From 68247cd7fc3b899527fc9512f68db8446cea3941 Mon Sep 17 00:00:00 2001
From: =?utf8?q?=C3=89tienne=20Mollier?= <emollier@debian.org>
Date: Tue, 29 Nov 2022 21:55:48 +0100
Subject: [PATCH] Import python-pysam_0.20.0+ds.orig.tar.xz

[dgit import orig python-pysam_0.20.0+ds.orig.tar.xz]
---
 .travis.disabled.yml                          |    114 +
 AUTHORS                                       |     43 +
 COPYING                                       |     21 +
 Containerfile                                 |     13 +
 INSTALL                                       |    102 +
 MANIFEST.in                                   |     54 +
 NEWS                                          |    850 +
 README.rst                                    |     53 +
 bcftools/HMM.c                                |    509 +
 bcftools/HMM.c.pysam.c                        |    511 +
 bcftools/HMM.h                                |    138 +
 bcftools/LICENSE                              |    773 +
 bcftools/README                               |     27 +
 bcftools/abuf.c                               |    802 +
 bcftools/abuf.c.pysam.c                       |    804 +
 bcftools/abuf.h                               |     78 +
 bcftools/bam2bcf.c                            |   1232 +
 bcftools/bam2bcf.c.pysam.c                    |   1234 +
 bcftools/bam2bcf.h                            |    171 +
 bcftools/bam2bcf_indel.c                      |    947 +
 bcftools/bam2bcf_indel.c.pysam.c              |    949 +
 bcftools/bam_sample.c                         |    398 +
 bcftools/bam_sample.c.pysam.c                 |    400 +
 bcftools/bam_sample.h                         |     50 +
 bcftools/bcftools.h                           |    143 +
 bcftools/bcftools.pysam.c                     |     83 +
 bcftools/bcftools.pysam.h                     |     74 +
 bcftools/bin.c                                |    106 +
 bcftools/bin.c.pysam.c                        |    108 +
 bcftools/bin.h                                |     65 +
 bcftools/call.h                               |    149 +
 bcftools/ccall.c                              |    338 +
 bcftools/ccall.c.pysam.c                      |    340 +
 bcftools/cols.c                               |    109 +
 bcftools/cols.c.pysam.c                       |    111 +
 bcftools/cols.h                               |     51 +
 bcftools/consensus.c                          |   1173 +
 bcftools/consensus.c.pysam.c                  |   1175 +
 bcftools/convert.c                            |   1709 +
 bcftools/convert.c.pysam.c                    |   1711 +
 bcftools/convert.h                            |     47 +
 bcftools/csq.c                                |   4395 +
 bcftools/csq.c.pysam.c                        |   4397 +
 bcftools/dbuf.h                               |     71 +
 bcftools/dist.c                               |    124 +
 bcftools/dist.c.pysam.c                       |    126 +
 bcftools/dist.h                               |     98 +
 bcftools/em.c                                 |    259 +
 bcftools/em.c.pysam.c                         |    261 +
 bcftools/extsort.c                            |    250 +
 bcftools/extsort.c.pysam.c                    |    252 +
 bcftools/extsort.h                            |     56 +
 bcftools/filter.c                             |   3671 +
 bcftools/filter.c.pysam.c                     |   3673 +
 bcftools/filter.h                             |     64 +
 bcftools/gvcf.c                               |    227 +
 bcftools/gvcf.c.pysam.c                       |    229 +
 bcftools/gvcf.h                               |     41 +
 bcftools/hclust.c                             |    401 +
 bcftools/hclust.c.pysam.c                     |    403 +
 bcftools/hclust.h                             |     77 +
 bcftools/hex.h                                |     95 +
 bcftools/khash_str2str.h                      |    106 +
 bcftools/kheap.h                              |    174 +
 bcftools/kmin.c                               |    209 +
 bcftools/kmin.c.pysam.c                       |    211 +
 bcftools/kmin.h                               |     46 +
 bcftools/main.c                               |    310 +
 bcftools/main.c.pysam.c                       |    312 +
 bcftools/mcall.c                              |   1685 +
 bcftools/mcall.c.pysam.c                      |   1687 +
 bcftools/mpileup.c                            |   1558 +
 bcftools/mpileup.c.pysam.c                    |   1560 +
 bcftools/mw.h                                 |   1944 +
 bcftools/ploidy.c                             |    268 +
 bcftools/ploidy.c.pysam.c                     |    270 +
 bcftools/ploidy.h                             |    129 +
 bcftools/prob1.c                              |    524 +
 bcftools/prob1.c.pysam.c                      |    526 +
 bcftools/prob1.h                              |     93 +
 bcftools/rbuf.h                               |    261 +
 bcftools/regidx.c                             |    650 +
 bcftools/regidx.c.pysam.c                     |    652 +
 bcftools/regidx.h                             |    222 +
 bcftools/reheader.c                           |    764 +
 bcftools/reheader.c.pysam.c                   |    766 +
 bcftools/smpl_ilist.c                         |    170 +
 bcftools/smpl_ilist.c.pysam.c                 |    172 +
 bcftools/smpl_ilist.h                         |     53 +
 bcftools/str_finder.c                         |    270 +
 bcftools/str_finder.c.pysam.c                 |    272 +
 bcftools/str_finder.h                         |     64 +
 bcftools/tabix.c                              |    131 +
 bcftools/tabix.c.pysam.c                      |    133 +
 bcftools/tsv2vcf.c                            |    135 +
 bcftools/tsv2vcf.c.pysam.c                    |    137 +
 bcftools/tsv2vcf.h                            |     86 +
 bcftools/utlist.h                             |    761 +
 bcftools/variantkey.h                         |    583 +
 bcftools/vcfannotate.c                        |   3524 +
 bcftools/vcfannotate.c.pysam.c                |   3526 +
 bcftools/vcfbuf.c                             |    562 +
 bcftools/vcfbuf.c.pysam.c                     |    564 +
 bcftools/vcfbuf.h                             |    122 +
 bcftools/vcfcall.c                            |   1179 +
 bcftools/vcfcall.c.pysam.c                    |   1181 +
 bcftools/vcfcnv.c                             |   1438 +
 bcftools/vcfcnv.c.pysam.c                     |   1440 +
 bcftools/vcfconcat.c                          |   1062 +
 bcftools/vcfconcat.c.pysam.c                  |   1064 +
 bcftools/vcfconvert.c                         |   1677 +
 bcftools/vcfconvert.c.pysam.c                 |   1679 +
 bcftools/vcffilter.c                          |    722 +
 bcftools/vcffilter.c.pysam.c                  |    724 +
 bcftools/vcfgtcheck.c                         |   1277 +
 bcftools/vcfgtcheck.c.pysam.c                 |   1279 +
 bcftools/vcfhead.c                            |    133 +
 bcftools/vcfhead.c.pysam.c                    |    135 +
 bcftools/vcfindex.c                           |    334 +
 bcftools/vcfindex.c.pysam.c                   |    336 +
 bcftools/vcfisec.c                            |    652 +
 bcftools/vcfisec.c.pysam.c                    |    654 +
 bcftools/vcfmerge.c                           |   3330 +
 bcftools/vcfmerge.c.pysam.c                   |   3332 +
 bcftools/vcfnorm.c                            |   2295 +
 bcftools/vcfnorm.c.pysam.c                    |   2297 +
 bcftools/vcfplugin.c                          |    822 +
 bcftools/vcfplugin.c.pysam.c                  |    824 +
 bcftools/vcfquery.c                           |    447 +
 bcftools/vcfquery.c.pysam.c                   |    449 +
 bcftools/vcfroh.c                             |   1301 +
 bcftools/vcfroh.c.pysam.c                     |   1303 +
 bcftools/vcfsom.c                             |    718 +
 bcftools/vcfsom.c.pysam.c                     |    720 +
 bcftools/vcfsort.c                            |    443 +
 bcftools/vcfsort.c.pysam.c                    |    445 +
 bcftools/vcfstats.c                           |   1915 +
 bcftools/vcfstats.c.pysam.c                   |   1917 +
 bcftools/vcfview.c                            |    801 +
 bcftools/vcfview.c.pysam.c                    |    803 +
 bcftools/vcmp.c                               |    155 +
 bcftools/vcmp.c.pysam.c                       |    157 +
 bcftools/vcmp.h                               |     63 +
 bcftools/version.c                            |    109 +
 bcftools/version.c.pysam.c                    |    111 +
 bcftools/version.sh                           |     36 +
 cy_build.py                                   |     90 +
 devtools/buildwheels.sh                       |     73 +
 devtools/conda-recipe/build.sh                |      8 +
 devtools/conda-recipe/meta.yaml               |     29 +
 devtools/import.py                            |    262 +
 devtools/install-CGAT-tools.sh                |    282 +
 devtools/run_tests_travis.sh                  |    126 +
 doc/Makefile                                  |     96 +
 doc/api.rst                                   |    230 +
 doc/benchmarking.rst                          |     70 +
 doc/conf.py                                   |    228 +
 doc/developer.rst                             |     80 +
 doc/faq.rst                                   |    278 +
 doc/glossary.rst                              |    144 +
 doc/index.rst                                 |     84 +
 doc/installation.rst                          |    108 +
 doc/make.bat                                  |    112 +
 doc/release.rst                               |    841 +
 doc/usage.rst                                 |    423 +
 import/pysam.c                                |     83 +
 import/pysam.h                                |     74 +
 .../BuildRead.pyx                             |     24 +
 .../PysamTestModule_link_pre_489/__init__.py  |      3 +
 linker_tests/link_pre_489/cy_build.py         |     86 +
 linker_tests/link_pre_489/setup.py            |     28 +
 .../link_pre_489/tests/test_module.py         |     15 +
 .../BuildRead.pyx                             |     24 +
 .../__init__.py                               |      3 +
 linker_tests/link_with_rpath/setup.py         |     36 +
 .../link_with_rpath/tests/test_module.py      |     15 +
 .../BuildRead.pyx                             |     24 +
 .../__init__.py                               |      3 +
 linker_tests/link_without_rpath/setup.py      |     35 +
 .../link_without_rpath/tests/test_module.py   |     15 +
 pysam/Pileup.py                               |    282 +
 pysam/VCF.py.obsolete                         |   1087 +
 pysam/__init__.py                             |    100 +
 pysam/alternatives.py.obsolete                |     82 +
 pysam/bcftools.py                             |     29 +
 pysam/cbcftools_util.h                        |      6 +
 pysam/csamtools_util.h                        |      6 +
 pysam/htslib_util.c                           |    159 +
 pysam/htslib_util.h                           |     97 +
 pysam/include/__init__.py                     |      0
 pysam/libcalignedsegment.pxd                  |    102 +
 pysam/libcalignedsegment.pyi                  |    222 +
 pysam/libcalignedsegment.pyx                  |   3409 +
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 pysam/libcvcf.pxd                             |      2 +
 pysam/libcvcf.pyi                             |      0
 pysam/libcvcf.pyx                             |   1203 +
 pysam/py.typed                                |      0
 pysam/pysam_stream.h                          |     13 +
 pysam/pysam_util.c                            |     36 +
 pysam/pysam_util.h                            |      5 +
 pysam/samtools.py                             |     55 +
 pysam/utils.py                                |    111 +
 pysam/version.h                               |      5 +
 pysam/version.py                              |      6 +
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 requirements.txt                              |      1 +
 samtools/LICENSE                              |     33 +
 samtools/README                               |    126 +
 samtools/amplicon_stats.c                     |   1754 +
 samtools/amplicon_stats.c.pysam.c             |   1756 +
 samtools/bam.c                                |    267 +
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 samtools/bam_addrprg.c.pysam.c                |    501 +
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 samtools/bam_consensus.c                      |   1712 +
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 samtools/bam_flags.c                          |     86 +
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 samtools/bam_lpileup.c                        |    225 +
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 samtools/bam_rmdup.c                          |    325 +
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 samtools/faidx.c                              |    415 +
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 samtools/lz4/LICENSE                          |     24 +
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 create mode 100644 tests/pysam_data/ex10.sam
 create mode 100644 tests/pysam_data/ex3.sam
 create mode 100644 tests/pysam_data/ex4.sam
 create mode 100644 tests/pysam_data/ex5.sam
 create mode 100644 tests/pysam_data/ex6.sam
 create mode 100644 tests/pysam_data/ex7.sam.donottest
 create mode 100644 tests/pysam_data/ex8.sam
 create mode 100644 tests/pysam_data/ex9_fail.sam
 create mode 100644 tests/pysam_data/ex9_nofail.sam
 create mode 100644 tests/pysam_data/ex_spliced.sam
 create mode 100644 tests/pysam_data/example_aligned_pairs.sam
 create mode 100644 tests/pysam_data/example_btag.sam
 create mode 100644 tests/pysam_data/example_dash_in_chr.sam
 create mode 100644 tests/pysam_data/example_empty_header.sam
 create mode 100644 tests/pysam_data/example_empty_with_header.sam
 create mode 100644 tests/pysam_data/example_reverse_complement.sam
 create mode 100644 tests/pysam_data/example_unmapped_reads_no_sq.sam
 create mode 100644 tests/pysam_data/faidx_empty_seq.fq
 create mode 100644 tests/pysam_data/faidx_ex1.fa
 create mode 100644 tests/pysam_data/faidx_ex1.fq
 create mode 100644 tests/pysam_data/issue100.sam
 create mode 100644 tests/pysam_data/rg_with_tab.sam
 create mode 100644 tests/pysam_data/softclip.sam
 create mode 100644 tests/pysam_data/tag_bug.sam
 create mode 100644 tests/pysam_data/test.gtf
 create mode 100644 tests/pysam_data/test.gtf.gz
 create mode 100644 tests/pysam_data/test_mapped_unmapped.sam
 create mode 100644 tests/pysam_data/test_query_position.sam
 create mode 100644 tests/pysam_data/test_unaligned.sam
 create mode 100644 tests/refactoring.pl
 create mode 100644 tests/refactoring.txt
 create mode 100644 tests/samtools_test.py
 create mode 100644 tests/tabix_bench.py
 create mode 100644 tests/tabix_data/Makefile
 create mode 100644 tests/tabix_data/empty.bed.gz
 create mode 100644 tests/tabix_data/example.bed
 create mode 100644 tests/tabix_data/example.gff2.gz
 create mode 100644 tests/tabix_data/example.gff3.gz
 create mode 100644 tests/tabix_data/example.gtf.gz
 create mode 100644 tests/tabix_data/example.gtf.gz.tbi
 create mode 100644 tests/tabix_data/example.sam.gz
 create mode 100644 tests/tabix_data/example.vcf.gz
 create mode 100644 tests/tabix_data/example.vcf40
 create mode 100644 tests/tabix_data/example_0v23.bed.gz
 create mode 100644 tests/tabix_data/example_0v23.bed.gz.tbi
 create mode 100644 tests/tabix_data/example_0v23.vcf.gz
 create mode 100644 tests/tabix_data/example_0v23.vcf.gz.tbi
 create mode 100644 tests/tabix_data/example_0v26.bed.gz
 create mode 100644 tests/tabix_data/example_0v26.bed.gz.tbi
 create mode 100644 tests/tabix_data/example_0v26.vcf.gz
 create mode 100644 tests/tabix_data/example_0v26.vcf.gz.tbi
 create mode 100644 tests/tabix_data/example_badcomments.bed.gz
 create mode 100644 tests/tabix_data/example_badcomments.gtf.gz
 create mode 100644 tests/tabix_data/example_badcomments.sam.gz
 create mode 100644 tests/tabix_data/example_badcomments.vcf.gz
 create mode 100644 tests/tabix_data/example_comments.bed.gz
 create mode 100644 tests/tabix_data/example_comments.gtf.gz
 create mode 100644 tests/tabix_data/example_comments.sam.gz
 create mode 100644 tests/tabix_data/example_comments.vcf.gz
 create mode 100644 tests/tabix_data/example_large.bed
 create mode 100644 tests/tabix_data/example_large.bed.gz
 create mode 100644 tests/tabix_data/example_unicode.vcf
 create mode 100644 tests/tabix_data/fivecolumns.bed
 create mode 100644 tests/tabix_data/gtf_toofew_fields.gtf.gz
 create mode 100644 tests/tabix_data/gtf_toomany_fields.gtf.gz
 create mode 100644 tests/tabix_data/gtf_wrong_fields.gtf.gz
 create mode 100644 tests/tabix_data/vcf/10.vcf
 create mode 100644 tests/tabix_data/vcf/11.vcf
 create mode 100644 tests/tabix_data/vcf/12.vcf
 create mode 100644 tests/tabix_data/vcf/13.vcf
 create mode 100644 tests/tabix_data/vcf/15.vcf
 create mode 100644 tests/tabix_data/vcf/16.vcf
 create mode 100644 tests/tabix_data/vcf/18.vcf
 create mode 100644 tests/tabix_data/vcf/2.vcf
 create mode 100644 tests/tabix_data/vcf/20.vcf
 create mode 100644 tests/tabix_data/vcf/21.vcf
 create mode 100644 tests/tabix_data/vcf/22.vcf
 create mode 100644 tests/tabix_data/vcf/23.vcf
 create mode 100644 tests/tabix_data/vcf/24.vcf
 create mode 100644 tests/tabix_data/vcf/3.vcf
 create mode 100644 tests/tabix_data/vcf/4.vcf
 create mode 100644 tests/tabix_data/vcf/5.vcf
 create mode 100644 tests/tabix_data/vcf/6.vcf
 create mode 100644 tests/tabix_data/vcf/7.vcf
 create mode 100644 tests/tabix_data/vcf/8.vcf
 create mode 100644 tests/tabix_data/vcf/9.vcf
 create mode 100644 tests/tabix_data/vcf/README.txt
 create mode 100644 tests/tabix_data/vcf/issue85.vcf
 create mode 100644 tests/tabix_data/vcf/vcf_v42.vcf
 create mode 100644 tests/tabix_test.py
 create mode 100644 tests/tabixproxies_test.py
 create mode 100644 tests/test_samtools_python.py

diff --git a/.travis.disabled.yml b/.travis.disabled.yml
new file mode 100644
index 0000000..5b7bcc8
--- /dev/null
+++ b/.travis.disabled.yml
@@ -0,0 +1,114 @@
+os:
+  - linux
+  - osx
+
+language: c
+
+stages:
+  - test
+  - name: deploy
+    if: tag IS present
+
+env:
+  matrix:
+    - CONDA_PY=2.7
+    - CONDA_PY=3.6
+    - CONDA_PY=3.7
+    - CONDA_PY=3.8
+  global:
+    - PYSAM_LINKING_TEST=1
+    - TWINE_USERNAME=grepall
+    - secure: bTbky3Un19NAl62lix8bMLmBv9IGNhFkRXlZH+B253nYub7jwQwPQKum3ct9ea+XHJT5//uM0B8WAF6eyugpNkPQ7+S7SEH5BJuCt30nv6qvGhSO2AffZKeHEDnfW2kqGrivn87TqeomlSBlO742CD/V0wOIUwkTT9tutd+E7FU=
+
+_cibw_common: &cibw_common
+  addons: {}
+  install:
+    - python3 -m pip install cibuildwheel>=1.1.0 twine
+  script:
+    - set -e
+    - cibuildwheel --output-dir dist
+    - twine check dist/*
+    - twine upload --skip-existing dist/*
+
+_cibw_linux: &cibw_linux
+  stage: deploy
+  os: linux
+  language: python
+  python: '3.5'
+  services:
+    - docker
+  <<: *cibw_common
+
+_cibw_linux_aarch64: &cibw_linux_aarch64
+  stage: deploy
+  os: linux
+  arch: arm64
+  language: python
+  python: '3.9'
+  services:
+    - docker
+  <<: *cibw_common
+
+matrix:
+  include:
+    - stage: deploy
+      os: linux
+      language: python
+      python: '3.5'
+      addons:
+        apt:
+          packages:
+            - gcc
+            - g++
+            - libcurl4-openssl-dev  # for libcurl support in sdist
+            - libssl-dev  # for s3 support in sdist
+      install:
+        - python3 -m pip install Cython twine
+      script:
+        - set -e
+        - python3 setup.py build_ext --inplace
+        - python3 setup.py sdist
+        - twine check dist/*
+        - twine upload --skip-existing dist/*
+    - <<: *cibw_linux
+      env:
+        - CIBW_BUILD="*_x86_64"
+        - CIBW_BEFORE_BUILD="yum install -y zlib-devel bzip2-devel xz-devel && python -m pip install -r requirements.txt"
+        - CIBW_ENVIRONMENT='HTSLIB_CONFIGURE_OPTIONS="--disable-libcurl"'
+        - CIBW_REPAIR_WHEEL_COMMAND_LINUX='auditwheel repair -L . -w {dest_dir} {wheel}'
+        - CIBW_TEST_COMMAND='python -c "import pysam"'
+    - <<: *cibw_linux
+      env:
+        - CIBW_BUILD="*_i686"
+        - CIBW_BEFORE_BUILD="yum install -y zlib-devel bzip2-devel xz-devel && python -m pip install -r requirements.txt"
+        - CIBW_ENVIRONMENT='HTSLIB_CONFIGURE_OPTIONS="--disable-libcurl"'
+        - CIBW_REPAIR_WHEEL_COMMAND_LINUX='auditwheel repair -L . -w {dest_dir} {wheel}'
+        - CIBW_TEST_COMMAND='python -c "import pysam"'
+    - <<: *cibw_linux_aarch64
+      env:
+        - CIBW_BUILD="*_aarch64"
+        - CIBW_BEFORE_BUILD="yum install -y zlib-devel bzip2-devel xz-devel && python -m pip install -r requirements.txt"
+        - CIBW_ENVIRONMENT='HTSLIB_CONFIGURE_OPTIONS="--disable-libcurl"'
+        - CIBW_REPAIR_WHEEL_COMMAND_LINUX='auditwheel repair -L . -w {dest_dir} {wheel}'
+        - CIBW_TEST_COMMAND='python -c "import pysam"'
+    - stage: deploy
+      os: osx
+      language: generic
+      env:
+        - CIBW_BEFORE_BUILD="python -m pip install -r requirements.txt"
+        - CIBW_ENVIRONMENT='HTSLIB_CONFIGURE_OPTIONS="--disable-libcurl"'
+        - CIBW_TEST_COMMAND='python -c "import pysam"'
+      <<: *cibw_common
+
+addons:
+  apt:
+    packages:
+    - gcc
+    - g++
+
+script:
+  - ./devtools/run_tests_travis.sh
+
+notifications:
+  email:
+    - andreas.heger@gmail.com
diff --git a/AUTHORS b/AUTHORS
new file mode 100644
index 0000000..4e9c5eb
--- /dev/null
+++ b/AUTHORS
@@ -0,0 +1,43 @@
+Many people have contributed to pysam. The list of github contributors
+is the best place to get a full list of authors and their contributions.
+The list and summary below is a out-of-date and represents the earlier
+stages of the project.
+
+List of contributors:
+
+Andreas Heger, Tildon Grant Belgard, Florian Finkernagel, Leo
+Goodstadt, Martin Goodson all contributed code to pysam.
+
+John Marshall has been looking after pysam and its community for
+several years, as well as making many code contributions and improving
+the engineering of pysam.
+
+Kevin B. Jacobs implemented a Cython wrapper for the VCF/BCF
+reader/writer in htslib.
+
+Gerton Lunter provided a validating VCF parser.
+
+Marcel Martin implemented python 3 compatibility.
+Ben Schiller contributed a Windows compatible clone.
+
+The sources in the directory samtools are from the samtools project:
+http://samtools.sourceforge.net/. All of these are available under the
+MIT licence. The attributions for this code are as follows:
+
+Heng Li from the Sanger Institute wrote most of the initial source code
+of SAMtools and various converters.
+
+Bob Handsaker from the Broad Institute is a major contributor to the
+SAM/BAM specification. He designed and implemented the BGZF format, the
+underlying indexable compression format for the BAM format. BGZF does
+not support arithmetic between file offsets.
+
+Jue Ruan for the Beijing Genome Institute designed and implemented the
+RAZF format, an alternative indexable compression format. RAZF supports
+arithmetic between file offsets, at the cost of increased index file
+size and the full compatibility with gzip. RAZF is optional and only
+used in `faidx' for indexing RAZF compressed fasta files.
+
+Colin Hercus updated novo2sam.pl to support gapped alignment by
+novoalign.
+
diff --git a/COPYING b/COPYING
new file mode 100644
index 0000000..82fa2f4
--- /dev/null
+++ b/COPYING
@@ -0,0 +1,21 @@
+The MIT License
+
+Copyright (c) 2008-2009 Genome Research Ltd.
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.
\ No newline at end of file
diff --git a/Containerfile b/Containerfile
new file mode 100644
index 0000000..633f07e
--- /dev/null
+++ b/Containerfile
@@ -0,0 +1,13 @@
+FROM ubi8:latest
+
+RUN yum update \
+  && yum install -y python3-pip python3-devel pigz \
+  && cd /usr/local/bin \
+  && ln -s /usr/bin/python3 python \
+  && pip3 --no-cache-dir install --upgrade pip \
+  && yum clean all \
+  && echo "system packages installed"
+
+RUN python -m pip install pysam
+
+WORKDIR /opt/
diff --git a/INSTALL b/INSTALL
new file mode 100644
index 0000000..5016dcc
--- /dev/null
+++ b/INSTALL
@@ -0,0 +1,102 @@
+An online version of the installation instructions can be found here:
+http://pysam.readthedocs.io/en/latest/installation.html
+
+================
+Installing pysam
+================
+
+Pysam can be installed through conda_, pypi_ and from the repository.
+The recommended way to install pysam is through conda/bioconda.
+
+Conda installation
+==================
+
+To install pysam in your current conda_ environment, type::
+
+   conda config --add channels r
+   conda config --add channels bioconda
+   conda install pysam
+
+This will install pysam from the bioconda_ channel and automatically
+makes sure that dependencies are installed. Also, compilation flags
+will be set automatically, which will potentially save a lot of
+trouble on OS X.
+
+Pypi installation
+=================
+
+Pysam provides a python interface to the functionality contained
+within the htslib_ C library. There are two ways that these two
+can be combined, ``builtin`` and ``external``.
+
+Builtin
+-------
+
+The typical installation will be through pypi_::
+
+   pip install pysam
+
+This will compile the ``builtin`` htslib source code within pysam.
+
+htslib_ can be configured at compilation to turn on additional
+features such support using encrypted configurations, enable plugins,
+and more. See the htslib_ project for more information on these.
+
+Pysam will attempt to configure htslib_ to turn on some advanced
+features. If these fail, for example due to missing library
+dependencies (`libcurl`, `libcrypto`), it will fall back to
+conservative defaults.
+
+Options can be passed to the configure script explicitly by
+setting the environment variable `HTSLIB_CONFIGURE_OPTIONS`.
+For example::
+
+  export HTSLIB_CONFIGURE_OPTIONS=--enable-plugins
+  pip install pysam
+
+External
+--------
+
+pysam can be combined with an externally installed htslib_
+library. This is a good way to avoid duplication of libraries. To link
+against an externally installed library, set the environment variables
+`HTSLIB_LIBRARY_DIR` and `HTSLIB_INCLUDE_DIR` before installing::
+
+   export HTSLIB_LIBRARY_DIR=/usr/local/lib
+   export HTSLIB_INCLUDE_DIR=/usr/local/include
+   pip install pysam
+
+Note that the location of the file :file:`libhts.so` needs to be known
+to the linker once you run pysam, for example by setting the
+environment-varirable `LD_LIBRARY_PATH`.
+
+Note that generally the pysam and htslib version need to be compatible. See
+the release notes for more information.
+
+Installation from repository
+============================
+
+pysam depends on cython_ to provide the connectivity to the htslib_ C
+library. The installation of the source tarball (:file:`.tar.gz`)
+contains pre-built C-files and cython needs not be present
+during installation. However, when installing from the repository,
+cython needs to be installed beforehand.
+
+To install from repository, type::
+
+    python setup.py install
+
+For compilation options, see the section on Pypi installation above.
+
+Requirements
+============
+
+Depending on the installation method, requirements for building pysam differ.
+
+When installing through conda_, dependencies will be resolved by the
+package manager. The pip_ installation and installation from source
+require a C compiler and its standard libraries as well as all
+requirements for building htslib. Htslib requirements are listed in
+the htslib/INSTALL file.
+
+Installing from the repository will require cython_ to be installed.
diff --git a/MANIFEST.in b/MANIFEST.in
new file mode 100644
index 0000000..25e9a1a
--- /dev/null
+++ b/MANIFEST.in
@@ -0,0 +1,54 @@
+#
+# Use .add_data_files and .add_data_dir methods in a appropriate
+# setup.py files to include non-python files such as documentation,
+# data, etc files to distribution. Avoid using MANIFEST.in for that.
+#
+include MANIFEST.in
+include COPYING
+include NEWS
+include INSTALL
+include KNOWN_BUGS
+include THANKS
+include cy_build.py
+include requirements.txt
+include pysam/libc*.pxd
+include pysam/libc*.pyx
+include pysam/libc*.c
+include pysam/*.c
+include pysam/*.h
+exclude pysam/config.py
+
+include win32/*.[ch]
+
+# exclude tests from pypi tar-ball - they
+# require additional data
+prune tests/
+
+# samtools
+include samtools/LICENSE samtools/README samtools/lz4/LICENSE
+recursive-include samtools *.[ch]
+include samtools/version.sh
+exclude samtools/*config*.h
+
+# bcftools
+include bcftools/LICENSE bcftools/README
+include bcftools/*.[ch]
+include bcftools/version.sh
+exclude bcftools/*config*.h
+
+# htslib
+include htslib/LICENSE htslib/README
+recursive-include htslib *.[ch]
+exclude htslib/*config*.h
+
+include htslib/configure.ac htslib/m4/*.m4 htslib/*.in
+include htslib/configure htslib/version.sh
+include htslib/Makefile htslib/*.mk
+exclude htslib/config.mk htslib/htscodecs.mk
+
+include cy_build.py
+include requirements.txt
+
+# documentation
+include doc/*.py doc/*.rst
+include doc/Makefile doc/make.bat
diff --git a/NEWS b/NEWS
new file mode 100644
index 0000000..a0078cb
--- /dev/null
+++ b/NEWS
@@ -0,0 +1,850 @@
+An online version of the installation instructions can be found here:
+http://pysam.readthedocs.io/en/latest/release.html
+
+=============
+Release notes
+=============
+
+Release 0.20.0
+==============
+
+This release wraps htslib/bcftools version 1.16 and samtools version 1.16.1.
+
+* [#1113] Full compatibility with setuptools v62.1.0's build directory name changes
+* [#1121] Build-time symbol check portability improved
+* [#1122] Fix setting sample genotype using .alleles property
+* [#1128] Fix test suite failure when using a libdeflate-enabled samtools
+
+Many additional type hints have been provided by the community,
+thanks!
+
+Release 0.19.1
+==============
+
+This release wraps htslib/samtools/bcftools version 1.15.1.
+
+* [#1104] add an add_samples() method to quickly add multiple samples
+  to VCF.
+
+Release 0.19.0
+==============
+
+This release wraps htslib/samtools/bcftools version 1.15.
+
+* [#1085] Improve getopt()/getopt_long() resetting when running samtools/bcftools commands
+
+* [#1078] Support BAM_CPAD in get_aligned_pairs
+
+* [#1063] Run flake8 and fix some linting issues
+
+* [#1088] Add AlignedSegment is_mapped/mate_is_mapped/is_forward/mate_is_forward properties
+
+* Write an absent AlignedSegment.qual as all-bytes-0xff
+
+* Fix BGZFile.read() behaviour near or at EOF
+
+* First API for the htslib modified bases interface
+  
+Release 0.18.0
+==============
+
+This release wraps htslib/samtools/bcftools version 1.14.
+
+* [#1048] and [#1060], clarify documentation of index statistics with CRAM files
+* Prevent "retval may be used uninitialised" warning.
+* Add new "samples" subcommand to pysam/samtools.py
+* Introduce TupleProxyIterator iterator object class
+
+Release 0.17.0
+==============
+
+This release wraps htslib/samtools/bcftools version 1.13. Corresponding
+to new samtools commands, `pysam.samtools` now has additional functions
+`ampliconclip`, `ampliconstats`, `fqimport`, and `version`.
+
+Bugs fixed:
+
+* [#447] The maximum QNAME length is fully restored to 254
+* [#506, #958, #1000] Don't crash the Python interpreter on ``pysam.bcftools.*()`` errors
+* [#603] count_coverage: ignore reads that have no SEQ field
+* [#928] Fix ``pysam.bcftools.mpileup()`` segmentation fault
+* [#983] Add win32/\*.[ch] to MANIFEST.in
+* [#994] Raise exception in ``get_tid()`` if header could not be parsed
+* [#995] Choose TBI/CSI in ``tabix_index()`` via both min_shift and csi
+* [#996] ``AlignmentFile.fetch()`` now works with large chromosomes longer than 2\ :sup:`29` bases
+* [#1019] Fix Sphinx documentation generation by avoiding Python 2 ``ur'string'`` syntax
+* [#1035] Improved handling of file iteration errors
+* [#1038] ``tabix_index()`` no longer leaks file descriptors
+* [#1040] ``print(aligned_segment)`` now prints the correct TLEN value
+  (it also now prints RNAME/RNEXT more clearly and prints POS/PNEXT 1-based)
+* *setup.py* longer uses ``setup(use_2to3)`` for compatibility with setuptools >= v58.0.0
+
+New facilities:
+
+* [PR #963] Additional VCF classes are exposed to pysam programmers
+* [#998, PR #1001] Add ``get/set_encoding_error_handler()`` to control UTF-8 conversion
+* [PR #1012] Running ``python setup.py sdist`` now automatically runs cythonize
+* Running tests with ``pytest`` now automatically runs ``make`` to generate test data
+
+Documentation improvements:
+
+* [#726] Clarify get_forward_sequence/get_forward_qualities documentation
+* [#865] Improved example
+* [#968] ``get_index_statstics`` parameters
+* [#986] Clarify ``VariantFile.fetch`` start/stop region parameters are 0-based and half-open.
+* [#990] Corrected ``PileupColumn.get_query_sequences`` documentation
+* [#999] Fix documentation for ``AlignmentFile.get_reference_length()``
+* [#1002] Document the default min_base_quality for ``pileup()``
+
+
+Release 0.16.0
+==============
+
+This release wraps htslib/bcftools version 1.10.2 and samtools version
+1.10. The following bugs reported against pysam are fixed due to this:
+
+* [#447] Writing out QNAME longer than 251 characters corrupts BAM
+* [#640, #734, #843] Setting VariantRecord pos or stop raises error
+* [#738, #919] FastxFile truncates concatenated plain gzip compressed files
+
+Additional bugfixes:
+
+* [#840] Pileup doesn't work on python3 when `index_filename` is used
+* [#886] FastqProxy raises ValueError when instantiated from python
+* [#904] VariantFile.fetch() throws ValueError on files with no records
+* [#909] Fix incorrect quoting in VariantFile contig records
+* [#915, #916] Implement pileup() for unindexed files and/or SAM files
+
+Backwards incompatible changes:
+
+* The `samtools import` command was removed in samtools 1.10, so pysam
+  no longer exports a `samimport` function. Use `pysam.view()` instead.
+
+
+Release 0.15.4
+==============
+
+Bugfix release. Principal reason for release is to update cython
+version in order to fix pip install pysam with python 3.8.
+
+* [#879] Fix add_meta function in libcbcf.pyx, so meta-information
+  lines in header added with this function have double-quoting rules
+  in accordance to rules specified in VCF4.2 and VCF4.3 specifications
+* [#863] Force arg to bytes to support non-ASCII encoding
+* [#875] Bump minimum Cython version
+* [#868] Prevent segfault on Python 2.7 AlignedSegment.compare(other=None)
+* [#867] Fix wheel building on TravisCI
+* [#863] Force arg to bytes to support non-ASCII encoding
+* [#799] disambiguate interpretation of bcf_read return code
+* [#841] Fix silent truncation of FASTQ with bad q strings
+* [#846] Prevent segmentation fault on ID, when handling malformed records
+* [#829] Run configure with the correct CC/CFLAGS/LDFLAGS env vars
+
+Release 0.15.3
+==============
+
+Bugfix release.
+
+* [#824] allow reading of UTF-8 encoded text in VCF/BCF files.
+* [#780] close all filehandles before opening new ones in pysam_dispatch
+* [#773] do not cache VariantRecord.id to avoid memory leak
+* [#781] default of multiple_iterators=True is changed to False for
+  CRAM files.
+* [#825] fix collections.abc import
+* [#825] use bcf_hdr_format instead of bcf_hdr_fmt_text, fix memcpy
+  bug when setting FORMAT fields.
+* [#804] Use HTSlib's kstring_t, which reallocates and enlarges its
+  memory as needed, rather than a fixed-size char buffer.
+* [#814] Build wheels and upload them to PyPI
+* [#755] Allow passing flags and arguments to index methods
+* [#763] Strip \0 in header check
+* [#761] Test Tabix index contents, not the compression
+
+Release 0.15.2
+==============
+
+Bugfix release.
+
+* [#746] catch pileup itorator out-of-scope segfaults
+* [#747] fix faixd fetch with region
+* [#748] increase max_pos to (1<<31)-1
+* [#645] Add missing macOS stub files in `MANIFEST.in`, @SoapZA
+* [#737] Fix bug in get_aligned_pairs, @bkohrn
+
+Release 0.15.1
+==============
+
+Bugfix release.
+
+* [#716] raise ValueError if tid is out of range when writing
+* [#697] release version using cython 0.28.5 for python 3.7
+  compatibility
+
+Release 0.15.0
+==============
+
+This release wraps htslib (and friends) version 1.9.
+
+* [#673] permit dash in chromosome name of region string
+* [#656] Support `text` when opening a SAM file for writing
+* [#658] return None in get_forward_sequence if sequence not in record
+* [#683] allow lower case bases in MD tags
+* Ensure that = and X CIGAR ops are treated the same as M
+
+Release 0.14.1
+==============
+
+This is mostly a bugfix release, though bcftools has now also been
+upgraded to 1.7.0.
+
+* [#621] Add a warning to count_coverage when an alignment has an
+  empty QUAL field
+* [#635] Speed-up of AlignedSegment.find_intro()
+* treat border case of all bases in pileup column below quality score
+* [#634] Fix access to pileup reference_sequence
+
+Release 0.14.0
+==============
+
+This release wraps htslib/samtools versions 1.7.0.
+
+* SAM/BAM/CRAM headers are now managed by a separate AlignmentHeader
+  class.
+* AlignmentFile.header.as_dict() returns an ordered dictionary.
+* Use "stop" instead of "end" to ensure consistency to
+  VariantFile. The end designations have been kept for backwards
+  compatibility.
+
+* [#611] and [#293] CRAM repeated fetch now works, each iterator
+  reloads index if multiple_iterators=True
+* [#608] pysam now wraps htslib 1.7 and samtools 1.7.
+* [#580] reference_name and next_reference_name can now be set to "*"
+  (will be converted to None to indicate an unmapped location)
+* [#302] providing no coordinate to count_coverage will not count from
+  start/end of contig.
+* [#325] @SQ records will be automatically added to header if they are
+  absent from text section of header.
+* [#529] add get_forward_sequence() and get_forward_qualities()
+  methods
+* [#577] add from_string() and to_dict()/from_dict() methods to
+  AlignedSegment. Rename tostring() to to_string() throughout for
+  consistency
+* [#589] return None from build_alignment_sequence if no MD tag is set
+* [#528] add PileupColumn.__len__ method
+
+Backwards incompatible changes:
+
+* AlignmentFile.header now returns an AlignmentHeader object. Use
+  AlignmentFile.header.to_dict() to get the dictionary as
+  previously. Most dictionary accessor methods (keys(), values(),
+  __getitem__, ...) have been implemented to ensure some level of
+  backwards compatibility when only reading.
+
+  The rationale for this change is to have consistency between
+  AlignmentFile and VariantFile.
+
+* AlignmentFile and FastaFile now raise IOError instead of OSError
+
+Medium term we plan to have a 1.0 release. The pysam
+interface has grown over the years and the API is cluttered with
+deprecated names (Samfile, getrname(), gettid(), ...). To work towards
+this, the next release (0.15.0) will yield DeprecationWarnings
+for any parts of the API that are considered obsolete and will not be
+in 1.0. Once 1.0 has been reached, we will use semantic versioning.
+
+Release 0.13.0
+===============
+
+This release wraps htslib/samtools/bcftools versions 1.6.0 and
+contains a series of bugfixes.
+
+* [#544] reading header from remote TabixFiles now works.
+* [#531] add missing tag types H and A. A python float will now be
+  added as 'f' type instead of 'd' type.
+* [#543] use FastaFile instead of Fastafile in pileup.
+* [#546] set is_modified flag in setAttribute so updated attributes
+  are output.
+* [#537] allow tabix index files to be created in a custom location.
+* [#530] add get_index_statistics() method
+
+Release 0.12.0.1
+================
+
+Bugfix release to solve compilation issue due to missinge
+bcftools/config.h file.
+
+Release 0.12.0
+==============
+
+This release wraps htslib/samtools/bcftools versions 1.5.0 and
+contains a series of bugfixes.
+
+* [#473] A new FastxRecord class that can be instantiated from class and
+  modified in-place. Replaces PersistentFastqProxy.
+* [#521] In AligmentFile, Simplify file detection logic and allow remote index files
+  * Removed attempts to guess data and index file names; this is magic left
+    to htslib.
+  * Removed file existence check prior to opening files with htslib
+  * Better error checking after opening files that raise the appropriate
+    error (IOError for when errno is set, ValueError otherwise for backward
+    compatibility).
+  * Report IO errors when loading an index by name.
+  * Allow remote indices (tested using S3 signed URLs).
+  * Document filepath_index and make it an alias for index_filename.
+  * Added a require_index parameter to AlignmentFile
+* [#526] handle unset ref when creating new records
+* [#513] fix bcf_translate to skip deleted FORMAT fields to avoid
+  segfaults
+* [#516] expose IO errors via IOError exceptions
+* [#487] add tabix line_skip, remove 'pileup' preset
+* add FastxRecord, replaces PersistentFastqProxy (still present for
+  backwards compatibility)
+* [#496] upgrade to htslib/samtools/bcftools versions 1.5
+* add start/stop to AlignmentFile.fetch() to be consistent with
+  VariantFile.fetch(). "end" is kept for backwards compatibility.
+* [#512] add get_index_statistics() method to AlignmentFile.
+
+Upcoming changes:
+
+In the next release we are plannig to separate the header information
+from AlignmentFile into a separate class AlignmentHeader. This layout
+is similar to VariantFile/VariantHeader. With this change we will
+ensure that an AlignedSegment record will be linked to a header so
+that chromosome names can be automatically translated from the numeric
+representation. As a consequence, the way new AlignedSegment records
+are created will need to change as the constructor requires a header::
+
+    header = pysam.AlignmentHeader(
+        reference_names=["chr1", "chr2"],
+        reference_lengths=[1000, 1000])
+
+    read = pysam.AlignedSegment(header)
+
+This will affect all code that instantiates AlignedSegment objects
+directly. We have not yet merged to allow users to provide feed-back.
+The pull-request is here: https://github.com/pysam-developers/pysam/pull/518
+Please comment on github.
+
+Release 0.11.2.2
+================
+
+Bugfix release to address two issues:
+
+* Changes in 0.11.2.1 broke the GTF/GFF3 parser. Corrected and
+  more tests have been added.
+* [#479] Correct VariantRecord edge cases described in issue
+
+Release 0.11.2.1
+================
+
+Release to fix release tar-ball containing 0.11.1 pre-compiled
+C-files.
+
+Release 0.11.2
+==============
+
+This release wraps htslib/samtools/bcfools versions 1.4.1 in response
+to a security fix in these libraries. Additionally the following
+issues have been fixed:
+
+* [#452] add GFF3 support for tabix parsers
+* [#461] Multiple fixes related to VariantRecordInfo and handling of INFO/END
+* [#447] limit query name to 251 characters (only partially addresses issue)
+
+VariantFile and related object fixes
+
+* Restore VariantFile.\_\_dealloc\_\_
+* Correct handling of bcf_str_missing in bcf_array_to_object and
+  bcf_object_to_array
+* Added update() and pop() methods to some dict-like proxy objects
+* scalar INFO entries could not be set again after being deleted
+* VariantRecordInfo.__delitem__ now allows unset flags to be deleted without
+  raising a KeyError
+* Multiple other fixes for VariantRecordInfo methods
+* INFO/END is now accessible only via VariantRecord.stop and
+  VariantRecord.rlen.  Even if present behind the scenes, it is no longer
+  accessible via VariantRecordInfo.
+* Add argument to issue a warning instead of an exception if input appears
+  to be truncated
+
+Other features and fixes:
+
+* Make AlignmentFile \_\_dealloc\_\_ and close more
+  stringent
+* Add argument AlignmentFile to issue a warning instead of an
+  exception if input appears to be truncated
+
+Release 0.11.1
+==============
+
+Bugfix release
+
+* [#440] add deprecated 'always' option to infer_query_length for backwards compatibility.
+
+Release 0.11.0
+==============
+
+This release wraps the latest versions of htslib/samtools/bcftools and
+implements a few bugfixes.
+
+* [#413] Wrap HTSlib/Samtools/BCFtools 1.4
+* [#422] Fix missing pysam.sort.usage() message
+* [#411] Fix BGZfile initialization bug
+* [#412] Add seek support for BGZFile
+* [#395] Make BGZfile iterable
+* [#433] Correct getQueryEnd
+* [#419] Export SAM enums such as pysam.CMATCH
+* [#415] Fix access by tid in AlignmentFile.fetch()
+* [#405] Writing SAM now outputs a header by default.
+* [#332] split infer_query_length(always) into infer_query_length and infer_read_length
+
+Release 0.10.0
+==============
+
+This release implements further functionality in the VariantFile API
+and includes several bugfixes:
+
+* treat special case -c option in samtools view outputs to stdout even
+  if -o given, fixes #315
+* permit reading BAM files with CSI index, closes #370
+* raise Error if query name exceeds maximum length, fixes #373
+* new method to compute hash value for AlignedSegment
+* AlignmentFile, VariantFile and TabixFile all inherit from HTSFile
+* Avoid segfault by detecting out of range reference_id and
+  next_reference in AlignedSegment.tostring
+* Issue #355: Implement streams using file descriptors for VariantFile
+* upgrade to htslib 1.3.2
+* fix compilation with musl libc
+* Issue #316, #360: Rename all Cython modules to have lib as a prefix
+* Issue #332, hardclipped bases in cigar included by
+  pysam.AlignedSegment.infer_query_length()
+* Added support for Python 3.6 filename encoding protocol
+* Issue #371, fix incorrect parsing of scalar INFO and FORMAT fields in VariantRecord
+* Issue #331, fix failure in VariantFile.reset() method
+* Issue #314, add VariantHeader.new_record(), VariantFile.new_record() and
+  VariantRecord.copy() methods to create new VariantRecord objects
+* Added VariantRecordFilter.add() method to allow setting new VariantRecord filters
+* Preliminary (potentially unsafe) support for removing and altering header metadata
+* Many minor fixes and improvements to VariantFile and related objects
+
+Please note that all internal cython extensions now have a lib prefix
+to facilitate linking against pysam extension modules. Any user cython
+extensions using cimport to import pysam definitions will need
+changes, for example::
+
+   cimport pysam.csamtools
+
+will become::
+
+   cimport pysam.libcsamtools
+
+Release 0.9.1
+=============
+
+This is a bugfix release addressing some installation problems
+in pysam 0.9.0, in particular:
+
+* patch included htslib to work with older libcurl versions, fixes #262.
+* do not require cython for python 3 install, fixes #260
+* FastaFile does not accept filepath_index any more, see #270
+* add AlignedSegment.get_cigar_stats method.
+* py3 bugfix in VariantFile.subset_samples, fixes #272
+* add missing sysconfig import, fixes #278
+* do not redirect stdout, but instead write to a separately
+  created file. This should resolve issues when pysam is used
+  in notebooks or other environments that redirect stdout.
+* wrap htslib-1.3.1, samtools-1.3.1 and bcftools-1.3.1
+* use bgzf throughout instead of gzip
+* allow specifying a fasta reference for CRAM file when opening
+  for both read and write, fixes #280
+
+Release 0.9.0
+=============
+
+Overview
+--------
+
+The 0.9.0 release upgrades htslib to htslib 1.3 and numerous other
+enhancements and bugfixes. See below for a detailed list.
+
+`Htslib 1.3 <https://github.com/samtools/htslib/releases/tag/1.3>`_
+comes with additional capabilities for remote file access which depend
+on the presence of optional system libraries. As a consequence, the
+installation script :file:`setup.py` has become more complex. For an
+overview, see :ref:`installation`.  We have tested installation on
+linux and OS X, but could not capture all variations. It is possible
+that a 0.9.1 release might follow soon addressing installation issues.
+
+The :py:class:`~.pysam.VariantFile` class provides access to
+:term:`vcf` and :term:`bcf` formatted files. The class is certainly
+usable and interface is reaching completion, but the API and the
+functionality is subject to change.
+
+Detailed release notes
+----------------------
+
+* upgrade to htslib 1.3
+* python 3 compatibility tested throughout.
+* added a first set of bcftools commands in the pysam.bcftools
+  submodule.
+* samtools commands are now in the pysam.samtools module. For
+  backwards compatibility they are still imported into the pysam
+  namespace.
+* samtools/bcftools return stdout as a single (byte) string. As output
+  can be binary (VCF.gz, BAM) this is necessary to ensure py2/py3
+  compatibility. To replicate the previous behaviour in py2.7, use::
+
+     pysam.samtools.view(self.filename).splitlines(True)
+
+* get_tags() returns the tag type as a character, not an integer (#214)
+* TabixFile now raises ValueError on indices created by tabix <1.0 (#206)
+* improve OSX installation and develop mode
+* FastxIterator now handles empty sequences (#204)
+* TabixFile.isremote is not TabixFile.is_remote in line with AlignmentFile
+* AlignmentFile.count() has extra optional argument read_callback
+* setup.py has been changed to:
+   * install a single builtin htslib library. Previously, each pysam
+     module contained its own version. This reduces compilation time
+     and code bloat.
+   * run configure for the builtin htslib library in order to detect
+     optional libraries such as libcurl. Configure behaviour can be
+     controlled by setting the environment variable
+     HTSLIB_CONFIGURE_OPTIONS.
+* get_reference_sequence() now returns the reference sequence and not
+  something looking like it. This bug had effects on
+  get_aligned_pairs(with_seq=True), see #225. If you have relied on on
+  get_aligned_pairs(with_seq=True) in pysam-0.8.4, please check your
+  results.
+* improved autodetection of file formats in AlignmentFile and VariantFile.
+
+Release 0.8.4
+=============
+
+This release contains numerous bugfixes and a first implementation of
+a pythonic interface to VCF/BCF files. Note that this code is still
+incomplete and preliminary, but does offer a nearly complete immutable
+Pythonic interface to VCF/BCF metadata and data with reading and
+writing capability.
+
+Potential isses when upgrading from v0.8.3:
+
+* binary tags are now returned as python arrays
+
+* renamed several methods for pep8 compatibility, old names still retained for
+  backwards compatibility, but should be considered deprecated.
+   * gettid() is now get_tid()
+   * getrname() is now get_reference_name()
+   * parseRegion() is now parse_region()
+
+* some methods have changed for pep8 compatibility without the old
+  names being present:
+   * fromQualityString() is now qualitystring_to_array()
+   * toQualityString() is now qualities_to_qualitystring()
+
+* faidx now returns strings and not binary strings in py3.
+
+* The cython components have been broken up into smaller files with
+  more specific content. This will affect users using the cython
+  interfaces.
+
+Edited list of commit log changes:
+
+*    fixes AlignmentFile.check_index to return True
+*    add RG/PM header tag - closes #179
+*    add with_seq option to get_aligned_pairs
+*    use char * inside reconsituteReferenceSequence
+*    add soft clipping for get_reference_sequence
+*    add get_reference_sequence
+*    queryEnd now computes length from cigar string if no sequence present, closes #176
+*    tolerate missing space at end of gtf files, closes #162
+*    do not raise Error when receiving output on stderr
+*    add docu about fetching without index, closes #170
+*    FastaFile and FastxFile now return strings in python3, closes #173
+*    py3 compat: relative -> absolute imports.
+*    add reference_name and next_reference_name attributes to AlignedSegment
+*    add function signatures to cvcf cython.  Added note about other VCF code.
+*    add context manager functions to FastaFile
+*    add reference_name and next_reference_name attributes to AlignedSegment
+*    PileupColumn also gets a reference_name attribute.
+*    add context manager functions to FastaFile
+*    TabixFile.header for remote files raises AttributeError, fixes #157
+*    add context manager interface to TabixFile, closes #165
+*    change ctypedef enum to typedef enum for cython 0.23
+*    add function signatures to cvcf cython, also added note about other VCF code
+*    remove exception for custom upper-case header record tags.
+*    rename VALID_HEADER_FIELDS to KNOWN_HEADER_FIELDS
+*    fix header record tag parsing for custom tags.
+*    use cython.str in count_coverage, fixes #141
+*    avoid maketrans (issues with python3)
+*    refactoring: AlignedSegment now in separate module
+*    do not execute remote tests if URL not available
+*    fix the unmapped count, incl reads with no SQ group
+*    add raw output to tags
+*    added write access for binary tags
+*    bugfix in call to resize
+*    implemented writing of binary tags from arrays
+*    implemented convert_binary_tag to use arrays
+*    add special cases for reads that are unmapped or whose mates are unmapped.
+*    rename TabProxies to ctabixproxies
+*    remove underscores from utility functions
+*    move utility methods into cutils
+*    remove callback argument to fetch - closes #128
+*    avoid calling close in dealloc
+*    add unit tests for File object opening
+*    change AlignmentFile.open to filepath_or_object
+*    implement copy.copy, close #65
+*    add chaching of array attributes in AlignedSegment, closes #121
+*    add export of Fastafile
+*    remove superfluous pysam_dispatch
+*    use persist option in FastqFile
+*    get_tag: expose tag type if requested with `with_value_type`
+*    fix to allow reading vcf record info via tabix-based vcf reader
+*    add pFastqProxy and pFastqFile objects to make it possible to work with multiple fastq records per file handle, unlike FastqProxy/FastqFile.
+*    release GIL around htslib IO operations
+*    More work on read/write support, API improvements
+*    add `phased` property on `VariantRecordSample`
+*    add mutable properties to VariantRecord
+*    BCF fixes and start of read/write support
+*    VariantHeaderRecord objects now act like mappings for attributes.
+*    add VariantHeader.alts dict from alt ID->Record.
+*    Bug fix to strong representation of structured header records.
+*    VariantHeader is now mutable
+
+
+Release 0.8.3
+=============
+
+* samtools command now accept the "catch_stdout" option.
+
+* get_aligned_pairs now works for soft-clipped reads.
+
+* query_position is now None when a PileupRead is not aligned
+  to a particular position.
+
+* AlignedSegments are now comparable and hashable.
+
+Release 0.8.2.1
+===============
+
+* Installation bugfix release.
+
+Release 0.8.2
+=============
+
+* Pysam now wraps htslib 1.2.1 and samtools version 1.2.
+
+* Added CRAM file support to pysam.
+
+* New alignment info interface.
+   * opt() and setTag are deprecated, use get_tag() and set_tag()
+     instead.
+   * added has_tag()
+   * tags is deprecated, use get_tags() and set_tags() instead.
+
+* FastqFile is now FastxFile to reflect that the latter permits
+  iteration over both fastq- and fasta-formatted files.
+
+* A Cython wrapper for htslib VCF/BCF reader/writer. The wrapper
+  provides a nearly complete Pythonic interface to VCF/BCF metadata
+  with reading and writing capability. However, the interface is still
+  incomplete and preliminary and lacks capability to mutate the
+  resulting data.
+
+Release 0.8.1
+=============
+
+* Pysam now wraps htslib and samtools versions 1.1.
+
+* Bugfixes, most notable:
+  * issue #43: uncompressed BAM output
+  * issue #42: skip tests requiring network if none available
+  * issue #19: multiple iterators can now be made to work on the same tabix file
+  * issue #24: All strings returned from/passed to the pysam API are now unicode in python 3
+  * issue #5:  type guessing for lists of integers fixed
+
+* API changes for consistency. The old API is still present,
+  but deprecated.
+  In particular:
+
+  * Tabixfile -> TabixFile
+  * Fastafile -> FastaFile
+  * Fastqfile -> FastqFile
+  * Samfile -> AlignmentFile
+  * AlignedRead -> AlignedSegment
+     * qname -> query_name
+     * tid -> reference_id
+     * pos -> reference_start
+     * mapq -> mapping_quality
+     * rnext -> next_reference_id
+     * pnext -> next_reference_start
+     * cigar -> cigartuples
+     * cigarstring -> cigarstring
+     * tlen -> template_length
+     * seq -> query_sequence
+     * qual -> query_qualities, now returns array
+     * qqual -> query_alignment_qualities, now returns array
+     * tags -> tags
+     * alen -> reference_length, reference is always "alignment", so removed
+     * aend -> reference_end
+     * rlen -> query_length
+     * query -> query_alignment_sequence
+     * qstart -> query_alignment_start
+     * qend -> query_alignment_end
+     * qlen -> query_alignment_length
+     * mrnm -> next_reference_id
+     * mpos -> next_reference_start
+     * rname -> reference_id
+     * isize -> template_length
+     * blocks -> get_blocks()
+     * aligned_pairs -> get_aligned_pairs()
+     * inferred_length -> infer_query_length()
+     * positions -> get_reference_positions()
+     * overlap() -> get_overlap()
+
+  * All strings are now passed to or received from the pysam API
+    as strings, no more bytes.
+
+Other changes:
+   * AlignmentFile.fetch(reopen) option is now multiple_iterators. The
+     default changed to not reopen a file unless requested by the user.
+   * FastaFile.getReferenceLength is now FastaFile.get_reference_length
+
+Backwards incompatible changes
+
+* Empty cigarstring now returns None (instead of '')
+* Empty cigar now returns None (instead of [])
+* When using the extension classes in cython modules, AlignedRead
+  needs to be substituted with AlignedSegment.
+* fancy_str() has been removed
+* qual, qqual now return arrays
+
+Release 0.8.0
+=============
+
+* Disabled features
+   * IteratorColumn.setMask() disabled as htslib does not implement
+     this functionality?
+
+* Not implemented yet:
+   * reading SAM files without header
+
+Tabix files between version 0.7.8 and 0.8.0 are
+not compatible and need to be re-indexed.
+
+While version 0.7.8 and 0.8.0 should be mostly
+compatible, there are some notable exceptions:
+
+* tabix iterators will fail if there are comments
+  in the middle or the end of a file.
+
+* tabix raises always ValueError for invalid intervals.
+  Previously, different types of errors were raised
+  (KeyError, IndexError, ValueError) depending on
+  the type of invalid intervals (missing chromosome,
+  out-of-range, malformatted interval).
+
+
+Release 0.7.8
+=============
+
+* added AlignedRead.setTag method
+* added AlignedRead.blocks
+* unsetting CIGAR strings is now possible
+* empty CIGAR string returns empty list
+* added reopen flag to Samfile.fetch()
+* various bugfixes
+
+Release 0.7.7
+=============
+
+* added Fastafile.references, .nreferences and .lengths
+* tabix_iterator now uses kseq.h for python 2.7
+
+Release 0.7.6
+=============
+
+* added inferred_length property
+* issue 122: MACOSX getline missing, now it works?
+* seq and qual can be set None
+* added Fastqfile
+
+Release 0.7.5
+=============
+
+* switch to samtools 0.1.19
+* issue 122: MACOSX getline missing
+* issue 130: clean up tempfiles
+* various other bugfixes
+
+Release 0.7.4
+=============
+
+* further bugfixes to setup.py and package layout
+
+Release 0.7.3
+=============
+
+* further bugfixes to setup.py
+* upgraded distribute_setup.py to 0.6.34
+
+Release 0.7.2
+=============
+
+* bugfix in installer - failed when cython not present
+* changed installation locations of shared libraries
+
+Release 0.7.1
+=============
+
+* bugfix: missing PP tag PG records in header
+* added pre-built .c files to distribution
+
+Release 0.7
+===========
+
+* switch to tabix 0.2.6
+* added cigarstring field
+* python3 compatibility
+* added B tag handling
+* added check_sq and check_header options to Samfile.__init__
+* added lazy GTF parsing to tabix
+* reworked support for VCF format parsing
+* bugfixes
+
+Release 0.6
+===========
+
+* switch to samtools 0.1.18
+* various bugfixes
+* removed references to deprecated 'samtools pileup' functionality
+* AlignedRead.tags now returns an empty list if there are no tags.
+* added pnext, rnext and tlen
+
+Release 0.5
+===========
+
+* switch to samtools 0.1.16 and tabix 0.2.5
+* improved tabix parsing, added vcf support
+* re-organized code to permit linking against pysam
+* various bugfixes
+* added Samfile.positions and Samfile.overlap
+
+Release 0.4
+===========
+
+* switch to samtools 0.1.12a and tabix 0.2.3
+* added snp and indel calling.
+* switch from pyrex to cython
+* changed handling of samtools stderr
+* various bugfixes
+* added Samfile.count and Samfile.mate
+* deprecated AlignedRead.rname, added AlignedRead.tid
+
+Release 0.3
+===========
+
+* switch to samtools 0.1.8
+* added support for tabix files
+* numerous bugfixes including
+* permit simultaneous iterators on the same file
+* working access to remote files
diff --git a/README.rst b/README.rst
new file mode 100644
index 0000000..9a66049
--- /dev/null
+++ b/README.rst
@@ -0,0 +1,53 @@
+=====
+Pysam
+=====
+
+|build-status| |docs|
+
+Pysam is a python module for reading and manipulating files in the
+SAM/BAM format. The SAM/BAM format is a way to store efficiently large
+numbers of alignments (`Li 2009`_), such as those routinely created by
+next-generation sequencing methods.
+
+Pysam is a lightweight wrapper of the samtools_ C-API. Pysam also
+includes an interface for tabix_.
+
+If you are using the conda packaging manager (e.g. miniconda or anaconda),
+you can install pysam from the `bioconda channel <https://bioconda.github.io/>`_::
+
+   conda config --add channels defaults
+   conda config --add channels conda-forge
+   conda config --add channels bioconda
+   conda install pysam
+
+Installation through bioconda is the recommended way to install pysam
+as it resolves non-python dependencies and uses pre-configured
+compilation options. Especially for OS X this will potentially save a
+lot of trouble.
+
+The current version of pysam wraps 3rd-party code from htslib-1.16, samtools-1.16.1, and bcftools-1.16.
+
+Pysam is available through `pypi
+<https://pypi.python.org/pypi/pysam>`_. To install, type::
+
+   pip install pysam
+
+Pysam documentation is available
+`here <http://pysam.readthedocs.org/en/latest/>`_
+
+Questions and comments are very welcome and should be sent to the
+`pysam user group <http://groups.google.com/group/pysam-user-group>`_
+
+.. _samtools: http://samtools.sourceforge.net/
+.. _tabix: http://samtools.sourceforge.net/tabix.shtml
+.. _Li 2009: http://www.ncbi.nlm.nih.gov/pubmed/19505943
+
+.. |build-status| image:: https://travis-ci.org/pysam-developers/pysam.svg
+    :alt: build status
+    :scale: 100%
+    :target: https://travis-ci.org/pysam-developers/pysam
+
+.. |docs| image:: https://readthedocs.org/projects/pysam/badge/?version=latest
+    :alt: Documentation Status
+    :scale: 100%
+    :target: https://pysam.readthedocs.org/en/latest/?badge=latest
diff --git a/bcftools/HMM.c b/bcftools/HMM.c
new file mode 100644
index 0000000..c2d302f
--- /dev/null
+++ b/bcftools/HMM.c
@@ -0,0 +1,509 @@
+/* The MIT License
+
+   Copyright (c) 2014-2017 Genome Research Ltd.
+
+   Author: Petr Danecek <pd3@sanger.ac.uk>
+
+   Permission is hereby granted, free of charge, to any person obtaining a copy
+   of this software and associated documentation files (the "Software"), to deal
+   in the Software without restriction, including without limitation the rights
+   to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+   copies of the Software, and to permit persons to whom the Software is
+   furnished to do so, subject to the following conditions:
+
+   The above copyright notice and this permission notice shall be included in
+   all copies or substantial portions of the Software.
+
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+   IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+   FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+   AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+   LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+   OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+   THE SOFTWARE.
+
+ */
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <assert.h>
+#include <htslib/hts.h>
+#include "HMM.h"
+
+typedef struct
+{
+    int nstates;            // number of hmm's states
+    uint32_t snap_at_pos;   // snapshot at this position, 0 when inactive
+    double *vit_prob;       // viterbi probabilities, NULL for uniform probs
+    double *fwd_prob;       // transition probabilities
+    double *bwd_prob;       // transition probabilities
+}
+snapshot_t;
+
+struct _hmm_t
+{
+    int nstates;    // number of states
+
+    double *vprob, *vprob_tmp;  // viterbi probs [nstates]
+    uint8_t *vpath;             // viterbi path [nstates*nvpath]
+    double *bwd, *bwd_tmp;      // bwd probs [nstates]
+    double *fwd;                // fwd probs [nstates*(nfwd+1)]
+    int nvpath, nfwd;
+
+    int ntprob_arr;             // number of pre-calculated tprob matrices
+    double *curr_tprob, *tmp;   // Temporary arrays; curr_tprob is short lived, valid only for
+                                //  one site (that is, one step of Viterbi algorithm)
+    double *tprob_arr;          // Array of transition matrices, precalculated to ntprob_arr
+                                //  positions. The first matrix is the initial tprob matrix
+                                //  set by hmm_init() or hmm_set_tprob()
+    set_tprob_f set_tprob;      // Optional user function to set / modify transition probabilities
+                                //  at each site (one step of Viterbi algorithm)
+    void *set_tprob_data;
+    snapshot_t init, state;     // Initial and current state probs. Set state from snapshot if prev_snap_pos!=0 or from init otherwise
+    snapshot_t *snapshot;       //  snapshot->snap_at_pos  .. request a snapshot at this position
+                                //  hmm->state.snap_at_pos .. the current state comes from snapshot made at this position
+};
+
+uint8_t *hmm_get_viterbi_path(hmm_t *hmm) { return hmm->vpath; }
+double *hmm_get_tprob(hmm_t *hmm) { return hmm->tprob_arr; }
+int hmm_get_nstates(hmm_t *hmm) { return hmm->nstates; }
+double *hmm_get_fwd_bwd_prob(hmm_t *hmm) { return hmm->fwd; }
+
+static inline void multiply_matrix(int n, double *a, double *b, double *dst, double *tmp)
+{
+    double *out = dst;
+    if ( a==dst || b==dst )
+        out = tmp;
+
+    int i,j,k;
+    for (i=0; i<n; i++)
+    {
+        for (j=0; j<n; j++)
+        {
+            double val = 0;
+            for (k=0; k<n; k++) val += MAT(a,n,i,k)*MAT(b,n,k,j);
+            MAT(out,n,i,j) = val;
+        }
+    }
+    if ( out!=dst )
+        memcpy(dst,out,sizeof(double)*n*n);
+}
+
+void hmm_init_states(hmm_t *hmm, double *probs)
+{
+    hmm->init.snap_at_pos = hmm->state.snap_at_pos = 0;
+
+    if ( !hmm->init.vit_prob )
+        hmm->init.vit_prob = (double*) malloc(sizeof(double)*hmm->nstates);
+    if ( !hmm->init.fwd_prob )
+        hmm->init.fwd_prob = (double*) malloc(sizeof(double)*hmm->nstates);
+    if ( !hmm->init.bwd_prob )
+        hmm->init.bwd_prob = (double*) malloc(sizeof(double)*hmm->nstates);
+
+    if ( !hmm->state.vit_prob )
+        hmm->state.vit_prob = (double*) malloc(sizeof(double)*hmm->nstates);
+    if ( !hmm->state.fwd_prob )
+        hmm->state.fwd_prob = (double*) malloc(sizeof(double)*hmm->nstates);
+    if ( !hmm->state.bwd_prob )
+        hmm->state.bwd_prob = (double*) malloc(sizeof(double)*hmm->nstates);
+    
+    int i;
+    if ( probs )
+    {
+        memcpy(hmm->init.vit_prob,probs,sizeof(double)*hmm->nstates);
+        double sum = 0;
+        for (i=0; i<hmm->nstates; i++) sum += hmm->init.vit_prob[i];
+        for (i=0; i<hmm->nstates; i++) hmm->init.vit_prob[i] /= sum;
+    }
+    else
+        for (i=0; i<hmm->nstates; i++) hmm->init.vit_prob[i] = 1./hmm->nstates;
+
+    memcpy(hmm->init.fwd_prob,hmm->init.vit_prob,sizeof(double)*hmm->nstates);  // these remain unchanged
+    memcpy(hmm->init.bwd_prob,hmm->init.vit_prob,sizeof(double)*hmm->nstates);
+    memcpy(hmm->state.vit_prob,hmm->init.vit_prob,sizeof(double)*hmm->nstates); // can be changed by snapshotting
+    memcpy(hmm->state.fwd_prob,hmm->init.fwd_prob,sizeof(double)*hmm->nstates);
+    memcpy(hmm->state.bwd_prob,hmm->init.bwd_prob,sizeof(double)*hmm->nstates);
+}
+hmm_t *hmm_init(int nstates, double *tprob, int ntprob)
+{
+    hmm_t *hmm = (hmm_t*) calloc(1,sizeof(hmm_t));
+    hmm->nstates = nstates;
+    hmm->curr_tprob = (double*) malloc(sizeof(double)*nstates*nstates);
+    hmm->tmp = (double*) malloc(sizeof(double)*nstates*nstates);
+    hmm_set_tprob(hmm, tprob, ntprob);
+    hmm_init_states(hmm, NULL);
+    return hmm;
+}
+
+void *hmm_snapshot(hmm_t *hmm, void *_snapshot, uint32_t pos)
+{
+    snapshot_t *snapshot = (snapshot_t*) _snapshot;
+    if ( snapshot && snapshot->nstates!=hmm->nstates )
+    {
+        free(snapshot);
+        snapshot = NULL;
+    }
+    if ( !snapshot )
+    {
+        // Allocate the snapshot as a single memory block so that it can be
+        // free()-ed by the user. So make sure the arrays are aligned..
+        size_t str_size = sizeof(snapshot_t);
+        size_t dbl_size = sizeof(double);
+        size_t pad_size = (dbl_size - str_size % dbl_size) % dbl_size;
+        uint8_t *mem = (uint8_t*) malloc(str_size + pad_size + dbl_size*2*hmm->nstates);
+        snapshot = (snapshot_t*) mem;
+        snapshot->nstates  = hmm->nstates;
+        snapshot->vit_prob = (double*) (mem + str_size + pad_size);
+        snapshot->fwd_prob = snapshot->vit_prob + hmm->nstates;
+    }
+    snapshot->snap_at_pos = pos;
+    hmm->snapshot = snapshot;
+    return snapshot;
+}
+void hmm_restore(hmm_t *hmm, void *_snapshot)
+{
+    snapshot_t *snapshot = (snapshot_t*) _snapshot;
+    if ( !snapshot || !snapshot->snap_at_pos ) 
+    {
+        hmm->state.snap_at_pos = 0;
+        memcpy(hmm->state.vit_prob,hmm->init.vit_prob,sizeof(double)*hmm->nstates);
+        memcpy(hmm->state.fwd_prob,hmm->init.fwd_prob,sizeof(double)*hmm->nstates);
+    }
+    else
+    {
+        hmm->state.snap_at_pos = snapshot->snap_at_pos;
+        memcpy(hmm->state.vit_prob,snapshot->vit_prob,sizeof(double)*hmm->nstates);
+        memcpy(hmm->state.fwd_prob,snapshot->fwd_prob,sizeof(double)*hmm->nstates);
+    }
+}
+void hmm_reset(hmm_t *hmm, void *_snapshot)
+{
+    snapshot_t *snapshot = (snapshot_t*) _snapshot;
+    if ( snapshot ) snapshot->snap_at_pos = 0;
+    hmm->state.snap_at_pos = 0;
+    memcpy(hmm->state.vit_prob,hmm->init.vit_prob,sizeof(double)*hmm->nstates);
+    memcpy(hmm->state.fwd_prob,hmm->init.fwd_prob,sizeof(double)*hmm->nstates);
+}
+
+void hmm_set_tprob(hmm_t *hmm, double *tprob, int ntprob)
+{
+    hmm->ntprob_arr = ntprob;
+    if ( ntprob<=0 ) ntprob = 1;
+
+    if ( !hmm->tprob_arr )
+        hmm->tprob_arr  = (double*) malloc(sizeof(double)*hmm->nstates*hmm->nstates*ntprob);
+
+    memcpy(hmm->tprob_arr,tprob,sizeof(double)*hmm->nstates*hmm->nstates);
+
+    int i;
+    for (i=1; i<ntprob; i++)
+        multiply_matrix(hmm->nstates, hmm->tprob_arr, hmm->tprob_arr+(i-1)*hmm->nstates*hmm->nstates, hmm->tprob_arr+i*hmm->nstates*hmm->nstates, hmm->tmp);
+}
+
+void hmm_set_tprob_func(hmm_t *hmm, set_tprob_f set_tprob, void *data)
+{
+    hmm->set_tprob = set_tprob;
+    hmm->set_tprob_data = data;
+}
+
+static void _set_tprob(hmm_t *hmm, int pos_diff)
+{
+    assert( pos_diff>=0 );
+
+    int i, n;
+
+    n = hmm->ntprob_arr ? pos_diff % hmm->ntprob_arr : 0;  // n-th precalculated matrix
+    memcpy(hmm->curr_tprob, hmm->tprob_arr+n*hmm->nstates*hmm->nstates, sizeof(*hmm->curr_tprob)*hmm->nstates*hmm->nstates);
+
+    if ( hmm->ntprob_arr > 0  )
+    {
+        n = pos_diff / hmm->ntprob_arr;  // number of full blocks to jump
+        for (i=0; i<n; i++)
+            multiply_matrix(hmm->nstates, hmm->tprob_arr+(hmm->ntprob_arr-1)*hmm->nstates*hmm->nstates, hmm->curr_tprob, hmm->curr_tprob, hmm->tmp);
+    }
+}
+
+void hmm_run_viterbi(hmm_t *hmm, int n, double *eprobs, uint32_t *sites)
+{
+    // Init arrays when run for the first time
+    if ( hmm->nvpath < n )
+    {
+        hmm->nvpath = n;
+        hmm->vpath  = (uint8_t*) realloc(hmm->vpath, sizeof(uint8_t)*hmm->nvpath*hmm->nstates);
+    }
+    if ( !hmm->vprob )
+    {
+        hmm->vprob     = (double*) malloc(sizeof(double)*hmm->nstates);
+        hmm->vprob_tmp = (double*) malloc(sizeof(double)*hmm->nstates);
+    }
+
+    // Init all states with equal likelihood
+    int i,j, nstates = hmm->nstates;
+    memcpy(hmm->vprob, hmm->state.vit_prob, sizeof(*hmm->state.vit_prob)*nstates);
+    uint32_t prev_pos = hmm->state.snap_at_pos ? hmm->state.snap_at_pos : sites[0];
+
+    // Run Viterbi
+    for (i=0; i<n; i++)
+    {
+        uint8_t *vpath = &hmm->vpath[i*nstates];
+        double *eprob  = &eprobs[i*nstates];
+
+        int pos_diff = sites[i] == prev_pos ? 0 : sites[i] - prev_pos - 1;
+        _set_tprob(hmm, pos_diff);
+        if ( hmm->set_tprob ) hmm->set_tprob(hmm, prev_pos, sites[i], hmm->set_tprob_data, hmm->curr_tprob);
+        prev_pos = sites[i];
+
+        double vnorm = 0;
+        for (j=0; j<nstates; j++)
+        {
+            double vmax = 0;
+            int k, k_vmax = 0;
+            for (k=0; k<nstates; k++)
+            {
+                double pval = hmm->vprob[k] * MAT(hmm->curr_tprob,hmm->nstates,j,k);
+                if ( vmax < pval ) { vmax = pval; k_vmax = k; }
+            }
+            vpath[j] = k_vmax;
+            hmm->vprob_tmp[j] = vmax * eprob[j];
+            vnorm += hmm->vprob_tmp[j];
+        }
+        for (j=0; j<nstates; j++) hmm->vprob_tmp[j] /= vnorm;
+        double *tmp = hmm->vprob; hmm->vprob = hmm->vprob_tmp; hmm->vprob_tmp = tmp;
+
+        if ( hmm->snapshot && sites[i]==hmm->snapshot->snap_at_pos )
+            memcpy(hmm->snapshot->vit_prob, hmm->vprob, sizeof(*hmm->vprob)*nstates);
+    }
+
+    // Find the most likely state
+    int iptr = 0;
+    for (i=1; i<nstates; i++) 
+        if ( hmm->vprob[iptr] < hmm->vprob[i] ) iptr = i;
+
+    // Trace back the Viterbi path, we are reusing vpath for storing the states (vpath[i*nstates])
+    for (i=n-1; i>=0; i--)
+    {
+        assert( iptr<nstates && hmm->vpath[i*nstates + iptr]<nstates );
+        iptr = hmm->vpath[i*nstates + iptr];
+        hmm->vpath[i*nstates] = iptr;     // reusing the array for different purpose here
+    }
+}
+
+void hmm_run_fwd_bwd(hmm_t *hmm, int n, double *eprobs, uint32_t *sites)
+{
+    // Init arrays when run for the first time
+    if ( hmm->nfwd < n )
+    {
+        hmm->nfwd = n;
+        hmm->fwd  = (double*) realloc(hmm->fwd, sizeof(double)*(hmm->nfwd+1)*hmm->nstates);
+    }
+    if ( !hmm->bwd )
+    {
+        hmm->bwd     = (double*) malloc(sizeof(double)*hmm->nstates);
+        hmm->bwd_tmp = (double*) malloc(sizeof(double)*hmm->nstates);
+    }
+
+
+    int i,j,k, nstates = hmm->nstates;
+    memcpy(hmm->fwd, hmm->state.fwd_prob, sizeof(*hmm->state.fwd_prob)*nstates);
+    memcpy(hmm->bwd, hmm->state.bwd_prob, sizeof(*hmm->state.bwd_prob)*nstates);
+    uint32_t prev_pos = hmm->state.snap_at_pos ? hmm->state.snap_at_pos : sites[0];
+
+    // Run fwd 
+    for (i=0; i<n; i++)
+    {
+        double *fwd_prev = &hmm->fwd[i*nstates];
+        double *fwd      = &hmm->fwd[(i+1)*nstates];
+        double *eprob    = &eprobs[i*nstates];
+
+        int pos_diff = sites[i] == prev_pos ? 0 : sites[i] - prev_pos - 1;
+
+        _set_tprob(hmm, pos_diff);
+        if ( hmm->set_tprob ) hmm->set_tprob(hmm, prev_pos, sites[i], hmm->set_tprob_data, hmm->curr_tprob);
+        prev_pos = sites[i];
+
+        double norm = 0;
+        for (j=0; j<nstates; j++)
+        {
+            double pval = 0;
+            for (k=0; k<nstates; k++)
+                pval += fwd_prev[k] * MAT(hmm->curr_tprob,hmm->nstates,j,k);
+            fwd[j] = pval * eprob[j];
+            norm += fwd[j];
+        }
+        for (j=0; j<nstates; j++) fwd[j] /= norm;
+
+        if ( hmm->snapshot && sites[i]==hmm->snapshot->snap_at_pos )
+            memcpy(hmm->snapshot->fwd_prob, fwd, sizeof(*fwd)*nstates);
+    }
+
+    // Run bwd
+    double *bwd = hmm->bwd, *bwd_tmp = hmm->bwd_tmp;
+    prev_pos = sites[n-1];
+    for (i=0; i<n; i++)
+    {
+        double *fwd   = &hmm->fwd[(n-i)*nstates];
+        double *eprob = &eprobs[(n-i-1)*nstates];
+        
+        int pos_diff = sites[n-i-1] == prev_pos ? 0 : prev_pos - sites[n-i-1] - 1;
+
+        _set_tprob(hmm, pos_diff);
+        if ( hmm->set_tprob ) hmm->set_tprob(hmm, sites[n-i-1], prev_pos, hmm->set_tprob_data, hmm->curr_tprob);
+        prev_pos = sites[n-i-1];
+
+        double bwd_norm = 0;
+        for (j=0; j<nstates; j++)
+        {
+            double pval = 0;
+            for (k=0; k<nstates; k++)
+                pval += bwd[k] * eprob[k] * MAT(hmm->curr_tprob,hmm->nstates,k,j);
+            bwd_tmp[j] = pval;
+            bwd_norm += pval;
+        }
+        double norm = 0;
+        for (j=0; j<nstates; j++)
+        {
+            bwd_tmp[j] /= bwd_norm;
+            fwd[j] *= bwd_tmp[j];   // fwd now stores fwd*bwd
+            norm += fwd[j];
+        }
+        for (j=0; j<nstates; j++) fwd[j] /= norm;
+        double *tmp = bwd_tmp; bwd_tmp = bwd; bwd = tmp;
+    }
+}
+
+double *hmm_run_baum_welch(hmm_t *hmm, int n, double *eprobs, uint32_t *sites)
+{
+    // Init arrays when run for the first time
+    if ( hmm->nfwd < n )
+    {
+        hmm->nfwd = n;
+        hmm->fwd  = (double*) realloc(hmm->fwd, sizeof(double)*(hmm->nfwd+1)*hmm->nstates);
+    }
+    if ( !hmm->bwd )
+    {
+        hmm->bwd     = (double*) malloc(sizeof(double)*hmm->nstates);
+        hmm->bwd_tmp = (double*) malloc(sizeof(double)*hmm->nstates);
+    }
+
+    // Init all states with equal likelihood
+    int i,j,k, nstates = hmm->nstates;
+    memcpy(hmm->fwd, hmm->state.fwd_prob, sizeof(*hmm->state.fwd_prob)*nstates);
+    memcpy(hmm->bwd, hmm->state.bwd_prob, sizeof(*hmm->state.bwd_prob)*nstates);
+    uint32_t prev_pos = hmm->state.snap_at_pos ? hmm->state.snap_at_pos : sites[0];
+
+    // New transition matrix: temporary values
+    double *tmp_xi = (double*) calloc(nstates*nstates,sizeof(double));
+    double *tmp_gamma = (double*) calloc(nstates,sizeof(double));
+    double *fwd_bwd = (double*) malloc(sizeof(double)*nstates);
+
+    // Run fwd 
+    for (i=0; i<n; i++)
+    {
+        double *fwd_prev = &hmm->fwd[i*nstates];
+        double *fwd      = &hmm->fwd[(i+1)*nstates];
+        double *eprob    = &eprobs[i*nstates];
+
+        int pos_diff = sites[i] == prev_pos ? 0 : sites[i] - prev_pos - 1;
+
+        _set_tprob(hmm, pos_diff);
+        if ( hmm->set_tprob ) hmm->set_tprob(hmm, prev_pos, sites[i], hmm->set_tprob_data, hmm->curr_tprob);
+        prev_pos = sites[i];
+
+        double norm = 0;
+        for (j=0; j<nstates; j++)
+        {
+            double pval = 0;
+            for (k=0; k<nstates; k++)
+                pval += fwd_prev[k] * MAT(hmm->curr_tprob,hmm->nstates,j,k);
+            fwd[j] = pval * eprob[j];
+            norm += fwd[j];
+        }
+        for (j=0; j<nstates; j++) fwd[j] /= norm;
+    }
+
+    // Run bwd
+    double *bwd = hmm->bwd, *bwd_tmp = hmm->bwd_tmp;
+    prev_pos = sites[n-1];
+    for (i=0; i<n; i++)
+    {
+        double *fwd   = &hmm->fwd[(n-i)*nstates];
+        double *eprob = &eprobs[(n-i-1)*nstates];
+        
+        int pos_diff = sites[n-i-1] == prev_pos ? 0 : prev_pos - sites[n-i-1] - 1;
+
+        _set_tprob(hmm, pos_diff);
+        if ( hmm->set_tprob ) hmm->set_tprob(hmm, sites[n-i-1], prev_pos, hmm->set_tprob_data, hmm->curr_tprob);
+        prev_pos = sites[n-i-1];
+
+        double bwd_norm = 0;
+        for (j=0; j<nstates; j++)
+        {
+            double pval = 0;
+            for (k=0; k<nstates; k++)
+                pval += bwd[k] * eprob[k] * MAT(hmm->curr_tprob,hmm->nstates,k,j);
+            bwd_tmp[j] = pval;
+            bwd_norm += pval;
+        }
+        double norm = 0;
+        for (j=0; j<nstates; j++)
+        {
+            bwd_tmp[j] /= bwd_norm;
+            fwd_bwd[j] = fwd[j]*bwd_tmp[j];
+            norm += fwd_bwd[j];
+        }
+        for (j=0; j<nstates; j++) 
+        {
+            fwd_bwd[j] /= norm;
+            tmp_gamma[j] += fwd_bwd[j];
+        }
+
+        for (j=0; j<nstates; j++)
+        {
+            for (k=0; k<nstates; k++)
+            {
+                MAT(tmp_xi,nstates,k,j) += fwd[j]*bwd[k]*MAT(hmm->tprob_arr,hmm->nstates,k,j)*eprob[k] / norm;
+            }
+        }
+
+        for (j=0; j<nstates; j++) fwd[j] = fwd_bwd[j];    // fwd now stores fwd*bwd
+
+        double *tmp = bwd_tmp; bwd_tmp = bwd; bwd = tmp;
+    }
+    for (j=0; j<nstates; j++)
+    {
+        double norm = 0;
+        for (k=0; k<nstates; k++)
+        {
+            MAT(hmm->curr_tprob,nstates,k,j) = MAT(tmp_xi,nstates,k,j) / tmp_gamma[j];
+            norm += MAT(hmm->curr_tprob,nstates,k,j);
+        }
+        for (k=0; k<nstates; k++)
+            MAT(hmm->curr_tprob,nstates,k,j) /= norm;
+    }
+    free(tmp_gamma);
+    free(tmp_xi);
+    free(fwd_bwd);
+    return hmm->curr_tprob;
+}
+
+void hmm_destroy(hmm_t *hmm)
+{
+    free(hmm->init.vit_prob);
+    free(hmm->init.fwd_prob);
+    free(hmm->init.bwd_prob);
+    free(hmm->state.vit_prob);
+    free(hmm->state.fwd_prob);
+    free(hmm->state.bwd_prob);
+    free(hmm->vprob);
+    free(hmm->vprob_tmp);
+    free(hmm->vpath);
+    free(hmm->curr_tprob);
+    free(hmm->tmp);
+    free(hmm->tprob_arr);
+    free(hmm->fwd);
+    free(hmm->bwd);
+    free(hmm->bwd_tmp);
+    free(hmm);
+}
+
diff --git a/bcftools/HMM.c.pysam.c b/bcftools/HMM.c.pysam.c
new file mode 100644
index 0000000..d039367
--- /dev/null
+++ b/bcftools/HMM.c.pysam.c
@@ -0,0 +1,511 @@
+#include "bcftools.pysam.h"
+
+/* The MIT License
+
+   Copyright (c) 2014-2017 Genome Research Ltd.
+
+   Author: Petr Danecek <pd3@sanger.ac.uk>
+
+   Permission is hereby granted, free of charge, to any person obtaining a copy
+   of this software and associated documentation files (the "Software"), to deal
+   in the Software without restriction, including without limitation the rights
+   to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+   copies of the Software, and to permit persons to whom the Software is
+   furnished to do so, subject to the following conditions:
+
+   The above copyright notice and this permission notice shall be included in
+   all copies or substantial portions of the Software.
+
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+   IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+   FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+   AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+   LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+   OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+   THE SOFTWARE.
+
+ */
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <assert.h>
+#include <htslib/hts.h>
+#include "HMM.h"
+
+typedef struct
+{
+    int nstates;            // number of hmm's states
+    uint32_t snap_at_pos;   // snapshot at this position, 0 when inactive
+    double *vit_prob;       // viterbi probabilities, NULL for uniform probs
+    double *fwd_prob;       // transition probabilities
+    double *bwd_prob;       // transition probabilities
+}
+snapshot_t;
+
+struct _hmm_t
+{
+    int nstates;    // number of states
+
+    double *vprob, *vprob_tmp;  // viterbi probs [nstates]
+    uint8_t *vpath;             // viterbi path [nstates*nvpath]
+    double *bwd, *bwd_tmp;      // bwd probs [nstates]
+    double *fwd;                // fwd probs [nstates*(nfwd+1)]
+    int nvpath, nfwd;
+
+    int ntprob_arr;             // number of pre-calculated tprob matrices
+    double *curr_tprob, *tmp;   // Temporary arrays; curr_tprob is short lived, valid only for
+                                //  one site (that is, one step of Viterbi algorithm)
+    double *tprob_arr;          // Array of transition matrices, precalculated to ntprob_arr
+                                //  positions. The first matrix is the initial tprob matrix
+                                //  set by hmm_init() or hmm_set_tprob()
+    set_tprob_f set_tprob;      // Optional user function to set / modify transition probabilities
+                                //  at each site (one step of Viterbi algorithm)
+    void *set_tprob_data;
+    snapshot_t init, state;     // Initial and current state probs. Set state from snapshot if prev_snap_pos!=0 or from init otherwise
+    snapshot_t *snapshot;       //  snapshot->snap_at_pos  .. request a snapshot at this position
+                                //  hmm->state.snap_at_pos .. the current state comes from snapshot made at this position
+};
+
+uint8_t *hmm_get_viterbi_path(hmm_t *hmm) { return hmm->vpath; }
+double *hmm_get_tprob(hmm_t *hmm) { return hmm->tprob_arr; }
+int hmm_get_nstates(hmm_t *hmm) { return hmm->nstates; }
+double *hmm_get_fwd_bwd_prob(hmm_t *hmm) { return hmm->fwd; }
+
+static inline void multiply_matrix(int n, double *a, double *b, double *dst, double *tmp)
+{
+    double *out = dst;
+    if ( a==dst || b==dst )
+        out = tmp;
+
+    int i,j,k;
+    for (i=0; i<n; i++)
+    {
+        for (j=0; j<n; j++)
+        {
+            double val = 0;
+            for (k=0; k<n; k++) val += MAT(a,n,i,k)*MAT(b,n,k,j);
+            MAT(out,n,i,j) = val;
+        }
+    }
+    if ( out!=dst )
+        memcpy(dst,out,sizeof(double)*n*n);
+}
+
+void hmm_init_states(hmm_t *hmm, double *probs)
+{
+    hmm->init.snap_at_pos = hmm->state.snap_at_pos = 0;
+
+    if ( !hmm->init.vit_prob )
+        hmm->init.vit_prob = (double*) malloc(sizeof(double)*hmm->nstates);
+    if ( !hmm->init.fwd_prob )
+        hmm->init.fwd_prob = (double*) malloc(sizeof(double)*hmm->nstates);
+    if ( !hmm->init.bwd_prob )
+        hmm->init.bwd_prob = (double*) malloc(sizeof(double)*hmm->nstates);
+
+    if ( !hmm->state.vit_prob )
+        hmm->state.vit_prob = (double*) malloc(sizeof(double)*hmm->nstates);
+    if ( !hmm->state.fwd_prob )
+        hmm->state.fwd_prob = (double*) malloc(sizeof(double)*hmm->nstates);
+    if ( !hmm->state.bwd_prob )
+        hmm->state.bwd_prob = (double*) malloc(sizeof(double)*hmm->nstates);
+    
+    int i;
+    if ( probs )
+    {
+        memcpy(hmm->init.vit_prob,probs,sizeof(double)*hmm->nstates);
+        double sum = 0;
+        for (i=0; i<hmm->nstates; i++) sum += hmm->init.vit_prob[i];
+        for (i=0; i<hmm->nstates; i++) hmm->init.vit_prob[i] /= sum;
+    }
+    else
+        for (i=0; i<hmm->nstates; i++) hmm->init.vit_prob[i] = 1./hmm->nstates;
+
+    memcpy(hmm->init.fwd_prob,hmm->init.vit_prob,sizeof(double)*hmm->nstates);  // these remain unchanged
+    memcpy(hmm->init.bwd_prob,hmm->init.vit_prob,sizeof(double)*hmm->nstates);
+    memcpy(hmm->state.vit_prob,hmm->init.vit_prob,sizeof(double)*hmm->nstates); // can be changed by snapshotting
+    memcpy(hmm->state.fwd_prob,hmm->init.fwd_prob,sizeof(double)*hmm->nstates);
+    memcpy(hmm->state.bwd_prob,hmm->init.bwd_prob,sizeof(double)*hmm->nstates);
+}
+hmm_t *hmm_init(int nstates, double *tprob, int ntprob)
+{
+    hmm_t *hmm = (hmm_t*) calloc(1,sizeof(hmm_t));
+    hmm->nstates = nstates;
+    hmm->curr_tprob = (double*) malloc(sizeof(double)*nstates*nstates);
+    hmm->tmp = (double*) malloc(sizeof(double)*nstates*nstates);
+    hmm_set_tprob(hmm, tprob, ntprob);
+    hmm_init_states(hmm, NULL);
+    return hmm;
+}
+
+void *hmm_snapshot(hmm_t *hmm, void *_snapshot, uint32_t pos)
+{
+    snapshot_t *snapshot = (snapshot_t*) _snapshot;
+    if ( snapshot && snapshot->nstates!=hmm->nstates )
+    {
+        free(snapshot);
+        snapshot = NULL;
+    }
+    if ( !snapshot )
+    {
+        // Allocate the snapshot as a single memory block so that it can be
+        // free()-ed by the user. So make sure the arrays are aligned..
+        size_t str_size = sizeof(snapshot_t);
+        size_t dbl_size = sizeof(double);
+        size_t pad_size = (dbl_size - str_size % dbl_size) % dbl_size;
+        uint8_t *mem = (uint8_t*) malloc(str_size + pad_size + dbl_size*2*hmm->nstates);
+        snapshot = (snapshot_t*) mem;
+        snapshot->nstates  = hmm->nstates;
+        snapshot->vit_prob = (double*) (mem + str_size + pad_size);
+        snapshot->fwd_prob = snapshot->vit_prob + hmm->nstates;
+    }
+    snapshot->snap_at_pos = pos;
+    hmm->snapshot = snapshot;
+    return snapshot;
+}
+void hmm_restore(hmm_t *hmm, void *_snapshot)
+{
+    snapshot_t *snapshot = (snapshot_t*) _snapshot;
+    if ( !snapshot || !snapshot->snap_at_pos ) 
+    {
+        hmm->state.snap_at_pos = 0;
+        memcpy(hmm->state.vit_prob,hmm->init.vit_prob,sizeof(double)*hmm->nstates);
+        memcpy(hmm->state.fwd_prob,hmm->init.fwd_prob,sizeof(double)*hmm->nstates);
+    }
+    else
+    {
+        hmm->state.snap_at_pos = snapshot->snap_at_pos;
+        memcpy(hmm->state.vit_prob,snapshot->vit_prob,sizeof(double)*hmm->nstates);
+        memcpy(hmm->state.fwd_prob,snapshot->fwd_prob,sizeof(double)*hmm->nstates);
+    }
+}
+void hmm_reset(hmm_t *hmm, void *_snapshot)
+{
+    snapshot_t *snapshot = (snapshot_t*) _snapshot;
+    if ( snapshot ) snapshot->snap_at_pos = 0;
+    hmm->state.snap_at_pos = 0;
+    memcpy(hmm->state.vit_prob,hmm->init.vit_prob,sizeof(double)*hmm->nstates);
+    memcpy(hmm->state.fwd_prob,hmm->init.fwd_prob,sizeof(double)*hmm->nstates);
+}
+
+void hmm_set_tprob(hmm_t *hmm, double *tprob, int ntprob)
+{
+    hmm->ntprob_arr = ntprob;
+    if ( ntprob<=0 ) ntprob = 1;
+
+    if ( !hmm->tprob_arr )
+        hmm->tprob_arr  = (double*) malloc(sizeof(double)*hmm->nstates*hmm->nstates*ntprob);
+
+    memcpy(hmm->tprob_arr,tprob,sizeof(double)*hmm->nstates*hmm->nstates);
+
+    int i;
+    for (i=1; i<ntprob; i++)
+        multiply_matrix(hmm->nstates, hmm->tprob_arr, hmm->tprob_arr+(i-1)*hmm->nstates*hmm->nstates, hmm->tprob_arr+i*hmm->nstates*hmm->nstates, hmm->tmp);
+}
+
+void hmm_set_tprob_func(hmm_t *hmm, set_tprob_f set_tprob, void *data)
+{
+    hmm->set_tprob = set_tprob;
+    hmm->set_tprob_data = data;
+}
+
+static void _set_tprob(hmm_t *hmm, int pos_diff)
+{
+    assert( pos_diff>=0 );
+
+    int i, n;
+
+    n = hmm->ntprob_arr ? pos_diff % hmm->ntprob_arr : 0;  // n-th precalculated matrix
+    memcpy(hmm->curr_tprob, hmm->tprob_arr+n*hmm->nstates*hmm->nstates, sizeof(*hmm->curr_tprob)*hmm->nstates*hmm->nstates);
+
+    if ( hmm->ntprob_arr > 0  )
+    {
+        n = pos_diff / hmm->ntprob_arr;  // number of full blocks to jump
+        for (i=0; i<n; i++)
+            multiply_matrix(hmm->nstates, hmm->tprob_arr+(hmm->ntprob_arr-1)*hmm->nstates*hmm->nstates, hmm->curr_tprob, hmm->curr_tprob, hmm->tmp);
+    }
+}
+
+void hmm_run_viterbi(hmm_t *hmm, int n, double *eprobs, uint32_t *sites)
+{
+    // Init arrays when run for the first time
+    if ( hmm->nvpath < n )
+    {
+        hmm->nvpath = n;
+        hmm->vpath  = (uint8_t*) realloc(hmm->vpath, sizeof(uint8_t)*hmm->nvpath*hmm->nstates);
+    }
+    if ( !hmm->vprob )
+    {
+        hmm->vprob     = (double*) malloc(sizeof(double)*hmm->nstates);
+        hmm->vprob_tmp = (double*) malloc(sizeof(double)*hmm->nstates);
+    }
+
+    // Init all states with equal likelihood
+    int i,j, nstates = hmm->nstates;
+    memcpy(hmm->vprob, hmm->state.vit_prob, sizeof(*hmm->state.vit_prob)*nstates);
+    uint32_t prev_pos = hmm->state.snap_at_pos ? hmm->state.snap_at_pos : sites[0];
+
+    // Run Viterbi
+    for (i=0; i<n; i++)
+    {
+        uint8_t *vpath = &hmm->vpath[i*nstates];
+        double *eprob  = &eprobs[i*nstates];
+
+        int pos_diff = sites[i] == prev_pos ? 0 : sites[i] - prev_pos - 1;
+        _set_tprob(hmm, pos_diff);
+        if ( hmm->set_tprob ) hmm->set_tprob(hmm, prev_pos, sites[i], hmm->set_tprob_data, hmm->curr_tprob);
+        prev_pos = sites[i];
+
+        double vnorm = 0;
+        for (j=0; j<nstates; j++)
+        {
+            double vmax = 0;
+            int k, k_vmax = 0;
+            for (k=0; k<nstates; k++)
+            {
+                double pval = hmm->vprob[k] * MAT(hmm->curr_tprob,hmm->nstates,j,k);
+                if ( vmax < pval ) { vmax = pval; k_vmax = k; }
+            }
+            vpath[j] = k_vmax;
+            hmm->vprob_tmp[j] = vmax * eprob[j];
+            vnorm += hmm->vprob_tmp[j];
+        }
+        for (j=0; j<nstates; j++) hmm->vprob_tmp[j] /= vnorm;
+        double *tmp = hmm->vprob; hmm->vprob = hmm->vprob_tmp; hmm->vprob_tmp = tmp;
+
+        if ( hmm->snapshot && sites[i]==hmm->snapshot->snap_at_pos )
+            memcpy(hmm->snapshot->vit_prob, hmm->vprob, sizeof(*hmm->vprob)*nstates);
+    }
+
+    // Find the most likely state
+    int iptr = 0;
+    for (i=1; i<nstates; i++) 
+        if ( hmm->vprob[iptr] < hmm->vprob[i] ) iptr = i;
+
+    // Trace back the Viterbi path, we are reusing vpath for storing the states (vpath[i*nstates])
+    for (i=n-1; i>=0; i--)
+    {
+        assert( iptr<nstates && hmm->vpath[i*nstates + iptr]<nstates );
+        iptr = hmm->vpath[i*nstates + iptr];
+        hmm->vpath[i*nstates] = iptr;     // reusing the array for different purpose here
+    }
+}
+
+void hmm_run_fwd_bwd(hmm_t *hmm, int n, double *eprobs, uint32_t *sites)
+{
+    // Init arrays when run for the first time
+    if ( hmm->nfwd < n )
+    {
+        hmm->nfwd = n;
+        hmm->fwd  = (double*) realloc(hmm->fwd, sizeof(double)*(hmm->nfwd+1)*hmm->nstates);
+    }
+    if ( !hmm->bwd )
+    {
+        hmm->bwd     = (double*) malloc(sizeof(double)*hmm->nstates);
+        hmm->bwd_tmp = (double*) malloc(sizeof(double)*hmm->nstates);
+    }
+
+
+    int i,j,k, nstates = hmm->nstates;
+    memcpy(hmm->fwd, hmm->state.fwd_prob, sizeof(*hmm->state.fwd_prob)*nstates);
+    memcpy(hmm->bwd, hmm->state.bwd_prob, sizeof(*hmm->state.bwd_prob)*nstates);
+    uint32_t prev_pos = hmm->state.snap_at_pos ? hmm->state.snap_at_pos : sites[0];
+
+    // Run fwd 
+    for (i=0; i<n; i++)
+    {
+        double *fwd_prev = &hmm->fwd[i*nstates];
+        double *fwd      = &hmm->fwd[(i+1)*nstates];
+        double *eprob    = &eprobs[i*nstates];
+
+        int pos_diff = sites[i] == prev_pos ? 0 : sites[i] - prev_pos - 1;
+
+        _set_tprob(hmm, pos_diff);
+        if ( hmm->set_tprob ) hmm->set_tprob(hmm, prev_pos, sites[i], hmm->set_tprob_data, hmm->curr_tprob);
+        prev_pos = sites[i];
+
+        double norm = 0;
+        for (j=0; j<nstates; j++)
+        {
+            double pval = 0;
+            for (k=0; k<nstates; k++)
+                pval += fwd_prev[k] * MAT(hmm->curr_tprob,hmm->nstates,j,k);
+            fwd[j] = pval * eprob[j];
+            norm += fwd[j];
+        }
+        for (j=0; j<nstates; j++) fwd[j] /= norm;
+
+        if ( hmm->snapshot && sites[i]==hmm->snapshot->snap_at_pos )
+            memcpy(hmm->snapshot->fwd_prob, fwd, sizeof(*fwd)*nstates);
+    }
+
+    // Run bwd
+    double *bwd = hmm->bwd, *bwd_tmp = hmm->bwd_tmp;
+    prev_pos = sites[n-1];
+    for (i=0; i<n; i++)
+    {
+        double *fwd   = &hmm->fwd[(n-i)*nstates];
+        double *eprob = &eprobs[(n-i-1)*nstates];
+        
+        int pos_diff = sites[n-i-1] == prev_pos ? 0 : prev_pos - sites[n-i-1] - 1;
+
+        _set_tprob(hmm, pos_diff);
+        if ( hmm->set_tprob ) hmm->set_tprob(hmm, sites[n-i-1], prev_pos, hmm->set_tprob_data, hmm->curr_tprob);
+        prev_pos = sites[n-i-1];
+
+        double bwd_norm = 0;
+        for (j=0; j<nstates; j++)
+        {
+            double pval = 0;
+            for (k=0; k<nstates; k++)
+                pval += bwd[k] * eprob[k] * MAT(hmm->curr_tprob,hmm->nstates,k,j);
+            bwd_tmp[j] = pval;
+            bwd_norm += pval;
+        }
+        double norm = 0;
+        for (j=0; j<nstates; j++)
+        {
+            bwd_tmp[j] /= bwd_norm;
+            fwd[j] *= bwd_tmp[j];   // fwd now stores fwd*bwd
+            norm += fwd[j];
+        }
+        for (j=0; j<nstates; j++) fwd[j] /= norm;
+        double *tmp = bwd_tmp; bwd_tmp = bwd; bwd = tmp;
+    }
+}
+
+double *hmm_run_baum_welch(hmm_t *hmm, int n, double *eprobs, uint32_t *sites)
+{
+    // Init arrays when run for the first time
+    if ( hmm->nfwd < n )
+    {
+        hmm->nfwd = n;
+        hmm->fwd  = (double*) realloc(hmm->fwd, sizeof(double)*(hmm->nfwd+1)*hmm->nstates);
+    }
+    if ( !hmm->bwd )
+    {
+        hmm->bwd     = (double*) malloc(sizeof(double)*hmm->nstates);
+        hmm->bwd_tmp = (double*) malloc(sizeof(double)*hmm->nstates);
+    }
+
+    // Init all states with equal likelihood
+    int i,j,k, nstates = hmm->nstates;
+    memcpy(hmm->fwd, hmm->state.fwd_prob, sizeof(*hmm->state.fwd_prob)*nstates);
+    memcpy(hmm->bwd, hmm->state.bwd_prob, sizeof(*hmm->state.bwd_prob)*nstates);
+    uint32_t prev_pos = hmm->state.snap_at_pos ? hmm->state.snap_at_pos : sites[0];
+
+    // New transition matrix: temporary values
+    double *tmp_xi = (double*) calloc(nstates*nstates,sizeof(double));
+    double *tmp_gamma = (double*) calloc(nstates,sizeof(double));
+    double *fwd_bwd = (double*) malloc(sizeof(double)*nstates);
+
+    // Run fwd 
+    for (i=0; i<n; i++)
+    {
+        double *fwd_prev = &hmm->fwd[i*nstates];
+        double *fwd      = &hmm->fwd[(i+1)*nstates];
+        double *eprob    = &eprobs[i*nstates];
+
+        int pos_diff = sites[i] == prev_pos ? 0 : sites[i] - prev_pos - 1;
+
+        _set_tprob(hmm, pos_diff);
+        if ( hmm->set_tprob ) hmm->set_tprob(hmm, prev_pos, sites[i], hmm->set_tprob_data, hmm->curr_tprob);
+        prev_pos = sites[i];
+
+        double norm = 0;
+        for (j=0; j<nstates; j++)
+        {
+            double pval = 0;
+            for (k=0; k<nstates; k++)
+                pval += fwd_prev[k] * MAT(hmm->curr_tprob,hmm->nstates,j,k);
+            fwd[j] = pval * eprob[j];
+            norm += fwd[j];
+        }
+        for (j=0; j<nstates; j++) fwd[j] /= norm;
+    }
+
+    // Run bwd
+    double *bwd = hmm->bwd, *bwd_tmp = hmm->bwd_tmp;
+    prev_pos = sites[n-1];
+    for (i=0; i<n; i++)
+    {
+        double *fwd   = &hmm->fwd[(n-i)*nstates];
+        double *eprob = &eprobs[(n-i-1)*nstates];
+        
+        int pos_diff = sites[n-i-1] == prev_pos ? 0 : prev_pos - sites[n-i-1] - 1;
+
+        _set_tprob(hmm, pos_diff);
+        if ( hmm->set_tprob ) hmm->set_tprob(hmm, sites[n-i-1], prev_pos, hmm->set_tprob_data, hmm->curr_tprob);
+        prev_pos = sites[n-i-1];
+
+        double bwd_norm = 0;
+        for (j=0; j<nstates; j++)
+        {
+            double pval = 0;
+            for (k=0; k<nstates; k++)
+                pval += bwd[k] * eprob[k] * MAT(hmm->curr_tprob,hmm->nstates,k,j);
+            bwd_tmp[j] = pval;
+            bwd_norm += pval;
+        }
+        double norm = 0;
+        for (j=0; j<nstates; j++)
+        {
+            bwd_tmp[j] /= bwd_norm;
+            fwd_bwd[j] = fwd[j]*bwd_tmp[j];
+            norm += fwd_bwd[j];
+        }
+        for (j=0; j<nstates; j++) 
+        {
+            fwd_bwd[j] /= norm;
+            tmp_gamma[j] += fwd_bwd[j];
+        }
+
+        for (j=0; j<nstates; j++)
+        {
+            for (k=0; k<nstates; k++)
+            {
+                MAT(tmp_xi,nstates,k,j) += fwd[j]*bwd[k]*MAT(hmm->tprob_arr,hmm->nstates,k,j)*eprob[k] / norm;
+            }
+        }
+
+        for (j=0; j<nstates; j++) fwd[j] = fwd_bwd[j];    // fwd now stores fwd*bwd
+
+        double *tmp = bwd_tmp; bwd_tmp = bwd; bwd = tmp;
+    }
+    for (j=0; j<nstates; j++)
+    {
+        double norm = 0;
+        for (k=0; k<nstates; k++)
+        {
+            MAT(hmm->curr_tprob,nstates,k,j) = MAT(tmp_xi,nstates,k,j) / tmp_gamma[j];
+            norm += MAT(hmm->curr_tprob,nstates,k,j);
+        }
+        for (k=0; k<nstates; k++)
+            MAT(hmm->curr_tprob,nstates,k,j) /= norm;
+    }
+    free(tmp_gamma);
+    free(tmp_xi);
+    free(fwd_bwd);
+    return hmm->curr_tprob;
+}
+
+void hmm_destroy(hmm_t *hmm)
+{
+    free(hmm->init.vit_prob);
+    free(hmm->init.fwd_prob);
+    free(hmm->init.bwd_prob);
+    free(hmm->state.vit_prob);
+    free(hmm->state.fwd_prob);
+    free(hmm->state.bwd_prob);
+    free(hmm->vprob);
+    free(hmm->vprob_tmp);
+    free(hmm->vpath);
+    free(hmm->curr_tprob);
+    free(hmm->tmp);
+    free(hmm->tprob_arr);
+    free(hmm->fwd);
+    free(hmm->bwd);
+    free(hmm->bwd_tmp);
+    free(hmm);
+}
+
diff --git a/bcftools/HMM.h b/bcftools/HMM.h
new file mode 100644
index 0000000..3a6cab3
--- /dev/null
+++ b/bcftools/HMM.h
@@ -0,0 +1,138 @@
+/* The MIT License
+
+   Copyright (c) 2014-2016 Genome Research Ltd.
+
+   Author: Petr Danecek <pd3@sanger.ac.uk>
+
+   Permission is hereby granted, free of charge, to any person obtaining a copy
+   of this software and associated documentation files (the "Software"), to deal
+   in the Software without restriction, including without limitation the rights
+   to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+   copies of the Software, and to permit persons to whom the Software is
+   furnished to do so, subject to the following conditions:
+
+   The above copyright notice and this permission notice shall be included in
+   all copies or substantial portions of the Software.
+
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+   IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+   FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+   AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+   LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+   OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+   THE SOFTWARE.
+
+ */
+
+#ifndef __HMM_H__
+#define __HMM_H__
+
+#define MAT(matrix,ndim,i,j) (matrix)[(ndim)*(i)+(j)]       // P(i|j), that is, transition j->i
+
+typedef struct _hmm_t hmm_t;
+
+typedef void (*set_tprob_f) (hmm_t *hmm, uint32_t prev_pos, uint32_t pos, void *data, double *tprob);
+
+/**
+ *   hmm_init() - initialize HMM
+ *   @nstates:  number of states
+ *   @tprob:    transition probabilities matrix (nstates x nstates), for elements ordering
+ *              see the MAT macro above.
+ *   @ntprob:   number of precalculated tprob matrices or 0 for constant probs, independent
+ *              of distance
+ */
+hmm_t *hmm_init(int nstates, double *tprob, int ntprob);
+void hmm_set_tprob(hmm_t *hmm, double *tprob, int ntprob);
+
+#define HMM_VIT 1
+#define HMM_FWD 2
+#define HMM_BWD 4
+
+/**
+ *   hmm_init_states() - initial state probabilities
+ *   @probs:  initial state probabilities or NULL to reset to default
+ *
+ *   If uncalled, all states are initialized with the same likelihood
+ */
+void hmm_init_states(hmm_t *hmm, double *probs);
+
+/**
+ *   hmm_snapshot() - take the model's snapshot, intended for sliding HMM
+ *   @snapshot: NULL or snapshot returned by previous hmm_snapshot() call, must be free()-ed by the caller
+ *   @pos:      take the snapshot at this position
+ *
+ *   If both restore() and snapshot() are needed, restore() must be called first.
+ */
+void *hmm_snapshot(hmm_t *hmm, void *snapshot, uint32_t pos);
+
+/**
+ *   hmm_restore() - restore model's snapshot, intended for sliding HMM
+ *   @snapshot: snapshot returned by hmm_snapshot() call or NULL to reset
+ *   @isite:    take the snapshot at i-th step
+ *
+ *   If both restore() and snapshot() are needed, restore() must be called first.
+ */
+void hmm_restore(hmm_t *hmm, void *snapshot);
+void hmm_reset(hmm_t *hmm, void *snapshot);
+
+/**
+ *   hmm_get_tprob() - return the array of transition matrices, precalculated
+ *      to ntprob positions. The first matrix is the initial tprob matrix
+ *      set by hmm_init() or hmm_set_tprob()
+ */
+double *hmm_get_tprob(hmm_t *hmm);
+int hmm_get_nstates(hmm_t *hmm);
+
+/**
+ *   hmm_set_tprob_func() - custom setter of transition probabilities
+ */
+void hmm_set_tprob_func(hmm_t *hmm, set_tprob_f set_tprob, void *data);
+
+/**
+ *   hmm_run_viterbi() - run Viterbi algorithm
+ *   @nsites:   number of sites 
+ *   @eprob:    emission probabilities for each site and state (nsites x nstates)
+ *   @sites:    list of positions
+ *
+ *   When done, hmm->vpath[] contains the calculated Viterbi path. The states
+ *   are indexed starting from 0, a state at i-th site can be accessed as
+ *   vpath[nstates*i].
+ */
+void hmm_run_viterbi(hmm_t *hmm, int nsites, double *eprob, uint32_t *sites);
+
+/**
+ *   hmm_get_viterbi_path() - the viterbi path: state at ith site is the
+ *      (nstates*isite)-th element
+ */
+uint8_t *hmm_get_viterbi_path(hmm_t *hmm);
+
+/**
+ *   hmm_run_fwd_bwd() - run the forward-backward algorithm
+ *   @nsites:   number of sites 
+ *   @eprob:    emission probabilities for each site and state (nsites x nstates)
+ *   @sites:    list of positions
+ */
+void hmm_run_fwd_bwd(hmm_t *hmm, int nsites, double *eprob, uint32_t *sites);
+
+/**
+ *   hmm_get_fwd_bwd_prob() - the probability of i-th state at j-th site can
+ *      be accessed as fwd_bwd[j*nstates+i].
+ */
+double *hmm_get_fwd_bwd_prob(hmm_t *hmm);
+
+/**
+ *   hmm_run_baum_welch() - run one iteration of Baum-Welch algorithm
+ *   @nsites:   number of sites 
+ *   @eprob:    emission probabilities for each site and state (nsites x nstates)
+ *   @sites:    list of positions
+ *
+ *   Same as hmm_run_fwd_bwd, in addition a pointer to a matrix with the new
+ *   transition probabilities is returned. In this verison, emission
+ *   probabilities are not updated.
+ */
+double *hmm_run_baum_welch(hmm_t *hmm, int nsites, double *eprob, uint32_t *sites);
+
+void hmm_destroy(hmm_t *hmm);
+
+#endif
+
diff --git a/bcftools/LICENSE b/bcftools/LICENSE
new file mode 100644
index 0000000..f223b09
--- /dev/null
+++ b/bcftools/LICENSE
@@ -0,0 +1,773 @@
+This software is available to you under a choice of one of two licenses. You
+may chose to be licensed under the terms of the MIT/Expat license or the GNU
+General Public License (GPL), both included below. If compiled with the GNU
+Scientific Library (which is optional and disabled by default as explained in
+the INSTALL document), the use of this software is governed by the GPL license.
+
+
+-----------------------------------------------------------------------------
+
+The MIT/Expat License
+
+Copyright (C) 2012-2021 Genome Research Ltd.
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.
+
+
+[The use of a range of years within a copyright notice in this distribution
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+first and last year specified and all consecutive years between them.
+
+For example, a copyright notice that reads "Copyright (C) 2005, 2007-2009,
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+that reads "Copyright (C) 2005-2012" should be interpreted as being identical
+to a notice that reads "Copyright (C) 2005, 2006, 2007, 2008, 2009, 2010,
+2011, 2012".]
+
+
+-----------------------------------------------------------------------------
+
+
+GNU GENERAL PUBLIC LICENSE
+Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
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+                     END OF TERMS AND CONDITIONS
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+    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
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+    <program>  Copyright (C) <year>  <name of author>
+    This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+    This is free software, and you are welcome to redistribute it
+    under certain conditions; type `show c' for details.
+
+The hypothetical commands `show w' and `show c' should show the appropriate
+parts of the General Public License.  Of course, your program's commands
+might be different; for a GUI interface, you would use an "about box".
+
+  You should also get your employer (if you work as a programmer) or school,
+if any, to sign a "copyright disclaimer" for the program, if necessary.
+For more information on this, and how to apply and follow the GNU GPL, see
+<http://www.gnu.org/licenses/>.
+
+  The GNU General Public License does not permit incorporating your program
+into proprietary programs.  If your program is a subroutine library, you
+may consider it more useful to permit linking proprietary applications with
+the library.  If this is what you want to do, use the GNU Lesser General
+Public License instead of this License.  But first, please read
+<http://www.gnu.org/philosophy/why-not-lgpl.html>.
+
+
+-----------------------------------------------------------------------------
+
+LICENSE FOR VariantKey (https://github.com/Genomicsplc/variantkey)
+
+The MIT License
+
+Copyright (c) 2017-2018 GENOMICS plc
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.
+
+-----------------------------------------------------------------------------
+
+LICENSE for utlist.h
+
+Copyright (c) 2007-2014, Troy D. Hanson   http://troydhanson.github.com/uthash/
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+    * Redistributions of source code must retain the above copyright
+      notice, this list of conditions and the following disclaimer.
+
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+PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
diff --git a/bcftools/README b/bcftools/README
new file mode 100644
index 0000000..fff0cb7
--- /dev/null
+++ b/bcftools/README
@@ -0,0 +1,27 @@
+BCFtools implements utilities for variant calling (in conjunction with
+SAMtools) and manipulating VCF and BCF files.  The program is intended
+to replace the Perl-based tools from vcftools.
+
+See INSTALL for building and installation instructions.
+
+Please cite this paper when using BCFtools for your publications:
+
+Twelve years of SAMtools and BCFtools
+Petr Danecek, James K Bonfield, Jennifer Liddle, John Marshall, Valeriu Ohan, Martin O Pollard, Andrew Whitwham, Thomas Keane, Shane A McCarthy, Robert M Davies, Heng Li
+GigaScience, Volume 10, Issue 2, February 2021, giab008, https://doi.org/10.1093/gigascience/giab008
+
+@article{10.1093/gigascience/giab008,
+    author = {Danecek, Petr and Bonfield, James K and Liddle, Jennifer and Marshall, John and Ohan, Valeriu and Pollard, Martin O and Whitwham, Andrew and Keane, Thomas and McCarthy, Shane A and Davies, Robert M and Li, Heng},
+    title = "{Twelve years of SAMtools and BCFtools}",
+    journal = {GigaScience},
+    volume = {10},
+    number = {2},
+    year = {2021},
+    month = {02},
+    abstract = "{SAMtools and BCFtools are widely used programs for processing and analysing high-throughput sequencing data. They include tools for file format conversion and manipulation, sorting, querying, statistics, variant calling, and effect analysis amongst other methods.The first version appeared online 12 years ago and has been maintained and further developed ever since, with many new features and improvements added over the years. The SAMtools and BCFtools packages represent a unique collection of tools that have been used in numerous other software projects and countless genomic pipelines.Both SAMtools and BCFtools are freely available on GitHub under the permissive MIT licence, free for both non-commercial and commercial use. Both packages have been installed \\&gt;1 million times via Bioconda. The source code and documentation are available from https://www.htslib.org.}",
+    issn = {2047-217X},
+    doi = {10.1093/gigascience/giab008},
+    url = {https://doi.org/10.1093/gigascience/giab008},
+    note = {giab008},
+    eprint = {https://academic.oup.com/gigascience/article-pdf/10/2/giab008/36332246/giab008.pdf},
+}
diff --git a/bcftools/abuf.c b/bcftools/abuf.c
new file mode 100644
index 0000000..78682d6
--- /dev/null
+++ b/bcftools/abuf.c
@@ -0,0 +1,802 @@
+/* The MIT License
+
+   Copyright (c) 2021-2022 Genome Research Ltd.
+
+   Author: Petr Danecek <pd3@sanger.ac.uk>
+
+   Permission is hereby granted, free of charge, to any person obtaining a copy
+   of this software and associated documentation files (the "Software"), to deal
+   in the Software without restriction, including without limitation the rights
+   to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+   copies of the Software, and to permit persons to whom the Software is
+   furnished to do so, subject to the following conditions:
+
+   The above copyright notice and this permission notice shall be included in
+   all copies or substantial portions of the Software.
+
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+   IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+   FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+   AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+   LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+   OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+   THE SOFTWARE.
+
+ */
+
+#include <assert.h>
+#include <strings.h>
+#include <htslib/vcf.h>
+#include <ctype.h>
+#include "bcftools.h"
+#include "abuf.h"
+#include "rbuf.h"
+
+typedef enum
+{
+    M_FIRST, M_SUM
+}
+merge_rule_t;
+
+typedef struct
+{
+    kstring_t ref, alt;
+    int ial;        // the index of the original ALT allele, 1-based
+    int beg, end;   // 0-based inclusive offsets to ref,alt
+}
+atom_t;
+
+typedef struct
+{
+    bcf1_t *rec;
+    int nori, nout;     // number of ALTs in the input, and VCF rows on output
+    uint8_t *tbl;       // nori columns, nout rows; indicates allele contribution to output rows, see "The atomization works as follows" below
+    uint8_t *overlaps;  // is the star allele needed for this variant?
+    atom_t **atoms;
+    int matoms, mtbl, moverlaps;
+    char *info_tag;
+}
+split_t;
+
+struct _abuf_t
+{
+    abuf_opt_t mode;
+    split_t split;
+    atom_t *atoms;
+    int natoms, matoms;
+    const bcf_hdr_t *hdr;
+    bcf_hdr_t *out_hdr;
+    bcf1_t **vcf;       // dimensions stored in rbuf
+    rbuf_t rbuf;
+
+    kstring_t tmps;
+    void *tmp, *tmp2;
+    int32_t *gt, *tmpi;
+    int ngt, mgt, ntmpi, mtmpi, mtmp, mtmp2;
+    int star_allele;
+};
+
+abuf_t *abuf_init(const bcf_hdr_t *hdr, abuf_opt_t mode)
+{
+    if ( mode!=SPLIT ) error("todo\n");
+    abuf_t *buf = (abuf_t*) calloc(1,sizeof(abuf_t));
+    buf->hdr  = hdr;
+    buf->out_hdr = (bcf_hdr_t*) hdr;
+    buf->mode = mode;
+    buf->star_allele = 1;
+    rbuf_init(&buf->rbuf, 0);
+    return buf;
+}
+
+void abuf_destroy(abuf_t *buf)
+{
+    int i;
+    for (i=0; i<buf->matoms; i++)
+    {
+        free(buf->atoms[i].ref.s);
+        free(buf->atoms[i].alt.s);
+    }
+    free(buf->atoms);
+    free(buf->split.atoms);
+    free(buf->split.overlaps);
+    free(buf->split.tbl);
+    for (i=0; i<buf->rbuf.m; i++)
+        if ( buf->vcf[i] ) bcf_destroy(buf->vcf[i]);
+    free(buf->vcf);
+    free(buf->gt);
+    free(buf->tmpi);
+    free(buf->tmp);
+    free(buf->tmp2);
+    free(buf->tmps.s);
+    free(buf);
+}
+
+void abuf_set(abuf_t *buf, abuf_opt_t key, void *value)
+{
+    if ( key==BCF_HDR ) { buf->out_hdr = *((bcf_hdr_t**)value); return; }
+    if ( key==INFO_TAG )
+    {
+        buf->split.info_tag = *((char**)value);
+        bcf_hdr_printf(buf->out_hdr,"##INFO=<ID=%s,Number=1,Type=String,Description=\"Original variant. Format: CHR|POS|REF|ALT|USED_ALT_IDX\">",buf->split.info_tag);
+        return;
+    }
+    if ( key==STAR_ALLELE ) { buf->star_allele = *((int*)value); return; }
+}
+
+/*
+    Split alleles into primitivs, e.g.
+        CC>TT  becomes  C>T,C>T
+        GCGT>GTGA  becomes C>T,T>A
+
+    There is no sequence alignment, just trimming and hungry matching
+    from left side.
+*/
+static void _atomize_allele(abuf_t *buf, bcf1_t *rec, int ial)
+{
+    // Trim identical sequence from right
+    char *ref = rec->d.allele[0];
+    char *alt = rec->d.allele[ial];
+    int rlen = strlen(ref);
+    int alen = strlen(alt);
+    while ( rlen>1 && alen>1 && ref[rlen-1]==alt[alen-1] ) rlen--, alen--;
+    int Mlen = rlen > alen ? rlen : alen;
+
+    atom_t *atom = NULL;
+    int i;
+    for (i=0; i<Mlen; i++)
+    {
+        char refb = i<rlen ? ref[i] : '-';
+        char altb = i<alen ? alt[i] : '-';
+        if ( refb!=altb )
+        {
+            if ( refb=='-' || altb=='-' )
+            {
+                assert(atom);
+                if ( altb!='-' ) kputc(altb, &atom->alt);
+                if ( refb!='-' ) { kputc(refb, &atom->ref); atom->end++; }
+            }
+            else
+            {
+                buf->natoms++;
+                hts_expand0(atom_t,buf->natoms,buf->matoms,buf->atoms);
+                atom = &buf->atoms[buf->natoms-1];
+                atom->ref.l = 0;
+                atom->alt.l = 0;
+                kputc(refb, &atom->ref);
+                kputc(altb, &atom->alt);
+                atom->beg = atom->end = i;
+                atom->ial = ial;
+            }
+            continue;
+        }
+        if ( i+1>=rlen || i+1>=alen )   // is the next base a deletion?
+        {
+            buf->natoms++;
+            hts_expand0(atom_t,buf->natoms,buf->matoms,buf->atoms);
+            atom = &buf->atoms[buf->natoms-1];
+            atom->ref.l = 0;
+            atom->alt.l = 0;
+            kputc(refb, &atom->ref);
+            kputc(altb, &atom->alt);
+            atom->beg = atom->end = i;
+            atom->ial = ial;
+        }
+    }
+}
+static int _atoms_inconsistent(const atom_t *a, const atom_t *b)
+{
+    if ( a->beg < b->beg ) return -1;
+    if ( a->beg > b->beg ) return 1;
+    int rcmp = strcasecmp(a->ref.s,b->ref.s);
+    if ( rcmp ) return rcmp;
+    return strcasecmp(a->alt.s,b->alt.s);
+}
+/*
+    For reproducibility of tests on different platforms, we need to guarantee the same order of identical
+    atoms originating from different source ALTs.  Even though they are consistent, different values can be
+    picked for VCF annotations as currently the values from the one that comes first are used.
+*/
+static int _cmp_atoms(const void *aptr, const void *bptr)
+{
+    const atom_t *a = (const atom_t*) aptr;
+    const atom_t *b = (const atom_t*) bptr;
+    int rcmp = _atoms_inconsistent(a,b);
+    if ( rcmp ) return rcmp;
+    if ( a->ial < b->ial ) return -1;
+    if ( a->ial > b->ial ) return 1;
+    return 0;
+}
+static void _split_table_init(abuf_t *buf, bcf1_t *rec, int natoms)
+{
+    buf->split.rec  = rec;
+    buf->split.nori = rec->n_allele - 1;
+    buf->split.nout = 0;
+    hts_expand(uint8_t,buf->split.nori*natoms,buf->split.mtbl,buf->split.tbl);
+    hts_expand(atom_t*,natoms,buf->split.matoms,buf->split.atoms);
+    hts_expand(uint8_t,natoms,buf->split.moverlaps,buf->split.overlaps);
+    memset(buf->split.overlaps,0,sizeof(*buf->split.overlaps)*natoms);
+}
+static void _split_table_new(abuf_t *buf, atom_t *atom)
+{
+    int i, iout = buf->split.nout++;
+    buf->split.atoms[iout] = atom;
+    uint8_t *ptr = buf->split.tbl + iout*buf->split.nori;
+    for (i=0; i<buf->split.nori; i++) ptr[i] = 0;
+    ptr[atom->ial-1] = 1;
+}
+static void _split_table_overlap(abuf_t *buf, int iout, atom_t *atom)
+{
+    uint8_t *ptr = buf->split.tbl + iout*buf->split.nori;
+    ptr[atom->ial-1] = _atoms_inconsistent(atom,buf->split.atoms[iout]) ? 2 : 1;
+    buf->split.overlaps[iout] = 1;
+}
+#if 0
+static void _split_table_print(abuf_t *buf)
+{
+    int i,j;
+    for (i=0; i<buf->split.nout; i++)
+    {
+        atom_t *atom = buf->split.atoms[i];
+        uint8_t *ptr = buf->split.tbl + i*buf->split.nori;
+        fprintf(stderr,"%d\t%s\t%s",(int)buf->split.rec->pos+1+atom->beg,atom->ref.s,atom->alt.s);
+        for (j=0; j<buf->split.nori; j++) fprintf(stderr,"\t%d",(int)ptr[j]);
+        fprintf(stderr,"\n");
+    }
+}
+static void _split_table_print_atoms(abuf_t *buf)
+{
+    int i;
+    for (i=0; i<buf->natoms; i++)
+    {
+        atom_t *atom = &buf->atoms[i];
+        fprintf(stderr,"atom%d %p: ialt=%d %s>%s %d-%d\n",i,atom,atom->ial,atom->ref.s,atom->alt.s,atom->beg,atom->end);
+    }
+}
+#endif
+static inline uint8_t _has_star_allele(abuf_t *buf, int iout)
+{
+    if ( !buf->star_allele ) return 0;
+    return buf->split.overlaps[iout];
+}
+static inline int _split_table_get_ial(abuf_t *buf, int irow, int ial)
+{
+    if ( !ial ) return ial;
+    return buf->split.tbl[irow*buf->split.nori + ial - 1];
+}
+static void _split_table_set_chrom_qual(abuf_t *buf)
+{
+    int iout,j;
+    bcf1_t *rec = buf->split.rec;
+    for (iout=0; iout<buf->split.nout; iout++)
+    {
+        rbuf_expand0(&buf->rbuf, bcf1_t*, buf->rbuf.n+1, buf->vcf);
+        j = rbuf_append(&buf->rbuf);
+        if ( !buf->vcf[j] ) buf->vcf[j] = bcf_init1();
+        bcf1_t *out = buf->vcf[j];
+        bcf_clear1(out);
+
+        atom_t *atom = buf->split.atoms[iout];
+        out->rid = rec->rid;
+        out->pos = rec->pos + atom->beg;
+        bcf_update_id(buf->out_hdr, out, rec->d.id);
+
+        const char *als[3];
+        als[0] = atom->ref.s;
+        als[1] = atom->alt.s;
+        als[2] = "*";
+        int nals = _has_star_allele(buf,iout) ? 3 : 2;
+        bcf_update_alleles(buf->out_hdr, out, als, nals);
+
+        if ( bcf_float_is_missing(rec->qual) )
+            bcf_float_set_missing(out->qual);
+        else
+            out->qual = rec->qual;
+
+        bcf_update_filter(buf->out_hdr, out, rec->d.flt, rec->d.n_flt);
+    }
+}
+int copy_string_field(char *src, int isrc, int src_len, kstring_t *dst, int idst);
+static void _split_table_set_info(abuf_t *buf, bcf_info_t *info, merge_rule_t mode)
+{
+    const char *tag = bcf_hdr_int2id(buf->hdr,BCF_DT_ID,info->key);
+    int type = bcf_hdr_id2type(buf->hdr,BCF_HL_INFO,info->key);
+    int len  = bcf_hdr_id2length(buf->hdr,BCF_HL_INFO,info->key);
+    if ( len==BCF_VL_G ) return;                                                // todo: Number=G INFO tags
+    if ( type==BCF_HT_LONG ) return;                                            // todo: 64bit integers
+
+    bcf1_t *rec = buf->split.rec;
+    int mtmp = ( type==BCF_HT_INT || type==BCF_HT_REAL ) ? buf->mtmp/4 : buf->mtmp;
+    int nval = bcf_get_info_values(buf->hdr,rec,tag,&buf->tmp,&mtmp,type);
+    if ( type==BCF_HT_INT || type==BCF_HT_REAL ) buf->mtmp = mtmp*4;
+
+    // Check for incorrect number of values. Note this check does not consider all values missing
+    // and will remove annotations that don't pass.
+    if ( type==BCF_HT_INT || type==BCF_HT_REAL )
+    {
+        if ( (len==BCF_VL_A && nval != rec->n_allele - 1) || (len==BCF_VL_R && nval != rec->n_allele) ) return;
+    }
+
+    if ( buf->mtmp2 < buf->mtmp )
+    {
+        buf->tmp2  = realloc(buf->tmp2, buf->mtmp);
+        if ( !buf->tmp2 ) error("Failed to alloc %d bytes\n", buf->mtmp);
+        buf->mtmp2 = buf->mtmp;
+    }
+
+    const int num_size = 4;
+    assert( num_size==sizeof(int32_t) && num_size==sizeof(float) );
+    int32_t missing = bcf_int32_missing;
+    void *missing_ptr = (void*)&missing;
+    if ( type==BCF_HT_REAL ) bcf_float_set_missing(*((float*)missing_ptr));
+    int32_t vector_end = bcf_int32_vector_end;
+    void *vector_end_ptr = (void*)&vector_end;
+    if ( type==BCF_HT_REAL ) bcf_float_set_vector_end(*((float*)vector_end_ptr));
+
+    int iout,i;
+    for (iout=0; iout<buf->split.nout; iout++)
+    {
+        bcf1_t *out = buf->vcf[rbuf_kth(&buf->rbuf,iout)];
+        int star_allele = _has_star_allele(buf,iout);
+        int ret = 0;
+        if ( len==BCF_VL_FIXED || len==BCF_VL_VAR )
+            ret = bcf_update_info(buf->out_hdr, out, tag, type==BCF_HT_FLAG ? NULL : buf->tmp, nval, type);
+        else if ( len==BCF_VL_A && type!=BCF_HT_STR )
+        {
+            int iori = buf->split.atoms[iout]->ial - 1;
+            assert( iori<nval );
+            if ( !memcmp(vector_end_ptr,buf->tmp+num_size*iori,num_size) )
+                memcpy(buf->tmp2,missing_ptr,num_size);
+            else
+                memcpy(buf->tmp2,buf->tmp+num_size*iori,num_size);
+            if ( star_allele )
+                memcpy(buf->tmp2+num_size,missing_ptr,num_size);
+            ret = bcf_update_info(buf->out_hdr, out, tag, buf->tmp2, 1 + star_allele, type);
+        }
+        else if ( len==BCF_VL_A && type==BCF_HT_STR )
+        {
+            int iori = buf->split.atoms[iout]->ial - 1;
+            kstring_t dst;
+            dst.l = 0; dst.m = buf->mtmp2; dst.s = (char*)buf->tmp2;
+            kputc('.',&dst);
+            if ( star_allele ) kputs(",.",&dst);
+            copy_string_field(buf->tmp, iori, nval, &dst, 0);
+            if ( star_allele ) copy_string_field(".", 0, 1, &dst, 1);
+            buf->mtmp2 = dst.m;
+            buf->tmp2  = dst.s;
+            ret = bcf_update_info(buf->out_hdr, out, tag, buf->tmp2, dst.l, type);
+        }
+        else if ( len==BCF_VL_R && type!=BCF_HT_STR )
+        {
+            memcpy(buf->tmp2,buf->tmp,num_size);   // REF contributes to all records
+            int iori = buf->split.atoms[iout]->ial;
+            assert( iori<nval && iori<=buf->split.nori );
+            if ( !memcmp(vector_end_ptr,buf->tmp+num_size*iori,num_size) )
+                memcpy(buf->tmp2+num_size,missing_ptr,num_size);
+            else
+                memcpy(buf->tmp2+num_size,buf->tmp+num_size*iori,num_size);
+            if ( type==BCF_HT_INT && mode==M_SUM )
+            {
+                uint8_t *tbl = buf->split.tbl + iout*buf->split.nori;
+                for (i=iori; i<buf->split.nori; i++)
+                {
+                    if ( tbl[i]==1 ) ((int32_t*)buf->tmp2)[1] += ((int32_t*)buf->tmp)[i+1];
+                }
+            }
+            if ( star_allele )
+                memcpy(buf->tmp2+2*num_size,missing_ptr,num_size);
+            ret = bcf_update_info(buf->out_hdr, out, tag, buf->tmp2, 2 + star_allele, type);
+        }
+        else if ( len==BCF_VL_R && type==BCF_HT_STR )
+        {
+            int iori = buf->split.atoms[iout]->ial - 1;
+            kstring_t dst;
+            dst.l = 0; dst.m = buf->mtmp2; dst.s = (char*)buf->tmp2;
+            kputs(".,.",&dst);
+            if ( star_allele ) kputs(",.",&dst);
+            copy_string_field(buf->tmp, 0, nval, &dst, 0);
+            copy_string_field(buf->tmp, iori+1, nval, &dst, 1);
+            if ( star_allele ) copy_string_field(".", 0, 1, &dst, 2);
+            buf->mtmp2 = dst.m;
+            buf->tmp2  = dst.s;
+            ret = bcf_update_info(buf->out_hdr, out, tag, buf->tmp2, dst.l, type);
+        }
+        if ( ret!=0 ) error("An error occurred while updating INFO/%s\n",tag);
+    }
+}
+static void _split_table_set_history(abuf_t *buf)
+{
+    int i,j;
+    bcf1_t *rec = buf->split.rec;
+    buf->tmps.l = 0;
+    ksprintf(&buf->tmps,"%s|%"PRIhts_pos"|%s|",bcf_seqname(buf->hdr,rec),rec->pos+1,rec->d.allele[0]);
+    for (i=1; i<rec->n_allele; i++)
+    {
+        kputs(rec->d.allele[i],&buf->tmps);
+        if ( i+1<rec->n_allele ) kputc(',',&buf->tmps);
+        else kputc(',',&buf->tmps);
+    }
+    int len = buf->tmps.l;
+    buf->tmps.s[buf->tmps.l-1] = '|';
+
+    for (i=0; i<buf->split.nout; i++)
+    {
+        buf->tmps.l = len;
+        bcf1_t *out = buf->vcf[rbuf_kth(&buf->rbuf,i)];
+        uint8_t *ptr = buf->split.tbl + i*buf->split.nori;
+        for (j=0; j<buf->split.nori; j++)
+        {
+            if ( ptr[j]!=1 ) continue;
+            kputw(j+1,&buf->tmps);
+            kputc(',',&buf->tmps);
+        }
+        buf->tmps.s[--buf->tmps.l] = 0;
+        if ( (bcf_update_info_string(buf->out_hdr, out, buf->split.info_tag, buf->tmps.s))!=0 )
+            error("An error occurred while updating INFO/%s\n",buf->split.info_tag);
+    }
+}
+static void _split_table_set_gt(abuf_t *buf)
+{
+    int nsmpl = bcf_hdr_nsamples(buf->hdr);
+    if ( !nsmpl ) return;
+
+    bcf1_t *rec = buf->split.rec;
+    buf->ngt = bcf_get_genotypes(buf->hdr, rec, &buf->gt, &buf->mgt);
+    if ( buf->ngt<=0 ) return;
+    else
+        hts_expand(int32_t,buf->ngt,buf->mtmpi,buf->tmpi);
+
+    int iout,i,j;
+    for (iout=0; iout<buf->split.nout; iout++)
+    {
+        bcf1_t *out = buf->vcf[rbuf_kth(&buf->rbuf,iout)];
+        int star_allele = _has_star_allele(buf,iout);
+        int max_ploidy = buf->ngt/nsmpl;
+        int32_t *src = buf->gt, *dst = buf->tmpi;
+        for (i=0; i<nsmpl; i++)
+        {
+            for (j=0; j<max_ploidy; j++)
+            {
+                if ( src[j]==bcf_int32_vector_end || bcf_gt_is_missing(src[j]) )
+                {
+                    dst[j] = src[j];
+                    continue;
+                }
+                int iori = bcf_gt_allele(src[j]);
+                if ( iori<0 || iori>=rec->n_allele )
+                    error("Out-of-bounds genotypes at %s:%"PRIhts_pos"\n",bcf_seqname(buf->hdr,rec),rec->pos+1);
+                int ial = _split_table_get_ial(buf,iout,iori);
+                if ( ial==2 && !star_allele )
+                {
+                    dst[j] = bcf_gt_missing;
+                    if ( bcf_gt_is_phased(src[j]) ) dst[j] |= 1;
+                }
+                else
+                    dst[j] = bcf_gt_is_phased(src[j]) ? bcf_gt_phased(ial) : bcf_gt_unphased(ial);
+            }
+            src += max_ploidy;
+            dst += max_ploidy;
+        }
+        bcf_update_genotypes(buf->out_hdr,out,buf->tmpi,buf->ngt);
+    }
+}
+static void _split_table_set_format(abuf_t *buf, bcf_fmt_t *fmt, merge_rule_t mode)
+{
+    int nsmpl = bcf_hdr_nsamples(buf->hdr);
+    if ( !nsmpl ) return;
+
+    const char *tag = bcf_hdr_int2id(buf->hdr,BCF_DT_ID,fmt->id);
+    if ( tag[0]=='G' && tag[1]=='T' && !tag[2] )        // FORMAT/GT
+    {
+        _split_table_set_gt(buf);
+        return;
+    }
+
+    int type = bcf_hdr_id2type(buf->hdr,BCF_HL_FMT,fmt->id);
+    int len  = bcf_hdr_id2length(buf->hdr,BCF_HL_FMT,fmt->id);
+    if ( type==BCF_HT_STR && len==BCF_VL_G ) return;                            // possible todo: Number=G for strings
+    if ( type==BCF_HT_LONG ) return;                                            // todo: 64bit integers
+
+    const int num_size = 4;
+    assert( num_size==sizeof(int32_t) && num_size==sizeof(float) );
+    int32_t missing = bcf_int32_missing;
+    void *missing_ptr = (void*)&missing;
+    if ( type==BCF_HT_REAL ) bcf_float_set_missing(*((float*)missing_ptr));
+    int32_t vector_end = bcf_int32_vector_end;
+    void *vector_end_ptr = (void*)&vector_end;
+    if ( type==BCF_HT_REAL ) bcf_float_set_vector_end(*((float*)vector_end_ptr));
+
+    bcf1_t *rec = buf->split.rec;
+    int mtmp = ( type==BCF_HT_INT || type==BCF_HT_REAL ) ? buf->mtmp/num_size : buf->mtmp;  // number of items
+    int nval = bcf_get_format_values(buf->hdr,rec,tag,&buf->tmp,&mtmp,type);
+    if ( type==BCF_HT_INT || type==BCF_HT_REAL ) buf->mtmp = mtmp*num_size;                 // number of bytes
+
+    if ( type==BCF_HT_INT || type==BCF_HT_REAL )
+    {
+        if ( len==BCF_VL_G && nval!=nsmpl*rec->n_allele && nval!=nsmpl*rec->n_allele*(rec->n_allele+1)/2 ) return;      // not haploid nor diploid
+
+        // Check for incorrect number of values. Note this check does not consider all values missing
+        // and will remove annotations that don't pass.
+        if ( (len==BCF_VL_A && nval != nsmpl*(rec->n_allele - 1)) || (len==BCF_VL_R && nval != nsmpl*rec->n_allele) ) return;
+    }
+
+    // Increase buffer size to accommodate star allele
+    int nval1 = nval / nsmpl;
+    mtmp = buf->mtmp;
+    if ( type==BCF_HT_INT || type==BCF_HT_REAL )
+    {
+        if ( (len==BCF_VL_A || len==BCF_VL_R) && mtmp < num_size*nsmpl*(nval1+1) ) mtmp = num_size*nsmpl*(nval1+1); // +1 for the possibility of the star allele
+        else if ( len==BCF_VL_G && mtmp < num_size*nsmpl*(nval1+3) ) mtmp = num_size*nsmpl*(nval1+3);
+    }
+    else if ( type==BCF_HT_STR )
+    {
+        if ( (len==BCF_VL_A || len==BCF_VL_R) && mtmp < nsmpl*(nval1+2) ) mtmp = nsmpl*(nval1+2); // +2 for the possibility of the star allele, ",."
+        else if ( len==BCF_VL_G && mtmp < nsmpl*(nval1+6) ) mtmp = nsmpl*(nval1+6);
+    }
+
+    if ( buf->mtmp2 < mtmp )
+    {
+        buf->tmp2  = realloc(buf->tmp2, mtmp);
+        if ( !buf->tmp2 ) error("Failed to alloc %d bytes\n", mtmp);
+        buf->mtmp2 = mtmp;
+    }
+
+    int iout, i, j;
+    for (iout=0; iout<buf->split.nout; iout++)
+    {
+        int star_allele = _has_star_allele(buf,iout);
+        bcf1_t *out = buf->vcf[rbuf_kth(&buf->rbuf,iout)];
+        int ret = 0;
+        if ( len==BCF_VL_FIXED || len==BCF_VL_VAR )
+            ret = bcf_update_format(buf->out_hdr, out, tag, buf->tmp, nval, type);
+        else if ( len==BCF_VL_A && type!=BCF_HT_STR )
+        {
+            int iori = buf->split.atoms[iout]->ial - 1;
+            assert( iori<nval );
+            for (i=0; i<nsmpl; i++)
+            {
+                void *src = buf->tmp  + nval1*num_size*i;
+                void *dst = buf->tmp2 + num_size*i*(star_allele+1);
+                if ( !memcmp(vector_end_ptr,src+iori*num_size,num_size) )
+                    memcpy(dst,missing_ptr,num_size);
+                else
+                    memcpy(dst,src+iori*num_size,num_size);
+                if ( star_allele )
+                    memcpy(dst+num_size,missing_ptr,num_size);
+            }
+            ret = bcf_update_format(buf->out_hdr, out, tag, buf->tmp2, nsmpl*(star_allele+1), type);
+        }
+        else if ( (len==BCF_VL_A || len==BCF_VL_R) && type==BCF_HT_STR )
+        {
+            int ioff = len==BCF_VL_R ? 1 : 0;
+            int iori = buf->split.atoms[iout]->ial - 1;
+            int nval1_dst = star_allele ? nval1 + 2 : nval1;
+            memset(buf->tmp2,0,nval1_dst*nsmpl);
+            for (i=0; i<nsmpl; i++)
+            {
+                kstring_t dst;
+                dst.l = 0; dst.m = nval1_dst; dst.s = (char*)buf->tmp2 + nval1_dst*i;
+                kputc_('.',&dst);
+                if ( star_allele ) kputsn_(",.",2,&dst);
+                if ( len==BCF_VL_R )
+                {
+                    kputsn_(",.",2,&dst);
+                    copy_string_field(buf->tmp+nval1*i, 0, nval1, &dst, 0);
+                }
+                copy_string_field(buf->tmp+nval1*i, iori+ioff, nval1, &dst, 0+ioff);
+                if ( star_allele ) copy_string_field(".", 0, 1, &dst, 1+ioff);
+            }
+            ret = bcf_update_format(buf->out_hdr, out, tag, buf->tmp2, nval1_dst*nsmpl, type);
+        }
+        else if ( len==BCF_VL_R && type!=BCF_HT_STR )
+        {
+            int iori = buf->split.atoms[iout]->ial;
+            assert( iori<=nval );
+            for (i=0; i<nsmpl; i++)
+            {
+                void *src = buf->tmp  + nval1*num_size*i;
+                void *dst = buf->tmp2 + num_size*i*(star_allele+2);
+                memcpy(dst,src,num_size);
+                memcpy(dst+num_size,src+iori*num_size,num_size);
+                if ( type==BCF_HT_INT && mode==M_SUM )
+                {
+                    uint8_t *tbl = buf->split.tbl + iout*buf->split.nori;
+                    for (j=iori; j<buf->split.nori; j++)
+                        if ( tbl[j]==1 ) ((int32_t*)dst)[1] += ((int32_t*)src)[j+1];
+                }
+                if ( star_allele )
+                    memcpy(dst+num_size*2,missing_ptr,num_size);
+            }
+            ret = bcf_update_format(buf->out_hdr, out, tag, buf->tmp2, nsmpl*(star_allele+2), type);
+        }
+        else if ( len==BCF_VL_G && type!=BCF_HT_STR )
+        {
+            int iori = buf->split.atoms[iout]->ial;
+            int i01  = bcf_alleles2gt(0,iori);
+            int i11  = bcf_alleles2gt(iori,iori);
+            assert( iori<nval );
+            #define BRANCH(type_t, is_missing, is_vector_end, set_missing, set_vector_end) { \
+                for (i=0; i<nsmpl; i++) \
+                { \
+                    type_t *src = (type_t*)buf->tmp + i*nval1; \
+                    type_t *dst = (type_t*)buf->tmp2 + i*3*(1+star_allele); \
+                    int n=0; /* determine ploidy of this genotype */ \
+                    while ( n<nval1 && !(is_vector_end) ) { n++; src++; } \
+                    src = (type_t*)buf->tmp + i*nval1; \
+                    memcpy(dst++,src,sizeof(type)); \
+                    int nmiss = 0, nend = 0; \
+                    if ( n==rec->n_allele ) /* haploid */ \
+                    { \
+                        memcpy(dst++,src+iori,sizeof(type)); \
+                        if ( star_allele ) { nmiss = 1; nend = 3; } \
+                        else nend = 1; \
+                    } \
+                    else if ( n==nval1 ) \
+                    { \
+                        memcpy(dst++,src+i01,sizeof(type)); \
+                        memcpy(dst++,src+i11,sizeof(type)); \
+                        if ( star_allele ) nmiss = 3; \
+                    } \
+                    else if ( n==1 && is_missing ) \
+                    { \
+                        if ( star_allele ) nend = 5; \
+                        else nend = 2; \
+                    } \
+                    else  \
+                        error("Incorrect number of values at %s:%"PRIhts_pos" .. tag=FORMAT/%s Number=G nAlleles=%d nValues=%d, %d-th sample\n", \
+                                bcf_seqname(buf->hdr,rec),rec->pos+1,tag,rec->n_allele,n,i+1); \
+                    for (j=0; j<nmiss; j++) { set_missing; dst++; } \
+                    for (j=0; j<nend; j++) { set_vector_end; dst++; } \
+                } \
+            }
+            switch (type)
+            {
+                case BCF_HT_INT:  BRANCH(int32_t, *src==bcf_int32_missing, *src==bcf_int32_vector_end, *dst=bcf_int32_missing, *dst=bcf_int32_vector_end); break;
+                case BCF_HT_REAL: BRANCH(float, bcf_float_is_missing(*src), bcf_float_is_vector_end(*src), bcf_float_set_missing(*dst), bcf_float_set_vector_end(*dst)); break;
+                default: error("Unexpected case: %d\n", type);
+            }
+            #undef BRANCH
+            ret = bcf_update_format(buf->out_hdr, out, tag, buf->tmp2, 3*(1+star_allele)*nsmpl, type);
+        }
+        if ( ret!=0 ) error("An error occurred while updating FORMAT/%s\n",tag);
+    }
+}
+static inline int _is_acgtn(char *seq)
+{
+    while ( *seq )
+    {
+        char c = toupper(*seq);
+        if ( c!='A' && c!='C' && c!='G' && c!='T' && c!='N' ) return 0;
+        seq++;
+    }
+    return 1;
+}
+/*
+    The atomization works as follows:
+    - Atomize each alternate allele separately by leaving out sequence identical to the reference. No
+      alignment is performed, just greedy trimming of the end, then from left. This operation returns
+      a list of atoms (atom_t) which carry fragments of REF,ALT and their positions as 0-based offsets
+      to the original REF allele
+    - Sort atoms by POS, REF and ALT. Each unique atom (POS+REF+ALT) forms a new VCF record, each
+      with a single ALT.
+    - For each new VCF record determine how to translate the original allele index (iori) to this new
+      record:
+        - 1: the original allele matches the atom
+        - 0: the original allele does not overlap this atom or the overlapping part matches the REF
+             allele
+        - 2 (or equivalently "."): there is a mismatch between the original allele and the atom
+      The mapping is encoded in a table with columns corresponding to the original ALTs and rows
+      to the new POS+ALTs (atoms). The table is initialized to 0, then we set 1's for matching
+      atoms and 2's for overlapping mismatching atoms.
+
+    Note that different ALT alleles can result in the same atom (the same output line) and this code
+    does not know how to reconcile possibly conflicting VCF annotations. This could be improved
+    and merge logic provided, similarly to `merge -l`. For example, the allelic depths (AD) should
+    be summed for the same atomized output allele. However, this level of complexity is not addressed
+    in this initial draft. Higher priority for now is to provide the inverse "join" operation.
+
+    Update 2021-04-09:
+        Tags QS,AD are now automatically incremented as they should be, for both INFO and FORMAT.
+        Note that the code will fail on missing values (todo) and it needs to be generalized and
+        made customizable.
+*/
+void _abuf_split(abuf_t *buf, bcf1_t *rec)
+{
+    int i,j;
+    if ( rec->n_allele < 2 )
+    {
+        rbuf_expand0(&buf->rbuf, bcf1_t*, buf->rbuf.n+1, buf->vcf);
+        int j = rbuf_append(&buf->rbuf);
+        if ( buf->vcf[j] ) bcf_destroy(buf->vcf[j]);
+        buf->vcf[j] = bcf_dup(rec);
+        return;
+    }
+    for (i=0; i<rec->n_allele; i++)
+    {
+        if ( _is_acgtn(rec->d.allele[i]) ) continue;
+        rbuf_expand0(&buf->rbuf, bcf1_t*, buf->rbuf.n+1, buf->vcf);
+        int j = rbuf_append(&buf->rbuf);
+        if ( buf->vcf[j] ) bcf_destroy(buf->vcf[j]);
+        buf->vcf[j] = bcf_dup(rec);
+        return;
+    }
+
+    buf->natoms = 0;
+    for (i=1; i<rec->n_allele; i++) _atomize_allele(buf,rec,i);
+    qsort(buf->atoms,buf->natoms,sizeof(*buf->atoms),_cmp_atoms);
+    _split_table_init(buf,rec,buf->natoms);
+    for (i=0; i<buf->natoms; i++)
+    {
+        if ( i && !_atoms_inconsistent(&buf->atoms[i-1],&buf->atoms[i]) ) continue;
+        _split_table_new(buf, &buf->atoms[i]);  // add a new unique output atom
+    }
+    for (i=0; i<buf->natoms; i++)
+    {
+        // Looping over sorted list of all atoms with possible duplicates from different source ALT alleles
+        atom_t *atom = &buf->atoms[i];
+        for (j=0; j<buf->split.nout; j++)
+        {
+            atom_t *out = buf->split.atoms[j];
+            if ( atom == out ) continue;            // table already set to 1
+            if ( atom->beg > out->end ) continue;   // cannot overlap this output atom
+            if ( atom->end < out->beg ) break;      // this atom is ahead of all subsequent output records
+            _split_table_overlap(buf, j, atom);
+        }
+    }
+    assert( !buf->rbuf.n ); // all records should be flushed first in the SPLIT mode
+
+    // Create the output records, transferring all annotations:
+    // CHROM-QUAL
+    _split_table_set_chrom_qual(buf);
+
+    // INFO
+    for (i=0; i<rec->n_info; i++)
+    {
+        // this implementation of merging rules is temporary: generalize and made customizable through the API
+        merge_rule_t mode = M_FIRST;
+        const char *tag = bcf_hdr_int2id(buf->hdr,BCF_DT_ID,rec->d.info[i].key);
+        if ( !strcmp(tag,"QS") || !strcmp(tag,"AD") ) mode = M_SUM;
+
+        _split_table_set_info(buf, &rec->d.info[i], mode);
+    }
+
+    // Set INFO tag showing the original record
+    if ( buf->split.info_tag )
+        _split_table_set_history(buf);
+
+    // FORMAT
+    for (i=0; i<rec->n_fmt; i++)
+    {
+        // this implementation of merging rules is temporary: generalize and made customizable through the API
+        merge_rule_t mode = M_FIRST;
+        const char *tag = bcf_hdr_int2id(buf->hdr,BCF_DT_ID,rec->d.fmt[i].id);
+        if ( !strcmp(tag,"QS") || !strcmp(tag,"AD") ) mode = M_SUM;
+
+        _split_table_set_format(buf, &rec->d.fmt[i], mode);
+    }
+
+    // Check that at least one FORMAT field was added, if not, the number of samples must be set manually
+    for (i=0; i<buf->split.nout; i++)
+    {
+        bcf1_t *out = buf->vcf[rbuf_kth(&buf->rbuf,i)];
+        if ( !out->n_sample ) out->n_sample = rec->n_sample;
+    }
+}
+
+void abuf_push(abuf_t *buf, bcf1_t *rec)
+{
+    bcf_unpack(rec, BCF_UN_ALL);
+    if ( buf->mode==SPLIT ) _abuf_split(buf,rec);
+}
+
+bcf1_t *abuf_flush(abuf_t *buf, int flush_all)
+{
+    int i;
+
+    if ( buf->rbuf.n==0 ) return NULL;
+    if ( flush_all ) goto ret;
+
+ret:
+    i = rbuf_shift(&buf->rbuf);
+    return buf->vcf[i];
+}
+
diff --git a/bcftools/abuf.c.pysam.c b/bcftools/abuf.c.pysam.c
new file mode 100644
index 0000000..d85a54c
--- /dev/null
+++ b/bcftools/abuf.c.pysam.c
@@ -0,0 +1,804 @@
+#include "bcftools.pysam.h"
+
+/* The MIT License
+
+   Copyright (c) 2021-2022 Genome Research Ltd.
+
+   Author: Petr Danecek <pd3@sanger.ac.uk>
+
+   Permission is hereby granted, free of charge, to any person obtaining a copy
+   of this software and associated documentation files (the "Software"), to deal
+   in the Software without restriction, including without limitation the rights
+   to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+   copies of the Software, and to permit persons to whom the Software is
+   furnished to do so, subject to the following conditions:
+
+   The above copyright notice and this permission notice shall be included in
+   all copies or substantial portions of the Software.
+
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+   IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+   FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+   AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+   LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+   OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+   THE SOFTWARE.
+
+ */
+
+#include <assert.h>
+#include <strings.h>
+#include <htslib/vcf.h>
+#include <ctype.h>
+#include "bcftools.h"
+#include "abuf.h"
+#include "rbuf.h"
+
+typedef enum
+{
+    M_FIRST, M_SUM
+}
+merge_rule_t;
+
+typedef struct
+{
+    kstring_t ref, alt;
+    int ial;        // the index of the original ALT allele, 1-based
+    int beg, end;   // 0-based inclusive offsets to ref,alt
+}
+atom_t;
+
+typedef struct
+{
+    bcf1_t *rec;
+    int nori, nout;     // number of ALTs in the input, and VCF rows on output
+    uint8_t *tbl;       // nori columns, nout rows; indicates allele contribution to output rows, see "The atomization works as follows" below
+    uint8_t *overlaps;  // is the star allele needed for this variant?
+    atom_t **atoms;
+    int matoms, mtbl, moverlaps;
+    char *info_tag;
+}
+split_t;
+
+struct _abuf_t
+{
+    abuf_opt_t mode;
+    split_t split;
+    atom_t *atoms;
+    int natoms, matoms;
+    const bcf_hdr_t *hdr;
+    bcf_hdr_t *out_hdr;
+    bcf1_t **vcf;       // dimensions stored in rbuf
+    rbuf_t rbuf;
+
+    kstring_t tmps;
+    void *tmp, *tmp2;
+    int32_t *gt, *tmpi;
+    int ngt, mgt, ntmpi, mtmpi, mtmp, mtmp2;
+    int star_allele;
+};
+
+abuf_t *abuf_init(const bcf_hdr_t *hdr, abuf_opt_t mode)
+{
+    if ( mode!=SPLIT ) error("todo\n");
+    abuf_t *buf = (abuf_t*) calloc(1,sizeof(abuf_t));
+    buf->hdr  = hdr;
+    buf->out_hdr = (bcf_hdr_t*) hdr;
+    buf->mode = mode;
+    buf->star_allele = 1;
+    rbuf_init(&buf->rbuf, 0);
+    return buf;
+}
+
+void abuf_destroy(abuf_t *buf)
+{
+    int i;
+    for (i=0; i<buf->matoms; i++)
+    {
+        free(buf->atoms[i].ref.s);
+        free(buf->atoms[i].alt.s);
+    }
+    free(buf->atoms);
+    free(buf->split.atoms);
+    free(buf->split.overlaps);
+    free(buf->split.tbl);
+    for (i=0; i<buf->rbuf.m; i++)
+        if ( buf->vcf[i] ) bcf_destroy(buf->vcf[i]);
+    free(buf->vcf);
+    free(buf->gt);
+    free(buf->tmpi);
+    free(buf->tmp);
+    free(buf->tmp2);
+    free(buf->tmps.s);
+    free(buf);
+}
+
+void abuf_set(abuf_t *buf, abuf_opt_t key, void *value)
+{
+    if ( key==BCF_HDR ) { buf->out_hdr = *((bcf_hdr_t**)value); return; }
+    if ( key==INFO_TAG )
+    {
+        buf->split.info_tag = *((char**)value);
+        bcf_hdr_printf(buf->out_hdr,"##INFO=<ID=%s,Number=1,Type=String,Description=\"Original variant. Format: CHR|POS|REF|ALT|USED_ALT_IDX\">",buf->split.info_tag);
+        return;
+    }
+    if ( key==STAR_ALLELE ) { buf->star_allele = *((int*)value); return; }
+}
+
+/*
+    Split alleles into primitivs, e.g.
+        CC>TT  becomes  C>T,C>T
+        GCGT>GTGA  becomes C>T,T>A
+
+    There is no sequence alignment, just trimming and hungry matching
+    from left side.
+*/
+static void _atomize_allele(abuf_t *buf, bcf1_t *rec, int ial)
+{
+    // Trim identical sequence from right
+    char *ref = rec->d.allele[0];
+    char *alt = rec->d.allele[ial];
+    int rlen = strlen(ref);
+    int alen = strlen(alt);
+    while ( rlen>1 && alen>1 && ref[rlen-1]==alt[alen-1] ) rlen--, alen--;
+    int Mlen = rlen > alen ? rlen : alen;
+
+    atom_t *atom = NULL;
+    int i;
+    for (i=0; i<Mlen; i++)
+    {
+        char refb = i<rlen ? ref[i] : '-';
+        char altb = i<alen ? alt[i] : '-';
+        if ( refb!=altb )
+        {
+            if ( refb=='-' || altb=='-' )
+            {
+                assert(atom);
+                if ( altb!='-' ) kputc(altb, &atom->alt);
+                if ( refb!='-' ) { kputc(refb, &atom->ref); atom->end++; }
+            }
+            else
+            {
+                buf->natoms++;
+                hts_expand0(atom_t,buf->natoms,buf->matoms,buf->atoms);
+                atom = &buf->atoms[buf->natoms-1];
+                atom->ref.l = 0;
+                atom->alt.l = 0;
+                kputc(refb, &atom->ref);
+                kputc(altb, &atom->alt);
+                atom->beg = atom->end = i;
+                atom->ial = ial;
+            }
+            continue;
+        }
+        if ( i+1>=rlen || i+1>=alen )   // is the next base a deletion?
+        {
+            buf->natoms++;
+            hts_expand0(atom_t,buf->natoms,buf->matoms,buf->atoms);
+            atom = &buf->atoms[buf->natoms-1];
+            atom->ref.l = 0;
+            atom->alt.l = 0;
+            kputc(refb, &atom->ref);
+            kputc(altb, &atom->alt);
+            atom->beg = atom->end = i;
+            atom->ial = ial;
+        }
+    }
+}
+static int _atoms_inconsistent(const atom_t *a, const atom_t *b)
+{
+    if ( a->beg < b->beg ) return -1;
+    if ( a->beg > b->beg ) return 1;
+    int rcmp = strcasecmp(a->ref.s,b->ref.s);
+    if ( rcmp ) return rcmp;
+    return strcasecmp(a->alt.s,b->alt.s);
+}
+/*
+    For reproducibility of tests on different platforms, we need to guarantee the same order of identical
+    atoms originating from different source ALTs.  Even though they are consistent, different values can be
+    picked for VCF annotations as currently the values from the one that comes first are used.
+*/
+static int _cmp_atoms(const void *aptr, const void *bptr)
+{
+    const atom_t *a = (const atom_t*) aptr;
+    const atom_t *b = (const atom_t*) bptr;
+    int rcmp = _atoms_inconsistent(a,b);
+    if ( rcmp ) return rcmp;
+    if ( a->ial < b->ial ) return -1;
+    if ( a->ial > b->ial ) return 1;
+    return 0;
+}
+static void _split_table_init(abuf_t *buf, bcf1_t *rec, int natoms)
+{
+    buf->split.rec  = rec;
+    buf->split.nori = rec->n_allele - 1;
+    buf->split.nout = 0;
+    hts_expand(uint8_t,buf->split.nori*natoms,buf->split.mtbl,buf->split.tbl);
+    hts_expand(atom_t*,natoms,buf->split.matoms,buf->split.atoms);
+    hts_expand(uint8_t,natoms,buf->split.moverlaps,buf->split.overlaps);
+    memset(buf->split.overlaps,0,sizeof(*buf->split.overlaps)*natoms);
+}
+static void _split_table_new(abuf_t *buf, atom_t *atom)
+{
+    int i, iout = buf->split.nout++;
+    buf->split.atoms[iout] = atom;
+    uint8_t *ptr = buf->split.tbl + iout*buf->split.nori;
+    for (i=0; i<buf->split.nori; i++) ptr[i] = 0;
+    ptr[atom->ial-1] = 1;
+}
+static void _split_table_overlap(abuf_t *buf, int iout, atom_t *atom)
+{
+    uint8_t *ptr = buf->split.tbl + iout*buf->split.nori;
+    ptr[atom->ial-1] = _atoms_inconsistent(atom,buf->split.atoms[iout]) ? 2 : 1;
+    buf->split.overlaps[iout] = 1;
+}
+#if 0
+static void _split_table_print(abuf_t *buf)
+{
+    int i,j;
+    for (i=0; i<buf->split.nout; i++)
+    {
+        atom_t *atom = buf->split.atoms[i];
+        uint8_t *ptr = buf->split.tbl + i*buf->split.nori;
+        fprintf(bcftools_stderr,"%d\t%s\t%s",(int)buf->split.rec->pos+1+atom->beg,atom->ref.s,atom->alt.s);
+        for (j=0; j<buf->split.nori; j++) fprintf(bcftools_stderr,"\t%d",(int)ptr[j]);
+        fprintf(bcftools_stderr,"\n");
+    }
+}
+static void _split_table_print_atoms(abuf_t *buf)
+{
+    int i;
+    for (i=0; i<buf->natoms; i++)
+    {
+        atom_t *atom = &buf->atoms[i];
+        fprintf(bcftools_stderr,"atom%d %p: ialt=%d %s>%s %d-%d\n",i,atom,atom->ial,atom->ref.s,atom->alt.s,atom->beg,atom->end);
+    }
+}
+#endif
+static inline uint8_t _has_star_allele(abuf_t *buf, int iout)
+{
+    if ( !buf->star_allele ) return 0;
+    return buf->split.overlaps[iout];
+}
+static inline int _split_table_get_ial(abuf_t *buf, int irow, int ial)
+{
+    if ( !ial ) return ial;
+    return buf->split.tbl[irow*buf->split.nori + ial - 1];
+}
+static void _split_table_set_chrom_qual(abuf_t *buf)
+{
+    int iout,j;
+    bcf1_t *rec = buf->split.rec;
+    for (iout=0; iout<buf->split.nout; iout++)
+    {
+        rbuf_expand0(&buf->rbuf, bcf1_t*, buf->rbuf.n+1, buf->vcf);
+        j = rbuf_append(&buf->rbuf);
+        if ( !buf->vcf[j] ) buf->vcf[j] = bcf_init1();
+        bcf1_t *out = buf->vcf[j];
+        bcf_clear1(out);
+
+        atom_t *atom = buf->split.atoms[iout];
+        out->rid = rec->rid;
+        out->pos = rec->pos + atom->beg;
+        bcf_update_id(buf->out_hdr, out, rec->d.id);
+
+        const char *als[3];
+        als[0] = atom->ref.s;
+        als[1] = atom->alt.s;
+        als[2] = "*";
+        int nals = _has_star_allele(buf,iout) ? 3 : 2;
+        bcf_update_alleles(buf->out_hdr, out, als, nals);
+
+        if ( bcf_float_is_missing(rec->qual) )
+            bcf_float_set_missing(out->qual);
+        else
+            out->qual = rec->qual;
+
+        bcf_update_filter(buf->out_hdr, out, rec->d.flt, rec->d.n_flt);
+    }
+}
+int copy_string_field(char *src, int isrc, int src_len, kstring_t *dst, int idst);
+static void _split_table_set_info(abuf_t *buf, bcf_info_t *info, merge_rule_t mode)
+{
+    const char *tag = bcf_hdr_int2id(buf->hdr,BCF_DT_ID,info->key);
+    int type = bcf_hdr_id2type(buf->hdr,BCF_HL_INFO,info->key);
+    int len  = bcf_hdr_id2length(buf->hdr,BCF_HL_INFO,info->key);
+    if ( len==BCF_VL_G ) return;                                                // todo: Number=G INFO tags
+    if ( type==BCF_HT_LONG ) return;                                            // todo: 64bit integers
+
+    bcf1_t *rec = buf->split.rec;
+    int mtmp = ( type==BCF_HT_INT || type==BCF_HT_REAL ) ? buf->mtmp/4 : buf->mtmp;
+    int nval = bcf_get_info_values(buf->hdr,rec,tag,&buf->tmp,&mtmp,type);
+    if ( type==BCF_HT_INT || type==BCF_HT_REAL ) buf->mtmp = mtmp*4;
+
+    // Check for incorrect number of values. Note this check does not consider all values missing
+    // and will remove annotations that don't pass.
+    if ( type==BCF_HT_INT || type==BCF_HT_REAL )
+    {
+        if ( (len==BCF_VL_A && nval != rec->n_allele - 1) || (len==BCF_VL_R && nval != rec->n_allele) ) return;
+    }
+
+    if ( buf->mtmp2 < buf->mtmp )
+    {
+        buf->tmp2  = realloc(buf->tmp2, buf->mtmp);
+        if ( !buf->tmp2 ) error("Failed to alloc %d bytes\n", buf->mtmp);
+        buf->mtmp2 = buf->mtmp;
+    }
+
+    const int num_size = 4;
+    assert( num_size==sizeof(int32_t) && num_size==sizeof(float) );
+    int32_t missing = bcf_int32_missing;
+    void *missing_ptr = (void*)&missing;
+    if ( type==BCF_HT_REAL ) bcf_float_set_missing(*((float*)missing_ptr));
+    int32_t vector_end = bcf_int32_vector_end;
+    void *vector_end_ptr = (void*)&vector_end;
+    if ( type==BCF_HT_REAL ) bcf_float_set_vector_end(*((float*)vector_end_ptr));
+
+    int iout,i;
+    for (iout=0; iout<buf->split.nout; iout++)
+    {
+        bcf1_t *out = buf->vcf[rbuf_kth(&buf->rbuf,iout)];
+        int star_allele = _has_star_allele(buf,iout);
+        int ret = 0;
+        if ( len==BCF_VL_FIXED || len==BCF_VL_VAR )
+            ret = bcf_update_info(buf->out_hdr, out, tag, type==BCF_HT_FLAG ? NULL : buf->tmp, nval, type);
+        else if ( len==BCF_VL_A && type!=BCF_HT_STR )
+        {
+            int iori = buf->split.atoms[iout]->ial - 1;
+            assert( iori<nval );
+            if ( !memcmp(vector_end_ptr,buf->tmp+num_size*iori,num_size) )
+                memcpy(buf->tmp2,missing_ptr,num_size);
+            else
+                memcpy(buf->tmp2,buf->tmp+num_size*iori,num_size);
+            if ( star_allele )
+                memcpy(buf->tmp2+num_size,missing_ptr,num_size);
+            ret = bcf_update_info(buf->out_hdr, out, tag, buf->tmp2, 1 + star_allele, type);
+        }
+        else if ( len==BCF_VL_A && type==BCF_HT_STR )
+        {
+            int iori = buf->split.atoms[iout]->ial - 1;
+            kstring_t dst;
+            dst.l = 0; dst.m = buf->mtmp2; dst.s = (char*)buf->tmp2;
+            kputc('.',&dst);
+            if ( star_allele ) kputs(",.",&dst);
+            copy_string_field(buf->tmp, iori, nval, &dst, 0);
+            if ( star_allele ) copy_string_field(".", 0, 1, &dst, 1);
+            buf->mtmp2 = dst.m;
+            buf->tmp2  = dst.s;
+            ret = bcf_update_info(buf->out_hdr, out, tag, buf->tmp2, dst.l, type);
+        }
+        else if ( len==BCF_VL_R && type!=BCF_HT_STR )
+        {
+            memcpy(buf->tmp2,buf->tmp,num_size);   // REF contributes to all records
+            int iori = buf->split.atoms[iout]->ial;
+            assert( iori<nval && iori<=buf->split.nori );
+            if ( !memcmp(vector_end_ptr,buf->tmp+num_size*iori,num_size) )
+                memcpy(buf->tmp2+num_size,missing_ptr,num_size);
+            else
+                memcpy(buf->tmp2+num_size,buf->tmp+num_size*iori,num_size);
+            if ( type==BCF_HT_INT && mode==M_SUM )
+            {
+                uint8_t *tbl = buf->split.tbl + iout*buf->split.nori;
+                for (i=iori; i<buf->split.nori; i++)
+                {
+                    if ( tbl[i]==1 ) ((int32_t*)buf->tmp2)[1] += ((int32_t*)buf->tmp)[i+1];
+                }
+            }
+            if ( star_allele )
+                memcpy(buf->tmp2+2*num_size,missing_ptr,num_size);
+            ret = bcf_update_info(buf->out_hdr, out, tag, buf->tmp2, 2 + star_allele, type);
+        }
+        else if ( len==BCF_VL_R && type==BCF_HT_STR )
+        {
+            int iori = buf->split.atoms[iout]->ial - 1;
+            kstring_t dst;
+            dst.l = 0; dst.m = buf->mtmp2; dst.s = (char*)buf->tmp2;
+            kputs(".,.",&dst);
+            if ( star_allele ) kputs(",.",&dst);
+            copy_string_field(buf->tmp, 0, nval, &dst, 0);
+            copy_string_field(buf->tmp, iori+1, nval, &dst, 1);
+            if ( star_allele ) copy_string_field(".", 0, 1, &dst, 2);
+            buf->mtmp2 = dst.m;
+            buf->tmp2  = dst.s;
+            ret = bcf_update_info(buf->out_hdr, out, tag, buf->tmp2, dst.l, type);
+        }
+        if ( ret!=0 ) error("An error occurred while updating INFO/%s\n",tag);
+    }
+}
+static void _split_table_set_history(abuf_t *buf)
+{
+    int i,j;
+    bcf1_t *rec = buf->split.rec;
+    buf->tmps.l = 0;
+    ksprintf(&buf->tmps,"%s|%"PRIhts_pos"|%s|",bcf_seqname(buf->hdr,rec),rec->pos+1,rec->d.allele[0]);
+    for (i=1; i<rec->n_allele; i++)
+    {
+        kputs(rec->d.allele[i],&buf->tmps);
+        if ( i+1<rec->n_allele ) kputc(',',&buf->tmps);
+        else kputc(',',&buf->tmps);
+    }
+    int len = buf->tmps.l;
+    buf->tmps.s[buf->tmps.l-1] = '|';
+
+    for (i=0; i<buf->split.nout; i++)
+    {
+        buf->tmps.l = len;
+        bcf1_t *out = buf->vcf[rbuf_kth(&buf->rbuf,i)];
+        uint8_t *ptr = buf->split.tbl + i*buf->split.nori;
+        for (j=0; j<buf->split.nori; j++)
+        {
+            if ( ptr[j]!=1 ) continue;
+            kputw(j+1,&buf->tmps);
+            kputc(',',&buf->tmps);
+        }
+        buf->tmps.s[--buf->tmps.l] = 0;
+        if ( (bcf_update_info_string(buf->out_hdr, out, buf->split.info_tag, buf->tmps.s))!=0 )
+            error("An error occurred while updating INFO/%s\n",buf->split.info_tag);
+    }
+}
+static void _split_table_set_gt(abuf_t *buf)
+{
+    int nsmpl = bcf_hdr_nsamples(buf->hdr);
+    if ( !nsmpl ) return;
+
+    bcf1_t *rec = buf->split.rec;
+    buf->ngt = bcf_get_genotypes(buf->hdr, rec, &buf->gt, &buf->mgt);
+    if ( buf->ngt<=0 ) return;
+    else
+        hts_expand(int32_t,buf->ngt,buf->mtmpi,buf->tmpi);
+
+    int iout,i,j;
+    for (iout=0; iout<buf->split.nout; iout++)
+    {
+        bcf1_t *out = buf->vcf[rbuf_kth(&buf->rbuf,iout)];
+        int star_allele = _has_star_allele(buf,iout);
+        int max_ploidy = buf->ngt/nsmpl;
+        int32_t *src = buf->gt, *dst = buf->tmpi;
+        for (i=0; i<nsmpl; i++)
+        {
+            for (j=0; j<max_ploidy; j++)
+            {
+                if ( src[j]==bcf_int32_vector_end || bcf_gt_is_missing(src[j]) )
+                {
+                    dst[j] = src[j];
+                    continue;
+                }
+                int iori = bcf_gt_allele(src[j]);
+                if ( iori<0 || iori>=rec->n_allele )
+                    error("Out-of-bounds genotypes at %s:%"PRIhts_pos"\n",bcf_seqname(buf->hdr,rec),rec->pos+1);
+                int ial = _split_table_get_ial(buf,iout,iori);
+                if ( ial==2 && !star_allele )
+                {
+                    dst[j] = bcf_gt_missing;
+                    if ( bcf_gt_is_phased(src[j]) ) dst[j] |= 1;
+                }
+                else
+                    dst[j] = bcf_gt_is_phased(src[j]) ? bcf_gt_phased(ial) : bcf_gt_unphased(ial);
+            }
+            src += max_ploidy;
+            dst += max_ploidy;
+        }
+        bcf_update_genotypes(buf->out_hdr,out,buf->tmpi,buf->ngt);
+    }
+}
+static void _split_table_set_format(abuf_t *buf, bcf_fmt_t *fmt, merge_rule_t mode)
+{
+    int nsmpl = bcf_hdr_nsamples(buf->hdr);
+    if ( !nsmpl ) return;
+
+    const char *tag = bcf_hdr_int2id(buf->hdr,BCF_DT_ID,fmt->id);
+    if ( tag[0]=='G' && tag[1]=='T' && !tag[2] )        // FORMAT/GT
+    {
+        _split_table_set_gt(buf);
+        return;
+    }
+
+    int type = bcf_hdr_id2type(buf->hdr,BCF_HL_FMT,fmt->id);
+    int len  = bcf_hdr_id2length(buf->hdr,BCF_HL_FMT,fmt->id);
+    if ( type==BCF_HT_STR && len==BCF_VL_G ) return;                            // possible todo: Number=G for strings
+    if ( type==BCF_HT_LONG ) return;                                            // todo: 64bit integers
+
+    const int num_size = 4;
+    assert( num_size==sizeof(int32_t) && num_size==sizeof(float) );
+    int32_t missing = bcf_int32_missing;
+    void *missing_ptr = (void*)&missing;
+    if ( type==BCF_HT_REAL ) bcf_float_set_missing(*((float*)missing_ptr));
+    int32_t vector_end = bcf_int32_vector_end;
+    void *vector_end_ptr = (void*)&vector_end;
+    if ( type==BCF_HT_REAL ) bcf_float_set_vector_end(*((float*)vector_end_ptr));
+
+    bcf1_t *rec = buf->split.rec;
+    int mtmp = ( type==BCF_HT_INT || type==BCF_HT_REAL ) ? buf->mtmp/num_size : buf->mtmp;  // number of items
+    int nval = bcf_get_format_values(buf->hdr,rec,tag,&buf->tmp,&mtmp,type);
+    if ( type==BCF_HT_INT || type==BCF_HT_REAL ) buf->mtmp = mtmp*num_size;                 // number of bytes
+
+    if ( type==BCF_HT_INT || type==BCF_HT_REAL )
+    {
+        if ( len==BCF_VL_G && nval!=nsmpl*rec->n_allele && nval!=nsmpl*rec->n_allele*(rec->n_allele+1)/2 ) return;      // not haploid nor diploid
+
+        // Check for incorrect number of values. Note this check does not consider all values missing
+        // and will remove annotations that don't pass.
+        if ( (len==BCF_VL_A && nval != nsmpl*(rec->n_allele - 1)) || (len==BCF_VL_R && nval != nsmpl*rec->n_allele) ) return;
+    }
+
+    // Increase buffer size to accommodate star allele
+    int nval1 = nval / nsmpl;
+    mtmp = buf->mtmp;
+    if ( type==BCF_HT_INT || type==BCF_HT_REAL )
+    {
+        if ( (len==BCF_VL_A || len==BCF_VL_R) && mtmp < num_size*nsmpl*(nval1+1) ) mtmp = num_size*nsmpl*(nval1+1); // +1 for the possibility of the star allele
+        else if ( len==BCF_VL_G && mtmp < num_size*nsmpl*(nval1+3) ) mtmp = num_size*nsmpl*(nval1+3);
+    }
+    else if ( type==BCF_HT_STR )
+    {
+        if ( (len==BCF_VL_A || len==BCF_VL_R) && mtmp < nsmpl*(nval1+2) ) mtmp = nsmpl*(nval1+2); // +2 for the possibility of the star allele, ",."
+        else if ( len==BCF_VL_G && mtmp < nsmpl*(nval1+6) ) mtmp = nsmpl*(nval1+6);
+    }
+
+    if ( buf->mtmp2 < mtmp )
+    {
+        buf->tmp2  = realloc(buf->tmp2, mtmp);
+        if ( !buf->tmp2 ) error("Failed to alloc %d bytes\n", mtmp);
+        buf->mtmp2 = mtmp;
+    }
+
+    int iout, i, j;
+    for (iout=0; iout<buf->split.nout; iout++)
+    {
+        int star_allele = _has_star_allele(buf,iout);
+        bcf1_t *out = buf->vcf[rbuf_kth(&buf->rbuf,iout)];
+        int ret = 0;
+        if ( len==BCF_VL_FIXED || len==BCF_VL_VAR )
+            ret = bcf_update_format(buf->out_hdr, out, tag, buf->tmp, nval, type);
+        else if ( len==BCF_VL_A && type!=BCF_HT_STR )
+        {
+            int iori = buf->split.atoms[iout]->ial - 1;
+            assert( iori<nval );
+            for (i=0; i<nsmpl; i++)
+            {
+                void *src = buf->tmp  + nval1*num_size*i;
+                void *dst = buf->tmp2 + num_size*i*(star_allele+1);
+                if ( !memcmp(vector_end_ptr,src+iori*num_size,num_size) )
+                    memcpy(dst,missing_ptr,num_size);
+                else
+                    memcpy(dst,src+iori*num_size,num_size);
+                if ( star_allele )
+                    memcpy(dst+num_size,missing_ptr,num_size);
+            }
+            ret = bcf_update_format(buf->out_hdr, out, tag, buf->tmp2, nsmpl*(star_allele+1), type);
+        }
+        else if ( (len==BCF_VL_A || len==BCF_VL_R) && type==BCF_HT_STR )
+        {
+            int ioff = len==BCF_VL_R ? 1 : 0;
+            int iori = buf->split.atoms[iout]->ial - 1;
+            int nval1_dst = star_allele ? nval1 + 2 : nval1;
+            memset(buf->tmp2,0,nval1_dst*nsmpl);
+            for (i=0; i<nsmpl; i++)
+            {
+                kstring_t dst;
+                dst.l = 0; dst.m = nval1_dst; dst.s = (char*)buf->tmp2 + nval1_dst*i;
+                kputc_('.',&dst);
+                if ( star_allele ) kputsn_(",.",2,&dst);
+                if ( len==BCF_VL_R )
+                {
+                    kputsn_(",.",2,&dst);
+                    copy_string_field(buf->tmp+nval1*i, 0, nval1, &dst, 0);
+                }
+                copy_string_field(buf->tmp+nval1*i, iori+ioff, nval1, &dst, 0+ioff);
+                if ( star_allele ) copy_string_field(".", 0, 1, &dst, 1+ioff);
+            }
+            ret = bcf_update_format(buf->out_hdr, out, tag, buf->tmp2, nval1_dst*nsmpl, type);
+        }
+        else if ( len==BCF_VL_R && type!=BCF_HT_STR )
+        {
+            int iori = buf->split.atoms[iout]->ial;
+            assert( iori<=nval );
+            for (i=0; i<nsmpl; i++)
+            {
+                void *src = buf->tmp  + nval1*num_size*i;
+                void *dst = buf->tmp2 + num_size*i*(star_allele+2);
+                memcpy(dst,src,num_size);
+                memcpy(dst+num_size,src+iori*num_size,num_size);
+                if ( type==BCF_HT_INT && mode==M_SUM )
+                {
+                    uint8_t *tbl = buf->split.tbl + iout*buf->split.nori;
+                    for (j=iori; j<buf->split.nori; j++)
+                        if ( tbl[j]==1 ) ((int32_t*)dst)[1] += ((int32_t*)src)[j+1];
+                }
+                if ( star_allele )
+                    memcpy(dst+num_size*2,missing_ptr,num_size);
+            }
+            ret = bcf_update_format(buf->out_hdr, out, tag, buf->tmp2, nsmpl*(star_allele+2), type);
+        }
+        else if ( len==BCF_VL_G && type!=BCF_HT_STR )
+        {
+            int iori = buf->split.atoms[iout]->ial;
+            int i01  = bcf_alleles2gt(0,iori);
+            int i11  = bcf_alleles2gt(iori,iori);
+            assert( iori<nval );
+            #define BRANCH(type_t, is_missing, is_vector_end, set_missing, set_vector_end) { \
+                for (i=0; i<nsmpl; i++) \
+                { \
+                    type_t *src = (type_t*)buf->tmp + i*nval1; \
+                    type_t *dst = (type_t*)buf->tmp2 + i*3*(1+star_allele); \
+                    int n=0; /* determine ploidy of this genotype */ \
+                    while ( n<nval1 && !(is_vector_end) ) { n++; src++; } \
+                    src = (type_t*)buf->tmp + i*nval1; \
+                    memcpy(dst++,src,sizeof(type)); \
+                    int nmiss = 0, nend = 0; \
+                    if ( n==rec->n_allele ) /* haploid */ \
+                    { \
+                        memcpy(dst++,src+iori,sizeof(type)); \
+                        if ( star_allele ) { nmiss = 1; nend = 3; } \
+                        else nend = 1; \
+                    } \
+                    else if ( n==nval1 ) \
+                    { \
+                        memcpy(dst++,src+i01,sizeof(type)); \
+                        memcpy(dst++,src+i11,sizeof(type)); \
+                        if ( star_allele ) nmiss = 3; \
+                    } \
+                    else if ( n==1 && is_missing ) \
+                    { \
+                        if ( star_allele ) nend = 5; \
+                        else nend = 2; \
+                    } \
+                    else  \
+                        error("Incorrect number of values at %s:%"PRIhts_pos" .. tag=FORMAT/%s Number=G nAlleles=%d nValues=%d, %d-th sample\n", \
+                                bcf_seqname(buf->hdr,rec),rec->pos+1,tag,rec->n_allele,n,i+1); \
+                    for (j=0; j<nmiss; j++) { set_missing; dst++; } \
+                    for (j=0; j<nend; j++) { set_vector_end; dst++; } \
+                } \
+            }
+            switch (type)
+            {
+                case BCF_HT_INT:  BRANCH(int32_t, *src==bcf_int32_missing, *src==bcf_int32_vector_end, *dst=bcf_int32_missing, *dst=bcf_int32_vector_end); break;
+                case BCF_HT_REAL: BRANCH(float, bcf_float_is_missing(*src), bcf_float_is_vector_end(*src), bcf_float_set_missing(*dst), bcf_float_set_vector_end(*dst)); break;
+                default: error("Unexpected case: %d\n", type);
+            }
+            #undef BRANCH
+            ret = bcf_update_format(buf->out_hdr, out, tag, buf->tmp2, 3*(1+star_allele)*nsmpl, type);
+        }
+        if ( ret!=0 ) error("An error occurred while updating FORMAT/%s\n",tag);
+    }
+}
+static inline int _is_acgtn(char *seq)
+{
+    while ( *seq )
+    {
+        char c = toupper(*seq);
+        if ( c!='A' && c!='C' && c!='G' && c!='T' && c!='N' ) return 0;
+        seq++;
+    }
+    return 1;
+}
+/*
+    The atomization works as follows:
+    - Atomize each alternate allele separately by leaving out sequence identical to the reference. No
+      alignment is performed, just greedy trimming of the end, then from left. This operation returns
+      a list of atoms (atom_t) which carry fragments of REF,ALT and their positions as 0-based offsets
+      to the original REF allele
+    - Sort atoms by POS, REF and ALT. Each unique atom (POS+REF+ALT) forms a new VCF record, each
+      with a single ALT.
+    - For each new VCF record determine how to translate the original allele index (iori) to this new
+      record:
+        - 1: the original allele matches the atom
+        - 0: the original allele does not overlap this atom or the overlapping part matches the REF
+             allele
+        - 2 (or equivalently "."): there is a mismatch between the original allele and the atom
+      The mapping is encoded in a table with columns corresponding to the original ALTs and rows
+      to the new POS+ALTs (atoms). The table is initialized to 0, then we set 1's for matching
+      atoms and 2's for overlapping mismatching atoms.
+
+    Note that different ALT alleles can result in the same atom (the same output line) and this code
+    does not know how to reconcile possibly conflicting VCF annotations. This could be improved
+    and merge logic provided, similarly to `merge -l`. For example, the allelic depths (AD) should
+    be summed for the same atomized output allele. However, this level of complexity is not addressed
+    in this initial draft. Higher priority for now is to provide the inverse "join" operation.
+
+    Update 2021-04-09:
+        Tags QS,AD are now automatically incremented as they should be, for both INFO and FORMAT.
+        Note that the code will fail on missing values (todo) and it needs to be generalized and
+        made customizable.
+*/
+void _abuf_split(abuf_t *buf, bcf1_t *rec)
+{
+    int i,j;
+    if ( rec->n_allele < 2 )
+    {
+        rbuf_expand0(&buf->rbuf, bcf1_t*, buf->rbuf.n+1, buf->vcf);
+        int j = rbuf_append(&buf->rbuf);
+        if ( buf->vcf[j] ) bcf_destroy(buf->vcf[j]);
+        buf->vcf[j] = bcf_dup(rec);
+        return;
+    }
+    for (i=0; i<rec->n_allele; i++)
+    {
+        if ( _is_acgtn(rec->d.allele[i]) ) continue;
+        rbuf_expand0(&buf->rbuf, bcf1_t*, buf->rbuf.n+1, buf->vcf);
+        int j = rbuf_append(&buf->rbuf);
+        if ( buf->vcf[j] ) bcf_destroy(buf->vcf[j]);
+        buf->vcf[j] = bcf_dup(rec);
+        return;
+    }
+
+    buf->natoms = 0;
+    for (i=1; i<rec->n_allele; i++) _atomize_allele(buf,rec,i);
+    qsort(buf->atoms,buf->natoms,sizeof(*buf->atoms),_cmp_atoms);
+    _split_table_init(buf,rec,buf->natoms);
+    for (i=0; i<buf->natoms; i++)
+    {
+        if ( i && !_atoms_inconsistent(&buf->atoms[i-1],&buf->atoms[i]) ) continue;
+        _split_table_new(buf, &buf->atoms[i]);  // add a new unique output atom
+    }
+    for (i=0; i<buf->natoms; i++)
+    {
+        // Looping over sorted list of all atoms with possible duplicates from different source ALT alleles
+        atom_t *atom = &buf->atoms[i];
+        for (j=0; j<buf->split.nout; j++)
+        {
+            atom_t *out = buf->split.atoms[j];
+            if ( atom == out ) continue;            // table already set to 1
+            if ( atom->beg > out->end ) continue;   // cannot overlap this output atom
+            if ( atom->end < out->beg ) break;      // this atom is ahead of all subsequent output records
+            _split_table_overlap(buf, j, atom);
+        }
+    }
+    assert( !buf->rbuf.n ); // all records should be flushed first in the SPLIT mode
+
+    // Create the output records, transferring all annotations:
+    // CHROM-QUAL
+    _split_table_set_chrom_qual(buf);
+
+    // INFO
+    for (i=0; i<rec->n_info; i++)
+    {
+        // this implementation of merging rules is temporary: generalize and made customizable through the API
+        merge_rule_t mode = M_FIRST;
+        const char *tag = bcf_hdr_int2id(buf->hdr,BCF_DT_ID,rec->d.info[i].key);
+        if ( !strcmp(tag,"QS") || !strcmp(tag,"AD") ) mode = M_SUM;
+
+        _split_table_set_info(buf, &rec->d.info[i], mode);
+    }
+
+    // Set INFO tag showing the original record
+    if ( buf->split.info_tag )
+        _split_table_set_history(buf);
+
+    // FORMAT
+    for (i=0; i<rec->n_fmt; i++)
+    {
+        // this implementation of merging rules is temporary: generalize and made customizable through the API
+        merge_rule_t mode = M_FIRST;
+        const char *tag = bcf_hdr_int2id(buf->hdr,BCF_DT_ID,rec->d.fmt[i].id);
+        if ( !strcmp(tag,"QS") || !strcmp(tag,"AD") ) mode = M_SUM;
+
+        _split_table_set_format(buf, &rec->d.fmt[i], mode);
+    }
+
+    // Check that at least one FORMAT field was added, if not, the number of samples must be set manually
+    for (i=0; i<buf->split.nout; i++)
+    {
+        bcf1_t *out = buf->vcf[rbuf_kth(&buf->rbuf,i)];
+        if ( !out->n_sample ) out->n_sample = rec->n_sample;
+    }
+}
+
+void abuf_push(abuf_t *buf, bcf1_t *rec)
+{
+    bcf_unpack(rec, BCF_UN_ALL);
+    if ( buf->mode==SPLIT ) _abuf_split(buf,rec);
+}
+
+bcf1_t *abuf_flush(abuf_t *buf, int flush_all)
+{
+    int i;
+
+    if ( buf->rbuf.n==0 ) return NULL;
+    if ( flush_all ) goto ret;
+
+ret:
+    i = rbuf_shift(&buf->rbuf);
+    return buf->vcf[i];
+}
+
diff --git a/bcftools/abuf.h b/bcftools/abuf.h
new file mode 100644
index 0000000..5fc1e00
--- /dev/null
+++ b/bcftools/abuf.h
@@ -0,0 +1,78 @@
+/* The MIT License
+
+   Copyright (c) 2021 Genome Research Ltd.
+
+   Author: Petr Danecek <pd3@sanger.ac.uk>
+   
+   Permission is hereby granted, free of charge, to any person obtaining a copy
+   of this software and associated documentation files (the "Software"), to deal
+   in the Software without restriction, including without limitation the rights
+   to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+   copies of the Software, and to permit persons to whom the Software is
+   furnished to do so, subject to the following conditions:
+   
+   The above copyright notice and this permission notice shall be included in
+   all copies or substantial portions of the Software.
+   
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+   IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+   FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+   AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+   LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+   OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+   THE SOFTWARE.
+
+ */
+
+/*
+    Atomize/deatomize complex variants
+*/
+
+#ifndef __ABUF_H__
+#define __ABUF_H__
+
+#include <htslib/vcf.h>
+
+typedef struct _abuf_t abuf_t;
+
+// Modes of operation
+typedef enum
+{
+    NONE,
+
+    // mode of operation, to be passed to abuf_init
+    SPLIT,
+    JOIN,
+
+    BCF_HDR,        // should the records be annotated, a writable bcf header is required
+    INFO_TAG,       // set BCF_HDR first
+    STAR_ALLELE     // 1: use STAR allele (the default), 0: set overlaps to missing
+}
+abuf_opt_t;
+
+#define abuf_set_opt(buf,type,key,value) { type tmp = value; abuf_set(buf, key, (void*)&tmp); }
+void abuf_set(abuf_t *buf, abuf_opt_t key, void *value);
+
+/*
+ *  abuf_init() - init buffer
+ *  @win:   number of sites (>0) or bp (<0)
+ */
+abuf_t *abuf_init(const bcf_hdr_t *hdr, abuf_opt_t mode);
+void abuf_destroy(abuf_t *buf);
+
+/*
+ *  abuf_push() - Push a new site for analysis
+ */
+void abuf_push(abuf_t *buf, bcf1_t *rec);
+
+/*
+ *  abuf_flush() - Return next buffered record
+ *  @flush_all: Set to 1 if no more overlapping records are coming (e.g. end of chromosome or end of file),
+ *              the buffer can be emptied.
+ *  return:     The next atomized/deatomized VCF record or NULL if no record is ready. The returned
+ *              structure will be cleaned by abuf.
+ */
+bcf1_t *abuf_flush(abuf_t *buf, int flush_all);
+
+#endif
+
diff --git a/bcftools/bam2bcf.c b/bcftools/bam2bcf.c
new file mode 100644
index 0000000..d373e99
--- /dev/null
+++ b/bcftools/bam2bcf.c
@@ -0,0 +1,1232 @@
+/*  bam2bcf.c -- variant calling.
+
+    Copyright (C) 2010-2012 Broad Institute.
+    Copyright (C) 2012-2022 Genome Research Ltd.
+
+    Author: Heng Li <lh3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <math.h>
+#include <stdint.h>
+#include <assert.h>
+#include <float.h>
+#include <htslib/hts.h>
+#include <htslib/sam.h>
+#include <htslib/kstring.h>
+#include <htslib/kfunc.h>
+#include "bam2bcf.h"
+
+extern  void ks_introsort_uint32_t(size_t n, uint32_t a[]);
+
+#define CALL_DEFTHETA 0.83
+#define DEF_MAPQ 20
+
+#define CAP_DIST 25
+
+bcf_callaux_t *bcf_call_init(double theta, int min_baseQ, int max_baseQ,
+                             int delta_baseQ)
+{
+    bcf_callaux_t *bca;
+    if (theta <= 0.) theta = CALL_DEFTHETA;
+    bca = (bcf_callaux_t*) calloc(1, sizeof(bcf_callaux_t));
+    bca->capQ = 60;
+    bca->openQ = 40; bca->extQ = 20; bca->tandemQ = 100;
+    bca->min_baseQ = min_baseQ;
+    bca->max_baseQ = max_baseQ;
+    bca->delta_baseQ = delta_baseQ;
+    bca->e = errmod_init(1. - theta);
+    bca->min_frac = 0.002;
+    bca->min_support = 1;
+    bca->per_sample_flt = 0;
+    bca->npos = 100;
+    bca->ref_pos = (int*) malloc(bca->npos*sizeof(int));
+    bca->alt_pos = (int*) malloc(bca->npos*sizeof(int));
+    bca->iref_pos= (int*) malloc(bca->npos*sizeof(int));
+    bca->ialt_pos= (int*) malloc(bca->npos*sizeof(int));
+    bca->nqual = 60;
+    bca->ref_mq  = (int*) malloc(bca->nqual*sizeof(int));
+    bca->alt_mq  = (int*) malloc(bca->nqual*sizeof(int));
+    bca->iref_mq = (int*) malloc(bca->nqual*sizeof(int));
+    bca->ialt_mq = (int*) malloc(bca->nqual*sizeof(int));
+    bca->ref_bq  = (int*) malloc(bca->nqual*sizeof(int));
+    bca->alt_bq  = (int*) malloc(bca->nqual*sizeof(int));
+    bca->fwd_mqs = (int*) malloc(bca->nqual*sizeof(int));
+    bca->rev_mqs = (int*) malloc(bca->nqual*sizeof(int));
+    return bca;
+}
+
+void bcf_call_destroy(bcf_callaux_t *bca)
+{
+    if (bca == 0) return;
+    errmod_destroy(bca->e);
+    if (bca->npos) {
+        free(bca->ref_pos);  free(bca->alt_pos);
+        free(bca->iref_pos); free(bca->ialt_pos);
+        bca->npos = 0;
+    }
+    free(bca->ref_mq); free(bca->alt_mq);
+    free(bca->iref_mq); free(bca->ialt_mq);
+    free(bca->ref_bq); free(bca->alt_bq);
+    free(bca->fwd_mqs); free(bca->rev_mqs);
+    bca->nqual = 0;
+    free(bca->bases); free(bca->inscns); free(bca);
+}
+
+static int get_aux_nm(bam1_t *rec, int32_t qpos, int is_ref)
+{
+    uint8_t *nm_tag = bam_aux_get(rec, "NM");
+    if ( !nm_tag ) return -1;
+    int64_t nm = bam_aux2i(nm_tag);
+
+    // Count indels as single events, not as the number of inserted/deleted
+    // bases (which is what NM does). Add soft clips as mismatches.
+    int i;
+    for (i=0; i < rec->core.n_cigar; i++)
+    {
+        int val = bam_get_cigar(rec)[i] & BAM_CIGAR_MASK;
+        if ( val==BAM_CSOFT_CLIP )
+        {
+            nm += bam_get_cigar(rec)[i] >> BAM_CIGAR_SHIFT;
+        }
+        else if ( val==BAM_CINS || val==BAM_CDEL )
+        {
+            val = bam_get_cigar(rec)[i] >> BAM_CIGAR_SHIFT;
+            if ( val > 1 ) nm -= val - 1;
+        }
+    }
+
+    // Take into account MNPs, 2% of de novo SNVs appear within 20bp of another de novo SNV
+    //      http://www.genome.org/cgi/doi/10.1101/gr.239756.118
+    nm -= is_ref ? 1 : 2;
+
+    if ( nm < 0 ) nm = 0;
+    if ( nm >= B2B_N_NM ) nm = B2B_N_NM - 1;
+
+    return nm;
+}
+
+// position in the sequence with respect to the aligned part of the read
+static int get_position(const bam_pileup1_t *p, int *len,
+                        int *sc_len, int *sc_dist) {
+    int i, j, edist = p->qpos + 1;
+    int sc_left = 0, sc_right = 0;
+    int sc_left_dist = -1, sc_right_dist = -1;
+
+    // left end
+    for (i = 0; i < p->b->core.n_cigar; i++) {
+        int cig  = bam_get_cigar(p->b)[i] & BAM_CIGAR_MASK;
+        if (cig == BAM_CHARD_CLIP)
+            continue;
+        else if (cig == BAM_CSOFT_CLIP)
+            sc_left += bam_get_cigar(p->b)[i] >> BAM_CIGAR_SHIFT;
+        else
+            break;
+    }
+    if (sc_left)
+        sc_left_dist = p->qpos+1 - sc_left;
+    edist -= sc_left;
+
+    // right end
+    for (j = p->b->core.n_cigar-1; j >= i; j--) {
+        int cig  = bam_get_cigar(p->b)[j] & BAM_CIGAR_MASK;
+        if (cig == BAM_CHARD_CLIP)
+            continue;
+        else if (cig == BAM_CSOFT_CLIP)
+            sc_right += bam_get_cigar(p->b)[j] >> BAM_CIGAR_SHIFT;
+        else
+            break;
+    }
+    if (sc_right)
+        sc_right_dist = p->b->core.l_qseq - sc_right - p->qpos;
+
+    // Distance to nearest soft-clips and length of that clip.
+    if (sc_left_dist >= 0) {
+        if (sc_right_dist < 0 || sc_left_dist < sc_right_dist) {
+            *sc_len  = sc_left;
+            *sc_dist = sc_left_dist;
+        }
+    } else if (sc_right_dist >= 0) {
+        *sc_len  = sc_right;
+        *sc_dist = sc_right_dist;
+    } else {
+        *sc_len  = 0;
+        *sc_dist = 0;
+    }
+
+    *len = p->b->core.l_qseq - sc_left - sc_right;
+    return edist;
+}
+
+void bcf_callaux_clean(bcf_callaux_t *bca, bcf_call_t *call)
+{
+    memset(bca->ref_pos,0,sizeof(int)*bca->npos);
+    memset(bca->alt_pos,0,sizeof(int)*bca->npos);
+    memset(bca->iref_pos,0,sizeof(int)*bca->npos);
+    memset(bca->ialt_pos,0,sizeof(int)*bca->npos);
+    memset(bca->ref_mq,0,sizeof(int)*bca->nqual);
+    memset(bca->alt_mq,0,sizeof(int)*bca->nqual);
+    memset(bca->iref_mq,0,sizeof(int)*bca->nqual);
+    memset(bca->ialt_mq,0,sizeof(int)*bca->nqual);
+    memset(bca->ref_bq,0,sizeof(int)*bca->nqual);
+    memset(bca->alt_bq,0,sizeof(int)*bca->nqual);
+    memset(bca->fwd_mqs,0,sizeof(int)*bca->nqual);
+    memset(bca->rev_mqs,0,sizeof(int)*bca->nqual);
+    if ( call->ADF ) memset(call->ADF,0,sizeof(int32_t)*(call->n+1)*B2B_MAX_ALLELES);
+    if ( call->ADR ) memset(call->ADR,0,sizeof(int32_t)*(call->n+1)*B2B_MAX_ALLELES);
+    if ( call->SCR ) memset(call->SCR,0,sizeof(*call->SCR)*(call->n+1));
+    if ( call->SCR ) memset(call->SCR,0,sizeof(*call->SCR)*(call->n+1));
+    if ( bca->fmt_flag&B2B_FMT_NMBZ )
+    {
+        memset(call->ref_nm,0,sizeof(*call->ref_nm)*(call->n+1)*B2B_N_NM);
+        memset(call->alt_nm,0,sizeof(*call->alt_nm)*(call->n+1)*B2B_N_NM);
+    }
+    else
+    {
+        memset(call->ref_nm,0,sizeof(*call->ref_nm)*B2B_N_NM);
+        memset(call->alt_nm,0,sizeof(*call->alt_nm)*B2B_N_NM);
+    }
+    memset(call->QS,0,sizeof(*call->QS)*call->n*B2B_MAX_ALLELES);
+    memset(bca->ref_scl,  0, 100*sizeof(int));
+    memset(bca->alt_scl,  0, 100*sizeof(int));
+    memset(bca->iref_scl, 0, 100*sizeof(int));
+    memset(bca->ialt_scl, 0, 100*sizeof(int));
+}
+
+/*
+    Notes:
+    - Called from bam_plcmd.c by mpileup. Amongst other things, sets the bcf_callret1_t.QS frequencies
+        which are carried over via bcf_call_combine and bcf_call2bcf to the output BCF as the INFO/QS and FMT/QS annotations.
+        Later it's used for multiallelic calling by `call -m`, `call -mG` and `+trio-dnm`.
+    - ref_base is the 4-bit representation of the reference base. It is negative if we are looking at an indel.
+ */
+/*
+ * This function is called once for each sample.
+ * _n is number of pilesups pl contributing reads to this sample
+ * pl is pointer to array of _n pileups (one pileup per read)
+ * ref_base is the 4-bit representation of the reference base. It is negative if we are looking at an indel.
+ * bca is the settings to perform calls across all samples
+ * r is the returned value of the call
+ */
+int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base, bcf_callaux_t *bca, bcf_callret1_t *r)
+{
+    int i, n, ref4, is_indel, ori_depth = 0;
+
+    // clean from previous run
+    r->ori_depth = 0;
+    r->mq0 = 0;
+    memset(r->anno,0,sizeof(double)*16);
+    memset(r->p,0,sizeof(float)*25);
+    r->SCR = 0;
+
+    if (ref_base >= 0) {
+        ref4 = seq_nt16_int[ref_base];
+        is_indel = 0;
+    } else ref4 = 4, is_indel = 1;
+    if (_n == 0) return -1;
+    // enlarge the bases array if necessary
+    if (bca->max_bases < _n) {
+        bca->max_bases = _n;
+        kroundup32(bca->max_bases);
+        bca->bases = (uint16_t*)realloc(bca->bases, 2 * bca->max_bases);
+    }
+
+    // fill the bases array
+    double nqual_over_60 = bca->nqual / 60.0;
+    int ADR_ref_missed[4] = {0};
+    int ADF_ref_missed[4] = {0};
+    for (i = n = 0; i < _n; ++i) {
+        const bam_pileup1_t *p = pl + i;
+        int q, b, mapQ, baseQ, is_diff, min_dist, seqQ;
+        if ( bca->fmt_flag&(B2B_INFO_SCR|B2B_FMT_SCR) && PLP_HAS_SOFT_CLIP(p->cd.i) ) r->SCR++;
+        if (p->is_refskip || (p->b->core.flag&BAM_FUNMAP)) continue;
+        if (p->is_del && !is_indel) continue;
+        ++ori_depth;
+        if (is_indel)
+        {
+            b = p->aux>>16&0x3f;
+            seqQ = q = (p->aux & 0xff); // mp2 + builtin indel-bias
+            if (q < bca->min_baseQ)
+            {
+                if (!p->indel && b < 4)
+                {
+                    if (bam_is_rev(p->b))
+                        ADR_ref_missed[b]++;
+                    else
+                        ADF_ref_missed[b]++;
+                }
+                continue;
+            }
+            if (p->indel == 0 && (q < _n/2 || _n > 20)) {
+                // high quality indel calls without p->indel set aren't
+                // particularly indicative of being a good REF match either,
+                // at least not in low coverage.  So require solid coverage
+                // before we start utilising such quals.
+                b = 0;
+                q = (int)bam_get_qual(p->b)[p->qpos];
+                seqQ = (3*seqQ + 2*q)/8;
+            }
+            if (_n > 20 && seqQ > 40) seqQ = 40;
+            baseQ  = p->aux>>8&0xff;
+
+            is_diff = (b != 0);
+        }
+        else
+        {
+            b = bam_seqi(bam_get_seq(p->b), p->qpos); // base
+            b = seq_nt16_int[b? b : ref_base]; // b is the 2-bit base
+
+            // Lowest of this and neighbour quality values
+            uint8_t *qual = bam_get_qual(p->b);
+            q = qual[p->qpos];
+            if (p->qpos > 0 &&
+                q > qual[p->qpos-1]+bca->delta_baseQ)
+                q = qual[p->qpos-1]+bca->delta_baseQ;
+            if (p->qpos+1 < p->b->core.l_qseq &&
+                q > qual[p->qpos+1]+bca->delta_baseQ)
+                q = qual[p->qpos+1]+bca->delta_baseQ;
+
+            if (q < bca->min_baseQ) continue;
+            if (q > bca->max_baseQ) q = bca->max_baseQ;
+            baseQ = q;
+            seqQ  = 99;
+            is_diff = (ref4 < 4 && b == ref4)? 0 : 1;
+        }
+        mapQ  = p->b->core.qual < 255? p->b->core.qual : DEF_MAPQ; // special case for mapQ==255
+        if ( !mapQ ) r->mq0++;
+        if (q > seqQ) q = seqQ;
+        mapQ = mapQ < bca->capQ? mapQ : bca->capQ;
+        if (q > mapQ) q = mapQ;
+        if (q > 63) q = 63;
+        if (q < 4) q = 4;       // MQ=0 reads count as BQ=4
+        bca->bases[n++] = q<<5 | (int)bam_is_rev(p->b)<<4 | b;
+        // collect annotations
+        if (b < 4)
+        {
+            r->QS[b] += q;
+            if ( r->ADF )
+            {
+                if ( bam_is_rev(p->b) )
+                    r->ADR[b]++;
+                else
+                    r->ADF[b]++;
+            }
+        }
+        ++r->anno[0<<2|is_diff<<1|bam_is_rev(p->b)];
+        min_dist = p->b->core.l_qseq - 1 - p->qpos;
+        if (min_dist > p->qpos) min_dist = p->qpos;
+        if (min_dist > CAP_DIST) min_dist = CAP_DIST;
+        r->anno[1<<2|is_diff<<1|0] += baseQ;
+        r->anno[1<<2|is_diff<<1|1] += baseQ * baseQ;
+        r->anno[2<<2|is_diff<<1|0] += mapQ;
+        r->anno[2<<2|is_diff<<1|1] += mapQ * mapQ;
+        r->anno[3<<2|is_diff<<1|0] += min_dist;
+        r->anno[3<<2|is_diff<<1|1] += min_dist * min_dist;
+
+        // collect for bias tests
+        if ( baseQ > 59 ) baseQ = 59;
+        if ( mapQ > 59 ) mapQ = 59;
+        int len, epos = 0, sc_len = 0, sc_dist = 0;
+        if ( bca->fmt_flag & (B2B_INFO_RPB|B2B_INFO_VDB|B2B_INFO_SCB) )
+        {
+            int pos = get_position(p, &len, &sc_len, &sc_dist);
+            epos = (double)pos/(len+1) * bca->npos;
+
+            if (sc_len) {
+                sc_len = 15.0*sc_len / sc_dist;
+                if (sc_len > 99) sc_len = 99;
+            }
+        }
+        int imq  = mapQ * nqual_over_60;
+        int ibq  = baseQ * nqual_over_60;
+        int inm  = get_aux_nm(p->b,p->qpos,is_diff?0:1);
+
+        if ( bam_is_rev(p->b) )
+            bca->rev_mqs[imq]++;
+        else
+            bca->fwd_mqs[imq]++;
+
+        if ( !is_diff )
+        {
+            bca->ref_pos[epos]++;
+            bca->ref_bq[ibq]++;
+            bca->ref_mq[imq]++;
+            bca->ref_scl[sc_len]++;
+            if ( inm>=0 )
+            {
+                bca->ref_nm[inm]++;
+                if ( r->ref_nm ) r->ref_nm[inm]++;
+            }
+        }
+        else
+        {
+            bca->alt_pos[epos]++;
+            bca->alt_bq[ibq]++;
+            bca->alt_mq[imq]++;
+            bca->alt_scl[sc_len]++;
+            if ( inm>=0 )
+            {
+                bca->alt_nm[inm]++;
+                if ( r->alt_nm ) r->alt_nm[inm]++;
+            }
+        }
+    }
+
+    // Compensate for AD not being counted on low quality REF indel matches.
+    if ( r->ADF && bca->ambig_reads==B2B_INC_AD0 )
+    {
+        for (i=0; i<4; i++)
+        {
+            r->ADR[0] += ADR_ref_missed[i];
+            r->ADF[0] += ADF_ref_missed[i];
+        }
+    }
+    else if ( r->ADF && bca->ambig_reads==B2B_INC_AD )
+    {
+        int dp = 0, dp_ambig = 0;
+        for (i=0; i<4; i++) dp += r->ADR[i];
+        for (i=0; i<4; i++) dp_ambig += ADR_ref_missed[i];
+        if ( dp )
+            for (i=0; i<4; i++) r->ADR[i] += lroundf((float)dp_ambig * r->ADR[i]/dp);
+        dp = 0, dp_ambig = 0;
+        for (i=0; i<4; i++) dp += r->ADF[i];
+        for (i=0; i<4; i++) dp_ambig += ADF_ref_missed[i];
+        if ( dp )
+            for (i=0; i<4; i++) r->ADF[i] += lroundf((float)dp_ambig * r->ADF[i]/dp);
+    }
+
+    r->ori_depth = ori_depth;
+    // glfgen
+    errmod_cal(bca->e, n, 5, bca->bases, r->p); // calculate PL of each genotype
+    return n;
+}
+
+
+/*
+ *  calc_vdb() - returns value between zero (most biased) and one (no bias)
+ *               on success, or HUGE_VAL when VDB cannot be calculated because
+ *               of insufficient depth (<2x)
+ *
+ *  Variant Distance Bias tests if the variant bases are positioned within the
+ *  reads with sufficient randomness. Unlike other tests, it looks only at
+ *  variant reads and therefore gives different kind of information than Read
+ *  Position Bias for instance. VDB was developed for detecting artefacts in
+ *  RNA-seq calls where reads from spliced transcripts span splice site
+ *  boundaries.  The current implementation differs somewhat from the original
+ *  version described in supplementary material of PMID:22524474, but the idea
+ *  remains the same. (Here the random variable tested is the average distance
+ *  from the averaged position, not the average pairwise distance.)
+ *
+ *  For coverage of 2x, the calculation is exact but is approximated for the
+ *  rest. The result is most accurate between 4-200x. For 3x or >200x, the
+ *  reported values are slightly more favourable than those of a true random
+ *  distribution.
+ */
+double calc_vdb(int *pos, int npos)
+{
+    // Note well: the parameters were obtained by fitting to simulated data of
+    // 100bp reads. This assumes rescaling to 100bp in bcf_call_glfgen().
+    const int readlen = 100;
+    assert( npos==readlen );
+
+    #define nparam 15
+    const float param[nparam][3] = { {3,0.079,18}, {4,0.09,19.8}, {5,0.1,20.5}, {6,0.11,21.5},
+        {7,0.125,21.6}, {8,0.135,22}, {9,0.14,22.2}, {10,0.153,22.3}, {15,0.19,22.8},
+        {20,0.22,23.2}, {30,0.26,23.4}, {40,0.29,23.5}, {50,0.35,23.65}, {100,0.5,23.7},
+        {200,0.7,23.7} };
+
+    int i, dp = 0;
+    float mean_pos = 0, mean_diff = 0;
+    for (i=0; i<npos; i++)
+    {
+        if ( !pos[i] ) continue;
+        dp += pos[i];
+        mean_pos += pos[i]*i;
+    }
+    if ( dp<2 ) return HUGE_VAL;     // one or zero reads can be placed anywhere
+
+    mean_pos /= dp;
+    for (i=0; i<npos; i++)
+    {
+        if ( !pos[i] ) continue;
+        mean_diff += pos[i] * fabs(i - mean_pos);
+    }
+    mean_diff /= dp;
+
+    int ipos = mean_diff;   // tuned for float-to-int implicit conversion
+    if ( dp==2 )
+        return (2*readlen-2*(ipos+1)-1)*(ipos+1)/(readlen-1)/(readlen*0.5);
+
+    if ( dp>=200 )
+        i = nparam; // shortcut for big depths
+    else
+    {
+        for (i=0; i<nparam; i++)
+            if ( param[i][0]>=dp ) break;
+    }
+    float pshift, pscale;
+    if ( i==nparam )
+    {
+        // the depth is too high, go with 200x
+        pscale = param[nparam-1][1];
+        pshift = param[nparam-1][2];
+    }
+    else if ( i>0 && param[i][0]!=dp )
+    {
+        // linear interpolation of parameters
+        pscale = (param[i-1][1] + param[i][1])*0.5;
+        pshift = (param[i-1][2] + param[i][2])*0.5;
+    }
+    else
+    {
+        pscale = param[i][1];
+        pshift = param[i][2];
+    }
+    return 0.5*kf_erfc(-(mean_diff-pshift)*pscale);
+}
+
+double calc_chisq_bias(int *a, int *b, int n)
+{
+    int na = 0, nb = 0, i, ndf = n;
+    for (i=0; i<n; i++) na += a[i];
+    for (i=0; i<n; i++) nb += b[i];
+    if ( !na || !nb ) return HUGE_VAL;
+
+    double chisq = 0;
+    for (i=0; i<n; i++)
+    {
+        if ( !a[i] && !b[i] ) ndf--;
+        else
+        {
+            double tmp = a[i] - b[i];
+            chisq += tmp*tmp/(a[i]+b[i]);
+        }
+    }
+    /*
+        kf_gammq: incomplete gamma function Q(a,x) = 1 - P(a,x) = Gamma(a,x)/Gamma(a)
+        1 if the distributions are identical, 0 if very different
+    */
+    double prob = kf_gammaq(0.5*ndf, 0.5*chisq);
+    return prob;
+}
+
+static double mann_whitney_1947_(int n, int m, int U)
+{
+     if (U<0) return 0;
+     if (n==0||m==0) return U==0 ? 1 : 0;
+    return (double)n/(n+m)*mann_whitney_1947_(n-1,m,U-m) + (double)m/(n+m)*mann_whitney_1947_(n,m-1,U);
+}
+
+double mann_whitney_1947(int n, int m, int U)
+{
+    #include "mw.h"
+
+    assert(n >= 2 && m >= 2);
+
+    return (n < 8 && m < 8 && U < 50)
+        ? mw[n-2][m-2][U]
+        : mann_whitney_1947_(n,m,U);
+}
+
+double mann_whitney_1947_cdf(int n, int m, int U)
+{
+    int i;
+    double sum = 0;
+    for (i=0; i<=U; i++)
+        sum += mann_whitney_1947(n,m,i);
+    return sum;
+}
+
+double calc_mwu_bias_cdf(int *a, int *b, int n)
+{
+    int na = 0, nb = 0, i;
+    double U = 0;
+    //double ties = 0;
+    for (i=0; i<n; i++)
+    {
+        na += a[i];
+        U  += a[i] * (nb + b[i]*0.5);
+        nb += b[i];
+        // if ( a[i] && b[i] )
+        // {
+        //     double tie = a[i] + b[i];
+        //     ties += (tie*tie-1)*tie;
+        // }
+    }
+    if ( !na || !nb ) return HUGE_VAL;
+
+    // Always work with the smaller U
+    double U_min = ((double)na * nb) - U;
+    if ( U < U_min ) U_min = U;
+
+    if ( na==1 ) return 2.0 * (floor(U_min)+1) / (nb+1);
+    if ( nb==1 ) return 2.0 * (floor(U_min)+1) / (na+1);
+
+    // Normal approximation, very good for na>=8 && nb>=8 and reasonable if na<8 or nb<8
+    if ( na>=8 || nb>=8 )
+    {
+        double mean = ((double)na*nb)*0.5;
+        // Correction for ties:
+        //      double N = na+nb;
+        //      double var2 = (N*N-1)*N-ties;
+        //      if ( var2==0 ) return 1.0;
+        //      var2 *= ((double)na*nb)/N/(N-1)/12.0;
+        // No correction for ties:
+        double var2 = ((double)na*nb)*(na+nb+1)/12.0;
+        double z = (U_min - mean)/sqrt(2*var2);   // z is N(0,1)
+        return 2.0 - kf_erfc(z);  // which is 1 + erf(z)
+    }
+
+    // Exact calculation
+    double pval = 2*mann_whitney_1947_cdf(na,nb,U_min);
+    return pval>1 ? 1 : pval;
+}
+
+double calc_mwu_bias(int *a, int *b, int n, int left)
+{
+    int na = 0, nb = 0, i;
+    double U = 0;
+    // double ties = 0;
+    for (i=0; i<n; i++)
+    {
+        if (!a[i]) {
+            if (!b[i]) continue;
+            nb += b[i];
+        } else if (!b[i]) {
+            na += a[i];
+            U  += a[i] * nb;
+        } else {
+            na += a[i];
+            U  += a[i] * (nb + b[i]*0.5);
+            nb += b[i];
+            // double tie = a[i] + b[i];
+            // ties += (tie*tie-1)*tie;
+        }
+    }
+    if ( !na || !nb ) return HUGE_VAL;
+    if ( na==1 || nb==1 ) return 1.0;       // Flat probability, all U values are equally likely
+
+    double mean = ((double)na*nb)*0.5;
+    if (left && U > mean) return 1; // for MQB which is asymmetrical
+    if ( na==2 || nb==2 )
+    {
+        // Linear approximation
+        return U>mean ? (2.0*mean-U)/mean : U/mean;
+    }
+    // Correction for ties:
+    //      double N = na+nb;
+    //      double var2 = (N*N-1)*N-ties;
+    //      if ( var2==0 ) return 1.0;
+    //      var2 *= ((double)na*nb)/N/(N-1)/12.0;
+    // No correction for ties:
+    double var2 = ((double)na*nb)*(na+nb+1)/12.0;
+    if ( na>=8 || nb>=8 )
+    {
+        // Normal approximation, very good for na>=8 && nb>=8 and reasonable if na<8 or nb<8
+        return exp(-0.5*(U-mean)*(U-mean)/var2);
+    }
+
+    // Exact calculation
+    return mann_whitney_1947(na,nb,U) * sqrt(2*M_PI*var2);
+}
+
+// A Z-score version of the above function.
+//
+// See "Normal approximation and tie correction" at
+// https://en.wikipedia.org/wiki/Mann%E2%80%93Whitney_U_test
+//
+// The Z score is the number of standard deviations above or below the mean
+// with 0 being equality of the two distributions and +ve/-ve from there.
+//
+// This is a more robust score to filter on.
+double calc_mwu_biasZ(int *a, int *b, int n, int left_only, int do_Z) {
+    int i;
+    int64_t t;
+
+    // Optimisation
+    for (i = 0; i < n; i++)
+        if (b[i])
+            break;
+    int b_empty = (i == n);
+
+    // Count equal (e), less-than (l) and greater-than (g) permutations.
+    int e = 0, l = 0, na = 0, nb = 0;
+    if (b_empty) {
+        for (t = 0, i = n-1; i >= 0; i--) {
+            na += a[i];
+            t += (a[i]*a[i]-1)*a[i];  // adjustment score for ties
+        }
+    } else {
+        for (t = 0, i = n-1; i >= 0; i--) {
+            // Combinations of a[i] and b[j] for i==j
+            e += a[i]*b[i];
+
+            // nb is running total of b[i+1]..b[n-1].
+            // Therefore a[i]*nb is the number of combinations of a[i] and b[j]
+            // for all i < j.
+            l += a[i]*nb;    // a<b
+
+            na += a[i];
+            nb += b[i];
+            int p = a[i]+b[i];
+            t += (p*p-1)*p;  // adjustment score for ties
+        }
+    }
+
+    if (!na || !nb)
+        return HUGE_VAL;
+
+    double U, m;
+    U = l + e*0.5; // Mann-Whitney U score
+    m = na*nb / 2.0;
+
+    // With ties adjustment
+    double var2 = (na*nb)/12.0 * ((na+nb+1) - t/(double)((na+nb)*(na+nb-1)));
+    // var = na*nb*(na+nb+1)/12.0; // simpler; minus tie adjustment
+    if (var2 <= 0)
+        return do_Z ? 0 : 1;
+
+    if (do_Z) {
+        // S.D. normalised Z-score
+        //Z = (U - m - (U-m >= 0 ? 0.5 : -0.5)) / sd; // gatk method?
+        return (U - m) / sqrt(var2);
+    }
+
+    // Else U score, which can be asymmetric for some data types.
+    if (left_only && U > m)
+        return HUGE_VAL; // one-sided, +ve bias is OK, -ve is not.
+
+    if (na >= 8 || nb >= 8) {
+        // Normal approximation, very good for na>=8 && nb>=8 and
+        // reasonable if na<8 or nb<8
+        return exp(-0.5*(U-m)*(U-m)/var2);
+    }
+
+    // Exact calculation
+    if (na==1 || nb == 1)
+        return mann_whitney_1947_(na, nb, U) * sqrt(2*M_PI*var2);
+    else
+        return mann_whitney_1947(na, nb, U) * sqrt(2*M_PI*var2);
+}
+
+static inline double logsumexp2(double a, double b)
+{
+    if ( a>b )
+        return log(1 + exp(b-a)) + a;
+    else
+        return log(1 + exp(a-b)) + b;
+}
+
+void calc_SegBias(const bcf_callret1_t *bcr, bcf_call_t *call)
+{
+    call->seg_bias = HUGE_VAL;
+    if ( !bcr ) return;
+
+    int nr = call->anno[2] + call->anno[3]; // number of observed non-reference reads
+    if ( !nr ) return;
+
+    int avg_dp = (call->anno[0] + call->anno[1] + nr) / call->n;    // average depth
+    double M   = floor((double)nr / avg_dp + 0.5);   // an approximate number of variants samples in the population
+    if ( M>call->n ) M = call->n;       // clamp M at the number of samples
+    else if ( M==0 ) M = 1;
+    double f = M / 2. / call->n;        // allele frequency
+    double p = (double) nr / call->n;   // number of variant reads per sample expected if variant not real (poisson)
+    double q = (double) nr / M;         // number of variant reads per sample expected if variant is real (poisson)
+    double sum = 0;
+    const double log2 = log(2.0);
+
+    // fprintf(stderr,"M=%.1f  p=%e q=%e f=%f  dp=%d\n",M,p,q,f,avg_dp);
+    int i;
+    for (i=0; i<call->n; i++)
+    {
+        int oi = bcr[i].anno[2] + bcr[i].anno[3];       // observed number of non-ref reads
+        double tmp;
+        if ( oi )
+        {
+            // tmp = log(f) + oi*log(q/p) - q + log(2*(1-f) + f*pow(2,oi)*exp(-q)) + p; // this can under/overflow
+            tmp = logsumexp2(log(2*(1-f)), log(f) + oi*log2 - q);
+            tmp += log(f) + oi*log(q/p) - q + p;
+        }
+        else
+            tmp = log(2*f*(1-f)*exp(-q) + f*f*exp(-2*q) + (1-f)*(1-f)) + p;
+        sum += tmp;
+        // fprintf(stderr,"oi=%d %e\n", oi,tmp);
+    }
+    call->seg_bias = sum;
+}
+
+/**
+ *  bcf_call_combine() - sets the PL array and VDB, RPB annotations, finds the top two alleles
+ *  @n:         number of samples
+ *  @calls:     each sample's calls
+ *  @bca:       auxiliary data structure for holding temporary values
+ *  @ref_base:  the reference base
+ *  @call:      filled with the annotations
+ *
+ *  Combines calls across the various samples being studied
+ *  1. For each allele at each base across all samples the quality is summed so
+ *     you end up with a set of quality sums for each allele present 2. The quality
+ *     sums are sorted.
+ *  3. Using the sorted quality sums we now create the allele ordering array
+ *     A\subN. This is done by doing the following:
+ *     a) If the reference allele is known it always comes first, otherwise N
+ *        comes first.
+ *     b) Then the rest of the alleles are output in descending order of quality
+ *        sum (which we already know the qsum array was sorted).  Any allelles with
+ *        qsum 0 will be excluded.
+ *  4. Using the allele ordering array we create the genotype ordering array.
+ *     In the worst case with an unknown reference this will be:  A0/A0 A1/A0 A1/A1
+ *     A2/A0 A2/A1 A2/A2 A3/A0 A3/A1 A3/A2 A3/A3 A4/A0 A4/A1 A4/A2 A4/A3 A4/A4
+ *  5. The genotype ordering array is then used to extract data from the error
+ *     model 5*5 matrix and is used to produce a Phread likelihood array for each
+ *     sample.
+ */
+int bcf_call_combine(int n, const bcf_callret1_t *calls, bcf_callaux_t *bca, int ref_base /*4-bit*/, bcf_call_t *call)
+{
+    int ref4, i, j;
+    float qsum[B2B_MAX_ALLELES] = {0,0,0,0,0};
+    if (ref_base >= 0) {
+        call->ori_ref = ref4 = seq_nt16_int[ref_base];
+        if (ref4 > 4) ref4 = 4;
+    } else call->ori_ref = -1, ref4 = 0;
+
+    // calculate qsum, this is done by summing normalized qsum across all samples,
+    // to account for differences in coverage
+    for (i = 0; i < n; ++i)
+    {
+        float sum = 0;
+        for (j = 0; j < 4; ++j) sum += calls[i].QS[j];
+        if ( sum )
+            for (j = 0; j < 4; j++) qsum[j] += (float)calls[i].QS[j] / sum;
+    }
+
+    // sort qsum in ascending order (insertion sort)
+    float *ptr[5], *tmp;
+    for (i=0; i<5; i++) ptr[i] = &qsum[i];
+    for (i=1; i<4; i++)
+        for (j=i; j>0 && *ptr[j] < *ptr[j-1]; j--)
+            tmp = ptr[j], ptr[j] = ptr[j-1], ptr[j-1] = tmp;
+
+    // Set the reference allele and alternative allele(s)
+    for (i=0; i<5; i++) call->a[i] = -1;
+    for (i=0; i<B2B_MAX_ALLELES; i++) call->qsum[i] = 0;
+    call->unseen = -1;
+    call->a[0] = ref4;
+    for (i=3, j=1; i>=0; i--)   // i: alleles sorted by QS; j, a[j]: output allele ordering
+    {
+        int ipos = ptr[i] - qsum;   // position in sorted qsum array
+        if ( ipos==ref4 )
+            call->qsum[0] = qsum[ipos];    // REF's qsum
+        else
+        {
+            if ( !qsum[ipos] ) break;       // qsum is 0, this and consequent alleles are not seen in the pileup
+            call->qsum[j] = qsum[ipos];
+            call->a[j++]  = ipos;
+        }
+    }
+    if (ref_base >= 0)
+    {
+        // for SNPs, find the "unseen" base
+        if (((ref4 < 4 && j < 4) || (ref4 == 4 && j < 5)) && i >= 0)
+            call->unseen = j, call->a[j++] = ptr[i] - qsum;
+        call->n_alleles = j;
+    }
+    else
+    {
+        call->n_alleles = j;
+        if (call->n_alleles == 1) return -1; // no reliable supporting read. stop doing anything
+    }
+    int has_alt = (call->n_alleles==2 && call->unseen!=-1) ? 0 : 1;
+    /*
+     * Set the phread likelihood array (call->PL) This array is 15 entries long
+     * for each sample because that is size of an upper or lower triangle of a
+     * worst case 5x5 matrix of possible genotypes. This worst case matrix will
+     * occur when all 4 possible alleles are present and the reference allele
+     * is unknown.  The sides of the matrix will correspond to the reference
+     * allele (if known) followed by the alleles present in descending order of
+     * quality sum
+     */
+    {
+        int x, g[15], z;
+        double sum_min = 0.;
+        x = call->n_alleles * (call->n_alleles + 1) / 2;
+        // get the possible genotypes
+        // this is done by creating an ordered list of locations g for call (allele a, allele b) in the genotype likelihood matrix
+        for (i = z = 0; i < call->n_alleles; ++i) {
+            for (j = 0; j <= i; ++j) {
+                g[z++] = call->a[j] * 5 + call->a[i];
+            }
+        }
+        // for each sample calculate the PL
+        for (i = 0; i < n; ++i)
+        {
+            int32_t *PL = call->PL + x * i;
+            const bcf_callret1_t *r = calls + i;
+            float min = FLT_MAX;
+            for (j = 0; j < x; ++j) {
+                if (min > r->p[g[j]]) min = r->p[g[j]];
+            }
+            sum_min += min;
+            for (j = 0; j < x; ++j) {
+                int y;
+                y = (int)(r->p[g[j]] - min + .499);
+                if (y > 255) y = 255;
+                PL[j] = y;
+            }
+        }
+        if ( call->DP4 )
+        {
+            for (i=0; i<n; i++)
+            {
+                call->DP4[4*i]   = calls[i].anno[0];
+                call->DP4[4*i+1] = calls[i].anno[1];
+                call->DP4[4*i+2] = calls[i].anno[2];
+                call->DP4[4*i+3] = calls[i].anno[3];
+            }
+        }
+        if ( call->SCR )
+        {
+            for (i=0; i<n; i++)
+            {
+                call->SCR[0]  += calls[i].SCR;
+                call->SCR[1+i] = calls[i].SCR;
+            }
+        }
+        if ( call->ADF )
+        {
+            assert( call->n_alleles<=B2B_MAX_ALLELES );   // this is always true for SNPs and so far for indels as well
+
+            // reorder ADR,ADF to match the allele ordering at this site
+            int32_t tmp[B2B_MAX_ALLELES];
+            int32_t *adr = call->ADR + B2B_MAX_ALLELES, *adr_out = call->ADR + B2B_MAX_ALLELES;
+            int32_t *adf = call->ADF + B2B_MAX_ALLELES, *adf_out = call->ADF + B2B_MAX_ALLELES;
+            int32_t *adr_tot = call->ADR;   // the first bin stores total counts per site
+            int32_t *adf_tot = call->ADF;
+            for (i=0; i<n; i++)
+            {
+                for (j=0; j<call->n_alleles; j++)
+                {
+                    tmp[j] = adr[ call->a[j] ];
+                    adr_tot[j] += tmp[j];
+                }
+                for (j=0; j<call->n_alleles; j++) adr_out[j] = tmp[j];
+                for (j=0; j<call->n_alleles; j++)
+                {
+                    tmp[j] = adf[ call->a[j] ];
+                    adf_tot[j] += tmp[j];
+                }
+                for (j=0; j<call->n_alleles; j++) adf_out[j] = tmp[j];
+                adf_out += call->n_alleles;
+                adr_out += call->n_alleles;
+                adr += B2B_MAX_ALLELES;
+                adf += B2B_MAX_ALLELES;
+            }
+        }
+        if ( bca->fmt_flag & B2B_FMT_QS )
+        {
+            assert( call->n_alleles<=B2B_MAX_ALLELES );   // this is always true for SNPs and so far for indels as well
+
+            // reorder QS to match the allele ordering at this site
+            int32_t tmp[B2B_MAX_ALLELES];
+            int32_t *qs = call->QS, *qs_out = call->QS;
+            for (i=0; i<n; i++)
+            {
+                for (j=0; j<call->n_alleles; j++) tmp[j] = qs[ call->a[j] ];
+                for (j=0; j<call->n_alleles; j++) qs_out[j] = tmp[j] < BCF_MAX_BT_INT32 ? tmp[j] : BCF_MAX_BT_INT32;
+                qs_out += call->n_alleles;
+                qs += B2B_MAX_ALLELES;
+            }
+        }
+
+//      if (ref_base < 0) fprintf(stderr, "%d,%d,%f,%d\n", call->n_alleles, x, sum_min, call->unseen);
+        call->shift = (int)(sum_min + .499);
+    }
+    // combine annotations
+    memset(call->anno, 0, 16 * sizeof(double));
+    call->ori_depth = 0;
+    call->depth     = 0;
+    call->mq0       = 0;
+    for (i = 0; i < n; ++i) {
+        call->depth += calls[i].anno[0] + calls[i].anno[1] + calls[i].anno[2] + calls[i].anno[3];
+        call->ori_depth += calls[i].ori_depth;
+        call->mq0 += calls[i].mq0;
+        for (j = 0; j < 16; ++j) call->anno[j] += calls[i].anno[j];
+    }
+
+    // No need to calculate MWU tests when there is no ALT allele, this should speed up things slightly
+    if ( !has_alt ) return 0;
+
+    calc_SegBias(calls, call);
+
+    // calc_chisq_bias("XPOS", call->bcf_hdr->id[BCF_DT_CTG][call->tid].key, call->pos, bca->ref_pos, bca->alt_pos, bca->npos);
+    // calc_chisq_bias("XMQ", call->bcf_hdr->id[BCF_DT_CTG][call->tid].key, call->pos, bca->ref_mq, bca->alt_mq, bca->nqual);
+    // calc_chisq_bias("XBQ", call->bcf_hdr->id[BCF_DT_CTG][call->tid].key, call->pos, bca->ref_bq, bca->alt_bq, bca->nqual);
+
+    if (bca->fmt_flag & B2B_INFO_ZSCORE) {
+        // U z-normalised as +/- number of standard deviations from mean.
+        if (call->ori_ref < 0) {    // indel
+            if (bca->fmt_flag & B2B_INFO_RPB)
+                call->mwu_pos = calc_mwu_biasZ(bca->iref_pos, bca->ialt_pos,
+                                               bca->npos, 0, 1);
+            call->mwu_mq  = calc_mwu_biasZ(bca->iref_mq,  bca->ialt_mq,
+                                           bca->nqual,1,1);
+            if ( bca->fmt_flag & B2B_INFO_SCB )
+                call->mwu_sc  = calc_mwu_biasZ(bca->iref_scl, bca->ialt_scl,
+                                               100, 0,1);
+        } else {
+            if (bca->fmt_flag & B2B_INFO_RPB)
+                call->mwu_pos = calc_mwu_biasZ(bca->ref_pos, bca->alt_pos,
+                                               bca->npos, 0, 1);
+            call->mwu_mq  = calc_mwu_biasZ(bca->ref_mq,  bca->alt_mq,
+                                           bca->nqual,1,1);
+            call->mwu_bq  = calc_mwu_biasZ(bca->ref_bq,  bca->alt_bq,
+                                           bca->nqual,0,1);
+            call->mwu_mqs = calc_mwu_biasZ(bca->fwd_mqs, bca->rev_mqs,
+                                           bca->nqual,0,1);
+            if ( bca->fmt_flag & B2B_INFO_SCB )
+                call->mwu_sc  = calc_mwu_biasZ(bca->ref_scl, bca->alt_scl,
+                                               100, 0,1);
+        }
+        call->mwu_nm[0] = calc_mwu_biasZ(bca->ref_nm, bca->alt_nm, B2B_N_NM,0,1);
+        if ( bca->fmt_flag & B2B_FMT_NMBZ )
+        {
+            for (i=0; i<n; i++)
+            {
+                float val = calc_mwu_biasZ(calls[i].ref_nm, calls[i].alt_nm, B2B_N_NM,0,1);
+                call->mwu_nm[i+1] = val!=HUGE_VAL ? val : 0;
+            }
+        }
+    } else {
+        // Old method; U as probability between 0 and 1
+        if ( bca->fmt_flag & B2B_INFO_RPB )
+            call->mwu_pos = calc_mwu_biasZ(bca->ref_pos, bca->alt_pos,
+                                           bca->npos, 0, 0);
+        call->mwu_mq  = calc_mwu_biasZ(bca->ref_mq,  bca->alt_mq,
+                                       bca->nqual, 1, 0);
+        call->mwu_bq  = calc_mwu_biasZ(bca->ref_bq,  bca->alt_bq,
+                                       bca->nqual, 0, 0);
+        call->mwu_mqs = calc_mwu_biasZ(bca->fwd_mqs, bca->rev_mqs,
+                                       bca->nqual, 0, 0);
+    }
+
+#if CDF_MWU_TESTS
+    // CDF version of MWU tests is not calculated by default
+    if ( bca->fmt_flag & B2B_INFO_RPB )
+        call->mwu_pos_cdf = calc_mwu_bias_cdf(bca->ref_pos, bca->alt_pos, bca->npos);
+    call->mwu_mq_cdf  = calc_mwu_bias_cdf(bca->ref_mq,  bca->alt_mq,  bca->nqual);
+    call->mwu_bq_cdf  = calc_mwu_bias_cdf(bca->ref_bq,  bca->alt_bq,  bca->nqual);
+    call->mwu_mqs_cdf = calc_mwu_bias_cdf(bca->fwd_mqs, bca->rev_mqs, bca->nqual);
+#endif
+
+    if ( bca->fmt_flag & B2B_INFO_VDB )
+        call->vdb = calc_vdb(bca->alt_pos, bca->npos);
+
+    return 0;
+}
+
+int bcf_call2bcf(bcf_call_t *bc, bcf1_t *rec, bcf_callret1_t *bcr, int fmt_flag, const bcf_callaux_t *bca, const char *ref)
+{
+    extern double kt_fisher_exact(int n11, int n12, int n21, int n22, double *_left, double *_right, double *two);
+    int i, j, nals = 1, has_alt = 0;
+
+    bcf_hdr_t *hdr = bc->bcf_hdr;
+    rec->rid  = bc->tid;
+    rec->pos  = bc->pos;
+    rec->qual = 0;
+
+    bc->tmp.l = 0;
+    if (bc->ori_ref < 0)    // indel
+    {
+        // REF
+        kputc(ref[bc->pos], &bc->tmp);
+        for (j = 0; j < bca->indelreg; ++j) kputc(ref[bc->pos+1+j], &bc->tmp);
+
+        // ALT
+        for (i=1; i<4; i++)
+        {
+            if (bc->a[i] < 0) break;
+            kputc(',', &bc->tmp); kputc(ref[bc->pos], &bc->tmp);
+
+            if (bca->indel_types[bc->a[i]] < 0) { // deletion
+                for (j = -bca->indel_types[bc->a[i]]; j < bca->indelreg; ++j)
+                    kputc(ref[bc->pos+1+j], &bc->tmp);
+            } else { // insertion; cannot be a reference unless a bug
+                char *inscns = &bca->inscns[bc->a[i] * bca->maxins];
+                for (j = 0; j < bca->indel_types[bc->a[i]]; ++j)
+                    kputc("ACGTN"[(int)inscns[j]], &bc->tmp);
+                for (j = 0; j < bca->indelreg; ++j) kputc(ref[bc->pos+1+j], &bc->tmp);
+            }
+            nals++;
+            has_alt = 1;
+        }
+    }
+    else    // SNP
+    {
+        kputc("ACGTN"[bc->ori_ref], &bc->tmp);
+        for (i=1; i<5; i++)
+        {
+            if (bc->a[i] < 0) break;
+            kputc(',', &bc->tmp);
+            if ( bc->unseen==i ) kputs("<*>", &bc->tmp);
+            else
+            {
+                kputc("ACGT"[bc->a[i]], &bc->tmp);
+                has_alt = 1;
+            }
+            nals++;
+        }
+    }
+    bcf_update_alleles_str(hdr, rec, bc->tmp.s);
+
+    bc->tmp.l = 0;
+
+    // INFO
+    if (bc->ori_ref < 0)
+    {
+        bcf_update_info_flag(hdr, rec, "INDEL", NULL, 1);
+        bcf_update_info_int32(hdr, rec, "IDV", &bca->max_support, 1);
+        bcf_update_info_float(hdr, rec, "IMF", &bca->max_frac, 1);
+    }
+    bcf_update_info_int32(hdr, rec, "DP", &bc->ori_depth, 1);
+    if ( fmt_flag&B2B_INFO_ADF )
+        bcf_update_info_int32(hdr, rec, "ADF", bc->ADF, rec->n_allele);
+    if ( fmt_flag&B2B_INFO_ADR )
+        bcf_update_info_int32(hdr, rec, "ADR", bc->ADR, rec->n_allele);
+    if ( fmt_flag&(B2B_INFO_AD|B2B_INFO_DPR) )
+    {
+        for (i=0; i<rec->n_allele; i++) bc->ADF[i] += bc->ADR[i];
+        if ( fmt_flag&B2B_INFO_AD )
+            bcf_update_info_int32(hdr, rec, "AD", bc->ADF, rec->n_allele);
+        if ( fmt_flag&B2B_INFO_DPR )
+            bcf_update_info_int32(hdr, rec, "DPR", bc->ADF, rec->n_allele);
+    }
+    if ( fmt_flag&B2B_INFO_SCR )
+        bcf_update_info_int32(hdr, rec, "SCR", bc->SCR, 1);
+
+    float tmpf[16];
+    for (i=0; i<16; i++) tmpf[i] = bc->anno[i];
+    bcf_update_info_float(hdr, rec, "I16", tmpf, 16);
+    bcf_update_info_float(hdr, rec, "QS", bc->qsum, nals);
+
+    if ( has_alt )
+    {
+        if ( bc->vdb != HUGE_VAL )      bcf_update_info_float(hdr, rec, "VDB", &bc->vdb, 1);
+        if ( bc->seg_bias != HUGE_VAL ) bcf_update_info_float(hdr, rec, "SGB", &bc->seg_bias, 1);
+
+        if (bca->fmt_flag & B2B_INFO_ZSCORE) {
+            if ( bc->mwu_pos != HUGE_VAL )
+                bcf_update_info_float(hdr, rec, "RPBZ", &bc->mwu_pos, 1);
+            if ( bc->mwu_mq != HUGE_VAL )
+                bcf_update_info_float(hdr, rec, "MQBZ", &bc->mwu_mq, 1);
+            if ( bc->mwu_mqs != HUGE_VAL )
+                bcf_update_info_float(hdr, rec, "MQSBZ", &bc->mwu_mqs, 1);
+            if ( bc->mwu_bq != HUGE_VAL )
+                bcf_update_info_float(hdr, rec, "BQBZ", &bc->mwu_bq, 1);
+            if ( bc->mwu_nm[0] != HUGE_VAL )
+                bcf_update_info_float(hdr, rec, "NMBZ", bc->mwu_nm, 1);
+            if ( bc->mwu_sc != HUGE_VAL )
+                bcf_update_info_float(hdr, rec, "SCBZ", &bc->mwu_sc, 1);
+        } else {
+            if ( bc->mwu_pos != HUGE_VAL )
+                bcf_update_info_float(hdr, rec, "RPB", &bc->mwu_pos, 1);
+            if ( bc->mwu_mq != HUGE_VAL )
+                bcf_update_info_float(hdr, rec, "MQB", &bc->mwu_mq, 1);
+            if ( bc->mwu_mqs != HUGE_VAL )
+                bcf_update_info_float(hdr, rec, "MQSB", &bc->mwu_mqs, 1);
+            if ( bc->mwu_bq != HUGE_VAL )
+                bcf_update_info_float(hdr, rec, "BQB", &bc->mwu_bq, 1);
+        }
+
+        if ( bc->strand_bias != HUGE_VAL )
+            bcf_update_info_float(hdr, rec, "FS", &bc->strand_bias, 1);
+
+#if CDF_MWU_TESTS
+        if ( bc->mwu_pos_cdf != HUGE_VAL )  bcf_update_info_float(hdr, rec, "RPB2", &bc->mwu_pos_cdf, 1);
+        if ( bc->mwu_mq_cdf != HUGE_VAL )   bcf_update_info_float(hdr, rec, "MQB2", &bc->mwu_mq_cdf, 1);
+        if ( bc->mwu_mqs_cdf != HUGE_VAL )  bcf_update_info_float(hdr, rec, "MQSB2", &bc->mwu_mqs_cdf, 1);
+        if ( bc->mwu_bq_cdf != HUGE_VAL )   bcf_update_info_float(hdr, rec, "BQB2", &bc->mwu_bq_cdf, 1);
+#endif
+    }
+
+    tmpf[0] = bc->ori_depth ? (float)bc->mq0/bc->ori_depth : 0;
+    bcf_update_info_float(hdr, rec, "MQ0F", tmpf, 1);
+
+    // FORMAT
+    rec->n_sample = bc->n;
+    bcf_update_format_int32(hdr, rec, "PL", bc->PL, nals*(nals+1)/2 * rec->n_sample);
+    if ( fmt_flag&B2B_FMT_DP )
+    {
+        int32_t *ptr = (int32_t*) bc->fmt_arr;
+        for (i=0; i<bc->n; i++)
+            ptr[i] = bc->DP4[4*i] + bc->DP4[4*i+1] + bc->DP4[4*i+2] + bc->DP4[4*i+3];
+        bcf_update_format_int32(hdr, rec, "DP", bc->fmt_arr, rec->n_sample);
+    }
+    if ( fmt_flag&B2B_FMT_DV )
+    {
+        int32_t *ptr = (int32_t*) bc->fmt_arr;
+        for (i=0; i<bc->n; i++)
+            ptr[i] = bc->DP4[4*i+2] + bc->DP4[4*i+3];
+        bcf_update_format_int32(hdr, rec, "DV", bc->fmt_arr, rec->n_sample);
+    }
+    if ( fmt_flag&B2B_FMT_SP )
+    {
+        int32_t *ptr = (int32_t*) bc->fmt_arr;
+        for (i=0; i<bc->n; i++)
+        {
+            int fwd_ref = bc->DP4[4*i], rev_ref =  bc->DP4[4*i+1], fwd_alt = bc->DP4[4*i+2], rev_alt = bc->DP4[4*i+3];
+            if ( fwd_ref+rev_ref<2 || fwd_alt+rev_alt<2 || fwd_ref+fwd_alt<2 || rev_ref+rev_alt<2 )
+                ptr[i] = 0;
+            else
+            {
+                double left, right, two;
+                kt_fisher_exact(fwd_ref, rev_ref, fwd_alt, rev_alt, &left, &right, &two);
+                int32_t x = (int)(-4.343 * log(two) + .499);
+                if (x > 255) x = 255;
+                ptr[i] = x;
+            }
+        }
+        bcf_update_format_int32(hdr, rec, "SP", bc->fmt_arr, rec->n_sample);
+    }
+    if ( fmt_flag&B2B_FMT_DP4 )
+        bcf_update_format_int32(hdr, rec, "DP4", bc->DP4, rec->n_sample*4);
+    if ( fmt_flag&B2B_FMT_ADF )
+        bcf_update_format_int32(hdr, rec, "ADF", bc->ADF+B2B_MAX_ALLELES, rec->n_sample*rec->n_allele);
+    if ( fmt_flag&B2B_FMT_ADR )
+        bcf_update_format_int32(hdr, rec, "ADR", bc->ADR+B2B_MAX_ALLELES, rec->n_sample*rec->n_allele);
+    if ( fmt_flag&(B2B_FMT_AD|B2B_FMT_DPR) )
+    {
+        for (i=0; i<rec->n_sample*rec->n_allele; i++) bc->ADF[B2B_MAX_ALLELES+i] += bc->ADR[B2B_MAX_ALLELES+i];
+        if ( fmt_flag&B2B_FMT_AD )
+            bcf_update_format_int32(hdr, rec, "AD", bc->ADF+B2B_MAX_ALLELES, rec->n_sample*rec->n_allele);
+        if ( fmt_flag&B2B_FMT_DPR )
+            bcf_update_format_int32(hdr, rec, "DPR", bc->ADF+B2B_MAX_ALLELES, rec->n_sample*rec->n_allele);
+    }
+    if ( fmt_flag&B2B_FMT_SCR )
+        bcf_update_format_int32(hdr, rec, "SCR", bc->SCR+1, rec->n_sample);
+    if ( fmt_flag&B2B_FMT_QS )
+        bcf_update_format_int32(hdr, rec, "QS", bc->QS, rec->n_sample*rec->n_allele);
+
+    if ( has_alt )
+    {
+        if ( fmt_flag&B2B_FMT_NMBZ )
+            bcf_update_format_float(hdr, rec, "NMBZ", bc->mwu_nm+1, rec->n_sample);
+    }
+
+    return 0;
+}
diff --git a/bcftools/bam2bcf.c.pysam.c b/bcftools/bam2bcf.c.pysam.c
new file mode 100644
index 0000000..24c4270
--- /dev/null
+++ b/bcftools/bam2bcf.c.pysam.c
@@ -0,0 +1,1234 @@
+#include "bcftools.pysam.h"
+
+/*  bam2bcf.c -- variant calling.
+
+    Copyright (C) 2010-2012 Broad Institute.
+    Copyright (C) 2012-2022 Genome Research Ltd.
+
+    Author: Heng Li <lh3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <math.h>
+#include <stdint.h>
+#include <assert.h>
+#include <float.h>
+#include <htslib/hts.h>
+#include <htslib/sam.h>
+#include <htslib/kstring.h>
+#include <htslib/kfunc.h>
+#include "bam2bcf.h"
+
+extern  void ks_introsort_uint32_t(size_t n, uint32_t a[]);
+
+#define CALL_DEFTHETA 0.83
+#define DEF_MAPQ 20
+
+#define CAP_DIST 25
+
+bcf_callaux_t *bcf_call_init(double theta, int min_baseQ, int max_baseQ,
+                             int delta_baseQ)
+{
+    bcf_callaux_t *bca;
+    if (theta <= 0.) theta = CALL_DEFTHETA;
+    bca = (bcf_callaux_t*) calloc(1, sizeof(bcf_callaux_t));
+    bca->capQ = 60;
+    bca->openQ = 40; bca->extQ = 20; bca->tandemQ = 100;
+    bca->min_baseQ = min_baseQ;
+    bca->max_baseQ = max_baseQ;
+    bca->delta_baseQ = delta_baseQ;
+    bca->e = errmod_init(1. - theta);
+    bca->min_frac = 0.002;
+    bca->min_support = 1;
+    bca->per_sample_flt = 0;
+    bca->npos = 100;
+    bca->ref_pos = (int*) malloc(bca->npos*sizeof(int));
+    bca->alt_pos = (int*) malloc(bca->npos*sizeof(int));
+    bca->iref_pos= (int*) malloc(bca->npos*sizeof(int));
+    bca->ialt_pos= (int*) malloc(bca->npos*sizeof(int));
+    bca->nqual = 60;
+    bca->ref_mq  = (int*) malloc(bca->nqual*sizeof(int));
+    bca->alt_mq  = (int*) malloc(bca->nqual*sizeof(int));
+    bca->iref_mq = (int*) malloc(bca->nqual*sizeof(int));
+    bca->ialt_mq = (int*) malloc(bca->nqual*sizeof(int));
+    bca->ref_bq  = (int*) malloc(bca->nqual*sizeof(int));
+    bca->alt_bq  = (int*) malloc(bca->nqual*sizeof(int));
+    bca->fwd_mqs = (int*) malloc(bca->nqual*sizeof(int));
+    bca->rev_mqs = (int*) malloc(bca->nqual*sizeof(int));
+    return bca;
+}
+
+void bcf_call_destroy(bcf_callaux_t *bca)
+{
+    if (bca == 0) return;
+    errmod_destroy(bca->e);
+    if (bca->npos) {
+        free(bca->ref_pos);  free(bca->alt_pos);
+        free(bca->iref_pos); free(bca->ialt_pos);
+        bca->npos = 0;
+    }
+    free(bca->ref_mq); free(bca->alt_mq);
+    free(bca->iref_mq); free(bca->ialt_mq);
+    free(bca->ref_bq); free(bca->alt_bq);
+    free(bca->fwd_mqs); free(bca->rev_mqs);
+    bca->nqual = 0;
+    free(bca->bases); free(bca->inscns); free(bca);
+}
+
+static int get_aux_nm(bam1_t *rec, int32_t qpos, int is_ref)
+{
+    uint8_t *nm_tag = bam_aux_get(rec, "NM");
+    if ( !nm_tag ) return -1;
+    int64_t nm = bam_aux2i(nm_tag);
+
+    // Count indels as single events, not as the number of inserted/deleted
+    // bases (which is what NM does). Add soft clips as mismatches.
+    int i;
+    for (i=0; i < rec->core.n_cigar; i++)
+    {
+        int val = bam_get_cigar(rec)[i] & BAM_CIGAR_MASK;
+        if ( val==BAM_CSOFT_CLIP )
+        {
+            nm += bam_get_cigar(rec)[i] >> BAM_CIGAR_SHIFT;
+        }
+        else if ( val==BAM_CINS || val==BAM_CDEL )
+        {
+            val = bam_get_cigar(rec)[i] >> BAM_CIGAR_SHIFT;
+            if ( val > 1 ) nm -= val - 1;
+        }
+    }
+
+    // Take into account MNPs, 2% of de novo SNVs appear within 20bp of another de novo SNV
+    //      http://www.genome.org/cgi/doi/10.1101/gr.239756.118
+    nm -= is_ref ? 1 : 2;
+
+    if ( nm < 0 ) nm = 0;
+    if ( nm >= B2B_N_NM ) nm = B2B_N_NM - 1;
+
+    return nm;
+}
+
+// position in the sequence with respect to the aligned part of the read
+static int get_position(const bam_pileup1_t *p, int *len,
+                        int *sc_len, int *sc_dist) {
+    int i, j, edist = p->qpos + 1;
+    int sc_left = 0, sc_right = 0;
+    int sc_left_dist = -1, sc_right_dist = -1;
+
+    // left end
+    for (i = 0; i < p->b->core.n_cigar; i++) {
+        int cig  = bam_get_cigar(p->b)[i] & BAM_CIGAR_MASK;
+        if (cig == BAM_CHARD_CLIP)
+            continue;
+        else if (cig == BAM_CSOFT_CLIP)
+            sc_left += bam_get_cigar(p->b)[i] >> BAM_CIGAR_SHIFT;
+        else
+            break;
+    }
+    if (sc_left)
+        sc_left_dist = p->qpos+1 - sc_left;
+    edist -= sc_left;
+
+    // right end
+    for (j = p->b->core.n_cigar-1; j >= i; j--) {
+        int cig  = bam_get_cigar(p->b)[j] & BAM_CIGAR_MASK;
+        if (cig == BAM_CHARD_CLIP)
+            continue;
+        else if (cig == BAM_CSOFT_CLIP)
+            sc_right += bam_get_cigar(p->b)[j] >> BAM_CIGAR_SHIFT;
+        else
+            break;
+    }
+    if (sc_right)
+        sc_right_dist = p->b->core.l_qseq - sc_right - p->qpos;
+
+    // Distance to nearest soft-clips and length of that clip.
+    if (sc_left_dist >= 0) {
+        if (sc_right_dist < 0 || sc_left_dist < sc_right_dist) {
+            *sc_len  = sc_left;
+            *sc_dist = sc_left_dist;
+        }
+    } else if (sc_right_dist >= 0) {
+        *sc_len  = sc_right;
+        *sc_dist = sc_right_dist;
+    } else {
+        *sc_len  = 0;
+        *sc_dist = 0;
+    }
+
+    *len = p->b->core.l_qseq - sc_left - sc_right;
+    return edist;
+}
+
+void bcf_callaux_clean(bcf_callaux_t *bca, bcf_call_t *call)
+{
+    memset(bca->ref_pos,0,sizeof(int)*bca->npos);
+    memset(bca->alt_pos,0,sizeof(int)*bca->npos);
+    memset(bca->iref_pos,0,sizeof(int)*bca->npos);
+    memset(bca->ialt_pos,0,sizeof(int)*bca->npos);
+    memset(bca->ref_mq,0,sizeof(int)*bca->nqual);
+    memset(bca->alt_mq,0,sizeof(int)*bca->nqual);
+    memset(bca->iref_mq,0,sizeof(int)*bca->nqual);
+    memset(bca->ialt_mq,0,sizeof(int)*bca->nqual);
+    memset(bca->ref_bq,0,sizeof(int)*bca->nqual);
+    memset(bca->alt_bq,0,sizeof(int)*bca->nqual);
+    memset(bca->fwd_mqs,0,sizeof(int)*bca->nqual);
+    memset(bca->rev_mqs,0,sizeof(int)*bca->nqual);
+    if ( call->ADF ) memset(call->ADF,0,sizeof(int32_t)*(call->n+1)*B2B_MAX_ALLELES);
+    if ( call->ADR ) memset(call->ADR,0,sizeof(int32_t)*(call->n+1)*B2B_MAX_ALLELES);
+    if ( call->SCR ) memset(call->SCR,0,sizeof(*call->SCR)*(call->n+1));
+    if ( call->SCR ) memset(call->SCR,0,sizeof(*call->SCR)*(call->n+1));
+    if ( bca->fmt_flag&B2B_FMT_NMBZ )
+    {
+        memset(call->ref_nm,0,sizeof(*call->ref_nm)*(call->n+1)*B2B_N_NM);
+        memset(call->alt_nm,0,sizeof(*call->alt_nm)*(call->n+1)*B2B_N_NM);
+    }
+    else
+    {
+        memset(call->ref_nm,0,sizeof(*call->ref_nm)*B2B_N_NM);
+        memset(call->alt_nm,0,sizeof(*call->alt_nm)*B2B_N_NM);
+    }
+    memset(call->QS,0,sizeof(*call->QS)*call->n*B2B_MAX_ALLELES);
+    memset(bca->ref_scl,  0, 100*sizeof(int));
+    memset(bca->alt_scl,  0, 100*sizeof(int));
+    memset(bca->iref_scl, 0, 100*sizeof(int));
+    memset(bca->ialt_scl, 0, 100*sizeof(int));
+}
+
+/*
+    Notes:
+    - Called from bam_plcmd.c by mpileup. Amongst other things, sets the bcf_callret1_t.QS frequencies
+        which are carried over via bcf_call_combine and bcf_call2bcf to the output BCF as the INFO/QS and FMT/QS annotations.
+        Later it's used for multiallelic calling by `call -m`, `call -mG` and `+trio-dnm`.
+    - ref_base is the 4-bit representation of the reference base. It is negative if we are looking at an indel.
+ */
+/*
+ * This function is called once for each sample.
+ * _n is number of pilesups pl contributing reads to this sample
+ * pl is pointer to array of _n pileups (one pileup per read)
+ * ref_base is the 4-bit representation of the reference base. It is negative if we are looking at an indel.
+ * bca is the settings to perform calls across all samples
+ * r is the returned value of the call
+ */
+int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base, bcf_callaux_t *bca, bcf_callret1_t *r)
+{
+    int i, n, ref4, is_indel, ori_depth = 0;
+
+    // clean from previous run
+    r->ori_depth = 0;
+    r->mq0 = 0;
+    memset(r->anno,0,sizeof(double)*16);
+    memset(r->p,0,sizeof(float)*25);
+    r->SCR = 0;
+
+    if (ref_base >= 0) {
+        ref4 = seq_nt16_int[ref_base];
+        is_indel = 0;
+    } else ref4 = 4, is_indel = 1;
+    if (_n == 0) return -1;
+    // enlarge the bases array if necessary
+    if (bca->max_bases < _n) {
+        bca->max_bases = _n;
+        kroundup32(bca->max_bases);
+        bca->bases = (uint16_t*)realloc(bca->bases, 2 * bca->max_bases);
+    }
+
+    // fill the bases array
+    double nqual_over_60 = bca->nqual / 60.0;
+    int ADR_ref_missed[4] = {0};
+    int ADF_ref_missed[4] = {0};
+    for (i = n = 0; i < _n; ++i) {
+        const bam_pileup1_t *p = pl + i;
+        int q, b, mapQ, baseQ, is_diff, min_dist, seqQ;
+        if ( bca->fmt_flag&(B2B_INFO_SCR|B2B_FMT_SCR) && PLP_HAS_SOFT_CLIP(p->cd.i) ) r->SCR++;
+        if (p->is_refskip || (p->b->core.flag&BAM_FUNMAP)) continue;
+        if (p->is_del && !is_indel) continue;
+        ++ori_depth;
+        if (is_indel)
+        {
+            b = p->aux>>16&0x3f;
+            seqQ = q = (p->aux & 0xff); // mp2 + builtin indel-bias
+            if (q < bca->min_baseQ)
+            {
+                if (!p->indel && b < 4)
+                {
+                    if (bam_is_rev(p->b))
+                        ADR_ref_missed[b]++;
+                    else
+                        ADF_ref_missed[b]++;
+                }
+                continue;
+            }
+            if (p->indel == 0 && (q < _n/2 || _n > 20)) {
+                // high quality indel calls without p->indel set aren't
+                // particularly indicative of being a good REF match either,
+                // at least not in low coverage.  So require solid coverage
+                // before we start utilising such quals.
+                b = 0;
+                q = (int)bam_get_qual(p->b)[p->qpos];
+                seqQ = (3*seqQ + 2*q)/8;
+            }
+            if (_n > 20 && seqQ > 40) seqQ = 40;
+            baseQ  = p->aux>>8&0xff;
+
+            is_diff = (b != 0);
+        }
+        else
+        {
+            b = bam_seqi(bam_get_seq(p->b), p->qpos); // base
+            b = seq_nt16_int[b? b : ref_base]; // b is the 2-bit base
+
+            // Lowest of this and neighbour quality values
+            uint8_t *qual = bam_get_qual(p->b);
+            q = qual[p->qpos];
+            if (p->qpos > 0 &&
+                q > qual[p->qpos-1]+bca->delta_baseQ)
+                q = qual[p->qpos-1]+bca->delta_baseQ;
+            if (p->qpos+1 < p->b->core.l_qseq &&
+                q > qual[p->qpos+1]+bca->delta_baseQ)
+                q = qual[p->qpos+1]+bca->delta_baseQ;
+
+            if (q < bca->min_baseQ) continue;
+            if (q > bca->max_baseQ) q = bca->max_baseQ;
+            baseQ = q;
+            seqQ  = 99;
+            is_diff = (ref4 < 4 && b == ref4)? 0 : 1;
+        }
+        mapQ  = p->b->core.qual < 255? p->b->core.qual : DEF_MAPQ; // special case for mapQ==255
+        if ( !mapQ ) r->mq0++;
+        if (q > seqQ) q = seqQ;
+        mapQ = mapQ < bca->capQ? mapQ : bca->capQ;
+        if (q > mapQ) q = mapQ;
+        if (q > 63) q = 63;
+        if (q < 4) q = 4;       // MQ=0 reads count as BQ=4
+        bca->bases[n++] = q<<5 | (int)bam_is_rev(p->b)<<4 | b;
+        // collect annotations
+        if (b < 4)
+        {
+            r->QS[b] += q;
+            if ( r->ADF )
+            {
+                if ( bam_is_rev(p->b) )
+                    r->ADR[b]++;
+                else
+                    r->ADF[b]++;
+            }
+        }
+        ++r->anno[0<<2|is_diff<<1|bam_is_rev(p->b)];
+        min_dist = p->b->core.l_qseq - 1 - p->qpos;
+        if (min_dist > p->qpos) min_dist = p->qpos;
+        if (min_dist > CAP_DIST) min_dist = CAP_DIST;
+        r->anno[1<<2|is_diff<<1|0] += baseQ;
+        r->anno[1<<2|is_diff<<1|1] += baseQ * baseQ;
+        r->anno[2<<2|is_diff<<1|0] += mapQ;
+        r->anno[2<<2|is_diff<<1|1] += mapQ * mapQ;
+        r->anno[3<<2|is_diff<<1|0] += min_dist;
+        r->anno[3<<2|is_diff<<1|1] += min_dist * min_dist;
+
+        // collect for bias tests
+        if ( baseQ > 59 ) baseQ = 59;
+        if ( mapQ > 59 ) mapQ = 59;
+        int len, epos = 0, sc_len = 0, sc_dist = 0;
+        if ( bca->fmt_flag & (B2B_INFO_RPB|B2B_INFO_VDB|B2B_INFO_SCB) )
+        {
+            int pos = get_position(p, &len, &sc_len, &sc_dist);
+            epos = (double)pos/(len+1) * bca->npos;
+
+            if (sc_len) {
+                sc_len = 15.0*sc_len / sc_dist;
+                if (sc_len > 99) sc_len = 99;
+            }
+        }
+        int imq  = mapQ * nqual_over_60;
+        int ibq  = baseQ * nqual_over_60;
+        int inm  = get_aux_nm(p->b,p->qpos,is_diff?0:1);
+
+        if ( bam_is_rev(p->b) )
+            bca->rev_mqs[imq]++;
+        else
+            bca->fwd_mqs[imq]++;
+
+        if ( !is_diff )
+        {
+            bca->ref_pos[epos]++;
+            bca->ref_bq[ibq]++;
+            bca->ref_mq[imq]++;
+            bca->ref_scl[sc_len]++;
+            if ( inm>=0 )
+            {
+                bca->ref_nm[inm]++;
+                if ( r->ref_nm ) r->ref_nm[inm]++;
+            }
+        }
+        else
+        {
+            bca->alt_pos[epos]++;
+            bca->alt_bq[ibq]++;
+            bca->alt_mq[imq]++;
+            bca->alt_scl[sc_len]++;
+            if ( inm>=0 )
+            {
+                bca->alt_nm[inm]++;
+                if ( r->alt_nm ) r->alt_nm[inm]++;
+            }
+        }
+    }
+
+    // Compensate for AD not being counted on low quality REF indel matches.
+    if ( r->ADF && bca->ambig_reads==B2B_INC_AD0 )
+    {
+        for (i=0; i<4; i++)
+        {
+            r->ADR[0] += ADR_ref_missed[i];
+            r->ADF[0] += ADF_ref_missed[i];
+        }
+    }
+    else if ( r->ADF && bca->ambig_reads==B2B_INC_AD )
+    {
+        int dp = 0, dp_ambig = 0;
+        for (i=0; i<4; i++) dp += r->ADR[i];
+        for (i=0; i<4; i++) dp_ambig += ADR_ref_missed[i];
+        if ( dp )
+            for (i=0; i<4; i++) r->ADR[i] += lroundf((float)dp_ambig * r->ADR[i]/dp);
+        dp = 0, dp_ambig = 0;
+        for (i=0; i<4; i++) dp += r->ADF[i];
+        for (i=0; i<4; i++) dp_ambig += ADF_ref_missed[i];
+        if ( dp )
+            for (i=0; i<4; i++) r->ADF[i] += lroundf((float)dp_ambig * r->ADF[i]/dp);
+    }
+
+    r->ori_depth = ori_depth;
+    // glfgen
+    errmod_cal(bca->e, n, 5, bca->bases, r->p); // calculate PL of each genotype
+    return n;
+}
+
+
+/*
+ *  calc_vdb() - returns value between zero (most biased) and one (no bias)
+ *               on success, or HUGE_VAL when VDB cannot be calculated because
+ *               of insufficient depth (<2x)
+ *
+ *  Variant Distance Bias tests if the variant bases are positioned within the
+ *  reads with sufficient randomness. Unlike other tests, it looks only at
+ *  variant reads and therefore gives different kind of information than Read
+ *  Position Bias for instance. VDB was developed for detecting artefacts in
+ *  RNA-seq calls where reads from spliced transcripts span splice site
+ *  boundaries.  The current implementation differs somewhat from the original
+ *  version described in supplementary material of PMID:22524474, but the idea
+ *  remains the same. (Here the random variable tested is the average distance
+ *  from the averaged position, not the average pairwise distance.)
+ *
+ *  For coverage of 2x, the calculation is exact but is approximated for the
+ *  rest. The result is most accurate between 4-200x. For 3x or >200x, the
+ *  reported values are slightly more favourable than those of a true random
+ *  distribution.
+ */
+double calc_vdb(int *pos, int npos)
+{
+    // Note well: the parameters were obtained by fitting to simulated data of
+    // 100bp reads. This assumes rescaling to 100bp in bcf_call_glfgen().
+    const int readlen = 100;
+    assert( npos==readlen );
+
+    #define nparam 15
+    const float param[nparam][3] = { {3,0.079,18}, {4,0.09,19.8}, {5,0.1,20.5}, {6,0.11,21.5},
+        {7,0.125,21.6}, {8,0.135,22}, {9,0.14,22.2}, {10,0.153,22.3}, {15,0.19,22.8},
+        {20,0.22,23.2}, {30,0.26,23.4}, {40,0.29,23.5}, {50,0.35,23.65}, {100,0.5,23.7},
+        {200,0.7,23.7} };
+
+    int i, dp = 0;
+    float mean_pos = 0, mean_diff = 0;
+    for (i=0; i<npos; i++)
+    {
+        if ( !pos[i] ) continue;
+        dp += pos[i];
+        mean_pos += pos[i]*i;
+    }
+    if ( dp<2 ) return HUGE_VAL;     // one or zero reads can be placed anywhere
+
+    mean_pos /= dp;
+    for (i=0; i<npos; i++)
+    {
+        if ( !pos[i] ) continue;
+        mean_diff += pos[i] * fabs(i - mean_pos);
+    }
+    mean_diff /= dp;
+
+    int ipos = mean_diff;   // tuned for float-to-int implicit conversion
+    if ( dp==2 )
+        return (2*readlen-2*(ipos+1)-1)*(ipos+1)/(readlen-1)/(readlen*0.5);
+
+    if ( dp>=200 )
+        i = nparam; // shortcut for big depths
+    else
+    {
+        for (i=0; i<nparam; i++)
+            if ( param[i][0]>=dp ) break;
+    }
+    float pshift, pscale;
+    if ( i==nparam )
+    {
+        // the depth is too high, go with 200x
+        pscale = param[nparam-1][1];
+        pshift = param[nparam-1][2];
+    }
+    else if ( i>0 && param[i][0]!=dp )
+    {
+        // linear interpolation of parameters
+        pscale = (param[i-1][1] + param[i][1])*0.5;
+        pshift = (param[i-1][2] + param[i][2])*0.5;
+    }
+    else
+    {
+        pscale = param[i][1];
+        pshift = param[i][2];
+    }
+    return 0.5*kf_erfc(-(mean_diff-pshift)*pscale);
+}
+
+double calc_chisq_bias(int *a, int *b, int n)
+{
+    int na = 0, nb = 0, i, ndf = n;
+    for (i=0; i<n; i++) na += a[i];
+    for (i=0; i<n; i++) nb += b[i];
+    if ( !na || !nb ) return HUGE_VAL;
+
+    double chisq = 0;
+    for (i=0; i<n; i++)
+    {
+        if ( !a[i] && !b[i] ) ndf--;
+        else
+        {
+            double tmp = a[i] - b[i];
+            chisq += tmp*tmp/(a[i]+b[i]);
+        }
+    }
+    /*
+        kf_gammq: incomplete gamma function Q(a,x) = 1 - P(a,x) = Gamma(a,x)/Gamma(a)
+        1 if the distributions are identical, 0 if very different
+    */
+    double prob = kf_gammaq(0.5*ndf, 0.5*chisq);
+    return prob;
+}
+
+static double mann_whitney_1947_(int n, int m, int U)
+{
+     if (U<0) return 0;
+     if (n==0||m==0) return U==0 ? 1 : 0;
+    return (double)n/(n+m)*mann_whitney_1947_(n-1,m,U-m) + (double)m/(n+m)*mann_whitney_1947_(n,m-1,U);
+}
+
+double mann_whitney_1947(int n, int m, int U)
+{
+    #include "mw.h"
+
+    assert(n >= 2 && m >= 2);
+
+    return (n < 8 && m < 8 && U < 50)
+        ? mw[n-2][m-2][U]
+        : mann_whitney_1947_(n,m,U);
+}
+
+double mann_whitney_1947_cdf(int n, int m, int U)
+{
+    int i;
+    double sum = 0;
+    for (i=0; i<=U; i++)
+        sum += mann_whitney_1947(n,m,i);
+    return sum;
+}
+
+double calc_mwu_bias_cdf(int *a, int *b, int n)
+{
+    int na = 0, nb = 0, i;
+    double U = 0;
+    //double ties = 0;
+    for (i=0; i<n; i++)
+    {
+        na += a[i];
+        U  += a[i] * (nb + b[i]*0.5);
+        nb += b[i];
+        // if ( a[i] && b[i] )
+        // {
+        //     double tie = a[i] + b[i];
+        //     ties += (tie*tie-1)*tie;
+        // }
+    }
+    if ( !na || !nb ) return HUGE_VAL;
+
+    // Always work with the smaller U
+    double U_min = ((double)na * nb) - U;
+    if ( U < U_min ) U_min = U;
+
+    if ( na==1 ) return 2.0 * (floor(U_min)+1) / (nb+1);
+    if ( nb==1 ) return 2.0 * (floor(U_min)+1) / (na+1);
+
+    // Normal approximation, very good for na>=8 && nb>=8 and reasonable if na<8 or nb<8
+    if ( na>=8 || nb>=8 )
+    {
+        double mean = ((double)na*nb)*0.5;
+        // Correction for ties:
+        //      double N = na+nb;
+        //      double var2 = (N*N-1)*N-ties;
+        //      if ( var2==0 ) return 1.0;
+        //      var2 *= ((double)na*nb)/N/(N-1)/12.0;
+        // No correction for ties:
+        double var2 = ((double)na*nb)*(na+nb+1)/12.0;
+        double z = (U_min - mean)/sqrt(2*var2);   // z is N(0,1)
+        return 2.0 - kf_erfc(z);  // which is 1 + erf(z)
+    }
+
+    // Exact calculation
+    double pval = 2*mann_whitney_1947_cdf(na,nb,U_min);
+    return pval>1 ? 1 : pval;
+}
+
+double calc_mwu_bias(int *a, int *b, int n, int left)
+{
+    int na = 0, nb = 0, i;
+    double U = 0;
+    // double ties = 0;
+    for (i=0; i<n; i++)
+    {
+        if (!a[i]) {
+            if (!b[i]) continue;
+            nb += b[i];
+        } else if (!b[i]) {
+            na += a[i];
+            U  += a[i] * nb;
+        } else {
+            na += a[i];
+            U  += a[i] * (nb + b[i]*0.5);
+            nb += b[i];
+            // double tie = a[i] + b[i];
+            // ties += (tie*tie-1)*tie;
+        }
+    }
+    if ( !na || !nb ) return HUGE_VAL;
+    if ( na==1 || nb==1 ) return 1.0;       // Flat probability, all U values are equally likely
+
+    double mean = ((double)na*nb)*0.5;
+    if (left && U > mean) return 1; // for MQB which is asymmetrical
+    if ( na==2 || nb==2 )
+    {
+        // Linear approximation
+        return U>mean ? (2.0*mean-U)/mean : U/mean;
+    }
+    // Correction for ties:
+    //      double N = na+nb;
+    //      double var2 = (N*N-1)*N-ties;
+    //      if ( var2==0 ) return 1.0;
+    //      var2 *= ((double)na*nb)/N/(N-1)/12.0;
+    // No correction for ties:
+    double var2 = ((double)na*nb)*(na+nb+1)/12.0;
+    if ( na>=8 || nb>=8 )
+    {
+        // Normal approximation, very good for na>=8 && nb>=8 and reasonable if na<8 or nb<8
+        return exp(-0.5*(U-mean)*(U-mean)/var2);
+    }
+
+    // Exact calculation
+    return mann_whitney_1947(na,nb,U) * sqrt(2*M_PI*var2);
+}
+
+// A Z-score version of the above function.
+//
+// See "Normal approximation and tie correction" at
+// https://en.wikipedia.org/wiki/Mann%E2%80%93Whitney_U_test
+//
+// The Z score is the number of standard deviations above or below the mean
+// with 0 being equality of the two distributions and +ve/-ve from there.
+//
+// This is a more robust score to filter on.
+double calc_mwu_biasZ(int *a, int *b, int n, int left_only, int do_Z) {
+    int i;
+    int64_t t;
+
+    // Optimisation
+    for (i = 0; i < n; i++)
+        if (b[i])
+            break;
+    int b_empty = (i == n);
+
+    // Count equal (e), less-than (l) and greater-than (g) permutations.
+    int e = 0, l = 0, na = 0, nb = 0;
+    if (b_empty) {
+        for (t = 0, i = n-1; i >= 0; i--) {
+            na += a[i];
+            t += (a[i]*a[i]-1)*a[i];  // adjustment score for ties
+        }
+    } else {
+        for (t = 0, i = n-1; i >= 0; i--) {
+            // Combinations of a[i] and b[j] for i==j
+            e += a[i]*b[i];
+
+            // nb is running total of b[i+1]..b[n-1].
+            // Therefore a[i]*nb is the number of combinations of a[i] and b[j]
+            // for all i < j.
+            l += a[i]*nb;    // a<b
+
+            na += a[i];
+            nb += b[i];
+            int p = a[i]+b[i];
+            t += (p*p-1)*p;  // adjustment score for ties
+        }
+    }
+
+    if (!na || !nb)
+        return HUGE_VAL;
+
+    double U, m;
+    U = l + e*0.5; // Mann-Whitney U score
+    m = na*nb / 2.0;
+
+    // With ties adjustment
+    double var2 = (na*nb)/12.0 * ((na+nb+1) - t/(double)((na+nb)*(na+nb-1)));
+    // var = na*nb*(na+nb+1)/12.0; // simpler; minus tie adjustment
+    if (var2 <= 0)
+        return do_Z ? 0 : 1;
+
+    if (do_Z) {
+        // S.D. normalised Z-score
+        //Z = (U - m - (U-m >= 0 ? 0.5 : -0.5)) / sd; // gatk method?
+        return (U - m) / sqrt(var2);
+    }
+
+    // Else U score, which can be asymmetric for some data types.
+    if (left_only && U > m)
+        return HUGE_VAL; // one-sided, +ve bias is OK, -ve is not.
+
+    if (na >= 8 || nb >= 8) {
+        // Normal approximation, very good for na>=8 && nb>=8 and
+        // reasonable if na<8 or nb<8
+        return exp(-0.5*(U-m)*(U-m)/var2);
+    }
+
+    // Exact calculation
+    if (na==1 || nb == 1)
+        return mann_whitney_1947_(na, nb, U) * sqrt(2*M_PI*var2);
+    else
+        return mann_whitney_1947(na, nb, U) * sqrt(2*M_PI*var2);
+}
+
+static inline double logsumexp2(double a, double b)
+{
+    if ( a>b )
+        return log(1 + exp(b-a)) + a;
+    else
+        return log(1 + exp(a-b)) + b;
+}
+
+void calc_SegBias(const bcf_callret1_t *bcr, bcf_call_t *call)
+{
+    call->seg_bias = HUGE_VAL;
+    if ( !bcr ) return;
+
+    int nr = call->anno[2] + call->anno[3]; // number of observed non-reference reads
+    if ( !nr ) return;
+
+    int avg_dp = (call->anno[0] + call->anno[1] + nr) / call->n;    // average depth
+    double M   = floor((double)nr / avg_dp + 0.5);   // an approximate number of variants samples in the population
+    if ( M>call->n ) M = call->n;       // clamp M at the number of samples
+    else if ( M==0 ) M = 1;
+    double f = M / 2. / call->n;        // allele frequency
+    double p = (double) nr / call->n;   // number of variant reads per sample expected if variant not real (poisson)
+    double q = (double) nr / M;         // number of variant reads per sample expected if variant is real (poisson)
+    double sum = 0;
+    const double log2 = log(2.0);
+
+    // fprintf(bcftools_stderr,"M=%.1f  p=%e q=%e f=%f  dp=%d\n",M,p,q,f,avg_dp);
+    int i;
+    for (i=0; i<call->n; i++)
+    {
+        int oi = bcr[i].anno[2] + bcr[i].anno[3];       // observed number of non-ref reads
+        double tmp;
+        if ( oi )
+        {
+            // tmp = log(f) + oi*log(q/p) - q + log(2*(1-f) + f*pow(2,oi)*exp(-q)) + p; // this can under/overflow
+            tmp = logsumexp2(log(2*(1-f)), log(f) + oi*log2 - q);
+            tmp += log(f) + oi*log(q/p) - q + p;
+        }
+        else
+            tmp = log(2*f*(1-f)*exp(-q) + f*f*exp(-2*q) + (1-f)*(1-f)) + p;
+        sum += tmp;
+        // fprintf(bcftools_stderr,"oi=%d %e\n", oi,tmp);
+    }
+    call->seg_bias = sum;
+}
+
+/**
+ *  bcf_call_combine() - sets the PL array and VDB, RPB annotations, finds the top two alleles
+ *  @n:         number of samples
+ *  @calls:     each sample's calls
+ *  @bca:       auxiliary data structure for holding temporary values
+ *  @ref_base:  the reference base
+ *  @call:      filled with the annotations
+ *
+ *  Combines calls across the various samples being studied
+ *  1. For each allele at each base across all samples the quality is summed so
+ *     you end up with a set of quality sums for each allele present 2. The quality
+ *     sums are sorted.
+ *  3. Using the sorted quality sums we now create the allele ordering array
+ *     A\subN. This is done by doing the following:
+ *     a) If the reference allele is known it always comes first, otherwise N
+ *        comes first.
+ *     b) Then the rest of the alleles are output in descending order of quality
+ *        sum (which we already know the qsum array was sorted).  Any allelles with
+ *        qsum 0 will be excluded.
+ *  4. Using the allele ordering array we create the genotype ordering array.
+ *     In the worst case with an unknown reference this will be:  A0/A0 A1/A0 A1/A1
+ *     A2/A0 A2/A1 A2/A2 A3/A0 A3/A1 A3/A2 A3/A3 A4/A0 A4/A1 A4/A2 A4/A3 A4/A4
+ *  5. The genotype ordering array is then used to extract data from the error
+ *     model 5*5 matrix and is used to produce a Phread likelihood array for each
+ *     sample.
+ */
+int bcf_call_combine(int n, const bcf_callret1_t *calls, bcf_callaux_t *bca, int ref_base /*4-bit*/, bcf_call_t *call)
+{
+    int ref4, i, j;
+    float qsum[B2B_MAX_ALLELES] = {0,0,0,0,0};
+    if (ref_base >= 0) {
+        call->ori_ref = ref4 = seq_nt16_int[ref_base];
+        if (ref4 > 4) ref4 = 4;
+    } else call->ori_ref = -1, ref4 = 0;
+
+    // calculate qsum, this is done by summing normalized qsum across all samples,
+    // to account for differences in coverage
+    for (i = 0; i < n; ++i)
+    {
+        float sum = 0;
+        for (j = 0; j < 4; ++j) sum += calls[i].QS[j];
+        if ( sum )
+            for (j = 0; j < 4; j++) qsum[j] += (float)calls[i].QS[j] / sum;
+    }
+
+    // sort qsum in ascending order (insertion sort)
+    float *ptr[5], *tmp;
+    for (i=0; i<5; i++) ptr[i] = &qsum[i];
+    for (i=1; i<4; i++)
+        for (j=i; j>0 && *ptr[j] < *ptr[j-1]; j--)
+            tmp = ptr[j], ptr[j] = ptr[j-1], ptr[j-1] = tmp;
+
+    // Set the reference allele and alternative allele(s)
+    for (i=0; i<5; i++) call->a[i] = -1;
+    for (i=0; i<B2B_MAX_ALLELES; i++) call->qsum[i] = 0;
+    call->unseen = -1;
+    call->a[0] = ref4;
+    for (i=3, j=1; i>=0; i--)   // i: alleles sorted by QS; j, a[j]: output allele ordering
+    {
+        int ipos = ptr[i] - qsum;   // position in sorted qsum array
+        if ( ipos==ref4 )
+            call->qsum[0] = qsum[ipos];    // REF's qsum
+        else
+        {
+            if ( !qsum[ipos] ) break;       // qsum is 0, this and consequent alleles are not seen in the pileup
+            call->qsum[j] = qsum[ipos];
+            call->a[j++]  = ipos;
+        }
+    }
+    if (ref_base >= 0)
+    {
+        // for SNPs, find the "unseen" base
+        if (((ref4 < 4 && j < 4) || (ref4 == 4 && j < 5)) && i >= 0)
+            call->unseen = j, call->a[j++] = ptr[i] - qsum;
+        call->n_alleles = j;
+    }
+    else
+    {
+        call->n_alleles = j;
+        if (call->n_alleles == 1) return -1; // no reliable supporting read. stop doing anything
+    }
+    int has_alt = (call->n_alleles==2 && call->unseen!=-1) ? 0 : 1;
+    /*
+     * Set the phread likelihood array (call->PL) This array is 15 entries long
+     * for each sample because that is size of an upper or lower triangle of a
+     * worst case 5x5 matrix of possible genotypes. This worst case matrix will
+     * occur when all 4 possible alleles are present and the reference allele
+     * is unknown.  The sides of the matrix will correspond to the reference
+     * allele (if known) followed by the alleles present in descending order of
+     * quality sum
+     */
+    {
+        int x, g[15], z;
+        double sum_min = 0.;
+        x = call->n_alleles * (call->n_alleles + 1) / 2;
+        // get the possible genotypes
+        // this is done by creating an ordered list of locations g for call (allele a, allele b) in the genotype likelihood matrix
+        for (i = z = 0; i < call->n_alleles; ++i) {
+            for (j = 0; j <= i; ++j) {
+                g[z++] = call->a[j] * 5 + call->a[i];
+            }
+        }
+        // for each sample calculate the PL
+        for (i = 0; i < n; ++i)
+        {
+            int32_t *PL = call->PL + x * i;
+            const bcf_callret1_t *r = calls + i;
+            float min = FLT_MAX;
+            for (j = 0; j < x; ++j) {
+                if (min > r->p[g[j]]) min = r->p[g[j]];
+            }
+            sum_min += min;
+            for (j = 0; j < x; ++j) {
+                int y;
+                y = (int)(r->p[g[j]] - min + .499);
+                if (y > 255) y = 255;
+                PL[j] = y;
+            }
+        }
+        if ( call->DP4 )
+        {
+            for (i=0; i<n; i++)
+            {
+                call->DP4[4*i]   = calls[i].anno[0];
+                call->DP4[4*i+1] = calls[i].anno[1];
+                call->DP4[4*i+2] = calls[i].anno[2];
+                call->DP4[4*i+3] = calls[i].anno[3];
+            }
+        }
+        if ( call->SCR )
+        {
+            for (i=0; i<n; i++)
+            {
+                call->SCR[0]  += calls[i].SCR;
+                call->SCR[1+i] = calls[i].SCR;
+            }
+        }
+        if ( call->ADF )
+        {
+            assert( call->n_alleles<=B2B_MAX_ALLELES );   // this is always true for SNPs and so far for indels as well
+
+            // reorder ADR,ADF to match the allele ordering at this site
+            int32_t tmp[B2B_MAX_ALLELES];
+            int32_t *adr = call->ADR + B2B_MAX_ALLELES, *adr_out = call->ADR + B2B_MAX_ALLELES;
+            int32_t *adf = call->ADF + B2B_MAX_ALLELES, *adf_out = call->ADF + B2B_MAX_ALLELES;
+            int32_t *adr_tot = call->ADR;   // the first bin stores total counts per site
+            int32_t *adf_tot = call->ADF;
+            for (i=0; i<n; i++)
+            {
+                for (j=0; j<call->n_alleles; j++)
+                {
+                    tmp[j] = adr[ call->a[j] ];
+                    adr_tot[j] += tmp[j];
+                }
+                for (j=0; j<call->n_alleles; j++) adr_out[j] = tmp[j];
+                for (j=0; j<call->n_alleles; j++)
+                {
+                    tmp[j] = adf[ call->a[j] ];
+                    adf_tot[j] += tmp[j];
+                }
+                for (j=0; j<call->n_alleles; j++) adf_out[j] = tmp[j];
+                adf_out += call->n_alleles;
+                adr_out += call->n_alleles;
+                adr += B2B_MAX_ALLELES;
+                adf += B2B_MAX_ALLELES;
+            }
+        }
+        if ( bca->fmt_flag & B2B_FMT_QS )
+        {
+            assert( call->n_alleles<=B2B_MAX_ALLELES );   // this is always true for SNPs and so far for indels as well
+
+            // reorder QS to match the allele ordering at this site
+            int32_t tmp[B2B_MAX_ALLELES];
+            int32_t *qs = call->QS, *qs_out = call->QS;
+            for (i=0; i<n; i++)
+            {
+                for (j=0; j<call->n_alleles; j++) tmp[j] = qs[ call->a[j] ];
+                for (j=0; j<call->n_alleles; j++) qs_out[j] = tmp[j] < BCF_MAX_BT_INT32 ? tmp[j] : BCF_MAX_BT_INT32;
+                qs_out += call->n_alleles;
+                qs += B2B_MAX_ALLELES;
+            }
+        }
+
+//      if (ref_base < 0) fprintf(bcftools_stderr, "%d,%d,%f,%d\n", call->n_alleles, x, sum_min, call->unseen);
+        call->shift = (int)(sum_min + .499);
+    }
+    // combine annotations
+    memset(call->anno, 0, 16 * sizeof(double));
+    call->ori_depth = 0;
+    call->depth     = 0;
+    call->mq0       = 0;
+    for (i = 0; i < n; ++i) {
+        call->depth += calls[i].anno[0] + calls[i].anno[1] + calls[i].anno[2] + calls[i].anno[3];
+        call->ori_depth += calls[i].ori_depth;
+        call->mq0 += calls[i].mq0;
+        for (j = 0; j < 16; ++j) call->anno[j] += calls[i].anno[j];
+    }
+
+    // No need to calculate MWU tests when there is no ALT allele, this should speed up things slightly
+    if ( !has_alt ) return 0;
+
+    calc_SegBias(calls, call);
+
+    // calc_chisq_bias("XPOS", call->bcf_hdr->id[BCF_DT_CTG][call->tid].key, call->pos, bca->ref_pos, bca->alt_pos, bca->npos);
+    // calc_chisq_bias("XMQ", call->bcf_hdr->id[BCF_DT_CTG][call->tid].key, call->pos, bca->ref_mq, bca->alt_mq, bca->nqual);
+    // calc_chisq_bias("XBQ", call->bcf_hdr->id[BCF_DT_CTG][call->tid].key, call->pos, bca->ref_bq, bca->alt_bq, bca->nqual);
+
+    if (bca->fmt_flag & B2B_INFO_ZSCORE) {
+        // U z-normalised as +/- number of standard deviations from mean.
+        if (call->ori_ref < 0) {    // indel
+            if (bca->fmt_flag & B2B_INFO_RPB)
+                call->mwu_pos = calc_mwu_biasZ(bca->iref_pos, bca->ialt_pos,
+                                               bca->npos, 0, 1);
+            call->mwu_mq  = calc_mwu_biasZ(bca->iref_mq,  bca->ialt_mq,
+                                           bca->nqual,1,1);
+            if ( bca->fmt_flag & B2B_INFO_SCB )
+                call->mwu_sc  = calc_mwu_biasZ(bca->iref_scl, bca->ialt_scl,
+                                               100, 0,1);
+        } else {
+            if (bca->fmt_flag & B2B_INFO_RPB)
+                call->mwu_pos = calc_mwu_biasZ(bca->ref_pos, bca->alt_pos,
+                                               bca->npos, 0, 1);
+            call->mwu_mq  = calc_mwu_biasZ(bca->ref_mq,  bca->alt_mq,
+                                           bca->nqual,1,1);
+            call->mwu_bq  = calc_mwu_biasZ(bca->ref_bq,  bca->alt_bq,
+                                           bca->nqual,0,1);
+            call->mwu_mqs = calc_mwu_biasZ(bca->fwd_mqs, bca->rev_mqs,
+                                           bca->nqual,0,1);
+            if ( bca->fmt_flag & B2B_INFO_SCB )
+                call->mwu_sc  = calc_mwu_biasZ(bca->ref_scl, bca->alt_scl,
+                                               100, 0,1);
+        }
+        call->mwu_nm[0] = calc_mwu_biasZ(bca->ref_nm, bca->alt_nm, B2B_N_NM,0,1);
+        if ( bca->fmt_flag & B2B_FMT_NMBZ )
+        {
+            for (i=0; i<n; i++)
+            {
+                float val = calc_mwu_biasZ(calls[i].ref_nm, calls[i].alt_nm, B2B_N_NM,0,1);
+                call->mwu_nm[i+1] = val!=HUGE_VAL ? val : 0;
+            }
+        }
+    } else {
+        // Old method; U as probability between 0 and 1
+        if ( bca->fmt_flag & B2B_INFO_RPB )
+            call->mwu_pos = calc_mwu_biasZ(bca->ref_pos, bca->alt_pos,
+                                           bca->npos, 0, 0);
+        call->mwu_mq  = calc_mwu_biasZ(bca->ref_mq,  bca->alt_mq,
+                                       bca->nqual, 1, 0);
+        call->mwu_bq  = calc_mwu_biasZ(bca->ref_bq,  bca->alt_bq,
+                                       bca->nqual, 0, 0);
+        call->mwu_mqs = calc_mwu_biasZ(bca->fwd_mqs, bca->rev_mqs,
+                                       bca->nqual, 0, 0);
+    }
+
+#if CDF_MWU_TESTS
+    // CDF version of MWU tests is not calculated by default
+    if ( bca->fmt_flag & B2B_INFO_RPB )
+        call->mwu_pos_cdf = calc_mwu_bias_cdf(bca->ref_pos, bca->alt_pos, bca->npos);
+    call->mwu_mq_cdf  = calc_mwu_bias_cdf(bca->ref_mq,  bca->alt_mq,  bca->nqual);
+    call->mwu_bq_cdf  = calc_mwu_bias_cdf(bca->ref_bq,  bca->alt_bq,  bca->nqual);
+    call->mwu_mqs_cdf = calc_mwu_bias_cdf(bca->fwd_mqs, bca->rev_mqs, bca->nqual);
+#endif
+
+    if ( bca->fmt_flag & B2B_INFO_VDB )
+        call->vdb = calc_vdb(bca->alt_pos, bca->npos);
+
+    return 0;
+}
+
+int bcf_call2bcf(bcf_call_t *bc, bcf1_t *rec, bcf_callret1_t *bcr, int fmt_flag, const bcf_callaux_t *bca, const char *ref)
+{
+    extern double kt_fisher_exact(int n11, int n12, int n21, int n22, double *_left, double *_right, double *two);
+    int i, j, nals = 1, has_alt = 0;
+
+    bcf_hdr_t *hdr = bc->bcf_hdr;
+    rec->rid  = bc->tid;
+    rec->pos  = bc->pos;
+    rec->qual = 0;
+
+    bc->tmp.l = 0;
+    if (bc->ori_ref < 0)    // indel
+    {
+        // REF
+        kputc(ref[bc->pos], &bc->tmp);
+        for (j = 0; j < bca->indelreg; ++j) kputc(ref[bc->pos+1+j], &bc->tmp);
+
+        // ALT
+        for (i=1; i<4; i++)
+        {
+            if (bc->a[i] < 0) break;
+            kputc(',', &bc->tmp); kputc(ref[bc->pos], &bc->tmp);
+
+            if (bca->indel_types[bc->a[i]] < 0) { // deletion
+                for (j = -bca->indel_types[bc->a[i]]; j < bca->indelreg; ++j)
+                    kputc(ref[bc->pos+1+j], &bc->tmp);
+            } else { // insertion; cannot be a reference unless a bug
+                char *inscns = &bca->inscns[bc->a[i] * bca->maxins];
+                for (j = 0; j < bca->indel_types[bc->a[i]]; ++j)
+                    kputc("ACGTN"[(int)inscns[j]], &bc->tmp);
+                for (j = 0; j < bca->indelreg; ++j) kputc(ref[bc->pos+1+j], &bc->tmp);
+            }
+            nals++;
+            has_alt = 1;
+        }
+    }
+    else    // SNP
+    {
+        kputc("ACGTN"[bc->ori_ref], &bc->tmp);
+        for (i=1; i<5; i++)
+        {
+            if (bc->a[i] < 0) break;
+            kputc(',', &bc->tmp);
+            if ( bc->unseen==i ) kputs("<*>", &bc->tmp);
+            else
+            {
+                kputc("ACGT"[bc->a[i]], &bc->tmp);
+                has_alt = 1;
+            }
+            nals++;
+        }
+    }
+    bcf_update_alleles_str(hdr, rec, bc->tmp.s);
+
+    bc->tmp.l = 0;
+
+    // INFO
+    if (bc->ori_ref < 0)
+    {
+        bcf_update_info_flag(hdr, rec, "INDEL", NULL, 1);
+        bcf_update_info_int32(hdr, rec, "IDV", &bca->max_support, 1);
+        bcf_update_info_float(hdr, rec, "IMF", &bca->max_frac, 1);
+    }
+    bcf_update_info_int32(hdr, rec, "DP", &bc->ori_depth, 1);
+    if ( fmt_flag&B2B_INFO_ADF )
+        bcf_update_info_int32(hdr, rec, "ADF", bc->ADF, rec->n_allele);
+    if ( fmt_flag&B2B_INFO_ADR )
+        bcf_update_info_int32(hdr, rec, "ADR", bc->ADR, rec->n_allele);
+    if ( fmt_flag&(B2B_INFO_AD|B2B_INFO_DPR) )
+    {
+        for (i=0; i<rec->n_allele; i++) bc->ADF[i] += bc->ADR[i];
+        if ( fmt_flag&B2B_INFO_AD )
+            bcf_update_info_int32(hdr, rec, "AD", bc->ADF, rec->n_allele);
+        if ( fmt_flag&B2B_INFO_DPR )
+            bcf_update_info_int32(hdr, rec, "DPR", bc->ADF, rec->n_allele);
+    }
+    if ( fmt_flag&B2B_INFO_SCR )
+        bcf_update_info_int32(hdr, rec, "SCR", bc->SCR, 1);
+
+    float tmpf[16];
+    for (i=0; i<16; i++) tmpf[i] = bc->anno[i];
+    bcf_update_info_float(hdr, rec, "I16", tmpf, 16);
+    bcf_update_info_float(hdr, rec, "QS", bc->qsum, nals);
+
+    if ( has_alt )
+    {
+        if ( bc->vdb != HUGE_VAL )      bcf_update_info_float(hdr, rec, "VDB", &bc->vdb, 1);
+        if ( bc->seg_bias != HUGE_VAL ) bcf_update_info_float(hdr, rec, "SGB", &bc->seg_bias, 1);
+
+        if (bca->fmt_flag & B2B_INFO_ZSCORE) {
+            if ( bc->mwu_pos != HUGE_VAL )
+                bcf_update_info_float(hdr, rec, "RPBZ", &bc->mwu_pos, 1);
+            if ( bc->mwu_mq != HUGE_VAL )
+                bcf_update_info_float(hdr, rec, "MQBZ", &bc->mwu_mq, 1);
+            if ( bc->mwu_mqs != HUGE_VAL )
+                bcf_update_info_float(hdr, rec, "MQSBZ", &bc->mwu_mqs, 1);
+            if ( bc->mwu_bq != HUGE_VAL )
+                bcf_update_info_float(hdr, rec, "BQBZ", &bc->mwu_bq, 1);
+            if ( bc->mwu_nm[0] != HUGE_VAL )
+                bcf_update_info_float(hdr, rec, "NMBZ", bc->mwu_nm, 1);
+            if ( bc->mwu_sc != HUGE_VAL )
+                bcf_update_info_float(hdr, rec, "SCBZ", &bc->mwu_sc, 1);
+        } else {
+            if ( bc->mwu_pos != HUGE_VAL )
+                bcf_update_info_float(hdr, rec, "RPB", &bc->mwu_pos, 1);
+            if ( bc->mwu_mq != HUGE_VAL )
+                bcf_update_info_float(hdr, rec, "MQB", &bc->mwu_mq, 1);
+            if ( bc->mwu_mqs != HUGE_VAL )
+                bcf_update_info_float(hdr, rec, "MQSB", &bc->mwu_mqs, 1);
+            if ( bc->mwu_bq != HUGE_VAL )
+                bcf_update_info_float(hdr, rec, "BQB", &bc->mwu_bq, 1);
+        }
+
+        if ( bc->strand_bias != HUGE_VAL )
+            bcf_update_info_float(hdr, rec, "FS", &bc->strand_bias, 1);
+
+#if CDF_MWU_TESTS
+        if ( bc->mwu_pos_cdf != HUGE_VAL )  bcf_update_info_float(hdr, rec, "RPB2", &bc->mwu_pos_cdf, 1);
+        if ( bc->mwu_mq_cdf != HUGE_VAL )   bcf_update_info_float(hdr, rec, "MQB2", &bc->mwu_mq_cdf, 1);
+        if ( bc->mwu_mqs_cdf != HUGE_VAL )  bcf_update_info_float(hdr, rec, "MQSB2", &bc->mwu_mqs_cdf, 1);
+        if ( bc->mwu_bq_cdf != HUGE_VAL )   bcf_update_info_float(hdr, rec, "BQB2", &bc->mwu_bq_cdf, 1);
+#endif
+    }
+
+    tmpf[0] = bc->ori_depth ? (float)bc->mq0/bc->ori_depth : 0;
+    bcf_update_info_float(hdr, rec, "MQ0F", tmpf, 1);
+
+    // FORMAT
+    rec->n_sample = bc->n;
+    bcf_update_format_int32(hdr, rec, "PL", bc->PL, nals*(nals+1)/2 * rec->n_sample);
+    if ( fmt_flag&B2B_FMT_DP )
+    {
+        int32_t *ptr = (int32_t*) bc->fmt_arr;
+        for (i=0; i<bc->n; i++)
+            ptr[i] = bc->DP4[4*i] + bc->DP4[4*i+1] + bc->DP4[4*i+2] + bc->DP4[4*i+3];
+        bcf_update_format_int32(hdr, rec, "DP", bc->fmt_arr, rec->n_sample);
+    }
+    if ( fmt_flag&B2B_FMT_DV )
+    {
+        int32_t *ptr = (int32_t*) bc->fmt_arr;
+        for (i=0; i<bc->n; i++)
+            ptr[i] = bc->DP4[4*i+2] + bc->DP4[4*i+3];
+        bcf_update_format_int32(hdr, rec, "DV", bc->fmt_arr, rec->n_sample);
+    }
+    if ( fmt_flag&B2B_FMT_SP )
+    {
+        int32_t *ptr = (int32_t*) bc->fmt_arr;
+        for (i=0; i<bc->n; i++)
+        {
+            int fwd_ref = bc->DP4[4*i], rev_ref =  bc->DP4[4*i+1], fwd_alt = bc->DP4[4*i+2], rev_alt = bc->DP4[4*i+3];
+            if ( fwd_ref+rev_ref<2 || fwd_alt+rev_alt<2 || fwd_ref+fwd_alt<2 || rev_ref+rev_alt<2 )
+                ptr[i] = 0;
+            else
+            {
+                double left, right, two;
+                kt_fisher_exact(fwd_ref, rev_ref, fwd_alt, rev_alt, &left, &right, &two);
+                int32_t x = (int)(-4.343 * log(two) + .499);
+                if (x > 255) x = 255;
+                ptr[i] = x;
+            }
+        }
+        bcf_update_format_int32(hdr, rec, "SP", bc->fmt_arr, rec->n_sample);
+    }
+    if ( fmt_flag&B2B_FMT_DP4 )
+        bcf_update_format_int32(hdr, rec, "DP4", bc->DP4, rec->n_sample*4);
+    if ( fmt_flag&B2B_FMT_ADF )
+        bcf_update_format_int32(hdr, rec, "ADF", bc->ADF+B2B_MAX_ALLELES, rec->n_sample*rec->n_allele);
+    if ( fmt_flag&B2B_FMT_ADR )
+        bcf_update_format_int32(hdr, rec, "ADR", bc->ADR+B2B_MAX_ALLELES, rec->n_sample*rec->n_allele);
+    if ( fmt_flag&(B2B_FMT_AD|B2B_FMT_DPR) )
+    {
+        for (i=0; i<rec->n_sample*rec->n_allele; i++) bc->ADF[B2B_MAX_ALLELES+i] += bc->ADR[B2B_MAX_ALLELES+i];
+        if ( fmt_flag&B2B_FMT_AD )
+            bcf_update_format_int32(hdr, rec, "AD", bc->ADF+B2B_MAX_ALLELES, rec->n_sample*rec->n_allele);
+        if ( fmt_flag&B2B_FMT_DPR )
+            bcf_update_format_int32(hdr, rec, "DPR", bc->ADF+B2B_MAX_ALLELES, rec->n_sample*rec->n_allele);
+    }
+    if ( fmt_flag&B2B_FMT_SCR )
+        bcf_update_format_int32(hdr, rec, "SCR", bc->SCR+1, rec->n_sample);
+    if ( fmt_flag&B2B_FMT_QS )
+        bcf_update_format_int32(hdr, rec, "QS", bc->QS, rec->n_sample*rec->n_allele);
+
+    if ( has_alt )
+    {
+        if ( fmt_flag&B2B_FMT_NMBZ )
+            bcf_update_format_float(hdr, rec, "NMBZ", bc->mwu_nm+1, rec->n_sample);
+    }
+
+    return 0;
+}
diff --git a/bcftools/bam2bcf.h b/bcftools/bam2bcf.h
new file mode 100644
index 0000000..c256b26
--- /dev/null
+++ b/bcftools/bam2bcf.h
@@ -0,0 +1,171 @@
+/*  bam2bcf.h -- variant calling.
+
+    Copyright (C) 2010-2012 Broad Institute.
+    Copyright (C) 2012-2022 Genome Research Ltd.
+
+    Author: Heng Li <lh3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#ifndef BAM2BCF_H
+#define BAM2BCF_H
+
+#include <stdint.h>
+#include <htslib/hts.h>
+#include <htslib/vcf.h>
+
+/**
+ *  A simplified version of Mann-Whitney U-test is calculated
+ *  by default (no CDF) because it is faster and seems to work
+ *  better in machine learning filtering. When enabled by setting
+ *  CDF_MWU_TESTS, additional annotations will appear on mpileup's
+ *  output (RPB2 in addition to RPB, etc.).
+ */
+#ifndef CDF_MWU_TESTS
+#define CDF_MWU_TESTS 0
+#endif
+
+#define B2B_INDEL_NULL 10000
+
+#define B2B_FMT_DP      (1<<0)
+#define B2B_FMT_SP      (1<<1)
+#define B2B_FMT_DV      (1<<2)
+#define B2B_FMT_DP4     (1<<3)
+#define B2B_FMT_DPR     (1<<4)
+#define B2B_INFO_DPR    (1<<5)
+#define B2B_FMT_AD      (1<<6)
+#define B2B_FMT_ADF     (1<<7)
+#define B2B_FMT_ADR     (1<<8)
+#define B2B_INFO_AD     (1<<9)
+#define B2B_INFO_ADF    (1<<10)
+#define B2B_INFO_ADR    (1<<11)
+#define B2B_INFO_SCR    (1<<12)
+#define B2B_FMT_SCR     (1<<13)
+#define B2B_INFO_VDB    (1<<14)
+#define B2B_INFO_RPB    (1<<15)
+#define B2B_FMT_QS      (1<<16)
+#define B2B_INFO_SCB    (1<<17)
+#define B2B_FMT_NMBZ    (1<<18) // per-sample NMBZ
+#define B2B_INFO_ZSCORE (1<<30) // MWU as-is or Z-normalised
+
+#define B2B_MAX_ALLELES 5
+#define B2B_N_NM 32             // number of NMBZ bins, i.e. max number of mismatches
+
+
+#define B2B_DROP      0
+#define B2B_INC_AD    1
+#define B2B_INC_AD0   2
+
+#define PLP_HAS_SOFT_CLIP(i) ((i)&1)
+#define PLP_HAS_INDEL(i)     ((i)&2)
+#define PLP_SAMPLE_ID(i)     ((i)>>2)
+
+#define PLP_SET_SOFT_CLIP(i)     ((i)|=1)
+#define PLP_SET_INDEL(i)         ((i)|=2)
+#define PLP_SET_SAMPLE_ID(i,n)   ((i)|=(n)<<2)
+
+typedef struct __bcf_callaux_t {
+    int fmt_flag, ambig_reads;
+    int capQ, min_baseQ, max_baseQ, delta_baseQ;
+    int openQ, extQ, tandemQ; // for indels
+    uint32_t min_support, max_support; // for collecting indel candidates
+    double min_frac; // for collecting indel candidates
+    float max_frac; // for collecting indel candidates
+    int per_sample_flt; // indel filtering strategy
+    int *ref_pos, *alt_pos, npos, *ref_mq, *alt_mq, *ref_bq, *alt_bq, *fwd_mqs, *rev_mqs, nqual; // for bias tests
+    int *iref_pos, *ialt_pos, *iref_mq, *ialt_mq; // for indels
+    int ref_scl[100], alt_scl[100];   // soft-clip length bias; SNP
+    int iref_scl[100], ialt_scl[100]; // soft-clip length bias; INDEL
+    // for internal uses
+    int max_bases;
+    int indel_types[4];     // indel lengths
+    int indel_win_size;
+    int maxins, indelreg;
+    int read_len;
+    char *inscns;
+    uint16_t *bases;        // 5bit: unused, 6:quality, 1:is_rev, 4:2-bit base or indel allele (index to bcf_callaux_t.indel_types)
+    errmod_t *e;
+    void *rghash;
+    float indel_bias;  // adjusts indel score threshold; lower => call more.
+    int32_t *ref_nm, *alt_nm;   // pointers to bcf_call_t.{ref_nm,alt_nm}
+} bcf_callaux_t;
+
+// per-sample values
+typedef struct {
+    uint32_t ori_depth;     // ori_depth = anno[0..3] but before --min-BQ is applied
+    unsigned int mq0;
+    int32_t *ADF, *ADR, SCR, *QS;   // FMT/QS
+    int32_t *ref_nm, *alt_nm;
+    // The fields are:
+    //      depth fwd   .. ref (0) and non-ref (2)
+    //      depth rev   .. ref (1) and non-ref (3)
+    //      baseQ       .. ref (4) and non-ref (6)
+    //      baseQ^2     .. ref (5) and non-ref (7)
+    //      mapQ        .. ref (8) and non-ref (10)
+    //      mapQ^2      .. ref (9) and non-ref (11)
+    //      minDist     .. ref (12) and non-ref (14)
+    //      minDist^2   .. ref (13) and non-ref (15)
+    // Note that this probably needs a more thorough fix: int types in
+    // bcf_call_t do overflow with high-coverage data, such as exomes, and
+    // BCFv2 supports only floats which may not suffice.
+    double anno[16];
+    float p[25];        // phred-scaled likelihood of each genotype
+} bcf_callret1_t;
+
+// values for all samples
+typedef struct {
+    int tid, pos;
+    bcf_hdr_t *bcf_hdr;
+    int a[5]; // alleles: ref, alt, alt2, alt3
+    float qsum[B2B_MAX_ALLELES];  // INFO/QS tag
+    int n, n_alleles, shift, ori_ref, unseen;
+    int n_supp; // number of supporting non-reference reads
+    double anno[16];
+    unsigned int depth, ori_depth, mq0;
+    int32_t *PL, *DP4, *ADR, *ADF, *SCR, *QS, *ref_nm, *alt_nm;
+    uint8_t *fmt_arr;
+    float vdb; // variant distance bias
+    float mwu_pos, mwu_mq, mwu_bq, mwu_mqs, mwu_sc, *mwu_nm;
+#if CDF_MWU_TESTS
+    float mwu_pos_cdf, mwu_mq_cdf, mwu_bq_cdf, mwu_mqs_cdf;
+#endif
+    float seg_bias;
+    float strand_bias; // phred-scaled fisher-exact test
+    kstring_t tmp;
+} bcf_call_t;
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+    bcf_callaux_t *bcf_call_init(double theta, int min_baseQ, int max_baseQ,
+                                 int delta_baseQ);
+    void bcf_call_destroy(bcf_callaux_t *bca);
+    int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base, bcf_callaux_t *bca, bcf_callret1_t *r);
+    int bcf_call_combine(int n, const bcf_callret1_t *calls, bcf_callaux_t *bca, int ref_base /*4-bit*/, bcf_call_t *call);
+    int bcf_call2bcf(bcf_call_t *bc, bcf1_t *b, bcf_callret1_t *bcr, int fmt_flag,
+                     const bcf_callaux_t *bca, const char *ref);
+    int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_callaux_t *bca, const char *ref);
+    void bcf_callaux_clean(bcf_callaux_t *bca, bcf_call_t *call);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif
diff --git a/bcftools/bam2bcf_indel.c b/bcftools/bam2bcf_indel.c
new file mode 100644
index 0000000..108d505
--- /dev/null
+++ b/bcftools/bam2bcf_indel.c
@@ -0,0 +1,947 @@
+/*  bam2bcf_indel.c -- indel caller.
+
+    Copyright (C) 2010, 2011 Broad Institute.
+    Copyright (C) 2012-2014,2016-2017, 2021 Genome Research Ltd.
+
+    Author: Heng Li <lh3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <assert.h>
+#include <ctype.h>
+#include <string.h>
+#include <math.h>
+#include <htslib/hts.h>
+#include <htslib/sam.h>
+#include <htslib/khash_str2int.h>
+#include "bam2bcf.h"
+#include "str_finder.h"
+
+#include <htslib/ksort.h>
+KSORT_INIT_GENERIC(uint32_t)
+
+#define MINUS_CONST 0x10000000
+
+#define MAX_TYPES 64
+
+// Take a reference position tpos and convert to a query position (returned).
+// This uses the CIGAR string plus alignment c->pos to do the mapping.
+//
+// *_tpos is returned as tpos if query overlaps tpos, but for deletions
+// it'll be either the start (is_left) or end (!is_left) ref position.
+static int tpos2qpos(const bam1_core_t *c, const uint32_t *cigar, int32_t tpos, int is_left, int32_t *_tpos)
+{
+    // x = pos in ref, y = pos in query seq
+    int k, x = c->pos, y = 0, last_y = 0;
+    *_tpos = c->pos;
+    for (k = 0; k < c->n_cigar; ++k) {
+        int op = cigar[k] & BAM_CIGAR_MASK;
+        int l = cigar[k] >> BAM_CIGAR_SHIFT;
+        if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) {
+            if (c->pos > tpos) return y;
+            if (x + l > tpos) {
+                *_tpos = tpos;
+                return y + (tpos - x);
+            }
+            x += l; y += l;
+            last_y = y;
+        } else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) y += l;
+        else if (op == BAM_CDEL || op == BAM_CREF_SKIP) {
+            if (x + l > tpos) {
+                *_tpos = is_left? x : x + l;
+                return y;
+            }
+            x += l;
+        }
+    }
+    *_tpos = x;
+    return last_y;
+}
+
+// FIXME: check if the inserted sequence is consistent with the homopolymer run
+// l is the relative gap length and l_run is the length of the homopolymer on the reference
+static inline int est_seqQ(const bcf_callaux_t *bca, int l, int l_run)
+{
+    int q, qh;
+    q = bca->openQ + bca->extQ * (abs(l) - 1);
+    qh = l_run >= 3? (int)(bca->tandemQ * (double)abs(l) / l_run + .499) : 1000;
+    return q < qh? q : qh;
+}
+
+static inline int est_indelreg(int pos, const char *ref, int l, char *ins4)
+{
+    int i, j, max = 0, max_i = pos, score = 0;
+    l = abs(l);
+    for (i = pos + 1, j = 0; ref[i]; ++i, ++j) {
+        if (ins4) score += (toupper(ref[i]) != "ACGTN"[(int)ins4[j%l]])? -10 : 1;
+        else score += (toupper(ref[i]) != toupper(ref[pos+1+j%l]))? -10 : 1;
+        if (score < 0) break;
+        if (max < score) max = score, max_i = i;
+    }
+    return max_i - pos;
+}
+
+// Identify spft-clip length, position in seq, and clipped seq len
+static inline void get_pos(const bcf_callaux_t *bca, bam_pileup1_t *p,
+                           int *sc_len_r, int *slen_r, int *epos_r, int *end) {
+    bam1_t *b = p->b;
+    int sc_len = 0, sc_dist = -1, at_left = 1;
+    int epos = p->qpos, slen = b->core.l_qseq;
+    int k;
+    uint32_t *cigar = bam_get_cigar(b);
+    *end = -1;
+    for (k = 0; k < b->core.n_cigar; k++) {
+        int op = bam_cigar_op(cigar[k]);
+        if (op == BAM_CSOFT_CLIP) {
+            slen -= bam_cigar_oplen(cigar[k]);
+            if (at_left) {
+                // left end
+                sc_len += bam_cigar_oplen(cigar[k]);
+                epos -= sc_len; // don't count SC in seq pos
+                sc_dist = epos;
+                *end = 0;
+            } else {
+                // right end
+                int srlen = bam_cigar_oplen(cigar[k]);
+                int rd = b->core.l_qseq - srlen - p->qpos;
+                if (sc_dist < 0 || sc_dist > rd) {
+                    // closer to right end than left
+                    // FIXME: compensate for indel length too?
+                    sc_dist = rd;
+                    sc_len = srlen;
+                    *end = 1;
+                }
+            }
+        } else if (op != BAM_CHARD_CLIP) {
+            at_left = 0;
+        }
+    }
+
+    if (p->indel > 0 && slen - (epos+p->indel) < epos)
+        epos += p->indel-1; // end of insertion, if near end of seq
+
+    // slen is now length of sequence minus soft-clips and
+    // epos is position of indel in seq minus left-clip.
+    *epos_r = (double)epos / (slen+1) * bca->npos;
+
+    if (sc_len) {
+        // scale importance of clip by distance to closest end
+        *sc_len_r = 15.0*sc_len / (sc_dist+1);
+        if (*sc_len_r > 99) *sc_len_r = 99;
+    } else {
+        *sc_len_r = 0;
+    }
+
+    *slen_r = slen;
+}
+
+// Part of bcf_call_gap_prep.
+//
+// Scans the pileup to identify all the different sizes of indels
+// present.
+//
+// Returns types and fills out n_types_r,  max_rd_len_r and ref_type_r,
+//         or NULL on error.
+static int *bcf_cgp_find_types(int n, int *n_plp, bam_pileup1_t **plp,
+                               int pos, bcf_callaux_t *bca, const char *ref,
+                               int *max_rd_len_r, int *n_types_r,
+                               int *ref_type_r, int *N_r) {
+    int i, j, t, s, N, m, max_rd_len, n_types;
+    int n_alt = 0, n_tot = 0, indel_support_ok = 0;
+    uint32_t *aux;
+    int *types;
+
+    // N is the total number of reads
+    for (s = N = 0; s < n; ++s)
+        N += n_plp[s];
+
+    bca->max_support = bca->max_frac = 0;
+    aux = (uint32_t*) calloc(N + 1, 4);
+    if (!aux)
+        return NULL;
+
+    m = max_rd_len = 0;
+    aux[m++] = MINUS_CONST; // zero indel is always a type (REF)
+
+    // Fill out aux[] array with all the non-zero indel sizes.
+    // Also tally number with indels (n_alt) and total (n_tot).
+    for (s = 0; s < n; ++s) {
+        int na = 0, nt = 0;
+        for (i = 0; i < n_plp[s]; ++i) {
+            const bam_pileup1_t *p = plp[s] + i;
+            ++nt;
+            if (p->indel != 0) {
+                ++na;
+                aux[m++] = MINUS_CONST + p->indel;
+            }
+
+            // FIXME: cache me in pileup struct.
+            j = bam_cigar2qlen(p->b->core.n_cigar, bam_get_cigar(p->b));
+            if (j > max_rd_len) max_rd_len = j;
+        }
+        double frac = (double)na/nt;
+        if ( !indel_support_ok && na >= bca->min_support
+             && frac >= bca->min_frac )
+            indel_support_ok = 1;
+        if ( na > bca->max_support && frac > 0 )
+            bca->max_support = na, bca->max_frac = frac;
+
+        n_alt += na;
+        n_tot += nt;
+    }
+
+    // Sort aux[] and dedup
+    ks_introsort(uint32_t, m, aux);
+    for (i = 1, n_types = 1; i < m; ++i)
+        if (aux[i] != aux[i-1]) ++n_types;
+
+    // Taking totals makes it hard to call rare indels (IMF filter)
+    if ( !bca->per_sample_flt )
+        indel_support_ok = ( (double)n_alt / n_tot < bca->min_frac
+                             || n_alt < bca->min_support )
+            ? 0 : 1;
+    if ( n_types == 1 || !indel_support_ok ) { // then skip
+        free(aux);
+        return NULL;
+    }
+
+    // Bail out if we have far too many types of indel
+    if (n_types >= MAX_TYPES) {
+        free(aux);
+        // TODO revisit how/whether to control printing this warning
+        if (hts_verbose >= 2)
+            fprintf(stderr, "[%s] excessive INDEL alleles at position %d. "
+                    "Skip the position.\n", __func__, pos + 1);
+        return NULL;
+    }
+
+    // To prevent long stretches of N's to be mistaken for indels
+    // (sometimes thousands of bases), check the number of N's in the
+    // sequence and skip places where half or more reference bases are Ns.
+    int nN=0, i_end = pos + (2*bca->indel_win_size < max_rd_len
+                            ?2*bca->indel_win_size : max_rd_len);
+    for (i=pos; i<i_end && ref[i]; i++)
+        nN += ref[i] == 'N';
+    if ( nN*2>(i-pos) ) {
+        free(aux);
+        return NULL;
+    }
+
+    // Finally fill out the types[] array detailing the size of insertion
+    // or deletion.
+    types = (int*)calloc(n_types, sizeof(int));
+    if (!types) {
+        free(aux);
+        return NULL;
+    }
+    t = 0;
+    types[t++] = aux[0] - MINUS_CONST;
+    for (i = 1; i < m; ++i)
+        if (aux[i] != aux[i-1])
+            types[t++] = aux[i] - MINUS_CONST;
+    free(aux);
+
+    // Find reference type; types[?] == 0)
+    for (t = 0; t < n_types; ++t)
+        if (types[t] == 0) break;
+
+    *ref_type_r   = t;
+    *n_types_r    = n_types;
+    *max_rd_len_r = max_rd_len;
+    *N_r          = N;
+
+    return types;
+}
+
+// Part of bcf_call_gap_prep.
+//
+// Construct per-sample consensus.
+//
+// Returns an array of consensus seqs,
+//         or NULL on failure.
+static char **bcf_cgp_ref_sample(int n, int *n_plp, bam_pileup1_t **plp,
+                                 int pos, bcf_callaux_t *bca, const char *ref,
+                                 int left, int right) {
+    int i, k, s, L = right - left + 1, max_i, max2_i;
+    char **ref_sample; // returned
+    uint32_t *cns = NULL, max, max2;
+    char *ref0 = NULL, *r;
+    ref_sample = (char**) calloc(n, sizeof(char*));
+    cns = (uint32_t*) calloc(L, 4);
+    ref0 = (char*) calloc(L, 1);
+    if (!ref_sample || !cns || !ref0) {
+        n = 0;
+        goto err;
+    }
+
+    // Convert ref ASCII to 0-15.
+    for (i = 0; i < right - left; ++i)
+        ref0[i] = seq_nt16_table[(int)ref[i+left]];
+
+    // NB: one consensus per sample 'n', not per indel type.
+    // FIXME: consider fixing this.  We should compute alignments vs
+    // types, not vs samples?  Or types/sample combined?
+    for (s = 0; s < n; ++s) {
+        r = ref_sample[s] = (char*) calloc(L, 1);
+        if (!r) {
+            n = s-1;
+            goto err;
+        }
+
+        memset(cns, 0, sizeof(int) * L);
+
+        // collect ref and non-ref counts in cns
+        for (i = 0; i < n_plp[s]; ++i) {
+            bam_pileup1_t *p = plp[s] + i;
+            bam1_t *b = p->b;
+            uint32_t *cigar = bam_get_cigar(b);
+            uint8_t *seq = bam_get_seq(b);
+            int x = b->core.pos, y = 0;
+
+            // TODO: pileup exposes pileup_ind, but we also need e.g.
+            // pileup_len to know how much of the current CIGAR op-len
+            // we've used (or have remaining).  If we had that, we
+            // could start at p->qpos without having to scan through
+            // the entire CIGAR string until we find it.
+            //
+            // Without it about all we could do is have a side channel
+            // to cache the last known coords.  Messy, so punt for now.
+            // This is no longer the bottle neck until we get to 1000s of
+            // CIGAR ops.
+
+            for (k = 0; k < b->core.n_cigar; ++k) {
+                int op = cigar[k]&0xf;
+                int j, l = cigar[k]>>4;
+                if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) {
+                    if (x + l >= left) {
+                        j = left - x > 0 ? left - x : 0;
+                        int j_end = right - x < l ? right - x : l;
+                        for (; j < j_end; j++)
+                            // Append to cns.  Note this is ref coords,
+                            // so insertions aren't in cns and deletions
+                            // will have lower coverage.
+
+                            // FIXME: want true consensus (with ins) per
+                            // type, so we can independently compare each
+                            // seq to each consensus and see which it
+                            // matches best, so we get proper GT analysis.
+                            cns[x+j-left] +=
+                                (bam_seqi(seq, y+j) == ref0[x+j-left])
+                                ? 1        // REF
+                                : (1<<16); // ALT
+                    }
+                    x += l; y += l;
+                } else if (op == BAM_CDEL || op == BAM_CREF_SKIP) {
+                    x += l;
+                } else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) {
+                    y += l;
+                }
+
+                if (x > right)
+                    break;
+            }
+        }
+
+        // Determine a sample specific reference.
+        for (i = 0; i < right - left; ++i)
+            r[i] = ref0[i];
+
+        // Find deepest and 2nd deepest ALT region (max & max2).
+        max = max2 = 0; max_i = max2_i = -1;
+        for (i = 0; i < right - left; ++i) {
+            if (cns[i]>>16 >= max>>16)
+                max2 = max, max2_i = max_i, max = cns[i], max_i = i;
+            else if (cns[i]>>16 >= max2>>16)
+                max2 = cns[i], max2_i = i;
+        }
+
+        // Masks mismatches present in at least 70% of the reads with 'N'.
+        // This code is nREF/(nREF+n_ALT) >= 70% for deepest region.
+        // The effect is that at least 30% of bases differing to REF will
+        // use "N" in consensus, so we don't penalise ALT or REF when
+        // aligning against it.  (A poor man IUPAC code)
+        //
+        // Why is it only done in two loci at most?
+        if ((double)(max&0xffff) / ((max&0xffff) + (max>>16)) >= 0.7)
+            max_i = -1;
+        if ((double)(max2&0xffff) / ((max2&0xffff) + (max2>>16)) >= 0.7)
+            max2_i = -1;
+        if (max_i >= 0) r[max_i] = 15;
+        if (max2_i >= 0) r[max2_i] = 15;
+
+        //for (i = 0; i < right - left; ++i)
+        //    fputc("=ACMGRSVTWYHKDBN"[(int)r[i]], stderr);
+        //fputc('\n', stderr);
+    }
+
+    free(ref0);
+    free(cns);
+
+    return ref_sample;
+
+ err:
+    free(ref0);
+    free(cns);
+    if (ref_sample) {
+        for (s = 0; s < n; s++)
+            free(ref_sample[s]);
+        free(ref_sample);
+    }
+
+    return NULL;
+}
+
+// The length of the homopolymer run around the current position
+static int bcf_cgp_l_run(const char *ref, int pos) {
+    int i, l_run;
+
+    int c = seq_nt16_table[(int)ref[pos + 1]];
+    if (c == 15) {
+        l_run = 1;
+    } else {
+        for (i = pos + 2; ref[i]; ++i)
+            if (seq_nt16_table[(int)ref[i]] != c) break;
+        l_run = i;
+        for (i = pos; i >= 0; --i)
+            if (seq_nt16_table[(int)ref[i]] != c) break;
+        l_run -= i + 1;
+    }
+
+    return l_run;
+}
+
+
+// Compute the consensus for this sample 's', minus indels which
+// get added later.
+static char *bcf_cgp_calc_cons(int n, int *n_plp, bam_pileup1_t **plp,
+                               int pos, int *types, int n_types,
+                               int max_ins, int s) {
+    int i, j, t, k;
+    int *inscns_aux = (int*)calloc(5 * n_types * max_ins, sizeof(int));
+    if (!inscns_aux)
+        return NULL;
+
+    // Count the number of occurrences of each base at each position for
+    // each type of insertion.
+    for (t = 0; t < n_types; ++t) {
+        if (types[t] > 0) {
+            for (s = 0; s < n; ++s) {
+                for (i = 0; i < n_plp[s]; ++i) {
+                    bam_pileup1_t *p = plp[s] + i;
+                    if (p->indel == types[t]) {
+                        uint8_t *seq = bam_get_seq(p->b);
+                        for (k = 1; k <= p->indel; ++k) {
+                            int c = seq_nt16_int[bam_seqi(seq, p->qpos + k)];
+                            assert(c<5);
+                            ++inscns_aux[(t*max_ins+(k-1))*5 + c];
+                        }
+                    }
+                }
+            }
+        }
+    }
+
+    // Use the majority rule to construct the consensus
+    char *inscns = (char *)calloc(n_types * max_ins, 1);
+    for (t = 0; t < n_types; ++t) {
+        for (j = 0; j < types[t]; ++j) {
+            int max = 0, max_k = -1, *ia = &inscns_aux[(t*max_ins+j)*5];
+            for (k = 0; k < 5; ++k)
+                if (ia[k] > max)
+                    max = ia[k], max_k = k;
+            inscns[t*max_ins + j] = max ? max_k : 4;
+            if (max_k == 4) {
+                // discard insertions which contain N's
+                types[t] = 0;
+                break;
+            }
+        }
+    }
+    free(inscns_aux);
+
+    return inscns;
+}
+
+#ifndef MIN
+#  define MIN(a,b) ((a)<(b)?(a):(b))
+#endif
+
+// Part of bcf_call_gap_prep.
+//
+// Realign using BAQ to get an alignment score of a single read vs
+// a haplotype consensus.
+//
+// Fills out score
+// Returns 0 on success,
+//        <0 on error
+static int bcf_cgp_align_score(bam_pileup1_t *p, bcf_callaux_t *bca,
+                               int type, uint8_t *ref2, uint8_t *query,
+                               int r_start, int r_end, int long_read,
+                               int tbeg, int tend,
+                               int left, int right,
+                               int qbeg, int qend,
+                               int qpos, int max_deletion,
+                               int *score) {
+    // Illumina
+    probaln_par_t apf = { 1e-4, 1e-2, 10 };
+
+    // Parameters that work better on PacBio CCS 15k.
+    // We should consider querying the header and RG PU field.
+    // See also htslib/realn.c:sam_prob_realn()
+    if (long_read) {
+        apf.d = 1e-3;
+        apf.e = 1e-1;
+    }
+
+    type = abs(type);
+    apf.bw = type + 3;
+    int l, sc;
+    const uint8_t *qual = bam_get_qual(p->b), *bq;
+    uint8_t *qq;
+
+    // Get segment of quality, either ZQ tag or if absent QUAL.
+    if (!(qq = (uint8_t*) calloc(qend - qbeg, 1)))
+        return -1;
+    bq = (uint8_t*)bam_aux_get(p->b, "ZQ");
+    if (bq) ++bq; // skip type
+    for (l = qbeg; l < qend; ++l) {
+        int qval = bq? qual[l] + (bq[l] - 64) : qual[l];
+        if (qval > 30)
+            qval = 30;
+        if (qval < 7)
+            qval = 7;
+        qq[l - qbeg] = qval;
+    }
+
+    // The bottom 8 bits are length-normalised score while
+    // the top bits are unnormalised.
+    sc = probaln_glocal(ref2 + tbeg - left, tend - tbeg + type,
+                        query, qend - qbeg, qq, &apf, 0, 0);
+    if (sc < 0) {
+        *score = 0xffffff;
+        free(qq);
+        return 0;
+    }
+
+    // used for adjusting indelQ below
+    l = (int)(100. * sc / (qend - qbeg) + .499) * bca->indel_bias;
+    *score = sc<<8 | MIN(255, l);
+
+    rep_ele *reps, *elt, *tmp;
+    uint8_t *seg = ref2 + tbeg - left;
+    int seg_len = tend - tbeg + type;
+
+    // Note: although seg moves (tbeg varies), ref2 is reused many times
+    // so we could factor out some find_STR calls.  However it's not the
+    // bottleneck for now.
+
+    // FIXME: need to make this work on IUPAC.
+    reps = find_STR((char *)seg, seg_len, 0);
+    int iscore = 0;
+
+    // Identify STRs in ref covering the indel up to
+    // (or close to) the end of the sequence.
+    // Those having an indel and right at the sequence
+    // end do not confirm the total length of indel
+    // size.  Specifically a *lack* of indel at the
+    // end, where we know indels occur in other
+    // sequences, is a possible reference bias.
+    //
+    // This is emphasised further if the sequence ends with
+    // soft clipping.
+    DL_FOREACH_SAFE(reps, elt, tmp) {
+        if (elt->start <= qpos && elt->end >= qpos) {
+            iscore += (elt->end-elt->start) / elt->rep_len;  // c
+            if (elt->start+tbeg <= r_start ||
+                elt->end+tbeg   >= r_end)
+                iscore += 2*(elt->end-elt->start);
+       }
+
+        DL_DELETE(reps, elt);
+        free(elt);
+    }
+
+    // Apply STR score to existing indelQ
+    l  =  (*score&0xff)*.8 + iscore*2;
+    *score = (*score & ~0xff) | MIN(255, l);
+
+    free(qq);
+
+    return 0;
+}
+
+// Part of bcf_call_gap_prep.
+//
+// Returns n_alt on success
+//         -1 on failure
+static int bcf_cgp_compute_indelQ(int n, int *n_plp, bam_pileup1_t **plp,
+                                  bcf_callaux_t *bca, char *inscns,
+                                  int l_run, int max_ins,
+                                  int ref_type, int *types, int n_types,
+                                  int *score) {
+    // FIXME: n_types has a maximum; no need to alloc - use a #define?
+    int sc[MAX_TYPES], sumq[MAX_TYPES], s, i, j, t, K, n_alt, tmp;
+    memset(sumq, 0, n_types * sizeof(int));
+    for (s = K = 0; s < n; ++s) {
+        for (i = 0; i < n_plp[s]; ++i, ++K) {
+            bam_pileup1_t *p = plp[s] + i;
+            int *sct = &score[K*n_types], seqQ, indelQ;
+            for (t = 0; t < n_types; ++t) sc[t] = sct[t]<<6 | t;
+            for (t = 1; t < n_types; ++t) // insertion sort
+                for (j = t; j > 0 && sc[j] < sc[j-1]; --j)
+                    tmp = sc[j], sc[j] = sc[j-1], sc[j-1] = tmp;
+
+            /* errmod_cal() assumes that if the call is wrong, the
+             * likelihoods of other events are equal. This is about
+             * right for substitutions, but is not desired for
+             * indels. To reuse errmod_cal(), I have to make
+             * compromise for multi-allelic indels.
+             */
+            if ((sc[0]&0x3f) == ref_type) {
+                indelQ = (sc[1]>>14) - (sc[0]>>14);
+                seqQ = est_seqQ(bca, types[sc[1]&0x3f], l_run);
+            } else {
+                for (t = 0; t < n_types; ++t) // look for the reference type
+                    if ((sc[t]&0x3f) == ref_type) break;
+                indelQ = (sc[t]>>14) - (sc[0]>>14);
+                seqQ = est_seqQ(bca, types[sc[0]&0x3f], l_run);
+            }
+            tmp = sc[0]>>6 & 0xff;
+            // reduce indelQ
+            indelQ = tmp > 111? 0 : (int)((1. - tmp/111.) * indelQ + .499);
+
+            // Doesn't really help accuracy, but permits -h to take
+            // affect still.
+            if (indelQ > seqQ) indelQ = seqQ;
+            if (indelQ > 255) indelQ = 255;
+            if (seqQ > 255) seqQ = 255;
+            p->aux = (sc[0]&0x3f)<<16 | seqQ<<8 | indelQ; // use 22 bits in total
+            sumq[sc[0]&0x3f] += indelQ < seqQ? indelQ : seqQ;
+            //              fprintf(stderr, "pos=%d read=%d:%d name=%s call=%d indelQ=%d seqQ=%d\n", pos, s, i, bam1_qname(p->b), types[sc[0]&0x3f], indelQ, seqQ);
+        }
+    }
+    // determine bca->indel_types[] and bca->inscns
+    bca->maxins = max_ins;
+    bca->inscns = (char*) realloc(bca->inscns, bca->maxins * 4);
+    if (bca->maxins && !bca->inscns)
+        return -1;
+    for (t = 0; t < n_types; ++t)
+        sumq[t] = sumq[t]<<6 | t;
+    for (t = 1; t < n_types; ++t) // insertion sort
+        for (j = t; j > 0 && sumq[j] > sumq[j-1]; --j)
+            tmp = sumq[j], sumq[j] = sumq[j-1], sumq[j-1] = tmp;
+    for (t = 0; t < n_types; ++t) // look for the reference type
+        if ((sumq[t]&0x3f) == ref_type) break;
+    if (t) { // then move the reference type to the first
+        tmp = sumq[t];
+        for (; t > 0; --t) sumq[t] = sumq[t-1];
+        sumq[0] = tmp;
+    }
+    for (t = 0; t < 4; ++t) bca->indel_types[t] = B2B_INDEL_NULL;
+    for (t = 0; t < 4 && t < n_types; ++t) {
+        bca->indel_types[t] = types[sumq[t]&0x3f];
+        if (bca->maxins)
+            memcpy(&bca->inscns[t * bca->maxins],
+                   &inscns[(sumq[t]&0x3f) * max_ins], bca->maxins);
+    }
+    // update p->aux
+    for (s = n_alt = 0; s < n; ++s) {
+        for (i = 0; i < n_plp[s]; ++i) {
+            bam_pileup1_t *p = plp[s] + i;
+            int x = types[p->aux>>16&0x3f];
+            for (j = 0; j < 4; ++j)
+                if (x == bca->indel_types[j]) break;
+            p->aux = j<<16 | (j == 4? 0 : (p->aux&0xffff));
+            if ((p->aux>>16&0x3f) > 0) ++n_alt;
+            //fprintf(stderr, "X pos=%d read=%d:%d name=%s call=%d type=%d seqQ=%d indelQ=%d\n", pos, s, i, bam_get_qname(p->b), (p->aux>>16)&0x3f, bca->indel_types[(p->aux>>16)&0x3f], (p->aux>>8)&0xff, p->aux&0xff);
+        }
+    }
+
+    return n_alt;
+}
+
+/*
+FIXME: with high number of samples, do we handle IMF correctly?  Is it
+fraction of indels across entire data set, or just fraction for this
+specific sample? Needs to check bca->per_sample_flt (--per-sample-mF) opt.
+ */
+
+/*
+    notes:
+    - n .. number of samples
+    - the routine sets bam_pileup1_t.aux of each read as follows:
+        - 6: unused
+        - 6: the call; index to bcf_callaux_t.indel_types   .. (aux>>16)&0x3f
+        - 8: estimated sequence quality                     .. (aux>>8)&0xff
+        - 8: indel quality                                  .. aux&0xff
+ */
+int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos,
+                      bcf_callaux_t *bca, const char *ref)
+{
+    if (ref == 0 || bca == 0) return -1;
+
+    int i, s, j, k, t, n_types, *types, max_rd_len, left, right, max_ins;
+    int *score, max_ref2;
+    int N, K, l_run, ref_type, n_alt;
+    char *inscns = 0, *ref2, *query, **ref_sample;
+
+    // determine if there is a gap
+    for (s = N = 0; s < n; ++s) {
+        for (i = 0; i < n_plp[s]; ++i)
+            if (plp[s][i].indel != 0) break;
+        if (i < n_plp[s]) break;
+    }
+    if (s == n)
+        // there is no indel at this position.
+        return -1;
+
+    // find out how many types of indels are present
+    types = bcf_cgp_find_types(n, n_plp, plp, pos, bca, ref,
+                               &max_rd_len, &n_types, &ref_type, &N);
+    if (!types)
+        return -1;
+
+
+    // calculate left and right boundary
+    left = pos > bca->indel_win_size ? pos - bca->indel_win_size : 0;
+    right = pos + bca->indel_win_size;
+    if (types[0] < 0) right -= types[0];
+
+    // in case the alignments stand out the reference
+    for (i = pos; i < right; ++i)
+        if (ref[i] == 0) break;
+    right = i;
+
+
+    /* The following call fixes a long-existing flaw in the INDEL
+     * calling model: the interference of nearby SNPs. However, it also
+     * reduces the power because sometimes, substitutions caused by
+     * indels are not distinguishable from true mutations. Multiple
+     * sequence realignment helps to increase the power.
+     *
+     * Masks mismatches present in at least 70% of the reads with 'N'.
+     */
+    ref_sample = bcf_cgp_ref_sample(n, n_plp, plp, pos, bca, ref, left, right);
+
+    // The length of the homopolymer run around the current position
+    l_run = bcf_cgp_l_run(ref, pos);
+
+    // construct the consensus sequence (minus indels, which are added later)
+    max_ins = types[n_types - 1];   // max_ins is at least 0
+    if (max_ins > 0) {
+        inscns = bcf_cgp_calc_cons(n, n_plp, plp, pos,
+                                   types, n_types, max_ins, s);
+        if (!inscns)
+            return -1;
+    }
+
+    // compute the likelihood given each type of indel for each read
+    max_ref2 = right - left + 2 + 2 * (max_ins > -types[0]? max_ins : -types[0]);
+    ref2  = (char*) calloc(max_ref2, 1);
+    query = (char*) calloc(right - left + max_rd_len + max_ins + 2, 1);
+    score = (int*) calloc(N * n_types, sizeof(int));
+    bca->indelreg = 0;
+    double nqual_over_60 = bca->nqual / 60.0;
+
+    for (t = 0; t < n_types; ++t) {
+        int l, ir;
+
+        // compute indelreg
+        if (types[t] == 0)
+            ir = 0;
+        else if (types[t] > 0)
+            ir = est_indelreg(pos, ref, types[t], &inscns[t*max_ins]);
+        else
+            ir = est_indelreg(pos, ref, -types[t], 0);
+
+        if (ir > bca->indelreg)
+            bca->indelreg = ir;
+
+        // Identify max deletion length
+        int max_deletion = 0;
+        for (s = 0; s < n; ++s) {
+            for (i = 0; i < n_plp[s]; ++i, ++K) {
+                bam_pileup1_t *p = plp[s] + i;
+                if (max_deletion < -p->indel)
+                    max_deletion = -p->indel;
+            }
+        }
+
+        // Realignment score, computed via BAQ
+        for (s = K = 0; s < n; ++s) {
+            // Construct ref2 from ref_sample, inscns and indels.
+            // This is now the true sample consensus (possibly prepended
+            // and appended with reference if sample data doesn't span
+            // the full length).
+            for (k = 0, j = left; j <= pos; ++j)
+                ref2[k++] = seq_nt16_int[(int)ref_sample[s][j-left]];
+
+            if (types[t] <= 0)
+                j += -types[t];
+            else
+                for (l = 0; l < types[t]; ++l)
+                    ref2[k++] = inscns[t*max_ins + l];
+
+            for (; j < right && ref[j]; ++j)
+                ref2[k++] = seq_nt16_int[(int)ref_sample[s][j-left]];
+            for (; k < max_ref2; ++k)
+                ref2[k] = 4;
+
+            if (right > j)
+                right = j;
+
+            // align each read to ref2
+            for (i = 0; i < n_plp[s]; ++i, ++K) {
+                bam_pileup1_t *p = plp[s] + i;
+
+                // Some basic ref vs alt stats.
+                int imq = p->b->core.qual > 59 ? 59 : p->b->core.qual;
+                imq *= nqual_over_60;
+
+                int sc_len, slen, epos, sc_end;
+
+                // Only need to gather stats on one type, as it's
+                // identical calculation for all the subsequent ones
+                // and we're sharing the same stats array
+                if (t == 0) {
+                    // Gather stats for INFO field to aid filtering.
+                    // mq and sc_len not very helpful for filtering, but could
+                    // help in assigning a better QUAL value.
+                    //
+                    // Pos is slightly useful.
+                    // Base qual can be useful, but need qual prior to BAQ?
+                    // May need to cache orig quals in aux tag so we can fetch
+                    // them even after mpileup step.
+                    get_pos(bca, p, &sc_len, &slen, &epos, &sc_end);
+
+                    assert(imq >= 0 && imq < bca->nqual);
+                    assert(epos >= 0 && epos < bca->npos);
+                    assert(sc_len >= 0 && sc_len < 100);
+                    if (p->indel) {
+                        bca->ialt_mq[imq]++;
+                        bca->ialt_scl[sc_len]++;
+                        bca->ialt_pos[epos]++;
+                    } else {
+                        bca->iref_mq[imq]++;
+                        bca->iref_scl[sc_len]++;
+                        bca->iref_pos[epos]++;
+                    }
+                }
+
+                int qbeg, qpos, qend, tbeg, tend, kk;
+                uint8_t *seq = bam_get_seq(p->b);
+                uint32_t *cigar = bam_get_cigar(p->b);
+                if (p->b->core.flag & BAM_FUNMAP) continue;
+
+                // FIXME: the following loop should be better moved outside;
+                // nonetheless, realignment should be much slower anyway.
+                for (kk = 0; kk < p->b->core.n_cigar; ++kk)
+                    if ((cigar[kk]&BAM_CIGAR_MASK) == BAM_CREF_SKIP)
+                        break;
+                if (kk < p->b->core.n_cigar)
+                    continue;
+
+                // determine the start and end of sequences for alignment
+                // FIXME: loops over CIGAR multiple times
+                int left2 = left, right2 = right;
+                if (p->b->core.l_qseq > 1000) {
+                    // long read data needs less context.  It also tends to
+                    // have many more candidate indels to investigate so
+                    // speed here matters more.
+                    if (pos - left >= bca->indel_win_size)
+                        left2 += bca->indel_win_size/2;
+                    if (right-pos >= bca->indel_win_size)
+                        right2 -= bca->indel_win_size/2;
+                }
+
+                int r_start = p->b->core.pos;
+                int r_end = bam_cigar2rlen(p->b->core.n_cigar,
+                                           bam_get_cigar(p->b))
+                            -1 + r_start;
+
+                qbeg = tpos2qpos(&p->b->core, bam_get_cigar(p->b), left2,
+                                 0, &tbeg);
+                qpos = tpos2qpos(&p->b->core, bam_get_cigar(p->b), pos,
+                                     0, &tend) - qbeg;
+                qend = tpos2qpos(&p->b->core, bam_get_cigar(p->b), right2,
+                                 1, &tend);
+
+                if (types[t] < 0) {
+                    int l = -types[t];
+                    tbeg = tbeg - l > left?  tbeg - l : left;
+                }
+
+                // write the query sequence
+                for (l = qbeg; l < qend; ++l)
+                    query[l - qbeg] = seq_nt16_int[bam_seqi(seq, l)];
+
+                // A fudge for now.  Consider checking SAM header for
+                // RG platform field.
+                int long_read = p->b->core.l_qseq > 1000;
+
+                // do realignment; this is the bottleneck
+                if (tend > tbeg) {
+                    if (bcf_cgp_align_score(p, bca, types[t],
+                                            (uint8_t *)ref2 + left2-left,
+                                            (uint8_t *)query,
+                                            r_start, r_end, long_read,
+                                            tbeg, tend, left2, right2,
+                                            qbeg, qend, qpos, max_deletion,
+                                            &score[K*n_types + t]) < 0) {
+                        score[K*n_types + t] = 0xffffff;
+                        return -1;
+                    }
+                } else {
+                    // place holder large cost for reads that cover the
+                    // region entirely within a deletion (thus tend < tbeg).
+                    score[K*n_types + t] = 0xffffff;
+                }
+#if 0
+                for (l = 0; l < tend - tbeg + abs(types[t]); ++l)
+                    fputc("ACGTN"[(int)ref2[tbeg-left+l]], stderr);
+                fputc('\n', stderr);
+                for (l = 0; l < qend - qbeg; ++l)
+                    fputc("ACGTN"[(int)query[l]], stderr);
+                fputc('\n', stderr);
+                fprintf(stderr, "pos=%d type=%d read=%d:%d name=%s "
+                        "qbeg=%d tbeg=%d score=%d\n",
+                        pos, types[t], s, i, bam_get_qname(p->b),
+                        qbeg, tbeg, sc);
+#endif
+            }
+        }
+    }
+
+    // compute indelQ
+    n_alt = bcf_cgp_compute_indelQ(n, n_plp, plp, bca, inscns, l_run, max_ins,
+                                   ref_type, types, n_types, score);
+
+    // free
+    free(ref2);
+    free(query);
+    free(score);
+
+    for (i = 0; i < n; ++i)
+        free(ref_sample[i]);
+
+    free(ref_sample);
+    free(types); free(inscns);
+
+    return n_alt > 0? 0 : -1;
+}
diff --git a/bcftools/bam2bcf_indel.c.pysam.c b/bcftools/bam2bcf_indel.c.pysam.c
new file mode 100644
index 0000000..c2287de
--- /dev/null
+++ b/bcftools/bam2bcf_indel.c.pysam.c
@@ -0,0 +1,949 @@
+#include "bcftools.pysam.h"
+
+/*  bam2bcf_indel.c -- indel caller.
+
+    Copyright (C) 2010, 2011 Broad Institute.
+    Copyright (C) 2012-2014,2016-2017, 2021 Genome Research Ltd.
+
+    Author: Heng Li <lh3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <assert.h>
+#include <ctype.h>
+#include <string.h>
+#include <math.h>
+#include <htslib/hts.h>
+#include <htslib/sam.h>
+#include <htslib/khash_str2int.h>
+#include "bam2bcf.h"
+#include "str_finder.h"
+
+#include <htslib/ksort.h>
+KSORT_INIT_GENERIC(uint32_t)
+
+#define MINUS_CONST 0x10000000
+
+#define MAX_TYPES 64
+
+// Take a reference position tpos and convert to a query position (returned).
+// This uses the CIGAR string plus alignment c->pos to do the mapping.
+//
+// *_tpos is returned as tpos if query overlaps tpos, but for deletions
+// it'll be either the start (is_left) or end (!is_left) ref position.
+static int tpos2qpos(const bam1_core_t *c, const uint32_t *cigar, int32_t tpos, int is_left, int32_t *_tpos)
+{
+    // x = pos in ref, y = pos in query seq
+    int k, x = c->pos, y = 0, last_y = 0;
+    *_tpos = c->pos;
+    for (k = 0; k < c->n_cigar; ++k) {
+        int op = cigar[k] & BAM_CIGAR_MASK;
+        int l = cigar[k] >> BAM_CIGAR_SHIFT;
+        if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) {
+            if (c->pos > tpos) return y;
+            if (x + l > tpos) {
+                *_tpos = tpos;
+                return y + (tpos - x);
+            }
+            x += l; y += l;
+            last_y = y;
+        } else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) y += l;
+        else if (op == BAM_CDEL || op == BAM_CREF_SKIP) {
+            if (x + l > tpos) {
+                *_tpos = is_left? x : x + l;
+                return y;
+            }
+            x += l;
+        }
+    }
+    *_tpos = x;
+    return last_y;
+}
+
+// FIXME: check if the inserted sequence is consistent with the homopolymer run
+// l is the relative gap length and l_run is the length of the homopolymer on the reference
+static inline int est_seqQ(const bcf_callaux_t *bca, int l, int l_run)
+{
+    int q, qh;
+    q = bca->openQ + bca->extQ * (abs(l) - 1);
+    qh = l_run >= 3? (int)(bca->tandemQ * (double)abs(l) / l_run + .499) : 1000;
+    return q < qh? q : qh;
+}
+
+static inline int est_indelreg(int pos, const char *ref, int l, char *ins4)
+{
+    int i, j, max = 0, max_i = pos, score = 0;
+    l = abs(l);
+    for (i = pos + 1, j = 0; ref[i]; ++i, ++j) {
+        if (ins4) score += (toupper(ref[i]) != "ACGTN"[(int)ins4[j%l]])? -10 : 1;
+        else score += (toupper(ref[i]) != toupper(ref[pos+1+j%l]))? -10 : 1;
+        if (score < 0) break;
+        if (max < score) max = score, max_i = i;
+    }
+    return max_i - pos;
+}
+
+// Identify spft-clip length, position in seq, and clipped seq len
+static inline void get_pos(const bcf_callaux_t *bca, bam_pileup1_t *p,
+                           int *sc_len_r, int *slen_r, int *epos_r, int *end) {
+    bam1_t *b = p->b;
+    int sc_len = 0, sc_dist = -1, at_left = 1;
+    int epos = p->qpos, slen = b->core.l_qseq;
+    int k;
+    uint32_t *cigar = bam_get_cigar(b);
+    *end = -1;
+    for (k = 0; k < b->core.n_cigar; k++) {
+        int op = bam_cigar_op(cigar[k]);
+        if (op == BAM_CSOFT_CLIP) {
+            slen -= bam_cigar_oplen(cigar[k]);
+            if (at_left) {
+                // left end
+                sc_len += bam_cigar_oplen(cigar[k]);
+                epos -= sc_len; // don't count SC in seq pos
+                sc_dist = epos;
+                *end = 0;
+            } else {
+                // right end
+                int srlen = bam_cigar_oplen(cigar[k]);
+                int rd = b->core.l_qseq - srlen - p->qpos;
+                if (sc_dist < 0 || sc_dist > rd) {
+                    // closer to right end than left
+                    // FIXME: compensate for indel length too?
+                    sc_dist = rd;
+                    sc_len = srlen;
+                    *end = 1;
+                }
+            }
+        } else if (op != BAM_CHARD_CLIP) {
+            at_left = 0;
+        }
+    }
+
+    if (p->indel > 0 && slen - (epos+p->indel) < epos)
+        epos += p->indel-1; // end of insertion, if near end of seq
+
+    // slen is now length of sequence minus soft-clips and
+    // epos is position of indel in seq minus left-clip.
+    *epos_r = (double)epos / (slen+1) * bca->npos;
+
+    if (sc_len) {
+        // scale importance of clip by distance to closest end
+        *sc_len_r = 15.0*sc_len / (sc_dist+1);
+        if (*sc_len_r > 99) *sc_len_r = 99;
+    } else {
+        *sc_len_r = 0;
+    }
+
+    *slen_r = slen;
+}
+
+// Part of bcf_call_gap_prep.
+//
+// Scans the pileup to identify all the different sizes of indels
+// present.
+//
+// Returns types and fills out n_types_r,  max_rd_len_r and ref_type_r,
+//         or NULL on error.
+static int *bcf_cgp_find_types(int n, int *n_plp, bam_pileup1_t **plp,
+                               int pos, bcf_callaux_t *bca, const char *ref,
+                               int *max_rd_len_r, int *n_types_r,
+                               int *ref_type_r, int *N_r) {
+    int i, j, t, s, N, m, max_rd_len, n_types;
+    int n_alt = 0, n_tot = 0, indel_support_ok = 0;
+    uint32_t *aux;
+    int *types;
+
+    // N is the total number of reads
+    for (s = N = 0; s < n; ++s)
+        N += n_plp[s];
+
+    bca->max_support = bca->max_frac = 0;
+    aux = (uint32_t*) calloc(N + 1, 4);
+    if (!aux)
+        return NULL;
+
+    m = max_rd_len = 0;
+    aux[m++] = MINUS_CONST; // zero indel is always a type (REF)
+
+    // Fill out aux[] array with all the non-zero indel sizes.
+    // Also tally number with indels (n_alt) and total (n_tot).
+    for (s = 0; s < n; ++s) {
+        int na = 0, nt = 0;
+        for (i = 0; i < n_plp[s]; ++i) {
+            const bam_pileup1_t *p = plp[s] + i;
+            ++nt;
+            if (p->indel != 0) {
+                ++na;
+                aux[m++] = MINUS_CONST + p->indel;
+            }
+
+            // FIXME: cache me in pileup struct.
+            j = bam_cigar2qlen(p->b->core.n_cigar, bam_get_cigar(p->b));
+            if (j > max_rd_len) max_rd_len = j;
+        }
+        double frac = (double)na/nt;
+        if ( !indel_support_ok && na >= bca->min_support
+             && frac >= bca->min_frac )
+            indel_support_ok = 1;
+        if ( na > bca->max_support && frac > 0 )
+            bca->max_support = na, bca->max_frac = frac;
+
+        n_alt += na;
+        n_tot += nt;
+    }
+
+    // Sort aux[] and dedup
+    ks_introsort(uint32_t, m, aux);
+    for (i = 1, n_types = 1; i < m; ++i)
+        if (aux[i] != aux[i-1]) ++n_types;
+
+    // Taking totals makes it hard to call rare indels (IMF filter)
+    if ( !bca->per_sample_flt )
+        indel_support_ok = ( (double)n_alt / n_tot < bca->min_frac
+                             || n_alt < bca->min_support )
+            ? 0 : 1;
+    if ( n_types == 1 || !indel_support_ok ) { // then skip
+        free(aux);
+        return NULL;
+    }
+
+    // Bail out if we have far too many types of indel
+    if (n_types >= MAX_TYPES) {
+        free(aux);
+        // TODO revisit how/whether to control printing this warning
+        if (hts_verbose >= 2)
+            fprintf(bcftools_stderr, "[%s] excessive INDEL alleles at position %d. "
+                    "Skip the position.\n", __func__, pos + 1);
+        return NULL;
+    }
+
+    // To prevent long stretches of N's to be mistaken for indels
+    // (sometimes thousands of bases), check the number of N's in the
+    // sequence and skip places where half or more reference bases are Ns.
+    int nN=0, i_end = pos + (2*bca->indel_win_size < max_rd_len
+                            ?2*bca->indel_win_size : max_rd_len);
+    for (i=pos; i<i_end && ref[i]; i++)
+        nN += ref[i] == 'N';
+    if ( nN*2>(i-pos) ) {
+        free(aux);
+        return NULL;
+    }
+
+    // Finally fill out the types[] array detailing the size of insertion
+    // or deletion.
+    types = (int*)calloc(n_types, sizeof(int));
+    if (!types) {
+        free(aux);
+        return NULL;
+    }
+    t = 0;
+    types[t++] = aux[0] - MINUS_CONST;
+    for (i = 1; i < m; ++i)
+        if (aux[i] != aux[i-1])
+            types[t++] = aux[i] - MINUS_CONST;
+    free(aux);
+
+    // Find reference type; types[?] == 0)
+    for (t = 0; t < n_types; ++t)
+        if (types[t] == 0) break;
+
+    *ref_type_r   = t;
+    *n_types_r    = n_types;
+    *max_rd_len_r = max_rd_len;
+    *N_r          = N;
+
+    return types;
+}
+
+// Part of bcf_call_gap_prep.
+//
+// Construct per-sample consensus.
+//
+// Returns an array of consensus seqs,
+//         or NULL on failure.
+static char **bcf_cgp_ref_sample(int n, int *n_plp, bam_pileup1_t **plp,
+                                 int pos, bcf_callaux_t *bca, const char *ref,
+                                 int left, int right) {
+    int i, k, s, L = right - left + 1, max_i, max2_i;
+    char **ref_sample; // returned
+    uint32_t *cns = NULL, max, max2;
+    char *ref0 = NULL, *r;
+    ref_sample = (char**) calloc(n, sizeof(char*));
+    cns = (uint32_t*) calloc(L, 4);
+    ref0 = (char*) calloc(L, 1);
+    if (!ref_sample || !cns || !ref0) {
+        n = 0;
+        goto err;
+    }
+
+    // Convert ref ASCII to 0-15.
+    for (i = 0; i < right - left; ++i)
+        ref0[i] = seq_nt16_table[(int)ref[i+left]];
+
+    // NB: one consensus per sample 'n', not per indel type.
+    // FIXME: consider fixing this.  We should compute alignments vs
+    // types, not vs samples?  Or types/sample combined?
+    for (s = 0; s < n; ++s) {
+        r = ref_sample[s] = (char*) calloc(L, 1);
+        if (!r) {
+            n = s-1;
+            goto err;
+        }
+
+        memset(cns, 0, sizeof(int) * L);
+
+        // collect ref and non-ref counts in cns
+        for (i = 0; i < n_plp[s]; ++i) {
+            bam_pileup1_t *p = plp[s] + i;
+            bam1_t *b = p->b;
+            uint32_t *cigar = bam_get_cigar(b);
+            uint8_t *seq = bam_get_seq(b);
+            int x = b->core.pos, y = 0;
+
+            // TODO: pileup exposes pileup_ind, but we also need e.g.
+            // pileup_len to know how much of the current CIGAR op-len
+            // we've used (or have remaining).  If we had that, we
+            // could start at p->qpos without having to scan through
+            // the entire CIGAR string until we find it.
+            //
+            // Without it about all we could do is have a side channel
+            // to cache the last known coords.  Messy, so punt for now.
+            // This is no longer the bottle neck until we get to 1000s of
+            // CIGAR ops.
+
+            for (k = 0; k < b->core.n_cigar; ++k) {
+                int op = cigar[k]&0xf;
+                int j, l = cigar[k]>>4;
+                if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) {
+                    if (x + l >= left) {
+                        j = left - x > 0 ? left - x : 0;
+                        int j_end = right - x < l ? right - x : l;
+                        for (; j < j_end; j++)
+                            // Append to cns.  Note this is ref coords,
+                            // so insertions aren't in cns and deletions
+                            // will have lower coverage.
+
+                            // FIXME: want true consensus (with ins) per
+                            // type, so we can independently compare each
+                            // seq to each consensus and see which it
+                            // matches best, so we get proper GT analysis.
+                            cns[x+j-left] +=
+                                (bam_seqi(seq, y+j) == ref0[x+j-left])
+                                ? 1        // REF
+                                : (1<<16); // ALT
+                    }
+                    x += l; y += l;
+                } else if (op == BAM_CDEL || op == BAM_CREF_SKIP) {
+                    x += l;
+                } else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) {
+                    y += l;
+                }
+
+                if (x > right)
+                    break;
+            }
+        }
+
+        // Determine a sample specific reference.
+        for (i = 0; i < right - left; ++i)
+            r[i] = ref0[i];
+
+        // Find deepest and 2nd deepest ALT region (max & max2).
+        max = max2 = 0; max_i = max2_i = -1;
+        for (i = 0; i < right - left; ++i) {
+            if (cns[i]>>16 >= max>>16)
+                max2 = max, max2_i = max_i, max = cns[i], max_i = i;
+            else if (cns[i]>>16 >= max2>>16)
+                max2 = cns[i], max2_i = i;
+        }
+
+        // Masks mismatches present in at least 70% of the reads with 'N'.
+        // This code is nREF/(nREF+n_ALT) >= 70% for deepest region.
+        // The effect is that at least 30% of bases differing to REF will
+        // use "N" in consensus, so we don't penalise ALT or REF when
+        // aligning against it.  (A poor man IUPAC code)
+        //
+        // Why is it only done in two loci at most?
+        if ((double)(max&0xffff) / ((max&0xffff) + (max>>16)) >= 0.7)
+            max_i = -1;
+        if ((double)(max2&0xffff) / ((max2&0xffff) + (max2>>16)) >= 0.7)
+            max2_i = -1;
+        if (max_i >= 0) r[max_i] = 15;
+        if (max2_i >= 0) r[max2_i] = 15;
+
+        //for (i = 0; i < right - left; ++i)
+        //    fputc("=ACMGRSVTWYHKDBN"[(int)r[i]], bcftools_stderr);
+        //fputc('\n', bcftools_stderr);
+    }
+
+    free(ref0);
+    free(cns);
+
+    return ref_sample;
+
+ err:
+    free(ref0);
+    free(cns);
+    if (ref_sample) {
+        for (s = 0; s < n; s++)
+            free(ref_sample[s]);
+        free(ref_sample);
+    }
+
+    return NULL;
+}
+
+// The length of the homopolymer run around the current position
+static int bcf_cgp_l_run(const char *ref, int pos) {
+    int i, l_run;
+
+    int c = seq_nt16_table[(int)ref[pos + 1]];
+    if (c == 15) {
+        l_run = 1;
+    } else {
+        for (i = pos + 2; ref[i]; ++i)
+            if (seq_nt16_table[(int)ref[i]] != c) break;
+        l_run = i;
+        for (i = pos; i >= 0; --i)
+            if (seq_nt16_table[(int)ref[i]] != c) break;
+        l_run -= i + 1;
+    }
+
+    return l_run;
+}
+
+
+// Compute the consensus for this sample 's', minus indels which
+// get added later.
+static char *bcf_cgp_calc_cons(int n, int *n_plp, bam_pileup1_t **plp,
+                               int pos, int *types, int n_types,
+                               int max_ins, int s) {
+    int i, j, t, k;
+    int *inscns_aux = (int*)calloc(5 * n_types * max_ins, sizeof(int));
+    if (!inscns_aux)
+        return NULL;
+
+    // Count the number of occurrences of each base at each position for
+    // each type of insertion.
+    for (t = 0; t < n_types; ++t) {
+        if (types[t] > 0) {
+            for (s = 0; s < n; ++s) {
+                for (i = 0; i < n_plp[s]; ++i) {
+                    bam_pileup1_t *p = plp[s] + i;
+                    if (p->indel == types[t]) {
+                        uint8_t *seq = bam_get_seq(p->b);
+                        for (k = 1; k <= p->indel; ++k) {
+                            int c = seq_nt16_int[bam_seqi(seq, p->qpos + k)];
+                            assert(c<5);
+                            ++inscns_aux[(t*max_ins+(k-1))*5 + c];
+                        }
+                    }
+                }
+            }
+        }
+    }
+
+    // Use the majority rule to construct the consensus
+    char *inscns = (char *)calloc(n_types * max_ins, 1);
+    for (t = 0; t < n_types; ++t) {
+        for (j = 0; j < types[t]; ++j) {
+            int max = 0, max_k = -1, *ia = &inscns_aux[(t*max_ins+j)*5];
+            for (k = 0; k < 5; ++k)
+                if (ia[k] > max)
+                    max = ia[k], max_k = k;
+            inscns[t*max_ins + j] = max ? max_k : 4;
+            if (max_k == 4) {
+                // discard insertions which contain N's
+                types[t] = 0;
+                break;
+            }
+        }
+    }
+    free(inscns_aux);
+
+    return inscns;
+}
+
+#ifndef MIN
+#  define MIN(a,b) ((a)<(b)?(a):(b))
+#endif
+
+// Part of bcf_call_gap_prep.
+//
+// Realign using BAQ to get an alignment score of a single read vs
+// a haplotype consensus.
+//
+// Fills out score
+// Returns 0 on success,
+//        <0 on error
+static int bcf_cgp_align_score(bam_pileup1_t *p, bcf_callaux_t *bca,
+                               int type, uint8_t *ref2, uint8_t *query,
+                               int r_start, int r_end, int long_read,
+                               int tbeg, int tend,
+                               int left, int right,
+                               int qbeg, int qend,
+                               int qpos, int max_deletion,
+                               int *score) {
+    // Illumina
+    probaln_par_t apf = { 1e-4, 1e-2, 10 };
+
+    // Parameters that work better on PacBio CCS 15k.
+    // We should consider querying the header and RG PU field.
+    // See also htslib/realn.c:sam_prob_realn()
+    if (long_read) {
+        apf.d = 1e-3;
+        apf.e = 1e-1;
+    }
+
+    type = abs(type);
+    apf.bw = type + 3;
+    int l, sc;
+    const uint8_t *qual = bam_get_qual(p->b), *bq;
+    uint8_t *qq;
+
+    // Get segment of quality, either ZQ tag or if absent QUAL.
+    if (!(qq = (uint8_t*) calloc(qend - qbeg, 1)))
+        return -1;
+    bq = (uint8_t*)bam_aux_get(p->b, "ZQ");
+    if (bq) ++bq; // skip type
+    for (l = qbeg; l < qend; ++l) {
+        int qval = bq? qual[l] + (bq[l] - 64) : qual[l];
+        if (qval > 30)
+            qval = 30;
+        if (qval < 7)
+            qval = 7;
+        qq[l - qbeg] = qval;
+    }
+
+    // The bottom 8 bits are length-normalised score while
+    // the top bits are unnormalised.
+    sc = probaln_glocal(ref2 + tbeg - left, tend - tbeg + type,
+                        query, qend - qbeg, qq, &apf, 0, 0);
+    if (sc < 0) {
+        *score = 0xffffff;
+        free(qq);
+        return 0;
+    }
+
+    // used for adjusting indelQ below
+    l = (int)(100. * sc / (qend - qbeg) + .499) * bca->indel_bias;
+    *score = sc<<8 | MIN(255, l);
+
+    rep_ele *reps, *elt, *tmp;
+    uint8_t *seg = ref2 + tbeg - left;
+    int seg_len = tend - tbeg + type;
+
+    // Note: although seg moves (tbeg varies), ref2 is reused many times
+    // so we could factor out some find_STR calls.  However it's not the
+    // bottleneck for now.
+
+    // FIXME: need to make this work on IUPAC.
+    reps = find_STR((char *)seg, seg_len, 0);
+    int iscore = 0;
+
+    // Identify STRs in ref covering the indel up to
+    // (or close to) the end of the sequence.
+    // Those having an indel and right at the sequence
+    // end do not confirm the total length of indel
+    // size.  Specifically a *lack* of indel at the
+    // end, where we know indels occur in other
+    // sequences, is a possible reference bias.
+    //
+    // This is emphasised further if the sequence ends with
+    // soft clipping.
+    DL_FOREACH_SAFE(reps, elt, tmp) {
+        if (elt->start <= qpos && elt->end >= qpos) {
+            iscore += (elt->end-elt->start) / elt->rep_len;  // c
+            if (elt->start+tbeg <= r_start ||
+                elt->end+tbeg   >= r_end)
+                iscore += 2*(elt->end-elt->start);
+       }
+
+        DL_DELETE(reps, elt);
+        free(elt);
+    }
+
+    // Apply STR score to existing indelQ
+    l  =  (*score&0xff)*.8 + iscore*2;
+    *score = (*score & ~0xff) | MIN(255, l);
+
+    free(qq);
+
+    return 0;
+}
+
+// Part of bcf_call_gap_prep.
+//
+// Returns n_alt on success
+//         -1 on failure
+static int bcf_cgp_compute_indelQ(int n, int *n_plp, bam_pileup1_t **plp,
+                                  bcf_callaux_t *bca, char *inscns,
+                                  int l_run, int max_ins,
+                                  int ref_type, int *types, int n_types,
+                                  int *score) {
+    // FIXME: n_types has a maximum; no need to alloc - use a #define?
+    int sc[MAX_TYPES], sumq[MAX_TYPES], s, i, j, t, K, n_alt, tmp;
+    memset(sumq, 0, n_types * sizeof(int));
+    for (s = K = 0; s < n; ++s) {
+        for (i = 0; i < n_plp[s]; ++i, ++K) {
+            bam_pileup1_t *p = plp[s] + i;
+            int *sct = &score[K*n_types], seqQ, indelQ;
+            for (t = 0; t < n_types; ++t) sc[t] = sct[t]<<6 | t;
+            for (t = 1; t < n_types; ++t) // insertion sort
+                for (j = t; j > 0 && sc[j] < sc[j-1]; --j)
+                    tmp = sc[j], sc[j] = sc[j-1], sc[j-1] = tmp;
+
+            /* errmod_cal() assumes that if the call is wrong, the
+             * likelihoods of other events are equal. This is about
+             * right for substitutions, but is not desired for
+             * indels. To reuse errmod_cal(), I have to make
+             * compromise for multi-allelic indels.
+             */
+            if ((sc[0]&0x3f) == ref_type) {
+                indelQ = (sc[1]>>14) - (sc[0]>>14);
+                seqQ = est_seqQ(bca, types[sc[1]&0x3f], l_run);
+            } else {
+                for (t = 0; t < n_types; ++t) // look for the reference type
+                    if ((sc[t]&0x3f) == ref_type) break;
+                indelQ = (sc[t]>>14) - (sc[0]>>14);
+                seqQ = est_seqQ(bca, types[sc[0]&0x3f], l_run);
+            }
+            tmp = sc[0]>>6 & 0xff;
+            // reduce indelQ
+            indelQ = tmp > 111? 0 : (int)((1. - tmp/111.) * indelQ + .499);
+
+            // Doesn't really help accuracy, but permits -h to take
+            // affect still.
+            if (indelQ > seqQ) indelQ = seqQ;
+            if (indelQ > 255) indelQ = 255;
+            if (seqQ > 255) seqQ = 255;
+            p->aux = (sc[0]&0x3f)<<16 | seqQ<<8 | indelQ; // use 22 bits in total
+            sumq[sc[0]&0x3f] += indelQ < seqQ? indelQ : seqQ;
+            //              fprintf(bcftools_stderr, "pos=%d read=%d:%d name=%s call=%d indelQ=%d seqQ=%d\n", pos, s, i, bam1_qname(p->b), types[sc[0]&0x3f], indelQ, seqQ);
+        }
+    }
+    // determine bca->indel_types[] and bca->inscns
+    bca->maxins = max_ins;
+    bca->inscns = (char*) realloc(bca->inscns, bca->maxins * 4);
+    if (bca->maxins && !bca->inscns)
+        return -1;
+    for (t = 0; t < n_types; ++t)
+        sumq[t] = sumq[t]<<6 | t;
+    for (t = 1; t < n_types; ++t) // insertion sort
+        for (j = t; j > 0 && sumq[j] > sumq[j-1]; --j)
+            tmp = sumq[j], sumq[j] = sumq[j-1], sumq[j-1] = tmp;
+    for (t = 0; t < n_types; ++t) // look for the reference type
+        if ((sumq[t]&0x3f) == ref_type) break;
+    if (t) { // then move the reference type to the first
+        tmp = sumq[t];
+        for (; t > 0; --t) sumq[t] = sumq[t-1];
+        sumq[0] = tmp;
+    }
+    for (t = 0; t < 4; ++t) bca->indel_types[t] = B2B_INDEL_NULL;
+    for (t = 0; t < 4 && t < n_types; ++t) {
+        bca->indel_types[t] = types[sumq[t]&0x3f];
+        if (bca->maxins)
+            memcpy(&bca->inscns[t * bca->maxins],
+                   &inscns[(sumq[t]&0x3f) * max_ins], bca->maxins);
+    }
+    // update p->aux
+    for (s = n_alt = 0; s < n; ++s) {
+        for (i = 0; i < n_plp[s]; ++i) {
+            bam_pileup1_t *p = plp[s] + i;
+            int x = types[p->aux>>16&0x3f];
+            for (j = 0; j < 4; ++j)
+                if (x == bca->indel_types[j]) break;
+            p->aux = j<<16 | (j == 4? 0 : (p->aux&0xffff));
+            if ((p->aux>>16&0x3f) > 0) ++n_alt;
+            //fprintf(bcftools_stderr, "X pos=%d read=%d:%d name=%s call=%d type=%d seqQ=%d indelQ=%d\n", pos, s, i, bam_get_qname(p->b), (p->aux>>16)&0x3f, bca->indel_types[(p->aux>>16)&0x3f], (p->aux>>8)&0xff, p->aux&0xff);
+        }
+    }
+
+    return n_alt;
+}
+
+/*
+FIXME: with high number of samples, do we handle IMF correctly?  Is it
+fraction of indels across entire data set, or just fraction for this
+specific sample? Needs to check bca->per_sample_flt (--per-sample-mF) opt.
+ */
+
+/*
+    notes:
+    - n .. number of samples
+    - the routine sets bam_pileup1_t.aux of each read as follows:
+        - 6: unused
+        - 6: the call; index to bcf_callaux_t.indel_types   .. (aux>>16)&0x3f
+        - 8: estimated sequence quality                     .. (aux>>8)&0xff
+        - 8: indel quality                                  .. aux&0xff
+ */
+int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos,
+                      bcf_callaux_t *bca, const char *ref)
+{
+    if (ref == 0 || bca == 0) return -1;
+
+    int i, s, j, k, t, n_types, *types, max_rd_len, left, right, max_ins;
+    int *score, max_ref2;
+    int N, K, l_run, ref_type, n_alt;
+    char *inscns = 0, *ref2, *query, **ref_sample;
+
+    // determine if there is a gap
+    for (s = N = 0; s < n; ++s) {
+        for (i = 0; i < n_plp[s]; ++i)
+            if (plp[s][i].indel != 0) break;
+        if (i < n_plp[s]) break;
+    }
+    if (s == n)
+        // there is no indel at this position.
+        return -1;
+
+    // find out how many types of indels are present
+    types = bcf_cgp_find_types(n, n_plp, plp, pos, bca, ref,
+                               &max_rd_len, &n_types, &ref_type, &N);
+    if (!types)
+        return -1;
+
+
+    // calculate left and right boundary
+    left = pos > bca->indel_win_size ? pos - bca->indel_win_size : 0;
+    right = pos + bca->indel_win_size;
+    if (types[0] < 0) right -= types[0];
+
+    // in case the alignments stand out the reference
+    for (i = pos; i < right; ++i)
+        if (ref[i] == 0) break;
+    right = i;
+
+
+    /* The following call fixes a long-existing flaw in the INDEL
+     * calling model: the interference of nearby SNPs. However, it also
+     * reduces the power because sometimes, substitutions caused by
+     * indels are not distinguishable from true mutations. Multiple
+     * sequence realignment helps to increase the power.
+     *
+     * Masks mismatches present in at least 70% of the reads with 'N'.
+     */
+    ref_sample = bcf_cgp_ref_sample(n, n_plp, plp, pos, bca, ref, left, right);
+
+    // The length of the homopolymer run around the current position
+    l_run = bcf_cgp_l_run(ref, pos);
+
+    // construct the consensus sequence (minus indels, which are added later)
+    max_ins = types[n_types - 1];   // max_ins is at least 0
+    if (max_ins > 0) {
+        inscns = bcf_cgp_calc_cons(n, n_plp, plp, pos,
+                                   types, n_types, max_ins, s);
+        if (!inscns)
+            return -1;
+    }
+
+    // compute the likelihood given each type of indel for each read
+    max_ref2 = right - left + 2 + 2 * (max_ins > -types[0]? max_ins : -types[0]);
+    ref2  = (char*) calloc(max_ref2, 1);
+    query = (char*) calloc(right - left + max_rd_len + max_ins + 2, 1);
+    score = (int*) calloc(N * n_types, sizeof(int));
+    bca->indelreg = 0;
+    double nqual_over_60 = bca->nqual / 60.0;
+
+    for (t = 0; t < n_types; ++t) {
+        int l, ir;
+
+        // compute indelreg
+        if (types[t] == 0)
+            ir = 0;
+        else if (types[t] > 0)
+            ir = est_indelreg(pos, ref, types[t], &inscns[t*max_ins]);
+        else
+            ir = est_indelreg(pos, ref, -types[t], 0);
+
+        if (ir > bca->indelreg)
+            bca->indelreg = ir;
+
+        // Identify max deletion length
+        int max_deletion = 0;
+        for (s = 0; s < n; ++s) {
+            for (i = 0; i < n_plp[s]; ++i, ++K) {
+                bam_pileup1_t *p = plp[s] + i;
+                if (max_deletion < -p->indel)
+                    max_deletion = -p->indel;
+            }
+        }
+
+        // Realignment score, computed via BAQ
+        for (s = K = 0; s < n; ++s) {
+            // Construct ref2 from ref_sample, inscns and indels.
+            // This is now the true sample consensus (possibly prepended
+            // and appended with reference if sample data doesn't span
+            // the full length).
+            for (k = 0, j = left; j <= pos; ++j)
+                ref2[k++] = seq_nt16_int[(int)ref_sample[s][j-left]];
+
+            if (types[t] <= 0)
+                j += -types[t];
+            else
+                for (l = 0; l < types[t]; ++l)
+                    ref2[k++] = inscns[t*max_ins + l];
+
+            for (; j < right && ref[j]; ++j)
+                ref2[k++] = seq_nt16_int[(int)ref_sample[s][j-left]];
+            for (; k < max_ref2; ++k)
+                ref2[k] = 4;
+
+            if (right > j)
+                right = j;
+
+            // align each read to ref2
+            for (i = 0; i < n_plp[s]; ++i, ++K) {
+                bam_pileup1_t *p = plp[s] + i;
+
+                // Some basic ref vs alt stats.
+                int imq = p->b->core.qual > 59 ? 59 : p->b->core.qual;
+                imq *= nqual_over_60;
+
+                int sc_len, slen, epos, sc_end;
+
+                // Only need to gather stats on one type, as it's
+                // identical calculation for all the subsequent ones
+                // and we're sharing the same stats array
+                if (t == 0) {
+                    // Gather stats for INFO field to aid filtering.
+                    // mq and sc_len not very helpful for filtering, but could
+                    // help in assigning a better QUAL value.
+                    //
+                    // Pos is slightly useful.
+                    // Base qual can be useful, but need qual prior to BAQ?
+                    // May need to cache orig quals in aux tag so we can fetch
+                    // them even after mpileup step.
+                    get_pos(bca, p, &sc_len, &slen, &epos, &sc_end);
+
+                    assert(imq >= 0 && imq < bca->nqual);
+                    assert(epos >= 0 && epos < bca->npos);
+                    assert(sc_len >= 0 && sc_len < 100);
+                    if (p->indel) {
+                        bca->ialt_mq[imq]++;
+                        bca->ialt_scl[sc_len]++;
+                        bca->ialt_pos[epos]++;
+                    } else {
+                        bca->iref_mq[imq]++;
+                        bca->iref_scl[sc_len]++;
+                        bca->iref_pos[epos]++;
+                    }
+                }
+
+                int qbeg, qpos, qend, tbeg, tend, kk;
+                uint8_t *seq = bam_get_seq(p->b);
+                uint32_t *cigar = bam_get_cigar(p->b);
+                if (p->b->core.flag & BAM_FUNMAP) continue;
+
+                // FIXME: the following loop should be better moved outside;
+                // nonetheless, realignment should be much slower anyway.
+                for (kk = 0; kk < p->b->core.n_cigar; ++kk)
+                    if ((cigar[kk]&BAM_CIGAR_MASK) == BAM_CREF_SKIP)
+                        break;
+                if (kk < p->b->core.n_cigar)
+                    continue;
+
+                // determine the start and end of sequences for alignment
+                // FIXME: loops over CIGAR multiple times
+                int left2 = left, right2 = right;
+                if (p->b->core.l_qseq > 1000) {
+                    // long read data needs less context.  It also tends to
+                    // have many more candidate indels to investigate so
+                    // speed here matters more.
+                    if (pos - left >= bca->indel_win_size)
+                        left2 += bca->indel_win_size/2;
+                    if (right-pos >= bca->indel_win_size)
+                        right2 -= bca->indel_win_size/2;
+                }
+
+                int r_start = p->b->core.pos;
+                int r_end = bam_cigar2rlen(p->b->core.n_cigar,
+                                           bam_get_cigar(p->b))
+                            -1 + r_start;
+
+                qbeg = tpos2qpos(&p->b->core, bam_get_cigar(p->b), left2,
+                                 0, &tbeg);
+                qpos = tpos2qpos(&p->b->core, bam_get_cigar(p->b), pos,
+                                     0, &tend) - qbeg;
+                qend = tpos2qpos(&p->b->core, bam_get_cigar(p->b), right2,
+                                 1, &tend);
+
+                if (types[t] < 0) {
+                    int l = -types[t];
+                    tbeg = tbeg - l > left?  tbeg - l : left;
+                }
+
+                // write the query sequence
+                for (l = qbeg; l < qend; ++l)
+                    query[l - qbeg] = seq_nt16_int[bam_seqi(seq, l)];
+
+                // A fudge for now.  Consider checking SAM header for
+                // RG platform field.
+                int long_read = p->b->core.l_qseq > 1000;
+
+                // do realignment; this is the bottleneck
+                if (tend > tbeg) {
+                    if (bcf_cgp_align_score(p, bca, types[t],
+                                            (uint8_t *)ref2 + left2-left,
+                                            (uint8_t *)query,
+                                            r_start, r_end, long_read,
+                                            tbeg, tend, left2, right2,
+                                            qbeg, qend, qpos, max_deletion,
+                                            &score[K*n_types + t]) < 0) {
+                        score[K*n_types + t] = 0xffffff;
+                        return -1;
+                    }
+                } else {
+                    // place holder large cost for reads that cover the
+                    // region entirely within a deletion (thus tend < tbeg).
+                    score[K*n_types + t] = 0xffffff;
+                }
+#if 0
+                for (l = 0; l < tend - tbeg + abs(types[t]); ++l)
+                    fputc("ACGTN"[(int)ref2[tbeg-left+l]], bcftools_stderr);
+                fputc('\n', bcftools_stderr);
+                for (l = 0; l < qend - qbeg; ++l)
+                    fputc("ACGTN"[(int)query[l]], bcftools_stderr);
+                fputc('\n', bcftools_stderr);
+                fprintf(bcftools_stderr, "pos=%d type=%d read=%d:%d name=%s "
+                        "qbeg=%d tbeg=%d score=%d\n",
+                        pos, types[t], s, i, bam_get_qname(p->b),
+                        qbeg, tbeg, sc);
+#endif
+            }
+        }
+    }
+
+    // compute indelQ
+    n_alt = bcf_cgp_compute_indelQ(n, n_plp, plp, bca, inscns, l_run, max_ins,
+                                   ref_type, types, n_types, score);
+
+    // free
+    free(ref2);
+    free(query);
+    free(score);
+
+    for (i = 0; i < n; ++i)
+        free(ref_sample[i]);
+
+    free(ref_sample);
+    free(types); free(inscns);
+
+    return n_alt > 0? 0 : -1;
+}
diff --git a/bcftools/bam_sample.c b/bcftools/bam_sample.c
new file mode 100644
index 0000000..d8c10b8
--- /dev/null
+++ b/bcftools/bam_sample.c
@@ -0,0 +1,398 @@
+/*  bam_sample.c -- group data by sample.
+
+    Copyright (C) 2010, 2011 Broad Institute.
+    Copyright (C) 2013, 2016-2022 Genome Research Ltd.
+
+    Author: Heng Li <lh3@sanger.ac.uk>, Petr Danecek <pd3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <stdlib.h>
+#include <string.h>
+#include <ctype.h>
+#include <htslib/hts.h>
+#include <htslib/kstring.h>
+#include <htslib/khash_str2int.h>
+#include <khash_str2str.h>
+#include "bam_sample.h"
+#include "bcftools.h"
+
+
+typedef struct
+{
+    char *fname;
+    void *rg2idx;       // hash: read group name to BCF output sample index. Maintained by bsmpl_add_readgroup
+    int default_idx;    // default BCF output sample index, set only when all readgroups are treated as one sample
+}
+file_t;
+
+struct _bam_smpl_t
+{
+    kstring_t tmp;
+    file_t *files;
+    int ignore_rg, nsmpl, nfiles;
+    char **smpl;        // list of BCF output sample names. Maintained by bsmpl_add_readgroup
+    void *sample_list;  // hash: BAM input sample name to BCF output sample name. This is the -s/-S list
+    int sample_logic;   // the -s/-S logic, 1: include, 0: exclude
+    void *rg_list;      // hash: BAM/rg_id to sample name or */rg_id for global ids. This is the -G list
+    int rg_logic;       // the -G logic, 1: include, 0: exclude
+    void *name2idx;     // hash: BCF output sample name to BCF output sample index. Maintained by bsmpl_add_readgroup
+};
+
+bam_smpl_t *bam_smpl_init(void)
+{
+    bam_smpl_t *bsmpl;
+    bsmpl = (bam_smpl_t*) calloc(1, sizeof(bam_smpl_t));
+    bsmpl->name2idx = khash_str2int_init();
+    return bsmpl;
+}
+
+void bam_smpl_destroy(bam_smpl_t *bsmpl)
+{
+    if ( !bsmpl ) return;
+    if ( bsmpl->name2idx ) khash_str2int_destroy_free(bsmpl->name2idx);
+    if ( bsmpl->sample_list ) khash_str2str_destroy_free_all(bsmpl->sample_list);
+    if ( bsmpl->rg_list ) khash_str2str_destroy_free_all(bsmpl->rg_list);
+    int i;
+    for (i=0; i<bsmpl->nfiles; i++)
+    {
+        file_t *file = &bsmpl->files[i];
+        if ( file->rg2idx ) khash_str2int_destroy_free(file->rg2idx);
+        free(file->fname);
+    }
+    free(bsmpl->smpl);
+    free(bsmpl->files);
+    free(bsmpl->tmp.s);
+    free(bsmpl);
+}
+
+void bam_smpl_ignore_readgroups(bam_smpl_t* bsmpl)
+{
+    bsmpl->ignore_rg = 1;
+}
+
+static void bsmpl_add_readgroup(bam_smpl_t *bsmpl, file_t *file, const char *rg_id, const char *smpl_name)
+{
+    int ismpl = -1;
+    if ( smpl_name )
+    {
+        if ( khash_str2int_get(bsmpl->name2idx,smpl_name,&ismpl) < 0 )
+        {
+            // new sample
+            bsmpl->nsmpl++;
+            bsmpl->smpl = (char**) realloc(bsmpl->smpl,sizeof(char*)*bsmpl->nsmpl);
+            bsmpl->smpl[bsmpl->nsmpl-1] = strdup(smpl_name);
+            ismpl = khash_str2int_inc(bsmpl->name2idx,bsmpl->smpl[bsmpl->nsmpl-1]);
+        }
+    }
+    if ( !strcmp("*",rg_id) )
+    {
+        // all read groups in the bam treated as the same sample
+        file->default_idx = ismpl;
+        return;
+    }
+    if ( !file->rg2idx ) file->rg2idx = khash_str2int_init();
+    if ( khash_str2int_has_key(file->rg2idx,rg_id) ) return;    // duplicate @RG:ID
+    khash_str2int_set(file->rg2idx, strdup(rg_id), ismpl);
+}
+static int bsmpl_keep_readgroup(bam_smpl_t *bsmpl, file_t *file, const char *rg_id, const char **smpl_name)
+{
+    char *rg_smpl = khash_str2str_get(bsmpl->rg_list,rg_id);    // unique read group present in one bam only
+    if ( !rg_smpl )
+    {
+        // read group specific to this bam
+        bsmpl->tmp.l = 0;
+        ksprintf(&bsmpl->tmp,"%s\t%s",rg_id,file->fname);
+        rg_smpl = khash_str2str_get(bsmpl->rg_list,bsmpl->tmp.s);
+    }
+    if ( !rg_smpl )
+    {
+        // any read group in this file?
+        bsmpl->tmp.l = 0;
+        ksprintf(&bsmpl->tmp,"*\t%s",file->fname);
+        rg_smpl = khash_str2str_get(bsmpl->rg_list,bsmpl->tmp.s);
+    }
+    if ( !rg_smpl && bsmpl->rg_logic ) return 0;
+    if ( rg_smpl && !bsmpl->rg_logic ) return 0;
+
+    if ( rg_smpl && rg_smpl[0]!='\t' ) *smpl_name = rg_smpl;    // rename the sample
+    return 1;
+}
+
+/*
+    The logic of this function is a bit complicated because we want to work
+    also with broken bams containing read groups that are not listed in the
+    header. The desired behavior is as follows:
+        - when -G is given, read groups which are not listed in the header must
+          be given explicitly using the "?" symbol in -G.
+          Otherwise:
+        - if the bam has no header, all reads in the file are assigned to a
+          single sample named after the file
+        - if there is at least one sample defined in the header, reads with no
+          read group id or with a read group id not listed in the header are
+          assigned to the first sample encountered in the header
+*/
+int bam_smpl_add_bam(bam_smpl_t *bsmpl, char *bam_hdr, const char *fname)
+{
+    bsmpl->nfiles++;
+    bsmpl->files = (file_t*) realloc(bsmpl->files,bsmpl->nfiles*sizeof(file_t));
+    file_t *file = &bsmpl->files[bsmpl->nfiles-1];
+    memset(file,0,sizeof(file_t));
+    file->fname  = strdup(fname);
+    file->default_idx = -1;
+
+    if ( bsmpl->ignore_rg || !bam_hdr )
+    {
+        // The option --ignore-RG is set or there is no BAM header: use the file name as the sample name
+        bsmpl_add_readgroup(bsmpl,file,"*",file->fname);
+        return bsmpl->nfiles-1;
+    }
+
+    void *bam_smpls = khash_str2int_init();
+    int first_smpl = -1, nskipped = 0;
+    const char *p = bam_hdr, *q, *r;
+    while (p != NULL && (q = strstr(p, "@RG")) != 0)
+    {
+        char *eol = strchr(q + 3, '\n');
+        if (q > bam_hdr && *(q - 1) != '\n') { // @RG must be at start of line
+            p = eol;
+            continue;
+        }
+        p = q + 3;
+        if ((q = strstr(p, "\tID:")) != 0) q += 4;
+        if ((r = strstr(p, "\tSM:")) != 0) r += 4;
+        if (r && q)
+        {
+            char *u, *v;
+            int ioq, ior;
+            for (u = (char*)q; *u && *u != '\t' && *u != '\n'; ++u);
+            for (v = (char*)r; *v && *v != '\t' && *v != '\n'; ++v);
+            ioq = *u; ior = *v; *u = *v = '\0';
+
+            // q now points to a null terminated read group id
+            // r points to a null terminated sample name
+            if ( !strcmp("*",q) || !strcmp("?",q) )
+                error("Error: the read group IDs \"*\" and \"?\" have a special meaning in the mpileup code. Please fix the code or the bam: %s\n", fname);
+
+            int accept_rg = 1;
+            if ( bsmpl->sample_list )
+            {
+                // restrict samples based on the -s/-S options
+                char *name = khash_str2str_get(bsmpl->sample_list,r);
+                if ( bsmpl->sample_logic==0 )
+                    accept_rg = name ? 0 : 1;
+                else if ( !name )
+                    accept_rg = 0;
+                else
+                    r = name;
+            }
+            if ( accept_rg && bsmpl->rg_list )
+            {
+                // restrict readgroups based on the -G option, possibly renaming the sample
+                accept_rg = bsmpl_keep_readgroup(bsmpl,file,q,&r);
+            }
+            if ( accept_rg )
+                bsmpl_add_readgroup(bsmpl,file,q,r);
+            else
+            {
+                bsmpl_add_readgroup(bsmpl,file,q,NULL); // ignore this RG but note that it was seen in the header
+                nskipped++;
+            }
+
+            if ( first_smpl<0 )
+                khash_str2int_get(bsmpl->name2idx,r,&first_smpl);
+            if ( !khash_str2int_has_key(bam_smpls,r) )
+                khash_str2int_inc(bam_smpls,strdup(r));
+
+            *u = ioq; *v = ior;
+        }
+        else
+            break;
+        p = eol;
+    }
+    int nsmpls = khash_str2int_size(bam_smpls);
+    khash_str2int_destroy_free(bam_smpls);
+
+    const char *smpl_name = NULL;
+    int accept_null_rg = 1;
+    if ( bsmpl->rg_list && !bsmpl_keep_readgroup(bsmpl,file,"?",&smpl_name) ) accept_null_rg = 0;
+    if ( bsmpl->sample_list && first_smpl==-1 ) accept_null_rg = 0;
+
+    if ( !accept_null_rg && first_smpl==-1 )
+    {
+        // no suitable read group is available in this bam: ignore the whole file.
+        free(file->fname);
+        if ( file->rg2idx ) khash_str2int_destroy_free(file->rg2idx);
+        bsmpl->nfiles--;
+        return -1;
+    }
+    if ( !accept_null_rg ) return bsmpl->nfiles-1;
+    if ( nsmpls==1 && !nskipped )
+    {
+        file->default_idx = first_smpl;
+        return bsmpl->nfiles-1;
+    }
+    if ( !smpl_name ) smpl_name = first_smpl==-1 ? file->fname : bsmpl->smpl[first_smpl];
+
+    bsmpl_add_readgroup(bsmpl,file,"?",smpl_name);
+    return bsmpl->nfiles-1;
+}
+
+const char **bam_smpl_get_samples(bam_smpl_t *bsmpl, int *nsmpl)
+{
+    *nsmpl = bsmpl->nsmpl;
+    return (const char**)bsmpl->smpl;
+}
+
+int bam_smpl_get_sample_id(bam_smpl_t *bsmpl, int bam_id, bam1_t *bam_rec)
+{
+    file_t *file = &bsmpl->files[bam_id];
+    if ( file->default_idx >= 0 ) return file->default_idx;
+
+    char *aux_rg = (char*) bam_aux_get(bam_rec, "RG");
+    aux_rg = aux_rg ? aux_rg+1 : "?";
+
+    int rg_id;
+    if ( khash_str2int_get(file->rg2idx, aux_rg, &rg_id)==0 ) return rg_id;
+    if ( khash_str2int_get(file->rg2idx, "?", &rg_id)==0 ) return rg_id;
+    return -1;
+}
+
+int bam_smpl_add_samples(bam_smpl_t *bsmpl, char *list, int is_file)
+{
+    if ( list[0]!='^' ) bsmpl->sample_logic = 1;
+    else list++;
+
+    int i, nsamples = 0;
+    char **samples = hts_readlist(list, is_file, &nsamples);
+    if ( !samples || !nsamples ) return 0;
+
+    kstring_t ori = {0,0,0};
+    kstring_t ren = {0,0,0};
+
+    bsmpl->sample_list = khash_str2str_init();
+    for (i=0; i<nsamples; i++)
+    {
+        char *ptr = samples[i];
+        ori.l = ren.l = 0;
+        int escaped = 0;
+        while ( *ptr )
+        {
+            if ( *ptr=='\\' && !escaped ) { escaped = 1; ptr++; continue; }
+            if ( isspace(*ptr) && !escaped ) break;
+            kputc(*ptr, &ori);
+            escaped = 0;
+            ptr++;
+        }
+        if ( *ptr )
+        {
+            while ( *ptr && isspace(*ptr) ) ptr++;
+            while ( *ptr )
+            {
+                if ( *ptr=='\\' && !escaped ) { escaped = 1; ptr++; continue; }
+                if ( isspace(*ptr) && !escaped ) break;
+                kputc(*ptr, &ren);
+                escaped = 0;
+                ptr++;
+            }
+        }
+        khash_str2str_set(bsmpl->sample_list,strdup(ori.s),strdup(ren.l?ren.s:ori.s));
+        free(samples[i]);
+    }
+    free(samples);
+    free(ori.s);
+    free(ren.s);
+    return nsamples;
+}
+
+int bam_smpl_add_readgroups(bam_smpl_t *bsmpl, char *list, int is_file)
+{
+    if ( list[0]!='^' ) bsmpl->rg_logic = 1;
+    else list++;
+
+    int i, nrows  = 0;
+    char **rows = hts_readlist(list, is_file, &nrows);
+    if ( !rows || !nrows ) return 0;
+
+    kstring_t fld1 = {0,0,0};
+    kstring_t fld2 = {0,0,0};
+    kstring_t fld3 = {0,0,0};
+
+    bsmpl->rg_list = khash_str2str_init();
+    for (i=0; i<nrows; i++)
+    {
+        char *ptr = rows[i];
+        fld1.l = fld2.l = fld3.l = 0;
+        int escaped = 0;
+        while ( *ptr )
+        {
+            if ( *ptr=='\\' && !escaped ) { escaped = 1; ptr++; continue; }
+            if ( isspace(*ptr) && !escaped ) break;
+            kputc(*ptr, &fld1);
+            escaped = 0;
+            ptr++;
+        }
+        if ( *ptr )
+        {
+            while ( *ptr && isspace(*ptr) ) ptr++;
+            while ( *ptr )
+            {
+                if ( *ptr=='\\' && !escaped ) { escaped = 1; ptr++; continue; }
+                if ( isspace(*ptr) && !escaped ) break;
+                kputc(*ptr, &fld2);
+                escaped = 0;
+                ptr++;
+            }
+        }
+        if ( *ptr )
+        {
+            while ( *ptr && isspace(*ptr) ) ptr++;
+            while ( *ptr )
+            {
+                if ( *ptr=='\\' && !escaped ) { escaped = 1; ptr++; continue; }
+                if ( isspace(*ptr) && !escaped ) break;
+                kputc(*ptr, &fld3);
+                escaped = 0;
+                ptr++;
+            }
+        }
+        if ( fld3.l )
+        {
+            // ID FILE SAMPLE
+            kputc('\t',&fld1);
+            kputs(fld2.s,&fld1);
+            fld2.l = 0;
+            kputs(fld3.s,&fld2);
+        }
+        // fld2.s now contains a new sample name. If NULL, use \t to keep the bam header name
+        char *value = khash_str2str_get(bsmpl->rg_list,fld1.s);
+        if ( !value )
+            khash_str2str_set(bsmpl->rg_list,strdup(fld1.s),strdup(fld2.l?fld2.s:"\t"));
+        else if ( strcmp(value,fld2.l?fld2.s:"\t") )
+            error("Error: The read group \"%s\" was assigned to two different samples: \"%s\" and \"%s\"\n", fld1.s,value,fld2.l?fld2.s:"\t");
+        free(rows[i]);
+    }
+    free(rows);
+    free(fld1.s);
+    free(fld2.s);
+    free(fld3.s);
+    return nrows;
+}
+
+
diff --git a/bcftools/bam_sample.c.pysam.c b/bcftools/bam_sample.c.pysam.c
new file mode 100644
index 0000000..9384470
--- /dev/null
+++ b/bcftools/bam_sample.c.pysam.c
@@ -0,0 +1,400 @@
+#include "bcftools.pysam.h"
+
+/*  bam_sample.c -- group data by sample.
+
+    Copyright (C) 2010, 2011 Broad Institute.
+    Copyright (C) 2013, 2016-2022 Genome Research Ltd.
+
+    Author: Heng Li <lh3@sanger.ac.uk>, Petr Danecek <pd3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <stdlib.h>
+#include <string.h>
+#include <ctype.h>
+#include <htslib/hts.h>
+#include <htslib/kstring.h>
+#include <htslib/khash_str2int.h>
+#include <khash_str2str.h>
+#include "bam_sample.h"
+#include "bcftools.h"
+
+
+typedef struct
+{
+    char *fname;
+    void *rg2idx;       // hash: read group name to BCF output sample index. Maintained by bsmpl_add_readgroup
+    int default_idx;    // default BCF output sample index, set only when all readgroups are treated as one sample
+}
+file_t;
+
+struct _bam_smpl_t
+{
+    kstring_t tmp;
+    file_t *files;
+    int ignore_rg, nsmpl, nfiles;
+    char **smpl;        // list of BCF output sample names. Maintained by bsmpl_add_readgroup
+    void *sample_list;  // hash: BAM input sample name to BCF output sample name. This is the -s/-S list
+    int sample_logic;   // the -s/-S logic, 1: include, 0: exclude
+    void *rg_list;      // hash: BAM/rg_id to sample name or */rg_id for global ids. This is the -G list
+    int rg_logic;       // the -G logic, 1: include, 0: exclude
+    void *name2idx;     // hash: BCF output sample name to BCF output sample index. Maintained by bsmpl_add_readgroup
+};
+
+bam_smpl_t *bam_smpl_init(void)
+{
+    bam_smpl_t *bsmpl;
+    bsmpl = (bam_smpl_t*) calloc(1, sizeof(bam_smpl_t));
+    bsmpl->name2idx = khash_str2int_init();
+    return bsmpl;
+}
+
+void bam_smpl_destroy(bam_smpl_t *bsmpl)
+{
+    if ( !bsmpl ) return;
+    if ( bsmpl->name2idx ) khash_str2int_destroy_free(bsmpl->name2idx);
+    if ( bsmpl->sample_list ) khash_str2str_destroy_free_all(bsmpl->sample_list);
+    if ( bsmpl->rg_list ) khash_str2str_destroy_free_all(bsmpl->rg_list);
+    int i;
+    for (i=0; i<bsmpl->nfiles; i++)
+    {
+        file_t *file = &bsmpl->files[i];
+        if ( file->rg2idx ) khash_str2int_destroy_free(file->rg2idx);
+        free(file->fname);
+    }
+    free(bsmpl->smpl);
+    free(bsmpl->files);
+    free(bsmpl->tmp.s);
+    free(bsmpl);
+}
+
+void bam_smpl_ignore_readgroups(bam_smpl_t* bsmpl)
+{
+    bsmpl->ignore_rg = 1;
+}
+
+static void bsmpl_add_readgroup(bam_smpl_t *bsmpl, file_t *file, const char *rg_id, const char *smpl_name)
+{
+    int ismpl = -1;
+    if ( smpl_name )
+    {
+        if ( khash_str2int_get(bsmpl->name2idx,smpl_name,&ismpl) < 0 )
+        {
+            // new sample
+            bsmpl->nsmpl++;
+            bsmpl->smpl = (char**) realloc(bsmpl->smpl,sizeof(char*)*bsmpl->nsmpl);
+            bsmpl->smpl[bsmpl->nsmpl-1] = strdup(smpl_name);
+            ismpl = khash_str2int_inc(bsmpl->name2idx,bsmpl->smpl[bsmpl->nsmpl-1]);
+        }
+    }
+    if ( !strcmp("*",rg_id) )
+    {
+        // all read groups in the bam treated as the same sample
+        file->default_idx = ismpl;
+        return;
+    }
+    if ( !file->rg2idx ) file->rg2idx = khash_str2int_init();
+    if ( khash_str2int_has_key(file->rg2idx,rg_id) ) return;    // duplicate @RG:ID
+    khash_str2int_set(file->rg2idx, strdup(rg_id), ismpl);
+}
+static int bsmpl_keep_readgroup(bam_smpl_t *bsmpl, file_t *file, const char *rg_id, const char **smpl_name)
+{
+    char *rg_smpl = khash_str2str_get(bsmpl->rg_list,rg_id);    // unique read group present in one bam only
+    if ( !rg_smpl )
+    {
+        // read group specific to this bam
+        bsmpl->tmp.l = 0;
+        ksprintf(&bsmpl->tmp,"%s\t%s",rg_id,file->fname);
+        rg_smpl = khash_str2str_get(bsmpl->rg_list,bsmpl->tmp.s);
+    }
+    if ( !rg_smpl )
+    {
+        // any read group in this file?
+        bsmpl->tmp.l = 0;
+        ksprintf(&bsmpl->tmp,"*\t%s",file->fname);
+        rg_smpl = khash_str2str_get(bsmpl->rg_list,bsmpl->tmp.s);
+    }
+    if ( !rg_smpl && bsmpl->rg_logic ) return 0;
+    if ( rg_smpl && !bsmpl->rg_logic ) return 0;
+
+    if ( rg_smpl && rg_smpl[0]!='\t' ) *smpl_name = rg_smpl;    // rename the sample
+    return 1;
+}
+
+/*
+    The logic of this function is a bit complicated because we want to work
+    also with broken bams containing read groups that are not listed in the
+    header. The desired behavior is as follows:
+        - when -G is given, read groups which are not listed in the header must
+          be given explicitly using the "?" symbol in -G.
+          Otherwise:
+        - if the bam has no header, all reads in the file are assigned to a
+          single sample named after the file
+        - if there is at least one sample defined in the header, reads with no
+          read group id or with a read group id not listed in the header are
+          assigned to the first sample encountered in the header
+*/
+int bam_smpl_add_bam(bam_smpl_t *bsmpl, char *bam_hdr, const char *fname)
+{
+    bsmpl->nfiles++;
+    bsmpl->files = (file_t*) realloc(bsmpl->files,bsmpl->nfiles*sizeof(file_t));
+    file_t *file = &bsmpl->files[bsmpl->nfiles-1];
+    memset(file,0,sizeof(file_t));
+    file->fname  = strdup(fname);
+    file->default_idx = -1;
+
+    if ( bsmpl->ignore_rg || !bam_hdr )
+    {
+        // The option --ignore-RG is set or there is no BAM header: use the file name as the sample name
+        bsmpl_add_readgroup(bsmpl,file,"*",file->fname);
+        return bsmpl->nfiles-1;
+    }
+
+    void *bam_smpls = khash_str2int_init();
+    int first_smpl = -1, nskipped = 0;
+    const char *p = bam_hdr, *q, *r;
+    while (p != NULL && (q = strstr(p, "@RG")) != 0)
+    {
+        char *eol = strchr(q + 3, '\n');
+        if (q > bam_hdr && *(q - 1) != '\n') { // @RG must be at start of line
+            p = eol;
+            continue;
+        }
+        p = q + 3;
+        if ((q = strstr(p, "\tID:")) != 0) q += 4;
+        if ((r = strstr(p, "\tSM:")) != 0) r += 4;
+        if (r && q)
+        {
+            char *u, *v;
+            int ioq, ior;
+            for (u = (char*)q; *u && *u != '\t' && *u != '\n'; ++u);
+            for (v = (char*)r; *v && *v != '\t' && *v != '\n'; ++v);
+            ioq = *u; ior = *v; *u = *v = '\0';
+
+            // q now points to a null terminated read group id
+            // r points to a null terminated sample name
+            if ( !strcmp("*",q) || !strcmp("?",q) )
+                error("Error: the read group IDs \"*\" and \"?\" have a special meaning in the mpileup code. Please fix the code or the bam: %s\n", fname);
+
+            int accept_rg = 1;
+            if ( bsmpl->sample_list )
+            {
+                // restrict samples based on the -s/-S options
+                char *name = khash_str2str_get(bsmpl->sample_list,r);
+                if ( bsmpl->sample_logic==0 )
+                    accept_rg = name ? 0 : 1;
+                else if ( !name )
+                    accept_rg = 0;
+                else
+                    r = name;
+            }
+            if ( accept_rg && bsmpl->rg_list )
+            {
+                // restrict readgroups based on the -G option, possibly renaming the sample
+                accept_rg = bsmpl_keep_readgroup(bsmpl,file,q,&r);
+            }
+            if ( accept_rg )
+                bsmpl_add_readgroup(bsmpl,file,q,r);
+            else
+            {
+                bsmpl_add_readgroup(bsmpl,file,q,NULL); // ignore this RG but note that it was seen in the header
+                nskipped++;
+            }
+
+            if ( first_smpl<0 )
+                khash_str2int_get(bsmpl->name2idx,r,&first_smpl);
+            if ( !khash_str2int_has_key(bam_smpls,r) )
+                khash_str2int_inc(bam_smpls,strdup(r));
+
+            *u = ioq; *v = ior;
+        }
+        else
+            break;
+        p = eol;
+    }
+    int nsmpls = khash_str2int_size(bam_smpls);
+    khash_str2int_destroy_free(bam_smpls);
+
+    const char *smpl_name = NULL;
+    int accept_null_rg = 1;
+    if ( bsmpl->rg_list && !bsmpl_keep_readgroup(bsmpl,file,"?",&smpl_name) ) accept_null_rg = 0;
+    if ( bsmpl->sample_list && first_smpl==-1 ) accept_null_rg = 0;
+
+    if ( !accept_null_rg && first_smpl==-1 )
+    {
+        // no suitable read group is available in this bam: ignore the whole file.
+        free(file->fname);
+        if ( file->rg2idx ) khash_str2int_destroy_free(file->rg2idx);
+        bsmpl->nfiles--;
+        return -1;
+    }
+    if ( !accept_null_rg ) return bsmpl->nfiles-1;
+    if ( nsmpls==1 && !nskipped )
+    {
+        file->default_idx = first_smpl;
+        return bsmpl->nfiles-1;
+    }
+    if ( !smpl_name ) smpl_name = first_smpl==-1 ? file->fname : bsmpl->smpl[first_smpl];
+
+    bsmpl_add_readgroup(bsmpl,file,"?",smpl_name);
+    return bsmpl->nfiles-1;
+}
+
+const char **bam_smpl_get_samples(bam_smpl_t *bsmpl, int *nsmpl)
+{
+    *nsmpl = bsmpl->nsmpl;
+    return (const char**)bsmpl->smpl;
+}
+
+int bam_smpl_get_sample_id(bam_smpl_t *bsmpl, int bam_id, bam1_t *bam_rec)
+{
+    file_t *file = &bsmpl->files[bam_id];
+    if ( file->default_idx >= 0 ) return file->default_idx;
+
+    char *aux_rg = (char*) bam_aux_get(bam_rec, "RG");
+    aux_rg = aux_rg ? aux_rg+1 : "?";
+
+    int rg_id;
+    if ( khash_str2int_get(file->rg2idx, aux_rg, &rg_id)==0 ) return rg_id;
+    if ( khash_str2int_get(file->rg2idx, "?", &rg_id)==0 ) return rg_id;
+    return -1;
+}
+
+int bam_smpl_add_samples(bam_smpl_t *bsmpl, char *list, int is_file)
+{
+    if ( list[0]!='^' ) bsmpl->sample_logic = 1;
+    else list++;
+
+    int i, nsamples = 0;
+    char **samples = hts_readlist(list, is_file, &nsamples);
+    if ( !samples || !nsamples ) return 0;
+
+    kstring_t ori = {0,0,0};
+    kstring_t ren = {0,0,0};
+
+    bsmpl->sample_list = khash_str2str_init();
+    for (i=0; i<nsamples; i++)
+    {
+        char *ptr = samples[i];
+        ori.l = ren.l = 0;
+        int escaped = 0;
+        while ( *ptr )
+        {
+            if ( *ptr=='\\' && !escaped ) { escaped = 1; ptr++; continue; }
+            if ( isspace(*ptr) && !escaped ) break;
+            kputc(*ptr, &ori);
+            escaped = 0;
+            ptr++;
+        }
+        if ( *ptr )
+        {
+            while ( *ptr && isspace(*ptr) ) ptr++;
+            while ( *ptr )
+            {
+                if ( *ptr=='\\' && !escaped ) { escaped = 1; ptr++; continue; }
+                if ( isspace(*ptr) && !escaped ) break;
+                kputc(*ptr, &ren);
+                escaped = 0;
+                ptr++;
+            }
+        }
+        khash_str2str_set(bsmpl->sample_list,strdup(ori.s),strdup(ren.l?ren.s:ori.s));
+        free(samples[i]);
+    }
+    free(samples);
+    free(ori.s);
+    free(ren.s);
+    return nsamples;
+}
+
+int bam_smpl_add_readgroups(bam_smpl_t *bsmpl, char *list, int is_file)
+{
+    if ( list[0]!='^' ) bsmpl->rg_logic = 1;
+    else list++;
+
+    int i, nrows  = 0;
+    char **rows = hts_readlist(list, is_file, &nrows);
+    if ( !rows || !nrows ) return 0;
+
+    kstring_t fld1 = {0,0,0};
+    kstring_t fld2 = {0,0,0};
+    kstring_t fld3 = {0,0,0};
+
+    bsmpl->rg_list = khash_str2str_init();
+    for (i=0; i<nrows; i++)
+    {
+        char *ptr = rows[i];
+        fld1.l = fld2.l = fld3.l = 0;
+        int escaped = 0;
+        while ( *ptr )
+        {
+            if ( *ptr=='\\' && !escaped ) { escaped = 1; ptr++; continue; }
+            if ( isspace(*ptr) && !escaped ) break;
+            kputc(*ptr, &fld1);
+            escaped = 0;
+            ptr++;
+        }
+        if ( *ptr )
+        {
+            while ( *ptr && isspace(*ptr) ) ptr++;
+            while ( *ptr )
+            {
+                if ( *ptr=='\\' && !escaped ) { escaped = 1; ptr++; continue; }
+                if ( isspace(*ptr) && !escaped ) break;
+                kputc(*ptr, &fld2);
+                escaped = 0;
+                ptr++;
+            }
+        }
+        if ( *ptr )
+        {
+            while ( *ptr && isspace(*ptr) ) ptr++;
+            while ( *ptr )
+            {
+                if ( *ptr=='\\' && !escaped ) { escaped = 1; ptr++; continue; }
+                if ( isspace(*ptr) && !escaped ) break;
+                kputc(*ptr, &fld3);
+                escaped = 0;
+                ptr++;
+            }
+        }
+        if ( fld3.l )
+        {
+            // ID FILE SAMPLE
+            kputc('\t',&fld1);
+            kputs(fld2.s,&fld1);
+            fld2.l = 0;
+            kputs(fld3.s,&fld2);
+        }
+        // fld2.s now contains a new sample name. If NULL, use \t to keep the bam header name
+        char *value = khash_str2str_get(bsmpl->rg_list,fld1.s);
+        if ( !value )
+            khash_str2str_set(bsmpl->rg_list,strdup(fld1.s),strdup(fld2.l?fld2.s:"\t"));
+        else if ( strcmp(value,fld2.l?fld2.s:"\t") )
+            error("Error: The read group \"%s\" was assigned to two different samples: \"%s\" and \"%s\"\n", fld1.s,value,fld2.l?fld2.s:"\t");
+        free(rows[i]);
+    }
+    free(rows);
+    free(fld1.s);
+    free(fld2.s);
+    free(fld3.s);
+    return nrows;
+}
+
+
diff --git a/bcftools/bam_sample.h b/bcftools/bam_sample.h
new file mode 100644
index 0000000..5cbcc39
--- /dev/null
+++ b/bcftools/bam_sample.h
@@ -0,0 +1,50 @@
+/*  bam_sample.h -- group data by sample.
+
+    Copyright (C) 2010 Broad Institute.
+    Copyright (C) 2016 Genome Research Ltd.
+
+    Author: Heng Li <lh3@sanger.ac.uk>, Petr Danecek <pd3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#ifndef BAM_SAMPLE_H
+#define BAM_SAMPLE_H
+
+#include <htslib/sam.h>
+
+typedef struct _bam_smpl_t bam_smpl_t;
+
+bam_smpl_t *bam_smpl_init(void);
+
+int bam_smpl_add_samples(bam_smpl_t *bsmpl, char *list, int is_file);
+int bam_smpl_add_readgroups(bam_smpl_t *bsmpl, char *list, int is_file);
+void bam_smpl_ignore_readgroups(bam_smpl_t* bsmpl);
+
+// The above should be called only before bams are added. Returns the BAM id
+// to be passed to bam_smpl_get_sample_id() later. It is safe to assume
+// sequential numbering, starting from 0.
+//
+int bam_smpl_add_bam(bam_smpl_t *bsmpl, char *bam_hdr, const char *fname);
+
+const char **bam_smpl_get_samples(bam_smpl_t *bsmpl, int *nsmpl);
+int bam_smpl_get_sample_id(bam_smpl_t *bsmpl, int bam_id, bam1_t *bam_rec);
+
+void bam_smpl_destroy(bam_smpl_t *bsmpl);
+
+#endif
diff --git a/bcftools/bcftools.h b/bcftools/bcftools.h
new file mode 100644
index 0000000..a915802
--- /dev/null
+++ b/bcftools/bcftools.h
@@ -0,0 +1,143 @@
+/*  bcftools.h -- utility function declarations.
+
+    Copyright (C) 2013-2022 Genome Research Ltd.
+
+    Author: Petr Danecek <pd3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.  */
+
+#ifndef BCFTOOLS_H
+#define BCFTOOLS_H
+
+#include <stdarg.h>
+#include <htslib/hts_defs.h>
+#include <htslib/vcf.h>
+#include <htslib/synced_bcf_reader.h>
+#include <math.h>
+
+#define FT_TAB_TEXT 0       // custom tab-delimited text file
+#define FT_GZ 1
+#define FT_VCF 2
+#define FT_VCF_GZ (FT_GZ|FT_VCF)
+#define FT_BCF (1<<2)
+#define FT_BCF_GZ (FT_GZ|FT_BCF)
+#define FT_STDIN (1<<3)
+
+char *bcftools_version(void);
+
+/// Report an error and exit -1
+void error(const char *format, ...) HTS_NORETURN HTS_FORMAT(HTS_PRINTF_FMT, 1, 2);
+
+/// Report an error and exit -1.  If errno != 0, appends strerror(errno).
+//  Note: unlike error() above, the message should not end with "\n" as a
+//  newline will be added by the function.
+void error_errno(const char *format, ...) HTS_NORETURN HTS_FORMAT(HTS_PRINTF_FMT, 1, 2);
+
+void bcf_hdr_append_version(bcf_hdr_t *hdr, int argc, char **argv, const char *cmd);
+const char *hts_bcf_wmode(int file_type);
+const char *hts_bcf_wmode2(int file_type, const char *fname);
+void set_wmode(char dst[8], int file_type, const char *fname, int compression_level);  // clevel: 0-9 with or zb type, -1 unset
+char *init_tmp_prefix(const char *prefix);
+int read_AF(bcf_sr_regions_t *tgt, bcf1_t *line, double *alt_freq);
+int parse_overlap_option(const char *arg);
+
+void *smalloc(size_t size);     // safe malloc
+
+static inline int iupac2bitmask(char iupac)
+{
+    const int A = 1;
+    const int C = 2;
+    const int G = 4;
+    const int T = 8;
+    if ( iupac >= 97 ) iupac -= 32;
+    if ( iupac == 'A' ) return A;
+    if ( iupac == 'C' ) return C;
+    if ( iupac == 'G' ) return G;
+    if ( iupac == 'T' ) return T;
+    if ( iupac == 'M' ) return A|C;
+    if ( iupac == 'R' ) return A|G;
+    if ( iupac == 'W' ) return A|T;
+    if ( iupac == 'S' ) return C|G;
+    if ( iupac == 'Y' ) return C|T;
+    if ( iupac == 'K' ) return G|T;
+    if ( iupac == 'V' ) return A|C|G;
+    if ( iupac == 'H' ) return A|C|T;
+    if ( iupac == 'D' ) return A|G|T;
+    if ( iupac == 'B' ) return C|G|T;
+    if ( iupac == 'N' ) return A|C|G|T;
+    return -1;
+}
+static inline char bitmask2iupac(int bitmask)
+{
+    const char iupac[16] = {'.','A','C','M','G','R','S','V','T','W','Y','H','K','D','B','N'};
+    if ( bitmask <= 0 || bitmask > 15 ) return 0;
+    return iupac[bitmask];
+}
+
+static inline int iupac_consistent(char iupac, char nt)
+{
+    static const char iupac_mask[90] = {
+        0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
+        0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
+        0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,14,2,
+        13,0,0,4,11,0,0,12,0,3,15,0,0,0,5,6,8,0,7,9,0,10
+    };
+    if ( iupac > 89 ) return 0;
+    if ( nt > 90 ) nt -=  32;  // lowercase 
+    if ( nt=='A' ) nt = 1;
+    else if ( nt=='C' ) nt = 2;
+    else if ( nt=='G' ) nt = 4;
+    else if ( nt=='T' ) nt = 8;
+    return iupac_mask[(int)iupac] & nt ? 1 : 0;
+}
+
+static inline char nt_to_upper(char nt)
+{
+    if ( nt < 97 ) return nt;
+    return nt - 32;
+}
+
+static inline double phred_score(double prob)
+{
+    if ( prob==0 ) return 99;
+    prob = -4.3429*log(prob);
+    return prob>99 ? 99 : prob;
+}
+
+static const uint64_t bcf_double_missing    = 0x7ff0000000000001;
+static const uint64_t bcf_double_vector_end = 0x7ff0000000000002;
+static inline void bcf_double_set(double *ptr, uint64_t value)
+{
+    union { uint64_t i; double d; } u;
+    u.i = value;
+    *ptr = u.d;
+}
+static inline int bcf_double_test(double d, uint64_t value)
+{
+    union { uint64_t i; double d; } u;
+    u.d = d;
+    return u.i==value ? 1 : 0;
+}
+#define bcf_double_set_vector_end(x) bcf_double_set(&(x),bcf_double_vector_end)
+#define bcf_double_set_missing(x)    bcf_double_set(&(x),bcf_double_missing)
+#define bcf_double_is_vector_end(x)  bcf_double_test((x),bcf_double_vector_end)
+#define bcf_double_is_missing(x)     bcf_double_test((x),bcf_double_missing)
+#define bcf_double_is_missing_or_vector_end(x)     (bcf_double_test((x),bcf_double_missing) || bcf_double_test((x),bcf_double_vector_end))
+
+#endif
diff --git a/bcftools/bcftools.pysam.c b/bcftools/bcftools.pysam.c
new file mode 100644
index 0000000..e7f620a
--- /dev/null
+++ b/bcftools/bcftools.pysam.c
@@ -0,0 +1,83 @@
+#include <getopt.h>
+#include <unistd.h>
+#include <setjmp.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+
+#include "bcftools.pysam.h"
+
+FILE * bcftools_stderr = NULL;
+FILE * bcftools_stdout = NULL;
+const char * bcftools_stdout_fn = NULL;
+
+
+FILE * bcftools_set_stderr(int fd)
+{
+  if (bcftools_stderr != NULL)
+    fclose(bcftools_stderr);
+  bcftools_stderr = fdopen(fd, "w");
+  return bcftools_stderr;
+}
+
+void bcftools_close_stderr(void)
+{
+  fclose(bcftools_stderr);
+  bcftools_stderr = NULL;
+}
+
+FILE * bcftools_set_stdout(int fd)
+{
+  if (bcftools_stdout != NULL)
+    fclose(bcftools_stdout);
+  bcftools_stdout = fdopen(fd, "w");
+  if (bcftools_stdout == NULL)
+    {
+      fprintf(bcftools_stderr, "could not set stdout to fd %i", fd);
+    }
+  return bcftools_stdout;
+}
+
+void bcftools_set_stdout_fn(const char *fn)
+{
+  bcftools_stdout_fn = fn;
+}
+
+void bcftools_close_stdout(void)
+{
+  fclose(bcftools_stdout);
+  bcftools_stdout = NULL;
+}
+
+int bcftools_puts(const char *s)
+{
+  if (fputs(s, bcftools_stdout) == EOF) return EOF;
+  return putc('\n', bcftools_stdout);
+}
+
+
+static jmp_buf bcftools_jmpbuf;
+static int bcftools_status = 0;
+
+int bcftools_dispatch(int argc, char *argv[])
+{
+  /* Reset getopt()/getopt_long() processing. */
+#if defined __GLIBC__
+  optind = 0;
+#elif defined _OPTRESET || defined _OPTRESET_DECLARED
+  optreset = optind = 1;
+#else
+  optind = 1;
+#endif
+
+  if (setjmp(bcftools_jmpbuf) == 0)
+    return bcftools_main(argc, argv);
+  else
+    return bcftools_status;
+}
+
+void bcftools_exit(int status)
+{
+  bcftools_status = status;
+  longjmp(bcftools_jmpbuf, 1);
+}
diff --git a/bcftools/bcftools.pysam.h b/bcftools/bcftools.pysam.h
new file mode 100644
index 0000000..e6717bb
--- /dev/null
+++ b/bcftools/bcftools.pysam.h
@@ -0,0 +1,74 @@
+#ifndef bcftools_PYSAM_H
+#define bcftools_PYSAM_H
+
+#include <stdio.h>
+
+#ifndef __has_attribute
+#define __has_attribute(attribute) 0
+#endif
+#ifndef PYSAM_NORETURN
+#if __has_attribute(__noreturn__) || __GNUC__ >= 3
+#define PYSAM_NORETURN __attribute__((__noreturn__))
+#else
+#define PYSAM_NORETURN
+#endif
+#endif
+
+extern FILE * bcftools_stderr;
+
+extern FILE * bcftools_stdout;
+
+extern const char * bcftools_stdout_fn;
+
+/*! set pysam standard error to point to file descriptor
+
+  Setting the stderr will close the previous stderr.
+ */
+FILE * bcftools_set_stderr(int fd);
+
+/*! set pysam standard output to point to file descriptor
+
+  Setting the stdout will close the previous stdout.
+ */
+FILE * bcftools_set_stdout(int fd);
+
+/*! set pysam standard output to point to filename
+
+ */
+void bcftools_set_stdout_fn(const char * fn);
+
+/*! close pysam standard error and set to NULL
+  
+ */
+void bcftools_close_stderr(void);
+
+/*! close pysam standard output and set to NULL
+  
+ */
+void bcftools_close_stdout(void);
+
+int bcftools_puts(const char *s);
+
+int bcftools_dispatch(int argc, char *argv[]);
+
+void PYSAM_NORETURN bcftools_exit(int status);
+
+extern int bcftools_main(int argc, char *argv[]);
+
+/* Define these only in samtools/bcftools C source, not Cython code. */
+#if !(defined CYTHON_ABI || defined CYTHON_HEX_VERSION)
+
+/*! Several non-static function names are used in both samtools and bcftools.
+    Both libcsamtools.so and libcbcftools.so are loaded simultaneously, leading
+    to collisions and wrong functions being called. #define these names so the
+    actual symbol names include distinct prefixes to avoid collisions.
+ */
+#define main_consensus bcftools_main_consensus
+#define main_reheader bcftools_main_reheader
+#define bam_smpl_init bcftools_bam_smpl_init
+#define bam_smpl_destroy bcftools_bam_smpl_destroy
+#define read_file_list bcftools_read_file_list
+
+#endif
+
+#endif
diff --git a/bcftools/bin.c b/bcftools/bin.c
new file mode 100644
index 0000000..645012e
--- /dev/null
+++ b/bcftools/bin.c
@@ -0,0 +1,106 @@
+/* The MIT License
+
+   Copyright (c) 2016-2022 Genome Research Ltd.
+
+   Author: Petr Danecek <pd3@sanger.ac.uk>
+   
+   Permission is hereby granted, free of charge, to any person obtaining a copy
+   of this software and associated documentation files (the "Software"), to deal
+   in the Software without restriction, including without limitation the rights
+   to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+   copies of the Software, and to permit persons to whom the Software is
+   furnished to do so, subject to the following conditions:
+   
+   The above copyright notice and this permission notice shall be included in
+   all copies or substantial portions of the Software.
+   
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+   IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+   FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+   AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+   LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+   OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+   THE SOFTWARE.
+
+ */
+
+#include <stdio.h>
+#include <assert.h>
+#include "bcftools.h"
+#include "bin.h"
+
+struct _bin_t
+{
+    float *bins;
+    int nbins;
+};
+
+bin_t *bin_init(const char *list_def, float min, float max)
+{
+    bin_t *bin = (bin_t*) calloc(1,sizeof(bin_t));
+
+    // a comma indicates a list, otherwise a file
+    int is_file = strchr(list_def,',') ? 0 : 1;
+    int i, nlist;
+    char **list = hts_readlist(list_def, is_file, &nlist);
+    if ( !list ) error("Error: failed to read %s\n",list_def);
+    bin->nbins = nlist;
+    bin->bins  = (float*) malloc(sizeof(float)*nlist);
+    for (i=0; i<nlist; i++)
+    {
+        char *tmp;
+        bin->bins[i] = strtod(list[i],&tmp);
+        if ( *tmp ) error("Could not parse %s: %s\n", list_def, list[i]);
+        if ( min!=max && (bin->bins[i]<min || bin->bins[i]>max) )
+            error("Expected values from the interval [%f,%f], found %s\n", min, max, list[i]);
+        free(list[i]); 
+    }
+    free(list);
+
+    if ( min!=max )
+    {
+        // make sure we've got both boundaries: min,max.
+        assert( nlist>1 );
+        float max_err = (bin->bins[1] - bin->bins[0])*1e-6;
+        if ( fabs(bin->bins[0] - min) > max_err )
+        {
+            bin->bins = (float*) realloc(bin->bins, (++bin->nbins)*sizeof(float));
+            memmove(bin->bins+1, bin->bins, sizeof(float)*(bin->nbins-1));
+            bin->bins[0] = min;
+        }
+        if ( fabs(bin->bins[bin->nbins-1] - max) > max_err ) 
+        {
+            bin->bins = (float*) realloc(bin->bins, (++bin->nbins)*sizeof(float));
+            bin->bins[bin->nbins-1] = max;
+        }
+    }
+    return bin;
+}
+
+void bin_destroy(bin_t *bin)
+{
+    free(bin->bins);
+    free(bin);
+}
+
+int bin_get_size(bin_t *bin) { return bin->nbins; }
+
+float bin_get_value(bin_t *bin, int idx) { return bin->bins[idx]; }
+
+int bin_get_idx(bin_t *bin, float value)
+{
+    if ( bin->bins[bin->nbins-1] < value ) return bin->nbins-1;
+
+    // Binary search in half-closed,half-open intervals [)
+    int imin = 0, imax = bin->nbins - 2;
+    while ( imin<imax )
+    {
+        int i = (imin+imax)/2;
+        if ( value < bin->bins[i] ) imax = i - 1;
+        else if ( value > bin->bins[i] ) imin = i + 1;
+        else return i;
+    }
+    if ( bin->bins[imax] <= value ) return imax;
+    return imin - 1;
+}
+
diff --git a/bcftools/bin.c.pysam.c b/bcftools/bin.c.pysam.c
new file mode 100644
index 0000000..683d69c
--- /dev/null
+++ b/bcftools/bin.c.pysam.c
@@ -0,0 +1,108 @@
+#include "bcftools.pysam.h"
+
+/* The MIT License
+
+   Copyright (c) 2016-2022 Genome Research Ltd.
+
+   Author: Petr Danecek <pd3@sanger.ac.uk>
+   
+   Permission is hereby granted, free of charge, to any person obtaining a copy
+   of this software and associated documentation files (the "Software"), to deal
+   in the Software without restriction, including without limitation the rights
+   to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+   copies of the Software, and to permit persons to whom the Software is
+   furnished to do so, subject to the following conditions:
+   
+   The above copyright notice and this permission notice shall be included in
+   all copies or substantial portions of the Software.
+   
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+   IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+   FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+   AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+   LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+   OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+   THE SOFTWARE.
+
+ */
+
+#include <stdio.h>
+#include <assert.h>
+#include "bcftools.h"
+#include "bin.h"
+
+struct _bin_t
+{
+    float *bins;
+    int nbins;
+};
+
+bin_t *bin_init(const char *list_def, float min, float max)
+{
+    bin_t *bin = (bin_t*) calloc(1,sizeof(bin_t));
+
+    // a comma indicates a list, otherwise a file
+    int is_file = strchr(list_def,',') ? 0 : 1;
+    int i, nlist;
+    char **list = hts_readlist(list_def, is_file, &nlist);
+    if ( !list ) error("Error: failed to read %s\n",list_def);
+    bin->nbins = nlist;
+    bin->bins  = (float*) malloc(sizeof(float)*nlist);
+    for (i=0; i<nlist; i++)
+    {
+        char *tmp;
+        bin->bins[i] = strtod(list[i],&tmp);
+        if ( *tmp ) error("Could not parse %s: %s\n", list_def, list[i]);
+        if ( min!=max && (bin->bins[i]<min || bin->bins[i]>max) )
+            error("Expected values from the interval [%f,%f], found %s\n", min, max, list[i]);
+        free(list[i]); 
+    }
+    free(list);
+
+    if ( min!=max )
+    {
+        // make sure we've got both boundaries: min,max.
+        assert( nlist>1 );
+        float max_err = (bin->bins[1] - bin->bins[0])*1e-6;
+        if ( fabs(bin->bins[0] - min) > max_err )
+        {
+            bin->bins = (float*) realloc(bin->bins, (++bin->nbins)*sizeof(float));
+            memmove(bin->bins+1, bin->bins, sizeof(float)*(bin->nbins-1));
+            bin->bins[0] = min;
+        }
+        if ( fabs(bin->bins[bin->nbins-1] - max) > max_err ) 
+        {
+            bin->bins = (float*) realloc(bin->bins, (++bin->nbins)*sizeof(float));
+            bin->bins[bin->nbins-1] = max;
+        }
+    }
+    return bin;
+}
+
+void bin_destroy(bin_t *bin)
+{
+    free(bin->bins);
+    free(bin);
+}
+
+int bin_get_size(bin_t *bin) { return bin->nbins; }
+
+float bin_get_value(bin_t *bin, int idx) { return bin->bins[idx]; }
+
+int bin_get_idx(bin_t *bin, float value)
+{
+    if ( bin->bins[bin->nbins-1] < value ) return bin->nbins-1;
+
+    // Binary search in half-closed,half-open intervals [)
+    int imin = 0, imax = bin->nbins - 2;
+    while ( imin<imax )
+    {
+        int i = (imin+imax)/2;
+        if ( value < bin->bins[i] ) imax = i - 1;
+        else if ( value > bin->bins[i] ) imin = i + 1;
+        else return i;
+    }
+    if ( bin->bins[imax] <= value ) return imax;
+    return imin - 1;
+}
+
diff --git a/bcftools/bin.h b/bcftools/bin.h
new file mode 100644
index 0000000..ab9e5b1
--- /dev/null
+++ b/bcftools/bin.h
@@ -0,0 +1,65 @@
+/* The MIT License
+
+   Copyright (c) 2016 Genome Research Ltd.
+
+   Author: Petr Danecek <pd3@sanger.ac.uk>
+   
+   Permission is hereby granted, free of charge, to any person obtaining a copy
+   of this software and associated documentation files (the "Software"), to deal
+   in the Software without restriction, including without limitation the rights
+   to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+   copies of the Software, and to permit persons to whom the Software is
+   furnished to do so, subject to the following conditions:
+   
+   The above copyright notice and this permission notice shall be included in
+   all copies or substantial portions of the Software.
+   
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+   IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+   FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+   AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+   LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+   OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+   THE SOFTWARE.
+
+ */
+
+/*
+    Simple binning of float values into predefined bins
+*/
+
+#ifndef __BIN_H__
+#define __BIN_H__
+
+#include <stdio.h>
+
+typedef struct _bin_t bin_t;
+
+/*
+ *  bin_init() - init bins
+ *  @list: list of half-open intervals [). If the list does not contain commas,
+ *      it is interpreted as a file name.
+ *  @min,max:  extreme values. This is for user convenience so that well-known
+ *      extremes can be left out from the list. Ignored if min=max
+ */
+bin_t *bin_init(const char *list, float min, float max);
+void bin_destroy(bin_t *bin);
+
+/*
+ *  bin_get_size() - number of boundaries, subtract 1 to get the number of bins
+ */
+int bin_get_size(bin_t *bin);
+
+/*
+   bin_get_idx() - find the bin index which corresponds to the value (binary search)
+   Returns the bin index 0 <= idx <= size-2 or -1,size-1 for out of range values.
+ */
+int bin_get_idx(bin_t *bin, float value);
+
+/*
+   bin_get_value() - get the i-th boundary value, i=0,..,size-1
+ */
+float bin_get_value(bin_t *bin, int ith);
+
+#endif
+
diff --git a/bcftools/call.h b/bcftools/call.h
new file mode 100644
index 0000000..16bf0b6
--- /dev/null
+++ b/bcftools/call.h
@@ -0,0 +1,149 @@
+/*  call.h -- variant calling declarations.
+
+    Copyright (C) 2013-2015, 2019-2020 Genome Research Ltd.
+
+    Author: Petr Danecek <pd3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.  */
+
+#ifndef __CALL_H__
+#define __CALL_H__
+
+#include <htslib/vcf.h>
+#include <htslib/synced_bcf_reader.h>
+#include "vcmp.h"
+
+#define CALL_KEEPALT        1
+#define CALL_VARONLY        (1<<1)
+#define CALL_CONSTR_TRIO    (1<<2)
+#define CALL_CONSTR_ALLELES (1<<3)
+//
+#define CALL_FMT_PV4        (1<<5)
+#define CALL_FMT_GQ         (1<<6)
+#define CALL_FMT_GP         (1<<7)
+
+#define FATHER 0
+#define MOTHER 1
+#define CHILD  2
+typedef struct
+{
+    char *name;
+    int sample[3];  // father, mother, child
+    int type;       // see FTYPE_* definitions in mcall.c
+}
+family_t;
+
+// For the single-sample and grouped -G calling
+typedef struct
+{
+    double ref_lk, max_lk, lk_sum;
+    float *qsum;    // QS(quality sum) values
+    int nqsum;
+    uint32_t *smpl, nsmpl;
+    uint32_t nals, als;
+}
+smpl_grp_t;
+
+// For the `-C alleles -i` constrained calling
+typedef struct
+{
+    uint32_t n:31, used:1;
+    char **allele;
+}
+tgt_als_t;
+
+typedef struct _ccall_t ccall_t;
+typedef struct
+{
+    // mcall only
+    int npdg;
+    int *als_map, nals_map; // mapping from full set of alleles to trimmed set of alleles (old -> new)
+    int *pl_map, npl_map;   // same as above for PLs, but reverse (new -> old)
+    char **als;             // array to hold the trimmed set of alleles to appear on output
+    int nals;               // size of the als array
+    int als_new, nals_new;  // bitmask with final alleles and their number
+    family_t *fams;         // list of families and samples for trio calling
+    int nfams, mfams;
+    int ntrio[5][5];        // possible trio genotype combinations and their counts; first idx:
+    uint16_t *trio[5][5];   //  family type, second index: allele count (2-4, first two are unused)
+    double *GLs;
+    float *GPs;             // FORMAT/GP: posterior probabilities
+    int32_t *GQs, *ADs;     // FORMAT/GQ: genotype qualities; AD: allelic depth for -G
+    int32_t *itmp;          // temporary int array, used for new PLs with CALL_CONSTR_ALLELES
+    int n_itmp, nGPs, nADs;
+    vcmp_t *vcmp;
+    double trio_Pm_SNPs, trio_Pm_del, trio_Pm_ins;      // P(mendelian) for trio calling, see mcall_call_trio_genotypes()
+    int32_t *ugts, *cgts;   // unconstraind and constrained GTs
+    uint32_t output_tags;
+    char *prior_AN, *prior_AC;  // reference panel AF tags (AF=AC/AN)
+    tgt_als_t *tgt_als;         // for CALL_CONSTR_ALLELES
+    char *sample_groups;        // for single-sample or grouped calling with -G
+    char *sample_groups_tag;    // for -G [AD|QS:]
+    smpl_grp_t *smpl_grp;
+    int nsmpl_grp;
+
+    // ccall only
+    double indel_frac, min_perm_p, min_lrt;
+    double prior_type, pref;
+    int ngrp1_samples, n_perm;
+    char *prior_file;
+    ccall_t *cdat;
+
+    // shared
+    bcf_srs_t *srs;         // BCF synced readers holding target alleles for CALL_CONSTR_ALLELES
+    bcf1_t *rec;
+    bcf_hdr_t *hdr;
+    uint32_t flag;          // One or more of the CALL_* flags defined above
+    uint8_t *ploidy, all_diploid, unseen;
+
+    double pl2p[256];       // PL to 10^(-PL/10) table
+    int32_t *PLs;           // VCF PL likelihoods (rw)
+    int nPLs, mPLs, nac;
+    int32_t *gts, *ac;      // GTs and AC (w)
+    double *pdg;            // PLs converted to P(D|G)
+    float *anno16; int n16; // see anno[16] in bam2bcf.h
+    double theta;           // prior
+}
+call_t;
+
+void error(const char *format, ...);
+
+/*
+ *  call() - return -1 value on critical error; -2 to skip the site; or the number of non-reference
+ *            alleles on success.
+ */
+int mcall(call_t *call, bcf1_t *rec);    // multiallic and rare-variant calling model
+int ccall(call_t *call, bcf1_t *rec);    // the default consensus calling model
+int qcall(call_t *call, bcf1_t *rec);    // QCall output
+
+void mcall_init(call_t *call);
+void ccall_init(call_t *call);
+void qcall_init(call_t *call);
+
+void mcall_destroy(call_t *call);
+void ccall_destroy(call_t *call);
+void qcall_destroy(call_t *call);
+
+void call_init_pl2p(call_t *call);
+uint32_t *call_trio_prep(int is_x, int is_son);
+
+void init_allele_trimming_maps(call_t *call, int nals_ori, int als_out);
+void mcall_trim_and_update_numberR(call_t *call, bcf1_t *rec, int nals_ori, int nals_new);
+
+#endif
diff --git a/bcftools/ccall.c b/bcftools/ccall.c
new file mode 100644
index 0000000..6bf987b
--- /dev/null
+++ b/bcftools/ccall.c
@@ -0,0 +1,338 @@
+/*  ccall.c -- consensus variant calling.
+
+    Copyright (C) 2013-2014 Genome Research Ltd.
+    Portions copyright (C) 2010 Broad Institute.
+
+    Author: Petr Danecek <pd3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.  */
+
+#include <math.h>
+#include <assert.h>
+#include <htslib/kfunc.h>
+#include "call.h"
+#include "kmin.h"
+#include "prob1.h"
+
+// Most of the original -c calling was moved to bcftools as it was
+// and its data structures were wrapped into the ccal_t to make it
+// functional quickly. This is not the desired state.
+struct _ccall_t
+{
+    bcf_p1aux_t *p1;
+};
+
+void ccall_init(call_t *call)
+{
+    call->cdat = (ccall_t*) calloc(1,sizeof(ccall_t));
+    call_init_pl2p(call);
+    call->cdat->p1 = bcf_p1_init(bcf_hdr_nsamples(call->hdr), call->ploidy);
+    call->gts = (int*) calloc(bcf_hdr_nsamples(call->hdr)*2,sizeof(int));   // assuming at most diploid everywhere
+    call->nals_map = 5;
+    call->als_map  = (int*) malloc(sizeof(int)*call->nals_map);
+
+    bcf_hdr_append(call->hdr,"##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">");
+    if ( call->output_tags & CALL_FMT_GQ )
+    {
+        bcf_hdr_append(call->hdr,"##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">");
+        call->GQs = (int32_t*) malloc(sizeof(int32_t)*bcf_hdr_nsamples(call->hdr));
+    }
+    if ( call->output_tags & CALL_FMT_GP )
+        error("Sorry, -f GP is not supported with -c\n");
+    bcf_hdr_append(call->hdr,"##INFO=<ID=AF1,Number=1,Type=Float,Description=\"Max-likelihood estimate of the first ALT allele frequency (assuming HWE)\">");
+    // Todo: groups not migrated to 'bcftools call' yet
+    bcf_hdr_append(call->hdr,"##INFO=<ID=AF2,Number=1,Type=Float,Description=\"Max-likelihood estimate of the first and second group ALT allele frequency (assuming HWE)\">");
+    bcf_hdr_append(call->hdr,"##INFO=<ID=AC1,Number=1,Type=Float,Description=\"Max-likelihood estimate of the first ALT allele count (no HWE assumption)\">");
+    bcf_hdr_append(call->hdr,"##INFO=<ID=MQ,Number=1,Type=Integer,Description=\"Root-mean-square mapping quality of covering reads\">\n");
+    bcf_hdr_append(call->hdr,"##INFO=<ID=FQ,Number=1,Type=Float,Description=\"Phred probability of all samples being the same\">\n");
+    bcf_hdr_append(call->hdr,"##INFO=<ID=PV4,Number=4,Type=Float,Description=\"P-values for strand bias, baseQ bias, mapQ bias and tail distance bias\">\n");
+    bcf_hdr_append(call->hdr,"##INFO=<ID=G3,Number=3,Type=Float,Description=\"ML estimate of genotype frequencies\">\n");
+    bcf_hdr_append(call->hdr,"##INFO=<ID=HWE,Number=1,Type=Float,Description=\"Chi^2 based HWE test P-value based on G3\">\n");
+    // bcf_hdr_append(call->hdr,);
+    // bcf_hdr_append(call->hdr,);
+    bcf_hdr_append(call->hdr,"##INFO=<ID=DP4,Number=4,Type=Integer,Description=\"Number of high-quality ref-forward , ref-reverse, alt-forward and alt-reverse bases\">");
+
+    return;
+}
+void ccall_destroy(call_t *call)
+{
+    free(call->itmp);
+    free(call->als_map);
+    free(call->gts);
+    free(call->anno16);
+    free(call->PLs);
+    free(call->GQs);
+    free(call->pdg);
+    bcf_p1_destroy(call->cdat->p1);
+    free(call->cdat);
+    return;
+}
+
+// Inits P(D|G): convert PLs from log space, only two alleles (three PLs) are used.
+// NB: The original samtools calling code uses pdgs in reverse order (AA comes
+// first, RR last), while the -m calling model uses the canonical order.
+static void set_pdg3(double *pl2p, int *PLs, double *pdg, int n_smpl, int n_gt)
+{
+    int i;
+    for (i=0; i<n_smpl; i++)
+    {
+        pdg[2] = pl2p[ PLs[0] ];
+        pdg[1] = pl2p[ PLs[1] ];
+        pdg[0] = pl2p[ PLs[2] ];
+        PLs += n_gt;
+        pdg += 3;
+    }
+}
+
+static double ttest(int n1, int n2, float a[4])
+{
+    extern double kf_betai(double a, double b, double x);
+    double t, v, u1, u2;
+    if (n1 == 0 || n2 == 0 || n1 + n2 < 3) return 1.0;
+    u1 = (double)a[0] / n1; u2 = (double)a[2] / n2;
+    if (u1 <= u2) return 1.;
+    t = (u1 - u2) / sqrt(((a[1] - n1 * u1 * u1) + (a[3] - n2 * u2 * u2)) / (n1 + n2 - 2) * (1./n1 + 1./n2));
+    v = n1 + n2 - 2;
+    return t < 0.? 1. : .5 * kf_betai(.5*v, .5, v/(v+t*t));
+}
+
+static int test16_core(float anno[16], anno16_t *a)
+{
+    extern double kt_fisher_exact(int n11, int n12, int n21, int n22, double *_left, double *_right, double *two);
+    double left, right;
+    int i;
+    a->p[0] = a->p[1] = a->p[2] = a->p[3] = 1.;
+    for (i=0; i<4; i++) a->d[i] = anno[i];
+    a->depth = anno[0] + anno[1] + anno[2] + anno[3];
+    a->is_tested = (anno[0] + anno[1] > 0 && anno[2] + anno[3] > 0);
+    if (a->depth == 0) return -1;
+    a->mq = (int)(sqrt((anno[9] + anno[11]) / a->depth) + .499);
+    kt_fisher_exact(anno[0], anno[1], anno[2], anno[3], &left, &right, &a->p[0]);
+    for (i = 1; i < 4; ++i)
+        a->p[i] = ttest(anno[0] + anno[1], anno[2] + anno[3], anno+4*i);
+    return 0;
+}
+
+int test16(float *anno16, anno16_t *a)
+{
+    a->p[0] = a->p[1] = a->p[2] = a->p[3] = 1.;
+    a->d[0] = a->d[1] = a->d[2] = a->d[3] = 0.;
+    a->mq = a->depth = a->is_tested = 0;
+    return test16_core(anno16, a);
+}
+static int update_bcf1(call_t *call, bcf1_t *rec, const bcf_p1rst_t *pr, double em[10])
+{
+    int has_I16, is_var;
+    float fq, r;
+    anno16_t a;
+    float tmpf[4], tmpi;
+
+    bcf_get_info_float(call->hdr, rec, "I16", &call->anno16, &call->n16);
+
+    has_I16 = test16(call->anno16, &a) >= 0? 1 : 0;
+
+    // print EM
+    if (em[0] >= 0)
+    {
+        tmpf[0] = 1 - em[0];
+        bcf_update_info_float(call->hdr, rec, "AF1", tmpf, 1);
+    }
+    if (em[4] >= 0 && em[4] <= 0.05)
+    {
+        tmpf[0] = em[3]; tmpf[1] = em[2]; tmpf[2] = em[1]; tmpf[3] = em[4];
+        bcf_update_info_float(call->hdr, rec, "G3", tmpf, 3);
+        bcf_update_info_float(call->hdr, rec, "HWE", &tmpf[3], 1);
+    }
+    if (em[5] >= 0 && em[6] >= 0)
+    {
+        tmpf[0] = 1 - em[5]; tmpf[1] = 1 - em[6];
+        bcf_update_info_float(call->hdr, rec, "AF2", tmpf, 2);
+    }
+    if (em[7] >= 0)
+    {
+        tmpf[0] = em[7];
+        bcf_update_info_float(call->hdr, rec, "LRT", tmpf, 1);
+    }
+    if (em[8] >= 0)
+    {
+        tmpf[0] = em[8];
+        bcf_update_info_float(call->hdr, rec, "LRT2", tmpf, 1);
+    }
+
+    bcf_p1aux_t *p1 = call->cdat->p1;
+    if (p1->cons_llr > 0)
+    {
+        tmpi = p1->cons_llr;
+        bcf_update_info_int32(call->hdr, rec, "CLR", &tmpi, 1);
+        // todo: trio calling with -c
+        if (p1->cons_gt > 0)
+        {
+            char tmp[4];
+            tmp[0] = p1->cons_gt&0xff; tmp[1] = p1->cons_gt>>8&0xff; tmp[2] = p1->cons_gt>>16&0xff; tmp[3] = 0;
+            bcf_update_info_string(call->hdr, rec, "UGT", tmp);
+            tmp[0] = p1->cons_gt>>32&0xff; tmp[1] = p1->cons_gt>>40&0xff; tmp[2] = p1->cons_gt>>48&0xff;
+            bcf_update_info_string(call->hdr, rec, "CGT", tmp);
+        }
+    }
+    is_var = (pr->p_ref < call->pref);
+    r = is_var? pr->p_ref : pr->p_var;
+
+    bcf_update_info_int32(call->hdr, rec, "AC1", &pr->ac, 1);
+    int32_t dp[4]; dp[0] = call->anno16[0]; dp[1] = call->anno16[1]; dp[2] = call->anno16[2]; dp[3] = call->anno16[3];
+    bcf_update_info_int32(call->hdr, rec, "DP4", dp, 4);
+    bcf_update_info_int32(call->hdr, rec, "MQ", &a.mq, 1);
+
+    fq = pr->p_ref_folded < 0.5? -4.343 * log(pr->p_ref_folded) : 4.343 * log(pr->p_var_folded);
+    if (fq < -999) fq = -999;
+    if (fq > 999) fq = 999;
+    bcf_update_info_float(call->hdr, rec, "FQ", &fq, 1);
+
+    assert( pr->cmp[0]<0 );
+    // todo
+    //  if (pr->cmp[0] >= 0.) { // two sample groups
+    //      int i, q[3];
+    //      for (i = 1; i < 3; ++i) {
+    //          double x = pr->cmp[i] + pr->cmp[0]/2.;
+    //          q[i] = x == 0? 255 : (int)(-4.343 * log(x) + .499);
+    //          if (q[i] > 255) q[i] = 255;
+    //      }
+    //      if (pr->perm_rank >= 0) ksprintf(&s, "PR=%d;", pr->perm_rank);
+    //
+    //      ksprintf(&s, "PCHI2=%.3g;PC2=%d,%d;", q[1], q[2], pr->p_chi2);
+    //  }
+
+    if (has_I16 && a.is_tested)
+    {
+        int i;
+        for (i=0; i<4; i++) tmpf[i] = a.p[i];
+        bcf_update_info_float(call->hdr, rec, "PV4", tmpf, 4);
+    }
+    bcf_update_info_int32(call->hdr, rec, "I16", NULL, 0);     // remove I16 tag
+    bcf_update_info_int32(call->hdr, rec, "QS", NULL, 0);      // remove QS tag
+
+    rec->qual = r < 1e-100? 999 : -4.343 * log(r);
+    if (rec->qual > 999) rec->qual = 999;
+
+    // Remove unused alleles
+    int nals_ori = rec->n_allele, nals = !is_var && !(call->flag & CALL_KEEPALT) ? 1 : pr->rank0 < 2? 2 : pr->rank0+1;
+    if ( call->flag & CALL_KEEPALT && call->unseen==nals-1 ) nals--;
+    
+    if ( nals<rec->n_allele )
+    {
+        bcf_update_alleles(call->hdr, rec, (const char**)rec->d.allele, nals);
+
+        // Update PLs
+        int npls_src = call->nPLs / rec->n_sample, npls_dst = nals*(nals+1)/2;
+        int *pls_src = call->PLs - npls_src, *pls_dst = call->PLs - npls_dst;
+        int isample, i;
+        for (isample = 0; isample < rec->n_sample; isample++)
+        {
+            pls_src += npls_src;
+            pls_dst += npls_dst;
+            if ( !call->ploidy || call->ploidy[isample]==2 )
+            {
+                for (i=0; i<npls_dst; i++)
+                    pls_dst[i] =  pls_src[i];
+            }
+            else
+            {
+                for (i=0; i<nals; i++)
+                {
+                    int isrc = (i+1)*(i+2)/2-1;
+                    pls_dst[i] = pls_src[isrc];
+                }
+                if (i<npls_dst) pls_dst[i] = bcf_int32_vector_end;
+            }
+        }
+        bcf_update_format_int32(call->hdr, rec, "PL", call->PLs, npls_dst*rec->n_sample);
+    }
+
+    // Call genotypes
+    int i;
+    for (i=0; i<rec->n_sample; i++)
+    {
+        int x = ( is_var || call->output_tags & CALL_FMT_GQ ) ? bcf_p1_call_gt(p1, pr->f_exp, i, is_var) : 2;
+        int gt = x&3;
+        if ( !call->ploidy || call->ploidy[i]==2 )
+        {
+            if ( gt==1 )
+            {
+                call->gts[2*i]   = bcf_gt_unphased(0);
+                call->gts[2*i+1] = bcf_gt_unphased(1);
+            }
+            else if ( gt==0 )
+            {
+                call->gts[2*i]   = bcf_gt_unphased(1);
+                call->gts[2*i+1] = bcf_gt_unphased(1);
+            }
+            else
+            {
+                call->gts[2*i]   = bcf_gt_unphased(0);
+                call->gts[2*i+1] = bcf_gt_unphased(0);
+            }
+            if ( call->output_tags & CALL_FMT_GQ ) call->GQs[i] = x>>2;
+        }
+        else
+        {
+            if ( gt==0 ) call->gts[2*i] = bcf_gt_unphased(1);
+            else call->gts[2*i] = bcf_gt_unphased(0);
+            call->gts[2*i+1] = bcf_int32_vector_end;
+            if ( call->output_tags & CALL_FMT_GQ ) call->GQs[i] = bcf_int32_missing;
+        }
+    }
+    bcf_update_genotypes(call->hdr, rec, call->gts, rec->n_sample*2);
+    if ( call->output_tags & CALL_FMT_GQ )
+        bcf_update_format_int32(call->hdr, rec, "GQ", call->GQs, rec->n_sample);
+
+    // trim Number=R tags
+    int out_als = 0;
+    for (i=0; i<nals; i++) out_als |= 1<<i;
+    init_allele_trimming_maps(call, nals_ori, out_als);
+    mcall_trim_and_update_numberR(call, rec, nals_ori, nals);
+
+    return is_var;
+}
+
+
+int ccall(call_t *call, bcf1_t *rec)
+{
+    int nsmpl = bcf_hdr_nsamples(call->hdr);
+
+    // Get the genotype likelihoods
+    int nals = rec->n_allele;
+    call->nPLs = bcf_get_format_int32(call->hdr, rec, "PL", &call->PLs, &call->mPLs);
+    if ( call->nPLs!=nsmpl*nals*(nals+1)/2 && call->nPLs!=nsmpl*nals )  // diploid+haploid or haploid only
+        error("Wrong number of PL fields? nals=%d npl=%d\n", nals,call->nPLs);
+
+    // Convert PLs to probabilities, only first two alleles are considered
+    int ngts = nals*(nals+1)/2;
+    hts_expand(double, 3*nsmpl, call->npdg, call->pdg);
+    set_pdg3(call->pl2p, call->PLs, call->pdg, nsmpl, ngts);
+
+    double em[10] = {-1.,-1.,-1.,-1.,-1.,-1.,-1.,-1.,-1.,-1.};
+    int ret = bcf_em1(call, rec, call->ngrp1_samples, 0x1ff, em);
+
+    bcf_p1rst_t pr;
+    int do_contrast = (em[7] >= 0 && em[7] < call->min_lrt) ? 1 : 0;
+    ret = bcf_p1_cal(call, rec, do_contrast, call->cdat->p1, &pr);
+    if (pr.p_ref >= call->pref && (call->flag & CALL_VARONLY)) return 0;
+    if (ret >= 0) ret = update_bcf1(call, rec, &pr, em);
+    return ret;
+}
+
diff --git a/bcftools/ccall.c.pysam.c b/bcftools/ccall.c.pysam.c
new file mode 100644
index 0000000..eb7c615
--- /dev/null
+++ b/bcftools/ccall.c.pysam.c
@@ -0,0 +1,340 @@
+#include "bcftools.pysam.h"
+
+/*  ccall.c -- consensus variant calling.
+
+    Copyright (C) 2013-2014 Genome Research Ltd.
+    Portions copyright (C) 2010 Broad Institute.
+
+    Author: Petr Danecek <pd3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.  */
+
+#include <math.h>
+#include <assert.h>
+#include <htslib/kfunc.h>
+#include "call.h"
+#include "kmin.h"
+#include "prob1.h"
+
+// Most of the original -c calling was moved to bcftools as it was
+// and its data structures were wrapped into the ccal_t to make it
+// functional quickly. This is not the desired state.
+struct _ccall_t
+{
+    bcf_p1aux_t *p1;
+};
+
+void ccall_init(call_t *call)
+{
+    call->cdat = (ccall_t*) calloc(1,sizeof(ccall_t));
+    call_init_pl2p(call);
+    call->cdat->p1 = bcf_p1_init(bcf_hdr_nsamples(call->hdr), call->ploidy);
+    call->gts = (int*) calloc(bcf_hdr_nsamples(call->hdr)*2,sizeof(int));   // assuming at most diploid everywhere
+    call->nals_map = 5;
+    call->als_map  = (int*) malloc(sizeof(int)*call->nals_map);
+
+    bcf_hdr_append(call->hdr,"##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">");
+    if ( call->output_tags & CALL_FMT_GQ )
+    {
+        bcf_hdr_append(call->hdr,"##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">");
+        call->GQs = (int32_t*) malloc(sizeof(int32_t)*bcf_hdr_nsamples(call->hdr));
+    }
+    if ( call->output_tags & CALL_FMT_GP )
+        error("Sorry, -f GP is not supported with -c\n");
+    bcf_hdr_append(call->hdr,"##INFO=<ID=AF1,Number=1,Type=Float,Description=\"Max-likelihood estimate of the first ALT allele frequency (assuming HWE)\">");
+    // Todo: groups not migrated to 'bcftools call' yet
+    bcf_hdr_append(call->hdr,"##INFO=<ID=AF2,Number=1,Type=Float,Description=\"Max-likelihood estimate of the first and second group ALT allele frequency (assuming HWE)\">");
+    bcf_hdr_append(call->hdr,"##INFO=<ID=AC1,Number=1,Type=Float,Description=\"Max-likelihood estimate of the first ALT allele count (no HWE assumption)\">");
+    bcf_hdr_append(call->hdr,"##INFO=<ID=MQ,Number=1,Type=Integer,Description=\"Root-mean-square mapping quality of covering reads\">\n");
+    bcf_hdr_append(call->hdr,"##INFO=<ID=FQ,Number=1,Type=Float,Description=\"Phred probability of all samples being the same\">\n");
+    bcf_hdr_append(call->hdr,"##INFO=<ID=PV4,Number=4,Type=Float,Description=\"P-values for strand bias, baseQ bias, mapQ bias and tail distance bias\">\n");
+    bcf_hdr_append(call->hdr,"##INFO=<ID=G3,Number=3,Type=Float,Description=\"ML estimate of genotype frequencies\">\n");
+    bcf_hdr_append(call->hdr,"##INFO=<ID=HWE,Number=1,Type=Float,Description=\"Chi^2 based HWE test P-value based on G3\">\n");
+    // bcf_hdr_append(call->hdr,);
+    // bcf_hdr_append(call->hdr,);
+    bcf_hdr_append(call->hdr,"##INFO=<ID=DP4,Number=4,Type=Integer,Description=\"Number of high-quality ref-forward , ref-reverse, alt-forward and alt-reverse bases\">");
+
+    return;
+}
+void ccall_destroy(call_t *call)
+{
+    free(call->itmp);
+    free(call->als_map);
+    free(call->gts);
+    free(call->anno16);
+    free(call->PLs);
+    free(call->GQs);
+    free(call->pdg);
+    bcf_p1_destroy(call->cdat->p1);
+    free(call->cdat);
+    return;
+}
+
+// Inits P(D|G): convert PLs from log space, only two alleles (three PLs) are used.
+// NB: The original samtools calling code uses pdgs in reverse order (AA comes
+// first, RR last), while the -m calling model uses the canonical order.
+static void set_pdg3(double *pl2p, int *PLs, double *pdg, int n_smpl, int n_gt)
+{
+    int i;
+    for (i=0; i<n_smpl; i++)
+    {
+        pdg[2] = pl2p[ PLs[0] ];
+        pdg[1] = pl2p[ PLs[1] ];
+        pdg[0] = pl2p[ PLs[2] ];
+        PLs += n_gt;
+        pdg += 3;
+    }
+}
+
+static double ttest(int n1, int n2, float a[4])
+{
+    extern double kf_betai(double a, double b, double x);
+    double t, v, u1, u2;
+    if (n1 == 0 || n2 == 0 || n1 + n2 < 3) return 1.0;
+    u1 = (double)a[0] / n1; u2 = (double)a[2] / n2;
+    if (u1 <= u2) return 1.;
+    t = (u1 - u2) / sqrt(((a[1] - n1 * u1 * u1) + (a[3] - n2 * u2 * u2)) / (n1 + n2 - 2) * (1./n1 + 1./n2));
+    v = n1 + n2 - 2;
+    return t < 0.? 1. : .5 * kf_betai(.5*v, .5, v/(v+t*t));
+}
+
+static int test16_core(float anno[16], anno16_t *a)
+{
+    extern double kt_fisher_exact(int n11, int n12, int n21, int n22, double *_left, double *_right, double *two);
+    double left, right;
+    int i;
+    a->p[0] = a->p[1] = a->p[2] = a->p[3] = 1.;
+    for (i=0; i<4; i++) a->d[i] = anno[i];
+    a->depth = anno[0] + anno[1] + anno[2] + anno[3];
+    a->is_tested = (anno[0] + anno[1] > 0 && anno[2] + anno[3] > 0);
+    if (a->depth == 0) return -1;
+    a->mq = (int)(sqrt((anno[9] + anno[11]) / a->depth) + .499);
+    kt_fisher_exact(anno[0], anno[1], anno[2], anno[3], &left, &right, &a->p[0]);
+    for (i = 1; i < 4; ++i)
+        a->p[i] = ttest(anno[0] + anno[1], anno[2] + anno[3], anno+4*i);
+    return 0;
+}
+
+int test16(float *anno16, anno16_t *a)
+{
+    a->p[0] = a->p[1] = a->p[2] = a->p[3] = 1.;
+    a->d[0] = a->d[1] = a->d[2] = a->d[3] = 0.;
+    a->mq = a->depth = a->is_tested = 0;
+    return test16_core(anno16, a);
+}
+static int update_bcf1(call_t *call, bcf1_t *rec, const bcf_p1rst_t *pr, double em[10])
+{
+    int has_I16, is_var;
+    float fq, r;
+    anno16_t a;
+    float tmpf[4], tmpi;
+
+    bcf_get_info_float(call->hdr, rec, "I16", &call->anno16, &call->n16);
+
+    has_I16 = test16(call->anno16, &a) >= 0? 1 : 0;
+
+    // print EM
+    if (em[0] >= 0)
+    {
+        tmpf[0] = 1 - em[0];
+        bcf_update_info_float(call->hdr, rec, "AF1", tmpf, 1);
+    }
+    if (em[4] >= 0 && em[4] <= 0.05)
+    {
+        tmpf[0] = em[3]; tmpf[1] = em[2]; tmpf[2] = em[1]; tmpf[3] = em[4];
+        bcf_update_info_float(call->hdr, rec, "G3", tmpf, 3);
+        bcf_update_info_float(call->hdr, rec, "HWE", &tmpf[3], 1);
+    }
+    if (em[5] >= 0 && em[6] >= 0)
+    {
+        tmpf[0] = 1 - em[5]; tmpf[1] = 1 - em[6];
+        bcf_update_info_float(call->hdr, rec, "AF2", tmpf, 2);
+    }
+    if (em[7] >= 0)
+    {
+        tmpf[0] = em[7];
+        bcf_update_info_float(call->hdr, rec, "LRT", tmpf, 1);
+    }
+    if (em[8] >= 0)
+    {
+        tmpf[0] = em[8];
+        bcf_update_info_float(call->hdr, rec, "LRT2", tmpf, 1);
+    }
+
+    bcf_p1aux_t *p1 = call->cdat->p1;
+    if (p1->cons_llr > 0)
+    {
+        tmpi = p1->cons_llr;
+        bcf_update_info_int32(call->hdr, rec, "CLR", &tmpi, 1);
+        // todo: trio calling with -c
+        if (p1->cons_gt > 0)
+        {
+            char tmp[4];
+            tmp[0] = p1->cons_gt&0xff; tmp[1] = p1->cons_gt>>8&0xff; tmp[2] = p1->cons_gt>>16&0xff; tmp[3] = 0;
+            bcf_update_info_string(call->hdr, rec, "UGT", tmp);
+            tmp[0] = p1->cons_gt>>32&0xff; tmp[1] = p1->cons_gt>>40&0xff; tmp[2] = p1->cons_gt>>48&0xff;
+            bcf_update_info_string(call->hdr, rec, "CGT", tmp);
+        }
+    }
+    is_var = (pr->p_ref < call->pref);
+    r = is_var? pr->p_ref : pr->p_var;
+
+    bcf_update_info_int32(call->hdr, rec, "AC1", &pr->ac, 1);
+    int32_t dp[4]; dp[0] = call->anno16[0]; dp[1] = call->anno16[1]; dp[2] = call->anno16[2]; dp[3] = call->anno16[3];
+    bcf_update_info_int32(call->hdr, rec, "DP4", dp, 4);
+    bcf_update_info_int32(call->hdr, rec, "MQ", &a.mq, 1);
+
+    fq = pr->p_ref_folded < 0.5? -4.343 * log(pr->p_ref_folded) : 4.343 * log(pr->p_var_folded);
+    if (fq < -999) fq = -999;
+    if (fq > 999) fq = 999;
+    bcf_update_info_float(call->hdr, rec, "FQ", &fq, 1);
+
+    assert( pr->cmp[0]<0 );
+    // todo
+    //  if (pr->cmp[0] >= 0.) { // two sample groups
+    //      int i, q[3];
+    //      for (i = 1; i < 3; ++i) {
+    //          double x = pr->cmp[i] + pr->cmp[0]/2.;
+    //          q[i] = x == 0? 255 : (int)(-4.343 * log(x) + .499);
+    //          if (q[i] > 255) q[i] = 255;
+    //      }
+    //      if (pr->perm_rank >= 0) ksprintf(&s, "PR=%d;", pr->perm_rank);
+    //
+    //      ksprintf(&s, "PCHI2=%.3g;PC2=%d,%d;", q[1], q[2], pr->p_chi2);
+    //  }
+
+    if (has_I16 && a.is_tested)
+    {
+        int i;
+        for (i=0; i<4; i++) tmpf[i] = a.p[i];
+        bcf_update_info_float(call->hdr, rec, "PV4", tmpf, 4);
+    }
+    bcf_update_info_int32(call->hdr, rec, "I16", NULL, 0);     // remove I16 tag
+    bcf_update_info_int32(call->hdr, rec, "QS", NULL, 0);      // remove QS tag
+
+    rec->qual = r < 1e-100? 999 : -4.343 * log(r);
+    if (rec->qual > 999) rec->qual = 999;
+
+    // Remove unused alleles
+    int nals_ori = rec->n_allele, nals = !is_var && !(call->flag & CALL_KEEPALT) ? 1 : pr->rank0 < 2? 2 : pr->rank0+1;
+    if ( call->flag & CALL_KEEPALT && call->unseen==nals-1 ) nals--;
+    
+    if ( nals<rec->n_allele )
+    {
+        bcf_update_alleles(call->hdr, rec, (const char**)rec->d.allele, nals);
+
+        // Update PLs
+        int npls_src = call->nPLs / rec->n_sample, npls_dst = nals*(nals+1)/2;
+        int *pls_src = call->PLs - npls_src, *pls_dst = call->PLs - npls_dst;
+        int isample, i;
+        for (isample = 0; isample < rec->n_sample; isample++)
+        {
+            pls_src += npls_src;
+            pls_dst += npls_dst;
+            if ( !call->ploidy || call->ploidy[isample]==2 )
+            {
+                for (i=0; i<npls_dst; i++)
+                    pls_dst[i] =  pls_src[i];
+            }
+            else
+            {
+                for (i=0; i<nals; i++)
+                {
+                    int isrc = (i+1)*(i+2)/2-1;
+                    pls_dst[i] = pls_src[isrc];
+                }
+                if (i<npls_dst) pls_dst[i] = bcf_int32_vector_end;
+            }
+        }
+        bcf_update_format_int32(call->hdr, rec, "PL", call->PLs, npls_dst*rec->n_sample);
+    }
+
+    // Call genotypes
+    int i;
+    for (i=0; i<rec->n_sample; i++)
+    {
+        int x = ( is_var || call->output_tags & CALL_FMT_GQ ) ? bcf_p1_call_gt(p1, pr->f_exp, i, is_var) : 2;
+        int gt = x&3;
+        if ( !call->ploidy || call->ploidy[i]==2 )
+        {
+            if ( gt==1 )
+            {
+                call->gts[2*i]   = bcf_gt_unphased(0);
+                call->gts[2*i+1] = bcf_gt_unphased(1);
+            }
+            else if ( gt==0 )
+            {
+                call->gts[2*i]   = bcf_gt_unphased(1);
+                call->gts[2*i+1] = bcf_gt_unphased(1);
+            }
+            else
+            {
+                call->gts[2*i]   = bcf_gt_unphased(0);
+                call->gts[2*i+1] = bcf_gt_unphased(0);
+            }
+            if ( call->output_tags & CALL_FMT_GQ ) call->GQs[i] = x>>2;
+        }
+        else
+        {
+            if ( gt==0 ) call->gts[2*i] = bcf_gt_unphased(1);
+            else call->gts[2*i] = bcf_gt_unphased(0);
+            call->gts[2*i+1] = bcf_int32_vector_end;
+            if ( call->output_tags & CALL_FMT_GQ ) call->GQs[i] = bcf_int32_missing;
+        }
+    }
+    bcf_update_genotypes(call->hdr, rec, call->gts, rec->n_sample*2);
+    if ( call->output_tags & CALL_FMT_GQ )
+        bcf_update_format_int32(call->hdr, rec, "GQ", call->GQs, rec->n_sample);
+
+    // trim Number=R tags
+    int out_als = 0;
+    for (i=0; i<nals; i++) out_als |= 1<<i;
+    init_allele_trimming_maps(call, nals_ori, out_als);
+    mcall_trim_and_update_numberR(call, rec, nals_ori, nals);
+
+    return is_var;
+}
+
+
+int ccall(call_t *call, bcf1_t *rec)
+{
+    int nsmpl = bcf_hdr_nsamples(call->hdr);
+
+    // Get the genotype likelihoods
+    int nals = rec->n_allele;
+    call->nPLs = bcf_get_format_int32(call->hdr, rec, "PL", &call->PLs, &call->mPLs);
+    if ( call->nPLs!=nsmpl*nals*(nals+1)/2 && call->nPLs!=nsmpl*nals )  // diploid+haploid or haploid only
+        error("Wrong number of PL fields? nals=%d npl=%d\n", nals,call->nPLs);
+
+    // Convert PLs to probabilities, only first two alleles are considered
+    int ngts = nals*(nals+1)/2;
+    hts_expand(double, 3*nsmpl, call->npdg, call->pdg);
+    set_pdg3(call->pl2p, call->PLs, call->pdg, nsmpl, ngts);
+
+    double em[10] = {-1.,-1.,-1.,-1.,-1.,-1.,-1.,-1.,-1.,-1.};
+    int ret = bcf_em1(call, rec, call->ngrp1_samples, 0x1ff, em);
+
+    bcf_p1rst_t pr;
+    int do_contrast = (em[7] >= 0 && em[7] < call->min_lrt) ? 1 : 0;
+    ret = bcf_p1_cal(call, rec, do_contrast, call->cdat->p1, &pr);
+    if (pr.p_ref >= call->pref && (call->flag & CALL_VARONLY)) return 0;
+    if (ret >= 0) ret = update_bcf1(call, rec, &pr, em);
+    return ret;
+}
+
diff --git a/bcftools/cols.c b/bcftools/cols.c
new file mode 100644
index 0000000..30ca365
--- /dev/null
+++ b/bcftools/cols.c
@@ -0,0 +1,109 @@
+/* 
+    Copyright (C) 2019 Genome Research Ltd.
+    
+    Author: Petr Danecek <pd3@sanger.ac.uk>
+    
+    Permission is hereby granted, free of charge, to any person obtaining a copy
+    of this software and associated documentation files (the "Software"), to deal
+    in the Software without restriction, including without limitation the rights
+    to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+    copies of the Software, and to permit persons to whom the Software is
+    furnished to do so, subject to the following conditions:
+    
+    The above copyright notice and this permission notice shall be included in
+    all copies or substantial portions of the Software.
+    
+    THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+    IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+    FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+    THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+    LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+    FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+    DEALINGS IN THE SOFTWARE.
+*/
+
+#include <string.h>
+#include "cols.h"
+
+cols_t *cols_split(const char *line, cols_t *cols, char delim)
+{
+    if ( !cols ) cols = (cols_t*) calloc(1,sizeof(cols_t));
+    if ( cols->rmme ) free(cols->rmme);
+    cols->n = 0;
+    cols->rmme = strdup(line);
+    char *ss = cols->rmme;
+    while (1)
+    {
+        char *se = ss;
+        while ( *se && *se!=delim ) se++;
+        char tmp = *se;
+        *se = 0;
+        cols->n++;
+        if ( cols->n > cols->m )
+        {
+            cols->m += 10;
+            cols->off = (char**) realloc(cols->off, sizeof(*cols->off)*cols->m);
+        }
+        cols->off[ cols->n - 1 ] = ss;
+        if ( !tmp ) break;
+        ss = se + 1;
+    }
+    return cols;
+}
+
+void cols_append(cols_t *cols, char *str)
+{
+    if ( cols->rmme )
+    {
+        size_t str_len = strlen(str);
+        size_t lst_len = strlen(cols->off[ cols->n - 1 ]);
+        size_t tot_len = 2 + str_len + lst_len + (cols->off[ cols->n - 1 ] - cols->rmme);
+
+        cols_t *tmp_cols = (cols_t*)calloc(1,sizeof(cols_t));
+        tmp_cols->rmme = (char*) calloc(tot_len,1);
+        tmp_cols->off  = (char**) calloc(cols->n+1,sizeof(*tmp_cols->off));
+
+        char *ptr = tmp_cols->rmme;
+        int i;
+        for (i=0; i<cols->n; i++)
+        {
+            size_t len = strlen(cols->off[i]);
+            memcpy(ptr, cols->off[i], len);
+            tmp_cols->off[i] = ptr;
+            ptr += len + 1;
+        }
+        memcpy(ptr, str, str_len);
+        tmp_cols->off[i] = ptr;
+
+        free(cols->off);
+        free(cols->rmme);
+        cols->rmme = tmp_cols->rmme;
+        cols->off  = tmp_cols->off;
+        cols->n    = cols->n+1;
+        cols->m    = cols->n;
+        free(tmp_cols);
+        return;
+    }
+    cols->n++;
+    if ( cols->n > cols->m )
+    {
+        cols->m++;
+        cols->off = (char**) realloc(cols->off,sizeof(*cols->off)*cols->m);
+    }
+    cols->off[cols->n-1] = str;
+}
+void cols_clear(cols_t *cols)
+{
+    if ( !cols ) return;
+    free(cols->rmme);
+    free(cols->off);
+    cols->rmme = NULL;
+    cols->off  = NULL;
+}
+void cols_destroy(cols_t *cols)
+{
+    if ( !cols ) return;
+    cols_clear(cols);
+    free(cols);
+}
+
diff --git a/bcftools/cols.c.pysam.c b/bcftools/cols.c.pysam.c
new file mode 100644
index 0000000..b8309cc
--- /dev/null
+++ b/bcftools/cols.c.pysam.c
@@ -0,0 +1,111 @@
+#include "bcftools.pysam.h"
+
+/* 
+    Copyright (C) 2019 Genome Research Ltd.
+    
+    Author: Petr Danecek <pd3@sanger.ac.uk>
+    
+    Permission is hereby granted, free of charge, to any person obtaining a copy
+    of this software and associated documentation files (the "Software"), to deal
+    in the Software without restriction, including without limitation the rights
+    to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+    copies of the Software, and to permit persons to whom the Software is
+    furnished to do so, subject to the following conditions:
+    
+    The above copyright notice and this permission notice shall be included in
+    all copies or substantial portions of the Software.
+    
+    THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+    IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+    FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+    THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+    LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+    FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+    DEALINGS IN THE SOFTWARE.
+*/
+
+#include <string.h>
+#include "cols.h"
+
+cols_t *cols_split(const char *line, cols_t *cols, char delim)
+{
+    if ( !cols ) cols = (cols_t*) calloc(1,sizeof(cols_t));
+    if ( cols->rmme ) free(cols->rmme);
+    cols->n = 0;
+    cols->rmme = strdup(line);
+    char *ss = cols->rmme;
+    while (1)
+    {
+        char *se = ss;
+        while ( *se && *se!=delim ) se++;
+        char tmp = *se;
+        *se = 0;
+        cols->n++;
+        if ( cols->n > cols->m )
+        {
+            cols->m += 10;
+            cols->off = (char**) realloc(cols->off, sizeof(*cols->off)*cols->m);
+        }
+        cols->off[ cols->n - 1 ] = ss;
+        if ( !tmp ) break;
+        ss = se + 1;
+    }
+    return cols;
+}
+
+void cols_append(cols_t *cols, char *str)
+{
+    if ( cols->rmme )
+    {
+        size_t str_len = strlen(str);
+        size_t lst_len = strlen(cols->off[ cols->n - 1 ]);
+        size_t tot_len = 2 + str_len + lst_len + (cols->off[ cols->n - 1 ] - cols->rmme);
+
+        cols_t *tmp_cols = (cols_t*)calloc(1,sizeof(cols_t));
+        tmp_cols->rmme = (char*) calloc(tot_len,1);
+        tmp_cols->off  = (char**) calloc(cols->n+1,sizeof(*tmp_cols->off));
+
+        char *ptr = tmp_cols->rmme;
+        int i;
+        for (i=0; i<cols->n; i++)
+        {
+            size_t len = strlen(cols->off[i]);
+            memcpy(ptr, cols->off[i], len);
+            tmp_cols->off[i] = ptr;
+            ptr += len + 1;
+        }
+        memcpy(ptr, str, str_len);
+        tmp_cols->off[i] = ptr;
+
+        free(cols->off);
+        free(cols->rmme);
+        cols->rmme = tmp_cols->rmme;
+        cols->off  = tmp_cols->off;
+        cols->n    = cols->n+1;
+        cols->m    = cols->n;
+        free(tmp_cols);
+        return;
+    }
+    cols->n++;
+    if ( cols->n > cols->m )
+    {
+        cols->m++;
+        cols->off = (char**) realloc(cols->off,sizeof(*cols->off)*cols->m);
+    }
+    cols->off[cols->n-1] = str;
+}
+void cols_clear(cols_t *cols)
+{
+    if ( !cols ) return;
+    free(cols->rmme);
+    free(cols->off);
+    cols->rmme = NULL;
+    cols->off  = NULL;
+}
+void cols_destroy(cols_t *cols)
+{
+    if ( !cols ) return;
+    cols_clear(cols);
+    free(cols);
+}
+
diff --git a/bcftools/cols.h b/bcftools/cols.h
new file mode 100644
index 0000000..577f2d1
--- /dev/null
+++ b/bcftools/cols.h
@@ -0,0 +1,51 @@
+/* 
+    Copyright (C) 2019 Genome Research Ltd.
+    
+    Author: Petr Danecek <pd3@sanger.ac.uk>
+    
+    Permission is hereby granted, free of charge, to any person obtaining a copy
+    of this software and associated documentation files (the "Software"), to deal
+    in the Software without restriction, including without limitation the rights
+    to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+    copies of the Software, and to permit persons to whom the Software is
+    furnished to do so, subject to the following conditions:
+    
+    The above copyright notice and this permission notice shall be included in
+    all copies or substantial portions of the Software.
+    
+    THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+    IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+    FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+    THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+    LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+    FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+    DEALINGS IN THE SOFTWARE.
+*/
+
+#ifndef __COLS_H__
+#define __COLS_H__
+
+#include <stdlib.h>
+
+typedef struct
+{
+    int n,m;
+    char **off, *rmme;
+}
+cols_t;
+
+/*
+    cols_split() can be called repeatedly to split new strings, memory is allocated
+    and deallocated automatically
+*/
+cols_t *cols_split(const char *line, cols_t *cols, char delim);
+
+/* 
+    Although cols_append() can be combined with cols_split(), it is much slower and
+    the string must exist throughout the life of cols unless initialized with cols_split().
+*/
+void cols_append(cols_t *cols, char *str);
+void cols_clear(cols_t *cols);
+void cols_destroy(cols_t *cols);
+
+#endif
diff --git a/bcftools/consensus.c b/bcftools/consensus.c
new file mode 100644
index 0000000..84ae905
--- /dev/null
+++ b/bcftools/consensus.c
@@ -0,0 +1,1173 @@
+/* The MIT License
+
+   Copyright (c) 2014-2022 Genome Research Ltd.
+
+   Author: Petr Danecek <pd3@sanger.ac.uk>
+
+   Permission is hereby granted, free of charge, to any person obtaining a copy
+   of this software and associated documentation files (the "Software"), to deal
+   in the Software without restriction, including without limitation the rights
+   to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+   copies of the Software, and to permit persons to whom the Software is
+   furnished to do so, subject to the following conditions:
+
+   The above copyright notice and this permission notice shall be included in
+   all copies or substantial portions of the Software.
+
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+   IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+   FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+   AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+   LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+   OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+   THE SOFTWARE.
+
+ */
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <strings.h>
+#include <assert.h>
+#include <errno.h>
+#include <getopt.h>
+#include <unistd.h>
+#include <ctype.h>
+#include <htslib/vcf.h>
+#include <htslib/kstring.h>
+#include <htslib/synced_bcf_reader.h>
+#include <htslib/kseq.h>
+#include <htslib/bgzf.h>
+#include "regidx.h"
+#include "bcftools.h"
+#include "rbuf.h"
+#include "filter.h"
+
+// Logic of the filters: include or exclude sites which match the filters?
+#define FLT_INCLUDE 1
+#define FLT_EXCLUDE 2
+
+#define PICK_REF   1
+#define PICK_ALT   2
+#define PICK_LONG  4
+#define PICK_SHORT 8
+#define PICK_IUPAC 16
+
+#define TO_UPPER 0
+#define TO_LOWER 1
+
+typedef struct
+{
+    int num;                // number of ungapped blocks in this chain
+    int *block_lengths;     // length of the ungapped blocks in this chain
+    int *ref_gaps;          // length of the gaps on the reference sequence between blocks
+    int *alt_gaps;          // length of the gaps on the alternative sequence between blocks
+    int ori_pos;
+    int ref_last_block_ori; // start position on the reference sequence of the following ungapped block (0-based)
+    int alt_last_block_ori; // start position on the alternative sequence of the following ungapped block (0-based)
+}
+chain_t;
+
+#define MASK_LC 1
+#define MASK_UC 2
+#define MASK_SKIP(x) (((x)->with!=MASK_LC && (x)->with!=MASK_UC) ? 1 : 0)
+typedef struct
+{
+    char *fname, with;
+    regidx_t *idx;
+    regitr_t *itr;
+}
+mask_t;
+
+typedef struct
+{
+    kstring_t fa_buf;   // buffered reference sequence
+    int fa_ori_pos;     // start position of the fa_buffer (wrt original sequence)
+    int fa_frz_pos;     // protected position to avoid conflicting variants (last pos for SNPs/ins)
+    int fa_mod_off;     // position difference of fa_frz_pos in the ori and modified sequence (ins positive)
+    int fa_frz_mod;     // the fa_buf offset of the protected fa_frz_pos position, includes the modified sequence
+    int fa_end_pos;     // region's end position in the original sequence
+    int fa_length;      // region's length in the original sequence (in case end_pos not provided in the FASTA header)
+    int fa_case;        // output upper case or lower case: TO_UPPER|TO_LOWER
+    int fa_src_pos;     // last genomic coordinate read from the input fasta (0-based)
+    char prev_base;     // this is only to validate the REF allele in the VCF - the modified fa_buf cannot be used for inserts following deletions, see 600#issuecomment-383186778
+    int prev_base_pos;  // the position of prev_base
+    int prev_is_insert;
+
+    rbuf_t vcf_rbuf;
+    bcf1_t **vcf_buf;
+    int nvcf_buf, rid;
+    char *chr, *chr_prefix;
+
+    mask_t *mask;
+    int nmask;
+
+    int chain_id;       // chain_id, to provide a unique ID to each chain in the chain output
+    chain_t *chain;     // chain structure to store the sequence of ungapped blocks between the ref and alt sequences
+                        // Note that the chain is re-initialised for each chromosome/seq_region
+
+    filter_t *filter;
+    char *filter_str;
+    int filter_logic;   // include or exclude sites which match the filters? One of FLT_INCLUDE/FLT_EXCLUDE
+
+    bcf_srs_t *files;
+    bcf_hdr_t *hdr;
+    FILE *fp_out;
+    FILE *fp_chain;
+    char **argv;
+    int argc, output_iupac, haplotype, allele, isample, napplied;
+    uint8_t *iupac_bitmask;
+    int miupac_bitmask;
+    char *fname, *ref_fname, *sample, *output_fname, *mask_fname, *chain_fname, missing_allele, absent_allele;
+    char mark_del, mark_ins, mark_snv;
+}
+args_t;
+
+static void destroy_chain(chain_t *chain)
+{
+    if ( !chain ) return;
+    free(chain->ref_gaps);
+    free(chain->alt_gaps);
+    free(chain->block_lengths);
+    free(chain);
+}
+static chain_t* init_chain(chain_t *chain, int ref_ori_pos)
+{
+    if ( chain ) destroy_chain(chain);
+    chain = (chain_t*) calloc(1,sizeof(chain_t));
+    chain->num = 0;
+    chain->block_lengths = NULL;
+    chain->ref_gaps = NULL;
+    chain->alt_gaps = NULL;
+    chain->ori_pos = ref_ori_pos;
+    chain->ref_last_block_ori = ref_ori_pos;
+    chain->alt_last_block_ori = ref_ori_pos;
+    return chain;
+}
+
+static void print_chain(args_t *args)
+{
+    /*
+        Example chain format (see: https://genome.ucsc.edu/goldenPath/help/chain.html):
+        chain 1 500 + 480 500 1 501 + 480 501 1
+        12 3 1
+        1 0 3
+        484
+
+        chain line is:
+        - chain
+        - score (sum of the length of ungapped block in this case)
+        - ref_seqname (from the fasta header, parsed by htslib)
+        - ref_seqlength (from the fasta header)
+        - ref_strand (+ or -; always + for bcf-consensus)
+        - ref_start (as defined in the fasta header)
+        - ref_end (as defined in the fasta header)
+        - alt_seqname (same as ref_seqname as bcf-consensus only considers SNPs and indels)
+        - alt_seqlength (adjusted to match the length of the alt sequence)
+        - alt_strand (+ or -; always + for bcf-consensus)
+        - alt_start (same as ref_start, as no edits are recorded/applied before that position)
+        - alt_end (adjusted to match the length of the alt sequence)
+        - chain_num (just an auto-increment id)
+
+        the other (sorted) lines are:
+        - length of the ungapped alignment block
+        - gap on the ref sequence between this and the next block (all but the last line)
+        - gap on the alt sequence between this and the next block (all but the last line)
+    */
+    chain_t *chain = args->chain;
+    int n = chain->num;
+    int ref_end_pos = args->fa_length + chain->ori_pos;
+    int last_block_size = ref_end_pos - chain->ref_last_block_ori;
+    int alt_end_pos = chain->alt_last_block_ori + last_block_size;
+    int score = 0;
+    for (n=0; n<chain->num; n++) {
+        score += chain->block_lengths[n];
+    }
+    score += last_block_size;
+    fprintf(args->fp_chain, "chain %d %s %d + %d %d %s %d + %d %d %d\n", score, args->chr, ref_end_pos, chain->ori_pos, ref_end_pos, args->chr, alt_end_pos, chain->ori_pos, alt_end_pos, ++args->chain_id);
+    for (n=0; n<chain->num; n++) {
+        fprintf(args->fp_chain, "%d %d %d\n", chain->block_lengths[n], chain->ref_gaps[n], chain->alt_gaps[n]);
+    }
+    fprintf(args->fp_chain, "%d\n\n", last_block_size);
+}
+
+static void push_chain_gap(chain_t *chain, int ref_start, int ref_len, int alt_start, int alt_len)
+{
+    // fprintf(stderr, "push_chain_gap(chain=%p, ref_start=%d, ref_len=%d, alt_start=%d, alt_len=%d)\n", chain, ref_start, ref_len, alt_start, alt_len);
+    int num = chain->num;
+
+    if (num && ref_start <= chain->ref_last_block_ori) {
+        // In case this variant is back-to-back with the previous one
+        chain->ref_last_block_ori = ref_start + ref_len;
+        chain->alt_last_block_ori = alt_start + alt_len;
+        chain->ref_gaps[num-1] += ref_len;
+        chain->alt_gaps[num-1] += alt_len;
+
+    } else {
+        // Extend the ungapped blocks, store the gap length
+        chain->block_lengths = (int*) realloc(chain->block_lengths, (num + 1) * sizeof(int));
+        chain->ref_gaps = (int*) realloc(chain->ref_gaps, (num + 1) * sizeof(int));
+        chain->alt_gaps = (int*) realloc(chain->alt_gaps, (num + 1) * sizeof(int));
+        chain->block_lengths[num] = ref_start - chain->ref_last_block_ori;
+        chain->ref_gaps[num] = ref_len;
+        chain->alt_gaps[num] = alt_len;
+        // Update the start positions of the next block
+        chain->ref_last_block_ori = ref_start + ref_len;
+        chain->alt_last_block_ori = alt_start + alt_len;
+        // Increment the number of ungapped blocks
+        chain->num++;
+    }
+}
+
+static void init_data(args_t *args)
+{
+    args->files = bcf_sr_init();
+    args->files->require_index = 1;
+    if ( !bcf_sr_add_reader(args->files,args->fname) ) error("Failed to read from %s: %s\n", !strcmp("-",args->fname)?"standard input":args->fname, bcf_sr_strerror(args->files->errnum));
+    args->hdr = args->files->readers[0].header;
+    args->isample = -1;
+    if ( args->sample )
+    {
+        args->isample = bcf_hdr_id2int(args->hdr,BCF_DT_SAMPLE,args->sample);
+        if ( args->isample<0 ) error("No such sample: %s\n", args->sample);
+    }
+    if ( (args->haplotype || args->allele) && args->isample<0 )
+    {
+        if ( bcf_hdr_nsamples(args->hdr) > 1 ) error("The --sample option is expected with --haplotype\n");
+        args->isample = 0;
+    }
+    int i;
+    for (i=0; i<args->nmask; i++)
+    {
+        mask_t *mask = &args->mask[i];
+        mask->idx = regidx_init(mask->fname,NULL,NULL,0,NULL);
+        if ( !mask->idx ) error("Failed to initialize mask regions\n");
+        mask->itr = regitr_init(mask->idx);
+    }
+    // In case we want to store the chains
+    if ( args->chain_fname )
+    {
+        args->fp_chain = fopen(args->chain_fname,"w");
+        if ( ! args->fp_chain ) error("Failed to create %s: %s\n", args->chain_fname, strerror(errno));
+        args->chain_id = 0;
+    }
+    rbuf_init(&args->vcf_rbuf, 100);
+    args->vcf_buf = (bcf1_t**) calloc(args->vcf_rbuf.m, sizeof(bcf1_t*));
+    if ( args->output_fname ) {
+        args->fp_out = fopen(args->output_fname,"w");
+        if ( ! args->fp_out ) error("Failed to create %s: %s\n", args->output_fname, strerror(errno));
+    }
+    else args->fp_out = stdout;
+    if ( args->isample<0 ) fprintf(stderr,"Note: the --sample option not given, applying all records regardless of the genotype\n");
+    if ( args->filter_str )
+        args->filter = filter_init(args->hdr, args->filter_str);
+    args->rid = -1;
+}
+static void add_mask(args_t *args, char *fname)
+{
+    args->nmask++;
+    args->mask = (mask_t*)realloc(args->mask,args->nmask*sizeof(*args->mask));
+    mask_t *mask = &args->mask[args->nmask-1];
+    mask->fname = fname;
+    mask->with  = 'N';
+}
+static void add_mask_with(args_t *args, char *with)
+{
+    if ( !args->nmask ) error("The --mask-with option must follow --mask\n");
+    mask_t *mask = &args->mask[args->nmask-1];
+    if ( !strcasecmp(with,"uc") ) mask->with = MASK_UC;
+    else if ( !strcasecmp(with,"lc") ) mask->with = MASK_LC;
+    else if ( strlen(with)!=1 ) error("Expected \"lc\", \"uc\", or a single character with the --mask-with option\n");
+    else mask->with = *with;
+}
+static void destroy_data(args_t *args)
+{
+    free(args->iupac_bitmask);
+    if (args->filter) filter_destroy(args->filter);
+    bcf_sr_destroy(args->files);
+    int i;
+    for (i=0; i<args->vcf_rbuf.m; i++)
+        if ( args->vcf_buf[i] ) bcf_destroy1(args->vcf_buf[i]);
+    free(args->vcf_buf);
+    free(args->fa_buf.s);
+    free(args->chr);
+    for (i=0; i<args->nmask; i++)
+    {
+        mask_t *mask = &args->mask[i];
+        regidx_destroy(mask->idx);
+        regitr_destroy(mask->itr);
+    }
+    free(args->mask);
+    if ( args->chain_fname )
+        if ( fclose(args->fp_chain) ) error("Close failed: %s\n", args->chain_fname);
+    if ( fclose(args->fp_out) ) error("Close failed: %s\n", args->output_fname);
+    destroy_chain(args->chain);
+}
+
+static void init_region(args_t *args, char *line)
+{
+    char *ss, *se = line;
+    while ( *se && !isspace(*se) && *se!=':' ) se++;
+    int from = 0, to = 0;
+    char tmp = 0, *tmp_ptr = NULL;
+    if ( *se )
+    {
+        tmp = *se; *se = 0; tmp_ptr = se;
+        ss = ++se;
+        from = strtol(ss,&se,10);
+        if ( ss==se || !*se || *se!='-' ) from = 0;
+        else
+        {
+            from--;
+            ss = ++se;
+            to = strtol(ss,&se,10);
+            if ( ss==se || (*se && !isspace(*se)) ) { from = 0; to = 0; }
+            else to--;
+        }
+    }
+    free(args->chr);
+    args->chr = strdup(line);
+    args->rid = bcf_hdr_name2id(args->hdr,line);
+    if ( args->rid<0 ) fprintf(stderr,"Warning: Sequence \"%s\" not in %s\n", line,args->fname);
+    args->prev_base_pos = -1;
+    args->fa_buf.l  = 0;
+    args->fa_length = 0;
+    args->fa_end_pos = to;
+    args->fa_ori_pos = from;
+    args->fa_src_pos = from;
+    args->fa_mod_off = 0;
+    args->fa_frz_pos = -1;
+    args->fa_frz_mod = -1;
+    args->fa_case    = -1;
+    args->vcf_rbuf.n = 0;
+    bcf_sr_seek(args->files,line,args->fa_ori_pos);
+    if ( tmp_ptr ) *tmp_ptr = tmp;
+    fprintf(args->fp_out,">%s%s\n",args->chr_prefix?args->chr_prefix:"",line);
+    if ( args->chain_fname )
+        args->chain = init_chain(args->chain, args->fa_ori_pos);
+}
+
+static bcf1_t **next_vcf_line(args_t *args)
+{
+    if ( args->vcf_rbuf.n )
+    {
+        int i = rbuf_shift(&args->vcf_rbuf);
+        return &args->vcf_buf[i];
+    }
+    while ( bcf_sr_next_line(args->files) )
+    {
+        if ( args->filter )
+        {
+            int is_ok = filter_test(args->filter, bcf_sr_get_line(args->files,0), NULL);
+            if ( args->filter_logic & FLT_EXCLUDE ) is_ok = is_ok ? 0 : 1;
+            if ( !is_ok ) continue;
+        }
+        return &args->files->readers[0].buffer[0];
+    }
+    return NULL;
+}
+static void unread_vcf_line(args_t *args, bcf1_t **rec_ptr)
+{
+    bcf1_t *rec = *rec_ptr;
+    if ( args->vcf_rbuf.n >= args->vcf_rbuf.m )
+        error("FIXME: too many overlapping records near %s:%"PRId64"\n", bcf_seqname(args->hdr,rec),(int64_t) rec->pos+1);
+
+    // Insert the new record in the buffer. The line would be overwritten in
+    // the next bcf_sr_next_line call, therefore we need to swap it with an
+    // unused one
+    int i = rbuf_append(&args->vcf_rbuf);
+    if ( !args->vcf_buf[i] ) args->vcf_buf[i] = bcf_init1();
+    bcf1_t *tmp = rec; *rec_ptr = args->vcf_buf[i]; args->vcf_buf[i] = tmp;
+}
+static void flush_fa_buffer(args_t *args, int len)
+{
+    if ( !args->fa_buf.l ) return;
+    int nwr = 0;
+    while ( nwr + 60 <= args->fa_buf.l )
+    {
+        if ( fwrite(args->fa_buf.s+nwr,1,60,args->fp_out) != 60 ) error("Could not write: %s\n", args->output_fname);
+        if ( fwrite("\n",1,1,args->fp_out) != 1 ) error("Could not write: %s\n", args->output_fname);
+        nwr += 60;
+    }
+    if ( nwr )
+        args->fa_ori_pos += nwr;
+
+    args->fa_frz_mod -= nwr;
+
+    if ( len )
+    {
+        // not finished on this chr yet and the buffer cannot be emptied completely
+        if ( nwr && nwr < args->fa_buf.l )
+            memmove(args->fa_buf.s,args->fa_buf.s+nwr,args->fa_buf.l-nwr);
+        args->fa_buf.l -= nwr;
+        return;
+    }
+
+    // empty the whole buffer
+    if ( nwr == args->fa_buf.l ) { args->fa_buf.l = 0; return; }
+
+    if ( fwrite(args->fa_buf.s+nwr,1,args->fa_buf.l - nwr,args->fp_out) != args->fa_buf.l - nwr ) error("Could not write: %s\n", args->output_fname);
+    if ( fwrite("\n",1,1,args->fp_out) != 1 ) error("Could not write: %s\n", args->output_fname);
+
+    args->fa_ori_pos += args->fa_buf.l - nwr - args->fa_mod_off;
+    args->fa_mod_off = 0;
+    args->fa_buf.l = 0;
+}
+static void apply_absent(args_t *args, hts_pos_t pos)
+{
+    if ( !args->fa_buf.l || pos <= args->fa_frz_pos + 1 || pos <= args->fa_ori_pos ) return;
+
+    int ie = pos && pos - args->fa_ori_pos + args->fa_mod_off < args->fa_buf.l ? pos - args->fa_ori_pos + args->fa_mod_off : args->fa_buf.l;
+    int ib = args->fa_frz_mod < 0 ? 0 : args->fa_frz_mod;
+    int i;
+    for (i=ib; i<ie; i++)
+        args->fa_buf.s[i] = args->absent_allele;
+}
+static void freeze_ref(args_t *args, bcf1_t *rec)
+{
+    if ( args->fa_frz_pos >= rec->pos + rec->rlen - 1 ) return;
+    args->fa_frz_pos = rec->pos + rec->rlen - 1;
+    args->fa_frz_mod = rec->pos - args->fa_ori_pos + args->fa_mod_off + rec->rlen;
+}
+static char *mark_del(char *ref, int rlen, char *alt, int mark)
+{
+    char *out = malloc(rlen+1);
+    int i;
+    if ( alt )
+    {
+        int nalt = strlen(alt);
+        for (i=0; i<nalt; i++) out[i] = alt[i];
+    }
+    else    // symbolic <DEL>
+    {
+        int nref = strlen(ref);
+        for (i=0; i<nref; i++) out[i] = ref[i];
+    }
+    for (; i<rlen; i++) out[i] = mark;
+    out[rlen] = 0;
+    return out;
+}
+static void mark_ins(char *ref, char *alt, char mark)
+{
+    int i, nref = strlen(ref), nalt = strlen(alt);
+    if ( mark=='l' )
+        for (i=nref; i<nalt; i++) alt[i] = tolower(alt[i]);
+    else
+        for (i=nref; i<nalt; i++) alt[i] = toupper(alt[i]);
+}
+static void mark_snv(char *ref, char *alt, char mark)
+{
+    int i, nref = strlen(ref), nalt = strlen(alt);
+    int n = nref < nalt ? nref : nalt;
+    if ( mark=='l' )
+    {
+        for (i=0; i<n; i++)
+            if ( tolower(ref[i])!=tolower(alt[i]) ) alt[i] = tolower(alt[i]);
+    }
+    else
+    {
+        for (i=0; i<n; i++)
+            if ( tolower(ref[i])!=tolower(alt[i]) ) alt[i] = toupper(alt[i]);
+    }
+}
+static void apply_variant(args_t *args, bcf1_t *rec)
+{
+    static int warned_haplotype = 0;
+
+    if ( args->absent_allele ) apply_absent(args, rec->pos);
+    if ( rec->n_allele==1 && !args->missing_allele && !args->absent_allele ) { return; }
+
+    int i,j;
+    if ( args->mask )
+    {
+        char *chr = (char*)bcf_hdr_id2name(args->hdr,args->rid);
+        int start = rec->pos;
+        int end   = rec->pos + rec->rlen - 1;
+        for (i=0; i<args->nmask; i++)
+        {
+            mask_t *mask = &args->mask[i];
+            if ( MASK_SKIP(mask) && regidx_overlap(mask->idx, chr,start,end,NULL) ) return;
+        }
+    }
+
+    int ialt = 1;    // the alternate allele
+    if ( args->isample >= 0 )
+    {
+        bcf_unpack(rec, BCF_UN_FMT);
+        bcf_fmt_t *fmt = bcf_get_fmt(args->hdr, rec, "GT");
+        if ( !fmt ) return;
+
+        if ( fmt->type!=BCF_BT_INT8 )
+            error("Todo: GT field represented with BCF_BT_INT8, too many alleles at %s:%"PRId64"?\n",bcf_seqname(args->hdr,rec),(int64_t) rec->pos+1);
+        uint8_t *ptr = fmt->p + fmt->size*args->isample;
+
+        enum { use_hap, use_iupac, pick_one } action = use_hap;
+        if ( args->allele==PICK_IUPAC )
+        {
+            if ( !args->haplotype ) action = use_iupac;
+            if ( !bcf_gt_is_phased(ptr[0]) && !bcf_gt_is_phased(ptr[fmt->n-1]) ) action = use_iupac;
+        }
+        else if ( args->output_iupac ) action = use_iupac;
+        else if ( !args->haplotype ) action = pick_one;
+
+        if ( action==use_hap )
+        {
+            if ( args->haplotype > fmt->n )
+            {
+                if ( bcf_gt_is_missing(ptr[fmt->n-1]) || bcf_gt_is_missing(ptr[0]) )
+                {
+                    if ( !args->missing_allele ) return;
+                    ialt = -1;
+                }
+                else
+                {
+                    if ( !warned_haplotype )
+                    {
+                        fprintf(stderr, "Can't apply %d-th haplotype at %s:%"PRId64". (This warning is printed only once.)\n", args->haplotype,bcf_seqname(args->hdr,rec),(int64_t) rec->pos+1);
+                        warned_haplotype = 1;
+                    }
+                    return;
+                }
+            }
+            else
+            {
+                ialt = (int8_t)ptr[args->haplotype-1];
+                if ( bcf_gt_is_missing(ialt) || ialt==bcf_int8_vector_end )
+                {
+                    if ( !args->missing_allele ) return;
+                    ialt = -1;
+                }
+                else
+                    ialt = bcf_gt_allele(ialt);
+            }
+        }
+        else if ( action==use_iupac )
+        {
+            ialt = -1;
+            int is_missing = 0, alen = 0, mlen = 0, fallback_alt = -1;
+            for (i=0; i<fmt->n; i++)
+            {
+                if ( bcf_gt_is_missing(ptr[i]) ) { is_missing = 1; continue; }
+                if ( ptr[i]==(uint8_t)bcf_int8_vector_end ) break;
+                int jalt = bcf_gt_allele(ptr[i]);
+                if ( jalt >= rec->n_allele ) error("Invalid VCF, too few ALT alleles at %s:%"PRId64"\n", bcf_seqname(args->hdr,rec),(int64_t) rec->pos+1);
+                if ( fallback_alt <= 0 ) fallback_alt = jalt;
+
+                int l = strlen(rec->d.allele[jalt]);
+                for (j=0; j<l; j++)
+                    if ( iupac2bitmask(rec->d.allele[jalt][j]) < 0 ) break;
+                if ( j<l ) continue; // symbolic allele, breakpoint or invalid character in the allele
+
+                if ( l > mlen )
+                {
+                    hts_expand(uint8_t,l,args->miupac_bitmask,args->iupac_bitmask);
+                    for (j=mlen; j<l; j++) args->iupac_bitmask[j] = 0;
+                    mlen = l;
+                }
+                if ( jalt>0 && l>alen )
+                {
+                    alen = l;
+                    ialt = jalt;
+                }
+                for (j=0; j<l; j++)
+                    args->iupac_bitmask[j] |= iupac2bitmask(rec->d.allele[jalt][j]);
+            }
+            if ( alen > 0 )
+                for (j=0; j<alen; j++) rec->d.allele[ialt][j] = bitmask2iupac(args->iupac_bitmask[j]);
+            else if ( fallback_alt >= 0 )
+                ialt = fallback_alt;
+            else if ( is_missing && !args->missing_allele ) return;
+        }
+        else
+        {
+            int is_hom = 1;
+            for (i=0; i<fmt->n; i++)
+            {
+                if ( bcf_gt_is_missing(ptr[i]) )
+                {
+                    if ( !args->missing_allele ) return;  // ignore missing or half-missing genotypes
+                    ialt = -1;
+                    break;
+                }
+                if ( ptr[i]==(uint8_t)bcf_int8_vector_end ) break;
+                ialt = bcf_gt_allele(ptr[i]);
+                if ( i>0 && ialt!=bcf_gt_allele(ptr[i-1]) ) { is_hom = 0; break; }
+            }
+            if ( !is_hom )
+            {
+                int prev_len = 0, jalt;
+                for (i=0; i<fmt->n; i++)
+                {
+                    if ( ptr[i]==(uint8_t)bcf_int8_vector_end ) break;
+                    jalt = bcf_gt_allele(ptr[i]);
+                    if ( rec->n_allele <= jalt ) error("Broken VCF, too few alts at %s:%"PRId64"\n", bcf_seqname(args->hdr,rec),(int64_t) rec->pos+1);
+                    if ( args->allele & (PICK_LONG|PICK_SHORT) )
+                    {
+                        int len = jalt==0 ? rec->rlen : strlen(rec->d.allele[jalt]);
+                        if ( i==0 ) ialt = jalt, prev_len = len;
+                        else if ( len == prev_len )
+                        {
+                            if ( args->allele & PICK_REF && jalt==0 ) ialt = jalt, prev_len = len;
+                            else if ( args->allele & PICK_ALT && ialt==0 ) ialt = jalt, prev_len = len;
+                        }
+                        else if ( args->allele & PICK_LONG && len > prev_len ) ialt = jalt, prev_len = len;
+                        else if ( args->allele & PICK_SHORT && len < prev_len ) ialt = jalt, prev_len = len;
+                    }
+                    else
+                    {
+                        if ( args->allele & PICK_REF && jalt==0 ) ialt = jalt;
+                        else if ( args->allele & PICK_ALT && ialt==0 ) ialt = jalt;
+                    }
+                }
+            }
+        }
+        if ( !ialt )
+        {
+            // ref allele
+            if ( args->absent_allele ) freeze_ref(args,rec);
+            return;
+        }
+        if ( rec->n_allele <= ialt ) error("Broken VCF, too few alts at %s:%"PRId64"\n", bcf_seqname(args->hdr,rec),(int64_t) rec->pos+1);
+    }
+    else if ( args->output_iupac && rec->n_allele>1 )
+    {
+        int ialt, alen = 0, mlen = 0;
+        for (i=0; i<rec->n_allele; i++)
+        {
+            int l = strlen(rec->d.allele[i]);
+            for (j=0; j<l; j++)
+                if ( iupac2bitmask(rec->d.allele[i][j]) < 0 ) break;
+            if ( j<l ) continue;    // symbolic allele, breakpoint or invalid character in the allele
+
+            if ( l > mlen )
+            {
+                hts_expand(uint8_t,l,args->miupac_bitmask,args->iupac_bitmask);
+                for (j=mlen; j<l; j++) args->iupac_bitmask[j] = 0;
+                mlen = l;
+            }
+            if ( i>0 && l>alen )
+            {
+                alen = l;
+                ialt = i;
+            }
+            for (j=0; j<l; j++)
+                args->iupac_bitmask[j] |= iupac2bitmask(rec->d.allele[i][j]);
+        }
+        if ( alen > 0 )
+            for (j=0; j<alen; j++) rec->d.allele[ialt][j] = bitmask2iupac(args->iupac_bitmask[j]);
+        else
+            ialt = 1;
+    }
+
+    if ( rec->n_allele==1 && ialt!=-1 )
+    {
+        // non-missing reference
+        if ( args->absent_allele ) freeze_ref(args,rec);
+        return;
+    }
+    if ( ialt==-1 )
+    {
+        char alleles[4];
+        alleles[0] = rec->d.allele[0][0];
+        alleles[1] = ',';
+        alleles[2] = args->missing_allele;
+        alleles[3] = 0;
+        bcf_update_alleles_str(args->hdr, rec, alleles);
+        ialt = 1;
+    }
+
+    // For some variant types POS+REF refer to the base *before* the event; in such case set trim_beg
+    int trim_beg = 0;
+    int var_type = bcf_get_variant_type(rec,ialt);
+    int var_len  = rec->d.var[ialt].n;
+    if ( var_type & VCF_INDEL )
+    {
+        // normally indel starts one base after, but not if the first base of the fa reference is deleted
+        if ( rec->d.allele[0][0] == rec->d.allele[ialt][0] )
+            trim_beg = 1;
+        else
+            trim_beg = 0;
+    }
+    else if ( (var_type & VCF_OTHER) && !strcasecmp(rec->d.allele[ialt],"<DEL>") )
+    {
+        trim_beg = 1;
+        var_len  = 1 - rec->rlen;
+    }
+    else if ( (var_type & VCF_OTHER) && !strncasecmp(rec->d.allele[ialt],"<INS",4) ) trim_beg = 1;
+
+    // Overlapping variant?
+    if ( rec->pos <= args->fa_frz_pos )
+    {
+        // Can be still OK iff this is an insertion (and which does not follow another insertion, see #888).
+        // This still may not be enough for more complicated cases with multiple duplicate positions
+        // and other types in between. In such case let the user normalize the VCF and remove duplicates.
+
+        int overlap = 0;
+        if ( rec->pos < args->fa_frz_pos || !trim_beg || var_len==0 || args->prev_is_insert ) overlap = 1;
+
+        if ( overlap )
+        {
+            fprintf(stderr,"The site %s:%"PRId64" overlaps with another variant, skipping...\n", bcf_seqname(args->hdr,rec),(int64_t) rec->pos+1);
+            return;
+        }
+
+    }
+
+    char *alt_allele = rec->d.allele[ialt];
+    int rmme_alt = 0;
+
+    int len_diff = 0, alen = 0;
+    int idx = rec->pos - args->fa_ori_pos + args->fa_mod_off;
+    if ( idx<0 )
+    {
+        fprintf(stderr,"Warning: ignoring overlapping variant starting at %s:%"PRId64"\n", bcf_seqname(args->hdr,rec),(int64_t) rec->pos+1);
+        return;
+    }
+    if ( rec->rlen > args->fa_buf.l - idx )
+    {
+        rec->rlen = args->fa_buf.l - idx;
+        if ( alt_allele[0]!='<' )
+        {
+            alen = strlen(alt_allele);
+            if ( alen > rec->rlen )
+            {
+                fprintf(stderr,"Warning: trimming variant \"%s\" starting at %s:%"PRId64"\n", alt_allele,bcf_seqname(args->hdr,rec),(int64_t) rec->pos+1);
+                alt_allele[rec->rlen] = 0;
+            }
+        }
+    }
+    if ( idx>=args->fa_buf.l )
+        error("FIXME: %s:%"PRId64" .. idx=%d, ori_pos=%d, len=%"PRIu64", off=%d\n",bcf_seqname(args->hdr,rec),(int64_t) rec->pos+1,idx,args->fa_ori_pos,(uint64_t)args->fa_buf.l,args->fa_mod_off);
+
+    // sanity check the reference base
+    if ( alt_allele[0]=='<' )
+    {
+        // TODO: symbolic deletions probably need more work above with PICK_SHORT|PICK_LONG
+
+        if ( strcasecmp(alt_allele,"<DEL>") && strcasecmp(alt_allele,"<*>") && strcasecmp(alt_allele,"<NON_REF>") )
+            error("Symbolic alleles other than <DEL>, <*> or <NON_REF> are currently not supported, e.g. \"%s\" at %s:%"PRId64".\n"
+                  "Please use filtering expressions to exclude such sites, for example by running with: -e 'ALT~\"<.*>\"'\n",
+                alt_allele,bcf_seqname(args->hdr,rec),(int64_t) rec->pos+1);
+        if ( !strcasecmp(alt_allele,"<DEL>") )
+        {
+            static int multibase_ref_del_warned = 0;
+            if ( rec->d.allele[0][1]!=0 && !multibase_ref_del_warned )
+            {
+                fprintf(stderr,
+                    "Warning: one REF base is expected with <DEL>, assuming the actual deletion starts at POS+1 at %s:%"PRId64".\n"
+                    "         (This warning is printed only once.)\n", bcf_seqname(args->hdr,rec),(int64_t) rec->pos+1);
+                multibase_ref_del_warned = 1;
+            }
+            if ( args->mark_del )   // insert dashes instead of delete sequence
+            {
+                alt_allele = mark_del(rec->d.allele[0], rec->rlen, NULL, args->mark_del);
+                alen = rec->rlen;
+                len_diff = 0;
+                rmme_alt = 1;
+            }
+            else
+            {
+                len_diff = 1-rec->rlen;
+                alt_allele = rec->d.allele[0];     // according to VCF spec, the first REF base must precede the event
+                alen = 1;
+            }
+        }
+        else
+        {
+            // <*>  or <NON_REF> .. gVCF, evidence for the reference allele throughout the whole block
+            freeze_ref(args,rec);
+            return;
+        }
+    }
+    else if ( strncasecmp(rec->d.allele[0],args->fa_buf.s+idx,rec->rlen) )
+    {
+        // This is hacky, handle a special case: if SNP or an insert follows a deletion (AAC>A, C>CAA),
+        // the reference base in fa_buf is lost and the check fails. We do not keep a buffer
+        // with the original sequence as it should not be necessary, we should encounter max
+        // one base overlap
+
+        int fail = 1;
+        if ( args->prev_base_pos==rec->pos && toupper(rec->d.allele[0][0])==toupper(args->prev_base) )
+        {
+            if ( rec->rlen==1 ) fail = 0;
+            else if ( !strncasecmp(rec->d.allele[0]+1,args->fa_buf.s+idx+1,rec->rlen-1) ) fail = 0;
+        }
+
+        if ( fail )
+        {
+            char tmp = 0;
+            if ( args->fa_buf.l - idx > rec->rlen )
+            {
+                tmp = args->fa_buf.s[idx+rec->rlen];
+                args->fa_buf.s[idx+rec->rlen] = 0;
+            }
+            error(
+                    "The fasta sequence does not match the REF allele at %s:%"PRId64":\n"
+                    "   REF .vcf: [%s]\n"
+                    "   ALT .vcf: [%s]\n"
+                    "   REF .fa : [%s]%c%s\n",
+                    bcf_seqname(args->hdr,rec),(int64_t) rec->pos+1, rec->d.allele[0], alt_allele, args->fa_buf.s+idx,
+                    tmp?tmp:' ',tmp?args->fa_buf.s+idx+rec->rlen+1:""
+                 );
+        }
+        alen = strlen(alt_allele);
+        len_diff = alen - rec->rlen;
+
+        if ( args->mark_del && len_diff<0 )
+        {
+            alt_allele = mark_del(rec->d.allele[0], rec->rlen, alt_allele, args->mark_del);
+            alen = rec->rlen;
+            len_diff = 0;
+            rmme_alt = 1;
+        }
+    }
+    else
+    {
+        alen = strlen(alt_allele);
+        len_diff = alen - rec->rlen;
+
+        if ( args->mark_del && len_diff<0 )
+        {
+            alt_allele = mark_del(rec->d.allele[0], rec->rlen, alt_allele, args->mark_del);
+            alen = rec->rlen;
+            len_diff = 0;
+            rmme_alt = 1;
+        }
+    }
+
+    args->fa_case = toupper(args->fa_buf.s[idx])==args->fa_buf.s[idx] ? TO_UPPER : TO_LOWER;
+    if ( args->fa_case==TO_UPPER )
+        for (i=0; i<alen; i++) alt_allele[i] = toupper(alt_allele[i]);
+    else
+        for (i=0; i<alen; i++) alt_allele[i] = tolower(alt_allele[i]);
+
+    if ( args->mark_ins && len_diff>0 )
+        mark_ins(rec->d.allele[0], alt_allele, args->mark_ins);
+    if ( args->mark_snv )
+        mark_snv(rec->d.allele[0], alt_allele, args->mark_snv);
+
+    if ( len_diff <= 0 )
+    {
+        // deletion or same size event
+        assert( args->fa_buf.l >= idx+rec->rlen );
+        args->prev_base = args->fa_buf.s[idx+rec->rlen-1];
+        args->prev_base_pos = rec->pos + rec->rlen - 1;
+        args->prev_is_insert = 0;
+        args->fa_frz_mod = idx + alen;
+
+        for (i=trim_beg; i<alen; i++)
+            args->fa_buf.s[idx+i] = alt_allele[i];
+
+        if ( len_diff )
+            memmove(args->fa_buf.s+idx+alen,args->fa_buf.s+idx+rec->rlen,args->fa_buf.l-idx-rec->rlen);
+    }
+    else
+    {
+        args->prev_is_insert = 1;
+        args->prev_base_pos = rec->pos;
+
+        // insertion
+        ks_resize(&args->fa_buf, args->fa_buf.l + len_diff);
+        memmove(args->fa_buf.s + idx + rec->rlen + len_diff, args->fa_buf.s + idx + rec->rlen, args->fa_buf.l - idx - rec->rlen);
+
+        // This can get tricky, make sure the bases unchanged by the insertion do not overwrite preceeding variants.
+        // For example, here we want to get TAA:
+        //      POS REF ALT
+        //      1   C   T
+        //      1   C   CAA
+        int ibeg = 0;
+        while ( ibeg<alen && rec->d.allele[0][ibeg]==alt_allele[ibeg] && rec->pos + ibeg <= args->prev_base_pos  ) ibeg++;
+        for (i=ibeg; i<alen; i++)
+            args->fa_buf.s[idx+i] = alt_allele[i];
+
+        args->fa_frz_mod = idx + alen - ibeg + 1;
+    }
+    if (args->chain && len_diff != 0)
+    {
+        // If first nucleotide of both REF and ALT are the same... (indels typically include the nucleotide before the variant)
+        if ( strncasecmp(rec->d.allele[0],alt_allele,1) == 0)
+        {
+            // ...extend the block by 1 bp: start is 1 bp further and alleles are 1 bp shorter
+            push_chain_gap(args->chain, rec->pos + 1, rec->rlen - 1, rec->pos + 1 + args->fa_mod_off, alen - 1);
+        }
+        else
+        {
+            // otherwise, just the coordinates of the variant as given
+            push_chain_gap(args->chain, rec->pos, rec->rlen, rec->pos + args->fa_mod_off, alen);
+        }
+    }
+    args->fa_buf.l += len_diff;
+    args->fa_mod_off += len_diff;
+    args->fa_frz_pos  = rec->pos + rec->rlen - 1;
+    args->napplied++;
+    if ( rmme_alt ) free(alt_allele);
+}
+
+
+static void mask_region(args_t *args, char *seq, int len)
+{
+    int start = args->fa_src_pos - len;
+    int end   = args->fa_src_pos;
+    int i;
+
+    for (i=0; i<args->nmask; i++)
+    {
+        mask_t *mask = &args->mask[i];
+        if ( !regidx_overlap(mask->idx, args->chr,start,end, mask->itr) ) continue;
+
+        int idx_start, idx_end, j;
+        while ( regitr_overlap(mask->itr) )
+        {
+            idx_start = mask->itr->beg - start;
+            idx_end   = mask->itr->end - start;
+            if ( idx_start < 0 ) idx_start = 0;
+            if ( idx_end >= len ) idx_end = len - 1;
+            if ( mask->with==MASK_UC )
+                for (j=idx_start; j<=idx_end; j++) seq[j] = toupper(seq[j]);
+            else if ( mask->with==MASK_LC )
+                for (j=idx_start; j<=idx_end; j++) seq[j] = tolower(seq[j]);
+            else
+                for (j=idx_start; j<=idx_end; j++) seq[j] = mask->with;
+        }
+    }
+}
+
+static void consensus(args_t *args)
+{
+    BGZF *fasta = bgzf_open(args->ref_fname, "r");
+    if ( !fasta ) error("Error reading %s\n", args->ref_fname);
+    kstring_t str = {0,0,0};
+    while ( bgzf_getline(fasta, '\n', &str) > 0 )
+    {
+        if ( str.s[0]=='>' )
+        {
+            // new sequence encountered
+            if ( args->chain ) print_chain(args);
+
+            // apply all cached variants and variants that might have been missed because of short fasta (see test/consensus.9.*)
+            bcf1_t **rec_ptr = NULL;
+            while ( args->rid>=0 && (rec_ptr = next_vcf_line(args)) )
+            {
+                bcf1_t *rec = *rec_ptr;
+                if ( rec->rid!=args->rid || ( args->fa_end_pos && rec->pos > args->fa_end_pos ) ) break;
+                apply_variant(args, rec);
+            }
+            if ( args->absent_allele )
+            {
+                int pos = 0;
+                if ( args->vcf_rbuf.n && args->vcf_buf[args->vcf_rbuf.f]->rid==args->rid )
+                    pos = args->vcf_buf[args->vcf_rbuf.f]->pos;
+                apply_absent(args, pos);
+            }
+            flush_fa_buffer(args, 0);
+            init_region(args, str.s+1);
+            continue;
+        }
+        args->fa_length  += str.l;
+        args->fa_src_pos += str.l;
+
+        // determine if uppercase or lowercase is used in this fasta file
+        if ( args->fa_case==-1 ) args->fa_case = toupper(str.s[0])==str.s[0] ? 1 : 0;
+
+        if ( args->mask ) mask_region(args, str.s, str.l);
+        kputs(str.s, &args->fa_buf);
+
+        bcf1_t **rec_ptr = NULL;
+        while ( args->rid>=0 && (rec_ptr = next_vcf_line(args)) )
+        {
+            bcf1_t *rec = *rec_ptr;
+
+            // still the same chr and the same region? if not, fasta buf can be flushed
+            if ( rec->rid!=args->rid || ( args->fa_end_pos && rec->pos > args->fa_end_pos ) )
+            {
+                // save the vcf record until next time and flush
+                unread_vcf_line(args, rec_ptr);
+                rec_ptr = NULL;
+                break;
+            }
+
+            // is the vcf record well beyond cached fasta buffer? if yes, the buf can be flushed
+            if ( args->fa_ori_pos + args->fa_buf.l - args->fa_mod_off <= rec->pos )
+            {
+                unread_vcf_line(args, rec_ptr);
+                rec_ptr = NULL;
+                break;
+            }
+
+            // is the cached fasta buffer full enough? if not, read more fasta, no flushing
+            if ( args->fa_ori_pos + args->fa_buf.l - args->fa_mod_off < rec->pos + rec->rlen )
+            {
+                unread_vcf_line(args, rec_ptr);
+                break;
+            }
+            apply_variant(args, rec);
+        }
+        if ( !rec_ptr )
+        {
+            if ( args->absent_allele ) apply_absent(args, args->fa_ori_pos - args->fa_mod_off + args->fa_buf.l);
+            flush_fa_buffer(args, 60);
+        }
+    }
+    bcf1_t **rec_ptr = NULL;
+    while ( args->rid>=0 && (rec_ptr = next_vcf_line(args)) )
+    {
+        bcf1_t *rec = *rec_ptr;
+        if ( rec->rid!=args->rid ) break;
+        if ( args->fa_end_pos && rec->pos > args->fa_end_pos ) break;
+        if ( args->fa_ori_pos + args->fa_buf.l - args->fa_mod_off <= rec->pos ) break;
+        apply_variant(args, rec);
+    }
+    if (args->chain) print_chain(args);
+    if ( args->absent_allele ) apply_absent(args, HTS_POS_MAX);
+    flush_fa_buffer(args, 0);
+    bgzf_close(fasta);
+    free(str.s);
+    fprintf(stderr,"Applied %d variants\n", args->napplied);
+}
+
+static void usage(args_t *args)
+{
+    fprintf(stderr, "\n");
+    fprintf(stderr, "About: Create consensus sequence by applying VCF variants to a reference fasta\n");
+    fprintf(stderr, "       file. By default, the program will apply all ALT variants. Using the\n");
+    fprintf(stderr, "       --sample (and, optionally, --haplotype) option will apply genotype\n");
+    fprintf(stderr, "       (or haplotype) calls from FORMAT/GT. The program ignores allelic depth\n");
+    fprintf(stderr, "       information, such as INFO/AD or FORMAT/AD.\n");
+    fprintf(stderr, "Usage: bcftools consensus [OPTIONS] <file.vcf.gz>\n");
+    fprintf(stderr, "Options:\n");
+    fprintf(stderr, "    -c, --chain FILE               write a chain file for liftover\n");
+    fprintf(stderr, "    -a, --absent CHAR              replace positions absent from VCF with CHAR\n");
+    fprintf(stderr, "    -e, --exclude EXPR             exclude sites for which the expression is true (see man page for details)\n");
+    fprintf(stderr, "    -f, --fasta-ref FILE           reference sequence in fasta format\n");
+    fprintf(stderr, "    -H, --haplotype WHICH          choose which allele to use from the FORMAT/GT field, note\n");
+    fprintf(stderr, "                                   the codes are case-insensitive:\n");
+    fprintf(stderr, "                                       1: first allele from GT, regardless of phasing\n");
+    fprintf(stderr, "                                       2: second allele from GT, regardless of phasing\n");
+    fprintf(stderr, "                                       R: REF allele in het genotypes\n");
+    fprintf(stderr, "                                       A: ALT allele\n");
+    fprintf(stderr, "                                       I: IUPAC code for all genotypes\n");
+    fprintf(stderr, "                                       LR,LA: longer allele and REF/ALT if equal length\n");
+    fprintf(stderr, "                                       SR,SA: shorter allele and REF/ALT if equal length\n");
+    fprintf(stderr, "                                       1pIu,2pIu: first/second allele for phased and IUPAC code for unphased GTs\n");
+    fprintf(stderr, "    -i, --include EXPR             select sites for which the expression is true (see man page for details)\n");
+    fprintf(stderr, "    -I, --iupac-codes              output variants in the form of IUPAC ambiguity codes\n");
+    fprintf(stderr, "        --mark-del CHAR            instead of removing sequence, insert CHAR for deletions\n");
+    fprintf(stderr, "        --mark-ins uc|lc           highlight insertions in uppercase (uc) or lowercase (lc), leaving the rest as is\n");
+    fprintf(stderr, "        --mark-snv uc|lc           highlight substitutions in uppercase (uc) or lowercase (lc), leaving the rest as is\n");
+    fprintf(stderr, "    -m, --mask FILE                replace regions according to the next --mask-with option. The default is --mask-with N\n");
+    fprintf(stderr, "        --mask-with CHAR|uc|lc     replace with CHAR (skips overlapping variants); change to uppercase (uc) or lowercase (lc)\n");
+    fprintf(stderr, "    -M, --missing CHAR             output CHAR instead of skipping a missing genotype \"./.\"\n");
+    fprintf(stderr, "    -o, --output FILE              write output to a file [standard output]\n");
+    fprintf(stderr, "    -p, --prefix STRING            prefix to add to output sequence names\n");
+    fprintf(stderr, "    -s, --sample NAME              apply variants of the given sample\n");
+    fprintf(stderr, "Examples:\n");
+    fprintf(stderr, "   # Get the consensus for one region. The fasta header lines are then expected\n");
+    fprintf(stderr, "   # in the form \">chr:from-to\".\n");
+    fprintf(stderr, "   samtools faidx ref.fa 8:11870-11890 | bcftools consensus in.vcf.gz > out.fa\n");
+    fprintf(stderr, "\n");
+    fprintf(stderr, "   # See also http://samtools.github.io/bcftools/howtos/consensus-sequence.html\n");
+    fprintf(stderr, "\n");
+    exit(1);
+}
+
+int main_consensus(int argc, char *argv[])
+{
+    args_t *args = (args_t*) calloc(1,sizeof(args_t));
+    args->argc   = argc; args->argv = argv;
+
+    static struct option loptions[] =
+    {
+        {"mark-del",required_argument,NULL,1},
+        {"mark-ins",required_argument,NULL,2},
+        {"mark-snv",required_argument,NULL,3},
+        {"mask-with",1,0,4},
+        {"exclude",required_argument,NULL,'e'},
+        {"include",required_argument,NULL,'i'},
+        {"sample",1,0,'s'},
+        {"iupac-codes",0,0,'I'},
+        {"haplotype",1,0,'H'},
+        {"output",1,0,'o'},
+        {"fasta-ref",1,0,'f'},
+        {"mask",1,0,'m'},
+        {"missing",1,0,'M'},
+        {"absent",1,0,'a'},
+        {"chain",1,0,'c'},
+        {"prefix",required_argument,0,'p'},
+        {0,0,0,0}
+    };
+    int c;
+    while ((c = getopt_long(argc, argv, "h?s:1Ii:e:H:f:o:m:c:M:p:a:",loptions,NULL)) >= 0)
+    {
+        switch (c)
+        {
+            case  1 : args->mark_del = optarg[0]; break;
+            case  2 :
+                if ( !strcasecmp(optarg,"uc") ) args->mark_ins = 'u';
+                else if ( !strcasecmp(optarg,"lc") ) args->mark_ins = 'l';
+                else error("The argument is not recognised: --mark-ins %s\n",optarg);
+                break;
+            case  3 :
+                if ( !strcasecmp(optarg,"uc") ) args->mark_snv = 'u';
+                else if ( !strcasecmp(optarg,"lc") ) args->mark_snv = 'l';
+                else error("The argument is not recognised: --mark-snv %s\n",optarg);
+                break;
+            case 'p': args->chr_prefix = optarg; break;
+            case 's': args->sample = optarg; break;
+            case 'o': args->output_fname = optarg; break;
+            case 'I': args->output_iupac = 1; break;
+            case 'e':
+                if ( args->filter_str ) error("Error: only one -i or -e expression can be given, and they cannot be combined\n");
+                args->filter_str = optarg; args->filter_logic |= FLT_EXCLUDE; break;
+            case 'i':
+                if ( args->filter_str ) error("Error: only one -i or -e expression can be given, and they cannot be combined\n");
+                args->filter_str = optarg; args->filter_logic |= FLT_INCLUDE; break;
+            case 'f': args->ref_fname = optarg; break;
+            case 'm': add_mask(args,optarg); break;
+            case  4 : add_mask_with(args,optarg); break;
+            case 'a':
+                args->absent_allele = optarg[0];
+                if ( optarg[1]!=0 ) error("Expected single character with -a, got \"%s\"\n", optarg);
+                break;
+            case 'M':
+                args->missing_allele = optarg[0];
+                if ( optarg[1]!=0 ) error("Expected single character with -M, got \"%s\"\n", optarg);
+                break;
+            case 'c': args->chain_fname = optarg; break;
+            case 'H':
+                if ( !strcasecmp(optarg,"R") ) args->allele |= PICK_REF;
+                else if ( !strcasecmp(optarg,"A") ) args->allele |= PICK_ALT;
+                else if ( !strcasecmp(optarg,"L") ) args->allele |= PICK_LONG|PICK_REF;
+                else if ( !strcasecmp(optarg,"S") ) args->allele |= PICK_SHORT|PICK_REF;
+                else if ( !strcasecmp(optarg,"LR") ) args->allele |= PICK_LONG|PICK_REF;
+                else if ( !strcasecmp(optarg,"LA") ) args->allele |= PICK_LONG|PICK_ALT;
+                else if ( !strcasecmp(optarg,"SR") ) args->allele |= PICK_SHORT|PICK_REF;
+                else if ( !strcasecmp(optarg,"SA") ) args->allele |= PICK_SHORT|PICK_ALT;
+                else if ( !strcasecmp(optarg,"I") ) args->allele |= PICK_IUPAC;
+                else if ( !strcasecmp(optarg,"1pIu") ) args->allele |= PICK_IUPAC, args->haplotype = 1;
+                else if ( !strcasecmp(optarg,"2pIu") ) args->allele |= PICK_IUPAC, args->haplotype = 2;
+                else
+                {
+                    char *tmp;
+                    args->haplotype = strtol(optarg, &tmp, 10);
+                    if ( tmp==optarg || *tmp ) error("Error: Could not parse --haplotype %s, expected numeric argument\n", optarg);
+                    if ( args->haplotype <=0 ) error("Error: Expected positive integer with --haplotype\n");
+                }
+                break;
+            default: usage(args); break;
+        }
+    }
+    if ( optind>=argc ) usage(args);
+    args->fname = argv[optind];
+
+    if ( !args->ref_fname && !isatty(fileno((FILE *)stdin)) ) args->ref_fname = "-";
+    if ( !args->ref_fname ) usage(args);
+
+    init_data(args);
+    consensus(args);
+    destroy_data(args);
+    free(args);
+
+    return 0;
+}
+
+
diff --git a/bcftools/consensus.c.pysam.c b/bcftools/consensus.c.pysam.c
new file mode 100644
index 0000000..4af9c18
--- /dev/null
+++ b/bcftools/consensus.c.pysam.c
@@ -0,0 +1,1175 @@
+#include "bcftools.pysam.h"
+
+/* The MIT License
+
+   Copyright (c) 2014-2022 Genome Research Ltd.
+
+   Author: Petr Danecek <pd3@sanger.ac.uk>
+
+   Permission is hereby granted, free of charge, to any person obtaining a copy
+   of this software and associated documentation files (the "Software"), to deal
+   in the Software without restriction, including without limitation the rights
+   to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+   copies of the Software, and to permit persons to whom the Software is
+   furnished to do so, subject to the following conditions:
+
+   The above copyright notice and this permission notice shall be included in
+   all copies or substantial portions of the Software.
+
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+   IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+   FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+   AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+   LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+   OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+   THE SOFTWARE.
+
+ */
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <strings.h>
+#include <assert.h>
+#include <errno.h>
+#include <getopt.h>
+#include <unistd.h>
+#include <ctype.h>
+#include <htslib/vcf.h>
+#include <htslib/kstring.h>
+#include <htslib/synced_bcf_reader.h>
+#include <htslib/kseq.h>
+#include <htslib/bgzf.h>
+#include "regidx.h"
+#include "bcftools.h"
+#include "rbuf.h"
+#include "filter.h"
+
+// Logic of the filters: include or exclude sites which match the filters?
+#define FLT_INCLUDE 1
+#define FLT_EXCLUDE 2
+
+#define PICK_REF   1
+#define PICK_ALT   2
+#define PICK_LONG  4
+#define PICK_SHORT 8
+#define PICK_IUPAC 16
+
+#define TO_UPPER 0
+#define TO_LOWER 1
+
+typedef struct
+{
+    int num;                // number of ungapped blocks in this chain
+    int *block_lengths;     // length of the ungapped blocks in this chain
+    int *ref_gaps;          // length of the gaps on the reference sequence between blocks
+    int *alt_gaps;          // length of the gaps on the alternative sequence between blocks
+    int ori_pos;
+    int ref_last_block_ori; // start position on the reference sequence of the following ungapped block (0-based)
+    int alt_last_block_ori; // start position on the alternative sequence of the following ungapped block (0-based)
+}
+chain_t;
+
+#define MASK_LC 1
+#define MASK_UC 2
+#define MASK_SKIP(x) (((x)->with!=MASK_LC && (x)->with!=MASK_UC) ? 1 : 0)
+typedef struct
+{
+    char *fname, with;
+    regidx_t *idx;
+    regitr_t *itr;
+}
+mask_t;
+
+typedef struct
+{
+    kstring_t fa_buf;   // buffered reference sequence
+    int fa_ori_pos;     // start position of the fa_buffer (wrt original sequence)
+    int fa_frz_pos;     // protected position to avoid conflicting variants (last pos for SNPs/ins)
+    int fa_mod_off;     // position difference of fa_frz_pos in the ori and modified sequence (ins positive)
+    int fa_frz_mod;     // the fa_buf offset of the protected fa_frz_pos position, includes the modified sequence
+    int fa_end_pos;     // region's end position in the original sequence
+    int fa_length;      // region's length in the original sequence (in case end_pos not provided in the FASTA header)
+    int fa_case;        // output upper case or lower case: TO_UPPER|TO_LOWER
+    int fa_src_pos;     // last genomic coordinate read from the input fasta (0-based)
+    char prev_base;     // this is only to validate the REF allele in the VCF - the modified fa_buf cannot be used for inserts following deletions, see 600#issuecomment-383186778
+    int prev_base_pos;  // the position of prev_base
+    int prev_is_insert;
+
+    rbuf_t vcf_rbuf;
+    bcf1_t **vcf_buf;
+    int nvcf_buf, rid;
+    char *chr, *chr_prefix;
+
+    mask_t *mask;
+    int nmask;
+
+    int chain_id;       // chain_id, to provide a unique ID to each chain in the chain output
+    chain_t *chain;     // chain structure to store the sequence of ungapped blocks between the ref and alt sequences
+                        // Note that the chain is re-initialised for each chromosome/seq_region
+
+    filter_t *filter;
+    char *filter_str;
+    int filter_logic;   // include or exclude sites which match the filters? One of FLT_INCLUDE/FLT_EXCLUDE
+
+    bcf_srs_t *files;
+    bcf_hdr_t *hdr;
+    FILE *fp_out;
+    FILE *fp_chain;
+    char **argv;
+    int argc, output_iupac, haplotype, allele, isample, napplied;
+    uint8_t *iupac_bitmask;
+    int miupac_bitmask;
+    char *fname, *ref_fname, *sample, *output_fname, *mask_fname, *chain_fname, missing_allele, absent_allele;
+    char mark_del, mark_ins, mark_snv;
+}
+args_t;
+
+static void destroy_chain(chain_t *chain)
+{
+    if ( !chain ) return;
+    free(chain->ref_gaps);
+    free(chain->alt_gaps);
+    free(chain->block_lengths);
+    free(chain);
+}
+static chain_t* init_chain(chain_t *chain, int ref_ori_pos)
+{
+    if ( chain ) destroy_chain(chain);
+    chain = (chain_t*) calloc(1,sizeof(chain_t));
+    chain->num = 0;
+    chain->block_lengths = NULL;
+    chain->ref_gaps = NULL;
+    chain->alt_gaps = NULL;
+    chain->ori_pos = ref_ori_pos;
+    chain->ref_last_block_ori = ref_ori_pos;
+    chain->alt_last_block_ori = ref_ori_pos;
+    return chain;
+}
+
+static void print_chain(args_t *args)
+{
+    /*
+        Example chain format (see: https://genome.ucsc.edu/goldenPath/help/chain.html):
+        chain 1 500 + 480 500 1 501 + 480 501 1
+        12 3 1
+        1 0 3
+        484
+
+        chain line is:
+        - chain
+        - score (sum of the length of ungapped block in this case)
+        - ref_seqname (from the fasta header, parsed by htslib)
+        - ref_seqlength (from the fasta header)
+        - ref_strand (+ or -; always + for bcf-consensus)
+        - ref_start (as defined in the fasta header)
+        - ref_end (as defined in the fasta header)
+        - alt_seqname (same as ref_seqname as bcf-consensus only considers SNPs and indels)
+        - alt_seqlength (adjusted to match the length of the alt sequence)
+        - alt_strand (+ or -; always + for bcf-consensus)
+        - alt_start (same as ref_start, as no edits are recorded/applied before that position)
+        - alt_end (adjusted to match the length of the alt sequence)
+        - chain_num (just an auto-increment id)
+
+        the other (sorted) lines are:
+        - length of the ungapped alignment block
+        - gap on the ref sequence between this and the next block (all but the last line)
+        - gap on the alt sequence between this and the next block (all but the last line)
+    */
+    chain_t *chain = args->chain;
+    int n = chain->num;
+    int ref_end_pos = args->fa_length + chain->ori_pos;
+    int last_block_size = ref_end_pos - chain->ref_last_block_ori;
+    int alt_end_pos = chain->alt_last_block_ori + last_block_size;
+    int score = 0;
+    for (n=0; n<chain->num; n++) {
+        score += chain->block_lengths[n];
+    }
+    score += last_block_size;
+    fprintf(args->fp_chain, "chain %d %s %d + %d %d %s %d + %d %d %d\n", score, args->chr, ref_end_pos, chain->ori_pos, ref_end_pos, args->chr, alt_end_pos, chain->ori_pos, alt_end_pos, ++args->chain_id);
+    for (n=0; n<chain->num; n++) {
+        fprintf(args->fp_chain, "%d %d %d\n", chain->block_lengths[n], chain->ref_gaps[n], chain->alt_gaps[n]);
+    }
+    fprintf(args->fp_chain, "%d\n\n", last_block_size);
+}
+
+static void push_chain_gap(chain_t *chain, int ref_start, int ref_len, int alt_start, int alt_len)
+{
+    // fprintf(bcftools_stderr, "push_chain_gap(chain=%p, ref_start=%d, ref_len=%d, alt_start=%d, alt_len=%d)\n", chain, ref_start, ref_len, alt_start, alt_len);
+    int num = chain->num;
+
+    if (num && ref_start <= chain->ref_last_block_ori) {
+        // In case this variant is back-to-back with the previous one
+        chain->ref_last_block_ori = ref_start + ref_len;
+        chain->alt_last_block_ori = alt_start + alt_len;
+        chain->ref_gaps[num-1] += ref_len;
+        chain->alt_gaps[num-1] += alt_len;
+
+    } else {
+        // Extend the ungapped blocks, store the gap length
+        chain->block_lengths = (int*) realloc(chain->block_lengths, (num + 1) * sizeof(int));
+        chain->ref_gaps = (int*) realloc(chain->ref_gaps, (num + 1) * sizeof(int));
+        chain->alt_gaps = (int*) realloc(chain->alt_gaps, (num + 1) * sizeof(int));
+        chain->block_lengths[num] = ref_start - chain->ref_last_block_ori;
+        chain->ref_gaps[num] = ref_len;
+        chain->alt_gaps[num] = alt_len;
+        // Update the start positions of the next block
+        chain->ref_last_block_ori = ref_start + ref_len;
+        chain->alt_last_block_ori = alt_start + alt_len;
+        // Increment the number of ungapped blocks
+        chain->num++;
+    }
+}
+
+static void init_data(args_t *args)
+{
+    args->files = bcf_sr_init();
+    args->files->require_index = 1;
+    if ( !bcf_sr_add_reader(args->files,args->fname) ) error("Failed to read from %s: %s\n", !strcmp("-",args->fname)?"standard input":args->fname, bcf_sr_strerror(args->files->errnum));
+    args->hdr = args->files->readers[0].header;
+    args->isample = -1;
+    if ( args->sample )
+    {
+        args->isample = bcf_hdr_id2int(args->hdr,BCF_DT_SAMPLE,args->sample);
+        if ( args->isample<0 ) error("No such sample: %s\n", args->sample);
+    }
+    if ( (args->haplotype || args->allele) && args->isample<0 )
+    {
+        if ( bcf_hdr_nsamples(args->hdr) > 1 ) error("The --sample option is expected with --haplotype\n");
+        args->isample = 0;
+    }
+    int i;
+    for (i=0; i<args->nmask; i++)
+    {
+        mask_t *mask = &args->mask[i];
+        mask->idx = regidx_init(mask->fname,NULL,NULL,0,NULL);
+        if ( !mask->idx ) error("Failed to initialize mask regions\n");
+        mask->itr = regitr_init(mask->idx);
+    }
+    // In case we want to store the chains
+    if ( args->chain_fname )
+    {
+        args->fp_chain = fopen(args->chain_fname,"w");
+        if ( ! args->fp_chain ) error("Failed to create %s: %s\n", args->chain_fname, strerror(errno));
+        args->chain_id = 0;
+    }
+    rbuf_init(&args->vcf_rbuf, 100);
+    args->vcf_buf = (bcf1_t**) calloc(args->vcf_rbuf.m, sizeof(bcf1_t*));
+    if ( args->output_fname ) {
+        args->fp_out = fopen(args->output_fname,"w");
+        if ( ! args->fp_out ) error("Failed to create %s: %s\n", args->output_fname, strerror(errno));
+    }
+    else args->fp_out = bcftools_stdout;
+    if ( args->isample<0 ) fprintf(bcftools_stderr,"Note: the --sample option not given, applying all records regardless of the genotype\n");
+    if ( args->filter_str )
+        args->filter = filter_init(args->hdr, args->filter_str);
+    args->rid = -1;
+}
+static void add_mask(args_t *args, char *fname)
+{
+    args->nmask++;
+    args->mask = (mask_t*)realloc(args->mask,args->nmask*sizeof(*args->mask));
+    mask_t *mask = &args->mask[args->nmask-1];
+    mask->fname = fname;
+    mask->with  = 'N';
+}
+static void add_mask_with(args_t *args, char *with)
+{
+    if ( !args->nmask ) error("The --mask-with option must follow --mask\n");
+    mask_t *mask = &args->mask[args->nmask-1];
+    if ( !strcasecmp(with,"uc") ) mask->with = MASK_UC;
+    else if ( !strcasecmp(with,"lc") ) mask->with = MASK_LC;
+    else if ( strlen(with)!=1 ) error("Expected \"lc\", \"uc\", or a single character with the --mask-with option\n");
+    else mask->with = *with;
+}
+static void destroy_data(args_t *args)
+{
+    free(args->iupac_bitmask);
+    if (args->filter) filter_destroy(args->filter);
+    bcf_sr_destroy(args->files);
+    int i;
+    for (i=0; i<args->vcf_rbuf.m; i++)
+        if ( args->vcf_buf[i] ) bcf_destroy1(args->vcf_buf[i]);
+    free(args->vcf_buf);
+    free(args->fa_buf.s);
+    free(args->chr);
+    for (i=0; i<args->nmask; i++)
+    {
+        mask_t *mask = &args->mask[i];
+        regidx_destroy(mask->idx);
+        regitr_destroy(mask->itr);
+    }
+    free(args->mask);
+    if ( args->chain_fname )
+        if ( fclose(args->fp_chain) ) error("Close failed: %s\n", args->chain_fname);
+    if ( fclose(args->fp_out) ) error("Close failed: %s\n", args->output_fname);
+    destroy_chain(args->chain);
+}
+
+static void init_region(args_t *args, char *line)
+{
+    char *ss, *se = line;
+    while ( *se && !isspace(*se) && *se!=':' ) se++;
+    int from = 0, to = 0;
+    char tmp = 0, *tmp_ptr = NULL;
+    if ( *se )
+    {
+        tmp = *se; *se = 0; tmp_ptr = se;
+        ss = ++se;
+        from = strtol(ss,&se,10);
+        if ( ss==se || !*se || *se!='-' ) from = 0;
+        else
+        {
+            from--;
+            ss = ++se;
+            to = strtol(ss,&se,10);
+            if ( ss==se || (*se && !isspace(*se)) ) { from = 0; to = 0; }
+            else to--;
+        }
+    }
+    free(args->chr);
+    args->chr = strdup(line);
+    args->rid = bcf_hdr_name2id(args->hdr,line);
+    if ( args->rid<0 ) fprintf(bcftools_stderr,"Warning: Sequence \"%s\" not in %s\n", line,args->fname);
+    args->prev_base_pos = -1;
+    args->fa_buf.l  = 0;
+    args->fa_length = 0;
+    args->fa_end_pos = to;
+    args->fa_ori_pos = from;
+    args->fa_src_pos = from;
+    args->fa_mod_off = 0;
+    args->fa_frz_pos = -1;
+    args->fa_frz_mod = -1;
+    args->fa_case    = -1;
+    args->vcf_rbuf.n = 0;
+    bcf_sr_seek(args->files,line,args->fa_ori_pos);
+    if ( tmp_ptr ) *tmp_ptr = tmp;
+    fprintf(args->fp_out,">%s%s\n",args->chr_prefix?args->chr_prefix:"",line);
+    if ( args->chain_fname )
+        args->chain = init_chain(args->chain, args->fa_ori_pos);
+}
+
+static bcf1_t **next_vcf_line(args_t *args)
+{
+    if ( args->vcf_rbuf.n )
+    {
+        int i = rbuf_shift(&args->vcf_rbuf);
+        return &args->vcf_buf[i];
+    }
+    while ( bcf_sr_next_line(args->files) )
+    {
+        if ( args->filter )
+        {
+            int is_ok = filter_test(args->filter, bcf_sr_get_line(args->files,0), NULL);
+            if ( args->filter_logic & FLT_EXCLUDE ) is_ok = is_ok ? 0 : 1;
+            if ( !is_ok ) continue;
+        }
+        return &args->files->readers[0].buffer[0];
+    }
+    return NULL;
+}
+static void unread_vcf_line(args_t *args, bcf1_t **rec_ptr)
+{
+    bcf1_t *rec = *rec_ptr;
+    if ( args->vcf_rbuf.n >= args->vcf_rbuf.m )
+        error("FIXME: too many overlapping records near %s:%"PRId64"\n", bcf_seqname(args->hdr,rec),(int64_t) rec->pos+1);
+
+    // Insert the new record in the buffer. The line would be overwritten in
+    // the next bcf_sr_next_line call, therefore we need to swap it with an
+    // unused one
+    int i = rbuf_append(&args->vcf_rbuf);
+    if ( !args->vcf_buf[i] ) args->vcf_buf[i] = bcf_init1();
+    bcf1_t *tmp = rec; *rec_ptr = args->vcf_buf[i]; args->vcf_buf[i] = tmp;
+}
+static void flush_fa_buffer(args_t *args, int len)
+{
+    if ( !args->fa_buf.l ) return;
+    int nwr = 0;
+    while ( nwr + 60 <= args->fa_buf.l )
+    {
+        if ( fwrite(args->fa_buf.s+nwr,1,60,args->fp_out) != 60 ) error("Could not write: %s\n", args->output_fname);
+        if ( fwrite("\n",1,1,args->fp_out) != 1 ) error("Could not write: %s\n", args->output_fname);
+        nwr += 60;
+    }
+    if ( nwr )
+        args->fa_ori_pos += nwr;
+
+    args->fa_frz_mod -= nwr;
+
+    if ( len )
+    {
+        // not finished on this chr yet and the buffer cannot be emptied completely
+        if ( nwr && nwr < args->fa_buf.l )
+            memmove(args->fa_buf.s,args->fa_buf.s+nwr,args->fa_buf.l-nwr);
+        args->fa_buf.l -= nwr;
+        return;
+    }
+
+    // empty the whole buffer
+    if ( nwr == args->fa_buf.l ) { args->fa_buf.l = 0; return; }
+
+    if ( fwrite(args->fa_buf.s+nwr,1,args->fa_buf.l - nwr,args->fp_out) != args->fa_buf.l - nwr ) error("Could not write: %s\n", args->output_fname);
+    if ( fwrite("\n",1,1,args->fp_out) != 1 ) error("Could not write: %s\n", args->output_fname);
+
+    args->fa_ori_pos += args->fa_buf.l - nwr - args->fa_mod_off;
+    args->fa_mod_off = 0;
+    args->fa_buf.l = 0;
+}
+static void apply_absent(args_t *args, hts_pos_t pos)
+{
+    if ( !args->fa_buf.l || pos <= args->fa_frz_pos + 1 || pos <= args->fa_ori_pos ) return;
+
+    int ie = pos && pos - args->fa_ori_pos + args->fa_mod_off < args->fa_buf.l ? pos - args->fa_ori_pos + args->fa_mod_off : args->fa_buf.l;
+    int ib = args->fa_frz_mod < 0 ? 0 : args->fa_frz_mod;
+    int i;
+    for (i=ib; i<ie; i++)
+        args->fa_buf.s[i] = args->absent_allele;
+}
+static void freeze_ref(args_t *args, bcf1_t *rec)
+{
+    if ( args->fa_frz_pos >= rec->pos + rec->rlen - 1 ) return;
+    args->fa_frz_pos = rec->pos + rec->rlen - 1;
+    args->fa_frz_mod = rec->pos - args->fa_ori_pos + args->fa_mod_off + rec->rlen;
+}
+static char *mark_del(char *ref, int rlen, char *alt, int mark)
+{
+    char *out = malloc(rlen+1);
+    int i;
+    if ( alt )
+    {
+        int nalt = strlen(alt);
+        for (i=0; i<nalt; i++) out[i] = alt[i];
+    }
+    else    // symbolic <DEL>
+    {
+        int nref = strlen(ref);
+        for (i=0; i<nref; i++) out[i] = ref[i];
+    }
+    for (; i<rlen; i++) out[i] = mark;
+    out[rlen] = 0;
+    return out;
+}
+static void mark_ins(char *ref, char *alt, char mark)
+{
+    int i, nref = strlen(ref), nalt = strlen(alt);
+    if ( mark=='l' )
+        for (i=nref; i<nalt; i++) alt[i] = tolower(alt[i]);
+    else
+        for (i=nref; i<nalt; i++) alt[i] = toupper(alt[i]);
+}
+static void mark_snv(char *ref, char *alt, char mark)
+{
+    int i, nref = strlen(ref), nalt = strlen(alt);
+    int n = nref < nalt ? nref : nalt;
+    if ( mark=='l' )
+    {
+        for (i=0; i<n; i++)
+            if ( tolower(ref[i])!=tolower(alt[i]) ) alt[i] = tolower(alt[i]);
+    }
+    else
+    {
+        for (i=0; i<n; i++)
+            if ( tolower(ref[i])!=tolower(alt[i]) ) alt[i] = toupper(alt[i]);
+    }
+}
+static void apply_variant(args_t *args, bcf1_t *rec)
+{
+    static int warned_haplotype = 0;
+
+    if ( args->absent_allele ) apply_absent(args, rec->pos);
+    if ( rec->n_allele==1 && !args->missing_allele && !args->absent_allele ) { return; }
+
+    int i,j;
+    if ( args->mask )
+    {
+        char *chr = (char*)bcf_hdr_id2name(args->hdr,args->rid);
+        int start = rec->pos;
+        int end   = rec->pos + rec->rlen - 1;
+        for (i=0; i<args->nmask; i++)
+        {
+            mask_t *mask = &args->mask[i];
+            if ( MASK_SKIP(mask) && regidx_overlap(mask->idx, chr,start,end,NULL) ) return;
+        }
+    }
+
+    int ialt = 1;    // the alternate allele
+    if ( args->isample >= 0 )
+    {
+        bcf_unpack(rec, BCF_UN_FMT);
+        bcf_fmt_t *fmt = bcf_get_fmt(args->hdr, rec, "GT");
+        if ( !fmt ) return;
+
+        if ( fmt->type!=BCF_BT_INT8 )
+            error("Todo: GT field represented with BCF_BT_INT8, too many alleles at %s:%"PRId64"?\n",bcf_seqname(args->hdr,rec),(int64_t) rec->pos+1);
+        uint8_t *ptr = fmt->p + fmt->size*args->isample;
+
+        enum { use_hap, use_iupac, pick_one } action = use_hap;
+        if ( args->allele==PICK_IUPAC )
+        {
+            if ( !args->haplotype ) action = use_iupac;
+            if ( !bcf_gt_is_phased(ptr[0]) && !bcf_gt_is_phased(ptr[fmt->n-1]) ) action = use_iupac;
+        }
+        else if ( args->output_iupac ) action = use_iupac;
+        else if ( !args->haplotype ) action = pick_one;
+
+        if ( action==use_hap )
+        {
+            if ( args->haplotype > fmt->n )
+            {
+                if ( bcf_gt_is_missing(ptr[fmt->n-1]) || bcf_gt_is_missing(ptr[0]) )
+                {
+                    if ( !args->missing_allele ) return;
+                    ialt = -1;
+                }
+                else
+                {
+                    if ( !warned_haplotype )
+                    {
+                        fprintf(bcftools_stderr, "Can't apply %d-th haplotype at %s:%"PRId64". (This warning is printed only once.)\n", args->haplotype,bcf_seqname(args->hdr,rec),(int64_t) rec->pos+1);
+                        warned_haplotype = 1;
+                    }
+                    return;
+                }
+            }
+            else
+            {
+                ialt = (int8_t)ptr[args->haplotype-1];
+                if ( bcf_gt_is_missing(ialt) || ialt==bcf_int8_vector_end )
+                {
+                    if ( !args->missing_allele ) return;
+                    ialt = -1;
+                }
+                else
+                    ialt = bcf_gt_allele(ialt);
+            }
+        }
+        else if ( action==use_iupac )
+        {
+            ialt = -1;
+            int is_missing = 0, alen = 0, mlen = 0, fallback_alt = -1;
+            for (i=0; i<fmt->n; i++)
+            {
+                if ( bcf_gt_is_missing(ptr[i]) ) { is_missing = 1; continue; }
+                if ( ptr[i]==(uint8_t)bcf_int8_vector_end ) break;
+                int jalt = bcf_gt_allele(ptr[i]);
+                if ( jalt >= rec->n_allele ) error("Invalid VCF, too few ALT alleles at %s:%"PRId64"\n", bcf_seqname(args->hdr,rec),(int64_t) rec->pos+1);
+                if ( fallback_alt <= 0 ) fallback_alt = jalt;
+
+                int l = strlen(rec->d.allele[jalt]);
+                for (j=0; j<l; j++)
+                    if ( iupac2bitmask(rec->d.allele[jalt][j]) < 0 ) break;
+                if ( j<l ) continue; // symbolic allele, breakpoint or invalid character in the allele
+
+                if ( l > mlen )
+                {
+                    hts_expand(uint8_t,l,args->miupac_bitmask,args->iupac_bitmask);
+                    for (j=mlen; j<l; j++) args->iupac_bitmask[j] = 0;
+                    mlen = l;
+                }
+                if ( jalt>0 && l>alen )
+                {
+                    alen = l;
+                    ialt = jalt;
+                }
+                for (j=0; j<l; j++)
+                    args->iupac_bitmask[j] |= iupac2bitmask(rec->d.allele[jalt][j]);
+            }
+            if ( alen > 0 )
+                for (j=0; j<alen; j++) rec->d.allele[ialt][j] = bitmask2iupac(args->iupac_bitmask[j]);
+            else if ( fallback_alt >= 0 )
+                ialt = fallback_alt;
+            else if ( is_missing && !args->missing_allele ) return;
+        }
+        else
+        {
+            int is_hom = 1;
+            for (i=0; i<fmt->n; i++)
+            {
+                if ( bcf_gt_is_missing(ptr[i]) )
+                {
+                    if ( !args->missing_allele ) return;  // ignore missing or half-missing genotypes
+                    ialt = -1;
+                    break;
+                }
+                if ( ptr[i]==(uint8_t)bcf_int8_vector_end ) break;
+                ialt = bcf_gt_allele(ptr[i]);
+                if ( i>0 && ialt!=bcf_gt_allele(ptr[i-1]) ) { is_hom = 0; break; }
+            }
+            if ( !is_hom )
+            {
+                int prev_len = 0, jalt;
+                for (i=0; i<fmt->n; i++)
+                {
+                    if ( ptr[i]==(uint8_t)bcf_int8_vector_end ) break;
+                    jalt = bcf_gt_allele(ptr[i]);
+                    if ( rec->n_allele <= jalt ) error("Broken VCF, too few alts at %s:%"PRId64"\n", bcf_seqname(args->hdr,rec),(int64_t) rec->pos+1);
+                    if ( args->allele & (PICK_LONG|PICK_SHORT) )
+                    {
+                        int len = jalt==0 ? rec->rlen : strlen(rec->d.allele[jalt]);
+                        if ( i==0 ) ialt = jalt, prev_len = len;
+                        else if ( len == prev_len )
+                        {
+                            if ( args->allele & PICK_REF && jalt==0 ) ialt = jalt, prev_len = len;
+                            else if ( args->allele & PICK_ALT && ialt==0 ) ialt = jalt, prev_len = len;
+                        }
+                        else if ( args->allele & PICK_LONG && len > prev_len ) ialt = jalt, prev_len = len;
+                        else if ( args->allele & PICK_SHORT && len < prev_len ) ialt = jalt, prev_len = len;
+                    }
+                    else
+                    {
+                        if ( args->allele & PICK_REF && jalt==0 ) ialt = jalt;
+                        else if ( args->allele & PICK_ALT && ialt==0 ) ialt = jalt;
+                    }
+                }
+            }
+        }
+        if ( !ialt )
+        {
+            // ref allele
+            if ( args->absent_allele ) freeze_ref(args,rec);
+            return;
+        }
+        if ( rec->n_allele <= ialt ) error("Broken VCF, too few alts at %s:%"PRId64"\n", bcf_seqname(args->hdr,rec),(int64_t) rec->pos+1);
+    }
+    else if ( args->output_iupac && rec->n_allele>1 )
+    {
+        int ialt, alen = 0, mlen = 0;
+        for (i=0; i<rec->n_allele; i++)
+        {
+            int l = strlen(rec->d.allele[i]);
+            for (j=0; j<l; j++)
+                if ( iupac2bitmask(rec->d.allele[i][j]) < 0 ) break;
+            if ( j<l ) continue;    // symbolic allele, breakpoint or invalid character in the allele
+
+            if ( l > mlen )
+            {
+                hts_expand(uint8_t,l,args->miupac_bitmask,args->iupac_bitmask);
+                for (j=mlen; j<l; j++) args->iupac_bitmask[j] = 0;
+                mlen = l;
+            }
+            if ( i>0 && l>alen )
+            {
+                alen = l;
+                ialt = i;
+            }
+            for (j=0; j<l; j++)
+                args->iupac_bitmask[j] |= iupac2bitmask(rec->d.allele[i][j]);
+        }
+        if ( alen > 0 )
+            for (j=0; j<alen; j++) rec->d.allele[ialt][j] = bitmask2iupac(args->iupac_bitmask[j]);
+        else
+            ialt = 1;
+    }
+
+    if ( rec->n_allele==1 && ialt!=-1 )
+    {
+        // non-missing reference
+        if ( args->absent_allele ) freeze_ref(args,rec);
+        return;
+    }
+    if ( ialt==-1 )
+    {
+        char alleles[4];
+        alleles[0] = rec->d.allele[0][0];
+        alleles[1] = ',';
+        alleles[2] = args->missing_allele;
+        alleles[3] = 0;
+        bcf_update_alleles_str(args->hdr, rec, alleles);
+        ialt = 1;
+    }
+
+    // For some variant types POS+REF refer to the base *before* the event; in such case set trim_beg
+    int trim_beg = 0;
+    int var_type = bcf_get_variant_type(rec,ialt);
+    int var_len  = rec->d.var[ialt].n;
+    if ( var_type & VCF_INDEL )
+    {
+        // normally indel starts one base after, but not if the first base of the fa reference is deleted
+        if ( rec->d.allele[0][0] == rec->d.allele[ialt][0] )
+            trim_beg = 1;
+        else
+            trim_beg = 0;
+    }
+    else if ( (var_type & VCF_OTHER) && !strcasecmp(rec->d.allele[ialt],"<DEL>") )
+    {
+        trim_beg = 1;
+        var_len  = 1 - rec->rlen;
+    }
+    else if ( (var_type & VCF_OTHER) && !strncasecmp(rec->d.allele[ialt],"<INS",4) ) trim_beg = 1;
+
+    // Overlapping variant?
+    if ( rec->pos <= args->fa_frz_pos )
+    {
+        // Can be still OK iff this is an insertion (and which does not follow another insertion, see #888).
+        // This still may not be enough for more complicated cases with multiple duplicate positions
+        // and other types in between. In such case let the user normalize the VCF and remove duplicates.
+
+        int overlap = 0;
+        if ( rec->pos < args->fa_frz_pos || !trim_beg || var_len==0 || args->prev_is_insert ) overlap = 1;
+
+        if ( overlap )
+        {
+            fprintf(bcftools_stderr,"The site %s:%"PRId64" overlaps with another variant, skipping...\n", bcf_seqname(args->hdr,rec),(int64_t) rec->pos+1);
+            return;
+        }
+
+    }
+
+    char *alt_allele = rec->d.allele[ialt];
+    int rmme_alt = 0;
+
+    int len_diff = 0, alen = 0;
+    int idx = rec->pos - args->fa_ori_pos + args->fa_mod_off;
+    if ( idx<0 )
+    {
+        fprintf(bcftools_stderr,"Warning: ignoring overlapping variant starting at %s:%"PRId64"\n", bcf_seqname(args->hdr,rec),(int64_t) rec->pos+1);
+        return;
+    }
+    if ( rec->rlen > args->fa_buf.l - idx )
+    {
+        rec->rlen = args->fa_buf.l - idx;
+        if ( alt_allele[0]!='<' )
+        {
+            alen = strlen(alt_allele);
+            if ( alen > rec->rlen )
+            {
+                fprintf(bcftools_stderr,"Warning: trimming variant \"%s\" starting at %s:%"PRId64"\n", alt_allele,bcf_seqname(args->hdr,rec),(int64_t) rec->pos+1);
+                alt_allele[rec->rlen] = 0;
+            }
+        }
+    }
+    if ( idx>=args->fa_buf.l )
+        error("FIXME: %s:%"PRId64" .. idx=%d, ori_pos=%d, len=%"PRIu64", off=%d\n",bcf_seqname(args->hdr,rec),(int64_t) rec->pos+1,idx,args->fa_ori_pos,(uint64_t)args->fa_buf.l,args->fa_mod_off);
+
+    // sanity check the reference base
+    if ( alt_allele[0]=='<' )
+    {
+        // TODO: symbolic deletions probably need more work above with PICK_SHORT|PICK_LONG
+
+        if ( strcasecmp(alt_allele,"<DEL>") && strcasecmp(alt_allele,"<*>") && strcasecmp(alt_allele,"<NON_REF>") )
+            error("Symbolic alleles other than <DEL>, <*> or <NON_REF> are currently not supported, e.g. \"%s\" at %s:%"PRId64".\n"
+                  "Please use filtering expressions to exclude such sites, for example by running with: -e 'ALT~\"<.*>\"'\n",
+                alt_allele,bcf_seqname(args->hdr,rec),(int64_t) rec->pos+1);
+        if ( !strcasecmp(alt_allele,"<DEL>") )
+        {
+            static int multibase_ref_del_warned = 0;
+            if ( rec->d.allele[0][1]!=0 && !multibase_ref_del_warned )
+            {
+                fprintf(bcftools_stderr,
+                    "Warning: one REF base is expected with <DEL>, assuming the actual deletion starts at POS+1 at %s:%"PRId64".\n"
+                    "         (This warning is printed only once.)\n", bcf_seqname(args->hdr,rec),(int64_t) rec->pos+1);
+                multibase_ref_del_warned = 1;
+            }
+            if ( args->mark_del )   // insert dashes instead of delete sequence
+            {
+                alt_allele = mark_del(rec->d.allele[0], rec->rlen, NULL, args->mark_del);
+                alen = rec->rlen;
+                len_diff = 0;
+                rmme_alt = 1;
+            }
+            else
+            {
+                len_diff = 1-rec->rlen;
+                alt_allele = rec->d.allele[0];     // according to VCF spec, the first REF base must precede the event
+                alen = 1;
+            }
+        }
+        else
+        {
+            // <*>  or <NON_REF> .. gVCF, evidence for the reference allele throughout the whole block
+            freeze_ref(args,rec);
+            return;
+        }
+    }
+    else if ( strncasecmp(rec->d.allele[0],args->fa_buf.s+idx,rec->rlen) )
+    {
+        // This is hacky, handle a special case: if SNP or an insert follows a deletion (AAC>A, C>CAA),
+        // the reference base in fa_buf is lost and the check fails. We do not keep a buffer
+        // with the original sequence as it should not be necessary, we should encounter max
+        // one base overlap
+
+        int fail = 1;
+        if ( args->prev_base_pos==rec->pos && toupper(rec->d.allele[0][0])==toupper(args->prev_base) )
+        {
+            if ( rec->rlen==1 ) fail = 0;
+            else if ( !strncasecmp(rec->d.allele[0]+1,args->fa_buf.s+idx+1,rec->rlen-1) ) fail = 0;
+        }
+
+        if ( fail )
+        {
+            char tmp = 0;
+            if ( args->fa_buf.l - idx > rec->rlen )
+            {
+                tmp = args->fa_buf.s[idx+rec->rlen];
+                args->fa_buf.s[idx+rec->rlen] = 0;
+            }
+            error(
+                    "The fasta sequence does not match the REF allele at %s:%"PRId64":\n"
+                    "   REF .vcf: [%s]\n"
+                    "   ALT .vcf: [%s]\n"
+                    "   REF .fa : [%s]%c%s\n",
+                    bcf_seqname(args->hdr,rec),(int64_t) rec->pos+1, rec->d.allele[0], alt_allele, args->fa_buf.s+idx,
+                    tmp?tmp:' ',tmp?args->fa_buf.s+idx+rec->rlen+1:""
+                 );
+        }
+        alen = strlen(alt_allele);
+        len_diff = alen - rec->rlen;
+
+        if ( args->mark_del && len_diff<0 )
+        {
+            alt_allele = mark_del(rec->d.allele[0], rec->rlen, alt_allele, args->mark_del);
+            alen = rec->rlen;
+            len_diff = 0;
+            rmme_alt = 1;
+        }
+    }
+    else
+    {
+        alen = strlen(alt_allele);
+        len_diff = alen - rec->rlen;
+
+        if ( args->mark_del && len_diff<0 )
+        {
+            alt_allele = mark_del(rec->d.allele[0], rec->rlen, alt_allele, args->mark_del);
+            alen = rec->rlen;
+            len_diff = 0;
+            rmme_alt = 1;
+        }
+    }
+
+    args->fa_case = toupper(args->fa_buf.s[idx])==args->fa_buf.s[idx] ? TO_UPPER : TO_LOWER;
+    if ( args->fa_case==TO_UPPER )
+        for (i=0; i<alen; i++) alt_allele[i] = toupper(alt_allele[i]);
+    else
+        for (i=0; i<alen; i++) alt_allele[i] = tolower(alt_allele[i]);
+
+    if ( args->mark_ins && len_diff>0 )
+        mark_ins(rec->d.allele[0], alt_allele, args->mark_ins);
+    if ( args->mark_snv )
+        mark_snv(rec->d.allele[0], alt_allele, args->mark_snv);
+
+    if ( len_diff <= 0 )
+    {
+        // deletion or same size event
+        assert( args->fa_buf.l >= idx+rec->rlen );
+        args->prev_base = args->fa_buf.s[idx+rec->rlen-1];
+        args->prev_base_pos = rec->pos + rec->rlen - 1;
+        args->prev_is_insert = 0;
+        args->fa_frz_mod = idx + alen;
+
+        for (i=trim_beg; i<alen; i++)
+            args->fa_buf.s[idx+i] = alt_allele[i];
+
+        if ( len_diff )
+            memmove(args->fa_buf.s+idx+alen,args->fa_buf.s+idx+rec->rlen,args->fa_buf.l-idx-rec->rlen);
+    }
+    else
+    {
+        args->prev_is_insert = 1;
+        args->prev_base_pos = rec->pos;
+
+        // insertion
+        ks_resize(&args->fa_buf, args->fa_buf.l + len_diff);
+        memmove(args->fa_buf.s + idx + rec->rlen + len_diff, args->fa_buf.s + idx + rec->rlen, args->fa_buf.l - idx - rec->rlen);
+
+        // This can get tricky, make sure the bases unchanged by the insertion do not overwrite preceeding variants.
+        // For example, here we want to get TAA:
+        //      POS REF ALT
+        //      1   C   T
+        //      1   C   CAA
+        int ibeg = 0;
+        while ( ibeg<alen && rec->d.allele[0][ibeg]==alt_allele[ibeg] && rec->pos + ibeg <= args->prev_base_pos  ) ibeg++;
+        for (i=ibeg; i<alen; i++)
+            args->fa_buf.s[idx+i] = alt_allele[i];
+
+        args->fa_frz_mod = idx + alen - ibeg + 1;
+    }
+    if (args->chain && len_diff != 0)
+    {
+        // If first nucleotide of both REF and ALT are the same... (indels typically include the nucleotide before the variant)
+        if ( strncasecmp(rec->d.allele[0],alt_allele,1) == 0)
+        {
+            // ...extend the block by 1 bp: start is 1 bp further and alleles are 1 bp shorter
+            push_chain_gap(args->chain, rec->pos + 1, rec->rlen - 1, rec->pos + 1 + args->fa_mod_off, alen - 1);
+        }
+        else
+        {
+            // otherwise, just the coordinates of the variant as given
+            push_chain_gap(args->chain, rec->pos, rec->rlen, rec->pos + args->fa_mod_off, alen);
+        }
+    }
+    args->fa_buf.l += len_diff;
+    args->fa_mod_off += len_diff;
+    args->fa_frz_pos  = rec->pos + rec->rlen - 1;
+    args->napplied++;
+    if ( rmme_alt ) free(alt_allele);
+}
+
+
+static void mask_region(args_t *args, char *seq, int len)
+{
+    int start = args->fa_src_pos - len;
+    int end   = args->fa_src_pos;
+    int i;
+
+    for (i=0; i<args->nmask; i++)
+    {
+        mask_t *mask = &args->mask[i];
+        if ( !regidx_overlap(mask->idx, args->chr,start,end, mask->itr) ) continue;
+
+        int idx_start, idx_end, j;
+        while ( regitr_overlap(mask->itr) )
+        {
+            idx_start = mask->itr->beg - start;
+            idx_end   = mask->itr->end - start;
+            if ( idx_start < 0 ) idx_start = 0;
+            if ( idx_end >= len ) idx_end = len - 1;
+            if ( mask->with==MASK_UC )
+                for (j=idx_start; j<=idx_end; j++) seq[j] = toupper(seq[j]);
+            else if ( mask->with==MASK_LC )
+                for (j=idx_start; j<=idx_end; j++) seq[j] = tolower(seq[j]);
+            else
+                for (j=idx_start; j<=idx_end; j++) seq[j] = mask->with;
+        }
+    }
+}
+
+static void consensus(args_t *args)
+{
+    BGZF *fasta = bgzf_open(args->ref_fname, "r");
+    if ( !fasta ) error("Error reading %s\n", args->ref_fname);
+    kstring_t str = {0,0,0};
+    while ( bgzf_getline(fasta, '\n', &str) > 0 )
+    {
+        if ( str.s[0]=='>' )
+        {
+            // new sequence encountered
+            if ( args->chain ) print_chain(args);
+
+            // apply all cached variants and variants that might have been missed because of short fasta (see test/consensus.9.*)
+            bcf1_t **rec_ptr = NULL;
+            while ( args->rid>=0 && (rec_ptr = next_vcf_line(args)) )
+            {
+                bcf1_t *rec = *rec_ptr;
+                if ( rec->rid!=args->rid || ( args->fa_end_pos && rec->pos > args->fa_end_pos ) ) break;
+                apply_variant(args, rec);
+            }
+            if ( args->absent_allele )
+            {
+                int pos = 0;
+                if ( args->vcf_rbuf.n && args->vcf_buf[args->vcf_rbuf.f]->rid==args->rid )
+                    pos = args->vcf_buf[args->vcf_rbuf.f]->pos;
+                apply_absent(args, pos);
+            }
+            flush_fa_buffer(args, 0);
+            init_region(args, str.s+1);
+            continue;
+        }
+        args->fa_length  += str.l;
+        args->fa_src_pos += str.l;
+
+        // determine if uppercase or lowercase is used in this fasta file
+        if ( args->fa_case==-1 ) args->fa_case = toupper(str.s[0])==str.s[0] ? 1 : 0;
+
+        if ( args->mask ) mask_region(args, str.s, str.l);
+        kputs(str.s, &args->fa_buf);
+
+        bcf1_t **rec_ptr = NULL;
+        while ( args->rid>=0 && (rec_ptr = next_vcf_line(args)) )
+        {
+            bcf1_t *rec = *rec_ptr;
+
+            // still the same chr and the same region? if not, fasta buf can be flushed
+            if ( rec->rid!=args->rid || ( args->fa_end_pos && rec->pos > args->fa_end_pos ) )
+            {
+                // save the vcf record until next time and flush
+                unread_vcf_line(args, rec_ptr);
+                rec_ptr = NULL;
+                break;
+            }
+
+            // is the vcf record well beyond cached fasta buffer? if yes, the buf can be flushed
+            if ( args->fa_ori_pos + args->fa_buf.l - args->fa_mod_off <= rec->pos )
+            {
+                unread_vcf_line(args, rec_ptr);
+                rec_ptr = NULL;
+                break;
+            }
+
+            // is the cached fasta buffer full enough? if not, read more fasta, no flushing
+            if ( args->fa_ori_pos + args->fa_buf.l - args->fa_mod_off < rec->pos + rec->rlen )
+            {
+                unread_vcf_line(args, rec_ptr);
+                break;
+            }
+            apply_variant(args, rec);
+        }
+        if ( !rec_ptr )
+        {
+            if ( args->absent_allele ) apply_absent(args, args->fa_ori_pos - args->fa_mod_off + args->fa_buf.l);
+            flush_fa_buffer(args, 60);
+        }
+    }
+    bcf1_t **rec_ptr = NULL;
+    while ( args->rid>=0 && (rec_ptr = next_vcf_line(args)) )
+    {
+        bcf1_t *rec = *rec_ptr;
+        if ( rec->rid!=args->rid ) break;
+        if ( args->fa_end_pos && rec->pos > args->fa_end_pos ) break;
+        if ( args->fa_ori_pos + args->fa_buf.l - args->fa_mod_off <= rec->pos ) break;
+        apply_variant(args, rec);
+    }
+    if (args->chain) print_chain(args);
+    if ( args->absent_allele ) apply_absent(args, HTS_POS_MAX);
+    flush_fa_buffer(args, 0);
+    bgzf_close(fasta);
+    free(str.s);
+    fprintf(bcftools_stderr,"Applied %d variants\n", args->napplied);
+}
+
+static void usage(args_t *args)
+{
+    fprintf(bcftools_stderr, "\n");
+    fprintf(bcftools_stderr, "About: Create consensus sequence by applying VCF variants to a reference fasta\n");
+    fprintf(bcftools_stderr, "       file. By default, the program will apply all ALT variants. Using the\n");
+    fprintf(bcftools_stderr, "       --sample (and, optionally, --haplotype) option will apply genotype\n");
+    fprintf(bcftools_stderr, "       (or haplotype) calls from FORMAT/GT. The program ignores allelic depth\n");
+    fprintf(bcftools_stderr, "       information, such as INFO/AD or FORMAT/AD.\n");
+    fprintf(bcftools_stderr, "Usage: bcftools consensus [OPTIONS] <file.vcf.gz>\n");
+    fprintf(bcftools_stderr, "Options:\n");
+    fprintf(bcftools_stderr, "    -c, --chain FILE               write a chain file for liftover\n");
+    fprintf(bcftools_stderr, "    -a, --absent CHAR              replace positions absent from VCF with CHAR\n");
+    fprintf(bcftools_stderr, "    -e, --exclude EXPR             exclude sites for which the expression is true (see man page for details)\n");
+    fprintf(bcftools_stderr, "    -f, --fasta-ref FILE           reference sequence in fasta format\n");
+    fprintf(bcftools_stderr, "    -H, --haplotype WHICH          choose which allele to use from the FORMAT/GT field, note\n");
+    fprintf(bcftools_stderr, "                                   the codes are case-insensitive:\n");
+    fprintf(bcftools_stderr, "                                       1: first allele from GT, regardless of phasing\n");
+    fprintf(bcftools_stderr, "                                       2: second allele from GT, regardless of phasing\n");
+    fprintf(bcftools_stderr, "                                       R: REF allele in het genotypes\n");
+    fprintf(bcftools_stderr, "                                       A: ALT allele\n");
+    fprintf(bcftools_stderr, "                                       I: IUPAC code for all genotypes\n");
+    fprintf(bcftools_stderr, "                                       LR,LA: longer allele and REF/ALT if equal length\n");
+    fprintf(bcftools_stderr, "                                       SR,SA: shorter allele and REF/ALT if equal length\n");
+    fprintf(bcftools_stderr, "                                       1pIu,2pIu: first/second allele for phased and IUPAC code for unphased GTs\n");
+    fprintf(bcftools_stderr, "    -i, --include EXPR             select sites for which the expression is true (see man page for details)\n");
+    fprintf(bcftools_stderr, "    -I, --iupac-codes              output variants in the form of IUPAC ambiguity codes\n");
+    fprintf(bcftools_stderr, "        --mark-del CHAR            instead of removing sequence, insert CHAR for deletions\n");
+    fprintf(bcftools_stderr, "        --mark-ins uc|lc           highlight insertions in uppercase (uc) or lowercase (lc), leaving the rest as is\n");
+    fprintf(bcftools_stderr, "        --mark-snv uc|lc           highlight substitutions in uppercase (uc) or lowercase (lc), leaving the rest as is\n");
+    fprintf(bcftools_stderr, "    -m, --mask FILE                replace regions according to the next --mask-with option. The default is --mask-with N\n");
+    fprintf(bcftools_stderr, "        --mask-with CHAR|uc|lc     replace with CHAR (skips overlapping variants); change to uppercase (uc) or lowercase (lc)\n");
+    fprintf(bcftools_stderr, "    -M, --missing CHAR             output CHAR instead of skipping a missing genotype \"./.\"\n");
+    fprintf(bcftools_stderr, "    -o, --output FILE              write output to a file [standard output]\n");
+    fprintf(bcftools_stderr, "    -p, --prefix STRING            prefix to add to output sequence names\n");
+    fprintf(bcftools_stderr, "    -s, --sample NAME              apply variants of the given sample\n");
+    fprintf(bcftools_stderr, "Examples:\n");
+    fprintf(bcftools_stderr, "   # Get the consensus for one region. The fasta header lines are then expected\n");
+    fprintf(bcftools_stderr, "   # in the form \">chr:from-to\".\n");
+    fprintf(bcftools_stderr, "   samtools faidx ref.fa 8:11870-11890 | bcftools consensus in.vcf.gz > out.fa\n");
+    fprintf(bcftools_stderr, "\n");
+    fprintf(bcftools_stderr, "   # See also http://samtools.github.io/bcftools/howtos/consensus-sequence.html\n");
+    fprintf(bcftools_stderr, "\n");
+    bcftools_exit(1);
+}
+
+int main_consensus(int argc, char *argv[])
+{
+    args_t *args = (args_t*) calloc(1,sizeof(args_t));
+    args->argc   = argc; args->argv = argv;
+
+    static struct option loptions[] =
+    {
+        {"mark-del",required_argument,NULL,1},
+        {"mark-ins",required_argument,NULL,2},
+        {"mark-snv",required_argument,NULL,3},
+        {"mask-with",1,0,4},
+        {"exclude",required_argument,NULL,'e'},
+        {"include",required_argument,NULL,'i'},
+        {"sample",1,0,'s'},
+        {"iupac-codes",0,0,'I'},
+        {"haplotype",1,0,'H'},
+        {"output",1,0,'o'},
+        {"fasta-ref",1,0,'f'},
+        {"mask",1,0,'m'},
+        {"missing",1,0,'M'},
+        {"absent",1,0,'a'},
+        {"chain",1,0,'c'},
+        {"prefix",required_argument,0,'p'},
+        {0,0,0,0}
+    };
+    int c;
+    while ((c = getopt_long(argc, argv, "h?s:1Ii:e:H:f:o:m:c:M:p:a:",loptions,NULL)) >= 0)
+    {
+        switch (c)
+        {
+            case  1 : args->mark_del = optarg[0]; break;
+            case  2 :
+                if ( !strcasecmp(optarg,"uc") ) args->mark_ins = 'u';
+                else if ( !strcasecmp(optarg,"lc") ) args->mark_ins = 'l';
+                else error("The argument is not recognised: --mark-ins %s\n",optarg);
+                break;
+            case  3 :
+                if ( !strcasecmp(optarg,"uc") ) args->mark_snv = 'u';
+                else if ( !strcasecmp(optarg,"lc") ) args->mark_snv = 'l';
+                else error("The argument is not recognised: --mark-snv %s\n",optarg);
+                break;
+            case 'p': args->chr_prefix = optarg; break;
+            case 's': args->sample = optarg; break;
+            case 'o': args->output_fname = optarg; break;
+            case 'I': args->output_iupac = 1; break;
+            case 'e':
+                if ( args->filter_str ) error("Error: only one -i or -e expression can be given, and they cannot be combined\n");
+                args->filter_str = optarg; args->filter_logic |= FLT_EXCLUDE; break;
+            case 'i':
+                if ( args->filter_str ) error("Error: only one -i or -e expression can be given, and they cannot be combined\n");
+                args->filter_str = optarg; args->filter_logic |= FLT_INCLUDE; break;
+            case 'f': args->ref_fname = optarg; break;
+            case 'm': add_mask(args,optarg); break;
+            case  4 : add_mask_with(args,optarg); break;
+            case 'a':
+                args->absent_allele = optarg[0];
+                if ( optarg[1]!=0 ) error("Expected single character with -a, got \"%s\"\n", optarg);
+                break;
+            case 'M':
+                args->missing_allele = optarg[0];
+                if ( optarg[1]!=0 ) error("Expected single character with -M, got \"%s\"\n", optarg);
+                break;
+            case 'c': args->chain_fname = optarg; break;
+            case 'H':
+                if ( !strcasecmp(optarg,"R") ) args->allele |= PICK_REF;
+                else if ( !strcasecmp(optarg,"A") ) args->allele |= PICK_ALT;
+                else if ( !strcasecmp(optarg,"L") ) args->allele |= PICK_LONG|PICK_REF;
+                else if ( !strcasecmp(optarg,"S") ) args->allele |= PICK_SHORT|PICK_REF;
+                else if ( !strcasecmp(optarg,"LR") ) args->allele |= PICK_LONG|PICK_REF;
+                else if ( !strcasecmp(optarg,"LA") ) args->allele |= PICK_LONG|PICK_ALT;
+                else if ( !strcasecmp(optarg,"SR") ) args->allele |= PICK_SHORT|PICK_REF;
+                else if ( !strcasecmp(optarg,"SA") ) args->allele |= PICK_SHORT|PICK_ALT;
+                else if ( !strcasecmp(optarg,"I") ) args->allele |= PICK_IUPAC;
+                else if ( !strcasecmp(optarg,"1pIu") ) args->allele |= PICK_IUPAC, args->haplotype = 1;
+                else if ( !strcasecmp(optarg,"2pIu") ) args->allele |= PICK_IUPAC, args->haplotype = 2;
+                else
+                {
+                    char *tmp;
+                    args->haplotype = strtol(optarg, &tmp, 10);
+                    if ( tmp==optarg || *tmp ) error("Error: Could not parse --haplotype %s, expected numeric argument\n", optarg);
+                    if ( args->haplotype <=0 ) error("Error: Expected positive integer with --haplotype\n");
+                }
+                break;
+            default: usage(args); break;
+        }
+    }
+    if ( optind>=argc ) usage(args);
+    args->fname = argv[optind];
+
+    if ( !args->ref_fname && !isatty(fileno((FILE *)stdin)) ) args->ref_fname = "-";
+    if ( !args->ref_fname ) usage(args);
+
+    init_data(args);
+    consensus(args);
+    destroy_data(args);
+    free(args);
+
+    return 0;
+}
+
+
diff --git a/bcftools/convert.c b/bcftools/convert.c
new file mode 100644
index 0000000..5317cb8
--- /dev/null
+++ b/bcftools/convert.c
@@ -0,0 +1,1709 @@
+/*  convert.c -- functions for converting between VCF/BCF and related formats.
+
+    Copyright (C) 2013-2022 Genome Research Ltd.
+
+    Author: Petr Danecek <pd3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.  */
+
+#include <stdio.h>
+#include <unistd.h>
+#include <getopt.h>
+#include <assert.h>
+#include <ctype.h>
+#include <string.h>
+#include <errno.h>
+#include <sys/stat.h>
+#include <sys/types.h>
+#define __STDC_FORMAT_MACROS
+#include <inttypes.h>
+#include <math.h>
+#include <htslib/vcf.h>
+#include <htslib/synced_bcf_reader.h>
+#include <htslib/vcfutils.h>
+#include <htslib/kfunc.h>
+#include <htslib/khash_str2int.h>
+#include "bcftools.h"
+#include "variantkey.h"
+#include "convert.h"
+#include "filter.h"
+
+#define T_CHROM   1
+#define T_POS     2
+#define T_ID      3
+#define T_REF     4
+#define T_ALT     5
+#define T_QUAL    6
+#define T_FILTER  7
+#define T_INFO    8
+#define T_FORMAT  9
+#define T_SAMPLE  10
+#define T_SEP     11
+#define T_IS_TS   12
+#define T_TYPE    13
+#define T_MASK    14
+#define T_GT      15
+#define T_TGT     16
+#define T_LINE    17
+#define T_CHROM_POS_ID 18   // not publicly advertised
+#define T_GT_TO_PROB3  19   // not publicly advertised
+#define T_PL_TO_PROB3  20   // not publicly advertised
+#define T_GP_TO_PROB3  21   // not publicly advertised
+#define T_FIRST_ALT    22   // not publicly advertised
+#define T_IUPAC_GT     23
+#define T_GT_TO_HAP    24   // not publicly advertised
+#define T_GT_TO_HAP2   25   // not publicly advertised
+#define T_TBCSQ        26
+#define T_END          27
+#define T_POS0         28
+#define T_END0         29
+#define T_RSX          30   // RSID HEX
+#define T_VKX          31   // VARIANTKEY HEX
+#define T_PBINOM       32
+#define T_NPASS        33
+
+typedef struct _fmt_t
+{
+    int type, id, is_gt_field, ready, subscript;
+    char *key;
+    bcf_fmt_t *fmt;
+    void *usr;                  // user data (optional)
+    void (*handler)(convert_t *, bcf1_t *, struct _fmt_t *, int, kstring_t *);
+    void (*destroy)(void*);     // clean user data (optional)
+}
+fmt_t;
+
+struct _convert_t
+{
+    fmt_t *fmt;
+    int nfmt, mfmt;
+    int nsamples, *samples;
+    bcf_hdr_t *header;
+    int max_unpack;
+    char *format_str;
+    bcf_srs_t *readers; // required only for %MASK
+    int nreaders;
+    void *dat;
+    int ndat;
+    char *undef_info_tag;
+    void *used_tags_hash;
+    char **used_tags_list;
+    int nused_tags;
+    int allow_undef_tags;
+    uint8_t **subset_samples;
+};
+
+typedef struct
+{
+    kstring_t hap1,hap2;
+    char **str;
+    int n, m;
+}
+bcsq_t;
+
+static void process_chrom(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str) { kputs(convert->header->id[BCF_DT_CTG][line->rid].key, str); }
+static void process_pos(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str) { kputw(line->pos+1, str); }
+static void process_pos0(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str) { kputw(line->pos, str); }
+static void process_end(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str) { kputw(line->pos+line->rlen, str); }
+static void process_end0(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str) { kputw(line->pos+line->rlen-1, str); }
+static void process_id(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str) { kputs(line->d.id, str); }
+static void process_ref(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str) { kputs(line->d.allele[0], str); }
+static void process_alt(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str)
+{
+    int i;
+    if ( line->n_allele==1 )
+    {
+        kputc('.', str);
+        return;
+    }
+    if ( fmt->subscript>=0 )
+    {
+        if ( line->n_allele > fmt->subscript+1 )
+            kputs(line->d.allele[fmt->subscript+1], str);
+        else
+            kputc('.', str);
+        return;
+    }
+    for (i=1; i<line->n_allele; i++)
+    {
+        if ( i>1 ) kputc(',', str);
+        kputs(line->d.allele[i], str);
+    }
+}
+static void process_first_alt(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str)
+{
+    if ( line->n_allele==1 )
+        kputc('.', str);
+    else
+        kputs(line->d.allele[1], str);
+}
+static void process_qual(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str)
+{
+    if ( bcf_float_is_missing(line->qual) ) kputc('.', str);
+    else kputd(line->qual, str);
+}
+static void process_filter(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str)
+{
+    int i;
+    if ( line->d.n_flt )
+    {
+        for (i=0; i<line->d.n_flt; i++)
+        {
+            if (i) kputc(';', str);
+            kputs(convert->header->id[BCF_DT_ID][line->d.flt[i]].key, str);
+        }
+    }
+    else kputc('.', str);
+}
+static inline int32_t bcf_array_ivalue(void *bcf_array, int type, int idx)
+{
+    if ( type==BCF_BT_INT8 )
+    {
+        int8_t val = ((int8_t*)bcf_array)[idx];
+        if ( val==bcf_int8_missing ) return bcf_int32_missing;
+        if ( val==bcf_int8_vector_end ) return bcf_int32_vector_end;
+        return val;
+    }
+    if ( type==BCF_BT_INT16 )
+    {
+        int16_t val = ((int16_t*)bcf_array)[idx];
+        if ( val==bcf_int16_missing ) return bcf_int32_missing;
+        if ( val==bcf_int16_vector_end ) return bcf_int32_vector_end;
+        return val;
+    }
+    return ((int32_t*)bcf_array)[idx];
+}
+static inline void _copy_field(char *src, uint32_t len, int idx, kstring_t *str)
+{
+    int n = 0, ibeg = 0;
+    while ( src[ibeg] && ibeg<len && n < idx )
+    {
+        if ( src[ibeg]==',' ) n++;
+        ibeg++;
+    }
+    if ( ibeg==len ) { kputc('.', str); return; }
+
+    int iend = ibeg;
+    while ( src[iend] && src[iend]!=',' && iend<len ) iend++;
+
+    if ( iend>ibeg )
+        kputsn(src+ibeg, iend-ibeg, str);
+    else
+        kputc('.', str);
+}
+static void process_info(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str)
+{
+    int i;
+    if ( !fmt->key )    // the whole INFO column
+    {
+        int first = 1;
+        for (i=0; i<line->n_info; i++)
+        {
+            bcf_info_t *inf = &line->d.info[i];
+            if ( !inf->vptr ) continue;
+            if ( !first ) kputc(';', str);
+            first = 0;
+            if ( inf->key >= convert->header->n[BCF_DT_ID] ) continue;
+            kputs(convert->header->id[BCF_DT_ID][inf->key].key, str);
+            if ( inf->len <= 0 ) continue;
+            kputc('=', str);
+            if ( inf->len == 1 )
+            {
+                switch (inf->type)
+                {
+                    case BCF_BT_INT8:  if ( inf->v1.i==bcf_int8_missing ) kputc('.', str); else kputw(inf->v1.i, str); break;
+                    case BCF_BT_INT16: if ( inf->v1.i==bcf_int16_missing ) kputc('.', str); else kputw(inf->v1.i, str); break;
+                    case BCF_BT_INT32: if ( inf->v1.i==bcf_int32_missing ) kputc('.', str); else kputw(inf->v1.i, str); break;
+                    case BCF_BT_FLOAT: if ( bcf_float_is_missing(inf->v1.f) ) kputc('.', str); else kputd(inf->v1.f, str); break;
+                    case BCF_BT_CHAR:  kputc(inf->v1.i, str); break;
+                    default: error("Unexpected type %d", inf->type); break;
+                }
+            }
+            else bcf_fmt_array(str, inf->len, inf->type, inf->vptr);
+        }
+        if ( first ) kputc('.', str);
+        return;
+    }
+
+    if ( fmt->id<0 )
+    {
+        kputc('.', str);
+        return;
+    }
+
+    for (i=0; i<line->n_info; i++)
+        if ( line->d.info[i].key == fmt->id ) break;
+
+    // output "." if the tag is not present
+    if ( i==line->n_info )
+    {
+        kputc('.', str);
+        return;
+    }
+
+    bcf_info_t *info = &line->d.info[i];
+
+    // if this is a flag, output 1
+    if ( info->len <=0 )
+    {
+        kputc('1', str);
+        return;
+    }
+
+    if ( info->len == 1 )
+    {
+        switch (info->type)
+        {
+            case BCF_BT_INT8:  if ( info->v1.i==bcf_int8_missing ) kputc('.', str); else kputw(info->v1.i, str); break;
+            case BCF_BT_INT16: if ( info->v1.i==bcf_int16_missing ) kputc('.', str); else kputw(info->v1.i, str); break;
+            case BCF_BT_INT32: if ( info->v1.i==bcf_int32_missing ) kputc('.', str); else kputw(info->v1.i, str); break;
+            case BCF_BT_FLOAT: if ( bcf_float_is_missing(info->v1.f) ) kputc('.', str); else kputd(info->v1.f, str); break;
+            case BCF_BT_CHAR:  kputc(info->v1.i, str); break;
+            default: fprintf(stderr,"todo: type %d\n", info->type); exit(1); break;
+        }
+    }
+    else if ( fmt->subscript >=0 )
+    {
+        if ( info->len <= fmt->subscript )
+        {
+            kputc('.', str);
+            return;
+        }
+        #define BRANCH(type_t, is_missing, is_vector_end, kprint) { \
+            type_t val = ((type_t *) info->vptr)[fmt->subscript]; \
+            if ( is_missing || is_vector_end ) kputc('.',str); \
+            else kprint; \
+        }
+        switch (info->type)
+        {
+            case BCF_BT_INT8:  BRANCH(int8_t,  val==bcf_int8_missing,  val==bcf_int8_vector_end,  kputw(val, str)); break;
+            case BCF_BT_INT16: BRANCH(int16_t, val==bcf_int16_missing, val==bcf_int16_vector_end, kputw(val, str)); break;
+            case BCF_BT_INT32: BRANCH(int32_t, val==bcf_int32_missing, val==bcf_int32_vector_end, kputw(val, str)); break;
+            case BCF_BT_FLOAT: BRANCH(float,   bcf_float_is_missing(val), bcf_float_is_vector_end(val), kputd(val, str)); break;
+            case BCF_BT_CHAR:  _copy_field((char*)info->vptr, info->vptr_len, fmt->subscript, str); break;
+            default: fprintf(stderr,"todo: type %d\n", info->type); exit(1); break;
+        }
+        #undef BRANCH
+    }
+    else
+        bcf_fmt_array(str, info->len, info->type, info->vptr);
+}
+static void init_format(convert_t *convert, bcf1_t *line, fmt_t *fmt)
+{
+    fmt->id = bcf_hdr_id2int(convert->header, BCF_DT_ID, fmt->key);
+    if ( !bcf_hdr_idinfo_exists(convert->header,BCF_HL_FMT,fmt->id) ) fmt->id = -1;
+    fmt->fmt = NULL;
+    if ( fmt->id >= 0 )
+    {
+        int i;
+        for (i=0; i<(int)line->n_fmt; i++)
+            if ( line->d.fmt[i].id==fmt->id ) { fmt->fmt = &line->d.fmt[i]; break; }
+    }
+    else if ( !convert->allow_undef_tags )
+        error("Error: no such tag defined in the VCF header: FORMAT/%s\n", fmt->key);
+
+    fmt->ready = 1;
+}
+static void process_complete_format(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str)
+{
+    if ( convert->nsamples )
+    {
+        int i,j;
+        if ( line->n_fmt)
+        {
+            int gt_i = -1;
+            bcf_fmt_t *fmt = line->d.fmt;
+            int first = 1;
+            for (i=0; i<(int)line->n_fmt; i++)
+            {
+                if ( !fmt[i].p || fmt[i].id<0 ) continue;
+                if ( !first ) kputc(':', str);
+                first = 0;
+                kputs(convert->header->id[BCF_DT_ID][fmt[i].id].key, str);
+                if ( strcmp(convert->header->id[BCF_DT_ID][fmt[i].id].key, "GT") == 0) gt_i = i;
+            }
+            if ( first ) kputc('.', str);
+            for (j=0; j<convert->nsamples; j++)
+            {
+                kputc('\t', str);
+                first = 1;
+                for (i=0; i<(int)line->n_fmt; i++)
+                {
+                    bcf_fmt_t *f = &fmt[i];
+                    if ( !f->p ) continue;
+                    if ( !first ) kputc(':', str);
+                    first = 0;
+                    if (gt_i == i)
+                        bcf_format_gt(f,convert->samples[j],str);
+                    else
+                        bcf_fmt_array(str, f->n, f->type, f->p + convert->samples[j] * f->size);
+                }
+                if ( first ) kputc('.', str);
+            }
+        }
+        else
+            for (j=0; j<=line->n_sample; j++)
+                kputs("\t.", str);
+    }
+    else
+        kputc('.',str);
+}
+static void process_format(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str)
+{
+    if ( !fmt->ready )
+        init_format(convert, line, fmt);
+
+    if ( fmt->fmt==NULL )
+    {
+        kputc('.', str);
+        return;
+    }
+    else if ( fmt->subscript >=0 )
+    {
+        if ( fmt->fmt->n <= fmt->subscript )
+        {
+            kputc('.', str);
+            return;
+        }
+        if ( fmt->fmt->type == BCF_BT_FLOAT )
+        {
+            float *ptr = (float*)(fmt->fmt->p + isample*fmt->fmt->size);
+            if ( bcf_float_is_missing(ptr[fmt->subscript]) || bcf_float_is_vector_end(ptr[fmt->subscript]) )
+                kputc('.', str);
+            else
+                kputd(ptr[fmt->subscript], str);
+        }
+        else if ( fmt->fmt->type != BCF_BT_CHAR )
+        {
+            int32_t ival = bcf_array_ivalue(fmt->fmt->p+isample*fmt->fmt->size,fmt->fmt->type,fmt->subscript);
+            if ( ival==bcf_int32_missing || ival==bcf_int32_vector_end )
+                kputc('.', str);
+            else
+                kputw(ival, str);
+        }
+        else if ( fmt->fmt->type == BCF_BT_CHAR )
+            _copy_field((char*)(fmt->fmt->p + isample*fmt->fmt->size), fmt->fmt->size, fmt->subscript, str);
+        else error("TODO: %s:%d .. fmt->type=%d\n", __FILE__,__LINE__, fmt->fmt->type);
+    }
+    else
+        bcf_fmt_array(str, fmt->fmt->n, fmt->fmt->type, fmt->fmt->p + isample*fmt->fmt->size);
+}
+static void process_gt(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str)
+{
+    if ( !fmt->ready )
+        init_format(convert, line, fmt);
+
+    if ( fmt->fmt==NULL )
+    {
+        kputc('.', str);
+        return;
+    }
+    bcf_format_gt(fmt->fmt, isample, str);
+}
+static void process_tgt(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str)
+{
+    if ( !fmt->ready )
+        init_format(convert, line, fmt);
+
+    if ( fmt->fmt==NULL )
+    {
+        kputc('.', str);
+        return;
+    }
+
+    assert( fmt->fmt->type==BCF_BT_INT8 );
+
+    int l;
+    int8_t *x = (int8_t*)(fmt->fmt->p + isample*fmt->fmt->size); // FIXME: does not work with n_alt >= 64
+    for (l = 0; l < fmt->fmt->n && x[l] != bcf_int8_vector_end; ++l)
+    {
+        if (l) kputc("/|"[x[l]&1], str);
+        if (x[l]>>1)
+        {
+            int ial = (x[l]>>1) - 1;
+            kputs(line->d.allele[ial], str);
+        }
+        else
+            kputc('.', str);
+    }
+    if (l == 0) kputc('.', str);
+}
+static void destroy_tbcsq(void *usr)
+{
+    if ( !usr ) return;
+    bcsq_t *csq = (bcsq_t*) usr;
+    free(csq->hap1.s);
+    free(csq->hap2.s);
+    if ( csq->n )
+        free(csq->str[0]);
+    free(csq->str);
+    free(csq);
+}
+static void process_tbcsq(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str)
+{
+    if ( !fmt->ready )
+    {
+        init_format(convert, line, fmt);
+
+        bcsq_t *csq;
+        if ( fmt->usr )
+        {
+            csq = (bcsq_t*) fmt->usr;
+            if ( csq->n )
+                free(csq->str[0]);
+            csq->n = 0;
+        }
+        else
+            csq = (bcsq_t*) calloc(1,sizeof(bcsq_t));
+        fmt->usr = csq;
+
+        int i=0, len = 0;
+        char *tmp = NULL;
+        if ( bcf_get_info_string(convert->header,line,fmt->key,&tmp,&len)<0 )
+        {
+            csq->n = 0;
+            return;
+        }
+        do
+        {
+            csq->n++;
+            hts_expand(char*, csq->n, csq->m, csq->str);
+            csq->str[ csq->n-1 ] = tmp + i;
+            while ( i<len && tmp[i]!=',' ) i++;
+            if ( i<len && tmp[i]==',' ) tmp[i++] = 0;
+        }
+        while ( i<len );
+    }
+
+    bcsq_t *csq = (bcsq_t*)fmt->usr;
+
+    if ( fmt->fmt==NULL || !csq->n ) return;
+
+    csq->hap1.l = 0;
+    csq->hap2.l = 0;
+
+    int mask = fmt->subscript==0 ? 3 : 1;   // merge both haplotypes if subscript==0
+
+    #define BRANCH(type_t, nbits) { \
+        type_t *x = (type_t*)(fmt->fmt->p + isample*fmt->fmt->size); \
+        int i,j; \
+        if ( fmt->subscript<=0 || fmt->subscript==1 ) \
+        { \
+            for (j=0; j < fmt->fmt->n; j++) \
+            { \
+                type_t val = x[j]; \
+                if ( !val ) continue; \
+                for (i=0; i<nbits; i+=2) \
+                    if ( val & (mask<<i) ) { kputs(csq->str[(j*30+i)/2], &csq->hap1); kputc_(',', &csq->hap1); } \
+            } \
+        } \
+        if ( fmt->subscript<0 || fmt->subscript==2 ) \
+        { \
+            for (j=0; j < fmt->fmt->n; j++) \
+            { \
+                type_t val = x[j]; \
+                if ( !val ) continue; \
+                for (i=1; i<nbits; i+=2) \
+                    if ( val & (1<<i) ) { kputs(csq->str[(j*30+i)/2], &csq->hap2); kputc_(',', &csq->hap2); } \
+            } \
+        } \
+    }
+    switch (fmt->fmt->type)
+    {
+        case BCF_BT_INT8:  BRANCH(uint8_t, 8); break;
+        case BCF_BT_INT16: BRANCH(uint16_t,16); break;
+        case BCF_BT_INT32: BRANCH(uint32_t,30); break;  // 2 bytes unused to account for the reserved BCF values
+        default: error("Unexpected type: %d\n", fmt->fmt->type); exit(1); break;
+    }
+    #undef BRANCH
+
+    if ( !csq->hap1.l && !csq->hap2.l ) return;
+
+    if ( csq->hap1.l ) csq->hap1.s[--csq->hap1.l] = 0;
+    if ( csq->hap2.l ) csq->hap2.s[--csq->hap2.l] = 0;
+
+    if ( fmt->subscript<0 )
+    {
+        kputs(csq->hap1.l?csq->hap1.s:".", str);
+        kputc_('\t', str);
+        kputs(csq->hap2.l?csq->hap2.s:".", str);
+    }
+    else if ( fmt->subscript<2 )
+        kputs(csq->hap1.l?csq->hap1.s:".", str);
+    else
+        kputs(csq->hap2.l?csq->hap2.s:".", str);
+}
+static void init_format_iupac(convert_t *convert, bcf1_t *line, fmt_t *fmt)
+{
+    init_format(convert, line, fmt);
+    if ( fmt->fmt==NULL ) return;
+
+    // Init mapping between alleles and IUPAC table
+    hts_expand(uint8_t, line->n_allele, convert->ndat, convert->dat);
+    int8_t *dat = (int8_t*)convert->dat;
+    int i;
+    for (i=0; i<line->n_allele; i++)
+    {
+        if ( line->d.allele[i][1] ) dat[i] = -1;
+        else
+        {
+            switch (line->d.allele[i][0])
+            {
+                case 'A': dat[i] = 0; break;
+                case 'C': dat[i] = 1; break;
+                case 'G': dat[i] = 2; break;
+                case 'T': dat[i] = 3; break;
+                case 'a': dat[i] = 0; break;
+                case 'c': dat[i] = 1; break;
+                case 'g': dat[i] = 2; break;
+                case 't': dat[i] = 3; break;
+                default: dat[i] = -1;
+            }
+        }
+    }
+}
+static void process_iupac_gt(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str)
+{
+    if ( !fmt->ready )
+        init_format_iupac(convert, line, fmt);
+
+    if ( fmt->fmt==NULL )
+    {
+        kputc('.', str);
+        return;
+    }
+
+    assert( fmt->fmt->type==BCF_BT_INT8 );
+
+    static const char iupac[4][4] = { {'A','M','R','W'},{'M','C','S','Y'},{'R','S','G','K'},{'W','Y','K','T'} };
+    int8_t *dat = (int8_t*)convert->dat;
+
+    int8_t *x = (int8_t*)(fmt->fmt->p + isample*fmt->fmt->size); // FIXME: does not work with n_alt >= 64
+    int l = 0;
+    while ( l<fmt->fmt->n && x[l]!=bcf_int8_vector_end && x[l]!=bcf_int8_missing ) l++;
+
+    if ( l==2 )
+    {
+        // diploid
+        int ia = (x[0]>>1) - 1, ib = (x[1]>>1) - 1;
+        if ( ia>=0 && ia<line->n_allele && ib>=0 && ib<line->n_allele && dat[ia]>=0 && dat[ib]>=0 )
+        {
+            kputc(iupac[dat[ia]][dat[ib]], str);
+            return;
+        }
+    }
+    for (l = 0; l < fmt->fmt->n && x[l] != bcf_int8_vector_end; ++l)
+    {
+        if (l) kputc("/|"[x[l]&1], str);
+        if (x[l]>>1)
+        {
+            int ial = (x[l]>>1) - 1;
+            kputs(line->d.allele[ial], str);
+        }
+        else
+            kputc('.', str);
+    }
+    if (l == 0) kputc('.', str);
+}
+static void process_sample(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str)
+{
+    kputs(convert->header->samples[isample], str);
+}
+static void process_sep(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str) { if (fmt->key) kputs(fmt->key, str); }
+static void process_is_ts(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str)
+{
+    int is_ts = 0;
+    if ( bcf_get_variant_types(line) & (VCF_SNP|VCF_MNP) )
+        is_ts = abs(bcf_acgt2int(*line->d.allele[0])-bcf_acgt2int(*line->d.allele[1])) == 2 ? 1 : 0;
+    kputc(is_ts ? '1' : '0', str);
+}
+static void process_type(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str)
+{
+    int line_type = bcf_get_variant_types(line);
+    int i = 0;
+    if ( line_type == VCF_REF ) { kputs("REF", str); i++; }
+    if ( line_type & VCF_SNP ) { if (i) kputc(',',str); kputs("SNP", str); i++; }
+    if ( line_type & VCF_MNP ) { if (i) kputc(',',str); kputs("MNP", str); i++; }
+    if ( line_type & VCF_INDEL ) { if (i) kputc(',',str); kputs("INDEL", str); i++; }
+    if ( line_type & VCF_OTHER ) { if (i) kputc(',',str); kputs("OTHER", str); i++; }
+    if ( line_type & VCF_BND ) { if (i) kputc(',',str); kputs("BND", str); i++; }
+    if ( line_type & VCF_OVERLAP ) { if (i) kputc(',',str); kputs("OVERLAP", str); i++; }
+}
+static void process_line(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str)
+{
+    vcf_format1(convert->header, line, str);
+}
+static void process_chrom_pos_id(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str)
+{
+    if ( line->d.id[0]!='.' || line->d.id[1] )
+    {
+        // ID is present
+        kputs(line->d.id, str);
+    }
+    else
+    {
+        // use CHROM:POS instead of ID
+        kputs(convert->header->id[BCF_DT_CTG][line->rid].key, str);
+        kputc(':', str);
+        kputw(line->pos+1, str);
+    }
+}
+static void process_gt_to_prob3(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str)
+{
+    int m,n,i;
+
+    m = convert->ndat / sizeof(int32_t);
+    n = bcf_get_genotypes(convert->header,line,&convert->dat,&m);
+    convert->ndat = m * sizeof(int32_t);
+
+    if ( n<=0 )
+    {
+        // Throw an error or silently proceed?
+        //
+        // for (i=0; i<convert->nsamples; i++) kputs(" 0.33 0.33 0.33", str);
+        // return;
+
+        error("Error parsing GT tag at %s:%"PRId64"\n", bcf_seqname(convert->header,line),(int64_t) line->pos+1);
+    }
+
+    n /= convert->nsamples;
+    for (i=0; i<convert->nsamples; i++)
+    {
+        int32_t *ptr = (int32_t*)convert->dat + i*n;
+        int j;
+        for (j=0; j<n; j++)
+            if ( ptr[j]==bcf_int32_vector_end ) break;
+
+        if ( j==2 )
+        {
+            // diploid
+            if ( bcf_gt_is_missing(ptr[0]) )
+                kputs(" 0.33 0.33 0.33", str);
+            else if ( bcf_gt_allele(ptr[0])!=bcf_gt_allele(ptr[1]) )
+                kputs(" 0 1 0", str);       // HET
+            else if ( bcf_gt_allele(ptr[0])==1 )
+                kputs(" 0 0 1", str);       // ALT HOM, first ALT allele
+            else
+                kputs(" 1 0 0", str);       // REF HOM or something else than first ALT
+        }
+        else if ( j==1 )
+        {
+            // haploid
+            if ( bcf_gt_is_missing(ptr[0]) )
+                kputs(" 0.5 0.0 0.5", str);
+            else if ( bcf_gt_allele(ptr[0])==1 )
+                kputs(" 0 0 1", str);       // first ALT allele
+            else
+                kputs(" 1 0 0", str);       // REF or something else than first ALT
+        }
+        else error("FIXME: not ready for ploidy %d\n", j);
+    }
+}
+static void process_pl_to_prob3(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str)
+{
+    int m,n,i;
+
+    m = convert->ndat / sizeof(int32_t);
+    n = bcf_get_format_int32(convert->header,line,"PL",&convert->dat,&m);
+    convert->ndat = m * sizeof(int32_t);
+
+    if ( n<=0 )
+    {
+        // Throw an error or silently proceed?
+        //
+        // for (i=0; i<convert->nsamples; i++) kputs(" 0.33 0.33 0.33", str);
+        // return;
+
+        error("Error parsing PL tag at %s:%"PRId64"\n", bcf_seqname(convert->header,line),(int64_t) line->pos+1);
+    }
+
+    n /= convert->nsamples;
+    for (i=0; i<convert->nsamples; i++)
+    {
+        int32_t *ptr = (int32_t*)convert->dat + i*n;
+        int j;
+        float sum = 0;
+        for (j=0; j<n; j++)
+        {
+            if ( ptr[j]==bcf_int32_vector_end ) break;
+            sum += pow(10,-0.1*ptr[j]);
+        }
+        if ( j==line->n_allele )
+        {
+            // haploid
+            kputc(' ',str);
+            ksprintf(str,"%f",pow(10,-0.1*ptr[0])/sum);
+            kputs(" 0 ", str);
+            ksprintf(str,"%f",pow(10,-0.1*ptr[1])/sum);
+        }
+        else
+        {
+            // diploid
+            kputc(' ',str);
+            ksprintf(str,"%f",pow(10,-0.1*ptr[0])/sum);
+            kputc(' ',str);
+            ksprintf(str,"%f",pow(10,-0.1*ptr[1])/sum);
+            kputc(' ',str);
+            ksprintf(str,"%f",pow(10,-0.1*ptr[2])/sum);
+        }
+    }
+}
+static void process_gp_to_prob3(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str)
+{
+    int m,n,i;
+
+    m = convert->ndat / sizeof(float);
+    n = bcf_get_format_float(convert->header,line,"GP",&convert->dat,&m);
+    convert->ndat = m * sizeof(float);
+
+    if ( n<=0 )
+    {
+        // Throw an error or silently proceed?
+        //
+        // for (i=0; i<convert->nsamples; i++) kputs(" 0.33 0.33 0.33", str);
+        // return;
+
+        error("Error parsing GP tag at %s:%"PRId64"\n", bcf_seqname(convert->header,line),(int64_t) line->pos+1);
+    }
+
+    n /= convert->nsamples;
+    for (i=0; i<convert->nsamples; i++)
+    {
+        float *ptr = (float*)convert->dat + i*n;
+        int j;
+        for (j=0; j<n; j++)
+        {
+            if ( bcf_float_is_vector_end(ptr[j]) ) break;
+            if ( bcf_float_is_missing(ptr[j]) ) { ptr[j]=0; continue; }
+            if ( ptr[j]<0 || ptr[j]>1 ) error("[%s:%"PRId64":%f] GP value outside range [0,1]; bcftools convert expects the VCF4.3+ spec for the GP field encoding genotype posterior probabilities", bcf_seqname(convert->header,line),(int64_t) line->pos+1,ptr[j]);
+        }
+        if ( j==line->n_allele )
+            ksprintf(str," %f %f %f",ptr[0],0.,ptr[1]); // haploid
+        else
+            ksprintf(str," %f %f %f",ptr[0],ptr[1],ptr[2]); // diploid
+    }
+}
+
+static void process_gt_to_hap(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str)
+{
+    // https://mathgen.stats.ox.ac.uk/impute/impute_v2.html#-known_haps_g
+
+    // File containing known haplotypes for the study cohort. The format
+    // is the same as the output format from IMPUTE2's -phase option:
+    // five header columns (as in the -g file) followed by two columns
+    // (haplotypes) per individual. Allowed values in the haplotype
+    // columns are 0, 1, and ?.
+
+    // If your study dataset is fully phased, you can replace the -g file
+    // with a -known_haps_g file. This will cause IMPUTE2 to perform
+    // haploid imputation, although it will still report diploid imputation
+    // probabilities in the main output file. If any genotypes are missing,
+    // they can be marked as '? ?' (two question marks separated by one
+    // space) in the input file. (The program does not allow just one
+    // allele from a diploid genotype to be missing.) If the reference
+    // panels are also phased, IMPUTE2 will perform a single, fast
+    // imputation step rather than its standard MCMC module this is how
+    // the program imputes into pre-phased GWAS haplotypes.
+
+    // The -known_haps_g file can also be used to specify study
+    // genotypes that are "partially" phased, in the sense that some
+    // genotypes are phased relative to a fixed reference point while
+    // others are not. We anticipate that this will be most useful when
+    // trying to phase resequencing data onto a scaffold of known
+    // haplotypes. To mark a known genotype as unphased, place an
+    // asterisk immediately after each allele, with no space between
+    // the allele (0/1) and the asterisk (*); e.g., "0* 1*" for a
+    // heterozygous genotype of unknown phase.
+
+    int i, gt_id = bcf_hdr_id2int(convert->header, BCF_DT_ID, "GT");
+    if ( !bcf_hdr_idinfo_exists(convert->header,BCF_HL_FMT,gt_id) )
+        error("FORMAT/GT tag not present at %s:%"PRId64"\n", bcf_seqname(convert->header, line),(int64_t) line->pos+1);
+    if ( !(line->unpacked & BCF_UN_FMT) ) bcf_unpack(line, BCF_UN_FMT);
+    bcf_fmt_t *fmt_gt = NULL;
+    for (i=0; i<line->n_fmt; i++)
+        if ( line->d.fmt[i].id==gt_id ) { fmt_gt = &line->d.fmt[i]; break; }
+    if ( !fmt_gt )
+        error("FORMAT/GT tag not present at %s:%"PRId64"\n", bcf_seqname(convert->header, line),(int64_t) line->pos+1);
+
+    // Alloc all memory in advance to avoid kput routines. The biggest allowed allele index is 99
+    if ( line->n_allele > 100 )
+        error("Too many alleles (%d) at %s:%"PRId64"\n", line->n_allele, bcf_seqname(convert->header, line),(int64_t) line->pos+1);
+    if ( ks_resize(str, str->l+convert->nsamples*8) != 0 )
+        error("Could not alloc %" PRIu64 " bytes\n", (uint64_t)(str->l + convert->nsamples*8));
+
+    if ( fmt_gt->type!=BCF_BT_INT8 )    // todo: use BRANCH_INT if the VCF is valid
+        error("Uh, too many alleles (%d) or redundant BCF representation at %s:%"PRId64"\n", line->n_allele, bcf_seqname(convert->header, line),(int64_t) line->pos+1);
+    if ( fmt_gt->n!=1 && fmt_gt->n!=2 )
+        error("Uh, ploidy of %d not supported, see %s:%"PRId64"\n", fmt_gt->n, bcf_seqname(convert->header, line),(int64_t) line->pos+1);
+
+    int8_t *ptr = ((int8_t*) fmt_gt->p) - fmt_gt->n;
+    for (i=0; i<convert->nsamples; i++)
+    {
+        ptr += fmt_gt->n;
+        if ( fmt_gt->n==1 ) // haploid genotypes
+        {
+            if ( ptr[0]==2 ) /* 0 */
+            {
+                str->s[str->l++] = '0'; str->s[str->l++] = ' '; str->s[str->l++] = '-'; str->s[str->l++] = ' ';
+            }
+            else if ( ptr[0]==bcf_int8_missing )   /* . */
+            {
+                str->s[str->l++] = '?'; str->s[str->l++] = ' '; str->s[str->l++] = '?'; str->s[str->l++] = ' ';
+            }
+            else if ( ptr[0]==4 ) /* 1 */
+            {
+                str->s[str->l++] = '1'; str->s[str->l++] = ' '; str->s[str->l++] = '-'; str->s[str->l++] = ' ';
+            }
+            else
+            {
+                kputw(bcf_gt_allele(ptr[0]),str); str->s[str->l++] = ' '; str->s[str->l++] = '-'; str->s[str->l++] = ' ';
+            }
+        }
+        else if ( ptr[0]==2 )
+        {
+            if ( ptr[1]==3 ) /* 0|0 */
+            {
+                str->s[str->l++] = '0'; str->s[str->l++] = ' '; str->s[str->l++] = '0'; str->s[str->l++] = ' ';
+            }
+            else if ( ptr[1]==5 ) /* 0|1 */
+            {
+                str->s[str->l++] = '0'; str->s[str->l++] = ' '; str->s[str->l++] = '1'; str->s[str->l++] = ' ';
+            }
+            else if ( ptr[1]==bcf_int8_vector_end ) /* 0 */
+            {
+                str->s[str->l++] = '0'; str->s[str->l++] = ' '; str->s[str->l++] = '-'; str->s[str->l++] = ' ';
+            }
+            else if ( ptr[1]==2 ) /* 0/0 */
+            {
+                str->s[str->l++] = '0'; str->s[str->l++] = '*'; str->s[str->l++] = ' '; str->s[str->l++] = '0'; str->s[str->l++] = '*'; str->s[str->l++] = ' ';
+            }
+            else if ( ptr[1]==4 ) /* 0/1 */
+            {
+                str->s[str->l++] = '0'; str->s[str->l++] = '*'; str->s[str->l++] = ' '; str->s[str->l++] = '1'; str->s[str->l++] = '*'; str->s[str->l++] = ' ';
+            }
+            else if ( bcf_gt_is_missing(ptr[1]) ) /* 0/. */
+            {
+                str->s[str->l++] = '?'; str->s[str->l++] = ' '; str->s[str->l++] = '?'; str->s[str->l++] = ' ';
+            }
+            else if ( bcf_gt_is_phased(ptr[1]) ) /* 0|x */
+            {
+                str->s[str->l++] = '0'; str->s[str->l++] = ' ';
+                kputw(bcf_gt_allele(ptr[1]),str);
+                str->s[str->l++] = ' ';
+            }
+            else /* 0/x */
+            {
+                str->s[str->l++] = '0'; str->s[str->l++] = '*'; str->s[str->l++] = ' ';
+                kputw(bcf_gt_allele(ptr[1]),str);
+                str->s[str->l++] = '*'; str->s[str->l++] = ' ';
+            }
+        }
+        else if ( ptr[0]==4 )
+        {
+            if ( ptr[1]==3 ) /* 1|0 */
+            {
+                str->s[str->l++] = '1'; str->s[str->l++] = ' '; str->s[str->l++] = '0'; str->s[str->l++] = ' ';
+            }
+            else if ( ptr[1]==5 ) /* 1|1 */
+            {
+                str->s[str->l++] = '1'; str->s[str->l++] = ' '; str->s[str->l++] = '1'; str->s[str->l++] = ' ';
+            }
+            else if ( ptr[1]==bcf_int8_vector_end ) /* 1 */
+            {
+                str->s[str->l++] = '1'; str->s[str->l++] = ' '; str->s[str->l++] = '-'; str->s[str->l++] = ' ';
+            }
+            else if ( ptr[1]==2 ) /* 1/0 */
+            {
+                str->s[str->l++] = '1'; str->s[str->l++] = '*'; str->s[str->l++] = ' '; str->s[str->l++] = '0'; str->s[str->l++] = '*'; str->s[str->l++] = ' ';
+            }
+            else if ( ptr[1]==4 ) /* 1/1 */
+            {
+                str->s[str->l++] = '1'; str->s[str->l++] = '*'; str->s[str->l++] = ' '; str->s[str->l++] = '1'; str->s[str->l++] = '*'; str->s[str->l++] = ' ';
+            }
+            else if ( bcf_gt_is_missing(ptr[1]) ) /* 1/. */
+            {
+                str->s[str->l++] = '?'; str->s[str->l++] = ' '; str->s[str->l++] = '?'; str->s[str->l++] = ' ';
+            }
+            else if ( bcf_gt_is_phased(ptr[1]) )    /* 1|x */
+            {
+                str->s[str->l++] = '1'; str->s[str->l++] = ' ';
+                kputw(bcf_gt_allele(ptr[1]),str);
+                str->s[str->l++] = ' ';
+            }
+            else /* 1/x */
+            {
+                str->s[str->l++] = '1'; str->s[str->l++] = '*'; str->s[str->l++] = ' ';
+                kputw(bcf_gt_allele(ptr[1]),str);
+                str->s[str->l++] = '*'; str->s[str->l++] = ' ';
+            }
+        }
+        else if ( bcf_gt_is_missing(ptr[0]) )
+        {
+            if ( ptr[1]==bcf_int8_vector_end )
+            {
+                str->s[str->l++] = '?'; str->s[str->l++] = ' '; str->s[str->l++] = '-'; str->s[str->l++] = ' ';
+            }
+            else
+            {
+                str->s[str->l++] = '?'; str->s[str->l++] = ' '; str->s[str->l++] = '?'; str->s[str->l++] = ' ';
+            }
+        }
+        else if ( ptr[1]==bcf_int8_vector_end )
+        {
+            /* use REF for something else than first ALT */
+            str->s[str->l++] = '0'; str->s[str->l++] = ' '; str->s[str->l++] = '-'; str->s[str->l++] = ' ';
+        }
+        else
+        {
+            kputw(bcf_gt_allele(ptr[0]),str);
+            if ( bcf_gt_is_phased(ptr[1]) ) str->s[str->l++] = '*';
+            str->s[str->l++] = ' ';
+            kputw(bcf_gt_allele(ptr[1]),str);
+            if ( bcf_gt_is_phased(ptr[1]) ) str->s[str->l++] = '*';
+            str->s[str->l++] = ' ';
+        }
+    }
+    str->s[--str->l] = 0;     // delete the last space
+}
+static void process_gt_to_hap2(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str)
+{
+    // same as process_gt_to_hap but converts haploid genotypes into diploid
+
+    int i, gt_id = bcf_hdr_id2int(convert->header, BCF_DT_ID, "GT");
+    if ( !bcf_hdr_idinfo_exists(convert->header,BCF_HL_FMT,gt_id) )
+        error("FORMAT/GT tag not present at %s:%"PRId64"\n", bcf_seqname(convert->header, line),(int64_t) line->pos+1);
+    if ( !(line->unpacked & BCF_UN_FMT) ) bcf_unpack(line, BCF_UN_FMT);
+    bcf_fmt_t *fmt_gt = NULL;
+    for (i=0; i<line->n_fmt; i++)
+        if ( line->d.fmt[i].id==gt_id ) { fmt_gt = &line->d.fmt[i]; break; }
+    if ( !fmt_gt )
+        error("FORMAT/GT tag not present at %s:%"PRId64"\n", bcf_seqname(convert->header, line),(int64_t)  line->pos+1);
+
+    // Alloc all memory in advance to avoid kput routines. The biggest allowed allele index is 99
+    if ( line->n_allele > 100 )
+        error("Too many alleles (%d) at %s:%"PRId64"\n", line->n_allele, bcf_seqname(convert->header, line),(int64_t) line->pos+1);
+    if ( ks_resize(str, str->l+convert->nsamples*8) != 0 )
+        error("Could not alloc %" PRIu64 " bytes\n", (uint64_t)(str->l + convert->nsamples*8));
+
+    if ( fmt_gt->type!=BCF_BT_INT8 )    // todo: use BRANCH_INT if the VCF is valid
+        error("Uh, too many alleles (%d) or redundant BCF representation at %s:%"PRId64"\n", line->n_allele, bcf_seqname(convert->header, line),(int64_t) line->pos+1);
+
+    int8_t *ptr = ((int8_t*) fmt_gt->p) - fmt_gt->n;
+    for (i=0; i<convert->nsamples; i++)
+    {
+        ptr += fmt_gt->n;
+        if ( ptr[0]==2 )
+        {
+            if ( ptr[1]==3 ) /* 0|0 */
+            {
+                str->s[str->l++] = '0'; str->s[str->l++] = ' '; str->s[str->l++] = '0'; str->s[str->l++] = ' ';
+            }
+            else if ( ptr[1]==5 ) /* 0|1 */
+            {
+                str->s[str->l++] = '0'; str->s[str->l++] = ' '; str->s[str->l++] = '1'; str->s[str->l++] = ' ';
+            }
+            else if ( ptr[1]==bcf_int8_vector_end ) /* 0 -> 0|0 */
+            {
+                str->s[str->l++] = '0'; str->s[str->l++] = ' '; str->s[str->l++] = '0'; str->s[str->l++] = ' ';
+            }
+            else if ( ptr[1]==2 ) /* 0/0 */
+            {
+                str->s[str->l++] = '0'; str->s[str->l++] = '*'; str->s[str->l++] = ' '; str->s[str->l++] = '0'; str->s[str->l++] = '*'; str->s[str->l++] = ' ';
+            }
+            else if ( ptr[1]==4 ) /* 0/1 */
+            {
+                str->s[str->l++] = '0'; str->s[str->l++] = '*'; str->s[str->l++] = ' '; str->s[str->l++] = '1'; str->s[str->l++] = '*'; str->s[str->l++] = ' ';
+            }
+            else if ( bcf_gt_is_missing(ptr[1]) ) /* 0/. */
+            {
+                str->s[str->l++] = '?'; str->s[str->l++] = ' '; str->s[str->l++] = '?'; str->s[str->l++] = ' ';
+            }
+            else if ( bcf_gt_is_phased(ptr[1]) ) /* 0|x */
+            {
+                str->s[str->l++] = '0'; str->s[str->l++] = ' ';
+                kputw(bcf_gt_allele(ptr[1]),str);
+                str->s[str->l++] = ' ';
+            }
+            else /* 0/x */
+            {
+                str->s[str->l++] = '0'; str->s[str->l++] = '*'; str->s[str->l++] = ' ';
+                kputw(bcf_gt_allele(ptr[1]),str);
+                str->s[str->l++] = '*'; str->s[str->l++] = ' ';
+            }
+        }
+        else if ( ptr[0]==4 )
+        {
+            if ( ptr[1]==3 ) /* 1|0 */
+            {
+                str->s[str->l++] = '1'; str->s[str->l++] = ' '; str->s[str->l++] = '0'; str->s[str->l++] = ' ';
+            }
+            else if ( ptr[1]==5 ) /* 1|1 */
+            {
+                str->s[str->l++] = '1'; str->s[str->l++] = ' '; str->s[str->l++] = '1'; str->s[str->l++] = ' ';
+            }
+            else if ( ptr[1]==bcf_int8_vector_end ) /* 1 -> 1|1 */
+            {
+                str->s[str->l++] = '1'; str->s[str->l++] = ' '; str->s[str->l++] = '1'; str->s[str->l++] = ' ';
+            }
+            else if ( ptr[1]==2 ) /* 1/0 */
+            {
+                str->s[str->l++] = '1'; str->s[str->l++] = '*'; str->s[str->l++] = ' '; str->s[str->l++] = '0'; str->s[str->l++] = '*'; str->s[str->l++] = ' ';
+            }
+            else if ( ptr[1]==4 ) /* 1/1 */
+            {
+                str->s[str->l++] = '1'; str->s[str->l++] = '*'; str->s[str->l++] = ' '; str->s[str->l++] = '1'; str->s[str->l++] = '*'; str->s[str->l++] = ' ';
+            }
+            else if ( bcf_gt_is_missing(ptr[1]) ) /* 1/. */
+            {
+                str->s[str->l++] = '?'; str->s[str->l++] = ' '; str->s[str->l++] = '?'; str->s[str->l++] = ' ';
+            }
+            else if ( bcf_gt_is_phased(ptr[1]) )    /* 1|x */
+            {
+                str->s[str->l++] = '1'; str->s[str->l++] = ' ';
+                kputw(bcf_gt_allele(ptr[1]),str);
+                str->s[str->l++] = ' ';
+            }
+            else /* 1/x */
+            {
+                str->s[str->l++] = '1'; str->s[str->l++] = '*'; str->s[str->l++] = ' ';
+                kputw(bcf_gt_allele(ptr[1]),str);
+                str->s[str->l++] = '*'; str->s[str->l++] = ' ';
+            }
+        }
+        else if ( bcf_gt_is_missing(ptr[0]) )
+        {
+            str->s[str->l++] = '?'; str->s[str->l++] = ' '; str->s[str->l++] = '?'; str->s[str->l++] = ' ';
+        }
+        else if ( ptr[1]==bcf_int8_vector_end )
+        {
+            /* use REF for something else than first ALT */
+            str->s[str->l++] = '0'; str->s[str->l++] = ' '; str->s[str->l++] = '0'; str->s[str->l++] = ' ';
+        }
+        else
+        {
+            kputw(bcf_gt_allele(ptr[0]),str);
+            if ( bcf_gt_is_phased(ptr[1]) ) str->s[str->l++] = '*';
+            str->s[str->l++] = ' ';
+            kputw(bcf_gt_allele(ptr[1]),str);
+            if ( bcf_gt_is_phased(ptr[1]) ) str->s[str->l++] = '*';
+            str->s[str->l++] = ' ';
+        }
+    }
+    str->s[--str->l] = 0;     // delete the last space
+}
+
+static void process_rsid_hex(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str)
+{
+    char *ptr = line->d.id;
+    ptr += 2; // remove 'rs'
+    ksprintf(str, "%08" PRIx32 "", (uint32_t)strtoul(ptr, NULL, 10));
+}
+
+static void process_variantkey_hex(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str)
+{
+    uint64_t vk = variantkey(
+        convert->header->id[BCF_DT_CTG][line->rid].key,
+        strlen(convert->header->id[BCF_DT_CTG][line->rid].key),
+        line->pos,
+        line->d.allele[0],
+        strlen(line->d.allele[0]),
+        line->d.allele[1],
+        strlen(line->d.allele[1]));
+    ksprintf(str, "%016" PRIx64 "", vk);
+}
+
+static void process_npass(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str)
+{
+    int i, nsmpl = 0;
+    filter_t *flt = (filter_t*) fmt->usr;
+    const uint8_t *smpl;
+    filter_test(flt,line,&smpl);
+    for (i=0; i<convert->nsamples; i++)
+        if ( smpl[i] ) nsmpl++;
+    kputd(nsmpl, str);
+}
+static void destroy_npass(void *usr)
+{
+    filter_destroy((filter_t*)usr);
+}
+
+static void process_pbinom(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str)
+{
+    int i;
+    if ( !fmt->ready )
+    {
+        fmt->fmt = NULL;    // AD
+        fmt->usr = NULL;    // GT
+
+        for (i=0; i<(int)line->n_fmt; i++)
+            if ( line->d.fmt[i].id==fmt->id ) { fmt->fmt = &line->d.fmt[i]; break; }
+
+        // Check that the first field is GT
+        int gt_id = bcf_hdr_id2int(convert->header, BCF_DT_ID, "GT");
+        if ( !bcf_hdr_idinfo_exists(convert->header, BCF_HL_FMT, fmt->id)  ) error("Error: FORMAT/GT is not defined in the header\n");
+        for (i=0; i<(int)line->n_fmt; i++)
+            if ( line->d.fmt[i].id==gt_id ) { fmt->usr = &line->d.fmt[i]; break; }  // it should always be first according to VCF spec, but...
+
+        if ( fmt->usr && line->d.fmt[i].type!=BCF_BT_INT8 )   // skip sites with many alleles
+            fmt->usr = NULL;
+
+        fmt->ready = 1;
+    }
+    bcf_fmt_t *gt_fmt = (bcf_fmt_t*) fmt->usr;
+    if ( !fmt->fmt || !gt_fmt || gt_fmt->n!=2 ) goto invalid;
+
+    int n[2] = {0,0};
+    int8_t *gt = (int8_t*)(gt_fmt->p + isample*gt_fmt->size);
+    for (i=0; i<2; i++)
+    {
+        if ( bcf_gt_is_missing(gt[i]) || gt[i] == bcf_int8_vector_end ) goto invalid;
+        int al = bcf_gt_allele(gt[i]);
+        if ( al > line->n_allele || al >= fmt->fmt->n ) goto invalid;
+
+        #define BRANCH(type_t, missing, vector_end) { \
+            type_t val = ((type_t *) fmt->fmt->p)[al + isample*fmt->fmt->n]; \
+            if ( val==missing || val==vector_end ) goto invalid; \
+            else n[i] = val; \
+        }
+        switch (fmt->fmt->type)
+        {
+            case BCF_BT_INT8:  BRANCH(int8_t,  bcf_int8_missing,  bcf_int8_vector_end); break;
+            case BCF_BT_INT16: BRANCH(int16_t, bcf_int16_missing, bcf_int16_vector_end); break;
+            case BCF_BT_INT32: BRANCH(int32_t, bcf_int32_missing, bcf_int32_vector_end); break;
+            default: goto invalid; break;
+        }
+        #undef BRANCH
+    }
+
+    if ( n[0]==n[1] ) kputc(n[0]==0 ? '.':'0', str);
+    else
+    {
+        double pval = n[0] < n[1] ? kf_betai(n[1], n[0] + 1, 0.5) : kf_betai(n[0], n[1] + 1, 0.5);
+        pval *= 2;
+        if ( pval>=1 ) pval = 0;     // this can happen, machine precision error, eg. kf_betai(1,0,0.5)
+        else
+            pval = -4.34294481903*log(pval);
+        kputd(pval, str);
+    }
+    return;
+
+invalid:
+    kputc('.', str);
+}
+
+static void _used_tags_add(convert_t *convert, int type, char *key)
+{
+    kstring_t str = {0,0,0};
+    ksprintf(&str,"%s/%s",type==T_INFO?"INFO":"FORMAT",key);
+    khash_str2int_inc(convert->used_tags_hash,str.s);
+    convert->nused_tags++;
+    convert->used_tags_list = (char**)realloc(convert->used_tags_list,sizeof(*convert->used_tags_list)*convert->nused_tags);
+    convert->used_tags_list[convert->nused_tags-1] = str.s;
+}
+
+
+#define _SET_NON_FORMAT_TAGS(function,key,...) \
+    if ( !strcmp("CHROM",key) ) { function(__VA_ARGS__, T_CHROM); } \
+    else if ( !strcmp("POS",key) ) { function(__VA_ARGS__, T_POS); } \
+    else if ( !strcmp("POS0",key) ) { function(__VA_ARGS__, T_POS0); } \
+    else if ( !strcmp("END",key) ) { function(__VA_ARGS__, T_END); } \
+    else if ( !strcmp("END0",key) ) { function(__VA_ARGS__, T_END0); } \
+    else if ( !strcmp("ID",key) ) { function(__VA_ARGS__, T_ID); } \
+    else if ( !strcmp("REF",key) ) { function(__VA_ARGS__, T_REF); } \
+    else if ( !strcmp("FIRST_ALT",key) ) { function(__VA_ARGS__, T_FIRST_ALT); } \
+    else if ( !strcmp("QUAL",key) ) { function(__VA_ARGS__, T_QUAL); } \
+    else if ( !strcmp("TYPE",key) ) { function(__VA_ARGS__, T_TYPE); } \
+    else if ( !strcmp("FILTER",key) ) { function(__VA_ARGS__, T_FILTER); } \
+    else if ( !strcmp("IS_TS",key) ) { function(__VA_ARGS__, T_IS_TS); } \
+    else if ( !strcmp("MASK",key) ) { function(__VA_ARGS__, T_MASK); } \
+    else if ( !strcmp("LINE",key) ) { function(__VA_ARGS__, T_LINE); }
+
+static void set_type(fmt_t *fmt, int type) { fmt->type = type; }
+static fmt_t *register_tag(convert_t *convert, char *key, int is_gtf, int type)
+{
+    convert->nfmt++;
+    if ( convert->nfmt > convert->mfmt )
+    {
+        convert->mfmt += 10;
+        convert->fmt   = (fmt_t*) realloc(convert->fmt, convert->mfmt*sizeof(fmt_t));
+    }
+    fmt_t *fmt = &convert->fmt[ convert->nfmt-1 ];
+    fmt->type  = type;
+    fmt->key   = key ? strdup(key) : NULL;
+    fmt->is_gt_field = is_gtf;
+    fmt->subscript = -1;
+    fmt->usr     = NULL;
+    fmt->destroy = NULL;
+
+    // Allow non-format tags, such as CHROM, INFO, etc., to appear amongst the format tags.
+    if ( key )
+    {
+        int id = bcf_hdr_id2int(convert->header, BCF_DT_ID, key);
+        if ( fmt->type==T_FORMAT && !bcf_hdr_idinfo_exists(convert->header,BCF_HL_FMT,id) )
+        {
+            _SET_NON_FORMAT_TAGS(set_type,key,fmt)
+           else if ( !strcmp("ALT",key) ) { fmt->type = T_ALT; }
+           else if ( !strcmp("_CHROM_POS_ID",key) ) { fmt->type = T_CHROM_POS_ID; }
+            else if ( !strcmp("RSX",key) ) { fmt->type = T_RSX; }
+            else if ( !strcmp("VKX",key) ) { fmt->type = T_VKX; }
+            else if ( id>=0 && bcf_hdr_idinfo_exists(convert->header,BCF_HL_INFO,id) )
+            {
+                fmt->type = T_INFO;
+                _used_tags_add(convert,T_INFO,key);
+            }
+        }
+        else if ( fmt->type==T_PBINOM )
+        {
+            fmt->id = bcf_hdr_id2int(convert->header, BCF_DT_ID, fmt->key);
+            if ( !bcf_hdr_idinfo_exists(convert->header,BCF_HL_FMT, fmt->id)  ) error("No such FORMAT tag defined in the header: %s\n", fmt->key);
+            _used_tags_add(convert,T_FORMAT,key);
+        }
+        else if ( fmt->type==T_NPASS )
+        {
+            filter_t *flt = filter_init(convert->header,key);
+            convert->max_unpack |= filter_max_unpack(flt);
+            fmt->usr = (void*) flt;
+        }
+    }
+
+    switch (fmt->type)
+    {
+        case T_FIRST_ALT: fmt->handler = &process_first_alt; break;
+        case T_CHROM_POS_ID: fmt->handler = &process_chrom_pos_id; break;
+        case T_GT_TO_PROB3: fmt->handler = &process_gt_to_prob3; break;
+        case T_PL_TO_PROB3: fmt->handler = &process_pl_to_prob3; break;
+        case T_GP_TO_PROB3: fmt->handler = &process_gp_to_prob3; break;
+        case T_CHROM: fmt->handler = &process_chrom; break;
+        case T_POS: fmt->handler = &process_pos; break;
+        case T_POS0: fmt->handler = &process_pos0; break;
+        case T_END: fmt->handler = &process_end; convert->max_unpack |= BCF_UN_INFO; break;
+        case T_END0: fmt->handler = &process_end0; convert->max_unpack |= BCF_UN_INFO; break;
+        case T_ID: fmt->handler = &process_id; break;
+        case T_REF: fmt->handler = &process_ref; break;
+        case T_ALT: fmt->handler = &process_alt; break;
+        case T_QUAL: fmt->handler = &process_qual; break;
+        case T_FILTER: fmt->handler = &process_filter; convert->max_unpack |= BCF_UN_FLT; break;
+        case T_INFO: fmt->handler = &process_info; convert->max_unpack |= BCF_UN_INFO; break;
+        case T_FORMAT: fmt->handler = fmt->key ? &process_format : &process_complete_format; convert->max_unpack |= BCF_UN_FMT; break;
+        case T_SAMPLE: fmt->handler = &process_sample; break;
+        case T_SEP: fmt->handler = &process_sep; break;
+        case T_IS_TS: fmt->handler = &process_is_ts; break;
+        case T_TYPE: fmt->handler = &process_type; break;
+        case T_MASK: fmt->handler = NULL; break;
+        case T_GT: fmt->handler = &process_gt; convert->max_unpack |= BCF_UN_FMT; break;
+        case T_TGT: fmt->handler = &process_tgt; convert->max_unpack |= BCF_UN_FMT; break;
+        case T_IUPAC_GT: fmt->handler = &process_iupac_gt; convert->max_unpack |= BCF_UN_FMT; break;
+        case T_GT_TO_HAP: fmt->handler = &process_gt_to_hap; convert->max_unpack |= BCF_UN_FMT; break;
+        case T_GT_TO_HAP2: fmt->handler = &process_gt_to_hap2; convert->max_unpack |= BCF_UN_FMT; break;
+        case T_TBCSQ: fmt->handler = &process_tbcsq; fmt->destroy = &destroy_tbcsq; convert->max_unpack |= BCF_UN_FMT; break;
+        case T_LINE: fmt->handler = &process_line; convert->max_unpack |= BCF_UN_FMT; break;
+        case T_RSX: fmt->handler = &process_rsid_hex; break;
+        case T_VKX: fmt->handler = &process_variantkey_hex; break;
+        case T_PBINOM: fmt->handler = &process_pbinom; convert->max_unpack |= BCF_UN_FMT; break;
+        case T_NPASS: fmt->handler = &process_npass; fmt->destroy = &destroy_npass; break;
+        default: error("TODO: handler for type %d\n", fmt->type);
+    }
+    if ( key && fmt->type==T_INFO )
+    {
+        fmt->id = bcf_hdr_id2int(convert->header, BCF_DT_ID, key);
+        if ( !bcf_hdr_idinfo_exists(convert->header,BCF_HL_INFO,fmt->id) )
+        {
+            fmt->id = -1;
+            convert->undef_info_tag = strdup(key);
+        }
+    }
+    return fmt;
+}
+
+static int parse_subscript(char **p)
+{
+    char *q = *p;
+    if ( *q!='{' ) return -1;
+    q++;
+    while ( *q && *q!='}' && isdigit(*q) ) q++;
+    if ( *q!='}' ) return -1;
+    int idx = atoi((*p)+1);
+    *p = q+1;
+    return idx;
+}
+
+static char *parse_tag(convert_t *convert, char *p, int is_gtf)
+{
+    char *q = ++p;
+    while ( *q && (isalnum(*q) || *q=='_' || *q=='.') ) q++;
+    kstring_t str = {0,0,0};
+    if ( q-p==0 ) error("Could not parse format string: %s\n", convert->format_str);
+    kputsn(p, q-p, &str);
+    if ( is_gtf )
+    {
+        if ( !strcmp(str.s, "SAMPLE") ) register_tag(convert, "SAMPLE", is_gtf, T_SAMPLE);
+        else if ( !strcmp(str.s, "GT") ) register_tag(convert, "GT", is_gtf, T_GT);
+        else if ( !strcmp(str.s, "TGT") ) register_tag(convert, "GT", is_gtf, T_TGT);
+        else if ( !strcmp(str.s, "TBCSQ") )
+        {
+            fmt_t *fmt = register_tag(convert, "BCSQ", is_gtf, T_TBCSQ);
+            fmt->subscript = parse_subscript(&q);
+            if ( fmt->subscript==-1 )
+            {
+                if ( !strncmp(q,"{*}",3) ) { fmt->subscript = 0; q += 3; }
+            }
+            else fmt->subscript++;
+        }
+        else if ( !strcmp(str.s, "IUPACGT") ) register_tag(convert, "GT", is_gtf, T_IUPAC_GT);
+        else if ( !strcmp(str.s, "INFO") )
+        {
+            if ( *q!='/' )
+            {
+                int id = bcf_hdr_id2int(convert->header, BCF_DT_ID, str.s);
+                if ( bcf_hdr_idinfo_exists(convert->header,BCF_HL_INFO,id) )
+                    error("Could not parse format string \"%s\". Did you mean %%INFO/%s?\n", convert->format_str,str.s);
+                else
+                    error("Could not parse format string: %s\n", convert->format_str);
+            }
+            p = ++q;
+            str.l = 0;
+            while ( *q && (isalnum(*q) || *q=='_' || *q=='.') ) q++;
+            if ( q-p==0 ) error("Could not parse format string: %s\n", convert->format_str);
+            kputsn(p, q-p, &str);
+            fmt_t *fmt = register_tag(convert, str.s, is_gtf, T_INFO);
+            fmt->subscript = parse_subscript(&q);
+            _used_tags_add(convert,T_INFO,str.s);
+        }
+        else if ( !strcmp(str.s,"PBINOM") )
+        {
+            if ( *q!='(' ) error("Could not parse the expression: %s\n", convert->format_str);
+            p = ++q;
+            str.l = 0;
+            while ( *q && *q!=')' ) q++;
+            if ( q-p==0 ) error("Could not parse format string: %s\n", convert->format_str);
+            kputsn(p, q-p, &str);
+            register_tag(convert, str.s, is_gtf, T_PBINOM);
+            q++;
+        }
+        else if ( !strcmp(str.s,"N_PASS") )
+            error("N_PASS() must be placed outside the square brackets\n");
+        else
+        {
+            fmt_t *fmt = register_tag(convert, str.s, is_gtf, T_FORMAT);
+            fmt->subscript = parse_subscript(&q);
+        }
+    }
+    else
+    {
+        _SET_NON_FORMAT_TAGS(register_tag, str.s, convert, str.s, is_gtf)
+        else if ( !strcmp(str.s, "ALT") )
+        {
+            fmt_t *fmt = register_tag(convert, str.s, is_gtf, T_ALT);
+            fmt->subscript = parse_subscript(&q);
+        }
+        else if ( !strcmp(str.s, "_CHROM_POS_ID") ) register_tag(convert, str.s, is_gtf, T_CHROM_POS_ID);
+        else if ( !strcmp(str.s, "_GT_TO_PROB3") ) register_tag(convert, str.s, is_gtf, T_GT_TO_PROB3);
+        else if ( !strcmp(str.s, "_PL_TO_PROB3") ) register_tag(convert, str.s, is_gtf, T_PL_TO_PROB3);
+        else if ( !strcmp(str.s, "_GP_TO_PROB3") ) register_tag(convert, str.s, is_gtf, T_GP_TO_PROB3);
+        else if ( !strcmp(str.s, "_GT_TO_HAP") ) register_tag(convert, str.s, is_gtf, T_GT_TO_HAP);
+        else if ( !strcmp(str.s, "_GT_TO_HAP2") ) register_tag(convert, str.s, is_gtf, T_GT_TO_HAP2);
+        else if ( !strcmp(str.s, "RSX") ) register_tag(convert, str.s, is_gtf, T_RSX);
+        else if ( !strcmp(str.s, "VKX") ) register_tag(convert, str.s, is_gtf, T_VKX);
+        else if ( !strcmp(str.s,"PBINOM") ) error("Error: PBINOM() is currently supported only with FORMAT tags. (todo)\n");
+        else if ( !strcmp(str.s, "INFO") )
+        {
+            if ( *q=='/' )
+            {
+                p = ++q;
+                str.l = 0;
+                while ( *q && (isalnum(*q) || *q=='_' || *q=='.') ) q++;
+                if ( q-p==0 ) error("Could not parse format string: %s\n", convert->format_str);
+                kputsn(p, q-p, &str);
+                fmt_t *fmt = register_tag(convert, str.s, is_gtf, T_INFO);
+                fmt->subscript = parse_subscript(&q);
+                _used_tags_add(convert,T_INFO,str.s);
+            }
+            else
+                register_tag(convert, NULL, is_gtf, T_INFO);    // the whole INFO
+        }
+        else if ( !strcmp(str.s, "FORMAT") )
+             register_tag(convert, NULL, 0, T_FORMAT);
+        else if ( !strcmp(str.s,"N_PASS") )
+        {
+            if ( *q!='(' ) error("Could not parse the expression: %s\n", convert->format_str);
+            p = ++q;
+            str.l = 0;
+            int nopen = 1;
+            while ( *q && nopen )
+            {
+                if ( *q=='(' ) nopen++;
+                else if ( *q==')' ) nopen--;
+                q++;
+            }
+            if ( q-p==0 || nopen ) error("Could not parse format string: %s\n", convert->format_str);
+            kputsn(p, q-p-1, &str);
+            register_tag(convert, str.s, is_gtf, T_NPASS);
+        }
+        else
+        {
+            fmt_t *fmt = register_tag(convert, str.s, is_gtf, T_INFO);
+            fmt->subscript = parse_subscript(&q);
+            _used_tags_add(convert,T_INFO,str.s);
+        }
+    }
+    free(str.s);
+    return q;
+}
+
+static char *parse_sep(convert_t *convert, char *p, int is_gtf)
+{
+    char *q = p;
+    kstring_t str = {0,0,0};
+    while ( *q && *q!='[' && *q!=']' && *q!='%' )
+    {
+        if ( *q=='\\' )
+        {
+            q++;
+            if ( *q=='n' ) kputc('\n', &str);
+            else if ( *q=='t' ) kputc('\t', &str);
+            else kputc(*q, &str);
+        }
+        else kputc(*q, &str);
+        q++;
+    }
+    if ( !str.l ) error("Could not parse format string: %s\n", convert->format_str);
+    register_tag(convert, str.s, is_gtf, T_SEP);
+    free(str.s);
+    return q;
+}
+
+convert_t *convert_init(bcf_hdr_t *hdr, int *samples, int nsamples, const char *format_str)
+{
+    convert_t *convert = (convert_t*) calloc(1,sizeof(convert_t));
+    convert->header = hdr;
+    convert->format_str = strdup(format_str);
+    convert->max_unpack = BCF_UN_STR;
+    convert->used_tags_hash = khash_str2int_init();
+
+    int i, is_gtf = 0;
+    char *p = convert->format_str;
+    while ( *p )
+    {
+        //fprintf(stderr,"<%s>\n", p);
+        switch (*p)
+        {
+            case '[': is_gtf = 1; p++; break;
+            case ']': is_gtf = 0; register_tag(convert, NULL, 0, T_SEP); p++; break;
+            case '%': p = parse_tag(convert, p, is_gtf); break;
+            default:  p = parse_sep(convert, p, is_gtf); break;
+        }
+    }
+    if ( is_gtf )
+        error("Could not parse the format string, missing the square bracket \"]\": %s\n", convert->format_str);
+
+    if ( nsamples )
+    {
+        convert->nsamples = nsamples;
+        convert->samples = (int*) malloc(sizeof(int)*nsamples);
+        for (i=0; i<convert->nsamples; i++) convert->samples[i] = samples[i];
+    }
+    else
+    {
+        convert->nsamples = bcf_hdr_nsamples(convert->header);
+        convert->samples = (int*) malloc(sizeof(int)*convert->nsamples);
+        for (i=0; i<convert->nsamples; i++) convert->samples[i] = i;
+    }
+    return convert;
+}
+
+void convert_destroy(convert_t *convert)
+{
+    int i;
+    for (i=0; i<convert->nfmt; i++)
+    {
+        if ( convert->fmt[i].destroy ) convert->fmt[i].destroy(convert->fmt[i].usr);
+        free(convert->fmt[i].key);
+    }
+    if ( convert->nused_tags )
+    {
+        for (i=0; i<convert->nused_tags; i++) free(convert->used_tags_list[i]);
+        free(convert->used_tags_list);
+    }
+    khash_str2int_destroy(convert->used_tags_hash);
+    free(convert->fmt);
+    free(convert->undef_info_tag);
+    free(convert->dat);
+    free(convert->samples);
+    free(convert->format_str);
+    free(convert);
+}
+
+
+int convert_header(convert_t *convert, kstring_t *str)
+{
+    int i, icol = 0, l_ori = str->l;
+    bcf_hdr_t *hdr = convert->header;
+
+    // Supress the header output if LINE is present
+    for (i=0; i<convert->nfmt; i++)
+        if ( convert->fmt[i].type == T_LINE ) break;
+    if ( i!=convert->nfmt )
+        return str->l - l_ori;
+
+    kputs("# ", str);
+    for (i=0; i<convert->nfmt; i++)
+    {
+        // Genotype fields
+        if ( convert->fmt[i].is_gt_field )
+        {
+            int j = i, js, k;
+            while ( convert->fmt[j].is_gt_field ) j++;
+            for (js=0; js<convert->nsamples; js++)
+            {
+                int ks = convert->samples[js];
+                for (k=i; k<j; k++)
+                {
+                    if ( convert->fmt[k].type == T_SEP )
+                    {
+                        if ( convert->fmt[k].key ) kputs(convert->fmt[k].key, str);
+                    }
+                    else if ( convert->fmt[k].type == T_SAMPLE )
+                        ksprintf(str, "[%d]%s", ++icol, convert->fmt[k].key);
+                    else
+                        ksprintf(str, "[%d]%s:%s", ++icol, hdr->samples[ks], convert->fmt[k].key);
+                }
+            }
+            i = j-1;
+            continue;
+        }
+        // Fixed fields
+        if ( convert->fmt[i].type == T_SEP )
+        {
+            if ( convert->fmt[i].key ) kputs(convert->fmt[i].key, str);
+            continue;
+        }
+        ksprintf(str, "[%d]%s", ++icol, convert->fmt[i].key);
+    }
+    return str->l - l_ori;
+}
+
+int convert_line(convert_t *convert, bcf1_t *line, kstring_t *str)
+{
+    if ( !convert->allow_undef_tags && convert->undef_info_tag )
+    {
+        kstring_t msg = {0,0,0};
+        ksprintf(&msg,"Error: no such tag defined in the VCF header: INFO/%s", convert->undef_info_tag);
+
+        int hdr_id = bcf_hdr_id2int(convert->header,BCF_DT_ID,convert->undef_info_tag);
+        if ( hdr_id>=0 && bcf_hdr_idinfo_exists(convert->header,BCF_HL_FMT,hdr_id) )
+            ksprintf(&msg,". FORMAT fields must be enclosed in square brackets, e.g. \"[ %%%s]\"", convert->undef_info_tag);
+        error("%s\n", msg.s);
+    }
+
+    int l_ori = str->l;
+    bcf_unpack(line, convert->max_unpack);
+
+    int i, ir;
+    str->l = 0;
+    for (i=0; i<convert->nfmt; i++)
+    {
+        // Genotype fields.
+        if ( convert->fmt[i].is_gt_field )
+        {
+            int j = i, js, k;
+            while ( j<convert->nfmt && convert->fmt[j].is_gt_field )
+            {
+                convert->fmt[j].ready = 0;
+                j++;
+            }
+            for (js=0; js<convert->nsamples; js++)
+            {
+                // Skip samples when filtering was requested
+                int ks = convert->samples[js];
+                if ( convert->subset_samples && *convert->subset_samples && !(*convert->subset_samples)[ks] ) continue;
+
+                // Here comes a hack designed for TBCSQ. When running on large files,
+                // such as 1000GP, there are too many empty fields in the output and
+                // it's very very slow. Therefore in case the handler does not add
+                // anything to the string, we trim all genotype fields enclosed in square
+                // brackets here. This may be changed in future, time will show...
+                size_t l_start = str->l;
+
+                for (k=i; k<j; k++)
+                {
+                    if ( convert->fmt[k].type == T_MASK )
+                    {
+                        for (ir=0; ir<convert->nreaders; ir++)
+                            kputc(bcf_sr_has_line(convert->readers,ir)?'1':'0', str);
+                    }
+                    else if ( convert->fmt[k].handler )
+                    {
+                        size_t l = str->l;
+                        convert->fmt[k].handler(convert, line, &convert->fmt[k], ks, str);
+                        if ( l==str->l ) { str->l = l_start; break; }  // only TBCSQ does this
+                    }
+                }
+            }
+            i = j-1;
+            continue;
+        }
+        // Fixed fields
+        if ( convert->fmt[i].type == T_MASK )
+        {
+            for (ir=0; ir<convert->nreaders; ir++)
+                kputc(bcf_sr_has_line(convert->readers,ir)?'1':'0', str);
+        }
+        else if ( convert->fmt[i].handler )
+            convert->fmt[i].handler(convert, line, &convert->fmt[i], -1, str);
+
+    }
+    return str->l - l_ori;
+}
+
+int convert_set_option(convert_t *convert, enum convert_option opt, ...)
+{
+    int ret = 0;
+    va_list args;
+
+    va_start(args, opt);
+    switch (opt)
+    {
+        case allow_undef_tags:
+            convert->allow_undef_tags = va_arg(args, int);
+            break;
+        case subset_samples:
+            convert->subset_samples = va_arg(args, uint8_t**);
+            break;
+        default:
+            ret = -1;
+    }
+    va_end(args);
+    return ret;
+}
+
+int convert_max_unpack(convert_t *convert)
+{
+    return convert->max_unpack;
+}
+
+int convert_is_tag_used(convert_t *convert, char *tag)
+{
+    return khash_str2int_has_key(convert->used_tags_hash, tag);
+}
+const char **convert_list_used_tags(convert_t *convert, int *ntags)
+{
+    *ntags = convert->nused_tags;
+    return (const char **)convert->used_tags_list;
+}
+
diff --git a/bcftools/convert.c.pysam.c b/bcftools/convert.c.pysam.c
new file mode 100644
index 0000000..6b9e851
--- /dev/null
+++ b/bcftools/convert.c.pysam.c
@@ -0,0 +1,1711 @@
+#include "bcftools.pysam.h"
+
+/*  convert.c -- functions for converting between VCF/BCF and related formats.
+
+    Copyright (C) 2013-2022 Genome Research Ltd.
+
+    Author: Petr Danecek <pd3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.  */
+
+#include <stdio.h>
+#include <unistd.h>
+#include <getopt.h>
+#include <assert.h>
+#include <ctype.h>
+#include <string.h>
+#include <errno.h>
+#include <sys/stat.h>
+#include <sys/types.h>
+#define __STDC_FORMAT_MACROS
+#include <inttypes.h>
+#include <math.h>
+#include <htslib/vcf.h>
+#include <htslib/synced_bcf_reader.h>
+#include <htslib/vcfutils.h>
+#include <htslib/kfunc.h>
+#include <htslib/khash_str2int.h>
+#include "bcftools.h"
+#include "variantkey.h"
+#include "convert.h"
+#include "filter.h"
+
+#define T_CHROM   1
+#define T_POS     2
+#define T_ID      3
+#define T_REF     4
+#define T_ALT     5
+#define T_QUAL    6
+#define T_FILTER  7
+#define T_INFO    8
+#define T_FORMAT  9
+#define T_SAMPLE  10
+#define T_SEP     11
+#define T_IS_TS   12
+#define T_TYPE    13
+#define T_MASK    14
+#define T_GT      15
+#define T_TGT     16
+#define T_LINE    17
+#define T_CHROM_POS_ID 18   // not publicly advertised
+#define T_GT_TO_PROB3  19   // not publicly advertised
+#define T_PL_TO_PROB3  20   // not publicly advertised
+#define T_GP_TO_PROB3  21   // not publicly advertised
+#define T_FIRST_ALT    22   // not publicly advertised
+#define T_IUPAC_GT     23
+#define T_GT_TO_HAP    24   // not publicly advertised
+#define T_GT_TO_HAP2   25   // not publicly advertised
+#define T_TBCSQ        26
+#define T_END          27
+#define T_POS0         28
+#define T_END0         29
+#define T_RSX          30   // RSID HEX
+#define T_VKX          31   // VARIANTKEY HEX
+#define T_PBINOM       32
+#define T_NPASS        33
+
+typedef struct _fmt_t
+{
+    int type, id, is_gt_field, ready, subscript;
+    char *key;
+    bcf_fmt_t *fmt;
+    void *usr;                  // user data (optional)
+    void (*handler)(convert_t *, bcf1_t *, struct _fmt_t *, int, kstring_t *);
+    void (*destroy)(void*);     // clean user data (optional)
+}
+fmt_t;
+
+struct _convert_t
+{
+    fmt_t *fmt;
+    int nfmt, mfmt;
+    int nsamples, *samples;
+    bcf_hdr_t *header;
+    int max_unpack;
+    char *format_str;
+    bcf_srs_t *readers; // required only for %MASK
+    int nreaders;
+    void *dat;
+    int ndat;
+    char *undef_info_tag;
+    void *used_tags_hash;
+    char **used_tags_list;
+    int nused_tags;
+    int allow_undef_tags;
+    uint8_t **subset_samples;
+};
+
+typedef struct
+{
+    kstring_t hap1,hap2;
+    char **str;
+    int n, m;
+}
+bcsq_t;
+
+static void process_chrom(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str) { kputs(convert->header->id[BCF_DT_CTG][line->rid].key, str); }
+static void process_pos(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str) { kputw(line->pos+1, str); }
+static void process_pos0(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str) { kputw(line->pos, str); }
+static void process_end(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str) { kputw(line->pos+line->rlen, str); }
+static void process_end0(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str) { kputw(line->pos+line->rlen-1, str); }
+static void process_id(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str) { kputs(line->d.id, str); }
+static void process_ref(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str) { kputs(line->d.allele[0], str); }
+static void process_alt(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str)
+{
+    int i;
+    if ( line->n_allele==1 )
+    {
+        kputc('.', str);
+        return;
+    }
+    if ( fmt->subscript>=0 )
+    {
+        if ( line->n_allele > fmt->subscript+1 )
+            kputs(line->d.allele[fmt->subscript+1], str);
+        else
+            kputc('.', str);
+        return;
+    }
+    for (i=1; i<line->n_allele; i++)
+    {
+        if ( i>1 ) kputc(',', str);
+        kputs(line->d.allele[i], str);
+    }
+}
+static void process_first_alt(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str)
+{
+    if ( line->n_allele==1 )
+        kputc('.', str);
+    else
+        kputs(line->d.allele[1], str);
+}
+static void process_qual(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str)
+{
+    if ( bcf_float_is_missing(line->qual) ) kputc('.', str);
+    else kputd(line->qual, str);
+}
+static void process_filter(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str)
+{
+    int i;
+    if ( line->d.n_flt )
+    {
+        for (i=0; i<line->d.n_flt; i++)
+        {
+            if (i) kputc(';', str);
+            kputs(convert->header->id[BCF_DT_ID][line->d.flt[i]].key, str);
+        }
+    }
+    else kputc('.', str);
+}
+static inline int32_t bcf_array_ivalue(void *bcf_array, int type, int idx)
+{
+    if ( type==BCF_BT_INT8 )
+    {
+        int8_t val = ((int8_t*)bcf_array)[idx];
+        if ( val==bcf_int8_missing ) return bcf_int32_missing;
+        if ( val==bcf_int8_vector_end ) return bcf_int32_vector_end;
+        return val;
+    }
+    if ( type==BCF_BT_INT16 )
+    {
+        int16_t val = ((int16_t*)bcf_array)[idx];
+        if ( val==bcf_int16_missing ) return bcf_int32_missing;
+        if ( val==bcf_int16_vector_end ) return bcf_int32_vector_end;
+        return val;
+    }
+    return ((int32_t*)bcf_array)[idx];
+}
+static inline void _copy_field(char *src, uint32_t len, int idx, kstring_t *str)
+{
+    int n = 0, ibeg = 0;
+    while ( src[ibeg] && ibeg<len && n < idx )
+    {
+        if ( src[ibeg]==',' ) n++;
+        ibeg++;
+    }
+    if ( ibeg==len ) { kputc('.', str); return; }
+
+    int iend = ibeg;
+    while ( src[iend] && src[iend]!=',' && iend<len ) iend++;
+
+    if ( iend>ibeg )
+        kputsn(src+ibeg, iend-ibeg, str);
+    else
+        kputc('.', str);
+}
+static void process_info(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str)
+{
+    int i;
+    if ( !fmt->key )    // the whole INFO column
+    {
+        int first = 1;
+        for (i=0; i<line->n_info; i++)
+        {
+            bcf_info_t *inf = &line->d.info[i];
+            if ( !inf->vptr ) continue;
+            if ( !first ) kputc(';', str);
+            first = 0;
+            if ( inf->key >= convert->header->n[BCF_DT_ID] ) continue;
+            kputs(convert->header->id[BCF_DT_ID][inf->key].key, str);
+            if ( inf->len <= 0 ) continue;
+            kputc('=', str);
+            if ( inf->len == 1 )
+            {
+                switch (inf->type)
+                {
+                    case BCF_BT_INT8:  if ( inf->v1.i==bcf_int8_missing ) kputc('.', str); else kputw(inf->v1.i, str); break;
+                    case BCF_BT_INT16: if ( inf->v1.i==bcf_int16_missing ) kputc('.', str); else kputw(inf->v1.i, str); break;
+                    case BCF_BT_INT32: if ( inf->v1.i==bcf_int32_missing ) kputc('.', str); else kputw(inf->v1.i, str); break;
+                    case BCF_BT_FLOAT: if ( bcf_float_is_missing(inf->v1.f) ) kputc('.', str); else kputd(inf->v1.f, str); break;
+                    case BCF_BT_CHAR:  kputc(inf->v1.i, str); break;
+                    default: error("Unexpected type %d", inf->type); break;
+                }
+            }
+            else bcf_fmt_array(str, inf->len, inf->type, inf->vptr);
+        }
+        if ( first ) kputc('.', str);
+        return;
+    }
+
+    if ( fmt->id<0 )
+    {
+        kputc('.', str);
+        return;
+    }
+
+    for (i=0; i<line->n_info; i++)
+        if ( line->d.info[i].key == fmt->id ) break;
+
+    // output "." if the tag is not present
+    if ( i==line->n_info )
+    {
+        kputc('.', str);
+        return;
+    }
+
+    bcf_info_t *info = &line->d.info[i];
+
+    // if this is a flag, output 1
+    if ( info->len <=0 )
+    {
+        kputc('1', str);
+        return;
+    }
+
+    if ( info->len == 1 )
+    {
+        switch (info->type)
+        {
+            case BCF_BT_INT8:  if ( info->v1.i==bcf_int8_missing ) kputc('.', str); else kputw(info->v1.i, str); break;
+            case BCF_BT_INT16: if ( info->v1.i==bcf_int16_missing ) kputc('.', str); else kputw(info->v1.i, str); break;
+            case BCF_BT_INT32: if ( info->v1.i==bcf_int32_missing ) kputc('.', str); else kputw(info->v1.i, str); break;
+            case BCF_BT_FLOAT: if ( bcf_float_is_missing(info->v1.f) ) kputc('.', str); else kputd(info->v1.f, str); break;
+            case BCF_BT_CHAR:  kputc(info->v1.i, str); break;
+            default: fprintf(bcftools_stderr,"todo: type %d\n", info->type); bcftools_exit(1); break;
+        }
+    }
+    else if ( fmt->subscript >=0 )
+    {
+        if ( info->len <= fmt->subscript )
+        {
+            kputc('.', str);
+            return;
+        }
+        #define BRANCH(type_t, is_missing, is_vector_end, kprint) { \
+            type_t val = ((type_t *) info->vptr)[fmt->subscript]; \
+            if ( is_missing || is_vector_end ) kputc('.',str); \
+            else kprint; \
+        }
+        switch (info->type)
+        {
+            case BCF_BT_INT8:  BRANCH(int8_t,  val==bcf_int8_missing,  val==bcf_int8_vector_end,  kputw(val, str)); break;
+            case BCF_BT_INT16: BRANCH(int16_t, val==bcf_int16_missing, val==bcf_int16_vector_end, kputw(val, str)); break;
+            case BCF_BT_INT32: BRANCH(int32_t, val==bcf_int32_missing, val==bcf_int32_vector_end, kputw(val, str)); break;
+            case BCF_BT_FLOAT: BRANCH(float,   bcf_float_is_missing(val), bcf_float_is_vector_end(val), kputd(val, str)); break;
+            case BCF_BT_CHAR:  _copy_field((char*)info->vptr, info->vptr_len, fmt->subscript, str); break;
+            default: fprintf(bcftools_stderr,"todo: type %d\n", info->type); bcftools_exit(1); break;
+        }
+        #undef BRANCH
+    }
+    else
+        bcf_fmt_array(str, info->len, info->type, info->vptr);
+}
+static void init_format(convert_t *convert, bcf1_t *line, fmt_t *fmt)
+{
+    fmt->id = bcf_hdr_id2int(convert->header, BCF_DT_ID, fmt->key);
+    if ( !bcf_hdr_idinfo_exists(convert->header,BCF_HL_FMT,fmt->id) ) fmt->id = -1;
+    fmt->fmt = NULL;
+    if ( fmt->id >= 0 )
+    {
+        int i;
+        for (i=0; i<(int)line->n_fmt; i++)
+            if ( line->d.fmt[i].id==fmt->id ) { fmt->fmt = &line->d.fmt[i]; break; }
+    }
+    else if ( !convert->allow_undef_tags )
+        error("Error: no such tag defined in the VCF header: FORMAT/%s\n", fmt->key);
+
+    fmt->ready = 1;
+}
+static void process_complete_format(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str)
+{
+    if ( convert->nsamples )
+    {
+        int i,j;
+        if ( line->n_fmt)
+        {
+            int gt_i = -1;
+            bcf_fmt_t *fmt = line->d.fmt;
+            int first = 1;
+            for (i=0; i<(int)line->n_fmt; i++)
+            {
+                if ( !fmt[i].p || fmt[i].id<0 ) continue;
+                if ( !first ) kputc(':', str);
+                first = 0;
+                kputs(convert->header->id[BCF_DT_ID][fmt[i].id].key, str);
+                if ( strcmp(convert->header->id[BCF_DT_ID][fmt[i].id].key, "GT") == 0) gt_i = i;
+            }
+            if ( first ) kputc('.', str);
+            for (j=0; j<convert->nsamples; j++)
+            {
+                kputc('\t', str);
+                first = 1;
+                for (i=0; i<(int)line->n_fmt; i++)
+                {
+                    bcf_fmt_t *f = &fmt[i];
+                    if ( !f->p ) continue;
+                    if ( !first ) kputc(':', str);
+                    first = 0;
+                    if (gt_i == i)
+                        bcf_format_gt(f,convert->samples[j],str);
+                    else
+                        bcf_fmt_array(str, f->n, f->type, f->p + convert->samples[j] * f->size);
+                }
+                if ( first ) kputc('.', str);
+            }
+        }
+        else
+            for (j=0; j<=line->n_sample; j++)
+                kputs("\t.", str);
+    }
+    else
+        kputc('.',str);
+}
+static void process_format(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str)
+{
+    if ( !fmt->ready )
+        init_format(convert, line, fmt);
+
+    if ( fmt->fmt==NULL )
+    {
+        kputc('.', str);
+        return;
+    }
+    else if ( fmt->subscript >=0 )
+    {
+        if ( fmt->fmt->n <= fmt->subscript )
+        {
+            kputc('.', str);
+            return;
+        }
+        if ( fmt->fmt->type == BCF_BT_FLOAT )
+        {
+            float *ptr = (float*)(fmt->fmt->p + isample*fmt->fmt->size);
+            if ( bcf_float_is_missing(ptr[fmt->subscript]) || bcf_float_is_vector_end(ptr[fmt->subscript]) )
+                kputc('.', str);
+            else
+                kputd(ptr[fmt->subscript], str);
+        }
+        else if ( fmt->fmt->type != BCF_BT_CHAR )
+        {
+            int32_t ival = bcf_array_ivalue(fmt->fmt->p+isample*fmt->fmt->size,fmt->fmt->type,fmt->subscript);
+            if ( ival==bcf_int32_missing || ival==bcf_int32_vector_end )
+                kputc('.', str);
+            else
+                kputw(ival, str);
+        }
+        else if ( fmt->fmt->type == BCF_BT_CHAR )
+            _copy_field((char*)(fmt->fmt->p + isample*fmt->fmt->size), fmt->fmt->size, fmt->subscript, str);
+        else error("TODO: %s:%d .. fmt->type=%d\n", __FILE__,__LINE__, fmt->fmt->type);
+    }
+    else
+        bcf_fmt_array(str, fmt->fmt->n, fmt->fmt->type, fmt->fmt->p + isample*fmt->fmt->size);
+}
+static void process_gt(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str)
+{
+    if ( !fmt->ready )
+        init_format(convert, line, fmt);
+
+    if ( fmt->fmt==NULL )
+    {
+        kputc('.', str);
+        return;
+    }
+    bcf_format_gt(fmt->fmt, isample, str);
+}
+static void process_tgt(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str)
+{
+    if ( !fmt->ready )
+        init_format(convert, line, fmt);
+
+    if ( fmt->fmt==NULL )
+    {
+        kputc('.', str);
+        return;
+    }
+
+    assert( fmt->fmt->type==BCF_BT_INT8 );
+
+    int l;
+    int8_t *x = (int8_t*)(fmt->fmt->p + isample*fmt->fmt->size); // FIXME: does not work with n_alt >= 64
+    for (l = 0; l < fmt->fmt->n && x[l] != bcf_int8_vector_end; ++l)
+    {
+        if (l) kputc("/|"[x[l]&1], str);
+        if (x[l]>>1)
+        {
+            int ial = (x[l]>>1) - 1;
+            kputs(line->d.allele[ial], str);
+        }
+        else
+            kputc('.', str);
+    }
+    if (l == 0) kputc('.', str);
+}
+static void destroy_tbcsq(void *usr)
+{
+    if ( !usr ) return;
+    bcsq_t *csq = (bcsq_t*) usr;
+    free(csq->hap1.s);
+    free(csq->hap2.s);
+    if ( csq->n )
+        free(csq->str[0]);
+    free(csq->str);
+    free(csq);
+}
+static void process_tbcsq(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str)
+{
+    if ( !fmt->ready )
+    {
+        init_format(convert, line, fmt);
+
+        bcsq_t *csq;
+        if ( fmt->usr )
+        {
+            csq = (bcsq_t*) fmt->usr;
+            if ( csq->n )
+                free(csq->str[0]);
+            csq->n = 0;
+        }
+        else
+            csq = (bcsq_t*) calloc(1,sizeof(bcsq_t));
+        fmt->usr = csq;
+
+        int i=0, len = 0;
+        char *tmp = NULL;
+        if ( bcf_get_info_string(convert->header,line,fmt->key,&tmp,&len)<0 )
+        {
+            csq->n = 0;
+            return;
+        }
+        do
+        {
+            csq->n++;
+            hts_expand(char*, csq->n, csq->m, csq->str);
+            csq->str[ csq->n-1 ] = tmp + i;
+            while ( i<len && tmp[i]!=',' ) i++;
+            if ( i<len && tmp[i]==',' ) tmp[i++] = 0;
+        }
+        while ( i<len );
+    }
+
+    bcsq_t *csq = (bcsq_t*)fmt->usr;
+
+    if ( fmt->fmt==NULL || !csq->n ) return;
+
+    csq->hap1.l = 0;
+    csq->hap2.l = 0;
+
+    int mask = fmt->subscript==0 ? 3 : 1;   // merge both haplotypes if subscript==0
+
+    #define BRANCH(type_t, nbits) { \
+        type_t *x = (type_t*)(fmt->fmt->p + isample*fmt->fmt->size); \
+        int i,j; \
+        if ( fmt->subscript<=0 || fmt->subscript==1 ) \
+        { \
+            for (j=0; j < fmt->fmt->n; j++) \
+            { \
+                type_t val = x[j]; \
+                if ( !val ) continue; \
+                for (i=0; i<nbits; i+=2) \
+                    if ( val & (mask<<i) ) { kputs(csq->str[(j*30+i)/2], &csq->hap1); kputc_(',', &csq->hap1); } \
+            } \
+        } \
+        if ( fmt->subscript<0 || fmt->subscript==2 ) \
+        { \
+            for (j=0; j < fmt->fmt->n; j++) \
+            { \
+                type_t val = x[j]; \
+                if ( !val ) continue; \
+                for (i=1; i<nbits; i+=2) \
+                    if ( val & (1<<i) ) { kputs(csq->str[(j*30+i)/2], &csq->hap2); kputc_(',', &csq->hap2); } \
+            } \
+        } \
+    }
+    switch (fmt->fmt->type)
+    {
+        case BCF_BT_INT8:  BRANCH(uint8_t, 8); break;
+        case BCF_BT_INT16: BRANCH(uint16_t,16); break;
+        case BCF_BT_INT32: BRANCH(uint32_t,30); break;  // 2 bytes unused to account for the reserved BCF values
+        default: error("Unexpected type: %d\n", fmt->fmt->type); bcftools_exit(1); break;
+    }
+    #undef BRANCH
+
+    if ( !csq->hap1.l && !csq->hap2.l ) return;
+
+    if ( csq->hap1.l ) csq->hap1.s[--csq->hap1.l] = 0;
+    if ( csq->hap2.l ) csq->hap2.s[--csq->hap2.l] = 0;
+
+    if ( fmt->subscript<0 )
+    {
+        kputs(csq->hap1.l?csq->hap1.s:".", str);
+        kputc_('\t', str);
+        kputs(csq->hap2.l?csq->hap2.s:".", str);
+    }
+    else if ( fmt->subscript<2 )
+        kputs(csq->hap1.l?csq->hap1.s:".", str);
+    else
+        kputs(csq->hap2.l?csq->hap2.s:".", str);
+}
+static void init_format_iupac(convert_t *convert, bcf1_t *line, fmt_t *fmt)
+{
+    init_format(convert, line, fmt);
+    if ( fmt->fmt==NULL ) return;
+
+    // Init mapping between alleles and IUPAC table
+    hts_expand(uint8_t, line->n_allele, convert->ndat, convert->dat);
+    int8_t *dat = (int8_t*)convert->dat;
+    int i;
+    for (i=0; i<line->n_allele; i++)
+    {
+        if ( line->d.allele[i][1] ) dat[i] = -1;
+        else
+        {
+            switch (line->d.allele[i][0])
+            {
+                case 'A': dat[i] = 0; break;
+                case 'C': dat[i] = 1; break;
+                case 'G': dat[i] = 2; break;
+                case 'T': dat[i] = 3; break;
+                case 'a': dat[i] = 0; break;
+                case 'c': dat[i] = 1; break;
+                case 'g': dat[i] = 2; break;
+                case 't': dat[i] = 3; break;
+                default: dat[i] = -1;
+            }
+        }
+    }
+}
+static void process_iupac_gt(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str)
+{
+    if ( !fmt->ready )
+        init_format_iupac(convert, line, fmt);
+
+    if ( fmt->fmt==NULL )
+    {
+        kputc('.', str);
+        return;
+    }
+
+    assert( fmt->fmt->type==BCF_BT_INT8 );
+
+    static const char iupac[4][4] = { {'A','M','R','W'},{'M','C','S','Y'},{'R','S','G','K'},{'W','Y','K','T'} };
+    int8_t *dat = (int8_t*)convert->dat;
+
+    int8_t *x = (int8_t*)(fmt->fmt->p + isample*fmt->fmt->size); // FIXME: does not work with n_alt >= 64
+    int l = 0;
+    while ( l<fmt->fmt->n && x[l]!=bcf_int8_vector_end && x[l]!=bcf_int8_missing ) l++;
+
+    if ( l==2 )
+    {
+        // diploid
+        int ia = (x[0]>>1) - 1, ib = (x[1]>>1) - 1;
+        if ( ia>=0 && ia<line->n_allele && ib>=0 && ib<line->n_allele && dat[ia]>=0 && dat[ib]>=0 )
+        {
+            kputc(iupac[dat[ia]][dat[ib]], str);
+            return;
+        }
+    }
+    for (l = 0; l < fmt->fmt->n && x[l] != bcf_int8_vector_end; ++l)
+    {
+        if (l) kputc("/|"[x[l]&1], str);
+        if (x[l]>>1)
+        {
+            int ial = (x[l]>>1) - 1;
+            kputs(line->d.allele[ial], str);
+        }
+        else
+            kputc('.', str);
+    }
+    if (l == 0) kputc('.', str);
+}
+static void process_sample(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str)
+{
+    kputs(convert->header->samples[isample], str);
+}
+static void process_sep(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str) { if (fmt->key) kputs(fmt->key, str); }
+static void process_is_ts(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str)
+{
+    int is_ts = 0;
+    if ( bcf_get_variant_types(line) & (VCF_SNP|VCF_MNP) )
+        is_ts = abs(bcf_acgt2int(*line->d.allele[0])-bcf_acgt2int(*line->d.allele[1])) == 2 ? 1 : 0;
+    kputc(is_ts ? '1' : '0', str);
+}
+static void process_type(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str)
+{
+    int line_type = bcf_get_variant_types(line);
+    int i = 0;
+    if ( line_type == VCF_REF ) { kputs("REF", str); i++; }
+    if ( line_type & VCF_SNP ) { if (i) kputc(',',str); kputs("SNP", str); i++; }
+    if ( line_type & VCF_MNP ) { if (i) kputc(',',str); kputs("MNP", str); i++; }
+    if ( line_type & VCF_INDEL ) { if (i) kputc(',',str); kputs("INDEL", str); i++; }
+    if ( line_type & VCF_OTHER ) { if (i) kputc(',',str); kputs("OTHER", str); i++; }
+    if ( line_type & VCF_BND ) { if (i) kputc(',',str); kputs("BND", str); i++; }
+    if ( line_type & VCF_OVERLAP ) { if (i) kputc(',',str); kputs("OVERLAP", str); i++; }
+}
+static void process_line(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str)
+{
+    vcf_format1(convert->header, line, str);
+}
+static void process_chrom_pos_id(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str)
+{
+    if ( line->d.id[0]!='.' || line->d.id[1] )
+    {
+        // ID is present
+        kputs(line->d.id, str);
+    }
+    else
+    {
+        // use CHROM:POS instead of ID
+        kputs(convert->header->id[BCF_DT_CTG][line->rid].key, str);
+        kputc(':', str);
+        kputw(line->pos+1, str);
+    }
+}
+static void process_gt_to_prob3(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str)
+{
+    int m,n,i;
+
+    m = convert->ndat / sizeof(int32_t);
+    n = bcf_get_genotypes(convert->header,line,&convert->dat,&m);
+    convert->ndat = m * sizeof(int32_t);
+
+    if ( n<=0 )
+    {
+        // Throw an error or silently proceed?
+        //
+        // for (i=0; i<convert->nsamples; i++) kputs(" 0.33 0.33 0.33", str);
+        // return;
+
+        error("Error parsing GT tag at %s:%"PRId64"\n", bcf_seqname(convert->header,line),(int64_t) line->pos+1);
+    }
+
+    n /= convert->nsamples;
+    for (i=0; i<convert->nsamples; i++)
+    {
+        int32_t *ptr = (int32_t*)convert->dat + i*n;
+        int j;
+        for (j=0; j<n; j++)
+            if ( ptr[j]==bcf_int32_vector_end ) break;
+
+        if ( j==2 )
+        {
+            // diploid
+            if ( bcf_gt_is_missing(ptr[0]) )
+                kputs(" 0.33 0.33 0.33", str);
+            else if ( bcf_gt_allele(ptr[0])!=bcf_gt_allele(ptr[1]) )
+                kputs(" 0 1 0", str);       // HET
+            else if ( bcf_gt_allele(ptr[0])==1 )
+                kputs(" 0 0 1", str);       // ALT HOM, first ALT allele
+            else
+                kputs(" 1 0 0", str);       // REF HOM or something else than first ALT
+        }
+        else if ( j==1 )
+        {
+            // haploid
+            if ( bcf_gt_is_missing(ptr[0]) )
+                kputs(" 0.5 0.0 0.5", str);
+            else if ( bcf_gt_allele(ptr[0])==1 )
+                kputs(" 0 0 1", str);       // first ALT allele
+            else
+                kputs(" 1 0 0", str);       // REF or something else than first ALT
+        }
+        else error("FIXME: not ready for ploidy %d\n", j);
+    }
+}
+static void process_pl_to_prob3(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str)
+{
+    int m,n,i;
+
+    m = convert->ndat / sizeof(int32_t);
+    n = bcf_get_format_int32(convert->header,line,"PL",&convert->dat,&m);
+    convert->ndat = m * sizeof(int32_t);
+
+    if ( n<=0 )
+    {
+        // Throw an error or silently proceed?
+        //
+        // for (i=0; i<convert->nsamples; i++) kputs(" 0.33 0.33 0.33", str);
+        // return;
+
+        error("Error parsing PL tag at %s:%"PRId64"\n", bcf_seqname(convert->header,line),(int64_t) line->pos+1);
+    }
+
+    n /= convert->nsamples;
+    for (i=0; i<convert->nsamples; i++)
+    {
+        int32_t *ptr = (int32_t*)convert->dat + i*n;
+        int j;
+        float sum = 0;
+        for (j=0; j<n; j++)
+        {
+            if ( ptr[j]==bcf_int32_vector_end ) break;
+            sum += pow(10,-0.1*ptr[j]);
+        }
+        if ( j==line->n_allele )
+        {
+            // haploid
+            kputc(' ',str);
+            ksprintf(str,"%f",pow(10,-0.1*ptr[0])/sum);
+            kputs(" 0 ", str);
+            ksprintf(str,"%f",pow(10,-0.1*ptr[1])/sum);
+        }
+        else
+        {
+            // diploid
+            kputc(' ',str);
+            ksprintf(str,"%f",pow(10,-0.1*ptr[0])/sum);
+            kputc(' ',str);
+            ksprintf(str,"%f",pow(10,-0.1*ptr[1])/sum);
+            kputc(' ',str);
+            ksprintf(str,"%f",pow(10,-0.1*ptr[2])/sum);
+        }
+    }
+}
+static void process_gp_to_prob3(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str)
+{
+    int m,n,i;
+
+    m = convert->ndat / sizeof(float);
+    n = bcf_get_format_float(convert->header,line,"GP",&convert->dat,&m);
+    convert->ndat = m * sizeof(float);
+
+    if ( n<=0 )
+    {
+        // Throw an error or silently proceed?
+        //
+        // for (i=0; i<convert->nsamples; i++) kputs(" 0.33 0.33 0.33", str);
+        // return;
+
+        error("Error parsing GP tag at %s:%"PRId64"\n", bcf_seqname(convert->header,line),(int64_t) line->pos+1);
+    }
+
+    n /= convert->nsamples;
+    for (i=0; i<convert->nsamples; i++)
+    {
+        float *ptr = (float*)convert->dat + i*n;
+        int j;
+        for (j=0; j<n; j++)
+        {
+            if ( bcf_float_is_vector_end(ptr[j]) ) break;
+            if ( bcf_float_is_missing(ptr[j]) ) { ptr[j]=0; continue; }
+            if ( ptr[j]<0 || ptr[j]>1 ) error("[%s:%"PRId64":%f] GP value outside range [0,1]; bcftools convert expects the VCF4.3+ spec for the GP field encoding genotype posterior probabilities", bcf_seqname(convert->header,line),(int64_t) line->pos+1,ptr[j]);
+        }
+        if ( j==line->n_allele )
+            ksprintf(str," %f %f %f",ptr[0],0.,ptr[1]); // haploid
+        else
+            ksprintf(str," %f %f %f",ptr[0],ptr[1],ptr[2]); // diploid
+    }
+}
+
+static void process_gt_to_hap(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str)
+{
+    // https://mathgen.stats.ox.ac.uk/impute/impute_v2.html#-known_haps_g
+
+    // File containing known haplotypes for the study cohort. The format
+    // is the same as the output format from IMPUTE2's -phase option:
+    // five header columns (as in the -g file) followed by two columns
+    // (haplotypes) per individual. Allowed values in the haplotype
+    // columns are 0, 1, and ?.
+
+    // If your study dataset is fully phased, you can replace the -g file
+    // with a -known_haps_g file. This will cause IMPUTE2 to perform
+    // haploid imputation, although it will still report diploid imputation
+    // probabilities in the main output file. If any genotypes are missing,
+    // they can be marked as '? ?' (two question marks separated by one
+    // space) in the input file. (The program does not allow just one
+    // allele from a diploid genotype to be missing.) If the reference
+    // panels are also phased, IMPUTE2 will perform a single, fast
+    // imputation step rather than its standard MCMC module this is how
+    // the program imputes into pre-phased GWAS haplotypes.
+
+    // The -known_haps_g file can also be used to specify study
+    // genotypes that are "partially" phased, in the sense that some
+    // genotypes are phased relative to a fixed reference point while
+    // others are not. We anticipate that this will be most useful when
+    // trying to phase resequencing data onto a scaffold of known
+    // haplotypes. To mark a known genotype as unphased, place an
+    // asterisk immediately after each allele, with no space between
+    // the allele (0/1) and the asterisk (*); e.g., "0* 1*" for a
+    // heterozygous genotype of unknown phase.
+
+    int i, gt_id = bcf_hdr_id2int(convert->header, BCF_DT_ID, "GT");
+    if ( !bcf_hdr_idinfo_exists(convert->header,BCF_HL_FMT,gt_id) )
+        error("FORMAT/GT tag not present at %s:%"PRId64"\n", bcf_seqname(convert->header, line),(int64_t) line->pos+1);
+    if ( !(line->unpacked & BCF_UN_FMT) ) bcf_unpack(line, BCF_UN_FMT);
+    bcf_fmt_t *fmt_gt = NULL;
+    for (i=0; i<line->n_fmt; i++)
+        if ( line->d.fmt[i].id==gt_id ) { fmt_gt = &line->d.fmt[i]; break; }
+    if ( !fmt_gt )
+        error("FORMAT/GT tag not present at %s:%"PRId64"\n", bcf_seqname(convert->header, line),(int64_t) line->pos+1);
+
+    // Alloc all memory in advance to avoid kput routines. The biggest allowed allele index is 99
+    if ( line->n_allele > 100 )
+        error("Too many alleles (%d) at %s:%"PRId64"\n", line->n_allele, bcf_seqname(convert->header, line),(int64_t) line->pos+1);
+    if ( ks_resize(str, str->l+convert->nsamples*8) != 0 )
+        error("Could not alloc %" PRIu64 " bytes\n", (uint64_t)(str->l + convert->nsamples*8));
+
+    if ( fmt_gt->type!=BCF_BT_INT8 )    // todo: use BRANCH_INT if the VCF is valid
+        error("Uh, too many alleles (%d) or redundant BCF representation at %s:%"PRId64"\n", line->n_allele, bcf_seqname(convert->header, line),(int64_t) line->pos+1);
+    if ( fmt_gt->n!=1 && fmt_gt->n!=2 )
+        error("Uh, ploidy of %d not supported, see %s:%"PRId64"\n", fmt_gt->n, bcf_seqname(convert->header, line),(int64_t) line->pos+1);
+
+    int8_t *ptr = ((int8_t*) fmt_gt->p) - fmt_gt->n;
+    for (i=0; i<convert->nsamples; i++)
+    {
+        ptr += fmt_gt->n;
+        if ( fmt_gt->n==1 ) // haploid genotypes
+        {
+            if ( ptr[0]==2 ) /* 0 */
+            {
+                str->s[str->l++] = '0'; str->s[str->l++] = ' '; str->s[str->l++] = '-'; str->s[str->l++] = ' ';
+            }
+            else if ( ptr[0]==bcf_int8_missing )   /* . */
+            {
+                str->s[str->l++] = '?'; str->s[str->l++] = ' '; str->s[str->l++] = '?'; str->s[str->l++] = ' ';
+            }
+            else if ( ptr[0]==4 ) /* 1 */
+            {
+                str->s[str->l++] = '1'; str->s[str->l++] = ' '; str->s[str->l++] = '-'; str->s[str->l++] = ' ';
+            }
+            else
+            {
+                kputw(bcf_gt_allele(ptr[0]),str); str->s[str->l++] = ' '; str->s[str->l++] = '-'; str->s[str->l++] = ' ';
+            }
+        }
+        else if ( ptr[0]==2 )
+        {
+            if ( ptr[1]==3 ) /* 0|0 */
+            {
+                str->s[str->l++] = '0'; str->s[str->l++] = ' '; str->s[str->l++] = '0'; str->s[str->l++] = ' ';
+            }
+            else if ( ptr[1]==5 ) /* 0|1 */
+            {
+                str->s[str->l++] = '0'; str->s[str->l++] = ' '; str->s[str->l++] = '1'; str->s[str->l++] = ' ';
+            }
+            else if ( ptr[1]==bcf_int8_vector_end ) /* 0 */
+            {
+                str->s[str->l++] = '0'; str->s[str->l++] = ' '; str->s[str->l++] = '-'; str->s[str->l++] = ' ';
+            }
+            else if ( ptr[1]==2 ) /* 0/0 */
+            {
+                str->s[str->l++] = '0'; str->s[str->l++] = '*'; str->s[str->l++] = ' '; str->s[str->l++] = '0'; str->s[str->l++] = '*'; str->s[str->l++] = ' ';
+            }
+            else if ( ptr[1]==4 ) /* 0/1 */
+            {
+                str->s[str->l++] = '0'; str->s[str->l++] = '*'; str->s[str->l++] = ' '; str->s[str->l++] = '1'; str->s[str->l++] = '*'; str->s[str->l++] = ' ';
+            }
+            else if ( bcf_gt_is_missing(ptr[1]) ) /* 0/. */
+            {
+                str->s[str->l++] = '?'; str->s[str->l++] = ' '; str->s[str->l++] = '?'; str->s[str->l++] = ' ';
+            }
+            else if ( bcf_gt_is_phased(ptr[1]) ) /* 0|x */
+            {
+                str->s[str->l++] = '0'; str->s[str->l++] = ' ';
+                kputw(bcf_gt_allele(ptr[1]),str);
+                str->s[str->l++] = ' ';
+            }
+            else /* 0/x */
+            {
+                str->s[str->l++] = '0'; str->s[str->l++] = '*'; str->s[str->l++] = ' ';
+                kputw(bcf_gt_allele(ptr[1]),str);
+                str->s[str->l++] = '*'; str->s[str->l++] = ' ';
+            }
+        }
+        else if ( ptr[0]==4 )
+        {
+            if ( ptr[1]==3 ) /* 1|0 */
+            {
+                str->s[str->l++] = '1'; str->s[str->l++] = ' '; str->s[str->l++] = '0'; str->s[str->l++] = ' ';
+            }
+            else if ( ptr[1]==5 ) /* 1|1 */
+            {
+                str->s[str->l++] = '1'; str->s[str->l++] = ' '; str->s[str->l++] = '1'; str->s[str->l++] = ' ';
+            }
+            else if ( ptr[1]==bcf_int8_vector_end ) /* 1 */
+            {
+                str->s[str->l++] = '1'; str->s[str->l++] = ' '; str->s[str->l++] = '-'; str->s[str->l++] = ' ';
+            }
+            else if ( ptr[1]==2 ) /* 1/0 */
+            {
+                str->s[str->l++] = '1'; str->s[str->l++] = '*'; str->s[str->l++] = ' '; str->s[str->l++] = '0'; str->s[str->l++] = '*'; str->s[str->l++] = ' ';
+            }
+            else if ( ptr[1]==4 ) /* 1/1 */
+            {
+                str->s[str->l++] = '1'; str->s[str->l++] = '*'; str->s[str->l++] = ' '; str->s[str->l++] = '1'; str->s[str->l++] = '*'; str->s[str->l++] = ' ';
+            }
+            else if ( bcf_gt_is_missing(ptr[1]) ) /* 1/. */
+            {
+                str->s[str->l++] = '?'; str->s[str->l++] = ' '; str->s[str->l++] = '?'; str->s[str->l++] = ' ';
+            }
+            else if ( bcf_gt_is_phased(ptr[1]) )    /* 1|x */
+            {
+                str->s[str->l++] = '1'; str->s[str->l++] = ' ';
+                kputw(bcf_gt_allele(ptr[1]),str);
+                str->s[str->l++] = ' ';
+            }
+            else /* 1/x */
+            {
+                str->s[str->l++] = '1'; str->s[str->l++] = '*'; str->s[str->l++] = ' ';
+                kputw(bcf_gt_allele(ptr[1]),str);
+                str->s[str->l++] = '*'; str->s[str->l++] = ' ';
+            }
+        }
+        else if ( bcf_gt_is_missing(ptr[0]) )
+        {
+            if ( ptr[1]==bcf_int8_vector_end )
+            {
+                str->s[str->l++] = '?'; str->s[str->l++] = ' '; str->s[str->l++] = '-'; str->s[str->l++] = ' ';
+            }
+            else
+            {
+                str->s[str->l++] = '?'; str->s[str->l++] = ' '; str->s[str->l++] = '?'; str->s[str->l++] = ' ';
+            }
+        }
+        else if ( ptr[1]==bcf_int8_vector_end )
+        {
+            /* use REF for something else than first ALT */
+            str->s[str->l++] = '0'; str->s[str->l++] = ' '; str->s[str->l++] = '-'; str->s[str->l++] = ' ';
+        }
+        else
+        {
+            kputw(bcf_gt_allele(ptr[0]),str);
+            if ( bcf_gt_is_phased(ptr[1]) ) str->s[str->l++] = '*';
+            str->s[str->l++] = ' ';
+            kputw(bcf_gt_allele(ptr[1]),str);
+            if ( bcf_gt_is_phased(ptr[1]) ) str->s[str->l++] = '*';
+            str->s[str->l++] = ' ';
+        }
+    }
+    str->s[--str->l] = 0;     // delete the last space
+}
+static void process_gt_to_hap2(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str)
+{
+    // same as process_gt_to_hap but converts haploid genotypes into diploid
+
+    int i, gt_id = bcf_hdr_id2int(convert->header, BCF_DT_ID, "GT");
+    if ( !bcf_hdr_idinfo_exists(convert->header,BCF_HL_FMT,gt_id) )
+        error("FORMAT/GT tag not present at %s:%"PRId64"\n", bcf_seqname(convert->header, line),(int64_t) line->pos+1);
+    if ( !(line->unpacked & BCF_UN_FMT) ) bcf_unpack(line, BCF_UN_FMT);
+    bcf_fmt_t *fmt_gt = NULL;
+    for (i=0; i<line->n_fmt; i++)
+        if ( line->d.fmt[i].id==gt_id ) { fmt_gt = &line->d.fmt[i]; break; }
+    if ( !fmt_gt )
+        error("FORMAT/GT tag not present at %s:%"PRId64"\n", bcf_seqname(convert->header, line),(int64_t)  line->pos+1);
+
+    // Alloc all memory in advance to avoid kput routines. The biggest allowed allele index is 99
+    if ( line->n_allele > 100 )
+        error("Too many alleles (%d) at %s:%"PRId64"\n", line->n_allele, bcf_seqname(convert->header, line),(int64_t) line->pos+1);
+    if ( ks_resize(str, str->l+convert->nsamples*8) != 0 )
+        error("Could not alloc %" PRIu64 " bytes\n", (uint64_t)(str->l + convert->nsamples*8));
+
+    if ( fmt_gt->type!=BCF_BT_INT8 )    // todo: use BRANCH_INT if the VCF is valid
+        error("Uh, too many alleles (%d) or redundant BCF representation at %s:%"PRId64"\n", line->n_allele, bcf_seqname(convert->header, line),(int64_t) line->pos+1);
+
+    int8_t *ptr = ((int8_t*) fmt_gt->p) - fmt_gt->n;
+    for (i=0; i<convert->nsamples; i++)
+    {
+        ptr += fmt_gt->n;
+        if ( ptr[0]==2 )
+        {
+            if ( ptr[1]==3 ) /* 0|0 */
+            {
+                str->s[str->l++] = '0'; str->s[str->l++] = ' '; str->s[str->l++] = '0'; str->s[str->l++] = ' ';
+            }
+            else if ( ptr[1]==5 ) /* 0|1 */
+            {
+                str->s[str->l++] = '0'; str->s[str->l++] = ' '; str->s[str->l++] = '1'; str->s[str->l++] = ' ';
+            }
+            else if ( ptr[1]==bcf_int8_vector_end ) /* 0 -> 0|0 */
+            {
+                str->s[str->l++] = '0'; str->s[str->l++] = ' '; str->s[str->l++] = '0'; str->s[str->l++] = ' ';
+            }
+            else if ( ptr[1]==2 ) /* 0/0 */
+            {
+                str->s[str->l++] = '0'; str->s[str->l++] = '*'; str->s[str->l++] = ' '; str->s[str->l++] = '0'; str->s[str->l++] = '*'; str->s[str->l++] = ' ';
+            }
+            else if ( ptr[1]==4 ) /* 0/1 */
+            {
+                str->s[str->l++] = '0'; str->s[str->l++] = '*'; str->s[str->l++] = ' '; str->s[str->l++] = '1'; str->s[str->l++] = '*'; str->s[str->l++] = ' ';
+            }
+            else if ( bcf_gt_is_missing(ptr[1]) ) /* 0/. */
+            {
+                str->s[str->l++] = '?'; str->s[str->l++] = ' '; str->s[str->l++] = '?'; str->s[str->l++] = ' ';
+            }
+            else if ( bcf_gt_is_phased(ptr[1]) ) /* 0|x */
+            {
+                str->s[str->l++] = '0'; str->s[str->l++] = ' ';
+                kputw(bcf_gt_allele(ptr[1]),str);
+                str->s[str->l++] = ' ';
+            }
+            else /* 0/x */
+            {
+                str->s[str->l++] = '0'; str->s[str->l++] = '*'; str->s[str->l++] = ' ';
+                kputw(bcf_gt_allele(ptr[1]),str);
+                str->s[str->l++] = '*'; str->s[str->l++] = ' ';
+            }
+        }
+        else if ( ptr[0]==4 )
+        {
+            if ( ptr[1]==3 ) /* 1|0 */
+            {
+                str->s[str->l++] = '1'; str->s[str->l++] = ' '; str->s[str->l++] = '0'; str->s[str->l++] = ' ';
+            }
+            else if ( ptr[1]==5 ) /* 1|1 */
+            {
+                str->s[str->l++] = '1'; str->s[str->l++] = ' '; str->s[str->l++] = '1'; str->s[str->l++] = ' ';
+            }
+            else if ( ptr[1]==bcf_int8_vector_end ) /* 1 -> 1|1 */
+            {
+                str->s[str->l++] = '1'; str->s[str->l++] = ' '; str->s[str->l++] = '1'; str->s[str->l++] = ' ';
+            }
+            else if ( ptr[1]==2 ) /* 1/0 */
+            {
+                str->s[str->l++] = '1'; str->s[str->l++] = '*'; str->s[str->l++] = ' '; str->s[str->l++] = '0'; str->s[str->l++] = '*'; str->s[str->l++] = ' ';
+            }
+            else if ( ptr[1]==4 ) /* 1/1 */
+            {
+                str->s[str->l++] = '1'; str->s[str->l++] = '*'; str->s[str->l++] = ' '; str->s[str->l++] = '1'; str->s[str->l++] = '*'; str->s[str->l++] = ' ';
+            }
+            else if ( bcf_gt_is_missing(ptr[1]) ) /* 1/. */
+            {
+                str->s[str->l++] = '?'; str->s[str->l++] = ' '; str->s[str->l++] = '?'; str->s[str->l++] = ' ';
+            }
+            else if ( bcf_gt_is_phased(ptr[1]) )    /* 1|x */
+            {
+                str->s[str->l++] = '1'; str->s[str->l++] = ' ';
+                kputw(bcf_gt_allele(ptr[1]),str);
+                str->s[str->l++] = ' ';
+            }
+            else /* 1/x */
+            {
+                str->s[str->l++] = '1'; str->s[str->l++] = '*'; str->s[str->l++] = ' ';
+                kputw(bcf_gt_allele(ptr[1]),str);
+                str->s[str->l++] = '*'; str->s[str->l++] = ' ';
+            }
+        }
+        else if ( bcf_gt_is_missing(ptr[0]) )
+        {
+            str->s[str->l++] = '?'; str->s[str->l++] = ' '; str->s[str->l++] = '?'; str->s[str->l++] = ' ';
+        }
+        else if ( ptr[1]==bcf_int8_vector_end )
+        {
+            /* use REF for something else than first ALT */
+            str->s[str->l++] = '0'; str->s[str->l++] = ' '; str->s[str->l++] = '0'; str->s[str->l++] = ' ';
+        }
+        else
+        {
+            kputw(bcf_gt_allele(ptr[0]),str);
+            if ( bcf_gt_is_phased(ptr[1]) ) str->s[str->l++] = '*';
+            str->s[str->l++] = ' ';
+            kputw(bcf_gt_allele(ptr[1]),str);
+            if ( bcf_gt_is_phased(ptr[1]) ) str->s[str->l++] = '*';
+            str->s[str->l++] = ' ';
+        }
+    }
+    str->s[--str->l] = 0;     // delete the last space
+}
+
+static void process_rsid_hex(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str)
+{
+    char *ptr = line->d.id;
+    ptr += 2; // remove 'rs'
+    ksprintf(str, "%08" PRIx32 "", (uint32_t)strtoul(ptr, NULL, 10));
+}
+
+static void process_variantkey_hex(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str)
+{
+    uint64_t vk = variantkey(
+        convert->header->id[BCF_DT_CTG][line->rid].key,
+        strlen(convert->header->id[BCF_DT_CTG][line->rid].key),
+        line->pos,
+        line->d.allele[0],
+        strlen(line->d.allele[0]),
+        line->d.allele[1],
+        strlen(line->d.allele[1]));
+    ksprintf(str, "%016" PRIx64 "", vk);
+}
+
+static void process_npass(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str)
+{
+    int i, nsmpl = 0;
+    filter_t *flt = (filter_t*) fmt->usr;
+    const uint8_t *smpl;
+    filter_test(flt,line,&smpl);
+    for (i=0; i<convert->nsamples; i++)
+        if ( smpl[i] ) nsmpl++;
+    kputd(nsmpl, str);
+}
+static void destroy_npass(void *usr)
+{
+    filter_destroy((filter_t*)usr);
+}
+
+static void process_pbinom(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str)
+{
+    int i;
+    if ( !fmt->ready )
+    {
+        fmt->fmt = NULL;    // AD
+        fmt->usr = NULL;    // GT
+
+        for (i=0; i<(int)line->n_fmt; i++)
+            if ( line->d.fmt[i].id==fmt->id ) { fmt->fmt = &line->d.fmt[i]; break; }
+
+        // Check that the first field is GT
+        int gt_id = bcf_hdr_id2int(convert->header, BCF_DT_ID, "GT");
+        if ( !bcf_hdr_idinfo_exists(convert->header, BCF_HL_FMT, fmt->id)  ) error("Error: FORMAT/GT is not defined in the header\n");
+        for (i=0; i<(int)line->n_fmt; i++)
+            if ( line->d.fmt[i].id==gt_id ) { fmt->usr = &line->d.fmt[i]; break; }  // it should always be first according to VCF spec, but...
+
+        if ( fmt->usr && line->d.fmt[i].type!=BCF_BT_INT8 )   // skip sites with many alleles
+            fmt->usr = NULL;
+
+        fmt->ready = 1;
+    }
+    bcf_fmt_t *gt_fmt = (bcf_fmt_t*) fmt->usr;
+    if ( !fmt->fmt || !gt_fmt || gt_fmt->n!=2 ) goto invalid;
+
+    int n[2] = {0,0};
+    int8_t *gt = (int8_t*)(gt_fmt->p + isample*gt_fmt->size);
+    for (i=0; i<2; i++)
+    {
+        if ( bcf_gt_is_missing(gt[i]) || gt[i] == bcf_int8_vector_end ) goto invalid;
+        int al = bcf_gt_allele(gt[i]);
+        if ( al > line->n_allele || al >= fmt->fmt->n ) goto invalid;
+
+        #define BRANCH(type_t, missing, vector_end) { \
+            type_t val = ((type_t *) fmt->fmt->p)[al + isample*fmt->fmt->n]; \
+            if ( val==missing || val==vector_end ) goto invalid; \
+            else n[i] = val; \
+        }
+        switch (fmt->fmt->type)
+        {
+            case BCF_BT_INT8:  BRANCH(int8_t,  bcf_int8_missing,  bcf_int8_vector_end); break;
+            case BCF_BT_INT16: BRANCH(int16_t, bcf_int16_missing, bcf_int16_vector_end); break;
+            case BCF_BT_INT32: BRANCH(int32_t, bcf_int32_missing, bcf_int32_vector_end); break;
+            default: goto invalid; break;
+        }
+        #undef BRANCH
+    }
+
+    if ( n[0]==n[1] ) kputc(n[0]==0 ? '.':'0', str);
+    else
+    {
+        double pval = n[0] < n[1] ? kf_betai(n[1], n[0] + 1, 0.5) : kf_betai(n[0], n[1] + 1, 0.5);
+        pval *= 2;
+        if ( pval>=1 ) pval = 0;     // this can happen, machine precision error, eg. kf_betai(1,0,0.5)
+        else
+            pval = -4.34294481903*log(pval);
+        kputd(pval, str);
+    }
+    return;
+
+invalid:
+    kputc('.', str);
+}
+
+static void _used_tags_add(convert_t *convert, int type, char *key)
+{
+    kstring_t str = {0,0,0};
+    ksprintf(&str,"%s/%s",type==T_INFO?"INFO":"FORMAT",key);
+    khash_str2int_inc(convert->used_tags_hash,str.s);
+    convert->nused_tags++;
+    convert->used_tags_list = (char**)realloc(convert->used_tags_list,sizeof(*convert->used_tags_list)*convert->nused_tags);
+    convert->used_tags_list[convert->nused_tags-1] = str.s;
+}
+
+
+#define _SET_NON_FORMAT_TAGS(function,key,...) \
+    if ( !strcmp("CHROM",key) ) { function(__VA_ARGS__, T_CHROM); } \
+    else if ( !strcmp("POS",key) ) { function(__VA_ARGS__, T_POS); } \
+    else if ( !strcmp("POS0",key) ) { function(__VA_ARGS__, T_POS0); } \
+    else if ( !strcmp("END",key) ) { function(__VA_ARGS__, T_END); } \
+    else if ( !strcmp("END0",key) ) { function(__VA_ARGS__, T_END0); } \
+    else if ( !strcmp("ID",key) ) { function(__VA_ARGS__, T_ID); } \
+    else if ( !strcmp("REF",key) ) { function(__VA_ARGS__, T_REF); } \
+    else if ( !strcmp("FIRST_ALT",key) ) { function(__VA_ARGS__, T_FIRST_ALT); } \
+    else if ( !strcmp("QUAL",key) ) { function(__VA_ARGS__, T_QUAL); } \
+    else if ( !strcmp("TYPE",key) ) { function(__VA_ARGS__, T_TYPE); } \
+    else if ( !strcmp("FILTER",key) ) { function(__VA_ARGS__, T_FILTER); } \
+    else if ( !strcmp("IS_TS",key) ) { function(__VA_ARGS__, T_IS_TS); } \
+    else if ( !strcmp("MASK",key) ) { function(__VA_ARGS__, T_MASK); } \
+    else if ( !strcmp("LINE",key) ) { function(__VA_ARGS__, T_LINE); }
+
+static void set_type(fmt_t *fmt, int type) { fmt->type = type; }
+static fmt_t *register_tag(convert_t *convert, char *key, int is_gtf, int type)
+{
+    convert->nfmt++;
+    if ( convert->nfmt > convert->mfmt )
+    {
+        convert->mfmt += 10;
+        convert->fmt   = (fmt_t*) realloc(convert->fmt, convert->mfmt*sizeof(fmt_t));
+    }
+    fmt_t *fmt = &convert->fmt[ convert->nfmt-1 ];
+    fmt->type  = type;
+    fmt->key   = key ? strdup(key) : NULL;
+    fmt->is_gt_field = is_gtf;
+    fmt->subscript = -1;
+    fmt->usr     = NULL;
+    fmt->destroy = NULL;
+
+    // Allow non-format tags, such as CHROM, INFO, etc., to appear amongst the format tags.
+    if ( key )
+    {
+        int id = bcf_hdr_id2int(convert->header, BCF_DT_ID, key);
+        if ( fmt->type==T_FORMAT && !bcf_hdr_idinfo_exists(convert->header,BCF_HL_FMT,id) )
+        {
+            _SET_NON_FORMAT_TAGS(set_type,key,fmt)
+           else if ( !strcmp("ALT",key) ) { fmt->type = T_ALT; }
+           else if ( !strcmp("_CHROM_POS_ID",key) ) { fmt->type = T_CHROM_POS_ID; }
+            else if ( !strcmp("RSX",key) ) { fmt->type = T_RSX; }
+            else if ( !strcmp("VKX",key) ) { fmt->type = T_VKX; }
+            else if ( id>=0 && bcf_hdr_idinfo_exists(convert->header,BCF_HL_INFO,id) )
+            {
+                fmt->type = T_INFO;
+                _used_tags_add(convert,T_INFO,key);
+            }
+        }
+        else if ( fmt->type==T_PBINOM )
+        {
+            fmt->id = bcf_hdr_id2int(convert->header, BCF_DT_ID, fmt->key);
+            if ( !bcf_hdr_idinfo_exists(convert->header,BCF_HL_FMT, fmt->id)  ) error("No such FORMAT tag defined in the header: %s\n", fmt->key);
+            _used_tags_add(convert,T_FORMAT,key);
+        }
+        else if ( fmt->type==T_NPASS )
+        {
+            filter_t *flt = filter_init(convert->header,key);
+            convert->max_unpack |= filter_max_unpack(flt);
+            fmt->usr = (void*) flt;
+        }
+    }
+
+    switch (fmt->type)
+    {
+        case T_FIRST_ALT: fmt->handler = &process_first_alt; break;
+        case T_CHROM_POS_ID: fmt->handler = &process_chrom_pos_id; break;
+        case T_GT_TO_PROB3: fmt->handler = &process_gt_to_prob3; break;
+        case T_PL_TO_PROB3: fmt->handler = &process_pl_to_prob3; break;
+        case T_GP_TO_PROB3: fmt->handler = &process_gp_to_prob3; break;
+        case T_CHROM: fmt->handler = &process_chrom; break;
+        case T_POS: fmt->handler = &process_pos; break;
+        case T_POS0: fmt->handler = &process_pos0; break;
+        case T_END: fmt->handler = &process_end; convert->max_unpack |= BCF_UN_INFO; break;
+        case T_END0: fmt->handler = &process_end0; convert->max_unpack |= BCF_UN_INFO; break;
+        case T_ID: fmt->handler = &process_id; break;
+        case T_REF: fmt->handler = &process_ref; break;
+        case T_ALT: fmt->handler = &process_alt; break;
+        case T_QUAL: fmt->handler = &process_qual; break;
+        case T_FILTER: fmt->handler = &process_filter; convert->max_unpack |= BCF_UN_FLT; break;
+        case T_INFO: fmt->handler = &process_info; convert->max_unpack |= BCF_UN_INFO; break;
+        case T_FORMAT: fmt->handler = fmt->key ? &process_format : &process_complete_format; convert->max_unpack |= BCF_UN_FMT; break;
+        case T_SAMPLE: fmt->handler = &process_sample; break;
+        case T_SEP: fmt->handler = &process_sep; break;
+        case T_IS_TS: fmt->handler = &process_is_ts; break;
+        case T_TYPE: fmt->handler = &process_type; break;
+        case T_MASK: fmt->handler = NULL; break;
+        case T_GT: fmt->handler = &process_gt; convert->max_unpack |= BCF_UN_FMT; break;
+        case T_TGT: fmt->handler = &process_tgt; convert->max_unpack |= BCF_UN_FMT; break;
+        case T_IUPAC_GT: fmt->handler = &process_iupac_gt; convert->max_unpack |= BCF_UN_FMT; break;
+        case T_GT_TO_HAP: fmt->handler = &process_gt_to_hap; convert->max_unpack |= BCF_UN_FMT; break;
+        case T_GT_TO_HAP2: fmt->handler = &process_gt_to_hap2; convert->max_unpack |= BCF_UN_FMT; break;
+        case T_TBCSQ: fmt->handler = &process_tbcsq; fmt->destroy = &destroy_tbcsq; convert->max_unpack |= BCF_UN_FMT; break;
+        case T_LINE: fmt->handler = &process_line; convert->max_unpack |= BCF_UN_FMT; break;
+        case T_RSX: fmt->handler = &process_rsid_hex; break;
+        case T_VKX: fmt->handler = &process_variantkey_hex; break;
+        case T_PBINOM: fmt->handler = &process_pbinom; convert->max_unpack |= BCF_UN_FMT; break;
+        case T_NPASS: fmt->handler = &process_npass; fmt->destroy = &destroy_npass; break;
+        default: error("TODO: handler for type %d\n", fmt->type);
+    }
+    if ( key && fmt->type==T_INFO )
+    {
+        fmt->id = bcf_hdr_id2int(convert->header, BCF_DT_ID, key);
+        if ( !bcf_hdr_idinfo_exists(convert->header,BCF_HL_INFO,fmt->id) )
+        {
+            fmt->id = -1;
+            convert->undef_info_tag = strdup(key);
+        }
+    }
+    return fmt;
+}
+
+static int parse_subscript(char **p)
+{
+    char *q = *p;
+    if ( *q!='{' ) return -1;
+    q++;
+    while ( *q && *q!='}' && isdigit(*q) ) q++;
+    if ( *q!='}' ) return -1;
+    int idx = atoi((*p)+1);
+    *p = q+1;
+    return idx;
+}
+
+static char *parse_tag(convert_t *convert, char *p, int is_gtf)
+{
+    char *q = ++p;
+    while ( *q && (isalnum(*q) || *q=='_' || *q=='.') ) q++;
+    kstring_t str = {0,0,0};
+    if ( q-p==0 ) error("Could not parse format string: %s\n", convert->format_str);
+    kputsn(p, q-p, &str);
+    if ( is_gtf )
+    {
+        if ( !strcmp(str.s, "SAMPLE") ) register_tag(convert, "SAMPLE", is_gtf, T_SAMPLE);
+        else if ( !strcmp(str.s, "GT") ) register_tag(convert, "GT", is_gtf, T_GT);
+        else if ( !strcmp(str.s, "TGT") ) register_tag(convert, "GT", is_gtf, T_TGT);
+        else if ( !strcmp(str.s, "TBCSQ") )
+        {
+            fmt_t *fmt = register_tag(convert, "BCSQ", is_gtf, T_TBCSQ);
+            fmt->subscript = parse_subscript(&q);
+            if ( fmt->subscript==-1 )
+            {
+                if ( !strncmp(q,"{*}",3) ) { fmt->subscript = 0; q += 3; }
+            }
+            else fmt->subscript++;
+        }
+        else if ( !strcmp(str.s, "IUPACGT") ) register_tag(convert, "GT", is_gtf, T_IUPAC_GT);
+        else if ( !strcmp(str.s, "INFO") )
+        {
+            if ( *q!='/' )
+            {
+                int id = bcf_hdr_id2int(convert->header, BCF_DT_ID, str.s);
+                if ( bcf_hdr_idinfo_exists(convert->header,BCF_HL_INFO,id) )
+                    error("Could not parse format string \"%s\". Did you mean %%INFO/%s?\n", convert->format_str,str.s);
+                else
+                    error("Could not parse format string: %s\n", convert->format_str);
+            }
+            p = ++q;
+            str.l = 0;
+            while ( *q && (isalnum(*q) || *q=='_' || *q=='.') ) q++;
+            if ( q-p==0 ) error("Could not parse format string: %s\n", convert->format_str);
+            kputsn(p, q-p, &str);
+            fmt_t *fmt = register_tag(convert, str.s, is_gtf, T_INFO);
+            fmt->subscript = parse_subscript(&q);
+            _used_tags_add(convert,T_INFO,str.s);
+        }
+        else if ( !strcmp(str.s,"PBINOM") )
+        {
+            if ( *q!='(' ) error("Could not parse the expression: %s\n", convert->format_str);
+            p = ++q;
+            str.l = 0;
+            while ( *q && *q!=')' ) q++;
+            if ( q-p==0 ) error("Could not parse format string: %s\n", convert->format_str);
+            kputsn(p, q-p, &str);
+            register_tag(convert, str.s, is_gtf, T_PBINOM);
+            q++;
+        }
+        else if ( !strcmp(str.s,"N_PASS") )
+            error("N_PASS() must be placed outside the square brackets\n");
+        else
+        {
+            fmt_t *fmt = register_tag(convert, str.s, is_gtf, T_FORMAT);
+            fmt->subscript = parse_subscript(&q);
+        }
+    }
+    else
+    {
+        _SET_NON_FORMAT_TAGS(register_tag, str.s, convert, str.s, is_gtf)
+        else if ( !strcmp(str.s, "ALT") )
+        {
+            fmt_t *fmt = register_tag(convert, str.s, is_gtf, T_ALT);
+            fmt->subscript = parse_subscript(&q);
+        }
+        else if ( !strcmp(str.s, "_CHROM_POS_ID") ) register_tag(convert, str.s, is_gtf, T_CHROM_POS_ID);
+        else if ( !strcmp(str.s, "_GT_TO_PROB3") ) register_tag(convert, str.s, is_gtf, T_GT_TO_PROB3);
+        else if ( !strcmp(str.s, "_PL_TO_PROB3") ) register_tag(convert, str.s, is_gtf, T_PL_TO_PROB3);
+        else if ( !strcmp(str.s, "_GP_TO_PROB3") ) register_tag(convert, str.s, is_gtf, T_GP_TO_PROB3);
+        else if ( !strcmp(str.s, "_GT_TO_HAP") ) register_tag(convert, str.s, is_gtf, T_GT_TO_HAP);
+        else if ( !strcmp(str.s, "_GT_TO_HAP2") ) register_tag(convert, str.s, is_gtf, T_GT_TO_HAP2);
+        else if ( !strcmp(str.s, "RSX") ) register_tag(convert, str.s, is_gtf, T_RSX);
+        else if ( !strcmp(str.s, "VKX") ) register_tag(convert, str.s, is_gtf, T_VKX);
+        else if ( !strcmp(str.s,"PBINOM") ) error("Error: PBINOM() is currently supported only with FORMAT tags. (todo)\n");
+        else if ( !strcmp(str.s, "INFO") )
+        {
+            if ( *q=='/' )
+            {
+                p = ++q;
+                str.l = 0;
+                while ( *q && (isalnum(*q) || *q=='_' || *q=='.') ) q++;
+                if ( q-p==0 ) error("Could not parse format string: %s\n", convert->format_str);
+                kputsn(p, q-p, &str);
+                fmt_t *fmt = register_tag(convert, str.s, is_gtf, T_INFO);
+                fmt->subscript = parse_subscript(&q);
+                _used_tags_add(convert,T_INFO,str.s);
+            }
+            else
+                register_tag(convert, NULL, is_gtf, T_INFO);    // the whole INFO
+        }
+        else if ( !strcmp(str.s, "FORMAT") )
+             register_tag(convert, NULL, 0, T_FORMAT);
+        else if ( !strcmp(str.s,"N_PASS") )
+        {
+            if ( *q!='(' ) error("Could not parse the expression: %s\n", convert->format_str);
+            p = ++q;
+            str.l = 0;
+            int nopen = 1;
+            while ( *q && nopen )
+            {
+                if ( *q=='(' ) nopen++;
+                else if ( *q==')' ) nopen--;
+                q++;
+            }
+            if ( q-p==0 || nopen ) error("Could not parse format string: %s\n", convert->format_str);
+            kputsn(p, q-p-1, &str);
+            register_tag(convert, str.s, is_gtf, T_NPASS);
+        }
+        else
+        {
+            fmt_t *fmt = register_tag(convert, str.s, is_gtf, T_INFO);
+            fmt->subscript = parse_subscript(&q);
+            _used_tags_add(convert,T_INFO,str.s);
+        }
+    }
+    free(str.s);
+    return q;
+}
+
+static char *parse_sep(convert_t *convert, char *p, int is_gtf)
+{
+    char *q = p;
+    kstring_t str = {0,0,0};
+    while ( *q && *q!='[' && *q!=']' && *q!='%' )
+    {
+        if ( *q=='\\' )
+        {
+            q++;
+            if ( *q=='n' ) kputc('\n', &str);
+            else if ( *q=='t' ) kputc('\t', &str);
+            else kputc(*q, &str);
+        }
+        else kputc(*q, &str);
+        q++;
+    }
+    if ( !str.l ) error("Could not parse format string: %s\n", convert->format_str);
+    register_tag(convert, str.s, is_gtf, T_SEP);
+    free(str.s);
+    return q;
+}
+
+convert_t *convert_init(bcf_hdr_t *hdr, int *samples, int nsamples, const char *format_str)
+{
+    convert_t *convert = (convert_t*) calloc(1,sizeof(convert_t));
+    convert->header = hdr;
+    convert->format_str = strdup(format_str);
+    convert->max_unpack = BCF_UN_STR;
+    convert->used_tags_hash = khash_str2int_init();
+
+    int i, is_gtf = 0;
+    char *p = convert->format_str;
+    while ( *p )
+    {
+        //fprintf(bcftools_stderr,"<%s>\n", p);
+        switch (*p)
+        {
+            case '[': is_gtf = 1; p++; break;
+            case ']': is_gtf = 0; register_tag(convert, NULL, 0, T_SEP); p++; break;
+            case '%': p = parse_tag(convert, p, is_gtf); break;
+            default:  p = parse_sep(convert, p, is_gtf); break;
+        }
+    }
+    if ( is_gtf )
+        error("Could not parse the format string, missing the square bracket \"]\": %s\n", convert->format_str);
+
+    if ( nsamples )
+    {
+        convert->nsamples = nsamples;
+        convert->samples = (int*) malloc(sizeof(int)*nsamples);
+        for (i=0; i<convert->nsamples; i++) convert->samples[i] = samples[i];
+    }
+    else
+    {
+        convert->nsamples = bcf_hdr_nsamples(convert->header);
+        convert->samples = (int*) malloc(sizeof(int)*convert->nsamples);
+        for (i=0; i<convert->nsamples; i++) convert->samples[i] = i;
+    }
+    return convert;
+}
+
+void convert_destroy(convert_t *convert)
+{
+    int i;
+    for (i=0; i<convert->nfmt; i++)
+    {
+        if ( convert->fmt[i].destroy ) convert->fmt[i].destroy(convert->fmt[i].usr);
+        free(convert->fmt[i].key);
+    }
+    if ( convert->nused_tags )
+    {
+        for (i=0; i<convert->nused_tags; i++) free(convert->used_tags_list[i]);
+        free(convert->used_tags_list);
+    }
+    khash_str2int_destroy(convert->used_tags_hash);
+    free(convert->fmt);
+    free(convert->undef_info_tag);
+    free(convert->dat);
+    free(convert->samples);
+    free(convert->format_str);
+    free(convert);
+}
+
+
+int convert_header(convert_t *convert, kstring_t *str)
+{
+    int i, icol = 0, l_ori = str->l;
+    bcf_hdr_t *hdr = convert->header;
+
+    // Supress the header output if LINE is present
+    for (i=0; i<convert->nfmt; i++)
+        if ( convert->fmt[i].type == T_LINE ) break;
+    if ( i!=convert->nfmt )
+        return str->l - l_ori;
+
+    kputs("# ", str);
+    for (i=0; i<convert->nfmt; i++)
+    {
+        // Genotype fields
+        if ( convert->fmt[i].is_gt_field )
+        {
+            int j = i, js, k;
+            while ( convert->fmt[j].is_gt_field ) j++;
+            for (js=0; js<convert->nsamples; js++)
+            {
+                int ks = convert->samples[js];
+                for (k=i; k<j; k++)
+                {
+                    if ( convert->fmt[k].type == T_SEP )
+                    {
+                        if ( convert->fmt[k].key ) kputs(convert->fmt[k].key, str);
+                    }
+                    else if ( convert->fmt[k].type == T_SAMPLE )
+                        ksprintf(str, "[%d]%s", ++icol, convert->fmt[k].key);
+                    else
+                        ksprintf(str, "[%d]%s:%s", ++icol, hdr->samples[ks], convert->fmt[k].key);
+                }
+            }
+            i = j-1;
+            continue;
+        }
+        // Fixed fields
+        if ( convert->fmt[i].type == T_SEP )
+        {
+            if ( convert->fmt[i].key ) kputs(convert->fmt[i].key, str);
+            continue;
+        }
+        ksprintf(str, "[%d]%s", ++icol, convert->fmt[i].key);
+    }
+    return str->l - l_ori;
+}
+
+int convert_line(convert_t *convert, bcf1_t *line, kstring_t *str)
+{
+    if ( !convert->allow_undef_tags && convert->undef_info_tag )
+    {
+        kstring_t msg = {0,0,0};
+        ksprintf(&msg,"Error: no such tag defined in the VCF header: INFO/%s", convert->undef_info_tag);
+
+        int hdr_id = bcf_hdr_id2int(convert->header,BCF_DT_ID,convert->undef_info_tag);
+        if ( hdr_id>=0 && bcf_hdr_idinfo_exists(convert->header,BCF_HL_FMT,hdr_id) )
+            ksprintf(&msg,". FORMAT fields must be enclosed in square brackets, e.g. \"[ %%%s]\"", convert->undef_info_tag);
+        error("%s\n", msg.s);
+    }
+
+    int l_ori = str->l;
+    bcf_unpack(line, convert->max_unpack);
+
+    int i, ir;
+    str->l = 0;
+    for (i=0; i<convert->nfmt; i++)
+    {
+        // Genotype fields.
+        if ( convert->fmt[i].is_gt_field )
+        {
+            int j = i, js, k;
+            while ( j<convert->nfmt && convert->fmt[j].is_gt_field )
+            {
+                convert->fmt[j].ready = 0;
+                j++;
+            }
+            for (js=0; js<convert->nsamples; js++)
+            {
+                // Skip samples when filtering was requested
+                int ks = convert->samples[js];
+                if ( convert->subset_samples && *convert->subset_samples && !(*convert->subset_samples)[ks] ) continue;
+
+                // Here comes a hack designed for TBCSQ. When running on large files,
+                // such as 1000GP, there are too many empty fields in the output and
+                // it's very very slow. Therefore in case the handler does not add
+                // anything to the string, we trim all genotype fields enclosed in square
+                // brackets here. This may be changed in future, time will show...
+                size_t l_start = str->l;
+
+                for (k=i; k<j; k++)
+                {
+                    if ( convert->fmt[k].type == T_MASK )
+                    {
+                        for (ir=0; ir<convert->nreaders; ir++)
+                            kputc(bcf_sr_has_line(convert->readers,ir)?'1':'0', str);
+                    }
+                    else if ( convert->fmt[k].handler )
+                    {
+                        size_t l = str->l;
+                        convert->fmt[k].handler(convert, line, &convert->fmt[k], ks, str);
+                        if ( l==str->l ) { str->l = l_start; break; }  // only TBCSQ does this
+                    }
+                }
+            }
+            i = j-1;
+            continue;
+        }
+        // Fixed fields
+        if ( convert->fmt[i].type == T_MASK )
+        {
+            for (ir=0; ir<convert->nreaders; ir++)
+                kputc(bcf_sr_has_line(convert->readers,ir)?'1':'0', str);
+        }
+        else if ( convert->fmt[i].handler )
+            convert->fmt[i].handler(convert, line, &convert->fmt[i], -1, str);
+
+    }
+    return str->l - l_ori;
+}
+
+int convert_set_option(convert_t *convert, enum convert_option opt, ...)
+{
+    int ret = 0;
+    va_list args;
+
+    va_start(args, opt);
+    switch (opt)
+    {
+        case allow_undef_tags:
+            convert->allow_undef_tags = va_arg(args, int);
+            break;
+        case subset_samples:
+            convert->subset_samples = va_arg(args, uint8_t**);
+            break;
+        default:
+            ret = -1;
+    }
+    va_end(args);
+    return ret;
+}
+
+int convert_max_unpack(convert_t *convert)
+{
+    return convert->max_unpack;
+}
+
+int convert_is_tag_used(convert_t *convert, char *tag)
+{
+    return khash_str2int_has_key(convert->used_tags_hash, tag);
+}
+const char **convert_list_used_tags(convert_t *convert, int *ntags)
+{
+    *ntags = convert->nused_tags;
+    return (const char **)convert->used_tags_list;
+}
+
diff --git a/bcftools/convert.h b/bcftools/convert.h
new file mode 100644
index 0000000..5bbbc2c
--- /dev/null
+++ b/bcftools/convert.h
@@ -0,0 +1,47 @@
+/*  convert.h -- functions for converting between VCF/BCF and related formats.
+
+    Copyright (C) 2014-2021 Genome Research Ltd.
+
+    Author: Petr Danecek <pd3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.  */
+
+#ifndef __CONVERT_H__
+#define __CONVERT_H__
+
+#include <htslib/vcf.h>
+
+typedef struct _convert_t convert_t;
+enum convert_option
+{
+    allow_undef_tags,
+    subset_samples,
+};
+
+convert_t *convert_init(bcf_hdr_t *hdr, int *samples, int nsamples, const char *str);
+void convert_destroy(convert_t *convert);
+int convert_set_option(convert_t *convert, enum convert_option opt, ...);
+int convert_header(convert_t *convert, kstring_t *str);
+int convert_line(convert_t *convert, bcf1_t *rec, kstring_t *str);
+int convert_max_unpack(convert_t *convert);
+int convert_is_tag_used(convert_t *convert, char *tag);
+const char **convert_list_used_tags(convert_t *convert, int *ntags);
+
+#endif
+
diff --git a/bcftools/csq.c b/bcftools/csq.c
new file mode 100644
index 0000000..de0d7a9
--- /dev/null
+++ b/bcftools/csq.c
@@ -0,0 +1,4395 @@
+/* The MIT License
+
+   Copyright (c) 2016-2021 Genome Research Ltd.
+
+   Author: Petr Danecek <pd3@sanger.ac.uk>
+   
+   Permission is hereby granted, free of charge, to any person obtaining a copy
+   of this software and associated documentation files (the "Software"), to deal
+   in the Software without restriction, including without limitation the rights
+   to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+   copies of the Software, and to permit persons to whom the Software is
+   furnished to do so, subject to the following conditions:
+   
+   The above copyright notice and this permission notice shall be included in
+   all copies or substantial portions of the Software.
+   
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+   IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+   FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+   AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+   LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+   OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+   THE SOFTWARE.
+
+ */
+/*
+    Things that would be nice to have
+        - dynamic N_REF_PAD
+        - for stop-lost events (also in frameshifts) report the number of truncated aa's
+        - memory could be greatly reduced by indexing gff (but it is quite compact already)
+        - deletions that go beyond transcript boundaries are not checked at sequence level
+            - alloc tscript->ref in hap_finalize, introduce fa_off_beg:16,fa_off_end:16
+            - see test/csq/ENST00000573314/insertion-overlap.vcf #1476288882
+
+    Read about transcript types here
+        http://vega.sanger.ac.uk/info/about/gene_and_transcript_types.html
+        http://www.ensembl.org/info/genome/variation/predicted_data.html
+        http://www.gencodegenes.org/gencode_biotypes.html
+
+    List of supported biotypes
+        antisense
+        IG_C_gene
+        IG_D_gene
+        IG_J_gene
+        IG_LV_gene
+        IG_V_gene
+        lincRNA
+        macro_lncRNA
+        miRNA
+        misc_RNA
+        Mt_rRNA
+        Mt_tRNA
+        polymorphic_pseudogene
+        processed_transcript
+        protein_coding
+        ribozyme
+        rRNA
+        sRNA
+        scRNA
+        scaRNA
+        sense_intronic
+        sense_overlapping
+        snRNA
+        snoRNA
+        TR_C_gene
+        TR_D_gene
+        TR_J_gene
+        TR_V_gene
+
+    The gff parsing logic
+        We collect features such by combining gff lines A,B,C as follows:
+            A .. gene line with a supported biotype
+                    A.ID=~/^gene:/
+
+            B .. transcript line referencing A with supported biotype
+                    B.ID=~/^transcript:/ && B.Parent=~/^gene:A.ID/
+
+            C .. corresponding CDS, exon, and UTR lines:
+                    C[3] in {"CDS","exon","three_prime_UTR","five_prime_UTR"} && C.Parent=~/^transcript:B.ID/ 
+
+        For coding biotypes ("protein_coding" or "polymorphic_pseudogene") the
+        complete chain link C -> B -> A is required. For the rest, link B -> A suffices.
+        
+                
+    The supported consequence types, sorted by impact:
+        splice_acceptor_variant .. end region of an intron changed (2bp at the 3' end of an intron)
+        splice_donor_variant    .. start region of an intron changed (2bp at the 5' end of an intron)
+        stop_gained             .. DNA sequence variant resulting in a stop codon
+        frameshift_variant      .. number of inserted/deleted bases not a multiple of three, disrupted translational frame
+        stop_lost               .. elongated transcript, stop codon changed
+        start_lost              .. the first codon changed
+        inframe_altering        .. combination of indels leading to unchanged reading frame and length
+        inframe_insertion       .. inserted coding sequence, unchanged reading frame
+        inframe_deletion        .. deleted coding sequence, unchanged reading frame
+        missense_variant        .. amino acid (aa) change, unchanged length
+        splice_region_variant   .. change within 1-3 bases of the exon or 3-8 bases of the intron
+        synonymous_variant      .. DNA sequence variant resulting in no amino acid change
+        stop_retained_variant   .. different stop codon
+        start_retained_variant  .. start codon retained by indel realignment
+        non_coding_variant      .. variant in non-coding sequence, such as RNA gene
+        5_prime_UTR_variant
+        3_prime_UTR_variant
+        intron_variant          .. reported only if none of the above
+        intergenic_variant      .. reported only if none of the above
+
+
+    The annotation algorithm.
+        The algorithm checks if the variant falls in a region of a supported type. The
+        search is performed in the following order, until a match is found:
+            1. idx_cds(gf_cds_t) - lookup CDS by position, create haplotypes, call consequences
+            2. idx_utr(gf_utr_t) - check UTR hits
+            3. idx_exon(gf_exon_t) - check for splice variants
+            4. idx_tscript(tscript_t) - check for intronic variants, RNAs, etc.
+
+        These regidx indexes are created by parsing a gff3 file as follows:
+            1.  create the array "ftr" of all UTR, CDS, exons. This will be
+            processed later and pruned based on transcript types we want to keep.
+            In the same go, create the hash "id2tr" of transcripts to keep
+            (based on biotype) which maps from transcript_id to a transcript. At
+            the same time also build the hash "gid2gene" which maps from gene_id to
+            gf_gene_t pointer.
+            
+            2.  build "idx_cds", "idx_tscript", "idx_utr" and "idx_exon" indexes.
+            Use only features from "ftr" which are present in "id2tr".
+
+            3.  clean data that won't be needed anymore: ftr, id2tr, gid2gene.
+        
+    Data structures.
+        idx_cds, idx_utr, idx_exon, idx_tscript:
+            as described above, regidx structures for fast lookup of exons/transcripts
+            overlapping a region, the payload is a pointer to tscript.cds
+*/
+ 
+#include <stdio.h>
+#include <stdlib.h>
+#include <assert.h>
+#include <getopt.h>
+#include <math.h>
+#include <inttypes.h>
+#include <htslib/hts.h>
+#include <htslib/vcf.h>
+#include <htslib/synced_bcf_reader.h>
+#include <htslib/khash.h>
+#include <htslib/khash_str2int.h>
+#include <htslib/kseq.h>
+#include <htslib/faidx.h>
+#include <errno.h>
+#include <unistd.h>
+#include <ctype.h>
+#include "bcftools.h"
+#include "filter.h"
+#include "regidx.h"
+#include "kheap.h"
+#include "smpl_ilist.h"
+#include "rbuf.h"
+
+#ifndef __FUNCTION__
+#  define __FUNCTION__ __func__
+#endif
+
+// Logic of the filters: include or exclude sites which match the filters?
+#define FLT_INCLUDE 1
+#define FLT_EXCLUDE 2
+
+// Definition of splice_region, splice_acceptor and splice_donor
+#define N_SPLICE_DONOR         2      
+#define N_SPLICE_REGION_EXON   3 
+#define N_SPLICE_REGION_INTRON 8 
+
+#define N_REF_PAD 10    // number of bases to avoid boundary effects
+
+#define STRAND_REV 0
+#define STRAND_FWD 1
+
+#define TRIM_NONE   0
+#define TRIM_5PRIME 1
+#define TRIM_3PRIME 2
+
+// How to treat phased/unphased genotypes
+#define PHASE_REQUIRE 0     // --phase r
+#define PHASE_MERGE   1     // --phase m
+#define PHASE_AS_IS   2     // --phase a
+#define PHASE_SKIP    3     // --phase s
+#define PHASE_NON_REF 4     // --phase R
+#define PHASE_DROP_GT 5     // --samples -
+
+// Node types in the haplotype tree
+#define HAP_CDS   0
+#define HAP_ROOT  1 
+#define HAP_SSS   2     // start/stop/splice
+
+#define CSQ_PRINTED_UPSTREAM    (1<<0)
+#define CSQ_SYNONYMOUS_VARIANT  (1<<1)
+#define CSQ_MISSENSE_VARIANT    (1<<2)
+#define CSQ_STOP_LOST           (1<<3)
+#define CSQ_STOP_GAINED         (1<<4)
+#define CSQ_INFRAME_DELETION    (1<<5)
+#define CSQ_INFRAME_INSERTION   (1<<6)
+#define CSQ_FRAMESHIFT_VARIANT  (1<<7)
+#define CSQ_SPLICE_ACCEPTOR     (1<<8)
+#define CSQ_SPLICE_DONOR        (1<<9)
+#define CSQ_START_LOST          (1<<10)
+#define CSQ_SPLICE_REGION       (1<<11)
+#define CSQ_STOP_RETAINED       (1<<12)
+#define CSQ_UTR5                (1<<13)
+#define CSQ_UTR3                (1<<14)
+#define CSQ_NON_CODING          (1<<15)
+#define CSQ_INTRON              (1<<16)
+//#define CSQ_INTERGENIC          (1<<17)
+#define CSQ_INFRAME_ALTERING    (1<<18)
+#define CSQ_UPSTREAM_STOP       (1<<19)     // adds * in front of the csq string
+#define CSQ_INCOMPLETE_CDS      (1<<20)     // to remove START/STOP in incomplete CDS, see ENSG00000173376/synon.vcf
+#define CSQ_CODING_SEQUENCE     (1<<21)     // cannot tell exactly what it is, but it does affect the coding sequence
+#define CSQ_ELONGATION          (1<<22)     // symbolic insertion
+#define CSQ_START_RETAINED      (1<<23)
+
+// Haplotype-aware consequences, printed in one vcf record only, the rest has a reference @12345
+#define CSQ_COMPOUND (CSQ_SYNONYMOUS_VARIANT|CSQ_MISSENSE_VARIANT|CSQ_STOP_LOST|CSQ_STOP_GAINED| \
+                      CSQ_INFRAME_DELETION|CSQ_INFRAME_INSERTION|CSQ_FRAMESHIFT_VARIANT| \
+                      CSQ_START_LOST|CSQ_STOP_RETAINED|CSQ_INFRAME_ALTERING|CSQ_INCOMPLETE_CDS| \
+                      CSQ_UPSTREAM_STOP|CSQ_START_RETAINED)
+#define CSQ_START_STOP          (CSQ_STOP_LOST|CSQ_STOP_GAINED|CSQ_STOP_RETAINED|CSQ_START_LOST|CSQ_START_RETAINED)
+
+#define CSQ_PRN_STRAND(csq)     ((csq)&CSQ_COMPOUND && !((csq)&(CSQ_SPLICE_ACCEPTOR|CSQ_SPLICE_DONOR|CSQ_SPLICE_REGION)))
+#define CSQ_PRN_TSCRIPT         (~(CSQ_INTRON|CSQ_NON_CODING))
+#define CSQ_PRN_BIOTYPE         CSQ_NON_CODING
+
+// see kput_vcsq()
+const char *csq_strings[] = 
+{
+    NULL, 
+    "synonymous", 
+    "missense", 
+    "stop_lost", 
+    "stop_gained", 
+    "inframe_deletion", 
+    "inframe_insertion", 
+    "frameshift", 
+    "splice_acceptor", 
+    "splice_donor", 
+    "start_lost", 
+    "splice_region", 
+    "stop_retained", 
+    "5_prime_utr", 
+    "3_prime_utr", 
+    "non_coding", 
+    "intron", 
+    "intergenic",
+    "inframe_altering",
+    NULL,
+    NULL,
+    "coding_sequence",
+    "feature_elongation",
+    "start_retained"
+};
+
+
+// GFF line types
+#define GFF_TSCRIPT_LINE 1
+#define GFF_GENE_LINE    2
+
+
+/* 
+    Genomic features, for fast lookup by position to overlapping features
+*/
+#define GF_coding_bit 6
+#define GF_is_coding(x) ((x) & (1<<GF_coding_bit))
+#define GF_MT_rRNA                       1                      // non-coding: 1, 2, ...
+#define GF_MT_tRNA                       2
+#define GF_lincRNA                       3
+#define GF_miRNA                         4
+#define GF_MISC_RNA                      5
+#define GF_rRNA                          6
+#define GF_snRNA                         7
+#define GF_snoRNA                        8
+#define GF_PROCESSED_TRANSCRIPT          9
+#define GF_ANTISENSE                    10
+#define GF_macro_lncRNA                 11
+#define GF_ribozyme                     12
+#define GF_sRNA                         13
+#define GF_scRNA                        14
+#define GF_scaRNA                       15
+#define GF_SENSE_INTRONIC               16
+#define GF_SENSE_OVERLAPPING            17
+#define GF_PSEUDOGENE                   18
+#define GF_PROCESSED_PSEUDOGENE         19
+#define GF_ARTIFACT                     20
+#define GF_IG_PSEUDOGENE                21
+#define GF_IG_C_PSEUDOGENE              22
+#define GF_IG_J_PSEUDOGENE              23
+#define GF_IG_V_PSEUDOGENE              24
+#define GF_TR_V_PSEUDOGENE              25
+#define GF_TR_J_PSEUDOGENE              26
+#define GF_MT_tRNA_PSEUDOGENE           27
+#define GF_misc_RNA_PSEUDOGENE          28
+#define GF_miRNA_PSEUDOGENE             29
+#define GF_RIBOZYME                     30
+#define GF_RETAINED_INTRON              31
+#define GF_RETROTRANSPOSED              32
+#define GF_tRNA_PSEUDOGENE              33
+#define GF_TRANSCRIBED_PROCESSED_PSEUDOGENE     34
+#define GF_TRANSCRIBED_UNPROCESSED_PSEUDOGENE   35
+#define GF_TRANSCRIBED_UNITARY_PSEUDOGENE       36
+#define GF_TRANSLATED_UNPROCESSED_PSEUDOGENE    37
+#define GF_TRANSLATED_PROCESSED_PSEUDOGENE      38
+#define GF_KNOWN_NCRNA                          39
+#define GF_UNITARY_PSEUDOGENE                   40
+#define GF_UNPROCESSED_PSEUDOGENE               41
+#define GF_LRG_GENE                             42
+#define GF_3PRIME_OVERLAPPING_ncRNA             43
+#define GF_DISRUPTED_DOMAIN                     44
+#define GF_vaultRNA                             45
+#define GF_BIDIRECTIONAL_PROMOTER_lncRNA        46
+#define GF_AMBIGUOUS_ORF                        47
+#define GF_PROTEIN_CODING               (1|(1<<GF_coding_bit))  // coding: 65, 66, ...
+#define GF_POLYMORPHIC_PSEUDOGENE       (2|(1<<GF_coding_bit))
+#define GF_IG_C                         (3|(1<<GF_coding_bit))
+#define GF_IG_D                         (4|(1<<GF_coding_bit))
+#define GF_IG_J                         (5|(1<<GF_coding_bit))
+#define GF_IG_LV                        (6|(1<<GF_coding_bit))
+#define GF_IG_V                         (7|(1<<GF_coding_bit))
+#define GF_TR_C                         (8|(1<<GF_coding_bit))
+#define GF_TR_D                         (9|(1<<GF_coding_bit))
+#define GF_TR_J                        (10|(1<<GF_coding_bit))
+#define GF_TR_V                        (11|(1<<GF_coding_bit))
+#define GF_NMD                         (12|(1<<GF_coding_bit))
+#define GF_NON_STOP_DECAY              (13|(1<<GF_coding_bit))
+#define GF_CDS      ((1<<(GF_coding_bit+1))+1)                  // special types: 129, 130, ...
+#define GF_EXON     ((1<<(GF_coding_bit+1))+2)
+#define GF_UTR3     ((1<<(GF_coding_bit+1))+3)
+#define GF_UTR5     ((1<<(GF_coding_bit+1))+4)
+// GF_MAX = (1<<30)-1, see hap_node_t
+
+#define CDS_PHASE_UNKN 3
+typedef struct _tscript_t tscript_t;
+typedef struct
+{
+    tscript_t *tr;      // transcript
+    uint32_t beg;       // the start coordinate of the CDS (on the reference strand, 0-based)
+    uint32_t pos;       // 0-based index of the first exon base within the transcript (only to
+                        //  update hap_node_t.sbeg in hap_init, could be calculated on the fly)
+    uint32_t len;       // exon length
+    uint32_t icds:30,   // exon index within the transcript
+             phase:2;   // offset of the CDS: 0,1,2 or 3 for unknown
+}
+gf_cds_t;
+typedef struct
+{
+    char *name;           // human readable name, e.g. ORF45
+    uint32_t iseq;
+}
+gf_gene_t;
+typedef struct
+{
+    uint32_t beg,end;
+    tscript_t *tr;
+}
+gf_exon_t;
+typedef enum { prime3, prime5 } utr_t;
+typedef struct
+{
+    utr_t which;
+    uint32_t beg,end;
+    tscript_t *tr;
+}
+gf_utr_t;
+
+
+/*
+    Structures related to VCF output:
+
+    vcsq_t
+        information required to assemble consequence lines such as "inframe_deletion|XYZ|ENST01|+|5TY>5I|121ACG>A+124TA>T"
+
+    vrec_t
+        single VCF record and csq tied to this record. (Haplotype can have multiple
+        consequences in several VCF records. Each record can have multiple consequences
+        from multiple haplotypes.)
+
+    csq_t
+        a top-level consequence tied to a haplotype
+
+    vbuf_t
+    pos2vbuf
+        VCF records with the same position clustered together for a fast lookup via pos2vbuf
+*/
+typedef struct _vbuf_t vbuf_t;
+typedef struct _vcsq_t vcsq_t;
+struct _vcsq_t
+{
+    uint32_t strand:1,
+             type:31;   // one of CSQ_* types
+    uint32_t trid;
+    uint32_t vcf_ial;
+    uint32_t biotype;   // one of GF_* types
+    char *gene;         // gene name
+    bcf1_t *ref;        // if type&CSQ_PRINTED_UPSTREAM, ref consequence "@1234"
+    kstring_t vstr;     // variant string, eg 5TY>5I|121ACG>A+124TA>T
+};
+typedef struct
+{
+    bcf1_t *line;
+    uint32_t *fmt_bm;   // bitmask of sample consequences with first/second haplotype interleaved
+    uint32_t nfmt:4,    // the bitmask size (the number of integers per sample)
+             nvcsq:28, mvcsq;
+    vcsq_t *vcsq;       // there can be multiple consequences for a single VCF record
+}
+vrec_t;
+typedef struct
+{
+    uint32_t pos;
+    vrec_t *vrec;   // vcf line that this csq is tied to; needed when printing haplotypes (hap_stage_vcf)
+    int idx;        // 0-based index of the csq at the VCF line, for FMT/BCSQ
+    vcsq_t type;
+}
+csq_t;
+struct _vbuf_t
+{
+    vrec_t **vrec;   // buffer of VCF lines with the same position
+    int n, m;
+    uint32_t keep_until;    // the maximum transcript end position
+};
+KHASH_MAP_INIT_INT(pos2vbuf, vbuf_t*)
+
+
+/*
+    Structures related to haplotype-aware consequences in coding regions
+
+    hap_node_t
+        node of a haplotype tree. Each transcript has one tree
+
+    tscript_t
+        despite its general name, it is intended for coding transcripts only
+
+    hap_t
+    hstack_t
+        for traversal of the haplotype tree and braking combined
+        consequences into independent parts
+*/
+typedef struct _hap_node_t hap_node_t;
+struct _hap_node_t
+{
+    char *seq;          // cds segment [parent_node,this_node)
+    char *var;          // variant "ref>alt"
+    uint32_t type:2,    // HAP_ROOT or HAP_CDS
+             csq:30;    // this node's consequence
+    int dlen;           // alt minus ref length: <0 del, >0 ins, 0 substitution
+    uint32_t rbeg;      // variant's VCF position (0-based, inclusive)
+    int32_t rlen;       // variant's rlen; alen=rlen+dlen; fake for non CDS types
+    uint32_t sbeg;      // variant's position on the spliced reference transcript (0-based, inclusive, N_REF_PAD not included)
+    uint32_t icds;      // which exon does this node's variant overlaps
+    hap_node_t **child, *prev;  // children haplotypes and previous coding node
+    int nchild, mchild;
+    bcf1_t *cur_rec, *rec;      // current VCF record and node's VCF record
+    int vcf_ial;                // which VCF allele generated this node
+    uint32_t nend;              // number of haplotypes ending in this node
+    int *cur_child, mcur_child; // mapping from the allele to the currently active child
+    csq_t *csq_list;            // list of haplotype's consequences, broken by position (each corresponds to a VCF record)
+    int ncsq_list, mcsq_list;
+};
+struct _tscript_t
+{
+    uint32_t id;        // transcript id
+    uint32_t beg,end;   // transcript's beg and end coordinate (ref strand, 0-based, inclusive)
+    uint32_t strand:1,  // STRAND_REV or STRAND_FWD
+             ncds:31,   // number of exons
+             mcds;
+    gf_cds_t **cds;     // ordered list of exons
+    char *ref;          // reference sequence, padded with N_REF_PAD bases on both ends
+    char *sref;         // spliced reference sequence, padded with N_REF_PAD bases on both ends
+    hap_node_t *root;   // root of the haplotype tree
+    hap_node_t **hap;   // pointer to haplotype leaves, two for each sample
+    int nhap, nsref;    // number of haplotypes and length of sref, including 2*N_REF_PAD
+    uint32_t trim:2,    // complete, 5' or 3' trimmed, see TRIM_* types
+             type:30;   // one of GF_* types
+    gf_gene_t *gene;
+};
+static inline int cmp_tscript(tscript_t **a, tscript_t **b)
+{
+    return ( (*a)->end  < (*b)->end ) ? 1 : 0;
+}
+KHEAP_INIT(trhp, tscript_t*, cmp_tscript)
+typedef khp_trhp_t tr_heap_t;
+typedef struct
+{
+    hap_node_t *node;   // current node
+    int ichild;         // current child in the active node
+    int dlen;           // total dlen, from the root to the active node
+    size_t slen;        // total sequence length, from the root to the active node
+}
+hstack_t;
+typedef struct
+{
+    int mstack;
+    hstack_t *stack;
+    tscript_t *tr;      // tr->ref: spliced transcript on ref strand
+    kstring_t sseq;     // spliced haplotype sequence on ref strand
+    kstring_t tseq;     // the variable part of translated haplotype transcript, coding strand
+    kstring_t tref;     // the variable part of translated reference transcript, coding strand
+    uint32_t sbeg;      // stack's sbeg, for cases first node's type is HAP_SSS
+    int upstream_stop;
+}
+hap_t;
+
+
+/*
+    Helper structures, only for initialization
+    
+    ftr_t
+        temporary list of all exons, CDS, UTRs 
+*/
+KHASH_MAP_INIT_INT(int2tscript, tscript_t*)
+KHASH_MAP_INIT_INT(int2gene, gf_gene_t*)
+typedef struct
+{
+    int type;       // GF_CDS, GF_EXON, GF_5UTR, GF_3UTR
+    uint32_t beg;
+    uint32_t end;
+    uint32_t trid;
+    uint32_t strand:1;   // STRAND_REV,STRAND_FWD
+    uint32_t phase:2;    // 0, 1, 2, or 3 for unknown
+    uint32_t iseq:29;
+}
+ftr_t;
+/*
+    Mapping from GFF ID string (such as ENST00000450305 or Zm00001d027230_P001)
+    to integer id.  To keep the memory requirements low, the original version
+    relied on IDs in the form of a string prefix and a numerical id.  However,
+    it turns out that this assumption is not valid for some ensembl GFFs, see
+    for example Zea_mays.AGPv4.36.gff3.gz
+ */
+typedef struct
+{
+    void *str2id;       // khash_str2int
+    int nstr, mstr;
+    char **str;         // numeric id to string
+}
+id_tbl_t;
+typedef struct
+{
+    // all exons, CDS, UTRs
+    ftr_t *ftr;
+    int nftr, mftr;
+
+    // mapping from gene id to gf_gene_t
+    kh_int2gene_t *gid2gene;
+
+    // mapping from transcript id to tscript, for quick CDS anchoring
+    kh_int2tscript_t *id2tr;
+
+    // sequences
+    void *seq2int;  // str2int hash
+    char **seq;
+    int nseq, mseq;
+
+    // ignored biotypes
+    void *ignored_biotypes;
+
+    id_tbl_t gene_ids;   // temporary table for mapping between gene id (eg. Zm00001d027245) and a numeric idx
+}
+aux_t;
+
+typedef struct _args_t
+{
+    // the main regidx lookups, from chr:beg-end to overlapping features and
+    // index iterator
+    regidx_t *idx_cds, *idx_utr, *idx_exon, *idx_tscript;
+    regitr_t *itr;
+
+    // temporary structures, deleted after initializtion
+    aux_t init;
+
+    // text tab-delimited output (out) or vcf/bcf output (out_fh)
+    FILE *out;
+    htsFile *out_fh;
+
+    // vcf
+    bcf_srs_t *sr;
+    bcf_hdr_t *hdr;
+    int hdr_nsmpl;          // actual number of samples in the vcf, for bcf_update_format_values()
+
+    // include or exclude sites which match the filters
+    filter_t *filter;
+    char *filter_str;
+    int filter_logic;       // FLT_INCLUDE or FLT_EXCLUDE
+
+    // samples to process
+    int sample_is_file;
+    char *sample_list;
+    smpl_ilist_t *smpl;
+
+    char *outdir, **argv, *fa_fname, *gff_fname, *output_fname;
+    char *bcsq_tag;
+    int argc, output_type, clevel;
+    int phase, verbosity, local_csq, record_cmd_line;
+    int ncsq2_max, nfmt_bcsq;   // maximum number of csq per site that can be accessed from FORMAT/BCSQ (*2 and 1 bit skipped to avoid BCF missing values)
+    int ncsq2_small_warned;
+    int brief_predictions;
+    
+    int rid;                    // current chromosome
+    tr_heap_t *active_tr;       // heap of active transcripts for quick flushing
+    hap_t *hap;                 // transcript haplotype recursion
+    vbuf_t **vcf_buf;           // buffered VCF lines to annotate with CSQ and flush
+    rbuf_t vcf_rbuf;            // round buffer indexes to vcf_buf
+    kh_pos2vbuf_t *pos2vbuf;    // fast lookup of buffered lines by position
+    tscript_t **rm_tr;          // buffer of transcripts to clean
+    int nrm_tr, mrm_tr;
+    csq_t *csq_buf;             // pool of csq not managed by hap_node_t, i.e. non-CDS csqs
+    int ncsq_buf, mcsq_buf;
+    id_tbl_t tscript_ids;       // mapping between transcript id (eg. Zm00001d027245_T001) and a numeric idx
+    int force;                  // force run under various conditions. Currently only to skip out-of-phase transcripts
+    int n_threads;              // extra compression/decompression threads
+
+    faidx_t *fai;
+    kstring_t str, str2;
+    int32_t *gt_arr, mgt_arr;
+}
+args_t;
+
+// AAA, AAC, ...
+const char *gencode = "KNKNTTTTRSRSIIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVV*Y*YSSSS*CWCLFLF";
+const uint8_t nt4[] =
+{
+    4,4,4,4, 4,4,4,4, 4,4,4,4, 4,4,4,4,
+    4,4,4,4, 4,4,4,4, 4,4,4,4, 4,4,4,4,
+    4,4,4,4, 4,4,4,4, 4,4,4,4, 4,4,4,4,
+    4,4,4,4, 4,4,4,4, 4,4,4,4, 4,4,4,4,
+    4,0,4,1, 4,4,4,2, 4,4,4,4, 4,4,4,4,
+    4,4,4,4, 3,4,4,4, 4,4,4,4, 4,4,4,4,
+    4,0,4,1, 4,4,4,2, 4,4,4,4, 4,4,4,4,
+    4,4,4,4, 3
+};
+const uint8_t cnt4[] =
+{
+    4,4,4,4, 4,4,4,4, 4,4,4,4, 4,4,4,4,
+    4,4,4,4, 4,4,4,4, 4,4,4,4, 4,4,4,4,
+    4,4,4,4, 4,4,4,4, 4,4,4,4, 4,4,4,4,
+    4,4,4,4, 4,4,4,4, 4,4,4,4, 4,4,4,4,
+    4,3,4,2, 4,4,4,1, 4,4,4,4, 4,4,4,4,
+    4,4,4,4, 0,4,4,4, 4,4,4,4, 4,4,4,4,
+    4,3,4,2, 4,4,4,1, 4,4,4,4, 4,4,4,4,
+    4,4,4,4, 0
+};
+#define dna2aa(x)  gencode[  nt4[(uint8_t)(x)[0]]<<4 |  nt4[(uint8_t)(x)[1]]<<2 |  nt4[(uint8_t)(x)[2]] ]
+#define cdna2aa(x) gencode[ cnt4[(uint8_t)(x)[2]]<<4 | cnt4[(uint8_t)(x)[1]]<<2 | cnt4[(uint8_t)(x)[0]] ]
+
+static const char *gf_strings_noncoding[] = 
+{ 
+    "MT_rRNA", "MT_tRNA", "lincRNA", "miRNA", "misc_RNA", "rRNA", "snRNA", "snoRNA", "processed_transcript",
+    "antisense", "macro_lncRNA", "ribozyme", "sRNA", "scRNA", "scaRNA", "sense_intronic", "sense_overlapping",
+    "pseudogene", "processed_pseudogene", "artifact", "IG_pseudogene", "IG_C_pseudogene", "IG_J_pseudogene", 
+    "IG_V_pseudogene", "TR_V_pseudogene", "TR_J_pseudogene", "MT_tRNA_pseudogene", "misc_RNA_pseudogene", 
+    "miRNA_pseudogene", "ribozyme", "retained_intron", "retrotransposed", "Trna_pseudogene", "transcribed_processed_pseudogene", 
+    "transcribed_unprocessed_pseudogene", "transcribed_unitary_pseudogene",    "translated_unprocessed_pseudogene",
+    "translated_processed_pseudogene", "known_ncRNA", "unitary_pseudogene", "unprocessed_pseudogene",
+    "LRG_gene", "3_prime_overlapping_ncRNA", "disrupted_domain", "vaultRNA", "bidirectional_promoter_lncRNA", "ambiguous_orf"
+};
+static const char *gf_strings_coding[] = { "protein_coding", "polymorphic_pseudogene", "IG_C", "IG_D", "IG_J", "IG_LV", "IG_V", "TR_C", "TR_D", "TR_J", "TR_V", "NMD", "non_stop_decay"};
+static const char *gf_strings_special[] = { "CDS", "exon", "3_prime_UTR", "5_prime_UTR" };
+
+const char *gf_type2gff_string(int type)
+{
+    if ( !GF_is_coding(type) )
+    {
+        if ( type < (1<<GF_coding_bit) ) return gf_strings_noncoding[type-1];
+        type &= (1<<(GF_coding_bit+1)) - 1;
+        return gf_strings_special[type - 1];
+    }
+    type &= (1<<GF_coding_bit) - 1;
+    return gf_strings_coding[type - 1];
+}
+
+/*
+    gff parsing functions
+*/
+static inline int feature_set_seq(args_t *args, char *chr_beg, char *chr_end)
+{
+    aux_t *aux = &args->init;
+    char c = chr_end[1];
+    chr_end[1] = 0;
+    int iseq;
+    if ( khash_str2int_get(aux->seq2int, chr_beg, &iseq)!=0 )
+    {
+        // check for possible mismatch in chromosome naming convention such as chrX vs X
+        char *new_chr = NULL;
+        if ( faidx_has_seq(args->fai,chr_beg) )
+            new_chr = strdup(chr_beg);                  // valid chr name, the same in gff and faidx
+        else
+        {
+            int len = strlen(chr_beg);
+            if ( !strncmp("chr",chr_beg,3) && len>3 )
+                new_chr = strdup(chr_beg+3);            // gff has the prefix, faidx does not
+            else
+            {
+                new_chr = malloc(len+4);                // gff does not have the prefix, faidx has
+                memcpy(new_chr,"chr",3);
+                memcpy(new_chr+3,chr_beg,len);
+                new_chr[len+3] = 0;
+            }
+            if ( !faidx_has_seq(args->fai,new_chr) )    // modification did not help, this sequence is not in fai
+            {
+                static int unkwn_chr_warned = 0;
+                if ( !unkwn_chr_warned && args->verbosity>0 )
+                    fprintf(stderr,"Warning: GFF chromosome \"%s\" not part of the reference genome\n",chr_beg);
+                unkwn_chr_warned = 1;
+                free(new_chr);
+                new_chr = strdup(chr_beg);              // use the original sequence name
+            }
+        }
+        if ( khash_str2int_get(aux->seq2int, new_chr, &iseq)!=0 )
+        {
+            hts_expand(char*, aux->nseq+1, aux->mseq, aux->seq);
+            aux->seq[aux->nseq] = new_chr;
+            iseq = khash_str2int_inc(aux->seq2int, aux->seq[aux->nseq]);
+            aux->nseq++;
+            assert( aux->nseq < 1<<29 );  // see gf_gene_t.iseq and ftr_t.iseq
+        }
+        else
+            free(new_chr);
+    }
+    chr_end[1] = c;
+    return iseq;
+}
+static inline char *gff_skip(const char *line, char *ss)
+{
+    while ( *ss && *ss!='\t' ) ss++;
+    if ( !*ss ) error("[%s:%d %s] Could not parse the line: %s\n",__FILE__,__LINE__,__FUNCTION__,line);
+    return ss+1;
+}
+static inline void gff_parse_chr(const char *line, char **chr_beg, char **chr_end)
+{
+    char *se = (char*) line;
+    while ( *se && *se!='\t' ) se++;
+    if ( !*se ) error("[%s:%d %s] Could not parse the line: %s\n",__FILE__,__LINE__,__FUNCTION__,line);
+    *chr_beg = (char*) line;
+    *chr_end = se-1;
+}
+static inline char *gff_parse_beg_end(const char *line, char *ss, uint32_t *beg, uint32_t *end)
+{
+    char *se = ss;
+    *beg = strtol(ss, &se, 10) - 1;
+    if ( ss==se ) error("[%s:%d %s] Could not parse the line:\n\t%s\n\t%s\n",__FILE__,__LINE__,__FUNCTION__,line,ss);
+    ss = se+1;
+    *end = strtol(ss, &se, 10) - 1;
+    if ( ss==se ) error("[%s:%d %s] Could not parse the line: %s\n",__FILE__,__LINE__,__FUNCTION__,line);
+    return se+1;
+}
+static void gff_id_init(id_tbl_t *tbl)
+{
+    memset(tbl, 0, sizeof(*tbl));
+    tbl->str2id = khash_str2int_init();
+}
+static void gff_id_destroy(id_tbl_t *tbl)
+{
+    khash_str2int_destroy_free(tbl->str2id);
+    free(tbl->str);
+}
+static inline uint32_t gff_id_parse(id_tbl_t *tbl, const char *line, const char *needle, char *ss)
+{
+    ss = strstr(ss,needle);     // e.g. "ID=transcript:"
+    if ( !ss ) error("[%s:%d %s] Could not parse the line, \"%s\" not present: %s\n",__FILE__,__LINE__,__FUNCTION__,needle,line);
+    ss += strlen(needle);
+
+    char *se = ss;
+    while ( *se && *se!=';' && !isspace(*se) ) se++;
+    char tmp = *se;
+    *se = 0;
+
+    int id;
+    if ( khash_str2int_get(tbl->str2id, ss, &id) < 0 )
+    {
+        id = tbl->nstr++;
+        hts_expand(char*, tbl->nstr, tbl->mstr, tbl->str);
+        tbl->str[id] = strdup(ss);
+        khash_str2int_set(tbl->str2id, tbl->str[id], id);
+    }
+    *se = tmp;
+
+    return id;
+}
+static inline int gff_parse_type(char *line)
+{
+    line = strstr(line,"ID=");
+    if ( !line ) return -1;
+    line += 3;
+    if ( !strncmp(line,"transcript:",11) ) return GFF_TSCRIPT_LINE;
+    else if ( !strncmp(line,"gene:",5) ) return GFF_GENE_LINE;
+    return -1;
+}
+static inline int gff_parse_biotype(char *_line)
+{
+    char *line = strstr(_line,"biotype=");
+    if ( !line ) return -1;
+
+    line += 8;
+    switch (*line)
+    {
+        case 'p': 
+            if ( !strncmp(line,"protein_coding",14) ) return GF_PROTEIN_CODING;
+            else if ( !strncmp(line,"pseudogene",10) ) return GF_PSEUDOGENE;
+            else if ( !strncmp(line,"processed_transcript",20) ) return GF_PROCESSED_TRANSCRIPT;
+            else if ( !strncmp(line,"processed_pseudogene",20) ) return GF_PROCESSED_PSEUDOGENE;
+            else if ( !strncmp(line,"polymorphic_pseudogene",22) ) return GF_POLYMORPHIC_PSEUDOGENE;
+            break;
+        case 'a':
+            if ( !strncmp(line,"artifact",8) ) return GF_ARTIFACT;
+            else if ( !strncmp(line,"antisense",9) ) return GF_ANTISENSE;
+            else if ( !strncmp(line,"ambiguous_orf",13) ) return GF_AMBIGUOUS_ORF;
+            break;
+        case 'I':
+            if ( !strncmp(line,"IG_C_gene",9) ) return GF_IG_C;
+            else if ( !strncmp(line,"IG_D_gene",9) ) return GF_IG_D;
+            else if ( !strncmp(line,"IG_J_gene",9) ) return GF_IG_J;
+            else if ( !strncmp(line,"IG_LV_gene",10) ) return GF_IG_LV;
+            else if ( !strncmp(line,"IG_V_gene",9) ) return GF_IG_V;
+            else if ( !strncmp(line,"IG_pseudogene",13) ) return GF_IG_PSEUDOGENE;
+            else if ( !strncmp(line,"IG_C_pseudogene",15) ) return GF_IG_C_PSEUDOGENE;
+            else if ( !strncmp(line,"IG_J_pseudogene",15) ) return GF_IG_J_PSEUDOGENE;
+            else if ( !strncmp(line,"IG_V_pseudogene",15) ) return GF_IG_V_PSEUDOGENE;
+            break;
+        case 'T':
+            if ( !strncmp(line,"TR_C_gene",9) ) return GF_TR_C;
+            else if ( !strncmp(line,"TR_D_gene",9) ) return GF_TR_D;
+            else if ( !strncmp(line,"TR_J_gene",9) ) return GF_TR_J;
+            else if ( !strncmp(line,"TR_V_gene",9) ) return GF_TR_V;
+            else if ( !strncmp(line,"TR_V_pseudogene",15) ) return GF_TR_V_PSEUDOGENE;
+            else if ( !strncmp(line,"TR_J_pseudogene",15) ) return GF_TR_J_PSEUDOGENE;
+            break;
+        case 'M':
+            if ( !strncmp(line,"Mt_tRNA_pseudogene",18) ) return GF_MT_tRNA_PSEUDOGENE;
+            else if ( !strncmp(line,"Mt_tRNA",7) ) return GF_MT_tRNA;
+            else if ( !strncmp(line,"Mt_rRNA",7) ) return GF_MT_tRNA;
+            break;
+        case 'l':
+            if ( !strncmp(line,"lincRNA",7) ) return GF_lincRNA;
+            break;
+        case 'm':
+            if ( !strncmp(line,"macro_lncRNA",12) ) return GF_macro_lncRNA;
+            else if ( !strncmp(line,"misc_RNA_pseudogene",19) ) return GF_misc_RNA_PSEUDOGENE;
+            else if ( !strncmp(line,"miRNA_pseudogene",16) ) return GF_miRNA_PSEUDOGENE;
+            else if ( !strncmp(line,"miRNA",5) ) return GF_miRNA;
+            else if ( !strncmp(line,"misc_RNA",8) ) return GF_MISC_RNA;
+            break;
+        case 'r':
+            if ( !strncmp(line,"rRNA",4) ) return GF_rRNA;
+            else if ( !strncmp(line,"ribozyme",8) ) return GF_RIBOZYME;
+            else if ( !strncmp(line,"retained_intron",15) ) return GF_RETAINED_INTRON;
+            else if ( !strncmp(line,"retrotransposed",15) ) return GF_RETROTRANSPOSED;
+            break;
+        case 's':
+            if ( !strncmp(line,"snRNA",5) ) return GF_snRNA;
+            else if ( !strncmp(line,"sRNA",4) ) return GF_sRNA;
+            else if ( !strncmp(line,"scRNA",5) ) return GF_scRNA;
+            else if ( !strncmp(line,"scaRNA",6) ) return GF_scaRNA;
+            else if ( !strncmp(line,"snoRNA",6) ) return GF_snoRNA;
+            else if ( !strncmp(line,"sense_intronic",14) ) return GF_SENSE_INTRONIC;
+            else if ( !strncmp(line,"sense_overlapping",17) ) return GF_SENSE_OVERLAPPING;
+            break;
+        case 't':
+            if ( !strncmp(line,"tRNA_pseudogene",15) ) return GF_tRNA_PSEUDOGENE;
+            else if ( !strncmp(line,"transcribed_processed_pseudogene",32) ) return GF_TRANSCRIBED_PROCESSED_PSEUDOGENE;
+            else if ( !strncmp(line,"transcribed_unprocessed_pseudogene",34) ) return GF_TRANSCRIBED_UNPROCESSED_PSEUDOGENE; 
+            else if ( !strncmp(line,"transcribed_unitary_pseudogene",30) ) return GF_TRANSCRIBED_UNITARY_PSEUDOGENE;
+            else if ( !strncmp(line,"translated_unprocessed_pseudogene",33) ) return GF_TRANSLATED_UNPROCESSED_PSEUDOGENE;
+            else if ( !strncmp(line,"translated_processed_pseudogene",31) ) return GF_TRANSLATED_PROCESSED_PSEUDOGENE;
+            break;
+        case 'n':
+            if ( !strncmp(line,"nonsense_mediated_decay",23) ) return GF_NMD;
+            else if ( !strncmp(line,"non_stop_decay",14) ) return GF_NON_STOP_DECAY;
+            break;
+        case 'k':
+            if ( !strncmp(line,"known_ncrna",11) ) return GF_KNOWN_NCRNA;
+            break;
+        case 'u':
+            if ( !strncmp(line,"unitary_pseudogene",18) ) return GF_UNITARY_PSEUDOGENE;
+            else if ( !strncmp(line,"unprocessed_pseudogene",22) ) return GF_UNPROCESSED_PSEUDOGENE;
+            break;
+        case 'L':
+            if ( !strncmp(line,"LRG_gene",8) ) return GF_LRG_GENE;
+            break;
+        case '3':
+            if ( !strncmp(line,"3prime_overlapping_ncRNA",24) ) return GF_3PRIME_OVERLAPPING_ncRNA;
+            break;
+        case 'd':
+            if ( !strncmp(line,"disrupted_domain",16) ) return GF_DISRUPTED_DOMAIN;
+            break;
+        case 'v':
+            if ( !strncmp(line,"vaultRNA",8) ) return GF_vaultRNA;
+            break;
+        case 'b':
+            if ( !strncmp(line,"bidirectional_promoter_lncRNA",29) ) return GF_BIDIRECTIONAL_PROMOTER_lncRNA;
+            break;
+    }
+    return 0;
+}
+static inline int gff_ignored_biotype(args_t *args, char *ss)
+{
+    ss = strstr(ss,"biotype=");
+    if ( !ss ) return 0;
+
+    ss += 8;
+    char *se = ss, tmp;
+    while ( *se && *se!=';' ) se++;
+    tmp = *se;
+    *se = 0;
+
+    char *key = ss;
+    int n = 0;
+    if ( khash_str2int_get(args->init.ignored_biotypes, ss, &n)!=0 ) key = strdup(ss);
+    khash_str2int_set(args->init.ignored_biotypes, key, n+1);
+
+    *se = tmp;
+    return 1;
+}
+gf_gene_t *gene_init(aux_t *aux, uint32_t gene_id)
+{
+    khint_t k = kh_get(int2gene, aux->gid2gene, (int)gene_id);
+    gf_gene_t *gene = (k == kh_end(aux->gid2gene)) ? NULL : kh_val(aux->gid2gene, k);
+    if ( !gene )
+    {
+        gene = (gf_gene_t*) calloc(1,sizeof(gf_gene_t));
+        int ret;
+        k = kh_put(int2gene, aux->gid2gene, (int)gene_id, &ret);
+        kh_val(aux->gid2gene,k) = gene;
+    }
+    return gene;
+}
+void gff_parse_transcript(args_t *args, const char *line, char *ss, ftr_t *ftr)
+{
+    aux_t *aux = &args->init;
+    int biotype = gff_parse_biotype(ss);
+    if ( biotype <= 0 )
+    {
+        if ( !gff_ignored_biotype(args, ss) && args->verbosity > 0 ) fprintf(stderr,"ignored transcript: %s\n",line);
+        return;
+    }
+
+    // create a mapping from transcript_id to gene_id
+    uint32_t trid = gff_id_parse(&args->tscript_ids, line, "ID=transcript:", ss);
+    uint32_t gene_id = gff_id_parse(&args->init.gene_ids, line, "Parent=gene:", ss);
+
+    tscript_t *tr = (tscript_t*) calloc(1,sizeof(tscript_t));
+    tr->id     = trid;
+    tr->strand = ftr->strand;
+    tr->gene   = gene_init(aux, gene_id);
+    tr->type   = biotype;
+    tr->beg    = ftr->beg;
+    tr->end    = ftr->end;
+
+    khint_t k;
+    int ret;
+    k = kh_put(int2tscript, aux->id2tr, (int)trid, &ret);
+    kh_val(aux->id2tr,k) = tr;
+}
+void gff_parse_gene(args_t *args, const char *line, char *ss, char *chr_beg, char *chr_end, ftr_t *ftr)
+{
+    int biotype = gff_parse_biotype(ss);
+    if ( biotype <= 0 )
+    {
+        if ( !gff_ignored_biotype(args, ss) && args->verbosity > 0 ) fprintf(stderr,"ignored gene: %s\n",line);
+        return;
+    }
+
+    aux_t *aux = &args->init;
+
+    // substring search for "ID=gene:ENSG00000437963"
+    uint32_t gene_id = gff_id_parse(&aux->gene_ids, line, "ID=gene:", ss);
+    gf_gene_t *gene = gene_init(aux, gene_id);
+    assert( !gene->name );      // the gene_id should be unique
+
+    gene->iseq = feature_set_seq(args, chr_beg,chr_end);
+
+    // substring search for "Name=OR4F5"
+    ss = strstr(chr_end+2,"Name=");
+    if ( ss )
+    {
+        ss += 5;
+        char *se = ss;
+        while ( *se && *se!=';' && !isspace(*se) ) se++;
+        gene->name = (char*) malloc(se-ss+1);
+        memcpy(gene->name,ss,se-ss);
+        gene->name[se-ss] = 0;
+    }
+    else
+        gene->name = strdup(aux->gene_ids.str[gene_id]); // Name=<GeneName> field is not present, use the gene ID instead
+}
+int gff_parse(args_t *args, char *line, ftr_t *ftr)
+{
+    // - skip empty lines and commented lines
+    // - columns 
+    //      1.      chr
+    //      2.      <skip>
+    //      3.      CDS, transcript, gene, ...
+    //      4-5.    beg,end
+    //      6.      <skip>
+    //      7.      strand
+    //      8.      phase
+    //      9.      Parent=transcript:ENST(\d+);ID=... etc
+
+    char *ss = line;
+    if ( !*ss ) return -1;      // skip blank lines
+    if ( *ss=='#' ) return -1;  // skip comments
+
+    char *chr_beg, *chr_end;
+    gff_parse_chr(line, &chr_beg, &chr_end);
+    ss = gff_skip(line, chr_end + 2);
+
+    // 3. column: is this a CDS, transcript, gene, etc.
+    if ( !strncmp("exon\t",ss,5) ) { ftr->type = GF_EXON; ss += 5; }
+    else if ( !strncmp("CDS\t",ss,4) ) { ftr->type = GF_CDS; ss += 4; }
+    else if ( !strncmp("three_prime_UTR\t",ss,16) ) { ftr->type = GF_UTR3; ss += 16; }
+    else if ( !strncmp("five_prime_UTR\t",ss,15) ) { ftr->type = GF_UTR5; ss += 15; }
+    else
+    {
+        ss = gff_skip(line, ss);
+        ss = gff_parse_beg_end(line, ss, &ftr->beg,&ftr->end);
+        ss = gff_skip(line, ss);
+        int type = gff_parse_type(ss);
+        if ( type!=GFF_TSCRIPT_LINE && type!=GFF_GENE_LINE ) 
+        {
+            // we ignore these, debug print to see new types:
+            ss = strstr(ss,"ID=");
+            if ( !ss ) return -1;   // no ID, ignore the line
+            if ( !strncmp("chromosome",ss+3,10) ) return -1;
+            if ( !strncmp("supercontig",ss+3,11) ) return -1;
+            if ( args->verbosity > 0 ) fprintf(stderr,"ignored: %s\n", line);
+            return -1;
+        }
+
+        // 7. column: strand
+        if ( *ss == '+' ) ftr->strand = STRAND_FWD;
+        else if ( *ss == '-' ) ftr->strand = STRAND_REV;
+        else error("Unknown strand: %c .. %s\n", *ss,ss);
+
+        if ( type==GFF_TSCRIPT_LINE )
+            gff_parse_transcript(args, line, ss, ftr);
+        else
+            gff_parse_gene(args, line, ss, chr_beg, chr_end, ftr);
+
+        return -1;
+    }
+    ss = gff_parse_beg_end(line, ss, &ftr->beg,&ftr->end);
+    ss = gff_skip(line, ss);
+
+    // 7. column: strand
+    if ( *ss == '+' ) ftr->strand = STRAND_FWD;
+    else if ( *ss == '-' ) ftr->strand = STRAND_REV;
+    else { if ( args->verbosity > 0 ) fprintf(stderr,"Skipping unknown strand: %c\n", *ss); return -1; }
+    ss += 2;
+
+    // 8. column: phase (codon offset)
+    if ( *ss == '0' ) ftr->phase = 0;
+    else if ( *ss == '1' ) ftr->phase = 1;
+    else if ( *ss == '2' ) ftr->phase = 2;
+    else if ( *ss == '.' ) ftr->phase = CDS_PHASE_UNKN;     // exons and even CDS in some GFFs do not have phase
+    else { if ( args->verbosity > 0 ) fprintf(stderr,"Skipping unknown phase: %c, %s\n", *ss, line); return -1; }
+    ss += 2;
+
+    // substring search for "Parent=transcript:ENST00000437963"
+    ftr->trid = gff_id_parse(&args->tscript_ids, line, "Parent=transcript:", ss);
+    ftr->iseq = feature_set_seq(args, chr_beg,chr_end);
+    return 0;
+}
+
+static int cmp_cds_ptr(const void *a, const void *b)
+{
+    // comparison function for qsort of transcripts's CDS
+    if ( (*((gf_cds_t**)a))->beg < (*((gf_cds_t**)b))->beg ) return -1;
+    if ( (*((gf_cds_t**)a))->beg > (*((gf_cds_t**)b))->beg ) return 1;
+    return 0;
+}
+
+static inline void chr_beg_end(aux_t *aux, int iseq, char **chr_beg, char **chr_end)
+{
+    *chr_beg = *chr_end = aux->seq[iseq];
+    while ( (*chr_end)[1] ) (*chr_end)++;
+}
+tscript_t *tscript_init(aux_t *aux, uint32_t trid)
+{
+    khint_t k = kh_get(int2tscript, aux->id2tr, (int)trid);
+    tscript_t *tr = (k == kh_end(aux->id2tr)) ? NULL : kh_val(aux->id2tr, k);
+    assert( tr );
+    return tr;
+}
+void register_cds(args_t *args, ftr_t *ftr)
+{
+    // Make the CDS searchable via idx_cds. Note we do not malloc tr->cds just yet.
+    //  ftr is the result of parsing a gff CDS line
+    aux_t *aux = &args->init;
+
+    tscript_t *tr = tscript_init(aux, ftr->trid);
+    if ( tr->strand != ftr->strand ) error("Conflicting strand in transcript %"PRIu32" .. %d vs %d\n",ftr->trid,tr->strand,ftr->strand);
+    
+    gf_cds_t *cds = (gf_cds_t*) malloc(sizeof(gf_cds_t));
+    cds->tr    = tr;
+    cds->beg   = ftr->beg;
+    cds->len   = ftr->end - ftr->beg + 1;
+    cds->icds  = 0;     // to keep valgrind on mac happy
+    cds->phase = ftr->phase;
+    
+    hts_expand(gf_cds_t*,tr->ncds+1,tr->mcds,tr->cds);
+    tr->cds[tr->ncds++] = cds;
+}
+void register_utr(args_t *args, ftr_t *ftr)
+{
+    aux_t *aux = &args->init;
+    gf_utr_t *utr = (gf_utr_t*) malloc(sizeof(gf_utr_t));
+    utr->which = ftr->type==GF_UTR3 ? prime3 : prime5;
+    utr->beg   = ftr->beg;
+    utr->end   = ftr->end;
+    utr->tr    = tscript_init(aux, ftr->trid);
+
+    char *chr_beg, *chr_end;
+    chr_beg_end(&args->init, utr->tr->gene->iseq, &chr_beg, &chr_end);
+    regidx_push(args->idx_utr, chr_beg,chr_end, utr->beg,utr->end, &utr);
+}
+void register_exon(args_t *args, ftr_t *ftr)
+{
+    aux_t *aux = &args->init;
+    gf_exon_t *exon = (gf_exon_t*) malloc(sizeof(gf_exon_t));
+    exon->beg = ftr->beg;
+    exon->end = ftr->end;
+    exon->tr  = tscript_init(aux, ftr->trid);
+
+    char *chr_beg, *chr_end;
+    chr_beg_end(&args->init, exon->tr->gene->iseq, &chr_beg, &chr_end);
+    regidx_push(args->idx_exon, chr_beg,chr_end, exon->beg - N_SPLICE_REGION_INTRON, exon->end + N_SPLICE_REGION_INTRON, &exon);
+}
+
+void tscript_init_cds(args_t *args)
+{
+    aux_t *aux = &args->init;
+
+    // Sort CDS in all transcripts, set offsets, check their phase, length, create index (idx_cds)
+    khint_t k;
+    int warn_phase_unkn = 0;
+    for (k=0; k<kh_end(aux->id2tr); k++)
+    {
+        if ( !kh_exist(aux->id2tr, k) ) continue;
+        tscript_t *tr = (tscript_t*) kh_val(aux->id2tr, k);
+
+        // position-to-tscript lookup
+        char *chr_beg, *chr_end;
+        chr_beg_end(aux, tr->gene->iseq, &chr_beg, &chr_end);
+        regidx_push(args->idx_tscript, chr_beg, chr_end, tr->beg, tr->end, &tr);
+
+        if ( !tr->ncds ) continue;      // transcript with no CDS
+
+        // sort CDs
+        qsort(tr->cds, tr->ncds, sizeof(gf_cds_t*), cmp_cds_ptr);
+
+        // trim non-coding start
+        int i, len = 0;
+        if ( tr->strand==STRAND_FWD )
+        {
+            if ( tr->cds[0]->phase != CDS_PHASE_UNKN )
+            {
+                if ( tr->cds[0]->phase ) tr->trim |= TRIM_5PRIME;
+                tr->cds[0]->beg += tr->cds[0]->phase;
+                tr->cds[0]->len -= tr->cds[0]->phase;
+                tr->cds[0]->phase = 0;
+            }
+
+            // sanity check phase; the phase number in gff tells us how many bases to skip in this
+            // feature to reach the first base of the next codon
+            int tscript_ok = 1;
+            for (i=0; i<tr->ncds; i++)
+            {
+                if ( tr->cds[i]->phase == CDS_PHASE_UNKN )
+                {
+                    warn_phase_unkn = 1;
+                    len += tr->cds[i]->len;
+                    continue;
+                }
+                int phase = tr->cds[i]->phase ? 3 - tr->cds[i]->phase : 0;
+                if ( phase!=len%3 )
+                {
+                    if ( args->force )
+                    {
+                        if ( args->verbosity > 0 )
+                            fprintf(stderr,"Warning: the GFF has inconsistent phase column in transcript %s, skipping. CDS pos=%d: phase!=len%%3 (phase=%d, len=%d)\n",
+                                args->tscript_ids.str[tr->id],tr->cds[i]->beg+1,phase,len);
+                        tscript_ok = 0;
+                        break;
+                    }
+                    error("Error: GFF3 assumption failed for transcript %s, CDS=%d: phase!=len%%3 (phase=%d, len=%d). Use the --force option to proceed anyway (at your own risk).\n",
+                            args->tscript_ids.str[tr->id],tr->cds[i]->beg+1,phase,len);
+                }
+                len += tr->cds[i]->len; 
+            }
+            if ( !tscript_ok ) continue;    // skip this transcript
+        }
+        else
+        {
+            if ( tr->cds[tr->ncds-1]->phase != CDS_PHASE_UNKN )
+            {
+                // Check that the phase is not bigger than CDS length. Curiously, this can really happen,
+                // see Mus_musculus.GRCm38.85.gff3.gz, transcript:ENSMUST00000163141
+                // todo: the same for the fwd strand
+                i = tr->ncds - 1;
+                int phase = tr->cds[i]->phase;
+                if ( phase ) tr->trim |= TRIM_5PRIME;
+                while ( i>=0 && phase > tr->cds[i]->len )
+                {
+                    phase -= tr->cds[i]->len;
+                    tr->cds[i]->phase = 0;
+                    tr->cds[i]->len   = 0;
+                    i--;
+                }
+                tr->cds[i]->len  -= tr->cds[i]->phase;
+                tr->cds[i]->phase = 0;
+            }
+
+            // sanity check phase
+            int tscript_ok = 1;
+            for (i=tr->ncds-1; i>=0; i--)
+            {
+                if ( tr->cds[i]->phase == CDS_PHASE_UNKN )
+                {
+                    warn_phase_unkn = 1;
+                    len += tr->cds[i]->len;
+                    continue;
+                }
+                int phase = tr->cds[i]->phase ? 3 - tr->cds[i]->phase : 0;
+                if ( phase!=len%3)
+                {
+                    if ( args->force )
+                    {
+                        if ( args->verbosity > 0 )
+                            fprintf(stderr,"Warning: the GFF has inconsistent phase column in transcript %s, skipping. CDS pos=%d: phase!=len%%3 (phase=%d, len=%d)\n",
+                                args->tscript_ids.str[tr->id],tr->cds[i]->beg+1,phase,len);
+                        tscript_ok = 0;
+                        break;
+                    }
+                    error("Error: GFF3 assumption failed for transcript %s, CDS=%d: phase!=len%%3 (phase=%d, len=%d). Use the --force option to proceed anyway (at your own risk).\n",
+                        args->tscript_ids.str[tr->id],tr->cds[i]->beg+1,phase,len);
+                }
+                len += tr->cds[i]->len;
+            }
+            if ( !tscript_ok ) continue;    // skip this transcript
+        }
+
+        // set len. At the same check that CDS within a transcript do not overlap
+        len = 0;
+        for (i=0; i<tr->ncds; i++)
+        {
+            tr->cds[i]->icds = i;
+            len += tr->cds[i]->len; 
+            if ( !i ) continue;
+
+            gf_cds_t *a = tr->cds[i-1];
+            gf_cds_t *b = tr->cds[i];
+            if ( a->beg + a->len - 1 >= b->beg ) 
+            {
+                if ( args->force )
+                {
+                    fprintf(stderr,"Warning: GFF contains overlapping CDS %s: %"PRIu32"-%"PRIu32" and %"PRIu32"-%"PRIu32".\n",
+                        args->tscript_ids.str[tr->id], a->beg+1,a->beg+a->len, b->beg+1,b->beg+b->len);
+                }
+                else
+                    error("Error: CDS overlap in the transcript %s: %"PRIu32"-%"PRIu32" and %"PRIu32"-%"PRIu32", is this intended (e.g. ribosomal slippage)?\n"
+                          "       Use the --force option to override (at your own risk).\n", 
+                            args->tscript_ids.str[tr->id], a->beg+1,a->beg+a->len, b->beg+1,b->beg+b->len);
+            }
+        }
+        if ( len%3 != 0 )
+        {
+            // There are 13k transcripts with incomplete 3' CDS. See for example ENST00000524289
+            //  http://sep2015.archive.ensembl.org/Homo_sapiens/Transcript/Sequence_cDNA?db=core;g=ENSG00000155868;r=5:157138846-157159019;t=ENST00000524289
+            // Also, the incomplete CDS can be too short (1 or 2bp), so it is not enough to trim the last one.
+
+            tr->trim |= TRIM_3PRIME;
+            if ( tr->strand==STRAND_FWD )
+            {
+                i = tr->ncds - 1;
+                while ( i>=0 && len%3 )
+                {
+                    int dlen = tr->cds[i]->len >= len%3 ? len%3 : tr->cds[i]->len;
+                    tr->cds[i]->len -= dlen;
+                    len -= dlen;
+                    i--;
+                }
+            }
+            else
+            {
+                i = 0;
+                while ( i<tr->ncds && len%3 )
+                {
+                    int dlen = tr->cds[i]->len >= len%3 ? len%3 : tr->cds[i]->len;
+                    tr->cds[i]->len -= dlen;
+                    tr->cds[i]->beg += dlen;
+                    len -= dlen;
+                    i++;
+                }
+            }
+        }
+
+        // set CDS offsets and insert into regidx
+        len=0;
+        for (i=0; i<tr->ncds; i++)
+        {
+            tr->cds[i]->pos = len;
+            len += tr->cds[i]->len;
+            regidx_push(args->idx_cds, chr_beg,chr_end, tr->cds[i]->beg,tr->cds[i]->beg+tr->cds[i]->len-1, &tr->cds[i]);
+        }
+    }
+    if ( warn_phase_unkn && args->verbosity > 0 )
+        fprintf(stderr,"Warning: encountered CDS with phase column unset, could not verify reading frame\n");
+}
+
+void regidx_free_gf(void *payload) { free(*((gf_cds_t**)payload)); }
+void regidx_free_tscript(void *payload) { tscript_t *tr = *((tscript_t**)payload); free(tr->cds); free(tr); }
+
+void init_gff(args_t *args)
+{
+    aux_t *aux = &args->init;
+    aux->seq2int   = khash_str2int_init();   // chrom's numeric id
+    aux->gid2gene  = kh_init(int2gene);      // gene id to gf_gene_t, for idx_gene
+    aux->id2tr     = kh_init(int2tscript);   // transcript id to tscript_t
+    args->idx_tscript = regidx_init(NULL, NULL, regidx_free_tscript, sizeof(tscript_t*), NULL);
+    aux->ignored_biotypes = khash_str2int_init();
+    gff_id_init(&aux->gene_ids);
+    gff_id_init(&args->tscript_ids);
+
+    // parse gff
+    kstring_t str = {0,0,0};
+    htsFile *fp = hts_open(args->gff_fname,"r");
+    if ( !fp ) error("Failed to read %s\n", args->gff_fname);
+    while ( hts_getline(fp, KS_SEP_LINE, &str) > 0 )
+    {
+        hts_expand(ftr_t, aux->nftr+1, aux->mftr, aux->ftr);
+        int ret = gff_parse(args, str.s, aux->ftr + aux->nftr);
+        if ( !ret ) aux->nftr++;
+    }
+    free(str.s);
+    if ( hts_close(fp)!=0 ) error("Close failed: %s\n", args->gff_fname);
+
+
+    // process gff information: connect CDS and exons to transcripts
+    args->idx_cds  = regidx_init(NULL, NULL, regidx_free_gf, sizeof(gf_cds_t*), NULL);
+    args->idx_utr  = regidx_init(NULL, NULL, regidx_free_gf, sizeof(gf_utr_t*), NULL);
+    args->idx_exon = regidx_init(NULL, NULL, regidx_free_gf, sizeof(gf_exon_t*), NULL);
+    args->itr      = regitr_init(NULL);
+
+    int i;
+    for (i=0; i<aux->nftr; i++)
+    {
+        ftr_t *ftr = &aux->ftr[i];
+
+        // check whether to keep this feature: is there a mapping trid -> gene_id -> gene?
+        khint_t k = kh_get(int2tscript, aux->id2tr, (int)ftr->trid);
+        if ( k==kh_end(aux->id2tr) ) continue;       // no such transcript
+
+        tscript_t *tr = kh_val(aux->id2tr,k);
+        if ( !tr->gene->name )
+        {
+            // not a supported biotype (e.g. gene:pseudogene, transcript:processed_transcript)
+            regidx_free_tscript(&tr);
+            kh_del(int2tscript, aux->id2tr,k);
+            continue;
+        }
+
+        // populate regidx by category: 
+        //      ftr->type   .. GF_CDS, GF_EXON, GF_UTR3, GF_UTR5
+        //      gene->type  .. GF_PROTEIN_CODING, GF_MT_rRNA, GF_IG_C, ...
+        if ( ftr->type==GF_CDS ) register_cds(args, ftr);
+        else if ( ftr->type==GF_EXON ) register_exon(args, ftr);
+        else if ( ftr->type==GF_UTR5 ) register_utr(args, ftr);
+        else if ( ftr->type==GF_UTR3 ) register_utr(args, ftr);
+        else
+            error("something: %s\t%d\t%d\t%s\t%s\n", aux->seq[ftr->iseq],ftr->beg+1,ftr->end+1,args->tscript_ids.str[ftr->trid],gf_type2gff_string(ftr->type));
+    }
+    tscript_init_cds(args);
+
+    if ( args->verbosity > 0 )
+    {
+        fprintf(stderr,"Indexed %d transcripts, %d exons, %d CDSs, %d UTRs\n", 
+                regidx_nregs(args->idx_tscript),
+                regidx_nregs(args->idx_exon),
+                regidx_nregs(args->idx_cds),
+                regidx_nregs(args->idx_utr));
+    }
+
+    free(aux->ftr);
+    khash_str2int_destroy_free(aux->seq2int);
+    // keeping only to destroy the genes at the end: kh_destroy(int2gene,aux->gid2gene);
+    kh_destroy(int2tscript,aux->id2tr);
+    free(aux->seq);
+    gff_id_destroy(&aux->gene_ids);
+
+    if ( args->verbosity > 0 && khash_str2int_size(aux->ignored_biotypes) )
+    {
+        khash_t(str2int) *ign = (khash_t(str2int)*)aux->ignored_biotypes;
+        fprintf(stderr,"Ignored the following biotypes:\n");
+        for (i = kh_begin(ign); i < kh_end(ign); i++)
+        {
+            if ( !kh_exist(ign,i)) continue;
+            const char *biotype = kh_key(ign,i);
+            if ( !strcmp(biotype,"TCE") ) biotype = "TCE (\"To be Experimentally Confirmed\")";
+            fprintf(stderr,"\t%dx\t.. %s\n", kh_value(ign,i), biotype);
+        }
+    }
+    khash_str2int_destroy_free(aux->ignored_biotypes);
+}
+
+static inline int ncsq2_to_nfmt(int ncsq2)
+{
+    return 1 + (ncsq2 - 1) / 30;
+}
+static inline void icsq2_to_bit(int icsq2, int *ival, int *ibit)
+{
+    *ival = icsq2 / 30;
+    *ibit = icsq2 % 30;
+}
+
+void init_data(args_t *args)
+{
+    args->nfmt_bcsq = ncsq2_to_nfmt(args->ncsq2_max);
+
+    args->fai = fai_load(args->fa_fname);
+    if ( !args->fai ) error("Failed to load the fai index: %s\n", args->fa_fname);
+
+    if ( args->verbosity > 0 ) fprintf(stderr,"Parsing %s ...\n", args->gff_fname);
+    init_gff(args);
+
+    args->rid = -1;
+
+    if ( args->filter_str )
+        args->filter = filter_init(args->hdr, args->filter_str);
+
+    args->pos2vbuf  = kh_init(pos2vbuf);
+    args->active_tr = khp_init(trhp);
+    args->hap = (hap_t*) calloc(1,sizeof(hap_t));
+
+    // init samples
+    if ( !bcf_hdr_nsamples(args->hdr) ) args->phase = PHASE_DROP_GT;
+    if ( args->sample_list && !strcmp("-",args->sample_list) )
+    {
+        // ignore all samples
+        if ( args->output_type==FT_TAB_TEXT ) 
+        {
+            // significant speedup for plain VCFs
+            if (bcf_hdr_set_samples(args->hdr,NULL,0) < 0)
+                error_errno("[%s] Couldn't build sample filter", __func__);
+        }
+        args->phase = PHASE_DROP_GT;
+    }
+    else
+        args->smpl = smpl_ilist_init(args->hdr, args->sample_list, args->sample_is_file, SMPL_STRICT);
+    args->hdr_nsmpl = args->phase==PHASE_DROP_GT ? 0 : bcf_hdr_nsamples(args->hdr);
+
+    if ( args->output_type==FT_TAB_TEXT )
+    {
+        args->out = args->output_fname ? fopen(args->output_fname,"w") : stdout;
+        if ( !args->out ) error("Failed to write to %s: %s\n", !strcmp("-",args->output_fname)?"standard output":args->output_fname,strerror(errno));
+
+        fprintf(args->out,"# This file was produced by: bcftools +csq(%s+htslib-%s)\n", bcftools_version(),hts_version());
+        fprintf(args->out,"# The command line was:\tbcftools +%s", args->argv[0]);
+        int i;
+        for (i=1; i<args->argc; i++)
+            fprintf(args->out," %s",args->argv[i]);
+        fprintf(args->out,"\n");
+        fprintf(args->out,"# LOG\t[2]Message\n");
+        fprintf(args->out,"# CSQ"); i = 1;
+        fprintf(args->out,"\t[%d]Sample", ++i);
+        fprintf(args->out,"\t[%d]Haplotype", ++i);
+        fprintf(args->out,"\t[%d]Chromosome", ++i);
+        fprintf(args->out,"\t[%d]Position", ++i);
+        fprintf(args->out,"\t[%d]Consequence", ++i);
+        fprintf(args->out,"\n");
+    }
+    else
+    {
+        char wmode[8];
+        set_wmode(wmode,args->output_type,args->output_fname,args->clevel);
+        args->out_fh = hts_open(args->output_fname ? args->output_fname : "-", wmode);
+        if ( args->out_fh == NULL ) error("[%s] Error: cannot write to %s: %s\n", __func__,args->output_fname? args->output_fname : "standard output", strerror(errno));
+        if ( args->n_threads > 0)
+            hts_set_opt(args->out_fh, HTS_OPT_THREAD_POOL, args->sr->p);
+        if ( args->record_cmd_line ) bcf_hdr_append_version(args->hdr,args->argc,args->argv,"bcftools/csq");
+        bcf_hdr_printf(args->hdr,"##INFO=<ID=%s,Number=.,Type=String,Description=\"%s consequence annotation from BCFtools/csq, see http://samtools.github.io/bcftools/howtos/csq-calling.html for details. Format: Consequence|gene|transcript|biotype|strand|amino_acid_change|dna_change\">",args->bcsq_tag, args->local_csq ? "Local" : "Haplotype-aware");
+        if ( args->hdr_nsmpl ) 
+            bcf_hdr_printf(args->hdr,"##FORMAT=<ID=%s,Number=.,Type=Integer,Description=\"Bitmask of indexes to INFO/BCSQ, with interleaved first/second haplotype. Use \\\"bcftools query -f'[%%CHROM\\t%%POS\\t%%SAMPLE\\t%%TBCSQ\\n]'\\\" to translate.\">",args->bcsq_tag);
+        if ( bcf_hdr_write(args->out_fh, args->hdr)!=0 ) error("[%s] Error: cannot write the header to %s\n", __func__,args->output_fname?args->output_fname:"standard output");
+    }
+    if ( args->verbosity > 0 ) fprintf(stderr,"Calling...\n");
+}
+
+void destroy_data(args_t *args)
+{
+    if ( args->ncsq2_small_warned )
+        fprintf(stderr,
+            "Note: Some samples had too many consequences to be represented in %d bytes. If you need to record them all,\n"
+            "      the limit can be increased by running with `--ncsq %d`.\n",ncsq2_to_nfmt(args->ncsq2_max)/8,1+args->ncsq2_small_warned/2);
+
+    regidx_destroy(args->idx_cds);
+    regidx_destroy(args->idx_utr);
+    regidx_destroy(args->idx_exon);
+    regidx_destroy(args->idx_tscript);
+    regitr_destroy(args->itr);
+
+    khint_t k,i,j;
+    for (k=0; k<kh_end(args->init.gid2gene); k++)
+    {
+        if ( !kh_exist(args->init.gid2gene, k) ) continue;
+        gf_gene_t *gene = (gf_gene_t*) kh_val(args->init.gid2gene, k);
+        free(gene->name);
+        free(gene);
+    }
+    kh_destroy(int2gene,args->init.gid2gene);
+
+    if ( args->filter )
+        filter_destroy(args->filter);
+
+    khp_destroy(trhp,args->active_tr);
+    kh_destroy(pos2vbuf,args->pos2vbuf);
+    if ( args->smpl ) smpl_ilist_destroy(args->smpl);
+    int ret;
+    if ( args->out_fh )
+        ret = hts_close(args->out_fh);
+    else
+        ret = fclose(args->out);
+    if ( ret ) error("Error: close failed .. %s\n", args->output_fname?args->output_fname:"stdout");
+    for (i=0; i<args->vcf_rbuf.m; i++)
+    {
+        vbuf_t *vbuf = args->vcf_buf[i];
+        if ( !vbuf ) continue;
+        for (j=0; j<vbuf->m; j++)
+        {
+            if ( !vbuf->vrec[j] ) continue;
+            if ( vbuf->vrec[j]->line ) bcf_destroy(vbuf->vrec[j]->line);
+            free(vbuf->vrec[j]->fmt_bm);
+            free(vbuf->vrec[j]->vcsq);
+            free(vbuf->vrec[j]);
+        }
+        free(vbuf->vrec);
+        free(vbuf);
+    }
+    free(args->vcf_buf);
+    free(args->rm_tr);
+    free(args->csq_buf);
+    free(args->hap->stack);
+    free(args->hap->sseq.s);
+    free(args->hap->tseq.s);
+    free(args->hap->tref.s);
+    free(args->hap);
+    fai_destroy(args->fai);
+    free(args->gt_arr);
+    free(args->str.s);
+    free(args->str2.s);
+    gff_id_destroy(&args->tscript_ids);
+}
+
+/*
+    The splice_* functions are for consquences around splice sites: start,stop,splice_*
+ */
+#define SPLICE_VAR_REF 0   // ref: ACGT>ACGT, csq not applicable, skip completely
+#define SPLICE_OUTSIDE 1   // splice acceptor or similar; csq set and is done, does not overlap the region
+#define SPLICE_INSIDE  2   // overlaps coding region; csq can be set but coding prediction is needed 
+#define SPLICE_OVERLAP 3   // indel overlaps region boundary, csq set but could not determine csq
+typedef struct
+{
+    tscript_t *tr;
+    struct {
+        int32_t pos, rlen, alen, ial;
+        char *ref, *alt;
+        bcf1_t *rec;
+    } vcf;
+    uint16_t check_acceptor:1,  // check distance from exon start (fwd) or end (rev)
+             check_start:1,     // this is the first coding exon (relative to transcript orientation), check first (fwd) or last (rev) codon 
+             check_stop:1,      // this is the last coding exon (relative to transcript orientation), check last (fwd) or first (rev) codon
+             check_donor:1,     // as with check_acceptor
+             check_region_beg:1,    // do/don't check for splices at this end, eg. in the first or last exon
+             check_region_end:1,    // 
+             check_utr:1,           // check splice sites (acceptor/donor/region_*) only if not in utr
+             set_refalt:1;          // set kref,kalt, if set, check also for synonymous events
+    uint32_t csq;
+    int tbeg, tend;             // number of trimmed bases from beg and end of ref,alt allele
+    uint32_t ref_beg,           // ref coordinates with spurious bases removed, ACC>AC can become AC>A or CC>C, whichever gives 
+             ref_end;           // a more conservative csq (the first and last base in kref.s)
+    kstring_t kref, kalt;       // trimmed alleles, set only with SPLICE_OLAP
+}
+splice_t;
+void splice_init(splice_t *splice, bcf1_t *rec)
+{
+    memset(splice,0,sizeof(*splice));
+    splice->vcf.rec  = rec;
+    splice->vcf.pos  = rec->pos;
+    splice->vcf.rlen = rec->rlen;
+    splice->vcf.ref  = rec->d.allele[0];
+    splice->csq      = 0;
+}
+static inline void splice_build_hap(splice_t *splice, uint32_t beg, int len)
+{
+    // len>0 .. beg is the first base, del filled from right
+    // len<0 .. beg is the last base, del filled from left
+
+    int rlen, alen, rbeg, abeg;     // first base to include (ref coordinates)
+    if ( len<0 )
+    {
+        rlen = alen = -len;
+        rbeg = beg - rlen + 1;
+        int dlen = splice->vcf.alen - splice->vcf.rlen;
+        if ( dlen<0 && beg < splice->ref_end ) // incomplete del, beg is in the middle
+            dlen += splice->ref_end - beg;
+        abeg = rbeg + dlen;
+    }
+    else
+    {
+        rbeg = abeg = beg;
+        rlen = alen = len;
+        // check for incomplete del as above??
+    }
+
+#define XDBG 0
+#if XDBG
+fprintf(stderr,"build_hap:  rbeg=%d + %d    abeg=%d \n",rbeg,rlen,abeg);
+#endif 
+    splice->kref.l = 0;
+    splice->kalt.l = 0;
+
+    // add the part before vcf.ref, in the vcf.ref and after vcf.ref
+    int roff;   // how many vcf.ref bases already used
+    if ( rbeg < splice->vcf.pos )
+    {
+        assert( splice->tr->beg <= rbeg );  // this can be extended thanks to N_REF_PAD
+        kputsn(splice->tr->ref + N_REF_PAD + rbeg - splice->tr->beg, splice->vcf.pos - rbeg, &splice->kref);
+        roff = 0;
+    }
+    else
+        roff = rbeg - splice->vcf.pos;
+#if XDBG
+fprintf(stderr,"r1: %s  roff=%d\n",splice->kref.s,roff);
+#endif
+
+    if ( roff < splice->vcf.rlen && splice->kref.l < rlen )
+    {
+        int len = splice->vcf.rlen - roff;  // len still available in vcf.ref
+        if ( len > rlen - splice->kref.l ) len = rlen - splice->kref.l; // how much of ref allele is still needed
+        kputsn(splice->vcf.ref + roff, len, &splice->kref);
+    }
+#if XDBG
+fprintf(stderr,"r2: %s\n",splice->kref.s);
+#endif
+
+    uint32_t end = splice->vcf.pos + splice->vcf.rlen;    // position just after the ref allele
+    if ( splice->kref.l < rlen )
+    {
+        if ( end + rlen - splice->kref.l - 1 > splice->tr->end ) // trim, the requested sequence is too long (could be extended, see N_REF_PAD)
+            rlen -= end + rlen - splice->kref.l - 1 - splice->tr->end;
+        if ( splice->kref.l < rlen )
+            kputsn(splice->tr->ref + N_REF_PAD + end - splice->tr->beg, rlen - splice->kref.l, &splice->kref);
+    }
+#if XDBG
+fprintf(stderr,"r3: %s\n",splice->kref.s);
+#endif
+
+
+    int aoff;
+    if ( abeg < splice->vcf.pos )
+    {
+        assert( splice->tr->beg <= abeg );
+        kputsn(splice->tr->ref + N_REF_PAD + abeg - splice->tr->beg, splice->vcf.pos - abeg, &splice->kalt);
+        aoff = 0;
+    }
+    else
+        aoff = abeg - splice->vcf.pos;
+#if XDBG
+fprintf(stderr,"a1: %s  aoff=%d\n",splice->kalt.s,aoff);
+#endif
+
+    if ( aoff < splice->vcf.alen && splice->kalt.l < alen )
+    {
+        int len = splice->vcf.alen - aoff;  // len still available in vcf.alt
+        if ( len > alen - splice->kalt.l ) len = alen - splice->kalt.l; // how much of alt allele is still needed
+        kputsn(splice->vcf.alt + aoff, len, &splice->kalt);
+        aoff -= len;
+    }
+    if ( aoff < 0 ) aoff = 0;
+    else aoff--;
+#if XDBG
+fprintf(stderr,"a2: %s  aoff=%d\n",splice->kalt.s,aoff);
+#endif
+
+    end = splice->vcf.pos + splice->vcf.rlen;    // position just after the ref allele
+    if ( splice->kalt.l < alen )
+    {
+        if ( end + alen + aoff - splice->kalt.l - 1 > splice->tr->end ) // trim, the requested sequence is too long
+            alen -= end + alen + aoff - splice->kalt.l - 1 - splice->tr->end;
+        if ( alen > 0 && alen > splice->kalt.l )
+            kputsn(splice->tr->ref + aoff + N_REF_PAD + end - splice->tr->beg, alen - splice->kalt.l, &splice->kalt);
+    }
+#if XDBG
+fprintf(stderr,"a3: %s\n",splice->kalt.s);
+fprintf(stderr," [%s]\n [%s]\n\n",splice->kref.s,splice->kalt.s);
+#endif
+}
+void csq_stage(args_t *args, csq_t *csq, bcf1_t *rec);
+static inline int csq_stage_utr(args_t *args, regitr_t *itr, bcf1_t *rec, uint32_t trid, uint32_t type, int ial)
+{
+    while ( regitr_overlap(itr) )
+    {
+        gf_utr_t *utr = regitr_payload(itr, gf_utr_t*);
+        tscript_t *tr = utr->tr;
+        if ( tr->id != trid ) continue;
+        csq_t csq; 
+        memset(&csq, 0, sizeof(csq_t));
+        csq.pos          = rec->pos;
+        csq.type.type    = (utr->which==prime5 ? CSQ_UTR5 : CSQ_UTR3) | type;
+        csq.type.biotype = tr->type;
+        csq.type.strand  = tr->strand;
+        csq.type.trid    = tr->id;
+        csq.type.vcf_ial = ial;
+        csq.type.gene    = tr->gene->name;
+        csq_stage(args, &csq, rec);
+        return csq.type.type;
+    }
+    return 0;
+}
+static inline void csq_stage_splice(args_t *args, bcf1_t *rec, tscript_t *tr, uint32_t type, int ial)
+{
+#if XDBG
+fprintf(stderr,"csq_stage_splice %d: type=%d\n",rec->pos+1,type);
+#endif
+    if ( !type ) return;
+    csq_t csq; 
+    memset(&csq, 0, sizeof(csq_t));
+    csq.pos          = rec->pos;
+    csq.type.type    = type;
+    csq.type.biotype = tr->type;
+    csq.type.strand  = tr->strand;
+    csq.type.trid    = tr->id;
+    csq.type.vcf_ial = ial;
+    csq.type.gene    = tr->gene->name;
+    csq_stage(args, &csq, rec);
+}
+static inline int splice_csq_ins(args_t *args, splice_t *splice, uint32_t ex_beg, uint32_t ex_end)
+{
+    // coordinates that matter for consequences, eg AC>ACG trimmed to C>CG, 1bp
+    // before and after the inserted bases
+    if ( splice->tbeg || splice->vcf.ref[0]!=splice->vcf.alt[0] )
+    {
+        splice->ref_beg = splice->vcf.pos + splice->tbeg - 1;
+        splice->ref_end = splice->vcf.pos + splice->vcf.rlen - splice->tend;
+    }
+    else
+    {
+        if ( splice->tend ) splice->tend--;
+        splice->ref_beg = splice->vcf.pos;
+        splice->ref_end = splice->vcf.pos + splice->vcf.rlen - splice->tend;
+    }
+#if XDBG
+fprintf(stderr,"ins: %s>%s .. ex=%d,%d  beg,end=%d,%d  tbeg,tend=%d,%d  check_utr=%d start,stop,beg,end=%d,%d,%d,%d\n", splice->vcf.ref,splice->vcf.alt,ex_beg,ex_end,splice->ref_beg,splice->ref_end,splice->tbeg,splice->tend,splice->check_utr,splice->check_start,splice->check_stop,splice->check_region_beg,splice->check_region_end);
+#endif
+
+    int ret;
+    if ( splice->ref_beg >= ex_end )   // fully outside, beyond the exon
+    {
+        if ( splice->check_utr )
+        {
+            regitr_t *itr = regitr_init(NULL);
+            const char *chr = bcf_seqname(args->hdr,splice->vcf.rec);
+            if ( regidx_overlap(args->idx_utr,chr,splice->ref_beg+1,splice->ref_beg+1, itr) )     // adjacent utr
+            {
+                ret = csq_stage_utr(args, itr, splice->vcf.rec, splice->tr->id, splice->csq, splice->vcf.ial);
+                if ( ret!=0 ) 
+                {
+                    regitr_destroy(itr);
+                    return SPLICE_OUTSIDE; // overlaps utr
+                }
+            }
+            regitr_destroy(itr);
+        }
+        if ( !splice->check_region_end ) return SPLICE_OUTSIDE;
+        char *ref = NULL, *alt = NULL;
+        if ( splice->set_refalt )   // seq identity is checked only when tr->ref is available
+        {
+            splice_build_hap(splice, ex_end+1, N_SPLICE_REGION_INTRON);
+            ref = splice->kref.s, alt = splice->kalt.s;
+        }
+        if ( splice->ref_beg < ex_end + N_SPLICE_REGION_INTRON && splice->ref_end > ex_end + N_SPLICE_DONOR )
+        {
+            splice->csq |= CSQ_SPLICE_REGION;
+            if ( ref && !strncmp(ref,alt,N_SPLICE_REGION_INTRON) ) splice->csq |= CSQ_SYNONYMOUS_VARIANT;
+        }
+        if ( splice->ref_beg < ex_end + N_SPLICE_DONOR )
+        {
+            if ( splice->check_donor && splice->tr->strand==STRAND_FWD ) splice->csq |= CSQ_SPLICE_DONOR;
+            if ( splice->check_acceptor && splice->tr->strand==STRAND_REV ) splice->csq |= CSQ_SPLICE_ACCEPTOR;
+            if ( ref && !strncmp(ref,alt,N_SPLICE_DONOR) ) splice->csq |= CSQ_SYNONYMOUS_VARIANT;
+        }
+        csq_stage_splice(args, splice->vcf.rec, splice->tr, splice->csq, splice->vcf.ial);
+        return SPLICE_OUTSIDE;
+    }
+    if ( splice->ref_end < ex_beg || (splice->ref_end == ex_beg && !splice->check_region_beg) )    // fully outside, before the exon
+    {
+        if ( splice->check_utr )
+        {
+            regitr_t *itr = regitr_init(NULL);
+            const char *chr = bcf_seqname(args->hdr,splice->vcf.rec);
+            if ( regidx_overlap(args->idx_utr,chr,splice->ref_end-1,splice->ref_end-1, itr) )     // adjacent utr
+            {
+                ret = csq_stage_utr(args, itr, splice->vcf.rec, splice->tr->id, splice->csq, splice->vcf.ial);
+                if ( ret!=0 )
+                {
+                    regitr_destroy(itr);
+                    return SPLICE_OUTSIDE; // overlaps utr
+                }
+            }
+            regitr_destroy(itr);
+        }
+        if ( !splice->check_region_beg ) return SPLICE_OUTSIDE;
+        char *ref = NULL, *alt = NULL;
+        if ( splice->set_refalt )   // seq identity is checked only when tr->ref is available
+        {
+            splice_build_hap(splice, ex_beg - N_SPLICE_REGION_INTRON, N_SPLICE_REGION_INTRON);
+            ref = splice->kref.s, alt = splice->kalt.s;
+        }
+        if ( splice->ref_end > ex_beg - N_SPLICE_REGION_INTRON && splice->ref_beg < ex_beg - N_SPLICE_DONOR )
+        {
+            splice->csq |= CSQ_SPLICE_REGION;
+            if ( ref && !strncmp(ref,alt,N_SPLICE_REGION_INTRON) ) splice->csq |= CSQ_SYNONYMOUS_VARIANT;
+        }
+        if ( splice->ref_end > ex_beg - N_SPLICE_DONOR )
+        {
+            if ( splice->check_donor && splice->tr->strand==STRAND_REV ) splice->csq |= CSQ_SPLICE_DONOR;
+            if ( splice->check_acceptor && splice->tr->strand==STRAND_FWD ) splice->csq |= CSQ_SPLICE_ACCEPTOR;
+            if ( ref && !strncmp(ref+N_SPLICE_REGION_INTRON-N_SPLICE_DONOR,alt+N_SPLICE_REGION_INTRON-N_SPLICE_DONOR,N_SPLICE_DONOR) ) splice->csq |= CSQ_SYNONYMOUS_VARIANT;
+        }
+        csq_stage_splice(args, splice->vcf.rec, splice->tr, splice->csq, splice->vcf.ial);
+        return SPLICE_OUTSIDE;
+    }
+    // overlaps the exon or inside the exon
+    // possible todo: find better alignment for frameshifting variants?
+    if ( splice->ref_beg <= ex_beg + 2 )    // in the first 3bp
+    {
+        if ( splice->check_region_beg ) splice->csq |= CSQ_SPLICE_REGION;
+        if ( splice->tr->strand==STRAND_FWD ) { if ( splice->check_start ) splice->csq |= CSQ_START_LOST; }
+        else { if ( splice->check_stop ) splice->csq |= CSQ_STOP_LOST; }
+    }
+    if ( splice->ref_end > ex_end - 2 )
+    {
+        if ( splice->check_region_end ) splice->csq |= CSQ_SPLICE_REGION;
+        if ( splice->tr->strand==STRAND_REV ) { if ( splice->check_start ) splice->csq |= CSQ_START_LOST; }
+        else { if ( splice->check_stop ) splice->csq |= CSQ_STOP_LOST; }
+    }
+    if ( splice->set_refalt )
+    {
+        // Make sure the variant will not end up left aligned to avoid overlapping vcf records
+        //      splice_build_hap(splice, splice->ref_beg, splice->vcf.alen - splice->tend - splice->tbeg + 1);
+        //      splice->vcf.rlen -= splice->tbeg + splice->tend - 1;
+        //      if ( splice->kref.l > splice->vcf.rlen ) { splice->kref.l = splice->vcf.rlen;  splice->kref.s[splice->kref.l] = 0; }
+        if ( splice->ref_beg < splice->vcf.pos )    // this must have been caused by too much trimming from right
+        {
+            int dlen = splice->vcf.pos - splice->ref_beg;
+            assert( dlen==1 );
+            splice->tbeg += dlen;
+            if ( splice->tbeg + splice->tend == splice->vcf.rlen ) splice->tend -= dlen;
+            splice->ref_beg = splice->vcf.pos;
+        }
+        if ( splice->ref_end==ex_beg ) splice->tend--;  // prevent zero-length ref allele
+        splice_build_hap(splice, splice->ref_beg, splice->vcf.alen - splice->tend - splice->tbeg + 1);
+        splice->vcf.rlen -= splice->tbeg + splice->tend - 1;
+        if ( splice->kref.l > splice->vcf.rlen ) { splice->kref.l = splice->vcf.rlen;  splice->kref.s[splice->kref.l] = 0; }
+    }
+    csq_stage_splice(args, splice->vcf.rec, splice->tr, splice->csq, splice->vcf.ial);
+    return SPLICE_INSIDE;
+}
+
+int shifted_del_synonymous(args_t *args, splice_t *splice, uint32_t ex_beg, uint32_t ex_end)
+{
+    static int small_ref_padding_warned = 0;
+    tscript_t *tr = splice->tr;
+
+    // We know the VCF record overlaps the exon, but does it overlap the start codon?
+    if ( tr->strand==STRAND_REV && splice->vcf.pos + splice->vcf.rlen + 2 <= ex_end ) return 0;
+    if ( tr->strand==STRAND_FWD && splice->vcf.pos >= ex_beg + 3 ) return 0;
+
+#if XDBG
+    fprintf(stderr,"shifted_del_synonymous: %d-%d  %s\n",ex_beg,ex_end, tr->strand==STRAND_FWD?"fwd":"rev");
+    fprintf(stderr,"   %d  ..  %s > %s\n",splice->vcf.pos+1,splice->vcf.ref,splice->vcf.alt);
+#endif
+
+    // is there enough ref sequence for the extension? All coordinates are 0-based
+    int ref_len = strlen(splice->vcf.ref);
+    int alt_len = strlen(splice->vcf.alt);
+    assert( ref_len > alt_len );
+    int ndel = ref_len - alt_len;
+
+    if ( tr->strand==STRAND_REV )
+    {
+        int32_t vcf_ref_end = splice->vcf.pos + ref_len - 1;  // end pos of the VCF REF allele
+        int32_t tr_ref_end  = splice->tr->end + N_REF_PAD;    // the end pos of accessible cached ref seq
+        if ( vcf_ref_end + ndel > tr_ref_end )
+        {
+            if ( !small_ref_padding_warned )
+            {
+                fprintf(stderr,"Warning: Could not verify synonymous start/stop at %s:%d due to small N_REF_PAD. (Improve me?)\n",bcf_seqname(args->hdr,splice->vcf.rec),splice->vcf.pos+1);
+                small_ref_padding_warned = 1;
+            }
+            return 0;
+        }
+
+        char *ptr_vcf = splice->vcf.ref + alt_len;                         // the first deleted base in the VCF REF allele
+        char *ptr_ref = splice->tr->ref + N_REF_PAD + (vcf_ref_end + 1 - splice->tr->beg);  // the first ref base after the ndel bases deleted
+#if XDBG
+        fprintf(stderr,"vcf: %s\nref: %s\n",ptr_vcf,ptr_ref);
+#endif
+        int i = 0;
+        while ( ptr_vcf[i] && ptr_vcf[i]==ptr_ref[i] ) i++;
+        if ( ptr_vcf[i] ) return 0;       // the deleted sequence cannot be replaced
+    }
+    else 
+    {
+        // STRAND_FWD
+        int32_t vcf_block_beg = splice->vcf.pos + ref_len - 2*ndel;        // the position of the first base of the ref block that could potentially replace the deletion
+        if ( vcf_block_beg < 0 ) return 0;
+
+#if XDBG
+        fprintf(stderr,"vcf_block_beg: %d\n",vcf_block_beg+1);
+#endif
+
+        if ( N_REF_PAD + vcf_block_beg < ex_beg )
+        {
+            if ( !small_ref_padding_warned )
+            {
+                fprintf(stderr,"Warning: Could not verify synonymous start/stop at %s:%d due to small N_REF_PAD. (Improve me?)\n",bcf_seqname(args->hdr,splice->vcf.rec),splice->vcf.pos+1);
+                small_ref_padding_warned = 1;
+            }
+            return 0;
+        }
+
+        char *ptr_vcf = splice->vcf.ref + alt_len;                                      // the first deleted base in the VCF REF allele
+        char *ptr_ref = splice->tr->ref + N_REF_PAD + vcf_block_beg - splice->tr->beg;  // the replacement ref block
+#if XDBG
+        fprintf(stderr,"vcf: %s\nref: %s\n",ptr_vcf,ptr_ref);
+#endif
+
+        int i = 0;
+        while ( ptr_vcf[i] && ptr_vcf[i]==ptr_ref[i] ) i++;
+        if ( ptr_vcf[i] ) return 0;       // the deleted sequence cannot be replaced
+    }
+
+    return 1;
+}
+
+static inline int splice_csq_del(args_t *args, splice_t *splice, uint32_t ex_beg, uint32_t ex_end)
+{
+    if ( splice->check_start )
+    {
+        // check for synonymous start
+        //      test/csq/ENST00000375992/incorrect-synon-del-not-start-lost.txt
+        //      test/csq/ENST00000368801.2/start-lost.txt
+        //      test/csq/ENST00000318249.2/synonymous-start-lost.txt
+        int is_synonymous = shifted_del_synonymous(args, splice, ex_beg, ex_end);
+        if ( is_synonymous )
+        {
+            splice->csq |= CSQ_START_RETAINED;
+            return SPLICE_OVERLAP;
+        }
+    }
+
+    // coordinates that matter for consequences, eg AC>ACG trimmed to C>CG
+    splice->ref_beg = splice->vcf.pos + splice->tbeg - 1;                       // 1b before the deleted base
+    splice->ref_end = splice->vcf.pos + splice->vcf.rlen - splice->tend - 1;    // the last deleted base
+
+#if XDBG
+fprintf(stderr,"splice_csq_del: %s>%s .. ex=%d,%d  beg,end=%d,%d  tbeg,tend=%d,%d  check_utr=%d start,stop,beg,end=%d,%d,%d,%d\n", splice->vcf.ref,splice->vcf.alt,ex_beg,ex_end,splice->ref_beg,splice->ref_end,splice->tbeg,splice->tend,splice->check_utr,splice->check_start,splice->check_stop,splice->check_region_beg,splice->check_region_end);
+#endif
+
+    if ( splice->ref_beg + 1 < ex_beg )     // the part before the exon; ref_beg is off by -1
+    {
+        if ( splice->check_region_beg )
+        {
+            int csq = 0;
+            if ( splice->check_utr )
+            {
+                regitr_t *itr = regitr_init(NULL);
+                const char *chr = bcf_seqname(args->hdr,splice->vcf.rec);
+                if ( regidx_overlap(args->idx_utr,chr,splice->ref_beg,ex_beg-1, itr) )     // adjacent utr
+                    csq = csq_stage_utr(args, itr, splice->vcf.rec, splice->tr->id, splice->csq, splice->vcf.ial);
+                regitr_destroy(itr);
+            }
+            if ( !csq )
+            {
+                char *ref = NULL, *alt = NULL;
+                if ( splice->set_refalt )   // seq identity is checked only when tr->ref is available
+                {
+                    // filling from the left does not work for ENST00000341065/frame3.vcf
+                    //    CAG.GTGGCCAG      CAG.GTGGCCAG
+                    //    CA-.--GGCCAG  vs  CAG.---GCCAG
+                    //  splice_build_hap(splice, ex_beg-1, -N_SPLICE_REGION_INTRON);
+                    //
+                    // filling from the right:
+                    splice_build_hap(splice, ex_beg - N_SPLICE_REGION_INTRON, N_SPLICE_REGION_INTRON);
+                    ref = splice->kref.s, alt = splice->kalt.s;
+                }
+                if ( splice->ref_end >= ex_beg - N_SPLICE_REGION_INTRON && splice->ref_beg < ex_beg - N_SPLICE_DONOR )
+                {
+                    splice->csq |= CSQ_SPLICE_REGION;
+                    if ( ref && alt && !strncmp(ref,alt,N_SPLICE_REGION_INTRON) ) splice->csq |= CSQ_SYNONYMOUS_VARIANT;
+                }
+                if ( splice->ref_end >= ex_beg - N_SPLICE_DONOR )
+                {
+                    if ( splice->check_donor && splice->tr->strand==STRAND_REV ) splice->csq |= CSQ_SPLICE_DONOR;
+                    if ( splice->check_acceptor && splice->tr->strand==STRAND_FWD ) splice->csq |= CSQ_SPLICE_ACCEPTOR;
+                    if ( ref && alt && !strncmp(ref+N_SPLICE_REGION_INTRON-N_SPLICE_DONOR,alt+N_SPLICE_REGION_INTRON-N_SPLICE_DONOR,N_SPLICE_DONOR) ) splice->csq |= CSQ_SYNONYMOUS_VARIANT;
+                }
+            }
+        }
+        if ( splice->ref_end >= ex_beg ) 
+        {
+            splice->tbeg = splice->ref_beg - splice->vcf.pos + 1;
+            splice->ref_beg = ex_beg - 1;
+            if ( splice->tbeg + splice->tend == splice->vcf.alen )
+            {
+                // the deletion overlaps ex_beg and cannot be easily realigned to the right
+                if ( !splice->tend )
+                {
+                    splice->csq |= CSQ_CODING_SEQUENCE;
+                    return SPLICE_OVERLAP;
+                }
+                splice->tend--;
+            }
+        }
+    }
+    if ( ex_end < splice->ref_end )     // the part after the exon
+    {
+        if ( splice->check_region_end )
+        {
+            int csq = 0;
+            if ( splice->check_utr )
+            {
+                regitr_t *itr = regitr_init(NULL);
+                const char *chr = bcf_seqname(args->hdr,splice->vcf.rec);
+                if ( regidx_overlap(args->idx_utr,chr,ex_end+1,splice->ref_end, itr) )     // adjacent utr
+                    csq = csq_stage_utr(args, itr, splice->vcf.rec, splice->tr->id, splice->csq, splice->vcf.ial);
+                regitr_destroy(itr);
+            }
+            if ( !csq )
+            {
+                char *ref = NULL, *alt = NULL;
+                if ( splice->set_refalt )   // seq identity is checked only when tr->ref is available
+                {
+                    splice_build_hap(splice, ex_end+1, N_SPLICE_REGION_INTRON);  // ref,alt positioned at the first intron base
+                    ref = splice->kref.s, alt = splice->kalt.s;
+                }
+                if ( splice->ref_beg < ex_end + N_SPLICE_REGION_INTRON && splice->ref_end > ex_end + N_SPLICE_DONOR )
+                {
+                    splice->csq |= CSQ_SPLICE_REGION;
+                    if ( ref && alt && !strncmp(ref,alt,N_SPLICE_REGION_INTRON) ) splice->csq |= CSQ_SYNONYMOUS_VARIANT;
+                }
+                if ( splice->ref_beg < ex_end + N_SPLICE_DONOR )
+                {
+                    if ( splice->check_donor && splice->tr->strand==STRAND_FWD ) splice->csq |= CSQ_SPLICE_DONOR;
+                    if ( splice->check_acceptor && splice->tr->strand==STRAND_REV ) splice->csq |= CSQ_SPLICE_ACCEPTOR;
+                    if ( ref && alt && !strncmp(ref+N_SPLICE_REGION_INTRON-N_SPLICE_DONOR,alt+N_SPLICE_REGION_INTRON-N_SPLICE_DONOR,N_SPLICE_DONOR) ) splice->csq |= CSQ_SYNONYMOUS_VARIANT;
+                }
+            }
+        }
+        if ( splice->ref_beg < ex_end ) 
+        {
+            splice->tend = splice->vcf.rlen - (splice->ref_end - splice->vcf.pos + 1);
+            splice->ref_end = ex_end;
+        }
+    }
+    if ( splice->ref_end < ex_beg || splice->ref_beg >= ex_end )
+    {
+        csq_stage_splice(args, splice->vcf.rec, splice->tr, splice->csq, splice->vcf.ial);
+        return SPLICE_OUTSIDE;
+    }
+    if ( splice->ref_beg < ex_beg + 2 ) // ref_beg is off by -1
+    {
+        if ( splice->check_region_beg ) splice->csq |= CSQ_SPLICE_REGION;
+        if ( splice->tr->strand==STRAND_FWD ) { if ( splice->check_start ) splice->csq |= CSQ_START_LOST; }
+        else { if ( splice->check_stop ) splice->csq |= CSQ_STOP_LOST; }
+    }
+    if ( splice->ref_end > ex_end - 3 )
+    {
+        if ( splice->check_region_end ) splice->csq |= CSQ_SPLICE_REGION;
+        if ( splice->tr->strand==STRAND_REV ) { if ( splice->check_start ) splice->csq |= CSQ_START_LOST; }
+        else { if ( splice->check_stop ) splice->csq |= CSQ_STOP_LOST; }
+    }
+    if ( splice->set_refalt )
+    {
+        if ( splice->tbeg>0 ) splice->tbeg--;  //why is this?
+        if ( splice->vcf.rlen > splice->tbeg + splice->tend && splice->vcf.alen > splice->tbeg + splice->tend )
+        {
+            splice->vcf.rlen -= splice->tbeg + splice->tend;
+            splice->vcf.alen -= splice->tbeg + splice->tend;
+        }
+        splice->kref.l = 0; kputsn(splice->vcf.ref + splice->tbeg, splice->vcf.rlen, &splice->kref); 
+        splice->kalt.l = 0; kputsn(splice->vcf.alt + splice->tbeg, splice->vcf.alen, &splice->kalt); 
+        if ( (splice->ref_beg+1 < ex_beg && splice->ref_end >= ex_beg) || (splice->ref_beg+1 < ex_end && splice->ref_end >= ex_end) ) // ouch, ugly ENST00000409523/long-overlapping-del.vcf
+        {
+            splice->csq |= (splice->ref_end - splice->ref_beg)%3 ? CSQ_FRAMESHIFT_VARIANT : CSQ_INFRAME_DELETION;
+            return SPLICE_OVERLAP;
+        }
+    }
+    csq_stage_splice(args, splice->vcf.rec, splice->tr, splice->csq, splice->vcf.ial);
+    return SPLICE_INSIDE;
+}
+
+static inline int splice_csq_mnp(args_t *args, splice_t *splice, uint32_t ex_beg, uint32_t ex_end)
+{
+    // not a real variant, can be ignored: eg ACGT>ACGT
+    if ( splice->tbeg + splice->tend == splice->vcf.rlen ) return SPLICE_VAR_REF;
+
+    splice->ref_beg = splice->vcf.pos + splice->tbeg;
+    splice->ref_end = splice->vcf.pos + splice->vcf.rlen - splice->tend - 1;
+
+#if XDBG
+fprintf(stderr,"mnp: %s>%s .. ex=%d,%d  beg,end=%d,%d  tbeg,tend=%d,%d  check_utr=%d start,stop,beg,end=%d,%d,%d,%d\n", splice->vcf.ref,splice->vcf.alt,ex_beg,ex_end,splice->ref_beg,splice->ref_end,splice->tbeg,splice->tend,splice->check_utr,splice->check_start,splice->check_stop,splice->check_region_beg,splice->check_region_end);
+#endif
+
+    if ( splice->ref_beg < ex_beg )     // the part before the exon
+    {
+        if ( splice->check_region_beg )
+        {
+            int csq = 0;
+            if ( splice->check_utr )
+            {
+                regitr_t *itr = regitr_init(NULL);
+                const char *chr = bcf_seqname(args->hdr,splice->vcf.rec);
+                if ( regidx_overlap(args->idx_utr,chr,splice->ref_beg,ex_beg-1, itr) )     // adjacent utr
+                    csq = csq_stage_utr(args, itr, splice->vcf.rec, splice->tr->id, splice->csq, splice->vcf.ial);
+                regitr_destroy(itr);
+            }
+            if ( !csq )
+            {
+                if ( splice->ref_end >= ex_beg - N_SPLICE_REGION_INTRON && splice->ref_beg < ex_beg - N_SPLICE_DONOR )
+                    splice->csq |= CSQ_SPLICE_REGION;
+                if ( splice->ref_end >= ex_beg - N_SPLICE_DONOR )
+                {
+                    if ( splice->check_donor && splice->tr->strand==STRAND_REV ) splice->csq |= CSQ_SPLICE_DONOR;
+                    if ( splice->check_acceptor && splice->tr->strand==STRAND_FWD ) splice->csq |= CSQ_SPLICE_ACCEPTOR;
+                }
+            }
+        }
+        if ( splice->ref_end >= ex_beg ) 
+        {
+            splice->tbeg = splice->ref_beg - splice->vcf.pos;
+            splice->ref_beg = ex_beg;
+        }
+    }
+    if ( ex_end < splice->ref_end )     // the part after the exon
+    {
+        if ( splice->check_region_end )
+        {
+            int csq = 0;
+            if ( splice->check_utr )
+            {
+                regitr_t *itr = regitr_init(NULL);
+                const char *chr = bcf_seqname(args->hdr,splice->vcf.rec);
+                if ( regidx_overlap(args->idx_utr,chr,ex_end+1,splice->ref_end, itr) )     // adjacent utr
+                    csq = csq_stage_utr(args, itr, splice->vcf.rec, splice->tr->id, splice->csq, splice->vcf.ial);
+                regitr_destroy(itr);
+            }
+            if ( !csq )
+            {
+                if ( splice->ref_beg <= ex_end + N_SPLICE_REGION_INTRON && splice->ref_end > ex_end + N_SPLICE_DONOR )
+                    splice->csq |= CSQ_SPLICE_REGION;
+                if ( splice->ref_beg <= ex_end + N_SPLICE_DONOR )
+                {
+                    if ( splice->check_donor && splice->tr->strand==STRAND_FWD ) splice->csq |= CSQ_SPLICE_DONOR;
+                    if ( splice->check_acceptor && splice->tr->strand==STRAND_REV ) splice->csq |= CSQ_SPLICE_ACCEPTOR;
+                }
+            }
+        }
+        if ( splice->ref_beg <= ex_end ) 
+        {
+            splice->tend = splice->vcf.rlen - (splice->ref_end - splice->vcf.pos + 1);
+            splice->ref_end = ex_end;
+        }
+    }
+    if ( splice->ref_end < ex_beg || splice->ref_beg > ex_end )
+    {
+        csq_stage_splice(args, splice->vcf.rec, splice->tr, splice->csq, splice->vcf.ial);
+        return SPLICE_OUTSIDE;
+    }
+
+    if ( splice->ref_beg < ex_beg + 3 )
+    {
+        if ( splice->check_region_beg ) splice->csq |= CSQ_SPLICE_REGION;
+        if ( splice->tr->strand==STRAND_FWD ) { if ( splice->check_start ) splice->csq |= CSQ_START_LOST; }
+        else { if ( splice->check_stop ) splice->csq |= CSQ_STOP_LOST; }
+    }
+    if ( splice->ref_end > ex_end - 3 )
+    {
+        if ( splice->check_region_end ) splice->csq |= CSQ_SPLICE_REGION;
+        if ( splice->tr->strand==STRAND_REV ) { if ( splice->check_start ) splice->csq |= CSQ_START_LOST; }
+        else { if ( splice->check_stop ) splice->csq |= CSQ_STOP_LOST; }
+    }
+    if ( splice->set_refalt )
+    {
+        splice->vcf.rlen -= splice->tbeg + splice->tend;
+        splice->kref.l = 0; kputsn(splice->vcf.ref + splice->tbeg, splice->vcf.rlen, &splice->kref); 
+        splice->kalt.l = 0; kputsn(splice->vcf.alt + splice->tbeg, splice->vcf.rlen, &splice->kalt); 
+    }
+    csq_stage_splice(args, splice->vcf.rec, splice->tr, splice->csq, splice->vcf.ial);
+    return SPLICE_INSIDE;
+}
+static inline int splice_csq(args_t *args, splice_t *splice, uint32_t ex_beg, uint32_t ex_end)
+{
+    splice->vcf.alen = strlen(splice->vcf.alt);
+
+    int rlen1 = splice->vcf.rlen - 1, alen1 = splice->vcf.alen - 1, i = 0;
+    splice->tbeg = 0, splice->tend = 0;
+
+    // trim from the right, then from the left
+    while ( i<=rlen1 && i<=alen1 )
+    {
+        if ( splice->vcf.ref[rlen1-i] != splice->vcf.alt[alen1-i] ) break;
+        i++;
+    }
+    splice->tend = i;
+    rlen1 -= i, alen1 -= i, i = 0;
+    while ( i<=rlen1 && i<=alen1 )
+    {
+        if ( splice->vcf.ref[i] != splice->vcf.alt[i] ) break;
+        i++;
+    }
+    splice->tbeg = i;
+
+    // The mnp, ins and del code was split into near-identical functions for clarity and debugging;
+    // possible todo: generalize once stable
+    if ( splice->vcf.rlen==splice->vcf.alen ) return splice_csq_mnp(args, splice, ex_beg, ex_end);
+    if ( splice->vcf.rlen < splice->vcf.alen ) return splice_csq_ins(args, splice, ex_beg, ex_end);
+    if ( splice->vcf.rlen > splice->vcf.alen ) return splice_csq_del(args, splice, ex_beg, ex_end);
+
+    return 0;
+}
+
+
+// return value: 0 added, 1 overlapping variant, 2 silent discard (intronic,alt=ref)
+int hap_init(args_t *args, hap_node_t *parent, hap_node_t *child, gf_cds_t *cds, bcf1_t *rec, int ial)
+{
+    int i;
+    kstring_t str = {0,0,0};
+    tscript_t *tr = cds->tr;
+    child->icds = cds->icds;     // index of cds in the tscript's list of exons
+    child->vcf_ial = ial;
+
+    splice_t splice;
+    splice_init(&splice, rec);
+    splice.tr = tr;
+    splice.vcf.ial  = ial;
+    splice.vcf.alt  = rec->d.allele[ial];
+    splice.check_acceptor = splice.check_donor = splice.set_refalt = splice.check_utr = 1;
+    if ( !(tr->trim & TRIM_5PRIME) )
+    {
+        if ( tr->strand==STRAND_FWD ) { if ( child->icds==0 ) splice.check_start = 1; }
+        else { if ( child->icds==tr->ncds-1 ) splice.check_start = 1; }
+    }
+    if ( !(tr->trim & TRIM_3PRIME) )
+    {
+        if ( tr->strand==STRAND_FWD ) { if ( child->icds==tr->ncds-1 ) splice.check_stop = 1; }
+        else { if ( child->icds==0 ) splice.check_stop = 1; }
+    }
+    if ( splice.check_start )   // do not check starts in incomplete CDS, defined as not starting with M
+    {
+        if ( tr->strand==STRAND_FWD ) { if ( dna2aa(tr->ref+N_REF_PAD+cds->beg-tr->beg) != 'M' ) splice.check_start = 0; }
+        else { if ( cdna2aa(tr->ref+N_REF_PAD+cds->beg-tr->beg+cds->len-3) != 'M' ) splice.check_start = 0; }
+    }
+    if ( child->icds!=0 ) splice.check_region_beg = 1;
+    if ( child->icds!=tr->ncds-1 ) splice.check_region_end = 1;
+
+#if XDBG
+fprintf(stderr,"\nhap_init: %d [%s][%s]   check start:%d,stop:%d\n",splice.vcf.pos+1,splice.vcf.ref,splice.vcf.alt,splice.check_start,splice.check_stop);
+#endif
+    int ret = splice_csq(args, &splice, cds->beg, cds->beg + cds->len - 1);
+#if XDBG
+fprintf(stderr,"cds splice_csq: %d [%s][%s] .. beg,end=%d %d, ret=%d, csq=%d\n\n",splice.vcf.pos+1,splice.kref.s,splice.kalt.s,splice.ref_beg+1,splice.ref_end+1,ret,splice.csq);
+#endif
+
+    if ( ret==SPLICE_VAR_REF ) return 2;  // not a variant, eg REF=CA ALT=CA
+    if ( ret==SPLICE_OUTSIDE || ret==SPLICE_OVERLAP || splice.csq==CSQ_START_LOST )  // not a coding csq
+    {
+        free(splice.kref.s);
+        free(splice.kalt.s);
+
+        if ( !splice.csq ) return 2;        // fully intronic, no csq
+
+        // splice_region/acceptor/donor
+        child->seq  = NULL;
+        child->sbeg = 0;
+        child->rbeg = rec->pos;
+        child->rlen = 0;
+        child->dlen = 0;
+        kputs(rec->d.allele[0],&str);
+        kputc('>',&str);
+        kputs(rec->d.allele[ial],&str);
+        child->var  = str.s;
+        child->type = HAP_SSS;
+        child->csq  = splice.csq;
+        child->rec  = rec;
+        return 0;
+    }
+    if ( splice.csq & CSQ_SYNONYMOUS_VARIANT ) splice.csq &= ~CSQ_SYNONYMOUS_VARIANT;   // synonymous&splice,frame could become synonymous&frame,splice
+
+    int dbeg = 0;
+    if ( splice.ref_beg < cds->beg )
+    {
+        // The vcf record overlaps the exon boundary, but the variant itself
+        // should fit inside since we are here. This will need more work.
+        // #1475227917
+        dbeg = cds->beg - splice.ref_beg;
+        splice.kref.l -= dbeg;
+        splice.ref_beg = cds->beg;
+        assert( dbeg <= splice.kalt.l );
+    }
+
+    assert( parent->type!=HAP_SSS );
+    if ( parent->type==HAP_CDS )    
+    {
+        i = parent->icds;
+        if ( i!=cds->icds )
+        {
+            // the variant is on a new exon, finish up the previous
+            int len = tr->cds[i]->len - parent->rbeg - parent->rlen + tr->cds[i]->beg;
+            if ( len > 0 )
+                kputsn_(tr->ref + N_REF_PAD + parent->rbeg + parent->rlen - tr->beg, len, &str);
+        }
+
+        // append any skipped non-variant exons
+        while ( ++i < cds->icds )
+            kputsn_(tr->ref + N_REF_PAD + tr->cds[i]->beg - tr->beg, tr->cds[i]->len, &str);
+
+        if ( parent->icds==child->icds )
+        {
+            int len = splice.ref_beg - parent->rbeg - parent->rlen;
+            if ( len < 0 )   // overlapping variants
+            {
+                free(str.s);
+                free(splice.kref.s);
+                free(splice.kalt.s);
+                return 1;
+            }
+            kputsn_(tr->ref + N_REF_PAD + parent->rbeg + parent->rlen - tr->beg, len, &str);
+        }
+        else
+            kputsn_(tr->ref + N_REF_PAD + cds->beg - tr->beg, splice.ref_beg - cds->beg, &str);
+    }
+    kputs(splice.kalt.s + dbeg, &str);
+
+    child->seq  = str.s;
+    child->sbeg = cds->pos + (splice.ref_beg - cds->beg);
+    child->rbeg = splice.ref_beg;
+    child->rlen = splice.kref.l;
+    child->type = HAP_CDS;
+    child->prev = parent;
+    child->rec  = rec;
+    child->csq  = splice.csq;
+
+    // set vlen and the "ref>alt" string
+    {
+        int rlen = strlen(rec->d.allele[0]);
+        int alen = strlen(rec->d.allele[ial]);
+        child->dlen = alen - rlen;
+        child->var  = (char*) malloc(rlen+alen+2);
+        memcpy(child->var,rec->d.allele[0],rlen);
+        child->var[rlen] = '>';
+        memcpy(child->var+rlen+1,rec->d.allele[ial],alen);
+        child->var[rlen+alen+1] = 0;
+    }
+
+    // yuck, the whole CDS is modified/deleted, not ready for this, todo.
+    if ( child->rbeg + child->rlen > cds->beg + cds->len )
+    {
+        child->type = HAP_SSS;
+        if ( !child->csq ) child->csq |= CSQ_CODING_SEQUENCE;  // hack, specifically for ENST00000390520/deletion-overlap.vcf
+    }
+
+
+    free(splice.kref.s);
+    free(splice.kalt.s);
+    return 0;
+}
+void hap_destroy(hap_node_t *hap)
+{
+    int i;
+    for (i=0; i<hap->nchild; i++)
+        if ( hap->child[i] ) hap_destroy(hap->child[i]);
+    for (i=0; i<hap->mcsq_list; i++) free(hap->csq_list[i].type.vstr.s);
+    free(hap->csq_list);
+    free(hap->child);
+    free(hap->cur_child);
+    free(hap->seq);
+    free(hap->var);
+    free(hap);
+}
+
+
+/*
+    ref:    spliced reference and its length (ref.l)
+    seq:    part of the spliced query transcript on the reference strand to translate, its 
+                length (seq.l) and the total length of the complete transcript (seq.m)
+    sbeg:   seq offset within the spliced query transcript
+    rbeg:   seq offset within ref, 0-based
+    rend:   last base of seq within ref, plus one. If seq does not contain indels, it is rend=rbeg+seq->l
+    strand: coding strand - 0:rev, 1:fwd
+    tseq:   translated sequence (aa)
+    fill:   frameshift, fill until the end (strand=fwd) or from the start (strand=rev)
+ */
+void cds_translate(kstring_t *_ref, kstring_t *_seq, uint32_t sbeg, uint32_t rbeg, uint32_t rend, int strand, kstring_t *tseq, int fill)
+{
+#if XDBG
+fprintf(stderr,"\ntranslate: %d %d %d  fill=%d  seq.l=%d\n",sbeg,rbeg,rend,fill,(int)_seq->l);
+#endif
+    char tmp[3], *codon, *end;
+    int i, len, npad;
+
+    kstring_t ref = *_ref;
+    kstring_t seq = *_seq;
+
+    tseq->l = 0;
+    if ( !seq.l )
+    {
+        kputc('?', tseq);
+        return;
+    }
+
+#define DBG 0
+#if DBG
+ fprintf(stderr,"translate: sbeg,rbeg,rend=%d %d %d  fill=%d  seq.l=%d\n",sbeg,rbeg,rend,fill,(int)_seq->l);
+ fprintf(stderr,"    ref: l=%d %s\n", (int)ref.l,ref.s);
+ fprintf(stderr,"    seq: l=%d m=%d ", (int)seq.l,(int)seq.m);
+ for (i=0; i<seq.l; i++) fprintf(stderr,"%c",seq.s[i]); fprintf(stderr,"\n");
+ fprintf(stderr,"    sbeg,rbeg,rend: %d,%d,%d\n", sbeg,rbeg,rend);
+ fprintf(stderr,"    strand,fill: %d,%d\n", strand,fill);
+#endif
+
+    if ( strand==STRAND_FWD )
+    {
+        // left padding
+        npad = sbeg % 3;
+#if DBG>1
+        fprintf(stderr,"    npad: %d\n",npad);
+#endif
+        assert( npad<=rbeg );
+
+        for (i=0; i<npad; i++)
+            tmp[i] = ref.s[rbeg+i-npad+N_REF_PAD];
+        for (; i<3 && i-npad<seq.l; i++)
+            tmp[i] = seq.s[i-npad];
+        len = seq.l - i + npad;    // the remaining length of padded sseq
+#if DBG>1
+        fprintf(stderr,"\t i=%d\n", i);
+#endif
+        if ( i==3 )
+        {
+            kputc_(dna2aa(tmp), tseq);
+#if DBG>1
+            fprintf(stderr,"[1]%c%c%c\n",tmp[0],tmp[1],tmp[2]);
+#endif
+            codon = seq.s + 3 - npad;        // next codon
+            end   = codon + len - 1 - (len % 3);    // last position of a valid codon
+            while ( codon < end )
+            {
+                kputc_(dna2aa(codon), tseq);
+#if DBG>1
+                fprintf(stderr,"[2]%c%c%c\n",codon[0],codon[1],codon[2]);
+#endif
+                codon += 3;
+            }
+            end = seq.s + seq.l - 1;
+            for (i=0; codon+i<=end; i++) tmp[i] = codon[i];
+        }
+
+        // right padding
+        codon = ref.s + rend + N_REF_PAD;
+        if ( i>0 )
+        {
+#if DBG>1
+            if(i==1)fprintf(stderr,"[3]%c\n",tmp[0]);
+            if(i==2)fprintf(stderr,"[3]%c%c\n",tmp[0],tmp[1]);
+#endif
+            for (; i<3; i++)
+            {
+                tmp[i] = *codon;
+                codon++;
+            }
+            kputc_(dna2aa(tmp), tseq);
+#if DBG>1
+            fprintf(stderr,"[4]%c%c%c\n",tmp[0],tmp[1],tmp[2]);
+#endif
+        }
+        if ( fill!=0 )
+        {
+            end = ref.s + ref.l - N_REF_PAD;
+            while ( codon+3 <= end )
+            {
+                kputc_(dna2aa(codon), tseq);
+#if DBG>1
+                fprintf(stderr,"[5]%c%c%c\t%c\n",codon[0],codon[1],codon[2],dna2aa(codon));
+#endif
+                codon += 3;
+            }
+        }
+    }
+    else    // STRAND_REV
+    {
+        // right padding - number of bases to take from ref
+        npad = (seq.m - (sbeg + seq.l)) % 3; 
+#if DBG>1
+        fprintf(stderr,"    npad: %d\n",npad);
+#endif
+        if ( !(npad>=0 && sbeg+seq.l+npad<=seq.m) ) fprintf(stderr,"sbeg=%d  seq.l=%d seq.m=%d npad=%d\n",sbeg,(int)seq.l,(int)seq.m,npad);
+        assert( npad>=0 && sbeg+seq.l+npad<=seq.m );  // todo: first codon on the rev strand
+
+        if ( npad==2 )
+        {
+            tmp[1] = ref.s[rend+N_REF_PAD];
+            tmp[2] = ref.s[rend+N_REF_PAD+1];
+            i = 0;
+        }
+        else if ( npad==1 )
+        {
+            tmp[2] = ref.s[rend+N_REF_PAD];
+            i = 1;
+        }
+        else
+            i = 2;
+
+        end = seq.s + seq.l;
+        for (; i>=0 && end>seq.s; i--) tmp[i] = *(--end);
+#if DBG>1
+        fprintf(stderr,"\t i=%d\n", i);
+        if(i==1)fprintf(stderr,"[0]  %c\n",tmp[2]);
+        if(i==0)fprintf(stderr,"[0] %c%c\n",tmp[1],tmp[2]);
+#endif
+        if ( i==-1 )
+        {
+#if DBG>1
+            fprintf(stderr,"[1]%c%c%c\t%c\n",tmp[0],tmp[1],tmp[2], cdna2aa(tmp));
+#endif
+            kputc_(cdna2aa(tmp), tseq);
+            codon = end - 3;
+            while ( codon >= seq.s )
+            {
+                kputc_(cdna2aa(codon), tseq);
+#if DBG>1
+                fprintf(stderr,"[2]%c%c%c\t%c\n",codon[0],codon[1],codon[2], cdna2aa(codon));
+#endif
+                codon -= 3;
+            }
+            if ( seq.s-codon==2 )
+            {
+                tmp[2] = seq.s[0]; 
+                i = 1;
+            }
+            else if ( seq.s-codon==1 )
+            {
+                tmp[1] = seq.s[0]; 
+                tmp[2] = seq.s[1];
+                i = 0;
+            }
+            else
+                i = -1;
+#if DBG>1
+            if(i==1)fprintf(stderr,"[3]   %c\n",tmp[2]);
+            if(i==0)fprintf(stderr,"[3] %c%c\n",tmp[1],tmp[2]);
+#endif
+        }
+        // left padding
+        end = ref.s + N_REF_PAD + rbeg;
+        if ( i>=0 )
+        {
+            for (; i>=0 && end>=ref.s; i--) tmp[i] = *(--end);
+            kputc_(cdna2aa(tmp), tseq);
+#if DBG>1
+            fprintf(stderr,"[4]%c%c%c\t%c\n",tmp[0],tmp[1],tmp[2],cdna2aa(tmp));
+#endif
+        }
+        if ( fill!=0 )
+        {
+            codon = end - 3;
+            while ( codon >= ref.s + N_REF_PAD )
+            {
+                kputc_(cdna2aa(codon), tseq);
+#if DBG>1
+                fprintf(stderr,"[5]%c%c%c\t%c\n",codon[0],codon[1],codon[2],cdna2aa(codon));
+#endif
+                codon -= 3;
+            }
+        }
+    }
+    kputc_(0,tseq); tseq->l--;
+#if DBG
+ fprintf(stderr,"    tseq: %s\n", tseq->s);
+#endif
+}
+
+void tscript_splice_ref(tscript_t *tr)
+{
+    int i, len = 0;
+    for (i=0; i<tr->ncds; i++) 
+        len += tr->cds[i]->len;
+
+    tr->nsref = len + 2*N_REF_PAD;
+    tr->sref  = (char*) malloc(len + 1 + 2*N_REF_PAD);
+    len = 0;
+
+    memcpy(tr->sref, tr->ref + tr->cds[0]->beg - tr->beg, N_REF_PAD);
+    len += N_REF_PAD;
+
+    for (i=0; i<tr->ncds; i++)
+    {
+        memcpy(tr->sref + len, tr->ref + N_REF_PAD + tr->cds[i]->beg - tr->beg, tr->cds[i]->len);
+        len += tr->cds[i]->len;
+    }
+    memcpy(tr->sref + len, tr->ref + N_REF_PAD + tr->cds[tr->ncds-1]->beg - tr->beg, N_REF_PAD);
+    len += N_REF_PAD;
+
+    tr->sref[len] = 0;
+}
+
+// returns: 0 if consequence was added, 1 if it already exists or could not be added
+int csq_push(args_t *args, csq_t *csq, bcf1_t *rec)
+{
+#if XDBG
+fprintf(stderr,"csq_push: %d .. %d\n",rec->pos+1,csq->type.type);
+#endif
+    khint_t k = kh_get(pos2vbuf, args->pos2vbuf, (int)csq->pos);
+    vbuf_t *vbuf = (k == kh_end(args->pos2vbuf)) ? NULL : kh_val(args->pos2vbuf, k);
+    if ( !vbuf ) error("This should not happen. %s:%d  %s\n",bcf_seqname(args->hdr,rec),csq->pos+1,csq->type.vstr.s);
+
+    int i;
+    for (i=0; i<vbuf->n; i++)
+        if ( vbuf->vrec[i]->line==rec ) break;
+    if ( i==vbuf->n ) error("This should not happen.. %s:%d  %s\n", bcf_seqname(args->hdr,rec),csq->pos+1,csq->type.vstr.s);
+    vrec_t *vrec = vbuf->vrec[i];
+
+    // if the variant overlaps donor/acceptor and also splice region, report only donor/acceptor
+    if ( csq->type.type & CSQ_SPLICE_REGION && csq->type.type & (CSQ_SPLICE_DONOR|CSQ_SPLICE_ACCEPTOR) ) 
+        csq->type.type &= ~CSQ_SPLICE_REGION;
+
+    if ( csq->type.type & CSQ_PRINTED_UPSTREAM )
+    {
+        for (i=0; i<vrec->nvcsq; i++)
+        {
+            // Same as below, to avoid records like
+            //      3630 .. @3632,stop_lost|AL627309.1|ENST00000423372|protein_coding|-
+            //      3632 .. stop_lost|AL627309.1|ENST00000423372|protein_coding|-|260*>260G|3630T>A+3632A>C
+            if ( csq->type.type&CSQ_START_STOP && vrec->vcsq[i].type&CSQ_START_STOP )
+            {
+                vrec->vcsq[i] = csq->type;
+                goto exit_duplicate;
+            }
+            if ( !(vrec->vcsq[i].type & CSQ_PRINTED_UPSTREAM) ) continue;
+            if ( csq->type.ref != vrec->vcsq[i].ref ) continue;
+            goto exit_duplicate;
+        }
+    }
+    else if ( csq->type.type & CSQ_COMPOUND )
+    {
+        for (i=0; i<vrec->nvcsq; i++)
+        {
+            if ( csq->type.trid != vrec->vcsq[i].trid && (csq->type.type|vrec->vcsq[i].type)&CSQ_PRN_TSCRIPT ) continue;
+            if ( csq->type.biotype != vrec->vcsq[i].biotype ) continue;
+            if ( csq->type.gene != vrec->vcsq[i].gene ) continue;
+            if ( csq->type.vcf_ial != vrec->vcsq[i].vcf_ial ) continue;
+            if ( (csq->type.type&CSQ_UPSTREAM_STOP)^(vrec->vcsq[i].type&CSQ_UPSTREAM_STOP) ) continue;  // both must or mustn't have upstream_stop
+            if ( csq->type.vstr.s || vrec->vcsq[i].vstr.s ) 
+            {
+                // This is a bit hacky, but we want a simpler and more predictable output. The splice_csq() function
+                // can trigger stop/start events based on indel overlap, then another stop/start event can be triggered
+                // from add_csq() or test_cds_local() based on sequence comparison, and on output we could find two
+                // consequences:
+                //      stop_lost|AL627309.1|ENST00000423372|protein_coding|-
+                //      stop_lost&inframe_insertion|AL627309.1|ENST00000423372|protein_coding|-|260*>260CL|3630T>TAAA
+                if ( !csq->type.vstr.s || !vrec->vcsq[i].vstr.s ) 
+                {
+                    if ( csq->type.type&CSQ_START_STOP && vrec->vcsq[i].type&CSQ_START_STOP )
+                    {
+                        vrec->vcsq[i].type |= csq->type.type;
+
+                        // remove stop_lost&synonymous if stop_retained set
+                        if ( vrec->vcsq[i].type&CSQ_STOP_RETAINED ) 
+                            vrec->vcsq[i].type &= ~(CSQ_STOP_LOST|CSQ_SYNONYMOUS_VARIANT);
+
+                        if ( !vrec->vcsq[i].vstr.s ) vrec->vcsq[i].vstr = csq->type.vstr;
+                        goto exit_duplicate;
+                    }
+                    continue;
+                }
+                if ( strcmp(csq->type.vstr.s,vrec->vcsq[i].vstr.s) ) continue;
+            }
+            vrec->vcsq[i].type |= csq->type.type; 
+            goto exit_duplicate;
+        }
+    }
+    else
+    {
+        for (i=0; i<vrec->nvcsq; i++)
+        {
+            if ( csq->type.trid != vrec->vcsq[i].trid && (csq->type.type|vrec->vcsq[i].type)&CSQ_PRN_TSCRIPT) continue;
+            if ( csq->type.biotype != vrec->vcsq[i].biotype ) continue;
+            if ( !(vrec->vcsq[i].type & CSQ_COMPOUND) ) 
+            {
+                vrec->vcsq[i].type |= csq->type.type;
+                goto exit_duplicate;
+            }
+            if ( vrec->vcsq[i].type==(vrec->vcsq[i].type|csq->type.type) ) goto exit_duplicate;
+        }
+    }
+    // no such csq yet in this vcf record
+    csq->vrec = vrec;
+    csq->idx  = vrec->nvcsq++;
+    hts_expand0(vcsq_t, vrec->nvcsq, vrec->mvcsq, vrec->vcsq);
+    vrec->vcsq[i] = csq->type;
+    return 0;
+
+exit_duplicate:
+    csq->vrec = vrec;
+    csq->idx  = i;
+    return 1;
+}
+
+//  soff .. position of the variant within the trimmed query transcript
+//  sbeg .. position of the variant within the query transcript
+//  rbeg .. position on the reference transcript (if there are no indels, then rbeg=send)
+//  rpos .. VCF position
+#define node2soff(i) (hap->stack[i].slen - (hap->stack[i].node->rlen + hap->stack[i].node->dlen))
+#define node2sbeg(i) (hap->sbeg + node2soff(i))
+#define node2send(i) (hap->sbeg + hap->stack[i].slen)
+#define node2rbeg(i) (hap->stack[i].node->sbeg)
+#define node2rend(i) (hap->stack[i].node->sbeg + hap->stack[i].node->rlen)
+#define node2rpos(i) (hap->stack[i].node->rec->pos)
+
+void kput_vcsq(args_t *args, vcsq_t *csq, kstring_t *str)
+{
+    // Remove start/stop from incomplete CDS, but only if there is another
+    // consequence as something must be reported
+    if ( csq->type & CSQ_INCOMPLETE_CDS && (csq->type & ~(CSQ_START_STOP|CSQ_INCOMPLETE_CDS|CSQ_UPSTREAM_STOP)) ) csq->type &= ~(CSQ_START_STOP|CSQ_INCOMPLETE_CDS);
+
+    // Remove missense from start/stops
+    if ( csq->type & CSQ_START_STOP && csq->type & CSQ_MISSENSE_VARIANT ) csq->type &= ~CSQ_MISSENSE_VARIANT;
+
+    if ( csq->type & CSQ_PRINTED_UPSTREAM && csq->ref )
+    {
+        kputc_('@',str);
+        kputw(csq->ref->pos+1, str);
+        return;
+    }
+    if ( csq->type & CSQ_UPSTREAM_STOP )
+        kputc_('*',str);
+
+    int i, n = sizeof(csq_strings)/sizeof(char*);
+    for (i=1; i<n; i++)
+        if ( csq_strings[i] && csq->type&(1<<i) ) { kputs(csq_strings[i],str); break; }
+    i++;
+    for (; i<n; i++)
+        if ( csq_strings[i] && csq->type&(1<<i) ) { kputc_('&',str); kputs(csq_strings[i],str); }
+
+    kputc_('|', str);
+    if ( csq->gene ) kputs(csq->gene , str);
+
+    kputc_('|', str);
+    if ( csq->type & CSQ_PRN_TSCRIPT ) kputs(args->tscript_ids.str[csq->trid], str);
+
+    kputc_('|', str);
+    kputs(gf_type2gff_string(csq->biotype), str);
+
+    if ( CSQ_PRN_STRAND(csq->type) || csq->vstr.l )
+        kputs(csq->strand==STRAND_FWD ? "|+" : "|-", str);
+
+    if ( csq->vstr.l )
+        kputs(csq->vstr.s, str);
+}
+
+void kprint_aa_prediction(args_t *args, int beg, kstring_t *aa, kstring_t *str)
+{
+    if ( !args->brief_predictions || (int)aa->l - args->brief_predictions < 3 )
+        kputs(aa->s, str);
+    else
+    {
+        int i, len = aa->l;
+        if ( aa->s[len-1]=='*' ) len--;
+        for (i=0; i<len && i<args->brief_predictions; i++) kputc(aa->s[i], str);
+        kputs("..", str);
+        kputw(beg+len, str);
+    }
+}
+
+void hap_add_csq(args_t *args, hap_t *hap, hap_node_t *node, int tlen, int ibeg, int iend, int dlen, int indel)
+{
+    int i;
+    tscript_t *tr = hap->tr;
+    int ref_node = tr->strand==STRAND_FWD ? ibeg : iend;
+    int icsq = node->ncsq_list++;
+    hts_expand0(csq_t,node->ncsq_list,node->mcsq_list,node->csq_list);
+    csq_t *csq = &node->csq_list[icsq];
+    csq->pos  = hap->stack[ref_node].node->rec->pos;
+    csq->type.trid    = tr->id;
+    csq->type.vcf_ial = node->vcf_ial;
+    csq->type.gene    = tr->gene->name;
+    csq->type.strand  = tr->strand;
+    csq->type.biotype = tr->type;
+
+    // only now we see the translated sequence and can determine if the stop/start changes are real
+    int rm_csq = 0; 
+    csq->type.type = 0;
+    for (i=ibeg; i<=iend; i++)
+        csq->type.type |= hap->stack[i].node->csq & CSQ_COMPOUND;
+    if ( dlen==0 && indel ) csq->type.type |= CSQ_INFRAME_ALTERING;
+
+    int has_upstream_stop = hap->upstream_stop;
+    if ( hap->stack[ibeg].node->type != HAP_SSS )
+    {
+        // check for truncating stops
+        for (i=0; i<hap->tref.l; i++)
+            if ( hap->tref.s[i]=='*' ) break;
+        if ( i!=hap->tref.l )
+        {
+            hap->tref.l = i+1;
+            hap->tref.s[i+1] = 0;
+        }
+        for (i=0; i<hap->tseq.l; i++)
+            if ( hap->tseq.s[i]=='*' ) break;
+        if ( i!=hap->tseq.l )
+        {
+            hap->tseq.l = i+1;
+            hap->tseq.s[i+1] = 0;
+            hap->upstream_stop = 1;
+        }
+        if ( csq->type.type & CSQ_STOP_LOST )
+        {
+            if ( hap->tref.s[hap->tref.l-1]=='*' && hap->tref.s[hap->tref.l-1] == hap->tseq.s[hap->tseq.l-1] ) 
+            {
+                rm_csq |= CSQ_STOP_LOST;
+                csq->type.type |= CSQ_STOP_RETAINED;
+            }
+            else if ( hap->tref.s[hap->tref.l-1]!='*' )
+            {
+                // This is CDS 3' incomplete ENSG00000173376/synon.vcf, can also be missense
+                // We observe in real data a change to a stop, ENST00000528237/retained-stop-incomplete-cds.vcf
+                if ( hap->tseq.s[hap->tseq.l-1] == '*' )
+                {
+                    rm_csq |= CSQ_STOP_GAINED;
+                    csq->type.type |= CSQ_STOP_RETAINED;
+                }
+                else
+                    csq->type.type |= CSQ_INCOMPLETE_CDS;
+            }
+        }
+        if ( csq->type.type & CSQ_START_LOST && hap->tref.s[0]!='M' )
+        {
+            rm_csq |= CSQ_START_LOST;
+            csq->type.type &= ~CSQ_START_LOST;
+        }
+        if ( dlen!=0 )
+        {
+            if ( dlen%3 )
+                csq->type.type |= CSQ_FRAMESHIFT_VARIANT;
+            else if ( dlen<0 )
+                csq->type.type |= CSQ_INFRAME_DELETION;
+            else
+                csq->type.type |= CSQ_INFRAME_INSERTION;
+            if ( hap->tref.s[hap->tref.l-1]!='*' && hap->tseq.s[hap->tseq.l-1]=='*' )
+                csq->type.type |= CSQ_STOP_GAINED;
+        }
+        else
+        {
+            for (i=0; i<hap->tref.l; i++) 
+                if ( hap->tref.s[i] != hap->tseq.s[i] ) break;
+            if ( i==hap->tref.l )
+                csq->type.type |= CSQ_SYNONYMOUS_VARIANT;
+            else if ( hap->tref.s[i] ==  '*' )
+                csq->type.type |= CSQ_STOP_LOST;
+            else if ( hap->tseq.s[i] ==  '*' )
+                csq->type.type |= CSQ_STOP_GAINED;
+            else
+                csq->type.type |= CSQ_MISSENSE_VARIANT;
+        }
+    }
+    // Check if compound inframe variants are real inframes, or if the stop codon occurs before the frameshift can be restored
+    if ( ibeg!=iend && (csq->type.type & (CSQ_INFRAME_DELETION|CSQ_INFRAME_INSERTION|CSQ_INFRAME_ALTERING)) && hap->tseq.s[hap->tseq.l-1]=='*' )
+    {
+        rm_csq |= CSQ_INFRAME_DELETION | CSQ_INFRAME_INSERTION | CSQ_INFRAME_ALTERING;
+        csq->type.type |= CSQ_FRAMESHIFT_VARIANT | CSQ_STOP_GAINED;
+    }
+    if ( has_upstream_stop ) csq->type.type |= CSQ_UPSTREAM_STOP;
+    csq->type.type &= ~rm_csq;
+
+    if ( hap->stack[ibeg].node->type == HAP_SSS  )
+    {
+        node->csq_list[icsq].type.type   |= hap->stack[ibeg].node->csq & ~rm_csq;
+        node->csq_list[icsq].type.ref     = hap->stack[ibeg].node->rec;
+        node->csq_list[icsq].type.biotype = tr->type;
+        csq_push(args, node->csq_list+icsq, hap->stack[ibeg].node->rec);
+        return;
+    }
+
+    kstring_t str = node->csq_list[icsq].type.vstr;
+    str.l = 0;
+
+    // create the aa variant string
+    int aa_rbeg = tr->strand==STRAND_FWD ? node2rbeg(ibeg)/3+1 : (hap->tr->nsref - 2*N_REF_PAD - node2rend(iend))/3+1;
+    int aa_sbeg = tr->strand==STRAND_FWD ? node2sbeg(ibeg)/3+1 : (tlen - node2send(iend))/3+1;
+    kputc_('|', &str);
+    kputw(aa_rbeg, &str);
+    kprint_aa_prediction(args,aa_rbeg,&hap->tref,&str);
+    if ( !(csq->type.type & CSQ_SYNONYMOUS_VARIANT) )
+    {
+        kputc_('>', &str);
+        kputw(aa_sbeg, &str);
+        kprint_aa_prediction(args,aa_sbeg,&hap->tseq,&str);
+    }
+    kputc_('|', &str);
+
+    // create the dna variant string and, in case of combined variants,
+    // insert silent CSQ_PRINTED_UPSTREAM variants
+    for (i=ibeg; i<=iend; i++)
+    {
+        if ( i>ibeg ) kputc_('+', &str);
+        kputw(node2rpos(i)+1, &str);
+        kputs(hap->stack[i].node->var, &str);
+    }
+    node->csq_list[icsq].type.vstr = str;
+    csq_push(args, node->csq_list+icsq, hap->stack[ref_node].node->rec);
+
+    for (i=ibeg; i<=iend; i++)
+    {
+        // csq are printed at one position only for combined variants, the rest is
+        // silent and references the first
+        if ( hap->stack[i].node->csq & ~CSQ_COMPOUND )
+        {
+            node->ncsq_list++;
+            hts_expand0(csq_t,node->ncsq_list,node->mcsq_list,node->csq_list);
+            csq_t *tmp_csq = &node->csq_list[node->ncsq_list - 1];
+            tmp_csq->pos  = hap->stack[i].node->rec->pos;
+            tmp_csq->type.trid    = tr->id;
+            //??tmp_csq->type.vcf_ial = node->vcf_ial;  .. this should not be needed for non-compound variants
+            tmp_csq->type.gene    = tr->gene->name;
+            tmp_csq->type.strand  = tr->strand;
+            tmp_csq->type.type    = hap->stack[i].node->csq & ~CSQ_COMPOUND & ~rm_csq;
+            tmp_csq->type.biotype = tr->type;
+            tmp_csq->type.vstr.l  = 0;
+            kputs(str.s,&tmp_csq->type.vstr);
+            csq_push(args, tmp_csq, hap->stack[i].node->rec);
+        }
+        if ( i!=ref_node && (node->csq_list[icsq].type.type & CSQ_COMPOUND || !(hap->stack[i].node->csq & ~CSQ_COMPOUND)) )
+        {
+            node->ncsq_list++;
+            hts_expand0(csq_t,node->ncsq_list,node->mcsq_list,node->csq_list);
+            csq_t *tmp_csq = &node->csq_list[node->ncsq_list - 1];
+            tmp_csq->pos  = hap->stack[i].node->rec->pos;
+            tmp_csq->type.trid    = tr->id;
+            //??tmp_csq->type.vcf_ial = node->vcf_ial;  .. this should not be needed for non-compound variants
+            tmp_csq->type.gene    = tr->gene->name;
+            tmp_csq->type.strand  = tr->strand;
+            tmp_csq->type.type    = CSQ_PRINTED_UPSTREAM | hap->stack[i].node->csq;
+            tmp_csq->type.biotype = tr->type;
+            tmp_csq->type.ref     = hap->stack[ref_node].node->rec;
+            tmp_csq->type.vstr.l  = 0;
+            csq_push(args, tmp_csq, hap->stack[i].node->rec);
+        }
+    }
+}
+
+
+void hap_finalize(args_t *args, hap_t *hap)
+{
+    tscript_t *tr = hap->tr;
+    if ( !tr->sref )
+        tscript_splice_ref(tr);
+
+    kstring_t sref;
+    sref.s = tr->sref;
+    sref.l = tr->nsref;
+    sref.m = sref.l;
+
+    int istack = 0;
+    hts_expand(hstack_t,1,hap->mstack,hap->stack);
+
+    hap->sseq.l = 0;
+    hap->tseq.l = 0;
+    hap->stack[0].node = tr->root;
+    hap->stack[0].ichild = -1;
+    hap->stack[0].slen = 0;
+    hap->stack[0].dlen = 0;
+
+    while ( istack>=0 )
+    {
+        hstack_t *stack  = &hap->stack[istack];
+        hap_node_t *node = hap->stack[istack].node;
+        while ( ++hap->stack[istack].ichild < node->nchild )
+        {
+            if ( node->child[stack->ichild] ) break;
+        }
+        if ( stack->ichild == node->nchild ) { istack--; continue; }
+
+        node = node->child[stack->ichild];
+
+        istack++;
+        hts_expand(hstack_t,istack+1,hap->mstack,hap->stack);
+        stack = &hap->stack[istack-1];
+
+        hap->stack[istack].node = node;
+        hap->stack[istack].ichild = -1;
+
+        hap->sseq.l = stack->slen;
+        if ( node->type==HAP_CDS ) kputs(node->seq, &hap->sseq);
+        hap->stack[istack].slen = hap->sseq.l;
+        hap->stack[istack].dlen = hap->stack[istack-1].dlen + node->dlen;
+
+        if ( !node->nend ) continue;    // not a leaf node
+
+        // The spliced sequence has been built for the current haplotype and stored
+        // in hap->sseq. Now we break it and output as independent parts
+        
+        kstring_t sseq;
+        sseq.m = sref.m - 2*N_REF_PAD + hap->stack[istack].dlen;  // total length of the spliced query transcript
+        hap->upstream_stop = 0;
+
+        int i = 1, dlen = 0, ibeg, indel = 0;
+        hap->sbeg = hap->stack[i].node->sbeg;
+        assert( hap->stack[istack].node->type != HAP_SSS );
+        if ( tr->strand==STRAND_FWD )
+        {
+            i = 0, ibeg = -1;
+            while ( ++i <= istack )
+            {
+                assert( hap->stack[i].node->type != HAP_SSS );
+
+                dlen += hap->stack[i].node->dlen;
+                if ( hap->stack[i].node->dlen ) indel = 1;
+
+                // This condition extends compound variants.
+                if ( i<istack )
+                {
+                    if ( dlen%3 )   // frameshift
+                    {
+                        if ( ibeg==-1 ) ibeg = i;
+                        continue;
+                    }
+                    // the last base of the current variant vs the first base of the next
+                    // variant: are they in the same codon? (forward strand)
+                    int icur  = node2sbeg(i);
+                    int inext = node2sbeg(i+1);
+                    if ( hap->stack[i].node->dlen > 0 ) icur += hap->stack[i].node->dlen;
+                    else if ( hap->stack[i].node->dlen < 0 ) icur++;
+                    if ( icur/3 == inext/3 )    // in the same codon, can't be flushed yet
+                    {
+                        if ( ibeg==-1 ) ibeg = i;
+                        continue;
+                    }
+                }
+                if ( ibeg<0 ) ibeg = i;
+
+                int ioff = node2soff(ibeg);
+                int icur = node2sbeg(ibeg);
+                int rbeg = node2rbeg(ibeg);
+                int rend = node2rend(i);
+                int fill = dlen%3;
+
+                // alt
+                if ( hap->sseq.l )
+                {
+                    sseq.l = hap->stack[i].slen - ioff;
+                    sseq.s = hap->sseq.s + ioff;
+                }
+                else    // splice site overlap, see #1475227917
+                    sseq.l = fill = 0;
+                cds_translate(&sref, &sseq, icur,rbeg,rend, tr->strand, &hap->tseq, fill);
+
+                // ref
+                sseq.l = node2rend(i) - rbeg;
+                sseq.s = sref.s + N_REF_PAD + rbeg;
+                sseq.m = sref.m - 2*N_REF_PAD;
+                cds_translate(&sref, &sseq, rbeg,rbeg,rend, tr->strand, &hap->tref, fill);
+                sseq.m = sref.m - 2*N_REF_PAD + hap->stack[istack].dlen;
+
+                hap_add_csq(args,hap,node,0, ibeg,i,dlen,indel);
+                ibeg = -1;
+                dlen = 0;
+                indel = 0;
+            }
+        }
+        else
+        {
+            i = istack + 1, ibeg = -1;
+            while ( --i > 0 )
+            {
+                assert ( hap->stack[i].node->type != HAP_SSS );
+                dlen += hap->stack[i].node->dlen;
+                if ( hap->stack[i].node->dlen ) indel = 1;
+                if ( i>1 )
+                {
+                    if ( dlen%3 )
+                    {
+                        if ( ibeg==-1 ) ibeg = i;
+                        continue;
+                    }
+                    // the last base of the current variant vs the first base of the next
+                    // variant: are they in the same codon? (reverse strand)
+                    int icur  = sseq.m - 1 - node2sbeg(i);
+                    int inext = sseq.m - 1 - node2sbeg(i-1);
+                    if ( hap->stack[i].node->dlen > 0 ) icur += hap->stack[i].node->dlen - 1;
+                    else if ( hap->stack[i].node->dlen < 0 ) icur -= hap->stack[i].node->dlen;
+                    if ( hap->stack[i-1].node->dlen > 0 ) inext -= hap->stack[i-1].node->dlen;
+                    if ( icur/3 == inext/3 )
+                    {
+                        if ( ibeg==-1 ) ibeg = i;
+                        continue;
+                    }
+                }
+                if ( ibeg<0 ) ibeg = i;
+                int ioff = node2soff(i);
+                int icur = node2sbeg(i);
+                int rbeg = node2rbeg(i);
+                int rend = node2rend(ibeg);
+                int fill = dlen%3;
+
+                // alt
+                if ( hap->sseq.l )
+                {
+                    sseq.l = hap->stack[ibeg].slen - ioff;
+                    sseq.s = hap->sseq.s + ioff;
+                }
+                else    // splice site overlap, see #1475227917
+                    sseq.l = fill = 0;
+                cds_translate(&sref, &sseq, icur,rbeg,rend, tr->strand, &hap->tseq, fill);
+
+                // ref
+                sseq.l = node2rend(ibeg) - rbeg;
+                sseq.s = sref.s + N_REF_PAD + rbeg;
+                sseq.m = sref.m - 2*N_REF_PAD;
+                cds_translate(&sref, &sseq, rbeg,rbeg,rend, tr->strand, &hap->tref, fill);
+                sseq.m = sref.m - 2*N_REF_PAD + hap->stack[istack].dlen;
+
+                hap_add_csq(args,hap,node,sseq.m, i,ibeg,dlen,indel);
+                ibeg = -1;
+                dlen = 0;
+                indel = 0;
+            }
+        }
+    }
+}
+
+static inline void csq_print_text(args_t *args, csq_t *csq, int ismpl, int ihap)
+{
+    if ( csq->type.type & CSQ_PRINTED_UPSTREAM ) return;
+
+    char *smpl = ismpl >= 0 ? args->hdr->samples[ismpl] : "-";
+    const char *chr = bcf_hdr_id2name(args->hdr,args->rid);
+
+    fprintf(args->out,"CSQ\t%s\t", smpl);
+    if ( ihap>0 )
+        fprintf(args->out,"%d", ihap);
+    else
+        fprintf(args->out,"-");
+
+    args->str.l = 0;
+    kput_vcsq(args, &csq->type, &args->str);
+    fprintf(args->out,"\t%s\t%d\t%s\n",chr,csq->pos+1,args->str.s);
+}
+static inline void hap_print_text(args_t *args, tscript_t *tr, int ismpl, int ihap, hap_node_t *node)
+{
+    if ( !node || !node->ncsq_list ) return;
+
+    char *smpl = ismpl >= 0 ? args->hdr->samples[ismpl] : "-";
+    const char *chr = bcf_hdr_id2name(args->hdr,args->rid);
+
+    int i;
+    for (i=0; i<node->ncsq_list; i++)
+    {
+        csq_t *csq = node->csq_list + i;
+        if ( csq->type.type & CSQ_PRINTED_UPSTREAM ) continue;
+        assert( csq->type.vstr.l );
+
+        fprintf(args->out,"CSQ\t%s\t", smpl);
+        if ( ihap>0 )
+            fprintf(args->out,"%d", ihap);
+        else
+            fprintf(args->out,"-");
+
+        args->str.l = 0;
+        kput_vcsq(args, &csq->type, &args->str);
+        fprintf(args->out,"\t%s\t%d\t%s\n",chr,csq->pos+1,args->str.s);
+    }
+}
+
+static inline void hap_stage_vcf(args_t *args, tscript_t *tr, int ismpl, int ihap, hap_node_t *node)
+{
+    if ( !node || !node->ncsq_list || ismpl<0 ) return;
+
+    int i;
+    for (i=0; i<node->ncsq_list; i++)
+    {
+        csq_t *csq = node->csq_list + i;
+        vrec_t *vrec = csq->vrec;
+        int icsq2 = 2*csq->idx + ihap;
+        if ( icsq2 >= args->ncsq2_max ) // more than ncsq2_max consequences, so can't fit it in FMT
+        {
+            if ( args->verbosity && (!args->ncsq2_small_warned || args->verbosity > 1) )
+            {
+                fprintf(stderr,
+                    "Warning: Too many consequences for sample %s at %s:%"PRId64", keeping the first %d and skipping the rest.\n",
+                    args->hdr->samples[ismpl],bcf_hdr_id2name(args->hdr,args->rid),(int64_t) vrec->line->pos+1,csq->idx);
+                if ( !args->ncsq2_small_warned )
+                    fprintf(stderr,"         The limit can be increased by setting the --ncsq parameter. This warning is printed only once.\n");
+            }
+            if ( args->ncsq2_small_warned < icsq2 ) args->ncsq2_small_warned = icsq2;
+            break;
+        }
+        int ival, ibit;
+        icsq2_to_bit(icsq2, &ival,&ibit);
+        if ( vrec->nfmt < 1 + ival ) vrec->nfmt = 1 + ival;
+        vrec->fmt_bm[ismpl*args->nfmt_bcsq + ival] |= 1 << ibit;
+    }
+}
+
+void hap_flush(args_t *args, uint32_t pos)
+{
+    int i,j;
+    tr_heap_t *heap = args->active_tr;
+    while ( heap->ndat && heap->dat[0]->end<=pos )
+    {
+        tscript_t *tr = heap->dat[0];
+        khp_delete(trhp, heap);
+        args->hap->tr = tr;
+        if ( tr->root && tr->root->nchild ) // normal, non-localized calling
+        {
+            hap_finalize(args, args->hap);
+
+            if ( args->output_type==FT_TAB_TEXT )   // plain text output, not a vcf
+            {
+                if ( args->phase==PHASE_DROP_GT )
+                    hap_print_text(args, tr, -1,0, tr->hap[0]);
+                else
+                {
+                    for (i=0; i<args->smpl->n; i++)
+                    {
+                        for (j=0; j<2; j++)
+                            hap_print_text(args, tr, args->smpl->idx[i],j+1, tr->hap[i*2+j]);
+                    }
+                }
+            }
+            else if ( args->phase!=PHASE_DROP_GT )
+            {
+                for (i=0; i<args->smpl->n; i++)
+                {
+                    for (j=0; j<2; j++)
+                        hap_stage_vcf(args, tr, args->smpl->idx[i],j, tr->hap[i*2+j]);
+                }
+            }
+        }
+
+        // mark the transcript for deletion. Cannot delete it immediately because
+        // by-position VCF output will need them when flushed by vcf_buf_push
+        args->nrm_tr++;
+        hts_expand(tscript_t*,args->nrm_tr,args->mrm_tr,args->rm_tr);
+        args->rm_tr[args->nrm_tr-1] = tr;
+    }
+}
+
+#define SWAP(type_t, a, b) { type_t t = a; a = b; b = t; }
+
+vbuf_t *vbuf_push(args_t *args, bcf1_t **rec_ptr)
+{
+    int i;
+
+    assert(rec_ptr);
+    bcf1_t *rec = *rec_ptr;
+
+    // check for duplicate records
+    i = args->vcf_rbuf.n ? rbuf_last(&args->vcf_rbuf) : -1;
+    if ( i<0 || args->vcf_buf[i]->vrec[0]->line->pos!=rec->pos ) 
+    {
+        // vcf record with a new pos
+        rbuf_expand0(&args->vcf_rbuf, vbuf_t*, args->vcf_rbuf.n+1, args->vcf_buf);
+        i = rbuf_append(&args->vcf_rbuf);
+        if ( !args->vcf_buf[i] ) args->vcf_buf[i] = (vbuf_t*) calloc(1,sizeof(vbuf_t));
+        args->vcf_buf[i]->n = 0;
+        args->vcf_buf[i]->keep_until = 0;
+    }
+    vbuf_t *vbuf = args->vcf_buf[i];
+    vbuf->n++;
+    hts_expand0(vrec_t*, vbuf->n, vbuf->m, vbuf->vrec);
+    if ( !vbuf->vrec[vbuf->n - 1] )
+        vbuf->vrec[vbuf->n - 1] = (vrec_t*) calloc(1,sizeof(vrec_t));
+
+    vrec_t *vrec = vbuf->vrec[vbuf->n - 1];
+    if ( args->phase!=PHASE_DROP_GT && args->smpl->n )
+    {
+        if ( !vrec->fmt_bm ) vrec->fmt_bm = (uint32_t*) calloc(args->hdr_nsmpl,sizeof(*vrec->fmt_bm) * args->nfmt_bcsq);
+        else memset(vrec->fmt_bm,0,args->hdr_nsmpl*sizeof(*vrec->fmt_bm) * args->nfmt_bcsq);
+    }
+    if ( !vrec->line ) vrec->line = bcf_init1();
+    SWAP(bcf1_t*, (*rec_ptr), vrec->line);
+
+    int ret;
+    khint_t k = kh_put(pos2vbuf, args->pos2vbuf, (int)rec->pos, &ret);
+    kh_val(args->pos2vbuf,k) = vbuf;
+
+    return vbuf;
+}
+
+void vbuf_flush(args_t *args, uint32_t pos)
+{
+    int i,j;
+    while ( args->vcf_rbuf.n )
+    {
+        vbuf_t *vbuf;
+        if ( !args->local_csq && args->active_tr->ndat )
+        {
+            // check if the first active transcript starts beyond the first buffered VCF record,
+            // cannot output buffered VCF lines (args.vbuf) until the active transcripts are gone
+            vbuf = args->vcf_buf[ args->vcf_rbuf.f ];
+            if ( vbuf->keep_until > pos ) break;
+            assert( vbuf->n );
+        }
+
+        i = rbuf_shift(&args->vcf_rbuf);
+        assert( i>=0 );
+        vbuf = args->vcf_buf[i];
+        int pos = vbuf->n ? vbuf->vrec[0]->line->pos : -1;
+        for (i=0; i<vbuf->n; i++)
+        {
+            vrec_t *vrec = vbuf->vrec[i];
+            if ( !args->out_fh ) // not a VCF output
+            {
+                vrec->nvcsq = 0;
+                continue;
+            }
+            if ( !vrec->nvcsq )
+            {
+                if ( bcf_write(args->out_fh, args->hdr, vrec->line)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->output_fname?args->output_fname:"standard output");
+                int save_pos = vrec->line->pos;
+                bcf_empty(vrec->line);
+                vrec->line->pos = save_pos;  // this is necessary for compound variants
+                continue;
+            }
+            
+            args->str.l = 0;
+            kput_vcsq(args, &vrec->vcsq[0], &args->str);
+            for (j=1; j<vrec->nvcsq; j++)
+            {
+                kputc_(',', &args->str);
+                kput_vcsq(args, &vrec->vcsq[j], &args->str);
+            }
+            bcf_update_info_string(args->hdr, vrec->line, args->bcsq_tag, args->str.s);
+            if ( args->hdr_nsmpl )
+            {
+                if ( vrec->nfmt < args->nfmt_bcsq )
+                    for (j=1; j<args->hdr_nsmpl; j++)
+                        memmove(&vrec->fmt_bm[j*vrec->nfmt], &vrec->fmt_bm[j*args->nfmt_bcsq], vrec->nfmt*sizeof(*vrec->fmt_bm));
+                bcf_update_format_int32(args->hdr, vrec->line, args->bcsq_tag, vrec->fmt_bm, args->hdr_nsmpl*vrec->nfmt);
+            }
+            vrec->nvcsq = 0;
+            if ( bcf_write(args->out_fh, args->hdr, vrec->line)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->output_fname?args->output_fname:"standard output");
+            int save_pos = vrec->line->pos;
+            bcf_empty(vrec->line);
+            vrec->line->pos = save_pos;
+        }
+        if ( pos!=-1 )
+        {
+            khint_t k = kh_get(pos2vbuf, args->pos2vbuf, pos);
+            if ( k != kh_end(args->pos2vbuf) ) kh_del(pos2vbuf, args->pos2vbuf, k);
+        }
+        vbuf->n = 0;
+    }
+    if ( args->active_tr->ndat ) return;
+
+    for (i=0; i<args->nrm_tr; i++)
+    {
+        tscript_t *tr = args->rm_tr[i];
+        if ( tr->root ) hap_destroy(tr->root);
+        tr->root = NULL;
+        free(tr->hap);
+        free(tr->ref);
+        free(tr->sref);
+    }
+    args->nrm_tr = 0;
+    args->ncsq_buf = 0;
+}
+
+void tscript_init_ref(args_t *args, tscript_t *tr, const char *chr)
+{
+    int i, len;
+    int pad_beg = tr->beg >= N_REF_PAD ? N_REF_PAD : tr->beg;
+
+    tr->ref = faidx_fetch_seq(args->fai, chr, tr->beg - pad_beg, tr->end + N_REF_PAD, &len);
+    if ( !tr->ref )
+        error("faidx_fetch_seq failed %s:%d-%d\n", chr,tr->beg+1,tr->end+1);
+
+    int pad_end = len - (tr->end - tr->beg + 1 + pad_beg);
+    if ( pad_beg + pad_end != 2*N_REF_PAD )
+    {
+        char *ref = (char*) malloc(tr->end - tr->beg + 1 + 2*N_REF_PAD + 1);
+        for (i=0; i < N_REF_PAD - pad_beg; i++) ref[i] = 'N';
+        memcpy(ref+i, tr->ref, len);
+        len += i;
+        for (i=0; i < N_REF_PAD - pad_end; i++) ref[i+len] = 'N';
+        ref[i+len] = 0;
+        free(tr->ref);
+        tr->ref = ref;
+    }
+}
+
+static void sanity_check_ref(args_t *args, tscript_t *tr, bcf1_t *rec)
+{
+    int vbeg = 0;
+    int rbeg = rec->pos - tr->beg + N_REF_PAD;
+    if ( rbeg < 0 ) { vbeg += abs(rbeg); rbeg = 0; }
+    char *ref = tr->ref + rbeg;
+    char *vcf = rec->d.allele[0] + vbeg;
+    assert( vcf - rec->d.allele[0] < strlen(rec->d.allele[0]) && ref - tr->ref < tr->end - tr->beg + 2*N_REF_PAD );
+    int i = 0;
+    while ( ref[i] && vcf[i] )
+    {
+        if ( ref[i]!=vcf[i] && toupper(ref[i])!=toupper(vcf[i]) ) 
+            error("Error: the fasta reference does not match the VCF REF allele at %s:%"PRId64" .. fasta=%c vcf=%c\n",
+                    bcf_seqname(args->hdr,rec),(int64_t) rec->pos+vbeg+1,ref[i],vcf[i]);
+        i++;
+    }
+}
+
+int test_cds_local(args_t *args, bcf1_t *rec)
+{
+    int i,j, ret = 0;
+    const char *chr = bcf_seqname(args->hdr,rec);
+    // note that the off-by-one extension of rlen is deliberate to account for insertions
+    if ( !regidx_overlap(args->idx_cds,chr,rec->pos,rec->pos+rec->rlen, args->itr) ) return 0;
+
+    // structures to fake the normal test_cds machinery
+    hap_node_t root, node;
+    root.type  = HAP_ROOT;
+    kstring_t *tref = &args->hap->tref, *tseq = &args->hap->tseq;
+
+    while ( regitr_overlap(args->itr) )
+    {
+        gf_cds_t *cds = regitr_payload(args->itr,gf_cds_t*);
+        tscript_t *tr = cds->tr;
+        if ( !GF_is_coding(tr->type) ) continue;
+        ret = 1;
+
+        if ( !tr->ref )
+        {
+            tscript_init_ref(args, tr, chr);
+            tscript_splice_ref(tr);
+            khp_insert(trhp, args->active_tr, &tr);     // only to clean the reference afterwards
+        }
+
+        sanity_check_ref(args, tr, rec);
+
+        kstring_t sref;
+        sref.s = tr->sref;
+        sref.l = tr->nsref;
+        sref.m = sref.l;
+
+        for (i=1; i<rec->n_allele; i++)
+        {
+            if ( rec->d.allele[i][0]=='<' || rec->d.allele[i][0]=='*' ) { continue; }
+            if ( hap_init(args, &root, &node, cds, rec, i)!=0 ) continue;
+
+            csq_t csq; 
+            memset(&csq, 0, sizeof(csq_t));
+            csq.pos          = rec->pos;
+            csq.type.biotype = tr->type;
+            csq.type.strand  = tr->strand;
+            csq.type.trid    = tr->id;
+            csq.type.vcf_ial = i;
+            csq.type.gene    = tr->gene->name;
+
+            int csq_type = node.csq;
+
+            // code repetition: it would be nice to reuse the code from hap_add_csq, needs refactoring though
+            if ( node.type == HAP_SSS )
+            {
+                csq.type.type = csq_type;
+                csq_stage(args, &csq, rec);
+            }
+            else
+            {
+                kstring_t sseq;
+                sseq.m = sref.m - 2*N_REF_PAD + node.dlen;
+                sseq.s = node.seq;
+                int alen = sseq.l = strlen(sseq.s);
+                int fill = node.dlen%3 && alen ? 1 : 0; // see #1475227917
+                cds_translate(&sref, &sseq, node.sbeg,node.sbeg,node.sbeg+node.rlen, tr->strand, tseq, fill);
+
+                sseq.m = sref.m - 2*N_REF_PAD;
+                sseq.s = sref.s + N_REF_PAD + node.sbeg;
+                sseq.l = node.rlen;
+                cds_translate(&sref, &sseq, node.sbeg,node.sbeg,node.sbeg+node.rlen, tr->strand, tref, fill);
+
+                // check for truncating stops
+                for (j=0; j<tref->l; j++)
+                    if ( tref->s[j]=='*' ) break;
+                if ( j!=tref->l )
+                {
+                    tref->l = j+1;
+                    tref->s[j+1] = 0;
+                }
+                for (j=0; j<tseq->l; j++)
+                    if ( tseq->s[j]=='*' ) break;
+                if ( j!=tseq->l )
+                {
+                    tseq->l = j+1;
+                    tseq->s[j+1] = 0;
+                }
+                if ( csq_type & CSQ_STOP_LOST )
+                {
+                    if ( tref->s[tref->l-1]=='*' && tref->s[tref->l-1] == tseq->s[tseq->l-1] ) 
+                    {
+                        csq_type &= ~CSQ_STOP_LOST;
+                        csq_type |= CSQ_STOP_RETAINED;
+                    }
+                    else if (tref->s[tref->l-1]!='*' )
+                    {
+                        // This is CDS 3' incomplete ENSG00000173376/synon.vcf, can also be missense
+                        // We observe in real data a change to a stop, ENST00000528237/retained-stop-incomplete-cds.vcf
+                        if ( tseq->s[tseq->l-1] == '*' )
+                        {
+                            csq_type &= ~CSQ_STOP_GAINED;
+                            csq_type |= CSQ_STOP_RETAINED;
+                        }
+                        else
+                            csq_type |= CSQ_INCOMPLETE_CDS;
+                    }
+                }
+                if ( csq_type & CSQ_START_LOST && tref->s[0]!='M' )
+                    csq_type &= ~CSQ_START_LOST;
+                if ( node.dlen!=0 )
+                {
+                    if ( node.dlen%3 )
+                        csq_type |= CSQ_FRAMESHIFT_VARIANT;
+                    else if ( node.dlen<0 )
+                        csq_type |= CSQ_INFRAME_DELETION;
+                    else
+                        csq_type |= CSQ_INFRAME_INSERTION;
+                    if ( tref->s[tref->l-1]!='*' && tseq->s[tseq->l-1]=='*' )
+                        csq_type |= CSQ_STOP_GAINED;
+                }
+                else
+                {
+                    for (j=0; j<tref->l; j++) 
+                        if ( tref->s[j] != tseq->s[j] ) break;
+                    if ( j==tref->l )
+                        csq_type |= CSQ_SYNONYMOUS_VARIANT;
+                    else if ( tref->s[j] ==  '*' )
+                        csq_type |= CSQ_STOP_LOST;
+                    else if ( tseq->s[j] ==  '*' )
+                        csq_type |= CSQ_STOP_GAINED;
+                    else
+                        csq_type |= CSQ_MISSENSE_VARIANT;
+                }
+                if ( csq_type & CSQ_COMPOUND )
+                {
+                    // create the aa variant string
+                    kstring_t str = {0,0,0};
+                    int aa_rbeg = tr->strand==STRAND_FWD ? node.sbeg/3+1 : (tr->nsref - 2*N_REF_PAD - node.sbeg - node.rlen)/3+1;
+                    int aa_sbeg = tr->strand==STRAND_FWD ? node.sbeg/3+1 : (tr->nsref - 2*N_REF_PAD + node.dlen - node.sbeg - alen)/3+1;
+                    kputc_('|', &str);
+                    kputw(aa_rbeg, &str);
+                    kprint_aa_prediction(args,aa_rbeg,tref,&str);
+                    if ( !(csq_type & CSQ_SYNONYMOUS_VARIANT) )
+                    {
+                        kputc_('>', &str);
+                        kputw(aa_sbeg, &str);
+                        kprint_aa_prediction(args,aa_sbeg,tseq,&str);
+                    }
+                    kputc_('|', &str);
+                    kputw(rec->pos+1, &str);
+                    kputs(node.var, &str);
+                    csq.type.vstr = str;
+                    csq.type.type = csq_type & CSQ_COMPOUND;
+                    csq_stage(args, &csq, rec);
+
+                    // all this only to clean vstr when vrec is flushed
+                    if ( !tr->root )
+                        tr->root = (hap_node_t*) calloc(1,sizeof(hap_node_t));
+                    tr->root->ncsq_list++;
+                    hts_expand0(csq_t,tr->root->ncsq_list,tr->root->mcsq_list,tr->root->csq_list);
+                    csq_t *rm_csq = tr->root->csq_list + tr->root->ncsq_list - 1;
+                    rm_csq->type.vstr = str;            
+                }
+                if ( csq_type & ~CSQ_COMPOUND )
+                {
+                    csq.type.type = csq_type & ~CSQ_COMPOUND;
+                    csq.type.vstr.l = 0;
+                    csq_stage(args, &csq, rec);
+                }
+            }
+            free(node.seq);
+            free(node.var);
+        }
+    }
+    return ret;
+}
+
+int test_cds(args_t *args, bcf1_t *rec, vbuf_t *vbuf)
+{
+    static int overlaps_warned = 0, multiploid_warned = 0;
+
+    int i, ret = 0, hap_ret;
+    const char *chr = bcf_seqname(args->hdr,rec);
+    // note that the off-by-one extension of rlen is deliberate to account for insertions
+    if ( !regidx_overlap(args->idx_cds,chr,rec->pos,rec->pos+rec->rlen, args->itr) ) return 0;
+    while ( regitr_overlap(args->itr) )
+    {
+        gf_cds_t *cds = regitr_payload(args->itr,gf_cds_t*);
+        tscript_t *tr = cds->tr;
+        if ( !GF_is_coding(tr->type) ) continue;
+        if ( vbuf->keep_until < tr->end ) vbuf->keep_until = tr->end;
+        ret = 1;
+        if ( !tr->root )
+        {
+            // initialize the transcript and its haplotype tree, fetch the reference sequence
+            tscript_init_ref(args, tr, chr);
+
+            tr->root = (hap_node_t*) calloc(1,sizeof(hap_node_t));
+            tr->nhap = args->phase==PHASE_DROP_GT ? 1 : 2*args->smpl->n;     // maximum ploidy = diploid
+            tr->hap  = (hap_node_t**) malloc(tr->nhap*sizeof(hap_node_t*));
+            for (i=0; i<tr->nhap; i++) tr->hap[i] = NULL;
+            tr->root->nend = tr->nhap;
+            tr->root->type = HAP_ROOT;
+
+            khp_insert(trhp, args->active_tr, &tr);
+        }
+
+        sanity_check_ref(args, tr, rec);
+
+        if ( args->phase==PHASE_DROP_GT )
+        {
+            if ( rec->d.allele[1][0]=='<' || rec->d.allele[1][0]=='*' ) { continue; }
+            hap_node_t *parent = tr->hap[0] ? tr->hap[0] : tr->root;
+            hap_node_t *child  = (hap_node_t*)calloc(1,sizeof(hap_node_t));
+            hap_ret = hap_init(args, parent, child, cds, rec, 1);
+            if ( hap_ret!=0 )
+            {
+                // overlapping or intron variant, cannot apply
+                if ( hap_ret==1 )
+                {
+                    if ( args->verbosity && (!overlaps_warned || args->verbosity > 1) )
+                    {
+                        fprintf(stderr,
+                            "Warning: Skipping overlapping variants at %s:%"PRId64"\t%s>%s.\n",
+                            chr,(int64_t) rec->pos+1,rec->d.allele[0],rec->d.allele[1]);
+                        if ( !overlaps_warned )
+                            fprintf(stderr,"         This message is printed only once, the verbosity can be increased with `--verbose 2`\n");
+                        overlaps_warned = 1;
+                    }
+                    if ( args->out ) 
+                        fprintf(args->out,"LOG\tWarning: Skipping overlapping variants at %s:%"PRId64"\t%s>%s\n", chr,(int64_t) rec->pos+1,rec->d.allele[0],rec->d.allele[1]);
+                }
+                else ret = 1;   // prevent reporting as intron in test_tscript
+                hap_destroy(child);
+                continue;
+            }
+            if ( child->type==HAP_SSS )
+            {
+                csq_t csq; 
+                memset(&csq, 0, sizeof(csq_t));
+                csq.pos          = rec->pos;
+                csq.type.biotype = tr->type;
+                csq.type.strand  = tr->strand;
+                csq.type.trid    = tr->id;
+                csq.type.vcf_ial = 1;
+                csq.type.gene    = tr->gene->name;
+                csq.type.type = child->csq;
+                csq_stage(args, &csq, rec);
+                hap_destroy(child);
+                ret = 1;
+                continue;
+            }
+            parent->nend--;
+            parent->nchild = 1;
+            parent->mchild = 1;
+            parent->child  = (hap_node_t**) malloc(sizeof(hap_node_t*));
+            parent->child[0] = child;
+            tr->hap[0] = child;
+            tr->hap[0]->nend = 1;
+            continue;
+        }
+
+        // apply the VCF variants and extend the haplotype tree
+        int j, ismpl, ihap, ngts = bcf_get_genotypes(args->hdr, rec, &args->gt_arr, &args->mgt_arr);
+        ngts /= bcf_hdr_nsamples(args->hdr);
+        if ( ngts!=1 && ngts!=2 ) 
+        {
+            if ( args->verbosity && (!multiploid_warned || args->verbosity > 1) )
+            {
+                fprintf(stderr,
+                    "Warning: Skipping site with non-diploid/non-haploid genotypes at %s:%"PRId64"\t%s>%s.\n",
+                    chr,(int64_t) rec->pos+1,rec->d.allele[0],rec->d.allele[1]);
+                if ( !multiploid_warned )
+                    fprintf(stderr,"         This message is printed only once, the verbosity can be increased with `--verbose 2`\n");
+                multiploid_warned = 1;
+            }
+            if ( args->out ) 
+                fprintf(args->out,"LOG\tWarning: Skipping site with non-diploid/non-haploid genotypes at %s:%"PRId64"\t%s>%s\n", chr,(int64_t) rec->pos+1,rec->d.allele[0],rec->d.allele[1]);
+            continue;
+        }
+        for (ismpl=0; ismpl<args->smpl->n; ismpl++)
+        {
+            int32_t *gt = args->gt_arr + args->smpl->idx[ismpl]*ngts;
+            if ( gt[0]==bcf_gt_missing ) continue;
+
+            if ( ngts>1 && gt[1]!=bcf_gt_missing && gt[1]!=bcf_int32_vector_end && bcf_gt_allele(gt[0])!=bcf_gt_allele(gt[1]) )
+            {
+                if ( args->phase==PHASE_MERGE )
+                {
+                    if ( !bcf_gt_allele(gt[0]) ) gt[0] = gt[1];
+                }
+                if ( !bcf_gt_is_phased(gt[0]) && !bcf_gt_is_phased(gt[1]) )
+                {
+                    if ( args->phase==PHASE_REQUIRE )
+                        error("Unphased heterozygous genotype at %s:%"PRId64", sample %s. See the --phase option.\n", chr,(int64_t) rec->pos+1,args->hdr->samples[args->smpl->idx[ismpl]]);
+                    if ( args->phase==PHASE_SKIP )
+                        continue;
+                    if ( args->phase==PHASE_NON_REF )
+                    {
+                        if ( !bcf_gt_allele(gt[0]) ) gt[0] = gt[1];
+                        else if ( !bcf_gt_allele(gt[1]) ) gt[1] = gt[0];
+                    }
+                }
+            }
+
+            for (ihap=0; ihap<ngts; ihap++)
+            {
+                if ( gt[ihap]==bcf_gt_missing || gt[ihap]==bcf_int32_vector_end ) continue;
+
+                i = 2*ismpl + ihap;
+
+                int ial = bcf_gt_allele(gt[ihap]);
+                if ( !ial ) continue;
+                assert( ial < rec->n_allele );
+                if ( rec->d.allele[ial][0]=='<' || rec->d.allele[ial][0]=='*' ) { continue; }
+
+                hap_node_t *parent = tr->hap[i] ? tr->hap[i] : tr->root;
+                if ( parent->cur_rec==rec && parent->cur_child[ial]>=0 )
+                {
+                    // this haplotype has been seen in another sample
+                    tr->hap[i] = parent->child[ parent->cur_child[ial] ];
+                    tr->hap[i]->nend++;
+                    parent->nend--;
+                    continue;
+                }
+
+                hap_node_t *child = (hap_node_t*)calloc(1,sizeof(hap_node_t));
+                hap_ret = hap_init(args, parent, child, cds, rec, ial);
+                if ( hap_ret!=0 )
+                {
+                    // overlapping or intron variant, cannot apply
+                    if ( hap_ret==1 )
+                    {
+                        if ( args->verbosity && (!overlaps_warned || args->verbosity > 1) )
+                        {
+                            fprintf(stderr,
+                                    "Warning: Skipping overlapping variants at %s:%"PRId64", sample %s\t%s>%s.\n",
+                                    chr,(int64_t) rec->pos+1,args->hdr->samples[args->smpl->idx[ismpl]],rec->d.allele[0],rec->d.allele[ial]);
+                            if ( !overlaps_warned )
+                                fprintf(stderr,"         This message is printed only once, the verbosity can be increased with `--verbose 2`\n");
+                            overlaps_warned = 1;
+                        }
+                        if ( args->out  )
+                            fprintf(args->out,"LOG\tWarning: Skipping overlapping variants at %s:%"PRId64", sample %s\t%s>%s\n",
+                                    chr,(int64_t) rec->pos+1,args->hdr->samples[args->smpl->idx[ismpl]],rec->d.allele[0],rec->d.allele[ial]);
+                    }
+                    hap_destroy(child);
+                    continue;
+                }
+                if ( child->type==HAP_SSS )
+                {
+                    csq_t csq; 
+                    memset(&csq, 0, sizeof(csq_t));
+                    csq.pos          = rec->pos;
+                    csq.type.biotype = tr->type;
+                    csq.type.strand  = tr->strand;
+                    csq.type.trid    = tr->id;
+                    csq.type.vcf_ial = ial;
+                    csq.type.gene    = tr->gene->name;
+                    csq.type.type = child->csq;
+                    csq_stage(args, &csq, rec);
+                    hap_destroy(child);
+                    continue;
+                }
+                if ( parent->cur_rec!=rec )
+                {
+                    hts_expand(int,rec->n_allele,parent->mcur_child,parent->cur_child);
+                    for (j=0; j<rec->n_allele; j++) parent->cur_child[j] = -1;
+                    parent->cur_rec = rec;
+                }
+
+                j = parent->nchild++;
+                hts_expand0(hap_node_t*,parent->nchild,parent->mchild,parent->child);
+                parent->cur_child[ial] = j;
+                parent->child[j] = child;
+                tr->hap[i] = child;
+                tr->hap[i]->nend++;
+                parent->nend--;
+            }
+        }
+    }
+    return ret;
+}
+
+void csq_stage(args_t *args, csq_t *csq, bcf1_t *rec)
+{
+    // known issues: tab output leads to unsorted output. This is because
+    // coding haplotypes are printed in one go and buffering is not used
+    // with tab output. VCF output is OK though.
+    if ( csq_push(args, csq, rec)!=0 && args->phase==PHASE_DROP_GT ) return;    // the consequence already exists
+
+    int i,j,ngt = 0;
+    if ( args->phase!=PHASE_DROP_GT )
+    {
+        ngt = bcf_get_genotypes(args->hdr, rec, &args->gt_arr, &args->mgt_arr);
+        if ( ngt>0 ) ngt /= bcf_hdr_nsamples(args->hdr);
+    }
+    if ( ngt<=0 )
+    {
+        if ( args->output_type==FT_TAB_TEXT )
+            csq_print_text(args, csq, -1,0);
+        return;
+    }
+    assert( ngt<=2 );
+
+    if ( args->output_type==FT_TAB_TEXT )
+    {
+        for (i=0; i<args->smpl->n; i++)
+        {
+            int32_t *gt = args->gt_arr + args->smpl->idx[i]*ngt;
+            for (j=0; j<ngt; j++)
+            {
+                if ( gt[j]==bcf_gt_missing || gt[j]==bcf_int32_vector_end ) continue;
+                int ial = bcf_gt_allele(gt[j]);
+                if ( !ial || ial!=csq->type.vcf_ial ) continue;
+                csq_print_text(args, csq, args->smpl->idx[i],j+1);
+            }
+        }
+        return;
+    }
+
+    vrec_t *vrec = csq->vrec;
+    for (i=0; i<args->smpl->n; i++)
+    {
+        int32_t *gt = args->gt_arr + args->smpl->idx[i]*ngt;
+        for (j=0; j<ngt; j++)
+        {
+            if ( gt[j]==bcf_gt_missing || gt[j]==bcf_int32_vector_end ) continue;
+            int ial = bcf_gt_allele(gt[j]);
+            if ( !ial || ial!=csq->type.vcf_ial ) continue;
+
+            int icsq2 = 2*csq->idx + j;
+            if ( icsq2 >= args->ncsq2_max ) // more than ncsq_max consequences, so can't fit it in FMT
+            {
+                int ismpl = args->smpl->idx[i];
+                if ( args->verbosity && (!args->ncsq2_small_warned || args->verbosity > 1) )
+                {
+                    fprintf(stderr,
+                            "Warning: Too many consequences for sample %s at %s:%"PRId64", keeping the first %d and skipping the rest.\n",
+                            args->hdr->samples[ismpl],bcf_hdr_id2name(args->hdr,args->rid),(int64_t) vrec->line->pos+1,icsq2+1);
+                    if ( !args->ncsq2_small_warned )
+                        fprintf(stderr,"         The limit can be increased by setting the --ncsq parameter. This warning is printed only once.\n");
+                    args->ncsq2_small_warned = 1;
+                }
+                if ( args->ncsq2_small_warned < icsq2 ) args->ncsq2_small_warned = icsq2;
+                break;
+            }
+            int ival, ibit;
+            icsq2_to_bit(icsq2, &ival,&ibit);
+            if ( vrec->nfmt < 1 + ival ) vrec->nfmt = 1 + ival;
+            vrec->fmt_bm[i*args->nfmt_bcsq + ival] |= 1 << ibit;
+        }
+    }
+}
+int test_utr(args_t *args, bcf1_t *rec)
+{
+    const char *chr = bcf_seqname(args->hdr,rec);
+    // note that the off-by-one extension of rlen is deliberate to account for insertions
+    if ( !regidx_overlap(args->idx_utr,chr,rec->pos,rec->pos+rec->rlen, args->itr) ) return 0;
+
+    splice_t splice;
+    splice_init(&splice, rec);
+
+    int i, ret = 0;
+    while ( regitr_overlap(args->itr) )
+    {
+        gf_utr_t *utr = regitr_payload(args->itr, gf_utr_t*);
+        tscript_t *tr = splice.tr = utr->tr;
+        for (i=1; i<rec->n_allele; i++)
+        {
+            if ( rec->d.allele[i][0]=='<' || rec->d.allele[i][0]=='*' ) { continue; }
+            splice.vcf.alt = rec->d.allele[i];
+            splice.csq     = 0;
+            int splice_ret = splice_csq(args, &splice, utr->beg, utr->end);
+            if ( splice_ret!=SPLICE_INSIDE && splice_ret!=SPLICE_OVERLAP ) continue;
+            csq_t csq; 
+            memset(&csq, 0, sizeof(csq_t));
+            csq.pos          = rec->pos;
+            csq.type.type    = utr->which==prime5 ? CSQ_UTR5 : CSQ_UTR3;
+            csq.type.biotype = tr->type;
+            csq.type.strand  = tr->strand;
+            csq.type.trid    = tr->id;
+            csq.type.vcf_ial = i;
+            csq.type.gene    = tr->gene->name;
+            csq_stage(args, &csq, rec);
+            ret = 1;
+        }
+    }
+    assert(!splice.kref.s);
+    assert(!splice.kalt.s);
+    return ret;
+}
+int test_splice(args_t *args, bcf1_t *rec)
+{
+    const char *chr = bcf_seqname(args->hdr,rec);
+    if ( !regidx_overlap(args->idx_exon,chr,rec->pos,rec->pos + rec->rlen, args->itr) ) return 0;
+
+    splice_t splice;
+    splice_init(&splice, rec);
+    splice.check_acceptor = splice.check_donor = 1;
+
+    int i, ret = 0;
+    while ( regitr_overlap(args->itr) )
+    {
+        gf_exon_t *exon = regitr_payload(args->itr, gf_exon_t*);
+        splice.tr = exon->tr;
+        if ( !splice.tr->ncds ) continue;  // not a coding transcript, no interest in splice sites
+
+        splice.check_region_beg = splice.tr->beg==exon->beg ? 0 : 1;
+        splice.check_region_end = splice.tr->end==exon->end ? 0 : 1;
+
+        for (i=1; i<rec->n_allele; i++)
+        {
+            if ( rec->d.allele[1][0]=='<' || rec->d.allele[1][0]=='*' ) { continue; }
+            splice.vcf.alt = rec->d.allele[i];
+            splice.csq     = 0;
+            splice_csq(args, &splice, exon->beg, exon->end);
+            if ( splice.csq ) ret = 1;
+        }
+    }
+    free(splice.kref.s);
+    free(splice.kalt.s);
+    return ret;
+}
+int test_tscript(args_t *args, bcf1_t *rec)
+{
+    const char *chr = bcf_seqname(args->hdr,rec);
+    if ( !regidx_overlap(args->idx_tscript,chr,rec->pos,rec->pos+rec->rlen, args->itr) ) return 0;
+
+    splice_t splice;
+    splice_init(&splice, rec);
+
+    int i, ret = 0;
+    while ( regitr_overlap(args->itr) )
+    {
+        tscript_t *tr = splice.tr = regitr_payload(args->itr, tscript_t*);
+        for (i=1; i<rec->n_allele; i++)
+        {
+            if ( rec->d.allele[i][0]=='<' || rec->d.allele[i][0]=='*' ) { continue; }
+            splice.vcf.alt = rec->d.allele[i];
+            splice.csq     = 0;
+            int splice_ret = splice_csq(args, &splice, tr->beg, tr->end);
+            if ( splice_ret!=SPLICE_INSIDE && splice_ret!=SPLICE_OVERLAP ) continue;    // SPLICE_OUTSIDE or SPLICE_REF
+            csq_t csq; 
+            memset(&csq, 0, sizeof(csq_t));
+            csq.pos          = rec->pos;
+            csq.type.type    = GF_is_coding(tr->type) ? CSQ_INTRON : CSQ_NON_CODING;
+            csq.type.biotype = tr->type;
+            csq.type.strand  = tr->strand;
+            csq.type.trid    = tr->id;
+            csq.type.gene    = tr->gene->name;
+            csq_stage(args, &csq, rec);
+            ret = 1;
+        }
+    }
+    assert(!splice.kref.s);
+    assert(!splice.kalt.s);
+    return ret;
+}
+
+void test_symbolic_alt(args_t *args, bcf1_t *rec)
+{
+    static int warned = 0;
+    if ( args->verbosity && (!warned && args->verbosity > 0) )
+    {
+        fprintf(stderr,"Warning: The support for symbolic ALT insertions is experimental.\n");
+        warned = 1;
+    }
+
+    const char *chr = bcf_seqname(args->hdr,rec);
+
+    // only insertions atm
+    int beg = rec->pos + 1;
+    int end = beg;
+    int csq_class = CSQ_ELONGATION;
+
+    int hit = 0;
+    if ( regidx_overlap(args->idx_cds,chr,beg,end, args->itr) )
+    {
+        while ( regitr_overlap(args->itr) )
+        {
+            csq_t csq; 
+            memset(&csq, 0, sizeof(csq_t));
+            gf_cds_t *cds    = regitr_payload(args->itr,gf_cds_t*);
+            tscript_t *tr    = cds->tr;
+            csq.type.type    = (GF_is_coding(tr->type) ? CSQ_CODING_SEQUENCE : CSQ_NON_CODING) | csq_class;
+            csq.pos          = rec->pos;
+            csq.type.biotype = tr->type;
+            csq.type.strand  = tr->strand;
+            csq.type.trid    = tr->id;
+            csq.type.gene    = tr->gene->name;
+            csq_stage(args, &csq, rec);
+            hit = 1;
+        }
+    }
+    if ( regidx_overlap(args->idx_utr,chr,beg,end, args->itr) )
+    {
+        while ( regitr_overlap(args->itr) )
+        {
+            csq_t csq; 
+            memset(&csq, 0, sizeof(csq_t));
+            gf_utr_t *utr    = regitr_payload(args->itr, gf_utr_t*);
+            tscript_t *tr    = utr->tr;
+            csq.type.type    = (utr->which==prime5 ? CSQ_UTR5 : CSQ_UTR3) | csq_class;
+            csq.pos          = rec->pos;
+            csq.type.biotype = tr->type;
+            csq.type.strand  = tr->strand;
+            csq.type.trid    = tr->id;
+            csq.type.gene    = tr->gene->name;
+            csq_stage(args, &csq, rec);
+            hit = 1;
+        }
+    }
+    if ( regidx_overlap(args->idx_exon,chr,beg,end, args->itr) )
+    {
+        splice_t splice;
+        splice_init(&splice, rec);
+        splice.check_acceptor = splice.check_donor = 1;
+
+        while ( regitr_overlap(args->itr) )
+        {
+            gf_exon_t *exon = regitr_payload(args->itr, gf_exon_t*);
+            splice.tr = exon->tr;
+            if ( !splice.tr->ncds ) continue;  // not a coding transcript, no interest in splice sites
+            splice.check_region_beg = splice.tr->beg==exon->beg ? 0 : 1;
+            splice.check_region_end = splice.tr->end==exon->end ? 0 : 1;
+            splice.vcf.alt = rec->d.allele[1];
+            splice.csq     = csq_class;
+            splice_csq(args, &splice, exon->beg, exon->end);
+            if ( splice.csq ) hit = 1;
+        }
+    }
+    if ( !hit && regidx_overlap(args->idx_tscript,chr,beg,end, args->itr) )
+    {
+        splice_t splice;
+        splice_init(&splice, rec);
+
+        while ( regitr_overlap(args->itr) )
+        {
+            csq_t csq; 
+            memset(&csq, 0, sizeof(csq_t));
+            tscript_t *tr = splice.tr = regitr_payload(args->itr, tscript_t*);
+            splice.vcf.alt = rec->d.allele[1];
+            splice.csq     = csq_class;
+            int splice_ret = splice_csq(args, &splice, tr->beg, tr->end);
+            if ( splice_ret!=SPLICE_INSIDE && splice_ret!=SPLICE_OVERLAP ) continue;    // SPLICE_OUTSIDE or SPLICE_REF
+            csq.type.type    = (GF_is_coding(tr->type) ? CSQ_INTRON : CSQ_NON_CODING) | csq_class;
+            csq.pos          = rec->pos;
+            csq.type.biotype = tr->type;
+            csq.type.strand  = tr->strand;
+            csq.type.trid    = tr->id;
+            csq.type.gene    = tr->gene->name;
+            csq_stage(args, &csq, rec);
+        }
+    }
+}
+
+void debug_print_buffers(args_t *args, int pos)
+{
+    int i,j;
+    fprintf(stderr,"debug_print_buffers at %d\n", pos);
+    fprintf(stderr,"vbufs:\n");
+    for (i=0; i<args->vcf_rbuf.n; i++)
+    {
+        int k = rbuf_kth(&args->vcf_rbuf, i);
+        vbuf_t *vbuf = args->vcf_buf[k];
+
+        fprintf(stderr,"\tvbuf %d:\n", i);
+        for (j=0; j<vbuf->n; j++)
+        {
+            vrec_t *vrec = vbuf->vrec[j];
+            fprintf(stderr,"\t\t%"PRId64" .. nvcsq=%d\n", (int64_t) vrec->line->pos+1, vrec->nvcsq);
+        }
+    }
+    fprintf(stderr,"pos2vbuf:");
+    khint_t k;
+    for (k = 0; k < kh_end(args->pos2vbuf); ++k)
+        if (kh_exist(args->pos2vbuf, k)) fprintf(stderr," %d",1+(int)kh_key(args->pos2vbuf, k));
+    fprintf(stderr,"\n");
+    fprintf(stderr,"active_tr: %d\n", args->active_tr->ndat);
+}
+
+static void process(args_t *args, bcf1_t **rec_ptr)
+{
+    if ( !rec_ptr )
+    {
+        hap_flush(args, REGIDX_MAX);
+        vbuf_flush(args, REGIDX_MAX);
+        return;
+    }
+
+    bcf1_t *rec = *rec_ptr;
+    static int32_t prev_rid = -1, prev_pos = -1;
+    if ( prev_rid!=rec->rid )
+    {
+        prev_rid = rec->rid;
+        prev_pos = rec->pos;
+
+        // Common error is to use different naming conventions in the fasta and the VCF (e.g. X vs chrX).
+        // Perform a simple sanity check (that does not catch much), the chromosome must be present in the
+        // reference file
+        if ( !faidx_has_seq(args->fai,bcf_seqname(args->hdr,rec)) )
+            error("Error: the chromosome \"%s\" is not present in %s\n",bcf_seqname(args->hdr,rec),args->fa_fname);
+    }
+    if ( prev_pos > rec->pos )
+        error("Error: The file is not sorted, %s:%d comes before %s:%"PRId64"\n",bcf_seqname(args->hdr,rec),prev_pos+1,bcf_seqname(args->hdr,rec),(int64_t) rec->pos+1);
+
+    int call_csq = 1;
+    if ( rec->n_allele < 2 ) call_csq = 0;   // no alternate allele
+    else if ( rec->n_allele==2 && (rec->d.allele[1][0]=='*' || rec->d.allele[1][1]=='*') ) call_csq = 0;     // gVCF, not an alt allele
+    else if ( rec->d.allele[1][0]=='<' )
+    {
+        if ( strncmp("<INS",rec->d.allele[1], 4) ) call_csq = 0;    // only <INS[:.*]> is supported at the moment
+    }
+    if ( call_csq && args->filter )
+    {
+        call_csq = filter_test(args->filter, rec, NULL);
+        if ( args->filter_logic==FLT_EXCLUDE ) call_csq = call_csq ? 0 : 1;
+    }
+    if ( !call_csq )
+    {
+        if ( !args->out_fh ) return;    // not a VCF output
+        vbuf_push(args, rec_ptr);
+        hap_flush(args, rec->pos-1);
+        vbuf_flush(args, rec->pos-1);
+        return;
+    }
+
+    if ( args->rid != rec->rid ) 
+    {
+        hap_flush(args, REGIDX_MAX);
+        vbuf_flush(args, REGIDX_MAX);
+    }
+    args->rid = rec->rid;
+    vbuf_t *vbuf = vbuf_push(args, rec_ptr);
+
+    if ( rec->d.allele[1][0]!='<' )
+    {
+        int hit = args->local_csq ? test_cds_local(args, rec) : test_cds(args, rec, vbuf);
+        hit += test_utr(args, rec);
+        hit += test_splice(args, rec);
+        if ( !hit ) test_tscript(args, rec);
+    }
+    else
+        test_symbolic_alt(args, rec);
+
+    if ( rec->pos > 0 )
+    {
+        hap_flush(args, rec->pos-1);
+        vbuf_flush(args, rec->pos-1);
+    }
+
+    return;
+}
+
+static const char *usage(void)
+{
+    return 
+        "\n"
+        "About: Haplotype-aware consequence caller.\n"
+        "Usage: bcftools csq [OPTIONS] in.vcf\n"
+        "\n"
+        "Required options:\n"
+        "   -f, --fasta-ref FILE              Reference file in fasta format\n"
+        "   -g, --gff-annot FILE              GFF3 annotation file\n"
+        "\n"
+        "CSQ options:\n"
+        "   -B, --trim-protein-seq INT        Abbreviate protein-changing predictions to max INT aminoacids\n" 
+        "   -c, --custom-tag STRING           Use this tag instead of the default BCSQ\n"
+        "   -l, --local-csq                   Localized predictions, consider only one VCF record at a time\n"
+        "   -n, --ncsq INT                    Maximum number of per-haplotype consequences to consider for each site [15]\n"
+        "   -p, --phase a|m|r|R|s             How to handle unphased heterozygous genotypes: [r]\n"
+        "                                       a: take GTs as is, create haplotypes regardless of phase (0/1 -> 0|1)\n"
+        "                                       m: merge *all* GTs into a single haplotype (0/1 -> 1, 1/2 -> 1)\n"
+        "                                       r: require phased GTs, throw an error on unphased het GTs\n"
+        "                                       R: create non-reference haplotypes if possible (0/1 -> 1|1, 1/2 -> 1|2)\n"
+        "                                       s: skip unphased hets\n"
+        "Options:\n"
+        "   -e, --exclude EXPR                Exclude sites for which the expression is true\n"
+        "       --force                       Run even if some sanity checks fail\n"
+        "   -i, --include EXPR                Select sites for which the expression is true\n"
+        "       --no-version                  Do not append version and command line to the header\n"
+        "   -o, --output FILE                 Write output to a file [standard output]\n"
+        "   -O, --output-type b|u|z|v|t[0-9]  b: compressed BCF, u: uncompressed BCF, z: compressed VCF\n"
+        "                                     v: uncompressed VCF, t: plain tab-delimited text output, 0-9: compression level [v]\n"
+        "   -r, --regions REGION              Restrict to comma-separated list of regions\n"
+        "   -R, --regions-file FILE           Restrict to regions listed in a file\n"
+        "       --regions-overlap 0|1|2       Include if POS in the region (0), record overlaps (1), variant overlaps (2) [1]\n"
+        "   -s, --samples -|LIST              Samples to include or \"-\" to apply all variants and ignore samples\n"
+        "   -S, --samples-file FILE           Samples to include\n"
+        "   -t, --targets REGION              Similar to -r but streams rather than index-jumps\n"
+        "   -T, --targets-file FILE           Similar to -R but streams rather than index-jumps\n"
+        "       --targets-overlap 0|1|2       Include if POS in the region (0), record overlaps (1), variant overlaps (2) [0]\n"
+        "       --threads INT                 Use multithreading with <int> worker threads [0]\n"
+        "   -v, --verbose INT                 Verbosity level 0-2 [1]\n"
+        "\n"
+        "Example:\n"
+        "   bcftools csq -f hs37d5.fa -g Homo_sapiens.GRCh37.82.gff3.gz in.vcf\n"
+        "\n"
+        "   # GFF3 annotation files can be downloaded from Ensembl. e.g. for human:\n"
+        "   ftp://ftp.ensembl.org/pub/current_gff3/homo_sapiens/\n"
+        "   ftp://ftp.ensembl.org/pub/grch37/release-84/gff3/homo_sapiens/\n"
+        "\n";
+}
+
+int main_csq(int argc, char *argv[])
+{
+    args_t *args = (args_t*) calloc(1,sizeof(args_t));
+    args->argc = argc; args->argv = argv;
+    args->output_type = FT_VCF;
+    args->bcsq_tag = "BCSQ";
+    args->ncsq2_max = 2*(16-1);      // 1 bit is reserved for BCF missing values
+    args->verbosity = 1;
+    args->record_cmd_line = 1;
+    args->clevel = -1;
+
+    static struct option loptions[] =
+    {
+        {"force",0,0,1},
+        {"threads",required_argument,NULL,2},
+        {"help",0,0,'h'},
+        {"ncsq",1,0,'n'},
+        {"brief-predictions",no_argument,0,'b'},
+        {"trim-protein-seq",required_argument,0,'B'},
+        {"custom-tag",1,0,'c'},
+        {"local-csq",0,0,'l'},
+        {"gff-annot",1,0,'g'},
+        {"fasta-ref",1,0,'f'},
+        {"include",1,0,'i'},
+        {"exclude",1,0,'e'},
+        {"output",1,0,'o'},
+        {"output-type",1,NULL,'O'},
+        {"phase",1,0,'p'},
+        {"quiet",0,0,'q'},
+        {"verbose",1,0,'v'},
+        {"regions",1,0,'r'},
+        {"regions-file",1,0,'R'},
+        {"regions-overlap",required_argument,NULL,4},
+        {"samples",1,0,'s'},
+        {"samples-file",1,0,'S'},
+        {"targets",1,0,'t'},
+        {"targets-file",1,0,'T'},
+        {"targets-overlap",required_argument,NULL,5},
+        {"no-version",no_argument,NULL,3},
+        {0,0,0,0}
+    };
+    int c, targets_is_file = 0, regions_is_file = 0; 
+    int regions_overlap = 1;
+    int targets_overlap = 0;
+    char *targets_list = NULL, *regions_list = NULL, *tmp;
+    while ((c = getopt_long(argc, argv, "?hr:R:t:T:i:e:f:o:O:g:s:S:p:qc:ln:bB:v:",loptions,NULL)) >= 0)
+    {
+        switch (c) 
+        {
+            case  1 : args->force = 1; break;
+            case  2 :
+                args->n_threads = strtol(optarg,&tmp,10);
+                if ( *tmp ) error("Could not parse argument: --threads  %s\n", optarg);
+                break;
+            case  3 : args->record_cmd_line = 0; break;
+            case 'b':
+                    args->brief_predictions = 1;
+                    fprintf(stderr,"Warning: the -b option will be removed in future versions. Please use -B 1 instead.\n");
+                    break;
+            case 'B': 
+                    args->brief_predictions = strtol(optarg,&tmp,10);
+                    if ( *tmp || args->brief_predictions<1 ) error("Could not parse argument: --trim-protein-seq %s\n", optarg);
+                    break;
+            case 'l': args->local_csq = 1; break;
+            case 'c': args->bcsq_tag = optarg; break;
+            case 'q': error("Error: the -q option has been deprecated, use -v, --verbose instead.\n"); break;
+            case 'v': 
+                args->verbosity = atoi(optarg);
+                if ( args->verbosity<0 || args->verbosity>2 ) error("Error: expected integer 0-2 with -v, --verbose\n");
+                break;
+            case 'p':
+                switch (optarg[0]) 
+                {
+                    case 'a': args->phase = PHASE_AS_IS; break;
+                    case 'm': args->phase = PHASE_MERGE; break;
+                    case 'r': args->phase = PHASE_REQUIRE; break;
+                    case 'R': args->phase = PHASE_NON_REF; break;
+                    case 's': args->phase = PHASE_SKIP; break;
+                    default: error("The -p code \"%s\" not recognised\n", optarg);
+                }
+                break;
+            case 'f': args->fa_fname = optarg; break;
+            case 'g': args->gff_fname = optarg; break;
+            case 'n': 
+                args->ncsq2_max = 2 * atoi(optarg);
+                if ( args->ncsq2_max <= 0 ) error("Expected positive integer with -n, got %s\n", optarg);
+                break;
+            case 'o': args->output_fname = optarg; break;
+            case 'O':
+                      switch (optarg[0]) {
+                          case 't': args->output_type = FT_TAB_TEXT; break;
+                          case 'b': args->output_type = FT_BCF_GZ; break;
+                          case 'u': args->output_type = FT_BCF; break;
+                          case 'z': args->output_type = FT_VCF_GZ; break;
+                          case 'v': args->output_type = FT_VCF; break;
+                          default:
+                          {
+                              args->clevel = strtol(optarg,&tmp,10);
+                              if ( *tmp || args->clevel<0 || args->clevel>9 ) error("The output type \"%s\" not recognised\n", optarg);
+                          }
+                      }
+                      if ( optarg[1] )
+                      {
+                          args->clevel = strtol(optarg+1,&tmp,10);
+                          if ( *tmp || args->clevel<0 || args->clevel>9 ) error("Could not parse argument: --output-type %s\n", optarg+1);
+                      }
+                      break;
+            case 'e':
+                if ( args->filter_str ) error("Error: only one -i or -e expression can be given, and they cannot be combined\n");
+                args->filter_str = optarg; args->filter_logic |= FLT_EXCLUDE; break;
+            case 'i':
+                if ( args->filter_str ) error("Error: only one -i or -e expression can be given, and they cannot be combined\n");
+                args->filter_str = optarg; args->filter_logic |= FLT_INCLUDE; break;
+            case 'r': regions_list = optarg; break;
+            case 'R': regions_list = optarg; regions_is_file = 1; break;
+            case 's': args->sample_list = optarg; break;
+            case 'S': args->sample_list = optarg; args->sample_is_file = 1; break;
+            case 't': targets_list = optarg; break;
+            case 'T': targets_list = optarg; targets_is_file = 1; break;
+            case  4 :
+                regions_overlap = parse_overlap_option(optarg);
+                if ( regions_overlap < 0 ) error("Could not parse: --regions-overlap %s\n",optarg);
+                break;
+            case  5 :
+                targets_overlap = parse_overlap_option(optarg);
+                if ( targets_overlap < 0 ) error("Could not parse: --targets-overlap %s\n",optarg);
+                break;
+            case 'h':
+            case '?': error("%s",usage());
+            default: error("The option not recognised: %s\n\n", optarg); break;
+        }
+    }
+    char *fname = NULL;
+    if ( optind==argc )
+    {
+        if ( !isatty(fileno((FILE *)stdin)) ) fname = "-";  // reading from stdin
+        else error("%s", usage());
+    }
+    else fname = argv[optind];
+    if ( argc - optind>1 ) error("%s", usage());
+    if ( !args->fa_fname ) error("Missing the --fa-ref option\n");
+    if ( !args->gff_fname ) error("Missing the --gff option\n");
+    args->sr = bcf_sr_init();
+    if ( targets_list )
+    {
+        bcf_sr_set_opt(args->sr,BCF_SR_TARGETS_OVERLAP,targets_overlap);
+        if ( bcf_sr_set_targets(args->sr, targets_list, targets_is_file, 0)<0 )
+            error("Failed to read the targets: %s\n", targets_list);
+    }
+    if ( regions_list )
+    {
+        bcf_sr_set_opt(args->sr,BCF_SR_REGIONS_OVERLAP,regions_overlap);
+        if ( bcf_sr_set_regions(args->sr, regions_list, regions_is_file)<0 )
+            error("Failed to read the regions: %s\n", regions_list);
+    }
+    if ( bcf_sr_set_threads(args->sr, args->n_threads)<0 ) error("Failed to create %d extra threads\n", args->n_threads);
+    if ( !bcf_sr_add_reader(args->sr, fname) )
+        error("Failed to read from %s: %s\n", !strcmp("-",fname)?"standard input":fname,bcf_sr_strerror(args->sr->errnum));
+    args->hdr = bcf_sr_get_header(args->sr,0);
+
+    init_data(args);
+    while ( bcf_sr_next_line(args->sr) )
+    {
+        process(args, &args->sr->readers[0].buffer[0]);
+    }
+    process(args,NULL);
+
+    destroy_data(args);
+    bcf_sr_destroy(args->sr);
+    free(args);
+    return 0;
+}
+
diff --git a/bcftools/csq.c.pysam.c b/bcftools/csq.c.pysam.c
new file mode 100644
index 0000000..e4abf4b
--- /dev/null
+++ b/bcftools/csq.c.pysam.c
@@ -0,0 +1,4397 @@
+#include "bcftools.pysam.h"
+
+/* The MIT License
+
+   Copyright (c) 2016-2021 Genome Research Ltd.
+
+   Author: Petr Danecek <pd3@sanger.ac.uk>
+   
+   Permission is hereby granted, free of charge, to any person obtaining a copy
+   of this software and associated documentation files (the "Software"), to deal
+   in the Software without restriction, including without limitation the rights
+   to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+   copies of the Software, and to permit persons to whom the Software is
+   furnished to do so, subject to the following conditions:
+   
+   The above copyright notice and this permission notice shall be included in
+   all copies or substantial portions of the Software.
+   
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+   IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+   FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+   AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+   LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+   OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+   THE SOFTWARE.
+
+ */
+/*
+    Things that would be nice to have
+        - dynamic N_REF_PAD
+        - for stop-lost events (also in frameshifts) report the number of truncated aa's
+        - memory could be greatly reduced by indexing gff (but it is quite compact already)
+        - deletions that go beyond transcript boundaries are not checked at sequence level
+            - alloc tscript->ref in hap_finalize, introduce fa_off_beg:16,fa_off_end:16
+            - see test/csq/ENST00000573314/insertion-overlap.vcf #1476288882
+
+    Read about transcript types here
+        http://vega.sanger.ac.uk/info/about/gene_and_transcript_types.html
+        http://www.ensembl.org/info/genome/variation/predicted_data.html
+        http://www.gencodegenes.org/gencode_biotypes.html
+
+    List of supported biotypes
+        antisense
+        IG_C_gene
+        IG_D_gene
+        IG_J_gene
+        IG_LV_gene
+        IG_V_gene
+        lincRNA
+        macro_lncRNA
+        miRNA
+        misc_RNA
+        Mt_rRNA
+        Mt_tRNA
+        polymorphic_pseudogene
+        processed_transcript
+        protein_coding
+        ribozyme
+        rRNA
+        sRNA
+        scRNA
+        scaRNA
+        sense_intronic
+        sense_overlapping
+        snRNA
+        snoRNA
+        TR_C_gene
+        TR_D_gene
+        TR_J_gene
+        TR_V_gene
+
+    The gff parsing logic
+        We collect features such by combining gff lines A,B,C as follows:
+            A .. gene line with a supported biotype
+                    A.ID=~/^gene:/
+
+            B .. transcript line referencing A with supported biotype
+                    B.ID=~/^transcript:/ && B.Parent=~/^gene:A.ID/
+
+            C .. corresponding CDS, exon, and UTR lines:
+                    C[3] in {"CDS","exon","three_prime_UTR","five_prime_UTR"} && C.Parent=~/^transcript:B.ID/ 
+
+        For coding biotypes ("protein_coding" or "polymorphic_pseudogene") the
+        complete chain link C -> B -> A is required. For the rest, link B -> A suffices.
+        
+                
+    The supported consequence types, sorted by impact:
+        splice_acceptor_variant .. end region of an intron changed (2bp at the 3' end of an intron)
+        splice_donor_variant    .. start region of an intron changed (2bp at the 5' end of an intron)
+        stop_gained             .. DNA sequence variant resulting in a stop codon
+        frameshift_variant      .. number of inserted/deleted bases not a multiple of three, disrupted translational frame
+        stop_lost               .. elongated transcript, stop codon changed
+        start_lost              .. the first codon changed
+        inframe_altering        .. combination of indels leading to unchanged reading frame and length
+        inframe_insertion       .. inserted coding sequence, unchanged reading frame
+        inframe_deletion        .. deleted coding sequence, unchanged reading frame
+        missense_variant        .. amino acid (aa) change, unchanged length
+        splice_region_variant   .. change within 1-3 bases of the exon or 3-8 bases of the intron
+        synonymous_variant      .. DNA sequence variant resulting in no amino acid change
+        stop_retained_variant   .. different stop codon
+        start_retained_variant  .. start codon retained by indel realignment
+        non_coding_variant      .. variant in non-coding sequence, such as RNA gene
+        5_prime_UTR_variant
+        3_prime_UTR_variant
+        intron_variant          .. reported only if none of the above
+        intergenic_variant      .. reported only if none of the above
+
+
+    The annotation algorithm.
+        The algorithm checks if the variant falls in a region of a supported type. The
+        search is performed in the following order, until a match is found:
+            1. idx_cds(gf_cds_t) - lookup CDS by position, create haplotypes, call consequences
+            2. idx_utr(gf_utr_t) - check UTR hits
+            3. idx_exon(gf_exon_t) - check for splice variants
+            4. idx_tscript(tscript_t) - check for intronic variants, RNAs, etc.
+
+        These regidx indexes are created by parsing a gff3 file as follows:
+            1.  create the array "ftr" of all UTR, CDS, exons. This will be
+            processed later and pruned based on transcript types we want to keep.
+            In the same go, create the hash "id2tr" of transcripts to keep
+            (based on biotype) which maps from transcript_id to a transcript. At
+            the same time also build the hash "gid2gene" which maps from gene_id to
+            gf_gene_t pointer.
+            
+            2.  build "idx_cds", "idx_tscript", "idx_utr" and "idx_exon" indexes.
+            Use only features from "ftr" which are present in "id2tr".
+
+            3.  clean data that won't be needed anymore: ftr, id2tr, gid2gene.
+        
+    Data structures.
+        idx_cds, idx_utr, idx_exon, idx_tscript:
+            as described above, regidx structures for fast lookup of exons/transcripts
+            overlapping a region, the payload is a pointer to tscript.cds
+*/
+ 
+#include <stdio.h>
+#include <stdlib.h>
+#include <assert.h>
+#include <getopt.h>
+#include <math.h>
+#include <inttypes.h>
+#include <htslib/hts.h>
+#include <htslib/vcf.h>
+#include <htslib/synced_bcf_reader.h>
+#include <htslib/khash.h>
+#include <htslib/khash_str2int.h>
+#include <htslib/kseq.h>
+#include <htslib/faidx.h>
+#include <errno.h>
+#include <unistd.h>
+#include <ctype.h>
+#include "bcftools.h"
+#include "filter.h"
+#include "regidx.h"
+#include "kheap.h"
+#include "smpl_ilist.h"
+#include "rbuf.h"
+
+#ifndef __FUNCTION__
+#  define __FUNCTION__ __func__
+#endif
+
+// Logic of the filters: include or exclude sites which match the filters?
+#define FLT_INCLUDE 1
+#define FLT_EXCLUDE 2
+
+// Definition of splice_region, splice_acceptor and splice_donor
+#define N_SPLICE_DONOR         2      
+#define N_SPLICE_REGION_EXON   3 
+#define N_SPLICE_REGION_INTRON 8 
+
+#define N_REF_PAD 10    // number of bases to avoid boundary effects
+
+#define STRAND_REV 0
+#define STRAND_FWD 1
+
+#define TRIM_NONE   0
+#define TRIM_5PRIME 1
+#define TRIM_3PRIME 2
+
+// How to treat phased/unphased genotypes
+#define PHASE_REQUIRE 0     // --phase r
+#define PHASE_MERGE   1     // --phase m
+#define PHASE_AS_IS   2     // --phase a
+#define PHASE_SKIP    3     // --phase s
+#define PHASE_NON_REF 4     // --phase R
+#define PHASE_DROP_GT 5     // --samples -
+
+// Node types in the haplotype tree
+#define HAP_CDS   0
+#define HAP_ROOT  1 
+#define HAP_SSS   2     // start/stop/splice
+
+#define CSQ_PRINTED_UPSTREAM    (1<<0)
+#define CSQ_SYNONYMOUS_VARIANT  (1<<1)
+#define CSQ_MISSENSE_VARIANT    (1<<2)
+#define CSQ_STOP_LOST           (1<<3)
+#define CSQ_STOP_GAINED         (1<<4)
+#define CSQ_INFRAME_DELETION    (1<<5)
+#define CSQ_INFRAME_INSERTION   (1<<6)
+#define CSQ_FRAMESHIFT_VARIANT  (1<<7)
+#define CSQ_SPLICE_ACCEPTOR     (1<<8)
+#define CSQ_SPLICE_DONOR        (1<<9)
+#define CSQ_START_LOST          (1<<10)
+#define CSQ_SPLICE_REGION       (1<<11)
+#define CSQ_STOP_RETAINED       (1<<12)
+#define CSQ_UTR5                (1<<13)
+#define CSQ_UTR3                (1<<14)
+#define CSQ_NON_CODING          (1<<15)
+#define CSQ_INTRON              (1<<16)
+//#define CSQ_INTERGENIC          (1<<17)
+#define CSQ_INFRAME_ALTERING    (1<<18)
+#define CSQ_UPSTREAM_STOP       (1<<19)     // adds * in front of the csq string
+#define CSQ_INCOMPLETE_CDS      (1<<20)     // to remove START/STOP in incomplete CDS, see ENSG00000173376/synon.vcf
+#define CSQ_CODING_SEQUENCE     (1<<21)     // cannot tell exactly what it is, but it does affect the coding sequence
+#define CSQ_ELONGATION          (1<<22)     // symbolic insertion
+#define CSQ_START_RETAINED      (1<<23)
+
+// Haplotype-aware consequences, printed in one vcf record only, the rest has a reference @12345
+#define CSQ_COMPOUND (CSQ_SYNONYMOUS_VARIANT|CSQ_MISSENSE_VARIANT|CSQ_STOP_LOST|CSQ_STOP_GAINED| \
+                      CSQ_INFRAME_DELETION|CSQ_INFRAME_INSERTION|CSQ_FRAMESHIFT_VARIANT| \
+                      CSQ_START_LOST|CSQ_STOP_RETAINED|CSQ_INFRAME_ALTERING|CSQ_INCOMPLETE_CDS| \
+                      CSQ_UPSTREAM_STOP|CSQ_START_RETAINED)
+#define CSQ_START_STOP          (CSQ_STOP_LOST|CSQ_STOP_GAINED|CSQ_STOP_RETAINED|CSQ_START_LOST|CSQ_START_RETAINED)
+
+#define CSQ_PRN_STRAND(csq)     ((csq)&CSQ_COMPOUND && !((csq)&(CSQ_SPLICE_ACCEPTOR|CSQ_SPLICE_DONOR|CSQ_SPLICE_REGION)))
+#define CSQ_PRN_TSCRIPT         (~(CSQ_INTRON|CSQ_NON_CODING))
+#define CSQ_PRN_BIOTYPE         CSQ_NON_CODING
+
+// see kput_vcsq()
+const char *csq_strings[] = 
+{
+    NULL, 
+    "synonymous", 
+    "missense", 
+    "stop_lost", 
+    "stop_gained", 
+    "inframe_deletion", 
+    "inframe_insertion", 
+    "frameshift", 
+    "splice_acceptor", 
+    "splice_donor", 
+    "start_lost", 
+    "splice_region", 
+    "stop_retained", 
+    "5_prime_utr", 
+    "3_prime_utr", 
+    "non_coding", 
+    "intron", 
+    "intergenic",
+    "inframe_altering",
+    NULL,
+    NULL,
+    "coding_sequence",
+    "feature_elongation",
+    "start_retained"
+};
+
+
+// GFF line types
+#define GFF_TSCRIPT_LINE 1
+#define GFF_GENE_LINE    2
+
+
+/* 
+    Genomic features, for fast lookup by position to overlapping features
+*/
+#define GF_coding_bit 6
+#define GF_is_coding(x) ((x) & (1<<GF_coding_bit))
+#define GF_MT_rRNA                       1                      // non-coding: 1, 2, ...
+#define GF_MT_tRNA                       2
+#define GF_lincRNA                       3
+#define GF_miRNA                         4
+#define GF_MISC_RNA                      5
+#define GF_rRNA                          6
+#define GF_snRNA                         7
+#define GF_snoRNA                        8
+#define GF_PROCESSED_TRANSCRIPT          9
+#define GF_ANTISENSE                    10
+#define GF_macro_lncRNA                 11
+#define GF_ribozyme                     12
+#define GF_sRNA                         13
+#define GF_scRNA                        14
+#define GF_scaRNA                       15
+#define GF_SENSE_INTRONIC               16
+#define GF_SENSE_OVERLAPPING            17
+#define GF_PSEUDOGENE                   18
+#define GF_PROCESSED_PSEUDOGENE         19
+#define GF_ARTIFACT                     20
+#define GF_IG_PSEUDOGENE                21
+#define GF_IG_C_PSEUDOGENE              22
+#define GF_IG_J_PSEUDOGENE              23
+#define GF_IG_V_PSEUDOGENE              24
+#define GF_TR_V_PSEUDOGENE              25
+#define GF_TR_J_PSEUDOGENE              26
+#define GF_MT_tRNA_PSEUDOGENE           27
+#define GF_misc_RNA_PSEUDOGENE          28
+#define GF_miRNA_PSEUDOGENE             29
+#define GF_RIBOZYME                     30
+#define GF_RETAINED_INTRON              31
+#define GF_RETROTRANSPOSED              32
+#define GF_tRNA_PSEUDOGENE              33
+#define GF_TRANSCRIBED_PROCESSED_PSEUDOGENE     34
+#define GF_TRANSCRIBED_UNPROCESSED_PSEUDOGENE   35
+#define GF_TRANSCRIBED_UNITARY_PSEUDOGENE       36
+#define GF_TRANSLATED_UNPROCESSED_PSEUDOGENE    37
+#define GF_TRANSLATED_PROCESSED_PSEUDOGENE      38
+#define GF_KNOWN_NCRNA                          39
+#define GF_UNITARY_PSEUDOGENE                   40
+#define GF_UNPROCESSED_PSEUDOGENE               41
+#define GF_LRG_GENE                             42
+#define GF_3PRIME_OVERLAPPING_ncRNA             43
+#define GF_DISRUPTED_DOMAIN                     44
+#define GF_vaultRNA                             45
+#define GF_BIDIRECTIONAL_PROMOTER_lncRNA        46
+#define GF_AMBIGUOUS_ORF                        47
+#define GF_PROTEIN_CODING               (1|(1<<GF_coding_bit))  // coding: 65, 66, ...
+#define GF_POLYMORPHIC_PSEUDOGENE       (2|(1<<GF_coding_bit))
+#define GF_IG_C                         (3|(1<<GF_coding_bit))
+#define GF_IG_D                         (4|(1<<GF_coding_bit))
+#define GF_IG_J                         (5|(1<<GF_coding_bit))
+#define GF_IG_LV                        (6|(1<<GF_coding_bit))
+#define GF_IG_V                         (7|(1<<GF_coding_bit))
+#define GF_TR_C                         (8|(1<<GF_coding_bit))
+#define GF_TR_D                         (9|(1<<GF_coding_bit))
+#define GF_TR_J                        (10|(1<<GF_coding_bit))
+#define GF_TR_V                        (11|(1<<GF_coding_bit))
+#define GF_NMD                         (12|(1<<GF_coding_bit))
+#define GF_NON_STOP_DECAY              (13|(1<<GF_coding_bit))
+#define GF_CDS      ((1<<(GF_coding_bit+1))+1)                  // special types: 129, 130, ...
+#define GF_EXON     ((1<<(GF_coding_bit+1))+2)
+#define GF_UTR3     ((1<<(GF_coding_bit+1))+3)
+#define GF_UTR5     ((1<<(GF_coding_bit+1))+4)
+// GF_MAX = (1<<30)-1, see hap_node_t
+
+#define CDS_PHASE_UNKN 3
+typedef struct _tscript_t tscript_t;
+typedef struct
+{
+    tscript_t *tr;      // transcript
+    uint32_t beg;       // the start coordinate of the CDS (on the reference strand, 0-based)
+    uint32_t pos;       // 0-based index of the first exon base within the transcript (only to
+                        //  update hap_node_t.sbeg in hap_init, could be calculated on the fly)
+    uint32_t len;       // exon length
+    uint32_t icds:30,   // exon index within the transcript
+             phase:2;   // offset of the CDS: 0,1,2 or 3 for unknown
+}
+gf_cds_t;
+typedef struct
+{
+    char *name;           // human readable name, e.g. ORF45
+    uint32_t iseq;
+}
+gf_gene_t;
+typedef struct
+{
+    uint32_t beg,end;
+    tscript_t *tr;
+}
+gf_exon_t;
+typedef enum { prime3, prime5 } utr_t;
+typedef struct
+{
+    utr_t which;
+    uint32_t beg,end;
+    tscript_t *tr;
+}
+gf_utr_t;
+
+
+/*
+    Structures related to VCF output:
+
+    vcsq_t
+        information required to assemble consequence lines such as "inframe_deletion|XYZ|ENST01|+|5TY>5I|121ACG>A+124TA>T"
+
+    vrec_t
+        single VCF record and csq tied to this record. (Haplotype can have multiple
+        consequences in several VCF records. Each record can have multiple consequences
+        from multiple haplotypes.)
+
+    csq_t
+        a top-level consequence tied to a haplotype
+
+    vbuf_t
+    pos2vbuf
+        VCF records with the same position clustered together for a fast lookup via pos2vbuf
+*/
+typedef struct _vbuf_t vbuf_t;
+typedef struct _vcsq_t vcsq_t;
+struct _vcsq_t
+{
+    uint32_t strand:1,
+             type:31;   // one of CSQ_* types
+    uint32_t trid;
+    uint32_t vcf_ial;
+    uint32_t biotype;   // one of GF_* types
+    char *gene;         // gene name
+    bcf1_t *ref;        // if type&CSQ_PRINTED_UPSTREAM, ref consequence "@1234"
+    kstring_t vstr;     // variant string, eg 5TY>5I|121ACG>A+124TA>T
+};
+typedef struct
+{
+    bcf1_t *line;
+    uint32_t *fmt_bm;   // bitmask of sample consequences with first/second haplotype interleaved
+    uint32_t nfmt:4,    // the bitmask size (the number of integers per sample)
+             nvcsq:28, mvcsq;
+    vcsq_t *vcsq;       // there can be multiple consequences for a single VCF record
+}
+vrec_t;
+typedef struct
+{
+    uint32_t pos;
+    vrec_t *vrec;   // vcf line that this csq is tied to; needed when printing haplotypes (hap_stage_vcf)
+    int idx;        // 0-based index of the csq at the VCF line, for FMT/BCSQ
+    vcsq_t type;
+}
+csq_t;
+struct _vbuf_t
+{
+    vrec_t **vrec;   // buffer of VCF lines with the same position
+    int n, m;
+    uint32_t keep_until;    // the maximum transcript end position
+};
+KHASH_MAP_INIT_INT(pos2vbuf, vbuf_t*)
+
+
+/*
+    Structures related to haplotype-aware consequences in coding regions
+
+    hap_node_t
+        node of a haplotype tree. Each transcript has one tree
+
+    tscript_t
+        despite its general name, it is intended for coding transcripts only
+
+    hap_t
+    hstack_t
+        for traversal of the haplotype tree and braking combined
+        consequences into independent parts
+*/
+typedef struct _hap_node_t hap_node_t;
+struct _hap_node_t
+{
+    char *seq;          // cds segment [parent_node,this_node)
+    char *var;          // variant "ref>alt"
+    uint32_t type:2,    // HAP_ROOT or HAP_CDS
+             csq:30;    // this node's consequence
+    int dlen;           // alt minus ref length: <0 del, >0 ins, 0 substitution
+    uint32_t rbeg;      // variant's VCF position (0-based, inclusive)
+    int32_t rlen;       // variant's rlen; alen=rlen+dlen; fake for non CDS types
+    uint32_t sbeg;      // variant's position on the spliced reference transcript (0-based, inclusive, N_REF_PAD not included)
+    uint32_t icds;      // which exon does this node's variant overlaps
+    hap_node_t **child, *prev;  // children haplotypes and previous coding node
+    int nchild, mchild;
+    bcf1_t *cur_rec, *rec;      // current VCF record and node's VCF record
+    int vcf_ial;                // which VCF allele generated this node
+    uint32_t nend;              // number of haplotypes ending in this node
+    int *cur_child, mcur_child; // mapping from the allele to the currently active child
+    csq_t *csq_list;            // list of haplotype's consequences, broken by position (each corresponds to a VCF record)
+    int ncsq_list, mcsq_list;
+};
+struct _tscript_t
+{
+    uint32_t id;        // transcript id
+    uint32_t beg,end;   // transcript's beg and end coordinate (ref strand, 0-based, inclusive)
+    uint32_t strand:1,  // STRAND_REV or STRAND_FWD
+             ncds:31,   // number of exons
+             mcds;
+    gf_cds_t **cds;     // ordered list of exons
+    char *ref;          // reference sequence, padded with N_REF_PAD bases on both ends
+    char *sref;         // spliced reference sequence, padded with N_REF_PAD bases on both ends
+    hap_node_t *root;   // root of the haplotype tree
+    hap_node_t **hap;   // pointer to haplotype leaves, two for each sample
+    int nhap, nsref;    // number of haplotypes and length of sref, including 2*N_REF_PAD
+    uint32_t trim:2,    // complete, 5' or 3' trimmed, see TRIM_* types
+             type:30;   // one of GF_* types
+    gf_gene_t *gene;
+};
+static inline int cmp_tscript(tscript_t **a, tscript_t **b)
+{
+    return ( (*a)->end  < (*b)->end ) ? 1 : 0;
+}
+KHEAP_INIT(trhp, tscript_t*, cmp_tscript)
+typedef khp_trhp_t tr_heap_t;
+typedef struct
+{
+    hap_node_t *node;   // current node
+    int ichild;         // current child in the active node
+    int dlen;           // total dlen, from the root to the active node
+    size_t slen;        // total sequence length, from the root to the active node
+}
+hstack_t;
+typedef struct
+{
+    int mstack;
+    hstack_t *stack;
+    tscript_t *tr;      // tr->ref: spliced transcript on ref strand
+    kstring_t sseq;     // spliced haplotype sequence on ref strand
+    kstring_t tseq;     // the variable part of translated haplotype transcript, coding strand
+    kstring_t tref;     // the variable part of translated reference transcript, coding strand
+    uint32_t sbeg;      // stack's sbeg, for cases first node's type is HAP_SSS
+    int upstream_stop;
+}
+hap_t;
+
+
+/*
+    Helper structures, only for initialization
+    
+    ftr_t
+        temporary list of all exons, CDS, UTRs 
+*/
+KHASH_MAP_INIT_INT(int2tscript, tscript_t*)
+KHASH_MAP_INIT_INT(int2gene, gf_gene_t*)
+typedef struct
+{
+    int type;       // GF_CDS, GF_EXON, GF_5UTR, GF_3UTR
+    uint32_t beg;
+    uint32_t end;
+    uint32_t trid;
+    uint32_t strand:1;   // STRAND_REV,STRAND_FWD
+    uint32_t phase:2;    // 0, 1, 2, or 3 for unknown
+    uint32_t iseq:29;
+}
+ftr_t;
+/*
+    Mapping from GFF ID string (such as ENST00000450305 or Zm00001d027230_P001)
+    to integer id.  To keep the memory requirements low, the original version
+    relied on IDs in the form of a string prefix and a numerical id.  However,
+    it turns out that this assumption is not valid for some ensembl GFFs, see
+    for example Zea_mays.AGPv4.36.gff3.gz
+ */
+typedef struct
+{
+    void *str2id;       // khash_str2int
+    int nstr, mstr;
+    char **str;         // numeric id to string
+}
+id_tbl_t;
+typedef struct
+{
+    // all exons, CDS, UTRs
+    ftr_t *ftr;
+    int nftr, mftr;
+
+    // mapping from gene id to gf_gene_t
+    kh_int2gene_t *gid2gene;
+
+    // mapping from transcript id to tscript, for quick CDS anchoring
+    kh_int2tscript_t *id2tr;
+
+    // sequences
+    void *seq2int;  // str2int hash
+    char **seq;
+    int nseq, mseq;
+
+    // ignored biotypes
+    void *ignored_biotypes;
+
+    id_tbl_t gene_ids;   // temporary table for mapping between gene id (eg. Zm00001d027245) and a numeric idx
+}
+aux_t;
+
+typedef struct _args_t
+{
+    // the main regidx lookups, from chr:beg-end to overlapping features and
+    // index iterator
+    regidx_t *idx_cds, *idx_utr, *idx_exon, *idx_tscript;
+    regitr_t *itr;
+
+    // temporary structures, deleted after initializtion
+    aux_t init;
+
+    // text tab-delimited output (out) or vcf/bcf output (out_fh)
+    FILE *out;
+    htsFile *out_fh;
+
+    // vcf
+    bcf_srs_t *sr;
+    bcf_hdr_t *hdr;
+    int hdr_nsmpl;          // actual number of samples in the vcf, for bcf_update_format_values()
+
+    // include or exclude sites which match the filters
+    filter_t *filter;
+    char *filter_str;
+    int filter_logic;       // FLT_INCLUDE or FLT_EXCLUDE
+
+    // samples to process
+    int sample_is_file;
+    char *sample_list;
+    smpl_ilist_t *smpl;
+
+    char *outdir, **argv, *fa_fname, *gff_fname, *output_fname;
+    char *bcsq_tag;
+    int argc, output_type, clevel;
+    int phase, verbosity, local_csq, record_cmd_line;
+    int ncsq2_max, nfmt_bcsq;   // maximum number of csq per site that can be accessed from FORMAT/BCSQ (*2 and 1 bit skipped to avoid BCF missing values)
+    int ncsq2_small_warned;
+    int brief_predictions;
+    
+    int rid;                    // current chromosome
+    tr_heap_t *active_tr;       // heap of active transcripts for quick flushing
+    hap_t *hap;                 // transcript haplotype recursion
+    vbuf_t **vcf_buf;           // buffered VCF lines to annotate with CSQ and flush
+    rbuf_t vcf_rbuf;            // round buffer indexes to vcf_buf
+    kh_pos2vbuf_t *pos2vbuf;    // fast lookup of buffered lines by position
+    tscript_t **rm_tr;          // buffer of transcripts to clean
+    int nrm_tr, mrm_tr;
+    csq_t *csq_buf;             // pool of csq not managed by hap_node_t, i.e. non-CDS csqs
+    int ncsq_buf, mcsq_buf;
+    id_tbl_t tscript_ids;       // mapping between transcript id (eg. Zm00001d027245_T001) and a numeric idx
+    int force;                  // force run under various conditions. Currently only to skip out-of-phase transcripts
+    int n_threads;              // extra compression/decompression threads
+
+    faidx_t *fai;
+    kstring_t str, str2;
+    int32_t *gt_arr, mgt_arr;
+}
+args_t;
+
+// AAA, AAC, ...
+const char *gencode = "KNKNTTTTRSRSIIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVV*Y*YSSSS*CWCLFLF";
+const uint8_t nt4[] =
+{
+    4,4,4,4, 4,4,4,4, 4,4,4,4, 4,4,4,4,
+    4,4,4,4, 4,4,4,4, 4,4,4,4, 4,4,4,4,
+    4,4,4,4, 4,4,4,4, 4,4,4,4, 4,4,4,4,
+    4,4,4,4, 4,4,4,4, 4,4,4,4, 4,4,4,4,
+    4,0,4,1, 4,4,4,2, 4,4,4,4, 4,4,4,4,
+    4,4,4,4, 3,4,4,4, 4,4,4,4, 4,4,4,4,
+    4,0,4,1, 4,4,4,2, 4,4,4,4, 4,4,4,4,
+    4,4,4,4, 3
+};
+const uint8_t cnt4[] =
+{
+    4,4,4,4, 4,4,4,4, 4,4,4,4, 4,4,4,4,
+    4,4,4,4, 4,4,4,4, 4,4,4,4, 4,4,4,4,
+    4,4,4,4, 4,4,4,4, 4,4,4,4, 4,4,4,4,
+    4,4,4,4, 4,4,4,4, 4,4,4,4, 4,4,4,4,
+    4,3,4,2, 4,4,4,1, 4,4,4,4, 4,4,4,4,
+    4,4,4,4, 0,4,4,4, 4,4,4,4, 4,4,4,4,
+    4,3,4,2, 4,4,4,1, 4,4,4,4, 4,4,4,4,
+    4,4,4,4, 0
+};
+#define dna2aa(x)  gencode[  nt4[(uint8_t)(x)[0]]<<4 |  nt4[(uint8_t)(x)[1]]<<2 |  nt4[(uint8_t)(x)[2]] ]
+#define cdna2aa(x) gencode[ cnt4[(uint8_t)(x)[2]]<<4 | cnt4[(uint8_t)(x)[1]]<<2 | cnt4[(uint8_t)(x)[0]] ]
+
+static const char *gf_strings_noncoding[] = 
+{ 
+    "MT_rRNA", "MT_tRNA", "lincRNA", "miRNA", "misc_RNA", "rRNA", "snRNA", "snoRNA", "processed_transcript",
+    "antisense", "macro_lncRNA", "ribozyme", "sRNA", "scRNA", "scaRNA", "sense_intronic", "sense_overlapping",
+    "pseudogene", "processed_pseudogene", "artifact", "IG_pseudogene", "IG_C_pseudogene", "IG_J_pseudogene", 
+    "IG_V_pseudogene", "TR_V_pseudogene", "TR_J_pseudogene", "MT_tRNA_pseudogene", "misc_RNA_pseudogene", 
+    "miRNA_pseudogene", "ribozyme", "retained_intron", "retrotransposed", "Trna_pseudogene", "transcribed_processed_pseudogene", 
+    "transcribed_unprocessed_pseudogene", "transcribed_unitary_pseudogene",    "translated_unprocessed_pseudogene",
+    "translated_processed_pseudogene", "known_ncRNA", "unitary_pseudogene", "unprocessed_pseudogene",
+    "LRG_gene", "3_prime_overlapping_ncRNA", "disrupted_domain", "vaultRNA", "bidirectional_promoter_lncRNA", "ambiguous_orf"
+};
+static const char *gf_strings_coding[] = { "protein_coding", "polymorphic_pseudogene", "IG_C", "IG_D", "IG_J", "IG_LV", "IG_V", "TR_C", "TR_D", "TR_J", "TR_V", "NMD", "non_stop_decay"};
+static const char *gf_strings_special[] = { "CDS", "exon", "3_prime_UTR", "5_prime_UTR" };
+
+const char *gf_type2gff_string(int type)
+{
+    if ( !GF_is_coding(type) )
+    {
+        if ( type < (1<<GF_coding_bit) ) return gf_strings_noncoding[type-1];
+        type &= (1<<(GF_coding_bit+1)) - 1;
+        return gf_strings_special[type - 1];
+    }
+    type &= (1<<GF_coding_bit) - 1;
+    return gf_strings_coding[type - 1];
+}
+
+/*
+    gff parsing functions
+*/
+static inline int feature_set_seq(args_t *args, char *chr_beg, char *chr_end)
+{
+    aux_t *aux = &args->init;
+    char c = chr_end[1];
+    chr_end[1] = 0;
+    int iseq;
+    if ( khash_str2int_get(aux->seq2int, chr_beg, &iseq)!=0 )
+    {
+        // check for possible mismatch in chromosome naming convention such as chrX vs X
+        char *new_chr = NULL;
+        if ( faidx_has_seq(args->fai,chr_beg) )
+            new_chr = strdup(chr_beg);                  // valid chr name, the same in gff and faidx
+        else
+        {
+            int len = strlen(chr_beg);
+            if ( !strncmp("chr",chr_beg,3) && len>3 )
+                new_chr = strdup(chr_beg+3);            // gff has the prefix, faidx does not
+            else
+            {
+                new_chr = malloc(len+4);                // gff does not have the prefix, faidx has
+                memcpy(new_chr,"chr",3);
+                memcpy(new_chr+3,chr_beg,len);
+                new_chr[len+3] = 0;
+            }
+            if ( !faidx_has_seq(args->fai,new_chr) )    // modification did not help, this sequence is not in fai
+            {
+                static int unkwn_chr_warned = 0;
+                if ( !unkwn_chr_warned && args->verbosity>0 )
+                    fprintf(bcftools_stderr,"Warning: GFF chromosome \"%s\" not part of the reference genome\n",chr_beg);
+                unkwn_chr_warned = 1;
+                free(new_chr);
+                new_chr = strdup(chr_beg);              // use the original sequence name
+            }
+        }
+        if ( khash_str2int_get(aux->seq2int, new_chr, &iseq)!=0 )
+        {
+            hts_expand(char*, aux->nseq+1, aux->mseq, aux->seq);
+            aux->seq[aux->nseq] = new_chr;
+            iseq = khash_str2int_inc(aux->seq2int, aux->seq[aux->nseq]);
+            aux->nseq++;
+            assert( aux->nseq < 1<<29 );  // see gf_gene_t.iseq and ftr_t.iseq
+        }
+        else
+            free(new_chr);
+    }
+    chr_end[1] = c;
+    return iseq;
+}
+static inline char *gff_skip(const char *line, char *ss)
+{
+    while ( *ss && *ss!='\t' ) ss++;
+    if ( !*ss ) error("[%s:%d %s] Could not parse the line: %s\n",__FILE__,__LINE__,__FUNCTION__,line);
+    return ss+1;
+}
+static inline void gff_parse_chr(const char *line, char **chr_beg, char **chr_end)
+{
+    char *se = (char*) line;
+    while ( *se && *se!='\t' ) se++;
+    if ( !*se ) error("[%s:%d %s] Could not parse the line: %s\n",__FILE__,__LINE__,__FUNCTION__,line);
+    *chr_beg = (char*) line;
+    *chr_end = se-1;
+}
+static inline char *gff_parse_beg_end(const char *line, char *ss, uint32_t *beg, uint32_t *end)
+{
+    char *se = ss;
+    *beg = strtol(ss, &se, 10) - 1;
+    if ( ss==se ) error("[%s:%d %s] Could not parse the line:\n\t%s\n\t%s\n",__FILE__,__LINE__,__FUNCTION__,line,ss);
+    ss = se+1;
+    *end = strtol(ss, &se, 10) - 1;
+    if ( ss==se ) error("[%s:%d %s] Could not parse the line: %s\n",__FILE__,__LINE__,__FUNCTION__,line);
+    return se+1;
+}
+static void gff_id_init(id_tbl_t *tbl)
+{
+    memset(tbl, 0, sizeof(*tbl));
+    tbl->str2id = khash_str2int_init();
+}
+static void gff_id_destroy(id_tbl_t *tbl)
+{
+    khash_str2int_destroy_free(tbl->str2id);
+    free(tbl->str);
+}
+static inline uint32_t gff_id_parse(id_tbl_t *tbl, const char *line, const char *needle, char *ss)
+{
+    ss = strstr(ss,needle);     // e.g. "ID=transcript:"
+    if ( !ss ) error("[%s:%d %s] Could not parse the line, \"%s\" not present: %s\n",__FILE__,__LINE__,__FUNCTION__,needle,line);
+    ss += strlen(needle);
+
+    char *se = ss;
+    while ( *se && *se!=';' && !isspace(*se) ) se++;
+    char tmp = *se;
+    *se = 0;
+
+    int id;
+    if ( khash_str2int_get(tbl->str2id, ss, &id) < 0 )
+    {
+        id = tbl->nstr++;
+        hts_expand(char*, tbl->nstr, tbl->mstr, tbl->str);
+        tbl->str[id] = strdup(ss);
+        khash_str2int_set(tbl->str2id, tbl->str[id], id);
+    }
+    *se = tmp;
+
+    return id;
+}
+static inline int gff_parse_type(char *line)
+{
+    line = strstr(line,"ID=");
+    if ( !line ) return -1;
+    line += 3;
+    if ( !strncmp(line,"transcript:",11) ) return GFF_TSCRIPT_LINE;
+    else if ( !strncmp(line,"gene:",5) ) return GFF_GENE_LINE;
+    return -1;
+}
+static inline int gff_parse_biotype(char *_line)
+{
+    char *line = strstr(_line,"biotype=");
+    if ( !line ) return -1;
+
+    line += 8;
+    switch (*line)
+    {
+        case 'p': 
+            if ( !strncmp(line,"protein_coding",14) ) return GF_PROTEIN_CODING;
+            else if ( !strncmp(line,"pseudogene",10) ) return GF_PSEUDOGENE;
+            else if ( !strncmp(line,"processed_transcript",20) ) return GF_PROCESSED_TRANSCRIPT;
+            else if ( !strncmp(line,"processed_pseudogene",20) ) return GF_PROCESSED_PSEUDOGENE;
+            else if ( !strncmp(line,"polymorphic_pseudogene",22) ) return GF_POLYMORPHIC_PSEUDOGENE;
+            break;
+        case 'a':
+            if ( !strncmp(line,"artifact",8) ) return GF_ARTIFACT;
+            else if ( !strncmp(line,"antisense",9) ) return GF_ANTISENSE;
+            else if ( !strncmp(line,"ambiguous_orf",13) ) return GF_AMBIGUOUS_ORF;
+            break;
+        case 'I':
+            if ( !strncmp(line,"IG_C_gene",9) ) return GF_IG_C;
+            else if ( !strncmp(line,"IG_D_gene",9) ) return GF_IG_D;
+            else if ( !strncmp(line,"IG_J_gene",9) ) return GF_IG_J;
+            else if ( !strncmp(line,"IG_LV_gene",10) ) return GF_IG_LV;
+            else if ( !strncmp(line,"IG_V_gene",9) ) return GF_IG_V;
+            else if ( !strncmp(line,"IG_pseudogene",13) ) return GF_IG_PSEUDOGENE;
+            else if ( !strncmp(line,"IG_C_pseudogene",15) ) return GF_IG_C_PSEUDOGENE;
+            else if ( !strncmp(line,"IG_J_pseudogene",15) ) return GF_IG_J_PSEUDOGENE;
+            else if ( !strncmp(line,"IG_V_pseudogene",15) ) return GF_IG_V_PSEUDOGENE;
+            break;
+        case 'T':
+            if ( !strncmp(line,"TR_C_gene",9) ) return GF_TR_C;
+            else if ( !strncmp(line,"TR_D_gene",9) ) return GF_TR_D;
+            else if ( !strncmp(line,"TR_J_gene",9) ) return GF_TR_J;
+            else if ( !strncmp(line,"TR_V_gene",9) ) return GF_TR_V;
+            else if ( !strncmp(line,"TR_V_pseudogene",15) ) return GF_TR_V_PSEUDOGENE;
+            else if ( !strncmp(line,"TR_J_pseudogene",15) ) return GF_TR_J_PSEUDOGENE;
+            break;
+        case 'M':
+            if ( !strncmp(line,"Mt_tRNA_pseudogene",18) ) return GF_MT_tRNA_PSEUDOGENE;
+            else if ( !strncmp(line,"Mt_tRNA",7) ) return GF_MT_tRNA;
+            else if ( !strncmp(line,"Mt_rRNA",7) ) return GF_MT_tRNA;
+            break;
+        case 'l':
+            if ( !strncmp(line,"lincRNA",7) ) return GF_lincRNA;
+            break;
+        case 'm':
+            if ( !strncmp(line,"macro_lncRNA",12) ) return GF_macro_lncRNA;
+            else if ( !strncmp(line,"misc_RNA_pseudogene",19) ) return GF_misc_RNA_PSEUDOGENE;
+            else if ( !strncmp(line,"miRNA_pseudogene",16) ) return GF_miRNA_PSEUDOGENE;
+            else if ( !strncmp(line,"miRNA",5) ) return GF_miRNA;
+            else if ( !strncmp(line,"misc_RNA",8) ) return GF_MISC_RNA;
+            break;
+        case 'r':
+            if ( !strncmp(line,"rRNA",4) ) return GF_rRNA;
+            else if ( !strncmp(line,"ribozyme",8) ) return GF_RIBOZYME;
+            else if ( !strncmp(line,"retained_intron",15) ) return GF_RETAINED_INTRON;
+            else if ( !strncmp(line,"retrotransposed",15) ) return GF_RETROTRANSPOSED;
+            break;
+        case 's':
+            if ( !strncmp(line,"snRNA",5) ) return GF_snRNA;
+            else if ( !strncmp(line,"sRNA",4) ) return GF_sRNA;
+            else if ( !strncmp(line,"scRNA",5) ) return GF_scRNA;
+            else if ( !strncmp(line,"scaRNA",6) ) return GF_scaRNA;
+            else if ( !strncmp(line,"snoRNA",6) ) return GF_snoRNA;
+            else if ( !strncmp(line,"sense_intronic",14) ) return GF_SENSE_INTRONIC;
+            else if ( !strncmp(line,"sense_overlapping",17) ) return GF_SENSE_OVERLAPPING;
+            break;
+        case 't':
+            if ( !strncmp(line,"tRNA_pseudogene",15) ) return GF_tRNA_PSEUDOGENE;
+            else if ( !strncmp(line,"transcribed_processed_pseudogene",32) ) return GF_TRANSCRIBED_PROCESSED_PSEUDOGENE;
+            else if ( !strncmp(line,"transcribed_unprocessed_pseudogene",34) ) return GF_TRANSCRIBED_UNPROCESSED_PSEUDOGENE; 
+            else if ( !strncmp(line,"transcribed_unitary_pseudogene",30) ) return GF_TRANSCRIBED_UNITARY_PSEUDOGENE;
+            else if ( !strncmp(line,"translated_unprocessed_pseudogene",33) ) return GF_TRANSLATED_UNPROCESSED_PSEUDOGENE;
+            else if ( !strncmp(line,"translated_processed_pseudogene",31) ) return GF_TRANSLATED_PROCESSED_PSEUDOGENE;
+            break;
+        case 'n':
+            if ( !strncmp(line,"nonsense_mediated_decay",23) ) return GF_NMD;
+            else if ( !strncmp(line,"non_stop_decay",14) ) return GF_NON_STOP_DECAY;
+            break;
+        case 'k':
+            if ( !strncmp(line,"known_ncrna",11) ) return GF_KNOWN_NCRNA;
+            break;
+        case 'u':
+            if ( !strncmp(line,"unitary_pseudogene",18) ) return GF_UNITARY_PSEUDOGENE;
+            else if ( !strncmp(line,"unprocessed_pseudogene",22) ) return GF_UNPROCESSED_PSEUDOGENE;
+            break;
+        case 'L':
+            if ( !strncmp(line,"LRG_gene",8) ) return GF_LRG_GENE;
+            break;
+        case '3':
+            if ( !strncmp(line,"3prime_overlapping_ncRNA",24) ) return GF_3PRIME_OVERLAPPING_ncRNA;
+            break;
+        case 'd':
+            if ( !strncmp(line,"disrupted_domain",16) ) return GF_DISRUPTED_DOMAIN;
+            break;
+        case 'v':
+            if ( !strncmp(line,"vaultRNA",8) ) return GF_vaultRNA;
+            break;
+        case 'b':
+            if ( !strncmp(line,"bidirectional_promoter_lncRNA",29) ) return GF_BIDIRECTIONAL_PROMOTER_lncRNA;
+            break;
+    }
+    return 0;
+}
+static inline int gff_ignored_biotype(args_t *args, char *ss)
+{
+    ss = strstr(ss,"biotype=");
+    if ( !ss ) return 0;
+
+    ss += 8;
+    char *se = ss, tmp;
+    while ( *se && *se!=';' ) se++;
+    tmp = *se;
+    *se = 0;
+
+    char *key = ss;
+    int n = 0;
+    if ( khash_str2int_get(args->init.ignored_biotypes, ss, &n)!=0 ) key = strdup(ss);
+    khash_str2int_set(args->init.ignored_biotypes, key, n+1);
+
+    *se = tmp;
+    return 1;
+}
+gf_gene_t *gene_init(aux_t *aux, uint32_t gene_id)
+{
+    khint_t k = kh_get(int2gene, aux->gid2gene, (int)gene_id);
+    gf_gene_t *gene = (k == kh_end(aux->gid2gene)) ? NULL : kh_val(aux->gid2gene, k);
+    if ( !gene )
+    {
+        gene = (gf_gene_t*) calloc(1,sizeof(gf_gene_t));
+        int ret;
+        k = kh_put(int2gene, aux->gid2gene, (int)gene_id, &ret);
+        kh_val(aux->gid2gene,k) = gene;
+    }
+    return gene;
+}
+void gff_parse_transcript(args_t *args, const char *line, char *ss, ftr_t *ftr)
+{
+    aux_t *aux = &args->init;
+    int biotype = gff_parse_biotype(ss);
+    if ( biotype <= 0 )
+    {
+        if ( !gff_ignored_biotype(args, ss) && args->verbosity > 0 ) fprintf(bcftools_stderr,"ignored transcript: %s\n",line);
+        return;
+    }
+
+    // create a mapping from transcript_id to gene_id
+    uint32_t trid = gff_id_parse(&args->tscript_ids, line, "ID=transcript:", ss);
+    uint32_t gene_id = gff_id_parse(&args->init.gene_ids, line, "Parent=gene:", ss);
+
+    tscript_t *tr = (tscript_t*) calloc(1,sizeof(tscript_t));
+    tr->id     = trid;
+    tr->strand = ftr->strand;
+    tr->gene   = gene_init(aux, gene_id);
+    tr->type   = biotype;
+    tr->beg    = ftr->beg;
+    tr->end    = ftr->end;
+
+    khint_t k;
+    int ret;
+    k = kh_put(int2tscript, aux->id2tr, (int)trid, &ret);
+    kh_val(aux->id2tr,k) = tr;
+}
+void gff_parse_gene(args_t *args, const char *line, char *ss, char *chr_beg, char *chr_end, ftr_t *ftr)
+{
+    int biotype = gff_parse_biotype(ss);
+    if ( biotype <= 0 )
+    {
+        if ( !gff_ignored_biotype(args, ss) && args->verbosity > 0 ) fprintf(bcftools_stderr,"ignored gene: %s\n",line);
+        return;
+    }
+
+    aux_t *aux = &args->init;
+
+    // substring search for "ID=gene:ENSG00000437963"
+    uint32_t gene_id = gff_id_parse(&aux->gene_ids, line, "ID=gene:", ss);
+    gf_gene_t *gene = gene_init(aux, gene_id);
+    assert( !gene->name );      // the gene_id should be unique
+
+    gene->iseq = feature_set_seq(args, chr_beg,chr_end);
+
+    // substring search for "Name=OR4F5"
+    ss = strstr(chr_end+2,"Name=");
+    if ( ss )
+    {
+        ss += 5;
+        char *se = ss;
+        while ( *se && *se!=';' && !isspace(*se) ) se++;
+        gene->name = (char*) malloc(se-ss+1);
+        memcpy(gene->name,ss,se-ss);
+        gene->name[se-ss] = 0;
+    }
+    else
+        gene->name = strdup(aux->gene_ids.str[gene_id]); // Name=<GeneName> field is not present, use the gene ID instead
+}
+int gff_parse(args_t *args, char *line, ftr_t *ftr)
+{
+    // - skip empty lines and commented lines
+    // - columns 
+    //      1.      chr
+    //      2.      <skip>
+    //      3.      CDS, transcript, gene, ...
+    //      4-5.    beg,end
+    //      6.      <skip>
+    //      7.      strand
+    //      8.      phase
+    //      9.      Parent=transcript:ENST(\d+);ID=... etc
+
+    char *ss = line;
+    if ( !*ss ) return -1;      // skip blank lines
+    if ( *ss=='#' ) return -1;  // skip comments
+
+    char *chr_beg, *chr_end;
+    gff_parse_chr(line, &chr_beg, &chr_end);
+    ss = gff_skip(line, chr_end + 2);
+
+    // 3. column: is this a CDS, transcript, gene, etc.
+    if ( !strncmp("exon\t",ss,5) ) { ftr->type = GF_EXON; ss += 5; }
+    else if ( !strncmp("CDS\t",ss,4) ) { ftr->type = GF_CDS; ss += 4; }
+    else if ( !strncmp("three_prime_UTR\t",ss,16) ) { ftr->type = GF_UTR3; ss += 16; }
+    else if ( !strncmp("five_prime_UTR\t",ss,15) ) { ftr->type = GF_UTR5; ss += 15; }
+    else
+    {
+        ss = gff_skip(line, ss);
+        ss = gff_parse_beg_end(line, ss, &ftr->beg,&ftr->end);
+        ss = gff_skip(line, ss);
+        int type = gff_parse_type(ss);
+        if ( type!=GFF_TSCRIPT_LINE && type!=GFF_GENE_LINE ) 
+        {
+            // we ignore these, debug print to see new types:
+            ss = strstr(ss,"ID=");
+            if ( !ss ) return -1;   // no ID, ignore the line
+            if ( !strncmp("chromosome",ss+3,10) ) return -1;
+            if ( !strncmp("supercontig",ss+3,11) ) return -1;
+            if ( args->verbosity > 0 ) fprintf(bcftools_stderr,"ignored: %s\n", line);
+            return -1;
+        }
+
+        // 7. column: strand
+        if ( *ss == '+' ) ftr->strand = STRAND_FWD;
+        else if ( *ss == '-' ) ftr->strand = STRAND_REV;
+        else error("Unknown strand: %c .. %s\n", *ss,ss);
+
+        if ( type==GFF_TSCRIPT_LINE )
+            gff_parse_transcript(args, line, ss, ftr);
+        else
+            gff_parse_gene(args, line, ss, chr_beg, chr_end, ftr);
+
+        return -1;
+    }
+    ss = gff_parse_beg_end(line, ss, &ftr->beg,&ftr->end);
+    ss = gff_skip(line, ss);
+
+    // 7. column: strand
+    if ( *ss == '+' ) ftr->strand = STRAND_FWD;
+    else if ( *ss == '-' ) ftr->strand = STRAND_REV;
+    else { if ( args->verbosity > 0 ) fprintf(bcftools_stderr,"Skipping unknown strand: %c\n", *ss); return -1; }
+    ss += 2;
+
+    // 8. column: phase (codon offset)
+    if ( *ss == '0' ) ftr->phase = 0;
+    else if ( *ss == '1' ) ftr->phase = 1;
+    else if ( *ss == '2' ) ftr->phase = 2;
+    else if ( *ss == '.' ) ftr->phase = CDS_PHASE_UNKN;     // exons and even CDS in some GFFs do not have phase
+    else { if ( args->verbosity > 0 ) fprintf(bcftools_stderr,"Skipping unknown phase: %c, %s\n", *ss, line); return -1; }
+    ss += 2;
+
+    // substring search for "Parent=transcript:ENST00000437963"
+    ftr->trid = gff_id_parse(&args->tscript_ids, line, "Parent=transcript:", ss);
+    ftr->iseq = feature_set_seq(args, chr_beg,chr_end);
+    return 0;
+}
+
+static int cmp_cds_ptr(const void *a, const void *b)
+{
+    // comparison function for qsort of transcripts's CDS
+    if ( (*((gf_cds_t**)a))->beg < (*((gf_cds_t**)b))->beg ) return -1;
+    if ( (*((gf_cds_t**)a))->beg > (*((gf_cds_t**)b))->beg ) return 1;
+    return 0;
+}
+
+static inline void chr_beg_end(aux_t *aux, int iseq, char **chr_beg, char **chr_end)
+{
+    *chr_beg = *chr_end = aux->seq[iseq];
+    while ( (*chr_end)[1] ) (*chr_end)++;
+}
+tscript_t *tscript_init(aux_t *aux, uint32_t trid)
+{
+    khint_t k = kh_get(int2tscript, aux->id2tr, (int)trid);
+    tscript_t *tr = (k == kh_end(aux->id2tr)) ? NULL : kh_val(aux->id2tr, k);
+    assert( tr );
+    return tr;
+}
+void register_cds(args_t *args, ftr_t *ftr)
+{
+    // Make the CDS searchable via idx_cds. Note we do not malloc tr->cds just yet.
+    //  ftr is the result of parsing a gff CDS line
+    aux_t *aux = &args->init;
+
+    tscript_t *tr = tscript_init(aux, ftr->trid);
+    if ( tr->strand != ftr->strand ) error("Conflicting strand in transcript %"PRIu32" .. %d vs %d\n",ftr->trid,tr->strand,ftr->strand);
+    
+    gf_cds_t *cds = (gf_cds_t*) malloc(sizeof(gf_cds_t));
+    cds->tr    = tr;
+    cds->beg   = ftr->beg;
+    cds->len   = ftr->end - ftr->beg + 1;
+    cds->icds  = 0;     // to keep valgrind on mac happy
+    cds->phase = ftr->phase;
+    
+    hts_expand(gf_cds_t*,tr->ncds+1,tr->mcds,tr->cds);
+    tr->cds[tr->ncds++] = cds;
+}
+void register_utr(args_t *args, ftr_t *ftr)
+{
+    aux_t *aux = &args->init;
+    gf_utr_t *utr = (gf_utr_t*) malloc(sizeof(gf_utr_t));
+    utr->which = ftr->type==GF_UTR3 ? prime3 : prime5;
+    utr->beg   = ftr->beg;
+    utr->end   = ftr->end;
+    utr->tr    = tscript_init(aux, ftr->trid);
+
+    char *chr_beg, *chr_end;
+    chr_beg_end(&args->init, utr->tr->gene->iseq, &chr_beg, &chr_end);
+    regidx_push(args->idx_utr, chr_beg,chr_end, utr->beg,utr->end, &utr);
+}
+void register_exon(args_t *args, ftr_t *ftr)
+{
+    aux_t *aux = &args->init;
+    gf_exon_t *exon = (gf_exon_t*) malloc(sizeof(gf_exon_t));
+    exon->beg = ftr->beg;
+    exon->end = ftr->end;
+    exon->tr  = tscript_init(aux, ftr->trid);
+
+    char *chr_beg, *chr_end;
+    chr_beg_end(&args->init, exon->tr->gene->iseq, &chr_beg, &chr_end);
+    regidx_push(args->idx_exon, chr_beg,chr_end, exon->beg - N_SPLICE_REGION_INTRON, exon->end + N_SPLICE_REGION_INTRON, &exon);
+}
+
+void tscript_init_cds(args_t *args)
+{
+    aux_t *aux = &args->init;
+
+    // Sort CDS in all transcripts, set offsets, check their phase, length, create index (idx_cds)
+    khint_t k;
+    int warn_phase_unkn = 0;
+    for (k=0; k<kh_end(aux->id2tr); k++)
+    {
+        if ( !kh_exist(aux->id2tr, k) ) continue;
+        tscript_t *tr = (tscript_t*) kh_val(aux->id2tr, k);
+
+        // position-to-tscript lookup
+        char *chr_beg, *chr_end;
+        chr_beg_end(aux, tr->gene->iseq, &chr_beg, &chr_end);
+        regidx_push(args->idx_tscript, chr_beg, chr_end, tr->beg, tr->end, &tr);
+
+        if ( !tr->ncds ) continue;      // transcript with no CDS
+
+        // sort CDs
+        qsort(tr->cds, tr->ncds, sizeof(gf_cds_t*), cmp_cds_ptr);
+
+        // trim non-coding start
+        int i, len = 0;
+        if ( tr->strand==STRAND_FWD )
+        {
+            if ( tr->cds[0]->phase != CDS_PHASE_UNKN )
+            {
+                if ( tr->cds[0]->phase ) tr->trim |= TRIM_5PRIME;
+                tr->cds[0]->beg += tr->cds[0]->phase;
+                tr->cds[0]->len -= tr->cds[0]->phase;
+                tr->cds[0]->phase = 0;
+            }
+
+            // sanity check phase; the phase number in gff tells us how many bases to skip in this
+            // feature to reach the first base of the next codon
+            int tscript_ok = 1;
+            for (i=0; i<tr->ncds; i++)
+            {
+                if ( tr->cds[i]->phase == CDS_PHASE_UNKN )
+                {
+                    warn_phase_unkn = 1;
+                    len += tr->cds[i]->len;
+                    continue;
+                }
+                int phase = tr->cds[i]->phase ? 3 - tr->cds[i]->phase : 0;
+                if ( phase!=len%3 )
+                {
+                    if ( args->force )
+                    {
+                        if ( args->verbosity > 0 )
+                            fprintf(bcftools_stderr,"Warning: the GFF has inconsistent phase column in transcript %s, skipping. CDS pos=%d: phase!=len%%3 (phase=%d, len=%d)\n",
+                                args->tscript_ids.str[tr->id],tr->cds[i]->beg+1,phase,len);
+                        tscript_ok = 0;
+                        break;
+                    }
+                    error("Error: GFF3 assumption failed for transcript %s, CDS=%d: phase!=len%%3 (phase=%d, len=%d). Use the --force option to proceed anyway (at your own risk).\n",
+                            args->tscript_ids.str[tr->id],tr->cds[i]->beg+1,phase,len);
+                }
+                len += tr->cds[i]->len; 
+            }
+            if ( !tscript_ok ) continue;    // skip this transcript
+        }
+        else
+        {
+            if ( tr->cds[tr->ncds-1]->phase != CDS_PHASE_UNKN )
+            {
+                // Check that the phase is not bigger than CDS length. Curiously, this can really happen,
+                // see Mus_musculus.GRCm38.85.gff3.gz, transcript:ENSMUST00000163141
+                // todo: the same for the fwd strand
+                i = tr->ncds - 1;
+                int phase = tr->cds[i]->phase;
+                if ( phase ) tr->trim |= TRIM_5PRIME;
+                while ( i>=0 && phase > tr->cds[i]->len )
+                {
+                    phase -= tr->cds[i]->len;
+                    tr->cds[i]->phase = 0;
+                    tr->cds[i]->len   = 0;
+                    i--;
+                }
+                tr->cds[i]->len  -= tr->cds[i]->phase;
+                tr->cds[i]->phase = 0;
+            }
+
+            // sanity check phase
+            int tscript_ok = 1;
+            for (i=tr->ncds-1; i>=0; i--)
+            {
+                if ( tr->cds[i]->phase == CDS_PHASE_UNKN )
+                {
+                    warn_phase_unkn = 1;
+                    len += tr->cds[i]->len;
+                    continue;
+                }
+                int phase = tr->cds[i]->phase ? 3 - tr->cds[i]->phase : 0;
+                if ( phase!=len%3)
+                {
+                    if ( args->force )
+                    {
+                        if ( args->verbosity > 0 )
+                            fprintf(bcftools_stderr,"Warning: the GFF has inconsistent phase column in transcript %s, skipping. CDS pos=%d: phase!=len%%3 (phase=%d, len=%d)\n",
+                                args->tscript_ids.str[tr->id],tr->cds[i]->beg+1,phase,len);
+                        tscript_ok = 0;
+                        break;
+                    }
+                    error("Error: GFF3 assumption failed for transcript %s, CDS=%d: phase!=len%%3 (phase=%d, len=%d). Use the --force option to proceed anyway (at your own risk).\n",
+                        args->tscript_ids.str[tr->id],tr->cds[i]->beg+1,phase,len);
+                }
+                len += tr->cds[i]->len;
+            }
+            if ( !tscript_ok ) continue;    // skip this transcript
+        }
+
+        // set len. At the same check that CDS within a transcript do not overlap
+        len = 0;
+        for (i=0; i<tr->ncds; i++)
+        {
+            tr->cds[i]->icds = i;
+            len += tr->cds[i]->len; 
+            if ( !i ) continue;
+
+            gf_cds_t *a = tr->cds[i-1];
+            gf_cds_t *b = tr->cds[i];
+            if ( a->beg + a->len - 1 >= b->beg ) 
+            {
+                if ( args->force )
+                {
+                    fprintf(bcftools_stderr,"Warning: GFF contains overlapping CDS %s: %"PRIu32"-%"PRIu32" and %"PRIu32"-%"PRIu32".\n",
+                        args->tscript_ids.str[tr->id], a->beg+1,a->beg+a->len, b->beg+1,b->beg+b->len);
+                }
+                else
+                    error("Error: CDS overlap in the transcript %s: %"PRIu32"-%"PRIu32" and %"PRIu32"-%"PRIu32", is this intended (e.g. ribosomal slippage)?\n"
+                          "       Use the --force option to override (at your own risk).\n", 
+                            args->tscript_ids.str[tr->id], a->beg+1,a->beg+a->len, b->beg+1,b->beg+b->len);
+            }
+        }
+        if ( len%3 != 0 )
+        {
+            // There are 13k transcripts with incomplete 3' CDS. See for example ENST00000524289
+            //  http://sep2015.archive.ensembl.org/Homo_sapiens/Transcript/Sequence_cDNA?db=core;g=ENSG00000155868;r=5:157138846-157159019;t=ENST00000524289
+            // Also, the incomplete CDS can be too short (1 or 2bp), so it is not enough to trim the last one.
+
+            tr->trim |= TRIM_3PRIME;
+            if ( tr->strand==STRAND_FWD )
+            {
+                i = tr->ncds - 1;
+                while ( i>=0 && len%3 )
+                {
+                    int dlen = tr->cds[i]->len >= len%3 ? len%3 : tr->cds[i]->len;
+                    tr->cds[i]->len -= dlen;
+                    len -= dlen;
+                    i--;
+                }
+            }
+            else
+            {
+                i = 0;
+                while ( i<tr->ncds && len%3 )
+                {
+                    int dlen = tr->cds[i]->len >= len%3 ? len%3 : tr->cds[i]->len;
+                    tr->cds[i]->len -= dlen;
+                    tr->cds[i]->beg += dlen;
+                    len -= dlen;
+                    i++;
+                }
+            }
+        }
+
+        // set CDS offsets and insert into regidx
+        len=0;
+        for (i=0; i<tr->ncds; i++)
+        {
+            tr->cds[i]->pos = len;
+            len += tr->cds[i]->len;
+            regidx_push(args->idx_cds, chr_beg,chr_end, tr->cds[i]->beg,tr->cds[i]->beg+tr->cds[i]->len-1, &tr->cds[i]);
+        }
+    }
+    if ( warn_phase_unkn && args->verbosity > 0 )
+        fprintf(bcftools_stderr,"Warning: encountered CDS with phase column unset, could not verify reading frame\n");
+}
+
+void regidx_free_gf(void *payload) { free(*((gf_cds_t**)payload)); }
+void regidx_free_tscript(void *payload) { tscript_t *tr = *((tscript_t**)payload); free(tr->cds); free(tr); }
+
+void init_gff(args_t *args)
+{
+    aux_t *aux = &args->init;
+    aux->seq2int   = khash_str2int_init();   // chrom's numeric id
+    aux->gid2gene  = kh_init(int2gene);      // gene id to gf_gene_t, for idx_gene
+    aux->id2tr     = kh_init(int2tscript);   // transcript id to tscript_t
+    args->idx_tscript = regidx_init(NULL, NULL, regidx_free_tscript, sizeof(tscript_t*), NULL);
+    aux->ignored_biotypes = khash_str2int_init();
+    gff_id_init(&aux->gene_ids);
+    gff_id_init(&args->tscript_ids);
+
+    // parse gff
+    kstring_t str = {0,0,0};
+    htsFile *fp = hts_open(args->gff_fname,"r");
+    if ( !fp ) error("Failed to read %s\n", args->gff_fname);
+    while ( hts_getline(fp, KS_SEP_LINE, &str) > 0 )
+    {
+        hts_expand(ftr_t, aux->nftr+1, aux->mftr, aux->ftr);
+        int ret = gff_parse(args, str.s, aux->ftr + aux->nftr);
+        if ( !ret ) aux->nftr++;
+    }
+    free(str.s);
+    if ( hts_close(fp)!=0 ) error("Close failed: %s\n", args->gff_fname);
+
+
+    // process gff information: connect CDS and exons to transcripts
+    args->idx_cds  = regidx_init(NULL, NULL, regidx_free_gf, sizeof(gf_cds_t*), NULL);
+    args->idx_utr  = regidx_init(NULL, NULL, regidx_free_gf, sizeof(gf_utr_t*), NULL);
+    args->idx_exon = regidx_init(NULL, NULL, regidx_free_gf, sizeof(gf_exon_t*), NULL);
+    args->itr      = regitr_init(NULL);
+
+    int i;
+    for (i=0; i<aux->nftr; i++)
+    {
+        ftr_t *ftr = &aux->ftr[i];
+
+        // check whether to keep this feature: is there a mapping trid -> gene_id -> gene?
+        khint_t k = kh_get(int2tscript, aux->id2tr, (int)ftr->trid);
+        if ( k==kh_end(aux->id2tr) ) continue;       // no such transcript
+
+        tscript_t *tr = kh_val(aux->id2tr,k);
+        if ( !tr->gene->name )
+        {
+            // not a supported biotype (e.g. gene:pseudogene, transcript:processed_transcript)
+            regidx_free_tscript(&tr);
+            kh_del(int2tscript, aux->id2tr,k);
+            continue;
+        }
+
+        // populate regidx by category: 
+        //      ftr->type   .. GF_CDS, GF_EXON, GF_UTR3, GF_UTR5
+        //      gene->type  .. GF_PROTEIN_CODING, GF_MT_rRNA, GF_IG_C, ...
+        if ( ftr->type==GF_CDS ) register_cds(args, ftr);
+        else if ( ftr->type==GF_EXON ) register_exon(args, ftr);
+        else if ( ftr->type==GF_UTR5 ) register_utr(args, ftr);
+        else if ( ftr->type==GF_UTR3 ) register_utr(args, ftr);
+        else
+            error("something: %s\t%d\t%d\t%s\t%s\n", aux->seq[ftr->iseq],ftr->beg+1,ftr->end+1,args->tscript_ids.str[ftr->trid],gf_type2gff_string(ftr->type));
+    }
+    tscript_init_cds(args);
+
+    if ( args->verbosity > 0 )
+    {
+        fprintf(bcftools_stderr,"Indexed %d transcripts, %d exons, %d CDSs, %d UTRs\n", 
+                regidx_nregs(args->idx_tscript),
+                regidx_nregs(args->idx_exon),
+                regidx_nregs(args->idx_cds),
+                regidx_nregs(args->idx_utr));
+    }
+
+    free(aux->ftr);
+    khash_str2int_destroy_free(aux->seq2int);
+    // keeping only to destroy the genes at the end: kh_destroy(int2gene,aux->gid2gene);
+    kh_destroy(int2tscript,aux->id2tr);
+    free(aux->seq);
+    gff_id_destroy(&aux->gene_ids);
+
+    if ( args->verbosity > 0 && khash_str2int_size(aux->ignored_biotypes) )
+    {
+        khash_t(str2int) *ign = (khash_t(str2int)*)aux->ignored_biotypes;
+        fprintf(bcftools_stderr,"Ignored the following biotypes:\n");
+        for (i = kh_begin(ign); i < kh_end(ign); i++)
+        {
+            if ( !kh_exist(ign,i)) continue;
+            const char *biotype = kh_key(ign,i);
+            if ( !strcmp(biotype,"TCE") ) biotype = "TCE (\"To be Experimentally Confirmed\")";
+            fprintf(bcftools_stderr,"\t%dx\t.. %s\n", kh_value(ign,i), biotype);
+        }
+    }
+    khash_str2int_destroy_free(aux->ignored_biotypes);
+}
+
+static inline int ncsq2_to_nfmt(int ncsq2)
+{
+    return 1 + (ncsq2 - 1) / 30;
+}
+static inline void icsq2_to_bit(int icsq2, int *ival, int *ibit)
+{
+    *ival = icsq2 / 30;
+    *ibit = icsq2 % 30;
+}
+
+void init_data(args_t *args)
+{
+    args->nfmt_bcsq = ncsq2_to_nfmt(args->ncsq2_max);
+
+    args->fai = fai_load(args->fa_fname);
+    if ( !args->fai ) error("Failed to load the fai index: %s\n", args->fa_fname);
+
+    if ( args->verbosity > 0 ) fprintf(bcftools_stderr,"Parsing %s ...\n", args->gff_fname);
+    init_gff(args);
+
+    args->rid = -1;
+
+    if ( args->filter_str )
+        args->filter = filter_init(args->hdr, args->filter_str);
+
+    args->pos2vbuf  = kh_init(pos2vbuf);
+    args->active_tr = khp_init(trhp);
+    args->hap = (hap_t*) calloc(1,sizeof(hap_t));
+
+    // init samples
+    if ( !bcf_hdr_nsamples(args->hdr) ) args->phase = PHASE_DROP_GT;
+    if ( args->sample_list && !strcmp("-",args->sample_list) )
+    {
+        // ignore all samples
+        if ( args->output_type==FT_TAB_TEXT ) 
+        {
+            // significant speedup for plain VCFs
+            if (bcf_hdr_set_samples(args->hdr,NULL,0) < 0)
+                error_errno("[%s] Couldn't build sample filter", __func__);
+        }
+        args->phase = PHASE_DROP_GT;
+    }
+    else
+        args->smpl = smpl_ilist_init(args->hdr, args->sample_list, args->sample_is_file, SMPL_STRICT);
+    args->hdr_nsmpl = args->phase==PHASE_DROP_GT ? 0 : bcf_hdr_nsamples(args->hdr);
+
+    if ( args->output_type==FT_TAB_TEXT )
+    {
+        args->out = args->output_fname ? fopen(args->output_fname,"w") : bcftools_stdout;
+        if ( !args->out ) error("Failed to write to %s: %s\n", !strcmp("-",args->output_fname)?"standard output":args->output_fname,strerror(errno));
+
+        fprintf(args->out,"# This file was produced by: bcftools +csq(%s+htslib-%s)\n", bcftools_version(),hts_version());
+        fprintf(args->out,"# The command line was:\tbcftools +%s", args->argv[0]);
+        int i;
+        for (i=1; i<args->argc; i++)
+            fprintf(args->out," %s",args->argv[i]);
+        fprintf(args->out,"\n");
+        fprintf(args->out,"# LOG\t[2]Message\n");
+        fprintf(args->out,"# CSQ"); i = 1;
+        fprintf(args->out,"\t[%d]Sample", ++i);
+        fprintf(args->out,"\t[%d]Haplotype", ++i);
+        fprintf(args->out,"\t[%d]Chromosome", ++i);
+        fprintf(args->out,"\t[%d]Position", ++i);
+        fprintf(args->out,"\t[%d]Consequence", ++i);
+        fprintf(args->out,"\n");
+    }
+    else
+    {
+        char wmode[8];
+        set_wmode(wmode,args->output_type,args->output_fname,args->clevel);
+        args->out_fh = hts_open(args->output_fname ? args->output_fname : "-", wmode);
+        if ( args->out_fh == NULL ) error("[%s] Error: cannot write to %s: %s\n", __func__,args->output_fname? args->output_fname : "standard output", strerror(errno));
+        if ( args->n_threads > 0)
+            hts_set_opt(args->out_fh, HTS_OPT_THREAD_POOL, args->sr->p);
+        if ( args->record_cmd_line ) bcf_hdr_append_version(args->hdr,args->argc,args->argv,"bcftools/csq");
+        bcf_hdr_printf(args->hdr,"##INFO=<ID=%s,Number=.,Type=String,Description=\"%s consequence annotation from BCFtools/csq, see http://samtools.github.io/bcftools/howtos/csq-calling.html for details. Format: Consequence|gene|transcript|biotype|strand|amino_acid_change|dna_change\">",args->bcsq_tag, args->local_csq ? "Local" : "Haplotype-aware");
+        if ( args->hdr_nsmpl ) 
+            bcf_hdr_printf(args->hdr,"##FORMAT=<ID=%s,Number=.,Type=Integer,Description=\"Bitmask of indexes to INFO/BCSQ, with interleaved first/second haplotype. Use \\\"bcftools query -f'[%%CHROM\\t%%POS\\t%%SAMPLE\\t%%TBCSQ\\n]'\\\" to translate.\">",args->bcsq_tag);
+        if ( bcf_hdr_write(args->out_fh, args->hdr)!=0 ) error("[%s] Error: cannot write the header to %s\n", __func__,args->output_fname?args->output_fname:"standard output");
+    }
+    if ( args->verbosity > 0 ) fprintf(bcftools_stderr,"Calling...\n");
+}
+
+void destroy_data(args_t *args)
+{
+    if ( args->ncsq2_small_warned )
+        fprintf(bcftools_stderr,
+            "Note: Some samples had too many consequences to be represented in %d bytes. If you need to record them all,\n"
+            "      the limit can be increased by running with `--ncsq %d`.\n",ncsq2_to_nfmt(args->ncsq2_max)/8,1+args->ncsq2_small_warned/2);
+
+    regidx_destroy(args->idx_cds);
+    regidx_destroy(args->idx_utr);
+    regidx_destroy(args->idx_exon);
+    regidx_destroy(args->idx_tscript);
+    regitr_destroy(args->itr);
+
+    khint_t k,i,j;
+    for (k=0; k<kh_end(args->init.gid2gene); k++)
+    {
+        if ( !kh_exist(args->init.gid2gene, k) ) continue;
+        gf_gene_t *gene = (gf_gene_t*) kh_val(args->init.gid2gene, k);
+        free(gene->name);
+        free(gene);
+    }
+    kh_destroy(int2gene,args->init.gid2gene);
+
+    if ( args->filter )
+        filter_destroy(args->filter);
+
+    khp_destroy(trhp,args->active_tr);
+    kh_destroy(pos2vbuf,args->pos2vbuf);
+    if ( args->smpl ) smpl_ilist_destroy(args->smpl);
+    int ret;
+    if ( args->out_fh )
+        ret = hts_close(args->out_fh);
+    else
+        ret = fclose(args->out);
+    if ( ret ) error("Error: close failed .. %s\n", args->output_fname?args->output_fname:"bcftools_stdout");
+    for (i=0; i<args->vcf_rbuf.m; i++)
+    {
+        vbuf_t *vbuf = args->vcf_buf[i];
+        if ( !vbuf ) continue;
+        for (j=0; j<vbuf->m; j++)
+        {
+            if ( !vbuf->vrec[j] ) continue;
+            if ( vbuf->vrec[j]->line ) bcf_destroy(vbuf->vrec[j]->line);
+            free(vbuf->vrec[j]->fmt_bm);
+            free(vbuf->vrec[j]->vcsq);
+            free(vbuf->vrec[j]);
+        }
+        free(vbuf->vrec);
+        free(vbuf);
+    }
+    free(args->vcf_buf);
+    free(args->rm_tr);
+    free(args->csq_buf);
+    free(args->hap->stack);
+    free(args->hap->sseq.s);
+    free(args->hap->tseq.s);
+    free(args->hap->tref.s);
+    free(args->hap);
+    fai_destroy(args->fai);
+    free(args->gt_arr);
+    free(args->str.s);
+    free(args->str2.s);
+    gff_id_destroy(&args->tscript_ids);
+}
+
+/*
+    The splice_* functions are for consquences around splice sites: start,stop,splice_*
+ */
+#define SPLICE_VAR_REF 0   // ref: ACGT>ACGT, csq not applicable, skip completely
+#define SPLICE_OUTSIDE 1   // splice acceptor or similar; csq set and is done, does not overlap the region
+#define SPLICE_INSIDE  2   // overlaps coding region; csq can be set but coding prediction is needed 
+#define SPLICE_OVERLAP 3   // indel overlaps region boundary, csq set but could not determine csq
+typedef struct
+{
+    tscript_t *tr;
+    struct {
+        int32_t pos, rlen, alen, ial;
+        char *ref, *alt;
+        bcf1_t *rec;
+    } vcf;
+    uint16_t check_acceptor:1,  // check distance from exon start (fwd) or end (rev)
+             check_start:1,     // this is the first coding exon (relative to transcript orientation), check first (fwd) or last (rev) codon 
+             check_stop:1,      // this is the last coding exon (relative to transcript orientation), check last (fwd) or first (rev) codon
+             check_donor:1,     // as with check_acceptor
+             check_region_beg:1,    // do/don't check for splices at this end, eg. in the first or last exon
+             check_region_end:1,    // 
+             check_utr:1,           // check splice sites (acceptor/donor/region_*) only if not in utr
+             set_refalt:1;          // set kref,kalt, if set, check also for synonymous events
+    uint32_t csq;
+    int tbeg, tend;             // number of trimmed bases from beg and end of ref,alt allele
+    uint32_t ref_beg,           // ref coordinates with spurious bases removed, ACC>AC can become AC>A or CC>C, whichever gives 
+             ref_end;           // a more conservative csq (the first and last base in kref.s)
+    kstring_t kref, kalt;       // trimmed alleles, set only with SPLICE_OLAP
+}
+splice_t;
+void splice_init(splice_t *splice, bcf1_t *rec)
+{
+    memset(splice,0,sizeof(*splice));
+    splice->vcf.rec  = rec;
+    splice->vcf.pos  = rec->pos;
+    splice->vcf.rlen = rec->rlen;
+    splice->vcf.ref  = rec->d.allele[0];
+    splice->csq      = 0;
+}
+static inline void splice_build_hap(splice_t *splice, uint32_t beg, int len)
+{
+    // len>0 .. beg is the first base, del filled from right
+    // len<0 .. beg is the last base, del filled from left
+
+    int rlen, alen, rbeg, abeg;     // first base to include (ref coordinates)
+    if ( len<0 )
+    {
+        rlen = alen = -len;
+        rbeg = beg - rlen + 1;
+        int dlen = splice->vcf.alen - splice->vcf.rlen;
+        if ( dlen<0 && beg < splice->ref_end ) // incomplete del, beg is in the middle
+            dlen += splice->ref_end - beg;
+        abeg = rbeg + dlen;
+    }
+    else
+    {
+        rbeg = abeg = beg;
+        rlen = alen = len;
+        // check for incomplete del as above??
+    }
+
+#define XDBG 0
+#if XDBG
+fprintf(bcftools_stderr,"build_hap:  rbeg=%d + %d    abeg=%d \n",rbeg,rlen,abeg);
+#endif 
+    splice->kref.l = 0;
+    splice->kalt.l = 0;
+
+    // add the part before vcf.ref, in the vcf.ref and after vcf.ref
+    int roff;   // how many vcf.ref bases already used
+    if ( rbeg < splice->vcf.pos )
+    {
+        assert( splice->tr->beg <= rbeg );  // this can be extended thanks to N_REF_PAD
+        kputsn(splice->tr->ref + N_REF_PAD + rbeg - splice->tr->beg, splice->vcf.pos - rbeg, &splice->kref);
+        roff = 0;
+    }
+    else
+        roff = rbeg - splice->vcf.pos;
+#if XDBG
+fprintf(bcftools_stderr,"r1: %s  roff=%d\n",splice->kref.s,roff);
+#endif
+
+    if ( roff < splice->vcf.rlen && splice->kref.l < rlen )
+    {
+        int len = splice->vcf.rlen - roff;  // len still available in vcf.ref
+        if ( len > rlen - splice->kref.l ) len = rlen - splice->kref.l; // how much of ref allele is still needed
+        kputsn(splice->vcf.ref + roff, len, &splice->kref);
+    }
+#if XDBG
+fprintf(bcftools_stderr,"r2: %s\n",splice->kref.s);
+#endif
+
+    uint32_t end = splice->vcf.pos + splice->vcf.rlen;    // position just after the ref allele
+    if ( splice->kref.l < rlen )
+    {
+        if ( end + rlen - splice->kref.l - 1 > splice->tr->end ) // trim, the requested sequence is too long (could be extended, see N_REF_PAD)
+            rlen -= end + rlen - splice->kref.l - 1 - splice->tr->end;
+        if ( splice->kref.l < rlen )
+            kputsn(splice->tr->ref + N_REF_PAD + end - splice->tr->beg, rlen - splice->kref.l, &splice->kref);
+    }
+#if XDBG
+fprintf(bcftools_stderr,"r3: %s\n",splice->kref.s);
+#endif
+
+
+    int aoff;
+    if ( abeg < splice->vcf.pos )
+    {
+        assert( splice->tr->beg <= abeg );
+        kputsn(splice->tr->ref + N_REF_PAD + abeg - splice->tr->beg, splice->vcf.pos - abeg, &splice->kalt);
+        aoff = 0;
+    }
+    else
+        aoff = abeg - splice->vcf.pos;
+#if XDBG
+fprintf(bcftools_stderr,"a1: %s  aoff=%d\n",splice->kalt.s,aoff);
+#endif
+
+    if ( aoff < splice->vcf.alen && splice->kalt.l < alen )
+    {
+        int len = splice->vcf.alen - aoff;  // len still available in vcf.alt
+        if ( len > alen - splice->kalt.l ) len = alen - splice->kalt.l; // how much of alt allele is still needed
+        kputsn(splice->vcf.alt + aoff, len, &splice->kalt);
+        aoff -= len;
+    }
+    if ( aoff < 0 ) aoff = 0;
+    else aoff--;
+#if XDBG
+fprintf(bcftools_stderr,"a2: %s  aoff=%d\n",splice->kalt.s,aoff);
+#endif
+
+    end = splice->vcf.pos + splice->vcf.rlen;    // position just after the ref allele
+    if ( splice->kalt.l < alen )
+    {
+        if ( end + alen + aoff - splice->kalt.l - 1 > splice->tr->end ) // trim, the requested sequence is too long
+            alen -= end + alen + aoff - splice->kalt.l - 1 - splice->tr->end;
+        if ( alen > 0 && alen > splice->kalt.l )
+            kputsn(splice->tr->ref + aoff + N_REF_PAD + end - splice->tr->beg, alen - splice->kalt.l, &splice->kalt);
+    }
+#if XDBG
+fprintf(bcftools_stderr,"a3: %s\n",splice->kalt.s);
+fprintf(bcftools_stderr," [%s]\n [%s]\n\n",splice->kref.s,splice->kalt.s);
+#endif
+}
+void csq_stage(args_t *args, csq_t *csq, bcf1_t *rec);
+static inline int csq_stage_utr(args_t *args, regitr_t *itr, bcf1_t *rec, uint32_t trid, uint32_t type, int ial)
+{
+    while ( regitr_overlap(itr) )
+    {
+        gf_utr_t *utr = regitr_payload(itr, gf_utr_t*);
+        tscript_t *tr = utr->tr;
+        if ( tr->id != trid ) continue;
+        csq_t csq; 
+        memset(&csq, 0, sizeof(csq_t));
+        csq.pos          = rec->pos;
+        csq.type.type    = (utr->which==prime5 ? CSQ_UTR5 : CSQ_UTR3) | type;
+        csq.type.biotype = tr->type;
+        csq.type.strand  = tr->strand;
+        csq.type.trid    = tr->id;
+        csq.type.vcf_ial = ial;
+        csq.type.gene    = tr->gene->name;
+        csq_stage(args, &csq, rec);
+        return csq.type.type;
+    }
+    return 0;
+}
+static inline void csq_stage_splice(args_t *args, bcf1_t *rec, tscript_t *tr, uint32_t type, int ial)
+{
+#if XDBG
+fprintf(bcftools_stderr,"csq_stage_splice %d: type=%d\n",rec->pos+1,type);
+#endif
+    if ( !type ) return;
+    csq_t csq; 
+    memset(&csq, 0, sizeof(csq_t));
+    csq.pos          = rec->pos;
+    csq.type.type    = type;
+    csq.type.biotype = tr->type;
+    csq.type.strand  = tr->strand;
+    csq.type.trid    = tr->id;
+    csq.type.vcf_ial = ial;
+    csq.type.gene    = tr->gene->name;
+    csq_stage(args, &csq, rec);
+}
+static inline int splice_csq_ins(args_t *args, splice_t *splice, uint32_t ex_beg, uint32_t ex_end)
+{
+    // coordinates that matter for consequences, eg AC>ACG trimmed to C>CG, 1bp
+    // before and after the inserted bases
+    if ( splice->tbeg || splice->vcf.ref[0]!=splice->vcf.alt[0] )
+    {
+        splice->ref_beg = splice->vcf.pos + splice->tbeg - 1;
+        splice->ref_end = splice->vcf.pos + splice->vcf.rlen - splice->tend;
+    }
+    else
+    {
+        if ( splice->tend ) splice->tend--;
+        splice->ref_beg = splice->vcf.pos;
+        splice->ref_end = splice->vcf.pos + splice->vcf.rlen - splice->tend;
+    }
+#if XDBG
+fprintf(bcftools_stderr,"ins: %s>%s .. ex=%d,%d  beg,end=%d,%d  tbeg,tend=%d,%d  check_utr=%d start,stop,beg,end=%d,%d,%d,%d\n", splice->vcf.ref,splice->vcf.alt,ex_beg,ex_end,splice->ref_beg,splice->ref_end,splice->tbeg,splice->tend,splice->check_utr,splice->check_start,splice->check_stop,splice->check_region_beg,splice->check_region_end);
+#endif
+
+    int ret;
+    if ( splice->ref_beg >= ex_end )   // fully outside, beyond the exon
+    {
+        if ( splice->check_utr )
+        {
+            regitr_t *itr = regitr_init(NULL);
+            const char *chr = bcf_seqname(args->hdr,splice->vcf.rec);
+            if ( regidx_overlap(args->idx_utr,chr,splice->ref_beg+1,splice->ref_beg+1, itr) )     // adjacent utr
+            {
+                ret = csq_stage_utr(args, itr, splice->vcf.rec, splice->tr->id, splice->csq, splice->vcf.ial);
+                if ( ret!=0 ) 
+                {
+                    regitr_destroy(itr);
+                    return SPLICE_OUTSIDE; // overlaps utr
+                }
+            }
+            regitr_destroy(itr);
+        }
+        if ( !splice->check_region_end ) return SPLICE_OUTSIDE;
+        char *ref = NULL, *alt = NULL;
+        if ( splice->set_refalt )   // seq identity is checked only when tr->ref is available
+        {
+            splice_build_hap(splice, ex_end+1, N_SPLICE_REGION_INTRON);
+            ref = splice->kref.s, alt = splice->kalt.s;
+        }
+        if ( splice->ref_beg < ex_end + N_SPLICE_REGION_INTRON && splice->ref_end > ex_end + N_SPLICE_DONOR )
+        {
+            splice->csq |= CSQ_SPLICE_REGION;
+            if ( ref && !strncmp(ref,alt,N_SPLICE_REGION_INTRON) ) splice->csq |= CSQ_SYNONYMOUS_VARIANT;
+        }
+        if ( splice->ref_beg < ex_end + N_SPLICE_DONOR )
+        {
+            if ( splice->check_donor && splice->tr->strand==STRAND_FWD ) splice->csq |= CSQ_SPLICE_DONOR;
+            if ( splice->check_acceptor && splice->tr->strand==STRAND_REV ) splice->csq |= CSQ_SPLICE_ACCEPTOR;
+            if ( ref && !strncmp(ref,alt,N_SPLICE_DONOR) ) splice->csq |= CSQ_SYNONYMOUS_VARIANT;
+        }
+        csq_stage_splice(args, splice->vcf.rec, splice->tr, splice->csq, splice->vcf.ial);
+        return SPLICE_OUTSIDE;
+    }
+    if ( splice->ref_end < ex_beg || (splice->ref_end == ex_beg && !splice->check_region_beg) )    // fully outside, before the exon
+    {
+        if ( splice->check_utr )
+        {
+            regitr_t *itr = regitr_init(NULL);
+            const char *chr = bcf_seqname(args->hdr,splice->vcf.rec);
+            if ( regidx_overlap(args->idx_utr,chr,splice->ref_end-1,splice->ref_end-1, itr) )     // adjacent utr
+            {
+                ret = csq_stage_utr(args, itr, splice->vcf.rec, splice->tr->id, splice->csq, splice->vcf.ial);
+                if ( ret!=0 )
+                {
+                    regitr_destroy(itr);
+                    return SPLICE_OUTSIDE; // overlaps utr
+                }
+            }
+            regitr_destroy(itr);
+        }
+        if ( !splice->check_region_beg ) return SPLICE_OUTSIDE;
+        char *ref = NULL, *alt = NULL;
+        if ( splice->set_refalt )   // seq identity is checked only when tr->ref is available
+        {
+            splice_build_hap(splice, ex_beg - N_SPLICE_REGION_INTRON, N_SPLICE_REGION_INTRON);
+            ref = splice->kref.s, alt = splice->kalt.s;
+        }
+        if ( splice->ref_end > ex_beg - N_SPLICE_REGION_INTRON && splice->ref_beg < ex_beg - N_SPLICE_DONOR )
+        {
+            splice->csq |= CSQ_SPLICE_REGION;
+            if ( ref && !strncmp(ref,alt,N_SPLICE_REGION_INTRON) ) splice->csq |= CSQ_SYNONYMOUS_VARIANT;
+        }
+        if ( splice->ref_end > ex_beg - N_SPLICE_DONOR )
+        {
+            if ( splice->check_donor && splice->tr->strand==STRAND_REV ) splice->csq |= CSQ_SPLICE_DONOR;
+            if ( splice->check_acceptor && splice->tr->strand==STRAND_FWD ) splice->csq |= CSQ_SPLICE_ACCEPTOR;
+            if ( ref && !strncmp(ref+N_SPLICE_REGION_INTRON-N_SPLICE_DONOR,alt+N_SPLICE_REGION_INTRON-N_SPLICE_DONOR,N_SPLICE_DONOR) ) splice->csq |= CSQ_SYNONYMOUS_VARIANT;
+        }
+        csq_stage_splice(args, splice->vcf.rec, splice->tr, splice->csq, splice->vcf.ial);
+        return SPLICE_OUTSIDE;
+    }
+    // overlaps the exon or inside the exon
+    // possible todo: find better alignment for frameshifting variants?
+    if ( splice->ref_beg <= ex_beg + 2 )    // in the first 3bp
+    {
+        if ( splice->check_region_beg ) splice->csq |= CSQ_SPLICE_REGION;
+        if ( splice->tr->strand==STRAND_FWD ) { if ( splice->check_start ) splice->csq |= CSQ_START_LOST; }
+        else { if ( splice->check_stop ) splice->csq |= CSQ_STOP_LOST; }
+    }
+    if ( splice->ref_end > ex_end - 2 )
+    {
+        if ( splice->check_region_end ) splice->csq |= CSQ_SPLICE_REGION;
+        if ( splice->tr->strand==STRAND_REV ) { if ( splice->check_start ) splice->csq |= CSQ_START_LOST; }
+        else { if ( splice->check_stop ) splice->csq |= CSQ_STOP_LOST; }
+    }
+    if ( splice->set_refalt )
+    {
+        // Make sure the variant will not end up left aligned to avoid overlapping vcf records
+        //      splice_build_hap(splice, splice->ref_beg, splice->vcf.alen - splice->tend - splice->tbeg + 1);
+        //      splice->vcf.rlen -= splice->tbeg + splice->tend - 1;
+        //      if ( splice->kref.l > splice->vcf.rlen ) { splice->kref.l = splice->vcf.rlen;  splice->kref.s[splice->kref.l] = 0; }
+        if ( splice->ref_beg < splice->vcf.pos )    // this must have been caused by too much trimming from right
+        {
+            int dlen = splice->vcf.pos - splice->ref_beg;
+            assert( dlen==1 );
+            splice->tbeg += dlen;
+            if ( splice->tbeg + splice->tend == splice->vcf.rlen ) splice->tend -= dlen;
+            splice->ref_beg = splice->vcf.pos;
+        }
+        if ( splice->ref_end==ex_beg ) splice->tend--;  // prevent zero-length ref allele
+        splice_build_hap(splice, splice->ref_beg, splice->vcf.alen - splice->tend - splice->tbeg + 1);
+        splice->vcf.rlen -= splice->tbeg + splice->tend - 1;
+        if ( splice->kref.l > splice->vcf.rlen ) { splice->kref.l = splice->vcf.rlen;  splice->kref.s[splice->kref.l] = 0; }
+    }
+    csq_stage_splice(args, splice->vcf.rec, splice->tr, splice->csq, splice->vcf.ial);
+    return SPLICE_INSIDE;
+}
+
+int shifted_del_synonymous(args_t *args, splice_t *splice, uint32_t ex_beg, uint32_t ex_end)
+{
+    static int small_ref_padding_warned = 0;
+    tscript_t *tr = splice->tr;
+
+    // We know the VCF record overlaps the exon, but does it overlap the start codon?
+    if ( tr->strand==STRAND_REV && splice->vcf.pos + splice->vcf.rlen + 2 <= ex_end ) return 0;
+    if ( tr->strand==STRAND_FWD && splice->vcf.pos >= ex_beg + 3 ) return 0;
+
+#if XDBG
+    fprintf(bcftools_stderr,"shifted_del_synonymous: %d-%d  %s\n",ex_beg,ex_end, tr->strand==STRAND_FWD?"fwd":"rev");
+    fprintf(bcftools_stderr,"   %d  ..  %s > %s\n",splice->vcf.pos+1,splice->vcf.ref,splice->vcf.alt);
+#endif
+
+    // is there enough ref sequence for the extension? All coordinates are 0-based
+    int ref_len = strlen(splice->vcf.ref);
+    int alt_len = strlen(splice->vcf.alt);
+    assert( ref_len > alt_len );
+    int ndel = ref_len - alt_len;
+
+    if ( tr->strand==STRAND_REV )
+    {
+        int32_t vcf_ref_end = splice->vcf.pos + ref_len - 1;  // end pos of the VCF REF allele
+        int32_t tr_ref_end  = splice->tr->end + N_REF_PAD;    // the end pos of accessible cached ref seq
+        if ( vcf_ref_end + ndel > tr_ref_end )
+        {
+            if ( !small_ref_padding_warned )
+            {
+                fprintf(bcftools_stderr,"Warning: Could not verify synonymous start/stop at %s:%d due to small N_REF_PAD. (Improve me?)\n",bcf_seqname(args->hdr,splice->vcf.rec),splice->vcf.pos+1);
+                small_ref_padding_warned = 1;
+            }
+            return 0;
+        }
+
+        char *ptr_vcf = splice->vcf.ref + alt_len;                         // the first deleted base in the VCF REF allele
+        char *ptr_ref = splice->tr->ref + N_REF_PAD + (vcf_ref_end + 1 - splice->tr->beg);  // the first ref base after the ndel bases deleted
+#if XDBG
+        fprintf(bcftools_stderr,"vcf: %s\nref: %s\n",ptr_vcf,ptr_ref);
+#endif
+        int i = 0;
+        while ( ptr_vcf[i] && ptr_vcf[i]==ptr_ref[i] ) i++;
+        if ( ptr_vcf[i] ) return 0;       // the deleted sequence cannot be replaced
+    }
+    else 
+    {
+        // STRAND_FWD
+        int32_t vcf_block_beg = splice->vcf.pos + ref_len - 2*ndel;        // the position of the first base of the ref block that could potentially replace the deletion
+        if ( vcf_block_beg < 0 ) return 0;
+
+#if XDBG
+        fprintf(bcftools_stderr,"vcf_block_beg: %d\n",vcf_block_beg+1);
+#endif
+
+        if ( N_REF_PAD + vcf_block_beg < ex_beg )
+        {
+            if ( !small_ref_padding_warned )
+            {
+                fprintf(bcftools_stderr,"Warning: Could not verify synonymous start/stop at %s:%d due to small N_REF_PAD. (Improve me?)\n",bcf_seqname(args->hdr,splice->vcf.rec),splice->vcf.pos+1);
+                small_ref_padding_warned = 1;
+            }
+            return 0;
+        }
+
+        char *ptr_vcf = splice->vcf.ref + alt_len;                                      // the first deleted base in the VCF REF allele
+        char *ptr_ref = splice->tr->ref + N_REF_PAD + vcf_block_beg - splice->tr->beg;  // the replacement ref block
+#if XDBG
+        fprintf(bcftools_stderr,"vcf: %s\nref: %s\n",ptr_vcf,ptr_ref);
+#endif
+
+        int i = 0;
+        while ( ptr_vcf[i] && ptr_vcf[i]==ptr_ref[i] ) i++;
+        if ( ptr_vcf[i] ) return 0;       // the deleted sequence cannot be replaced
+    }
+
+    return 1;
+}
+
+static inline int splice_csq_del(args_t *args, splice_t *splice, uint32_t ex_beg, uint32_t ex_end)
+{
+    if ( splice->check_start )
+    {
+        // check for synonymous start
+        //      test/csq/ENST00000375992/incorrect-synon-del-not-start-lost.txt
+        //      test/csq/ENST00000368801.2/start-lost.txt
+        //      test/csq/ENST00000318249.2/synonymous-start-lost.txt
+        int is_synonymous = shifted_del_synonymous(args, splice, ex_beg, ex_end);
+        if ( is_synonymous )
+        {
+            splice->csq |= CSQ_START_RETAINED;
+            return SPLICE_OVERLAP;
+        }
+    }
+
+    // coordinates that matter for consequences, eg AC>ACG trimmed to C>CG
+    splice->ref_beg = splice->vcf.pos + splice->tbeg - 1;                       // 1b before the deleted base
+    splice->ref_end = splice->vcf.pos + splice->vcf.rlen - splice->tend - 1;    // the last deleted base
+
+#if XDBG
+fprintf(bcftools_stderr,"splice_csq_del: %s>%s .. ex=%d,%d  beg,end=%d,%d  tbeg,tend=%d,%d  check_utr=%d start,stop,beg,end=%d,%d,%d,%d\n", splice->vcf.ref,splice->vcf.alt,ex_beg,ex_end,splice->ref_beg,splice->ref_end,splice->tbeg,splice->tend,splice->check_utr,splice->check_start,splice->check_stop,splice->check_region_beg,splice->check_region_end);
+#endif
+
+    if ( splice->ref_beg + 1 < ex_beg )     // the part before the exon; ref_beg is off by -1
+    {
+        if ( splice->check_region_beg )
+        {
+            int csq = 0;
+            if ( splice->check_utr )
+            {
+                regitr_t *itr = regitr_init(NULL);
+                const char *chr = bcf_seqname(args->hdr,splice->vcf.rec);
+                if ( regidx_overlap(args->idx_utr,chr,splice->ref_beg,ex_beg-1, itr) )     // adjacent utr
+                    csq = csq_stage_utr(args, itr, splice->vcf.rec, splice->tr->id, splice->csq, splice->vcf.ial);
+                regitr_destroy(itr);
+            }
+            if ( !csq )
+            {
+                char *ref = NULL, *alt = NULL;
+                if ( splice->set_refalt )   // seq identity is checked only when tr->ref is available
+                {
+                    // filling from the left does not work for ENST00000341065/frame3.vcf
+                    //    CAG.GTGGCCAG      CAG.GTGGCCAG
+                    //    CA-.--GGCCAG  vs  CAG.---GCCAG
+                    //  splice_build_hap(splice, ex_beg-1, -N_SPLICE_REGION_INTRON);
+                    //
+                    // filling from the right:
+                    splice_build_hap(splice, ex_beg - N_SPLICE_REGION_INTRON, N_SPLICE_REGION_INTRON);
+                    ref = splice->kref.s, alt = splice->kalt.s;
+                }
+                if ( splice->ref_end >= ex_beg - N_SPLICE_REGION_INTRON && splice->ref_beg < ex_beg - N_SPLICE_DONOR )
+                {
+                    splice->csq |= CSQ_SPLICE_REGION;
+                    if ( ref && alt && !strncmp(ref,alt,N_SPLICE_REGION_INTRON) ) splice->csq |= CSQ_SYNONYMOUS_VARIANT;
+                }
+                if ( splice->ref_end >= ex_beg - N_SPLICE_DONOR )
+                {
+                    if ( splice->check_donor && splice->tr->strand==STRAND_REV ) splice->csq |= CSQ_SPLICE_DONOR;
+                    if ( splice->check_acceptor && splice->tr->strand==STRAND_FWD ) splice->csq |= CSQ_SPLICE_ACCEPTOR;
+                    if ( ref && alt && !strncmp(ref+N_SPLICE_REGION_INTRON-N_SPLICE_DONOR,alt+N_SPLICE_REGION_INTRON-N_SPLICE_DONOR,N_SPLICE_DONOR) ) splice->csq |= CSQ_SYNONYMOUS_VARIANT;
+                }
+            }
+        }
+        if ( splice->ref_end >= ex_beg ) 
+        {
+            splice->tbeg = splice->ref_beg - splice->vcf.pos + 1;
+            splice->ref_beg = ex_beg - 1;
+            if ( splice->tbeg + splice->tend == splice->vcf.alen )
+            {
+                // the deletion overlaps ex_beg and cannot be easily realigned to the right
+                if ( !splice->tend )
+                {
+                    splice->csq |= CSQ_CODING_SEQUENCE;
+                    return SPLICE_OVERLAP;
+                }
+                splice->tend--;
+            }
+        }
+    }
+    if ( ex_end < splice->ref_end )     // the part after the exon
+    {
+        if ( splice->check_region_end )
+        {
+            int csq = 0;
+            if ( splice->check_utr )
+            {
+                regitr_t *itr = regitr_init(NULL);
+                const char *chr = bcf_seqname(args->hdr,splice->vcf.rec);
+                if ( regidx_overlap(args->idx_utr,chr,ex_end+1,splice->ref_end, itr) )     // adjacent utr
+                    csq = csq_stage_utr(args, itr, splice->vcf.rec, splice->tr->id, splice->csq, splice->vcf.ial);
+                regitr_destroy(itr);
+            }
+            if ( !csq )
+            {
+                char *ref = NULL, *alt = NULL;
+                if ( splice->set_refalt )   // seq identity is checked only when tr->ref is available
+                {
+                    splice_build_hap(splice, ex_end+1, N_SPLICE_REGION_INTRON);  // ref,alt positioned at the first intron base
+                    ref = splice->kref.s, alt = splice->kalt.s;
+                }
+                if ( splice->ref_beg < ex_end + N_SPLICE_REGION_INTRON && splice->ref_end > ex_end + N_SPLICE_DONOR )
+                {
+                    splice->csq |= CSQ_SPLICE_REGION;
+                    if ( ref && alt && !strncmp(ref,alt,N_SPLICE_REGION_INTRON) ) splice->csq |= CSQ_SYNONYMOUS_VARIANT;
+                }
+                if ( splice->ref_beg < ex_end + N_SPLICE_DONOR )
+                {
+                    if ( splice->check_donor && splice->tr->strand==STRAND_FWD ) splice->csq |= CSQ_SPLICE_DONOR;
+                    if ( splice->check_acceptor && splice->tr->strand==STRAND_REV ) splice->csq |= CSQ_SPLICE_ACCEPTOR;
+                    if ( ref && alt && !strncmp(ref+N_SPLICE_REGION_INTRON-N_SPLICE_DONOR,alt+N_SPLICE_REGION_INTRON-N_SPLICE_DONOR,N_SPLICE_DONOR) ) splice->csq |= CSQ_SYNONYMOUS_VARIANT;
+                }
+            }
+        }
+        if ( splice->ref_beg < ex_end ) 
+        {
+            splice->tend = splice->vcf.rlen - (splice->ref_end - splice->vcf.pos + 1);
+            splice->ref_end = ex_end;
+        }
+    }
+    if ( splice->ref_end < ex_beg || splice->ref_beg >= ex_end )
+    {
+        csq_stage_splice(args, splice->vcf.rec, splice->tr, splice->csq, splice->vcf.ial);
+        return SPLICE_OUTSIDE;
+    }
+    if ( splice->ref_beg < ex_beg + 2 ) // ref_beg is off by -1
+    {
+        if ( splice->check_region_beg ) splice->csq |= CSQ_SPLICE_REGION;
+        if ( splice->tr->strand==STRAND_FWD ) { if ( splice->check_start ) splice->csq |= CSQ_START_LOST; }
+        else { if ( splice->check_stop ) splice->csq |= CSQ_STOP_LOST; }
+    }
+    if ( splice->ref_end > ex_end - 3 )
+    {
+        if ( splice->check_region_end ) splice->csq |= CSQ_SPLICE_REGION;
+        if ( splice->tr->strand==STRAND_REV ) { if ( splice->check_start ) splice->csq |= CSQ_START_LOST; }
+        else { if ( splice->check_stop ) splice->csq |= CSQ_STOP_LOST; }
+    }
+    if ( splice->set_refalt )
+    {
+        if ( splice->tbeg>0 ) splice->tbeg--;  //why is this?
+        if ( splice->vcf.rlen > splice->tbeg + splice->tend && splice->vcf.alen > splice->tbeg + splice->tend )
+        {
+            splice->vcf.rlen -= splice->tbeg + splice->tend;
+            splice->vcf.alen -= splice->tbeg + splice->tend;
+        }
+        splice->kref.l = 0; kputsn(splice->vcf.ref + splice->tbeg, splice->vcf.rlen, &splice->kref); 
+        splice->kalt.l = 0; kputsn(splice->vcf.alt + splice->tbeg, splice->vcf.alen, &splice->kalt); 
+        if ( (splice->ref_beg+1 < ex_beg && splice->ref_end >= ex_beg) || (splice->ref_beg+1 < ex_end && splice->ref_end >= ex_end) ) // ouch, ugly ENST00000409523/long-overlapping-del.vcf
+        {
+            splice->csq |= (splice->ref_end - splice->ref_beg)%3 ? CSQ_FRAMESHIFT_VARIANT : CSQ_INFRAME_DELETION;
+            return SPLICE_OVERLAP;
+        }
+    }
+    csq_stage_splice(args, splice->vcf.rec, splice->tr, splice->csq, splice->vcf.ial);
+    return SPLICE_INSIDE;
+}
+
+static inline int splice_csq_mnp(args_t *args, splice_t *splice, uint32_t ex_beg, uint32_t ex_end)
+{
+    // not a real variant, can be ignored: eg ACGT>ACGT
+    if ( splice->tbeg + splice->tend == splice->vcf.rlen ) return SPLICE_VAR_REF;
+
+    splice->ref_beg = splice->vcf.pos + splice->tbeg;
+    splice->ref_end = splice->vcf.pos + splice->vcf.rlen - splice->tend - 1;
+
+#if XDBG
+fprintf(bcftools_stderr,"mnp: %s>%s .. ex=%d,%d  beg,end=%d,%d  tbeg,tend=%d,%d  check_utr=%d start,stop,beg,end=%d,%d,%d,%d\n", splice->vcf.ref,splice->vcf.alt,ex_beg,ex_end,splice->ref_beg,splice->ref_end,splice->tbeg,splice->tend,splice->check_utr,splice->check_start,splice->check_stop,splice->check_region_beg,splice->check_region_end);
+#endif
+
+    if ( splice->ref_beg < ex_beg )     // the part before the exon
+    {
+        if ( splice->check_region_beg )
+        {
+            int csq = 0;
+            if ( splice->check_utr )
+            {
+                regitr_t *itr = regitr_init(NULL);
+                const char *chr = bcf_seqname(args->hdr,splice->vcf.rec);
+                if ( regidx_overlap(args->idx_utr,chr,splice->ref_beg,ex_beg-1, itr) )     // adjacent utr
+                    csq = csq_stage_utr(args, itr, splice->vcf.rec, splice->tr->id, splice->csq, splice->vcf.ial);
+                regitr_destroy(itr);
+            }
+            if ( !csq )
+            {
+                if ( splice->ref_end >= ex_beg - N_SPLICE_REGION_INTRON && splice->ref_beg < ex_beg - N_SPLICE_DONOR )
+                    splice->csq |= CSQ_SPLICE_REGION;
+                if ( splice->ref_end >= ex_beg - N_SPLICE_DONOR )
+                {
+                    if ( splice->check_donor && splice->tr->strand==STRAND_REV ) splice->csq |= CSQ_SPLICE_DONOR;
+                    if ( splice->check_acceptor && splice->tr->strand==STRAND_FWD ) splice->csq |= CSQ_SPLICE_ACCEPTOR;
+                }
+            }
+        }
+        if ( splice->ref_end >= ex_beg ) 
+        {
+            splice->tbeg = splice->ref_beg - splice->vcf.pos;
+            splice->ref_beg = ex_beg;
+        }
+    }
+    if ( ex_end < splice->ref_end )     // the part after the exon
+    {
+        if ( splice->check_region_end )
+        {
+            int csq = 0;
+            if ( splice->check_utr )
+            {
+                regitr_t *itr = regitr_init(NULL);
+                const char *chr = bcf_seqname(args->hdr,splice->vcf.rec);
+                if ( regidx_overlap(args->idx_utr,chr,ex_end+1,splice->ref_end, itr) )     // adjacent utr
+                    csq = csq_stage_utr(args, itr, splice->vcf.rec, splice->tr->id, splice->csq, splice->vcf.ial);
+                regitr_destroy(itr);
+            }
+            if ( !csq )
+            {
+                if ( splice->ref_beg <= ex_end + N_SPLICE_REGION_INTRON && splice->ref_end > ex_end + N_SPLICE_DONOR )
+                    splice->csq |= CSQ_SPLICE_REGION;
+                if ( splice->ref_beg <= ex_end + N_SPLICE_DONOR )
+                {
+                    if ( splice->check_donor && splice->tr->strand==STRAND_FWD ) splice->csq |= CSQ_SPLICE_DONOR;
+                    if ( splice->check_acceptor && splice->tr->strand==STRAND_REV ) splice->csq |= CSQ_SPLICE_ACCEPTOR;
+                }
+            }
+        }
+        if ( splice->ref_beg <= ex_end ) 
+        {
+            splice->tend = splice->vcf.rlen - (splice->ref_end - splice->vcf.pos + 1);
+            splice->ref_end = ex_end;
+        }
+    }
+    if ( splice->ref_end < ex_beg || splice->ref_beg > ex_end )
+    {
+        csq_stage_splice(args, splice->vcf.rec, splice->tr, splice->csq, splice->vcf.ial);
+        return SPLICE_OUTSIDE;
+    }
+
+    if ( splice->ref_beg < ex_beg + 3 )
+    {
+        if ( splice->check_region_beg ) splice->csq |= CSQ_SPLICE_REGION;
+        if ( splice->tr->strand==STRAND_FWD ) { if ( splice->check_start ) splice->csq |= CSQ_START_LOST; }
+        else { if ( splice->check_stop ) splice->csq |= CSQ_STOP_LOST; }
+    }
+    if ( splice->ref_end > ex_end - 3 )
+    {
+        if ( splice->check_region_end ) splice->csq |= CSQ_SPLICE_REGION;
+        if ( splice->tr->strand==STRAND_REV ) { if ( splice->check_start ) splice->csq |= CSQ_START_LOST; }
+        else { if ( splice->check_stop ) splice->csq |= CSQ_STOP_LOST; }
+    }
+    if ( splice->set_refalt )
+    {
+        splice->vcf.rlen -= splice->tbeg + splice->tend;
+        splice->kref.l = 0; kputsn(splice->vcf.ref + splice->tbeg, splice->vcf.rlen, &splice->kref); 
+        splice->kalt.l = 0; kputsn(splice->vcf.alt + splice->tbeg, splice->vcf.rlen, &splice->kalt); 
+    }
+    csq_stage_splice(args, splice->vcf.rec, splice->tr, splice->csq, splice->vcf.ial);
+    return SPLICE_INSIDE;
+}
+static inline int splice_csq(args_t *args, splice_t *splice, uint32_t ex_beg, uint32_t ex_end)
+{
+    splice->vcf.alen = strlen(splice->vcf.alt);
+
+    int rlen1 = splice->vcf.rlen - 1, alen1 = splice->vcf.alen - 1, i = 0;
+    splice->tbeg = 0, splice->tend = 0;
+
+    // trim from the right, then from the left
+    while ( i<=rlen1 && i<=alen1 )
+    {
+        if ( splice->vcf.ref[rlen1-i] != splice->vcf.alt[alen1-i] ) break;
+        i++;
+    }
+    splice->tend = i;
+    rlen1 -= i, alen1 -= i, i = 0;
+    while ( i<=rlen1 && i<=alen1 )
+    {
+        if ( splice->vcf.ref[i] != splice->vcf.alt[i] ) break;
+        i++;
+    }
+    splice->tbeg = i;
+
+    // The mnp, ins and del code was split into near-identical functions for clarity and debugging;
+    // possible todo: generalize once stable
+    if ( splice->vcf.rlen==splice->vcf.alen ) return splice_csq_mnp(args, splice, ex_beg, ex_end);
+    if ( splice->vcf.rlen < splice->vcf.alen ) return splice_csq_ins(args, splice, ex_beg, ex_end);
+    if ( splice->vcf.rlen > splice->vcf.alen ) return splice_csq_del(args, splice, ex_beg, ex_end);
+
+    return 0;
+}
+
+
+// return value: 0 added, 1 overlapping variant, 2 silent discard (intronic,alt=ref)
+int hap_init(args_t *args, hap_node_t *parent, hap_node_t *child, gf_cds_t *cds, bcf1_t *rec, int ial)
+{
+    int i;
+    kstring_t str = {0,0,0};
+    tscript_t *tr = cds->tr;
+    child->icds = cds->icds;     // index of cds in the tscript's list of exons
+    child->vcf_ial = ial;
+
+    splice_t splice;
+    splice_init(&splice, rec);
+    splice.tr = tr;
+    splice.vcf.ial  = ial;
+    splice.vcf.alt  = rec->d.allele[ial];
+    splice.check_acceptor = splice.check_donor = splice.set_refalt = splice.check_utr = 1;
+    if ( !(tr->trim & TRIM_5PRIME) )
+    {
+        if ( tr->strand==STRAND_FWD ) { if ( child->icds==0 ) splice.check_start = 1; }
+        else { if ( child->icds==tr->ncds-1 ) splice.check_start = 1; }
+    }
+    if ( !(tr->trim & TRIM_3PRIME) )
+    {
+        if ( tr->strand==STRAND_FWD ) { if ( child->icds==tr->ncds-1 ) splice.check_stop = 1; }
+        else { if ( child->icds==0 ) splice.check_stop = 1; }
+    }
+    if ( splice.check_start )   // do not check starts in incomplete CDS, defined as not starting with M
+    {
+        if ( tr->strand==STRAND_FWD ) { if ( dna2aa(tr->ref+N_REF_PAD+cds->beg-tr->beg) != 'M' ) splice.check_start = 0; }
+        else { if ( cdna2aa(tr->ref+N_REF_PAD+cds->beg-tr->beg+cds->len-3) != 'M' ) splice.check_start = 0; }
+    }
+    if ( child->icds!=0 ) splice.check_region_beg = 1;
+    if ( child->icds!=tr->ncds-1 ) splice.check_region_end = 1;
+
+#if XDBG
+fprintf(bcftools_stderr,"\nhap_init: %d [%s][%s]   check start:%d,stop:%d\n",splice.vcf.pos+1,splice.vcf.ref,splice.vcf.alt,splice.check_start,splice.check_stop);
+#endif
+    int ret = splice_csq(args, &splice, cds->beg, cds->beg + cds->len - 1);
+#if XDBG
+fprintf(bcftools_stderr,"cds splice_csq: %d [%s][%s] .. beg,end=%d %d, ret=%d, csq=%d\n\n",splice.vcf.pos+1,splice.kref.s,splice.kalt.s,splice.ref_beg+1,splice.ref_end+1,ret,splice.csq);
+#endif
+
+    if ( ret==SPLICE_VAR_REF ) return 2;  // not a variant, eg REF=CA ALT=CA
+    if ( ret==SPLICE_OUTSIDE || ret==SPLICE_OVERLAP || splice.csq==CSQ_START_LOST )  // not a coding csq
+    {
+        free(splice.kref.s);
+        free(splice.kalt.s);
+
+        if ( !splice.csq ) return 2;        // fully intronic, no csq
+
+        // splice_region/acceptor/donor
+        child->seq  = NULL;
+        child->sbeg = 0;
+        child->rbeg = rec->pos;
+        child->rlen = 0;
+        child->dlen = 0;
+        kputs(rec->d.allele[0],&str);
+        kputc('>',&str);
+        kputs(rec->d.allele[ial],&str);
+        child->var  = str.s;
+        child->type = HAP_SSS;
+        child->csq  = splice.csq;
+        child->rec  = rec;
+        return 0;
+    }
+    if ( splice.csq & CSQ_SYNONYMOUS_VARIANT ) splice.csq &= ~CSQ_SYNONYMOUS_VARIANT;   // synonymous&splice,frame could become synonymous&frame,splice
+
+    int dbeg = 0;
+    if ( splice.ref_beg < cds->beg )
+    {
+        // The vcf record overlaps the exon boundary, but the variant itself
+        // should fit inside since we are here. This will need more work.
+        // #1475227917
+        dbeg = cds->beg - splice.ref_beg;
+        splice.kref.l -= dbeg;
+        splice.ref_beg = cds->beg;
+        assert( dbeg <= splice.kalt.l );
+    }
+
+    assert( parent->type!=HAP_SSS );
+    if ( parent->type==HAP_CDS )    
+    {
+        i = parent->icds;
+        if ( i!=cds->icds )
+        {
+            // the variant is on a new exon, finish up the previous
+            int len = tr->cds[i]->len - parent->rbeg - parent->rlen + tr->cds[i]->beg;
+            if ( len > 0 )
+                kputsn_(tr->ref + N_REF_PAD + parent->rbeg + parent->rlen - tr->beg, len, &str);
+        }
+
+        // append any skipped non-variant exons
+        while ( ++i < cds->icds )
+            kputsn_(tr->ref + N_REF_PAD + tr->cds[i]->beg - tr->beg, tr->cds[i]->len, &str);
+
+        if ( parent->icds==child->icds )
+        {
+            int len = splice.ref_beg - parent->rbeg - parent->rlen;
+            if ( len < 0 )   // overlapping variants
+            {
+                free(str.s);
+                free(splice.kref.s);
+                free(splice.kalt.s);
+                return 1;
+            }
+            kputsn_(tr->ref + N_REF_PAD + parent->rbeg + parent->rlen - tr->beg, len, &str);
+        }
+        else
+            kputsn_(tr->ref + N_REF_PAD + cds->beg - tr->beg, splice.ref_beg - cds->beg, &str);
+    }
+    kputs(splice.kalt.s + dbeg, &str);
+
+    child->seq  = str.s;
+    child->sbeg = cds->pos + (splice.ref_beg - cds->beg);
+    child->rbeg = splice.ref_beg;
+    child->rlen = splice.kref.l;
+    child->type = HAP_CDS;
+    child->prev = parent;
+    child->rec  = rec;
+    child->csq  = splice.csq;
+
+    // set vlen and the "ref>alt" string
+    {
+        int rlen = strlen(rec->d.allele[0]);
+        int alen = strlen(rec->d.allele[ial]);
+        child->dlen = alen - rlen;
+        child->var  = (char*) malloc(rlen+alen+2);
+        memcpy(child->var,rec->d.allele[0],rlen);
+        child->var[rlen] = '>';
+        memcpy(child->var+rlen+1,rec->d.allele[ial],alen);
+        child->var[rlen+alen+1] = 0;
+    }
+
+    // yuck, the whole CDS is modified/deleted, not ready for this, todo.
+    if ( child->rbeg + child->rlen > cds->beg + cds->len )
+    {
+        child->type = HAP_SSS;
+        if ( !child->csq ) child->csq |= CSQ_CODING_SEQUENCE;  // hack, specifically for ENST00000390520/deletion-overlap.vcf
+    }
+
+
+    free(splice.kref.s);
+    free(splice.kalt.s);
+    return 0;
+}
+void hap_destroy(hap_node_t *hap)
+{
+    int i;
+    for (i=0; i<hap->nchild; i++)
+        if ( hap->child[i] ) hap_destroy(hap->child[i]);
+    for (i=0; i<hap->mcsq_list; i++) free(hap->csq_list[i].type.vstr.s);
+    free(hap->csq_list);
+    free(hap->child);
+    free(hap->cur_child);
+    free(hap->seq);
+    free(hap->var);
+    free(hap);
+}
+
+
+/*
+    ref:    spliced reference and its length (ref.l)
+    seq:    part of the spliced query transcript on the reference strand to translate, its 
+                length (seq.l) and the total length of the complete transcript (seq.m)
+    sbeg:   seq offset within the spliced query transcript
+    rbeg:   seq offset within ref, 0-based
+    rend:   last base of seq within ref, plus one. If seq does not contain indels, it is rend=rbeg+seq->l
+    strand: coding strand - 0:rev, 1:fwd
+    tseq:   translated sequence (aa)
+    fill:   frameshift, fill until the end (strand=fwd) or from the start (strand=rev)
+ */
+void cds_translate(kstring_t *_ref, kstring_t *_seq, uint32_t sbeg, uint32_t rbeg, uint32_t rend, int strand, kstring_t *tseq, int fill)
+{
+#if XDBG
+fprintf(bcftools_stderr,"\ntranslate: %d %d %d  fill=%d  seq.l=%d\n",sbeg,rbeg,rend,fill,(int)_seq->l);
+#endif
+    char tmp[3], *codon, *end;
+    int i, len, npad;
+
+    kstring_t ref = *_ref;
+    kstring_t seq = *_seq;
+
+    tseq->l = 0;
+    if ( !seq.l )
+    {
+        kputc('?', tseq);
+        return;
+    }
+
+#define DBG 0
+#if DBG
+ fprintf(bcftools_stderr,"translate: sbeg,rbeg,rend=%d %d %d  fill=%d  seq.l=%d\n",sbeg,rbeg,rend,fill,(int)_seq->l);
+ fprintf(bcftools_stderr,"    ref: l=%d %s\n", (int)ref.l,ref.s);
+ fprintf(bcftools_stderr,"    seq: l=%d m=%d ", (int)seq.l,(int)seq.m);
+ for (i=0; i<seq.l; i++) fprintf(bcftools_stderr,"%c",seq.s[i]); fprintf(bcftools_stderr,"\n");
+ fprintf(bcftools_stderr,"    sbeg,rbeg,rend: %d,%d,%d\n", sbeg,rbeg,rend);
+ fprintf(bcftools_stderr,"    strand,fill: %d,%d\n", strand,fill);
+#endif
+
+    if ( strand==STRAND_FWD )
+    {
+        // left padding
+        npad = sbeg % 3;
+#if DBG>1
+        fprintf(bcftools_stderr,"    npad: %d\n",npad);
+#endif
+        assert( npad<=rbeg );
+
+        for (i=0; i<npad; i++)
+            tmp[i] = ref.s[rbeg+i-npad+N_REF_PAD];
+        for (; i<3 && i-npad<seq.l; i++)
+            tmp[i] = seq.s[i-npad];
+        len = seq.l - i + npad;    // the remaining length of padded sseq
+#if DBG>1
+        fprintf(bcftools_stderr,"\t i=%d\n", i);
+#endif
+        if ( i==3 )
+        {
+            kputc_(dna2aa(tmp), tseq);
+#if DBG>1
+            fprintf(bcftools_stderr,"[1]%c%c%c\n",tmp[0],tmp[1],tmp[2]);
+#endif
+            codon = seq.s + 3 - npad;        // next codon
+            end   = codon + len - 1 - (len % 3);    // last position of a valid codon
+            while ( codon < end )
+            {
+                kputc_(dna2aa(codon), tseq);
+#if DBG>1
+                fprintf(bcftools_stderr,"[2]%c%c%c\n",codon[0],codon[1],codon[2]);
+#endif
+                codon += 3;
+            }
+            end = seq.s + seq.l - 1;
+            for (i=0; codon+i<=end; i++) tmp[i] = codon[i];
+        }
+
+        // right padding
+        codon = ref.s + rend + N_REF_PAD;
+        if ( i>0 )
+        {
+#if DBG>1
+            if(i==1)fprintf(bcftools_stderr,"[3]%c\n",tmp[0]);
+            if(i==2)fprintf(bcftools_stderr,"[3]%c%c\n",tmp[0],tmp[1]);
+#endif
+            for (; i<3; i++)
+            {
+                tmp[i] = *codon;
+                codon++;
+            }
+            kputc_(dna2aa(tmp), tseq);
+#if DBG>1
+            fprintf(bcftools_stderr,"[4]%c%c%c\n",tmp[0],tmp[1],tmp[2]);
+#endif
+        }
+        if ( fill!=0 )
+        {
+            end = ref.s + ref.l - N_REF_PAD;
+            while ( codon+3 <= end )
+            {
+                kputc_(dna2aa(codon), tseq);
+#if DBG>1
+                fprintf(bcftools_stderr,"[5]%c%c%c\t%c\n",codon[0],codon[1],codon[2],dna2aa(codon));
+#endif
+                codon += 3;
+            }
+        }
+    }
+    else    // STRAND_REV
+    {
+        // right padding - number of bases to take from ref
+        npad = (seq.m - (sbeg + seq.l)) % 3; 
+#if DBG>1
+        fprintf(bcftools_stderr,"    npad: %d\n",npad);
+#endif
+        if ( !(npad>=0 && sbeg+seq.l+npad<=seq.m) ) fprintf(bcftools_stderr,"sbeg=%d  seq.l=%d seq.m=%d npad=%d\n",sbeg,(int)seq.l,(int)seq.m,npad);
+        assert( npad>=0 && sbeg+seq.l+npad<=seq.m );  // todo: first codon on the rev strand
+
+        if ( npad==2 )
+        {
+            tmp[1] = ref.s[rend+N_REF_PAD];
+            tmp[2] = ref.s[rend+N_REF_PAD+1];
+            i = 0;
+        }
+        else if ( npad==1 )
+        {
+            tmp[2] = ref.s[rend+N_REF_PAD];
+            i = 1;
+        }
+        else
+            i = 2;
+
+        end = seq.s + seq.l;
+        for (; i>=0 && end>seq.s; i--) tmp[i] = *(--end);
+#if DBG>1
+        fprintf(bcftools_stderr,"\t i=%d\n", i);
+        if(i==1)fprintf(bcftools_stderr,"[0]  %c\n",tmp[2]);
+        if(i==0)fprintf(bcftools_stderr,"[0] %c%c\n",tmp[1],tmp[2]);
+#endif
+        if ( i==-1 )
+        {
+#if DBG>1
+            fprintf(bcftools_stderr,"[1]%c%c%c\t%c\n",tmp[0],tmp[1],tmp[2], cdna2aa(tmp));
+#endif
+            kputc_(cdna2aa(tmp), tseq);
+            codon = end - 3;
+            while ( codon >= seq.s )
+            {
+                kputc_(cdna2aa(codon), tseq);
+#if DBG>1
+                fprintf(bcftools_stderr,"[2]%c%c%c\t%c\n",codon[0],codon[1],codon[2], cdna2aa(codon));
+#endif
+                codon -= 3;
+            }
+            if ( seq.s-codon==2 )
+            {
+                tmp[2] = seq.s[0]; 
+                i = 1;
+            }
+            else if ( seq.s-codon==1 )
+            {
+                tmp[1] = seq.s[0]; 
+                tmp[2] = seq.s[1];
+                i = 0;
+            }
+            else
+                i = -1;
+#if DBG>1
+            if(i==1)fprintf(bcftools_stderr,"[3]   %c\n",tmp[2]);
+            if(i==0)fprintf(bcftools_stderr,"[3] %c%c\n",tmp[1],tmp[2]);
+#endif
+        }
+        // left padding
+        end = ref.s + N_REF_PAD + rbeg;
+        if ( i>=0 )
+        {
+            for (; i>=0 && end>=ref.s; i--) tmp[i] = *(--end);
+            kputc_(cdna2aa(tmp), tseq);
+#if DBG>1
+            fprintf(bcftools_stderr,"[4]%c%c%c\t%c\n",tmp[0],tmp[1],tmp[2],cdna2aa(tmp));
+#endif
+        }
+        if ( fill!=0 )
+        {
+            codon = end - 3;
+            while ( codon >= ref.s + N_REF_PAD )
+            {
+                kputc_(cdna2aa(codon), tseq);
+#if DBG>1
+                fprintf(bcftools_stderr,"[5]%c%c%c\t%c\n",codon[0],codon[1],codon[2],cdna2aa(codon));
+#endif
+                codon -= 3;
+            }
+        }
+    }
+    kputc_(0,tseq); tseq->l--;
+#if DBG
+ fprintf(bcftools_stderr,"    tseq: %s\n", tseq->s);
+#endif
+}
+
+void tscript_splice_ref(tscript_t *tr)
+{
+    int i, len = 0;
+    for (i=0; i<tr->ncds; i++) 
+        len += tr->cds[i]->len;
+
+    tr->nsref = len + 2*N_REF_PAD;
+    tr->sref  = (char*) malloc(len + 1 + 2*N_REF_PAD);
+    len = 0;
+
+    memcpy(tr->sref, tr->ref + tr->cds[0]->beg - tr->beg, N_REF_PAD);
+    len += N_REF_PAD;
+
+    for (i=0; i<tr->ncds; i++)
+    {
+        memcpy(tr->sref + len, tr->ref + N_REF_PAD + tr->cds[i]->beg - tr->beg, tr->cds[i]->len);
+        len += tr->cds[i]->len;
+    }
+    memcpy(tr->sref + len, tr->ref + N_REF_PAD + tr->cds[tr->ncds-1]->beg - tr->beg, N_REF_PAD);
+    len += N_REF_PAD;
+
+    tr->sref[len] = 0;
+}
+
+// returns: 0 if consequence was added, 1 if it already exists or could not be added
+int csq_push(args_t *args, csq_t *csq, bcf1_t *rec)
+{
+#if XDBG
+fprintf(bcftools_stderr,"csq_push: %d .. %d\n",rec->pos+1,csq->type.type);
+#endif
+    khint_t k = kh_get(pos2vbuf, args->pos2vbuf, (int)csq->pos);
+    vbuf_t *vbuf = (k == kh_end(args->pos2vbuf)) ? NULL : kh_val(args->pos2vbuf, k);
+    if ( !vbuf ) error("This should not happen. %s:%d  %s\n",bcf_seqname(args->hdr,rec),csq->pos+1,csq->type.vstr.s);
+
+    int i;
+    for (i=0; i<vbuf->n; i++)
+        if ( vbuf->vrec[i]->line==rec ) break;
+    if ( i==vbuf->n ) error("This should not happen.. %s:%d  %s\n", bcf_seqname(args->hdr,rec),csq->pos+1,csq->type.vstr.s);
+    vrec_t *vrec = vbuf->vrec[i];
+
+    // if the variant overlaps donor/acceptor and also splice region, report only donor/acceptor
+    if ( csq->type.type & CSQ_SPLICE_REGION && csq->type.type & (CSQ_SPLICE_DONOR|CSQ_SPLICE_ACCEPTOR) ) 
+        csq->type.type &= ~CSQ_SPLICE_REGION;
+
+    if ( csq->type.type & CSQ_PRINTED_UPSTREAM )
+    {
+        for (i=0; i<vrec->nvcsq; i++)
+        {
+            // Same as below, to avoid records like
+            //      3630 .. @3632,stop_lost|AL627309.1|ENST00000423372|protein_coding|-
+            //      3632 .. stop_lost|AL627309.1|ENST00000423372|protein_coding|-|260*>260G|3630T>A+3632A>C
+            if ( csq->type.type&CSQ_START_STOP && vrec->vcsq[i].type&CSQ_START_STOP )
+            {
+                vrec->vcsq[i] = csq->type;
+                goto exit_duplicate;
+            }
+            if ( !(vrec->vcsq[i].type & CSQ_PRINTED_UPSTREAM) ) continue;
+            if ( csq->type.ref != vrec->vcsq[i].ref ) continue;
+            goto exit_duplicate;
+        }
+    }
+    else if ( csq->type.type & CSQ_COMPOUND )
+    {
+        for (i=0; i<vrec->nvcsq; i++)
+        {
+            if ( csq->type.trid != vrec->vcsq[i].trid && (csq->type.type|vrec->vcsq[i].type)&CSQ_PRN_TSCRIPT ) continue;
+            if ( csq->type.biotype != vrec->vcsq[i].biotype ) continue;
+            if ( csq->type.gene != vrec->vcsq[i].gene ) continue;
+            if ( csq->type.vcf_ial != vrec->vcsq[i].vcf_ial ) continue;
+            if ( (csq->type.type&CSQ_UPSTREAM_STOP)^(vrec->vcsq[i].type&CSQ_UPSTREAM_STOP) ) continue;  // both must or mustn't have upstream_stop
+            if ( csq->type.vstr.s || vrec->vcsq[i].vstr.s ) 
+            {
+                // This is a bit hacky, but we want a simpler and more predictable output. The splice_csq() function
+                // can trigger stop/start events based on indel overlap, then another stop/start event can be triggered
+                // from add_csq() or test_cds_local() based on sequence comparison, and on output we could find two
+                // consequences:
+                //      stop_lost|AL627309.1|ENST00000423372|protein_coding|-
+                //      stop_lost&inframe_insertion|AL627309.1|ENST00000423372|protein_coding|-|260*>260CL|3630T>TAAA
+                if ( !csq->type.vstr.s || !vrec->vcsq[i].vstr.s ) 
+                {
+                    if ( csq->type.type&CSQ_START_STOP && vrec->vcsq[i].type&CSQ_START_STOP )
+                    {
+                        vrec->vcsq[i].type |= csq->type.type;
+
+                        // remove stop_lost&synonymous if stop_retained set
+                        if ( vrec->vcsq[i].type&CSQ_STOP_RETAINED ) 
+                            vrec->vcsq[i].type &= ~(CSQ_STOP_LOST|CSQ_SYNONYMOUS_VARIANT);
+
+                        if ( !vrec->vcsq[i].vstr.s ) vrec->vcsq[i].vstr = csq->type.vstr;
+                        goto exit_duplicate;
+                    }
+                    continue;
+                }
+                if ( strcmp(csq->type.vstr.s,vrec->vcsq[i].vstr.s) ) continue;
+            }
+            vrec->vcsq[i].type |= csq->type.type; 
+            goto exit_duplicate;
+        }
+    }
+    else
+    {
+        for (i=0; i<vrec->nvcsq; i++)
+        {
+            if ( csq->type.trid != vrec->vcsq[i].trid && (csq->type.type|vrec->vcsq[i].type)&CSQ_PRN_TSCRIPT) continue;
+            if ( csq->type.biotype != vrec->vcsq[i].biotype ) continue;
+            if ( !(vrec->vcsq[i].type & CSQ_COMPOUND) ) 
+            {
+                vrec->vcsq[i].type |= csq->type.type;
+                goto exit_duplicate;
+            }
+            if ( vrec->vcsq[i].type==(vrec->vcsq[i].type|csq->type.type) ) goto exit_duplicate;
+        }
+    }
+    // no such csq yet in this vcf record
+    csq->vrec = vrec;
+    csq->idx  = vrec->nvcsq++;
+    hts_expand0(vcsq_t, vrec->nvcsq, vrec->mvcsq, vrec->vcsq);
+    vrec->vcsq[i] = csq->type;
+    return 0;
+
+exit_duplicate:
+    csq->vrec = vrec;
+    csq->idx  = i;
+    return 1;
+}
+
+//  soff .. position of the variant within the trimmed query transcript
+//  sbeg .. position of the variant within the query transcript
+//  rbeg .. position on the reference transcript (if there are no indels, then rbeg=send)
+//  rpos .. VCF position
+#define node2soff(i) (hap->stack[i].slen - (hap->stack[i].node->rlen + hap->stack[i].node->dlen))
+#define node2sbeg(i) (hap->sbeg + node2soff(i))
+#define node2send(i) (hap->sbeg + hap->stack[i].slen)
+#define node2rbeg(i) (hap->stack[i].node->sbeg)
+#define node2rend(i) (hap->stack[i].node->sbeg + hap->stack[i].node->rlen)
+#define node2rpos(i) (hap->stack[i].node->rec->pos)
+
+void kput_vcsq(args_t *args, vcsq_t *csq, kstring_t *str)
+{
+    // Remove start/stop from incomplete CDS, but only if there is another
+    // consequence as something must be reported
+    if ( csq->type & CSQ_INCOMPLETE_CDS && (csq->type & ~(CSQ_START_STOP|CSQ_INCOMPLETE_CDS|CSQ_UPSTREAM_STOP)) ) csq->type &= ~(CSQ_START_STOP|CSQ_INCOMPLETE_CDS);
+
+    // Remove missense from start/stops
+    if ( csq->type & CSQ_START_STOP && csq->type & CSQ_MISSENSE_VARIANT ) csq->type &= ~CSQ_MISSENSE_VARIANT;
+
+    if ( csq->type & CSQ_PRINTED_UPSTREAM && csq->ref )
+    {
+        kputc_('@',str);
+        kputw(csq->ref->pos+1, str);
+        return;
+    }
+    if ( csq->type & CSQ_UPSTREAM_STOP )
+        kputc_('*',str);
+
+    int i, n = sizeof(csq_strings)/sizeof(char*);
+    for (i=1; i<n; i++)
+        if ( csq_strings[i] && csq->type&(1<<i) ) { kputs(csq_strings[i],str); break; }
+    i++;
+    for (; i<n; i++)
+        if ( csq_strings[i] && csq->type&(1<<i) ) { kputc_('&',str); kputs(csq_strings[i],str); }
+
+    kputc_('|', str);
+    if ( csq->gene ) kputs(csq->gene , str);
+
+    kputc_('|', str);
+    if ( csq->type & CSQ_PRN_TSCRIPT ) kputs(args->tscript_ids.str[csq->trid], str);
+
+    kputc_('|', str);
+    kputs(gf_type2gff_string(csq->biotype), str);
+
+    if ( CSQ_PRN_STRAND(csq->type) || csq->vstr.l )
+        kputs(csq->strand==STRAND_FWD ? "|+" : "|-", str);
+
+    if ( csq->vstr.l )
+        kputs(csq->vstr.s, str);
+}
+
+void kprint_aa_prediction(args_t *args, int beg, kstring_t *aa, kstring_t *str)
+{
+    if ( !args->brief_predictions || (int)aa->l - args->brief_predictions < 3 )
+        kputs(aa->s, str);
+    else
+    {
+        int i, len = aa->l;
+        if ( aa->s[len-1]=='*' ) len--;
+        for (i=0; i<len && i<args->brief_predictions; i++) kputc(aa->s[i], str);
+        kputs("..", str);
+        kputw(beg+len, str);
+    }
+}
+
+void hap_add_csq(args_t *args, hap_t *hap, hap_node_t *node, int tlen, int ibeg, int iend, int dlen, int indel)
+{
+    int i;
+    tscript_t *tr = hap->tr;
+    int ref_node = tr->strand==STRAND_FWD ? ibeg : iend;
+    int icsq = node->ncsq_list++;
+    hts_expand0(csq_t,node->ncsq_list,node->mcsq_list,node->csq_list);
+    csq_t *csq = &node->csq_list[icsq];
+    csq->pos  = hap->stack[ref_node].node->rec->pos;
+    csq->type.trid    = tr->id;
+    csq->type.vcf_ial = node->vcf_ial;
+    csq->type.gene    = tr->gene->name;
+    csq->type.strand  = tr->strand;
+    csq->type.biotype = tr->type;
+
+    // only now we see the translated sequence and can determine if the stop/start changes are real
+    int rm_csq = 0; 
+    csq->type.type = 0;
+    for (i=ibeg; i<=iend; i++)
+        csq->type.type |= hap->stack[i].node->csq & CSQ_COMPOUND;
+    if ( dlen==0 && indel ) csq->type.type |= CSQ_INFRAME_ALTERING;
+
+    int has_upstream_stop = hap->upstream_stop;
+    if ( hap->stack[ibeg].node->type != HAP_SSS )
+    {
+        // check for truncating stops
+        for (i=0; i<hap->tref.l; i++)
+            if ( hap->tref.s[i]=='*' ) break;
+        if ( i!=hap->tref.l )
+        {
+            hap->tref.l = i+1;
+            hap->tref.s[i+1] = 0;
+        }
+        for (i=0; i<hap->tseq.l; i++)
+            if ( hap->tseq.s[i]=='*' ) break;
+        if ( i!=hap->tseq.l )
+        {
+            hap->tseq.l = i+1;
+            hap->tseq.s[i+1] = 0;
+            hap->upstream_stop = 1;
+        }
+        if ( csq->type.type & CSQ_STOP_LOST )
+        {
+            if ( hap->tref.s[hap->tref.l-1]=='*' && hap->tref.s[hap->tref.l-1] == hap->tseq.s[hap->tseq.l-1] ) 
+            {
+                rm_csq |= CSQ_STOP_LOST;
+                csq->type.type |= CSQ_STOP_RETAINED;
+            }
+            else if ( hap->tref.s[hap->tref.l-1]!='*' )
+            {
+                // This is CDS 3' incomplete ENSG00000173376/synon.vcf, can also be missense
+                // We observe in real data a change to a stop, ENST00000528237/retained-stop-incomplete-cds.vcf
+                if ( hap->tseq.s[hap->tseq.l-1] == '*' )
+                {
+                    rm_csq |= CSQ_STOP_GAINED;
+                    csq->type.type |= CSQ_STOP_RETAINED;
+                }
+                else
+                    csq->type.type |= CSQ_INCOMPLETE_CDS;
+            }
+        }
+        if ( csq->type.type & CSQ_START_LOST && hap->tref.s[0]!='M' )
+        {
+            rm_csq |= CSQ_START_LOST;
+            csq->type.type &= ~CSQ_START_LOST;
+        }
+        if ( dlen!=0 )
+        {
+            if ( dlen%3 )
+                csq->type.type |= CSQ_FRAMESHIFT_VARIANT;
+            else if ( dlen<0 )
+                csq->type.type |= CSQ_INFRAME_DELETION;
+            else
+                csq->type.type |= CSQ_INFRAME_INSERTION;
+            if ( hap->tref.s[hap->tref.l-1]!='*' && hap->tseq.s[hap->tseq.l-1]=='*' )
+                csq->type.type |= CSQ_STOP_GAINED;
+        }
+        else
+        {
+            for (i=0; i<hap->tref.l; i++) 
+                if ( hap->tref.s[i] != hap->tseq.s[i] ) break;
+            if ( i==hap->tref.l )
+                csq->type.type |= CSQ_SYNONYMOUS_VARIANT;
+            else if ( hap->tref.s[i] ==  '*' )
+                csq->type.type |= CSQ_STOP_LOST;
+            else if ( hap->tseq.s[i] ==  '*' )
+                csq->type.type |= CSQ_STOP_GAINED;
+            else
+                csq->type.type |= CSQ_MISSENSE_VARIANT;
+        }
+    }
+    // Check if compound inframe variants are real inframes, or if the stop codon occurs before the frameshift can be restored
+    if ( ibeg!=iend && (csq->type.type & (CSQ_INFRAME_DELETION|CSQ_INFRAME_INSERTION|CSQ_INFRAME_ALTERING)) && hap->tseq.s[hap->tseq.l-1]=='*' )
+    {
+        rm_csq |= CSQ_INFRAME_DELETION | CSQ_INFRAME_INSERTION | CSQ_INFRAME_ALTERING;
+        csq->type.type |= CSQ_FRAMESHIFT_VARIANT | CSQ_STOP_GAINED;
+    }
+    if ( has_upstream_stop ) csq->type.type |= CSQ_UPSTREAM_STOP;
+    csq->type.type &= ~rm_csq;
+
+    if ( hap->stack[ibeg].node->type == HAP_SSS  )
+    {
+        node->csq_list[icsq].type.type   |= hap->stack[ibeg].node->csq & ~rm_csq;
+        node->csq_list[icsq].type.ref     = hap->stack[ibeg].node->rec;
+        node->csq_list[icsq].type.biotype = tr->type;
+        csq_push(args, node->csq_list+icsq, hap->stack[ibeg].node->rec);
+        return;
+    }
+
+    kstring_t str = node->csq_list[icsq].type.vstr;
+    str.l = 0;
+
+    // create the aa variant string
+    int aa_rbeg = tr->strand==STRAND_FWD ? node2rbeg(ibeg)/3+1 : (hap->tr->nsref - 2*N_REF_PAD - node2rend(iend))/3+1;
+    int aa_sbeg = tr->strand==STRAND_FWD ? node2sbeg(ibeg)/3+1 : (tlen - node2send(iend))/3+1;
+    kputc_('|', &str);
+    kputw(aa_rbeg, &str);
+    kprint_aa_prediction(args,aa_rbeg,&hap->tref,&str);
+    if ( !(csq->type.type & CSQ_SYNONYMOUS_VARIANT) )
+    {
+        kputc_('>', &str);
+        kputw(aa_sbeg, &str);
+        kprint_aa_prediction(args,aa_sbeg,&hap->tseq,&str);
+    }
+    kputc_('|', &str);
+
+    // create the dna variant string and, in case of combined variants,
+    // insert silent CSQ_PRINTED_UPSTREAM variants
+    for (i=ibeg; i<=iend; i++)
+    {
+        if ( i>ibeg ) kputc_('+', &str);
+        kputw(node2rpos(i)+1, &str);
+        kputs(hap->stack[i].node->var, &str);
+    }
+    node->csq_list[icsq].type.vstr = str;
+    csq_push(args, node->csq_list+icsq, hap->stack[ref_node].node->rec);
+
+    for (i=ibeg; i<=iend; i++)
+    {
+        // csq are printed at one position only for combined variants, the rest is
+        // silent and references the first
+        if ( hap->stack[i].node->csq & ~CSQ_COMPOUND )
+        {
+            node->ncsq_list++;
+            hts_expand0(csq_t,node->ncsq_list,node->mcsq_list,node->csq_list);
+            csq_t *tmp_csq = &node->csq_list[node->ncsq_list - 1];
+            tmp_csq->pos  = hap->stack[i].node->rec->pos;
+            tmp_csq->type.trid    = tr->id;
+            //??tmp_csq->type.vcf_ial = node->vcf_ial;  .. this should not be needed for non-compound variants
+            tmp_csq->type.gene    = tr->gene->name;
+            tmp_csq->type.strand  = tr->strand;
+            tmp_csq->type.type    = hap->stack[i].node->csq & ~CSQ_COMPOUND & ~rm_csq;
+            tmp_csq->type.biotype = tr->type;
+            tmp_csq->type.vstr.l  = 0;
+            kputs(str.s,&tmp_csq->type.vstr);
+            csq_push(args, tmp_csq, hap->stack[i].node->rec);
+        }
+        if ( i!=ref_node && (node->csq_list[icsq].type.type & CSQ_COMPOUND || !(hap->stack[i].node->csq & ~CSQ_COMPOUND)) )
+        {
+            node->ncsq_list++;
+            hts_expand0(csq_t,node->ncsq_list,node->mcsq_list,node->csq_list);
+            csq_t *tmp_csq = &node->csq_list[node->ncsq_list - 1];
+            tmp_csq->pos  = hap->stack[i].node->rec->pos;
+            tmp_csq->type.trid    = tr->id;
+            //??tmp_csq->type.vcf_ial = node->vcf_ial;  .. this should not be needed for non-compound variants
+            tmp_csq->type.gene    = tr->gene->name;
+            tmp_csq->type.strand  = tr->strand;
+            tmp_csq->type.type    = CSQ_PRINTED_UPSTREAM | hap->stack[i].node->csq;
+            tmp_csq->type.biotype = tr->type;
+            tmp_csq->type.ref     = hap->stack[ref_node].node->rec;
+            tmp_csq->type.vstr.l  = 0;
+            csq_push(args, tmp_csq, hap->stack[i].node->rec);
+        }
+    }
+}
+
+
+void hap_finalize(args_t *args, hap_t *hap)
+{
+    tscript_t *tr = hap->tr;
+    if ( !tr->sref )
+        tscript_splice_ref(tr);
+
+    kstring_t sref;
+    sref.s = tr->sref;
+    sref.l = tr->nsref;
+    sref.m = sref.l;
+
+    int istack = 0;
+    hts_expand(hstack_t,1,hap->mstack,hap->stack);
+
+    hap->sseq.l = 0;
+    hap->tseq.l = 0;
+    hap->stack[0].node = tr->root;
+    hap->stack[0].ichild = -1;
+    hap->stack[0].slen = 0;
+    hap->stack[0].dlen = 0;
+
+    while ( istack>=0 )
+    {
+        hstack_t *stack  = &hap->stack[istack];
+        hap_node_t *node = hap->stack[istack].node;
+        while ( ++hap->stack[istack].ichild < node->nchild )
+        {
+            if ( node->child[stack->ichild] ) break;
+        }
+        if ( stack->ichild == node->nchild ) { istack--; continue; }
+
+        node = node->child[stack->ichild];
+
+        istack++;
+        hts_expand(hstack_t,istack+1,hap->mstack,hap->stack);
+        stack = &hap->stack[istack-1];
+
+        hap->stack[istack].node = node;
+        hap->stack[istack].ichild = -1;
+
+        hap->sseq.l = stack->slen;
+        if ( node->type==HAP_CDS ) kputs(node->seq, &hap->sseq);
+        hap->stack[istack].slen = hap->sseq.l;
+        hap->stack[istack].dlen = hap->stack[istack-1].dlen + node->dlen;
+
+        if ( !node->nend ) continue;    // not a leaf node
+
+        // The spliced sequence has been built for the current haplotype and stored
+        // in hap->sseq. Now we break it and output as independent parts
+        
+        kstring_t sseq;
+        sseq.m = sref.m - 2*N_REF_PAD + hap->stack[istack].dlen;  // total length of the spliced query transcript
+        hap->upstream_stop = 0;
+
+        int i = 1, dlen = 0, ibeg, indel = 0;
+        hap->sbeg = hap->stack[i].node->sbeg;
+        assert( hap->stack[istack].node->type != HAP_SSS );
+        if ( tr->strand==STRAND_FWD )
+        {
+            i = 0, ibeg = -1;
+            while ( ++i <= istack )
+            {
+                assert( hap->stack[i].node->type != HAP_SSS );
+
+                dlen += hap->stack[i].node->dlen;
+                if ( hap->stack[i].node->dlen ) indel = 1;
+
+                // This condition extends compound variants.
+                if ( i<istack )
+                {
+                    if ( dlen%3 )   // frameshift
+                    {
+                        if ( ibeg==-1 ) ibeg = i;
+                        continue;
+                    }
+                    // the last base of the current variant vs the first base of the next
+                    // variant: are they in the same codon? (forward strand)
+                    int icur  = node2sbeg(i);
+                    int inext = node2sbeg(i+1);
+                    if ( hap->stack[i].node->dlen > 0 ) icur += hap->stack[i].node->dlen;
+                    else if ( hap->stack[i].node->dlen < 0 ) icur++;
+                    if ( icur/3 == inext/3 )    // in the same codon, can't be flushed yet
+                    {
+                        if ( ibeg==-1 ) ibeg = i;
+                        continue;
+                    }
+                }
+                if ( ibeg<0 ) ibeg = i;
+
+                int ioff = node2soff(ibeg);
+                int icur = node2sbeg(ibeg);
+                int rbeg = node2rbeg(ibeg);
+                int rend = node2rend(i);
+                int fill = dlen%3;
+
+                // alt
+                if ( hap->sseq.l )
+                {
+                    sseq.l = hap->stack[i].slen - ioff;
+                    sseq.s = hap->sseq.s + ioff;
+                }
+                else    // splice site overlap, see #1475227917
+                    sseq.l = fill = 0;
+                cds_translate(&sref, &sseq, icur,rbeg,rend, tr->strand, &hap->tseq, fill);
+
+                // ref
+                sseq.l = node2rend(i) - rbeg;
+                sseq.s = sref.s + N_REF_PAD + rbeg;
+                sseq.m = sref.m - 2*N_REF_PAD;
+                cds_translate(&sref, &sseq, rbeg,rbeg,rend, tr->strand, &hap->tref, fill);
+                sseq.m = sref.m - 2*N_REF_PAD + hap->stack[istack].dlen;
+
+                hap_add_csq(args,hap,node,0, ibeg,i,dlen,indel);
+                ibeg = -1;
+                dlen = 0;
+                indel = 0;
+            }
+        }
+        else
+        {
+            i = istack + 1, ibeg = -1;
+            while ( --i > 0 )
+            {
+                assert ( hap->stack[i].node->type != HAP_SSS );
+                dlen += hap->stack[i].node->dlen;
+                if ( hap->stack[i].node->dlen ) indel = 1;
+                if ( i>1 )
+                {
+                    if ( dlen%3 )
+                    {
+                        if ( ibeg==-1 ) ibeg = i;
+                        continue;
+                    }
+                    // the last base of the current variant vs the first base of the next
+                    // variant: are they in the same codon? (reverse strand)
+                    int icur  = sseq.m - 1 - node2sbeg(i);
+                    int inext = sseq.m - 1 - node2sbeg(i-1);
+                    if ( hap->stack[i].node->dlen > 0 ) icur += hap->stack[i].node->dlen - 1;
+                    else if ( hap->stack[i].node->dlen < 0 ) icur -= hap->stack[i].node->dlen;
+                    if ( hap->stack[i-1].node->dlen > 0 ) inext -= hap->stack[i-1].node->dlen;
+                    if ( icur/3 == inext/3 )
+                    {
+                        if ( ibeg==-1 ) ibeg = i;
+                        continue;
+                    }
+                }
+                if ( ibeg<0 ) ibeg = i;
+                int ioff = node2soff(i);
+                int icur = node2sbeg(i);
+                int rbeg = node2rbeg(i);
+                int rend = node2rend(ibeg);
+                int fill = dlen%3;
+
+                // alt
+                if ( hap->sseq.l )
+                {
+                    sseq.l = hap->stack[ibeg].slen - ioff;
+                    sseq.s = hap->sseq.s + ioff;
+                }
+                else    // splice site overlap, see #1475227917
+                    sseq.l = fill = 0;
+                cds_translate(&sref, &sseq, icur,rbeg,rend, tr->strand, &hap->tseq, fill);
+
+                // ref
+                sseq.l = node2rend(ibeg) - rbeg;
+                sseq.s = sref.s + N_REF_PAD + rbeg;
+                sseq.m = sref.m - 2*N_REF_PAD;
+                cds_translate(&sref, &sseq, rbeg,rbeg,rend, tr->strand, &hap->tref, fill);
+                sseq.m = sref.m - 2*N_REF_PAD + hap->stack[istack].dlen;
+
+                hap_add_csq(args,hap,node,sseq.m, i,ibeg,dlen,indel);
+                ibeg = -1;
+                dlen = 0;
+                indel = 0;
+            }
+        }
+    }
+}
+
+static inline void csq_print_text(args_t *args, csq_t *csq, int ismpl, int ihap)
+{
+    if ( csq->type.type & CSQ_PRINTED_UPSTREAM ) return;
+
+    char *smpl = ismpl >= 0 ? args->hdr->samples[ismpl] : "-";
+    const char *chr = bcf_hdr_id2name(args->hdr,args->rid);
+
+    fprintf(args->out,"CSQ\t%s\t", smpl);
+    if ( ihap>0 )
+        fprintf(args->out,"%d", ihap);
+    else
+        fprintf(args->out,"-");
+
+    args->str.l = 0;
+    kput_vcsq(args, &csq->type, &args->str);
+    fprintf(args->out,"\t%s\t%d\t%s\n",chr,csq->pos+1,args->str.s);
+}
+static inline void hap_print_text(args_t *args, tscript_t *tr, int ismpl, int ihap, hap_node_t *node)
+{
+    if ( !node || !node->ncsq_list ) return;
+
+    char *smpl = ismpl >= 0 ? args->hdr->samples[ismpl] : "-";
+    const char *chr = bcf_hdr_id2name(args->hdr,args->rid);
+
+    int i;
+    for (i=0; i<node->ncsq_list; i++)
+    {
+        csq_t *csq = node->csq_list + i;
+        if ( csq->type.type & CSQ_PRINTED_UPSTREAM ) continue;
+        assert( csq->type.vstr.l );
+
+        fprintf(args->out,"CSQ\t%s\t", smpl);
+        if ( ihap>0 )
+            fprintf(args->out,"%d", ihap);
+        else
+            fprintf(args->out,"-");
+
+        args->str.l = 0;
+        kput_vcsq(args, &csq->type, &args->str);
+        fprintf(args->out,"\t%s\t%d\t%s\n",chr,csq->pos+1,args->str.s);
+    }
+}
+
+static inline void hap_stage_vcf(args_t *args, tscript_t *tr, int ismpl, int ihap, hap_node_t *node)
+{
+    if ( !node || !node->ncsq_list || ismpl<0 ) return;
+
+    int i;
+    for (i=0; i<node->ncsq_list; i++)
+    {
+        csq_t *csq = node->csq_list + i;
+        vrec_t *vrec = csq->vrec;
+        int icsq2 = 2*csq->idx + ihap;
+        if ( icsq2 >= args->ncsq2_max ) // more than ncsq2_max consequences, so can't fit it in FMT
+        {
+            if ( args->verbosity && (!args->ncsq2_small_warned || args->verbosity > 1) )
+            {
+                fprintf(bcftools_stderr,
+                    "Warning: Too many consequences for sample %s at %s:%"PRId64", keeping the first %d and skipping the rest.\n",
+                    args->hdr->samples[ismpl],bcf_hdr_id2name(args->hdr,args->rid),(int64_t) vrec->line->pos+1,csq->idx);
+                if ( !args->ncsq2_small_warned )
+                    fprintf(bcftools_stderr,"         The limit can be increased by setting the --ncsq parameter. This warning is printed only once.\n");
+            }
+            if ( args->ncsq2_small_warned < icsq2 ) args->ncsq2_small_warned = icsq2;
+            break;
+        }
+        int ival, ibit;
+        icsq2_to_bit(icsq2, &ival,&ibit);
+        if ( vrec->nfmt < 1 + ival ) vrec->nfmt = 1 + ival;
+        vrec->fmt_bm[ismpl*args->nfmt_bcsq + ival] |= 1 << ibit;
+    }
+}
+
+void hap_flush(args_t *args, uint32_t pos)
+{
+    int i,j;
+    tr_heap_t *heap = args->active_tr;
+    while ( heap->ndat && heap->dat[0]->end<=pos )
+    {
+        tscript_t *tr = heap->dat[0];
+        khp_delete(trhp, heap);
+        args->hap->tr = tr;
+        if ( tr->root && tr->root->nchild ) // normal, non-localized calling
+        {
+            hap_finalize(args, args->hap);
+
+            if ( args->output_type==FT_TAB_TEXT )   // plain text output, not a vcf
+            {
+                if ( args->phase==PHASE_DROP_GT )
+                    hap_print_text(args, tr, -1,0, tr->hap[0]);
+                else
+                {
+                    for (i=0; i<args->smpl->n; i++)
+                    {
+                        for (j=0; j<2; j++)
+                            hap_print_text(args, tr, args->smpl->idx[i],j+1, tr->hap[i*2+j]);
+                    }
+                }
+            }
+            else if ( args->phase!=PHASE_DROP_GT )
+            {
+                for (i=0; i<args->smpl->n; i++)
+                {
+                    for (j=0; j<2; j++)
+                        hap_stage_vcf(args, tr, args->smpl->idx[i],j, tr->hap[i*2+j]);
+                }
+            }
+        }
+
+        // mark the transcript for deletion. Cannot delete it immediately because
+        // by-position VCF output will need them when flushed by vcf_buf_push
+        args->nrm_tr++;
+        hts_expand(tscript_t*,args->nrm_tr,args->mrm_tr,args->rm_tr);
+        args->rm_tr[args->nrm_tr-1] = tr;
+    }
+}
+
+#define SWAP(type_t, a, b) { type_t t = a; a = b; b = t; }
+
+vbuf_t *vbuf_push(args_t *args, bcf1_t **rec_ptr)
+{
+    int i;
+
+    assert(rec_ptr);
+    bcf1_t *rec = *rec_ptr;
+
+    // check for duplicate records
+    i = args->vcf_rbuf.n ? rbuf_last(&args->vcf_rbuf) : -1;
+    if ( i<0 || args->vcf_buf[i]->vrec[0]->line->pos!=rec->pos ) 
+    {
+        // vcf record with a new pos
+        rbuf_expand0(&args->vcf_rbuf, vbuf_t*, args->vcf_rbuf.n+1, args->vcf_buf);
+        i = rbuf_append(&args->vcf_rbuf);
+        if ( !args->vcf_buf[i] ) args->vcf_buf[i] = (vbuf_t*) calloc(1,sizeof(vbuf_t));
+        args->vcf_buf[i]->n = 0;
+        args->vcf_buf[i]->keep_until = 0;
+    }
+    vbuf_t *vbuf = args->vcf_buf[i];
+    vbuf->n++;
+    hts_expand0(vrec_t*, vbuf->n, vbuf->m, vbuf->vrec);
+    if ( !vbuf->vrec[vbuf->n - 1] )
+        vbuf->vrec[vbuf->n - 1] = (vrec_t*) calloc(1,sizeof(vrec_t));
+
+    vrec_t *vrec = vbuf->vrec[vbuf->n - 1];
+    if ( args->phase!=PHASE_DROP_GT && args->smpl->n )
+    {
+        if ( !vrec->fmt_bm ) vrec->fmt_bm = (uint32_t*) calloc(args->hdr_nsmpl,sizeof(*vrec->fmt_bm) * args->nfmt_bcsq);
+        else memset(vrec->fmt_bm,0,args->hdr_nsmpl*sizeof(*vrec->fmt_bm) * args->nfmt_bcsq);
+    }
+    if ( !vrec->line ) vrec->line = bcf_init1();
+    SWAP(bcf1_t*, (*rec_ptr), vrec->line);
+
+    int ret;
+    khint_t k = kh_put(pos2vbuf, args->pos2vbuf, (int)rec->pos, &ret);
+    kh_val(args->pos2vbuf,k) = vbuf;
+
+    return vbuf;
+}
+
+void vbuf_flush(args_t *args, uint32_t pos)
+{
+    int i,j;
+    while ( args->vcf_rbuf.n )
+    {
+        vbuf_t *vbuf;
+        if ( !args->local_csq && args->active_tr->ndat )
+        {
+            // check if the first active transcript starts beyond the first buffered VCF record,
+            // cannot output buffered VCF lines (args.vbuf) until the active transcripts are gone
+            vbuf = args->vcf_buf[ args->vcf_rbuf.f ];
+            if ( vbuf->keep_until > pos ) break;
+            assert( vbuf->n );
+        }
+
+        i = rbuf_shift(&args->vcf_rbuf);
+        assert( i>=0 );
+        vbuf = args->vcf_buf[i];
+        int pos = vbuf->n ? vbuf->vrec[0]->line->pos : -1;
+        for (i=0; i<vbuf->n; i++)
+        {
+            vrec_t *vrec = vbuf->vrec[i];
+            if ( !args->out_fh ) // not a VCF output
+            {
+                vrec->nvcsq = 0;
+                continue;
+            }
+            if ( !vrec->nvcsq )
+            {
+                if ( bcf_write(args->out_fh, args->hdr, vrec->line)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->output_fname?args->output_fname:"standard output");
+                int save_pos = vrec->line->pos;
+                bcf_empty(vrec->line);
+                vrec->line->pos = save_pos;  // this is necessary for compound variants
+                continue;
+            }
+            
+            args->str.l = 0;
+            kput_vcsq(args, &vrec->vcsq[0], &args->str);
+            for (j=1; j<vrec->nvcsq; j++)
+            {
+                kputc_(',', &args->str);
+                kput_vcsq(args, &vrec->vcsq[j], &args->str);
+            }
+            bcf_update_info_string(args->hdr, vrec->line, args->bcsq_tag, args->str.s);
+            if ( args->hdr_nsmpl )
+            {
+                if ( vrec->nfmt < args->nfmt_bcsq )
+                    for (j=1; j<args->hdr_nsmpl; j++)
+                        memmove(&vrec->fmt_bm[j*vrec->nfmt], &vrec->fmt_bm[j*args->nfmt_bcsq], vrec->nfmt*sizeof(*vrec->fmt_bm));
+                bcf_update_format_int32(args->hdr, vrec->line, args->bcsq_tag, vrec->fmt_bm, args->hdr_nsmpl*vrec->nfmt);
+            }
+            vrec->nvcsq = 0;
+            if ( bcf_write(args->out_fh, args->hdr, vrec->line)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->output_fname?args->output_fname:"standard output");
+            int save_pos = vrec->line->pos;
+            bcf_empty(vrec->line);
+            vrec->line->pos = save_pos;
+        }
+        if ( pos!=-1 )
+        {
+            khint_t k = kh_get(pos2vbuf, args->pos2vbuf, pos);
+            if ( k != kh_end(args->pos2vbuf) ) kh_del(pos2vbuf, args->pos2vbuf, k);
+        }
+        vbuf->n = 0;
+    }
+    if ( args->active_tr->ndat ) return;
+
+    for (i=0; i<args->nrm_tr; i++)
+    {
+        tscript_t *tr = args->rm_tr[i];
+        if ( tr->root ) hap_destroy(tr->root);
+        tr->root = NULL;
+        free(tr->hap);
+        free(tr->ref);
+        free(tr->sref);
+    }
+    args->nrm_tr = 0;
+    args->ncsq_buf = 0;
+}
+
+void tscript_init_ref(args_t *args, tscript_t *tr, const char *chr)
+{
+    int i, len;
+    int pad_beg = tr->beg >= N_REF_PAD ? N_REF_PAD : tr->beg;
+
+    tr->ref = faidx_fetch_seq(args->fai, chr, tr->beg - pad_beg, tr->end + N_REF_PAD, &len);
+    if ( !tr->ref )
+        error("faidx_fetch_seq failed %s:%d-%d\n", chr,tr->beg+1,tr->end+1);
+
+    int pad_end = len - (tr->end - tr->beg + 1 + pad_beg);
+    if ( pad_beg + pad_end != 2*N_REF_PAD )
+    {
+        char *ref = (char*) malloc(tr->end - tr->beg + 1 + 2*N_REF_PAD + 1);
+        for (i=0; i < N_REF_PAD - pad_beg; i++) ref[i] = 'N';
+        memcpy(ref+i, tr->ref, len);
+        len += i;
+        for (i=0; i < N_REF_PAD - pad_end; i++) ref[i+len] = 'N';
+        ref[i+len] = 0;
+        free(tr->ref);
+        tr->ref = ref;
+    }
+}
+
+static void sanity_check_ref(args_t *args, tscript_t *tr, bcf1_t *rec)
+{
+    int vbeg = 0;
+    int rbeg = rec->pos - tr->beg + N_REF_PAD;
+    if ( rbeg < 0 ) { vbeg += abs(rbeg); rbeg = 0; }
+    char *ref = tr->ref + rbeg;
+    char *vcf = rec->d.allele[0] + vbeg;
+    assert( vcf - rec->d.allele[0] < strlen(rec->d.allele[0]) && ref - tr->ref < tr->end - tr->beg + 2*N_REF_PAD );
+    int i = 0;
+    while ( ref[i] && vcf[i] )
+    {
+        if ( ref[i]!=vcf[i] && toupper(ref[i])!=toupper(vcf[i]) ) 
+            error("Error: the fasta reference does not match the VCF REF allele at %s:%"PRId64" .. fasta=%c vcf=%c\n",
+                    bcf_seqname(args->hdr,rec),(int64_t) rec->pos+vbeg+1,ref[i],vcf[i]);
+        i++;
+    }
+}
+
+int test_cds_local(args_t *args, bcf1_t *rec)
+{
+    int i,j, ret = 0;
+    const char *chr = bcf_seqname(args->hdr,rec);
+    // note that the off-by-one extension of rlen is deliberate to account for insertions
+    if ( !regidx_overlap(args->idx_cds,chr,rec->pos,rec->pos+rec->rlen, args->itr) ) return 0;
+
+    // structures to fake the normal test_cds machinery
+    hap_node_t root, node;
+    root.type  = HAP_ROOT;
+    kstring_t *tref = &args->hap->tref, *tseq = &args->hap->tseq;
+
+    while ( regitr_overlap(args->itr) )
+    {
+        gf_cds_t *cds = regitr_payload(args->itr,gf_cds_t*);
+        tscript_t *tr = cds->tr;
+        if ( !GF_is_coding(tr->type) ) continue;
+        ret = 1;
+
+        if ( !tr->ref )
+        {
+            tscript_init_ref(args, tr, chr);
+            tscript_splice_ref(tr);
+            khp_insert(trhp, args->active_tr, &tr);     // only to clean the reference afterwards
+        }
+
+        sanity_check_ref(args, tr, rec);
+
+        kstring_t sref;
+        sref.s = tr->sref;
+        sref.l = tr->nsref;
+        sref.m = sref.l;
+
+        for (i=1; i<rec->n_allele; i++)
+        {
+            if ( rec->d.allele[i][0]=='<' || rec->d.allele[i][0]=='*' ) { continue; }
+            if ( hap_init(args, &root, &node, cds, rec, i)!=0 ) continue;
+
+            csq_t csq; 
+            memset(&csq, 0, sizeof(csq_t));
+            csq.pos          = rec->pos;
+            csq.type.biotype = tr->type;
+            csq.type.strand  = tr->strand;
+            csq.type.trid    = tr->id;
+            csq.type.vcf_ial = i;
+            csq.type.gene    = tr->gene->name;
+
+            int csq_type = node.csq;
+
+            // code repetition: it would be nice to reuse the code from hap_add_csq, needs refactoring though
+            if ( node.type == HAP_SSS )
+            {
+                csq.type.type = csq_type;
+                csq_stage(args, &csq, rec);
+            }
+            else
+            {
+                kstring_t sseq;
+                sseq.m = sref.m - 2*N_REF_PAD + node.dlen;
+                sseq.s = node.seq;
+                int alen = sseq.l = strlen(sseq.s);
+                int fill = node.dlen%3 && alen ? 1 : 0; // see #1475227917
+                cds_translate(&sref, &sseq, node.sbeg,node.sbeg,node.sbeg+node.rlen, tr->strand, tseq, fill);
+
+                sseq.m = sref.m - 2*N_REF_PAD;
+                sseq.s = sref.s + N_REF_PAD + node.sbeg;
+                sseq.l = node.rlen;
+                cds_translate(&sref, &sseq, node.sbeg,node.sbeg,node.sbeg+node.rlen, tr->strand, tref, fill);
+
+                // check for truncating stops
+                for (j=0; j<tref->l; j++)
+                    if ( tref->s[j]=='*' ) break;
+                if ( j!=tref->l )
+                {
+                    tref->l = j+1;
+                    tref->s[j+1] = 0;
+                }
+                for (j=0; j<tseq->l; j++)
+                    if ( tseq->s[j]=='*' ) break;
+                if ( j!=tseq->l )
+                {
+                    tseq->l = j+1;
+                    tseq->s[j+1] = 0;
+                }
+                if ( csq_type & CSQ_STOP_LOST )
+                {
+                    if ( tref->s[tref->l-1]=='*' && tref->s[tref->l-1] == tseq->s[tseq->l-1] ) 
+                    {
+                        csq_type &= ~CSQ_STOP_LOST;
+                        csq_type |= CSQ_STOP_RETAINED;
+                    }
+                    else if (tref->s[tref->l-1]!='*' )
+                    {
+                        // This is CDS 3' incomplete ENSG00000173376/synon.vcf, can also be missense
+                        // We observe in real data a change to a stop, ENST00000528237/retained-stop-incomplete-cds.vcf
+                        if ( tseq->s[tseq->l-1] == '*' )
+                        {
+                            csq_type &= ~CSQ_STOP_GAINED;
+                            csq_type |= CSQ_STOP_RETAINED;
+                        }
+                        else
+                            csq_type |= CSQ_INCOMPLETE_CDS;
+                    }
+                }
+                if ( csq_type & CSQ_START_LOST && tref->s[0]!='M' )
+                    csq_type &= ~CSQ_START_LOST;
+                if ( node.dlen!=0 )
+                {
+                    if ( node.dlen%3 )
+                        csq_type |= CSQ_FRAMESHIFT_VARIANT;
+                    else if ( node.dlen<0 )
+                        csq_type |= CSQ_INFRAME_DELETION;
+                    else
+                        csq_type |= CSQ_INFRAME_INSERTION;
+                    if ( tref->s[tref->l-1]!='*' && tseq->s[tseq->l-1]=='*' )
+                        csq_type |= CSQ_STOP_GAINED;
+                }
+                else
+                {
+                    for (j=0; j<tref->l; j++) 
+                        if ( tref->s[j] != tseq->s[j] ) break;
+                    if ( j==tref->l )
+                        csq_type |= CSQ_SYNONYMOUS_VARIANT;
+                    else if ( tref->s[j] ==  '*' )
+                        csq_type |= CSQ_STOP_LOST;
+                    else if ( tseq->s[j] ==  '*' )
+                        csq_type |= CSQ_STOP_GAINED;
+                    else
+                        csq_type |= CSQ_MISSENSE_VARIANT;
+                }
+                if ( csq_type & CSQ_COMPOUND )
+                {
+                    // create the aa variant string
+                    kstring_t str = {0,0,0};
+                    int aa_rbeg = tr->strand==STRAND_FWD ? node.sbeg/3+1 : (tr->nsref - 2*N_REF_PAD - node.sbeg - node.rlen)/3+1;
+                    int aa_sbeg = tr->strand==STRAND_FWD ? node.sbeg/3+1 : (tr->nsref - 2*N_REF_PAD + node.dlen - node.sbeg - alen)/3+1;
+                    kputc_('|', &str);
+                    kputw(aa_rbeg, &str);
+                    kprint_aa_prediction(args,aa_rbeg,tref,&str);
+                    if ( !(csq_type & CSQ_SYNONYMOUS_VARIANT) )
+                    {
+                        kputc_('>', &str);
+                        kputw(aa_sbeg, &str);
+                        kprint_aa_prediction(args,aa_sbeg,tseq,&str);
+                    }
+                    kputc_('|', &str);
+                    kputw(rec->pos+1, &str);
+                    kputs(node.var, &str);
+                    csq.type.vstr = str;
+                    csq.type.type = csq_type & CSQ_COMPOUND;
+                    csq_stage(args, &csq, rec);
+
+                    // all this only to clean vstr when vrec is flushed
+                    if ( !tr->root )
+                        tr->root = (hap_node_t*) calloc(1,sizeof(hap_node_t));
+                    tr->root->ncsq_list++;
+                    hts_expand0(csq_t,tr->root->ncsq_list,tr->root->mcsq_list,tr->root->csq_list);
+                    csq_t *rm_csq = tr->root->csq_list + tr->root->ncsq_list - 1;
+                    rm_csq->type.vstr = str;            
+                }
+                if ( csq_type & ~CSQ_COMPOUND )
+                {
+                    csq.type.type = csq_type & ~CSQ_COMPOUND;
+                    csq.type.vstr.l = 0;
+                    csq_stage(args, &csq, rec);
+                }
+            }
+            free(node.seq);
+            free(node.var);
+        }
+    }
+    return ret;
+}
+
+int test_cds(args_t *args, bcf1_t *rec, vbuf_t *vbuf)
+{
+    static int overlaps_warned = 0, multiploid_warned = 0;
+
+    int i, ret = 0, hap_ret;
+    const char *chr = bcf_seqname(args->hdr,rec);
+    // note that the off-by-one extension of rlen is deliberate to account for insertions
+    if ( !regidx_overlap(args->idx_cds,chr,rec->pos,rec->pos+rec->rlen, args->itr) ) return 0;
+    while ( regitr_overlap(args->itr) )
+    {
+        gf_cds_t *cds = regitr_payload(args->itr,gf_cds_t*);
+        tscript_t *tr = cds->tr;
+        if ( !GF_is_coding(tr->type) ) continue;
+        if ( vbuf->keep_until < tr->end ) vbuf->keep_until = tr->end;
+        ret = 1;
+        if ( !tr->root )
+        {
+            // initialize the transcript and its haplotype tree, fetch the reference sequence
+            tscript_init_ref(args, tr, chr);
+
+            tr->root = (hap_node_t*) calloc(1,sizeof(hap_node_t));
+            tr->nhap = args->phase==PHASE_DROP_GT ? 1 : 2*args->smpl->n;     // maximum ploidy = diploid
+            tr->hap  = (hap_node_t**) malloc(tr->nhap*sizeof(hap_node_t*));
+            for (i=0; i<tr->nhap; i++) tr->hap[i] = NULL;
+            tr->root->nend = tr->nhap;
+            tr->root->type = HAP_ROOT;
+
+            khp_insert(trhp, args->active_tr, &tr);
+        }
+
+        sanity_check_ref(args, tr, rec);
+
+        if ( args->phase==PHASE_DROP_GT )
+        {
+            if ( rec->d.allele[1][0]=='<' || rec->d.allele[1][0]=='*' ) { continue; }
+            hap_node_t *parent = tr->hap[0] ? tr->hap[0] : tr->root;
+            hap_node_t *child  = (hap_node_t*)calloc(1,sizeof(hap_node_t));
+            hap_ret = hap_init(args, parent, child, cds, rec, 1);
+            if ( hap_ret!=0 )
+            {
+                // overlapping or intron variant, cannot apply
+                if ( hap_ret==1 )
+                {
+                    if ( args->verbosity && (!overlaps_warned || args->verbosity > 1) )
+                    {
+                        fprintf(bcftools_stderr,
+                            "Warning: Skipping overlapping variants at %s:%"PRId64"\t%s>%s.\n",
+                            chr,(int64_t) rec->pos+1,rec->d.allele[0],rec->d.allele[1]);
+                        if ( !overlaps_warned )
+                            fprintf(bcftools_stderr,"         This message is printed only once, the verbosity can be increased with `--verbose 2`\n");
+                        overlaps_warned = 1;
+                    }
+                    if ( args->out ) 
+                        fprintf(args->out,"LOG\tWarning: Skipping overlapping variants at %s:%"PRId64"\t%s>%s\n", chr,(int64_t) rec->pos+1,rec->d.allele[0],rec->d.allele[1]);
+                }
+                else ret = 1;   // prevent reporting as intron in test_tscript
+                hap_destroy(child);
+                continue;
+            }
+            if ( child->type==HAP_SSS )
+            {
+                csq_t csq; 
+                memset(&csq, 0, sizeof(csq_t));
+                csq.pos          = rec->pos;
+                csq.type.biotype = tr->type;
+                csq.type.strand  = tr->strand;
+                csq.type.trid    = tr->id;
+                csq.type.vcf_ial = 1;
+                csq.type.gene    = tr->gene->name;
+                csq.type.type = child->csq;
+                csq_stage(args, &csq, rec);
+                hap_destroy(child);
+                ret = 1;
+                continue;
+            }
+            parent->nend--;
+            parent->nchild = 1;
+            parent->mchild = 1;
+            parent->child  = (hap_node_t**) malloc(sizeof(hap_node_t*));
+            parent->child[0] = child;
+            tr->hap[0] = child;
+            tr->hap[0]->nend = 1;
+            continue;
+        }
+
+        // apply the VCF variants and extend the haplotype tree
+        int j, ismpl, ihap, ngts = bcf_get_genotypes(args->hdr, rec, &args->gt_arr, &args->mgt_arr);
+        ngts /= bcf_hdr_nsamples(args->hdr);
+        if ( ngts!=1 && ngts!=2 ) 
+        {
+            if ( args->verbosity && (!multiploid_warned || args->verbosity > 1) )
+            {
+                fprintf(bcftools_stderr,
+                    "Warning: Skipping site with non-diploid/non-haploid genotypes at %s:%"PRId64"\t%s>%s.\n",
+                    chr,(int64_t) rec->pos+1,rec->d.allele[0],rec->d.allele[1]);
+                if ( !multiploid_warned )
+                    fprintf(bcftools_stderr,"         This message is printed only once, the verbosity can be increased with `--verbose 2`\n");
+                multiploid_warned = 1;
+            }
+            if ( args->out ) 
+                fprintf(args->out,"LOG\tWarning: Skipping site with non-diploid/non-haploid genotypes at %s:%"PRId64"\t%s>%s\n", chr,(int64_t) rec->pos+1,rec->d.allele[0],rec->d.allele[1]);
+            continue;
+        }
+        for (ismpl=0; ismpl<args->smpl->n; ismpl++)
+        {
+            int32_t *gt = args->gt_arr + args->smpl->idx[ismpl]*ngts;
+            if ( gt[0]==bcf_gt_missing ) continue;
+
+            if ( ngts>1 && gt[1]!=bcf_gt_missing && gt[1]!=bcf_int32_vector_end && bcf_gt_allele(gt[0])!=bcf_gt_allele(gt[1]) )
+            {
+                if ( args->phase==PHASE_MERGE )
+                {
+                    if ( !bcf_gt_allele(gt[0]) ) gt[0] = gt[1];
+                }
+                if ( !bcf_gt_is_phased(gt[0]) && !bcf_gt_is_phased(gt[1]) )
+                {
+                    if ( args->phase==PHASE_REQUIRE )
+                        error("Unphased heterozygous genotype at %s:%"PRId64", sample %s. See the --phase option.\n", chr,(int64_t) rec->pos+1,args->hdr->samples[args->smpl->idx[ismpl]]);
+                    if ( args->phase==PHASE_SKIP )
+                        continue;
+                    if ( args->phase==PHASE_NON_REF )
+                    {
+                        if ( !bcf_gt_allele(gt[0]) ) gt[0] = gt[1];
+                        else if ( !bcf_gt_allele(gt[1]) ) gt[1] = gt[0];
+                    }
+                }
+            }
+
+            for (ihap=0; ihap<ngts; ihap++)
+            {
+                if ( gt[ihap]==bcf_gt_missing || gt[ihap]==bcf_int32_vector_end ) continue;
+
+                i = 2*ismpl + ihap;
+
+                int ial = bcf_gt_allele(gt[ihap]);
+                if ( !ial ) continue;
+                assert( ial < rec->n_allele );
+                if ( rec->d.allele[ial][0]=='<' || rec->d.allele[ial][0]=='*' ) { continue; }
+
+                hap_node_t *parent = tr->hap[i] ? tr->hap[i] : tr->root;
+                if ( parent->cur_rec==rec && parent->cur_child[ial]>=0 )
+                {
+                    // this haplotype has been seen in another sample
+                    tr->hap[i] = parent->child[ parent->cur_child[ial] ];
+                    tr->hap[i]->nend++;
+                    parent->nend--;
+                    continue;
+                }
+
+                hap_node_t *child = (hap_node_t*)calloc(1,sizeof(hap_node_t));
+                hap_ret = hap_init(args, parent, child, cds, rec, ial);
+                if ( hap_ret!=0 )
+                {
+                    // overlapping or intron variant, cannot apply
+                    if ( hap_ret==1 )
+                    {
+                        if ( args->verbosity && (!overlaps_warned || args->verbosity > 1) )
+                        {
+                            fprintf(bcftools_stderr,
+                                    "Warning: Skipping overlapping variants at %s:%"PRId64", sample %s\t%s>%s.\n",
+                                    chr,(int64_t) rec->pos+1,args->hdr->samples[args->smpl->idx[ismpl]],rec->d.allele[0],rec->d.allele[ial]);
+                            if ( !overlaps_warned )
+                                fprintf(bcftools_stderr,"         This message is printed only once, the verbosity can be increased with `--verbose 2`\n");
+                            overlaps_warned = 1;
+                        }
+                        if ( args->out  )
+                            fprintf(args->out,"LOG\tWarning: Skipping overlapping variants at %s:%"PRId64", sample %s\t%s>%s\n",
+                                    chr,(int64_t) rec->pos+1,args->hdr->samples[args->smpl->idx[ismpl]],rec->d.allele[0],rec->d.allele[ial]);
+                    }
+                    hap_destroy(child);
+                    continue;
+                }
+                if ( child->type==HAP_SSS )
+                {
+                    csq_t csq; 
+                    memset(&csq, 0, sizeof(csq_t));
+                    csq.pos          = rec->pos;
+                    csq.type.biotype = tr->type;
+                    csq.type.strand  = tr->strand;
+                    csq.type.trid    = tr->id;
+                    csq.type.vcf_ial = ial;
+                    csq.type.gene    = tr->gene->name;
+                    csq.type.type = child->csq;
+                    csq_stage(args, &csq, rec);
+                    hap_destroy(child);
+                    continue;
+                }
+                if ( parent->cur_rec!=rec )
+                {
+                    hts_expand(int,rec->n_allele,parent->mcur_child,parent->cur_child);
+                    for (j=0; j<rec->n_allele; j++) parent->cur_child[j] = -1;
+                    parent->cur_rec = rec;
+                }
+
+                j = parent->nchild++;
+                hts_expand0(hap_node_t*,parent->nchild,parent->mchild,parent->child);
+                parent->cur_child[ial] = j;
+                parent->child[j] = child;
+                tr->hap[i] = child;
+                tr->hap[i]->nend++;
+                parent->nend--;
+            }
+        }
+    }
+    return ret;
+}
+
+void csq_stage(args_t *args, csq_t *csq, bcf1_t *rec)
+{
+    // known issues: tab output leads to unsorted output. This is because
+    // coding haplotypes are printed in one go and buffering is not used
+    // with tab output. VCF output is OK though.
+    if ( csq_push(args, csq, rec)!=0 && args->phase==PHASE_DROP_GT ) return;    // the consequence already exists
+
+    int i,j,ngt = 0;
+    if ( args->phase!=PHASE_DROP_GT )
+    {
+        ngt = bcf_get_genotypes(args->hdr, rec, &args->gt_arr, &args->mgt_arr);
+        if ( ngt>0 ) ngt /= bcf_hdr_nsamples(args->hdr);
+    }
+    if ( ngt<=0 )
+    {
+        if ( args->output_type==FT_TAB_TEXT )
+            csq_print_text(args, csq, -1,0);
+        return;
+    }
+    assert( ngt<=2 );
+
+    if ( args->output_type==FT_TAB_TEXT )
+    {
+        for (i=0; i<args->smpl->n; i++)
+        {
+            int32_t *gt = args->gt_arr + args->smpl->idx[i]*ngt;
+            for (j=0; j<ngt; j++)
+            {
+                if ( gt[j]==bcf_gt_missing || gt[j]==bcf_int32_vector_end ) continue;
+                int ial = bcf_gt_allele(gt[j]);
+                if ( !ial || ial!=csq->type.vcf_ial ) continue;
+                csq_print_text(args, csq, args->smpl->idx[i],j+1);
+            }
+        }
+        return;
+    }
+
+    vrec_t *vrec = csq->vrec;
+    for (i=0; i<args->smpl->n; i++)
+    {
+        int32_t *gt = args->gt_arr + args->smpl->idx[i]*ngt;
+        for (j=0; j<ngt; j++)
+        {
+            if ( gt[j]==bcf_gt_missing || gt[j]==bcf_int32_vector_end ) continue;
+            int ial = bcf_gt_allele(gt[j]);
+            if ( !ial || ial!=csq->type.vcf_ial ) continue;
+
+            int icsq2 = 2*csq->idx + j;
+            if ( icsq2 >= args->ncsq2_max ) // more than ncsq_max consequences, so can't fit it in FMT
+            {
+                int ismpl = args->smpl->idx[i];
+                if ( args->verbosity && (!args->ncsq2_small_warned || args->verbosity > 1) )
+                {
+                    fprintf(bcftools_stderr,
+                            "Warning: Too many consequences for sample %s at %s:%"PRId64", keeping the first %d and skipping the rest.\n",
+                            args->hdr->samples[ismpl],bcf_hdr_id2name(args->hdr,args->rid),(int64_t) vrec->line->pos+1,icsq2+1);
+                    if ( !args->ncsq2_small_warned )
+                        fprintf(bcftools_stderr,"         The limit can be increased by setting the --ncsq parameter. This warning is printed only once.\n");
+                    args->ncsq2_small_warned = 1;
+                }
+                if ( args->ncsq2_small_warned < icsq2 ) args->ncsq2_small_warned = icsq2;
+                break;
+            }
+            int ival, ibit;
+            icsq2_to_bit(icsq2, &ival,&ibit);
+            if ( vrec->nfmt < 1 + ival ) vrec->nfmt = 1 + ival;
+            vrec->fmt_bm[i*args->nfmt_bcsq + ival] |= 1 << ibit;
+        }
+    }
+}
+int test_utr(args_t *args, bcf1_t *rec)
+{
+    const char *chr = bcf_seqname(args->hdr,rec);
+    // note that the off-by-one extension of rlen is deliberate to account for insertions
+    if ( !regidx_overlap(args->idx_utr,chr,rec->pos,rec->pos+rec->rlen, args->itr) ) return 0;
+
+    splice_t splice;
+    splice_init(&splice, rec);
+
+    int i, ret = 0;
+    while ( regitr_overlap(args->itr) )
+    {
+        gf_utr_t *utr = regitr_payload(args->itr, gf_utr_t*);
+        tscript_t *tr = splice.tr = utr->tr;
+        for (i=1; i<rec->n_allele; i++)
+        {
+            if ( rec->d.allele[i][0]=='<' || rec->d.allele[i][0]=='*' ) { continue; }
+            splice.vcf.alt = rec->d.allele[i];
+            splice.csq     = 0;
+            int splice_ret = splice_csq(args, &splice, utr->beg, utr->end);
+            if ( splice_ret!=SPLICE_INSIDE && splice_ret!=SPLICE_OVERLAP ) continue;
+            csq_t csq; 
+            memset(&csq, 0, sizeof(csq_t));
+            csq.pos          = rec->pos;
+            csq.type.type    = utr->which==prime5 ? CSQ_UTR5 : CSQ_UTR3;
+            csq.type.biotype = tr->type;
+            csq.type.strand  = tr->strand;
+            csq.type.trid    = tr->id;
+            csq.type.vcf_ial = i;
+            csq.type.gene    = tr->gene->name;
+            csq_stage(args, &csq, rec);
+            ret = 1;
+        }
+    }
+    assert(!splice.kref.s);
+    assert(!splice.kalt.s);
+    return ret;
+}
+int test_splice(args_t *args, bcf1_t *rec)
+{
+    const char *chr = bcf_seqname(args->hdr,rec);
+    if ( !regidx_overlap(args->idx_exon,chr,rec->pos,rec->pos + rec->rlen, args->itr) ) return 0;
+
+    splice_t splice;
+    splice_init(&splice, rec);
+    splice.check_acceptor = splice.check_donor = 1;
+
+    int i, ret = 0;
+    while ( regitr_overlap(args->itr) )
+    {
+        gf_exon_t *exon = regitr_payload(args->itr, gf_exon_t*);
+        splice.tr = exon->tr;
+        if ( !splice.tr->ncds ) continue;  // not a coding transcript, no interest in splice sites
+
+        splice.check_region_beg = splice.tr->beg==exon->beg ? 0 : 1;
+        splice.check_region_end = splice.tr->end==exon->end ? 0 : 1;
+
+        for (i=1; i<rec->n_allele; i++)
+        {
+            if ( rec->d.allele[1][0]=='<' || rec->d.allele[1][0]=='*' ) { continue; }
+            splice.vcf.alt = rec->d.allele[i];
+            splice.csq     = 0;
+            splice_csq(args, &splice, exon->beg, exon->end);
+            if ( splice.csq ) ret = 1;
+        }
+    }
+    free(splice.kref.s);
+    free(splice.kalt.s);
+    return ret;
+}
+int test_tscript(args_t *args, bcf1_t *rec)
+{
+    const char *chr = bcf_seqname(args->hdr,rec);
+    if ( !regidx_overlap(args->idx_tscript,chr,rec->pos,rec->pos+rec->rlen, args->itr) ) return 0;
+
+    splice_t splice;
+    splice_init(&splice, rec);
+
+    int i, ret = 0;
+    while ( regitr_overlap(args->itr) )
+    {
+        tscript_t *tr = splice.tr = regitr_payload(args->itr, tscript_t*);
+        for (i=1; i<rec->n_allele; i++)
+        {
+            if ( rec->d.allele[i][0]=='<' || rec->d.allele[i][0]=='*' ) { continue; }
+            splice.vcf.alt = rec->d.allele[i];
+            splice.csq     = 0;
+            int splice_ret = splice_csq(args, &splice, tr->beg, tr->end);
+            if ( splice_ret!=SPLICE_INSIDE && splice_ret!=SPLICE_OVERLAP ) continue;    // SPLICE_OUTSIDE or SPLICE_REF
+            csq_t csq; 
+            memset(&csq, 0, sizeof(csq_t));
+            csq.pos          = rec->pos;
+            csq.type.type    = GF_is_coding(tr->type) ? CSQ_INTRON : CSQ_NON_CODING;
+            csq.type.biotype = tr->type;
+            csq.type.strand  = tr->strand;
+            csq.type.trid    = tr->id;
+            csq.type.gene    = tr->gene->name;
+            csq_stage(args, &csq, rec);
+            ret = 1;
+        }
+    }
+    assert(!splice.kref.s);
+    assert(!splice.kalt.s);
+    return ret;
+}
+
+void test_symbolic_alt(args_t *args, bcf1_t *rec)
+{
+    static int warned = 0;
+    if ( args->verbosity && (!warned && args->verbosity > 0) )
+    {
+        fprintf(bcftools_stderr,"Warning: The support for symbolic ALT insertions is experimental.\n");
+        warned = 1;
+    }
+
+    const char *chr = bcf_seqname(args->hdr,rec);
+
+    // only insertions atm
+    int beg = rec->pos + 1;
+    int end = beg;
+    int csq_class = CSQ_ELONGATION;
+
+    int hit = 0;
+    if ( regidx_overlap(args->idx_cds,chr,beg,end, args->itr) )
+    {
+        while ( regitr_overlap(args->itr) )
+        {
+            csq_t csq; 
+            memset(&csq, 0, sizeof(csq_t));
+            gf_cds_t *cds    = regitr_payload(args->itr,gf_cds_t*);
+            tscript_t *tr    = cds->tr;
+            csq.type.type    = (GF_is_coding(tr->type) ? CSQ_CODING_SEQUENCE : CSQ_NON_CODING) | csq_class;
+            csq.pos          = rec->pos;
+            csq.type.biotype = tr->type;
+            csq.type.strand  = tr->strand;
+            csq.type.trid    = tr->id;
+            csq.type.gene    = tr->gene->name;
+            csq_stage(args, &csq, rec);
+            hit = 1;
+        }
+    }
+    if ( regidx_overlap(args->idx_utr,chr,beg,end, args->itr) )
+    {
+        while ( regitr_overlap(args->itr) )
+        {
+            csq_t csq; 
+            memset(&csq, 0, sizeof(csq_t));
+            gf_utr_t *utr    = regitr_payload(args->itr, gf_utr_t*);
+            tscript_t *tr    = utr->tr;
+            csq.type.type    = (utr->which==prime5 ? CSQ_UTR5 : CSQ_UTR3) | csq_class;
+            csq.pos          = rec->pos;
+            csq.type.biotype = tr->type;
+            csq.type.strand  = tr->strand;
+            csq.type.trid    = tr->id;
+            csq.type.gene    = tr->gene->name;
+            csq_stage(args, &csq, rec);
+            hit = 1;
+        }
+    }
+    if ( regidx_overlap(args->idx_exon,chr,beg,end, args->itr) )
+    {
+        splice_t splice;
+        splice_init(&splice, rec);
+        splice.check_acceptor = splice.check_donor = 1;
+
+        while ( regitr_overlap(args->itr) )
+        {
+            gf_exon_t *exon = regitr_payload(args->itr, gf_exon_t*);
+            splice.tr = exon->tr;
+            if ( !splice.tr->ncds ) continue;  // not a coding transcript, no interest in splice sites
+            splice.check_region_beg = splice.tr->beg==exon->beg ? 0 : 1;
+            splice.check_region_end = splice.tr->end==exon->end ? 0 : 1;
+            splice.vcf.alt = rec->d.allele[1];
+            splice.csq     = csq_class;
+            splice_csq(args, &splice, exon->beg, exon->end);
+            if ( splice.csq ) hit = 1;
+        }
+    }
+    if ( !hit && regidx_overlap(args->idx_tscript,chr,beg,end, args->itr) )
+    {
+        splice_t splice;
+        splice_init(&splice, rec);
+
+        while ( regitr_overlap(args->itr) )
+        {
+            csq_t csq; 
+            memset(&csq, 0, sizeof(csq_t));
+            tscript_t *tr = splice.tr = regitr_payload(args->itr, tscript_t*);
+            splice.vcf.alt = rec->d.allele[1];
+            splice.csq     = csq_class;
+            int splice_ret = splice_csq(args, &splice, tr->beg, tr->end);
+            if ( splice_ret!=SPLICE_INSIDE && splice_ret!=SPLICE_OVERLAP ) continue;    // SPLICE_OUTSIDE or SPLICE_REF
+            csq.type.type    = (GF_is_coding(tr->type) ? CSQ_INTRON : CSQ_NON_CODING) | csq_class;
+            csq.pos          = rec->pos;
+            csq.type.biotype = tr->type;
+            csq.type.strand  = tr->strand;
+            csq.type.trid    = tr->id;
+            csq.type.gene    = tr->gene->name;
+            csq_stage(args, &csq, rec);
+        }
+    }
+}
+
+void debug_print_buffers(args_t *args, int pos)
+{
+    int i,j;
+    fprintf(bcftools_stderr,"debug_print_buffers at %d\n", pos);
+    fprintf(bcftools_stderr,"vbufs:\n");
+    for (i=0; i<args->vcf_rbuf.n; i++)
+    {
+        int k = rbuf_kth(&args->vcf_rbuf, i);
+        vbuf_t *vbuf = args->vcf_buf[k];
+
+        fprintf(bcftools_stderr,"\tvbuf %d:\n", i);
+        for (j=0; j<vbuf->n; j++)
+        {
+            vrec_t *vrec = vbuf->vrec[j];
+            fprintf(bcftools_stderr,"\t\t%"PRId64" .. nvcsq=%d\n", (int64_t) vrec->line->pos+1, vrec->nvcsq);
+        }
+    }
+    fprintf(bcftools_stderr,"pos2vbuf:");
+    khint_t k;
+    for (k = 0; k < kh_end(args->pos2vbuf); ++k)
+        if (kh_exist(args->pos2vbuf, k)) fprintf(bcftools_stderr," %d",1+(int)kh_key(args->pos2vbuf, k));
+    fprintf(bcftools_stderr,"\n");
+    fprintf(bcftools_stderr,"active_tr: %d\n", args->active_tr->ndat);
+}
+
+static void process(args_t *args, bcf1_t **rec_ptr)
+{
+    if ( !rec_ptr )
+    {
+        hap_flush(args, REGIDX_MAX);
+        vbuf_flush(args, REGIDX_MAX);
+        return;
+    }
+
+    bcf1_t *rec = *rec_ptr;
+    static int32_t prev_rid = -1, prev_pos = -1;
+    if ( prev_rid!=rec->rid )
+    {
+        prev_rid = rec->rid;
+        prev_pos = rec->pos;
+
+        // Common error is to use different naming conventions in the fasta and the VCF (e.g. X vs chrX).
+        // Perform a simple sanity check (that does not catch much), the chromosome must be present in the
+        // reference file
+        if ( !faidx_has_seq(args->fai,bcf_seqname(args->hdr,rec)) )
+            error("Error: the chromosome \"%s\" is not present in %s\n",bcf_seqname(args->hdr,rec),args->fa_fname);
+    }
+    if ( prev_pos > rec->pos )
+        error("Error: The file is not sorted, %s:%d comes before %s:%"PRId64"\n",bcf_seqname(args->hdr,rec),prev_pos+1,bcf_seqname(args->hdr,rec),(int64_t) rec->pos+1);
+
+    int call_csq = 1;
+    if ( rec->n_allele < 2 ) call_csq = 0;   // no alternate allele
+    else if ( rec->n_allele==2 && (rec->d.allele[1][0]=='*' || rec->d.allele[1][1]=='*') ) call_csq = 0;     // gVCF, not an alt allele
+    else if ( rec->d.allele[1][0]=='<' )
+    {
+        if ( strncmp("<INS",rec->d.allele[1], 4) ) call_csq = 0;    // only <INS[:.*]> is supported at the moment
+    }
+    if ( call_csq && args->filter )
+    {
+        call_csq = filter_test(args->filter, rec, NULL);
+        if ( args->filter_logic==FLT_EXCLUDE ) call_csq = call_csq ? 0 : 1;
+    }
+    if ( !call_csq )
+    {
+        if ( !args->out_fh ) return;    // not a VCF output
+        vbuf_push(args, rec_ptr);
+        hap_flush(args, rec->pos-1);
+        vbuf_flush(args, rec->pos-1);
+        return;
+    }
+
+    if ( args->rid != rec->rid ) 
+    {
+        hap_flush(args, REGIDX_MAX);
+        vbuf_flush(args, REGIDX_MAX);
+    }
+    args->rid = rec->rid;
+    vbuf_t *vbuf = vbuf_push(args, rec_ptr);
+
+    if ( rec->d.allele[1][0]!='<' )
+    {
+        int hit = args->local_csq ? test_cds_local(args, rec) : test_cds(args, rec, vbuf);
+        hit += test_utr(args, rec);
+        hit += test_splice(args, rec);
+        if ( !hit ) test_tscript(args, rec);
+    }
+    else
+        test_symbolic_alt(args, rec);
+
+    if ( rec->pos > 0 )
+    {
+        hap_flush(args, rec->pos-1);
+        vbuf_flush(args, rec->pos-1);
+    }
+
+    return;
+}
+
+static const char *usage(void)
+{
+    return 
+        "\n"
+        "About: Haplotype-aware consequence caller.\n"
+        "Usage: bcftools csq [OPTIONS] in.vcf\n"
+        "\n"
+        "Required options:\n"
+        "   -f, --fasta-ref FILE              Reference file in fasta format\n"
+        "   -g, --gff-annot FILE              GFF3 annotation file\n"
+        "\n"
+        "CSQ options:\n"
+        "   -B, --trim-protein-seq INT        Abbreviate protein-changing predictions to max INT aminoacids\n" 
+        "   -c, --custom-tag STRING           Use this tag instead of the default BCSQ\n"
+        "   -l, --local-csq                   Localized predictions, consider only one VCF record at a time\n"
+        "   -n, --ncsq INT                    Maximum number of per-haplotype consequences to consider for each site [15]\n"
+        "   -p, --phase a|m|r|R|s             How to handle unphased heterozygous genotypes: [r]\n"
+        "                                       a: take GTs as is, create haplotypes regardless of phase (0/1 -> 0|1)\n"
+        "                                       m: merge *all* GTs into a single haplotype (0/1 -> 1, 1/2 -> 1)\n"
+        "                                       r: require phased GTs, throw an error on unphased het GTs\n"
+        "                                       R: create non-reference haplotypes if possible (0/1 -> 1|1, 1/2 -> 1|2)\n"
+        "                                       s: skip unphased hets\n"
+        "Options:\n"
+        "   -e, --exclude EXPR                Exclude sites for which the expression is true\n"
+        "       --force                       Run even if some sanity checks fail\n"
+        "   -i, --include EXPR                Select sites for which the expression is true\n"
+        "       --no-version                  Do not append version and command line to the header\n"
+        "   -o, --output FILE                 Write output to a file [standard output]\n"
+        "   -O, --output-type b|u|z|v|t[0-9]  b: compressed BCF, u: uncompressed BCF, z: compressed VCF\n"
+        "                                     v: uncompressed VCF, t: plain tab-delimited text output, 0-9: compression level [v]\n"
+        "   -r, --regions REGION              Restrict to comma-separated list of regions\n"
+        "   -R, --regions-file FILE           Restrict to regions listed in a file\n"
+        "       --regions-overlap 0|1|2       Include if POS in the region (0), record overlaps (1), variant overlaps (2) [1]\n"
+        "   -s, --samples -|LIST              Samples to include or \"-\" to apply all variants and ignore samples\n"
+        "   -S, --samples-file FILE           Samples to include\n"
+        "   -t, --targets REGION              Similar to -r but streams rather than index-jumps\n"
+        "   -T, --targets-file FILE           Similar to -R but streams rather than index-jumps\n"
+        "       --targets-overlap 0|1|2       Include if POS in the region (0), record overlaps (1), variant overlaps (2) [0]\n"
+        "       --threads INT                 Use multithreading with <int> worker threads [0]\n"
+        "   -v, --verbose INT                 Verbosity level 0-2 [1]\n"
+        "\n"
+        "Example:\n"
+        "   bcftools csq -f hs37d5.fa -g Homo_sapiens.GRCh37.82.gff3.gz in.vcf\n"
+        "\n"
+        "   # GFF3 annotation files can be downloaded from Ensembl. e.g. for human:\n"
+        "   ftp://ftp.ensembl.org/pub/current_gff3/homo_sapiens/\n"
+        "   ftp://ftp.ensembl.org/pub/grch37/release-84/gff3/homo_sapiens/\n"
+        "\n";
+}
+
+int main_csq(int argc, char *argv[])
+{
+    args_t *args = (args_t*) calloc(1,sizeof(args_t));
+    args->argc = argc; args->argv = argv;
+    args->output_type = FT_VCF;
+    args->bcsq_tag = "BCSQ";
+    args->ncsq2_max = 2*(16-1);      // 1 bit is reserved for BCF missing values
+    args->verbosity = 1;
+    args->record_cmd_line = 1;
+    args->clevel = -1;
+
+    static struct option loptions[] =
+    {
+        {"force",0,0,1},
+        {"threads",required_argument,NULL,2},
+        {"help",0,0,'h'},
+        {"ncsq",1,0,'n'},
+        {"brief-predictions",no_argument,0,'b'},
+        {"trim-protein-seq",required_argument,0,'B'},
+        {"custom-tag",1,0,'c'},
+        {"local-csq",0,0,'l'},
+        {"gff-annot",1,0,'g'},
+        {"fasta-ref",1,0,'f'},
+        {"include",1,0,'i'},
+        {"exclude",1,0,'e'},
+        {"output",1,0,'o'},
+        {"output-type",1,NULL,'O'},
+        {"phase",1,0,'p'},
+        {"quiet",0,0,'q'},
+        {"verbose",1,0,'v'},
+        {"regions",1,0,'r'},
+        {"regions-file",1,0,'R'},
+        {"regions-overlap",required_argument,NULL,4},
+        {"samples",1,0,'s'},
+        {"samples-file",1,0,'S'},
+        {"targets",1,0,'t'},
+        {"targets-file",1,0,'T'},
+        {"targets-overlap",required_argument,NULL,5},
+        {"no-version",no_argument,NULL,3},
+        {0,0,0,0}
+    };
+    int c, targets_is_file = 0, regions_is_file = 0; 
+    int regions_overlap = 1;
+    int targets_overlap = 0;
+    char *targets_list = NULL, *regions_list = NULL, *tmp;
+    while ((c = getopt_long(argc, argv, "?hr:R:t:T:i:e:f:o:O:g:s:S:p:qc:ln:bB:v:",loptions,NULL)) >= 0)
+    {
+        switch (c) 
+        {
+            case  1 : args->force = 1; break;
+            case  2 :
+                args->n_threads = strtol(optarg,&tmp,10);
+                if ( *tmp ) error("Could not parse argument: --threads  %s\n", optarg);
+                break;
+            case  3 : args->record_cmd_line = 0; break;
+            case 'b':
+                    args->brief_predictions = 1;
+                    fprintf(bcftools_stderr,"Warning: the -b option will be removed in future versions. Please use -B 1 instead.\n");
+                    break;
+            case 'B': 
+                    args->brief_predictions = strtol(optarg,&tmp,10);
+                    if ( *tmp || args->brief_predictions<1 ) error("Could not parse argument: --trim-protein-seq %s\n", optarg);
+                    break;
+            case 'l': args->local_csq = 1; break;
+            case 'c': args->bcsq_tag = optarg; break;
+            case 'q': error("Error: the -q option has been deprecated, use -v, --verbose instead.\n"); break;
+            case 'v': 
+                args->verbosity = atoi(optarg);
+                if ( args->verbosity<0 || args->verbosity>2 ) error("Error: expected integer 0-2 with -v, --verbose\n");
+                break;
+            case 'p':
+                switch (optarg[0]) 
+                {
+                    case 'a': args->phase = PHASE_AS_IS; break;
+                    case 'm': args->phase = PHASE_MERGE; break;
+                    case 'r': args->phase = PHASE_REQUIRE; break;
+                    case 'R': args->phase = PHASE_NON_REF; break;
+                    case 's': args->phase = PHASE_SKIP; break;
+                    default: error("The -p code \"%s\" not recognised\n", optarg);
+                }
+                break;
+            case 'f': args->fa_fname = optarg; break;
+            case 'g': args->gff_fname = optarg; break;
+            case 'n': 
+                args->ncsq2_max = 2 * atoi(optarg);
+                if ( args->ncsq2_max <= 0 ) error("Expected positive integer with -n, got %s\n", optarg);
+                break;
+            case 'o': args->output_fname = optarg; break;
+            case 'O':
+                      switch (optarg[0]) {
+                          case 't': args->output_type = FT_TAB_TEXT; break;
+                          case 'b': args->output_type = FT_BCF_GZ; break;
+                          case 'u': args->output_type = FT_BCF; break;
+                          case 'z': args->output_type = FT_VCF_GZ; break;
+                          case 'v': args->output_type = FT_VCF; break;
+                          default:
+                          {
+                              args->clevel = strtol(optarg,&tmp,10);
+                              if ( *tmp || args->clevel<0 || args->clevel>9 ) error("The output type \"%s\" not recognised\n", optarg);
+                          }
+                      }
+                      if ( optarg[1] )
+                      {
+                          args->clevel = strtol(optarg+1,&tmp,10);
+                          if ( *tmp || args->clevel<0 || args->clevel>9 ) error("Could not parse argument: --output-type %s\n", optarg+1);
+                      }
+                      break;
+            case 'e':
+                if ( args->filter_str ) error("Error: only one -i or -e expression can be given, and they cannot be combined\n");
+                args->filter_str = optarg; args->filter_logic |= FLT_EXCLUDE; break;
+            case 'i':
+                if ( args->filter_str ) error("Error: only one -i or -e expression can be given, and they cannot be combined\n");
+                args->filter_str = optarg; args->filter_logic |= FLT_INCLUDE; break;
+            case 'r': regions_list = optarg; break;
+            case 'R': regions_list = optarg; regions_is_file = 1; break;
+            case 's': args->sample_list = optarg; break;
+            case 'S': args->sample_list = optarg; args->sample_is_file = 1; break;
+            case 't': targets_list = optarg; break;
+            case 'T': targets_list = optarg; targets_is_file = 1; break;
+            case  4 :
+                regions_overlap = parse_overlap_option(optarg);
+                if ( regions_overlap < 0 ) error("Could not parse: --regions-overlap %s\n",optarg);
+                break;
+            case  5 :
+                targets_overlap = parse_overlap_option(optarg);
+                if ( targets_overlap < 0 ) error("Could not parse: --targets-overlap %s\n",optarg);
+                break;
+            case 'h':
+            case '?': error("%s",usage());
+            default: error("The option not recognised: %s\n\n", optarg); break;
+        }
+    }
+    char *fname = NULL;
+    if ( optind==argc )
+    {
+        if ( !isatty(fileno((FILE *)stdin)) ) fname = "-";  // reading from stdin
+        else error("%s", usage());
+    }
+    else fname = argv[optind];
+    if ( argc - optind>1 ) error("%s", usage());
+    if ( !args->fa_fname ) error("Missing the --fa-ref option\n");
+    if ( !args->gff_fname ) error("Missing the --gff option\n");
+    args->sr = bcf_sr_init();
+    if ( targets_list )
+    {
+        bcf_sr_set_opt(args->sr,BCF_SR_TARGETS_OVERLAP,targets_overlap);
+        if ( bcf_sr_set_targets(args->sr, targets_list, targets_is_file, 0)<0 )
+            error("Failed to read the targets: %s\n", targets_list);
+    }
+    if ( regions_list )
+    {
+        bcf_sr_set_opt(args->sr,BCF_SR_REGIONS_OVERLAP,regions_overlap);
+        if ( bcf_sr_set_regions(args->sr, regions_list, regions_is_file)<0 )
+            error("Failed to read the regions: %s\n", regions_list);
+    }
+    if ( bcf_sr_set_threads(args->sr, args->n_threads)<0 ) error("Failed to create %d extra threads\n", args->n_threads);
+    if ( !bcf_sr_add_reader(args->sr, fname) )
+        error("Failed to read from %s: %s\n", !strcmp("-",fname)?"standard input":fname,bcf_sr_strerror(args->sr->errnum));
+    args->hdr = bcf_sr_get_header(args->sr,0);
+
+    init_data(args);
+    while ( bcf_sr_next_line(args->sr) )
+    {
+        process(args, &args->sr->readers[0].buffer[0]);
+    }
+    process(args,NULL);
+
+    destroy_data(args);
+    bcf_sr_destroy(args->sr);
+    free(args);
+    return 0;
+}
+
diff --git a/bcftools/dbuf.h b/bcftools/dbuf.h
new file mode 100644
index 0000000..80b5958
--- /dev/null
+++ b/bcftools/dbuf.h
@@ -0,0 +1,71 @@
+/* The MIT License
+
+   Copyright (c) 2022 Genome Research Ltd.
+
+   Author: Petr Danecek <pd3@sanger.ac.uk>
+
+   Permission is hereby granted, free of charge, to any person obtaining a copy
+   of this software and associated documentation files (the "Software"), to deal
+   in the Software without restriction, including without limitation the rights
+   to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+   copies of the Software, and to permit persons to whom the Software is
+   furnished to do so, subject to the following conditions:
+
+   The above copyright notice and this permission notice shall be included in
+   all copies or substantial portions of the Software.
+
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+   IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+   FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+   AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+   LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+   OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+   THE SOFTWARE.
+
+ */
+
+/*
+    Simple data buffer
+*/
+
+#ifndef __DBUF_H__
+#define __DBUF_H__
+
+#include <htslib/hts.h>
+
+typedef struct
+{
+    size_t n,m;
+    void **dat;
+}
+dbuf_t;
+
+static inline dbuf_t *dbuf_push(dbuf_t *buf, void *ptr)
+{
+    if ( !buf ) buf = calloc(1,sizeof(dbuf_t));
+    buf->n++;
+    hts_expand(void*,buf->n,buf->m,buf->dat);
+    buf->dat[buf->n-1] = ptr;
+    return buf;
+}
+
+static inline void *dbuf_ith(dbuf_t *buf, int i)
+{
+    return buf->dat[i];
+}
+
+static inline size_t dbuf_n(dbuf_t *buf)
+{
+    return buf->n;
+}
+
+static inline void dbuf_destroy_free(dbuf_t *buf)
+{
+    int i;
+    for (i=0; i<buf->n; i++) free(buf->dat[i]);
+    free(buf->dat);
+    free(buf);
+}
+
+#endif
+
diff --git a/bcftools/dist.c b/bcftools/dist.c
new file mode 100644
index 0000000..094fc73
--- /dev/null
+++ b/bcftools/dist.c
@@ -0,0 +1,124 @@
+/* The MIT License
+
+   Copyright (c) 2016-2020 Genome Research Ltd.
+
+   Author: Petr Danecek <pd3@sanger.ac.uk>
+   
+   Permission is hereby granted, free of charge, to any person obtaining a copy
+   of this software and associated documentation files (the "Software"), to deal
+   in the Software without restriction, including without limitation the rights
+   to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+   copies of the Software, and to permit persons to whom the Software is
+   furnished to do so, subject to the following conditions:
+   
+   The above copyright notice and this permission notice shall be included in
+   all copies or substantial portions of the Software.
+   
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+   IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+   FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+   AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+   LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+   OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+   THE SOFTWARE.
+
+ */
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <math.h>
+#include <string.h>
+#include <assert.h>
+#include "dist.h"
+
+extern void error(const char *format, ...);
+
+struct _dist_t
+{
+    uint64_t *bins, nvalues;
+    int nbins;
+    int npow;   // the number of orders of magnitude to represent exactly
+    int nexact; // pow(10,npow)
+    int nlevel;
+};
+
+dist_t *dist_init(int npow)
+{
+    dist_t *dist = (dist_t*) calloc(1,sizeof(dist_t));
+    dist->npow   = npow;
+    dist->nexact = pow(10,npow);
+    dist->nlevel = dist->nexact - pow(10,npow-1);
+    return dist;
+}
+
+void dist_destroy(dist_t *dist)
+{
+    if ( !dist ) return;
+    free(dist->bins);
+    free(dist);
+}
+
+int dist_nbins(dist_t *dist)
+{
+    return dist->nbins;
+}
+
+int dist_nvalues(dist_t *dist)
+{
+    return dist->nvalues;
+}
+
+uint32_t dist_insert(dist_t *dist, uint32_t value)
+{
+    int ibin;
+
+    if ( value <= dist->nexact ) 
+        ibin = value;
+    else
+    {
+        int npow  = (int) log10(value);
+        int level = npow - dist->npow + 1;
+        uint32_t step = pow(10, level);
+        ibin = dist->nexact + dist->nlevel*(level-1) + (value - pow(10,npow)) / step;
+    }
+
+    if ( ibin >= dist->nbins )
+    {
+        dist->bins = (uint64_t*) realloc(dist->bins, sizeof(*dist->bins)*(ibin+1));
+        memset(dist->bins + dist->nbins, 0, (ibin+1 - dist->nbins)*sizeof(*dist->bins));
+        dist->nbins = ibin+1;
+    }
+    dist->bins[ibin]++;
+    dist->nvalues++;
+    return ibin;
+}
+uint32_t dist_insert_n(dist_t *dist, uint32_t value, uint32_t cnt)
+{
+    if ( !cnt ) return 0;
+    int ibin = dist_insert(dist, value);
+    dist->bins[ibin] += cnt - 1;
+    dist->nvalues += cnt;
+    return ibin;
+}
+
+uint64_t dist_get(dist_t *dist, uint32_t idx, uint32_t *beg, uint32_t *end)
+{
+    if ( idx < dist->nexact )
+    {
+        if ( beg ) *beg = idx;
+        if ( end ) *end = idx + 1;
+    }
+    else
+    {
+        int level = (idx - dist->nexact) / dist->nlevel + 1;
+        int bin   = idx - dist->nexact - dist->nlevel*(level-1);
+
+        uint32_t step  = pow(10, level);
+        uint32_t value = pow(10, level + dist->npow - 1) + step*bin;
+
+        if ( beg ) *beg = value;
+        if ( end ) *end = value + step;
+    }
+    return dist->bins[idx];
+}
+
diff --git a/bcftools/dist.c.pysam.c b/bcftools/dist.c.pysam.c
new file mode 100644
index 0000000..f3f0915
--- /dev/null
+++ b/bcftools/dist.c.pysam.c
@@ -0,0 +1,126 @@
+#include "bcftools.pysam.h"
+
+/* The MIT License
+
+   Copyright (c) 2016-2020 Genome Research Ltd.
+
+   Author: Petr Danecek <pd3@sanger.ac.uk>
+   
+   Permission is hereby granted, free of charge, to any person obtaining a copy
+   of this software and associated documentation files (the "Software"), to deal
+   in the Software without restriction, including without limitation the rights
+   to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+   copies of the Software, and to permit persons to whom the Software is
+   furnished to do so, subject to the following conditions:
+   
+   The above copyright notice and this permission notice shall be included in
+   all copies or substantial portions of the Software.
+   
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+   IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+   FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+   AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+   LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+   OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+   THE SOFTWARE.
+
+ */
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <math.h>
+#include <string.h>
+#include <assert.h>
+#include "dist.h"
+
+extern void error(const char *format, ...);
+
+struct _dist_t
+{
+    uint64_t *bins, nvalues;
+    int nbins;
+    int npow;   // the number of orders of magnitude to represent exactly
+    int nexact; // pow(10,npow)
+    int nlevel;
+};
+
+dist_t *dist_init(int npow)
+{
+    dist_t *dist = (dist_t*) calloc(1,sizeof(dist_t));
+    dist->npow   = npow;
+    dist->nexact = pow(10,npow);
+    dist->nlevel = dist->nexact - pow(10,npow-1);
+    return dist;
+}
+
+void dist_destroy(dist_t *dist)
+{
+    if ( !dist ) return;
+    free(dist->bins);
+    free(dist);
+}
+
+int dist_nbins(dist_t *dist)
+{
+    return dist->nbins;
+}
+
+int dist_nvalues(dist_t *dist)
+{
+    return dist->nvalues;
+}
+
+uint32_t dist_insert(dist_t *dist, uint32_t value)
+{
+    int ibin;
+
+    if ( value <= dist->nexact ) 
+        ibin = value;
+    else
+    {
+        int npow  = (int) log10(value);
+        int level = npow - dist->npow + 1;
+        uint32_t step = pow(10, level);
+        ibin = dist->nexact + dist->nlevel*(level-1) + (value - pow(10,npow)) / step;
+    }
+
+    if ( ibin >= dist->nbins )
+    {
+        dist->bins = (uint64_t*) realloc(dist->bins, sizeof(*dist->bins)*(ibin+1));
+        memset(dist->bins + dist->nbins, 0, (ibin+1 - dist->nbins)*sizeof(*dist->bins));
+        dist->nbins = ibin+1;
+    }
+    dist->bins[ibin]++;
+    dist->nvalues++;
+    return ibin;
+}
+uint32_t dist_insert_n(dist_t *dist, uint32_t value, uint32_t cnt)
+{
+    if ( !cnt ) return 0;
+    int ibin = dist_insert(dist, value);
+    dist->bins[ibin] += cnt - 1;
+    dist->nvalues += cnt;
+    return ibin;
+}
+
+uint64_t dist_get(dist_t *dist, uint32_t idx, uint32_t *beg, uint32_t *end)
+{
+    if ( idx < dist->nexact )
+    {
+        if ( beg ) *beg = idx;
+        if ( end ) *end = idx + 1;
+    }
+    else
+    {
+        int level = (idx - dist->nexact) / dist->nlevel + 1;
+        int bin   = idx - dist->nexact - dist->nlevel*(level-1);
+
+        uint32_t step  = pow(10, level);
+        uint32_t value = pow(10, level + dist->npow - 1) + step*bin;
+
+        if ( beg ) *beg = value;
+        if ( end ) *end = value + step;
+    }
+    return dist->bins[idx];
+}
+
diff --git a/bcftools/dist.h b/bcftools/dist.h
new file mode 100644
index 0000000..5c9c571
--- /dev/null
+++ b/bcftools/dist.h
@@ -0,0 +1,98 @@
+/* The MIT License
+
+   Copyright (c) 2016-2020 Genome Research Ltd.
+
+   Author: Petr Danecek <pd3@sanger.ac.uk>
+   
+   Permission is hereby granted, free of charge, to any person obtaining a copy
+   of this software and associated documentation files (the "Software"), to deal
+   in the Software without restriction, including without limitation the rights
+   to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+   copies of the Software, and to permit persons to whom the Software is
+   furnished to do so, subject to the following conditions:
+   
+   The above copyright notice and this permission notice shall be included in
+   all copies or substantial portions of the Software.
+   
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+   IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+   FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+   AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+   LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+   OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+   THE SOFTWARE.
+
+ */
+/*
+    Logarithmic binning
+
+    Example of usage:
+
+        // Initialize, make the binning exact up to 10^4, then add a log-step
+        dist_t *dist = dist_init(4);
+
+        // Insert values
+        int i;
+        for (i=0; i<1e6; i++)
+            dist_insert(dist, i);
+
+        // Number of bins used
+        int n = dist_n(dist);
+
+        // Now print the distribution
+        uint32_t beg, end;
+        for (i=0; i<n; i++)
+        {
+            // Raw count in the bin. The boundaries beg,end are optional, 
+            // and can be used to plot correctly the density
+            uint64_t cnt = dist_get(dist, i, &beg, &end);
+            if ( !cnt ) continue;
+
+            // Print the interval, count and density
+            printf("%u\t%u\t%"PRIu64"\t%f\n", beg, end, cnt, (double)cnt/(end-beg));
+        }
+
+        // Clean up
+        dist_destroy(dist);
+ */
+
+#ifndef __DIST_H__
+#define __DIST_H__
+
+#include <stdio.h>
+#include <inttypes.h>
+
+typedef struct _dist_t dist_t;
+
+/*
+ *  dist_init() - init bins
+ */
+dist_t *dist_init(int npow);
+void dist_destroy(dist_t *dist);
+
+/*
+    dist_nbins() - get the number of bins
+ */
+int dist_nbins(dist_t *dist);
+
+/*
+    dist_nvalues() - get the total number of values inserted
+ */
+int dist_nvalues(dist_t *dist);
+
+/*
+    dist_insert()   - insert new value
+    dist_insert_n() - insert new value n times
+ */
+uint32_t dist_insert(dist_t *dist, uint32_t value);
+uint32_t dist_insert_n(dist_t *dist, uint32_t value, uint32_t cnt);
+
+/*
+   dist_get() 
+   @idx:        from the interval [0,dist_n-1]
+   @beg,end:    [beg,end)
+ */
+uint64_t dist_get(dist_t *dist, uint32_t idx, uint32_t *beg, uint32_t *end);
+
+#endif
+
diff --git a/bcftools/em.c b/bcftools/em.c
new file mode 100644
index 0000000..baa3490
--- /dev/null
+++ b/bcftools/em.c
@@ -0,0 +1,259 @@
+/*  em.c -- mathematical functions.
+
+    Copyright (C) 2010, 2011 Broad Institute.
+    Portions copyright (C) 2013-2014 Genome Research Ltd.
+
+    Author: Heng Li <lh3@live.co.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.  */
+
+#include <stdlib.h>
+#include <string.h>
+#include <math.h>
+#include <htslib/vcf.h>
+#include "kmin.h"
+#include "call.h"
+
+#define ITER_MAX 50
+#define ITER_TRY 10
+#define EPS 1e-5
+
+extern double kf_gammaq(double, double);
+
+/*
+    Generic routines
+ */
+
+// estimate site allele frequency in a very naive and inaccurate way
+static double est_freq(int n, const double *pdg)
+{
+    int i, gcnt[3], tmp1;
+    // get a rough estimate of the genotype frequency
+    gcnt[0] = gcnt[1] = gcnt[2] = 0;
+    for (i = 0; i < n; ++i) {
+        const double *p = pdg + i * 3;
+        if (p[0] != 1. || p[1] != 1. || p[2] != 1.) {
+            int which = p[0] > p[1]? 0 : 1;
+            which = p[which] > p[2]? which : 2;
+            ++gcnt[which];
+        }
+    }
+    tmp1 = gcnt[0] + gcnt[1] + gcnt[2];
+    return (tmp1 == 0)? -1.0 : (.5 * gcnt[1] + gcnt[2]) / tmp1;
+}
+
+/*
+    Single-locus EM
+ */
+
+typedef struct {
+    int beg, end;
+    const double *pdg;
+} minaux1_t;
+
+static double prob1(double f, void *data)
+{
+    minaux1_t *a = (minaux1_t*)data;
+    double p = 1., l = 0., f3[3];
+    int i;
+//  printf("brent %lg\n", f);
+    if (f < 0 || f > 1) return 1e300;
+    f3[0] = (1.-f)*(1.-f); f3[1] = 2.*f*(1.-f); f3[2] = f*f;
+    for (i = a->beg; i < a->end; ++i) {
+        const double *pdg = a->pdg + i * 3;
+        p *= pdg[0] * f3[0] + pdg[1] * f3[1] + pdg[2] * f3[2];
+        if (p < 1e-200) l -= log(p), p = 1.;
+    }
+    return l - log(p);
+}
+
+// one EM iteration for allele frequency estimate
+static double freq_iter(double *f, const double *_pdg, int beg, int end)
+{
+    double f0 = *f, f3[3], err;
+    int i;
+//  printf("em %lg\n", *f);
+    f3[0] = (1.-f0)*(1.-f0); f3[1] = 2.*f0*(1.-f0); f3[2] = f0*f0;
+    for (i = beg, f0 = 0.; i < end; ++i) {
+        const double *pdg = _pdg + i * 3;
+        f0 += (pdg[1] * f3[1] + 2. * pdg[2] * f3[2])
+            / (pdg[0] * f3[0] + pdg[1] * f3[1] + pdg[2] * f3[2]);
+    }
+    f0 /= (end - beg) * 2;
+    err = fabs(f0 - *f);
+    *f = f0;
+    return err;
+}
+
+/* The following function combines EM and Brent's method. When the signal from
+ * the data is strong, EM is faster but sometimes, EM may converge very slowly.
+ * When this happens, we switch to Brent's method. The idea is learned from
+ * Rasmus Nielsen.
+ */
+static double freqml(double f0, int beg, int end, const double *pdg)
+{
+    int i;
+    double f;
+    for (i = 0, f = f0; i < ITER_TRY; ++i)
+        if (freq_iter(&f, pdg, beg, end) < EPS) break;
+    if (i == ITER_TRY) { // haven't converged yet; try Brent's method
+        minaux1_t a;
+        a.beg = beg; a.end = end; a.pdg = pdg;
+        kmin_brent(prob1, f0 == f? .5*f0 : f0, f, (void*)&a, EPS, &f);
+    }
+    return f;
+}
+
+// one EM iteration for genotype frequency estimate
+static double g3_iter(double g[3], const double *_pdg, int beg, int end)
+{
+    double err, gg[3];
+    int i;
+    gg[0] = gg[1] = gg[2] = 0.;
+//  printf("%lg,%lg,%lg\n", g[0], g[1], g[2]);
+    for (i = beg; i < end; ++i) {
+        double sum, tmp[3];
+        const double *pdg = _pdg + i * 3;
+        tmp[0] = pdg[0] * g[0]; tmp[1] = pdg[1] * g[1]; tmp[2] = pdg[2] * g[2];
+        sum = (tmp[0] + tmp[1] + tmp[2]) * (end - beg);
+        gg[0] += tmp[0] / sum; gg[1] += tmp[1] / sum; gg[2] += tmp[2] / sum;
+    }
+    err = fabs(gg[0] - g[0]) > fabs(gg[1] - g[1])? fabs(gg[0] - g[0]) : fabs(gg[1] - g[1]);
+    err = err > fabs(gg[2] - g[2])? err : fabs(gg[2] - g[2]);
+    g[0] = gg[0]; g[1] = gg[1]; g[2] = gg[2];
+    return err;
+}
+
+// perform likelihood ratio test
+static double lk_ratio_test(int n, int n1, const double *pdg, double f3[3][3])
+{
+    double r;
+    int i;
+    for (i = 0, r = 1.; i < n1; ++i) {
+        const double *p = pdg + i * 3;
+        r *= (p[0] * f3[1][0] + p[1] * f3[1][1] + p[2] * f3[1][2])
+            / (p[0] * f3[0][0] + p[1] * f3[0][1] + p[2] * f3[0][2]);
+    }
+    for (; i < n; ++i) {
+        const double *p = pdg + i * 3;
+        r *= (p[0] * f3[2][0] + p[1] * f3[2][1] + p[2] * f3[2][2])
+            / (p[0] * f3[0][0] + p[1] * f3[0][1] + p[2] * f3[0][2]);
+    }
+    return r;
+}
+
+// x[0]: ref frequency
+// x[1..3]: alt-alt, alt-ref, ref-ref frequenc
+// x[4]: HWE P-value
+// x[5..6]: group1 freq, group2 freq
+// x[7]: 1-degree P-value
+// x[8]: 2-degree P-value
+int bcf_em1(call_t *call, const bcf1_t *rec, int n1, int flag, double x[10])
+{
+    double *pdg;
+    int i, n; //, n2;
+    if (rec->n_allele < 2) return -1; // one allele only
+    // initialization
+    if (n1 < 0 || n1 > rec->n_sample) n1 = 0;
+    if (flag & 1<<7) flag |= 7<<5; // compute group freq if LRT is required
+    if (flag & 0xf<<1) flag |= 0xf<<1;
+    n = rec->n_sample; //n2 = n - n1;
+    pdg = call->pdg;
+    if (pdg == 0) return -1;
+    for (i = 0; i < 10; ++i) x[i] = -1.; // set to negative
+    {
+        if ((x[0] = est_freq(n, pdg)) < 0.) return -1; // no data
+        x[0] = freqml(x[0], 0, n, pdg);
+    }
+    if (flag & (0xf<<1|3<<8)) { // estimate the genotype frequency and test HWE
+        double *g = x + 1, f3[3], r;
+        f3[0] = g[0] = (1 - x[0]) * (1 - x[0]);
+        f3[1] = g[1] = 2 * x[0] * (1 - x[0]);
+        f3[2] = g[2] = x[0] * x[0];
+        for (i = 0; i < ITER_MAX; ++i)
+            if (g3_iter(g, pdg, 0, n) < EPS) break;
+        // Hardy-Weinberg equilibrium (HWE)
+        for (i = 0, r = 1.; i < n; ++i) {
+            double *p = pdg + i * 3;
+            r *= (p[0] * g[0] + p[1] * g[1] + p[2] * g[2]) / (p[0] * f3[0] + p[1] * f3[1] + p[2] * f3[2]);
+        }
+        x[4] = kf_gammaq(.5, log(r));
+    }
+    if ((flag & 7<<5) && n1 > 0 && n1 < n) { // group frequency
+        x[5] = freqml(x[0], 0, n1, pdg);
+        x[6] = freqml(x[0], n1, n, pdg);
+    }
+    if ((flag & 1<<7) && n1 > 0 && n1 < n) { // 1-degree P-value
+        double f[3], f3[3][3], tmp;
+        f[0] = x[0]; f[1] = x[5]; f[2] = x[6];
+        for (i = 0; i < 3; ++i)
+            f3[i][0] = (1-f[i])*(1-f[i]), f3[i][1] = 2*f[i]*(1-f[i]), f3[i][2] = f[i]*f[i];
+        tmp = log(lk_ratio_test(n, n1, pdg, f3));
+        if (tmp < 0) tmp = 0;
+        x[7] = kf_gammaq(.5, tmp);
+    }
+    if ((flag & 3<<8) && n1 > 0 && n1 < n) { // 2-degree P-value
+        double g[3][3], tmp;
+        for (i = 0; i < 3; ++i) memcpy(g[i], x + 1, 3 * sizeof(double));
+        for (i = 0; i < ITER_MAX; ++i)
+            if (g3_iter(g[1], pdg, 0, n1) < EPS) break;
+        for (i = 0; i < ITER_MAX; ++i)
+            if (g3_iter(g[2], pdg, n1, n) < EPS) break;
+        tmp = log(lk_ratio_test(n, n1, pdg, g));
+        if (tmp < 0) tmp = 0;
+        x[8] = kf_gammaq(1., tmp);
+    }
+    return 0;
+}
+
+/*
+    Two-locus EM (LD)
+ */
+
+#define _G1(h, k) ((h>>1&1) + (k>>1&1))
+#define _G2(h, k) ((h&1) + (k&1))
+
+#if 0
+// 0: the previous site; 1: the current site
+static int pair_freq_iter(int n, double *pdg[2], double f[4])
+{
+    double ff[4];
+    int i, k, h;
+//  printf("%lf,%lf,%lf,%lf\n", f[0], f[1], f[2], f[3]);
+    memset(ff, 0, 4 * sizeof(double));
+    for (i = 0; i < n; ++i) {
+        double *p[2], sum, tmp;
+        p[0] = pdg[0] + i * 3; p[1] = pdg[1] + i * 3;
+        for (k = 0, sum = 0.; k < 4; ++k)
+            for (h = 0; h < 4; ++h)
+                sum += f[k] * f[h] * p[0][_G1(k,h)] * p[1][_G2(k,h)];
+        for (k = 0; k < 4; ++k) {
+            tmp = f[0] * (p[0][_G1(0,k)] * p[1][_G2(0,k)] + p[0][_G1(k,0)] * p[1][_G2(k,0)])
+                + f[1] * (p[0][_G1(1,k)] * p[1][_G2(1,k)] + p[0][_G1(k,1)] * p[1][_G2(k,1)])
+                + f[2] * (p[0][_G1(2,k)] * p[1][_G2(2,k)] + p[0][_G1(k,2)] * p[1][_G2(k,2)])
+                + f[3] * (p[0][_G1(3,k)] * p[1][_G2(3,k)] + p[0][_G1(k,3)] * p[1][_G2(k,3)]);
+            ff[k] += f[k] * tmp / sum;
+        }
+    }
+    for (k = 0; k < 4; ++k) f[k] = ff[k] / (2 * n);
+    return 0;
+}
+#endif
+
+
diff --git a/bcftools/em.c.pysam.c b/bcftools/em.c.pysam.c
new file mode 100644
index 0000000..37a3dea
--- /dev/null
+++ b/bcftools/em.c.pysam.c
@@ -0,0 +1,261 @@
+#include "bcftools.pysam.h"
+
+/*  em.c -- mathematical functions.
+
+    Copyright (C) 2010, 2011 Broad Institute.
+    Portions copyright (C) 2013-2014 Genome Research Ltd.
+
+    Author: Heng Li <lh3@live.co.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.  */
+
+#include <stdlib.h>
+#include <string.h>
+#include <math.h>
+#include <htslib/vcf.h>
+#include "kmin.h"
+#include "call.h"
+
+#define ITER_MAX 50
+#define ITER_TRY 10
+#define EPS 1e-5
+
+extern double kf_gammaq(double, double);
+
+/*
+    Generic routines
+ */
+
+// estimate site allele frequency in a very naive and inaccurate way
+static double est_freq(int n, const double *pdg)
+{
+    int i, gcnt[3], tmp1;
+    // get a rough estimate of the genotype frequency
+    gcnt[0] = gcnt[1] = gcnt[2] = 0;
+    for (i = 0; i < n; ++i) {
+        const double *p = pdg + i * 3;
+        if (p[0] != 1. || p[1] != 1. || p[2] != 1.) {
+            int which = p[0] > p[1]? 0 : 1;
+            which = p[which] > p[2]? which : 2;
+            ++gcnt[which];
+        }
+    }
+    tmp1 = gcnt[0] + gcnt[1] + gcnt[2];
+    return (tmp1 == 0)? -1.0 : (.5 * gcnt[1] + gcnt[2]) / tmp1;
+}
+
+/*
+    Single-locus EM
+ */
+
+typedef struct {
+    int beg, end;
+    const double *pdg;
+} minaux1_t;
+
+static double prob1(double f, void *data)
+{
+    minaux1_t *a = (minaux1_t*)data;
+    double p = 1., l = 0., f3[3];
+    int i;
+//  fprintf(bcftools_stdout, "brent %lg\n", f);
+    if (f < 0 || f > 1) return 1e300;
+    f3[0] = (1.-f)*(1.-f); f3[1] = 2.*f*(1.-f); f3[2] = f*f;
+    for (i = a->beg; i < a->end; ++i) {
+        const double *pdg = a->pdg + i * 3;
+        p *= pdg[0] * f3[0] + pdg[1] * f3[1] + pdg[2] * f3[2];
+        if (p < 1e-200) l -= log(p), p = 1.;
+    }
+    return l - log(p);
+}
+
+// one EM iteration for allele frequency estimate
+static double freq_iter(double *f, const double *_pdg, int beg, int end)
+{
+    double f0 = *f, f3[3], err;
+    int i;
+//  fprintf(bcftools_stdout, "em %lg\n", *f);
+    f3[0] = (1.-f0)*(1.-f0); f3[1] = 2.*f0*(1.-f0); f3[2] = f0*f0;
+    for (i = beg, f0 = 0.; i < end; ++i) {
+        const double *pdg = _pdg + i * 3;
+        f0 += (pdg[1] * f3[1] + 2. * pdg[2] * f3[2])
+            / (pdg[0] * f3[0] + pdg[1] * f3[1] + pdg[2] * f3[2]);
+    }
+    f0 /= (end - beg) * 2;
+    err = fabs(f0 - *f);
+    *f = f0;
+    return err;
+}
+
+/* The following function combines EM and Brent's method. When the signal from
+ * the data is strong, EM is faster but sometimes, EM may converge very slowly.
+ * When this happens, we switch to Brent's method. The idea is learned from
+ * Rasmus Nielsen.
+ */
+static double freqml(double f0, int beg, int end, const double *pdg)
+{
+    int i;
+    double f;
+    for (i = 0, f = f0; i < ITER_TRY; ++i)
+        if (freq_iter(&f, pdg, beg, end) < EPS) break;
+    if (i == ITER_TRY) { // haven't converged yet; try Brent's method
+        minaux1_t a;
+        a.beg = beg; a.end = end; a.pdg = pdg;
+        kmin_brent(prob1, f0 == f? .5*f0 : f0, f, (void*)&a, EPS, &f);
+    }
+    return f;
+}
+
+// one EM iteration for genotype frequency estimate
+static double g3_iter(double g[3], const double *_pdg, int beg, int end)
+{
+    double err, gg[3];
+    int i;
+    gg[0] = gg[1] = gg[2] = 0.;
+//  fprintf(bcftools_stdout, "%lg,%lg,%lg\n", g[0], g[1], g[2]);
+    for (i = beg; i < end; ++i) {
+        double sum, tmp[3];
+        const double *pdg = _pdg + i * 3;
+        tmp[0] = pdg[0] * g[0]; tmp[1] = pdg[1] * g[1]; tmp[2] = pdg[2] * g[2];
+        sum = (tmp[0] + tmp[1] + tmp[2]) * (end - beg);
+        gg[0] += tmp[0] / sum; gg[1] += tmp[1] / sum; gg[2] += tmp[2] / sum;
+    }
+    err = fabs(gg[0] - g[0]) > fabs(gg[1] - g[1])? fabs(gg[0] - g[0]) : fabs(gg[1] - g[1]);
+    err = err > fabs(gg[2] - g[2])? err : fabs(gg[2] - g[2]);
+    g[0] = gg[0]; g[1] = gg[1]; g[2] = gg[2];
+    return err;
+}
+
+// perform likelihood ratio test
+static double lk_ratio_test(int n, int n1, const double *pdg, double f3[3][3])
+{
+    double r;
+    int i;
+    for (i = 0, r = 1.; i < n1; ++i) {
+        const double *p = pdg + i * 3;
+        r *= (p[0] * f3[1][0] + p[1] * f3[1][1] + p[2] * f3[1][2])
+            / (p[0] * f3[0][0] + p[1] * f3[0][1] + p[2] * f3[0][2]);
+    }
+    for (; i < n; ++i) {
+        const double *p = pdg + i * 3;
+        r *= (p[0] * f3[2][0] + p[1] * f3[2][1] + p[2] * f3[2][2])
+            / (p[0] * f3[0][0] + p[1] * f3[0][1] + p[2] * f3[0][2]);
+    }
+    return r;
+}
+
+// x[0]: ref frequency
+// x[1..3]: alt-alt, alt-ref, ref-ref frequenc
+// x[4]: HWE P-value
+// x[5..6]: group1 freq, group2 freq
+// x[7]: 1-degree P-value
+// x[8]: 2-degree P-value
+int bcf_em1(call_t *call, const bcf1_t *rec, int n1, int flag, double x[10])
+{
+    double *pdg;
+    int i, n; //, n2;
+    if (rec->n_allele < 2) return -1; // one allele only
+    // initialization
+    if (n1 < 0 || n1 > rec->n_sample) n1 = 0;
+    if (flag & 1<<7) flag |= 7<<5; // compute group freq if LRT is required
+    if (flag & 0xf<<1) flag |= 0xf<<1;
+    n = rec->n_sample; //n2 = n - n1;
+    pdg = call->pdg;
+    if (pdg == 0) return -1;
+    for (i = 0; i < 10; ++i) x[i] = -1.; // set to negative
+    {
+        if ((x[0] = est_freq(n, pdg)) < 0.) return -1; // no data
+        x[0] = freqml(x[0], 0, n, pdg);
+    }
+    if (flag & (0xf<<1|3<<8)) { // estimate the genotype frequency and test HWE
+        double *g = x + 1, f3[3], r;
+        f3[0] = g[0] = (1 - x[0]) * (1 - x[0]);
+        f3[1] = g[1] = 2 * x[0] * (1 - x[0]);
+        f3[2] = g[2] = x[0] * x[0];
+        for (i = 0; i < ITER_MAX; ++i)
+            if (g3_iter(g, pdg, 0, n) < EPS) break;
+        // Hardy-Weinberg equilibrium (HWE)
+        for (i = 0, r = 1.; i < n; ++i) {
+            double *p = pdg + i * 3;
+            r *= (p[0] * g[0] + p[1] * g[1] + p[2] * g[2]) / (p[0] * f3[0] + p[1] * f3[1] + p[2] * f3[2]);
+        }
+        x[4] = kf_gammaq(.5, log(r));
+    }
+    if ((flag & 7<<5) && n1 > 0 && n1 < n) { // group frequency
+        x[5] = freqml(x[0], 0, n1, pdg);
+        x[6] = freqml(x[0], n1, n, pdg);
+    }
+    if ((flag & 1<<7) && n1 > 0 && n1 < n) { // 1-degree P-value
+        double f[3], f3[3][3], tmp;
+        f[0] = x[0]; f[1] = x[5]; f[2] = x[6];
+        for (i = 0; i < 3; ++i)
+            f3[i][0] = (1-f[i])*(1-f[i]), f3[i][1] = 2*f[i]*(1-f[i]), f3[i][2] = f[i]*f[i];
+        tmp = log(lk_ratio_test(n, n1, pdg, f3));
+        if (tmp < 0) tmp = 0;
+        x[7] = kf_gammaq(.5, tmp);
+    }
+    if ((flag & 3<<8) && n1 > 0 && n1 < n) { // 2-degree P-value
+        double g[3][3], tmp;
+        for (i = 0; i < 3; ++i) memcpy(g[i], x + 1, 3 * sizeof(double));
+        for (i = 0; i < ITER_MAX; ++i)
+            if (g3_iter(g[1], pdg, 0, n1) < EPS) break;
+        for (i = 0; i < ITER_MAX; ++i)
+            if (g3_iter(g[2], pdg, n1, n) < EPS) break;
+        tmp = log(lk_ratio_test(n, n1, pdg, g));
+        if (tmp < 0) tmp = 0;
+        x[8] = kf_gammaq(1., tmp);
+    }
+    return 0;
+}
+
+/*
+    Two-locus EM (LD)
+ */
+
+#define _G1(h, k) ((h>>1&1) + (k>>1&1))
+#define _G2(h, k) ((h&1) + (k&1))
+
+#if 0
+// 0: the previous site; 1: the current site
+static int pair_freq_iter(int n, double *pdg[2], double f[4])
+{
+    double ff[4];
+    int i, k, h;
+//  fprintf(bcftools_stdout, "%lf,%lf,%lf,%lf\n", f[0], f[1], f[2], f[3]);
+    memset(ff, 0, 4 * sizeof(double));
+    for (i = 0; i < n; ++i) {
+        double *p[2], sum, tmp;
+        p[0] = pdg[0] + i * 3; p[1] = pdg[1] + i * 3;
+        for (k = 0, sum = 0.; k < 4; ++k)
+            for (h = 0; h < 4; ++h)
+                sum += f[k] * f[h] * p[0][_G1(k,h)] * p[1][_G2(k,h)];
+        for (k = 0; k < 4; ++k) {
+            tmp = f[0] * (p[0][_G1(0,k)] * p[1][_G2(0,k)] + p[0][_G1(k,0)] * p[1][_G2(k,0)])
+                + f[1] * (p[0][_G1(1,k)] * p[1][_G2(1,k)] + p[0][_G1(k,1)] * p[1][_G2(k,1)])
+                + f[2] * (p[0][_G1(2,k)] * p[1][_G2(2,k)] + p[0][_G1(k,2)] * p[1][_G2(k,2)])
+                + f[3] * (p[0][_G1(3,k)] * p[1][_G2(3,k)] + p[0][_G1(k,3)] * p[1][_G2(k,3)]);
+            ff[k] += f[k] * tmp / sum;
+        }
+    }
+    for (k = 0; k < 4; ++k) f[k] = ff[k] / (2 * n);
+    return 0;
+}
+#endif
+
+
diff --git a/bcftools/extsort.c b/bcftools/extsort.c
new file mode 100644
index 0000000..014e03b
--- /dev/null
+++ b/bcftools/extsort.c
@@ -0,0 +1,250 @@
+/*  ext-sort.h -- sort on disk
+
+   Copyright (C) 2020-2021 Genome Research Ltd.
+
+   Author: Petr Danecek <pd3@sanger.ac.uk>
+   
+   Permission is hereby granted, free of charge, to any person obtaining a copy
+   of this software and associated documentation files (the "Software"), to deal
+   in the Software without restriction, including without limitation the rights
+   to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+   copies of the Software, and to permit persons to whom the Software is
+   furnished to do so, subject to the following conditions:
+   
+   The above copyright notice and this permission notice shall be included in
+   all copies or substantial portions of the Software.
+   
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+   IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+   FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+   AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+   LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+   OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+   THE SOFTWARE.
+
+ */
+
+#include <stdio.h>
+#include <unistd.h>     // for unlink()
+#include <sys/stat.h>   // for chmod()
+#include <assert.h>
+#include <fcntl.h>
+#ifdef _WIN32
+#include <windows.h>
+#endif
+#include "bcftools.h"
+#include "extsort.h"
+#include "kheap.h"
+
+typedef struct
+{
+    extsort_t *es;  // this is to get access to extsort_cmp_f from kheap
+    int fd;
+    char *fname;
+    void *dat;
+}
+blk_t;
+
+static inline int blk_is_smaller(blk_t **aptr, blk_t **bptr);
+KHEAP_INIT(blk, blk_t*, blk_is_smaller)     /* defines khp_blk_t */
+
+struct _extsort_t
+{
+    size_t dat_size, mem, max_mem;
+    char *tmp_prefix;
+    extsort_cmp_f cmp;
+
+    size_t nbuf, mbuf, nblk;
+    blk_t **blk;
+    void **buf, *tmp_dat;
+    khp_blk_t *bhp;
+};
+
+static inline int blk_is_smaller(blk_t **aptr, blk_t **bptr)
+{
+    blk_t *a = *aptr;
+    blk_t *b = *bptr;
+    int ret = a->es->cmp(&a->dat,&b->dat);
+    if ( ret < 0 ) return 1;
+    return 0;
+}
+
+size_t parse_mem_string(const char *str);
+
+void extsort_set(extsort_t *es, extsort_opt_t key, void *value)
+{
+    if ( key==DAT_SIZE ) { es->dat_size = *((size_t*)value); return; }
+    if ( key==MAX_MEM )
+    {
+        es->max_mem = parse_mem_string(*((const char**)value));
+        if ( es->max_mem <=0 ) error("Could not parse the memory string, expected positive number: %s\n",*((const char**)value));
+        return;
+    }
+    if ( key==TMP_PREFIX ) { es->tmp_prefix = init_tmp_prefix(*((const char**)value)); return; }
+    if ( key==FUNC_CMP ) { es->cmp = *((extsort_cmp_f*)value); return; }
+}
+
+extsort_t *extsort_alloc(void)
+{
+    extsort_t *es = (extsort_t*) calloc(1,sizeof(*es));
+    es->max_mem = 100e6;
+    return es;
+}
+void extsort_init(extsort_t *es)
+{
+    assert( es->cmp );
+    assert( es->dat_size );
+    if ( !es->tmp_prefix ) es->tmp_prefix = init_tmp_prefix(NULL);
+    es->tmp_dat = malloc(es->dat_size);
+}
+
+void extsort_destroy(extsort_t *es)
+{
+    int i;
+    for (i=0; i<es->nblk; i++)
+    {
+        blk_t *blk = es->blk[i];
+        if ( blk->fd!=-1 )
+#ifdef _WIN32
+            _close(blk->fd);
+#else
+            close(blk->fd);
+#endif
+        free(blk->fname);
+        free(blk->dat);
+        free(blk);
+    }
+    free(es->tmp_dat);
+    free(es->tmp_prefix);
+    free(es->blk);
+    khp_destroy(blk, es->bhp);
+    free(es);
+}
+
+static void _buf_flush(extsort_t *es)
+{
+    int i;
+    if ( !es->nbuf ) return;
+
+    qsort(es->buf, es->nbuf, sizeof(void*), es->cmp);
+
+    es->nblk++;
+    es->blk = (blk_t**) realloc(es->blk, sizeof(blk_t*)*es->nblk);
+    es->blk[es->nblk-1] = (blk_t*) calloc(1,sizeof(blk_t));
+    blk_t *blk = es->blk[es->nblk-1];
+    blk->es    = es;
+    blk->dat   = malloc(es->dat_size);
+    blk->fname = strdup(es->tmp_prefix);
+    #ifdef _WIN32
+        for (i=0; i<100000; i++)
+        {
+            memcpy(blk->fname,es->tmp_prefix,strlen(es->tmp_prefix));
+            mktemp(blk->fname);
+            blk->fd = _open(blk->fname, O_RDWR|O_CREAT|O_EXCL|O_BINARY|O_TEMPORARY, 0600);
+            if ( blk->fd==-1 )
+            {
+                if ( errno==EEXIST ) continue; 
+                error("Error: failed to open a temporary file %s\n",blk->fname);
+            }
+            break;
+        }
+        if ( !blk->fd ) error("Error: failed to create a unique temporary file name from %s\n",es->tmp_prefix);
+        if ( _chmod(blk->fname, S_IRUSR|S_IWUSR)!=0 ) error("Error: failed to set permissions of the temporary file %s\n",blk->fname);
+    #else
+        if ( (blk->fd = mkstemp(blk->fname))==-1 )
+            error("Error: failed to open a temporary file %s\n",blk->fname);
+        if ( fchmod(blk->fd,S_IRUSR|S_IWUSR)!=0 ) error("Error: failed to set permissions of the temporary file %s\n",blk->fname);
+        unlink(blk->fname); // should auto delete when closed on linux, the descriptor remains open
+    #endif
+
+    for (i=0; i<es->nbuf; i++)
+    {
+        #ifdef _WIN32
+            if ( _write(blk->fd, es->buf[i], es->dat_size)!=es->dat_size ) error("Error: failed to write %zu bytes to the temporary file %s\n",es->dat_size,blk->fname);
+        #else
+            if ( write(blk->fd, es->buf[i], es->dat_size)!=es->dat_size ) error("Error: failed to write %zu bytes to the temporary file %s\n",es->dat_size,blk->fname);
+        #endif
+        free(es->buf[i]);
+    }
+#ifdef _WIN32
+    if ( _lseek(blk->fd,0,SEEK_SET)!=0 ) error("Error: failed to lseek() to the start of the temporary file %s\n", blk->fname);
+#else
+    if ( lseek(blk->fd,0,SEEK_SET)!=0 ) error("Error: failed to lseek() to the start of the temporary file %s\n", blk->fname);
+#endif
+
+    es->nbuf = 0;
+    es->mem  = 0;
+}
+
+void extsort_push(extsort_t *es, void *dat)
+{
+    int delta = sizeof(void*) + es->dat_size;
+    if ( es->nbuf && es->mem + delta > es->max_mem ) _buf_flush(es);
+    es->nbuf++;
+    es->mem += delta;
+    hts_expand(void*, es->nbuf, es->mbuf, es->buf);
+    es->buf[es->nbuf-1] = dat;
+}
+
+// return number of elements read
+static ssize_t _blk_read(extsort_t *es, blk_t *blk)
+{
+    ssize_t ret = 0;
+    if ( blk->fd==-1 ) return ret;
+#ifdef _WIN32
+    ret = _read(blk->fd, blk->dat, es->dat_size);
+#else
+    ret = read(blk->fd, blk->dat, es->dat_size);
+#endif
+    if ( ret < 0 ) error("Error: failed to read from the temporary file %s\n", blk->fname);
+    if ( ret == 0 )
+    {
+#ifdef _WIN32
+        if ( _close(blk->fd)!=0 ) error("Error: failed to close the temporary file %s\n", blk->fname);
+#else
+        if ( close(blk->fd)!=0 ) error("Error: failed to close the temporary file %s\n", blk->fname);
+#endif
+        blk->fd = -1;
+        return ret;
+    }
+    if ( ret < es->dat_size ) error("Error: failed to read %zu bytes from the temporary file %s\n",es->dat_size,blk->fname);
+    return ret;
+}
+
+void extsort_sort(extsort_t *es)
+{
+    _buf_flush(es);
+    free(es->buf);
+    es->buf = NULL;
+    es->bhp = khp_init(blk);
+
+    // open all blocks, read one record from each, create a heap
+    int i;
+    for (i=0; i<es->nblk; i++)
+    {
+        blk_t *blk = es->blk[i];
+#ifdef _WIN32
+        if ( _lseek(blk->fd,0,SEEK_SET)!=0 ) error("Error: failed to lseek() to the start of the temporary file %s\n", blk->fname);
+#else
+        if ( lseek(blk->fd,0,SEEK_SET)!=0 ) error("Error: failed to lseek() to the start of the temporary file %s\n", blk->fname);
+#endif
+        int ret = _blk_read(es, blk);
+        if ( ret ) khp_insert(blk, es->bhp, &blk);
+    }
+}
+
+void *extsort_shift(extsort_t *es)
+{
+    if ( !es->bhp->ndat ) return NULL;
+    blk_t *blk = es->bhp->dat[0];
+
+    // swap the pointer which keeps the location of user data so that it is not overwritten by the next read
+    void *tmp = es->tmp_dat; es->tmp_dat = blk->dat; blk->dat = tmp;
+    khp_delete(blk, es->bhp);
+
+    int ret = _blk_read(es, blk);
+    if ( ret ) khp_insert(blk, es->bhp, &blk);
+
+    return es->tmp_dat;
+}
+
diff --git a/bcftools/extsort.c.pysam.c b/bcftools/extsort.c.pysam.c
new file mode 100644
index 0000000..1b410a7
--- /dev/null
+++ b/bcftools/extsort.c.pysam.c
@@ -0,0 +1,252 @@
+#include "bcftools.pysam.h"
+
+/*  ext-sort.h -- sort on disk
+
+   Copyright (C) 2020-2021 Genome Research Ltd.
+
+   Author: Petr Danecek <pd3@sanger.ac.uk>
+   
+   Permission is hereby granted, free of charge, to any person obtaining a copy
+   of this software and associated documentation files (the "Software"), to deal
+   in the Software without restriction, including without limitation the rights
+   to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+   copies of the Software, and to permit persons to whom the Software is
+   furnished to do so, subject to the following conditions:
+   
+   The above copyright notice and this permission notice shall be included in
+   all copies or substantial portions of the Software.
+   
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+   IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+   FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+   AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+   LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+   OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+   THE SOFTWARE.
+
+ */
+
+#include <stdio.h>
+#include <unistd.h>     // for unlink()
+#include <sys/stat.h>   // for chmod()
+#include <assert.h>
+#include <fcntl.h>
+#ifdef _WIN32
+#include <windows.h>
+#endif
+#include "bcftools.h"
+#include "extsort.h"
+#include "kheap.h"
+
+typedef struct
+{
+    extsort_t *es;  // this is to get access to extsort_cmp_f from kheap
+    int fd;
+    char *fname;
+    void *dat;
+}
+blk_t;
+
+static inline int blk_is_smaller(blk_t **aptr, blk_t **bptr);
+KHEAP_INIT(blk, blk_t*, blk_is_smaller)     /* defines khp_blk_t */
+
+struct _extsort_t
+{
+    size_t dat_size, mem, max_mem;
+    char *tmp_prefix;
+    extsort_cmp_f cmp;
+
+    size_t nbuf, mbuf, nblk;
+    blk_t **blk;
+    void **buf, *tmp_dat;
+    khp_blk_t *bhp;
+};
+
+static inline int blk_is_smaller(blk_t **aptr, blk_t **bptr)
+{
+    blk_t *a = *aptr;
+    blk_t *b = *bptr;
+    int ret = a->es->cmp(&a->dat,&b->dat);
+    if ( ret < 0 ) return 1;
+    return 0;
+}
+
+size_t parse_mem_string(const char *str);
+
+void extsort_set(extsort_t *es, extsort_opt_t key, void *value)
+{
+    if ( key==DAT_SIZE ) { es->dat_size = *((size_t*)value); return; }
+    if ( key==MAX_MEM )
+    {
+        es->max_mem = parse_mem_string(*((const char**)value));
+        if ( es->max_mem <=0 ) error("Could not parse the memory string, expected positive number: %s\n",*((const char**)value));
+        return;
+    }
+    if ( key==TMP_PREFIX ) { es->tmp_prefix = init_tmp_prefix(*((const char**)value)); return; }
+    if ( key==FUNC_CMP ) { es->cmp = *((extsort_cmp_f*)value); return; }
+}
+
+extsort_t *extsort_alloc(void)
+{
+    extsort_t *es = (extsort_t*) calloc(1,sizeof(*es));
+    es->max_mem = 100e6;
+    return es;
+}
+void extsort_init(extsort_t *es)
+{
+    assert( es->cmp );
+    assert( es->dat_size );
+    if ( !es->tmp_prefix ) es->tmp_prefix = init_tmp_prefix(NULL);
+    es->tmp_dat = malloc(es->dat_size);
+}
+
+void extsort_destroy(extsort_t *es)
+{
+    int i;
+    for (i=0; i<es->nblk; i++)
+    {
+        blk_t *blk = es->blk[i];
+        if ( blk->fd!=-1 )
+#ifdef _WIN32
+            _close(blk->fd);
+#else
+            close(blk->fd);
+#endif
+        free(blk->fname);
+        free(blk->dat);
+        free(blk);
+    }
+    free(es->tmp_dat);
+    free(es->tmp_prefix);
+    free(es->blk);
+    khp_destroy(blk, es->bhp);
+    free(es);
+}
+
+static void _buf_flush(extsort_t *es)
+{
+    int i;
+    if ( !es->nbuf ) return;
+
+    qsort(es->buf, es->nbuf, sizeof(void*), es->cmp);
+
+    es->nblk++;
+    es->blk = (blk_t**) realloc(es->blk, sizeof(blk_t*)*es->nblk);
+    es->blk[es->nblk-1] = (blk_t*) calloc(1,sizeof(blk_t));
+    blk_t *blk = es->blk[es->nblk-1];
+    blk->es    = es;
+    blk->dat   = malloc(es->dat_size);
+    blk->fname = strdup(es->tmp_prefix);
+    #ifdef _WIN32
+        for (i=0; i<100000; i++)
+        {
+            memcpy(blk->fname,es->tmp_prefix,strlen(es->tmp_prefix));
+            mktemp(blk->fname);
+            blk->fd = _open(blk->fname, O_RDWR|O_CREAT|O_EXCL|O_BINARY|O_TEMPORARY, 0600);
+            if ( blk->fd==-1 )
+            {
+                if ( errno==EEXIST ) continue; 
+                error("Error: failed to open a temporary file %s\n",blk->fname);
+            }
+            break;
+        }
+        if ( !blk->fd ) error("Error: failed to create a unique temporary file name from %s\n",es->tmp_prefix);
+        if ( _chmod(blk->fname, S_IRUSR|S_IWUSR)!=0 ) error("Error: failed to set permissions of the temporary file %s\n",blk->fname);
+    #else
+        if ( (blk->fd = mkstemp(blk->fname))==-1 )
+            error("Error: failed to open a temporary file %s\n",blk->fname);
+        if ( fchmod(blk->fd,S_IRUSR|S_IWUSR)!=0 ) error("Error: failed to set permissions of the temporary file %s\n",blk->fname);
+        unlink(blk->fname); // should auto delete when closed on linux, the descriptor remains open
+    #endif
+
+    for (i=0; i<es->nbuf; i++)
+    {
+        #ifdef _WIN32
+            if ( _write(blk->fd, es->buf[i], es->dat_size)!=es->dat_size ) error("Error: failed to write %zu bytes to the temporary file %s\n",es->dat_size,blk->fname);
+        #else
+            if ( write(blk->fd, es->buf[i], es->dat_size)!=es->dat_size ) error("Error: failed to write %zu bytes to the temporary file %s\n",es->dat_size,blk->fname);
+        #endif
+        free(es->buf[i]);
+    }
+#ifdef _WIN32
+    if ( _lseek(blk->fd,0,SEEK_SET)!=0 ) error("Error: failed to lseek() to the start of the temporary file %s\n", blk->fname);
+#else
+    if ( lseek(blk->fd,0,SEEK_SET)!=0 ) error("Error: failed to lseek() to the start of the temporary file %s\n", blk->fname);
+#endif
+
+    es->nbuf = 0;
+    es->mem  = 0;
+}
+
+void extsort_push(extsort_t *es, void *dat)
+{
+    int delta = sizeof(void*) + es->dat_size;
+    if ( es->nbuf && es->mem + delta > es->max_mem ) _buf_flush(es);
+    es->nbuf++;
+    es->mem += delta;
+    hts_expand(void*, es->nbuf, es->mbuf, es->buf);
+    es->buf[es->nbuf-1] = dat;
+}
+
+// return number of elements read
+static ssize_t _blk_read(extsort_t *es, blk_t *blk)
+{
+    ssize_t ret = 0;
+    if ( blk->fd==-1 ) return ret;
+#ifdef _WIN32
+    ret = _read(blk->fd, blk->dat, es->dat_size);
+#else
+    ret = read(blk->fd, blk->dat, es->dat_size);
+#endif
+    if ( ret < 0 ) error("Error: failed to read from the temporary file %s\n", blk->fname);
+    if ( ret == 0 )
+    {
+#ifdef _WIN32
+        if ( _close(blk->fd)!=0 ) error("Error: failed to close the temporary file %s\n", blk->fname);
+#else
+        if ( close(blk->fd)!=0 ) error("Error: failed to close the temporary file %s\n", blk->fname);
+#endif
+        blk->fd = -1;
+        return ret;
+    }
+    if ( ret < es->dat_size ) error("Error: failed to read %zu bytes from the temporary file %s\n",es->dat_size,blk->fname);
+    return ret;
+}
+
+void extsort_sort(extsort_t *es)
+{
+    _buf_flush(es);
+    free(es->buf);
+    es->buf = NULL;
+    es->bhp = khp_init(blk);
+
+    // open all blocks, read one record from each, create a heap
+    int i;
+    for (i=0; i<es->nblk; i++)
+    {
+        blk_t *blk = es->blk[i];
+#ifdef _WIN32
+        if ( _lseek(blk->fd,0,SEEK_SET)!=0 ) error("Error: failed to lseek() to the start of the temporary file %s\n", blk->fname);
+#else
+        if ( lseek(blk->fd,0,SEEK_SET)!=0 ) error("Error: failed to lseek() to the start of the temporary file %s\n", blk->fname);
+#endif
+        int ret = _blk_read(es, blk);
+        if ( ret ) khp_insert(blk, es->bhp, &blk);
+    }
+}
+
+void *extsort_shift(extsort_t *es)
+{
+    if ( !es->bhp->ndat ) return NULL;
+    blk_t *blk = es->bhp->dat[0];
+
+    // swap the pointer which keeps the location of user data so that it is not overwritten by the next read
+    void *tmp = es->tmp_dat; es->tmp_dat = blk->dat; blk->dat = tmp;
+    khp_delete(blk, es->bhp);
+
+    int ret = _blk_read(es, blk);
+    if ( ret ) khp_insert(blk, es->bhp, &blk);
+
+    return es->tmp_dat;
+}
+
diff --git a/bcftools/extsort.h b/bcftools/extsort.h
new file mode 100644
index 0000000..ba6282e
--- /dev/null
+++ b/bcftools/extsort.h
@@ -0,0 +1,56 @@
+/*  ext-sort.h -- sort on disk
+
+   Copyright (C) 2020 Genome Research Ltd.
+
+   Author: Petr Danecek <pd3@sanger.ac.uk>
+   
+   Permission is hereby granted, free of charge, to any person obtaining a copy
+   of this software and associated documentation files (the "Software"), to deal
+   in the Software without restriction, including without limitation the rights
+   to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+   copies of the Software, and to permit persons to whom the Software is
+   furnished to do so, subject to the following conditions:
+   
+   The above copyright notice and this permission notice shall be included in
+   all copies or substantial portions of the Software.
+   
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+   IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+   FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+   AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+   LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+   OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+   THE SOFTWARE.
+
+ */
+
+#ifndef __EXTSORT_H__
+#define __EXTSORT_H__
+
+//todo: return status to all functions
+
+typedef struct _extsort_t extsort_t;
+
+typedef int (*extsort_cmp_f) (const void *aptr, const void *bptr);
+
+// Modes of operation
+typedef enum
+{
+    DAT_SIZE,       // size_t        .. assuming constant size records for now
+    TMP_PREFIX,     // const char*   .. prefix of temporary files, XXXXXX will be appended
+    MAX_MEM,        // const char*   .. maximum memory to use, e.g. 100MB
+    FUNC_CMP,       // extsort_cmp_f .. sort function
+}
+extsort_opt_t;
+
+#define extsort_set_opt(es,type,key,value) { type tmp = value; extsort_set(es, key, (void*)&tmp); }
+
+extsort_t *extsort_alloc(void);
+void extsort_set(extsort_t *es, extsort_opt_t key, void *value);
+void extsort_init(extsort_t *es);
+void extsort_push(extsort_t *es, void *dat);    // dat will be freed by extsort later
+void extsort_sort(extsort_t *es);
+void *extsort_shift(extsort_t *es);
+void extsort_destroy(extsort_t *es);
+
+#endif
diff --git a/bcftools/filter.c b/bcftools/filter.c
new file mode 100644
index 0000000..d545608
--- /dev/null
+++ b/bcftools/filter.c
@@ -0,0 +1,3671 @@
+/*  filter.c -- filter expressions.
+
+    Copyright (C) 2013-2022 Genome Research Ltd.
+
+    Author: Petr Danecek <pd3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.  */
+
+#include <ctype.h>
+#include <stdlib.h>
+#include <strings.h>
+#include <assert.h>
+#include <errno.h>
+#include <math.h>
+#include <sys/types.h>
+#include <inttypes.h>
+#ifndef _WIN32
+#include <pwd.h>
+#endif
+#include <regex.h>
+#include <htslib/khash_str2int.h>
+#include <htslib/hts_defs.h>
+#include <htslib/vcfutils.h>
+#include <htslib/kfunc.h>
+#include "config.h"
+#include "filter.h"
+#include "bcftools.h"
+
+#if ENABLE_PERL_FILTERS
+#  define filter_t perl_filter_t
+#  include <EXTERN.h>
+#  include <perl.h>
+#  undef filter_t
+#  define my_perl perl
+
+static int filter_ninit = 0;
+#endif
+
+
+#ifndef __FUNCTION__
+#  define __FUNCTION__ __func__
+#endif
+
+typedef struct _token_t
+{
+    // read-only values, same for all VCF lines
+    int tok_type;       // one of the TOK_* keys below
+    int nargs;          // with TOK_PERLSUB the first argument is the name of the subroutine
+    char *key;          // set only for string constants, otherwise NULL
+    char *tag;          // for debugging and printout only, VCF tag name
+    double threshold;   // filtering threshold
+    int is_constant;    // the threshold is set
+    int hdr_id, tag_type;   // BCF header lookup ID and one of BCF_HL_* types
+    int idx;            // 0-based index to VCF vectors,
+                        //  -2: list (e.g. [0,1,2] or [1..3] or [1..] or any field[*], which is equivalent to [0..])
+    int *idxs;          // set indexes to 0 to exclude, to 1 to include, and last element negative if unlimited; used by VCF retrievers only
+    int nidxs, nuidxs;  // size of idxs array and the number of elements set to 1
+    uint8_t *usmpl;     // bitmask of used samples as set by idx, set for FORMAT fields, NULL otherwise
+    int nsamples;       // number of samples for format fields, 0 for info and other fields
+    void (*setter)(filter_t *, bcf1_t *, struct _token_t *);
+    int (*func)(filter_t *, bcf1_t *, struct _token_t *rtok, struct _token_t **stack, int nstack);
+    void (*comparator)(struct _token_t *, struct _token_t *, struct _token_t *rtok, bcf1_t *);
+    void *hash;         // test presence of str value in the hash via comparator
+    regex_t *regex;     // precompiled regex for string comparison
+
+    // modified on filter evaluation at each VCF line
+    double *values;
+    kstring_t str_value;
+    int is_str, is_missing; // is_missing is set only for constants, variables are controled via nvalues
+    int pass_site;          // -1 not applicable, 0 fails, >0 pass
+    uint8_t *pass_samples;  // status of individual samples
+    int nvalues, mvalues;   // number of used values: n=0 for missing values, n=1 for scalars, for strings n=str_value.l
+    int nval1;              // number of per-sample fields or string length
+}
+token_t;
+
+struct _filter_t
+{
+    bcf_hdr_t *hdr;
+    char *str;
+    int nfilters;
+    token_t *filters, **flt_stack;  // filtering input tokens (in RPN) and evaluation stack
+    int32_t *tmpi;
+    float   *tmpf;
+    kstring_t tmps;
+    int max_unpack, mtmpi, mtmpf, nsamples;
+#if ENABLE_PERL_FILTERS
+    PerlInterpreter *perl;
+#endif
+};
+
+
+#define TOK_VAL     0
+#define TOK_LFT     1       // (
+#define TOK_RGT     2       // )
+#define TOK_LE      3       // less or equal
+#define TOK_LT      4       // less than
+#define TOK_EQ      5       // equal
+#define TOK_BT      6       // bigger than
+#define TOK_BE      7       // bigger or equal
+#define TOK_NE      8       // not equal
+#define TOK_OR      9       // |
+#define TOK_AND     10      // &
+#define TOK_ADD     11      // +
+#define TOK_SUB     12      // -
+#define TOK_MULT    13      // *
+#define TOK_DIV     14      // /
+#define TOK_MAX     15
+#define TOK_MIN     16
+#define TOK_AVG     17
+#define TOK_AND_VEC 18      // &&   (operator applied in samples)
+#define TOK_OR_VEC  19      // ||   (operator applied in samples)
+#define TOK_LIKE    20      //  ~ regular expression
+#define TOK_NLIKE   21      // !~ regular expression
+#define TOK_SUM     22
+#define TOK_ABS     23
+#define TOK_LEN     24
+#define TOK_FUNC    25
+#define TOK_CNT     26
+#define TOK_PERLSUB 27
+#define TOK_BINOM   28
+#define TOK_PHRED   29
+#define TOK_MEDIAN  30
+#define TOK_STDEV   31
+#define TOK_sMAX    32
+#define TOK_sMIN    33
+#define TOK_sAVG    34
+#define TOK_sMEDIAN 35
+#define TOK_sSTDEV  36
+#define TOK_sSUM    37
+#define TOK_IN      38      // contains, e.g. FILTER~"A"
+#define TOK_NOT_IN  39      // does not contain, e.g. FILTER!~"A"
+#define TOK_MODULO  40      // %
+
+//                      0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40
+//                        ( ) [ < = > ] ! | &  +  -  *  /  M  m  a  A  O  ~  ^  S  .  l  f  c  p  b  P  i  s                          %
+static int op_prec[] = {0,1,1,5,5,5,5,5,5,2,3, 6, 6, 7, 7, 8, 8, 8, 3, 2, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 7 };
+#define TOKEN_STRING "x()[<=>]!|&+-*/MmaAO~^S.lfcpis"       // this is only for debugging, not maintained diligently
+
+static void cmp_vector_strings(token_t *atok, token_t *btok, token_t *rtok);
+
+// Return negative values if it is a function with variable number of arguments
+static int filters_next_token(char **str, int *len)
+{
+    char *tmp = *str;
+    while ( *tmp && isspace(*tmp) ) tmp++;
+    *str = tmp;
+    *len = 0;
+
+    // test for doubles: d.ddde[+-]dd
+    if ( isdigit(*str[0]) || *str[0]=='.' )   // strtod would eat +/-
+    {
+        double HTS_UNUSED v = strtod(*str, &tmp);
+        if ( *str!=tmp && (!tmp[0] || !isalnum(tmp[0])) )
+        {
+            *len = tmp - (*str);
+            return TOK_VAL;
+        }
+        tmp = *str;
+    }
+
+    if ( !strncasecmp(tmp,"SMPL_MAX(",9) ) { (*str) += 8; return TOK_sMAX; }
+    if ( !strncasecmp(tmp,"SMPL_MIN(",9) ) { (*str) += 8; return TOK_sMIN; }
+    if ( !strncasecmp(tmp,"SMPL_MEAN(",10) ) { (*str) += 9; return TOK_sAVG; }
+    if ( !strncasecmp(tmp,"SMPL_MEDIAN(",12) ) { (*str) += 11; return TOK_sMEDIAN; }
+    if ( !strncasecmp(tmp,"SMPL_AVG(",9) ) { (*str) += 8; return TOK_sAVG; }
+    if ( !strncasecmp(tmp,"SMPL_STDEV(",11) ) { (*str) += 10; return TOK_sSTDEV; }
+    if ( !strncasecmp(tmp,"SMPL_SUM(",9) ) { (*str) += 8; return TOK_sSUM; }
+    if ( !strncasecmp(tmp,"sMAX(",5) ) { (*str) += 4; return TOK_sMAX; }
+    if ( !strncasecmp(tmp,"sMIN(",5) ) { (*str) += 4; return TOK_sMIN; }
+    if ( !strncasecmp(tmp,"sMEAN(",6) ) { (*str) += 5; return TOK_sAVG; }
+    if ( !strncasecmp(tmp,"sMEDIAN(",8) ) { (*str) += 7; return TOK_sMEDIAN; }
+    if ( !strncasecmp(tmp,"sAVG(",5) ) { (*str) += 4; return TOK_sAVG; }
+    if ( !strncasecmp(tmp,"sSTDEV(",7) ) { (*str) += 6; return TOK_sSTDEV; }
+    if ( !strncasecmp(tmp,"sSUM(",5) ) { (*str) += 4; return TOK_sSUM; }
+    if ( !strncasecmp(tmp,"MAX(",4) ) { (*str) += 3; return TOK_MAX; }
+    if ( !strncasecmp(tmp,"MIN(",4) ) { (*str) += 3; return TOK_MIN; }
+    if ( !strncasecmp(tmp,"MEAN(",5) ) { (*str) += 4; return TOK_AVG; }
+    if ( !strncasecmp(tmp,"MEDIAN(",7) ) { (*str) += 6; return TOK_MEDIAN; }
+    if ( !strncasecmp(tmp,"AVG(",4) ) { (*str) += 3; return TOK_AVG; }
+    if ( !strncasecmp(tmp,"STDEV(",6) ) { (*str) += 5; return TOK_STDEV; }
+    if ( !strncasecmp(tmp,"SUM(",4) ) { (*str) += 3; return TOK_SUM; }
+    if ( !strncasecmp(tmp,"ABS(",4) ) { (*str) += 3; return TOK_ABS; }
+    if ( !strncasecmp(tmp,"COUNT(",4) ) { (*str) += 5; return TOK_CNT; }
+    if ( !strncasecmp(tmp,"STRLEN(",7) ) { (*str) += 6; return TOK_LEN; }
+    if ( !strncasecmp(tmp,"BINOM(",6) ) { (*str) += 5; return -TOK_BINOM; }
+    if ( !strncasecmp(tmp,"PHRED(",6) ) { (*str) += 5; return TOK_PHRED; }
+    if ( !strncasecmp(tmp,"%MAX(",5) ) { (*str) += 4; return TOK_MAX; } // for backward compatibility
+    if ( !strncasecmp(tmp,"%MIN(",5) ) { (*str) += 4; return TOK_MIN; } // for backward compatibility
+    if ( !strncasecmp(tmp,"%AVG(",5) ) { (*str) += 4; return TOK_AVG; } // for backward compatibility
+    if ( !strncasecmp(tmp,"%SUM(",5) ) { (*str) += 4; return TOK_SUM; } // for backward compatibility
+    if ( !strncasecmp(tmp,"INFO/",5) ) tmp += 5;
+    if ( !strncasecmp(tmp,"FORMAT/",7) ) tmp += 7;
+    if ( !strncasecmp(tmp,"FMT/",4) ) tmp += 4;
+    if ( !strncasecmp(tmp,"PERL.",5) ) { (*str) += 5; return -TOK_PERLSUB; }
+    if ( !strncasecmp(tmp,"N_PASS(",7) ) { *len = 6; (*str) += 6; return -TOK_FUNC; }
+    if ( !strncasecmp(tmp,"F_PASS(",7) ) { *len = 6; (*str) += 6; return -TOK_FUNC; }
+    if ( !strncasecmp(tmp,"%ILEN",5) ) { *len = 5; return TOK_VAL; }    // to be able to distinguish between INFO/ILEN and on-the-fly ILEN
+
+    if ( tmp[0]=='@' )  // file name
+    {
+        while ( *tmp && !isspace(*tmp) && *tmp!='=' && *tmp!='!' ) tmp++;
+        *len = tmp - (*str);
+        return TOK_VAL;
+    }
+
+    int square_brackets = 0;
+    while ( tmp[0] )
+    {
+        if ( !square_brackets )
+        {
+            if ( tmp[0]=='"' ) break;
+            if ( tmp[0]=='\'' ) break;
+            if ( isspace(tmp[0]) ) break;
+            if ( tmp[0]=='<' ) break;
+            if ( tmp[0]=='>' ) break;
+            if ( tmp[0]=='=' ) break;
+            if ( tmp[0]=='!' ) break;
+            if ( tmp[0]=='&' ) break;
+            if ( tmp[0]=='|' ) break;
+            if ( tmp[0]=='(' ) break;
+            if ( tmp[0]==')' ) break;
+            if ( tmp[0]=='+' ) break;
+            if ( tmp[0]=='*' ) break;
+            if ( tmp[0]=='-' ) break;
+            if ( tmp[0]=='/' ) break;
+            if ( tmp[0]=='~' ) break;
+            if ( tmp[0]=='%' ) break;
+        }
+        if ( tmp[0]==']' ) { if (square_brackets) tmp++; break; }
+        if ( tmp[0]=='[' ) square_brackets++;
+        tmp++;
+    }
+    if ( tmp > *str )
+    {
+        *len = tmp - (*str);
+        return TOK_VAL;
+    }
+    if ( tmp[0]=='"' || tmp[0]=='\'' )
+    {
+        int quote = tmp[0];
+        tmp++;
+        while ( *tmp && tmp[0]!=quote ) tmp++;
+        if ( !*tmp ) return -1;     // missing quotes
+        *len = tmp - (*str) + 1;
+        return TOK_VAL;
+    }
+    if ( tmp[0]=='!' )
+    {
+        if ( tmp[1]=='=' ) { (*str) += 2; return TOK_NE; }
+        if ( tmp[1]=='~' ) { (*str) += 2; return TOK_NLIKE; }
+    }
+    if ( tmp[0]=='<' )
+    {
+        if ( tmp[1]=='=' ) { (*str) += 2; return TOK_LE; }
+        (*str) += 1; return TOK_LT;
+    }
+    if ( tmp[0]=='>' )
+    {
+        if ( tmp[1]=='=' ) { (*str) += 2; return TOK_BE; }
+        (*str) += 1; return TOK_BT;
+    }
+    if ( tmp[0]=='=' )
+    {
+        if ( tmp[1]=='=' ) { (*str) += 2; return TOK_EQ; }
+        (*str) += 1; return TOK_EQ;
+    }
+    if ( tmp[0]=='(' ) { (*str) += 1; return TOK_LFT; }
+    if ( tmp[0]==')' ) { (*str) += 1; return TOK_RGT; }
+    if ( tmp[0]=='&' && tmp[1]=='&' ) { (*str) += 2; return TOK_AND_VEC; }
+    if ( tmp[0]=='|' && tmp[1]=='|' ) { (*str) += 2; return TOK_OR_VEC; }
+    if ( tmp[0]=='&' ) { (*str) += 1; return TOK_AND; }
+    if ( tmp[0]=='|' ) { (*str) += 1; return TOK_OR; }
+    if ( tmp[0]=='+' ) { (*str) += 1; return TOK_ADD; }
+    if ( tmp[0]=='-' ) { (*str) += 1; return TOK_SUB; }
+    if ( tmp[0]=='*' ) { (*str) += 1; return TOK_MULT; }
+    if ( tmp[0]=='/' ) { (*str) += 1; return TOK_DIV; }
+    if ( tmp[0]=='~' ) { (*str) += 1; return TOK_LIKE; }
+    if ( tmp[0]=='%' ) { (*str) += 1; return TOK_MODULO; }
+
+    *len = tmp - (*str);
+    return TOK_VAL;
+}
+
+
+/*
+    Simple path expansion, expands ~/, ~user, $var. The result must be freed by the caller.
+
+    Based on jkb's staden code with some adjustments.
+    https://sourceforge.net/p/staden/code/HEAD/tree/staden/trunk/src/Misc/getfile.c#l123
+*/
+char *expand_path(char *path)
+{
+    kstring_t str = {0,0,0};
+
+    if ( path[0] == '~' )
+    {
+        if ( !path[1] || path[1] == '/' )
+        {
+#ifdef _WIN32
+            kputs(getenv("HOMEDRIVE"), &str);
+            kputs(getenv("HOMEPATH"), &str);
+#else
+            // ~ or ~/path
+            kputs(getenv("HOME"), &str);
+            if ( path[1] ) kputs(path+1, &str);
+#endif
+        }
+#ifndef _WIN32
+        else
+        {
+            // user name: ~pd3/path
+            char *end = path;
+            while ( *end && *end!='/' ) end++;
+            kputsn(path+1, end-path-1, &str);
+            struct passwd *pwentry = getpwnam(str.s);
+            str.l = 0;
+
+            if ( !pwentry ) kputsn(path, end-path, &str);
+            else kputs(pwentry->pw_dir, &str);
+            kputs(end, &str);
+        }
+#endif
+        return ks_release(&str);
+    }
+    if ( path[0] == '$' )
+    {
+        char *var = getenv(path+1);
+        if ( var ) {
+            kputs(var, &str);
+            return ks_release(&str);
+        }
+    }
+
+    return strdup(path);
+}
+
+static void filters_set_qual(filter_t *flt, bcf1_t *line, token_t *tok)
+{
+    float *ptr = &line->qual;
+    if ( bcf_float_is_missing(*ptr) )
+        bcf_double_set_missing(tok->values[0]);
+    else
+        tok->values[0] = (double)line->qual;
+    tok->nvalues  = 1;
+}
+static void filters_set_type(filter_t *flt, bcf1_t *line, token_t *tok)
+{
+    tok->values[0] = bcf_get_variant_types(line);
+    if ( !tok->values[0] ) tok->values[0] = 1;      // mistake in htslib: VCF_* should start with 1
+    else tok->values[0] = ((int)tok->values[0]) << 1;
+    tok->nvalues = 1;
+}
+static void filters_set_info(filter_t *flt, bcf1_t *line, token_t *tok)
+{
+    assert( tok->hdr_id >=0  );
+    int i;
+    for (i=0; i<line->n_info; i++)
+        if ( line->d.info[i].key == tok->hdr_id ) break;
+
+    if ( i==line->n_info )
+        tok->nvalues = tok->str_value.l = 0;
+    else if ( line->d.info[i].type==BCF_BT_CHAR )
+    {
+        int n = line->d.info[i].len;
+        if ( n >= tok->str_value.m )
+        {
+            tok->str_value.m = n + 1;
+            tok->str_value.s = (char*) realloc(tok->str_value.s, tok->str_value.m);
+            if ( !tok->str_value.s ) error("Failed to alloc %d bytes\n", (int)tok->str_value.m);
+        }
+        memcpy(tok->str_value.s, line->d.info[i].vptr, n);
+        tok->str_value.s[n] = 0;
+        tok->nvalues = tok->str_value.l = n;
+    }
+    else if ( line->d.info[i].type==BCF_BT_FLOAT )
+    {
+        if ( bcf_float_is_missing(line->d.info[i].v1.f) ) tok->nvalues = 0;
+        else
+        {
+            tok->values[0] = line->d.info[i].v1.f;
+            tok->nvalues   = 1;
+        }
+        tok->str_value.l = 0;
+    }
+    else
+    {
+        tok->str_value.l = 0;
+        if ( line->d.info[i].type==BCF_BT_INT8 && line->d.info[i].v1.i==bcf_int8_missing ) tok->nvalues = 0;
+        else if ( line->d.info[i].type==BCF_BT_INT16 && line->d.info[i].v1.i==bcf_int16_missing ) tok->nvalues = 0;
+        else if ( line->d.info[i].type==BCF_BT_INT32 && line->d.info[i].v1.i==bcf_int32_missing ) tok->nvalues = 0;
+        else
+        {
+            tok->values[0] = line->d.info[i].v1.i;
+            tok->nvalues   = 1;
+        }
+    }
+}
+static void filters_cmp_bit_and(token_t *atok, token_t *btok, token_t *rtok, bcf1_t *line)
+{
+    int a = (int)(atok->nvalues?atok->values[0]:atok->threshold);
+    int b = (int)(btok->nvalues?btok->values[0]:btok->threshold);
+    if ( rtok->tok_type==TOK_LIKE )
+        rtok->pass_site = a&b ? 1 : 0;
+    else
+        rtok->pass_site = a&b ? 0 : 1;
+}
+static void filters_cmp_filter(token_t *atok, token_t *btok, token_t *rtok, bcf1_t *line)
+{
+    // the btok values contain FILTER ids obtained by parsing the user expression
+    int i,j;
+    if ( rtok->tok_type==TOK_NOT_IN )   // fail if the query expression is a subset of the VCF FILTER
+    {
+        if ( !btok->nvalues )   // the query expression is ".", pass everything unless the VCF is also "."
+        {
+            if ( line->d.n_flt ) rtok->pass_site = 1;
+            return;
+        }
+        if ( !line->d.n_flt )   // no filters at this VCF line and the query expression has a value
+        {
+            rtok->pass_site = 1;
+            return;
+        }
+        for (j=0; j<btok->nvalues; j++) // some query expression value must be absent from VCF in order to pass
+        {
+            for (i=0; i<line->d.n_flt; i++)
+                if ( btok->values[j]==line->d.flt[i] ) break;
+            if ( i==line->d.n_flt ) break;  // the query is not in the VCF
+        }
+        if ( j!=btok->nvalues ) rtok->pass_site = 1;
+        return;
+    }
+    else if ( rtok->tok_type==TOK_IN )
+    {
+        if ( !btok->nvalues )   // the query expression is ".", fail everything unless the VCF is also "."
+        {
+            if ( !line->d.n_flt ) rtok->pass_site = 1;
+            return;
+        }
+        if ( !line->d.n_flt ) return;   // no filters at this VCF line and the query expression has a value
+        for (j=0; j<btok->nvalues; j++) // all of the query values must be present in the VCF in order to pass
+        {
+            for (i=0; i<line->d.n_flt; i++)
+                if ( btok->values[j]==line->d.flt[i] ) break;
+            if ( i==line->d.n_flt ) break;  // the query is not in the VCF
+        }
+        if ( j==btok->nvalues ) rtok->pass_site = 1;
+        return;
+    }
+    else if ( rtok->tok_type==TOK_NE )  // require anything but exact match
+    {
+        if ( btok->nvalues != line->d.n_flt )
+        {
+            rtok->pass_site = 1;
+            return;
+        }
+        if ( !btok->nvalues ) return;
+        for (j=0; j<btok->nvalues; j++) // some of the query values must be absent from the VCF in order to pass
+        {
+            for (i=0; i<line->d.n_flt; i++)
+                if ( btok->values[j]==line->d.flt[i] ) break;
+            if ( i==line->d.n_flt ) break;  // the query is not in the VCF
+        }
+        if ( j!=btok->nvalues ) rtok->pass_site = 1;
+        return;
+    }
+    else if ( rtok->tok_type==TOK_EQ )  // require exact match
+    {
+        if ( btok->nvalues != line->d.n_flt ) return;
+        if ( !btok->nvalues )
+        {
+            rtok->pass_site = 1;
+            return;
+        }
+        for (j=0; j<btok->nvalues; j++) // all of the query values must be present in the VCF in order to pass
+        {
+            for (i=0; i<line->d.n_flt; i++)
+                if ( btok->values[j]==line->d.flt[i] ) break;
+            if ( i==line->d.n_flt ) break;  // the query is not in the VCF
+        }
+        if ( j==btok->nvalues ) rtok->pass_site = 1;
+        return;
+    }
+    else
+        error("Only ==, !=, ~, and !~ operators are supported for FILTER\n");
+    return;
+}
+static void filters_cmp_id(token_t *atok, token_t *btok, token_t *rtok, bcf1_t *line)
+{
+    if ( btok->hash )
+    {
+        token_t *tmp = atok; atok = btok; btok = tmp;
+    }
+    if ( atok->hash )
+    {
+        if ( rtok->tok_type!=TOK_EQ && rtok->tok_type!=TOK_NE )
+            error("Only == and != operators are supported for strings read from a file\n");
+
+        int ret = khash_str2int_has_key(atok->hash, line->d.id);
+        if ( rtok->tok_type==TOK_NE ) ret = ret ? 0 : 1;
+        rtok->pass_site = ret;
+        return;
+    }
+
+    if ( !btok->str_value.l ) error("Error occurred while evaluating the expression\n");
+
+    if ( rtok->tok_type==TOK_EQ )
+        rtok->pass_site = strcmp(btok->str_value.s,line->d.id) ? 0 : 1;
+    else if ( rtok->tok_type==TOK_NE )
+        rtok->pass_site = strcmp(btok->str_value.s,line->d.id) ? 1 : 0;
+    else
+    {
+        if ( rtok->tok_type!=TOK_LIKE && rtok->tok_type!=TOK_NLIKE )
+            error("Only the following operators are supported for querying ID: ==, !=, ~, !~; the operator type %d is not supported (%p %p)\n",
+                rtok->tok_type,atok->regex,btok->regex);
+
+        regex_t *regex = atok->regex ? atok->regex : (btok->regex ? btok->regex : NULL);
+        if ( !regex ) error("fixme: regex initialization failed\n");
+        rtok->pass_site = regexec(regex,line->d.id, 0,NULL,0) ? 0 : 1;
+        if ( rtok->tok_type==TOK_NLIKE ) rtok->pass_site = rtok->pass_site ? 0 : 1;
+    }
+}
+
+/**
+ *  bcf_get_info_value() - get single INFO value, int64_t or double
+ *  @line:      BCF line
+ *  @info_id:   tag ID, as returned by bcf_hdr_id2int
+ *  @ivec:      0-based index to retrieve, -1 when single value is expected
+ *  @vptr:      pointer to memory location of sufficient size to accomodate
+ *              info_id's type
+ *
+ *  The returned value is -1 if tag is not present, 0 if present but
+ *  values is missing or ivec is out of range, and 1 on success.
+ */
+static int bcf_get_info_value(bcf1_t *line, int info_id, int ivec, void *value)
+{
+    int j;
+    for (j=0; j<line->n_info; j++)
+        if ( line->d.info[j].key == info_id ) break;
+    if ( j==line->n_info ) return -1;
+
+    bcf_info_t *info = &line->d.info[j];
+    if ( info->len == 1 )
+    {
+        if ( info->type==BCF_BT_FLOAT ) *((double*)value) = info->v1.f;
+        else if ( info->type==BCF_BT_INT8 || info->type==BCF_BT_INT16 || info->type==BCF_BT_INT32 ) *((int64_t*)value) = info->v1.i;
+        return 1;
+    }
+
+    if ( ivec<0 ) ivec = 0;
+
+    #define BRANCH(type_t, is_missing, is_vector_end, out_type_t) { \
+        type_t *p = (type_t *) info->vptr; \
+        for (j=0; j<ivec && j<info->len; j++) \
+        { \
+            if ( is_vector_end ) return 0; \
+        } \
+        if ( is_missing ) return 0; \
+        *((out_type_t*)value) = p[j]; \
+        return 1; \
+    }
+    switch (info->type) {
+        case BCF_BT_INT8:  BRANCH(int8_t,  p[j]==bcf_int8_missing,  p[j]==bcf_int8_vector_end,  int64_t); break;
+        case BCF_BT_INT16: BRANCH(int16_t, p[j]==bcf_int16_missing, p[j]==bcf_int16_vector_end, int64_t); break;
+        case BCF_BT_INT32: BRANCH(int32_t, p[j]==bcf_int32_missing, p[j]==bcf_int32_vector_end, int64_t); break;
+        case BCF_BT_FLOAT: BRANCH(float,   bcf_float_is_missing(p[j]), bcf_float_is_vector_end(p[j]), double); break;
+        default: fprintf(stderr,"todo: type %d\n", info->type); exit(1); break;
+    }
+    #undef BRANCH
+    return -1;  // this shouldn't happen
+}
+
+static void filters_set_chrom(filter_t *flt, bcf1_t *line, token_t *tok)
+{
+    tok->str_value.l = 0;
+    kputs(bcf_seqname(flt->hdr,line), &tok->str_value);
+    tok->nvalues = tok->str_value.l;
+    tok->is_str  = 1;
+}
+
+static void filters_set_pos(filter_t *flt, bcf1_t *line, token_t *tok)
+{
+    tok->values[0] = line->pos+1;
+    tok->nvalues = 1;
+}
+
+static void filters_set_info_int(filter_t *flt, bcf1_t *line, token_t *tok)
+{
+    if ( tok->idx==-2 )
+    {
+        tok->nvalues = bcf_get_info_int32(flt->hdr,line,tok->tag,&flt->tmpi,&flt->mtmpi);
+        if ( tok->nvalues<=0 ) tok->nvalues = 0;
+        else
+        {
+            hts_expand(double,tok->nvalues,tok->mvalues,tok->values);
+            int i, j = 0, end = tok->idxs[tok->nidxs-1] < 0 ? tok->nvalues - 1 : tok->nidxs - 1;
+            if ( end >= tok->nvalues ) end = tok->nvalues - 1;
+            for (i=0; i<=end; i++)
+                if ( i>=tok->nidxs || tok->idxs[i] ) tok->values[j++] = flt->tmpi[i];
+            tok->nvalues = j;
+        }
+    }
+    else
+    {
+        int64_t value = 0;
+        if ( bcf_get_info_value(line,tok->hdr_id,tok->idx,&value) <= 0 )
+            tok->nvalues = 0;
+        else
+        {
+            tok->values[0] = value;
+            tok->nvalues = 1;
+        }
+    }
+}
+
+static void filters_set_info_float(filter_t *flt, bcf1_t *line, token_t *tok)
+{
+    if ( tok->idx==-2 )
+    {
+        tok->nvalues = bcf_get_info_float(flt->hdr,line,tok->tag,&flt->tmpf,&flt->mtmpf);
+        if ( tok->nvalues<=0 ) tok->nvalues = 0;
+        else
+        {
+            hts_expand(double,tok->nvalues,tok->mvalues,tok->values);
+            int i, j = 0, end = tok->idxs[tok->nidxs-1] < 0 ? tok->nvalues - 1 : tok->nidxs - 1;
+            if ( end >= tok->nvalues ) end = tok->nvalues - 1;
+            for (i=0; i<=end; i++)
+                if ( i>=tok->nidxs || tok->idxs[i] )
+                {
+                    if ( bcf_float_is_missing(flt->tmpf[i]) ) bcf_double_set_missing(tok->values[j]);
+                    else tok->values[j] = flt->tmpf[i];
+                    j++;
+                }
+            tok->nvalues = j;
+        }
+    }
+    else
+    {
+        double value;
+        if ( bcf_get_info_value(line,tok->hdr_id,tok->idx,&value) <= 0 )
+            tok->nvalues = 0;
+        else
+        {
+            tok->values[0] = value;
+            tok->nvalues = 1;
+        }
+    }
+}
+
+static void filters_set_info_string(filter_t *flt, bcf1_t *line, token_t *tok)
+{
+    int32_t m = tok->str_value.m;
+    int n = bcf_get_info_string(flt->hdr,line,tok->tag,&tok->str_value.s,&m);
+    tok->str_value.m = m;
+    if ( n<0 ) { tok->nvalues = tok->str_value.l = 0; return; }
+
+    if ( tok->idx>=0 )
+    {
+        // get ith field (i=tok->idx)
+        int i = 0;
+        char *ss = tok->str_value.s, *se = tok->str_value.s + n;
+        while ( ss<se && i<tok->idx )
+        {
+            if ( *ss==',' ) i++;
+            ss++;
+        }
+        if ( ss==se || i!=tok->idx ) { tok->nvalues = tok->str_value.l = 0; return; }
+        se = ss;
+        while ( se - tok->str_value.s < n && *se!=',' ) se++;
+        if ( ss==tok->str_value.s ) *se = 0;
+        else
+        {
+            memmove(tok->str_value.s, ss, se-ss);
+            tok->str_value.s[se-ss] = 0;
+        }
+        tok->str_value.l = se - ss;
+    }
+    else if ( tok->idx==-2 && tok->idxs[0]==-1 )    // keep all values, TAG[*]
+        tok->str_value.l = n;
+    else if ( tok->idx==-2 )
+    {
+        flt->tmps.l = 0;
+        ks_resize(&flt->tmps, n);
+        int i, iend = tok->idxs[tok->nidxs-1] < 0 ? n - 1 : tok->nidxs - 1;
+        if ( iend >= n ) iend = n - 1;
+        char *beg = tok->str_value.s, *dst = flt->tmps.s;
+        for (i=0; i<=iend; i++)
+        {
+            char *end = beg;
+            while ( *end && *end!=',' ) end++;
+            if ( i>=tok->nidxs || tok->idxs[i] )
+            {
+                memcpy(dst, beg, end - beg);
+                dst += end - beg;
+                dst[0] = ',';
+                dst++;
+            }
+            beg = end+1;
+        }
+        dst[0] = 0;
+        tok->str_value.l = dst - flt->tmps.s;
+
+        #define SWAP(type_t, a, b) { type_t t = a; a = b; b = t; }
+        SWAP(char *, flt->tmps.s, tok->str_value.s);
+        SWAP(size_t, flt->tmps.m, tok->str_value.m);
+    }
+    tok->nvalues = tok->str_value.l;
+}
+
+static void filters_set_info_flag(filter_t *flt, bcf1_t *line, token_t *tok)
+{
+    int j;
+    for (j=0; j<line->n_info; j++)
+        if ( line->d.info[j].key == tok->hdr_id ) break;
+    tok->values[0] = j==line->n_info ? 0 : 1;
+    tok->nvalues = 1;
+}
+
+static void filters_set_format_int(filter_t *flt, bcf1_t *line, token_t *tok)
+{
+    if ( line->n_sample != tok->nsamples )
+        error("Incorrect number of FORMAT fields at %s:%"PRId64" .. %s, %d vs %d\n", bcf_seqname(flt->hdr,line),(int64_t) line->pos+1,tok->tag,line->n_sample,tok->nsamples);
+
+    int nvals;
+    if ( (nvals=bcf_get_format_int32(flt->hdr,line,tok->tag,&flt->tmpi,&flt->mtmpi))<0 )
+    {
+        tok->nvalues = 0;
+        return;
+    }
+    int i, nsrc1 = nvals / tok->nsamples;
+    tok->nval1 = tok->idx >= 0 ? 1 : (tok->nuidxs ? tok->nuidxs : nsrc1);
+    tok->nvalues = tok->nval1*tok->nsamples;
+    hts_expand(double, tok->nvalues, tok->mvalues, tok->values);
+
+    if ( tok->idx >= 0 )    // scalar or vector index
+    {
+        for (i=0; i<tok->nsamples; i++)
+        {
+            if ( !tok->usmpl[i] ) continue;
+            int32_t *ptr = flt->tmpi + i*nsrc1;
+            if ( tok->idx>=nsrc1 || ptr[tok->idx]==bcf_int32_missing )
+                bcf_double_set_missing(tok->values[i]);
+            else if ( ptr[tok->idx]==bcf_int32_vector_end )
+                bcf_double_set_vector_end(tok->values[i]);
+            else
+                tok->values[i] = ptr[tok->idx];
+        }
+    }
+    else
+    {
+        int kend = tok->idxs[tok->nidxs-1] < 0 ? tok->nval1 : tok->nidxs;
+        for (i=0; i<tok->nsamples; i++)
+        {
+            if ( !tok->usmpl[i] ) continue;
+            int32_t *src = flt->tmpi + i*nsrc1;
+            double  *dst = tok->values + i*tok->nval1;
+            int k, j = 0;
+            for (k=0; k<kend; k++)
+            {
+                if ( k<tok->nidxs && !tok->idxs[k] ) continue;
+                if ( src[k]==bcf_int32_missing )
+                    bcf_double_set_missing(dst[j]);
+                else if ( src[k]==bcf_int32_vector_end )
+                    bcf_double_set_vector_end(dst[j]);
+                else
+                    dst[j] = src[k];
+                j++;
+            }
+            if ( j==0 )
+            {
+                bcf_double_set_missing(dst[j]);
+                j++;
+            }
+            while (j < tok->nval1)
+            {
+                bcf_double_set_vector_end(dst[j]);
+                j++;
+            }
+        }
+    }
+}
+static void filters_set_format_float(filter_t *flt, bcf1_t *line, token_t *tok)
+{
+    if ( line->n_sample != tok->nsamples )
+        error("Incorrect number of FORMAT fields at %s:%"PRId64" .. %s, %d vs %d\n", bcf_seqname(flt->hdr,line),(int64_t) line->pos+1,tok->tag,line->n_sample,tok->nsamples);
+
+    int nvals;
+    if ( (nvals=bcf_get_format_float(flt->hdr,line,tok->tag,&flt->tmpf,&flt->mtmpf))<0 )
+    {
+        tok->nvalues = 0;
+        return;
+    }
+    int i, nsrc1 = nvals / tok->nsamples;
+    tok->nval1 = tok->idx >= 0 ? 1 : (tok->nuidxs ? tok->nuidxs : nsrc1);
+    tok->nvalues = tok->nval1*tok->nsamples;
+    hts_expand(double, tok->nvalues, tok->mvalues, tok->values);
+
+    if ( tok->idx >= 0 )    // scalar or vector index
+    {
+        for (i=0; i<tok->nsamples; i++)
+        {
+            if ( !tok->usmpl[i] ) continue;
+            float *ptr = flt->tmpf + i*nsrc1;
+            if ( tok->idx>=nsrc1 || bcf_float_is_missing(ptr[tok->idx]) )
+                bcf_double_set_missing(tok->values[i]);
+            else if ( bcf_float_is_vector_end(ptr[tok->idx]) )
+                bcf_double_set_vector_end(tok->values[i]);
+            else
+                tok->values[i] = ptr[tok->idx];
+        }
+    }
+    else
+    {
+        int kend = tok->idxs[tok->nidxs-1] < 0 ? tok->nval1 : tok->nidxs;
+        for (i=0; i<tok->nsamples; i++)
+        {
+            if ( !tok->usmpl[i] ) continue;
+            float *src = flt->tmpf + i*nsrc1;
+            double  *dst = tok->values + i*tok->nval1;
+            int k, j = 0;
+            for (k=0; k<kend; k++)
+            {
+                if ( k<tok->nidxs && !tok->idxs[k] ) continue;
+                if ( bcf_float_is_missing(src[k]) )
+                    bcf_double_set_missing(dst[j]);
+                else if ( bcf_float_is_vector_end(src[k]) )
+                    bcf_double_set_vector_end(dst[j]);
+                else
+                    dst[j] = src[k];
+                j++;
+            }
+            if ( j==0 )
+            {
+                bcf_double_set_missing(dst[j]);
+                j++;
+            }
+            while (j < tok->nval1)
+            {
+                bcf_double_set_vector_end(dst[j]);
+                j++;
+            }
+        }
+    }
+}
+static void filters_set_format_string(filter_t *flt, bcf1_t *line, token_t *tok)
+{
+    if ( line->n_sample != tok->nsamples )
+        error("Incorrect number of FORMAT fields at %s:%"PRId64" .. %s, %d vs %d\n", bcf_seqname(flt->hdr,line),(int64_t) line->pos+1,tok->tag,line->n_sample,tok->nsamples);
+
+    int i, ndim = tok->str_value.m;
+    int nstr = bcf_get_format_char(flt->hdr, line, tok->tag, &tok->str_value.s, &ndim);
+    tok->str_value.m = ndim;
+    tok->str_value.l = tok->nvalues = 0;
+
+    if ( nstr<0 ) return;
+
+    tok->nvalues = tok->str_value.l = nstr;
+    tok->nval1   = nstr / tok->nsamples;
+    for (i=0; i<tok->nsamples; i++)
+    {
+        if ( !tok->usmpl[i] ) continue;
+        char *src = tok->str_value.s + i*tok->nval1, *dst = src;
+        int ibeg = 0, idx = 0;
+        while ( ibeg < tok->nval1 )
+        {
+            int iend = ibeg;
+            while ( iend < tok->nval1 && src[iend] && src[iend]!=',' ) iend++;
+
+            int keep = 0;
+            if ( tok->idx >= 0 )
+            {
+                if ( tok->idx==idx ) keep = 1;
+            }
+            else if ( idx < tok->nidxs )
+            {
+                if ( tok->idxs[idx] != 0 ) keep = 1;
+            }
+            else if ( tok->idxs[tok->nidxs-1] < 0 )
+                keep = 1;
+
+            if ( keep )
+            {
+                if ( ibeg!=0 ) memmove(dst, src+ibeg, iend-ibeg+1);
+                dst += iend - ibeg + 1;
+                if ( tok->idx>=0 ) break;
+            }
+            if ( !src[iend] ) break;
+            ibeg = iend + 1;
+            idx++;
+        }
+        if ( dst==src ) { dst[0] = '.'; dst+=2; }
+        if ( dst - src < tok->nval1 ) memset(dst-1, 0, tok->nval1 - (dst - src));
+    }
+}
+static void _filters_set_genotype(filter_t *flt, bcf1_t *line, token_t *tok, int type)
+{
+    bcf_fmt_t *fmt = bcf_get_fmt(flt->hdr, line, "GT");
+    if ( !fmt )
+    {
+        tok->nvalues = tok->str_value.l = 0;
+        return;
+    }
+
+    int i,j, nsmpl = bcf_hdr_nsamples(flt->hdr), nvals1 = type==2 ? 3 : 4;
+    if ( tok->str_value.m <= nvals1*nsmpl )
+    {
+        tok->str_value.m = nvals1*nsmpl + 1;
+        tok->str_value.s = (char*)realloc(tok->str_value.s, tok->str_value.m);
+    }
+
+#define BRANCH_INT(type_t,vector_end) \
+    { \
+        for (i=0; i<line->n_sample; i++) \
+        { \
+            type_t *ptr = (type_t*) (fmt->p + i*fmt->size); \
+            int is_het = 0, has_ref = 0, missing = 0; \
+            for (j=0; j<fmt->n; j++) \
+            { \
+                if ( ptr[j]==vector_end ) break; /* smaller ploidy */ \
+                if ( bcf_gt_is_missing(ptr[j]) ) { missing=1; break; } /* missing allele */ \
+                int ial = ptr[j]; \
+                if ( bcf_gt_allele(ial)==0 ) has_ref = 1; \
+                if ( j>0 ) \
+                { \
+                    int jal = ptr[j-1]; \
+                    if ( bcf_gt_allele(ial)!=bcf_gt_allele(jal) ) is_het = 1; \
+                } \
+            } \
+            char *dst = &tok->str_value.s[nvals1*i]; \
+            if ( type==4 ) \
+            { \
+                if ( !j || missing ) dst[0]='m', dst[1]='i', dst[2]='s', dst[3] = 0; /* mis, missing genotype */ \
+                else if ( !has_ref ) dst[0]='a', dst[1]='l', dst[2]='t', dst[3] = 0; /* alt, no ref, must have alt allele */ \
+                else if ( !is_het ) dst[0]='r', dst[1]='e', dst[2]='f', dst[3] = 0; /* ref, must be ref-only, no alt alelle */ \
+                else dst[0]='a', dst[1]='l', dst[2]='t', dst[3] = 0; /* alt, is het, has alt allele */ \
+            } \
+            else if ( !j || missing ) dst[0]='.', dst[1]=0; /* ., missing genotype */ \
+            else if ( type==3 ) \
+            { \
+                if ( j==1 ) dst[0]='h', dst[1]='a', dst[2]='p', dst[3] = 0; /* hap, haploid */ \
+                else if ( !is_het ) dst[0]='h', dst[1]='o', dst[2]='m', dst[3] = 0; /* hom */ \
+                else dst[0]='h', dst[1]='e', dst[2]='t', dst[3] = 0; /* het */ \
+            } \
+            else \
+            { \
+                if ( j==1 ) \
+                { \
+                    if ( has_ref ) dst[0]='r', dst[1]=0; /* r, haploid */ \
+                    else dst[0]='a', dst[1]=0; /* a, haploid */ \
+                } \
+                else if ( !is_het ) \
+                { \
+                    if ( has_ref ) dst[0]='r', dst[1]='r', dst[2] = 0; /* rr */ \
+                    else dst[0]='a', dst[1]='a', dst[2] = 0; /* aa */ \
+                } \
+                else \
+                { \
+                    if ( has_ref ) dst[0]='r', dst[1]='a', dst[2] = 0; /* ra */ \
+                    else dst[0]='a', dst[1]='A', dst[2] = 0; /* aA */ \
+                } \
+            } \
+        } \
+    }
+    switch (fmt->type) {
+        case BCF_BT_INT8:  BRANCH_INT(int8_t,  bcf_int8_vector_end); break;
+        case BCF_BT_INT16: BRANCH_INT(int16_t, bcf_int16_vector_end); break;
+        case BCF_BT_INT32: BRANCH_INT(int32_t, bcf_int32_vector_end); break;
+        default: error("The GT type is not lineognised: %d at %s:%"PRId64"\n",fmt->type, bcf_seqname(flt->hdr,line),(int64_t) line->pos+1); break;
+    }
+#undef BRANCH_INT
+    assert( tok->nsamples == nsmpl );
+    tok->nvalues = tok->str_value.l = nvals1*nsmpl;
+    tok->str_value.s[tok->str_value.l] = 0;
+    tok->nval1 = nvals1;
+}
+static void filters_set_genotype2(filter_t *flt, bcf1_t *line, token_t *tok) { _filters_set_genotype(flt, line, tok, 2); }
+static void filters_set_genotype3(filter_t *flt, bcf1_t *line, token_t *tok) { _filters_set_genotype(flt, line, tok, 3); }
+static void filters_set_genotype4(filter_t *flt, bcf1_t *line, token_t *tok) { _filters_set_genotype(flt, line, tok, 4); }
+
+static void filters_set_genotype_string(filter_t *flt, bcf1_t *line, token_t *tok)
+{
+    bcf_fmt_t *fmt = bcf_get_fmt(flt->hdr, line, "GT");
+    if ( !fmt )
+    {
+        tok->nvalues = 0;
+        return;
+    }
+    int i, blen = 4, nsmpl = line->n_sample;
+
+gt_length_too_big:
+    tok->str_value.l = 0;
+    for (i=0; i<nsmpl; i++)
+    {
+        size_t plen = tok->str_value.l;
+        bcf_format_gt(fmt, i, &tok->str_value);
+        kputc_(0, &tok->str_value);
+        if ( tok->str_value.l - plen > blen )
+        {
+            // too many alternate alleles or ploidy is too large, the genotype does not fit
+            // three characters ("0/0" vs "10/10").
+            blen *= 2;
+            goto gt_length_too_big;
+        }
+
+        plen = tok->str_value.l - plen;
+        while ( plen < blen )
+        {
+            kputc_(0, &tok->str_value);
+            plen++;
+        }
+    }
+    assert( tok->nsamples == nsmpl );
+    tok->nvalues = tok->str_value.l;
+    tok->nval1 = blen;
+}
+static void filters_set_ilen(filter_t *flt, bcf1_t *line, token_t *tok)
+{
+    tok->nvalues = line->n_allele - 1;
+    hts_expand(double,tok->nvalues,tok->mvalues,tok->values);
+
+    int i, rlen = strlen(line->d.allele[0]);
+    for (i=1; i<line->n_allele; i++)
+    {
+        int alen = strlen(line->d.allele[i]);
+        if ( rlen==alen ) bcf_double_set_missing(tok->values[i-1]);
+        else tok->values[i-1] = alen - rlen;
+    }
+}
+static void filters_set_ref_string(filter_t *flt, bcf1_t *line, token_t *tok)
+{
+    tok->str_value.l = 0;
+    kputs(line->d.allele[0], &tok->str_value);
+    tok->nvalues = tok->str_value.l;
+}
+static void filters_set_alt_string(filter_t *flt, bcf1_t *line, token_t *tok)
+{
+    tok->str_value.l = 0;
+    if ( tok->idx>=0 )
+    {
+        if ( line->n_allele > tok->idx + 1 )
+            kputs(line->d.allele[tok->idx + 1], &tok->str_value);
+        else
+            kputc('.', &tok->str_value);
+    }
+    else if ( tok->idx==-2 )
+    {
+        int i, end = tok->nuidxs ? tok->nuidxs : line->n_allele - 1;
+        if ( end >= line->n_allele - 1 ) end = line->n_allele - 2;
+        for (i=0; i<=end; i++)
+            if ( i>=tok->nidxs || tok->idxs[i] )
+            {
+                if ( tok->str_value.l ) kputc(',', &tok->str_value);
+                kputs(line->d.allele[i+1], &tok->str_value);
+            }
+    }
+    else if ( line->n_allele>1 )
+    {
+        kputs(line->d.allele[1], &tok->str_value);
+        int i;
+        for (i=2; i<line->n_allele; i++)
+        {
+            kputc(',', &tok->str_value);
+            kputs(line->d.allele[i], &tok->str_value);
+        }
+    }
+    else if ( line->n_allele==1 )
+        kputc('.', &tok->str_value);
+    tok->nvalues = tok->str_value.l;
+}
+static void filters_set_nmissing(filter_t *flt, bcf1_t *line, token_t *tok)
+{
+    bcf_unpack(line, BCF_UN_FMT);
+    if ( !line->n_sample )
+    {
+        tok->nvalues = 1;
+        tok->values[0] = 0;
+        return;
+    }
+
+    int i,igt = bcf_hdr_id2int(flt->hdr, BCF_DT_ID, "GT");
+    bcf_fmt_t *fmt = NULL;
+    for (i=0; i<line->n_fmt; i++)
+        if ( line->d.fmt[i].id==igt ) { fmt = &line->d.fmt[i]; break; }
+    if ( !fmt )
+    {
+        tok->nvalues = 0;
+        return;
+    }
+
+    int j,nmissing = 0;
+    #define BRANCH(type_t, is_vector_end) { \
+        for (i=0; i<line->n_sample; i++) \
+        { \
+            type_t *ptr = (type_t *) (fmt->p + i*fmt->size); \
+            for (j=0; j<fmt->n; j++) \
+            { \
+                if ( ptr[j]==is_vector_end ) break; \
+                if ( ptr[j]==bcf_gt_missing ) { nmissing++; break; } \
+            } \
+        } \
+    }
+    switch (fmt->type) {
+        case BCF_BT_INT8:  BRANCH(int8_t,  bcf_int8_vector_end); break;
+        case BCF_BT_INT16: BRANCH(int16_t, bcf_int16_vector_end); break;
+        case BCF_BT_INT32: BRANCH(int32_t, bcf_int32_vector_end); break;
+        default: fprintf(stderr,"todo: type %d\n", fmt->type); exit(1); break;
+    }
+    #undef BRANCH
+    tok->nvalues = 1;
+    tok->values[0] = tok->tag[0]=='N' ? nmissing : (double)nmissing / line->n_sample;
+}
+static int func_npass(filter_t *flt, bcf1_t *line, token_t *rtok, token_t **stack, int nstack)
+{
+    if ( nstack==0 ) error("Error parsing the expression\n");
+    token_t *tok = stack[nstack - 1];
+    if ( !tok->nsamples ) error("The function %s works with FORMAT fields\n", rtok->tag);
+    assert(tok->usmpl);
+
+    int i, npass = 0;
+    for (i=0; i<tok->nsamples; i++)
+    {
+        if ( !tok->usmpl[i] ) continue;
+        if ( tok->pass_samples[i] ) npass++;
+    }
+    hts_expand(double,1,rtok->mvalues,rtok->values);
+    rtok->nsamples = 0;
+    rtok->nvalues = 1;
+    rtok->values[0] = rtok->tag[0]=='N' ? npass : (line->n_sample ? 1.0*npass/line->n_sample : 0);
+
+    return 1;
+}
+static void filters_set_nalt(filter_t *flt, bcf1_t *line, token_t *tok)
+{
+    tok->nvalues = 1;
+    tok->values[0] = line->n_allele - 1;
+}
+static void filters_set_ac(filter_t *flt, bcf1_t *line, token_t *tok)
+{
+    hts_expand(int32_t, line->n_allele, flt->mtmpi, flt->tmpi);
+    if ( !bcf_calc_ac(flt->hdr, line, flt->tmpi, BCF_UN_INFO|BCF_UN_FMT) )
+    {
+        tok->nvalues = 0;
+        return;
+    }
+    int i, an = flt->tmpi[0];
+    for (i=1; i<line->n_allele; i++) an += flt->tmpi[i];
+    if ( !an )
+    {
+        tok->nvalues = 0;
+        return;
+    }
+    flt->tmpi[0] = an;  // for filters_set_[mac|af|maf]
+    if ( tok->idx>=0 )
+    {
+        tok->nvalues = 1;
+        tok->values[0] = tok->idx+1<line->n_allele ? flt->tmpi[tok->idx+1] : 0;
+    }
+    else if ( line->n_allele==1 )   // no ALT
+    {
+        tok->nvalues = 1;
+        tok->values[0] = 0;
+    }
+    else
+    {
+        hts_expand(double,line->n_allele,tok->mvalues,tok->values);
+        for (i=1; i<line->n_allele; i++)
+            tok->values[i-1] = flt->tmpi[i];
+        tok->nvalues = line->n_allele - 1;
+    }
+}
+static void filters_set_an(filter_t *flt, bcf1_t *line, token_t *tok)
+{
+    filters_set_ac(flt,line,tok);
+    tok->values[0] = tok->nvalues ? flt->tmpi[0] : 0;
+    tok->nvalues = 1;
+}
+static void filters_set_mac(filter_t *flt, bcf1_t *line, token_t *tok)
+{
+    filters_set_ac(flt,line,tok);
+    if ( !tok->nvalues ) return;
+    int i, an = flt->tmpi[0];
+    for (i=0; i<tok->nvalues; i++)
+        if ( tok->values[i] > an*0.5 ) tok->values[i] = an - tok->values[i];
+}
+static void filters_set_af(filter_t *flt, bcf1_t *line, token_t *tok)
+{
+    filters_set_ac(flt,line,tok);
+    if ( !tok->nvalues ) return;
+    int i, an = flt->tmpi[0];
+    for (i=0; i<tok->nvalues; i++)
+        tok->values[i] /= (double)an;
+}
+static void filters_set_maf(filter_t *flt, bcf1_t *line, token_t *tok)
+{
+    filters_set_ac(flt,line,tok);
+    if ( !tok->nvalues ) return;
+    int i, an = flt->tmpi[0];
+    for (i=0; i<tok->nvalues; i++)
+    {
+        tok->values[i] /= (double)an;
+        if ( tok->values[i] > 0.5 ) tok->values[i] = 1 - tok->values[i];
+    }
+}
+
+static int func_max(filter_t *flt, bcf1_t *line, token_t *rtok, token_t **stack, int nstack)
+{
+    token_t *tok = stack[nstack - 1];
+    rtok->nvalues = 0;
+    if ( !tok->nvalues ) return 1;
+    double *ptr, val = -HUGE_VAL;
+    int i,j, has_value = 0;
+    if ( tok->nsamples )
+    {
+        for (i=0; i<tok->nsamples; i++)
+        {
+            if ( !tok->usmpl[i] ) continue;
+            ptr = tok->values + i*tok->nval1;
+            for (j=0; j<tok->nval1; j++)
+            {
+                if ( bcf_double_is_missing_or_vector_end(ptr[j]) ) continue;
+                has_value = 1;
+                if ( val < ptr[j] ) val = ptr[j];
+            }
+        }
+    }
+    else
+    {
+        for (i=0; i<tok->nvalues; i++)
+        {
+            if ( bcf_double_is_missing_or_vector_end(tok->values[i]) ) continue;
+            has_value = 1;
+            if ( val < tok->values[i] ) val = tok->values[i];
+        }
+    }
+    if ( has_value )
+    {
+        rtok->values[0] = val;
+        rtok->nvalues = has_value;
+    }
+    return 1;
+}
+static int func_smpl_max(filter_t *flt, bcf1_t *line, token_t *rtok, token_t **stack, int nstack)
+{
+    token_t *tok = stack[nstack - 1];
+    if ( !tok->nsamples ) return func_max(flt,line,rtok,stack,nstack);
+    rtok->nsamples = tok->nsamples;
+    rtok->nvalues  = tok->nsamples;
+    rtok->nval1 = 1;
+    hts_expand(double,rtok->nvalues,rtok->mvalues,rtok->values);
+    assert(tok->usmpl);
+    if ( !rtok->usmpl ) rtok->usmpl = (uint8_t*) malloc(tok->nsamples);
+    memcpy(rtok->usmpl, tok->usmpl, tok->nsamples);
+    int i, j, has_value;
+    double val, *ptr;
+    for (i=0; i<tok->nsamples; i++)
+    {
+        if ( !rtok->usmpl[i] ) continue;
+        val = -HUGE_VAL;
+        has_value = 0;
+        ptr = tok->values + i*tok->nval1;
+        for (j=0; j<tok->nval1; j++)
+        {
+            if ( bcf_double_is_missing_or_vector_end(ptr[j]) ) continue;
+            has_value = 1;
+            if ( val < ptr[j] ) val = ptr[j];
+        }
+        if ( has_value ) rtok->values[i] = val;
+        else bcf_double_set_missing(rtok->values[i]);
+    }
+    return 1;
+}
+static int func_min(filter_t *flt, bcf1_t *line, token_t *rtok, token_t **stack, int nstack)
+{
+    token_t *tok = stack[nstack - 1];
+    rtok->nvalues = 0;
+    if ( !tok->nvalues ) return 1;
+    double *ptr, val = HUGE_VAL;
+    int i,j, has_value = 0;
+    if ( tok->nsamples )
+    {
+        for (i=0; i<tok->nsamples; i++)
+        {
+            if ( !tok->usmpl[i] ) continue;
+            ptr = tok->values + i*tok->nval1;
+            for (j=0; j<tok->nval1; j++)
+            {
+                if ( bcf_double_is_missing_or_vector_end(ptr[j]) ) continue;
+                has_value = 1;
+                if ( val > ptr[j] ) val = ptr[j];
+            }
+        }
+    }
+    else
+    {
+        for (i=0; i<tok->nvalues; i++)
+        {
+            if ( bcf_double_is_missing_or_vector_end(tok->values[i]) ) continue;
+            has_value = 1;
+            if ( val > tok->values[i] ) val = tok->values[i];
+        }
+    }
+    if ( has_value )
+    {
+        rtok->values[0] = val;
+        rtok->nvalues = has_value;
+    }
+    return 1;
+}
+static int func_smpl_min(filter_t *flt, bcf1_t *line, token_t *rtok, token_t **stack, int nstack)
+{
+    token_t *tok = stack[nstack - 1];
+    if ( !tok->nsamples ) return func_min(flt,line,rtok,stack,nstack);
+    rtok->nsamples = tok->nsamples;
+    rtok->nvalues  = tok->nsamples;
+    rtok->nval1 = 1;
+    hts_expand(double,rtok->nvalues,rtok->mvalues,rtok->values);
+    assert(tok->usmpl);
+    if ( !rtok->usmpl ) rtok->usmpl = (uint8_t*) malloc(tok->nsamples);
+    memcpy(rtok->usmpl, tok->usmpl, tok->nsamples);
+    int i, j, has_value;
+    double val, *ptr;
+    for (i=0; i<tok->nsamples; i++)
+    {
+        if ( !rtok->usmpl[i] ) continue;
+        val = HUGE_VAL;
+        has_value = 0;
+        ptr = tok->values + i*tok->nval1;
+        for (j=0; j<tok->nval1; j++)
+        {
+            if ( bcf_double_is_missing_or_vector_end(ptr[j]) ) continue;
+            has_value = 1;
+            if ( val > ptr[j] ) val = ptr[j];
+        }
+        if ( has_value ) rtok->values[i] = val;
+        else bcf_double_set_missing(rtok->values[i]);
+    }
+    return 1;
+}
+static int func_avg(filter_t *flt, bcf1_t *line, token_t *rtok, token_t **stack, int nstack)
+{
+    token_t *tok = stack[nstack - 1];
+    rtok->nvalues = 0;
+    if ( !tok->nvalues ) return 1;
+    double *ptr, val = 0;
+    int i,j, n = 0;
+    if ( tok->nsamples )
+    {
+        for (i=0; i<tok->nsamples; i++)
+        {
+            if ( !tok->usmpl[i] ) continue;
+            ptr = tok->values + i*tok->nval1;
+            for (j=0; j<tok->nval1; j++)
+            {
+                if ( bcf_double_is_missing_or_vector_end(ptr[j]) ) continue;
+                val += ptr[j];
+                n++;
+            }
+        }
+    }
+    else
+    {
+        for (i=0; i<tok->nvalues; i++)
+            if ( !bcf_double_is_missing_or_vector_end(tok->values[i]) ) { val += tok->values[i]; n++; }
+    }
+    if ( n )
+    {
+        rtok->values[0] = val / n;
+        rtok->nvalues   = 1;
+    }
+    return 1;
+}
+static int func_smpl_avg(filter_t *flt, bcf1_t *line, token_t *rtok, token_t **stack, int nstack)
+{
+    token_t *tok = stack[nstack - 1];
+    if ( !tok->nsamples ) return func_avg(flt,line,rtok,stack,nstack);
+    rtok->nsamples = tok->nsamples;
+    rtok->nvalues  = tok->nsamples;
+    rtok->nval1 = 1;
+    hts_expand(double,rtok->nvalues,rtok->mvalues,rtok->values);
+    assert(tok->usmpl);
+    if ( !rtok->usmpl ) rtok->usmpl = (uint8_t*) malloc(tok->nsamples);
+    memcpy(rtok->usmpl, tok->usmpl, tok->nsamples);
+    int i, j, n;
+    double val, *ptr;
+    for (i=0; i<tok->nsamples; i++)
+    {
+        if ( !rtok->usmpl[i] ) continue;
+        val = 0;
+        n = 0;
+        ptr = tok->values + i*tok->nval1;
+        for (j=0; j<tok->nval1; j++)
+        {
+            if ( !bcf_double_is_missing_or_vector_end(ptr[j]) ) { val += ptr[j]; n++; }
+        }
+        if ( n ) rtok->values[i] = val / n;
+        else bcf_double_set_missing(rtok->values[i]);
+    }
+    return 1;
+}
+static int compare_doubles(const void *lhs, const void *rhs)
+{
+    double arg1 = *(const double*) lhs;
+    double arg2 = *(const double*) rhs;
+    if (arg1 < arg2) return -1;
+    if (arg1 > arg2) return 1;
+    return 0;
+}
+static int func_median(filter_t *flt, bcf1_t *line, token_t *rtok, token_t **stack, int nstack)
+{
+    token_t *tok = stack[nstack - 1];
+    rtok->nvalues = 0;
+    if ( !tok->nvalues ) return 1;
+    // sweep through all tok->values and while excluding all missing values reuse the very same array
+    int i,j,k = 0, n = 0;
+    if ( tok->nsamples )
+    {
+        for (i=0; i<tok->nsamples; i++)
+        {
+            if ( !tok->usmpl[i] ) { k += tok->nval1; continue; }
+            for (j=0; j<tok->nval1; k++,j++)
+            {
+                if ( bcf_double_is_missing_or_vector_end(tok->values[k]) ) continue;
+                if ( n < k ) tok->values[n] = tok->values[k];
+                n++;
+            }
+        }
+    }
+    else
+    {
+        for (i=0; i<tok->nvalues; i++)
+        {
+            if ( bcf_double_is_missing_or_vector_end(tok->values[i]) ) continue;
+            if ( n < i ) tok->values[n] = tok->values[i];
+            n++;
+        }
+    }
+    if ( !n ) return 1;
+    if ( n==1 ) rtok->values[0] = tok->values[0];
+    else
+    {
+        qsort(tok->values, n, sizeof(double), compare_doubles);
+        rtok->values[0] = n % 2 ? tok->values[n/2] : (tok->values[n/2-1] + tok->values[n/2]) * 0.5;
+    }
+    rtok->nvalues = 1;
+    return 1;
+}
+static int func_smpl_median(filter_t *flt, bcf1_t *line, token_t *rtok, token_t **stack, int nstack)
+{
+    token_t *tok = stack[nstack - 1];
+    if ( !tok->nsamples ) return func_avg(flt,line,rtok,stack,nstack);
+    rtok->nsamples = tok->nsamples;
+    rtok->nvalues  = tok->nsamples;
+    rtok->nval1 = 1;
+    hts_expand(double,rtok->nvalues,rtok->mvalues,rtok->values);
+    assert(tok->usmpl);
+    if ( !rtok->usmpl ) rtok->usmpl = (uint8_t*) malloc(tok->nsamples);
+    memcpy(rtok->usmpl, tok->usmpl, tok->nsamples);
+    int i, j, n;
+    double *ptr;
+    for (i=0; i<tok->nsamples; i++)
+    {
+        if ( !rtok->usmpl[i] ) continue;
+        n = 0;
+        ptr = tok->values + i*tok->nval1;
+        for (j=0; j<tok->nval1; j++)
+        {
+            if ( bcf_double_is_missing_or_vector_end(ptr[j]) ) continue;
+            if ( n < j ) ptr[n] = ptr[j];
+            n++;
+        }
+        if ( n==0 )
+            bcf_double_set_missing(rtok->values[i]);
+        else if ( n==1 )
+            rtok->values[i] = ptr[0];
+        else
+        {
+            qsort(ptr, n, sizeof(double), compare_doubles);
+            rtok->values[i] = n % 2 ? ptr[n/2] : (ptr[n/2-1] + ptr[n/2]) * 0.5;
+        }
+    }
+    return 1;
+}
+static int func_stddev(filter_t *flt, bcf1_t *line, token_t *rtok, token_t **stack, int nstack)
+{
+    token_t *tok = stack[nstack - 1];
+    rtok->nvalues = 0;
+    if ( !tok->nvalues ) return 1;
+    // sweep through all tok->values and while excluding all missing values reuse the very same array
+    int i,j,k = 0, n = 0;
+    if ( tok->nsamples )
+    {
+        for (i=0; i<tok->nsamples; i++)
+        {
+            if ( !tok->usmpl[i] ) { k += tok->nval1; continue; }
+            for (j=0; j<tok->nval1; k++,j++)
+            {
+                if ( bcf_double_is_missing_or_vector_end(tok->values[k]) ) continue;
+                if ( n < k ) tok->values[n] = tok->values[k];
+                n++;
+            }
+        }
+    }
+    else
+    {
+        for (i=0; i<tok->nvalues; i++)
+        {
+            if ( bcf_double_is_missing_or_vector_end(tok->values[i]) ) continue;
+            if ( n < i ) tok->values[n] = tok->values[i];
+            n++;
+        }
+    }
+    if ( !n ) return 1;
+    if ( n==1 ) rtok->values[0] = 0;
+    else
+    {
+        double sdev = 0, avg = 0;
+        for (i=0; i<n; i++) avg += tok->values[i];
+        avg /= n;
+        for (i=0; i<n; i++) sdev += (tok->values[i] - avg) * (tok->values[i] - avg);
+        rtok->values[0] = sqrt(sdev/n);
+    }
+    rtok->nvalues = 1;
+    return 1;
+}
+static int func_smpl_stddev(filter_t *flt, bcf1_t *line, token_t *rtok, token_t **stack, int nstack)
+{
+    token_t *tok = stack[nstack - 1];
+    if ( !tok->nsamples ) return func_avg(flt,line,rtok,stack,nstack);
+    rtok->nsamples = tok->nsamples;
+    rtok->nvalues  = tok->nsamples;
+    rtok->nval1 = 1;
+    hts_expand(double,rtok->nvalues,rtok->mvalues,rtok->values);
+    assert(tok->usmpl);
+    if ( !rtok->usmpl ) rtok->usmpl = (uint8_t*) malloc(tok->nsamples);
+    memcpy(rtok->usmpl, tok->usmpl, tok->nsamples);
+    int i, j, n;
+    double *ptr;
+    for (i=0; i<tok->nsamples; i++)
+    {
+        if ( !rtok->usmpl[i] ) continue;
+        n = 0;
+        ptr = tok->values + i*tok->nval1;
+        for (j=0; j<tok->nval1; j++)
+        {
+            if ( bcf_double_is_missing_or_vector_end(ptr[j]) ) continue;
+            if ( n < j ) ptr[n] = ptr[j];
+            n++;
+        }
+        if ( n==0 )
+            bcf_double_set_missing(rtok->values[i]);
+        else if ( n==1 )
+            rtok->values[i] = 0;
+        else
+        {
+            double sdev = 0, avg = 0;
+            for (j=0; j<n; j++) avg += ptr[j];
+            avg /= n;
+            for (j=0; j<n; j++) sdev += (ptr[j] - avg) * (ptr[j] - avg);
+            rtok->values[i] = sqrt(sdev/n);
+        }
+    }
+    return 1;
+}
+static int func_sum(filter_t *flt, bcf1_t *line, token_t *rtok, token_t **stack, int nstack)
+{
+    rtok->nvalues = 0;
+    token_t *tok = stack[nstack - 1];
+    if ( !tok->nvalues ) return 1;
+    double *ptr, val = 0;
+    int i,j, n = 0;
+    if ( tok->nsamples )
+    {
+        for (i=0; i<tok->nsamples; i++)
+        {
+            if ( !tok->usmpl[i] ) continue;
+            ptr = tok->values + i*tok->nval1;
+            for (j=0; j<tok->nval1; j++)
+            {
+                if ( bcf_double_is_missing_or_vector_end(ptr[j]) ) continue;
+                val += ptr[j];
+                n++;
+            }
+        }
+    }
+    else
+    {
+        for (i=0; i<tok->nvalues; i++)
+            if ( !bcf_double_is_missing_or_vector_end(tok->values[i]) ) { val += tok->values[i]; n++; }
+    }
+    if ( n )
+    {
+        rtok->values[0] = val;
+        rtok->nvalues   = 1;
+    }
+    return 1;
+}
+static int func_smpl_sum(filter_t *flt, bcf1_t *line, token_t *rtok, token_t **stack, int nstack)
+{
+    token_t *tok = stack[nstack - 1];
+    if ( !tok->nsamples ) return func_avg(flt,line,rtok,stack,nstack);
+    rtok->nsamples = tok->nsamples;
+    rtok->nvalues  = tok->nsamples;
+    rtok->nval1 = 1;
+    hts_expand(double,rtok->nvalues,rtok->mvalues,rtok->values);
+    assert(tok->usmpl);
+    if ( !rtok->usmpl ) rtok->usmpl = (uint8_t*) malloc(tok->nsamples);
+    memcpy(rtok->usmpl, tok->usmpl, tok->nsamples);
+    int i, j, has_value;
+    double val, *ptr;
+    for (i=0; i<tok->nsamples; i++)
+    {
+        if ( !rtok->usmpl[i] ) continue;
+        val = 0;
+        has_value = 0;
+        ptr = tok->values + i*tok->nval1;
+        for (j=0; j<tok->nval1; j++)
+        {
+            if ( bcf_double_is_missing_or_vector_end(ptr[j]) ) continue;
+            has_value = 1;
+            val += ptr[j];
+        }
+        if ( has_value ) rtok->values[i] = val;
+        else bcf_double_set_missing(rtok->values[i]);
+    }
+    return 1;
+}
+static int func_abs(filter_t *flt, bcf1_t *line, token_t *rtok, token_t **stack, int nstack)
+{
+    token_t *tok = stack[nstack - 1];
+    if ( tok->is_str ) error("ABS() can be applied only on numeric values\n");
+    rtok->nsamples = tok->nsamples;
+    rtok->nvalues = tok->nvalues;
+    rtok->nval1 = tok->nval1;
+    hts_expand(double,rtok->nvalues,rtok->mvalues,rtok->values);
+    if ( tok->usmpl )
+    {
+        if ( !rtok->usmpl ) rtok->usmpl = (uint8_t*) malloc(tok->nsamples);
+        memcpy(rtok->usmpl, tok->usmpl, tok->nsamples);
+    }
+    if ( !tok->nvalues ) return 1;
+    hts_expand(double, rtok->nvalues, rtok->mvalues, rtok->values);
+    int i,j,k = 0;
+    if ( tok->usmpl )
+    {
+        for (i=0; i<tok->nsamples; i++)
+        {
+            if ( !tok->usmpl[i] ) { k+= tok->nval1; continue; }
+            for (j=0; j<tok->nval1; k++,j++)
+            {
+                if ( bcf_double_is_missing_or_vector_end(tok->values[k]) ) bcf_double_set_missing(rtok->values[k]);
+                else rtok->values[k] = fabs(tok->values[k]);
+            }
+        }
+    }
+    else
+    {
+        for (i=0; i<tok->nvalues; i++)
+        {
+            if ( tok->usmpl && !tok->usmpl[i] ) continue;
+            if ( bcf_double_is_missing(tok->values[i]) ) bcf_double_set_missing(rtok->values[i]);
+            else if ( !bcf_double_is_vector_end(tok->values[i]) ) rtok->values[i] = fabs(tok->values[i]);
+        }
+    }
+    return 1;
+}
+static int func_count(filter_t *flt, bcf1_t *line, token_t *rtok, token_t **stack, int nstack)
+{
+    token_t *tok = stack[nstack - 1];
+    int i,j, cnt = 0;
+    if ( tok->tag && tok->nsamples )
+    {
+        // raw number of values in a FMT tag, e.g. COUNT(FMT/TAG)
+        if ( tok->is_str ) error("todo: Type=String for COUNT on FORMAT fields?\n");
+        for (i=0; i<tok->nsamples; i++)
+        {
+            if ( !tok->usmpl[i] ) continue;
+            double *ptr = tok->values + i*tok->nval1;
+            for (j=0; j<tok->nval1; j++)
+                if ( !bcf_double_is_missing_or_vector_end(ptr[j]) ) cnt++;
+        }
+    }
+    else if ( tok->nsamples )
+    {
+        // number of samples that pass a processed FMT tag
+        for (i=0; i<tok->nsamples; i++)
+            if ( tok->pass_samples[i] ) cnt++;
+    }
+    else if ( tok->is_str )
+    {
+        if ( tok->str_value.l ) cnt = 1;
+        for (i=0; i<tok->str_value.l; i++) if ( tok->str_value.s[i]==',' ) cnt++;
+    }
+    else
+        cnt = tok->nvalues;
+
+    rtok->nvalues = 1;
+    rtok->values[0] = cnt;
+    return 1;
+}
+static int func_strlen(filter_t *flt, bcf1_t *line, token_t *rtok, token_t **stack, int nstack)
+{
+    token_t *tok = stack[nstack - 1];
+    rtok->nvalues = rtok->str_value.l = 0;
+    if ( !tok->str_value.l ) return 1;
+
+    if ( tok->idx==-2 )
+    {
+        int i = 0;
+        char *ss = tok->str_value.s;
+        while ( *ss )
+        {
+            char *se = ss;
+            while ( *se && *se!=',' ) se++;
+            hts_expand(double, i+1, rtok->mvalues, rtok->values);
+            if ( !*se ) rtok->values[i] = strlen(ss);
+            else
+            {
+                *se = 0;
+                rtok->values[i] = strlen(ss);
+                *se = ',';
+            }
+            ss = *se ? se + 1 : se;
+            i++;
+        }
+        rtok->nvalues = i;
+    }
+    else
+    {
+        if ( !tok->str_value.s[1] && tok->str_value.s[0]=='.' )
+            rtok->values[0] = 0;
+        else
+            rtok->values[0] = strlen(tok->str_value.s);
+        rtok->nvalues = 1;
+    }
+    return 1;
+}
+static inline double calc_binom(int na, int nb)
+{
+    if ( na==0 && nb==0 ) return -1;
+    if ( na==nb ) return 1;
+
+    // kfunc.h implements kf_betai, which is the regularized beta function  P(X<=k/N;p) = I_{1-p}(N-k,k+1)
+
+    double pval = na < nb ? kf_betai(nb, na + 1, 0.5) : kf_betai(na, nb + 1, 0.5);
+    pval *= 2;
+    if ( pval>1 ) pval = 1;     // this can happen, machine precision error, eg. kf_betai(1,0,0.5)
+
+    return pval;
+}
+static int func_binom(filter_t *flt, bcf1_t *line, token_t *rtok, token_t **stack, int nstack)
+{
+    int i, istack = nstack - rtok->nargs;
+
+    if ( rtok->nargs!=2 && rtok->nargs!=1 ) error("Error: binom() takes one or two arguments\n");
+    assert( istack>=0 );
+
+    // The expected mean is 0.5. Should we support also prob!=0.5?
+    //
+    //  double prob = 0.5;
+    //  if ( nstack==3 )
+    //  {
+    //      // three parameters, the first one must be a scalar:  binom(0.25,AD[0],AD[1])
+    //      if ( !stack[istack]->is_constant )
+    //          error("The first argument of binom() must be a numeric constant if three parameters are given\n");
+    //      prob = stack[istack]->threshold;
+    //      istack++;
+    //  }
+    //  else if ( nstack==2 && stack[istack]->is_constant )
+    //  {
+    //      // two parameters, the first can be a scalar:  binom(0.25,AD) or binom(AD[0],AD[1])
+    //      prob = stack[istack]->threshold;
+    //      istack++;
+    //  }
+
+    token_t *tok = stack[istack];
+    if ( tok->nsamples )
+    {
+        // working with a FORMAT tag
+        rtok->nval1    = 1;
+        rtok->nvalues  = tok->nsamples;
+        rtok->nsamples = tok->nsamples;
+        hts_expand(double, rtok->nvalues, rtok->mvalues, rtok->values);
+        assert(tok->usmpl);
+        if ( !rtok->usmpl ) rtok->usmpl = (uint8_t*) malloc(tok->nsamples);
+        memcpy(rtok->usmpl, tok->usmpl, tok->nsamples);
+
+        if ( istack+1==nstack )
+        {
+            // determine the index from the GT field: binom(AD)
+            int ngt = bcf_get_genotypes(flt->hdr, line, &flt->tmpi, &flt->mtmpi);
+            int max_ploidy = ngt/line->n_sample;
+            if ( ngt <= 0 || max_ploidy < 2 ) // GT not present or not diploid, cannot set
+            {
+                for (i=0; i<rtok->nsamples; i++)
+                    if ( rtok->usmpl[i] ) bcf_double_set_missing(rtok->values[i]);
+                return rtok->nargs;
+            }
+            for (i=0; i<rtok->nsamples; i++)
+            {
+                if ( !rtok->usmpl[i] ) continue;
+                int32_t *ptr = flt->tmpi + i*max_ploidy;
+                if ( bcf_gt_is_missing(ptr[0]) || bcf_gt_is_missing(ptr[1]) || ptr[1]==bcf_int32_vector_end )
+                {
+                    bcf_double_set_missing(rtok->values[i]);
+                    continue;
+                }
+                int idx1 = bcf_gt_allele(ptr[0]);
+                int idx2 = bcf_gt_allele(ptr[1]);
+                if ( idx1>=line->n_allele ) error("Incorrect allele index at %s:%"PRId64", sample %s\n", bcf_seqname(flt->hdr,line),(int64_t) line->pos+1,flt->hdr->samples[i]);
+                if ( idx2>=line->n_allele ) error("Incorrect allele index at %s:%"PRId64", sample %s\n", bcf_seqname(flt->hdr,line),(int64_t) line->pos+1,flt->hdr->samples[i]);
+                double *vals = tok->values + tok->nval1*i;
+                if ( bcf_double_is_missing_or_vector_end(vals[idx1]) || bcf_double_is_missing_or_vector_end(vals[idx2]) )
+                {
+                    bcf_double_set_missing(rtok->values[i]);
+                    continue;
+                }
+                rtok->values[i] = calc_binom(vals[idx1],vals[idx2]);
+                if ( rtok->values[i] < 0 )
+                {
+                    bcf_double_set_missing(rtok->values[i]);
+                    continue;
+                }
+            }
+        }
+        else
+        {
+            // the fields given explicitly: binom(AD[:0],AD[:1])
+            token_t *tok2 = stack[istack+1];
+            if ( tok->nval1!=1 || tok2->nval1!=1 )
+                error("Expected one value per binom() argument, found %d and %d at %s:%"PRId64"\n",tok->nval1,tok2->nval1, bcf_seqname(flt->hdr,line),(int64_t) line->pos+1);
+            for (i=0; i<rtok->nsamples; i++)
+            {
+                if ( !rtok->usmpl[i] ) continue;
+                double *ptr1 = tok->values + tok->nval1*i;
+                double *ptr2 = tok2->values + tok2->nval1*i;
+                if ( bcf_double_is_missing_or_vector_end(ptr1[0]) || bcf_double_is_missing_or_vector_end(ptr2[0]) )
+                {
+                    bcf_double_set_missing(rtok->values[i]);
+                    continue;
+                }
+                rtok->values[i] = calc_binom(ptr1[0],ptr2[0]);
+                if ( rtok->values[i] < 0 )
+                {
+                    bcf_double_set_missing(rtok->values[i]);
+                    continue;
+                }
+            }
+        }
+    }
+    else
+    {
+        // working with an INFO tag
+        rtok->nvalues  = 1;
+        hts_expand(double, rtok->nvalues, rtok->mvalues, rtok->values);
+
+        double *ptr1 = NULL, *ptr2 = NULL;
+        if ( istack+1==nstack )
+        {
+            // only one tag, expecting two values: binom(INFO/AD)
+            if ( tok->nvalues==2 )
+            {
+                ptr1 = &tok->values[0];
+                ptr2 = &tok->values[1];
+            }
+        }
+        else
+        {
+            // two tags, expecting one value in each: binom(INFO/AD[0],INFO/AD[1])
+            token_t *tok2 = stack[istack+1];
+            if ( tok->nvalues==1 && tok2->nvalues==1 )
+            {
+                ptr1 = &tok->values[0];
+                ptr2 = &tok2->values[0];
+            }
+        }
+        if ( !ptr1 || !ptr2 || bcf_double_is_missing_or_vector_end(ptr1[0]) || bcf_double_is_missing_or_vector_end(ptr2[0]) )
+            bcf_double_set_missing(rtok->values[0]);
+        else
+        {
+            rtok->values[0] = calc_binom(ptr1[0],ptr2[0]);
+            if ( rtok->values[0] < 0 )
+                bcf_double_set_missing(rtok->values[0]);
+        }
+    }
+    return rtok->nargs;
+}
+static int func_phred(filter_t *flt, bcf1_t *line, token_t *rtok, token_t **stack, int nstack)
+{
+    token_t *tok = stack[nstack - 1];
+    if ( tok->is_str ) error("PHRED() can be applied only on numeric values\n");
+
+    rtok->nsamples = tok->nsamples;
+    rtok->nval1 = tok->nval1;
+    memcpy(rtok->pass_samples, tok->pass_samples, rtok->nsamples*sizeof(*rtok->pass_samples));
+    assert(tok->usmpl);
+    if ( !rtok->usmpl )
+    {
+        rtok->usmpl = (uint8_t*) malloc(tok->nsamples*sizeof(*rtok->usmpl));
+        memcpy(rtok->usmpl, tok->usmpl, tok->nsamples*sizeof(*rtok->usmpl));
+    }
+    rtok->nvalues = tok->nvalues;
+    if ( !tok->nvalues ) return 1;
+
+    hts_expand(double, rtok->nvalues, rtok->mvalues, rtok->values);
+    int i,j,k = 0;
+    if ( tok->usmpl )
+    {
+        for (i=0; i<tok->nsamples; i++)
+        {
+            if ( !tok->usmpl[i] ) { k+= tok->nval1; continue; }
+            for (j=0; j<tok->nval1; k++,j++)
+            {
+                if ( bcf_double_is_missing_or_vector_end(tok->values[k]) ) bcf_double_set_missing(rtok->values[k]);
+                else rtok->values[k] = -4.34294481903*log(tok->values[k]);
+            }
+        }
+    }
+    else
+    {
+        for (i=0; i<tok->nvalues; i++)
+        {
+            if ( bcf_double_is_missing_or_vector_end(tok->values[i]) ) bcf_double_set_missing(rtok->values[i]);
+            else rtok->values[i] = -4.34294481903*log(tok->values[i]);
+        }
+    }
+    return 1;
+}
+inline static void tok_init_values(token_t *atok, token_t *btok, token_t *rtok)
+{
+    token_t *tok;
+    if ( (atok->nsamples || btok->nsamples) && (!atok->nsamples || !btok->nsamples) )
+        tok = atok->nsamples ? atok : btok;
+    else
+        tok = atok->nvalues > btok->nvalues ? atok : btok;
+    rtok->nvalues = tok->nvalues;
+    rtok->nval1   = tok->nval1;
+    hts_expand(double, rtok->nvalues, rtok->mvalues, rtok->values);
+}
+inline static void tok_init_samples(token_t *atok, token_t *btok, token_t *rtok)
+{
+    if ( (atok->nsamples || btok->nsamples) && !rtok->nsamples )
+    {
+        rtok->nsamples = atok->nsamples ? atok->nsamples : btok->nsamples;
+        rtok->usmpl = (uint8_t*) calloc(rtok->nsamples,1);
+        int i;
+        for (i=0; i<atok->nsamples; i++) rtok->usmpl[i] |= atok->usmpl[i];
+        for (i=0; i<btok->nsamples; i++) rtok->usmpl[i] |= btok->usmpl[i];
+    }
+    if (rtok->nsamples)
+        memset(rtok->pass_samples, 0, rtok->nsamples);
+}
+
+#define VECTOR_ARITHMETICS(atok,btok,_rtok,AOP,TYPE) \
+{ \
+    token_t *rtok = _rtok; \
+    int i, has_values = 0; \
+    if ( atok->nvalues && btok->nvalues ) \
+    { \
+        tok_init_values(atok, btok, rtok); \
+        tok_init_samples(atok, btok, rtok); \
+        if ( (atok->nsamples && btok->nsamples) || (!atok->nsamples && !btok->nsamples)) \
+        { \
+            assert( atok->nsamples==btok->nsamples ); \
+            for (i=0; i<atok->nvalues; i++) \
+            { \
+                if ( bcf_double_is_missing_or_vector_end(atok->values[i]) || bcf_double_is_missing_or_vector_end(btok->values[i]) ) \
+                { \
+                    bcf_double_set_missing(rtok->values[i]); \
+                    continue; \
+                } \
+                has_values = 1; \
+                rtok->values[i] = TYPE atok->values[i] AOP TYPE btok->values[i]; \
+            } \
+        } \
+        else if ( atok->nsamples ) \
+        { \
+            assert( btok->nvalues==1 ); \
+            if ( !bcf_double_is_missing_or_vector_end(btok->values[0]) ) \
+            { \
+                for (i=0; i<atok->nvalues; i++) \
+                { \
+                    if ( bcf_double_is_missing_or_vector_end(atok->values[i]) ) \
+                    { \
+                        bcf_double_set_missing(rtok->values[i]); \
+                        continue; \
+                    } \
+                    has_values = 1; \
+                    rtok->values[i] = TYPE atok->values[i] AOP TYPE btok->values[0]; \
+                } \
+            } \
+        } \
+        else \
+        { \
+            assert( atok->nvalues==1 ); \
+            if ( !bcf_double_is_missing_or_vector_end(atok->values[0]) ) \
+            { \
+                for (i=0; i<btok->nvalues; i++) \
+                { \
+                    if ( bcf_double_is_missing_or_vector_end(btok->values[i]) ) \
+                    { \
+                        bcf_double_set_missing(rtok->values[i]); \
+                        continue; \
+                    } \
+                    has_values = 1; \
+                    rtok->values[i] = TYPE atok->values[0] AOP TYPE btok->values[i]; \
+                } \
+            } \
+        } \
+    } \
+    if ( !has_values ) rtok->nvalues = 0; \
+}
+
+static int vector_logic_or(filter_t *filter, bcf1_t *line, token_t *rtok, token_t **stack, int nstack)
+{
+    if ( nstack < 2 ) error("Error occurred while processing the filter \"%s\"\n", filter->str);
+
+    token_t *atok = stack[nstack-2];
+    token_t *btok = stack[nstack-1];
+    tok_init_samples(atok, btok, rtok);
+
+    if ( !atok->pass_site && !btok->pass_site ) return 2;
+
+    rtok->pass_site = 1;
+    if ( !atok->nsamples && !btok->nsamples ) return 2;
+
+    int i;
+    if ( rtok->tok_type==TOK_OR_VEC )   // ||, select all samples if one is true
+    {
+        if ( (!atok->nsamples && !atok->pass_site) || (!btok->nsamples && !btok->pass_site) )
+        {
+            // These two conditions are to ensure the following does not set all samples
+            // at sites with QUAL<=30:
+            //      QUAL>30 || FMT/GQ>30
+
+            token_t *tok = atok->nsamples ? atok : btok;
+            for (i=0; i<rtok->nsamples; i++)
+            {
+                if ( !rtok->usmpl[i] ) continue;
+                rtok->pass_samples[i] = tok->pass_samples[i];
+            }
+        }
+        else
+        {
+            for (i=0; i<rtok->nsamples; i++)
+            {
+                if ( !rtok->usmpl[i] ) continue;
+                rtok->pass_samples[i] = 1;
+            }
+        }
+        return 2;
+    }
+
+    //  |, only select samples which are actually true
+
+    if ( !atok->nsamples || !btok->nsamples )
+    {
+        token_t *tok = atok->nsamples ? atok : btok;
+        for (i=0; i<rtok->nsamples; i++)
+        {
+            if ( !rtok->usmpl[i] ) continue;
+            rtok->pass_samples[i] = tok->pass_samples[i];
+        }
+        return 2;
+    }
+
+    assert( atok->nsamples==btok->nsamples );
+
+    for (i=0; i<rtok->nsamples; i++)
+    {
+        if ( !rtok->usmpl[i] ) continue;
+        rtok->pass_samples[i] = atok->pass_samples[i] | btok->pass_samples[i];
+    }
+    return 2;
+}
+static int vector_logic_and(filter_t *filter, bcf1_t *line, token_t *rtok, token_t **stack, int nstack)
+{
+    if ( nstack < 2 ) error("Error occurred while processing the filter \"%s\". (nstack=%d)\n", filter->str,nstack);
+
+    token_t *atok = stack[nstack-2];
+    token_t *btok = stack[nstack-1];
+    tok_init_samples(atok, btok, rtok);
+
+    if ( !atok->pass_site || !btok->pass_site ) return 2;
+    if ( !atok->nsamples && !btok->nsamples ) { rtok->pass_site = 1; return 2; }
+
+    int i;
+    if ( !atok->nsamples || !btok->nsamples )
+    {
+        token_t *tok = atok->nsamples ? atok : btok;
+        for (i=0; i<rtok->nsamples; i++)
+        {
+            if ( !rtok->usmpl[i] ) continue;
+            rtok->pass_samples[i] = tok->pass_samples[i];
+        }
+        rtok->pass_site = 1;
+        return 2;
+    }
+
+    assert( atok->nsamples==btok->nsamples );
+    if ( rtok->tok_type==TOK_AND_VEC )  // &&, can be true in different samples
+    {
+        for (i=0; i<rtok->nsamples; i++)
+        {
+            if ( !rtok->usmpl[i] ) continue;
+            rtok->pass_samples[i] = atok->pass_samples[i] | btok->pass_samples[i];
+        }
+        rtok->pass_site = 1;
+    }
+    else    // &, must be true within one sample
+    {
+        for (i=0; i<rtok->nsamples; i++)
+        {
+            if ( !rtok->usmpl[i] ) continue;
+            rtok->pass_samples[i] = atok->pass_samples[i] & btok->pass_samples[i];
+            if ( rtok->pass_samples[i] ) rtok->pass_site = 1;
+        }
+    }
+    return 2;
+}
+
+#define CMP_VECTORS(atok,btok,_rtok,CMP_OP,missing_logic) \
+{ \
+    token_t *rtok = _rtok; \
+    int i, j, k; \
+    tok_init_samples(atok, btok, rtok); \
+    if ( !atok->nsamples && !btok->nsamples ) \
+    { \
+        if ( !atok->nvalues && !btok->nvalues ) { rtok->pass_site = missing_logic[2]; } \
+        else if ( !atok->nvalues || !btok->nvalues ) \
+        { \
+            token_t *tok = atok->nvalues ? atok : btok; \
+            for (j=0; j<tok->nvalues; j++) \
+            { \
+                if ( bcf_double_is_missing_or_vector_end(tok->values[j]) ) \
+                { \
+                    if ( missing_logic[2] ) { rtok->pass_site = 1; break; } \
+                } \
+                else if ( missing_logic[1] ) {  rtok->pass_site = 1; break; } \
+            } \
+        } \
+        else \
+        { \
+            for (i=0; i<atok->nvalues; i++) \
+            { \
+                int amiss = bcf_double_is_missing_or_vector_end(atok->values[i]) ? 1 : 0; \
+                for (j=0; j<btok->nvalues; j++) \
+                { \
+                    int nmiss = amiss + (bcf_double_is_missing_or_vector_end(btok->values[j]) ? 1 : 0); \
+                    if ( nmiss ) \
+                    { \
+                        if ( missing_logic[nmiss] ) { rtok->pass_site = 1; i = atok->nvalues; break; } \
+                    } \
+                    else if ( atok->values[i] > 16777216 || btok->values[j] > 16777216 ) /* Ugly, see #871 */ \
+                    { \
+                        if ( atok->values[i] CMP_OP btok->values[j] ) { rtok->pass_site = 1; i = atok->nvalues; break; } \
+                    } \
+                    else if ( (float)atok->values[i] CMP_OP (float)btok->values[j] ) { rtok->pass_site = 1; i = atok->nvalues; break; } \
+                } \
+            } \
+        } \
+    } \
+    else \
+    { \
+        if ( !atok->nvalues && !btok->nvalues ) \
+        { \
+            if ( missing_logic[2] ) \
+            { \
+                for (i=0; i<rtok->nsamples; i++) \
+                    if ( rtok->usmpl[i] ) { rtok->pass_samples[i] = missing_logic[2]; rtok->pass_site = 1; } \
+            } \
+        } \
+        else if ( !atok->nvalues || !btok->nvalues ) \
+        { \
+            token_t *tok = atok->nvalues ? atok : btok; \
+            if ( !tok->nsamples ) \
+            { \
+                int miss = 0; \
+                for (j=0; j<tok->nvalues; j++) \
+                    miss |= bcf_double_is_missing_or_vector_end(tok->values[j]) ? 1 : 0; \
+                if ( missing_logic[++miss] ) \
+                { \
+                    for (i=0; i<rtok->nsamples; i++) \
+                        if ( rtok->usmpl[i] ) { rtok->pass_samples[i] = missing_logic[miss]; rtok->pass_site = 1; } \
+                } \
+            } \
+            else \
+                for (i=0; i<tok->nsamples; i++) \
+                { \
+                    if ( !rtok->usmpl[i] ) continue; \
+                    double *ptr = tok->values + i*tok->nval1; \
+                    int miss = 0; \
+                    for (j=0; j<tok->nval1; j++) \
+                        miss |= bcf_double_is_missing_or_vector_end(ptr[j]) ? 1 : 0; \
+                    if ( missing_logic[++miss] ) { rtok->pass_samples[i] = missing_logic[miss]; rtok->pass_site = 1; } \
+                } \
+        } \
+        else if ( atok->nsamples && btok->nsamples ) \
+        { \
+            if ( atok->nval1!=btok->nval1 ) error("Incompatible number of per-sample values in comparison: %d vs %d\n",atok->nval1,btok->nval1); \
+            if ( atok->nsamples!=btok->nsamples ) error("Incompatible number samples in comparison: %d vs %d\n",atok->nsamples,btok->nsamples); \
+            for (i=0; i<atok->nsamples; i++) \
+            { \
+                if ( !atok->usmpl[i] || !btok->usmpl[i] ) { rtok->usmpl[i] = 0; continue; } \
+                double *aptr = atok->values + i*atok->nval1; \
+                double *bptr = btok->values + i*btok->nval1; \
+                for (j=0; j<atok->nval1; j++) \
+                { \
+                    int nmiss = bcf_double_is_missing_or_vector_end(aptr[j]) ? 1 : 0; \
+                    if ( nmiss && !missing_logic[0] ) continue; /* any is missing => result is false */ \
+                    nmiss += (bcf_double_is_missing_or_vector_end(bptr[j]) ? 1 : 0); \
+                    if ( nmiss ) \
+                    { \
+                        if ( missing_logic[nmiss] ) { rtok->pass_samples[i] = 1; rtok->pass_site = 1; break; } \
+                    } \
+                    else if ( aptr[j] > 16777216 || bptr[j] > 16777216 ) /* Ugly, see #871 */ \
+                    { \
+                        if ( aptr[j] CMP_OP bptr[j] ) { rtok->pass_samples[i] = 1; rtok->pass_site = 1; break; } \
+                    } \
+                    else if ( (float)aptr[j] CMP_OP (float)bptr[j] ) { rtok->pass_samples[i] = 1; rtok->pass_site = 1; break; } \
+                } \
+            } \
+        } \
+        else if ( atok->nsamples )\
+        { \
+            for (i=0; i<atok->nsamples; i++) \
+            { \
+                if ( !rtok->usmpl[i] ) continue; \
+                double *aptr = atok->values + i*atok->nval1; \
+                double *bptr = btok->values + i*btok->nval1; \
+                for (j=0; j<atok->nval1; j++) \
+                { \
+                    int miss = bcf_double_is_missing_or_vector_end(aptr[j]) ? 1 : 0; \
+                    if ( miss && !missing_logic[0] ) continue; /* any is missing => result is false */ \
+                    for (k=0; k<btok->nvalues; k++) \
+                    { \
+                        int nmiss = miss + (bcf_double_is_missing_or_vector_end(bptr[k]) ? 1 : 0); \
+                        if ( nmiss ) \
+                        { \
+                            if ( missing_logic[nmiss] ) { rtok->pass_samples[i] = 1; rtok->pass_site = 1; j = atok->nval1; break; } \
+                        } \
+                        else if ( aptr[j] > 16777216 || bptr[k] > 16777216 ) /* Ugly, see #871 */ \
+                        { \
+                            if ( aptr[j] CMP_OP bptr[k] ) { rtok->pass_samples[i] = 1; rtok->pass_site = 1; j = atok->nval1; break; } \
+                        } \
+                        else if ( (float)aptr[j] CMP_OP (float)bptr[k] ) { rtok->pass_samples[i] = 1; rtok->pass_site = 1; j = atok->nval1; break; } \
+                    } \
+                } \
+            } \
+        } \
+        else /* btok->nsamples */ \
+        { \
+            for (i=0; i<btok->nsamples; i++) \
+            { \
+                if ( !rtok->usmpl[i] ) continue; \
+                double *aptr = atok->values + i*atok->nval1; \
+                double *bptr = btok->values + i*btok->nval1; \
+                for (j=0; j<btok->nval1; j++) \
+                { \
+                    int miss = bcf_double_is_missing_or_vector_end(bptr[j]) ? 1 : 0; \
+                    if ( miss && !missing_logic[0] ) continue; /* any is missing => result is false */ \
+                    for (k=0; k<atok->nvalues; k++) \
+                    { \
+                        int nmiss = miss + (bcf_double_is_missing_or_vector_end(aptr[k]) ? 1 : 0); \
+                        if ( nmiss ) \
+                        { \
+                            if ( missing_logic[nmiss] ) { rtok->pass_samples[i] = 1; rtok->pass_site = 1; j = btok->nval1; break; } \
+                        } \
+                        else if ( bptr[j] > 16777216 || aptr[k] > 16777216 ) /* Ugly, see #871 */ \
+                        { \
+                            if ( aptr[k] CMP_OP bptr[j] ) { rtok->pass_samples[i] = 1; rtok->pass_site = 1; j = btok->nval1; break; } \
+                        } \
+                        else if ( (float)aptr[k] CMP_OP (float)bptr[j] ) { rtok->pass_samples[i] = 1; rtok->pass_site = 1; j = btok->nval1; break; } \
+                    } \
+                } \
+            } \
+        } \
+    } \
+}
+static int _regex_vector_strings(regex_t *regex, char *str, size_t len, int logic, int *missing_logic)
+{
+    char *end = str + len;
+    while ( str < end && *str )
+    {
+        char *mid = str;
+        while ( mid < end && *mid && *mid!=',' ) mid++;
+        int miss = mid - str == 1 && str[0]=='.' ? 1 : 0;
+        if ( miss && missing_logic[miss] ) return 1;
+        char tmp = *mid; *mid = 0;
+        int match = regexec(regex, str, 0,NULL,0) ? 0 : 1;
+        *mid = tmp;
+        if ( logic==TOK_NLIKE ) match = match ? 0 : 1;
+        if ( match ) return 1;
+        if ( !*mid ) break;
+        str = mid + 1;
+    }
+    return 0;
+}
+static inline int _has_missing_string(char *beg)
+{
+    while ( *beg )
+    {
+        char *end = beg;
+        while ( *end && *end!=',' ) end++;
+        if ( end-beg==1 && beg[0]=='.' ) return 1;
+        if ( !*end ) break;
+        beg = end + 1;
+    }
+    return 0;
+}
+
+// Compare two strings with multiple fields, for example "A,B,.,C"=="X,Y,A".
+// Returns 1 if any field matches, otherwise returns 0
+static inline int _match_vector_strings(char *abeg, size_t alen, char *bstr, size_t blen, int logic, int *missing_logic)
+{
+    char *aend = abeg + alen;
+    char *bend = bstr + blen;
+    while ( abeg < aend && *abeg )
+    {
+        char *amid = abeg;
+        while ( amid < aend && *amid && *amid!=',' ) amid++;
+        int miss = amid - abeg == 1 && abeg[0]=='.' ? 1 : 0;
+        char *bbeg = bstr;
+        while ( bbeg < bend && *bbeg )
+        {
+            char *bmid = bbeg;
+            while ( bmid < bend && *bmid && *bmid!=',' ) bmid++;
+            int nmiss = miss + (bmid - bbeg == 1 && bbeg[0]=='.' ? 1 : 0);
+            if ( nmiss )
+            {
+                if ( missing_logic[nmiss] ) return 1;
+            }
+            else
+            {
+                int match = amid-abeg==bmid-bbeg && !strncmp(abeg,bbeg,amid-abeg) ? 1 : 0;
+                if ( logic==TOK_NE ) match = match==1 ? 0 : 1;
+                if ( match ) return 1;
+            }
+            if ( !*bmid ) break;
+            bbeg = bmid + 1;
+        }
+        if ( !*amid ) break;
+        abeg = amid + 1;
+    }
+    return 0;
+}
+static void cmp_vector_strings(token_t *atok, token_t *btok, token_t *rtok)
+{
+    tok_init_samples(atok, btok, rtok);
+
+    int i, logic = rtok->tok_type;     // TOK_EQ, TOK_NE, TOK_LIKE, TOK_NLIKE
+    regex_t *regex = atok->regex ? atok->regex : (btok->regex ? btok->regex : NULL);
+
+    assert( atok->nvalues==atok->str_value.l && btok->nvalues==btok->str_value.l );
+    assert( !atok->nsamples || !btok->nsamples );
+    assert( (!regex && (logic==TOK_EQ || logic==TOK_NE)) || (regex && (logic==TOK_LIKE || logic==TOK_NLIKE)) );
+
+    int missing_logic[] = {0,0,0};
+    if ( logic==TOK_EQ || logic==TOK_LIKE ) missing_logic[0] = missing_logic[2] = 1;
+    else if ( logic==TOK_NE || logic==TOK_NLIKE ) missing_logic[0] = missing_logic[1] = 1;
+
+    if ( !atok->nsamples && !btok->nsamples )
+    {
+        if ( !atok->nvalues && !btok->nvalues ) { rtok->pass_site = missing_logic[2]; return; }
+        if ( !atok->nvalues || !btok->nvalues )
+        {
+            int miss = _has_missing_string(atok->nvalues ? atok->str_value.s : btok->str_value.s);
+            if ( missing_logic[miss+1] ) rtok->pass_site = 1;
+            return;
+        }
+        if ( !regex )
+            rtok->pass_site = _match_vector_strings(atok->str_value.s, atok->str_value.l, btok->str_value.s, btok->str_value.l, logic, missing_logic);
+        else
+        {
+            token_t *tok = atok->regex ? btok : atok;
+            rtok->pass_site = _regex_vector_strings(regex, tok->str_value.s, tok->str_value.l, logic, missing_logic);
+        }
+        return;
+    }
+
+    // The case of (!atok->nsamples || !btok->nsamples)
+
+    if ( !atok->nvalues && !btok->nvalues )
+    {
+        if ( missing_logic[2] )
+        {
+            for (i=0; i<rtok->nsamples; i++)
+                if ( rtok->usmpl[i] ) { rtok->pass_samples[i] = missing_logic[2]; rtok->pass_site = 1; }
+        }
+        return;
+    }
+    if ( !atok->nvalues || !btok->nvalues )
+    {
+        token_t *tok = atok->nvalues ? atok : btok;
+        if ( !tok->nsamples )
+        {
+            int miss = _has_missing_string(tok->str_value.s);
+            if ( !missing_logic[miss+1] ) return;
+            for (i=0; i<rtok->nsamples; i++)
+                if ( rtok->usmpl[i] ) { rtok->pass_samples[i] = 1; rtok->pass_site = 1; }
+        }
+        else
+            for (i=0; i<tok->nsamples; i++)
+            {
+                if ( !rtok->usmpl[i] ) continue;
+                int miss = _has_missing_string(tok->str_value.s + i*tok->nval1);
+                if ( missing_logic[miss+1] ) { rtok->pass_samples[i] = 1; rtok->pass_site = 1; }
+            }
+        return;
+    }
+
+    // The case of (!atok->nsamples || !btok->nsamples) && (atok->nvalues && btok->nvalues)
+    token_t *xtok = atok->nsamples ? atok : btok;
+    token_t *ytok = atok->nsamples ? btok : atok;
+    assert( regex==ytok->regex );
+    for (i=0; i<xtok->nsamples; i++)
+    {
+        if ( !rtok->usmpl[i] ) continue;
+        int match;
+        if ( regex )
+            match = _regex_vector_strings(regex, xtok->str_value.s + i*xtok->nval1, xtok->nval1, logic, missing_logic);
+        else
+            match = _match_vector_strings(xtok->str_value.s + i*xtok->nval1, xtok->nval1, ytok->str_value.s, ytok->str_value.l, logic, missing_logic);
+        if ( match ) { rtok->pass_samples[i] = 1; rtok->pass_site = 1; }
+    }
+}
+
+static int parse_idxs(char *tag_idx, int **idxs, int *nidxs, int *idx)
+{
+    // TAG[], TAG[*] .. any field; sets idx=-2, idxs[0]=-1
+    if ( *tag_idx==0 || !strcmp("*", tag_idx) )
+    {
+        *idxs = (int*) malloc(sizeof(int));
+        (*idxs)[0] = -1;
+        *nidxs     = 1;
+        *idx       = -2;
+        return 0;
+    }
+
+    // TAG[integer] .. one field; idx positive
+    char *end, *beg = tag_idx;
+    *idx = strtol(tag_idx, &end, 10);
+    if ( *idx >= 0 && *end==0 ) return 0;
+
+    // TAG[0,1] or TAG[0-2] or [1-] etc; idx=-2, idxs[...]=0,0,1,1,..
+    int i, ibeg = -1;
+    while ( *beg )
+    {
+        int num = strtol(beg, &end, 10);
+        if ( end[0]==',' ) beg = end + 1;
+        else if ( end[0]==0 ) beg = end;
+        else if ( end[0]=='-' ) { beg = end + 1; ibeg = num; continue; }
+        else return -1;
+        if ( num >= *nidxs )
+        {
+            *idxs = (int*) realloc(*idxs, sizeof(int)*(num+1));
+            memset(*idxs + *nidxs, 0, sizeof(int)*(num - *nidxs + 1));
+            *nidxs = num + 1;
+        }
+        if ( ibeg>=0 )
+        {
+            for (i=ibeg; i<=num; i++) (*idxs)[i] = 1;
+            ibeg = -1;
+        }
+        (*idxs)[num] = 1;
+    }
+    if ( ibeg >=0 )
+    {
+        if ( ibeg >= *nidxs )
+        {
+            *idxs = (int*) realloc(*idxs, sizeof(int)*(ibeg+1));
+            memset(*idxs + *nidxs, 0, sizeof(int)*(ibeg - *nidxs + 1));
+            *nidxs = ibeg + 1;
+        }
+        (*idxs)[ibeg] = -1;
+    }
+    *idx = -2;
+    return 0;
+}
+
+static void parse_tag_idx(bcf_hdr_t *hdr, int is_fmt, char *tag, char *tag_idx, token_t *tok)   // tag_idx points just after "TAG["
+{
+    int i, len = strlen(tag_idx);
+    if ( tag_idx[len-1] == ']' ) tag_idx[len-1] = 0;
+    char *ori = strdup(tag_idx);
+
+    assert( !tok->idxs && !tok->usmpl );
+    int *idxs1 = NULL, nidxs1 = 0, idx1 = 0;
+    int *idxs2 = NULL, nidxs2 = 0, idx2 = 0;
+
+    int set_samples = 0;
+    char *colon = strrchr(tag_idx, ':');
+    if ( tag_idx[0]=='@' )     // file list with sample names
+    {
+        if ( !is_fmt ) error("Could not parse \"%s\". (Not a FORMAT tag yet a sample list provided.)\n", ori);
+        char *fname = expand_path(tag_idx+1);
+#ifdef _WIN32
+        if (fname && strlen(fname) > 2 && fname[1] == ':') // Deal with Windows paths, such as 'C:\..'
+            colon = strrchr(fname+2, ':');
+#endif
+        int nsmpl;
+        char **list = hts_readlist(fname, 1, &nsmpl);
+        if ( !list && colon )
+        {
+            if ( parse_idxs(colon+1, &idxs2, &nidxs2, &idx2) != 0 ) error("Could not parse the index: %s\n", ori);
+            tok->idxs  = idxs2;
+            tok->nidxs = nidxs2;
+            tok->idx   = idx2;
+            colon = strrchr(fname, ':');
+            *colon = 0;
+            list = hts_readlist(fname, 1, &nsmpl);
+        }
+        if ( !list ) error("Could not read: %s\n", fname);
+        free(fname);
+        tok->nsamples = bcf_hdr_nsamples(hdr);
+        tok->usmpl = (uint8_t*) calloc(tok->nsamples,1);
+        for (i=0; i<nsmpl; i++)
+        {
+            int ismpl = bcf_hdr_id2int(hdr,BCF_DT_SAMPLE,list[i]);
+            if ( ismpl<0 ) error("No such sample in the VCF: \"%s\"\n", list[i]);
+            free(list[i]);
+            tok->usmpl[ismpl] = 1;
+        }
+        free(list);
+        if ( !colon )
+        {
+            tok->idxs = (int*) malloc(sizeof(int));
+            tok->idxs[0] = -1;
+            tok->nidxs   = 1;
+            tok->idx     = -2;
+        }
+    }
+    else if ( colon )
+    {
+        if ( !is_fmt ) error("Could not parse the index \"%s\". (Not a FORMAT tag yet sample index implied.)\n", ori);
+        *colon = 0;
+        if ( parse_idxs(tag_idx, &idxs1, &nidxs1, &idx1) != 0 ) error("Could not parse the index: %s\n", ori);
+        if ( parse_idxs(colon+1, &idxs2, &nidxs2, &idx2) != 0 ) error("Could not parse the index: %s\n", ori);
+        tok->idxs  = idxs2;
+        tok->nidxs = nidxs2;
+        tok->idx   = idx2;
+        set_samples = 1;
+    }
+    else
+    {
+        if ( parse_idxs(tag_idx, &idxs1, &nidxs1, &idx1) != 0 ) error("Could not parse the index: %s\n", ori);
+        if ( is_fmt )
+        {
+            if ( nidxs1==1 && idxs1[0]==-1 )
+            {
+                tok->idxs = (int*) malloc(sizeof(int));
+                tok->idxs[0] = -1;
+                tok->nidxs   = 1;
+                tok->idx     = -2;
+            }
+            else if ( bcf_hdr_id2number(hdr,BCF_HL_FMT,tok->hdr_id)!=1 )
+                error("The FORMAT tag %s can have multiple subfields, run as %s[sample:subfield]\n", tag,tag);
+            else
+                tok->idx = 0;
+            set_samples = 1;
+        }
+        else
+        {
+            tok->idxs  = idxs1;
+            tok->nidxs = nidxs1;
+            tok->idx   = idx1;
+        }
+    }
+
+    if ( set_samples )
+    {
+        tok->nsamples = bcf_hdr_nsamples(hdr);
+        tok->usmpl = (uint8_t*) calloc(tok->nsamples,1);
+        if ( idx1>=0 )
+        {
+            if ( idx1 >= bcf_hdr_nsamples(hdr) ) error("The sample index is too large: %s\n", ori);
+            tok->usmpl[idx1] = 1;
+        }
+        else if ( idx1==-2 )
+        {
+            for (i=0; i<nidxs1; i++)
+            {
+                if ( idxs1[i]==0 ) continue;
+                if ( idxs1[i]==-1 ) break;
+                if ( i >= bcf_hdr_nsamples(hdr) ) error("The sample index is too large: %s\n", ori);
+                tok->usmpl[i] = 1;
+            }
+            if ( nidxs1 && idxs1[nidxs1-1]==-1 )    // open range, such as "7-"
+            {
+                for (; i<tok->nsamples; i++) tok->usmpl[i] = 1;
+            }
+        }
+        else error("todo: %s:%d .. %d\n", __FILE__,__LINE__, idx2);
+        free(idxs1);
+    }
+    free(ori);
+
+    if ( tok->nidxs && tok->idxs[tok->nidxs-1]!=-1 )
+    {
+        for (i=0; i<tok->nidxs; i++) if ( tok->idxs[i] ) tok->nuidxs++;
+    }
+}
+static int max_ac_an_unpack(bcf_hdr_t *hdr)
+{
+    int hdr_id = bcf_hdr_id2int(hdr,BCF_DT_ID,"AC");
+    if ( hdr_id<0 ) return BCF_UN_FMT;
+    if ( !bcf_hdr_idinfo_exists(hdr,BCF_HL_INFO,hdr_id) ) return BCF_UN_FMT;
+
+    hdr_id = bcf_hdr_id2int(hdr,BCF_DT_ID,"AN");
+    if ( hdr_id<0 ) return BCF_UN_FMT;
+    if ( !bcf_hdr_idinfo_exists(hdr,BCF_HL_INFO,hdr_id) ) return BCF_UN_FMT;
+
+    return BCF_UN_INFO;
+}
+static int filters_init1(filter_t *filter, char *str, int len, token_t *tok)
+{
+    tok->tag_type  = -1;
+    tok->tok_type  = TOK_VAL;
+    tok->hdr_id    = -1;
+    tok->pass_site = -1;
+    tok->idx       = 0;
+
+    // is this a string constant?
+    if ( str[0]=='"' || str[0]=='\'' )
+    {
+        int quote = str[0];
+        if ( str[len-1] != quote ) error("TODO: [%s]\n", filter->str);
+        tok->key = (char*) calloc(len-1,sizeof(char));
+        hts_expand(double,1,tok->mvalues,tok->values);
+        tok->values[0] = len-2;
+        memcpy(tok->key,str+1,len-2);
+        tok->key[len-2] = 0;
+        tok->is_str = 1;
+        tok->nvalues = len-2;
+        if ( !strcmp(".",tok->key) ) tok->is_missing = 1;
+        return 0;
+    }
+
+    // is it a file?
+    if ( str[0]=='@' )
+    {
+        tok->tag = (char*) calloc(len+1,sizeof(char));
+        memcpy(tok->tag,str,len);
+        tok->tag[len] = 0;
+        char *fname = expand_path(tok->tag+1);
+        int i, n;
+        char **list = hts_readlist(fname, 1, &n);
+        if ( !list ) error("Could not read: %s\n", fname);
+        free(fname);
+        tok->hash = khash_str2int_init();
+        for (i=0; i<n; i++)
+        {
+            char *se = list[i];
+            while ( *se && !isspace(*se) ) se++;
+            *se = 0;
+            if ( !khash_str2int_has_key(tok->hash,list[i]) )
+                khash_str2int_inc(tok->hash,list[i]);
+            else
+                free(list[i]);
+        }
+        free(list);
+        return 0;
+    }
+
+    int is_fmt = -1;
+    if ( !strncasecmp(str,"FMT/",4) ) { str += 4; len -= 4; is_fmt = 1; }
+    else if ( !strncasecmp(str,"FORMAT/",7) ) { str += 7; len -= 7; is_fmt = 1; }
+    else
+    {
+        if ( !strncasecmp(str,"INFO/",5) ) { is_fmt = 0; str += 5; len -= 5; }
+        else if ( !strncasecmp(str,"QUAL",len) || !strncmp(str,"%QUAL",len) /* for backward compatibility */ )
+        {
+            tok->setter = filters_set_qual;
+            tok->tag = strdup("QUAL");
+            return 0;
+        }
+        else if ( !strncasecmp(str,"TYPE",len) || !strncmp(str,"%TYPE",len) /* for backward compatibility */ )
+        {
+            tok->setter = filters_set_type;
+            tok->tag = strdup("TYPE");
+            return 0;
+        }
+        else if ( !strncasecmp(str,"FILTER",len) || !strncmp(str,"%FILTER",len) /* for backward compatibility */ )
+        {
+            tok->comparator = filters_cmp_filter;
+            tok->tag = strdup("FILTER");
+            filter->max_unpack |= BCF_UN_FLT;
+            tok->tag_type = BCF_HL_FLT;
+            return 0;
+        }
+        else if ( !strncasecmp(str,"ID",len) || !strncasecmp(str,"%ID",len) /* for backward compatibility */ )
+        {
+            tok->comparator = filters_cmp_id;
+            tok->tag = strdup("ID");
+            return 0;
+        }
+        else if ( !strncasecmp(str,"CHROM",len) )
+        {
+            tok->setter = &filters_set_chrom;
+            tok->tag = strdup("CHROM");
+            return 0;
+        }
+        else if ( !strncasecmp(str,"POS",len) )
+        {
+            tok->setter = &filters_set_pos;
+            tok->tag = strdup("POS");
+            return 0;
+        }
+        else if ( !strncasecmp(str,"REF",len) )
+        {
+            tok->setter = &filters_set_ref_string;
+            tok->is_str = 1;
+            tok->tag = strdup("REF");
+            return 0;
+        }
+        else if ( !strncasecmp(str,"ALT",len) )
+        {
+            tok->setter = &filters_set_alt_string;
+            tok->is_str = 1;
+            tok->tag = strdup("ALT");
+            tok->idxs = (int*) malloc(sizeof(int));
+            tok->idxs[0] = -1;
+            tok->nidxs   = 1;
+            tok->idx     = -2;
+            return 0;
+        }
+        else if ( !strncasecmp(str,"N_ALT",len) )
+        {
+            tok->setter = &filters_set_nalt;
+            tok->tag = strdup("N_ALT");
+            return 0;
+        }
+        else if ( !strncasecmp(str,"N_SAMPLES",len) )
+        {
+            tok->tok_type = TOK_VAL;
+            tok->threshold = bcf_hdr_nsamples(filter->hdr);
+            tok->is_constant = 1;
+            return 0;
+        }
+        else if ( !strncasecmp(str,"N_MISSING",len) )
+        {
+            filter->max_unpack |= BCF_UN_FMT;
+            tok->setter = &filters_set_nmissing;
+            tok->tag = strdup("N_MISSING");
+            return 0;
+        }
+        else if ( !strncasecmp(str,"F_MISSING",len) )
+        {
+            filter->max_unpack |= BCF_UN_FMT;
+            tok->setter = &filters_set_nmissing;
+            tok->tag = strdup("F_MISSING");
+            return 0;
+        }
+    }
+
+    // does it have array subscript?
+    int is_array = 0;
+    kstring_t tmp = {0,0,0};
+    kputsn(str, len, &tmp);
+    if ( tmp.s[tmp.l-1] == ']' )
+    {
+        int i;
+        for (i=0; i<tmp.l; i++)
+            if ( tmp.s[i]=='[' ) { tmp.s[i] = 0; is_array = i+1; break; }
+    }
+    tok->hdr_id = bcf_hdr_id2int(filter->hdr,BCF_DT_ID,tmp.s);
+    if ( is_fmt==-1 )
+    {
+        if ( tok->hdr_id >=0 )
+        {
+            int is_info = bcf_hdr_idinfo_exists(filter->hdr,BCF_HL_INFO,tok->hdr_id) ? 1 : 0;
+            is_fmt = bcf_hdr_idinfo_exists(filter->hdr,BCF_HL_FMT,tok->hdr_id) ? 1 : 0;
+            if ( is_info && is_fmt )
+                error("Error: ambiguous filtering expression, both INFO/%s and FORMAT/%s are defined in the VCF header.\n" , tmp.s,tmp.s);
+        }
+        if ( is_fmt==-1 ) is_fmt = 0;
+    }
+    if ( is_array )
+        parse_tag_idx(filter->hdr, is_fmt, tmp.s, tmp.s+is_array, tok);
+    else if ( is_fmt && !tok->nsamples )
+    {
+        int i;
+        tok->nsamples = bcf_hdr_nsamples(filter->hdr);
+        tok->usmpl = (uint8_t*) malloc(tok->nsamples);
+        for (i=0; i<tok->nsamples; i++) tok->usmpl[i] = 1;
+    }
+
+    tok->tag_type = is_fmt ? BCF_HL_FMT : BCF_HL_INFO;
+    if ( is_fmt ) filter->max_unpack |= BCF_UN_FMT;
+    if ( tok->hdr_id>=0 )
+    {
+        if ( is_fmt && !strcmp("GT",tmp.s) )
+        {
+            tok->setter = &filters_set_genotype_string; tok->is_str = 1;
+        }
+        else if ( is_fmt )
+        {
+            if ( !bcf_hdr_idinfo_exists(filter->hdr,BCF_HL_FMT,tok->hdr_id) )
+                error("No such FORMAT field: %s\n", tmp.s);
+            if ( bcf_hdr_id2number(filter->hdr,BCF_HL_FMT,tok->hdr_id)!=1 && !is_array )
+            {
+                tok->idxs = (int*) malloc(sizeof(int));
+                tok->idxs[0] = -1;
+                tok->nidxs   = 1;
+                tok->idx     = -2;
+            }
+            switch ( bcf_hdr_id2type(filter->hdr,BCF_HL_FMT,tok->hdr_id) )
+            {
+                case BCF_HT_INT:  tok->setter = &filters_set_format_int; break;
+                case BCF_HT_REAL: tok->setter = &filters_set_format_float; break;
+                case BCF_HT_STR:  tok->setter = &filters_set_format_string; tok->is_str = 1; break;
+                default: error("[%s:%d %s] FIXME\n", __FILE__,__LINE__,__FUNCTION__);
+            }
+        }
+        else if ( !bcf_hdr_idinfo_exists(filter->hdr,BCF_HL_INFO,tok->hdr_id) )
+            error("No such INFO field: %s\n", tmp.s);
+        else
+        {
+            if ( bcf_hdr_id2type(filter->hdr,BCF_HL_INFO,tok->hdr_id) == BCF_HT_FLAG )
+                tok->setter = filters_set_info_flag;
+            else
+            {
+                if ( bcf_hdr_id2type(filter->hdr,BCF_HL_INFO,tok->hdr_id) == BCF_HT_STR ) tok->is_str = 1;
+                if ( bcf_hdr_id2number(filter->hdr,BCF_HL_INFO,tok->hdr_id)==1 )
+                    tok->setter = filters_set_info;
+                else
+                {
+                    switch ( bcf_hdr_id2type(filter->hdr,BCF_HL_INFO,tok->hdr_id) )
+                    {
+                        case BCF_HT_INT:  tok->setter = &filters_set_info_int; break;
+                        case BCF_HT_REAL: tok->setter = &filters_set_info_float; break;
+                        case BCF_HT_STR:  tok->setter = &filters_set_info_string; tok->is_str = 1; break;
+                        default: error("[%s:%d %s] FIXME\n", __FILE__,__LINE__,__FUNCTION__);
+                    }
+                    if (!is_array)
+                    {
+                        tok->idx = -2;
+                        tok->idxs = (int*) malloc(sizeof(int));
+                        tok->idxs[0] = -1;
+                        tok->nidxs   = 1;
+                    }
+                }
+            }
+            filter->max_unpack |= BCF_UN_INFO;
+        }
+        tok->tag = strdup(tmp.s);
+        if ( tmp.s ) free(tmp.s);
+        return 0;
+    }
+    else if ( !strcasecmp(tmp.s,"ALT") )
+    {
+        tok->setter = &filters_set_alt_string;
+        tok->is_str = 1;
+        tok->tag = strdup(tmp.s);
+        free(tmp.s);
+        return 0;
+    }
+    else if ( !strcasecmp(tmp.s,"AN") )
+    {
+        filter->max_unpack |= BCF_UN_FMT;
+        tok->setter = &filters_set_an;
+        tok->tag = strdup("AN");
+        free(tmp.s);
+        return 0;
+    }
+    else if ( !strcasecmp(tmp.s,"AC") )
+    {
+        filter->max_unpack |= BCF_UN_FMT;
+        tok->setter = &filters_set_ac;
+        tok->tag = strdup("AC");
+        free(tmp.s);
+        return 0;
+    }
+    else if ( !strcasecmp(tmp.s,"MAC") )
+    {
+        filter->max_unpack |= max_ac_an_unpack(filter->hdr);
+        tok->setter = &filters_set_mac;
+        tok->tag = strdup("MAC");
+        free(tmp.s);
+        return 0;
+    }
+    else if ( !strcasecmp(tmp.s,"AF") )
+    {
+        filter->max_unpack |= max_ac_an_unpack(filter->hdr);
+        tok->setter = &filters_set_af;
+        tok->tag = strdup("AF");
+        free(tmp.s);
+        return 0;
+    }
+    else if ( !strcasecmp(tmp.s,"MAF") )
+    {
+        filter->max_unpack |= max_ac_an_unpack(filter->hdr);
+        tok->setter = &filters_set_maf;
+        tok->tag = strdup("MAF");
+        free(tmp.s);
+        return 0;
+    }
+    else if ( !strcasecmp(tmp.s,"ILEN") || !strcasecmp(tmp.s,"%ILEN") )
+    {
+        filter->max_unpack |= BCF_UN_STR;
+        tok->setter = &filters_set_ilen;
+        tok->tag = strdup("ILEN");
+        free(tmp.s);
+        return 0;
+    }
+
+    // is it a value? Here we parse as integer/float separately and use strtof
+    // rather than strtod, because the more accurate double representation
+    // would invalidate floating point comparisons like QUAL=59.2, obtained via
+    // htslib/vcf parser.
+    // Update: use strtod() and force floats only in comparisons
+    char *end;
+    tok->threshold = strtol(tmp.s, &end, 10);   // integer?
+    if ( end - tmp.s != strlen(tmp.s) )
+    {
+        errno = 0;
+        tok->threshold = strtod(tmp.s, &end);   // float?
+        if ( errno!=0 || end!=tmp.s+len ) error("[%s:%d %s] Error: the tag \"%s\" is not defined in the VCF header\n", __FILE__,__LINE__,__FUNCTION__,tmp.s);
+    }
+    tok->is_constant = 1;
+
+    if ( tmp.s ) free(tmp.s);
+    return 0;
+}
+
+
+static void filter_debug_print(token_t *toks, token_t **tok_ptrs, int ntoks)
+{
+    int i;
+    for (i=0; i<ntoks; i++)
+    {
+        token_t *tok = toks ? &toks[i] : tok_ptrs[i];
+        if ( tok->tok_type==TOK_VAL )
+        {
+            if ( tok->key )
+                fprintf(stderr,"%s", tok->key);
+            else if ( tok->tag )
+                fprintf(stderr,"%s", tok->tag);
+            else
+                fprintf(stderr,"%e", tok->threshold);
+        }
+        else
+            fprintf(stderr,"%c", TOKEN_STRING[tok->tok_type]);
+        if ( tok->setter ) fprintf(stderr,"\t[setter %p]", tok->setter);
+        fprintf(stderr,"\n");
+    }
+}
+
+static void str_to_lower(char *str)
+{
+    while ( *str ) { *str = tolower(*str); str++; }
+}
+static int perl_exec(filter_t *flt, bcf1_t *line, token_t *rtok, token_t **stack, int nstack)
+{
+#if ENABLE_PERL_FILTERS
+
+    PerlInterpreter *perl = flt->perl;
+    if ( !perl ) error("Error: perl expression without a perl script name\n");
+
+    dSP;
+    ENTER;
+    SAVETMPS;
+
+    PUSHMARK(SP);
+    int i,j, istack = nstack - rtok->nargs;
+    for (i=istack+1; i<nstack; i++)
+    {
+        token_t *tok = stack[i];
+        if ( tok->is_str )
+            XPUSHs(sv_2mortal(newSVpvn(tok->str_value.s,tok->str_value.l)));
+        else if ( tok->nvalues==1 )
+            XPUSHs(sv_2mortal(newSVnv(tok->values[0])));
+        else if ( tok->nvalues>1 )
+        {
+            AV *av = newAV();
+            for (j=0; j<tok->nvalues; j++) av_push(av, newSVnv(tok->values[j]));
+            SV *rv = newRV_inc((SV*)av);
+            XPUSHs(rv);
+        }
+        else
+        {
+            bcf_double_set_missing(tok->values[0]);
+            XPUSHs(sv_2mortal(newSVnv(tok->values[0])));
+        }
+    }
+    PUTBACK;
+
+    // A possible future todo: provide a means to select samples and indexes,
+    // expressions like this don't work yet
+    //          perl.filter(FMT/AD)[1:0]
+
+    int nret = call_pv(stack[istack]->str_value.s, G_ARRAY);
+
+    SPAGAIN;
+
+    rtok->nvalues = nret;
+    hts_expand(double, rtok->nvalues, rtok->mvalues, rtok->values);
+    for (i=nret; i>0; i--)
+    {
+        rtok->values[i-1] = (double) POPn;
+        if ( isnan(rtok->values[i-1]) ) bcf_double_set_missing(rtok->values[i-1]);
+    }
+
+    PUTBACK;
+    FREETMPS;
+    LEAVE;
+
+#else
+    error("\nPerl filtering requires running `configure --enable-perl-filters` at compile time.\n\n");
+#endif
+    return rtok->nargs;
+}
+static void perl_init(filter_t *filter, char **str)
+{
+    char *beg = *str;
+    while ( *beg && isspace(*beg) ) beg++;
+    if ( !*beg ) return;
+    if ( strncasecmp("perl:", beg, 5) ) return;
+#if ENABLE_PERL_FILTERS
+    beg += 5;
+    char *end = beg;
+    while ( *end && *end!=';' ) end++;  // for now not escaping semicolons
+    *str = end+1;
+
+    if ( ++filter_ninit == 1 )
+    {
+        // must be executed only once, even for multiple filters; first time here
+        int argc = 0;
+        char **argv = NULL;
+        char **env  = NULL;
+        PERL_SYS_INIT3(&argc, &argv, &env);
+    }
+
+    filter->perl = perl_alloc();
+    PerlInterpreter *perl = filter->perl;
+
+    if ( !perl ) error("perl_alloc failed\n");
+    perl_construct(perl);
+
+    // name of the perl script to run
+    char *rmme = (char*) calloc(end - beg + 1,1);
+    memcpy(rmme, beg, end - beg);
+    char *argv[] = { "", "" };
+    argv[1] = expand_path(rmme);
+    free(rmme);
+
+    PL_origalen = 1;    // don't allow $0 change
+    int ret = perl_parse(filter->perl, NULL, 2, argv, NULL);
+    PL_exit_flags |= PERL_EXIT_DESTRUCT_END;
+    if ( ret ) error("Failed to parse: %s\n", argv[1]);
+    free(argv[1]);
+
+    perl_run(perl);
+#else
+    error("\nPerl filtering requires running `configure --enable-perl-filters` at compile time.\n\n");
+#endif
+}
+static void perl_destroy(filter_t *filter)
+{
+#if ENABLE_PERL_FILTERS
+    if ( !filter->perl ) return;
+
+    PerlInterpreter *perl = filter->perl;
+    perl_destruct(perl);
+    perl_free(perl);
+    if ( --filter_ninit <= 0  )
+    {
+        // similarly to PERL_SYS_INIT3, can must be executed only once? todo: test
+        PERL_SYS_TERM();
+    }
+#endif
+}
+
+
+// Parse filter expression and convert to reverse polish notation. Dijkstra's shunting-yard algorithm
+filter_t *filter_init(bcf_hdr_t *hdr, const char *str)
+{
+    filter_t *filter = (filter_t *) calloc(1,sizeof(filter_t));
+    filter->str = strdup(str);
+    filter->hdr = hdr;
+    filter->max_unpack |= BCF_UN_STR;
+
+    int nops = 0, mops = 0;    // operators stack
+    int nout = 0, mout = 0;    // filter tokens, RPN
+    token_t *out = NULL;
+    token_t *ops = NULL;
+    char *tmp = filter->str;
+    perl_init(filter, &tmp);
+
+    int last_op = -1;
+    while ( *tmp )
+    {
+        int len, ret;
+        ret = filters_next_token(&tmp, &len);
+        if ( ret==-1 ) error("Missing quotes in: %s\n", str);
+
+        // fprintf(stderr,"token=[%c] .. [%s] %d\n", TOKEN_STRING[ret], tmp, len);
+        // int i; for (i=0; i<nops; i++) fprintf(stderr," .%c", TOKEN_STRING[ops[i].tok_type]); fprintf(stderr,"\n");
+
+        if ( ret==TOK_LFT )         // left bracket
+        {
+            nops++;
+            hts_expand0(token_t, nops, mops, ops);
+            ops[nops-1].tok_type = ret;
+        }
+        else if ( ret==TOK_RGT )    // right bracket
+        {
+            while ( nops>0 && ops[nops-1].tok_type!=TOK_LFT )
+            {
+                nout++;
+                hts_expand0(token_t, nout, mout, out);
+                out[nout-1] = ops[nops-1];
+                memset(&ops[nops-1],0,sizeof(token_t));
+                nops--;
+            }
+            if ( nops<=0 ) error("Could not parse: %s\n", str);
+            memset(&ops[nops-1],0,sizeof(token_t));
+            nops--;
+        }
+        else if ( ret!=TOK_VAL )    // one of the operators
+        {
+            // detect unary minus: replace -value with -1*(value)
+            if ( ret==TOK_SUB && last_op!=TOK_VAL && last_op!=TOK_RGT )
+            {
+                nout++;
+                hts_expand0(token_t, nout, mout, out);
+                token_t *tok = &out[nout-1];
+                tok->tok_type  = TOK_VAL;
+                tok->hdr_id    = -1;
+                tok->pass_site = -1;
+                tok->threshold = -1.0;
+                tok->is_constant = 1;
+                ret = TOK_MULT;
+            }
+            else if ( ret == -TOK_FUNC )
+            {
+                // this is different from TOK_PERLSUB,TOK_BINOM in that the expression inside the
+                // brackets gets evaluated as normal expression
+                nops++;
+                hts_expand0(token_t, nops, mops, ops);
+                token_t *tok = &ops[nops-1];
+                tok->tok_type  = -ret;
+                tok->hdr_id    = -1;
+                tok->pass_site = -1;
+                tok->threshold = -1.0;
+                if ( !strncasecmp(tmp-len,"N_PASS",6) )
+                {
+                    filter->max_unpack |= BCF_UN_FMT;
+                    tok->func = func_npass;
+                    tok->tag = strdup("N_PASS");
+                }
+                else if ( !strncasecmp(tmp-len,"F_PASS",6) )
+                {
+                    filter->max_unpack |= BCF_UN_FMT;
+                    tok->func = func_npass;
+                    tok->tag = strdup("F_PASS");
+                }
+                else error("The function \"%s\" is not supported\n", tmp-len);
+                continue;
+            }
+            else if ( ret < 0 )     // variable number of arguments: TOK_PERLSUB,TOK_BINOM
+            {
+                ret = -ret;
+
+                tmp += len;
+                char *beg = tmp;
+                kstring_t rmme = {0,0,0};
+                int i, margs, nargs = 0;
+
+                if ( ret == TOK_PERLSUB )
+                {
+                    while ( *beg && ((isalnum(*beg) && !ispunct(*beg)) || *beg=='_') ) beg++;
+                    if ( *beg!='(' ) error("Could not parse the expression: %s\n", str);
+
+                    // the subroutine name
+                    kputc('"', &rmme);
+                    kputsn(tmp, beg-tmp, &rmme);
+                    kputc('"', &rmme);
+                    nout++;
+                    hts_expand0(token_t, nout, mout, out);
+                    filters_init1(filter, rmme.s, rmme.l, &out[nout-1]);
+                    nargs++;
+                }
+                char *end = beg;
+                while ( *end && *end!=')' ) end++;
+                if ( !*end ) error("Could not parse the expression: %s\n", str);
+
+                // subroutine arguments
+                rmme.l = 0;
+                kputsn(beg+1, end-beg-1, &rmme);
+                char **rmme_list = hts_readlist(rmme.s, 0, &margs);
+                for (i=0; i<margs; i++)
+                {
+                    nargs++;
+                    nout++;
+                    hts_expand0(token_t, nout, mout, out);
+                    filters_init1(filter, rmme_list[i], strlen(rmme_list[i]), &out[nout-1]);
+                    free(rmme_list[i]);
+                }
+                free(rmme_list);
+                free(rmme.s);
+
+                nout++;
+                hts_expand0(token_t, nout, mout, out);
+                token_t *tok = &out[nout-1];
+                tok->tok_type  = ret;
+                tok->nargs     = nargs;
+                tok->hdr_id    = -1;
+                tok->pass_site = -1;
+                tok->threshold = -1.0;
+
+                tmp = end + 1;
+                continue;
+            }
+            else
+            {
+                while ( nops>0 && op_prec[ret] < op_prec[ops[nops-1].tok_type] )
+                {
+                    nout++;
+                    hts_expand0(token_t, nout, mout, out);
+                    out[nout-1] = ops[nops-1];
+                    memset(&ops[nops-1],0,sizeof(token_t));
+                    nops--;
+                }
+            }
+            nops++;
+            hts_expand0(token_t, nops, mops, ops);
+            ops[nops-1].tok_type = ret;
+        }
+        else if ( !len )
+        {
+            if ( *tmp && !isspace(*tmp) ) error("Could not parse the expression: [%s]\n", str);
+            break;     // all tokens read
+        }
+        else           // annotation name or filtering value
+        {
+            nout++;
+            hts_expand0(token_t, nout, mout, out);
+            if ( tmp[len-1]==',' )
+                filters_init1(filter, tmp, len-1, &out[nout-1]);
+            else
+                filters_init1(filter, tmp, len, &out[nout-1]);
+            tmp += len;
+        }
+        last_op = ret;
+    }
+    while ( nops>0 )
+    {
+        if ( ops[nops-1].tok_type==TOK_LFT || ops[nops-1].tok_type==TOK_RGT ) error("Could not parse the expression: [%s]\n", filter->str);
+        nout++;
+        hts_expand0(token_t, nout, mout, out);
+        out[nout-1] = ops[nops-1];
+        memset(&ops[nops-1],0,sizeof(token_t));
+        nops--;
+    }
+
+    // In the special cases of TYPE and FILTER the BCF header IDs are yet unknown. Walk through the
+    // list of operators and convert the strings (e.g. "PASS") to BCF ids. The string value token must be
+    // just before or after the FILTER token and they must be followed with a comparison operator.
+    // At this point we also initialize regex expressions which, in RPN, must preceed the LIKE/NLIKE operator.
+    // Additionally, treat "." as missing value rather than a string in numeric equalities; that
+    // @file is only used with ID; etc.
+    // This code is fragile: improve me.
+    static int comma_separator_warned = 0;
+    int i;
+    for (i=0; i<nout; i++)
+    {
+        if ( i+1<nout && (out[i].tok_type==TOK_LT || out[i].tok_type==TOK_BT) && out[i+1].tok_type==TOK_EQ )
+            error("Error parsing the expression: \"%s\"\n", filter->str);
+
+        if ( out[i].hash )
+        {
+            int j = out[i+1].tok_type==TOK_VAL ? i+1 : i-1;
+            if ( out[j].comparator!=filters_cmp_id )
+                error("Error: could not parse the expression. Note that the \"@file_name\" syntax can be currently used with ID column only.\n");
+        }
+        if ( out[i].tok_type==TOK_OR || out[i].tok_type==TOK_OR_VEC )
+            out[i].func = vector_logic_or;
+        if ( out[i].tok_type==TOK_AND || out[i].tok_type==TOK_AND_VEC )
+            out[i].func = vector_logic_and;
+        if ( out[i].tok_type==TOK_EQ || out[i].tok_type==TOK_NE )
+        {
+            // Look for j="." and k numeric type
+            int j = i-1, k = i-2;
+            if ( !out[j].is_str ) { k = i-1, j = i-2; }
+            if ( out[j].is_str && out[j].key && !strcmp(".",out[j].key) )
+            {
+                int set_missing = 0;
+                if ( out[k].hdr_id>0 )
+                {
+                    int type = bcf_hdr_id2type(filter->hdr,out[k].tag_type,out[k].hdr_id);
+                    if ( type==BCF_HT_INT ) set_missing = 1;
+                    else if ( type==BCF_HT_REAL ) set_missing = 1;
+                }
+                else if ( !strcmp("QUAL",out[k].tag) ) set_missing = 1;
+                if ( set_missing ) { out[j].is_str = 0; out[j].is_missing = 1; bcf_double_set_missing(out[j].values[0]); }
+            }
+        }
+        if ( out[i].tok_type==TOK_LIKE || out[i].tok_type==TOK_NLIKE )
+        {
+            int j = i-1;
+            if ( !out[j].key )
+                error("Could not parse the expression, wrong value for regex operator: %s\n", filter->str);
+            out[j].regex = (regex_t *) malloc(sizeof(regex_t));
+            int cflags = REG_NOSUB;
+            int len = strlen(out[j].key);
+            if ( len>2 && out[j].key[len-1]=='i' && out[j].key[len-2]=='/' && out[j].key[len-3]!='\\'  )
+            {
+                out[j].key[len-2] = 0;
+                cflags |= REG_ICASE;
+            }
+            if ( regcomp(out[j].regex, out[j].key, cflags) )
+                error("Could not compile the regex expression \"%s\": %s\n", out[j].key,filter->str);
+        }
+        if ( out[i].is_str && out[i].tok_type==TOK_VAL && out[i].key && strchr(out[i].key,',') )
+        {
+            int print_note = 0;
+            if ( out[i+1].tok_type==TOK_EQ || (out[i+1].is_str && out[i+2].tok_type==TOK_EQ) ) print_note = 1;
+            else if ( out[i+1].tok_type==TOK_NE || (out[i+1].is_str && out[i+2].tok_type==TOK_NE) ) print_note = 1;
+            if ( print_note && !comma_separator_warned )
+            {
+                comma_separator_warned = 1;
+                fprintf(stderr,
+                    "Warning: comma is interpreted as a separator and OR logic is used in string comparisons.\n"
+                    "         (Search the manual for \"Comma in strings\" to learn more.)\n");
+            }
+        }
+        if ( out[i].tok_type!=TOK_VAL ) continue;
+        if ( !out[i].tag ) continue;
+        if ( out[i].setter==filters_set_type )
+        {
+            if ( i+1==nout ) error("Could not parse the expression: %s\n", filter->str);
+            int itok, ival;
+            if ( out[i+1].tok_type==TOK_EQ || out[i+1].tok_type==TOK_NE ) ival = i - 1, itok = i + 1;
+            else if ( out[i+1].tok_type==TOK_LIKE || out[i+1].tok_type==TOK_NLIKE ) ival = i - 1, itok = i + 1;
+            else if ( out[i+2].tok_type==TOK_EQ || out[i+2].tok_type==TOK_NE ) itok = i + 2, ival = i + 1;
+            else if ( out[i+2].tok_type==TOK_LIKE || out[i+2].tok_type==TOK_NLIKE ) itok = i + 2, ival = i + 1;
+            else error("[%s:%d %s] Could not parse the expression: %s\n",  __FILE__,__LINE__,__FUNCTION__, filter->str);
+            if ( !strcasecmp(out[ival].key,"snp") || !strcasecmp(out[ival].key,"snps") ) { out[ival].threshold = VCF_SNP<<1; out[ival].is_str = 0; }
+            else if ( !strcasecmp(out[ival].key,"indel") || !strcasecmp(out[ival].key,"indels") ) { out[ival].threshold = VCF_INDEL<<1; out[ival].is_str = 0; }
+            else if ( !strcasecmp(out[ival].key,"mnp") || !strcasecmp(out[ival].key,"mnps") ) { out[ival].threshold = VCF_MNP<<1; out[ival].is_str = 0; }
+            else if ( !strcasecmp(out[ival].key,"other") ) { out[ival].threshold = VCF_OTHER<<1; out[ival].is_str = 0; }
+            else if ( !strcasecmp(out[ival].key,"bnd") ) { out[ival].threshold = VCF_BND<<1; out[ival].is_str = 0; }
+            else if ( !strcasecmp(out[ival].key,"overlap") ) { out[ival].threshold = VCF_OVERLAP<<1; out[ival].is_str = 0; }
+            else if ( !strcasecmp(out[ival].key,"ref") ) { out[ival].threshold = 1; out[ival].is_str = 0; }
+            else error("The type \"%s\" not recognised: %s\n", out[ival].key, filter->str);
+            out[ival].is_constant = 1;
+            if ( out[itok].tok_type==TOK_LIKE || out[itok].tok_type==TOK_NLIKE ) out[itok].comparator = filters_cmp_bit_and;
+            out[ival].tag = out[ival].key; out[ival].key = NULL;
+            i = itok;
+            continue;
+        }
+        if ( !strcmp(out[i].tag,"GT") )
+        {
+            if ( i+1==nout ) error("Could not parse the expression: %s\n", filter->str);
+            int ival;
+            if ( out[i+1].tok_type==TOK_EQ || out[i+1].tok_type==TOK_NE ) ival = i - 1;
+            else if ( out[i+1].tok_type==TOK_LIKE || out[i+1].tok_type==TOK_NLIKE ) ival = i - 1;
+            else if ( out[i+2].tok_type==TOK_EQ || out[i+2].tok_type==TOK_NE ) ival = i + 1;
+            else if ( out[i+2].tok_type==TOK_LIKE || out[i+2].tok_type==TOK_NLIKE ) ival = i + 1;
+            else error("[%s:%d %s] Could not parse the expression: %s\n",  __FILE__,__LINE__,__FUNCTION__, filter->str);
+
+            if ( !out[ival].key ) error("Comparison between samples is not supported, sorry!\n");
+
+            // assign correct setters and unify expressions, eg ar->ra, HOM->hom, etc
+            if ( !strcasecmp(out[ival].key,"hom") ) { out[i].setter = filters_set_genotype3;  str_to_lower(out[ival].key); }
+            else if ( !strcasecmp(out[ival].key,"het") ) { out[i].setter = filters_set_genotype3;  str_to_lower(out[ival].key); }
+            else if ( !strcasecmp(out[ival].key,"hap") ) { out[i].setter = filters_set_genotype3;  str_to_lower(out[ival].key); }
+            else if ( !strcasecmp(out[ival].key,"mis") ) { out[i].setter = filters_set_genotype4;  str_to_lower(out[ival].key); }
+            else if ( !strcasecmp(out[ival].key,"ref") ) { out[i].setter = filters_set_genotype4;  str_to_lower(out[ival].key); }
+            else if ( !strcasecmp(out[ival].key,"alt") ) { out[i].setter = filters_set_genotype4;  str_to_lower(out[ival].key); }
+            else if ( !strcasecmp(out[ival].key,"rr") ) { out[i].setter = filters_set_genotype2;  str_to_lower(out[ival].key); }
+            else if ( !strcasecmp(out[ival].key,"ra") || !strcasecmp(out[ival].key,"ar") ) { out[i].setter = filters_set_genotype2; out[ival].key[0]='r'; out[ival].key[1]='a'; }   // ra
+            else if ( !strcmp(out[ival].key,"aA") || !strcmp(out[ival].key,"Aa") ) { out[i].setter = filters_set_genotype2; out[ival].key[0]='a'; out[ival].key[1]='A'; }   // aA
+            else if ( !strcasecmp(out[ival].key,"aa") ) { out[i].setter = filters_set_genotype2; out[ival].key[0]='a'; out[ival].key[1]='a'; }  // aa
+            else if ( !strcasecmp(out[ival].key,"a") ) { out[i].setter = filters_set_genotype2; out[ival].key[0]='a'; out[ival].key[1]=0; }  // a
+            else if ( !strcasecmp(out[ival].key,"r") ) { out[i].setter = filters_set_genotype2; out[ival].key[0]='r'; out[ival].key[1]=0; }  // r
+            continue;
+        }
+        if ( out[i].tag_type==BCF_HL_FLT )
+        {
+            if ( i+1==nout ) error("Could not parse the expression: %s\n", filter->str);
+            int itok = i, ival;
+            if ( out[i+1].tok_type==TOK_EQ || out[i+1].tok_type==TOK_NE ) ival = i - 1;
+            else if ( out[i+1].tok_type==TOK_LIKE ) out[i+1].tok_type = TOK_IN, ival = i - 1;
+            else if ( out[i+1].tok_type==TOK_NLIKE ) out[i+1].tok_type = TOK_NOT_IN, ival = i - 1;
+            else if ( out[i+2].tok_type==TOK_EQ || out[i+2].tok_type==TOK_NE ) ival = ++i;
+            else if ( out[i+2].tok_type==TOK_LIKE ) out[i+2].tok_type = TOK_IN, ival = ++i;
+            else if ( out[i+2].tok_type==TOK_NLIKE ) out[i+2].tok_type = TOK_NOT_IN, ival = ++i;
+            else error("[%s:%d %s] Could not parse the expression: %s\n",  __FILE__,__LINE__,__FUNCTION__, filter->str);
+            if ( out[ival].tok_type!=TOK_VAL || !out[ival].key )
+                error("[%s:%d %s] Could not parse the expression, an unquoted string value perhaps? %s\n", __FILE__,__LINE__,__FUNCTION__, filter->str);
+            token_t *tok = &out[ival];
+            char *bp = tok->key;
+            tok->nvalues = 0;
+            int has_missing = 0;
+            while ( *bp )
+            {
+                char tmp, *ep = bp;
+                while ( *ep && *ep!=';' ) ep++;
+                tmp = *ep;
+                *ep = 0;
+                if ( !strcmp(".",bp) ) has_missing = 1;
+                else
+                {
+                    tok->nvalues++;
+                    hts_expand(double,tok->nvalues,tok->mvalues,tok->values);
+                    int id = bcf_hdr_id2int(filter->hdr, BCF_DT_ID, bp);
+                    if ( !bcf_hdr_idinfo_exists(filter->hdr,BCF_HL_FLT,id) )
+                        error("The filter \"%s\" not present in the VCF header\n", bp);
+                    tok->values[tok->nvalues-1] = id;
+                }
+                *ep = tmp;
+                if ( !tmp ) break;
+                bp = ep + 1;
+            }
+            if ( has_missing && tok->nvalues ) error("The FILTER expression cannot contain missing value AND filters: \"%s\" (%d)\n",tok->key,tok->nvalues);
+            out[ival].tag = tok->key;
+            tok->key = NULL;
+            out[itok].hdr_id = tok->hdr_id;
+            continue;
+        }
+    }
+    filter->nsamples = filter->max_unpack&BCF_UN_FMT ? bcf_hdr_nsamples(filter->hdr) : 0;
+    for (i=0; i<nout; i++)
+    {
+        if ( out[i].tok_type==TOK_MAX )      { out[i].func = func_max; out[i].tok_type = TOK_FUNC; }
+        else if ( out[i].tok_type==TOK_MIN ) { out[i].func = func_min; out[i].tok_type = TOK_FUNC; }
+        else if ( out[i].tok_type==TOK_AVG ) { out[i].func = func_avg; out[i].tok_type = TOK_FUNC; }
+        else if ( out[i].tok_type==TOK_MEDIAN ) { out[i].func = func_median; out[i].tok_type = TOK_FUNC; }
+        else if ( out[i].tok_type==TOK_AVG ) { out[i].func = func_avg; out[i].tok_type = TOK_FUNC; }
+        else if ( out[i].tok_type==TOK_STDEV ) { out[i].func = func_stddev; out[i].tok_type = TOK_FUNC; }
+        else if ( out[i].tok_type==TOK_SUM ) { out[i].func = func_sum; out[i].tok_type = TOK_FUNC; }
+        else if ( out[i].tok_type==TOK_ABS ) { out[i].func = func_abs; out[i].tok_type = TOK_FUNC; }
+        else if ( out[i].tok_type==TOK_CNT ) { out[i].func = func_count; out[i].tok_type = TOK_FUNC; }
+        else if ( out[i].tok_type==TOK_LEN ) { out[i].func = func_strlen; out[i].tok_type = TOK_FUNC; }
+        else if ( out[i].tok_type==TOK_PHRED ) { out[i].func = func_phred; out[i].tok_type = TOK_FUNC; }
+        else if ( out[i].tok_type==TOK_BINOM ) { out[i].func = func_binom; out[i].tok_type = TOK_FUNC; }
+        else if ( out[i].tok_type==TOK_PERLSUB ) { out[i].func = perl_exec; out[i].tok_type = TOK_FUNC; }
+        else if ( out[i].tok_type==TOK_sMAX ) { out[i].func = func_smpl_max; out[i].tok_type = TOK_FUNC; }
+        else if ( out[i].tok_type==TOK_sMIN ) { out[i].func = func_smpl_min; out[i].tok_type = TOK_FUNC; }
+        else if ( out[i].tok_type==TOK_sAVG ) { out[i].func = func_smpl_avg; out[i].tok_type = TOK_FUNC; }
+        else if ( out[i].tok_type==TOK_sMEDIAN ) { out[i].func = func_smpl_median; out[i].tok_type = TOK_FUNC; }
+        else if ( out[i].tok_type==TOK_sSTDEV ) { out[i].func = func_smpl_stddev; out[i].tok_type = TOK_FUNC; }
+        else if ( out[i].tok_type==TOK_sSUM ) { out[i].func = func_smpl_sum; out[i].tok_type = TOK_FUNC; }
+        hts_expand0(double,1,out[i].mvalues,out[i].values);
+        if ( filter->nsamples )
+        {
+            out[i].pass_samples = (uint8_t*)malloc(filter->nsamples);
+            int j;
+            for (j=0; j<filter->nsamples; j++) out[i].pass_samples[j] = 0;
+        }
+    }
+
+    if (0) filter_debug_print(out, NULL, nout);
+
+    if ( mops ) free(ops);
+    filter->filters   = out;
+    filter->nfilters  = nout;
+    filter->flt_stack = (token_t **)malloc(sizeof(token_t*)*nout);
+    return filter;
+}
+
+void filter_destroy(filter_t *filter)
+{
+    perl_destroy(filter);
+    int i;
+    for (i=0; i<filter->nfilters; i++)
+    {
+        if ( filter->filters[i].key ) free(filter->filters[i].key);
+        free(filter->filters[i].str_value.s);
+        free(filter->filters[i].tag);
+        free(filter->filters[i].idxs);
+        free(filter->filters[i].usmpl);
+        free(filter->filters[i].values);
+        free(filter->filters[i].pass_samples);
+        if (filter->filters[i].hash) khash_str2int_destroy_free(filter->filters[i].hash);
+        if (filter->filters[i].regex)
+        {
+            regfree(filter->filters[i].regex);
+            free(filter->filters[i].regex);
+        }
+    }
+    free(filter->filters);
+    free(filter->flt_stack);
+    free(filter->str);
+    free(filter->tmpi);
+    free(filter->tmpf);
+    free(filter->tmps.s);
+    free(filter);
+}
+
+int filter_test(filter_t *filter, bcf1_t *line, const uint8_t **samples)
+{
+    bcf_unpack(line, filter->max_unpack);
+
+    int i, nstack = 0;
+    for (i=0; i<filter->nfilters; i++)
+    {
+        filter->filters[i].pass_site = 0;
+        if ( filter->filters[i].tok_type == TOK_VAL )
+        {
+            if ( filter->filters[i].setter )    // variable, query the VCF line
+                filter->filters[i].setter(filter, line, &filter->filters[i]);
+            else if ( filter->filters[i].key )  // string constant
+            {
+                filter->filters[i].str_value.l = 0;
+                kputs(filter->filters[i].key, &filter->filters[i].str_value);
+                filter->filters[i].nvalues = filter->filters[i].str_value.l;
+            }
+            else if ( filter->filters[i].is_constant )   // numeric constant
+            {
+                filter->filters[i].values[0] = filter->filters[i].threshold;
+                filter->filters[i].nvalues   = 1;
+            }
+            filter->flt_stack[nstack++] = &filter->filters[i];
+            continue;
+        }
+        else if ( filter->filters[i].func )
+        {
+            int nargs = filter->filters[i].func(filter, line, &filter->filters[i], filter->flt_stack, nstack);
+            filter->flt_stack[nstack-nargs] = &filter->filters[i];
+            if ( --nargs > 0 ) nstack -= nargs;
+            continue;
+        }
+        if ( nstack<2 )
+            error("Error occurred while processing the filter \"%s\" (1:%d)\n", filter->str,nstack);  // too few values left on the stack
+
+        int is_str  = filter->flt_stack[nstack-1]->is_str + filter->flt_stack[nstack-2]->is_str;
+
+        if ( filter->filters[i].tok_type == TOK_ADD )
+        {
+            VECTOR_ARITHMETICS(filter->flt_stack[nstack-2],filter->flt_stack[nstack-1],&filter->filters[i],+,(double));
+            filter->flt_stack[nstack-2] = &filter->filters[i];
+            nstack--;
+            continue;
+        }
+        else if ( filter->filters[i].tok_type == TOK_SUB )
+        {
+            VECTOR_ARITHMETICS(filter->flt_stack[nstack-2],filter->flt_stack[nstack-1],&filter->filters[i],-,(double));
+            filter->flt_stack[nstack-2] = &filter->filters[i];
+            nstack--;
+            continue;
+        }
+        else if ( filter->filters[i].tok_type == TOK_MULT )
+        {
+            VECTOR_ARITHMETICS(filter->flt_stack[nstack-2],filter->flt_stack[nstack-1],&filter->filters[i],*,(double));
+            filter->flt_stack[nstack-2] = &filter->filters[i];
+            nstack--;
+            continue;
+        }
+        else if ( filter->filters[i].tok_type == TOK_DIV )
+        {
+            VECTOR_ARITHMETICS(filter->flt_stack[nstack-2],filter->flt_stack[nstack-1],&filter->filters[i],/,(double));
+            filter->flt_stack[nstack-2] = &filter->filters[i];
+            nstack--;
+            continue;
+        }
+        else if ( filter->filters[i].tok_type == TOK_MODULO )
+        {
+            VECTOR_ARITHMETICS(filter->flt_stack[nstack-2],filter->flt_stack[nstack-1],&filter->filters[i],%,(int));
+            filter->flt_stack[nstack-2] = &filter->filters[i];
+            nstack--;
+            continue;
+        }
+
+        // ideally, these comparators would become func, but this would require more work in init1()
+        if ( filter->filters[i].comparator )
+        {
+            filter->filters[i].comparator(filter->flt_stack[nstack-1],filter->flt_stack[nstack-2],&filter->filters[i],line);
+        }
+        else if ( filter->flt_stack[nstack-1]->comparator )
+        {
+            filter->flt_stack[nstack-1]->comparator(filter->flt_stack[nstack-1],filter->flt_stack[nstack-2],&filter->filters[i],line);
+        }
+        else if ( filter->flt_stack[nstack-2]->comparator )
+        {
+            filter->flt_stack[nstack-2]->comparator(filter->flt_stack[nstack-2],filter->flt_stack[nstack-1],&filter->filters[i],line);
+        }
+        else if ( is_str==2 )
+        {
+            cmp_vector_strings(filter->flt_stack[nstack-2],filter->flt_stack[nstack-1],&filter->filters[i]);
+        }
+        else
+        {
+            if ( is_str==1 ) error("Error: cannot use arithmetic operators to compare strings and numbers\n");
+
+            // Determine what to do with one [1] or both [2] sides missing. The first field [0] gives [1]|[2]
+            int missing_logic[] = {0,0,0};
+            if ( filter->filters[i].tok_type == TOK_EQ ) { missing_logic[0] = missing_logic[2] = 1; }
+            if ( filter->filters[i].tok_type == TOK_NE ) { missing_logic[0] = missing_logic[1] = 1; }
+
+            if ( filter->filters[i].tok_type == TOK_EQ )
+                CMP_VECTORS(filter->flt_stack[nstack-2],filter->flt_stack[nstack-1],&filter->filters[i],==,missing_logic)
+            else if ( filter->filters[i].tok_type == TOK_NE )
+                CMP_VECTORS(filter->flt_stack[nstack-2],filter->flt_stack[nstack-1],&filter->filters[i],!=,missing_logic)
+            else if ( filter->filters[i].tok_type == TOK_LE )
+                CMP_VECTORS(filter->flt_stack[nstack-2],filter->flt_stack[nstack-1],&filter->filters[i],<=,missing_logic)
+            else if ( filter->filters[i].tok_type == TOK_LT )
+                CMP_VECTORS(filter->flt_stack[nstack-2],filter->flt_stack[nstack-1],&filter->filters[i],<,missing_logic)
+            else if ( filter->filters[i].tok_type == TOK_BT )
+                CMP_VECTORS(filter->flt_stack[nstack-2],filter->flt_stack[nstack-1],&filter->filters[i],>,missing_logic)
+            else if ( filter->filters[i].tok_type == TOK_BE )
+                CMP_VECTORS(filter->flt_stack[nstack-2],filter->flt_stack[nstack-1],&filter->filters[i],>=,missing_logic)
+            else
+                error("todo: %s:%d .. type=%d\n", __FILE__,__LINE__,filter->filters[i].tok_type);
+        }
+        filter->flt_stack[nstack-2] = &filter->filters[i];
+        nstack--;
+    }
+    if ( nstack>1 ) error("Error occurred while processing the filter \"%s\" (2:%d)\n", filter->str,nstack);    // too few values left on the stack
+    if ( samples )
+    {
+        *samples = filter->max_unpack&BCF_UN_FMT ? filter->flt_stack[0]->pass_samples : NULL;
+        if ( *samples && !filter->flt_stack[0]->nsamples )
+        {
+            for (i=0; i<filter->nsamples; i++)
+                filter->flt_stack[0]->pass_samples[i] = filter->flt_stack[0]->pass_site;
+        }
+    }
+    return filter->flt_stack[0]->pass_site;
+}
+
+int filter_max_unpack(filter_t *flt)
+{
+    return flt->max_unpack;
+}
+
+const double *filter_get_doubles(filter_t *filter, int *nval, int *nval1)
+{
+    token_t *tok = filter->flt_stack[0];
+    if ( tok->nvalues )
+    {
+        *nval  = tok->nvalues;
+        *nval1 = tok->nval1;
+    }
+    else
+    {
+        if ( !tok->values ) error("fixme in filter_get_doubles(): %s\n", filter->str);
+        *nval  = 1;
+        *nval1 = 1;
+        tok->values[0] = filter->flt_stack[0]->pass_site;
+    }
+    return tok->values;
+}
+
+void filter_set_samples(filter_t *filter, const uint8_t *samples)
+{
+    int i,j;
+    for (i=0; i<filter->nfilters; i++)
+    {
+        if ( !filter->filters[i].nsamples ) continue;
+        for (j=0; j<filter->filters[i].nsamples; j++) filter->filters[i].usmpl[j] = samples[j];
+    }
+}
+
diff --git a/bcftools/filter.c.pysam.c b/bcftools/filter.c.pysam.c
new file mode 100644
index 0000000..d15586c
--- /dev/null
+++ b/bcftools/filter.c.pysam.c
@@ -0,0 +1,3673 @@
+#include "bcftools.pysam.h"
+
+/*  filter.c -- filter expressions.
+
+    Copyright (C) 2013-2022 Genome Research Ltd.
+
+    Author: Petr Danecek <pd3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.  */
+
+#include <ctype.h>
+#include <stdlib.h>
+#include <strings.h>
+#include <assert.h>
+#include <errno.h>
+#include <math.h>
+#include <sys/types.h>
+#include <inttypes.h>
+#ifndef _WIN32
+#include <pwd.h>
+#endif
+#include <regex.h>
+#include <htslib/khash_str2int.h>
+#include <htslib/hts_defs.h>
+#include <htslib/vcfutils.h>
+#include <htslib/kfunc.h>
+#include "config.h"
+#include "filter.h"
+#include "bcftools.h"
+
+#if ENABLE_PERL_FILTERS
+#  define filter_t perl_filter_t
+#  include <EXTERN.h>
+#  include <perl.h>
+#  undef filter_t
+#  define my_perl perl
+
+static int filter_ninit = 0;
+#endif
+
+
+#ifndef __FUNCTION__
+#  define __FUNCTION__ __func__
+#endif
+
+typedef struct _token_t
+{
+    // read-only values, same for all VCF lines
+    int tok_type;       // one of the TOK_* keys below
+    int nargs;          // with TOK_PERLSUB the first argument is the name of the subroutine
+    char *key;          // set only for string constants, otherwise NULL
+    char *tag;          // for debugging and printout only, VCF tag name
+    double threshold;   // filtering threshold
+    int is_constant;    // the threshold is set
+    int hdr_id, tag_type;   // BCF header lookup ID and one of BCF_HL_* types
+    int idx;            // 0-based index to VCF vectors,
+                        //  -2: list (e.g. [0,1,2] or [1..3] or [1..] or any field[*], which is equivalent to [0..])
+    int *idxs;          // set indexes to 0 to exclude, to 1 to include, and last element negative if unlimited; used by VCF retrievers only
+    int nidxs, nuidxs;  // size of idxs array and the number of elements set to 1
+    uint8_t *usmpl;     // bitmask of used samples as set by idx, set for FORMAT fields, NULL otherwise
+    int nsamples;       // number of samples for format fields, 0 for info and other fields
+    void (*setter)(filter_t *, bcf1_t *, struct _token_t *);
+    int (*func)(filter_t *, bcf1_t *, struct _token_t *rtok, struct _token_t **stack, int nstack);
+    void (*comparator)(struct _token_t *, struct _token_t *, struct _token_t *rtok, bcf1_t *);
+    void *hash;         // test presence of str value in the hash via comparator
+    regex_t *regex;     // precompiled regex for string comparison
+
+    // modified on filter evaluation at each VCF line
+    double *values;
+    kstring_t str_value;
+    int is_str, is_missing; // is_missing is set only for constants, variables are controled via nvalues
+    int pass_site;          // -1 not applicable, 0 fails, >0 pass
+    uint8_t *pass_samples;  // status of individual samples
+    int nvalues, mvalues;   // number of used values: n=0 for missing values, n=1 for scalars, for strings n=str_value.l
+    int nval1;              // number of per-sample fields or string length
+}
+token_t;
+
+struct _filter_t
+{
+    bcf_hdr_t *hdr;
+    char *str;
+    int nfilters;
+    token_t *filters, **flt_stack;  // filtering input tokens (in RPN) and evaluation stack
+    int32_t *tmpi;
+    float   *tmpf;
+    kstring_t tmps;
+    int max_unpack, mtmpi, mtmpf, nsamples;
+#if ENABLE_PERL_FILTERS
+    PerlInterpreter *perl;
+#endif
+};
+
+
+#define TOK_VAL     0
+#define TOK_LFT     1       // (
+#define TOK_RGT     2       // )
+#define TOK_LE      3       // less or equal
+#define TOK_LT      4       // less than
+#define TOK_EQ      5       // equal
+#define TOK_BT      6       // bigger than
+#define TOK_BE      7       // bigger or equal
+#define TOK_NE      8       // not equal
+#define TOK_OR      9       // |
+#define TOK_AND     10      // &
+#define TOK_ADD     11      // +
+#define TOK_SUB     12      // -
+#define TOK_MULT    13      // *
+#define TOK_DIV     14      // /
+#define TOK_MAX     15
+#define TOK_MIN     16
+#define TOK_AVG     17
+#define TOK_AND_VEC 18      // &&   (operator applied in samples)
+#define TOK_OR_VEC  19      // ||   (operator applied in samples)
+#define TOK_LIKE    20      //  ~ regular expression
+#define TOK_NLIKE   21      // !~ regular expression
+#define TOK_SUM     22
+#define TOK_ABS     23
+#define TOK_LEN     24
+#define TOK_FUNC    25
+#define TOK_CNT     26
+#define TOK_PERLSUB 27
+#define TOK_BINOM   28
+#define TOK_PHRED   29
+#define TOK_MEDIAN  30
+#define TOK_STDEV   31
+#define TOK_sMAX    32
+#define TOK_sMIN    33
+#define TOK_sAVG    34
+#define TOK_sMEDIAN 35
+#define TOK_sSTDEV  36
+#define TOK_sSUM    37
+#define TOK_IN      38      // contains, e.g. FILTER~"A"
+#define TOK_NOT_IN  39      // does not contain, e.g. FILTER!~"A"
+#define TOK_MODULO  40      // %
+
+//                      0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40
+//                        ( ) [ < = > ] ! | &  +  -  *  /  M  m  a  A  O  ~  ^  S  .  l  f  c  p  b  P  i  s                          %
+static int op_prec[] = {0,1,1,5,5,5,5,5,5,2,3, 6, 6, 7, 7, 8, 8, 8, 3, 2, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 7 };
+#define TOKEN_STRING "x()[<=>]!|&+-*/MmaAO~^S.lfcpis"       // this is only for debugging, not maintained diligently
+
+static void cmp_vector_strings(token_t *atok, token_t *btok, token_t *rtok);
+
+// Return negative values if it is a function with variable number of arguments
+static int filters_next_token(char **str, int *len)
+{
+    char *tmp = *str;
+    while ( *tmp && isspace(*tmp) ) tmp++;
+    *str = tmp;
+    *len = 0;
+
+    // test for doubles: d.ddde[+-]dd
+    if ( isdigit(*str[0]) || *str[0]=='.' )   // strtod would eat +/-
+    {
+        double HTS_UNUSED v = strtod(*str, &tmp);
+        if ( *str!=tmp && (!tmp[0] || !isalnum(tmp[0])) )
+        {
+            *len = tmp - (*str);
+            return TOK_VAL;
+        }
+        tmp = *str;
+    }
+
+    if ( !strncasecmp(tmp,"SMPL_MAX(",9) ) { (*str) += 8; return TOK_sMAX; }
+    if ( !strncasecmp(tmp,"SMPL_MIN(",9) ) { (*str) += 8; return TOK_sMIN; }
+    if ( !strncasecmp(tmp,"SMPL_MEAN(",10) ) { (*str) += 9; return TOK_sAVG; }
+    if ( !strncasecmp(tmp,"SMPL_MEDIAN(",12) ) { (*str) += 11; return TOK_sMEDIAN; }
+    if ( !strncasecmp(tmp,"SMPL_AVG(",9) ) { (*str) += 8; return TOK_sAVG; }
+    if ( !strncasecmp(tmp,"SMPL_STDEV(",11) ) { (*str) += 10; return TOK_sSTDEV; }
+    if ( !strncasecmp(tmp,"SMPL_SUM(",9) ) { (*str) += 8; return TOK_sSUM; }
+    if ( !strncasecmp(tmp,"sMAX(",5) ) { (*str) += 4; return TOK_sMAX; }
+    if ( !strncasecmp(tmp,"sMIN(",5) ) { (*str) += 4; return TOK_sMIN; }
+    if ( !strncasecmp(tmp,"sMEAN(",6) ) { (*str) += 5; return TOK_sAVG; }
+    if ( !strncasecmp(tmp,"sMEDIAN(",8) ) { (*str) += 7; return TOK_sMEDIAN; }
+    if ( !strncasecmp(tmp,"sAVG(",5) ) { (*str) += 4; return TOK_sAVG; }
+    if ( !strncasecmp(tmp,"sSTDEV(",7) ) { (*str) += 6; return TOK_sSTDEV; }
+    if ( !strncasecmp(tmp,"sSUM(",5) ) { (*str) += 4; return TOK_sSUM; }
+    if ( !strncasecmp(tmp,"MAX(",4) ) { (*str) += 3; return TOK_MAX; }
+    if ( !strncasecmp(tmp,"MIN(",4) ) { (*str) += 3; return TOK_MIN; }
+    if ( !strncasecmp(tmp,"MEAN(",5) ) { (*str) += 4; return TOK_AVG; }
+    if ( !strncasecmp(tmp,"MEDIAN(",7) ) { (*str) += 6; return TOK_MEDIAN; }
+    if ( !strncasecmp(tmp,"AVG(",4) ) { (*str) += 3; return TOK_AVG; }
+    if ( !strncasecmp(tmp,"STDEV(",6) ) { (*str) += 5; return TOK_STDEV; }
+    if ( !strncasecmp(tmp,"SUM(",4) ) { (*str) += 3; return TOK_SUM; }
+    if ( !strncasecmp(tmp,"ABS(",4) ) { (*str) += 3; return TOK_ABS; }
+    if ( !strncasecmp(tmp,"COUNT(",4) ) { (*str) += 5; return TOK_CNT; }
+    if ( !strncasecmp(tmp,"STRLEN(",7) ) { (*str) += 6; return TOK_LEN; }
+    if ( !strncasecmp(tmp,"BINOM(",6) ) { (*str) += 5; return -TOK_BINOM; }
+    if ( !strncasecmp(tmp,"PHRED(",6) ) { (*str) += 5; return TOK_PHRED; }
+    if ( !strncasecmp(tmp,"%MAX(",5) ) { (*str) += 4; return TOK_MAX; } // for backward compatibility
+    if ( !strncasecmp(tmp,"%MIN(",5) ) { (*str) += 4; return TOK_MIN; } // for backward compatibility
+    if ( !strncasecmp(tmp,"%AVG(",5) ) { (*str) += 4; return TOK_AVG; } // for backward compatibility
+    if ( !strncasecmp(tmp,"%SUM(",5) ) { (*str) += 4; return TOK_SUM; } // for backward compatibility
+    if ( !strncasecmp(tmp,"INFO/",5) ) tmp += 5;
+    if ( !strncasecmp(tmp,"FORMAT/",7) ) tmp += 7;
+    if ( !strncasecmp(tmp,"FMT/",4) ) tmp += 4;
+    if ( !strncasecmp(tmp,"PERL.",5) ) { (*str) += 5; return -TOK_PERLSUB; }
+    if ( !strncasecmp(tmp,"N_PASS(",7) ) { *len = 6; (*str) += 6; return -TOK_FUNC; }
+    if ( !strncasecmp(tmp,"F_PASS(",7) ) { *len = 6; (*str) += 6; return -TOK_FUNC; }
+    if ( !strncasecmp(tmp,"%ILEN",5) ) { *len = 5; return TOK_VAL; }    // to be able to distinguish between INFO/ILEN and on-the-fly ILEN
+
+    if ( tmp[0]=='@' )  // file name
+    {
+        while ( *tmp && !isspace(*tmp) && *tmp!='=' && *tmp!='!' ) tmp++;
+        *len = tmp - (*str);
+        return TOK_VAL;
+    }
+
+    int square_brackets = 0;
+    while ( tmp[0] )
+    {
+        if ( !square_brackets )
+        {
+            if ( tmp[0]=='"' ) break;
+            if ( tmp[0]=='\'' ) break;
+            if ( isspace(tmp[0]) ) break;
+            if ( tmp[0]=='<' ) break;
+            if ( tmp[0]=='>' ) break;
+            if ( tmp[0]=='=' ) break;
+            if ( tmp[0]=='!' ) break;
+            if ( tmp[0]=='&' ) break;
+            if ( tmp[0]=='|' ) break;
+            if ( tmp[0]=='(' ) break;
+            if ( tmp[0]==')' ) break;
+            if ( tmp[0]=='+' ) break;
+            if ( tmp[0]=='*' ) break;
+            if ( tmp[0]=='-' ) break;
+            if ( tmp[0]=='/' ) break;
+            if ( tmp[0]=='~' ) break;
+            if ( tmp[0]=='%' ) break;
+        }
+        if ( tmp[0]==']' ) { if (square_brackets) tmp++; break; }
+        if ( tmp[0]=='[' ) square_brackets++;
+        tmp++;
+    }
+    if ( tmp > *str )
+    {
+        *len = tmp - (*str);
+        return TOK_VAL;
+    }
+    if ( tmp[0]=='"' || tmp[0]=='\'' )
+    {
+        int quote = tmp[0];
+        tmp++;
+        while ( *tmp && tmp[0]!=quote ) tmp++;
+        if ( !*tmp ) return -1;     // missing quotes
+        *len = tmp - (*str) + 1;
+        return TOK_VAL;
+    }
+    if ( tmp[0]=='!' )
+    {
+        if ( tmp[1]=='=' ) { (*str) += 2; return TOK_NE; }
+        if ( tmp[1]=='~' ) { (*str) += 2; return TOK_NLIKE; }
+    }
+    if ( tmp[0]=='<' )
+    {
+        if ( tmp[1]=='=' ) { (*str) += 2; return TOK_LE; }
+        (*str) += 1; return TOK_LT;
+    }
+    if ( tmp[0]=='>' )
+    {
+        if ( tmp[1]=='=' ) { (*str) += 2; return TOK_BE; }
+        (*str) += 1; return TOK_BT;
+    }
+    if ( tmp[0]=='=' )
+    {
+        if ( tmp[1]=='=' ) { (*str) += 2; return TOK_EQ; }
+        (*str) += 1; return TOK_EQ;
+    }
+    if ( tmp[0]=='(' ) { (*str) += 1; return TOK_LFT; }
+    if ( tmp[0]==')' ) { (*str) += 1; return TOK_RGT; }
+    if ( tmp[0]=='&' && tmp[1]=='&' ) { (*str) += 2; return TOK_AND_VEC; }
+    if ( tmp[0]=='|' && tmp[1]=='|' ) { (*str) += 2; return TOK_OR_VEC; }
+    if ( tmp[0]=='&' ) { (*str) += 1; return TOK_AND; }
+    if ( tmp[0]=='|' ) { (*str) += 1; return TOK_OR; }
+    if ( tmp[0]=='+' ) { (*str) += 1; return TOK_ADD; }
+    if ( tmp[0]=='-' ) { (*str) += 1; return TOK_SUB; }
+    if ( tmp[0]=='*' ) { (*str) += 1; return TOK_MULT; }
+    if ( tmp[0]=='/' ) { (*str) += 1; return TOK_DIV; }
+    if ( tmp[0]=='~' ) { (*str) += 1; return TOK_LIKE; }
+    if ( tmp[0]=='%' ) { (*str) += 1; return TOK_MODULO; }
+
+    *len = tmp - (*str);
+    return TOK_VAL;
+}
+
+
+/*
+    Simple path expansion, expands ~/, ~user, $var. The result must be freed by the caller.
+
+    Based on jkb's staden code with some adjustments.
+    https://sourceforge.net/p/staden/code/HEAD/tree/staden/trunk/src/Misc/getfile.c#l123
+*/
+char *expand_path(char *path)
+{
+    kstring_t str = {0,0,0};
+
+    if ( path[0] == '~' )
+    {
+        if ( !path[1] || path[1] == '/' )
+        {
+#ifdef _WIN32
+            kputs(getenv("HOMEDRIVE"), &str);
+            kputs(getenv("HOMEPATH"), &str);
+#else
+            // ~ or ~/path
+            kputs(getenv("HOME"), &str);
+            if ( path[1] ) kputs(path+1, &str);
+#endif
+        }
+#ifndef _WIN32
+        else
+        {
+            // user name: ~pd3/path
+            char *end = path;
+            while ( *end && *end!='/' ) end++;
+            kputsn(path+1, end-path-1, &str);
+            struct passwd *pwentry = getpwnam(str.s);
+            str.l = 0;
+
+            if ( !pwentry ) kputsn(path, end-path, &str);
+            else kputs(pwentry->pw_dir, &str);
+            kputs(end, &str);
+        }
+#endif
+        return ks_release(&str);
+    }
+    if ( path[0] == '$' )
+    {
+        char *var = getenv(path+1);
+        if ( var ) {
+            kputs(var, &str);
+            return ks_release(&str);
+        }
+    }
+
+    return strdup(path);
+}
+
+static void filters_set_qual(filter_t *flt, bcf1_t *line, token_t *tok)
+{
+    float *ptr = &line->qual;
+    if ( bcf_float_is_missing(*ptr) )
+        bcf_double_set_missing(tok->values[0]);
+    else
+        tok->values[0] = (double)line->qual;
+    tok->nvalues  = 1;
+}
+static void filters_set_type(filter_t *flt, bcf1_t *line, token_t *tok)
+{
+    tok->values[0] = bcf_get_variant_types(line);
+    if ( !tok->values[0] ) tok->values[0] = 1;      // mistake in htslib: VCF_* should start with 1
+    else tok->values[0] = ((int)tok->values[0]) << 1;
+    tok->nvalues = 1;
+}
+static void filters_set_info(filter_t *flt, bcf1_t *line, token_t *tok)
+{
+    assert( tok->hdr_id >=0  );
+    int i;
+    for (i=0; i<line->n_info; i++)
+        if ( line->d.info[i].key == tok->hdr_id ) break;
+
+    if ( i==line->n_info )
+        tok->nvalues = tok->str_value.l = 0;
+    else if ( line->d.info[i].type==BCF_BT_CHAR )
+    {
+        int n = line->d.info[i].len;
+        if ( n >= tok->str_value.m )
+        {
+            tok->str_value.m = n + 1;
+            tok->str_value.s = (char*) realloc(tok->str_value.s, tok->str_value.m);
+            if ( !tok->str_value.s ) error("Failed to alloc %d bytes\n", (int)tok->str_value.m);
+        }
+        memcpy(tok->str_value.s, line->d.info[i].vptr, n);
+        tok->str_value.s[n] = 0;
+        tok->nvalues = tok->str_value.l = n;
+    }
+    else if ( line->d.info[i].type==BCF_BT_FLOAT )
+    {
+        if ( bcf_float_is_missing(line->d.info[i].v1.f) ) tok->nvalues = 0;
+        else
+        {
+            tok->values[0] = line->d.info[i].v1.f;
+            tok->nvalues   = 1;
+        }
+        tok->str_value.l = 0;
+    }
+    else
+    {
+        tok->str_value.l = 0;
+        if ( line->d.info[i].type==BCF_BT_INT8 && line->d.info[i].v1.i==bcf_int8_missing ) tok->nvalues = 0;
+        else if ( line->d.info[i].type==BCF_BT_INT16 && line->d.info[i].v1.i==bcf_int16_missing ) tok->nvalues = 0;
+        else if ( line->d.info[i].type==BCF_BT_INT32 && line->d.info[i].v1.i==bcf_int32_missing ) tok->nvalues = 0;
+        else
+        {
+            tok->values[0] = line->d.info[i].v1.i;
+            tok->nvalues   = 1;
+        }
+    }
+}
+static void filters_cmp_bit_and(token_t *atok, token_t *btok, token_t *rtok, bcf1_t *line)
+{
+    int a = (int)(atok->nvalues?atok->values[0]:atok->threshold);
+    int b = (int)(btok->nvalues?btok->values[0]:btok->threshold);
+    if ( rtok->tok_type==TOK_LIKE )
+        rtok->pass_site = a&b ? 1 : 0;
+    else
+        rtok->pass_site = a&b ? 0 : 1;
+}
+static void filters_cmp_filter(token_t *atok, token_t *btok, token_t *rtok, bcf1_t *line)
+{
+    // the btok values contain FILTER ids obtained by parsing the user expression
+    int i,j;
+    if ( rtok->tok_type==TOK_NOT_IN )   // fail if the query expression is a subset of the VCF FILTER
+    {
+        if ( !btok->nvalues )   // the query expression is ".", pass everything unless the VCF is also "."
+        {
+            if ( line->d.n_flt ) rtok->pass_site = 1;
+            return;
+        }
+        if ( !line->d.n_flt )   // no filters at this VCF line and the query expression has a value
+        {
+            rtok->pass_site = 1;
+            return;
+        }
+        for (j=0; j<btok->nvalues; j++) // some query expression value must be absent from VCF in order to pass
+        {
+            for (i=0; i<line->d.n_flt; i++)
+                if ( btok->values[j]==line->d.flt[i] ) break;
+            if ( i==line->d.n_flt ) break;  // the query is not in the VCF
+        }
+        if ( j!=btok->nvalues ) rtok->pass_site = 1;
+        return;
+    }
+    else if ( rtok->tok_type==TOK_IN )
+    {
+        if ( !btok->nvalues )   // the query expression is ".", fail everything unless the VCF is also "."
+        {
+            if ( !line->d.n_flt ) rtok->pass_site = 1;
+            return;
+        }
+        if ( !line->d.n_flt ) return;   // no filters at this VCF line and the query expression has a value
+        for (j=0; j<btok->nvalues; j++) // all of the query values must be present in the VCF in order to pass
+        {
+            for (i=0; i<line->d.n_flt; i++)
+                if ( btok->values[j]==line->d.flt[i] ) break;
+            if ( i==line->d.n_flt ) break;  // the query is not in the VCF
+        }
+        if ( j==btok->nvalues ) rtok->pass_site = 1;
+        return;
+    }
+    else if ( rtok->tok_type==TOK_NE )  // require anything but exact match
+    {
+        if ( btok->nvalues != line->d.n_flt )
+        {
+            rtok->pass_site = 1;
+            return;
+        }
+        if ( !btok->nvalues ) return;
+        for (j=0; j<btok->nvalues; j++) // some of the query values must be absent from the VCF in order to pass
+        {
+            for (i=0; i<line->d.n_flt; i++)
+                if ( btok->values[j]==line->d.flt[i] ) break;
+            if ( i==line->d.n_flt ) break;  // the query is not in the VCF
+        }
+        if ( j!=btok->nvalues ) rtok->pass_site = 1;
+        return;
+    }
+    else if ( rtok->tok_type==TOK_EQ )  // require exact match
+    {
+        if ( btok->nvalues != line->d.n_flt ) return;
+        if ( !btok->nvalues )
+        {
+            rtok->pass_site = 1;
+            return;
+        }
+        for (j=0; j<btok->nvalues; j++) // all of the query values must be present in the VCF in order to pass
+        {
+            for (i=0; i<line->d.n_flt; i++)
+                if ( btok->values[j]==line->d.flt[i] ) break;
+            if ( i==line->d.n_flt ) break;  // the query is not in the VCF
+        }
+        if ( j==btok->nvalues ) rtok->pass_site = 1;
+        return;
+    }
+    else
+        error("Only ==, !=, ~, and !~ operators are supported for FILTER\n");
+    return;
+}
+static void filters_cmp_id(token_t *atok, token_t *btok, token_t *rtok, bcf1_t *line)
+{
+    if ( btok->hash )
+    {
+        token_t *tmp = atok; atok = btok; btok = tmp;
+    }
+    if ( atok->hash )
+    {
+        if ( rtok->tok_type!=TOK_EQ && rtok->tok_type!=TOK_NE )
+            error("Only == and != operators are supported for strings read from a file\n");
+
+        int ret = khash_str2int_has_key(atok->hash, line->d.id);
+        if ( rtok->tok_type==TOK_NE ) ret = ret ? 0 : 1;
+        rtok->pass_site = ret;
+        return;
+    }
+
+    if ( !btok->str_value.l ) error("Error occurred while evaluating the expression\n");
+
+    if ( rtok->tok_type==TOK_EQ )
+        rtok->pass_site = strcmp(btok->str_value.s,line->d.id) ? 0 : 1;
+    else if ( rtok->tok_type==TOK_NE )
+        rtok->pass_site = strcmp(btok->str_value.s,line->d.id) ? 1 : 0;
+    else
+    {
+        if ( rtok->tok_type!=TOK_LIKE && rtok->tok_type!=TOK_NLIKE )
+            error("Only the following operators are supported for querying ID: ==, !=, ~, !~; the operator type %d is not supported (%p %p)\n",
+                rtok->tok_type,atok->regex,btok->regex);
+
+        regex_t *regex = atok->regex ? atok->regex : (btok->regex ? btok->regex : NULL);
+        if ( !regex ) error("fixme: regex initialization failed\n");
+        rtok->pass_site = regexec(regex,line->d.id, 0,NULL,0) ? 0 : 1;
+        if ( rtok->tok_type==TOK_NLIKE ) rtok->pass_site = rtok->pass_site ? 0 : 1;
+    }
+}
+
+/**
+ *  bcf_get_info_value() - get single INFO value, int64_t or double
+ *  @line:      BCF line
+ *  @info_id:   tag ID, as returned by bcf_hdr_id2int
+ *  @ivec:      0-based index to retrieve, -1 when single value is expected
+ *  @vptr:      pointer to memory location of sufficient size to accomodate
+ *              info_id's type
+ *
+ *  The returned value is -1 if tag is not present, 0 if present but
+ *  values is missing or ivec is out of range, and 1 on success.
+ */
+static int bcf_get_info_value(bcf1_t *line, int info_id, int ivec, void *value)
+{
+    int j;
+    for (j=0; j<line->n_info; j++)
+        if ( line->d.info[j].key == info_id ) break;
+    if ( j==line->n_info ) return -1;
+
+    bcf_info_t *info = &line->d.info[j];
+    if ( info->len == 1 )
+    {
+        if ( info->type==BCF_BT_FLOAT ) *((double*)value) = info->v1.f;
+        else if ( info->type==BCF_BT_INT8 || info->type==BCF_BT_INT16 || info->type==BCF_BT_INT32 ) *((int64_t*)value) = info->v1.i;
+        return 1;
+    }
+
+    if ( ivec<0 ) ivec = 0;
+
+    #define BRANCH(type_t, is_missing, is_vector_end, out_type_t) { \
+        type_t *p = (type_t *) info->vptr; \
+        for (j=0; j<ivec && j<info->len; j++) \
+        { \
+            if ( is_vector_end ) return 0; \
+        } \
+        if ( is_missing ) return 0; \
+        *((out_type_t*)value) = p[j]; \
+        return 1; \
+    }
+    switch (info->type) {
+        case BCF_BT_INT8:  BRANCH(int8_t,  p[j]==bcf_int8_missing,  p[j]==bcf_int8_vector_end,  int64_t); break;
+        case BCF_BT_INT16: BRANCH(int16_t, p[j]==bcf_int16_missing, p[j]==bcf_int16_vector_end, int64_t); break;
+        case BCF_BT_INT32: BRANCH(int32_t, p[j]==bcf_int32_missing, p[j]==bcf_int32_vector_end, int64_t); break;
+        case BCF_BT_FLOAT: BRANCH(float,   bcf_float_is_missing(p[j]), bcf_float_is_vector_end(p[j]), double); break;
+        default: fprintf(bcftools_stderr,"todo: type %d\n", info->type); bcftools_exit(1); break;
+    }
+    #undef BRANCH
+    return -1;  // this shouldn't happen
+}
+
+static void filters_set_chrom(filter_t *flt, bcf1_t *line, token_t *tok)
+{
+    tok->str_value.l = 0;
+    kputs(bcf_seqname(flt->hdr,line), &tok->str_value);
+    tok->nvalues = tok->str_value.l;
+    tok->is_str  = 1;
+}
+
+static void filters_set_pos(filter_t *flt, bcf1_t *line, token_t *tok)
+{
+    tok->values[0] = line->pos+1;
+    tok->nvalues = 1;
+}
+
+static void filters_set_info_int(filter_t *flt, bcf1_t *line, token_t *tok)
+{
+    if ( tok->idx==-2 )
+    {
+        tok->nvalues = bcf_get_info_int32(flt->hdr,line,tok->tag,&flt->tmpi,&flt->mtmpi);
+        if ( tok->nvalues<=0 ) tok->nvalues = 0;
+        else
+        {
+            hts_expand(double,tok->nvalues,tok->mvalues,tok->values);
+            int i, j = 0, end = tok->idxs[tok->nidxs-1] < 0 ? tok->nvalues - 1 : tok->nidxs - 1;
+            if ( end >= tok->nvalues ) end = tok->nvalues - 1;
+            for (i=0; i<=end; i++)
+                if ( i>=tok->nidxs || tok->idxs[i] ) tok->values[j++] = flt->tmpi[i];
+            tok->nvalues = j;
+        }
+    }
+    else
+    {
+        int64_t value = 0;
+        if ( bcf_get_info_value(line,tok->hdr_id,tok->idx,&value) <= 0 )
+            tok->nvalues = 0;
+        else
+        {
+            tok->values[0] = value;
+            tok->nvalues = 1;
+        }
+    }
+}
+
+static void filters_set_info_float(filter_t *flt, bcf1_t *line, token_t *tok)
+{
+    if ( tok->idx==-2 )
+    {
+        tok->nvalues = bcf_get_info_float(flt->hdr,line,tok->tag,&flt->tmpf,&flt->mtmpf);
+        if ( tok->nvalues<=0 ) tok->nvalues = 0;
+        else
+        {
+            hts_expand(double,tok->nvalues,tok->mvalues,tok->values);
+            int i, j = 0, end = tok->idxs[tok->nidxs-1] < 0 ? tok->nvalues - 1 : tok->nidxs - 1;
+            if ( end >= tok->nvalues ) end = tok->nvalues - 1;
+            for (i=0; i<=end; i++)
+                if ( i>=tok->nidxs || tok->idxs[i] )
+                {
+                    if ( bcf_float_is_missing(flt->tmpf[i]) ) bcf_double_set_missing(tok->values[j]);
+                    else tok->values[j] = flt->tmpf[i];
+                    j++;
+                }
+            tok->nvalues = j;
+        }
+    }
+    else
+    {
+        double value;
+        if ( bcf_get_info_value(line,tok->hdr_id,tok->idx,&value) <= 0 )
+            tok->nvalues = 0;
+        else
+        {
+            tok->values[0] = value;
+            tok->nvalues = 1;
+        }
+    }
+}
+
+static void filters_set_info_string(filter_t *flt, bcf1_t *line, token_t *tok)
+{
+    int32_t m = tok->str_value.m;
+    int n = bcf_get_info_string(flt->hdr,line,tok->tag,&tok->str_value.s,&m);
+    tok->str_value.m = m;
+    if ( n<0 ) { tok->nvalues = tok->str_value.l = 0; return; }
+
+    if ( tok->idx>=0 )
+    {
+        // get ith field (i=tok->idx)
+        int i = 0;
+        char *ss = tok->str_value.s, *se = tok->str_value.s + n;
+        while ( ss<se && i<tok->idx )
+        {
+            if ( *ss==',' ) i++;
+            ss++;
+        }
+        if ( ss==se || i!=tok->idx ) { tok->nvalues = tok->str_value.l = 0; return; }
+        se = ss;
+        while ( se - tok->str_value.s < n && *se!=',' ) se++;
+        if ( ss==tok->str_value.s ) *se = 0;
+        else
+        {
+            memmove(tok->str_value.s, ss, se-ss);
+            tok->str_value.s[se-ss] = 0;
+        }
+        tok->str_value.l = se - ss;
+    }
+    else if ( tok->idx==-2 && tok->idxs[0]==-1 )    // keep all values, TAG[*]
+        tok->str_value.l = n;
+    else if ( tok->idx==-2 )
+    {
+        flt->tmps.l = 0;
+        ks_resize(&flt->tmps, n);
+        int i, iend = tok->idxs[tok->nidxs-1] < 0 ? n - 1 : tok->nidxs - 1;
+        if ( iend >= n ) iend = n - 1;
+        char *beg = tok->str_value.s, *dst = flt->tmps.s;
+        for (i=0; i<=iend; i++)
+        {
+            char *end = beg;
+            while ( *end && *end!=',' ) end++;
+            if ( i>=tok->nidxs || tok->idxs[i] )
+            {
+                memcpy(dst, beg, end - beg);
+                dst += end - beg;
+                dst[0] = ',';
+                dst++;
+            }
+            beg = end+1;
+        }
+        dst[0] = 0;
+        tok->str_value.l = dst - flt->tmps.s;
+
+        #define SWAP(type_t, a, b) { type_t t = a; a = b; b = t; }
+        SWAP(char *, flt->tmps.s, tok->str_value.s);
+        SWAP(size_t, flt->tmps.m, tok->str_value.m);
+    }
+    tok->nvalues = tok->str_value.l;
+}
+
+static void filters_set_info_flag(filter_t *flt, bcf1_t *line, token_t *tok)
+{
+    int j;
+    for (j=0; j<line->n_info; j++)
+        if ( line->d.info[j].key == tok->hdr_id ) break;
+    tok->values[0] = j==line->n_info ? 0 : 1;
+    tok->nvalues = 1;
+}
+
+static void filters_set_format_int(filter_t *flt, bcf1_t *line, token_t *tok)
+{
+    if ( line->n_sample != tok->nsamples )
+        error("Incorrect number of FORMAT fields at %s:%"PRId64" .. %s, %d vs %d\n", bcf_seqname(flt->hdr,line),(int64_t) line->pos+1,tok->tag,line->n_sample,tok->nsamples);
+
+    int nvals;
+    if ( (nvals=bcf_get_format_int32(flt->hdr,line,tok->tag,&flt->tmpi,&flt->mtmpi))<0 )
+    {
+        tok->nvalues = 0;
+        return;
+    }
+    int i, nsrc1 = nvals / tok->nsamples;
+    tok->nval1 = tok->idx >= 0 ? 1 : (tok->nuidxs ? tok->nuidxs : nsrc1);
+    tok->nvalues = tok->nval1*tok->nsamples;
+    hts_expand(double, tok->nvalues, tok->mvalues, tok->values);
+
+    if ( tok->idx >= 0 )    // scalar or vector index
+    {
+        for (i=0; i<tok->nsamples; i++)
+        {
+            if ( !tok->usmpl[i] ) continue;
+            int32_t *ptr = flt->tmpi + i*nsrc1;
+            if ( tok->idx>=nsrc1 || ptr[tok->idx]==bcf_int32_missing )
+                bcf_double_set_missing(tok->values[i]);
+            else if ( ptr[tok->idx]==bcf_int32_vector_end )
+                bcf_double_set_vector_end(tok->values[i]);
+            else
+                tok->values[i] = ptr[tok->idx];
+        }
+    }
+    else
+    {
+        int kend = tok->idxs[tok->nidxs-1] < 0 ? tok->nval1 : tok->nidxs;
+        for (i=0; i<tok->nsamples; i++)
+        {
+            if ( !tok->usmpl[i] ) continue;
+            int32_t *src = flt->tmpi + i*nsrc1;
+            double  *dst = tok->values + i*tok->nval1;
+            int k, j = 0;
+            for (k=0; k<kend; k++)
+            {
+                if ( k<tok->nidxs && !tok->idxs[k] ) continue;
+                if ( src[k]==bcf_int32_missing )
+                    bcf_double_set_missing(dst[j]);
+                else if ( src[k]==bcf_int32_vector_end )
+                    bcf_double_set_vector_end(dst[j]);
+                else
+                    dst[j] = src[k];
+                j++;
+            }
+            if ( j==0 )
+            {
+                bcf_double_set_missing(dst[j]);
+                j++;
+            }
+            while (j < tok->nval1)
+            {
+                bcf_double_set_vector_end(dst[j]);
+                j++;
+            }
+        }
+    }
+}
+static void filters_set_format_float(filter_t *flt, bcf1_t *line, token_t *tok)
+{
+    if ( line->n_sample != tok->nsamples )
+        error("Incorrect number of FORMAT fields at %s:%"PRId64" .. %s, %d vs %d\n", bcf_seqname(flt->hdr,line),(int64_t) line->pos+1,tok->tag,line->n_sample,tok->nsamples);
+
+    int nvals;
+    if ( (nvals=bcf_get_format_float(flt->hdr,line,tok->tag,&flt->tmpf,&flt->mtmpf))<0 )
+    {
+        tok->nvalues = 0;
+        return;
+    }
+    int i, nsrc1 = nvals / tok->nsamples;
+    tok->nval1 = tok->idx >= 0 ? 1 : (tok->nuidxs ? tok->nuidxs : nsrc1);
+    tok->nvalues = tok->nval1*tok->nsamples;
+    hts_expand(double, tok->nvalues, tok->mvalues, tok->values);
+
+    if ( tok->idx >= 0 )    // scalar or vector index
+    {
+        for (i=0; i<tok->nsamples; i++)
+        {
+            if ( !tok->usmpl[i] ) continue;
+            float *ptr = flt->tmpf + i*nsrc1;
+            if ( tok->idx>=nsrc1 || bcf_float_is_missing(ptr[tok->idx]) )
+                bcf_double_set_missing(tok->values[i]);
+            else if ( bcf_float_is_vector_end(ptr[tok->idx]) )
+                bcf_double_set_vector_end(tok->values[i]);
+            else
+                tok->values[i] = ptr[tok->idx];
+        }
+    }
+    else
+    {
+        int kend = tok->idxs[tok->nidxs-1] < 0 ? tok->nval1 : tok->nidxs;
+        for (i=0; i<tok->nsamples; i++)
+        {
+            if ( !tok->usmpl[i] ) continue;
+            float *src = flt->tmpf + i*nsrc1;
+            double  *dst = tok->values + i*tok->nval1;
+            int k, j = 0;
+            for (k=0; k<kend; k++)
+            {
+                if ( k<tok->nidxs && !tok->idxs[k] ) continue;
+                if ( bcf_float_is_missing(src[k]) )
+                    bcf_double_set_missing(dst[j]);
+                else if ( bcf_float_is_vector_end(src[k]) )
+                    bcf_double_set_vector_end(dst[j]);
+                else
+                    dst[j] = src[k];
+                j++;
+            }
+            if ( j==0 )
+            {
+                bcf_double_set_missing(dst[j]);
+                j++;
+            }
+            while (j < tok->nval1)
+            {
+                bcf_double_set_vector_end(dst[j]);
+                j++;
+            }
+        }
+    }
+}
+static void filters_set_format_string(filter_t *flt, bcf1_t *line, token_t *tok)
+{
+    if ( line->n_sample != tok->nsamples )
+        error("Incorrect number of FORMAT fields at %s:%"PRId64" .. %s, %d vs %d\n", bcf_seqname(flt->hdr,line),(int64_t) line->pos+1,tok->tag,line->n_sample,tok->nsamples);
+
+    int i, ndim = tok->str_value.m;
+    int nstr = bcf_get_format_char(flt->hdr, line, tok->tag, &tok->str_value.s, &ndim);
+    tok->str_value.m = ndim;
+    tok->str_value.l = tok->nvalues = 0;
+
+    if ( nstr<0 ) return;
+
+    tok->nvalues = tok->str_value.l = nstr;
+    tok->nval1   = nstr / tok->nsamples;
+    for (i=0; i<tok->nsamples; i++)
+    {
+        if ( !tok->usmpl[i] ) continue;
+        char *src = tok->str_value.s + i*tok->nval1, *dst = src;
+        int ibeg = 0, idx = 0;
+        while ( ibeg < tok->nval1 )
+        {
+            int iend = ibeg;
+            while ( iend < tok->nval1 && src[iend] && src[iend]!=',' ) iend++;
+
+            int keep = 0;
+            if ( tok->idx >= 0 )
+            {
+                if ( tok->idx==idx ) keep = 1;
+            }
+            else if ( idx < tok->nidxs )
+            {
+                if ( tok->idxs[idx] != 0 ) keep = 1;
+            }
+            else if ( tok->idxs[tok->nidxs-1] < 0 )
+                keep = 1;
+
+            if ( keep )
+            {
+                if ( ibeg!=0 ) memmove(dst, src+ibeg, iend-ibeg+1);
+                dst += iend - ibeg + 1;
+                if ( tok->idx>=0 ) break;
+            }
+            if ( !src[iend] ) break;
+            ibeg = iend + 1;
+            idx++;
+        }
+        if ( dst==src ) { dst[0] = '.'; dst+=2; }
+        if ( dst - src < tok->nval1 ) memset(dst-1, 0, tok->nval1 - (dst - src));
+    }
+}
+static void _filters_set_genotype(filter_t *flt, bcf1_t *line, token_t *tok, int type)
+{
+    bcf_fmt_t *fmt = bcf_get_fmt(flt->hdr, line, "GT");
+    if ( !fmt )
+    {
+        tok->nvalues = tok->str_value.l = 0;
+        return;
+    }
+
+    int i,j, nsmpl = bcf_hdr_nsamples(flt->hdr), nvals1 = type==2 ? 3 : 4;
+    if ( tok->str_value.m <= nvals1*nsmpl )
+    {
+        tok->str_value.m = nvals1*nsmpl + 1;
+        tok->str_value.s = (char*)realloc(tok->str_value.s, tok->str_value.m);
+    }
+
+#define BRANCH_INT(type_t,vector_end) \
+    { \
+        for (i=0; i<line->n_sample; i++) \
+        { \
+            type_t *ptr = (type_t*) (fmt->p + i*fmt->size); \
+            int is_het = 0, has_ref = 0, missing = 0; \
+            for (j=0; j<fmt->n; j++) \
+            { \
+                if ( ptr[j]==vector_end ) break; /* smaller ploidy */ \
+                if ( bcf_gt_is_missing(ptr[j]) ) { missing=1; break; } /* missing allele */ \
+                int ial = ptr[j]; \
+                if ( bcf_gt_allele(ial)==0 ) has_ref = 1; \
+                if ( j>0 ) \
+                { \
+                    int jal = ptr[j-1]; \
+                    if ( bcf_gt_allele(ial)!=bcf_gt_allele(jal) ) is_het = 1; \
+                } \
+            } \
+            char *dst = &tok->str_value.s[nvals1*i]; \
+            if ( type==4 ) \
+            { \
+                if ( !j || missing ) dst[0]='m', dst[1]='i', dst[2]='s', dst[3] = 0; /* mis, missing genotype */ \
+                else if ( !has_ref ) dst[0]='a', dst[1]='l', dst[2]='t', dst[3] = 0; /* alt, no ref, must have alt allele */ \
+                else if ( !is_het ) dst[0]='r', dst[1]='e', dst[2]='f', dst[3] = 0; /* ref, must be ref-only, no alt alelle */ \
+                else dst[0]='a', dst[1]='l', dst[2]='t', dst[3] = 0; /* alt, is het, has alt allele */ \
+            } \
+            else if ( !j || missing ) dst[0]='.', dst[1]=0; /* ., missing genotype */ \
+            else if ( type==3 ) \
+            { \
+                if ( j==1 ) dst[0]='h', dst[1]='a', dst[2]='p', dst[3] = 0; /* hap, haploid */ \
+                else if ( !is_het ) dst[0]='h', dst[1]='o', dst[2]='m', dst[3] = 0; /* hom */ \
+                else dst[0]='h', dst[1]='e', dst[2]='t', dst[3] = 0; /* het */ \
+            } \
+            else \
+            { \
+                if ( j==1 ) \
+                { \
+                    if ( has_ref ) dst[0]='r', dst[1]=0; /* r, haploid */ \
+                    else dst[0]='a', dst[1]=0; /* a, haploid */ \
+                } \
+                else if ( !is_het ) \
+                { \
+                    if ( has_ref ) dst[0]='r', dst[1]='r', dst[2] = 0; /* rr */ \
+                    else dst[0]='a', dst[1]='a', dst[2] = 0; /* aa */ \
+                } \
+                else \
+                { \
+                    if ( has_ref ) dst[0]='r', dst[1]='a', dst[2] = 0; /* ra */ \
+                    else dst[0]='a', dst[1]='A', dst[2] = 0; /* aA */ \
+                } \
+            } \
+        } \
+    }
+    switch (fmt->type) {
+        case BCF_BT_INT8:  BRANCH_INT(int8_t,  bcf_int8_vector_end); break;
+        case BCF_BT_INT16: BRANCH_INT(int16_t, bcf_int16_vector_end); break;
+        case BCF_BT_INT32: BRANCH_INT(int32_t, bcf_int32_vector_end); break;
+        default: error("The GT type is not lineognised: %d at %s:%"PRId64"\n",fmt->type, bcf_seqname(flt->hdr,line),(int64_t) line->pos+1); break;
+    }
+#undef BRANCH_INT
+    assert( tok->nsamples == nsmpl );
+    tok->nvalues = tok->str_value.l = nvals1*nsmpl;
+    tok->str_value.s[tok->str_value.l] = 0;
+    tok->nval1 = nvals1;
+}
+static void filters_set_genotype2(filter_t *flt, bcf1_t *line, token_t *tok) { _filters_set_genotype(flt, line, tok, 2); }
+static void filters_set_genotype3(filter_t *flt, bcf1_t *line, token_t *tok) { _filters_set_genotype(flt, line, tok, 3); }
+static void filters_set_genotype4(filter_t *flt, bcf1_t *line, token_t *tok) { _filters_set_genotype(flt, line, tok, 4); }
+
+static void filters_set_genotype_string(filter_t *flt, bcf1_t *line, token_t *tok)
+{
+    bcf_fmt_t *fmt = bcf_get_fmt(flt->hdr, line, "GT");
+    if ( !fmt )
+    {
+        tok->nvalues = 0;
+        return;
+    }
+    int i, blen = 4, nsmpl = line->n_sample;
+
+gt_length_too_big:
+    tok->str_value.l = 0;
+    for (i=0; i<nsmpl; i++)
+    {
+        size_t plen = tok->str_value.l;
+        bcf_format_gt(fmt, i, &tok->str_value);
+        kputc_(0, &tok->str_value);
+        if ( tok->str_value.l - plen > blen )
+        {
+            // too many alternate alleles or ploidy is too large, the genotype does not fit
+            // three characters ("0/0" vs "10/10").
+            blen *= 2;
+            goto gt_length_too_big;
+        }
+
+        plen = tok->str_value.l - plen;
+        while ( plen < blen )
+        {
+            kputc_(0, &tok->str_value);
+            plen++;
+        }
+    }
+    assert( tok->nsamples == nsmpl );
+    tok->nvalues = tok->str_value.l;
+    tok->nval1 = blen;
+}
+static void filters_set_ilen(filter_t *flt, bcf1_t *line, token_t *tok)
+{
+    tok->nvalues = line->n_allele - 1;
+    hts_expand(double,tok->nvalues,tok->mvalues,tok->values);
+
+    int i, rlen = strlen(line->d.allele[0]);
+    for (i=1; i<line->n_allele; i++)
+    {
+        int alen = strlen(line->d.allele[i]);
+        if ( rlen==alen ) bcf_double_set_missing(tok->values[i-1]);
+        else tok->values[i-1] = alen - rlen;
+    }
+}
+static void filters_set_ref_string(filter_t *flt, bcf1_t *line, token_t *tok)
+{
+    tok->str_value.l = 0;
+    kputs(line->d.allele[0], &tok->str_value);
+    tok->nvalues = tok->str_value.l;
+}
+static void filters_set_alt_string(filter_t *flt, bcf1_t *line, token_t *tok)
+{
+    tok->str_value.l = 0;
+    if ( tok->idx>=0 )
+    {
+        if ( line->n_allele > tok->idx + 1 )
+            kputs(line->d.allele[tok->idx + 1], &tok->str_value);
+        else
+            kputc('.', &tok->str_value);
+    }
+    else if ( tok->idx==-2 )
+    {
+        int i, end = tok->nuidxs ? tok->nuidxs : line->n_allele - 1;
+        if ( end >= line->n_allele - 1 ) end = line->n_allele - 2;
+        for (i=0; i<=end; i++)
+            if ( i>=tok->nidxs || tok->idxs[i] )
+            {
+                if ( tok->str_value.l ) kputc(',', &tok->str_value);
+                kputs(line->d.allele[i+1], &tok->str_value);
+            }
+    }
+    else if ( line->n_allele>1 )
+    {
+        kputs(line->d.allele[1], &tok->str_value);
+        int i;
+        for (i=2; i<line->n_allele; i++)
+        {
+            kputc(',', &tok->str_value);
+            kputs(line->d.allele[i], &tok->str_value);
+        }
+    }
+    else if ( line->n_allele==1 )
+        kputc('.', &tok->str_value);
+    tok->nvalues = tok->str_value.l;
+}
+static void filters_set_nmissing(filter_t *flt, bcf1_t *line, token_t *tok)
+{
+    bcf_unpack(line, BCF_UN_FMT);
+    if ( !line->n_sample )
+    {
+        tok->nvalues = 1;
+        tok->values[0] = 0;
+        return;
+    }
+
+    int i,igt = bcf_hdr_id2int(flt->hdr, BCF_DT_ID, "GT");
+    bcf_fmt_t *fmt = NULL;
+    for (i=0; i<line->n_fmt; i++)
+        if ( line->d.fmt[i].id==igt ) { fmt = &line->d.fmt[i]; break; }
+    if ( !fmt )
+    {
+        tok->nvalues = 0;
+        return;
+    }
+
+    int j,nmissing = 0;
+    #define BRANCH(type_t, is_vector_end) { \
+        for (i=0; i<line->n_sample; i++) \
+        { \
+            type_t *ptr = (type_t *) (fmt->p + i*fmt->size); \
+            for (j=0; j<fmt->n; j++) \
+            { \
+                if ( ptr[j]==is_vector_end ) break; \
+                if ( ptr[j]==bcf_gt_missing ) { nmissing++; break; } \
+            } \
+        } \
+    }
+    switch (fmt->type) {
+        case BCF_BT_INT8:  BRANCH(int8_t,  bcf_int8_vector_end); break;
+        case BCF_BT_INT16: BRANCH(int16_t, bcf_int16_vector_end); break;
+        case BCF_BT_INT32: BRANCH(int32_t, bcf_int32_vector_end); break;
+        default: fprintf(bcftools_stderr,"todo: type %d\n", fmt->type); bcftools_exit(1); break;
+    }
+    #undef BRANCH
+    tok->nvalues = 1;
+    tok->values[0] = tok->tag[0]=='N' ? nmissing : (double)nmissing / line->n_sample;
+}
+static int func_npass(filter_t *flt, bcf1_t *line, token_t *rtok, token_t **stack, int nstack)
+{
+    if ( nstack==0 ) error("Error parsing the expression\n");
+    token_t *tok = stack[nstack - 1];
+    if ( !tok->nsamples ) error("The function %s works with FORMAT fields\n", rtok->tag);
+    assert(tok->usmpl);
+
+    int i, npass = 0;
+    for (i=0; i<tok->nsamples; i++)
+    {
+        if ( !tok->usmpl[i] ) continue;
+        if ( tok->pass_samples[i] ) npass++;
+    }
+    hts_expand(double,1,rtok->mvalues,rtok->values);
+    rtok->nsamples = 0;
+    rtok->nvalues = 1;
+    rtok->values[0] = rtok->tag[0]=='N' ? npass : (line->n_sample ? 1.0*npass/line->n_sample : 0);
+
+    return 1;
+}
+static void filters_set_nalt(filter_t *flt, bcf1_t *line, token_t *tok)
+{
+    tok->nvalues = 1;
+    tok->values[0] = line->n_allele - 1;
+}
+static void filters_set_ac(filter_t *flt, bcf1_t *line, token_t *tok)
+{
+    hts_expand(int32_t, line->n_allele, flt->mtmpi, flt->tmpi);
+    if ( !bcf_calc_ac(flt->hdr, line, flt->tmpi, BCF_UN_INFO|BCF_UN_FMT) )
+    {
+        tok->nvalues = 0;
+        return;
+    }
+    int i, an = flt->tmpi[0];
+    for (i=1; i<line->n_allele; i++) an += flt->tmpi[i];
+    if ( !an )
+    {
+        tok->nvalues = 0;
+        return;
+    }
+    flt->tmpi[0] = an;  // for filters_set_[mac|af|maf]
+    if ( tok->idx>=0 )
+    {
+        tok->nvalues = 1;
+        tok->values[0] = tok->idx+1<line->n_allele ? flt->tmpi[tok->idx+1] : 0;
+    }
+    else if ( line->n_allele==1 )   // no ALT
+    {
+        tok->nvalues = 1;
+        tok->values[0] = 0;
+    }
+    else
+    {
+        hts_expand(double,line->n_allele,tok->mvalues,tok->values);
+        for (i=1; i<line->n_allele; i++)
+            tok->values[i-1] = flt->tmpi[i];
+        tok->nvalues = line->n_allele - 1;
+    }
+}
+static void filters_set_an(filter_t *flt, bcf1_t *line, token_t *tok)
+{
+    filters_set_ac(flt,line,tok);
+    tok->values[0] = tok->nvalues ? flt->tmpi[0] : 0;
+    tok->nvalues = 1;
+}
+static void filters_set_mac(filter_t *flt, bcf1_t *line, token_t *tok)
+{
+    filters_set_ac(flt,line,tok);
+    if ( !tok->nvalues ) return;
+    int i, an = flt->tmpi[0];
+    for (i=0; i<tok->nvalues; i++)
+        if ( tok->values[i] > an*0.5 ) tok->values[i] = an - tok->values[i];
+}
+static void filters_set_af(filter_t *flt, bcf1_t *line, token_t *tok)
+{
+    filters_set_ac(flt,line,tok);
+    if ( !tok->nvalues ) return;
+    int i, an = flt->tmpi[0];
+    for (i=0; i<tok->nvalues; i++)
+        tok->values[i] /= (double)an;
+}
+static void filters_set_maf(filter_t *flt, bcf1_t *line, token_t *tok)
+{
+    filters_set_ac(flt,line,tok);
+    if ( !tok->nvalues ) return;
+    int i, an = flt->tmpi[0];
+    for (i=0; i<tok->nvalues; i++)
+    {
+        tok->values[i] /= (double)an;
+        if ( tok->values[i] > 0.5 ) tok->values[i] = 1 - tok->values[i];
+    }
+}
+
+static int func_max(filter_t *flt, bcf1_t *line, token_t *rtok, token_t **stack, int nstack)
+{
+    token_t *tok = stack[nstack - 1];
+    rtok->nvalues = 0;
+    if ( !tok->nvalues ) return 1;
+    double *ptr, val = -HUGE_VAL;
+    int i,j, has_value = 0;
+    if ( tok->nsamples )
+    {
+        for (i=0; i<tok->nsamples; i++)
+        {
+            if ( !tok->usmpl[i] ) continue;
+            ptr = tok->values + i*tok->nval1;
+            for (j=0; j<tok->nval1; j++)
+            {
+                if ( bcf_double_is_missing_or_vector_end(ptr[j]) ) continue;
+                has_value = 1;
+                if ( val < ptr[j] ) val = ptr[j];
+            }
+        }
+    }
+    else
+    {
+        for (i=0; i<tok->nvalues; i++)
+        {
+            if ( bcf_double_is_missing_or_vector_end(tok->values[i]) ) continue;
+            has_value = 1;
+            if ( val < tok->values[i] ) val = tok->values[i];
+        }
+    }
+    if ( has_value )
+    {
+        rtok->values[0] = val;
+        rtok->nvalues = has_value;
+    }
+    return 1;
+}
+static int func_smpl_max(filter_t *flt, bcf1_t *line, token_t *rtok, token_t **stack, int nstack)
+{
+    token_t *tok = stack[nstack - 1];
+    if ( !tok->nsamples ) return func_max(flt,line,rtok,stack,nstack);
+    rtok->nsamples = tok->nsamples;
+    rtok->nvalues  = tok->nsamples;
+    rtok->nval1 = 1;
+    hts_expand(double,rtok->nvalues,rtok->mvalues,rtok->values);
+    assert(tok->usmpl);
+    if ( !rtok->usmpl ) rtok->usmpl = (uint8_t*) malloc(tok->nsamples);
+    memcpy(rtok->usmpl, tok->usmpl, tok->nsamples);
+    int i, j, has_value;
+    double val, *ptr;
+    for (i=0; i<tok->nsamples; i++)
+    {
+        if ( !rtok->usmpl[i] ) continue;
+        val = -HUGE_VAL;
+        has_value = 0;
+        ptr = tok->values + i*tok->nval1;
+        for (j=0; j<tok->nval1; j++)
+        {
+            if ( bcf_double_is_missing_or_vector_end(ptr[j]) ) continue;
+            has_value = 1;
+            if ( val < ptr[j] ) val = ptr[j];
+        }
+        if ( has_value ) rtok->values[i] = val;
+        else bcf_double_set_missing(rtok->values[i]);
+    }
+    return 1;
+}
+static int func_min(filter_t *flt, bcf1_t *line, token_t *rtok, token_t **stack, int nstack)
+{
+    token_t *tok = stack[nstack - 1];
+    rtok->nvalues = 0;
+    if ( !tok->nvalues ) return 1;
+    double *ptr, val = HUGE_VAL;
+    int i,j, has_value = 0;
+    if ( tok->nsamples )
+    {
+        for (i=0; i<tok->nsamples; i++)
+        {
+            if ( !tok->usmpl[i] ) continue;
+            ptr = tok->values + i*tok->nval1;
+            for (j=0; j<tok->nval1; j++)
+            {
+                if ( bcf_double_is_missing_or_vector_end(ptr[j]) ) continue;
+                has_value = 1;
+                if ( val > ptr[j] ) val = ptr[j];
+            }
+        }
+    }
+    else
+    {
+        for (i=0; i<tok->nvalues; i++)
+        {
+            if ( bcf_double_is_missing_or_vector_end(tok->values[i]) ) continue;
+            has_value = 1;
+            if ( val > tok->values[i] ) val = tok->values[i];
+        }
+    }
+    if ( has_value )
+    {
+        rtok->values[0] = val;
+        rtok->nvalues = has_value;
+    }
+    return 1;
+}
+static int func_smpl_min(filter_t *flt, bcf1_t *line, token_t *rtok, token_t **stack, int nstack)
+{
+    token_t *tok = stack[nstack - 1];
+    if ( !tok->nsamples ) return func_min(flt,line,rtok,stack,nstack);
+    rtok->nsamples = tok->nsamples;
+    rtok->nvalues  = tok->nsamples;
+    rtok->nval1 = 1;
+    hts_expand(double,rtok->nvalues,rtok->mvalues,rtok->values);
+    assert(tok->usmpl);
+    if ( !rtok->usmpl ) rtok->usmpl = (uint8_t*) malloc(tok->nsamples);
+    memcpy(rtok->usmpl, tok->usmpl, tok->nsamples);
+    int i, j, has_value;
+    double val, *ptr;
+    for (i=0; i<tok->nsamples; i++)
+    {
+        if ( !rtok->usmpl[i] ) continue;
+        val = HUGE_VAL;
+        has_value = 0;
+        ptr = tok->values + i*tok->nval1;
+        for (j=0; j<tok->nval1; j++)
+        {
+            if ( bcf_double_is_missing_or_vector_end(ptr[j]) ) continue;
+            has_value = 1;
+            if ( val > ptr[j] ) val = ptr[j];
+        }
+        if ( has_value ) rtok->values[i] = val;
+        else bcf_double_set_missing(rtok->values[i]);
+    }
+    return 1;
+}
+static int func_avg(filter_t *flt, bcf1_t *line, token_t *rtok, token_t **stack, int nstack)
+{
+    token_t *tok = stack[nstack - 1];
+    rtok->nvalues = 0;
+    if ( !tok->nvalues ) return 1;
+    double *ptr, val = 0;
+    int i,j, n = 0;
+    if ( tok->nsamples )
+    {
+        for (i=0; i<tok->nsamples; i++)
+        {
+            if ( !tok->usmpl[i] ) continue;
+            ptr = tok->values + i*tok->nval1;
+            for (j=0; j<tok->nval1; j++)
+            {
+                if ( bcf_double_is_missing_or_vector_end(ptr[j]) ) continue;
+                val += ptr[j];
+                n++;
+            }
+        }
+    }
+    else
+    {
+        for (i=0; i<tok->nvalues; i++)
+            if ( !bcf_double_is_missing_or_vector_end(tok->values[i]) ) { val += tok->values[i]; n++; }
+    }
+    if ( n )
+    {
+        rtok->values[0] = val / n;
+        rtok->nvalues   = 1;
+    }
+    return 1;
+}
+static int func_smpl_avg(filter_t *flt, bcf1_t *line, token_t *rtok, token_t **stack, int nstack)
+{
+    token_t *tok = stack[nstack - 1];
+    if ( !tok->nsamples ) return func_avg(flt,line,rtok,stack,nstack);
+    rtok->nsamples = tok->nsamples;
+    rtok->nvalues  = tok->nsamples;
+    rtok->nval1 = 1;
+    hts_expand(double,rtok->nvalues,rtok->mvalues,rtok->values);
+    assert(tok->usmpl);
+    if ( !rtok->usmpl ) rtok->usmpl = (uint8_t*) malloc(tok->nsamples);
+    memcpy(rtok->usmpl, tok->usmpl, tok->nsamples);
+    int i, j, n;
+    double val, *ptr;
+    for (i=0; i<tok->nsamples; i++)
+    {
+        if ( !rtok->usmpl[i] ) continue;
+        val = 0;
+        n = 0;
+        ptr = tok->values + i*tok->nval1;
+        for (j=0; j<tok->nval1; j++)
+        {
+            if ( !bcf_double_is_missing_or_vector_end(ptr[j]) ) { val += ptr[j]; n++; }
+        }
+        if ( n ) rtok->values[i] = val / n;
+        else bcf_double_set_missing(rtok->values[i]);
+    }
+    return 1;
+}
+static int compare_doubles(const void *lhs, const void *rhs)
+{
+    double arg1 = *(const double*) lhs;
+    double arg2 = *(const double*) rhs;
+    if (arg1 < arg2) return -1;
+    if (arg1 > arg2) return 1;
+    return 0;
+}
+static int func_median(filter_t *flt, bcf1_t *line, token_t *rtok, token_t **stack, int nstack)
+{
+    token_t *tok = stack[nstack - 1];
+    rtok->nvalues = 0;
+    if ( !tok->nvalues ) return 1;
+    // sweep through all tok->values and while excluding all missing values reuse the very same array
+    int i,j,k = 0, n = 0;
+    if ( tok->nsamples )
+    {
+        for (i=0; i<tok->nsamples; i++)
+        {
+            if ( !tok->usmpl[i] ) { k += tok->nval1; continue; }
+            for (j=0; j<tok->nval1; k++,j++)
+            {
+                if ( bcf_double_is_missing_or_vector_end(tok->values[k]) ) continue;
+                if ( n < k ) tok->values[n] = tok->values[k];
+                n++;
+            }
+        }
+    }
+    else
+    {
+        for (i=0; i<tok->nvalues; i++)
+        {
+            if ( bcf_double_is_missing_or_vector_end(tok->values[i]) ) continue;
+            if ( n < i ) tok->values[n] = tok->values[i];
+            n++;
+        }
+    }
+    if ( !n ) return 1;
+    if ( n==1 ) rtok->values[0] = tok->values[0];
+    else
+    {
+        qsort(tok->values, n, sizeof(double), compare_doubles);
+        rtok->values[0] = n % 2 ? tok->values[n/2] : (tok->values[n/2-1] + tok->values[n/2]) * 0.5;
+    }
+    rtok->nvalues = 1;
+    return 1;
+}
+static int func_smpl_median(filter_t *flt, bcf1_t *line, token_t *rtok, token_t **stack, int nstack)
+{
+    token_t *tok = stack[nstack - 1];
+    if ( !tok->nsamples ) return func_avg(flt,line,rtok,stack,nstack);
+    rtok->nsamples = tok->nsamples;
+    rtok->nvalues  = tok->nsamples;
+    rtok->nval1 = 1;
+    hts_expand(double,rtok->nvalues,rtok->mvalues,rtok->values);
+    assert(tok->usmpl);
+    if ( !rtok->usmpl ) rtok->usmpl = (uint8_t*) malloc(tok->nsamples);
+    memcpy(rtok->usmpl, tok->usmpl, tok->nsamples);
+    int i, j, n;
+    double *ptr;
+    for (i=0; i<tok->nsamples; i++)
+    {
+        if ( !rtok->usmpl[i] ) continue;
+        n = 0;
+        ptr = tok->values + i*tok->nval1;
+        for (j=0; j<tok->nval1; j++)
+        {
+            if ( bcf_double_is_missing_or_vector_end(ptr[j]) ) continue;
+            if ( n < j ) ptr[n] = ptr[j];
+            n++;
+        }
+        if ( n==0 )
+            bcf_double_set_missing(rtok->values[i]);
+        else if ( n==1 )
+            rtok->values[i] = ptr[0];
+        else
+        {
+            qsort(ptr, n, sizeof(double), compare_doubles);
+            rtok->values[i] = n % 2 ? ptr[n/2] : (ptr[n/2-1] + ptr[n/2]) * 0.5;
+        }
+    }
+    return 1;
+}
+static int func_stddev(filter_t *flt, bcf1_t *line, token_t *rtok, token_t **stack, int nstack)
+{
+    token_t *tok = stack[nstack - 1];
+    rtok->nvalues = 0;
+    if ( !tok->nvalues ) return 1;
+    // sweep through all tok->values and while excluding all missing values reuse the very same array
+    int i,j,k = 0, n = 0;
+    if ( tok->nsamples )
+    {
+        for (i=0; i<tok->nsamples; i++)
+        {
+            if ( !tok->usmpl[i] ) { k += tok->nval1; continue; }
+            for (j=0; j<tok->nval1; k++,j++)
+            {
+                if ( bcf_double_is_missing_or_vector_end(tok->values[k]) ) continue;
+                if ( n < k ) tok->values[n] = tok->values[k];
+                n++;
+            }
+        }
+    }
+    else
+    {
+        for (i=0; i<tok->nvalues; i++)
+        {
+            if ( bcf_double_is_missing_or_vector_end(tok->values[i]) ) continue;
+            if ( n < i ) tok->values[n] = tok->values[i];
+            n++;
+        }
+    }
+    if ( !n ) return 1;
+    if ( n==1 ) rtok->values[0] = 0;
+    else
+    {
+        double sdev = 0, avg = 0;
+        for (i=0; i<n; i++) avg += tok->values[i];
+        avg /= n;
+        for (i=0; i<n; i++) sdev += (tok->values[i] - avg) * (tok->values[i] - avg);
+        rtok->values[0] = sqrt(sdev/n);
+    }
+    rtok->nvalues = 1;
+    return 1;
+}
+static int func_smpl_stddev(filter_t *flt, bcf1_t *line, token_t *rtok, token_t **stack, int nstack)
+{
+    token_t *tok = stack[nstack - 1];
+    if ( !tok->nsamples ) return func_avg(flt,line,rtok,stack,nstack);
+    rtok->nsamples = tok->nsamples;
+    rtok->nvalues  = tok->nsamples;
+    rtok->nval1 = 1;
+    hts_expand(double,rtok->nvalues,rtok->mvalues,rtok->values);
+    assert(tok->usmpl);
+    if ( !rtok->usmpl ) rtok->usmpl = (uint8_t*) malloc(tok->nsamples);
+    memcpy(rtok->usmpl, tok->usmpl, tok->nsamples);
+    int i, j, n;
+    double *ptr;
+    for (i=0; i<tok->nsamples; i++)
+    {
+        if ( !rtok->usmpl[i] ) continue;
+        n = 0;
+        ptr = tok->values + i*tok->nval1;
+        for (j=0; j<tok->nval1; j++)
+        {
+            if ( bcf_double_is_missing_or_vector_end(ptr[j]) ) continue;
+            if ( n < j ) ptr[n] = ptr[j];
+            n++;
+        }
+        if ( n==0 )
+            bcf_double_set_missing(rtok->values[i]);
+        else if ( n==1 )
+            rtok->values[i] = 0;
+        else
+        {
+            double sdev = 0, avg = 0;
+            for (j=0; j<n; j++) avg += ptr[j];
+            avg /= n;
+            for (j=0; j<n; j++) sdev += (ptr[j] - avg) * (ptr[j] - avg);
+            rtok->values[i] = sqrt(sdev/n);
+        }
+    }
+    return 1;
+}
+static int func_sum(filter_t *flt, bcf1_t *line, token_t *rtok, token_t **stack, int nstack)
+{
+    rtok->nvalues = 0;
+    token_t *tok = stack[nstack - 1];
+    if ( !tok->nvalues ) return 1;
+    double *ptr, val = 0;
+    int i,j, n = 0;
+    if ( tok->nsamples )
+    {
+        for (i=0; i<tok->nsamples; i++)
+        {
+            if ( !tok->usmpl[i] ) continue;
+            ptr = tok->values + i*tok->nval1;
+            for (j=0; j<tok->nval1; j++)
+            {
+                if ( bcf_double_is_missing_or_vector_end(ptr[j]) ) continue;
+                val += ptr[j];
+                n++;
+            }
+        }
+    }
+    else
+    {
+        for (i=0; i<tok->nvalues; i++)
+            if ( !bcf_double_is_missing_or_vector_end(tok->values[i]) ) { val += tok->values[i]; n++; }
+    }
+    if ( n )
+    {
+        rtok->values[0] = val;
+        rtok->nvalues   = 1;
+    }
+    return 1;
+}
+static int func_smpl_sum(filter_t *flt, bcf1_t *line, token_t *rtok, token_t **stack, int nstack)
+{
+    token_t *tok = stack[nstack - 1];
+    if ( !tok->nsamples ) return func_avg(flt,line,rtok,stack,nstack);
+    rtok->nsamples = tok->nsamples;
+    rtok->nvalues  = tok->nsamples;
+    rtok->nval1 = 1;
+    hts_expand(double,rtok->nvalues,rtok->mvalues,rtok->values);
+    assert(tok->usmpl);
+    if ( !rtok->usmpl ) rtok->usmpl = (uint8_t*) malloc(tok->nsamples);
+    memcpy(rtok->usmpl, tok->usmpl, tok->nsamples);
+    int i, j, has_value;
+    double val, *ptr;
+    for (i=0; i<tok->nsamples; i++)
+    {
+        if ( !rtok->usmpl[i] ) continue;
+        val = 0;
+        has_value = 0;
+        ptr = tok->values + i*tok->nval1;
+        for (j=0; j<tok->nval1; j++)
+        {
+            if ( bcf_double_is_missing_or_vector_end(ptr[j]) ) continue;
+            has_value = 1;
+            val += ptr[j];
+        }
+        if ( has_value ) rtok->values[i] = val;
+        else bcf_double_set_missing(rtok->values[i]);
+    }
+    return 1;
+}
+static int func_abs(filter_t *flt, bcf1_t *line, token_t *rtok, token_t **stack, int nstack)
+{
+    token_t *tok = stack[nstack - 1];
+    if ( tok->is_str ) error("ABS() can be applied only on numeric values\n");
+    rtok->nsamples = tok->nsamples;
+    rtok->nvalues = tok->nvalues;
+    rtok->nval1 = tok->nval1;
+    hts_expand(double,rtok->nvalues,rtok->mvalues,rtok->values);
+    if ( tok->usmpl )
+    {
+        if ( !rtok->usmpl ) rtok->usmpl = (uint8_t*) malloc(tok->nsamples);
+        memcpy(rtok->usmpl, tok->usmpl, tok->nsamples);
+    }
+    if ( !tok->nvalues ) return 1;
+    hts_expand(double, rtok->nvalues, rtok->mvalues, rtok->values);
+    int i,j,k = 0;
+    if ( tok->usmpl )
+    {
+        for (i=0; i<tok->nsamples; i++)
+        {
+            if ( !tok->usmpl[i] ) { k+= tok->nval1; continue; }
+            for (j=0; j<tok->nval1; k++,j++)
+            {
+                if ( bcf_double_is_missing_or_vector_end(tok->values[k]) ) bcf_double_set_missing(rtok->values[k]);
+                else rtok->values[k] = fabs(tok->values[k]);
+            }
+        }
+    }
+    else
+    {
+        for (i=0; i<tok->nvalues; i++)
+        {
+            if ( tok->usmpl && !tok->usmpl[i] ) continue;
+            if ( bcf_double_is_missing(tok->values[i]) ) bcf_double_set_missing(rtok->values[i]);
+            else if ( !bcf_double_is_vector_end(tok->values[i]) ) rtok->values[i] = fabs(tok->values[i]);
+        }
+    }
+    return 1;
+}
+static int func_count(filter_t *flt, bcf1_t *line, token_t *rtok, token_t **stack, int nstack)
+{
+    token_t *tok = stack[nstack - 1];
+    int i,j, cnt = 0;
+    if ( tok->tag && tok->nsamples )
+    {
+        // raw number of values in a FMT tag, e.g. COUNT(FMT/TAG)
+        if ( tok->is_str ) error("todo: Type=String for COUNT on FORMAT fields?\n");
+        for (i=0; i<tok->nsamples; i++)
+        {
+            if ( !tok->usmpl[i] ) continue;
+            double *ptr = tok->values + i*tok->nval1;
+            for (j=0; j<tok->nval1; j++)
+                if ( !bcf_double_is_missing_or_vector_end(ptr[j]) ) cnt++;
+        }
+    }
+    else if ( tok->nsamples )
+    {
+        // number of samples that pass a processed FMT tag
+        for (i=0; i<tok->nsamples; i++)
+            if ( tok->pass_samples[i] ) cnt++;
+    }
+    else if ( tok->is_str )
+    {
+        if ( tok->str_value.l ) cnt = 1;
+        for (i=0; i<tok->str_value.l; i++) if ( tok->str_value.s[i]==',' ) cnt++;
+    }
+    else
+        cnt = tok->nvalues;
+
+    rtok->nvalues = 1;
+    rtok->values[0] = cnt;
+    return 1;
+}
+static int func_strlen(filter_t *flt, bcf1_t *line, token_t *rtok, token_t **stack, int nstack)
+{
+    token_t *tok = stack[nstack - 1];
+    rtok->nvalues = rtok->str_value.l = 0;
+    if ( !tok->str_value.l ) return 1;
+
+    if ( tok->idx==-2 )
+    {
+        int i = 0;
+        char *ss = tok->str_value.s;
+        while ( *ss )
+        {
+            char *se = ss;
+            while ( *se && *se!=',' ) se++;
+            hts_expand(double, i+1, rtok->mvalues, rtok->values);
+            if ( !*se ) rtok->values[i] = strlen(ss);
+            else
+            {
+                *se = 0;
+                rtok->values[i] = strlen(ss);
+                *se = ',';
+            }
+            ss = *se ? se + 1 : se;
+            i++;
+        }
+        rtok->nvalues = i;
+    }
+    else
+    {
+        if ( !tok->str_value.s[1] && tok->str_value.s[0]=='.' )
+            rtok->values[0] = 0;
+        else
+            rtok->values[0] = strlen(tok->str_value.s);
+        rtok->nvalues = 1;
+    }
+    return 1;
+}
+static inline double calc_binom(int na, int nb)
+{
+    if ( na==0 && nb==0 ) return -1;
+    if ( na==nb ) return 1;
+
+    // kfunc.h implements kf_betai, which is the regularized beta function  P(X<=k/N;p) = I_{1-p}(N-k,k+1)
+
+    double pval = na < nb ? kf_betai(nb, na + 1, 0.5) : kf_betai(na, nb + 1, 0.5);
+    pval *= 2;
+    if ( pval>1 ) pval = 1;     // this can happen, machine precision error, eg. kf_betai(1,0,0.5)
+
+    return pval;
+}
+static int func_binom(filter_t *flt, bcf1_t *line, token_t *rtok, token_t **stack, int nstack)
+{
+    int i, istack = nstack - rtok->nargs;
+
+    if ( rtok->nargs!=2 && rtok->nargs!=1 ) error("Error: binom() takes one or two arguments\n");
+    assert( istack>=0 );
+
+    // The expected mean is 0.5. Should we support also prob!=0.5?
+    //
+    //  double prob = 0.5;
+    //  if ( nstack==3 )
+    //  {
+    //      // three parameters, the first one must be a scalar:  binom(0.25,AD[0],AD[1])
+    //      if ( !stack[istack]->is_constant )
+    //          error("The first argument of binom() must be a numeric constant if three parameters are given\n");
+    //      prob = stack[istack]->threshold;
+    //      istack++;
+    //  }
+    //  else if ( nstack==2 && stack[istack]->is_constant )
+    //  {
+    //      // two parameters, the first can be a scalar:  binom(0.25,AD) or binom(AD[0],AD[1])
+    //      prob = stack[istack]->threshold;
+    //      istack++;
+    //  }
+
+    token_t *tok = stack[istack];
+    if ( tok->nsamples )
+    {
+        // working with a FORMAT tag
+        rtok->nval1    = 1;
+        rtok->nvalues  = tok->nsamples;
+        rtok->nsamples = tok->nsamples;
+        hts_expand(double, rtok->nvalues, rtok->mvalues, rtok->values);
+        assert(tok->usmpl);
+        if ( !rtok->usmpl ) rtok->usmpl = (uint8_t*) malloc(tok->nsamples);
+        memcpy(rtok->usmpl, tok->usmpl, tok->nsamples);
+
+        if ( istack+1==nstack )
+        {
+            // determine the index from the GT field: binom(AD)
+            int ngt = bcf_get_genotypes(flt->hdr, line, &flt->tmpi, &flt->mtmpi);
+            int max_ploidy = ngt/line->n_sample;
+            if ( ngt <= 0 || max_ploidy < 2 ) // GT not present or not diploid, cannot set
+            {
+                for (i=0; i<rtok->nsamples; i++)
+                    if ( rtok->usmpl[i] ) bcf_double_set_missing(rtok->values[i]);
+                return rtok->nargs;
+            }
+            for (i=0; i<rtok->nsamples; i++)
+            {
+                if ( !rtok->usmpl[i] ) continue;
+                int32_t *ptr = flt->tmpi + i*max_ploidy;
+                if ( bcf_gt_is_missing(ptr[0]) || bcf_gt_is_missing(ptr[1]) || ptr[1]==bcf_int32_vector_end )
+                {
+                    bcf_double_set_missing(rtok->values[i]);
+                    continue;
+                }
+                int idx1 = bcf_gt_allele(ptr[0]);
+                int idx2 = bcf_gt_allele(ptr[1]);
+                if ( idx1>=line->n_allele ) error("Incorrect allele index at %s:%"PRId64", sample %s\n", bcf_seqname(flt->hdr,line),(int64_t) line->pos+1,flt->hdr->samples[i]);
+                if ( idx2>=line->n_allele ) error("Incorrect allele index at %s:%"PRId64", sample %s\n", bcf_seqname(flt->hdr,line),(int64_t) line->pos+1,flt->hdr->samples[i]);
+                double *vals = tok->values + tok->nval1*i;
+                if ( bcf_double_is_missing_or_vector_end(vals[idx1]) || bcf_double_is_missing_or_vector_end(vals[idx2]) )
+                {
+                    bcf_double_set_missing(rtok->values[i]);
+                    continue;
+                }
+                rtok->values[i] = calc_binom(vals[idx1],vals[idx2]);
+                if ( rtok->values[i] < 0 )
+                {
+                    bcf_double_set_missing(rtok->values[i]);
+                    continue;
+                }
+            }
+        }
+        else
+        {
+            // the fields given explicitly: binom(AD[:0],AD[:1])
+            token_t *tok2 = stack[istack+1];
+            if ( tok->nval1!=1 || tok2->nval1!=1 )
+                error("Expected one value per binom() argument, found %d and %d at %s:%"PRId64"\n",tok->nval1,tok2->nval1, bcf_seqname(flt->hdr,line),(int64_t) line->pos+1);
+            for (i=0; i<rtok->nsamples; i++)
+            {
+                if ( !rtok->usmpl[i] ) continue;
+                double *ptr1 = tok->values + tok->nval1*i;
+                double *ptr2 = tok2->values + tok2->nval1*i;
+                if ( bcf_double_is_missing_or_vector_end(ptr1[0]) || bcf_double_is_missing_or_vector_end(ptr2[0]) )
+                {
+                    bcf_double_set_missing(rtok->values[i]);
+                    continue;
+                }
+                rtok->values[i] = calc_binom(ptr1[0],ptr2[0]);
+                if ( rtok->values[i] < 0 )
+                {
+                    bcf_double_set_missing(rtok->values[i]);
+                    continue;
+                }
+            }
+        }
+    }
+    else
+    {
+        // working with an INFO tag
+        rtok->nvalues  = 1;
+        hts_expand(double, rtok->nvalues, rtok->mvalues, rtok->values);
+
+        double *ptr1 = NULL, *ptr2 = NULL;
+        if ( istack+1==nstack )
+        {
+            // only one tag, expecting two values: binom(INFO/AD)
+            if ( tok->nvalues==2 )
+            {
+                ptr1 = &tok->values[0];
+                ptr2 = &tok->values[1];
+            }
+        }
+        else
+        {
+            // two tags, expecting one value in each: binom(INFO/AD[0],INFO/AD[1])
+            token_t *tok2 = stack[istack+1];
+            if ( tok->nvalues==1 && tok2->nvalues==1 )
+            {
+                ptr1 = &tok->values[0];
+                ptr2 = &tok2->values[0];
+            }
+        }
+        if ( !ptr1 || !ptr2 || bcf_double_is_missing_or_vector_end(ptr1[0]) || bcf_double_is_missing_or_vector_end(ptr2[0]) )
+            bcf_double_set_missing(rtok->values[0]);
+        else
+        {
+            rtok->values[0] = calc_binom(ptr1[0],ptr2[0]);
+            if ( rtok->values[0] < 0 )
+                bcf_double_set_missing(rtok->values[0]);
+        }
+    }
+    return rtok->nargs;
+}
+static int func_phred(filter_t *flt, bcf1_t *line, token_t *rtok, token_t **stack, int nstack)
+{
+    token_t *tok = stack[nstack - 1];
+    if ( tok->is_str ) error("PHRED() can be applied only on numeric values\n");
+
+    rtok->nsamples = tok->nsamples;
+    rtok->nval1 = tok->nval1;
+    memcpy(rtok->pass_samples, tok->pass_samples, rtok->nsamples*sizeof(*rtok->pass_samples));
+    assert(tok->usmpl);
+    if ( !rtok->usmpl )
+    {
+        rtok->usmpl = (uint8_t*) malloc(tok->nsamples*sizeof(*rtok->usmpl));
+        memcpy(rtok->usmpl, tok->usmpl, tok->nsamples*sizeof(*rtok->usmpl));
+    }
+    rtok->nvalues = tok->nvalues;
+    if ( !tok->nvalues ) return 1;
+
+    hts_expand(double, rtok->nvalues, rtok->mvalues, rtok->values);
+    int i,j,k = 0;
+    if ( tok->usmpl )
+    {
+        for (i=0; i<tok->nsamples; i++)
+        {
+            if ( !tok->usmpl[i] ) { k+= tok->nval1; continue; }
+            for (j=0; j<tok->nval1; k++,j++)
+            {
+                if ( bcf_double_is_missing_or_vector_end(tok->values[k]) ) bcf_double_set_missing(rtok->values[k]);
+                else rtok->values[k] = -4.34294481903*log(tok->values[k]);
+            }
+        }
+    }
+    else
+    {
+        for (i=0; i<tok->nvalues; i++)
+        {
+            if ( bcf_double_is_missing_or_vector_end(tok->values[i]) ) bcf_double_set_missing(rtok->values[i]);
+            else rtok->values[i] = -4.34294481903*log(tok->values[i]);
+        }
+    }
+    return 1;
+}
+inline static void tok_init_values(token_t *atok, token_t *btok, token_t *rtok)
+{
+    token_t *tok;
+    if ( (atok->nsamples || btok->nsamples) && (!atok->nsamples || !btok->nsamples) )
+        tok = atok->nsamples ? atok : btok;
+    else
+        tok = atok->nvalues > btok->nvalues ? atok : btok;
+    rtok->nvalues = tok->nvalues;
+    rtok->nval1   = tok->nval1;
+    hts_expand(double, rtok->nvalues, rtok->mvalues, rtok->values);
+}
+inline static void tok_init_samples(token_t *atok, token_t *btok, token_t *rtok)
+{
+    if ( (atok->nsamples || btok->nsamples) && !rtok->nsamples )
+    {
+        rtok->nsamples = atok->nsamples ? atok->nsamples : btok->nsamples;
+        rtok->usmpl = (uint8_t*) calloc(rtok->nsamples,1);
+        int i;
+        for (i=0; i<atok->nsamples; i++) rtok->usmpl[i] |= atok->usmpl[i];
+        for (i=0; i<btok->nsamples; i++) rtok->usmpl[i] |= btok->usmpl[i];
+    }
+    if (rtok->nsamples)
+        memset(rtok->pass_samples, 0, rtok->nsamples);
+}
+
+#define VECTOR_ARITHMETICS(atok,btok,_rtok,AOP,TYPE) \
+{ \
+    token_t *rtok = _rtok; \
+    int i, has_values = 0; \
+    if ( atok->nvalues && btok->nvalues ) \
+    { \
+        tok_init_values(atok, btok, rtok); \
+        tok_init_samples(atok, btok, rtok); \
+        if ( (atok->nsamples && btok->nsamples) || (!atok->nsamples && !btok->nsamples)) \
+        { \
+            assert( atok->nsamples==btok->nsamples ); \
+            for (i=0; i<atok->nvalues; i++) \
+            { \
+                if ( bcf_double_is_missing_or_vector_end(atok->values[i]) || bcf_double_is_missing_or_vector_end(btok->values[i]) ) \
+                { \
+                    bcf_double_set_missing(rtok->values[i]); \
+                    continue; \
+                } \
+                has_values = 1; \
+                rtok->values[i] = TYPE atok->values[i] AOP TYPE btok->values[i]; \
+            } \
+        } \
+        else if ( atok->nsamples ) \
+        { \
+            assert( btok->nvalues==1 ); \
+            if ( !bcf_double_is_missing_or_vector_end(btok->values[0]) ) \
+            { \
+                for (i=0; i<atok->nvalues; i++) \
+                { \
+                    if ( bcf_double_is_missing_or_vector_end(atok->values[i]) ) \
+                    { \
+                        bcf_double_set_missing(rtok->values[i]); \
+                        continue; \
+                    } \
+                    has_values = 1; \
+                    rtok->values[i] = TYPE atok->values[i] AOP TYPE btok->values[0]; \
+                } \
+            } \
+        } \
+        else \
+        { \
+            assert( atok->nvalues==1 ); \
+            if ( !bcf_double_is_missing_or_vector_end(atok->values[0]) ) \
+            { \
+                for (i=0; i<btok->nvalues; i++) \
+                { \
+                    if ( bcf_double_is_missing_or_vector_end(btok->values[i]) ) \
+                    { \
+                        bcf_double_set_missing(rtok->values[i]); \
+                        continue; \
+                    } \
+                    has_values = 1; \
+                    rtok->values[i] = TYPE atok->values[0] AOP TYPE btok->values[i]; \
+                } \
+            } \
+        } \
+    } \
+    if ( !has_values ) rtok->nvalues = 0; \
+}
+
+static int vector_logic_or(filter_t *filter, bcf1_t *line, token_t *rtok, token_t **stack, int nstack)
+{
+    if ( nstack < 2 ) error("Error occurred while processing the filter \"%s\"\n", filter->str);
+
+    token_t *atok = stack[nstack-2];
+    token_t *btok = stack[nstack-1];
+    tok_init_samples(atok, btok, rtok);
+
+    if ( !atok->pass_site && !btok->pass_site ) return 2;
+
+    rtok->pass_site = 1;
+    if ( !atok->nsamples && !btok->nsamples ) return 2;
+
+    int i;
+    if ( rtok->tok_type==TOK_OR_VEC )   // ||, select all samples if one is true
+    {
+        if ( (!atok->nsamples && !atok->pass_site) || (!btok->nsamples && !btok->pass_site) )
+        {
+            // These two conditions are to ensure the following does not set all samples
+            // at sites with QUAL<=30:
+            //      QUAL>30 || FMT/GQ>30
+
+            token_t *tok = atok->nsamples ? atok : btok;
+            for (i=0; i<rtok->nsamples; i++)
+            {
+                if ( !rtok->usmpl[i] ) continue;
+                rtok->pass_samples[i] = tok->pass_samples[i];
+            }
+        }
+        else
+        {
+            for (i=0; i<rtok->nsamples; i++)
+            {
+                if ( !rtok->usmpl[i] ) continue;
+                rtok->pass_samples[i] = 1;
+            }
+        }
+        return 2;
+    }
+
+    //  |, only select samples which are actually true
+
+    if ( !atok->nsamples || !btok->nsamples )
+    {
+        token_t *tok = atok->nsamples ? atok : btok;
+        for (i=0; i<rtok->nsamples; i++)
+        {
+            if ( !rtok->usmpl[i] ) continue;
+            rtok->pass_samples[i] = tok->pass_samples[i];
+        }
+        return 2;
+    }
+
+    assert( atok->nsamples==btok->nsamples );
+
+    for (i=0; i<rtok->nsamples; i++)
+    {
+        if ( !rtok->usmpl[i] ) continue;
+        rtok->pass_samples[i] = atok->pass_samples[i] | btok->pass_samples[i];
+    }
+    return 2;
+}
+static int vector_logic_and(filter_t *filter, bcf1_t *line, token_t *rtok, token_t **stack, int nstack)
+{
+    if ( nstack < 2 ) error("Error occurred while processing the filter \"%s\". (nstack=%d)\n", filter->str,nstack);
+
+    token_t *atok = stack[nstack-2];
+    token_t *btok = stack[nstack-1];
+    tok_init_samples(atok, btok, rtok);
+
+    if ( !atok->pass_site || !btok->pass_site ) return 2;
+    if ( !atok->nsamples && !btok->nsamples ) { rtok->pass_site = 1; return 2; }
+
+    int i;
+    if ( !atok->nsamples || !btok->nsamples )
+    {
+        token_t *tok = atok->nsamples ? atok : btok;
+        for (i=0; i<rtok->nsamples; i++)
+        {
+            if ( !rtok->usmpl[i] ) continue;
+            rtok->pass_samples[i] = tok->pass_samples[i];
+        }
+        rtok->pass_site = 1;
+        return 2;
+    }
+
+    assert( atok->nsamples==btok->nsamples );
+    if ( rtok->tok_type==TOK_AND_VEC )  // &&, can be true in different samples
+    {
+        for (i=0; i<rtok->nsamples; i++)
+        {
+            if ( !rtok->usmpl[i] ) continue;
+            rtok->pass_samples[i] = atok->pass_samples[i] | btok->pass_samples[i];
+        }
+        rtok->pass_site = 1;
+    }
+    else    // &, must be true within one sample
+    {
+        for (i=0; i<rtok->nsamples; i++)
+        {
+            if ( !rtok->usmpl[i] ) continue;
+            rtok->pass_samples[i] = atok->pass_samples[i] & btok->pass_samples[i];
+            if ( rtok->pass_samples[i] ) rtok->pass_site = 1;
+        }
+    }
+    return 2;
+}
+
+#define CMP_VECTORS(atok,btok,_rtok,CMP_OP,missing_logic) \
+{ \
+    token_t *rtok = _rtok; \
+    int i, j, k; \
+    tok_init_samples(atok, btok, rtok); \
+    if ( !atok->nsamples && !btok->nsamples ) \
+    { \
+        if ( !atok->nvalues && !btok->nvalues ) { rtok->pass_site = missing_logic[2]; } \
+        else if ( !atok->nvalues || !btok->nvalues ) \
+        { \
+            token_t *tok = atok->nvalues ? atok : btok; \
+            for (j=0; j<tok->nvalues; j++) \
+            { \
+                if ( bcf_double_is_missing_or_vector_end(tok->values[j]) ) \
+                { \
+                    if ( missing_logic[2] ) { rtok->pass_site = 1; break; } \
+                } \
+                else if ( missing_logic[1] ) {  rtok->pass_site = 1; break; } \
+            } \
+        } \
+        else \
+        { \
+            for (i=0; i<atok->nvalues; i++) \
+            { \
+                int amiss = bcf_double_is_missing_or_vector_end(atok->values[i]) ? 1 : 0; \
+                for (j=0; j<btok->nvalues; j++) \
+                { \
+                    int nmiss = amiss + (bcf_double_is_missing_or_vector_end(btok->values[j]) ? 1 : 0); \
+                    if ( nmiss ) \
+                    { \
+                        if ( missing_logic[nmiss] ) { rtok->pass_site = 1; i = atok->nvalues; break; } \
+                    } \
+                    else if ( atok->values[i] > 16777216 || btok->values[j] > 16777216 ) /* Ugly, see #871 */ \
+                    { \
+                        if ( atok->values[i] CMP_OP btok->values[j] ) { rtok->pass_site = 1; i = atok->nvalues; break; } \
+                    } \
+                    else if ( (float)atok->values[i] CMP_OP (float)btok->values[j] ) { rtok->pass_site = 1; i = atok->nvalues; break; } \
+                } \
+            } \
+        } \
+    } \
+    else \
+    { \
+        if ( !atok->nvalues && !btok->nvalues ) \
+        { \
+            if ( missing_logic[2] ) \
+            { \
+                for (i=0; i<rtok->nsamples; i++) \
+                    if ( rtok->usmpl[i] ) { rtok->pass_samples[i] = missing_logic[2]; rtok->pass_site = 1; } \
+            } \
+        } \
+        else if ( !atok->nvalues || !btok->nvalues ) \
+        { \
+            token_t *tok = atok->nvalues ? atok : btok; \
+            if ( !tok->nsamples ) \
+            { \
+                int miss = 0; \
+                for (j=0; j<tok->nvalues; j++) \
+                    miss |= bcf_double_is_missing_or_vector_end(tok->values[j]) ? 1 : 0; \
+                if ( missing_logic[++miss] ) \
+                { \
+                    for (i=0; i<rtok->nsamples; i++) \
+                        if ( rtok->usmpl[i] ) { rtok->pass_samples[i] = missing_logic[miss]; rtok->pass_site = 1; } \
+                } \
+            } \
+            else \
+                for (i=0; i<tok->nsamples; i++) \
+                { \
+                    if ( !rtok->usmpl[i] ) continue; \
+                    double *ptr = tok->values + i*tok->nval1; \
+                    int miss = 0; \
+                    for (j=0; j<tok->nval1; j++) \
+                        miss |= bcf_double_is_missing_or_vector_end(ptr[j]) ? 1 : 0; \
+                    if ( missing_logic[++miss] ) { rtok->pass_samples[i] = missing_logic[miss]; rtok->pass_site = 1; } \
+                } \
+        } \
+        else if ( atok->nsamples && btok->nsamples ) \
+        { \
+            if ( atok->nval1!=btok->nval1 ) error("Incompatible number of per-sample values in comparison: %d vs %d\n",atok->nval1,btok->nval1); \
+            if ( atok->nsamples!=btok->nsamples ) error("Incompatible number samples in comparison: %d vs %d\n",atok->nsamples,btok->nsamples); \
+            for (i=0; i<atok->nsamples; i++) \
+            { \
+                if ( !atok->usmpl[i] || !btok->usmpl[i] ) { rtok->usmpl[i] = 0; continue; } \
+                double *aptr = atok->values + i*atok->nval1; \
+                double *bptr = btok->values + i*btok->nval1; \
+                for (j=0; j<atok->nval1; j++) \
+                { \
+                    int nmiss = bcf_double_is_missing_or_vector_end(aptr[j]) ? 1 : 0; \
+                    if ( nmiss && !missing_logic[0] ) continue; /* any is missing => result is false */ \
+                    nmiss += (bcf_double_is_missing_or_vector_end(bptr[j]) ? 1 : 0); \
+                    if ( nmiss ) \
+                    { \
+                        if ( missing_logic[nmiss] ) { rtok->pass_samples[i] = 1; rtok->pass_site = 1; break; } \
+                    } \
+                    else if ( aptr[j] > 16777216 || bptr[j] > 16777216 ) /* Ugly, see #871 */ \
+                    { \
+                        if ( aptr[j] CMP_OP bptr[j] ) { rtok->pass_samples[i] = 1; rtok->pass_site = 1; break; } \
+                    } \
+                    else if ( (float)aptr[j] CMP_OP (float)bptr[j] ) { rtok->pass_samples[i] = 1; rtok->pass_site = 1; break; } \
+                } \
+            } \
+        } \
+        else if ( atok->nsamples )\
+        { \
+            for (i=0; i<atok->nsamples; i++) \
+            { \
+                if ( !rtok->usmpl[i] ) continue; \
+                double *aptr = atok->values + i*atok->nval1; \
+                double *bptr = btok->values + i*btok->nval1; \
+                for (j=0; j<atok->nval1; j++) \
+                { \
+                    int miss = bcf_double_is_missing_or_vector_end(aptr[j]) ? 1 : 0; \
+                    if ( miss && !missing_logic[0] ) continue; /* any is missing => result is false */ \
+                    for (k=0; k<btok->nvalues; k++) \
+                    { \
+                        int nmiss = miss + (bcf_double_is_missing_or_vector_end(bptr[k]) ? 1 : 0); \
+                        if ( nmiss ) \
+                        { \
+                            if ( missing_logic[nmiss] ) { rtok->pass_samples[i] = 1; rtok->pass_site = 1; j = atok->nval1; break; } \
+                        } \
+                        else if ( aptr[j] > 16777216 || bptr[k] > 16777216 ) /* Ugly, see #871 */ \
+                        { \
+                            if ( aptr[j] CMP_OP bptr[k] ) { rtok->pass_samples[i] = 1; rtok->pass_site = 1; j = atok->nval1; break; } \
+                        } \
+                        else if ( (float)aptr[j] CMP_OP (float)bptr[k] ) { rtok->pass_samples[i] = 1; rtok->pass_site = 1; j = atok->nval1; break; } \
+                    } \
+                } \
+            } \
+        } \
+        else /* btok->nsamples */ \
+        { \
+            for (i=0; i<btok->nsamples; i++) \
+            { \
+                if ( !rtok->usmpl[i] ) continue; \
+                double *aptr = atok->values + i*atok->nval1; \
+                double *bptr = btok->values + i*btok->nval1; \
+                for (j=0; j<btok->nval1; j++) \
+                { \
+                    int miss = bcf_double_is_missing_or_vector_end(bptr[j]) ? 1 : 0; \
+                    if ( miss && !missing_logic[0] ) continue; /* any is missing => result is false */ \
+                    for (k=0; k<atok->nvalues; k++) \
+                    { \
+                        int nmiss = miss + (bcf_double_is_missing_or_vector_end(aptr[k]) ? 1 : 0); \
+                        if ( nmiss ) \
+                        { \
+                            if ( missing_logic[nmiss] ) { rtok->pass_samples[i] = 1; rtok->pass_site = 1; j = btok->nval1; break; } \
+                        } \
+                        else if ( bptr[j] > 16777216 || aptr[k] > 16777216 ) /* Ugly, see #871 */ \
+                        { \
+                            if ( aptr[k] CMP_OP bptr[j] ) { rtok->pass_samples[i] = 1; rtok->pass_site = 1; j = btok->nval1; break; } \
+                        } \
+                        else if ( (float)aptr[k] CMP_OP (float)bptr[j] ) { rtok->pass_samples[i] = 1; rtok->pass_site = 1; j = btok->nval1; break; } \
+                    } \
+                } \
+            } \
+        } \
+    } \
+}
+static int _regex_vector_strings(regex_t *regex, char *str, size_t len, int logic, int *missing_logic)
+{
+    char *end = str + len;
+    while ( str < end && *str )
+    {
+        char *mid = str;
+        while ( mid < end && *mid && *mid!=',' ) mid++;
+        int miss = mid - str == 1 && str[0]=='.' ? 1 : 0;
+        if ( miss && missing_logic[miss] ) return 1;
+        char tmp = *mid; *mid = 0;
+        int match = regexec(regex, str, 0,NULL,0) ? 0 : 1;
+        *mid = tmp;
+        if ( logic==TOK_NLIKE ) match = match ? 0 : 1;
+        if ( match ) return 1;
+        if ( !*mid ) break;
+        str = mid + 1;
+    }
+    return 0;
+}
+static inline int _has_missing_string(char *beg)
+{
+    while ( *beg )
+    {
+        char *end = beg;
+        while ( *end && *end!=',' ) end++;
+        if ( end-beg==1 && beg[0]=='.' ) return 1;
+        if ( !*end ) break;
+        beg = end + 1;
+    }
+    return 0;
+}
+
+// Compare two strings with multiple fields, for example "A,B,.,C"=="X,Y,A".
+// Returns 1 if any field matches, otherwise returns 0
+static inline int _match_vector_strings(char *abeg, size_t alen, char *bstr, size_t blen, int logic, int *missing_logic)
+{
+    char *aend = abeg + alen;
+    char *bend = bstr + blen;
+    while ( abeg < aend && *abeg )
+    {
+        char *amid = abeg;
+        while ( amid < aend && *amid && *amid!=',' ) amid++;
+        int miss = amid - abeg == 1 && abeg[0]=='.' ? 1 : 0;
+        char *bbeg = bstr;
+        while ( bbeg < bend && *bbeg )
+        {
+            char *bmid = bbeg;
+            while ( bmid < bend && *bmid && *bmid!=',' ) bmid++;
+            int nmiss = miss + (bmid - bbeg == 1 && bbeg[0]=='.' ? 1 : 0);
+            if ( nmiss )
+            {
+                if ( missing_logic[nmiss] ) return 1;
+            }
+            else
+            {
+                int match = amid-abeg==bmid-bbeg && !strncmp(abeg,bbeg,amid-abeg) ? 1 : 0;
+                if ( logic==TOK_NE ) match = match==1 ? 0 : 1;
+                if ( match ) return 1;
+            }
+            if ( !*bmid ) break;
+            bbeg = bmid + 1;
+        }
+        if ( !*amid ) break;
+        abeg = amid + 1;
+    }
+    return 0;
+}
+static void cmp_vector_strings(token_t *atok, token_t *btok, token_t *rtok)
+{
+    tok_init_samples(atok, btok, rtok);
+
+    int i, logic = rtok->tok_type;     // TOK_EQ, TOK_NE, TOK_LIKE, TOK_NLIKE
+    regex_t *regex = atok->regex ? atok->regex : (btok->regex ? btok->regex : NULL);
+
+    assert( atok->nvalues==atok->str_value.l && btok->nvalues==btok->str_value.l );
+    assert( !atok->nsamples || !btok->nsamples );
+    assert( (!regex && (logic==TOK_EQ || logic==TOK_NE)) || (regex && (logic==TOK_LIKE || logic==TOK_NLIKE)) );
+
+    int missing_logic[] = {0,0,0};
+    if ( logic==TOK_EQ || logic==TOK_LIKE ) missing_logic[0] = missing_logic[2] = 1;
+    else if ( logic==TOK_NE || logic==TOK_NLIKE ) missing_logic[0] = missing_logic[1] = 1;
+
+    if ( !atok->nsamples && !btok->nsamples )
+    {
+        if ( !atok->nvalues && !btok->nvalues ) { rtok->pass_site = missing_logic[2]; return; }
+        if ( !atok->nvalues || !btok->nvalues )
+        {
+            int miss = _has_missing_string(atok->nvalues ? atok->str_value.s : btok->str_value.s);
+            if ( missing_logic[miss+1] ) rtok->pass_site = 1;
+            return;
+        }
+        if ( !regex )
+            rtok->pass_site = _match_vector_strings(atok->str_value.s, atok->str_value.l, btok->str_value.s, btok->str_value.l, logic, missing_logic);
+        else
+        {
+            token_t *tok = atok->regex ? btok : atok;
+            rtok->pass_site = _regex_vector_strings(regex, tok->str_value.s, tok->str_value.l, logic, missing_logic);
+        }
+        return;
+    }
+
+    // The case of (!atok->nsamples || !btok->nsamples)
+
+    if ( !atok->nvalues && !btok->nvalues )
+    {
+        if ( missing_logic[2] )
+        {
+            for (i=0; i<rtok->nsamples; i++)
+                if ( rtok->usmpl[i] ) { rtok->pass_samples[i] = missing_logic[2]; rtok->pass_site = 1; }
+        }
+        return;
+    }
+    if ( !atok->nvalues || !btok->nvalues )
+    {
+        token_t *tok = atok->nvalues ? atok : btok;
+        if ( !tok->nsamples )
+        {
+            int miss = _has_missing_string(tok->str_value.s);
+            if ( !missing_logic[miss+1] ) return;
+            for (i=0; i<rtok->nsamples; i++)
+                if ( rtok->usmpl[i] ) { rtok->pass_samples[i] = 1; rtok->pass_site = 1; }
+        }
+        else
+            for (i=0; i<tok->nsamples; i++)
+            {
+                if ( !rtok->usmpl[i] ) continue;
+                int miss = _has_missing_string(tok->str_value.s + i*tok->nval1);
+                if ( missing_logic[miss+1] ) { rtok->pass_samples[i] = 1; rtok->pass_site = 1; }
+            }
+        return;
+    }
+
+    // The case of (!atok->nsamples || !btok->nsamples) && (atok->nvalues && btok->nvalues)
+    token_t *xtok = atok->nsamples ? atok : btok;
+    token_t *ytok = atok->nsamples ? btok : atok;
+    assert( regex==ytok->regex );
+    for (i=0; i<xtok->nsamples; i++)
+    {
+        if ( !rtok->usmpl[i] ) continue;
+        int match;
+        if ( regex )
+            match = _regex_vector_strings(regex, xtok->str_value.s + i*xtok->nval1, xtok->nval1, logic, missing_logic);
+        else
+            match = _match_vector_strings(xtok->str_value.s + i*xtok->nval1, xtok->nval1, ytok->str_value.s, ytok->str_value.l, logic, missing_logic);
+        if ( match ) { rtok->pass_samples[i] = 1; rtok->pass_site = 1; }
+    }
+}
+
+static int parse_idxs(char *tag_idx, int **idxs, int *nidxs, int *idx)
+{
+    // TAG[], TAG[*] .. any field; sets idx=-2, idxs[0]=-1
+    if ( *tag_idx==0 || !strcmp("*", tag_idx) )
+    {
+        *idxs = (int*) malloc(sizeof(int));
+        (*idxs)[0] = -1;
+        *nidxs     = 1;
+        *idx       = -2;
+        return 0;
+    }
+
+    // TAG[integer] .. one field; idx positive
+    char *end, *beg = tag_idx;
+    *idx = strtol(tag_idx, &end, 10);
+    if ( *idx >= 0 && *end==0 ) return 0;
+
+    // TAG[0,1] or TAG[0-2] or [1-] etc; idx=-2, idxs[...]=0,0,1,1,..
+    int i, ibeg = -1;
+    while ( *beg )
+    {
+        int num = strtol(beg, &end, 10);
+        if ( end[0]==',' ) beg = end + 1;
+        else if ( end[0]==0 ) beg = end;
+        else if ( end[0]=='-' ) { beg = end + 1; ibeg = num; continue; }
+        else return -1;
+        if ( num >= *nidxs )
+        {
+            *idxs = (int*) realloc(*idxs, sizeof(int)*(num+1));
+            memset(*idxs + *nidxs, 0, sizeof(int)*(num - *nidxs + 1));
+            *nidxs = num + 1;
+        }
+        if ( ibeg>=0 )
+        {
+            for (i=ibeg; i<=num; i++) (*idxs)[i] = 1;
+            ibeg = -1;
+        }
+        (*idxs)[num] = 1;
+    }
+    if ( ibeg >=0 )
+    {
+        if ( ibeg >= *nidxs )
+        {
+            *idxs = (int*) realloc(*idxs, sizeof(int)*(ibeg+1));
+            memset(*idxs + *nidxs, 0, sizeof(int)*(ibeg - *nidxs + 1));
+            *nidxs = ibeg + 1;
+        }
+        (*idxs)[ibeg] = -1;
+    }
+    *idx = -2;
+    return 0;
+}
+
+static void parse_tag_idx(bcf_hdr_t *hdr, int is_fmt, char *tag, char *tag_idx, token_t *tok)   // tag_idx points just after "TAG["
+{
+    int i, len = strlen(tag_idx);
+    if ( tag_idx[len-1] == ']' ) tag_idx[len-1] = 0;
+    char *ori = strdup(tag_idx);
+
+    assert( !tok->idxs && !tok->usmpl );
+    int *idxs1 = NULL, nidxs1 = 0, idx1 = 0;
+    int *idxs2 = NULL, nidxs2 = 0, idx2 = 0;
+
+    int set_samples = 0;
+    char *colon = strrchr(tag_idx, ':');
+    if ( tag_idx[0]=='@' )     // file list with sample names
+    {
+        if ( !is_fmt ) error("Could not parse \"%s\". (Not a FORMAT tag yet a sample list provided.)\n", ori);
+        char *fname = expand_path(tag_idx+1);
+#ifdef _WIN32
+        if (fname && strlen(fname) > 2 && fname[1] == ':') // Deal with Windows paths, such as 'C:\..'
+            colon = strrchr(fname+2, ':');
+#endif
+        int nsmpl;
+        char **list = hts_readlist(fname, 1, &nsmpl);
+        if ( !list && colon )
+        {
+            if ( parse_idxs(colon+1, &idxs2, &nidxs2, &idx2) != 0 ) error("Could not parse the index: %s\n", ori);
+            tok->idxs  = idxs2;
+            tok->nidxs = nidxs2;
+            tok->idx   = idx2;
+            colon = strrchr(fname, ':');
+            *colon = 0;
+            list = hts_readlist(fname, 1, &nsmpl);
+        }
+        if ( !list ) error("Could not read: %s\n", fname);
+        free(fname);
+        tok->nsamples = bcf_hdr_nsamples(hdr);
+        tok->usmpl = (uint8_t*) calloc(tok->nsamples,1);
+        for (i=0; i<nsmpl; i++)
+        {
+            int ismpl = bcf_hdr_id2int(hdr,BCF_DT_SAMPLE,list[i]);
+            if ( ismpl<0 ) error("No such sample in the VCF: \"%s\"\n", list[i]);
+            free(list[i]);
+            tok->usmpl[ismpl] = 1;
+        }
+        free(list);
+        if ( !colon )
+        {
+            tok->idxs = (int*) malloc(sizeof(int));
+            tok->idxs[0] = -1;
+            tok->nidxs   = 1;
+            tok->idx     = -2;
+        }
+    }
+    else if ( colon )
+    {
+        if ( !is_fmt ) error("Could not parse the index \"%s\". (Not a FORMAT tag yet sample index implied.)\n", ori);
+        *colon = 0;
+        if ( parse_idxs(tag_idx, &idxs1, &nidxs1, &idx1) != 0 ) error("Could not parse the index: %s\n", ori);
+        if ( parse_idxs(colon+1, &idxs2, &nidxs2, &idx2) != 0 ) error("Could not parse the index: %s\n", ori);
+        tok->idxs  = idxs2;
+        tok->nidxs = nidxs2;
+        tok->idx   = idx2;
+        set_samples = 1;
+    }
+    else
+    {
+        if ( parse_idxs(tag_idx, &idxs1, &nidxs1, &idx1) != 0 ) error("Could not parse the index: %s\n", ori);
+        if ( is_fmt )
+        {
+            if ( nidxs1==1 && idxs1[0]==-1 )
+            {
+                tok->idxs = (int*) malloc(sizeof(int));
+                tok->idxs[0] = -1;
+                tok->nidxs   = 1;
+                tok->idx     = -2;
+            }
+            else if ( bcf_hdr_id2number(hdr,BCF_HL_FMT,tok->hdr_id)!=1 )
+                error("The FORMAT tag %s can have multiple subfields, run as %s[sample:subfield]\n", tag,tag);
+            else
+                tok->idx = 0;
+            set_samples = 1;
+        }
+        else
+        {
+            tok->idxs  = idxs1;
+            tok->nidxs = nidxs1;
+            tok->idx   = idx1;
+        }
+    }
+
+    if ( set_samples )
+    {
+        tok->nsamples = bcf_hdr_nsamples(hdr);
+        tok->usmpl = (uint8_t*) calloc(tok->nsamples,1);
+        if ( idx1>=0 )
+        {
+            if ( idx1 >= bcf_hdr_nsamples(hdr) ) error("The sample index is too large: %s\n", ori);
+            tok->usmpl[idx1] = 1;
+        }
+        else if ( idx1==-2 )
+        {
+            for (i=0; i<nidxs1; i++)
+            {
+                if ( idxs1[i]==0 ) continue;
+                if ( idxs1[i]==-1 ) break;
+                if ( i >= bcf_hdr_nsamples(hdr) ) error("The sample index is too large: %s\n", ori);
+                tok->usmpl[i] = 1;
+            }
+            if ( nidxs1 && idxs1[nidxs1-1]==-1 )    // open range, such as "7-"
+            {
+                for (; i<tok->nsamples; i++) tok->usmpl[i] = 1;
+            }
+        }
+        else error("todo: %s:%d .. %d\n", __FILE__,__LINE__, idx2);
+        free(idxs1);
+    }
+    free(ori);
+
+    if ( tok->nidxs && tok->idxs[tok->nidxs-1]!=-1 )
+    {
+        for (i=0; i<tok->nidxs; i++) if ( tok->idxs[i] ) tok->nuidxs++;
+    }
+}
+static int max_ac_an_unpack(bcf_hdr_t *hdr)
+{
+    int hdr_id = bcf_hdr_id2int(hdr,BCF_DT_ID,"AC");
+    if ( hdr_id<0 ) return BCF_UN_FMT;
+    if ( !bcf_hdr_idinfo_exists(hdr,BCF_HL_INFO,hdr_id) ) return BCF_UN_FMT;
+
+    hdr_id = bcf_hdr_id2int(hdr,BCF_DT_ID,"AN");
+    if ( hdr_id<0 ) return BCF_UN_FMT;
+    if ( !bcf_hdr_idinfo_exists(hdr,BCF_HL_INFO,hdr_id) ) return BCF_UN_FMT;
+
+    return BCF_UN_INFO;
+}
+static int filters_init1(filter_t *filter, char *str, int len, token_t *tok)
+{
+    tok->tag_type  = -1;
+    tok->tok_type  = TOK_VAL;
+    tok->hdr_id    = -1;
+    tok->pass_site = -1;
+    tok->idx       = 0;
+
+    // is this a string constant?
+    if ( str[0]=='"' || str[0]=='\'' )
+    {
+        int quote = str[0];
+        if ( str[len-1] != quote ) error("TODO: [%s]\n", filter->str);
+        tok->key = (char*) calloc(len-1,sizeof(char));
+        hts_expand(double,1,tok->mvalues,tok->values);
+        tok->values[0] = len-2;
+        memcpy(tok->key,str+1,len-2);
+        tok->key[len-2] = 0;
+        tok->is_str = 1;
+        tok->nvalues = len-2;
+        if ( !strcmp(".",tok->key) ) tok->is_missing = 1;
+        return 0;
+    }
+
+    // is it a file?
+    if ( str[0]=='@' )
+    {
+        tok->tag = (char*) calloc(len+1,sizeof(char));
+        memcpy(tok->tag,str,len);
+        tok->tag[len] = 0;
+        char *fname = expand_path(tok->tag+1);
+        int i, n;
+        char **list = hts_readlist(fname, 1, &n);
+        if ( !list ) error("Could not read: %s\n", fname);
+        free(fname);
+        tok->hash = khash_str2int_init();
+        for (i=0; i<n; i++)
+        {
+            char *se = list[i];
+            while ( *se && !isspace(*se) ) se++;
+            *se = 0;
+            if ( !khash_str2int_has_key(tok->hash,list[i]) )
+                khash_str2int_inc(tok->hash,list[i]);
+            else
+                free(list[i]);
+        }
+        free(list);
+        return 0;
+    }
+
+    int is_fmt = -1;
+    if ( !strncasecmp(str,"FMT/",4) ) { str += 4; len -= 4; is_fmt = 1; }
+    else if ( !strncasecmp(str,"FORMAT/",7) ) { str += 7; len -= 7; is_fmt = 1; }
+    else
+    {
+        if ( !strncasecmp(str,"INFO/",5) ) { is_fmt = 0; str += 5; len -= 5; }
+        else if ( !strncasecmp(str,"QUAL",len) || !strncmp(str,"%QUAL",len) /* for backward compatibility */ )
+        {
+            tok->setter = filters_set_qual;
+            tok->tag = strdup("QUAL");
+            return 0;
+        }
+        else if ( !strncasecmp(str,"TYPE",len) || !strncmp(str,"%TYPE",len) /* for backward compatibility */ )
+        {
+            tok->setter = filters_set_type;
+            tok->tag = strdup("TYPE");
+            return 0;
+        }
+        else if ( !strncasecmp(str,"FILTER",len) || !strncmp(str,"%FILTER",len) /* for backward compatibility */ )
+        {
+            tok->comparator = filters_cmp_filter;
+            tok->tag = strdup("FILTER");
+            filter->max_unpack |= BCF_UN_FLT;
+            tok->tag_type = BCF_HL_FLT;
+            return 0;
+        }
+        else if ( !strncasecmp(str,"ID",len) || !strncasecmp(str,"%ID",len) /* for backward compatibility */ )
+        {
+            tok->comparator = filters_cmp_id;
+            tok->tag = strdup("ID");
+            return 0;
+        }
+        else if ( !strncasecmp(str,"CHROM",len) )
+        {
+            tok->setter = &filters_set_chrom;
+            tok->tag = strdup("CHROM");
+            return 0;
+        }
+        else if ( !strncasecmp(str,"POS",len) )
+        {
+            tok->setter = &filters_set_pos;
+            tok->tag = strdup("POS");
+            return 0;
+        }
+        else if ( !strncasecmp(str,"REF",len) )
+        {
+            tok->setter = &filters_set_ref_string;
+            tok->is_str = 1;
+            tok->tag = strdup("REF");
+            return 0;
+        }
+        else if ( !strncasecmp(str,"ALT",len) )
+        {
+            tok->setter = &filters_set_alt_string;
+            tok->is_str = 1;
+            tok->tag = strdup("ALT");
+            tok->idxs = (int*) malloc(sizeof(int));
+            tok->idxs[0] = -1;
+            tok->nidxs   = 1;
+            tok->idx     = -2;
+            return 0;
+        }
+        else if ( !strncasecmp(str,"N_ALT",len) )
+        {
+            tok->setter = &filters_set_nalt;
+            tok->tag = strdup("N_ALT");
+            return 0;
+        }
+        else if ( !strncasecmp(str,"N_SAMPLES",len) )
+        {
+            tok->tok_type = TOK_VAL;
+            tok->threshold = bcf_hdr_nsamples(filter->hdr);
+            tok->is_constant = 1;
+            return 0;
+        }
+        else if ( !strncasecmp(str,"N_MISSING",len) )
+        {
+            filter->max_unpack |= BCF_UN_FMT;
+            tok->setter = &filters_set_nmissing;
+            tok->tag = strdup("N_MISSING");
+            return 0;
+        }
+        else if ( !strncasecmp(str,"F_MISSING",len) )
+        {
+            filter->max_unpack |= BCF_UN_FMT;
+            tok->setter = &filters_set_nmissing;
+            tok->tag = strdup("F_MISSING");
+            return 0;
+        }
+    }
+
+    // does it have array subscript?
+    int is_array = 0;
+    kstring_t tmp = {0,0,0};
+    kputsn(str, len, &tmp);
+    if ( tmp.s[tmp.l-1] == ']' )
+    {
+        int i;
+        for (i=0; i<tmp.l; i++)
+            if ( tmp.s[i]=='[' ) { tmp.s[i] = 0; is_array = i+1; break; }
+    }
+    tok->hdr_id = bcf_hdr_id2int(filter->hdr,BCF_DT_ID,tmp.s);
+    if ( is_fmt==-1 )
+    {
+        if ( tok->hdr_id >=0 )
+        {
+            int is_info = bcf_hdr_idinfo_exists(filter->hdr,BCF_HL_INFO,tok->hdr_id) ? 1 : 0;
+            is_fmt = bcf_hdr_idinfo_exists(filter->hdr,BCF_HL_FMT,tok->hdr_id) ? 1 : 0;
+            if ( is_info && is_fmt )
+                error("Error: ambiguous filtering expression, both INFO/%s and FORMAT/%s are defined in the VCF header.\n" , tmp.s,tmp.s);
+        }
+        if ( is_fmt==-1 ) is_fmt = 0;
+    }
+    if ( is_array )
+        parse_tag_idx(filter->hdr, is_fmt, tmp.s, tmp.s+is_array, tok);
+    else if ( is_fmt && !tok->nsamples )
+    {
+        int i;
+        tok->nsamples = bcf_hdr_nsamples(filter->hdr);
+        tok->usmpl = (uint8_t*) malloc(tok->nsamples);
+        for (i=0; i<tok->nsamples; i++) tok->usmpl[i] = 1;
+    }
+
+    tok->tag_type = is_fmt ? BCF_HL_FMT : BCF_HL_INFO;
+    if ( is_fmt ) filter->max_unpack |= BCF_UN_FMT;
+    if ( tok->hdr_id>=0 )
+    {
+        if ( is_fmt && !strcmp("GT",tmp.s) )
+        {
+            tok->setter = &filters_set_genotype_string; tok->is_str = 1;
+        }
+        else if ( is_fmt )
+        {
+            if ( !bcf_hdr_idinfo_exists(filter->hdr,BCF_HL_FMT,tok->hdr_id) )
+                error("No such FORMAT field: %s\n", tmp.s);
+            if ( bcf_hdr_id2number(filter->hdr,BCF_HL_FMT,tok->hdr_id)!=1 && !is_array )
+            {
+                tok->idxs = (int*) malloc(sizeof(int));
+                tok->idxs[0] = -1;
+                tok->nidxs   = 1;
+                tok->idx     = -2;
+            }
+            switch ( bcf_hdr_id2type(filter->hdr,BCF_HL_FMT,tok->hdr_id) )
+            {
+                case BCF_HT_INT:  tok->setter = &filters_set_format_int; break;
+                case BCF_HT_REAL: tok->setter = &filters_set_format_float; break;
+                case BCF_HT_STR:  tok->setter = &filters_set_format_string; tok->is_str = 1; break;
+                default: error("[%s:%d %s] FIXME\n", __FILE__,__LINE__,__FUNCTION__);
+            }
+        }
+        else if ( !bcf_hdr_idinfo_exists(filter->hdr,BCF_HL_INFO,tok->hdr_id) )
+            error("No such INFO field: %s\n", tmp.s);
+        else
+        {
+            if ( bcf_hdr_id2type(filter->hdr,BCF_HL_INFO,tok->hdr_id) == BCF_HT_FLAG )
+                tok->setter = filters_set_info_flag;
+            else
+            {
+                if ( bcf_hdr_id2type(filter->hdr,BCF_HL_INFO,tok->hdr_id) == BCF_HT_STR ) tok->is_str = 1;
+                if ( bcf_hdr_id2number(filter->hdr,BCF_HL_INFO,tok->hdr_id)==1 )
+                    tok->setter = filters_set_info;
+                else
+                {
+                    switch ( bcf_hdr_id2type(filter->hdr,BCF_HL_INFO,tok->hdr_id) )
+                    {
+                        case BCF_HT_INT:  tok->setter = &filters_set_info_int; break;
+                        case BCF_HT_REAL: tok->setter = &filters_set_info_float; break;
+                        case BCF_HT_STR:  tok->setter = &filters_set_info_string; tok->is_str = 1; break;
+                        default: error("[%s:%d %s] FIXME\n", __FILE__,__LINE__,__FUNCTION__);
+                    }
+                    if (!is_array)
+                    {
+                        tok->idx = -2;
+                        tok->idxs = (int*) malloc(sizeof(int));
+                        tok->idxs[0] = -1;
+                        tok->nidxs   = 1;
+                    }
+                }
+            }
+            filter->max_unpack |= BCF_UN_INFO;
+        }
+        tok->tag = strdup(tmp.s);
+        if ( tmp.s ) free(tmp.s);
+        return 0;
+    }
+    else if ( !strcasecmp(tmp.s,"ALT") )
+    {
+        tok->setter = &filters_set_alt_string;
+        tok->is_str = 1;
+        tok->tag = strdup(tmp.s);
+        free(tmp.s);
+        return 0;
+    }
+    else if ( !strcasecmp(tmp.s,"AN") )
+    {
+        filter->max_unpack |= BCF_UN_FMT;
+        tok->setter = &filters_set_an;
+        tok->tag = strdup("AN");
+        free(tmp.s);
+        return 0;
+    }
+    else if ( !strcasecmp(tmp.s,"AC") )
+    {
+        filter->max_unpack |= BCF_UN_FMT;
+        tok->setter = &filters_set_ac;
+        tok->tag = strdup("AC");
+        free(tmp.s);
+        return 0;
+    }
+    else if ( !strcasecmp(tmp.s,"MAC") )
+    {
+        filter->max_unpack |= max_ac_an_unpack(filter->hdr);
+        tok->setter = &filters_set_mac;
+        tok->tag = strdup("MAC");
+        free(tmp.s);
+        return 0;
+    }
+    else if ( !strcasecmp(tmp.s,"AF") )
+    {
+        filter->max_unpack |= max_ac_an_unpack(filter->hdr);
+        tok->setter = &filters_set_af;
+        tok->tag = strdup("AF");
+        free(tmp.s);
+        return 0;
+    }
+    else if ( !strcasecmp(tmp.s,"MAF") )
+    {
+        filter->max_unpack |= max_ac_an_unpack(filter->hdr);
+        tok->setter = &filters_set_maf;
+        tok->tag = strdup("MAF");
+        free(tmp.s);
+        return 0;
+    }
+    else if ( !strcasecmp(tmp.s,"ILEN") || !strcasecmp(tmp.s,"%ILEN") )
+    {
+        filter->max_unpack |= BCF_UN_STR;
+        tok->setter = &filters_set_ilen;
+        tok->tag = strdup("ILEN");
+        free(tmp.s);
+        return 0;
+    }
+
+    // is it a value? Here we parse as integer/float separately and use strtof
+    // rather than strtod, because the more accurate double representation
+    // would invalidate floating point comparisons like QUAL=59.2, obtained via
+    // htslib/vcf parser.
+    // Update: use strtod() and force floats only in comparisons
+    char *end;
+    tok->threshold = strtol(tmp.s, &end, 10);   // integer?
+    if ( end - tmp.s != strlen(tmp.s) )
+    {
+        errno = 0;
+        tok->threshold = strtod(tmp.s, &end);   // float?
+        if ( errno!=0 || end!=tmp.s+len ) error("[%s:%d %s] Error: the tag \"%s\" is not defined in the VCF header\n", __FILE__,__LINE__,__FUNCTION__,tmp.s);
+    }
+    tok->is_constant = 1;
+
+    if ( tmp.s ) free(tmp.s);
+    return 0;
+}
+
+
+static void filter_debug_print(token_t *toks, token_t **tok_ptrs, int ntoks)
+{
+    int i;
+    for (i=0; i<ntoks; i++)
+    {
+        token_t *tok = toks ? &toks[i] : tok_ptrs[i];
+        if ( tok->tok_type==TOK_VAL )
+        {
+            if ( tok->key )
+                fprintf(bcftools_stderr,"%s", tok->key);
+            else if ( tok->tag )
+                fprintf(bcftools_stderr,"%s", tok->tag);
+            else
+                fprintf(bcftools_stderr,"%e", tok->threshold);
+        }
+        else
+            fprintf(bcftools_stderr,"%c", TOKEN_STRING[tok->tok_type]);
+        if ( tok->setter ) fprintf(bcftools_stderr,"\t[setter %p]", tok->setter);
+        fprintf(bcftools_stderr,"\n");
+    }
+}
+
+static void str_to_lower(char *str)
+{
+    while ( *str ) { *str = tolower(*str); str++; }
+}
+static int perl_exec(filter_t *flt, bcf1_t *line, token_t *rtok, token_t **stack, int nstack)
+{
+#if ENABLE_PERL_FILTERS
+
+    PerlInterpreter *perl = flt->perl;
+    if ( !perl ) error("Error: perl expression without a perl script name\n");
+
+    dSP;
+    ENTER;
+    SAVETMPS;
+
+    PUSHMARK(SP);
+    int i,j, istack = nstack - rtok->nargs;
+    for (i=istack+1; i<nstack; i++)
+    {
+        token_t *tok = stack[i];
+        if ( tok->is_str )
+            XPUSHs(sv_2mortal(newSVpvn(tok->str_value.s,tok->str_value.l)));
+        else if ( tok->nvalues==1 )
+            XPUSHs(sv_2mortal(newSVnv(tok->values[0])));
+        else if ( tok->nvalues>1 )
+        {
+            AV *av = newAV();
+            for (j=0; j<tok->nvalues; j++) av_push(av, newSVnv(tok->values[j]));
+            SV *rv = newRV_inc((SV*)av);
+            XPUSHs(rv);
+        }
+        else
+        {
+            bcf_double_set_missing(tok->values[0]);
+            XPUSHs(sv_2mortal(newSVnv(tok->values[0])));
+        }
+    }
+    PUTBACK;
+
+    // A possible future todo: provide a means to select samples and indexes,
+    // expressions like this don't work yet
+    //          perl.filter(FMT/AD)[1:0]
+
+    int nret = call_pv(stack[istack]->str_value.s, G_ARRAY);
+
+    SPAGAIN;
+
+    rtok->nvalues = nret;
+    hts_expand(double, rtok->nvalues, rtok->mvalues, rtok->values);
+    for (i=nret; i>0; i--)
+    {
+        rtok->values[i-1] = (double) POPn;
+        if ( isnan(rtok->values[i-1]) ) bcf_double_set_missing(rtok->values[i-1]);
+    }
+
+    PUTBACK;
+    FREETMPS;
+    LEAVE;
+
+#else
+    error("\nPerl filtering requires running `configure --enable-perl-filters` at compile time.\n\n");
+#endif
+    return rtok->nargs;
+}
+static void perl_init(filter_t *filter, char **str)
+{
+    char *beg = *str;
+    while ( *beg && isspace(*beg) ) beg++;
+    if ( !*beg ) return;
+    if ( strncasecmp("perl:", beg, 5) ) return;
+#if ENABLE_PERL_FILTERS
+    beg += 5;
+    char *end = beg;
+    while ( *end && *end!=';' ) end++;  // for now not escaping semicolons
+    *str = end+1;
+
+    if ( ++filter_ninit == 1 )
+    {
+        // must be executed only once, even for multiple filters; first time here
+        int argc = 0;
+        char **argv = NULL;
+        char **env  = NULL;
+        PERL_SYS_INIT3(&argc, &argv, &env);
+    }
+
+    filter->perl = perl_alloc();
+    PerlInterpreter *perl = filter->perl;
+
+    if ( !perl ) error("perl_alloc failed\n");
+    perl_construct(perl);
+
+    // name of the perl script to run
+    char *rmme = (char*) calloc(end - beg + 1,1);
+    memcpy(rmme, beg, end - beg);
+    char *argv[] = { "", "" };
+    argv[1] = expand_path(rmme);
+    free(rmme);
+
+    PL_origalen = 1;    // don't allow $0 change
+    int ret = perl_parse(filter->perl, NULL, 2, argv, NULL);
+    PL_exit_flags |= PERL_EXIT_DESTRUCT_END;
+    if ( ret ) error("Failed to parse: %s\n", argv[1]);
+    free(argv[1]);
+
+    perl_run(perl);
+#else
+    error("\nPerl filtering requires running `configure --enable-perl-filters` at compile time.\n\n");
+#endif
+}
+static void perl_destroy(filter_t *filter)
+{
+#if ENABLE_PERL_FILTERS
+    if ( !filter->perl ) return;
+
+    PerlInterpreter *perl = filter->perl;
+    perl_destruct(perl);
+    perl_free(perl);
+    if ( --filter_ninit <= 0  )
+    {
+        // similarly to PERL_SYS_INIT3, can must be executed only once? todo: test
+        PERL_SYS_TERM();
+    }
+#endif
+}
+
+
+// Parse filter expression and convert to reverse polish notation. Dijkstra's shunting-yard algorithm
+filter_t *filter_init(bcf_hdr_t *hdr, const char *str)
+{
+    filter_t *filter = (filter_t *) calloc(1,sizeof(filter_t));
+    filter->str = strdup(str);
+    filter->hdr = hdr;
+    filter->max_unpack |= BCF_UN_STR;
+
+    int nops = 0, mops = 0;    // operators stack
+    int nout = 0, mout = 0;    // filter tokens, RPN
+    token_t *out = NULL;
+    token_t *ops = NULL;
+    char *tmp = filter->str;
+    perl_init(filter, &tmp);
+
+    int last_op = -1;
+    while ( *tmp )
+    {
+        int len, ret;
+        ret = filters_next_token(&tmp, &len);
+        if ( ret==-1 ) error("Missing quotes in: %s\n", str);
+
+        // fprintf(bcftools_stderr,"token=[%c] .. [%s] %d\n", TOKEN_STRING[ret], tmp, len);
+        // int i; for (i=0; i<nops; i++) fprintf(bcftools_stderr," .%c", TOKEN_STRING[ops[i].tok_type]); fprintf(bcftools_stderr,"\n");
+
+        if ( ret==TOK_LFT )         // left bracket
+        {
+            nops++;
+            hts_expand0(token_t, nops, mops, ops);
+            ops[nops-1].tok_type = ret;
+        }
+        else if ( ret==TOK_RGT )    // right bracket
+        {
+            while ( nops>0 && ops[nops-1].tok_type!=TOK_LFT )
+            {
+                nout++;
+                hts_expand0(token_t, nout, mout, out);
+                out[nout-1] = ops[nops-1];
+                memset(&ops[nops-1],0,sizeof(token_t));
+                nops--;
+            }
+            if ( nops<=0 ) error("Could not parse: %s\n", str);
+            memset(&ops[nops-1],0,sizeof(token_t));
+            nops--;
+        }
+        else if ( ret!=TOK_VAL )    // one of the operators
+        {
+            // detect unary minus: replace -value with -1*(value)
+            if ( ret==TOK_SUB && last_op!=TOK_VAL && last_op!=TOK_RGT )
+            {
+                nout++;
+                hts_expand0(token_t, nout, mout, out);
+                token_t *tok = &out[nout-1];
+                tok->tok_type  = TOK_VAL;
+                tok->hdr_id    = -1;
+                tok->pass_site = -1;
+                tok->threshold = -1.0;
+                tok->is_constant = 1;
+                ret = TOK_MULT;
+            }
+            else if ( ret == -TOK_FUNC )
+            {
+                // this is different from TOK_PERLSUB,TOK_BINOM in that the expression inside the
+                // brackets gets evaluated as normal expression
+                nops++;
+                hts_expand0(token_t, nops, mops, ops);
+                token_t *tok = &ops[nops-1];
+                tok->tok_type  = -ret;
+                tok->hdr_id    = -1;
+                tok->pass_site = -1;
+                tok->threshold = -1.0;
+                if ( !strncasecmp(tmp-len,"N_PASS",6) )
+                {
+                    filter->max_unpack |= BCF_UN_FMT;
+                    tok->func = func_npass;
+                    tok->tag = strdup("N_PASS");
+                }
+                else if ( !strncasecmp(tmp-len,"F_PASS",6) )
+                {
+                    filter->max_unpack |= BCF_UN_FMT;
+                    tok->func = func_npass;
+                    tok->tag = strdup("F_PASS");
+                }
+                else error("The function \"%s\" is not supported\n", tmp-len);
+                continue;
+            }
+            else if ( ret < 0 )     // variable number of arguments: TOK_PERLSUB,TOK_BINOM
+            {
+                ret = -ret;
+
+                tmp += len;
+                char *beg = tmp;
+                kstring_t rmme = {0,0,0};
+                int i, margs, nargs = 0;
+
+                if ( ret == TOK_PERLSUB )
+                {
+                    while ( *beg && ((isalnum(*beg) && !ispunct(*beg)) || *beg=='_') ) beg++;
+                    if ( *beg!='(' ) error("Could not parse the expression: %s\n", str);
+
+                    // the subroutine name
+                    kputc('"', &rmme);
+                    kputsn(tmp, beg-tmp, &rmme);
+                    kputc('"', &rmme);
+                    nout++;
+                    hts_expand0(token_t, nout, mout, out);
+                    filters_init1(filter, rmme.s, rmme.l, &out[nout-1]);
+                    nargs++;
+                }
+                char *end = beg;
+                while ( *end && *end!=')' ) end++;
+                if ( !*end ) error("Could not parse the expression: %s\n", str);
+
+                // subroutine arguments
+                rmme.l = 0;
+                kputsn(beg+1, end-beg-1, &rmme);
+                char **rmme_list = hts_readlist(rmme.s, 0, &margs);
+                for (i=0; i<margs; i++)
+                {
+                    nargs++;
+                    nout++;
+                    hts_expand0(token_t, nout, mout, out);
+                    filters_init1(filter, rmme_list[i], strlen(rmme_list[i]), &out[nout-1]);
+                    free(rmme_list[i]);
+                }
+                free(rmme_list);
+                free(rmme.s);
+
+                nout++;
+                hts_expand0(token_t, nout, mout, out);
+                token_t *tok = &out[nout-1];
+                tok->tok_type  = ret;
+                tok->nargs     = nargs;
+                tok->hdr_id    = -1;
+                tok->pass_site = -1;
+                tok->threshold = -1.0;
+
+                tmp = end + 1;
+                continue;
+            }
+            else
+            {
+                while ( nops>0 && op_prec[ret] < op_prec[ops[nops-1].tok_type] )
+                {
+                    nout++;
+                    hts_expand0(token_t, nout, mout, out);
+                    out[nout-1] = ops[nops-1];
+                    memset(&ops[nops-1],0,sizeof(token_t));
+                    nops--;
+                }
+            }
+            nops++;
+            hts_expand0(token_t, nops, mops, ops);
+            ops[nops-1].tok_type = ret;
+        }
+        else if ( !len )
+        {
+            if ( *tmp && !isspace(*tmp) ) error("Could not parse the expression: [%s]\n", str);
+            break;     // all tokens read
+        }
+        else           // annotation name or filtering value
+        {
+            nout++;
+            hts_expand0(token_t, nout, mout, out);
+            if ( tmp[len-1]==',' )
+                filters_init1(filter, tmp, len-1, &out[nout-1]);
+            else
+                filters_init1(filter, tmp, len, &out[nout-1]);
+            tmp += len;
+        }
+        last_op = ret;
+    }
+    while ( nops>0 )
+    {
+        if ( ops[nops-1].tok_type==TOK_LFT || ops[nops-1].tok_type==TOK_RGT ) error("Could not parse the expression: [%s]\n", filter->str);
+        nout++;
+        hts_expand0(token_t, nout, mout, out);
+        out[nout-1] = ops[nops-1];
+        memset(&ops[nops-1],0,sizeof(token_t));
+        nops--;
+    }
+
+    // In the special cases of TYPE and FILTER the BCF header IDs are yet unknown. Walk through the
+    // list of operators and convert the strings (e.g. "PASS") to BCF ids. The string value token must be
+    // just before or after the FILTER token and they must be followed with a comparison operator.
+    // At this point we also initialize regex expressions which, in RPN, must preceed the LIKE/NLIKE operator.
+    // Additionally, treat "." as missing value rather than a string in numeric equalities; that
+    // @file is only used with ID; etc.
+    // This code is fragile: improve me.
+    static int comma_separator_warned = 0;
+    int i;
+    for (i=0; i<nout; i++)
+    {
+        if ( i+1<nout && (out[i].tok_type==TOK_LT || out[i].tok_type==TOK_BT) && out[i+1].tok_type==TOK_EQ )
+            error("Error parsing the expression: \"%s\"\n", filter->str);
+
+        if ( out[i].hash )
+        {
+            int j = out[i+1].tok_type==TOK_VAL ? i+1 : i-1;
+            if ( out[j].comparator!=filters_cmp_id )
+                error("Error: could not parse the expression. Note that the \"@file_name\" syntax can be currently used with ID column only.\n");
+        }
+        if ( out[i].tok_type==TOK_OR || out[i].tok_type==TOK_OR_VEC )
+            out[i].func = vector_logic_or;
+        if ( out[i].tok_type==TOK_AND || out[i].tok_type==TOK_AND_VEC )
+            out[i].func = vector_logic_and;
+        if ( out[i].tok_type==TOK_EQ || out[i].tok_type==TOK_NE )
+        {
+            // Look for j="." and k numeric type
+            int j = i-1, k = i-2;
+            if ( !out[j].is_str ) { k = i-1, j = i-2; }
+            if ( out[j].is_str && out[j].key && !strcmp(".",out[j].key) )
+            {
+                int set_missing = 0;
+                if ( out[k].hdr_id>0 )
+                {
+                    int type = bcf_hdr_id2type(filter->hdr,out[k].tag_type,out[k].hdr_id);
+                    if ( type==BCF_HT_INT ) set_missing = 1;
+                    else if ( type==BCF_HT_REAL ) set_missing = 1;
+                }
+                else if ( !strcmp("QUAL",out[k].tag) ) set_missing = 1;
+                if ( set_missing ) { out[j].is_str = 0; out[j].is_missing = 1; bcf_double_set_missing(out[j].values[0]); }
+            }
+        }
+        if ( out[i].tok_type==TOK_LIKE || out[i].tok_type==TOK_NLIKE )
+        {
+            int j = i-1;
+            if ( !out[j].key )
+                error("Could not parse the expression, wrong value for regex operator: %s\n", filter->str);
+            out[j].regex = (regex_t *) malloc(sizeof(regex_t));
+            int cflags = REG_NOSUB;
+            int len = strlen(out[j].key);
+            if ( len>2 && out[j].key[len-1]=='i' && out[j].key[len-2]=='/' && out[j].key[len-3]!='\\'  )
+            {
+                out[j].key[len-2] = 0;
+                cflags |= REG_ICASE;
+            }
+            if ( regcomp(out[j].regex, out[j].key, cflags) )
+                error("Could not compile the regex expression \"%s\": %s\n", out[j].key,filter->str);
+        }
+        if ( out[i].is_str && out[i].tok_type==TOK_VAL && out[i].key && strchr(out[i].key,',') )
+        {
+            int print_note = 0;
+            if ( out[i+1].tok_type==TOK_EQ || (out[i+1].is_str && out[i+2].tok_type==TOK_EQ) ) print_note = 1;
+            else if ( out[i+1].tok_type==TOK_NE || (out[i+1].is_str && out[i+2].tok_type==TOK_NE) ) print_note = 1;
+            if ( print_note && !comma_separator_warned )
+            {
+                comma_separator_warned = 1;
+                fprintf(bcftools_stderr,
+                    "Warning: comma is interpreted as a separator and OR logic is used in string comparisons.\n"
+                    "         (Search the manual for \"Comma in strings\" to learn more.)\n");
+            }
+        }
+        if ( out[i].tok_type!=TOK_VAL ) continue;
+        if ( !out[i].tag ) continue;
+        if ( out[i].setter==filters_set_type )
+        {
+            if ( i+1==nout ) error("Could not parse the expression: %s\n", filter->str);
+            int itok, ival;
+            if ( out[i+1].tok_type==TOK_EQ || out[i+1].tok_type==TOK_NE ) ival = i - 1, itok = i + 1;
+            else if ( out[i+1].tok_type==TOK_LIKE || out[i+1].tok_type==TOK_NLIKE ) ival = i - 1, itok = i + 1;
+            else if ( out[i+2].tok_type==TOK_EQ || out[i+2].tok_type==TOK_NE ) itok = i + 2, ival = i + 1;
+            else if ( out[i+2].tok_type==TOK_LIKE || out[i+2].tok_type==TOK_NLIKE ) itok = i + 2, ival = i + 1;
+            else error("[%s:%d %s] Could not parse the expression: %s\n",  __FILE__,__LINE__,__FUNCTION__, filter->str);
+            if ( !strcasecmp(out[ival].key,"snp") || !strcasecmp(out[ival].key,"snps") ) { out[ival].threshold = VCF_SNP<<1; out[ival].is_str = 0; }
+            else if ( !strcasecmp(out[ival].key,"indel") || !strcasecmp(out[ival].key,"indels") ) { out[ival].threshold = VCF_INDEL<<1; out[ival].is_str = 0; }
+            else if ( !strcasecmp(out[ival].key,"mnp") || !strcasecmp(out[ival].key,"mnps") ) { out[ival].threshold = VCF_MNP<<1; out[ival].is_str = 0; }
+            else if ( !strcasecmp(out[ival].key,"other") ) { out[ival].threshold = VCF_OTHER<<1; out[ival].is_str = 0; }
+            else if ( !strcasecmp(out[ival].key,"bnd") ) { out[ival].threshold = VCF_BND<<1; out[ival].is_str = 0; }
+            else if ( !strcasecmp(out[ival].key,"overlap") ) { out[ival].threshold = VCF_OVERLAP<<1; out[ival].is_str = 0; }
+            else if ( !strcasecmp(out[ival].key,"ref") ) { out[ival].threshold = 1; out[ival].is_str = 0; }
+            else error("The type \"%s\" not recognised: %s\n", out[ival].key, filter->str);
+            out[ival].is_constant = 1;
+            if ( out[itok].tok_type==TOK_LIKE || out[itok].tok_type==TOK_NLIKE ) out[itok].comparator = filters_cmp_bit_and;
+            out[ival].tag = out[ival].key; out[ival].key = NULL;
+            i = itok;
+            continue;
+        }
+        if ( !strcmp(out[i].tag,"GT") )
+        {
+            if ( i+1==nout ) error("Could not parse the expression: %s\n", filter->str);
+            int ival;
+            if ( out[i+1].tok_type==TOK_EQ || out[i+1].tok_type==TOK_NE ) ival = i - 1;
+            else if ( out[i+1].tok_type==TOK_LIKE || out[i+1].tok_type==TOK_NLIKE ) ival = i - 1;
+            else if ( out[i+2].tok_type==TOK_EQ || out[i+2].tok_type==TOK_NE ) ival = i + 1;
+            else if ( out[i+2].tok_type==TOK_LIKE || out[i+2].tok_type==TOK_NLIKE ) ival = i + 1;
+            else error("[%s:%d %s] Could not parse the expression: %s\n",  __FILE__,__LINE__,__FUNCTION__, filter->str);
+
+            if ( !out[ival].key ) error("Comparison between samples is not supported, sorry!\n");
+
+            // assign correct setters and unify expressions, eg ar->ra, HOM->hom, etc
+            if ( !strcasecmp(out[ival].key,"hom") ) { out[i].setter = filters_set_genotype3;  str_to_lower(out[ival].key); }
+            else if ( !strcasecmp(out[ival].key,"het") ) { out[i].setter = filters_set_genotype3;  str_to_lower(out[ival].key); }
+            else if ( !strcasecmp(out[ival].key,"hap") ) { out[i].setter = filters_set_genotype3;  str_to_lower(out[ival].key); }
+            else if ( !strcasecmp(out[ival].key,"mis") ) { out[i].setter = filters_set_genotype4;  str_to_lower(out[ival].key); }
+            else if ( !strcasecmp(out[ival].key,"ref") ) { out[i].setter = filters_set_genotype4;  str_to_lower(out[ival].key); }
+            else if ( !strcasecmp(out[ival].key,"alt") ) { out[i].setter = filters_set_genotype4;  str_to_lower(out[ival].key); }
+            else if ( !strcasecmp(out[ival].key,"rr") ) { out[i].setter = filters_set_genotype2;  str_to_lower(out[ival].key); }
+            else if ( !strcasecmp(out[ival].key,"ra") || !strcasecmp(out[ival].key,"ar") ) { out[i].setter = filters_set_genotype2; out[ival].key[0]='r'; out[ival].key[1]='a'; }   // ra
+            else if ( !strcmp(out[ival].key,"aA") || !strcmp(out[ival].key,"Aa") ) { out[i].setter = filters_set_genotype2; out[ival].key[0]='a'; out[ival].key[1]='A'; }   // aA
+            else if ( !strcasecmp(out[ival].key,"aa") ) { out[i].setter = filters_set_genotype2; out[ival].key[0]='a'; out[ival].key[1]='a'; }  // aa
+            else if ( !strcasecmp(out[ival].key,"a") ) { out[i].setter = filters_set_genotype2; out[ival].key[0]='a'; out[ival].key[1]=0; }  // a
+            else if ( !strcasecmp(out[ival].key,"r") ) { out[i].setter = filters_set_genotype2; out[ival].key[0]='r'; out[ival].key[1]=0; }  // r
+            continue;
+        }
+        if ( out[i].tag_type==BCF_HL_FLT )
+        {
+            if ( i+1==nout ) error("Could not parse the expression: %s\n", filter->str);
+            int itok = i, ival;
+            if ( out[i+1].tok_type==TOK_EQ || out[i+1].tok_type==TOK_NE ) ival = i - 1;
+            else if ( out[i+1].tok_type==TOK_LIKE ) out[i+1].tok_type = TOK_IN, ival = i - 1;
+            else if ( out[i+1].tok_type==TOK_NLIKE ) out[i+1].tok_type = TOK_NOT_IN, ival = i - 1;
+            else if ( out[i+2].tok_type==TOK_EQ || out[i+2].tok_type==TOK_NE ) ival = ++i;
+            else if ( out[i+2].tok_type==TOK_LIKE ) out[i+2].tok_type = TOK_IN, ival = ++i;
+            else if ( out[i+2].tok_type==TOK_NLIKE ) out[i+2].tok_type = TOK_NOT_IN, ival = ++i;
+            else error("[%s:%d %s] Could not parse the expression: %s\n",  __FILE__,__LINE__,__FUNCTION__, filter->str);
+            if ( out[ival].tok_type!=TOK_VAL || !out[ival].key )
+                error("[%s:%d %s] Could not parse the expression, an unquoted string value perhaps? %s\n", __FILE__,__LINE__,__FUNCTION__, filter->str);
+            token_t *tok = &out[ival];
+            char *bp = tok->key;
+            tok->nvalues = 0;
+            int has_missing = 0;
+            while ( *bp )
+            {
+                char tmp, *ep = bp;
+                while ( *ep && *ep!=';' ) ep++;
+                tmp = *ep;
+                *ep = 0;
+                if ( !strcmp(".",bp) ) has_missing = 1;
+                else
+                {
+                    tok->nvalues++;
+                    hts_expand(double,tok->nvalues,tok->mvalues,tok->values);
+                    int id = bcf_hdr_id2int(filter->hdr, BCF_DT_ID, bp);
+                    if ( !bcf_hdr_idinfo_exists(filter->hdr,BCF_HL_FLT,id) )
+                        error("The filter \"%s\" not present in the VCF header\n", bp);
+                    tok->values[tok->nvalues-1] = id;
+                }
+                *ep = tmp;
+                if ( !tmp ) break;
+                bp = ep + 1;
+            }
+            if ( has_missing && tok->nvalues ) error("The FILTER expression cannot contain missing value AND filters: \"%s\" (%d)\n",tok->key,tok->nvalues);
+            out[ival].tag = tok->key;
+            tok->key = NULL;
+            out[itok].hdr_id = tok->hdr_id;
+            continue;
+        }
+    }
+    filter->nsamples = filter->max_unpack&BCF_UN_FMT ? bcf_hdr_nsamples(filter->hdr) : 0;
+    for (i=0; i<nout; i++)
+    {
+        if ( out[i].tok_type==TOK_MAX )      { out[i].func = func_max; out[i].tok_type = TOK_FUNC; }
+        else if ( out[i].tok_type==TOK_MIN ) { out[i].func = func_min; out[i].tok_type = TOK_FUNC; }
+        else if ( out[i].tok_type==TOK_AVG ) { out[i].func = func_avg; out[i].tok_type = TOK_FUNC; }
+        else if ( out[i].tok_type==TOK_MEDIAN ) { out[i].func = func_median; out[i].tok_type = TOK_FUNC; }
+        else if ( out[i].tok_type==TOK_AVG ) { out[i].func = func_avg; out[i].tok_type = TOK_FUNC; }
+        else if ( out[i].tok_type==TOK_STDEV ) { out[i].func = func_stddev; out[i].tok_type = TOK_FUNC; }
+        else if ( out[i].tok_type==TOK_SUM ) { out[i].func = func_sum; out[i].tok_type = TOK_FUNC; }
+        else if ( out[i].tok_type==TOK_ABS ) { out[i].func = func_abs; out[i].tok_type = TOK_FUNC; }
+        else if ( out[i].tok_type==TOK_CNT ) { out[i].func = func_count; out[i].tok_type = TOK_FUNC; }
+        else if ( out[i].tok_type==TOK_LEN ) { out[i].func = func_strlen; out[i].tok_type = TOK_FUNC; }
+        else if ( out[i].tok_type==TOK_PHRED ) { out[i].func = func_phred; out[i].tok_type = TOK_FUNC; }
+        else if ( out[i].tok_type==TOK_BINOM ) { out[i].func = func_binom; out[i].tok_type = TOK_FUNC; }
+        else if ( out[i].tok_type==TOK_PERLSUB ) { out[i].func = perl_exec; out[i].tok_type = TOK_FUNC; }
+        else if ( out[i].tok_type==TOK_sMAX ) { out[i].func = func_smpl_max; out[i].tok_type = TOK_FUNC; }
+        else if ( out[i].tok_type==TOK_sMIN ) { out[i].func = func_smpl_min; out[i].tok_type = TOK_FUNC; }
+        else if ( out[i].tok_type==TOK_sAVG ) { out[i].func = func_smpl_avg; out[i].tok_type = TOK_FUNC; }
+        else if ( out[i].tok_type==TOK_sMEDIAN ) { out[i].func = func_smpl_median; out[i].tok_type = TOK_FUNC; }
+        else if ( out[i].tok_type==TOK_sSTDEV ) { out[i].func = func_smpl_stddev; out[i].tok_type = TOK_FUNC; }
+        else if ( out[i].tok_type==TOK_sSUM ) { out[i].func = func_smpl_sum; out[i].tok_type = TOK_FUNC; }
+        hts_expand0(double,1,out[i].mvalues,out[i].values);
+        if ( filter->nsamples )
+        {
+            out[i].pass_samples = (uint8_t*)malloc(filter->nsamples);
+            int j;
+            for (j=0; j<filter->nsamples; j++) out[i].pass_samples[j] = 0;
+        }
+    }
+
+    if (0) filter_debug_print(out, NULL, nout);
+
+    if ( mops ) free(ops);
+    filter->filters   = out;
+    filter->nfilters  = nout;
+    filter->flt_stack = (token_t **)malloc(sizeof(token_t*)*nout);
+    return filter;
+}
+
+void filter_destroy(filter_t *filter)
+{
+    perl_destroy(filter);
+    int i;
+    for (i=0; i<filter->nfilters; i++)
+    {
+        if ( filter->filters[i].key ) free(filter->filters[i].key);
+        free(filter->filters[i].str_value.s);
+        free(filter->filters[i].tag);
+        free(filter->filters[i].idxs);
+        free(filter->filters[i].usmpl);
+        free(filter->filters[i].values);
+        free(filter->filters[i].pass_samples);
+        if (filter->filters[i].hash) khash_str2int_destroy_free(filter->filters[i].hash);
+        if (filter->filters[i].regex)
+        {
+            regfree(filter->filters[i].regex);
+            free(filter->filters[i].regex);
+        }
+    }
+    free(filter->filters);
+    free(filter->flt_stack);
+    free(filter->str);
+    free(filter->tmpi);
+    free(filter->tmpf);
+    free(filter->tmps.s);
+    free(filter);
+}
+
+int filter_test(filter_t *filter, bcf1_t *line, const uint8_t **samples)
+{
+    bcf_unpack(line, filter->max_unpack);
+
+    int i, nstack = 0;
+    for (i=0; i<filter->nfilters; i++)
+    {
+        filter->filters[i].pass_site = 0;
+        if ( filter->filters[i].tok_type == TOK_VAL )
+        {
+            if ( filter->filters[i].setter )    // variable, query the VCF line
+                filter->filters[i].setter(filter, line, &filter->filters[i]);
+            else if ( filter->filters[i].key )  // string constant
+            {
+                filter->filters[i].str_value.l = 0;
+                kputs(filter->filters[i].key, &filter->filters[i].str_value);
+                filter->filters[i].nvalues = filter->filters[i].str_value.l;
+            }
+            else if ( filter->filters[i].is_constant )   // numeric constant
+            {
+                filter->filters[i].values[0] = filter->filters[i].threshold;
+                filter->filters[i].nvalues   = 1;
+            }
+            filter->flt_stack[nstack++] = &filter->filters[i];
+            continue;
+        }
+        else if ( filter->filters[i].func )
+        {
+            int nargs = filter->filters[i].func(filter, line, &filter->filters[i], filter->flt_stack, nstack);
+            filter->flt_stack[nstack-nargs] = &filter->filters[i];
+            if ( --nargs > 0 ) nstack -= nargs;
+            continue;
+        }
+        if ( nstack<2 )
+            error("Error occurred while processing the filter \"%s\" (1:%d)\n", filter->str,nstack);  // too few values left on the stack
+
+        int is_str  = filter->flt_stack[nstack-1]->is_str + filter->flt_stack[nstack-2]->is_str;
+
+        if ( filter->filters[i].tok_type == TOK_ADD )
+        {
+            VECTOR_ARITHMETICS(filter->flt_stack[nstack-2],filter->flt_stack[nstack-1],&filter->filters[i],+,(double));
+            filter->flt_stack[nstack-2] = &filter->filters[i];
+            nstack--;
+            continue;
+        }
+        else if ( filter->filters[i].tok_type == TOK_SUB )
+        {
+            VECTOR_ARITHMETICS(filter->flt_stack[nstack-2],filter->flt_stack[nstack-1],&filter->filters[i],-,(double));
+            filter->flt_stack[nstack-2] = &filter->filters[i];
+            nstack--;
+            continue;
+        }
+        else if ( filter->filters[i].tok_type == TOK_MULT )
+        {
+            VECTOR_ARITHMETICS(filter->flt_stack[nstack-2],filter->flt_stack[nstack-1],&filter->filters[i],*,(double));
+            filter->flt_stack[nstack-2] = &filter->filters[i];
+            nstack--;
+            continue;
+        }
+        else if ( filter->filters[i].tok_type == TOK_DIV )
+        {
+            VECTOR_ARITHMETICS(filter->flt_stack[nstack-2],filter->flt_stack[nstack-1],&filter->filters[i],/,(double));
+            filter->flt_stack[nstack-2] = &filter->filters[i];
+            nstack--;
+            continue;
+        }
+        else if ( filter->filters[i].tok_type == TOK_MODULO )
+        {
+            VECTOR_ARITHMETICS(filter->flt_stack[nstack-2],filter->flt_stack[nstack-1],&filter->filters[i],%,(int));
+            filter->flt_stack[nstack-2] = &filter->filters[i];
+            nstack--;
+            continue;
+        }
+
+        // ideally, these comparators would become func, but this would require more work in init1()
+        if ( filter->filters[i].comparator )
+        {
+            filter->filters[i].comparator(filter->flt_stack[nstack-1],filter->flt_stack[nstack-2],&filter->filters[i],line);
+        }
+        else if ( filter->flt_stack[nstack-1]->comparator )
+        {
+            filter->flt_stack[nstack-1]->comparator(filter->flt_stack[nstack-1],filter->flt_stack[nstack-2],&filter->filters[i],line);
+        }
+        else if ( filter->flt_stack[nstack-2]->comparator )
+        {
+            filter->flt_stack[nstack-2]->comparator(filter->flt_stack[nstack-2],filter->flt_stack[nstack-1],&filter->filters[i],line);
+        }
+        else if ( is_str==2 )
+        {
+            cmp_vector_strings(filter->flt_stack[nstack-2],filter->flt_stack[nstack-1],&filter->filters[i]);
+        }
+        else
+        {
+            if ( is_str==1 ) error("Error: cannot use arithmetic operators to compare strings and numbers\n");
+
+            // Determine what to do with one [1] or both [2] sides missing. The first field [0] gives [1]|[2]
+            int missing_logic[] = {0,0,0};
+            if ( filter->filters[i].tok_type == TOK_EQ ) { missing_logic[0] = missing_logic[2] = 1; }
+            if ( filter->filters[i].tok_type == TOK_NE ) { missing_logic[0] = missing_logic[1] = 1; }
+
+            if ( filter->filters[i].tok_type == TOK_EQ )
+                CMP_VECTORS(filter->flt_stack[nstack-2],filter->flt_stack[nstack-1],&filter->filters[i],==,missing_logic)
+            else if ( filter->filters[i].tok_type == TOK_NE )
+                CMP_VECTORS(filter->flt_stack[nstack-2],filter->flt_stack[nstack-1],&filter->filters[i],!=,missing_logic)
+            else if ( filter->filters[i].tok_type == TOK_LE )
+                CMP_VECTORS(filter->flt_stack[nstack-2],filter->flt_stack[nstack-1],&filter->filters[i],<=,missing_logic)
+            else if ( filter->filters[i].tok_type == TOK_LT )
+                CMP_VECTORS(filter->flt_stack[nstack-2],filter->flt_stack[nstack-1],&filter->filters[i],<,missing_logic)
+            else if ( filter->filters[i].tok_type == TOK_BT )
+                CMP_VECTORS(filter->flt_stack[nstack-2],filter->flt_stack[nstack-1],&filter->filters[i],>,missing_logic)
+            else if ( filter->filters[i].tok_type == TOK_BE )
+                CMP_VECTORS(filter->flt_stack[nstack-2],filter->flt_stack[nstack-1],&filter->filters[i],>=,missing_logic)
+            else
+                error("todo: %s:%d .. type=%d\n", __FILE__,__LINE__,filter->filters[i].tok_type);
+        }
+        filter->flt_stack[nstack-2] = &filter->filters[i];
+        nstack--;
+    }
+    if ( nstack>1 ) error("Error occurred while processing the filter \"%s\" (2:%d)\n", filter->str,nstack);    // too few values left on the stack
+    if ( samples )
+    {
+        *samples = filter->max_unpack&BCF_UN_FMT ? filter->flt_stack[0]->pass_samples : NULL;
+        if ( *samples && !filter->flt_stack[0]->nsamples )
+        {
+            for (i=0; i<filter->nsamples; i++)
+                filter->flt_stack[0]->pass_samples[i] = filter->flt_stack[0]->pass_site;
+        }
+    }
+    return filter->flt_stack[0]->pass_site;
+}
+
+int filter_max_unpack(filter_t *flt)
+{
+    return flt->max_unpack;
+}
+
+const double *filter_get_doubles(filter_t *filter, int *nval, int *nval1)
+{
+    token_t *tok = filter->flt_stack[0];
+    if ( tok->nvalues )
+    {
+        *nval  = tok->nvalues;
+        *nval1 = tok->nval1;
+    }
+    else
+    {
+        if ( !tok->values ) error("fixme in filter_get_doubles(): %s\n", filter->str);
+        *nval  = 1;
+        *nval1 = 1;
+        tok->values[0] = filter->flt_stack[0]->pass_site;
+    }
+    return tok->values;
+}
+
+void filter_set_samples(filter_t *filter, const uint8_t *samples)
+{
+    int i,j;
+    for (i=0; i<filter->nfilters; i++)
+    {
+        if ( !filter->filters[i].nsamples ) continue;
+        for (j=0; j<filter->filters[i].nsamples; j++) filter->filters[i].usmpl[j] = samples[j];
+    }
+}
+
diff --git a/bcftools/filter.h b/bcftools/filter.h
new file mode 100644
index 0000000..243e3b6
--- /dev/null
+++ b/bcftools/filter.h
@@ -0,0 +1,64 @@
+/*  filter.h -- filter expressions.
+
+    Copyright (C) 2013-2021 Genome Research Ltd.
+
+    Author: Petr Danecek <pd3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.  */
+
+#ifndef __FILTER_H__
+#define __FILTER_H__
+
+#include <htslib/vcf.h>
+
+typedef struct _filter_t filter_t;
+
+/**
+  *  @hdr:  BCF header file
+  *  @str:  see the bcftools filter command help for description
+  */
+filter_t *filter_init(bcf_hdr_t *hdr, const char *str);
+
+void filter_destroy(filter_t *filter);
+
+/**
+  *  filter_test() - test whether the BCF record passes the test
+  *  @samples:  if not NULL, a pointer to an array with samples statuses is
+  *             stored in the location referenced by @samples. The pointer
+  *             will be set to NULL if the FORMAT fields were not queried.
+  *  Returns 1 if the expression is true and 0 if false.
+  */
+int filter_test(filter_t *filter, bcf1_t *rec, const uint8_t **samples);
+
+/**
+  *  filter_set_samples() - restrict filtering expression to samples.
+  *             Call after filter_init().
+  *  @samples:  use samples set to 1, ignore samples set 0
+  */
+void filter_set_samples(filter_t *filter, const uint8_t *samples);
+
+/**
+  *  filter_get_doubles() - return a pointer to values from the last filter_test() evaluation
+  */
+const double *filter_get_doubles(filter_t *filter, int *nval, int *nval1);
+
+void filter_expression_info(FILE *fp);
+int filter_max_unpack(filter_t *filter);
+
+#endif
diff --git a/bcftools/gvcf.c b/bcftools/gvcf.c
new file mode 100644
index 0000000..c7b2e77
--- /dev/null
+++ b/bcftools/gvcf.c
@@ -0,0 +1,227 @@
+/*  gvcf.c -- support for gVCF files.
+
+    Copyright (C) 2014-2015 Genome Research Ltd.
+
+    Author: Petr Danecek <pd3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include "gvcf.h"
+#include "bcftools.h"
+
+struct _gvcf_t
+{
+    int *dp_range, ndp_range;   // per-sample DP ranges
+    int prev_range;             // 0 if not in a block
+    int32_t *dp, mdp, *pl, mpl, npl;
+    int32_t *tmp, mtmp, *gts, ngts,mgts, nqsum,mqsum;
+    float *qsum;
+    int32_t rid, start, end, min_dp;
+    kstring_t als;
+    bcf1_t *line;
+};
+
+void gvcf_update_header(gvcf_t *gvcf, bcf_hdr_t *hdr)
+{
+    bcf_hdr_append(hdr,"##INFO=<ID=END,Number=1,Type=Integer,Description=\"End position of the variant described in this record\">");
+    bcf_hdr_append(hdr,"##INFO=<ID=MinDP,Number=1,Type=Integer,Description=\"Minimum per-sample depth in this gVCF block\">");
+}
+
+gvcf_t *gvcf_init(const char *dp_ranges)
+{
+    gvcf_t *gvcf = (gvcf_t*) calloc(1,sizeof(gvcf_t));
+    gvcf->line = bcf_init();
+
+    int n = 1;
+    const char *ss = dp_ranges;
+    while ( *ss )
+    {
+        if ( *ss==',' ) n++;
+        ss++;
+    }
+    gvcf->ndp_range = n;
+    gvcf->dp_range  = (int*) malloc(sizeof(int)*gvcf->ndp_range);
+
+    n  = 0;
+    ss = dp_ranges;
+    while ( *ss )
+    {
+        char *se = (char*) ss;
+        gvcf->dp_range[n++] = strtol(ss,&se,10);
+        if ( se==ss ) return NULL;
+        if ( *se==',' && se[1] ) { ss = se+1; continue; }
+        else if ( !*se ) break;
+        return NULL;
+    }
+    return gvcf;
+}
+
+void gvcf_destroy(gvcf_t *gvcf)
+{
+    free(gvcf->dp_range);
+    free(gvcf->dp);
+    free(gvcf->pl);
+    free(gvcf->tmp);
+    free(gvcf->qsum);
+    free(gvcf->gts);
+    free(gvcf->als.s);
+    if ( gvcf->line ) bcf_destroy(gvcf->line);
+    free(gvcf);
+}
+
+bcf1_t *gvcf_write(gvcf_t *gvcf, htsFile *fh, bcf_hdr_t *hdr, bcf1_t *rec, int is_ref)
+{
+    int i, ret, nsmpl = bcf_hdr_nsamples(hdr);
+    int can_collapse = is_ref ? 1 : 0;
+    int32_t dp_range = 0, min_dp = 0;
+
+    // No record and nothing to flush?
+    if ( !rec && !gvcf->prev_range ) return NULL;
+
+    // Flush gVCF block if there are no more records, chr changed, a gap
+    // encountered, or other conditions not met (block broken by a non-ref or DP too low).
+    int needs_flush = can_collapse ? 0 : 1;
+
+
+    // Can the record be included in a gVCF block? That is, is this a ref-only site?
+    if ( rec && can_collapse )
+    {
+        bcf_unpack(rec, BCF_UN_ALL);
+
+        // per-sample depth
+        ret = bcf_get_format_int32(hdr, rec, "DP", &gvcf->tmp, &gvcf->mtmp);
+        if ( ret==nsmpl )
+        {
+            min_dp = gvcf->tmp[0];
+            for (i=1; i<nsmpl; i++)
+                if ( min_dp > gvcf->tmp[i] ) min_dp = gvcf->tmp[i];
+
+            for (i=0; i<gvcf->ndp_range; i++)
+                if ( min_dp < gvcf->dp_range[i] ) break;
+
+            dp_range = i;
+            if ( !dp_range )
+            {
+                // leave the record unchanged, DP is too small. Alternatively, return NULL here
+                // to skip these sites
+                needs_flush  = 1;
+                can_collapse = 0;
+            }
+        }
+        else
+            needs_flush = 1;       // DP field not present
+    }
+
+    if ( gvcf->prev_range && gvcf->prev_range!=dp_range ) needs_flush = 1;
+    if ( !rec || gvcf->rid!=rec->rid || rec->pos > gvcf->end+1 ) needs_flush = 1;
+
+    // If prev_range is set, something can be flushed
+    if ( gvcf->prev_range && needs_flush )
+    {
+        // mpileup can output two records with the same position, SNP and
+        // indel. Make sure the end position does not include the non-variant
+        // SNP position just before the indel.
+        if ( rec && rec->rid==gvcf->rid && rec->pos==gvcf->end ) gvcf->end--;
+
+        gvcf->end++;    // from 0-based to 1-based coordinate
+
+        bcf_clear1(gvcf->line);
+        gvcf->line->rid  = gvcf->rid;
+        gvcf->line->pos  = gvcf->start;
+        gvcf->line->rlen = gvcf->end - gvcf->start;
+        bcf_update_alleles_str(hdr, gvcf->line, gvcf->als.s);
+        if ( gvcf->start+1 < gvcf->end )    // create gVCF record only if it spans at least two sites
+            bcf_update_info_int32(hdr, gvcf->line, "END", &gvcf->end, 1);
+        bcf_update_info_int32(hdr, gvcf->line, "MinDP", &gvcf->min_dp, 1);
+        if ( gvcf->nqsum>0 )
+            bcf_update_info_float(hdr, gvcf->line, "QS", gvcf->qsum, gvcf->nqsum);
+        if ( gvcf->ngts )
+            bcf_update_genotypes(hdr,gvcf->line,gvcf->gts,gvcf->ngts);
+        if ( gvcf->npl>0 )
+            bcf_update_format_int32(hdr, gvcf->line, "PL", gvcf->pl, gvcf->npl);
+        bcf_update_format_int32(hdr, gvcf->line, "DP", gvcf->dp, nsmpl);
+        if ( bcf_write1(fh, hdr, gvcf->line)!=0 ) error("[%s] Error: failed to write the record\n", __func__);
+        gvcf->prev_range = 0;
+        gvcf->rid  = -1;
+        gvcf->npl  = 0;
+        gvcf->nqsum = 0;
+        gvcf->ngts  = 0;
+
+        if ( !rec ) return NULL;     // just flushing the buffer, this was last record
+    }
+
+    if ( can_collapse )
+    {
+        if ( !gvcf->prev_range )
+        {
+            hts_expand(int32_t,nsmpl,gvcf->mdp,gvcf->dp);
+            memcpy(gvcf->dp,gvcf->tmp,nsmpl*sizeof(int32_t));   // tmp still contains DP from rec
+            gvcf->npl = bcf_get_format_int32(hdr, rec, "PL", &gvcf->pl, &gvcf->mpl);
+
+            gvcf->nqsum = bcf_get_info_float(hdr,rec,"QS",&gvcf->qsum,&gvcf->mqsum);
+            gvcf->ngts  = bcf_get_genotypes(hdr,rec,&gvcf->gts,&gvcf->mgts);
+
+            gvcf->rid    = rec->rid;
+            gvcf->start  = rec->pos;
+            gvcf->als.l = 0;
+            kputs(rec->d.allele[0],&gvcf->als);
+            for (i=1; i<rec->n_allele; i++)
+            {
+                kputc(',',&gvcf->als);
+                kputs(rec->d.allele[i],&gvcf->als);
+            }
+            gvcf->min_dp = min_dp;
+        }
+        else
+        {
+            if ( gvcf->min_dp > min_dp ) gvcf->min_dp = min_dp;
+            for (i=0; i<nsmpl; i++)
+                if ( gvcf->dp[i] > gvcf->tmp[i] ) gvcf->dp[i] = gvcf->tmp[i];
+            ret = bcf_get_format_int32(hdr, rec, "PL", &gvcf->tmp, &gvcf->mtmp);
+            if ( ret>=0 )
+            {
+                if ( ret!=nsmpl*3 ) error("Unexpected number of PL fields\n");
+                for (i=0; i<nsmpl; i++)
+                {
+                    if ( gvcf->pl[3*i+1] > gvcf->tmp[3*i+1] )
+                    {
+                        gvcf->pl[3*i+1] = gvcf->tmp[3*i+1];
+                        gvcf->pl[3*i+2] = gvcf->tmp[3*i+2];
+                    }
+                    else if ( gvcf->pl[3*i+1]==gvcf->tmp[3*i+1] && gvcf->pl[3*i+2] > gvcf->tmp[3*i+2] )
+                        gvcf->pl[3*i+2] = gvcf->tmp[3*i+2];
+                }
+            }
+            else
+                gvcf->npl = 0;
+        }
+        gvcf->prev_range = dp_range;
+        if ( bcf_get_info_int32(hdr,rec,"END",&gvcf->tmp,&gvcf->mtmp)==1 )
+            gvcf->end = gvcf->tmp[0] - 1;   // from 1-based to 0-based
+        else
+            gvcf->end = rec->pos;
+        return NULL;
+    }
+
+    if ( is_ref && min_dp )
+        bcf_update_info_int32(hdr, rec, "MinDP", &min_dp, 1);
+
+    return rec;
+}
+
diff --git a/bcftools/gvcf.c.pysam.c b/bcftools/gvcf.c.pysam.c
new file mode 100644
index 0000000..bd881f4
--- /dev/null
+++ b/bcftools/gvcf.c.pysam.c
@@ -0,0 +1,229 @@
+#include "bcftools.pysam.h"
+
+/*  gvcf.c -- support for gVCF files.
+
+    Copyright (C) 2014-2015 Genome Research Ltd.
+
+    Author: Petr Danecek <pd3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include "gvcf.h"
+#include "bcftools.h"
+
+struct _gvcf_t
+{
+    int *dp_range, ndp_range;   // per-sample DP ranges
+    int prev_range;             // 0 if not in a block
+    int32_t *dp, mdp, *pl, mpl, npl;
+    int32_t *tmp, mtmp, *gts, ngts,mgts, nqsum,mqsum;
+    float *qsum;
+    int32_t rid, start, end, min_dp;
+    kstring_t als;
+    bcf1_t *line;
+};
+
+void gvcf_update_header(gvcf_t *gvcf, bcf_hdr_t *hdr)
+{
+    bcf_hdr_append(hdr,"##INFO=<ID=END,Number=1,Type=Integer,Description=\"End position of the variant described in this record\">");
+    bcf_hdr_append(hdr,"##INFO=<ID=MinDP,Number=1,Type=Integer,Description=\"Minimum per-sample depth in this gVCF block\">");
+}
+
+gvcf_t *gvcf_init(const char *dp_ranges)
+{
+    gvcf_t *gvcf = (gvcf_t*) calloc(1,sizeof(gvcf_t));
+    gvcf->line = bcf_init();
+
+    int n = 1;
+    const char *ss = dp_ranges;
+    while ( *ss )
+    {
+        if ( *ss==',' ) n++;
+        ss++;
+    }
+    gvcf->ndp_range = n;
+    gvcf->dp_range  = (int*) malloc(sizeof(int)*gvcf->ndp_range);
+
+    n  = 0;
+    ss = dp_ranges;
+    while ( *ss )
+    {
+        char *se = (char*) ss;
+        gvcf->dp_range[n++] = strtol(ss,&se,10);
+        if ( se==ss ) return NULL;
+        if ( *se==',' && se[1] ) { ss = se+1; continue; }
+        else if ( !*se ) break;
+        return NULL;
+    }
+    return gvcf;
+}
+
+void gvcf_destroy(gvcf_t *gvcf)
+{
+    free(gvcf->dp_range);
+    free(gvcf->dp);
+    free(gvcf->pl);
+    free(gvcf->tmp);
+    free(gvcf->qsum);
+    free(gvcf->gts);
+    free(gvcf->als.s);
+    if ( gvcf->line ) bcf_destroy(gvcf->line);
+    free(gvcf);
+}
+
+bcf1_t *gvcf_write(gvcf_t *gvcf, htsFile *fh, bcf_hdr_t *hdr, bcf1_t *rec, int is_ref)
+{
+    int i, ret, nsmpl = bcf_hdr_nsamples(hdr);
+    int can_collapse = is_ref ? 1 : 0;
+    int32_t dp_range = 0, min_dp = 0;
+
+    // No record and nothing to flush?
+    if ( !rec && !gvcf->prev_range ) return NULL;
+
+    // Flush gVCF block if there are no more records, chr changed, a gap
+    // encountered, or other conditions not met (block broken by a non-ref or DP too low).
+    int needs_flush = can_collapse ? 0 : 1;
+
+
+    // Can the record be included in a gVCF block? That is, is this a ref-only site?
+    if ( rec && can_collapse )
+    {
+        bcf_unpack(rec, BCF_UN_ALL);
+
+        // per-sample depth
+        ret = bcf_get_format_int32(hdr, rec, "DP", &gvcf->tmp, &gvcf->mtmp);
+        if ( ret==nsmpl )
+        {
+            min_dp = gvcf->tmp[0];
+            for (i=1; i<nsmpl; i++)
+                if ( min_dp > gvcf->tmp[i] ) min_dp = gvcf->tmp[i];
+
+            for (i=0; i<gvcf->ndp_range; i++)
+                if ( min_dp < gvcf->dp_range[i] ) break;
+
+            dp_range = i;
+            if ( !dp_range )
+            {
+                // leave the record unchanged, DP is too small. Alternatively, return NULL here
+                // to skip these sites
+                needs_flush  = 1;
+                can_collapse = 0;
+            }
+        }
+        else
+            needs_flush = 1;       // DP field not present
+    }
+
+    if ( gvcf->prev_range && gvcf->prev_range!=dp_range ) needs_flush = 1;
+    if ( !rec || gvcf->rid!=rec->rid || rec->pos > gvcf->end+1 ) needs_flush = 1;
+
+    // If prev_range is set, something can be flushed
+    if ( gvcf->prev_range && needs_flush )
+    {
+        // mpileup can output two records with the same position, SNP and
+        // indel. Make sure the end position does not include the non-variant
+        // SNP position just before the indel.
+        if ( rec && rec->rid==gvcf->rid && rec->pos==gvcf->end ) gvcf->end--;
+
+        gvcf->end++;    // from 0-based to 1-based coordinate
+
+        bcf_clear1(gvcf->line);
+        gvcf->line->rid  = gvcf->rid;
+        gvcf->line->pos  = gvcf->start;
+        gvcf->line->rlen = gvcf->end - gvcf->start;
+        bcf_update_alleles_str(hdr, gvcf->line, gvcf->als.s);
+        if ( gvcf->start+1 < gvcf->end )    // create gVCF record only if it spans at least two sites
+            bcf_update_info_int32(hdr, gvcf->line, "END", &gvcf->end, 1);
+        bcf_update_info_int32(hdr, gvcf->line, "MinDP", &gvcf->min_dp, 1);
+        if ( gvcf->nqsum>0 )
+            bcf_update_info_float(hdr, gvcf->line, "QS", gvcf->qsum, gvcf->nqsum);
+        if ( gvcf->ngts )
+            bcf_update_genotypes(hdr,gvcf->line,gvcf->gts,gvcf->ngts);
+        if ( gvcf->npl>0 )
+            bcf_update_format_int32(hdr, gvcf->line, "PL", gvcf->pl, gvcf->npl);
+        bcf_update_format_int32(hdr, gvcf->line, "DP", gvcf->dp, nsmpl);
+        if ( bcf_write1(fh, hdr, gvcf->line)!=0 ) error("[%s] Error: failed to write the record\n", __func__);
+        gvcf->prev_range = 0;
+        gvcf->rid  = -1;
+        gvcf->npl  = 0;
+        gvcf->nqsum = 0;
+        gvcf->ngts  = 0;
+
+        if ( !rec ) return NULL;     // just flushing the buffer, this was last record
+    }
+
+    if ( can_collapse )
+    {
+        if ( !gvcf->prev_range )
+        {
+            hts_expand(int32_t,nsmpl,gvcf->mdp,gvcf->dp);
+            memcpy(gvcf->dp,gvcf->tmp,nsmpl*sizeof(int32_t));   // tmp still contains DP from rec
+            gvcf->npl = bcf_get_format_int32(hdr, rec, "PL", &gvcf->pl, &gvcf->mpl);
+
+            gvcf->nqsum = bcf_get_info_float(hdr,rec,"QS",&gvcf->qsum,&gvcf->mqsum);
+            gvcf->ngts  = bcf_get_genotypes(hdr,rec,&gvcf->gts,&gvcf->mgts);
+
+            gvcf->rid    = rec->rid;
+            gvcf->start  = rec->pos;
+            gvcf->als.l = 0;
+            kputs(rec->d.allele[0],&gvcf->als);
+            for (i=1; i<rec->n_allele; i++)
+            {
+                kputc(',',&gvcf->als);
+                kputs(rec->d.allele[i],&gvcf->als);
+            }
+            gvcf->min_dp = min_dp;
+        }
+        else
+        {
+            if ( gvcf->min_dp > min_dp ) gvcf->min_dp = min_dp;
+            for (i=0; i<nsmpl; i++)
+                if ( gvcf->dp[i] > gvcf->tmp[i] ) gvcf->dp[i] = gvcf->tmp[i];
+            ret = bcf_get_format_int32(hdr, rec, "PL", &gvcf->tmp, &gvcf->mtmp);
+            if ( ret>=0 )
+            {
+                if ( ret!=nsmpl*3 ) error("Unexpected number of PL fields\n");
+                for (i=0; i<nsmpl; i++)
+                {
+                    if ( gvcf->pl[3*i+1] > gvcf->tmp[3*i+1] )
+                    {
+                        gvcf->pl[3*i+1] = gvcf->tmp[3*i+1];
+                        gvcf->pl[3*i+2] = gvcf->tmp[3*i+2];
+                    }
+                    else if ( gvcf->pl[3*i+1]==gvcf->tmp[3*i+1] && gvcf->pl[3*i+2] > gvcf->tmp[3*i+2] )
+                        gvcf->pl[3*i+2] = gvcf->tmp[3*i+2];
+                }
+            }
+            else
+                gvcf->npl = 0;
+        }
+        gvcf->prev_range = dp_range;
+        if ( bcf_get_info_int32(hdr,rec,"END",&gvcf->tmp,&gvcf->mtmp)==1 )
+            gvcf->end = gvcf->tmp[0] - 1;   // from 1-based to 0-based
+        else
+            gvcf->end = rec->pos;
+        return NULL;
+    }
+
+    if ( is_ref && min_dp )
+        bcf_update_info_int32(hdr, rec, "MinDP", &min_dp, 1);
+
+    return rec;
+}
+
diff --git a/bcftools/gvcf.h b/bcftools/gvcf.h
new file mode 100644
index 0000000..784e1f6
--- /dev/null
+++ b/bcftools/gvcf.h
@@ -0,0 +1,41 @@
+/* gvcf.[ch] - Helper functions for gVCF support
+
+   The MIT License
+
+   Copyright (c) 2015 Genome Research Ltd.
+
+   Author: Petr Danecek <pd3@sanger.ac.uk>
+   
+   Permission is hereby granted, free of charge, to any person obtaining a copy
+   of this software and associated documentation files (the "Software"), to deal
+   in the Software without restriction, including without limitation the rights
+   to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+   copies of the Software, and to permit persons to whom the Software is
+   furnished to do so, subject to the following conditions:
+   
+   The above copyright notice and this permission notice shall be included in
+   all copies or substantial portions of the Software.
+   
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+   IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+   FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+   AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+   LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+   OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+   THE SOFTWARE.
+
+ */
+
+#ifndef __GVCF_H__
+#define __GVCF_H__
+
+#include "bcftools.h"
+
+typedef struct _gvcf_t gvcf_t;
+
+gvcf_t *gvcf_init(const char *dp_ranges);
+void gvcf_update_header(gvcf_t *gvcf, bcf_hdr_t *hdr);
+bcf1_t *gvcf_write(gvcf_t *gvcf, htsFile *fh, bcf_hdr_t *hdr, bcf1_t *rec, int is_ref);
+void gvcf_destroy(gvcf_t *gvcf);
+
+#endif
diff --git a/bcftools/hclust.c b/bcftools/hclust.c
new file mode 100644
index 0000000..945c70e
--- /dev/null
+++ b/bcftools/hclust.c
@@ -0,0 +1,401 @@
+/* The MIT License
+
+   Copyright (c) 2016 Genome Research Ltd.
+
+   Author: Petr Danecek <pd3@sanger.ac.uk>
+   
+   Permission is hereby granted, free of charge, to any person obtaining a copy
+   of this software and associated documentation files (the "Software"), to deal
+   in the Software without restriction, including without limitation the rights
+   to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+   copies of the Software, and to permit persons to whom the Software is
+   furnished to do so, subject to the following conditions:
+   
+   The above copyright notice and this permission notice shall be included in
+   all copies or substantial portions of the Software.
+   
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+   IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+   FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+   AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+   LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+   OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+   THE SOFTWARE.
+
+ */
+
+#include <htslib/hts.h>
+#include <htslib/kstring.h>
+#include <stdlib.h>
+#include <assert.h>
+#include "bcftools.h"
+#include "hclust.h"
+
+typedef struct _node_t
+{
+    struct _node_t *akid, *bkid, *next, *prev, *parent;
+    int id, idx;    // id: unique node id; idx: current index to pdist
+    float value;    // max pairwise dist of elements within the node
+}
+node_t;
+
+struct _hclust_t
+{
+    int ndat, nclust;       // ndat: number of elements (pdist matrix size); nclust: current number of clusters
+    float *pdist;           // pairwise cluster distances, diagonal matrix accessed via the PDIST macro
+    node_t *first, *last;   // clusters are maintained in a double-linked list
+    node_t **rmme;          // convenience array to remove all allocated nodes at the end
+    int nrmme;
+    kstring_t str;          // (for debugging) pointer to str.s is returned by create_dot()
+    char **dbg;             // (for debugging) created by create_list() via set_threshold() and returned by explain()
+    int ndbg, mdbg;
+};
+
+node_t *append_node(hclust_t *clust, int idx)
+{
+    node_t *node = (node_t*) calloc(1,sizeof(node_t));
+
+    clust->nclust++;
+    node->id  = clust->nrmme;
+    node->idx = idx;
+    if ( !clust->first )
+    {
+        clust->first = node; 
+        clust->last  = node; 
+    }
+    else
+    {
+        node->prev = clust->last;
+        clust->last->next = node; 
+        clust->last = node; 
+    }
+    
+    if ( clust->nrmme >= clust->ndat*2 ) error("hclust fixme: %d vs %d\n",clust->nrmme,clust->ndat);
+    clust->rmme[clust->nrmme++] = node;
+
+    return node;
+}
+void remove_node(hclust_t *clust, node_t *node)
+{
+    if ( node==clust->first ) clust->first = node->next;
+    if ( node==clust->last ) clust->last = node->prev;
+    if ( node->next ) node->next->prev = node->prev;
+    if ( node->prev ) node->prev->next = node->next;
+    clust->nclust--;
+}
+
+#if DEBUG
+void hclust_debug(hclust_t *clust)
+{
+    int i;
+    fprintf(stderr,"nrmme=%d  nclust=%d\n", clust->nrmme,clust->nclust);
+    for (i=0; i<clust->nrmme; i++)
+    {
+        node_t *node = clust->rmme[i];
+        int akid  = node->akid ? node->akid->id : -1;
+        int bkid  = node->bkid ? node->bkid->id : -1;
+        int akidx = node->akid ? node->akid->idx : -1;
+        int bkidx = node->bkid ? node->bkid->idx : -1;
+        fprintf(stderr,"\t%d\t%d\t%f\t%d %d\t%d %d\n",node->id,node->idx,node->value,akid,bkid,akidx,bkidx);
+    }
+
+    int j;
+    for (i=1; i<clust->ndat; i++)
+    {
+        int active = 0;
+        node_t *node = clust->first;
+        while (node)
+        {
+            if ( node->idx==i ) { active=1; break; }
+            node = node->next;
+        }
+        fprintf(stderr,"%2d%c ",i,active?'*':' ');
+        for (j=0; j<i; j++)
+        {
+            if ( PDIST(clust->pdist,i,j)==9 )
+                fprintf(stderr,"  -----  ");
+            else
+                fprintf(stderr," %f", PDIST(clust->pdist,i,j));
+        }
+        fprintf(stderr,"\n");
+    }
+    for (j=0; j<clust->ndat-1; j++) fprintf(stderr,"  %6d ",j); fprintf(stderr,"\n");
+}
+#endif
+
+hclust_t *hclust_init(int n, float *pdist)
+{
+    hclust_t *clust = (hclust_t*) calloc(1,sizeof(hclust_t));
+    clust->ndat  = n;
+    clust->pdist = pdist;
+    clust->rmme = (node_t**) calloc(n*2,sizeof(node_t*));
+
+    // init clusters
+    int i;
+    for (i=0; i<clust->ndat; i++) append_node(clust,i);
+
+    // build the tree
+    while ( clust->nclust>1 )
+    {
+        // find two clusters with minimum distance
+        float min_value = HUGE_VAL;
+        node_t *iclust = clust->first->next;
+        node_t *min_iclust = NULL, *min_jclust = NULL;
+        while ( iclust )
+        {
+            node_t *jclust = clust->first;
+            while ( jclust!=iclust )
+            {
+                float value = PDIST(clust->pdist,iclust->idx,jclust->idx);
+                if ( value < min_value ) 
+                { 
+                    min_value  = value;
+                    min_iclust = iclust;
+                    min_jclust = jclust; 
+                }
+                jclust = jclust->next;
+            }
+            iclust = iclust->next;
+        }
+        assert( min_iclust && min_jclust ); // pdist contains inf or nan, fix the caller
+        remove_node(clust,min_iclust);
+        remove_node(clust,min_jclust);
+
+        // update the pairwise distances. We keep the matrix and as we are moving up the
+        // tree, we use fewer columns/rows as the number of clusters decreases: we reuse
+        // i-th and leave j-th unused. Inter-cluster distance is defined as maximum distance
+        // between pairwise distances of elements within the cluster.
+        iclust = clust->first;
+        while ( iclust )
+        {
+            if ( PDIST(clust->pdist,iclust->idx,min_iclust->idx) < PDIST(clust->pdist,iclust->idx,min_jclust->idx) )
+                PDIST(clust->pdist,iclust->idx,min_iclust->idx) = PDIST(clust->pdist,iclust->idx,min_jclust->idx);
+            iclust = iclust->next;
+        }
+
+        node_t *node = append_node(clust,min_iclust->idx);
+        node->akid  = min_iclust;
+        node->bkid  = min_jclust;
+        node->value = min_value;
+        node->akid->parent = node;
+        node->bkid->parent = node;
+    }
+
+    return clust;
+}
+void hclust_destroy(hclust_t *clust)
+{
+    int i;
+    for (i=0; i<clust->nrmme; i++) free(clust->rmme[i]);
+    free(clust->rmme);
+    free(clust->dbg);
+    free(clust->str.s);
+    free(clust);
+}
+
+char *hclust_create_dot(hclust_t *clust, char **labels, float th)
+{
+    clust->str.l = 0;
+    ksprintf(&clust->str,"digraph myGraph {");
+
+    int i;
+    for (i=0; i<clust->nrmme; i++)
+    {
+        node_t *node = clust->rmme[i];
+        if ( node->value )
+            ksprintf(&clust->str,"\"%d\" [label=\"%f\"];", node->id,node->value);
+        else
+            ksprintf(&clust->str,"\"%d\" [label=\"%s\"];", node->id,labels[node->idx]);
+    }
+    for (i=0; i<clust->nrmme; i++)
+    {
+        node_t *node = clust->rmme[i];
+        if ( node->akid )
+        {
+            if ( node->value >= th && node->akid && node->akid->value < th )
+                ksprintf(&clust->str,"\"%d\" -> \"%d\" [color=\"#D43F3A\" penwidth=3];", node->id,node->akid->id);
+            else
+                ksprintf(&clust->str,"\"%d\" -> \"%d\";", node->id,node->akid->id);
+        }
+
+        if ( node->bkid )
+        {
+            if ( node->value >= th && node->bkid && node->bkid->value < th )
+                ksprintf(&clust->str,"\"%d\" -> \"%d\" [color=\"#D43F3A\" penwidth=3];", node->id,node->bkid->id);
+            else
+                ksprintf(&clust->str,"\"%d\" -> \"%d\";", node->id,node->bkid->id);
+        }
+    }
+    ksprintf(&clust->str,"};");
+    return clust->str.s;
+}
+char **hclust_explain(hclust_t *clust, int *nlines)
+{
+    clust->ndbg = 0;
+    char *beg = clust->str.s;
+    while ( *beg )
+    {
+        char *end = beg;
+        while ( *end && *end!='\n' ) end++;
+        clust->ndbg++;
+        hts_expand(char*,clust->ndbg,clust->mdbg,clust->dbg);
+        clust->dbg[clust->ndbg-1] = beg;
+        if ( !*end ) break;
+        *end = 0;
+        beg = end + 1;
+    }
+
+    *nlines = clust->ndbg;
+    return clust->dbg;
+}
+
+cluster_t *append_cluster(node_t *node, cluster_t *cluster, int *nclust, node_t **stack)
+{
+    (*nclust)++;
+    cluster = (cluster_t*) realloc(cluster,sizeof(cluster_t)*(*nclust));
+    cluster_t *clust = &cluster[*nclust-1];
+    clust->nmemb = 0;
+    clust->memb  = NULL;
+    clust->dist  = node->value;
+
+    int nstack = 1;
+    stack[0] = node;
+
+    while ( nstack )
+    {
+        node_t *node = stack[--nstack];
+        node_t *akid = node->akid;
+        node_t *bkid = node->bkid;
+        if ( node->akid )
+        {
+            stack[nstack++] = akid;
+            stack[nstack++] = bkid;
+        }
+        else    
+        {
+            clust->nmemb++;
+            clust->memb = (int*) realloc(clust->memb,sizeof(int)*clust->nmemb);
+            clust->memb[clust->nmemb-1] = node->id;
+        }
+    }
+    return cluster;
+}
+
+int cmp_nodes(const void *a, const void *b)
+{
+    const node_t *an = *((const node_t**) a);
+    const node_t *bn = *((const node_t**) b);
+    if ( an->value < bn->value ) return -1;
+    if ( an->value > bn->value ) return 1;
+    return 0;
+}
+
+float calc_dev(node_t **dat, int n)
+{
+    float avg = 0, dev = 0;
+    int i;
+    for (i=0; i<n; i++) avg += dat[i]->value;
+    avg /= n;
+    for (i=0; i<n; i++) dev += (dat[i]->value - avg)*(dat[i]->value - avg);
+    return sqrt(dev/n);
+}
+
+/*
+    Heuristics to determine clustering cutoff: sort nodes by distance and
+    split into two groups by minimizing the standard deviation.
+    This works best when two elements from a single different sample are
+    included in the mix.
+        - min_inter_dist .. smaller values are always considered identical
+        - max_intra_dist .. larger values are always considered different
+ */
+float hclust_set_threshold(hclust_t *clust, float min_inter_dist, float max_intra_dist)
+{
+    node_t **dat = clust->rmme + clust->ndat;
+    int i, ndat = clust->nrmme - clust->ndat;
+ 
+    qsort(dat, ndat, sizeof(dat), cmp_nodes);
+
+    clust->str.l = 0;
+    float th, min_dev = HUGE_VAL;
+    int imin = -1;
+    for (i=0; i<ndat; i++)
+    {
+        float dev = 0;
+        if ( i>0 ) dev += calc_dev(dat,i);
+        if ( i+1<ndat ) dev += calc_dev(dat+i,ndat-i);
+        th  = dat[i]->value;
+        ksprintf(&clust->str,"DEV\t%f\t%f\n",th,dev);
+        if ( min_dev > dev && th >= min_inter_dist ) { min_dev = dev; imin = i; }
+    }
+    if ( max_intra_dist > 0 )
+        th = max_intra_dist;  // use fixed cutoff, the above was only for debugging output
+    else
+    {
+        // dynamic cutoff
+        max_intra_dist = fabs(max_intra_dist);
+        th = imin==-1 ? max_intra_dist : dat[imin]->value;
+        if ( th > max_intra_dist ) th = max_intra_dist;
+    }
+    ksprintf(&clust->str,"TH\t%f\n", th);
+    ksprintf(&clust->str,"MAX_DIST\t%f\n", dat[ndat-1]->value);
+    ksprintf(&clust->str,"MIN_INTER\t%f\n", min_inter_dist);
+    ksprintf(&clust->str,"MAX_INTRA\t%f\n", max_intra_dist);
+    return th;
+} 
+
+cluster_t *hclust_create_list(hclust_t *clust, float min_inter_dist, float *max_intra_dist, int *nclust)
+{
+    float cutoff = *max_intra_dist = hclust_set_threshold(clust, min_inter_dist, *max_intra_dist);
+
+    node_t **stack = (node_t**) malloc(sizeof(node_t*)*clust->ndat);
+    node_t **tmp = (node_t**) malloc(sizeof(node_t*)*clust->ndat);
+    stack[0] = clust->first;
+    int nstack = 1;
+    
+    cluster_t *cluster = NULL;
+    int ncluster = 0;
+
+    if ( stack[0]->value < cutoff )
+    {
+        // all values are within the limits - create a single cluster
+        cluster = append_cluster(stack[0], cluster, &ncluster, tmp);
+        nstack = 0;
+    }
+
+    while ( nstack )
+    {
+        node_t *node = stack[--nstack];
+        node_t *akid = node->akid;
+        node_t *bkid = node->bkid;
+        if ( !akid )
+        {
+            cluster = append_cluster(node, cluster, &ncluster, tmp);
+            continue;
+        }
+
+        if ( node->value >= cutoff && akid->value < cutoff )
+            cluster = append_cluster(akid, cluster, &ncluster, tmp);
+        else    
+            stack[nstack++] = akid;
+
+        if ( node->value >= cutoff && bkid->value < cutoff )
+            cluster = append_cluster(bkid, cluster, &ncluster, tmp);
+        else    
+            stack[nstack++] = bkid;
+    }
+
+    free(tmp);
+    free(stack);
+
+    *nclust = ncluster;
+    return cluster;
+}
+
+void hclust_destroy_list(cluster_t *clust, int nclust)
+{
+    int i;
+    for (i=0; i<nclust; i++) free(clust[i].memb);
+    free(clust);
+}
+
+
diff --git a/bcftools/hclust.c.pysam.c b/bcftools/hclust.c.pysam.c
new file mode 100644
index 0000000..0a90af8
--- /dev/null
+++ b/bcftools/hclust.c.pysam.c
@@ -0,0 +1,403 @@
+#include "bcftools.pysam.h"
+
+/* The MIT License
+
+   Copyright (c) 2016 Genome Research Ltd.
+
+   Author: Petr Danecek <pd3@sanger.ac.uk>
+   
+   Permission is hereby granted, free of charge, to any person obtaining a copy
+   of this software and associated documentation files (the "Software"), to deal
+   in the Software without restriction, including without limitation the rights
+   to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+   copies of the Software, and to permit persons to whom the Software is
+   furnished to do so, subject to the following conditions:
+   
+   The above copyright notice and this permission notice shall be included in
+   all copies or substantial portions of the Software.
+   
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+   IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+   FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+   AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+   LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+   OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+   THE SOFTWARE.
+
+ */
+
+#include <htslib/hts.h>
+#include <htslib/kstring.h>
+#include <stdlib.h>
+#include <assert.h>
+#include "bcftools.h"
+#include "hclust.h"
+
+typedef struct _node_t
+{
+    struct _node_t *akid, *bkid, *next, *prev, *parent;
+    int id, idx;    // id: unique node id; idx: current index to pdist
+    float value;    // max pairwise dist of elements within the node
+}
+node_t;
+
+struct _hclust_t
+{
+    int ndat, nclust;       // ndat: number of elements (pdist matrix size); nclust: current number of clusters
+    float *pdist;           // pairwise cluster distances, diagonal matrix accessed via the PDIST macro
+    node_t *first, *last;   // clusters are maintained in a double-linked list
+    node_t **rmme;          // convenience array to remove all allocated nodes at the end
+    int nrmme;
+    kstring_t str;          // (for debugging) pointer to str.s is returned by create_dot()
+    char **dbg;             // (for debugging) created by create_list() via set_threshold() and returned by explain()
+    int ndbg, mdbg;
+};
+
+node_t *append_node(hclust_t *clust, int idx)
+{
+    node_t *node = (node_t*) calloc(1,sizeof(node_t));
+
+    clust->nclust++;
+    node->id  = clust->nrmme;
+    node->idx = idx;
+    if ( !clust->first )
+    {
+        clust->first = node; 
+        clust->last  = node; 
+    }
+    else
+    {
+        node->prev = clust->last;
+        clust->last->next = node; 
+        clust->last = node; 
+    }
+    
+    if ( clust->nrmme >= clust->ndat*2 ) error("hclust fixme: %d vs %d\n",clust->nrmme,clust->ndat);
+    clust->rmme[clust->nrmme++] = node;
+
+    return node;
+}
+void remove_node(hclust_t *clust, node_t *node)
+{
+    if ( node==clust->first ) clust->first = node->next;
+    if ( node==clust->last ) clust->last = node->prev;
+    if ( node->next ) node->next->prev = node->prev;
+    if ( node->prev ) node->prev->next = node->next;
+    clust->nclust--;
+}
+
+#if DEBUG
+void hclust_debug(hclust_t *clust)
+{
+    int i;
+    fprintf(bcftools_stderr,"nrmme=%d  nclust=%d\n", clust->nrmme,clust->nclust);
+    for (i=0; i<clust->nrmme; i++)
+    {
+        node_t *node = clust->rmme[i];
+        int akid  = node->akid ? node->akid->id : -1;
+        int bkid  = node->bkid ? node->bkid->id : -1;
+        int akidx = node->akid ? node->akid->idx : -1;
+        int bkidx = node->bkid ? node->bkid->idx : -1;
+        fprintf(bcftools_stderr,"\t%d\t%d\t%f\t%d %d\t%d %d\n",node->id,node->idx,node->value,akid,bkid,akidx,bkidx);
+    }
+
+    int j;
+    for (i=1; i<clust->ndat; i++)
+    {
+        int active = 0;
+        node_t *node = clust->first;
+        while (node)
+        {
+            if ( node->idx==i ) { active=1; break; }
+            node = node->next;
+        }
+        fprintf(bcftools_stderr,"%2d%c ",i,active?'*':' ');
+        for (j=0; j<i; j++)
+        {
+            if ( PDIST(clust->pdist,i,j)==9 )
+                fprintf(bcftools_stderr,"  -----  ");
+            else
+                fprintf(bcftools_stderr," %f", PDIST(clust->pdist,i,j));
+        }
+        fprintf(bcftools_stderr,"\n");
+    }
+    for (j=0; j<clust->ndat-1; j++) fprintf(bcftools_stderr,"  %6d ",j); fprintf(bcftools_stderr,"\n");
+}
+#endif
+
+hclust_t *hclust_init(int n, float *pdist)
+{
+    hclust_t *clust = (hclust_t*) calloc(1,sizeof(hclust_t));
+    clust->ndat  = n;
+    clust->pdist = pdist;
+    clust->rmme = (node_t**) calloc(n*2,sizeof(node_t*));
+
+    // init clusters
+    int i;
+    for (i=0; i<clust->ndat; i++) append_node(clust,i);
+
+    // build the tree
+    while ( clust->nclust>1 )
+    {
+        // find two clusters with minimum distance
+        float min_value = HUGE_VAL;
+        node_t *iclust = clust->first->next;
+        node_t *min_iclust = NULL, *min_jclust = NULL;
+        while ( iclust )
+        {
+            node_t *jclust = clust->first;
+            while ( jclust!=iclust )
+            {
+                float value = PDIST(clust->pdist,iclust->idx,jclust->idx);
+                if ( value < min_value ) 
+                { 
+                    min_value  = value;
+                    min_iclust = iclust;
+                    min_jclust = jclust; 
+                }
+                jclust = jclust->next;
+            }
+            iclust = iclust->next;
+        }
+        assert( min_iclust && min_jclust ); // pdist contains inf or nan, fix the caller
+        remove_node(clust,min_iclust);
+        remove_node(clust,min_jclust);
+
+        // update the pairwise distances. We keep the matrix and as we are moving up the
+        // tree, we use fewer columns/rows as the number of clusters decreases: we reuse
+        // i-th and leave j-th unused. Inter-cluster distance is defined as maximum distance
+        // between pairwise distances of elements within the cluster.
+        iclust = clust->first;
+        while ( iclust )
+        {
+            if ( PDIST(clust->pdist,iclust->idx,min_iclust->idx) < PDIST(clust->pdist,iclust->idx,min_jclust->idx) )
+                PDIST(clust->pdist,iclust->idx,min_iclust->idx) = PDIST(clust->pdist,iclust->idx,min_jclust->idx);
+            iclust = iclust->next;
+        }
+
+        node_t *node = append_node(clust,min_iclust->idx);
+        node->akid  = min_iclust;
+        node->bkid  = min_jclust;
+        node->value = min_value;
+        node->akid->parent = node;
+        node->bkid->parent = node;
+    }
+
+    return clust;
+}
+void hclust_destroy(hclust_t *clust)
+{
+    int i;
+    for (i=0; i<clust->nrmme; i++) free(clust->rmme[i]);
+    free(clust->rmme);
+    free(clust->dbg);
+    free(clust->str.s);
+    free(clust);
+}
+
+char *hclust_create_dot(hclust_t *clust, char **labels, float th)
+{
+    clust->str.l = 0;
+    ksprintf(&clust->str,"digraph myGraph {");
+
+    int i;
+    for (i=0; i<clust->nrmme; i++)
+    {
+        node_t *node = clust->rmme[i];
+        if ( node->value )
+            ksprintf(&clust->str,"\"%d\" [label=\"%f\"];", node->id,node->value);
+        else
+            ksprintf(&clust->str,"\"%d\" [label=\"%s\"];", node->id,labels[node->idx]);
+    }
+    for (i=0; i<clust->nrmme; i++)
+    {
+        node_t *node = clust->rmme[i];
+        if ( node->akid )
+        {
+            if ( node->value >= th && node->akid && node->akid->value < th )
+                ksprintf(&clust->str,"\"%d\" -> \"%d\" [color=\"#D43F3A\" penwidth=3];", node->id,node->akid->id);
+            else
+                ksprintf(&clust->str,"\"%d\" -> \"%d\";", node->id,node->akid->id);
+        }
+
+        if ( node->bkid )
+        {
+            if ( node->value >= th && node->bkid && node->bkid->value < th )
+                ksprintf(&clust->str,"\"%d\" -> \"%d\" [color=\"#D43F3A\" penwidth=3];", node->id,node->bkid->id);
+            else
+                ksprintf(&clust->str,"\"%d\" -> \"%d\";", node->id,node->bkid->id);
+        }
+    }
+    ksprintf(&clust->str,"};");
+    return clust->str.s;
+}
+char **hclust_explain(hclust_t *clust, int *nlines)
+{
+    clust->ndbg = 0;
+    char *beg = clust->str.s;
+    while ( *beg )
+    {
+        char *end = beg;
+        while ( *end && *end!='\n' ) end++;
+        clust->ndbg++;
+        hts_expand(char*,clust->ndbg,clust->mdbg,clust->dbg);
+        clust->dbg[clust->ndbg-1] = beg;
+        if ( !*end ) break;
+        *end = 0;
+        beg = end + 1;
+    }
+
+    *nlines = clust->ndbg;
+    return clust->dbg;
+}
+
+cluster_t *append_cluster(node_t *node, cluster_t *cluster, int *nclust, node_t **stack)
+{
+    (*nclust)++;
+    cluster = (cluster_t*) realloc(cluster,sizeof(cluster_t)*(*nclust));
+    cluster_t *clust = &cluster[*nclust-1];
+    clust->nmemb = 0;
+    clust->memb  = NULL;
+    clust->dist  = node->value;
+
+    int nstack = 1;
+    stack[0] = node;
+
+    while ( nstack )
+    {
+        node_t *node = stack[--nstack];
+        node_t *akid = node->akid;
+        node_t *bkid = node->bkid;
+        if ( node->akid )
+        {
+            stack[nstack++] = akid;
+            stack[nstack++] = bkid;
+        }
+        else    
+        {
+            clust->nmemb++;
+            clust->memb = (int*) realloc(clust->memb,sizeof(int)*clust->nmemb);
+            clust->memb[clust->nmemb-1] = node->id;
+        }
+    }
+    return cluster;
+}
+
+int cmp_nodes(const void *a, const void *b)
+{
+    const node_t *an = *((const node_t**) a);
+    const node_t *bn = *((const node_t**) b);
+    if ( an->value < bn->value ) return -1;
+    if ( an->value > bn->value ) return 1;
+    return 0;
+}
+
+float calc_dev(node_t **dat, int n)
+{
+    float avg = 0, dev = 0;
+    int i;
+    for (i=0; i<n; i++) avg += dat[i]->value;
+    avg /= n;
+    for (i=0; i<n; i++) dev += (dat[i]->value - avg)*(dat[i]->value - avg);
+    return sqrt(dev/n);
+}
+
+/*
+    Heuristics to determine clustering cutoff: sort nodes by distance and
+    split into two groups by minimizing the standard deviation.
+    This works best when two elements from a single different sample are
+    included in the mix.
+        - min_inter_dist .. smaller values are always considered identical
+        - max_intra_dist .. larger values are always considered different
+ */
+float hclust_set_threshold(hclust_t *clust, float min_inter_dist, float max_intra_dist)
+{
+    node_t **dat = clust->rmme + clust->ndat;
+    int i, ndat = clust->nrmme - clust->ndat;
+ 
+    qsort(dat, ndat, sizeof(dat), cmp_nodes);
+
+    clust->str.l = 0;
+    float th, min_dev = HUGE_VAL;
+    int imin = -1;
+    for (i=0; i<ndat; i++)
+    {
+        float dev = 0;
+        if ( i>0 ) dev += calc_dev(dat,i);
+        if ( i+1<ndat ) dev += calc_dev(dat+i,ndat-i);
+        th  = dat[i]->value;
+        ksprintf(&clust->str,"DEV\t%f\t%f\n",th,dev);
+        if ( min_dev > dev && th >= min_inter_dist ) { min_dev = dev; imin = i; }
+    }
+    if ( max_intra_dist > 0 )
+        th = max_intra_dist;  // use fixed cutoff, the above was only for debugging output
+    else
+    {
+        // dynamic cutoff
+        max_intra_dist = fabs(max_intra_dist);
+        th = imin==-1 ? max_intra_dist : dat[imin]->value;
+        if ( th > max_intra_dist ) th = max_intra_dist;
+    }
+    ksprintf(&clust->str,"TH\t%f\n", th);
+    ksprintf(&clust->str,"MAX_DIST\t%f\n", dat[ndat-1]->value);
+    ksprintf(&clust->str,"MIN_INTER\t%f\n", min_inter_dist);
+    ksprintf(&clust->str,"MAX_INTRA\t%f\n", max_intra_dist);
+    return th;
+} 
+
+cluster_t *hclust_create_list(hclust_t *clust, float min_inter_dist, float *max_intra_dist, int *nclust)
+{
+    float cutoff = *max_intra_dist = hclust_set_threshold(clust, min_inter_dist, *max_intra_dist);
+
+    node_t **stack = (node_t**) malloc(sizeof(node_t*)*clust->ndat);
+    node_t **tmp = (node_t**) malloc(sizeof(node_t*)*clust->ndat);
+    stack[0] = clust->first;
+    int nstack = 1;
+    
+    cluster_t *cluster = NULL;
+    int ncluster = 0;
+
+    if ( stack[0]->value < cutoff )
+    {
+        // all values are within the limits - create a single cluster
+        cluster = append_cluster(stack[0], cluster, &ncluster, tmp);
+        nstack = 0;
+    }
+
+    while ( nstack )
+    {
+        node_t *node = stack[--nstack];
+        node_t *akid = node->akid;
+        node_t *bkid = node->bkid;
+        if ( !akid )
+        {
+            cluster = append_cluster(node, cluster, &ncluster, tmp);
+            continue;
+        }
+
+        if ( node->value >= cutoff && akid->value < cutoff )
+            cluster = append_cluster(akid, cluster, &ncluster, tmp);
+        else    
+            stack[nstack++] = akid;
+
+        if ( node->value >= cutoff && bkid->value < cutoff )
+            cluster = append_cluster(bkid, cluster, &ncluster, tmp);
+        else    
+            stack[nstack++] = bkid;
+    }
+
+    free(tmp);
+    free(stack);
+
+    *nclust = ncluster;
+    return cluster;
+}
+
+void hclust_destroy_list(cluster_t *clust, int nclust)
+{
+    int i;
+    for (i=0; i<nclust; i++) free(clust[i].memb);
+    free(clust);
+}
+
+
diff --git a/bcftools/hclust.h b/bcftools/hclust.h
new file mode 100644
index 0000000..43d333f
--- /dev/null
+++ b/bcftools/hclust.h
@@ -0,0 +1,77 @@
+/* The MIT License
+
+   Copyright (c) 2016 Genome Research Ltd.
+
+   Author: Petr Danecek <pd3@sanger.ac.uk>
+   
+   Permission is hereby granted, free of charge, to any person obtaining a copy
+   of this software and associated documentation files (the "Software"), to deal
+   in the Software without restriction, including without limitation the rights
+   to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+   copies of the Software, and to permit persons to whom the Software is
+   furnished to do so, subject to the following conditions:
+   
+   The above copyright notice and this permission notice shall be included in
+   all copies or substantial portions of the Software.
+   
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+   IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+   FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+   AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+   LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+   OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+   THE SOFTWARE.
+
+ */
+
+/*
+    Simple hierarchical clustering
+*/
+
+#ifndef __HCLUST_H__
+#define __HCLUST_H__
+
+#include <stdio.h>
+
+typedef struct _hclust_t hclust_t;
+
+typedef struct
+{
+    float dist;
+    int nmemb, *memb;
+}
+cluster_t;
+
+#define PDIST(mat,a,b) (mat)[((a)>(b)?((a)*((a)-1)/2+(b)):((b)*((b)-1)/2+(a)))]
+
+/*
+ *  hclust_init() - init and run clustering
+ *  @n:     number of elements
+ *  @pdist: pairwise distances. The array will be modified by hclust and
+ *          must exist until hclust_destroy() is called
+ */
+hclust_t *hclust_init(int n, float *pdist);
+void hclust_destroy(hclust_t *clust);
+
+/*
+ *  hclust_create_list() - returns a list of clusters
+ *  @min_inter_dist: minimum inter-cluster distance. If smaller, elements are considered
+ *                   homogenous, belonging to the same cluster.
+ *  @max_intra_dist: maximum intra-cluster distance allowed. If smaller than 0,
+ *                   the threshold can be heuristically lowered, otherwise considered
+ *                   a fixed cutoff. The pointer will be filled to the cutoff actually used.
+ */
+cluster_t *hclust_create_list(hclust_t *clust, float min_inter_dist, float *max_intra_dist, int *nclust);
+void hclust_destroy_list(cluster_t *clust, int nclust);
+
+/* 
+ *  Access debugging data used in the decision making process.  Note that this
+ *  must be called immediately after hclust_create_list because other calls,
+ *  such as hclust_create_dot(), invalidate the temporary data structures.
+ */
+char **hclust_explain(hclust_t *clust, int *nlines);
+
+char *hclust_create_dot(hclust_t *clust, char **labels, float th);
+
+#endif
+
diff --git a/bcftools/hex.h b/bcftools/hex.h
new file mode 100644
index 0000000..d915b28
--- /dev/null
+++ b/bcftools/hex.h
@@ -0,0 +1,95 @@
+// VariantKey
+//
+// hex.h
+//
+// @category   Libraries
+// @author     Nicola Asuni <nicola.asuni@genomicsplc.com>
+// @copyright  2017-2018 GENOMICS plc
+// @license    MIT (see LICENSE)
+// @link       https://github.com/genomicsplc/variantkey
+//
+// LICENSE
+//
+// Copyright (c) 2017-2018 GENOMICS plc
+//
+// Permission is hereby granted, free of charge, to any person obtaining a copy
+// of this software and associated documentation files (the "Software"), to deal
+// in the Software without restriction, including without limitation the rights
+// to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+// copies of the Software, and to permit persons to whom the Software is
+// furnished to do so, subject to the following conditions:
+//
+// The above copyright notice and this permission notice shall be included in
+// all copies or substantial portions of the Software.
+//
+// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+// OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+// THE SOFTWARE.
+
+/**
+ * @file hex.h
+ * @brief Utility functions to manipulate strings.
+ *
+ * Collection of utility functions to manipulate strings.
+ */
+
+#ifndef ASTRING_H
+#define ASTRING_H
+
+#include <inttypes.h>
+#include <stdio.h>
+
+/** @brief Returns uint64_t hexadecimal string (16 characters).
+ *
+ * @param n     Number to parse
+ * @param str   String buffer to be returned (it must be sized 17 bytes at least).
+ *
+ * @return      Upon successful return, these function returns the number of characters processed
+ *              (excluding the null byte used to end output to strings).
+ *              If the buffer size is not sufficient, then the return value is the number of characters required for
+ *              buffer string, including the terminating null byte.
+ */
+static inline size_t hex_uint64_t(uint64_t n, char *str)
+{
+    return sprintf(str, "%016" PRIx64, n);
+}
+
+/** @brief Parses a 16 chars hexadecimal string and returns the code.
+ *
+ * @param s    Hexadecimal string to parse (it must contain 16 hexadecimal characters).
+ *
+ * @return uint64_t unsigned integer number.
+ */
+static inline uint64_t parse_hex_uint64_t(const char *s)
+{
+    uint64_t v = 0;
+    uint8_t b;
+    size_t i;
+    for (i = 0; i < 16; i++)
+    {
+        b = s[i];
+        if (b >= 'a')
+        {
+            b -= ('a' - 10); // a-f
+        }
+        else
+        {
+            if (b >= 'A')
+            {
+                b -= ('A' - 10); // A-F
+            }
+            else
+            {
+                b -= '0'; // 0-9
+            }
+        }
+        v = ((v << 4) | b);
+    }
+    return v;
+}
+
+#endif  // ASTRING_H
diff --git a/bcftools/khash_str2str.h b/bcftools/khash_str2str.h
new file mode 100644
index 0000000..4a5bd12
--- /dev/null
+++ b/bcftools/khash_str2str.h
@@ -0,0 +1,106 @@
+/*  khash_str2str.h -- C-string to C-string hash table.
+
+    Copyright (C) 2014,2016 Genome Research Ltd.
+
+    Author: Petr Danecek <pd3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#ifndef KHASH_STR2STR_H
+#define KHASH_STR2STR_H
+
+#include <htslib/khash.h>
+
+KHASH_MAP_INIT_STR(str2str, const char*)
+
+/*
+ *  Wrappers for khash dictionaries used by mpileup.
+ */
+
+static inline void *khash_str2str_init(void)
+{
+    return kh_init(str2str);
+}
+
+/*
+ *  Destroy the hash structure, but not the keys
+ */
+static inline void khash_str2str_destroy(void *_hash)
+{
+    khash_t(str2str) *hash = (khash_t(str2str)*)_hash;
+    if (hash) kh_destroy(str2str, hash); // Note that strings are not freed.
+}
+
+/*
+ *  Destroys both the hash structure and the keys
+ */
+static inline void khash_str2str_destroy_free(void *_hash)
+{
+    khash_t(str2str) *hash = (khash_t(str2str)*)_hash;
+    khint_t k;
+    if (hash == 0) return;
+    for (k = 0; k < kh_end(hash); ++k)
+        if (kh_exist(hash, k)) free((char*)kh_key(hash, k));
+    kh_destroy(str2str, hash);
+}
+
+/*
+ *  Destroys the hash structure, the keys and the values
+ */
+static inline void khash_str2str_destroy_free_all(void *_hash)
+{
+    khash_t(str2str) *hash = (khash_t(str2str)*)_hash;
+    khint_t k;
+    if (hash == 0) return;
+    for (k = 0; k < kh_end(hash); ++k)
+        if (kh_exist(hash, k))
+        {
+            free((char*)kh_key(hash, k));
+            free((char*)kh_val(hash, k));
+        }
+    kh_destroy(str2str, hash);
+}
+
+/*
+ *  Returns value if key exists or NULL if not
+ */
+static inline char *khash_str2str_get(void *_hash, const char *str)
+{
+    khash_t(str2str) *hash = (khash_t(str2str)*)_hash;
+    khint_t k = kh_get(str2str, hash, str);
+    if ( k == kh_end(hash) ) return NULL;
+    return (char*)kh_val(hash, k);
+}
+
+/*
+ *  Set a new key,value pair. On success returns the bin index, on
+ *  error -1 is returned.
+ */
+static inline int khash_str2str_set(void *_hash, const char *str, const char *value)
+{
+    khint_t k;
+    int ret;
+    khash_t(str2str) *hash = (khash_t(str2str)*)_hash;
+    if ( !hash ) return -1;
+    k = kh_put(str2str, hash, str, &ret);
+    kh_val(hash,k) = value;
+    return k;
+}
+
+#endif
diff --git a/bcftools/kheap.h b/bcftools/kheap.h
new file mode 100644
index 0000000..cb5dda4
--- /dev/null
+++ b/bcftools/kheap.h
@@ -0,0 +1,174 @@
+/* The MIT License
+
+   Copyright (C) 2016 Genome Research Ltd.
+
+   Author: Petr Danecek <pd3@sanger.ac.uk>
+
+   Permission is hereby granted, free of charge, to any person obtaining a copy
+   of this software and associated documentation files (the "Software"), to deal
+   in the Software without restriction, including without limitation the rights
+   to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+   copies of the Software, and to permit persons to whom the Software is
+   furnished to do so, subject to the following conditions:
+   
+   The above copyright notice and this permission notice shall be included in
+   all copies or substantial portions of the Software.
+   
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+   IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+   FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+   AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+   LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+   OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+   THE SOFTWARE.
+
+ */
+/*
+    Usage example:
+
+        #include "kheap.h"
+
+        // First we prepare the user data to store, in this example it is a
+        // struct with a single element "key", and a comparator function
+        // "is_smaller".  In this example the comparator defines a min heap (as
+        // opposed to a max heap).
+        typedef struct
+        {
+            uint32_t key; 
+        } 
+        data_t;
+        static inline int is_smaller(data_t *a, data_t *b)
+        {
+            return a->key < b->key ? 1 : 0; 
+        }
+        data_t data[3] = { {3}, {2}, {1} };
+
+
+        // Heap declaration, "mh" is an arbitrary string.  The typedef is not
+        // required, it is just a convenience shortcut so that we can use
+        // "heap_t" instead of the generic "khp_mh_t" automatically created by
+        // the KHEAP_INIT macro.
+        KHEAP_INIT(mh, data_t, is_smaller)
+        typedef khp_mh_t heap_t;
+
+        // Initialize the heap, insert the test data, then retrieve them back,
+        // sorted. Multiple heaps with the same name "mh" can be created and
+        // used simultaneously, as long as they all use the same data type
+        // "data_t".
+        heap_t *heap = khp_init(mh);
+
+        // When inserting a new element, the heap stores a copy of the memory
+        // area pointed to by the third argument.
+        for (int i=0; i<3; i++)
+            khp_insert(mh, heap, &data[i]);
+
+        while (heap->ndat)
+        {
+            printf("%d\n", heap->dat[0].pos);
+            khp_delete(mh, heap);
+        }
+
+        // Clean up
+        khp_destroy(mh, heap);
+
+*/
+
+#ifndef __KHEAP_H__
+#define __KHEAP_H__
+
+#include <stdlib.h>
+
+#ifndef kroundup32
+#define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
+#endif
+
+#ifndef kh_inline
+#ifdef _MSC_VER
+#define kh_inline __inline
+#else
+#define kh_inline inline
+#endif
+#endif /* kh_inline */
+
+#ifndef klib_unused
+#if (defined __clang__ && __clang_major__ >= 3) || (defined __GNUC__ && __GNUC__ >= 3)
+#define klib_unused __attribute__ ((__unused__))
+#else
+#define klib_unused
+#endif
+#endif /* klib_unused */
+
+
+#define __KHEAP_TYPE(name, kheap_t) \
+    typedef struct {                \
+        int ndat, mdat;             \
+        kheap_t *dat;               \
+        kheap_t tmp;                \
+    } khp_##name##_t;
+
+#define khp_parent(i) (((i)-1)/2)
+#define khp_lchild(i) (2*(i)+1)
+#define khp_rchild(i) (2*(i)+2)
+#define khp_swap(hp,i,j) {               \
+        ((hp)->tmp)    = ((hp)->dat[i]); \
+        ((hp)->dat[i]) = ((hp)->dat[j]); \
+        ((hp)->dat[j]) = ((hp)->tmp);    \
+    }
+
+#define __KHEAP_IMPL(name, SCOPE, kheap_t, __cmp)                       \
+    SCOPE khp_##name##_t *khp_init_##name(void)                         \
+    {                                                                   \
+        return (khp_##name##_t*)calloc(1, sizeof(khp_##name##_t));      \
+    }                                                                   \
+    SCOPE void khp_destroy_##name(khp_##name##_t *heap)                 \
+    {                                                                   \
+        if (heap) free(heap->dat);                                      \
+        free(heap);                                                     \
+    }                                                                   \
+    SCOPE int khp_insert_##name(khp_##name##_t *heap, kheap_t *dat)     \
+    {                                                                   \
+        heap->ndat++;                                                   \
+        if ( heap->ndat > heap->mdat )                                  \
+        {                                                               \
+            heap->mdat = heap->ndat;                                    \
+            kroundup32(heap->mdat);                                     \
+            heap->dat = (kheap_t*)realloc(heap->dat, heap->mdat*sizeof(kheap_t));         \
+            memset(heap->dat + heap->ndat, 0, (heap->mdat - heap->ndat)*sizeof(kheap_t)); \
+        }                                                               \
+        int i = heap->ndat - 1;                                         \
+        while ( i && __cmp(dat,&heap->dat[khp_parent(i)]) )             \
+        {                                                               \
+            heap->dat[i] = heap->dat[khp_parent(i)];                    \
+            i = khp_parent(i);                                          \
+        }                                                               \
+        heap->dat[i] = *dat;                                            \
+        return i;                                                       \
+    }                                                                   \
+    SCOPE void khp_heapify_##name(khp_##name##_t *heap, int i)          \
+    {                                                                   \
+/*todo: loop instead of a recursive function? */ \
+        int extreme = khp_lchild(i) < heap->ndat && __cmp(&heap->dat[khp_lchild(i)],&heap->dat[i]) ? khp_lchild(i) : i;     \
+        if ( khp_rchild(i) < heap->ndat && __cmp(&heap->dat[khp_rchild(i)],&heap->dat[extreme]) ) extreme = khp_rchild(i);  \
+        if ( extreme != i )                                             \
+        {                                                               \
+            khp_swap(heap,i,extreme);                                   \
+            khp_heapify_##name(heap,extreme);                           \
+        }                                                               \
+    }                                                                   \
+    SCOPE void khp_delete_##name(khp_##name##_t *heap)                  \
+    {                                                                   \
+        if ( !heap || !heap->ndat ) return;                             \
+        heap->dat[0] = heap->dat[--heap->ndat];                         \
+        khp_heapify_##name(heap, 0);                                    \
+    }                                                                   \
+
+#define KHEAP_INIT(name, kheap_t, __cmp)            \
+    __KHEAP_TYPE(name, kheap_t)                     \
+    __KHEAP_IMPL(name, static kh_inline klib_unused, kheap_t, __cmp)
+
+#define khp_init(name) khp_init_##name()
+#define khp_destroy(name, heap) khp_destroy_##name(heap)
+#define khp_insert(name, heap, dat) khp_insert_##name(heap, dat)
+#define khp_delete(name, heap) khp_delete_##name(heap)
+
+#endif
diff --git a/bcftools/kmin.c b/bcftools/kmin.c
new file mode 100644
index 0000000..5b8193b
--- /dev/null
+++ b/bcftools/kmin.c
@@ -0,0 +1,209 @@
+/* The MIT License
+
+   Copyright (c) 2008, 2010 by Attractive Chaos <attractor@live.co.uk>
+
+   Permission is hereby granted, free of charge, to any person obtaining
+   a copy of this software and associated documentation files (the
+   "Software"), to deal in the Software without restriction, including
+   without limitation the rights to use, copy, modify, merge, publish,
+   distribute, sublicense, and/or sell copies of the Software, and to
+   permit persons to whom the Software is furnished to do so, subject to
+   the following conditions:
+
+   The above copyright notice and this permission notice shall be
+   included in all copies or substantial portions of the Software.
+
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+   EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+   MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+   NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
+   BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+   ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+   CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+   SOFTWARE.
+*/
+
+/* Hooke-Jeeves algorithm for nonlinear minimization
+ 
+   Based on the pseudocodes by Bell and Pike (CACM 9(9):684-685), and
+   the revision by Tomlin and Smith (CACM 12(11):637-638). Both of the
+   papers are comments on Kaupe's Algorithm 178 "Direct Search" (ACM
+   6(6):313-314). The original algorithm was designed by Hooke and
+   Jeeves (ACM 8:212-229). This program is further revised according to
+   Johnson's implementation at Netlib (opt/hooke.c).
+ 
+   Hooke-Jeeves algorithm is very simple and it works quite well on a
+   few examples. However, it might fail to converge due to its heuristic
+   nature. A possible improvement, as is suggested by Johnson, may be to
+   choose a small r at the beginning to quickly approach to the minimum
+   and a large r at later step to hit the minimum.
+ */
+
+#include <stdlib.h>
+#include <string.h>
+#include <math.h>
+#include "kmin.h"
+
+static double __kmin_hj_aux(kmin_f func, int n, double *x1, void *data, double fx1, double *dx, int *n_calls)
+{
+	int k, j = *n_calls;
+	double ftmp;
+	for (k = 0; k != n; ++k) {
+		x1[k] += dx[k];
+		ftmp = func(n, x1, data); ++j;
+		if (ftmp < fx1) fx1 = ftmp;
+		else { /* search the opposite direction */
+			dx[k] = 0.0 - dx[k];
+			x1[k] += dx[k] + dx[k];
+			ftmp = func(n, x1, data); ++j;
+			if (ftmp < fx1) fx1 = ftmp;
+			else x1[k] -= dx[k]; /* back to the original x[k] */
+		}
+	}
+	*n_calls = j;
+	return fx1; /* here: fx1=f(n,x1) */
+}
+
+double kmin_hj(kmin_f func, int n, double *x, void *data, double r, double eps, int max_calls)
+{
+	double fx, fx1, *x1, *dx, radius;
+	int k, n_calls = 0;
+	x1 = (double*)calloc(n, sizeof(double));
+	dx = (double*)calloc(n, sizeof(double));
+	for (k = 0; k != n; ++k) { /* initial directions, based on MGJ */
+		dx[k] = fabs(x[k]) * r;
+		if (dx[k] == 0) dx[k] = r;
+	}
+	radius = r;
+	fx1 = fx = func(n, x, data); ++n_calls;
+	for (;;) {
+		memcpy(x1, x, n * sizeof(double)); /* x1 = x */
+		fx1 = __kmin_hj_aux(func, n, x1, data, fx, dx, &n_calls);
+		while (fx1 < fx) {
+			for (k = 0; k != n; ++k) {
+				double t = x[k];
+				dx[k] = x1[k] > x[k]? fabs(dx[k]) : 0.0 - fabs(dx[k]);
+				x[k] = x1[k];
+				x1[k] = x1[k] + x1[k] - t;
+			}
+			fx = fx1;
+			if (n_calls >= max_calls) break;
+			fx1 = func(n, x1, data); ++n_calls;
+			fx1 = __kmin_hj_aux(func, n, x1, data, fx1, dx, &n_calls);
+			if (fx1 >= fx) break;
+			for (k = 0; k != n; ++k)
+				if (fabs(x1[k] - x[k]) > .5 * fabs(dx[k])) break;
+			if (k == n) break;
+		}
+		if (radius >= eps) {
+			if (n_calls >= max_calls) break;
+			radius *= r;
+			for (k = 0; k != n; ++k) dx[k] *= r;
+		} else break; /* converge */
+	}
+	free(x1); free(dx);
+	return fx1;
+}
+
+// I copied this function somewhere several years ago with some of my modifications, but I forgot the source.
+double kmin_brent(kmin1_f func, double a, double b, void *data, double tol, double *xmin)
+{
+	double bound, u, r, q, fu, tmp, fa, fb, fc, c;
+	const double gold1 = 1.6180339887;
+	const double gold2 = 0.3819660113;
+	const double tiny = 1e-20;
+	const int max_iter = 100;
+
+	double e, d, w, v, mid, tol1, tol2, p, eold, fv, fw;
+	int iter;
+
+	fa = func(a, data); fb = func(b, data);
+	if (fb > fa) { // swap, such that f(a) > f(b)
+		tmp = a; a = b; b = tmp;
+		tmp = fa; fa = fb; fb = tmp;
+	}
+	c = b + gold1 * (b - a), fc = func(c, data); // golden section extrapolation
+	while (fb > fc) {
+		bound = b + 100.0 * (c - b); // the farthest point where we want to go
+		r = (b - a) * (fb - fc);
+		q = (b - c) * (fb - fa);
+		if (fabs(q - r) < tiny) { // avoid 0 denominator
+			tmp = q > r? tiny : 0.0 - tiny;
+		} else tmp = q - r;
+		u = b - ((b - c) * q - (b - a) * r) / (2.0 * tmp); // u is the parabolic extrapolation point
+		if ((b > u && u > c) || (b < u && u < c)) { // u lies between b and c
+			fu = func(u, data);
+			if (fu < fc) { // (b,u,c) bracket the minimum
+				a = b; b = u; fa = fb; fb = fu;
+				break;
+			} else if (fu > fb) { // (a,b,u) bracket the minimum
+				c = u; fc = fu;
+				break;
+			}
+			u = c + gold1 * (c - b); fu = func(u, data); // golden section extrapolation
+		} else if ((c > u && u > bound) || (c < u && u < bound)) { // u lies between c and bound
+			fu = func(u, data);
+			if (fu < fc) { // fb > fc > fu
+				b = c; c = u; u = c + gold1 * (c - b);
+				fb = fc; fc = fu; fu = func(u, data);
+			} else { // (b,c,u) bracket the minimum
+				a = b; b = c; c = u;
+				fa = fb; fb = fc; fc = fu;
+				break;
+			}
+		} else if ((u > bound && bound > c) || (u < bound && bound < c)) { // u goes beyond the bound
+			u = bound; fu = func(u, data);
+		} else { // u goes the other way around, use golden section extrapolation
+			u = c + gold1 * (c - b); fu = func(u, data);
+		}
+		a = b; b = c; c = u;
+		fa = fb; fb = fc; fc = fu;
+	}
+	if (a > c) u = a, a = c, c = u; // swap
+
+	// now, a<b<c, fa>fb and fb<fc, move on to Brent's algorithm
+	e = d = 0.0;
+	w = v = b; fv = fw = fb;
+	for (iter = 0; iter != max_iter; ++iter) {
+		mid = 0.5 * (a + c);
+		tol2 = 2.0 * (tol1 = tol * fabs(b) + tiny);
+		if (fabs(b - mid) <= (tol2 - 0.5 * (c - a))) {
+			*xmin = b; return fb; // found
+		}
+		if (fabs(e) > tol1) {
+			// related to parabolic interpolation
+			r = (b - w) * (fb - fv);
+			q = (b - v) * (fb - fw);
+			p = (b - v) * q - (b - w) * r;
+			q = 2.0 * (q - r);
+			if (q > 0.0) p = 0.0 - p;
+			else q = 0.0 - q;
+			eold = e; e = d;
+			if (fabs(p) >= fabs(0.5 * q * eold) || p <= q * (a - b) || p >= q * (c - b)) {
+				d = gold2 * (e = (b >= mid ? a - b : c - b));
+			} else {
+				d = p / q; u = b + d; // actual parabolic interpolation happens here
+				if (u - a < tol2 || c - u < tol2)
+					d = (mid > b)? tol1 : 0.0 - tol1;
+			}
+		} else d = gold2 * (e = (b >= mid ? a - b : c - b)); // golden section interpolation
+		u = fabs(d) >= tol1 ? b + d : b + (d > 0.0? tol1 : -tol1);
+		fu = func(u, data);
+		if (fu <= fb) { // u is the minimum point so far
+			if (u >= b) a = b;
+			else c = b;
+			v = w; w = b; b = u; fv = fw; fw = fb; fb = fu;
+		} else { // adjust (a,c) and (u,v,w)
+			if (u < b) a = u;
+			else c = u;
+			if (fu <= fw || w == b) {
+				v = w; w = u;
+				fv = fw; fw = fu;
+			} else if (fu <= fv || v == b || v == w) {
+				v = u; fv = fu;
+			}
+		}
+	}
+	*xmin = b;
+	return fb;
+}
diff --git a/bcftools/kmin.c.pysam.c b/bcftools/kmin.c.pysam.c
new file mode 100644
index 0000000..f0ccb98
--- /dev/null
+++ b/bcftools/kmin.c.pysam.c
@@ -0,0 +1,211 @@
+#include "bcftools.pysam.h"
+
+/* The MIT License
+
+   Copyright (c) 2008, 2010 by Attractive Chaos <attractor@live.co.uk>
+
+   Permission is hereby granted, free of charge, to any person obtaining
+   a copy of this software and associated documentation files (the
+   "Software"), to deal in the Software without restriction, including
+   without limitation the rights to use, copy, modify, merge, publish,
+   distribute, sublicense, and/or sell copies of the Software, and to
+   permit persons to whom the Software is furnished to do so, subject to
+   the following conditions:
+
+   The above copyright notice and this permission notice shall be
+   included in all copies or substantial portions of the Software.
+
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+   EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+   MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+   NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
+   BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+   ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+   CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+   SOFTWARE.
+*/
+
+/* Hooke-Jeeves algorithm for nonlinear minimization
+ 
+   Based on the pseudocodes by Bell and Pike (CACM 9(9):684-685), and
+   the revision by Tomlin and Smith (CACM 12(11):637-638). Both of the
+   papers are comments on Kaupe's Algorithm 178 "Direct Search" (ACM
+   6(6):313-314). The original algorithm was designed by Hooke and
+   Jeeves (ACM 8:212-229). This program is further revised according to
+   Johnson's implementation at Netlib (opt/hooke.c).
+ 
+   Hooke-Jeeves algorithm is very simple and it works quite well on a
+   few examples. However, it might fail to converge due to its heuristic
+   nature. A possible improvement, as is suggested by Johnson, may be to
+   choose a small r at the beginning to quickly approach to the minimum
+   and a large r at later step to hit the minimum.
+ */
+
+#include <stdlib.h>
+#include <string.h>
+#include <math.h>
+#include "kmin.h"
+
+static double __kmin_hj_aux(kmin_f func, int n, double *x1, void *data, double fx1, double *dx, int *n_calls)
+{
+	int k, j = *n_calls;
+	double ftmp;
+	for (k = 0; k != n; ++k) {
+		x1[k] += dx[k];
+		ftmp = func(n, x1, data); ++j;
+		if (ftmp < fx1) fx1 = ftmp;
+		else { /* search the opposite direction */
+			dx[k] = 0.0 - dx[k];
+			x1[k] += dx[k] + dx[k];
+			ftmp = func(n, x1, data); ++j;
+			if (ftmp < fx1) fx1 = ftmp;
+			else x1[k] -= dx[k]; /* back to the original x[k] */
+		}
+	}
+	*n_calls = j;
+	return fx1; /* here: fx1=f(n,x1) */
+}
+
+double kmin_hj(kmin_f func, int n, double *x, void *data, double r, double eps, int max_calls)
+{
+	double fx, fx1, *x1, *dx, radius;
+	int k, n_calls = 0;
+	x1 = (double*)calloc(n, sizeof(double));
+	dx = (double*)calloc(n, sizeof(double));
+	for (k = 0; k != n; ++k) { /* initial directions, based on MGJ */
+		dx[k] = fabs(x[k]) * r;
+		if (dx[k] == 0) dx[k] = r;
+	}
+	radius = r;
+	fx1 = fx = func(n, x, data); ++n_calls;
+	for (;;) {
+		memcpy(x1, x, n * sizeof(double)); /* x1 = x */
+		fx1 = __kmin_hj_aux(func, n, x1, data, fx, dx, &n_calls);
+		while (fx1 < fx) {
+			for (k = 0; k != n; ++k) {
+				double t = x[k];
+				dx[k] = x1[k] > x[k]? fabs(dx[k]) : 0.0 - fabs(dx[k]);
+				x[k] = x1[k];
+				x1[k] = x1[k] + x1[k] - t;
+			}
+			fx = fx1;
+			if (n_calls >= max_calls) break;
+			fx1 = func(n, x1, data); ++n_calls;
+			fx1 = __kmin_hj_aux(func, n, x1, data, fx1, dx, &n_calls);
+			if (fx1 >= fx) break;
+			for (k = 0; k != n; ++k)
+				if (fabs(x1[k] - x[k]) > .5 * fabs(dx[k])) break;
+			if (k == n) break;
+		}
+		if (radius >= eps) {
+			if (n_calls >= max_calls) break;
+			radius *= r;
+			for (k = 0; k != n; ++k) dx[k] *= r;
+		} else break; /* converge */
+	}
+	free(x1); free(dx);
+	return fx1;
+}
+
+// I copied this function somewhere several years ago with some of my modifications, but I forgot the source.
+double kmin_brent(kmin1_f func, double a, double b, void *data, double tol, double *xmin)
+{
+	double bound, u, r, q, fu, tmp, fa, fb, fc, c;
+	const double gold1 = 1.6180339887;
+	const double gold2 = 0.3819660113;
+	const double tiny = 1e-20;
+	const int max_iter = 100;
+
+	double e, d, w, v, mid, tol1, tol2, p, eold, fv, fw;
+	int iter;
+
+	fa = func(a, data); fb = func(b, data);
+	if (fb > fa) { // swap, such that f(a) > f(b)
+		tmp = a; a = b; b = tmp;
+		tmp = fa; fa = fb; fb = tmp;
+	}
+	c = b + gold1 * (b - a), fc = func(c, data); // golden section extrapolation
+	while (fb > fc) {
+		bound = b + 100.0 * (c - b); // the farthest point where we want to go
+		r = (b - a) * (fb - fc);
+		q = (b - c) * (fb - fa);
+		if (fabs(q - r) < tiny) { // avoid 0 denominator
+			tmp = q > r? tiny : 0.0 - tiny;
+		} else tmp = q - r;
+		u = b - ((b - c) * q - (b - a) * r) / (2.0 * tmp); // u is the parabolic extrapolation point
+		if ((b > u && u > c) || (b < u && u < c)) { // u lies between b and c
+			fu = func(u, data);
+			if (fu < fc) { // (b,u,c) bracket the minimum
+				a = b; b = u; fa = fb; fb = fu;
+				break;
+			} else if (fu > fb) { // (a,b,u) bracket the minimum
+				c = u; fc = fu;
+				break;
+			}
+			u = c + gold1 * (c - b); fu = func(u, data); // golden section extrapolation
+		} else if ((c > u && u > bound) || (c < u && u < bound)) { // u lies between c and bound
+			fu = func(u, data);
+			if (fu < fc) { // fb > fc > fu
+				b = c; c = u; u = c + gold1 * (c - b);
+				fb = fc; fc = fu; fu = func(u, data);
+			} else { // (b,c,u) bracket the minimum
+				a = b; b = c; c = u;
+				fa = fb; fb = fc; fc = fu;
+				break;
+			}
+		} else if ((u > bound && bound > c) || (u < bound && bound < c)) { // u goes beyond the bound
+			u = bound; fu = func(u, data);
+		} else { // u goes the other way around, use golden section extrapolation
+			u = c + gold1 * (c - b); fu = func(u, data);
+		}
+		a = b; b = c; c = u;
+		fa = fb; fb = fc; fc = fu;
+	}
+	if (a > c) u = a, a = c, c = u; // swap
+
+	// now, a<b<c, fa>fb and fb<fc, move on to Brent's algorithm
+	e = d = 0.0;
+	w = v = b; fv = fw = fb;
+	for (iter = 0; iter != max_iter; ++iter) {
+		mid = 0.5 * (a + c);
+		tol2 = 2.0 * (tol1 = tol * fabs(b) + tiny);
+		if (fabs(b - mid) <= (tol2 - 0.5 * (c - a))) {
+			*xmin = b; return fb; // found
+		}
+		if (fabs(e) > tol1) {
+			// related to parabolic interpolation
+			r = (b - w) * (fb - fv);
+			q = (b - v) * (fb - fw);
+			p = (b - v) * q - (b - w) * r;
+			q = 2.0 * (q - r);
+			if (q > 0.0) p = 0.0 - p;
+			else q = 0.0 - q;
+			eold = e; e = d;
+			if (fabs(p) >= fabs(0.5 * q * eold) || p <= q * (a - b) || p >= q * (c - b)) {
+				d = gold2 * (e = (b >= mid ? a - b : c - b));
+			} else {
+				d = p / q; u = b + d; // actual parabolic interpolation happens here
+				if (u - a < tol2 || c - u < tol2)
+					d = (mid > b)? tol1 : 0.0 - tol1;
+			}
+		} else d = gold2 * (e = (b >= mid ? a - b : c - b)); // golden section interpolation
+		u = fabs(d) >= tol1 ? b + d : b + (d > 0.0? tol1 : -tol1);
+		fu = func(u, data);
+		if (fu <= fb) { // u is the minimum point so far
+			if (u >= b) a = b;
+			else c = b;
+			v = w; w = b; b = u; fv = fw; fw = fb; fb = fu;
+		} else { // adjust (a,c) and (u,v,w)
+			if (u < b) a = u;
+			else c = u;
+			if (fu <= fw || w == b) {
+				v = w; w = u;
+				fv = fw; fw = fu;
+			} else if (fu <= fv || v == b || v == w) {
+				v = u; fv = fu;
+			}
+		}
+	}
+	*xmin = b;
+	return fb;
+}
diff --git a/bcftools/kmin.h b/bcftools/kmin.h
new file mode 100644
index 0000000..6feba45
--- /dev/null
+++ b/bcftools/kmin.h
@@ -0,0 +1,46 @@
+/*
+   Copyright (c) 2008, 2010 by Attractive Chaos <attractor@live.co.uk>
+
+   Permission is hereby granted, free of charge, to any person obtaining
+   a copy of this software and associated documentation files (the
+   "Software"), to deal in the Software without restriction, including
+   without limitation the rights to use, copy, modify, merge, publish,
+   distribute, sublicense, and/or sell copies of the Software, and to
+   permit persons to whom the Software is furnished to do so, subject to
+   the following conditions:
+
+   The above copyright notice and this permission notice shall be
+   included in all copies or substantial portions of the Software.
+
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+   EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+   MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+   NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
+   BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+   ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+   CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+   SOFTWARE.
+*/
+
+#ifndef KMIN_H
+#define KMIN_H
+
+#define KMIN_RADIUS  0.5
+#define KMIN_EPS     1e-7
+#define KMIN_MAXCALL 50000
+
+typedef double (*kmin_f)(int, double*, void*);
+typedef double (*kmin1_f)(double, void*);
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+	double kmin_hj(kmin_f func, int n, double *x, void *data, double r, double eps, int max_calls);
+	double kmin_brent(kmin1_f func, double a, double b, void *data, double tol, double *xmin);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif
diff --git a/bcftools/main.c b/bcftools/main.c
new file mode 100644
index 0000000..3a0d557
--- /dev/null
+++ b/bcftools/main.c
@@ -0,0 +1,310 @@
+/*  main.c -- main bcftools command front-end.
+
+    Copyright (C) 2012-2021 Genome Research Ltd.
+
+    Author: Petr Danecek <pd3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.  */
+
+#include "config.h"
+#include <stdio.h>
+#include <stdlib.h>
+#include <unistd.h>
+#include <string.h>
+#include <ctype.h>
+#include <htslib/hts.h>
+#include "version.h"
+#include "bcftools.h"
+
+int main_tabix(int argc, char *argv[]);
+int main_vcfindex(int argc, char *argv[]);
+int main_vcfstats(int argc, char *argv[]);
+int main_vcfisec(int argc, char *argv[]);
+int main_vcfmerge(int argc, char *argv[]);
+int main_vcfquery(int argc, char *argv[]);
+int main_vcffilter(int argc, char *argv[]);
+int main_vcfsom(int argc, char *argv[]);
+int main_vcfnorm(int argc, char *argv[]);
+int main_vcfgtcheck(int argc, char *argv[]);
+int main_vcfview(int argc, char *argv[]);
+int main_vcfhead(int argc, char *argv[]);
+int main_vcfcall(int argc, char *argv[]);
+int main_vcfannotate(int argc, char *argv[]);
+int main_vcfroh(int argc, char *argv[]);
+int main_vcfconcat(int argc, char *argv[]);
+int main_reheader(int argc, char *argv[]);
+int main_vcfconvert(int argc, char *argv[]);
+int main_vcfcnv(int argc, char *argv[]);
+#if USE_GPL
+int main_polysomy(int argc, char *argv[]);
+#endif
+#ifdef ENABLE_BCF_PLUGINS
+int main_plugin(int argc, char *argv[]);
+int count_plugins(void);
+#endif
+int main_consensus(int argc, char *argv[]);
+int main_csq(int argc, char *argv[]);
+int main_mpileup(int argc, char *argv[]);
+int main_sort(int argc, char *argv[]);
+
+typedef struct
+{
+    int (*func)(int, char*[]);
+    const char *alias, *help;
+}
+cmd_t;
+
+static cmd_t cmds[] =
+{
+    { .func  = NULL,
+      .alias = "Indexing",
+      .help  = NULL
+    },
+    { .func = main_vcfindex,
+      .alias = "index",
+      .help = "index VCF/BCF files"
+    },
+    { .func = main_tabix,
+      .alias = "tabix",
+      .help = "-tabix for BGZF'd BED, GFF, SAM, VCF and more" // do not advertise; only keep here for testing
+    },
+
+    { .func  = NULL,
+      .alias = "VCF/BCF manipulation",
+      .help  = NULL
+    },
+
+    { .func  = main_vcfannotate,
+      .alias = "annotate",
+      .help  = "annotate and edit VCF/BCF files",
+    },
+    { .func  = main_vcfconcat,
+      .alias = "concat",
+      .help  = "concatenate VCF/BCF files from the same set of samples"
+    },
+    { .func  = main_vcfconvert,
+      .alias = "convert",
+      .help  = "convert VCF/BCF files to different formats and back"
+    },
+    { .func  = main_vcfhead,
+      .alias = "head",
+      .help  = "view VCF/BCF file headers"
+    },
+    { .func  = main_vcfisec,
+      .alias = "isec",
+      .help  = "intersections of VCF/BCF files"
+    },
+    { .func  = main_vcfmerge,
+      .alias = "merge",
+      .help  = "merge VCF/BCF files files from non-overlapping sample sets"
+    },
+    { .func  = main_vcfnorm,
+      .alias = "norm",
+      .help  = "left-align and normalize indels"
+    },
+#ifdef ENABLE_BCF_PLUGINS
+    { .func  = main_plugin,
+      .alias = "plugin",
+      .help  = "user-defined plugins"
+    },
+#endif
+    { .func  = main_vcfquery,
+      .alias = "query",
+      .help  = "transform VCF/BCF into user-defined formats"
+    },
+    { .func  = main_reheader,
+      .alias = "reheader",
+      .help  = "modify VCF/BCF header, change sample names"
+    },
+    { .func  = main_sort,
+      .alias = "sort",
+      .help  = "sort VCF/BCF file"
+    },
+    { .func  = main_vcfview,
+      .alias = "view",
+      .help  = "VCF/BCF conversion, view, subset and filter VCF/BCF files"
+    },
+
+    { .func  = NULL,
+      .alias = "VCF/BCF analysis",
+      .help  = NULL
+    },
+
+    { .func  = main_vcfcall,
+      .alias = "call",
+      .help  = "SNP/indel calling"
+    },
+    { .func  = main_consensus,
+      .alias = "consensus",
+      .help  = "create consensus sequence by applying VCF variants"
+    },
+    { .func  = main_vcfcnv,
+      .alias = "cnv",
+      .help  = "HMM CNV calling"
+    },
+    { .func  = main_csq,
+      .alias = "csq",
+      .help  = "call variation consequences"
+    },
+    { .func  = main_vcffilter,
+      .alias = "filter",
+      .help  = "filter VCF/BCF files using fixed thresholds"
+    },
+    { .func  = main_vcfgtcheck,
+      .alias = "gtcheck",
+      .help  = "check sample concordance, detect sample swaps and contamination"
+    },
+    { .func  = main_mpileup,
+        .alias = "mpileup",
+        .help  = "multi-way pileup producing genotype likelihoods"
+    },
+#if USE_GPL
+    { .func  = main_polysomy,
+      .alias = "polysomy",
+      .help  = "detect number of chromosomal copies",
+    },
+#endif
+    { .func  = main_vcfroh,
+      .alias = "roh",
+      .help  = "identify runs of autozygosity (HMM)",
+    },
+    { .func  = main_vcfstats,
+      .alias = "stats",
+      .help  = "produce VCF/BCF stats"
+    },
+
+    { .func  = main_vcfsom,
+      .alias = "som",
+      .help  = "-filter using Self-Organized Maps (experimental)"   // do not advertise
+
+    },
+    { .func  = NULL,
+      .alias = NULL,
+      .help  = NULL
+    }
+};
+
+char *bcftools_version(void)
+{
+    return BCFTOOLS_VERSION;
+}
+
+static void usage(FILE *fp)
+{
+    fprintf(fp, "\n");
+    fprintf(fp, "Program: bcftools (Tools for variant calling and manipulating VCFs and BCFs)\n");
+#if USE_GPL
+    fprintf(fp, "License: GNU GPLv3+, due to use of the GNU Scientific Library\n");
+#endif
+    fprintf(fp, "Version: %s (using htslib %s)\n", bcftools_version(), hts_version());
+    fprintf(fp, "\n");
+    fprintf(fp, "Usage:   bcftools [--version|--version-only] [--help] <command> <argument>\n");
+    fprintf(fp, "\n");
+    fprintf(fp, "Commands:\n");
+
+    int i = 0;
+    const char *sep = NULL;
+    while (cmds[i].alias)
+    {
+        if ( !cmds[i].func ) sep = cmds[i].alias;
+        if ( sep )
+        {
+            fprintf(fp, "\n -- %s\n", sep);
+            sep = NULL;
+        }
+        if ( cmds[i].func && cmds[i].help[0]!='-' ) fprintf(fp, "    %-12s %s\n", cmds[i].alias, cmds[i].help);
+        i++;
+    }
+#if ENABLE_BCF_PLUGINS
+    fprintf(fp,"\n -- Plugins (collection of programs for calling, file manipulation & analysis)\n");
+    int nplugins = count_plugins();
+    if ( nplugins )
+        fprintf(fp,"    %d plugins available, run \"bcftools plugin -lv\" to see a complete list\n", nplugins);
+    else
+        fprintf(fp,"    0 plugins available, run \"bcftools plugin -l\" for help\n");
+#endif
+    fprintf(fp,"\n");
+    fprintf(fp,
+            " Most commands accept VCF, bgzipped VCF, and BCF with the file type detected\n"
+            " automatically even when streaming from a pipe. Indexed VCF and BCF will work\n"
+            " in all situations. Un-indexed VCF and BCF and streams will work in most but\n"
+            " not all situations.\n");
+    fprintf(fp,"\n");
+}
+
+// This is a tricky one, but on Windows the filename wildcard expansion is done by
+// the application and not by the shell, as traditionally it never had a "shell".
+// Even now, DOS and Powershell do not do this expansion (but bash does).
+//
+// This means that Mingw/Msys implements code before main() that takes e.g. "*" and
+// expands it up to a list of matching filenames.  This in turn breaks things like
+// specifying "*" as a region (all the unmapped reads).  We take a hard line here -
+// filename expansion is the task of the shell, not our application!
+#ifdef _WIN32
+int _CRT_glob = 0;
+#endif
+
+int main(int argc, char *argv[])
+{
+    if (argc < 2) { usage(stderr); return 1; }
+
+    if (strcmp(argv[1], "version") == 0 || strcmp(argv[1], "--version") == 0 || strcmp(argv[1], "-v") == 0) {
+        printf("bcftools %s\nUsing htslib %s\nCopyright (C) 2022 Genome Research Ltd.\n", bcftools_version(), hts_version());
+#if USE_GPL
+        printf("License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>\n");
+#else
+        printf("License Expat: The MIT/Expat license\n");
+#endif
+        printf("This is free software: you are free to change and redistribute it.\nThere is NO WARRANTY, to the extent permitted by law.\n");
+        return 0;
+    }
+    else if (strcmp(argv[1], "--version-only") == 0) {
+        printf("%s+htslib-%s\n", bcftools_version(), hts_version());
+        return 0;
+    }
+    else if (strcmp(argv[1], "help") == 0 || strcmp(argv[1], "--help") == 0 || strcmp(argv[1], "-h") == 0) {
+        if (argc == 2) { usage(stdout); return 0; }
+        // Otherwise change "bcftools help COMMAND [...]" to "bcftools COMMAND";
+        // main_xyz() functions by convention display the subcommand's usage
+        // when invoked without any arguments.
+        argv++;
+        argc = 2;
+    }
+    else if ( argv[1][0]=='+' )
+    {
+        // "bcftools plugin name" can be run as "bcftools +name"
+        argv[1]++;
+        argv[0] = "plugin";
+        argv--;
+        argc++;
+    }
+
+    int i = 0;
+    while (cmds[i].alias)
+    {
+        if (cmds[i].func && strcmp(argv[1],cmds[i].alias)==0)
+        {
+            return cmds[i].func(argc-1,argv+1);
+        }
+        i++;
+    }
+    fprintf(stderr, "[E::%s] unrecognized command '%s'\n", __func__, argv[1]);
+    return 1;
+}
+
diff --git a/bcftools/main.c.pysam.c b/bcftools/main.c.pysam.c
new file mode 100644
index 0000000..535813c
--- /dev/null
+++ b/bcftools/main.c.pysam.c
@@ -0,0 +1,312 @@
+#include "bcftools.pysam.h"
+
+/*  main.c -- main bcftools command front-end.
+
+    Copyright (C) 2012-2021 Genome Research Ltd.
+
+    Author: Petr Danecek <pd3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.  */
+
+#include "config.h"
+#include <stdio.h>
+#include <stdlib.h>
+#include <unistd.h>
+#include <string.h>
+#include <ctype.h>
+#include <htslib/hts.h>
+#include "version.h"
+#include "bcftools.h"
+
+int main_tabix(int argc, char *argv[]);
+int main_vcfindex(int argc, char *argv[]);
+int main_vcfstats(int argc, char *argv[]);
+int main_vcfisec(int argc, char *argv[]);
+int main_vcfmerge(int argc, char *argv[]);
+int main_vcfquery(int argc, char *argv[]);
+int main_vcffilter(int argc, char *argv[]);
+int main_vcfsom(int argc, char *argv[]);
+int main_vcfnorm(int argc, char *argv[]);
+int main_vcfgtcheck(int argc, char *argv[]);
+int main_vcfview(int argc, char *argv[]);
+int main_vcfhead(int argc, char *argv[]);
+int main_vcfcall(int argc, char *argv[]);
+int main_vcfannotate(int argc, char *argv[]);
+int main_vcfroh(int argc, char *argv[]);
+int main_vcfconcat(int argc, char *argv[]);
+int main_reheader(int argc, char *argv[]);
+int main_vcfconvert(int argc, char *argv[]);
+int main_vcfcnv(int argc, char *argv[]);
+#if USE_GPL
+int main_polysomy(int argc, char *argv[]);
+#endif
+#ifdef ENABLE_BCF_PLUGINS
+int main_plugin(int argc, char *argv[]);
+int count_plugins(void);
+#endif
+int main_consensus(int argc, char *argv[]);
+int main_csq(int argc, char *argv[]);
+int main_mpileup(int argc, char *argv[]);
+int main_sort(int argc, char *argv[]);
+
+typedef struct
+{
+    int (*func)(int, char*[]);
+    const char *alias, *help;
+}
+cmd_t;
+
+static cmd_t cmds[] =
+{
+    { .func  = NULL,
+      .alias = "Indexing",
+      .help  = NULL
+    },
+    { .func = main_vcfindex,
+      .alias = "index",
+      .help = "index VCF/BCF files"
+    },
+    { .func = main_tabix,
+      .alias = "tabix",
+      .help = "-tabix for BGZF'd BED, GFF, SAM, VCF and more" // do not advertise; only keep here for testing
+    },
+
+    { .func  = NULL,
+      .alias = "VCF/BCF manipulation",
+      .help  = NULL
+    },
+
+    { .func  = main_vcfannotate,
+      .alias = "annotate",
+      .help  = "annotate and edit VCF/BCF files",
+    },
+    { .func  = main_vcfconcat,
+      .alias = "concat",
+      .help  = "concatenate VCF/BCF files from the same set of samples"
+    },
+    { .func  = main_vcfconvert,
+      .alias = "convert",
+      .help  = "convert VCF/BCF files to different formats and back"
+    },
+    { .func  = main_vcfhead,
+      .alias = "head",
+      .help  = "view VCF/BCF file headers"
+    },
+    { .func  = main_vcfisec,
+      .alias = "isec",
+      .help  = "intersections of VCF/BCF files"
+    },
+    { .func  = main_vcfmerge,
+      .alias = "merge",
+      .help  = "merge VCF/BCF files files from non-overlapping sample sets"
+    },
+    { .func  = main_vcfnorm,
+      .alias = "norm",
+      .help  = "left-align and normalize indels"
+    },
+#ifdef ENABLE_BCF_PLUGINS
+    { .func  = main_plugin,
+      .alias = "plugin",
+      .help  = "user-defined plugins"
+    },
+#endif
+    { .func  = main_vcfquery,
+      .alias = "query",
+      .help  = "transform VCF/BCF into user-defined formats"
+    },
+    { .func  = main_reheader,
+      .alias = "reheader",
+      .help  = "modify VCF/BCF header, change sample names"
+    },
+    { .func  = main_sort,
+      .alias = "sort",
+      .help  = "sort VCF/BCF file"
+    },
+    { .func  = main_vcfview,
+      .alias = "view",
+      .help  = "VCF/BCF conversion, view, subset and filter VCF/BCF files"
+    },
+
+    { .func  = NULL,
+      .alias = "VCF/BCF analysis",
+      .help  = NULL
+    },
+
+    { .func  = main_vcfcall,
+      .alias = "call",
+      .help  = "SNP/indel calling"
+    },
+    { .func  = main_consensus,
+      .alias = "consensus",
+      .help  = "create consensus sequence by applying VCF variants"
+    },
+    { .func  = main_vcfcnv,
+      .alias = "cnv",
+      .help  = "HMM CNV calling"
+    },
+    { .func  = main_csq,
+      .alias = "csq",
+      .help  = "call variation consequences"
+    },
+    { .func  = main_vcffilter,
+      .alias = "filter",
+      .help  = "filter VCF/BCF files using fixed thresholds"
+    },
+    { .func  = main_vcfgtcheck,
+      .alias = "gtcheck",
+      .help  = "check sample concordance, detect sample swaps and contamination"
+    },
+    { .func  = main_mpileup,
+        .alias = "mpileup",
+        .help  = "multi-way pileup producing genotype likelihoods"
+    },
+#if USE_GPL
+    { .func  = main_polysomy,
+      .alias = "polysomy",
+      .help  = "detect number of chromosomal copies",
+    },
+#endif
+    { .func  = main_vcfroh,
+      .alias = "roh",
+      .help  = "identify runs of autozygosity (HMM)",
+    },
+    { .func  = main_vcfstats,
+      .alias = "stats",
+      .help  = "produce VCF/BCF stats"
+    },
+
+    { .func  = main_vcfsom,
+      .alias = "som",
+      .help  = "-filter using Self-Organized Maps (experimental)"   // do not advertise
+
+    },
+    { .func  = NULL,
+      .alias = NULL,
+      .help  = NULL
+    }
+};
+
+char *bcftools_version(void)
+{
+    return BCFTOOLS_VERSION;
+}
+
+static void usage(FILE *fp)
+{
+    fprintf(fp, "\n");
+    fprintf(fp, "Program: bcftools (Tools for variant calling and manipulating VCFs and BCFs)\n");
+#if USE_GPL
+    fprintf(fp, "License: GNU GPLv3+, due to use of the GNU Scientific Library\n");
+#endif
+    fprintf(fp, "Version: %s (using htslib %s)\n", bcftools_version(), hts_version());
+    fprintf(fp, "\n");
+    fprintf(fp, "Usage:   bcftools [--version|--version-only] [--help] <command> <argument>\n");
+    fprintf(fp, "\n");
+    fprintf(fp, "Commands:\n");
+
+    int i = 0;
+    const char *sep = NULL;
+    while (cmds[i].alias)
+    {
+        if ( !cmds[i].func ) sep = cmds[i].alias;
+        if ( sep )
+        {
+            fprintf(fp, "\n -- %s\n", sep);
+            sep = NULL;
+        }
+        if ( cmds[i].func && cmds[i].help[0]!='-' ) fprintf(fp, "    %-12s %s\n", cmds[i].alias, cmds[i].help);
+        i++;
+    }
+#if ENABLE_BCF_PLUGINS
+    fprintf(fp,"\n -- Plugins (collection of programs for calling, file manipulation & analysis)\n");
+    int nplugins = count_plugins();
+    if ( nplugins )
+        fprintf(fp,"    %d plugins available, run \"bcftools plugin -lv\" to see a complete list\n", nplugins);
+    else
+        fprintf(fp,"    0 plugins available, run \"bcftools plugin -l\" for help\n");
+#endif
+    fprintf(fp,"\n");
+    fprintf(fp,
+            " Most commands accept VCF, bgzipped VCF, and BCF with the file type detected\n"
+            " automatically even when streaming from a pipe. Indexed VCF and BCF will work\n"
+            " in all situations. Un-indexed VCF and BCF and streams will work in most but\n"
+            " not all situations.\n");
+    fprintf(fp,"\n");
+}
+
+// This is a tricky one, but on Windows the filename wildcard expansion is done by
+// the application and not by the shell, as traditionally it never had a "shell".
+// Even now, DOS and Powershell do not do this expansion (but bash does).
+//
+// This means that Mingw/Msys implements code before main() that takes e.g. "*" and
+// expands it up to a list of matching filenames.  This in turn breaks things like
+// specifying "*" as a region (all the unmapped reads).  We take a hard line here -
+// filename expansion is the task of the shell, not our application!
+#ifdef _WIN32
+int _CRT_glob = 0;
+#endif
+
+int bcftools_main(int argc, char *argv[])
+{
+    if (argc < 2) { usage(bcftools_stderr); return 1; }
+
+    if (strcmp(argv[1], "version") == 0 || strcmp(argv[1], "--version") == 0 || strcmp(argv[1], "-v") == 0) {
+        fprintf(bcftools_stdout, "bcftools %s\nUsing htslib %s\nCopyright (C) 2022 Genome Research Ltd.\n", bcftools_version(), hts_version());
+#if USE_GPL
+        fprintf(bcftools_stdout, "License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>\n");
+#else
+        fprintf(bcftools_stdout, "License Expat: The MIT/Expat license\n");
+#endif
+        fprintf(bcftools_stdout, "This is free software: you are free to change and redistribute it.\nThere is NO WARRANTY, to the extent permitted by law.\n");
+        return 0;
+    }
+    else if (strcmp(argv[1], "--version-only") == 0) {
+        fprintf(bcftools_stdout, "%s+htslib-%s\n", bcftools_version(), hts_version());
+        return 0;
+    }
+    else if (strcmp(argv[1], "help") == 0 || strcmp(argv[1], "--help") == 0 || strcmp(argv[1], "-h") == 0) {
+        if (argc == 2) { usage(bcftools_stdout); return 0; }
+        // Otherwise change "bcftools help COMMAND [...]" to "bcftools COMMAND";
+        // main_xyz() functions by convention display the subcommand's usage
+        // when invoked without any arguments.
+        argv++;
+        argc = 2;
+    }
+    else if ( argv[1][0]=='+' )
+    {
+        // "bcftools plugin name" can be run as "bcftools +name"
+        argv[1]++;
+        argv[0] = "plugin";
+        argv--;
+        argc++;
+    }
+
+    int i = 0;
+    while (cmds[i].alias)
+    {
+        if (cmds[i].func && strcmp(argv[1],cmds[i].alias)==0)
+        {
+            return cmds[i].func(argc-1,argv+1);
+        }
+        i++;
+    }
+    fprintf(bcftools_stderr, "[E::%s] unrecognized command '%s'\n", __func__, argv[1]);
+    return 1;
+}
+
diff --git a/bcftools/mcall.c b/bcftools/mcall.c
new file mode 100644
index 0000000..5761896
--- /dev/null
+++ b/bcftools/mcall.c
@@ -0,0 +1,1685 @@
+/*  mcall.c -- multiallelic and rare variant calling.
+
+    Copyright (C) 2012-2021 Genome Research Ltd.
+
+    Author: Petr Danecek <pd3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.  */
+
+#include <assert.h>
+#include <math.h>
+#include <inttypes.h>
+#include <ctype.h>
+#include <htslib/kfunc.h>
+#include <htslib/khash_str2int.h>
+#include "call.h"
+#include "prob1.h"
+
+// Using priors for GTs does not seem to be mathematically justified. Although
+// it seems effective in removing false calls, it also flips a significant
+// proportion of HET genotypes. Better is to filter by FORMAT/GQ using
+// `bcftools filter`.
+#define USE_PRIOR_FOR_GTS 0
+
+// Go with uniform PLs for samples with no coverage. If unset, missing
+// genotypes is reported instead.
+#define FLAT_PDG_FOR_MISSING 0
+
+int test16(float *anno16, anno16_t *a);
+
+void qcall_init(call_t *call) { return; }
+void qcall_destroy(call_t *call) { return; }
+int qcall(call_t *call, bcf1_t *rec)
+{
+    // QCall format:
+    //  chromosome, position, reference allele, depth, mapping quality, 0, ..
+    error("TODO: qcall output\n");
+    return 0;
+}
+
+void call_init_pl2p(call_t *call)
+{
+    int i;
+    for (i=0; i<256; i++)
+        call->pl2p[i] = pow(10., -i/10.);
+}
+
+// Macros for accessing call->trio and call->ntrio
+#define FTYPE_222 0     // family type: all diploid
+#define FTYPE_121 1     // chrX, the child is a boy
+#define FTYPE_122 2     // chrX, a girl
+#define FTYPE_101 3     // chrY, boy
+#define FTYPE_100 4     // chrY, girl
+
+#define GT_SKIP 0xf     // empty genotype (chrY in females)
+
+#define IS_POW2(x) (!((x) & ((x) - 1)))    // zero is permitted
+#define IS_HOM(x)  IS_POW2(x)
+
+// Pkij = P(k|i,j) tells how likely it is to be a het if the parents
+// are homs etc. The consistency of i,j,k has been already checked.
+// Parameters are alleles and ploidy of father, mother, kid
+// Returns 2/Pkij.
+int calc_Pkij(int fals, int mals, int kals, int fpl, int mpl, int kpl)
+{
+    int als = fals|mals|kals;
+    if ( IS_HOM(als) ) return 2;    // all are the same: child must be a HOM, P=1
+
+    if ( fpl==1 )
+    {
+        if ( kpl==1 )   // chr X, the child is a boy, the copy is inherited from the mother
+        {
+            if ( IS_HOM(mals) ) return 2;   // 0 11 -> P(1) = 1
+            return 4;                       // 0 01 -> P(0) = P(1) = 1/2
+        }
+        // chr X, the child is a girl
+        if ( IS_HOM(mals) ) return 2;       // 0 11 -> P(01) = 1
+        return 4;                           // 0 01 -> P(00) = P(01) = 1/2
+    }
+
+    if ( IS_HOM(fals) && IS_HOM(mals) ) return 2;   // 00 11 01, the child must be a HET, P=1
+    if ( !IS_HOM(fals) && !IS_HOM(mals) )
+    {
+        if ( IS_HOM(kals) ) return 8;   // 01 01 00 or 01 01 11, P(k=HOM) = 1/4
+        return 4;                       // 01 01 01, P(k=HET) = 1/2
+    }
+    return 4;   // 00 01, P(k=HET) = P(k=HOM) = 1/2
+}
+
+// Initialize ntrio and trio: ntrio lists the number of possible
+// genotypes given combination of haploid/diploid genomes and the
+// number of alleles. trio lists allowed genotype combinations:
+//      4bit: 2/Pkij, 4: father, 4: mother, 4: child
+// See also mcall_call_trio_genotypes()
+//
+static void mcall_init_trios(call_t *call)
+{
+    if ( call->prior_AN )
+    {
+        int id = bcf_hdr_id2int(call->hdr,BCF_DT_ID,call->prior_AN);
+        if ( id==-1 ) error("No such tag \"%s\"\n", call->prior_AN);
+        if ( !bcf_hdr_idinfo_exists(call->hdr,BCF_HL_FMT,id) )  error("No such FORMAT tag \"%s\"\n", call->prior_AN);
+        id = bcf_hdr_id2int(call->hdr,BCF_DT_ID,call->prior_AC);
+        if ( id==-1 ) error("No such tag \"%s\"\n", call->prior_AC);
+        if ( !bcf_hdr_idinfo_exists(call->hdr,BCF_HL_FMT,id) )  error("No such FORMAT tag \"%s\"\n", call->prior_AC);
+    }
+
+    // 23, 138, 478 possible diploid trio genotypes with 2, 3, 4 alleles
+    call->ntrio[FTYPE_222][2] = 15; call->ntrio[FTYPE_222][3] = 78;  call->ntrio[FTYPE_222][4] = 250;
+    call->ntrio[FTYPE_121][2] = 8;  call->ntrio[FTYPE_121][3] = 27;  call->ntrio[FTYPE_121][4] = 64;
+    call->ntrio[FTYPE_122][2] = 8;  call->ntrio[FTYPE_122][3] = 27;  call->ntrio[FTYPE_122][4] = 64;
+    call->ntrio[FTYPE_101][2] = 2;  call->ntrio[FTYPE_101][3] = 3;   call->ntrio[FTYPE_101][4] = 4;
+    call->ntrio[FTYPE_100][2] = 2;  call->ntrio[FTYPE_100][3] = 3;   call->ntrio[FTYPE_100][4] = 4;
+
+    int nals, itype;
+    for (itype=0; itype<=4; itype++)
+    {
+        for (nals=2; nals<=4; nals++)
+            call->trio[itype][nals] = (uint16_t*) malloc(sizeof(uint16_t)*call->ntrio[itype][nals]);
+    }
+
+    // max 10 possible diploid genotypes
+    int gts[10];
+    for (nals=2; nals<=4; nals++)
+    {
+        int i,j,k, n = 0, ngts = 0;
+        for (i=0; i<nals; i++)
+            for (j=0; j<=i; j++)
+                gts[ngts++] = 1<<i | 1<<j;
+
+        // 222: all diploid
+        // i,j,k: father, mother, child
+        for (i=0; i<ngts; i++)
+            for (j=0; j<ngts; j++)
+                for (k=0; k<ngts; k++)
+                {
+                    if ( ((gts[i]|gts[j])&gts[k]) != gts[k] ) continue;             // k not present in neither i nor j
+                    if ( !(gts[i] & gts[k]) || !(gts[j] & gts[k]) ) continue;       // one copy from father, one from mother
+                    int Pkij = calc_Pkij(gts[i],gts[j],gts[k], 2,2,2);
+                    call->trio[FTYPE_222][nals][n++] = Pkij<<12 | i<<8 | j<<4 | k;  // father, mother, child
+                }
+        assert( n==call->ntrio[FTYPE_222][nals] );
+
+        // 121: chrX, boy
+        n = 0;
+        for (i=0; i<ngts; i++)
+            for (j=0; j<ngts; j++)
+                for (k=0; k<ngts; k++)
+                {
+                    if ( !IS_HOM(gts[i]) || !IS_HOM(gts[k]) ) continue;   // father nor boy can be diploid
+                    if ( ((gts[i]|gts[j])&gts[k]) != gts[k] ) continue;
+                    if ( !(gts[j] & gts[k]) ) continue;     // boy must inherit the copy from mother
+                    int Pkij = calc_Pkij(gts[i],gts[j],gts[k], 1,2,1);
+                    call->trio[FTYPE_121][nals][n++] = Pkij<<12 | i<<8 | j<<4 | k;
+                }
+        assert( n==call->ntrio[FTYPE_121][nals] );
+
+        // 122: chrX, girl
+        n = 0;
+        for (i=0; i<ngts; i++)
+            for (j=0; j<ngts; j++)
+                for (k=0; k<ngts; k++)
+                {
+                    if ( !IS_HOM(gts[i]) ) continue;
+                    if ( ((gts[i]|gts[j])&gts[k]) != gts[k] ) continue;
+                    if ( !(gts[i] & gts[k]) ) continue;     // girl must inherit one copy from the father and one from the mother
+                    if ( !(gts[j] & gts[k]) ) continue;
+                    int Pkij = calc_Pkij(gts[i],gts[j],gts[k], 1,2,2);
+                    call->trio[FTYPE_122][nals][n++] = Pkij<<12 | i<<8 | j<<4 | k;
+                }
+        assert( n==call->ntrio[FTYPE_122][nals] );
+
+        // 101: chrY, boy
+        n = 0;
+        for (i=0; i<ngts; i++)
+            for (k=0; k<ngts; k++)
+            {
+                if ( !IS_HOM(gts[i]) || !IS_HOM(gts[k]) ) continue;
+                if ( (gts[i]&gts[k]) != gts[k] ) continue;
+                call->trio[FTYPE_101][nals][n++] = 1<<12 | i<<8 | GT_SKIP<<4 | k;
+            }
+        assert( n==call->ntrio[FTYPE_101][nals] );
+
+        // 100: chrY, girl
+        n = 0;
+        for (i=0; i<ngts; i++)
+        {
+            if ( !IS_POW2(gts[i]) ) continue;
+            call->trio[FTYPE_100][nals][n++] = 1<<12 | i<<8 | GT_SKIP<<4 | GT_SKIP;
+        }
+        assert( n==call->ntrio[FTYPE_100][nals] );
+
+    }
+    call->GLs = (double*) calloc(bcf_hdr_nsamples(call->hdr)*10,sizeof(double));
+
+    int i, j;
+    for (i=0; i<call->nfams; i++)
+    {
+        family_t *fam = &call->fams[i];
+        int ploidy[3];
+        for (j=0; j<3; j++)
+            ploidy[j] = call->ploidy[fam->sample[j]];
+
+        if ( ploidy[FATHER]==2 )    // not X, not Y
+        {
+            if ( ploidy[MOTHER]!=2 || ploidy[CHILD]!=2 )
+                error("Incorrect ploidy: %d %d %d\n", ploidy[FATHER],ploidy[MOTHER],ploidy[CHILD]);
+            fam->type = FTYPE_222;
+            continue;
+        }
+        if ( ploidy[FATHER]!=1 || ploidy[MOTHER]==1 )
+                error("Incorrect ploidy: %d %d %d\n", ploidy[FATHER],ploidy[MOTHER],ploidy[CHILD]);
+        if ( ploidy[MOTHER]==2 )    // X
+        {
+            if ( ploidy[CHILD]==0 )
+                error("Incorrect ploidy: %d %d %d\n", ploidy[FATHER],ploidy[MOTHER],ploidy[CHILD]);
+            fam->type = ploidy[CHILD]==2 ? FTYPE_122 : FTYPE_121;   // a girl or a boy
+        }
+        else    // Y
+        {
+            if ( ploidy[CHILD]==2 )
+                error("Incorrect ploidy: %d %d %d\n", ploidy[FATHER],ploidy[MOTHER],ploidy[CHILD]);
+            fam->type = ploidy[CHILD]==0 ? FTYPE_100 : FTYPE_101;   // a girl or a boy
+        }
+    }
+}
+static void mcall_destroy_trios(call_t *call)
+{
+    int i, j;
+    for (i=2; i<=4; i++)
+        for (j=0; j<=4; j++)
+            free(call->trio[j][i]);
+}
+
+static void init_sample_groups(call_t *call)
+{
+    int i, nsmpl = bcf_hdr_nsamples(call->hdr);
+    if ( !call->sample_groups )
+    {
+        // standard pooled calling, all samples in the same group
+        call->nsmpl_grp = 1;
+        call->smpl_grp  = (smpl_grp_t*)calloc(1,sizeof(*call->smpl_grp));
+        call->smpl_grp[0].nsmpl = nsmpl;
+        call->smpl_grp[0].smpl  = (uint32_t*)calloc(call->smpl_grp[0].nsmpl,sizeof(uint32_t));
+        for (i=0; i<nsmpl; i++)
+            call->smpl_grp[0].smpl[i] = i;
+        return;
+    }
+
+    if ( call->sample_groups_tag )
+    {
+        // Is the tag defined in the header?
+        int tag_id = bcf_hdr_id2int(call->hdr,BCF_DT_ID,call->sample_groups_tag);
+        if ( tag_id==-1 ) error("No such tag \"%s\"\n",call->sample_groups_tag);
+        if ( !bcf_hdr_idinfo_exists(call->hdr,BCF_HL_FMT,tag_id) )  error("No such FORMAT tag \"%s\"\n", call->sample_groups_tag);
+    }
+    else
+    {
+        int tag_id = bcf_hdr_id2int(call->hdr,BCF_DT_ID,"QS");
+        if ( tag_id >= 0 && bcf_hdr_idinfo_exists(call->hdr,BCF_HL_FMT,tag_id) ) call->sample_groups_tag = "QS";
+        else
+        {
+            tag_id = bcf_hdr_id2int(call->hdr,BCF_DT_ID,"AD");
+            if ( tag_id >= 0 && bcf_hdr_idinfo_exists(call->hdr,BCF_HL_FMT,tag_id) ) call->sample_groups_tag = "AD";
+            else error("Error: neither \"AD\" nor \"QS\" FORMAT tag exists and no alternative given with -G\n");
+        }
+    }
+
+    // Read samples/groups
+    if ( !strcmp("-",call->sample_groups) )
+    {
+        // single-sample calling, each sample creates its own group
+        call->nsmpl_grp = nsmpl;
+        call->smpl_grp  = (smpl_grp_t*)calloc(nsmpl,sizeof(*call->smpl_grp));
+        for (i=0; i<nsmpl; i++)
+        {
+            call->smpl_grp[i].nsmpl = 1;
+            call->smpl_grp[i].smpl  = (uint32_t*)calloc(call->smpl_grp[i].nsmpl,sizeof(uint32_t));
+            call->smpl_grp[i].smpl[0] = i;
+        }
+    }
+    else
+    {
+        int nlines;
+        char **lines = hts_readlist(call->sample_groups, 1, &nlines);
+        if ( !lines ) error("Could not read the file: %s\n", call->sample_groups);
+
+        uint32_t *smpl2grp = (uint32_t*)calloc(nsmpl,sizeof(uint32_t));
+        uint32_t *grp2n = (uint32_t*)calloc(nsmpl,sizeof(uint32_t));
+        void *grp2idx = khash_str2int_init();
+
+        call->nsmpl_grp = 0;
+        for (i=0; i<nlines; i++)
+        {
+            char *ptr = lines[i];
+            while ( *ptr && !isspace(*ptr) ) ptr++;
+            if ( !*ptr ) error("Could not parse the line in %s, expected a sample name followed by tab and a population name: %s\n",call->sample_groups,lines[i]);
+            char *tmp = ptr;
+            while ( *ptr && isspace(*ptr) ) ptr++;
+            if ( !*ptr ) error("Could not parse the line in %s, expected a sample name followed by tab and a population name: %s\n",call->sample_groups,lines[i]);
+            *tmp = 0;
+            int ismpl = bcf_hdr_id2int(call->hdr, BCF_DT_SAMPLE, lines[i]); 
+            if ( ismpl<0 ) continue;
+            if ( smpl2grp[ismpl] ) error("Error: the sample \"%s\" is listed twice in %s\n", lines[i],call->sample_groups);
+            if ( !khash_str2int_has_key(grp2idx,ptr+1) )
+            {
+                khash_str2int_set(grp2idx, ptr+1, call->nsmpl_grp);
+                call->nsmpl_grp++;
+            }
+            int igrp = -1;
+            if ( khash_str2int_get(grp2idx, ptr+1, &igrp)!=0 )
+                error("This should not happen, fixme: %s\n",ptr+1);
+            grp2n[igrp]++;
+            smpl2grp[ismpl] = igrp+1;   // +1 to distinguish unlisted samples
+        }
+        khash_str2int_destroy(grp2idx);
+        if ( !call->nsmpl_grp ) error("Could not parse the file, no matching samples found: %s\n", call->sample_groups);
+
+        call->smpl_grp = (smpl_grp_t*)calloc(call->nsmpl_grp,sizeof(*call->smpl_grp));
+        for (i=0; i<nsmpl; i++)
+        {
+            if ( !smpl2grp[i] ) error("Error: The sample \"%s\" is not listed in %s\n",call->hdr->samples[i],call->sample_groups);
+            int igrp = smpl2grp[i] - 1;
+            if ( !call->smpl_grp[igrp].nsmpl ) 
+                call->smpl_grp[igrp].smpl = (uint32_t*)calloc(grp2n[igrp],sizeof(uint32_t));
+            call->smpl_grp[igrp].smpl[call->smpl_grp[igrp].nsmpl] = i;
+            call->smpl_grp[igrp].nsmpl++;
+        }
+        free(smpl2grp);
+        free(grp2n);
+        for (i=0; i<nlines; i++) free(lines[i]);
+        free(lines);
+    }
+}
+static void destroy_sample_groups(call_t *call)
+{
+    int i;
+    for (i=0; i<call->nsmpl_grp; i++)
+    {
+        free(call->smpl_grp[i].qsum);
+        free(call->smpl_grp[i].smpl);
+    }
+    free(call->smpl_grp);
+}
+
+void mcall_init(call_t *call)
+{
+    init_sample_groups(call);
+    call_init_pl2p(call);
+
+    call->nals_map = 5;
+    call->als_map  = (int*) malloc(sizeof(int)*call->nals_map);
+    call->npl_map  = 5*(5+1)/2;     // will be expanded later if necessary
+    call->pl_map   = (int*) malloc(sizeof(int)*call->npl_map);
+    call->gts  = (int32_t*) calloc(bcf_hdr_nsamples(call->hdr)*2,sizeof(int32_t));   // assuming at most diploid everywhere
+
+    if ( call->flag & CALL_CONSTR_TRIO )
+    {
+        call->cgts = (int32_t*) calloc(bcf_hdr_nsamples(call->hdr),sizeof(int32_t));
+        call->ugts = (int32_t*) calloc(bcf_hdr_nsamples(call->hdr),sizeof(int32_t));
+        mcall_init_trios(call);
+        bcf_hdr_append(call->hdr,"##FORMAT=<ID=CGT,Number=1,Type=Integer,Description=\"Constrained Genotype (0-based index to Number=G ordering).\">");
+        bcf_hdr_append(call->hdr,"##FORMAT=<ID=UGT,Number=1,Type=Integer,Description=\"Unconstrained Genotype (0-based index to Number=G ordering).\">");
+    }
+    if ( call->flag & CALL_CONSTR_ALLELES ) call->vcmp = vcmp_init();
+
+    bcf_hdr_append(call->hdr,"##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">");
+    if ( call->output_tags & CALL_FMT_GQ )
+        bcf_hdr_append(call->hdr,"##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Phred-scaled Genotype Quality\">");
+    if ( call->output_tags & CALL_FMT_GP )
+        bcf_hdr_append(call->hdr,"##FORMAT=<ID=GP,Number=G,Type=Float,Description=\"Genotype posterior probabilities in the range 0 to 1\">");
+    if ( call->output_tags & (CALL_FMT_GQ|CALL_FMT_GP) )
+        call->GQs = (int32_t*) malloc(sizeof(int32_t)*bcf_hdr_nsamples(call->hdr));
+    bcf_hdr_append(call->hdr,"##INFO=<ID=AC,Number=A,Type=Integer,Description=\"Allele count in genotypes for each ALT allele, in the same order as listed\">");
+    bcf_hdr_append(call->hdr,"##INFO=<ID=AN,Number=1,Type=Integer,Description=\"Total number of alleles in called genotypes\">");
+    bcf_hdr_append(call->hdr,"##INFO=<ID=DP4,Number=4,Type=Integer,Description=\"Number of high-quality ref-forward , ref-reverse, alt-forward and alt-reverse bases\">");
+    bcf_hdr_append(call->hdr,"##INFO=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality\">");
+    if ( call->output_tags & CALL_FMT_PV4 )
+        bcf_hdr_append(call->hdr,"##INFO=<ID=PV4,Number=4,Type=Float,Description=\"P-values for strand bias, baseQ bias, mapQ bias and tail distance bias\">\n");
+
+    // init the prior
+    if ( call->theta>0 )
+    {
+        int i, n = 0;
+        if ( !call->ploidy ) n = 2*bcf_hdr_nsamples(call->hdr); // all are diploid
+        else
+        {
+            for (i=0; i<bcf_hdr_nsamples(call->hdr); i++)
+                n += call->ploidy[i];
+        }
+        // Watterson factor, here aM_1 = aM_2 = 1
+        double aM = 1;
+        for (i=2; i<n; i++) aM += 1./i;
+        call->theta *= aM;
+        if ( call->theta >= 1 )
+        {
+            fprintf(stderr,"The prior is too big (theta*aM=%.2f), going with 0.99\n", call->theta);
+            call->theta = 0.99;
+        }
+        call->theta = log(call->theta);
+    }
+}
+
+void mcall_destroy(call_t *call)
+{
+    destroy_sample_groups(call);
+    if (call->vcmp) vcmp_destroy(call->vcmp);
+    free(call->itmp);
+    mcall_destroy_trios(call);
+    free(call->GPs);
+    free(call->ADs);
+    free(call->GLs);
+    free(call->GQs);
+    free(call->anno16);
+    free(call->PLs);
+    free(call->als_map);
+    free(call->pl_map);
+    free(call->gts); free(call->cgts); free(call->ugts);
+    free(call->pdg);
+    free(call->als);
+    free(call->ac);
+    return;
+}
+
+
+// Inits P(D|G): convert PLs from log space and normalize. In case of zero
+// depth, missing PLs are all zero. In this case, pdg's are set to 0
+// so that the corresponding genotypes can be set as missing and the
+// qual calculation is not affected.
+// Missing values are replaced by generic likelihoods when X (unseen allele) is
+// present.
+// NB: While the -m callig model uses the pdgs in canonical order,
+// the original samtools -c calling code uses pdgs in reverse order (AA comes
+// first, RR last).
+// NB: Ploidy is not taken into account here, which is incorrect.
+void set_pdg(double *pl2p, int *PLs, double *pdg, int n_smpl, int n_gt, int unseen)
+{
+    int i, j, nals;
+
+    // find out the number of alleles, expecting diploid genotype likelihoods
+    bcf_gt2alleles(n_gt-1, &i, &nals);
+    assert( i==nals );
+    nals++;
+
+    for (i=0; i<n_smpl; i++)
+    {
+        double sum = 0;
+        for (j=0; j<n_gt; j++)
+        {
+            if ( PLs[j]==bcf_int32_vector_end )
+            {
+                // We expect diploid genotype likelihoods. If not diploid, treat as missing
+                j = 0;
+                break;
+            }
+            if ( PLs[j]==bcf_int32_missing ) break;
+            pdg[j] = PLs[j] < 256 ? pl2p[PLs[j]] : pow(10., -PLs[j]/10.);
+            sum += pdg[j];
+        }
+
+        if ( j==0 )
+        {
+            // First value is missing (LK of RR), this indicates that
+            // all values are missing.
+            j = sum = n_gt;
+        }
+        else if ( j<n_gt && unseen<0 )
+        {
+            // Some of the values are missing and the unseen allele LK is not
+            // available. In such a case, we set LK to a very small value.
+            sum = 0;
+            for (j=0; j<n_gt; j++)
+            {
+                assert( PLs[j]!=bcf_int32_vector_end );
+                if ( PLs[j]==bcf_int32_missing ) PLs[j] = 255;
+                pdg[j] = PLs[j] < 256 ? pl2p[PLs[j]] : pow(10., -PLs[j]/10.);
+                sum += pdg[j];
+            }
+        }
+        if ( j<n_gt )
+        {
+            // Missing values present, fill with unseen allele LK. This can be only
+            // as good as the merge was.
+            int ia,ib, k;
+            j = 0;
+            sum = 0;
+            for (ia=0; ia<nals; ia++)
+            {
+                for (ib=0; ib<=ia; ib++)
+                {
+                    if ( PLs[j]==bcf_int32_missing )
+                    {
+                        k = bcf_alleles2gt(ia,unseen);
+                        if ( PLs[k]==bcf_int32_missing ) k = bcf_alleles2gt(ib,unseen);
+                        if ( PLs[k]==bcf_int32_missing ) k = bcf_alleles2gt(unseen,unseen);
+                        if ( PLs[k]==bcf_int32_missing )
+                        {
+                            // The PLs for unseen allele X are not present as well as for ia, ib.
+                            // This can happen with incremental calling, when one of the merged
+                            // files had all alleles A,C,G,T, in such a case, X was not present.
+                            // Use a very small value instead.
+                            PLs[j] = 255;
+                        }
+                        else
+                            PLs[j] = PLs[k];
+                    }
+                    pdg[j] = pl2p[ PLs[j] ];
+                    sum += pdg[j];
+                    j++;
+                }
+            }
+        }
+        // Normalize: sum_i pdg_i = 1
+        if ( sum==n_gt )
+        {
+            // all missing
+            #if FLAT_PDG_FOR_MISSING
+                for (j=0; j<n_gt; j++) pdg[j] = 1./n_gt;
+            #else
+                for (j=0; j<n_gt; j++) pdg[j] = 0;
+            #endif
+        }
+        else
+            for (j=0; j<n_gt; j++) pdg[j] /= sum;
+
+        PLs += n_gt;
+        pdg += n_gt;
+    }
+}
+
+// Create mapping between old and new (trimmed) alleles
+void init_allele_trimming_maps(call_t *call, int nals_ori, int als_out)
+{
+    int i, j, nout = 0;
+
+    // als_map: old(i) -> new(j)
+    for (i=0; i<nals_ori; i++)
+    {
+        if ( als_out & (1<<i) ) call->als_map[i] = nout++;
+        else call->als_map[i] = -1;
+    }
+
+    if ( !call->pl_map ) return;
+
+    // pl_map: new(k) -> old(l)
+    int k = 0, l = 0;
+    for (i=0; i<nals_ori; i++)
+    {
+        for (j=0; j<=i; j++)
+        {
+            if ( (als_out & (1<<i)) && (als_out & (1<<j)) ) call->pl_map[k++] = l;
+            l++;
+        }
+    }
+}
+
+/** log(exp(a)+exp(b)) */
+static inline double logsumexp2(double a, double b)
+{
+    if ( a>b )
+        return log(1 + exp(b-a)) + a;
+    else
+        return log(1 + exp(a-b)) + b;
+}
+
+// Macro to set the most likely alleles
+#define UPDATE_MAX_LKs(als,sum) { \
+     if ( max_lk<lk_tot && lk_tot_set ) { max_lk = lk_tot; max_als = (als); } \
+     if ( sum ) lk_sum = logsumexp2(lk_tot,lk_sum); \
+}
+
+#define SWAP(type_t,x,y) {type_t tmp; tmp = x; x = y; y = tmp; }
+
+// Determine the most likely combination of alleles. In this implementation,
+// at most tri-allelic sites are considered. Returns the number of alleles.
+static int mcall_find_best_alleles(call_t *call, int nals, smpl_grp_t *grp)
+{
+    int ia,ib,ic;   // iterators over up to three alleles
+    int max_als=0;  // most likely combination of alleles
+    double ref_lk = -HUGE_VAL, max_lk = -HUGE_VAL; // likelihood of the reference and of most likely combination of alleles
+    double lk_sum = -HUGE_VAL;    // for normalizing the likelihoods
+    int nsmpl = grp->nsmpl;
+    int ngts  = nals*(nals+1)/2;
+
+    // Single allele
+    for (ia=0; ia<nals; ia++)
+    {
+        double lk_tot  = 0;
+        int lk_tot_set = 0;
+        int iaa = (ia+1)*(ia+2)/2-1;    // index in PL which corresponds to the homozygous "ia/ia" genotype
+        int ismpl;
+        for (ismpl=0; ismpl<nsmpl; ismpl++)
+        {
+            double *pdg = call->pdg + grp->smpl[ismpl]*ngts + iaa;
+            if ( *pdg ) { lk_tot += log(*pdg); lk_tot_set = 1; }
+        }
+        if ( ia==0 ) ref_lk = lk_tot;   // likelihood of 0/0 for all samples
+        else lk_tot += call->theta; // the prior
+        UPDATE_MAX_LKs(1<<ia, ia>0 && lk_tot_set);
+    }
+
+    // Two alleles
+    if ( nals>1 )
+    {
+        for (ia=0; ia<nals; ia++)
+        {
+            if ( grp->qsum[ia]==0 ) continue;
+            int iaa = (ia+1)*(ia+2)/2-1;
+            for (ib=0; ib<ia; ib++)
+            {
+                if ( grp->qsum[ib]==0 ) continue;
+                double lk_tot  = 0;
+                int lk_tot_set = 0;
+                double fa  = grp->qsum[ia]/(grp->qsum[ia] + grp->qsum[ib]);
+                double fb  = grp->qsum[ib]/(grp->qsum[ia] + grp->qsum[ib]);
+                double fa2 = fa*fa;
+                double fb2 = fb*fb;
+                double fab = 2*fa*fb;
+                int is, ibb = (ib+1)*(ib+2)/2-1, iab = iaa - ia + ib;
+                for (is=0; is<nsmpl; is++)
+                {
+                    int ismpl = grp->smpl[is];
+                    double *pdg = call->pdg + ismpl*ngts;
+                    double val = 0;
+                    if ( !call->ploidy || call->ploidy[ismpl]==2 )
+                        val = fa2*pdg[iaa] + fb2*pdg[ibb] + fab*pdg[iab];
+                    else if ( call->ploidy && call->ploidy[ismpl]==1 )
+                        val = fa*pdg[iaa] + fb*pdg[ibb];
+                    if ( val ) { lk_tot += log(val); lk_tot_set = 1; }
+                }
+                if ( ia!=0 ) lk_tot += call->theta;    // the prior
+                if ( ib!=0 ) lk_tot += call->theta;
+                UPDATE_MAX_LKs(1<<ia|1<<ib, lk_tot_set);
+            }
+        }
+    }
+
+    // Three alleles
+    if ( nals>2 )
+    {
+        for (ia=0; ia<nals; ia++)
+        {
+            if ( grp->qsum[ia]==0 ) continue;
+            int iaa = (ia+1)*(ia+2)/2-1;
+            for (ib=0; ib<ia; ib++)
+            {
+                if ( grp->qsum[ib]==0 ) continue;
+                int ibb = (ib+1)*(ib+2)/2-1;
+                int iab = iaa - ia + ib;
+                for (ic=0; ic<ib; ic++)
+                {
+                    if ( grp->qsum[ic]==0 ) continue;
+                    double lk_tot  = 0;
+                    int lk_tot_set = 0;
+
+                    double fa  = grp->qsum[ia]/(grp->qsum[ia] + grp->qsum[ib] + grp->qsum[ic]);
+                    double fb  = grp->qsum[ib]/(grp->qsum[ia] + grp->qsum[ib] + grp->qsum[ic]);
+                    double fc  = grp->qsum[ic]/(grp->qsum[ia] + grp->qsum[ib] + grp->qsum[ic]);
+                    double fa2 = fa*fa;
+                    double fb2 = fb*fb;
+                    double fc2 = fc*fc;
+                    double fab = 2*fa*fb, fac = 2*fa*fc, fbc = 2*fb*fc;
+                    int is, icc = (ic+1)*(ic+2)/2-1;
+                    int iac = iaa - ia + ic, ibc = ibb - ib + ic;
+                    for (is=0; is<nsmpl; is++)
+                    {
+                        int ismpl = grp->smpl[is];
+                        double *pdg = call->pdg + ismpl*ngts;
+                        double val = 0;
+                        if ( !call->ploidy || call->ploidy[ismpl]==2 )
+                            val = fa2*pdg[iaa] + fb2*pdg[ibb] + fc2*pdg[icc] + fab*pdg[iab] + fac*pdg[iac] + fbc*pdg[ibc];
+                        else if ( call->ploidy && call->ploidy[ismpl]==1 )
+                            val = fa*pdg[iaa] + fb*pdg[ibb] + fc*pdg[icc];
+                        if ( val ) { lk_tot += log(val); lk_tot_set = 1; }
+                    }
+                    if ( ia!=0 ) lk_tot += call->theta;    // the prior
+                    if ( ib!=0 ) lk_tot += call->theta;    // the prior
+                    if ( ic!=0 ) lk_tot += call->theta;    // the prior
+                    UPDATE_MAX_LKs(1<<ia|1<<ib|1<<ic, lk_tot_set);
+                }
+            }
+        }
+    }
+
+    int i, n = 0;
+    for (i=0; i<nals; i++) if ( max_als & 1<<i) n++;
+
+    grp->max_lk = max_lk;
+    grp->ref_lk = ref_lk;
+    grp->lk_sum = lk_sum;
+    grp->als  = max_als;
+    grp->nals = n;
+
+    return n;
+}
+
+// Sets GT=0/0 or GT=. if PL=0,0,0
+static void mcall_set_ref_genotypes(call_t *call, int nals_ori)
+{
+    int i;
+    int ngts  = nals_ori*(nals_ori+1)/2;            // need this to distinguish between GT=0/0 vs GT=.
+    int nsmpl = bcf_hdr_nsamples(call->hdr);
+
+    for (i=0; i<nals_ori; i++) call->ac[i] = 0;     // nals_new<=nals_ori, never mind setting extra 0's
+
+    // Set all genotypes to 0/0 or 0
+    int *gts    = call->gts;
+    double *pdg = call->pdg;
+    int isample;
+    for (isample = 0; isample < nsmpl; isample++)
+    {
+        int ploidy = call->ploidy ? call->ploidy[isample] : 2;
+        for (i=0; i<ngts; i++) if ( pdg[i]!=0.0 ) break;
+        if ( i==ngts || !ploidy )
+        {
+            gts[0] = bcf_gt_missing;
+            gts[1] = ploidy==2 ? bcf_gt_missing : bcf_int32_vector_end;
+        }
+        else
+        {
+            gts[0] = bcf_gt_unphased(0);
+            gts[1] = ploidy==2 ? bcf_gt_unphased(0) : bcf_int32_vector_end;
+            call->ac[0] += ploidy;
+        }
+        gts += 2;
+        pdg += ngts;
+    }
+}
+
+static void mcall_call_genotypes(call_t *call, int nals_ori, smpl_grp_t *grp)
+{
+    int ia, ib, i;
+    int ngts_ori = nals_ori*(nals_ori+1)/2; 
+    int ngts_new = call->nals_new*(call->nals_new+1)/2;
+    int nsmpl = grp->nsmpl;
+
+    #if USE_PRIOR_FOR_GTS
+        float prior = exp(call->theta);
+    #endif
+
+    int is;
+    for (is = 0; is < nsmpl; is++)
+    {
+        int ismpl   = grp->smpl[is];
+        double *pdg = call->pdg + ismpl*ngts_ori;
+        float *gps  = call->GPs + ismpl*ngts_new;
+        int *gts    = call->gts + ismpl*2;
+
+        int ploidy = call->ploidy ? call->ploidy[ismpl] : 2;
+        assert( ploidy>=0 && ploidy<=2 );
+
+        if ( !ploidy )
+        {
+            gts[0] = bcf_gt_missing;
+            gts[1] = bcf_int32_vector_end;
+            gps[0] = -1;
+            continue;
+        }
+
+        #if !FLAT_PDG_FOR_MISSING
+            // Skip samples with zero depth, they have all pdg's equal to 0
+            for (i=0; i<ngts_ori; i++) if ( pdg[i]!=0.0 ) break;
+            if ( i==ngts_ori )
+            {
+                gts[0] = bcf_gt_missing;
+                gts[1] = ploidy==2 ? bcf_gt_missing : bcf_int32_vector_end;
+                gps[0] = -1;
+                continue;
+            }
+        #endif
+
+        // Default fallback for the case all LKs are the same
+        gts[0] = bcf_gt_unphased(0);
+        gts[1] = ploidy==2 ? bcf_gt_unphased(0) : bcf_int32_vector_end;
+
+        // Non-zero depth, determine the most likely genotype
+        double best_lk = 0;
+        for (ia=0; ia<nals_ori; ia++)
+        {
+            if ( !(grp->als & 1<<ia) ) continue;    // ia-th allele not in the final selection, skip
+            int iaa = (ia+1)*(ia+2)/2-1;                // PL index of the ia/ia genotype
+            double lk = ploidy==2 ? pdg[iaa]*grp->qsum[ia]*grp->qsum[ia] : pdg[iaa]*grp->qsum[ia];
+            #if USE_PRIOR_FOR_GTS
+                if ( ia!=0 ) lk *= prior;
+            #endif
+            int igt  = ploidy==2 ? bcf_alleles2gt(call->als_map[ia],call->als_map[ia]) : call->als_map[ia];
+            gps[igt] = lk;
+            if ( best_lk < lk )
+            {
+                best_lk = lk;
+                gts[0] = bcf_gt_unphased(call->als_map[ia]);
+            }
+        }
+        if ( ploidy==2 )
+        {
+            gts[1] = gts[0];
+            for (ia=0; ia<nals_ori; ia++)
+            {
+                if ( !(grp->als & 1<<ia) ) continue;
+                int iaa = (ia+1)*(ia+2)/2-1;
+                for (ib=0; ib<ia; ib++)
+                {
+                    if ( !(grp->als & 1<<ib) ) continue;
+                    int iab = iaa - ia + ib;
+                    double lk = 2*pdg[iab]*grp->qsum[ia]*grp->qsum[ib];
+                    #if USE_PRIOR_FOR_GTS
+                        if ( ia!=0 ) lk *= prior;
+                        if ( ib!=0 ) lk *= prior;
+                    #endif
+                    int igt  = bcf_alleles2gt(call->als_map[ia],call->als_map[ib]);
+                    gps[igt] = lk;
+                    if ( best_lk < lk )
+                    {
+                        best_lk = lk;
+                        gts[0] = bcf_gt_unphased(call->als_map[ib]);
+                        gts[1] = bcf_gt_unphased(call->als_map[ia]);
+                    }
+                }
+            }
+        }
+        else
+            gts[1] = bcf_int32_vector_end;
+
+        call->ac[ bcf_gt_allele(gts[0]) ]++;
+        if ( gts[1]!=bcf_int32_vector_end ) call->ac[ bcf_gt_allele(gts[1]) ]++;
+    }
+    if ( !(call->output_tags & (CALL_FMT_GQ|CALL_FMT_GP)) ) return;
+    double max, sum;
+    for (is=0; is<nsmpl; is++)
+    {
+        int ismpl  = grp->smpl[is];
+        float *gps = call->GPs + ismpl*ngts_new;
+
+        int nmax;
+        if ( call->ploidy )
+        {
+            if ( call->ploidy[ismpl]==2 ) nmax = ngts_new;
+            else if ( call->ploidy[ismpl]==1 ) nmax = grp->nals;
+            else nmax = 0;
+        }
+        else nmax = ngts_new;
+
+        max = gps[0];
+        if ( max<0 || nmax==0 )
+        {
+            // no call
+            if ( call->output_tags & CALL_FMT_GP )
+            {
+                for (i=0; i<nmax; i++) gps[i] = 0;
+                if ( nmax==0 ) { bcf_float_set_missing(gps[i]); nmax++; }
+                if ( nmax < ngts_new ) bcf_float_set_vector_end(gps[nmax]);
+            }
+            call->GQs[ismpl] = 0;
+            continue;
+        }
+        sum = gps[0];
+        for (i=1; i<nmax; i++)
+        {
+            if ( max < gps[i] ) max = gps[i];
+            sum += gps[i];
+        }
+        max = -4.34294*log(1 - max/sum);
+        call->GQs[ismpl] = max<=INT8_MAX ? max : INT8_MAX;
+        if ( call->output_tags & CALL_FMT_GP )
+        {
+            assert( max );
+            for (i=0; i<nmax; i++) gps[i] = gps[i]/sum;
+            for (; i<ngts_new; i++) bcf_float_set_vector_end(gps[i]);
+        }
+    }
+}
+
+
+/**
+    Pm = P(mendelian) .. parameter to vary, 1-Pm is the probability of novel mutation.
+                         When trio_Pm_ins is negative, Pm is calculated dynamically
+                         according to indel length. For simplicity, only the
+                         first ALT is considered.
+    Pkij = P(k|i,j)   .. probability that the genotype combination i,j,k is consistent
+                         with mendelian inheritance (the likelihood that offspring
+                         of two HETs is a HOM is smaller than it being a HET)
+
+    P_uc(F=i,M=j,K=k) = P(F=i) . P(M=j) . P(K=k)  .. unconstrained P
+    P_c(F=i,M=j,K=k) = P_uc . Pkij                .. constrained P
+    P(F=i,M=j,K=k) = P_uc . (1 - Pm) + P_c . Pm
+                   = P_uc . [1 - Pm + Pkij . Pm]
+
+    We choose genotype combination i,j,k which maximizes P(F=i,M=j,K=k). This
+    probability gives the quality GQ(Trio).
+    Individual qualities are calculated as
+        GQ(F=i,M=j,K=k) = P(F=i,M=j,K=k) / \sum_{x,y} P(F=i,M=x,K=y)
+ */
+#if 0
+static void mcall_call_trio_genotypes(call_t *call, bcf1_t *rec, int nals, int nals_new, int als_new)
+{
+    int ia, ib, i;
+    int nsmpl    = bcf_hdr_nsamples(call->hdr);
+    int ngts     = nals*(nals+1)/2;
+    int nout_gts = nals_new*(nals_new+1)/2;
+    double *gls  = call->GLs - nout_gts;
+    double *pdg  = call->pdg - ngts;
+
+    // Calculate individuals' genotype likelihoods P(X=i)
+    int isample;
+    for (isample = 0; isample < nsmpl; isample++)
+    {
+        int ploidy = call->ploidy ? call->ploidy[isample] : 2;
+        int32_t *gts = call->ugts + isample;
+
+        gls += nout_gts;
+        pdg += ngts;
+
+        // Skip samples with all pdg's equal to 1. These have zero depth.
+        for (i=0; i<ngts; i++) if ( pdg[i]!=0.0 ) break;
+        if ( i==ngts || !ploidy )
+        {
+            gts[0] = -1;
+            gls[0] = 1;
+            continue;
+        }
+
+        for (i=0; i<nout_gts; i++) gls[i] = -HUGE_VAL;
+
+        grp1_t *grp = &call->smpl_grp.grp[call->smpl_grp.smpl2grp[isample]];
+        double sum_lk  = 0;
+        double best_lk = 0;
+        for (ia=0; ia<nals; ia++)
+        {
+            if ( !(als_new & 1<<ia) ) continue;     // ia-th allele not in the final selection, skip
+            int iaa   = bcf_alleles2gt(ia,ia);      // PL index of the ia/ia genotype
+            int idx   = bcf_alleles2gt(call->als_map[ia],call->als_map[ia]);
+            double lk = ploidy==2 ? pdg[iaa]*grp->qsum[ia]*grp->qsum[ia] : pdg[iaa]*grp->qsum[ia];
+            sum_lk   += lk;
+            gls[idx]  = lk;
+            if ( best_lk < lk )
+            {
+                best_lk = lk;
+                gts[0] = bcf_alleles2gt(call->als_map[ia],call->als_map[ia]);
+            }
+        }
+        if ( ploidy==2 )
+        {
+            for (ia=0; ia<nals; ia++)
+            {
+                if ( !(als_new & 1<<ia) ) continue;
+                for (ib=0; ib<ia; ib++)
+                {
+                    if ( !(als_new & 1<<ib) ) continue;
+                    int iab   = bcf_alleles2gt(ia,ib);
+                    int idx   = bcf_alleles2gt(call->als_map[ia],call->als_map[ib]);
+                    double lk = 2*pdg[iab]*grp->qsum[ia]*grp->qsum[ib];
+                    sum_lk   += lk;
+                    gls[idx]  = lk;
+                    if ( best_lk < lk )
+                    {
+                        best_lk = lk;
+                        gts[0] = bcf_alleles2gt(call->als_map[ib],call->als_map[ia]);
+                    }
+                }
+            }
+        }
+        for (i=0; i<nout_gts; i++)
+            if ( gls[i]!=-HUGE_VAL ) gls[i] = log(gls[i]/sum_lk);
+    }
+
+    // Set novel mutation rate for this site: using first ALT allele for simplicity.
+    double trio_Pm;
+    if ( call->trio_Pm_ins<0 && call->trio_Pm_del<0 ) trio_Pm = call->trio_Pm_SNPs;     // the same Pm for indels and SNPs requested
+    else
+    {
+        int ret = bcf_get_variant_types(rec);
+        if ( !(ret & VCF_INDEL) ) trio_Pm = call->trio_Pm_SNPs;
+        else
+        {
+            if ( call->trio_Pm_ins<0 )  // dynamic calculation, trio_Pm_del holds the scaling factor
+            {
+                trio_Pm = rec->d.var[1].n<0 ? -21.9313 - 0.2856*rec->d.var[1].n : -22.8689 + 0.2994*rec->d.var[1].n;
+                trio_Pm = 1 - call->trio_Pm_del * exp(trio_Pm);
+            }
+            else                        // snps and indels set explicitly
+            {
+                trio_Pm = rec->d.var[1].n<0 ? call->trio_Pm_del : call->trio_Pm_ins;
+            }
+        }
+    }
+
+    // Calculate constrained likelihoods and determine genotypes
+    int ifm;
+    for (ifm=0; ifm<call->nfams; ifm++)
+    {
+        family_t *fam = &call->fams[ifm];
+        int ntrio = call->ntrio[fam->type][nals_new];
+        uint16_t *trio = call->trio[fam->type][nals_new];
+
+        // Unconstrained likelihood
+        int uc_itr = 0;
+        double uc_lk = 0;
+        for (i=0; i<3; i++)     // for father, mother, child
+        {
+            int ismpl = fam->sample[i];
+            double *gl = call->GLs + nout_gts*ismpl;
+            if ( gl[0]==1 ) continue;
+            int j, jmax = 0;
+            double max  = gl[0];
+            for (j=1; j<nout_gts; j++)
+                if ( max < gl[j] ) { max = gl[j]; jmax = j; }
+            uc_lk += max;
+            uc_itr |= jmax << ((2-i)*4);
+        }
+
+        // Best constrained likelihood
+        int c_itr = -1, itr, uc_is_mendelian = 0;
+        double c_lk = -HUGE_VAL;
+        for (itr=0; itr<ntrio; itr++)   // for each trio genotype combination
+        {
+            double lk = 0;
+            int npresent = 0;
+            for (i=0; i<3; i++)     // for father, mother, child
+            {
+                int ismpl = fam->sample[i];
+                double *gl = call->GLs + nout_gts*ismpl;
+                if ( gl[0]==1 ) continue;
+                int igt = trio[itr]>>((2-i)*4) & 0xf;
+                assert( !call->ploidy || call->ploidy[ismpl]>0 );
+                if ( igt==GT_SKIP ) continue;
+                lk += gl[igt];
+                npresent++;
+                // fprintf(stderr," %e", gl[igt]);
+            }
+            // fprintf(stderr,"\t\t");
+            double Pkij = npresent==3 ? (double)2/(trio[itr]>>12) : 1;  // with missing genotypes Pkij's are different
+            lk += log(1 - trio_Pm * (1 - Pkij));
+            // fprintf(stderr,"%d%d%d\t%e\t%.2f\n", trio[itr]>>8&0xf,trio[itr]>>4&0xf,trio[itr]&0xf, lk, Pkij);
+            if ( c_lk < lk ) { c_lk = lk; c_itr = trio[itr]; }
+            if ( uc_itr==trio[itr] ) uc_is_mendelian = 1;
+        }
+
+        if ( !uc_is_mendelian )
+        {
+            uc_lk += log(1 - trio_Pm);
+            // fprintf(stderr,"c_lk=%e uc_lk=%e c_itr=%d%d%d uc_itr=%d%d%d\n", c_lk,uc_lk,c_itr>>8&0xf,c_itr>>4&0xf,c_itr&0xf,uc_itr>>8&0xf,uc_itr>>4&0xf,uc_itr&0xf);
+            if ( c_lk < uc_lk ) { c_lk = uc_lk; c_itr = uc_itr; }
+        }
+        // fprintf(stderr,"best_lk=%e best_itr=%d%d%d uc_itr=%d%d%d\n", c_lk,c_itr>>8&0xf,c_itr>>4&0xf,c_itr&0xf,uc_itr>>8&0xf,uc_itr>>4&0xf,uc_itr&0xf);
+
+        // Set genotypes for father, mother, child and calculate genotype qualities
+        for (i=0; i<3; i++)
+        {
+            // GT
+            int ismpl    = fam->sample[i];
+            int igt      = c_itr>>((2-i)*4) & 0xf;
+            double *gl   = call->GLs + nout_gts*ismpl;
+            int32_t *gts = call->cgts + ismpl;
+            if ( gl[0]==1 || igt==GT_SKIP )    // zero depth, set missing genotypes
+            {
+                gts[0] = -1;
+                // bcf_float_set_missing(call->GQs[ismpl]);
+                continue;
+            }
+            gts[0] = igt;
+
+            #if 0
+                // todo: Genotype Qualities
+                //
+                // GQ: for each family member i sum over all genotypes j,k keeping igt fixed
+                double lk_sum = 0;
+                for (itr=0; itr<ntrio; itr++)
+                {
+                    if ( igt != (trio[itr]>>((2-i)*4) & 0xf) ) continue;
+                    double lk = 0;
+                    int j;
+                    for (j=0; j<3; j++)
+                    {
+                        int jsmpl = fam->sample[j];
+                        double *gl = call->GLs + ngts*jsmpl;
+                        if ( gl[0]==1 ) continue;
+                        int jgt = trio[itr]>>((2-j)*4) & 0xf;
+                        if ( jgt==GT_SKIP ) continue;
+                        lk += gl[jgt];
+                    }
+                    double Pkij = (double)2/(trio[itr]>>12);
+                    lk += log(1 - trio_Pm * (1 - Pkij));
+                    lk_sum = logsumexp2(lk_sum, lk);
+                }
+                if ( !uc_is_mendelian && (best_itr>>((2-i)*4)&0xf)==(uc_itr>>((2-i)*4)&0xf) ) lk_sum = logsumexp2(lk_sum,uc_lk);
+                call->GQs[ismpl] = -4.3429*(best_lk - lk_sum);
+            #endif
+        }
+    }
+
+    for (i=0; i<4; i++) call->ac[i] = 0;
+    call->nhets = 0;
+    call->ndiploid = 0;
+
+    // Test if CGT,UGT are needed
+    int ucgts_needed = 0;
+    int32_t *cgts = call->cgts - 1;
+    int32_t *ugts = call->ugts - 1;
+    int32_t *gts  = call->gts - 2;
+    for (isample = 0; isample < nsmpl; isample++)
+    {
+        int ploidy = call->ploidy ? call->ploidy[isample] : 2;
+        cgts++;
+        ugts++;
+        gts += 2;
+        if ( ugts[0]==-1 )
+        {
+            gts[0] = bcf_gt_missing;
+            gts[1] = ploidy==2 ? bcf_gt_missing : bcf_int32_vector_end;
+            continue;
+        }
+        int a,b;
+        if ( cgts[0]!=ugts[0] )
+        {
+            bcf_gt2alleles(cgts[0], &a, &b);
+            gts[0] = bcf_gt_unphased(a);
+            gts[1] = ploidy==1 ? bcf_int32_vector_end : bcf_gt_unphased(b);
+        }
+        else
+        {
+            bcf_gt2alleles(ugts[0], &a, &b);
+            gts[0] = bcf_gt_unphased(a);
+            gts[1] = ploidy==1 ? bcf_int32_vector_end : bcf_gt_unphased(b);
+        }
+        if ( cgts[0]!=ugts[0] ) ucgts_needed = 1;
+        call->ac[a]++;
+        if ( ploidy==2 )
+        {
+            call->ac[b]++;
+            call->ndiploid++;
+            if ( a!=b ) call->nhets++;
+        }
+    }
+    if ( ucgts_needed )
+    {
+        // Some GTs are different
+        bcf_update_format_int32(call->hdr,rec,"UGT",call->ugts,nsmpl);
+        bcf_update_format_int32(call->hdr,rec,"CGT",call->cgts,nsmpl);
+    }
+}
+#endif
+
+static void mcall_trim_and_update_PLs(call_t *call, bcf1_t *rec, int nals_ori, int nals_new)
+{
+    int npls_src = nals_ori*(nals_ori+1)/2;
+    int npls_dst = nals_new*(nals_new+1)/2;     // number of PL values in diploid samples, ori and new
+    if ( call->all_diploid && npls_src == npls_dst ) return;
+
+    int *pls_src = call->PLs, *pls_dst = call->PLs;
+
+    int nsmpl = bcf_hdr_nsamples(call->hdr);
+    int isample, ia;
+    for (isample = 0; isample < nsmpl; isample++)
+    {
+        int ploidy = call->ploidy ? call->ploidy[isample] : 2;
+        if ( ploidy==2 )
+        {
+            for (ia=0; ia<npls_dst; ia++)
+                pls_dst[ia] =  pls_src[ call->pl_map[ia] ];
+        }
+        else if ( ploidy==1 )
+        {
+            for (ia=0; ia<nals_new; ia++)
+            {
+                int isrc = (ia+1)*(ia+2)/2-1;
+                pls_dst[ia] = pls_src[ call->pl_map[isrc] ];
+            }
+            if ( ia<npls_dst ) pls_dst[ia] = bcf_int32_vector_end;
+        }
+        else
+        {
+            pls_dst[0] = bcf_int32_missing;
+            pls_dst[1] = bcf_int32_vector_end;  // relying on nals_new>1 in mcall()
+        }
+        pls_src += npls_src;
+        pls_dst += npls_dst;
+    }
+    bcf_update_format_int32(call->hdr, rec, "PL", call->PLs, npls_dst*nsmpl);
+}
+
+void mcall_trim_and_update_numberR(call_t *call, bcf1_t *rec, int nals_ori, int nals_new)
+{
+    if ( nals_ori==nals_new ) return;
+
+    int i,j, nret, size = sizeof(float);
+
+    void *tmp_ori = call->itmp, *tmp_new = call->PLs;  // reusing PLs storage which is not used at this point
+    int ntmp_ori = call->n_itmp, ntmp_new = call->mPLs;
+
+    // INFO fields
+    for (i=0; i<rec->n_info; i++)
+    {
+        bcf_info_t *info = &rec->d.info[i];
+        int vlen = bcf_hdr_id2length(call->hdr,BCF_HL_INFO,info->key);
+        if ( vlen!=BCF_VL_R ) continue; // not a Number=R tag
+
+        int type  = bcf_hdr_id2type(call->hdr,BCF_HL_INFO,info->key);
+        const char *key = bcf_hdr_int2id(call->hdr,BCF_DT_ID,info->key);
+        nret = bcf_get_info_values(call->hdr, rec, key, &tmp_ori, &ntmp_ori, type);
+        if ( nret<=0 ) continue;
+
+        if ( nals_new==1 )
+            bcf_update_info_int32(call->hdr, rec, key, tmp_ori, 1);     // has to be the REF, the order could not change
+        else
+        {
+            for (j=0; j<nals_ori; j++)
+            {
+                int k = call->als_map[j];
+                if ( k==-1 ) continue;   // to be dropped
+                memcpy((char *)tmp_new+size*k, (char *)tmp_ori+size*j, size);
+            }
+            bcf_update_info_int32(call->hdr, rec, key, tmp_new, nals_new);
+        }
+    }
+
+    // FORMAT fields
+    for (i=0; i<rec->n_fmt; i++)
+    {
+        bcf_fmt_t *fmt = &rec->d.fmt[i];
+        int vlen = bcf_hdr_id2length(call->hdr,BCF_HL_FMT,fmt->id);
+        if ( vlen!=BCF_VL_R ) continue; // not a Number=R tag
+
+        int type = bcf_hdr_id2type(call->hdr,BCF_HL_FMT,fmt->id);
+        const char *key = bcf_hdr_int2id(call->hdr,BCF_DT_ID,fmt->id);
+        nret = bcf_get_format_values(call->hdr, rec, key, &tmp_ori, &ntmp_ori, type);
+        if (nret<=0) continue;
+        int nsmpl = bcf_hdr_nsamples(call->hdr);
+
+        assert( nret==nals_ori*nsmpl );
+
+        for (j=0; j<nsmpl; j++)
+        {
+            char *ptr_src = (char *)tmp_ori + j*nals_ori*size;
+            char *ptr_dst = (char *)tmp_new + j*nals_new*size;
+            int k;
+            for (k=0; k<nals_ori; k++)
+            {
+                int l = call->als_map[k];
+                if ( l==-1 ) continue;   // to be dropped
+                memcpy(ptr_dst+size*l, ptr_src+size*k, size);
+            }
+        }
+        bcf_update_format_int32(call->hdr, rec, key, tmp_new, nals_new*nsmpl);
+    }
+
+    call->PLs    = (int32_t*) tmp_new;
+    call->mPLs   = ntmp_new;
+    call->itmp   = (int32_t*) tmp_ori;
+    call->n_itmp = ntmp_ori;
+}
+
+
+// NB: in this function we temporarily use calls->als_map for a different
+// purpose to store mapping from new (target) alleles to original alleles.
+//
+static int mcall_constrain_alleles(call_t *call, bcf1_t *rec, int *unseen)
+{
+    assert( call->tgt_als->n );
+    if ( call->tgt_als->n>5 ) error("Maximum accepted number of alleles is 5, got %d\n", call->tgt_als->n);
+    hts_expand(char*,call->tgt_als->n+1,call->nals,call->als);
+
+    int has_new = 0;
+
+    int i, j, nals = 1;
+    for (i=1; i<call->nals_map; i++) call->als_map[i] = -1;
+
+    if ( vcmp_set_ref(call->vcmp, rec->d.allele[0], call->tgt_als->allele[0]) < 0 )
+        error("The reference alleles are not compatible at %s:%d .. %s vs %s\n", call->hdr->id[BCF_DT_CTG][rec->rid].key,rec->pos+1,call->tgt_als->allele[0],rec->d.allele[0]);
+
+    // create mapping from new to old alleles
+    call->als[0] = call->tgt_als->allele[0];
+    call->als_map[0] = 0;
+
+    for (i=1; i<call->tgt_als->n; i++)
+    {
+        call->als[nals] = call->tgt_als->allele[i];
+        j = vcmp_find_allele(call->vcmp, rec->d.allele+1, rec->n_allele - 1, call->tgt_als->allele[i]);
+
+        // if ( j+1==*unseen )
+        // { 
+        //     fprintf(stderr,"Fixme? Cannot constrain to %d-th allele (%s); j=%d,unseen=%d. VCF=",i,call->tgt_als->allele[i],j,*unseen);
+        //     int k;
+        //     for (k=0; k<rec->n_allele; k++) fprintf(stderr,"%s%s",k==0?"":",",rec->d.allele[k]);
+        //     fprintf(stderr,"\tTAB=");
+        //     for (k=0; k<call->tgt_als->n; k++) fprintf(stderr,"%s%s",k==0?"":",",call->tgt_als->allele[k]);
+        //     fprintf(stderr,"\n");
+        //     return -1;
+        // }
+        
+        if ( j>=0 )
+        {
+            // existing allele
+            call->als_map[nals] = j+1;
+        }
+        else
+        {
+            // There is a new allele in targets which is not present in VCF.
+            // We use the X allele to estimate PLs. Note that X may not be
+            // present at multiallelic indels sites. In that case we use the
+            // last allele anyway, because the least likely allele comes last
+            // in mpileup's ALT output.
+            call->als_map[nals] = (*unseen)>=0 ? *unseen : rec->n_allele - 1;
+            has_new = 1;
+        }
+        nals++;
+    }
+    if ( *unseen )
+    {
+        call->als_map[nals] = *unseen;
+        call->als[nals] = rec->d.allele[*unseen];
+        nals++;
+    }
+
+    if ( !has_new && nals==rec->n_allele ) return 0;
+    bcf_update_alleles(call->hdr, rec, (const char**)call->als, nals);
+
+    // create mapping from new PL to old PL
+    int k = 0;
+    for (i=0; i<nals; i++)
+    {
+        for (j=0; j<=i; j++)
+        {
+            int a = call->als_map[i], b = call->als_map[j];
+            call->pl_map[k++] = a>b ? a*(a+1)/2 + b : b*(b+1)/2 + a;
+        }
+    }
+
+    // update PL
+    call->nPLs = bcf_get_format_int32(call->hdr, rec, "PL", &call->PLs, &call->mPLs);
+    int nsmpl  = bcf_hdr_nsamples(call->hdr);
+    int npls_ori = call->nPLs / nsmpl;
+    int npls_new = k;
+    hts_expand(int32_t,npls_new*nsmpl,call->n_itmp,call->itmp);
+    int *ori_pl = call->PLs, *new_pl = call->itmp;
+    for (i=0; i<nsmpl; i++)
+    {
+        for (k=0; k<npls_new; k++)
+        {
+            new_pl[k] = ori_pl[call->pl_map[k]];
+            if ( new_pl[k]==bcf_int32_missing && *unseen>=0 )
+            {
+                // missing value, and there is an unseen allele: identify the
+                // alleles and use the lk of either AX or XX
+                int k_ori = call->pl_map[k], ia, ib;
+                bcf_gt2alleles(k_ori, &ia, &ib);
+                k_ori = bcf_alleles2gt(ia,*unseen);
+                if ( ori_pl[k_ori]==bcf_int32_missing ) k_ori = bcf_alleles2gt(ib,*unseen);
+                if ( ori_pl[k_ori]==bcf_int32_missing ) k_ori = bcf_alleles2gt(*unseen,*unseen);
+                new_pl[k] = ori_pl[k_ori];
+            }
+            if ( !k && new_pl[k]==bcf_int32_vector_end ) new_pl[k]=bcf_int32_missing;
+        }
+        ori_pl += npls_ori;
+        new_pl += npls_new;
+    }
+    bcf_update_format_int32(call->hdr, rec, "PL", call->itmp, npls_new*nsmpl);
+
+    // update QS, use temporarily call->GPs to store the values
+    int nqs = bcf_get_info_float(call->hdr, rec, "QS", &call->smpl_grp[0].qsum, &call->smpl_grp[0].nqsum);
+    hts_expand(float,nals,call->nGPs,call->GPs);
+    for (i=0; i<nals; i++)
+        call->GPs[i] = call->als_map[i]<nqs ? call->smpl_grp[0].qsum[call->als_map[i]] : 0;
+    bcf_update_info_float(call->hdr, rec, "QS", call->GPs, nals);
+
+    // update any Number=R tags
+    void *tmp_ori = call->itmp, *tmp_new = call->PLs;  // reusing PLs storage which is not used at this point
+    int ntmp_ori = call->n_itmp, ntmp_new = call->mPLs;
+    for (i=0; i<rec->n_fmt; i++)
+    {
+        bcf_fmt_t *fmt = &rec->d.fmt[i];
+        int vlen = bcf_hdr_id2length(call->hdr,BCF_HL_FMT,fmt->id);
+        if ( vlen!=BCF_VL_R ) continue; // not a Number=R tag
+
+        // NB:works only for BCF_HT_INT and BCF_HT_REAL
+        int type = bcf_hdr_id2type(call->hdr,BCF_HL_FMT,fmt->id);
+        assert( type==BCF_HT_INT || type==BCF_HT_REAL );
+        assert( sizeof(float)==sizeof(int32_t) );
+
+        const char *key = bcf_hdr_int2id(call->hdr,BCF_DT_ID,fmt->id);
+        int nret = bcf_get_format_values(call->hdr, rec, key, &tmp_ori, &ntmp_ori, type);
+        if (nret<=0) continue;
+        int nsmpl = bcf_hdr_nsamples(call->hdr);
+        int size1 = sizeof(float);
+        hts_expand(float, nsmpl * nals, ntmp_new, tmp_new);
+        for (j=0; j<nsmpl; j++)
+        {
+            uint8_t *ptr_ori = (uint8_t *) tmp_ori + j*size1*fmt->n;
+            uint8_t *ptr_new = (uint8_t *) tmp_new + j*nals*size1;
+            for (k=0; k<nals; k++)
+            {
+                uint8_t *dst = ptr_new + size1*k;
+                uint8_t *src = ptr_ori + size1*call->als_map[k];
+                memcpy(dst,src,size1);
+            }
+        }
+        nret = bcf_update_format(call->hdr, rec, key, tmp_new, nsmpl*nals, type);
+        assert( nret==0 );
+    }
+    call->PLs    = (int32_t*) tmp_new;
+    call->mPLs   = ntmp_new;
+    call->itmp   = (int32_t*) tmp_ori;
+    call->n_itmp = ntmp_ori;
+
+    if ( *unseen ) *unseen = nals-1;
+    return 0;
+}
+
+
+/**
+  *  This function implements the multiallelic calling model. It has two major parts:
+  *   1) determine the most likely set of alleles and calculate the quality of ref/non-ref site
+  *   2) determine and set the genotypes
+  *  In various places in between, the BCF record gets updated.
+  */
+int mcall(call_t *call, bcf1_t *rec)
+{
+    int i,j, unseen = call->unseen;
+
+    // Force alleles when calling genotypes given alleles was requested
+    if ( call->flag & CALL_CONSTR_ALLELES && mcall_constrain_alleles(call, rec, &unseen)!=0 ) return -2;
+
+    int nsmpl    = bcf_hdr_nsamples(call->hdr);
+    int nals_ori = rec->n_allele;
+    hts_expand(int,nals_ori,call->nac,call->ac);
+    hts_expand(int,nals_ori,call->nals_map,call->als_map);
+    hts_expand(int,nals_ori*(nals_ori+1)/2,call->npl_map,call->pl_map);
+
+    // Get the genotype likelihoods
+    call->nPLs = bcf_get_format_int32(call->hdr, rec, "PL", &call->PLs, &call->mPLs);
+    if ( call->nPLs!=nsmpl*nals_ori*(nals_ori+1)/2 && call->nPLs!=nsmpl*nals_ori )  // a mixture of diploid and haploid or haploid only
+        error("Wrong number of PL fields? nals=%d npl=%d\n", nals_ori,call->nPLs);
+
+    // Convert PLs to probabilities
+    int ngts_ori = nals_ori*(nals_ori+1)/2;
+    hts_expand(double, call->nPLs, call->npdg, call->pdg);
+    set_pdg(call->pl2p, call->PLs, call->pdg, nsmpl, ngts_ori, unseen);
+
+    // Get sum of qualities, serves as an AF estimate, f_x = QS/N in Eq. 1 in call-m math notes.
+    if ( call->nsmpl_grp == 1  )
+    {
+        int nqs = bcf_get_info_float(call->hdr, rec, "QS", &call->smpl_grp[0].qsum, &call->smpl_grp[0].nqsum);
+        if ( nqs<=0 ) error("The QS annotation not present at %s:%d\n", bcf_seqname(call->hdr,rec),rec->pos+1);
+        if ( nqs < nals_ori )
+        {
+            // Some of the listed alleles do not have the corresponding QS field. This is
+            // typically ref-only site with <*> in ALT.
+            hts_expand(float,nals_ori,call->smpl_grp[0].nqsum,call->smpl_grp[0].qsum);
+            for (i=nqs; i<nals_ori; i++) call->smpl_grp[0].qsum[i] = 0;
+        }
+    }
+    else
+    {
+        for (j=0; j<call->nsmpl_grp; j++)
+        {
+            hts_expand(float,nals_ori,call->smpl_grp[j].nqsum,call->smpl_grp[j].qsum);
+            memset(call->smpl_grp[j].qsum, 0, sizeof(float)*nals_ori);
+        }
+
+        // Use FORMAT/AD or FORMAT/QS
+        int nad = bcf_get_format_int32(call->hdr, rec, call->sample_groups_tag, &call->ADs, &call->nADs);
+        if ( nad<1 ) error("Error: FORMAT/%s is required with the -G option, mpileup must be run with \"-a AD\" or \"-a QS\"\n",call->sample_groups_tag);
+        nad /= bcf_hdr_nsamples(call->hdr);
+        for (i=0; i<call->nsmpl_grp; i++)
+        {
+            int is;
+            smpl_grp_t *grp = &call->smpl_grp[i];
+            hts_expand(float,nals_ori,grp->nqsum,grp->qsum);
+            for (j=0; j<nals_ori; j++) grp->qsum[j] = 0;
+            for (is=0; is<grp->nsmpl; is++)
+            {
+                int ismpl = grp->smpl[is];
+                int32_t *ptr = call->ADs + ismpl*nad;
+                float sum = 0;
+                for (j=0; j<nad; j++)
+                {
+                    if ( ptr[j]==bcf_int32_vector_end ) break;
+                    if ( ptr[j]!=bcf_int32_missing ) sum += ptr[j];
+                }
+                if ( sum )
+                {
+                    for (j=0; j<nad; j++)
+                    {
+                        if ( ptr[j]==bcf_int32_vector_end ) break;
+                        if ( ptr[j]!=bcf_int32_missing ) grp->qsum[j] += ptr[j]/sum;
+                    }
+                }
+            }
+        }
+    }
+
+    // If available, take into account reference panel AFs
+    if ( call->prior_AN && bcf_get_info_int32(call->hdr, rec, call->prior_AN ,&call->ac, &call->nac)==1 )
+    {
+        int an = call->ac[0];   // number of alleles total, procede only if not zero; reuse call->ac
+        if ( an > 0 && bcf_get_info_int32(call->hdr, rec, call->prior_AC ,&call->ac, &call->nac)==nals_ori-1 )    // number of ALT alleles
+        {
+            int ac0 = an;       // this will become the number of REFs
+            for (i=0; i<nals_ori-1; i++)
+            {
+                if ( call->ac[i]==bcf_int32_vector_end ) break;
+                if ( call->ac[i]==bcf_int32_missing ) continue;
+                ac0 -= call->ac[i];
+
+                // here an*0.5 is the number of samples in the populatio and ac*0.5 is the AF weighted by the number of samples
+                for (j=0; j<call->nsmpl_grp; j++)
+                    call->smpl_grp[j].qsum[i+1] = (call->smpl_grp[j].qsum[i+1] + 0.5*call->ac[i]) / (call->smpl_grp[j].nsmpl + 0.5*an);
+            }
+            if ( ac0<0 ) error("Incorrect %s,%s values at %s:%d\n", call->prior_AN,call->prior_AC,bcf_seqname(call->hdr,rec),rec->pos+1);
+            for (j=0; j<call->nsmpl_grp; j++)
+                call->smpl_grp[j].qsum[0] = (call->smpl_grp[j].qsum[0] + 0.5*ac0) / (call->smpl_grp[j].nsmpl + 0.5*an);
+        }
+    }
+
+    // normalize so that QS sums to 1 for each group
+    for (j=0; j<call->nsmpl_grp; j++)
+    {
+        float sum = 0;
+        for (i=0; i<nals_ori; i++) sum += call->smpl_grp[j].qsum[i];
+        if ( sum ) for (i=0; i<nals_ori; i++) call->smpl_grp[j].qsum[i] /= sum;
+    }
+
+    bcf_update_info_int32(call->hdr, rec, "QS", NULL, 0);      // remove QS tag
+
+    if ( nals_ori > 8*sizeof(call->als_new) )
+    { 
+        fprintf(stderr,"Too many alleles at %s:%"PRId64", skipping.\n", bcf_seqname(call->hdr,rec),(int64_t) rec->pos+1);
+        return 0; 
+    }
+
+    // For each group find the best combination of alleles
+    call->als_new = 0;
+    double ref_lk = -HUGE_VAL, lk_sum = -HUGE_VAL, max_qual = -HUGE_VAL;
+    for (j=0; j<call->nsmpl_grp; j++)
+    {
+        smpl_grp_t *grp = &call->smpl_grp[j];
+        mcall_find_best_alleles(call, nals_ori, grp);
+        call->als_new |= grp->als;
+        if ( grp->max_lk==-HUGE_VAL ) continue;
+        double qual = -4.343*(grp->ref_lk - logsumexp2(grp->lk_sum,grp->ref_lk));
+        if ( max_qual < qual )
+        {
+            max_qual = qual;
+            lk_sum = grp->lk_sum;
+            ref_lk = grp->ref_lk;
+        }
+    }
+
+    // Make sure the REF allele is always present
+    if ( !(call->als_new&1) ) call->als_new |= 1;
+
+    int is_variant = call->als_new==1 ? 0 : 1;
+    if ( call->flag & CALL_VARONLY && !is_variant ) return 0;
+
+    call->nals_new = 0;
+    for (i=0; i<nals_ori; i++)
+    {
+        if ( i>0 && i==unseen ) continue;
+        if ( call->flag & CALL_KEEPALT ) call->als_new |= 1<<i;
+        if ( call->als_new & (1<<i) ) call->nals_new++;
+    }
+
+    init_allele_trimming_maps(call,nals_ori,call->als_new);
+
+    int nAC = 0;
+    if ( call->als_new==1 )   // only REF allele on output
+    {
+        mcall_set_ref_genotypes(call,nals_ori);
+        bcf_update_format_int32(call->hdr, rec, "PL", NULL, 0);    // remove PL, useless now
+    }
+    else if ( !is_variant )
+    {
+        mcall_set_ref_genotypes(call,nals_ori);     // running with -A, prevent mcall_call_genotypes from putting some ALT back
+        mcall_trim_and_update_PLs(call, rec, nals_ori, call->nals_new);
+    }
+    else
+    {
+        // The most likely set of alleles includes non-reference allele (or was enforced), call genotypes.
+        // Note that it is a valid outcome if the called genotypes exclude some of the ALTs.
+        int ngts_new = call->nals_new*(call->nals_new+1)/2;
+        hts_expand(float,ngts_new*nsmpl,call->nGPs,call->GPs);
+        for (i=0; i<call->nals_new; i++) call->ac[i] = 0;
+
+        if ( call->flag & CALL_CONSTR_TRIO && call->nals_new>4 )
+        { 
+            fprintf(stderr,"Too many alleles at %s:%"PRId64", skipping.\n", bcf_seqname(call->hdr,rec),(int64_t) rec->pos+1);
+            return 0; 
+        }
+        if ( call->output_tags & (CALL_FMT_GQ|CALL_FMT_GP) )
+        {
+            memset(call->GPs,0,nsmpl*ngts_new*sizeof(*call->GPs));
+            memset(call->GQs,0,nsmpl*sizeof(*call->GQs));
+        }
+        for (i=0; i<call->nsmpl_grp; i++)
+        {
+            if ( call->flag & CALL_CONSTR_TRIO )
+                error("todo: constrained trio calling temporarily disabled\n");   //mcall_call_trio_genotypes(call,rec,nals,&call->smpl_grp[i]);
+            else
+                mcall_call_genotypes(call,nals_ori,&call->smpl_grp[i]);
+        }
+
+        // Skip the site if all samples are 0/0. This can happen occasionally.
+        for (i=1; i<call->nals_new; i++) nAC += call->ac[i];
+        if ( !nAC && call->flag & CALL_VARONLY ) return 0;
+
+        if ( call->output_tags & CALL_FMT_GP )
+            bcf_update_format_float(call->hdr, rec, "GP", call->GPs, nsmpl*ngts_new);
+        if ( call->output_tags & CALL_FMT_GQ )
+            bcf_update_format_int32(call->hdr, rec, "GQ", call->GQs, nsmpl);
+
+        mcall_trim_and_update_PLs(call,rec,nals_ori,call->nals_new);
+    }
+    if ( nals_ori!=call->nals_new )
+        mcall_trim_and_update_numberR(call,rec,nals_ori,call->nals_new);
+
+    // Set QUAL
+    if ( nAC )
+    {
+        // Quality of a variant site. fabs() to avoid negative zeros in VCF output when CALL_KEEPALT is set
+        rec->qual = max_qual;
+    }
+    else
+    {
+        // Set the quality of a REF site
+        if ( lk_sum!=-HUGE_VAL )  // no support from (high quality) reads, so QUAL=1-prior
+            rec->qual = -4.343*(lk_sum - logsumexp2(lk_sum,ref_lk));
+        else if ( call->ac[0] )
+            rec->qual = call->theta ? -4.343*call->theta : 0;
+        else
+            bcf_float_set_missing(rec->qual);
+    }
+
+    // AC, AN
+    if ( call->nals_new>1 ) bcf_update_info_int32(call->hdr, rec, "AC", call->ac+1, call->nals_new-1);
+    nAC += call->ac[0];
+    bcf_update_info_int32(call->hdr, rec, "AN", &nAC, 1);
+
+    // Remove unused alleles
+    hts_expand(char*,call->nals_new,call->nals,call->als);
+    for (i=0; i<nals_ori; i++)
+        if ( call->als_map[i]>=0 ) call->als[call->als_map[i]] = rec->d.allele[i];
+    bcf_update_alleles(call->hdr, rec, (const char**)call->als, call->nals_new);
+    bcf_update_genotypes(call->hdr, rec, call->gts, nsmpl*2);
+
+    // DP4 and PV4 tags
+    if ( bcf_get_info_float(call->hdr, rec, "I16", &call->anno16, &call->n16)==16 )
+    {
+        int32_t dp[4]; dp[0] = call->anno16[0]; dp[1] = call->anno16[1]; dp[2] = call->anno16[2]; dp[3] = call->anno16[3];
+        bcf_update_info_int32(call->hdr, rec, "DP4", dp, 4);
+
+        int32_t mq = (call->anno16[8]+call->anno16[10])/(call->anno16[0]+call->anno16[1]+call->anno16[2]+call->anno16[3]);
+        bcf_update_info_int32(call->hdr, rec, "MQ", &mq, 1);
+
+        if ( call->output_tags & CALL_FMT_PV4 )
+        {
+            anno16_t a;
+            float tmpf[4];
+            int is_tested = test16(call->anno16, &a) >= 0 && a.is_tested ? 1 : 0;
+            if ( is_tested ) 
+            {
+                for (i=0; i<4; i++) tmpf[i] = a.p[i];
+                bcf_update_info_float(call->hdr, rec, "PV4", tmpf, 4);
+            }
+        }
+    }
+
+    bcf_update_info_int32(call->hdr, rec, "I16", NULL, 0);     // remove I16 tag
+
+    return call->nals_new;
+}
+
diff --git a/bcftools/mcall.c.pysam.c b/bcftools/mcall.c.pysam.c
new file mode 100644
index 0000000..ea57344
--- /dev/null
+++ b/bcftools/mcall.c.pysam.c
@@ -0,0 +1,1687 @@
+#include "bcftools.pysam.h"
+
+/*  mcall.c -- multiallelic and rare variant calling.
+
+    Copyright (C) 2012-2021 Genome Research Ltd.
+
+    Author: Petr Danecek <pd3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.  */
+
+#include <assert.h>
+#include <math.h>
+#include <inttypes.h>
+#include <ctype.h>
+#include <htslib/kfunc.h>
+#include <htslib/khash_str2int.h>
+#include "call.h"
+#include "prob1.h"
+
+// Using priors for GTs does not seem to be mathematically justified. Although
+// it seems effective in removing false calls, it also flips a significant
+// proportion of HET genotypes. Better is to filter by FORMAT/GQ using
+// `bcftools filter`.
+#define USE_PRIOR_FOR_GTS 0
+
+// Go with uniform PLs for samples with no coverage. If unset, missing
+// genotypes is reported instead.
+#define FLAT_PDG_FOR_MISSING 0
+
+int test16(float *anno16, anno16_t *a);
+
+void qcall_init(call_t *call) { return; }
+void qcall_destroy(call_t *call) { return; }
+int qcall(call_t *call, bcf1_t *rec)
+{
+    // QCall format:
+    //  chromosome, position, reference allele, depth, mapping quality, 0, ..
+    error("TODO: qcall output\n");
+    return 0;
+}
+
+void call_init_pl2p(call_t *call)
+{
+    int i;
+    for (i=0; i<256; i++)
+        call->pl2p[i] = pow(10., -i/10.);
+}
+
+// Macros for accessing call->trio and call->ntrio
+#define FTYPE_222 0     // family type: all diploid
+#define FTYPE_121 1     // chrX, the child is a boy
+#define FTYPE_122 2     // chrX, a girl
+#define FTYPE_101 3     // chrY, boy
+#define FTYPE_100 4     // chrY, girl
+
+#define GT_SKIP 0xf     // empty genotype (chrY in females)
+
+#define IS_POW2(x) (!((x) & ((x) - 1)))    // zero is permitted
+#define IS_HOM(x)  IS_POW2(x)
+
+// Pkij = P(k|i,j) tells how likely it is to be a het if the parents
+// are homs etc. The consistency of i,j,k has been already checked.
+// Parameters are alleles and ploidy of father, mother, kid
+// Returns 2/Pkij.
+int calc_Pkij(int fals, int mals, int kals, int fpl, int mpl, int kpl)
+{
+    int als = fals|mals|kals;
+    if ( IS_HOM(als) ) return 2;    // all are the same: child must be a HOM, P=1
+
+    if ( fpl==1 )
+    {
+        if ( kpl==1 )   // chr X, the child is a boy, the copy is inherited from the mother
+        {
+            if ( IS_HOM(mals) ) return 2;   // 0 11 -> P(1) = 1
+            return 4;                       // 0 01 -> P(0) = P(1) = 1/2
+        }
+        // chr X, the child is a girl
+        if ( IS_HOM(mals) ) return 2;       // 0 11 -> P(01) = 1
+        return 4;                           // 0 01 -> P(00) = P(01) = 1/2
+    }
+
+    if ( IS_HOM(fals) && IS_HOM(mals) ) return 2;   // 00 11 01, the child must be a HET, P=1
+    if ( !IS_HOM(fals) && !IS_HOM(mals) )
+    {
+        if ( IS_HOM(kals) ) return 8;   // 01 01 00 or 01 01 11, P(k=HOM) = 1/4
+        return 4;                       // 01 01 01, P(k=HET) = 1/2
+    }
+    return 4;   // 00 01, P(k=HET) = P(k=HOM) = 1/2
+}
+
+// Initialize ntrio and trio: ntrio lists the number of possible
+// genotypes given combination of haploid/diploid genomes and the
+// number of alleles. trio lists allowed genotype combinations:
+//      4bit: 2/Pkij, 4: father, 4: mother, 4: child
+// See also mcall_call_trio_genotypes()
+//
+static void mcall_init_trios(call_t *call)
+{
+    if ( call->prior_AN )
+    {
+        int id = bcf_hdr_id2int(call->hdr,BCF_DT_ID,call->prior_AN);
+        if ( id==-1 ) error("No such tag \"%s\"\n", call->prior_AN);
+        if ( !bcf_hdr_idinfo_exists(call->hdr,BCF_HL_FMT,id) )  error("No such FORMAT tag \"%s\"\n", call->prior_AN);
+        id = bcf_hdr_id2int(call->hdr,BCF_DT_ID,call->prior_AC);
+        if ( id==-1 ) error("No such tag \"%s\"\n", call->prior_AC);
+        if ( !bcf_hdr_idinfo_exists(call->hdr,BCF_HL_FMT,id) )  error("No such FORMAT tag \"%s\"\n", call->prior_AC);
+    }
+
+    // 23, 138, 478 possible diploid trio genotypes with 2, 3, 4 alleles
+    call->ntrio[FTYPE_222][2] = 15; call->ntrio[FTYPE_222][3] = 78;  call->ntrio[FTYPE_222][4] = 250;
+    call->ntrio[FTYPE_121][2] = 8;  call->ntrio[FTYPE_121][3] = 27;  call->ntrio[FTYPE_121][4] = 64;
+    call->ntrio[FTYPE_122][2] = 8;  call->ntrio[FTYPE_122][3] = 27;  call->ntrio[FTYPE_122][4] = 64;
+    call->ntrio[FTYPE_101][2] = 2;  call->ntrio[FTYPE_101][3] = 3;   call->ntrio[FTYPE_101][4] = 4;
+    call->ntrio[FTYPE_100][2] = 2;  call->ntrio[FTYPE_100][3] = 3;   call->ntrio[FTYPE_100][4] = 4;
+
+    int nals, itype;
+    for (itype=0; itype<=4; itype++)
+    {
+        for (nals=2; nals<=4; nals++)
+            call->trio[itype][nals] = (uint16_t*) malloc(sizeof(uint16_t)*call->ntrio[itype][nals]);
+    }
+
+    // max 10 possible diploid genotypes
+    int gts[10];
+    for (nals=2; nals<=4; nals++)
+    {
+        int i,j,k, n = 0, ngts = 0;
+        for (i=0; i<nals; i++)
+            for (j=0; j<=i; j++)
+                gts[ngts++] = 1<<i | 1<<j;
+
+        // 222: all diploid
+        // i,j,k: father, mother, child
+        for (i=0; i<ngts; i++)
+            for (j=0; j<ngts; j++)
+                for (k=0; k<ngts; k++)
+                {
+                    if ( ((gts[i]|gts[j])&gts[k]) != gts[k] ) continue;             // k not present in neither i nor j
+                    if ( !(gts[i] & gts[k]) || !(gts[j] & gts[k]) ) continue;       // one copy from father, one from mother
+                    int Pkij = calc_Pkij(gts[i],gts[j],gts[k], 2,2,2);
+                    call->trio[FTYPE_222][nals][n++] = Pkij<<12 | i<<8 | j<<4 | k;  // father, mother, child
+                }
+        assert( n==call->ntrio[FTYPE_222][nals] );
+
+        // 121: chrX, boy
+        n = 0;
+        for (i=0; i<ngts; i++)
+            for (j=0; j<ngts; j++)
+                for (k=0; k<ngts; k++)
+                {
+                    if ( !IS_HOM(gts[i]) || !IS_HOM(gts[k]) ) continue;   // father nor boy can be diploid
+                    if ( ((gts[i]|gts[j])&gts[k]) != gts[k] ) continue;
+                    if ( !(gts[j] & gts[k]) ) continue;     // boy must inherit the copy from mother
+                    int Pkij = calc_Pkij(gts[i],gts[j],gts[k], 1,2,1);
+                    call->trio[FTYPE_121][nals][n++] = Pkij<<12 | i<<8 | j<<4 | k;
+                }
+        assert( n==call->ntrio[FTYPE_121][nals] );
+
+        // 122: chrX, girl
+        n = 0;
+        for (i=0; i<ngts; i++)
+            for (j=0; j<ngts; j++)
+                for (k=0; k<ngts; k++)
+                {
+                    if ( !IS_HOM(gts[i]) ) continue;
+                    if ( ((gts[i]|gts[j])&gts[k]) != gts[k] ) continue;
+                    if ( !(gts[i] & gts[k]) ) continue;     // girl must inherit one copy from the father and one from the mother
+                    if ( !(gts[j] & gts[k]) ) continue;
+                    int Pkij = calc_Pkij(gts[i],gts[j],gts[k], 1,2,2);
+                    call->trio[FTYPE_122][nals][n++] = Pkij<<12 | i<<8 | j<<4 | k;
+                }
+        assert( n==call->ntrio[FTYPE_122][nals] );
+
+        // 101: chrY, boy
+        n = 0;
+        for (i=0; i<ngts; i++)
+            for (k=0; k<ngts; k++)
+            {
+                if ( !IS_HOM(gts[i]) || !IS_HOM(gts[k]) ) continue;
+                if ( (gts[i]&gts[k]) != gts[k] ) continue;
+                call->trio[FTYPE_101][nals][n++] = 1<<12 | i<<8 | GT_SKIP<<4 | k;
+            }
+        assert( n==call->ntrio[FTYPE_101][nals] );
+
+        // 100: chrY, girl
+        n = 0;
+        for (i=0; i<ngts; i++)
+        {
+            if ( !IS_POW2(gts[i]) ) continue;
+            call->trio[FTYPE_100][nals][n++] = 1<<12 | i<<8 | GT_SKIP<<4 | GT_SKIP;
+        }
+        assert( n==call->ntrio[FTYPE_100][nals] );
+
+    }
+    call->GLs = (double*) calloc(bcf_hdr_nsamples(call->hdr)*10,sizeof(double));
+
+    int i, j;
+    for (i=0; i<call->nfams; i++)
+    {
+        family_t *fam = &call->fams[i];
+        int ploidy[3];
+        for (j=0; j<3; j++)
+            ploidy[j] = call->ploidy[fam->sample[j]];
+
+        if ( ploidy[FATHER]==2 )    // not X, not Y
+        {
+            if ( ploidy[MOTHER]!=2 || ploidy[CHILD]!=2 )
+                error("Incorrect ploidy: %d %d %d\n", ploidy[FATHER],ploidy[MOTHER],ploidy[CHILD]);
+            fam->type = FTYPE_222;
+            continue;
+        }
+        if ( ploidy[FATHER]!=1 || ploidy[MOTHER]==1 )
+                error("Incorrect ploidy: %d %d %d\n", ploidy[FATHER],ploidy[MOTHER],ploidy[CHILD]);
+        if ( ploidy[MOTHER]==2 )    // X
+        {
+            if ( ploidy[CHILD]==0 )
+                error("Incorrect ploidy: %d %d %d\n", ploidy[FATHER],ploidy[MOTHER],ploidy[CHILD]);
+            fam->type = ploidy[CHILD]==2 ? FTYPE_122 : FTYPE_121;   // a girl or a boy
+        }
+        else    // Y
+        {
+            if ( ploidy[CHILD]==2 )
+                error("Incorrect ploidy: %d %d %d\n", ploidy[FATHER],ploidy[MOTHER],ploidy[CHILD]);
+            fam->type = ploidy[CHILD]==0 ? FTYPE_100 : FTYPE_101;   // a girl or a boy
+        }
+    }
+}
+static void mcall_destroy_trios(call_t *call)
+{
+    int i, j;
+    for (i=2; i<=4; i++)
+        for (j=0; j<=4; j++)
+            free(call->trio[j][i]);
+}
+
+static void init_sample_groups(call_t *call)
+{
+    int i, nsmpl = bcf_hdr_nsamples(call->hdr);
+    if ( !call->sample_groups )
+    {
+        // standard pooled calling, all samples in the same group
+        call->nsmpl_grp = 1;
+        call->smpl_grp  = (smpl_grp_t*)calloc(1,sizeof(*call->smpl_grp));
+        call->smpl_grp[0].nsmpl = nsmpl;
+        call->smpl_grp[0].smpl  = (uint32_t*)calloc(call->smpl_grp[0].nsmpl,sizeof(uint32_t));
+        for (i=0; i<nsmpl; i++)
+            call->smpl_grp[0].smpl[i] = i;
+        return;
+    }
+
+    if ( call->sample_groups_tag )
+    {
+        // Is the tag defined in the header?
+        int tag_id = bcf_hdr_id2int(call->hdr,BCF_DT_ID,call->sample_groups_tag);
+        if ( tag_id==-1 ) error("No such tag \"%s\"\n",call->sample_groups_tag);
+        if ( !bcf_hdr_idinfo_exists(call->hdr,BCF_HL_FMT,tag_id) )  error("No such FORMAT tag \"%s\"\n", call->sample_groups_tag);
+    }
+    else
+    {
+        int tag_id = bcf_hdr_id2int(call->hdr,BCF_DT_ID,"QS");
+        if ( tag_id >= 0 && bcf_hdr_idinfo_exists(call->hdr,BCF_HL_FMT,tag_id) ) call->sample_groups_tag = "QS";
+        else
+        {
+            tag_id = bcf_hdr_id2int(call->hdr,BCF_DT_ID,"AD");
+            if ( tag_id >= 0 && bcf_hdr_idinfo_exists(call->hdr,BCF_HL_FMT,tag_id) ) call->sample_groups_tag = "AD";
+            else error("Error: neither \"AD\" nor \"QS\" FORMAT tag exists and no alternative given with -G\n");
+        }
+    }
+
+    // Read samples/groups
+    if ( !strcmp("-",call->sample_groups) )
+    {
+        // single-sample calling, each sample creates its own group
+        call->nsmpl_grp = nsmpl;
+        call->smpl_grp  = (smpl_grp_t*)calloc(nsmpl,sizeof(*call->smpl_grp));
+        for (i=0; i<nsmpl; i++)
+        {
+            call->smpl_grp[i].nsmpl = 1;
+            call->smpl_grp[i].smpl  = (uint32_t*)calloc(call->smpl_grp[i].nsmpl,sizeof(uint32_t));
+            call->smpl_grp[i].smpl[0] = i;
+        }
+    }
+    else
+    {
+        int nlines;
+        char **lines = hts_readlist(call->sample_groups, 1, &nlines);
+        if ( !lines ) error("Could not read the file: %s\n", call->sample_groups);
+
+        uint32_t *smpl2grp = (uint32_t*)calloc(nsmpl,sizeof(uint32_t));
+        uint32_t *grp2n = (uint32_t*)calloc(nsmpl,sizeof(uint32_t));
+        void *grp2idx = khash_str2int_init();
+
+        call->nsmpl_grp = 0;
+        for (i=0; i<nlines; i++)
+        {
+            char *ptr = lines[i];
+            while ( *ptr && !isspace(*ptr) ) ptr++;
+            if ( !*ptr ) error("Could not parse the line in %s, expected a sample name followed by tab and a population name: %s\n",call->sample_groups,lines[i]);
+            char *tmp = ptr;
+            while ( *ptr && isspace(*ptr) ) ptr++;
+            if ( !*ptr ) error("Could not parse the line in %s, expected a sample name followed by tab and a population name: %s\n",call->sample_groups,lines[i]);
+            *tmp = 0;
+            int ismpl = bcf_hdr_id2int(call->hdr, BCF_DT_SAMPLE, lines[i]); 
+            if ( ismpl<0 ) continue;
+            if ( smpl2grp[ismpl] ) error("Error: the sample \"%s\" is listed twice in %s\n", lines[i],call->sample_groups);
+            if ( !khash_str2int_has_key(grp2idx,ptr+1) )
+            {
+                khash_str2int_set(grp2idx, ptr+1, call->nsmpl_grp);
+                call->nsmpl_grp++;
+            }
+            int igrp = -1;
+            if ( khash_str2int_get(grp2idx, ptr+1, &igrp)!=0 )
+                error("This should not happen, fixme: %s\n",ptr+1);
+            grp2n[igrp]++;
+            smpl2grp[ismpl] = igrp+1;   // +1 to distinguish unlisted samples
+        }
+        khash_str2int_destroy(grp2idx);
+        if ( !call->nsmpl_grp ) error("Could not parse the file, no matching samples found: %s\n", call->sample_groups);
+
+        call->smpl_grp = (smpl_grp_t*)calloc(call->nsmpl_grp,sizeof(*call->smpl_grp));
+        for (i=0; i<nsmpl; i++)
+        {
+            if ( !smpl2grp[i] ) error("Error: The sample \"%s\" is not listed in %s\n",call->hdr->samples[i],call->sample_groups);
+            int igrp = smpl2grp[i] - 1;
+            if ( !call->smpl_grp[igrp].nsmpl ) 
+                call->smpl_grp[igrp].smpl = (uint32_t*)calloc(grp2n[igrp],sizeof(uint32_t));
+            call->smpl_grp[igrp].smpl[call->smpl_grp[igrp].nsmpl] = i;
+            call->smpl_grp[igrp].nsmpl++;
+        }
+        free(smpl2grp);
+        free(grp2n);
+        for (i=0; i<nlines; i++) free(lines[i]);
+        free(lines);
+    }
+}
+static void destroy_sample_groups(call_t *call)
+{
+    int i;
+    for (i=0; i<call->nsmpl_grp; i++)
+    {
+        free(call->smpl_grp[i].qsum);
+        free(call->smpl_grp[i].smpl);
+    }
+    free(call->smpl_grp);
+}
+
+void mcall_init(call_t *call)
+{
+    init_sample_groups(call);
+    call_init_pl2p(call);
+
+    call->nals_map = 5;
+    call->als_map  = (int*) malloc(sizeof(int)*call->nals_map);
+    call->npl_map  = 5*(5+1)/2;     // will be expanded later if necessary
+    call->pl_map   = (int*) malloc(sizeof(int)*call->npl_map);
+    call->gts  = (int32_t*) calloc(bcf_hdr_nsamples(call->hdr)*2,sizeof(int32_t));   // assuming at most diploid everywhere
+
+    if ( call->flag & CALL_CONSTR_TRIO )
+    {
+        call->cgts = (int32_t*) calloc(bcf_hdr_nsamples(call->hdr),sizeof(int32_t));
+        call->ugts = (int32_t*) calloc(bcf_hdr_nsamples(call->hdr),sizeof(int32_t));
+        mcall_init_trios(call);
+        bcf_hdr_append(call->hdr,"##FORMAT=<ID=CGT,Number=1,Type=Integer,Description=\"Constrained Genotype (0-based index to Number=G ordering).\">");
+        bcf_hdr_append(call->hdr,"##FORMAT=<ID=UGT,Number=1,Type=Integer,Description=\"Unconstrained Genotype (0-based index to Number=G ordering).\">");
+    }
+    if ( call->flag & CALL_CONSTR_ALLELES ) call->vcmp = vcmp_init();
+
+    bcf_hdr_append(call->hdr,"##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">");
+    if ( call->output_tags & CALL_FMT_GQ )
+        bcf_hdr_append(call->hdr,"##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Phred-scaled Genotype Quality\">");
+    if ( call->output_tags & CALL_FMT_GP )
+        bcf_hdr_append(call->hdr,"##FORMAT=<ID=GP,Number=G,Type=Float,Description=\"Genotype posterior probabilities in the range 0 to 1\">");
+    if ( call->output_tags & (CALL_FMT_GQ|CALL_FMT_GP) )
+        call->GQs = (int32_t*) malloc(sizeof(int32_t)*bcf_hdr_nsamples(call->hdr));
+    bcf_hdr_append(call->hdr,"##INFO=<ID=AC,Number=A,Type=Integer,Description=\"Allele count in genotypes for each ALT allele, in the same order as listed\">");
+    bcf_hdr_append(call->hdr,"##INFO=<ID=AN,Number=1,Type=Integer,Description=\"Total number of alleles in called genotypes\">");
+    bcf_hdr_append(call->hdr,"##INFO=<ID=DP4,Number=4,Type=Integer,Description=\"Number of high-quality ref-forward , ref-reverse, alt-forward and alt-reverse bases\">");
+    bcf_hdr_append(call->hdr,"##INFO=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality\">");
+    if ( call->output_tags & CALL_FMT_PV4 )
+        bcf_hdr_append(call->hdr,"##INFO=<ID=PV4,Number=4,Type=Float,Description=\"P-values for strand bias, baseQ bias, mapQ bias and tail distance bias\">\n");
+
+    // init the prior
+    if ( call->theta>0 )
+    {
+        int i, n = 0;
+        if ( !call->ploidy ) n = 2*bcf_hdr_nsamples(call->hdr); // all are diploid
+        else
+        {
+            for (i=0; i<bcf_hdr_nsamples(call->hdr); i++)
+                n += call->ploidy[i];
+        }
+        // Watterson factor, here aM_1 = aM_2 = 1
+        double aM = 1;
+        for (i=2; i<n; i++) aM += 1./i;
+        call->theta *= aM;
+        if ( call->theta >= 1 )
+        {
+            fprintf(bcftools_stderr,"The prior is too big (theta*aM=%.2f), going with 0.99\n", call->theta);
+            call->theta = 0.99;
+        }
+        call->theta = log(call->theta);
+    }
+}
+
+void mcall_destroy(call_t *call)
+{
+    destroy_sample_groups(call);
+    if (call->vcmp) vcmp_destroy(call->vcmp);
+    free(call->itmp);
+    mcall_destroy_trios(call);
+    free(call->GPs);
+    free(call->ADs);
+    free(call->GLs);
+    free(call->GQs);
+    free(call->anno16);
+    free(call->PLs);
+    free(call->als_map);
+    free(call->pl_map);
+    free(call->gts); free(call->cgts); free(call->ugts);
+    free(call->pdg);
+    free(call->als);
+    free(call->ac);
+    return;
+}
+
+
+// Inits P(D|G): convert PLs from log space and normalize. In case of zero
+// depth, missing PLs are all zero. In this case, pdg's are set to 0
+// so that the corresponding genotypes can be set as missing and the
+// qual calculation is not affected.
+// Missing values are replaced by generic likelihoods when X (unseen allele) is
+// present.
+// NB: While the -m callig model uses the pdgs in canonical order,
+// the original samtools -c calling code uses pdgs in reverse order (AA comes
+// first, RR last).
+// NB: Ploidy is not taken into account here, which is incorrect.
+void set_pdg(double *pl2p, int *PLs, double *pdg, int n_smpl, int n_gt, int unseen)
+{
+    int i, j, nals;
+
+    // find out the number of alleles, expecting diploid genotype likelihoods
+    bcf_gt2alleles(n_gt-1, &i, &nals);
+    assert( i==nals );
+    nals++;
+
+    for (i=0; i<n_smpl; i++)
+    {
+        double sum = 0;
+        for (j=0; j<n_gt; j++)
+        {
+            if ( PLs[j]==bcf_int32_vector_end )
+            {
+                // We expect diploid genotype likelihoods. If not diploid, treat as missing
+                j = 0;
+                break;
+            }
+            if ( PLs[j]==bcf_int32_missing ) break;
+            pdg[j] = PLs[j] < 256 ? pl2p[PLs[j]] : pow(10., -PLs[j]/10.);
+            sum += pdg[j];
+        }
+
+        if ( j==0 )
+        {
+            // First value is missing (LK of RR), this indicates that
+            // all values are missing.
+            j = sum = n_gt;
+        }
+        else if ( j<n_gt && unseen<0 )
+        {
+            // Some of the values are missing and the unseen allele LK is not
+            // available. In such a case, we set LK to a very small value.
+            sum = 0;
+            for (j=0; j<n_gt; j++)
+            {
+                assert( PLs[j]!=bcf_int32_vector_end );
+                if ( PLs[j]==bcf_int32_missing ) PLs[j] = 255;
+                pdg[j] = PLs[j] < 256 ? pl2p[PLs[j]] : pow(10., -PLs[j]/10.);
+                sum += pdg[j];
+            }
+        }
+        if ( j<n_gt )
+        {
+            // Missing values present, fill with unseen allele LK. This can be only
+            // as good as the merge was.
+            int ia,ib, k;
+            j = 0;
+            sum = 0;
+            for (ia=0; ia<nals; ia++)
+            {
+                for (ib=0; ib<=ia; ib++)
+                {
+                    if ( PLs[j]==bcf_int32_missing )
+                    {
+                        k = bcf_alleles2gt(ia,unseen);
+                        if ( PLs[k]==bcf_int32_missing ) k = bcf_alleles2gt(ib,unseen);
+                        if ( PLs[k]==bcf_int32_missing ) k = bcf_alleles2gt(unseen,unseen);
+                        if ( PLs[k]==bcf_int32_missing )
+                        {
+                            // The PLs for unseen allele X are not present as well as for ia, ib.
+                            // This can happen with incremental calling, when one of the merged
+                            // files had all alleles A,C,G,T, in such a case, X was not present.
+                            // Use a very small value instead.
+                            PLs[j] = 255;
+                        }
+                        else
+                            PLs[j] = PLs[k];
+                    }
+                    pdg[j] = pl2p[ PLs[j] ];
+                    sum += pdg[j];
+                    j++;
+                }
+            }
+        }
+        // Normalize: sum_i pdg_i = 1
+        if ( sum==n_gt )
+        {
+            // all missing
+            #if FLAT_PDG_FOR_MISSING
+                for (j=0; j<n_gt; j++) pdg[j] = 1./n_gt;
+            #else
+                for (j=0; j<n_gt; j++) pdg[j] = 0;
+            #endif
+        }
+        else
+            for (j=0; j<n_gt; j++) pdg[j] /= sum;
+
+        PLs += n_gt;
+        pdg += n_gt;
+    }
+}
+
+// Create mapping between old and new (trimmed) alleles
+void init_allele_trimming_maps(call_t *call, int nals_ori, int als_out)
+{
+    int i, j, nout = 0;
+
+    // als_map: old(i) -> new(j)
+    for (i=0; i<nals_ori; i++)
+    {
+        if ( als_out & (1<<i) ) call->als_map[i] = nout++;
+        else call->als_map[i] = -1;
+    }
+
+    if ( !call->pl_map ) return;
+
+    // pl_map: new(k) -> old(l)
+    int k = 0, l = 0;
+    for (i=0; i<nals_ori; i++)
+    {
+        for (j=0; j<=i; j++)
+        {
+            if ( (als_out & (1<<i)) && (als_out & (1<<j)) ) call->pl_map[k++] = l;
+            l++;
+        }
+    }
+}
+
+/** log(exp(a)+exp(b)) */
+static inline double logsumexp2(double a, double b)
+{
+    if ( a>b )
+        return log(1 + exp(b-a)) + a;
+    else
+        return log(1 + exp(a-b)) + b;
+}
+
+// Macro to set the most likely alleles
+#define UPDATE_MAX_LKs(als,sum) { \
+     if ( max_lk<lk_tot && lk_tot_set ) { max_lk = lk_tot; max_als = (als); } \
+     if ( sum ) lk_sum = logsumexp2(lk_tot,lk_sum); \
+}
+
+#define SWAP(type_t,x,y) {type_t tmp; tmp = x; x = y; y = tmp; }
+
+// Determine the most likely combination of alleles. In this implementation,
+// at most tri-allelic sites are considered. Returns the number of alleles.
+static int mcall_find_best_alleles(call_t *call, int nals, smpl_grp_t *grp)
+{
+    int ia,ib,ic;   // iterators over up to three alleles
+    int max_als=0;  // most likely combination of alleles
+    double ref_lk = -HUGE_VAL, max_lk = -HUGE_VAL; // likelihood of the reference and of most likely combination of alleles
+    double lk_sum = -HUGE_VAL;    // for normalizing the likelihoods
+    int nsmpl = grp->nsmpl;
+    int ngts  = nals*(nals+1)/2;
+
+    // Single allele
+    for (ia=0; ia<nals; ia++)
+    {
+        double lk_tot  = 0;
+        int lk_tot_set = 0;
+        int iaa = (ia+1)*(ia+2)/2-1;    // index in PL which corresponds to the homozygous "ia/ia" genotype
+        int ismpl;
+        for (ismpl=0; ismpl<nsmpl; ismpl++)
+        {
+            double *pdg = call->pdg + grp->smpl[ismpl]*ngts + iaa;
+            if ( *pdg ) { lk_tot += log(*pdg); lk_tot_set = 1; }
+        }
+        if ( ia==0 ) ref_lk = lk_tot;   // likelihood of 0/0 for all samples
+        else lk_tot += call->theta; // the prior
+        UPDATE_MAX_LKs(1<<ia, ia>0 && lk_tot_set);
+    }
+
+    // Two alleles
+    if ( nals>1 )
+    {
+        for (ia=0; ia<nals; ia++)
+        {
+            if ( grp->qsum[ia]==0 ) continue;
+            int iaa = (ia+1)*(ia+2)/2-1;
+            for (ib=0; ib<ia; ib++)
+            {
+                if ( grp->qsum[ib]==0 ) continue;
+                double lk_tot  = 0;
+                int lk_tot_set = 0;
+                double fa  = grp->qsum[ia]/(grp->qsum[ia] + grp->qsum[ib]);
+                double fb  = grp->qsum[ib]/(grp->qsum[ia] + grp->qsum[ib]);
+                double fa2 = fa*fa;
+                double fb2 = fb*fb;
+                double fab = 2*fa*fb;
+                int is, ibb = (ib+1)*(ib+2)/2-1, iab = iaa - ia + ib;
+                for (is=0; is<nsmpl; is++)
+                {
+                    int ismpl = grp->smpl[is];
+                    double *pdg = call->pdg + ismpl*ngts;
+                    double val = 0;
+                    if ( !call->ploidy || call->ploidy[ismpl]==2 )
+                        val = fa2*pdg[iaa] + fb2*pdg[ibb] + fab*pdg[iab];
+                    else if ( call->ploidy && call->ploidy[ismpl]==1 )
+                        val = fa*pdg[iaa] + fb*pdg[ibb];
+                    if ( val ) { lk_tot += log(val); lk_tot_set = 1; }
+                }
+                if ( ia!=0 ) lk_tot += call->theta;    // the prior
+                if ( ib!=0 ) lk_tot += call->theta;
+                UPDATE_MAX_LKs(1<<ia|1<<ib, lk_tot_set);
+            }
+        }
+    }
+
+    // Three alleles
+    if ( nals>2 )
+    {
+        for (ia=0; ia<nals; ia++)
+        {
+            if ( grp->qsum[ia]==0 ) continue;
+            int iaa = (ia+1)*(ia+2)/2-1;
+            for (ib=0; ib<ia; ib++)
+            {
+                if ( grp->qsum[ib]==0 ) continue;
+                int ibb = (ib+1)*(ib+2)/2-1;
+                int iab = iaa - ia + ib;
+                for (ic=0; ic<ib; ic++)
+                {
+                    if ( grp->qsum[ic]==0 ) continue;
+                    double lk_tot  = 0;
+                    int lk_tot_set = 0;
+
+                    double fa  = grp->qsum[ia]/(grp->qsum[ia] + grp->qsum[ib] + grp->qsum[ic]);
+                    double fb  = grp->qsum[ib]/(grp->qsum[ia] + grp->qsum[ib] + grp->qsum[ic]);
+                    double fc  = grp->qsum[ic]/(grp->qsum[ia] + grp->qsum[ib] + grp->qsum[ic]);
+                    double fa2 = fa*fa;
+                    double fb2 = fb*fb;
+                    double fc2 = fc*fc;
+                    double fab = 2*fa*fb, fac = 2*fa*fc, fbc = 2*fb*fc;
+                    int is, icc = (ic+1)*(ic+2)/2-1;
+                    int iac = iaa - ia + ic, ibc = ibb - ib + ic;
+                    for (is=0; is<nsmpl; is++)
+                    {
+                        int ismpl = grp->smpl[is];
+                        double *pdg = call->pdg + ismpl*ngts;
+                        double val = 0;
+                        if ( !call->ploidy || call->ploidy[ismpl]==2 )
+                            val = fa2*pdg[iaa] + fb2*pdg[ibb] + fc2*pdg[icc] + fab*pdg[iab] + fac*pdg[iac] + fbc*pdg[ibc];
+                        else if ( call->ploidy && call->ploidy[ismpl]==1 )
+                            val = fa*pdg[iaa] + fb*pdg[ibb] + fc*pdg[icc];
+                        if ( val ) { lk_tot += log(val); lk_tot_set = 1; }
+                    }
+                    if ( ia!=0 ) lk_tot += call->theta;    // the prior
+                    if ( ib!=0 ) lk_tot += call->theta;    // the prior
+                    if ( ic!=0 ) lk_tot += call->theta;    // the prior
+                    UPDATE_MAX_LKs(1<<ia|1<<ib|1<<ic, lk_tot_set);
+                }
+            }
+        }
+    }
+
+    int i, n = 0;
+    for (i=0; i<nals; i++) if ( max_als & 1<<i) n++;
+
+    grp->max_lk = max_lk;
+    grp->ref_lk = ref_lk;
+    grp->lk_sum = lk_sum;
+    grp->als  = max_als;
+    grp->nals = n;
+
+    return n;
+}
+
+// Sets GT=0/0 or GT=. if PL=0,0,0
+static void mcall_set_ref_genotypes(call_t *call, int nals_ori)
+{
+    int i;
+    int ngts  = nals_ori*(nals_ori+1)/2;            // need this to distinguish between GT=0/0 vs GT=.
+    int nsmpl = bcf_hdr_nsamples(call->hdr);
+
+    for (i=0; i<nals_ori; i++) call->ac[i] = 0;     // nals_new<=nals_ori, never mind setting extra 0's
+
+    // Set all genotypes to 0/0 or 0
+    int *gts    = call->gts;
+    double *pdg = call->pdg;
+    int isample;
+    for (isample = 0; isample < nsmpl; isample++)
+    {
+        int ploidy = call->ploidy ? call->ploidy[isample] : 2;
+        for (i=0; i<ngts; i++) if ( pdg[i]!=0.0 ) break;
+        if ( i==ngts || !ploidy )
+        {
+            gts[0] = bcf_gt_missing;
+            gts[1] = ploidy==2 ? bcf_gt_missing : bcf_int32_vector_end;
+        }
+        else
+        {
+            gts[0] = bcf_gt_unphased(0);
+            gts[1] = ploidy==2 ? bcf_gt_unphased(0) : bcf_int32_vector_end;
+            call->ac[0] += ploidy;
+        }
+        gts += 2;
+        pdg += ngts;
+    }
+}
+
+static void mcall_call_genotypes(call_t *call, int nals_ori, smpl_grp_t *grp)
+{
+    int ia, ib, i;
+    int ngts_ori = nals_ori*(nals_ori+1)/2; 
+    int ngts_new = call->nals_new*(call->nals_new+1)/2;
+    int nsmpl = grp->nsmpl;
+
+    #if USE_PRIOR_FOR_GTS
+        float prior = exp(call->theta);
+    #endif
+
+    int is;
+    for (is = 0; is < nsmpl; is++)
+    {
+        int ismpl   = grp->smpl[is];
+        double *pdg = call->pdg + ismpl*ngts_ori;
+        float *gps  = call->GPs + ismpl*ngts_new;
+        int *gts    = call->gts + ismpl*2;
+
+        int ploidy = call->ploidy ? call->ploidy[ismpl] : 2;
+        assert( ploidy>=0 && ploidy<=2 );
+
+        if ( !ploidy )
+        {
+            gts[0] = bcf_gt_missing;
+            gts[1] = bcf_int32_vector_end;
+            gps[0] = -1;
+            continue;
+        }
+
+        #if !FLAT_PDG_FOR_MISSING
+            // Skip samples with zero depth, they have all pdg's equal to 0
+            for (i=0; i<ngts_ori; i++) if ( pdg[i]!=0.0 ) break;
+            if ( i==ngts_ori )
+            {
+                gts[0] = bcf_gt_missing;
+                gts[1] = ploidy==2 ? bcf_gt_missing : bcf_int32_vector_end;
+                gps[0] = -1;
+                continue;
+            }
+        #endif
+
+        // Default fallback for the case all LKs are the same
+        gts[0] = bcf_gt_unphased(0);
+        gts[1] = ploidy==2 ? bcf_gt_unphased(0) : bcf_int32_vector_end;
+
+        // Non-zero depth, determine the most likely genotype
+        double best_lk = 0;
+        for (ia=0; ia<nals_ori; ia++)
+        {
+            if ( !(grp->als & 1<<ia) ) continue;    // ia-th allele not in the final selection, skip
+            int iaa = (ia+1)*(ia+2)/2-1;                // PL index of the ia/ia genotype
+            double lk = ploidy==2 ? pdg[iaa]*grp->qsum[ia]*grp->qsum[ia] : pdg[iaa]*grp->qsum[ia];
+            #if USE_PRIOR_FOR_GTS
+                if ( ia!=0 ) lk *= prior;
+            #endif
+            int igt  = ploidy==2 ? bcf_alleles2gt(call->als_map[ia],call->als_map[ia]) : call->als_map[ia];
+            gps[igt] = lk;
+            if ( best_lk < lk )
+            {
+                best_lk = lk;
+                gts[0] = bcf_gt_unphased(call->als_map[ia]);
+            }
+        }
+        if ( ploidy==2 )
+        {
+            gts[1] = gts[0];
+            for (ia=0; ia<nals_ori; ia++)
+            {
+                if ( !(grp->als & 1<<ia) ) continue;
+                int iaa = (ia+1)*(ia+2)/2-1;
+                for (ib=0; ib<ia; ib++)
+                {
+                    if ( !(grp->als & 1<<ib) ) continue;
+                    int iab = iaa - ia + ib;
+                    double lk = 2*pdg[iab]*grp->qsum[ia]*grp->qsum[ib];
+                    #if USE_PRIOR_FOR_GTS
+                        if ( ia!=0 ) lk *= prior;
+                        if ( ib!=0 ) lk *= prior;
+                    #endif
+                    int igt  = bcf_alleles2gt(call->als_map[ia],call->als_map[ib]);
+                    gps[igt] = lk;
+                    if ( best_lk < lk )
+                    {
+                        best_lk = lk;
+                        gts[0] = bcf_gt_unphased(call->als_map[ib]);
+                        gts[1] = bcf_gt_unphased(call->als_map[ia]);
+                    }
+                }
+            }
+        }
+        else
+            gts[1] = bcf_int32_vector_end;
+
+        call->ac[ bcf_gt_allele(gts[0]) ]++;
+        if ( gts[1]!=bcf_int32_vector_end ) call->ac[ bcf_gt_allele(gts[1]) ]++;
+    }
+    if ( !(call->output_tags & (CALL_FMT_GQ|CALL_FMT_GP)) ) return;
+    double max, sum;
+    for (is=0; is<nsmpl; is++)
+    {
+        int ismpl  = grp->smpl[is];
+        float *gps = call->GPs + ismpl*ngts_new;
+
+        int nmax;
+        if ( call->ploidy )
+        {
+            if ( call->ploidy[ismpl]==2 ) nmax = ngts_new;
+            else if ( call->ploidy[ismpl]==1 ) nmax = grp->nals;
+            else nmax = 0;
+        }
+        else nmax = ngts_new;
+
+        max = gps[0];
+        if ( max<0 || nmax==0 )
+        {
+            // no call
+            if ( call->output_tags & CALL_FMT_GP )
+            {
+                for (i=0; i<nmax; i++) gps[i] = 0;
+                if ( nmax==0 ) { bcf_float_set_missing(gps[i]); nmax++; }
+                if ( nmax < ngts_new ) bcf_float_set_vector_end(gps[nmax]);
+            }
+            call->GQs[ismpl] = 0;
+            continue;
+        }
+        sum = gps[0];
+        for (i=1; i<nmax; i++)
+        {
+            if ( max < gps[i] ) max = gps[i];
+            sum += gps[i];
+        }
+        max = -4.34294*log(1 - max/sum);
+        call->GQs[ismpl] = max<=INT8_MAX ? max : INT8_MAX;
+        if ( call->output_tags & CALL_FMT_GP )
+        {
+            assert( max );
+            for (i=0; i<nmax; i++) gps[i] = gps[i]/sum;
+            for (; i<ngts_new; i++) bcf_float_set_vector_end(gps[i]);
+        }
+    }
+}
+
+
+/**
+    Pm = P(mendelian) .. parameter to vary, 1-Pm is the probability of novel mutation.
+                         When trio_Pm_ins is negative, Pm is calculated dynamically
+                         according to indel length. For simplicity, only the
+                         first ALT is considered.
+    Pkij = P(k|i,j)   .. probability that the genotype combination i,j,k is consistent
+                         with mendelian inheritance (the likelihood that offspring
+                         of two HETs is a HOM is smaller than it being a HET)
+
+    P_uc(F=i,M=j,K=k) = P(F=i) . P(M=j) . P(K=k)  .. unconstrained P
+    P_c(F=i,M=j,K=k) = P_uc . Pkij                .. constrained P
+    P(F=i,M=j,K=k) = P_uc . (1 - Pm) + P_c . Pm
+                   = P_uc . [1 - Pm + Pkij . Pm]
+
+    We choose genotype combination i,j,k which maximizes P(F=i,M=j,K=k). This
+    probability gives the quality GQ(Trio).
+    Individual qualities are calculated as
+        GQ(F=i,M=j,K=k) = P(F=i,M=j,K=k) / \sum_{x,y} P(F=i,M=x,K=y)
+ */
+#if 0
+static void mcall_call_trio_genotypes(call_t *call, bcf1_t *rec, int nals, int nals_new, int als_new)
+{
+    int ia, ib, i;
+    int nsmpl    = bcf_hdr_nsamples(call->hdr);
+    int ngts     = nals*(nals+1)/2;
+    int nout_gts = nals_new*(nals_new+1)/2;
+    double *gls  = call->GLs - nout_gts;
+    double *pdg  = call->pdg - ngts;
+
+    // Calculate individuals' genotype likelihoods P(X=i)
+    int isample;
+    for (isample = 0; isample < nsmpl; isample++)
+    {
+        int ploidy = call->ploidy ? call->ploidy[isample] : 2;
+        int32_t *gts = call->ugts + isample;
+
+        gls += nout_gts;
+        pdg += ngts;
+
+        // Skip samples with all pdg's equal to 1. These have zero depth.
+        for (i=0; i<ngts; i++) if ( pdg[i]!=0.0 ) break;
+        if ( i==ngts || !ploidy )
+        {
+            gts[0] = -1;
+            gls[0] = 1;
+            continue;
+        }
+
+        for (i=0; i<nout_gts; i++) gls[i] = -HUGE_VAL;
+
+        grp1_t *grp = &call->smpl_grp.grp[call->smpl_grp.smpl2grp[isample]];
+        double sum_lk  = 0;
+        double best_lk = 0;
+        for (ia=0; ia<nals; ia++)
+        {
+            if ( !(als_new & 1<<ia) ) continue;     // ia-th allele not in the final selection, skip
+            int iaa   = bcf_alleles2gt(ia,ia);      // PL index of the ia/ia genotype
+            int idx   = bcf_alleles2gt(call->als_map[ia],call->als_map[ia]);
+            double lk = ploidy==2 ? pdg[iaa]*grp->qsum[ia]*grp->qsum[ia] : pdg[iaa]*grp->qsum[ia];
+            sum_lk   += lk;
+            gls[idx]  = lk;
+            if ( best_lk < lk )
+            {
+                best_lk = lk;
+                gts[0] = bcf_alleles2gt(call->als_map[ia],call->als_map[ia]);
+            }
+        }
+        if ( ploidy==2 )
+        {
+            for (ia=0; ia<nals; ia++)
+            {
+                if ( !(als_new & 1<<ia) ) continue;
+                for (ib=0; ib<ia; ib++)
+                {
+                    if ( !(als_new & 1<<ib) ) continue;
+                    int iab   = bcf_alleles2gt(ia,ib);
+                    int idx   = bcf_alleles2gt(call->als_map[ia],call->als_map[ib]);
+                    double lk = 2*pdg[iab]*grp->qsum[ia]*grp->qsum[ib];
+                    sum_lk   += lk;
+                    gls[idx]  = lk;
+                    if ( best_lk < lk )
+                    {
+                        best_lk = lk;
+                        gts[0] = bcf_alleles2gt(call->als_map[ib],call->als_map[ia]);
+                    }
+                }
+            }
+        }
+        for (i=0; i<nout_gts; i++)
+            if ( gls[i]!=-HUGE_VAL ) gls[i] = log(gls[i]/sum_lk);
+    }
+
+    // Set novel mutation rate for this site: using first ALT allele for simplicity.
+    double trio_Pm;
+    if ( call->trio_Pm_ins<0 && call->trio_Pm_del<0 ) trio_Pm = call->trio_Pm_SNPs;     // the same Pm for indels and SNPs requested
+    else
+    {
+        int ret = bcf_get_variant_types(rec);
+        if ( !(ret & VCF_INDEL) ) trio_Pm = call->trio_Pm_SNPs;
+        else
+        {
+            if ( call->trio_Pm_ins<0 )  // dynamic calculation, trio_Pm_del holds the scaling factor
+            {
+                trio_Pm = rec->d.var[1].n<0 ? -21.9313 - 0.2856*rec->d.var[1].n : -22.8689 + 0.2994*rec->d.var[1].n;
+                trio_Pm = 1 - call->trio_Pm_del * exp(trio_Pm);
+            }
+            else                        // snps and indels set explicitly
+            {
+                trio_Pm = rec->d.var[1].n<0 ? call->trio_Pm_del : call->trio_Pm_ins;
+            }
+        }
+    }
+
+    // Calculate constrained likelihoods and determine genotypes
+    int ifm;
+    for (ifm=0; ifm<call->nfams; ifm++)
+    {
+        family_t *fam = &call->fams[ifm];
+        int ntrio = call->ntrio[fam->type][nals_new];
+        uint16_t *trio = call->trio[fam->type][nals_new];
+
+        // Unconstrained likelihood
+        int uc_itr = 0;
+        double uc_lk = 0;
+        for (i=0; i<3; i++)     // for father, mother, child
+        {
+            int ismpl = fam->sample[i];
+            double *gl = call->GLs + nout_gts*ismpl;
+            if ( gl[0]==1 ) continue;
+            int j, jmax = 0;
+            double max  = gl[0];
+            for (j=1; j<nout_gts; j++)
+                if ( max < gl[j] ) { max = gl[j]; jmax = j; }
+            uc_lk += max;
+            uc_itr |= jmax << ((2-i)*4);
+        }
+
+        // Best constrained likelihood
+        int c_itr = -1, itr, uc_is_mendelian = 0;
+        double c_lk = -HUGE_VAL;
+        for (itr=0; itr<ntrio; itr++)   // for each trio genotype combination
+        {
+            double lk = 0;
+            int npresent = 0;
+            for (i=0; i<3; i++)     // for father, mother, child
+            {
+                int ismpl = fam->sample[i];
+                double *gl = call->GLs + nout_gts*ismpl;
+                if ( gl[0]==1 ) continue;
+                int igt = trio[itr]>>((2-i)*4) & 0xf;
+                assert( !call->ploidy || call->ploidy[ismpl]>0 );
+                if ( igt==GT_SKIP ) continue;
+                lk += gl[igt];
+                npresent++;
+                // fprintf(bcftools_stderr," %e", gl[igt]);
+            }
+            // fprintf(bcftools_stderr,"\t\t");
+            double Pkij = npresent==3 ? (double)2/(trio[itr]>>12) : 1;  // with missing genotypes Pkij's are different
+            lk += log(1 - trio_Pm * (1 - Pkij));
+            // fprintf(bcftools_stderr,"%d%d%d\t%e\t%.2f\n", trio[itr]>>8&0xf,trio[itr]>>4&0xf,trio[itr]&0xf, lk, Pkij);
+            if ( c_lk < lk ) { c_lk = lk; c_itr = trio[itr]; }
+            if ( uc_itr==trio[itr] ) uc_is_mendelian = 1;
+        }
+
+        if ( !uc_is_mendelian )
+        {
+            uc_lk += log(1 - trio_Pm);
+            // fprintf(bcftools_stderr,"c_lk=%e uc_lk=%e c_itr=%d%d%d uc_itr=%d%d%d\n", c_lk,uc_lk,c_itr>>8&0xf,c_itr>>4&0xf,c_itr&0xf,uc_itr>>8&0xf,uc_itr>>4&0xf,uc_itr&0xf);
+            if ( c_lk < uc_lk ) { c_lk = uc_lk; c_itr = uc_itr; }
+        }
+        // fprintf(bcftools_stderr,"best_lk=%e best_itr=%d%d%d uc_itr=%d%d%d\n", c_lk,c_itr>>8&0xf,c_itr>>4&0xf,c_itr&0xf,uc_itr>>8&0xf,uc_itr>>4&0xf,uc_itr&0xf);
+
+        // Set genotypes for father, mother, child and calculate genotype qualities
+        for (i=0; i<3; i++)
+        {
+            // GT
+            int ismpl    = fam->sample[i];
+            int igt      = c_itr>>((2-i)*4) & 0xf;
+            double *gl   = call->GLs + nout_gts*ismpl;
+            int32_t *gts = call->cgts + ismpl;
+            if ( gl[0]==1 || igt==GT_SKIP )    // zero depth, set missing genotypes
+            {
+                gts[0] = -1;
+                // bcf_float_set_missing(call->GQs[ismpl]);
+                continue;
+            }
+            gts[0] = igt;
+
+            #if 0
+                // todo: Genotype Qualities
+                //
+                // GQ: for each family member i sum over all genotypes j,k keeping igt fixed
+                double lk_sum = 0;
+                for (itr=0; itr<ntrio; itr++)
+                {
+                    if ( igt != (trio[itr]>>((2-i)*4) & 0xf) ) continue;
+                    double lk = 0;
+                    int j;
+                    for (j=0; j<3; j++)
+                    {
+                        int jsmpl = fam->sample[j];
+                        double *gl = call->GLs + ngts*jsmpl;
+                        if ( gl[0]==1 ) continue;
+                        int jgt = trio[itr]>>((2-j)*4) & 0xf;
+                        if ( jgt==GT_SKIP ) continue;
+                        lk += gl[jgt];
+                    }
+                    double Pkij = (double)2/(trio[itr]>>12);
+                    lk += log(1 - trio_Pm * (1 - Pkij));
+                    lk_sum = logsumexp2(lk_sum, lk);
+                }
+                if ( !uc_is_mendelian && (best_itr>>((2-i)*4)&0xf)==(uc_itr>>((2-i)*4)&0xf) ) lk_sum = logsumexp2(lk_sum,uc_lk);
+                call->GQs[ismpl] = -4.3429*(best_lk - lk_sum);
+            #endif
+        }
+    }
+
+    for (i=0; i<4; i++) call->ac[i] = 0;
+    call->nhets = 0;
+    call->ndiploid = 0;
+
+    // Test if CGT,UGT are needed
+    int ucgts_needed = 0;
+    int32_t *cgts = call->cgts - 1;
+    int32_t *ugts = call->ugts - 1;
+    int32_t *gts  = call->gts - 2;
+    for (isample = 0; isample < nsmpl; isample++)
+    {
+        int ploidy = call->ploidy ? call->ploidy[isample] : 2;
+        cgts++;
+        ugts++;
+        gts += 2;
+        if ( ugts[0]==-1 )
+        {
+            gts[0] = bcf_gt_missing;
+            gts[1] = ploidy==2 ? bcf_gt_missing : bcf_int32_vector_end;
+            continue;
+        }
+        int a,b;
+        if ( cgts[0]!=ugts[0] )
+        {
+            bcf_gt2alleles(cgts[0], &a, &b);
+            gts[0] = bcf_gt_unphased(a);
+            gts[1] = ploidy==1 ? bcf_int32_vector_end : bcf_gt_unphased(b);
+        }
+        else
+        {
+            bcf_gt2alleles(ugts[0], &a, &b);
+            gts[0] = bcf_gt_unphased(a);
+            gts[1] = ploidy==1 ? bcf_int32_vector_end : bcf_gt_unphased(b);
+        }
+        if ( cgts[0]!=ugts[0] ) ucgts_needed = 1;
+        call->ac[a]++;
+        if ( ploidy==2 )
+        {
+            call->ac[b]++;
+            call->ndiploid++;
+            if ( a!=b ) call->nhets++;
+        }
+    }
+    if ( ucgts_needed )
+    {
+        // Some GTs are different
+        bcf_update_format_int32(call->hdr,rec,"UGT",call->ugts,nsmpl);
+        bcf_update_format_int32(call->hdr,rec,"CGT",call->cgts,nsmpl);
+    }
+}
+#endif
+
+static void mcall_trim_and_update_PLs(call_t *call, bcf1_t *rec, int nals_ori, int nals_new)
+{
+    int npls_src = nals_ori*(nals_ori+1)/2;
+    int npls_dst = nals_new*(nals_new+1)/2;     // number of PL values in diploid samples, ori and new
+    if ( call->all_diploid && npls_src == npls_dst ) return;
+
+    int *pls_src = call->PLs, *pls_dst = call->PLs;
+
+    int nsmpl = bcf_hdr_nsamples(call->hdr);
+    int isample, ia;
+    for (isample = 0; isample < nsmpl; isample++)
+    {
+        int ploidy = call->ploidy ? call->ploidy[isample] : 2;
+        if ( ploidy==2 )
+        {
+            for (ia=0; ia<npls_dst; ia++)
+                pls_dst[ia] =  pls_src[ call->pl_map[ia] ];
+        }
+        else if ( ploidy==1 )
+        {
+            for (ia=0; ia<nals_new; ia++)
+            {
+                int isrc = (ia+1)*(ia+2)/2-1;
+                pls_dst[ia] = pls_src[ call->pl_map[isrc] ];
+            }
+            if ( ia<npls_dst ) pls_dst[ia] = bcf_int32_vector_end;
+        }
+        else
+        {
+            pls_dst[0] = bcf_int32_missing;
+            pls_dst[1] = bcf_int32_vector_end;  // relying on nals_new>1 in mcall()
+        }
+        pls_src += npls_src;
+        pls_dst += npls_dst;
+    }
+    bcf_update_format_int32(call->hdr, rec, "PL", call->PLs, npls_dst*nsmpl);
+}
+
+void mcall_trim_and_update_numberR(call_t *call, bcf1_t *rec, int nals_ori, int nals_new)
+{
+    if ( nals_ori==nals_new ) return;
+
+    int i,j, nret, size = sizeof(float);
+
+    void *tmp_ori = call->itmp, *tmp_new = call->PLs;  // reusing PLs storage which is not used at this point
+    int ntmp_ori = call->n_itmp, ntmp_new = call->mPLs;
+
+    // INFO fields
+    for (i=0; i<rec->n_info; i++)
+    {
+        bcf_info_t *info = &rec->d.info[i];
+        int vlen = bcf_hdr_id2length(call->hdr,BCF_HL_INFO,info->key);
+        if ( vlen!=BCF_VL_R ) continue; // not a Number=R tag
+
+        int type  = bcf_hdr_id2type(call->hdr,BCF_HL_INFO,info->key);
+        const char *key = bcf_hdr_int2id(call->hdr,BCF_DT_ID,info->key);
+        nret = bcf_get_info_values(call->hdr, rec, key, &tmp_ori, &ntmp_ori, type);
+        if ( nret<=0 ) continue;
+
+        if ( nals_new==1 )
+            bcf_update_info_int32(call->hdr, rec, key, tmp_ori, 1);     // has to be the REF, the order could not change
+        else
+        {
+            for (j=0; j<nals_ori; j++)
+            {
+                int k = call->als_map[j];
+                if ( k==-1 ) continue;   // to be dropped
+                memcpy((char *)tmp_new+size*k, (char *)tmp_ori+size*j, size);
+            }
+            bcf_update_info_int32(call->hdr, rec, key, tmp_new, nals_new);
+        }
+    }
+
+    // FORMAT fields
+    for (i=0; i<rec->n_fmt; i++)
+    {
+        bcf_fmt_t *fmt = &rec->d.fmt[i];
+        int vlen = bcf_hdr_id2length(call->hdr,BCF_HL_FMT,fmt->id);
+        if ( vlen!=BCF_VL_R ) continue; // not a Number=R tag
+
+        int type = bcf_hdr_id2type(call->hdr,BCF_HL_FMT,fmt->id);
+        const char *key = bcf_hdr_int2id(call->hdr,BCF_DT_ID,fmt->id);
+        nret = bcf_get_format_values(call->hdr, rec, key, &tmp_ori, &ntmp_ori, type);
+        if (nret<=0) continue;
+        int nsmpl = bcf_hdr_nsamples(call->hdr);
+
+        assert( nret==nals_ori*nsmpl );
+
+        for (j=0; j<nsmpl; j++)
+        {
+            char *ptr_src = (char *)tmp_ori + j*nals_ori*size;
+            char *ptr_dst = (char *)tmp_new + j*nals_new*size;
+            int k;
+            for (k=0; k<nals_ori; k++)
+            {
+                int l = call->als_map[k];
+                if ( l==-1 ) continue;   // to be dropped
+                memcpy(ptr_dst+size*l, ptr_src+size*k, size);
+            }
+        }
+        bcf_update_format_int32(call->hdr, rec, key, tmp_new, nals_new*nsmpl);
+    }
+
+    call->PLs    = (int32_t*) tmp_new;
+    call->mPLs   = ntmp_new;
+    call->itmp   = (int32_t*) tmp_ori;
+    call->n_itmp = ntmp_ori;
+}
+
+
+// NB: in this function we temporarily use calls->als_map for a different
+// purpose to store mapping from new (target) alleles to original alleles.
+//
+static int mcall_constrain_alleles(call_t *call, bcf1_t *rec, int *unseen)
+{
+    assert( call->tgt_als->n );
+    if ( call->tgt_als->n>5 ) error("Maximum accepted number of alleles is 5, got %d\n", call->tgt_als->n);
+    hts_expand(char*,call->tgt_als->n+1,call->nals,call->als);
+
+    int has_new = 0;
+
+    int i, j, nals = 1;
+    for (i=1; i<call->nals_map; i++) call->als_map[i] = -1;
+
+    if ( vcmp_set_ref(call->vcmp, rec->d.allele[0], call->tgt_als->allele[0]) < 0 )
+        error("The reference alleles are not compatible at %s:%d .. %s vs %s\n", call->hdr->id[BCF_DT_CTG][rec->rid].key,rec->pos+1,call->tgt_als->allele[0],rec->d.allele[0]);
+
+    // create mapping from new to old alleles
+    call->als[0] = call->tgt_als->allele[0];
+    call->als_map[0] = 0;
+
+    for (i=1; i<call->tgt_als->n; i++)
+    {
+        call->als[nals] = call->tgt_als->allele[i];
+        j = vcmp_find_allele(call->vcmp, rec->d.allele+1, rec->n_allele - 1, call->tgt_als->allele[i]);
+
+        // if ( j+1==*unseen )
+        // { 
+        //     fprintf(bcftools_stderr,"Fixme? Cannot constrain to %d-th allele (%s); j=%d,unseen=%d. VCF=",i,call->tgt_als->allele[i],j,*unseen);
+        //     int k;
+        //     for (k=0; k<rec->n_allele; k++) fprintf(bcftools_stderr,"%s%s",k==0?"":",",rec->d.allele[k]);
+        //     fprintf(bcftools_stderr,"\tTAB=");
+        //     for (k=0; k<call->tgt_als->n; k++) fprintf(bcftools_stderr,"%s%s",k==0?"":",",call->tgt_als->allele[k]);
+        //     fprintf(bcftools_stderr,"\n");
+        //     return -1;
+        // }
+        
+        if ( j>=0 )
+        {
+            // existing allele
+            call->als_map[nals] = j+1;
+        }
+        else
+        {
+            // There is a new allele in targets which is not present in VCF.
+            // We use the X allele to estimate PLs. Note that X may not be
+            // present at multiallelic indels sites. In that case we use the
+            // last allele anyway, because the least likely allele comes last
+            // in mpileup's ALT output.
+            call->als_map[nals] = (*unseen)>=0 ? *unseen : rec->n_allele - 1;
+            has_new = 1;
+        }
+        nals++;
+    }
+    if ( *unseen )
+    {
+        call->als_map[nals] = *unseen;
+        call->als[nals] = rec->d.allele[*unseen];
+        nals++;
+    }
+
+    if ( !has_new && nals==rec->n_allele ) return 0;
+    bcf_update_alleles(call->hdr, rec, (const char**)call->als, nals);
+
+    // create mapping from new PL to old PL
+    int k = 0;
+    for (i=0; i<nals; i++)
+    {
+        for (j=0; j<=i; j++)
+        {
+            int a = call->als_map[i], b = call->als_map[j];
+            call->pl_map[k++] = a>b ? a*(a+1)/2 + b : b*(b+1)/2 + a;
+        }
+    }
+
+    // update PL
+    call->nPLs = bcf_get_format_int32(call->hdr, rec, "PL", &call->PLs, &call->mPLs);
+    int nsmpl  = bcf_hdr_nsamples(call->hdr);
+    int npls_ori = call->nPLs / nsmpl;
+    int npls_new = k;
+    hts_expand(int32_t,npls_new*nsmpl,call->n_itmp,call->itmp);
+    int *ori_pl = call->PLs, *new_pl = call->itmp;
+    for (i=0; i<nsmpl; i++)
+    {
+        for (k=0; k<npls_new; k++)
+        {
+            new_pl[k] = ori_pl[call->pl_map[k]];
+            if ( new_pl[k]==bcf_int32_missing && *unseen>=0 )
+            {
+                // missing value, and there is an unseen allele: identify the
+                // alleles and use the lk of either AX or XX
+                int k_ori = call->pl_map[k], ia, ib;
+                bcf_gt2alleles(k_ori, &ia, &ib);
+                k_ori = bcf_alleles2gt(ia,*unseen);
+                if ( ori_pl[k_ori]==bcf_int32_missing ) k_ori = bcf_alleles2gt(ib,*unseen);
+                if ( ori_pl[k_ori]==bcf_int32_missing ) k_ori = bcf_alleles2gt(*unseen,*unseen);
+                new_pl[k] = ori_pl[k_ori];
+            }
+            if ( !k && new_pl[k]==bcf_int32_vector_end ) new_pl[k]=bcf_int32_missing;
+        }
+        ori_pl += npls_ori;
+        new_pl += npls_new;
+    }
+    bcf_update_format_int32(call->hdr, rec, "PL", call->itmp, npls_new*nsmpl);
+
+    // update QS, use temporarily call->GPs to store the values
+    int nqs = bcf_get_info_float(call->hdr, rec, "QS", &call->smpl_grp[0].qsum, &call->smpl_grp[0].nqsum);
+    hts_expand(float,nals,call->nGPs,call->GPs);
+    for (i=0; i<nals; i++)
+        call->GPs[i] = call->als_map[i]<nqs ? call->smpl_grp[0].qsum[call->als_map[i]] : 0;
+    bcf_update_info_float(call->hdr, rec, "QS", call->GPs, nals);
+
+    // update any Number=R tags
+    void *tmp_ori = call->itmp, *tmp_new = call->PLs;  // reusing PLs storage which is not used at this point
+    int ntmp_ori = call->n_itmp, ntmp_new = call->mPLs;
+    for (i=0; i<rec->n_fmt; i++)
+    {
+        bcf_fmt_t *fmt = &rec->d.fmt[i];
+        int vlen = bcf_hdr_id2length(call->hdr,BCF_HL_FMT,fmt->id);
+        if ( vlen!=BCF_VL_R ) continue; // not a Number=R tag
+
+        // NB:works only for BCF_HT_INT and BCF_HT_REAL
+        int type = bcf_hdr_id2type(call->hdr,BCF_HL_FMT,fmt->id);
+        assert( type==BCF_HT_INT || type==BCF_HT_REAL );
+        assert( sizeof(float)==sizeof(int32_t) );
+
+        const char *key = bcf_hdr_int2id(call->hdr,BCF_DT_ID,fmt->id);
+        int nret = bcf_get_format_values(call->hdr, rec, key, &tmp_ori, &ntmp_ori, type);
+        if (nret<=0) continue;
+        int nsmpl = bcf_hdr_nsamples(call->hdr);
+        int size1 = sizeof(float);
+        hts_expand(float, nsmpl * nals, ntmp_new, tmp_new);
+        for (j=0; j<nsmpl; j++)
+        {
+            uint8_t *ptr_ori = (uint8_t *) tmp_ori + j*size1*fmt->n;
+            uint8_t *ptr_new = (uint8_t *) tmp_new + j*nals*size1;
+            for (k=0; k<nals; k++)
+            {
+                uint8_t *dst = ptr_new + size1*k;
+                uint8_t *src = ptr_ori + size1*call->als_map[k];
+                memcpy(dst,src,size1);
+            }
+        }
+        nret = bcf_update_format(call->hdr, rec, key, tmp_new, nsmpl*nals, type);
+        assert( nret==0 );
+    }
+    call->PLs    = (int32_t*) tmp_new;
+    call->mPLs   = ntmp_new;
+    call->itmp   = (int32_t*) tmp_ori;
+    call->n_itmp = ntmp_ori;
+
+    if ( *unseen ) *unseen = nals-1;
+    return 0;
+}
+
+
+/**
+  *  This function implements the multiallelic calling model. It has two major parts:
+  *   1) determine the most likely set of alleles and calculate the quality of ref/non-ref site
+  *   2) determine and set the genotypes
+  *  In various places in between, the BCF record gets updated.
+  */
+int mcall(call_t *call, bcf1_t *rec)
+{
+    int i,j, unseen = call->unseen;
+
+    // Force alleles when calling genotypes given alleles was requested
+    if ( call->flag & CALL_CONSTR_ALLELES && mcall_constrain_alleles(call, rec, &unseen)!=0 ) return -2;
+
+    int nsmpl    = bcf_hdr_nsamples(call->hdr);
+    int nals_ori = rec->n_allele;
+    hts_expand(int,nals_ori,call->nac,call->ac);
+    hts_expand(int,nals_ori,call->nals_map,call->als_map);
+    hts_expand(int,nals_ori*(nals_ori+1)/2,call->npl_map,call->pl_map);
+
+    // Get the genotype likelihoods
+    call->nPLs = bcf_get_format_int32(call->hdr, rec, "PL", &call->PLs, &call->mPLs);
+    if ( call->nPLs!=nsmpl*nals_ori*(nals_ori+1)/2 && call->nPLs!=nsmpl*nals_ori )  // a mixture of diploid and haploid or haploid only
+        error("Wrong number of PL fields? nals=%d npl=%d\n", nals_ori,call->nPLs);
+
+    // Convert PLs to probabilities
+    int ngts_ori = nals_ori*(nals_ori+1)/2;
+    hts_expand(double, call->nPLs, call->npdg, call->pdg);
+    set_pdg(call->pl2p, call->PLs, call->pdg, nsmpl, ngts_ori, unseen);
+
+    // Get sum of qualities, serves as an AF estimate, f_x = QS/N in Eq. 1 in call-m math notes.
+    if ( call->nsmpl_grp == 1  )
+    {
+        int nqs = bcf_get_info_float(call->hdr, rec, "QS", &call->smpl_grp[0].qsum, &call->smpl_grp[0].nqsum);
+        if ( nqs<=0 ) error("The QS annotation not present at %s:%d\n", bcf_seqname(call->hdr,rec),rec->pos+1);
+        if ( nqs < nals_ori )
+        {
+            // Some of the listed alleles do not have the corresponding QS field. This is
+            // typically ref-only site with <*> in ALT.
+            hts_expand(float,nals_ori,call->smpl_grp[0].nqsum,call->smpl_grp[0].qsum);
+            for (i=nqs; i<nals_ori; i++) call->smpl_grp[0].qsum[i] = 0;
+        }
+    }
+    else
+    {
+        for (j=0; j<call->nsmpl_grp; j++)
+        {
+            hts_expand(float,nals_ori,call->smpl_grp[j].nqsum,call->smpl_grp[j].qsum);
+            memset(call->smpl_grp[j].qsum, 0, sizeof(float)*nals_ori);
+        }
+
+        // Use FORMAT/AD or FORMAT/QS
+        int nad = bcf_get_format_int32(call->hdr, rec, call->sample_groups_tag, &call->ADs, &call->nADs);
+        if ( nad<1 ) error("Error: FORMAT/%s is required with the -G option, mpileup must be run with \"-a AD\" or \"-a QS\"\n",call->sample_groups_tag);
+        nad /= bcf_hdr_nsamples(call->hdr);
+        for (i=0; i<call->nsmpl_grp; i++)
+        {
+            int is;
+            smpl_grp_t *grp = &call->smpl_grp[i];
+            hts_expand(float,nals_ori,grp->nqsum,grp->qsum);
+            for (j=0; j<nals_ori; j++) grp->qsum[j] = 0;
+            for (is=0; is<grp->nsmpl; is++)
+            {
+                int ismpl = grp->smpl[is];
+                int32_t *ptr = call->ADs + ismpl*nad;
+                float sum = 0;
+                for (j=0; j<nad; j++)
+                {
+                    if ( ptr[j]==bcf_int32_vector_end ) break;
+                    if ( ptr[j]!=bcf_int32_missing ) sum += ptr[j];
+                }
+                if ( sum )
+                {
+                    for (j=0; j<nad; j++)
+                    {
+                        if ( ptr[j]==bcf_int32_vector_end ) break;
+                        if ( ptr[j]!=bcf_int32_missing ) grp->qsum[j] += ptr[j]/sum;
+                    }
+                }
+            }
+        }
+    }
+
+    // If available, take into account reference panel AFs
+    if ( call->prior_AN && bcf_get_info_int32(call->hdr, rec, call->prior_AN ,&call->ac, &call->nac)==1 )
+    {
+        int an = call->ac[0];   // number of alleles total, procede only if not zero; reuse call->ac
+        if ( an > 0 && bcf_get_info_int32(call->hdr, rec, call->prior_AC ,&call->ac, &call->nac)==nals_ori-1 )    // number of ALT alleles
+        {
+            int ac0 = an;       // this will become the number of REFs
+            for (i=0; i<nals_ori-1; i++)
+            {
+                if ( call->ac[i]==bcf_int32_vector_end ) break;
+                if ( call->ac[i]==bcf_int32_missing ) continue;
+                ac0 -= call->ac[i];
+
+                // here an*0.5 is the number of samples in the populatio and ac*0.5 is the AF weighted by the number of samples
+                for (j=0; j<call->nsmpl_grp; j++)
+                    call->smpl_grp[j].qsum[i+1] = (call->smpl_grp[j].qsum[i+1] + 0.5*call->ac[i]) / (call->smpl_grp[j].nsmpl + 0.5*an);
+            }
+            if ( ac0<0 ) error("Incorrect %s,%s values at %s:%d\n", call->prior_AN,call->prior_AC,bcf_seqname(call->hdr,rec),rec->pos+1);
+            for (j=0; j<call->nsmpl_grp; j++)
+                call->smpl_grp[j].qsum[0] = (call->smpl_grp[j].qsum[0] + 0.5*ac0) / (call->smpl_grp[j].nsmpl + 0.5*an);
+        }
+    }
+
+    // normalize so that QS sums to 1 for each group
+    for (j=0; j<call->nsmpl_grp; j++)
+    {
+        float sum = 0;
+        for (i=0; i<nals_ori; i++) sum += call->smpl_grp[j].qsum[i];
+        if ( sum ) for (i=0; i<nals_ori; i++) call->smpl_grp[j].qsum[i] /= sum;
+    }
+
+    bcf_update_info_int32(call->hdr, rec, "QS", NULL, 0);      // remove QS tag
+
+    if ( nals_ori > 8*sizeof(call->als_new) )
+    { 
+        fprintf(bcftools_stderr,"Too many alleles at %s:%"PRId64", skipping.\n", bcf_seqname(call->hdr,rec),(int64_t) rec->pos+1);
+        return 0; 
+    }
+
+    // For each group find the best combination of alleles
+    call->als_new = 0;
+    double ref_lk = -HUGE_VAL, lk_sum = -HUGE_VAL, max_qual = -HUGE_VAL;
+    for (j=0; j<call->nsmpl_grp; j++)
+    {
+        smpl_grp_t *grp = &call->smpl_grp[j];
+        mcall_find_best_alleles(call, nals_ori, grp);
+        call->als_new |= grp->als;
+        if ( grp->max_lk==-HUGE_VAL ) continue;
+        double qual = -4.343*(grp->ref_lk - logsumexp2(grp->lk_sum,grp->ref_lk));
+        if ( max_qual < qual )
+        {
+            max_qual = qual;
+            lk_sum = grp->lk_sum;
+            ref_lk = grp->ref_lk;
+        }
+    }
+
+    // Make sure the REF allele is always present
+    if ( !(call->als_new&1) ) call->als_new |= 1;
+
+    int is_variant = call->als_new==1 ? 0 : 1;
+    if ( call->flag & CALL_VARONLY && !is_variant ) return 0;
+
+    call->nals_new = 0;
+    for (i=0; i<nals_ori; i++)
+    {
+        if ( i>0 && i==unseen ) continue;
+        if ( call->flag & CALL_KEEPALT ) call->als_new |= 1<<i;
+        if ( call->als_new & (1<<i) ) call->nals_new++;
+    }
+
+    init_allele_trimming_maps(call,nals_ori,call->als_new);
+
+    int nAC = 0;
+    if ( call->als_new==1 )   // only REF allele on output
+    {
+        mcall_set_ref_genotypes(call,nals_ori);
+        bcf_update_format_int32(call->hdr, rec, "PL", NULL, 0);    // remove PL, useless now
+    }
+    else if ( !is_variant )
+    {
+        mcall_set_ref_genotypes(call,nals_ori);     // running with -A, prevent mcall_call_genotypes from putting some ALT back
+        mcall_trim_and_update_PLs(call, rec, nals_ori, call->nals_new);
+    }
+    else
+    {
+        // The most likely set of alleles includes non-reference allele (or was enforced), call genotypes.
+        // Note that it is a valid outcome if the called genotypes exclude some of the ALTs.
+        int ngts_new = call->nals_new*(call->nals_new+1)/2;
+        hts_expand(float,ngts_new*nsmpl,call->nGPs,call->GPs);
+        for (i=0; i<call->nals_new; i++) call->ac[i] = 0;
+
+        if ( call->flag & CALL_CONSTR_TRIO && call->nals_new>4 )
+        { 
+            fprintf(bcftools_stderr,"Too many alleles at %s:%"PRId64", skipping.\n", bcf_seqname(call->hdr,rec),(int64_t) rec->pos+1);
+            return 0; 
+        }
+        if ( call->output_tags & (CALL_FMT_GQ|CALL_FMT_GP) )
+        {
+            memset(call->GPs,0,nsmpl*ngts_new*sizeof(*call->GPs));
+            memset(call->GQs,0,nsmpl*sizeof(*call->GQs));
+        }
+        for (i=0; i<call->nsmpl_grp; i++)
+        {
+            if ( call->flag & CALL_CONSTR_TRIO )
+                error("todo: constrained trio calling temporarily disabled\n");   //mcall_call_trio_genotypes(call,rec,nals,&call->smpl_grp[i]);
+            else
+                mcall_call_genotypes(call,nals_ori,&call->smpl_grp[i]);
+        }
+
+        // Skip the site if all samples are 0/0. This can happen occasionally.
+        for (i=1; i<call->nals_new; i++) nAC += call->ac[i];
+        if ( !nAC && call->flag & CALL_VARONLY ) return 0;
+
+        if ( call->output_tags & CALL_FMT_GP )
+            bcf_update_format_float(call->hdr, rec, "GP", call->GPs, nsmpl*ngts_new);
+        if ( call->output_tags & CALL_FMT_GQ )
+            bcf_update_format_int32(call->hdr, rec, "GQ", call->GQs, nsmpl);
+
+        mcall_trim_and_update_PLs(call,rec,nals_ori,call->nals_new);
+    }
+    if ( nals_ori!=call->nals_new )
+        mcall_trim_and_update_numberR(call,rec,nals_ori,call->nals_new);
+
+    // Set QUAL
+    if ( nAC )
+    {
+        // Quality of a variant site. fabs() to avoid negative zeros in VCF output when CALL_KEEPALT is set
+        rec->qual = max_qual;
+    }
+    else
+    {
+        // Set the quality of a REF site
+        if ( lk_sum!=-HUGE_VAL )  // no support from (high quality) reads, so QUAL=1-prior
+            rec->qual = -4.343*(lk_sum - logsumexp2(lk_sum,ref_lk));
+        else if ( call->ac[0] )
+            rec->qual = call->theta ? -4.343*call->theta : 0;
+        else
+            bcf_float_set_missing(rec->qual);
+    }
+
+    // AC, AN
+    if ( call->nals_new>1 ) bcf_update_info_int32(call->hdr, rec, "AC", call->ac+1, call->nals_new-1);
+    nAC += call->ac[0];
+    bcf_update_info_int32(call->hdr, rec, "AN", &nAC, 1);
+
+    // Remove unused alleles
+    hts_expand(char*,call->nals_new,call->nals,call->als);
+    for (i=0; i<nals_ori; i++)
+        if ( call->als_map[i]>=0 ) call->als[call->als_map[i]] = rec->d.allele[i];
+    bcf_update_alleles(call->hdr, rec, (const char**)call->als, call->nals_new);
+    bcf_update_genotypes(call->hdr, rec, call->gts, nsmpl*2);
+
+    // DP4 and PV4 tags
+    if ( bcf_get_info_float(call->hdr, rec, "I16", &call->anno16, &call->n16)==16 )
+    {
+        int32_t dp[4]; dp[0] = call->anno16[0]; dp[1] = call->anno16[1]; dp[2] = call->anno16[2]; dp[3] = call->anno16[3];
+        bcf_update_info_int32(call->hdr, rec, "DP4", dp, 4);
+
+        int32_t mq = (call->anno16[8]+call->anno16[10])/(call->anno16[0]+call->anno16[1]+call->anno16[2]+call->anno16[3]);
+        bcf_update_info_int32(call->hdr, rec, "MQ", &mq, 1);
+
+        if ( call->output_tags & CALL_FMT_PV4 )
+        {
+            anno16_t a;
+            float tmpf[4];
+            int is_tested = test16(call->anno16, &a) >= 0 && a.is_tested ? 1 : 0;
+            if ( is_tested ) 
+            {
+                for (i=0; i<4; i++) tmpf[i] = a.p[i];
+                bcf_update_info_float(call->hdr, rec, "PV4", tmpf, 4);
+            }
+        }
+    }
+
+    bcf_update_info_int32(call->hdr, rec, "I16", NULL, 0);     // remove I16 tag
+
+    return call->nals_new;
+}
+
diff --git a/bcftools/mpileup.c b/bcftools/mpileup.c
new file mode 100644
index 0000000..fc4f4b1
--- /dev/null
+++ b/bcftools/mpileup.c
@@ -0,0 +1,1558 @@
+/*  mpileup.c -- mpileup subcommand. Previously bam_plcmd.c from samtools
+
+    Copyright (C) 2008-2022 Genome Research Ltd.
+    Portions copyright (C) 2009-2012 Broad Institute.
+
+    Author: Heng Li <lh3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <unistd.h>
+#include <ctype.h>
+#include <string.h>
+#include <strings.h>
+#include <limits.h>
+#include <inttypes.h>
+#include <errno.h>
+#include <sys/stat.h>
+#include <getopt.h>
+#include <htslib/sam.h>
+#include <htslib/faidx.h>
+#include <htslib/kstring.h>
+#include <htslib/khash_str2int.h>
+#include <htslib/hts_os.h>
+#include <assert.h>
+#include "regidx.h"
+#include "bcftools.h"
+#include "bam2bcf.h"
+#include "bam_sample.h"
+#include "gvcf.h"
+
+#define MPLP_BCF        1
+#define MPLP_VCF        (1<<1)
+#define MPLP_NO_COMP    (1<<2)
+#define MPLP_NO_ORPHAN  (1<<3)
+#define MPLP_REALN      (1<<4)
+#define MPLP_NO_INDEL   (1<<5)
+#define MPLP_REDO_BAQ   (1<<6)
+#define MPLP_ILLUMINA13 (1<<7)
+#define MPLP_IGNORE_RG  (1<<8)
+#define MPLP_PRINT_POS  (1<<9)
+#define MPLP_PRINT_MAPQ (1<<10)
+#define MPLP_PER_SAMPLE (1<<11)
+#define MPLP_SMART_OVERLAPS (1<<12)
+#define MPLP_REALN_PARTIAL  (1<<13)
+
+typedef struct _mplp_aux_t mplp_aux_t;
+typedef struct _mplp_pileup_t mplp_pileup_t;
+
+// Data shared by all bam files
+typedef struct {
+    int min_mq, flag, min_baseQ, max_baseQ, delta_baseQ, capQ_thres, max_depth,
+        max_indel_depth, max_read_len, fmt_flag, ambig_reads;
+    int rflag_skip_any_unset, rflag_skip_all_unset, rflag_skip_any_set, rflag_skip_all_set, output_type;
+    int openQ, extQ, tandemQ, min_support, indel_win_size; // for indels
+    double min_frac; // for indels
+    double indel_bias;
+    char *reg_fname, *pl_list, *fai_fname, *output_fname;
+    int reg_is_file, record_cmd_line, n_threads, clevel;
+    faidx_t *fai;
+    regidx_t *bed, *reg;    // bed: skipping regions, reg: index-jump to regions
+    regitr_t *bed_itr, *reg_itr;
+    int bed_logic;          // 1: include region, 0: exclude region
+    gvcf_t *gvcf;
+
+    // auxiliary structures for calling
+    bcf_callaux_t *bca;
+    bcf_callret1_t *bcr;
+    bcf_call_t bc;
+    bam_mplp_t iter;
+    mplp_aux_t **mplp_data;
+    int nfiles;
+    char **files;
+    mplp_pileup_t *gplp;
+    int *n_plp;
+    const bam_pileup1_t **plp;
+    bam_smpl_t *bsmpl;
+    kstring_t buf;
+    bcf1_t *bcf_rec;
+    htsFile *bcf_fp;
+    bcf_hdr_t *bcf_hdr;
+    int argc;
+    char **argv;
+} mplp_conf_t;
+
+typedef struct {
+    char *ref[2];
+    int ref_id[2];
+    int ref_len[2];
+} mplp_ref_t;
+
+#define MPLP_REF_INIT {{NULL,NULL},{-1,-1},{0,0}}
+
+// Data specific to each bam file
+struct _mplp_aux_t {
+    samFile *fp;
+    hts_itr_t *iter;
+    bam_hdr_t *h;
+    mplp_ref_t *ref;
+    const mplp_conf_t *conf;
+    int bam_id;
+    hts_idx_t *idx;     // maintained only with more than one -r regions
+};
+
+// Data passed to htslib/mpileup
+struct _mplp_pileup_t {
+    int n;
+    int *n_plp, *m_plp;
+    bam_pileup1_t **plp;
+};
+
+static int mplp_get_ref(mplp_aux_t *ma, int tid,  char **ref, int *ref_len) {
+    mplp_ref_t *r = ma->ref;
+
+    //printf("get ref %d {%d/%p, %d/%p}\n", tid, r->ref_id[0], r->ref[0], r->ref_id[1], r->ref[1]);
+
+    if (!r || !ma->conf->fai) {
+        *ref = NULL;
+        return 0;
+    }
+
+    // Do we need to reference count this so multiple mplp_aux_t can
+    // track which references are in use?
+    // For now we just cache the last two. Sufficient?
+    if (tid == r->ref_id[0]) {
+        *ref = r->ref[0];
+        *ref_len = r->ref_len[0];
+        return 1;
+    }
+    if (tid == r->ref_id[1]) {
+        // Last, swap over
+        int tmp;
+        tmp = r->ref_id[0];  r->ref_id[0]  = r->ref_id[1];  r->ref_id[1]  = tmp;
+        tmp = r->ref_len[0]; r->ref_len[0] = r->ref_len[1]; r->ref_len[1] = tmp;
+
+        char *tc;
+        tc = r->ref[0]; r->ref[0] = r->ref[1]; r->ref[1] = tc;
+        *ref = r->ref[0];
+        *ref_len = r->ref_len[0];
+        return 1;
+    }
+
+    // New, so migrate to old and load new
+    free(r->ref[1]);
+    r->ref[1]     = r->ref[0];
+    r->ref_id[1]  = r->ref_id[0];
+    r->ref_len[1] = r->ref_len[0];
+
+    r->ref_id[0] = tid;
+    r->ref[0] = faidx_fetch_seq(ma->conf->fai,
+                                ma->h->target_name[r->ref_id[0]],
+                                0,
+                                INT_MAX,
+                                &r->ref_len[0]);
+
+    if (!r->ref[0]) {
+        r->ref[0] = NULL;
+        r->ref_id[0] = -1;
+        r->ref_len[0] = 0;
+        *ref = NULL;
+        return 0;
+    }
+
+    *ref = r->ref[0];
+    *ref_len = r->ref_len[0];
+    return 1;
+}
+
+static int mplp_func(void *data, bam1_t *b)
+{
+    char *ref;
+    mplp_aux_t *ma = (mplp_aux_t*)data;
+    int ret, ref_len;
+    while (1)
+    {
+        int has_ref;
+        ret = ma->iter? sam_itr_next(ma->fp, ma->iter, b) : sam_read1(ma->fp, ma->h, b);
+        if (ret < 0) break;
+        // The 'B' cigar operation is not part of the specification, considering as obsolete.
+        //  bam_remove_B(b);
+        if (b->core.tid < 0 || (b->core.flag&BAM_FUNMAP)) continue; // exclude unmapped reads
+        if (ma->conf->rflag_skip_any_unset && (ma->conf->rflag_skip_any_unset&b->core.flag)!=ma->conf->rflag_skip_any_unset) continue;
+        if (ma->conf->rflag_skip_all_set && (ma->conf->rflag_skip_all_set&b->core.flag)==ma->conf->rflag_skip_all_set) continue;
+        if (ma->conf->rflag_skip_all_unset && !(ma->conf->rflag_skip_all_unset&b->core.flag)) continue;
+        if (ma->conf->rflag_skip_any_set && ma->conf->rflag_skip_any_set&b->core.flag) continue;
+        if (ma->conf->bed)
+        {
+            // test overlap
+            regitr_t *itr = ma->conf->bed_itr;
+            int beg = b->core.pos, end = bam_endpos(b)-1;
+            int overlap = regidx_overlap(ma->conf->bed, ma->h->target_name[b->core.tid],beg,end, itr);
+            if ( !ma->conf->bed_logic && !overlap )
+            {
+                // exclude only reads which are fully contained in the region
+                while ( regitr_overlap(itr) )
+                {
+                    if ( beg < itr->beg ) { overlap = 1; break; }
+                    if ( end > itr->end ) { overlap = 1; break; }
+                }
+            }
+            if ( !overlap ) continue;
+        }
+        if ( bam_smpl_get_sample_id(ma->conf->bsmpl,ma->bam_id,b)<0 ) continue;
+        if (ma->conf->flag & MPLP_ILLUMINA13) {
+            int i;
+            uint8_t *qual = bam_get_qual(b);
+            for (i = 0; i < b->core.l_qseq; ++i)
+                qual[i] = qual[i] > 31? qual[i] - 31 : 0;
+        }
+
+        if (ma->conf->fai && b->core.tid >= 0) {
+            has_ref = mplp_get_ref(ma, b->core.tid, &ref, &ref_len);
+            if (has_ref && ref_len <= b->core.pos) { // exclude reads outside of the reference sequence
+                fprintf(stderr,"[%s] Skipping because %"PRId64" is outside of %d [ref:%d]\n",
+                        __func__, (int64_t) b->core.pos, ref_len, b->core.tid);
+                continue;
+            }
+        } else {
+            has_ref = 0;
+        }
+
+        // Allow sufficient room for bam_aux_append of ZQ tag without
+        // a realloc and consequent breakage of pileup's cached pointers.
+        if (has_ref && (ma->conf->flag &MPLP_REALN) && !bam_aux_get(b, "ZQ")) {
+            // Doing sam_prob_realn later is problematic as it adds to
+            // the tag list (ZQ or BQ), which causes a realloc of b->data.
+            // This happens after pileup has built a hash table on the
+            // read name.  It's a deficiency in pileup IMO.
+
+            // We could implement a new sam_prob_realn that returns ZQ
+            // somewhere else and cache it ourselves (pileup clientdata),
+            // but for now we simply use a workaround.
+            //
+            // We create a fake tag of the correct length, which we remove
+            // just prior calling sam_prob_realn so we can guarantee there is
+            // room. (We can't just make room now as bam_copy1 removes it
+            // again).
+            if (b->core.l_qseq > 500) {
+                uint8_t *ZQ = malloc((uint32_t)b->core.l_qseq+1);
+                memset(ZQ, '@', b->core.l_qseq);
+                ZQ[b->core.l_qseq] = 0;
+                bam_aux_append(b, "_Q", 'Z', b->core.l_qseq+1, ZQ);
+                free(ZQ);
+            } else {
+                static uint8_t ZQ[501] =
+                    "@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@"
+                    "@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@"
+                    "@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@"
+                    "@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@"
+                    "@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@"
+                    "@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@"
+                    "@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@"
+                    "@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@"
+                    "@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@"
+                    "@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@";
+                ZQ[b->core.l_qseq] = 0;
+                bam_aux_append(b, "_Q", 'Z', b->core.l_qseq+1, ZQ);
+                ZQ[b->core.l_qseq] = '@';
+            }
+        }
+
+        if (has_ref && ma->conf->capQ_thres > 10) {
+            int q = sam_cap_mapq(b, ref, ref_len, ma->conf->capQ_thres);
+            if (q < 0) continue;    // skip
+            else if (b->core.qual > q) b->core.qual = q;
+        }
+        if (b->core.qual < ma->conf->min_mq) continue;
+        else if ((ma->conf->flag&MPLP_NO_ORPHAN) && (b->core.flag&BAM_FPAIRED) && !(b->core.flag&BAM_FPROPER_PAIR)) continue;
+
+        return ret;
+    };
+    return ret;
+}
+
+// Called once per new bam added to the pileup.
+// We cache sample information here so we don't have to keep recomputing this
+// on each and every pileup column. If FMT/SCR annotation is requested, a flag
+// is set to indicate the presence of a soft clip.
+//
+// Cd is an arbitrary block of data we can write into, which ends up in
+// the pileup structures. We stash the sample ID there:
+//      has_soft_clip .. cd->i & 1
+//      sample_id     .. cd->i >> 1
+static int pileup_constructor(void *data, const bam1_t *b, bam_pileup_cd *cd)
+{
+    mplp_aux_t *ma = (mplp_aux_t *)data;
+    int n = bam_smpl_get_sample_id(ma->conf->bsmpl, ma->bam_id, (bam1_t *)b);
+    cd->i = 0;
+    PLP_SET_SAMPLE_ID(cd->i, n);
+    // Whether read has a soft-clip is used in mplp_realn's heuristics.
+    // TODO: consider whether clip length is beneficial to use?
+    int i;
+    for (i=0; i<b->core.n_cigar; i++) {
+        int cig = bam_get_cigar(b)[i] & BAM_CIGAR_MASK;
+        if (cig == BAM_CSOFT_CLIP) {
+            PLP_SET_SOFT_CLIP(cd->i);
+            break;
+        }
+    }
+
+    if (ma->conf->flag & MPLP_REALN) {
+        int i;
+        // int tot_ins = 0;
+        // int p = 0;
+        uint32_t *cigar = bam_get_cigar(b);
+        for (i=0; i<b->core.n_cigar; i++) {
+            int cig = cigar[i] & BAM_CIGAR_MASK;
+            // if (bam_cigar_type(cig) & 2)
+            //     p += cigar[i] >> BAM_CIGAR_SHIFT;
+            if (cig == BAM_CINS || cig == BAM_CDEL || cig == BAM_CREF_SKIP) {
+                // tot_ins += cigar[i] >> BAM_CIGAR_SHIFT;
+                // Possible further optimsation, check tot_ins==1 later
+                // (and remove break) so we can detect single bp indels.
+                // We may want to focus BAQ on more complex regions only.
+                PLP_SET_INDEL(cd->i);
+                break;
+            }
+
+            // TODO: proper p->cd struct and have cd->i as a size rather
+            // than a flag.
+
+            // Then aggregate together the sizes and if just 1 size for all
+            // reads or 2 sizes for approx 50/50 split in all reads, then
+            // treat this as a well-aligned variant and don't run BAQ.
+        }
+    }
+
+    return 0;
+}
+
+static void group_smpl(mplp_pileup_t *m, bam_smpl_t *bsmpl, int n, int *n_plp, const bam_pileup1_t **plp)
+{
+    int i, j;
+    memset(m->n_plp, 0, m->n * sizeof(int));
+    for (i = 0; i < n; ++i) // iterate over all bams
+    {
+        for (j = 0; j < n_plp[i]; ++j)  // iterate over all reads available at this position
+        {
+            const bam_pileup1_t *p = plp[i] + j;
+            int id = PLP_SAMPLE_ID(p->cd.i);
+            if (m->n_plp[id] == m->m_plp[id])
+            {
+                m->m_plp[id] = m->m_plp[id]? m->m_plp[id]<<1 : 8;
+                m->plp[id] = (bam_pileup1_t*) realloc(m->plp[id], sizeof(bam_pileup1_t) * m->m_plp[id]);
+            }
+            m->plp[id][m->n_plp[id]++] = *p;
+        }
+    }
+}
+
+static void flush_bcf_records(mplp_conf_t *conf, htsFile *fp, bcf_hdr_t *hdr, bcf1_t *rec)
+{
+    if ( !conf->gvcf )
+    {
+        if ( rec && bcf_write1(fp, hdr, rec)!=0 ) error("[%s] Error: failed to write the record to %s\n", __func__,conf->output_fname?conf->output_fname:"standard output");
+        return;
+    }
+
+    if ( !rec )
+    {
+        gvcf_write(conf->gvcf, fp, hdr, NULL, 0);
+        return;
+    }
+
+    int is_ref = 0;
+    if ( rec->n_allele==1 ) is_ref = 1;
+    else if ( rec->n_allele==2 )
+    {
+        // second allele is mpileup's X, not a variant
+        if ( rec->d.allele[1][0]=='<' && rec->d.allele[1][1]=='*' && rec->d.allele[1][2]=='>' ) is_ref = 1;
+    }
+    rec = gvcf_write(conf->gvcf, fp, hdr, rec, is_ref);
+    if ( rec && bcf_write1(fp,hdr,rec)!=0 ) error("[%s] Error: failed to write the record to %s\n", __func__,conf->output_fname?conf->output_fname:"standard output");
+}
+
+/*
+ * Loops for an indel at this position.
+ *
+ * Only reads that overlap an indel loci get realigned.  This considerably
+ * reduces the cost of running BAQ while keeping the main benefits.
+ *
+ * TODO: also consider only realigning reads that don't span the indel
+ * by more than a certain amount either-side.  Ie focus BAQ only on reads
+ * ending adjacent to the indel, where the alignment is most likely to
+ * be wrong.  (2nd TODO: do this based on sequence context; STRs bad, unique
+ * data good.)
+ *
+ * NB: this may sadly realign after we've already used the data.  Hmm...
+ */
+static void mplp_realn(int n, int *n_plp, const bam_pileup1_t **plp,
+                       int flag, int max_read_len,
+                       char *ref, int ref_len, int pos) {
+    int i, j, has_indel = 0, has_clip = 0, nt = 0;
+    int min_indel = INT_MAX, max_indel = INT_MIN;
+
+    // Is an indel present.
+    // NB: don't bother even checking if very long as almost guaranteed
+    // to have indel (and likely soft-clips too).
+    for (i = 0; i < n; i++) { // iterate over bams
+        nt += n_plp[i];
+        for (j = 0; j < n_plp[i]; j++) { // iterate over reads
+            bam_pileup1_t *p = (bam_pileup1_t *)plp[i] + j;
+            has_indel += (PLP_HAS_INDEL(p->cd.i) || p->indel) ? 1 : 0;
+            // Has_clip is almost always true for very long reads
+            // (eg PacBio CCS), but these rarely matter as the clip
+            // is likely a long way from this indel.
+            has_clip  += (PLP_HAS_SOFT_CLIP(p->cd.i))         ? 1 : 0;
+            if (max_indel < p->indel)
+                max_indel = p->indel;
+            if (min_indel > p->indel)
+                min_indel = p->indel;
+        }
+    }
+
+    if (flag & MPLP_REALN_PARTIAL) {
+        if (has_indel == 0 ||
+            (has_clip < 0.2*nt && max_indel == min_indel &&
+             (has_indel < 0.1*nt /*|| has_indel > 0.9*nt*/ || has_indel == 1)))
+            return;
+    }
+
+    // Realign
+    for (i = 0; i < n; i++) { // iterate over bams
+        for (j = 0; j < n_plp[i]; j++) { // iterate over reads
+            const bam_pileup1_t *p = plp[i] + j;
+            bam1_t *b = p->b;
+
+            // Avoid doing multiple times.
+            //
+            // Note we cannot modify p->cd.i here with a PLP_SET macro
+            // because the cd item is held by mpileup in an lbnode_t
+            // struct and copied over to the pileup struct for each
+            // iteration, essentially making p->cd.i read only.
+            //
+            // We could use our own structure (p->cd.p), allocated during
+            // the constructor, but for simplicity we play dirty and
+            // abuse an unused flag bit instead.
+            if (b->core.flag & 32768)
+                continue;
+            b->core.flag |= 32768;
+
+            if (b->core.l_qseq > max_read_len)
+                continue;
+
+            // Check p->cigar_ind and see what cigar elements are before
+            // and after.  How close is this location to the end of the
+            // read?  Only realign if we don't span by more than X bases.
+            //
+            // Again, best only done on deeper data as BAQ helps
+            // disproportionately more on shallow data sets.
+            //
+            // This rescues some of the false negatives that are caused by
+            // systematic reduction in quality due to sample vs ref alignment.
+
+// At deep coverage we skip realigning more reads as we have sufficient depth.
+// This rescues for false negatives.  At shallow depth we pay for this with
+// more FP so are more stringent on spanning size.
+#define REALN_DIST (40+10*(nt<40)+10*(nt<20))
+            uint32_t *cig = bam_get_cigar(b);
+            int ncig = b->core.n_cigar;
+
+            // Don't realign reads where indel is in middle?
+            // On long read data we don't care about soft-clips at the ends.
+            // For short read data, we always calc BAQ on these as they're
+            // a common source of false positives.
+            if ((flag & MPLP_REALN_PARTIAL) && nt > 15 && ncig > 1) {
+                // Left & right cigar op match.
+                int lr = b->core.l_qseq > 500;
+                int lm = 0, rm = 0, k;
+                for (k = 0; k < ncig; k++) {
+                    int cop = bam_cigar_op(cig[k]);
+                    if (lr && (cop == BAM_CHARD_CLIP || cop == BAM_CSOFT_CLIP))
+                        continue;
+
+                    if (cop == BAM_CMATCH || cop == BAM_CDIFF ||
+                        cop == BAM_CEQUAL)
+                        lm += bam_cigar_oplen(cig[k]);
+                    else
+                        break;
+                }
+
+                for (k = ncig-1; k >= 0; k--) {
+                    int cop = bam_cigar_op(cig[k]);
+                    if (lr && (cop == BAM_CHARD_CLIP || cop == BAM_CSOFT_CLIP))
+                        continue;
+
+                    if (cop == BAM_CMATCH || cop == BAM_CDIFF ||
+                        cop == BAM_CEQUAL)
+                        rm += bam_cigar_oplen(cig[k]);
+                    else
+                        break;
+                }
+
+                if (lm >= REALN_DIST*4 && rm >= REALN_DIST*4)
+                    continue;
+
+                if (lm >= REALN_DIST && rm >= REALN_DIST &&
+                    has_clip < (0.15+0.05*(nt>20))*nt)
+                    continue;
+            }
+
+            if (b->core.l_qseq > 500) {
+                // don't do BAQ on long-read data if it's going to
+                // cause us to have a large band-with and costly in CPU
+                int rl = bam_cigar2rlen(b->core.n_cigar, bam_get_cigar(b));
+                if (abs(rl - b->core.l_qseq) * b->core.l_qseq >= 500000)
+                    continue;
+            }
+
+            // Fudge: make room for ZQ tag.
+            uint8_t *_Q = bam_aux_get(b, "_Q");
+            if (_Q) bam_aux_del(b, _Q);
+            sam_prob_realn(b, ref, ref_len, (flag & MPLP_REDO_BAQ) ? 7 : 3);
+        }
+    }
+
+    return;
+}
+
+static int mpileup_reg(mplp_conf_t *conf, uint32_t beg, uint32_t end)
+{
+    bam_hdr_t *hdr = conf->mplp_data[0]->h; // header of first file in input list
+
+    int ret, i, tid, pos, ref_len;
+    char *ref;
+
+    while ( (ret=bam_mplp_auto(conf->iter, &tid, &pos, conf->n_plp, conf->plp)) > 0)
+    {
+        if ( pos<beg || pos>end ) continue;
+        if ( conf->bed && tid >= 0 )
+        {
+            int overlap = regidx_overlap(conf->bed, hdr->target_name[tid], pos, pos, NULL);
+            if ( !conf->bed_logic ) overlap = overlap ? 0 : 1;
+            if ( !overlap ) continue;
+        }
+        int has_ref = mplp_get_ref(conf->mplp_data[0], tid, &ref, &ref_len);
+        if (has_ref && (conf->flag & MPLP_REALN))
+            mplp_realn(conf->nfiles, conf->n_plp, conf->plp, conf->flag,
+                       conf->max_read_len, ref, ref_len, pos);
+
+        int total_depth, _ref0, ref16;
+        for (i = total_depth = 0; i < conf->nfiles; ++i) total_depth += conf->n_plp[i];
+        group_smpl(conf->gplp, conf->bsmpl, conf->nfiles, conf->n_plp, conf->plp);
+        _ref0 = (ref && pos < ref_len)? ref[pos] : 'N';
+        ref16 = seq_nt16_table[_ref0];
+        bcf_callaux_clean(conf->bca, &conf->bc);
+        for (i = 0; i < conf->gplp->n; ++i)
+            bcf_call_glfgen(conf->gplp->n_plp[i], conf->gplp->plp[i], ref16, conf->bca, conf->bcr + i);
+        conf->bc.tid = tid; conf->bc.pos = pos;
+        bcf_call_combine(conf->gplp->n, conf->bcr, conf->bca, ref16, &conf->bc);
+        bcf_clear1(conf->bcf_rec);
+        bcf_call2bcf(&conf->bc, conf->bcf_rec, conf->bcr, conf->fmt_flag,
+                     conf->bca, 0);
+        flush_bcf_records(conf, conf->bcf_fp, conf->bcf_hdr, conf->bcf_rec);
+
+        // call indels; todo: subsampling with total_depth>max_indel_depth instead of ignoring?
+        // check me: rghash in bcf_call_gap_prep() should have no effect, reads mplp_func already excludes them
+        if (!(conf->flag&MPLP_NO_INDEL) && total_depth < conf->max_indel_depth
+            && (bcf_callaux_clean(conf->bca, &conf->bc),
+                bcf_call_gap_prep(conf->gplp->n, conf->gplp->n_plp, conf->gplp->plp, pos, conf->bca, ref) >= 0))
+        {
+            for (i = 0; i < conf->gplp->n; ++i)
+                bcf_call_glfgen(conf->gplp->n_plp[i], conf->gplp->plp[i], -1, conf->bca, conf->bcr + i);
+            if (bcf_call_combine(conf->gplp->n, conf->bcr, conf->bca, -1, &conf->bc) >= 0)
+            {
+                bcf_clear1(conf->bcf_rec);
+                bcf_call2bcf(&conf->bc, conf->bcf_rec, conf->bcr, conf->fmt_flag, conf->bca, ref);
+                flush_bcf_records(conf, conf->bcf_fp, conf->bcf_hdr, conf->bcf_rec);
+            }
+        }
+    }
+    return 0;
+}
+
+static int mpileup(mplp_conf_t *conf)
+{
+    if (conf->nfiles == 0) {
+        fprintf(stderr,"[%s] no input file/data given\n", __func__);
+        exit(EXIT_FAILURE);
+    }
+
+    mplp_ref_t mp_ref = MPLP_REF_INIT;
+    conf->gplp = (mplp_pileup_t *) calloc(1,sizeof(mplp_pileup_t));
+    conf->mplp_data = (mplp_aux_t**) calloc(conf->nfiles, sizeof(mplp_aux_t*));
+    conf->plp = (const bam_pileup1_t**) calloc(conf->nfiles, sizeof(bam_pileup1_t*));
+    conf->n_plp = (int*) calloc(conf->nfiles, sizeof(int));
+
+    // Allow to run mpileup on multiple regions in one go. This comes at cost: the bai index
+    // must be kept in the memory for the whole time which can be a problem with many bams.
+    // Therefore if none or only one region is requested, we initialize the bam iterator as
+    // before and free the index. Only when multiple regions are queried, we keep the index.
+    int nregs = 0;
+    if ( conf->reg_fname )
+    {
+        if ( conf->reg_is_file )
+        {
+            conf->reg = regidx_init(conf->reg_fname,NULL,NULL,0,NULL);
+            if ( !conf->reg ) {
+                fprintf(stderr,"Could not parse the regions: %s\n", conf->reg_fname);
+                exit(EXIT_FAILURE);
+            }
+        }
+        else
+        {
+            conf->reg = regidx_init(NULL,regidx_parse_reg,NULL,sizeof(char*),NULL);
+            if ( regidx_insert_list(conf->reg,conf->reg_fname,',') !=0 ) {
+                fprintf(stderr,"Could not parse the regions: %s\n", conf->reg_fname);
+                exit(EXIT_FAILURE);
+            }
+        }
+        nregs = regidx_nregs(conf->reg);
+        conf->reg_itr = regitr_init(conf->reg);
+        regitr_loop(conf->reg_itr);   // region iterator now positioned at the first region
+    }
+
+    // read the header of each file in the list and initialize data
+    // beware: mpileup has always assumed that tid's are consistent in the headers, add sanity check at least!
+    bam_hdr_t *hdr = NULL;      // header of first file in input list
+    int i;
+    for (i = 0; i < conf->nfiles; ++i) {
+        bam_hdr_t *h_tmp;
+        conf->mplp_data[i] = (mplp_aux_t*) calloc(1, sizeof(mplp_aux_t));
+        conf->mplp_data[i]->fp = sam_open(conf->files[i], "rb");
+        if ( !conf->mplp_data[i]->fp )
+        {
+            fprintf(stderr, "[%s] failed to open %s: %s\n", __func__, conf->files[i], strerror(errno));
+            exit(EXIT_FAILURE);
+        }
+        if (hts_set_opt(conf->mplp_data[i]->fp, CRAM_OPT_DECODE_MD, 1)) {
+            fprintf(stderr, "Failed to set CRAM_OPT_DECODE_MD value\n");
+            exit(EXIT_FAILURE);
+        }
+        if (conf->fai_fname && hts_set_fai_filename(conf->mplp_data[i]->fp, conf->fai_fname) != 0) {
+            fprintf(stderr, "[%s] failed to process %s: %s\n",
+                    __func__, conf->fai_fname, strerror(errno));
+            exit(EXIT_FAILURE);
+        }
+        conf->mplp_data[i]->conf = conf;
+        conf->mplp_data[i]->ref = &mp_ref;
+        h_tmp = sam_hdr_read(conf->mplp_data[i]->fp);
+        if ( !h_tmp ) {
+            fprintf(stderr,"[%s] fail to read the header of %s\n", __func__, conf->files[i]);
+            exit(EXIT_FAILURE);
+        }
+        conf->mplp_data[i]->h = i ? hdr : h_tmp; // for j==0, "h" has not been set yet
+        conf->mplp_data[i]->bam_id = bam_smpl_add_bam(conf->bsmpl,h_tmp->text,conf->files[i]);
+        if ( conf->mplp_data[i]->bam_id<0 )
+        {
+            // no usable readgroups in this bam, it can be skipped
+            sam_close(conf->mplp_data[i]->fp);
+            free(conf->mplp_data[i]);
+            bam_hdr_destroy(h_tmp);
+            free(conf->files[i]);
+            if ( i+1<conf->nfiles ) memmove(&conf->files[i],&conf->files[i+1],sizeof(*conf->files)*(conf->nfiles-i-1));
+            conf->nfiles--;
+            i--;
+            continue;
+        }
+        if (conf->reg) {
+            hts_idx_t *idx = sam_index_load(conf->mplp_data[i]->fp, conf->files[i]);
+            if (idx == NULL) {
+                fprintf(stderr, "[%s] fail to load index for %s\n", __func__, conf->files[i]);
+                exit(EXIT_FAILURE);
+            }
+            conf->buf.l = 0;
+            ksprintf(&conf->buf,"%s:%u-%u",conf->reg_itr->seq,conf->reg_itr->beg+1,conf->reg_itr->end+1);
+            conf->mplp_data[i]->iter = sam_itr_querys(idx, conf->mplp_data[i]->h, conf->buf.s);
+            if ( !conf->mplp_data[i]->iter )
+            {
+                conf->mplp_data[i]->iter = sam_itr_querys(idx, conf->mplp_data[i]->h, conf->reg_itr->seq);
+                if ( conf->mplp_data[i]->iter ) {
+                    fprintf(stderr,"[E::%s] fail to parse region '%s'\n", __func__, conf->buf.s);
+                    exit(EXIT_FAILURE);
+                }
+                fprintf(stderr,"[E::%s] the sequence \"%s\" not found: %s\n",__func__,conf->reg_itr->seq,conf->files[i]);
+                exit(EXIT_FAILURE);
+            }
+            if ( nregs==1 ) // no need to keep the index in memory
+               hts_idx_destroy(idx);
+            else
+                conf->mplp_data[i]->idx = idx;
+        }
+
+        if ( !hdr ) hdr = h_tmp; /* save the header of first file in list */
+        else {
+            // FIXME: check consistency between h and h_tmp
+            bam_hdr_destroy(h_tmp);
+
+            // we store only the first file's header; it's (alleged to be)
+            // compatible with the i-th file's target_name lookup needs
+            conf->mplp_data[i]->h = hdr;
+        }
+    }
+    if ( !hdr ) {
+        fprintf(stderr, "[%s] failed to find a file header with usable read groups\n", __func__);
+        exit(EXIT_FAILURE);
+    }
+    // allocate data storage proportionate to number of samples being studied sm->n
+    bam_smpl_get_samples(conf->bsmpl, &conf->gplp->n);
+    conf->gplp->n_plp = (int*) calloc(conf->gplp->n, sizeof(int));
+    conf->gplp->m_plp = (int*) calloc(conf->gplp->n, sizeof(int));
+    conf->gplp->plp = (bam_pileup1_t**) calloc(conf->gplp->n, sizeof(bam_pileup1_t*));
+
+    fprintf(stderr, "[%s] %d samples in %d input files\n", __func__, conf->gplp->n, conf->nfiles);
+    // write the VCF header
+    char wmode[8];
+    set_wmode(wmode,conf->output_type,conf->output_fname,conf->clevel);
+    conf->bcf_fp = hts_open(conf->output_fname ? conf->output_fname : "-", wmode);
+    if (conf->bcf_fp == NULL) {
+        fprintf(stderr, "[%s] failed to write to %s: %s\n", __func__, conf->output_fname? conf->output_fname : "standard output", strerror(errno));
+        exit(EXIT_FAILURE);
+    }
+    if ( conf->n_threads ) hts_set_threads(conf->bcf_fp, conf->n_threads);
+
+    // BCF header creation
+    conf->bcf_hdr = bcf_hdr_init("w");
+    conf->buf.l = 0;
+
+    if (conf->record_cmd_line)
+    {
+        ksprintf(&conf->buf, "##bcftoolsVersion=%s+htslib-%s\n",bcftools_version(),hts_version());
+        bcf_hdr_append(conf->bcf_hdr, conf->buf.s);
+
+        conf->buf.l = 0;
+        ksprintf(&conf->buf, "##bcftoolsCommand=mpileup");
+        for (i=1; i<conf->argc; i++) ksprintf(&conf->buf, " %s", conf->argv[i]);
+        kputc('\n', &conf->buf);
+        bcf_hdr_append(conf->bcf_hdr, conf->buf.s);
+    }
+
+    if (conf->fai_fname)
+    {
+        conf->buf.l = 0;
+        ksprintf(&conf->buf, "##reference=file://%s\n", conf->fai_fname);
+        bcf_hdr_append(conf->bcf_hdr, conf->buf.s);
+    }
+
+    // Translate BAM @SQ tags to BCF ##contig tags
+    // todo: use/write new BAM header manipulation routines, fill also UR, M5
+    for (i=0; i<hdr->n_targets; i++)
+    {
+        conf->buf.l = 0;
+        ksprintf(&conf->buf, "##contig=<ID=%s,length=%d>", hdr->target_name[i], hdr->target_len[i]);
+        bcf_hdr_append(conf->bcf_hdr, conf->buf.s);
+    }
+    conf->buf.l = 0;
+
+    bcf_hdr_append(conf->bcf_hdr,"##ALT=<ID=*,Description=\"Represents allele(s) other than observed.\">");
+    bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=INDEL,Number=0,Type=Flag,Description=\"Indicates that the variant is an INDEL.\">");
+    bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=IDV,Number=1,Type=Integer,Description=\"Maximum number of raw reads supporting an indel\">");
+    bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=IMF,Number=1,Type=Float,Description=\"Maximum fraction of raw reads supporting an indel\">");
+    bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Raw read depth\">");
+    if ( conf->fmt_flag&B2B_INFO_VDB )
+        bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=VDB,Number=1,Type=Float,Description=\"Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)\",Version=\"3\">");
+
+    if (conf->fmt_flag & B2B_INFO_ZSCORE) {
+        if ( conf->fmt_flag&B2B_INFO_RPB )
+            bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=RPBZ,Number=1,Type=Float,Description=\"Mann-Whitney U-z test of Read Position Bias (closer to 0 is better)\">");
+        bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=MQBZ,Number=1,Type=Float,Description=\"Mann-Whitney U-z test of Mapping Quality Bias (closer to 0 is better)\">");
+        bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=BQBZ,Number=1,Type=Float,Description=\"Mann-Whitney U-z test of Base Quality Bias (closer to 0 is better)\">");
+        bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=MQSBZ,Number=1,Type=Float,Description=\"Mann-Whitney U-z test of Mapping Quality vs Strand Bias (closer to 0 is better)\">");
+        bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=NMBZ,Number=1,Type=Float,Description=\"Mann-Whitney U-z test of Number of Mismatches within supporting reads (closer to 0 is better)\">");
+        if ( conf->fmt_flag&B2B_FMT_NMBZ )
+            bcf_hdr_append(conf->bcf_hdr,"##FORMAT=<ID=NMBZ,Number=1,Type=Float,Description=\"Mann-Whitney U-z test of Number of Mismatches within supporting reads (closer to 0 is better)\">");
+        if ( conf->fmt_flag&B2B_INFO_SCB )
+            bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=SCBZ,Number=1,Type=Float,Description=\"Mann-Whitney U-z test of Soft-Clip Length Bias (closer to 0 is better)\">");
+    } else {
+        if ( conf->fmt_flag&B2B_INFO_RPB )
+            bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=RPB,Number=1,Type=Float,Description=\"Mann-Whitney U test of Read Position Bias (bigger is better)\">");
+        bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=MQB,Number=1,Type=Float,Description=\"Mann-Whitney U test of Mapping Quality Bias (bigger is better)\">");
+        bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=BQB,Number=1,Type=Float,Description=\"Mann-Whitney U test of Base Quality Bias (bigger is better)\">");
+        bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=MQSB,Number=1,Type=Float,Description=\"Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better)\">");
+    }
+
+    bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=FS,Number=1,Type=Float,Description=\"Phred-scaled p-value using Fisher's exact test to detect strand bias\">");
+#if CDF_MWU_TESTS
+    bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=RPB2,Number=1,Type=Float,Description=\"Mann-Whitney U test of Read Position Bias [CDF] (bigger is better)\">");
+    bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=MQB2,Number=1,Type=Float,Description=\"Mann-Whitney U test of Mapping Quality Bias [CDF] (bigger is better)\">");
+    bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=BQB2,Number=1,Type=Float,Description=\"Mann-Whitney U test of Base Quality Bias [CDF] (bigger is better)\">");
+    bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=MQSB2,Number=1,Type=Float,Description=\"Mann-Whitney U test of Mapping Quality vs Strand Bias [CDF] (bigger is better)\">");
+#endif
+    bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=SGB,Number=1,Type=Float,Description=\"Segregation based metric.\">");
+    bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=MQ0F,Number=1,Type=Float,Description=\"Fraction of MQ0 reads (smaller is better)\">");
+    bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=I16,Number=16,Type=Float,Description=\"Auxiliary tag used for calling, see description of bcf_callret1_t in bam2bcf.h\">");
+    bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=QS,Number=R,Type=Float,Description=\"Auxiliary tag used for calling\">");
+    bcf_hdr_append(conf->bcf_hdr,"##FORMAT=<ID=PL,Number=G,Type=Integer,Description=\"List of Phred-scaled genotype likelihoods\">");
+    if ( conf->fmt_flag&B2B_FMT_DP )
+        bcf_hdr_append(conf->bcf_hdr,"##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Number of high-quality bases\">");
+    if ( conf->fmt_flag&B2B_FMT_DV )
+        bcf_hdr_append(conf->bcf_hdr,"##FORMAT=<ID=DV,Number=1,Type=Integer,Description=\"Number of high-quality non-reference bases\">");
+    if ( conf->fmt_flag&B2B_FMT_DPR )
+        bcf_hdr_append(conf->bcf_hdr,"##FORMAT=<ID=DPR,Number=R,Type=Integer,Description=\"Number of high-quality bases observed for each allele\">");
+    if ( conf->fmt_flag&B2B_INFO_DPR )
+        bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=DPR,Number=R,Type=Integer,Description=\"Number of high-quality bases observed for each allele\">");
+    if ( conf->fmt_flag&B2B_FMT_DP4 )
+        bcf_hdr_append(conf->bcf_hdr,"##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"Number of high-quality ref-fwd, ref-reverse, alt-fwd and alt-reverse bases\">");
+    if ( conf->fmt_flag&B2B_FMT_SP )
+        bcf_hdr_append(conf->bcf_hdr,"##FORMAT=<ID=SP,Number=1,Type=Integer,Description=\"Phred-scaled strand bias P-value\">");
+    if ( conf->fmt_flag&B2B_FMT_AD )
+        bcf_hdr_append(conf->bcf_hdr,"##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths (high-quality bases)\">");
+    if ( conf->fmt_flag&B2B_FMT_ADF )
+        bcf_hdr_append(conf->bcf_hdr,"##FORMAT=<ID=ADF,Number=R,Type=Integer,Description=\"Allelic depths on the forward strand (high-quality bases)\">");
+    if ( conf->fmt_flag&B2B_FMT_ADR )
+        bcf_hdr_append(conf->bcf_hdr,"##FORMAT=<ID=ADR,Number=R,Type=Integer,Description=\"Allelic depths on the reverse strand (high-quality bases)\">");
+    if ( conf->fmt_flag&B2B_FMT_QS )
+        bcf_hdr_append(conf->bcf_hdr,"##FORMAT=<ID=QS,Number=R,Type=Integer,Description=\"Phred-score allele quality sum used by `call -mG` and `+trio-dnm`\">");
+    if ( conf->fmt_flag&B2B_INFO_AD )
+        bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=AD,Number=R,Type=Integer,Description=\"Total allelic depths (high-quality bases)\">");
+    if ( conf->fmt_flag&B2B_INFO_ADF )
+        bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=ADF,Number=R,Type=Integer,Description=\"Total allelic depths on the forward strand (high-quality bases)\">");
+    if ( conf->fmt_flag&B2B_INFO_SCR )
+        bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=SCR,Number=1,Type=Integer,Description=\"Number of soft-clipped reads (at high-quality bases)\">");
+    if ( conf->fmt_flag&B2B_FMT_SCR )
+        bcf_hdr_append(conf->bcf_hdr,"##FORMAT=<ID=SCR,Number=1,Type=Integer,Description=\"Per-sample number of soft-clipped reads (at high-quality bases)\">");
+    if ( conf->fmt_flag&B2B_INFO_ADR )
+        bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=ADR,Number=R,Type=Integer,Description=\"Total allelic depths on the reverse strand (high-quality bases)\">");
+    if ( conf->gvcf )
+        gvcf_update_header(conf->gvcf, conf->bcf_hdr);
+
+    int nsmpl;
+    const char **smpl = bam_smpl_get_samples(conf->bsmpl, &nsmpl);
+    for (i=0; i<nsmpl; i++)
+        bcf_hdr_add_sample(conf->bcf_hdr, smpl[i]);
+    if ( bcf_hdr_write(conf->bcf_fp, conf->bcf_hdr)!=0 ) error("[%s] Error: failed to write the header to %s\n",__func__,conf->output_fname?conf->output_fname:"standard output");
+
+    conf->bca = bcf_call_init(-1., conf->min_baseQ, conf->max_baseQ,
+                              conf->delta_baseQ);
+    conf->bcr = (bcf_callret1_t*) calloc(nsmpl, sizeof(bcf_callret1_t));
+    conf->bca->openQ = conf->openQ, conf->bca->extQ = conf->extQ, conf->bca->tandemQ = conf->tandemQ;
+    conf->bca->indel_bias = conf->indel_bias;
+    conf->bca->min_frac = conf->min_frac;
+    conf->bca->min_support = conf->min_support;
+    conf->bca->per_sample_flt = conf->flag & MPLP_PER_SAMPLE;
+    conf->bca->fmt_flag = conf->fmt_flag;
+    conf->bca->ambig_reads = conf->ambig_reads;
+    conf->bca->indel_win_size = conf->indel_win_size;
+
+    conf->bc.bcf_hdr = conf->bcf_hdr;
+    conf->bc.n  = nsmpl;
+    conf->bc.PL = (int32_t*) malloc(15 * nsmpl * sizeof(*conf->bc.PL));
+    conf->bc.QS = (int32_t*) malloc(nsmpl*sizeof(*conf->bc.QS)*B2B_MAX_ALLELES);
+    for (i=0; i<nsmpl; i++)
+        conf->bcr[i].QS = conf->bc.QS + i*B2B_MAX_ALLELES;
+    if (conf->fmt_flag)
+    {
+        assert( sizeof(float)==sizeof(int32_t) );
+        conf->bc.DP4 = (int32_t*) malloc(nsmpl * sizeof(int32_t) * 4);
+        conf->bc.fmt_arr = (uint8_t*) malloc(nsmpl * sizeof(float)); // all fmt_flag fields, float and int32
+        if ( conf->fmt_flag&(B2B_INFO_DPR|B2B_FMT_DPR|B2B_INFO_AD|B2B_INFO_ADF|B2B_INFO_ADR|B2B_FMT_AD|B2B_FMT_ADF|B2B_FMT_ADR) )
+        {
+            // first B2B_MAX_ALLELES fields for total numbers, the rest per-sample
+            conf->bc.ADR = (int32_t*) malloc((nsmpl+1)*B2B_MAX_ALLELES*sizeof(int32_t));
+            conf->bc.ADF = (int32_t*) malloc((nsmpl+1)*B2B_MAX_ALLELES*sizeof(int32_t));
+            for (i=0; i<nsmpl; i++)
+            {
+                conf->bcr[i].ADR = conf->bc.ADR + (i+1)*B2B_MAX_ALLELES;
+                conf->bcr[i].ADF = conf->bc.ADF + (i+1)*B2B_MAX_ALLELES;
+            }
+        }
+        if ( conf->fmt_flag&(B2B_INFO_SCR|B2B_FMT_SCR) )
+            conf->bc.SCR = (int32_t*) malloc((nsmpl+1)*sizeof(*conf->bc.SCR));
+    }
+    int nnmbz = (conf->fmt_flag&B2B_FMT_NMBZ) ? nsmpl + 1 : 1;
+    conf->bc.ref_nm = (int32_t*) malloc(sizeof(*conf->bc.ref_nm) * nnmbz * B2B_N_NM);
+    conf->bc.alt_nm = (int32_t*) malloc(sizeof(*conf->bc.alt_nm) * nnmbz * B2B_N_NM);
+    conf->bc.mwu_nm = (float*) malloc((nsmpl+1)*sizeof(*conf->bc.mwu_nm));
+    conf->bca->ref_nm = conf->bc.ref_nm;     // this is just to make the arrays available in bcf_call_glfgen()
+    conf->bca->alt_nm = conf->bc.alt_nm;
+    if ( conf->fmt_flag&B2B_FMT_NMBZ )
+    {
+        for (i=0; i<nsmpl; i++) conf->bcr[i].ref_nm = conf->bc.ref_nm + (i+1)*B2B_N_NM;
+        for (i=0; i<nsmpl; i++) conf->bcr[i].alt_nm = conf->bc.alt_nm + (i+1)*B2B_N_NM;
+    }
+
+    // init mpileup
+    conf->iter = bam_mplp_init(conf->nfiles, mplp_func, (void**)conf->mplp_data);
+    if ( conf->flag & MPLP_SMART_OVERLAPS ) bam_mplp_init_overlaps(conf->iter);
+    fprintf(stderr, "[%s] maximum number of reads per input file set to -d %d\n",  __func__, conf->max_depth);
+    if ( (double)conf->max_depth * conf->nfiles > 1<<20)
+        fprintf(stderr, "Warning: Potential memory hog, up to %.0fM reads in the pileup!\n", (double)conf->max_depth*conf->nfiles);
+    if ( (double)conf->max_depth * conf->nfiles / nsmpl < 250 )
+        fprintf(stderr, "Note: The maximum per-sample depth with -d %d is %.1fx\n", conf->max_depth,(double)conf->max_depth * conf->nfiles / nsmpl);
+    bam_mplp_set_maxcnt(conf->iter, conf->max_depth);
+    conf->max_indel_depth = conf->max_indel_depth * nsmpl;
+    conf->bcf_rec = bcf_init1();
+    bam_mplp_constructor(conf->iter, pileup_constructor);
+
+    // Run mpileup for multiple regions
+    if ( nregs )
+    {
+        int ireg = 0;
+        do
+        {
+            // first region is already positioned
+            if ( ireg++ > 0 )
+            {
+                conf->buf.l = 0;
+                ksprintf(&conf->buf,"%s:%u-%u",conf->reg_itr->seq,conf->reg_itr->beg+1,conf->reg_itr->end+1);
+
+                for (i=0; i<conf->nfiles; i++)
+                {
+                    hts_itr_destroy(conf->mplp_data[i]->iter);
+                    conf->mplp_data[i]->iter = sam_itr_querys(conf->mplp_data[i]->idx, conf->mplp_data[i]->h, conf->buf.s);
+                    if ( !conf->mplp_data[i]->iter )
+                    {
+                        conf->mplp_data[i]->iter = sam_itr_querys(conf->mplp_data[i]->idx, conf->mplp_data[i]->h, conf->reg_itr->seq);
+                        if ( conf->mplp_data[i]->iter ) {
+                            fprintf(stderr,"[E::%s] fail to parse region '%s'\n", __func__, conf->buf.s);
+                            exit(EXIT_FAILURE);
+                        }
+                        fprintf(stderr,"[E::%s] the sequence \"%s\" not found: %s\n",__func__,conf->reg_itr->seq,conf->files[i]);
+                        exit(EXIT_FAILURE);
+                    }
+                    bam_mplp_reset(conf->iter);
+                }
+            }
+            mpileup_reg(conf,conf->reg_itr->beg,conf->reg_itr->end);
+        }
+        while ( regitr_loop(conf->reg_itr) );
+    }
+    else
+        mpileup_reg(conf,0,UINT32_MAX);
+
+    flush_bcf_records(conf, conf->bcf_fp, conf->bcf_hdr, NULL);
+
+    // clean up
+    free(conf->bc.tmp.s);
+    bcf_destroy1(conf->bcf_rec);
+    if (conf->bcf_fp)
+    {
+        if ( hts_close(conf->bcf_fp)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,conf->output_fname);
+        bcf_hdr_destroy(conf->bcf_hdr);
+        bcf_call_destroy(conf->bca);
+        free(conf->bc.PL);
+        free(conf->bc.DP4);
+        free(conf->bc.ADR);
+        free(conf->bc.ADF);
+        free(conf->bc.SCR);
+        free(conf->bc.QS);
+        free(conf->bc.ref_nm);
+        free(conf->bc.alt_nm);
+        free(conf->bc.fmt_arr);
+        free(conf->bc.mwu_nm);
+        free(conf->bcr);
+    }
+    if ( conf->gvcf ) gvcf_destroy(conf->gvcf);
+    free(conf->buf.s);
+    for (i = 0; i < conf->gplp->n; ++i) free(conf->gplp->plp[i]);
+    free(conf->gplp->plp); free(conf->gplp->n_plp); free(conf->gplp->m_plp); free(conf->gplp);
+    bam_mplp_destroy(conf->iter);
+    bam_hdr_destroy(hdr);
+    for (i = 0; i < conf->nfiles; ++i) {
+        if ( nregs>1 ) hts_idx_destroy(conf->mplp_data[i]->idx);
+        sam_close(conf->mplp_data[i]->fp);
+        if ( conf->mplp_data[i]->iter) hts_itr_destroy(conf->mplp_data[i]->iter);
+        free(conf->mplp_data[i]);
+    }
+    if ( conf->reg_itr ) regitr_destroy(conf->reg_itr);
+    free(conf->mplp_data); free(conf->plp); free(conf->n_plp);
+    free(mp_ref.ref[0]);
+    free(mp_ref.ref[1]);
+    return 0;
+}
+
+static int is_url(const char *s)
+{
+    static const char uri_scheme_chars[] =
+        "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789+.-";
+    return s[strspn(s, uri_scheme_chars)] == ':';
+}
+
+#define MAX_PATH_LEN 1024
+int read_file_list(const char *file_list,int *n,char **argv[])
+{
+    char buf[MAX_PATH_LEN];
+    int len, nfiles = 0;
+    char **files = NULL;
+    struct stat sb;
+
+    *n = 0;
+    *argv = NULL;
+
+    FILE *fh = fopen(file_list,"r");
+    if ( !fh )
+    {
+        fprintf(stderr,"%s: %s\n", file_list,strerror(errno));
+        return 1;
+    }
+
+    files = (char**) calloc(nfiles,sizeof(char*));
+    nfiles = 0;
+    while ( fgets(buf,MAX_PATH_LEN,fh) )
+    {
+        // allow empty lines and trailing spaces
+        len = strlen(buf);
+        while ( len>0 && isspace(buf[len-1]) ) len--;
+        if ( !len ) continue;
+
+        // check sanity of the file list
+        buf[len] = 0;
+        if (! (is_url(buf) || stat(buf, &sb) == 0))
+        {
+            // no such file, check if it is safe to print its name
+            int i, safe_to_print = 1;
+            for (i=0; i<len; i++)
+                if (!isprint(buf[i])) { safe_to_print = 0; break; }
+            if ( safe_to_print )
+                fprintf(stderr,"The file list \"%s\" appears broken, could not locate: %s\n", file_list,buf);
+            else
+                fprintf(stderr,"Does the file \"%s\" really contain a list of files and do all exist?\n", file_list);
+            return 1;
+        }
+
+        nfiles++;
+        files = (char**) realloc(files,nfiles*sizeof(char*));
+        files[nfiles-1] = strdup(buf);
+    }
+    if ( fclose(fh)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,file_list);
+    if ( !nfiles )
+    {
+        fprintf(stderr,"No files read from %s\n", file_list);
+        return 1;
+    }
+    *argv = files;
+    *n    = nfiles;
+    return 0;
+}
+#undef MAX_PATH_LEN
+
+int parse_format_flag(const char *str)
+{
+    int i, flag = 0, n_tags;
+    char **tags = hts_readlist(str, 0, &n_tags);
+    for(i=0; i<n_tags; i++)
+    {
+        if ( !strcasecmp(tags[i],"DP") || !strcasecmp(tags[i],"FORMAT/DP") || !strcasecmp(tags[i],"FMT/DP") ) flag |= B2B_FMT_DP;
+        else if ( !strcasecmp(tags[i],"DV") || !strcasecmp(tags[i],"FORMAT/DV") || !strcasecmp(tags[i],"FMT/DV") ) { flag |= B2B_FMT_DV; fprintf(stderr, "[warning] tag DV functional, but deprecated. Please switch to `AD` in future.\n"); }
+        else if ( !strcasecmp(tags[i],"SP") || !strcasecmp(tags[i],"FORMAT/SP") || !strcasecmp(tags[i],"FMT/SP") ) flag |= B2B_FMT_SP;
+        else if ( !strcasecmp(tags[i],"DP4") || !strcasecmp(tags[i],"FORMAT/DP4") || !strcasecmp(tags[i],"FMT/DP4") ) { flag |= B2B_FMT_DP4; fprintf(stderr, "[warning] tag DP4 functional, but deprecated. Please switch to `ADF` and `ADR` in future.\n"); }
+        else if ( !strcasecmp(tags[i],"DPR") || !strcasecmp(tags[i],"FORMAT/DPR") || !strcasecmp(tags[i],"FMT/DPR") ) { flag |= B2B_FMT_DPR; fprintf(stderr, "[warning] tag DPR functional, but deprecated. Please switch to `AD` in future.\n"); }
+        else if ( !strcasecmp(tags[i],"INFO/DPR") ) { flag |= B2B_INFO_DPR; fprintf(stderr, "[warning] tag INFO/DPR functional, but deprecated. Please switch to `INFO/AD` in future.\n"); }
+        else if ( !strcasecmp(tags[i],"AD") || !strcasecmp(tags[i],"FORMAT/AD") || !strcasecmp(tags[i],"FMT/AD") ) flag |= B2B_FMT_AD;
+        else if ( !strcasecmp(tags[i],"ADF") || !strcasecmp(tags[i],"FORMAT/ADF") || !strcasecmp(tags[i],"FMT/ADF") ) flag |= B2B_FMT_ADF;
+        else if ( !strcasecmp(tags[i],"ADR") || !strcasecmp(tags[i],"FORMAT/ADR") || !strcasecmp(tags[i],"FMT/ADR") ) flag |= B2B_FMT_ADR;
+        else if ( !strcasecmp(tags[i],"SCR") || !strcasecmp(tags[i],"FORMAT/SCR") || !strcasecmp(tags[i],"FMT/SCR") ) flag |= B2B_FMT_SCR;
+        else if ( !strcasecmp(tags[i],"QS") || !strcasecmp(tags[i],"FORMAT/QS") || !strcasecmp(tags[i],"FMT/QS") ) flag |= B2B_FMT_QS;
+        else if ( !strcasecmp(tags[i],"NMBZ") || !strcasecmp(tags[i],"FORMAT/NMBZ") || !strcasecmp(tags[i],"FMT/NMBZ") ) flag |= B2B_FMT_NMBZ;
+        else if ( !strcasecmp(tags[i],"INFO/SCR") ) flag |= B2B_INFO_SCR;
+        else if ( !strcasecmp(tags[i],"INFO/AD") ) flag |= B2B_INFO_AD;
+        else if ( !strcasecmp(tags[i],"INFO/ADF") ) flag |= B2B_INFO_ADF;
+        else if ( !strcasecmp(tags[i],"INFO/ADR") ) flag |= B2B_INFO_ADR;
+        else if ( !strcasecmp(tags[i],"SCB") || !strcasecmp(tags[i],"INFO/SCB")) flag |= B2B_INFO_SCB;
+        else
+        {
+            fprintf(stderr,"Could not parse tag \"%s\" in \"%s\"\n", tags[i], str);
+            exit(EXIT_FAILURE);
+        }
+        free(tags[i]);
+    }
+    if (n_tags) free(tags);
+    return flag;
+}
+
+// todo: make it possible to turn off some annotations or change the defaults,
+//      specifically RPB, VDB, MWU, SGB tests. It would be good to do some
+//      benchmarking first to see if it's worth it.
+static void list_annotations(FILE *fp)
+{
+    fprintf(fp,
+"\n"
+"FORMAT annotation tags available (\"FORMAT/\" prefix is optional):\n"
+"\n"
+"  FORMAT/AD   .. Allelic depth (Number=R,Type=Integer)\n"
+"  FORMAT/ADF  .. Allelic depths on the forward strand (Number=R,Type=Integer)\n"
+"  FORMAT/ADR  .. Allelic depths on the reverse strand (Number=R,Type=Integer)\n"
+"  FORMAT/DP   .. Number of high-quality bases (Number=1,Type=Integer)\n"
+"  FORMAT/NMBZ .. Mann-Whitney U-z test of Number of Mismatches within supporting reads (Number=1,Type=Float)\n"
+"  FORMAT/QS   .. Allele phred-score quality sum for use with `call -mG` and +trio-dnm (Number=R,Type=Integer)\n"
+"  FORMAT/SP   .. Phred-scaled strand bias P-value (Number=1,Type=Integer)\n"
+"  FORMAT/SCR  .. Number of soft-clipped reads (Number=1,Type=Integer)\n"
+"\n"
+"INFO annotation tags available:\n"
+"\n"
+"  INFO/AD  .. Total allelic depth (Number=R,Type=Integer)\n"
+"  INFO/ADF .. Total allelic depths on the forward strand (Number=R,Type=Integer)\n"
+"  INFO/ADR .. Total allelic depths on the reverse strand (Number=R,Type=Integer)\n"
+"  INFO/SCR .. Number of soft-clipped reads (Number=1,Type=Integer)\n"
+"\n");
+}
+
+static void print_usage(FILE *fp, const mplp_conf_t *mplp)
+{
+    char *tmp_skip_all_set = bam_flag2str(mplp->rflag_skip_all_set);
+    char *tmp_skip_any_unset = bam_flag2str(mplp->rflag_skip_any_unset);
+    char *tmp_skip_all_unset = bam_flag2str(mplp->rflag_skip_all_unset);
+    char *tmp_skip_any_set = bam_flag2str(mplp->rflag_skip_any_set);
+
+    // Display usage information, formatted for the standard 80 columns.
+    // (The unusual string formatting here aids the readability of this
+    // source code in 80 columns, to the extent that's possible.)
+
+    fprintf(fp,
+        "\n"
+        "Usage: bcftools mpileup [options] in1.bam [in2.bam [...]]\n"
+        "\n"
+        "Input options:\n"
+        "  -6, --illumina1.3+      Quality is in the Illumina-1.3+ encoding\n"
+        "  -A, --count-orphans     Do not discard anomalous read pairs\n"
+        "  -b, --bam-list FILE     List of input BAM filenames, one per line\n"
+        "  -B, --no-BAQ            Disable BAQ (per-Base Alignment Quality)\n"
+        "  -C, --adjust-MQ INT     Adjust mapping quality [0]\n"
+        "  -D, --full-BAQ          Apply BAQ everywhere, not just in problematic regions\n"
+        "  -d, --max-depth INT     Max raw per-file depth; avoids excessive memory usage [%d]\n", mplp->max_depth);
+            fprintf(fp,
+        "  -E, --redo-BAQ          Recalculate BAQ on the fly, ignore existing BQs\n"
+        "  -f, --fasta-ref FILE    Faidx indexed reference sequence file\n"
+        "      --no-reference      Do not require fasta reference file\n"
+        "  -G, --read-groups FILE  Select or exclude read groups listed in the file\n"
+        "  -q, --min-MQ INT        Skip alignments with mapQ smaller than INT [%d]\n", mplp->min_mq);
+    fprintf(fp,
+        "  -Q, --min-BQ INT        Skip bases with baseQ/BAQ smaller than INT [%d]\n", mplp->min_baseQ);
+    fprintf(fp,
+        "      --max-BQ INT        Limit baseQ/BAQ to no more than INT [%d]\n", mplp->max_baseQ);
+    fprintf(fp,
+        "      --delta-BQ INT      Use neighbour_qual + INT if less than qual [%d]\n", mplp->delta_baseQ);
+    fprintf(fp,
+        "  -r, --regions REG[,...] Comma separated list of regions in which pileup is generated\n"
+        "  -R, --regions-file FILE Restrict to regions listed in a file\n"
+        "      --ignore-RG         Ignore RG tags (one BAM = one sample)\n"
+        "  --ls, --skip-all-set STR|INT  Skip reads with all of the bits set []\n");
+    fprintf(fp,
+        "  --ns, --skip-any-set STR|INT  Skip reads with any of the bits set [%s]\n", tmp_skip_any_set);
+    fprintf(fp,
+        "  --lu, --skip-all-unset STR|INT  Skip reads with all of the bits unset []\n"
+        "  --nu, --skip-any-unset STR|INT  Skip reads with any of the bits unset []\n");
+    fprintf(fp,
+        "  -s, --samples LIST      Comma separated list of samples to include\n"
+        "  -S, --samples-file FILE File of samples to include\n"
+        "  -t, --targets REG[,...] Similar to -r but streams rather than index-jumps\n"
+        "  -T, --targets-file FILE Similar to -R but streams rather than index-jumps\n"
+        "  -x, --ignore-overlaps   Disable read-pair overlap detection\n"
+        "      --seed INT          Random number seed used for sampling deep regions [0]\n"
+        "\n"
+        "Output options:\n"
+        "  -a, --annotate LIST     Optional tags to output; '\\?' to list available tags []\n"
+        "  -g, --gvcf INT[,...]    Group non-variant sites into gVCF blocks according\n"
+        "                          To minimum per-sample DP\n"
+        "      --no-version        Do not append version and command line to the header\n"
+        "  -o, --output FILE       Write output to FILE [standard output]\n"
+        "  -O, --output-type TYPE  'b' compressed BCF; 'u' uncompressed BCF;\n"
+        "                          'z' compressed VCF; 'v' uncompressed VCF; 0-9 compression level [v]\n"
+        "  -U, --mwu-u             Use older probability scale for Mann-Whitney U test\n"
+        "      --threads INT       Use multithreading with INT worker threads [0]\n"
+        "\n"
+        "SNP/INDEL genotype likelihoods options:\n"
+        "  -X, --config STR        Specify platform specific profiles (see below)\n"
+        "  -e, --ext-prob INT      Phred-scaled gap extension seq error probability [%d]\n", mplp->extQ);
+    fprintf(fp,
+        "  -F, --gap-frac FLOAT    Minimum fraction of gapped reads [%g]\n", mplp->min_frac);
+    fprintf(fp,
+        "  -h, --tandem-qual INT   Coefficient for homopolymer errors [%d]\n", mplp->tandemQ);
+    fprintf(fp,
+        "  -I, --skip-indels       Do not perform indel calling\n"
+        "  -L, --max-idepth INT    Maximum per-file depth for INDEL calling [%d]\n", mplp->max_indel_depth);
+    fprintf(fp,
+        "  -m, --min-ireads INT    Minimum number gapped reads for indel candidates [%d]\n", mplp->min_support);
+    fprintf(fp,
+        "  -M, --max-read-len INT  Maximum length of read to pass to BAQ algorithm [%d]\n", mplp->max_read_len);
+    fprintf(fp,
+        "  -o, --open-prob INT     Phred-scaled gap open seq error probability [%d]\n", mplp->openQ);
+    fprintf(fp,
+        "  -p, --per-sample-mF     Apply -m and -F per-sample for increased sensitivity\n"
+        "  -P, --platforms STR     Comma separated list of platforms for indels [all]\n"
+        "  --ar, --ambig-reads STR   What to do with ambiguous indel reads: drop,incAD,incAD0 [drop]\n");
+    fprintf(fp,
+        "      --indel-bias FLOAT  Raise to favour recall over precision [%.2f]\n", mplp->indel_bias);
+    fprintf(fp,
+        "      --indel-size INT    Approximate maximum indel size considered [%d]\n", mplp->indel_win_size);
+    fprintf(fp,"\n");
+    fprintf(fp,
+        "Configuration profiles activated with -X, --config:\n"
+        "    1.12:        -Q13 -h100 -m1 -F0.002\n"
+        "    illumina:    [ default values ]\n"
+        "    ont:         -B -Q5 --max-BQ 30 -I [also try eg |bcftools call -P0.01]\n"
+        "    pacbio-ccs:  -D -Q5 --max-BQ 50 -F0.1 -o25 -e1 --delta-BQ 10 -M99999\n"
+        "\n"
+        "Notes: Assuming diploid individuals.\n"
+        "\n"
+        "Example:\n"
+        "   # See also http://samtools.github.io/bcftools/howtos/variant-calling.html\n"
+        "   bcftools mpileup -Ou -f reference.fa alignments.bam | bcftools call -mv -Ob -o calls.bcf\n"
+        "\n");
+
+    free(tmp_skip_all_set);
+    free(tmp_skip_any_unset);
+    free(tmp_skip_all_unset);
+    free(tmp_skip_any_set);
+}
+
+int main_mpileup(int argc, char *argv[])
+{
+    int c;
+    const char *file_list = NULL;
+    char **fn = NULL;
+    int nfiles = 0, use_orphan = 0, noref = 0;
+    mplp_conf_t mplp;
+    memset(&mplp, 0, sizeof(mplp_conf_t));
+    mplp.min_baseQ = 1;
+    mplp.max_baseQ = 60;
+    mplp.delta_baseQ = 30;
+    mplp.capQ_thres = 0;
+    mplp.max_depth = 250; mplp.max_indel_depth = 250;
+    mplp.openQ = 40; mplp.extQ = 20; mplp.tandemQ = 500;
+    mplp.min_frac = 0.05; mplp.indel_bias = 1.0; mplp.min_support = 2;
+    mplp.flag = MPLP_NO_ORPHAN | MPLP_REALN | MPLP_REALN_PARTIAL
+              | MPLP_SMART_OVERLAPS;
+    mplp.argc = argc; mplp.argv = argv;
+    mplp.rflag_skip_any_set = BAM_FUNMAP | BAM_FSECONDARY | BAM_FQCFAIL | BAM_FDUP;
+    mplp.output_fname = NULL;
+    mplp.output_type = FT_VCF;
+    mplp.record_cmd_line = 1;
+    mplp.n_threads = 0;
+    mplp.bsmpl = bam_smpl_init();
+    // the default to be changed in future, see also parse_format_flag()
+    mplp.fmt_flag = B2B_INFO_VDB|B2B_INFO_RPB|B2B_INFO_SCB|B2B_INFO_ZSCORE;
+    mplp.max_read_len = 500;
+    mplp.ambig_reads = B2B_DROP;
+    mplp.indel_win_size = 110;
+    mplp.clevel = -1;
+    hts_srand48(0);
+
+    static const struct option lopts[] =
+    {
+        {"nu", required_argument, NULL, 16},
+        {"lu", required_argument, NULL, 17},
+        {"rf", required_argument, NULL, 17},   // old --rf, --incl-flags = --lu, --skip-all-unset
+        {"ns", required_argument, NULL, 18},
+        {"ff", required_argument, NULL, 18},   // old --ff, --excl-flags = --ns, --skip-any-set
+        {"ls", required_argument, NULL, 19},
+        {"skip-any-unset", required_argument, NULL, 16},
+        {"skip-all-unset", required_argument, NULL, 17},
+        {"skip-any-set", required_argument, NULL, 18},
+        {"skip-all-set", required_argument, NULL, 19},
+        {"output", required_argument, NULL, 3},
+        {"open-prob", required_argument, NULL, 4},
+        {"ignore-RG", no_argument, NULL, 5},
+        {"ignore-rg", no_argument, NULL, 5},
+        {"gvcf", required_argument, NULL, 'g'},
+        {"no-reference", no_argument, NULL, 7},
+        {"no-version", no_argument, NULL, 8},
+        {"threads",required_argument,NULL,9},
+        {"illumina1.3+", no_argument, NULL, '6'},
+        {"count-orphans", no_argument, NULL, 'A'},
+        {"bam-list", required_argument, NULL, 'b'},
+        {"no-BAQ", no_argument, NULL, 'B'},
+        {"no-baq", no_argument, NULL, 'B'},
+        {"full-BAQ", no_argument, NULL, 'D'},
+        {"full-baq", no_argument, NULL, 'D'},
+        {"adjust-MQ", required_argument, NULL, 'C'},
+        {"adjust-mq", required_argument, NULL, 'C'},
+        {"max-depth", required_argument, NULL, 'd'},
+        {"redo-BAQ", no_argument, NULL, 'E'},
+        {"redo-baq", no_argument, NULL, 'E'},
+        {"fasta-ref", required_argument, NULL, 'f'},
+        {"read-groups", required_argument, NULL, 'G'},
+        {"region", required_argument, NULL, 'r'},
+        {"regions", required_argument, NULL, 'r'},
+        {"regions-file", required_argument, NULL, 'R'},
+        {"targets", required_argument, NULL, 't'},
+        {"targets-file", required_argument, NULL, 'T'},
+        {"min-MQ", required_argument, NULL, 'q'},
+        {"min-mq", required_argument, NULL, 'q'},
+        {"min-BQ", required_argument, NULL, 'Q'},
+        {"min-bq", required_argument, NULL, 'Q'},
+        {"max-bq", required_argument, NULL, 11},
+        {"max-BQ", required_argument, NULL, 11},
+        {"delta-BQ", required_argument, NULL, 12},
+        {"ignore-overlaps", no_argument, NULL, 'x'},
+        {"output-type", required_argument, NULL, 'O'},
+        {"samples", required_argument, NULL, 's'},
+        {"samples-file", required_argument, NULL, 'S'},
+        {"annotate", required_argument, NULL, 'a'},
+        {"ext-prob", required_argument, NULL, 'e'},
+        {"gap-frac", required_argument, NULL, 'F'},
+        {"indel-bias", required_argument, NULL, 10},
+        {"indel-size", required_argument, NULL, 15},
+        {"tandem-qual", required_argument, NULL, 'h'},
+        {"skip-indels", no_argument, NULL, 'I'},
+        {"max-idepth", required_argument, NULL, 'L'},
+        {"min-ireads", required_argument, NULL, 'm'},
+        {"per-sample-mF", no_argument, NULL, 'p'},
+        {"per-sample-mf", no_argument, NULL, 'p'},
+        {"platforms", required_argument, NULL, 'P'},
+        {"max-read-len", required_argument, NULL, 'M'},
+        {"config", required_argument, NULL, 'X'},
+        {"mwu-u", no_argument, NULL, 'U'},
+        {"seed", required_argument, NULL, 13},
+        {"ambig-reads", required_argument, NULL, 14},
+        {"ar", required_argument, NULL, 14},
+        {NULL, 0, NULL, 0}
+    };
+    while ((c = getopt_long(argc, argv, "Ag:f:r:R:q:Q:C:BDd:L:b:P:po:e:h:Im:F:EG:6O:xa:s:S:t:T:M:X:U",lopts,NULL)) >= 0) {
+        switch (c) {
+        case 'x': mplp.flag &= ~MPLP_SMART_OVERLAPS; break;
+        case  16 :
+            mplp.rflag_skip_any_unset = bam_str2flag(optarg);
+            if ( mplp.rflag_skip_any_unset <0 ) { fprintf(stderr,"Could not parse --nf %s\n", optarg); return 1; }
+            break;
+        case  17 :
+            mplp.rflag_skip_all_unset = bam_str2flag(optarg);
+            if ( mplp.rflag_skip_all_unset<0 ) { fprintf(stderr,"Could not parse --if %s\n", optarg); return 1; }
+            break;
+        case  18 :
+            mplp.rflag_skip_any_set = bam_str2flag(optarg);
+            if ( mplp.rflag_skip_any_set <0 ) { fprintf(stderr,"Could not parse --ef %s\n", optarg); return 1; }
+            break;
+        case  19 :
+            mplp.rflag_skip_all_set = bam_str2flag(optarg);
+            if ( mplp.rflag_skip_all_set <0 ) { fprintf(stderr,"Could not parse --df %s\n", optarg); return 1; }
+            break;
+        case  3 : mplp.output_fname = optarg; break;
+        case  4 : mplp.openQ = atoi(optarg); break;
+        case  5 : bam_smpl_ignore_readgroups(mplp.bsmpl); break;
+        case 'g':
+            mplp.gvcf = gvcf_init(optarg);
+            if ( !mplp.gvcf ) error("Could not parse: --gvcf %s\n", optarg);
+            break;
+        case 'f':
+            mplp.fai = fai_load(optarg);
+            if (mplp.fai == NULL) return 1;
+            mplp.fai_fname = optarg;
+            break;
+        case  7 : noref = 1; break;
+        case  8 : mplp.record_cmd_line = 0; break;
+        case  9 : mplp.n_threads = strtol(optarg, 0, 0); break;
+        case 'd': mplp.max_depth = atoi(optarg); break;
+        case 'r': mplp.reg_fname = strdup(optarg); break;
+        case 'R': mplp.reg_fname = strdup(optarg); mplp.reg_is_file = 1; break;
+        case 't':
+                  // In the original version the whole BAM was streamed which is inefficient
+                  //  with few BED intervals and big BAMs. Todo: devise a heuristic to determine
+                  //  best strategy, that is streaming or jumping.
+                  if ( optarg[0]=='^' ) optarg++;
+                  else mplp.bed_logic = 1;
+                  mplp.bed = regidx_init(NULL,regidx_parse_reg,NULL,0,NULL);
+                  mplp.bed_itr = regitr_init(mplp.bed);
+                  if ( regidx_insert_list(mplp.bed,optarg,',') !=0 )
+                  {
+                      fprintf(stderr,"Could not parse the targets: %s\n", optarg);
+                      exit(EXIT_FAILURE);
+                  }
+                  break;
+        case 'T':
+                  if ( optarg[0]=='^' ) optarg++;
+                  else mplp.bed_logic = 1;
+                  mplp.bed = regidx_init(optarg,NULL,NULL,0,NULL);
+                  if (!mplp.bed) { fprintf(stderr, "bcftools mpileup: Could not read file \"%s\"", optarg); return 1; }
+                  break;
+        case 'P': mplp.pl_list = strdup(optarg); break;
+        case 'p': mplp.flag |= MPLP_PER_SAMPLE; break;
+        case 'B': mplp.flag &= ~MPLP_REALN; break;
+        case 'D': mplp.flag &= ~MPLP_REALN_PARTIAL; break;
+        case 'I': mplp.flag |= MPLP_NO_INDEL; break;
+        case 'E': mplp.flag |= MPLP_REDO_BAQ; break;
+        case '6': mplp.flag |= MPLP_ILLUMINA13; break;
+        case 's': if ( bam_smpl_add_samples(mplp.bsmpl,optarg,0)<0 ) error("Could not read samples: %s\n",optarg); break;
+        case 'S': if ( bam_smpl_add_samples(mplp.bsmpl,optarg,1)<0 ) error("Could not read samples: %s\n",optarg); break;
+        case 'O':
+            switch (optarg[0]) {
+                case 'b': mplp.output_type = FT_BCF_GZ; break;
+                case 'u': mplp.output_type = FT_BCF; break;
+                case 'z': mplp.output_type = FT_VCF_GZ; break;
+                case 'v': mplp.output_type = FT_VCF; break;
+                default:
+                {
+                    char *tmp;
+                    mplp.clevel = strtol(optarg,&tmp,10);
+                    if ( *tmp || mplp.clevel<0 || mplp.clevel>9 ) error("The output type \"%s\" not recognised\n", optarg);
+                }
+            }
+            if ( optarg[1] )
+            {
+                char *tmp;
+                mplp.clevel = strtol(optarg+1,&tmp,10);
+                if ( *tmp || mplp.clevel<0 || mplp.clevel>9 ) error("Could not parse argument: --output-type %s\n", optarg+1);
+            }
+            break;
+        case 'C': mplp.capQ_thres = atoi(optarg); break;
+        case 'q': mplp.min_mq = atoi(optarg); break;
+        case 'Q': mplp.min_baseQ = atoi(optarg); break;
+        case  11: mplp.max_baseQ = atoi(optarg); break;
+        case  12: mplp.delta_baseQ = atoi(optarg); break;
+        case 'b': file_list = optarg; break;
+        case 'o': {
+                char *end;
+                long value = strtol(optarg, &end, 10);
+                // Distinguish between -o INT and -o FILE (a bit of a hack!)
+                if (*end == '\0') mplp.openQ = value;
+                else mplp.output_fname = optarg;
+            }
+            break;
+        case 'e': mplp.extQ = atoi(optarg); break;
+        case 'h': mplp.tandemQ = atoi(optarg); break;
+        case 10: // --indel-bias (inverted so higher => more indels called)
+            if (atof(optarg) < 1e-2)
+                mplp.indel_bias = 1/1e2;
+            else
+                mplp.indel_bias = 1/atof(optarg);
+            break;
+        case  15: {
+                char *tmp;
+                mplp.indel_win_size = strtol(optarg,&tmp,10);
+                if ( *tmp ) error("Could not parse argument: --indel-size %s\n", optarg);
+                if ( mplp.indel_win_size < 110 )
+                {
+                    mplp.indel_win_size = 110;
+                    fprintf(stderr,"Warning: running with --indel-size %d, the requested value is too small\n",mplp.indel_win_size);
+                }
+            }
+            break;
+        case 'A': use_orphan = 1; break;
+        case 'F': mplp.min_frac = atof(optarg); break;
+        case 'm': mplp.min_support = atoi(optarg); break;
+        case 'L': mplp.max_indel_depth = atoi(optarg); break;
+        case 'G': bam_smpl_add_readgroups(mplp.bsmpl, optarg, 1); break;
+        case 'a':
+            if (optarg[0]=='?') {
+                list_annotations(stderr);
+                return 1;
+            }
+            mplp.fmt_flag |= parse_format_flag(optarg);
+        break;
+        case 'M': mplp.max_read_len = atoi(optarg); break;
+        case 'U': mplp.fmt_flag &= ~B2B_INFO_ZSCORE; break;
+        case 'X':
+            if (strcasecmp(optarg, "pacbio-ccs") == 0) {
+                mplp.min_frac = 0.1;
+                mplp.min_baseQ = 5;
+                mplp.max_baseQ = 50;
+                mplp.delta_baseQ = 10;
+                mplp.openQ = 25;
+                mplp.extQ = 1;
+                mplp.flag |= MPLP_REALN_PARTIAL;
+                mplp.max_read_len = 99999;
+            } else if (strcasecmp(optarg, "ont") == 0) {
+                fprintf(stderr, "For ONT it may be beneficial to also run bcftools call with "
+                        "a higher -P, eg -P0.01 or -P 0.1\n");
+                mplp.min_baseQ = 5;
+                mplp.max_baseQ = 30;
+                mplp.flag &= ~MPLP_REALN;
+                mplp.flag |= MPLP_NO_INDEL;
+            } else if (strcasecmp(optarg, "1.12") == 0) {
+                // 1.12 and earlier
+                mplp.min_frac = 0.002;
+                mplp.min_support = 1;
+                mplp.min_baseQ = 13;
+                mplp.tandemQ = 100;
+                mplp.flag &= ~MPLP_REALN_PARTIAL;
+                mplp.flag |= MPLP_REALN;
+            } else if (strcasecmp(optarg, "illumina") == 0) {
+                mplp.flag |= MPLP_REALN_PARTIAL;
+            } else {
+                fprintf(stderr, "Unknown configuration name '%s'\n"
+                        "Please choose from 1.12, illumina, pacbio-ccs or ont\n",
+                        optarg);
+                return 1;
+            }
+            break;
+        case 13: hts_srand48(atoi(optarg)); break;
+        case 14:
+            if ( !strcasecmp(optarg,"drop") ) mplp.ambig_reads = B2B_DROP;
+            else if ( !strcasecmp(optarg,"incAD") ) mplp.ambig_reads = B2B_INC_AD;
+            else if ( !strcasecmp(optarg,"incAD0") ) mplp.ambig_reads = B2B_INC_AD0;
+            else error("The option to --ambig-reads not recognised: %s\n",optarg);
+            break;
+        default:
+            fprintf(stderr,"Invalid option: '%c'\n", c);
+            return 1;
+        }
+    }
+
+    if ( mplp.gvcf && !(mplp.fmt_flag&B2B_FMT_DP) )
+    {
+        fprintf(stderr,"[warning] The -a DP option is required with --gvcf, switching on.\n");
+        mplp.fmt_flag |= B2B_FMT_DP;
+    }
+    if ( mplp.flag&(MPLP_BCF|MPLP_VCF|MPLP_NO_COMP) )
+    {
+        if ( mplp.flag&MPLP_VCF )
+        {
+            if ( mplp.flag&MPLP_NO_COMP ) mplp.output_type = FT_VCF;
+            else mplp.output_type = FT_VCF_GZ;
+        }
+        else if ( mplp.flag&MPLP_BCF )
+        {
+            if ( mplp.flag&MPLP_NO_COMP ) mplp.output_type = FT_BCF;
+            else mplp.output_type = FT_BCF_GZ;
+        }
+    }
+    if ( !(mplp.flag&MPLP_REALN) && mplp.flag&MPLP_REDO_BAQ )
+    {
+        fprintf(stderr,"Error: The -B option cannot be combined with -E\n");
+        return 1;
+    }
+    if (use_orphan) mplp.flag &= ~MPLP_NO_ORPHAN;
+    if (argc == 1)
+    {
+        print_usage(stderr, &mplp);
+        return 1;
+    }
+    if (!mplp.fai && !noref) {
+        fprintf(stderr,"Error: mpileup requires the --fasta-ref option by default; use --no-reference to run without a fasta reference\n");
+        return 1;
+    }
+    int ret,i;
+    if (file_list)
+    {
+        if ( read_file_list(file_list,&nfiles,&fn) ) return 1;
+        mplp.files  = fn;
+        mplp.nfiles = nfiles;
+    }
+    else
+    {
+        mplp.nfiles = argc - optind;
+        mplp.files  = (char**) malloc(mplp.nfiles*sizeof(char*));
+        for (i=0; i<mplp.nfiles; i++) mplp.files[i] = strdup(argv[optind+i]);
+    }
+    ret = mpileup(&mplp);
+
+    for (i=0; i<mplp.nfiles; i++) free(mplp.files[i]);
+    free(mplp.files);
+    free(mplp.reg_fname); free(mplp.pl_list);
+    if (mplp.fai) fai_destroy(mplp.fai);
+    if (mplp.bed) regidx_destroy(mplp.bed);
+    if (mplp.bed_itr) regitr_destroy(mplp.bed_itr);
+    if (mplp.reg) regidx_destroy(mplp.reg);
+    bam_smpl_destroy(mplp.bsmpl);
+
+    return ret;
+}
diff --git a/bcftools/mpileup.c.pysam.c b/bcftools/mpileup.c.pysam.c
new file mode 100644
index 0000000..6e0ae5b
--- /dev/null
+++ b/bcftools/mpileup.c.pysam.c
@@ -0,0 +1,1560 @@
+#include "bcftools.pysam.h"
+
+/*  mpileup.c -- mpileup subcommand. Previously bam_plcmd.c from samtools
+
+    Copyright (C) 2008-2022 Genome Research Ltd.
+    Portions copyright (C) 2009-2012 Broad Institute.
+
+    Author: Heng Li <lh3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <unistd.h>
+#include <ctype.h>
+#include <string.h>
+#include <strings.h>
+#include <limits.h>
+#include <inttypes.h>
+#include <errno.h>
+#include <sys/stat.h>
+#include <getopt.h>
+#include <htslib/sam.h>
+#include <htslib/faidx.h>
+#include <htslib/kstring.h>
+#include <htslib/khash_str2int.h>
+#include <htslib/hts_os.h>
+#include <assert.h>
+#include "regidx.h"
+#include "bcftools.h"
+#include "bam2bcf.h"
+#include "bam_sample.h"
+#include "gvcf.h"
+
+#define MPLP_BCF        1
+#define MPLP_VCF        (1<<1)
+#define MPLP_NO_COMP    (1<<2)
+#define MPLP_NO_ORPHAN  (1<<3)
+#define MPLP_REALN      (1<<4)
+#define MPLP_NO_INDEL   (1<<5)
+#define MPLP_REDO_BAQ   (1<<6)
+#define MPLP_ILLUMINA13 (1<<7)
+#define MPLP_IGNORE_RG  (1<<8)
+#define MPLP_PRINT_POS  (1<<9)
+#define MPLP_PRINT_MAPQ (1<<10)
+#define MPLP_PER_SAMPLE (1<<11)
+#define MPLP_SMART_OVERLAPS (1<<12)
+#define MPLP_REALN_PARTIAL  (1<<13)
+
+typedef struct _mplp_aux_t mplp_aux_t;
+typedef struct _mplp_pileup_t mplp_pileup_t;
+
+// Data shared by all bam files
+typedef struct {
+    int min_mq, flag, min_baseQ, max_baseQ, delta_baseQ, capQ_thres, max_depth,
+        max_indel_depth, max_read_len, fmt_flag, ambig_reads;
+    int rflag_skip_any_unset, rflag_skip_all_unset, rflag_skip_any_set, rflag_skip_all_set, output_type;
+    int openQ, extQ, tandemQ, min_support, indel_win_size; // for indels
+    double min_frac; // for indels
+    double indel_bias;
+    char *reg_fname, *pl_list, *fai_fname, *output_fname;
+    int reg_is_file, record_cmd_line, n_threads, clevel;
+    faidx_t *fai;
+    regidx_t *bed, *reg;    // bed: skipping regions, reg: index-jump to regions
+    regitr_t *bed_itr, *reg_itr;
+    int bed_logic;          // 1: include region, 0: exclude region
+    gvcf_t *gvcf;
+
+    // auxiliary structures for calling
+    bcf_callaux_t *bca;
+    bcf_callret1_t *bcr;
+    bcf_call_t bc;
+    bam_mplp_t iter;
+    mplp_aux_t **mplp_data;
+    int nfiles;
+    char **files;
+    mplp_pileup_t *gplp;
+    int *n_plp;
+    const bam_pileup1_t **plp;
+    bam_smpl_t *bsmpl;
+    kstring_t buf;
+    bcf1_t *bcf_rec;
+    htsFile *bcf_fp;
+    bcf_hdr_t *bcf_hdr;
+    int argc;
+    char **argv;
+} mplp_conf_t;
+
+typedef struct {
+    char *ref[2];
+    int ref_id[2];
+    int ref_len[2];
+} mplp_ref_t;
+
+#define MPLP_REF_INIT {{NULL,NULL},{-1,-1},{0,0}}
+
+// Data specific to each bam file
+struct _mplp_aux_t {
+    samFile *fp;
+    hts_itr_t *iter;
+    bam_hdr_t *h;
+    mplp_ref_t *ref;
+    const mplp_conf_t *conf;
+    int bam_id;
+    hts_idx_t *idx;     // maintained only with more than one -r regions
+};
+
+// Data passed to htslib/mpileup
+struct _mplp_pileup_t {
+    int n;
+    int *n_plp, *m_plp;
+    bam_pileup1_t **plp;
+};
+
+static int mplp_get_ref(mplp_aux_t *ma, int tid,  char **ref, int *ref_len) {
+    mplp_ref_t *r = ma->ref;
+
+    //printf("get ref %d {%d/%p, %d/%p}\n", tid, r->ref_id[0], r->ref[0], r->ref_id[1], r->ref[1]);
+
+    if (!r || !ma->conf->fai) {
+        *ref = NULL;
+        return 0;
+    }
+
+    // Do we need to reference count this so multiple mplp_aux_t can
+    // track which references are in use?
+    // For now we just cache the last two. Sufficient?
+    if (tid == r->ref_id[0]) {
+        *ref = r->ref[0];
+        *ref_len = r->ref_len[0];
+        return 1;
+    }
+    if (tid == r->ref_id[1]) {
+        // Last, swap over
+        int tmp;
+        tmp = r->ref_id[0];  r->ref_id[0]  = r->ref_id[1];  r->ref_id[1]  = tmp;
+        tmp = r->ref_len[0]; r->ref_len[0] = r->ref_len[1]; r->ref_len[1] = tmp;
+
+        char *tc;
+        tc = r->ref[0]; r->ref[0] = r->ref[1]; r->ref[1] = tc;
+        *ref = r->ref[0];
+        *ref_len = r->ref_len[0];
+        return 1;
+    }
+
+    // New, so migrate to old and load new
+    free(r->ref[1]);
+    r->ref[1]     = r->ref[0];
+    r->ref_id[1]  = r->ref_id[0];
+    r->ref_len[1] = r->ref_len[0];
+
+    r->ref_id[0] = tid;
+    r->ref[0] = faidx_fetch_seq(ma->conf->fai,
+                                ma->h->target_name[r->ref_id[0]],
+                                0,
+                                INT_MAX,
+                                &r->ref_len[0]);
+
+    if (!r->ref[0]) {
+        r->ref[0] = NULL;
+        r->ref_id[0] = -1;
+        r->ref_len[0] = 0;
+        *ref = NULL;
+        return 0;
+    }
+
+    *ref = r->ref[0];
+    *ref_len = r->ref_len[0];
+    return 1;
+}
+
+static int mplp_func(void *data, bam1_t *b)
+{
+    char *ref;
+    mplp_aux_t *ma = (mplp_aux_t*)data;
+    int ret, ref_len;
+    while (1)
+    {
+        int has_ref;
+        ret = ma->iter? sam_itr_next(ma->fp, ma->iter, b) : sam_read1(ma->fp, ma->h, b);
+        if (ret < 0) break;
+        // The 'B' cigar operation is not part of the specification, considering as obsolete.
+        //  bam_remove_B(b);
+        if (b->core.tid < 0 || (b->core.flag&BAM_FUNMAP)) continue; // exclude unmapped reads
+        if (ma->conf->rflag_skip_any_unset && (ma->conf->rflag_skip_any_unset&b->core.flag)!=ma->conf->rflag_skip_any_unset) continue;
+        if (ma->conf->rflag_skip_all_set && (ma->conf->rflag_skip_all_set&b->core.flag)==ma->conf->rflag_skip_all_set) continue;
+        if (ma->conf->rflag_skip_all_unset && !(ma->conf->rflag_skip_all_unset&b->core.flag)) continue;
+        if (ma->conf->rflag_skip_any_set && ma->conf->rflag_skip_any_set&b->core.flag) continue;
+        if (ma->conf->bed)
+        {
+            // test overlap
+            regitr_t *itr = ma->conf->bed_itr;
+            int beg = b->core.pos, end = bam_endpos(b)-1;
+            int overlap = regidx_overlap(ma->conf->bed, ma->h->target_name[b->core.tid],beg,end, itr);
+            if ( !ma->conf->bed_logic && !overlap )
+            {
+                // exclude only reads which are fully contained in the region
+                while ( regitr_overlap(itr) )
+                {
+                    if ( beg < itr->beg ) { overlap = 1; break; }
+                    if ( end > itr->end ) { overlap = 1; break; }
+                }
+            }
+            if ( !overlap ) continue;
+        }
+        if ( bam_smpl_get_sample_id(ma->conf->bsmpl,ma->bam_id,b)<0 ) continue;
+        if (ma->conf->flag & MPLP_ILLUMINA13) {
+            int i;
+            uint8_t *qual = bam_get_qual(b);
+            for (i = 0; i < b->core.l_qseq; ++i)
+                qual[i] = qual[i] > 31? qual[i] - 31 : 0;
+        }
+
+        if (ma->conf->fai && b->core.tid >= 0) {
+            has_ref = mplp_get_ref(ma, b->core.tid, &ref, &ref_len);
+            if (has_ref && ref_len <= b->core.pos) { // exclude reads outside of the reference sequence
+                fprintf(bcftools_stderr,"[%s] Skipping because %"PRId64" is outside of %d [ref:%d]\n",
+                        __func__, (int64_t) b->core.pos, ref_len, b->core.tid);
+                continue;
+            }
+        } else {
+            has_ref = 0;
+        }
+
+        // Allow sufficient room for bam_aux_append of ZQ tag without
+        // a realloc and consequent breakage of pileup's cached pointers.
+        if (has_ref && (ma->conf->flag &MPLP_REALN) && !bam_aux_get(b, "ZQ")) {
+            // Doing sam_prob_realn later is problematic as it adds to
+            // the tag list (ZQ or BQ), which causes a realloc of b->data.
+            // This happens after pileup has built a hash table on the
+            // read name.  It's a deficiency in pileup IMO.
+
+            // We could implement a new sam_prob_realn that returns ZQ
+            // somewhere else and cache it ourselves (pileup clientdata),
+            // but for now we simply use a workaround.
+            //
+            // We create a fake tag of the correct length, which we remove
+            // just prior calling sam_prob_realn so we can guarantee there is
+            // room. (We can't just make room now as bam_copy1 removes it
+            // again).
+            if (b->core.l_qseq > 500) {
+                uint8_t *ZQ = malloc((uint32_t)b->core.l_qseq+1);
+                memset(ZQ, '@', b->core.l_qseq);
+                ZQ[b->core.l_qseq] = 0;
+                bam_aux_append(b, "_Q", 'Z', b->core.l_qseq+1, ZQ);
+                free(ZQ);
+            } else {
+                static uint8_t ZQ[501] =
+                    "@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@"
+                    "@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@"
+                    "@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@"
+                    "@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@"
+                    "@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@"
+                    "@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@"
+                    "@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@"
+                    "@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@"
+                    "@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@"
+                    "@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@";
+                ZQ[b->core.l_qseq] = 0;
+                bam_aux_append(b, "_Q", 'Z', b->core.l_qseq+1, ZQ);
+                ZQ[b->core.l_qseq] = '@';
+            }
+        }
+
+        if (has_ref && ma->conf->capQ_thres > 10) {
+            int q = sam_cap_mapq(b, ref, ref_len, ma->conf->capQ_thres);
+            if (q < 0) continue;    // skip
+            else if (b->core.qual > q) b->core.qual = q;
+        }
+        if (b->core.qual < ma->conf->min_mq) continue;
+        else if ((ma->conf->flag&MPLP_NO_ORPHAN) && (b->core.flag&BAM_FPAIRED) && !(b->core.flag&BAM_FPROPER_PAIR)) continue;
+
+        return ret;
+    };
+    return ret;
+}
+
+// Called once per new bam added to the pileup.
+// We cache sample information here so we don't have to keep recomputing this
+// on each and every pileup column. If FMT/SCR annotation is requested, a flag
+// is set to indicate the presence of a soft clip.
+//
+// Cd is an arbitrary block of data we can write into, which ends up in
+// the pileup structures. We stash the sample ID there:
+//      has_soft_clip .. cd->i & 1
+//      sample_id     .. cd->i >> 1
+static int pileup_constructor(void *data, const bam1_t *b, bam_pileup_cd *cd)
+{
+    mplp_aux_t *ma = (mplp_aux_t *)data;
+    int n = bam_smpl_get_sample_id(ma->conf->bsmpl, ma->bam_id, (bam1_t *)b);
+    cd->i = 0;
+    PLP_SET_SAMPLE_ID(cd->i, n);
+    // Whether read has a soft-clip is used in mplp_realn's heuristics.
+    // TODO: consider whether clip length is beneficial to use?
+    int i;
+    for (i=0; i<b->core.n_cigar; i++) {
+        int cig = bam_get_cigar(b)[i] & BAM_CIGAR_MASK;
+        if (cig == BAM_CSOFT_CLIP) {
+            PLP_SET_SOFT_CLIP(cd->i);
+            break;
+        }
+    }
+
+    if (ma->conf->flag & MPLP_REALN) {
+        int i;
+        // int tot_ins = 0;
+        // int p = 0;
+        uint32_t *cigar = bam_get_cigar(b);
+        for (i=0; i<b->core.n_cigar; i++) {
+            int cig = cigar[i] & BAM_CIGAR_MASK;
+            // if (bam_cigar_type(cig) & 2)
+            //     p += cigar[i] >> BAM_CIGAR_SHIFT;
+            if (cig == BAM_CINS || cig == BAM_CDEL || cig == BAM_CREF_SKIP) {
+                // tot_ins += cigar[i] >> BAM_CIGAR_SHIFT;
+                // Possible further optimsation, check tot_ins==1 later
+                // (and remove break) so we can detect single bp indels.
+                // We may want to focus BAQ on more complex regions only.
+                PLP_SET_INDEL(cd->i);
+                break;
+            }
+
+            // TODO: proper p->cd struct and have cd->i as a size rather
+            // than a flag.
+
+            // Then aggregate together the sizes and if just 1 size for all
+            // reads or 2 sizes for approx 50/50 split in all reads, then
+            // treat this as a well-aligned variant and don't run BAQ.
+        }
+    }
+
+    return 0;
+}
+
+static void group_smpl(mplp_pileup_t *m, bam_smpl_t *bsmpl, int n, int *n_plp, const bam_pileup1_t **plp)
+{
+    int i, j;
+    memset(m->n_plp, 0, m->n * sizeof(int));
+    for (i = 0; i < n; ++i) // iterate over all bams
+    {
+        for (j = 0; j < n_plp[i]; ++j)  // iterate over all reads available at this position
+        {
+            const bam_pileup1_t *p = plp[i] + j;
+            int id = PLP_SAMPLE_ID(p->cd.i);
+            if (m->n_plp[id] == m->m_plp[id])
+            {
+                m->m_plp[id] = m->m_plp[id]? m->m_plp[id]<<1 : 8;
+                m->plp[id] = (bam_pileup1_t*) realloc(m->plp[id], sizeof(bam_pileup1_t) * m->m_plp[id]);
+            }
+            m->plp[id][m->n_plp[id]++] = *p;
+        }
+    }
+}
+
+static void flush_bcf_records(mplp_conf_t *conf, htsFile *fp, bcf_hdr_t *hdr, bcf1_t *rec)
+{
+    if ( !conf->gvcf )
+    {
+        if ( rec && bcf_write1(fp, hdr, rec)!=0 ) error("[%s] Error: failed to write the record to %s\n", __func__,conf->output_fname?conf->output_fname:"standard output");
+        return;
+    }
+
+    if ( !rec )
+    {
+        gvcf_write(conf->gvcf, fp, hdr, NULL, 0);
+        return;
+    }
+
+    int is_ref = 0;
+    if ( rec->n_allele==1 ) is_ref = 1;
+    else if ( rec->n_allele==2 )
+    {
+        // second allele is mpileup's X, not a variant
+        if ( rec->d.allele[1][0]=='<' && rec->d.allele[1][1]=='*' && rec->d.allele[1][2]=='>' ) is_ref = 1;
+    }
+    rec = gvcf_write(conf->gvcf, fp, hdr, rec, is_ref);
+    if ( rec && bcf_write1(fp,hdr,rec)!=0 ) error("[%s] Error: failed to write the record to %s\n", __func__,conf->output_fname?conf->output_fname:"standard output");
+}
+
+/*
+ * Loops for an indel at this position.
+ *
+ * Only reads that overlap an indel loci get realigned.  This considerably
+ * reduces the cost of running BAQ while keeping the main benefits.
+ *
+ * TODO: also consider only realigning reads that don't span the indel
+ * by more than a certain amount either-side.  Ie focus BAQ only on reads
+ * ending adjacent to the indel, where the alignment is most likely to
+ * be wrong.  (2nd TODO: do this based on sequence context; STRs bad, unique
+ * data good.)
+ *
+ * NB: this may sadly realign after we've already used the data.  Hmm...
+ */
+static void mplp_realn(int n, int *n_plp, const bam_pileup1_t **plp,
+                       int flag, int max_read_len,
+                       char *ref, int ref_len, int pos) {
+    int i, j, has_indel = 0, has_clip = 0, nt = 0;
+    int min_indel = INT_MAX, max_indel = INT_MIN;
+
+    // Is an indel present.
+    // NB: don't bother even checking if very long as almost guaranteed
+    // to have indel (and likely soft-clips too).
+    for (i = 0; i < n; i++) { // iterate over bams
+        nt += n_plp[i];
+        for (j = 0; j < n_plp[i]; j++) { // iterate over reads
+            bam_pileup1_t *p = (bam_pileup1_t *)plp[i] + j;
+            has_indel += (PLP_HAS_INDEL(p->cd.i) || p->indel) ? 1 : 0;
+            // Has_clip is almost always true for very long reads
+            // (eg PacBio CCS), but these rarely matter as the clip
+            // is likely a long way from this indel.
+            has_clip  += (PLP_HAS_SOFT_CLIP(p->cd.i))         ? 1 : 0;
+            if (max_indel < p->indel)
+                max_indel = p->indel;
+            if (min_indel > p->indel)
+                min_indel = p->indel;
+        }
+    }
+
+    if (flag & MPLP_REALN_PARTIAL) {
+        if (has_indel == 0 ||
+            (has_clip < 0.2*nt && max_indel == min_indel &&
+             (has_indel < 0.1*nt /*|| has_indel > 0.9*nt*/ || has_indel == 1)))
+            return;
+    }
+
+    // Realign
+    for (i = 0; i < n; i++) { // iterate over bams
+        for (j = 0; j < n_plp[i]; j++) { // iterate over reads
+            const bam_pileup1_t *p = plp[i] + j;
+            bam1_t *b = p->b;
+
+            // Avoid doing multiple times.
+            //
+            // Note we cannot modify p->cd.i here with a PLP_SET macro
+            // because the cd item is held by mpileup in an lbnode_t
+            // struct and copied over to the pileup struct for each
+            // iteration, essentially making p->cd.i read only.
+            //
+            // We could use our own structure (p->cd.p), allocated during
+            // the constructor, but for simplicity we play dirty and
+            // abuse an unused flag bit instead.
+            if (b->core.flag & 32768)
+                continue;
+            b->core.flag |= 32768;
+
+            if (b->core.l_qseq > max_read_len)
+                continue;
+
+            // Check p->cigar_ind and see what cigar elements are before
+            // and after.  How close is this location to the end of the
+            // read?  Only realign if we don't span by more than X bases.
+            //
+            // Again, best only done on deeper data as BAQ helps
+            // disproportionately more on shallow data sets.
+            //
+            // This rescues some of the false negatives that are caused by
+            // systematic reduction in quality due to sample vs ref alignment.
+
+// At deep coverage we skip realigning more reads as we have sufficient depth.
+// This rescues for false negatives.  At shallow depth we pay for this with
+// more FP so are more stringent on spanning size.
+#define REALN_DIST (40+10*(nt<40)+10*(nt<20))
+            uint32_t *cig = bam_get_cigar(b);
+            int ncig = b->core.n_cigar;
+
+            // Don't realign reads where indel is in middle?
+            // On long read data we don't care about soft-clips at the ends.
+            // For short read data, we always calc BAQ on these as they're
+            // a common source of false positives.
+            if ((flag & MPLP_REALN_PARTIAL) && nt > 15 && ncig > 1) {
+                // Left & right cigar op match.
+                int lr = b->core.l_qseq > 500;
+                int lm = 0, rm = 0, k;
+                for (k = 0; k < ncig; k++) {
+                    int cop = bam_cigar_op(cig[k]);
+                    if (lr && (cop == BAM_CHARD_CLIP || cop == BAM_CSOFT_CLIP))
+                        continue;
+
+                    if (cop == BAM_CMATCH || cop == BAM_CDIFF ||
+                        cop == BAM_CEQUAL)
+                        lm += bam_cigar_oplen(cig[k]);
+                    else
+                        break;
+                }
+
+                for (k = ncig-1; k >= 0; k--) {
+                    int cop = bam_cigar_op(cig[k]);
+                    if (lr && (cop == BAM_CHARD_CLIP || cop == BAM_CSOFT_CLIP))
+                        continue;
+
+                    if (cop == BAM_CMATCH || cop == BAM_CDIFF ||
+                        cop == BAM_CEQUAL)
+                        rm += bam_cigar_oplen(cig[k]);
+                    else
+                        break;
+                }
+
+                if (lm >= REALN_DIST*4 && rm >= REALN_DIST*4)
+                    continue;
+
+                if (lm >= REALN_DIST && rm >= REALN_DIST &&
+                    has_clip < (0.15+0.05*(nt>20))*nt)
+                    continue;
+            }
+
+            if (b->core.l_qseq > 500) {
+                // don't do BAQ on long-read data if it's going to
+                // cause us to have a large band-with and costly in CPU
+                int rl = bam_cigar2rlen(b->core.n_cigar, bam_get_cigar(b));
+                if (abs(rl - b->core.l_qseq) * b->core.l_qseq >= 500000)
+                    continue;
+            }
+
+            // Fudge: make room for ZQ tag.
+            uint8_t *_Q = bam_aux_get(b, "_Q");
+            if (_Q) bam_aux_del(b, _Q);
+            sam_prob_realn(b, ref, ref_len, (flag & MPLP_REDO_BAQ) ? 7 : 3);
+        }
+    }
+
+    return;
+}
+
+static int mpileup_reg(mplp_conf_t *conf, uint32_t beg, uint32_t end)
+{
+    bam_hdr_t *hdr = conf->mplp_data[0]->h; // header of first file in input list
+
+    int ret, i, tid, pos, ref_len;
+    char *ref;
+
+    while ( (ret=bam_mplp_auto(conf->iter, &tid, &pos, conf->n_plp, conf->plp)) > 0)
+    {
+        if ( pos<beg || pos>end ) continue;
+        if ( conf->bed && tid >= 0 )
+        {
+            int overlap = regidx_overlap(conf->bed, hdr->target_name[tid], pos, pos, NULL);
+            if ( !conf->bed_logic ) overlap = overlap ? 0 : 1;
+            if ( !overlap ) continue;
+        }
+        int has_ref = mplp_get_ref(conf->mplp_data[0], tid, &ref, &ref_len);
+        if (has_ref && (conf->flag & MPLP_REALN))
+            mplp_realn(conf->nfiles, conf->n_plp, conf->plp, conf->flag,
+                       conf->max_read_len, ref, ref_len, pos);
+
+        int total_depth, _ref0, ref16;
+        for (i = total_depth = 0; i < conf->nfiles; ++i) total_depth += conf->n_plp[i];
+        group_smpl(conf->gplp, conf->bsmpl, conf->nfiles, conf->n_plp, conf->plp);
+        _ref0 = (ref && pos < ref_len)? ref[pos] : 'N';
+        ref16 = seq_nt16_table[_ref0];
+        bcf_callaux_clean(conf->bca, &conf->bc);
+        for (i = 0; i < conf->gplp->n; ++i)
+            bcf_call_glfgen(conf->gplp->n_plp[i], conf->gplp->plp[i], ref16, conf->bca, conf->bcr + i);
+        conf->bc.tid = tid; conf->bc.pos = pos;
+        bcf_call_combine(conf->gplp->n, conf->bcr, conf->bca, ref16, &conf->bc);
+        bcf_clear1(conf->bcf_rec);
+        bcf_call2bcf(&conf->bc, conf->bcf_rec, conf->bcr, conf->fmt_flag,
+                     conf->bca, 0);
+        flush_bcf_records(conf, conf->bcf_fp, conf->bcf_hdr, conf->bcf_rec);
+
+        // call indels; todo: subsampling with total_depth>max_indel_depth instead of ignoring?
+        // check me: rghash in bcf_call_gap_prep() should have no effect, reads mplp_func already excludes them
+        if (!(conf->flag&MPLP_NO_INDEL) && total_depth < conf->max_indel_depth
+            && (bcf_callaux_clean(conf->bca, &conf->bc),
+                bcf_call_gap_prep(conf->gplp->n, conf->gplp->n_plp, conf->gplp->plp, pos, conf->bca, ref) >= 0))
+        {
+            for (i = 0; i < conf->gplp->n; ++i)
+                bcf_call_glfgen(conf->gplp->n_plp[i], conf->gplp->plp[i], -1, conf->bca, conf->bcr + i);
+            if (bcf_call_combine(conf->gplp->n, conf->bcr, conf->bca, -1, &conf->bc) >= 0)
+            {
+                bcf_clear1(conf->bcf_rec);
+                bcf_call2bcf(&conf->bc, conf->bcf_rec, conf->bcr, conf->fmt_flag, conf->bca, ref);
+                flush_bcf_records(conf, conf->bcf_fp, conf->bcf_hdr, conf->bcf_rec);
+            }
+        }
+    }
+    return 0;
+}
+
+static int mpileup(mplp_conf_t *conf)
+{
+    if (conf->nfiles == 0) {
+        fprintf(bcftools_stderr,"[%s] no input file/data given\n", __func__);
+        bcftools_exit(EXIT_FAILURE);
+    }
+
+    mplp_ref_t mp_ref = MPLP_REF_INIT;
+    conf->gplp = (mplp_pileup_t *) calloc(1,sizeof(mplp_pileup_t));
+    conf->mplp_data = (mplp_aux_t**) calloc(conf->nfiles, sizeof(mplp_aux_t*));
+    conf->plp = (const bam_pileup1_t**) calloc(conf->nfiles, sizeof(bam_pileup1_t*));
+    conf->n_plp = (int*) calloc(conf->nfiles, sizeof(int));
+
+    // Allow to run mpileup on multiple regions in one go. This comes at cost: the bai index
+    // must be kept in the memory for the whole time which can be a problem with many bams.
+    // Therefore if none or only one region is requested, we initialize the bam iterator as
+    // before and free the index. Only when multiple regions are queried, we keep the index.
+    int nregs = 0;
+    if ( conf->reg_fname )
+    {
+        if ( conf->reg_is_file )
+        {
+            conf->reg = regidx_init(conf->reg_fname,NULL,NULL,0,NULL);
+            if ( !conf->reg ) {
+                fprintf(bcftools_stderr,"Could not parse the regions: %s\n", conf->reg_fname);
+                bcftools_exit(EXIT_FAILURE);
+            }
+        }
+        else
+        {
+            conf->reg = regidx_init(NULL,regidx_parse_reg,NULL,sizeof(char*),NULL);
+            if ( regidx_insert_list(conf->reg,conf->reg_fname,',') !=0 ) {
+                fprintf(bcftools_stderr,"Could not parse the regions: %s\n", conf->reg_fname);
+                bcftools_exit(EXIT_FAILURE);
+            }
+        }
+        nregs = regidx_nregs(conf->reg);
+        conf->reg_itr = regitr_init(conf->reg);
+        regitr_loop(conf->reg_itr);   // region iterator now positioned at the first region
+    }
+
+    // read the header of each file in the list and initialize data
+    // beware: mpileup has always assumed that tid's are consistent in the headers, add sanity check at least!
+    bam_hdr_t *hdr = NULL;      // header of first file in input list
+    int i;
+    for (i = 0; i < conf->nfiles; ++i) {
+        bam_hdr_t *h_tmp;
+        conf->mplp_data[i] = (mplp_aux_t*) calloc(1, sizeof(mplp_aux_t));
+        conf->mplp_data[i]->fp = sam_open(conf->files[i], "rb");
+        if ( !conf->mplp_data[i]->fp )
+        {
+            fprintf(bcftools_stderr, "[%s] failed to open %s: %s\n", __func__, conf->files[i], strerror(errno));
+            bcftools_exit(EXIT_FAILURE);
+        }
+        if (hts_set_opt(conf->mplp_data[i]->fp, CRAM_OPT_DECODE_MD, 1)) {
+            fprintf(bcftools_stderr, "Failed to set CRAM_OPT_DECODE_MD value\n");
+            bcftools_exit(EXIT_FAILURE);
+        }
+        if (conf->fai_fname && hts_set_fai_filename(conf->mplp_data[i]->fp, conf->fai_fname) != 0) {
+            fprintf(bcftools_stderr, "[%s] failed to process %s: %s\n",
+                    __func__, conf->fai_fname, strerror(errno));
+            bcftools_exit(EXIT_FAILURE);
+        }
+        conf->mplp_data[i]->conf = conf;
+        conf->mplp_data[i]->ref = &mp_ref;
+        h_tmp = sam_hdr_read(conf->mplp_data[i]->fp);
+        if ( !h_tmp ) {
+            fprintf(bcftools_stderr,"[%s] fail to read the header of %s\n", __func__, conf->files[i]);
+            bcftools_exit(EXIT_FAILURE);
+        }
+        conf->mplp_data[i]->h = i ? hdr : h_tmp; // for j==0, "h" has not been set yet
+        conf->mplp_data[i]->bam_id = bam_smpl_add_bam(conf->bsmpl,h_tmp->text,conf->files[i]);
+        if ( conf->mplp_data[i]->bam_id<0 )
+        {
+            // no usable readgroups in this bam, it can be skipped
+            sam_close(conf->mplp_data[i]->fp);
+            free(conf->mplp_data[i]);
+            bam_hdr_destroy(h_tmp);
+            free(conf->files[i]);
+            if ( i+1<conf->nfiles ) memmove(&conf->files[i],&conf->files[i+1],sizeof(*conf->files)*(conf->nfiles-i-1));
+            conf->nfiles--;
+            i--;
+            continue;
+        }
+        if (conf->reg) {
+            hts_idx_t *idx = sam_index_load(conf->mplp_data[i]->fp, conf->files[i]);
+            if (idx == NULL) {
+                fprintf(bcftools_stderr, "[%s] fail to load index for %s\n", __func__, conf->files[i]);
+                bcftools_exit(EXIT_FAILURE);
+            }
+            conf->buf.l = 0;
+            ksprintf(&conf->buf,"%s:%u-%u",conf->reg_itr->seq,conf->reg_itr->beg+1,conf->reg_itr->end+1);
+            conf->mplp_data[i]->iter = sam_itr_querys(idx, conf->mplp_data[i]->h, conf->buf.s);
+            if ( !conf->mplp_data[i]->iter )
+            {
+                conf->mplp_data[i]->iter = sam_itr_querys(idx, conf->mplp_data[i]->h, conf->reg_itr->seq);
+                if ( conf->mplp_data[i]->iter ) {
+                    fprintf(bcftools_stderr,"[E::%s] fail to parse region '%s'\n", __func__, conf->buf.s);
+                    bcftools_exit(EXIT_FAILURE);
+                }
+                fprintf(bcftools_stderr,"[E::%s] the sequence \"%s\" not found: %s\n",__func__,conf->reg_itr->seq,conf->files[i]);
+                bcftools_exit(EXIT_FAILURE);
+            }
+            if ( nregs==1 ) // no need to keep the index in memory
+               hts_idx_destroy(idx);
+            else
+                conf->mplp_data[i]->idx = idx;
+        }
+
+        if ( !hdr ) hdr = h_tmp; /* save the header of first file in list */
+        else {
+            // FIXME: check consistency between h and h_tmp
+            bam_hdr_destroy(h_tmp);
+
+            // we store only the first file's header; it's (alleged to be)
+            // compatible with the i-th file's target_name lookup needs
+            conf->mplp_data[i]->h = hdr;
+        }
+    }
+    if ( !hdr ) {
+        fprintf(bcftools_stderr, "[%s] failed to find a file header with usable read groups\n", __func__);
+        bcftools_exit(EXIT_FAILURE);
+    }
+    // allocate data storage proportionate to number of samples being studied sm->n
+    bam_smpl_get_samples(conf->bsmpl, &conf->gplp->n);
+    conf->gplp->n_plp = (int*) calloc(conf->gplp->n, sizeof(int));
+    conf->gplp->m_plp = (int*) calloc(conf->gplp->n, sizeof(int));
+    conf->gplp->plp = (bam_pileup1_t**) calloc(conf->gplp->n, sizeof(bam_pileup1_t*));
+
+    fprintf(bcftools_stderr, "[%s] %d samples in %d input files\n", __func__, conf->gplp->n, conf->nfiles);
+    // write the VCF header
+    char wmode[8];
+    set_wmode(wmode,conf->output_type,conf->output_fname,conf->clevel);
+    conf->bcf_fp = hts_open(conf->output_fname ? conf->output_fname : "-", wmode);
+    if (conf->bcf_fp == NULL) {
+        fprintf(bcftools_stderr, "[%s] failed to write to %s: %s\n", __func__, conf->output_fname? conf->output_fname : "standard output", strerror(errno));
+        bcftools_exit(EXIT_FAILURE);
+    }
+    if ( conf->n_threads ) hts_set_threads(conf->bcf_fp, conf->n_threads);
+
+    // BCF header creation
+    conf->bcf_hdr = bcf_hdr_init("w");
+    conf->buf.l = 0;
+
+    if (conf->record_cmd_line)
+    {
+        ksprintf(&conf->buf, "##bcftoolsVersion=%s+htslib-%s\n",bcftools_version(),hts_version());
+        bcf_hdr_append(conf->bcf_hdr, conf->buf.s);
+
+        conf->buf.l = 0;
+        ksprintf(&conf->buf, "##bcftoolsCommand=mpileup");
+        for (i=1; i<conf->argc; i++) ksprintf(&conf->buf, " %s", conf->argv[i]);
+        kputc('\n', &conf->buf);
+        bcf_hdr_append(conf->bcf_hdr, conf->buf.s);
+    }
+
+    if (conf->fai_fname)
+    {
+        conf->buf.l = 0;
+        ksprintf(&conf->buf, "##reference=file://%s\n", conf->fai_fname);
+        bcf_hdr_append(conf->bcf_hdr, conf->buf.s);
+    }
+
+    // Translate BAM @SQ tags to BCF ##contig tags
+    // todo: use/write new BAM header manipulation routines, fill also UR, M5
+    for (i=0; i<hdr->n_targets; i++)
+    {
+        conf->buf.l = 0;
+        ksprintf(&conf->buf, "##contig=<ID=%s,length=%d>", hdr->target_name[i], hdr->target_len[i]);
+        bcf_hdr_append(conf->bcf_hdr, conf->buf.s);
+    }
+    conf->buf.l = 0;
+
+    bcf_hdr_append(conf->bcf_hdr,"##ALT=<ID=*,Description=\"Represents allele(s) other than observed.\">");
+    bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=INDEL,Number=0,Type=Flag,Description=\"Indicates that the variant is an INDEL.\">");
+    bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=IDV,Number=1,Type=Integer,Description=\"Maximum number of raw reads supporting an indel\">");
+    bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=IMF,Number=1,Type=Float,Description=\"Maximum fraction of raw reads supporting an indel\">");
+    bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Raw read depth\">");
+    if ( conf->fmt_flag&B2B_INFO_VDB )
+        bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=VDB,Number=1,Type=Float,Description=\"Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)\",Version=\"3\">");
+
+    if (conf->fmt_flag & B2B_INFO_ZSCORE) {
+        if ( conf->fmt_flag&B2B_INFO_RPB )
+            bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=RPBZ,Number=1,Type=Float,Description=\"Mann-Whitney U-z test of Read Position Bias (closer to 0 is better)\">");
+        bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=MQBZ,Number=1,Type=Float,Description=\"Mann-Whitney U-z test of Mapping Quality Bias (closer to 0 is better)\">");
+        bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=BQBZ,Number=1,Type=Float,Description=\"Mann-Whitney U-z test of Base Quality Bias (closer to 0 is better)\">");
+        bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=MQSBZ,Number=1,Type=Float,Description=\"Mann-Whitney U-z test of Mapping Quality vs Strand Bias (closer to 0 is better)\">");
+        bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=NMBZ,Number=1,Type=Float,Description=\"Mann-Whitney U-z test of Number of Mismatches within supporting reads (closer to 0 is better)\">");
+        if ( conf->fmt_flag&B2B_FMT_NMBZ )
+            bcf_hdr_append(conf->bcf_hdr,"##FORMAT=<ID=NMBZ,Number=1,Type=Float,Description=\"Mann-Whitney U-z test of Number of Mismatches within supporting reads (closer to 0 is better)\">");
+        if ( conf->fmt_flag&B2B_INFO_SCB )
+            bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=SCBZ,Number=1,Type=Float,Description=\"Mann-Whitney U-z test of Soft-Clip Length Bias (closer to 0 is better)\">");
+    } else {
+        if ( conf->fmt_flag&B2B_INFO_RPB )
+            bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=RPB,Number=1,Type=Float,Description=\"Mann-Whitney U test of Read Position Bias (bigger is better)\">");
+        bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=MQB,Number=1,Type=Float,Description=\"Mann-Whitney U test of Mapping Quality Bias (bigger is better)\">");
+        bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=BQB,Number=1,Type=Float,Description=\"Mann-Whitney U test of Base Quality Bias (bigger is better)\">");
+        bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=MQSB,Number=1,Type=Float,Description=\"Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better)\">");
+    }
+
+    bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=FS,Number=1,Type=Float,Description=\"Phred-scaled p-value using Fisher's exact test to detect strand bias\">");
+#if CDF_MWU_TESTS
+    bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=RPB2,Number=1,Type=Float,Description=\"Mann-Whitney U test of Read Position Bias [CDF] (bigger is better)\">");
+    bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=MQB2,Number=1,Type=Float,Description=\"Mann-Whitney U test of Mapping Quality Bias [CDF] (bigger is better)\">");
+    bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=BQB2,Number=1,Type=Float,Description=\"Mann-Whitney U test of Base Quality Bias [CDF] (bigger is better)\">");
+    bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=MQSB2,Number=1,Type=Float,Description=\"Mann-Whitney U test of Mapping Quality vs Strand Bias [CDF] (bigger is better)\">");
+#endif
+    bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=SGB,Number=1,Type=Float,Description=\"Segregation based metric.\">");
+    bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=MQ0F,Number=1,Type=Float,Description=\"Fraction of MQ0 reads (smaller is better)\">");
+    bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=I16,Number=16,Type=Float,Description=\"Auxiliary tag used for calling, see description of bcf_callret1_t in bam2bcf.h\">");
+    bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=QS,Number=R,Type=Float,Description=\"Auxiliary tag used for calling\">");
+    bcf_hdr_append(conf->bcf_hdr,"##FORMAT=<ID=PL,Number=G,Type=Integer,Description=\"List of Phred-scaled genotype likelihoods\">");
+    if ( conf->fmt_flag&B2B_FMT_DP )
+        bcf_hdr_append(conf->bcf_hdr,"##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Number of high-quality bases\">");
+    if ( conf->fmt_flag&B2B_FMT_DV )
+        bcf_hdr_append(conf->bcf_hdr,"##FORMAT=<ID=DV,Number=1,Type=Integer,Description=\"Number of high-quality non-reference bases\">");
+    if ( conf->fmt_flag&B2B_FMT_DPR )
+        bcf_hdr_append(conf->bcf_hdr,"##FORMAT=<ID=DPR,Number=R,Type=Integer,Description=\"Number of high-quality bases observed for each allele\">");
+    if ( conf->fmt_flag&B2B_INFO_DPR )
+        bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=DPR,Number=R,Type=Integer,Description=\"Number of high-quality bases observed for each allele\">");
+    if ( conf->fmt_flag&B2B_FMT_DP4 )
+        bcf_hdr_append(conf->bcf_hdr,"##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"Number of high-quality ref-fwd, ref-reverse, alt-fwd and alt-reverse bases\">");
+    if ( conf->fmt_flag&B2B_FMT_SP )
+        bcf_hdr_append(conf->bcf_hdr,"##FORMAT=<ID=SP,Number=1,Type=Integer,Description=\"Phred-scaled strand bias P-value\">");
+    if ( conf->fmt_flag&B2B_FMT_AD )
+        bcf_hdr_append(conf->bcf_hdr,"##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths (high-quality bases)\">");
+    if ( conf->fmt_flag&B2B_FMT_ADF )
+        bcf_hdr_append(conf->bcf_hdr,"##FORMAT=<ID=ADF,Number=R,Type=Integer,Description=\"Allelic depths on the forward strand (high-quality bases)\">");
+    if ( conf->fmt_flag&B2B_FMT_ADR )
+        bcf_hdr_append(conf->bcf_hdr,"##FORMAT=<ID=ADR,Number=R,Type=Integer,Description=\"Allelic depths on the reverse strand (high-quality bases)\">");
+    if ( conf->fmt_flag&B2B_FMT_QS )
+        bcf_hdr_append(conf->bcf_hdr,"##FORMAT=<ID=QS,Number=R,Type=Integer,Description=\"Phred-score allele quality sum used by `call -mG` and `+trio-dnm`\">");
+    if ( conf->fmt_flag&B2B_INFO_AD )
+        bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=AD,Number=R,Type=Integer,Description=\"Total allelic depths (high-quality bases)\">");
+    if ( conf->fmt_flag&B2B_INFO_ADF )
+        bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=ADF,Number=R,Type=Integer,Description=\"Total allelic depths on the forward strand (high-quality bases)\">");
+    if ( conf->fmt_flag&B2B_INFO_SCR )
+        bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=SCR,Number=1,Type=Integer,Description=\"Number of soft-clipped reads (at high-quality bases)\">");
+    if ( conf->fmt_flag&B2B_FMT_SCR )
+        bcf_hdr_append(conf->bcf_hdr,"##FORMAT=<ID=SCR,Number=1,Type=Integer,Description=\"Per-sample number of soft-clipped reads (at high-quality bases)\">");
+    if ( conf->fmt_flag&B2B_INFO_ADR )
+        bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=ADR,Number=R,Type=Integer,Description=\"Total allelic depths on the reverse strand (high-quality bases)\">");
+    if ( conf->gvcf )
+        gvcf_update_header(conf->gvcf, conf->bcf_hdr);
+
+    int nsmpl;
+    const char **smpl = bam_smpl_get_samples(conf->bsmpl, &nsmpl);
+    for (i=0; i<nsmpl; i++)
+        bcf_hdr_add_sample(conf->bcf_hdr, smpl[i]);
+    if ( bcf_hdr_write(conf->bcf_fp, conf->bcf_hdr)!=0 ) error("[%s] Error: failed to write the header to %s\n",__func__,conf->output_fname?conf->output_fname:"standard output");
+
+    conf->bca = bcf_call_init(-1., conf->min_baseQ, conf->max_baseQ,
+                              conf->delta_baseQ);
+    conf->bcr = (bcf_callret1_t*) calloc(nsmpl, sizeof(bcf_callret1_t));
+    conf->bca->openQ = conf->openQ, conf->bca->extQ = conf->extQ, conf->bca->tandemQ = conf->tandemQ;
+    conf->bca->indel_bias = conf->indel_bias;
+    conf->bca->min_frac = conf->min_frac;
+    conf->bca->min_support = conf->min_support;
+    conf->bca->per_sample_flt = conf->flag & MPLP_PER_SAMPLE;
+    conf->bca->fmt_flag = conf->fmt_flag;
+    conf->bca->ambig_reads = conf->ambig_reads;
+    conf->bca->indel_win_size = conf->indel_win_size;
+
+    conf->bc.bcf_hdr = conf->bcf_hdr;
+    conf->bc.n  = nsmpl;
+    conf->bc.PL = (int32_t*) malloc(15 * nsmpl * sizeof(*conf->bc.PL));
+    conf->bc.QS = (int32_t*) malloc(nsmpl*sizeof(*conf->bc.QS)*B2B_MAX_ALLELES);
+    for (i=0; i<nsmpl; i++)
+        conf->bcr[i].QS = conf->bc.QS + i*B2B_MAX_ALLELES;
+    if (conf->fmt_flag)
+    {
+        assert( sizeof(float)==sizeof(int32_t) );
+        conf->bc.DP4 = (int32_t*) malloc(nsmpl * sizeof(int32_t) * 4);
+        conf->bc.fmt_arr = (uint8_t*) malloc(nsmpl * sizeof(float)); // all fmt_flag fields, float and int32
+        if ( conf->fmt_flag&(B2B_INFO_DPR|B2B_FMT_DPR|B2B_INFO_AD|B2B_INFO_ADF|B2B_INFO_ADR|B2B_FMT_AD|B2B_FMT_ADF|B2B_FMT_ADR) )
+        {
+            // first B2B_MAX_ALLELES fields for total numbers, the rest per-sample
+            conf->bc.ADR = (int32_t*) malloc((nsmpl+1)*B2B_MAX_ALLELES*sizeof(int32_t));
+            conf->bc.ADF = (int32_t*) malloc((nsmpl+1)*B2B_MAX_ALLELES*sizeof(int32_t));
+            for (i=0; i<nsmpl; i++)
+            {
+                conf->bcr[i].ADR = conf->bc.ADR + (i+1)*B2B_MAX_ALLELES;
+                conf->bcr[i].ADF = conf->bc.ADF + (i+1)*B2B_MAX_ALLELES;
+            }
+        }
+        if ( conf->fmt_flag&(B2B_INFO_SCR|B2B_FMT_SCR) )
+            conf->bc.SCR = (int32_t*) malloc((nsmpl+1)*sizeof(*conf->bc.SCR));
+    }
+    int nnmbz = (conf->fmt_flag&B2B_FMT_NMBZ) ? nsmpl + 1 : 1;
+    conf->bc.ref_nm = (int32_t*) malloc(sizeof(*conf->bc.ref_nm) * nnmbz * B2B_N_NM);
+    conf->bc.alt_nm = (int32_t*) malloc(sizeof(*conf->bc.alt_nm) * nnmbz * B2B_N_NM);
+    conf->bc.mwu_nm = (float*) malloc((nsmpl+1)*sizeof(*conf->bc.mwu_nm));
+    conf->bca->ref_nm = conf->bc.ref_nm;     // this is just to make the arrays available in bcf_call_glfgen()
+    conf->bca->alt_nm = conf->bc.alt_nm;
+    if ( conf->fmt_flag&B2B_FMT_NMBZ )
+    {
+        for (i=0; i<nsmpl; i++) conf->bcr[i].ref_nm = conf->bc.ref_nm + (i+1)*B2B_N_NM;
+        for (i=0; i<nsmpl; i++) conf->bcr[i].alt_nm = conf->bc.alt_nm + (i+1)*B2B_N_NM;
+    }
+
+    // init mpileup
+    conf->iter = bam_mplp_init(conf->nfiles, mplp_func, (void**)conf->mplp_data);
+    if ( conf->flag & MPLP_SMART_OVERLAPS ) bam_mplp_init_overlaps(conf->iter);
+    fprintf(bcftools_stderr, "[%s] maximum number of reads per input file set to -d %d\n",  __func__, conf->max_depth);
+    if ( (double)conf->max_depth * conf->nfiles > 1<<20)
+        fprintf(bcftools_stderr, "Warning: Potential memory hog, up to %.0fM reads in the pileup!\n", (double)conf->max_depth*conf->nfiles);
+    if ( (double)conf->max_depth * conf->nfiles / nsmpl < 250 )
+        fprintf(bcftools_stderr, "Note: The maximum per-sample depth with -d %d is %.1fx\n", conf->max_depth,(double)conf->max_depth * conf->nfiles / nsmpl);
+    bam_mplp_set_maxcnt(conf->iter, conf->max_depth);
+    conf->max_indel_depth = conf->max_indel_depth * nsmpl;
+    conf->bcf_rec = bcf_init1();
+    bam_mplp_constructor(conf->iter, pileup_constructor);
+
+    // Run mpileup for multiple regions
+    if ( nregs )
+    {
+        int ireg = 0;
+        do
+        {
+            // first region is already positioned
+            if ( ireg++ > 0 )
+            {
+                conf->buf.l = 0;
+                ksprintf(&conf->buf,"%s:%u-%u",conf->reg_itr->seq,conf->reg_itr->beg+1,conf->reg_itr->end+1);
+
+                for (i=0; i<conf->nfiles; i++)
+                {
+                    hts_itr_destroy(conf->mplp_data[i]->iter);
+                    conf->mplp_data[i]->iter = sam_itr_querys(conf->mplp_data[i]->idx, conf->mplp_data[i]->h, conf->buf.s);
+                    if ( !conf->mplp_data[i]->iter )
+                    {
+                        conf->mplp_data[i]->iter = sam_itr_querys(conf->mplp_data[i]->idx, conf->mplp_data[i]->h, conf->reg_itr->seq);
+                        if ( conf->mplp_data[i]->iter ) {
+                            fprintf(bcftools_stderr,"[E::%s] fail to parse region '%s'\n", __func__, conf->buf.s);
+                            bcftools_exit(EXIT_FAILURE);
+                        }
+                        fprintf(bcftools_stderr,"[E::%s] the sequence \"%s\" not found: %s\n",__func__,conf->reg_itr->seq,conf->files[i]);
+                        bcftools_exit(EXIT_FAILURE);
+                    }
+                    bam_mplp_reset(conf->iter);
+                }
+            }
+            mpileup_reg(conf,conf->reg_itr->beg,conf->reg_itr->end);
+        }
+        while ( regitr_loop(conf->reg_itr) );
+    }
+    else
+        mpileup_reg(conf,0,UINT32_MAX);
+
+    flush_bcf_records(conf, conf->bcf_fp, conf->bcf_hdr, NULL);
+
+    // clean up
+    free(conf->bc.tmp.s);
+    bcf_destroy1(conf->bcf_rec);
+    if (conf->bcf_fp)
+    {
+        if ( hts_close(conf->bcf_fp)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,conf->output_fname);
+        bcf_hdr_destroy(conf->bcf_hdr);
+        bcf_call_destroy(conf->bca);
+        free(conf->bc.PL);
+        free(conf->bc.DP4);
+        free(conf->bc.ADR);
+        free(conf->bc.ADF);
+        free(conf->bc.SCR);
+        free(conf->bc.QS);
+        free(conf->bc.ref_nm);
+        free(conf->bc.alt_nm);
+        free(conf->bc.fmt_arr);
+        free(conf->bc.mwu_nm);
+        free(conf->bcr);
+    }
+    if ( conf->gvcf ) gvcf_destroy(conf->gvcf);
+    free(conf->buf.s);
+    for (i = 0; i < conf->gplp->n; ++i) free(conf->gplp->plp[i]);
+    free(conf->gplp->plp); free(conf->gplp->n_plp); free(conf->gplp->m_plp); free(conf->gplp);
+    bam_mplp_destroy(conf->iter);
+    bam_hdr_destroy(hdr);
+    for (i = 0; i < conf->nfiles; ++i) {
+        if ( nregs>1 ) hts_idx_destroy(conf->mplp_data[i]->idx);
+        sam_close(conf->mplp_data[i]->fp);
+        if ( conf->mplp_data[i]->iter) hts_itr_destroy(conf->mplp_data[i]->iter);
+        free(conf->mplp_data[i]);
+    }
+    if ( conf->reg_itr ) regitr_destroy(conf->reg_itr);
+    free(conf->mplp_data); free(conf->plp); free(conf->n_plp);
+    free(mp_ref.ref[0]);
+    free(mp_ref.ref[1]);
+    return 0;
+}
+
+static int is_url(const char *s)
+{
+    static const char uri_scheme_chars[] =
+        "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789+.-";
+    return s[strspn(s, uri_scheme_chars)] == ':';
+}
+
+#define MAX_PATH_LEN 1024
+int read_file_list(const char *file_list,int *n,char **argv[])
+{
+    char buf[MAX_PATH_LEN];
+    int len, nfiles = 0;
+    char **files = NULL;
+    struct stat sb;
+
+    *n = 0;
+    *argv = NULL;
+
+    FILE *fh = fopen(file_list,"r");
+    if ( !fh )
+    {
+        fprintf(bcftools_stderr,"%s: %s\n", file_list,strerror(errno));
+        return 1;
+    }
+
+    files = (char**) calloc(nfiles,sizeof(char*));
+    nfiles = 0;
+    while ( fgets(buf,MAX_PATH_LEN,fh) )
+    {
+        // allow empty lines and trailing spaces
+        len = strlen(buf);
+        while ( len>0 && isspace(buf[len-1]) ) len--;
+        if ( !len ) continue;
+
+        // check sanity of the file list
+        buf[len] = 0;
+        if (! (is_url(buf) || stat(buf, &sb) == 0))
+        {
+            // no such file, check if it is safe to print its name
+            int i, safe_to_print = 1;
+            for (i=0; i<len; i++)
+                if (!isprint(buf[i])) { safe_to_print = 0; break; }
+            if ( safe_to_print )
+                fprintf(bcftools_stderr,"The file list \"%s\" appears broken, could not locate: %s\n", file_list,buf);
+            else
+                fprintf(bcftools_stderr,"Does the file \"%s\" really contain a list of files and do all exist?\n", file_list);
+            return 1;
+        }
+
+        nfiles++;
+        files = (char**) realloc(files,nfiles*sizeof(char*));
+        files[nfiles-1] = strdup(buf);
+    }
+    if ( fclose(fh)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,file_list);
+    if ( !nfiles )
+    {
+        fprintf(bcftools_stderr,"No files read from %s\n", file_list);
+        return 1;
+    }
+    *argv = files;
+    *n    = nfiles;
+    return 0;
+}
+#undef MAX_PATH_LEN
+
+int parse_format_flag(const char *str)
+{
+    int i, flag = 0, n_tags;
+    char **tags = hts_readlist(str, 0, &n_tags);
+    for(i=0; i<n_tags; i++)
+    {
+        if ( !strcasecmp(tags[i],"DP") || !strcasecmp(tags[i],"FORMAT/DP") || !strcasecmp(tags[i],"FMT/DP") ) flag |= B2B_FMT_DP;
+        else if ( !strcasecmp(tags[i],"DV") || !strcasecmp(tags[i],"FORMAT/DV") || !strcasecmp(tags[i],"FMT/DV") ) { flag |= B2B_FMT_DV; fprintf(bcftools_stderr, "[warning] tag DV functional, but deprecated. Please switch to `AD` in future.\n"); }
+        else if ( !strcasecmp(tags[i],"SP") || !strcasecmp(tags[i],"FORMAT/SP") || !strcasecmp(tags[i],"FMT/SP") ) flag |= B2B_FMT_SP;
+        else if ( !strcasecmp(tags[i],"DP4") || !strcasecmp(tags[i],"FORMAT/DP4") || !strcasecmp(tags[i],"FMT/DP4") ) { flag |= B2B_FMT_DP4; fprintf(bcftools_stderr, "[warning] tag DP4 functional, but deprecated. Please switch to `ADF` and `ADR` in future.\n"); }
+        else if ( !strcasecmp(tags[i],"DPR") || !strcasecmp(tags[i],"FORMAT/DPR") || !strcasecmp(tags[i],"FMT/DPR") ) { flag |= B2B_FMT_DPR; fprintf(bcftools_stderr, "[warning] tag DPR functional, but deprecated. Please switch to `AD` in future.\n"); }
+        else if ( !strcasecmp(tags[i],"INFO/DPR") ) { flag |= B2B_INFO_DPR; fprintf(bcftools_stderr, "[warning] tag INFO/DPR functional, but deprecated. Please switch to `INFO/AD` in future.\n"); }
+        else if ( !strcasecmp(tags[i],"AD") || !strcasecmp(tags[i],"FORMAT/AD") || !strcasecmp(tags[i],"FMT/AD") ) flag |= B2B_FMT_AD;
+        else if ( !strcasecmp(tags[i],"ADF") || !strcasecmp(tags[i],"FORMAT/ADF") || !strcasecmp(tags[i],"FMT/ADF") ) flag |= B2B_FMT_ADF;
+        else if ( !strcasecmp(tags[i],"ADR") || !strcasecmp(tags[i],"FORMAT/ADR") || !strcasecmp(tags[i],"FMT/ADR") ) flag |= B2B_FMT_ADR;
+        else if ( !strcasecmp(tags[i],"SCR") || !strcasecmp(tags[i],"FORMAT/SCR") || !strcasecmp(tags[i],"FMT/SCR") ) flag |= B2B_FMT_SCR;
+        else if ( !strcasecmp(tags[i],"QS") || !strcasecmp(tags[i],"FORMAT/QS") || !strcasecmp(tags[i],"FMT/QS") ) flag |= B2B_FMT_QS;
+        else if ( !strcasecmp(tags[i],"NMBZ") || !strcasecmp(tags[i],"FORMAT/NMBZ") || !strcasecmp(tags[i],"FMT/NMBZ") ) flag |= B2B_FMT_NMBZ;
+        else if ( !strcasecmp(tags[i],"INFO/SCR") ) flag |= B2B_INFO_SCR;
+        else if ( !strcasecmp(tags[i],"INFO/AD") ) flag |= B2B_INFO_AD;
+        else if ( !strcasecmp(tags[i],"INFO/ADF") ) flag |= B2B_INFO_ADF;
+        else if ( !strcasecmp(tags[i],"INFO/ADR") ) flag |= B2B_INFO_ADR;
+        else if ( !strcasecmp(tags[i],"SCB") || !strcasecmp(tags[i],"INFO/SCB")) flag |= B2B_INFO_SCB;
+        else
+        {
+            fprintf(bcftools_stderr,"Could not parse tag \"%s\" in \"%s\"\n", tags[i], str);
+            bcftools_exit(EXIT_FAILURE);
+        }
+        free(tags[i]);
+    }
+    if (n_tags) free(tags);
+    return flag;
+}
+
+// todo: make it possible to turn off some annotations or change the defaults,
+//      specifically RPB, VDB, MWU, SGB tests. It would be good to do some
+//      benchmarking first to see if it's worth it.
+static void list_annotations(FILE *fp)
+{
+    fprintf(fp,
+"\n"
+"FORMAT annotation tags available (\"FORMAT/\" prefix is optional):\n"
+"\n"
+"  FORMAT/AD   .. Allelic depth (Number=R,Type=Integer)\n"
+"  FORMAT/ADF  .. Allelic depths on the forward strand (Number=R,Type=Integer)\n"
+"  FORMAT/ADR  .. Allelic depths on the reverse strand (Number=R,Type=Integer)\n"
+"  FORMAT/DP   .. Number of high-quality bases (Number=1,Type=Integer)\n"
+"  FORMAT/NMBZ .. Mann-Whitney U-z test of Number of Mismatches within supporting reads (Number=1,Type=Float)\n"
+"  FORMAT/QS   .. Allele phred-score quality sum for use with `call -mG` and +trio-dnm (Number=R,Type=Integer)\n"
+"  FORMAT/SP   .. Phred-scaled strand bias P-value (Number=1,Type=Integer)\n"
+"  FORMAT/SCR  .. Number of soft-clipped reads (Number=1,Type=Integer)\n"
+"\n"
+"INFO annotation tags available:\n"
+"\n"
+"  INFO/AD  .. Total allelic depth (Number=R,Type=Integer)\n"
+"  INFO/ADF .. Total allelic depths on the forward strand (Number=R,Type=Integer)\n"
+"  INFO/ADR .. Total allelic depths on the reverse strand (Number=R,Type=Integer)\n"
+"  INFO/SCR .. Number of soft-clipped reads (Number=1,Type=Integer)\n"
+"\n");
+}
+
+static void print_usage(FILE *fp, const mplp_conf_t *mplp)
+{
+    char *tmp_skip_all_set = bam_flag2str(mplp->rflag_skip_all_set);
+    char *tmp_skip_any_unset = bam_flag2str(mplp->rflag_skip_any_unset);
+    char *tmp_skip_all_unset = bam_flag2str(mplp->rflag_skip_all_unset);
+    char *tmp_skip_any_set = bam_flag2str(mplp->rflag_skip_any_set);
+
+    // Display usage information, formatted for the standard 80 columns.
+    // (The unusual string formatting here aids the readability of this
+    // source code in 80 columns, to the extent that's possible.)
+
+    fprintf(fp,
+        "\n"
+        "Usage: bcftools mpileup [options] in1.bam [in2.bam [...]]\n"
+        "\n"
+        "Input options:\n"
+        "  -6, --illumina1.3+      Quality is in the Illumina-1.3+ encoding\n"
+        "  -A, --count-orphans     Do not discard anomalous read pairs\n"
+        "  -b, --bam-list FILE     List of input BAM filenames, one per line\n"
+        "  -B, --no-BAQ            Disable BAQ (per-Base Alignment Quality)\n"
+        "  -C, --adjust-MQ INT     Adjust mapping quality [0]\n"
+        "  -D, --full-BAQ          Apply BAQ everywhere, not just in problematic regions\n"
+        "  -d, --max-depth INT     Max raw per-file depth; avoids excessive memory usage [%d]\n", mplp->max_depth);
+            fprintf(fp,
+        "  -E, --redo-BAQ          Recalculate BAQ on the fly, ignore existing BQs\n"
+        "  -f, --fasta-ref FILE    Faidx indexed reference sequence file\n"
+        "      --no-reference      Do not require fasta reference file\n"
+        "  -G, --read-groups FILE  Select or exclude read groups listed in the file\n"
+        "  -q, --min-MQ INT        Skip alignments with mapQ smaller than INT [%d]\n", mplp->min_mq);
+    fprintf(fp,
+        "  -Q, --min-BQ INT        Skip bases with baseQ/BAQ smaller than INT [%d]\n", mplp->min_baseQ);
+    fprintf(fp,
+        "      --max-BQ INT        Limit baseQ/BAQ to no more than INT [%d]\n", mplp->max_baseQ);
+    fprintf(fp,
+        "      --delta-BQ INT      Use neighbour_qual + INT if less than qual [%d]\n", mplp->delta_baseQ);
+    fprintf(fp,
+        "  -r, --regions REG[,...] Comma separated list of regions in which pileup is generated\n"
+        "  -R, --regions-file FILE Restrict to regions listed in a file\n"
+        "      --ignore-RG         Ignore RG tags (one BAM = one sample)\n"
+        "  --ls, --skip-all-set STR|INT  Skip reads with all of the bits set []\n");
+    fprintf(fp,
+        "  --ns, --skip-any-set STR|INT  Skip reads with any of the bits set [%s]\n", tmp_skip_any_set);
+    fprintf(fp,
+        "  --lu, --skip-all-unset STR|INT  Skip reads with all of the bits unset []\n"
+        "  --nu, --skip-any-unset STR|INT  Skip reads with any of the bits unset []\n");
+    fprintf(fp,
+        "  -s, --samples LIST      Comma separated list of samples to include\n"
+        "  -S, --samples-file FILE File of samples to include\n"
+        "  -t, --targets REG[,...] Similar to -r but streams rather than index-jumps\n"
+        "  -T, --targets-file FILE Similar to -R but streams rather than index-jumps\n"
+        "  -x, --ignore-overlaps   Disable read-pair overlap detection\n"
+        "      --seed INT          Random number seed used for sampling deep regions [0]\n"
+        "\n"
+        "Output options:\n"
+        "  -a, --annotate LIST     Optional tags to output; '\\?' to list available tags []\n"
+        "  -g, --gvcf INT[,...]    Group non-variant sites into gVCF blocks according\n"
+        "                          To minimum per-sample DP\n"
+        "      --no-version        Do not append version and command line to the header\n"
+        "  -o, --output FILE       Write output to FILE [standard output]\n"
+        "  -O, --output-type TYPE  'b' compressed BCF; 'u' uncompressed BCF;\n"
+        "                          'z' compressed VCF; 'v' uncompressed VCF; 0-9 compression level [v]\n"
+        "  -U, --mwu-u             Use older probability scale for Mann-Whitney U test\n"
+        "      --threads INT       Use multithreading with INT worker threads [0]\n"
+        "\n"
+        "SNP/INDEL genotype likelihoods options:\n"
+        "  -X, --config STR        Specify platform specific profiles (see below)\n"
+        "  -e, --ext-prob INT      Phred-scaled gap extension seq error probability [%d]\n", mplp->extQ);
+    fprintf(fp,
+        "  -F, --gap-frac FLOAT    Minimum fraction of gapped reads [%g]\n", mplp->min_frac);
+    fprintf(fp,
+        "  -h, --tandem-qual INT   Coefficient for homopolymer errors [%d]\n", mplp->tandemQ);
+    fprintf(fp,
+        "  -I, --skip-indels       Do not perform indel calling\n"
+        "  -L, --max-idepth INT    Maximum per-file depth for INDEL calling [%d]\n", mplp->max_indel_depth);
+    fprintf(fp,
+        "  -m, --min-ireads INT    Minimum number gapped reads for indel candidates [%d]\n", mplp->min_support);
+    fprintf(fp,
+        "  -M, --max-read-len INT  Maximum length of read to pass to BAQ algorithm [%d]\n", mplp->max_read_len);
+    fprintf(fp,
+        "  -o, --open-prob INT     Phred-scaled gap open seq error probability [%d]\n", mplp->openQ);
+    fprintf(fp,
+        "  -p, --per-sample-mF     Apply -m and -F per-sample for increased sensitivity\n"
+        "  -P, --platforms STR     Comma separated list of platforms for indels [all]\n"
+        "  --ar, --ambig-reads STR   What to do with ambiguous indel reads: drop,incAD,incAD0 [drop]\n");
+    fprintf(fp,
+        "      --indel-bias FLOAT  Raise to favour recall over precision [%.2f]\n", mplp->indel_bias);
+    fprintf(fp,
+        "      --indel-size INT    Approximate maximum indel size considered [%d]\n", mplp->indel_win_size);
+    fprintf(fp,"\n");
+    fprintf(fp,
+        "Configuration profiles activated with -X, --config:\n"
+        "    1.12:        -Q13 -h100 -m1 -F0.002\n"
+        "    illumina:    [ default values ]\n"
+        "    ont:         -B -Q5 --max-BQ 30 -I [also try eg |bcftools call -P0.01]\n"
+        "    pacbio-ccs:  -D -Q5 --max-BQ 50 -F0.1 -o25 -e1 --delta-BQ 10 -M99999\n"
+        "\n"
+        "Notes: Assuming diploid individuals.\n"
+        "\n"
+        "Example:\n"
+        "   # See also http://samtools.github.io/bcftools/howtos/variant-calling.html\n"
+        "   bcftools mpileup -Ou -f reference.fa alignments.bam | bcftools call -mv -Ob -o calls.bcf\n"
+        "\n");
+
+    free(tmp_skip_all_set);
+    free(tmp_skip_any_unset);
+    free(tmp_skip_all_unset);
+    free(tmp_skip_any_set);
+}
+
+int main_mpileup(int argc, char *argv[])
+{
+    int c;
+    const char *file_list = NULL;
+    char **fn = NULL;
+    int nfiles = 0, use_orphan = 0, noref = 0;
+    mplp_conf_t mplp;
+    memset(&mplp, 0, sizeof(mplp_conf_t));
+    mplp.min_baseQ = 1;
+    mplp.max_baseQ = 60;
+    mplp.delta_baseQ = 30;
+    mplp.capQ_thres = 0;
+    mplp.max_depth = 250; mplp.max_indel_depth = 250;
+    mplp.openQ = 40; mplp.extQ = 20; mplp.tandemQ = 500;
+    mplp.min_frac = 0.05; mplp.indel_bias = 1.0; mplp.min_support = 2;
+    mplp.flag = MPLP_NO_ORPHAN | MPLP_REALN | MPLP_REALN_PARTIAL
+              | MPLP_SMART_OVERLAPS;
+    mplp.argc = argc; mplp.argv = argv;
+    mplp.rflag_skip_any_set = BAM_FUNMAP | BAM_FSECONDARY | BAM_FQCFAIL | BAM_FDUP;
+    mplp.output_fname = NULL;
+    mplp.output_type = FT_VCF;
+    mplp.record_cmd_line = 1;
+    mplp.n_threads = 0;
+    mplp.bsmpl = bam_smpl_init();
+    // the default to be changed in future, see also parse_format_flag()
+    mplp.fmt_flag = B2B_INFO_VDB|B2B_INFO_RPB|B2B_INFO_SCB|B2B_INFO_ZSCORE;
+    mplp.max_read_len = 500;
+    mplp.ambig_reads = B2B_DROP;
+    mplp.indel_win_size = 110;
+    mplp.clevel = -1;
+    hts_srand48(0);
+
+    static const struct option lopts[] =
+    {
+        {"nu", required_argument, NULL, 16},
+        {"lu", required_argument, NULL, 17},
+        {"rf", required_argument, NULL, 17},   // old --rf, --incl-flags = --lu, --skip-all-unset
+        {"ns", required_argument, NULL, 18},
+        {"ff", required_argument, NULL, 18},   // old --ff, --excl-flags = --ns, --skip-any-set
+        {"ls", required_argument, NULL, 19},
+        {"skip-any-unset", required_argument, NULL, 16},
+        {"skip-all-unset", required_argument, NULL, 17},
+        {"skip-any-set", required_argument, NULL, 18},
+        {"skip-all-set", required_argument, NULL, 19},
+        {"output", required_argument, NULL, 3},
+        {"open-prob", required_argument, NULL, 4},
+        {"ignore-RG", no_argument, NULL, 5},
+        {"ignore-rg", no_argument, NULL, 5},
+        {"gvcf", required_argument, NULL, 'g'},
+        {"no-reference", no_argument, NULL, 7},
+        {"no-version", no_argument, NULL, 8},
+        {"threads",required_argument,NULL,9},
+        {"illumina1.3+", no_argument, NULL, '6'},
+        {"count-orphans", no_argument, NULL, 'A'},
+        {"bam-list", required_argument, NULL, 'b'},
+        {"no-BAQ", no_argument, NULL, 'B'},
+        {"no-baq", no_argument, NULL, 'B'},
+        {"full-BAQ", no_argument, NULL, 'D'},
+        {"full-baq", no_argument, NULL, 'D'},
+        {"adjust-MQ", required_argument, NULL, 'C'},
+        {"adjust-mq", required_argument, NULL, 'C'},
+        {"max-depth", required_argument, NULL, 'd'},
+        {"redo-BAQ", no_argument, NULL, 'E'},
+        {"redo-baq", no_argument, NULL, 'E'},
+        {"fasta-ref", required_argument, NULL, 'f'},
+        {"read-groups", required_argument, NULL, 'G'},
+        {"region", required_argument, NULL, 'r'},
+        {"regions", required_argument, NULL, 'r'},
+        {"regions-file", required_argument, NULL, 'R'},
+        {"targets", required_argument, NULL, 't'},
+        {"targets-file", required_argument, NULL, 'T'},
+        {"min-MQ", required_argument, NULL, 'q'},
+        {"min-mq", required_argument, NULL, 'q'},
+        {"min-BQ", required_argument, NULL, 'Q'},
+        {"min-bq", required_argument, NULL, 'Q'},
+        {"max-bq", required_argument, NULL, 11},
+        {"max-BQ", required_argument, NULL, 11},
+        {"delta-BQ", required_argument, NULL, 12},
+        {"ignore-overlaps", no_argument, NULL, 'x'},
+        {"output-type", required_argument, NULL, 'O'},
+        {"samples", required_argument, NULL, 's'},
+        {"samples-file", required_argument, NULL, 'S'},
+        {"annotate", required_argument, NULL, 'a'},
+        {"ext-prob", required_argument, NULL, 'e'},
+        {"gap-frac", required_argument, NULL, 'F'},
+        {"indel-bias", required_argument, NULL, 10},
+        {"indel-size", required_argument, NULL, 15},
+        {"tandem-qual", required_argument, NULL, 'h'},
+        {"skip-indels", no_argument, NULL, 'I'},
+        {"max-idepth", required_argument, NULL, 'L'},
+        {"min-ireads", required_argument, NULL, 'm'},
+        {"per-sample-mF", no_argument, NULL, 'p'},
+        {"per-sample-mf", no_argument, NULL, 'p'},
+        {"platforms", required_argument, NULL, 'P'},
+        {"max-read-len", required_argument, NULL, 'M'},
+        {"config", required_argument, NULL, 'X'},
+        {"mwu-u", no_argument, NULL, 'U'},
+        {"seed", required_argument, NULL, 13},
+        {"ambig-reads", required_argument, NULL, 14},
+        {"ar", required_argument, NULL, 14},
+        {NULL, 0, NULL, 0}
+    };
+    while ((c = getopt_long(argc, argv, "Ag:f:r:R:q:Q:C:BDd:L:b:P:po:e:h:Im:F:EG:6O:xa:s:S:t:T:M:X:U",lopts,NULL)) >= 0) {
+        switch (c) {
+        case 'x': mplp.flag &= ~MPLP_SMART_OVERLAPS; break;
+        case  16 :
+            mplp.rflag_skip_any_unset = bam_str2flag(optarg);
+            if ( mplp.rflag_skip_any_unset <0 ) { fprintf(bcftools_stderr,"Could not parse --nf %s\n", optarg); return 1; }
+            break;
+        case  17 :
+            mplp.rflag_skip_all_unset = bam_str2flag(optarg);
+            if ( mplp.rflag_skip_all_unset<0 ) { fprintf(bcftools_stderr,"Could not parse --if %s\n", optarg); return 1; }
+            break;
+        case  18 :
+            mplp.rflag_skip_any_set = bam_str2flag(optarg);
+            if ( mplp.rflag_skip_any_set <0 ) { fprintf(bcftools_stderr,"Could not parse --ef %s\n", optarg); return 1; }
+            break;
+        case  19 :
+            mplp.rflag_skip_all_set = bam_str2flag(optarg);
+            if ( mplp.rflag_skip_all_set <0 ) { fprintf(bcftools_stderr,"Could not parse --df %s\n", optarg); return 1; }
+            break;
+        case  3 : mplp.output_fname = optarg; break;
+        case  4 : mplp.openQ = atoi(optarg); break;
+        case  5 : bam_smpl_ignore_readgroups(mplp.bsmpl); break;
+        case 'g':
+            mplp.gvcf = gvcf_init(optarg);
+            if ( !mplp.gvcf ) error("Could not parse: --gvcf %s\n", optarg);
+            break;
+        case 'f':
+            mplp.fai = fai_load(optarg);
+            if (mplp.fai == NULL) return 1;
+            mplp.fai_fname = optarg;
+            break;
+        case  7 : noref = 1; break;
+        case  8 : mplp.record_cmd_line = 0; break;
+        case  9 : mplp.n_threads = strtol(optarg, 0, 0); break;
+        case 'd': mplp.max_depth = atoi(optarg); break;
+        case 'r': mplp.reg_fname = strdup(optarg); break;
+        case 'R': mplp.reg_fname = strdup(optarg); mplp.reg_is_file = 1; break;
+        case 't':
+                  // In the original version the whole BAM was streamed which is inefficient
+                  //  with few BED intervals and big BAMs. Todo: devise a heuristic to determine
+                  //  best strategy, that is streaming or jumping.
+                  if ( optarg[0]=='^' ) optarg++;
+                  else mplp.bed_logic = 1;
+                  mplp.bed = regidx_init(NULL,regidx_parse_reg,NULL,0,NULL);
+                  mplp.bed_itr = regitr_init(mplp.bed);
+                  if ( regidx_insert_list(mplp.bed,optarg,',') !=0 )
+                  {
+                      fprintf(bcftools_stderr,"Could not parse the targets: %s\n", optarg);
+                      bcftools_exit(EXIT_FAILURE);
+                  }
+                  break;
+        case 'T':
+                  if ( optarg[0]=='^' ) optarg++;
+                  else mplp.bed_logic = 1;
+                  mplp.bed = regidx_init(optarg,NULL,NULL,0,NULL);
+                  if (!mplp.bed) { fprintf(bcftools_stderr, "bcftools mpileup: Could not read file \"%s\"", optarg); return 1; }
+                  break;
+        case 'P': mplp.pl_list = strdup(optarg); break;
+        case 'p': mplp.flag |= MPLP_PER_SAMPLE; break;
+        case 'B': mplp.flag &= ~MPLP_REALN; break;
+        case 'D': mplp.flag &= ~MPLP_REALN_PARTIAL; break;
+        case 'I': mplp.flag |= MPLP_NO_INDEL; break;
+        case 'E': mplp.flag |= MPLP_REDO_BAQ; break;
+        case '6': mplp.flag |= MPLP_ILLUMINA13; break;
+        case 's': if ( bam_smpl_add_samples(mplp.bsmpl,optarg,0)<0 ) error("Could not read samples: %s\n",optarg); break;
+        case 'S': if ( bam_smpl_add_samples(mplp.bsmpl,optarg,1)<0 ) error("Could not read samples: %s\n",optarg); break;
+        case 'O':
+            switch (optarg[0]) {
+                case 'b': mplp.output_type = FT_BCF_GZ; break;
+                case 'u': mplp.output_type = FT_BCF; break;
+                case 'z': mplp.output_type = FT_VCF_GZ; break;
+                case 'v': mplp.output_type = FT_VCF; break;
+                default:
+                {
+                    char *tmp;
+                    mplp.clevel = strtol(optarg,&tmp,10);
+                    if ( *tmp || mplp.clevel<0 || mplp.clevel>9 ) error("The output type \"%s\" not recognised\n", optarg);
+                }
+            }
+            if ( optarg[1] )
+            {
+                char *tmp;
+                mplp.clevel = strtol(optarg+1,&tmp,10);
+                if ( *tmp || mplp.clevel<0 || mplp.clevel>9 ) error("Could not parse argument: --output-type %s\n", optarg+1);
+            }
+            break;
+        case 'C': mplp.capQ_thres = atoi(optarg); break;
+        case 'q': mplp.min_mq = atoi(optarg); break;
+        case 'Q': mplp.min_baseQ = atoi(optarg); break;
+        case  11: mplp.max_baseQ = atoi(optarg); break;
+        case  12: mplp.delta_baseQ = atoi(optarg); break;
+        case 'b': file_list = optarg; break;
+        case 'o': {
+                char *end;
+                long value = strtol(optarg, &end, 10);
+                // Distinguish between -o INT and -o FILE (a bit of a hack!)
+                if (*end == '\0') mplp.openQ = value;
+                else mplp.output_fname = optarg;
+            }
+            break;
+        case 'e': mplp.extQ = atoi(optarg); break;
+        case 'h': mplp.tandemQ = atoi(optarg); break;
+        case 10: // --indel-bias (inverted so higher => more indels called)
+            if (atof(optarg) < 1e-2)
+                mplp.indel_bias = 1/1e2;
+            else
+                mplp.indel_bias = 1/atof(optarg);
+            break;
+        case  15: {
+                char *tmp;
+                mplp.indel_win_size = strtol(optarg,&tmp,10);
+                if ( *tmp ) error("Could not parse argument: --indel-size %s\n", optarg);
+                if ( mplp.indel_win_size < 110 )
+                {
+                    mplp.indel_win_size = 110;
+                    fprintf(bcftools_stderr,"Warning: running with --indel-size %d, the requested value is too small\n",mplp.indel_win_size);
+                }
+            }
+            break;
+        case 'A': use_orphan = 1; break;
+        case 'F': mplp.min_frac = atof(optarg); break;
+        case 'm': mplp.min_support = atoi(optarg); break;
+        case 'L': mplp.max_indel_depth = atoi(optarg); break;
+        case 'G': bam_smpl_add_readgroups(mplp.bsmpl, optarg, 1); break;
+        case 'a':
+            if (optarg[0]=='?') {
+                list_annotations(bcftools_stderr);
+                return 1;
+            }
+            mplp.fmt_flag |= parse_format_flag(optarg);
+        break;
+        case 'M': mplp.max_read_len = atoi(optarg); break;
+        case 'U': mplp.fmt_flag &= ~B2B_INFO_ZSCORE; break;
+        case 'X':
+            if (strcasecmp(optarg, "pacbio-ccs") == 0) {
+                mplp.min_frac = 0.1;
+                mplp.min_baseQ = 5;
+                mplp.max_baseQ = 50;
+                mplp.delta_baseQ = 10;
+                mplp.openQ = 25;
+                mplp.extQ = 1;
+                mplp.flag |= MPLP_REALN_PARTIAL;
+                mplp.max_read_len = 99999;
+            } else if (strcasecmp(optarg, "ont") == 0) {
+                fprintf(bcftools_stderr, "For ONT it may be beneficial to also run bcftools call with "
+                        "a higher -P, eg -P0.01 or -P 0.1\n");
+                mplp.min_baseQ = 5;
+                mplp.max_baseQ = 30;
+                mplp.flag &= ~MPLP_REALN;
+                mplp.flag |= MPLP_NO_INDEL;
+            } else if (strcasecmp(optarg, "1.12") == 0) {
+                // 1.12 and earlier
+                mplp.min_frac = 0.002;
+                mplp.min_support = 1;
+                mplp.min_baseQ = 13;
+                mplp.tandemQ = 100;
+                mplp.flag &= ~MPLP_REALN_PARTIAL;
+                mplp.flag |= MPLP_REALN;
+            } else if (strcasecmp(optarg, "illumina") == 0) {
+                mplp.flag |= MPLP_REALN_PARTIAL;
+            } else {
+                fprintf(bcftools_stderr, "Unknown configuration name '%s'\n"
+                        "Please choose from 1.12, illumina, pacbio-ccs or ont\n",
+                        optarg);
+                return 1;
+            }
+            break;
+        case 13: hts_srand48(atoi(optarg)); break;
+        case 14:
+            if ( !strcasecmp(optarg,"drop") ) mplp.ambig_reads = B2B_DROP;
+            else if ( !strcasecmp(optarg,"incAD") ) mplp.ambig_reads = B2B_INC_AD;
+            else if ( !strcasecmp(optarg,"incAD0") ) mplp.ambig_reads = B2B_INC_AD0;
+            else error("The option to --ambig-reads not recognised: %s\n",optarg);
+            break;
+        default:
+            fprintf(bcftools_stderr,"Invalid option: '%c'\n", c);
+            return 1;
+        }
+    }
+
+    if ( mplp.gvcf && !(mplp.fmt_flag&B2B_FMT_DP) )
+    {
+        fprintf(bcftools_stderr,"[warning] The -a DP option is required with --gvcf, switching on.\n");
+        mplp.fmt_flag |= B2B_FMT_DP;
+    }
+    if ( mplp.flag&(MPLP_BCF|MPLP_VCF|MPLP_NO_COMP) )
+    {
+        if ( mplp.flag&MPLP_VCF )
+        {
+            if ( mplp.flag&MPLP_NO_COMP ) mplp.output_type = FT_VCF;
+            else mplp.output_type = FT_VCF_GZ;
+        }
+        else if ( mplp.flag&MPLP_BCF )
+        {
+            if ( mplp.flag&MPLP_NO_COMP ) mplp.output_type = FT_BCF;
+            else mplp.output_type = FT_BCF_GZ;
+        }
+    }
+    if ( !(mplp.flag&MPLP_REALN) && mplp.flag&MPLP_REDO_BAQ )
+    {
+        fprintf(bcftools_stderr,"Error: The -B option cannot be combined with -E\n");
+        return 1;
+    }
+    if (use_orphan) mplp.flag &= ~MPLP_NO_ORPHAN;
+    if (argc == 1)
+    {
+        print_usage(bcftools_stderr, &mplp);
+        return 1;
+    }
+    if (!mplp.fai && !noref) {
+        fprintf(bcftools_stderr,"Error: mpileup requires the --fasta-ref option by default; use --no-reference to run without a fasta reference\n");
+        return 1;
+    }
+    int ret,i;
+    if (file_list)
+    {
+        if ( read_file_list(file_list,&nfiles,&fn) ) return 1;
+        mplp.files  = fn;
+        mplp.nfiles = nfiles;
+    }
+    else
+    {
+        mplp.nfiles = argc - optind;
+        mplp.files  = (char**) malloc(mplp.nfiles*sizeof(char*));
+        for (i=0; i<mplp.nfiles; i++) mplp.files[i] = strdup(argv[optind+i]);
+    }
+    ret = mpileup(&mplp);
+
+    for (i=0; i<mplp.nfiles; i++) free(mplp.files[i]);
+    free(mplp.files);
+    free(mplp.reg_fname); free(mplp.pl_list);
+    if (mplp.fai) fai_destroy(mplp.fai);
+    if (mplp.bed) regidx_destroy(mplp.bed);
+    if (mplp.bed_itr) regitr_destroy(mplp.bed_itr);
+    if (mplp.reg) regidx_destroy(mplp.reg);
+    bam_smpl_destroy(mplp.bsmpl);
+
+    return ret;
+}
diff --git a/bcftools/mw.h b/bcftools/mw.h
new file mode 100644
index 0000000..3e68cbf
--- /dev/null
+++ b/bcftools/mw.h
@@ -0,0 +1,1944 @@
+/* mw.h -- a table of precomputed Mann Whitney coefficients (for bam2bcf.c)
+
+   The MIT License
+
+   Copyright (C) 2016 Genome Research Ltd.
+
+   Author: James Bonfield <jkb@sanger.ac.uk>
+
+   Permission is hereby granted, free of charge, to any person obtaining a copy
+   of this software and associated documentation files (the "Software"), to deal
+   in the Software without restriction, including without limitation the rights
+   to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+   copies of the Software, and to permit persons to whom the Software is
+   furnished to do so, subject to the following conditions:
+
+   The above copyright notice and this permission notice shall be included in
+   all copies or substantial portions of the Software.
+
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+   IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+   FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+   AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+   LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+   OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+   THE SOFTWARE.
+*/
+
+// Code to build this table is below
+#ifdef BUILD_MW
+#include <stdio.h>
+
+double mann_whitney_1947(int n, int m, int U)
+{
+    if (U<0) return 0;
+    if (n==0||m==0) return U==0 ? 1 : 0;
+    return (double)n/(n+m)*mann_whitney_1947(n-1,m,U-m) + (double)m/(n+m)*mann_whitney_1947(n,m-1,U);
+}
+
+int main(void) {
+    int i, j, k;
+    printf("static double mw[6][6][50] = // [2-7][2-7][0-49]\n{\n");
+    for (i = 2; i < 8; i++) {
+	printf("    {\n");
+	for (j = 2; j < 8; j++) {
+	    printf("        {\n");
+	    for (k = 0; k < 50; k++) {
+		printf("            %.17f,\n", mann_whitney_1947(i,j,k));
+	    }
+	    printf("        },\n");
+	}
+	printf("    },\n");
+    }
+    printf("};\n");
+    return 0;
+}
+#endif
+
+static double mw[6][6][50] = // [2-7][2-7][0-49]
+{
+    {
+        {
+            0.16666666666666666,
+            0.16666666666666666,
+            0.33333333333333331,
+            0.16666666666666666,
+            0.16666666666666666,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+        },
+        {
+            0.09999999999999999,
+            0.09999999999999999,
+            0.19999999999999998,
+            0.20000000000000001,
+            0.20000000000000001,
+            0.10000000000000001,
+            0.10000000000000001,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+        },
+        {
+            0.06666666666666665,
+            0.06666666666666665,
+            0.13333333333333330,
+            0.13333333333333333,
+            0.20000000000000001,
+            0.13333333333333333,
+            0.13333333333333333,
+            0.06666666666666667,
+            0.06666666666666667,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+        },
+        {
+            0.04761904761904761,
+            0.04761904761904761,
+            0.09523809523809522,
+            0.09523809523809523,
+            0.14285714285714288,
+            0.14285714285714285,
+            0.14285714285714285,
+            0.09523809523809523,
+            0.09523809523809523,
+            0.04761904761904762,
+            0.04761904761904762,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+        },
+        {
+            0.03571428571428571,
+            0.03571428571428571,
+            0.07142857142857141,
+            0.07142857142857142,
+            0.10714285714285715,
+            0.10714285714285714,
+            0.14285714285714285,
+            0.10714285714285715,
+            0.10714285714285715,
+            0.07142857142857144,
+            0.07142857142857142,
+            0.03571428571428571,
+            0.03571428571428571,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+        },
+        {
+            0.02777777777777777,
+            0.02777777777777777,
+            0.05555555555555555,
+            0.05555555555555555,
+            0.08333333333333334,
+            0.08333333333333333,
+            0.11111111111111110,
+            0.11111111111111113,
+            0.11111111111111113,
+            0.08333333333333334,
+            0.08333333333333334,
+            0.05555555555555556,
+            0.05555555555555555,
+            0.02777777777777778,
+            0.02777777777777778,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+        },
+    },
+    {
+        {
+            0.10000000000000001,
+            0.10000000000000001,
+            0.20000000000000001,
+            0.20000000000000001,
+            0.19999999999999998,
+            0.09999999999999999,
+            0.09999999999999999,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+        },
+        {
+            0.05000000000000000,
+            0.05000000000000000,
+            0.10000000000000001,
+            0.14999999999999999,
+            0.14999999999999999,
+            0.14999999999999999,
+            0.14999999999999999,
+            0.10000000000000001,
+            0.05000000000000000,
+            0.05000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
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+            0.00641025641025641,
+            0.00407925407925408,
+            0.00291375291375291,
+            0.00174825174825175,
+            0.00116550116550117,
+            0.00058275058275058,
+            0.00058275058275058,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+        },
+        {
+            0.00029137529137529,
+            0.00029137529137529,
+            0.00058275058275058,
+            0.00087412587412587,
+            0.00145687645687646,
+            0.00203962703962704,
+            0.00320512820512821,
+            0.00437062937062937,
+            0.00582750582750583,
+            0.00757575757575758,
+            0.00990675990675991,
+            0.01223776223776224,
+            0.01544289044289044,
+            0.01835664335664336,
+            0.02185314685314686,
+            0.02534965034965035,
+            0.02913752913752913,
+            0.03263403263403263,
+            0.03642191142191141,
+            0.03962703962703962,
+            0.04254079254079253,
+            0.04516317016317015,
+            0.04720279720279719,
+            0.04836829836829836,
+            0.04924242424242423,
+            0.04924242424242423,
+            0.04836829836829836,
+            0.04720279720279719,
+            0.04516317016317015,
+            0.04254079254079253,
+            0.03962703962703962,
+            0.03642191142191141,
+            0.03263403263403263,
+            0.02913752913752913,
+            0.02534965034965035,
+            0.02185314685314686,
+            0.01835664335664336,
+            0.01544289044289044,
+            0.01223776223776224,
+            0.00990675990675991,
+            0.00757575757575758,
+            0.00582750582750583,
+            0.00437062937062937,
+            0.00320512820512821,
+            0.00203962703962704,
+            0.00145687645687646,
+            0.00087412587412587,
+            0.00058275058275058,
+            0.00029137529137529,
+            0.00029137529137529,
+        },
+    },
+};
diff --git a/bcftools/ploidy.c b/bcftools/ploidy.c
new file mode 100644
index 0000000..550ba87
--- /dev/null
+++ b/bcftools/ploidy.c
@@ -0,0 +1,268 @@
+/* 
+    Copyright (C) 2014-2016 Genome Research Ltd.
+
+    Author: Petr Danecek <pd3@sanger.ac.uk>
+
+    Permission is hereby granted, free of charge, to any person obtaining a copy
+    of this software and associated documentation files (the "Software"), to deal
+    in the Software without restriction, including without limitation the rights
+    to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+    copies of the Software, and to permit persons to whom the Software is
+    furnished to do so, subject to the following conditions:
+    
+    The above copyright notice and this permission notice shall be included in
+    all copies or substantial portions of the Software.
+    
+    THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+    IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+    FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+    AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+    LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+    OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+    THE SOFTWARE.
+*/
+
+#include <htslib/khash_str2int.h>
+#include <htslib/kseq.h>
+#include <htslib/hts.h>
+#include "bcftools.h"
+#include "ploidy.h"
+
+struct _ploidy_t
+{
+    int nsex, msex;     // number of genders, m:number of allocated elements in id2sex array
+    int dflt, min, max; // ploidy: default, min and max (only explicitly listed)
+    int *sex2dflt;
+    regidx_t *idx;
+    regitr_t *itr;
+    void *sex2id;
+    char **id2sex;
+    kstring_t tmp_str;
+};
+
+typedef struct
+{
+    int sex, ploidy;
+}
+sex_ploidy_t;
+
+
+regidx_t *ploidy_regions(ploidy_t *ploidy)
+{
+    return ploidy->idx;
+}
+
+int ploidy_parse(const char *line, char **chr_beg, char **chr_end, uint32_t *beg, uint32_t *end, void *payload, void *usr)
+{
+    int i, ret;
+    ploidy_t *ploidy = (ploidy_t*) usr;
+    void *sex2id = ploidy->sex2id;
+
+    // Check for special case of default ploidy "* * * <sex> <ploidy>"
+    int default_ploidy_def = 0;
+
+    char *ss = (char*) line;
+    while ( *ss && isspace(*ss) ) ss++;
+    if ( ss[0]=='*' && (!ss[1] || isspace(ss[1])) )
+        default_ploidy_def = 1; // definition of default ploidy, chr="*"
+    else
+    {
+        // Fill CHR,FROM,TO
+        ret = regidx_parse_tab(line,chr_beg,chr_end,beg,end,NULL,NULL);
+        if ( ret!=0 ) return ret;
+    }
+
+    // Skip the fields already parsed by regidx_parse_tab
+    ss = (char*) line;
+    while ( *ss && isspace(*ss) ) ss++;
+    for (i=0; i<3; i++)
+    {
+        while ( *ss && !isspace(*ss) ) ss++;
+        if ( !*ss ) return -2;  // wrong number of fields
+        while ( *ss && isspace(*ss) ) ss++;
+    }
+    if ( !*ss ) return -2;
+
+    // Parse the payload
+    char *se = ss;
+    while ( *se && !isspace(*se) ) se++;
+    if ( !*se || se==ss ) error("Could not parse: %s\n", line);
+    ploidy->tmp_str.l = 0;
+    kputsn(ss,se-ss,&ploidy->tmp_str);
+
+    sex_ploidy_t *sp = (sex_ploidy_t*) payload;
+    if ( khash_str2int_get(sex2id, ploidy->tmp_str.s, &sp->sex) != 0 )
+    {
+        ploidy->nsex++;
+        hts_expand0(char*,ploidy->nsex,ploidy->msex,ploidy->id2sex);
+        ploidy->id2sex[ploidy->nsex-1] = strdup(ploidy->tmp_str.s);
+        sp->sex = khash_str2int_inc(ploidy->sex2id, ploidy->id2sex[ploidy->nsex-1]);
+        ploidy->sex2dflt = (int*) realloc(ploidy->sex2dflt,sizeof(int)*ploidy->nsex);
+        ploidy->sex2dflt[ploidy->nsex-1] = -1;
+    }
+
+    ss = se;
+    while ( *se && isspace(*se) ) se++;
+    if ( !*se ) error("Could not parse: %s\n", line);
+    sp->ploidy = strtol(ss,&se,10);
+    if ( ss==se ) error("Could not parse: %s\n", line);
+    if ( ploidy->min<0 || sp->ploidy < ploidy->min ) ploidy->min = sp->ploidy;
+    if ( ploidy->max<0 || sp->ploidy > ploidy->max ) ploidy->max = sp->ploidy;
+
+    // Special case, chr="*" stands for a default value
+    if ( default_ploidy_def )
+    {
+        ploidy->sex2dflt[ploidy->nsex-1] = sp->ploidy;
+        return -1;
+    }
+
+    return 0;
+}
+
+static void _set_defaults(ploidy_t *ploidy, int dflt)
+{
+    int i;
+    if ( khash_str2int_get(ploidy->sex2id, "*", &i) == 0 ) dflt = ploidy->sex2dflt[i];
+    for (i=0; i<ploidy->nsex; i++)
+        if ( ploidy->sex2dflt[i]==-1 ) ploidy->sex2dflt[i] = dflt;
+
+    ploidy->dflt = dflt;
+    if ( ploidy->min<0 || dflt < ploidy->min ) ploidy->min = dflt;
+    if ( ploidy->max<0 || dflt > ploidy->max ) ploidy->max = dflt;
+}
+
+ploidy_t *ploidy_init(const char *fname, int dflt)
+{
+    ploidy_t *pld = (ploidy_t*) calloc(1,sizeof(ploidy_t));
+    if ( !pld ) return NULL;
+
+    pld->min = pld->max = -1;
+    pld->sex2id = khash_str2int_init();
+    pld->idx = regidx_init(fname,ploidy_parse,NULL,sizeof(sex_ploidy_t),pld);
+    if ( !pld->idx )
+    {
+        ploidy_destroy(pld);
+        return NULL;
+    }
+    pld->itr = regitr_init(pld->idx);
+    _set_defaults(pld,dflt);
+    return pld;
+}
+
+ploidy_t *ploidy_init_string(const char *str, int dflt)
+{
+    ploidy_t *pld = (ploidy_t*) calloc(1,sizeof(ploidy_t));
+    if ( !pld ) return NULL;
+
+    pld->min = pld->max = -1;
+    pld->sex2id = khash_str2int_init();
+    pld->idx = regidx_init(NULL,ploidy_parse,NULL,sizeof(sex_ploidy_t),pld);
+    pld->itr = regitr_init(pld->idx);
+
+    kstring_t tmp = {0,0,0};
+    const char *ss = str;
+    while ( *ss )
+    {
+        while ( *ss && isspace(*ss) ) ss++;
+        const char *se = ss;
+        while ( *se && *se!='\r' && *se!='\n' ) se++;
+        tmp.l = 0;
+        kputsn(ss, se-ss, &tmp);
+        regidx_insert(pld->idx,tmp.s);
+        while ( *se && isspace(*se) ) se++;
+        ss = se;
+    }
+    free(tmp.s);
+
+    _set_defaults(pld,dflt);
+    return pld;
+}
+
+void ploidy_destroy(ploidy_t *ploidy)
+{
+    if ( ploidy->sex2id ) khash_str2int_destroy_free(ploidy->sex2id);
+    if ( ploidy->itr ) regitr_destroy(ploidy->itr);
+    if ( ploidy->idx ) regidx_destroy(ploidy->idx);
+    free(ploidy->id2sex);
+    free(ploidy->tmp_str.s);
+    free(ploidy->sex2dflt);
+    free(ploidy);
+}
+
+int ploidy_query(ploidy_t *ploidy, char *seq, int pos, int *sex2ploidy, int *min, int *max)
+{
+    int i, ret = regidx_overlap(ploidy->idx, seq,pos,pos, ploidy->itr);
+
+    if ( !sex2ploidy && !min && !max ) return ret;
+
+    if ( !ret )
+    {
+        // no overlap
+        if ( min ) *min = ploidy->dflt;
+        if ( max ) *max = ploidy->dflt;
+        if ( sex2ploidy )
+            for (i=0; i<ploidy->nsex; i++) sex2ploidy[i] = ploidy->sex2dflt[i];
+        return 0;
+    }
+
+    int _min = INT_MAX, _max = -1;
+    if ( sex2ploidy ) for (i=0; i<ploidy->nsex; i++) sex2ploidy[i] = ploidy->dflt;
+
+    while ( regitr_overlap(ploidy->itr) )
+    {
+        int sex = regitr_payload(ploidy->itr,sex_ploidy_t).sex;
+        int pld = regitr_payload(ploidy->itr,sex_ploidy_t).ploidy;
+        if ( pld!=ploidy->dflt ) 
+        {
+            if ( sex2ploidy ) sex2ploidy[ sex ] = pld;
+            if ( _min > pld ) _min = pld;
+            if ( _max < pld ) _max = pld;
+        }
+    }
+    if ( _max==-1 ) _max = _min = ploidy->dflt;
+    if ( max ) *max = _max;
+    if ( min ) *min = _min;
+
+    return 1;
+}
+
+int ploidy_nsex(ploidy_t *ploidy)
+{
+    return ploidy->nsex;
+}
+
+char *ploidy_id2sex(ploidy_t *ploidy, int id)
+{
+    if ( id<0 || id>=ploidy->nsex ) return NULL;
+    return ploidy->id2sex[id];
+}
+
+int ploidy_sex2id(ploidy_t *ploidy, char *sex)
+{
+    int id;
+    if ( khash_str2int_get(ploidy->sex2id,sex,&id)!=0 ) return -1;
+    return id;
+}
+
+int ploidy_add_sex(ploidy_t *ploidy, const char *sex)
+{
+    int id;
+    if ( khash_str2int_get(ploidy->sex2id, sex, &id)==0 ) return id;
+    ploidy->nsex++;
+    hts_expand0(char*,ploidy->nsex,ploidy->msex,ploidy->id2sex);
+    ploidy->id2sex[ploidy->nsex-1] = strdup(sex);
+    ploidy->sex2dflt = (int*) realloc(ploidy->sex2dflt,sizeof(int)*ploidy->nsex);
+    ploidy->sex2dflt[ploidy->nsex-1] = ploidy->dflt;
+    return khash_str2int_inc(ploidy->sex2id, ploidy->id2sex[ploidy->nsex-1]);
+}
+
+int ploidy_max(ploidy_t *ploidy)
+{
+    return ploidy->dflt > ploidy->max ? ploidy->dflt : ploidy->max;
+}
+
+int ploidy_min(ploidy_t *ploidy)
+{
+    return ploidy->dflt < ploidy->min ? ploidy->dflt : ploidy->min;
+}
+
diff --git a/bcftools/ploidy.c.pysam.c b/bcftools/ploidy.c.pysam.c
new file mode 100644
index 0000000..aee0c56
--- /dev/null
+++ b/bcftools/ploidy.c.pysam.c
@@ -0,0 +1,270 @@
+#include "bcftools.pysam.h"
+
+/* 
+    Copyright (C) 2014-2016 Genome Research Ltd.
+
+    Author: Petr Danecek <pd3@sanger.ac.uk>
+
+    Permission is hereby granted, free of charge, to any person obtaining a copy
+    of this software and associated documentation files (the "Software"), to deal
+    in the Software without restriction, including without limitation the rights
+    to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+    copies of the Software, and to permit persons to whom the Software is
+    furnished to do so, subject to the following conditions:
+    
+    The above copyright notice and this permission notice shall be included in
+    all copies or substantial portions of the Software.
+    
+    THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+    IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+    FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+    AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+    LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+    OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+    THE SOFTWARE.
+*/
+
+#include <htslib/khash_str2int.h>
+#include <htslib/kseq.h>
+#include <htslib/hts.h>
+#include "bcftools.h"
+#include "ploidy.h"
+
+struct _ploidy_t
+{
+    int nsex, msex;     // number of genders, m:number of allocated elements in id2sex array
+    int dflt, min, max; // ploidy: default, min and max (only explicitly listed)
+    int *sex2dflt;
+    regidx_t *idx;
+    regitr_t *itr;
+    void *sex2id;
+    char **id2sex;
+    kstring_t tmp_str;
+};
+
+typedef struct
+{
+    int sex, ploidy;
+}
+sex_ploidy_t;
+
+
+regidx_t *ploidy_regions(ploidy_t *ploidy)
+{
+    return ploidy->idx;
+}
+
+int ploidy_parse(const char *line, char **chr_beg, char **chr_end, uint32_t *beg, uint32_t *end, void *payload, void *usr)
+{
+    int i, ret;
+    ploidy_t *ploidy = (ploidy_t*) usr;
+    void *sex2id = ploidy->sex2id;
+
+    // Check for special case of default ploidy "* * * <sex> <ploidy>"
+    int default_ploidy_def = 0;
+
+    char *ss = (char*) line;
+    while ( *ss && isspace(*ss) ) ss++;
+    if ( ss[0]=='*' && (!ss[1] || isspace(ss[1])) )
+        default_ploidy_def = 1; // definition of default ploidy, chr="*"
+    else
+    {
+        // Fill CHR,FROM,TO
+        ret = regidx_parse_tab(line,chr_beg,chr_end,beg,end,NULL,NULL);
+        if ( ret!=0 ) return ret;
+    }
+
+    // Skip the fields already parsed by regidx_parse_tab
+    ss = (char*) line;
+    while ( *ss && isspace(*ss) ) ss++;
+    for (i=0; i<3; i++)
+    {
+        while ( *ss && !isspace(*ss) ) ss++;
+        if ( !*ss ) return -2;  // wrong number of fields
+        while ( *ss && isspace(*ss) ) ss++;
+    }
+    if ( !*ss ) return -2;
+
+    // Parse the payload
+    char *se = ss;
+    while ( *se && !isspace(*se) ) se++;
+    if ( !*se || se==ss ) error("Could not parse: %s\n", line);
+    ploidy->tmp_str.l = 0;
+    kputsn(ss,se-ss,&ploidy->tmp_str);
+
+    sex_ploidy_t *sp = (sex_ploidy_t*) payload;
+    if ( khash_str2int_get(sex2id, ploidy->tmp_str.s, &sp->sex) != 0 )
+    {
+        ploidy->nsex++;
+        hts_expand0(char*,ploidy->nsex,ploidy->msex,ploidy->id2sex);
+        ploidy->id2sex[ploidy->nsex-1] = strdup(ploidy->tmp_str.s);
+        sp->sex = khash_str2int_inc(ploidy->sex2id, ploidy->id2sex[ploidy->nsex-1]);
+        ploidy->sex2dflt = (int*) realloc(ploidy->sex2dflt,sizeof(int)*ploidy->nsex);
+        ploidy->sex2dflt[ploidy->nsex-1] = -1;
+    }
+
+    ss = se;
+    while ( *se && isspace(*se) ) se++;
+    if ( !*se ) error("Could not parse: %s\n", line);
+    sp->ploidy = strtol(ss,&se,10);
+    if ( ss==se ) error("Could not parse: %s\n", line);
+    if ( ploidy->min<0 || sp->ploidy < ploidy->min ) ploidy->min = sp->ploidy;
+    if ( ploidy->max<0 || sp->ploidy > ploidy->max ) ploidy->max = sp->ploidy;
+
+    // Special case, chr="*" stands for a default value
+    if ( default_ploidy_def )
+    {
+        ploidy->sex2dflt[ploidy->nsex-1] = sp->ploidy;
+        return -1;
+    }
+
+    return 0;
+}
+
+static void _set_defaults(ploidy_t *ploidy, int dflt)
+{
+    int i;
+    if ( khash_str2int_get(ploidy->sex2id, "*", &i) == 0 ) dflt = ploidy->sex2dflt[i];
+    for (i=0; i<ploidy->nsex; i++)
+        if ( ploidy->sex2dflt[i]==-1 ) ploidy->sex2dflt[i] = dflt;
+
+    ploidy->dflt = dflt;
+    if ( ploidy->min<0 || dflt < ploidy->min ) ploidy->min = dflt;
+    if ( ploidy->max<0 || dflt > ploidy->max ) ploidy->max = dflt;
+}
+
+ploidy_t *ploidy_init(const char *fname, int dflt)
+{
+    ploidy_t *pld = (ploidy_t*) calloc(1,sizeof(ploidy_t));
+    if ( !pld ) return NULL;
+
+    pld->min = pld->max = -1;
+    pld->sex2id = khash_str2int_init();
+    pld->idx = regidx_init(fname,ploidy_parse,NULL,sizeof(sex_ploidy_t),pld);
+    if ( !pld->idx )
+    {
+        ploidy_destroy(pld);
+        return NULL;
+    }
+    pld->itr = regitr_init(pld->idx);
+    _set_defaults(pld,dflt);
+    return pld;
+}
+
+ploidy_t *ploidy_init_string(const char *str, int dflt)
+{
+    ploidy_t *pld = (ploidy_t*) calloc(1,sizeof(ploidy_t));
+    if ( !pld ) return NULL;
+
+    pld->min = pld->max = -1;
+    pld->sex2id = khash_str2int_init();
+    pld->idx = regidx_init(NULL,ploidy_parse,NULL,sizeof(sex_ploidy_t),pld);
+    pld->itr = regitr_init(pld->idx);
+
+    kstring_t tmp = {0,0,0};
+    const char *ss = str;
+    while ( *ss )
+    {
+        while ( *ss && isspace(*ss) ) ss++;
+        const char *se = ss;
+        while ( *se && *se!='\r' && *se!='\n' ) se++;
+        tmp.l = 0;
+        kputsn(ss, se-ss, &tmp);
+        regidx_insert(pld->idx,tmp.s);
+        while ( *se && isspace(*se) ) se++;
+        ss = se;
+    }
+    free(tmp.s);
+
+    _set_defaults(pld,dflt);
+    return pld;
+}
+
+void ploidy_destroy(ploidy_t *ploidy)
+{
+    if ( ploidy->sex2id ) khash_str2int_destroy_free(ploidy->sex2id);
+    if ( ploidy->itr ) regitr_destroy(ploidy->itr);
+    if ( ploidy->idx ) regidx_destroy(ploidy->idx);
+    free(ploidy->id2sex);
+    free(ploidy->tmp_str.s);
+    free(ploidy->sex2dflt);
+    free(ploidy);
+}
+
+int ploidy_query(ploidy_t *ploidy, char *seq, int pos, int *sex2ploidy, int *min, int *max)
+{
+    int i, ret = regidx_overlap(ploidy->idx, seq,pos,pos, ploidy->itr);
+
+    if ( !sex2ploidy && !min && !max ) return ret;
+
+    if ( !ret )
+    {
+        // no overlap
+        if ( min ) *min = ploidy->dflt;
+        if ( max ) *max = ploidy->dflt;
+        if ( sex2ploidy )
+            for (i=0; i<ploidy->nsex; i++) sex2ploidy[i] = ploidy->sex2dflt[i];
+        return 0;
+    }
+
+    int _min = INT_MAX, _max = -1;
+    if ( sex2ploidy ) for (i=0; i<ploidy->nsex; i++) sex2ploidy[i] = ploidy->dflt;
+
+    while ( regitr_overlap(ploidy->itr) )
+    {
+        int sex = regitr_payload(ploidy->itr,sex_ploidy_t).sex;
+        int pld = regitr_payload(ploidy->itr,sex_ploidy_t).ploidy;
+        if ( pld!=ploidy->dflt ) 
+        {
+            if ( sex2ploidy ) sex2ploidy[ sex ] = pld;
+            if ( _min > pld ) _min = pld;
+            if ( _max < pld ) _max = pld;
+        }
+    }
+    if ( _max==-1 ) _max = _min = ploidy->dflt;
+    if ( max ) *max = _max;
+    if ( min ) *min = _min;
+
+    return 1;
+}
+
+int ploidy_nsex(ploidy_t *ploidy)
+{
+    return ploidy->nsex;
+}
+
+char *ploidy_id2sex(ploidy_t *ploidy, int id)
+{
+    if ( id<0 || id>=ploidy->nsex ) return NULL;
+    return ploidy->id2sex[id];
+}
+
+int ploidy_sex2id(ploidy_t *ploidy, char *sex)
+{
+    int id;
+    if ( khash_str2int_get(ploidy->sex2id,sex,&id)!=0 ) return -1;
+    return id;
+}
+
+int ploidy_add_sex(ploidy_t *ploidy, const char *sex)
+{
+    int id;
+    if ( khash_str2int_get(ploidy->sex2id, sex, &id)==0 ) return id;
+    ploidy->nsex++;
+    hts_expand0(char*,ploidy->nsex,ploidy->msex,ploidy->id2sex);
+    ploidy->id2sex[ploidy->nsex-1] = strdup(sex);
+    ploidy->sex2dflt = (int*) realloc(ploidy->sex2dflt,sizeof(int)*ploidy->nsex);
+    ploidy->sex2dflt[ploidy->nsex-1] = ploidy->dflt;
+    return khash_str2int_inc(ploidy->sex2id, ploidy->id2sex[ploidy->nsex-1]);
+}
+
+int ploidy_max(ploidy_t *ploidy)
+{
+    return ploidy->dflt > ploidy->max ? ploidy->dflt : ploidy->max;
+}
+
+int ploidy_min(ploidy_t *ploidy)
+{
+    return ploidy->dflt < ploidy->min ? ploidy->dflt : ploidy->min;
+}
+
diff --git a/bcftools/ploidy.h b/bcftools/ploidy.h
new file mode 100644
index 0000000..7697c65
--- /dev/null
+++ b/bcftools/ploidy.h
@@ -0,0 +1,129 @@
+/* 
+    Copyright (C) 2014-2015 Genome Research Ltd.
+
+    Author: Petr Danecek <pd3@sanger.ac.uk>
+
+    Permission is hereby granted, free of charge, to any person obtaining a copy
+    of this software and associated documentation files (the "Software"), to deal
+    in the Software without restriction, including without limitation the rights
+    to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+    copies of the Software, and to permit persons to whom the Software is
+    furnished to do so, subject to the following conditions:
+    
+    The above copyright notice and this permission notice shall be included in
+    all copies or substantial portions of the Software.
+    
+    THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+    IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+    FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+    AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+    LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+    OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+    THE SOFTWARE.
+*/
+
+/*
+    Lookup from region and sex to ploidy.
+
+    Example of usage:
+
+        int default_ploidy = 2;
+        ploidy_t *pld = ploidy_init(fname, default_ploidy);
+
+        int nsex = ploidy_nsex(pld);
+        int *sex2ploidy = malloc(sizeof(int)*nsex);
+
+        ploidy_query(pld, "X",60000, sex2ploidy, NULL, NULL);
+        for (i=0; i<nsex; i++)
+            printf("ploidy of %s is %d\n", ploidy_id2sex(pld,i), sex2ploidy[i]);
+
+        ploidy_destroy(pld);
+
+    An example of ploidy file format follows. The coordinates are 1-based and
+    inclusive. The "*" records define the default ploidy for each sex. If not
+    present, the default_ploidy passed to ploidy_init is used instead:
+        X 1 60000 M 1
+        X 2699521 154931043 M 1
+        Y 1 59373566 M 1
+        Y 1 59373566 F 0
+        MT 1 16569 M 1
+        MT 1 16569 F 1
+        *  * *     M 2
+        *  * *     F 2
+*/
+
+#ifndef __PLOIDY_H__
+#define __PLOIDY_H__
+
+#include "regidx.h"
+
+typedef struct _ploidy_t ploidy_t;
+
+/*
+ *  ploidy_init()
+ *  @param fname:   input file name or NULL if default ploidy from example above should be used
+ *  @param dflt:    default ploidy to use for unlisted regions (the '* * *' records have precedence).
+ *
+ *  Returns new structure on success or NULL on error.
+ */
+ploidy_t *ploidy_init(const char *fname, int dflt);
+
+/* Same as ploidy_init() but the whole file is passed as a single string */
+ploidy_t *ploidy_init_string(const char *str, int dflt);
+
+/*
+ *  ploidy_destroy() - free memory allocated by ploidy_init
+ */
+void ploidy_destroy(ploidy_t *ploidy);
+
+/*
+ *  ploidy_query() - query ploidy at a position for all genders at once
+ *  @param seq: chromosome name
+ *  @param pos: 0-based position
+ *  @param sex2ploidy:  if not NULL, array will be filled with mapping from sex id to ploidy
+ *  @param min: if not NULL, minimum encountered encountered will be set
+ *  @param max: if not NULL, maximum encountered encountered will be set
+ *
+ *  Returns 1 if the position is listed in the regions or 0 otherwise.
+ */
+int ploidy_query(ploidy_t *ploidy, char *seq, int pos, int *sex2ploidy, int *min, int *max);
+
+/*
+ *  ploidy_nsex() - return number of recognised genders
+ */
+int ploidy_nsex(ploidy_t *ploidy);
+
+/*
+ *  ploidy_id2sex() - mapping between numeric gender id and name
+ *
+ *  Returns gender name (e.g. "M" or "F" in the example above)
+ *  or NULL if there is no such id.
+ */
+char *ploidy_id2sex(ploidy_t *ploidy, int id);
+
+/*
+ *  ploidy_sex2id() - mapping between gender name and its numeric id
+ *
+ *  Returns numeric id or -1 if not present.
+ */
+int ploidy_sex2id(ploidy_t *ploidy, char *sex);
+
+/*
+ *  ploidy_add_sex() - register new gender name. This function is
+ *      useful when gender has the default ploidy for all regions
+ *      and is not listed in the file passed to ploidy_init()
+ *
+ *  Returns numeric id of the added sex, regardless of whether the string was
+ *  newly added or was already present in the dictionary.
+ */
+int ploidy_add_sex(ploidy_t *ploidy, const char *sex);
+
+/** Returns region index for raw access */
+regidx_t *ploidy_regions(ploidy_t *ploidy);
+
+/** Return the minimum / maximum recognised ploidy  */
+int ploidy_max(ploidy_t *ploidy);
+int ploidy_min(ploidy_t *ploidy);
+
+#endif
+
diff --git a/bcftools/prob1.c b/bcftools/prob1.c
new file mode 100644
index 0000000..d298d6a
--- /dev/null
+++ b/bcftools/prob1.c
@@ -0,0 +1,524 @@
+/*  prob1.c -- mathematical utility functions.
+
+    Copyright (C) 2010, 2011 Broad Institute.
+    Copyright (C) 2012, 2013-2014, 2017 Genome Research Ltd.
+
+    Author: Heng Li <lh3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.  */
+
+#include <math.h>
+#include <stdlib.h>
+#include <string.h>
+#include <stdio.h>
+#include <errno.h>
+#include <assert.h>
+#include <limits.h>
+#include "prob1.h"
+
+#define MC_MAX_EM_ITER 16
+#define MC_EM_EPS 1e-5
+#define MC_DEF_INDEL 0.15
+
+void bcf_p1_indel_prior(bcf_p1aux_t *ma, double x)
+{
+    int i;
+    for (i = 0; i < ma->M; ++i)
+        ma->phi_indel[i] = ma->phi[i] * x;
+    ma->phi_indel[ma->M] = 1. - ma->phi[ma->M] * x;
+}
+
+static void init_prior(int type, double theta, int M, double *phi)
+{
+    int i;
+    if (type == MC_PTYPE_COND2) {
+        for (i = 0; i <= M; ++i)
+            phi[i] = 2. * (i + 1) / (M + 1) / (M + 2);
+    } else if (type == MC_PTYPE_FLAT) {
+        for (i = 0; i <= M; ++i)
+            phi[i] = 1. / (M + 1);
+    } else {
+        double sum;
+        for (i = 0, sum = 0.; i < M; ++i)
+            sum += (phi[i] = theta / (M - i));
+        phi[M] = 1. - sum;
+    }
+}
+
+void bcf_p1_init_prior(bcf_p1aux_t *ma, int type, double theta)
+{
+    init_prior(type, theta, ma->M, ma->phi);
+    bcf_p1_indel_prior(ma, MC_DEF_INDEL);
+}
+
+void bcf_p1_init_subprior(bcf_p1aux_t *ma, int type, double theta)
+{
+    if (ma->n1 <= 0 || ma->n1 >= ma->M) return;
+    init_prior(type, theta, 2*ma->n1, ma->phi1);
+    init_prior(type, theta, 2*(ma->n - ma->n1), ma->phi2);
+}
+
+
+/* Initialise a bcf_p1aux_t */
+bcf_p1aux_t *bcf_p1_init(int n_smpl, uint8_t *ploidy)
+{
+    bcf_p1aux_t *ma;
+    int i;
+    ma = (bcf_p1aux_t*) calloc(1, sizeof(bcf_p1aux_t));
+    ma->n1 = -1;
+    ma->n = n_smpl;
+    ma->M = 2 * n_smpl;
+    if (ploidy) {
+        ma->ploidy = (uint8_t*) malloc(n_smpl);
+        memcpy(ma->ploidy, ploidy, n_smpl);
+        for (i = 0, ma->M = 0; i < n_smpl; ++i) ma->M += ploidy[i];
+        if (ma->M == 2 * n_smpl) {
+            free(ma->ploidy);
+            ma->ploidy = 0;
+        }
+    }
+    ma->q2p = (double*) calloc(256, sizeof(double));
+    ma->pdg = (double*) calloc(3 * ma->n, sizeof(double));
+    ma->phi = (double*) calloc(ma->M + 1, sizeof(double));
+    ma->phi_indel = (double*) calloc(ma->M + 1, sizeof(double));
+    ma->phi1 = (double*) calloc(ma->M + 1, sizeof(double));
+    ma->phi2 = (double*) calloc(ma->M + 1, sizeof(double));
+    ma->z = (double*) calloc(ma->M + 1, sizeof(double));
+    ma->zswap = (double*) calloc(ma->M + 1, sizeof(double));
+    ma->z1 = (double*) calloc(ma->M + 1, sizeof(double)); // actually we do not need this large
+    ma->z2 = (double*) calloc(ma->M + 1, sizeof(double));
+    ma->afs = (double*) calloc(ma->M + 1, sizeof(double));
+    ma->afs1 = (double*) calloc(ma->M + 1, sizeof(double));
+    ma->lf = (double*) calloc(ma->M + 1, sizeof(double));
+    for (i = 0; i < 256; ++i)
+        ma->q2p[i] = pow(10., -i / 10.);
+    for (i = 0; i <= ma->M; ++i) ma->lf[i] = lgamma(i + 1);
+    bcf_p1_init_prior(ma, MC_PTYPE_FULL, 1e-3); // the simplest prior
+    return ma;
+}
+
+int bcf_p1_get_M(bcf_p1aux_t *b) { return b->M; }
+
+int bcf_p1_set_n1(bcf_p1aux_t *b, int n1)
+{
+    if (n1 == 0 || n1 >= b->n) return -1;
+    if (b->M != b->n * 2) {
+        fprintf(stderr, "[%s] unable to set `n1' when there are haploid samples.\n", __func__);
+        return -1;
+    }
+    b->n1 = n1;
+    return 0;
+}
+
+void bcf_p1_destroy(bcf_p1aux_t *ma)
+{
+    if (ma) {
+        int k;
+        free(ma->lf);
+        if (ma->hg && ma->n1 > 0) {
+            for (k = 0; k <= 2*ma->n1; ++k) free(ma->hg[k]);
+            free(ma->hg);
+        }
+        free(ma->ploidy); free(ma->q2p); free(ma->pdg);
+        free(ma->phi); free(ma->phi_indel); free(ma->phi1); free(ma->phi2);
+        free(ma->z); free(ma->zswap); free(ma->z1); free(ma->z2);
+        free(ma->afs); free(ma->afs1);
+        free(ma);
+    }
+}
+
+extern double kf_gammap(double s, double z);
+int test16(bcf1_t *b, anno16_t *a);
+
+/* Calculate P(D|g) */
+static int cal_pdg(const bcf1_t *b, bcf_p1aux_t *ma)
+{
+    int i, j;
+    long p_a[16], *p=p_a, tmp;
+    if (b->n_allele > 16)
+        p = (long*) malloc(b->n_allele * sizeof(long));
+    memset(p, 0, sizeof(long) * b->n_allele);
+
+    // Set P(D|g) for each sample and sum phread likelihoods across all samples to create lk
+    for (j = 0; j < ma->n; ++j) {
+        // Fetch the PL array for the sample
+        const int *pi = ma->PL + j * ma->PL_len;
+        // Fetch the P(D|g) array for the sample
+        double *pdg = ma->pdg + j * 3;
+        pdg[0] = ma->q2p[pi[2]]; pdg[1] = ma->q2p[pi[1]]; pdg[2] = ma->q2p[pi[0]];
+        for (i = 0; i < b->n_allele; ++i)
+            p[i] += (int)pi[(i+1)*(i+2)/2-1];
+    }
+    for (i = 0; i < b->n_allele; ++i) p[i] = p[i]<<4 | i;
+    for (i = 1; i < b->n_allele; ++i) // insertion sort
+        for (j = i; j > 0 && p[j] < p[j-1]; --j)
+            tmp = p[j], p[j] = p[j-1], p[j-1] = tmp;
+    for (i = b->n_allele - 1; i >= 0; --i)
+        if ((p[i]&0xf) == 0) break;
+    if (p != p_a)
+        free(p);
+    return i;
+}
+
+
+/* f0 is freq of the ref allele */
+int bcf_p1_call_gt(const bcf_p1aux_t *ma, double f0, int k, int is_var)
+{
+    double sum, g[3];
+    double max, f3[3], *pdg = ma->pdg + k * 3;
+    int q, i, max_i, ploidy;
+    /* determine ploidy */
+    ploidy = ma->ploidy? ma->ploidy[k] : 2;
+    if (ploidy == 2) {
+    /* given allele frequency we can determine how many of each
+     * genotype we have by HWE p=1-q PP=p^2 PQ&QP=2*p*q QQ=q^2 */
+        f3[0] = (1.-f0)*(1.-f0); f3[1] = 2.*f0*(1.-f0); f3[2] = f0*f0;
+    } else {
+        f3[0] = 1. - f0; f3[1] = 0; f3[2] = f0;
+    }
+    for (i = 0, sum = 0.; i < 3; ++i)
+        sum += (g[i] = pdg[i] * f3[i]);
+    /* normalise g and then determine max */
+    for (i = 0, max = -1., max_i = 0; i < 3; ++i) {
+        g[i] /= sum;
+        if (g[i] > max) max = g[i], max_i = i;
+    }
+    if ( !is_var ) { max_i = 2; max = g[2]; }   // force 0/0 genotype if the site is non-variant
+    max = 1. - max;
+    if (max < 1e-308) max = 1e-308;
+    q = (int)(-4.343 * log(max) + .499);
+    if (q > 99) q = 99;
+    return q<<2|max_i;
+}
+
+// If likelihoods fall below this they get squashed to 0
+#define TINY 1e-20
+static void mc_cal_y_core(bcf_p1aux_t *ma, int beg)
+{
+    double *z[2], *tmp, *pdg;
+    int _j, last_min, last_max;
+    assert(beg == 0 || ma->M == ma->n*2);
+    z[0] = ma->z;
+    z[1] = ma->zswap;
+    pdg = ma->pdg;
+    memset(z[0], 0, sizeof(double) * (ma->M + 1));
+    memset(z[1], 0, sizeof(double) * (ma->M + 1));
+    z[0][0] = 1.;
+    last_min = last_max = 0;
+    ma->t = 0.;
+    if (ma->M == ma->n * 2) {
+        int M = 0;
+        for (_j = beg; _j < ma->n; ++_j) {
+            int k, j = _j - beg, _min = last_min, _max = last_max, M0;
+            double p[3], sum;
+            M0 = M; M += 2;
+            // Fetch P(D|g) for this sample
+            pdg = ma->pdg + _j * 3;
+            p[0] = pdg[0]; p[1] = 2. * pdg[1]; p[2] = pdg[2];
+            for (; _min < _max && z[0][_min] < TINY; ++_min) z[0][_min] = z[1][_min] = 0.;
+            for (; _max > _min && z[0][_max] < TINY; --_max) z[0][_max] = z[1][_max] = 0.;
+            _max += 2;
+            if (_min == 0) k = 0, z[1][k] = (M0-k+1) * (M0-k+2) * p[0] * z[0][k];
+            if (_min <= 1) k = 1, z[1][k] = (M0-k+1) * (M0-k+2) * p[0] * z[0][k] + k*(M0-k+2) * p[1] * z[0][k-1];
+            for (k = _min < 2? 2 : _min; k <= _max; ++k)
+                z[1][k] = (M0-k+1)*(M0-k+2) * p[0] * z[0][k] + k*(M0-k+2) * p[1] * z[0][k-1] + k*(k-1)* p[2] * z[0][k-2];
+            for (k = _min, sum = 0.; k <= _max; ++k) sum += z[1][k];
+            ma->t += log(sum / (M * (M - 1.)));
+            for (k = _min; k <= _max; ++k) z[1][k] /= sum;
+            if (_min >= 1) z[1][_min-1] = 0.;
+            if (_min >= 2) z[1][_min-2] = 0.;
+            // If we are not on the last sample
+            if (j < ma->n - 1) z[1][_max+1] = z[1][_max+2] = 0.;
+            if (_j == ma->n1 - 1) { // set pop1; ma->n1==-1 when unset
+                ma->t1 = ma->t;
+                memcpy(ma->z1, z[1], sizeof(double) * (ma->n1 * 2 + 1));
+            }
+            tmp = z[0]; z[0] = z[1]; z[1] = tmp;
+            last_min = _min; last_max = _max;
+        }
+        //for (_j = 0; _j < last_min; ++_j) z[0][_j] = 0.; // TODO: are these necessary?
+        //for (_j = last_max + 1; _j < ma->M; ++_j) z[0][_j] = 0.;
+    } else { // this block is very similar to the block above; these two might be merged in future
+        int j, M = 0;
+        for (j = 0; j < ma->n; ++j) {
+            int k, M0, _min = last_min, _max = last_max;
+            double p[3], sum;
+            // Fetch P(D|g) for this sample
+            pdg = ma->pdg + j * 3;
+            for (; _min < _max && z[0][_min] < TINY; ++_min) z[0][_min] = z[1][_min] = 0.;
+            for (; _max > _min && z[0][_max] < TINY; --_max) z[0][_max] = z[1][_max] = 0.;
+            M0 = M;
+            M += ma->ploidy[j];
+            if (ma->ploidy[j] == 1) {
+                p[0] = pdg[0]; p[1] = pdg[2];
+                _max++;
+                if (_min == 0) k = 0, z[1][k] = (M0+1-k) * p[0] * z[0][k];
+                for (k = _min < 1? 1 : _min; k <= _max; ++k)
+                    z[1][k] = (M0+1-k) * p[0] * z[0][k] + k * p[1] * z[0][k-1];
+                for (k = _min, sum = 0.; k <= _max; ++k) sum += z[1][k];
+                ma->t += log(sum / M);
+                for (k = _min; k <= _max; ++k) z[1][k] /= sum;
+                if (_min >= 1) z[1][_min-1] = 0.;
+                // If we are not on the last sample
+                if (j < ma->n - 1) z[1][_max+1] = 0.;
+            } else if (ma->ploidy[j] == 2) {
+                p[0] = pdg[0]; p[1] = 2 * pdg[1]; p[2] = pdg[2];
+                _max += 2;
+                if (_min == 0) k = 0, z[1][k] = (M0-k+1) * (M0-k+2) * p[0] * z[0][k];
+                if (_min <= 1) k = 1, z[1][k] = (M0-k+1) * (M0-k+2) * p[0] * z[0][k] + k*(M0-k+2) * p[1] * z[0][k-1];
+                for (k = _min < 2? 2 : _min; k <= _max; ++k)
+                    z[1][k] = (M0-k+1)*(M0-k+2) * p[0] * z[0][k] + k*(M0-k+2) * p[1] * z[0][k-1] + k*(k-1)* p[2] * z[0][k-2];
+                for (k = _min, sum = 0.; k <= _max; ++k) sum += z[1][k];
+                ma->t += log(sum / (M * (M - 1.)));
+                for (k = _min; k <= _max; ++k) z[1][k] /= sum;
+                if (_min >= 1) z[1][_min-1] = 0.;
+                if (_min >= 2) z[1][_min-2] = 0.;
+                // If we are not on the last sample
+                if (j < ma->n - 1) z[1][_max+1] = z[1][_max+2] = 0.;
+            }
+            tmp = z[0]; z[0] = z[1]; z[1] = tmp;
+            last_min = _min; last_max = _max;
+        }
+    }
+    if (z[0] != ma->z) memcpy(ma->z, z[0], sizeof(double) * (ma->M + 1));
+}
+
+static void mc_cal_y(bcf_p1aux_t *ma)
+{
+    if (ma->n1 > 0 && ma->n1 < ma->n && ma->M == ma->n * 2) { // NB: ma->n1 is ineffective when there are haploid samples
+        int k;
+        long double x;
+        memset(ma->z1, 0, sizeof(double) * (2 * ma->n1 + 1));
+        memset(ma->z2, 0, sizeof(double) * (2 * (ma->n - ma->n1) + 1));
+        ma->t1 = ma->t2 = 0.;
+        mc_cal_y_core(ma, ma->n1);
+        ma->t2 = ma->t;
+        memcpy(ma->z2, ma->z, sizeof(double) * (2 * (ma->n - ma->n1) + 1));
+        mc_cal_y_core(ma, 0);
+        // rescale z
+        x = expl(ma->t - (ma->t1 + ma->t2));
+        for (k = 0; k <= ma->M; ++k) ma->z[k] *= x;
+    } else mc_cal_y_core(ma, 0);
+}
+
+#define CONTRAST_TINY 1e-30
+
+extern double kf_gammaq(double s, double z); // incomplete gamma function for chi^2 test
+
+static inline double chi2_test(int a, int b, int c, int d)
+{
+    double x, z;
+    x = (double)(a+b) * (c+d) * (b+d) * (a+c);
+    if (x == 0.) return 1;
+    z = a * d - b * c;
+    return kf_gammaq(.5, .5 * z * z * (a+b+c+d) / x);
+}
+
+// chi2=(a+b+c+d)(ad-bc)^2/[(a+b)(c+d)(a+c)(b+d)]
+static inline double contrast2_aux(const bcf_p1aux_t *p1, double sum, int k1, int k2, double x[3])
+{
+    double p = p1->phi[k1+k2] * p1->z1[k1] * p1->z2[k2] / sum * p1->hg[k1][k2];
+    int n1 = p1->n1, n2 = p1->n - p1->n1;
+    if (p < CONTRAST_TINY) return -1;
+    if (.5*k1/n1 < .5*k2/n2) x[1] += p;
+    else if (.5*k1/n1 > .5*k2/n2) x[2] += p;
+    else x[0] += p;
+    return p * chi2_test(k1, k2, (n1<<1) - k1, (n2<<1) - k2);
+}
+
+static double contrast2(bcf_p1aux_t *p1, double ret[3])
+{
+    int k, k1, k2, k10, k20, n1, n2;
+    double sum;
+    // get n1 and n2
+    n1 = p1->n1; n2 = p1->n - p1->n1;
+    if (n1 <= 0 || n2 <= 0) return 0.;
+    if (p1->hg == 0) { // initialize the hypergeometric distribution
+        /* NB: the hg matrix may take a lot of memory when there are many samples. There is a way
+           to avoid precomputing this matrix, but it is slower and quite intricate. The following
+           computation in this block can be accelerated with a similar strategy, but perhaps this
+           is not a serious concern for now. */
+        double tmp = lgamma(2*(n1+n2)+1) - (lgamma(2*n1+1) + lgamma(2*n2+1));
+        p1->hg = (double**) calloc(2*n1+1, sizeof(double*));
+        for (k1 = 0; k1 <= 2*n1; ++k1) {
+            p1->hg[k1] = (double*)calloc(2*n2+1, sizeof(double));
+            for (k2 = 0; k2 <= 2*n2; ++k2)
+                p1->hg[k1][k2] = exp(lgamma(k1+k2+1) + lgamma(p1->M-k1-k2+1) - (lgamma(k1+1) + lgamma(k2+1) + lgamma(2*n1-k1+1) + lgamma(2*n2-k2+1) + tmp));
+        }
+    }
+    { // compute
+        long double suml = 0;
+        for (k = 0; k <= p1->M; ++k) suml += p1->phi[k] * p1->z[k];
+        sum = suml;
+    }
+    { // get the max k1 and k2
+        double max;
+        int max_k;
+        for (k = 0, max = 0, max_k = -1; k <= 2*n1; ++k) {
+            double x = p1->phi1[k] * p1->z1[k];
+            if (x > max) max = x, max_k = k;
+        }
+        k10 = max_k;
+        for (k = 0, max = 0, max_k = -1; k <= 2*n2; ++k) {
+            double x = p1->phi2[k] * p1->z2[k];
+            if (x > max) max = x, max_k = k;
+        }
+        k20 = max_k;
+    }
+    { // We can do the following with one nested loop, but that is an O(N^2) thing. The following code block is much faster for large N.
+        double x[3], y;
+        long double z = 0., L[2];
+        x[0] = x[1] = x[2] = 0; L[0] = L[1] = 0;
+        for (k1 = k10; k1 >= 0; --k1) {
+            for (k2 = k20; k2 >= 0; --k2) {
+                if ((y = contrast2_aux(p1, sum, k1, k2, x)) < 0) break;
+                else z += y;
+            }
+            for (k2 = k20 + 1; k2 <= 2*n2; ++k2) {
+                if ((y = contrast2_aux(p1, sum, k1, k2, x)) < 0) break;
+                else z += y;
+            }
+        }
+        ret[0] = x[0]; ret[1] = x[1]; ret[2] = x[2];
+        x[0] = x[1] = x[2] = 0;
+        for (k1 = k10 + 1; k1 <= 2*n1; ++k1) {
+            for (k2 = k20; k2 >= 0; --k2) {
+                if ((y = contrast2_aux(p1, sum, k1, k2, x)) < 0) break;
+                else z += y;
+            }
+            for (k2 = k20 + 1; k2 <= 2*n2; ++k2) {
+                if ((y = contrast2_aux(p1, sum, k1, k2, x)) < 0) break;
+                else z += y;
+            }
+        }
+        ret[0] += x[0]; ret[1] += x[1]; ret[2] += x[2];
+        if (ret[0] + ret[1] + ret[2] < 0.95) { // in case of bad things happened
+            ret[0] = ret[1] = ret[2] = 0; L[0] = L[1] = 0;
+            for (k1 = 0, z = 0.; k1 <= 2*n1; ++k1)
+                for (k2 = 0; k2 <= 2*n2; ++k2)
+                    if ((y = contrast2_aux(p1, sum, k1, k2, ret)) >= 0) z += y;
+            if (ret[0] + ret[1] + ret[2] < 0.95) // It seems that this may be caused by floating point errors. I do not really understand why...
+                z = 1.0, ret[0] = ret[1] = ret[2] = 1./3;
+        }
+        return (double)z;
+    }
+}
+
+static double mc_cal_afs(bcf_p1aux_t *ma, double *p_ref_folded, double *p_var_folded)
+{
+    int k;
+    long double sum = 0., sum2;
+    double *phi = ma->is_indel? ma->phi_indel : ma->phi;
+    memset(ma->afs1, 0, sizeof(double) * (ma->M + 1));
+    mc_cal_y(ma);
+    // compute AFS
+    // MP15: is this using equation 20 from doi:10.1093/bioinformatics/btr509?
+    for (k = 0, sum = 0.; k <= ma->M; ++k)
+        sum += (long double)phi[k] * ma->z[k];
+    for (k = 0; k <= ma->M; ++k) {
+        ma->afs1[k] = phi[k] * ma->z[k] / sum;
+        if (isnan(ma->afs1[k]) || isinf(ma->afs1[k])) return -1.;
+    }
+    // compute folded variant probability
+    for (k = 0, sum = 0.; k <= ma->M; ++k)
+        sum += (long double)(phi[k] + phi[ma->M - k]) / 2. * ma->z[k];
+    for (k = 1, sum2 = 0.; k < ma->M; ++k)
+        sum2 += (long double)(phi[k] + phi[ma->M - k]) / 2. * ma->z[k];
+    *p_var_folded = sum2 / sum;
+    *p_ref_folded = (phi[k] + phi[ma->M - k]) / 2. * (ma->z[ma->M] + ma->z[0]) / sum;
+    // the expected frequency
+    for (k = 0, sum = 0.; k <= ma->M; ++k) {
+        ma->afs[k] += ma->afs1[k];
+        sum += k * ma->afs1[k];
+    }
+    return sum / ma->M;
+}
+
+int bcf_p1_cal(call_t *call, bcf1_t *b, int do_contrast, bcf_p1aux_t *ma, bcf_p1rst_t *rst)
+{
+    int i, k;
+    long double sum = 0.;
+    ma->is_indel = bcf_is_snp(b) ? 0 : 1;
+    rst->perm_rank = -1;
+
+    ma->PL = call->PLs;
+    ma->PL_len = call->nPLs / b->n_sample;
+    if (b->n_allele < 2) return -1; // FIXME: find a better solution
+
+    rst->rank0 = cal_pdg(b, ma);
+    rst->f_exp = mc_cal_afs(ma, &rst->p_ref_folded, &rst->p_var_folded);
+    rst->p_ref = ma->afs1[ma->M];
+    for (k = 0, sum = 0.; k < ma->M; ++k)
+        sum += ma->afs1[k];
+    rst->p_var = (double)sum;
+    { // compute the allele count
+        double max = -1;
+        rst->ac = -1;
+        for (k = 0; k <= ma->M; ++k)
+            if (max < ma->z[k]) max = ma->z[k], rst->ac = k;
+        rst->ac = ma->M - rst->ac;
+    }
+    // calculate f_flat and f_em
+    for (k = 0, sum = 0.; k <= ma->M; ++k)
+        sum += (long double)ma->z[k];
+    rst->f_flat = 0.;
+    for (k = 0; k <= ma->M; ++k) {
+        double p = ma->z[k] / sum;
+        rst->f_flat += k * p;
+    }
+    rst->f_flat /= ma->M;
+    { // estimate equal-tail credible interval (95% level)
+        int l, h;
+        double p;
+        for (i = 0, p = 0.; i <= ma->M; ++i)
+            if (p + ma->afs1[i] > 0.025) break;
+            else p += ma->afs1[i];
+        l = i;
+        for (i = ma->M, p = 0.; i >= 0; --i)
+            if (p + ma->afs1[i] > 0.025) break;
+            else p += ma->afs1[i];
+        h = i;
+        rst->cil = (double)(ma->M - h) / ma->M; rst->cih = (double)(ma->M - l) / ma->M;
+    }
+    if (ma->n1 > 0) { // compute LRT
+        double max0, max1, max2;
+        for (k = 0, max0 = -1; k <= ma->M; ++k)
+            if (max0 < ma->z[k]) max0 = ma->z[k];
+        for (k = 0, max1 = -1; k <= ma->n1 * 2; ++k)
+            if (max1 < ma->z1[k]) max1 = ma->z1[k];
+        for (k = 0, max2 = -1; k <= ma->M - ma->n1 * 2; ++k)
+            if (max2 < ma->z2[k]) max2 = ma->z2[k];
+        rst->lrt = log(max1 * max2 / max0);
+        rst->lrt = rst->lrt < 0? 1 : kf_gammaq(.5, rst->lrt);
+    } else rst->lrt = -1.0;
+    rst->cmp[0] = rst->cmp[1] = rst->cmp[2] = rst->p_chi2 = -1.0;
+    if (do_contrast && rst->p_var > 0.5) // skip contrast2() if the locus is a strong non-variant
+        rst->p_chi2 = contrast2(ma, rst->cmp);
+    return 0;
+}
+
+void bcf_p1_dump_afs(bcf_p1aux_t *ma)
+{
+    int k;
+    fprintf(stderr, "[afs]");
+    for (k = 0; k <= ma->M; ++k)
+        fprintf(stderr, " %d:%.3lf", k, ma->afs[ma->M - k]);
+    fprintf(stderr, "\n");
+    memset(ma->afs, 0, sizeof(double) * (ma->M + 1));
+}
diff --git a/bcftools/prob1.c.pysam.c b/bcftools/prob1.c.pysam.c
new file mode 100644
index 0000000..822d0c2
--- /dev/null
+++ b/bcftools/prob1.c.pysam.c
@@ -0,0 +1,526 @@
+#include "bcftools.pysam.h"
+
+/*  prob1.c -- mathematical utility functions.
+
+    Copyright (C) 2010, 2011 Broad Institute.
+    Copyright (C) 2012, 2013-2014, 2017 Genome Research Ltd.
+
+    Author: Heng Li <lh3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.  */
+
+#include <math.h>
+#include <stdlib.h>
+#include <string.h>
+#include <stdio.h>
+#include <errno.h>
+#include <assert.h>
+#include <limits.h>
+#include "prob1.h"
+
+#define MC_MAX_EM_ITER 16
+#define MC_EM_EPS 1e-5
+#define MC_DEF_INDEL 0.15
+
+void bcf_p1_indel_prior(bcf_p1aux_t *ma, double x)
+{
+    int i;
+    for (i = 0; i < ma->M; ++i)
+        ma->phi_indel[i] = ma->phi[i] * x;
+    ma->phi_indel[ma->M] = 1. - ma->phi[ma->M] * x;
+}
+
+static void init_prior(int type, double theta, int M, double *phi)
+{
+    int i;
+    if (type == MC_PTYPE_COND2) {
+        for (i = 0; i <= M; ++i)
+            phi[i] = 2. * (i + 1) / (M + 1) / (M + 2);
+    } else if (type == MC_PTYPE_FLAT) {
+        for (i = 0; i <= M; ++i)
+            phi[i] = 1. / (M + 1);
+    } else {
+        double sum;
+        for (i = 0, sum = 0.; i < M; ++i)
+            sum += (phi[i] = theta / (M - i));
+        phi[M] = 1. - sum;
+    }
+}
+
+void bcf_p1_init_prior(bcf_p1aux_t *ma, int type, double theta)
+{
+    init_prior(type, theta, ma->M, ma->phi);
+    bcf_p1_indel_prior(ma, MC_DEF_INDEL);
+}
+
+void bcf_p1_init_subprior(bcf_p1aux_t *ma, int type, double theta)
+{
+    if (ma->n1 <= 0 || ma->n1 >= ma->M) return;
+    init_prior(type, theta, 2*ma->n1, ma->phi1);
+    init_prior(type, theta, 2*(ma->n - ma->n1), ma->phi2);
+}
+
+
+/* Initialise a bcf_p1aux_t */
+bcf_p1aux_t *bcf_p1_init(int n_smpl, uint8_t *ploidy)
+{
+    bcf_p1aux_t *ma;
+    int i;
+    ma = (bcf_p1aux_t*) calloc(1, sizeof(bcf_p1aux_t));
+    ma->n1 = -1;
+    ma->n = n_smpl;
+    ma->M = 2 * n_smpl;
+    if (ploidy) {
+        ma->ploidy = (uint8_t*) malloc(n_smpl);
+        memcpy(ma->ploidy, ploidy, n_smpl);
+        for (i = 0, ma->M = 0; i < n_smpl; ++i) ma->M += ploidy[i];
+        if (ma->M == 2 * n_smpl) {
+            free(ma->ploidy);
+            ma->ploidy = 0;
+        }
+    }
+    ma->q2p = (double*) calloc(256, sizeof(double));
+    ma->pdg = (double*) calloc(3 * ma->n, sizeof(double));
+    ma->phi = (double*) calloc(ma->M + 1, sizeof(double));
+    ma->phi_indel = (double*) calloc(ma->M + 1, sizeof(double));
+    ma->phi1 = (double*) calloc(ma->M + 1, sizeof(double));
+    ma->phi2 = (double*) calloc(ma->M + 1, sizeof(double));
+    ma->z = (double*) calloc(ma->M + 1, sizeof(double));
+    ma->zswap = (double*) calloc(ma->M + 1, sizeof(double));
+    ma->z1 = (double*) calloc(ma->M + 1, sizeof(double)); // actually we do not need this large
+    ma->z2 = (double*) calloc(ma->M + 1, sizeof(double));
+    ma->afs = (double*) calloc(ma->M + 1, sizeof(double));
+    ma->afs1 = (double*) calloc(ma->M + 1, sizeof(double));
+    ma->lf = (double*) calloc(ma->M + 1, sizeof(double));
+    for (i = 0; i < 256; ++i)
+        ma->q2p[i] = pow(10., -i / 10.);
+    for (i = 0; i <= ma->M; ++i) ma->lf[i] = lgamma(i + 1);
+    bcf_p1_init_prior(ma, MC_PTYPE_FULL, 1e-3); // the simplest prior
+    return ma;
+}
+
+int bcf_p1_get_M(bcf_p1aux_t *b) { return b->M; }
+
+int bcf_p1_set_n1(bcf_p1aux_t *b, int n1)
+{
+    if (n1 == 0 || n1 >= b->n) return -1;
+    if (b->M != b->n * 2) {
+        fprintf(bcftools_stderr, "[%s] unable to set `n1' when there are haploid samples.\n", __func__);
+        return -1;
+    }
+    b->n1 = n1;
+    return 0;
+}
+
+void bcf_p1_destroy(bcf_p1aux_t *ma)
+{
+    if (ma) {
+        int k;
+        free(ma->lf);
+        if (ma->hg && ma->n1 > 0) {
+            for (k = 0; k <= 2*ma->n1; ++k) free(ma->hg[k]);
+            free(ma->hg);
+        }
+        free(ma->ploidy); free(ma->q2p); free(ma->pdg);
+        free(ma->phi); free(ma->phi_indel); free(ma->phi1); free(ma->phi2);
+        free(ma->z); free(ma->zswap); free(ma->z1); free(ma->z2);
+        free(ma->afs); free(ma->afs1);
+        free(ma);
+    }
+}
+
+extern double kf_gammap(double s, double z);
+int test16(bcf1_t *b, anno16_t *a);
+
+/* Calculate P(D|g) */
+static int cal_pdg(const bcf1_t *b, bcf_p1aux_t *ma)
+{
+    int i, j;
+    long p_a[16], *p=p_a, tmp;
+    if (b->n_allele > 16)
+        p = (long*) malloc(b->n_allele * sizeof(long));
+    memset(p, 0, sizeof(long) * b->n_allele);
+
+    // Set P(D|g) for each sample and sum phread likelihoods across all samples to create lk
+    for (j = 0; j < ma->n; ++j) {
+        // Fetch the PL array for the sample
+        const int *pi = ma->PL + j * ma->PL_len;
+        // Fetch the P(D|g) array for the sample
+        double *pdg = ma->pdg + j * 3;
+        pdg[0] = ma->q2p[pi[2]]; pdg[1] = ma->q2p[pi[1]]; pdg[2] = ma->q2p[pi[0]];
+        for (i = 0; i < b->n_allele; ++i)
+            p[i] += (int)pi[(i+1)*(i+2)/2-1];
+    }
+    for (i = 0; i < b->n_allele; ++i) p[i] = p[i]<<4 | i;
+    for (i = 1; i < b->n_allele; ++i) // insertion sort
+        for (j = i; j > 0 && p[j] < p[j-1]; --j)
+            tmp = p[j], p[j] = p[j-1], p[j-1] = tmp;
+    for (i = b->n_allele - 1; i >= 0; --i)
+        if ((p[i]&0xf) == 0) break;
+    if (p != p_a)
+        free(p);
+    return i;
+}
+
+
+/* f0 is freq of the ref allele */
+int bcf_p1_call_gt(const bcf_p1aux_t *ma, double f0, int k, int is_var)
+{
+    double sum, g[3];
+    double max, f3[3], *pdg = ma->pdg + k * 3;
+    int q, i, max_i, ploidy;
+    /* determine ploidy */
+    ploidy = ma->ploidy? ma->ploidy[k] : 2;
+    if (ploidy == 2) {
+    /* given allele frequency we can determine how many of each
+     * genotype we have by HWE p=1-q PP=p^2 PQ&QP=2*p*q QQ=q^2 */
+        f3[0] = (1.-f0)*(1.-f0); f3[1] = 2.*f0*(1.-f0); f3[2] = f0*f0;
+    } else {
+        f3[0] = 1. - f0; f3[1] = 0; f3[2] = f0;
+    }
+    for (i = 0, sum = 0.; i < 3; ++i)
+        sum += (g[i] = pdg[i] * f3[i]);
+    /* normalise g and then determine max */
+    for (i = 0, max = -1., max_i = 0; i < 3; ++i) {
+        g[i] /= sum;
+        if (g[i] > max) max = g[i], max_i = i;
+    }
+    if ( !is_var ) { max_i = 2; max = g[2]; }   // force 0/0 genotype if the site is non-variant
+    max = 1. - max;
+    if (max < 1e-308) max = 1e-308;
+    q = (int)(-4.343 * log(max) + .499);
+    if (q > 99) q = 99;
+    return q<<2|max_i;
+}
+
+// If likelihoods fall below this they get squashed to 0
+#define TINY 1e-20
+static void mc_cal_y_core(bcf_p1aux_t *ma, int beg)
+{
+    double *z[2], *tmp, *pdg;
+    int _j, last_min, last_max;
+    assert(beg == 0 || ma->M == ma->n*2);
+    z[0] = ma->z;
+    z[1] = ma->zswap;
+    pdg = ma->pdg;
+    memset(z[0], 0, sizeof(double) * (ma->M + 1));
+    memset(z[1], 0, sizeof(double) * (ma->M + 1));
+    z[0][0] = 1.;
+    last_min = last_max = 0;
+    ma->t = 0.;
+    if (ma->M == ma->n * 2) {
+        int M = 0;
+        for (_j = beg; _j < ma->n; ++_j) {
+            int k, j = _j - beg, _min = last_min, _max = last_max, M0;
+            double p[3], sum;
+            M0 = M; M += 2;
+            // Fetch P(D|g) for this sample
+            pdg = ma->pdg + _j * 3;
+            p[0] = pdg[0]; p[1] = 2. * pdg[1]; p[2] = pdg[2];
+            for (; _min < _max && z[0][_min] < TINY; ++_min) z[0][_min] = z[1][_min] = 0.;
+            for (; _max > _min && z[0][_max] < TINY; --_max) z[0][_max] = z[1][_max] = 0.;
+            _max += 2;
+            if (_min == 0) k = 0, z[1][k] = (M0-k+1) * (M0-k+2) * p[0] * z[0][k];
+            if (_min <= 1) k = 1, z[1][k] = (M0-k+1) * (M0-k+2) * p[0] * z[0][k] + k*(M0-k+2) * p[1] * z[0][k-1];
+            for (k = _min < 2? 2 : _min; k <= _max; ++k)
+                z[1][k] = (M0-k+1)*(M0-k+2) * p[0] * z[0][k] + k*(M0-k+2) * p[1] * z[0][k-1] + k*(k-1)* p[2] * z[0][k-2];
+            for (k = _min, sum = 0.; k <= _max; ++k) sum += z[1][k];
+            ma->t += log(sum / (M * (M - 1.)));
+            for (k = _min; k <= _max; ++k) z[1][k] /= sum;
+            if (_min >= 1) z[1][_min-1] = 0.;
+            if (_min >= 2) z[1][_min-2] = 0.;
+            // If we are not on the last sample
+            if (j < ma->n - 1) z[1][_max+1] = z[1][_max+2] = 0.;
+            if (_j == ma->n1 - 1) { // set pop1; ma->n1==-1 when unset
+                ma->t1 = ma->t;
+                memcpy(ma->z1, z[1], sizeof(double) * (ma->n1 * 2 + 1));
+            }
+            tmp = z[0]; z[0] = z[1]; z[1] = tmp;
+            last_min = _min; last_max = _max;
+        }
+        //for (_j = 0; _j < last_min; ++_j) z[0][_j] = 0.; // TODO: are these necessary?
+        //for (_j = last_max + 1; _j < ma->M; ++_j) z[0][_j] = 0.;
+    } else { // this block is very similar to the block above; these two might be merged in future
+        int j, M = 0;
+        for (j = 0; j < ma->n; ++j) {
+            int k, M0, _min = last_min, _max = last_max;
+            double p[3], sum;
+            // Fetch P(D|g) for this sample
+            pdg = ma->pdg + j * 3;
+            for (; _min < _max && z[0][_min] < TINY; ++_min) z[0][_min] = z[1][_min] = 0.;
+            for (; _max > _min && z[0][_max] < TINY; --_max) z[0][_max] = z[1][_max] = 0.;
+            M0 = M;
+            M += ma->ploidy[j];
+            if (ma->ploidy[j] == 1) {
+                p[0] = pdg[0]; p[1] = pdg[2];
+                _max++;
+                if (_min == 0) k = 0, z[1][k] = (M0+1-k) * p[0] * z[0][k];
+                for (k = _min < 1? 1 : _min; k <= _max; ++k)
+                    z[1][k] = (M0+1-k) * p[0] * z[0][k] + k * p[1] * z[0][k-1];
+                for (k = _min, sum = 0.; k <= _max; ++k) sum += z[1][k];
+                ma->t += log(sum / M);
+                for (k = _min; k <= _max; ++k) z[1][k] /= sum;
+                if (_min >= 1) z[1][_min-1] = 0.;
+                // If we are not on the last sample
+                if (j < ma->n - 1) z[1][_max+1] = 0.;
+            } else if (ma->ploidy[j] == 2) {
+                p[0] = pdg[0]; p[1] = 2 * pdg[1]; p[2] = pdg[2];
+                _max += 2;
+                if (_min == 0) k = 0, z[1][k] = (M0-k+1) * (M0-k+2) * p[0] * z[0][k];
+                if (_min <= 1) k = 1, z[1][k] = (M0-k+1) * (M0-k+2) * p[0] * z[0][k] + k*(M0-k+2) * p[1] * z[0][k-1];
+                for (k = _min < 2? 2 : _min; k <= _max; ++k)
+                    z[1][k] = (M0-k+1)*(M0-k+2) * p[0] * z[0][k] + k*(M0-k+2) * p[1] * z[0][k-1] + k*(k-1)* p[2] * z[0][k-2];
+                for (k = _min, sum = 0.; k <= _max; ++k) sum += z[1][k];
+                ma->t += log(sum / (M * (M - 1.)));
+                for (k = _min; k <= _max; ++k) z[1][k] /= sum;
+                if (_min >= 1) z[1][_min-1] = 0.;
+                if (_min >= 2) z[1][_min-2] = 0.;
+                // If we are not on the last sample
+                if (j < ma->n - 1) z[1][_max+1] = z[1][_max+2] = 0.;
+            }
+            tmp = z[0]; z[0] = z[1]; z[1] = tmp;
+            last_min = _min; last_max = _max;
+        }
+    }
+    if (z[0] != ma->z) memcpy(ma->z, z[0], sizeof(double) * (ma->M + 1));
+}
+
+static void mc_cal_y(bcf_p1aux_t *ma)
+{
+    if (ma->n1 > 0 && ma->n1 < ma->n && ma->M == ma->n * 2) { // NB: ma->n1 is ineffective when there are haploid samples
+        int k;
+        long double x;
+        memset(ma->z1, 0, sizeof(double) * (2 * ma->n1 + 1));
+        memset(ma->z2, 0, sizeof(double) * (2 * (ma->n - ma->n1) + 1));
+        ma->t1 = ma->t2 = 0.;
+        mc_cal_y_core(ma, ma->n1);
+        ma->t2 = ma->t;
+        memcpy(ma->z2, ma->z, sizeof(double) * (2 * (ma->n - ma->n1) + 1));
+        mc_cal_y_core(ma, 0);
+        // rescale z
+        x = expl(ma->t - (ma->t1 + ma->t2));
+        for (k = 0; k <= ma->M; ++k) ma->z[k] *= x;
+    } else mc_cal_y_core(ma, 0);
+}
+
+#define CONTRAST_TINY 1e-30
+
+extern double kf_gammaq(double s, double z); // incomplete gamma function for chi^2 test
+
+static inline double chi2_test(int a, int b, int c, int d)
+{
+    double x, z;
+    x = (double)(a+b) * (c+d) * (b+d) * (a+c);
+    if (x == 0.) return 1;
+    z = a * d - b * c;
+    return kf_gammaq(.5, .5 * z * z * (a+b+c+d) / x);
+}
+
+// chi2=(a+b+c+d)(ad-bc)^2/[(a+b)(c+d)(a+c)(b+d)]
+static inline double contrast2_aux(const bcf_p1aux_t *p1, double sum, int k1, int k2, double x[3])
+{
+    double p = p1->phi[k1+k2] * p1->z1[k1] * p1->z2[k2] / sum * p1->hg[k1][k2];
+    int n1 = p1->n1, n2 = p1->n - p1->n1;
+    if (p < CONTRAST_TINY) return -1;
+    if (.5*k1/n1 < .5*k2/n2) x[1] += p;
+    else if (.5*k1/n1 > .5*k2/n2) x[2] += p;
+    else x[0] += p;
+    return p * chi2_test(k1, k2, (n1<<1) - k1, (n2<<1) - k2);
+}
+
+static double contrast2(bcf_p1aux_t *p1, double ret[3])
+{
+    int k, k1, k2, k10, k20, n1, n2;
+    double sum;
+    // get n1 and n2
+    n1 = p1->n1; n2 = p1->n - p1->n1;
+    if (n1 <= 0 || n2 <= 0) return 0.;
+    if (p1->hg == 0) { // initialize the hypergeometric distribution
+        /* NB: the hg matrix may take a lot of memory when there are many samples. There is a way
+           to avoid precomputing this matrix, but it is slower and quite intricate. The following
+           computation in this block can be accelerated with a similar strategy, but perhaps this
+           is not a serious concern for now. */
+        double tmp = lgamma(2*(n1+n2)+1) - (lgamma(2*n1+1) + lgamma(2*n2+1));
+        p1->hg = (double**) calloc(2*n1+1, sizeof(double*));
+        for (k1 = 0; k1 <= 2*n1; ++k1) {
+            p1->hg[k1] = (double*)calloc(2*n2+1, sizeof(double));
+            for (k2 = 0; k2 <= 2*n2; ++k2)
+                p1->hg[k1][k2] = exp(lgamma(k1+k2+1) + lgamma(p1->M-k1-k2+1) - (lgamma(k1+1) + lgamma(k2+1) + lgamma(2*n1-k1+1) + lgamma(2*n2-k2+1) + tmp));
+        }
+    }
+    { // compute
+        long double suml = 0;
+        for (k = 0; k <= p1->M; ++k) suml += p1->phi[k] * p1->z[k];
+        sum = suml;
+    }
+    { // get the max k1 and k2
+        double max;
+        int max_k;
+        for (k = 0, max = 0, max_k = -1; k <= 2*n1; ++k) {
+            double x = p1->phi1[k] * p1->z1[k];
+            if (x > max) max = x, max_k = k;
+        }
+        k10 = max_k;
+        for (k = 0, max = 0, max_k = -1; k <= 2*n2; ++k) {
+            double x = p1->phi2[k] * p1->z2[k];
+            if (x > max) max = x, max_k = k;
+        }
+        k20 = max_k;
+    }
+    { // We can do the following with one nested loop, but that is an O(N^2) thing. The following code block is much faster for large N.
+        double x[3], y;
+        long double z = 0., L[2];
+        x[0] = x[1] = x[2] = 0; L[0] = L[1] = 0;
+        for (k1 = k10; k1 >= 0; --k1) {
+            for (k2 = k20; k2 >= 0; --k2) {
+                if ((y = contrast2_aux(p1, sum, k1, k2, x)) < 0) break;
+                else z += y;
+            }
+            for (k2 = k20 + 1; k2 <= 2*n2; ++k2) {
+                if ((y = contrast2_aux(p1, sum, k1, k2, x)) < 0) break;
+                else z += y;
+            }
+        }
+        ret[0] = x[0]; ret[1] = x[1]; ret[2] = x[2];
+        x[0] = x[1] = x[2] = 0;
+        for (k1 = k10 + 1; k1 <= 2*n1; ++k1) {
+            for (k2 = k20; k2 >= 0; --k2) {
+                if ((y = contrast2_aux(p1, sum, k1, k2, x)) < 0) break;
+                else z += y;
+            }
+            for (k2 = k20 + 1; k2 <= 2*n2; ++k2) {
+                if ((y = contrast2_aux(p1, sum, k1, k2, x)) < 0) break;
+                else z += y;
+            }
+        }
+        ret[0] += x[0]; ret[1] += x[1]; ret[2] += x[2];
+        if (ret[0] + ret[1] + ret[2] < 0.95) { // in case of bad things happened
+            ret[0] = ret[1] = ret[2] = 0; L[0] = L[1] = 0;
+            for (k1 = 0, z = 0.; k1 <= 2*n1; ++k1)
+                for (k2 = 0; k2 <= 2*n2; ++k2)
+                    if ((y = contrast2_aux(p1, sum, k1, k2, ret)) >= 0) z += y;
+            if (ret[0] + ret[1] + ret[2] < 0.95) // It seems that this may be caused by floating point errors. I do not really understand why...
+                z = 1.0, ret[0] = ret[1] = ret[2] = 1./3;
+        }
+        return (double)z;
+    }
+}
+
+static double mc_cal_afs(bcf_p1aux_t *ma, double *p_ref_folded, double *p_var_folded)
+{
+    int k;
+    long double sum = 0., sum2;
+    double *phi = ma->is_indel? ma->phi_indel : ma->phi;
+    memset(ma->afs1, 0, sizeof(double) * (ma->M + 1));
+    mc_cal_y(ma);
+    // compute AFS
+    // MP15: is this using equation 20 from doi:10.1093/bioinformatics/btr509?
+    for (k = 0, sum = 0.; k <= ma->M; ++k)
+        sum += (long double)phi[k] * ma->z[k];
+    for (k = 0; k <= ma->M; ++k) {
+        ma->afs1[k] = phi[k] * ma->z[k] / sum;
+        if (isnan(ma->afs1[k]) || isinf(ma->afs1[k])) return -1.;
+    }
+    // compute folded variant probability
+    for (k = 0, sum = 0.; k <= ma->M; ++k)
+        sum += (long double)(phi[k] + phi[ma->M - k]) / 2. * ma->z[k];
+    for (k = 1, sum2 = 0.; k < ma->M; ++k)
+        sum2 += (long double)(phi[k] + phi[ma->M - k]) / 2. * ma->z[k];
+    *p_var_folded = sum2 / sum;
+    *p_ref_folded = (phi[k] + phi[ma->M - k]) / 2. * (ma->z[ma->M] + ma->z[0]) / sum;
+    // the expected frequency
+    for (k = 0, sum = 0.; k <= ma->M; ++k) {
+        ma->afs[k] += ma->afs1[k];
+        sum += k * ma->afs1[k];
+    }
+    return sum / ma->M;
+}
+
+int bcf_p1_cal(call_t *call, bcf1_t *b, int do_contrast, bcf_p1aux_t *ma, bcf_p1rst_t *rst)
+{
+    int i, k;
+    long double sum = 0.;
+    ma->is_indel = bcf_is_snp(b) ? 0 : 1;
+    rst->perm_rank = -1;
+
+    ma->PL = call->PLs;
+    ma->PL_len = call->nPLs / b->n_sample;
+    if (b->n_allele < 2) return -1; // FIXME: find a better solution
+
+    rst->rank0 = cal_pdg(b, ma);
+    rst->f_exp = mc_cal_afs(ma, &rst->p_ref_folded, &rst->p_var_folded);
+    rst->p_ref = ma->afs1[ma->M];
+    for (k = 0, sum = 0.; k < ma->M; ++k)
+        sum += ma->afs1[k];
+    rst->p_var = (double)sum;
+    { // compute the allele count
+        double max = -1;
+        rst->ac = -1;
+        for (k = 0; k <= ma->M; ++k)
+            if (max < ma->z[k]) max = ma->z[k], rst->ac = k;
+        rst->ac = ma->M - rst->ac;
+    }
+    // calculate f_flat and f_em
+    for (k = 0, sum = 0.; k <= ma->M; ++k)
+        sum += (long double)ma->z[k];
+    rst->f_flat = 0.;
+    for (k = 0; k <= ma->M; ++k) {
+        double p = ma->z[k] / sum;
+        rst->f_flat += k * p;
+    }
+    rst->f_flat /= ma->M;
+    { // estimate equal-tail credible interval (95% level)
+        int l, h;
+        double p;
+        for (i = 0, p = 0.; i <= ma->M; ++i)
+            if (p + ma->afs1[i] > 0.025) break;
+            else p += ma->afs1[i];
+        l = i;
+        for (i = ma->M, p = 0.; i >= 0; --i)
+            if (p + ma->afs1[i] > 0.025) break;
+            else p += ma->afs1[i];
+        h = i;
+        rst->cil = (double)(ma->M - h) / ma->M; rst->cih = (double)(ma->M - l) / ma->M;
+    }
+    if (ma->n1 > 0) { // compute LRT
+        double max0, max1, max2;
+        for (k = 0, max0 = -1; k <= ma->M; ++k)
+            if (max0 < ma->z[k]) max0 = ma->z[k];
+        for (k = 0, max1 = -1; k <= ma->n1 * 2; ++k)
+            if (max1 < ma->z1[k]) max1 = ma->z1[k];
+        for (k = 0, max2 = -1; k <= ma->M - ma->n1 * 2; ++k)
+            if (max2 < ma->z2[k]) max2 = ma->z2[k];
+        rst->lrt = log(max1 * max2 / max0);
+        rst->lrt = rst->lrt < 0? 1 : kf_gammaq(.5, rst->lrt);
+    } else rst->lrt = -1.0;
+    rst->cmp[0] = rst->cmp[1] = rst->cmp[2] = rst->p_chi2 = -1.0;
+    if (do_contrast && rst->p_var > 0.5) // skip contrast2() if the locus is a strong non-variant
+        rst->p_chi2 = contrast2(ma, rst->cmp);
+    return 0;
+}
+
+void bcf_p1_dump_afs(bcf_p1aux_t *ma)
+{
+    int k;
+    fprintf(bcftools_stderr, "[afs]");
+    for (k = 0; k <= ma->M; ++k)
+        fprintf(bcftools_stderr, " %d:%.3lf", k, ma->afs[ma->M - k]);
+    fprintf(bcftools_stderr, "\n");
+    memset(ma->afs, 0, sizeof(double) * (ma->M + 1));
+}
diff --git a/bcftools/prob1.h b/bcftools/prob1.h
new file mode 100644
index 0000000..a562265
--- /dev/null
+++ b/bcftools/prob1.h
@@ -0,0 +1,93 @@
+/*  prob1.h -- mathematical utility functions.
+
+    Copyright (C) 2010, 2011 Broad Institute.
+    Copyright (C) 2012, 2013-2014 Genome Research Ltd.
+
+    Author: Heng Li <lh3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.  */
+
+#ifndef BCF_PROB1_H
+#define BCF_PROB1_H
+
+#include <htslib/vcf.h>
+#include "call.h"
+
+typedef struct {
+    int n; // Number of samples
+    int M; // Total number of chromosomes across all samples (n*2 if all samples are diploid)
+    int n1;
+    int is_indel;
+    uint8_t *ploidy; // haploid or diploid ONLY
+    double *q2p, *pdg; // q2p maps from phread scaled to real likelihood, pdg -> P(D|g)
+    double *phi; // Probability of seeing k reference alleles
+    double *phi_indel;
+    double *z, *zswap; // aux for afs
+    double *z1, *z2, *phi1, *phi2; // only calculated when n1 is set
+    double **hg; // hypergeometric distribution
+    double *lf; // log factorial
+    double t, t1, t2;
+    double *afs, *afs1; // afs: accumulative allele frequency spectrum (AFS); afs1: site posterior distribution
+    const int *PL; // point to PL
+    int PL_len;
+    int cons_llr;       // pair and trio calling
+    int64_t cons_gt;
+} bcf_p1aux_t;
+
+typedef struct {
+    int rank0, perm_rank; // NB: perm_rank is always set to -1 by bcf_p1_cal()
+    int ac; // ML alternative allele count
+    double f_exp, f_flat, p_ref_folded, p_ref, p_var_folded, p_var;
+    double cil, cih;
+    double cmp[3], p_chi2, lrt; // used by contrast2()
+} bcf_p1rst_t;
+
+typedef struct {
+    double p[4];
+    double edb, mqb, bqb;   // end distance bias, mapQ bias, baseQ bias
+    int mq, depth, is_tested, d[4];
+} anno16_t;
+
+#define MC_PTYPE_FULL  1
+#define MC_PTYPE_COND2 2
+#define MC_PTYPE_FLAT  3
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+    bcf_p1aux_t *bcf_p1_init(int n_smpl, uint8_t *ploidy);
+    void bcf_p1_init_prior(bcf_p1aux_t *ma, int type, double theta);
+    void bcf_p1_init_subprior(bcf_p1aux_t *ma, int type, double theta);
+    void bcf_p1_destroy(bcf_p1aux_t *ma);
+    void bcf_p1_set_ploidy(bcf1_t *b, bcf_p1aux_t *ma);
+    int bcf_p1_cal(call_t *call, bcf1_t *b, int do_contrast, bcf_p1aux_t *ma, bcf_p1rst_t *rst);
+    int bcf_p1_call_gt(const bcf_p1aux_t *ma, double f0, int k, int is_var);
+    void bcf_p1_dump_afs(bcf_p1aux_t *ma);
+    int bcf_p1_read_prior(bcf_p1aux_t *ma, const char *fn);
+    int bcf_p1_set_n1(bcf_p1aux_t *b, int n1);
+    void bcf_p1_set_folded(bcf_p1aux_t *p1a); // only effective when set_n1() is not called
+
+    int bcf_em1(call_t *call, const bcf1_t *b, int n1, int flag, double x[10]);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif
diff --git a/bcftools/rbuf.h b/bcftools/rbuf.h
new file mode 100644
index 0000000..ef2e206
--- /dev/null
+++ b/bcftools/rbuf.h
@@ -0,0 +1,261 @@
+/*  rbuf.h -- round buffers.
+
+    Copyright (C) 2013-2014, 2017 Genome Research Ltd.
+
+    Author: Petr Danecek <pd3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.  */
+
+#ifndef __RBUF_H__
+#define __RBUF_H__
+
+#include <string.h>
+
+typedef struct
+{
+    int m,n,f;    // m: allocated size, n: number of elements in the buffer, f: first element
+}
+rbuf_t;
+
+/**
+ *  rbuf_init() - initialize round buffer
+ *  @rbuf:  the rbuf_t holder
+ *  @size:  the maximum number of elements
+ *
+ */
+static inline void rbuf_init(rbuf_t *rbuf, int size)
+{
+    rbuf->m = size; rbuf->n = rbuf->f = 0;
+}
+/**
+ *  rbuf_kth() - get index of the k-th element of the round buffer
+ *  @rbuf:  the rbuf_t holder
+ *  @k:     0-based index. If negative, return k-th element from the end, 1-based
+ */
+static inline int rbuf_kth(rbuf_t *rbuf, int k)
+{
+    if ( k >= rbuf->n ) return -1;
+    if ( k < 0 )
+    {
+        k = rbuf->n + k; 
+        if ( k < 0 ) return -1;
+    }
+    int i = k + rbuf->f;
+    if ( i >= rbuf->m ) i -= rbuf->m;
+    return i;
+}
+/**
+ *  rbuf_last() - get index of the last element of the round buffer
+ *  @rbuf:  the rbuf_t holder
+ */
+#define rbuf_last(rbuf) rbuf_kth(rbuf, -1)
+
+/**
+ *  rbuf_l2ridx() - get 0-based rbuf index which corresponds to i-th linear index
+ *  @rbuf:  the rbuf_t holder
+ *  @idx:   0-based linear index
+ *
+ *  Returns 0-based circular index or -1 if out of bounds
+ */
+static inline int rbuf_l2ridx(rbuf_t *rbuf, int idx)
+{
+    if ( idx < 0 || idx >= rbuf->n ) return -1;
+    if ( idx >= rbuf->f )
+    {
+        int i = idx - rbuf->f;
+        if ( i >= rbuf->n ) return -1;
+        return i;
+    }
+    int i = rbuf->m - rbuf->f + idx;
+    if ( i >= rbuf->n ) return -1;
+    return i;
+}
+
+/**
+ *  rbuf_next() - get index of the next element in the round buffer
+ *  @rbuf:  the rbuf_t holder
+ *  @i:     pointer to the last rbuf index. Set to -1 before the first call.
+ *
+ *  Sets i to the next position in the buffer. The return value indicates if
+ *  the position points to a valid element (1) or if there are no more elements
+ *  after *i (0). When the end is reached, *i is set to the first element in the
+ *  buffer.
+ */
+static inline int rbuf_next(rbuf_t *rbuf, int *i)
+{
+    if ( !rbuf->n ) return 0;
+    if ( *i==-1 ) { *i = rbuf->f; return 1; }
+    int n = (rbuf->f <= *i) ? *i - rbuf->f + 1 : *i + rbuf->m - rbuf->f + 1;
+    if ( ++(*i) >= rbuf->m ) *i = 0;
+    if ( n < rbuf->n ) return 1;
+    *i = rbuf->f;
+    return 0;
+}
+/**
+ *  rbuf_prev() - get index of the previous element in the round buffer
+ *  @rbuf:  the rbuf_t holder
+ *  @i:     pointer to the last rbuf index. Set to -1 before the first call.
+ *
+ *  Sets i to the previous position in the buffer. The return value indicates if
+ *  the position points to a valid element (1) or if there are no more elements
+ *  before *i (0).
+ */
+static inline int rbuf_prev(rbuf_t *rbuf, int *i)
+{
+    if ( !rbuf->n || *i==rbuf->f ) return 0;
+    if ( *i==-1 )
+    {
+        *i = rbuf_last(rbuf);
+        return 1;
+    }
+    if ( --(*i) < 0 ) *i = rbuf->m - 1;
+    return 1;
+}
+/**
+ *  rbuf_prepend() - register new element at the start of the round buffer
+ *  @rbuf:  the rbuf_t holder
+ *
+ *  Returns index of the newly inserted element.
+ */
+static inline int rbuf_prepend(rbuf_t *rbuf)
+{
+    if ( rbuf->n < rbuf->m ) rbuf->n++;
+
+    rbuf->f = rbuf->f > 0 ? rbuf->f - 1 : rbuf->m - 1;
+    return rbuf->f;
+}
+/**
+ *  rbuf_append() - register new element at the end of the round buffer
+ *  @rbuf:  the rbuf_t holder
+ *
+ *  Returns index of the newly inserted element.
+ */
+static inline int rbuf_append(rbuf_t *rbuf)
+{
+    if ( rbuf->n < rbuf->m )
+    {
+        rbuf->n++;
+        int i = rbuf->f + rbuf->n;
+        return i <= rbuf->m ? i - 1 : i - rbuf->m - 1;
+    }
+
+    rbuf->f++;
+    if ( rbuf->f >= rbuf->m )
+    {
+        rbuf->f = 0;
+        return rbuf->m - 1;
+    }
+    return rbuf->f - 1;
+}
+/**
+ *  rbuf_shift() - removes first element from the buffer
+ *  @rbuf:  the rbuf_t holder
+ *
+ *  Returns index of the removed element.
+ */
+static inline int rbuf_shift(rbuf_t *rbuf)
+{
+    if ( !rbuf->n ) return -1;
+    int ret = rbuf->f;
+    rbuf->f++;
+    if ( rbuf->f >= rbuf->m ) rbuf->f = 0;
+    rbuf->n--;
+    return ret;
+}
+/**
+ *  rbuf_shift_n() - removes first n elements from the buffer
+ *  @rbuf:  the rbuf_t holder
+ *  @n:     number of elements to remove
+ */
+static inline void rbuf_shift_n(rbuf_t *rbuf, int n)
+{
+    if ( n >= rbuf->n )
+    {
+        rbuf->n = rbuf->f = 0;
+        return;
+    }
+    rbuf->n -= n;
+    rbuf->f += n;
+    if ( rbuf->f >= rbuf->m ) rbuf->f -= rbuf->m;
+}
+
+/**
+ *  rbuf_expand0() - expand round buffer and set the newly allocated elements to 0
+ *  @rbuf:      the rbuf holder
+ *  @type_t:    data type
+ *  @n:         requested number of elements
+ *  @data:      data array to be realloced
+ *
+ *  Note: The new array is linearized and leaves the rbuf.f offset untouched,
+ *  thus the size of the new buffer is determined by the current position.
+ */
+#define rbuf_expand0(rbuf,type_t,n,data) \
+{ \
+    if ( n > (rbuf)->m ) \
+    { \
+        int m = n + (rbuf)->f; \
+        m--, m|=m>>1, m|=m>>2, m|=m>>4, m|=m>>8, m|=m>>16, m++; /* kroundup32 */ \
+        data = (type_t*) realloc(data, sizeof(type_t)*m); \
+        type_t *ptr = data; \
+        memset(ptr+(rbuf)->m,0,sizeof(type_t)*(m-(rbuf)->m)); \
+        if ( (rbuf)->f ) \
+        { \
+            memcpy(ptr+(rbuf)->m,ptr,sizeof(type_t)*(rbuf)->f); \
+            memset(ptr,0,sizeof(type_t)*(rbuf)->f); \
+        } \
+        (rbuf)->m = m; \
+    } \
+}
+
+/**
+ *  rbuf_remove_kth() - remove k-th rbuf element (0-based) and memmove the data block
+ *  @rbuf:      the rbuf holder
+ *  @type_t:    data type
+ *  @k:         k-th element to remove
+ *  @data:      data array to be modified
+ */
+#define rbuf_remove_kth(rbuf, type_t, kth, data) \
+{ \
+    int k = rbuf_kth(rbuf, kth); \
+    if ( k < (rbuf)->f )    /* shrink from back */ \
+    { \
+        int l = rbuf_kth(rbuf, -1); \
+        if ( k < l ) \
+        { \
+            type_t tmp = (data)[k]; \
+            memmove(data+k, data+k+1, (l - k)*sizeof(type_t)); \
+            (data)[l] = tmp; \
+        } \
+        (rbuf)->n--; \
+    } \
+    else                    /* shrink from front */ \
+    { \
+        if ( k > (rbuf)->f ) \
+        { \
+            type_t tmp = (data)[k]; \
+            memmove(&data[(rbuf)->f+1], &data[(rbuf)->f], (k - (rbuf)->f)*sizeof(type_t)); \
+            (data)[(rbuf)->f] = tmp; \
+        } \
+        (rbuf)->f++; \
+        (rbuf)->n--; \
+        if ( (rbuf)->f == (rbuf)->m ) (rbuf)->f = 0; \
+    } \
+}
+
+#endif
diff --git a/bcftools/regidx.c b/bcftools/regidx.c
new file mode 100644
index 0000000..cdaf7ea
--- /dev/null
+++ b/bcftools/regidx.c
@@ -0,0 +1,650 @@
+/* 
+    Copyright (C) 2014-2018 Genome Research Ltd.
+
+    Author: Petr Danecek <pd3@sanger.ac.uk>
+
+    Permission is hereby granted, free of charge, to any person obtaining a copy
+    of this software and associated documentation files (the "Software"), to deal
+    in the Software without restriction, including without limitation the rights
+    to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+    copies of the Software, and to permit persons to whom the Software is
+    furnished to do so, subject to the following conditions:
+    
+    The above copyright notice and this permission notice shall be included in
+    all copies or substantial portions of the Software.
+    
+    THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+    IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+    FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+    AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+    LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+    OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+    THE SOFTWARE.
+*/
+
+#include <strings.h>
+#include <htslib/hts.h>
+#include <htslib/kstring.h>
+#include <htslib/kseq.h>
+#include <htslib/khash_str2int.h>
+#include "regidx.h"
+
+#define MAX_COOR_0 REGIDX_MAX   // CSI and hts_itr_query limit, 0-based
+
+#define iBIN(x) ((x)>>13)
+
+typedef struct
+{
+    uint32_t beg, end;
+}
+reg_t;
+
+typedef struct
+{
+    uint32_t pos, ireg;     // y-coordinate and a pointer to reglist.reg and reglist.dat
+}
+pos_t;
+
+typedef struct _reglist_t reglist_t;
+
+typedef struct
+{
+    uint32_t beg, end, ireg;      // query coordinates and the active region
+    regidx_t *ridx;
+    reglist_t *list;
+    int active;
+}
+_itr_t;
+
+// List of regions for one chromosome.
+struct _reglist_t
+{
+    uint32_t *idx, nidx;    // index to list.reg+1
+    uint32_t nreg, mreg;    // n:used, m:allocated
+    reg_t *reg;             // regions
+    void *dat;              // payload data
+    char *seq;              // sequence name
+    int unsorted;
+
+};
+
+// Container of all sequences
+struct _regidx_t
+{
+    int nseq, mseq;         // n:used, m:alloced
+    reglist_t *seq;         // regions for each sequence
+    void *seq2regs;         // hash for fast lookup from chr name to regions
+    char **seq_names;
+    regidx_free_f free;     // function to free any data allocated by regidx_parse_f
+    regidx_parse_f parse;   // parse one input line
+    void *usr;              // user data to pass to regidx_parse_f
+    int payload_size;
+    void *payload;          // temporary payload data set by regidx_parse_f (sequence is not known beforehand)
+    kstring_t str;
+};
+
+int regidx_seq_nregs(regidx_t *idx, const char *seq)
+{
+    int iseq;
+    if ( khash_str2int_get(idx->seq2regs, seq, &iseq)!=0 ) return 0; // no such sequence
+    return idx->seq[iseq].nreg;
+}
+
+int regidx_nregs(regidx_t *idx)
+{
+    int i, nreg = 0;
+    for (i=0; i<idx->nseq; i++) nreg += idx->seq[i].nreg;
+    return nreg;
+}
+
+char **regidx_seq_names(regidx_t *idx, int *n)
+{
+    *n = idx->nseq;
+    return idx->seq_names;
+}
+
+int regidx_insert_list(regidx_t *idx, char *line, char delim)
+{
+    kstring_t tmp = {0,0,0};
+    char *ss = line;
+    while ( *ss )
+    {
+        char *se = ss;
+        while ( *se && *se!=delim ) se++;
+        tmp.l = 0;
+        kputsn(ss, se-ss, &tmp);
+        if ( regidx_insert(idx,tmp.s) < 0 )
+        {
+            free(tmp.s);
+            return -1;
+        }
+        if ( !*se ) break;
+        ss = se+1;
+    }
+    free(tmp.s);
+    return 0;
+}
+
+static inline int cmp_regs(reg_t *a, reg_t *b)
+{
+    if ( a->beg < b->beg ) return -1;
+    if ( a->beg > b->beg ) return 1;
+    if ( a->end < b->end ) return 1;    // longer intervals come first
+    if ( a->end > b->end ) return -1;
+    return 0;
+}
+static int cmp_reg_ptrs(const void *a, const void *b)
+{
+    return cmp_regs((reg_t*)a,(reg_t*)b);
+}
+static int cmp_reg_ptrs2(const void *a, const void *b)
+{
+    return cmp_regs(*((reg_t**)a),*((reg_t**)b));
+}
+
+inline int regidx_push(regidx_t *idx, char *chr_beg, char *chr_end, uint32_t beg, uint32_t end, void *payload)
+{
+    if ( beg > MAX_COOR_0 ) beg = MAX_COOR_0;
+    if ( end > MAX_COOR_0 ) end = MAX_COOR_0;
+
+    int rid;
+    idx->str.l = 0;
+    kputsn(chr_beg, chr_end-chr_beg+1, &idx->str);
+    if ( khash_str2int_get(idx->seq2regs, idx->str.s, &rid)!=0 )
+    {
+        // new chromosome
+        idx->nseq++;
+        int m_prev = idx->mseq;
+        hts_expand0(reglist_t,idx->nseq,idx->mseq,idx->seq);
+        hts_expand0(char*,idx->nseq,m_prev,idx->seq_names);
+        idx->seq_names[idx->nseq-1] = strdup(idx->str.s);
+        rid = khash_str2int_inc(idx->seq2regs, idx->seq_names[idx->nseq-1]);
+    }
+
+    reglist_t *list = &idx->seq[rid];
+    list->seq = idx->seq_names[rid];
+    list->nreg++;
+    int mreg = list->mreg;
+    hts_expand(reg_t,list->nreg,list->mreg,list->reg);
+    list->reg[list->nreg-1].beg = beg;
+    list->reg[list->nreg-1].end = end;
+    if ( idx->payload_size )
+    {
+        if ( mreg != list->mreg ) list->dat = realloc(list->dat,idx->payload_size*list->mreg);
+        memcpy((char *)list->dat + idx->payload_size*(list->nreg-1), payload, idx->payload_size);
+    }
+    if ( !list->unsorted && list->nreg>1 && cmp_regs(&list->reg[list->nreg-2],&list->reg[list->nreg-1])>0 ) list->unsorted = 1;
+    return 0;
+}
+
+int regidx_insert(regidx_t *idx, char *line)
+{
+    if ( !line ) return 0;
+    char *chr_from, *chr_to;
+    uint32_t beg,end;
+    int ret = idx->parse(line,&chr_from,&chr_to,&beg,&end,idx->payload,idx->usr);
+    if ( ret==-2 ) return -1;   // error
+    if ( ret==-1 ) return 0;    // skip the line
+    regidx_push(idx, chr_from,chr_to,beg,end,idx->payload);
+    return 0;
+}
+
+regidx_t *regidx_init_string(const char *str, regidx_parse_f parser, regidx_free_f free_f, size_t payload_size, void *usr_dat)
+{
+    regidx_t *idx = (regidx_t*) calloc(1,sizeof(regidx_t));
+    if ( !idx ) return NULL;
+
+    idx->free  = free_f;
+    idx->parse = parser ? parser : regidx_parse_tab;
+    idx->usr   = usr_dat;
+    idx->seq2regs = khash_str2int_init();
+    idx->payload_size = payload_size;
+    if ( payload_size ) idx->payload = malloc(payload_size);
+
+    kstring_t tmp = {0,0,0};
+    const char *ss = str;
+    while ( *ss )
+    {
+        while ( *ss && isspace(*ss) ) ss++;
+        const char *se = ss;
+        while ( *se && *se!='\r' && *se!='\n' ) se++;
+        tmp.l = 0;
+        kputsn(ss, se-ss, &tmp);
+        regidx_insert(idx,tmp.s);
+        while ( *se && isspace(*se) ) se++;
+        ss = se;
+    }
+    free(tmp.s);
+    return idx;
+}
+
+regidx_t *regidx_init(const char *fname, regidx_parse_f parser, regidx_free_f free_f, size_t payload_size, void *usr_dat)
+{
+    if ( !parser )
+    {
+        if ( !fname ) parser = regidx_parse_tab;
+        else
+        {
+            int len = strlen(fname);
+            if ( len>=7 && !strcasecmp(".bed.gz",fname+len-7) )
+                parser = regidx_parse_bed;
+            else if ( len>=8 && !strcasecmp(".bed.bgz",fname+len-8) )
+                parser = regidx_parse_bed;
+            else if ( len>=4 && !strcasecmp(".bed",fname+len-4) )
+                parser = regidx_parse_bed;
+            else if ( len>=4 && !strcasecmp(".vcf",fname+len-4) )
+                parser = regidx_parse_vcf;
+            else if ( len>=7 && !strcasecmp(".vcf.gz",fname+len-7) )
+                parser = regidx_parse_vcf;
+            else
+                parser = regidx_parse_tab;
+        }
+    }
+
+    regidx_t *idx = (regidx_t*) calloc(1,sizeof(regidx_t));
+    idx->free  = free_f;
+    idx->parse = parser;
+    idx->usr   = usr_dat;
+    idx->seq2regs = khash_str2int_init();
+    idx->payload_size = payload_size;
+    if ( payload_size ) idx->payload = malloc(payload_size);
+
+    if ( !fname ) return idx;
+    
+    kstring_t str = {0,0,0};
+
+    htsFile *fp = hts_open(fname,"r");
+    if ( !fp ) goto error;
+
+    while ( hts_getline(fp, KS_SEP_LINE, &str) > 0 )
+    {
+        if ( regidx_insert(idx, str.s) ) goto error;
+    }
+
+    free(str.s);
+    if ( hts_close(fp)!=0 )
+    {
+        fprintf(stderr,"[%s] Error: close failed .. %s\n", __func__,fname);
+        goto error;
+    }
+    return idx;
+
+error:
+    free(str.s);
+    if ( fp ) hts_close(fp);
+    regidx_destroy(idx);
+    return NULL;
+}
+
+void regidx_destroy(regidx_t *idx)
+{
+    int i, j;
+    for (i=0; i<idx->nseq; i++)
+    {
+        reglist_t *list = &idx->seq[i];
+        if ( idx->free )
+        {
+            for (j=0; j<list->nreg; j++)
+                idx->free((char *)list->dat + idx->payload_size*j);
+        }
+        free(list->dat);
+        free(list->reg);
+        free(list->idx);
+    }
+    free(idx->seq_names);
+    free(idx->seq);
+    free(idx->str.s);
+    free(idx->payload);
+    khash_str2int_destroy_free(idx->seq2regs);
+    free(idx);
+}
+
+int _reglist_build_index(regidx_t *regidx, reglist_t *list)
+{
+    int i;
+    if ( list->unsorted )
+    {
+        if ( !regidx->payload_size )
+            qsort(list->reg,list->nreg,sizeof(reg_t),cmp_reg_ptrs);
+        else
+        {
+            reg_t **ptr = (reg_t**) malloc(sizeof(reg_t*)*list->nreg);
+            for (i=0; i<list->nreg; i++) ptr[i] = list->reg + i;
+            qsort(ptr,list->nreg,sizeof(*ptr),cmp_reg_ptrs2);
+
+            void *tmp_dat = malloc(regidx->payload_size*list->nreg);
+            for (i=0; i<list->nreg; i++)
+            {
+                size_t iori = ptr[i] - list->reg;
+                memcpy((char *)tmp_dat+i*regidx->payload_size,
+                       (char *)list->dat+iori*regidx->payload_size,
+                       regidx->payload_size);
+            }
+            free(list->dat);
+            list->dat = tmp_dat;
+
+            reg_t *tmp_reg = (reg_t*) malloc(sizeof(reg_t)*list->nreg);
+            for (i=0; i<list->nreg; i++)
+            {
+                size_t iori = ptr[i] - list->reg;
+                tmp_reg[i] = list->reg[iori];
+            }
+            free(ptr);
+            free(list->reg);
+            list->reg  = tmp_reg;
+            list->mreg = list->nreg;
+        }
+        list->unsorted = 0;
+    }
+
+    list->nidx = 0;
+    int j,k, midx = 0;
+    for (j=0; j<list->nreg; j++)
+    {
+        int ibeg = iBIN(list->reg[j].beg);
+        int iend = iBIN(list->reg[j].end);
+        if ( midx <= iend )
+        {
+            int old_midx = midx; 
+            midx = iend + 1;
+            kroundup32(midx);
+            list->idx = (uint32_t*) realloc(list->idx, midx*sizeof(uint32_t));
+            memset(list->idx+old_midx, 0, sizeof(uint32_t)*(midx-old_midx));
+        }
+        if ( ibeg==iend )
+        {
+            if ( !list->idx[ibeg] ) list->idx[ibeg] = j + 1;
+        }
+        else
+        {
+            for (k=ibeg; k<=iend; k++)
+                if ( !list->idx[k] ) list->idx[k] = j + 1;
+        }
+        if ( list->nidx < iend+1 ) list->nidx = iend+1;
+    }
+
+    return 0;
+}
+
+int regidx_overlap(regidx_t *regidx, const char *chr, uint32_t beg, uint32_t end, regitr_t *regitr)
+{
+    if ( regitr ) regitr->seq = NULL;
+
+    int iseq, ireg;
+    if ( khash_str2int_get(regidx->seq2regs, chr, &iseq)!=0 ) return 0;    // no such sequence
+
+    reglist_t *list = &regidx->seq[iseq];
+    if ( !list->nreg ) return 0;
+
+    if ( list->nreg==1 )
+    {
+        if ( beg > list->reg[0].end ) return 0;
+        if ( end < list->reg[0].beg ) return 0;
+        ireg = 0;
+    }
+    else
+    {
+        if ( !list->idx )
+            _reglist_build_index(regidx,list);
+
+        int ibeg = iBIN(beg);
+        if ( ibeg >= list->nidx ) return 0;     // beg is too big
+
+        // find a matching region
+        uint32_t i = list->idx[ibeg];
+        if ( !i )
+        {
+            int iend = iBIN(end);
+            if ( iend > list->nidx ) iend = list->nidx;
+            for (i=ibeg; i<=iend; i++)
+                if ( list->idx[i] ) break;
+            if ( i>iend ) return 0;
+            i = list->idx[i];
+        }
+        for (ireg=i-1; ireg<list->nreg; ireg++)
+        {
+            if ( list->reg[ireg].beg > end ) return 0;   // no match, past the query region
+            if ( list->reg[ireg].end >= beg && list->reg[ireg].beg <= end ) break; // found
+        }
+
+        if ( ireg >= list->nreg ) return 0;   // no match
+    }
+
+    if ( !regitr ) return 1;    // match, but no more info to save
+
+    // may need to iterate over the matching regions later
+    _itr_t *itr = (_itr_t*)regitr->itr;
+    itr->ridx = regidx;
+    itr->list = list;
+    itr->beg  = beg;
+    itr->end  = end;
+    itr->ireg = ireg;
+    itr->active = 0;
+
+    regitr->seq = list->seq;
+    regitr->beg = list->reg[ireg].beg;
+    regitr->end = list->reg[ireg].end;
+    if ( regidx->payload_size )
+        regitr->payload = (char *)list->dat + regidx->payload_size*ireg;
+
+    return 1;
+}
+
+int regidx_parse_bed(const char *line, char **chr_beg, char **chr_end, uint32_t *beg, uint32_t *end, void *payload, void *usr)
+{
+    char *ss = (char*) line;
+    while ( *ss && isspace(*ss) ) ss++;
+    if ( !*ss ) return -1;      // skip blank lines
+    if ( *ss=='#' ) return -1;  // skip comments
+    
+    char *se = ss;
+    while ( *se && !isspace(*se) ) se++;
+
+    *chr_beg = ss;
+    *chr_end = se-1;
+
+    if ( !*se )
+    {
+        // just the chromosome name
+        *beg = 0;
+        *end = MAX_COOR_0;
+        return 0;
+    }
+
+    ss = se+1;
+    *beg = strtod(ss, &se);
+    if ( ss==se ) { fprintf(stderr,"Could not parse bed line: %s\n", line); return -2; }
+
+    ss = se+1;
+    *end = strtod(ss, &se) - 1;
+    if ( ss==se ) { fprintf(stderr,"Could not parse bed line: %s\n", line); return -2; }
+    
+    return 0;
+}
+
+int regidx_parse_tab(const char *line, char **chr_beg, char **chr_end, uint32_t *beg, uint32_t *end, void *payload, void *usr)
+{
+    char *ss = (char*) line;
+    while ( *ss && isspace(*ss) ) ss++;
+    if ( !*ss ) return -1;      // skip blank lines
+    if ( *ss=='#' ) return -1;  // skip comments
+    
+    char *se = ss;
+    while ( *se && !isspace(*se) ) se++;
+
+    *chr_beg = ss;
+    *chr_end = se-1;
+
+    if ( !*se )
+    {
+        // just the chromosome name
+        *beg = 0;
+        *end = MAX_COOR_0;
+        return 0;
+    }
+
+    ss = se+1;
+    *beg = strtod(ss, &se);
+    if ( ss==se ) { fprintf(stderr,"Could not parse tab line: %s\n", line); return -2; }
+    if ( *beg==0 ) { fprintf(stderr,"Could not parse tab line, expected 1-based coordinate: %s\n", line); return -2; }
+    (*beg)--;
+
+    if ( !se[0] || !se[1] )
+        *end = *beg;
+    else
+    {
+        ss = se+1;
+        *end = strtod(ss, &se);
+        if ( ss==se || (*se && !isspace(*se)) ) *end = *beg;
+        else if ( *end==0 ) { fprintf(stderr,"Could not parse tab line, expected 1-based coordinate: %s\n", line); return -2; }
+        else (*end)--;
+    }
+    return 0;
+}
+
+int regidx_parse_vcf(const char *line, char **chr_beg, char **chr_end, uint32_t *beg, uint32_t *end, void *payload, void *usr)
+{
+    int ret = regidx_parse_tab(line, chr_beg, chr_end, beg, end, payload, usr);
+    if ( !ret ) *end = *beg;
+    return ret;
+}
+
+int regidx_parse_reg(const char *line, char **chr_beg, char **chr_end, uint32_t *beg, uint32_t *end, void *payload, void *usr)
+{
+    char *ss = (char*) line;
+    while ( *ss && isspace(*ss) ) ss++;
+    if ( !*ss ) return -1;      // skip blank lines
+    if ( *ss=='#' ) return -1;  // skip comments
+    
+    char *se = ss;
+    while ( *se && *se!=':' ) se++;
+
+    *chr_beg = ss;
+    *chr_end = se-1;
+
+    if ( !*se )
+    {
+        *beg = 0;
+        *end = MAX_COOR_0;
+        return 0;
+    }
+
+    ss = se+1;
+    *beg = strtod(ss, &se);
+    if ( ss==se ) { fprintf(stderr,"Could not parse reg line: %s\n", line); return -2; }
+    if ( *beg==0 ) { fprintf(stderr,"Could not parse reg line, expected 1-based coordinate: %s\n", line); return -2; }
+    (*beg)--;
+
+    if ( !se[0] || !se[1] )
+        *end = se[0]=='-' ? MAX_COOR_0 : *beg;
+    else
+    {
+        ss = se+1;
+        *end = strtod(ss, &se);
+        if ( ss==se ) *end = *beg;
+        else if ( *end==0 ) { fprintf(stderr,"Could not parse reg line, expected 1-based coordinate: %s\n", line); return -2; }
+        else (*end)--;
+    }
+    return 0;
+}
+
+regitr_t *regitr_init(regidx_t *regidx)
+{
+    regitr_t *regitr = (regitr_t*) calloc(1,sizeof(regitr_t));
+    regitr->itr  = (_itr_t*) calloc(1,sizeof(_itr_t));
+    _itr_t *itr = (_itr_t*) regitr->itr;
+    itr->ridx = regidx;
+    itr->list = NULL;
+    return regitr;
+}
+
+void regitr_reset(regidx_t *regidx, regitr_t *regitr)
+{
+    _itr_t *itr = (_itr_t*) regitr->itr;
+    memset(itr,0,sizeof(_itr_t));
+    itr->ridx = regidx;
+}
+
+void regitr_destroy(regitr_t *regitr)
+{
+    free(regitr->itr);
+    free(regitr);
+}
+
+int regitr_overlap(regitr_t *regitr)
+{
+    if ( !regitr->seq ) return 0;
+
+    _itr_t *itr = (_itr_t*) regitr->itr;
+    if ( !itr->active )
+    {
+        // is this the first call after regidx_overlap?
+        itr->active = 1;
+        itr->ireg++;
+        return 1;
+    }
+
+    reglist_t *list = itr->list;
+
+    int i;
+    for (i=itr->ireg; i<list->nreg; i++)
+    {
+        if ( list->reg[i].beg > itr->end ) return 0;   // no match, past the query region
+        if ( list->reg[i].end >= itr->beg && list->reg[i].beg <= itr->end ) break; // found
+    }
+
+    if ( i >= list->nreg ) return 0;   // no match
+
+    itr->ireg = i + 1;
+    regitr->seq = list->seq;
+    regitr->beg = list->reg[i].beg;
+    regitr->end = list->reg[i].end;
+    if ( itr->ridx->payload_size )
+        regitr->payload = (char *)list->dat + itr->ridx->payload_size*i;
+
+    return 1;
+}
+
+int regitr_loop(regitr_t *regitr)
+{
+    _itr_t *itr = (_itr_t*) regitr->itr;
+    regidx_t *regidx = itr->ridx;
+
+    if ( !itr->list )    // first time here
+    {
+        itr->list = regidx->seq;
+        itr->ireg = 0;
+    }
+
+    size_t iseq = itr->list - regidx->seq;
+    if ( iseq >= regidx->nseq ) return 0;
+
+    if ( itr->ireg >= itr->list->nreg )
+    {
+        iseq++;
+        if ( iseq >= regidx->nseq ) return 0; // no more sequences, done
+        itr->ireg = 0;
+        itr->list = &regidx->seq[iseq];
+    }
+
+    regitr->seq = itr->list->seq;
+    regitr->beg = itr->list->reg[itr->ireg].beg;
+    regitr->end = itr->list->reg[itr->ireg].end;
+    if ( regidx->payload_size )
+        regitr->payload = (char *)itr->list->dat + regidx->payload_size*itr->ireg;
+    itr->ireg++;
+
+    return 1;
+}
+
+
+void regitr_copy(regitr_t *dst, regitr_t *src)
+{
+    _itr_t *dst_itr = (_itr_t*) dst->itr;
+    _itr_t *src_itr = (_itr_t*) src->itr;
+    *dst_itr = *src_itr;
+    *dst = *src;
+    dst->itr = dst_itr;
+}
+
+
diff --git a/bcftools/regidx.c.pysam.c b/bcftools/regidx.c.pysam.c
new file mode 100644
index 0000000..4eb96e8
--- /dev/null
+++ b/bcftools/regidx.c.pysam.c
@@ -0,0 +1,652 @@
+#include "bcftools.pysam.h"
+
+/* 
+    Copyright (C) 2014-2018 Genome Research Ltd.
+
+    Author: Petr Danecek <pd3@sanger.ac.uk>
+
+    Permission is hereby granted, free of charge, to any person obtaining a copy
+    of this software and associated documentation files (the "Software"), to deal
+    in the Software without restriction, including without limitation the rights
+    to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+    copies of the Software, and to permit persons to whom the Software is
+    furnished to do so, subject to the following conditions:
+    
+    The above copyright notice and this permission notice shall be included in
+    all copies or substantial portions of the Software.
+    
+    THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+    IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+    FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+    AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+    LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+    OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+    THE SOFTWARE.
+*/
+
+#include <strings.h>
+#include <htslib/hts.h>
+#include <htslib/kstring.h>
+#include <htslib/kseq.h>
+#include <htslib/khash_str2int.h>
+#include "regidx.h"
+
+#define MAX_COOR_0 REGIDX_MAX   // CSI and hts_itr_query limit, 0-based
+
+#define iBIN(x) ((x)>>13)
+
+typedef struct
+{
+    uint32_t beg, end;
+}
+reg_t;
+
+typedef struct
+{
+    uint32_t pos, ireg;     // y-coordinate and a pointer to reglist.reg and reglist.dat
+}
+pos_t;
+
+typedef struct _reglist_t reglist_t;
+
+typedef struct
+{
+    uint32_t beg, end, ireg;      // query coordinates and the active region
+    regidx_t *ridx;
+    reglist_t *list;
+    int active;
+}
+_itr_t;
+
+// List of regions for one chromosome.
+struct _reglist_t
+{
+    uint32_t *idx, nidx;    // index to list.reg+1
+    uint32_t nreg, mreg;    // n:used, m:allocated
+    reg_t *reg;             // regions
+    void *dat;              // payload data
+    char *seq;              // sequence name
+    int unsorted;
+
+};
+
+// Container of all sequences
+struct _regidx_t
+{
+    int nseq, mseq;         // n:used, m:alloced
+    reglist_t *seq;         // regions for each sequence
+    void *seq2regs;         // hash for fast lookup from chr name to regions
+    char **seq_names;
+    regidx_free_f free;     // function to free any data allocated by regidx_parse_f
+    regidx_parse_f parse;   // parse one input line
+    void *usr;              // user data to pass to regidx_parse_f
+    int payload_size;
+    void *payload;          // temporary payload data set by regidx_parse_f (sequence is not known beforehand)
+    kstring_t str;
+};
+
+int regidx_seq_nregs(regidx_t *idx, const char *seq)
+{
+    int iseq;
+    if ( khash_str2int_get(idx->seq2regs, seq, &iseq)!=0 ) return 0; // no such sequence
+    return idx->seq[iseq].nreg;
+}
+
+int regidx_nregs(regidx_t *idx)
+{
+    int i, nreg = 0;
+    for (i=0; i<idx->nseq; i++) nreg += idx->seq[i].nreg;
+    return nreg;
+}
+
+char **regidx_seq_names(regidx_t *idx, int *n)
+{
+    *n = idx->nseq;
+    return idx->seq_names;
+}
+
+int regidx_insert_list(regidx_t *idx, char *line, char delim)
+{
+    kstring_t tmp = {0,0,0};
+    char *ss = line;
+    while ( *ss )
+    {
+        char *se = ss;
+        while ( *se && *se!=delim ) se++;
+        tmp.l = 0;
+        kputsn(ss, se-ss, &tmp);
+        if ( regidx_insert(idx,tmp.s) < 0 )
+        {
+            free(tmp.s);
+            return -1;
+        }
+        if ( !*se ) break;
+        ss = se+1;
+    }
+    free(tmp.s);
+    return 0;
+}
+
+static inline int cmp_regs(reg_t *a, reg_t *b)
+{
+    if ( a->beg < b->beg ) return -1;
+    if ( a->beg > b->beg ) return 1;
+    if ( a->end < b->end ) return 1;    // longer intervals come first
+    if ( a->end > b->end ) return -1;
+    return 0;
+}
+static int cmp_reg_ptrs(const void *a, const void *b)
+{
+    return cmp_regs((reg_t*)a,(reg_t*)b);
+}
+static int cmp_reg_ptrs2(const void *a, const void *b)
+{
+    return cmp_regs(*((reg_t**)a),*((reg_t**)b));
+}
+
+inline int regidx_push(regidx_t *idx, char *chr_beg, char *chr_end, uint32_t beg, uint32_t end, void *payload)
+{
+    if ( beg > MAX_COOR_0 ) beg = MAX_COOR_0;
+    if ( end > MAX_COOR_0 ) end = MAX_COOR_0;
+
+    int rid;
+    idx->str.l = 0;
+    kputsn(chr_beg, chr_end-chr_beg+1, &idx->str);
+    if ( khash_str2int_get(idx->seq2regs, idx->str.s, &rid)!=0 )
+    {
+        // new chromosome
+        idx->nseq++;
+        int m_prev = idx->mseq;
+        hts_expand0(reglist_t,idx->nseq,idx->mseq,idx->seq);
+        hts_expand0(char*,idx->nseq,m_prev,idx->seq_names);
+        idx->seq_names[idx->nseq-1] = strdup(idx->str.s);
+        rid = khash_str2int_inc(idx->seq2regs, idx->seq_names[idx->nseq-1]);
+    }
+
+    reglist_t *list = &idx->seq[rid];
+    list->seq = idx->seq_names[rid];
+    list->nreg++;
+    int mreg = list->mreg;
+    hts_expand(reg_t,list->nreg,list->mreg,list->reg);
+    list->reg[list->nreg-1].beg = beg;
+    list->reg[list->nreg-1].end = end;
+    if ( idx->payload_size )
+    {
+        if ( mreg != list->mreg ) list->dat = realloc(list->dat,idx->payload_size*list->mreg);
+        memcpy((char *)list->dat + idx->payload_size*(list->nreg-1), payload, idx->payload_size);
+    }
+    if ( !list->unsorted && list->nreg>1 && cmp_regs(&list->reg[list->nreg-2],&list->reg[list->nreg-1])>0 ) list->unsorted = 1;
+    return 0;
+}
+
+int regidx_insert(regidx_t *idx, char *line)
+{
+    if ( !line ) return 0;
+    char *chr_from, *chr_to;
+    uint32_t beg,end;
+    int ret = idx->parse(line,&chr_from,&chr_to,&beg,&end,idx->payload,idx->usr);
+    if ( ret==-2 ) return -1;   // error
+    if ( ret==-1 ) return 0;    // skip the line
+    regidx_push(idx, chr_from,chr_to,beg,end,idx->payload);
+    return 0;
+}
+
+regidx_t *regidx_init_string(const char *str, regidx_parse_f parser, regidx_free_f free_f, size_t payload_size, void *usr_dat)
+{
+    regidx_t *idx = (regidx_t*) calloc(1,sizeof(regidx_t));
+    if ( !idx ) return NULL;
+
+    idx->free  = free_f;
+    idx->parse = parser ? parser : regidx_parse_tab;
+    idx->usr   = usr_dat;
+    idx->seq2regs = khash_str2int_init();
+    idx->payload_size = payload_size;
+    if ( payload_size ) idx->payload = malloc(payload_size);
+
+    kstring_t tmp = {0,0,0};
+    const char *ss = str;
+    while ( *ss )
+    {
+        while ( *ss && isspace(*ss) ) ss++;
+        const char *se = ss;
+        while ( *se && *se!='\r' && *se!='\n' ) se++;
+        tmp.l = 0;
+        kputsn(ss, se-ss, &tmp);
+        regidx_insert(idx,tmp.s);
+        while ( *se && isspace(*se) ) se++;
+        ss = se;
+    }
+    free(tmp.s);
+    return idx;
+}
+
+regidx_t *regidx_init(const char *fname, regidx_parse_f parser, regidx_free_f free_f, size_t payload_size, void *usr_dat)
+{
+    if ( !parser )
+    {
+        if ( !fname ) parser = regidx_parse_tab;
+        else
+        {
+            int len = strlen(fname);
+            if ( len>=7 && !strcasecmp(".bed.gz",fname+len-7) )
+                parser = regidx_parse_bed;
+            else if ( len>=8 && !strcasecmp(".bed.bgz",fname+len-8) )
+                parser = regidx_parse_bed;
+            else if ( len>=4 && !strcasecmp(".bed",fname+len-4) )
+                parser = regidx_parse_bed;
+            else if ( len>=4 && !strcasecmp(".vcf",fname+len-4) )
+                parser = regidx_parse_vcf;
+            else if ( len>=7 && !strcasecmp(".vcf.gz",fname+len-7) )
+                parser = regidx_parse_vcf;
+            else
+                parser = regidx_parse_tab;
+        }
+    }
+
+    regidx_t *idx = (regidx_t*) calloc(1,sizeof(regidx_t));
+    idx->free  = free_f;
+    idx->parse = parser;
+    idx->usr   = usr_dat;
+    idx->seq2regs = khash_str2int_init();
+    idx->payload_size = payload_size;
+    if ( payload_size ) idx->payload = malloc(payload_size);
+
+    if ( !fname ) return idx;
+    
+    kstring_t str = {0,0,0};
+
+    htsFile *fp = hts_open(fname,"r");
+    if ( !fp ) goto error;
+
+    while ( hts_getline(fp, KS_SEP_LINE, &str) > 0 )
+    {
+        if ( regidx_insert(idx, str.s) ) goto error;
+    }
+
+    free(str.s);
+    if ( hts_close(fp)!=0 )
+    {
+        fprintf(bcftools_stderr,"[%s] Error: close failed .. %s\n", __func__,fname);
+        goto error;
+    }
+    return idx;
+
+error:
+    free(str.s);
+    if ( fp ) hts_close(fp);
+    regidx_destroy(idx);
+    return NULL;
+}
+
+void regidx_destroy(regidx_t *idx)
+{
+    int i, j;
+    for (i=0; i<idx->nseq; i++)
+    {
+        reglist_t *list = &idx->seq[i];
+        if ( idx->free )
+        {
+            for (j=0; j<list->nreg; j++)
+                idx->free((char *)list->dat + idx->payload_size*j);
+        }
+        free(list->dat);
+        free(list->reg);
+        free(list->idx);
+    }
+    free(idx->seq_names);
+    free(idx->seq);
+    free(idx->str.s);
+    free(idx->payload);
+    khash_str2int_destroy_free(idx->seq2regs);
+    free(idx);
+}
+
+int _reglist_build_index(regidx_t *regidx, reglist_t *list)
+{
+    int i;
+    if ( list->unsorted )
+    {
+        if ( !regidx->payload_size )
+            qsort(list->reg,list->nreg,sizeof(reg_t),cmp_reg_ptrs);
+        else
+        {
+            reg_t **ptr = (reg_t**) malloc(sizeof(reg_t*)*list->nreg);
+            for (i=0; i<list->nreg; i++) ptr[i] = list->reg + i;
+            qsort(ptr,list->nreg,sizeof(*ptr),cmp_reg_ptrs2);
+
+            void *tmp_dat = malloc(regidx->payload_size*list->nreg);
+            for (i=0; i<list->nreg; i++)
+            {
+                size_t iori = ptr[i] - list->reg;
+                memcpy((char *)tmp_dat+i*regidx->payload_size,
+                       (char *)list->dat+iori*regidx->payload_size,
+                       regidx->payload_size);
+            }
+            free(list->dat);
+            list->dat = tmp_dat;
+
+            reg_t *tmp_reg = (reg_t*) malloc(sizeof(reg_t)*list->nreg);
+            for (i=0; i<list->nreg; i++)
+            {
+                size_t iori = ptr[i] - list->reg;
+                tmp_reg[i] = list->reg[iori];
+            }
+            free(ptr);
+            free(list->reg);
+            list->reg  = tmp_reg;
+            list->mreg = list->nreg;
+        }
+        list->unsorted = 0;
+    }
+
+    list->nidx = 0;
+    int j,k, midx = 0;
+    for (j=0; j<list->nreg; j++)
+    {
+        int ibeg = iBIN(list->reg[j].beg);
+        int iend = iBIN(list->reg[j].end);
+        if ( midx <= iend )
+        {
+            int old_midx = midx; 
+            midx = iend + 1;
+            kroundup32(midx);
+            list->idx = (uint32_t*) realloc(list->idx, midx*sizeof(uint32_t));
+            memset(list->idx+old_midx, 0, sizeof(uint32_t)*(midx-old_midx));
+        }
+        if ( ibeg==iend )
+        {
+            if ( !list->idx[ibeg] ) list->idx[ibeg] = j + 1;
+        }
+        else
+        {
+            for (k=ibeg; k<=iend; k++)
+                if ( !list->idx[k] ) list->idx[k] = j + 1;
+        }
+        if ( list->nidx < iend+1 ) list->nidx = iend+1;
+    }
+
+    return 0;
+}
+
+int regidx_overlap(regidx_t *regidx, const char *chr, uint32_t beg, uint32_t end, regitr_t *regitr)
+{
+    if ( regitr ) regitr->seq = NULL;
+
+    int iseq, ireg;
+    if ( khash_str2int_get(regidx->seq2regs, chr, &iseq)!=0 ) return 0;    // no such sequence
+
+    reglist_t *list = &regidx->seq[iseq];
+    if ( !list->nreg ) return 0;
+
+    if ( list->nreg==1 )
+    {
+        if ( beg > list->reg[0].end ) return 0;
+        if ( end < list->reg[0].beg ) return 0;
+        ireg = 0;
+    }
+    else
+    {
+        if ( !list->idx )
+            _reglist_build_index(regidx,list);
+
+        int ibeg = iBIN(beg);
+        if ( ibeg >= list->nidx ) return 0;     // beg is too big
+
+        // find a matching region
+        uint32_t i = list->idx[ibeg];
+        if ( !i )
+        {
+            int iend = iBIN(end);
+            if ( iend > list->nidx ) iend = list->nidx;
+            for (i=ibeg; i<=iend; i++)
+                if ( list->idx[i] ) break;
+            if ( i>iend ) return 0;
+            i = list->idx[i];
+        }
+        for (ireg=i-1; ireg<list->nreg; ireg++)
+        {
+            if ( list->reg[ireg].beg > end ) return 0;   // no match, past the query region
+            if ( list->reg[ireg].end >= beg && list->reg[ireg].beg <= end ) break; // found
+        }
+
+        if ( ireg >= list->nreg ) return 0;   // no match
+    }
+
+    if ( !regitr ) return 1;    // match, but no more info to save
+
+    // may need to iterate over the matching regions later
+    _itr_t *itr = (_itr_t*)regitr->itr;
+    itr->ridx = regidx;
+    itr->list = list;
+    itr->beg  = beg;
+    itr->end  = end;
+    itr->ireg = ireg;
+    itr->active = 0;
+
+    regitr->seq = list->seq;
+    regitr->beg = list->reg[ireg].beg;
+    regitr->end = list->reg[ireg].end;
+    if ( regidx->payload_size )
+        regitr->payload = (char *)list->dat + regidx->payload_size*ireg;
+
+    return 1;
+}
+
+int regidx_parse_bed(const char *line, char **chr_beg, char **chr_end, uint32_t *beg, uint32_t *end, void *payload, void *usr)
+{
+    char *ss = (char*) line;
+    while ( *ss && isspace(*ss) ) ss++;
+    if ( !*ss ) return -1;      // skip blank lines
+    if ( *ss=='#' ) return -1;  // skip comments
+    
+    char *se = ss;
+    while ( *se && !isspace(*se) ) se++;
+
+    *chr_beg = ss;
+    *chr_end = se-1;
+
+    if ( !*se )
+    {
+        // just the chromosome name
+        *beg = 0;
+        *end = MAX_COOR_0;
+        return 0;
+    }
+
+    ss = se+1;
+    *beg = strtod(ss, &se);
+    if ( ss==se ) { fprintf(bcftools_stderr,"Could not parse bed line: %s\n", line); return -2; }
+
+    ss = se+1;
+    *end = strtod(ss, &se) - 1;
+    if ( ss==se ) { fprintf(bcftools_stderr,"Could not parse bed line: %s\n", line); return -2; }
+    
+    return 0;
+}
+
+int regidx_parse_tab(const char *line, char **chr_beg, char **chr_end, uint32_t *beg, uint32_t *end, void *payload, void *usr)
+{
+    char *ss = (char*) line;
+    while ( *ss && isspace(*ss) ) ss++;
+    if ( !*ss ) return -1;      // skip blank lines
+    if ( *ss=='#' ) return -1;  // skip comments
+    
+    char *se = ss;
+    while ( *se && !isspace(*se) ) se++;
+
+    *chr_beg = ss;
+    *chr_end = se-1;
+
+    if ( !*se )
+    {
+        // just the chromosome name
+        *beg = 0;
+        *end = MAX_COOR_0;
+        return 0;
+    }
+
+    ss = se+1;
+    *beg = strtod(ss, &se);
+    if ( ss==se ) { fprintf(bcftools_stderr,"Could not parse tab line: %s\n", line); return -2; }
+    if ( *beg==0 ) { fprintf(bcftools_stderr,"Could not parse tab line, expected 1-based coordinate: %s\n", line); return -2; }
+    (*beg)--;
+
+    if ( !se[0] || !se[1] )
+        *end = *beg;
+    else
+    {
+        ss = se+1;
+        *end = strtod(ss, &se);
+        if ( ss==se || (*se && !isspace(*se)) ) *end = *beg;
+        else if ( *end==0 ) { fprintf(bcftools_stderr,"Could not parse tab line, expected 1-based coordinate: %s\n", line); return -2; }
+        else (*end)--;
+    }
+    return 0;
+}
+
+int regidx_parse_vcf(const char *line, char **chr_beg, char **chr_end, uint32_t *beg, uint32_t *end, void *payload, void *usr)
+{
+    int ret = regidx_parse_tab(line, chr_beg, chr_end, beg, end, payload, usr);
+    if ( !ret ) *end = *beg;
+    return ret;
+}
+
+int regidx_parse_reg(const char *line, char **chr_beg, char **chr_end, uint32_t *beg, uint32_t *end, void *payload, void *usr)
+{
+    char *ss = (char*) line;
+    while ( *ss && isspace(*ss) ) ss++;
+    if ( !*ss ) return -1;      // skip blank lines
+    if ( *ss=='#' ) return -1;  // skip comments
+    
+    char *se = ss;
+    while ( *se && *se!=':' ) se++;
+
+    *chr_beg = ss;
+    *chr_end = se-1;
+
+    if ( !*se )
+    {
+        *beg = 0;
+        *end = MAX_COOR_0;
+        return 0;
+    }
+
+    ss = se+1;
+    *beg = strtod(ss, &se);
+    if ( ss==se ) { fprintf(bcftools_stderr,"Could not parse reg line: %s\n", line); return -2; }
+    if ( *beg==0 ) { fprintf(bcftools_stderr,"Could not parse reg line, expected 1-based coordinate: %s\n", line); return -2; }
+    (*beg)--;
+
+    if ( !se[0] || !se[1] )
+        *end = se[0]=='-' ? MAX_COOR_0 : *beg;
+    else
+    {
+        ss = se+1;
+        *end = strtod(ss, &se);
+        if ( ss==se ) *end = *beg;
+        else if ( *end==0 ) { fprintf(bcftools_stderr,"Could not parse reg line, expected 1-based coordinate: %s\n", line); return -2; }
+        else (*end)--;
+    }
+    return 0;
+}
+
+regitr_t *regitr_init(regidx_t *regidx)
+{
+    regitr_t *regitr = (regitr_t*) calloc(1,sizeof(regitr_t));
+    regitr->itr  = (_itr_t*) calloc(1,sizeof(_itr_t));
+    _itr_t *itr = (_itr_t*) regitr->itr;
+    itr->ridx = regidx;
+    itr->list = NULL;
+    return regitr;
+}
+
+void regitr_reset(regidx_t *regidx, regitr_t *regitr)
+{
+    _itr_t *itr = (_itr_t*) regitr->itr;
+    memset(itr,0,sizeof(_itr_t));
+    itr->ridx = regidx;
+}
+
+void regitr_destroy(regitr_t *regitr)
+{
+    free(regitr->itr);
+    free(regitr);
+}
+
+int regitr_overlap(regitr_t *regitr)
+{
+    if ( !regitr->seq ) return 0;
+
+    _itr_t *itr = (_itr_t*) regitr->itr;
+    if ( !itr->active )
+    {
+        // is this the first call after regidx_overlap?
+        itr->active = 1;
+        itr->ireg++;
+        return 1;
+    }
+
+    reglist_t *list = itr->list;
+
+    int i;
+    for (i=itr->ireg; i<list->nreg; i++)
+    {
+        if ( list->reg[i].beg > itr->end ) return 0;   // no match, past the query region
+        if ( list->reg[i].end >= itr->beg && list->reg[i].beg <= itr->end ) break; // found
+    }
+
+    if ( i >= list->nreg ) return 0;   // no match
+
+    itr->ireg = i + 1;
+    regitr->seq = list->seq;
+    regitr->beg = list->reg[i].beg;
+    regitr->end = list->reg[i].end;
+    if ( itr->ridx->payload_size )
+        regitr->payload = (char *)list->dat + itr->ridx->payload_size*i;
+
+    return 1;
+}
+
+int regitr_loop(regitr_t *regitr)
+{
+    _itr_t *itr = (_itr_t*) regitr->itr;
+    regidx_t *regidx = itr->ridx;
+
+    if ( !itr->list )    // first time here
+    {
+        itr->list = regidx->seq;
+        itr->ireg = 0;
+    }
+
+    size_t iseq = itr->list - regidx->seq;
+    if ( iseq >= regidx->nseq ) return 0;
+
+    if ( itr->ireg >= itr->list->nreg )
+    {
+        iseq++;
+        if ( iseq >= regidx->nseq ) return 0; // no more sequences, done
+        itr->ireg = 0;
+        itr->list = &regidx->seq[iseq];
+    }
+
+    regitr->seq = itr->list->seq;
+    regitr->beg = itr->list->reg[itr->ireg].beg;
+    regitr->end = itr->list->reg[itr->ireg].end;
+    if ( regidx->payload_size )
+        regitr->payload = (char *)itr->list->dat + regidx->payload_size*itr->ireg;
+    itr->ireg++;
+
+    return 1;
+}
+
+
+void regitr_copy(regitr_t *dst, regitr_t *src)
+{
+    _itr_t *dst_itr = (_itr_t*) dst->itr;
+    _itr_t *src_itr = (_itr_t*) src->itr;
+    *dst_itr = *src_itr;
+    *dst = *src;
+    dst->itr = dst_itr;
+}
+
+
diff --git a/bcftools/regidx.h b/bcftools/regidx.h
new file mode 100644
index 0000000..c40bbd8
--- /dev/null
+++ b/bcftools/regidx.h
@@ -0,0 +1,222 @@
+/* 
+    Copyright (C) 2014-2016, 2018 Genome Research Ltd.
+
+    Author: Petr Danecek <pd3@sanger.ac.uk>
+
+    Permission is hereby granted, free of charge, to any person obtaining a copy
+    of this software and associated documentation files (the "Software"), to deal
+    in the Software without restriction, including without limitation the rights
+    to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+    copies of the Software, and to permit persons to whom the Software is
+    furnished to do so, subject to the following conditions:
+    
+    The above copyright notice and this permission notice shall be included in
+    all copies or substantial portions of the Software.
+    
+    THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+    IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+    FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+    AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+    LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+    OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+    THE SOFTWARE.
+*/
+
+/*
+    Region indexing with an optional payload.
+
+    Example of usage:
+
+        // Init the parser and print regions. In this example the payload is a
+        // pointer to a string. For the description of parse_custom and
+        // free_custom functions, see regidx_parse_f and regidx_free_f below,
+        // and for working example see test/test-regidx.c.
+        regidx_t *idx = regidx_init(in_fname,parse_custom,free_custom,sizeof(char*),NULL);
+
+        // Query overlap with chr:beg-end (beg,end are 1-based coordinates)
+        regitr_t *itr = regitr_init(idx);
+        if ( regidx_overlap(idx, chr,beg-1,end-1, itr) ) printf("There is an overlap!\n");
+
+        while ( regitr_overlap(itr) )
+        {
+            printf("[%d,%d] overlaps with [%d,%d], payload=%s\n", beg,end, 
+                itr->beg+1, itr->end+1, regitr_payload(itr,char*));
+        }
+
+        regidx_destroy(idx);
+        regitr_destroy(itr);
+
+
+    Another example, loop over all regions:
+        
+        regidx_t *idx = regidx_init(in_fname,NULL,NULL,0,NULL);
+        regitr_t *itr = regitr_init(idx);
+
+        while ( regitr_loop(itr) )
+            printf("chr=%s  beg=%d  end=%d\n", itr->seq, itr->beg+1, itr->end+1);
+
+        regidx_destroy(idx);
+        regitr_destroy(itr);
+*/
+
+#ifndef __REGIDX_H__
+#define __REGIDX_H__
+
+#include <stdio.h>
+#include <inttypes.h>
+
+/* Avoid conflicts with HTSlib's regidx_* functions. */
+#define regidx_destroy bcftools_regidx_destroy
+#define regidx_init bcftools_regidx_init
+#define regidx_init_string bcftools_regidx_init_string
+#define regidx_insert bcftools_regidx_insert
+#define regidx_insert_list bcftools_regidx_insert_list
+#define regidx_nregs bcftools_regidx_nregs
+#define regidx_overlap bcftools_regidx_overlap
+#define regidx_parse_bed bcftools_regidx_parse_bed
+#define regidx_parse_reg bcftools_regidx_parse_reg
+#define regidx_parse_tab bcftools_regidx_parse_tab
+#define regidx_parse_vcf bcftools_regidx_parse_vcf
+#define regidx_push bcftools_regidx_push
+#define regidx_seq_names bcftools_regidx_seq_names
+#define regidx_seq_nregs bcftools_regidx_seq_nregs
+#define regitr_copy bcftools_regitr_copy
+#define regitr_destroy bcftools_regitr_destroy
+#define regitr_init bcftools_regitr_init
+#define regitr_loop bcftools_regitr_loop
+#define regitr_overlap bcftools_regitr_overlap
+#define regitr_reset bcftools_regitr_reset
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+#define REGIDX_MAX 2147483646       // maximum regidx coordinate (0-based)
+
+typedef struct _regidx_t regidx_t;
+typedef struct
+{
+    uint32_t beg,end;
+    void *payload;
+    char *seq;
+    void *itr;
+}
+regitr_t;
+
+#define regitr_payload(itr,type_t) (*((type_t*)(itr)->payload))
+
+/*
+ *  regidx_parse_f - Function to parse one input line, such as regidx_parse_bed
+ *  or regidx_parse_tab below. The function is expected to set `chr_from` and
+ *  `chr_to` to point to first and last character of chromosome name and set
+ *  coordinates `beg` and `end` (0-based, inclusive). If regidx_init() was
+ *  called with non-zero payload_size, the `payload` points to a memory
+ *  location of the payload_size and `usr` is the data passed to regidx_init().
+ *  Any memory allocated by the function will be freed by regidx_free_f called
+ *  by regidx_destroy().
+ *
+ *  Return value: 0 on success, -1 to skip a record, -2 on fatal error.
+ */
+typedef int  (*regidx_parse_f)(const char *line, char **chr_beg, char **chr_end, uint32_t *beg, uint32_t *end, void *payload, void *usr);
+typedef void (*regidx_free_f)(void *payload);
+
+/*
+ *  A note about the parsers: 
+ *      - leading spaces are ignored
+ *      - lines starting with "#" are ignored
+ */
+int regidx_parse_bed(const char*,char**,char**,uint32_t*,uint32_t*,void*,void*);   // CHROM or whitespace-sepatated CHROM,FROM,TO (0-based,right-open)
+int regidx_parse_tab(const char*,char**,char**,uint32_t*,uint32_t*,void*,void*);   // CHROM or whitespace-separated CHROM,POS (1-based, inclusive)
+int regidx_parse_reg(const char*,char**,char**,uint32_t*,uint32_t*,void*,void*);   // CHROM, CHROM:POS, CHROM:FROM-TO, CHROM:FROM- (1-based, inclusive)
+int regidx_parse_vcf(const char*,char**,char**,uint32_t*,uint32_t*,void*,void*);
+
+/*
+ *  regidx_init() - creates new index
+ *  regidx_init_string() - creates new index, from a string rather than from a file
+ *
+ *  @param fname:  input file name or NULL if regions will be added one-by-one via regidx_insert()
+ *  @param parsef: regidx_parse_bed, regidx_parse_tab or see description of regidx_parse_f. If NULL,
+ *                 the format will be autodected, currently either regidx_parse_tab (the default) or
+ *                 regidx_parse_bed (file must be named 'bed' or 'bed.gz') will be used. Note that
+ *                 the exact autodetection algorithm will change.
+ *  @param freef:  NULL or see description of regidx_parse_f
+ *  @param payload_size: 0 with regidx_parse_bed, regidx_parse_tab or see regidx_parse_f
+ *  @param usr:    optional user data passed to regidx_parse_f
+ *
+ *  Returns index on success or NULL on error.
+ */
+regidx_t *regidx_init(const char *fname, regidx_parse_f parsef, regidx_free_f freef, size_t payload_size, void *usr);
+regidx_t *regidx_init_string(const char *string, regidx_parse_f parsef, regidx_free_f freef, size_t payload_size, void *usr);
+
+/*
+ *  regidx_destroy() - free memory allocated by regidx_init
+ */
+void regidx_destroy(regidx_t *idx);
+
+/*
+ *  regidx_overlap() - check overlap of the location chr:from-to with regions
+ *  @param beg,end:     0-based start, end coordinate (inclusive)
+ *  @param itr:         pointer to iterator, can be NULL if regidx_loop not needed
+ *
+ *  Returns 0 if there is no overlap or 1 if overlap is found. The overlapping
+ *  regions can be iterated as shown in the example above.
+ */
+int regidx_overlap(regidx_t *idx, const char *chr, uint32_t beg, uint32_t end, regitr_t *itr);
+
+/*
+ *  regidx_insert() - add a new region. 
+ *  regidx_insert_list() - add new regions from a list
+ *  regidx_push() - low level insertion of a new region
+ *
+ *  Returns 0 on success or -1 on error.
+ */
+int regidx_insert(regidx_t *idx, char *line);
+int regidx_insert_list(regidx_t *idx, char *line, char delim);
+int regidx_push(regidx_t *idx, char *chr_beg, char *chr_end, uint32_t beg, uint32_t end, void *payload);
+
+/*
+ *  regidx_seq_names() - return list of all sequence names
+ */
+char **regidx_seq_names(regidx_t *idx, int *n);
+
+/*
+ *  regidx_seq_nregs() - number of regions
+ *  regidx_nregs()  - total number of regions
+ */
+int regidx_seq_nregs(regidx_t *idx, const char *seq);
+int regidx_nregs(regidx_t *idx);
+
+/*
+ *  regitr_init() - initialize an iterator. The idx parameter is required only
+ *                  with regitr_loop. If only regitr_overlap is called, NULL
+ *                  can be given.
+ *
+ *  regitr_reset() - initialize an iterator for a repeated regitr_loop cycle.
+ *                  Not required with regitr_overlap.
+ */
+regitr_t *regitr_init(regidx_t *idx);
+void regitr_destroy(regitr_t *itr);
+void regitr_reset(regidx_t *idx, regitr_t *itr);
+
+/*
+ *  regitr_overlap() - next overlapping region
+ *  Returns 0 when done or 1 when itr is set to next region
+ */
+int regitr_overlap(regitr_t *itr);
+
+/*
+ *  regitr_loop() - loop over all regions
+ *  Returns 0 when done or 1 when itr is set to next region
+ */
+int regitr_loop(regitr_t *itr);
+
+/*
+ *  regitr_copy() - create a copy of an iterator for a repeated iteration with regitr_loop
+ */
+void regitr_copy(regitr_t *dst, regitr_t *src);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif
diff --git a/bcftools/reheader.c b/bcftools/reheader.c
new file mode 100644
index 0000000..4458f27
--- /dev/null
+++ b/bcftools/reheader.c
@@ -0,0 +1,764 @@
+/*  reheader.c -- reheader subcommand.
+
+    Copyright (C) 2014-2022 Genome Research Ltd.
+
+    Author: Petr Danecek <pd3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.  */
+
+#include <stdio.h>
+#include <unistd.h>
+#include <getopt.h>
+#include <ctype.h>
+#include <string.h>
+#include <errno.h>
+#include <sys/stat.h>
+#include <sys/types.h>
+#include <inttypes.h>
+#include <fcntl.h>
+#include <math.h>
+#ifdef _WIN32
+#include <windows.h>
+#endif
+#include <htslib/vcf.h>
+#include <htslib/bgzf.h>
+#include <htslib/tbx.h> // for hts_get_bgzfp()
+#include <htslib/kseq.h>
+#include <htslib/thread_pool.h>
+#include <htslib/faidx.h>
+#include <htslib/khash_str2int.h>
+#include "bcftools.h"
+#include "khash_str2str.h"
+
+typedef struct _args_t
+{
+    char **argv, *fname, *samples_fname, *header_fname, *output_fname;
+    char *fai_fname, *rm_tmpfile, *tmp_prefix;
+    htsFile *fp;
+    htsFormat type;
+    htsThreadPool *threads;
+    int argc, n_threads;
+}
+args_t;
+
+static inline int is_escaped(const char *min, const char *str)
+{
+    int n = 0;
+    while ( --str>=min && *str=='\\' ) n++;
+    return n%2;
+}
+static char *copy_and_update_contig_line(faidx_t *fai, char *line, void *chr_seen, kstring_t *dst)
+{
+    kstring_t key = {0,0,0}, val = {0,0,0}, tmp = {0,0,0};
+    char *chr_name = NULL, *p, *q = line + 9;   // skip ##contig=
+    char *end = q;
+    int nopen = 1, chr_len = 0;
+    while ( *end && *end!='\n' ) end++;
+    while ( *q && *q!='\n' && nopen>0 )
+    {
+        p = ++q;
+        while ( *q && (*q==' ' || *q=='\t') ) { p++; q++; }
+        // ^[A-Za-z_][0-9A-Za-z_.]*$
+        if (p==q && *q && (isalpha(*q) || *q=='_'))
+        {
+            q++;
+            while ( *q && (isalnum(*q) || *q=='_' || *q=='.') ) q++;
+        }
+        int n = q-p;
+        int m = 0;
+        while ( *q && (*q==' ' || *q=='\t') ) { q++; m++; }
+        if ( *q!='=' || !n )
+        {
+            char *x = q;
+            while ( *x && *x!='\n' ) x++;
+            *x = '\0';
+            error("Could not parse the line: %s [%s][%s]\n", line,p,q);
+        }
+        key.l = 0;
+        kputsn(p,q-p-m,&key);
+        p = ++q;
+        while ( *q && (*q==' ' || *q=='\t') ) { p++; q++; }
+        int quoted = *p=='"' ? 1 : 0;
+        if ( quoted ) p++, q++;
+        while ( *q && *q != '\n' )
+        {
+            if ( quoted ) { if ( *q=='"' && !is_escaped(p,q) ) break; }
+            else
+            {
+                if ( *q=='<' ) nopen++;
+                if ( *q=='>' ) nopen--;
+                if ( !nopen ) break;
+                if ( *q==',' && nopen==1 ) break;
+            }
+            q++;
+        }
+        char *r = q;
+        while ( r > p && r[-1] == ' ' ) r--;
+        val.l = 0;
+        kputsn(p,r-p,&val);
+        if ( quoted && *q=='"' ) q++;
+        if ( *q=='>' ) { nopen--; q++; }
+        if ( !strcmp("length",key.s) ) continue;
+        if ( !strcmp("ID",key.s) )
+        {
+            if ( khash_str2int_has_key(chr_seen,val.s) ) continue;
+            chr_len = faidx_seq_len(fai, val.s);
+            if ( chr_len==-1 )
+            {
+                free(val.s); free(key.s); free(tmp.s);
+                return end;   // the sequence is not in fai, remove
+            }
+            chr_name = strdup(val.s);
+            khash_str2int_inc(chr_seen, chr_name);
+            continue;
+        }
+        kputc(',',&tmp);
+        kputs(key.s,&tmp);
+        kputc('=',&tmp);
+        if ( quoted ) kputc('"',&tmp);
+        kputs(val.s,&tmp);
+        if ( quoted ) kputc('"',&tmp);
+    }
+    if ( !chr_name ) return end;
+    ksprintf(dst,"##contig=<ID=%s,length=%d%s>",chr_name,chr_len,tmp.l ? tmp.s : "");
+    free(key.s); free(val.s); free(tmp.s);
+    return q;
+}
+char *init_tmp_prefix(const char *tmp_prefix)
+{
+    kstring_t prefix = {0,0,0};
+    if ( tmp_prefix )
+    {
+        ksprintf(&prefix,"%sXXXXXX",tmp_prefix);
+        return prefix.s;
+    }
+
+    char *tmpdir = getenv("TMPDIR");
+    if ( tmpdir )
+        kputs(tmpdir, &prefix);
+    else
+    {
+        #ifdef _WIN32
+            char tmp_path[MAX_PATH];
+            int ret = GetTempPath(MAX_PATH, tmp_path);
+            if (!ret || ret > MAX_PATH)
+                error("Could not get the path to the temporary folder\n");
+            kputs(tmp_path, &prefix);
+        #else
+            kputs("/tmp", &prefix);
+        #endif
+    }
+    kputs("/bcftools.XXXXXX", &prefix);
+    return prefix.s;
+}
+static void update_from_fai(args_t *args)
+{
+    if ( !strcmp("-",args->fname) )
+        error("Cannot use the --fai option when reading from standard input.\n");
+
+    faidx_t *fai = fai_load3(args->fai_fname,args->fai_fname,NULL,FAI_FASTA);
+    if ( !fai ) error("Could not parse %s\n", args->fai_fname);
+    args->rm_tmpfile = init_tmp_prefix(args->tmp_prefix);
+    int fd = mkstemp(args->rm_tmpfile);
+    if ( fd<0 ) error("Could not open a temporary file for writing: %s\n", args->rm_tmpfile);
+
+    // get a template header: either from the original VCF or from --header
+    char *ori_hdr_fname = args->header_fname ? args->header_fname : args->fname;
+    htsFile *fp = hts_open(ori_hdr_fname,"r");
+    if ( !fp ) error("Failed to open: %s\n", ori_hdr_fname);
+    bcf_hdr_t *hdr = bcf_hdr_read(fp);
+    if ( !hdr ) error("Failed to read the header: %s\n", ori_hdr_fname);
+    hts_close(fp);  // no need to check the return status here
+
+    // put the header in a text buffer
+    kstring_t hdr_txt_ori = {0,0,0}, hdr_txt_new = {0,0,0};
+    bcf_hdr_format(hdr, 0, &hdr_txt_ori);
+    bcf_hdr_destroy(hdr);
+
+    // update the existing contig lines and remove lines not present in the fai file
+    void *chr_seen = khash_str2int_init();
+    char *tmp, *beg = hdr_txt_ori.s;
+    while ( beg && *beg )
+    {
+        tmp = strstr(beg, "\n##contig=<");
+        if ( !tmp ) break;
+        kputsn(beg, tmp-beg+1, &hdr_txt_new);
+        size_t l_prev = hdr_txt_new.l;
+        beg = copy_and_update_contig_line(fai,tmp+1,chr_seen, &hdr_txt_new);
+        if ( l_prev==hdr_txt_new.l ) hdr_txt_new.l--;   // nothing was added, remove the newline
+    }
+    if ( !beg || !(tmp=strstr(beg,"\n#CHROM")) ) error("Failed to parse the header, #CHROM not found\n");
+    kputsn(beg, tmp-beg+1, &hdr_txt_new);
+
+    // add any new contig lines
+    int i, n = faidx_nseq(fai);
+    for (i=0; i<n; i++)
+    {
+        if ( khash_str2int_has_key(chr_seen,faidx_iseq(fai,i)) ) continue;
+        ksprintf(&hdr_txt_new,"##contig=<ID=%s,length=%d>\n",faidx_iseq(fai,i),faidx_seq_len(fai,faidx_iseq(fai,i)));
+    }
+    kputs(tmp+1,&hdr_txt_new);
+
+    if ( write(fd, hdr_txt_new.s, hdr_txt_new.l)!=hdr_txt_new.l ) error("Failed to write %zu bytes to %s\n", hdr_txt_new.l,args->rm_tmpfile);
+    if ( close(fd)!=0 ) error("Failed to close %s\n", args->rm_tmpfile);
+    args->header_fname = args->rm_tmpfile;
+
+    free(hdr_txt_ori.s);
+    free(hdr_txt_new.s);
+    fai_destroy(fai);
+    khash_str2int_destroy_free(chr_seen);
+}
+
+static void read_header_file(char *fname, kstring_t *hdr)
+{
+    kstring_t tmp = {0,0,0};
+    hdr->l = 0;
+
+    htsFile *fp = hts_open(fname, "r");
+    if ( !fp ) error("Could not read: %s\n", fname);
+    while ( hts_getline(fp, KS_SEP_LINE, &tmp) > 0 )
+    {
+        kputsn(tmp.s,tmp.l,hdr);
+        kputc('\n',hdr);
+    }
+    if ( hts_close(fp) ) error("Close failed: %s\n", fname);
+    free(tmp.s);
+
+    while ( hdr->l>0 && isspace(hdr->s[hdr->l-1]) ) hdr->l--;  // remove trailing newlines
+    kputc('\n',hdr);
+}
+
+static int set_sample_pairs(char **samples, int nsamples, kstring_t *hdr, int idx)
+{
+    int i, j, n;
+    kstring_t key = {0,0,0};
+    kstring_t val = {0,0,0};
+
+    // Are these samples "old-name new-name" pairs?
+    void *hash = khash_str2str_init();
+    for (i=0; i<nsamples; i++)
+    {
+        char *ptr = samples[i];
+        key.l = val.l = 0;
+        int escaped = 0;
+        while ( *ptr )
+        {
+            if ( *ptr=='\\' && !escaped ) { escaped = 1; ptr++; continue; }
+            if ( isspace(*ptr) && !escaped ) break;
+            kputc(*ptr, &key);
+            escaped = 0;
+            ptr++;
+        }
+        if ( !*ptr ) break;
+        while ( *ptr && isspace(*ptr) ) ptr++;
+        while ( *ptr )
+        {
+            if ( *ptr=='\\' && !escaped ) { escaped = 1; ptr++; continue; }
+            if ( isspace(*ptr) && !escaped ) break;
+            kputc(*ptr, &val);
+            escaped = 0;
+            ptr++;
+        }
+        khash_str2str_set(hash,strdup(key.s),strdup(val.s));
+    }
+    free(key.s);
+    free(val.s);
+    if ( i!=nsamples )  // not "old-name new-name" pairs
+    {
+        khash_str2str_destroy_free_all(hash);
+        return 0;
+    }
+
+    while ( hdr->l>0 && isspace(hdr->s[hdr->l-1]) ) hdr->l--;  // remove trailing newlines
+    hdr->s[hdr->l] = 0;
+
+    kstring_t tmp = {0,0,0};
+    i = j = n = 0;  // i:traverse the #CHROM line 1 by 1; j:points to the last column
+    while ( hdr->s[idx+i] )
+    {
+        if ( hdr->s[idx+i]=='\t' )
+        {
+            hdr->s[idx+i] = 0;
+
+            if ( ++n>9 )
+            {
+                char *new_name = khash_str2str_get(hash,hdr->s+idx+j);
+                kputs(new_name ? new_name : hdr->s+idx+j, &tmp);
+            }
+            else
+                kputs(hdr->s+idx+j, &tmp);
+
+            kputc('\t',&tmp);
+
+            j = ++i;
+            continue;
+        }
+        i++;
+    }
+    char *new_name = khash_str2str_get(hash,hdr->s+idx+j);
+    kputs(new_name ? new_name : hdr->s+idx+j, &tmp);
+
+    khash_str2str_destroy_free_all(hash);
+
+    hdr->l = idx;
+    kputs(tmp.s, hdr);
+    kputc('\n', hdr);
+    free(tmp.s);
+
+    return 1;
+}
+
+static void set_samples(char **samples, int nsamples, kstring_t *hdr)
+{
+    // Find the beginning of the #CHROM line
+    int i = hdr->l - 2, ncols = 0;
+    while ( i>=0 && hdr->s[i]!='\n' )
+    {
+        if ( hdr->s[i]=='\t' ) ncols++;
+        i--;
+    }
+    if ( i<0 || strncmp(hdr->s+i+1,"#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT",45) )
+    {
+        if ( i>0 && !strncmp(hdr->s+i+1,"#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO",38) )
+            error("Error: missing FORMAT fields, cowardly refusing to add samples\n");
+
+        error("Could not parse the header: %s\n", hdr->s);
+    }
+
+    // Are the samples "old-sample new-sample" pairs?
+    if ( set_sample_pairs(samples,nsamples,hdr, i+1) ) return;
+
+    // Replace all samples
+    if ( ncols!=nsamples+8 )
+        fprintf(stderr, "Warning: different number of samples: %d vs %d\n", nsamples,ncols-8);
+
+    ncols = 0;
+    while ( ncols!=9 )
+    {
+        i++;
+        if ( hdr->s[i]=='\t' ) ncols++;
+    }
+    hdr->l = i;
+
+    for (i=0; i<nsamples; i++)
+    {
+        kputc('\t', hdr);
+        kputs(samples[i], hdr);
+    }
+    kputc('\n', hdr);
+}
+
+BGZF *hts_get_bgzfp(htsFile *fp);
+static void reheader_vcf_gz(args_t *args)
+{
+    BGZF *fp = hts_get_bgzfp(args->fp);
+    if ( !fp || bgzf_read_block(fp) != 0 || !fp->block_length )
+        error("Failed to read %s: %s\n", args->fname, strerror(errno));
+
+    kstring_t hdr = {0,0,0};
+    char *buffer = (char*) fp->uncompressed_block;
+
+    // Read the header and find the position of the data block
+    if ( buffer[0]!='#' ) error("Could not parse the header, expected '#', found '%c'\n", buffer[0]);
+
+    int skip_until = 1;     // end of the header in the current uncompressed block
+    while (1)
+    {
+        if ( buffer[skip_until]=='\n' )
+        {
+            skip_until++;
+            if ( skip_until>=fp->block_length )
+            {
+                kputsn(buffer,skip_until,&hdr);
+                if ( bgzf_read_block(fp) != 0 ) error("Error reading %s\n", args->fname);
+                if ( !fp->block_length ) break;
+                skip_until = 0;
+            }
+            // The header has finished
+            if ( buffer[skip_until]!='#' )
+            {
+                kputsn(buffer,skip_until,&hdr);
+                break;
+            }
+        }
+        skip_until++;
+        if ( skip_until>=fp->block_length )
+        {
+            kputsn(buffer,fp->block_length,&hdr);
+            if ( bgzf_read_block(fp) != 0 ) error("Error reading %s\n", args->fname);
+            if ( !fp->block_length ) break;
+            skip_until = 0;
+        }
+    }
+
+    int nsamples = 0;
+    char **samples = NULL;
+    if ( args->samples_fname )
+    {
+        samples = hts_readlines(args->samples_fname, &nsamples);
+        if ( !samples || !nsamples ) error("Error reading the --samples file \"%s\"\n", args->samples_fname);
+    }
+    if ( args->header_fname )
+    {
+        free(hdr.s); hdr.s = NULL; hdr.l = hdr.m = 0;
+        read_header_file(args->header_fname, &hdr);
+    }
+    if ( samples )
+    {
+        set_samples(samples, nsamples, &hdr);
+        int i;
+        for (i=0; i<nsamples; i++) free(samples[i]);
+        free(samples);
+    }
+
+    // Output the modified header
+    BGZF *bgzf_out = bgzf_open(args->output_fname ? args->output_fname : "-","w");;
+    if ( bgzf_write(bgzf_out, hdr.s, hdr.l) < 0 ) error("Can't write BGZF header (code %d)\n", bgzf_out->errcode);
+    free(hdr.s);
+
+    // Output all remainig data read with the header block
+    if ( fp->block_length - skip_until > 0 )
+    {
+        if ( bgzf_write(bgzf_out, buffer+skip_until, fp->block_length-skip_until)<0 ) error("Error: %d\n",fp->errcode);
+    }
+    if ( bgzf_flush(bgzf_out)<0 ) error("Error: %d\n",bgzf_out->errcode);
+
+    // Stream the rest of the file without as it is, without decompressing
+    ssize_t nread;
+    const size_t page_size = 32768;
+    char *buf = (char*) malloc(page_size);
+    while (1)
+    {
+        nread = bgzf_raw_read(fp, buf, page_size);
+        if ( nread<=0 ) break;
+
+        int count = bgzf_raw_write(bgzf_out, buf, nread);
+        if (count != nread) error("Write failed, wrote %d instead of %d bytes.\n", count,(int)nread);
+    }
+    if (bgzf_close(bgzf_out) < 0) error("Error closing %s: %d\n",args->output_fname ? args->output_fname : "-",bgzf_out->errcode);
+    if (hts_close(args->fp)) error("Error closing %s: %d\n",args->fname,fp->errcode);
+    free(buf);
+}
+static void reheader_vcf(args_t *args)
+{
+    kstring_t hdr = {0,0,0};
+    htsFile *fp = args->fp;
+    while ( hts_getline(fp, KS_SEP_LINE, &fp->line) >=0 )
+    {
+        kputc('\n',&fp->line);  // hts_getline eats the newline character
+        if ( fp->line.s[0]!='#' ) break;
+        kputsn(fp->line.s,fp->line.l,&hdr);
+    }
+
+    int nsamples = 0;
+    char **samples = NULL;
+    if ( args->samples_fname )
+    {
+        samples = hts_readlines(args->samples_fname, &nsamples);
+        if ( !samples || !nsamples ) error("Error reading the --samples file \"%s\"\n", args->samples_fname);
+    }
+    if ( args->header_fname )
+    {
+        free(hdr.s); hdr.s = NULL; hdr.l = hdr.m = 0;
+        read_header_file(args->header_fname, &hdr);
+    }
+    if ( samples )
+    {
+        set_samples(samples, nsamples, &hdr);
+        int i;
+        for (i=0; i<nsamples; i++) free(samples[i]);
+        free(samples);
+    }
+
+    int out = args->output_fname ? open(args->output_fname, O_WRONLY|O_CREAT|O_TRUNC, 0666) : STDOUT_FILENO;
+    if ( out==-1 ) error("%s: %s\n", args->output_fname,strerror(errno));
+    if ( write(out, hdr.s, hdr.l)!=hdr.l ) error("Failed to write %"PRIu64" bytes\n", (uint64_t)hdr.l);
+    free(hdr.s);
+    if ( fp->line.l )
+    {
+        if ( write(out, fp->line.s, fp->line.l)!=fp->line.l ) error("Failed to write %"PRIu64" bytes\n", (uint64_t)fp->line.l);
+    }
+    while ( hts_getline(fp, KS_SEP_LINE, &fp->line) >=0 )   // uncompressed file implies small size, we don't worry about speed
+    {
+        kputc('\n',&fp->line);
+        if ( write(out, fp->line.s, fp->line.l)!=fp->line.l ) error("Failed to write %"PRIu64" bytes\n", (uint64_t)fp->line.l);
+    }
+    if ( hts_close(fp)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,args->fname);
+    if ( close(out)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,args->output_fname);
+}
+
+static bcf_hdr_t *strip_header(bcf_hdr_t *src, bcf_hdr_t *dst)
+{
+    bcf_hrec_t *src_hrec, *dst_hrec, *tmp;
+    bcf_hdr_t *out = bcf_hdr_init("r");
+    int i;
+    for (i=0; i<dst->nhrec; i++)
+    {
+        // first insert lines which do not code BCF ids, their order does not matter
+        dst_hrec = dst->hrec[i];
+        if ( dst_hrec->type==BCF_HL_FLT || dst_hrec->type==BCF_HL_INFO || dst_hrec->type==BCF_HL_FMT || dst_hrec->type== BCF_HL_CTG ) continue;
+        bcf_hdr_add_hrec(out, bcf_hrec_dup(dst_hrec));
+    }
+    for (i=0; i<src->nhrec; i++)
+    {
+        // now transfer header lines which define BCF ids
+        src_hrec = src->hrec[i];
+
+        if ( src_hrec->type==BCF_HL_FLT || src_hrec->type==BCF_HL_INFO || src_hrec->type==BCF_HL_FMT || src_hrec->type== BCF_HL_CTG )
+        {
+            int j = bcf_hrec_find_key(src_hrec, "ID");
+            dst_hrec = bcf_hdr_get_hrec(dst, src_hrec->type, "ID", src_hrec->vals[j], NULL);
+            if ( !dst_hrec ) continue;
+
+            tmp = bcf_hrec_dup(dst_hrec);
+
+            j = bcf_hrec_find_key(src_hrec, "IDX");
+            if ( j>=0 )
+            {
+                j = atoi(src_hrec->vals[j]);
+                if (hrec_add_idx(tmp, j) < 0)
+                    error_errno("[%s] Failed to add IDX header", __func__);
+            }
+            bcf_hdr_add_hrec(out, tmp);
+        }
+    }
+    if (bcf_hdr_sync(out) < 0)
+        error_errno("[%s] Failed to update header", __func__);
+    for (i=0; i<dst->nhrec; i++)
+    {
+        // finally add new structured fields
+        dst_hrec = dst->hrec[i];
+        if ( dst_hrec->type==BCF_HL_FLT || dst_hrec->type==BCF_HL_INFO || dst_hrec->type==BCF_HL_FMT || dst_hrec->type== BCF_HL_CTG )
+        {
+            int j = bcf_hrec_find_key(dst_hrec, "ID");
+            tmp = bcf_hdr_get_hrec(out, dst_hrec->type, "ID", dst_hrec->vals[j], NULL);
+            if ( !tmp )
+                bcf_hdr_add_hrec(out, bcf_hrec_dup(dst_hrec));
+        }
+    }
+    for (i=0; i<dst->n[BCF_DT_SAMPLE]; i++) bcf_hdr_add_sample(out, dst->samples[i]);
+    bcf_hdr_destroy(dst);
+    return out;
+}
+
+static void reheader_bcf(args_t *args, int is_compressed)
+{
+    htsFile *fp = args->fp;
+
+    if ( args->n_threads > 0 )
+    {
+        args->threads = (htsThreadPool *) calloc(1, sizeof(htsThreadPool));
+        if ( !args->threads ) error("Could not allocate memory\n");
+        if ( !(args->threads->pool = hts_tpool_init(args->n_threads)) ) error("Could not initialize threading\n");
+        hts_set_thread_pool(fp, args->threads);
+    }
+
+    bcf_hdr_t *hdr = bcf_hdr_read(fp); if ( !hdr ) error("Failed to read the header: %s\n", args->fname);
+    kstring_t htxt = {0,0,0};
+    bcf_hdr_format(hdr, 1, &htxt);
+
+    int i, nsamples = 0;
+    char **samples = NULL;
+    if ( args->samples_fname )
+    {
+        samples = hts_readlines(args->samples_fname, &nsamples);
+        if ( !samples || !nsamples ) error("Error reading the --samples file \"%s\"\n", args->samples_fname);
+    }
+    if ( args->header_fname )
+    {
+        free(htxt.s); htxt.s = NULL; htxt.l = htxt.m = 0;
+        read_header_file(args->header_fname, &htxt);
+    }
+    if ( samples )
+    {
+        set_samples(samples, nsamples, &htxt);
+        for (i=0; i<nsamples; i++) free(samples[i]);
+        free(samples);
+    }
+
+    bcf_hdr_t *hdr_out = bcf_hdr_init("r");
+    if ( bcf_hdr_parse(hdr_out, htxt.s) < 0 ) error("An error occurred while parsing the header\n");
+    if ( args->header_fname ) hdr_out = strip_header(hdr, hdr_out);
+
+    // write the header and the body
+    htsFile *fp_out = hts_open(args->output_fname ? args->output_fname : "-",is_compressed ? "wb" : "wbu");
+    if ( !fp_out ) error("%s: %s\n", args->output_fname ? args->output_fname : "-", strerror(errno));
+    if ( args->threads )
+        hts_set_thread_pool(fp_out, args->threads);
+    if ( bcf_hdr_write(fp_out, hdr_out)!=0 ) error("[%s] Error: cannot write the header to %s\n", __func__,args->output_fname ? args->output_fname : "standard output");
+
+    bcf1_t *rec = bcf_init();
+    while ( bcf_read(fp, hdr, rec)==0 )
+    {
+        // sanity checking, this slows things down. Make it optional?
+        bcf_unpack(rec, BCF_UN_ALL);
+        if ( rec->rid >= hdr_out->n[BCF_DT_CTG] || strcmp(bcf_hdr_int2id(hdr,BCF_DT_CTG,rec->rid),bcf_hdr_int2id(hdr_out,BCF_DT_CTG,rec->rid)) )
+            error("The CHROM is not defined: \"%s\"\n", bcf_hdr_int2id(hdr,BCF_DT_CTG,rec->rid));
+
+        for (i=0; i<rec->d.n_flt; i++)
+        {
+            int id = rec->d.flt[i];
+            if ( id >= hdr_out->n[BCF_DT_ID] ) break;
+            if ( !bcf_hdr_idinfo_exists(hdr_out,BCF_HL_FLT,id) ) break;
+            if ( strcmp(hdr->id[BCF_DT_ID][id].key,hdr_out->id[BCF_DT_ID][id].key) )
+                error("FIXME: Broken FILTER ids: %s vs %s\n", hdr->id[BCF_DT_ID][id].key,hdr_out->id[BCF_DT_ID][id].key);
+        }
+        if ( i!=rec->d.n_flt )
+            error("The FILTER is not defined: \"%s\"\n", bcf_hdr_int2id(hdr,BCF_DT_ID,rec->d.flt[i]));
+
+        for (i=0; i<rec->n_info; i++)
+        {
+            int id = rec->d.info[i].key;
+            if ( id >= hdr_out->n[BCF_DT_ID] ) break;
+            if ( !hdr_out->id[BCF_DT_ID][id].key ) break;
+            if ( !bcf_hdr_idinfo_exists(hdr_out,BCF_HL_INFO,id) ) break;
+            if ( strcmp(hdr->id[BCF_DT_ID][id].key,hdr_out->id[BCF_DT_ID][id].key) )
+                error("FIXME: Broken INFO ids: %s vs %s\n", hdr->id[BCF_DT_ID][id].key,hdr_out->id[BCF_DT_ID][id].key);
+        }
+        if ( i!=rec->n_info )
+            error("The INFO tag is not defined: \"%s\"\n", bcf_hdr_int2id(hdr,BCF_DT_ID,rec->d.info[i].key));
+
+        for (i=0; i<rec->n_fmt; i++)
+        {
+            int id = rec->d.fmt[i].id;
+            if ( id >= hdr_out->n[BCF_DT_ID] ) break;
+            if ( !hdr_out->id[BCF_DT_ID][id].key ) break;
+            if ( !bcf_hdr_idinfo_exists(hdr_out,BCF_HL_FMT,id) ) break;
+            if ( strcmp(hdr->id[BCF_DT_ID][id].key,hdr_out->id[BCF_DT_ID][id].key) )
+                error("FIXME: Broken FORMAT ids: %s vs %s\n", hdr->id[BCF_DT_ID][id].key,hdr_out->id[BCF_DT_ID][id].key);
+        }
+        if ( i!=rec->n_fmt )
+            error("The FORMAT tag is not defined: \"%s\"\n", bcf_hdr_int2id(hdr,BCF_DT_ID,rec->d.fmt[i].id));
+
+        if ( bcf_write(fp_out,hdr_out,rec)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->output_fname ? args->output_fname : "standard output");
+    }
+    bcf_destroy(rec);
+
+    free(htxt.s);
+    if ( hts_close(fp_out)!=0 ) error("[%s] Error: failed to close the file %s\n",__func__,args->output_fname ? args->output_fname : "standard output");
+    if ( hts_close(fp)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,args->fname);
+    bcf_hdr_destroy(hdr_out);
+    bcf_hdr_destroy(hdr);
+    if ( args->threads )
+    {
+        hts_tpool_destroy(args->threads->pool);
+        free(args->threads);
+    }
+}
+
+
+static void usage(args_t *args)
+{
+    fprintf(stderr, "\n");
+    fprintf(stderr, "About:   Modify header of VCF/BCF files, change sample names.\n");
+    fprintf(stderr, "Usage:   bcftools reheader [OPTIONS] <in.vcf.gz>\n");
+    fprintf(stderr, "\n");
+    fprintf(stderr, "Options:\n");
+    fprintf(stderr, "    -f, --fai FILE             update sequences and their lengths from the .fai file\n");
+    fprintf(stderr, "    -h, --header FILE          new header\n");
+    fprintf(stderr, "    -o, --output FILE          write output to a file [standard output]\n");
+    fprintf(stderr, "    -s, --samples FILE         new sample names\n");
+#ifdef _WIN32
+    fprintf(stderr, "    -T, --temp-prefix PATH     template for temporary file name [/bcftools.XXXXXX]\n");
+#else
+    fprintf(stderr, "    -T, --temp-prefix PATH     template for temporary file name [/tmp/bcftools.XXXXXX]\n");
+#endif
+    fprintf(stderr, "        --threads INT          use multithreading with <int> worker threads (BCF only) [0]\n");
+    fprintf(stderr, "\n");
+    fprintf(stderr, "Example:\n");
+    fprintf(stderr, "   # Write out the header to be modified\n");
+    fprintf(stderr, "   bcftools view -h old.bcf > header.txt\n");
+    fprintf(stderr, "\n");
+    fprintf(stderr, "   # Edit the header using your favorite text editor\n");
+    fprintf(stderr, "   vi header.txt\n");
+    fprintf(stderr, "\n");
+    fprintf(stderr, "   # Reheader the file\n");
+    fprintf(stderr, "   bcftools reheader -h header.txt -o new.bcf old.bcf\n");
+    fprintf(stderr, "\n");
+    exit(1);
+}
+
+int main_reheader(int argc, char *argv[])
+{
+    int c;
+    args_t *args  = (args_t*) calloc(1,sizeof(args_t));
+    args->argc    = argc; args->argv = argv;
+    
+    static struct option loptions[] =
+    {
+        {"temp-prefix",1,0,'T'},
+        {"fai",1,0,'f'},
+        {"output",1,0,'o'},
+        {"header",1,0,'h'},
+        {"samples",1,0,'s'},
+        {"threads",1,NULL,1},
+        {0,0,0,0}
+    };
+    while ((c = getopt_long(argc, argv, "s:h:o:f:T:",loptions,NULL)) >= 0)
+    {
+        switch (c)
+        {
+            case  1 : args->n_threads = strtol(optarg, 0, 0); break;
+            case 'T': args->tmp_prefix = optarg; break;
+            case 'f': args->fai_fname = optarg; break;
+            case 'o': args->output_fname = optarg; break;
+            case 's': args->samples_fname = optarg; break;
+            case 'h': args->header_fname = optarg; break;
+            case '?': usage(args); break;
+            default: error("Unknown argument: %s\n", optarg);
+        }
+    }
+
+    if ( optind>=argc )
+    {
+        if ( !isatty(fileno((FILE *)stdin)) ) args->fname = "-";  // reading from stdin
+        else usage(args);
+    }
+    else args->fname = argv[optind];
+
+    if ( args->fai_fname ) update_from_fai(args);
+    if ( !args->samples_fname && !args->header_fname ) usage(args);
+    if ( !args->fname ) usage(args);
+
+    args->fp = hts_open(args->fname,"r");
+    if ( !args->fp ) error("Failed to read from %s\n", !strcmp("-",args->fname)?"standard input":args->fname);
+    args->type = *hts_get_format(args->fp);
+
+    if ( args->type.format==vcf )
+    {
+        if ( args->type.compression==bgzf )
+            reheader_vcf_gz(args);
+        else if ( args->type.compression==no_compression )
+            reheader_vcf(args);
+        else if ( args->type.compression==gzip )
+            error("Error: cannot reheader gzip-compressed files, first convert with `bcftools view --output-type` to a supported format\n");
+        else
+            error("Error: the compression type of \"%s\" is not recognised/supported\n", args->fname);
+    }
+    else
+        reheader_bcf(args, args->type.compression==bgzf || args->type.compression==gzip);
+
+    if ( args->rm_tmpfile )
+    {
+        unlink(args->rm_tmpfile);
+        free(args->rm_tmpfile);
+    }
+    free(args);
+    return 0;
+}
diff --git a/bcftools/reheader.c.pysam.c b/bcftools/reheader.c.pysam.c
new file mode 100644
index 0000000..a069870
--- /dev/null
+++ b/bcftools/reheader.c.pysam.c
@@ -0,0 +1,766 @@
+#include "bcftools.pysam.h"
+
+/*  reheader.c -- reheader subcommand.
+
+    Copyright (C) 2014-2022 Genome Research Ltd.
+
+    Author: Petr Danecek <pd3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.  */
+
+#include <stdio.h>
+#include <unistd.h>
+#include <getopt.h>
+#include <ctype.h>
+#include <string.h>
+#include <errno.h>
+#include <sys/stat.h>
+#include <sys/types.h>
+#include <inttypes.h>
+#include <fcntl.h>
+#include <math.h>
+#ifdef _WIN32
+#include <windows.h>
+#endif
+#include <htslib/vcf.h>
+#include <htslib/bgzf.h>
+#include <htslib/tbx.h> // for hts_get_bgzfp()
+#include <htslib/kseq.h>
+#include <htslib/thread_pool.h>
+#include <htslib/faidx.h>
+#include <htslib/khash_str2int.h>
+#include "bcftools.h"
+#include "khash_str2str.h"
+
+typedef struct _args_t
+{
+    char **argv, *fname, *samples_fname, *header_fname, *output_fname;
+    char *fai_fname, *rm_tmpfile, *tmp_prefix;
+    htsFile *fp;
+    htsFormat type;
+    htsThreadPool *threads;
+    int argc, n_threads;
+}
+args_t;
+
+static inline int is_escaped(const char *min, const char *str)
+{
+    int n = 0;
+    while ( --str>=min && *str=='\\' ) n++;
+    return n%2;
+}
+static char *copy_and_update_contig_line(faidx_t *fai, char *line, void *chr_seen, kstring_t *dst)
+{
+    kstring_t key = {0,0,0}, val = {0,0,0}, tmp = {0,0,0};
+    char *chr_name = NULL, *p, *q = line + 9;   // skip ##contig=
+    char *end = q;
+    int nopen = 1, chr_len = 0;
+    while ( *end && *end!='\n' ) end++;
+    while ( *q && *q!='\n' && nopen>0 )
+    {
+        p = ++q;
+        while ( *q && (*q==' ' || *q=='\t') ) { p++; q++; }
+        // ^[A-Za-z_][0-9A-Za-z_.]*$
+        if (p==q && *q && (isalpha(*q) || *q=='_'))
+        {
+            q++;
+            while ( *q && (isalnum(*q) || *q=='_' || *q=='.') ) q++;
+        }
+        int n = q-p;
+        int m = 0;
+        while ( *q && (*q==' ' || *q=='\t') ) { q++; m++; }
+        if ( *q!='=' || !n )
+        {
+            char *x = q;
+            while ( *x && *x!='\n' ) x++;
+            *x = '\0';
+            error("Could not parse the line: %s [%s][%s]\n", line,p,q);
+        }
+        key.l = 0;
+        kputsn(p,q-p-m,&key);
+        p = ++q;
+        while ( *q && (*q==' ' || *q=='\t') ) { p++; q++; }
+        int quoted = *p=='"' ? 1 : 0;
+        if ( quoted ) p++, q++;
+        while ( *q && *q != '\n' )
+        {
+            if ( quoted ) { if ( *q=='"' && !is_escaped(p,q) ) break; }
+            else
+            {
+                if ( *q=='<' ) nopen++;
+                if ( *q=='>' ) nopen--;
+                if ( !nopen ) break;
+                if ( *q==',' && nopen==1 ) break;
+            }
+            q++;
+        }
+        char *r = q;
+        while ( r > p && r[-1] == ' ' ) r--;
+        val.l = 0;
+        kputsn(p,r-p,&val);
+        if ( quoted && *q=='"' ) q++;
+        if ( *q=='>' ) { nopen--; q++; }
+        if ( !strcmp("length",key.s) ) continue;
+        if ( !strcmp("ID",key.s) )
+        {
+            if ( khash_str2int_has_key(chr_seen,val.s) ) continue;
+            chr_len = faidx_seq_len(fai, val.s);
+            if ( chr_len==-1 )
+            {
+                free(val.s); free(key.s); free(tmp.s);
+                return end;   // the sequence is not in fai, remove
+            }
+            chr_name = strdup(val.s);
+            khash_str2int_inc(chr_seen, chr_name);
+            continue;
+        }
+        kputc(',',&tmp);
+        kputs(key.s,&tmp);
+        kputc('=',&tmp);
+        if ( quoted ) kputc('"',&tmp);
+        kputs(val.s,&tmp);
+        if ( quoted ) kputc('"',&tmp);
+    }
+    if ( !chr_name ) return end;
+    ksprintf(dst,"##contig=<ID=%s,length=%d%s>",chr_name,chr_len,tmp.l ? tmp.s : "");
+    free(key.s); free(val.s); free(tmp.s);
+    return q;
+}
+char *init_tmp_prefix(const char *tmp_prefix)
+{
+    kstring_t prefix = {0,0,0};
+    if ( tmp_prefix )
+    {
+        ksprintf(&prefix,"%sXXXXXX",tmp_prefix);
+        return prefix.s;
+    }
+
+    char *tmpdir = getenv("TMPDIR");
+    if ( tmpdir )
+        kputs(tmpdir, &prefix);
+    else
+    {
+        #ifdef _WIN32
+            char tmp_path[MAX_PATH];
+            int ret = GetTempPath(MAX_PATH, tmp_path);
+            if (!ret || ret > MAX_PATH)
+                error("Could not get the path to the temporary folder\n");
+            kputs(tmp_path, &prefix);
+        #else
+            kputs("/tmp", &prefix);
+        #endif
+    }
+    kputs("/bcftools.XXXXXX", &prefix);
+    return prefix.s;
+}
+static void update_from_fai(args_t *args)
+{
+    if ( !strcmp("-",args->fname) )
+        error("Cannot use the --fai option when reading from standard input.\n");
+
+    faidx_t *fai = fai_load3(args->fai_fname,args->fai_fname,NULL,FAI_FASTA);
+    if ( !fai ) error("Could not parse %s\n", args->fai_fname);
+    args->rm_tmpfile = init_tmp_prefix(args->tmp_prefix);
+    int fd = mkstemp(args->rm_tmpfile);
+    if ( fd<0 ) error("Could not open a temporary file for writing: %s\n", args->rm_tmpfile);
+
+    // get a template header: either from the original VCF or from --header
+    char *ori_hdr_fname = args->header_fname ? args->header_fname : args->fname;
+    htsFile *fp = hts_open(ori_hdr_fname,"r");
+    if ( !fp ) error("Failed to open: %s\n", ori_hdr_fname);
+    bcf_hdr_t *hdr = bcf_hdr_read(fp);
+    if ( !hdr ) error("Failed to read the header: %s\n", ori_hdr_fname);
+    hts_close(fp);  // no need to check the return status here
+
+    // put the header in a text buffer
+    kstring_t hdr_txt_ori = {0,0,0}, hdr_txt_new = {0,0,0};
+    bcf_hdr_format(hdr, 0, &hdr_txt_ori);
+    bcf_hdr_destroy(hdr);
+
+    // update the existing contig lines and remove lines not present in the fai file
+    void *chr_seen = khash_str2int_init();
+    char *tmp, *beg = hdr_txt_ori.s;
+    while ( beg && *beg )
+    {
+        tmp = strstr(beg, "\n##contig=<");
+        if ( !tmp ) break;
+        kputsn(beg, tmp-beg+1, &hdr_txt_new);
+        size_t l_prev = hdr_txt_new.l;
+        beg = copy_and_update_contig_line(fai,tmp+1,chr_seen, &hdr_txt_new);
+        if ( l_prev==hdr_txt_new.l ) hdr_txt_new.l--;   // nothing was added, remove the newline
+    }
+    if ( !beg || !(tmp=strstr(beg,"\n#CHROM")) ) error("Failed to parse the header, #CHROM not found\n");
+    kputsn(beg, tmp-beg+1, &hdr_txt_new);
+
+    // add any new contig lines
+    int i, n = faidx_nseq(fai);
+    for (i=0; i<n; i++)
+    {
+        if ( khash_str2int_has_key(chr_seen,faidx_iseq(fai,i)) ) continue;
+        ksprintf(&hdr_txt_new,"##contig=<ID=%s,length=%d>\n",faidx_iseq(fai,i),faidx_seq_len(fai,faidx_iseq(fai,i)));
+    }
+    kputs(tmp+1,&hdr_txt_new);
+
+    if ( write(fd, hdr_txt_new.s, hdr_txt_new.l)!=hdr_txt_new.l ) error("Failed to write %zu bytes to %s\n", hdr_txt_new.l,args->rm_tmpfile);
+    if ( close(fd)!=0 ) error("Failed to close %s\n", args->rm_tmpfile);
+    args->header_fname = args->rm_tmpfile;
+
+    free(hdr_txt_ori.s);
+    free(hdr_txt_new.s);
+    fai_destroy(fai);
+    khash_str2int_destroy_free(chr_seen);
+}
+
+static void read_header_file(char *fname, kstring_t *hdr)
+{
+    kstring_t tmp = {0,0,0};
+    hdr->l = 0;
+
+    htsFile *fp = hts_open(fname, "r");
+    if ( !fp ) error("Could not read: %s\n", fname);
+    while ( hts_getline(fp, KS_SEP_LINE, &tmp) > 0 )
+    {
+        kputsn(tmp.s,tmp.l,hdr);
+        kputc('\n',hdr);
+    }
+    if ( hts_close(fp) ) error("Close failed: %s\n", fname);
+    free(tmp.s);
+
+    while ( hdr->l>0 && isspace(hdr->s[hdr->l-1]) ) hdr->l--;  // remove trailing newlines
+    kputc('\n',hdr);
+}
+
+static int set_sample_pairs(char **samples, int nsamples, kstring_t *hdr, int idx)
+{
+    int i, j, n;
+    kstring_t key = {0,0,0};
+    kstring_t val = {0,0,0};
+
+    // Are these samples "old-name new-name" pairs?
+    void *hash = khash_str2str_init();
+    for (i=0; i<nsamples; i++)
+    {
+        char *ptr = samples[i];
+        key.l = val.l = 0;
+        int escaped = 0;
+        while ( *ptr )
+        {
+            if ( *ptr=='\\' && !escaped ) { escaped = 1; ptr++; continue; }
+            if ( isspace(*ptr) && !escaped ) break;
+            kputc(*ptr, &key);
+            escaped = 0;
+            ptr++;
+        }
+        if ( !*ptr ) break;
+        while ( *ptr && isspace(*ptr) ) ptr++;
+        while ( *ptr )
+        {
+            if ( *ptr=='\\' && !escaped ) { escaped = 1; ptr++; continue; }
+            if ( isspace(*ptr) && !escaped ) break;
+            kputc(*ptr, &val);
+            escaped = 0;
+            ptr++;
+        }
+        khash_str2str_set(hash,strdup(key.s),strdup(val.s));
+    }
+    free(key.s);
+    free(val.s);
+    if ( i!=nsamples )  // not "old-name new-name" pairs
+    {
+        khash_str2str_destroy_free_all(hash);
+        return 0;
+    }
+
+    while ( hdr->l>0 && isspace(hdr->s[hdr->l-1]) ) hdr->l--;  // remove trailing newlines
+    hdr->s[hdr->l] = 0;
+
+    kstring_t tmp = {0,0,0};
+    i = j = n = 0;  // i:traverse the #CHROM line 1 by 1; j:points to the last column
+    while ( hdr->s[idx+i] )
+    {
+        if ( hdr->s[idx+i]=='\t' )
+        {
+            hdr->s[idx+i] = 0;
+
+            if ( ++n>9 )
+            {
+                char *new_name = khash_str2str_get(hash,hdr->s+idx+j);
+                kputs(new_name ? new_name : hdr->s+idx+j, &tmp);
+            }
+            else
+                kputs(hdr->s+idx+j, &tmp);
+
+            kputc('\t',&tmp);
+
+            j = ++i;
+            continue;
+        }
+        i++;
+    }
+    char *new_name = khash_str2str_get(hash,hdr->s+idx+j);
+    kputs(new_name ? new_name : hdr->s+idx+j, &tmp);
+
+    khash_str2str_destroy_free_all(hash);
+
+    hdr->l = idx;
+    kputs(tmp.s, hdr);
+    kputc('\n', hdr);
+    free(tmp.s);
+
+    return 1;
+}
+
+static void set_samples(char **samples, int nsamples, kstring_t *hdr)
+{
+    // Find the beginning of the #CHROM line
+    int i = hdr->l - 2, ncols = 0;
+    while ( i>=0 && hdr->s[i]!='\n' )
+    {
+        if ( hdr->s[i]=='\t' ) ncols++;
+        i--;
+    }
+    if ( i<0 || strncmp(hdr->s+i+1,"#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT",45) )
+    {
+        if ( i>0 && !strncmp(hdr->s+i+1,"#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO",38) )
+            error("Error: missing FORMAT fields, cowardly refusing to add samples\n");
+
+        error("Could not parse the header: %s\n", hdr->s);
+    }
+
+    // Are the samples "old-sample new-sample" pairs?
+    if ( set_sample_pairs(samples,nsamples,hdr, i+1) ) return;
+
+    // Replace all samples
+    if ( ncols!=nsamples+8 )
+        fprintf(bcftools_stderr, "Warning: different number of samples: %d vs %d\n", nsamples,ncols-8);
+
+    ncols = 0;
+    while ( ncols!=9 )
+    {
+        i++;
+        if ( hdr->s[i]=='\t' ) ncols++;
+    }
+    hdr->l = i;
+
+    for (i=0; i<nsamples; i++)
+    {
+        kputc('\t', hdr);
+        kputs(samples[i], hdr);
+    }
+    kputc('\n', hdr);
+}
+
+BGZF *hts_get_bgzfp(htsFile *fp);
+static void reheader_vcf_gz(args_t *args)
+{
+    BGZF *fp = hts_get_bgzfp(args->fp);
+    if ( !fp || bgzf_read_block(fp) != 0 || !fp->block_length )
+        error("Failed to read %s: %s\n", args->fname, strerror(errno));
+
+    kstring_t hdr = {0,0,0};
+    char *buffer = (char*) fp->uncompressed_block;
+
+    // Read the header and find the position of the data block
+    if ( buffer[0]!='#' ) error("Could not parse the header, expected '#', found '%c'\n", buffer[0]);
+
+    int skip_until = 1;     // end of the header in the current uncompressed block
+    while (1)
+    {
+        if ( buffer[skip_until]=='\n' )
+        {
+            skip_until++;
+            if ( skip_until>=fp->block_length )
+            {
+                kputsn(buffer,skip_until,&hdr);
+                if ( bgzf_read_block(fp) != 0 ) error("Error reading %s\n", args->fname);
+                if ( !fp->block_length ) break;
+                skip_until = 0;
+            }
+            // The header has finished
+            if ( buffer[skip_until]!='#' )
+            {
+                kputsn(buffer,skip_until,&hdr);
+                break;
+            }
+        }
+        skip_until++;
+        if ( skip_until>=fp->block_length )
+        {
+            kputsn(buffer,fp->block_length,&hdr);
+            if ( bgzf_read_block(fp) != 0 ) error("Error reading %s\n", args->fname);
+            if ( !fp->block_length ) break;
+            skip_until = 0;
+        }
+    }
+
+    int nsamples = 0;
+    char **samples = NULL;
+    if ( args->samples_fname )
+    {
+        samples = hts_readlines(args->samples_fname, &nsamples);
+        if ( !samples || !nsamples ) error("Error reading the --samples file \"%s\"\n", args->samples_fname);
+    }
+    if ( args->header_fname )
+    {
+        free(hdr.s); hdr.s = NULL; hdr.l = hdr.m = 0;
+        read_header_file(args->header_fname, &hdr);
+    }
+    if ( samples )
+    {
+        set_samples(samples, nsamples, &hdr);
+        int i;
+        for (i=0; i<nsamples; i++) free(samples[i]);
+        free(samples);
+    }
+
+    // Output the modified header
+    BGZF *bgzf_out = bgzf_open(args->output_fname ? args->output_fname : "-","w");;
+    if ( bgzf_write(bgzf_out, hdr.s, hdr.l) < 0 ) error("Can't write BGZF header (code %d)\n", bgzf_out->errcode);
+    free(hdr.s);
+
+    // Output all remainig data read with the header block
+    if ( fp->block_length - skip_until > 0 )
+    {
+        if ( bgzf_write(bgzf_out, buffer+skip_until, fp->block_length-skip_until)<0 ) error("Error: %d\n",fp->errcode);
+    }
+    if ( bgzf_flush(bgzf_out)<0 ) error("Error: %d\n",bgzf_out->errcode);
+
+    // Stream the rest of the file without as it is, without decompressing
+    ssize_t nread;
+    const size_t page_size = 32768;
+    char *buf = (char*) malloc(page_size);
+    while (1)
+    {
+        nread = bgzf_raw_read(fp, buf, page_size);
+        if ( nread<=0 ) break;
+
+        int count = bgzf_raw_write(bgzf_out, buf, nread);
+        if (count != nread) error("Write failed, wrote %d instead of %d bytes.\n", count,(int)nread);
+    }
+    if (bgzf_close(bgzf_out) < 0) error("Error closing %s: %d\n",args->output_fname ? args->output_fname : "-",bgzf_out->errcode);
+    if (hts_close(args->fp)) error("Error closing %s: %d\n",args->fname,fp->errcode);
+    free(buf);
+}
+static void reheader_vcf(args_t *args)
+{
+    kstring_t hdr = {0,0,0};
+    htsFile *fp = args->fp;
+    while ( hts_getline(fp, KS_SEP_LINE, &fp->line) >=0 )
+    {
+        kputc('\n',&fp->line);  // hts_getline eats the newline character
+        if ( fp->line.s[0]!='#' ) break;
+        kputsn(fp->line.s,fp->line.l,&hdr);
+    }
+
+    int nsamples = 0;
+    char **samples = NULL;
+    if ( args->samples_fname )
+    {
+        samples = hts_readlines(args->samples_fname, &nsamples);
+        if ( !samples || !nsamples ) error("Error reading the --samples file \"%s\"\n", args->samples_fname);
+    }
+    if ( args->header_fname )
+    {
+        free(hdr.s); hdr.s = NULL; hdr.l = hdr.m = 0;
+        read_header_file(args->header_fname, &hdr);
+    }
+    if ( samples )
+    {
+        set_samples(samples, nsamples, &hdr);
+        int i;
+        for (i=0; i<nsamples; i++) free(samples[i]);
+        free(samples);
+    }
+
+    int out = args->output_fname ? open(args->output_fname, O_WRONLY|O_CREAT|O_TRUNC, 0666) : STDOUT_FILENO;
+    if ( out==-1 ) error("%s: %s\n", args->output_fname,strerror(errno));
+    if ( write(out, hdr.s, hdr.l)!=hdr.l ) error("Failed to write %"PRIu64" bytes\n", (uint64_t)hdr.l);
+    free(hdr.s);
+    if ( fp->line.l )
+    {
+        if ( write(out, fp->line.s, fp->line.l)!=fp->line.l ) error("Failed to write %"PRIu64" bytes\n", (uint64_t)fp->line.l);
+    }
+    while ( hts_getline(fp, KS_SEP_LINE, &fp->line) >=0 )   // uncompressed file implies small size, we don't worry about speed
+    {
+        kputc('\n',&fp->line);
+        if ( write(out, fp->line.s, fp->line.l)!=fp->line.l ) error("Failed to write %"PRIu64" bytes\n", (uint64_t)fp->line.l);
+    }
+    if ( hts_close(fp)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,args->fname);
+    if ( close(out)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,args->output_fname);
+}
+
+static bcf_hdr_t *strip_header(bcf_hdr_t *src, bcf_hdr_t *dst)
+{
+    bcf_hrec_t *src_hrec, *dst_hrec, *tmp;
+    bcf_hdr_t *out = bcf_hdr_init("r");
+    int i;
+    for (i=0; i<dst->nhrec; i++)
+    {
+        // first insert lines which do not code BCF ids, their order does not matter
+        dst_hrec = dst->hrec[i];
+        if ( dst_hrec->type==BCF_HL_FLT || dst_hrec->type==BCF_HL_INFO || dst_hrec->type==BCF_HL_FMT || dst_hrec->type== BCF_HL_CTG ) continue;
+        bcf_hdr_add_hrec(out, bcf_hrec_dup(dst_hrec));
+    }
+    for (i=0; i<src->nhrec; i++)
+    {
+        // now transfer header lines which define BCF ids
+        src_hrec = src->hrec[i];
+
+        if ( src_hrec->type==BCF_HL_FLT || src_hrec->type==BCF_HL_INFO || src_hrec->type==BCF_HL_FMT || src_hrec->type== BCF_HL_CTG )
+        {
+            int j = bcf_hrec_find_key(src_hrec, "ID");
+            dst_hrec = bcf_hdr_get_hrec(dst, src_hrec->type, "ID", src_hrec->vals[j], NULL);
+            if ( !dst_hrec ) continue;
+
+            tmp = bcf_hrec_dup(dst_hrec);
+
+            j = bcf_hrec_find_key(src_hrec, "IDX");
+            if ( j>=0 )
+            {
+                j = atoi(src_hrec->vals[j]);
+                if (hrec_add_idx(tmp, j) < 0)
+                    error_errno("[%s] Failed to add IDX header", __func__);
+            }
+            bcf_hdr_add_hrec(out, tmp);
+        }
+    }
+    if (bcf_hdr_sync(out) < 0)
+        error_errno("[%s] Failed to update header", __func__);
+    for (i=0; i<dst->nhrec; i++)
+    {
+        // finally add new structured fields
+        dst_hrec = dst->hrec[i];
+        if ( dst_hrec->type==BCF_HL_FLT || dst_hrec->type==BCF_HL_INFO || dst_hrec->type==BCF_HL_FMT || dst_hrec->type== BCF_HL_CTG )
+        {
+            int j = bcf_hrec_find_key(dst_hrec, "ID");
+            tmp = bcf_hdr_get_hrec(out, dst_hrec->type, "ID", dst_hrec->vals[j], NULL);
+            if ( !tmp )
+                bcf_hdr_add_hrec(out, bcf_hrec_dup(dst_hrec));
+        }
+    }
+    for (i=0; i<dst->n[BCF_DT_SAMPLE]; i++) bcf_hdr_add_sample(out, dst->samples[i]);
+    bcf_hdr_destroy(dst);
+    return out;
+}
+
+static void reheader_bcf(args_t *args, int is_compressed)
+{
+    htsFile *fp = args->fp;
+
+    if ( args->n_threads > 0 )
+    {
+        args->threads = (htsThreadPool *) calloc(1, sizeof(htsThreadPool));
+        if ( !args->threads ) error("Could not allocate memory\n");
+        if ( !(args->threads->pool = hts_tpool_init(args->n_threads)) ) error("Could not initialize threading\n");
+        hts_set_thread_pool(fp, args->threads);
+    }
+
+    bcf_hdr_t *hdr = bcf_hdr_read(fp); if ( !hdr ) error("Failed to read the header: %s\n", args->fname);
+    kstring_t htxt = {0,0,0};
+    bcf_hdr_format(hdr, 1, &htxt);
+
+    int i, nsamples = 0;
+    char **samples = NULL;
+    if ( args->samples_fname )
+    {
+        samples = hts_readlines(args->samples_fname, &nsamples);
+        if ( !samples || !nsamples ) error("Error reading the --samples file \"%s\"\n", args->samples_fname);
+    }
+    if ( args->header_fname )
+    {
+        free(htxt.s); htxt.s = NULL; htxt.l = htxt.m = 0;
+        read_header_file(args->header_fname, &htxt);
+    }
+    if ( samples )
+    {
+        set_samples(samples, nsamples, &htxt);
+        for (i=0; i<nsamples; i++) free(samples[i]);
+        free(samples);
+    }
+
+    bcf_hdr_t *hdr_out = bcf_hdr_init("r");
+    if ( bcf_hdr_parse(hdr_out, htxt.s) < 0 ) error("An error occurred while parsing the header\n");
+    if ( args->header_fname ) hdr_out = strip_header(hdr, hdr_out);
+
+    // write the header and the body
+    htsFile *fp_out = hts_open(args->output_fname ? args->output_fname : "-",is_compressed ? "wb" : "wbu");
+    if ( !fp_out ) error("%s: %s\n", args->output_fname ? args->output_fname : "-", strerror(errno));
+    if ( args->threads )
+        hts_set_thread_pool(fp_out, args->threads);
+    if ( bcf_hdr_write(fp_out, hdr_out)!=0 ) error("[%s] Error: cannot write the header to %s\n", __func__,args->output_fname ? args->output_fname : "standard output");
+
+    bcf1_t *rec = bcf_init();
+    while ( bcf_read(fp, hdr, rec)==0 )
+    {
+        // sanity checking, this slows things down. Make it optional?
+        bcf_unpack(rec, BCF_UN_ALL);
+        if ( rec->rid >= hdr_out->n[BCF_DT_CTG] || strcmp(bcf_hdr_int2id(hdr,BCF_DT_CTG,rec->rid),bcf_hdr_int2id(hdr_out,BCF_DT_CTG,rec->rid)) )
+            error("The CHROM is not defined: \"%s\"\n", bcf_hdr_int2id(hdr,BCF_DT_CTG,rec->rid));
+
+        for (i=0; i<rec->d.n_flt; i++)
+        {
+            int id = rec->d.flt[i];
+            if ( id >= hdr_out->n[BCF_DT_ID] ) break;
+            if ( !bcf_hdr_idinfo_exists(hdr_out,BCF_HL_FLT,id) ) break;
+            if ( strcmp(hdr->id[BCF_DT_ID][id].key,hdr_out->id[BCF_DT_ID][id].key) )
+                error("FIXME: Broken FILTER ids: %s vs %s\n", hdr->id[BCF_DT_ID][id].key,hdr_out->id[BCF_DT_ID][id].key);
+        }
+        if ( i!=rec->d.n_flt )
+            error("The FILTER is not defined: \"%s\"\n", bcf_hdr_int2id(hdr,BCF_DT_ID,rec->d.flt[i]));
+
+        for (i=0; i<rec->n_info; i++)
+        {
+            int id = rec->d.info[i].key;
+            if ( id >= hdr_out->n[BCF_DT_ID] ) break;
+            if ( !hdr_out->id[BCF_DT_ID][id].key ) break;
+            if ( !bcf_hdr_idinfo_exists(hdr_out,BCF_HL_INFO,id) ) break;
+            if ( strcmp(hdr->id[BCF_DT_ID][id].key,hdr_out->id[BCF_DT_ID][id].key) )
+                error("FIXME: Broken INFO ids: %s vs %s\n", hdr->id[BCF_DT_ID][id].key,hdr_out->id[BCF_DT_ID][id].key);
+        }
+        if ( i!=rec->n_info )
+            error("The INFO tag is not defined: \"%s\"\n", bcf_hdr_int2id(hdr,BCF_DT_ID,rec->d.info[i].key));
+
+        for (i=0; i<rec->n_fmt; i++)
+        {
+            int id = rec->d.fmt[i].id;
+            if ( id >= hdr_out->n[BCF_DT_ID] ) break;
+            if ( !hdr_out->id[BCF_DT_ID][id].key ) break;
+            if ( !bcf_hdr_idinfo_exists(hdr_out,BCF_HL_FMT,id) ) break;
+            if ( strcmp(hdr->id[BCF_DT_ID][id].key,hdr_out->id[BCF_DT_ID][id].key) )
+                error("FIXME: Broken FORMAT ids: %s vs %s\n", hdr->id[BCF_DT_ID][id].key,hdr_out->id[BCF_DT_ID][id].key);
+        }
+        if ( i!=rec->n_fmt )
+            error("The FORMAT tag is not defined: \"%s\"\n", bcf_hdr_int2id(hdr,BCF_DT_ID,rec->d.fmt[i].id));
+
+        if ( bcf_write(fp_out,hdr_out,rec)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->output_fname ? args->output_fname : "standard output");
+    }
+    bcf_destroy(rec);
+
+    free(htxt.s);
+    if ( hts_close(fp_out)!=0 ) error("[%s] Error: failed to close the file %s\n",__func__,args->output_fname ? args->output_fname : "standard output");
+    if ( hts_close(fp)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,args->fname);
+    bcf_hdr_destroy(hdr_out);
+    bcf_hdr_destroy(hdr);
+    if ( args->threads )
+    {
+        hts_tpool_destroy(args->threads->pool);
+        free(args->threads);
+    }
+}
+
+
+static void usage(args_t *args)
+{
+    fprintf(bcftools_stderr, "\n");
+    fprintf(bcftools_stderr, "About:   Modify header of VCF/BCF files, change sample names.\n");
+    fprintf(bcftools_stderr, "Usage:   bcftools reheader [OPTIONS] <in.vcf.gz>\n");
+    fprintf(bcftools_stderr, "\n");
+    fprintf(bcftools_stderr, "Options:\n");
+    fprintf(bcftools_stderr, "    -f, --fai FILE             update sequences and their lengths from the .fai file\n");
+    fprintf(bcftools_stderr, "    -h, --header FILE          new header\n");
+    fprintf(bcftools_stderr, "    -o, --output FILE          write output to a file [standard output]\n");
+    fprintf(bcftools_stderr, "    -s, --samples FILE         new sample names\n");
+#ifdef _WIN32
+    fprintf(bcftools_stderr, "    -T, --temp-prefix PATH     template for temporary file name [/bcftools.XXXXXX]\n");
+#else
+    fprintf(bcftools_stderr, "    -T, --temp-prefix PATH     template for temporary file name [/tmp/bcftools.XXXXXX]\n");
+#endif
+    fprintf(bcftools_stderr, "        --threads INT          use multithreading with <int> worker threads (BCF only) [0]\n");
+    fprintf(bcftools_stderr, "\n");
+    fprintf(bcftools_stderr, "Example:\n");
+    fprintf(bcftools_stderr, "   # Write out the header to be modified\n");
+    fprintf(bcftools_stderr, "   bcftools view -h old.bcf > header.txt\n");
+    fprintf(bcftools_stderr, "\n");
+    fprintf(bcftools_stderr, "   # Edit the header using your favorite text editor\n");
+    fprintf(bcftools_stderr, "   vi header.txt\n");
+    fprintf(bcftools_stderr, "\n");
+    fprintf(bcftools_stderr, "   # Reheader the file\n");
+    fprintf(bcftools_stderr, "   bcftools reheader -h header.txt -o new.bcf old.bcf\n");
+    fprintf(bcftools_stderr, "\n");
+    bcftools_exit(1);
+}
+
+int main_reheader(int argc, char *argv[])
+{
+    int c;
+    args_t *args  = (args_t*) calloc(1,sizeof(args_t));
+    args->argc    = argc; args->argv = argv;
+    
+    static struct option loptions[] =
+    {
+        {"temp-prefix",1,0,'T'},
+        {"fai",1,0,'f'},
+        {"output",1,0,'o'},
+        {"header",1,0,'h'},
+        {"samples",1,0,'s'},
+        {"threads",1,NULL,1},
+        {0,0,0,0}
+    };
+    while ((c = getopt_long(argc, argv, "s:h:o:f:T:",loptions,NULL)) >= 0)
+    {
+        switch (c)
+        {
+            case  1 : args->n_threads = strtol(optarg, 0, 0); break;
+            case 'T': args->tmp_prefix = optarg; break;
+            case 'f': args->fai_fname = optarg; break;
+            case 'o': args->output_fname = optarg; break;
+            case 's': args->samples_fname = optarg; break;
+            case 'h': args->header_fname = optarg; break;
+            case '?': usage(args); break;
+            default: error("Unknown argument: %s\n", optarg);
+        }
+    }
+
+    if ( optind>=argc )
+    {
+        if ( !isatty(fileno((FILE *)stdin)) ) args->fname = "-";  // reading from stdin
+        else usage(args);
+    }
+    else args->fname = argv[optind];
+
+    if ( args->fai_fname ) update_from_fai(args);
+    if ( !args->samples_fname && !args->header_fname ) usage(args);
+    if ( !args->fname ) usage(args);
+
+    args->fp = hts_open(args->fname,"r");
+    if ( !args->fp ) error("Failed to read from %s\n", !strcmp("-",args->fname)?"standard input":args->fname);
+    args->type = *hts_get_format(args->fp);
+
+    if ( args->type.format==vcf )
+    {
+        if ( args->type.compression==bgzf )
+            reheader_vcf_gz(args);
+        else if ( args->type.compression==no_compression )
+            reheader_vcf(args);
+        else if ( args->type.compression==gzip )
+            error("Error: cannot reheader gzip-compressed files, first convert with `bcftools view --output-type` to a supported format\n");
+        else
+            error("Error: the compression type of \"%s\" is not recognised/supported\n", args->fname);
+    }
+    else
+        reheader_bcf(args, args->type.compression==bgzf || args->type.compression==gzip);
+
+    if ( args->rm_tmpfile )
+    {
+        unlink(args->rm_tmpfile);
+        free(args->rm_tmpfile);
+    }
+    free(args);
+    return 0;
+}
diff --git a/bcftools/smpl_ilist.c b/bcftools/smpl_ilist.c
new file mode 100644
index 0000000..e3fbacc
--- /dev/null
+++ b/bcftools/smpl_ilist.c
@@ -0,0 +1,170 @@
+/* 
+    Copyright (C) 2016-2021 Genome Research Ltd.
+
+    Author: Petr Danecek <pd3@sanger.ac.uk>
+
+    Permission is hereby granted, free of charge, to any person obtaining a copy
+    of this software and associated documentation files (the "Software"), to deal
+    in the Software without restriction, including without limitation the rights
+    to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+    copies of the Software, and to permit persons to whom the Software is
+    furnished to do so, subject to the following conditions:
+    
+    The above copyright notice and this permission notice shall be included in
+    all copies or substantial portions of the Software.
+    
+    THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+    IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+    FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+    AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+    LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+    OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+    THE SOFTWARE.
+*/
+
+#include <ctype.h>
+#include "bcftools.h"
+#include "smpl_ilist.h"
+
+void smpl_ilist_destroy(smpl_ilist_t *smpl)
+{
+    int i;
+    if ( smpl->pair )
+    {
+        for (i=0; i<smpl->n; i++) free(smpl->pair[i]);
+        free(smpl->pair);
+    }
+    free(smpl->idx);
+    free(smpl);
+}
+
+static inline int is_space_or_escaped(const char *min, const char *str)
+{
+    if ( !isspace(*str) ) return 0;
+    int n = 0;
+    while ( --str>=min && *str=='\\' ) n++;
+    return n%2 ? 0 : 1;
+}
+smpl_ilist_t *smpl_ilist_init(bcf_hdr_t *hdr, char *sample_list, int is_file, int flags)
+{
+    smpl_ilist_t *smpl = (smpl_ilist_t*) calloc(1,sizeof(smpl_ilist_t));
+
+    int i;
+    if ( !sample_list )
+    {
+        smpl->n = bcf_hdr_nsamples(hdr);
+        smpl->idx = (int*) malloc(sizeof(int)*smpl->n);
+        for (i=0; i<smpl->n; i++) smpl->idx[i] = i;
+        return smpl;
+    }
+
+    int negate = sample_list[0]=='^' ? 1 : 0;
+    int nlist;
+    char **list = hts_readlist(negate?sample_list+1:sample_list, is_file, &nlist);
+    if ( !list ) error("Could not parse %s\n", sample_list);
+
+    if ( negate && (flags&SMPL_REORDER) ) flags &= ~SMPL_REORDER;
+
+    // preserve the VCF order unless flags&SMPL_REORDER is set
+    int j = 0;
+    int *tmp = (int*)calloc(bcf_hdr_nsamples(hdr),sizeof(int));
+    char **pair = NULL;
+    for (i=0; i<nlist; i++)
+    {
+        char *smpl1 = list[i];
+        char *smpl2 = NULL;
+
+        char *ptr = list[i];
+        while ( *ptr && !is_space_or_escaped(list[i], ptr) ) ptr++;
+        if ( *ptr )
+        {
+            *ptr = 0;
+            smpl2 = ptr+1;
+        }
+
+        char *smpl_name = flags&SMPL_PAIR2 && smpl2 ? smpl2 : smpl1;
+        int idx = bcf_hdr_id2int(hdr, BCF_DT_SAMPLE, smpl_name);
+        if ( idx<0 )
+        {
+            if ( !(flags&SMPL_STRICT) )
+            {
+                if ( flags&SMPL_VERBOSE ) fprintf(stderr,"No such sample: \"%s\"\n",smpl_name);
+                continue;
+            }
+            error("No such sample: \"%s\"\n", smpl_name);
+        }
+
+        if ( flags & SMPL_REORDER )
+        {
+            tmp[j++] = idx;
+        }
+        else
+        {
+            tmp[idx] = 1;
+            if ( smpl2 )
+            {
+                if ( !pair ) pair = (char**)calloc(bcf_hdr_nsamples(hdr),sizeof(char*));
+                if ( flags&SMPL_PAIR2 ) pair[idx] = strdup(smpl1);
+                else if ( flags&SMPL_PAIR1 ) pair[idx] = strdup(smpl2);
+            }
+        }
+        smpl->n++;
+    }
+
+    if ( flags & SMPL_REORDER )
+    {
+        smpl->idx = tmp;
+        for (i=0; i<nlist; i++) free(list[i]);
+        free(list);
+        return smpl;
+    }
+
+    if ( negate ) smpl->n = bcf_hdr_nsamples(hdr) - smpl->n;
+    smpl->idx = (int*) malloc(sizeof(int)*smpl->n);
+
+    j = 0;
+    if ( !negate )
+    {
+        if ( pair ) smpl->pair = (char**) calloc(smpl->n,sizeof(char*));
+        for (i=0; i<bcf_hdr_nsamples(hdr); i++)
+        {
+            if ( !tmp[i] ) continue;
+            smpl->idx[j] = i;
+            if ( pair && pair[i] ) smpl->pair[j] = pair[i];
+            j++;
+        }
+    }
+    else
+    {
+        for (i=0; i<bcf_hdr_nsamples(hdr); i++)
+            if ( !tmp[i] ) smpl->idx[j++] = i;
+    }
+
+    free(tmp);
+    free(pair);
+    for (i=0; i<nlist; i++) free(list[i]);
+    free(list);
+
+    return smpl;
+}
+
+smpl_ilist_t *smpl_ilist_map(bcf_hdr_t *hdr_a, bcf_hdr_t *hdr_b, int flags)
+{
+    if ( flags&SMPL_STRICT && bcf_hdr_nsamples(hdr_a)!=bcf_hdr_nsamples(hdr_b) )
+        error("Different number of samples: %d vs %d\n", bcf_hdr_nsamples(hdr_a),bcf_hdr_nsamples(hdr_b));
+
+    smpl_ilist_t *smpl = (smpl_ilist_t*) calloc(1,sizeof(smpl_ilist_t));
+
+    int i;
+    smpl->n = bcf_hdr_nsamples(hdr_a);
+    smpl->idx = (int*) malloc(sizeof(int)*smpl->n);
+    for (i=0; i<smpl->n; i++)
+    {
+        const char *name = bcf_hdr_int2id(hdr_a, BCF_DT_SAMPLE, i);
+        smpl->idx[i] = bcf_hdr_id2int(hdr_b, BCF_DT_SAMPLE, name);
+        if ( flags&SMPL_STRICT && smpl->idx[i]<0 ) 
+            error("The sample %s is not present in the second file\n", name);
+    }
+    return smpl;
+}
+
diff --git a/bcftools/smpl_ilist.c.pysam.c b/bcftools/smpl_ilist.c.pysam.c
new file mode 100644
index 0000000..68ed527
--- /dev/null
+++ b/bcftools/smpl_ilist.c.pysam.c
@@ -0,0 +1,172 @@
+#include "bcftools.pysam.h"
+
+/* 
+    Copyright (C) 2016-2021 Genome Research Ltd.
+
+    Author: Petr Danecek <pd3@sanger.ac.uk>
+
+    Permission is hereby granted, free of charge, to any person obtaining a copy
+    of this software and associated documentation files (the "Software"), to deal
+    in the Software without restriction, including without limitation the rights
+    to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+    copies of the Software, and to permit persons to whom the Software is
+    furnished to do so, subject to the following conditions:
+    
+    The above copyright notice and this permission notice shall be included in
+    all copies or substantial portions of the Software.
+    
+    THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+    IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+    FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+    AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+    LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+    OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+    THE SOFTWARE.
+*/
+
+#include <ctype.h>
+#include "bcftools.h"
+#include "smpl_ilist.h"
+
+void smpl_ilist_destroy(smpl_ilist_t *smpl)
+{
+    int i;
+    if ( smpl->pair )
+    {
+        for (i=0; i<smpl->n; i++) free(smpl->pair[i]);
+        free(smpl->pair);
+    }
+    free(smpl->idx);
+    free(smpl);
+}
+
+static inline int is_space_or_escaped(const char *min, const char *str)
+{
+    if ( !isspace(*str) ) return 0;
+    int n = 0;
+    while ( --str>=min && *str=='\\' ) n++;
+    return n%2 ? 0 : 1;
+}
+smpl_ilist_t *smpl_ilist_init(bcf_hdr_t *hdr, char *sample_list, int is_file, int flags)
+{
+    smpl_ilist_t *smpl = (smpl_ilist_t*) calloc(1,sizeof(smpl_ilist_t));
+
+    int i;
+    if ( !sample_list )
+    {
+        smpl->n = bcf_hdr_nsamples(hdr);
+        smpl->idx = (int*) malloc(sizeof(int)*smpl->n);
+        for (i=0; i<smpl->n; i++) smpl->idx[i] = i;
+        return smpl;
+    }
+
+    int negate = sample_list[0]=='^' ? 1 : 0;
+    int nlist;
+    char **list = hts_readlist(negate?sample_list+1:sample_list, is_file, &nlist);
+    if ( !list ) error("Could not parse %s\n", sample_list);
+
+    if ( negate && (flags&SMPL_REORDER) ) flags &= ~SMPL_REORDER;
+
+    // preserve the VCF order unless flags&SMPL_REORDER is set
+    int j = 0;
+    int *tmp = (int*)calloc(bcf_hdr_nsamples(hdr),sizeof(int));
+    char **pair = NULL;
+    for (i=0; i<nlist; i++)
+    {
+        char *smpl1 = list[i];
+        char *smpl2 = NULL;
+
+        char *ptr = list[i];
+        while ( *ptr && !is_space_or_escaped(list[i], ptr) ) ptr++;
+        if ( *ptr )
+        {
+            *ptr = 0;
+            smpl2 = ptr+1;
+        }
+
+        char *smpl_name = flags&SMPL_PAIR2 && smpl2 ? smpl2 : smpl1;
+        int idx = bcf_hdr_id2int(hdr, BCF_DT_SAMPLE, smpl_name);
+        if ( idx<0 )
+        {
+            if ( !(flags&SMPL_STRICT) )
+            {
+                if ( flags&SMPL_VERBOSE ) fprintf(bcftools_stderr,"No such sample: \"%s\"\n",smpl_name);
+                continue;
+            }
+            error("No such sample: \"%s\"\n", smpl_name);
+        }
+
+        if ( flags & SMPL_REORDER )
+        {
+            tmp[j++] = idx;
+        }
+        else
+        {
+            tmp[idx] = 1;
+            if ( smpl2 )
+            {
+                if ( !pair ) pair = (char**)calloc(bcf_hdr_nsamples(hdr),sizeof(char*));
+                if ( flags&SMPL_PAIR2 ) pair[idx] = strdup(smpl1);
+                else if ( flags&SMPL_PAIR1 ) pair[idx] = strdup(smpl2);
+            }
+        }
+        smpl->n++;
+    }
+
+    if ( flags & SMPL_REORDER )
+    {
+        smpl->idx = tmp;
+        for (i=0; i<nlist; i++) free(list[i]);
+        free(list);
+        return smpl;
+    }
+
+    if ( negate ) smpl->n = bcf_hdr_nsamples(hdr) - smpl->n;
+    smpl->idx = (int*) malloc(sizeof(int)*smpl->n);
+
+    j = 0;
+    if ( !negate )
+    {
+        if ( pair ) smpl->pair = (char**) calloc(smpl->n,sizeof(char*));
+        for (i=0; i<bcf_hdr_nsamples(hdr); i++)
+        {
+            if ( !tmp[i] ) continue;
+            smpl->idx[j] = i;
+            if ( pair && pair[i] ) smpl->pair[j] = pair[i];
+            j++;
+        }
+    }
+    else
+    {
+        for (i=0; i<bcf_hdr_nsamples(hdr); i++)
+            if ( !tmp[i] ) smpl->idx[j++] = i;
+    }
+
+    free(tmp);
+    free(pair);
+    for (i=0; i<nlist; i++) free(list[i]);
+    free(list);
+
+    return smpl;
+}
+
+smpl_ilist_t *smpl_ilist_map(bcf_hdr_t *hdr_a, bcf_hdr_t *hdr_b, int flags)
+{
+    if ( flags&SMPL_STRICT && bcf_hdr_nsamples(hdr_a)!=bcf_hdr_nsamples(hdr_b) )
+        error("Different number of samples: %d vs %d\n", bcf_hdr_nsamples(hdr_a),bcf_hdr_nsamples(hdr_b));
+
+    smpl_ilist_t *smpl = (smpl_ilist_t*) calloc(1,sizeof(smpl_ilist_t));
+
+    int i;
+    smpl->n = bcf_hdr_nsamples(hdr_a);
+    smpl->idx = (int*) malloc(sizeof(int)*smpl->n);
+    for (i=0; i<smpl->n; i++)
+    {
+        const char *name = bcf_hdr_int2id(hdr_a, BCF_DT_SAMPLE, i);
+        smpl->idx[i] = bcf_hdr_id2int(hdr_b, BCF_DT_SAMPLE, name);
+        if ( flags&SMPL_STRICT && smpl->idx[i]<0 ) 
+            error("The sample %s is not present in the second file\n", name);
+    }
+    return smpl;
+}
+
diff --git a/bcftools/smpl_ilist.h b/bcftools/smpl_ilist.h
new file mode 100644
index 0000000..79292c3
--- /dev/null
+++ b/bcftools/smpl_ilist.h
@@ -0,0 +1,53 @@
+/* 
+    Copyright (C) 2016-2021 Genome Research Ltd.
+
+    Author: Petr Danecek <pd3@sanger.ac.uk>
+
+    Permission is hereby granted, free of charge, to any person obtaining a copy
+    of this software and associated documentation files (the "Software"), to deal
+    in the Software without restriction, including without limitation the rights
+    to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+    copies of the Software, and to permit persons to whom the Software is
+    furnished to do so, subject to the following conditions:
+    
+    The above copyright notice and this permission notice shall be included in
+    all copies or substantial portions of the Software.
+    
+    THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+    IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+    FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+    AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+    LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+    OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+    THE SOFTWARE.
+*/
+/*
+    Parse --samples and --samples-file
+*/
+
+#ifndef __SMPL_ILIST_H__
+#define __SMPL_ILIST_H__
+
+#include <htslib/vcf.h>
+
+#define SMPL_NONE     0   // flexible error recovery
+#define SMPL_STRICT   1   // samples must exist
+#define SMPL_SINGLE   2   // single sample expected
+#define SMPL_PAIR1    4   // two samples expected, the first is from the bcf hdr
+#define SMPL_PAIR2    8   // two samples expected, the second is from the bcf hdr
+#define SMPL_VERBOSE 16   // print warnings 
+#define SMPL_REORDER 32   // reorder samples as asked, sample_list[i] points to the VCF header index
+
+typedef struct
+{
+    char **pair;    // the other sample in the pair
+    int *idx;       // index to bcf_hdr_t.samples; the first (SMPL_SINGLE|SMPL_PAIR1) or second sample (SMPL_PAIR2)
+    int n;
+}
+smpl_ilist_t;
+
+smpl_ilist_t *smpl_ilist_init(bcf_hdr_t *hdr, char *sample_list, int is_file, int flags);
+smpl_ilist_t *smpl_ilist_map(bcf_hdr_t *hdr_a, bcf_hdr_t *hdr_b, int flags);
+void smpl_ilist_destroy(smpl_ilist_t *smpl);
+
+#endif
diff --git a/bcftools/str_finder.c b/bcftools/str_finder.c
new file mode 100644
index 0000000..800cbfe
--- /dev/null
+++ b/bcftools/str_finder.c
@@ -0,0 +1,270 @@
+/*  str_finder.c -- Short Tandem Repeat finder.
+    Originally from Crumble (https://github.com/jkbonfield/crumble)
+
+    Copyright (C) 2015-2016, 2021 Genome Research Ltd.
+
+    Author: James Bonfield <jkb@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <stdint.h>
+#include <ctype.h>
+
+#include "str_finder.h"
+#include "utlist.h"
+
+#define MAX(a,b) ((a)>(b)?(a):(b))
+#define MIN(a,b) ((a)<(b)?(a):(b))
+
+typedef unsigned char uc;
+
+static void add_rep(rep_ele **list, char *cons, int clen, int pos, int rlen,
+		    int lower_only, unsigned int w) {
+    rep_ele *el, *tmp, *prev;
+    char *cp1, *cp2, *cp_end;
+    int i;
+
+    // Already handled this in previous overlap?
+    if (*list) {
+	tmp = DL_TAIL(*list);
+	if (tmp->start <= pos-rlen*2+1 && tmp->end >= pos)
+	    return;
+    }
+
+    // Find current and last occurence of repeated word.
+
+    cp2 = &cons[pos+1];
+    // If unpadded, this is quicker: cp1 = &cons[pos+1-rlen];
+
+    for (cp1 = &cons[pos], i = 1; i < rlen; cp1--) // compensate for pads
+	if (*cp1 == '*')
+	    continue;
+	else
+	    i++;
+    while (*cp1 == '*')
+	cp1--;
+
+
+    // Scan ahead to see how much further it goes.
+    cp_end = &cons[clen];
+    while (cp2 < cp_end) {
+	if (*cp1 != *cp2)
+	    break;
+
+	w<<=2;
+	w|=*cp2;
+	cp1++;
+	cp2++;
+    }
+
+    if (!(el = malloc(sizeof(*el))))
+	return;
+
+    el->end   = pos + cp2-&cons[pos+1];
+    el->rep_len = rlen;
+    pos++;
+    while (rlen--) {
+	while (cons[--pos] == '*');
+	while (cons[--pos] == '*');
+    }
+    //pos++;
+    while (pos > 1 && cons[pos-1] == '*') pos--;
+    el->start = pos;
+
+    // Check it meets the lower-case only criteria
+    if (lower_only) {
+	int lc = 0;
+	for (i = el->start; i <= el->end; i++) {
+	    if (islower(cons[i])) {
+		lc = 1;
+		break;
+	    }
+	}
+
+	if (!lc) {
+	    free(el);
+	    return;
+	}
+    }
+
+    // Remove any older items on the list that are entirely contained within el
+    if (*list) {
+	tmp = DL_TAIL(*list);
+	do {
+	    prev = tmp->prev;
+	    if (tmp->end < el->start)
+		break;
+
+	    if (tmp->start >= el->start) {
+		DL_DELETE(*list, tmp);
+		free(tmp);
+	    }
+
+	    if (tmp == DL_HEAD(*list))
+		break;
+	    tmp = prev;
+	} while (*list);
+    }
+
+    DL_APPEND(*list, el);
+
+    return;
+}
+
+/*
+ * Finds repeated homopolymers up to 8-mers.
+ * Note this assumes cons is 0-3, so N of 4 may rarely give false hits.
+ *
+ * Returns a list of rep_ele structs holding the start,end tuples of repeats;
+ *         NULL on failure.
+ */
+rep_ele *find_STR(char *cons, int len, int lower_only) {
+    int i, j;
+    uint32_t w = 0;
+    rep_ele *reps = NULL;
+
+    for (i = j = 0; i < len && j < 15; i++) {
+	if (cons[i] == '*') continue;
+
+	w <<= 2;
+	w |= cons[i];
+	//printf("%3d %c w=%08x\n", i, cons[i], w);
+	if (j>= 1 && (w&0x0003) == ((w>> 2)&0x0003))
+	    add_rep(&reps, cons, len, i, 1, lower_only, w);
+	if (j>= 3 && (w&0x000f) == ((w>> 4)&0x000f))
+	    add_rep(&reps, cons, len, i, 2, lower_only, w);
+	if (j>= 5 && (w&0x003f) == ((w>> 6)&0x003f))
+	    add_rep(&reps, cons, len, i, 3, lower_only, w);
+	if (j>= 7 && (w&0x00ff) == ((w>> 8)&0x00ff))
+	    add_rep(&reps, cons, len, i, 4, lower_only, w);
+	if (j>= 9 && (w&0x03ff) == ((w>>10)&0x03ff))
+	    add_rep(&reps, cons, len, i, 5, lower_only, w);
+	if (j>=11 && (w&0x0fff) == ((w>>12)&0x0fff))
+	    add_rep(&reps, cons, len, i, 6, lower_only, w);
+	if (j>=13 && (w&0x3fff) == ((w>>14)&0x3fff))
+	    add_rep(&reps, cons, len, i, 7, lower_only, w);
+
+	j++;
+    }
+
+    for (; i < len; i++) {	
+	if (cons[i] == '*') continue;
+
+	w <<= 2;
+	w |= cons[i];
+	//printf("%3d %c w=%08x\n", i, cons[i], w);
+	if ((w&0xffff) == ((w>>16)&0xffff)) 
+	    add_rep(&reps, cons, len, i, 8, lower_only, w);
+	else if ((w&0x3fff) == ((w>>14)&0x3fff)) 
+	    add_rep(&reps, cons, len, i, 7, lower_only, w);
+	else if ((w&0x0fff) == ((w>>12)&0x0fff)) 
+	    add_rep(&reps, cons, len, i, 6, lower_only, w);
+	else if ((w&0x03ff) == ((w>>10)&0x03ff)) 
+	    add_rep(&reps, cons, len, i, 5, lower_only, w);
+	else if ((w&0x00ff) == ((w>> 8)&0x00ff)) 
+	    add_rep(&reps, cons, len, i, 4, lower_only, w);
+	else if ((w&0x003f) == ((w>> 6)&0x003f)) 
+	    add_rep(&reps, cons, len, i, 3, lower_only, w);
+	else if ((w&0x000f) == ((w>> 4)&0x000f)) 
+	    add_rep(&reps, cons, len, i, 2, lower_only, w);
+	else if ((w&0x0003) == ((w>> 2)&0x0003)) 
+	    add_rep(&reps, cons, len, i, 1, lower_only, w);
+    }
+
+    return reps;
+}
+
+/* -----------------------------------------------------------------------------
+ * Computes repeat regions in the consensus and then provides a bit mask
+ * indicating the extend of the STRs.
+ *
+ * The purpose of this is to identify where a read needs to span the entire
+ * region in order to validate how many copies of a repeat word are present.
+ * This only really has a major impact when indels are involved.
+ *
+ * For example, given this multiple alignment:
+ *
+ * S1 GATCGGACGAGAG
+ * S2 GATCGGACGAGAGAGAGAGAGT
+ * S3 GATCGGACGAGAGAGAGAG**TCGGAC
+ * S4     GGACGAGAGAGAGAGAGTCGGAC
+ * S5        CGAGAGAGAGAG**TCGGAC
+ * S6              AGAGAGAGTCGGAC
+ *
+ * We have subseq of GAGAGAGAGAG** vs GAGAGAGAGAGAG. The first and last
+ * (S1 and S6) sequences do not span and so we do not know which allele they
+ * match. Specifically as the pad is at the right hand end, the alignment of
+ * S6 gives incorrect weight to the consensus as it is stating AG when it
+ * may actually be ** at that point.
+ *
+ * By identifying the repeats we can soft clip as follows:
+ *
+ * S1 GATCGGACgagag
+ * S2 GATCGGACGAGAGAGAGAGAGT
+ * S3 GATCGGACGAGAGAGAGAG**TCGGAC
+ * S4     GGACGAGAGAGAGAGAGTCGGAC
+ * S5        CGAGAGAGAGAG**TCGGAC
+ * S6              agagagagTCGGAC
+ *
+ * Returns an array of STR vs no-STR values.
+ *         0  => non repetitive.
+ *         1+ => repeat with consecutive bit-number for repeat size.
+ *
+ * Eg:  AGGGGAGGAGAAGAC
+ *       1111  1111
+ *         2222222
+ *              444444
+ * =>   011331137754440
+ */
+char *cons_mark_STR(char *cons, int len, int lower_only) {
+    rep_ele *reps, *elt, *tmp;
+    char *str;
+
+    str = calloc(1, len);
+    reps = find_STR(cons, len, lower_only);
+
+    DL_FOREACH_SAFE(reps, elt, tmp) {
+	int i, v = 0;
+	
+	//printf("%2d .. %2d %.*s\n", elt->start, elt->end,
+	//       elt->end - elt->start+1, &cons[elt->start]);
+
+	// What is there?
+	for (i = MAX(elt->start-1,0); i <= MIN(elt->end+1,len-1); i++)
+	    v |= str[i];
+
+	for (i = 0; i < 8; i++) {
+	    if (!(v&(1<<i)))
+		break;
+	}
+	v = (i == 8) ? 1 : (1<<i);
+
+	// Add new if available, or just overload 1 if not
+	for (i = elt->start; i <= elt->end; i++)
+	    str[i] |= v;
+
+	DL_DELETE(reps, elt);
+	free(elt);
+    }
+
+    return str;
+}
diff --git a/bcftools/str_finder.c.pysam.c b/bcftools/str_finder.c.pysam.c
new file mode 100644
index 0000000..296c867
--- /dev/null
+++ b/bcftools/str_finder.c.pysam.c
@@ -0,0 +1,272 @@
+#include "bcftools.pysam.h"
+
+/*  str_finder.c -- Short Tandem Repeat finder.
+    Originally from Crumble (https://github.com/jkbonfield/crumble)
+
+    Copyright (C) 2015-2016, 2021 Genome Research Ltd.
+
+    Author: James Bonfield <jkb@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <stdint.h>
+#include <ctype.h>
+
+#include "str_finder.h"
+#include "utlist.h"
+
+#define MAX(a,b) ((a)>(b)?(a):(b))
+#define MIN(a,b) ((a)<(b)?(a):(b))
+
+typedef unsigned char uc;
+
+static void add_rep(rep_ele **list, char *cons, int clen, int pos, int rlen,
+		    int lower_only, unsigned int w) {
+    rep_ele *el, *tmp, *prev;
+    char *cp1, *cp2, *cp_end;
+    int i;
+
+    // Already handled this in previous overlap?
+    if (*list) {
+	tmp = DL_TAIL(*list);
+	if (tmp->start <= pos-rlen*2+1 && tmp->end >= pos)
+	    return;
+    }
+
+    // Find current and last occurence of repeated word.
+
+    cp2 = &cons[pos+1];
+    // If unpadded, this is quicker: cp1 = &cons[pos+1-rlen];
+
+    for (cp1 = &cons[pos], i = 1; i < rlen; cp1--) // compensate for pads
+	if (*cp1 == '*')
+	    continue;
+	else
+	    i++;
+    while (*cp1 == '*')
+	cp1--;
+
+
+    // Scan ahead to see how much further it goes.
+    cp_end = &cons[clen];
+    while (cp2 < cp_end) {
+	if (*cp1 != *cp2)
+	    break;
+
+	w<<=2;
+	w|=*cp2;
+	cp1++;
+	cp2++;
+    }
+
+    if (!(el = malloc(sizeof(*el))))
+	return;
+
+    el->end   = pos + cp2-&cons[pos+1];
+    el->rep_len = rlen;
+    pos++;
+    while (rlen--) {
+	while (cons[--pos] == '*');
+	while (cons[--pos] == '*');
+    }
+    //pos++;
+    while (pos > 1 && cons[pos-1] == '*') pos--;
+    el->start = pos;
+
+    // Check it meets the lower-case only criteria
+    if (lower_only) {
+	int lc = 0;
+	for (i = el->start; i <= el->end; i++) {
+	    if (islower(cons[i])) {
+		lc = 1;
+		break;
+	    }
+	}
+
+	if (!lc) {
+	    free(el);
+	    return;
+	}
+    }
+
+    // Remove any older items on the list that are entirely contained within el
+    if (*list) {
+	tmp = DL_TAIL(*list);
+	do {
+	    prev = tmp->prev;
+	    if (tmp->end < el->start)
+		break;
+
+	    if (tmp->start >= el->start) {
+		DL_DELETE(*list, tmp);
+		free(tmp);
+	    }
+
+	    if (tmp == DL_HEAD(*list))
+		break;
+	    tmp = prev;
+	} while (*list);
+    }
+
+    DL_APPEND(*list, el);
+
+    return;
+}
+
+/*
+ * Finds repeated homopolymers up to 8-mers.
+ * Note this assumes cons is 0-3, so N of 4 may rarely give false hits.
+ *
+ * Returns a list of rep_ele structs holding the start,end tuples of repeats;
+ *         NULL on failure.
+ */
+rep_ele *find_STR(char *cons, int len, int lower_only) {
+    int i, j;
+    uint32_t w = 0;
+    rep_ele *reps = NULL;
+
+    for (i = j = 0; i < len && j < 15; i++) {
+	if (cons[i] == '*') continue;
+
+	w <<= 2;
+	w |= cons[i];
+	//printf("%3d %c w=%08x\n", i, cons[i], w);
+	if (j>= 1 && (w&0x0003) == ((w>> 2)&0x0003))
+	    add_rep(&reps, cons, len, i, 1, lower_only, w);
+	if (j>= 3 && (w&0x000f) == ((w>> 4)&0x000f))
+	    add_rep(&reps, cons, len, i, 2, lower_only, w);
+	if (j>= 5 && (w&0x003f) == ((w>> 6)&0x003f))
+	    add_rep(&reps, cons, len, i, 3, lower_only, w);
+	if (j>= 7 && (w&0x00ff) == ((w>> 8)&0x00ff))
+	    add_rep(&reps, cons, len, i, 4, lower_only, w);
+	if (j>= 9 && (w&0x03ff) == ((w>>10)&0x03ff))
+	    add_rep(&reps, cons, len, i, 5, lower_only, w);
+	if (j>=11 && (w&0x0fff) == ((w>>12)&0x0fff))
+	    add_rep(&reps, cons, len, i, 6, lower_only, w);
+	if (j>=13 && (w&0x3fff) == ((w>>14)&0x3fff))
+	    add_rep(&reps, cons, len, i, 7, lower_only, w);
+
+	j++;
+    }
+
+    for (; i < len; i++) {	
+	if (cons[i] == '*') continue;
+
+	w <<= 2;
+	w |= cons[i];
+	//printf("%3d %c w=%08x\n", i, cons[i], w);
+	if ((w&0xffff) == ((w>>16)&0xffff)) 
+	    add_rep(&reps, cons, len, i, 8, lower_only, w);
+	else if ((w&0x3fff) == ((w>>14)&0x3fff)) 
+	    add_rep(&reps, cons, len, i, 7, lower_only, w);
+	else if ((w&0x0fff) == ((w>>12)&0x0fff)) 
+	    add_rep(&reps, cons, len, i, 6, lower_only, w);
+	else if ((w&0x03ff) == ((w>>10)&0x03ff)) 
+	    add_rep(&reps, cons, len, i, 5, lower_only, w);
+	else if ((w&0x00ff) == ((w>> 8)&0x00ff)) 
+	    add_rep(&reps, cons, len, i, 4, lower_only, w);
+	else if ((w&0x003f) == ((w>> 6)&0x003f)) 
+	    add_rep(&reps, cons, len, i, 3, lower_only, w);
+	else if ((w&0x000f) == ((w>> 4)&0x000f)) 
+	    add_rep(&reps, cons, len, i, 2, lower_only, w);
+	else if ((w&0x0003) == ((w>> 2)&0x0003)) 
+	    add_rep(&reps, cons, len, i, 1, lower_only, w);
+    }
+
+    return reps;
+}
+
+/* -----------------------------------------------------------------------------
+ * Computes repeat regions in the consensus and then provides a bit mask
+ * indicating the extend of the STRs.
+ *
+ * The purpose of this is to identify where a read needs to span the entire
+ * region in order to validate how many copies of a repeat word are present.
+ * This only really has a major impact when indels are involved.
+ *
+ * For example, given this multiple alignment:
+ *
+ * S1 GATCGGACGAGAG
+ * S2 GATCGGACGAGAGAGAGAGAGT
+ * S3 GATCGGACGAGAGAGAGAG**TCGGAC
+ * S4     GGACGAGAGAGAGAGAGTCGGAC
+ * S5        CGAGAGAGAGAG**TCGGAC
+ * S6              AGAGAGAGTCGGAC
+ *
+ * We have subseq of GAGAGAGAGAG** vs GAGAGAGAGAGAG. The first and last
+ * (S1 and S6) sequences do not span and so we do not know which allele they
+ * match. Specifically as the pad is at the right hand end, the alignment of
+ * S6 gives incorrect weight to the consensus as it is stating AG when it
+ * may actually be ** at that point.
+ *
+ * By identifying the repeats we can soft clip as follows:
+ *
+ * S1 GATCGGACgagag
+ * S2 GATCGGACGAGAGAGAGAGAGT
+ * S3 GATCGGACGAGAGAGAGAG**TCGGAC
+ * S4     GGACGAGAGAGAGAGAGTCGGAC
+ * S5        CGAGAGAGAGAG**TCGGAC
+ * S6              agagagagTCGGAC
+ *
+ * Returns an array of STR vs no-STR values.
+ *         0  => non repetitive.
+ *         1+ => repeat with consecutive bit-number for repeat size.
+ *
+ * Eg:  AGGGGAGGAGAAGAC
+ *       1111  1111
+ *         2222222
+ *              444444
+ * =>   011331137754440
+ */
+char *cons_mark_STR(char *cons, int len, int lower_only) {
+    rep_ele *reps, *elt, *tmp;
+    char *str;
+
+    str = calloc(1, len);
+    reps = find_STR(cons, len, lower_only);
+
+    DL_FOREACH_SAFE(reps, elt, tmp) {
+	int i, v = 0;
+	
+	//printf("%2d .. %2d %.*s\n", elt->start, elt->end,
+	//       elt->end - elt->start+1, &cons[elt->start]);
+
+	// What is there?
+	for (i = MAX(elt->start-1,0); i <= MIN(elt->end+1,len-1); i++)
+	    v |= str[i];
+
+	for (i = 0; i < 8; i++) {
+	    if (!(v&(1<<i)))
+		break;
+	}
+	v = (i == 8) ? 1 : (1<<i);
+
+	// Add new if available, or just overload 1 if not
+	for (i = elt->start; i <= elt->end; i++)
+	    str[i] |= v;
+
+	DL_DELETE(reps, elt);
+	free(elt);
+    }
+
+    return str;
+}
diff --git a/bcftools/str_finder.h b/bcftools/str_finder.h
new file mode 100644
index 0000000..242f59e
--- /dev/null
+++ b/bcftools/str_finder.h
@@ -0,0 +1,64 @@
+/*  str_finder.c -- Short Tandem Repeat finder.
+    Originally from Crumble (https://github.com/jkbonfield/crumble)
+
+    Copyright (C) 2015-2016, 2021 Genome Research Ltd.
+
+    Author: James Bonfield <jkb@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#ifndef _STR_FINDER_H_
+#define _STR_FINDER_H_
+
+#include "utlist.h"
+
+typedef struct rep_ele {
+    int start, end, rep_len;
+    struct rep_ele *prev;
+    struct rep_ele *next;
+} rep_ele;
+
+/*
+ * Finds repeated homopolymers up to 8-mers.
+ *
+ * If lower_only is true then it only adds STRs for regions that
+ * contain at least one lower-case base. This can be used as a marker
+ * for looking for specific types of repeats.
+ * (One use for this is to only mark STRs that overlap a heterozygous
+ * indel region.)
+ *
+ * Returns a list of rep_ele structs holding the start,end tuples of repeats;
+ *         NULL on failure.
+ */
+rep_ele *find_STR(char *cons, int len, int lower_only);
+
+/*
+ * Returns an array of STR vs no-STR values.
+ *         0  => non repetitive.
+ *         1+ => repeat with consecutive bit-number for repeat size.
+ *
+ * Eg:  AGGGGAGGAGAAGAC
+ *       1111  1111
+ *         2222222
+ *              444444
+ * =>   011331137754440
+ */
+char *cons_mark_STR(char *cons, int len, int lower_only);
+
+#endif /* _STR_FINDER_H_ */
diff --git a/bcftools/tabix.c b/bcftools/tabix.c
new file mode 100644
index 0000000..639d954
--- /dev/null
+++ b/bcftools/tabix.c
@@ -0,0 +1,131 @@
+/*  tabix.c -- tabix subcommand.
+
+    Copyright (C) 2012 Broad Institute.
+    Copyright (C) 2013, 2016 Genome Research Ltd.
+
+    Author: Heng Li <lh3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.  */
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <unistd.h>
+#include <string.h>
+#include <strings.h>
+#include <htslib/bgzf.h>
+#include <htslib/tbx.h>
+
+int main_tabix(int argc, char *argv[])
+{
+    int c, min_shift = -1, is_force = 0, is_all = 0, detect = 1;
+    tbx_conf_t conf = tbx_conf_gff;
+    while ((c = getopt(argc, argv, "0fap:s:b:e:S:c:m:")) >= 0)
+        if (c == '0') conf.preset |= TBX_UCSC;
+        else if (c == 'f') is_force = 1;
+        else if (c == 'a') is_all = 1;
+        else if (c == 'm') min_shift = atoi(optarg);
+        else if (c == 's') conf.sc = atoi(optarg);
+        else if (c == 'b') conf.bc = atoi(optarg);
+        else if (c == 'e') conf.ec = atoi(optarg);
+        else if (c == 'c') conf.meta_char = *optarg;
+        else if (c == 'S') conf.line_skip = atoi(optarg);
+        else if (c == 'p') {
+            if (strcmp(optarg, "gff") == 0) conf = tbx_conf_gff;
+            else if (strcmp(optarg, "bed") == 0) conf = tbx_conf_bed;
+            else if (strcmp(optarg, "sam") == 0) conf = tbx_conf_sam;
+            else if (strcmp(optarg, "vcf") == 0) conf = tbx_conf_vcf;
+            else {
+                fprintf(stderr, "The type '%s' not recognised\n", optarg);
+                return 1;
+            detect = 0;
+            }
+
+        }
+    if (optind == argc) {
+        fprintf(stderr, "\nUsage: bcftools tabix [options] <in.gz> [reg1 [...]]\n\n");
+        fprintf(stderr, "Options: -p STR    preset: gff, bed, sam or vcf [gff]\n");
+        fprintf(stderr, "         -s INT    column number for sequence names (suppressed by -p) [1]\n");
+        fprintf(stderr, "         -b INT    column number for region start [4]\n");
+        fprintf(stderr, "         -e INT    column number for region end (if no end, set INT to -b) [5]\n");
+        fprintf(stderr, "         -0        specify coordinates are zero-based\n");
+        fprintf(stderr, "         -S INT    skip first INT lines [0]\n");
+        fprintf(stderr, "         -c CHAR   skip lines starting with CHAR [null]\n");
+        fprintf(stderr, "         -a        print all records\n");
+        fprintf(stderr, "         -f        force to overwrite existing index\n");
+        fprintf(stderr, "         -m INT    set the minimal interval size to 1<<INT; 0 for the old tabix index [0]\n");
+        fprintf(stderr, "\n");
+        return 1;
+    }
+    if (is_all) { // read without random access
+        kstring_t s;
+        BGZF *fp;
+        s.l = s.m = 0; s.s = 0;
+        fp = bgzf_open(argv[optind], "r");
+        while (bgzf_getline(fp, '\n', &s) >= 0) puts(s.s);
+        bgzf_close(fp);
+        free(s.s);
+    } else if (optind + 2 > argc) { // create index
+        if ( detect )
+        {
+            // auto-detect file type by file name
+            int l = strlen(argv[optind]);
+            if (l>=7 && strcasecmp(argv[optind]+l-7, ".gff.gz") == 0) conf = tbx_conf_gff;
+            else if (l>=7 && strcasecmp(argv[optind]+l-7, ".bed.gz") == 0) conf = tbx_conf_bed;
+            else if (l>=7 && strcasecmp(argv[optind]+l-7, ".sam.gz") == 0) conf = tbx_conf_sam;
+            else if (l>=7 && strcasecmp(argv[optind]+l-7, ".vcf.gz") == 0) conf = tbx_conf_vcf;
+        }
+
+        if (!is_force) {
+            char *fn;
+            FILE *fp;
+            fn = (char*)malloc(strlen(argv[optind]) + 5);
+            strcat(strcpy(fn, argv[optind]), min_shift <= 0? ".tbi" : ".csi");
+            if ((fp = fopen(fn, "rb")) != 0) {
+                fclose(fp);
+                free(fn);
+                fprintf(stderr, "[E::%s] the index file exists; use option '-f' to overwrite\n", __func__);
+                return 1;
+            }
+            free(fn);
+        }
+        if ( tbx_index_build(argv[optind], min_shift, &conf) )
+        {
+            fprintf(stderr,"tbx_index_build failed: Is the file bgzip-compressed? Was wrong -p [type] option used?\n");
+            return 1;
+        }
+    } else { // read with random access
+        tbx_t *tbx;
+        BGZF *fp;
+        kstring_t s;
+        int i;
+        if ((tbx = tbx_index_load(argv[optind])) == 0) return 1;
+        if ((fp = bgzf_open(argv[optind], "r")) == 0) return 1;
+        s.s = 0; s.l = s.m = 0;
+        for (i = optind + 1; i < argc; ++i) {
+            hts_itr_t *itr;
+            if ((itr = tbx_itr_querys(tbx, argv[i])) == 0) continue;
+            while (tbx_bgzf_itr_next(fp, tbx, itr, &s) >= 0) puts(s.s);
+            tbx_itr_destroy(itr);
+        }
+        free(s.s);
+        bgzf_close(fp);
+        tbx_destroy(tbx);
+    }
+    return 0;
+}
diff --git a/bcftools/tabix.c.pysam.c b/bcftools/tabix.c.pysam.c
new file mode 100644
index 0000000..4e51eaa
--- /dev/null
+++ b/bcftools/tabix.c.pysam.c
@@ -0,0 +1,133 @@
+#include "bcftools.pysam.h"
+
+/*  tabix.c -- tabix subcommand.
+
+    Copyright (C) 2012 Broad Institute.
+    Copyright (C) 2013, 2016 Genome Research Ltd.
+
+    Author: Heng Li <lh3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.  */
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <unistd.h>
+#include <string.h>
+#include <strings.h>
+#include <htslib/bgzf.h>
+#include <htslib/tbx.h>
+
+int main_tabix(int argc, char *argv[])
+{
+    int c, min_shift = -1, is_force = 0, is_all = 0, detect = 1;
+    tbx_conf_t conf = tbx_conf_gff;
+    while ((c = getopt(argc, argv, "0fap:s:b:e:S:c:m:")) >= 0)
+        if (c == '0') conf.preset |= TBX_UCSC;
+        else if (c == 'f') is_force = 1;
+        else if (c == 'a') is_all = 1;
+        else if (c == 'm') min_shift = atoi(optarg);
+        else if (c == 's') conf.sc = atoi(optarg);
+        else if (c == 'b') conf.bc = atoi(optarg);
+        else if (c == 'e') conf.ec = atoi(optarg);
+        else if (c == 'c') conf.meta_char = *optarg;
+        else if (c == 'S') conf.line_skip = atoi(optarg);
+        else if (c == 'p') {
+            if (strcmp(optarg, "gff") == 0) conf = tbx_conf_gff;
+            else if (strcmp(optarg, "bed") == 0) conf = tbx_conf_bed;
+            else if (strcmp(optarg, "sam") == 0) conf = tbx_conf_sam;
+            else if (strcmp(optarg, "vcf") == 0) conf = tbx_conf_vcf;
+            else {
+                fprintf(bcftools_stderr, "The type '%s' not recognised\n", optarg);
+                return 1;
+            detect = 0;
+            }
+
+        }
+    if (optind == argc) {
+        fprintf(bcftools_stderr, "\nUsage: bcftools tabix [options] <in.gz> [reg1 [...]]\n\n");
+        fprintf(bcftools_stderr, "Options: -p STR    preset: gff, bed, sam or vcf [gff]\n");
+        fprintf(bcftools_stderr, "         -s INT    column number for sequence names (suppressed by -p) [1]\n");
+        fprintf(bcftools_stderr, "         -b INT    column number for region start [4]\n");
+        fprintf(bcftools_stderr, "         -e INT    column number for region end (if no end, set INT to -b) [5]\n");
+        fprintf(bcftools_stderr, "         -0        specify coordinates are zero-based\n");
+        fprintf(bcftools_stderr, "         -S INT    skip first INT lines [0]\n");
+        fprintf(bcftools_stderr, "         -c CHAR   skip lines starting with CHAR [null]\n");
+        fprintf(bcftools_stderr, "         -a        print all records\n");
+        fprintf(bcftools_stderr, "         -f        force to overwrite existing index\n");
+        fprintf(bcftools_stderr, "         -m INT    set the minimal interval size to 1<<INT; 0 for the old tabix index [0]\n");
+        fprintf(bcftools_stderr, "\n");
+        return 1;
+    }
+    if (is_all) { // read without random access
+        kstring_t s;
+        BGZF *fp;
+        s.l = s.m = 0; s.s = 0;
+        fp = bgzf_open(argv[optind], "r");
+        while (bgzf_getline(fp, '\n', &s) >= 0) bcftools_puts(s.s);
+        bgzf_close(fp);
+        free(s.s);
+    } else if (optind + 2 > argc) { // create index
+        if ( detect )
+        {
+            // auto-detect file type by file name
+            int l = strlen(argv[optind]);
+            if (l>=7 && strcasecmp(argv[optind]+l-7, ".gff.gz") == 0) conf = tbx_conf_gff;
+            else if (l>=7 && strcasecmp(argv[optind]+l-7, ".bed.gz") == 0) conf = tbx_conf_bed;
+            else if (l>=7 && strcasecmp(argv[optind]+l-7, ".sam.gz") == 0) conf = tbx_conf_sam;
+            else if (l>=7 && strcasecmp(argv[optind]+l-7, ".vcf.gz") == 0) conf = tbx_conf_vcf;
+        }
+
+        if (!is_force) {
+            char *fn;
+            FILE *fp;
+            fn = (char*)malloc(strlen(argv[optind]) + 5);
+            strcat(strcpy(fn, argv[optind]), min_shift <= 0? ".tbi" : ".csi");
+            if ((fp = fopen(fn, "rb")) != 0) {
+                fclose(fp);
+                free(fn);
+                fprintf(bcftools_stderr, "[E::%s] the index file exists; use option '-f' to overwrite\n", __func__);
+                return 1;
+            }
+            free(fn);
+        }
+        if ( tbx_index_build(argv[optind], min_shift, &conf) )
+        {
+            fprintf(bcftools_stderr,"tbx_index_build failed: Is the file bgzip-compressed? Was wrong -p [type] option used?\n");
+            return 1;
+        }
+    } else { // read with random access
+        tbx_t *tbx;
+        BGZF *fp;
+        kstring_t s;
+        int i;
+        if ((tbx = tbx_index_load(argv[optind])) == 0) return 1;
+        if ((fp = bgzf_open(argv[optind], "r")) == 0) return 1;
+        s.s = 0; s.l = s.m = 0;
+        for (i = optind + 1; i < argc; ++i) {
+            hts_itr_t *itr;
+            if ((itr = tbx_itr_querys(tbx, argv[i])) == 0) continue;
+            while (tbx_bgzf_itr_next(fp, tbx, itr, &s) >= 0) bcftools_puts(s.s);
+            tbx_itr_destroy(itr);
+        }
+        free(s.s);
+        bgzf_close(fp);
+        tbx_destroy(tbx);
+    }
+    return 0;
+}
diff --git a/bcftools/tsv2vcf.c b/bcftools/tsv2vcf.c
new file mode 100644
index 0000000..596e75a
--- /dev/null
+++ b/bcftools/tsv2vcf.c
@@ -0,0 +1,135 @@
+/*  tsv2vcf.c -- convert from whitespace-separated fields to VCF
+
+    Copyright (C) 2014-2021 Genome Research Ltd.
+
+    Author: Petr Danecek <pd3@sanger.ac.uk>
+
+    Permission is hereby granted, free of charge, to any person obtaining a copy
+    of this software and associated documentation files (the "Software"), to deal
+    in the Software without restriction, including without limitation the rights
+    to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+    copies of the Software, and to permit persons to whom the Software is
+    furnished to do so, subject to the following conditions:
+    
+    The above copyright notice and this permission notice shall be included in
+    all copies or substantial portions of the Software.
+    
+    THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+    IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+    FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+    AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+    LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+    OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+    THE SOFTWARE.
+*/
+
+#include <ctype.h>
+#include <strings.h>
+#include "tsv2vcf.h"
+
+tsv_t *tsv_init(const char *str)
+{
+    tsv_t *tsv = (tsv_t *) calloc(1,sizeof(tsv_t));
+    kstring_t tmp = {0,0,0};
+    const char *ss = str, *se = ss;
+    tsv->ncols = 0;
+    while ( *ss )
+    {
+        if ( *se && *se!=',' ) { se++; continue; }
+        tsv->ncols++;
+        tsv->cols = (tsv_col_t*) realloc(tsv->cols,sizeof(tsv_col_t)*tsv->ncols);
+        tsv->cols[tsv->ncols-1].name   = NULL;
+        tsv->cols[tsv->ncols-1].setter = NULL;
+        tmp.l = 0;
+        kputsn(ss, se-ss, &tmp);
+        if ( strcasecmp("-",tmp.s) )
+            tsv->cols[tsv->ncols-1].name = strdup(tmp.s);
+        if ( !*se ) break;
+        ss = ++se;
+    }
+    free(tmp.s);
+    return tsv;
+}
+
+void tsv_destroy(tsv_t *tsv)
+{
+    int i;
+    for (i=0; i<tsv->ncols; i++) free(tsv->cols[i].name);
+    free(tsv->cols);
+    free(tsv);
+}
+
+int tsv_register(tsv_t *tsv, const char *id, tsv_setter_t setter, void *usr)
+{
+    int i;
+    for (i=0; i<tsv->ncols; i++)
+    {
+        if ( !tsv->cols[i].name || strcasecmp(tsv->cols[i].name,id) ) continue;
+        tsv->cols[i].setter = setter;
+        tsv->cols[i].usr    = usr;
+        return 0;
+    }
+    return -1;
+}
+
+int tsv_parse(tsv_t *tsv, bcf1_t *rec, char *str)
+{
+    int status = 0;
+    tsv->icol = 0;
+    tsv->ss = tsv->se = str;
+    while ( *tsv->ss && tsv->icol < tsv->ncols )
+    {
+        while ( *tsv->se && !isspace(*tsv->se) ) tsv->se++;
+        if ( tsv->cols[tsv->icol].setter )
+        {
+            int ret = tsv->cols[tsv->icol].setter(tsv,rec,tsv->cols[tsv->icol].usr);
+            if ( ret<0 ) return -1;
+            status++;
+        }
+        while ( *tsv->se && isspace(*tsv->se) ) tsv->se++;
+        tsv->ss = tsv->se;
+        tsv->icol++;
+    }
+    return status ? 0 : -1;
+}
+
+int tsv_setter_chrom(tsv_t *tsv, bcf1_t *rec, void *usr)
+{
+    char tmp = *tsv->se;
+    *tsv->se = 0;
+    rec->rid = bcf_hdr_name2id((bcf_hdr_t*)usr, tsv->ss);
+    *tsv->se = tmp;
+    return rec->rid==-1 ? -1 : 0;
+}
+
+int tsv_setter_pos(tsv_t *tsv, bcf1_t *rec, void *usr)
+{
+    char *endptr;
+    rec->pos = strtol(tsv->ss, &endptr, 10) - 1;
+    if ( tsv->ss==endptr ) return -1;
+    return 0;
+}
+
+int tsv_setter_id(tsv_t *tsv, bcf1_t *rec, void *usr)
+{
+    char tmp = *tsv->se;
+    *tsv->se = 0;
+    bcf_update_id((bcf_hdr_t*)usr, rec, tsv->ss);
+    *tsv->se = tmp;
+    return 0;
+}
+
+int tsv_setter_ref_alt(tsv_t *tsv, bcf1_t *rec, void *usr)
+{
+    bcf_hdr_t *hdr = (bcf_hdr_t*)usr;
+    char *sb = tsv->ss;
+    while ( *sb && !isspace(*sb) ) sb++;
+    if ( !*sb ) return -1;
+    char tmp = *sb;
+    *sb = ',';
+    bcf_update_alleles_str(hdr, rec, tsv->ss);
+    *sb = tmp;
+    return 0;
+}
+
+
diff --git a/bcftools/tsv2vcf.c.pysam.c b/bcftools/tsv2vcf.c.pysam.c
new file mode 100644
index 0000000..8c62157
--- /dev/null
+++ b/bcftools/tsv2vcf.c.pysam.c
@@ -0,0 +1,137 @@
+#include "bcftools.pysam.h"
+
+/*  tsv2vcf.c -- convert from whitespace-separated fields to VCF
+
+    Copyright (C) 2014-2021 Genome Research Ltd.
+
+    Author: Petr Danecek <pd3@sanger.ac.uk>
+
+    Permission is hereby granted, free of charge, to any person obtaining a copy
+    of this software and associated documentation files (the "Software"), to deal
+    in the Software without restriction, including without limitation the rights
+    to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+    copies of the Software, and to permit persons to whom the Software is
+    furnished to do so, subject to the following conditions:
+    
+    The above copyright notice and this permission notice shall be included in
+    all copies or substantial portions of the Software.
+    
+    THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+    IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+    FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+    AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+    LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+    OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+    THE SOFTWARE.
+*/
+
+#include <ctype.h>
+#include <strings.h>
+#include "tsv2vcf.h"
+
+tsv_t *tsv_init(const char *str)
+{
+    tsv_t *tsv = (tsv_t *) calloc(1,sizeof(tsv_t));
+    kstring_t tmp = {0,0,0};
+    const char *ss = str, *se = ss;
+    tsv->ncols = 0;
+    while ( *ss )
+    {
+        if ( *se && *se!=',' ) { se++; continue; }
+        tsv->ncols++;
+        tsv->cols = (tsv_col_t*) realloc(tsv->cols,sizeof(tsv_col_t)*tsv->ncols);
+        tsv->cols[tsv->ncols-1].name   = NULL;
+        tsv->cols[tsv->ncols-1].setter = NULL;
+        tmp.l = 0;
+        kputsn(ss, se-ss, &tmp);
+        if ( strcasecmp("-",tmp.s) )
+            tsv->cols[tsv->ncols-1].name = strdup(tmp.s);
+        if ( !*se ) break;
+        ss = ++se;
+    }
+    free(tmp.s);
+    return tsv;
+}
+
+void tsv_destroy(tsv_t *tsv)
+{
+    int i;
+    for (i=0; i<tsv->ncols; i++) free(tsv->cols[i].name);
+    free(tsv->cols);
+    free(tsv);
+}
+
+int tsv_register(tsv_t *tsv, const char *id, tsv_setter_t setter, void *usr)
+{
+    int i;
+    for (i=0; i<tsv->ncols; i++)
+    {
+        if ( !tsv->cols[i].name || strcasecmp(tsv->cols[i].name,id) ) continue;
+        tsv->cols[i].setter = setter;
+        tsv->cols[i].usr    = usr;
+        return 0;
+    }
+    return -1;
+}
+
+int tsv_parse(tsv_t *tsv, bcf1_t *rec, char *str)
+{
+    int status = 0;
+    tsv->icol = 0;
+    tsv->ss = tsv->se = str;
+    while ( *tsv->ss && tsv->icol < tsv->ncols )
+    {
+        while ( *tsv->se && !isspace(*tsv->se) ) tsv->se++;
+        if ( tsv->cols[tsv->icol].setter )
+        {
+            int ret = tsv->cols[tsv->icol].setter(tsv,rec,tsv->cols[tsv->icol].usr);
+            if ( ret<0 ) return -1;
+            status++;
+        }
+        while ( *tsv->se && isspace(*tsv->se) ) tsv->se++;
+        tsv->ss = tsv->se;
+        tsv->icol++;
+    }
+    return status ? 0 : -1;
+}
+
+int tsv_setter_chrom(tsv_t *tsv, bcf1_t *rec, void *usr)
+{
+    char tmp = *tsv->se;
+    *tsv->se = 0;
+    rec->rid = bcf_hdr_name2id((bcf_hdr_t*)usr, tsv->ss);
+    *tsv->se = tmp;
+    return rec->rid==-1 ? -1 : 0;
+}
+
+int tsv_setter_pos(tsv_t *tsv, bcf1_t *rec, void *usr)
+{
+    char *endptr;
+    rec->pos = strtol(tsv->ss, &endptr, 10) - 1;
+    if ( tsv->ss==endptr ) return -1;
+    return 0;
+}
+
+int tsv_setter_id(tsv_t *tsv, bcf1_t *rec, void *usr)
+{
+    char tmp = *tsv->se;
+    *tsv->se = 0;
+    bcf_update_id((bcf_hdr_t*)usr, rec, tsv->ss);
+    *tsv->se = tmp;
+    return 0;
+}
+
+int tsv_setter_ref_alt(tsv_t *tsv, bcf1_t *rec, void *usr)
+{
+    bcf_hdr_t *hdr = (bcf_hdr_t*)usr;
+    char *sb = tsv->ss;
+    while ( *sb && !isspace(*sb) ) sb++;
+    if ( !*sb ) return -1;
+    char tmp = *sb;
+    *sb = ',';
+    bcf_update_alleles_str(hdr, rec, tsv->ss);
+    *sb = tmp;
+    return 0;
+}
+
+
diff --git a/bcftools/tsv2vcf.h b/bcftools/tsv2vcf.h
new file mode 100644
index 0000000..68757d4
--- /dev/null
+++ b/bcftools/tsv2vcf.h
@@ -0,0 +1,86 @@
+/*  tsv2vcf.h -- convert from whitespace-separated fields to VCF
+
+    Copyright (C) 2014-2021 Genome Research Ltd.
+
+    Author: Petr Danecek <pd3@sanger.ac.uk>
+
+    Permission is hereby granted, free of charge, to any person obtaining a copy
+    of this software and associated documentation files (the "Software"), to deal
+    in the Software without restriction, including without limitation the rights
+    to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+    copies of the Software, and to permit persons to whom the Software is
+    furnished to do so, subject to the following conditions:
+    
+    The above copyright notice and this permission notice shall be included in
+    all copies or substantial portions of the Software.
+    
+    THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+    IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+    FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+    AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+    LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+    OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+    THE SOFTWARE.
+*/
+
+#ifndef __TSV2VCF_H__
+#define __TSV2VCF_H__
+
+#include <htslib/vcf.h>
+
+typedef struct _tsv_t tsv_t;
+typedef int (*tsv_setter_t)(tsv_t *, bcf1_t *, void *);
+
+typedef struct
+{
+    char *name;
+    tsv_setter_t setter;
+    void *usr;
+}
+tsv_col_t;
+
+struct _tsv_t
+{
+    int ncols, icol;
+    tsv_col_t *cols;
+    char *se, *ss;
+};
+
+tsv_t *tsv_init(const char *str);
+void tsv_destroy(tsv_t *tsv);
+int tsv_register(tsv_t *tsv, const char *id, tsv_setter_t setter, void *usr);
+
+/**
+ *  tsv_parse() - parse tsv line and fill VCF record
+ *  Returns 0 on success or -1 on parse error
+ */
+int tsv_parse(tsv_t *tsv, bcf1_t *rec, char *str);
+
+/**
+ *  tstv_next() - position ss,se to next field; first pass with ss=se=str
+ *  Returns 0 on success, or -1 if no more fields
+ */
+static inline int tsv_next(tsv_t *tsv)
+{
+    if ( !*tsv->se ) return -1;
+    if ( tsv->ss==tsv->se )
+    {
+        while ( *tsv->se && !isspace(*tsv->se) ) tsv->se++;
+        return 0;
+    }
+    while ( *tsv->se && isspace(*tsv->se) ) tsv->se++;
+    tsv->ss = tsv->se;
+    while ( *tsv->se && !isspace(*tsv->se) ) tsv->se++;
+    return 0;
+}
+
+/**
+ *  The setters return 0 on success or negative value if the line is to be skipped.
+ */
+int tsv_setter_chrom(tsv_t *tsv, bcf1_t *rec, void *usr);
+int tsv_setter_pos(tsv_t *tsv, bcf1_t *rec, void *usr);
+int tsv_setter_id(tsv_t *tsv, bcf1_t *rec, void *usr);
+int tsv_setter_ref_alt(tsv_t *tsv, bcf1_t *rec, void *usr);     // usr must point to bcf_hdr_t 
+
+#endif
+
diff --git a/bcftools/utlist.h b/bcftools/utlist.h
new file mode 100644
index 0000000..28cf8a3
--- /dev/null
+++ b/bcftools/utlist.h
@@ -0,0 +1,761 @@
+/*
+Copyright (c) 2007-2014, Troy D. Hanson   http://troydhanson.github.com/uthash/
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+    * Redistributions of source code must retain the above copyright
+      notice, this list of conditions and the following disclaimer.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS
+IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
+TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER
+OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+*/
+
+#ifndef UTLIST_H
+#define UTLIST_H
+
+#define UTLIST_VERSION 1.9.9
+
+#include <assert.h>
+
+/* 
+ * This file contains macros to manipulate singly and doubly-linked lists.
+ *
+ * 1. LL_ macros:  singly-linked lists.
+ * 2. DL_ macros:  doubly-linked lists.
+ * 3. CDL_ macros: circular doubly-linked lists.
+ *
+ * To use singly-linked lists, your structure must have a "next" pointer.
+ * To use doubly-linked lists, your structure must "prev" and "next" pointers.
+ * Either way, the pointer to the head of the list must be initialized to NULL.
+ * 
+ * ----------------.EXAMPLE -------------------------
+ * struct item {
+ *      int id;
+ *      struct item *prev, *next;
+ * }
+ *
+ * struct item *list = NULL:
+ *
+ * int main() {
+ *      struct item *item;
+ *      ... allocate and populate item ...
+ *      DL_APPEND(list, item);
+ * }
+ * --------------------------------------------------
+ *
+ * For doubly-linked lists, the append and delete macros are O(1)
+ * For singly-linked lists, append and delete are O(n) but prepend is O(1)
+ * The sort macro is O(n log(n)) for all types of single/double/circular lists.
+ */
+
+/* These macros use decltype or the earlier __typeof GNU extension.
+   As decltype is only available in newer compilers (VS2010 or gcc 4.3+
+   when compiling c++ code), this code uses whatever method is needed
+   or, for VS2008 where neither is available, uses casting workarounds. */
+#ifdef _MSC_VER            /* MS compiler */
+#if _MSC_VER >= 1600 && defined(__cplusplus)  /* VS2010 or newer in C++ mode */
+#define LDECLTYPE(x) decltype(x)
+#else                     /* VS2008 or older (or VS2010 in C mode) */
+#define NO_DECLTYPE
+#define LDECLTYPE(x) char*
+#endif
+#elif defined(__ICCARM__)
+#define NO_DECLTYPE
+#define LDECLTYPE(x) char*
+#else                      /* GNU, Sun and other compilers */
+#define LDECLTYPE(x) __typeof(x)
+#endif
+
+/* for VS2008 we use some workarounds to get around the lack of decltype,
+ * namely, we always reassign our tmp variable to the list head if we need
+ * to dereference its prev/next pointers, and save/restore the real head.*/
+#ifdef NO_DECLTYPE
+#define _SV(elt,list) _tmp = (char*)(list); {char **_alias = (char**)&(list); *_alias = (elt); }
+#define _NEXT(elt,list,next) ((char*)((list)->next))
+#define _NEXTASGN(elt,list,to,next) { char **_alias = (char**)&((list)->next); *_alias=(char*)(to); }
+/* #define _PREV(elt,list,prev) ((char*)((list)->prev)) */
+#define _PREVASGN(elt,list,to,prev) { char **_alias = (char**)&((list)->prev); *_alias=(char*)(to); }
+#define _RS(list) { char **_alias = (char**)&(list); *_alias=_tmp; }
+#define _CASTASGN(a,b) { char **_alias = (char**)&(a); *_alias=(char*)(b); }
+#else 
+#define _SV(elt,list)
+#define _NEXT(elt,list,next) ((elt)->next)
+#define _NEXTASGN(elt,list,to,next) ((elt)->next)=(to)
+/* #define _PREV(elt,list,prev) ((elt)->prev) */
+#define _PREVASGN(elt,list,to,prev) ((elt)->prev)=(to)
+#define _RS(list)
+#define _CASTASGN(a,b) (a)=(b)
+#endif
+
+/******************************************************************************
+ * The sort macro is an adaptation of Simon Tatham's O(n log(n)) mergesort    *
+ * Unwieldy variable names used here to avoid shadowing passed-in variables.  *
+ *****************************************************************************/
+#define LL_SORT(list, cmp)                                                                     \
+    LL_SORT2(list, cmp, next)
+
+#define LL_SORT2(list, cmp, next)                                                              \
+do {                                                                                           \
+  LDECLTYPE(list) _ls_p;                                                                       \
+  LDECLTYPE(list) _ls_q;                                                                       \
+  LDECLTYPE(list) _ls_e;                                                                       \
+  LDECLTYPE(list) _ls_tail;                                                                    \
+  int _ls_insize, _ls_nmerges, _ls_psize, _ls_qsize, _ls_i, _ls_looping;                       \
+  if (list) {                                                                                  \
+    _ls_insize = 1;                                                                            \
+    _ls_looping = 1;                                                                           \
+    while (_ls_looping) {                                                                      \
+      _CASTASGN(_ls_p,list);                                                                   \
+      list = NULL;                                                                             \
+      _ls_tail = NULL;                                                                         \
+      _ls_nmerges = 0;                                                                         \
+      while (_ls_p) {                                                                          \
+        _ls_nmerges++;                                                                         \
+        _ls_q = _ls_p;                                                                         \
+        _ls_psize = 0;                                                                         \
+        for (_ls_i = 0; _ls_i < _ls_insize; _ls_i++) {                                         \
+          _ls_psize++;                                                                         \
+          _SV(_ls_q,list); _ls_q = _NEXT(_ls_q,list,next); _RS(list);                          \
+          if (!_ls_q) break;                                                                   \
+        }                                                                                      \
+        _ls_qsize = _ls_insize;                                                                \
+        while (_ls_psize > 0 || (_ls_qsize > 0 && _ls_q)) {                                    \
+          if (_ls_psize == 0) {                                                                \
+            _ls_e = _ls_q; _SV(_ls_q,list); _ls_q =                                            \
+              _NEXT(_ls_q,list,next); _RS(list); _ls_qsize--;                                  \
+          } else if (_ls_qsize == 0 || !_ls_q) {                                               \
+            _ls_e = _ls_p; _SV(_ls_p,list); _ls_p =                                            \
+              _NEXT(_ls_p,list,next); _RS(list); _ls_psize--;                                  \
+          } else if (cmp(_ls_p,_ls_q) <= 0) {                                                  \
+            _ls_e = _ls_p; _SV(_ls_p,list); _ls_p =                                            \
+              _NEXT(_ls_p,list,next); _RS(list); _ls_psize--;                                  \
+          } else {                                                                             \
+            _ls_e = _ls_q; _SV(_ls_q,list); _ls_q =                                            \
+              _NEXT(_ls_q,list,next); _RS(list); _ls_qsize--;                                  \
+          }                                                                                    \
+          if (_ls_tail) {                                                                      \
+            _SV(_ls_tail,list); _NEXTASGN(_ls_tail,list,_ls_e,next); _RS(list);                \
+          } else {                                                                             \
+            _CASTASGN(list,_ls_e);                                                             \
+          }                                                                                    \
+          _ls_tail = _ls_e;                                                                    \
+        }                                                                                      \
+        _ls_p = _ls_q;                                                                         \
+      }                                                                                        \
+      if (_ls_tail) {                                                                          \
+        _SV(_ls_tail,list); _NEXTASGN(_ls_tail,list,NULL,next); _RS(list);                     \
+      }                                                                                        \
+      if (_ls_nmerges <= 1) {                                                                  \
+        _ls_looping=0;                                                                         \
+      }                                                                                        \
+      _ls_insize *= 2;                                                                         \
+    }                                                                                          \
+  }                                                                                            \
+} while (0)
+
+
+#define DL_SORT(list, cmp)                                                                     \
+    DL_SORT2(list, cmp, prev, next)
+
+#define DL_SORT2(list, cmp, prev, next)                                                        \
+do {                                                                                           \
+  LDECLTYPE(list) _ls_p;                                                                       \
+  LDECLTYPE(list) _ls_q;                                                                       \
+  LDECLTYPE(list) _ls_e;                                                                       \
+  LDECLTYPE(list) _ls_tail;                                                                    \
+  int _ls_insize, _ls_nmerges, _ls_psize, _ls_qsize, _ls_i, _ls_looping;                       \
+  if (list) {                                                                                  \
+    _ls_insize = 1;                                                                            \
+    _ls_looping = 1;                                                                           \
+    while (_ls_looping) {                                                                      \
+      _CASTASGN(_ls_p,list);                                                                   \
+      list = NULL;                                                                             \
+      _ls_tail = NULL;                                                                         \
+      _ls_nmerges = 0;                                                                         \
+      while (_ls_p) {                                                                          \
+        _ls_nmerges++;                                                                         \
+        _ls_q = _ls_p;                                                                         \
+        _ls_psize = 0;                                                                         \
+        for (_ls_i = 0; _ls_i < _ls_insize; _ls_i++) {                                         \
+          _ls_psize++;                                                                         \
+          _SV(_ls_q,list); _ls_q = _NEXT(_ls_q,list,next); _RS(list);                          \
+          if (!_ls_q) break;                                                                   \
+        }                                                                                      \
+        _ls_qsize = _ls_insize;                                                                \
+        while (_ls_psize > 0 || (_ls_qsize > 0 && _ls_q)) {                                    \
+          if (_ls_psize == 0) {                                                                \
+            _ls_e = _ls_q; _SV(_ls_q,list); _ls_q =                                            \
+              _NEXT(_ls_q,list,next); _RS(list); _ls_qsize--;                                  \
+          } else if (_ls_qsize == 0 || !_ls_q) {                                               \
+            _ls_e = _ls_p; _SV(_ls_p,list); _ls_p =                                            \
+              _NEXT(_ls_p,list,next); _RS(list); _ls_psize--;                                  \
+          } else if (cmp(_ls_p,_ls_q) <= 0) {                                                  \
+            _ls_e = _ls_p; _SV(_ls_p,list); _ls_p =                                            \
+              _NEXT(_ls_p,list,next); _RS(list); _ls_psize--;                                  \
+          } else {                                                                             \
+            _ls_e = _ls_q; _SV(_ls_q,list); _ls_q =                                            \
+              _NEXT(_ls_q,list,next); _RS(list); _ls_qsize--;                                  \
+          }                                                                                    \
+          if (_ls_tail) {                                                                      \
+            _SV(_ls_tail,list); _NEXTASGN(_ls_tail,list,_ls_e,next); _RS(list);                \
+          } else {                                                                             \
+            _CASTASGN(list,_ls_e);                                                             \
+          }                                                                                    \
+          _SV(_ls_e,list); _PREVASGN(_ls_e,list,_ls_tail,prev); _RS(list);                     \
+          _ls_tail = _ls_e;                                                                    \
+        }                                                                                      \
+        _ls_p = _ls_q;                                                                         \
+      }                                                                                        \
+      _CASTASGN(list->prev, _ls_tail);                                                         \
+      _SV(_ls_tail,list); _NEXTASGN(_ls_tail,list,NULL,next); _RS(list);                       \
+      if (_ls_nmerges <= 1) {                                                                  \
+        _ls_looping=0;                                                                         \
+      }                                                                                        \
+      _ls_insize *= 2;                                                                         \
+    }                                                                                          \
+  }                                                                                            \
+} while (0)
+
+
+#define DL_HEAD(list) (list)
+#define DL_TAIL(list) ((list) ? (list)->prev : NULL)
+
+#define CDL_SORT(list, cmp)                                                                    \
+    CDL_SORT2(list, cmp, prev, next)
+
+#define CDL_SORT2(list, cmp, prev, next)                                                       \
+do {                                                                                           \
+  LDECLTYPE(list) _ls_p;                                                                       \
+  LDECLTYPE(list) _ls_q;                                                                       \
+  LDECLTYPE(list) _ls_e;                                                                       \
+  LDECLTYPE(list) _ls_tail;                                                                    \
+  LDECLTYPE(list) _ls_oldhead;                                                                 \
+  LDECLTYPE(list) _tmp;                                                                        \
+  int _ls_insize, _ls_nmerges, _ls_psize, _ls_qsize, _ls_i, _ls_looping;                       \
+  if (list) {                                                                                  \
+    _ls_insize = 1;                                                                            \
+    _ls_looping = 1;                                                                           \
+    while (_ls_looping) {                                                                      \
+      _CASTASGN(_ls_p,list);                                                                   \
+      _CASTASGN(_ls_oldhead,list);                                                             \
+      list = NULL;                                                                             \
+      _ls_tail = NULL;                                                                         \
+      _ls_nmerges = 0;                                                                         \
+      while (_ls_p) {                                                                          \
+        _ls_nmerges++;                                                                         \
+        _ls_q = _ls_p;                                                                         \
+        _ls_psize = 0;                                                                         \
+        for (_ls_i = 0; _ls_i < _ls_insize; _ls_i++) {                                         \
+          _ls_psize++;                                                                         \
+          _SV(_ls_q,list);                                                                     \
+          if (_NEXT(_ls_q,list,next) == _ls_oldhead) {                                         \
+            _ls_q = NULL;                                                                      \
+          } else {                                                                             \
+            _ls_q = _NEXT(_ls_q,list,next);                                                    \
+          }                                                                                    \
+          _RS(list);                                                                           \
+          if (!_ls_q) break;                                                                   \
+        }                                                                                      \
+        _ls_qsize = _ls_insize;                                                                \
+        while (_ls_psize > 0 || (_ls_qsize > 0 && _ls_q)) {                                    \
+          if (_ls_psize == 0) {                                                                \
+            _ls_e = _ls_q; _SV(_ls_q,list); _ls_q =                                            \
+              _NEXT(_ls_q,list,next); _RS(list); _ls_qsize--;                                  \
+            if (_ls_q == _ls_oldhead) { _ls_q = NULL; }                                        \
+          } else if (_ls_qsize == 0 || !_ls_q) {                                               \
+            _ls_e = _ls_p; _SV(_ls_p,list); _ls_p =                                            \
+              _NEXT(_ls_p,list,next); _RS(list); _ls_psize--;                                  \
+            if (_ls_p == _ls_oldhead) { _ls_p = NULL; }                                        \
+          } else if (cmp(_ls_p,_ls_q) <= 0) {                                                  \
+            _ls_e = _ls_p; _SV(_ls_p,list); _ls_p =                                            \
+              _NEXT(_ls_p,list,next); _RS(list); _ls_psize--;                                  \
+            if (_ls_p == _ls_oldhead) { _ls_p = NULL; }                                        \
+          } else {                                                                             \
+            _ls_e = _ls_q; _SV(_ls_q,list); _ls_q =                                            \
+              _NEXT(_ls_q,list,next); _RS(list); _ls_qsize--;                                  \
+            if (_ls_q == _ls_oldhead) { _ls_q = NULL; }                                        \
+          }                                                                                    \
+          if (_ls_tail) {                                                                      \
+            _SV(_ls_tail,list); _NEXTASGN(_ls_tail,list,_ls_e,next); _RS(list);                \
+          } else {                                                                             \
+            _CASTASGN(list,_ls_e);                                                             \
+          }                                                                                    \
+          _SV(_ls_e,list); _PREVASGN(_ls_e,list,_ls_tail,prev); _RS(list);                     \
+          _ls_tail = _ls_e;                                                                    \
+        }                                                                                      \
+        _ls_p = _ls_q;                                                                         \
+      }                                                                                        \
+      _CASTASGN(list->prev,_ls_tail);                                                          \
+      _CASTASGN(_tmp,list);                                                                    \
+      _SV(_ls_tail,list); _NEXTASGN(_ls_tail,list,_tmp,next); _RS(list);                       \
+      if (_ls_nmerges <= 1) {                                                                  \
+        _ls_looping=0;                                                                         \
+      }                                                                                        \
+      _ls_insize *= 2;                                                                         \
+    }                                                                                          \
+  }                                                                                            \
+} while (0)
+
+/******************************************************************************
+ * singly linked list macros (non-circular)                                   *
+ *****************************************************************************/
+#define LL_PREPEND(head,add)                                                                   \
+    LL_PREPEND2(head,add,next)
+
+#define LL_PREPEND2(head,add,next)                                                             \
+do {                                                                                           \
+  (add)->next = head;                                                                          \
+  head = add;                                                                                  \
+} while (0)
+
+#define LL_CONCAT(head1,head2)                                                                 \
+    LL_CONCAT2(head1,head2,next)
+
+#define LL_CONCAT2(head1,head2,next)                                                           \
+do {                                                                                           \
+  LDECLTYPE(head1) _tmp;                                                                       \
+  if (head1) {                                                                                 \
+    _tmp = head1;                                                                              \
+    while (_tmp->next) { _tmp = _tmp->next; }                                                  \
+    _tmp->next=(head2);                                                                        \
+  } else {                                                                                     \
+    (head1)=(head2);                                                                           \
+  }                                                                                            \
+} while (0)
+
+#define LL_APPEND(head,add)                                                                    \
+    LL_APPEND2(head,add,next)
+
+#define LL_APPEND2(head,add,next)                                                              \
+do {                                                                                           \
+  LDECLTYPE(head) _tmp;                                                                        \
+  (add)->next=NULL;                                                                            \
+  if (head) {                                                                                  \
+    _tmp = head;                                                                               \
+    while (_tmp->next) { _tmp = _tmp->next; }                                                  \
+    _tmp->next=(add);                                                                          \
+  } else {                                                                                     \
+    (head)=(add);                                                                              \
+  }                                                                                            \
+} while (0)
+
+#define LL_DELETE(head,del)                                                                    \
+    LL_DELETE2(head,del,next)
+
+#define LL_DELETE2(head,del,next)                                                              \
+do {                                                                                           \
+  LDECLTYPE(head) _tmp;                                                                        \
+  if ((head) == (del)) {                                                                       \
+    (head)=(head)->next;                                                                       \
+  } else {                                                                                     \
+    _tmp = head;                                                                               \
+    while (_tmp->next && (_tmp->next != (del))) {                                              \
+      _tmp = _tmp->next;                                                                       \
+    }                                                                                          \
+    if (_tmp->next) {                                                                          \
+      _tmp->next = ((del)->next);                                                              \
+    }                                                                                          \
+  }                                                                                            \
+} while (0)
+
+/* Here are VS2008 replacements for LL_APPEND and LL_DELETE */
+#define LL_APPEND_VS2008(head,add)                                                             \
+    LL_APPEND2_VS2008(head,add,next)
+
+#define LL_APPEND2_VS2008(head,add,next)                                                       \
+do {                                                                                           \
+  if (head) {                                                                                  \
+    (add)->next = head;     /* use add->next as a temp variable */                             \
+    while ((add)->next->next) { (add)->next = (add)->next->next; }                             \
+    (add)->next->next=(add);                                                                   \
+  } else {                                                                                     \
+    (head)=(add);                                                                              \
+  }                                                                                            \
+  (add)->next=NULL;                                                                            \
+} while (0)
+
+#define LL_DELETE_VS2008(head,del)                                                             \
+    LL_DELETE2_VS2008(head,del,next)
+
+#define LL_DELETE2_VS2008(head,del,next)                                                       \
+do {                                                                                           \
+  if ((head) == (del)) {                                                                       \
+    (head)=(head)->next;                                                                       \
+  } else {                                                                                     \
+    char *_tmp = (char*)(head);                                                                \
+    while ((head)->next && ((head)->next != (del))) {                                          \
+      head = (head)->next;                                                                     \
+    }                                                                                          \
+    if ((head)->next) {                                                                        \
+      (head)->next = ((del)->next);                                                            \
+    }                                                                                          \
+    {                                                                                          \
+      char **_head_alias = (char**)&(head);                                                    \
+      *_head_alias = _tmp;                                                                     \
+    }                                                                                          \
+  }                                                                                            \
+} while (0)
+#ifdef NO_DECLTYPE
+#undef LL_APPEND
+#define LL_APPEND LL_APPEND_VS2008
+#undef LL_DELETE
+#define LL_DELETE LL_DELETE_VS2008
+#undef LL_DELETE2
+#define LL_DELETE2 LL_DELETE2_VS2008
+#undef LL_APPEND2
+#define LL_APPEND2 LL_APPEND2_VS2008
+#undef LL_CONCAT /* no LL_CONCAT_VS2008 */
+#undef DL_CONCAT /* no DL_CONCAT_VS2008 */
+#endif
+/* end VS2008 replacements */
+
+#define LL_COUNT(head,el,counter)                                                              \
+    LL_COUNT2(head,el,counter,next)                                                            \
+
+#define LL_COUNT2(head,el,counter,next)                                                        \
+{                                                                                              \
+    counter = 0;                                                                               \
+    LL_FOREACH2(head,el,next){ ++counter; }                                                    \
+}
+
+#define LL_FOREACH(head,el)                                                                    \
+    LL_FOREACH2(head,el,next)
+
+#define LL_FOREACH2(head,el,next)                                                              \
+    for(el=head;el;el=(el)->next)
+
+#define LL_FOREACH_SAFE(head,el,tmp)                                                           \
+    LL_FOREACH_SAFE2(head,el,tmp,next)
+
+#define LL_FOREACH_SAFE2(head,el,tmp,next)                                                     \
+  for((el)=(head);(el) && (tmp = (el)->next, 1); (el) = tmp)
+
+#define LL_SEARCH_SCALAR(head,out,field,val)                                                   \
+    LL_SEARCH_SCALAR2(head,out,field,val,next)
+
+#define LL_SEARCH_SCALAR2(head,out,field,val,next)                                             \
+do {                                                                                           \
+    LL_FOREACH2(head,out,next) {                                                               \
+      if ((out)->field == (val)) break;                                                        \
+    }                                                                                          \
+} while(0) 
+
+#define LL_SEARCH(head,out,elt,cmp)                                                            \
+    LL_SEARCH2(head,out,elt,cmp,next)
+
+#define LL_SEARCH2(head,out,elt,cmp,next)                                                      \
+do {                                                                                           \
+    LL_FOREACH2(head,out,next) {                                                               \
+      if ((cmp(out,elt))==0) break;                                                            \
+    }                                                                                          \
+} while(0) 
+
+#define LL_REPLACE_ELEM(head, el, add)                                                         \
+do {                                                                                           \
+ LDECLTYPE(head) _tmp;                                                                         \
+ assert(head != NULL);                                                                         \
+ assert(el != NULL);                                                                           \
+ assert(add != NULL);                                                                          \
+ (add)->next = (el)->next;                                                                     \
+ if ((head) == (el)) {                                                                         \
+  (head) = (add);                                                                              \
+ } else {                                                                                      \
+  _tmp = head;                                                                                 \
+  while (_tmp->next && (_tmp->next != (el))) {                                                 \
+   _tmp = _tmp->next;                                                                          \
+  }                                                                                            \
+  if (_tmp->next) {                                                                            \
+    _tmp->next = (add);                                                                        \
+  }                                                                                            \
+ }                                                                                             \
+} while (0)
+
+#define LL_PREPEND_ELEM(head, el, add)                                                         \
+do {                                                                                           \
+ LDECLTYPE(head) _tmp;                                                                         \
+ assert(head != NULL);                                                                         \
+ assert(el != NULL);                                                                           \
+ assert(add != NULL);                                                                          \
+ (add)->next = (el);                                                                           \
+ if ((head) == (el)) {                                                                         \
+  (head) = (add);                                                                              \
+ } else {                                                                                      \
+  _tmp = head;                                                                                 \
+  while (_tmp->next && (_tmp->next != (el))) {                                                 \
+   _tmp = _tmp->next;                                                                          \
+  }                                                                                            \
+  if (_tmp->next) {                                                                            \
+    _tmp->next = (add);                                                                        \
+  }                                                                                            \
+ }                                                                                             \
+} while (0)                                                                                    \
+
+
+/******************************************************************************
+ * doubly linked list macros (non-circular)                                   *
+ *****************************************************************************/
+#define DL_PREPEND(head,add)                                                                   \
+    DL_PREPEND2(head,add,prev,next)
+
+#define DL_PREPEND2(head,add,prev,next)                                                        \
+do {                                                                                           \
+ (add)->next = head;                                                                           \
+ if (head) {                                                                                   \
+   (add)->prev = (head)->prev;                                                                 \
+   (head)->prev = (add);                                                                       \
+ } else {                                                                                      \
+   (add)->prev = (add);                                                                        \
+ }                                                                                             \
+ (head) = (add);                                                                               \
+} while (0)
+
+#define DL_APPEND(head,add)                                                                    \
+    DL_APPEND2(head,add,prev,next)
+
+#define DL_APPEND2(head,add,prev,next)                                                         \
+do {                                                                                           \
+  if (head) {                                                                                  \
+      (add)->prev = (head)->prev;                                                              \
+      (head)->prev->next = (add);                                                              \
+      (head)->prev = (add);                                                                    \
+      (add)->next = NULL;                                                                      \
+  } else {                                                                                     \
+      (head)=(add);                                                                            \
+      (head)->prev = (head);                                                                   \
+      (head)->next = NULL;                                                                     \
+  }                                                                                            \
+} while (0) 
+
+#define DL_CONCAT(head1,head2)                                                                 \
+    DL_CONCAT2(head1,head2,prev,next)
+
+#define DL_CONCAT2(head1,head2,prev,next)                                                      \
+do {                                                                                           \
+  LDECLTYPE(head1) _tmp;                                                                       \
+  if (head2) {                                                                                 \
+    if (head1) {                                                                               \
+        _tmp = (head2)->prev;                                                                  \
+        (head2)->prev = (head1)->prev;                                                         \
+        (head1)->prev->next = (head2);                                                         \
+        (head1)->prev = _tmp;                                                                  \
+    } else {                                                                                   \
+        (head1)=(head2);                                                                       \
+    }                                                                                          \
+  }                                                                                            \
+} while (0) 
+
+#define DL_DELETE(head,del)                                                                    \
+    DL_DELETE2(head,del,prev,next)
+
+#define DL_DELETE2(head,del,prev,next)                                                         \
+do {                                                                                           \
+  assert((del)->prev != NULL);                                                                 \
+  if ((del)->prev == (del)) {                                                                  \
+      (head)=NULL;                                                                             \
+  } else if ((del)==(head)) {                                                                  \
+      (del)->next->prev = (del)->prev;                                                         \
+      (head) = (del)->next;                                                                    \
+  } else {                                                                                     \
+      (del)->prev->next = (del)->next;                                                         \
+      if ((del)->next) {                                                                       \
+          (del)->next->prev = (del)->prev;                                                     \
+      } else {                                                                                 \
+          (head)->prev = (del)->prev;                                                          \
+      }                                                                                        \
+  }                                                                                            \
+} while (0) 
+
+#define DL_COUNT(head,el,counter)                                                              \
+    DL_COUNT2(head,el,counter,next)                                                            \
+
+#define DL_COUNT2(head,el,counter,next)                                                        \
+{                                                                                              \
+    counter = 0;                                                                               \
+    DL_FOREACH2(head,el,next){ ++counter; }                                                    \
+}
+
+#define DL_FOREACH(head,el)                                                                    \
+    DL_FOREACH2(head,el,next)
+
+#define DL_FOREACH2(head,el,next)                                                              \
+    for(el=head;el;el=(el)->next)
+
+/* this version is safe for deleting the elements during iteration */
+#define DL_FOREACH_SAFE(head,el,tmp)                                                           \
+    DL_FOREACH_SAFE2(head,el,tmp,next)
+
+#define DL_FOREACH_SAFE2(head,el,tmp,next)                                                     \
+  for((el)=(head);(el) && (tmp = (el)->next, 1); (el) = tmp)
+
+/* these are identical to their singly-linked list counterparts */
+#define DL_SEARCH_SCALAR LL_SEARCH_SCALAR
+#define DL_SEARCH LL_SEARCH
+#define DL_SEARCH_SCALAR2 LL_SEARCH_SCALAR2
+#define DL_SEARCH2 LL_SEARCH2
+
+#define DL_REPLACE_ELEM(head, el, add)                                                         \
+do {                                                                                           \
+ assert(head != NULL);                                                                         \
+ assert(el != NULL);                                                                           \
+ assert(add != NULL);                                                                          \
+ if ((head) == (el)) {                                                                         \
+  (head) = (add);                                                                              \
+  (add)->next = (el)->next;                                                                    \
+  if ((el)->next == NULL) {                                                                    \
+   (add)->prev = (add);                                                                        \
+  } else {                                                                                     \
+   (add)->prev = (el)->prev;                                                                   \
+   (add)->next->prev = (add);                                                                  \
+  }                                                                                            \
+ } else {                                                                                      \
+  (add)->next = (el)->next;                                                                    \
+  (add)->prev = (el)->prev;                                                                    \
+  (add)->prev->next = (add);                                                                   \
+  if ((el)->next == NULL) {                                                                    \
+   (head)->prev = (add);                                                                       \
+  } else {                                                                                     \
+   (add)->next->prev = (add);                                                                  \
+  }                                                                                            \
+ }                                                                                             \
+} while (0)
+
+#define DL_PREPEND_ELEM(head, el, add)                                                         \
+do {                                                                                           \
+ assert(head != NULL);                                                                         \
+ assert(el != NULL);                                                                           \
+ assert(add != NULL);                                                                          \
+ (add)->next = (el);                                                                           \
+ (add)->prev = (el)->prev;                                                                     \
+ (el)->prev = (add);                                                                           \
+ if ((head) == (el)) {                                                                         \
+  (head) = (add);                                                                              \
+ } else {                                                                                      \
+  (add)->prev->next = (add);                                                                   \
+ }                                                                                             \
+} while (0)                                                                                    \
+
+
+/******************************************************************************
+ * circular doubly linked list macros                                         *
+ *****************************************************************************/
+#define CDL_PREPEND(head,add)                                                                  \
+    CDL_PREPEND2(head,add,prev,next)
+
+#define CDL_PREPEND2(head,add,prev,next)                                                       \
+do {                                                                                           \
+ if (head) {                                                                                   \
+   (add)->prev = (head)->prev;                                                                 \
+   (add)->next = (head);                                                                       \
+   (head)->prev = (add);                                                                       \
+   (add)->prev->next = (add);                                                                  \
+ } else {                                                                                      \
+   (add)->prev = (add);                                                                        \
+   (add)->next = (add);                                                                        \
+ }                                                                                             \
+(head)=(add);                                                                                  \
+} while (0)
+
+#define CDL_DELETE(head,del)                                                                   \
+    CDL_DELETE2(head,del,prev,next)
+
+#define CDL_DELETE2(head,del,prev,next)                                                        \
+do {                                                                                           \
+  if ( ((head)==(del)) && ((head)->next == (head))) {                                          \
+      (head) = 0L;                                                                             \
+  } else {                                                                                     \
+     (del)->next->prev = (del)->prev;                                                          \
+     (del)->prev->next = (del)->next;                                                          \
+     if ((del) == (head)) (head)=(del)->next;                                                  \
+  }                                                                                            \
+} while (0) 
+
+#define CDL_COUNT(head,el,counter)                                                             \
+    CDL_COUNT2(head,el,counter,next)                                                           \
+
+#define CDL_COUNT2(head, el, counter,next)                                                     \
+{                                                                                              \
+    counter = 0;                                                                               \
+    CDL_FOREACH2(head,el,next){ ++counter; }                                                   \
+}
+
+#define CDL_FOREACH(head,el)                                                                   \
+    CDL_FOREACH2(head,el,next)
+
+#define CDL_FOREACH2(head,el,next)                                                             \
+    for(el=head;el;el=((el)->next==head ? 0L : (el)->next)) 
+
+#define CDL_FOREACH_SAFE(head,el,tmp1,tmp2)                                                    \
+    CDL_FOREACH_SAFE2(head,el,tmp1,tmp2,prev,next)
+
+#define CDL_FOREACH_SAFE2(head,el,tmp1,tmp2,prev,next)                                         \
+  for((el)=(head), ((tmp1)=(head)?((head)->prev):NULL);                                        \
+      (el) && ((tmp2)=(el)->next, 1);                                                          \
+      ((el) = (((el)==(tmp1)) ? 0L : (tmp2))))
+
+#define CDL_SEARCH_SCALAR(head,out,field,val)                                                  \
+    CDL_SEARCH_SCALAR2(head,out,field,val,next)
+
+#define CDL_SEARCH_SCALAR2(head,out,field,val,next)                                            \
+do {                                                                                           \
+    CDL_FOREACH2(head,out,next) {                                                              \
+      if ((out)->field == (val)) break;                                                        \
+    }                                                                                          \
+} while(0) 
+
+#define CDL_SEARCH(head,out,elt,cmp)                                                           \
+    CDL_SEARCH2(head,out,elt,cmp,next)
+
+#define CDL_SEARCH2(head,out,elt,cmp,next)                                                     \
+do {                                                                                           \
+    CDL_FOREACH2(head,out,next) {                                                              \
+      if ((cmp(out,elt))==0) break;                                                            \
+    }                                                                                          \
+} while(0) 
+
+#define CDL_REPLACE_ELEM(head, el, add)                                                        \
+do {                                                                                           \
+ assert(head != NULL);                                                                         \
+ assert(el != NULL);                                                                           \
+ assert(add != NULL);                                                                          \
+ if ((el)->next == (el)) {                                                                     \
+  (add)->next = (add);                                                                         \
+  (add)->prev = (add);                                                                         \
+  (head) = (add);                                                                              \
+ } else {                                                                                      \
+  (add)->next = (el)->next;                                                                    \
+  (add)->prev = (el)->prev;                                                                    \
+  (add)->next->prev = (add);                                                                   \
+  (add)->prev->next = (add);                                                                   \
+  if ((head) == (el)) {                                                                        \
+   (head) = (add);                                                                             \
+  }                                                                                            \
+ }                                                                                             \
+} while (0)
+
+#define CDL_PREPEND_ELEM(head, el, add)                                                        \
+do {                                                                                           \
+ assert(head != NULL);                                                                         \
+ assert(el != NULL);                                                                           \
+ assert(add != NULL);                                                                          \
+ (add)->next = (el);                                                                           \
+ (add)->prev = (el)->prev;                                                                     \
+ (el)->prev = (add);                                                                           \
+ (add)->prev->next = (add);                                                                    \
+ if ((head) == (el)) {                                                                         \
+  (head) = (add);                                                                              \
+ }                                                                                             \
+} while (0)                                                                                    \
+
+#endif /* UTLIST_H */
+
diff --git a/bcftools/variantkey.h b/bcftools/variantkey.h
new file mode 100644
index 0000000..ccd4d8d
--- /dev/null
+++ b/bcftools/variantkey.h
@@ -0,0 +1,583 @@
+// VariantKey
+//
+// variantkey.h
+//
+// @category   Libraries
+// @author     Nicola Asuni <nicola.asuni@genomicsplc.com>
+// @copyright  2017-2018 GENOMICS plc
+// @license    MIT (see LICENSE)
+// @link       https://github.com/genomicsplc/variantkey
+//
+// LICENSE
+//
+// Copyright (c) 2017-2018 GENOMICS plc
+//
+// Permission is hereby granted, free of charge, to any person obtaining a copy
+// of this software and associated documentation files (the "Software"), to deal
+// in the Software without restriction, including without limitation the rights
+// to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+// copies of the Software, and to permit persons to whom the Software is
+// furnished to do so, subject to the following conditions:
+//
+// The above copyright notice and this permission notice shall be included in
+// all copies or substantial portions of the Software.
+//
+// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+// OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+// THE SOFTWARE.
+
+/**
+ * @file variantkey.h
+ * @brief VariantKey main functions.
+ *
+ * The functions provided here allows to generate and process a 64 bit Unsigned Integer Keys for Human Genetic Variants.
+ * The VariantKey is sortable for chromosome and position,
+ * and it is also fully reversible for variants with up to 11 bases between Reference and Alternate alleles.
+ * It can be used to sort, search and match variant-based data easily and very quickly.
+ */
+
+#ifndef VARIANTKEY_H
+#define VARIANTKEY_H
+
+#include <inttypes.h>
+#include <stddef.h>
+#include <stdio.h>
+#include "hex.h"
+
+#define VKMASK_CHROM    0xF800000000000000  //!< VariantKey binary mask for CHROM     [ 11111000 00000000 00000000 00000000 00000000 00000000 00000000 00000000 ]
+#define VKMASK_POS      0x07FFFFFF80000000  //!< VariantKey binary mask for POS       [ 00000111 11111111 11111111 11111111 10000000 00000000 00000000 00000000 ]
+#define VKMASK_CHROMPOS 0xFFFFFFFF80000000  //!< VariantKey binary mask for CHROM+POS [ 11111111 11111111 11111111 11111111 10000000 00000000 00000000 00000000 ]
+#define VKMASK_REFALT   0x000000007FFFFFFF  //!< VariantKey binary mask for REF+ALT   [ 00000000 00000000 00000000 00000000 01111111 11111111 11111111 11111111 ]
+#define VKSHIFT_CHROM   59 //!< CHROM LSB position from the VariantKey LSB
+#define VKSHIFT_POS     31 //!< POS LSB position from the VariantKey LSB
+
+/**
+ * VariantKey struct.
+ * Contains the numerically encoded VariantKey components (CHROM, POS, REF+ALT).
+ */
+typedef struct variantkey_t
+{
+    uint8_t chrom;   //!< Chromosome encoded number (only the LSB 5 bit are used)
+    uint32_t pos;    //!< Reference position, with the first base having position 0 (only the LSB 28 bit are used)
+    uint32_t refalt; //!< Code for Reference and Alternate allele (only the LSB 31 bits are used)
+} variantkey_t;
+
+/**
+ * Struct containing the minimum and maximum VariantKey values for range searches.
+ */
+typedef struct vkrange_t
+{
+    uint64_t min; //!< Minimum VariantKey value for any given REF+ALT encoding
+    uint64_t max; //!< Maximum VariantKey value for any given REF+ALT encoding
+} vkrange_t;
+
+/** @brief Returns chromosome numerical encoding.
+ *
+ * @param chrom  Chromosome. An identifier from the reference genome, no white-space permitted.
+ * @param size   Length of the chrom string, excluding the terminating null byte.
+ *
+ * @return CHROM code
+ */
+static inline uint8_t encode_chrom(const char *chrom, size_t size)
+{
+    // X > 23 ; Y > 24 ; M > 25
+    static const uint8_t onecharmap[] =
+    {
+        0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+        0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+        /*                                    M                                X  Y                  */
+        0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,25, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,23,24, 0, 0, 0, 0, 0, 0,
+        /*                                    m                                x  y                  */
+        0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,25, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,23,24, 0, 0, 0, 0, 0, 0,
+        0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+        0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+        0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+        0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+    };
+    // remove "chr" prefix
+    if ((size > 3)
+            && ((chrom[0] == 'c') || (chrom[0] == 'C'))
+            && ((chrom[1] == 'h') || (chrom[1] == 'H'))
+            && ((chrom[2] == 'r') || (chrom[2] == 'R')))
+    {
+        chrom += 3;
+        size -= 3;
+    }
+    if (size == 0)
+    {
+        return 0;
+    }
+    if ((chrom[0] <= '9') && (chrom[0] >= '0')) // Number
+    {
+        size_t i;
+        uint8_t v = (chrom[0] - '0');
+        for (i = 1; i < size; i++)
+        {
+            if ((chrom[i] > '9') || (chrom[i] < '0'))
+            {
+                return 0; // NA
+            }
+            v = ((v * 10) + (chrom[i] - '0'));
+        }
+        return v;
+    }
+    if ((size == 1) || ((size == 2) && ((chrom[1] == 'T') || (chrom[1] == 't'))))
+    {
+        return onecharmap[((uint8_t)chrom[0])];
+    }
+    return 0; // NA
+}
+
+/** @brief Decode the chromosome numerical code.
+ *
+ * @param code   CHROM code.
+ * @param chrom  CHROM string buffer to be returned. Its size should be enough to contain the results (max 4 bytes).
+ *
+ * @return If successful, the total number of characters written is returned,
+ *         excluding the null-character appended at the end of the string,
+ *         otherwise a negative number is returned in case of failure.
+ */
+static inline size_t decode_chrom(uint8_t code, char *chrom)
+{
+    if ((code < 1) || (code > 25))
+    {
+        return sprintf(chrom, "NA");
+    }
+    if (code < 23)
+    {
+        return sprintf(chrom, "%" PRIu8, code);
+    }
+    static const char *map[] = {"X", "Y", "MT"};
+    return sprintf(chrom, "%s", map[(code - 23)]);
+}
+
+static inline uint32_t encode_base(const uint8_t c)
+{
+    /*
+      Encode base:
+      A > 0
+      C > 1
+      G > 2
+      T > 3
+    */
+    static const uint32_t map[] =
+    {
+        4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,
+        4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,
+        /*A   C       G                         T*/
+        4,0,4,1,4,4,4,2,4,4,4,4,4,4,4,4,4,4,4,4,3,4,4,4,4,4,4,4,4,4,4,4,
+        /*a   c       g                         t*/
+        4,0,4,1,4,4,4,2,4,4,4,4,4,4,4,4,4,4,4,4,3,4,4,4,4,4,4,4,4,4,4,4,
+        4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,
+        4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,
+        4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,
+        4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,
+    };
+    return map[c];
+}
+
+static inline int encode_allele(uint32_t *h, uint8_t *bitpos, const char *str, size_t size)
+{
+    uint32_t v;
+    while (size--)
+    {
+        v = encode_base(*str++);
+        if (v > 3)
+        {
+            return -1;
+        }
+        *bitpos -= 2;
+        *h |= (v << *bitpos);
+    }
+    return 0;
+}
+
+static inline uint32_t encode_refalt_rev(const char *ref, size_t sizeref, const char *alt, size_t sizealt)
+{
+    //[******** ******** ******** ******** *RRRRAAA A1122334 45566778 8990011*]
+    uint32_t h = 0;
+    h |= ((uint32_t)(sizeref) << 27); // RRRR: length of (REF - 1)
+    h |= ((uint32_t)(sizealt) << 23); // AAAA: length of (ALT - 1)
+    uint8_t bitpos = 23;
+    if ((encode_allele(&h, &bitpos, ref, sizeref) < 0) || (encode_allele(&h, &bitpos, alt, sizealt) < 0))
+    {
+        return 0; // error code
+    }
+    return h;
+}
+
+// Mix two 32 bit hash numbers using a MurmurHash3-like algorithm
+static inline uint32_t muxhash(uint32_t k, uint32_t h)
+{
+    k *= 0xcc9e2d51;
+    k = (k >> 17) | (k << 15);
+    k *= 0x1b873593;
+    h ^= k;
+    h = (h >> 19) | (h << 13);
+    return ((h * 5) + 0xe6546b64);
+}
+
+static inline uint32_t encode_packchar(int c)
+{
+    if (c < 'A')
+    {
+        return 27;
+    }
+    if (c >= 'a')
+    {
+        return (uint32_t)(c - 'a' + 1);
+    }
+    return (uint32_t)(c - 'A' + 1);
+}
+
+// pack blocks of 6 characters in 32 bit (6 x 5 bit + 2 spare bit) [ 01111122 22233333 44444555 55666660 ]
+static inline uint32_t pack_chars_tail(const char *str, size_t size)
+{
+    uint32_t h = 0;
+    const char *pos = (str + size - 1);
+    switch (size)
+    {
+    case 5:
+        h ^= encode_packchar(*pos--) << (1 + (5 * 1));
+    // fall through
+    case 4:
+        h ^= encode_packchar(*pos--) << (1 + (5 * 2));
+    // fall through
+    case 3:
+        h ^= encode_packchar(*pos--) << (1 + (5 * 3));
+    // fall through
+    case 2:
+        h ^= encode_packchar(*pos--) << (1 + (5 * 4));
+    // fall through
+    case 1:
+        h ^= encode_packchar(*pos) << (1 + (5 * 5));
+    }
+    return h;
+}
+
+static inline uint32_t pack_chars(const char *str)
+{
+    const char *pos = (str + 5);
+    return ((encode_packchar(*pos) << 1)
+            ^ (encode_packchar(*(pos-1)) << (1 + (5 * 1)))
+            ^ (encode_packchar(*(pos-2)) << (1 + (5 * 2)))
+            ^ (encode_packchar(*(pos-3)) << (1 + (5 * 3)))
+            ^ (encode_packchar(*(pos-4)) << (1 + (5 * 4)))
+            ^ (encode_packchar(*(pos-5)) << (1 + (5 * 5))));
+}
+
+// Return a 32 bit hash of a nucleotide string
+static inline uint32_t hash32(const char *str, size_t size)
+{
+    uint32_t h = 0;
+    size_t len = 6;
+    while (size >= len)
+    {
+        h = muxhash(pack_chars(str), h);
+        str += len;
+        size -= len;
+    }
+    if (size > 0)
+    {
+        h = muxhash(pack_chars_tail(str, size), h);
+    }
+    return h;
+}
+
+static inline uint32_t encode_refalt_hash(const char *ref, size_t sizeref, const char *alt, size_t sizealt)
+{
+    // 0x3 is the separator character between REF and ALT [00000000 00000000 00000000 00000011]
+    uint32_t h = muxhash(hash32(alt, sizealt), muxhash(0x3, hash32(ref, sizeref)));
+    // MurmurHash3 finalization mix - force all bits of a hash block to avalanche
+    h ^= h >> 16;
+    h *= 0x85ebca6b;
+    h ^= h >> 13;
+    h *= 0xc2b2ae35;
+    h ^= h >> 16;
+    return ((h >> 1) | 0x1); // 0x1 is the set bit to indicate HASH mode [00000000 00000000 00000000 00000001]
+}
+
+/** @brief Returns reference+alternate numerical encoding.
+ *
+ * @param ref      Reference allele. String containing a sequence of nucleotide letters.
+ *                 The value in the pos field refers to the position of the first nucleotide in the String.
+ *                 Characters must be A-Z, a-z or *
+ * @param sizeref  Length of the ref string, excluding the terminating null byte.
+ * @param alt      Alternate non-reference allele string.
+ *                 Characters must be A-Z, a-z or *
+ * @param sizealt  Length of the alt string, excluding the terminating null byte.
+ *
+ * @return REF+ALT code
+ */
+static inline uint32_t encode_refalt(const char *ref, size_t sizeref, const char *alt, size_t sizealt)
+{
+    if ((sizeref + sizealt) <= 11)
+    {
+        uint32_t h = encode_refalt_rev(ref, sizeref, alt, sizealt);
+        if (h != 0)
+        {
+            return h;
+        }
+    }
+    return encode_refalt_hash(ref, sizeref, alt, sizealt);
+}
+
+static inline char decode_base(uint32_t code, int bitpos)
+{
+    static const char base[4] = {'A', 'C', 'G', 'T'};
+    return base[((code >> bitpos) & 0x3)]; // 0x3 is the 2 bit mask [00000011]
+}
+
+static inline size_t decode_refalt_rev(uint32_t code, char *ref, size_t *sizeref, char *alt, size_t *sizealt)
+{
+    *sizeref = (size_t)((code & 0x78000000) >> 27); // [01111000 00000000 00000000 00000000]
+    *sizealt = (size_t)((code & 0x07800000) >> 23); // [00000111 10000000 00000000 00000000]
+    switch (*sizeref)
+    {
+    case 10:
+        ref[9] = decode_base(code, (3 + (2 * 0)));
+    // fall through
+    case 9:
+        ref[8] = decode_base(code, (3 + (2 * 1)));
+    // fall through
+    case 8:
+        ref[7] = decode_base(code, (3 + (2 * 2)));
+    // fall through
+    case 7:
+        ref[6] = decode_base(code, (3 + (2 * 3)));
+    // fall through
+    case 6:
+        ref[5] = decode_base(code, (3 + (2 * 4)));
+    // fall through
+    case 5:
+        ref[4] = decode_base(code, (3 + (2 * 5)));
+    // fall through
+    case 4:
+        ref[3] = decode_base(code, (3 + (2 * 6)));
+    // fall through
+    case 3:
+        ref[2] = decode_base(code, (3 + (2 * 7)));
+    // fall through
+    case 2:
+        ref[1] = decode_base(code, (3 + (2 * 8)));
+    // fall through
+    case 1:
+        ref[0] = decode_base(code, (3 + (2 * 9)));
+    }
+    ref[*sizeref] = 0;
+    uint8_t bitpos = (23 - ((*sizeref) << 1));
+    switch (*sizealt)
+    {
+    case 10:
+        alt[9] = decode_base(code, bitpos - (2 * 10));
+    // fall through
+    case 9:
+        alt[8] = decode_base(code, bitpos - (2 * 9));
+    // fall through
+    case 8:
+        alt[7] = decode_base(code, bitpos - (2 * 8));
+    // fall through
+    case 7:
+        alt[6] = decode_base(code, bitpos - (2 * 7));
+    // fall through
+    case 6:
+        alt[5] = decode_base(code, bitpos - (2 * 6));
+    // fall through
+    case 5:
+        alt[4] = decode_base(code, bitpos - (2 * 5));
+    // fall through
+    case 4:
+        alt[3] = decode_base(code, bitpos - (2 * 4));
+    // fall through
+    case 3:
+        alt[2] = decode_base(code, bitpos - (2 * 3));
+    // fall through
+    case 2:
+        alt[1] = decode_base(code, bitpos - (2 * 2));
+    // fall through
+    case 1:
+        alt[0] = decode_base(code, bitpos - (2 * 1));
+    }
+    alt[*sizealt] = 0;
+    return (*sizeref + *sizealt);
+}
+
+/** @brief Decode the 32 bit REF+ALT code if reversible (if it has 11 or less bases in total and only contains ACGT letters).
+ *
+ * @param code     REF+ALT code
+ * @param ref      REF string buffer to be returned.
+ * @param sizeref  Pointer to the size of the ref buffer, excluding the terminating null byte.
+ *                 This will contain the final ref size.
+ * @param alt      ALT string buffer to be returned.
+ * @param sizealt  Pointer to the size of the alt buffer, excluding the terminating null byte.
+ *                 This will contain the final alt size.
+ *
+ * @return      If the code is reversible, then the total number of characters of REF+ALT is returned.
+ *              Otherwise 0 is returned.
+ */
+static inline size_t decode_refalt(uint32_t code, char *ref, size_t *sizeref, char *alt, size_t *sizealt)
+{
+    if (code & 0x1) // check last bit
+    {
+        return 0; // non-reversible encoding
+    }
+    return decode_refalt_rev(code, ref, sizeref, alt, sizealt);
+}
+
+/** @brief Returns a 64 bit variant key based on the pre-encoded CHROM, POS (0-based) and REF+ALT.
+ *
+ * @param chrom      Encoded Chromosome (see encode_chrom).
+ * @param pos        Position. The reference position, with the first base having position 0.
+ * @param refalt     Encoded Reference + Alternate (see encode_refalt).
+ *
+ * @return      VariantKey 64 bit code.
+ */
+static inline uint64_t encode_variantkey(uint8_t chrom, uint32_t pos, uint32_t refalt)
+{
+    return (((uint64_t)chrom << VKSHIFT_CHROM) | ((uint64_t)pos << VKSHIFT_POS) | (uint64_t)refalt);
+}
+
+/** @brief Extract the CHROM code from VariantKey.
+ *
+ * @param vk VariantKey code.
+ *
+ * @return CHROM code.
+ */
+static inline uint8_t extract_variantkey_chrom(uint64_t vk)
+{
+    return (uint8_t)((vk & VKMASK_CHROM) >> VKSHIFT_CHROM);
+}
+
+/** @brief Extract the POS code from VariantKey.
+ *
+ * @param vk VariantKey code.
+ *
+ * @return POS.
+ */
+static inline uint32_t extract_variantkey_pos(uint64_t vk)
+{
+    return (uint32_t)((vk & VKMASK_POS) >> VKSHIFT_POS);
+}
+
+/** @brief Extract the REF+ALT code from VariantKey.
+ *
+ * @param vk VariantKey code.
+ *
+ * @return REF+ALT code.
+ */
+static inline uint32_t extract_variantkey_refalt(uint64_t vk)
+{
+    return (uint32_t)(vk & VKMASK_REFALT);
+}
+
+/** @brief Decode a VariantKey code and returns the components as variantkey_t structure.
+ *
+ * @param code VariantKey code.
+ * @param vk   Decoded variantkey structure.
+ */
+static inline void decode_variantkey(uint64_t code, variantkey_t *vk)
+{
+    vk->chrom = extract_variantkey_chrom(code);
+    vk->pos = extract_variantkey_pos(code);
+    vk->refalt = extract_variantkey_refalt(code);
+}
+
+/** @brief Returns a 64 bit variant key based on CHROM, POS (0-based), REF, ALT.
+ *
+ * @param chrom      Chromosome. An identifier from the reference genome, no white-space or leading zeros permitted.
+ * @param sizechrom  Length of the chrom string, excluding the terminating null byte.
+ * @param pos        Position. The reference position, with the first base having position 0.
+ * @param ref        Reference allele. String containing a sequence of nucleotide letters.
+ *                   The value in the pos field refers to the position of the first nucleotide in the String.
+ *                   Characters must be A-Z, a-z or *
+ * @param sizeref    Length of the ref string, excluding the terminating null byte.
+ * @param alt        Alternate non-reference allele string.
+ *                   Characters must be A-Z, a-z or *
+ * @param sizealt    Length of the alt string, excluding the terminating null byte.
+ *
+ * @return      VariantKey 64 bit code.
+ */
+static inline uint64_t variantkey(const char *chrom, size_t sizechrom, uint32_t pos, const char *ref, size_t sizeref, const char *alt, size_t sizealt)
+{
+    return encode_variantkey(encode_chrom(chrom, sizechrom), pos, encode_refalt(ref, sizeref, alt, sizealt));
+}
+
+/** @brief Returns minimum and maximum VariantKeys for range searches.
+ *
+ * @param chrom     Chromosome encoded number.
+ * @param pos_min   Start reference position, with the first base having position 0.
+ * @param pos_max   End reference position, with the first base having position 0.
+ * @param range     VariantKey range values.
+ */
+static inline void variantkey_range(uint8_t chrom, uint32_t pos_min, uint32_t pos_max, vkrange_t *range)
+{
+    uint64_t c = ((uint64_t)chrom << VKSHIFT_CHROM);
+    range->min = (c | ((uint64_t)pos_min << VKSHIFT_POS));
+    range->max = (c | ((uint64_t)pos_max << VKSHIFT_POS) | VKMASK_REFALT);
+}
+
+static inline int8_t compare_uint64_t(uint64_t a, uint64_t b)
+{
+    return (a < b) ? -1 : (a > b);
+}
+
+/** @brief Compares two VariantKeys by chromosome only.
+ *
+ * @param vka    The first VariantKey to be compared.
+ * @param vkb    The second VariantKey to be compared.
+ *
+ * @return -1 if the first chromosome is smaller than the second, 0 if they are equal and 1 if the first is greater than the second.
+ */
+static inline int8_t compare_variantkey_chrom(uint64_t vka, uint64_t vkb)
+{
+    return compare_uint64_t((vka >> VKSHIFT_CHROM), (vkb >> VKSHIFT_CHROM));
+}
+
+/** @brief Compares two VariantKeys by chromosome and position.
+ *
+ * @param vka    The first VariantKey to be compared.
+ * @param vkb    The second VariantKey to be compared.
+ *
+ * @return -1 if the first CHROM+POS is smaller than the second, 0 if they are equal and 1 if the first is greater than the second.
+ */
+static inline int8_t compare_variantkey_chrom_pos(uint64_t vka, uint64_t vkb)
+{
+    return compare_uint64_t((vka >> VKSHIFT_POS), (vkb >> VKSHIFT_POS));
+}
+
+/** @brief Returns VariantKey hexadecimal string (16 characters).
+ *
+ * The string represent a 64 bit number or:
+ *   -  5 bit for CHROM
+ *   - 28 bit for POS
+ *   - 31 bit for REF+ALT
+ *
+ * @param vk    VariantKey code.
+ * @param str   String buffer to be returned (it must be sized 17 bytes at least).
+ *
+ * @return      Upon successful return, these function returns the number of characters processed
+ *              (excluding the null byte used to end output to strings).
+ *              If the buffer size is not sufficient, then the return value is the number of characters required for
+ *              buffer string, including the terminating null byte.
+ */
+static inline size_t variantkey_hex(uint64_t vk, char *str)
+{
+    return hex_uint64_t(vk, str);
+}
+
+/** @brief Parses a VariantKey hexadecimal string and returns the code.
+ *
+ * @param vs    VariantKey hexadecimal string (it must contain 16 hexadecimal characters).
+ *
+ * @return A VariantKey code.
+ */
+static inline uint64_t parse_variantkey_hex(const char *vs)
+{
+    return parse_hex_uint64_t(vs);
+}
+
+#endif  // VARIANTKEY_H
diff --git a/bcftools/vcfannotate.c b/bcftools/vcfannotate.c
new file mode 100644
index 0000000..d33fd90
--- /dev/null
+++ b/bcftools/vcfannotate.c
@@ -0,0 +1,3524 @@
+/*  vcfannotate.c -- Annotate and edit VCF/BCF files.
+
+    Copyright (C) 2013-2022 Genome Research Ltd.
+
+    Author: Petr Danecek <pd3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.  */
+
+#include <stdio.h>
+#include <strings.h>
+#include <unistd.h>
+#include <getopt.h>
+#include <assert.h>
+#include <ctype.h>
+#include <string.h>
+#include <errno.h>
+#include <sys/stat.h>
+#include <sys/types.h>
+#include <dirent.h>
+#include <math.h>
+#include <inttypes.h>
+#include <htslib/vcf.h>
+#include <htslib/synced_bcf_reader.h>
+#include <htslib/kseq.h>
+#include <htslib/khash_str2int.h>
+#include "bcftools.h"
+#include "vcmp.h"
+#include "filter.h"
+#include "convert.h"
+#include "smpl_ilist.h"
+#include "regidx.h"
+#include "dbuf.h"
+
+struct _args_t;
+
+typedef struct _rm_tag_t
+{
+    char *key;
+    int hdr_id;
+    void (*handler)(struct _args_t *, bcf1_t *, struct _rm_tag_t *);
+}
+rm_tag_t;
+
+typedef struct
+{
+    char **cols;
+    int ncols, mcols;
+    char **als;
+    int nals, mals;
+    kstring_t line;
+    int rid, start, end;
+}
+annot_line_t;
+
+#define REPLACE_MISSING     (1<<0)   // -c +TAG  .. replace only missing values
+#define REPLACE_ALL         (1<<1)   // -c TAG   .. replace both missing and existing values
+#define REPLACE_NON_MISSING (1<<2)   // -c -TAG  .. replace only if tgt is not missing
+#define SET_OR_APPEND       (1<<3)   // -c =TAG  .. set new value if missing or non-existent, append otherwise
+#define MATCH_VALUE         (1<<4)   // -c ~ID   .. do not set, just match the value
+#define CARRY_OVER_MISSING  (1<<5)   // -c .TAG  .. carry over source missing values as well
+#define MM_FIRST   0    // if multiple annotation lines overlap a VCF record, use the first, discarding the rest
+#define MM_APPEND  1    // append, possibly multiple times
+#define MM_UNIQUE  2    // append, only unique values
+#define MM_SUM     3
+#define MM_AVG     4
+#define MM_MIN     5
+#define MM_MAX     6
+#define MM_APPEND_MISSING 7     // missing values will be transferred as well
+typedef struct _annot_col_t
+{
+    int icol, replace, number;  // number: one of BCF_VL_* types
+    char *hdr_key_src, *hdr_key_dst;
+    // The setters return 0 on successful update of the bcf record, negative value (bcf_update_* return status) on errors,
+    // or 1 on (repeated partial updates) concluded with a src=NULL call
+    int (*setter)(struct _args_t *, bcf1_t *dst, struct _annot_col_t *, void *src); // the last is the annotation line, either src bcf1_t or annot_line_t
+    int (*getter)(struct _args_t *, bcf1_t *src, struct _annot_col_t *, void **ptr, int *mptr);
+    int merge_method;               // one of the MM_* defines
+    khash_t(str2int) *mm_str_hash;  // lookup table to ensure uniqueness of added string values
+    kstring_t mm_kstr;
+    size_t
+        mm_dbl_nalloc,  // the allocated size --merge-logic values array
+        mm_dbl_nused,   // the number of used elements in the mm_dbl array
+        mm_dbl_ndat;    // the number of merged rows (for calculating the average)
+    double
+        *mm_dbl;
+    void *ptr;
+    int mptr, done;
+}
+annot_col_t;
+
+// Logic of the filters: include or exclude sites which match the filters?
+#define FLT_INCLUDE 1
+#define FLT_EXCLUDE 2
+
+#define MARK_LISTED   1
+#define MARK_UNLISTED 2
+
+typedef struct _args_t
+{
+    bcf_srs_t *files;
+    bcf_hdr_t *hdr, *hdr_out, *tgts_hdr;
+    htsFile *out_fh;
+    int output_type, n_threads, clevel;
+    bcf_sr_regions_t *tgts;
+
+    regidx_t *tgt_idx;  // keep everything in memory only with .tab annotation file and -c BEG,END columns
+    regitr_t *tgt_itr;
+    int tgt_is_bed;
+
+    filter_t *filter;
+    char *filter_str;
+    int filter_logic;   // include or exclude sites which match the filters? One of FLT_INCLUDE/FLT_EXCLUDE
+    int keep_sites;
+
+    rm_tag_t *rm;           // tags scheduled for removal
+    int nrm;
+    int flt_keep_pass;      // when all filters removed, reset to PASS
+
+    vcmp_t *vcmp;           // for matching annotation and VCF lines by allele
+    annot_line_t *alines;   // buffered annotation lines
+    annot_line_t *aline_missing;
+    uint32_t *srt_alines;   // sorted indexes (iALT<<16 || iAline)
+    int nalines, malines, nsrt_alines, msrt_alines;
+    int ref_idx, alt_idx, chr_idx, beg_idx, end_idx;   // -1 if not present
+    annot_col_t *cols;      // column indexes and setters
+    int ncols;
+    int match_id;           // set iff `-c ~ID` given, -1 otherwise
+    int match_end;          // set iff `-c ~INFO/END` is given, -1 otherwise
+
+    char *set_ids_fmt;
+    convert_t *set_ids;
+    int set_ids_replace;
+
+    int nsmpl_annot;
+    int *sample_map, nsample_map, sample_is_file;   // map[idst] -> isrc
+    uint8_t *src_smpl_pld, *dst_smpl_pld;   // for Number=G format fields
+    int mtmpi, mtmpf, mtmps;
+    int mtmpi2, mtmpf2, mtmps2;
+    int mtmpi3, mtmpf3, mtmps3;
+    int32_t *tmpi, *tmpi2, *tmpi3;
+    float *tmpf, *tmpf2, *tmpf3;
+    char *tmps, *tmps2, **tmpp, **tmpp2;
+    kstring_t tmpks;
+
+    char **argv, *output_fname, *targets_fname, *regions_list, *header_fname;
+    char *remove_annots, *columns, *rename_chrs, *rename_annots, *sample_names, *mark_sites;
+    char **rename_annots_map;
+    char *min_overlap_str;
+    float min_overlap_ann, min_overlap_vcf;
+    int rename_annots_nmap;
+    kstring_t merge_method_str;
+    int argc, drop_header, record_cmd_line, tgts_is_vcf, mark_sites_logic, force, single_overlaps;
+    int columns_is_file, has_append_mode, pair_logic;
+    dbuf_t *header_lines;
+}
+args_t;
+
+char *msprintf(const char *fmt, ...);
+
+int parse_with_payload(const char *line, char **chr_beg, char **chr_end, uint32_t *beg, uint32_t *end, void *payload, void *usr)
+{
+    args_t *args = (args_t*) usr;
+    int ret = args->tgt_is_bed ? regidx_parse_bed(line, chr_beg, chr_end, beg, end, NULL, NULL) : regidx_parse_tab(line, chr_beg, chr_end, beg, end, NULL, NULL);
+    if ( ret<0 ) return ret;
+    *((char **)payload) = strdup(line);
+    return 0;
+}
+void free_payload(void *payload)
+{
+    char *str = *((char**)payload);
+    free(str);
+}
+
+void remove_id(args_t *args, bcf1_t *line, rm_tag_t *tag)
+{
+    bcf_update_id(args->hdr,line,NULL);
+}
+void remove_filter(args_t *args, bcf1_t *line, rm_tag_t *tag)
+{
+    if ( tag->key && tag->hdr_id<0 )
+    {
+        error("Error: Cannot proceed, not even with the --force option, bad things could happen.\n"
+              "       Note that \"bcftools annotate -x FILTER\" can be used to remove ALL filters.\n"
+              "       Even better, use \"bcftools view -h\" and \"bcftools reheader\" to fix the header!\n"
+              );
+    }
+    if ( !tag->key ) bcf_update_filter(args->hdr, line, NULL, args->flt_keep_pass);
+    else bcf_remove_filter(args->hdr, line, tag->hdr_id, args->flt_keep_pass);
+}
+void remove_qual(args_t *args, bcf1_t *line, rm_tag_t *tag)
+{
+    bcf_float_set_missing(line->qual);
+}
+void remove_info(args_t *args, bcf1_t *line, rm_tag_t *tag)
+{
+    // remove all INFO fields
+    if ( !(line->unpacked & BCF_UN_INFO) ) bcf_unpack(line, BCF_UN_INFO);
+
+    int i;
+    for (i=0; i<line->n_info; i++)
+    {
+        bcf_info_t *inf = &line->d.info[i];
+        if (  !strcmp("END",bcf_hdr_int2id(args->hdr,BCF_DT_ID,inf->key)) )
+            line->rlen = line->n_allele ? strlen(line->d.allele[0]) : 0;
+        if ( inf->vptr_free )
+        {
+            free(inf->vptr - inf->vptr_off);
+            inf->vptr_free = 0;
+        }
+        line->d.shared_dirty |= BCF1_DIRTY_INF;
+        inf->vptr = NULL;
+        inf->vptr_off = inf->vptr_len = 0;
+    }
+}
+void remove_info_tag(args_t *args, bcf1_t *line, rm_tag_t *tag)
+{
+    bcf_update_info(args->hdr, line, tag->key, NULL, 0, BCF_HT_INT);  // the type does not matter with n=0
+}
+void remove_format_tag(args_t *args, bcf1_t *line, rm_tag_t *tag)
+{
+    bcf_update_format(args->hdr, line, tag->key, NULL, 0, BCF_HT_INT);  // the type does not matter with n=0
+}
+void remove_format(args_t *args, bcf1_t *line, rm_tag_t *tag)
+{
+    // remove all FORMAT fields except GT
+    if ( !(line->unpacked & BCF_UN_FMT) ) bcf_unpack(line, BCF_UN_FMT);
+
+    int i;
+    for (i=0; i<line->n_fmt; i++)
+    {
+        bcf_fmt_t *fmt = &line->d.fmt[i];
+        const char *key = bcf_hdr_int2id(args->hdr,BCF_DT_ID,fmt->id);
+        if ( key[0]=='G' && key[1]=='T' && !key[2] ) continue;
+
+        if ( fmt->p_free )
+        {
+            free(fmt->p - fmt->p_off);
+            fmt->p_free = 0;
+        }
+        line->d.indiv_dirty = 1;
+        fmt->p = NULL;
+    }
+}
+
+#include "htslib/khash.h"
+KHASH_MAP_INIT_STR(vdict, bcf_idinfo_t)
+typedef khash_t(vdict) vdict_t;
+
+static void remove_hdr_lines(bcf_hdr_t *hdr, int type)
+{
+    int i = 0, nrm = 0;
+    while ( i<hdr->nhrec )
+    {
+        if ( hdr->hrec[i]->type!=type ) { i++; continue; }
+        bcf_hrec_t *hrec = hdr->hrec[i];
+        if ( type==BCF_HL_FMT || type==BCF_HL_INFO || type==BCF_HL_FMT || type== BCF_HL_CTG )
+        {
+            // everything except FORMAT/GT
+            int id = bcf_hrec_find_key(hrec, "ID");
+            if ( id>=0 )
+            {
+                if ( type==BCF_HL_FMT && !strcmp(hrec->vals[id],"GT") ) { i++; continue; }
+                vdict_t *d = type==BCF_HL_CTG ? (vdict_t*)hdr->dict[BCF_DT_CTG] : (vdict_t*)hdr->dict[BCF_DT_ID];
+                khint_t k = kh_get(vdict, d, hdr->hrec[i]->vals[id]);
+                kh_val(d, k).hrec[type==BCF_HL_CTG?0:type] = NULL;
+                kh_val(d, k).info[type] |= 0xf;
+            }
+        }
+        nrm++;
+        hdr->nhrec--;
+        if ( i < hdr->nhrec )
+            memmove(&hdr->hrec[i],&hdr->hrec[i+1],(hdr->nhrec-i)*sizeof(bcf_hrec_t*));
+        bcf_hrec_destroy(hrec);
+    }
+    if ( nrm ) {
+        if (bcf_hdr_sync(hdr) < 0)
+            error_errno("[%s] Failed to update header", __func__);
+    }
+}
+
+static void init_remove_annots(args_t *args)
+{
+    int keep_info = 0, keep_fmt = 0, keep_flt = 0;
+    void *keep = khash_str2int_init();
+    kstring_t str = {0,0,0};
+    char *ss = args->remove_annots;
+
+    int i, ntags, needs_info = 0;
+    if ( args->set_ids )
+    {
+        const char **tags = convert_list_used_tags(args->set_ids,&ntags);
+        for (i=0; i<ntags; i++)
+            if ( !strncmp("INFO/",tags[i],4) ) needs_info = 1;
+    }
+
+    while ( *ss )
+    {
+        args->nrm++;
+        args->rm = (rm_tag_t*) realloc(args->rm,sizeof(rm_tag_t)*args->nrm);
+        rm_tag_t *tag = &args->rm[args->nrm-1];
+        tag->key = NULL;
+
+        int type = BCF_HL_GEN;
+        if ( !strncasecmp("INFO/",ss,5) ) { type = BCF_HL_INFO; ss += 5; }
+        else if ( !strncasecmp("INF/",ss,4) ) { type = BCF_HL_INFO; ss += 4; }
+        else if ( !strncasecmp("FORMAT/",ss,7) ) { type = BCF_HL_FMT; ss += 7; }
+        else if ( !strncasecmp("FMT/",ss,4) ) { type = BCF_HL_FMT; ss += 4; }
+        else if ( !strncasecmp("FILTER/",ss,7) ) { type = BCF_HL_FLT; ss += 7; }
+        else if ( !strncasecmp("^INFO/",ss,6) ) { type = BCF_HL_INFO; ss += 6; keep_info = 1; }
+        else if ( !strncasecmp("^INF/",ss,5) ) { type = BCF_HL_INFO; ss += 5; keep_info = 1; }
+        else if ( !strncasecmp("^FORMAT/",ss,8) ) { type = BCF_HL_FMT; ss += 8; keep_fmt = 1; }
+        else if ( !strncasecmp("^FMT/",ss,5) ) { type = BCF_HL_FMT; ss += 5; keep_fmt = 1; }
+        else if ( !strncasecmp("^FILTER/",ss,8) ) { type = BCF_HL_FLT; ss += 8; keep_flt = 1; }
+
+        char *se = ss;
+        while ( *se && *se!=',' ) se++;
+        str.l = 0;
+        kputsn(ss, se-ss, &str);
+
+        if ( type==BCF_HL_FLT )
+        {
+            if ( !keep_flt )
+            {
+                args->flt_keep_pass = 1;
+                tag->handler = remove_filter;
+                tag->key = strdup(str.s);
+                tag->hdr_id = bcf_hdr_id2int(args->hdr, BCF_DT_ID, tag->key);
+                if ( !bcf_hdr_idinfo_exists(args->hdr,BCF_HL_FLT,tag->hdr_id) )
+                {
+                    if ( args->keep_sites )
+                        error("Error: The filter \"%s\" is not defined in the header, cannot use the -k option\n", str.s);
+                    else
+                        fprintf(stderr,"Warning: The filter \"%s\" is not defined in the header\n", str.s);
+                }
+                else if ( !args->keep_sites ) bcf_hdr_remove(args->hdr_out,BCF_HL_FLT,tag->key);
+            }
+            else
+            {
+                int value, ret = khash_str2int_get(keep, str.s, &value);
+                if ( ret==-1 ) khash_str2int_set(keep, strdup(str.s),1<<BCF_HL_FLT);
+                else khash_str2int_set(keep, str.s, value | 1<<BCF_HL_FLT);
+                args->nrm--;
+            }
+        }
+        else if ( type!=BCF_HL_GEN )
+        {
+            int id = bcf_hdr_id2int(args->hdr,BCF_DT_ID,str.s);
+            if ( !bcf_hdr_idinfo_exists(args->hdr,type,id) )
+            {
+                if ( args->keep_sites )
+                    error("Error: The tag \"%s\" is not defined in the header, cannot use the -k option\n", str.s);
+                else
+                    fprintf(stderr,"Warning: The tag \"%s\" not defined in the header\n", str.s);
+
+                tag->key = strdup(str.s);
+                if ( type==BCF_HL_INFO )
+                {
+                    tag->handler = remove_info_tag;
+                    if ( needs_info ) error("Error: `--remove INFO/%s` is executed first, cannot combine with `--set-id %s`\n",tag->key,args->set_ids_fmt);
+                }
+                else if ( type==BCF_HL_FMT ) tag->handler = remove_format_tag;
+            }
+            else if ( (type==BCF_HL_FMT && keep_fmt) || (type==BCF_HL_INFO && keep_info) )
+            {
+                int value, ret = khash_str2int_get(keep, str.s, &value);
+                if ( ret==-1 ) khash_str2int_set(keep, strdup(str.s),1<<type);
+                else khash_str2int_set(keep, str.s, value | 1<<type);
+                args->nrm--;
+            }
+            else
+            {
+                tag->key = strdup(str.s);
+                if ( type==BCF_HL_INFO )
+                {
+                    tag->handler = remove_info_tag;
+                    if ( needs_info ) error("Error: `--remove INFO/%s` is executed first, cannot combine with `--set-id %s`\n",tag->key,args->set_ids_fmt);
+                }
+                else if ( type==BCF_HL_FMT ) tag->handler = remove_format_tag;
+                if ( !args->keep_sites ) bcf_hdr_remove(args->hdr_out,type,tag->key);
+            }
+        }
+        else if ( !strcasecmp("ID",str.s) ) tag->handler = remove_id;
+        else if ( !strcasecmp("FILTER",str.s) )
+        {
+            tag->handler = remove_filter;
+            if ( !args->keep_sites ) remove_hdr_lines(args->hdr_out,BCF_HL_FLT);
+        }
+        else if ( !strcasecmp("QUAL",str.s) ) tag->handler = remove_qual;
+        else if ( !strcasecmp("INFO",str.s) )
+        {
+            if ( needs_info ) error("Error: `--remove INFO` is executed first, cannot combine with `--set-id %s`\n",args->set_ids_fmt);
+            tag->handler = remove_info;
+            if ( !args->keep_sites ) remove_hdr_lines(args->hdr_out,BCF_HL_INFO);
+        }
+        else if ( !strcasecmp("FMT",str.s) || !strcasecmp("FORMAT",str.s) )
+        {
+            tag->handler = remove_format;
+            if ( !args->keep_sites ) remove_hdr_lines(args->hdr_out,BCF_HL_FMT);
+        }
+        else if ( str.l )
+        {
+            int id = bcf_hdr_id2int(args->hdr, BCF_DT_ID, str.s);
+            if ( bcf_hdr_idinfo_exists(args->hdr,BCF_HL_INFO,id) ) error("Error: did you mean INFO/%s?\n",str.s);
+            if ( bcf_hdr_idinfo_exists(args->hdr,BCF_HL_FMT,id) ) error("Error: did you mean FORMAT/%s?\n",str.s);
+
+            if ( !args->keep_sites )
+            {
+                if ( str.s[0]=='#' && str.s[1]=='#' )
+                    bcf_hdr_remove(args->hdr_out,BCF_HL_GEN,str.s+2);
+                else
+                    bcf_hdr_remove(args->hdr_out,BCF_HL_STR,str.s);
+            }
+            args->nrm--;
+        }
+
+        ss = *se ? se+1 : se;
+    }
+    free(str.s);
+    if ( keep_flt || keep_info || keep_fmt )
+    {
+        int j;
+        for (j=0; j<args->hdr->nhrec; j++)
+        {
+            bcf_hrec_t *hrec = args->hdr->hrec[j];
+            if ( hrec->type!=BCF_HL_FLT && hrec->type!=BCF_HL_INFO && hrec->type!=BCF_HL_FMT ) continue;
+            if ( !keep_flt && hrec->type==BCF_HL_FLT ) continue;
+            if ( !keep_info && hrec->type==BCF_HL_INFO ) continue;
+            if ( !keep_fmt && hrec->type==BCF_HL_FMT ) continue;
+            int k = bcf_hrec_find_key(hrec,"ID");
+            assert( k>=0 ); // this should always be true for valid VCFs
+            int value, ret = khash_str2int_get(keep,hrec->vals[k],&value);
+            if ( ret==0 && value>>hrec->type ) // keep
+            {
+                if ( hrec->type==BCF_HL_FLT && !strcmp("PASS",hrec->vals[k]) ) args->flt_keep_pass = 1;
+                continue;
+            }
+            args->nrm++;
+            args->rm = (rm_tag_t*) realloc(args->rm,sizeof(rm_tag_t)*args->nrm);
+            rm_tag_t *tag = &args->rm[args->nrm-1];
+            if ( hrec->type==BCF_HL_INFO ) tag->handler = remove_info_tag;
+            else if ( hrec->type==BCF_HL_FMT ) tag->handler = remove_format_tag;
+            else
+            {
+                tag->handler = remove_filter;
+                tag->hdr_id = bcf_hdr_id2int(args->hdr, BCF_DT_ID, hrec->vals[k]);
+            }
+            tag->key = strdup(hrec->vals[k]);
+            if ( !args->keep_sites ) bcf_hdr_remove(args->hdr_out,hrec->type,tag->key);
+        }
+    }
+    khash_str2int_destroy_free(keep);
+    if ( !args->nrm ) error("No matching tag in -x %s\n", args->remove_annots);
+    if (bcf_hdr_sync(args->hdr_out) < 0)
+        error_errno("[%s] Failed to update header", __func__);
+}
+static void init_header_lines(args_t *args)
+{
+    if ( args->header_fname )
+    {
+        htsFile *file = hts_open(args->header_fname, "rb");
+        if ( !file ) error("Error reading %s\n", args->header_fname);
+        kstring_t str = {0,0,0};
+        while ( hts_getline(file, KS_SEP_LINE, &str) > 0 )
+        {
+            if ( bcf_hdr_append(args->hdr_out,str.s) ) error("Could not parse %s: %s\n", args->header_fname, str.s);
+            bcf_hdr_append(args->hdr,str.s);    // the input file may not have the header line if run with -h (and nothing else)
+        }
+        if ( hts_close(file)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,args->header_fname);
+        free(str.s);
+    }
+    if ( args->header_lines )
+    {
+        int i, n = dbuf_n(args->header_lines);
+        for (i=0; i<n; i++)
+        {
+            char *line = dbuf_ith(args->header_lines,i);
+            if ( bcf_hdr_append(args->hdr_out,line) ) error("Could not parse the header line: %s\n", line);
+            bcf_hdr_append(args->hdr,line);    // the input file may not have the header line if run with -H (and nothing else)
+        }
+        dbuf_destroy_free(args->header_lines);
+        args->header_lines = NULL;
+    }
+    if (bcf_hdr_sync(args->hdr_out) < 0)
+        error_errno("[%s] Failed to update output header", __func__);
+    if (bcf_hdr_sync(args->hdr) < 0)
+        error_errno("[%s] Failed to update input header", __func__);
+}
+static int vcf_getter_info_str2str(args_t *args, bcf1_t *rec, annot_col_t *col, void **ptr, int *mptr)
+{
+    return bcf_get_info_string(args->tgts_hdr,rec,col->hdr_key_src,ptr,mptr);
+}
+static int vcf_getter_id2str(args_t *args, bcf1_t *rec, annot_col_t *col, void **ptr, int *mptr)
+{
+    char *str = *((char**)ptr);
+    int len = strlen(rec->d.id);
+    if ( len >= *mptr ) str = realloc(str, len+1);
+    strcpy(str, rec->d.id);
+    *((char**)ptr) = str;
+    *mptr = len+1;
+    return len;
+}
+static int vcf_getter_filter2str(args_t *args, bcf1_t *rec, annot_col_t *col, void **ptr, int *mptr)
+{
+    kstring_t str;
+    str.s = *((char**)ptr);
+    str.m = *mptr;
+    str.l = 0;
+
+    int i;
+    if ( rec->d.n_flt )
+    {
+        for (i=0; i<rec->d.n_flt; i++)
+        {
+            if (i) kputc(';', &str);
+            kputs(bcf_hdr_int2id(args->tgts_hdr,BCF_DT_ID,rec->d.flt[i]), &str);
+        }
+    }
+    else kputc('.', &str);
+
+    *((char**)ptr) = str.s;
+    *mptr = str.m;
+    return str.l;
+}
+static int setter_filter(args_t *args, bcf1_t *line, annot_col_t *col, void *data)
+{
+    if ( !data ) error("Error: the --merge-logic option cannot be used with FILTER (yet?)\n");
+
+    // note: so far this works only with one filter, not a list of filters
+    annot_line_t *tab = (annot_line_t*) data;
+    if ( tab->cols[col->icol][0]=='.' && !tab->cols[col->icol][1] ) // don't overwrite with a missing value unless asked
+    {
+        if ( (col->replace & CARRY_OVER_MISSING) && (col->replace & (REPLACE_ALL|REPLACE_NON_MISSING)) ) bcf_update_filter(args->hdr_out,line,NULL,0);
+        return 0;
+    }
+    hts_expand(int,1,args->mtmpi,args->tmpi);
+    args->tmpi[0] = bcf_hdr_id2int(args->hdr_out, BCF_DT_ID, tab->cols[col->icol]);
+    if ( args->tmpi[0]<0 ) error("The FILTER \"%s\" is not defined in the header, was the -h option provided?\n", tab->cols[col->icol]);
+    if ( col->replace & SET_OR_APPEND ) return bcf_add_filter(args->hdr_out,line,args->tmpi[0]);
+    if ( !(col->replace & REPLACE_MISSING) )
+    {
+        bcf_update_filter(args->hdr_out,line,NULL,0);
+        return bcf_update_filter(args->hdr_out,line,args->tmpi,1);
+    }
+
+    // only update missing FILTER
+    if ( !(line->unpacked & BCF_UN_FLT) ) bcf_unpack(line, BCF_UN_FLT);
+    if ( !line->d.n_flt )
+        return bcf_update_filter(args->hdr_out,line,args->tmpi,1);
+
+    return 0;
+}
+static int vcf_setter_filter(args_t *args, bcf1_t *line, annot_col_t *col, void *data)
+{
+    int i, ret = 0;
+    bcf1_t *rec = (bcf1_t*) data;
+    if ( !(rec->unpacked & BCF_UN_FLT) ) bcf_unpack(rec, BCF_UN_FLT);
+    if ( !(line->unpacked & BCF_UN_FLT) ) bcf_unpack(line, BCF_UN_FLT);
+    if ( !rec->d.n_flt ) // don't overwrite with a missing value unless asked
+    {
+        if ( (col->replace & CARRY_OVER_MISSING) && (col->replace & (REPLACE_ALL|REPLACE_NON_MISSING)) ) bcf_update_filter(args->hdr_out,line,NULL,0);
+        return 0;
+    }
+    if ( col->replace & (SET_OR_APPEND|REPLACE_MISSING) )
+    {
+        if ( (col->replace & REPLACE_MISSING) && line->d.n_flt ) return 0; // only update missing FILTER
+        for (i=0; i<rec->d.n_flt; i++)
+        {
+            const char *flt = bcf_hdr_int2id(args->files->readers[1].header, BCF_DT_ID, rec->d.flt[i]);
+            if ( bcf_add_filter(args->hdr_out,line,bcf_hdr_id2int(args->hdr_out, BCF_DT_ID, flt)) < 0 ) ret = -1;
+        }
+        return ret;
+    }
+    hts_expand(int,rec->d.n_flt,args->mtmpi,args->tmpi);
+    for (i=0; i<rec->d.n_flt; i++)
+    {
+        const char *flt = bcf_hdr_int2id(args->files->readers[1].header, BCF_DT_ID, rec->d.flt[i]);
+        args->tmpi[i] = bcf_hdr_id2int(args->hdr_out, BCF_DT_ID, flt);
+    }
+    bcf_update_filter(args->hdr_out,line,NULL,0);
+    return bcf_update_filter(args->hdr_out,line,args->tmpi,rec->d.n_flt);
+}
+static int setter_pos(args_t *args, bcf1_t *line, annot_col_t *col, void *data)
+{
+    annot_line_t *tab = (annot_line_t*) data;
+    if ( tab->cols[col->icol] && tab->cols[col->icol][0]=='.' && !tab->cols[col->icol][1] ) return 0; // don't replace with "."
+    char *tmp;
+    int pos = strtol(tab->cols[col->icol], &tmp, 10);
+    if ( tmp==tab->cols[col->icol] )
+        error("Could not parse ~POS at %s:%"PRId64" .. [%s]\n",bcf_seqname(args->hdr,line),(int64_t)line->pos+1,tab->cols[col->icol]);
+    line->pos = pos - 1;
+    return 0;
+}
+static int setter_id(args_t *args, bcf1_t *line, annot_col_t *col, void *data)
+{
+    if ( !data ) error("Error: the --merge-logic option cannot be used with ID (yet?)\n");
+    if ( col->replace & MATCH_VALUE ) return 0;
+
+    // possible cases:
+    //      IN  ANNOT   OUT     ACHIEVED_BY
+    //      x   y       x        -c +ID
+    //      x   y       y        -c ID
+    //      x   y       x,y      -c =ID
+    //      x   .       x        -c +ID, ID
+    //      x   .       .        -x ID
+    //      .   y       y        -c +ID, -c ID
+    //
+    annot_line_t *tab = (annot_line_t*) data;
+    if ( tab->cols[col->icol] && tab->cols[col->icol][0]=='.' && !tab->cols[col->icol][1] ) return 0; // don't replace with "."
+    if ( col->replace & SET_OR_APPEND ) return bcf_add_id(args->hdr_out,line,tab->cols[col->icol]);
+    if ( !(col->replace & REPLACE_MISSING) ) return bcf_update_id(args->hdr_out,line,tab->cols[col->icol]);
+
+    // running with +ID, only update missing ids
+    if ( !line->d.id || (line->d.id[0]=='.' && !line->d.id[1]) )
+        return bcf_update_id(args->hdr_out,line,tab->cols[col->icol]);
+    return 0;
+}
+static int vcf_setter_id(args_t *args, bcf1_t *line, annot_col_t *col, void *data)
+{
+    if ( col->replace & MATCH_VALUE ) return 0;
+
+    bcf1_t *rec = (bcf1_t*) data;
+
+    char *id;
+    if ( col->getter )
+    {
+        int nret = col->getter(args,rec,col,&col->ptr,&col->mptr);
+        id = (char*) col->ptr;
+        if ( nret<=0 || (nret==1 && *id=='.') ) return 0;   // don't replace with "."
+    }
+    else
+    {
+        if ( rec->d.id && rec->d.id[0]=='.' && !rec->d.id[1] ) return 0;    // don't replace with "."
+        id = rec->d.id;
+    }
+    if ( col->replace & SET_OR_APPEND ) return bcf_add_id(args->hdr_out,line,id);
+    if ( !(col->replace & REPLACE_MISSING) ) return bcf_update_id(args->hdr_out,line,id);
+
+    // running with +ID, only update missing ids
+    if ( !line->d.id || (line->d.id[0]=='.' && !line->d.id[1]) )
+        return bcf_update_id(args->hdr_out,line,id);
+    return 0;
+}
+static int vcf_setter_ref(args_t *args, bcf1_t *line, annot_col_t *col, void *data)
+{
+    bcf1_t *rec = (bcf1_t*) data;
+    if ( !strcmp(rec->d.allele[0],line->d.allele[0]) ) return 0;    // no update necessary
+    const char **als = (const char**) malloc(sizeof(char*)*line->n_allele);
+    als[0] = rec->d.allele[0];
+    int i;
+    for (i=1; i<line->n_allele; i++) als[i] = line->d.allele[i];
+    int ret = bcf_update_alleles(args->hdr_out, line, als, line->n_allele);
+    free(als);
+    return ret;
+}
+static int vcf_setter_alt(args_t *args, bcf1_t *line, annot_col_t *col, void *data)
+{
+    bcf1_t *rec = (bcf1_t*) data;
+    int i;
+    if ( line->n_allele>1 && (col->replace & REPLACE_MISSING) ) return 0;
+    if ( rec->n_allele==line->n_allele )
+    {
+        for (i=1; i<rec->n_allele; i++) if ( strcmp(rec->d.allele[i],line->d.allele[i]) ) break;
+        if ( i==rec->n_allele ) return 0;   // no update necessary
+    }
+    const char **als = (const char**) malloc(sizeof(char*)*rec->n_allele);
+    als[0] = line->d.allele[0];
+    for (i=1; i<rec->n_allele; i++) als[i] = rec->d.allele[i];
+    int ret = bcf_update_alleles(args->hdr_out, line, als, rec->n_allele);
+    free(als);
+    return ret;
+}
+static int setter_qual(args_t *args, bcf1_t *line, annot_col_t *col, void *data)
+{
+    if ( !data ) error("Error: the --merge-logic option cannot be used with QUAL (yet?)\n");
+
+    annot_line_t *tab = (annot_line_t*) data;
+    char *str = tab->cols[col->icol];
+    if ( str[0]=='.' && str[1]==0 ) // don't overwrite with a missing value unless asked
+    {
+        if ( (col->replace & CARRY_OVER_MISSING) && (col->replace & (REPLACE_ALL|REPLACE_NON_MISSING)) ) bcf_float_set_missing(line->qual);
+        return 0;
+    }
+    if ( (col->replace & REPLACE_MISSING) && !bcf_float_is_missing(line->qual) ) return 0;
+
+    line->qual = strtod(str, &str);
+    if ( str == tab->cols[col->icol] )
+        error("Could not parse %s at %s:%"PRId64" .. [%s]\n", col->hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) line->pos+1,tab->cols[col->icol]);
+    return 0;
+}
+static int vcf_setter_qual(args_t *args, bcf1_t *line, annot_col_t *col, void *data)
+{
+    bcf1_t *rec = (bcf1_t*) data;
+    if ( bcf_float_is_missing(rec->qual) )  // don't overwrite with a missing value unless asked
+    {
+        if ( (col->replace & CARRY_OVER_MISSING) && (col->replace & (REPLACE_ALL|REPLACE_NON_MISSING)) ) bcf_float_set_missing(line->qual);
+        return 0;
+    }
+    if ( (col->replace & REPLACE_MISSING) && !bcf_float_is_missing(line->qual) ) return 0;
+    line->qual = rec->qual;
+    return 0;
+}
+static int setter_info_flag(args_t *args, bcf1_t *line, annot_col_t *col, void *data)
+{
+    if ( !data ) error("Error: the --merge-logic option cannot be used with INFO type=Flag (yet?)\n");
+
+    annot_line_t *tab = (annot_line_t*) data;
+    char *str = tab->cols[col->icol];
+    if ( str[0]=='.' && str[1]==0 ) // don't overwrite with a missing value unless asked
+    {
+        if ( (col->replace & CARRY_OVER_MISSING) && (col->replace & (REPLACE_ALL|REPLACE_NON_MISSING)) ) bcf_update_info_flag(args->hdr_out,line,col->hdr_key_dst,NULL,0);
+        return 0;
+    }
+
+    if ( str[0]=='1' && str[1]==0 ) return bcf_update_info_flag(args->hdr_out,line,col->hdr_key_dst,NULL,1);
+    if ( str[0]=='0' && str[1]==0 ) return bcf_update_info_flag(args->hdr_out,line,col->hdr_key_dst,NULL,0);
+    error("Could not parse %s at %s:%"PRId64" .. [%s]\n", col->hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) line->pos+1,tab->cols[col->icol]);
+    return -1;
+}
+static int vcf_setter_info_flag(args_t *args, bcf1_t *line, annot_col_t *col, void *data)
+{
+    bcf1_t *rec = (bcf1_t*) data;
+    int flag = bcf_get_info_flag(args->files->readers[1].header,rec,col->hdr_key_src,NULL,NULL);
+    bcf_update_info_flag(args->hdr_out,line,col->hdr_key_dst,NULL,flag);
+    return 0;
+}
+static int setter_ARinfo_int32(args_t *args, bcf1_t *line, annot_col_t *col, int nals, char **als, int ntmpi)
+{
+    if ( col->number==BCF_VL_A && ntmpi!=nals-1 && (ntmpi!=1 || args->tmpi[0]!=bcf_int32_missing || args->tmpi[1]!=bcf_int32_vector_end) )
+        error("Incorrect number of values (%d) for the %s tag at %s:%"PRId64"\n", ntmpi,col->hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) line->pos+1);
+    else if ( col->number==BCF_VL_R && ntmpi!=nals && (ntmpi!=1 || args->tmpi[0]!=bcf_int32_missing || args->tmpi[1]!=bcf_int32_vector_end) )
+        error("Incorrect number of values (%d) for the %s tag at %s:%"PRId64"\n", ntmpi,col->hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) line->pos+1);
+
+    int ndst = col->number==BCF_VL_A ? line->n_allele - 1 : line->n_allele;
+    int *map = vcmp_map_ARvalues(args->vcmp,ndst,nals,als,line->n_allele,line->d.allele);
+    if ( !map ) error("REF alleles not compatible at %s:%"PRId64"\n", bcf_seqname(args->hdr,line),(int64_t) line->pos+1);
+
+    // fill in any missing values in the target VCF (or all, if not present)
+    int ntmpi2 = bcf_get_info_float(args->hdr, line, col->hdr_key_dst, &args->tmpi2, &args->mtmpi2);
+    if ( ntmpi2 < ndst ) hts_expand(int32_t,ndst,args->mtmpi2,args->tmpi2);
+
+    int i;
+    for (i=0; i<ndst; i++)
+    {
+        if ( map[i]<0 )
+        {
+            if ( ntmpi2 < ndst ) args->tmpi2[i] = bcf_int32_missing;
+            continue;
+        }
+        if ( ntmpi2==ndst && (col->replace & REPLACE_MISSING)
+                && args->tmpi2[i]!=bcf_int32_missing
+                && args->tmpi2[i]!=bcf_int32_vector_end ) continue;
+
+        args->tmpi2[i] = args->tmpi[ map[i] ];
+    }
+    return bcf_update_info_int32(args->hdr_out,line,col->hdr_key_dst,args->tmpi2,ndst);
+}
+static int setter_info_int(args_t *args, bcf1_t *line, annot_col_t *col, void *data)
+{
+    annot_line_t *tab = (annot_line_t*) data;
+
+    // This is a bit hacky, only to reuse existing code with minimal changes:
+    //      -c =TAG will now behave as -l TAG:APPEND for integers
+    if ( col->replace & SET_OR_APPEND ) col->merge_method=MM_APPEND;
+
+    if ( !tab )
+    {
+        if ( col->merge_method!=MM_SUM && col->merge_method!=MM_AVG &&
+             col->merge_method!=MM_MIN && col->merge_method!=MM_MAX &&
+             col->merge_method!=MM_APPEND &&
+             col->merge_method!=MM_APPEND_MISSING )
+            error("Error: at the moment only the sum,avg,min,max,append,append-missing options are supported with --merge-logic for INFO type=Integer\n");
+    }
+
+    int i,ntmpi = 0;
+    if ( (col->replace & SET_OR_APPEND) && !col->mm_dbl_nused )
+    {
+        ntmpi = bcf_get_info_int32(args->hdr, line, col->hdr_key_dst, &args->tmpi, &args->mtmpi);
+        if ( ntmpi>0 && (args->tmpi[0]!=bcf_int32_missing || (col->replace & CARRY_OVER_MISSING)) )
+        {
+            col->mm_dbl_nused = col->mm_dbl_ndat = ntmpi;
+            hts_expand(double,col->mm_dbl_nused,col->mm_dbl_nalloc,col->mm_dbl);
+            for (i=0; i<ntmpi; i++)
+                col->mm_dbl[i] = args->tmpi[i];
+            col->mm_dbl_ndat = 1;
+        }
+        ntmpi = 0;
+    }
+    if ( tab )  // has data, not flushing yet
+    {
+        char *str = tab->cols[col->icol], *end = str;
+        if ( str[0]=='.' && str[1]==0 && col->merge_method!=MM_APPEND_MISSING && !(col->replace & CARRY_OVER_MISSING) ) return 1;
+
+        while ( *end )
+        {
+            ntmpi++;
+            hts_expand(int32_t,ntmpi,args->mtmpi,args->tmpi);
+            if ( str[0]=='.' && (str[1]==0 || str[1]==',') )
+            {
+                if ( col->merge_method==MM_APPEND_MISSING || (col->replace & CARRY_OVER_MISSING) )
+                    args->tmpi[ntmpi-1] = bcf_int32_missing;
+                else
+                    ntmpi--;
+                if ( str[1]==0 ) end = str+1;
+                str += 2;
+            }
+            else
+            {
+                args->tmpi[ntmpi-1] = strtol(str, &end, 10);
+                if ( end==str )
+                    error("Could not parse %s at %s:%"PRId64" .. [%s]\n", col->hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) line->pos+1,tab->cols[col->icol]);
+                str = end+1;
+            }
+        }
+        if ( col->merge_method!=MM_FIRST )
+        {
+            if ( !col->mm_dbl_nused )
+            {
+                col->mm_dbl_nused = ntmpi;
+                hts_expand(double,col->mm_dbl_nused,col->mm_dbl_nalloc,col->mm_dbl);
+                for (i=0; i<ntmpi; i++)
+                    col->mm_dbl[i] = args->tmpi[i];
+            }
+            else
+            {
+                if ( col->merge_method==MM_APPEND || col->merge_method==MM_APPEND_MISSING )
+                {
+                    int nori = col->mm_dbl_nused;
+                    col->mm_dbl_nused += ntmpi;
+                    hts_expand(double,col->mm_dbl_nused,col->mm_dbl_nalloc,col->mm_dbl);
+                    for (i=0; i<ntmpi; i++)
+                        col->mm_dbl[i+nori] = args->tmpi[i];
+                }
+                else
+                {
+                    if ( ntmpi!=col->mm_dbl_nused ) error("Error: cannot merge fields of unequal length\n");
+                    if ( col->merge_method==MM_SUM || col->merge_method==MM_AVG )
+                        for (i=0; i<ntmpi; i++) col->mm_dbl[i] += args->tmpi[i];
+                    else if ( col->merge_method==MM_MIN )
+                        for (i=0; i<ntmpi; i++) { if ( col->mm_dbl[i] > args->tmpi[i] ) col->mm_dbl[i] = args->tmpi[i]; }
+                    else if ( col->merge_method==MM_MAX )
+                        for (i=0; i<ntmpi; i++) { if ( col->mm_dbl[i] < args->tmpi[i] ) col->mm_dbl[i] = args->tmpi[i]; }
+                }
+            }
+            col->mm_dbl_ndat++;
+            return 1;
+        }
+    }
+    else if ( col->merge_method==MM_SUM || col->merge_method==MM_MIN || col->merge_method==MM_MAX || col->merge_method==MM_APPEND || col->merge_method==MM_APPEND_MISSING )
+    {
+        ntmpi = col->mm_dbl_nused;
+        hts_expand(int32_t,ntmpi,args->mtmpi,args->tmpi);
+        for (i=0; i<ntmpi; i++) args->tmpi[i] = col->mm_dbl[i];
+        col->mm_dbl_nused = col->mm_dbl_ndat = 0;
+    }
+    else if ( col->merge_method==MM_AVG )
+    {
+        ntmpi = col->mm_dbl_nused;
+        hts_expand(int32_t,ntmpi,args->mtmpi,args->tmpi);
+        for (i=0; i<ntmpi; i++) args->tmpi[i] = col->mm_dbl[i]/col->mm_dbl_ndat;
+        col->mm_dbl_nused = col->mm_dbl_ndat = 0;
+    }
+
+    if ( col->number==BCF_VL_A || col->number==BCF_VL_R )
+        return setter_ARinfo_int32(args,line,col,tab->nals,tab->als,ntmpi);
+
+    if ( col->replace & REPLACE_MISSING )
+    {
+        int ret = bcf_get_info_int32(args->hdr, line, col->hdr_key_dst, &args->tmpi2, &args->mtmpi2);
+        if ( ret>0 && args->tmpi2[0]!=bcf_int32_missing ) return 0;
+    }
+    return bcf_update_info_int32(args->hdr_out,line,col->hdr_key_dst,args->tmpi,ntmpi);
+}
+static int vcf_setter_info_int(args_t *args, bcf1_t *line, annot_col_t *col, void *data)
+{
+    bcf1_t *rec = (bcf1_t*) data;
+    int ntmpi = bcf_get_info_int32(args->files->readers[1].header,rec,col->hdr_key_src,&args->tmpi,&args->mtmpi);
+    if ( ntmpi < 0 ) return 0;    // nothing to add
+
+    if ( col->number==BCF_VL_A || col->number==BCF_VL_R )
+        return setter_ARinfo_int32(args,line,col,rec->n_allele,rec->d.allele,ntmpi);
+
+    if ( col->replace & REPLACE_MISSING )
+    {
+        int ret = bcf_get_info_int32(args->hdr, line, col->hdr_key_dst, &args->tmpi2, &args->mtmpi2);
+        if ( ret>0 && args->tmpi2[0]!=bcf_int32_missing ) return 0;
+    }
+
+    return bcf_update_info_int32(args->hdr_out,line,col->hdr_key_dst,args->tmpi,ntmpi);
+}
+static int setter_ARinfo_real(args_t *args, bcf1_t *line, annot_col_t *col, int nals, char **als, int ntmpf)
+{
+    if ( col->number==BCF_VL_A && ntmpf!=nals-1 && (ntmpf!=1 || !bcf_float_is_missing(args->tmpf[0]) || !bcf_float_is_vector_end(args->tmpf[0])) )
+        error("Incorrect number of values (%d) for the %s tag at %s:%"PRId64"\n", ntmpf,col->hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) line->pos+1);
+    else if ( col->number==BCF_VL_R && ntmpf!=nals && (ntmpf!=1 || !bcf_float_is_missing(args->tmpf[0]) || !bcf_float_is_vector_end(args->tmpf[0])) )
+        error("Incorrect number of values (%d) for the %s tag at %s:%"PRId64"\n", ntmpf,col->hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) line->pos+1);
+
+    int ndst = col->number==BCF_VL_A ? line->n_allele - 1 : line->n_allele;
+    int *map = vcmp_map_ARvalues(args->vcmp,ndst,nals,als,line->n_allele,line->d.allele);
+    if ( !map ) error("REF alleles not compatible at %s:%"PRId64"\n", bcf_seqname(args->hdr,line),(int64_t) line->pos+1);
+
+    // fill in any missing values in the target VCF (or all, if not present)
+    int ntmpf2 = bcf_get_info_float(args->hdr, line, col->hdr_key_dst, &args->tmpf2, &args->mtmpf2);
+    if ( ntmpf2 < ndst ) hts_expand(float,ndst,args->mtmpf2,args->tmpf2);
+
+    int i;
+    for (i=0; i<ndst; i++)
+    {
+        if ( map[i]<0 )
+        {
+            if ( ntmpf2 < ndst ) bcf_float_set_missing(args->tmpf2[i]);
+            continue;
+        }
+        if ( ntmpf2==ndst && (col->replace & REPLACE_MISSING)
+                && !bcf_float_is_missing(args->tmpf2[i])
+                && !bcf_float_is_vector_end(args->tmpf2[i]) ) continue;
+
+        args->tmpf2[i] = args->tmpf[ map[i] ];
+    }
+    return bcf_update_info_float(args->hdr_out,line,col->hdr_key_dst,args->tmpf2,ndst);
+}
+static int setter_info_real(args_t *args, bcf1_t *line, annot_col_t *col, void *data)
+{
+    annot_line_t *tab = (annot_line_t*) data;
+
+    // This is a bit hacky, only to reuse existing code with minimal changes:
+    //      -c =TAG will now behave as -l TAG:APPEND for floats
+    if ( col->replace & SET_OR_APPEND ) col->merge_method=MM_APPEND;
+
+    if ( !tab )
+    {
+        if ( col->merge_method!=MM_SUM && col->merge_method!=MM_AVG &&
+             col->merge_method!=MM_MIN && col->merge_method!=MM_MAX &&
+             col->merge_method!=MM_APPEND &&
+             col->merge_method!=MM_APPEND_MISSING )
+            error("Error: at the moment only the sum,avg,min,max,append,append-missing options are supported with --merge-logic for INFO type=Float\n");
+    }
+
+    int i,ntmpf = 0;
+    if ( (col->replace & SET_OR_APPEND) && !col->mm_dbl_nused )
+    {
+        ntmpf = bcf_get_info_float(args->hdr, line, col->hdr_key_dst, &args->tmpf, &args->mtmpf);
+        if ( ntmpf>0 && (!bcf_float_is_missing(args->tmpf[0]) || (col->replace & CARRY_OVER_MISSING)) )
+        {
+            col->mm_dbl_nused = ntmpf;
+            hts_expand(double,col->mm_dbl_nused,col->mm_dbl_nalloc,col->mm_dbl);
+            for (i=0; i<ntmpf; i++)
+                if ( bcf_float_is_missing(args->tmpf[i]) )
+                    bcf_double_set_missing(col->mm_dbl[i]);
+                else
+                    col->mm_dbl[i] = args->tmpf[i];
+            col->mm_dbl_ndat = 1;
+        }
+        ntmpf = 0;
+    }
+    if ( tab )  // data row, not just flushing
+    {
+        char *str = tab->cols[col->icol], *end = str;
+        if ( str[0]=='.' && str[1]==0 && col->merge_method!=MM_APPEND_MISSING && !(col->replace & CARRY_OVER_MISSING) ) return 1;
+
+        while ( *end )
+        {
+            ntmpf++;
+            hts_expand(float,ntmpf,args->mtmpf,args->tmpf);
+            if ( str[0]=='.' && (str[1]==0 || str[1]==',') )
+            {
+                if ( col->merge_method==MM_APPEND_MISSING || (col->replace & CARRY_OVER_MISSING) )
+                    bcf_float_set_missing(args->tmpf[ntmpf-1]);
+                else
+                    ntmpf--;
+                if ( str[1]==0 ) end = str+1;
+                str += 2;
+            }
+            else
+            {
+                args->tmpf[ntmpf-1] = strtod(str, &end);
+                if ( end==str )
+                    error("Could not parse %s at %s:%"PRId64" .. [%s]\n", col->hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) line->pos+1,tab->cols[col->icol]);
+                str = end+1;
+            }
+        }
+        if ( col->merge_method!=MM_FIRST )
+        {
+            if ( !col->mm_dbl_nused )
+            {
+                col->mm_dbl_nused = ntmpf;
+                hts_expand(double,col->mm_dbl_nused,col->mm_dbl_nalloc,col->mm_dbl);
+                for (i=0; i<ntmpf; i++)
+                {
+                    if ( bcf_float_is_missing(args->tmpf[i]) )
+                        bcf_double_set_missing(col->mm_dbl[i]);
+                    else
+                        col->mm_dbl[i] = args->tmpf[i];
+                }
+            }
+            else
+            {
+                if ( col->merge_method==MM_APPEND || col->merge_method==MM_APPEND_MISSING )
+                {
+                    int nori = col->mm_dbl_nused;
+                    col->mm_dbl_nused += ntmpf;
+                    hts_expand(double,col->mm_dbl_nused,col->mm_dbl_nalloc,col->mm_dbl);
+                    for (i=0; i<ntmpf; i++)
+                    {
+                        if ( bcf_float_is_missing(args->tmpf[i]) )
+                            bcf_double_set_missing(col->mm_dbl[i+nori]);
+                        else
+                            col->mm_dbl[i+nori] = args->tmpf[i];
+                    }
+                }
+                else
+                {
+                    if ( ntmpf!=col->mm_dbl_nused ) error("Error: cannot merge fields of unequal length\n");
+                    if ( col->merge_method==MM_SUM || col->merge_method==MM_AVG )
+                        for (i=0; i<ntmpf; i++) col->mm_dbl[i] += args->tmpf[i];
+                    else if ( col->merge_method==MM_MIN )
+                        for (i=0; i<ntmpf; i++) { if ( col->mm_dbl[i] > args->tmpf[i] ) col->mm_dbl[i] = args->tmpf[i]; }
+                    else if ( col->merge_method==MM_MAX )
+                        for (i=0; i<ntmpf; i++) { if ( col->mm_dbl[i] < args->tmpf[i] ) col->mm_dbl[i] = args->tmpf[i]; }
+                }
+            }
+            col->mm_dbl_ndat++;
+            return 1;
+        }
+    }
+    else if ( col->merge_method==MM_SUM || col->merge_method==MM_MIN || col->merge_method==MM_MAX || col->merge_method==MM_APPEND || col->merge_method==MM_APPEND_MISSING )
+    {
+        ntmpf = col->mm_dbl_nused;
+        hts_expand(int32_t,ntmpf,args->mtmpf,args->tmpf);
+        for (i=0; i<ntmpf; i++)
+        {
+            if ( bcf_double_is_missing(col->mm_dbl[i]) )
+                bcf_float_set_missing(args->tmpf[i]);
+            else
+                args->tmpf[i] = col->mm_dbl[i];
+        }
+        col->mm_dbl_nused = col->mm_dbl_ndat = 0;
+    }
+    else if ( col->merge_method==MM_AVG )
+    {
+        ntmpf = col->mm_dbl_nused;
+        hts_expand(int32_t,ntmpf,args->mtmpf,args->tmpf);
+        for (i=0; i<ntmpf; i++) args->tmpf[i] = col->mm_dbl[i]/col->mm_dbl_ndat;
+        col->mm_dbl_nused = col->mm_dbl_ndat = 0;
+    }
+
+    if ( col->number==BCF_VL_A || col->number==BCF_VL_R )
+        return setter_ARinfo_real(args,line,col,tab->nals,tab->als,ntmpf);
+
+    if ( col->replace & REPLACE_MISSING )
+    {
+        int ret = bcf_get_info_float(args->hdr, line, col->hdr_key_dst, &args->tmpf2, &args->mtmpf2);
+        if ( ret>0 && !bcf_float_is_missing(args->tmpf2[0]) ) return 0;
+    }
+
+    return bcf_update_info_float(args->hdr_out,line,col->hdr_key_dst,args->tmpf,ntmpf);
+}
+static int vcf_setter_info_real(args_t *args, bcf1_t *line, annot_col_t *col, void *data)
+{
+    bcf1_t *rec = (bcf1_t*) data;
+    int ntmpf = bcf_get_info_float(args->files->readers[1].header,rec,col->hdr_key_src,&args->tmpf,&args->mtmpf);
+    if ( ntmpf < 0 ) return 0;    // nothing to add
+
+    if ( col->number==BCF_VL_A || col->number==BCF_VL_R )
+        return setter_ARinfo_real(args,line,col,rec->n_allele,rec->d.allele,ntmpf);
+
+    if ( col->replace & REPLACE_MISSING )
+    {
+        int ret = bcf_get_info_float(args->hdr, line, col->hdr_key_dst, &args->tmpf2, &args->mtmpf2);
+        if ( ret>0 && !bcf_float_is_missing(args->tmpf2[0]) ) return 0;
+    }
+
+    return bcf_update_info_float(args->hdr_out,line,col->hdr_key_dst,args->tmpf,ntmpf);
+}
+int copy_string_field(char *src, int isrc, int src_len, kstring_t *dst, int idst); // see vcfmerge.c
+static int setter_ARinfo_string(args_t *args, bcf1_t *line, annot_col_t *col, int nals, char **als)
+{
+    assert( col->merge_method==MM_FIRST );
+
+    int nsrc = 1, lsrc = 0;
+    while ( args->tmps[lsrc] )
+    {
+        if ( args->tmps[lsrc]==',' ) nsrc++;
+        lsrc++;
+    }
+    if ( col->number==BCF_VL_A && nsrc!=nals-1 && (nsrc!=1 || args->tmps[0]!='.' || args->tmps[1]!=0 ) )
+        error("Incorrect number of values (%d) for the %s tag at %s:%"PRId64"\n", nsrc,col->hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) line->pos+1);
+    else if ( col->number==BCF_VL_R && nsrc!=nals && (nsrc!=1 || args->tmps[0]!='.' || args->tmps[1]!=0 ) )
+        error("Incorrect number of values (%d) for the %s tag at %s:%"PRId64"\n", nsrc,col->hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) line->pos+1);
+
+    int ndst = col->number==BCF_VL_A ? line->n_allele - 1 : line->n_allele;
+    int *map = vcmp_map_ARvalues(args->vcmp,ndst,nals,als,line->n_allele,line->d.allele);
+    if ( !map ) error("REF alleles not compatible at %s:%"PRId64"\n", bcf_seqname(args->hdr,line),(int64_t) line->pos+1);
+
+    // fill in any missing values in the target VCF (or all, if not present)
+    int i, empty = 0, nstr, mstr = args->tmpks.m;
+    nstr = bcf_get_info_string(args->hdr, line, col->hdr_key_dst, &args->tmpks.s, &mstr);
+    args->tmpks.m = mstr;
+    if ( nstr<0 || (nstr==1 && args->tmpks.s[0]=='.' && args->tmpks.s[1]==0) )
+    {
+        empty = 0;
+        args->tmpks.l = 0;
+        kputc('.',&args->tmpks);
+        for (i=1; i<ndst; i++) kputs(",.",&args->tmpks);
+    }
+    else args->tmpks.l = nstr;
+    for (i=0; i<ndst; i++)
+    {
+        if ( map[i]<0 )
+        {
+            if ( empty ) copy_string_field(".",0,1,&args->tmpks,i);
+            continue;
+        }
+        if ( col->replace & REPLACE_MISSING )
+        {
+            // Do not replace filled values. The field must be looked up again because
+            // of realloc in copy_string_field
+            int n = 0;
+            char *str = args->tmpks.s;
+            while ( *str && n<i )
+            {
+                if ( *str==',' ) n++;
+                str++;
+            }
+            if ( str[0]!='.' || (str[1]!=',' && str[1]!=0) ) continue;  // value already set
+        }
+        int ret = copy_string_field(args->tmps,map[i],lsrc,&args->tmpks,i);
+        if ( ret!=0 ) error("[%s:%d %s] Failed to copy a string field\n",  __FILE__,__LINE__,__func__);
+    }
+    return bcf_update_info_string(args->hdr_out,line,col->hdr_key_dst,args->tmpks.s);
+}
+void khash_str2int_clear_free(void *_hash)
+{
+    khash_t(str2int) *hash = (khash_t(str2int)*)_hash;
+    khint_t k;
+    if (hash == 0) return;
+    for (k = 0; k < kh_end(hash); ++k)
+        if (kh_exist(hash, k)) free((char*)kh_key(hash, k));
+    kh_clear(str2int, hash);
+}
+static int setter_info_str(args_t *args, bcf1_t *line, annot_col_t *col, void *data)
+{
+    if ( (col->replace & REPLACE_MISSING) && col->number!=BCF_VL_A && col->number!=BCF_VL_R )
+    {
+        int ret = bcf_get_info_string(args->hdr, line, col->hdr_key_dst, &args->tmps2, &args->mtmps2);
+        if ( ret>0 && (args->tmps2[0]!='.' || args->tmps2[1]!=0) ) return 0;
+    }
+
+    // This is a bit hacky, only to reuse existing code with minimal changes:
+    //      -c =TAG will now behave as -l TAG:unique for strings
+    if ( col->replace & SET_OR_APPEND ) col->merge_method=MM_UNIQUE;
+
+    annot_line_t *tab = (annot_line_t*) data;
+
+    int len = 0;
+    if ( tab )
+    {
+        len = strlen(tab->cols[col->icol]);
+        if ( !len ) return 0;
+        if ( len==1 && tab->cols[col->icol][0]=='.' && col->merge_method!=MM_APPEND_MISSING && !(col->replace & CARRY_OVER_MISSING) ) return 1;
+    }
+
+    if ( col->merge_method!=MM_FIRST )
+    {
+        if ( col->number==BCF_VL_A || col->number==BCF_VL_R )
+            error("Error: the --merge-logic option cannot be used with INFO tags Type=String,Number={A,R,G}\n");
+
+        if ( data )
+        {
+            assert( col->merge_method==MM_APPEND || col->merge_method==MM_APPEND_MISSING || col->merge_method==MM_UNIQUE );
+            if ( col->merge_method==MM_UNIQUE )
+            {
+                if ( !col->mm_str_hash ) col->mm_str_hash = (khash_t(str2int)*)khash_str2int_init();
+                if ( khash_str2int_has_key(col->mm_str_hash, tab->cols[col->icol]) ) return 1;
+                khash_str2int_inc(col->mm_str_hash, strdup(tab->cols[col->icol]));
+            }
+
+            if ( (col->replace & SET_OR_APPEND) && !col->mm_kstr.l )
+            {
+                int m = col->mm_kstr.m;
+                int n = bcf_get_info_string(args->hdr, line, col->hdr_key_dst, &col->mm_kstr.s, &m);
+                col->mm_kstr.m = m;
+                if ( n>0 && ((col->replace & CARRY_OVER_MISSING) || col->mm_kstr.s[0]!='.' || col->mm_kstr.s[1]) ) col->mm_kstr.l = n;
+            }
+
+            if ( col->mm_kstr.l ) kputc(',',&col->mm_kstr);
+            kputs(tab->cols[col->icol], &col->mm_kstr);
+            return 1;
+        }
+
+        if ( col->mm_kstr.l )
+        {
+            hts_expand(char,col->mm_kstr.l+1,args->mtmps,args->tmps);
+            memcpy(args->tmps,col->mm_kstr.s,col->mm_kstr.l+1);
+        }
+        else
+            return 0;
+
+        // flush the line
+        if ( col->merge_method==MM_UNIQUE )
+            khash_str2int_clear_free(col->mm_str_hash);
+        col->mm_kstr.l = 0;
+    }
+    else
+    {
+        assert(tab);
+        hts_expand(char,len+1,args->mtmps,args->tmps);
+        memcpy(args->tmps,tab->cols[col->icol],len+1);
+
+        if ( col->number==BCF_VL_A || col->number==BCF_VL_R )
+            return setter_ARinfo_string(args,line,col,tab->nals,tab->als);
+    }
+
+    return bcf_update_info_string(args->hdr_out,line,col->hdr_key_dst,args->tmps);
+}
+static int vcf_setter_info_str(args_t *args, bcf1_t *line, annot_col_t *col, void *data)
+{
+    bcf1_t *rec = (bcf1_t*) data;
+
+    if ( col->getter )
+        col->getter(args,rec,col,(void**)&args->tmps, &args->mtmps);
+    else
+    {
+        int ntmps = bcf_get_info_string(args->files->readers[1].header,rec,col->hdr_key_src,&args->tmps,&args->mtmps);
+        if ( ntmps < 0 ) return 0;    // nothing to add
+    }
+
+    if ( col->number==BCF_VL_A || col->number==BCF_VL_R )
+        return setter_ARinfo_string(args,line,col,rec->n_allele,rec->d.allele);
+
+    if ( col->replace & REPLACE_MISSING )
+    {
+        int ret = bcf_get_info_string(args->hdr, line, col->hdr_key_dst, &args->tmps2, &args->mtmps2);
+        if ( ret>0 && (args->tmps2[0]!='.' || args->tmps2[1]!=0) ) return 0;
+    }
+
+    return bcf_update_info_string(args->hdr_out,line,col->hdr_key_dst,args->tmps);
+}
+static int genotypes_to_string(args_t *args, int nsrc1, int32_t *src, int nsmpl_dst, kstring_t *str)
+{
+    int i, isrc, idst;
+    int blen = nsrc1 > 1 ? nsrc1 + 1 : 1;   // typically the genotypes take three bytes 0/1, no 0-termination is needed
+
+gt_length_too_big:
+    str->l = 0;
+    for (idst=0; idst<nsmpl_dst; idst++)
+    {
+        isrc = args->sample_map ? args->sample_map[idst] : idst;
+        if ( isrc==-1 )
+        {
+            kputc_('.', str);
+            for (i=1; i < blen; i++) kputc_(0, str);
+            continue;
+        }
+
+        size_t plen = str->l;
+        int32_t *ptr = src + isrc*nsrc1;
+        for (i=0; i<nsrc1 && ptr[i]!=bcf_int32_vector_end; i++)
+        {
+            if ( i ) kputc("/|"[bcf_gt_is_phased(ptr[i])], str);
+            if ( bcf_gt_is_missing(ptr[i]) ) kputc('.', str);
+            else kputw(bcf_gt_allele(ptr[i]), str);
+        }
+        if ( i==0 ) kputc('.', str);
+        if ( str->l - plen > blen )
+        {
+            // too many alternate alleles or ploidy is too large, the genotype does not fit
+            // three characters ("0/0" vs "10/10").
+            blen *= 2;
+            goto gt_length_too_big;
+        }
+        plen = str->l - plen;
+        while ( plen < blen )
+        {
+            kputc_(0, str);
+            plen++;
+        }
+    }
+    return 0;
+}
+static int vcf_setter_format_gt(args_t *args, bcf1_t *line, annot_col_t *col, void *data)
+{
+    bcf1_t *rec = (bcf1_t*) data;
+    int nsrc = bcf_get_genotypes(args->files->readers[1].header,rec,&args->tmpi,&args->mtmpi);
+    if ( nsrc==-3 ) return 0;    // the tag is not present
+    if ( nsrc<=0 ) return 1;     // error
+
+    // Genotypes are internally represented as integers. This is a complication when
+    // adding as a different Type=String field, such as FMT/newGT:=GT
+    if ( strcmp(col->hdr_key_src,col->hdr_key_dst) )
+    {
+        int nsmpl_dst = bcf_hdr_nsamples(args->hdr_out);
+        int nsmpl_src = bcf_hdr_nsamples(args->files->readers[1].header);
+        genotypes_to_string(args,nsrc/nsmpl_src,args->tmpi,nsmpl_dst,&args->tmpks);
+        return bcf_update_format_char(args->hdr_out,line,col->hdr_key_dst,args->tmpks.s,args->tmpks.l);
+    }
+
+    if ( !args->sample_map )
+        return bcf_update_genotypes(args->hdr_out,line,args->tmpi,nsrc);
+
+    int i, j, ndst = bcf_get_genotypes(args->hdr,line,&args->tmpi2,&args->mtmpi2);
+    if ( ndst > 0 ) ndst /= bcf_hdr_nsamples(args->hdr_out);
+    nsrc /= bcf_hdr_nsamples(args->files->readers[1].header);
+    if ( ndst<=0 )  // field not present in dst file
+    {
+        if ( col->replace & REPLACE_NON_MISSING ) return 0;
+        hts_expand(int32_t, nsrc*bcf_hdr_nsamples(args->hdr_out), args->mtmpi2, args->tmpi2);
+        for (i=0; i<bcf_hdr_nsamples(args->hdr_out); i++)
+        {
+            int32_t *dst = args->tmpi2 + nsrc*i;
+            if ( args->sample_map[i]==-1 )
+            {
+                dst[0] = bcf_gt_missing;
+                for (j=1; j<nsrc; j++) dst[j] = bcf_int32_vector_end;
+            }
+            else
+            {
+                int32_t *src = args->tmpi + nsrc*args->sample_map[i];
+                for (j=0; j<nsrc; j++) dst[j] = src[j];
+            }
+        }
+        return bcf_update_genotypes(args->hdr_out,line,args->tmpi2,nsrc*bcf_hdr_nsamples(args->hdr_out));
+    }
+    else if ( ndst >= nsrc )
+    {
+        for (i=0; i<bcf_hdr_nsamples(args->hdr_out); i++)
+        {
+            if ( args->sample_map[i]==-1 ) continue;
+            int32_t *src = args->tmpi  + nsrc*args->sample_map[i];
+            int32_t *dst = args->tmpi2 + ndst*i;
+            if ( (col->replace & REPLACE_NON_MISSING) && bcf_gt_is_missing(dst[0]) ) continue;
+            if ( (col->replace & REPLACE_MISSING)  && !bcf_gt_is_missing(dst[0]) ) continue;
+            for (j=0; j<nsrc; j++) dst[j] = src[j];
+            for (; j<ndst; j++) dst[j] = bcf_int32_vector_end;
+        }
+        return bcf_update_genotypes(args->hdr_out,line,args->tmpi2,ndst*bcf_hdr_nsamples(args->hdr_out));
+    }
+    else    // ndst < nsrc
+    {
+        hts_expand(int32_t, nsrc*bcf_hdr_nsamples(args->hdr_out), args->mtmpi3, args->tmpi3);
+        for (i=0; i<bcf_hdr_nsamples(args->hdr_out); i++)
+        {
+            int32_t *ori = args->tmpi2 + ndst*i;
+            int32_t *dst = args->tmpi3 + nsrc*i;
+            int keep_ori = 0;
+            if ( args->sample_map[i]==-1 ) keep_ori = 1;
+            else if ( (col->replace & REPLACE_NON_MISSING) && bcf_gt_is_missing(ori[0]) ) keep_ori = 1;
+            else if ( (col->replace & REPLACE_MISSING)  && !bcf_gt_is_missing(ori[0]) ) keep_ori = 1;
+            if ( keep_ori )
+            {
+                for (j=0; j<ndst; j++) dst[j] = ori[j];
+                for (; j<nsrc; j++) dst[j] = bcf_int32_vector_end;
+            }
+            else
+            {
+                int32_t *src = args->tmpi + nsrc*args->sample_map[i];
+                for (j=0; j<nsrc; j++) dst[j] = src[j];
+            }
+        }
+        return bcf_update_genotypes(args->hdr_out,line,args->tmpi3,nsrc*bcf_hdr_nsamples(args->hdr_out));
+    }
+}
+static int count_vals(annot_line_t *tab, int icol_beg, int icol_end)
+{
+    int i, nmax = 1;
+    for (i=icol_beg; i<icol_end; i++)
+    {
+        char *str = tab->cols[i], *end = str;
+        if ( str[0]=='.' && !str[1] )
+        {
+            // missing value
+            if ( !nmax ) nmax = 1;
+            continue;
+        }
+        int n = 1;
+        while ( *end )
+        {
+            if ( *end==',' ) n++;
+            end++;
+        }
+        if ( nmax<n ) nmax = n;
+    }
+    return nmax;
+}
+static int core_setter_format_int(args_t *args, bcf1_t *line, annot_col_t *col, int32_t *vals, int nvals)
+{
+    if ( !args->sample_map )
+        return bcf_update_format_int32(args->hdr_out,line,col->hdr_key_dst,vals,nvals*args->nsmpl_annot);
+
+    int i, j, ndst = bcf_get_format_int32(args->hdr,line,col->hdr_key_dst,&args->tmpi2,&args->mtmpi2);
+    if ( ndst > 0 ) ndst /= bcf_hdr_nsamples(args->hdr_out);
+    if ( ndst<=0 )
+    {
+        if ( col->replace & REPLACE_NON_MISSING ) return 0;    // overwrite only if present
+        hts_expand(int32_t, nvals*bcf_hdr_nsamples(args->hdr_out), args->mtmpi2, args->tmpi2);
+        for (i=0; i<bcf_hdr_nsamples(args->hdr_out); i++)
+        {
+            int32_t *dst = args->tmpi2 + nvals*i;
+            if ( args->sample_map[i]==-1 )
+            {
+                dst[0] = bcf_int32_missing;
+                for (j=1; j<nvals; j++) dst[j] = bcf_int32_vector_end;
+            }
+            else
+            {
+                int32_t *src = vals + nvals*args->sample_map[i];
+                for (j=0; j<nvals; j++) dst[j] = src[j];
+            }
+        }
+        return bcf_update_format_int32(args->hdr_out,line,col->hdr_key_dst,args->tmpi2,nvals*bcf_hdr_nsamples(args->hdr_out));
+    }
+    else if ( ndst >= nvals )
+    {
+        for (i=0; i<bcf_hdr_nsamples(args->hdr_out); i++)
+        {
+            if ( args->sample_map[i]==-1 ) continue;
+            int32_t *src = vals  + nvals*args->sample_map[i];
+            int32_t *dst = args->tmpi2 + ndst*i;
+            // possible cases:
+            //      in annot out
+            //       x  y     x     TAG,-TAG,=TAG    .. REPLACE_ALL, REPLACE_NON_MISSING, SET_OR_APPEND
+            //       x  y     y    +TAG              .. REPLACE_MISSING
+            //       .  y     .    =TAG              .. SET_OR_APPEND
+            //       .  y     y     TAG,+TAG,-TAG    .. REPLACE_ALL, REPLACE_MISSING, REPLACE_NON_MISSING
+            //       x  .     x     TAG,+TAG         .. REPLACE_ALL, REPLACE_MISSING
+            //       x  .     .    -TAG              .. REPLACE_NON_MISSING
+            if ( col->replace & REPLACE_NON_MISSING ) { if ( dst[0]==bcf_int32_missing ) continue; }
+            else if ( col->replace & REPLACE_MISSING ) { if ( dst[0]!=bcf_int32_missing ) continue; }
+            else if ( col->replace & REPLACE_ALL ) { if ( src[0]==bcf_int32_missing ) continue; }
+            for (j=0; j<nvals; j++) dst[j] = src[j];
+            for (; j<ndst; j++) dst[j] = bcf_int32_vector_end;
+        }
+        return bcf_update_format_int32(args->hdr_out,line,col->hdr_key_dst,args->tmpi2,ndst*bcf_hdr_nsamples(args->hdr_out));
+    }
+    else    // ndst < nvals
+    {
+        hts_expand(int32_t, nvals*bcf_hdr_nsamples(args->hdr_out), args->mtmpi3, args->tmpi3);
+        for (i=0; i<bcf_hdr_nsamples(args->hdr_out); i++)
+        {
+            int32_t *ann = vals + nvals*args->sample_map[i];
+            int32_t *ori = args->tmpi2 + ndst*i;                // ori vcf line
+            int32_t *dst = args->tmpi3 + nvals*i;               // expanded buffer
+            int use_new_ann = 1;
+            if ( args->sample_map[i]==-1 ) use_new_ann = 0;
+            else if ( col->replace & REPLACE_NON_MISSING ) { if ( ori[0]==bcf_int32_missing ) use_new_ann = 0; }
+            else if ( col->replace & REPLACE_MISSING ) { if ( ori[0]!=bcf_int32_missing ) use_new_ann = 0; }
+            else if ( col->replace & REPLACE_ALL ) { if ( ann[0]==bcf_int32_missing ) use_new_ann = 0; }
+            if ( !use_new_ann )
+            {
+                for (j=0; j<ndst; j++) dst[j] = ori[j];
+                for (; j<nvals; j++) dst[j] = bcf_int32_vector_end;
+            }
+            else
+                for (j=0; j<nvals; j++) dst[j] = ann[j];
+        }
+        return bcf_update_format_int32(args->hdr_out,line,col->hdr_key_dst,args->tmpi3,nvals*bcf_hdr_nsamples(args->hdr_out));
+    }
+}
+static int core_setter_format_real(args_t *args, bcf1_t *line, annot_col_t *col, float *vals, int nvals)
+{
+    if ( !args->sample_map )
+        return bcf_update_format_float(args->hdr_out,line,col->hdr_key_dst,vals,nvals*args->nsmpl_annot);
+
+    int i, j, ndst = bcf_get_format_float(args->hdr,line,col->hdr_key_dst,&args->tmpf2,&args->mtmpf2);
+    if ( ndst > 0 ) ndst /= bcf_hdr_nsamples(args->hdr_out);
+    if ( ndst<=0 )
+    {
+        if ( col->replace & REPLACE_NON_MISSING ) return 0;    // overwrite only if present
+        hts_expand(float, nvals*bcf_hdr_nsamples(args->hdr_out), args->mtmpf2, args->tmpf2);
+        for (i=0; i<bcf_hdr_nsamples(args->hdr_out); i++)
+        {
+            float *dst = args->tmpf2 + nvals*i;
+            if ( args->sample_map[i]==-1 )
+            {
+                bcf_float_set_missing(dst[0]);
+                for (j=1; j<nvals; j++) bcf_float_set_vector_end(dst[j]);
+            }
+            else
+            {
+                float *src = vals + nvals*args->sample_map[i];
+                for (j=0; j<nvals; j++) dst[j] = src[j];
+            }
+        }
+        return bcf_update_format_float(args->hdr_out,line,col->hdr_key_dst,args->tmpf2,nvals*bcf_hdr_nsamples(args->hdr_out));
+    }
+    else if ( ndst >= nvals )
+    {
+        for (i=0; i<bcf_hdr_nsamples(args->hdr_out); i++)
+        {
+            if ( args->sample_map[i]==-1 ) continue;
+            float *src = vals  + nvals*args->sample_map[i];
+            float *dst = args->tmpf2 + ndst*i;
+            if ( col->replace & REPLACE_NON_MISSING ) { if ( bcf_float_is_missing(dst[0]) ) continue; }
+            else if ( col->replace & REPLACE_MISSING ) { if ( !bcf_float_is_missing(dst[0]) ) continue; }
+            else if ( col->replace & REPLACE_ALL ) { if ( bcf_float_is_missing(src[0]) ) continue; }
+            for (j=0; j<nvals; j++) dst[j] = src[j];
+            for (; j<ndst; j++) bcf_float_set_vector_end(dst[j]);
+        }
+        return bcf_update_format_float(args->hdr_out,line,col->hdr_key_dst,args->tmpf2,ndst*bcf_hdr_nsamples(args->hdr_out));
+    }
+    else    // ndst < nvals
+    {
+        hts_expand(float, nvals*bcf_hdr_nsamples(args->hdr_out), args->mtmpf3, args->tmpf3);
+        for (i=0; i<bcf_hdr_nsamples(args->hdr_out); i++)
+        {
+            float *ann = vals + nvals*args->sample_map[i];
+            float *ori = args->tmpf2 + ndst*i;                // ori vcf line
+            float *dst = args->tmpf3 + nvals*i;               // expanded buffer
+            int use_new_ann = 1;
+            if ( args->sample_map[i]==-1 ) use_new_ann = 0;
+            else if ( col->replace & REPLACE_NON_MISSING ) { if ( bcf_float_is_missing(ori[0]) ) use_new_ann = 0; }
+            else if ( col->replace & REPLACE_MISSING ) { if ( !bcf_float_is_missing(ori[0]) ) use_new_ann = 0; }
+            else if ( col->replace & REPLACE_ALL ) { if ( bcf_float_is_missing(ann[0]) ) use_new_ann = 0; }
+            if ( !use_new_ann )
+            {
+                for (j=0; j<ndst; j++) dst[j] = ori[j];
+                for (; j<nvals; j++) bcf_float_set_vector_end(dst[j]);
+            }
+            else
+                for (j=0; j<nvals; j++) dst[j] = ann[j];
+        }
+        return bcf_update_format_float(args->hdr_out,line,col->hdr_key_dst,args->tmpf3,nvals*bcf_hdr_nsamples(args->hdr_out));
+    }
+}
+static int core_setter_format_str(args_t *args, bcf1_t *line, annot_col_t *col, char **vals)
+{
+    if ( !args->sample_map )
+        return bcf_update_format_string(args->hdr_out,line,col->hdr_key_dst,(const char**)vals,args->nsmpl_annot);
+
+    int i;
+    args->tmpp2[0] = args->tmps2;
+    int ret = bcf_get_format_string(args->hdr,line,col->hdr_key_dst,&args->tmpp2,&args->mtmps2);
+    args->tmps2 = args->tmpp2[0];   // tmps2 might be realloced
+
+    int nsmpl = bcf_hdr_nsamples(args->hdr_out);
+    if ( ret<=0 )   // not present in dst
+    {
+        hts_expand(char,bcf_hdr_nsamples(args->hdr_out)*2,args->mtmps2,args->tmps2);
+        char *tmp = args->tmps2;
+        for (i=0; i<nsmpl; i++)
+        {
+            tmp[0] = '.';
+            tmp[1] = 0;
+            args->tmpp2[i] = tmp;
+            tmp += 2;
+        }
+    }
+    for (i=0; i<nsmpl; i++)
+    {
+        if ( args->sample_map[i]==-1 ) continue;
+        char **src = vals + args->sample_map[i];
+        char **dst = args->tmpp2 + i;
+
+        if ( col->replace & REPLACE_NON_MISSING ) { if ( (*dst)[0]=='.' && (*dst)[1]==0 ) continue; }
+        else if ( col->replace & REPLACE_MISSING ) { if ( (*dst)[0]!='.' || (*dst)[1]!=0 ) continue; }
+        else if ( col->replace & REPLACE_ALL ) { if ( (*src)[0]=='.' && (*src)[1]==0 ) continue; }
+        *dst = *src;
+    }
+    return bcf_update_format_string(args->hdr_out,line,col->hdr_key_dst,(const char**)args->tmpp2,nsmpl);
+}
+static int setter_format_int(args_t *args, bcf1_t *line, annot_col_t *col, void *data)
+{
+    if ( !data ) error("Error: the --merge-logic option cannot be used with FORMAT tags (yet?)\n");
+
+    annot_line_t *tab = (annot_line_t*) data;
+    if ( col->icol+args->nsmpl_annot > tab->ncols )
+        error("Incorrect number of values for %s at %s:%"PRId64"\n",col->hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) line->pos+1);
+    int nvals = count_vals(tab,col->icol,col->icol+args->nsmpl_annot);
+    hts_expand(int32_t,nvals*args->nsmpl_annot,args->mtmpi,args->tmpi);
+
+    int icol = col->icol, ismpl;
+    for (ismpl=0; ismpl<args->nsmpl_annot; ismpl++)
+    {
+        int32_t *ptr = args->tmpi + ismpl*nvals;
+        int ival = 0;
+
+        char *str = tab->cols[icol];
+        while ( *str )
+        {
+            if ( str[0]=='.' && (!str[1] || str[1]==',') )  // missing value
+            {
+                ptr[ival++] = bcf_int32_missing;
+                str += str[1] ? 2 : 1;
+                continue;
+            }
+
+            char *end = str;
+            ptr[ival] = strtol(str, &end, 10);
+            if ( end==str )
+                error("Could not parse %s at %s:%"PRId64" .. [%s]\n", col->hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) line->pos+1,tab->cols[col->icol]);
+
+            ival++;
+            str = *end ? end+1 : end;
+        }
+        while ( ival<nvals ) ptr[ival++] = bcf_int32_vector_end;
+        icol++;
+    }
+    return core_setter_format_int(args,line,col,args->tmpi,nvals);
+}
+static int setter_format_real(args_t *args, bcf1_t *line, annot_col_t *col, void *data)
+{
+    if ( !data ) error("Error: the --merge-logic option cannot be used with FORMAT tags (yet?)\n");
+
+    annot_line_t *tab = (annot_line_t*) data;
+    if ( col->icol+args->nsmpl_annot > tab->ncols )
+        error("Incorrect number of values for %s at %s:%"PRId64"\n",col->hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) line->pos+1);
+    int nvals = count_vals(tab,col->icol,col->icol+args->nsmpl_annot);
+    hts_expand(float,nvals*args->nsmpl_annot,args->mtmpf,args->tmpf);
+
+    int icol = col->icol, ismpl;
+    for (ismpl=0; ismpl<args->nsmpl_annot; ismpl++)
+    {
+        float *ptr = args->tmpf + ismpl*nvals;
+        int ival = 0;
+
+        char *str = tab->cols[icol];
+        while ( *str )
+        {
+            if ( str[0]=='.' && (!str[1] || str[1]==',') )  // missing value
+            {
+                bcf_float_set_missing(ptr[ival]);
+                ival++;
+                str += str[1] ? 2 : 1;
+                continue;
+            }
+
+            char *end = str;
+            ptr[ival] = strtod(str, &end);
+            if ( end==str )
+                error("Could not parse %s at %s:%"PRId64" .. [%s]\n", col->hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) line->pos+1,tab->cols[col->icol]);
+
+            ival++;
+            str = *end ? end+1 : end;
+        }
+        while ( ival<nvals ) { bcf_float_set_vector_end(ptr[ival]); ival++; }
+        icol++;
+    }
+    return core_setter_format_real(args,line,col,args->tmpf,nvals);
+}
+static int setter_format_str(args_t *args, bcf1_t *line, annot_col_t *col, void *data)
+{
+    if ( !data ) error("Error: the --merge-logic option cannot be used with FORMAT tags (yet?)\n");
+
+    annot_line_t *tab = (annot_line_t*) data;
+    if ( col->icol+args->nsmpl_annot > tab->ncols )
+        error("Incorrect number of values for %s at %s:%"PRId64"\n",col->hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) line->pos+1);
+
+    int ismpl;
+    for (ismpl=0; ismpl<args->nsmpl_annot; ismpl++)
+        args->tmpp[ismpl] = tab->cols[col->icol + ismpl];
+
+    return core_setter_format_str(args,line,col,args->tmpp);
+}
+static int determine_ploidy(int nals, int *vals, int nvals1, uint8_t *smpl, int nsmpl)
+{
+    int i, j, ndip = nals*(nals+1)/2, max_ploidy = 0;
+    for (i=0; i<nsmpl; i++)
+    {
+        int *ptr = vals + i*nvals1;
+        int has_value = 0;
+        for (j=0; j<nvals1; j++)
+        {
+            if ( ptr[j]==bcf_int32_vector_end ) break;
+            if ( ptr[j]!=bcf_int32_missing ) has_value = 1;
+        }
+        if ( has_value )
+        {
+            if ( j==ndip )
+            {
+                smpl[i] = 2;
+                max_ploidy = 2;
+            }
+            else if ( j==nals )
+            {
+                smpl[i] = 1;
+                if ( !max_ploidy ) max_ploidy = 1;
+            }
+            else return -j;
+        }
+        else smpl[i] = 0;
+    }
+    return max_ploidy;
+}
+static int vcf_setter_format_int(args_t *args, bcf1_t *line, annot_col_t *col, void *data)
+{
+    bcf1_t *rec = (bcf1_t*) data;
+    int nsrc = bcf_get_format_int32(args->files->readers[1].header,rec,col->hdr_key_src,&args->tmpi,&args->mtmpi);
+    if ( nsrc==-3 ) return 0;    // the tag is not present
+    if ( nsrc<=0 ) return 1;     // error
+    int nsmpl_src = bcf_hdr_nsamples(args->files->readers[1].header);
+    int nsrc1 = nsrc / nsmpl_src;
+    if ( col->number!=BCF_VL_G && col->number!=BCF_VL_R && col->number!=BCF_VL_A )
+        return core_setter_format_int(args,line,col,args->tmpi,nsrc1);
+
+    // create mapping from src to dst genotypes, haploid and diploid version
+    int nmap_hap = col->number==BCF_VL_G || col->number==BCF_VL_R ? rec->n_allele : rec->n_allele - 1;
+    int *map_hap = vcmp_map_ARvalues(args->vcmp,nmap_hap,line->n_allele,line->d.allele,rec->n_allele,rec->d.allele);
+    if ( !map_hap ) error("REF alleles not compatible at %s:%"PRId64"\n", bcf_seqname(args->hdr,line),(int64_t) line->pos+1);
+
+    int i, j;
+    if ( rec->n_allele==line->n_allele )
+    {
+        // alleles unchanged?
+        for (i=0; i<rec->n_allele; i++) if ( map_hap[i]!=i ) break;
+        if ( i==rec->n_allele )
+            return core_setter_format_int(args,line,col,args->tmpi,nsrc1);
+    }
+
+    int nsmpl_dst = rec->n_sample;
+    int ndst  = bcf_get_format_int32(args->hdr,line,col->hdr_key_dst,&args->tmpi2,&args->mtmpi2);
+    int ndst1 = ndst / nsmpl_dst;
+    if ( ndst <= 0 )
+    {
+        if ( col->replace & REPLACE_NON_MISSING ) return 0;  // overwrite only if present
+        if ( col->number==BCF_VL_G )
+            ndst1 = line->n_allele*(line->n_allele+1)/2;
+        else
+            ndst1 = col->number==BCF_VL_A ? line->n_allele - 1 : line->n_allele;
+        hts_expand(int, ndst1*nsmpl_dst, args->mtmpi2, args->tmpi2);
+        for (i=0; i<nsmpl_dst; i++)
+        {
+            int32_t *dst = args->tmpi2 + i*ndst1;
+            for (j=0; j<ndst1; j++) dst[j] = bcf_int32_missing;
+        }
+    }
+
+    int nmap_dip = 0, *map_dip = NULL;
+    if ( col->number==BCF_VL_G )
+    {
+        map_dip = vcmp_map_dipGvalues(args->vcmp, &nmap_dip);
+        if ( !args->src_smpl_pld )
+        {
+            args->src_smpl_pld = (uint8_t*) malloc(nsmpl_src);
+            args->dst_smpl_pld = (uint8_t*) malloc(nsmpl_dst);
+        }
+        int pld_src = determine_ploidy(rec->n_allele, args->tmpi, nsrc1, args->src_smpl_pld, nsmpl_src);
+        if ( pld_src<0 )
+            error("Unexpected number of %s values (%d) for %d alleles at %s:%"PRId64"\n", col->hdr_key_src,-pld_src, rec->n_allele, bcf_seqname(bcf_sr_get_header(args->files,1),rec),(int64_t) rec->pos+1);
+        int pld_dst = determine_ploidy(line->n_allele, args->tmpi2, ndst1, args->dst_smpl_pld, nsmpl_dst);
+        if ( pld_dst<0 )
+            error("Unexpected number of %s values (%d) for %d alleles at %s:%"PRId64"\n", col->hdr_key_src,-pld_dst, line->n_allele, bcf_seqname(args->hdr,line),(int64_t) line->pos+1);
+
+        int ndst1_new = pld_dst==1 ? line->n_allele : line->n_allele*(line->n_allele+1)/2;
+        if ( ndst1_new != ndst1 )
+        {
+            if ( ndst1 ) error("todo: %s ndst1!=ndst .. %d %d  at %s:%"PRId64"\n",col->hdr_key_src,ndst1_new,ndst1,bcf_seqname(args->hdr,line),(int64_t) line->pos+1);
+            ndst1 = ndst1_new;
+            hts_expand(int32_t, ndst1*nsmpl_dst, args->mtmpi2, args->tmpi2);
+        }
+    }
+    else if ( !ndst1 )
+    {
+        ndst1 = col->number==BCF_VL_A ? line->n_allele - 1 : line->n_allele;
+        hts_expand(int32_t, ndst1*nsmpl_dst, args->mtmpi2, args->tmpi2);
+    }
+
+    for (i=0; i<nsmpl_dst; i++)
+    {
+        int ii = args->sample_map ? args->sample_map[i] : i;
+        int32_t *ptr_src = args->tmpi + i*nsrc1;
+        int32_t *ptr_dst = args->tmpi2 + ii*ndst1;
+
+        if ( col->number==BCF_VL_G )
+        {
+            if ( args->src_smpl_pld[ii] > 0 && args->dst_smpl_pld[i] > 0 && args->src_smpl_pld[ii]!=args->dst_smpl_pld[i] )
+                error("Sample ploidy differs at %s:%"PRId64"\n", bcf_seqname(args->hdr,line),(int64_t) line->pos+1);
+            if ( !args->dst_smpl_pld[i] )
+                for (j=0; j<ndst1; j++) ptr_dst[j] = bcf_int32_missing;
+        }
+        if ( col->number!=BCF_VL_G || args->src_smpl_pld[i]==1 )
+        {
+            for (j=0; j<nmap_hap; j++)
+            {
+                int k = map_hap[j];
+                if ( k>=0 ) ptr_dst[k] = ptr_src[j];
+            }
+            if ( col->number==BCF_VL_G )
+                for (j=line->n_allele; j<ndst1; j++) ptr_dst[j++] = bcf_int32_vector_end;
+        }
+        else
+        {
+            for (j=0; j<nmap_dip; j++)
+            {
+                int k = map_dip[j];
+                if ( k>=0 ) ptr_dst[k] = ptr_src[j];
+            }
+        }
+    }
+    return bcf_update_format_int32(args->hdr_out,line,col->hdr_key_dst,args->tmpi2,nsmpl_dst*ndst1);
+}
+static int vcf_setter_format_real(args_t *args, bcf1_t *line, annot_col_t *col, void *data)
+{
+    bcf1_t *rec = (bcf1_t*) data;
+    int nsrc = bcf_get_format_float(args->files->readers[1].header,rec,col->hdr_key_src,&args->tmpf,&args->mtmpf);
+    if ( nsrc==-3 ) return 0;    // the tag is not present
+    if ( nsrc<=0 ) return 1;     // error
+    int nsmpl_src = bcf_hdr_nsamples(args->files->readers[1].header);
+    int nsrc1 = nsrc / nsmpl_src;
+    if ( col->number!=BCF_VL_G && col->number!=BCF_VL_R && col->number!=BCF_VL_A )
+        return core_setter_format_real(args,line,col,args->tmpf,nsrc1);
+
+    // create mapping from src to dst genotypes, haploid and diploid version
+    int nmap_hap = col->number==BCF_VL_G || col->number==BCF_VL_R ? rec->n_allele : rec->n_allele - 1;
+    int *map_hap = vcmp_map_ARvalues(args->vcmp,nmap_hap,line->n_allele,line->d.allele,rec->n_allele,rec->d.allele);
+    if ( !map_hap ) error("REF alleles not compatible at %s:%"PRId64"\n", bcf_seqname(args->hdr,line),(int64_t) line->pos+1);
+
+    int i, j;
+    if ( rec->n_allele==line->n_allele )
+    {
+        // alleles unchanged?
+        for (i=0; i<rec->n_allele; i++) if ( map_hap[i]!=i ) break;
+        if ( i==rec->n_allele )
+            return core_setter_format_real(args,line,col,args->tmpf,nsrc1);
+    }
+
+    int nsmpl_dst = rec->n_sample;
+    int ndst  = bcf_get_format_float(args->hdr,line,col->hdr_key_dst,&args->tmpf2,&args->mtmpf2);
+    int ndst1 = ndst / nsmpl_dst;
+    if ( ndst <= 0 )
+    {
+        if ( col->replace & REPLACE_NON_MISSING ) return 0;  // overwrite only if present
+        if ( col->number==BCF_VL_G )
+            ndst1 = line->n_allele*(line->n_allele+1)/2;
+        else
+            ndst1 = col->number==BCF_VL_A ? line->n_allele - 1 : line->n_allele;
+        hts_expand(float, ndst1*nsmpl_dst, args->mtmpf2, args->tmpf2);
+        for (i=0; i<nsmpl_dst; i++)
+        {
+            float *dst = args->tmpf2 + i*ndst1;
+            for (j=0; j<ndst1; j++) bcf_float_set_missing(dst[j]);
+        }
+    }
+
+    int nmap_dip = 0, *map_dip = NULL;
+    if ( col->number==BCF_VL_G )
+    {
+        map_dip = vcmp_map_dipGvalues(args->vcmp, &nmap_dip);
+        if ( !args->src_smpl_pld )
+        {
+            args->src_smpl_pld = (uint8_t*) malloc(nsmpl_src);
+            args->dst_smpl_pld = (uint8_t*) malloc(nsmpl_dst);
+        }
+        int pld_src = determine_ploidy(rec->n_allele, args->tmpi, nsrc1, args->src_smpl_pld, nsmpl_src);
+        if ( pld_src<0 )
+            error("Unexpected number of %s values (%d) for %d alleles at %s:%"PRId64"\n", col->hdr_key_src,-pld_src, rec->n_allele, bcf_seqname(bcf_sr_get_header(args->files,1),rec),(int64_t) rec->pos+1);
+        int pld_dst = determine_ploidy(line->n_allele, args->tmpi2, ndst1, args->dst_smpl_pld, nsmpl_dst);
+        if ( pld_dst<0 )
+            error("Unexpected number of %s values (%d) for %d alleles at %s:%"PRId64"\n", col->hdr_key_src,-pld_dst, line->n_allele, bcf_seqname(args->hdr,line),(int64_t) line->pos+1);
+
+        int ndst1_new = pld_dst==1 ? line->n_allele : line->n_allele*(line->n_allele+1)/2;
+        if ( ndst1_new != ndst1 )
+        {
+            if ( ndst1 ) error("todo: %s ndst1!=ndst .. %d %d  at %s:%"PRId64"\n",col->hdr_key_src,ndst1_new,ndst1,bcf_seqname(args->hdr,line),(int64_t) line->pos+1);
+            ndst1 = ndst1_new;
+            hts_expand(float, ndst1*nsmpl_dst, args->mtmpf2, args->tmpf2);
+        }
+    }
+    else if ( !ndst1 )
+    {
+        ndst1 = col->number==BCF_VL_A ? line->n_allele - 1 : line->n_allele;
+        hts_expand(float, ndst1*nsmpl_dst, args->mtmpf2, args->tmpf2);
+    }
+
+    for (i=0; i<nsmpl_dst; i++)
+    {
+        int ii = args->sample_map ? args->sample_map[i] : i;
+        float *ptr_src = args->tmpf + i*nsrc1;
+        float *ptr_dst = args->tmpf2 + ii*ndst1;
+
+        if ( col->number==BCF_VL_G )
+        {
+            if ( args->src_smpl_pld[ii] > 0 && args->dst_smpl_pld[i] > 0 && args->src_smpl_pld[ii]!=args->dst_smpl_pld[i] )
+                error("Sample ploidy differs at %s:%"PRId64"\n", bcf_seqname(args->hdr,line),(int64_t) line->pos+1);
+            if ( !args->dst_smpl_pld[i] )
+                for (j=0; j<ndst1; j++) bcf_float_set_missing(ptr_dst[j]);
+        }
+        if ( col->number!=BCF_VL_G || args->src_smpl_pld[i]==1 )
+        {
+            for (j=0; j<nmap_hap; j++)
+            {
+                int k = map_hap[j];
+                if ( k>=0 )
+                {
+                    if ( bcf_float_is_missing(ptr_src[j]) ) bcf_float_set_missing(ptr_dst[k]);
+                    else if ( bcf_float_is_vector_end(ptr_src[j]) ) bcf_float_set_vector_end(ptr_dst[k]);
+                    else ptr_dst[k] = ptr_src[j];
+                }
+            }
+            if ( col->number==BCF_VL_G )
+                for (j=line->n_allele; j<ndst1; j++) bcf_float_set_vector_end(ptr_dst[j]);
+        }
+        else
+        {
+            for (j=0; j<nmap_dip; j++)
+            {
+                int k = map_dip[j];
+                if ( k>=0 )
+                {
+                    if ( bcf_float_is_missing(ptr_src[j]) ) bcf_float_set_missing(ptr_dst[k]);
+                    else if ( bcf_float_is_vector_end(ptr_src[j]) ) bcf_float_set_vector_end(ptr_dst[k]);
+                    else ptr_dst[k] = ptr_src[j];
+                }
+            }
+        }
+    }
+    return bcf_update_format_float(args->hdr_out,line,col->hdr_key_dst,args->tmpf2,nsmpl_dst*ndst1);
+}
+
+static int vcf_setter_format_str(args_t *args, bcf1_t *line, annot_col_t *col, void *data)
+{
+    bcf1_t *rec = (bcf1_t*) data;
+    args->tmpp[0] = args->tmps;
+    int ret = bcf_get_format_string(args->files->readers[1].header,rec,col->hdr_key_src,&args->tmpp,&args->mtmps);
+    args->tmps = args->tmpp[0]; // tmps might be realloced
+    if ( ret==-3 ) return 0;    // the tag is not present
+    if ( ret<=0 ) return 1;     // error
+    if ( strcmp("GT",col->hdr_key_dst) )
+        return core_setter_format_str(args,line,col,args->tmpp);
+
+    // Genotypes are internally represented as integers. This is a complication for FMT/GT:=oldGT
+    // First determine the maximum number of alleles per-sample ndst1
+    int nsmpl_src = bcf_hdr_nsamples(args->files->readers[1].header);
+    int nsmpl_dst = bcf_hdr_nsamples(args->hdr_out);
+    int isrc,idst, ndst1 = 0, nsrc1 = ret / nsmpl_src;
+    char *ptr = args->tmps, *ptr_end = ptr + ret;
+    while ( ptr < ptr_end )
+    {
+        char *smpl_end = ptr + nsrc1;
+        int n = 1;
+        while ( ptr < smpl_end )
+        {
+            if ( *ptr=='/' || *ptr=='|' ) n++;
+            ptr++;
+        }
+        if ( ndst1 < n ) ndst1 = n;
+    }
+    assert( ndst1 );
+
+    int ndst = ndst1*nsmpl_dst;
+    hts_expand(int32_t,ndst,args->mtmpi,args->tmpi);
+    hts_expand(char,ret+1,args->mtmps,args->tmps); args->tmps[ret] = 0; // the FORMAT string may not be 0-terminated
+    for (idst=0; idst<nsmpl_dst; idst++)
+    {
+        int i = 0, is_phased = 0;
+        int32_t *dst = args->tmpi + idst*ndst1;
+        isrc = args->sample_map ? args->sample_map[idst] : idst;
+        if ( isrc==-1 )
+        {
+            dst[0] = bcf_gt_missing;
+            for (i=1; i<ndst1; i++) dst[i] = bcf_int32_vector_end;
+            continue;
+        }
+        char *beg = args->tmps + isrc*nsrc1, *tmp;
+        char *keep_ptr = beg+nsrc1, keep = *keep_ptr; *keep_ptr = 0;
+        while ( *beg )
+        {
+            char *end = beg;
+            while ( *end && *end!='/' && *end!='|' ) end++;
+            if ( *beg=='.' && end-beg==1 ) dst[i] = bcf_gt_missing;
+            else
+            {
+                if ( *end=='|' ) is_phased = 1;
+                dst[i] = strtol(beg, &tmp, 10);
+                if ( tmp!=end )
+                    error("Could not parse the %s field at %s:%"PRId64" in %s\n", col->hdr_key_src,bcf_seqname(args->files->readers[1].header,rec),(int64_t) rec->pos+1,args->targets_fname);
+                if ( dst[i] >= line->n_allele )
+                    error("The source allele index is bigger than the number of destination alleles at %s:%"PRId64"\n", bcf_seqname(args->files->readers[1].header,rec),(int64_t) rec->pos+1);
+                dst[i] = is_phased ? bcf_gt_phased(dst[i]) : bcf_gt_unphased(dst[i]);
+            }
+            beg = *end ? end+1 : end;
+            i++;
+        }
+        *keep_ptr = keep;
+        for (; i<ndst1; i++) dst[i] = bcf_int32_vector_end;
+    }
+    return bcf_update_genotypes(args->hdr_out,line,args->tmpi,ndst);
+}
+static int init_sample_map(args_t *args, bcf_hdr_t *src, bcf_hdr_t *dst)
+{
+    int i;
+    if ( !args->sample_names )
+    {
+        args->nsmpl_annot = bcf_hdr_nsamples(dst);
+
+        // tab annotation file, expecting that all samples are present: sample map not needed
+        if ( !src ) return 0;
+
+        int nmatch = 0;
+        for (i=0; i<bcf_hdr_nsamples(src); i++)
+        {
+            int id = bcf_hdr_id2int(dst, BCF_DT_SAMPLE, src->samples[i]);
+            if ( id!=-1 ) nmatch++;
+        }
+        if ( !nmatch ) return -1;   // No matching samples found in the source and the destination file
+
+        args->nsample_map = bcf_hdr_nsamples(dst);
+        args->sample_map  = (int*) malloc(sizeof(int)*args->nsample_map);
+        for (i=0; i<args->nsample_map; i++)
+        {
+            int id = bcf_hdr_id2int(src, BCF_DT_SAMPLE, dst->samples[i]);
+            args->sample_map[i] = id;   // idst -> isrc, -1 if not present
+        }
+        return 1;
+    }
+
+    args->nsample_map = bcf_hdr_nsamples(dst);
+    args->sample_map  = (int*) malloc(sizeof(int)*args->nsample_map);
+    for (i=0; i<args->nsample_map; i++) args->sample_map[i] = -1;
+
+    int flags = !src ? SMPL_STRICT|SMPL_SINGLE : SMPL_STRICT|SMPL_SINGLE|SMPL_PAIR2; // is vcf vs tab annotation file
+    smpl_ilist_t *ilist = smpl_ilist_init(dst, args->sample_names, args->sample_is_file, flags);    // gives mapping dst->src
+    if ( !ilist || !ilist->n ) error("Could not parse the samples: %s\n", args->sample_names);
+    args->nsmpl_annot = ilist->n;
+    int need_sample_map = args->nsmpl_annot==bcf_hdr_nsamples(dst) ? 0 : 1;
+    for (i=0; i<args->nsmpl_annot; i++)
+    {
+        int idst = ilist->idx[i];
+        const char *src_name = ilist->pair && ilist->pair[i] ? ilist->pair[i] : bcf_hdr_int2id(dst, BCF_DT_SAMPLE, idst);
+        int isrc = i;
+        if ( src )     // the annotation file is a VCF, not a tab-delimited file
+        {
+            isrc = bcf_hdr_id2int(src, BCF_DT_SAMPLE, src_name);
+            if ( isrc==-1 ) error("Sample \"%s\" not found in the annotation file\n", src_name);
+        }
+        if ( isrc!=idst ) need_sample_map = 1;
+        args->sample_map[idst] = isrc;
+    }
+    smpl_ilist_destroy(ilist);
+    return need_sample_map;
+}
+static char *columns_complement(char *columns, void **skip_info, void **skip_fmt)
+{
+    kstring_t str = {0,0,0};
+    char *ss = columns, *se = ss;
+    while ( *ss )
+    {
+        if ( *se && *se!=',' ) { se++; continue; }
+        if ( *ss!='^' )
+        {
+            if ( str.l ) kputc(',',&str);
+            kputsn(ss, se-ss, &str);
+            if ( !*se ) break;
+            ss = ++se;
+            continue;
+        }
+
+        if ( !strncasecmp("^INFO/",ss,6) )
+        {
+            if ( !*skip_info )
+            {
+                *skip_info = khash_str2int_init();
+                if ( str.l ) kputc(',',&str);
+                kputs("INFO",&str);
+            }
+            char tmp = *se; *se = 0;
+            khash_str2int_inc(*skip_info, strdup(ss+6));
+            *se = tmp;
+        }
+        else if ( !strncasecmp("^FORMAT/",ss,8) || !strncasecmp("^FMT/",ss,5) )
+        {
+            int n = !strncasecmp("^FMT/",ss,5) ? 5 : 8;
+            if ( !*skip_fmt )
+            {
+                *skip_fmt = khash_str2int_init();
+                if ( str.l ) kputc(',',&str);
+                kputs("FORMAT",&str);
+            }
+            char tmp = *se; *se = 0;
+            khash_str2int_inc(*skip_fmt, strdup(ss+n));
+            *se = tmp;
+        }
+        else
+        {
+            if ( !*skip_info )
+            {
+                *skip_info = khash_str2int_init();
+                if ( str.l ) kputc(',',&str);
+                kputs("INFO",&str);
+            }
+            char tmp = *se; *se = 0;
+            khash_str2int_inc(*skip_info, strdup(ss+1));
+            *se = tmp;
+        }
+
+        if ( !*se ) break;
+        ss = ++se;
+    }
+    free(columns);
+    return str.s;
+}
+static void bcf_hrec_format_rename(bcf_hrec_t *hrec, char *tag, kstring_t *str)
+{
+    int j, nout = 0;
+    ksprintf(str, "##%s=<", hrec->key);
+    for (j=0; j<hrec->nkeys; j++)
+    {
+        if ( !strcmp("IDX",hrec->keys[j]) ) continue;
+        if ( nout ) kputc(',',str);
+        if ( !strcmp("ID", hrec->keys[j]) )
+            ksprintf(str,"%s=%s", hrec->keys[j], tag);
+        else
+            ksprintf(str,"%s=%s", hrec->keys[j], hrec->vals[j]);
+        nout++;
+    }
+    ksprintf(str,">\n");
+}
+static char *set_replace_mode(char *ss, int *replace)
+{
+    int mode = 0;
+    while (*ss)
+    {
+        if ( *ss=='+' ) mode |= REPLACE_MISSING;
+        else if ( *ss=='-' ) mode |= REPLACE_NON_MISSING;
+        else if ( *ss=='=' ) mode |= SET_OR_APPEND;
+        else if ( *ss=='.' ) mode |= CARRY_OVER_MISSING;
+        else break;
+        ss++;
+    }
+    if ( !mode ) mode = REPLACE_ALL;
+// is exactly one bit set?
+//    if ( mode && !(mode && ((mode & mode-1) == 0)) )
+    *replace = mode;
+    return ss;
+}
+static void rename_annots_push(args_t *args, char *src, char *dst);
+static void init_columns(args_t *args)
+{
+    int need_sample_map = 0;
+    int sample_map_ok = init_sample_map(args, args->tgts_is_vcf?args->files->readers[1].header:NULL, args->hdr);
+
+    kstring_t tmp = {0,0,0};
+    if ( args->columns_is_file )
+    {
+        int i,n;
+        char **str = hts_readlist(args->columns, args->columns_is_file, &n);
+        if ( !str ) error("Could not parse %s\n", args->columns);
+        for (i=0; i<n; i++)
+        {
+            char *ptr = str[i];
+            while ( *ptr && !isspace(*ptr) ) ptr++;
+            if ( *ptr )
+            {
+                *ptr = 0;
+                ptr++;
+                while ( *ptr && isspace(*ptr) ) ptr++;
+                if ( *ptr )
+                {
+                    if ( args->merge_method_str.l ) kputc(',',&args->merge_method_str);
+                    kputs(str[i],&args->merge_method_str);
+                    kputc(':',&args->merge_method_str);
+                    kputs(ptr,&args->merge_method_str);
+                }
+            }
+            if ( tmp.l ) kputc(',',&tmp);
+            kputs(str[i],&tmp);
+            free(str[i]);
+        }
+        free(str);
+        free(args->columns);
+        args->columns = tmp.s;
+        tmp.l = tmp.m = 0;
+        tmp.s = NULL;
+    }
+
+    void *skip_fmt = NULL, *skip_info = NULL;
+    if ( args->tgts_is_vcf )
+        args->columns = columns_complement(args->columns, &skip_info, &skip_fmt);
+
+    kstring_t str = {0,0,0};
+    char *ss = args->columns, *se = ss;
+    args->ncols = 0;
+    int icol = -1, has_fmt_str = 0;
+    while ( *ss )
+    {
+        char *ptr;
+        if ( *se && *se!=',' ) { se++; continue; }
+        int replace;
+        ss = set_replace_mode(ss, &replace);
+        icol++;
+        str.l = 0;
+        kputsn(ss, se-ss, &str);
+        if ( !str.s[0] || !strcasecmp("-",str.s) ) ;
+        else if ( !strcasecmp("CHROM",str.s) ) args->chr_idx = icol;
+        else if ( !strcasecmp("POS",str.s) ) args->beg_idx = icol;
+        else if ( !strcasecmp("FROM",str.s) || !strcasecmp("BEG",str.s) ) args->beg_idx = icol;
+        else if ( !strcasecmp("TO",str.s) || !strcasecmp("END",str.s) ) args->end_idx = icol;
+        else if ( !strcasecmp("REF",str.s) )
+        {
+            if ( args->tgts_is_vcf )
+            {
+                args->ncols++; args->cols = (annot_col_t*) realloc(args->cols,sizeof(annot_col_t)*args->ncols);
+                annot_col_t *col = &args->cols[args->ncols-1];
+                memset(col,0,sizeof(*col));
+                col->setter = vcf_setter_ref;
+                col->hdr_key_src = strdup(str.s);
+                col->hdr_key_dst = strdup(str.s);
+            }
+            else args->ref_idx = icol;
+        }
+        else if ( !strcasecmp("ALT",str.s) )
+        {
+            if ( args->tgts_is_vcf )
+            {
+                args->ncols++; args->cols = (annot_col_t*) realloc(args->cols,sizeof(annot_col_t)*args->ncols);
+                annot_col_t *col = &args->cols[args->ncols-1];
+                memset(col,0,sizeof(*col));
+                col->setter = vcf_setter_alt;
+                col->hdr_key_src = strdup(str.s);
+                col->hdr_key_dst = strdup(str.s);
+                col->replace = replace;
+                if ( args->pair_logic==-1 ) bcf_sr_set_opt(args->files,BCF_SR_PAIR_LOGIC,BCF_SR_PAIR_BOTH_REF);
+            }
+            else args->alt_idx = icol;
+        }
+        else if ( !strcasecmp("ID",str.s) || !strcasecmp("~ID",str.s) )
+        {
+            if ( replace & REPLACE_NON_MISSING ) error("Apologies, the -ID feature has not been implemented yet.\n");
+            if ( str.s[0]=='~' ) replace = MATCH_VALUE;
+            if ( args->tgts_is_vcf && (replace & MATCH_VALUE) ) error("todo: -c ~ID with -a VCF?\n");
+            args->ncols++; args->cols = (annot_col_t*) realloc(args->cols,sizeof(annot_col_t)*args->ncols);
+            annot_col_t *col = &args->cols[args->ncols-1];
+            memset(col,0,sizeof(*col));
+            col->icol = icol;
+            col->replace = replace;
+            col->setter = args->tgts_is_vcf ? vcf_setter_id : setter_id;
+            col->hdr_key_src = strdup(str.s);
+            col->hdr_key_dst = strdup(str.s);
+            if ( replace & MATCH_VALUE ) args->match_id = icol;
+        }
+        else if ( !strcasecmp("~INFO/END",str.s) && !args->tgts_is_vcf )
+        {
+            replace = MATCH_VALUE;
+            args->ncols++; args->cols = (annot_col_t*) realloc(args->cols,sizeof(annot_col_t)*args->ncols);
+            annot_col_t *col = &args->cols[args->ncols-1];
+            memset(col,0,sizeof(*col));
+            col->icol = icol;
+            col->replace = replace;
+            col->setter  = NULL;
+            col->hdr_key_src = strdup(str.s);
+            col->hdr_key_dst = strdup(str.s);
+            args->match_end = icol;
+        }
+        else if ( !strcasecmp("~POS",str.s) && !args->tgts_is_vcf )
+        {
+            if ( args->tgts_is_vcf ) error("Error: cannot use ~POS, position can be replaced only from a tab-delimited file\n");
+            args->ncols++; args->cols = (annot_col_t*) realloc(args->cols,sizeof(annot_col_t)*args->ncols);
+            annot_col_t *col = &args->cols[args->ncols-1];
+            memset(col,0,sizeof(*col));
+            col->icol = icol;
+            col->replace = replace;
+            col->setter  = setter_pos;
+            col->hdr_key_src = strdup(str.s);
+            col->hdr_key_dst = strdup(str.s);
+            args->match_end = icol;
+        }
+        else if ( !strncasecmp("ID:=",str.s,4) )    // transfer a tag from INFO to ID column
+        {
+            if ( !args->tgts_is_vcf ) error("The annotation source must be a VCF for \"%s\"\n",str.s);
+            if ( replace & REPLACE_NON_MISSING ) error("Apologies, the -ID feature has not been implemented yet.\n");
+            args->ncols++; args->cols = (annot_col_t*) realloc(args->cols,sizeof(annot_col_t)*args->ncols);
+            annot_col_t *col = &args->cols[args->ncols-1];
+            memset(col,0,sizeof(*col));
+            col->icol = icol;
+            col->replace = replace;
+            col->setter = vcf_setter_id;
+            col->getter = vcf_getter_info_str2str;
+            str.s[2] = 0;
+            col->hdr_key_dst = strdup(str.s);
+            col->hdr_key_src = strncasecmp("INFO/",str.s+4,5) ? strdup(str.s+4) : strdup(str.s+4+5);
+            int hdr_id = bcf_hdr_id2int(args->tgts_hdr, BCF_DT_ID,col->hdr_key_src);
+            if ( !bcf_hdr_idinfo_exists(args->tgts_hdr,BCF_HL_INFO,hdr_id) )
+                error("The INFO tag \"%s\" is not defined in %s\n", col->hdr_key_src, args->targets_fname);
+            if ( bcf_hdr_id2type(args->tgts_hdr,BCF_HL_INFO,hdr_id)!=BCF_HT_STR )
+                error("Only Type=String tags can be used to annotate the ID column\n");
+        }
+        else if ( (ptr=strstr(str.s,":=")) && !args->targets_fname )
+        {
+            *ptr = 0;
+            rename_annots_push(args,ptr+2,str.s);
+            *ptr = ':';
+        }
+        else if ( !strcasecmp("FILTER",str.s) )
+        {
+            if ( replace & REPLACE_NON_MISSING ) error("Apologies, the -FILTER feature has not been implemented yet.\n");
+            args->ncols++; args->cols = (annot_col_t*) realloc(args->cols,sizeof(annot_col_t)*args->ncols);
+            annot_col_t *col = &args->cols[args->ncols-1];
+            memset(col,0,sizeof(*col));
+            col->icol = icol;
+            col->replace = replace;
+            col->setter = args->tgts_is_vcf ? vcf_setter_filter : setter_filter;
+            col->hdr_key_src = strdup(str.s);
+            col->hdr_key_dst = strdup(str.s);
+            if ( args->tgts_is_vcf )
+            {
+                bcf_hdr_t *tgts_hdr = args->files->readers[1].header;
+                int j;
+                for (j=0; j<tgts_hdr->nhrec; j++)
+                {
+                    bcf_hrec_t *hrec = tgts_hdr->hrec[j];
+                    if ( hrec->type!=BCF_HL_FLT ) continue;
+                    int k = bcf_hrec_find_key(hrec,"ID");
+                    if ( k<0 ) error("[%s] Failed to parse the header, the ID attribute not found", __func__);
+                    tmp.l = 0;
+                    bcf_hrec_format(hrec, &tmp);
+                    bcf_hdr_append(args->hdr_out, tmp.s);
+                }
+                if (bcf_hdr_sync(args->hdr_out) < 0)
+                    error_errno("[%s] Failed to update header", __func__);
+            }
+        }
+        else if ( !strcasecmp("QUAL",str.s) )
+        {
+            if ( replace & REPLACE_NON_MISSING ) error("Apologies, the -QUAL feature has not been implemented yet.\n");
+            if ( replace & SET_OR_APPEND ) error("Apologies, the =QUAL feature has not been implemented yet.\n");
+            args->ncols++; args->cols = (annot_col_t*) realloc(args->cols,sizeof(annot_col_t)*args->ncols);
+            annot_col_t *col = &args->cols[args->ncols-1];
+            memset(col,0,sizeof(*col));
+            col->icol = icol;
+            col->replace = replace;
+            col->setter = args->tgts_is_vcf ? vcf_setter_qual : setter_qual;
+            col->hdr_key_src = strdup(str.s);
+            col->hdr_key_dst = strdup(str.s);
+        }
+        else if ( args->tgts_is_vcf && !strcasecmp("INFO",str.s) ) // All INFO fields
+        {
+            if ( replace & REPLACE_NON_MISSING ) error("Apologies, the -INFO/TAG feature has not been implemented yet.\n");
+            if ( replace & SET_OR_APPEND ) error("Apologies, the =INFO feature has not been implemented yet.\n");
+            bcf_hdr_t *tgts_hdr = args->files->readers[1].header;
+            int j;
+            for (j=0; j<tgts_hdr->nhrec; j++)
+            {
+                bcf_hrec_t *hrec = tgts_hdr->hrec[j];
+                if ( hrec->type!=BCF_HL_INFO ) continue;
+                int k = bcf_hrec_find_key(hrec,"ID");
+                assert( k>=0 ); // this should always be true for valid VCFs
+                if ( skip_info && khash_str2int_has_key(skip_info,hrec->vals[k]) ) continue;
+                tmp.l = 0;
+                bcf_hrec_format(hrec, &tmp);
+                bcf_hdr_append(args->hdr_out, tmp.s);
+                if (bcf_hdr_sync(args->hdr_out) < 0)
+                    error_errno("[%s] Failed to update header", __func__);
+                int hdr_id = bcf_hdr_id2int(args->hdr_out, BCF_DT_ID, hrec->vals[k]);
+                args->ncols++; args->cols = (annot_col_t*) realloc(args->cols,sizeof(annot_col_t)*args->ncols);
+                annot_col_t *col = &args->cols[args->ncols-1];
+                memset(col,0,sizeof(*col));
+                col->icol = -1;
+                col->replace = replace;
+                col->hdr_key_src = strdup(hrec->vals[k]);
+                col->hdr_key_dst = strdup(hrec->vals[k]);
+                col->number  = bcf_hdr_id2length(args->hdr_out,BCF_HL_INFO,hdr_id);
+                switch ( bcf_hdr_id2type(args->hdr_out,BCF_HL_INFO,hdr_id) )
+                {
+                    case BCF_HT_FLAG:   col->setter = vcf_setter_info_flag; break;
+                    case BCF_HT_INT:    col->setter = vcf_setter_info_int; break;
+                    case BCF_HT_REAL:   col->setter = vcf_setter_info_real; break;
+                    case BCF_HT_STR:    col->setter = vcf_setter_info_str; break;
+                    default: error("The type of %s not recognised (%d)\n", str.s,bcf_hdr_id2type(args->hdr_out,BCF_HL_INFO,hdr_id));
+                }
+            }
+        }
+        else if ( args->tgts_is_vcf && (!strcasecmp("FORMAT",str.s) || !strcasecmp("FMT",str.s)) ) // All FORMAT fields
+        {
+            bcf_hdr_t *tgts_hdr = args->files->readers[1].header;
+            need_sample_map = 1;
+            int j;
+            for (j=0; j<tgts_hdr->nhrec; j++)
+            {
+                bcf_hrec_t *hrec = tgts_hdr->hrec[j];
+                if ( hrec->type!=BCF_HL_FMT) continue;
+                int k = bcf_hrec_find_key(hrec,"ID");
+                assert( k>=0 ); // this should always be true for valid VCFs
+                if ( skip_fmt && khash_str2int_has_key(skip_fmt,hrec->vals[k]) ) continue;
+                tmp.l = 0;
+                bcf_hrec_format(hrec, &tmp);
+                bcf_hdr_append(args->hdr_out, tmp.s);
+                if (bcf_hdr_sync(args->hdr_out) < 0)
+                    error_errno("[%s] Failed to update header", __func__);
+                int hdr_id = bcf_hdr_id2int(args->hdr_out, BCF_DT_ID, hrec->vals[k]);
+                args->ncols++; args->cols = (annot_col_t*) realloc(args->cols,sizeof(annot_col_t)*args->ncols);
+                annot_col_t *col = &args->cols[args->ncols-1];
+                memset(col,0,sizeof(*col));
+                col->icol = -1;
+                col->replace = replace;
+                col->hdr_key_src = strdup(hrec->vals[k]);
+                col->hdr_key_dst = strdup(hrec->vals[k]);
+                if ( !strcasecmp("GT",col->hdr_key_src) )
+                {
+                    if ( !args->tgts_is_vcf ) error("The FORMAT/GT field can be currently populated only from a VCF\n");
+                    col->setter = vcf_setter_format_gt;
+                }
+                else
+                    switch ( bcf_hdr_id2type(args->hdr_out,BCF_HL_FMT,hdr_id) )
+                    {
+                        case BCF_HT_INT:    col->setter = vcf_setter_format_int; break;
+                        case BCF_HT_REAL:   col->setter = vcf_setter_format_real; break;
+                        case BCF_HT_STR:    col->setter = vcf_setter_format_str; has_fmt_str = 1; break;
+                        default: error("The type of %s not recognised (%d)\n", str.s,bcf_hdr_id2type(args->hdr_out,BCF_HL_FMT,hdr_id));
+                    }
+                hdr_id = bcf_hdr_id2int(tgts_hdr, BCF_DT_ID, hrec->vals[k]);
+                col->number = bcf_hdr_id2length(tgts_hdr,BCF_HL_FMT,hdr_id);
+            }
+        }
+        else if ( !strncasecmp("FORMAT/",str.s, 7) || !strncasecmp("FMT/",str.s,4) )
+        {
+            char *key_dst = str.s + (!strncasecmp("FMT/",str.s,4) ? 4 : 7);
+            char *key_src = strstr(key_dst,":=");
+            if ( key_src )
+            {
+                *key_src = 0;
+                key_src += 2;
+                if ( !strncasecmp("FORMAT/",key_src,7) ) key_src += 7;
+                else if ( !strncasecmp("FMT/",key_src,4) ) key_src += 4;
+            }
+            else
+                key_src = key_dst;
+            need_sample_map = 1;
+            if ( args->tgts_is_vcf )
+            {
+                bcf_hrec_t *hrec = bcf_hdr_get_hrec(args->files->readers[1].header, BCF_HL_FMT, "ID", key_src, NULL);
+                if ( !hrec ) error("No such annotation \"%s\" in %s\n", key_src,args->targets_fname);
+                tmp.l = 0;
+                bcf_hrec_format_rename(hrec, key_dst, &tmp);
+                bcf_hdr_append(args->hdr_out, tmp.s);
+                if (bcf_hdr_sync(args->hdr_out) < 0)
+                    error_errno("[%s] Failed to update header", __func__);
+            }
+            int hdr_id = bcf_hdr_id2int(args->hdr_out, BCF_DT_ID, key_dst);
+            if ( !bcf_hdr_idinfo_exists(args->hdr_out,BCF_HL_FMT,hdr_id) )
+                error("The FORMAT tag \"%s\" is not defined in %s, was the -h option provided?\n", str.s, args->targets_fname);
+            args->ncols++; args->cols = (annot_col_t*) realloc(args->cols,sizeof(annot_col_t)*args->ncols);
+            annot_col_t *col = &args->cols[args->ncols-1];
+            memset(col,0,sizeof(*col));
+            if ( !args->tgts_is_vcf )
+            {
+                col->icol = icol;
+                icol += args->nsmpl_annot - 1;
+            }
+            else
+                col->icol = -1;
+            col->replace = replace;
+            col->hdr_key_src = strdup(key_src);
+            col->hdr_key_dst = strdup(key_dst);
+            if ( !strcasecmp("GT",key_src) )
+            {
+                if ( !args->tgts_is_vcf ) error("The FORMAT/GT field can be currently populated only from a VCF\n");
+                col->setter = vcf_setter_format_gt;
+            }
+            else
+                switch ( bcf_hdr_id2type(args->hdr_out,BCF_HL_FMT,hdr_id) )
+                {
+                    case BCF_HT_INT:    col->setter = args->tgts_is_vcf ? vcf_setter_format_int  : setter_format_int; break;
+                    case BCF_HT_REAL:   col->setter = args->tgts_is_vcf ? vcf_setter_format_real : setter_format_real; break;
+                    case BCF_HT_STR:    col->setter = args->tgts_is_vcf ? vcf_setter_format_str  : setter_format_str; has_fmt_str = 1; break;
+                    default: error("The type of %s not recognised (%d)\n", str.s,bcf_hdr_id2type(args->hdr_out,BCF_HL_FMT,hdr_id));
+                }
+            if ( args->tgts_is_vcf )
+            {
+                bcf_hdr_t *tgts_hdr = args->files->readers[1].header;
+                hdr_id = bcf_hdr_id2int(tgts_hdr, BCF_DT_ID, col->hdr_key_src);
+                col->number = bcf_hdr_id2length(tgts_hdr,BCF_HL_FMT,hdr_id);
+            }
+        }
+        else
+        {
+            if ( replace & REPLACE_NON_MISSING ) error("Apologies, the -INFO/TAG feature has not been implemented yet.\n");
+            if ( replace & SET_OR_APPEND )
+            {
+                if ( args->tgts_is_vcf )
+                    error("Error: the =INFO/TAG feature is currently supported only with TAB annotation files and has limitations\n"
+                          "       (the annotation type is modified to \"Number=.\" and allele ordering is disregarded)\n");
+                fprintf(stderr,"Warning: the =INFO/TAG feature modifies the annotation to \"Number=.\" and disregards allele ordering\n");
+            }
+            int explicit_src_info = 0;
+            int explicit_dst_info = 0;
+            char *key_dst;
+            if ( !strncasecmp("INFO/",str.s,5) )
+            {
+                key_dst = str.s + 5;
+                explicit_dst_info = 1;
+            }
+            else if ( !strcasecmp("~INFO/END",str.s) )
+            {
+                key_dst = str.s + 6;
+                explicit_dst_info = 1;
+            }
+            else
+                key_dst = str.s;
+            char *key_src = strstr(key_dst,":=");
+            if ( key_src )
+            {
+                *key_src = 0;
+                key_src += 2;
+                if ( !strncasecmp("INFO/",key_src,5) )
+                {
+                    key_src += 5;
+                    explicit_src_info = 1;
+                }
+                else if ( !strncasecmp("FMT/",key_src,4) || !strncasecmp("FORMAT/",key_src,5) )
+                {
+                    key_src[-2] = ':';
+                    error("Did you mean \"FMT/%s\" rather than \"%s\"?\n",str.s,str.s);
+                }
+            }
+            else
+                key_src = key_dst;
+
+            args->ncols++; args->cols = (annot_col_t*) realloc(args->cols,sizeof(annot_col_t)*args->ncols);
+            annot_col_t *col = &args->cols[args->ncols-1];
+            memset(col,0,sizeof(*col));
+            col->icol = icol;
+            col->replace = replace;
+            col->hdr_key_src = strdup(key_src);
+            col->hdr_key_dst = strdup(key_dst);
+
+            int hdr_id = bcf_hdr_id2int(args->hdr_out, BCF_DT_ID, key_dst);
+            if ( !bcf_hdr_idinfo_exists(args->hdr_out,BCF_HL_INFO,hdr_id) )
+            {
+                if ( args->tgts_is_vcf ) // reading annotations from a VCF, add a new header line
+                {
+                    if ( !strcasecmp("ID",key_src) && !explicit_src_info )
+                    {
+                        // transferring ID column into a new INFO tag
+                        tmp.l = 0;
+                        ksprintf(&tmp,"##INFO=<ID=%s,Number=1,Type=String,Description=\"Transferred ID column\">",key_dst);
+                    }
+                    else if ( !strcasecmp("FILTER",key_src) && !explicit_src_info )
+                    {
+                        // transferring FILTER column into a new INFO tag
+                        tmp.l = 0;
+                        ksprintf(&tmp,"##INFO=<ID=%s,Number=1,Type=String,Description=\"Transferred FILTER column\">",key_dst);
+                    }
+                    else
+                    {
+                        bcf_hrec_t *hrec = bcf_hdr_get_hrec(args->files->readers[1].header, BCF_HL_INFO, "ID", key_src, NULL);
+                        if ( !hrec )
+                        {
+                            if ( explicit_dst_info+explicit_src_info==0 && bcf_hdr_get_hrec(args->files->readers[1].header, BCF_HL_FMT, "ID", key_src, NULL) )
+                                error("Did you mean \"FMT/%s\" rather than \"%s\"?\n",str.s,str.s);
+                            char *ptr = strchr(key_src,'=');
+                            if ( ptr )
+                            {
+                                *ptr = 0; tmp.l = 0; ksprintf(&tmp,"%s:=%s",key_src,ptr+1); *ptr = '=';
+                                error("The INFO tag \"%s\" is not defined, is this what you want \"%s\" ?\n",key_src,tmp.s);
+                            }
+                            error("The INFO tag \"%s\" is not defined in %s, was the -h option provided?\n", key_src,args->files->readers[1].fname);
+                        }
+                        tmp.l = 0;
+                        bcf_hrec_format_rename(hrec, key_dst, &tmp);
+                    }
+                    bcf_hdr_append(args->hdr_out, tmp.s);
+                    if (bcf_hdr_sync(args->hdr_out) < 0)
+                        error_errno("[%s] Failed to update header", __func__);
+                    hdr_id = bcf_hdr_id2int(args->hdr_out, BCF_DT_ID, key_dst);
+                }
+                else
+                    error("The INFO tag \"%s\" is not defined in %s, was the -h option provided?\n", key_dst, args->targets_fname);
+                assert( bcf_hdr_idinfo_exists(args->hdr_out,BCF_HL_INFO,hdr_id) );
+            }
+            if  ( args->tgts_is_vcf )
+            {
+                if ( !strcasecmp("ID",key_src) && !explicit_src_info ) col->getter = vcf_getter_id2str;
+                else if ( !strcasecmp("FILTER",key_src) && !explicit_src_info ) col->getter = vcf_getter_filter2str;
+            }
+            col->number = bcf_hdr_id2length(args->hdr_out,BCF_HL_INFO,hdr_id);
+            switch ( bcf_hdr_id2type(args->hdr_out,BCF_HL_INFO,hdr_id) )
+            {
+                case BCF_HT_FLAG:   col->setter = args->tgts_is_vcf ? vcf_setter_info_flag : setter_info_flag; break;
+                case BCF_HT_INT:    col->setter = args->tgts_is_vcf ? vcf_setter_info_int  : setter_info_int; break;
+                case BCF_HT_REAL:   col->setter = args->tgts_is_vcf ? vcf_setter_info_real : setter_info_real; break;
+                case BCF_HT_STR:    col->setter = args->tgts_is_vcf ? vcf_setter_info_str  : setter_info_str; break;
+                default: error("The type of %s not recognised (%d)\n", str.s,bcf_hdr_id2type(args->hdr_out,BCF_HL_INFO,hdr_id));
+            }
+            if ( replace & SET_OR_APPEND )   // change to Number=.
+            {
+                bcf_hrec_t *hrec = bcf_hdr_get_hrec(args->hdr_out, BCF_HL_INFO, "ID", key_dst, NULL);
+                if ( !hrec ) error("Uh, could not find the new tag \"%s\" in the header\n", key_dst);
+                hrec = bcf_hrec_dup(hrec);
+                int j = bcf_hrec_find_key(hrec, "Number");
+                if ( j<0 ) error("Uh, could not find the entry Number in the header record of %s\n",key_dst);
+                free(hrec->vals[j]);
+                hrec->vals[j] = strdup(".");
+                bcf_hdr_remove(args->hdr_out,BCF_HL_INFO, key_dst);
+                bcf_hdr_add_hrec(args->hdr_out, hrec);
+            }
+        }
+        if ( !*se ) break;
+        ss = ++se;
+    }
+    free(str.s);
+    free(tmp.s);
+    free(args->columns);
+    if ( skip_info ) khash_str2int_destroy_free(skip_info);
+    if ( skip_fmt ) khash_str2int_destroy_free(skip_fmt);
+    if ( has_fmt_str )
+    {
+        int n = bcf_hdr_nsamples(args->hdr_out);
+        if ( args->tgts_is_vcf && n<bcf_hdr_nsamples(args->files->readers[1].header) ) n = bcf_hdr_nsamples(args->files->readers[1].header);
+        args->tmpp  = (char**)malloc(sizeof(char*)*n);
+        args->tmpp2 = (char**)malloc(sizeof(char*)*n);
+    }
+    if ( !need_sample_map )
+    {
+        free(args->sample_map);
+        args->sample_map = NULL;
+    }
+    else if ( sample_map_ok<0 )
+        error("No matching samples in source and destination file?\n");
+}
+static void init_merge_method(args_t *args)
+{
+    int i;
+    for (i=0; i<args->ncols; i++)
+    {
+        args->cols[i].merge_method = MM_FIRST;
+        args->cols[i].mm_str_hash = NULL;
+        args->cols[i].mm_dbl = NULL;
+        args->cols[i].mm_dbl_nalloc = args->cols[i].mm_dbl_nused = args->cols[i].mm_dbl_ndat = 0;
+        memset(&args->cols[i].mm_kstr, 0, sizeof(args->cols[i].mm_kstr));
+    }
+    if ( !args->merge_method_str.l ) return;
+    if ( args->tgts_is_vcf ) error("Error: the --merge-logic is intended for use with BED or TAB-delimited files only.\n");
+    if ( !args->tgt_idx && !args->tgts ) error("Error: BEG,END (or FROM,TO) columns or REF,ALT columns are expected with the --merge-logic option.\n");
+    char *sb = args->merge_method_str.s;
+    while ( *sb )
+    {
+        char *se = sb;
+        while ( *se && *se!=',' ) se++;
+        args->tmpks.l = 0;
+        kputsn(sb, se-sb, &args->tmpks);
+        kputc(0, &args->tmpks);
+        char *mm_type_str = args->tmpks.s + args->tmpks.l;
+        while ( *mm_type_str!=':' && mm_type_str > args->tmpks.s ) mm_type_str--;
+        if ( *mm_type_str!=':' )
+            error("Error: could not parse the argument to --merge-logic: %s\n", args->merge_method_str.s);
+        *mm_type_str = 0;
+        mm_type_str++;
+        int mm_type = MM_FIRST;
+        if ( !strcasecmp("unique",mm_type_str) ) mm_type = MM_UNIQUE;
+        else if ( !strcasecmp("first",mm_type_str) ) mm_type = MM_FIRST;
+        else if ( !strcasecmp("append",mm_type_str) ) mm_type = MM_APPEND;
+        else if ( !strcasecmp("append-missing",mm_type_str) )
+        {
+            mm_type = MM_APPEND_MISSING;
+            if ( args->ref_idx!=-1 ) args->has_append_mode = 1;
+        }
+        else if ( !strcasecmp("sum",mm_type_str) ) mm_type = MM_SUM;
+        else if ( !strcasecmp("avg",mm_type_str) ) mm_type = MM_AVG;
+        else if ( !strcasecmp("min",mm_type_str) ) mm_type = MM_MIN;
+        else if ( !strcasecmp("max",mm_type_str) ) mm_type = MM_MAX;
+        else error("Error: could not parse --merge-logic %s, the logic \"%s\" is not recognised\n", args->merge_method_str.s,mm_type_str);
+        for (i=0; i<args->ncols; i++)
+        {
+            if ( strcmp(args->cols[i].hdr_key_dst,args->tmpks.s) ) continue;
+            if ( (mm_type==MM_APPEND || mm_type==MM_APPEND_MISSING) && args->cols[i].number!=BCF_VL_VAR )
+                error("Error: --merge-logic append can be requested only for tags of variable length (Number=.)\n");
+            args->cols[i].merge_method = mm_type;
+            break;
+        }
+        if ( i==args->ncols ) error("No such tag in the destination file: %s\n", args->tmpks.s);
+        sb = *se ? se + 1 : se;
+    }
+    if ( args->has_append_mode )
+    {
+        // create a missing line to insert missing values when VCF ALT finds no match in the annotation file
+        args->aline_missing = (annot_line_t*)calloc(1,sizeof(*args->aline_missing));
+        int ncol = 0;
+        for (i=0; i<args->ncols; i++)
+            if ( ncol < args->cols[i].icol + 1 ) ncol = args->cols[i].icol + 1;
+        if ( ncol < args->ref_idx + 1 ) ncol = args->ref_idx + 1;
+        args->aline_missing->mcols = ncol;
+        args->aline_missing->ncols = ncol;
+        args->aline_missing->cols = (char**) malloc(ncol*sizeof(char*));
+        for (i=0; i<ncol; i++)
+            args->aline_missing->cols[i] = strdup(".");
+    }
+}
+
+static void rename_chrs(args_t *args, char *fname)
+{
+    int n, i;
+    char **map = hts_readlist(fname, 1, &n);
+    if ( !map ) error("Could not read: %s\n", fname);
+    for (i=0; i<n; i++)
+    {
+        char *ss = map[i];
+        while ( *ss && !isspace(*ss) ) ss++;
+        if ( !*ss ) error("Could not parse: %s\n", fname);
+        *ss = 0;
+        int rid = bcf_hdr_name2id(args->hdr_out, map[i]);
+        bcf_hrec_t *hrec = bcf_hdr_get_hrec(args->hdr_out, BCF_HL_CTG, "ID", map[i], NULL);
+        if ( !hrec ) continue;  // the sequence not present
+        int j = bcf_hrec_find_key(hrec, "ID");
+        assert( j>=0 );
+        free(hrec->vals[j]);
+        ss++;
+        while ( *ss && isspace(*ss) ) ss++;
+        char *se = ss;
+        while ( *se && !isspace(*se) ) se++;
+        *se = 0;
+        hrec->vals[j] = strdup(ss);
+        args->hdr_out->id[BCF_DT_CTG][rid].key = hrec->vals[j];
+    }
+    for (i=0; i<n; i++) free(map[i]);
+    free(map);
+}
+// Dirty: this relies on bcf_hdr_sync NOT being called
+static int rename_annots_core(args_t *args, char *ori_tag, char *new_tag)
+{
+    int type;
+    if ( !strncasecmp("info/",ori_tag,5) ) type = BCF_HL_INFO, ori_tag += 5;
+    else if ( !strncasecmp("format/",ori_tag,7) ) type = BCF_HL_FMT, ori_tag += 7;
+    else if ( !strncasecmp("fmt/",ori_tag,4) ) type = BCF_HL_FMT, ori_tag += 4;
+    else if ( !strncasecmp("filter/",ori_tag,7) ) type = BCF_HL_FLT, ori_tag += 7;
+    else return -1;
+    if ( !strncasecmp("info/",new_tag,5) )
+    {
+        if ( type != BCF_HL_INFO ) error("Cannot transfer %s to INFO\n", ori_tag);
+        new_tag += 5;
+    }
+    else if ( !strncasecmp("format/",new_tag,7) )
+    {
+        if ( type != BCF_HL_FMT ) error("Cannot transfer %s to FORMAT\n", ori_tag);
+        new_tag += 7;
+    }
+    else if ( !strncasecmp("fmt/",new_tag,4) )
+    {
+        if ( type != BCF_HL_FMT ) error("Cannot transfer %s to FORMAT\n", ori_tag);
+        new_tag += 4;
+    }
+    else if ( !strncasecmp("filter/",new_tag,7) )
+    {
+        if ( type != BCF_HL_FLT ) error("Cannot transfer %s to FILTER\n", ori_tag);
+        new_tag += 7;
+    }
+    int id = bcf_hdr_id2int(args->hdr_out, BCF_DT_ID, ori_tag);
+    if ( id<0 ) return 1;
+    bcf_hrec_t *hrec = bcf_hdr_get_hrec(args->hdr_out, type, "ID", ori_tag, NULL);
+    if ( !hrec ) return 1;  // the ID attribute not present
+    int j = bcf_hrec_find_key(hrec, "ID");
+    assert( j>=0 );
+    free(hrec->vals[j]);
+    char *ptr = new_tag;
+    while ( *ptr && !isspace(*ptr) ) ptr++;
+    *ptr = 0;
+    hrec->vals[j] = strdup(new_tag);
+    args->hdr_out->id[BCF_DT_ID][id].key = hrec->vals[j];
+    return 0;
+}
+static void rename_annots(args_t *args)
+{
+    int i;
+    if ( args->rename_annots )
+    {
+        args->rename_annots_map = hts_readlist(args->rename_annots, 1, &args->rename_annots_nmap);
+        if ( !args->rename_annots_map ) error("Could not read: %s\n", args->rename_annots);
+    }
+    for (i=0; i<args->rename_annots_nmap; i++)
+    {
+        char *ptr = args->rename_annots_map[i];
+        while ( *ptr && !isspace(*ptr) ) ptr++;
+        if ( !*ptr ) error("Could not parse: %s\n", args->rename_annots_map[i]);
+        char *rmme = ptr;
+        *ptr = 0;
+        ptr++;
+        while ( *ptr && isspace(*ptr) ) ptr++;
+        if ( !*ptr ) { *rmme = ' '; error("Could not parse: %s\n", args->rename_annots_map[i]); }
+        if ( rename_annots_core(args, args->rename_annots_map[i], ptr) < 0 )
+            error("Could not parse \"%s %s\", expected INFO, FORMAT, or FILTER prefix\n",args->rename_annots_map[i],ptr);
+    }
+}
+static void rename_annots_push(args_t *args, char *src, char *dst)
+{
+    args->rename_annots_nmap++;
+    args->rename_annots_map = (char**)realloc(args->rename_annots_map,sizeof(*args->rename_annots_map)*args->rename_annots_nmap);
+    kstring_t str = {0,0,0};
+    ksprintf(&str,"%s %s",src,dst);
+    args->rename_annots_map[ args->rename_annots_nmap - 1 ] = str.s;
+}
+
+static void init_data(args_t *args)
+{
+    args->hdr = args->files->readers[0].header;
+    args->hdr_out = bcf_hdr_dup(args->hdr);
+
+    if ( args->set_ids_fmt )
+    {
+        if ( args->set_ids_fmt[0]=='+' ) { args->set_ids_replace = 0; args->set_ids_fmt++; }
+        args->set_ids = convert_init(args->hdr_out, NULL, 0, args->set_ids_fmt);
+    }
+    if ( args->remove_annots ) init_remove_annots(args);
+    if ( args->header_fname || args->header_lines ) init_header_lines(args);
+    if ( args->targets_fname && args->tgts_is_vcf )
+    {
+        // reading annots from a VCF
+        if ( !bcf_sr_add_reader(args->files, args->targets_fname) )
+            error("Failed to open %s: %s\n", args->targets_fname,bcf_sr_strerror(args->files->errnum));
+        args->tgts_hdr = args->files->readers[1].header;
+    }
+    if ( args->columns ) init_columns(args);
+    if ( args->targets_fname && !args->tgts_is_vcf )
+    {
+        if ( !args->columns ) error("The -c option not given\n");
+        if ( args->chr_idx==-1 ) error("The -c CHROM option not given\n");
+        if ( args->beg_idx==-1 ) error("The -c POS option not given\n");
+        if ( args->single_overlaps && args->merge_method_str.l ) error("The options --merge-logic and --single-overlaps cannot be combined\n");
+        if ( args->end_idx==-1 || (args->single_overlaps && !args->merge_method_str.l) )
+        {
+            args->end_idx = -args->beg_idx - 1;
+            args->tgts = bcf_sr_regions_init(args->targets_fname,1,args->chr_idx,args->beg_idx,args->end_idx);
+            if ( !args->tgts ) error("Could not initialize the annotation file: %s\n", args->targets_fname);
+            if ( !args->tgts->tbx ) error("Expected tabix-indexed annotation file: %s\n", args->targets_fname);
+        }
+        else
+        {
+            if ( args->ref_idx!=-1 ) error("Error: the REF columns will be ignored when BEG,END (or FROM,TO) is present. Replace END (or TO) with \"-\".\n");
+            int len = strlen(args->targets_fname);
+            if ( len>=7 && !strcasecmp(".bed.gz",args->targets_fname+len-7) ) args->tgt_is_bed = 1;
+            else if ( len>=8 && !strcasecmp(".bed.bgz",args->targets_fname+len-8) ) args->tgt_is_bed = 1;
+            else if ( len>=4 && !strcasecmp(".bed",args->targets_fname+len-4) ) args->tgt_is_bed = 1;
+            args->tgt_idx = regidx_init(args->targets_fname,parse_with_payload,free_payload,sizeof(char*),args);
+            if ( !args->tgt_idx ) error("Failed to parse: %s\n", args->targets_fname);
+            args->tgt_itr = regitr_init(args->tgt_idx);
+            args->nalines++;
+            hts_expand0(annot_line_t,args->nalines,args->malines,args->alines);
+        }
+        if ( args->min_overlap_str )
+        {
+            char *tmp = args->min_overlap_str;
+            if ( args->min_overlap_str[0] != ':' )
+            {
+                args->min_overlap_ann = strtod(args->min_overlap_str,&tmp);
+                if ( args->min_overlap_ann < 0 || args->min_overlap_ann > 1 || (*tmp && *tmp!=':') )
+                    error("Could not parse \"--min-overlap %s\", expected value(s) between 0-1\n", args->min_overlap_str);
+            }
+            if ( *tmp && *tmp==':' )
+            {
+                args->min_overlap_vcf = strtod(tmp+1,&tmp);
+                if ( args->min_overlap_vcf < 0 || args->min_overlap_vcf > 1 || *tmp )
+                    error("Could not parse \"--min-overlap %s\", expected value(s) between 0-1\n", args->min_overlap_str);
+            }
+        }
+    }
+    init_merge_method(args);
+    args->vcmp = vcmp_init();
+
+    if ( args->filter_str )
+        args->filter = filter_init(args->hdr, args->filter_str);
+
+    if ( args->mark_sites )
+    {
+        if ( !args->targets_fname ) error("The -a option not given\n");
+        bcf_hdr_printf(args->hdr_out,"##INFO=<ID=%s,Number=0,Type=Flag,Description=\"Sites %slisted in %s\">",
+            args->mark_sites,args->mark_sites_logic==MARK_LISTED?"":"not ",args->mark_sites);
+    }
+
+    if (args->record_cmd_line) bcf_hdr_append_version(args->hdr_out, args->argc, args->argv, "bcftools_annotate");
+    if ( !args->drop_header )
+    {
+        if ( args->rename_chrs ) rename_chrs(args, args->rename_chrs);
+        if ( args->rename_annots || args->rename_annots_map ) rename_annots(args);
+
+        char wmode[8];
+        set_wmode(wmode,args->output_type,args->output_fname,args->clevel);
+        args->out_fh = hts_open(args->output_fname ? args->output_fname : "-", wmode);
+        if ( args->out_fh == NULL ) error("[%s] Error: cannot write to \"%s\": %s\n", __func__,args->output_fname, strerror(errno));
+        if ( args->n_threads )
+            hts_set_opt(args->out_fh, HTS_OPT_THREAD_POOL, args->files->p);
+        if ( bcf_hdr_write(args->out_fh, args->hdr_out)!=0 ) error("[%s] Error: failed to write the header to %s\n", __func__,args->output_fname);
+    }
+}
+
+static void destroy_data(args_t *args)
+{
+    int i;
+    for (i=0; i<args->nrm; i++) free(args->rm[i].key);
+    free(args->rm);
+    if ( args->hdr_out ) bcf_hdr_destroy(args->hdr_out);
+    if (args->vcmp) vcmp_destroy(args->vcmp);
+    for (i=0; i<args->ncols; i++)
+    {
+        free(args->cols[i].hdr_key_src);
+        free(args->cols[i].hdr_key_dst);
+        free(args->cols[i].mm_kstr.s);
+        if ( args->cols[i].mm_str_hash ) khash_str2int_destroy_free(args->cols[i].mm_str_hash);
+        free(args->cols[i].mm_dbl);
+        free(args->cols[i].ptr);
+    }
+    free(args->cols);
+    if ( args->aline_missing )
+    {
+        for (i=0; i<args->aline_missing->ncols; i++) free(args->aline_missing->cols[i]);
+        free(args->aline_missing->cols);
+        free(args->aline_missing);
+    }
+    for (i=0; i<args->malines; i++)
+    {
+        free(args->alines[i].cols);
+        free(args->alines[i].als);
+        free(args->alines[i].line.s);
+    }
+    free(args->alines);
+    free(args->srt_alines);
+    if ( args->tgt_idx )
+    {
+        regidx_destroy(args->tgt_idx);
+        regitr_destroy(args->tgt_itr);
+    }
+    if ( args->rename_annots_map )
+    {
+        for (i=0; i<args->rename_annots_nmap; i++) free(args->rename_annots_map[i]);
+        free(args->rename_annots_map);
+    }
+    if ( args->tgts ) bcf_sr_regions_destroy(args->tgts);
+    free(args->tmpks.s);
+    free(args->tmpi);
+    free(args->tmpf);
+    free(args->tmps);
+    free(args->tmpp);
+    free(args->tmpi2);
+    free(args->tmpf2);
+    free(args->tmps2);
+    free(args->tmpp2);
+    free(args->tmpi3);
+    free(args->tmpf3);
+    free(args->src_smpl_pld);
+    free(args->dst_smpl_pld);
+    if ( args->set_ids )
+        convert_destroy(args->set_ids);
+    if ( args->filter )
+        filter_destroy(args->filter);
+    if (args->out_fh) hts_close(args->out_fh);
+    free(args->sample_map);
+    free(args->merge_method_str.s);
+}
+
+static void parse_annot_line(args_t *args, char *str, annot_line_t *tmp)
+{
+    tmp->line.l = 0;
+    kputs(str, &tmp->line);
+    char *s = tmp->line.s;
+    tmp->ncols = 1;
+    hts_expand(char*,tmp->ncols,tmp->mcols,tmp->cols);
+    tmp->cols[0] = s;
+    while ( *s )
+    {
+        if ( *s=='\t' )
+        {
+            tmp->ncols++;
+            hts_expand(char*,tmp->ncols,tmp->mcols,tmp->cols);
+            tmp->cols[tmp->ncols-1] = s+1;
+            *s = 0;
+        }
+        s++;
+    }
+    if ( args->ref_idx != -1 )
+    {
+        if ( args->ref_idx >= tmp->ncols )
+            error("Could not parse the line, expected %d+ columns, found %d:\n\t%s\n",args->ref_idx+1,tmp->ncols,str);
+        if ( args->alt_idx >= tmp->ncols )
+            error("Could not parse the line, expected %d+ columns, found %d:\n\t%s\n",args->alt_idx+1,tmp->ncols,str);
+        tmp->nals = 2;
+        hts_expand(char*,tmp->nals,tmp->mals,tmp->als);
+        tmp->als[0] = tmp->cols[args->ref_idx];
+        tmp->als[1] = s = tmp->cols[args->alt_idx];
+        while ( *s )
+        {
+            if ( *s==',' )
+            {
+                tmp->nals++;
+                hts_expand(char*,tmp->nals,tmp->mals,tmp->als);
+                tmp->als[tmp->nals-1] = s+1;
+                *s = 0;
+            }
+            s++;
+        }
+    }
+}
+static void buffer_annot_lines(args_t *args, bcf1_t *line, int start_pos, int end_pos)
+{
+    if ( args->nalines && args->alines[0].rid != line->rid ) args->nalines = 0;
+
+    int i = 0;
+    while ( i<args->nalines )
+    {
+        if ( line->pos > args->alines[i].end )
+        {
+            args->nalines--;
+            if ( args->nalines && i<args->nalines )
+            {
+                annot_line_t tmp = args->alines[i];
+                memmove(&args->alines[i],&args->alines[i+1],(args->nalines-i)*sizeof(annot_line_t));
+                args->alines[args->nalines] = tmp;
+            }
+        }
+        else i++;
+    }
+    if ( args->ref_idx==-1 && args->nalines ) return;
+
+    while ( !bcf_sr_regions_overlap(args->tgts, bcf_seqname(args->hdr,line), start_pos,end_pos) )
+    {
+        if ( args->nalines + 1 == 0xffff ) break;   // likely a symbolic allele, don't let the buffer overflow
+        args->nalines++;
+        hts_expand0(annot_line_t,args->nalines,args->malines,args->alines);
+        annot_line_t *tmp = &args->alines[args->nalines-1];
+        tmp->rid   = line->rid;
+        tmp->start = args->tgts->start;
+        tmp->end   = args->tgts->end;
+        parse_annot_line(args, args->tgts->line.s, tmp);
+        if ( args->ref_idx != -1 )
+        {
+            int iseq = args->tgts->iseq;
+            if ( bcf_sr_regions_next(args->tgts)<0 || args->tgts->iseq!=iseq ) break;
+        }
+        else break;
+    }
+}
+
+// search string in semicolon separated strings (xx vs aa;bb)
+static int str_match(char *needle, char *haystack)
+{
+    int len = strlen(needle);
+    char *ptr = haystack;
+    while ( *ptr && (ptr=strstr(ptr,needle)) )
+    {
+        if ( ptr[len]!=0 && ptr[len]!=';' ) ptr++;          // a prefix, not a match
+        else if ( ptr==haystack || ptr[-1]==';' ) return 1; // a match
+        ptr++;  // a suffix, not a match
+    }
+    return 0;
+}
+// search common string in semicolon separated strings (xx;yy;zz vs aa;bb)
+static int strstr_match(char *a, char *b)
+{
+    char *beg = a;
+    while ( *beg )
+    {
+        char *end = beg;
+        while ( *end && *end!=';' ) end++;
+        char tmp = *end;
+        if ( *end==';' ) *end = 0;
+        int ret = str_match(beg,b);
+        *end = tmp;
+        if ( ret || !*end ) return ret;
+        beg = end + 1;
+    }
+    return 0;
+}
+static void annotate(args_t *args, bcf1_t *line)
+{
+    int i, j;
+    for (i=0; i<args->nrm; i++)
+        args->rm[i].handler(args, line, &args->rm[i]);
+
+    int has_overlap = 0;
+    if ( args->tgt_idx )
+    {
+        for (j=0; j<args->ncols; j++) args->cols[j].done = 0;
+        if ( regidx_overlap(args->tgt_idx, bcf_seqname(args->hdr,line),line->pos,line->pos+line->rlen-1, args->tgt_itr) )
+        {
+            while ( regitr_overlap(args->tgt_itr) )
+            {
+                annot_line_t *tmp = &args->alines[0];
+                tmp->rid   = line->rid;
+                tmp->start = args->tgt_itr->beg;
+                tmp->end   = args->tgt_itr->end;
+
+                // Check min overlap
+                int len_ann = tmp->end - tmp->start + 1;
+                int len_vcf = line->rlen;
+                int isec = (tmp->end < line->pos+line->rlen-1 ? tmp->end : line->pos+line->rlen-1) - (tmp->start > line->pos ? tmp->start : line->pos) + 1;
+                assert( isec > 0 );
+                if ( args->min_overlap_ann && args->min_overlap_ann > (float)isec/len_ann ) continue;
+                if ( args->min_overlap_vcf && args->min_overlap_vcf > (float)isec/len_vcf ) continue;
+
+                parse_annot_line(args, regitr_payload(args->tgt_itr,char*), tmp);
+                for (j=0; j<args->ncols; j++)
+                {
+                    if ( args->cols[j].done==1 ) continue;
+                    int ret = args->cols[j].setter(args,line,&args->cols[j],tmp);
+                    if ( ret < 0 )
+                        error("fixme: Could not set %s at %s:%"PRId64"\n", args->cols[j].hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) line->pos+1);
+                    if ( ret==0 )
+                        args->cols[j].done = 1;
+                }
+            }
+            has_overlap = 1;
+        }
+        for (j=0; j<args->ncols; j++)
+        {
+            if ( args->cols[j].done==1 || args->cols[j].merge_method == MM_FIRST ) continue;
+            if ( !args->cols[j].setter ) continue;
+            if ( args->cols[j].setter(args,line,&args->cols[j],NULL) < 0 )
+                error("fixme: Could not set %s at %s:%"PRId64"\n", args->cols[j].hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) line->pos+1);
+        }
+    }
+    else if ( args->tgts )
+    {
+        // Buffer annotation lines. When multiple ALT alleles are present in the annotation file, at least one
+        // must match some of the VCF alleles. If the append-missing mode is set (and REF+ALT is requested), the
+        // buffered lines will annotate the VCF respecting the order in ALT and when no matching line is found
+        // for an ALT, missing value is appended instead.
+        int end_pos = line->pos + line->rlen - 1;
+        buffer_annot_lines(args, line, line->pos, end_pos);
+
+        args->nsrt_alines = 0;
+        hts_expand(uint32_t,args->nalines,args->msrt_alines,args->srt_alines);
+        if ( args->nalines >= 0xffff || line->n_allele >= 0xffff )
+            error("Error: too many alleles or annotation lines in the buffer at %s:%"PRId64" (todo:skip?)\n",bcf_seqname(args->hdr,line),(int64_t) line->pos+1);
+
+        kstring_t match_end = {0,0,0};
+        if ( args->match_end>=0 && bcf_get_info_int32(args->hdr,line,"END",&args->tmpi,&args->mtmpi)==1 )
+            kputw(args->tmpi[0],&match_end);
+
+        // Find matching lines
+        for (i=0; i<args->nalines; i++)
+        {
+            if ( line->pos > args->alines[i].end || end_pos < args->alines[i].start ) continue;
+            if ( args->ref_idx != -1 )  // REF+ALT matching requested
+            {
+                if ( line->pos!=args->alines[i].start || vcmp_set_ref(args->vcmp, line->d.allele[0], args->alines[i].als[0]) < 0 ) continue;   // refs are not compatible
+                for (j=1; j<args->alines[i].nals; j++)
+                {
+                    int ialt;
+                    if ( line->n_allele==1 && args->alines[i].als[j][0]=='.' && args->alines[i].als[j][1]==0 )  // match: no ALT allele in VCF and annot file has "."
+                        ialt = 0;
+                    else
+                    {
+                        ialt = vcmp_find_allele(args->vcmp, line->d.allele+1, line->n_allele - 1, args->alines[i].als[j]);
+                        if ( ialt < 0 ) continue;
+                        ialt++;
+                    }
+                    if ( args->match_id>=0 && !strstr_match(line->d.id,args->alines[i].cols[args->match_id]) ) continue;
+                    if ( args->match_end>=0 && match_end.l && strcmp(match_end.s,args->alines[i].cols[args->match_end]) ) continue;
+                    args->srt_alines[args->nsrt_alines++] = (ialt<<16) | i;
+                    has_overlap = 1;
+                    break;
+                }
+            }
+            else    // overlap, REF+ALT matching not requested
+            {
+                args->srt_alines[args->nsrt_alines++] = (0xffff<<16) | i;
+                has_overlap = 1;
+            }
+        }
+
+        free(match_end.s);
+
+        // Sort lines if needed
+        if ( args->has_append_mode )
+        {
+            // insertion sort by VCF ALT index (top bits) and alines index (low bits)
+            uint32_t tmp;
+            for (i=1; i<args->nsrt_alines; i++)
+                for (j=i; j>0 && args->srt_alines[j] < args->srt_alines[j-1]; j--)
+                    tmp = args->srt_alines[j], args->srt_alines[j] = args->srt_alines[j-1], args->srt_alines[j-1] = tmp;
+        }
+        // Annotate
+        for (j=0; j<args->ncols; j++) args->cols[j].done = 0;
+        int ialt_exp = 1;
+        for (i=0; i<args->nsrt_alines; i++)
+        {
+            int ialt = args->srt_alines[i] >> 16;
+            int ilin = args->srt_alines[i] & 0xffff;
+            if ( args->has_append_mode )
+            {
+                if ( ialt_exp > ialt ) continue;    // multiple annotation lines for the same position
+                if ( ialt_exp < ialt )
+                {
+                    // REF+ALT matching requested, append-missing mode: insert "." if no annotation line was found for the ALT
+                    while ( ialt_exp++ < ialt )
+                    {
+                        for (j=0; j<args->ncols; j++)
+                        {
+                            if ( args->cols[j].merge_method != MM_APPEND_MISSING ) continue;
+                            if ( args->cols[j].done==1 ) continue;
+                            if ( !args->cols[j].setter ) continue;
+                            int ret = args->cols[j].setter(args,line,&args->cols[j],args->aline_missing);
+                            if ( ret < 0 )
+                                error("fixme: Could not set missing %s at %s:%"PRId64"\n", args->cols[j].hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) line->pos+1);
+                            if ( ret==0 )
+                                args->cols[j].done = 1;
+                        }
+                    }
+                }
+            }
+            for (j=0; j<args->ncols; j++)
+            {
+                if ( args->cols[j].done==1 ) continue;
+                if ( !args->cols[j].setter ) continue;
+                int ret = args->cols[j].setter(args,line,&args->cols[j],&args->alines[ilin]);
+                if ( ret < 0 )
+                    error("fixme: Could not set %s at %s:%"PRId64"\n", args->cols[j].hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) line->pos+1);
+                if ( ret==0 )
+                    args->cols[j].done = 1;
+            }
+            ialt_exp = ialt + 1;
+        }
+        if ( args->nsrt_alines )
+        {
+            // In the append-missing mode fill missing values to all trailing ALTs, but only if at least one
+            // record was found. Otherwise leave the row will be left without annotation.
+            if ( args->has_append_mode && ialt_exp < line->n_allele )
+            {
+                while ( ialt_exp++ < line->n_allele )
+                {
+                    for (j=0; j<args->ncols; j++)
+                    {
+                        if ( args->cols[j].merge_method != MM_APPEND_MISSING ) continue;
+                        if ( args->cols[j].done==1 ) continue;
+                        if ( !args->cols[j].setter ) continue;
+                        int ret = args->cols[j].setter(args,line,&args->cols[j],args->aline_missing);
+                        if ( ret < 0 )
+                            error("fixme: Could not set missing %s at %s:%"PRId64"\n", args->cols[j].hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) line->pos+1);
+                        if ( ret==0 )
+                            args->cols[j].done = 1;
+                    }
+                }
+            }
+            // Flush
+            for (j=0; j<args->ncols; j++)
+            {
+                if ( args->cols[j].done==1 || args->cols[j].merge_method == MM_FIRST ) continue;
+                if ( !args->cols[j].setter ) continue;
+                int ret = args->cols[j].setter(args,line,&args->cols[j],NULL);
+                if ( ret < 0 )
+                    error("fixme: Could not set %s at %s:%"PRId64"\n", args->cols[j].hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) line->pos+1);
+            }
+        }
+    }
+    else if ( args->files->nreaders == 2 )
+    {
+        if ( bcf_sr_has_line(args->files,1) )
+        {
+            bcf1_t *aline = bcf_sr_get_line(args->files,1);
+            for (j=0; j<args->ncols; j++)
+            {
+                if ( !args->cols[j].setter ) continue;
+                if ( args->cols[j].setter(args,line,&args->cols[j],aline) )
+                    error("fixme: Could not set %s at %s:%"PRId64"\n", args->cols[j].hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) line->pos+1);
+            }
+
+            has_overlap = 1;
+        }
+    }
+    if ( args->set_ids )
+    {
+        args->tmpks.l = 0;
+        convert_line(args->set_ids, line, &args->tmpks);
+        if ( args->tmpks.l )
+        {
+            int replace = 0;
+            if ( args->set_ids_replace ) replace = 1;
+            else if ( !line->d.id || (line->d.id[0]=='.' && !line->d.id[1]) ) replace = 1;
+            if ( replace )
+                bcf_update_id(args->hdr_out,line,args->tmpks.s);
+        }
+    }
+
+    if ( args->mark_sites )
+    {
+        // ideally, we'd like to be far more general than this in future, see https://github.com/samtools/bcftools/issues/87
+        if ( args->mark_sites_logic==MARK_LISTED )
+            bcf_update_info_flag(args->hdr_out,line,args->mark_sites,NULL,has_overlap?1:0);
+        else
+            bcf_update_info_flag(args->hdr_out,line,args->mark_sites,NULL,has_overlap?0:1);
+    }
+}
+
+static void usage(args_t *args)
+{
+    fprintf(stderr, "\n");
+    fprintf(stderr, "About:   Annotate and edit VCF/BCF files.\n");
+    fprintf(stderr, "Usage:   bcftools annotate [options] VCF\n");
+    fprintf(stderr, "\n");
+    fprintf(stderr, "Options:\n");
+    fprintf(stderr, "   -a, --annotations FILE          VCF file or tabix-indexed FILE with annotations: CHR\\tPOS[\\tVALUE]+\n");
+    fprintf(stderr, "   -c, --columns LIST              List of columns in the annotation file, e.g. CHROM,POS,REF,ALT,-,INFO/TAG. See man page for details\n");
+    fprintf(stderr, "   -C, --columns-file FILE         Read -c columns from FILE, one name per row, with optional --merge-logic TYPE: NAME[ TYPE]\n");
+    fprintf(stderr, "   -e, --exclude EXPR              Exclude sites for which the expression is true (see man page for details)\n");
+    fprintf(stderr, "       --force                     Continue despite parsing error (at your own risk!)\n");
+    fprintf(stderr, "   -H, --header-line STR           Header line which should be appended to the VCF header, can be given multiple times\n");
+    fprintf(stderr, "   -h, --header-lines FILE         Lines which should be appended to the VCF header\n");
+    fprintf(stderr, "   -I, --set-id [+]FORMAT          Set ID column using a `bcftools query`-like expression, see man page for details\n");
+    fprintf(stderr, "   -i, --include EXPR              Select sites for which the expression is true (see man page for details)\n");
+    fprintf(stderr, "   -k, --keep-sites                Leave -i/-e sites unchanged instead of discarding them\n");
+    fprintf(stderr, "   -l, --merge-logic TAG:TYPE      Merge logic for multiple overlapping regions (see man page for details), EXPERIMENTAL\n");
+    fprintf(stderr, "   -m, --mark-sites [+-]TAG        Add INFO/TAG flag to sites which are (\"+\") or are not (\"-\") listed in the -a file\n");
+    fprintf(stderr, "       --min-overlap ANN:VCF       Required overlap as a fraction of variant in the -a file (ANN), the VCF (:VCF), or reciprocal (ANN:VCF)\n");
+    fprintf(stderr, "       --no-version                Do not append version and command line to the header\n");
+    fprintf(stderr, "   -o, --output FILE               Write output to a file [standard output]\n");
+    fprintf(stderr, "   -O, --output-type u|b|v|z[0-9]  u/b: un/compressed BCF, v/z: un/compressed VCF, 0-9: compression level [v]\n");
+    fprintf(stderr, "       --pair-logic STR            Matching records by <snps|indels|both|all|some|exact>, see man page for details [some]\n");
+    fprintf(stderr, "   -r, --regions REGION            Restrict to comma-separated list of regions\n");
+    fprintf(stderr, "   -R, --regions-file FILE         Restrict to regions listed in FILE\n");
+    fprintf(stderr, "       --regions-overlap 0|1|2     Include if POS in the region (0), record overlaps (1), variant overlaps (2) [1]\n");
+    fprintf(stderr, "       --rename-annots FILE        Rename annotations: TYPE/old\\tnew, where TYPE is one of FILTER,INFO,FORMAT\n");
+    fprintf(stderr, "       --rename-chrs FILE          Rename sequences according to the mapping: old\\tnew\n");
+    fprintf(stderr, "   -s, --samples [^]LIST           Comma separated list of samples to annotate (or exclude with \"^\" prefix)\n");
+    fprintf(stderr, "   -S, --samples-file [^]FILE      File of samples to annotate (or exclude with \"^\" prefix)\n");
+    fprintf(stderr, "       --single-overlaps           Keep memory low by avoiding complexities arising from handling multiple overlapping intervals\n");
+    fprintf(stderr, "   -x, --remove LIST               List of annotations (e.g. ID,INFO/DP,FORMAT/DP,FILTER) to remove (or keep with \"^\" prefix). See man page for details\n");
+    fprintf(stderr, "       --threads INT               Number of extra output compression threads [0]\n");
+    fprintf(stderr, "\n");
+    fprintf(stderr, "Examples:\n");
+    fprintf(stderr, "   http://samtools.github.io/bcftools/howtos/annotate.html\n");
+    fprintf(stderr, "\n");
+    exit(1);
+}
+
+int main_vcfannotate(int argc, char *argv[])
+{
+    int c;
+    args_t *args  = (args_t*) calloc(1,sizeof(args_t));
+    args->argc    = argc; args->argv = argv;
+    args->files   = bcf_sr_init();
+    args->output_fname = "-";
+    args->output_type = FT_VCF;
+    args->n_threads = 0;
+    args->record_cmd_line = 1;
+    args->ref_idx = args->alt_idx = args->chr_idx = args->beg_idx = args->end_idx = -1;
+    args->set_ids_replace = 1;
+    args->match_id = -1;
+    args->match_end = -1;
+    args->clevel = -1;
+    args->pair_logic = -1;
+    int regions_is_file = 0;
+    int regions_overlap = 1;
+
+    static struct option loptions[] =
+    {
+        {"keep-sites",no_argument,NULL,'k'},
+        {"mark-sites",required_argument,NULL,'m'},
+        {"set-id",required_argument,NULL,'I'},
+        {"output",required_argument,NULL,'o'},
+        {"output-type",required_argument,NULL,'O'},
+        {"threads",required_argument,NULL,9},
+        {"annotations",required_argument,NULL,'a'},
+        {"merge-logic",required_argument,NULL,'l'},
+        {"collapse",required_argument,NULL,2},
+        {"pair-logic",required_argument,NULL,2},
+        {"include",required_argument,NULL,'i'},
+        {"exclude",required_argument,NULL,'e'},
+        {"regions",required_argument,NULL,'r'},
+        {"regions-file",required_argument,NULL,'R'},
+        {"regions-overlap",required_argument,NULL,3},
+        {"remove",required_argument,NULL,'x'},
+        {"columns-file",required_argument,NULL,'C'},
+        {"columns",required_argument,NULL,'c'},
+        {"rename-annots",required_argument,NULL,11},
+        {"rename-chrs",required_argument,NULL,1},
+        {"header-lines",required_argument,NULL,'h'},
+        {"header-line",required_argument,NULL,'H'},
+        {"samples",required_argument,NULL,'s'},
+        {"samples-file",required_argument,NULL,'S'},
+        {"single-overlaps",no_argument,NULL,10},
+        {"min-overlap",required_argument,NULL,12},
+        {"no-version",no_argument,NULL,8},
+        {"force",no_argument,NULL,'f'},
+        {NULL,0,NULL,0}
+    };
+    char *tmp;
+    while ((c = getopt_long(argc, argv, "h:H:?o:O:r:R:a:x:c:C:i:e:S:s:I:m:kl:f",loptions,NULL)) >= 0)
+    {
+        switch (c) {
+            case 'f': args->force = 1; break;
+            case 'k': args->keep_sites = 1; break;
+            case 'm':
+                args->mark_sites_logic = MARK_LISTED;
+                if ( optarg[0]=='+' ) args->mark_sites = optarg+1;
+                else if ( optarg[0]=='-' ) { args->mark_sites = optarg+1; args->mark_sites_logic = MARK_UNLISTED; }
+                else args->mark_sites = optarg;
+                break;
+            case 'l':
+                if ( args->merge_method_str.l ) kputc(',',&args->merge_method_str);
+                kputs(optarg,&args->merge_method_str);
+                break;
+            case 'I': args->set_ids_fmt = optarg; break;
+            case 's': args->sample_names = optarg; break;
+            case 'S': args->sample_names = optarg; args->sample_is_file = 1; break;
+            case 'c': args->columns = strdup(optarg); break;
+            case 'C': args->columns = strdup(optarg); args->columns_is_file = 1; break;
+            case 'o': args->output_fname = optarg; break;
+            case 'O':
+                switch (optarg[0]) {
+                    case 'b': args->output_type = FT_BCF_GZ; break;
+                    case 'u': args->output_type = FT_BCF; break;
+                    case 'z': args->output_type = FT_VCF_GZ; break;
+                    case 'v': args->output_type = FT_VCF; break;
+                    default:
+                    {
+                        args->clevel = strtol(optarg,&tmp,10);
+                        if ( *tmp || args->clevel<0 || args->clevel>9 ) error("The output type \"%s\" not recognised\n", optarg);
+                    }
+                };
+                if ( optarg[1] )
+                {
+                    args->clevel = strtol(optarg+1,&tmp,10);
+                    if ( *tmp || args->clevel<0 || args->clevel>9 ) error("Could not parse argument: --compression-level %s\n", optarg+1);
+                }
+                break;
+            case 'e':
+                if ( args->filter_str ) error("Error: only one -i or -e expression can be given, and they cannot be combined\n");
+                args->filter_str = optarg; args->filter_logic |= FLT_EXCLUDE; break;
+            case 'i':
+                if ( args->filter_str ) error("Error: only one -i or -e expression can be given, and they cannot be combined\n");
+                args->filter_str = optarg; args->filter_logic |= FLT_INCLUDE; break;
+            case 'x': args->remove_annots = optarg; break;
+            case 'a': args->targets_fname = optarg; break;
+            case 'r': args->regions_list = optarg; break;
+            case 'R': args->regions_list = optarg; regions_is_file = 1; break;
+            case 'h': args->header_fname = optarg; break;
+            case 'H': args->header_lines = dbuf_push(args->header_lines,strdup(optarg)); break;
+            case  1 : args->rename_chrs = optarg; break;
+            case  2 :
+                if ( !strcmp(optarg,"snps") ) args->pair_logic |= BCF_SR_PAIR_SNP_REF;
+                else if ( !strcmp(optarg,"indels") ) args->pair_logic |= BCF_SR_PAIR_INDEL_REF;
+                else if ( !strcmp(optarg,"both") ) args->pair_logic |= BCF_SR_PAIR_BOTH_REF;
+                else if ( !strcmp(optarg,"any") ) args->pair_logic |= BCF_SR_PAIR_ANY;
+                else if ( !strcmp(optarg,"all") ) args->pair_logic |= BCF_SR_PAIR_ANY;
+                else if ( !strcmp(optarg,"some") ) args->pair_logic |= BCF_SR_PAIR_SOME;
+                else if ( !strcmp(optarg,"none") ) args->pair_logic = BCF_SR_PAIR_EXACT;
+                else if ( !strcmp(optarg,"exact") ) args->pair_logic = BCF_SR_PAIR_EXACT;
+                else error("The --pair-logic string \"%s\" not recognised.\n", optarg);
+                break;
+            case  3 :
+                regions_overlap = parse_overlap_option(optarg);
+                if ( regions_overlap < 0 ) error("Could not parse: --regions-overlap %s\n",optarg);
+                break;
+            case  9 : args->n_threads = strtol(optarg, 0, 0); break;
+            case  8 : args->record_cmd_line = 0; break;
+            case 10 : args->single_overlaps = 1; break;
+            case 11 : args->rename_annots = optarg; break;
+            case 12 : args->min_overlap_str = optarg; break;
+            case '?': usage(args); break;
+            default: error("Unknown argument: %s\n", optarg);
+        }
+    }
+
+    char *fname = NULL;
+    if ( optind>=argc )
+    {
+        if ( !isatty(fileno((FILE *)stdin)) ) fname = "-";  // reading from stdin
+        else usage(args);
+    }
+    else fname = argv[optind];
+
+    if ( args->regions_list )
+    {
+        bcf_sr_set_opt(args->files,BCF_SR_REGIONS_OVERLAP,regions_overlap);
+        if ( bcf_sr_set_regions(args->files, args->regions_list, regions_is_file)<0 )
+            error("Failed to read the regions: %s\n", args->regions_list);
+    }
+    if ( args->targets_fname )
+    {
+        htsFile *fp = hts_open(args->targets_fname,"r");
+        if ( !fp ) error("Failed to open %s\n", args->targets_fname);
+        htsFormat type = *hts_get_format(fp);
+        hts_close(fp);
+
+        if ( type.format==vcf || type.format==bcf )
+        {
+            args->tgts_is_vcf = 1;
+            args->files->require_index = 1;
+            bcf_sr_set_opt(args->files,BCF_SR_PAIR_LOGIC,args->pair_logic>=0 ? args->pair_logic : BCF_SR_PAIR_SOME);
+            if ( args->min_overlap_str ) error("The --min-overlap option cannot be used when annotating from a VCF\n");
+        }
+    }
+    if ( args->min_overlap_str && args->single_overlaps ) error("The options --single-overlaps and --min-overlap cannot be combined\n");
+    if ( bcf_sr_set_threads(args->files, args->n_threads)<0 ) error("Failed to create threads\n");
+    if ( !bcf_sr_add_reader(args->files, fname) ) error("Failed to read from %s: %s\n", !strcmp("-",fname)?"standard input":fname,bcf_sr_strerror(args->files->errnum));
+
+    static int line_errcode_warned = 0;
+    init_data(args);
+    while ( bcf_sr_next_line(args->files) )
+    {
+        if ( !bcf_sr_has_line(args->files,0) ) continue;
+        bcf1_t *line = bcf_sr_get_line(args->files,0);
+        if ( line->errcode )
+        {
+            if ( !args->force )
+                error("Encountered an error, cannot proceed. Please check the error output above.\n"
+                      "If feeling adventurous, use the --force option. (At your own risk!)\n");
+            else if ( !line_errcode_warned )
+            {
+                fprintf(stderr,
+                    "Warning: Encountered an error, proceeding only because --force was given.\n"
+                    "         Note that this can result in a segfault or a silent corruption of the output file!\n");
+                line_errcode_warned = 1;
+                line->errcode = 0;
+            }
+        }
+        if ( args->filter )
+        {
+            int pass = filter_test(args->filter, line, NULL);
+            if ( args->filter_logic & FLT_EXCLUDE ) pass = pass ? 0 : 1;
+            if ( !pass )
+            {
+                if ( args->keep_sites && bcf_write1(args->out_fh, args->hdr_out, line)!=0 ) error("[%s] Error: failed to write to %s\n", __func__,args->output_fname);
+                continue;
+            }
+        }
+        annotate(args, line);
+        if ( bcf_write1(args->out_fh, args->hdr_out, line)!=0 ) error("[%s] Error: failed to write to %s\n", __func__,args->output_fname);
+    }
+    destroy_data(args);
+    bcf_sr_destroy(args->files);
+    free(args);
+    return 0;
+}
diff --git a/bcftools/vcfannotate.c.pysam.c b/bcftools/vcfannotate.c.pysam.c
new file mode 100644
index 0000000..e45c305
--- /dev/null
+++ b/bcftools/vcfannotate.c.pysam.c
@@ -0,0 +1,3526 @@
+#include "bcftools.pysam.h"
+
+/*  vcfannotate.c -- Annotate and edit VCF/BCF files.
+
+    Copyright (C) 2013-2022 Genome Research Ltd.
+
+    Author: Petr Danecek <pd3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.  */
+
+#include <stdio.h>
+#include <strings.h>
+#include <unistd.h>
+#include <getopt.h>
+#include <assert.h>
+#include <ctype.h>
+#include <string.h>
+#include <errno.h>
+#include <sys/stat.h>
+#include <sys/types.h>
+#include <dirent.h>
+#include <math.h>
+#include <inttypes.h>
+#include <htslib/vcf.h>
+#include <htslib/synced_bcf_reader.h>
+#include <htslib/kseq.h>
+#include <htslib/khash_str2int.h>
+#include "bcftools.h"
+#include "vcmp.h"
+#include "filter.h"
+#include "convert.h"
+#include "smpl_ilist.h"
+#include "regidx.h"
+#include "dbuf.h"
+
+struct _args_t;
+
+typedef struct _rm_tag_t
+{
+    char *key;
+    int hdr_id;
+    void (*handler)(struct _args_t *, bcf1_t *, struct _rm_tag_t *);
+}
+rm_tag_t;
+
+typedef struct
+{
+    char **cols;
+    int ncols, mcols;
+    char **als;
+    int nals, mals;
+    kstring_t line;
+    int rid, start, end;
+}
+annot_line_t;
+
+#define REPLACE_MISSING     (1<<0)   // -c +TAG  .. replace only missing values
+#define REPLACE_ALL         (1<<1)   // -c TAG   .. replace both missing and existing values
+#define REPLACE_NON_MISSING (1<<2)   // -c -TAG  .. replace only if tgt is not missing
+#define SET_OR_APPEND       (1<<3)   // -c =TAG  .. set new value if missing or non-existent, append otherwise
+#define MATCH_VALUE         (1<<4)   // -c ~ID   .. do not set, just match the value
+#define CARRY_OVER_MISSING  (1<<5)   // -c .TAG  .. carry over source missing values as well
+#define MM_FIRST   0    // if multiple annotation lines overlap a VCF record, use the first, discarding the rest
+#define MM_APPEND  1    // append, possibly multiple times
+#define MM_UNIQUE  2    // append, only unique values
+#define MM_SUM     3
+#define MM_AVG     4
+#define MM_MIN     5
+#define MM_MAX     6
+#define MM_APPEND_MISSING 7     // missing values will be transferred as well
+typedef struct _annot_col_t
+{
+    int icol, replace, number;  // number: one of BCF_VL_* types
+    char *hdr_key_src, *hdr_key_dst;
+    // The setters return 0 on successful update of the bcf record, negative value (bcf_update_* return status) on errors,
+    // or 1 on (repeated partial updates) concluded with a src=NULL call
+    int (*setter)(struct _args_t *, bcf1_t *dst, struct _annot_col_t *, void *src); // the last is the annotation line, either src bcf1_t or annot_line_t
+    int (*getter)(struct _args_t *, bcf1_t *src, struct _annot_col_t *, void **ptr, int *mptr);
+    int merge_method;               // one of the MM_* defines
+    khash_t(str2int) *mm_str_hash;  // lookup table to ensure uniqueness of added string values
+    kstring_t mm_kstr;
+    size_t
+        mm_dbl_nalloc,  // the allocated size --merge-logic values array
+        mm_dbl_nused,   // the number of used elements in the mm_dbl array
+        mm_dbl_ndat;    // the number of merged rows (for calculating the average)
+    double
+        *mm_dbl;
+    void *ptr;
+    int mptr, done;
+}
+annot_col_t;
+
+// Logic of the filters: include or exclude sites which match the filters?
+#define FLT_INCLUDE 1
+#define FLT_EXCLUDE 2
+
+#define MARK_LISTED   1
+#define MARK_UNLISTED 2
+
+typedef struct _args_t
+{
+    bcf_srs_t *files;
+    bcf_hdr_t *hdr, *hdr_out, *tgts_hdr;
+    htsFile *out_fh;
+    int output_type, n_threads, clevel;
+    bcf_sr_regions_t *tgts;
+
+    regidx_t *tgt_idx;  // keep everything in memory only with .tab annotation file and -c BEG,END columns
+    regitr_t *tgt_itr;
+    int tgt_is_bed;
+
+    filter_t *filter;
+    char *filter_str;
+    int filter_logic;   // include or exclude sites which match the filters? One of FLT_INCLUDE/FLT_EXCLUDE
+    int keep_sites;
+
+    rm_tag_t *rm;           // tags scheduled for removal
+    int nrm;
+    int flt_keep_pass;      // when all filters removed, reset to PASS
+
+    vcmp_t *vcmp;           // for matching annotation and VCF lines by allele
+    annot_line_t *alines;   // buffered annotation lines
+    annot_line_t *aline_missing;
+    uint32_t *srt_alines;   // sorted indexes (iALT<<16 || iAline)
+    int nalines, malines, nsrt_alines, msrt_alines;
+    int ref_idx, alt_idx, chr_idx, beg_idx, end_idx;   // -1 if not present
+    annot_col_t *cols;      // column indexes and setters
+    int ncols;
+    int match_id;           // set iff `-c ~ID` given, -1 otherwise
+    int match_end;          // set iff `-c ~INFO/END` is given, -1 otherwise
+
+    char *set_ids_fmt;
+    convert_t *set_ids;
+    int set_ids_replace;
+
+    int nsmpl_annot;
+    int *sample_map, nsample_map, sample_is_file;   // map[idst] -> isrc
+    uint8_t *src_smpl_pld, *dst_smpl_pld;   // for Number=G format fields
+    int mtmpi, mtmpf, mtmps;
+    int mtmpi2, mtmpf2, mtmps2;
+    int mtmpi3, mtmpf3, mtmps3;
+    int32_t *tmpi, *tmpi2, *tmpi3;
+    float *tmpf, *tmpf2, *tmpf3;
+    char *tmps, *tmps2, **tmpp, **tmpp2;
+    kstring_t tmpks;
+
+    char **argv, *output_fname, *targets_fname, *regions_list, *header_fname;
+    char *remove_annots, *columns, *rename_chrs, *rename_annots, *sample_names, *mark_sites;
+    char **rename_annots_map;
+    char *min_overlap_str;
+    float min_overlap_ann, min_overlap_vcf;
+    int rename_annots_nmap;
+    kstring_t merge_method_str;
+    int argc, drop_header, record_cmd_line, tgts_is_vcf, mark_sites_logic, force, single_overlaps;
+    int columns_is_file, has_append_mode, pair_logic;
+    dbuf_t *header_lines;
+}
+args_t;
+
+char *msprintf(const char *fmt, ...);
+
+int parse_with_payload(const char *line, char **chr_beg, char **chr_end, uint32_t *beg, uint32_t *end, void *payload, void *usr)
+{
+    args_t *args = (args_t*) usr;
+    int ret = args->tgt_is_bed ? regidx_parse_bed(line, chr_beg, chr_end, beg, end, NULL, NULL) : regidx_parse_tab(line, chr_beg, chr_end, beg, end, NULL, NULL);
+    if ( ret<0 ) return ret;
+    *((char **)payload) = strdup(line);
+    return 0;
+}
+void free_payload(void *payload)
+{
+    char *str = *((char**)payload);
+    free(str);
+}
+
+void remove_id(args_t *args, bcf1_t *line, rm_tag_t *tag)
+{
+    bcf_update_id(args->hdr,line,NULL);
+}
+void remove_filter(args_t *args, bcf1_t *line, rm_tag_t *tag)
+{
+    if ( tag->key && tag->hdr_id<0 )
+    {
+        error("Error: Cannot proceed, not even with the --force option, bad things could happen.\n"
+              "       Note that \"bcftools annotate -x FILTER\" can be used to remove ALL filters.\n"
+              "       Even better, use \"bcftools view -h\" and \"bcftools reheader\" to fix the header!\n"
+              );
+    }
+    if ( !tag->key ) bcf_update_filter(args->hdr, line, NULL, args->flt_keep_pass);
+    else bcf_remove_filter(args->hdr, line, tag->hdr_id, args->flt_keep_pass);
+}
+void remove_qual(args_t *args, bcf1_t *line, rm_tag_t *tag)
+{
+    bcf_float_set_missing(line->qual);
+}
+void remove_info(args_t *args, bcf1_t *line, rm_tag_t *tag)
+{
+    // remove all INFO fields
+    if ( !(line->unpacked & BCF_UN_INFO) ) bcf_unpack(line, BCF_UN_INFO);
+
+    int i;
+    for (i=0; i<line->n_info; i++)
+    {
+        bcf_info_t *inf = &line->d.info[i];
+        if (  !strcmp("END",bcf_hdr_int2id(args->hdr,BCF_DT_ID,inf->key)) )
+            line->rlen = line->n_allele ? strlen(line->d.allele[0]) : 0;
+        if ( inf->vptr_free )
+        {
+            free(inf->vptr - inf->vptr_off);
+            inf->vptr_free = 0;
+        }
+        line->d.shared_dirty |= BCF1_DIRTY_INF;
+        inf->vptr = NULL;
+        inf->vptr_off = inf->vptr_len = 0;
+    }
+}
+void remove_info_tag(args_t *args, bcf1_t *line, rm_tag_t *tag)
+{
+    bcf_update_info(args->hdr, line, tag->key, NULL, 0, BCF_HT_INT);  // the type does not matter with n=0
+}
+void remove_format_tag(args_t *args, bcf1_t *line, rm_tag_t *tag)
+{
+    bcf_update_format(args->hdr, line, tag->key, NULL, 0, BCF_HT_INT);  // the type does not matter with n=0
+}
+void remove_format(args_t *args, bcf1_t *line, rm_tag_t *tag)
+{
+    // remove all FORMAT fields except GT
+    if ( !(line->unpacked & BCF_UN_FMT) ) bcf_unpack(line, BCF_UN_FMT);
+
+    int i;
+    for (i=0; i<line->n_fmt; i++)
+    {
+        bcf_fmt_t *fmt = &line->d.fmt[i];
+        const char *key = bcf_hdr_int2id(args->hdr,BCF_DT_ID,fmt->id);
+        if ( key[0]=='G' && key[1]=='T' && !key[2] ) continue;
+
+        if ( fmt->p_free )
+        {
+            free(fmt->p - fmt->p_off);
+            fmt->p_free = 0;
+        }
+        line->d.indiv_dirty = 1;
+        fmt->p = NULL;
+    }
+}
+
+#include "htslib/khash.h"
+KHASH_MAP_INIT_STR(vdict, bcf_idinfo_t)
+typedef khash_t(vdict) vdict_t;
+
+static void remove_hdr_lines(bcf_hdr_t *hdr, int type)
+{
+    int i = 0, nrm = 0;
+    while ( i<hdr->nhrec )
+    {
+        if ( hdr->hrec[i]->type!=type ) { i++; continue; }
+        bcf_hrec_t *hrec = hdr->hrec[i];
+        if ( type==BCF_HL_FMT || type==BCF_HL_INFO || type==BCF_HL_FMT || type== BCF_HL_CTG )
+        {
+            // everything except FORMAT/GT
+            int id = bcf_hrec_find_key(hrec, "ID");
+            if ( id>=0 )
+            {
+                if ( type==BCF_HL_FMT && !strcmp(hrec->vals[id],"GT") ) { i++; continue; }
+                vdict_t *d = type==BCF_HL_CTG ? (vdict_t*)hdr->dict[BCF_DT_CTG] : (vdict_t*)hdr->dict[BCF_DT_ID];
+                khint_t k = kh_get(vdict, d, hdr->hrec[i]->vals[id]);
+                kh_val(d, k).hrec[type==BCF_HL_CTG?0:type] = NULL;
+                kh_val(d, k).info[type] |= 0xf;
+            }
+        }
+        nrm++;
+        hdr->nhrec--;
+        if ( i < hdr->nhrec )
+            memmove(&hdr->hrec[i],&hdr->hrec[i+1],(hdr->nhrec-i)*sizeof(bcf_hrec_t*));
+        bcf_hrec_destroy(hrec);
+    }
+    if ( nrm ) {
+        if (bcf_hdr_sync(hdr) < 0)
+            error_errno("[%s] Failed to update header", __func__);
+    }
+}
+
+static void init_remove_annots(args_t *args)
+{
+    int keep_info = 0, keep_fmt = 0, keep_flt = 0;
+    void *keep = khash_str2int_init();
+    kstring_t str = {0,0,0};
+    char *ss = args->remove_annots;
+
+    int i, ntags, needs_info = 0;
+    if ( args->set_ids )
+    {
+        const char **tags = convert_list_used_tags(args->set_ids,&ntags);
+        for (i=0; i<ntags; i++)
+            if ( !strncmp("INFO/",tags[i],4) ) needs_info = 1;
+    }
+
+    while ( *ss )
+    {
+        args->nrm++;
+        args->rm = (rm_tag_t*) realloc(args->rm,sizeof(rm_tag_t)*args->nrm);
+        rm_tag_t *tag = &args->rm[args->nrm-1];
+        tag->key = NULL;
+
+        int type = BCF_HL_GEN;
+        if ( !strncasecmp("INFO/",ss,5) ) { type = BCF_HL_INFO; ss += 5; }
+        else if ( !strncasecmp("INF/",ss,4) ) { type = BCF_HL_INFO; ss += 4; }
+        else if ( !strncasecmp("FORMAT/",ss,7) ) { type = BCF_HL_FMT; ss += 7; }
+        else if ( !strncasecmp("FMT/",ss,4) ) { type = BCF_HL_FMT; ss += 4; }
+        else if ( !strncasecmp("FILTER/",ss,7) ) { type = BCF_HL_FLT; ss += 7; }
+        else if ( !strncasecmp("^INFO/",ss,6) ) { type = BCF_HL_INFO; ss += 6; keep_info = 1; }
+        else if ( !strncasecmp("^INF/",ss,5) ) { type = BCF_HL_INFO; ss += 5; keep_info = 1; }
+        else if ( !strncasecmp("^FORMAT/",ss,8) ) { type = BCF_HL_FMT; ss += 8; keep_fmt = 1; }
+        else if ( !strncasecmp("^FMT/",ss,5) ) { type = BCF_HL_FMT; ss += 5; keep_fmt = 1; }
+        else if ( !strncasecmp("^FILTER/",ss,8) ) { type = BCF_HL_FLT; ss += 8; keep_flt = 1; }
+
+        char *se = ss;
+        while ( *se && *se!=',' ) se++;
+        str.l = 0;
+        kputsn(ss, se-ss, &str);
+
+        if ( type==BCF_HL_FLT )
+        {
+            if ( !keep_flt )
+            {
+                args->flt_keep_pass = 1;
+                tag->handler = remove_filter;
+                tag->key = strdup(str.s);
+                tag->hdr_id = bcf_hdr_id2int(args->hdr, BCF_DT_ID, tag->key);
+                if ( !bcf_hdr_idinfo_exists(args->hdr,BCF_HL_FLT,tag->hdr_id) )
+                {
+                    if ( args->keep_sites )
+                        error("Error: The filter \"%s\" is not defined in the header, cannot use the -k option\n", str.s);
+                    else
+                        fprintf(bcftools_stderr,"Warning: The filter \"%s\" is not defined in the header\n", str.s);
+                }
+                else if ( !args->keep_sites ) bcf_hdr_remove(args->hdr_out,BCF_HL_FLT,tag->key);
+            }
+            else
+            {
+                int value, ret = khash_str2int_get(keep, str.s, &value);
+                if ( ret==-1 ) khash_str2int_set(keep, strdup(str.s),1<<BCF_HL_FLT);
+                else khash_str2int_set(keep, str.s, value | 1<<BCF_HL_FLT);
+                args->nrm--;
+            }
+        }
+        else if ( type!=BCF_HL_GEN )
+        {
+            int id = bcf_hdr_id2int(args->hdr,BCF_DT_ID,str.s);
+            if ( !bcf_hdr_idinfo_exists(args->hdr,type,id) )
+            {
+                if ( args->keep_sites )
+                    error("Error: The tag \"%s\" is not defined in the header, cannot use the -k option\n", str.s);
+                else
+                    fprintf(bcftools_stderr,"Warning: The tag \"%s\" not defined in the header\n", str.s);
+
+                tag->key = strdup(str.s);
+                if ( type==BCF_HL_INFO )
+                {
+                    tag->handler = remove_info_tag;
+                    if ( needs_info ) error("Error: `--remove INFO/%s` is executed first, cannot combine with `--set-id %s`\n",tag->key,args->set_ids_fmt);
+                }
+                else if ( type==BCF_HL_FMT ) tag->handler = remove_format_tag;
+            }
+            else if ( (type==BCF_HL_FMT && keep_fmt) || (type==BCF_HL_INFO && keep_info) )
+            {
+                int value, ret = khash_str2int_get(keep, str.s, &value);
+                if ( ret==-1 ) khash_str2int_set(keep, strdup(str.s),1<<type);
+                else khash_str2int_set(keep, str.s, value | 1<<type);
+                args->nrm--;
+            }
+            else
+            {
+                tag->key = strdup(str.s);
+                if ( type==BCF_HL_INFO )
+                {
+                    tag->handler = remove_info_tag;
+                    if ( needs_info ) error("Error: `--remove INFO/%s` is executed first, cannot combine with `--set-id %s`\n",tag->key,args->set_ids_fmt);
+                }
+                else if ( type==BCF_HL_FMT ) tag->handler = remove_format_tag;
+                if ( !args->keep_sites ) bcf_hdr_remove(args->hdr_out,type,tag->key);
+            }
+        }
+        else if ( !strcasecmp("ID",str.s) ) tag->handler = remove_id;
+        else if ( !strcasecmp("FILTER",str.s) )
+        {
+            tag->handler = remove_filter;
+            if ( !args->keep_sites ) remove_hdr_lines(args->hdr_out,BCF_HL_FLT);
+        }
+        else if ( !strcasecmp("QUAL",str.s) ) tag->handler = remove_qual;
+        else if ( !strcasecmp("INFO",str.s) )
+        {
+            if ( needs_info ) error("Error: `--remove INFO` is executed first, cannot combine with `--set-id %s`\n",args->set_ids_fmt);
+            tag->handler = remove_info;
+            if ( !args->keep_sites ) remove_hdr_lines(args->hdr_out,BCF_HL_INFO);
+        }
+        else if ( !strcasecmp("FMT",str.s) || !strcasecmp("FORMAT",str.s) )
+        {
+            tag->handler = remove_format;
+            if ( !args->keep_sites ) remove_hdr_lines(args->hdr_out,BCF_HL_FMT);
+        }
+        else if ( str.l )
+        {
+            int id = bcf_hdr_id2int(args->hdr, BCF_DT_ID, str.s);
+            if ( bcf_hdr_idinfo_exists(args->hdr,BCF_HL_INFO,id) ) error("Error: did you mean INFO/%s?\n",str.s);
+            if ( bcf_hdr_idinfo_exists(args->hdr,BCF_HL_FMT,id) ) error("Error: did you mean FORMAT/%s?\n",str.s);
+
+            if ( !args->keep_sites )
+            {
+                if ( str.s[0]=='#' && str.s[1]=='#' )
+                    bcf_hdr_remove(args->hdr_out,BCF_HL_GEN,str.s+2);
+                else
+                    bcf_hdr_remove(args->hdr_out,BCF_HL_STR,str.s);
+            }
+            args->nrm--;
+        }
+
+        ss = *se ? se+1 : se;
+    }
+    free(str.s);
+    if ( keep_flt || keep_info || keep_fmt )
+    {
+        int j;
+        for (j=0; j<args->hdr->nhrec; j++)
+        {
+            bcf_hrec_t *hrec = args->hdr->hrec[j];
+            if ( hrec->type!=BCF_HL_FLT && hrec->type!=BCF_HL_INFO && hrec->type!=BCF_HL_FMT ) continue;
+            if ( !keep_flt && hrec->type==BCF_HL_FLT ) continue;
+            if ( !keep_info && hrec->type==BCF_HL_INFO ) continue;
+            if ( !keep_fmt && hrec->type==BCF_HL_FMT ) continue;
+            int k = bcf_hrec_find_key(hrec,"ID");
+            assert( k>=0 ); // this should always be true for valid VCFs
+            int value, ret = khash_str2int_get(keep,hrec->vals[k],&value);
+            if ( ret==0 && value>>hrec->type ) // keep
+            {
+                if ( hrec->type==BCF_HL_FLT && !strcmp("PASS",hrec->vals[k]) ) args->flt_keep_pass = 1;
+                continue;
+            }
+            args->nrm++;
+            args->rm = (rm_tag_t*) realloc(args->rm,sizeof(rm_tag_t)*args->nrm);
+            rm_tag_t *tag = &args->rm[args->nrm-1];
+            if ( hrec->type==BCF_HL_INFO ) tag->handler = remove_info_tag;
+            else if ( hrec->type==BCF_HL_FMT ) tag->handler = remove_format_tag;
+            else
+            {
+                tag->handler = remove_filter;
+                tag->hdr_id = bcf_hdr_id2int(args->hdr, BCF_DT_ID, hrec->vals[k]);
+            }
+            tag->key = strdup(hrec->vals[k]);
+            if ( !args->keep_sites ) bcf_hdr_remove(args->hdr_out,hrec->type,tag->key);
+        }
+    }
+    khash_str2int_destroy_free(keep);
+    if ( !args->nrm ) error("No matching tag in -x %s\n", args->remove_annots);
+    if (bcf_hdr_sync(args->hdr_out) < 0)
+        error_errno("[%s] Failed to update header", __func__);
+}
+static void init_header_lines(args_t *args)
+{
+    if ( args->header_fname )
+    {
+        htsFile *file = hts_open(args->header_fname, "rb");
+        if ( !file ) error("Error reading %s\n", args->header_fname);
+        kstring_t str = {0,0,0};
+        while ( hts_getline(file, KS_SEP_LINE, &str) > 0 )
+        {
+            if ( bcf_hdr_append(args->hdr_out,str.s) ) error("Could not parse %s: %s\n", args->header_fname, str.s);
+            bcf_hdr_append(args->hdr,str.s);    // the input file may not have the header line if run with -h (and nothing else)
+        }
+        if ( hts_close(file)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,args->header_fname);
+        free(str.s);
+    }
+    if ( args->header_lines )
+    {
+        int i, n = dbuf_n(args->header_lines);
+        for (i=0; i<n; i++)
+        {
+            char *line = dbuf_ith(args->header_lines,i);
+            if ( bcf_hdr_append(args->hdr_out,line) ) error("Could not parse the header line: %s\n", line);
+            bcf_hdr_append(args->hdr,line);    // the input file may not have the header line if run with -H (and nothing else)
+        }
+        dbuf_destroy_free(args->header_lines);
+        args->header_lines = NULL;
+    }
+    if (bcf_hdr_sync(args->hdr_out) < 0)
+        error_errno("[%s] Failed to update output header", __func__);
+    if (bcf_hdr_sync(args->hdr) < 0)
+        error_errno("[%s] Failed to update input header", __func__);
+}
+static int vcf_getter_info_str2str(args_t *args, bcf1_t *rec, annot_col_t *col, void **ptr, int *mptr)
+{
+    return bcf_get_info_string(args->tgts_hdr,rec,col->hdr_key_src,ptr,mptr);
+}
+static int vcf_getter_id2str(args_t *args, bcf1_t *rec, annot_col_t *col, void **ptr, int *mptr)
+{
+    char *str = *((char**)ptr);
+    int len = strlen(rec->d.id);
+    if ( len >= *mptr ) str = realloc(str, len+1);
+    strcpy(str, rec->d.id);
+    *((char**)ptr) = str;
+    *mptr = len+1;
+    return len;
+}
+static int vcf_getter_filter2str(args_t *args, bcf1_t *rec, annot_col_t *col, void **ptr, int *mptr)
+{
+    kstring_t str;
+    str.s = *((char**)ptr);
+    str.m = *mptr;
+    str.l = 0;
+
+    int i;
+    if ( rec->d.n_flt )
+    {
+        for (i=0; i<rec->d.n_flt; i++)
+        {
+            if (i) kputc(';', &str);
+            kputs(bcf_hdr_int2id(args->tgts_hdr,BCF_DT_ID,rec->d.flt[i]), &str);
+        }
+    }
+    else kputc('.', &str);
+
+    *((char**)ptr) = str.s;
+    *mptr = str.m;
+    return str.l;
+}
+static int setter_filter(args_t *args, bcf1_t *line, annot_col_t *col, void *data)
+{
+    if ( !data ) error("Error: the --merge-logic option cannot be used with FILTER (yet?)\n");
+
+    // note: so far this works only with one filter, not a list of filters
+    annot_line_t *tab = (annot_line_t*) data;
+    if ( tab->cols[col->icol][0]=='.' && !tab->cols[col->icol][1] ) // don't overwrite with a missing value unless asked
+    {
+        if ( (col->replace & CARRY_OVER_MISSING) && (col->replace & (REPLACE_ALL|REPLACE_NON_MISSING)) ) bcf_update_filter(args->hdr_out,line,NULL,0);
+        return 0;
+    }
+    hts_expand(int,1,args->mtmpi,args->tmpi);
+    args->tmpi[0] = bcf_hdr_id2int(args->hdr_out, BCF_DT_ID, tab->cols[col->icol]);
+    if ( args->tmpi[0]<0 ) error("The FILTER \"%s\" is not defined in the header, was the -h option provided?\n", tab->cols[col->icol]);
+    if ( col->replace & SET_OR_APPEND ) return bcf_add_filter(args->hdr_out,line,args->tmpi[0]);
+    if ( !(col->replace & REPLACE_MISSING) )
+    {
+        bcf_update_filter(args->hdr_out,line,NULL,0);
+        return bcf_update_filter(args->hdr_out,line,args->tmpi,1);
+    }
+
+    // only update missing FILTER
+    if ( !(line->unpacked & BCF_UN_FLT) ) bcf_unpack(line, BCF_UN_FLT);
+    if ( !line->d.n_flt )
+        return bcf_update_filter(args->hdr_out,line,args->tmpi,1);
+
+    return 0;
+}
+static int vcf_setter_filter(args_t *args, bcf1_t *line, annot_col_t *col, void *data)
+{
+    int i, ret = 0;
+    bcf1_t *rec = (bcf1_t*) data;
+    if ( !(rec->unpacked & BCF_UN_FLT) ) bcf_unpack(rec, BCF_UN_FLT);
+    if ( !(line->unpacked & BCF_UN_FLT) ) bcf_unpack(line, BCF_UN_FLT);
+    if ( !rec->d.n_flt ) // don't overwrite with a missing value unless asked
+    {
+        if ( (col->replace & CARRY_OVER_MISSING) && (col->replace & (REPLACE_ALL|REPLACE_NON_MISSING)) ) bcf_update_filter(args->hdr_out,line,NULL,0);
+        return 0;
+    }
+    if ( col->replace & (SET_OR_APPEND|REPLACE_MISSING) )
+    {
+        if ( (col->replace & REPLACE_MISSING) && line->d.n_flt ) return 0; // only update missing FILTER
+        for (i=0; i<rec->d.n_flt; i++)
+        {
+            const char *flt = bcf_hdr_int2id(args->files->readers[1].header, BCF_DT_ID, rec->d.flt[i]);
+            if ( bcf_add_filter(args->hdr_out,line,bcf_hdr_id2int(args->hdr_out, BCF_DT_ID, flt)) < 0 ) ret = -1;
+        }
+        return ret;
+    }
+    hts_expand(int,rec->d.n_flt,args->mtmpi,args->tmpi);
+    for (i=0; i<rec->d.n_flt; i++)
+    {
+        const char *flt = bcf_hdr_int2id(args->files->readers[1].header, BCF_DT_ID, rec->d.flt[i]);
+        args->tmpi[i] = bcf_hdr_id2int(args->hdr_out, BCF_DT_ID, flt);
+    }
+    bcf_update_filter(args->hdr_out,line,NULL,0);
+    return bcf_update_filter(args->hdr_out,line,args->tmpi,rec->d.n_flt);
+}
+static int setter_pos(args_t *args, bcf1_t *line, annot_col_t *col, void *data)
+{
+    annot_line_t *tab = (annot_line_t*) data;
+    if ( tab->cols[col->icol] && tab->cols[col->icol][0]=='.' && !tab->cols[col->icol][1] ) return 0; // don't replace with "."
+    char *tmp;
+    int pos = strtol(tab->cols[col->icol], &tmp, 10);
+    if ( tmp==tab->cols[col->icol] )
+        error("Could not parse ~POS at %s:%"PRId64" .. [%s]\n",bcf_seqname(args->hdr,line),(int64_t)line->pos+1,tab->cols[col->icol]);
+    line->pos = pos - 1;
+    return 0;
+}
+static int setter_id(args_t *args, bcf1_t *line, annot_col_t *col, void *data)
+{
+    if ( !data ) error("Error: the --merge-logic option cannot be used with ID (yet?)\n");
+    if ( col->replace & MATCH_VALUE ) return 0;
+
+    // possible cases:
+    //      IN  ANNOT   OUT     ACHIEVED_BY
+    //      x   y       x        -c +ID
+    //      x   y       y        -c ID
+    //      x   y       x,y      -c =ID
+    //      x   .       x        -c +ID, ID
+    //      x   .       .        -x ID
+    //      .   y       y        -c +ID, -c ID
+    //
+    annot_line_t *tab = (annot_line_t*) data;
+    if ( tab->cols[col->icol] && tab->cols[col->icol][0]=='.' && !tab->cols[col->icol][1] ) return 0; // don't replace with "."
+    if ( col->replace & SET_OR_APPEND ) return bcf_add_id(args->hdr_out,line,tab->cols[col->icol]);
+    if ( !(col->replace & REPLACE_MISSING) ) return bcf_update_id(args->hdr_out,line,tab->cols[col->icol]);
+
+    // running with +ID, only update missing ids
+    if ( !line->d.id || (line->d.id[0]=='.' && !line->d.id[1]) )
+        return bcf_update_id(args->hdr_out,line,tab->cols[col->icol]);
+    return 0;
+}
+static int vcf_setter_id(args_t *args, bcf1_t *line, annot_col_t *col, void *data)
+{
+    if ( col->replace & MATCH_VALUE ) return 0;
+
+    bcf1_t *rec = (bcf1_t*) data;
+
+    char *id;
+    if ( col->getter )
+    {
+        int nret = col->getter(args,rec,col,&col->ptr,&col->mptr);
+        id = (char*) col->ptr;
+        if ( nret<=0 || (nret==1 && *id=='.') ) return 0;   // don't replace with "."
+    }
+    else
+    {
+        if ( rec->d.id && rec->d.id[0]=='.' && !rec->d.id[1] ) return 0;    // don't replace with "."
+        id = rec->d.id;
+    }
+    if ( col->replace & SET_OR_APPEND ) return bcf_add_id(args->hdr_out,line,id);
+    if ( !(col->replace & REPLACE_MISSING) ) return bcf_update_id(args->hdr_out,line,id);
+
+    // running with +ID, only update missing ids
+    if ( !line->d.id || (line->d.id[0]=='.' && !line->d.id[1]) )
+        return bcf_update_id(args->hdr_out,line,id);
+    return 0;
+}
+static int vcf_setter_ref(args_t *args, bcf1_t *line, annot_col_t *col, void *data)
+{
+    bcf1_t *rec = (bcf1_t*) data;
+    if ( !strcmp(rec->d.allele[0],line->d.allele[0]) ) return 0;    // no update necessary
+    const char **als = (const char**) malloc(sizeof(char*)*line->n_allele);
+    als[0] = rec->d.allele[0];
+    int i;
+    for (i=1; i<line->n_allele; i++) als[i] = line->d.allele[i];
+    int ret = bcf_update_alleles(args->hdr_out, line, als, line->n_allele);
+    free(als);
+    return ret;
+}
+static int vcf_setter_alt(args_t *args, bcf1_t *line, annot_col_t *col, void *data)
+{
+    bcf1_t *rec = (bcf1_t*) data;
+    int i;
+    if ( line->n_allele>1 && (col->replace & REPLACE_MISSING) ) return 0;
+    if ( rec->n_allele==line->n_allele )
+    {
+        for (i=1; i<rec->n_allele; i++) if ( strcmp(rec->d.allele[i],line->d.allele[i]) ) break;
+        if ( i==rec->n_allele ) return 0;   // no update necessary
+    }
+    const char **als = (const char**) malloc(sizeof(char*)*rec->n_allele);
+    als[0] = line->d.allele[0];
+    for (i=1; i<rec->n_allele; i++) als[i] = rec->d.allele[i];
+    int ret = bcf_update_alleles(args->hdr_out, line, als, rec->n_allele);
+    free(als);
+    return ret;
+}
+static int setter_qual(args_t *args, bcf1_t *line, annot_col_t *col, void *data)
+{
+    if ( !data ) error("Error: the --merge-logic option cannot be used with QUAL (yet?)\n");
+
+    annot_line_t *tab = (annot_line_t*) data;
+    char *str = tab->cols[col->icol];
+    if ( str[0]=='.' && str[1]==0 ) // don't overwrite with a missing value unless asked
+    {
+        if ( (col->replace & CARRY_OVER_MISSING) && (col->replace & (REPLACE_ALL|REPLACE_NON_MISSING)) ) bcf_float_set_missing(line->qual);
+        return 0;
+    }
+    if ( (col->replace & REPLACE_MISSING) && !bcf_float_is_missing(line->qual) ) return 0;
+
+    line->qual = strtod(str, &str);
+    if ( str == tab->cols[col->icol] )
+        error("Could not parse %s at %s:%"PRId64" .. [%s]\n", col->hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) line->pos+1,tab->cols[col->icol]);
+    return 0;
+}
+static int vcf_setter_qual(args_t *args, bcf1_t *line, annot_col_t *col, void *data)
+{
+    bcf1_t *rec = (bcf1_t*) data;
+    if ( bcf_float_is_missing(rec->qual) )  // don't overwrite with a missing value unless asked
+    {
+        if ( (col->replace & CARRY_OVER_MISSING) && (col->replace & (REPLACE_ALL|REPLACE_NON_MISSING)) ) bcf_float_set_missing(line->qual);
+        return 0;
+    }
+    if ( (col->replace & REPLACE_MISSING) && !bcf_float_is_missing(line->qual) ) return 0;
+    line->qual = rec->qual;
+    return 0;
+}
+static int setter_info_flag(args_t *args, bcf1_t *line, annot_col_t *col, void *data)
+{
+    if ( !data ) error("Error: the --merge-logic option cannot be used with INFO type=Flag (yet?)\n");
+
+    annot_line_t *tab = (annot_line_t*) data;
+    char *str = tab->cols[col->icol];
+    if ( str[0]=='.' && str[1]==0 ) // don't overwrite with a missing value unless asked
+    {
+        if ( (col->replace & CARRY_OVER_MISSING) && (col->replace & (REPLACE_ALL|REPLACE_NON_MISSING)) ) bcf_update_info_flag(args->hdr_out,line,col->hdr_key_dst,NULL,0);
+        return 0;
+    }
+
+    if ( str[0]=='1' && str[1]==0 ) return bcf_update_info_flag(args->hdr_out,line,col->hdr_key_dst,NULL,1);
+    if ( str[0]=='0' && str[1]==0 ) return bcf_update_info_flag(args->hdr_out,line,col->hdr_key_dst,NULL,0);
+    error("Could not parse %s at %s:%"PRId64" .. [%s]\n", col->hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) line->pos+1,tab->cols[col->icol]);
+    return -1;
+}
+static int vcf_setter_info_flag(args_t *args, bcf1_t *line, annot_col_t *col, void *data)
+{
+    bcf1_t *rec = (bcf1_t*) data;
+    int flag = bcf_get_info_flag(args->files->readers[1].header,rec,col->hdr_key_src,NULL,NULL);
+    bcf_update_info_flag(args->hdr_out,line,col->hdr_key_dst,NULL,flag);
+    return 0;
+}
+static int setter_ARinfo_int32(args_t *args, bcf1_t *line, annot_col_t *col, int nals, char **als, int ntmpi)
+{
+    if ( col->number==BCF_VL_A && ntmpi!=nals-1 && (ntmpi!=1 || args->tmpi[0]!=bcf_int32_missing || args->tmpi[1]!=bcf_int32_vector_end) )
+        error("Incorrect number of values (%d) for the %s tag at %s:%"PRId64"\n", ntmpi,col->hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) line->pos+1);
+    else if ( col->number==BCF_VL_R && ntmpi!=nals && (ntmpi!=1 || args->tmpi[0]!=bcf_int32_missing || args->tmpi[1]!=bcf_int32_vector_end) )
+        error("Incorrect number of values (%d) for the %s tag at %s:%"PRId64"\n", ntmpi,col->hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) line->pos+1);
+
+    int ndst = col->number==BCF_VL_A ? line->n_allele - 1 : line->n_allele;
+    int *map = vcmp_map_ARvalues(args->vcmp,ndst,nals,als,line->n_allele,line->d.allele);
+    if ( !map ) error("REF alleles not compatible at %s:%"PRId64"\n", bcf_seqname(args->hdr,line),(int64_t) line->pos+1);
+
+    // fill in any missing values in the target VCF (or all, if not present)
+    int ntmpi2 = bcf_get_info_float(args->hdr, line, col->hdr_key_dst, &args->tmpi2, &args->mtmpi2);
+    if ( ntmpi2 < ndst ) hts_expand(int32_t,ndst,args->mtmpi2,args->tmpi2);
+
+    int i;
+    for (i=0; i<ndst; i++)
+    {
+        if ( map[i]<0 )
+        {
+            if ( ntmpi2 < ndst ) args->tmpi2[i] = bcf_int32_missing;
+            continue;
+        }
+        if ( ntmpi2==ndst && (col->replace & REPLACE_MISSING)
+                && args->tmpi2[i]!=bcf_int32_missing
+                && args->tmpi2[i]!=bcf_int32_vector_end ) continue;
+
+        args->tmpi2[i] = args->tmpi[ map[i] ];
+    }
+    return bcf_update_info_int32(args->hdr_out,line,col->hdr_key_dst,args->tmpi2,ndst);
+}
+static int setter_info_int(args_t *args, bcf1_t *line, annot_col_t *col, void *data)
+{
+    annot_line_t *tab = (annot_line_t*) data;
+
+    // This is a bit hacky, only to reuse existing code with minimal changes:
+    //      -c =TAG will now behave as -l TAG:APPEND for integers
+    if ( col->replace & SET_OR_APPEND ) col->merge_method=MM_APPEND;
+
+    if ( !tab )
+    {
+        if ( col->merge_method!=MM_SUM && col->merge_method!=MM_AVG &&
+             col->merge_method!=MM_MIN && col->merge_method!=MM_MAX &&
+             col->merge_method!=MM_APPEND &&
+             col->merge_method!=MM_APPEND_MISSING )
+            error("Error: at the moment only the sum,avg,min,max,append,append-missing options are supported with --merge-logic for INFO type=Integer\n");
+    }
+
+    int i,ntmpi = 0;
+    if ( (col->replace & SET_OR_APPEND) && !col->mm_dbl_nused )
+    {
+        ntmpi = bcf_get_info_int32(args->hdr, line, col->hdr_key_dst, &args->tmpi, &args->mtmpi);
+        if ( ntmpi>0 && (args->tmpi[0]!=bcf_int32_missing || (col->replace & CARRY_OVER_MISSING)) )
+        {
+            col->mm_dbl_nused = col->mm_dbl_ndat = ntmpi;
+            hts_expand(double,col->mm_dbl_nused,col->mm_dbl_nalloc,col->mm_dbl);
+            for (i=0; i<ntmpi; i++)
+                col->mm_dbl[i] = args->tmpi[i];
+            col->mm_dbl_ndat = 1;
+        }
+        ntmpi = 0;
+    }
+    if ( tab )  // has data, not flushing yet
+    {
+        char *str = tab->cols[col->icol], *end = str;
+        if ( str[0]=='.' && str[1]==0 && col->merge_method!=MM_APPEND_MISSING && !(col->replace & CARRY_OVER_MISSING) ) return 1;
+
+        while ( *end )
+        {
+            ntmpi++;
+            hts_expand(int32_t,ntmpi,args->mtmpi,args->tmpi);
+            if ( str[0]=='.' && (str[1]==0 || str[1]==',') )
+            {
+                if ( col->merge_method==MM_APPEND_MISSING || (col->replace & CARRY_OVER_MISSING) )
+                    args->tmpi[ntmpi-1] = bcf_int32_missing;
+                else
+                    ntmpi--;
+                if ( str[1]==0 ) end = str+1;
+                str += 2;
+            }
+            else
+            {
+                args->tmpi[ntmpi-1] = strtol(str, &end, 10);
+                if ( end==str )
+                    error("Could not parse %s at %s:%"PRId64" .. [%s]\n", col->hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) line->pos+1,tab->cols[col->icol]);
+                str = end+1;
+            }
+        }
+        if ( col->merge_method!=MM_FIRST )
+        {
+            if ( !col->mm_dbl_nused )
+            {
+                col->mm_dbl_nused = ntmpi;
+                hts_expand(double,col->mm_dbl_nused,col->mm_dbl_nalloc,col->mm_dbl);
+                for (i=0; i<ntmpi; i++)
+                    col->mm_dbl[i] = args->tmpi[i];
+            }
+            else
+            {
+                if ( col->merge_method==MM_APPEND || col->merge_method==MM_APPEND_MISSING )
+                {
+                    int nori = col->mm_dbl_nused;
+                    col->mm_dbl_nused += ntmpi;
+                    hts_expand(double,col->mm_dbl_nused,col->mm_dbl_nalloc,col->mm_dbl);
+                    for (i=0; i<ntmpi; i++)
+                        col->mm_dbl[i+nori] = args->tmpi[i];
+                }
+                else
+                {
+                    if ( ntmpi!=col->mm_dbl_nused ) error("Error: cannot merge fields of unequal length\n");
+                    if ( col->merge_method==MM_SUM || col->merge_method==MM_AVG )
+                        for (i=0; i<ntmpi; i++) col->mm_dbl[i] += args->tmpi[i];
+                    else if ( col->merge_method==MM_MIN )
+                        for (i=0; i<ntmpi; i++) { if ( col->mm_dbl[i] > args->tmpi[i] ) col->mm_dbl[i] = args->tmpi[i]; }
+                    else if ( col->merge_method==MM_MAX )
+                        for (i=0; i<ntmpi; i++) { if ( col->mm_dbl[i] < args->tmpi[i] ) col->mm_dbl[i] = args->tmpi[i]; }
+                }
+            }
+            col->mm_dbl_ndat++;
+            return 1;
+        }
+    }
+    else if ( col->merge_method==MM_SUM || col->merge_method==MM_MIN || col->merge_method==MM_MAX || col->merge_method==MM_APPEND || col->merge_method==MM_APPEND_MISSING )
+    {
+        ntmpi = col->mm_dbl_nused;
+        hts_expand(int32_t,ntmpi,args->mtmpi,args->tmpi);
+        for (i=0; i<ntmpi; i++) args->tmpi[i] = col->mm_dbl[i];
+        col->mm_dbl_nused = col->mm_dbl_ndat = 0;
+    }
+    else if ( col->merge_method==MM_AVG )
+    {
+        ntmpi = col->mm_dbl_nused;
+        hts_expand(int32_t,ntmpi,args->mtmpi,args->tmpi);
+        for (i=0; i<ntmpi; i++) args->tmpi[i] = col->mm_dbl[i]/col->mm_dbl_ndat;
+        col->mm_dbl_nused = col->mm_dbl_ndat = 0;
+    }
+
+    if ( col->number==BCF_VL_A || col->number==BCF_VL_R )
+        return setter_ARinfo_int32(args,line,col,tab->nals,tab->als,ntmpi);
+
+    if ( col->replace & REPLACE_MISSING )
+    {
+        int ret = bcf_get_info_int32(args->hdr, line, col->hdr_key_dst, &args->tmpi2, &args->mtmpi2);
+        if ( ret>0 && args->tmpi2[0]!=bcf_int32_missing ) return 0;
+    }
+    return bcf_update_info_int32(args->hdr_out,line,col->hdr_key_dst,args->tmpi,ntmpi);
+}
+static int vcf_setter_info_int(args_t *args, bcf1_t *line, annot_col_t *col, void *data)
+{
+    bcf1_t *rec = (bcf1_t*) data;
+    int ntmpi = bcf_get_info_int32(args->files->readers[1].header,rec,col->hdr_key_src,&args->tmpi,&args->mtmpi);
+    if ( ntmpi < 0 ) return 0;    // nothing to add
+
+    if ( col->number==BCF_VL_A || col->number==BCF_VL_R )
+        return setter_ARinfo_int32(args,line,col,rec->n_allele,rec->d.allele,ntmpi);
+
+    if ( col->replace & REPLACE_MISSING )
+    {
+        int ret = bcf_get_info_int32(args->hdr, line, col->hdr_key_dst, &args->tmpi2, &args->mtmpi2);
+        if ( ret>0 && args->tmpi2[0]!=bcf_int32_missing ) return 0;
+    }
+
+    return bcf_update_info_int32(args->hdr_out,line,col->hdr_key_dst,args->tmpi,ntmpi);
+}
+static int setter_ARinfo_real(args_t *args, bcf1_t *line, annot_col_t *col, int nals, char **als, int ntmpf)
+{
+    if ( col->number==BCF_VL_A && ntmpf!=nals-1 && (ntmpf!=1 || !bcf_float_is_missing(args->tmpf[0]) || !bcf_float_is_vector_end(args->tmpf[0])) )
+        error("Incorrect number of values (%d) for the %s tag at %s:%"PRId64"\n", ntmpf,col->hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) line->pos+1);
+    else if ( col->number==BCF_VL_R && ntmpf!=nals && (ntmpf!=1 || !bcf_float_is_missing(args->tmpf[0]) || !bcf_float_is_vector_end(args->tmpf[0])) )
+        error("Incorrect number of values (%d) for the %s tag at %s:%"PRId64"\n", ntmpf,col->hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) line->pos+1);
+
+    int ndst = col->number==BCF_VL_A ? line->n_allele - 1 : line->n_allele;
+    int *map = vcmp_map_ARvalues(args->vcmp,ndst,nals,als,line->n_allele,line->d.allele);
+    if ( !map ) error("REF alleles not compatible at %s:%"PRId64"\n", bcf_seqname(args->hdr,line),(int64_t) line->pos+1);
+
+    // fill in any missing values in the target VCF (or all, if not present)
+    int ntmpf2 = bcf_get_info_float(args->hdr, line, col->hdr_key_dst, &args->tmpf2, &args->mtmpf2);
+    if ( ntmpf2 < ndst ) hts_expand(float,ndst,args->mtmpf2,args->tmpf2);
+
+    int i;
+    for (i=0; i<ndst; i++)
+    {
+        if ( map[i]<0 )
+        {
+            if ( ntmpf2 < ndst ) bcf_float_set_missing(args->tmpf2[i]);
+            continue;
+        }
+        if ( ntmpf2==ndst && (col->replace & REPLACE_MISSING)
+                && !bcf_float_is_missing(args->tmpf2[i])
+                && !bcf_float_is_vector_end(args->tmpf2[i]) ) continue;
+
+        args->tmpf2[i] = args->tmpf[ map[i] ];
+    }
+    return bcf_update_info_float(args->hdr_out,line,col->hdr_key_dst,args->tmpf2,ndst);
+}
+static int setter_info_real(args_t *args, bcf1_t *line, annot_col_t *col, void *data)
+{
+    annot_line_t *tab = (annot_line_t*) data;
+
+    // This is a bit hacky, only to reuse existing code with minimal changes:
+    //      -c =TAG will now behave as -l TAG:APPEND for floats
+    if ( col->replace & SET_OR_APPEND ) col->merge_method=MM_APPEND;
+
+    if ( !tab )
+    {
+        if ( col->merge_method!=MM_SUM && col->merge_method!=MM_AVG &&
+             col->merge_method!=MM_MIN && col->merge_method!=MM_MAX &&
+             col->merge_method!=MM_APPEND &&
+             col->merge_method!=MM_APPEND_MISSING )
+            error("Error: at the moment only the sum,avg,min,max,append,append-missing options are supported with --merge-logic for INFO type=Float\n");
+    }
+
+    int i,ntmpf = 0;
+    if ( (col->replace & SET_OR_APPEND) && !col->mm_dbl_nused )
+    {
+        ntmpf = bcf_get_info_float(args->hdr, line, col->hdr_key_dst, &args->tmpf, &args->mtmpf);
+        if ( ntmpf>0 && (!bcf_float_is_missing(args->tmpf[0]) || (col->replace & CARRY_OVER_MISSING)) )
+        {
+            col->mm_dbl_nused = ntmpf;
+            hts_expand(double,col->mm_dbl_nused,col->mm_dbl_nalloc,col->mm_dbl);
+            for (i=0; i<ntmpf; i++)
+                if ( bcf_float_is_missing(args->tmpf[i]) )
+                    bcf_double_set_missing(col->mm_dbl[i]);
+                else
+                    col->mm_dbl[i] = args->tmpf[i];
+            col->mm_dbl_ndat = 1;
+        }
+        ntmpf = 0;
+    }
+    if ( tab )  // data row, not just flushing
+    {
+        char *str = tab->cols[col->icol], *end = str;
+        if ( str[0]=='.' && str[1]==0 && col->merge_method!=MM_APPEND_MISSING && !(col->replace & CARRY_OVER_MISSING) ) return 1;
+
+        while ( *end )
+        {
+            ntmpf++;
+            hts_expand(float,ntmpf,args->mtmpf,args->tmpf);
+            if ( str[0]=='.' && (str[1]==0 || str[1]==',') )
+            {
+                if ( col->merge_method==MM_APPEND_MISSING || (col->replace & CARRY_OVER_MISSING) )
+                    bcf_float_set_missing(args->tmpf[ntmpf-1]);
+                else
+                    ntmpf--;
+                if ( str[1]==0 ) end = str+1;
+                str += 2;
+            }
+            else
+            {
+                args->tmpf[ntmpf-1] = strtod(str, &end);
+                if ( end==str )
+                    error("Could not parse %s at %s:%"PRId64" .. [%s]\n", col->hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) line->pos+1,tab->cols[col->icol]);
+                str = end+1;
+            }
+        }
+        if ( col->merge_method!=MM_FIRST )
+        {
+            if ( !col->mm_dbl_nused )
+            {
+                col->mm_dbl_nused = ntmpf;
+                hts_expand(double,col->mm_dbl_nused,col->mm_dbl_nalloc,col->mm_dbl);
+                for (i=0; i<ntmpf; i++)
+                {
+                    if ( bcf_float_is_missing(args->tmpf[i]) )
+                        bcf_double_set_missing(col->mm_dbl[i]);
+                    else
+                        col->mm_dbl[i] = args->tmpf[i];
+                }
+            }
+            else
+            {
+                if ( col->merge_method==MM_APPEND || col->merge_method==MM_APPEND_MISSING )
+                {
+                    int nori = col->mm_dbl_nused;
+                    col->mm_dbl_nused += ntmpf;
+                    hts_expand(double,col->mm_dbl_nused,col->mm_dbl_nalloc,col->mm_dbl);
+                    for (i=0; i<ntmpf; i++)
+                    {
+                        if ( bcf_float_is_missing(args->tmpf[i]) )
+                            bcf_double_set_missing(col->mm_dbl[i+nori]);
+                        else
+                            col->mm_dbl[i+nori] = args->tmpf[i];
+                    }
+                }
+                else
+                {
+                    if ( ntmpf!=col->mm_dbl_nused ) error("Error: cannot merge fields of unequal length\n");
+                    if ( col->merge_method==MM_SUM || col->merge_method==MM_AVG )
+                        for (i=0; i<ntmpf; i++) col->mm_dbl[i] += args->tmpf[i];
+                    else if ( col->merge_method==MM_MIN )
+                        for (i=0; i<ntmpf; i++) { if ( col->mm_dbl[i] > args->tmpf[i] ) col->mm_dbl[i] = args->tmpf[i]; }
+                    else if ( col->merge_method==MM_MAX )
+                        for (i=0; i<ntmpf; i++) { if ( col->mm_dbl[i] < args->tmpf[i] ) col->mm_dbl[i] = args->tmpf[i]; }
+                }
+            }
+            col->mm_dbl_ndat++;
+            return 1;
+        }
+    }
+    else if ( col->merge_method==MM_SUM || col->merge_method==MM_MIN || col->merge_method==MM_MAX || col->merge_method==MM_APPEND || col->merge_method==MM_APPEND_MISSING )
+    {
+        ntmpf = col->mm_dbl_nused;
+        hts_expand(int32_t,ntmpf,args->mtmpf,args->tmpf);
+        for (i=0; i<ntmpf; i++)
+        {
+            if ( bcf_double_is_missing(col->mm_dbl[i]) )
+                bcf_float_set_missing(args->tmpf[i]);
+            else
+                args->tmpf[i] = col->mm_dbl[i];
+        }
+        col->mm_dbl_nused = col->mm_dbl_ndat = 0;
+    }
+    else if ( col->merge_method==MM_AVG )
+    {
+        ntmpf = col->mm_dbl_nused;
+        hts_expand(int32_t,ntmpf,args->mtmpf,args->tmpf);
+        for (i=0; i<ntmpf; i++) args->tmpf[i] = col->mm_dbl[i]/col->mm_dbl_ndat;
+        col->mm_dbl_nused = col->mm_dbl_ndat = 0;
+    }
+
+    if ( col->number==BCF_VL_A || col->number==BCF_VL_R )
+        return setter_ARinfo_real(args,line,col,tab->nals,tab->als,ntmpf);
+
+    if ( col->replace & REPLACE_MISSING )
+    {
+        int ret = bcf_get_info_float(args->hdr, line, col->hdr_key_dst, &args->tmpf2, &args->mtmpf2);
+        if ( ret>0 && !bcf_float_is_missing(args->tmpf2[0]) ) return 0;
+    }
+
+    return bcf_update_info_float(args->hdr_out,line,col->hdr_key_dst,args->tmpf,ntmpf);
+}
+static int vcf_setter_info_real(args_t *args, bcf1_t *line, annot_col_t *col, void *data)
+{
+    bcf1_t *rec = (bcf1_t*) data;
+    int ntmpf = bcf_get_info_float(args->files->readers[1].header,rec,col->hdr_key_src,&args->tmpf,&args->mtmpf);
+    if ( ntmpf < 0 ) return 0;    // nothing to add
+
+    if ( col->number==BCF_VL_A || col->number==BCF_VL_R )
+        return setter_ARinfo_real(args,line,col,rec->n_allele,rec->d.allele,ntmpf);
+
+    if ( col->replace & REPLACE_MISSING )
+    {
+        int ret = bcf_get_info_float(args->hdr, line, col->hdr_key_dst, &args->tmpf2, &args->mtmpf2);
+        if ( ret>0 && !bcf_float_is_missing(args->tmpf2[0]) ) return 0;
+    }
+
+    return bcf_update_info_float(args->hdr_out,line,col->hdr_key_dst,args->tmpf,ntmpf);
+}
+int copy_string_field(char *src, int isrc, int src_len, kstring_t *dst, int idst); // see vcfmerge.c
+static int setter_ARinfo_string(args_t *args, bcf1_t *line, annot_col_t *col, int nals, char **als)
+{
+    assert( col->merge_method==MM_FIRST );
+
+    int nsrc = 1, lsrc = 0;
+    while ( args->tmps[lsrc] )
+    {
+        if ( args->tmps[lsrc]==',' ) nsrc++;
+        lsrc++;
+    }
+    if ( col->number==BCF_VL_A && nsrc!=nals-1 && (nsrc!=1 || args->tmps[0]!='.' || args->tmps[1]!=0 ) )
+        error("Incorrect number of values (%d) for the %s tag at %s:%"PRId64"\n", nsrc,col->hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) line->pos+1);
+    else if ( col->number==BCF_VL_R && nsrc!=nals && (nsrc!=1 || args->tmps[0]!='.' || args->tmps[1]!=0 ) )
+        error("Incorrect number of values (%d) for the %s tag at %s:%"PRId64"\n", nsrc,col->hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) line->pos+1);
+
+    int ndst = col->number==BCF_VL_A ? line->n_allele - 1 : line->n_allele;
+    int *map = vcmp_map_ARvalues(args->vcmp,ndst,nals,als,line->n_allele,line->d.allele);
+    if ( !map ) error("REF alleles not compatible at %s:%"PRId64"\n", bcf_seqname(args->hdr,line),(int64_t) line->pos+1);
+
+    // fill in any missing values in the target VCF (or all, if not present)
+    int i, empty = 0, nstr, mstr = args->tmpks.m;
+    nstr = bcf_get_info_string(args->hdr, line, col->hdr_key_dst, &args->tmpks.s, &mstr);
+    args->tmpks.m = mstr;
+    if ( nstr<0 || (nstr==1 && args->tmpks.s[0]=='.' && args->tmpks.s[1]==0) )
+    {
+        empty = 0;
+        args->tmpks.l = 0;
+        kputc('.',&args->tmpks);
+        for (i=1; i<ndst; i++) kputs(",.",&args->tmpks);
+    }
+    else args->tmpks.l = nstr;
+    for (i=0; i<ndst; i++)
+    {
+        if ( map[i]<0 )
+        {
+            if ( empty ) copy_string_field(".",0,1,&args->tmpks,i);
+            continue;
+        }
+        if ( col->replace & REPLACE_MISSING )
+        {
+            // Do not replace filled values. The field must be looked up again because
+            // of realloc in copy_string_field
+            int n = 0;
+            char *str = args->tmpks.s;
+            while ( *str && n<i )
+            {
+                if ( *str==',' ) n++;
+                str++;
+            }
+            if ( str[0]!='.' || (str[1]!=',' && str[1]!=0) ) continue;  // value already set
+        }
+        int ret = copy_string_field(args->tmps,map[i],lsrc,&args->tmpks,i);
+        if ( ret!=0 ) error("[%s:%d %s] Failed to copy a string field\n",  __FILE__,__LINE__,__func__);
+    }
+    return bcf_update_info_string(args->hdr_out,line,col->hdr_key_dst,args->tmpks.s);
+}
+void khash_str2int_clear_free(void *_hash)
+{
+    khash_t(str2int) *hash = (khash_t(str2int)*)_hash;
+    khint_t k;
+    if (hash == 0) return;
+    for (k = 0; k < kh_end(hash); ++k)
+        if (kh_exist(hash, k)) free((char*)kh_key(hash, k));
+    kh_clear(str2int, hash);
+}
+static int setter_info_str(args_t *args, bcf1_t *line, annot_col_t *col, void *data)
+{
+    if ( (col->replace & REPLACE_MISSING) && col->number!=BCF_VL_A && col->number!=BCF_VL_R )
+    {
+        int ret = bcf_get_info_string(args->hdr, line, col->hdr_key_dst, &args->tmps2, &args->mtmps2);
+        if ( ret>0 && (args->tmps2[0]!='.' || args->tmps2[1]!=0) ) return 0;
+    }
+
+    // This is a bit hacky, only to reuse existing code with minimal changes:
+    //      -c =TAG will now behave as -l TAG:unique for strings
+    if ( col->replace & SET_OR_APPEND ) col->merge_method=MM_UNIQUE;
+
+    annot_line_t *tab = (annot_line_t*) data;
+
+    int len = 0;
+    if ( tab )
+    {
+        len = strlen(tab->cols[col->icol]);
+        if ( !len ) return 0;
+        if ( len==1 && tab->cols[col->icol][0]=='.' && col->merge_method!=MM_APPEND_MISSING && !(col->replace & CARRY_OVER_MISSING) ) return 1;
+    }
+
+    if ( col->merge_method!=MM_FIRST )
+    {
+        if ( col->number==BCF_VL_A || col->number==BCF_VL_R )
+            error("Error: the --merge-logic option cannot be used with INFO tags Type=String,Number={A,R,G}\n");
+
+        if ( data )
+        {
+            assert( col->merge_method==MM_APPEND || col->merge_method==MM_APPEND_MISSING || col->merge_method==MM_UNIQUE );
+            if ( col->merge_method==MM_UNIQUE )
+            {
+                if ( !col->mm_str_hash ) col->mm_str_hash = (khash_t(str2int)*)khash_str2int_init();
+                if ( khash_str2int_has_key(col->mm_str_hash, tab->cols[col->icol]) ) return 1;
+                khash_str2int_inc(col->mm_str_hash, strdup(tab->cols[col->icol]));
+            }
+
+            if ( (col->replace & SET_OR_APPEND) && !col->mm_kstr.l )
+            {
+                int m = col->mm_kstr.m;
+                int n = bcf_get_info_string(args->hdr, line, col->hdr_key_dst, &col->mm_kstr.s, &m);
+                col->mm_kstr.m = m;
+                if ( n>0 && ((col->replace & CARRY_OVER_MISSING) || col->mm_kstr.s[0]!='.' || col->mm_kstr.s[1]) ) col->mm_kstr.l = n;
+            }
+
+            if ( col->mm_kstr.l ) kputc(',',&col->mm_kstr);
+            kputs(tab->cols[col->icol], &col->mm_kstr);
+            return 1;
+        }
+
+        if ( col->mm_kstr.l )
+        {
+            hts_expand(char,col->mm_kstr.l+1,args->mtmps,args->tmps);
+            memcpy(args->tmps,col->mm_kstr.s,col->mm_kstr.l+1);
+        }
+        else
+            return 0;
+
+        // flush the line
+        if ( col->merge_method==MM_UNIQUE )
+            khash_str2int_clear_free(col->mm_str_hash);
+        col->mm_kstr.l = 0;
+    }
+    else
+    {
+        assert(tab);
+        hts_expand(char,len+1,args->mtmps,args->tmps);
+        memcpy(args->tmps,tab->cols[col->icol],len+1);
+
+        if ( col->number==BCF_VL_A || col->number==BCF_VL_R )
+            return setter_ARinfo_string(args,line,col,tab->nals,tab->als);
+    }
+
+    return bcf_update_info_string(args->hdr_out,line,col->hdr_key_dst,args->tmps);
+}
+static int vcf_setter_info_str(args_t *args, bcf1_t *line, annot_col_t *col, void *data)
+{
+    bcf1_t *rec = (bcf1_t*) data;
+
+    if ( col->getter )
+        col->getter(args,rec,col,(void**)&args->tmps, &args->mtmps);
+    else
+    {
+        int ntmps = bcf_get_info_string(args->files->readers[1].header,rec,col->hdr_key_src,&args->tmps,&args->mtmps);
+        if ( ntmps < 0 ) return 0;    // nothing to add
+    }
+
+    if ( col->number==BCF_VL_A || col->number==BCF_VL_R )
+        return setter_ARinfo_string(args,line,col,rec->n_allele,rec->d.allele);
+
+    if ( col->replace & REPLACE_MISSING )
+    {
+        int ret = bcf_get_info_string(args->hdr, line, col->hdr_key_dst, &args->tmps2, &args->mtmps2);
+        if ( ret>0 && (args->tmps2[0]!='.' || args->tmps2[1]!=0) ) return 0;
+    }
+
+    return bcf_update_info_string(args->hdr_out,line,col->hdr_key_dst,args->tmps);
+}
+static int genotypes_to_string(args_t *args, int nsrc1, int32_t *src, int nsmpl_dst, kstring_t *str)
+{
+    int i, isrc, idst;
+    int blen = nsrc1 > 1 ? nsrc1 + 1 : 1;   // typically the genotypes take three bytes 0/1, no 0-termination is needed
+
+gt_length_too_big:
+    str->l = 0;
+    for (idst=0; idst<nsmpl_dst; idst++)
+    {
+        isrc = args->sample_map ? args->sample_map[idst] : idst;
+        if ( isrc==-1 )
+        {
+            kputc_('.', str);
+            for (i=1; i < blen; i++) kputc_(0, str);
+            continue;
+        }
+
+        size_t plen = str->l;
+        int32_t *ptr = src + isrc*nsrc1;
+        for (i=0; i<nsrc1 && ptr[i]!=bcf_int32_vector_end; i++)
+        {
+            if ( i ) kputc("/|"[bcf_gt_is_phased(ptr[i])], str);
+            if ( bcf_gt_is_missing(ptr[i]) ) kputc('.', str);
+            else kputw(bcf_gt_allele(ptr[i]), str);
+        }
+        if ( i==0 ) kputc('.', str);
+        if ( str->l - plen > blen )
+        {
+            // too many alternate alleles or ploidy is too large, the genotype does not fit
+            // three characters ("0/0" vs "10/10").
+            blen *= 2;
+            goto gt_length_too_big;
+        }
+        plen = str->l - plen;
+        while ( plen < blen )
+        {
+            kputc_(0, str);
+            plen++;
+        }
+    }
+    return 0;
+}
+static int vcf_setter_format_gt(args_t *args, bcf1_t *line, annot_col_t *col, void *data)
+{
+    bcf1_t *rec = (bcf1_t*) data;
+    int nsrc = bcf_get_genotypes(args->files->readers[1].header,rec,&args->tmpi,&args->mtmpi);
+    if ( nsrc==-3 ) return 0;    // the tag is not present
+    if ( nsrc<=0 ) return 1;     // error
+
+    // Genotypes are internally represented as integers. This is a complication when
+    // adding as a different Type=String field, such as FMT/newGT:=GT
+    if ( strcmp(col->hdr_key_src,col->hdr_key_dst) )
+    {
+        int nsmpl_dst = bcf_hdr_nsamples(args->hdr_out);
+        int nsmpl_src = bcf_hdr_nsamples(args->files->readers[1].header);
+        genotypes_to_string(args,nsrc/nsmpl_src,args->tmpi,nsmpl_dst,&args->tmpks);
+        return bcf_update_format_char(args->hdr_out,line,col->hdr_key_dst,args->tmpks.s,args->tmpks.l);
+    }
+
+    if ( !args->sample_map )
+        return bcf_update_genotypes(args->hdr_out,line,args->tmpi,nsrc);
+
+    int i, j, ndst = bcf_get_genotypes(args->hdr,line,&args->tmpi2,&args->mtmpi2);
+    if ( ndst > 0 ) ndst /= bcf_hdr_nsamples(args->hdr_out);
+    nsrc /= bcf_hdr_nsamples(args->files->readers[1].header);
+    if ( ndst<=0 )  // field not present in dst file
+    {
+        if ( col->replace & REPLACE_NON_MISSING ) return 0;
+        hts_expand(int32_t, nsrc*bcf_hdr_nsamples(args->hdr_out), args->mtmpi2, args->tmpi2);
+        for (i=0; i<bcf_hdr_nsamples(args->hdr_out); i++)
+        {
+            int32_t *dst = args->tmpi2 + nsrc*i;
+            if ( args->sample_map[i]==-1 )
+            {
+                dst[0] = bcf_gt_missing;
+                for (j=1; j<nsrc; j++) dst[j] = bcf_int32_vector_end;
+            }
+            else
+            {
+                int32_t *src = args->tmpi + nsrc*args->sample_map[i];
+                for (j=0; j<nsrc; j++) dst[j] = src[j];
+            }
+        }
+        return bcf_update_genotypes(args->hdr_out,line,args->tmpi2,nsrc*bcf_hdr_nsamples(args->hdr_out));
+    }
+    else if ( ndst >= nsrc )
+    {
+        for (i=0; i<bcf_hdr_nsamples(args->hdr_out); i++)
+        {
+            if ( args->sample_map[i]==-1 ) continue;
+            int32_t *src = args->tmpi  + nsrc*args->sample_map[i];
+            int32_t *dst = args->tmpi2 + ndst*i;
+            if ( (col->replace & REPLACE_NON_MISSING) && bcf_gt_is_missing(dst[0]) ) continue;
+            if ( (col->replace & REPLACE_MISSING)  && !bcf_gt_is_missing(dst[0]) ) continue;
+            for (j=0; j<nsrc; j++) dst[j] = src[j];
+            for (; j<ndst; j++) dst[j] = bcf_int32_vector_end;
+        }
+        return bcf_update_genotypes(args->hdr_out,line,args->tmpi2,ndst*bcf_hdr_nsamples(args->hdr_out));
+    }
+    else    // ndst < nsrc
+    {
+        hts_expand(int32_t, nsrc*bcf_hdr_nsamples(args->hdr_out), args->mtmpi3, args->tmpi3);
+        for (i=0; i<bcf_hdr_nsamples(args->hdr_out); i++)
+        {
+            int32_t *ori = args->tmpi2 + ndst*i;
+            int32_t *dst = args->tmpi3 + nsrc*i;
+            int keep_ori = 0;
+            if ( args->sample_map[i]==-1 ) keep_ori = 1;
+            else if ( (col->replace & REPLACE_NON_MISSING) && bcf_gt_is_missing(ori[0]) ) keep_ori = 1;
+            else if ( (col->replace & REPLACE_MISSING)  && !bcf_gt_is_missing(ori[0]) ) keep_ori = 1;
+            if ( keep_ori )
+            {
+                for (j=0; j<ndst; j++) dst[j] = ori[j];
+                for (; j<nsrc; j++) dst[j] = bcf_int32_vector_end;
+            }
+            else
+            {
+                int32_t *src = args->tmpi + nsrc*args->sample_map[i];
+                for (j=0; j<nsrc; j++) dst[j] = src[j];
+            }
+        }
+        return bcf_update_genotypes(args->hdr_out,line,args->tmpi3,nsrc*bcf_hdr_nsamples(args->hdr_out));
+    }
+}
+static int count_vals(annot_line_t *tab, int icol_beg, int icol_end)
+{
+    int i, nmax = 1;
+    for (i=icol_beg; i<icol_end; i++)
+    {
+        char *str = tab->cols[i], *end = str;
+        if ( str[0]=='.' && !str[1] )
+        {
+            // missing value
+            if ( !nmax ) nmax = 1;
+            continue;
+        }
+        int n = 1;
+        while ( *end )
+        {
+            if ( *end==',' ) n++;
+            end++;
+        }
+        if ( nmax<n ) nmax = n;
+    }
+    return nmax;
+}
+static int core_setter_format_int(args_t *args, bcf1_t *line, annot_col_t *col, int32_t *vals, int nvals)
+{
+    if ( !args->sample_map )
+        return bcf_update_format_int32(args->hdr_out,line,col->hdr_key_dst,vals,nvals*args->nsmpl_annot);
+
+    int i, j, ndst = bcf_get_format_int32(args->hdr,line,col->hdr_key_dst,&args->tmpi2,&args->mtmpi2);
+    if ( ndst > 0 ) ndst /= bcf_hdr_nsamples(args->hdr_out);
+    if ( ndst<=0 )
+    {
+        if ( col->replace & REPLACE_NON_MISSING ) return 0;    // overwrite only if present
+        hts_expand(int32_t, nvals*bcf_hdr_nsamples(args->hdr_out), args->mtmpi2, args->tmpi2);
+        for (i=0; i<bcf_hdr_nsamples(args->hdr_out); i++)
+        {
+            int32_t *dst = args->tmpi2 + nvals*i;
+            if ( args->sample_map[i]==-1 )
+            {
+                dst[0] = bcf_int32_missing;
+                for (j=1; j<nvals; j++) dst[j] = bcf_int32_vector_end;
+            }
+            else
+            {
+                int32_t *src = vals + nvals*args->sample_map[i];
+                for (j=0; j<nvals; j++) dst[j] = src[j];
+            }
+        }
+        return bcf_update_format_int32(args->hdr_out,line,col->hdr_key_dst,args->tmpi2,nvals*bcf_hdr_nsamples(args->hdr_out));
+    }
+    else if ( ndst >= nvals )
+    {
+        for (i=0; i<bcf_hdr_nsamples(args->hdr_out); i++)
+        {
+            if ( args->sample_map[i]==-1 ) continue;
+            int32_t *src = vals  + nvals*args->sample_map[i];
+            int32_t *dst = args->tmpi2 + ndst*i;
+            // possible cases:
+            //      in annot out
+            //       x  y     x     TAG,-TAG,=TAG    .. REPLACE_ALL, REPLACE_NON_MISSING, SET_OR_APPEND
+            //       x  y     y    +TAG              .. REPLACE_MISSING
+            //       .  y     .    =TAG              .. SET_OR_APPEND
+            //       .  y     y     TAG,+TAG,-TAG    .. REPLACE_ALL, REPLACE_MISSING, REPLACE_NON_MISSING
+            //       x  .     x     TAG,+TAG         .. REPLACE_ALL, REPLACE_MISSING
+            //       x  .     .    -TAG              .. REPLACE_NON_MISSING
+            if ( col->replace & REPLACE_NON_MISSING ) { if ( dst[0]==bcf_int32_missing ) continue; }
+            else if ( col->replace & REPLACE_MISSING ) { if ( dst[0]!=bcf_int32_missing ) continue; }
+            else if ( col->replace & REPLACE_ALL ) { if ( src[0]==bcf_int32_missing ) continue; }
+            for (j=0; j<nvals; j++) dst[j] = src[j];
+            for (; j<ndst; j++) dst[j] = bcf_int32_vector_end;
+        }
+        return bcf_update_format_int32(args->hdr_out,line,col->hdr_key_dst,args->tmpi2,ndst*bcf_hdr_nsamples(args->hdr_out));
+    }
+    else    // ndst < nvals
+    {
+        hts_expand(int32_t, nvals*bcf_hdr_nsamples(args->hdr_out), args->mtmpi3, args->tmpi3);
+        for (i=0; i<bcf_hdr_nsamples(args->hdr_out); i++)
+        {
+            int32_t *ann = vals + nvals*args->sample_map[i];
+            int32_t *ori = args->tmpi2 + ndst*i;                // ori vcf line
+            int32_t *dst = args->tmpi3 + nvals*i;               // expanded buffer
+            int use_new_ann = 1;
+            if ( args->sample_map[i]==-1 ) use_new_ann = 0;
+            else if ( col->replace & REPLACE_NON_MISSING ) { if ( ori[0]==bcf_int32_missing ) use_new_ann = 0; }
+            else if ( col->replace & REPLACE_MISSING ) { if ( ori[0]!=bcf_int32_missing ) use_new_ann = 0; }
+            else if ( col->replace & REPLACE_ALL ) { if ( ann[0]==bcf_int32_missing ) use_new_ann = 0; }
+            if ( !use_new_ann )
+            {
+                for (j=0; j<ndst; j++) dst[j] = ori[j];
+                for (; j<nvals; j++) dst[j] = bcf_int32_vector_end;
+            }
+            else
+                for (j=0; j<nvals; j++) dst[j] = ann[j];
+        }
+        return bcf_update_format_int32(args->hdr_out,line,col->hdr_key_dst,args->tmpi3,nvals*bcf_hdr_nsamples(args->hdr_out));
+    }
+}
+static int core_setter_format_real(args_t *args, bcf1_t *line, annot_col_t *col, float *vals, int nvals)
+{
+    if ( !args->sample_map )
+        return bcf_update_format_float(args->hdr_out,line,col->hdr_key_dst,vals,nvals*args->nsmpl_annot);
+
+    int i, j, ndst = bcf_get_format_float(args->hdr,line,col->hdr_key_dst,&args->tmpf2,&args->mtmpf2);
+    if ( ndst > 0 ) ndst /= bcf_hdr_nsamples(args->hdr_out);
+    if ( ndst<=0 )
+    {
+        if ( col->replace & REPLACE_NON_MISSING ) return 0;    // overwrite only if present
+        hts_expand(float, nvals*bcf_hdr_nsamples(args->hdr_out), args->mtmpf2, args->tmpf2);
+        for (i=0; i<bcf_hdr_nsamples(args->hdr_out); i++)
+        {
+            float *dst = args->tmpf2 + nvals*i;
+            if ( args->sample_map[i]==-1 )
+            {
+                bcf_float_set_missing(dst[0]);
+                for (j=1; j<nvals; j++) bcf_float_set_vector_end(dst[j]);
+            }
+            else
+            {
+                float *src = vals + nvals*args->sample_map[i];
+                for (j=0; j<nvals; j++) dst[j] = src[j];
+            }
+        }
+        return bcf_update_format_float(args->hdr_out,line,col->hdr_key_dst,args->tmpf2,nvals*bcf_hdr_nsamples(args->hdr_out));
+    }
+    else if ( ndst >= nvals )
+    {
+        for (i=0; i<bcf_hdr_nsamples(args->hdr_out); i++)
+        {
+            if ( args->sample_map[i]==-1 ) continue;
+            float *src = vals  + nvals*args->sample_map[i];
+            float *dst = args->tmpf2 + ndst*i;
+            if ( col->replace & REPLACE_NON_MISSING ) { if ( bcf_float_is_missing(dst[0]) ) continue; }
+            else if ( col->replace & REPLACE_MISSING ) { if ( !bcf_float_is_missing(dst[0]) ) continue; }
+            else if ( col->replace & REPLACE_ALL ) { if ( bcf_float_is_missing(src[0]) ) continue; }
+            for (j=0; j<nvals; j++) dst[j] = src[j];
+            for (; j<ndst; j++) bcf_float_set_vector_end(dst[j]);
+        }
+        return bcf_update_format_float(args->hdr_out,line,col->hdr_key_dst,args->tmpf2,ndst*bcf_hdr_nsamples(args->hdr_out));
+    }
+    else    // ndst < nvals
+    {
+        hts_expand(float, nvals*bcf_hdr_nsamples(args->hdr_out), args->mtmpf3, args->tmpf3);
+        for (i=0; i<bcf_hdr_nsamples(args->hdr_out); i++)
+        {
+            float *ann = vals + nvals*args->sample_map[i];
+            float *ori = args->tmpf2 + ndst*i;                // ori vcf line
+            float *dst = args->tmpf3 + nvals*i;               // expanded buffer
+            int use_new_ann = 1;
+            if ( args->sample_map[i]==-1 ) use_new_ann = 0;
+            else if ( col->replace & REPLACE_NON_MISSING ) { if ( bcf_float_is_missing(ori[0]) ) use_new_ann = 0; }
+            else if ( col->replace & REPLACE_MISSING ) { if ( !bcf_float_is_missing(ori[0]) ) use_new_ann = 0; }
+            else if ( col->replace & REPLACE_ALL ) { if ( bcf_float_is_missing(ann[0]) ) use_new_ann = 0; }
+            if ( !use_new_ann )
+            {
+                for (j=0; j<ndst; j++) dst[j] = ori[j];
+                for (; j<nvals; j++) bcf_float_set_vector_end(dst[j]);
+            }
+            else
+                for (j=0; j<nvals; j++) dst[j] = ann[j];
+        }
+        return bcf_update_format_float(args->hdr_out,line,col->hdr_key_dst,args->tmpf3,nvals*bcf_hdr_nsamples(args->hdr_out));
+    }
+}
+static int core_setter_format_str(args_t *args, bcf1_t *line, annot_col_t *col, char **vals)
+{
+    if ( !args->sample_map )
+        return bcf_update_format_string(args->hdr_out,line,col->hdr_key_dst,(const char**)vals,args->nsmpl_annot);
+
+    int i;
+    args->tmpp2[0] = args->tmps2;
+    int ret = bcf_get_format_string(args->hdr,line,col->hdr_key_dst,&args->tmpp2,&args->mtmps2);
+    args->tmps2 = args->tmpp2[0];   // tmps2 might be realloced
+
+    int nsmpl = bcf_hdr_nsamples(args->hdr_out);
+    if ( ret<=0 )   // not present in dst
+    {
+        hts_expand(char,bcf_hdr_nsamples(args->hdr_out)*2,args->mtmps2,args->tmps2);
+        char *tmp = args->tmps2;
+        for (i=0; i<nsmpl; i++)
+        {
+            tmp[0] = '.';
+            tmp[1] = 0;
+            args->tmpp2[i] = tmp;
+            tmp += 2;
+        }
+    }
+    for (i=0; i<nsmpl; i++)
+    {
+        if ( args->sample_map[i]==-1 ) continue;
+        char **src = vals + args->sample_map[i];
+        char **dst = args->tmpp2 + i;
+
+        if ( col->replace & REPLACE_NON_MISSING ) { if ( (*dst)[0]=='.' && (*dst)[1]==0 ) continue; }
+        else if ( col->replace & REPLACE_MISSING ) { if ( (*dst)[0]!='.' || (*dst)[1]!=0 ) continue; }
+        else if ( col->replace & REPLACE_ALL ) { if ( (*src)[0]=='.' && (*src)[1]==0 ) continue; }
+        *dst = *src;
+    }
+    return bcf_update_format_string(args->hdr_out,line,col->hdr_key_dst,(const char**)args->tmpp2,nsmpl);
+}
+static int setter_format_int(args_t *args, bcf1_t *line, annot_col_t *col, void *data)
+{
+    if ( !data ) error("Error: the --merge-logic option cannot be used with FORMAT tags (yet?)\n");
+
+    annot_line_t *tab = (annot_line_t*) data;
+    if ( col->icol+args->nsmpl_annot > tab->ncols )
+        error("Incorrect number of values for %s at %s:%"PRId64"\n",col->hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) line->pos+1);
+    int nvals = count_vals(tab,col->icol,col->icol+args->nsmpl_annot);
+    hts_expand(int32_t,nvals*args->nsmpl_annot,args->mtmpi,args->tmpi);
+
+    int icol = col->icol, ismpl;
+    for (ismpl=0; ismpl<args->nsmpl_annot; ismpl++)
+    {
+        int32_t *ptr = args->tmpi + ismpl*nvals;
+        int ival = 0;
+
+        char *str = tab->cols[icol];
+        while ( *str )
+        {
+            if ( str[0]=='.' && (!str[1] || str[1]==',') )  // missing value
+            {
+                ptr[ival++] = bcf_int32_missing;
+                str += str[1] ? 2 : 1;
+                continue;
+            }
+
+            char *end = str;
+            ptr[ival] = strtol(str, &end, 10);
+            if ( end==str )
+                error("Could not parse %s at %s:%"PRId64" .. [%s]\n", col->hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) line->pos+1,tab->cols[col->icol]);
+
+            ival++;
+            str = *end ? end+1 : end;
+        }
+        while ( ival<nvals ) ptr[ival++] = bcf_int32_vector_end;
+        icol++;
+    }
+    return core_setter_format_int(args,line,col,args->tmpi,nvals);
+}
+static int setter_format_real(args_t *args, bcf1_t *line, annot_col_t *col, void *data)
+{
+    if ( !data ) error("Error: the --merge-logic option cannot be used with FORMAT tags (yet?)\n");
+
+    annot_line_t *tab = (annot_line_t*) data;
+    if ( col->icol+args->nsmpl_annot > tab->ncols )
+        error("Incorrect number of values for %s at %s:%"PRId64"\n",col->hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) line->pos+1);
+    int nvals = count_vals(tab,col->icol,col->icol+args->nsmpl_annot);
+    hts_expand(float,nvals*args->nsmpl_annot,args->mtmpf,args->tmpf);
+
+    int icol = col->icol, ismpl;
+    for (ismpl=0; ismpl<args->nsmpl_annot; ismpl++)
+    {
+        float *ptr = args->tmpf + ismpl*nvals;
+        int ival = 0;
+
+        char *str = tab->cols[icol];
+        while ( *str )
+        {
+            if ( str[0]=='.' && (!str[1] || str[1]==',') )  // missing value
+            {
+                bcf_float_set_missing(ptr[ival]);
+                ival++;
+                str += str[1] ? 2 : 1;
+                continue;
+            }
+
+            char *end = str;
+            ptr[ival] = strtod(str, &end);
+            if ( end==str )
+                error("Could not parse %s at %s:%"PRId64" .. [%s]\n", col->hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) line->pos+1,tab->cols[col->icol]);
+
+            ival++;
+            str = *end ? end+1 : end;
+        }
+        while ( ival<nvals ) { bcf_float_set_vector_end(ptr[ival]); ival++; }
+        icol++;
+    }
+    return core_setter_format_real(args,line,col,args->tmpf,nvals);
+}
+static int setter_format_str(args_t *args, bcf1_t *line, annot_col_t *col, void *data)
+{
+    if ( !data ) error("Error: the --merge-logic option cannot be used with FORMAT tags (yet?)\n");
+
+    annot_line_t *tab = (annot_line_t*) data;
+    if ( col->icol+args->nsmpl_annot > tab->ncols )
+        error("Incorrect number of values for %s at %s:%"PRId64"\n",col->hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) line->pos+1);
+
+    int ismpl;
+    for (ismpl=0; ismpl<args->nsmpl_annot; ismpl++)
+        args->tmpp[ismpl] = tab->cols[col->icol + ismpl];
+
+    return core_setter_format_str(args,line,col,args->tmpp);
+}
+static int determine_ploidy(int nals, int *vals, int nvals1, uint8_t *smpl, int nsmpl)
+{
+    int i, j, ndip = nals*(nals+1)/2, max_ploidy = 0;
+    for (i=0; i<nsmpl; i++)
+    {
+        int *ptr = vals + i*nvals1;
+        int has_value = 0;
+        for (j=0; j<nvals1; j++)
+        {
+            if ( ptr[j]==bcf_int32_vector_end ) break;
+            if ( ptr[j]!=bcf_int32_missing ) has_value = 1;
+        }
+        if ( has_value )
+        {
+            if ( j==ndip )
+            {
+                smpl[i] = 2;
+                max_ploidy = 2;
+            }
+            else if ( j==nals )
+            {
+                smpl[i] = 1;
+                if ( !max_ploidy ) max_ploidy = 1;
+            }
+            else return -j;
+        }
+        else smpl[i] = 0;
+    }
+    return max_ploidy;
+}
+static int vcf_setter_format_int(args_t *args, bcf1_t *line, annot_col_t *col, void *data)
+{
+    bcf1_t *rec = (bcf1_t*) data;
+    int nsrc = bcf_get_format_int32(args->files->readers[1].header,rec,col->hdr_key_src,&args->tmpi,&args->mtmpi);
+    if ( nsrc==-3 ) return 0;    // the tag is not present
+    if ( nsrc<=0 ) return 1;     // error
+    int nsmpl_src = bcf_hdr_nsamples(args->files->readers[1].header);
+    int nsrc1 = nsrc / nsmpl_src;
+    if ( col->number!=BCF_VL_G && col->number!=BCF_VL_R && col->number!=BCF_VL_A )
+        return core_setter_format_int(args,line,col,args->tmpi,nsrc1);
+
+    // create mapping from src to dst genotypes, haploid and diploid version
+    int nmap_hap = col->number==BCF_VL_G || col->number==BCF_VL_R ? rec->n_allele : rec->n_allele - 1;
+    int *map_hap = vcmp_map_ARvalues(args->vcmp,nmap_hap,line->n_allele,line->d.allele,rec->n_allele,rec->d.allele);
+    if ( !map_hap ) error("REF alleles not compatible at %s:%"PRId64"\n", bcf_seqname(args->hdr,line),(int64_t) line->pos+1);
+
+    int i, j;
+    if ( rec->n_allele==line->n_allele )
+    {
+        // alleles unchanged?
+        for (i=0; i<rec->n_allele; i++) if ( map_hap[i]!=i ) break;
+        if ( i==rec->n_allele )
+            return core_setter_format_int(args,line,col,args->tmpi,nsrc1);
+    }
+
+    int nsmpl_dst = rec->n_sample;
+    int ndst  = bcf_get_format_int32(args->hdr,line,col->hdr_key_dst,&args->tmpi2,&args->mtmpi2);
+    int ndst1 = ndst / nsmpl_dst;
+    if ( ndst <= 0 )
+    {
+        if ( col->replace & REPLACE_NON_MISSING ) return 0;  // overwrite only if present
+        if ( col->number==BCF_VL_G )
+            ndst1 = line->n_allele*(line->n_allele+1)/2;
+        else
+            ndst1 = col->number==BCF_VL_A ? line->n_allele - 1 : line->n_allele;
+        hts_expand(int, ndst1*nsmpl_dst, args->mtmpi2, args->tmpi2);
+        for (i=0; i<nsmpl_dst; i++)
+        {
+            int32_t *dst = args->tmpi2 + i*ndst1;
+            for (j=0; j<ndst1; j++) dst[j] = bcf_int32_missing;
+        }
+    }
+
+    int nmap_dip = 0, *map_dip = NULL;
+    if ( col->number==BCF_VL_G )
+    {
+        map_dip = vcmp_map_dipGvalues(args->vcmp, &nmap_dip);
+        if ( !args->src_smpl_pld )
+        {
+            args->src_smpl_pld = (uint8_t*) malloc(nsmpl_src);
+            args->dst_smpl_pld = (uint8_t*) malloc(nsmpl_dst);
+        }
+        int pld_src = determine_ploidy(rec->n_allele, args->tmpi, nsrc1, args->src_smpl_pld, nsmpl_src);
+        if ( pld_src<0 )
+            error("Unexpected number of %s values (%d) for %d alleles at %s:%"PRId64"\n", col->hdr_key_src,-pld_src, rec->n_allele, bcf_seqname(bcf_sr_get_header(args->files,1),rec),(int64_t) rec->pos+1);
+        int pld_dst = determine_ploidy(line->n_allele, args->tmpi2, ndst1, args->dst_smpl_pld, nsmpl_dst);
+        if ( pld_dst<0 )
+            error("Unexpected number of %s values (%d) for %d alleles at %s:%"PRId64"\n", col->hdr_key_src,-pld_dst, line->n_allele, bcf_seqname(args->hdr,line),(int64_t) line->pos+1);
+
+        int ndst1_new = pld_dst==1 ? line->n_allele : line->n_allele*(line->n_allele+1)/2;
+        if ( ndst1_new != ndst1 )
+        {
+            if ( ndst1 ) error("todo: %s ndst1!=ndst .. %d %d  at %s:%"PRId64"\n",col->hdr_key_src,ndst1_new,ndst1,bcf_seqname(args->hdr,line),(int64_t) line->pos+1);
+            ndst1 = ndst1_new;
+            hts_expand(int32_t, ndst1*nsmpl_dst, args->mtmpi2, args->tmpi2);
+        }
+    }
+    else if ( !ndst1 )
+    {
+        ndst1 = col->number==BCF_VL_A ? line->n_allele - 1 : line->n_allele;
+        hts_expand(int32_t, ndst1*nsmpl_dst, args->mtmpi2, args->tmpi2);
+    }
+
+    for (i=0; i<nsmpl_dst; i++)
+    {
+        int ii = args->sample_map ? args->sample_map[i] : i;
+        int32_t *ptr_src = args->tmpi + i*nsrc1;
+        int32_t *ptr_dst = args->tmpi2 + ii*ndst1;
+
+        if ( col->number==BCF_VL_G )
+        {
+            if ( args->src_smpl_pld[ii] > 0 && args->dst_smpl_pld[i] > 0 && args->src_smpl_pld[ii]!=args->dst_smpl_pld[i] )
+                error("Sample ploidy differs at %s:%"PRId64"\n", bcf_seqname(args->hdr,line),(int64_t) line->pos+1);
+            if ( !args->dst_smpl_pld[i] )
+                for (j=0; j<ndst1; j++) ptr_dst[j] = bcf_int32_missing;
+        }
+        if ( col->number!=BCF_VL_G || args->src_smpl_pld[i]==1 )
+        {
+            for (j=0; j<nmap_hap; j++)
+            {
+                int k = map_hap[j];
+                if ( k>=0 ) ptr_dst[k] = ptr_src[j];
+            }
+            if ( col->number==BCF_VL_G )
+                for (j=line->n_allele; j<ndst1; j++) ptr_dst[j++] = bcf_int32_vector_end;
+        }
+        else
+        {
+            for (j=0; j<nmap_dip; j++)
+            {
+                int k = map_dip[j];
+                if ( k>=0 ) ptr_dst[k] = ptr_src[j];
+            }
+        }
+    }
+    return bcf_update_format_int32(args->hdr_out,line,col->hdr_key_dst,args->tmpi2,nsmpl_dst*ndst1);
+}
+static int vcf_setter_format_real(args_t *args, bcf1_t *line, annot_col_t *col, void *data)
+{
+    bcf1_t *rec = (bcf1_t*) data;
+    int nsrc = bcf_get_format_float(args->files->readers[1].header,rec,col->hdr_key_src,&args->tmpf,&args->mtmpf);
+    if ( nsrc==-3 ) return 0;    // the tag is not present
+    if ( nsrc<=0 ) return 1;     // error
+    int nsmpl_src = bcf_hdr_nsamples(args->files->readers[1].header);
+    int nsrc1 = nsrc / nsmpl_src;
+    if ( col->number!=BCF_VL_G && col->number!=BCF_VL_R && col->number!=BCF_VL_A )
+        return core_setter_format_real(args,line,col,args->tmpf,nsrc1);
+
+    // create mapping from src to dst genotypes, haploid and diploid version
+    int nmap_hap = col->number==BCF_VL_G || col->number==BCF_VL_R ? rec->n_allele : rec->n_allele - 1;
+    int *map_hap = vcmp_map_ARvalues(args->vcmp,nmap_hap,line->n_allele,line->d.allele,rec->n_allele,rec->d.allele);
+    if ( !map_hap ) error("REF alleles not compatible at %s:%"PRId64"\n", bcf_seqname(args->hdr,line),(int64_t) line->pos+1);
+
+    int i, j;
+    if ( rec->n_allele==line->n_allele )
+    {
+        // alleles unchanged?
+        for (i=0; i<rec->n_allele; i++) if ( map_hap[i]!=i ) break;
+        if ( i==rec->n_allele )
+            return core_setter_format_real(args,line,col,args->tmpf,nsrc1);
+    }
+
+    int nsmpl_dst = rec->n_sample;
+    int ndst  = bcf_get_format_float(args->hdr,line,col->hdr_key_dst,&args->tmpf2,&args->mtmpf2);
+    int ndst1 = ndst / nsmpl_dst;
+    if ( ndst <= 0 )
+    {
+        if ( col->replace & REPLACE_NON_MISSING ) return 0;  // overwrite only if present
+        if ( col->number==BCF_VL_G )
+            ndst1 = line->n_allele*(line->n_allele+1)/2;
+        else
+            ndst1 = col->number==BCF_VL_A ? line->n_allele - 1 : line->n_allele;
+        hts_expand(float, ndst1*nsmpl_dst, args->mtmpf2, args->tmpf2);
+        for (i=0; i<nsmpl_dst; i++)
+        {
+            float *dst = args->tmpf2 + i*ndst1;
+            for (j=0; j<ndst1; j++) bcf_float_set_missing(dst[j]);
+        }
+    }
+
+    int nmap_dip = 0, *map_dip = NULL;
+    if ( col->number==BCF_VL_G )
+    {
+        map_dip = vcmp_map_dipGvalues(args->vcmp, &nmap_dip);
+        if ( !args->src_smpl_pld )
+        {
+            args->src_smpl_pld = (uint8_t*) malloc(nsmpl_src);
+            args->dst_smpl_pld = (uint8_t*) malloc(nsmpl_dst);
+        }
+        int pld_src = determine_ploidy(rec->n_allele, args->tmpi, nsrc1, args->src_smpl_pld, nsmpl_src);
+        if ( pld_src<0 )
+            error("Unexpected number of %s values (%d) for %d alleles at %s:%"PRId64"\n", col->hdr_key_src,-pld_src, rec->n_allele, bcf_seqname(bcf_sr_get_header(args->files,1),rec),(int64_t) rec->pos+1);
+        int pld_dst = determine_ploidy(line->n_allele, args->tmpi2, ndst1, args->dst_smpl_pld, nsmpl_dst);
+        if ( pld_dst<0 )
+            error("Unexpected number of %s values (%d) for %d alleles at %s:%"PRId64"\n", col->hdr_key_src,-pld_dst, line->n_allele, bcf_seqname(args->hdr,line),(int64_t) line->pos+1);
+
+        int ndst1_new = pld_dst==1 ? line->n_allele : line->n_allele*(line->n_allele+1)/2;
+        if ( ndst1_new != ndst1 )
+        {
+            if ( ndst1 ) error("todo: %s ndst1!=ndst .. %d %d  at %s:%"PRId64"\n",col->hdr_key_src,ndst1_new,ndst1,bcf_seqname(args->hdr,line),(int64_t) line->pos+1);
+            ndst1 = ndst1_new;
+            hts_expand(float, ndst1*nsmpl_dst, args->mtmpf2, args->tmpf2);
+        }
+    }
+    else if ( !ndst1 )
+    {
+        ndst1 = col->number==BCF_VL_A ? line->n_allele - 1 : line->n_allele;
+        hts_expand(float, ndst1*nsmpl_dst, args->mtmpf2, args->tmpf2);
+    }
+
+    for (i=0; i<nsmpl_dst; i++)
+    {
+        int ii = args->sample_map ? args->sample_map[i] : i;
+        float *ptr_src = args->tmpf + i*nsrc1;
+        float *ptr_dst = args->tmpf2 + ii*ndst1;
+
+        if ( col->number==BCF_VL_G )
+        {
+            if ( args->src_smpl_pld[ii] > 0 && args->dst_smpl_pld[i] > 0 && args->src_smpl_pld[ii]!=args->dst_smpl_pld[i] )
+                error("Sample ploidy differs at %s:%"PRId64"\n", bcf_seqname(args->hdr,line),(int64_t) line->pos+1);
+            if ( !args->dst_smpl_pld[i] )
+                for (j=0; j<ndst1; j++) bcf_float_set_missing(ptr_dst[j]);
+        }
+        if ( col->number!=BCF_VL_G || args->src_smpl_pld[i]==1 )
+        {
+            for (j=0; j<nmap_hap; j++)
+            {
+                int k = map_hap[j];
+                if ( k>=0 )
+                {
+                    if ( bcf_float_is_missing(ptr_src[j]) ) bcf_float_set_missing(ptr_dst[k]);
+                    else if ( bcf_float_is_vector_end(ptr_src[j]) ) bcf_float_set_vector_end(ptr_dst[k]);
+                    else ptr_dst[k] = ptr_src[j];
+                }
+            }
+            if ( col->number==BCF_VL_G )
+                for (j=line->n_allele; j<ndst1; j++) bcf_float_set_vector_end(ptr_dst[j]);
+        }
+        else
+        {
+            for (j=0; j<nmap_dip; j++)
+            {
+                int k = map_dip[j];
+                if ( k>=0 )
+                {
+                    if ( bcf_float_is_missing(ptr_src[j]) ) bcf_float_set_missing(ptr_dst[k]);
+                    else if ( bcf_float_is_vector_end(ptr_src[j]) ) bcf_float_set_vector_end(ptr_dst[k]);
+                    else ptr_dst[k] = ptr_src[j];
+                }
+            }
+        }
+    }
+    return bcf_update_format_float(args->hdr_out,line,col->hdr_key_dst,args->tmpf2,nsmpl_dst*ndst1);
+}
+
+static int vcf_setter_format_str(args_t *args, bcf1_t *line, annot_col_t *col, void *data)
+{
+    bcf1_t *rec = (bcf1_t*) data;
+    args->tmpp[0] = args->tmps;
+    int ret = bcf_get_format_string(args->files->readers[1].header,rec,col->hdr_key_src,&args->tmpp,&args->mtmps);
+    args->tmps = args->tmpp[0]; // tmps might be realloced
+    if ( ret==-3 ) return 0;    // the tag is not present
+    if ( ret<=0 ) return 1;     // error
+    if ( strcmp("GT",col->hdr_key_dst) )
+        return core_setter_format_str(args,line,col,args->tmpp);
+
+    // Genotypes are internally represented as integers. This is a complication for FMT/GT:=oldGT
+    // First determine the maximum number of alleles per-sample ndst1
+    int nsmpl_src = bcf_hdr_nsamples(args->files->readers[1].header);
+    int nsmpl_dst = bcf_hdr_nsamples(args->hdr_out);
+    int isrc,idst, ndst1 = 0, nsrc1 = ret / nsmpl_src;
+    char *ptr = args->tmps, *ptr_end = ptr + ret;
+    while ( ptr < ptr_end )
+    {
+        char *smpl_end = ptr + nsrc1;
+        int n = 1;
+        while ( ptr < smpl_end )
+        {
+            if ( *ptr=='/' || *ptr=='|' ) n++;
+            ptr++;
+        }
+        if ( ndst1 < n ) ndst1 = n;
+    }
+    assert( ndst1 );
+
+    int ndst = ndst1*nsmpl_dst;
+    hts_expand(int32_t,ndst,args->mtmpi,args->tmpi);
+    hts_expand(char,ret+1,args->mtmps,args->tmps); args->tmps[ret] = 0; // the FORMAT string may not be 0-terminated
+    for (idst=0; idst<nsmpl_dst; idst++)
+    {
+        int i = 0, is_phased = 0;
+        int32_t *dst = args->tmpi + idst*ndst1;
+        isrc = args->sample_map ? args->sample_map[idst] : idst;
+        if ( isrc==-1 )
+        {
+            dst[0] = bcf_gt_missing;
+            for (i=1; i<ndst1; i++) dst[i] = bcf_int32_vector_end;
+            continue;
+        }
+        char *beg = args->tmps + isrc*nsrc1, *tmp;
+        char *keep_ptr = beg+nsrc1, keep = *keep_ptr; *keep_ptr = 0;
+        while ( *beg )
+        {
+            char *end = beg;
+            while ( *end && *end!='/' && *end!='|' ) end++;
+            if ( *beg=='.' && end-beg==1 ) dst[i] = bcf_gt_missing;
+            else
+            {
+                if ( *end=='|' ) is_phased = 1;
+                dst[i] = strtol(beg, &tmp, 10);
+                if ( tmp!=end )
+                    error("Could not parse the %s field at %s:%"PRId64" in %s\n", col->hdr_key_src,bcf_seqname(args->files->readers[1].header,rec),(int64_t) rec->pos+1,args->targets_fname);
+                if ( dst[i] >= line->n_allele )
+                    error("The source allele index is bigger than the number of destination alleles at %s:%"PRId64"\n", bcf_seqname(args->files->readers[1].header,rec),(int64_t) rec->pos+1);
+                dst[i] = is_phased ? bcf_gt_phased(dst[i]) : bcf_gt_unphased(dst[i]);
+            }
+            beg = *end ? end+1 : end;
+            i++;
+        }
+        *keep_ptr = keep;
+        for (; i<ndst1; i++) dst[i] = bcf_int32_vector_end;
+    }
+    return bcf_update_genotypes(args->hdr_out,line,args->tmpi,ndst);
+}
+static int init_sample_map(args_t *args, bcf_hdr_t *src, bcf_hdr_t *dst)
+{
+    int i;
+    if ( !args->sample_names )
+    {
+        args->nsmpl_annot = bcf_hdr_nsamples(dst);
+
+        // tab annotation file, expecting that all samples are present: sample map not needed
+        if ( !src ) return 0;
+
+        int nmatch = 0;
+        for (i=0; i<bcf_hdr_nsamples(src); i++)
+        {
+            int id = bcf_hdr_id2int(dst, BCF_DT_SAMPLE, src->samples[i]);
+            if ( id!=-1 ) nmatch++;
+        }
+        if ( !nmatch ) return -1;   // No matching samples found in the source and the destination file
+
+        args->nsample_map = bcf_hdr_nsamples(dst);
+        args->sample_map  = (int*) malloc(sizeof(int)*args->nsample_map);
+        for (i=0; i<args->nsample_map; i++)
+        {
+            int id = bcf_hdr_id2int(src, BCF_DT_SAMPLE, dst->samples[i]);
+            args->sample_map[i] = id;   // idst -> isrc, -1 if not present
+        }
+        return 1;
+    }
+
+    args->nsample_map = bcf_hdr_nsamples(dst);
+    args->sample_map  = (int*) malloc(sizeof(int)*args->nsample_map);
+    for (i=0; i<args->nsample_map; i++) args->sample_map[i] = -1;
+
+    int flags = !src ? SMPL_STRICT|SMPL_SINGLE : SMPL_STRICT|SMPL_SINGLE|SMPL_PAIR2; // is vcf vs tab annotation file
+    smpl_ilist_t *ilist = smpl_ilist_init(dst, args->sample_names, args->sample_is_file, flags);    // gives mapping dst->src
+    if ( !ilist || !ilist->n ) error("Could not parse the samples: %s\n", args->sample_names);
+    args->nsmpl_annot = ilist->n;
+    int need_sample_map = args->nsmpl_annot==bcf_hdr_nsamples(dst) ? 0 : 1;
+    for (i=0; i<args->nsmpl_annot; i++)
+    {
+        int idst = ilist->idx[i];
+        const char *src_name = ilist->pair && ilist->pair[i] ? ilist->pair[i] : bcf_hdr_int2id(dst, BCF_DT_SAMPLE, idst);
+        int isrc = i;
+        if ( src )     // the annotation file is a VCF, not a tab-delimited file
+        {
+            isrc = bcf_hdr_id2int(src, BCF_DT_SAMPLE, src_name);
+            if ( isrc==-1 ) error("Sample \"%s\" not found in the annotation file\n", src_name);
+        }
+        if ( isrc!=idst ) need_sample_map = 1;
+        args->sample_map[idst] = isrc;
+    }
+    smpl_ilist_destroy(ilist);
+    return need_sample_map;
+}
+static char *columns_complement(char *columns, void **skip_info, void **skip_fmt)
+{
+    kstring_t str = {0,0,0};
+    char *ss = columns, *se = ss;
+    while ( *ss )
+    {
+        if ( *se && *se!=',' ) { se++; continue; }
+        if ( *ss!='^' )
+        {
+            if ( str.l ) kputc(',',&str);
+            kputsn(ss, se-ss, &str);
+            if ( !*se ) break;
+            ss = ++se;
+            continue;
+        }
+
+        if ( !strncasecmp("^INFO/",ss,6) )
+        {
+            if ( !*skip_info )
+            {
+                *skip_info = khash_str2int_init();
+                if ( str.l ) kputc(',',&str);
+                kputs("INFO",&str);
+            }
+            char tmp = *se; *se = 0;
+            khash_str2int_inc(*skip_info, strdup(ss+6));
+            *se = tmp;
+        }
+        else if ( !strncasecmp("^FORMAT/",ss,8) || !strncasecmp("^FMT/",ss,5) )
+        {
+            int n = !strncasecmp("^FMT/",ss,5) ? 5 : 8;
+            if ( !*skip_fmt )
+            {
+                *skip_fmt = khash_str2int_init();
+                if ( str.l ) kputc(',',&str);
+                kputs("FORMAT",&str);
+            }
+            char tmp = *se; *se = 0;
+            khash_str2int_inc(*skip_fmt, strdup(ss+n));
+            *se = tmp;
+        }
+        else
+        {
+            if ( !*skip_info )
+            {
+                *skip_info = khash_str2int_init();
+                if ( str.l ) kputc(',',&str);
+                kputs("INFO",&str);
+            }
+            char tmp = *se; *se = 0;
+            khash_str2int_inc(*skip_info, strdup(ss+1));
+            *se = tmp;
+        }
+
+        if ( !*se ) break;
+        ss = ++se;
+    }
+    free(columns);
+    return str.s;
+}
+static void bcf_hrec_format_rename(bcf_hrec_t *hrec, char *tag, kstring_t *str)
+{
+    int j, nout = 0;
+    ksprintf(str, "##%s=<", hrec->key);
+    for (j=0; j<hrec->nkeys; j++)
+    {
+        if ( !strcmp("IDX",hrec->keys[j]) ) continue;
+        if ( nout ) kputc(',',str);
+        if ( !strcmp("ID", hrec->keys[j]) )
+            ksprintf(str,"%s=%s", hrec->keys[j], tag);
+        else
+            ksprintf(str,"%s=%s", hrec->keys[j], hrec->vals[j]);
+        nout++;
+    }
+    ksprintf(str,">\n");
+}
+static char *set_replace_mode(char *ss, int *replace)
+{
+    int mode = 0;
+    while (*ss)
+    {
+        if ( *ss=='+' ) mode |= REPLACE_MISSING;
+        else if ( *ss=='-' ) mode |= REPLACE_NON_MISSING;
+        else if ( *ss=='=' ) mode |= SET_OR_APPEND;
+        else if ( *ss=='.' ) mode |= CARRY_OVER_MISSING;
+        else break;
+        ss++;
+    }
+    if ( !mode ) mode = REPLACE_ALL;
+// is exactly one bit set?
+//    if ( mode && !(mode && ((mode & mode-1) == 0)) )
+    *replace = mode;
+    return ss;
+}
+static void rename_annots_push(args_t *args, char *src, char *dst);
+static void init_columns(args_t *args)
+{
+    int need_sample_map = 0;
+    int sample_map_ok = init_sample_map(args, args->tgts_is_vcf?args->files->readers[1].header:NULL, args->hdr);
+
+    kstring_t tmp = {0,0,0};
+    if ( args->columns_is_file )
+    {
+        int i,n;
+        char **str = hts_readlist(args->columns, args->columns_is_file, &n);
+        if ( !str ) error("Could not parse %s\n", args->columns);
+        for (i=0; i<n; i++)
+        {
+            char *ptr = str[i];
+            while ( *ptr && !isspace(*ptr) ) ptr++;
+            if ( *ptr )
+            {
+                *ptr = 0;
+                ptr++;
+                while ( *ptr && isspace(*ptr) ) ptr++;
+                if ( *ptr )
+                {
+                    if ( args->merge_method_str.l ) kputc(',',&args->merge_method_str);
+                    kputs(str[i],&args->merge_method_str);
+                    kputc(':',&args->merge_method_str);
+                    kputs(ptr,&args->merge_method_str);
+                }
+            }
+            if ( tmp.l ) kputc(',',&tmp);
+            kputs(str[i],&tmp);
+            free(str[i]);
+        }
+        free(str);
+        free(args->columns);
+        args->columns = tmp.s;
+        tmp.l = tmp.m = 0;
+        tmp.s = NULL;
+    }
+
+    void *skip_fmt = NULL, *skip_info = NULL;
+    if ( args->tgts_is_vcf )
+        args->columns = columns_complement(args->columns, &skip_info, &skip_fmt);
+
+    kstring_t str = {0,0,0};
+    char *ss = args->columns, *se = ss;
+    args->ncols = 0;
+    int icol = -1, has_fmt_str = 0;
+    while ( *ss )
+    {
+        char *ptr;
+        if ( *se && *se!=',' ) { se++; continue; }
+        int replace;
+        ss = set_replace_mode(ss, &replace);
+        icol++;
+        str.l = 0;
+        kputsn(ss, se-ss, &str);
+        if ( !str.s[0] || !strcasecmp("-",str.s) ) ;
+        else if ( !strcasecmp("CHROM",str.s) ) args->chr_idx = icol;
+        else if ( !strcasecmp("POS",str.s) ) args->beg_idx = icol;
+        else if ( !strcasecmp("FROM",str.s) || !strcasecmp("BEG",str.s) ) args->beg_idx = icol;
+        else if ( !strcasecmp("TO",str.s) || !strcasecmp("END",str.s) ) args->end_idx = icol;
+        else if ( !strcasecmp("REF",str.s) )
+        {
+            if ( args->tgts_is_vcf )
+            {
+                args->ncols++; args->cols = (annot_col_t*) realloc(args->cols,sizeof(annot_col_t)*args->ncols);
+                annot_col_t *col = &args->cols[args->ncols-1];
+                memset(col,0,sizeof(*col));
+                col->setter = vcf_setter_ref;
+                col->hdr_key_src = strdup(str.s);
+                col->hdr_key_dst = strdup(str.s);
+            }
+            else args->ref_idx = icol;
+        }
+        else if ( !strcasecmp("ALT",str.s) )
+        {
+            if ( args->tgts_is_vcf )
+            {
+                args->ncols++; args->cols = (annot_col_t*) realloc(args->cols,sizeof(annot_col_t)*args->ncols);
+                annot_col_t *col = &args->cols[args->ncols-1];
+                memset(col,0,sizeof(*col));
+                col->setter = vcf_setter_alt;
+                col->hdr_key_src = strdup(str.s);
+                col->hdr_key_dst = strdup(str.s);
+                col->replace = replace;
+                if ( args->pair_logic==-1 ) bcf_sr_set_opt(args->files,BCF_SR_PAIR_LOGIC,BCF_SR_PAIR_BOTH_REF);
+            }
+            else args->alt_idx = icol;
+        }
+        else if ( !strcasecmp("ID",str.s) || !strcasecmp("~ID",str.s) )
+        {
+            if ( replace & REPLACE_NON_MISSING ) error("Apologies, the -ID feature has not been implemented yet.\n");
+            if ( str.s[0]=='~' ) replace = MATCH_VALUE;
+            if ( args->tgts_is_vcf && (replace & MATCH_VALUE) ) error("todo: -c ~ID with -a VCF?\n");
+            args->ncols++; args->cols = (annot_col_t*) realloc(args->cols,sizeof(annot_col_t)*args->ncols);
+            annot_col_t *col = &args->cols[args->ncols-1];
+            memset(col,0,sizeof(*col));
+            col->icol = icol;
+            col->replace = replace;
+            col->setter = args->tgts_is_vcf ? vcf_setter_id : setter_id;
+            col->hdr_key_src = strdup(str.s);
+            col->hdr_key_dst = strdup(str.s);
+            if ( replace & MATCH_VALUE ) args->match_id = icol;
+        }
+        else if ( !strcasecmp("~INFO/END",str.s) && !args->tgts_is_vcf )
+        {
+            replace = MATCH_VALUE;
+            args->ncols++; args->cols = (annot_col_t*) realloc(args->cols,sizeof(annot_col_t)*args->ncols);
+            annot_col_t *col = &args->cols[args->ncols-1];
+            memset(col,0,sizeof(*col));
+            col->icol = icol;
+            col->replace = replace;
+            col->setter  = NULL;
+            col->hdr_key_src = strdup(str.s);
+            col->hdr_key_dst = strdup(str.s);
+            args->match_end = icol;
+        }
+        else if ( !strcasecmp("~POS",str.s) && !args->tgts_is_vcf )
+        {
+            if ( args->tgts_is_vcf ) error("Error: cannot use ~POS, position can be replaced only from a tab-delimited file\n");
+            args->ncols++; args->cols = (annot_col_t*) realloc(args->cols,sizeof(annot_col_t)*args->ncols);
+            annot_col_t *col = &args->cols[args->ncols-1];
+            memset(col,0,sizeof(*col));
+            col->icol = icol;
+            col->replace = replace;
+            col->setter  = setter_pos;
+            col->hdr_key_src = strdup(str.s);
+            col->hdr_key_dst = strdup(str.s);
+            args->match_end = icol;
+        }
+        else if ( !strncasecmp("ID:=",str.s,4) )    // transfer a tag from INFO to ID column
+        {
+            if ( !args->tgts_is_vcf ) error("The annotation source must be a VCF for \"%s\"\n",str.s);
+            if ( replace & REPLACE_NON_MISSING ) error("Apologies, the -ID feature has not been implemented yet.\n");
+            args->ncols++; args->cols = (annot_col_t*) realloc(args->cols,sizeof(annot_col_t)*args->ncols);
+            annot_col_t *col = &args->cols[args->ncols-1];
+            memset(col,0,sizeof(*col));
+            col->icol = icol;
+            col->replace = replace;
+            col->setter = vcf_setter_id;
+            col->getter = vcf_getter_info_str2str;
+            str.s[2] = 0;
+            col->hdr_key_dst = strdup(str.s);
+            col->hdr_key_src = strncasecmp("INFO/",str.s+4,5) ? strdup(str.s+4) : strdup(str.s+4+5);
+            int hdr_id = bcf_hdr_id2int(args->tgts_hdr, BCF_DT_ID,col->hdr_key_src);
+            if ( !bcf_hdr_idinfo_exists(args->tgts_hdr,BCF_HL_INFO,hdr_id) )
+                error("The INFO tag \"%s\" is not defined in %s\n", col->hdr_key_src, args->targets_fname);
+            if ( bcf_hdr_id2type(args->tgts_hdr,BCF_HL_INFO,hdr_id)!=BCF_HT_STR )
+                error("Only Type=String tags can be used to annotate the ID column\n");
+        }
+        else if ( (ptr=strstr(str.s,":=")) && !args->targets_fname )
+        {
+            *ptr = 0;
+            rename_annots_push(args,ptr+2,str.s);
+            *ptr = ':';
+        }
+        else if ( !strcasecmp("FILTER",str.s) )
+        {
+            if ( replace & REPLACE_NON_MISSING ) error("Apologies, the -FILTER feature has not been implemented yet.\n");
+            args->ncols++; args->cols = (annot_col_t*) realloc(args->cols,sizeof(annot_col_t)*args->ncols);
+            annot_col_t *col = &args->cols[args->ncols-1];
+            memset(col,0,sizeof(*col));
+            col->icol = icol;
+            col->replace = replace;
+            col->setter = args->tgts_is_vcf ? vcf_setter_filter : setter_filter;
+            col->hdr_key_src = strdup(str.s);
+            col->hdr_key_dst = strdup(str.s);
+            if ( args->tgts_is_vcf )
+            {
+                bcf_hdr_t *tgts_hdr = args->files->readers[1].header;
+                int j;
+                for (j=0; j<tgts_hdr->nhrec; j++)
+                {
+                    bcf_hrec_t *hrec = tgts_hdr->hrec[j];
+                    if ( hrec->type!=BCF_HL_FLT ) continue;
+                    int k = bcf_hrec_find_key(hrec,"ID");
+                    if ( k<0 ) error("[%s] Failed to parse the header, the ID attribute not found", __func__);
+                    tmp.l = 0;
+                    bcf_hrec_format(hrec, &tmp);
+                    bcf_hdr_append(args->hdr_out, tmp.s);
+                }
+                if (bcf_hdr_sync(args->hdr_out) < 0)
+                    error_errno("[%s] Failed to update header", __func__);
+            }
+        }
+        else if ( !strcasecmp("QUAL",str.s) )
+        {
+            if ( replace & REPLACE_NON_MISSING ) error("Apologies, the -QUAL feature has not been implemented yet.\n");
+            if ( replace & SET_OR_APPEND ) error("Apologies, the =QUAL feature has not been implemented yet.\n");
+            args->ncols++; args->cols = (annot_col_t*) realloc(args->cols,sizeof(annot_col_t)*args->ncols);
+            annot_col_t *col = &args->cols[args->ncols-1];
+            memset(col,0,sizeof(*col));
+            col->icol = icol;
+            col->replace = replace;
+            col->setter = args->tgts_is_vcf ? vcf_setter_qual : setter_qual;
+            col->hdr_key_src = strdup(str.s);
+            col->hdr_key_dst = strdup(str.s);
+        }
+        else if ( args->tgts_is_vcf && !strcasecmp("INFO",str.s) ) // All INFO fields
+        {
+            if ( replace & REPLACE_NON_MISSING ) error("Apologies, the -INFO/TAG feature has not been implemented yet.\n");
+            if ( replace & SET_OR_APPEND ) error("Apologies, the =INFO feature has not been implemented yet.\n");
+            bcf_hdr_t *tgts_hdr = args->files->readers[1].header;
+            int j;
+            for (j=0; j<tgts_hdr->nhrec; j++)
+            {
+                bcf_hrec_t *hrec = tgts_hdr->hrec[j];
+                if ( hrec->type!=BCF_HL_INFO ) continue;
+                int k = bcf_hrec_find_key(hrec,"ID");
+                assert( k>=0 ); // this should always be true for valid VCFs
+                if ( skip_info && khash_str2int_has_key(skip_info,hrec->vals[k]) ) continue;
+                tmp.l = 0;
+                bcf_hrec_format(hrec, &tmp);
+                bcf_hdr_append(args->hdr_out, tmp.s);
+                if (bcf_hdr_sync(args->hdr_out) < 0)
+                    error_errno("[%s] Failed to update header", __func__);
+                int hdr_id = bcf_hdr_id2int(args->hdr_out, BCF_DT_ID, hrec->vals[k]);
+                args->ncols++; args->cols = (annot_col_t*) realloc(args->cols,sizeof(annot_col_t)*args->ncols);
+                annot_col_t *col = &args->cols[args->ncols-1];
+                memset(col,0,sizeof(*col));
+                col->icol = -1;
+                col->replace = replace;
+                col->hdr_key_src = strdup(hrec->vals[k]);
+                col->hdr_key_dst = strdup(hrec->vals[k]);
+                col->number  = bcf_hdr_id2length(args->hdr_out,BCF_HL_INFO,hdr_id);
+                switch ( bcf_hdr_id2type(args->hdr_out,BCF_HL_INFO,hdr_id) )
+                {
+                    case BCF_HT_FLAG:   col->setter = vcf_setter_info_flag; break;
+                    case BCF_HT_INT:    col->setter = vcf_setter_info_int; break;
+                    case BCF_HT_REAL:   col->setter = vcf_setter_info_real; break;
+                    case BCF_HT_STR:    col->setter = vcf_setter_info_str; break;
+                    default: error("The type of %s not recognised (%d)\n", str.s,bcf_hdr_id2type(args->hdr_out,BCF_HL_INFO,hdr_id));
+                }
+            }
+        }
+        else if ( args->tgts_is_vcf && (!strcasecmp("FORMAT",str.s) || !strcasecmp("FMT",str.s)) ) // All FORMAT fields
+        {
+            bcf_hdr_t *tgts_hdr = args->files->readers[1].header;
+            need_sample_map = 1;
+            int j;
+            for (j=0; j<tgts_hdr->nhrec; j++)
+            {
+                bcf_hrec_t *hrec = tgts_hdr->hrec[j];
+                if ( hrec->type!=BCF_HL_FMT) continue;
+                int k = bcf_hrec_find_key(hrec,"ID");
+                assert( k>=0 ); // this should always be true for valid VCFs
+                if ( skip_fmt && khash_str2int_has_key(skip_fmt,hrec->vals[k]) ) continue;
+                tmp.l = 0;
+                bcf_hrec_format(hrec, &tmp);
+                bcf_hdr_append(args->hdr_out, tmp.s);
+                if (bcf_hdr_sync(args->hdr_out) < 0)
+                    error_errno("[%s] Failed to update header", __func__);
+                int hdr_id = bcf_hdr_id2int(args->hdr_out, BCF_DT_ID, hrec->vals[k]);
+                args->ncols++; args->cols = (annot_col_t*) realloc(args->cols,sizeof(annot_col_t)*args->ncols);
+                annot_col_t *col = &args->cols[args->ncols-1];
+                memset(col,0,sizeof(*col));
+                col->icol = -1;
+                col->replace = replace;
+                col->hdr_key_src = strdup(hrec->vals[k]);
+                col->hdr_key_dst = strdup(hrec->vals[k]);
+                if ( !strcasecmp("GT",col->hdr_key_src) )
+                {
+                    if ( !args->tgts_is_vcf ) error("The FORMAT/GT field can be currently populated only from a VCF\n");
+                    col->setter = vcf_setter_format_gt;
+                }
+                else
+                    switch ( bcf_hdr_id2type(args->hdr_out,BCF_HL_FMT,hdr_id) )
+                    {
+                        case BCF_HT_INT:    col->setter = vcf_setter_format_int; break;
+                        case BCF_HT_REAL:   col->setter = vcf_setter_format_real; break;
+                        case BCF_HT_STR:    col->setter = vcf_setter_format_str; has_fmt_str = 1; break;
+                        default: error("The type of %s not recognised (%d)\n", str.s,bcf_hdr_id2type(args->hdr_out,BCF_HL_FMT,hdr_id));
+                    }
+                hdr_id = bcf_hdr_id2int(tgts_hdr, BCF_DT_ID, hrec->vals[k]);
+                col->number = bcf_hdr_id2length(tgts_hdr,BCF_HL_FMT,hdr_id);
+            }
+        }
+        else if ( !strncasecmp("FORMAT/",str.s, 7) || !strncasecmp("FMT/",str.s,4) )
+        {
+            char *key_dst = str.s + (!strncasecmp("FMT/",str.s,4) ? 4 : 7);
+            char *key_src = strstr(key_dst,":=");
+            if ( key_src )
+            {
+                *key_src = 0;
+                key_src += 2;
+                if ( !strncasecmp("FORMAT/",key_src,7) ) key_src += 7;
+                else if ( !strncasecmp("FMT/",key_src,4) ) key_src += 4;
+            }
+            else
+                key_src = key_dst;
+            need_sample_map = 1;
+            if ( args->tgts_is_vcf )
+            {
+                bcf_hrec_t *hrec = bcf_hdr_get_hrec(args->files->readers[1].header, BCF_HL_FMT, "ID", key_src, NULL);
+                if ( !hrec ) error("No such annotation \"%s\" in %s\n", key_src,args->targets_fname);
+                tmp.l = 0;
+                bcf_hrec_format_rename(hrec, key_dst, &tmp);
+                bcf_hdr_append(args->hdr_out, tmp.s);
+                if (bcf_hdr_sync(args->hdr_out) < 0)
+                    error_errno("[%s] Failed to update header", __func__);
+            }
+            int hdr_id = bcf_hdr_id2int(args->hdr_out, BCF_DT_ID, key_dst);
+            if ( !bcf_hdr_idinfo_exists(args->hdr_out,BCF_HL_FMT,hdr_id) )
+                error("The FORMAT tag \"%s\" is not defined in %s, was the -h option provided?\n", str.s, args->targets_fname);
+            args->ncols++; args->cols = (annot_col_t*) realloc(args->cols,sizeof(annot_col_t)*args->ncols);
+            annot_col_t *col = &args->cols[args->ncols-1];
+            memset(col,0,sizeof(*col));
+            if ( !args->tgts_is_vcf )
+            {
+                col->icol = icol;
+                icol += args->nsmpl_annot - 1;
+            }
+            else
+                col->icol = -1;
+            col->replace = replace;
+            col->hdr_key_src = strdup(key_src);
+            col->hdr_key_dst = strdup(key_dst);
+            if ( !strcasecmp("GT",key_src) )
+            {
+                if ( !args->tgts_is_vcf ) error("The FORMAT/GT field can be currently populated only from a VCF\n");
+                col->setter = vcf_setter_format_gt;
+            }
+            else
+                switch ( bcf_hdr_id2type(args->hdr_out,BCF_HL_FMT,hdr_id) )
+                {
+                    case BCF_HT_INT:    col->setter = args->tgts_is_vcf ? vcf_setter_format_int  : setter_format_int; break;
+                    case BCF_HT_REAL:   col->setter = args->tgts_is_vcf ? vcf_setter_format_real : setter_format_real; break;
+                    case BCF_HT_STR:    col->setter = args->tgts_is_vcf ? vcf_setter_format_str  : setter_format_str; has_fmt_str = 1; break;
+                    default: error("The type of %s not recognised (%d)\n", str.s,bcf_hdr_id2type(args->hdr_out,BCF_HL_FMT,hdr_id));
+                }
+            if ( args->tgts_is_vcf )
+            {
+                bcf_hdr_t *tgts_hdr = args->files->readers[1].header;
+                hdr_id = bcf_hdr_id2int(tgts_hdr, BCF_DT_ID, col->hdr_key_src);
+                col->number = bcf_hdr_id2length(tgts_hdr,BCF_HL_FMT,hdr_id);
+            }
+        }
+        else
+        {
+            if ( replace & REPLACE_NON_MISSING ) error("Apologies, the -INFO/TAG feature has not been implemented yet.\n");
+            if ( replace & SET_OR_APPEND )
+            {
+                if ( args->tgts_is_vcf )
+                    error("Error: the =INFO/TAG feature is currently supported only with TAB annotation files and has limitations\n"
+                          "       (the annotation type is modified to \"Number=.\" and allele ordering is disregarded)\n");
+                fprintf(bcftools_stderr,"Warning: the =INFO/TAG feature modifies the annotation to \"Number=.\" and disregards allele ordering\n");
+            }
+            int explicit_src_info = 0;
+            int explicit_dst_info = 0;
+            char *key_dst;
+            if ( !strncasecmp("INFO/",str.s,5) )
+            {
+                key_dst = str.s + 5;
+                explicit_dst_info = 1;
+            }
+            else if ( !strcasecmp("~INFO/END",str.s) )
+            {
+                key_dst = str.s + 6;
+                explicit_dst_info = 1;
+            }
+            else
+                key_dst = str.s;
+            char *key_src = strstr(key_dst,":=");
+            if ( key_src )
+            {
+                *key_src = 0;
+                key_src += 2;
+                if ( !strncasecmp("INFO/",key_src,5) )
+                {
+                    key_src += 5;
+                    explicit_src_info = 1;
+                }
+                else if ( !strncasecmp("FMT/",key_src,4) || !strncasecmp("FORMAT/",key_src,5) )
+                {
+                    key_src[-2] = ':';
+                    error("Did you mean \"FMT/%s\" rather than \"%s\"?\n",str.s,str.s);
+                }
+            }
+            else
+                key_src = key_dst;
+
+            args->ncols++; args->cols = (annot_col_t*) realloc(args->cols,sizeof(annot_col_t)*args->ncols);
+            annot_col_t *col = &args->cols[args->ncols-1];
+            memset(col,0,sizeof(*col));
+            col->icol = icol;
+            col->replace = replace;
+            col->hdr_key_src = strdup(key_src);
+            col->hdr_key_dst = strdup(key_dst);
+
+            int hdr_id = bcf_hdr_id2int(args->hdr_out, BCF_DT_ID, key_dst);
+            if ( !bcf_hdr_idinfo_exists(args->hdr_out,BCF_HL_INFO,hdr_id) )
+            {
+                if ( args->tgts_is_vcf ) // reading annotations from a VCF, add a new header line
+                {
+                    if ( !strcasecmp("ID",key_src) && !explicit_src_info )
+                    {
+                        // transferring ID column into a new INFO tag
+                        tmp.l = 0;
+                        ksprintf(&tmp,"##INFO=<ID=%s,Number=1,Type=String,Description=\"Transferred ID column\">",key_dst);
+                    }
+                    else if ( !strcasecmp("FILTER",key_src) && !explicit_src_info )
+                    {
+                        // transferring FILTER column into a new INFO tag
+                        tmp.l = 0;
+                        ksprintf(&tmp,"##INFO=<ID=%s,Number=1,Type=String,Description=\"Transferred FILTER column\">",key_dst);
+                    }
+                    else
+                    {
+                        bcf_hrec_t *hrec = bcf_hdr_get_hrec(args->files->readers[1].header, BCF_HL_INFO, "ID", key_src, NULL);
+                        if ( !hrec )
+                        {
+                            if ( explicit_dst_info+explicit_src_info==0 && bcf_hdr_get_hrec(args->files->readers[1].header, BCF_HL_FMT, "ID", key_src, NULL) )
+                                error("Did you mean \"FMT/%s\" rather than \"%s\"?\n",str.s,str.s);
+                            char *ptr = strchr(key_src,'=');
+                            if ( ptr )
+                            {
+                                *ptr = 0; tmp.l = 0; ksprintf(&tmp,"%s:=%s",key_src,ptr+1); *ptr = '=';
+                                error("The INFO tag \"%s\" is not defined, is this what you want \"%s\" ?\n",key_src,tmp.s);
+                            }
+                            error("The INFO tag \"%s\" is not defined in %s, was the -h option provided?\n", key_src,args->files->readers[1].fname);
+                        }
+                        tmp.l = 0;
+                        bcf_hrec_format_rename(hrec, key_dst, &tmp);
+                    }
+                    bcf_hdr_append(args->hdr_out, tmp.s);
+                    if (bcf_hdr_sync(args->hdr_out) < 0)
+                        error_errno("[%s] Failed to update header", __func__);
+                    hdr_id = bcf_hdr_id2int(args->hdr_out, BCF_DT_ID, key_dst);
+                }
+                else
+                    error("The INFO tag \"%s\" is not defined in %s, was the -h option provided?\n", key_dst, args->targets_fname);
+                assert( bcf_hdr_idinfo_exists(args->hdr_out,BCF_HL_INFO,hdr_id) );
+            }
+            if  ( args->tgts_is_vcf )
+            {
+                if ( !strcasecmp("ID",key_src) && !explicit_src_info ) col->getter = vcf_getter_id2str;
+                else if ( !strcasecmp("FILTER",key_src) && !explicit_src_info ) col->getter = vcf_getter_filter2str;
+            }
+            col->number = bcf_hdr_id2length(args->hdr_out,BCF_HL_INFO,hdr_id);
+            switch ( bcf_hdr_id2type(args->hdr_out,BCF_HL_INFO,hdr_id) )
+            {
+                case BCF_HT_FLAG:   col->setter = args->tgts_is_vcf ? vcf_setter_info_flag : setter_info_flag; break;
+                case BCF_HT_INT:    col->setter = args->tgts_is_vcf ? vcf_setter_info_int  : setter_info_int; break;
+                case BCF_HT_REAL:   col->setter = args->tgts_is_vcf ? vcf_setter_info_real : setter_info_real; break;
+                case BCF_HT_STR:    col->setter = args->tgts_is_vcf ? vcf_setter_info_str  : setter_info_str; break;
+                default: error("The type of %s not recognised (%d)\n", str.s,bcf_hdr_id2type(args->hdr_out,BCF_HL_INFO,hdr_id));
+            }
+            if ( replace & SET_OR_APPEND )   // change to Number=.
+            {
+                bcf_hrec_t *hrec = bcf_hdr_get_hrec(args->hdr_out, BCF_HL_INFO, "ID", key_dst, NULL);
+                if ( !hrec ) error("Uh, could not find the new tag \"%s\" in the header\n", key_dst);
+                hrec = bcf_hrec_dup(hrec);
+                int j = bcf_hrec_find_key(hrec, "Number");
+                if ( j<0 ) error("Uh, could not find the entry Number in the header record of %s\n",key_dst);
+                free(hrec->vals[j]);
+                hrec->vals[j] = strdup(".");
+                bcf_hdr_remove(args->hdr_out,BCF_HL_INFO, key_dst);
+                bcf_hdr_add_hrec(args->hdr_out, hrec);
+            }
+        }
+        if ( !*se ) break;
+        ss = ++se;
+    }
+    free(str.s);
+    free(tmp.s);
+    free(args->columns);
+    if ( skip_info ) khash_str2int_destroy_free(skip_info);
+    if ( skip_fmt ) khash_str2int_destroy_free(skip_fmt);
+    if ( has_fmt_str )
+    {
+        int n = bcf_hdr_nsamples(args->hdr_out);
+        if ( args->tgts_is_vcf && n<bcf_hdr_nsamples(args->files->readers[1].header) ) n = bcf_hdr_nsamples(args->files->readers[1].header);
+        args->tmpp  = (char**)malloc(sizeof(char*)*n);
+        args->tmpp2 = (char**)malloc(sizeof(char*)*n);
+    }
+    if ( !need_sample_map )
+    {
+        free(args->sample_map);
+        args->sample_map = NULL;
+    }
+    else if ( sample_map_ok<0 )
+        error("No matching samples in source and destination file?\n");
+}
+static void init_merge_method(args_t *args)
+{
+    int i;
+    for (i=0; i<args->ncols; i++)
+    {
+        args->cols[i].merge_method = MM_FIRST;
+        args->cols[i].mm_str_hash = NULL;
+        args->cols[i].mm_dbl = NULL;
+        args->cols[i].mm_dbl_nalloc = args->cols[i].mm_dbl_nused = args->cols[i].mm_dbl_ndat = 0;
+        memset(&args->cols[i].mm_kstr, 0, sizeof(args->cols[i].mm_kstr));
+    }
+    if ( !args->merge_method_str.l ) return;
+    if ( args->tgts_is_vcf ) error("Error: the --merge-logic is intended for use with BED or TAB-delimited files only.\n");
+    if ( !args->tgt_idx && !args->tgts ) error("Error: BEG,END (or FROM,TO) columns or REF,ALT columns are expected with the --merge-logic option.\n");
+    char *sb = args->merge_method_str.s;
+    while ( *sb )
+    {
+        char *se = sb;
+        while ( *se && *se!=',' ) se++;
+        args->tmpks.l = 0;
+        kputsn(sb, se-sb, &args->tmpks);
+        kputc(0, &args->tmpks);
+        char *mm_type_str = args->tmpks.s + args->tmpks.l;
+        while ( *mm_type_str!=':' && mm_type_str > args->tmpks.s ) mm_type_str--;
+        if ( *mm_type_str!=':' )
+            error("Error: could not parse the argument to --merge-logic: %s\n", args->merge_method_str.s);
+        *mm_type_str = 0;
+        mm_type_str++;
+        int mm_type = MM_FIRST;
+        if ( !strcasecmp("unique",mm_type_str) ) mm_type = MM_UNIQUE;
+        else if ( !strcasecmp("first",mm_type_str) ) mm_type = MM_FIRST;
+        else if ( !strcasecmp("append",mm_type_str) ) mm_type = MM_APPEND;
+        else if ( !strcasecmp("append-missing",mm_type_str) )
+        {
+            mm_type = MM_APPEND_MISSING;
+            if ( args->ref_idx!=-1 ) args->has_append_mode = 1;
+        }
+        else if ( !strcasecmp("sum",mm_type_str) ) mm_type = MM_SUM;
+        else if ( !strcasecmp("avg",mm_type_str) ) mm_type = MM_AVG;
+        else if ( !strcasecmp("min",mm_type_str) ) mm_type = MM_MIN;
+        else if ( !strcasecmp("max",mm_type_str) ) mm_type = MM_MAX;
+        else error("Error: could not parse --merge-logic %s, the logic \"%s\" is not recognised\n", args->merge_method_str.s,mm_type_str);
+        for (i=0; i<args->ncols; i++)
+        {
+            if ( strcmp(args->cols[i].hdr_key_dst,args->tmpks.s) ) continue;
+            if ( (mm_type==MM_APPEND || mm_type==MM_APPEND_MISSING) && args->cols[i].number!=BCF_VL_VAR )
+                error("Error: --merge-logic append can be requested only for tags of variable length (Number=.)\n");
+            args->cols[i].merge_method = mm_type;
+            break;
+        }
+        if ( i==args->ncols ) error("No such tag in the destination file: %s\n", args->tmpks.s);
+        sb = *se ? se + 1 : se;
+    }
+    if ( args->has_append_mode )
+    {
+        // create a missing line to insert missing values when VCF ALT finds no match in the annotation file
+        args->aline_missing = (annot_line_t*)calloc(1,sizeof(*args->aline_missing));
+        int ncol = 0;
+        for (i=0; i<args->ncols; i++)
+            if ( ncol < args->cols[i].icol + 1 ) ncol = args->cols[i].icol + 1;
+        if ( ncol < args->ref_idx + 1 ) ncol = args->ref_idx + 1;
+        args->aline_missing->mcols = ncol;
+        args->aline_missing->ncols = ncol;
+        args->aline_missing->cols = (char**) malloc(ncol*sizeof(char*));
+        for (i=0; i<ncol; i++)
+            args->aline_missing->cols[i] = strdup(".");
+    }
+}
+
+static void rename_chrs(args_t *args, char *fname)
+{
+    int n, i;
+    char **map = hts_readlist(fname, 1, &n);
+    if ( !map ) error("Could not read: %s\n", fname);
+    for (i=0; i<n; i++)
+    {
+        char *ss = map[i];
+        while ( *ss && !isspace(*ss) ) ss++;
+        if ( !*ss ) error("Could not parse: %s\n", fname);
+        *ss = 0;
+        int rid = bcf_hdr_name2id(args->hdr_out, map[i]);
+        bcf_hrec_t *hrec = bcf_hdr_get_hrec(args->hdr_out, BCF_HL_CTG, "ID", map[i], NULL);
+        if ( !hrec ) continue;  // the sequence not present
+        int j = bcf_hrec_find_key(hrec, "ID");
+        assert( j>=0 );
+        free(hrec->vals[j]);
+        ss++;
+        while ( *ss && isspace(*ss) ) ss++;
+        char *se = ss;
+        while ( *se && !isspace(*se) ) se++;
+        *se = 0;
+        hrec->vals[j] = strdup(ss);
+        args->hdr_out->id[BCF_DT_CTG][rid].key = hrec->vals[j];
+    }
+    for (i=0; i<n; i++) free(map[i]);
+    free(map);
+}
+// Dirty: this relies on bcf_hdr_sync NOT being called
+static int rename_annots_core(args_t *args, char *ori_tag, char *new_tag)
+{
+    int type;
+    if ( !strncasecmp("info/",ori_tag,5) ) type = BCF_HL_INFO, ori_tag += 5;
+    else if ( !strncasecmp("format/",ori_tag,7) ) type = BCF_HL_FMT, ori_tag += 7;
+    else if ( !strncasecmp("fmt/",ori_tag,4) ) type = BCF_HL_FMT, ori_tag += 4;
+    else if ( !strncasecmp("filter/",ori_tag,7) ) type = BCF_HL_FLT, ori_tag += 7;
+    else return -1;
+    if ( !strncasecmp("info/",new_tag,5) )
+    {
+        if ( type != BCF_HL_INFO ) error("Cannot transfer %s to INFO\n", ori_tag);
+        new_tag += 5;
+    }
+    else if ( !strncasecmp("format/",new_tag,7) )
+    {
+        if ( type != BCF_HL_FMT ) error("Cannot transfer %s to FORMAT\n", ori_tag);
+        new_tag += 7;
+    }
+    else if ( !strncasecmp("fmt/",new_tag,4) )
+    {
+        if ( type != BCF_HL_FMT ) error("Cannot transfer %s to FORMAT\n", ori_tag);
+        new_tag += 4;
+    }
+    else if ( !strncasecmp("filter/",new_tag,7) )
+    {
+        if ( type != BCF_HL_FLT ) error("Cannot transfer %s to FILTER\n", ori_tag);
+        new_tag += 7;
+    }
+    int id = bcf_hdr_id2int(args->hdr_out, BCF_DT_ID, ori_tag);
+    if ( id<0 ) return 1;
+    bcf_hrec_t *hrec = bcf_hdr_get_hrec(args->hdr_out, type, "ID", ori_tag, NULL);
+    if ( !hrec ) return 1;  // the ID attribute not present
+    int j = bcf_hrec_find_key(hrec, "ID");
+    assert( j>=0 );
+    free(hrec->vals[j]);
+    char *ptr = new_tag;
+    while ( *ptr && !isspace(*ptr) ) ptr++;
+    *ptr = 0;
+    hrec->vals[j] = strdup(new_tag);
+    args->hdr_out->id[BCF_DT_ID][id].key = hrec->vals[j];
+    return 0;
+}
+static void rename_annots(args_t *args)
+{
+    int i;
+    if ( args->rename_annots )
+    {
+        args->rename_annots_map = hts_readlist(args->rename_annots, 1, &args->rename_annots_nmap);
+        if ( !args->rename_annots_map ) error("Could not read: %s\n", args->rename_annots);
+    }
+    for (i=0; i<args->rename_annots_nmap; i++)
+    {
+        char *ptr = args->rename_annots_map[i];
+        while ( *ptr && !isspace(*ptr) ) ptr++;
+        if ( !*ptr ) error("Could not parse: %s\n", args->rename_annots_map[i]);
+        char *rmme = ptr;
+        *ptr = 0;
+        ptr++;
+        while ( *ptr && isspace(*ptr) ) ptr++;
+        if ( !*ptr ) { *rmme = ' '; error("Could not parse: %s\n", args->rename_annots_map[i]); }
+        if ( rename_annots_core(args, args->rename_annots_map[i], ptr) < 0 )
+            error("Could not parse \"%s %s\", expected INFO, FORMAT, or FILTER prefix\n",args->rename_annots_map[i],ptr);
+    }
+}
+static void rename_annots_push(args_t *args, char *src, char *dst)
+{
+    args->rename_annots_nmap++;
+    args->rename_annots_map = (char**)realloc(args->rename_annots_map,sizeof(*args->rename_annots_map)*args->rename_annots_nmap);
+    kstring_t str = {0,0,0};
+    ksprintf(&str,"%s %s",src,dst);
+    args->rename_annots_map[ args->rename_annots_nmap - 1 ] = str.s;
+}
+
+static void init_data(args_t *args)
+{
+    args->hdr = args->files->readers[0].header;
+    args->hdr_out = bcf_hdr_dup(args->hdr);
+
+    if ( args->set_ids_fmt )
+    {
+        if ( args->set_ids_fmt[0]=='+' ) { args->set_ids_replace = 0; args->set_ids_fmt++; }
+        args->set_ids = convert_init(args->hdr_out, NULL, 0, args->set_ids_fmt);
+    }
+    if ( args->remove_annots ) init_remove_annots(args);
+    if ( args->header_fname || args->header_lines ) init_header_lines(args);
+    if ( args->targets_fname && args->tgts_is_vcf )
+    {
+        // reading annots from a VCF
+        if ( !bcf_sr_add_reader(args->files, args->targets_fname) )
+            error("Failed to open %s: %s\n", args->targets_fname,bcf_sr_strerror(args->files->errnum));
+        args->tgts_hdr = args->files->readers[1].header;
+    }
+    if ( args->columns ) init_columns(args);
+    if ( args->targets_fname && !args->tgts_is_vcf )
+    {
+        if ( !args->columns ) error("The -c option not given\n");
+        if ( args->chr_idx==-1 ) error("The -c CHROM option not given\n");
+        if ( args->beg_idx==-1 ) error("The -c POS option not given\n");
+        if ( args->single_overlaps && args->merge_method_str.l ) error("The options --merge-logic and --single-overlaps cannot be combined\n");
+        if ( args->end_idx==-1 || (args->single_overlaps && !args->merge_method_str.l) )
+        {
+            args->end_idx = -args->beg_idx - 1;
+            args->tgts = bcf_sr_regions_init(args->targets_fname,1,args->chr_idx,args->beg_idx,args->end_idx);
+            if ( !args->tgts ) error("Could not initialize the annotation file: %s\n", args->targets_fname);
+            if ( !args->tgts->tbx ) error("Expected tabix-indexed annotation file: %s\n", args->targets_fname);
+        }
+        else
+        {
+            if ( args->ref_idx!=-1 ) error("Error: the REF columns will be ignored when BEG,END (or FROM,TO) is present. Replace END (or TO) with \"-\".\n");
+            int len = strlen(args->targets_fname);
+            if ( len>=7 && !strcasecmp(".bed.gz",args->targets_fname+len-7) ) args->tgt_is_bed = 1;
+            else if ( len>=8 && !strcasecmp(".bed.bgz",args->targets_fname+len-8) ) args->tgt_is_bed = 1;
+            else if ( len>=4 && !strcasecmp(".bed",args->targets_fname+len-4) ) args->tgt_is_bed = 1;
+            args->tgt_idx = regidx_init(args->targets_fname,parse_with_payload,free_payload,sizeof(char*),args);
+            if ( !args->tgt_idx ) error("Failed to parse: %s\n", args->targets_fname);
+            args->tgt_itr = regitr_init(args->tgt_idx);
+            args->nalines++;
+            hts_expand0(annot_line_t,args->nalines,args->malines,args->alines);
+        }
+        if ( args->min_overlap_str )
+        {
+            char *tmp = args->min_overlap_str;
+            if ( args->min_overlap_str[0] != ':' )
+            {
+                args->min_overlap_ann = strtod(args->min_overlap_str,&tmp);
+                if ( args->min_overlap_ann < 0 || args->min_overlap_ann > 1 || (*tmp && *tmp!=':') )
+                    error("Could not parse \"--min-overlap %s\", expected value(s) between 0-1\n", args->min_overlap_str);
+            }
+            if ( *tmp && *tmp==':' )
+            {
+                args->min_overlap_vcf = strtod(tmp+1,&tmp);
+                if ( args->min_overlap_vcf < 0 || args->min_overlap_vcf > 1 || *tmp )
+                    error("Could not parse \"--min-overlap %s\", expected value(s) between 0-1\n", args->min_overlap_str);
+            }
+        }
+    }
+    init_merge_method(args);
+    args->vcmp = vcmp_init();
+
+    if ( args->filter_str )
+        args->filter = filter_init(args->hdr, args->filter_str);
+
+    if ( args->mark_sites )
+    {
+        if ( !args->targets_fname ) error("The -a option not given\n");
+        bcf_hdr_printf(args->hdr_out,"##INFO=<ID=%s,Number=0,Type=Flag,Description=\"Sites %slisted in %s\">",
+            args->mark_sites,args->mark_sites_logic==MARK_LISTED?"":"not ",args->mark_sites);
+    }
+
+    if (args->record_cmd_line) bcf_hdr_append_version(args->hdr_out, args->argc, args->argv, "bcftools_annotate");
+    if ( !args->drop_header )
+    {
+        if ( args->rename_chrs ) rename_chrs(args, args->rename_chrs);
+        if ( args->rename_annots || args->rename_annots_map ) rename_annots(args);
+
+        char wmode[8];
+        set_wmode(wmode,args->output_type,args->output_fname,args->clevel);
+        args->out_fh = hts_open(args->output_fname ? args->output_fname : "-", wmode);
+        if ( args->out_fh == NULL ) error("[%s] Error: cannot write to \"%s\": %s\n", __func__,args->output_fname, strerror(errno));
+        if ( args->n_threads )
+            hts_set_opt(args->out_fh, HTS_OPT_THREAD_POOL, args->files->p);
+        if ( bcf_hdr_write(args->out_fh, args->hdr_out)!=0 ) error("[%s] Error: failed to write the header to %s\n", __func__,args->output_fname);
+    }
+}
+
+static void destroy_data(args_t *args)
+{
+    int i;
+    for (i=0; i<args->nrm; i++) free(args->rm[i].key);
+    free(args->rm);
+    if ( args->hdr_out ) bcf_hdr_destroy(args->hdr_out);
+    if (args->vcmp) vcmp_destroy(args->vcmp);
+    for (i=0; i<args->ncols; i++)
+    {
+        free(args->cols[i].hdr_key_src);
+        free(args->cols[i].hdr_key_dst);
+        free(args->cols[i].mm_kstr.s);
+        if ( args->cols[i].mm_str_hash ) khash_str2int_destroy_free(args->cols[i].mm_str_hash);
+        free(args->cols[i].mm_dbl);
+        free(args->cols[i].ptr);
+    }
+    free(args->cols);
+    if ( args->aline_missing )
+    {
+        for (i=0; i<args->aline_missing->ncols; i++) free(args->aline_missing->cols[i]);
+        free(args->aline_missing->cols);
+        free(args->aline_missing);
+    }
+    for (i=0; i<args->malines; i++)
+    {
+        free(args->alines[i].cols);
+        free(args->alines[i].als);
+        free(args->alines[i].line.s);
+    }
+    free(args->alines);
+    free(args->srt_alines);
+    if ( args->tgt_idx )
+    {
+        regidx_destroy(args->tgt_idx);
+        regitr_destroy(args->tgt_itr);
+    }
+    if ( args->rename_annots_map )
+    {
+        for (i=0; i<args->rename_annots_nmap; i++) free(args->rename_annots_map[i]);
+        free(args->rename_annots_map);
+    }
+    if ( args->tgts ) bcf_sr_regions_destroy(args->tgts);
+    free(args->tmpks.s);
+    free(args->tmpi);
+    free(args->tmpf);
+    free(args->tmps);
+    free(args->tmpp);
+    free(args->tmpi2);
+    free(args->tmpf2);
+    free(args->tmps2);
+    free(args->tmpp2);
+    free(args->tmpi3);
+    free(args->tmpf3);
+    free(args->src_smpl_pld);
+    free(args->dst_smpl_pld);
+    if ( args->set_ids )
+        convert_destroy(args->set_ids);
+    if ( args->filter )
+        filter_destroy(args->filter);
+    if (args->out_fh) hts_close(args->out_fh);
+    free(args->sample_map);
+    free(args->merge_method_str.s);
+}
+
+static void parse_annot_line(args_t *args, char *str, annot_line_t *tmp)
+{
+    tmp->line.l = 0;
+    kputs(str, &tmp->line);
+    char *s = tmp->line.s;
+    tmp->ncols = 1;
+    hts_expand(char*,tmp->ncols,tmp->mcols,tmp->cols);
+    tmp->cols[0] = s;
+    while ( *s )
+    {
+        if ( *s=='\t' )
+        {
+            tmp->ncols++;
+            hts_expand(char*,tmp->ncols,tmp->mcols,tmp->cols);
+            tmp->cols[tmp->ncols-1] = s+1;
+            *s = 0;
+        }
+        s++;
+    }
+    if ( args->ref_idx != -1 )
+    {
+        if ( args->ref_idx >= tmp->ncols )
+            error("Could not parse the line, expected %d+ columns, found %d:\n\t%s\n",args->ref_idx+1,tmp->ncols,str);
+        if ( args->alt_idx >= tmp->ncols )
+            error("Could not parse the line, expected %d+ columns, found %d:\n\t%s\n",args->alt_idx+1,tmp->ncols,str);
+        tmp->nals = 2;
+        hts_expand(char*,tmp->nals,tmp->mals,tmp->als);
+        tmp->als[0] = tmp->cols[args->ref_idx];
+        tmp->als[1] = s = tmp->cols[args->alt_idx];
+        while ( *s )
+        {
+            if ( *s==',' )
+            {
+                tmp->nals++;
+                hts_expand(char*,tmp->nals,tmp->mals,tmp->als);
+                tmp->als[tmp->nals-1] = s+1;
+                *s = 0;
+            }
+            s++;
+        }
+    }
+}
+static void buffer_annot_lines(args_t *args, bcf1_t *line, int start_pos, int end_pos)
+{
+    if ( args->nalines && args->alines[0].rid != line->rid ) args->nalines = 0;
+
+    int i = 0;
+    while ( i<args->nalines )
+    {
+        if ( line->pos > args->alines[i].end )
+        {
+            args->nalines--;
+            if ( args->nalines && i<args->nalines )
+            {
+                annot_line_t tmp = args->alines[i];
+                memmove(&args->alines[i],&args->alines[i+1],(args->nalines-i)*sizeof(annot_line_t));
+                args->alines[args->nalines] = tmp;
+            }
+        }
+        else i++;
+    }
+    if ( args->ref_idx==-1 && args->nalines ) return;
+
+    while ( !bcf_sr_regions_overlap(args->tgts, bcf_seqname(args->hdr,line), start_pos,end_pos) )
+    {
+        if ( args->nalines + 1 == 0xffff ) break;   // likely a symbolic allele, don't let the buffer overflow
+        args->nalines++;
+        hts_expand0(annot_line_t,args->nalines,args->malines,args->alines);
+        annot_line_t *tmp = &args->alines[args->nalines-1];
+        tmp->rid   = line->rid;
+        tmp->start = args->tgts->start;
+        tmp->end   = args->tgts->end;
+        parse_annot_line(args, args->tgts->line.s, tmp);
+        if ( args->ref_idx != -1 )
+        {
+            int iseq = args->tgts->iseq;
+            if ( bcf_sr_regions_next(args->tgts)<0 || args->tgts->iseq!=iseq ) break;
+        }
+        else break;
+    }
+}
+
+// search string in semicolon separated strings (xx vs aa;bb)
+static int str_match(char *needle, char *haystack)
+{
+    int len = strlen(needle);
+    char *ptr = haystack;
+    while ( *ptr && (ptr=strstr(ptr,needle)) )
+    {
+        if ( ptr[len]!=0 && ptr[len]!=';' ) ptr++;          // a prefix, not a match
+        else if ( ptr==haystack || ptr[-1]==';' ) return 1; // a match
+        ptr++;  // a suffix, not a match
+    }
+    return 0;
+}
+// search common string in semicolon separated strings (xx;yy;zz vs aa;bb)
+static int strstr_match(char *a, char *b)
+{
+    char *beg = a;
+    while ( *beg )
+    {
+        char *end = beg;
+        while ( *end && *end!=';' ) end++;
+        char tmp = *end;
+        if ( *end==';' ) *end = 0;
+        int ret = str_match(beg,b);
+        *end = tmp;
+        if ( ret || !*end ) return ret;
+        beg = end + 1;
+    }
+    return 0;
+}
+static void annotate(args_t *args, bcf1_t *line)
+{
+    int i, j;
+    for (i=0; i<args->nrm; i++)
+        args->rm[i].handler(args, line, &args->rm[i]);
+
+    int has_overlap = 0;
+    if ( args->tgt_idx )
+    {
+        for (j=0; j<args->ncols; j++) args->cols[j].done = 0;
+        if ( regidx_overlap(args->tgt_idx, bcf_seqname(args->hdr,line),line->pos,line->pos+line->rlen-1, args->tgt_itr) )
+        {
+            while ( regitr_overlap(args->tgt_itr) )
+            {
+                annot_line_t *tmp = &args->alines[0];
+                tmp->rid   = line->rid;
+                tmp->start = args->tgt_itr->beg;
+                tmp->end   = args->tgt_itr->end;
+
+                // Check min overlap
+                int len_ann = tmp->end - tmp->start + 1;
+                int len_vcf = line->rlen;
+                int isec = (tmp->end < line->pos+line->rlen-1 ? tmp->end : line->pos+line->rlen-1) - (tmp->start > line->pos ? tmp->start : line->pos) + 1;
+                assert( isec > 0 );
+                if ( args->min_overlap_ann && args->min_overlap_ann > (float)isec/len_ann ) continue;
+                if ( args->min_overlap_vcf && args->min_overlap_vcf > (float)isec/len_vcf ) continue;
+
+                parse_annot_line(args, regitr_payload(args->tgt_itr,char*), tmp);
+                for (j=0; j<args->ncols; j++)
+                {
+                    if ( args->cols[j].done==1 ) continue;
+                    int ret = args->cols[j].setter(args,line,&args->cols[j],tmp);
+                    if ( ret < 0 )
+                        error("fixme: Could not set %s at %s:%"PRId64"\n", args->cols[j].hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) line->pos+1);
+                    if ( ret==0 )
+                        args->cols[j].done = 1;
+                }
+            }
+            has_overlap = 1;
+        }
+        for (j=0; j<args->ncols; j++)
+        {
+            if ( args->cols[j].done==1 || args->cols[j].merge_method == MM_FIRST ) continue;
+            if ( !args->cols[j].setter ) continue;
+            if ( args->cols[j].setter(args,line,&args->cols[j],NULL) < 0 )
+                error("fixme: Could not set %s at %s:%"PRId64"\n", args->cols[j].hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) line->pos+1);
+        }
+    }
+    else if ( args->tgts )
+    {
+        // Buffer annotation lines. When multiple ALT alleles are present in the annotation file, at least one
+        // must match some of the VCF alleles. If the append-missing mode is set (and REF+ALT is requested), the
+        // buffered lines will annotate the VCF respecting the order in ALT and when no matching line is found
+        // for an ALT, missing value is appended instead.
+        int end_pos = line->pos + line->rlen - 1;
+        buffer_annot_lines(args, line, line->pos, end_pos);
+
+        args->nsrt_alines = 0;
+        hts_expand(uint32_t,args->nalines,args->msrt_alines,args->srt_alines);
+        if ( args->nalines >= 0xffff || line->n_allele >= 0xffff )
+            error("Error: too many alleles or annotation lines in the buffer at %s:%"PRId64" (todo:skip?)\n",bcf_seqname(args->hdr,line),(int64_t) line->pos+1);
+
+        kstring_t match_end = {0,0,0};
+        if ( args->match_end>=0 && bcf_get_info_int32(args->hdr,line,"END",&args->tmpi,&args->mtmpi)==1 )
+            kputw(args->tmpi[0],&match_end);
+
+        // Find matching lines
+        for (i=0; i<args->nalines; i++)
+        {
+            if ( line->pos > args->alines[i].end || end_pos < args->alines[i].start ) continue;
+            if ( args->ref_idx != -1 )  // REF+ALT matching requested
+            {
+                if ( line->pos!=args->alines[i].start || vcmp_set_ref(args->vcmp, line->d.allele[0], args->alines[i].als[0]) < 0 ) continue;   // refs are not compatible
+                for (j=1; j<args->alines[i].nals; j++)
+                {
+                    int ialt;
+                    if ( line->n_allele==1 && args->alines[i].als[j][0]=='.' && args->alines[i].als[j][1]==0 )  // match: no ALT allele in VCF and annot file has "."
+                        ialt = 0;
+                    else
+                    {
+                        ialt = vcmp_find_allele(args->vcmp, line->d.allele+1, line->n_allele - 1, args->alines[i].als[j]);
+                        if ( ialt < 0 ) continue;
+                        ialt++;
+                    }
+                    if ( args->match_id>=0 && !strstr_match(line->d.id,args->alines[i].cols[args->match_id]) ) continue;
+                    if ( args->match_end>=0 && match_end.l && strcmp(match_end.s,args->alines[i].cols[args->match_end]) ) continue;
+                    args->srt_alines[args->nsrt_alines++] = (ialt<<16) | i;
+                    has_overlap = 1;
+                    break;
+                }
+            }
+            else    // overlap, REF+ALT matching not requested
+            {
+                args->srt_alines[args->nsrt_alines++] = (0xffff<<16) | i;
+                has_overlap = 1;
+            }
+        }
+
+        free(match_end.s);
+
+        // Sort lines if needed
+        if ( args->has_append_mode )
+        {
+            // insertion sort by VCF ALT index (top bits) and alines index (low bits)
+            uint32_t tmp;
+            for (i=1; i<args->nsrt_alines; i++)
+                for (j=i; j>0 && args->srt_alines[j] < args->srt_alines[j-1]; j--)
+                    tmp = args->srt_alines[j], args->srt_alines[j] = args->srt_alines[j-1], args->srt_alines[j-1] = tmp;
+        }
+        // Annotate
+        for (j=0; j<args->ncols; j++) args->cols[j].done = 0;
+        int ialt_exp = 1;
+        for (i=0; i<args->nsrt_alines; i++)
+        {
+            int ialt = args->srt_alines[i] >> 16;
+            int ilin = args->srt_alines[i] & 0xffff;
+            if ( args->has_append_mode )
+            {
+                if ( ialt_exp > ialt ) continue;    // multiple annotation lines for the same position
+                if ( ialt_exp < ialt )
+                {
+                    // REF+ALT matching requested, append-missing mode: insert "." if no annotation line was found for the ALT
+                    while ( ialt_exp++ < ialt )
+                    {
+                        for (j=0; j<args->ncols; j++)
+                        {
+                            if ( args->cols[j].merge_method != MM_APPEND_MISSING ) continue;
+                            if ( args->cols[j].done==1 ) continue;
+                            if ( !args->cols[j].setter ) continue;
+                            int ret = args->cols[j].setter(args,line,&args->cols[j],args->aline_missing);
+                            if ( ret < 0 )
+                                error("fixme: Could not set missing %s at %s:%"PRId64"\n", args->cols[j].hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) line->pos+1);
+                            if ( ret==0 )
+                                args->cols[j].done = 1;
+                        }
+                    }
+                }
+            }
+            for (j=0; j<args->ncols; j++)
+            {
+                if ( args->cols[j].done==1 ) continue;
+                if ( !args->cols[j].setter ) continue;
+                int ret = args->cols[j].setter(args,line,&args->cols[j],&args->alines[ilin]);
+                if ( ret < 0 )
+                    error("fixme: Could not set %s at %s:%"PRId64"\n", args->cols[j].hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) line->pos+1);
+                if ( ret==0 )
+                    args->cols[j].done = 1;
+            }
+            ialt_exp = ialt + 1;
+        }
+        if ( args->nsrt_alines )
+        {
+            // In the append-missing mode fill missing values to all trailing ALTs, but only if at least one
+            // record was found. Otherwise leave the row will be left without annotation.
+            if ( args->has_append_mode && ialt_exp < line->n_allele )
+            {
+                while ( ialt_exp++ < line->n_allele )
+                {
+                    for (j=0; j<args->ncols; j++)
+                    {
+                        if ( args->cols[j].merge_method != MM_APPEND_MISSING ) continue;
+                        if ( args->cols[j].done==1 ) continue;
+                        if ( !args->cols[j].setter ) continue;
+                        int ret = args->cols[j].setter(args,line,&args->cols[j],args->aline_missing);
+                        if ( ret < 0 )
+                            error("fixme: Could not set missing %s at %s:%"PRId64"\n", args->cols[j].hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) line->pos+1);
+                        if ( ret==0 )
+                            args->cols[j].done = 1;
+                    }
+                }
+            }
+            // Flush
+            for (j=0; j<args->ncols; j++)
+            {
+                if ( args->cols[j].done==1 || args->cols[j].merge_method == MM_FIRST ) continue;
+                if ( !args->cols[j].setter ) continue;
+                int ret = args->cols[j].setter(args,line,&args->cols[j],NULL);
+                if ( ret < 0 )
+                    error("fixme: Could not set %s at %s:%"PRId64"\n", args->cols[j].hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) line->pos+1);
+            }
+        }
+    }
+    else if ( args->files->nreaders == 2 )
+    {
+        if ( bcf_sr_has_line(args->files,1) )
+        {
+            bcf1_t *aline = bcf_sr_get_line(args->files,1);
+            for (j=0; j<args->ncols; j++)
+            {
+                if ( !args->cols[j].setter ) continue;
+                if ( args->cols[j].setter(args,line,&args->cols[j],aline) )
+                    error("fixme: Could not set %s at %s:%"PRId64"\n", args->cols[j].hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) line->pos+1);
+            }
+
+            has_overlap = 1;
+        }
+    }
+    if ( args->set_ids )
+    {
+        args->tmpks.l = 0;
+        convert_line(args->set_ids, line, &args->tmpks);
+        if ( args->tmpks.l )
+        {
+            int replace = 0;
+            if ( args->set_ids_replace ) replace = 1;
+            else if ( !line->d.id || (line->d.id[0]=='.' && !line->d.id[1]) ) replace = 1;
+            if ( replace )
+                bcf_update_id(args->hdr_out,line,args->tmpks.s);
+        }
+    }
+
+    if ( args->mark_sites )
+    {
+        // ideally, we'd like to be far more general than this in future, see https://github.com/samtools/bcftools/issues/87
+        if ( args->mark_sites_logic==MARK_LISTED )
+            bcf_update_info_flag(args->hdr_out,line,args->mark_sites,NULL,has_overlap?1:0);
+        else
+            bcf_update_info_flag(args->hdr_out,line,args->mark_sites,NULL,has_overlap?0:1);
+    }
+}
+
+static void usage(args_t *args)
+{
+    fprintf(bcftools_stderr, "\n");
+    fprintf(bcftools_stderr, "About:   Annotate and edit VCF/BCF files.\n");
+    fprintf(bcftools_stderr, "Usage:   bcftools annotate [options] VCF\n");
+    fprintf(bcftools_stderr, "\n");
+    fprintf(bcftools_stderr, "Options:\n");
+    fprintf(bcftools_stderr, "   -a, --annotations FILE          VCF file or tabix-indexed FILE with annotations: CHR\\tPOS[\\tVALUE]+\n");
+    fprintf(bcftools_stderr, "   -c, --columns LIST              List of columns in the annotation file, e.g. CHROM,POS,REF,ALT,-,INFO/TAG. See man page for details\n");
+    fprintf(bcftools_stderr, "   -C, --columns-file FILE         Read -c columns from FILE, one name per row, with optional --merge-logic TYPE: NAME[ TYPE]\n");
+    fprintf(bcftools_stderr, "   -e, --exclude EXPR              Exclude sites for which the expression is true (see man page for details)\n");
+    fprintf(bcftools_stderr, "       --force                     Continue despite parsing error (at your own risk!)\n");
+    fprintf(bcftools_stderr, "   -H, --header-line STR           Header line which should be appended to the VCF header, can be given multiple times\n");
+    fprintf(bcftools_stderr, "   -h, --header-lines FILE         Lines which should be appended to the VCF header\n");
+    fprintf(bcftools_stderr, "   -I, --set-id [+]FORMAT          Set ID column using a `bcftools query`-like expression, see man page for details\n");
+    fprintf(bcftools_stderr, "   -i, --include EXPR              Select sites for which the expression is true (see man page for details)\n");
+    fprintf(bcftools_stderr, "   -k, --keep-sites                Leave -i/-e sites unchanged instead of discarding them\n");
+    fprintf(bcftools_stderr, "   -l, --merge-logic TAG:TYPE      Merge logic for multiple overlapping regions (see man page for details), EXPERIMENTAL\n");
+    fprintf(bcftools_stderr, "   -m, --mark-sites [+-]TAG        Add INFO/TAG flag to sites which are (\"+\") or are not (\"-\") listed in the -a file\n");
+    fprintf(bcftools_stderr, "       --min-overlap ANN:VCF       Required overlap as a fraction of variant in the -a file (ANN), the VCF (:VCF), or reciprocal (ANN:VCF)\n");
+    fprintf(bcftools_stderr, "       --no-version                Do not append version and command line to the header\n");
+    fprintf(bcftools_stderr, "   -o, --output FILE               Write output to a file [standard output]\n");
+    fprintf(bcftools_stderr, "   -O, --output-type u|b|v|z[0-9]  u/b: un/compressed BCF, v/z: un/compressed VCF, 0-9: compression level [v]\n");
+    fprintf(bcftools_stderr, "       --pair-logic STR            Matching records by <snps|indels|both|all|some|exact>, see man page for details [some]\n");
+    fprintf(bcftools_stderr, "   -r, --regions REGION            Restrict to comma-separated list of regions\n");
+    fprintf(bcftools_stderr, "   -R, --regions-file FILE         Restrict to regions listed in FILE\n");
+    fprintf(bcftools_stderr, "       --regions-overlap 0|1|2     Include if POS in the region (0), record overlaps (1), variant overlaps (2) [1]\n");
+    fprintf(bcftools_stderr, "       --rename-annots FILE        Rename annotations: TYPE/old\\tnew, where TYPE is one of FILTER,INFO,FORMAT\n");
+    fprintf(bcftools_stderr, "       --rename-chrs FILE          Rename sequences according to the mapping: old\\tnew\n");
+    fprintf(bcftools_stderr, "   -s, --samples [^]LIST           Comma separated list of samples to annotate (or exclude with \"^\" prefix)\n");
+    fprintf(bcftools_stderr, "   -S, --samples-file [^]FILE      File of samples to annotate (or exclude with \"^\" prefix)\n");
+    fprintf(bcftools_stderr, "       --single-overlaps           Keep memory low by avoiding complexities arising from handling multiple overlapping intervals\n");
+    fprintf(bcftools_stderr, "   -x, --remove LIST               List of annotations (e.g. ID,INFO/DP,FORMAT/DP,FILTER) to remove (or keep with \"^\" prefix). See man page for details\n");
+    fprintf(bcftools_stderr, "       --threads INT               Number of extra output compression threads [0]\n");
+    fprintf(bcftools_stderr, "\n");
+    fprintf(bcftools_stderr, "Examples:\n");
+    fprintf(bcftools_stderr, "   http://samtools.github.io/bcftools/howtos/annotate.html\n");
+    fprintf(bcftools_stderr, "\n");
+    bcftools_exit(1);
+}
+
+int main_vcfannotate(int argc, char *argv[])
+{
+    int c;
+    args_t *args  = (args_t*) calloc(1,sizeof(args_t));
+    args->argc    = argc; args->argv = argv;
+    args->files   = bcf_sr_init();
+    args->output_fname = "-";
+    args->output_type = FT_VCF;
+    args->n_threads = 0;
+    args->record_cmd_line = 1;
+    args->ref_idx = args->alt_idx = args->chr_idx = args->beg_idx = args->end_idx = -1;
+    args->set_ids_replace = 1;
+    args->match_id = -1;
+    args->match_end = -1;
+    args->clevel = -1;
+    args->pair_logic = -1;
+    int regions_is_file = 0;
+    int regions_overlap = 1;
+
+    static struct option loptions[] =
+    {
+        {"keep-sites",no_argument,NULL,'k'},
+        {"mark-sites",required_argument,NULL,'m'},
+        {"set-id",required_argument,NULL,'I'},
+        {"output",required_argument,NULL,'o'},
+        {"output-type",required_argument,NULL,'O'},
+        {"threads",required_argument,NULL,9},
+        {"annotations",required_argument,NULL,'a'},
+        {"merge-logic",required_argument,NULL,'l'},
+        {"collapse",required_argument,NULL,2},
+        {"pair-logic",required_argument,NULL,2},
+        {"include",required_argument,NULL,'i'},
+        {"exclude",required_argument,NULL,'e'},
+        {"regions",required_argument,NULL,'r'},
+        {"regions-file",required_argument,NULL,'R'},
+        {"regions-overlap",required_argument,NULL,3},
+        {"remove",required_argument,NULL,'x'},
+        {"columns-file",required_argument,NULL,'C'},
+        {"columns",required_argument,NULL,'c'},
+        {"rename-annots",required_argument,NULL,11},
+        {"rename-chrs",required_argument,NULL,1},
+        {"header-lines",required_argument,NULL,'h'},
+        {"header-line",required_argument,NULL,'H'},
+        {"samples",required_argument,NULL,'s'},
+        {"samples-file",required_argument,NULL,'S'},
+        {"single-overlaps",no_argument,NULL,10},
+        {"min-overlap",required_argument,NULL,12},
+        {"no-version",no_argument,NULL,8},
+        {"force",no_argument,NULL,'f'},
+        {NULL,0,NULL,0}
+    };
+    char *tmp;
+    while ((c = getopt_long(argc, argv, "h:H:?o:O:r:R:a:x:c:C:i:e:S:s:I:m:kl:f",loptions,NULL)) >= 0)
+    {
+        switch (c) {
+            case 'f': args->force = 1; break;
+            case 'k': args->keep_sites = 1; break;
+            case 'm':
+                args->mark_sites_logic = MARK_LISTED;
+                if ( optarg[0]=='+' ) args->mark_sites = optarg+1;
+                else if ( optarg[0]=='-' ) { args->mark_sites = optarg+1; args->mark_sites_logic = MARK_UNLISTED; }
+                else args->mark_sites = optarg;
+                break;
+            case 'l':
+                if ( args->merge_method_str.l ) kputc(',',&args->merge_method_str);
+                kputs(optarg,&args->merge_method_str);
+                break;
+            case 'I': args->set_ids_fmt = optarg; break;
+            case 's': args->sample_names = optarg; break;
+            case 'S': args->sample_names = optarg; args->sample_is_file = 1; break;
+            case 'c': args->columns = strdup(optarg); break;
+            case 'C': args->columns = strdup(optarg); args->columns_is_file = 1; break;
+            case 'o': args->output_fname = optarg; break;
+            case 'O':
+                switch (optarg[0]) {
+                    case 'b': args->output_type = FT_BCF_GZ; break;
+                    case 'u': args->output_type = FT_BCF; break;
+                    case 'z': args->output_type = FT_VCF_GZ; break;
+                    case 'v': args->output_type = FT_VCF; break;
+                    default:
+                    {
+                        args->clevel = strtol(optarg,&tmp,10);
+                        if ( *tmp || args->clevel<0 || args->clevel>9 ) error("The output type \"%s\" not recognised\n", optarg);
+                    }
+                };
+                if ( optarg[1] )
+                {
+                    args->clevel = strtol(optarg+1,&tmp,10);
+                    if ( *tmp || args->clevel<0 || args->clevel>9 ) error("Could not parse argument: --compression-level %s\n", optarg+1);
+                }
+                break;
+            case 'e':
+                if ( args->filter_str ) error("Error: only one -i or -e expression can be given, and they cannot be combined\n");
+                args->filter_str = optarg; args->filter_logic |= FLT_EXCLUDE; break;
+            case 'i':
+                if ( args->filter_str ) error("Error: only one -i or -e expression can be given, and they cannot be combined\n");
+                args->filter_str = optarg; args->filter_logic |= FLT_INCLUDE; break;
+            case 'x': args->remove_annots = optarg; break;
+            case 'a': args->targets_fname = optarg; break;
+            case 'r': args->regions_list = optarg; break;
+            case 'R': args->regions_list = optarg; regions_is_file = 1; break;
+            case 'h': args->header_fname = optarg; break;
+            case 'H': args->header_lines = dbuf_push(args->header_lines,strdup(optarg)); break;
+            case  1 : args->rename_chrs = optarg; break;
+            case  2 :
+                if ( !strcmp(optarg,"snps") ) args->pair_logic |= BCF_SR_PAIR_SNP_REF;
+                else if ( !strcmp(optarg,"indels") ) args->pair_logic |= BCF_SR_PAIR_INDEL_REF;
+                else if ( !strcmp(optarg,"both") ) args->pair_logic |= BCF_SR_PAIR_BOTH_REF;
+                else if ( !strcmp(optarg,"any") ) args->pair_logic |= BCF_SR_PAIR_ANY;
+                else if ( !strcmp(optarg,"all") ) args->pair_logic |= BCF_SR_PAIR_ANY;
+                else if ( !strcmp(optarg,"some") ) args->pair_logic |= BCF_SR_PAIR_SOME;
+                else if ( !strcmp(optarg,"none") ) args->pair_logic = BCF_SR_PAIR_EXACT;
+                else if ( !strcmp(optarg,"exact") ) args->pair_logic = BCF_SR_PAIR_EXACT;
+                else error("The --pair-logic string \"%s\" not recognised.\n", optarg);
+                break;
+            case  3 :
+                regions_overlap = parse_overlap_option(optarg);
+                if ( regions_overlap < 0 ) error("Could not parse: --regions-overlap %s\n",optarg);
+                break;
+            case  9 : args->n_threads = strtol(optarg, 0, 0); break;
+            case  8 : args->record_cmd_line = 0; break;
+            case 10 : args->single_overlaps = 1; break;
+            case 11 : args->rename_annots = optarg; break;
+            case 12 : args->min_overlap_str = optarg; break;
+            case '?': usage(args); break;
+            default: error("Unknown argument: %s\n", optarg);
+        }
+    }
+
+    char *fname = NULL;
+    if ( optind>=argc )
+    {
+        if ( !isatty(fileno((FILE *)stdin)) ) fname = "-";  // reading from stdin
+        else usage(args);
+    }
+    else fname = argv[optind];
+
+    if ( args->regions_list )
+    {
+        bcf_sr_set_opt(args->files,BCF_SR_REGIONS_OVERLAP,regions_overlap);
+        if ( bcf_sr_set_regions(args->files, args->regions_list, regions_is_file)<0 )
+            error("Failed to read the regions: %s\n", args->regions_list);
+    }
+    if ( args->targets_fname )
+    {
+        htsFile *fp = hts_open(args->targets_fname,"r");
+        if ( !fp ) error("Failed to open %s\n", args->targets_fname);
+        htsFormat type = *hts_get_format(fp);
+        hts_close(fp);
+
+        if ( type.format==vcf || type.format==bcf )
+        {
+            args->tgts_is_vcf = 1;
+            args->files->require_index = 1;
+            bcf_sr_set_opt(args->files,BCF_SR_PAIR_LOGIC,args->pair_logic>=0 ? args->pair_logic : BCF_SR_PAIR_SOME);
+            if ( args->min_overlap_str ) error("The --min-overlap option cannot be used when annotating from a VCF\n");
+        }
+    }
+    if ( args->min_overlap_str && args->single_overlaps ) error("The options --single-overlaps and --min-overlap cannot be combined\n");
+    if ( bcf_sr_set_threads(args->files, args->n_threads)<0 ) error("Failed to create threads\n");
+    if ( !bcf_sr_add_reader(args->files, fname) ) error("Failed to read from %s: %s\n", !strcmp("-",fname)?"standard input":fname,bcf_sr_strerror(args->files->errnum));
+
+    static int line_errcode_warned = 0;
+    init_data(args);
+    while ( bcf_sr_next_line(args->files) )
+    {
+        if ( !bcf_sr_has_line(args->files,0) ) continue;
+        bcf1_t *line = bcf_sr_get_line(args->files,0);
+        if ( line->errcode )
+        {
+            if ( !args->force )
+                error("Encountered an error, cannot proceed. Please check the error output above.\n"
+                      "If feeling adventurous, use the --force option. (At your own risk!)\n");
+            else if ( !line_errcode_warned )
+            {
+                fprintf(bcftools_stderr,
+                    "Warning: Encountered an error, proceeding only because --force was given.\n"
+                    "         Note that this can result in a segfault or a silent corruption of the output file!\n");
+                line_errcode_warned = 1;
+                line->errcode = 0;
+            }
+        }
+        if ( args->filter )
+        {
+            int pass = filter_test(args->filter, line, NULL);
+            if ( args->filter_logic & FLT_EXCLUDE ) pass = pass ? 0 : 1;
+            if ( !pass )
+            {
+                if ( args->keep_sites && bcf_write1(args->out_fh, args->hdr_out, line)!=0 ) error("[%s] Error: failed to write to %s\n", __func__,args->output_fname);
+                continue;
+            }
+        }
+        annotate(args, line);
+        if ( bcf_write1(args->out_fh, args->hdr_out, line)!=0 ) error("[%s] Error: failed to write to %s\n", __func__,args->output_fname);
+    }
+    destroy_data(args);
+    bcf_sr_destroy(args->files);
+    free(args);
+    return 0;
+}
diff --git a/bcftools/vcfbuf.c b/bcftools/vcfbuf.c
new file mode 100644
index 0000000..9d60c49
--- /dev/null
+++ b/bcftools/vcfbuf.c
@@ -0,0 +1,562 @@
+/* The MIT License
+
+   Copyright (c) 2016-2022 Genome Research Ltd.
+
+   Author: Petr Danecek <pd3@sanger.ac.uk>
+
+   Permission is hereby granted, free of charge, to any person obtaining a copy
+   of this software and associated documentation files (the "Software"), to deal
+   in the Software without restriction, including without limitation the rights
+   to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+   copies of the Software, and to permit persons to whom the Software is
+   furnished to do so, subject to the following conditions:
+
+   The above copyright notice and this permission notice shall be included in
+   all copies or substantial portions of the Software.
+
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+   IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+   FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+   AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+   LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+   OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+   THE SOFTWARE.
+
+ */
+
+#include <assert.h>
+#include <strings.h>
+#include <htslib/vcf.h>
+#include <htslib/vcfutils.h>
+#include <htslib/hts_os.h>
+#include "bcftools.h"
+#include "vcfbuf.h"
+#include "rbuf.h"
+
+typedef struct
+{
+    double max[VCFBUF_LD_N];
+    int rand_missing, filter1;
+}
+ld_t;
+
+typedef struct
+{
+    bcf1_t *rec;
+    double af;
+    int af_set:1, filter:1, idx:30;
+}
+vcfrec_t;
+
+#define PRUNE_MODE_MAX_AF 1
+#define PRUNE_MODE_1ST    2
+#define PRUNE_MODE_RAND   3
+typedef struct
+{
+    int max_sites, mvrec, mac, mfarr, mode;
+    int *ac, *idx;
+    float *farr;
+    char *af_tag;
+    vcfrec_t **vrec;
+}
+prune_t;
+
+typedef struct
+{
+    int active;
+}
+rmdup_t;
+
+typedef struct
+{
+    int active, rid, end;
+}
+overlap_t;
+
+struct _vcfbuf_t
+{
+    int win, dummy;
+    bcf_hdr_t *hdr;
+    vcfrec_t *vcf;
+    rbuf_t rbuf;
+    ld_t ld;
+    prune_t prune;
+    overlap_t overlap;
+    rmdup_t rmdup;
+};
+
+vcfbuf_t *vcfbuf_init(bcf_hdr_t *hdr, int win)
+{
+    vcfbuf_t *buf = (vcfbuf_t*) calloc(1,sizeof(vcfbuf_t));
+    buf->hdr = hdr;
+    buf->win = win;
+    buf->overlap.rid = -1;
+    int i;
+    for (i=0; i<VCFBUF_LD_N; i++) buf->ld.max[i] = HUGE_VAL;
+    rbuf_init(&buf->rbuf, 0);
+    return buf;
+}
+
+void vcfbuf_destroy(vcfbuf_t *buf)
+{
+    int i;
+    for (i=0; i<buf->rbuf.m; i++)
+        if ( buf->vcf[i].rec ) bcf_destroy(buf->vcf[i].rec);
+    free(buf->vcf);
+    free(buf->prune.farr);
+    free(buf->prune.vrec);
+    free(buf->prune.ac);
+    free(buf->prune.idx);
+    free(buf);
+}
+
+void vcfbuf_set(vcfbuf_t *buf, vcfbuf_opt_t key, void *value)
+{
+    if ( key==LD_FILTER1 ) { buf->ld.filter1 = *((int*)value); return; }
+    if ( key==LD_RAND_MISSING ) { buf->ld.rand_missing = *((int*)value); return; }
+    if ( key==LD_MAX_R2 ) { buf->ld.max[VCFBUF_LD_IDX_R2] = *((double*)value); return; }
+    if ( key==LD_MAX_LD ) { buf->ld.max[VCFBUF_LD_IDX_LD] = *((double*)value); return; }
+    if ( key==LD_MAX_HD ) { buf->ld.max[VCFBUF_LD_IDX_HD] = *((double*)value); return; }
+
+    if ( key==VCFBUF_DUMMY ) { buf->dummy = *((int*)value); return; }
+    if ( key==VCFBUF_NSITES )
+    {
+        buf->prune.max_sites = *((int*)value);
+        if ( !buf->prune.mode ) buf->prune.mode = PRUNE_MODE_MAX_AF;
+        return;
+    }
+    if ( key==VCFBUF_AF_TAG ) { buf->prune.af_tag = *((char**)value); return; }
+    if ( key==VCFBUF_OVERLAP_WIN ) { buf->overlap.active = *((int*)value); return; }
+    if ( key==VCFBUF_RMDUP) { buf->rmdup.active = *((int*)value); return; }
+
+    if ( key==VCFBUF_NSITES_MODE )
+    {
+        char *mode = *((char**)value);
+        if ( !strcasecmp(mode,"maxAF") ) buf->prune.mode = PRUNE_MODE_MAX_AF;
+        else if ( !strcasecmp(mode,"1st") ) buf->prune.mode = PRUNE_MODE_1ST;
+        else if ( !strcasecmp(mode,"rand") ) buf->prune.mode = PRUNE_MODE_RAND;
+        else error("The mode \"%s\" is not recognised\n",mode);
+        return;
+    }
+}
+
+int vcfbuf_nsites(vcfbuf_t *buf)
+{
+    return buf->rbuf.n;
+}
+
+bcf1_t *vcfbuf_push(vcfbuf_t *buf, bcf1_t *rec)
+{
+    rbuf_expand0(&buf->rbuf, vcfrec_t, buf->rbuf.n+1, buf->vcf);
+
+    int i = rbuf_append(&buf->rbuf);
+    if ( !buf->vcf[i].rec ) buf->vcf[i].rec = bcf_init1();
+
+    bcf1_t *ret = buf->vcf[i].rec;
+    buf->vcf[i].rec = rec;
+    buf->vcf[i].af_set = 0;
+    buf->vcf[i].filter = buf->ld.filter1;
+    buf->ld.filter1 = 0;
+
+    return ret;
+}
+
+bcf1_t *vcfbuf_peek(vcfbuf_t *buf, int idx)
+{
+    int i = rbuf_kth(&buf->rbuf, idx);
+    return i<0 ? NULL : buf->vcf[i].rec;
+}
+
+bcf1_t *vcfbuf_remove(vcfbuf_t *buf, int idx)
+{
+    int i = rbuf_kth(&buf->rbuf, idx);
+    if ( i<0 ) return NULL;
+    bcf1_t *rec = buf->vcf[i].rec;
+	rbuf_remove_kth(&buf->rbuf, vcfrec_t, idx, buf->vcf);
+    return rec;
+}
+
+static int cmpvrec(const void *_a, const void *_b)
+{
+    vcfrec_t *a = *((vcfrec_t**) _a);
+    vcfrec_t *b = *((vcfrec_t**) _b);
+    if ( a->af < b->af ) return -1;
+    if ( a->af == b->af ) return 0;
+    return 1;
+}
+static int cmpint_desc(const void *_a, const void *_b)
+{
+    int a = *((int*)_a);
+    int b = *((int*)_b);
+    if ( a < b ) return 1;
+    if ( a == b ) return 0;
+    return -1;
+}
+
+static void _prune_sites(vcfbuf_t *buf, int flush_all)
+{
+    int nbuf = flush_all ? buf->rbuf.n : buf->rbuf.n - 1;
+
+    int nprune = nbuf - buf->prune.max_sites;
+    int i,k,irec = 0;
+    if ( buf->prune.mode==PRUNE_MODE_1ST )
+    {
+        int eoff = flush_all ? 1 : 2;
+        for (i=0; i<nprune; i++)
+            rbuf_remove_kth(&buf->rbuf, vcfrec_t, buf->rbuf.n - eoff, buf->vcf);
+        return;
+    }
+    if ( buf->prune.mode==PRUNE_MODE_RAND )
+    {
+        int eoff = flush_all ? 0 : 1;
+        for (i=0; i<nprune; i++)
+        {
+            int j = (buf->rbuf.n - eoff) * hts_drand48();
+            rbuf_remove_kth(&buf->rbuf, vcfrec_t, j, buf->vcf);
+        }
+        return;
+    }
+
+    if ( nbuf > buf->prune.mvrec )
+    {
+        buf->prune.idx   = (int*) realloc(buf->prune.idx, nbuf*sizeof(int));
+        buf->prune.vrec  = (vcfrec_t**) realloc(buf->prune.vrec, nbuf*sizeof(vcfrec_t*));
+        buf->prune.mvrec = nbuf;
+    }
+
+    // set allele frequency and prepare buffer for sorting
+    for (i=-1; rbuf_next(&buf->rbuf,&i) && irec<nbuf; )
+    {
+        bcf1_t *line = buf->vcf[i].rec;
+        if ( line->n_allele > buf->prune.mac )
+        {
+            buf->prune.ac = (int*) realloc(buf->prune.ac, line->n_allele*sizeof(*buf->prune.ac));
+            buf->prune.mac = line->n_allele;
+        }
+        if ( !buf->vcf[i].af_set )
+        {
+            buf->vcf[i].af = 0;
+            if ( buf->prune.af_tag )
+            {
+                if ( bcf_get_info_float(buf->hdr,line,buf->prune.af_tag,&buf->prune.farr, &buf->prune.mfarr) > 0 ) buf->vcf[i].af = buf->prune.farr[0];
+            }
+            else if ( bcf_calc_ac(buf->hdr, line, buf->prune.ac, BCF_UN_INFO|BCF_UN_FMT) )
+            {
+                int ntot = buf->prune.ac[0], nalt = 0;
+                for (k=1; k<line->n_allele; k++) nalt += buf->prune.ac[k];
+                buf->vcf[i].af = ntot ? (float)nalt/ntot : 0;
+            }
+            buf->vcf[i].af_set = 1;
+        }
+        buf->vcf[i].idx = irec;
+        buf->prune.vrec[irec++] = &buf->vcf[i];
+    }
+
+    // sort by allele frequency, low AF will be removed preferentially
+    qsort(buf->prune.vrec, nbuf, sizeof(*buf->prune.vrec), cmpvrec);
+
+    // sort the rbuf indexes to be pruned descendently so that j-th rbuf index
+    // is removed before i-th index if i<j
+    for (i=0; i<nprune; i++)
+        buf->prune.idx[i] = buf->prune.vrec[i]->idx;
+
+    qsort(buf->prune.idx, nprune, sizeof(int), cmpint_desc);
+
+    for (i=0; i<nprune; i++)
+        rbuf_remove_kth(&buf->rbuf, vcfrec_t, buf->prune.idx[i], buf->vcf);
+}
+
+static int _rmdup_can_flush(vcfbuf_t *buf, int flush_all)
+{
+    if ( flush_all ) return 1;
+
+    if ( buf->rbuf.n==1 ) return 0;
+
+    int k1 = rbuf_kth(&buf->rbuf, -1);
+    int k2 = rbuf_kth(&buf->rbuf, -2);
+
+    vcfrec_t *rec1 = &buf->vcf[k1];
+    vcfrec_t *rec2 = &buf->vcf[k2];
+
+    if ( rec1->rec->rid!=rec2->rec->rid ) return 1;
+    if ( rec1->rec->pos!=rec2->rec->pos ) return 1;
+
+    return 0;
+}
+
+static int _overlap_can_flush(vcfbuf_t *buf, int flush_all)
+{
+    if ( flush_all ) { buf->overlap.rid = -1; return 1; }
+
+    int i = rbuf_last(&buf->rbuf);
+    vcfrec_t *last = &buf->vcf[i];
+    if ( buf->overlap.rid != last->rec->rid ) buf->overlap.end = 0;
+
+    int beg_pos = last->rec->pos;
+    int end_pos = last->rec->pos + last->rec->rlen - 1;
+
+    // Assuming left-aligned indels. In case it is a deletion, the real variant
+    // starts one base after. If an insertion, the overlap with previous zero length.
+    int imin = last->rec->rlen;
+    for (i=0; i<last->rec->n_allele; i++)
+    {
+        char *ref = last->rec->d.allele[0];
+        char *alt = last->rec->d.allele[i];
+        if ( *alt == '<' ) continue;    // ignore symbolic alleles
+        while ( *ref && *alt && nt_to_upper(*ref)==nt_to_upper(*alt) ) { ref++; alt++; }
+        if ( imin > ref - last->rec->d.allele[0] ) imin = ref - last->rec->d.allele[0];
+    }
+
+    if ( beg_pos <= buf->overlap.end )
+    {
+        beg_pos += imin;
+        if ( beg_pos > end_pos ) end_pos = beg_pos;
+    }
+
+    if ( buf->rbuf.n==1 )
+    {
+        buf->overlap.rid = last->rec->rid;
+        buf->overlap.end = end_pos;
+        return 0;
+    }
+    if ( beg_pos <= buf->overlap.end )
+    {
+        if ( buf->overlap.end < end_pos ) buf->overlap.end = end_pos;
+        return 0;
+    }
+    return 1;
+}
+
+bcf1_t *vcfbuf_flush(vcfbuf_t *buf, int flush_all)
+{
+    int i,j;
+
+    if ( buf->rbuf.n==0 ) return NULL;
+    if ( flush_all || buf->dummy ) goto ret;
+
+    i = rbuf_kth(&buf->rbuf, 0);    // first
+    j = rbuf_last(&buf->rbuf);      // last
+
+    if ( buf->vcf[i].rec->rid != buf->vcf[j].rec->rid ) goto ret;
+    if ( buf->overlap.active && _overlap_can_flush(buf, flush_all) ) goto ret;
+    if ( buf->rmdup.active && _rmdup_can_flush(buf, flush_all) ) goto ret;
+
+    if ( buf->win > 0 )
+    {
+        if ( buf->rbuf.n <= buf->win ) return NULL;
+        goto ret;
+    }
+    else if ( buf->win < 0 )
+    {
+        if ( buf->vcf[i].rec->pos - buf->vcf[j].rec->pos > buf->win ) return NULL;
+        goto ret;
+    }
+    else
+        return NULL;
+
+ret:
+    if ( buf->prune.max_sites && buf->prune.max_sites < buf->rbuf.n ) _prune_sites(buf, flush_all);
+
+    i = rbuf_shift(&buf->rbuf);
+    return buf->vcf[i].rec;
+}
+
+static double _estimate_af(int8_t *ptr, int size, int nvals, int nsamples)
+{
+    int i,j, nref = 0, nalt = 0;
+    for (i=0; i<nsamples; i++)
+    {
+        for (j=0; j<nvals; j++)
+        {
+            if ( ptr[j]==bcf_gt_missing ) break;
+            if ( ptr[j]==bcf_int8_vector_end ) break;
+            if ( bcf_gt_allele(ptr[j]) ) nalt++;
+            else nref++;
+        }
+        ptr += size;
+    }
+    if ( nref+nalt == 0 ) return 0;
+    return (double)nalt/(nref+nalt);
+}
+
+/*
+    The `ld` is set to D approximated as suggested in https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2710162/
+        D =~ (GT correlation) * sqrt(Pa*(1-Pa)*Pb*(1-Pb))
+
+    and `hd` as proposed in Ragsdale, A. P., & Gravel, S. (2019). Unbiased estimation of linkage
+    disequilibrium from unphased data.  Molecular Biology and Evolution. doi:10.1093/molbev/msz265
+
+        \hat{D} = 1/[n*(n+1)]*[
+                             (n1 + n2/2 + n4/2 + n5/4)*(n5/4 + n6/2 + n8/2 + n9)
+                            -(n2/2 + n3 + n5/4 + n6/2)*(n4/2 + n5/4 + n7 + n8/2)
+                        ]
+    where n1,n2,..n9 are counts of RR/RR,RR/RA,..,AA/AA genotypes.
+
+    Returns 0 on success, -1 if the values could not be determined (missing genotypes)
+*/
+static int _calc_r2_ld(vcfbuf_t *buf, bcf1_t *arec, bcf1_t *brec, vcfbuf_ld_t *ld)
+{
+    if ( arec->n_sample!=brec->n_sample ) error("Different number of samples: %d vs %d\n",arec->n_sample,brec->n_sample);
+    assert( arec->n_sample );
+
+    int i,j,igt = bcf_hdr_id2int(buf->hdr, BCF_DT_ID, "GT");
+    bcf_unpack(arec, BCF_UN_FMT);
+    bcf_unpack(brec, BCF_UN_FMT);
+    bcf_fmt_t *afmt = NULL, *bfmt = NULL;
+    for (i=0; i<arec->n_fmt; i++)
+        if ( arec->d.fmt[i].id==igt ) { afmt = &arec->d.fmt[i]; break; }
+    if ( !afmt ) return -1;  // no GT tag
+    for (i=0; i<brec->n_fmt; i++)
+        if ( brec->d.fmt[i].id==igt ) { bfmt = &brec->d.fmt[i]; break; }
+    if ( !bfmt ) return -1;  // no GT tag
+
+    if ( afmt->n==0 ) return -1;   // empty?!
+    if ( bfmt->n==0 ) return -1;   // empty?!
+    if ( afmt->type!=BCF_BT_INT8 ) error("TODO: the GT fmt_type is not int8!\n");
+    if ( bfmt->type!=BCF_BT_INT8 ) error("TODO: the GT fmt_type is not int8!\n");
+
+    // Determine allele frequencies, this is to sample randomly missing genotypes
+    double aaf = 0, baf = 0;
+    if ( buf->ld.rand_missing )
+    {
+        aaf = _estimate_af((int8_t*)afmt->p, afmt->size, afmt->n, arec->n_sample);
+        baf = _estimate_af((int8_t*)bfmt->p, bfmt->size, bfmt->n, brec->n_sample);
+    }
+
+    // Calculate r2, lf, hd
+    double nhd[] = {0,0,0,0,0,0,0,0,0};
+    double ab = 0, aa = 0, bb = 0, a = 0, b = 0;
+    int nab = 0, ndiff = 0;
+    int an_tot = 0, bn_tot = 0;
+    for (i=0; i<arec->n_sample; i++)
+    {
+        int8_t *aptr = (int8_t*) (afmt->p + i*afmt->size);
+        int8_t *bptr = (int8_t*) (bfmt->p + i*bfmt->size);
+        int adsg = 0, bdsg = 0;     // dosages (0,1,2) at sites (a,b)
+        int an = 0, bn = 0;         // number of alleles at sites (a,b)
+        for (j=0; j<afmt->n; j++)
+        {
+            if ( aptr[j]==bcf_int8_vector_end ) break;
+            if ( aptr[j]==bcf_gt_missing )
+            {
+                if ( !buf->ld.rand_missing ) break;
+                if ( hts_drand48() >= aaf ) adsg += 1;
+            }
+            else if ( bcf_gt_allele(aptr[j]) ) adsg += 1;
+            an++;
+        }
+        for (j=0; j<bfmt->n; j++)
+        {
+            if ( bptr[j]==bcf_int8_vector_end ) break;
+            if ( bptr[j]==bcf_gt_missing )
+            {
+                if ( !buf->ld.rand_missing ) break;
+                if ( hts_drand48() >= baf ) bdsg += 1;
+            }
+            else if ( bcf_gt_allele(bptr[j]) ) bdsg += 1;
+            bn++;
+        }
+        if ( an && bn )
+        {
+            an_tot += an;
+            aa += adsg*adsg;
+            a  += adsg;
+
+            bn_tot += bn;
+            bb += bdsg*bdsg;
+            b  += bdsg;
+
+            if ( adsg!=bdsg ) ndiff++;
+            ab += adsg*bdsg;
+            nab++;
+        }
+        if ( an==2 && bn==2 )   // for now only diploid genotypes
+        {
+            assert( adsg<=2 && bdsg<=2 );
+            nhd[ bdsg*3 + adsg ]++;
+        }
+    }
+    if ( !nab ) return -1;  // no data in common for the two sites
+
+    double pa = a/an_tot;
+    double pb = b/bn_tot;
+    double cor;
+    if ( !ndiff ) cor = 1;
+    else
+    {
+        if ( aa == a*a/nab || bb == b*b/nab )     // zero variance, add small noise
+        {
+            aa += 1e-4;
+            bb += 1e-4;
+            ab += 1e-4;
+            a  += 1e-2;
+            b  += 1e-2;
+            nab++;
+        }
+        cor = (ab - a*b/nab) / sqrt(aa - a*a/nab) / sqrt(bb - b*b/nab);
+    }
+
+    ld->val[VCFBUF_LD_IDX_R2] = cor * cor;
+
+    // Lewontin's normalization of D. Also we cap at 1 as the calculation
+    // can result in values bigger than 1 for high AFs.
+    ld->val[VCFBUF_LD_IDX_LD] = cor * sqrt(pa*(1-pa)*pb*(1-pb));
+    double norm;
+    if ( ld->val[VCFBUF_LD_IDX_LD] < 0 )
+        norm = -pa*pb > -(1-pa)*(1-pb) ? -pa*pb : -(1-pa)*(1-pb);
+    else
+        norm = pa*(1-pb) > (1-pa)*pb ? pa*(1-pb) : (1-pa)*pb;
+    if ( norm )
+        ld->val[VCFBUF_LD_IDX_LD] = fabs(norm) > fabs(ld->val[VCFBUF_LD_IDX_LD]) ? ld->val[VCFBUF_LD_IDX_LD]/norm : 1;
+    if ( !ld->val[VCFBUF_LD_IDX_LD] )
+        ld->val[VCFBUF_LD_IDX_LD] = fabs(ld->val[VCFBUF_LD_IDX_LD]);    // avoid "-0" on output
+
+    ld->val[VCFBUF_LD_IDX_HD] =
+        (nhd[0] + nhd[1]/2. + nhd[3]/2. + nhd[4]/4.)*(nhd[4]/4. + nhd[5]/2. + nhd[7]/2. + nhd[8])
+        - (nhd[1]/2. + nhd[2] + nhd[4]/4. + nhd[5]/2.)*(nhd[3]/2. + nhd[4]/4. + nhd[6] + nhd[7]/2.);
+    ld->val[VCFBUF_LD_IDX_HD] /= nab;
+    ld->val[VCFBUF_LD_IDX_HD] /= nab+1;
+
+    return 0;
+}
+
+int vcfbuf_ld(vcfbuf_t *buf, bcf1_t *rec, vcfbuf_ld_t *ld)
+{
+    int ret = -1;
+    if ( !buf->rbuf.n ) return ret;
+
+    int j, i = buf->rbuf.f;
+
+    // Relying on vcfbuf being properly flushed - all sites in the buffer
+    // must come from the same chromosome
+    if ( buf->vcf[i].rec->rid != rec->rid ) return ret;
+
+    vcfbuf_ld_t tmp;
+    for (j=0; j<VCFBUF_LD_N; j++)
+    {
+        ld->val[j] = -HUGE_VAL;
+        ld->rec[j] = NULL;
+    }
+
+    for (i=-1; rbuf_next(&buf->rbuf,&i); )
+    {
+        if ( buf->vcf[i].filter ) continue;
+        if ( _calc_r2_ld(buf, buf->vcf[i].rec, rec, &tmp) < 0 ) continue;   // missing genotypes
+
+        int done = 0;
+        for (j=0; j<VCFBUF_LD_N; j++)
+        {
+            if ( ld->val[j] < tmp.val[j] )
+            {
+                ld->val[j] = tmp.val[j];
+                ld->rec[j] = buf->vcf[i].rec;
+            }
+            if ( buf->ld.max[j] < tmp.val[j] ) done = 1;
+            ret = 0;
+        }
+        if ( done ) return ret;
+    }
+    return ret;
+}
+
+
diff --git a/bcftools/vcfbuf.c.pysam.c b/bcftools/vcfbuf.c.pysam.c
new file mode 100644
index 0000000..7b1c40e
--- /dev/null
+++ b/bcftools/vcfbuf.c.pysam.c
@@ -0,0 +1,564 @@
+#include "bcftools.pysam.h"
+
+/* The MIT License
+
+   Copyright (c) 2016-2022 Genome Research Ltd.
+
+   Author: Petr Danecek <pd3@sanger.ac.uk>
+
+   Permission is hereby granted, free of charge, to any person obtaining a copy
+   of this software and associated documentation files (the "Software"), to deal
+   in the Software without restriction, including without limitation the rights
+   to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+   copies of the Software, and to permit persons to whom the Software is
+   furnished to do so, subject to the following conditions:
+
+   The above copyright notice and this permission notice shall be included in
+   all copies or substantial portions of the Software.
+
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+   IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+   FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+   AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+   LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+   OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+   THE SOFTWARE.
+
+ */
+
+#include <assert.h>
+#include <strings.h>
+#include <htslib/vcf.h>
+#include <htslib/vcfutils.h>
+#include <htslib/hts_os.h>
+#include "bcftools.h"
+#include "vcfbuf.h"
+#include "rbuf.h"
+
+typedef struct
+{
+    double max[VCFBUF_LD_N];
+    int rand_missing, filter1;
+}
+ld_t;
+
+typedef struct
+{
+    bcf1_t *rec;
+    double af;
+    int af_set:1, filter:1, idx:30;
+}
+vcfrec_t;
+
+#define PRUNE_MODE_MAX_AF 1
+#define PRUNE_MODE_1ST    2
+#define PRUNE_MODE_RAND   3
+typedef struct
+{
+    int max_sites, mvrec, mac, mfarr, mode;
+    int *ac, *idx;
+    float *farr;
+    char *af_tag;
+    vcfrec_t **vrec;
+}
+prune_t;
+
+typedef struct
+{
+    int active;
+}
+rmdup_t;
+
+typedef struct
+{
+    int active, rid, end;
+}
+overlap_t;
+
+struct _vcfbuf_t
+{
+    int win, dummy;
+    bcf_hdr_t *hdr;
+    vcfrec_t *vcf;
+    rbuf_t rbuf;
+    ld_t ld;
+    prune_t prune;
+    overlap_t overlap;
+    rmdup_t rmdup;
+};
+
+vcfbuf_t *vcfbuf_init(bcf_hdr_t *hdr, int win)
+{
+    vcfbuf_t *buf = (vcfbuf_t*) calloc(1,sizeof(vcfbuf_t));
+    buf->hdr = hdr;
+    buf->win = win;
+    buf->overlap.rid = -1;
+    int i;
+    for (i=0; i<VCFBUF_LD_N; i++) buf->ld.max[i] = HUGE_VAL;
+    rbuf_init(&buf->rbuf, 0);
+    return buf;
+}
+
+void vcfbuf_destroy(vcfbuf_t *buf)
+{
+    int i;
+    for (i=0; i<buf->rbuf.m; i++)
+        if ( buf->vcf[i].rec ) bcf_destroy(buf->vcf[i].rec);
+    free(buf->vcf);
+    free(buf->prune.farr);
+    free(buf->prune.vrec);
+    free(buf->prune.ac);
+    free(buf->prune.idx);
+    free(buf);
+}
+
+void vcfbuf_set(vcfbuf_t *buf, vcfbuf_opt_t key, void *value)
+{
+    if ( key==LD_FILTER1 ) { buf->ld.filter1 = *((int*)value); return; }
+    if ( key==LD_RAND_MISSING ) { buf->ld.rand_missing = *((int*)value); return; }
+    if ( key==LD_MAX_R2 ) { buf->ld.max[VCFBUF_LD_IDX_R2] = *((double*)value); return; }
+    if ( key==LD_MAX_LD ) { buf->ld.max[VCFBUF_LD_IDX_LD] = *((double*)value); return; }
+    if ( key==LD_MAX_HD ) { buf->ld.max[VCFBUF_LD_IDX_HD] = *((double*)value); return; }
+
+    if ( key==VCFBUF_DUMMY ) { buf->dummy = *((int*)value); return; }
+    if ( key==VCFBUF_NSITES )
+    {
+        buf->prune.max_sites = *((int*)value);
+        if ( !buf->prune.mode ) buf->prune.mode = PRUNE_MODE_MAX_AF;
+        return;
+    }
+    if ( key==VCFBUF_AF_TAG ) { buf->prune.af_tag = *((char**)value); return; }
+    if ( key==VCFBUF_OVERLAP_WIN ) { buf->overlap.active = *((int*)value); return; }
+    if ( key==VCFBUF_RMDUP) { buf->rmdup.active = *((int*)value); return; }
+
+    if ( key==VCFBUF_NSITES_MODE )
+    {
+        char *mode = *((char**)value);
+        if ( !strcasecmp(mode,"maxAF") ) buf->prune.mode = PRUNE_MODE_MAX_AF;
+        else if ( !strcasecmp(mode,"1st") ) buf->prune.mode = PRUNE_MODE_1ST;
+        else if ( !strcasecmp(mode,"rand") ) buf->prune.mode = PRUNE_MODE_RAND;
+        else error("The mode \"%s\" is not recognised\n",mode);
+        return;
+    }
+}
+
+int vcfbuf_nsites(vcfbuf_t *buf)
+{
+    return buf->rbuf.n;
+}
+
+bcf1_t *vcfbuf_push(vcfbuf_t *buf, bcf1_t *rec)
+{
+    rbuf_expand0(&buf->rbuf, vcfrec_t, buf->rbuf.n+1, buf->vcf);
+
+    int i = rbuf_append(&buf->rbuf);
+    if ( !buf->vcf[i].rec ) buf->vcf[i].rec = bcf_init1();
+
+    bcf1_t *ret = buf->vcf[i].rec;
+    buf->vcf[i].rec = rec;
+    buf->vcf[i].af_set = 0;
+    buf->vcf[i].filter = buf->ld.filter1;
+    buf->ld.filter1 = 0;
+
+    return ret;
+}
+
+bcf1_t *vcfbuf_peek(vcfbuf_t *buf, int idx)
+{
+    int i = rbuf_kth(&buf->rbuf, idx);
+    return i<0 ? NULL : buf->vcf[i].rec;
+}
+
+bcf1_t *vcfbuf_remove(vcfbuf_t *buf, int idx)
+{
+    int i = rbuf_kth(&buf->rbuf, idx);
+    if ( i<0 ) return NULL;
+    bcf1_t *rec = buf->vcf[i].rec;
+	rbuf_remove_kth(&buf->rbuf, vcfrec_t, idx, buf->vcf);
+    return rec;
+}
+
+static int cmpvrec(const void *_a, const void *_b)
+{
+    vcfrec_t *a = *((vcfrec_t**) _a);
+    vcfrec_t *b = *((vcfrec_t**) _b);
+    if ( a->af < b->af ) return -1;
+    if ( a->af == b->af ) return 0;
+    return 1;
+}
+static int cmpint_desc(const void *_a, const void *_b)
+{
+    int a = *((int*)_a);
+    int b = *((int*)_b);
+    if ( a < b ) return 1;
+    if ( a == b ) return 0;
+    return -1;
+}
+
+static void _prune_sites(vcfbuf_t *buf, int flush_all)
+{
+    int nbuf = flush_all ? buf->rbuf.n : buf->rbuf.n - 1;
+
+    int nprune = nbuf - buf->prune.max_sites;
+    int i,k,irec = 0;
+    if ( buf->prune.mode==PRUNE_MODE_1ST )
+    {
+        int eoff = flush_all ? 1 : 2;
+        for (i=0; i<nprune; i++)
+            rbuf_remove_kth(&buf->rbuf, vcfrec_t, buf->rbuf.n - eoff, buf->vcf);
+        return;
+    }
+    if ( buf->prune.mode==PRUNE_MODE_RAND )
+    {
+        int eoff = flush_all ? 0 : 1;
+        for (i=0; i<nprune; i++)
+        {
+            int j = (buf->rbuf.n - eoff) * hts_drand48();
+            rbuf_remove_kth(&buf->rbuf, vcfrec_t, j, buf->vcf);
+        }
+        return;
+    }
+
+    if ( nbuf > buf->prune.mvrec )
+    {
+        buf->prune.idx   = (int*) realloc(buf->prune.idx, nbuf*sizeof(int));
+        buf->prune.vrec  = (vcfrec_t**) realloc(buf->prune.vrec, nbuf*sizeof(vcfrec_t*));
+        buf->prune.mvrec = nbuf;
+    }
+
+    // set allele frequency and prepare buffer for sorting
+    for (i=-1; rbuf_next(&buf->rbuf,&i) && irec<nbuf; )
+    {
+        bcf1_t *line = buf->vcf[i].rec;
+        if ( line->n_allele > buf->prune.mac )
+        {
+            buf->prune.ac = (int*) realloc(buf->prune.ac, line->n_allele*sizeof(*buf->prune.ac));
+            buf->prune.mac = line->n_allele;
+        }
+        if ( !buf->vcf[i].af_set )
+        {
+            buf->vcf[i].af = 0;
+            if ( buf->prune.af_tag )
+            {
+                if ( bcf_get_info_float(buf->hdr,line,buf->prune.af_tag,&buf->prune.farr, &buf->prune.mfarr) > 0 ) buf->vcf[i].af = buf->prune.farr[0];
+            }
+            else if ( bcf_calc_ac(buf->hdr, line, buf->prune.ac, BCF_UN_INFO|BCF_UN_FMT) )
+            {
+                int ntot = buf->prune.ac[0], nalt = 0;
+                for (k=1; k<line->n_allele; k++) nalt += buf->prune.ac[k];
+                buf->vcf[i].af = ntot ? (float)nalt/ntot : 0;
+            }
+            buf->vcf[i].af_set = 1;
+        }
+        buf->vcf[i].idx = irec;
+        buf->prune.vrec[irec++] = &buf->vcf[i];
+    }
+
+    // sort by allele frequency, low AF will be removed preferentially
+    qsort(buf->prune.vrec, nbuf, sizeof(*buf->prune.vrec), cmpvrec);
+
+    // sort the rbuf indexes to be pruned descendently so that j-th rbuf index
+    // is removed before i-th index if i<j
+    for (i=0; i<nprune; i++)
+        buf->prune.idx[i] = buf->prune.vrec[i]->idx;
+
+    qsort(buf->prune.idx, nprune, sizeof(int), cmpint_desc);
+
+    for (i=0; i<nprune; i++)
+        rbuf_remove_kth(&buf->rbuf, vcfrec_t, buf->prune.idx[i], buf->vcf);
+}
+
+static int _rmdup_can_flush(vcfbuf_t *buf, int flush_all)
+{
+    if ( flush_all ) return 1;
+
+    if ( buf->rbuf.n==1 ) return 0;
+
+    int k1 = rbuf_kth(&buf->rbuf, -1);
+    int k2 = rbuf_kth(&buf->rbuf, -2);
+
+    vcfrec_t *rec1 = &buf->vcf[k1];
+    vcfrec_t *rec2 = &buf->vcf[k2];
+
+    if ( rec1->rec->rid!=rec2->rec->rid ) return 1;
+    if ( rec1->rec->pos!=rec2->rec->pos ) return 1;
+
+    return 0;
+}
+
+static int _overlap_can_flush(vcfbuf_t *buf, int flush_all)
+{
+    if ( flush_all ) { buf->overlap.rid = -1; return 1; }
+
+    int i = rbuf_last(&buf->rbuf);
+    vcfrec_t *last = &buf->vcf[i];
+    if ( buf->overlap.rid != last->rec->rid ) buf->overlap.end = 0;
+
+    int beg_pos = last->rec->pos;
+    int end_pos = last->rec->pos + last->rec->rlen - 1;
+
+    // Assuming left-aligned indels. In case it is a deletion, the real variant
+    // starts one base after. If an insertion, the overlap with previous zero length.
+    int imin = last->rec->rlen;
+    for (i=0; i<last->rec->n_allele; i++)
+    {
+        char *ref = last->rec->d.allele[0];
+        char *alt = last->rec->d.allele[i];
+        if ( *alt == '<' ) continue;    // ignore symbolic alleles
+        while ( *ref && *alt && nt_to_upper(*ref)==nt_to_upper(*alt) ) { ref++; alt++; }
+        if ( imin > ref - last->rec->d.allele[0] ) imin = ref - last->rec->d.allele[0];
+    }
+
+    if ( beg_pos <= buf->overlap.end )
+    {
+        beg_pos += imin;
+        if ( beg_pos > end_pos ) end_pos = beg_pos;
+    }
+
+    if ( buf->rbuf.n==1 )
+    {
+        buf->overlap.rid = last->rec->rid;
+        buf->overlap.end = end_pos;
+        return 0;
+    }
+    if ( beg_pos <= buf->overlap.end )
+    {
+        if ( buf->overlap.end < end_pos ) buf->overlap.end = end_pos;
+        return 0;
+    }
+    return 1;
+}
+
+bcf1_t *vcfbuf_flush(vcfbuf_t *buf, int flush_all)
+{
+    int i,j;
+
+    if ( buf->rbuf.n==0 ) return NULL;
+    if ( flush_all || buf->dummy ) goto ret;
+
+    i = rbuf_kth(&buf->rbuf, 0);    // first
+    j = rbuf_last(&buf->rbuf);      // last
+
+    if ( buf->vcf[i].rec->rid != buf->vcf[j].rec->rid ) goto ret;
+    if ( buf->overlap.active && _overlap_can_flush(buf, flush_all) ) goto ret;
+    if ( buf->rmdup.active && _rmdup_can_flush(buf, flush_all) ) goto ret;
+
+    if ( buf->win > 0 )
+    {
+        if ( buf->rbuf.n <= buf->win ) return NULL;
+        goto ret;
+    }
+    else if ( buf->win < 0 )
+    {
+        if ( buf->vcf[i].rec->pos - buf->vcf[j].rec->pos > buf->win ) return NULL;
+        goto ret;
+    }
+    else
+        return NULL;
+
+ret:
+    if ( buf->prune.max_sites && buf->prune.max_sites < buf->rbuf.n ) _prune_sites(buf, flush_all);
+
+    i = rbuf_shift(&buf->rbuf);
+    return buf->vcf[i].rec;
+}
+
+static double _estimate_af(int8_t *ptr, int size, int nvals, int nsamples)
+{
+    int i,j, nref = 0, nalt = 0;
+    for (i=0; i<nsamples; i++)
+    {
+        for (j=0; j<nvals; j++)
+        {
+            if ( ptr[j]==bcf_gt_missing ) break;
+            if ( ptr[j]==bcf_int8_vector_end ) break;
+            if ( bcf_gt_allele(ptr[j]) ) nalt++;
+            else nref++;
+        }
+        ptr += size;
+    }
+    if ( nref+nalt == 0 ) return 0;
+    return (double)nalt/(nref+nalt);
+}
+
+/*
+    The `ld` is set to D approximated as suggested in https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2710162/
+        D =~ (GT correlation) * sqrt(Pa*(1-Pa)*Pb*(1-Pb))
+
+    and `hd` as proposed in Ragsdale, A. P., & Gravel, S. (2019). Unbiased estimation of linkage
+    disequilibrium from unphased data.  Molecular Biology and Evolution. doi:10.1093/molbev/msz265
+
+        \hat{D} = 1/[n*(n+1)]*[
+                             (n1 + n2/2 + n4/2 + n5/4)*(n5/4 + n6/2 + n8/2 + n9)
+                            -(n2/2 + n3 + n5/4 + n6/2)*(n4/2 + n5/4 + n7 + n8/2)
+                        ]
+    where n1,n2,..n9 are counts of RR/RR,RR/RA,..,AA/AA genotypes.
+
+    Returns 0 on success, -1 if the values could not be determined (missing genotypes)
+*/
+static int _calc_r2_ld(vcfbuf_t *buf, bcf1_t *arec, bcf1_t *brec, vcfbuf_ld_t *ld)
+{
+    if ( arec->n_sample!=brec->n_sample ) error("Different number of samples: %d vs %d\n",arec->n_sample,brec->n_sample);
+    assert( arec->n_sample );
+
+    int i,j,igt = bcf_hdr_id2int(buf->hdr, BCF_DT_ID, "GT");
+    bcf_unpack(arec, BCF_UN_FMT);
+    bcf_unpack(brec, BCF_UN_FMT);
+    bcf_fmt_t *afmt = NULL, *bfmt = NULL;
+    for (i=0; i<arec->n_fmt; i++)
+        if ( arec->d.fmt[i].id==igt ) { afmt = &arec->d.fmt[i]; break; }
+    if ( !afmt ) return -1;  // no GT tag
+    for (i=0; i<brec->n_fmt; i++)
+        if ( brec->d.fmt[i].id==igt ) { bfmt = &brec->d.fmt[i]; break; }
+    if ( !bfmt ) return -1;  // no GT tag
+
+    if ( afmt->n==0 ) return -1;   // empty?!
+    if ( bfmt->n==0 ) return -1;   // empty?!
+    if ( afmt->type!=BCF_BT_INT8 ) error("TODO: the GT fmt_type is not int8!\n");
+    if ( bfmt->type!=BCF_BT_INT8 ) error("TODO: the GT fmt_type is not int8!\n");
+
+    // Determine allele frequencies, this is to sample randomly missing genotypes
+    double aaf = 0, baf = 0;
+    if ( buf->ld.rand_missing )
+    {
+        aaf = _estimate_af((int8_t*)afmt->p, afmt->size, afmt->n, arec->n_sample);
+        baf = _estimate_af((int8_t*)bfmt->p, bfmt->size, bfmt->n, brec->n_sample);
+    }
+
+    // Calculate r2, lf, hd
+    double nhd[] = {0,0,0,0,0,0,0,0,0};
+    double ab = 0, aa = 0, bb = 0, a = 0, b = 0;
+    int nab = 0, ndiff = 0;
+    int an_tot = 0, bn_tot = 0;
+    for (i=0; i<arec->n_sample; i++)
+    {
+        int8_t *aptr = (int8_t*) (afmt->p + i*afmt->size);
+        int8_t *bptr = (int8_t*) (bfmt->p + i*bfmt->size);
+        int adsg = 0, bdsg = 0;     // dosages (0,1,2) at sites (a,b)
+        int an = 0, bn = 0;         // number of alleles at sites (a,b)
+        for (j=0; j<afmt->n; j++)
+        {
+            if ( aptr[j]==bcf_int8_vector_end ) break;
+            if ( aptr[j]==bcf_gt_missing )
+            {
+                if ( !buf->ld.rand_missing ) break;
+                if ( hts_drand48() >= aaf ) adsg += 1;
+            }
+            else if ( bcf_gt_allele(aptr[j]) ) adsg += 1;
+            an++;
+        }
+        for (j=0; j<bfmt->n; j++)
+        {
+            if ( bptr[j]==bcf_int8_vector_end ) break;
+            if ( bptr[j]==bcf_gt_missing )
+            {
+                if ( !buf->ld.rand_missing ) break;
+                if ( hts_drand48() >= baf ) bdsg += 1;
+            }
+            else if ( bcf_gt_allele(bptr[j]) ) bdsg += 1;
+            bn++;
+        }
+        if ( an && bn )
+        {
+            an_tot += an;
+            aa += adsg*adsg;
+            a  += adsg;
+
+            bn_tot += bn;
+            bb += bdsg*bdsg;
+            b  += bdsg;
+
+            if ( adsg!=bdsg ) ndiff++;
+            ab += adsg*bdsg;
+            nab++;
+        }
+        if ( an==2 && bn==2 )   // for now only diploid genotypes
+        {
+            assert( adsg<=2 && bdsg<=2 );
+            nhd[ bdsg*3 + adsg ]++;
+        }
+    }
+    if ( !nab ) return -1;  // no data in common for the two sites
+
+    double pa = a/an_tot;
+    double pb = b/bn_tot;
+    double cor;
+    if ( !ndiff ) cor = 1;
+    else
+    {
+        if ( aa == a*a/nab || bb == b*b/nab )     // zero variance, add small noise
+        {
+            aa += 1e-4;
+            bb += 1e-4;
+            ab += 1e-4;
+            a  += 1e-2;
+            b  += 1e-2;
+            nab++;
+        }
+        cor = (ab - a*b/nab) / sqrt(aa - a*a/nab) / sqrt(bb - b*b/nab);
+    }
+
+    ld->val[VCFBUF_LD_IDX_R2] = cor * cor;
+
+    // Lewontin's normalization of D. Also we cap at 1 as the calculation
+    // can result in values bigger than 1 for high AFs.
+    ld->val[VCFBUF_LD_IDX_LD] = cor * sqrt(pa*(1-pa)*pb*(1-pb));
+    double norm;
+    if ( ld->val[VCFBUF_LD_IDX_LD] < 0 )
+        norm = -pa*pb > -(1-pa)*(1-pb) ? -pa*pb : -(1-pa)*(1-pb);
+    else
+        norm = pa*(1-pb) > (1-pa)*pb ? pa*(1-pb) : (1-pa)*pb;
+    if ( norm )
+        ld->val[VCFBUF_LD_IDX_LD] = fabs(norm) > fabs(ld->val[VCFBUF_LD_IDX_LD]) ? ld->val[VCFBUF_LD_IDX_LD]/norm : 1;
+    if ( !ld->val[VCFBUF_LD_IDX_LD] )
+        ld->val[VCFBUF_LD_IDX_LD] = fabs(ld->val[VCFBUF_LD_IDX_LD]);    // avoid "-0" on output
+
+    ld->val[VCFBUF_LD_IDX_HD] =
+        (nhd[0] + nhd[1]/2. + nhd[3]/2. + nhd[4]/4.)*(nhd[4]/4. + nhd[5]/2. + nhd[7]/2. + nhd[8])
+        - (nhd[1]/2. + nhd[2] + nhd[4]/4. + nhd[5]/2.)*(nhd[3]/2. + nhd[4]/4. + nhd[6] + nhd[7]/2.);
+    ld->val[VCFBUF_LD_IDX_HD] /= nab;
+    ld->val[VCFBUF_LD_IDX_HD] /= nab+1;
+
+    return 0;
+}
+
+int vcfbuf_ld(vcfbuf_t *buf, bcf1_t *rec, vcfbuf_ld_t *ld)
+{
+    int ret = -1;
+    if ( !buf->rbuf.n ) return ret;
+
+    int j, i = buf->rbuf.f;
+
+    // Relying on vcfbuf being properly flushed - all sites in the buffer
+    // must come from the same chromosome
+    if ( buf->vcf[i].rec->rid != rec->rid ) return ret;
+
+    vcfbuf_ld_t tmp;
+    for (j=0; j<VCFBUF_LD_N; j++)
+    {
+        ld->val[j] = -HUGE_VAL;
+        ld->rec[j] = NULL;
+    }
+
+    for (i=-1; rbuf_next(&buf->rbuf,&i); )
+    {
+        if ( buf->vcf[i].filter ) continue;
+        if ( _calc_r2_ld(buf, buf->vcf[i].rec, rec, &tmp) < 0 ) continue;   // missing genotypes
+
+        int done = 0;
+        for (j=0; j<VCFBUF_LD_N; j++)
+        {
+            if ( ld->val[j] < tmp.val[j] )
+            {
+                ld->val[j] = tmp.val[j];
+                ld->rec[j] = buf->vcf[i].rec;
+            }
+            if ( buf->ld.max[j] < tmp.val[j] ) done = 1;
+            ret = 0;
+        }
+        if ( done ) return ret;
+    }
+    return ret;
+}
+
+
diff --git a/bcftools/vcfbuf.h b/bcftools/vcfbuf.h
new file mode 100644
index 0000000..878fd10
--- /dev/null
+++ b/bcftools/vcfbuf.h
@@ -0,0 +1,122 @@
+/* The MIT License
+
+   Copyright (c) 2017-2022 Genome Research Ltd.
+
+   Author: Petr Danecek <pd3@sanger.ac.uk>
+
+   Permission is hereby granted, free of charge, to any person obtaining a copy
+   of this software and associated documentation files (the "Software"), to deal
+   in the Software without restriction, including without limitation the rights
+   to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+   copies of the Software, and to permit persons to whom the Software is
+   furnished to do so, subject to the following conditions:
+
+   The above copyright notice and this permission notice shall be included in
+   all copies or substantial portions of the Software.
+
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+   IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+   FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+   AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+   LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+   OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+   THE SOFTWARE.
+
+ */
+
+/*
+    Buffer VCF records and perform operations on the buffer
+*/
+
+#ifndef __VCFBUF_H__
+#define __VCFBUF_H__
+
+#include <htslib/vcf.h>
+
+typedef struct _vcfbuf_t vcfbuf_t;
+
+// Modes of operation
+typedef enum
+{
+    VCFBUF_DUMMY,           // the caller maintains the buffer via push/peek/flush, nothing is removed by vcfbuf
+
+    VCFBUF_OVERLAP_WIN,     // keep only overlapping variants in the window
+    VCFBUF_RMDUP,           // remove duplicate sites (completely)
+    VCFBUF_NSITES,          // leave at max this many sites in the window
+    VCFBUF_NSITES_MODE,     // one of: maxAF (keep sites with max AF), 1st (sites that come first), rand (pick randomly)
+    VCFBUF_AF_TAG,          // use this INFO tag with VCFBUF_NSITES
+
+    // LD related options
+    LD_RAND_MISSING,        // randomize rather than ignore missing genotypes
+    LD_FILTER1,             // exclude the next record inserted by vcfbuf_push() from LD analysis
+    LD_MAX_R2,              // If set, vcfbuf_ld() will stop at the first record that exceeds the R2,
+    LD_MAX_LD,              //      LD, or HD threshold. When multiple are set, the OR logic is applied
+    LD_MAX_HD,              //
+}
+vcfbuf_opt_t;
+
+#define vcfbuf_set_opt(buf,type,key,value) { type tmp = value; vcfbuf_set(buf, key, (void*)&tmp); }
+void vcfbuf_set(vcfbuf_t *buf, vcfbuf_opt_t key, void *value);
+
+
+/*
+ *  vcfbuf_init() - init buffer
+ *  @win:   number of sites (>0), bp (<0)
+ */
+vcfbuf_t *vcfbuf_init(bcf_hdr_t *hdr, int win);
+void vcfbuf_destroy(vcfbuf_t *buf);
+
+/*
+ *  vcfbuf_push() - push a new site for analysis
+ */
+bcf1_t *vcfbuf_push(vcfbuf_t *buf, bcf1_t *rec);
+
+/*
+ *  vcfbuf_peek() - return pointer to i-th record in the buffer but do not remove it from the buffer
+ *  @idx:  0-based index to buffered lines
+ */
+bcf1_t *vcfbuf_peek(vcfbuf_t *buf, int idx);
+
+/*
+ *  vcfbuf_remove() - return pointer to i-th record in the buffer and remove it from the buffer
+ *  @idx:  0-based index to buffered lines
+ */
+bcf1_t *vcfbuf_remove(vcfbuf_t *buf, int idx);
+
+/*
+ *  vcfbuf_flush() - returns the next record or NULL, depending on the mode of operation and
+ *      the content of the buffer
+ */
+bcf1_t *vcfbuf_flush(vcfbuf_t *buf, int flush_all);
+
+/*
+ *  vcfbuf_nsites() - return the number of sites in the buffer
+ */
+int vcfbuf_nsites(vcfbuf_t *buf);
+
+/*
+ *  vcfbuf_ld() - find records with maximum LD values or the values in first record that exceeds thresholds
+ *                set by vcfbuf_set_opt(..,LD_MAX*,..)
+ *
+ *  Returns 0 on success or -1 if no values were filled.
+ *
+ *  @val:  will be filled with the values
+ *          .. correlation coefficient r-squared
+ *          .. Lewontin's D' (PMID: 19433632)
+ *          .. Ragsdale's \hat{D} (doi:10.1093/molbev/msz265)
+ *  @rec: corresponding positions or NULL if the value(s) has not been set
+ */
+#define VCFBUF_LD_N 3
+#define VCFBUF_LD_IDX_R2 0
+#define VCFBUF_LD_IDX_LD 1
+#define VCFBUF_LD_IDX_HD 2
+typedef struct
+{
+    double val[VCFBUF_LD_N];    // r2, ld, hd
+    bcf1_t *rec[VCFBUF_LD_N];   // record with max r2, ld, hd
+}
+vcfbuf_ld_t;
+int vcfbuf_ld(vcfbuf_t *buf, bcf1_t *rec, vcfbuf_ld_t *ld);
+
+#endif
+
diff --git a/bcftools/vcfcall.c b/bcftools/vcfcall.c
new file mode 100644
index 0000000..4c9e88c
--- /dev/null
+++ b/bcftools/vcfcall.c
@@ -0,0 +1,1179 @@
+/*  vcfcall.c -- SNP/indel variant calling from VCF/BCF.
+
+    Copyright (C) 2013-2022 Genome Research Ltd.
+
+    Author: Petr Danecek <pd3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.  */
+
+#include <stdarg.h>
+#include <string.h>
+#include <strings.h>
+#include <assert.h>
+#include <errno.h>
+#include <unistd.h>
+#include <getopt.h>
+#include <math.h>
+#include <htslib/vcf.h>
+#include <time.h>
+#include <stdarg.h>
+#include <htslib/kfunc.h>
+#include <htslib/synced_bcf_reader.h>
+#include <htslib/khash_str2int.h>
+#include <ctype.h>
+#include "bcftools.h"
+#include "call.h"
+#include "prob1.h"
+#include "ploidy.h"
+#include "gvcf.h"
+#include "regidx.h"
+#include "vcfbuf.h"
+
+void error(const char *format, ...);
+
+#define CF_NO_GENO      1
+#define CF_INS_MISSED   (1<<1)
+#define CF_CCALL        (1<<2)
+//                      (1<<3)
+//                      (1<<4)
+//                      (1<<5)
+#define CF_ACGT_ONLY    (1<<6)
+#define CF_QCALL        (1<<7)
+#define CF_ADJLD        (1<<8)
+#define CF_NO_INDEL     (1<<9)
+#define CF_ANNO_MAX     (1<<10)
+#define CF_MCALL        (1<<11)
+#define CF_PAIRCALL     (1<<12)
+#define CF_QCNT         (1<<13)
+#define CF_INDEL_ONLY   (1<<14)
+
+typedef struct
+{
+    tgt_als_t *als;
+    int nmatch_als, ibuf;
+}
+rec_tgt_t;
+
+typedef struct
+{
+    int flag;   // combination of CF_* flags above
+    int output_type, n_threads, record_cmd_line, clevel;
+    htsFile *bcf_in, *out_fh;
+    char *bcf_fname, *output_fname;
+    char **samples;             // for subsampling and ploidy
+    int nsamples, *samples_map; // mapping from output sample names to original VCF
+    char *regions, *targets;    // regions to process
+    int regions_is_file, targets_is_file, regions_overlap;
+    regidx_t *tgt_idx;
+    regitr_t *tgt_itr, *tgt_itr_prev, *tgt_itr_tmp;
+    vcfbuf_t *vcfbuf;
+
+    char *samples_fname;
+    int samples_is_file;
+    int *sample2sex;    // mapping for ploidy. If negative, interpreted as -1*ploidy
+    int *sex2ploidy, *sex2ploidy_prev, nsex;
+    ploidy_t *ploidy;
+    gvcf_t *gvcf;
+
+    bcf1_t *missed_line;
+    call_t aux;     // parameters and temporary data
+    kstring_t str;
+
+    int argc;
+    char **argv;
+
+    //  int flag, prior_type, n1, n_sub, *sublist, n_perm;
+    //  uint32_t *trio_aux;
+    //  char *prior_file, **subsam;
+    //  uint8_t *ploidy;
+    //  double theta, pref, indel_frac, min_smpl_frac, min_lrt;
+    // Permutation tests
+    //  int n_perm, *seeds;
+    //  double min_perm_p;
+    //  void *bed;
+}
+args_t;
+
+static char **add_sample(void *name2idx, char **lines, int *nlines, int *mlines, char *name, char sex, int *ith)
+{
+    int ret = khash_str2int_get(name2idx, name, ith);
+    if ( ret==0 ) return lines;
+
+    hts_expand(char*,(*nlines+1),*mlines,lines);
+    int len = strlen(name);
+    lines[*nlines] = (char*) malloc(len+3);
+    memcpy(lines[*nlines],name,len);
+    lines[*nlines][len]   = ' ';
+    lines[*nlines][len+1] = sex;
+    lines[*nlines][len+2] = 0;
+    *ith = *nlines;
+    (*nlines)++;
+    khash_str2int_set(name2idx, strdup(name), *ith);
+    return lines;
+}
+
+typedef struct
+{
+    const char *alias, *about, *ploidy;
+}
+ploidy_predef_t;
+
+static ploidy_predef_t ploidy_predefs[] =
+{
+    { .alias  = "GRCh37",
+      .about  = "Human Genome reference assembly GRCh37 / hg19",
+      .ploidy =
+          "X 1 60000 M 1\n"
+          "X 2699521 154931043 M 1\n"
+          "Y 1 59373566 M 1\n"
+          "Y 1 59373566 F 0\n"
+          "MT 1 16569 M 1\n"
+          "MT 1 16569 F 1\n"
+          "chrX 1 60000 M 1\n"
+          "chrX 2699521 154931043 M 1\n"
+          "chrY 1 59373566 M 1\n"
+          "chrY 1 59373566 F 0\n"
+          "chrM 1 16569 M 1\n"
+          "chrM 1 16569 F 1\n"
+          "*  * *     M 2\n"
+          "*  * *     F 2\n"
+    },
+    { .alias  = "GRCh38",
+      .about  = "Human Genome reference assembly GRCh38 / hg38",
+      .ploidy =
+          "X 1 9999 M 1\n"
+          "X 2781480 155701381 M 1\n"
+          "Y 1 57227415 M 1\n"
+          "Y 1 57227415 F 0\n"
+          "MT 1 16569 M 1\n"
+          "MT 1 16569 F 1\n"
+          "chrX 1 9999 M 1\n"
+          "chrX 2781480 155701381 M 1\n"
+          "chrY 1 57227415 M 1\n"
+          "chrY 1 57227415 F 0\n"
+          "chrM 1 16569 M 1\n"
+          "chrM 1 16569 F 1\n"
+          "*  * *     M 2\n"
+          "*  * *     F 2\n"
+    },
+    { .alias  = "X",
+      .about  = "Treat male samples as haploid and female as diploid regardless of the chromosome name",
+      .ploidy =
+          "*  * *     M 1\n"
+          "*  * *     F 2\n"
+    },
+    { .alias  = "Y",
+      .about  = "Treat male samples as haploid and female as no-copy, regardless of the chromosome name",
+      .ploidy =
+          "*  * *     M 1\n"
+          "*  * *     F 0\n"
+    },
+    { .alias  = "1",
+      .about  = "Treat all samples as haploid",
+      .ploidy =
+          "*  * *     * 1\n"
+    },
+    { .alias  = "2",
+      .about  = "Treat all samples as diploid",
+      .ploidy =
+          "*  * *     * 2\n"
+    },
+    {
+        .alias  = NULL,
+        .about  = NULL,
+        .ploidy = NULL,
+    }
+};
+
+// only 5 columns are required and the first is ignored:
+//  ignored,sample,father(or 0),mother(or 0),sex(1=M,2=F)
+static char **parse_ped_samples(call_t *call, char **vals, int nvals, int *nsmpl)
+{
+    int i, j, mlines = 0, nlines = 0;
+    kstring_t str = {0,0,0}, fam_str = {0,0,0};
+    void *name2idx = khash_str2int_init();
+    char **lines = NULL;
+    for (i=0; i<nvals; i++)
+    {
+        str.l = 0;
+        kputs(vals[i], &str);
+        char *col_ends[5], *tmp = str.s;
+        j = 0;
+        while ( *tmp && j<5 )
+        {
+            if ( isspace(*tmp) )
+            {
+                *tmp = 0;
+                ++tmp;
+                while ( isspace(*tmp) ) tmp++;  // allow multiple spaces
+                col_ends[j] = tmp-1;
+                j++;
+                continue;
+            }
+            tmp++;
+        }
+        if ( j<4 ) break;
+
+        char sex;
+        if ( col_ends[3][1]=='1' ) sex = 'M';
+        else if ( col_ends[3][1]=='2' ) sex = 'F';
+        else break;
+
+        lines = add_sample(name2idx, lines, &nlines, &mlines, col_ends[0]+1, sex, &j);
+        if ( strcmp(col_ends[1]+1,"0") && strcmp(col_ends[2]+1,"0") )   // father and mother
+        {
+            call->nfams++;
+            hts_expand(family_t, call->nfams, call->mfams, call->fams);
+            family_t *fam = &call->fams[call->nfams-1];
+            fam_str.l = 0;
+            ksprintf(&fam_str,"father=%s, mother=%s, child=%s", col_ends[1]+1,col_ends[2]+1,col_ends[0]+1);
+            fam->name = strdup(fam_str.s);
+
+            if ( !khash_str2int_has_key(name2idx, col_ends[1]+1) )
+                lines = add_sample(name2idx, lines, &nlines, &mlines, col_ends[1]+1, 'M', &fam->sample[FATHER]);
+            if ( !khash_str2int_has_key(name2idx, col_ends[2]+1) )
+                lines = add_sample(name2idx, lines, &nlines, &mlines, col_ends[2]+1, 'F', &fam->sample[MOTHER]);
+
+            khash_str2int_get(name2idx, col_ends[0]+1, &fam->sample[CHILD]);
+            khash_str2int_get(name2idx, col_ends[1]+1, &fam->sample[FATHER]);
+            khash_str2int_get(name2idx, col_ends[2]+1, &fam->sample[MOTHER]);
+        }
+    }
+    free(str.s);
+    free(fam_str.s);
+    khash_str2int_destroy_free(name2idx);
+
+    if ( i!=nvals ) return NULL; // not a ped file
+
+    *nsmpl = nlines;
+    return lines;
+}
+
+
+/*
+ *  Reads sample names and their ploidy (optional) from a file.
+ *  Alternatively, if no such file exists, the file name is interpreted
+ *  as a comma-separated list of samples. When ploidy is not present,
+ *  the default ploidy 2 is assumed.
+ */
+static void set_samples(args_t *args, const char *fn, int is_file)
+{
+    int i, nlines;
+    char **lines = hts_readlist(fn, is_file, &nlines);
+    if ( !lines ) error("Could not read the file: %s\n", fn);
+
+    int nsmpls;
+    char **smpls = parse_ped_samples(&args->aux, lines, nlines, &nsmpls);
+    if ( smpls )
+    {
+        for (i=0; i<nlines; i++) free(lines[i]);
+        free(lines);
+        lines = smpls;
+        nlines = nsmpls;
+    }
+    else if ( is_file )
+        fprintf(stderr,"Note: could not parse as PED: %s\n",fn);
+
+    args->samples_map = (int*) malloc(sizeof(int)*bcf_hdr_nsamples(args->aux.hdr)); // for subsetting
+    args->sample2sex  = (int*) malloc(sizeof(int)*bcf_hdr_nsamples(args->aux.hdr));
+    int dflt_sex_id = ploidy_nsex(args->ploidy) - 1;
+    for (i=0; i<bcf_hdr_nsamples(args->aux.hdr); i++) args->sample2sex[i] = dflt_sex_id;
+
+    int *old2new = (int*) malloc(sizeof(int)*bcf_hdr_nsamples(args->aux.hdr));
+    for (i=0; i<bcf_hdr_nsamples(args->aux.hdr); i++) old2new[i] = -1;
+
+    int nsmpl = 0, map_needed = 0;
+    for (i=0; i<nlines; i++)
+    {
+        char *ss = lines[i];
+        while ( *ss && isspace(*ss) ) ss++;
+        if ( !*ss ) error("Could not parse: %s\n", lines[i]);
+        if ( *ss=='#' ) continue;
+        char *se = ss;
+        while ( *se && !isspace(*se) ) se++;
+        char x = *se, *xptr = se; *se = 0;
+
+        int ismpl = bcf_hdr_id2int(args->aux.hdr, BCF_DT_SAMPLE, ss);
+        if ( ismpl < 0 ) { fprintf(stderr,"Warning: No such sample in the VCF: %s\n",ss); continue; }
+        if ( old2new[ismpl] != -1 ) { fprintf(stderr,"Warning: The sample is listed multiple times: %s\n",ss); continue; }
+
+        ss = se+(x != '\0');
+        while ( *ss && isspace(*ss) ) ss++;
+        if ( !*ss ) ss = "2";   // default ploidy
+        se = ss;
+        while ( *se && !isspace(*se) ) se++;
+        if ( se==ss ) { *xptr = x; error("Could not parse: \"%s\"\n", lines[i]); }
+
+        if ( ss[1]==0 && (ss[0]=='0' || ss[0]=='1' || ss[0]=='2') )
+            args->sample2sex[nsmpl] = -1*(ss[0]-'0');
+        else
+            args->sample2sex[nsmpl] = ploidy_add_sex(args->ploidy, ss);
+
+        if ( ismpl!=nsmpl ) map_needed = 1;
+        args->samples_map[nsmpl] = ismpl;
+        old2new[ismpl] = nsmpl;
+        nsmpl++;
+    }
+
+    for (i=0; i<args->aux.nfams; i++)
+    {
+        int j, nmiss = 0;
+        family_t *fam = &args->aux.fams[i];
+        for (j=0; j<3; j++)
+        {
+            fam->sample[i] = old2new[fam->sample[i]];
+            if ( fam->sample[i]<0 ) nmiss++;
+        }
+        assert( nmiss==0 || nmiss==3 );
+    }
+    free(old2new);
+
+    if ( !map_needed ) { free(args->samples_map); args->samples_map = NULL; }
+
+    args->nsamples = nsmpl;
+    args->samples = lines;
+}
+
+static void init_missed_line(args_t *args)
+{
+    int i;
+    for (i=0; i<bcf_hdr_nsamples(args->aux.hdr); i++)
+    {
+        args->aux.gts[i*2]   = bcf_gt_missing;
+        args->aux.gts[i*2+1] = bcf_int32_vector_end;
+    }
+    args->missed_line = bcf_init1();
+    bcf_update_genotypes(args->aux.hdr, args->missed_line, args->aux.gts, 2*bcf_hdr_nsamples(args->aux.hdr));
+    bcf_float_set_missing(args->missed_line->qual);
+}
+
+static int tgt_parse(const char *line, char **chr_beg, char **chr_end, uint32_t *beg, uint32_t *end, void *payload, void *usr)
+{
+    char *ss = (char*) line;
+    while ( *ss && isspace(*ss) ) ss++;
+    if ( !*ss ) { fprintf(stderr,"Could not parse the line: %s\n", line); return -2; }
+    if ( *ss=='#' ) return -1;  // skip comments
+
+    char *se = ss;
+    while ( *se && !isspace(*se) ) se++;
+
+    *chr_beg = ss;
+    *chr_end = se-1;
+
+    if ( !*se ) { fprintf(stderr,"Could not parse the line: %s\n", line); return -2; }
+
+    ss = se+1;
+    *beg = strtod(ss, &se);
+    if ( ss==se ) { fprintf(stderr,"Could not parse tab line: %s\n", line); return -2; }
+    if ( *beg==0 ) { fprintf(stderr,"Could not parse tab line, expected 1-based coordinate: %s\n", line); return -2; }
+    (*beg)--;
+    *end = *beg;
+
+    if ( !usr ) return 0; // allele information not required
+
+    ss = se+1;
+    tgt_als_t *als = (tgt_als_t*)payload;
+    als->used   = 0;
+    als->n      = 0;
+    als->allele = NULL;
+    while ( *ss )
+    {
+        se = ss;
+        while ( *se && *se!=',' ) se++;
+        als->n++;
+        als->allele = (char**)realloc(als->allele,als->n*sizeof(*als->allele));
+        als->allele[als->n-1] = (char*)malloc(se-ss+1);
+        memcpy(als->allele[als->n-1],ss,se-ss);
+        als->allele[als->n-1][se-ss] = 0;
+        ss = se+1;
+        if ( !*se ) break;
+    }
+    return 0;
+}
+static void tgt_free(void *payload)
+{
+    tgt_als_t *als = (tgt_als_t*)payload;
+    int i;
+    for (i=0; i<als->n; i++) free(als->allele[i]);
+    free(als->allele);
+}
+static void tgt_flush_region(args_t *args, char *chr, uint32_t beg, uint32_t end)
+{
+    if ( !regidx_overlap(args->tgt_idx, chr,beg,end,args->tgt_itr_tmp) ) return;
+    while ( regitr_overlap(args->tgt_itr_tmp) )
+    {
+        if ( args->tgt_itr_tmp->beg < beg ) continue;
+
+        tgt_als_t *tgt_als = &regitr_payload(args->tgt_itr_tmp,tgt_als_t);
+        if ( tgt_als->used ) continue;
+
+        args->missed_line->rid  = bcf_hdr_name2id(args->aux.hdr,chr);
+        args->missed_line->pos  = args->tgt_itr_tmp->beg;
+        bcf_unpack(args->missed_line,BCF_UN_ALL);
+        bcf_update_alleles(args->aux.hdr, args->missed_line, (const char**)tgt_als->allele, tgt_als->n);
+        tgt_als->used = 1;
+        if ( bcf_write1(args->out_fh, args->aux.hdr, args->missed_line)!=0 ) error("[%s] Error: failed to write to %s\n", __func__,args->output_fname);
+    }
+}
+static void tgt_flush(args_t *args, bcf1_t *rec)
+{
+    if ( rec )
+    {
+        char *chr = (char*)bcf_seqname(args->aux.hdr,rec);
+
+        if ( !args->tgt_itr_prev )                  // first record
+            tgt_flush_region(args,chr,0,rec->pos-1);
+
+        else if ( strcmp(chr,args->tgt_itr_prev->seq) )  // first record on a new chromosome
+        {
+            tgt_flush_region(args,args->tgt_itr_prev->seq,args->tgt_itr_prev->beg+1,REGIDX_MAX);
+            tgt_flush_region(args,chr,0,rec->pos-1);
+        }
+        else                                        // another record on the same chromosome
+            tgt_flush_region(args,args->tgt_itr_prev->seq,args->tgt_itr_prev->beg,rec->pos-1);
+    }
+    else
+    {
+        // flush everything
+        if ( args->tgt_itr_prev )
+            tgt_flush_region(args,args->tgt_itr_prev->seq,args->tgt_itr_prev->beg,REGIDX_MAX);
+
+        int i, nchr = 0;
+        char **chr = regidx_seq_names(args->tgt_idx, &nchr);
+        for (i=0; i<nchr; i++)
+            tgt_flush_region(args,chr[i],0,REGIDX_MAX);
+    }
+}
+inline static int is_indel(int nals, char **als)
+{
+    // This is mpileup output, we can make some assumption:
+    //  - no MNPs
+    //  - "<*>" is not present at indels sites and there are no other symbolic alleles than <*>
+    if ( als[1][0]=='<' ) return 0;
+
+    int i;
+    for (i=0; i<nals; i++)
+    {
+        if ( als[i][0]=='<' ) continue;
+        if ( als[i][1] ) return 1;
+    }
+    return 0;
+}
+bcf1_t *next_line(args_t *args)
+{
+    bcf1_t *rec = NULL;
+    if ( !args->vcfbuf )
+    {
+        while ( bcf_sr_next_line(args->aux.srs) )
+        {
+            rec = args->aux.srs->readers[0].buffer[0];
+            if ( args->aux.srs->errnum || rec->errcode ) error("Error: could not parse the input VCF\n");
+            if ( args->tgt_idx )
+            {
+                if ( !regidx_overlap(args->tgt_idx, bcf_seqname(args->aux.hdr,rec),rec->pos,rec->pos,args->tgt_itr) ) continue;
+
+                // For backward compatibility: require the exact position, not an interval overlap
+                int pos_match = 0;
+                while ( regitr_overlap(args->tgt_itr) )
+                {
+                    if ( args->tgt_itr->beg != rec->pos ) continue;
+                    pos_match = 1;
+                    break;
+                }
+                if ( !pos_match ) continue;
+            }
+            if ( args->samples_map ) bcf_subset(args->aux.hdr, rec, args->nsamples, args->samples_map);
+            bcf_unpack(rec, BCF_UN_STR);
+            return rec;
+        }
+        return NULL;
+    }
+
+    // If we are here,-C alleles was given and vcfbuf and tgt_idx are set
+
+    // Fill the buffer with duplicate lines
+    int vcfbuf_full = 1;
+    int nbuf = vcfbuf_nsites(args->vcfbuf);
+    bcf1_t *rec0 = NULL, *recN = NULL;
+    if ( nbuf==0 ) vcfbuf_full = 0;
+    else if ( nbuf==1 )
+    {
+        vcfbuf_full = 0;
+        rec0 = vcfbuf_peek(args->vcfbuf, 0);
+    }
+    else
+    {
+        rec0 = vcfbuf_peek(args->vcfbuf, 0);
+        recN = vcfbuf_peek(args->vcfbuf, nbuf-1);
+        if ( rec0->rid == recN->rid && rec0->pos == recN->pos ) vcfbuf_full = 0;
+    }
+    if ( !vcfbuf_full )
+    {
+        while ( bcf_sr_next_line(args->aux.srs) )
+        {
+            rec = args->aux.srs->readers[0].buffer[0];
+            if ( args->aux.srs->errnum || rec->errcode ) error("Error: could not parse the input VCF\n");
+            if ( !regidx_overlap(args->tgt_idx, bcf_seqname(args->aux.hdr,rec),rec->pos,rec->pos,args->tgt_itr) ) continue;
+            // as above: require the exact position, not an interval overlap
+            int exact_match = 0;
+            while ( regitr_overlap(args->tgt_itr) )
+            {
+                if ( args->tgt_itr->beg != rec->pos ) continue;
+                exact_match = 1;
+                break;
+            }
+            if ( !exact_match ) continue;
+
+            if ( args->samples_map ) bcf_subset(args->aux.hdr, rec, args->nsamples, args->samples_map);
+            bcf_unpack(rec, BCF_UN_STR);
+            if ( !rec0 ) rec0 = rec;
+            recN = rec;
+            args->aux.srs->readers[0].buffer[0] = vcfbuf_push(args->vcfbuf, rec);
+            if ( rec0->rid!=recN->rid || rec0->pos!=recN->pos ) break;
+        }
+    }
+
+    nbuf = vcfbuf_nsites(args->vcfbuf);
+    int n, i,j;
+    for (n=nbuf; n>1; n--)
+    {
+        recN = vcfbuf_peek(args->vcfbuf, n-1);
+        if ( rec0->rid==recN->rid && rec0->pos==recN->pos ) break;
+    }
+    if ( n==0 )
+    {
+        assert( !nbuf );
+        return NULL;
+    }
+
+    // Find the VCF and tab record with the best matching combination of alleles, prioritize
+    // records of the same type (snp vs indel)
+    rec_tgt_t rec_tgt;
+    memset(&rec_tgt,0,sizeof(rec_tgt));
+    regidx_overlap(args->tgt_idx, bcf_seqname(args->aux.hdr,rec0),rec0->pos,rec0->pos,args->tgt_itr);
+    regitr_t *tmp_itr = regitr_init(args->tgt_idx);
+    regitr_copy(tmp_itr, args->tgt_itr);
+    for (i=0; i<n; i++)
+    {
+        rec = vcfbuf_peek(args->vcfbuf, i);
+        int rec_indel = is_indel(rec->n_allele, rec->d.allele) ? 1 : -1;
+        while ( regitr_overlap(tmp_itr) )
+        {
+            if ( tmp_itr->beg != rec->pos ) continue;
+            tgt_als_t *als = &regitr_payload(tmp_itr,tgt_als_t);
+            if ( als->used ) continue;
+            int nmatch_als = 0;
+            vcmp_t *vcmp = vcmp_init();
+            int ret = vcmp_set_ref(vcmp, rec->d.allele[0], als->allele[0]);
+            if ( ret==0 )
+            {
+                nmatch_als++;
+                if ( rec->n_allele > 1 && als->n > 1 )
+                {
+                    for (j=1; j<als->n; j++)
+                    {
+                        if ( vcmp_find_allele(vcmp, rec->d.allele+1, rec->n_allele-1, als->allele[j])>=0 ) nmatch_als++;
+                    }
+                }
+            }
+            int als_indel = is_indel(als->n, als->allele) ? 1 : -1;
+            nmatch_als *= rec_indel*als_indel;
+            if ( nmatch_als > rec_tgt.nmatch_als || !rec_tgt.als )
+            {
+                rec_tgt.nmatch_als = nmatch_als;
+                rec_tgt.als  = als;
+                rec_tgt.ibuf = i;
+            }
+            vcmp_destroy(vcmp);
+        }
+    }
+    regitr_destroy(tmp_itr);
+
+    args->aux.tgt_als = rec_tgt.als;
+    if ( rec_tgt.als ) rec_tgt.als->used = 1;
+
+    rec = vcfbuf_remove(args->vcfbuf, rec_tgt.ibuf);
+    return rec;
+}
+
+static void init_data(args_t *args)
+{
+    args->aux.srs = bcf_sr_init();
+
+    // Open files for input and output, initialize structures
+    if ( args->targets )
+    {
+        args->tgt_idx = regidx_init(args->targets, tgt_parse, args->aux.flag&CALL_CONSTR_ALLELES ? tgt_free : (regidx_free_f) NULL, sizeof(tgt_als_t), args->aux.flag&CALL_CONSTR_ALLELES ? args : NULL);
+        args->tgt_itr = regitr_init(args->tgt_idx);
+        args->tgt_itr_tmp = regitr_init(args->tgt_idx);
+    }
+
+    if ( args->regions )
+    {
+        bcf_sr_set_opt(args->aux.srs,BCF_SR_REGIONS_OVERLAP,args->regions_overlap);
+        if ( bcf_sr_set_regions(args->aux.srs, args->regions, args->regions_is_file)<0 )
+            error("Failed to read the regions: %s\n", args->regions);
+    }
+
+    if ( !bcf_sr_add_reader(args->aux.srs, args->bcf_fname) )
+        error("Failed to read from %s: %s\n", !strcmp("-",args->bcf_fname)?"standard input":args->bcf_fname,bcf_sr_strerror(args->aux.srs->errnum));
+    args->aux.hdr = bcf_sr_get_header(args->aux.srs,0);
+
+    int i;
+    if ( args->samples_fname )
+    {
+        set_samples(args, args->samples_fname, args->samples_is_file);
+        if ( args->aux.flag&CALL_CONSTR_TRIO )
+        {
+            if ( 3*args->aux.nfams!=args->nsamples ) error("Expected only trios in %s, sorry!\n", args->samples_fname);
+            fprintf(stderr,"Detected %d samples in %d trio families\n", args->nsamples,args->aux.nfams);
+        }
+    }
+    if ( args->ploidy  )
+    {
+        args->nsex = ploidy_nsex(args->ploidy);
+        args->sex2ploidy = (int*) calloc(args->nsex,sizeof(int));
+        args->sex2ploidy_prev = (int*) calloc(args->nsex,sizeof(int));
+        if ( !args->nsamples )
+        {
+            args->nsamples = bcf_hdr_nsamples(args->aux.hdr);
+            args->sample2sex = (int*) malloc(sizeof(int)*args->nsamples);
+            for (i=0; i<args->nsamples; i++) args->sample2sex[i] = args->nsex - 1;
+        }
+    }
+    if ( args->nsamples )
+    {
+        args->aux.ploidy = (uint8_t*) malloc(args->nsamples);
+        for (i=0; i<args->nsamples; i++) args->aux.ploidy[i] = ploidy_max(args->ploidy);
+        for (i=0; i<args->nsex; i++) args->sex2ploidy_prev[i] = ploidy_max(args->ploidy);
+        for (i=0; i<args->nsamples; i++)
+            if ( args->sample2sex[i] >= args->nsex ) args->sample2sex[i] = args->nsex - 1;
+    }
+
+    if ( args->gvcf )
+    {
+        int id = bcf_hdr_id2int(args->aux.hdr,BCF_DT_ID,"DP");
+        if ( id<0 || !bcf_hdr_idinfo_exists(args->aux.hdr,BCF_HL_FMT,id) ) error("--gvcf output mode requires FORMAT/DP tag, which is not present in the input header\n");
+        gvcf_update_header(args->gvcf, args->aux.hdr);
+    }
+
+    if ( args->samples_map )
+    {
+        args->aux.hdr = bcf_hdr_subset(bcf_sr_get_header(args->aux.srs,0), args->nsamples, args->samples, args->samples_map);
+        if ( !args->aux.hdr ) error("Error occurred while subsetting samples\n");
+        for (i=0; i<args->nsamples; i++)
+            if ( args->samples_map[i]<0 ) error("No such sample: %s\n", args->samples[i]);
+        if ( !bcf_hdr_nsamples(args->aux.hdr) ) error("No matching sample found\n");
+    }
+    else
+    {
+        args->aux.hdr = bcf_hdr_dup(bcf_sr_get_header(args->aux.srs,0));
+        if ( args->samples )
+        {
+            for (i=0; i<args->nsamples; i++)
+                if ( bcf_hdr_id2int(args->aux.hdr,BCF_DT_SAMPLE,args->samples[i])<0 )
+                    error("No such sample: %s\n", args->samples[i]);
+        }
+    }
+
+    if ( args->aux.flag & CALL_CONSTR_ALLELES )
+        args->vcfbuf = vcfbuf_init(args->aux.hdr, 0);
+
+    char wmode[8];
+    set_wmode(wmode,args->output_type,args->output_fname,args->clevel);
+    args->out_fh = hts_open(args->output_fname ? args->output_fname : "-", wmode);
+    if ( args->out_fh == NULL ) error("Error: cannot write to \"%s\": %s\n", args->output_fname, strerror(errno));
+    if ( args->n_threads ) hts_set_threads(args->out_fh, args->n_threads);
+
+    if ( args->flag & CF_QCALL )
+        return;
+
+    if ( args->flag & CF_MCALL )
+        mcall_init(&args->aux);
+
+    if ( args->flag & CF_CCALL )
+        ccall_init(&args->aux);
+
+    bcf_hdr_remove(args->aux.hdr, BCF_HL_INFO, "QS");
+    bcf_hdr_remove(args->aux.hdr, BCF_HL_INFO, "I16");
+
+    if (args->record_cmd_line) bcf_hdr_append_version(args->aux.hdr, args->argc, args->argv, "bcftools_call");
+    if ( bcf_hdr_write(args->out_fh, args->aux.hdr)!=0 ) error("[%s] Error: cannot write the header to %s\n", __func__,args->output_fname);
+
+    if ( args->flag&CF_INS_MISSED ) init_missed_line(args);
+}
+
+static void destroy_data(args_t *args)
+{
+    if ( args->vcfbuf ) vcfbuf_destroy(args->vcfbuf);
+    if ( args->tgt_idx )
+    {
+        regidx_destroy(args->tgt_idx);
+        regitr_destroy(args->tgt_itr);
+        regitr_destroy(args->tgt_itr_tmp);
+        if ( args->tgt_itr_prev ) regitr_destroy(args->tgt_itr_prev);
+    }
+    if ( args->flag & CF_CCALL ) ccall_destroy(&args->aux);
+    else if ( args->flag & CF_MCALL ) mcall_destroy(&args->aux);
+    else if ( args->flag & CF_QCALL ) qcall_destroy(&args->aux);
+    int i;
+    if ( args->samples )
+    {
+        for (i=0; i<args->nsamples; i++) free(args->samples[i]);
+    }
+    if ( args->aux.fams )
+    {
+        for (i=0; i<args->aux.nfams; i++) free(args->aux.fams[i].name);
+        free(args->aux.fams);
+    }
+    if ( args->missed_line ) bcf_destroy(args->missed_line);
+    ploidy_destroy(args->ploidy);
+    free(args->sex2ploidy);
+    free(args->sex2ploidy_prev);
+    free(args->samples);
+    free(args->samples_map);
+    free(args->sample2sex);
+    free(args->aux.ploidy);
+    free(args->str.s);
+    if ( args->gvcf ) gvcf_destroy(args->gvcf);
+    bcf_hdr_destroy(args->aux.hdr);
+    if ( hts_close(args->out_fh)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,args->output_fname);
+    bcf_sr_destroy(args->aux.srs);
+}
+
+void parse_novel_rate(args_t *args, const char *str)
+{
+    if ( sscanf(str,"%le,%le,%le",&args->aux.trio_Pm_SNPs,&args->aux.trio_Pm_del,&args->aux.trio_Pm_ins)==3 )  // explicit for all
+    {
+        args->aux.trio_Pm_SNPs = 1 - args->aux.trio_Pm_SNPs;
+        args->aux.trio_Pm_del  = 1 - args->aux.trio_Pm_del;
+        args->aux.trio_Pm_ins  = 1 - args->aux.trio_Pm_ins;
+    }
+    else if ( sscanf(str,"%le,%le",&args->aux.trio_Pm_SNPs,&args->aux.trio_Pm_del)==2 )   // dynamic for indels
+    {
+        args->aux.trio_Pm_SNPs = 1 - args->aux.trio_Pm_SNPs;
+        args->aux.trio_Pm_ins  = -1;    // negative value for dynamic calculation
+    }
+    else if ( sscanf(str,"%le",&args->aux.trio_Pm_SNPs)==1 )  // same for all
+    {
+        args->aux.trio_Pm_SNPs = 1 - args->aux.trio_Pm_SNPs;
+        args->aux.trio_Pm_del  = -1;
+        args->aux.trio_Pm_ins  = -1;
+    }
+    else error("Could not parse --novel-rate %s\n", str);
+}
+
+static void list_annotations(FILE *fp)
+{
+    fprintf(fp,
+        "\n"
+        "Optional INFO annotations available with -m (\"INFO/\" prefix is optional):\n"
+        "  INFO/PV4   .. P-values for strand bias, baseQ bias, mapQ bias and tail distance bias (Number=4,Type=Float)\n"
+        "\n"
+        "Optional FORMAT annotations available with -m (\"FORMAT/\" prefix is optional):\n"
+        "  FORMAT/GQ  .. Phred-scaled genotype quality (Number=1,Type=Integer)\n"
+        "  FORMAT/GP  .. Phred-scaled genotype posterior probabilities (Number=G,Type=Float)\n"
+        "\n");
+}
+
+static int parse_output_tags(const char *str)
+{
+    int flag = 0;
+    const char *ss = str;
+    while ( *ss )
+    {
+        const char *se = ss;
+        while ( *se && *se!=',' ) se++;
+        if ( !strncasecmp(ss,"GQ",se-ss) || !strncasecmp(ss,"FORMAT/GQ",se-ss) || !strncasecmp(ss,"FMT/GQ",se-ss)  ) flag |= CALL_FMT_GQ;
+        else if ( !strncasecmp(ss,"GP",se-ss) || !strncasecmp(ss,"FORMAT/GP",se-ss) || !strncasecmp(ss,"FMT/GP",se-ss) ) flag |= CALL_FMT_GP;
+        else if ( !strncasecmp(ss,"PV4",se-ss) || !strncasecmp(ss,"INFO/PV4",se-ss) ) flag |= CALL_FMT_PV4;
+        else
+        {
+            fprintf(stderr,"Could not parse \"%s\"\n", str);
+            exit(1);
+        }
+        if ( !*se ) break;
+        ss = se + 1;
+    }
+    return flag;
+}
+
+static void set_ploidy(args_t *args, bcf1_t *rec)
+{
+    ploidy_query(args->ploidy,(char*)bcf_seqname(args->aux.hdr,rec),rec->pos,args->sex2ploidy,NULL,NULL);
+
+    int i;
+    for (i=0; i<args->nsex; i++)
+        if ( args->sex2ploidy[i]!=args->sex2ploidy_prev[i] ) break;
+
+    if ( i==args->nsex ) return;    // ploidy same as previously
+
+    for (i=0; i<args->nsamples; i++)
+    {
+        if ( args->sample2sex[i]<0 )
+            args->aux.ploidy[i] = -1*args->sample2sex[i];
+        else
+            args->aux.ploidy[i] = args->sex2ploidy[args->sample2sex[i]];
+    }
+    int *tmp = args->sex2ploidy; args->sex2ploidy = args->sex2ploidy_prev; args->sex2ploidy_prev = tmp;
+}
+
+ploidy_t *init_ploidy(char *alias)
+{
+    const ploidy_predef_t *pld = ploidy_predefs;
+
+    int detailed = 0, len = strlen(alias);
+    if ( alias[len-1]=='?' ) { detailed = 1; alias[len-1] = 0; }
+
+    while ( pld->alias && strcasecmp(alias,pld->alias) ) pld++;
+
+    if ( !pld->alias )
+    {
+        fprintf(stderr,"\nPRE-DEFINED PLOIDY FILES\n\n");
+        fprintf(stderr," * Columns are: CHROM,FROM,TO,SEX,PLOIDY\n");
+        fprintf(stderr," * Coordinates are 1-based inclusive.\n");
+        fprintf(stderr," * A '*' means any value not otherwise defined.\n\n");
+        pld = ploidy_predefs;
+        while ( pld->alias )
+        {
+            fprintf(stderr,"%s\n   .. %s\n\n", pld->alias,pld->about);
+            if ( detailed )
+                fprintf(stderr,"%s\n", pld->ploidy);
+            pld++;
+        }
+        fprintf(stderr,"Run as --ploidy <alias> (e.g. --ploidy GRCh37).\n");
+        fprintf(stderr,"To see the detailed ploidy definition, append a question mark (e.g. --ploidy GRCh37?).\n");
+        fprintf(stderr,"\n");
+        exit(-1);
+    }
+    else if ( detailed )
+    {
+        fprintf(stderr,"%s", pld->ploidy);
+        exit(-1);
+    }
+    return ploidy_init_string(pld->ploidy,2);
+}
+
+static void usage(args_t *args)
+{
+    fprintf(stderr, "\n");
+    fprintf(stderr, "About:   SNP/indel variant calling from VCF/BCF. To be used in conjunction with bcftools mpileup.\n");
+    fprintf(stderr, "         This command replaces the former \"bcftools view\" caller. Some of the original\n");
+    fprintf(stderr, "         functionality has been temporarily lost in the process of transition to htslib,\n");
+    fprintf(stderr, "         but will be added back on popular demand. The original calling model can be\n");
+    fprintf(stderr, "         invoked with the -c option.\n");
+    fprintf(stderr, "Usage:   bcftools call [options] <in.vcf.gz>\n");
+    fprintf(stderr, "\n");
+    fprintf(stderr, "File format options:\n");
+    fprintf(stderr, "       --no-version                Do not append version and command line to the header\n");
+    fprintf(stderr, "   -o, --output FILE               Write output to a file [standard output]\n");
+    fprintf(stderr, "   -O, --output-type b|u|z|v       Output type: 'b' compressed BCF; 'u' uncompressed BCF; 'z' compressed VCF; 'v' uncompressed VCF [v]\n");
+    fprintf(stderr, "   -O, --output-type u|b|v|z[0-9]  u/b: un/compressed BCF, v/z: un/compressed VCF, 0-9: compression level [v]\n");
+    fprintf(stderr, "       --ploidy ASSEMBLY[?]        Predefined ploidy, 'list' to print available settings, append '?' for details [2]\n");
+    fprintf(stderr, "       --ploidy-file FILE          Space/tab-delimited list of CHROM,FROM,TO,SEX,PLOIDY\n");
+    fprintf(stderr, "   -r, --regions REGION            Restrict to comma-separated list of regions\n");
+    fprintf(stderr, "   -R, --regions-file FILE         Restrict to regions listed in a file\n");
+    fprintf(stderr, "       --regions-overlap 0|1|2     Include if POS in the region (0), record overlaps (1), variant overlaps (2) [1]\n");
+    fprintf(stderr, "   -s, --samples LIST              List of samples to include [all samples]\n");
+    fprintf(stderr, "   -S, --samples-file FILE         PED file or a file with an optional column with sex (see man page for details) [all samples]\n");
+    fprintf(stderr, "   -t, --targets REGION            Similar to -r but streams rather than index-jumps\n");
+    fprintf(stderr, "   -T, --targets-file FILE         Similar to -R but streams rather than index-jumps\n");
+    fprintf(stderr, "       --threads INT               Use multithreading with INT worker threads [0]\n");
+    fprintf(stderr, "\n");
+    fprintf(stderr, "Input/output options:\n");
+    fprintf(stderr, "   -A, --keep-alts                 Keep all possible alternate alleles at variant sites\n");
+    fprintf(stderr, "   -a, --annotate LIST             Optional tags to output (lowercase allowed); '?' to list available tags\n");
+    fprintf(stderr, "   -F, --prior-freqs AN,AC         Use prior allele frequencies, determined from these pre-filled tags\n");
+    fprintf(stderr, "   -G, --group-samples FILE|-      Group samples by population (file with \"sample\\tgroup\") or \"-\" for single-sample calling.\n");
+    fprintf(stderr, "                                   This requires FORMAT/QS or other Number=R,Type=Integer tag such as FORMAT/AD\n");
+    fprintf(stderr, "       --group-samples-tag TAG     The tag to use with -G, by default FORMAT/QS and FORMAT/AD are checked automatically\n");
+    fprintf(stderr, "   -g, --gvcf INT,[...]            Group non-variant sites into gVCF blocks by minimum per-sample DP\n");
+    fprintf(stderr, "   -i, --insert-missed             Output also sites missed by mpileup but present in -T\n");
+    fprintf(stderr, "   -M, --keep-masked-ref           Keep sites with masked reference allele (REF=N)\n");
+    fprintf(stderr, "   -V, --skip-variants TYPE        Skip indels/snps\n");
+    fprintf(stderr, "   -v, --variants-only             Output variant sites only\n");
+    fprintf(stderr, "\n");
+    fprintf(stderr, "Consensus/variant calling options:\n");
+    fprintf(stderr, "   -c, --consensus-caller          The original calling method (conflicts with -m)\n");
+    fprintf(stderr, "   -C, --constrain STR             One of: alleles, trio (see manual)\n");
+    fprintf(stderr, "   -m, --multiallelic-caller       Alternative model for multiallelic and rare-variant calling (conflicts with -c)\n");
+    fprintf(stderr, "   -n, --novel-rate FLOAT,[...]    Likelihood of novel mutation for constrained trio calling, see man page for details [1e-8,1e-9,1e-9]\n");
+    fprintf(stderr, "   -p, --pval-threshold FLOAT      Variant if P(ref|D)<FLOAT with -c [0.5]\n");
+    fprintf(stderr, "   -P, --prior FLOAT               Mutation rate (use bigger for greater sensitivity), use with -m [1.1e-3]\n");
+    fprintf(stderr, "\n");
+    fprintf(stderr, "Example:\n");
+    fprintf(stderr, "   # See also http://samtools.github.io/bcftools/howtos/variant-calling.html\n");
+    fprintf(stderr, "   bcftools mpileup -Ou -f reference.fa alignments.bam | bcftools call -mv -Ob -o calls.bcf\n");
+
+    // todo (and more)
+    // fprintf(stderr, "\nContrast calling and association test options:\n");
+    // fprintf(stderr, "       -1 INT    number of group-1 samples [0]\n");
+    // fprintf(stderr, "       -C FLOAT  posterior constrast for LRT<FLOAT and P(ref|D)<0.5 [%g]\n", args->aux.min_lrt);
+    // fprintf(stderr, "       -U INT    number of permutations for association testing (effective with -1) [0]\n");
+    // fprintf(stderr, "       -X FLOAT  only perform permutations for P(chi^2)<FLOAT [%g]\n", args->aux.min_perm_p);
+    fprintf(stderr, "\n");
+    exit(-1);
+}
+
+int main_vcfcall(int argc, char *argv[])
+{
+    char *ploidy_fname = NULL, *ploidy = NULL;
+    args_t args;
+    memset(&args, 0, sizeof(args_t));
+    args.argc = argc; args.argv = argv;
+    args.aux.prior_type = -1;
+    args.aux.indel_frac = -1;
+    args.aux.theta      = 1.1e-3;
+    args.aux.pref       = 0.5;
+    args.aux.min_perm_p = 0.01;
+    args.aux.min_lrt    = 1;
+    args.flag           = CF_ACGT_ONLY;
+    args.output_fname   = "-";
+    args.output_type    = FT_VCF;
+    args.n_threads = 0;
+    args.record_cmd_line = 1;
+    args.aux.trio_Pm_SNPs = 1 - 1e-8;
+    args.aux.trio_Pm_ins  = args.aux.trio_Pm_del  = 1 - 1e-9;
+    args.regions_overlap = 1;
+    args.clevel = -1;
+
+    int c;
+    static struct option loptions[] =
+    {
+        {"help",no_argument,NULL,'h'},
+        {"format-fields",required_argument,NULL,'f'},
+        {"annotate",required_argument,NULL,'a'},
+        {"prior-freqs",required_argument,NULL,'F'},
+        {"gvcf",required_argument,NULL,'g'},
+        {"group-samples",required_argument,NULL,'G'},
+        {"group-samples-tag",required_argument,NULL,3},
+        {"output",required_argument,NULL,'o'},
+        {"output-type",required_argument,NULL,'O'},
+        {"regions",required_argument,NULL,'r'},
+        {"regions-file",required_argument,NULL,'R'},
+        {"regions-overlap",required_argument,NULL,4},
+        {"samples",required_argument,NULL,'s'},
+        {"samples-file",required_argument,NULL,'S'},
+        {"targets",required_argument,NULL,'t'},
+        {"targets-file",required_argument,NULL,'T'},
+        {"threads",required_argument,NULL,9},
+        {"keep-alts",no_argument,NULL,'A'},
+        {"insert-missed",no_argument,NULL,'i'},
+        {"skip-Ns",no_argument,NULL,'N'},            // now the new default
+        {"keep-masked-refs",no_argument,NULL,'M'},
+        {"skip-variants",required_argument,NULL,'V'},
+        {"variants-only",no_argument,NULL,'v'},
+        {"consensus-caller",no_argument,NULL,'c'},
+        {"constrain",required_argument,NULL,'C'},
+        {"multiallelic-caller",no_argument,NULL,'m'},
+        {"pval-threshold",required_argument,NULL,'p'},
+        {"prior",required_argument,NULL,'P'},
+        {"novel-rate",required_argument,NULL,'n'},
+        {"ploidy",required_argument,NULL,1},
+        {"ploidy-file",required_argument,NULL,2},
+        {"chromosome-X",no_argument,NULL,'X'},
+        {"chromosome-Y",no_argument,NULL,'Y'},
+        {"no-version",no_argument,NULL,8},
+        {NULL,0,NULL,0}
+    };
+
+    char *tmp = NULL;
+    while ((c = getopt_long(argc, argv, "h?o:O:r:R:s:S:t:T:ANMV:vcmp:C:n:P:f:a:ig:XYF:G:", loptions, NULL)) >= 0)
+    {
+        switch (c)
+        {
+            case  2 : ploidy_fname = optarg; break;
+            case  1 : ploidy = optarg; break;
+            case 'X': ploidy = "X"; fprintf(stderr,"Warning: -X will be deprecated, please use --ploidy instead.\n"); break;
+            case 'Y': ploidy = "Y"; fprintf(stderr,"Warning: -Y will be deprecated, please use --ploidy instead.\n"); break;
+            case 'G': args.aux.sample_groups = optarg; break;
+            case  3 : args.aux.sample_groups_tag = optarg; break;
+            case 'f': fprintf(stderr,"Warning: -f, --format-fields will be deprecated, please use -a, --annotate instead.\n");
+            case 'a':
+                      if (optarg[0]=='?') { list_annotations(stderr); return 1; }
+                      args.aux.output_tags |= parse_output_tags(optarg);
+                      break;
+            case 'M': args.flag &= ~CF_ACGT_ONLY; break;     // keep sites where REF is N
+            case 'N': args.flag |= CF_ACGT_ONLY; break;      // omit sites where first base in REF is N (the new default)
+            case 'A': args.aux.flag |= CALL_KEEPALT; break;
+            case 'c': args.flag |= CF_CCALL; break;          // the original EM based calling method
+            case 'i': args.flag |= CF_INS_MISSED; break;
+            case 'v': args.aux.flag |= CALL_VARONLY; break;
+            case 'F':
+                args.aux.prior_AN = optarg;
+                args.aux.prior_AC = strchr(optarg,',');
+                if ( !args.aux.prior_AC ) error("Expected two tags with -F (e.g. AN,AC), got \"%s\"\n",optarg);
+                *args.aux.prior_AC = 0;
+                args.aux.prior_AC++;
+                break;
+            case 'g':
+                args.gvcf = gvcf_init(optarg);
+                if ( !args.gvcf ) error("Could not parse: --gvcf %s\n", optarg);
+                break;
+            case 'o': args.output_fname = optarg; break;
+            case 'O':
+                      switch (optarg[0]) {
+                          case 'b': args.output_type = FT_BCF_GZ; break;
+                          case 'u': args.output_type = FT_BCF; break;
+                          case 'z': args.output_type = FT_VCF_GZ; break;
+                          case 'v': args.output_type = FT_VCF; break;
+                          default:
+                          {
+                              args.clevel = strtol(optarg,&tmp,10);
+                              if ( *tmp || args.clevel<0 || args.clevel>9 ) error("The output type \"%s\" not recognised\n", optarg);
+                          }
+                      }
+                      if ( optarg[1] )
+                      {
+                          args.clevel = strtol(optarg+1,&tmp,10);
+                          if ( *tmp || args.clevel<0 || args.clevel>9 ) error("Could not parse argument: --compression-level %s\n", optarg+1);
+                      }
+                      break;
+            case 'C':
+                      if ( !strcasecmp(optarg,"alleles") ) args.aux.flag |= CALL_CONSTR_ALLELES;
+                      else if ( !strcasecmp(optarg,"trio") ) args.aux.flag |= CALL_CONSTR_TRIO;
+                      else error("Unknown argument to -C: \"%s\"\n", optarg);
+                      break;
+            case 'V':
+                      if ( !strcasecmp(optarg,"snps") ) args.flag |= CF_INDEL_ONLY;
+                      else if ( !strcasecmp(optarg,"indels") ) args.flag |= CF_NO_INDEL;
+                      else error("Unknown skip category \"%s\" (-S argument must be \"snps\" or \"indels\")\n", optarg);
+                      break;
+            case 'm': args.flag |= CF_MCALL; break;         // multiallelic calling method
+            case 'p':
+                args.aux.pref = strtod(optarg,&tmp);
+                if ( *tmp ) error("Could not parse: --pval-threshold %s\n", optarg);
+                break;
+            case 'P': args.aux.theta = strtod(optarg,&tmp);
+                      if ( *tmp ) error("Could not parse, expected float argument: -P %s\n", optarg);
+                      break;
+            case 'n': parse_novel_rate(&args,optarg); break;
+            case 'r': args.regions = optarg; break;
+            case 'R': args.regions = optarg; args.regions_is_file = 1; break;
+            case 't': args.targets = optarg; break;
+            case 'T': args.targets = optarg; args.targets_is_file = 1; break;
+            case 's': args.samples_fname = optarg; break;
+            case 'S': args.samples_fname = optarg; args.samples_is_file = 1; break;
+            case  9 : args.n_threads = strtol(optarg, 0, 0); break;
+            case  8 : args.record_cmd_line = 0; break;
+            case  4 :
+                args.regions_overlap = parse_overlap_option(optarg);
+                if ( args.regions_overlap < 0 ) error("Could not parse: --regions-overlap %s\n",optarg);
+                break;
+            default: usage(&args);
+        }
+    }
+    // Sanity check options and initialize
+    if ( ploidy_fname ) args.ploidy = ploidy_init(ploidy_fname, 2);
+    else if ( ploidy ) args.ploidy = init_ploidy(ploidy);
+
+    if ( optind>=argc )
+    {
+        if ( !isatty(fileno((FILE *)stdin)) ) args.bcf_fname = "-";  // reading from stdin
+        else usage(&args);
+    }
+    else args.bcf_fname = argv[optind++];
+
+    if ( !ploidy_fname && !ploidy )
+    {
+        if ( !args.samples_is_file ) fprintf(stderr,"Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid\n");
+        args.ploidy = ploidy_init_string("* * * 0 0\n* * * 1 1\n* * * 2 2\n",2);
+    }
+
+    if ( !args.ploidy ) error("Could not initialize ploidy\n");
+    if ( (args.flag & CF_CCALL ? 1 : 0) + (args.flag & CF_MCALL ? 1 : 0) + (args.flag & CF_QCALL ? 1 : 0) > 1 ) error("Only one of -c or -m options can be given\n");
+    if ( !(args.flag & CF_CCALL) && !(args.flag & CF_MCALL) && !(args.flag & CF_QCALL) ) error("Expected -c or -m option\n");
+    if ( (args.flag & CF_CCALL ? 1: 0) && args.gvcf ) error("gvcf -g option not functional with -c calling mode yet\n");
+    if ( args.aux.n_perm && args.aux.ngrp1_samples<=0 ) error("Expected -1 with -U\n");    // not sure about this, please fix
+    if ( args.aux.flag & CALL_CONSTR_ALLELES )
+    {
+        if ( !args.targets ) error("Expected -t or -T with \"-C alleles\"\n");
+        if ( !(args.flag & CF_MCALL) ) error("The \"-C alleles\" mode requires -m\n");
+    }
+    if ( args.flag & CF_INS_MISSED && !(args.aux.flag&CALL_CONSTR_ALLELES) ) error("The -i option requires -C alleles\n");
+    if ( args.aux.flag&CALL_VARONLY && args.gvcf ) error("The two options cannot be combined: --variants-only and --gvcf\n");
+    if ( args.aux.sample_groups && !(args.flag & CF_MCALL) ) error("The -G feature is supported only with the -m calling mode\n");
+    init_data(&args);
+
+    bcf1_t *bcf_rec;
+    while ( (bcf_rec = next_line(&args)) )
+    {
+        // Skip duplicate positions with all matching `-C alleles -T` used up
+        if ( args.aux.flag&CALL_CONSTR_ALLELES && !args.aux.tgt_als ) continue;
+
+        // Skip unwanted sites
+        int i, is_indel = bcf_is_snp(bcf_rec) ? 0 : 1;
+        if ( (args.flag & CF_INDEL_ONLY) && !is_indel ) continue;
+        if ( (args.flag & CF_NO_INDEL) && is_indel ) continue;
+        if ( (args.flag & CF_ACGT_ONLY) && (bcf_rec->d.allele[0][0]=='N' || bcf_rec->d.allele[0][0]=='n') ) continue;   // REF[0] is 'N'
+
+        // Which allele is symbolic? All SNPs should have it, but not indels
+        args.aux.unseen = 0;
+        for (i=1; i<bcf_rec->n_allele; i++)
+        {
+            if ( bcf_rec->d.allele[i][0]=='X' ) { args.aux.unseen = i; break; }  // old X
+            if ( bcf_rec->d.allele[i][0]=='<' )
+            {
+                if ( bcf_rec->d.allele[i][1]=='X' && bcf_rec->d.allele[i][2]=='>' ) { args.aux.unseen = i; break; } // old <X>
+                if ( bcf_rec->d.allele[i][1]=='*' && bcf_rec->d.allele[i][2]=='>' ) { args.aux.unseen = i; break; } // new <*>
+            }
+        }
+        int is_ref = (bcf_rec->n_allele==1 || (bcf_rec->n_allele==2 && args.aux.unseen>0)) ? 1 : 0;
+
+        if ( is_ref && args.aux.flag&CALL_VARONLY )
+            continue;
+
+        bcf_unpack(bcf_rec, BCF_UN_ALL);
+        if ( args.nsex ) set_ploidy(&args, bcf_rec);
+
+        // Various output modes: QCall output (todo)
+        if ( args.flag & CF_QCALL )
+        {
+            qcall(&args.aux, bcf_rec);
+            continue;
+        }
+
+        if ( args.flag & CF_INS_MISSED )
+        {
+            tgt_flush(&args,bcf_rec);
+            if ( !args.tgt_itr_prev ) args.tgt_itr_prev = regitr_init(args.tgt_idx);
+            regitr_copy(args.tgt_itr_prev, args.tgt_itr);
+        }
+
+        // Calling modes which output VCFs
+        int ret;
+        if ( args.flag & CF_MCALL )
+            ret = mcall(&args.aux, bcf_rec);
+        else
+            ret = ccall(&args.aux, bcf_rec);
+        if ( ret==-1 ) error("Something is wrong\n");
+        else if ( ret==-2 ) continue;   // skip the site
+
+        // Normal output
+        if ( (args.aux.flag & CALL_VARONLY) && ret==0 && !args.gvcf ) continue;     // not a variant
+        if ( args.gvcf )
+            bcf_rec = gvcf_write(args.gvcf, args.out_fh, args.aux.hdr, bcf_rec, ret==1?1:0);
+        if ( bcf_rec && bcf_write1(args.out_fh, args.aux.hdr, bcf_rec)!=0 ) error("[%s] Error: failed to write to %s\n", __func__,args.output_fname);
+    }
+    if ( args.gvcf ) gvcf_write(args.gvcf, args.out_fh, args.aux.hdr, NULL, 0);
+    if ( args.flag & CF_INS_MISSED ) tgt_flush(&args,NULL);
+    destroy_data(&args);
+    return 0;
+}
+
diff --git a/bcftools/vcfcall.c.pysam.c b/bcftools/vcfcall.c.pysam.c
new file mode 100644
index 0000000..c715c53
--- /dev/null
+++ b/bcftools/vcfcall.c.pysam.c
@@ -0,0 +1,1181 @@
+#include "bcftools.pysam.h"
+
+/*  vcfcall.c -- SNP/indel variant calling from VCF/BCF.
+
+    Copyright (C) 2013-2022 Genome Research Ltd.
+
+    Author: Petr Danecek <pd3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.  */
+
+#include <stdarg.h>
+#include <string.h>
+#include <strings.h>
+#include <assert.h>
+#include <errno.h>
+#include <unistd.h>
+#include <getopt.h>
+#include <math.h>
+#include <htslib/vcf.h>
+#include <time.h>
+#include <stdarg.h>
+#include <htslib/kfunc.h>
+#include <htslib/synced_bcf_reader.h>
+#include <htslib/khash_str2int.h>
+#include <ctype.h>
+#include "bcftools.h"
+#include "call.h"
+#include "prob1.h"
+#include "ploidy.h"
+#include "gvcf.h"
+#include "regidx.h"
+#include "vcfbuf.h"
+
+void error(const char *format, ...);
+
+#define CF_NO_GENO      1
+#define CF_INS_MISSED   (1<<1)
+#define CF_CCALL        (1<<2)
+//                      (1<<3)
+//                      (1<<4)
+//                      (1<<5)
+#define CF_ACGT_ONLY    (1<<6)
+#define CF_QCALL        (1<<7)
+#define CF_ADJLD        (1<<8)
+#define CF_NO_INDEL     (1<<9)
+#define CF_ANNO_MAX     (1<<10)
+#define CF_MCALL        (1<<11)
+#define CF_PAIRCALL     (1<<12)
+#define CF_QCNT         (1<<13)
+#define CF_INDEL_ONLY   (1<<14)
+
+typedef struct
+{
+    tgt_als_t *als;
+    int nmatch_als, ibuf;
+}
+rec_tgt_t;
+
+typedef struct
+{
+    int flag;   // combination of CF_* flags above
+    int output_type, n_threads, record_cmd_line, clevel;
+    htsFile *bcf_in, *out_fh;
+    char *bcf_fname, *output_fname;
+    char **samples;             // for subsampling and ploidy
+    int nsamples, *samples_map; // mapping from output sample names to original VCF
+    char *regions, *targets;    // regions to process
+    int regions_is_file, targets_is_file, regions_overlap;
+    regidx_t *tgt_idx;
+    regitr_t *tgt_itr, *tgt_itr_prev, *tgt_itr_tmp;
+    vcfbuf_t *vcfbuf;
+
+    char *samples_fname;
+    int samples_is_file;
+    int *sample2sex;    // mapping for ploidy. If negative, interpreted as -1*ploidy
+    int *sex2ploidy, *sex2ploidy_prev, nsex;
+    ploidy_t *ploidy;
+    gvcf_t *gvcf;
+
+    bcf1_t *missed_line;
+    call_t aux;     // parameters and temporary data
+    kstring_t str;
+
+    int argc;
+    char **argv;
+
+    //  int flag, prior_type, n1, n_sub, *sublist, n_perm;
+    //  uint32_t *trio_aux;
+    //  char *prior_file, **subsam;
+    //  uint8_t *ploidy;
+    //  double theta, pref, indel_frac, min_smpl_frac, min_lrt;
+    // Permutation tests
+    //  int n_perm, *seeds;
+    //  double min_perm_p;
+    //  void *bed;
+}
+args_t;
+
+static char **add_sample(void *name2idx, char **lines, int *nlines, int *mlines, char *name, char sex, int *ith)
+{
+    int ret = khash_str2int_get(name2idx, name, ith);
+    if ( ret==0 ) return lines;
+
+    hts_expand(char*,(*nlines+1),*mlines,lines);
+    int len = strlen(name);
+    lines[*nlines] = (char*) malloc(len+3);
+    memcpy(lines[*nlines],name,len);
+    lines[*nlines][len]   = ' ';
+    lines[*nlines][len+1] = sex;
+    lines[*nlines][len+2] = 0;
+    *ith = *nlines;
+    (*nlines)++;
+    khash_str2int_set(name2idx, strdup(name), *ith);
+    return lines;
+}
+
+typedef struct
+{
+    const char *alias, *about, *ploidy;
+}
+ploidy_predef_t;
+
+static ploidy_predef_t ploidy_predefs[] =
+{
+    { .alias  = "GRCh37",
+      .about  = "Human Genome reference assembly GRCh37 / hg19",
+      .ploidy =
+          "X 1 60000 M 1\n"
+          "X 2699521 154931043 M 1\n"
+          "Y 1 59373566 M 1\n"
+          "Y 1 59373566 F 0\n"
+          "MT 1 16569 M 1\n"
+          "MT 1 16569 F 1\n"
+          "chrX 1 60000 M 1\n"
+          "chrX 2699521 154931043 M 1\n"
+          "chrY 1 59373566 M 1\n"
+          "chrY 1 59373566 F 0\n"
+          "chrM 1 16569 M 1\n"
+          "chrM 1 16569 F 1\n"
+          "*  * *     M 2\n"
+          "*  * *     F 2\n"
+    },
+    { .alias  = "GRCh38",
+      .about  = "Human Genome reference assembly GRCh38 / hg38",
+      .ploidy =
+          "X 1 9999 M 1\n"
+          "X 2781480 155701381 M 1\n"
+          "Y 1 57227415 M 1\n"
+          "Y 1 57227415 F 0\n"
+          "MT 1 16569 M 1\n"
+          "MT 1 16569 F 1\n"
+          "chrX 1 9999 M 1\n"
+          "chrX 2781480 155701381 M 1\n"
+          "chrY 1 57227415 M 1\n"
+          "chrY 1 57227415 F 0\n"
+          "chrM 1 16569 M 1\n"
+          "chrM 1 16569 F 1\n"
+          "*  * *     M 2\n"
+          "*  * *     F 2\n"
+    },
+    { .alias  = "X",
+      .about  = "Treat male samples as haploid and female as diploid regardless of the chromosome name",
+      .ploidy =
+          "*  * *     M 1\n"
+          "*  * *     F 2\n"
+    },
+    { .alias  = "Y",
+      .about  = "Treat male samples as haploid and female as no-copy, regardless of the chromosome name",
+      .ploidy =
+          "*  * *     M 1\n"
+          "*  * *     F 0\n"
+    },
+    { .alias  = "1",
+      .about  = "Treat all samples as haploid",
+      .ploidy =
+          "*  * *     * 1\n"
+    },
+    { .alias  = "2",
+      .about  = "Treat all samples as diploid",
+      .ploidy =
+          "*  * *     * 2\n"
+    },
+    {
+        .alias  = NULL,
+        .about  = NULL,
+        .ploidy = NULL,
+    }
+};
+
+// only 5 columns are required and the first is ignored:
+//  ignored,sample,father(or 0),mother(or 0),sex(1=M,2=F)
+static char **parse_ped_samples(call_t *call, char **vals, int nvals, int *nsmpl)
+{
+    int i, j, mlines = 0, nlines = 0;
+    kstring_t str = {0,0,0}, fam_str = {0,0,0};
+    void *name2idx = khash_str2int_init();
+    char **lines = NULL;
+    for (i=0; i<nvals; i++)
+    {
+        str.l = 0;
+        kputs(vals[i], &str);
+        char *col_ends[5], *tmp = str.s;
+        j = 0;
+        while ( *tmp && j<5 )
+        {
+            if ( isspace(*tmp) )
+            {
+                *tmp = 0;
+                ++tmp;
+                while ( isspace(*tmp) ) tmp++;  // allow multiple spaces
+                col_ends[j] = tmp-1;
+                j++;
+                continue;
+            }
+            tmp++;
+        }
+        if ( j<4 ) break;
+
+        char sex;
+        if ( col_ends[3][1]=='1' ) sex = 'M';
+        else if ( col_ends[3][1]=='2' ) sex = 'F';
+        else break;
+
+        lines = add_sample(name2idx, lines, &nlines, &mlines, col_ends[0]+1, sex, &j);
+        if ( strcmp(col_ends[1]+1,"0") && strcmp(col_ends[2]+1,"0") )   // father and mother
+        {
+            call->nfams++;
+            hts_expand(family_t, call->nfams, call->mfams, call->fams);
+            family_t *fam = &call->fams[call->nfams-1];
+            fam_str.l = 0;
+            ksprintf(&fam_str,"father=%s, mother=%s, child=%s", col_ends[1]+1,col_ends[2]+1,col_ends[0]+1);
+            fam->name = strdup(fam_str.s);
+
+            if ( !khash_str2int_has_key(name2idx, col_ends[1]+1) )
+                lines = add_sample(name2idx, lines, &nlines, &mlines, col_ends[1]+1, 'M', &fam->sample[FATHER]);
+            if ( !khash_str2int_has_key(name2idx, col_ends[2]+1) )
+                lines = add_sample(name2idx, lines, &nlines, &mlines, col_ends[2]+1, 'F', &fam->sample[MOTHER]);
+
+            khash_str2int_get(name2idx, col_ends[0]+1, &fam->sample[CHILD]);
+            khash_str2int_get(name2idx, col_ends[1]+1, &fam->sample[FATHER]);
+            khash_str2int_get(name2idx, col_ends[2]+1, &fam->sample[MOTHER]);
+        }
+    }
+    free(str.s);
+    free(fam_str.s);
+    khash_str2int_destroy_free(name2idx);
+
+    if ( i!=nvals ) return NULL; // not a ped file
+
+    *nsmpl = nlines;
+    return lines;
+}
+
+
+/*
+ *  Reads sample names and their ploidy (optional) from a file.
+ *  Alternatively, if no such file exists, the file name is interpreted
+ *  as a comma-separated list of samples. When ploidy is not present,
+ *  the default ploidy 2 is assumed.
+ */
+static void set_samples(args_t *args, const char *fn, int is_file)
+{
+    int i, nlines;
+    char **lines = hts_readlist(fn, is_file, &nlines);
+    if ( !lines ) error("Could not read the file: %s\n", fn);
+
+    int nsmpls;
+    char **smpls = parse_ped_samples(&args->aux, lines, nlines, &nsmpls);
+    if ( smpls )
+    {
+        for (i=0; i<nlines; i++) free(lines[i]);
+        free(lines);
+        lines = smpls;
+        nlines = nsmpls;
+    }
+    else if ( is_file )
+        fprintf(bcftools_stderr,"Note: could not parse as PED: %s\n",fn);
+
+    args->samples_map = (int*) malloc(sizeof(int)*bcf_hdr_nsamples(args->aux.hdr)); // for subsetting
+    args->sample2sex  = (int*) malloc(sizeof(int)*bcf_hdr_nsamples(args->aux.hdr));
+    int dflt_sex_id = ploidy_nsex(args->ploidy) - 1;
+    for (i=0; i<bcf_hdr_nsamples(args->aux.hdr); i++) args->sample2sex[i] = dflt_sex_id;
+
+    int *old2new = (int*) malloc(sizeof(int)*bcf_hdr_nsamples(args->aux.hdr));
+    for (i=0; i<bcf_hdr_nsamples(args->aux.hdr); i++) old2new[i] = -1;
+
+    int nsmpl = 0, map_needed = 0;
+    for (i=0; i<nlines; i++)
+    {
+        char *ss = lines[i];
+        while ( *ss && isspace(*ss) ) ss++;
+        if ( !*ss ) error("Could not parse: %s\n", lines[i]);
+        if ( *ss=='#' ) continue;
+        char *se = ss;
+        while ( *se && !isspace(*se) ) se++;
+        char x = *se, *xptr = se; *se = 0;
+
+        int ismpl = bcf_hdr_id2int(args->aux.hdr, BCF_DT_SAMPLE, ss);
+        if ( ismpl < 0 ) { fprintf(bcftools_stderr,"Warning: No such sample in the VCF: %s\n",ss); continue; }
+        if ( old2new[ismpl] != -1 ) { fprintf(bcftools_stderr,"Warning: The sample is listed multiple times: %s\n",ss); continue; }
+
+        ss = se+(x != '\0');
+        while ( *ss && isspace(*ss) ) ss++;
+        if ( !*ss ) ss = "2";   // default ploidy
+        se = ss;
+        while ( *se && !isspace(*se) ) se++;
+        if ( se==ss ) { *xptr = x; error("Could not parse: \"%s\"\n", lines[i]); }
+
+        if ( ss[1]==0 && (ss[0]=='0' || ss[0]=='1' || ss[0]=='2') )
+            args->sample2sex[nsmpl] = -1*(ss[0]-'0');
+        else
+            args->sample2sex[nsmpl] = ploidy_add_sex(args->ploidy, ss);
+
+        if ( ismpl!=nsmpl ) map_needed = 1;
+        args->samples_map[nsmpl] = ismpl;
+        old2new[ismpl] = nsmpl;
+        nsmpl++;
+    }
+
+    for (i=0; i<args->aux.nfams; i++)
+    {
+        int j, nmiss = 0;
+        family_t *fam = &args->aux.fams[i];
+        for (j=0; j<3; j++)
+        {
+            fam->sample[i] = old2new[fam->sample[i]];
+            if ( fam->sample[i]<0 ) nmiss++;
+        }
+        assert( nmiss==0 || nmiss==3 );
+    }
+    free(old2new);
+
+    if ( !map_needed ) { free(args->samples_map); args->samples_map = NULL; }
+
+    args->nsamples = nsmpl;
+    args->samples = lines;
+}
+
+static void init_missed_line(args_t *args)
+{
+    int i;
+    for (i=0; i<bcf_hdr_nsamples(args->aux.hdr); i++)
+    {
+        args->aux.gts[i*2]   = bcf_gt_missing;
+        args->aux.gts[i*2+1] = bcf_int32_vector_end;
+    }
+    args->missed_line = bcf_init1();
+    bcf_update_genotypes(args->aux.hdr, args->missed_line, args->aux.gts, 2*bcf_hdr_nsamples(args->aux.hdr));
+    bcf_float_set_missing(args->missed_line->qual);
+}
+
+static int tgt_parse(const char *line, char **chr_beg, char **chr_end, uint32_t *beg, uint32_t *end, void *payload, void *usr)
+{
+    char *ss = (char*) line;
+    while ( *ss && isspace(*ss) ) ss++;
+    if ( !*ss ) { fprintf(bcftools_stderr,"Could not parse the line: %s\n", line); return -2; }
+    if ( *ss=='#' ) return -1;  // skip comments
+
+    char *se = ss;
+    while ( *se && !isspace(*se) ) se++;
+
+    *chr_beg = ss;
+    *chr_end = se-1;
+
+    if ( !*se ) { fprintf(bcftools_stderr,"Could not parse the line: %s\n", line); return -2; }
+
+    ss = se+1;
+    *beg = strtod(ss, &se);
+    if ( ss==se ) { fprintf(bcftools_stderr,"Could not parse tab line: %s\n", line); return -2; }
+    if ( *beg==0 ) { fprintf(bcftools_stderr,"Could not parse tab line, expected 1-based coordinate: %s\n", line); return -2; }
+    (*beg)--;
+    *end = *beg;
+
+    if ( !usr ) return 0; // allele information not required
+
+    ss = se+1;
+    tgt_als_t *als = (tgt_als_t*)payload;
+    als->used   = 0;
+    als->n      = 0;
+    als->allele = NULL;
+    while ( *ss )
+    {
+        se = ss;
+        while ( *se && *se!=',' ) se++;
+        als->n++;
+        als->allele = (char**)realloc(als->allele,als->n*sizeof(*als->allele));
+        als->allele[als->n-1] = (char*)malloc(se-ss+1);
+        memcpy(als->allele[als->n-1],ss,se-ss);
+        als->allele[als->n-1][se-ss] = 0;
+        ss = se+1;
+        if ( !*se ) break;
+    }
+    return 0;
+}
+static void tgt_free(void *payload)
+{
+    tgt_als_t *als = (tgt_als_t*)payload;
+    int i;
+    for (i=0; i<als->n; i++) free(als->allele[i]);
+    free(als->allele);
+}
+static void tgt_flush_region(args_t *args, char *chr, uint32_t beg, uint32_t end)
+{
+    if ( !regidx_overlap(args->tgt_idx, chr,beg,end,args->tgt_itr_tmp) ) return;
+    while ( regitr_overlap(args->tgt_itr_tmp) )
+    {
+        if ( args->tgt_itr_tmp->beg < beg ) continue;
+
+        tgt_als_t *tgt_als = &regitr_payload(args->tgt_itr_tmp,tgt_als_t);
+        if ( tgt_als->used ) continue;
+
+        args->missed_line->rid  = bcf_hdr_name2id(args->aux.hdr,chr);
+        args->missed_line->pos  = args->tgt_itr_tmp->beg;
+        bcf_unpack(args->missed_line,BCF_UN_ALL);
+        bcf_update_alleles(args->aux.hdr, args->missed_line, (const char**)tgt_als->allele, tgt_als->n);
+        tgt_als->used = 1;
+        if ( bcf_write1(args->out_fh, args->aux.hdr, args->missed_line)!=0 ) error("[%s] Error: failed to write to %s\n", __func__,args->output_fname);
+    }
+}
+static void tgt_flush(args_t *args, bcf1_t *rec)
+{
+    if ( rec )
+    {
+        char *chr = (char*)bcf_seqname(args->aux.hdr,rec);
+
+        if ( !args->tgt_itr_prev )                  // first record
+            tgt_flush_region(args,chr,0,rec->pos-1);
+
+        else if ( strcmp(chr,args->tgt_itr_prev->seq) )  // first record on a new chromosome
+        {
+            tgt_flush_region(args,args->tgt_itr_prev->seq,args->tgt_itr_prev->beg+1,REGIDX_MAX);
+            tgt_flush_region(args,chr,0,rec->pos-1);
+        }
+        else                                        // another record on the same chromosome
+            tgt_flush_region(args,args->tgt_itr_prev->seq,args->tgt_itr_prev->beg,rec->pos-1);
+    }
+    else
+    {
+        // flush everything
+        if ( args->tgt_itr_prev )
+            tgt_flush_region(args,args->tgt_itr_prev->seq,args->tgt_itr_prev->beg,REGIDX_MAX);
+
+        int i, nchr = 0;
+        char **chr = regidx_seq_names(args->tgt_idx, &nchr);
+        for (i=0; i<nchr; i++)
+            tgt_flush_region(args,chr[i],0,REGIDX_MAX);
+    }
+}
+inline static int is_indel(int nals, char **als)
+{
+    // This is mpileup output, we can make some assumption:
+    //  - no MNPs
+    //  - "<*>" is not present at indels sites and there are no other symbolic alleles than <*>
+    if ( als[1][0]=='<' ) return 0;
+
+    int i;
+    for (i=0; i<nals; i++)
+    {
+        if ( als[i][0]=='<' ) continue;
+        if ( als[i][1] ) return 1;
+    }
+    return 0;
+}
+bcf1_t *next_line(args_t *args)
+{
+    bcf1_t *rec = NULL;
+    if ( !args->vcfbuf )
+    {
+        while ( bcf_sr_next_line(args->aux.srs) )
+        {
+            rec = args->aux.srs->readers[0].buffer[0];
+            if ( args->aux.srs->errnum || rec->errcode ) error("Error: could not parse the input VCF\n");
+            if ( args->tgt_idx )
+            {
+                if ( !regidx_overlap(args->tgt_idx, bcf_seqname(args->aux.hdr,rec),rec->pos,rec->pos,args->tgt_itr) ) continue;
+
+                // For backward compatibility: require the exact position, not an interval overlap
+                int pos_match = 0;
+                while ( regitr_overlap(args->tgt_itr) )
+                {
+                    if ( args->tgt_itr->beg != rec->pos ) continue;
+                    pos_match = 1;
+                    break;
+                }
+                if ( !pos_match ) continue;
+            }
+            if ( args->samples_map ) bcf_subset(args->aux.hdr, rec, args->nsamples, args->samples_map);
+            bcf_unpack(rec, BCF_UN_STR);
+            return rec;
+        }
+        return NULL;
+    }
+
+    // If we are here,-C alleles was given and vcfbuf and tgt_idx are set
+
+    // Fill the buffer with duplicate lines
+    int vcfbuf_full = 1;
+    int nbuf = vcfbuf_nsites(args->vcfbuf);
+    bcf1_t *rec0 = NULL, *recN = NULL;
+    if ( nbuf==0 ) vcfbuf_full = 0;
+    else if ( nbuf==1 )
+    {
+        vcfbuf_full = 0;
+        rec0 = vcfbuf_peek(args->vcfbuf, 0);
+    }
+    else
+    {
+        rec0 = vcfbuf_peek(args->vcfbuf, 0);
+        recN = vcfbuf_peek(args->vcfbuf, nbuf-1);
+        if ( rec0->rid == recN->rid && rec0->pos == recN->pos ) vcfbuf_full = 0;
+    }
+    if ( !vcfbuf_full )
+    {
+        while ( bcf_sr_next_line(args->aux.srs) )
+        {
+            rec = args->aux.srs->readers[0].buffer[0];
+            if ( args->aux.srs->errnum || rec->errcode ) error("Error: could not parse the input VCF\n");
+            if ( !regidx_overlap(args->tgt_idx, bcf_seqname(args->aux.hdr,rec),rec->pos,rec->pos,args->tgt_itr) ) continue;
+            // as above: require the exact position, not an interval overlap
+            int exact_match = 0;
+            while ( regitr_overlap(args->tgt_itr) )
+            {
+                if ( args->tgt_itr->beg != rec->pos ) continue;
+                exact_match = 1;
+                break;
+            }
+            if ( !exact_match ) continue;
+
+            if ( args->samples_map ) bcf_subset(args->aux.hdr, rec, args->nsamples, args->samples_map);
+            bcf_unpack(rec, BCF_UN_STR);
+            if ( !rec0 ) rec0 = rec;
+            recN = rec;
+            args->aux.srs->readers[0].buffer[0] = vcfbuf_push(args->vcfbuf, rec);
+            if ( rec0->rid!=recN->rid || rec0->pos!=recN->pos ) break;
+        }
+    }
+
+    nbuf = vcfbuf_nsites(args->vcfbuf);
+    int n, i,j;
+    for (n=nbuf; n>1; n--)
+    {
+        recN = vcfbuf_peek(args->vcfbuf, n-1);
+        if ( rec0->rid==recN->rid && rec0->pos==recN->pos ) break;
+    }
+    if ( n==0 )
+    {
+        assert( !nbuf );
+        return NULL;
+    }
+
+    // Find the VCF and tab record with the best matching combination of alleles, prioritize
+    // records of the same type (snp vs indel)
+    rec_tgt_t rec_tgt;
+    memset(&rec_tgt,0,sizeof(rec_tgt));
+    regidx_overlap(args->tgt_idx, bcf_seqname(args->aux.hdr,rec0),rec0->pos,rec0->pos,args->tgt_itr);
+    regitr_t *tmp_itr = regitr_init(args->tgt_idx);
+    regitr_copy(tmp_itr, args->tgt_itr);
+    for (i=0; i<n; i++)
+    {
+        rec = vcfbuf_peek(args->vcfbuf, i);
+        int rec_indel = is_indel(rec->n_allele, rec->d.allele) ? 1 : -1;
+        while ( regitr_overlap(tmp_itr) )
+        {
+            if ( tmp_itr->beg != rec->pos ) continue;
+            tgt_als_t *als = &regitr_payload(tmp_itr,tgt_als_t);
+            if ( als->used ) continue;
+            int nmatch_als = 0;
+            vcmp_t *vcmp = vcmp_init();
+            int ret = vcmp_set_ref(vcmp, rec->d.allele[0], als->allele[0]);
+            if ( ret==0 )
+            {
+                nmatch_als++;
+                if ( rec->n_allele > 1 && als->n > 1 )
+                {
+                    for (j=1; j<als->n; j++)
+                    {
+                        if ( vcmp_find_allele(vcmp, rec->d.allele+1, rec->n_allele-1, als->allele[j])>=0 ) nmatch_als++;
+                    }
+                }
+            }
+            int als_indel = is_indel(als->n, als->allele) ? 1 : -1;
+            nmatch_als *= rec_indel*als_indel;
+            if ( nmatch_als > rec_tgt.nmatch_als || !rec_tgt.als )
+            {
+                rec_tgt.nmatch_als = nmatch_als;
+                rec_tgt.als  = als;
+                rec_tgt.ibuf = i;
+            }
+            vcmp_destroy(vcmp);
+        }
+    }
+    regitr_destroy(tmp_itr);
+
+    args->aux.tgt_als = rec_tgt.als;
+    if ( rec_tgt.als ) rec_tgt.als->used = 1;
+
+    rec = vcfbuf_remove(args->vcfbuf, rec_tgt.ibuf);
+    return rec;
+}
+
+static void init_data(args_t *args)
+{
+    args->aux.srs = bcf_sr_init();
+
+    // Open files for input and output, initialize structures
+    if ( args->targets )
+    {
+        args->tgt_idx = regidx_init(args->targets, tgt_parse, args->aux.flag&CALL_CONSTR_ALLELES ? tgt_free : (regidx_free_f) NULL, sizeof(tgt_als_t), args->aux.flag&CALL_CONSTR_ALLELES ? args : NULL);
+        args->tgt_itr = regitr_init(args->tgt_idx);
+        args->tgt_itr_tmp = regitr_init(args->tgt_idx);
+    }
+
+    if ( args->regions )
+    {
+        bcf_sr_set_opt(args->aux.srs,BCF_SR_REGIONS_OVERLAP,args->regions_overlap);
+        if ( bcf_sr_set_regions(args->aux.srs, args->regions, args->regions_is_file)<0 )
+            error("Failed to read the regions: %s\n", args->regions);
+    }
+
+    if ( !bcf_sr_add_reader(args->aux.srs, args->bcf_fname) )
+        error("Failed to read from %s: %s\n", !strcmp("-",args->bcf_fname)?"standard input":args->bcf_fname,bcf_sr_strerror(args->aux.srs->errnum));
+    args->aux.hdr = bcf_sr_get_header(args->aux.srs,0);
+
+    int i;
+    if ( args->samples_fname )
+    {
+        set_samples(args, args->samples_fname, args->samples_is_file);
+        if ( args->aux.flag&CALL_CONSTR_TRIO )
+        {
+            if ( 3*args->aux.nfams!=args->nsamples ) error("Expected only trios in %s, sorry!\n", args->samples_fname);
+            fprintf(bcftools_stderr,"Detected %d samples in %d trio families\n", args->nsamples,args->aux.nfams);
+        }
+    }
+    if ( args->ploidy  )
+    {
+        args->nsex = ploidy_nsex(args->ploidy);
+        args->sex2ploidy = (int*) calloc(args->nsex,sizeof(int));
+        args->sex2ploidy_prev = (int*) calloc(args->nsex,sizeof(int));
+        if ( !args->nsamples )
+        {
+            args->nsamples = bcf_hdr_nsamples(args->aux.hdr);
+            args->sample2sex = (int*) malloc(sizeof(int)*args->nsamples);
+            for (i=0; i<args->nsamples; i++) args->sample2sex[i] = args->nsex - 1;
+        }
+    }
+    if ( args->nsamples )
+    {
+        args->aux.ploidy = (uint8_t*) malloc(args->nsamples);
+        for (i=0; i<args->nsamples; i++) args->aux.ploidy[i] = ploidy_max(args->ploidy);
+        for (i=0; i<args->nsex; i++) args->sex2ploidy_prev[i] = ploidy_max(args->ploidy);
+        for (i=0; i<args->nsamples; i++)
+            if ( args->sample2sex[i] >= args->nsex ) args->sample2sex[i] = args->nsex - 1;
+    }
+
+    if ( args->gvcf )
+    {
+        int id = bcf_hdr_id2int(args->aux.hdr,BCF_DT_ID,"DP");
+        if ( id<0 || !bcf_hdr_idinfo_exists(args->aux.hdr,BCF_HL_FMT,id) ) error("--gvcf output mode requires FORMAT/DP tag, which is not present in the input header\n");
+        gvcf_update_header(args->gvcf, args->aux.hdr);
+    }
+
+    if ( args->samples_map )
+    {
+        args->aux.hdr = bcf_hdr_subset(bcf_sr_get_header(args->aux.srs,0), args->nsamples, args->samples, args->samples_map);
+        if ( !args->aux.hdr ) error("Error occurred while subsetting samples\n");
+        for (i=0; i<args->nsamples; i++)
+            if ( args->samples_map[i]<0 ) error("No such sample: %s\n", args->samples[i]);
+        if ( !bcf_hdr_nsamples(args->aux.hdr) ) error("No matching sample found\n");
+    }
+    else
+    {
+        args->aux.hdr = bcf_hdr_dup(bcf_sr_get_header(args->aux.srs,0));
+        if ( args->samples )
+        {
+            for (i=0; i<args->nsamples; i++)
+                if ( bcf_hdr_id2int(args->aux.hdr,BCF_DT_SAMPLE,args->samples[i])<0 )
+                    error("No such sample: %s\n", args->samples[i]);
+        }
+    }
+
+    if ( args->aux.flag & CALL_CONSTR_ALLELES )
+        args->vcfbuf = vcfbuf_init(args->aux.hdr, 0);
+
+    char wmode[8];
+    set_wmode(wmode,args->output_type,args->output_fname,args->clevel);
+    args->out_fh = hts_open(args->output_fname ? args->output_fname : "-", wmode);
+    if ( args->out_fh == NULL ) error("Error: cannot write to \"%s\": %s\n", args->output_fname, strerror(errno));
+    if ( args->n_threads ) hts_set_threads(args->out_fh, args->n_threads);
+
+    if ( args->flag & CF_QCALL )
+        return;
+
+    if ( args->flag & CF_MCALL )
+        mcall_init(&args->aux);
+
+    if ( args->flag & CF_CCALL )
+        ccall_init(&args->aux);
+
+    bcf_hdr_remove(args->aux.hdr, BCF_HL_INFO, "QS");
+    bcf_hdr_remove(args->aux.hdr, BCF_HL_INFO, "I16");
+
+    if (args->record_cmd_line) bcf_hdr_append_version(args->aux.hdr, args->argc, args->argv, "bcftools_call");
+    if ( bcf_hdr_write(args->out_fh, args->aux.hdr)!=0 ) error("[%s] Error: cannot write the header to %s\n", __func__,args->output_fname);
+
+    if ( args->flag&CF_INS_MISSED ) init_missed_line(args);
+}
+
+static void destroy_data(args_t *args)
+{
+    if ( args->vcfbuf ) vcfbuf_destroy(args->vcfbuf);
+    if ( args->tgt_idx )
+    {
+        regidx_destroy(args->tgt_idx);
+        regitr_destroy(args->tgt_itr);
+        regitr_destroy(args->tgt_itr_tmp);
+        if ( args->tgt_itr_prev ) regitr_destroy(args->tgt_itr_prev);
+    }
+    if ( args->flag & CF_CCALL ) ccall_destroy(&args->aux);
+    else if ( args->flag & CF_MCALL ) mcall_destroy(&args->aux);
+    else if ( args->flag & CF_QCALL ) qcall_destroy(&args->aux);
+    int i;
+    if ( args->samples )
+    {
+        for (i=0; i<args->nsamples; i++) free(args->samples[i]);
+    }
+    if ( args->aux.fams )
+    {
+        for (i=0; i<args->aux.nfams; i++) free(args->aux.fams[i].name);
+        free(args->aux.fams);
+    }
+    if ( args->missed_line ) bcf_destroy(args->missed_line);
+    ploidy_destroy(args->ploidy);
+    free(args->sex2ploidy);
+    free(args->sex2ploidy_prev);
+    free(args->samples);
+    free(args->samples_map);
+    free(args->sample2sex);
+    free(args->aux.ploidy);
+    free(args->str.s);
+    if ( args->gvcf ) gvcf_destroy(args->gvcf);
+    bcf_hdr_destroy(args->aux.hdr);
+    if ( hts_close(args->out_fh)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,args->output_fname);
+    bcf_sr_destroy(args->aux.srs);
+}
+
+void parse_novel_rate(args_t *args, const char *str)
+{
+    if ( sscanf(str,"%le,%le,%le",&args->aux.trio_Pm_SNPs,&args->aux.trio_Pm_del,&args->aux.trio_Pm_ins)==3 )  // explicit for all
+    {
+        args->aux.trio_Pm_SNPs = 1 - args->aux.trio_Pm_SNPs;
+        args->aux.trio_Pm_del  = 1 - args->aux.trio_Pm_del;
+        args->aux.trio_Pm_ins  = 1 - args->aux.trio_Pm_ins;
+    }
+    else if ( sscanf(str,"%le,%le",&args->aux.trio_Pm_SNPs,&args->aux.trio_Pm_del)==2 )   // dynamic for indels
+    {
+        args->aux.trio_Pm_SNPs = 1 - args->aux.trio_Pm_SNPs;
+        args->aux.trio_Pm_ins  = -1;    // negative value for dynamic calculation
+    }
+    else if ( sscanf(str,"%le",&args->aux.trio_Pm_SNPs)==1 )  // same for all
+    {
+        args->aux.trio_Pm_SNPs = 1 - args->aux.trio_Pm_SNPs;
+        args->aux.trio_Pm_del  = -1;
+        args->aux.trio_Pm_ins  = -1;
+    }
+    else error("Could not parse --novel-rate %s\n", str);
+}
+
+static void list_annotations(FILE *fp)
+{
+    fprintf(fp,
+        "\n"
+        "Optional INFO annotations available with -m (\"INFO/\" prefix is optional):\n"
+        "  INFO/PV4   .. P-values for strand bias, baseQ bias, mapQ bias and tail distance bias (Number=4,Type=Float)\n"
+        "\n"
+        "Optional FORMAT annotations available with -m (\"FORMAT/\" prefix is optional):\n"
+        "  FORMAT/GQ  .. Phred-scaled genotype quality (Number=1,Type=Integer)\n"
+        "  FORMAT/GP  .. Phred-scaled genotype posterior probabilities (Number=G,Type=Float)\n"
+        "\n");
+}
+
+static int parse_output_tags(const char *str)
+{
+    int flag = 0;
+    const char *ss = str;
+    while ( *ss )
+    {
+        const char *se = ss;
+        while ( *se && *se!=',' ) se++;
+        if ( !strncasecmp(ss,"GQ",se-ss) || !strncasecmp(ss,"FORMAT/GQ",se-ss) || !strncasecmp(ss,"FMT/GQ",se-ss)  ) flag |= CALL_FMT_GQ;
+        else if ( !strncasecmp(ss,"GP",se-ss) || !strncasecmp(ss,"FORMAT/GP",se-ss) || !strncasecmp(ss,"FMT/GP",se-ss) ) flag |= CALL_FMT_GP;
+        else if ( !strncasecmp(ss,"PV4",se-ss) || !strncasecmp(ss,"INFO/PV4",se-ss) ) flag |= CALL_FMT_PV4;
+        else
+        {
+            fprintf(bcftools_stderr,"Could not parse \"%s\"\n", str);
+            bcftools_exit(1);
+        }
+        if ( !*se ) break;
+        ss = se + 1;
+    }
+    return flag;
+}
+
+static void set_ploidy(args_t *args, bcf1_t *rec)
+{
+    ploidy_query(args->ploidy,(char*)bcf_seqname(args->aux.hdr,rec),rec->pos,args->sex2ploidy,NULL,NULL);
+
+    int i;
+    for (i=0; i<args->nsex; i++)
+        if ( args->sex2ploidy[i]!=args->sex2ploidy_prev[i] ) break;
+
+    if ( i==args->nsex ) return;    // ploidy same as previously
+
+    for (i=0; i<args->nsamples; i++)
+    {
+        if ( args->sample2sex[i]<0 )
+            args->aux.ploidy[i] = -1*args->sample2sex[i];
+        else
+            args->aux.ploidy[i] = args->sex2ploidy[args->sample2sex[i]];
+    }
+    int *tmp = args->sex2ploidy; args->sex2ploidy = args->sex2ploidy_prev; args->sex2ploidy_prev = tmp;
+}
+
+ploidy_t *init_ploidy(char *alias)
+{
+    const ploidy_predef_t *pld = ploidy_predefs;
+
+    int detailed = 0, len = strlen(alias);
+    if ( alias[len-1]=='?' ) { detailed = 1; alias[len-1] = 0; }
+
+    while ( pld->alias && strcasecmp(alias,pld->alias) ) pld++;
+
+    if ( !pld->alias )
+    {
+        fprintf(bcftools_stderr,"\nPRE-DEFINED PLOIDY FILES\n\n");
+        fprintf(bcftools_stderr," * Columns are: CHROM,FROM,TO,SEX,PLOIDY\n");
+        fprintf(bcftools_stderr," * Coordinates are 1-based inclusive.\n");
+        fprintf(bcftools_stderr," * A '*' means any value not otherwise defined.\n\n");
+        pld = ploidy_predefs;
+        while ( pld->alias )
+        {
+            fprintf(bcftools_stderr,"%s\n   .. %s\n\n", pld->alias,pld->about);
+            if ( detailed )
+                fprintf(bcftools_stderr,"%s\n", pld->ploidy);
+            pld++;
+        }
+        fprintf(bcftools_stderr,"Run as --ploidy <alias> (e.g. --ploidy GRCh37).\n");
+        fprintf(bcftools_stderr,"To see the detailed ploidy definition, append a question mark (e.g. --ploidy GRCh37?).\n");
+        fprintf(bcftools_stderr,"\n");
+        bcftools_exit(-1);
+    }
+    else if ( detailed )
+    {
+        fprintf(bcftools_stderr,"%s", pld->ploidy);
+        bcftools_exit(-1);
+    }
+    return ploidy_init_string(pld->ploidy,2);
+}
+
+static void usage(args_t *args)
+{
+    fprintf(bcftools_stderr, "\n");
+    fprintf(bcftools_stderr, "About:   SNP/indel variant calling from VCF/BCF. To be used in conjunction with bcftools mpileup.\n");
+    fprintf(bcftools_stderr, "         This command replaces the former \"bcftools view\" caller. Some of the original\n");
+    fprintf(bcftools_stderr, "         functionality has been temporarily lost in the process of transition to htslib,\n");
+    fprintf(bcftools_stderr, "         but will be added back on popular demand. The original calling model can be\n");
+    fprintf(bcftools_stderr, "         invoked with the -c option.\n");
+    fprintf(bcftools_stderr, "Usage:   bcftools call [options] <in.vcf.gz>\n");
+    fprintf(bcftools_stderr, "\n");
+    fprintf(bcftools_stderr, "File format options:\n");
+    fprintf(bcftools_stderr, "       --no-version                Do not append version and command line to the header\n");
+    fprintf(bcftools_stderr, "   -o, --output FILE               Write output to a file [standard output]\n");
+    fprintf(bcftools_stderr, "   -O, --output-type b|u|z|v       Output type: 'b' compressed BCF; 'u' uncompressed BCF; 'z' compressed VCF; 'v' uncompressed VCF [v]\n");
+    fprintf(bcftools_stderr, "   -O, --output-type u|b|v|z[0-9]  u/b: un/compressed BCF, v/z: un/compressed VCF, 0-9: compression level [v]\n");
+    fprintf(bcftools_stderr, "       --ploidy ASSEMBLY[?]        Predefined ploidy, 'list' to print available settings, append '?' for details [2]\n");
+    fprintf(bcftools_stderr, "       --ploidy-file FILE          Space/tab-delimited list of CHROM,FROM,TO,SEX,PLOIDY\n");
+    fprintf(bcftools_stderr, "   -r, --regions REGION            Restrict to comma-separated list of regions\n");
+    fprintf(bcftools_stderr, "   -R, --regions-file FILE         Restrict to regions listed in a file\n");
+    fprintf(bcftools_stderr, "       --regions-overlap 0|1|2     Include if POS in the region (0), record overlaps (1), variant overlaps (2) [1]\n");
+    fprintf(bcftools_stderr, "   -s, --samples LIST              List of samples to include [all samples]\n");
+    fprintf(bcftools_stderr, "   -S, --samples-file FILE         PED file or a file with an optional column with sex (see man page for details) [all samples]\n");
+    fprintf(bcftools_stderr, "   -t, --targets REGION            Similar to -r but streams rather than index-jumps\n");
+    fprintf(bcftools_stderr, "   -T, --targets-file FILE         Similar to -R but streams rather than index-jumps\n");
+    fprintf(bcftools_stderr, "       --threads INT               Use multithreading with INT worker threads [0]\n");
+    fprintf(bcftools_stderr, "\n");
+    fprintf(bcftools_stderr, "Input/output options:\n");
+    fprintf(bcftools_stderr, "   -A, --keep-alts                 Keep all possible alternate alleles at variant sites\n");
+    fprintf(bcftools_stderr, "   -a, --annotate LIST             Optional tags to output (lowercase allowed); '?' to list available tags\n");
+    fprintf(bcftools_stderr, "   -F, --prior-freqs AN,AC         Use prior allele frequencies, determined from these pre-filled tags\n");
+    fprintf(bcftools_stderr, "   -G, --group-samples FILE|-      Group samples by population (file with \"sample\\tgroup\") or \"-\" for single-sample calling.\n");
+    fprintf(bcftools_stderr, "                                   This requires FORMAT/QS or other Number=R,Type=Integer tag such as FORMAT/AD\n");
+    fprintf(bcftools_stderr, "       --group-samples-tag TAG     The tag to use with -G, by default FORMAT/QS and FORMAT/AD are checked automatically\n");
+    fprintf(bcftools_stderr, "   -g, --gvcf INT,[...]            Group non-variant sites into gVCF blocks by minimum per-sample DP\n");
+    fprintf(bcftools_stderr, "   -i, --insert-missed             Output also sites missed by mpileup but present in -T\n");
+    fprintf(bcftools_stderr, "   -M, --keep-masked-ref           Keep sites with masked reference allele (REF=N)\n");
+    fprintf(bcftools_stderr, "   -V, --skip-variants TYPE        Skip indels/snps\n");
+    fprintf(bcftools_stderr, "   -v, --variants-only             Output variant sites only\n");
+    fprintf(bcftools_stderr, "\n");
+    fprintf(bcftools_stderr, "Consensus/variant calling options:\n");
+    fprintf(bcftools_stderr, "   -c, --consensus-caller          The original calling method (conflicts with -m)\n");
+    fprintf(bcftools_stderr, "   -C, --constrain STR             One of: alleles, trio (see manual)\n");
+    fprintf(bcftools_stderr, "   -m, --multiallelic-caller       Alternative model for multiallelic and rare-variant calling (conflicts with -c)\n");
+    fprintf(bcftools_stderr, "   -n, --novel-rate FLOAT,[...]    Likelihood of novel mutation for constrained trio calling, see man page for details [1e-8,1e-9,1e-9]\n");
+    fprintf(bcftools_stderr, "   -p, --pval-threshold FLOAT      Variant if P(ref|D)<FLOAT with -c [0.5]\n");
+    fprintf(bcftools_stderr, "   -P, --prior FLOAT               Mutation rate (use bigger for greater sensitivity), use with -m [1.1e-3]\n");
+    fprintf(bcftools_stderr, "\n");
+    fprintf(bcftools_stderr, "Example:\n");
+    fprintf(bcftools_stderr, "   # See also http://samtools.github.io/bcftools/howtos/variant-calling.html\n");
+    fprintf(bcftools_stderr, "   bcftools mpileup -Ou -f reference.fa alignments.bam | bcftools call -mv -Ob -o calls.bcf\n");
+
+    // todo (and more)
+    // fprintf(bcftools_stderr, "\nContrast calling and association test options:\n");
+    // fprintf(bcftools_stderr, "       -1 INT    number of group-1 samples [0]\n");
+    // fprintf(bcftools_stderr, "       -C FLOAT  posterior constrast for LRT<FLOAT and P(ref|D)<0.5 [%g]\n", args->aux.min_lrt);
+    // fprintf(bcftools_stderr, "       -U INT    number of permutations for association testing (effective with -1) [0]\n");
+    // fprintf(bcftools_stderr, "       -X FLOAT  only perform permutations for P(chi^2)<FLOAT [%g]\n", args->aux.min_perm_p);
+    fprintf(bcftools_stderr, "\n");
+    bcftools_exit(-1);
+}
+
+int main_vcfcall(int argc, char *argv[])
+{
+    char *ploidy_fname = NULL, *ploidy = NULL;
+    args_t args;
+    memset(&args, 0, sizeof(args_t));
+    args.argc = argc; args.argv = argv;
+    args.aux.prior_type = -1;
+    args.aux.indel_frac = -1;
+    args.aux.theta      = 1.1e-3;
+    args.aux.pref       = 0.5;
+    args.aux.min_perm_p = 0.01;
+    args.aux.min_lrt    = 1;
+    args.flag           = CF_ACGT_ONLY;
+    args.output_fname   = "-";
+    args.output_type    = FT_VCF;
+    args.n_threads = 0;
+    args.record_cmd_line = 1;
+    args.aux.trio_Pm_SNPs = 1 - 1e-8;
+    args.aux.trio_Pm_ins  = args.aux.trio_Pm_del  = 1 - 1e-9;
+    args.regions_overlap = 1;
+    args.clevel = -1;
+
+    int c;
+    static struct option loptions[] =
+    {
+        {"help",no_argument,NULL,'h'},
+        {"format-fields",required_argument,NULL,'f'},
+        {"annotate",required_argument,NULL,'a'},
+        {"prior-freqs",required_argument,NULL,'F'},
+        {"gvcf",required_argument,NULL,'g'},
+        {"group-samples",required_argument,NULL,'G'},
+        {"group-samples-tag",required_argument,NULL,3},
+        {"output",required_argument,NULL,'o'},
+        {"output-type",required_argument,NULL,'O'},
+        {"regions",required_argument,NULL,'r'},
+        {"regions-file",required_argument,NULL,'R'},
+        {"regions-overlap",required_argument,NULL,4},
+        {"samples",required_argument,NULL,'s'},
+        {"samples-file",required_argument,NULL,'S'},
+        {"targets",required_argument,NULL,'t'},
+        {"targets-file",required_argument,NULL,'T'},
+        {"threads",required_argument,NULL,9},
+        {"keep-alts",no_argument,NULL,'A'},
+        {"insert-missed",no_argument,NULL,'i'},
+        {"skip-Ns",no_argument,NULL,'N'},            // now the new default
+        {"keep-masked-refs",no_argument,NULL,'M'},
+        {"skip-variants",required_argument,NULL,'V'},
+        {"variants-only",no_argument,NULL,'v'},
+        {"consensus-caller",no_argument,NULL,'c'},
+        {"constrain",required_argument,NULL,'C'},
+        {"multiallelic-caller",no_argument,NULL,'m'},
+        {"pval-threshold",required_argument,NULL,'p'},
+        {"prior",required_argument,NULL,'P'},
+        {"novel-rate",required_argument,NULL,'n'},
+        {"ploidy",required_argument,NULL,1},
+        {"ploidy-file",required_argument,NULL,2},
+        {"chromosome-X",no_argument,NULL,'X'},
+        {"chromosome-Y",no_argument,NULL,'Y'},
+        {"no-version",no_argument,NULL,8},
+        {NULL,0,NULL,0}
+    };
+
+    char *tmp = NULL;
+    while ((c = getopt_long(argc, argv, "h?o:O:r:R:s:S:t:T:ANMV:vcmp:C:n:P:f:a:ig:XYF:G:", loptions, NULL)) >= 0)
+    {
+        switch (c)
+        {
+            case  2 : ploidy_fname = optarg; break;
+            case  1 : ploidy = optarg; break;
+            case 'X': ploidy = "X"; fprintf(bcftools_stderr,"Warning: -X will be deprecated, please use --ploidy instead.\n"); break;
+            case 'Y': ploidy = "Y"; fprintf(bcftools_stderr,"Warning: -Y will be deprecated, please use --ploidy instead.\n"); break;
+            case 'G': args.aux.sample_groups = optarg; break;
+            case  3 : args.aux.sample_groups_tag = optarg; break;
+            case 'f': fprintf(bcftools_stderr,"Warning: -f, --format-fields will be deprecated, please use -a, --annotate instead.\n");
+            case 'a':
+                      if (optarg[0]=='?') { list_annotations(bcftools_stderr); return 1; }
+                      args.aux.output_tags |= parse_output_tags(optarg);
+                      break;
+            case 'M': args.flag &= ~CF_ACGT_ONLY; break;     // keep sites where REF is N
+            case 'N': args.flag |= CF_ACGT_ONLY; break;      // omit sites where first base in REF is N (the new default)
+            case 'A': args.aux.flag |= CALL_KEEPALT; break;
+            case 'c': args.flag |= CF_CCALL; break;          // the original EM based calling method
+            case 'i': args.flag |= CF_INS_MISSED; break;
+            case 'v': args.aux.flag |= CALL_VARONLY; break;
+            case 'F':
+                args.aux.prior_AN = optarg;
+                args.aux.prior_AC = strchr(optarg,',');
+                if ( !args.aux.prior_AC ) error("Expected two tags with -F (e.g. AN,AC), got \"%s\"\n",optarg);
+                *args.aux.prior_AC = 0;
+                args.aux.prior_AC++;
+                break;
+            case 'g':
+                args.gvcf = gvcf_init(optarg);
+                if ( !args.gvcf ) error("Could not parse: --gvcf %s\n", optarg);
+                break;
+            case 'o': args.output_fname = optarg; break;
+            case 'O':
+                      switch (optarg[0]) {
+                          case 'b': args.output_type = FT_BCF_GZ; break;
+                          case 'u': args.output_type = FT_BCF; break;
+                          case 'z': args.output_type = FT_VCF_GZ; break;
+                          case 'v': args.output_type = FT_VCF; break;
+                          default:
+                          {
+                              args.clevel = strtol(optarg,&tmp,10);
+                              if ( *tmp || args.clevel<0 || args.clevel>9 ) error("The output type \"%s\" not recognised\n", optarg);
+                          }
+                      }
+                      if ( optarg[1] )
+                      {
+                          args.clevel = strtol(optarg+1,&tmp,10);
+                          if ( *tmp || args.clevel<0 || args.clevel>9 ) error("Could not parse argument: --compression-level %s\n", optarg+1);
+                      }
+                      break;
+            case 'C':
+                      if ( !strcasecmp(optarg,"alleles") ) args.aux.flag |= CALL_CONSTR_ALLELES;
+                      else if ( !strcasecmp(optarg,"trio") ) args.aux.flag |= CALL_CONSTR_TRIO;
+                      else error("Unknown argument to -C: \"%s\"\n", optarg);
+                      break;
+            case 'V':
+                      if ( !strcasecmp(optarg,"snps") ) args.flag |= CF_INDEL_ONLY;
+                      else if ( !strcasecmp(optarg,"indels") ) args.flag |= CF_NO_INDEL;
+                      else error("Unknown skip category \"%s\" (-S argument must be \"snps\" or \"indels\")\n", optarg);
+                      break;
+            case 'm': args.flag |= CF_MCALL; break;         // multiallelic calling method
+            case 'p':
+                args.aux.pref = strtod(optarg,&tmp);
+                if ( *tmp ) error("Could not parse: --pval-threshold %s\n", optarg);
+                break;
+            case 'P': args.aux.theta = strtod(optarg,&tmp);
+                      if ( *tmp ) error("Could not parse, expected float argument: -P %s\n", optarg);
+                      break;
+            case 'n': parse_novel_rate(&args,optarg); break;
+            case 'r': args.regions = optarg; break;
+            case 'R': args.regions = optarg; args.regions_is_file = 1; break;
+            case 't': args.targets = optarg; break;
+            case 'T': args.targets = optarg; args.targets_is_file = 1; break;
+            case 's': args.samples_fname = optarg; break;
+            case 'S': args.samples_fname = optarg; args.samples_is_file = 1; break;
+            case  9 : args.n_threads = strtol(optarg, 0, 0); break;
+            case  8 : args.record_cmd_line = 0; break;
+            case  4 :
+                args.regions_overlap = parse_overlap_option(optarg);
+                if ( args.regions_overlap < 0 ) error("Could not parse: --regions-overlap %s\n",optarg);
+                break;
+            default: usage(&args);
+        }
+    }
+    // Sanity check options and initialize
+    if ( ploidy_fname ) args.ploidy = ploidy_init(ploidy_fname, 2);
+    else if ( ploidy ) args.ploidy = init_ploidy(ploidy);
+
+    if ( optind>=argc )
+    {
+        if ( !isatty(fileno((FILE *)stdin)) ) args.bcf_fname = "-";  // reading from stdin
+        else usage(&args);
+    }
+    else args.bcf_fname = argv[optind++];
+
+    if ( !ploidy_fname && !ploidy )
+    {
+        if ( !args.samples_is_file ) fprintf(bcftools_stderr,"Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid\n");
+        args.ploidy = ploidy_init_string("* * * 0 0\n* * * 1 1\n* * * 2 2\n",2);
+    }
+
+    if ( !args.ploidy ) error("Could not initialize ploidy\n");
+    if ( (args.flag & CF_CCALL ? 1 : 0) + (args.flag & CF_MCALL ? 1 : 0) + (args.flag & CF_QCALL ? 1 : 0) > 1 ) error("Only one of -c or -m options can be given\n");
+    if ( !(args.flag & CF_CCALL) && !(args.flag & CF_MCALL) && !(args.flag & CF_QCALL) ) error("Expected -c or -m option\n");
+    if ( (args.flag & CF_CCALL ? 1: 0) && args.gvcf ) error("gvcf -g option not functional with -c calling mode yet\n");
+    if ( args.aux.n_perm && args.aux.ngrp1_samples<=0 ) error("Expected -1 with -U\n");    // not sure about this, please fix
+    if ( args.aux.flag & CALL_CONSTR_ALLELES )
+    {
+        if ( !args.targets ) error("Expected -t or -T with \"-C alleles\"\n");
+        if ( !(args.flag & CF_MCALL) ) error("The \"-C alleles\" mode requires -m\n");
+    }
+    if ( args.flag & CF_INS_MISSED && !(args.aux.flag&CALL_CONSTR_ALLELES) ) error("The -i option requires -C alleles\n");
+    if ( args.aux.flag&CALL_VARONLY && args.gvcf ) error("The two options cannot be combined: --variants-only and --gvcf\n");
+    if ( args.aux.sample_groups && !(args.flag & CF_MCALL) ) error("The -G feature is supported only with the -m calling mode\n");
+    init_data(&args);
+
+    bcf1_t *bcf_rec;
+    while ( (bcf_rec = next_line(&args)) )
+    {
+        // Skip duplicate positions with all matching `-C alleles -T` used up
+        if ( args.aux.flag&CALL_CONSTR_ALLELES && !args.aux.tgt_als ) continue;
+
+        // Skip unwanted sites
+        int i, is_indel = bcf_is_snp(bcf_rec) ? 0 : 1;
+        if ( (args.flag & CF_INDEL_ONLY) && !is_indel ) continue;
+        if ( (args.flag & CF_NO_INDEL) && is_indel ) continue;
+        if ( (args.flag & CF_ACGT_ONLY) && (bcf_rec->d.allele[0][0]=='N' || bcf_rec->d.allele[0][0]=='n') ) continue;   // REF[0] is 'N'
+
+        // Which allele is symbolic? All SNPs should have it, but not indels
+        args.aux.unseen = 0;
+        for (i=1; i<bcf_rec->n_allele; i++)
+        {
+            if ( bcf_rec->d.allele[i][0]=='X' ) { args.aux.unseen = i; break; }  // old X
+            if ( bcf_rec->d.allele[i][0]=='<' )
+            {
+                if ( bcf_rec->d.allele[i][1]=='X' && bcf_rec->d.allele[i][2]=='>' ) { args.aux.unseen = i; break; } // old <X>
+                if ( bcf_rec->d.allele[i][1]=='*' && bcf_rec->d.allele[i][2]=='>' ) { args.aux.unseen = i; break; } // new <*>
+            }
+        }
+        int is_ref = (bcf_rec->n_allele==1 || (bcf_rec->n_allele==2 && args.aux.unseen>0)) ? 1 : 0;
+
+        if ( is_ref && args.aux.flag&CALL_VARONLY )
+            continue;
+
+        bcf_unpack(bcf_rec, BCF_UN_ALL);
+        if ( args.nsex ) set_ploidy(&args, bcf_rec);
+
+        // Various output modes: QCall output (todo)
+        if ( args.flag & CF_QCALL )
+        {
+            qcall(&args.aux, bcf_rec);
+            continue;
+        }
+
+        if ( args.flag & CF_INS_MISSED )
+        {
+            tgt_flush(&args,bcf_rec);
+            if ( !args.tgt_itr_prev ) args.tgt_itr_prev = regitr_init(args.tgt_idx);
+            regitr_copy(args.tgt_itr_prev, args.tgt_itr);
+        }
+
+        // Calling modes which output VCFs
+        int ret;
+        if ( args.flag & CF_MCALL )
+            ret = mcall(&args.aux, bcf_rec);
+        else
+            ret = ccall(&args.aux, bcf_rec);
+        if ( ret==-1 ) error("Something is wrong\n");
+        else if ( ret==-2 ) continue;   // skip the site
+
+        // Normal output
+        if ( (args.aux.flag & CALL_VARONLY) && ret==0 && !args.gvcf ) continue;     // not a variant
+        if ( args.gvcf )
+            bcf_rec = gvcf_write(args.gvcf, args.out_fh, args.aux.hdr, bcf_rec, ret==1?1:0);
+        if ( bcf_rec && bcf_write1(args.out_fh, args.aux.hdr, bcf_rec)!=0 ) error("[%s] Error: failed to write to %s\n", __func__,args.output_fname);
+    }
+    if ( args.gvcf ) gvcf_write(args.gvcf, args.out_fh, args.aux.hdr, NULL, 0);
+    if ( args.flag & CF_INS_MISSED ) tgt_flush(&args,NULL);
+    destroy_data(&args);
+    return 0;
+}
+
diff --git a/bcftools/vcfcnv.c b/bcftools/vcfcnv.c
new file mode 100644
index 0000000..0302261
--- /dev/null
+++ b/bcftools/vcfcnv.c
@@ -0,0 +1,1438 @@
+/* The MIT License
+
+   Copyright (c) 2014-2022 Genome Research Ltd.
+
+   Author: Petr Danecek <pd3@sanger.ac.uk>
+   
+   Permission is hereby granted, free of charge, to any person obtaining a copy
+   of this software and associated documentation files (the "Software"), to deal
+   in the Software without restriction, including without limitation the rights
+   to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+   copies of the Software, and to permit persons to whom the Software is
+   furnished to do so, subject to the following conditions:
+   
+   The above copyright notice and this permission notice shall be included in
+   all copies or substantial portions of the Software.
+   
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+   IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+   FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+   AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+   LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+   OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+   THE SOFTWARE.
+
+ */
+
+/*
+    Known issues:
+    - The --AF-file option behaves like --targets-file, sites not listed in the AFs
+      are skipped.
+*/
+
+#include <stdio.h>
+#include <unistd.h>
+#include <assert.h>
+#include <getopt.h>
+#include <math.h>
+#include <inttypes.h>
+#include <htslib/vcf.h>
+#include <htslib/synced_bcf_reader.h>
+#include <htslib/kstring.h>
+#include <htslib/kfunc.h>
+#include <htslib/khash_str2int.h>
+#include "bcftools.h"
+#include "HMM.h"
+#include "rbuf.h"
+
+#define DBG0 0
+
+#define N_STATES 4
+#define CN0 0
+#define CN1 1
+#define CN2 2
+#define CN3 3
+
+typedef struct
+{
+    float mean, dev2, norm;
+}
+gauss_param_t;
+
+typedef struct
+{
+    char *name;
+    int idx;    // VCF sample index
+    float *lrr,*baf, baf_dev2, baf_dev2_dflt, lrr_dev2;
+    float cell_frac, cell_frac_dflt;
+    gauss_param_t gauss_param[18];
+    double pobs[N_STATES];
+    FILE *dat_fh, *cn_fh, *summary_fh;
+    char *dat_fname, *cn_fname, *summary_fname;
+}
+sample_t;
+
+typedef struct _args_t
+{
+    bcf_srs_t *files;
+    bcf_hdr_t *hdr;
+    int prev_rid, ntot, nused;
+    sample_t query_sample, control_sample;
+
+    int nstates;    // number of states: N_STATES for one sample, N_STATES^2 for two samples
+    double lrr_bias, baf_bias;              // LRR/BAF weights
+    double same_prob, ij_prob;              // prior of both samples being the same and the transition probability P(i|j)
+    double err_prob;                        // constant probability of erroneous measurement
+    float *nonref_afs, nonref_af, nonref_af_dflt, fRR, fRA, fAA, *tmpf;
+    unsigned long int nRR, nRA, nAA;
+    int mtmpf;
+
+    double *tprob, *tprob_arr;  // array of transition matrices, precalculated up to ntprob_arr positions
+    double *iprobs;             // states' initial probabilities
+    int ntprob_arr;
+
+    hmm_t *hmm;
+    double *eprob;          // emission probs [nstates*nsites,msites]
+    uint32_t *sites;        // positions [nsites,msites]
+    int nsites, msites;
+
+    double baum_welch_th, optimize_frac; 
+    float plot_th;
+    FILE *summary_fh;
+    char **argv, *regions_list, *summary_fname, *output_dir;
+    char *targets_list, *af_fname;
+    int argc, verbose, lrr_smooth_win;
+}
+args_t;
+
+FILE *open_file(char **fname, const char *mode, const char *fmt, ...);
+
+static inline void hmm2cn_state(int nstates, int i, int *a, int *b)
+{
+    *a = i / N_STATES;
+    *b = i - (*a)*N_STATES;
+}
+static double *init_tprob_matrix(int ndim, double ij_prob, double same_prob)
+{
+    int i,j;
+    double *mat = (double*) malloc(sizeof(double)*ndim*ndim);
+
+    assert( ndim==N_STATES || ndim==N_STATES*N_STATES);
+
+    if ( ndim==N_STATES )   // one sample
+    {
+        double pii = 1 - ij_prob*(N_STATES-1);
+        if ( pii < ij_prob ) error("Error: -x set a bit too high, P(x|x) < P(x|y): %e vs %e\n", pii,ij_prob);
+        for (j=0; j<ndim; j++)
+        {
+            double sum = 0;
+            for (i=0; i<ndim; i++)
+            {
+                // transition from j-th to i-th state
+                if ( i==j )
+                    MAT(mat,ndim,i,j) = pii;
+                else
+                    MAT(mat,ndim,i,j) = ij_prob;
+
+                sum += MAT(mat,ndim,i,j);
+            }
+            assert( fabs(sum - 1.0)<1e-15 );
+        }
+    }
+    else    // two samples
+    {
+        // interpret ij_prob differently, as ii_prob in fact, so that for two
+        // samples the behaviour is somewhat closer to single sample calling
+        // with s=0. 
+        double pii = 1 - ij_prob*(N_STATES-1);
+        ij_prob = (1 - pii) / (ndim - 1);
+        for (j=0; j<ndim; j++)
+        {
+            int ja,jb;
+            hmm2cn_state(ndim, j, &ja, &jb);
+
+            double sum = 0;
+            for (i=0; i<ndim; i++)
+            {
+                int ia,ib;
+                hmm2cn_state(ndim, i, &ia, &ib);
+
+                // transition from (ja,jb)-th to (ia,ib)-th state
+                double pa = ja==ia ? pii : ij_prob;
+                double pb = jb==ib ? pii : ij_prob;
+
+                if ( ia==ib && ja==jb )
+                    MAT(mat,ndim,i,j) = pa*pb - pa*pb*same_prob + sqrt(pa*pb)*same_prob;
+                else if ( ia==ib )
+                    MAT(mat,ndim,i,j) = pa*pb;
+                else
+                    MAT(mat,ndim,i,j) = pa*pb*(1-same_prob);
+
+                sum += MAT(mat,ndim,i,j);
+            }
+            for (i=0; i<ndim; i++) MAT(mat,ndim,i,j) /= sum;
+        }
+    }
+    return mat;
+}
+
+static double *init_iprobs(int ndim, double same_prob)
+{
+    int i;
+    double *probs = (double*) malloc(sizeof(double)*ndim);
+
+    assert( ndim==N_STATES || ndim==N_STATES*N_STATES);
+
+    if ( ndim==N_STATES )   
+    {
+        // one sample: prior on CN2
+        for (i=0; i<ndim; i++) 
+            probs[i] = i==CN2 ? 0.5 : 0.5/3;
+    }
+    else
+    {
+        // two samples
+        double norm = 0;
+        for (i=0; i<ndim; i++) 
+        {
+            int ia,ib;
+            hmm2cn_state(ndim, i, &ia, &ib);
+
+            double pa = ia==CN2 ? 0.5 : 0.5/3;
+            double pb = ib==CN2 ? 0.5 : 0.5/3;
+
+            probs[i] = pa*pb;
+            if ( ia!=ib ) probs[i] *= 1-same_prob;
+
+            norm += probs[i];
+        }
+        for (i=0; i<ndim; i++) probs[i] /= norm;
+    }
+    return probs;
+}
+
+static void init_sample_files(sample_t *smpl, char *dir)
+{
+    smpl->dat_fh = open_file(&smpl->dat_fname,"w","%s/dat.%s.tab",dir,smpl->name);
+    if ( !smpl->dat_fh ) error("Error opening file: %s/dat.%s.tab\n",dir,smpl->name);
+
+    smpl->cn_fh  = open_file(&smpl->cn_fname,"w","%s/cn.%s.tab",dir,smpl->name);
+    if ( !smpl->cn_fh ) error("Error opening file: %s/cn.%s.tab\n",dir,smpl->name);
+
+    smpl->summary_fh = open_file(&smpl->summary_fname,"w","%s/summary.%s.tab",dir,smpl->name);
+    if ( !smpl->summary_fh ) error("Error opening file: %s/summary.%s.tab\n",dir,smpl->name);
+
+    fprintf(smpl->dat_fh,"# [1]Chromosome\t[2]Position\t[3]BAF\t[4]LRR\n");
+    fprintf(smpl->cn_fh,"# [1]Chromosome\t[2]Position\t[3]CN\t[4]P(CN0)\t[5]P(CN1)\t[6]P(CN2)\t[7]P(CN3)\n");
+    fprintf(smpl->summary_fh,"# RG, Regions [2]Chromosome\t[3]Start\t[4]End\t[5]Copy Number state\t[6]Quality\t[7]nSites\t[8]nHETs\n");
+}
+static void close_sample_files(sample_t *smpl)
+{
+    if ( fclose(smpl->dat_fh)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,smpl->dat_fname);
+    if ( fclose(smpl->cn_fh)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,smpl->cn_fname);
+    if ( fclose(smpl->summary_fh)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,smpl->summary_fname);
+}
+
+static double norm_cdf(double mean, double dev);
+static void init_data(args_t *args)
+{
+    args->prev_rid = -1;
+    args->hdr = args->files->readers[0].header;
+
+    if ( !args->query_sample.name )
+    {
+        if ( bcf_hdr_nsamples(args->hdr)>1 ) error("Multi-sample VCF, missing the -s option\n");
+        args->query_sample.name = strdup(args->hdr->samples[0]);
+    }
+    else 
+        if ( bcf_hdr_id2int(args->hdr,BCF_DT_SAMPLE,args->query_sample.name)<0 ) error("The sample \"%s\" not found\n", args->query_sample.name);
+    if ( !args->files->readers[0].file->is_bin )
+    {
+        int ret;
+        kstring_t tmp = {0,0,0};
+        if ( args->control_sample.name )
+        {
+            ksprintf(&tmp, "%s,%s", args->query_sample.name,args->control_sample.name);
+            ret = bcf_hdr_set_samples(args->hdr, tmp.s, 0);
+        }
+        else
+        {
+            ret = bcf_hdr_set_samples(args->hdr, args->query_sample.name, 0);
+            tmp.s = args->query_sample.name;
+        }
+        if ( ret<0 ) error("Error parsing the list of samples: %s\n", tmp.s);
+        else if ( ret>0 ) error("The sample not found in the VCF: %s\n", ret==1 ? args->query_sample.name : args->control_sample.name);
+
+        if ( args->control_sample.name ) free(tmp.s);
+    }
+    args->query_sample.idx = bcf_hdr_id2int(args->hdr,BCF_DT_SAMPLE,args->query_sample.name);
+    args->control_sample.idx = args->control_sample.name ? bcf_hdr_id2int(args->hdr,BCF_DT_SAMPLE,args->control_sample.name) : -1;
+    args->nstates = args->control_sample.name ? N_STATES*N_STATES : N_STATES;
+    args->tprob  = init_tprob_matrix(args->nstates, args->ij_prob, args->same_prob);
+    args->iprobs = init_iprobs(args->nstates, args->same_prob);
+    args->hmm = hmm_init(args->nstates, args->tprob, 10000);
+    hmm_init_states(args->hmm, args->iprobs);
+
+    args->summary_fh = stdout;
+    init_sample_files(&args->query_sample, args->output_dir);
+    if ( args->control_sample.name )
+    {
+        init_sample_files(&args->control_sample, args->output_dir);
+        args->summary_fh = open_file(&args->summary_fname,"w","%s/summary.tab",args->output_dir);
+    }
+    else
+        args->summary_fh = NULL;    // one sample only, no two-file summary
+        
+
+    int i;
+    FILE *fh = args->summary_fh ? args->summary_fh : args->query_sample.summary_fh;
+
+    fprintf(fh, "# This file was produced by: bcftools cnv(%s+htslib-%s)\n", bcftools_version(),hts_version());
+    fprintf(fh, "# The command line was:\tbcftools %s", args->argv[0]);
+    for (i=1; i<args->argc; i++) fprintf(fh, " %s",args->argv[i]);
+    if ( args->control_sample.name )
+        fprintf(fh, "\n#\n"
+                "# RG, Regions\t[2]Chromosome\t[3]Start\t[4]End\t[5]Copy number:%s\t[6]Copy number:%s\t[7]Quality"
+                "\t[8]nSites in (5)\t[9]nHETs in (5)\t[10]nSites in (6)\t[11]nHETs in(6)\n",
+                args->query_sample.name,args->control_sample.name
+               );
+    else
+        fprintf(fh, "\n#\n"
+                "# RG, Regions\t[2]Chromosome\t[3]Start\t[4]End\t[5]Copy number:%s\t[6]Quality\t[7]nSites\t[8]nHETs\n",
+                args->query_sample.name
+               );
+    if ( args->optimize_frac )
+    {
+        fprintf(args->query_sample.summary_fh, "# CF, cell fraction estimate\t[2]Chromosome\t[3]Start\t[4]End\t[5]Cell fraction\t[6]BAF deviation\n");
+        if ( args->control_sample.name )
+        {
+            fprintf(args->control_sample.summary_fh, "# CF, cell fraction estimate\t[2]Chromosome\t[3]Start\t[4]End\t[5]Cell fraction\t[6]BAF deviation\n");
+            fprintf(args->summary_fh, "# CF, cell fraction estimate\t[2]Chromosome\t[3]Start\t[4]End\t"
+                "[5]Cell fraction:%s\t[6]Cell fraction:%s\t[7]BAF deviation:%s\t[8]BAF deviation:%s\n",
+                args->query_sample.name,args->control_sample.name,
+                args->query_sample.name,args->control_sample.name
+                );
+        }
+    }
+}
+
+char *msprintf(const char *fmt, ...);
+static void py_plot_cnv(char *script, float th)
+{
+    if ( th>100 ) return;   // create no plots
+
+    char *cmd = msprintf("python %s -p %f", script, th);
+    int ret = system(cmd);
+    if ( ret) fprintf(stderr, "The command returned non-zero status %d: %s\n", ret, cmd);
+    free(cmd);
+}
+
+static void plot_sample(args_t *args, sample_t *smpl)
+{
+    char *fname;
+    FILE *fp = open_file(&fname,"w","%s/plot.%s.py",args->output_dir,smpl->name);
+    fprintf(fp,
+            "import matplotlib as mpl\n"
+            "mpl.use('Agg')\n"
+            "import matplotlib.pyplot as plt\n"
+            "import csv\n"
+            "import numpy as np\n"
+            "csv.register_dialect('tab', delimiter='\\t', quoting=csv.QUOTE_NONE)\n"
+            "\n"
+            "dat = {}\n"
+            "with open('%s', 'r') as f:\n"
+            "    reader = csv.reader(f, 'tab')\n"
+            "    for row in reader:\n"
+            "        chr = row[0]\n"
+            "        if chr[0]=='#': continue\n"
+            "        if chr not in dat: dat[chr] = []\n"
+            "        dat[chr].append([int(row[1]), float(row[2]), float(row[3])])\n"
+            "\n"
+            "cnv = {}\n"
+            "with open('%s', 'r') as f:\n"
+            "    reader = csv.reader(f, 'tab')\n"
+            "    for row in reader:\n"
+            "        chr = row[0]\n"
+            "        if chr[0]=='#': continue\n"
+            "        if chr not in cnv: cnv[chr] = []\n"
+            "        row[2] = int(row[2]) + 0.5\n"
+            "        row[1] = int(row[1])\n"
+            "        cnv[chr].append(row[1:])\n"
+            "\n"
+            "for chr in dat:\n"
+            "    fig,(ax1, ax2, ax3) = plt.subplots(3,1,figsize=(10,8),sharex=True)\n"
+            "    ax1.plot([x[0] for x in dat[chr]],[x[2] for x in dat[chr]], '.', ms=3)\n"
+            "    ax2.plot([x[0] for x in dat[chr]],[x[1] for x in dat[chr]], '.', ms=3)\n"
+            "    cn_dat = cnv[chr]\n"
+            "    xgrid = [float(x[0]) for x in cn_dat]\n"
+            "    ygrid = np.linspace(0,5,6)\n"
+            "    xgrid, ygrid = np.meshgrid(xgrid, ygrid)\n"
+            "    heat = np.zeros_like(xgrid)\n"
+            "    for x in range(len(heat[0])-1):\n"
+            "       heat[0][x] = cn_dat[x][2]\n"
+            "       heat[1][x] = cn_dat[x][3]\n"
+            "       heat[2][x] = cn_dat[x][4]\n"
+            "       heat[3][x] = cn_dat[x][5]\n"
+            "    mesh = ax3.pcolormesh(xgrid, ygrid, heat, cmap='bwr_r', shading='auto', alpha=0)\n"
+            "    mesh.set_clim(vmin=-1,vmax=1)\n"
+            "    ax3.plot([x[0] for x in cn_dat],[x[1] for x in cn_dat],'.-',ms=3,color='black')\n"
+            "    fig.suptitle('%s (chr '+chr+')')\n"
+            "    ax1.set_title('Log-R intensities Ratio',fontsize=10)\n"
+            "    ax2.set_title('B-Allele Frequency',fontsize=10)\n"
+            "    ax3.set_title('Copy Number Variation',fontsize=10)\n"
+            "    ax1.set_ylabel('LRR')\n"
+            "    ax2.set_ylabel('BAF')\n"
+            "    ax3.set_ylabel('CN')\n"
+            "    ax3.set_xlabel('Coordinate (chrom '+chr+')',fontsize=10)\n"
+            "    ax3.set_ylim(-0.1,4.1)\n"
+            "    ax3.set_yticks([0.5,1.5,2.5,3.5])\n"
+            "    ax3.set_yticklabels(['CN0','CN1','CN2','CN3'])\n"
+            "    plt.subplots_adjust(left=0.08,right=0.95,bottom=0.08,top=0.92)\n"
+            "    plt.savefig('%s/plot.%s.chr'+chr+'.png')\n"
+            "    plt.close()\n"
+            "\n", 
+            smpl->dat_fname,smpl->cn_fname,smpl->name,args->output_dir,smpl->name
+    );
+    fclose(fp);
+
+    py_plot_cnv(fname, args->plot_th);
+    free(fname);
+}
+
+static void create_plots(args_t *args)
+{
+    close_sample_files(&args->query_sample);
+    if ( args->control_sample.name ) close_sample_files(&args->control_sample);
+    if ( args->summary_fh ) fclose(args->summary_fh);
+
+    if ( !args->control_sample.name )
+    {
+        plot_sample(args, &args->query_sample);
+        return;
+    }
+
+    char *fname;
+    FILE *fp = open_file(&fname,"w","%s/plot.%s.%s.py",args->output_dir,args->control_sample.name,args->query_sample.name);
+    fprintf(fp,
+            "import matplotlib as mpl\n"
+            "mpl.use('Agg')\n"
+            "import matplotlib.pyplot as plt\n"
+            "import csv,argparse\n"
+            "import numpy as np\n"
+            "csv.register_dialect('tab', delimiter='\\t', quoting=csv.QUOTE_NONE)\n"
+            "\n"
+            "control_sample = '%s'\n"
+            "query_sample   = '%s'\n"
+            "\n"
+            "parser = argparse.ArgumentParser()\n"
+            "parser.add_argument('-p', '--plot-threshold', type=float)\n"
+            "parser.add_argument('-c', '--chromosome')\n"
+            "args = parser.parse_args()\n"
+            "if args.plot_threshold==None: args.plot_threshold = 0\n"
+            "\n"
+            "def chroms_to_plot(th):\n"
+            "   dat = {}\n"
+            "   with open('%s/summary.tab', 'r') as f:\n"
+            "       reader = csv.reader(f, 'tab')\n"
+            "       for row in reader:\n"
+            "           if row[0]!='RG': continue\n"
+            "           chr   = row[1]\n"
+            "           start = row[2]\n"
+            "           end   = row[3]\n"
+            "           qual  = float(row[6])\n"
+            "           if row[4]==row[5] and args.plot_threshold!=0: continue\n"
+            "           if chr not in dat: dat[chr] = 0.0\n"
+            "           if qual > dat[chr]: dat[chr] = qual\n"
+            "   out = {}\n"
+            "   for chr in dat:\n"
+            "       if (chr not in dat) or dat[chr]<th: continue\n"
+            "       out[chr] = 1\n"
+            "   return out\n"
+            "if args.chromosome!=None:\n"
+            "   plot_chroms = { args.chromosome:1 }\n"
+            "else:\n"
+            "   plot_chroms = chroms_to_plot(args.plot_threshold)\n"
+            "\n"
+            "def read_dat(file,dat,plot_chr):\n"
+            "   with open(file, 'r') as f:\n"
+            "       reader = csv.reader(f, 'tab')\n"
+            "       for row in reader:\n"
+            "           chr = row[0]\n"
+            "           if chr != plot_chr: continue\n"
+            "           dat.append([int(row[1]), float(row[2]), float(row[3])])\n"
+            "def read_cnv(file,cnv,plot_chr):\n"
+            "   with open(file, 'r') as f:\n"
+            "       reader = csv.reader(f, 'tab')\n"
+            "       for row in reader:\n"
+            "           chr = row[0]\n"
+            "           if chr != plot_chr: continue\n"
+            "           row[2] = int(row[2]) + 0.5\n"
+            "           row[1] = int(row[1])\n"
+            "           cnv.append(row[1:])\n"
+            "def find_diffs(a,b):\n"
+            "    out = []\n"
+            "    diff = []\n"
+            "    for i in range(len(a)):\n"
+            "        if a[i][1]!=b[i][1]:\n"
+            "            if i>0: diff.append([b[i-1][0],b[i-1][1],a[i-1][1]])\n"
+            "            diff.append([b[i][0],b[i][1],a[i][1]])\n"
+            "        elif len(diff):\n"
+            "            diff.append([b[i][0],b[i][1],a[i][1]])\n"
+            "            out.append(diff)\n"
+            "            diff = []\n"
+            "    if len(diff): out.append(diff)\n"
+            "    return out\n"
+            "\n"
+            "for chr in sorted(plot_chroms.keys()):\n"
+            "    control_dat = []\n"
+            "    control_cnv = []\n"
+            "    query_dat   = []\n"
+            "    query_cnv   = []\n"
+            "    read_dat('%s',control_dat,chr)\n"
+            "    read_dat('%s',query_dat,chr)\n"
+            "    read_cnv('%s',control_cnv,chr)\n"
+            "    read_cnv('%s',query_cnv,chr)\n"
+            "\n"
+            "    fig,(ax1,ax2,ax3,ax4,ax5,ax6) = plt.subplots(6,1,figsize=(10,8),sharex=True)\n"
+            "    ax1.plot([x[0] for x in control_dat],[x[2] for x in control_dat], '.', ms=3,color='red')\n"
+            "    ax2.plot([x[0] for x in control_dat],[x[1] for x in control_dat], '.', ms=3,color='red')\n"
+            "    cn_dat = control_cnv\n"
+            "    xgrid = [float(x[0]) for x in cn_dat]\n"
+            "    ygrid = np.linspace(0,5,6)\n"
+            "    xgrid, ygrid = np.meshgrid(xgrid, ygrid)\n"
+            "    heat = np.zeros_like(xgrid)\n"
+            "    for x in range(len(heat[0])-1):\n"
+            "       heat[0][x] = cn_dat[x][2]\n"
+            "       heat[1][x] = cn_dat[x][3]\n"
+            "       heat[2][x] = cn_dat[x][4]\n"
+            "       heat[3][x] = cn_dat[x][5]\n"
+            "    mesh = ax3.pcolormesh(xgrid, ygrid, heat, cmap='bwr', shading='auto', alpha=0)\n"
+            "    mesh.set_clim(vmin=-1,vmax=1)\n"
+            "    ax3.plot([x[0] for x in cn_dat],[x[1] for x in cn_dat],'-',ms=3,color='black',lw=1.7)\n"
+            "\n"
+            "    ax6.plot([x[0] for x in query_dat],[x[2] for x in query_dat], '.', ms=3)\n"
+            "    ax5.plot([x[0] for x in query_dat],[x[1] for x in query_dat], '.', ms=3)\n"
+            "    cn_dat = query_cnv\n"
+            "    xgrid = [float(x[0]) for x in cn_dat]\n"
+            "    ygrid = np.linspace(0,5,6)\n"
+            "    xgrid, ygrid = np.meshgrid(xgrid, ygrid)\n"
+            "    heat = np.zeros_like(xgrid)\n"
+            "    for x in range(len(heat[0])-1):\n"
+            "       heat[0][x] = cn_dat[x][2]\n"
+            "       heat[1][x] = cn_dat[x][3]\n"
+            "       heat[2][x] = cn_dat[x][4]\n"
+            "       heat[3][x] = cn_dat[x][5]\n"
+            "    mesh = ax4.pcolormesh(xgrid, ygrid, heat, cmap='bwr_r')\n"
+            "    mesh.set_clim(vmin=-1,vmax=1)\n"
+            "    ax4.plot([x[0] for x in cn_dat],[x[1] for x in cn_dat],'-',ms=3,color='black',lw=1.7)\n"
+            "    ax3.annotate(control_sample, xy=(0.02,0.1), xycoords='axes fraction', color='red',fontsize=12, va='bottom',ha='left')\n"
+            "    ax4.annotate(query_sample, xy=(0.02,0.9), xycoords='axes fraction', color='blue',fontsize=12, va='top',ha='left')\n"
+            "\n"
+            "    diffs = find_diffs(control_cnv,query_cnv)\n"
+            "    for diff in diffs:\n"
+            "        ax3.plot([x[0] for x in diff],[x[1] for x in diff],'-',ms=3,color='blue',lw=1.7)\n"
+            "        ax4.plot([x[0] for x in diff],[x[2] for x in diff],'-',ms=3,color='red',lw=1.7)\n"
+            "\n"
+            "    fig.suptitle('chr '+chr+', '+control_sample+' vs '+query_sample)\n"
+            "    ax1.tick_params(axis='both', labelsize=8)\n"
+            "    ax2.tick_params(axis='both', labelsize=8)\n"
+            "    ax3.tick_params(axis='both', labelsize=8)\n"
+            "    ax4.tick_params(axis='both', labelsize=8)\n"
+            "    ax5.tick_params(axis='both', labelsize=8)\n"
+            "    ax6.tick_params(axis='both', labelsize=8)\n"
+            "    ax6.set_xlabel('Coordinate (chrom '+chr+')',fontsize=8)\n"
+            "    ax1.set_ylabel('LRR')\n"
+            "    ax2.set_ylabel('BAF')\n"
+            "    ax3.set_ylabel('CN')\n"
+            "    ax6.set_ylabel('LRR')\n"
+            "    ax5.set_ylabel('BAF')\n"
+            "    ax4.set_ylabel('CN')\n"
+            "    ax3.set_ylim(-0.1,4.1)\n"
+            "    ax3.set_yticks([0.5,1.5,2.5,3.5])\n"
+            "    ax3.set_yticklabels(['CN0','CN1','CN2','CN3'])\n"
+            "    ax4.set_ylim(-0.1,4.1)\n"
+            "    ax4.set_yticks([0.5,1.5,2.5,3.5])\n"
+            "    ax4.set_yticklabels(['CN0','CN1','CN2','CN3'])\n"
+            "    plt.subplots_adjust(left=0.08,right=0.95,bottom=0.08,top=0.92,hspace=0)\n"
+            "    plt.savefig('%s/plot.%s.%s.chr'+chr+'.png')\n"
+            "    plt.close()\n"
+            "\n", 
+            args->control_sample.name,args->query_sample.name,
+            args->output_dir,
+            args->control_sample.dat_fname,args->query_sample.dat_fname,
+            args->control_sample.cn_fname,args->query_sample.cn_fname,
+            args->output_dir,args->control_sample.name,args->query_sample.name
+        );
+        fclose(fp);
+
+    py_plot_cnv(fname,args->plot_th);
+    free(fname);
+}
+
+static void destroy_data(args_t *args)
+{
+    bcf_sr_destroy(args->files);
+    hmm_destroy(args->hmm);
+    free(args->tmpf);
+    free(args->sites);
+    free(args->eprob);
+    free(args->tprob);
+    free(args->iprobs);
+    free(args->summary_fname);
+    free(args->nonref_afs);
+    free(args->query_sample.baf);
+    free(args->query_sample.lrr);
+    free(args->control_sample.baf);
+    free(args->control_sample.lrr);
+    free(args->query_sample.name);
+    free(args->query_sample.dat_fname);
+    free(args->query_sample.cn_fname);
+    free(args->query_sample.summary_fname);
+    free(args->control_sample.dat_fname);
+    free(args->control_sample.cn_fname);
+    free(args->control_sample.summary_fname);
+}
+
+static inline char copy_number_state(args_t *args, int istate, int ismpl)
+{
+    char code[] = "01234";
+    if ( !args->control_sample.name ) return code[istate];
+    int idx = ismpl ? istate - (istate/N_STATES)*N_STATES : istate/N_STATES;
+    return code[idx];
+}
+
+static double avg_ii_prob(int n, double *mat)
+{
+    int i;
+    double avg = 0;
+    for (i=0; i<n; i++) avg += MAT(mat,n,i,i);
+    return avg/n;
+}
+
+#define GAUSS_CN1_PK_R(smpl)    (&((smpl)->gauss_param[0]))
+#define GAUSS_CN1_PK_A(smpl)    (&((smpl)->gauss_param[1]))
+#define GAUSS_CN2_PK_RR(smpl)   (&((smpl)->gauss_param[2]))
+#define GAUSS_CN2_PK_RA(smpl)   (&((smpl)->gauss_param[3]))
+#define GAUSS_CN2_PK_AA(smpl)   (&((smpl)->gauss_param[4]))
+#define GAUSS_CN3_PK_RRR(smpl)  (&((smpl)->gauss_param[5]))
+#define GAUSS_CN3_PK_RRA(smpl)  (&((smpl)->gauss_param[6]))
+#define GAUSS_CN3_PK_RAA(smpl)  (&((smpl)->gauss_param[7]))
+#define GAUSS_CN3_PK_AAA(smpl)  (&((smpl)->gauss_param[8]))
+
+static inline double norm_prob(double baf, gauss_param_t *param)
+{
+    return exp(-(baf-param->mean)*(baf-param->mean)*0.5/param->dev2) / param->norm / sqrt(2*M_PI*param->dev2);
+}
+
+static int set_observed_prob(args_t *args, sample_t *smpl, int isite)
+{
+    float baf = smpl->baf[isite];
+    float lrr = args->lrr_bias>0 ? smpl->lrr[isite] : 0;
+
+    float fRR = args->fRR;
+    float fRA = args->fRA;
+    float fAA = args->fAA;
+
+    if ( baf<0 )
+    {
+        // no call: either some technical issue or the call could not be made because it is CN0
+        int i;
+        smpl->pobs[CN0] = 0.5;
+        for (i=1; i<N_STATES; i++) smpl->pobs[i] = (1.0-smpl->pobs[CN0])/(N_STATES-1);
+        return 0;
+    }
+
+    double cn1_baf = 
+        norm_prob(baf,GAUSS_CN1_PK_R(smpl)) * (fRR + fRA*0.5) +
+        norm_prob(baf,GAUSS_CN1_PK_A(smpl)) * (fAA + fRA*0.5) ;
+    double cn2_baf = 
+        norm_prob(baf,GAUSS_CN2_PK_RR(smpl)) * fRR + 
+        norm_prob(baf,GAUSS_CN2_PK_RA(smpl)) * fRA + 
+        norm_prob(baf,GAUSS_CN2_PK_AA(smpl)) * fAA;
+    double cn3_baf = 
+        norm_prob(baf,GAUSS_CN3_PK_RRR(smpl)) * fRR + 
+        norm_prob(baf,GAUSS_CN3_PK_RRA(smpl)) * fRA*0.5 + 
+        norm_prob(baf,GAUSS_CN3_PK_RAA(smpl)) * fRA*0.5 + 
+        norm_prob(baf,GAUSS_CN3_PK_AAA(smpl)) * fAA;
+
+    double norm = cn1_baf + cn2_baf + cn3_baf;
+    cn1_baf /= norm;
+    cn2_baf /= norm;
+    cn3_baf /= norm;
+
+    #if DBG0
+    if ( args->verbose ) fprintf(stderr,"%f\t%f %f %f\n", baf,cn1_baf,cn2_baf,cn3_baf);
+    #endif
+
+    double cn1_lrr = exp(-(lrr + 0.45)*(lrr + 0.45)/smpl->lrr_dev2);
+    double cn2_lrr = exp(-(lrr - 0.00)*(lrr - 0.00)/smpl->lrr_dev2);
+    double cn3_lrr = exp(-(lrr - 0.30)*(lrr - 0.30)/smpl->lrr_dev2);
+
+    smpl->pobs[CN0] = 0;
+    smpl->pobs[CN1] = args->err_prob + (1 - args->baf_bias + args->baf_bias*cn1_baf)*(1 - args->lrr_bias + args->lrr_bias*cn1_lrr);
+    smpl->pobs[CN2] = args->err_prob + (1 - args->baf_bias + args->baf_bias*cn2_baf)*(1 - args->lrr_bias + args->lrr_bias*cn2_lrr);
+    smpl->pobs[CN3] = args->err_prob + (1 - args->baf_bias + args->baf_bias*cn3_baf)*(1 - args->lrr_bias + args->lrr_bias*cn3_lrr);
+
+    return 0;
+}
+
+static void set_emission_prob(args_t *args, int isite)
+{
+    double *eprob = &args->eprob[args->nstates*isite];
+    int i;
+    for (i=0; i<N_STATES; i++)
+        eprob[i] = args->query_sample.pobs[i];
+}
+
+static void set_emission_prob2(args_t *args, int isite)
+{
+    double *eprob = &args->eprob[args->nstates*isite];
+    int i, j;
+    for (i=0; i<N_STATES; i++)
+    {
+        for (j=0; j<N_STATES; j++)
+        {
+            eprob[i*N_STATES+j] = args->query_sample.pobs[i]*args->control_sample.pobs[j];
+        }
+    }
+}
+
+static void set_gauss_params(args_t *args, sample_t *smpl);
+static double norm_cdf(double mean, double dev)
+{
+    double bot = 0, top = 1;
+    top = 1 - 0.5*erfc((top-mean)/(dev*sqrt(2)));
+    bot = 1 - 0.5*erfc((bot-mean)/(dev*sqrt(2)));
+    return top-bot;
+}
+
+static void set_emission_probs(args_t *args)
+{
+    if ( !args->af_fname )
+    {
+        args->fRR = 0.76;
+        args->fRA = 0.14;
+        args->fAA = 0.098;
+    }
+
+    set_gauss_params(args, &args->query_sample);
+    if ( args->control_sample.name ) set_gauss_params(args, &args->control_sample);
+
+    #if DBG0
+    args->verbose = 1;
+    args->query_sample.baf[0] = 0; set_observed_prob(args,&args->query_sample,0);
+    args->query_sample.baf[0] = 1/3.; set_observed_prob(args,&args->query_sample,0);
+    args->query_sample.baf[0] = 1/2.; set_observed_prob(args,&args->query_sample,0);
+    args->query_sample.baf[0] = 2/3.; set_observed_prob(args,&args->query_sample,0);
+    args->query_sample.baf[0] = 1; set_observed_prob(args,&args->query_sample,0);
+    args->verbose = 0;
+    #endif
+
+    int i;
+    for (i=0; i<args->nsites; i++)
+    {
+        if ( args->af_fname )
+        {
+            args->fRR = (1-args->nonref_afs[i])*(1-args->nonref_afs[i]);
+            args->fRA = 2*args->nonref_afs[i]*(1-args->nonref_afs[i]);
+            args->fAA = args->nonref_afs[i]*args->nonref_afs[i];
+        }
+        set_observed_prob(args,&args->query_sample,i);
+        if ( args->control_sample.name )
+        {
+            set_observed_prob(args,&args->control_sample,i);
+            set_emission_prob2(args,i);
+        }
+        else
+            set_emission_prob(args,i);
+    }
+}
+
+static void smooth_data(float *dat, int ndat, int win)
+{
+    if ( win<=1 ) return;
+
+    int i,j, k1 = win/2, k2 = win-k1;
+    rbuf_t rbuf;
+    rbuf_init(&rbuf,win);
+    float sum = 0, *buf = (float*)malloc(sizeof(float)*win);
+    for (i=0; i<k2; i++)
+    {
+        sum += dat[i];
+        int j = rbuf_append(&rbuf);
+        buf[j] = dat[i];
+    }
+    for (i=0; i<ndat; i++)
+    {
+        dat[i] = sum/rbuf.n;
+        if ( i>=k1 )
+        {
+            j = rbuf_shift(&rbuf);
+            sum -= buf[j];
+        }
+        if ( i+k2<ndat )
+        {
+            sum += dat[i+k2];
+            j = rbuf_append(&rbuf);
+            buf[j] = dat[i+k2];
+        }
+    }
+    free(buf);
+}
+
+static void set_gauss_params(args_t *args, sample_t *smpl)
+{
+    int i;
+    for (i=0; i<18; i++) smpl->gauss_param[i].dev2 = smpl->baf_dev2;
+
+    double dev = sqrt(smpl->baf_dev2);
+
+    GAUSS_CN1_PK_R(smpl)->mean = 0;
+    GAUSS_CN1_PK_A(smpl)->mean = 1;
+    GAUSS_CN1_PK_R(smpl)->norm = norm_cdf(GAUSS_CN1_PK_R(smpl)->mean,dev);
+    GAUSS_CN1_PK_A(smpl)->norm = norm_cdf(GAUSS_CN1_PK_A(smpl)->mean,dev);
+
+    GAUSS_CN2_PK_RR(smpl)->mean = 0;
+    GAUSS_CN2_PK_RA(smpl)->mean = 0.5;
+    GAUSS_CN2_PK_AA(smpl)->mean = 1;
+    GAUSS_CN2_PK_RR(smpl)->norm = norm_cdf(GAUSS_CN2_PK_RR(smpl)->mean,dev);
+    GAUSS_CN2_PK_RA(smpl)->norm = norm_cdf(GAUSS_CN2_PK_RA(smpl)->mean,dev);
+    GAUSS_CN2_PK_AA(smpl)->norm = norm_cdf(GAUSS_CN2_PK_AA(smpl)->mean,dev);
+
+    GAUSS_CN3_PK_RRR(smpl)->mean = 0;
+    GAUSS_CN3_PK_RRA(smpl)->mean = 1.0/(2+smpl->cell_frac);
+    GAUSS_CN3_PK_RAA(smpl)->mean = (1.0+smpl->cell_frac)/(2+smpl->cell_frac);
+    GAUSS_CN3_PK_AAA(smpl)->mean = 1;
+    GAUSS_CN3_PK_RRR(smpl)->norm = norm_cdf(GAUSS_CN3_PK_RRR(smpl)->mean,dev);
+    GAUSS_CN3_PK_RRA(smpl)->norm = norm_cdf(GAUSS_CN3_PK_RRA(smpl)->mean,dev);
+    GAUSS_CN3_PK_RAA(smpl)->norm = norm_cdf(GAUSS_CN3_PK_RAA(smpl)->mean,dev);
+    GAUSS_CN3_PK_AAA(smpl)->norm = norm_cdf(GAUSS_CN3_PK_AAA(smpl)->mean,dev);
+}
+
+static int update_sample_args(args_t *args, sample_t *smpl, int ismpl)
+{
+    hmm_t *hmm = args->hmm;
+    double *fwd = hmm_get_fwd_bwd_prob(hmm);
+    int nstates = hmm_get_nstates(hmm);
+
+    // estimate the BAF mean and deviation for CN3
+    double mean_cn3 = 0, norm_cn3 = 0;
+    double baf_dev2 = 0, baf_AA_dev2 = 0, norm_baf_AA_dev2 = 0;
+
+    // experimental: smooth CN3 probs to bias toward bigger events, this lowers
+    // the FP rate when the data is noisy
+    hts_expand(float,args->nsites,args->mtmpf,args->tmpf);
+    int i, j, k = 0;
+    for (i=0; i<args->nsites; i++)
+    {
+        float baf = smpl->baf[i];
+        if ( baf>4/5.) continue;        // skip AA genotypes
+        if ( baf>0.5 ) baf = 1 - baf;   // the bands should be symmetric
+        if ( baf<1/5.) continue;        // skip RR genotypes
+
+        double prob_cn3 = 0, *probs = fwd + i*nstates;
+        if ( !args->control_sample.name )
+        {
+            prob_cn3 = probs[CN3];
+        }
+        else if ( ismpl==0 )
+        {
+            // query sample: CN3 probability must be recovered from all states of the control sample
+            for (j=0; j<N_STATES; j++) prob_cn3 += probs[CN3*N_STATES+j];
+        }
+        else
+        {
+            // same as above but for control sample
+            for (j=0; j<N_STATES; j++) prob_cn3 += probs[CN3+j*N_STATES];
+        }
+        args->tmpf[k++] = prob_cn3;
+    }
+    smooth_data(args->tmpf, k, 50);
+    k = 0;
+    for (i=0; i<args->nsites; i++)
+    {
+        float baf = smpl->baf[i];
+        if ( baf>4/5.) { baf_AA_dev2 += (1.0-baf)*(1.0-baf); norm_baf_AA_dev2++; continue; }       // skip AA genotypes
+        if ( baf>0.5 ) baf = 1 - baf;   // the bands should be symmetric
+        if ( baf<1/5.) continue;        // skip RR genotypes
+
+        double prob_cn3 = args->tmpf[k++];
+        mean_cn3 += prob_cn3 * baf;
+        norm_cn3 += prob_cn3;
+    }
+    if ( !norm_cn3 )
+    {
+        smpl->cell_frac = 1.0;
+        return 1;
+    }
+    mean_cn3 /= norm_cn3;
+    k = 0;
+    for (i=0; i<args->nsites; i++)
+    {
+        float baf = smpl->baf[i];
+        if ( baf>0.5 ) baf = 1 - baf;   // the bands should be symmetric
+        if ( baf<1/5.) continue;        // skip RR,AA genotypes
+
+        double prob_cn3 = args->tmpf[k++];
+        baf_dev2 += prob_cn3 * (baf - mean_cn3)*(baf - mean_cn3);
+    }
+
+    /*
+        A noisy CN2 band is hard to distinguish from two CN3 bands which are
+        close to each other. Set a treshold on the minimum separation based
+        on the BAF deviation at p=0.95
+    */
+    baf_dev2 /= norm_cn3;
+    baf_AA_dev2 /= norm_baf_AA_dev2;
+    if ( baf_dev2 < baf_AA_dev2 )  baf_dev2 = baf_AA_dev2;
+    double max_mean_cn3 = 0.5 - sqrt(baf_dev2)*1.644854;    // R: qnorm(0.95)=1.644854
+    //fprintf(stderr,"dev=%f  AA_dev=%f  max_mean_cn3=%f  mean_cn3=%f\n", baf_dev2,baf_AA_dev2,max_mean_cn3,mean_cn3);
+    assert( max_mean_cn3>0 );
+
+    double new_frac = 1./mean_cn3 - 2;
+    if ( mean_cn3 > max_mean_cn3 || new_frac < args->optimize_frac )
+    {
+        // out of bounds, beyond our detection limits. Give up and say it converged
+        smpl->cell_frac = 1.0;
+        return 1;
+    }
+    if ( new_frac>1 ) new_frac = 1;
+    int converged = fabs(new_frac - smpl->cell_frac) < 1e-1 ? 1 : 0;
+
+    // Update dev2, but stay within safe limits
+    if ( baf_dev2 > 3*smpl->baf_dev2_dflt ) baf_dev2 = 3*smpl->baf_dev2_dflt;
+    else if ( baf_dev2 < 0.5*smpl->baf_dev2_dflt ) baf_dev2 = 0.5*smpl->baf_dev2_dflt;
+
+    smpl->cell_frac = new_frac;
+    smpl->baf_dev2  = baf_dev2;
+
+    return converged;
+}
+
+// Update parameters which depend on the estimated fraction of aberrant cells
+// in CN3.  Returns 0 if the current estimate did not need to be updated or 1
+// if there was a change.
+static int update_args(args_t *args)
+{
+    int converged = update_sample_args(args, &args->query_sample, 0);
+    if ( args->control_sample.name )
+    {
+        converged += update_sample_args(args, &args->control_sample, 1);
+        return converged==2 ? 0 : 1;
+    }
+    return converged ? 0 : 1;
+}
+
+// for an approximate estimate of the number of het genotypes in a region
+#define BAF_LIKELY_HET(val)   (val)>0.25 && (val)<0.75
+
+static void cnv_flush_viterbi(args_t *args)
+{
+    if ( !args->nsites ) return;
+
+    // Set HMM transition matrix for the new chromsome again. This is for case
+    // Baum-Welch was used, which is experimental, largerly unsupported and not
+    // done by default.
+    hmm_t *hmm = args->hmm;
+    hmm_set_tprob(args->hmm, args->tprob, 10000);
+
+    // Smooth LRR values to reduce noise
+    if ( args->lrr_bias > 0 )
+    {
+        smooth_data(args->query_sample.lrr,args->nsites, args->lrr_smooth_win);
+        if ( args->control_sample.name ) smooth_data(args->control_sample.lrr,args->nsites, args->lrr_smooth_win);
+    }
+
+    // Set the BAF peak likelihoods, such as P(RRR|CN3), taking account the
+    // estimated fraction of aberrant cells in the mixture. With the new chromosome,
+    // reset the fraction to the default value.
+    args->query_sample.cell_frac   = args->query_sample.cell_frac_dflt;
+    args->control_sample.cell_frac = args->control_sample.cell_frac_dflt;
+    args->query_sample.baf_dev2    = args->query_sample.baf_dev2_dflt;
+    args->control_sample.baf_dev2  = args->control_sample.baf_dev2_dflt;
+    set_gauss_params(args, &args->query_sample);
+    if ( args->control_sample.name ) set_gauss_params(args, &args->control_sample);
+
+    if ( args->optimize_frac )
+    {
+        int niter = 0;
+        fprintf(stderr,"Attempting to estimate the fraction of aberrant cells (chr %s):\n", bcf_hdr_id2name(args->hdr,args->prev_rid));
+        do
+        {
+            fprintf(stderr,"\t.. %f %f", args->query_sample.cell_frac,args->query_sample.baf_dev2);
+            if ( args->control_sample.name )
+                fprintf(stderr,"\t.. %f %f", args->control_sample.cell_frac,args->control_sample.baf_dev2);
+            fprintf(stderr,"\n");
+            set_emission_probs(args);
+            hmm_run_fwd_bwd(hmm, args->nsites, args->eprob, args->sites);
+        }
+        while ( update_args(args) && ++niter<20 );
+        if ( niter>=20 )
+        {
+            // no convergence
+            args->query_sample.cell_frac   = args->query_sample.cell_frac_dflt;
+            args->control_sample.cell_frac = args->control_sample.cell_frac_dflt;
+            args->query_sample.baf_dev2    = args->query_sample.baf_dev2_dflt;
+            args->control_sample.baf_dev2  = args->control_sample.baf_dev2_dflt;
+            set_gauss_params(args, &args->query_sample);
+            if ( args->control_sample.name ) set_gauss_params(args, &args->control_sample);
+        }
+
+        fprintf(stderr,"\t.. %f %f", args->query_sample.cell_frac,args->query_sample.baf_dev2);
+        if ( args->control_sample.name )
+            fprintf(stderr,"\t.. %f %f", args->control_sample.cell_frac,args->control_sample.baf_dev2);
+        fprintf(stderr,"\n");
+
+        fprintf(args->query_sample.summary_fh,"CF\t%s\t%d\t%d\t%.2f\t%f\n",
+            bcf_hdr_id2name(args->hdr,args->prev_rid),args->sites[0]+1,args->sites[args->nsites-1]+1,
+            args->query_sample.cell_frac,sqrt(args->query_sample.baf_dev2));
+        if ( args->control_sample.name )
+        {
+            fprintf(args->control_sample.summary_fh,"CF\t%s\t%d\t%d\t%.2f\t%f\n",
+                    bcf_hdr_id2name(args->hdr,args->prev_rid),args->sites[0]+1,args->sites[args->nsites-1]+1,
+                    args->control_sample.cell_frac,sqrt(args->control_sample.baf_dev2));
+            fprintf(args->summary_fh,"CF\t%s\t%d\t%d\t%.2f\t%.2f\t%f\t%f\n",
+                    bcf_hdr_id2name(args->hdr,args->prev_rid),args->sites[0]+1,args->sites[args->nsites-1]+1,
+                    args->query_sample.cell_frac, args->control_sample.cell_frac,
+                    sqrt(args->query_sample.baf_dev2), sqrt(args->control_sample.baf_dev2));
+        }
+    }
+    set_emission_probs(args);
+
+    while ( args->baum_welch_th!=0 )
+    {
+        int nstates = hmm_get_nstates(hmm);
+        double ori_ii = avg_ii_prob(nstates,hmm_get_tprob(hmm));
+        hmm_run_baum_welch(hmm, args->nsites, args->eprob, args->sites);
+        double new_ii = avg_ii_prob(nstates,hmm_get_tprob(hmm));
+        fprintf(stderr,"%e\t%e\t%e\n", ori_ii,new_ii,new_ii-ori_ii);
+        double *tprob = init_tprob_matrix(nstates, 1-new_ii, args->same_prob);
+        hmm_set_tprob(args->hmm, tprob, 10000);
+        double *tprob_arr = hmm_get_tprob(hmm);
+        free(tprob);
+        if ( fabs(new_ii - ori_ii) < args->baum_welch_th )
+        {
+            int i,j;
+            for (i=0; i<nstates; i++)
+            {
+                for (j=0; j<nstates; j++)
+                {
+                    printf(" %.15f", MAT(tprob_arr,nstates,j,i));
+                }
+                printf("\n");
+            }
+            break;
+        }
+    }
+    hmm_run_viterbi(hmm, args->nsites, args->eprob, args->sites);
+    hmm_run_fwd_bwd(hmm, args->nsites, args->eprob, args->sites);
+
+
+    // Output the results
+    uint8_t *vpath = hmm_get_viterbi_path(hmm);
+    double qual = 0, *fwd = hmm_get_fwd_bwd_prob(hmm);
+    int i,j, isite, start_cn = vpath[0], start_pos = args->sites[0], istart_pos = 0;
+    int ctrl_ntot = 0, smpl_ntot = 0, ctrl_nhet = 0, smpl_nhet = 0;
+    for (isite=0; isite<args->nsites; isite++)
+    {
+        int state = vpath[args->nstates*isite];
+        double *pval = fwd + isite*args->nstates;
+
+        qual += pval[start_cn];
+
+        // output CN and fwd-bwd likelihood for each site
+        if ( args->query_sample.cn_fh )
+        {
+            fprintf(args->query_sample.cn_fh, "%s\t%d\t%c", bcf_hdr_id2name(args->hdr,args->prev_rid), args->sites[isite]+1, copy_number_state(args,state,0));
+            if ( !args->control_sample.cn_fh )
+                for (i=0; i<args->nstates; i++) fprintf(args->query_sample.cn_fh, "\t%f", pval[i]);
+            else
+                for (i=0; i<N_STATES; i++)
+                {
+                    double sum = 0;
+                    for (j=0; j<N_STATES; j++) sum += pval[i*N_STATES+j];
+                    fprintf(args->query_sample.cn_fh, "\t%f", sum);
+                }
+            fprintf(args->query_sample.cn_fh, "\n");
+            if ( args->query_sample.baf[isite]>=0 )     // if non-missing
+            {
+                if ( BAF_LIKELY_HET(args->query_sample.baf[isite]) ) smpl_nhet++;
+                smpl_ntot++;
+            }
+        }
+        if ( args->control_sample.cn_fh )
+        {
+            fprintf(args->control_sample.cn_fh, "%s\t%d\t%c", bcf_hdr_id2name(args->hdr,args->prev_rid), args->sites[isite]+1, copy_number_state(args,state,1));
+            for (i=0; i<N_STATES; i++)
+            {
+                double sum = 0;
+                for (j=0; j<N_STATES; j++) sum += pval[i+N_STATES*j];
+                fprintf(args->control_sample.cn_fh, "\t%f", sum);
+            }
+            fprintf(args->control_sample.cn_fh, "\n");
+            if ( args->control_sample.baf[isite]>=0 )     // if non-missing
+            {
+                if ( BAF_LIKELY_HET(args->control_sample.baf[isite]) ) ctrl_nhet++;
+                ctrl_ntot++;
+            }
+        }
+
+        if ( start_cn != state )
+        {
+            char start_cn_query = copy_number_state(args,start_cn,0);
+            qual = phred_score(1 - qual/(isite - istart_pos));
+            fprintf(args->query_sample.summary_fh,"RG\t%s\t%d\t%d\t%c\t%.1f\t%d\t%d\n",
+                bcf_hdr_id2name(args->hdr,args->prev_rid), start_pos+1, args->sites[isite],start_cn_query,qual,smpl_ntot,smpl_nhet);
+
+            if ( args->control_sample.name )
+            {
+                // regions 0-based, half-open
+                char start_cn_ctrl = copy_number_state(args,start_cn,1);
+                fprintf(args->control_sample.summary_fh,"RG\t%s\t%d\t%d\t%c\t%.1f\t%d\t%d\n",
+                    bcf_hdr_id2name(args->hdr,args->prev_rid), start_pos+1, args->sites[isite],start_cn_ctrl,qual,ctrl_ntot,ctrl_nhet);
+                fprintf(args->summary_fh,"RG\t%s\t%d\t%d\t%c\t%c\t%.1f\t%d\t%d\t%d\t%d\n",
+                    bcf_hdr_id2name(args->hdr,args->prev_rid), start_pos+1, args->sites[isite],start_cn_query,start_cn_ctrl,qual,smpl_ntot,smpl_nhet,ctrl_ntot,ctrl_nhet);
+            }
+
+            istart_pos = isite;
+            start_pos = args->sites[isite];
+            start_cn = state;
+            qual = 0;
+            smpl_ntot = smpl_nhet = ctrl_ntot = ctrl_nhet = 0;
+        }
+    }
+    qual = phred_score(1 - qual/(isite - istart_pos));
+    char start_cn_query = copy_number_state(args,start_cn,0);
+    fprintf(args->query_sample.summary_fh,"RG\t%s\t%d\t%d\t%c\t%.1f\t%d\t%d\n",
+        bcf_hdr_id2name(args->hdr,args->prev_rid), start_pos+1, args->sites[isite-1]+1,start_cn_query,qual,smpl_ntot,smpl_nhet);
+    if ( args->control_sample.name )
+    {
+        char start_cn_ctrl = copy_number_state(args,start_cn,1);
+        fprintf(args->control_sample.summary_fh,"RG\t%s\t%d\t%d\t%c\t%.1f\t%d\t%d\n",
+            bcf_hdr_id2name(args->hdr,args->prev_rid), start_pos+1, args->sites[isite-1]+1,start_cn_ctrl,qual,ctrl_ntot,ctrl_nhet);
+        fprintf(args->summary_fh,"RG\t%s\t%d\t%d\t%c\t%c\t%.1f\t%d\t%d\t%d\t%d\n",
+            bcf_hdr_id2name(args->hdr,args->prev_rid), start_pos+1, args->sites[isite-1]+1,start_cn_query,start_cn_ctrl,qual,smpl_ntot,smpl_nhet,ctrl_ntot,ctrl_nhet);
+    }
+}
+
+static int parse_lrr_baf(sample_t *smpl, bcf_fmt_t *baf_fmt, bcf_fmt_t *lrr_fmt, float *baf, float *lrr)
+{
+    *baf = ((float*)(baf_fmt->p + baf_fmt->size*smpl->idx))[0];
+    if ( bcf_float_is_missing(*baf) || isnan(*baf) ) *baf = -0.1;    // arbitrary negative value == missing value
+
+    if ( lrr_fmt )
+    {
+        *lrr = ((float*)(lrr_fmt->p + lrr_fmt->size*smpl->idx))[0];
+        if ( bcf_float_is_missing(*lrr) || isnan(*lrr) ) { *lrr = 0; *baf = -0.1; }
+    }
+    else
+        *lrr = 0;
+
+    return *baf<0 ? 0 : 1;
+}
+
+static void cnv_next_line(args_t *args, bcf1_t *line)
+{
+    if ( !line ) 
+    {
+        // Done, flush viterbi
+        cnv_flush_viterbi(args);
+        return;
+    }
+
+    if ( line->rid!=args->prev_rid )
+    {
+        // New chromosome
+        cnv_flush_viterbi(args);
+        args->prev_rid = line->rid;
+        args->nsites = 0;
+        args->nRR = args->nAA = args->nRA = 0;
+    }
+
+    // Process line
+    args->ntot++;
+
+    bcf_fmt_t *baf_fmt, *lrr_fmt = NULL;
+    if ( !(baf_fmt = bcf_get_fmt(args->hdr, line, "BAF")) ) return; 
+    if ( args->lrr_bias>0 && !(lrr_fmt = bcf_get_fmt(args->hdr, line, "LRR")) ) return;
+
+    float baf1,lrr1,baf2,lrr2;
+    int ret = 0;
+    ret += parse_lrr_baf(&args->query_sample,  baf_fmt,lrr_fmt,&baf1,&lrr1);
+    ret += parse_lrr_baf(&args->control_sample,baf_fmt,lrr_fmt,&baf2,&lrr2);
+    if ( !ret ) return;
+
+    // Realloc buffers needed to store observed data and used by viterbi and fwd-bwd
+    args->nsites++;
+    int m = args->msites;
+    hts_expand(uint32_t,args->nsites,args->msites,args->sites);
+    if ( args->msites!=m )
+    {
+        args->eprob = (double*) realloc(args->eprob,sizeof(double)*args->msites*args->nstates);
+        if ( args->control_sample.name )
+        {
+            args->control_sample.lrr = (float*) realloc(args->control_sample.lrr,sizeof(float)*args->msites);
+            args->control_sample.baf = (float*) realloc(args->control_sample.baf,sizeof(float)*args->msites);
+        }
+        args->query_sample.lrr = (float*) realloc(args->query_sample.lrr,sizeof(float)*args->msites);
+        args->query_sample.baf = (float*) realloc(args->query_sample.baf,sizeof(float)*args->msites);
+        if ( args->af_fname )
+            args->nonref_afs = (float*) realloc(args->nonref_afs,sizeof(float)*args->msites);
+    }
+    args->sites[args->nsites-1] = line->pos;
+    args->query_sample.lrr[args->nsites-1] = lrr1;
+    args->query_sample.baf[args->nsites-1] = baf1;
+    if ( args->af_fname )
+    {
+        double alt_freq;
+        args->nonref_afs[args->nsites-1] = read_AF(args->files->targets,line,&alt_freq)<0 ? args->nonref_af_dflt : alt_freq;
+    }
+    if ( args->control_sample.name )
+    {
+        args->control_sample.lrr[args->nsites-1] = lrr2;
+        args->control_sample.baf[args->nsites-1] = baf2;
+        if ( baf2>=0 )  // skip missing values
+            fprintf(args->control_sample.dat_fh,"%s\t%"PRId64"\t%.3f\t%.3f\n",bcf_hdr_id2name(args->hdr,args->prev_rid), (int64_t) line->pos+1,baf2,lrr2);
+    }
+    if ( baf1>=0 )  // skip missing values
+        fprintf(args->query_sample.dat_fh,"%s\t%"PRId64"\t%.3f\t%.3f\n",bcf_hdr_id2name(args->hdr,args->prev_rid), (int64_t) line->pos+1,baf1,lrr1);
+
+    if ( baf1>=0 )
+    {
+        if ( baf1<1/5. ) args->nRR++;
+        else if ( baf1>4/5. ) args->nAA++;
+        else args->nRA++;
+    }
+    args->nused++;
+}
+
+static void usage(args_t *args)
+{
+    fprintf(stderr, "\n");
+    fprintf(stderr, "About:   Copy number variation caller, requires Illumina's B-allele frequency (BAF) and Log R\n");
+    fprintf(stderr, "         Ratio intensity (LRR). The HMM considers the following copy number states: CN 2\n");
+    fprintf(stderr, "         (normal), 1 (single-copy loss), 0 (complete loss), 3 (single-copy gain)\n");
+    fprintf(stderr, "Usage:   bcftools cnv [OPTIONS] FILE.vcf\n");
+    fprintf(stderr, "General Options:\n");
+    fprintf(stderr, "    -c, --control-sample STRING      Optional control sample name to highlight differences\n");
+    fprintf(stderr, "    -f, --AF-file FILE               Read allele frequencies from file (CHR\\tPOS\\tREF,ALT\\tAF)\n");
+    fprintf(stderr, "    -o, --output-dir PATH            \n");
+    fprintf(stderr, "    -p, --plot-threshold FLOAT       Plot aberrant chromosomes with quality at least FLOAT\n");
+    fprintf(stderr, "    -r, --regions REGION             Restrict to comma-separated list of regions\n");
+    fprintf(stderr, "    -R, --regions-file FILE          Restrict to regions listed in a file\n");
+    fprintf(stderr, "        --regions-overlap 0|1|2      Include if POS in the region (0), record overlaps (1), variant overlaps (2) [1]\n");
+    fprintf(stderr, "    -s, --query-sample STRING        Query samply name\n");
+    fprintf(stderr, "    -t, --targets REGION             Similar to -r but streams rather than index-jumps\n");
+    fprintf(stderr, "    -T, --targets-file FILE          Similar to -R but streams rather than index-jumps\n");
+    fprintf(stderr, "        --targets-overlap 0|1|2      Include if POS in the region (0), record overlaps (1), variant overlaps (2) [0]\n");
+    fprintf(stderr, "HMM Options:\n");
+    fprintf(stderr, "    -a, --aberrant FLOAT[,FLOAT]     Fraction of aberrant cells in query and control [1.0,1.0]\n");
+    fprintf(stderr, "    -b, --BAF-weight FLOAT           Relative contribution from BAF [1]\n");
+    fprintf(stderr, "    -d, --BAF-dev FLOAT[,FLOAT]      Expected BAF deviation in query and control [0.04,0.04]\n"); // experimental
+    fprintf(stderr, "    -e, --err-prob FLOAT             Uniform error probability [1e-4]\n");
+    fprintf(stderr, "    -k, --LRR-dev FLOAT[,FLOAT]      Expected LRR deviation [0.2,0.2]\n"); // experimental
+    fprintf(stderr, "    -l, --LRR-weight FLOAT           Relative contribution from LRR [0.2]\n");
+    fprintf(stderr, "    -L, --LRR-smooth-win INT         Window of LRR moving average smoothing [10]\n");
+    fprintf(stderr, "    -O, --optimize FLOAT             Estimate fraction of aberrant cells down to FLOAT [1.0]\n");
+    fprintf(stderr, "    -P, --same-prob FLOA>            Prior probability of -s/-c being the same [0.5]\n");
+    fprintf(stderr, "    -x, --xy-prob FLOAT              P(x|y) transition probability [1e-9]\n");
+    fprintf(stderr, "\n");
+    exit(1);
+}
+
+int main_vcfcnv(int argc, char *argv[])
+{
+    int c;
+    args_t *args    = (args_t*) calloc(1,sizeof(args_t));
+    args->argc      = argc; args->argv = argv;
+    args->files     = bcf_sr_init();
+    args->plot_th   = 1e9;   // by default plot none
+    args->nonref_af_dflt = 0.1;
+    args->lrr_smooth_win = 10;
+
+    args->query_sample.cell_frac_dflt = 1;
+    args->control_sample.cell_frac_dflt = 1;
+
+    // How much FORMAT/LRR and FORMAT/BAF matter
+    args->lrr_bias  = 0.2;
+    args->baf_bias  = 1.0;
+    args->err_prob  = 1e-4;
+
+    // Transition probability to a different state and the prior of both samples being the same
+    args->ij_prob   = 1e-9;
+    args->same_prob = 0.5;
+
+    // Squared std dev of BAF and LRR values (gaussian noise), estimated from real data (hets, one sample, one chr)
+    args->query_sample.baf_dev2_dflt = args->control_sample.baf_dev2_dflt = 0.04*0.04; // illumina: 0.03
+    args->query_sample.lrr_dev2 = args->control_sample.lrr_dev2 = 0.2*0.2; //0.20*0.20;   // illumina: 0.18
+
+    int regions_is_file = 0, targets_is_file = 0;
+    int regions_overlap = 1;
+    int targets_overlap = 0;
+
+    static struct option loptions[] = 
+    {
+        {"BAF-dev",1,0,'d'},
+        {"LRR-dev",1,0,'k'},
+        {"LRR-smooth-win",1,0,'L'},
+        {"AF-file",1,0,'f'},
+        {"baum-welch",1,0,'W'}, // hidden
+        {"optimize",1,0,'O'},
+        {"aberrant",1,0,'a'},
+        {"err-prob",1,0,'e'},
+        {"BAF-weight",1,0,'b'},
+        {"LRR-weight",1,0,'l'},
+        {"same-prob",1,0,'P'},
+        {"xy-prob",1,0,'x'},
+        {"query-sample",1,0,'s'},
+        {"control-sample",1,0,'c'},
+        {"targets",1,0,'t'},
+        {"targets-file",1,0,'T'},
+        {"targets-overlap",required_argument,NULL,4},
+        {"regions",1,0,'r'},
+        {"regions-file",1,0,'R'},
+        {"regions-overlap",required_argument,NULL,3},
+        {"plot-threshold",1,0,'p'},
+        {"output-dir",1,0,'o'},
+        {0,0,0,0}
+    };
+    char *tmp = NULL;
+    while ((c = getopt_long(argc, argv, "h?r:R:t:T:s:o:p:l:T:c:b:P:x:e:O:W:f:a:L:d:k:",loptions,NULL)) >= 0) {
+        switch (c) {
+            case 'L': 
+                args->lrr_smooth_win = strtol(optarg,&tmp,10);
+                if ( *tmp ) error("Could not parse: --LRR-smooth-win %s\n", optarg);
+                break;
+            case 'f': args->af_fname = optarg; break;
+            case 'O': 
+                args->optimize_frac = strtod(optarg,&tmp);
+                if ( *tmp ) error("Could not parse: -O %s\n", optarg);
+                break;
+            case 'd':
+                args->query_sample.baf_dev2_dflt = strtod(optarg,&tmp);
+                if ( *tmp )
+                {
+                    if ( *tmp!=',') error("Could not parse: -d %s\n", optarg);
+                    args->control_sample.baf_dev2_dflt = strtod(tmp+1,&tmp);
+                    if ( *tmp ) error("Could not parse: -d %s\n", optarg);
+                }
+                else
+                    args->control_sample.baf_dev2_dflt = args->query_sample.baf_dev2_dflt;
+                args->query_sample.baf_dev2_dflt   *= args->query_sample.baf_dev2_dflt;
+                args->control_sample.baf_dev2_dflt *= args->control_sample.baf_dev2_dflt;
+                break;
+            case 'k':
+                args->query_sample.lrr_dev2 = strtod(optarg,&tmp);
+                if ( *tmp )
+                {
+                    if ( *tmp!=',') error("Could not parse: -k %s\n", optarg);
+                    args->control_sample.lrr_dev2 = strtod(tmp+1,&tmp);
+                    if ( *tmp ) error("Could not parse: -d %s\n", optarg);
+                }
+                else
+                    args->control_sample.lrr_dev2 = args->query_sample.lrr_dev2;
+                args->query_sample.lrr_dev2   *= args->query_sample.lrr_dev2;
+                args->control_sample.lrr_dev2 *= args->control_sample.lrr_dev2;
+                break;
+            case 'a':
+                args->query_sample.cell_frac_dflt = strtod(optarg,&tmp);
+                if ( *tmp )
+                {
+                    if ( *tmp!=',') error("Could not parse: -a %s\n", optarg);
+                    args->control_sample.cell_frac_dflt = strtod(tmp+1,&tmp);
+                    if ( *tmp ) error("Could not parse: -a %s\n", optarg);
+                }
+                break;
+            case 'W':
+                args->baum_welch_th = strtod(optarg,&tmp);
+                if ( *tmp ) error("Could not parse: -W %s\n", optarg);
+                break;
+            case 'e': 
+                args->err_prob = strtod(optarg,&tmp);
+                if ( *tmp ) error("Could not parse: -e %s\n", optarg);
+                break;
+            case 'b': 
+                args->baf_bias = strtod(optarg,&tmp);
+                if ( *tmp ) error("Could not parse: -b %s\n", optarg);
+                break;
+            case 'x': 
+                args->ij_prob = strtod(optarg,&tmp);
+                if ( *tmp ) error("Could not parse: -x %s\n", optarg);
+                break;
+            case 'P': 
+                args->same_prob = strtod(optarg,&tmp);
+                if ( *tmp ) error("Could not parse: -P %s\n", optarg);
+                break;
+            case 'l': 
+                args->lrr_bias = strtod(optarg,&tmp);
+                if ( *tmp ) error("Could not parse: -l %s\n", optarg);
+                break;
+            case 'p': 
+                args->plot_th = strtod(optarg,&tmp);
+                if ( *tmp ) error("Could not parse: -p %s\n", optarg);
+                break;
+            case 'o': args->output_dir = optarg; break;
+            case 's': args->query_sample.name = strdup(optarg); break;
+            case 'c': args->control_sample.name = optarg; break;
+            case 't': args->targets_list = optarg; break;
+            case 'T': args->targets_list = optarg; targets_is_file = 1; break;
+            case 'r': args->regions_list = optarg; break;
+            case 'R': args->regions_list = optarg; regions_is_file = 1; break;
+            case  3 :
+                regions_overlap = parse_overlap_option(optarg);
+                if ( regions_overlap < 0 ) error("Could not parse: --regions-overlap %s\n",optarg);
+                break;
+            case  4 :
+                targets_overlap = parse_overlap_option(optarg);
+                if ( targets_overlap < 0 ) error("Could not parse: --targets-overlap %s\n",optarg);
+                break;
+            case 'h': 
+            case '?': usage(args); break;
+            default: error("Unknown argument: %s\n", optarg);
+        }
+    }
+
+    char *fname = NULL;
+    if ( optind>=argc )
+    {
+        if ( !isatty(fileno((FILE *)stdin)) ) fname = "-";
+    }
+    else fname = argv[optind];
+    if ( !fname ) usage(args);
+
+    if ( !args->output_dir ) error("Expected -o option\n");
+    if ( args->regions_list )
+    {
+        bcf_sr_set_opt(args->files,BCF_SR_REGIONS_OVERLAP,regions_overlap);
+        if ( bcf_sr_set_regions(args->files, args->regions_list, regions_is_file)<0 )
+            error("Failed to read the regions: %s\n", args->regions_list);
+    }
+    if ( args->targets_list )
+    {
+        bcf_sr_set_opt(args->files,BCF_SR_TARGETS_OVERLAP,targets_overlap);
+        if ( bcf_sr_set_targets(args->files, args->targets_list, targets_is_file, 0)<0 )
+            error("Failed to read the targets: %s\n", args->targets_list);
+    }
+    if ( args->af_fname )
+    {
+        if ( bcf_sr_set_targets(args->files, args->af_fname, 1, 3)<0 )
+            error("Failed to read the targets: %s\n", args->af_fname);
+    }
+    if ( !bcf_sr_add_reader(args->files, fname) )
+        error("Failed to read from %s: %s\n", !strcmp("-",fname)?"standard input":fname,bcf_sr_strerror(args->files->errnum));
+    
+    init_data(args);
+    while ( bcf_sr_next_line(args->files) )
+    {
+        bcf1_t *line = bcf_sr_get_line(args->files,0);
+        cnv_next_line(args, line);
+    }
+    cnv_next_line(args, NULL);
+    create_plots(args);
+    fprintf(stderr,"Number of lines: total/processed: %d/%d\n", args->ntot,args->nused);
+    destroy_data(args);
+    free(args);
+    return 0;
+}
+
+
diff --git a/bcftools/vcfcnv.c.pysam.c b/bcftools/vcfcnv.c.pysam.c
new file mode 100644
index 0000000..fd2e3bb
--- /dev/null
+++ b/bcftools/vcfcnv.c.pysam.c
@@ -0,0 +1,1440 @@
+#include "bcftools.pysam.h"
+
+/* The MIT License
+
+   Copyright (c) 2014-2022 Genome Research Ltd.
+
+   Author: Petr Danecek <pd3@sanger.ac.uk>
+   
+   Permission is hereby granted, free of charge, to any person obtaining a copy
+   of this software and associated documentation files (the "Software"), to deal
+   in the Software without restriction, including without limitation the rights
+   to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+   copies of the Software, and to permit persons to whom the Software is
+   furnished to do so, subject to the following conditions:
+   
+   The above copyright notice and this permission notice shall be included in
+   all copies or substantial portions of the Software.
+   
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+   IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+   FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+   AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+   LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+   OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+   THE SOFTWARE.
+
+ */
+
+/*
+    Known issues:
+    - The --AF-file option behaves like --targets-file, sites not listed in the AFs
+      are skipped.
+*/
+
+#include <stdio.h>
+#include <unistd.h>
+#include <assert.h>
+#include <getopt.h>
+#include <math.h>
+#include <inttypes.h>
+#include <htslib/vcf.h>
+#include <htslib/synced_bcf_reader.h>
+#include <htslib/kstring.h>
+#include <htslib/kfunc.h>
+#include <htslib/khash_str2int.h>
+#include "bcftools.h"
+#include "HMM.h"
+#include "rbuf.h"
+
+#define DBG0 0
+
+#define N_STATES 4
+#define CN0 0
+#define CN1 1
+#define CN2 2
+#define CN3 3
+
+typedef struct
+{
+    float mean, dev2, norm;
+}
+gauss_param_t;
+
+typedef struct
+{
+    char *name;
+    int idx;    // VCF sample index
+    float *lrr,*baf, baf_dev2, baf_dev2_dflt, lrr_dev2;
+    float cell_frac, cell_frac_dflt;
+    gauss_param_t gauss_param[18];
+    double pobs[N_STATES];
+    FILE *dat_fh, *cn_fh, *summary_fh;
+    char *dat_fname, *cn_fname, *summary_fname;
+}
+sample_t;
+
+typedef struct _args_t
+{
+    bcf_srs_t *files;
+    bcf_hdr_t *hdr;
+    int prev_rid, ntot, nused;
+    sample_t query_sample, control_sample;
+
+    int nstates;    // number of states: N_STATES for one sample, N_STATES^2 for two samples
+    double lrr_bias, baf_bias;              // LRR/BAF weights
+    double same_prob, ij_prob;              // prior of both samples being the same and the transition probability P(i|j)
+    double err_prob;                        // constant probability of erroneous measurement
+    float *nonref_afs, nonref_af, nonref_af_dflt, fRR, fRA, fAA, *tmpf;
+    unsigned long int nRR, nRA, nAA;
+    int mtmpf;
+
+    double *tprob, *tprob_arr;  // array of transition matrices, precalculated up to ntprob_arr positions
+    double *iprobs;             // states' initial probabilities
+    int ntprob_arr;
+
+    hmm_t *hmm;
+    double *eprob;          // emission probs [nstates*nsites,msites]
+    uint32_t *sites;        // positions [nsites,msites]
+    int nsites, msites;
+
+    double baum_welch_th, optimize_frac; 
+    float plot_th;
+    FILE *summary_fh;
+    char **argv, *regions_list, *summary_fname, *output_dir;
+    char *targets_list, *af_fname;
+    int argc, verbose, lrr_smooth_win;
+}
+args_t;
+
+FILE *open_file(char **fname, const char *mode, const char *fmt, ...);
+
+static inline void hmm2cn_state(int nstates, int i, int *a, int *b)
+{
+    *a = i / N_STATES;
+    *b = i - (*a)*N_STATES;
+}
+static double *init_tprob_matrix(int ndim, double ij_prob, double same_prob)
+{
+    int i,j;
+    double *mat = (double*) malloc(sizeof(double)*ndim*ndim);
+
+    assert( ndim==N_STATES || ndim==N_STATES*N_STATES);
+
+    if ( ndim==N_STATES )   // one sample
+    {
+        double pii = 1 - ij_prob*(N_STATES-1);
+        if ( pii < ij_prob ) error("Error: -x set a bit too high, P(x|x) < P(x|y): %e vs %e\n", pii,ij_prob);
+        for (j=0; j<ndim; j++)
+        {
+            double sum = 0;
+            for (i=0; i<ndim; i++)
+            {
+                // transition from j-th to i-th state
+                if ( i==j )
+                    MAT(mat,ndim,i,j) = pii;
+                else
+                    MAT(mat,ndim,i,j) = ij_prob;
+
+                sum += MAT(mat,ndim,i,j);
+            }
+            assert( fabs(sum - 1.0)<1e-15 );
+        }
+    }
+    else    // two samples
+    {
+        // interpret ij_prob differently, as ii_prob in fact, so that for two
+        // samples the behaviour is somewhat closer to single sample calling
+        // with s=0. 
+        double pii = 1 - ij_prob*(N_STATES-1);
+        ij_prob = (1 - pii) / (ndim - 1);
+        for (j=0; j<ndim; j++)
+        {
+            int ja,jb;
+            hmm2cn_state(ndim, j, &ja, &jb);
+
+            double sum = 0;
+            for (i=0; i<ndim; i++)
+            {
+                int ia,ib;
+                hmm2cn_state(ndim, i, &ia, &ib);
+
+                // transition from (ja,jb)-th to (ia,ib)-th state
+                double pa = ja==ia ? pii : ij_prob;
+                double pb = jb==ib ? pii : ij_prob;
+
+                if ( ia==ib && ja==jb )
+                    MAT(mat,ndim,i,j) = pa*pb - pa*pb*same_prob + sqrt(pa*pb)*same_prob;
+                else if ( ia==ib )
+                    MAT(mat,ndim,i,j) = pa*pb;
+                else
+                    MAT(mat,ndim,i,j) = pa*pb*(1-same_prob);
+
+                sum += MAT(mat,ndim,i,j);
+            }
+            for (i=0; i<ndim; i++) MAT(mat,ndim,i,j) /= sum;
+        }
+    }
+    return mat;
+}
+
+static double *init_iprobs(int ndim, double same_prob)
+{
+    int i;
+    double *probs = (double*) malloc(sizeof(double)*ndim);
+
+    assert( ndim==N_STATES || ndim==N_STATES*N_STATES);
+
+    if ( ndim==N_STATES )   
+    {
+        // one sample: prior on CN2
+        for (i=0; i<ndim; i++) 
+            probs[i] = i==CN2 ? 0.5 : 0.5/3;
+    }
+    else
+    {
+        // two samples
+        double norm = 0;
+        for (i=0; i<ndim; i++) 
+        {
+            int ia,ib;
+            hmm2cn_state(ndim, i, &ia, &ib);
+
+            double pa = ia==CN2 ? 0.5 : 0.5/3;
+            double pb = ib==CN2 ? 0.5 : 0.5/3;
+
+            probs[i] = pa*pb;
+            if ( ia!=ib ) probs[i] *= 1-same_prob;
+
+            norm += probs[i];
+        }
+        for (i=0; i<ndim; i++) probs[i] /= norm;
+    }
+    return probs;
+}
+
+static void init_sample_files(sample_t *smpl, char *dir)
+{
+    smpl->dat_fh = open_file(&smpl->dat_fname,"w","%s/dat.%s.tab",dir,smpl->name);
+    if ( !smpl->dat_fh ) error("Error opening file: %s/dat.%s.tab\n",dir,smpl->name);
+
+    smpl->cn_fh  = open_file(&smpl->cn_fname,"w","%s/cn.%s.tab",dir,smpl->name);
+    if ( !smpl->cn_fh ) error("Error opening file: %s/cn.%s.tab\n",dir,smpl->name);
+
+    smpl->summary_fh = open_file(&smpl->summary_fname,"w","%s/summary.%s.tab",dir,smpl->name);
+    if ( !smpl->summary_fh ) error("Error opening file: %s/summary.%s.tab\n",dir,smpl->name);
+
+    fprintf(smpl->dat_fh,"# [1]Chromosome\t[2]Position\t[3]BAF\t[4]LRR\n");
+    fprintf(smpl->cn_fh,"# [1]Chromosome\t[2]Position\t[3]CN\t[4]P(CN0)\t[5]P(CN1)\t[6]P(CN2)\t[7]P(CN3)\n");
+    fprintf(smpl->summary_fh,"# RG, Regions [2]Chromosome\t[3]Start\t[4]End\t[5]Copy Number state\t[6]Quality\t[7]nSites\t[8]nHETs\n");
+}
+static void close_sample_files(sample_t *smpl)
+{
+    if ( fclose(smpl->dat_fh)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,smpl->dat_fname);
+    if ( fclose(smpl->cn_fh)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,smpl->cn_fname);
+    if ( fclose(smpl->summary_fh)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,smpl->summary_fname);
+}
+
+static double norm_cdf(double mean, double dev);
+static void init_data(args_t *args)
+{
+    args->prev_rid = -1;
+    args->hdr = args->files->readers[0].header;
+
+    if ( !args->query_sample.name )
+    {
+        if ( bcf_hdr_nsamples(args->hdr)>1 ) error("Multi-sample VCF, missing the -s option\n");
+        args->query_sample.name = strdup(args->hdr->samples[0]);
+    }
+    else 
+        if ( bcf_hdr_id2int(args->hdr,BCF_DT_SAMPLE,args->query_sample.name)<0 ) error("The sample \"%s\" not found\n", args->query_sample.name);
+    if ( !args->files->readers[0].file->is_bin )
+    {
+        int ret;
+        kstring_t tmp = {0,0,0};
+        if ( args->control_sample.name )
+        {
+            ksprintf(&tmp, "%s,%s", args->query_sample.name,args->control_sample.name);
+            ret = bcf_hdr_set_samples(args->hdr, tmp.s, 0);
+        }
+        else
+        {
+            ret = bcf_hdr_set_samples(args->hdr, args->query_sample.name, 0);
+            tmp.s = args->query_sample.name;
+        }
+        if ( ret<0 ) error("Error parsing the list of samples: %s\n", tmp.s);
+        else if ( ret>0 ) error("The sample not found in the VCF: %s\n", ret==1 ? args->query_sample.name : args->control_sample.name);
+
+        if ( args->control_sample.name ) free(tmp.s);
+    }
+    args->query_sample.idx = bcf_hdr_id2int(args->hdr,BCF_DT_SAMPLE,args->query_sample.name);
+    args->control_sample.idx = args->control_sample.name ? bcf_hdr_id2int(args->hdr,BCF_DT_SAMPLE,args->control_sample.name) : -1;
+    args->nstates = args->control_sample.name ? N_STATES*N_STATES : N_STATES;
+    args->tprob  = init_tprob_matrix(args->nstates, args->ij_prob, args->same_prob);
+    args->iprobs = init_iprobs(args->nstates, args->same_prob);
+    args->hmm = hmm_init(args->nstates, args->tprob, 10000);
+    hmm_init_states(args->hmm, args->iprobs);
+
+    args->summary_fh = bcftools_stdout;
+    init_sample_files(&args->query_sample, args->output_dir);
+    if ( args->control_sample.name )
+    {
+        init_sample_files(&args->control_sample, args->output_dir);
+        args->summary_fh = open_file(&args->summary_fname,"w","%s/summary.tab",args->output_dir);
+    }
+    else
+        args->summary_fh = NULL;    // one sample only, no two-file summary
+        
+
+    int i;
+    FILE *fh = args->summary_fh ? args->summary_fh : args->query_sample.summary_fh;
+
+    fprintf(fh, "# This file was produced by: bcftools cnv(%s+htslib-%s)\n", bcftools_version(),hts_version());
+    fprintf(fh, "# The command line was:\tbcftools %s", args->argv[0]);
+    for (i=1; i<args->argc; i++) fprintf(fh, " %s",args->argv[i]);
+    if ( args->control_sample.name )
+        fprintf(fh, "\n#\n"
+                "# RG, Regions\t[2]Chromosome\t[3]Start\t[4]End\t[5]Copy number:%s\t[6]Copy number:%s\t[7]Quality"
+                "\t[8]nSites in (5)\t[9]nHETs in (5)\t[10]nSites in (6)\t[11]nHETs in(6)\n",
+                args->query_sample.name,args->control_sample.name
+               );
+    else
+        fprintf(fh, "\n#\n"
+                "# RG, Regions\t[2]Chromosome\t[3]Start\t[4]End\t[5]Copy number:%s\t[6]Quality\t[7]nSites\t[8]nHETs\n",
+                args->query_sample.name
+               );
+    if ( args->optimize_frac )
+    {
+        fprintf(args->query_sample.summary_fh, "# CF, cell fraction estimate\t[2]Chromosome\t[3]Start\t[4]End\t[5]Cell fraction\t[6]BAF deviation\n");
+        if ( args->control_sample.name )
+        {
+            fprintf(args->control_sample.summary_fh, "# CF, cell fraction estimate\t[2]Chromosome\t[3]Start\t[4]End\t[5]Cell fraction\t[6]BAF deviation\n");
+            fprintf(args->summary_fh, "# CF, cell fraction estimate\t[2]Chromosome\t[3]Start\t[4]End\t"
+                "[5]Cell fraction:%s\t[6]Cell fraction:%s\t[7]BAF deviation:%s\t[8]BAF deviation:%s\n",
+                args->query_sample.name,args->control_sample.name,
+                args->query_sample.name,args->control_sample.name
+                );
+        }
+    }
+}
+
+char *msprintf(const char *fmt, ...);
+static void py_plot_cnv(char *script, float th)
+{
+    if ( th>100 ) return;   // create no plots
+
+    char *cmd = msprintf("python %s -p %f", script, th);
+    int ret = system(cmd);
+    if ( ret) fprintf(bcftools_stderr, "The command returned non-zero status %d: %s\n", ret, cmd);
+    free(cmd);
+}
+
+static void plot_sample(args_t *args, sample_t *smpl)
+{
+    char *fname;
+    FILE *fp = open_file(&fname,"w","%s/plot.%s.py",args->output_dir,smpl->name);
+    fprintf(fp,
+            "import matplotlib as mpl\n"
+            "mpl.use('Agg')\n"
+            "import matplotlib.pyplot as plt\n"
+            "import csv\n"
+            "import numpy as np\n"
+            "csv.register_dialect('tab', delimiter='\\t', quoting=csv.QUOTE_NONE)\n"
+            "\n"
+            "dat = {}\n"
+            "with open('%s', 'r') as f:\n"
+            "    reader = csv.reader(f, 'tab')\n"
+            "    for row in reader:\n"
+            "        chr = row[0]\n"
+            "        if chr[0]=='#': continue\n"
+            "        if chr not in dat: dat[chr] = []\n"
+            "        dat[chr].append([int(row[1]), float(row[2]), float(row[3])])\n"
+            "\n"
+            "cnv = {}\n"
+            "with open('%s', 'r') as f:\n"
+            "    reader = csv.reader(f, 'tab')\n"
+            "    for row in reader:\n"
+            "        chr = row[0]\n"
+            "        if chr[0]=='#': continue\n"
+            "        if chr not in cnv: cnv[chr] = []\n"
+            "        row[2] = int(row[2]) + 0.5\n"
+            "        row[1] = int(row[1])\n"
+            "        cnv[chr].append(row[1:])\n"
+            "\n"
+            "for chr in dat:\n"
+            "    fig,(ax1, ax2, ax3) = plt.subplots(3,1,figsize=(10,8),sharex=True)\n"
+            "    ax1.plot([x[0] for x in dat[chr]],[x[2] for x in dat[chr]], '.', ms=3)\n"
+            "    ax2.plot([x[0] for x in dat[chr]],[x[1] for x in dat[chr]], '.', ms=3)\n"
+            "    cn_dat = cnv[chr]\n"
+            "    xgrid = [float(x[0]) for x in cn_dat]\n"
+            "    ygrid = np.linspace(0,5,6)\n"
+            "    xgrid, ygrid = np.meshgrid(xgrid, ygrid)\n"
+            "    heat = np.zeros_like(xgrid)\n"
+            "    for x in range(len(heat[0])-1):\n"
+            "       heat[0][x] = cn_dat[x][2]\n"
+            "       heat[1][x] = cn_dat[x][3]\n"
+            "       heat[2][x] = cn_dat[x][4]\n"
+            "       heat[3][x] = cn_dat[x][5]\n"
+            "    mesh = ax3.pcolormesh(xgrid, ygrid, heat, cmap='bwr_r', shading='auto', alpha=0)\n"
+            "    mesh.set_clim(vmin=-1,vmax=1)\n"
+            "    ax3.plot([x[0] for x in cn_dat],[x[1] for x in cn_dat],'.-',ms=3,color='black')\n"
+            "    fig.suptitle('%s (chr '+chr+')')\n"
+            "    ax1.set_title('Log-R intensities Ratio',fontsize=10)\n"
+            "    ax2.set_title('B-Allele Frequency',fontsize=10)\n"
+            "    ax3.set_title('Copy Number Variation',fontsize=10)\n"
+            "    ax1.set_ylabel('LRR')\n"
+            "    ax2.set_ylabel('BAF')\n"
+            "    ax3.set_ylabel('CN')\n"
+            "    ax3.set_xlabel('Coordinate (chrom '+chr+')',fontsize=10)\n"
+            "    ax3.set_ylim(-0.1,4.1)\n"
+            "    ax3.set_yticks([0.5,1.5,2.5,3.5])\n"
+            "    ax3.set_yticklabels(['CN0','CN1','CN2','CN3'])\n"
+            "    plt.subplots_adjust(left=0.08,right=0.95,bottom=0.08,top=0.92)\n"
+            "    plt.savefig('%s/plot.%s.chr'+chr+'.png')\n"
+            "    plt.close()\n"
+            "\n", 
+            smpl->dat_fname,smpl->cn_fname,smpl->name,args->output_dir,smpl->name
+    );
+    fclose(fp);
+
+    py_plot_cnv(fname, args->plot_th);
+    free(fname);
+}
+
+static void create_plots(args_t *args)
+{
+    close_sample_files(&args->query_sample);
+    if ( args->control_sample.name ) close_sample_files(&args->control_sample);
+    if ( args->summary_fh ) fclose(args->summary_fh);
+
+    if ( !args->control_sample.name )
+    {
+        plot_sample(args, &args->query_sample);
+        return;
+    }
+
+    char *fname;
+    FILE *fp = open_file(&fname,"w","%s/plot.%s.%s.py",args->output_dir,args->control_sample.name,args->query_sample.name);
+    fprintf(fp,
+            "import matplotlib as mpl\n"
+            "mpl.use('Agg')\n"
+            "import matplotlib.pyplot as plt\n"
+            "import csv,argparse\n"
+            "import numpy as np\n"
+            "csv.register_dialect('tab', delimiter='\\t', quoting=csv.QUOTE_NONE)\n"
+            "\n"
+            "control_sample = '%s'\n"
+            "query_sample   = '%s'\n"
+            "\n"
+            "parser = argparse.ArgumentParser()\n"
+            "parser.add_argument('-p', '--plot-threshold', type=float)\n"
+            "parser.add_argument('-c', '--chromosome')\n"
+            "args = parser.parse_args()\n"
+            "if args.plot_threshold==None: args.plot_threshold = 0\n"
+            "\n"
+            "def chroms_to_plot(th):\n"
+            "   dat = {}\n"
+            "   with open('%s/summary.tab', 'r') as f:\n"
+            "       reader = csv.reader(f, 'tab')\n"
+            "       for row in reader:\n"
+            "           if row[0]!='RG': continue\n"
+            "           chr   = row[1]\n"
+            "           start = row[2]\n"
+            "           end   = row[3]\n"
+            "           qual  = float(row[6])\n"
+            "           if row[4]==row[5] and args.plot_threshold!=0: continue\n"
+            "           if chr not in dat: dat[chr] = 0.0\n"
+            "           if qual > dat[chr]: dat[chr] = qual\n"
+            "   out = {}\n"
+            "   for chr in dat:\n"
+            "       if (chr not in dat) or dat[chr]<th: continue\n"
+            "       out[chr] = 1\n"
+            "   return out\n"
+            "if args.chromosome!=None:\n"
+            "   plot_chroms = { args.chromosome:1 }\n"
+            "else:\n"
+            "   plot_chroms = chroms_to_plot(args.plot_threshold)\n"
+            "\n"
+            "def read_dat(file,dat,plot_chr):\n"
+            "   with open(file, 'r') as f:\n"
+            "       reader = csv.reader(f, 'tab')\n"
+            "       for row in reader:\n"
+            "           chr = row[0]\n"
+            "           if chr != plot_chr: continue\n"
+            "           dat.append([int(row[1]), float(row[2]), float(row[3])])\n"
+            "def read_cnv(file,cnv,plot_chr):\n"
+            "   with open(file, 'r') as f:\n"
+            "       reader = csv.reader(f, 'tab')\n"
+            "       for row in reader:\n"
+            "           chr = row[0]\n"
+            "           if chr != plot_chr: continue\n"
+            "           row[2] = int(row[2]) + 0.5\n"
+            "           row[1] = int(row[1])\n"
+            "           cnv.append(row[1:])\n"
+            "def find_diffs(a,b):\n"
+            "    out = []\n"
+            "    diff = []\n"
+            "    for i in range(len(a)):\n"
+            "        if a[i][1]!=b[i][1]:\n"
+            "            if i>0: diff.append([b[i-1][0],b[i-1][1],a[i-1][1]])\n"
+            "            diff.append([b[i][0],b[i][1],a[i][1]])\n"
+            "        elif len(diff):\n"
+            "            diff.append([b[i][0],b[i][1],a[i][1]])\n"
+            "            out.append(diff)\n"
+            "            diff = []\n"
+            "    if len(diff): out.append(diff)\n"
+            "    return out\n"
+            "\n"
+            "for chr in sorted(plot_chroms.keys()):\n"
+            "    control_dat = []\n"
+            "    control_cnv = []\n"
+            "    query_dat   = []\n"
+            "    query_cnv   = []\n"
+            "    read_dat('%s',control_dat,chr)\n"
+            "    read_dat('%s',query_dat,chr)\n"
+            "    read_cnv('%s',control_cnv,chr)\n"
+            "    read_cnv('%s',query_cnv,chr)\n"
+            "\n"
+            "    fig,(ax1,ax2,ax3,ax4,ax5,ax6) = plt.subplots(6,1,figsize=(10,8),sharex=True)\n"
+            "    ax1.plot([x[0] for x in control_dat],[x[2] for x in control_dat], '.', ms=3,color='red')\n"
+            "    ax2.plot([x[0] for x in control_dat],[x[1] for x in control_dat], '.', ms=3,color='red')\n"
+            "    cn_dat = control_cnv\n"
+            "    xgrid = [float(x[0]) for x in cn_dat]\n"
+            "    ygrid = np.linspace(0,5,6)\n"
+            "    xgrid, ygrid = np.meshgrid(xgrid, ygrid)\n"
+            "    heat = np.zeros_like(xgrid)\n"
+            "    for x in range(len(heat[0])-1):\n"
+            "       heat[0][x] = cn_dat[x][2]\n"
+            "       heat[1][x] = cn_dat[x][3]\n"
+            "       heat[2][x] = cn_dat[x][4]\n"
+            "       heat[3][x] = cn_dat[x][5]\n"
+            "    mesh = ax3.pcolormesh(xgrid, ygrid, heat, cmap='bwr', shading='auto', alpha=0)\n"
+            "    mesh.set_clim(vmin=-1,vmax=1)\n"
+            "    ax3.plot([x[0] for x in cn_dat],[x[1] for x in cn_dat],'-',ms=3,color='black',lw=1.7)\n"
+            "\n"
+            "    ax6.plot([x[0] for x in query_dat],[x[2] for x in query_dat], '.', ms=3)\n"
+            "    ax5.plot([x[0] for x in query_dat],[x[1] for x in query_dat], '.', ms=3)\n"
+            "    cn_dat = query_cnv\n"
+            "    xgrid = [float(x[0]) for x in cn_dat]\n"
+            "    ygrid = np.linspace(0,5,6)\n"
+            "    xgrid, ygrid = np.meshgrid(xgrid, ygrid)\n"
+            "    heat = np.zeros_like(xgrid)\n"
+            "    for x in range(len(heat[0])-1):\n"
+            "       heat[0][x] = cn_dat[x][2]\n"
+            "       heat[1][x] = cn_dat[x][3]\n"
+            "       heat[2][x] = cn_dat[x][4]\n"
+            "       heat[3][x] = cn_dat[x][5]\n"
+            "    mesh = ax4.pcolormesh(xgrid, ygrid, heat, cmap='bwr_r')\n"
+            "    mesh.set_clim(vmin=-1,vmax=1)\n"
+            "    ax4.plot([x[0] for x in cn_dat],[x[1] for x in cn_dat],'-',ms=3,color='black',lw=1.7)\n"
+            "    ax3.annotate(control_sample, xy=(0.02,0.1), xycoords='axes fraction', color='red',fontsize=12, va='bottom',ha='left')\n"
+            "    ax4.annotate(query_sample, xy=(0.02,0.9), xycoords='axes fraction', color='blue',fontsize=12, va='top',ha='left')\n"
+            "\n"
+            "    diffs = find_diffs(control_cnv,query_cnv)\n"
+            "    for diff in diffs:\n"
+            "        ax3.plot([x[0] for x in diff],[x[1] for x in diff],'-',ms=3,color='blue',lw=1.7)\n"
+            "        ax4.plot([x[0] for x in diff],[x[2] for x in diff],'-',ms=3,color='red',lw=1.7)\n"
+            "\n"
+            "    fig.suptitle('chr '+chr+', '+control_sample+' vs '+query_sample)\n"
+            "    ax1.tick_params(axis='both', labelsize=8)\n"
+            "    ax2.tick_params(axis='both', labelsize=8)\n"
+            "    ax3.tick_params(axis='both', labelsize=8)\n"
+            "    ax4.tick_params(axis='both', labelsize=8)\n"
+            "    ax5.tick_params(axis='both', labelsize=8)\n"
+            "    ax6.tick_params(axis='both', labelsize=8)\n"
+            "    ax6.set_xlabel('Coordinate (chrom '+chr+')',fontsize=8)\n"
+            "    ax1.set_ylabel('LRR')\n"
+            "    ax2.set_ylabel('BAF')\n"
+            "    ax3.set_ylabel('CN')\n"
+            "    ax6.set_ylabel('LRR')\n"
+            "    ax5.set_ylabel('BAF')\n"
+            "    ax4.set_ylabel('CN')\n"
+            "    ax3.set_ylim(-0.1,4.1)\n"
+            "    ax3.set_yticks([0.5,1.5,2.5,3.5])\n"
+            "    ax3.set_yticklabels(['CN0','CN1','CN2','CN3'])\n"
+            "    ax4.set_ylim(-0.1,4.1)\n"
+            "    ax4.set_yticks([0.5,1.5,2.5,3.5])\n"
+            "    ax4.set_yticklabels(['CN0','CN1','CN2','CN3'])\n"
+            "    plt.subplots_adjust(left=0.08,right=0.95,bottom=0.08,top=0.92,hspace=0)\n"
+            "    plt.savefig('%s/plot.%s.%s.chr'+chr+'.png')\n"
+            "    plt.close()\n"
+            "\n", 
+            args->control_sample.name,args->query_sample.name,
+            args->output_dir,
+            args->control_sample.dat_fname,args->query_sample.dat_fname,
+            args->control_sample.cn_fname,args->query_sample.cn_fname,
+            args->output_dir,args->control_sample.name,args->query_sample.name
+        );
+        fclose(fp);
+
+    py_plot_cnv(fname,args->plot_th);
+    free(fname);
+}
+
+static void destroy_data(args_t *args)
+{
+    bcf_sr_destroy(args->files);
+    hmm_destroy(args->hmm);
+    free(args->tmpf);
+    free(args->sites);
+    free(args->eprob);
+    free(args->tprob);
+    free(args->iprobs);
+    free(args->summary_fname);
+    free(args->nonref_afs);
+    free(args->query_sample.baf);
+    free(args->query_sample.lrr);
+    free(args->control_sample.baf);
+    free(args->control_sample.lrr);
+    free(args->query_sample.name);
+    free(args->query_sample.dat_fname);
+    free(args->query_sample.cn_fname);
+    free(args->query_sample.summary_fname);
+    free(args->control_sample.dat_fname);
+    free(args->control_sample.cn_fname);
+    free(args->control_sample.summary_fname);
+}
+
+static inline char copy_number_state(args_t *args, int istate, int ismpl)
+{
+    char code[] = "01234";
+    if ( !args->control_sample.name ) return code[istate];
+    int idx = ismpl ? istate - (istate/N_STATES)*N_STATES : istate/N_STATES;
+    return code[idx];
+}
+
+static double avg_ii_prob(int n, double *mat)
+{
+    int i;
+    double avg = 0;
+    for (i=0; i<n; i++) avg += MAT(mat,n,i,i);
+    return avg/n;
+}
+
+#define GAUSS_CN1_PK_R(smpl)    (&((smpl)->gauss_param[0]))
+#define GAUSS_CN1_PK_A(smpl)    (&((smpl)->gauss_param[1]))
+#define GAUSS_CN2_PK_RR(smpl)   (&((smpl)->gauss_param[2]))
+#define GAUSS_CN2_PK_RA(smpl)   (&((smpl)->gauss_param[3]))
+#define GAUSS_CN2_PK_AA(smpl)   (&((smpl)->gauss_param[4]))
+#define GAUSS_CN3_PK_RRR(smpl)  (&((smpl)->gauss_param[5]))
+#define GAUSS_CN3_PK_RRA(smpl)  (&((smpl)->gauss_param[6]))
+#define GAUSS_CN3_PK_RAA(smpl)  (&((smpl)->gauss_param[7]))
+#define GAUSS_CN3_PK_AAA(smpl)  (&((smpl)->gauss_param[8]))
+
+static inline double norm_prob(double baf, gauss_param_t *param)
+{
+    return exp(-(baf-param->mean)*(baf-param->mean)*0.5/param->dev2) / param->norm / sqrt(2*M_PI*param->dev2);
+}
+
+static int set_observed_prob(args_t *args, sample_t *smpl, int isite)
+{
+    float baf = smpl->baf[isite];
+    float lrr = args->lrr_bias>0 ? smpl->lrr[isite] : 0;
+
+    float fRR = args->fRR;
+    float fRA = args->fRA;
+    float fAA = args->fAA;
+
+    if ( baf<0 )
+    {
+        // no call: either some technical issue or the call could not be made because it is CN0
+        int i;
+        smpl->pobs[CN0] = 0.5;
+        for (i=1; i<N_STATES; i++) smpl->pobs[i] = (1.0-smpl->pobs[CN0])/(N_STATES-1);
+        return 0;
+    }
+
+    double cn1_baf = 
+        norm_prob(baf,GAUSS_CN1_PK_R(smpl)) * (fRR + fRA*0.5) +
+        norm_prob(baf,GAUSS_CN1_PK_A(smpl)) * (fAA + fRA*0.5) ;
+    double cn2_baf = 
+        norm_prob(baf,GAUSS_CN2_PK_RR(smpl)) * fRR + 
+        norm_prob(baf,GAUSS_CN2_PK_RA(smpl)) * fRA + 
+        norm_prob(baf,GAUSS_CN2_PK_AA(smpl)) * fAA;
+    double cn3_baf = 
+        norm_prob(baf,GAUSS_CN3_PK_RRR(smpl)) * fRR + 
+        norm_prob(baf,GAUSS_CN3_PK_RRA(smpl)) * fRA*0.5 + 
+        norm_prob(baf,GAUSS_CN3_PK_RAA(smpl)) * fRA*0.5 + 
+        norm_prob(baf,GAUSS_CN3_PK_AAA(smpl)) * fAA;
+
+    double norm = cn1_baf + cn2_baf + cn3_baf;
+    cn1_baf /= norm;
+    cn2_baf /= norm;
+    cn3_baf /= norm;
+
+    #if DBG0
+    if ( args->verbose ) fprintf(bcftools_stderr,"%f\t%f %f %f\n", baf,cn1_baf,cn2_baf,cn3_baf);
+    #endif
+
+    double cn1_lrr = exp(-(lrr + 0.45)*(lrr + 0.45)/smpl->lrr_dev2);
+    double cn2_lrr = exp(-(lrr - 0.00)*(lrr - 0.00)/smpl->lrr_dev2);
+    double cn3_lrr = exp(-(lrr - 0.30)*(lrr - 0.30)/smpl->lrr_dev2);
+
+    smpl->pobs[CN0] = 0;
+    smpl->pobs[CN1] = args->err_prob + (1 - args->baf_bias + args->baf_bias*cn1_baf)*(1 - args->lrr_bias + args->lrr_bias*cn1_lrr);
+    smpl->pobs[CN2] = args->err_prob + (1 - args->baf_bias + args->baf_bias*cn2_baf)*(1 - args->lrr_bias + args->lrr_bias*cn2_lrr);
+    smpl->pobs[CN3] = args->err_prob + (1 - args->baf_bias + args->baf_bias*cn3_baf)*(1 - args->lrr_bias + args->lrr_bias*cn3_lrr);
+
+    return 0;
+}
+
+static void set_emission_prob(args_t *args, int isite)
+{
+    double *eprob = &args->eprob[args->nstates*isite];
+    int i;
+    for (i=0; i<N_STATES; i++)
+        eprob[i] = args->query_sample.pobs[i];
+}
+
+static void set_emission_prob2(args_t *args, int isite)
+{
+    double *eprob = &args->eprob[args->nstates*isite];
+    int i, j;
+    for (i=0; i<N_STATES; i++)
+    {
+        for (j=0; j<N_STATES; j++)
+        {
+            eprob[i*N_STATES+j] = args->query_sample.pobs[i]*args->control_sample.pobs[j];
+        }
+    }
+}
+
+static void set_gauss_params(args_t *args, sample_t *smpl);
+static double norm_cdf(double mean, double dev)
+{
+    double bot = 0, top = 1;
+    top = 1 - 0.5*erfc((top-mean)/(dev*sqrt(2)));
+    bot = 1 - 0.5*erfc((bot-mean)/(dev*sqrt(2)));
+    return top-bot;
+}
+
+static void set_emission_probs(args_t *args)
+{
+    if ( !args->af_fname )
+    {
+        args->fRR = 0.76;
+        args->fRA = 0.14;
+        args->fAA = 0.098;
+    }
+
+    set_gauss_params(args, &args->query_sample);
+    if ( args->control_sample.name ) set_gauss_params(args, &args->control_sample);
+
+    #if DBG0
+    args->verbose = 1;
+    args->query_sample.baf[0] = 0; set_observed_prob(args,&args->query_sample,0);
+    args->query_sample.baf[0] = 1/3.; set_observed_prob(args,&args->query_sample,0);
+    args->query_sample.baf[0] = 1/2.; set_observed_prob(args,&args->query_sample,0);
+    args->query_sample.baf[0] = 2/3.; set_observed_prob(args,&args->query_sample,0);
+    args->query_sample.baf[0] = 1; set_observed_prob(args,&args->query_sample,0);
+    args->verbose = 0;
+    #endif
+
+    int i;
+    for (i=0; i<args->nsites; i++)
+    {
+        if ( args->af_fname )
+        {
+            args->fRR = (1-args->nonref_afs[i])*(1-args->nonref_afs[i]);
+            args->fRA = 2*args->nonref_afs[i]*(1-args->nonref_afs[i]);
+            args->fAA = args->nonref_afs[i]*args->nonref_afs[i];
+        }
+        set_observed_prob(args,&args->query_sample,i);
+        if ( args->control_sample.name )
+        {
+            set_observed_prob(args,&args->control_sample,i);
+            set_emission_prob2(args,i);
+        }
+        else
+            set_emission_prob(args,i);
+    }
+}
+
+static void smooth_data(float *dat, int ndat, int win)
+{
+    if ( win<=1 ) return;
+
+    int i,j, k1 = win/2, k2 = win-k1;
+    rbuf_t rbuf;
+    rbuf_init(&rbuf,win);
+    float sum = 0, *buf = (float*)malloc(sizeof(float)*win);
+    for (i=0; i<k2; i++)
+    {
+        sum += dat[i];
+        int j = rbuf_append(&rbuf);
+        buf[j] = dat[i];
+    }
+    for (i=0; i<ndat; i++)
+    {
+        dat[i] = sum/rbuf.n;
+        if ( i>=k1 )
+        {
+            j = rbuf_shift(&rbuf);
+            sum -= buf[j];
+        }
+        if ( i+k2<ndat )
+        {
+            sum += dat[i+k2];
+            j = rbuf_append(&rbuf);
+            buf[j] = dat[i+k2];
+        }
+    }
+    free(buf);
+}
+
+static void set_gauss_params(args_t *args, sample_t *smpl)
+{
+    int i;
+    for (i=0; i<18; i++) smpl->gauss_param[i].dev2 = smpl->baf_dev2;
+
+    double dev = sqrt(smpl->baf_dev2);
+
+    GAUSS_CN1_PK_R(smpl)->mean = 0;
+    GAUSS_CN1_PK_A(smpl)->mean = 1;
+    GAUSS_CN1_PK_R(smpl)->norm = norm_cdf(GAUSS_CN1_PK_R(smpl)->mean,dev);
+    GAUSS_CN1_PK_A(smpl)->norm = norm_cdf(GAUSS_CN1_PK_A(smpl)->mean,dev);
+
+    GAUSS_CN2_PK_RR(smpl)->mean = 0;
+    GAUSS_CN2_PK_RA(smpl)->mean = 0.5;
+    GAUSS_CN2_PK_AA(smpl)->mean = 1;
+    GAUSS_CN2_PK_RR(smpl)->norm = norm_cdf(GAUSS_CN2_PK_RR(smpl)->mean,dev);
+    GAUSS_CN2_PK_RA(smpl)->norm = norm_cdf(GAUSS_CN2_PK_RA(smpl)->mean,dev);
+    GAUSS_CN2_PK_AA(smpl)->norm = norm_cdf(GAUSS_CN2_PK_AA(smpl)->mean,dev);
+
+    GAUSS_CN3_PK_RRR(smpl)->mean = 0;
+    GAUSS_CN3_PK_RRA(smpl)->mean = 1.0/(2+smpl->cell_frac);
+    GAUSS_CN3_PK_RAA(smpl)->mean = (1.0+smpl->cell_frac)/(2+smpl->cell_frac);
+    GAUSS_CN3_PK_AAA(smpl)->mean = 1;
+    GAUSS_CN3_PK_RRR(smpl)->norm = norm_cdf(GAUSS_CN3_PK_RRR(smpl)->mean,dev);
+    GAUSS_CN3_PK_RRA(smpl)->norm = norm_cdf(GAUSS_CN3_PK_RRA(smpl)->mean,dev);
+    GAUSS_CN3_PK_RAA(smpl)->norm = norm_cdf(GAUSS_CN3_PK_RAA(smpl)->mean,dev);
+    GAUSS_CN3_PK_AAA(smpl)->norm = norm_cdf(GAUSS_CN3_PK_AAA(smpl)->mean,dev);
+}
+
+static int update_sample_args(args_t *args, sample_t *smpl, int ismpl)
+{
+    hmm_t *hmm = args->hmm;
+    double *fwd = hmm_get_fwd_bwd_prob(hmm);
+    int nstates = hmm_get_nstates(hmm);
+
+    // estimate the BAF mean and deviation for CN3
+    double mean_cn3 = 0, norm_cn3 = 0;
+    double baf_dev2 = 0, baf_AA_dev2 = 0, norm_baf_AA_dev2 = 0;
+
+    // experimental: smooth CN3 probs to bias toward bigger events, this lowers
+    // the FP rate when the data is noisy
+    hts_expand(float,args->nsites,args->mtmpf,args->tmpf);
+    int i, j, k = 0;
+    for (i=0; i<args->nsites; i++)
+    {
+        float baf = smpl->baf[i];
+        if ( baf>4/5.) continue;        // skip AA genotypes
+        if ( baf>0.5 ) baf = 1 - baf;   // the bands should be symmetric
+        if ( baf<1/5.) continue;        // skip RR genotypes
+
+        double prob_cn3 = 0, *probs = fwd + i*nstates;
+        if ( !args->control_sample.name )
+        {
+            prob_cn3 = probs[CN3];
+        }
+        else if ( ismpl==0 )
+        {
+            // query sample: CN3 probability must be recovered from all states of the control sample
+            for (j=0; j<N_STATES; j++) prob_cn3 += probs[CN3*N_STATES+j];
+        }
+        else
+        {
+            // same as above but for control sample
+            for (j=0; j<N_STATES; j++) prob_cn3 += probs[CN3+j*N_STATES];
+        }
+        args->tmpf[k++] = prob_cn3;
+    }
+    smooth_data(args->tmpf, k, 50);
+    k = 0;
+    for (i=0; i<args->nsites; i++)
+    {
+        float baf = smpl->baf[i];
+        if ( baf>4/5.) { baf_AA_dev2 += (1.0-baf)*(1.0-baf); norm_baf_AA_dev2++; continue; }       // skip AA genotypes
+        if ( baf>0.5 ) baf = 1 - baf;   // the bands should be symmetric
+        if ( baf<1/5.) continue;        // skip RR genotypes
+
+        double prob_cn3 = args->tmpf[k++];
+        mean_cn3 += prob_cn3 * baf;
+        norm_cn3 += prob_cn3;
+    }
+    if ( !norm_cn3 )
+    {
+        smpl->cell_frac = 1.0;
+        return 1;
+    }
+    mean_cn3 /= norm_cn3;
+    k = 0;
+    for (i=0; i<args->nsites; i++)
+    {
+        float baf = smpl->baf[i];
+        if ( baf>0.5 ) baf = 1 - baf;   // the bands should be symmetric
+        if ( baf<1/5.) continue;        // skip RR,AA genotypes
+
+        double prob_cn3 = args->tmpf[k++];
+        baf_dev2 += prob_cn3 * (baf - mean_cn3)*(baf - mean_cn3);
+    }
+
+    /*
+        A noisy CN2 band is hard to distinguish from two CN3 bands which are
+        close to each other. Set a treshold on the minimum separation based
+        on the BAF deviation at p=0.95
+    */
+    baf_dev2 /= norm_cn3;
+    baf_AA_dev2 /= norm_baf_AA_dev2;
+    if ( baf_dev2 < baf_AA_dev2 )  baf_dev2 = baf_AA_dev2;
+    double max_mean_cn3 = 0.5 - sqrt(baf_dev2)*1.644854;    // R: qnorm(0.95)=1.644854
+    //fprintf(bcftools_stderr,"dev=%f  AA_dev=%f  max_mean_cn3=%f  mean_cn3=%f\n", baf_dev2,baf_AA_dev2,max_mean_cn3,mean_cn3);
+    assert( max_mean_cn3>0 );
+
+    double new_frac = 1./mean_cn3 - 2;
+    if ( mean_cn3 > max_mean_cn3 || new_frac < args->optimize_frac )
+    {
+        // out of bounds, beyond our detection limits. Give up and say it converged
+        smpl->cell_frac = 1.0;
+        return 1;
+    }
+    if ( new_frac>1 ) new_frac = 1;
+    int converged = fabs(new_frac - smpl->cell_frac) < 1e-1 ? 1 : 0;
+
+    // Update dev2, but stay within safe limits
+    if ( baf_dev2 > 3*smpl->baf_dev2_dflt ) baf_dev2 = 3*smpl->baf_dev2_dflt;
+    else if ( baf_dev2 < 0.5*smpl->baf_dev2_dflt ) baf_dev2 = 0.5*smpl->baf_dev2_dflt;
+
+    smpl->cell_frac = new_frac;
+    smpl->baf_dev2  = baf_dev2;
+
+    return converged;
+}
+
+// Update parameters which depend on the estimated fraction of aberrant cells
+// in CN3.  Returns 0 if the current estimate did not need to be updated or 1
+// if there was a change.
+static int update_args(args_t *args)
+{
+    int converged = update_sample_args(args, &args->query_sample, 0);
+    if ( args->control_sample.name )
+    {
+        converged += update_sample_args(args, &args->control_sample, 1);
+        return converged==2 ? 0 : 1;
+    }
+    return converged ? 0 : 1;
+}
+
+// for an approximate estimate of the number of het genotypes in a region
+#define BAF_LIKELY_HET(val)   (val)>0.25 && (val)<0.75
+
+static void cnv_flush_viterbi(args_t *args)
+{
+    if ( !args->nsites ) return;
+
+    // Set HMM transition matrix for the new chromsome again. This is for case
+    // Baum-Welch was used, which is experimental, largerly unsupported and not
+    // done by default.
+    hmm_t *hmm = args->hmm;
+    hmm_set_tprob(args->hmm, args->tprob, 10000);
+
+    // Smooth LRR values to reduce noise
+    if ( args->lrr_bias > 0 )
+    {
+        smooth_data(args->query_sample.lrr,args->nsites, args->lrr_smooth_win);
+        if ( args->control_sample.name ) smooth_data(args->control_sample.lrr,args->nsites, args->lrr_smooth_win);
+    }
+
+    // Set the BAF peak likelihoods, such as P(RRR|CN3), taking account the
+    // estimated fraction of aberrant cells in the mixture. With the new chromosome,
+    // reset the fraction to the default value.
+    args->query_sample.cell_frac   = args->query_sample.cell_frac_dflt;
+    args->control_sample.cell_frac = args->control_sample.cell_frac_dflt;
+    args->query_sample.baf_dev2    = args->query_sample.baf_dev2_dflt;
+    args->control_sample.baf_dev2  = args->control_sample.baf_dev2_dflt;
+    set_gauss_params(args, &args->query_sample);
+    if ( args->control_sample.name ) set_gauss_params(args, &args->control_sample);
+
+    if ( args->optimize_frac )
+    {
+        int niter = 0;
+        fprintf(bcftools_stderr,"Attempting to estimate the fraction of aberrant cells (chr %s):\n", bcf_hdr_id2name(args->hdr,args->prev_rid));
+        do
+        {
+            fprintf(bcftools_stderr,"\t.. %f %f", args->query_sample.cell_frac,args->query_sample.baf_dev2);
+            if ( args->control_sample.name )
+                fprintf(bcftools_stderr,"\t.. %f %f", args->control_sample.cell_frac,args->control_sample.baf_dev2);
+            fprintf(bcftools_stderr,"\n");
+            set_emission_probs(args);
+            hmm_run_fwd_bwd(hmm, args->nsites, args->eprob, args->sites);
+        }
+        while ( update_args(args) && ++niter<20 );
+        if ( niter>=20 )
+        {
+            // no convergence
+            args->query_sample.cell_frac   = args->query_sample.cell_frac_dflt;
+            args->control_sample.cell_frac = args->control_sample.cell_frac_dflt;
+            args->query_sample.baf_dev2    = args->query_sample.baf_dev2_dflt;
+            args->control_sample.baf_dev2  = args->control_sample.baf_dev2_dflt;
+            set_gauss_params(args, &args->query_sample);
+            if ( args->control_sample.name ) set_gauss_params(args, &args->control_sample);
+        }
+
+        fprintf(bcftools_stderr,"\t.. %f %f", args->query_sample.cell_frac,args->query_sample.baf_dev2);
+        if ( args->control_sample.name )
+            fprintf(bcftools_stderr,"\t.. %f %f", args->control_sample.cell_frac,args->control_sample.baf_dev2);
+        fprintf(bcftools_stderr,"\n");
+
+        fprintf(args->query_sample.summary_fh,"CF\t%s\t%d\t%d\t%.2f\t%f\n",
+            bcf_hdr_id2name(args->hdr,args->prev_rid),args->sites[0]+1,args->sites[args->nsites-1]+1,
+            args->query_sample.cell_frac,sqrt(args->query_sample.baf_dev2));
+        if ( args->control_sample.name )
+        {
+            fprintf(args->control_sample.summary_fh,"CF\t%s\t%d\t%d\t%.2f\t%f\n",
+                    bcf_hdr_id2name(args->hdr,args->prev_rid),args->sites[0]+1,args->sites[args->nsites-1]+1,
+                    args->control_sample.cell_frac,sqrt(args->control_sample.baf_dev2));
+            fprintf(args->summary_fh,"CF\t%s\t%d\t%d\t%.2f\t%.2f\t%f\t%f\n",
+                    bcf_hdr_id2name(args->hdr,args->prev_rid),args->sites[0]+1,args->sites[args->nsites-1]+1,
+                    args->query_sample.cell_frac, args->control_sample.cell_frac,
+                    sqrt(args->query_sample.baf_dev2), sqrt(args->control_sample.baf_dev2));
+        }
+    }
+    set_emission_probs(args);
+
+    while ( args->baum_welch_th!=0 )
+    {
+        int nstates = hmm_get_nstates(hmm);
+        double ori_ii = avg_ii_prob(nstates,hmm_get_tprob(hmm));
+        hmm_run_baum_welch(hmm, args->nsites, args->eprob, args->sites);
+        double new_ii = avg_ii_prob(nstates,hmm_get_tprob(hmm));
+        fprintf(bcftools_stderr,"%e\t%e\t%e\n", ori_ii,new_ii,new_ii-ori_ii);
+        double *tprob = init_tprob_matrix(nstates, 1-new_ii, args->same_prob);
+        hmm_set_tprob(args->hmm, tprob, 10000);
+        double *tprob_arr = hmm_get_tprob(hmm);
+        free(tprob);
+        if ( fabs(new_ii - ori_ii) < args->baum_welch_th )
+        {
+            int i,j;
+            for (i=0; i<nstates; i++)
+            {
+                for (j=0; j<nstates; j++)
+                {
+                    fprintf(bcftools_stdout, " %.15f", MAT(tprob_arr,nstates,j,i));
+                }
+                fprintf(bcftools_stdout, "\n");
+            }
+            break;
+        }
+    }
+    hmm_run_viterbi(hmm, args->nsites, args->eprob, args->sites);
+    hmm_run_fwd_bwd(hmm, args->nsites, args->eprob, args->sites);
+
+
+    // Output the results
+    uint8_t *vpath = hmm_get_viterbi_path(hmm);
+    double qual = 0, *fwd = hmm_get_fwd_bwd_prob(hmm);
+    int i,j, isite, start_cn = vpath[0], start_pos = args->sites[0], istart_pos = 0;
+    int ctrl_ntot = 0, smpl_ntot = 0, ctrl_nhet = 0, smpl_nhet = 0;
+    for (isite=0; isite<args->nsites; isite++)
+    {
+        int state = vpath[args->nstates*isite];
+        double *pval = fwd + isite*args->nstates;
+
+        qual += pval[start_cn];
+
+        // output CN and fwd-bwd likelihood for each site
+        if ( args->query_sample.cn_fh )
+        {
+            fprintf(args->query_sample.cn_fh, "%s\t%d\t%c", bcf_hdr_id2name(args->hdr,args->prev_rid), args->sites[isite]+1, copy_number_state(args,state,0));
+            if ( !args->control_sample.cn_fh )
+                for (i=0; i<args->nstates; i++) fprintf(args->query_sample.cn_fh, "\t%f", pval[i]);
+            else
+                for (i=0; i<N_STATES; i++)
+                {
+                    double sum = 0;
+                    for (j=0; j<N_STATES; j++) sum += pval[i*N_STATES+j];
+                    fprintf(args->query_sample.cn_fh, "\t%f", sum);
+                }
+            fprintf(args->query_sample.cn_fh, "\n");
+            if ( args->query_sample.baf[isite]>=0 )     // if non-missing
+            {
+                if ( BAF_LIKELY_HET(args->query_sample.baf[isite]) ) smpl_nhet++;
+                smpl_ntot++;
+            }
+        }
+        if ( args->control_sample.cn_fh )
+        {
+            fprintf(args->control_sample.cn_fh, "%s\t%d\t%c", bcf_hdr_id2name(args->hdr,args->prev_rid), args->sites[isite]+1, copy_number_state(args,state,1));
+            for (i=0; i<N_STATES; i++)
+            {
+                double sum = 0;
+                for (j=0; j<N_STATES; j++) sum += pval[i+N_STATES*j];
+                fprintf(args->control_sample.cn_fh, "\t%f", sum);
+            }
+            fprintf(args->control_sample.cn_fh, "\n");
+            if ( args->control_sample.baf[isite]>=0 )     // if non-missing
+            {
+                if ( BAF_LIKELY_HET(args->control_sample.baf[isite]) ) ctrl_nhet++;
+                ctrl_ntot++;
+            }
+        }
+
+        if ( start_cn != state )
+        {
+            char start_cn_query = copy_number_state(args,start_cn,0);
+            qual = phred_score(1 - qual/(isite - istart_pos));
+            fprintf(args->query_sample.summary_fh,"RG\t%s\t%d\t%d\t%c\t%.1f\t%d\t%d\n",
+                bcf_hdr_id2name(args->hdr,args->prev_rid), start_pos+1, args->sites[isite],start_cn_query,qual,smpl_ntot,smpl_nhet);
+
+            if ( args->control_sample.name )
+            {
+                // regions 0-based, half-open
+                char start_cn_ctrl = copy_number_state(args,start_cn,1);
+                fprintf(args->control_sample.summary_fh,"RG\t%s\t%d\t%d\t%c\t%.1f\t%d\t%d\n",
+                    bcf_hdr_id2name(args->hdr,args->prev_rid), start_pos+1, args->sites[isite],start_cn_ctrl,qual,ctrl_ntot,ctrl_nhet);
+                fprintf(args->summary_fh,"RG\t%s\t%d\t%d\t%c\t%c\t%.1f\t%d\t%d\t%d\t%d\n",
+                    bcf_hdr_id2name(args->hdr,args->prev_rid), start_pos+1, args->sites[isite],start_cn_query,start_cn_ctrl,qual,smpl_ntot,smpl_nhet,ctrl_ntot,ctrl_nhet);
+            }
+
+            istart_pos = isite;
+            start_pos = args->sites[isite];
+            start_cn = state;
+            qual = 0;
+            smpl_ntot = smpl_nhet = ctrl_ntot = ctrl_nhet = 0;
+        }
+    }
+    qual = phred_score(1 - qual/(isite - istart_pos));
+    char start_cn_query = copy_number_state(args,start_cn,0);
+    fprintf(args->query_sample.summary_fh,"RG\t%s\t%d\t%d\t%c\t%.1f\t%d\t%d\n",
+        bcf_hdr_id2name(args->hdr,args->prev_rid), start_pos+1, args->sites[isite-1]+1,start_cn_query,qual,smpl_ntot,smpl_nhet);
+    if ( args->control_sample.name )
+    {
+        char start_cn_ctrl = copy_number_state(args,start_cn,1);
+        fprintf(args->control_sample.summary_fh,"RG\t%s\t%d\t%d\t%c\t%.1f\t%d\t%d\n",
+            bcf_hdr_id2name(args->hdr,args->prev_rid), start_pos+1, args->sites[isite-1]+1,start_cn_ctrl,qual,ctrl_ntot,ctrl_nhet);
+        fprintf(args->summary_fh,"RG\t%s\t%d\t%d\t%c\t%c\t%.1f\t%d\t%d\t%d\t%d\n",
+            bcf_hdr_id2name(args->hdr,args->prev_rid), start_pos+1, args->sites[isite-1]+1,start_cn_query,start_cn_ctrl,qual,smpl_ntot,smpl_nhet,ctrl_ntot,ctrl_nhet);
+    }
+}
+
+static int parse_lrr_baf(sample_t *smpl, bcf_fmt_t *baf_fmt, bcf_fmt_t *lrr_fmt, float *baf, float *lrr)
+{
+    *baf = ((float*)(baf_fmt->p + baf_fmt->size*smpl->idx))[0];
+    if ( bcf_float_is_missing(*baf) || isnan(*baf) ) *baf = -0.1;    // arbitrary negative value == missing value
+
+    if ( lrr_fmt )
+    {
+        *lrr = ((float*)(lrr_fmt->p + lrr_fmt->size*smpl->idx))[0];
+        if ( bcf_float_is_missing(*lrr) || isnan(*lrr) ) { *lrr = 0; *baf = -0.1; }
+    }
+    else
+        *lrr = 0;
+
+    return *baf<0 ? 0 : 1;
+}
+
+static void cnv_next_line(args_t *args, bcf1_t *line)
+{
+    if ( !line ) 
+    {
+        // Done, flush viterbi
+        cnv_flush_viterbi(args);
+        return;
+    }
+
+    if ( line->rid!=args->prev_rid )
+    {
+        // New chromosome
+        cnv_flush_viterbi(args);
+        args->prev_rid = line->rid;
+        args->nsites = 0;
+        args->nRR = args->nAA = args->nRA = 0;
+    }
+
+    // Process line
+    args->ntot++;
+
+    bcf_fmt_t *baf_fmt, *lrr_fmt = NULL;
+    if ( !(baf_fmt = bcf_get_fmt(args->hdr, line, "BAF")) ) return; 
+    if ( args->lrr_bias>0 && !(lrr_fmt = bcf_get_fmt(args->hdr, line, "LRR")) ) return;
+
+    float baf1,lrr1,baf2,lrr2;
+    int ret = 0;
+    ret += parse_lrr_baf(&args->query_sample,  baf_fmt,lrr_fmt,&baf1,&lrr1);
+    ret += parse_lrr_baf(&args->control_sample,baf_fmt,lrr_fmt,&baf2,&lrr2);
+    if ( !ret ) return;
+
+    // Realloc buffers needed to store observed data and used by viterbi and fwd-bwd
+    args->nsites++;
+    int m = args->msites;
+    hts_expand(uint32_t,args->nsites,args->msites,args->sites);
+    if ( args->msites!=m )
+    {
+        args->eprob = (double*) realloc(args->eprob,sizeof(double)*args->msites*args->nstates);
+        if ( args->control_sample.name )
+        {
+            args->control_sample.lrr = (float*) realloc(args->control_sample.lrr,sizeof(float)*args->msites);
+            args->control_sample.baf = (float*) realloc(args->control_sample.baf,sizeof(float)*args->msites);
+        }
+        args->query_sample.lrr = (float*) realloc(args->query_sample.lrr,sizeof(float)*args->msites);
+        args->query_sample.baf = (float*) realloc(args->query_sample.baf,sizeof(float)*args->msites);
+        if ( args->af_fname )
+            args->nonref_afs = (float*) realloc(args->nonref_afs,sizeof(float)*args->msites);
+    }
+    args->sites[args->nsites-1] = line->pos;
+    args->query_sample.lrr[args->nsites-1] = lrr1;
+    args->query_sample.baf[args->nsites-1] = baf1;
+    if ( args->af_fname )
+    {
+        double alt_freq;
+        args->nonref_afs[args->nsites-1] = read_AF(args->files->targets,line,&alt_freq)<0 ? args->nonref_af_dflt : alt_freq;
+    }
+    if ( args->control_sample.name )
+    {
+        args->control_sample.lrr[args->nsites-1] = lrr2;
+        args->control_sample.baf[args->nsites-1] = baf2;
+        if ( baf2>=0 )  // skip missing values
+            fprintf(args->control_sample.dat_fh,"%s\t%"PRId64"\t%.3f\t%.3f\n",bcf_hdr_id2name(args->hdr,args->prev_rid), (int64_t) line->pos+1,baf2,lrr2);
+    }
+    if ( baf1>=0 )  // skip missing values
+        fprintf(args->query_sample.dat_fh,"%s\t%"PRId64"\t%.3f\t%.3f\n",bcf_hdr_id2name(args->hdr,args->prev_rid), (int64_t) line->pos+1,baf1,lrr1);
+
+    if ( baf1>=0 )
+    {
+        if ( baf1<1/5. ) args->nRR++;
+        else if ( baf1>4/5. ) args->nAA++;
+        else args->nRA++;
+    }
+    args->nused++;
+}
+
+static void usage(args_t *args)
+{
+    fprintf(bcftools_stderr, "\n");
+    fprintf(bcftools_stderr, "About:   Copy number variation caller, requires Illumina's B-allele frequency (BAF) and Log R\n");
+    fprintf(bcftools_stderr, "         Ratio intensity (LRR). The HMM considers the following copy number states: CN 2\n");
+    fprintf(bcftools_stderr, "         (normal), 1 (single-copy loss), 0 (complete loss), 3 (single-copy gain)\n");
+    fprintf(bcftools_stderr, "Usage:   bcftools cnv [OPTIONS] FILE.vcf\n");
+    fprintf(bcftools_stderr, "General Options:\n");
+    fprintf(bcftools_stderr, "    -c, --control-sample STRING      Optional control sample name to highlight differences\n");
+    fprintf(bcftools_stderr, "    -f, --AF-file FILE               Read allele frequencies from file (CHR\\tPOS\\tREF,ALT\\tAF)\n");
+    fprintf(bcftools_stderr, "    -o, --output-dir PATH            \n");
+    fprintf(bcftools_stderr, "    -p, --plot-threshold FLOAT       Plot aberrant chromosomes with quality at least FLOAT\n");
+    fprintf(bcftools_stderr, "    -r, --regions REGION             Restrict to comma-separated list of regions\n");
+    fprintf(bcftools_stderr, "    -R, --regions-file FILE          Restrict to regions listed in a file\n");
+    fprintf(bcftools_stderr, "        --regions-overlap 0|1|2      Include if POS in the region (0), record overlaps (1), variant overlaps (2) [1]\n");
+    fprintf(bcftools_stderr, "    -s, --query-sample STRING        Query samply name\n");
+    fprintf(bcftools_stderr, "    -t, --targets REGION             Similar to -r but streams rather than index-jumps\n");
+    fprintf(bcftools_stderr, "    -T, --targets-file FILE          Similar to -R but streams rather than index-jumps\n");
+    fprintf(bcftools_stderr, "        --targets-overlap 0|1|2      Include if POS in the region (0), record overlaps (1), variant overlaps (2) [0]\n");
+    fprintf(bcftools_stderr, "HMM Options:\n");
+    fprintf(bcftools_stderr, "    -a, --aberrant FLOAT[,FLOAT]     Fraction of aberrant cells in query and control [1.0,1.0]\n");
+    fprintf(bcftools_stderr, "    -b, --BAF-weight FLOAT           Relative contribution from BAF [1]\n");
+    fprintf(bcftools_stderr, "    -d, --BAF-dev FLOAT[,FLOAT]      Expected BAF deviation in query and control [0.04,0.04]\n"); // experimental
+    fprintf(bcftools_stderr, "    -e, --err-prob FLOAT             Uniform error probability [1e-4]\n");
+    fprintf(bcftools_stderr, "    -k, --LRR-dev FLOAT[,FLOAT]      Expected LRR deviation [0.2,0.2]\n"); // experimental
+    fprintf(bcftools_stderr, "    -l, --LRR-weight FLOAT           Relative contribution from LRR [0.2]\n");
+    fprintf(bcftools_stderr, "    -L, --LRR-smooth-win INT         Window of LRR moving average smoothing [10]\n");
+    fprintf(bcftools_stderr, "    -O, --optimize FLOAT             Estimate fraction of aberrant cells down to FLOAT [1.0]\n");
+    fprintf(bcftools_stderr, "    -P, --same-prob FLOA>            Prior probability of -s/-c being the same [0.5]\n");
+    fprintf(bcftools_stderr, "    -x, --xy-prob FLOAT              P(x|y) transition probability [1e-9]\n");
+    fprintf(bcftools_stderr, "\n");
+    bcftools_exit(1);
+}
+
+int main_vcfcnv(int argc, char *argv[])
+{
+    int c;
+    args_t *args    = (args_t*) calloc(1,sizeof(args_t));
+    args->argc      = argc; args->argv = argv;
+    args->files     = bcf_sr_init();
+    args->plot_th   = 1e9;   // by default plot none
+    args->nonref_af_dflt = 0.1;
+    args->lrr_smooth_win = 10;
+
+    args->query_sample.cell_frac_dflt = 1;
+    args->control_sample.cell_frac_dflt = 1;
+
+    // How much FORMAT/LRR and FORMAT/BAF matter
+    args->lrr_bias  = 0.2;
+    args->baf_bias  = 1.0;
+    args->err_prob  = 1e-4;
+
+    // Transition probability to a different state and the prior of both samples being the same
+    args->ij_prob   = 1e-9;
+    args->same_prob = 0.5;
+
+    // Squared std dev of BAF and LRR values (gaussian noise), estimated from real data (hets, one sample, one chr)
+    args->query_sample.baf_dev2_dflt = args->control_sample.baf_dev2_dflt = 0.04*0.04; // illumina: 0.03
+    args->query_sample.lrr_dev2 = args->control_sample.lrr_dev2 = 0.2*0.2; //0.20*0.20;   // illumina: 0.18
+
+    int regions_is_file = 0, targets_is_file = 0;
+    int regions_overlap = 1;
+    int targets_overlap = 0;
+
+    static struct option loptions[] = 
+    {
+        {"BAF-dev",1,0,'d'},
+        {"LRR-dev",1,0,'k'},
+        {"LRR-smooth-win",1,0,'L'},
+        {"AF-file",1,0,'f'},
+        {"baum-welch",1,0,'W'}, // hidden
+        {"optimize",1,0,'O'},
+        {"aberrant",1,0,'a'},
+        {"err-prob",1,0,'e'},
+        {"BAF-weight",1,0,'b'},
+        {"LRR-weight",1,0,'l'},
+        {"same-prob",1,0,'P'},
+        {"xy-prob",1,0,'x'},
+        {"query-sample",1,0,'s'},
+        {"control-sample",1,0,'c'},
+        {"targets",1,0,'t'},
+        {"targets-file",1,0,'T'},
+        {"targets-overlap",required_argument,NULL,4},
+        {"regions",1,0,'r'},
+        {"regions-file",1,0,'R'},
+        {"regions-overlap",required_argument,NULL,3},
+        {"plot-threshold",1,0,'p'},
+        {"output-dir",1,0,'o'},
+        {0,0,0,0}
+    };
+    char *tmp = NULL;
+    while ((c = getopt_long(argc, argv, "h?r:R:t:T:s:o:p:l:T:c:b:P:x:e:O:W:f:a:L:d:k:",loptions,NULL)) >= 0) {
+        switch (c) {
+            case 'L': 
+                args->lrr_smooth_win = strtol(optarg,&tmp,10);
+                if ( *tmp ) error("Could not parse: --LRR-smooth-win %s\n", optarg);
+                break;
+            case 'f': args->af_fname = optarg; break;
+            case 'O': 
+                args->optimize_frac = strtod(optarg,&tmp);
+                if ( *tmp ) error("Could not parse: -O %s\n", optarg);
+                break;
+            case 'd':
+                args->query_sample.baf_dev2_dflt = strtod(optarg,&tmp);
+                if ( *tmp )
+                {
+                    if ( *tmp!=',') error("Could not parse: -d %s\n", optarg);
+                    args->control_sample.baf_dev2_dflt = strtod(tmp+1,&tmp);
+                    if ( *tmp ) error("Could not parse: -d %s\n", optarg);
+                }
+                else
+                    args->control_sample.baf_dev2_dflt = args->query_sample.baf_dev2_dflt;
+                args->query_sample.baf_dev2_dflt   *= args->query_sample.baf_dev2_dflt;
+                args->control_sample.baf_dev2_dflt *= args->control_sample.baf_dev2_dflt;
+                break;
+            case 'k':
+                args->query_sample.lrr_dev2 = strtod(optarg,&tmp);
+                if ( *tmp )
+                {
+                    if ( *tmp!=',') error("Could not parse: -k %s\n", optarg);
+                    args->control_sample.lrr_dev2 = strtod(tmp+1,&tmp);
+                    if ( *tmp ) error("Could not parse: -d %s\n", optarg);
+                }
+                else
+                    args->control_sample.lrr_dev2 = args->query_sample.lrr_dev2;
+                args->query_sample.lrr_dev2   *= args->query_sample.lrr_dev2;
+                args->control_sample.lrr_dev2 *= args->control_sample.lrr_dev2;
+                break;
+            case 'a':
+                args->query_sample.cell_frac_dflt = strtod(optarg,&tmp);
+                if ( *tmp )
+                {
+                    if ( *tmp!=',') error("Could not parse: -a %s\n", optarg);
+                    args->control_sample.cell_frac_dflt = strtod(tmp+1,&tmp);
+                    if ( *tmp ) error("Could not parse: -a %s\n", optarg);
+                }
+                break;
+            case 'W':
+                args->baum_welch_th = strtod(optarg,&tmp);
+                if ( *tmp ) error("Could not parse: -W %s\n", optarg);
+                break;
+            case 'e': 
+                args->err_prob = strtod(optarg,&tmp);
+                if ( *tmp ) error("Could not parse: -e %s\n", optarg);
+                break;
+            case 'b': 
+                args->baf_bias = strtod(optarg,&tmp);
+                if ( *tmp ) error("Could not parse: -b %s\n", optarg);
+                break;
+            case 'x': 
+                args->ij_prob = strtod(optarg,&tmp);
+                if ( *tmp ) error("Could not parse: -x %s\n", optarg);
+                break;
+            case 'P': 
+                args->same_prob = strtod(optarg,&tmp);
+                if ( *tmp ) error("Could not parse: -P %s\n", optarg);
+                break;
+            case 'l': 
+                args->lrr_bias = strtod(optarg,&tmp);
+                if ( *tmp ) error("Could not parse: -l %s\n", optarg);
+                break;
+            case 'p': 
+                args->plot_th = strtod(optarg,&tmp);
+                if ( *tmp ) error("Could not parse: -p %s\n", optarg);
+                break;
+            case 'o': args->output_dir = optarg; break;
+            case 's': args->query_sample.name = strdup(optarg); break;
+            case 'c': args->control_sample.name = optarg; break;
+            case 't': args->targets_list = optarg; break;
+            case 'T': args->targets_list = optarg; targets_is_file = 1; break;
+            case 'r': args->regions_list = optarg; break;
+            case 'R': args->regions_list = optarg; regions_is_file = 1; break;
+            case  3 :
+                regions_overlap = parse_overlap_option(optarg);
+                if ( regions_overlap < 0 ) error("Could not parse: --regions-overlap %s\n",optarg);
+                break;
+            case  4 :
+                targets_overlap = parse_overlap_option(optarg);
+                if ( targets_overlap < 0 ) error("Could not parse: --targets-overlap %s\n",optarg);
+                break;
+            case 'h': 
+            case '?': usage(args); break;
+            default: error("Unknown argument: %s\n", optarg);
+        }
+    }
+
+    char *fname = NULL;
+    if ( optind>=argc )
+    {
+        if ( !isatty(fileno((FILE *)stdin)) ) fname = "-";
+    }
+    else fname = argv[optind];
+    if ( !fname ) usage(args);
+
+    if ( !args->output_dir ) error("Expected -o option\n");
+    if ( args->regions_list )
+    {
+        bcf_sr_set_opt(args->files,BCF_SR_REGIONS_OVERLAP,regions_overlap);
+        if ( bcf_sr_set_regions(args->files, args->regions_list, regions_is_file)<0 )
+            error("Failed to read the regions: %s\n", args->regions_list);
+    }
+    if ( args->targets_list )
+    {
+        bcf_sr_set_opt(args->files,BCF_SR_TARGETS_OVERLAP,targets_overlap);
+        if ( bcf_sr_set_targets(args->files, args->targets_list, targets_is_file, 0)<0 )
+            error("Failed to read the targets: %s\n", args->targets_list);
+    }
+    if ( args->af_fname )
+    {
+        if ( bcf_sr_set_targets(args->files, args->af_fname, 1, 3)<0 )
+            error("Failed to read the targets: %s\n", args->af_fname);
+    }
+    if ( !bcf_sr_add_reader(args->files, fname) )
+        error("Failed to read from %s: %s\n", !strcmp("-",fname)?"standard input":fname,bcf_sr_strerror(args->files->errnum));
+    
+    init_data(args);
+    while ( bcf_sr_next_line(args->files) )
+    {
+        bcf1_t *line = bcf_sr_get_line(args->files,0);
+        cnv_next_line(args, line);
+    }
+    cnv_next_line(args, NULL);
+    create_plots(args);
+    fprintf(bcftools_stderr,"Number of lines: total/processed: %d/%d\n", args->ntot,args->nused);
+    destroy_data(args);
+    free(args);
+    return 0;
+}
+
+
diff --git a/bcftools/vcfconcat.c b/bcftools/vcfconcat.c
new file mode 100644
index 0000000..0246b59
--- /dev/null
+++ b/bcftools/vcfconcat.c
@@ -0,0 +1,1062 @@
+/*  vcfconcat.c -- Concatenate or combine VCF/BCF files.
+
+    Copyright (C) 2013-2021 Genome Research Ltd.
+
+    Author: Petr Danecek <pd3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.  */
+
+#include <stdio.h>
+#include <unistd.h>
+#include <getopt.h>
+#include <string.h>
+#include <assert.h>
+#include <errno.h>
+#include <math.h>
+#include <inttypes.h>
+#include <htslib/vcf.h>
+#include <htslib/synced_bcf_reader.h>
+#include <htslib/kseq.h>
+#include <htslib/bgzf.h>
+#include <htslib/tbx.h> // for hts_get_bgzfp()
+#include <htslib/thread_pool.h>
+#include <sys/time.h>
+#include "bcftools.h"
+
+typedef struct _args_t
+{
+    bcf_srs_t *files;
+    htsFile *out_fh;
+    int output_type, n_threads, record_cmd_line, clevel;
+    bcf_hdr_t *out_hdr;
+    int *seen_seq;
+
+    // phasing
+    int *start_pos, start_tid, ifname;
+    int *swap_phase, nswap, *nmatch, *nmism;
+    bcf1_t **buf;
+    uint8_t *buf_mask;
+    int nbuf, mbuf, prev_chr, min_PQ, prev_pos_check;
+    int32_t *GTa, *GTb, mGTa, mGTb, *phase_qual, *phase_set;
+
+    char **argv, *output_fname, *file_list, **fnames, *remove_dups, *regions_list;
+    int argc, nfnames, allow_overlaps, phased_concat, regions_is_file, regions_overlap;
+    int compact_PS, phase_set_changed, naive_concat, naive_concat_trust_headers;
+    int verbose, explicit_output_type, ligate_force, ligate_warn;
+    htsThreadPool *tpool;
+}
+args_t;
+
+static void init_data(args_t *args)
+{
+    bcf1_t *line = NULL;
+
+    // With phased concat, the chunks overlap and come in the right order.  To
+    // avoid opening all files at once, store start positions to recognise need
+    // for the next one. This way we can keep only two open chunks at once.
+    if ( args->phased_concat )
+    {
+        args->start_pos = (int*) malloc(sizeof(int)*args->nfnames);
+        line = bcf_init();
+    }
+
+    if ( args->verbose ) fprintf(stderr,"Checking the headers and starting positions of %d files\n", args->nfnames);
+    kstring_t str = {0,0,0};
+    int i, prev_chrid = -1;
+    for (i=0; i<args->nfnames; i++)
+    {
+        htsFile *fp = hts_open(args->fnames[i], "r"); if ( !fp ) error("Failed to open: %s\n", args->fnames[i]);
+        bcf_hdr_t *hdr = bcf_hdr_read(fp); if ( !hdr ) error("Failed to parse header: %s\n", args->fnames[i]);
+        args->out_hdr = bcf_hdr_merge(args->out_hdr,hdr);
+        if ( bcf_hdr_nsamples(hdr) != bcf_hdr_nsamples(args->out_hdr) )
+            error("Different number of samples in %s. Perhaps \"bcftools merge\" is what you are looking for?\n", args->fnames[i]);
+
+        int j;
+        for (j=0; j<bcf_hdr_nsamples(hdr); j++)
+            if ( strcmp(args->out_hdr->samples[j],hdr->samples[j]) )
+                error("Different sample names in %s. Perhaps \"bcftools merge\" is what you are looking for?\n", args->fnames[i]);
+
+        if ( args->phased_concat )
+        {
+            int ret = bcf_read(fp, hdr, line);
+            if ( ret!=0 ) args->start_pos[i] = -2;  // empty file
+            else
+            {
+                int chrid = bcf_hdr_id2int(args->out_hdr,BCF_DT_CTG,bcf_seqname(hdr,line));
+                args->start_pos[i] = chrid==prev_chrid ? line->pos : -1;
+                prev_chrid = chrid;
+            }
+        }
+        bcf_hdr_destroy(hdr);
+        if ( hts_close(fp)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,args->fnames[i]);
+    }
+    free(str.s);
+    if ( line ) bcf_destroy(line);
+
+    args->seen_seq = (int*) calloc(args->out_hdr->n[BCF_DT_CTG],sizeof(int));
+
+    if ( args->phased_concat )
+    {
+        bcf_hdr_append(args->out_hdr,"##FORMAT=<ID=PQ,Number=1,Type=Integer,Description=\"Phasing Quality (bigger is better)\">");
+        bcf_hdr_append(args->out_hdr,"##FORMAT=<ID=PS,Number=1,Type=Integer,Description=\"Phase Set\">");
+    }
+    if (args->record_cmd_line) bcf_hdr_append_version(args->out_hdr, args->argc, args->argv, "bcftools_concat");
+    char wmode[8];
+    set_wmode(wmode,args->output_type,args->output_fname,args->clevel);
+    args->out_fh = hts_open(args->output_fname ? args->output_fname : "-", wmode);
+    if ( args->out_fh == NULL ) error("Can't write to \"%s\": %s\n", args->output_fname, strerror(errno));
+    if ( args->allow_overlaps || args->phased_concat )
+    {
+        args->files = bcf_sr_init();
+        args->files->require_index = 1;
+    }
+    if ( args->n_threads )
+    {
+        if ( args->files )
+        {
+            if ( bcf_sr_set_threads(args->files, args->n_threads)<0 ) error("Failed to create threads\n");
+            args->tpool = args->files->p;
+        }
+        else
+        {
+            args->tpool = (htsThreadPool*) calloc(1, sizeof(htsThreadPool));
+            if ( !args->tpool ) error("Failed to allocate memory\n");
+            if ( !(args->tpool->pool = hts_tpool_init(args->n_threads)) ) error("Failed to initialize %d threads\n",args->n_threads);
+        }
+        hts_set_opt(args->out_fh, HTS_OPT_THREAD_POOL, args->tpool);
+    }
+    if ( bcf_hdr_write(args->out_fh, args->out_hdr)!=0 ) error("[%s] Error: cannot write the header to %s\n", __func__,args->output_fname);
+
+    if ( args->allow_overlaps )
+    {
+        if ( args->regions_list )
+        {
+            bcf_sr_set_opt(args->files,BCF_SR_REGIONS_OVERLAP,args->regions_overlap);
+            if ( bcf_sr_set_regions(args->files, args->regions_list, args->regions_is_file)<0 )
+                error("Failed to read the regions: %s\n", args->regions_list);
+        }
+        if ( args->remove_dups )
+        {
+            if ( !strcmp(args->remove_dups,"snps") ) args->files->collapse |= COLLAPSE_SNPS;
+            else if ( !strcmp(args->remove_dups,"indels") ) args->files->collapse |= COLLAPSE_INDELS;
+            else if ( !strcmp(args->remove_dups,"both") ) args->files->collapse |= COLLAPSE_SNPS | COLLAPSE_INDELS;
+            else if ( !strcmp(args->remove_dups,"any") ) args->files->collapse |= COLLAPSE_ANY;
+            else if ( !strcmp(args->remove_dups,"all") ) args->files->collapse |= COLLAPSE_ANY;
+            else if ( !strcmp(args->remove_dups,"none") ) args->files->collapse = COLLAPSE_NONE;
+            else if ( !strcmp(args->remove_dups,"exact") ) args->files->collapse = COLLAPSE_NONE;
+            else error("The -D string \"%s\" not recognised.\n", args->remove_dups);
+        }
+        for (i=0; i<args->nfnames; i++)
+            if ( !bcf_sr_add_reader(args->files,args->fnames[i]) ) error("Failed to open %s: %s\n", args->fnames[i],bcf_sr_strerror(args->files->errnum));
+    }
+    else if ( args->phased_concat )
+    {
+        // Remove empty files from the list
+        int nok = 0;
+        while (1)
+        {
+            while ( nok<args->nfnames && args->start_pos[nok]!=-2 ) nok++;
+            if ( nok==args->nfnames ) break;
+
+            i = nok;
+            while ( i<args->nfnames && args->start_pos[i]==-2 ) i++;
+            if ( i==args->nfnames ) break;
+
+            int tmp = args->start_pos[nok]; args->start_pos[nok] = args->start_pos[i]; args->start_pos[i] = tmp;
+            char *str = args->fnames[nok]; args->fnames[nok] = args->fnames[i]; args->fnames[i] = str;
+        }
+        for (i=nok; i<args->nfnames; i++) free(args->fnames[i]);
+        args->nfnames = nok;
+
+        for (i=1; i<args->nfnames; i++)
+            if ( args->start_pos[i-1]!=-1 && args->start_pos[i]!=-1 && args->start_pos[i]<args->start_pos[i-1] )
+                error("The files not in ascending order: %d in %s, %d in %s\n", args->start_pos[i-1]+1,args->fnames[i-1],args->start_pos[i]+1,args->fnames[i]);
+
+        args->prev_chr = -1;
+        args->swap_phase = (int*) calloc(bcf_hdr_nsamples(args->out_hdr),sizeof(int));
+        args->nmatch = (int*) calloc(bcf_hdr_nsamples(args->out_hdr),sizeof(int));
+        args->nmism  = (int*) calloc(bcf_hdr_nsamples(args->out_hdr),sizeof(int));
+        args->phase_qual = (int32_t*) malloc(bcf_hdr_nsamples(args->out_hdr)*sizeof(int32_t));
+        args->phase_set  = (int32_t*) malloc(bcf_hdr_nsamples(args->out_hdr)*sizeof(int32_t));
+        args->ifname = 0;
+    }
+}
+
+static void destroy_data(args_t *args)
+{
+    int i;
+    if ( args->out_fh )
+    {
+        if ( hts_close(args->out_fh)!=0 ) error("hts_close error\n");
+    }
+    if ( args->tpool && !args->files )
+    {
+        hts_tpool_destroy(args->tpool->pool);
+        free(args->tpool);
+    }
+    if ( args->files ) bcf_sr_destroy(args->files);
+    if ( args->out_hdr ) bcf_hdr_destroy(args->out_hdr);
+    free(args->seen_seq);
+    free(args->start_pos);
+    free(args->swap_phase);
+    for (i=0; i<args->mbuf; i++) bcf_destroy(args->buf[i]);
+    free(args->buf);
+    free(args->buf_mask);
+    free(args->GTa);
+    free(args->GTb);
+    free(args->nmatch);
+    free(args->nmism);
+    free(args->phase_qual);
+    free(args->phase_set);
+    for (i=0; i<args->nfnames; i++) free(args->fnames[i]);
+    free(args->fnames);
+}
+
+int vcf_write_line(htsFile *fp, kstring_t *line);
+
+#define SWAP(type_t, a, b) { type_t t = a; a = b; b = t; }
+static void phase_update(args_t *args, bcf_hdr_t *hdr, bcf1_t *rec)
+{
+    int i, nGTs = bcf_get_genotypes(hdr, rec, &args->GTa, &args->mGTa);
+    if ( nGTs <= 0 ) return;    // GT field is not present
+    for (i=0; i<bcf_hdr_nsamples(hdr); i++)
+    {
+        if ( !args->swap_phase[i] ) continue;
+        int *gt = &args->GTa[i*2];
+        if ( bcf_gt_is_missing(gt[0]) || gt[1]==bcf_int32_vector_end ) continue;
+        if ( !bcf_gt_is_phased(gt[1]) ) continue;
+        SWAP(int, gt[0], gt[1]);
+        gt[1] |= 1;
+    }
+    bcf_update_genotypes(hdr,rec,args->GTa,nGTs);
+}
+
+static void phased_flush(args_t *args)
+{
+    if ( !args->nbuf ) return;
+
+    bcf_hdr_t *ahdr = args->files->readers[0].header;
+    bcf_hdr_t *bhdr = args->files->readers[1].header;
+
+    int i, j, nsmpl = bcf_hdr_nsamples(args->out_hdr);
+    static int gt_absent_warned = 0;
+    for (i=0; i<args->nbuf; i+=2)
+    {
+        if ( args->buf_mask[i/2]!=3 ) continue;
+
+        bcf1_t *arec = args->buf[i];
+        bcf1_t *brec = args->buf[i+1];
+
+        int nGTs = bcf_get_genotypes(ahdr, arec, &args->GTa, &args->mGTa);
+        if ( nGTs < 0 ) 
+        {
+            if ( !gt_absent_warned )
+            {
+                fprintf(stderr,"GT is not present at %s:%"PRId64". (This warning is printed only once.)\n", bcf_seqname(ahdr,arec), (int64_t) arec->pos+1);
+                gt_absent_warned = 1;
+            }
+            continue;
+        }
+        if ( nGTs != 2*nsmpl ) continue;    // not diploid
+        nGTs = bcf_get_genotypes(bhdr, brec, &args->GTb, &args->mGTb);
+        if ( nGTs < 0 )
+        {
+            if ( !gt_absent_warned )
+            {
+                fprintf(stderr,"GT is not present at %s:%"PRId64". (This warning is printed only once.)\n", bcf_seqname(bhdr,brec), (int64_t) brec->pos+1);
+                gt_absent_warned = 1;
+            }
+            continue;
+        }
+        if ( nGTs != 2*nsmpl ) continue;    // not diploid
+
+        for (j=0; j<nsmpl; j++)
+        {
+            int *gta = &args->GTa[j*2];
+            int *gtb = &args->GTb[j*2];
+            if ( gta[1]==bcf_int32_vector_end || gtb[1]==bcf_int32_vector_end ) continue;
+            if ( bcf_gt_is_missing(gta[0]) || bcf_gt_is_missing(gta[1]) || bcf_gt_is_missing(gtb[0]) || bcf_gt_is_missing(gtb[1]) ) continue;
+            if ( !bcf_gt_is_phased(gta[1]) || !bcf_gt_is_phased(gtb[1]) ) continue;
+            if ( bcf_gt_allele(gta[0])==bcf_gt_allele(gta[1]) || bcf_gt_allele(gtb[0])==bcf_gt_allele(gtb[1]) ) continue;
+            if ( bcf_gt_allele(gta[0])==bcf_gt_allele(gtb[0]) && bcf_gt_allele(gta[1])==bcf_gt_allele(gtb[1]) )
+            {
+                if ( args->swap_phase[j] ) args->nmism[j]++; else args->nmatch[j]++;
+            }
+            if ( bcf_gt_allele(gta[0])==bcf_gt_allele(gtb[1]) && bcf_gt_allele(gta[1])==bcf_gt_allele(gtb[0]) )
+            {
+                if ( args->swap_phase[j] ) args->nmatch[j]++; else args->nmism[j]++;
+            }
+        }
+    }
+    for (i=0; i<args->nbuf/2; i+=2)
+    {
+        bcf1_t *rec;
+        bcf_hdr_t *hdr;
+        int mask = args->buf_mask[i/2];
+        if ( mask & 1 ) { rec = args->buf[i]; hdr = args->files->readers[0].header; }
+        else { rec = args->buf[i+1]; hdr = args->files->readers[1].header; }
+        bcf_translate(args->out_hdr, hdr, rec);
+        if ( args->nswap && (mask&1) )
+            phase_update(args, args->out_hdr, rec);
+        if ( !args->compact_PS || args->phase_set_changed )
+        {
+            bcf_update_format_int32(args->out_hdr,rec,"PS",args->phase_set,nsmpl);
+            args->phase_set_changed = 0;
+        }
+        if ( bcf_write(args->out_fh, args->out_hdr, rec)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->output_fname);
+
+        if ( rec->pos < args->prev_pos_check ) error("FIXME, disorder: %s:%"PRId64" vs %d  [1]\n", bcf_seqname(hdr,rec),(int64_t)rec->pos+1,args->prev_pos_check+1);
+        args->prev_pos_check = rec->pos;
+    }
+    args->nswap = 0;
+    for (j=0; j<nsmpl; j++)
+    {
+        if ( args->nmatch[j] >= args->nmism[j] )
+            args->swap_phase[j] = 0;
+        else
+        {
+            args->swap_phase[j] = 1;
+            args->nswap++;
+        }
+        if ( args->nmatch[j] && args->nmism[j] )
+        {
+            // Entropy-inspired quality. The factor 0.7 shifts and scales to (0,1)
+            double f = (double)args->nmatch[j]/(args->nmatch[j]+args->nmism[j]);
+            args->phase_qual[j] = 99*(0.7 + f*log(f) + (1-f)*log(1-f))/0.7;
+        }
+        else
+            args->phase_qual[j] = 99;
+        args->nmatch[j] = 0;
+        args->nmism[j]  = 0;
+    }
+    int PQ_printed = 0;
+    for (; i<args->nbuf; i+=2)
+    {
+        bcf1_t *rec;
+        bcf_hdr_t *hdr;
+        int mask = args->buf_mask[i/2];
+        if ( mask & 2 ) { rec = args->buf[i+1]; hdr = args->files->readers[1].header; }
+        else { rec = args->buf[i]; hdr = args->files->readers[0].header; }
+        bcf_translate(args->out_hdr, hdr, rec);
+        if ( !PQ_printed && mask==3 )
+        {
+            bcf_update_format_int32(args->out_hdr,rec,"PQ",args->phase_qual,nsmpl);
+            PQ_printed = 1;
+            for (j=0; j<nsmpl; j++)
+                if ( args->phase_qual[j] < args->min_PQ ) 
+                {
+                    args->phase_set[j] = rec->pos+1;
+                    args->phase_set_changed = 1;
+                }
+                else if ( args->compact_PS ) args->phase_set[j] = bcf_int32_missing;
+        }
+        if ( args->nswap )
+            phase_update(args, args->out_hdr, rec);
+        if ( !args->compact_PS || args->phase_set_changed )
+        {
+            bcf_update_format_int32(args->out_hdr,rec,"PS",args->phase_set,nsmpl);
+            args->phase_set_changed = 0;
+        }
+        if ( bcf_write(args->out_fh, args->out_hdr, rec)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->output_fname);
+
+        if ( rec->pos < args->prev_pos_check ) error("FIXME, disorder: %s:%"PRId64" vs %d  [2]\n", bcf_seqname(hdr,rec),(int64_t)rec->pos+1,args->prev_pos_check+1);
+        args->prev_pos_check = rec->pos;
+    }
+    args->nbuf = 0;
+}
+
+static void phased_push(args_t *args, bcf1_t *arec, bcf1_t *brec, int is_overlap)
+{
+    bcf_hdr_t *ahdr = arec ? bcf_sr_get_header(args->files,0) : NULL;
+    bcf_hdr_t *bhdr = brec ? bcf_sr_get_header(args->files,1) : NULL;
+
+    if ( arec && arec->errcode )
+        error("Parse error at %s:%"PRId64", cannot proceed: %s\n", bcf_seqname(ahdr,arec),(int64_t) arec->pos+1, args->files->readers[0].fname);
+    if ( brec && brec->errcode )
+        error("Parse error at %s:%"PRId64", cannot proceed: %s\n", bcf_seqname(bhdr,brec),(int64_t) brec->pos+1, args->files->readers[1].fname);
+
+    int i, nsmpl = bcf_hdr_nsamples(args->out_hdr);
+    int chr_id = arec ? bcf_hdr_name2id(args->out_hdr,bcf_seqname(ahdr,arec)) : bcf_hdr_name2id(args->out_hdr,bcf_seqname(bhdr,brec));
+    if ( args->prev_chr<0 || args->prev_chr!=chr_id )
+    {
+        if ( args->prev_chr>=0 ) phased_flush(args);
+
+        for (i=0; i<nsmpl; i++)
+            args->phase_set[i] = arec ? arec->pos+1 : brec->pos+1;
+        args->phase_set_changed = 1;
+
+        if ( args->seen_seq[chr_id] ) error("The chromosome block %s is not contiguous\n", arec ? bcf_seqname(ahdr,arec) : bcf_seqname(bhdr,brec));
+        args->seen_seq[chr_id] = 1;
+        args->prev_chr = chr_id;
+        args->prev_pos_check = -1;
+    }
+
+    if ( !is_overlap )
+    {
+        assert(arec);
+
+        bcf_translate(args->out_hdr, ahdr, arec);
+        if ( args->nswap )
+            phase_update(args, args->out_hdr, arec);
+        if ( !args->compact_PS || args->phase_set_changed )
+        {
+            bcf_update_format_int32(args->out_hdr,arec,"PS",args->phase_set,nsmpl);
+            args->phase_set_changed = 0;
+        }
+        if ( bcf_write(args->out_fh, args->out_hdr, arec)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->output_fname);
+
+        if ( arec->pos < args->prev_pos_check )
+            error("FIXME, disorder: %s:%"PRId64" in %s vs %d written  [3]\n", bcf_seqname(ahdr,arec), (int64_t) arec->pos+1,args->files->readers[0].fname, args->prev_pos_check+1);
+        args->prev_pos_check = arec->pos;
+        return;
+    }
+
+    int m = args->mbuf;
+    args->nbuf += 2;
+    hts_expand(bcf1_t*,args->nbuf,args->mbuf,args->buf);
+    if ( m < args->mbuf ) args->buf_mask = (uint8_t*)realloc(args->buf_mask,sizeof(*args->buf_mask)*args->mbuf);
+    for (i=m; i<args->mbuf; i++)
+        args->buf[i] = bcf_init1();
+
+    if ( arec ) SWAP(bcf1_t*, args->files->readers[0].buffer[0], args->buf[args->nbuf-2]);
+    if ( brec ) SWAP(bcf1_t*, args->files->readers[1].buffer[0], args->buf[args->nbuf-1]);
+    args->buf_mask[args->nbuf/2-1] = (arec?1:0) | (brec?2:0);
+}
+
+static int _get_active_index(bcf_srs_t *sr)
+{
+    int i;
+    for (i=0; i<sr->nreaders; i++)
+        if ( bcf_sr_has_line(sr,i) ) return i;
+    return -1;
+}
+
+static void concat(args_t *args)
+{
+    static int site_drop_warned = 0;
+    int i;
+    if ( args->phased_concat )  // phased concat
+    {
+        // keep only two open files at a time
+        while ( args->ifname < args->nfnames )
+        {
+            int new_file = 0;
+            while ( args->files->nreaders < 2 && args->ifname < args->nfnames )
+            {
+                if ( !bcf_sr_add_reader(args->files,args->fnames[args->ifname]) ) error("Failed to open %s: %s\n", args->fnames[args->ifname],bcf_sr_strerror(args->files->errnum));
+                new_file = 1;
+
+                args->ifname++;
+                if ( args->start_pos[args->ifname-1]==-1 ) break;   // new chromosome, start with only one file open
+                if ( args->ifname < args->nfnames && args->start_pos[args->ifname]==-1 ) break; // next file starts on a different chromosome
+            }
+
+            // is there a line from the previous run? Seek the newly opened reader to that position
+            int seek_pos = -1;
+            int seek_chr = -1;
+            if ( bcf_sr_has_line(args->files,0) )
+            {
+                bcf1_t *line = bcf_sr_get_line(args->files,0);
+                bcf_sr_seek(args->files, bcf_seqname(args->files->readers[0].header,line), line->pos);
+                seek_pos = line->pos;
+                seek_chr = bcf_hdr_name2id(args->out_hdr, bcf_seqname(args->files->readers[0].header,line));
+            }
+            else if ( new_file )
+                bcf_sr_seek(args->files,NULL,0);  // set to start
+
+            int nret, ir;
+            while ( (nret = bcf_sr_next_line(args->files)) )
+            {
+                int is_overlap = args->files->nreaders==1 ? 0 : 1;
+                if ( !bcf_sr_has_line(args->files,0) )  // no input from the first reader
+                {
+                    // We are assuming that there is a perfect overlap, sites which are not present in both files are dropped
+                    if ( bcf_sr_region_done(args->files,0) )
+                    {
+                        phased_flush(args);
+                        bcf_sr_remove_reader(args->files, 0);
+                        is_overlap = 0;
+                    }
+                    else if ( args->ligate_warn )
+                    {
+                        if ( !site_drop_warned )
+                        {
+                            ir = _get_active_index(args->files);
+                            fprintf(stderr,
+                                "Warning: Dropping the site %s:%"PRId64". The --ligate option is intended for VCFs with perfect\n"
+                                "         overlap, sites in overlapping regions present in one but missing in other are dropped.\n"
+                                "         This warning is printed only once.\n",
+                                bcf_seqname(bcf_sr_get_header(args->files,ir),bcf_sr_get_line(args->files,ir)), (int64_t) bcf_sr_get_line(args->files,ir)->pos+1);
+                            site_drop_warned = 1;
+                        }
+                        continue;
+                    }
+                    else if ( !args->ligate_force )
+                    {
+                        ir = _get_active_index(args->files);
+                        error("Error: The --ligate option is intended for VCFs with perfect overlap, the site %s:%"PRId64" breaks the assumption\n",
+                            bcf_seqname(bcf_sr_get_header(args->files,ir),bcf_sr_get_line(args->files,ir)), (int64_t) bcf_sr_get_line(args->files,ir)->pos+1);
+                    }
+                }
+
+                // Get a line to learn about current position
+                ir = _get_active_index(args->files);
+                bcf1_t *line = bcf_sr_get_line(args->files,ir);
+
+                // This can happen after bcf_sr_seek: indel may start before the coordinate which we seek to.
+                if ( seek_chr>=0 && seek_pos>line->pos && seek_chr==bcf_hdr_name2id(args->out_hdr, bcf_seqname(args->files->readers[ir].header,line)) ) continue;
+                seek_pos = seek_chr = -1;
+
+                //  Check if the position overlaps with the next, yet unopened, reader
+                int must_seek = 0;
+                while ( args->ifname < args->nfnames && args->start_pos[args->ifname]!=-1 && line->pos >= args->start_pos[args->ifname] )
+                {
+                    must_seek = 1;
+                    if ( !bcf_sr_add_reader(args->files,args->fnames[args->ifname]) ) error("Failed to open %s: %s\n", args->fnames[args->ifname],bcf_sr_strerror(args->files->errnum));
+                    args->ifname++;
+                }
+                if ( must_seek )
+                {
+                    bcf_sr_seek(args->files, bcf_seqname(args->files->readers[ir].header,line), line->pos);
+                    seek_pos = line->pos;
+                    seek_chr = bcf_hdr_name2id(args->out_hdr, bcf_seqname(args->files->readers[ir].header,line));
+                    continue;
+                }
+
+                // We are assuming that there is a perfect overlap, sites which are not present in both files are dropped
+                if ( args->files->nreaders>1 && !bcf_sr_has_line(args->files,1) && !bcf_sr_region_done(args->files,1) && !args->ligate_force )
+                {
+                    if ( args->ligate_warn && !site_drop_warned )
+                    {
+                        ir = _get_active_index(args->files);
+                        fprintf(stderr,
+                                "Warning: Dropping the site %s:%"PRId64". The --ligate option is intended for VCFs with perfect\n"
+                                "         overlap, sites in overlapping regions present in one but missing in other are dropped.\n"
+                                "         This warning is printed only once.\n",
+                                bcf_seqname(bcf_sr_get_header(args->files,ir),line), (int64_t) line->pos+1);
+                        site_drop_warned = 1;
+                    }
+                    else if ( !args->ligate_warn )
+                    {
+                        ir = _get_active_index(args->files);
+                        error("Error: The --ligate option is intended for VCFs with perfect overlap, the site %s:%"PRId64" breaks the assumption\n",
+                            bcf_seqname(bcf_sr_get_header(args->files,ir),bcf_sr_get_line(args->files,ir)), (int64_t) bcf_sr_get_line(args->files,ir)->pos+1);
+                    }
+                    continue;
+                }
+
+                bcf1_t *line0 = bcf_sr_get_line(args->files,0);
+                bcf1_t *line1 = args->files->nreaders > 1 ? bcf_sr_get_line(args->files,1) : NULL;
+                phased_push(args, line0, line1, is_overlap);
+            }
+
+            if ( args->files->nreaders )
+            {
+                phased_flush(args);
+                while ( args->files->nreaders )
+                    bcf_sr_remove_reader(args->files, 0);
+            }
+        }
+    }
+    else if ( args->files )  // combining overlapping files, using synced reader
+    {
+        while ( bcf_sr_next_line(args->files) )
+        {
+            for (i=0; i<args->files->nreaders; i++)
+            {
+                bcf1_t *line = bcf_sr_get_line(args->files,i);
+                if ( !line ) continue;
+                bcf_translate(args->out_hdr, args->files->readers[i].header, line);
+                if ( bcf_write1(args->out_fh, args->out_hdr, line)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->output_fname);
+                if ( args->remove_dups ) break;
+            }
+        }
+    }
+    else    // concatenating
+    {
+        struct timeval t0, t1;
+        kstring_t tmp = {0,0,0};
+        int prev_chr_id = -1, prev_pos;
+        bcf1_t *line = bcf_init();
+        for (i=0; i<args->nfnames; i++)
+        {
+            if ( args->verbose )
+            {
+                fprintf(stderr,"Concatenating %s", args->fnames[i]);
+                gettimeofday(&t0, NULL);
+            }
+            htsFile *fp = hts_open(args->fnames[i], "r"); if ( !fp ) error("\nFailed to open: %s\n", args->fnames[i]);
+            if ( args->n_threads ) hts_set_opt(fp, HTS_OPT_THREAD_POOL, args->tpool);
+            bcf_hdr_t *hdr = bcf_hdr_read(fp); if ( !hdr ) error("\nFailed to parse header: %s\n", args->fnames[i]);
+            if ( !fp->is_bin && args->output_type&FT_VCF )
+            {
+                line->max_unpack = BCF_UN_STR;
+                // if VCF is on both input and output, avoid VCF to BCF conversion
+                while ( hts_getline(fp, KS_SEP_LINE, &fp->line) >=0 )
+                {
+                    char *str = fp->line.s;
+                    while ( *str && *str!='\t' ) str++;
+                    tmp.l = 0;
+                    kputsn(fp->line.s,str-fp->line.s,&tmp);
+                    int chr_id = bcf_hdr_name2id(args->out_hdr, tmp.s);
+                    if ( chr_id<0 ) error("\nThe sequence \"%s\" not defined in the header: %s\n(Quick workaround: index the file.)\n", tmp.s, args->fnames[i]);
+                    if ( prev_chr_id!=chr_id )
+                    {
+                        prev_pos = -1;
+                        if ( args->seen_seq[chr_id] )
+                            error("\nThe chromosome block %s is not contiguous, consider running with -a.\n", tmp.s);
+                    }
+                    char *end;
+                    int pos = strtol(str+1,&end,10) - 1;
+                    if ( end==str+1 ) error("Could not parse line: %s\n", fp->line.s);
+                    if ( prev_pos > pos )
+                        error("\nThe chromosome block %s is not sorted, consider running with -a.\n", tmp.s);
+                    args->seen_seq[chr_id] = 1;
+                    prev_chr_id = chr_id;
+
+                    if ( vcf_write_line(args->out_fh, &fp->line)!=0 ) error("\nFailed to write %"PRIu64" bytes\n", (uint64_t)fp->line.l);
+                }
+            }
+            else
+            {
+                // BCF conversion is required
+                line->max_unpack = 0;
+                while ( bcf_read(fp, hdr, line)==0 )
+                {
+                    bcf_translate(args->out_hdr, hdr, line);
+
+                    if ( prev_chr_id!=line->rid )
+                    {
+                        prev_pos = -1;
+                        if ( args->seen_seq[line->rid] )
+                            error("\nThe chromosome block %s is not contiguous, consider running with -a.\n", bcf_seqname(args->out_hdr, line));
+                    }
+                    if ( prev_pos > line->pos )
+                        error("\nThe chromosome block %s is not sorted, consider running with -a.\n", bcf_seqname(args->out_hdr, line));
+                    args->seen_seq[line->rid] = 1;
+                    prev_chr_id = line->rid;
+
+                    if ( bcf_write(args->out_fh, args->out_hdr, line)!=0 ) error("\nFailed to write\n");
+                }
+            }
+            bcf_hdr_destroy(hdr);
+            hts_close(fp);
+            if ( args->verbose )
+            {
+                gettimeofday(&t1, NULL);
+                double delta = (t1.tv_sec - t0.tv_sec) * 1e6 + (t1.tv_usec - t0.tv_usec);
+                fprintf(stderr,"\t%f seconds\n",delta/1e6);
+            }
+        }
+        bcf_destroy(line);
+        free(tmp.s);
+    }
+}
+
+int print_vcf_gz_header(BGZF *fp, BGZF *bgzf_out, int print_header, kstring_t *tmp)
+{
+    char *buffer = (char*) fp->uncompressed_block;
+
+    // Read the header and find the position of the data block
+    if ( buffer[0]!='#' ) error("Could not parse the header, expected '#', found '%c'\n", buffer[0]);
+
+    int nskip = 1;     // end of the header in the current uncompressed block
+    while (1)
+    {
+        if ( buffer[nskip]=='\n' )
+        {
+            nskip++;
+            if ( nskip>=fp->block_length )
+            {
+                kputsn(buffer,nskip,tmp);
+                if ( bgzf_read_block(fp) != 0 ) return -1;
+                if ( !fp->block_length ) break;
+                nskip = 0;
+            }
+            // The header has finished
+            if ( buffer[nskip]!='#' )
+            {
+                kputsn(buffer,nskip,tmp);
+                break;
+            }
+        }
+        nskip++;
+        if ( nskip>=fp->block_length )
+        {
+            kputsn(buffer,fp->block_length,tmp);
+            if ( bgzf_read_block(fp) != 0 ) return -1;
+            if ( !fp->block_length ) break;
+            nskip = 0;
+        }
+    }
+    if ( print_header )
+    {
+        if ( bgzf_write(bgzf_out,tmp->s,tmp->l) != tmp->l ) error("Failed to write %"PRIu64" bytes\n", (uint64_t)tmp->l);
+        tmp->l = 0;
+    }
+    return nskip;
+}
+
+static inline int unpackInt16(const uint8_t *buffer)
+{
+    return buffer[0] | buffer[1] << 8;
+}
+static int check_header(const uint8_t *header)
+{
+    if ( header[0] != 31 || header[1] != 139 || header[2] != 8 ) return -2;
+    return ((header[3] & 4) != 0
+            && unpackInt16((uint8_t*)&header[10]) == 6
+            && header[12] == 'B' && header[13] == 'C'
+            && unpackInt16((uint8_t*)&header[14]) == 2) ? 0 : -1;
+}
+static void _check_hrecs(const bcf_hdr_t *hdr0, const bcf_hdr_t *hdr, char *fname0, char *fname)
+{
+    int j;
+    for (j=0; j<hdr0->nhrec; j++)
+    {
+        bcf_hrec_t *hrec0 = hdr0->hrec[j];
+        if ( hrec0->type!=BCF_HL_FLT && hrec0->type!=BCF_HL_INFO && hrec0->type!=BCF_HL_FMT && hrec0->type!=BCF_HL_CTG ) continue;    // skip fiels w/o IDX
+        int itag = bcf_hrec_find_key(hrec0, "ID");
+        bcf_hrec_t *hrec = bcf_hdr_get_hrec(hdr, hrec0->type, "ID", hrec0->vals[itag], NULL);
+
+        char *type = NULL;
+        if ( hrec0->type==BCF_HL_FLT ) type = "FILTER";
+        if ( hrec0->type==BCF_HL_INFO ) type = "INFO";
+        if ( hrec0->type==BCF_HL_FMT ) type = "FORMAT";
+        if ( hrec0->type==BCF_HL_CTG ) type = "contig";
+
+        if ( !hrec )
+            error("Cannot use --naive, incompatible headers, the tag %s/%s not present in %s\n",type,hrec0->vals[itag],fname);
+
+        int idx0 = bcf_hrec_find_key(hrec0, "IDX");
+        int idx  = bcf_hrec_find_key(hrec,  "IDX");
+        if ( idx0<0 || idx<0 )
+            error("fixme: unexpected IDX<0 for %s/%s in %s or %s\n",type,hrec0->vals[itag],fname0,fname);
+        if ( strcmp(hrec0->vals[idx0],hrec->vals[idx]) )
+            error("Cannot use --naive, use --naive-force instead: different order the tag %s/%s in %s vs %s\n",type,hrec0->vals[itag],fname0,fname);
+    }
+}
+static void naive_concat_check_headers(args_t *args)
+{
+    fprintf(stderr,"Checking the headers of %d files.\n",args->nfnames);
+    bcf_hdr_t *hdr0 = NULL;
+    int i,j;
+    for (i=0; i<args->nfnames; i++)
+    {
+        htsFile *fp = hts_open(args->fnames[i], "r"); if ( !fp ) error("Failed to open: %s\n", args->fnames[i]);
+        bcf_hdr_t *hdr = bcf_hdr_read(fp); if ( !hdr ) error("Failed to parse header: %s\n", args->fnames[i]);
+        htsFormat type = *hts_get_format(fp);
+        hts_close(fp);
+
+        if ( i==0 )
+        {
+            hdr0 = hdr;
+            continue;
+        }
+
+        // check the samples
+        if ( bcf_hdr_nsamples(hdr0)!=bcf_hdr_nsamples(hdr) )
+            error("Cannot concatenate, different number of samples: %d vs %d in %s vs %s\n",bcf_hdr_nsamples(hdr0),bcf_hdr_nsamples(hdr),args->fnames[0],args->fnames[i]);
+        for (j=0; j<bcf_hdr_nsamples(hdr0); j++)
+            if ( strcmp(hdr0->samples[j],hdr->samples[j]) )
+                error("Cannot concatenate, different samples in %s vs %s\n",args->fnames[0],args->fnames[i]);
+
+        // if BCF, check if tag IDs are consistent in the dictionary of strings
+        if ( type.compression!=bgzf )
+            error("The --naive option works only for compressed BCFs or VCFs, sorry :-/\n");
+
+        _check_hrecs(hdr0,hdr,args->fnames[0],args->fnames[i]);
+        _check_hrecs(hdr,hdr0,args->fnames[i],args->fnames[0]);
+
+        bcf_hdr_destroy(hdr);
+    }
+    if ( hdr0 ) bcf_hdr_destroy(hdr0);
+    fprintf(stderr,"Done, the headers are compatible.\n");
+}
+static void naive_concat(args_t *args)
+{
+    if ( !args->naive_concat_trust_headers )
+        naive_concat_check_headers(args);
+
+    // only compressed BCF atm
+    BGZF *bgzf_out = bgzf_open(args->output_fname,"w");;
+
+    htsFormat output_type;
+    output_type.format = (args->output_type & FT_VCF) ? vcf : bcf;
+    output_type.compression = (args->output_type & FT_GZ) ? bgzf : no_compression;
+
+    struct timeval t0, t1;
+    const size_t page_size = BGZF_MAX_BLOCK_SIZE;
+    uint8_t *buf = (uint8_t*) malloc(page_size);
+    kstring_t tmp = {0,0,0};
+    int i, file_types = 0;
+    for (i=0; i<args->nfnames; i++)
+    {
+        if ( args->verbose )
+        {
+            fprintf(stderr,"Concatenating %s", args->fnames[i]);
+            gettimeofday(&t0, NULL);
+        }
+        htsFile *hts_fp = hts_open(args->fnames[i],"r");
+        if ( !hts_fp ) error("\nFailed to open: %s\n", args->fnames[i]);
+        htsFormat type = *hts_get_format(hts_fp);
+
+        if ( type.compression!=bgzf )
+            error("\nThe --naive option works only for compressed BCFs or VCFs\n");
+        file_types |= type.format==vcf ? 1 : 2;
+        if ( file_types==3 )
+            error("\nThe --naive option works only for compressed files of the same type, all BCFs or all VCFs\n");
+        if ( args->explicit_output_type )
+        {
+            if ( output_type.format!=type.format )
+                error("\nThe --naive option works only for the output of the same type, all BCFs or all VCFs\n");
+            if ( output_type.compression!=type.compression )
+                error("\nThe --naive option works only for the output of the same compression type\n");
+        }
+
+        BGZF *fp = hts_get_bgzfp(hts_fp);
+        if ( !fp || bgzf_read_block(fp) != 0 || !fp->block_length )
+            error("\nFailed to read %s: %s\n", args->fnames[i], strerror(errno));
+
+        int nskip;
+        if ( type.format==bcf )
+        {
+            uint8_t magic[5];
+            if ( bgzf_read(fp, magic, 5) != 5 ) error("\nFailed to read the BCF header in %s\n", args->fnames[i]);
+            if (strncmp((char*)magic, "BCF\2\2", 5) != 0) error("\nInvalid BCF magic string in %s\n", args->fnames[i]);
+
+            if ( bgzf_read(fp, &tmp.l, 4) != 4 ) error("\nFailed to read the BCF header in %s\n", args->fnames[i]);
+            hts_expand(char,tmp.l,tmp.m,tmp.s);
+            if ( bgzf_read(fp, tmp.s, tmp.l) != tmp.l ) error("\nFailed to read the BCF header in %s\n", args->fnames[i]);
+
+            // write only the first header
+            if ( i==0 )
+            {
+                if ( bgzf_write(bgzf_out, "BCF\2\2", 5) !=5 ) error("\nFailed to write %d bytes to %s\n", 5,args->output_fname);
+                if ( bgzf_write(bgzf_out, &tmp.l, 4) !=4 ) error("\nFailed to write %d bytes to %s\n", 4,args->output_fname);
+                if ( bgzf_write(bgzf_out, tmp.s, tmp.l) != tmp.l) error("\nFailed to write %"PRId64" bytes to %s\n", (uint64_t)tmp.l,args->output_fname);
+            }
+            nskip = fp->block_offset;
+        }
+        else
+        {
+            nskip = print_vcf_gz_header(fp, bgzf_out, i==0?1:0, &tmp);
+            if ( nskip==-1 ) error("\nError reading %s\n", args->fnames[i]);
+        }
+
+        // Output all non-header data that were read together with the header block
+        if ( fp->block_length - nskip > 0 )
+        {
+            if ( bgzf_write(bgzf_out, (char *)fp->uncompressed_block+nskip, fp->block_length-nskip)<0 ) error("\nError: %d\n",fp->errcode);
+        }
+        if ( bgzf_flush(bgzf_out)<0 ) error("\nError: %d\n",bgzf_out->errcode);
+
+
+        // Stream the rest of the file as it is, without recompressing, but remove BGZF EOF blocks
+        // The final bgzf eof block will be added by bgzf_close.
+        ssize_t nread, nblock, nwr;
+        const int nheader = 18, neof = 28;
+        const uint8_t *eof = (uint8_t*) "\037\213\010\4\0\0\0\0\0\377\6\0\102\103\2\0\033\0\3\0\0\0\0\0\0\0\0\0";
+        while (1)
+        {
+            nread = bgzf_raw_read(fp, buf, nheader);
+            if ( !nread ) break;
+            if ( nread != nheader || check_header(buf)!=0 ) error("\nCould not parse the header of a bgzf block: %s\n",args->fnames[i]);
+            nblock = unpackInt16(buf+16) + 1;
+            assert( nblock <= page_size && nblock >= nheader );
+            nread += bgzf_raw_read(fp, buf+nheader, nblock - nheader);
+            if ( nread!=nblock ) error("\nCould not read %"PRId64" bytes: %s\n",(uint64_t)nblock,args->fnames[i]);
+            if ( nread==neof && !memcmp(buf,eof,neof) ) continue;
+            nwr = bgzf_raw_write(bgzf_out, buf, nread);
+            if ( nwr != nread ) error("\nWrite failed, wrote %"PRId64" instead of %d bytes.\n", (uint64_t)nwr,(int)nread);
+        }
+        if (hts_close(hts_fp)) error("\nClose failed: %s\n",args->fnames[i]);
+        if ( args->verbose )
+        {
+            gettimeofday(&t1, NULL);
+            double delta = (t1.tv_sec - t0.tv_sec) * 1e6 + (t1.tv_usec - t0.tv_usec);
+            fprintf(stderr,"\t%f seconds\n",delta/1e6);
+        }
+    }
+    free(buf);
+    free(tmp.s);
+    if (bgzf_close(bgzf_out) < 0) error("Error: %d\n",bgzf_out->errcode);
+}
+
+static void usage(args_t *args)
+{
+    fprintf(stderr, "\n");
+    fprintf(stderr, "About:   Concatenate or combine VCF/BCF files. All source files must have the same sample\n");
+    fprintf(stderr, "         columns appearing in the same order. The program can be used, for example, to\n");
+    fprintf(stderr, "         concatenate chromosome VCFs into one VCF, or combine a SNP VCF and an indel\n");
+    fprintf(stderr, "         VCF into one. The input files must be sorted by chr and position. The files\n");
+    fprintf(stderr, "         must be given in the correct order to produce sorted VCF on output unless\n");
+    fprintf(stderr, "         the -a, --allow-overlaps option is specified. With the --naive option, the files\n");
+    fprintf(stderr, "         are concatenated without being recompressed, which is very fast.\n");
+    fprintf(stderr, "Usage:   bcftools concat [options] <A.vcf.gz> [<B.vcf.gz> [...]]\n");
+    fprintf(stderr, "\n");
+    fprintf(stderr, "Options:\n");
+    fprintf(stderr, "   -a, --allow-overlaps           First coordinate of the next file can precede last record of the current file.\n");
+    fprintf(stderr, "   -c, --compact-PS               Do not output PS tag at each site, only at the start of a new phase set block.\n");
+    fprintf(stderr, "   -d, --rm-dups STRING           Output duplicate records present in multiple files only once: <snps|indels|both|all|exact>\n");
+    fprintf(stderr, "   -D, --remove-duplicates        Alias for -d exact\n");
+    fprintf(stderr, "   -f, --file-list FILE           Read the list of files from a file.\n");
+    fprintf(stderr, "   -l, --ligate                   Ligate phased VCFs by matching phase at overlapping haplotypes\n");
+    fprintf(stderr, "       --ligate-force             Ligate even non-overlapping chunks, keep all sites\n");
+    fprintf(stderr, "       --ligate-warn              Drop sites in imperfect overlaps\n");
+    fprintf(stderr, "       --no-version               Do not append version and command line to the header\n");
+    fprintf(stderr, "   -n, --naive                    Concatenate files without recompression, a header check compatibility is performed\n");
+    fprintf(stderr, "       --naive-force              Same as --naive, but header compatibility is not checked. Dangerous, use with caution.\n");
+    fprintf(stderr, "   -o, --output FILE              Write output to a file [standard output]\n");
+    fprintf(stderr, "   -O, --output-type u|b|v|z[0-9] u/b: un/compressed BCF, v/z: un/compressed VCF, 0-9: compression level [v]\n");
+    fprintf(stderr, "   -q, --min-PQ INT               Break phase set if phasing quality is lower than <int> [30]\n");
+    fprintf(stderr, "   -r, --regions REGION           Restrict to comma-separated list of regions\n");
+    fprintf(stderr, "   -R, --regions-file FILE        Restrict to regions listed in a file\n");
+    fprintf(stderr, "       --regions-overlap 0|1|2    Include if POS in the region (0), record overlaps (1), variant overlaps (2) [1]\n");
+    fprintf(stderr, "       --threads INT              Use multithreading with <int> worker threads [0]\n");
+    fprintf(stderr, "   -v, --verbose 0|1              Set verbosity level [1]\n");
+    fprintf(stderr, "\n");
+    exit(1);
+}
+
+int main_vcfconcat(int argc, char *argv[])
+{
+    int c;
+    args_t *args  = (args_t*) calloc(1,sizeof(args_t));
+    args->argc    = argc; args->argv = argv;
+    args->output_fname = "-";
+    args->output_type = FT_VCF;
+    args->n_threads = 0;
+    args->record_cmd_line = 1;
+    args->min_PQ  = 30;
+    args->verbose = 1;
+    args->clevel = -1;
+
+    static struct option loptions[] =
+    {
+        {"verbose",required_argument,NULL,'v'},
+        {"naive",no_argument,NULL,'n'},
+        {"naive-force",no_argument,NULL,7},
+        {"compact-PS",no_argument,NULL,'c'},
+        {"regions",required_argument,NULL,'r'},
+        {"regions-file",required_argument,NULL,'R'},
+        {"regions-overlap",required_argument,NULL,12},
+        {"remove-duplicates",no_argument,NULL,'D'},
+        {"rm-dups",required_argument,NULL,'d'},
+        {"allow-overlaps",no_argument,NULL,'a'},
+        {"ligate",no_argument,NULL,'l'},
+        {"ligate-force",no_argument,NULL,10},
+        {"ligate-warn",no_argument,NULL,11},
+        {"output",required_argument,NULL,'o'},
+        {"output-type",required_argument,NULL,'O'},
+        {"threads",required_argument,NULL,9},
+        {"file-list",required_argument,NULL,'f'},
+        {"min-PQ",required_argument,NULL,'q'},
+        {"no-version",no_argument,NULL,8},
+        {NULL,0,NULL,0}
+    };
+    char *tmp;
+    while ((c = getopt_long(argc, argv, "h:?o:O:f:alq:Dd:r:R:cnv:",loptions,NULL)) >= 0)
+    {
+        switch (c) {
+            case 'c': args->compact_PS = 1; break;
+            case 'r': args->regions_list = optarg; break;
+            case 'R': args->regions_list = optarg; args->regions_is_file = 1; break;
+            case 'd': args->remove_dups = optarg; break;
+            case 'D': args->remove_dups = "exact"; break;
+            case 'q': 
+                args->min_PQ = strtol(optarg,&tmp,10);
+                if ( *tmp ) error("Could not parse argument: --min-PQ %s\n", optarg);
+                break;
+            case 'n': args->naive_concat = 1; break;
+            case 'a': args->allow_overlaps = 1; break;
+            case 'l': args->phased_concat = 1; break;
+            case 'f': args->file_list = optarg; break;
+            case 'o': args->output_fname = optarg; break;
+            case 'O':
+                args->explicit_output_type = 1;
+                switch (optarg[0]) {
+                    case 'b': args->output_type = FT_BCF_GZ; break;
+                    case 'u': args->output_type = FT_BCF; break;
+                    case 'z': args->output_type = FT_VCF_GZ; break;
+                    case 'v': args->output_type = FT_VCF; break;
+                    default:
+                    {
+                        args->clevel = strtol(optarg,&tmp,10);
+                        if ( *tmp || args->clevel<0 || args->clevel>9 ) error("The output type \"%s\" not recognised\n", optarg);
+                    }
+                };
+                if ( optarg[1] )
+                {
+                    args->clevel = strtol(optarg+1,&tmp,10);
+                    if ( *tmp || args->clevel<0 || args->clevel>9 ) error("Could not parse argument: --compression-level %s\n", optarg+1);
+                }
+                break;
+            case 10 : args->ligate_force = 1; break;
+            case 11 : args->ligate_warn  = 1; break;
+            case  9 : args->n_threads = strtol(optarg, 0, 0); break;
+            case  8 : args->record_cmd_line = 0; break;
+            case  7 : args->naive_concat = 1; args->naive_concat_trust_headers = 1; break;
+            case 12 :
+                args->regions_overlap = parse_overlap_option(optarg);
+                if ( args->regions_overlap < 0 ) error("Could not parse: --regions-overlap %s\n",optarg);
+                break;
+            case 'v':
+                      args->verbose = strtol(optarg, 0, 0);
+                      error("Error: currently only --verbose 0 or --verbose 1 is supported\n");
+                      break;
+            case 'h':
+            case '?': usage(args); break;
+            default: error("Unknown argument: %s\n", optarg);
+        }
+    }
+    while ( optind<argc )
+    {
+        args->nfnames++;
+        args->fnames = (char **)realloc(args->fnames,sizeof(char*)*args->nfnames);
+        args->fnames[args->nfnames-1] = strdup(argv[optind]);
+        optind++;
+    }
+    if ( args->ligate_force && args->ligate_warn ) error("The options cannot be combined: --ligate-force and --ligate-warn\n");
+    if ( args->allow_overlaps && args->phased_concat ) error("The options -a and -l should not be combined. Please run with -l only.\n");
+    if ( args->compact_PS && !args->phased_concat ) error("The -c option is intended only with -l\n");
+    if ( args->file_list )
+    {
+        if ( args->nfnames ) error("Cannot combine -l with file names on command line.\n");
+        args->fnames = hts_readlines(args->file_list, &args->nfnames);
+        if ( !args->fnames ) error("Could not read the file: %s\n", args->file_list);
+    }
+    if ( !args->nfnames ) usage(args);
+    if ( args->remove_dups && !args->allow_overlaps ) error("The -D option is supported only with -a\n");
+    if ( args->regions_list && !args->allow_overlaps ) error("The -r/-R option is supported only with -a\n");
+    if ( args->naive_concat )
+    {
+        if ( args->allow_overlaps ) error("The option --naive cannot be combined with --allow-overlaps\n");
+        if ( args->phased_concat ) error("The option --naive cannot be combined with --ligate\n");
+        naive_concat(args);
+        destroy_data(args);
+        free(args);
+        return 0;
+    }
+    init_data(args);
+    concat(args);
+    destroy_data(args);
+    free(args);
+    return 0;
+}
diff --git a/bcftools/vcfconcat.c.pysam.c b/bcftools/vcfconcat.c.pysam.c
new file mode 100644
index 0000000..e2cd43f
--- /dev/null
+++ b/bcftools/vcfconcat.c.pysam.c
@@ -0,0 +1,1064 @@
+#include "bcftools.pysam.h"
+
+/*  vcfconcat.c -- Concatenate or combine VCF/BCF files.
+
+    Copyright (C) 2013-2021 Genome Research Ltd.
+
+    Author: Petr Danecek <pd3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.  */
+
+#include <stdio.h>
+#include <unistd.h>
+#include <getopt.h>
+#include <string.h>
+#include <assert.h>
+#include <errno.h>
+#include <math.h>
+#include <inttypes.h>
+#include <htslib/vcf.h>
+#include <htslib/synced_bcf_reader.h>
+#include <htslib/kseq.h>
+#include <htslib/bgzf.h>
+#include <htslib/tbx.h> // for hts_get_bgzfp()
+#include <htslib/thread_pool.h>
+#include <sys/time.h>
+#include "bcftools.h"
+
+typedef struct _args_t
+{
+    bcf_srs_t *files;
+    htsFile *out_fh;
+    int output_type, n_threads, record_cmd_line, clevel;
+    bcf_hdr_t *out_hdr;
+    int *seen_seq;
+
+    // phasing
+    int *start_pos, start_tid, ifname;
+    int *swap_phase, nswap, *nmatch, *nmism;
+    bcf1_t **buf;
+    uint8_t *buf_mask;
+    int nbuf, mbuf, prev_chr, min_PQ, prev_pos_check;
+    int32_t *GTa, *GTb, mGTa, mGTb, *phase_qual, *phase_set;
+
+    char **argv, *output_fname, *file_list, **fnames, *remove_dups, *regions_list;
+    int argc, nfnames, allow_overlaps, phased_concat, regions_is_file, regions_overlap;
+    int compact_PS, phase_set_changed, naive_concat, naive_concat_trust_headers;
+    int verbose, explicit_output_type, ligate_force, ligate_warn;
+    htsThreadPool *tpool;
+}
+args_t;
+
+static void init_data(args_t *args)
+{
+    bcf1_t *line = NULL;
+
+    // With phased concat, the chunks overlap and come in the right order.  To
+    // avoid opening all files at once, store start positions to recognise need
+    // for the next one. This way we can keep only two open chunks at once.
+    if ( args->phased_concat )
+    {
+        args->start_pos = (int*) malloc(sizeof(int)*args->nfnames);
+        line = bcf_init();
+    }
+
+    if ( args->verbose ) fprintf(bcftools_stderr,"Checking the headers and starting positions of %d files\n", args->nfnames);
+    kstring_t str = {0,0,0};
+    int i, prev_chrid = -1;
+    for (i=0; i<args->nfnames; i++)
+    {
+        htsFile *fp = hts_open(args->fnames[i], "r"); if ( !fp ) error("Failed to open: %s\n", args->fnames[i]);
+        bcf_hdr_t *hdr = bcf_hdr_read(fp); if ( !hdr ) error("Failed to parse header: %s\n", args->fnames[i]);
+        args->out_hdr = bcf_hdr_merge(args->out_hdr,hdr);
+        if ( bcf_hdr_nsamples(hdr) != bcf_hdr_nsamples(args->out_hdr) )
+            error("Different number of samples in %s. Perhaps \"bcftools merge\" is what you are looking for?\n", args->fnames[i]);
+
+        int j;
+        for (j=0; j<bcf_hdr_nsamples(hdr); j++)
+            if ( strcmp(args->out_hdr->samples[j],hdr->samples[j]) )
+                error("Different sample names in %s. Perhaps \"bcftools merge\" is what you are looking for?\n", args->fnames[i]);
+
+        if ( args->phased_concat )
+        {
+            int ret = bcf_read(fp, hdr, line);
+            if ( ret!=0 ) args->start_pos[i] = -2;  // empty file
+            else
+            {
+                int chrid = bcf_hdr_id2int(args->out_hdr,BCF_DT_CTG,bcf_seqname(hdr,line));
+                args->start_pos[i] = chrid==prev_chrid ? line->pos : -1;
+                prev_chrid = chrid;
+            }
+        }
+        bcf_hdr_destroy(hdr);
+        if ( hts_close(fp)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,args->fnames[i]);
+    }
+    free(str.s);
+    if ( line ) bcf_destroy(line);
+
+    args->seen_seq = (int*) calloc(args->out_hdr->n[BCF_DT_CTG],sizeof(int));
+
+    if ( args->phased_concat )
+    {
+        bcf_hdr_append(args->out_hdr,"##FORMAT=<ID=PQ,Number=1,Type=Integer,Description=\"Phasing Quality (bigger is better)\">");
+        bcf_hdr_append(args->out_hdr,"##FORMAT=<ID=PS,Number=1,Type=Integer,Description=\"Phase Set\">");
+    }
+    if (args->record_cmd_line) bcf_hdr_append_version(args->out_hdr, args->argc, args->argv, "bcftools_concat");
+    char wmode[8];
+    set_wmode(wmode,args->output_type,args->output_fname,args->clevel);
+    args->out_fh = hts_open(args->output_fname ? args->output_fname : "-", wmode);
+    if ( args->out_fh == NULL ) error("Can't write to \"%s\": %s\n", args->output_fname, strerror(errno));
+    if ( args->allow_overlaps || args->phased_concat )
+    {
+        args->files = bcf_sr_init();
+        args->files->require_index = 1;
+    }
+    if ( args->n_threads )
+    {
+        if ( args->files )
+        {
+            if ( bcf_sr_set_threads(args->files, args->n_threads)<0 ) error("Failed to create threads\n");
+            args->tpool = args->files->p;
+        }
+        else
+        {
+            args->tpool = (htsThreadPool*) calloc(1, sizeof(htsThreadPool));
+            if ( !args->tpool ) error("Failed to allocate memory\n");
+            if ( !(args->tpool->pool = hts_tpool_init(args->n_threads)) ) error("Failed to initialize %d threads\n",args->n_threads);
+        }
+        hts_set_opt(args->out_fh, HTS_OPT_THREAD_POOL, args->tpool);
+    }
+    if ( bcf_hdr_write(args->out_fh, args->out_hdr)!=0 ) error("[%s] Error: cannot write the header to %s\n", __func__,args->output_fname);
+
+    if ( args->allow_overlaps )
+    {
+        if ( args->regions_list )
+        {
+            bcf_sr_set_opt(args->files,BCF_SR_REGIONS_OVERLAP,args->regions_overlap);
+            if ( bcf_sr_set_regions(args->files, args->regions_list, args->regions_is_file)<0 )
+                error("Failed to read the regions: %s\n", args->regions_list);
+        }
+        if ( args->remove_dups )
+        {
+            if ( !strcmp(args->remove_dups,"snps") ) args->files->collapse |= COLLAPSE_SNPS;
+            else if ( !strcmp(args->remove_dups,"indels") ) args->files->collapse |= COLLAPSE_INDELS;
+            else if ( !strcmp(args->remove_dups,"both") ) args->files->collapse |= COLLAPSE_SNPS | COLLAPSE_INDELS;
+            else if ( !strcmp(args->remove_dups,"any") ) args->files->collapse |= COLLAPSE_ANY;
+            else if ( !strcmp(args->remove_dups,"all") ) args->files->collapse |= COLLAPSE_ANY;
+            else if ( !strcmp(args->remove_dups,"none") ) args->files->collapse = COLLAPSE_NONE;
+            else if ( !strcmp(args->remove_dups,"exact") ) args->files->collapse = COLLAPSE_NONE;
+            else error("The -D string \"%s\" not recognised.\n", args->remove_dups);
+        }
+        for (i=0; i<args->nfnames; i++)
+            if ( !bcf_sr_add_reader(args->files,args->fnames[i]) ) error("Failed to open %s: %s\n", args->fnames[i],bcf_sr_strerror(args->files->errnum));
+    }
+    else if ( args->phased_concat )
+    {
+        // Remove empty files from the list
+        int nok = 0;
+        while (1)
+        {
+            while ( nok<args->nfnames && args->start_pos[nok]!=-2 ) nok++;
+            if ( nok==args->nfnames ) break;
+
+            i = nok;
+            while ( i<args->nfnames && args->start_pos[i]==-2 ) i++;
+            if ( i==args->nfnames ) break;
+
+            int tmp = args->start_pos[nok]; args->start_pos[nok] = args->start_pos[i]; args->start_pos[i] = tmp;
+            char *str = args->fnames[nok]; args->fnames[nok] = args->fnames[i]; args->fnames[i] = str;
+        }
+        for (i=nok; i<args->nfnames; i++) free(args->fnames[i]);
+        args->nfnames = nok;
+
+        for (i=1; i<args->nfnames; i++)
+            if ( args->start_pos[i-1]!=-1 && args->start_pos[i]!=-1 && args->start_pos[i]<args->start_pos[i-1] )
+                error("The files not in ascending order: %d in %s, %d in %s\n", args->start_pos[i-1]+1,args->fnames[i-1],args->start_pos[i]+1,args->fnames[i]);
+
+        args->prev_chr = -1;
+        args->swap_phase = (int*) calloc(bcf_hdr_nsamples(args->out_hdr),sizeof(int));
+        args->nmatch = (int*) calloc(bcf_hdr_nsamples(args->out_hdr),sizeof(int));
+        args->nmism  = (int*) calloc(bcf_hdr_nsamples(args->out_hdr),sizeof(int));
+        args->phase_qual = (int32_t*) malloc(bcf_hdr_nsamples(args->out_hdr)*sizeof(int32_t));
+        args->phase_set  = (int32_t*) malloc(bcf_hdr_nsamples(args->out_hdr)*sizeof(int32_t));
+        args->ifname = 0;
+    }
+}
+
+static void destroy_data(args_t *args)
+{
+    int i;
+    if ( args->out_fh )
+    {
+        if ( hts_close(args->out_fh)!=0 ) error("hts_close error\n");
+    }
+    if ( args->tpool && !args->files )
+    {
+        hts_tpool_destroy(args->tpool->pool);
+        free(args->tpool);
+    }
+    if ( args->files ) bcf_sr_destroy(args->files);
+    if ( args->out_hdr ) bcf_hdr_destroy(args->out_hdr);
+    free(args->seen_seq);
+    free(args->start_pos);
+    free(args->swap_phase);
+    for (i=0; i<args->mbuf; i++) bcf_destroy(args->buf[i]);
+    free(args->buf);
+    free(args->buf_mask);
+    free(args->GTa);
+    free(args->GTb);
+    free(args->nmatch);
+    free(args->nmism);
+    free(args->phase_qual);
+    free(args->phase_set);
+    for (i=0; i<args->nfnames; i++) free(args->fnames[i]);
+    free(args->fnames);
+}
+
+int vcf_write_line(htsFile *fp, kstring_t *line);
+
+#define SWAP(type_t, a, b) { type_t t = a; a = b; b = t; }
+static void phase_update(args_t *args, bcf_hdr_t *hdr, bcf1_t *rec)
+{
+    int i, nGTs = bcf_get_genotypes(hdr, rec, &args->GTa, &args->mGTa);
+    if ( nGTs <= 0 ) return;    // GT field is not present
+    for (i=0; i<bcf_hdr_nsamples(hdr); i++)
+    {
+        if ( !args->swap_phase[i] ) continue;
+        int *gt = &args->GTa[i*2];
+        if ( bcf_gt_is_missing(gt[0]) || gt[1]==bcf_int32_vector_end ) continue;
+        if ( !bcf_gt_is_phased(gt[1]) ) continue;
+        SWAP(int, gt[0], gt[1]);
+        gt[1] |= 1;
+    }
+    bcf_update_genotypes(hdr,rec,args->GTa,nGTs);
+}
+
+static void phased_flush(args_t *args)
+{
+    if ( !args->nbuf ) return;
+
+    bcf_hdr_t *ahdr = args->files->readers[0].header;
+    bcf_hdr_t *bhdr = args->files->readers[1].header;
+
+    int i, j, nsmpl = bcf_hdr_nsamples(args->out_hdr);
+    static int gt_absent_warned = 0;
+    for (i=0; i<args->nbuf; i+=2)
+    {
+        if ( args->buf_mask[i/2]!=3 ) continue;
+
+        bcf1_t *arec = args->buf[i];
+        bcf1_t *brec = args->buf[i+1];
+
+        int nGTs = bcf_get_genotypes(ahdr, arec, &args->GTa, &args->mGTa);
+        if ( nGTs < 0 ) 
+        {
+            if ( !gt_absent_warned )
+            {
+                fprintf(bcftools_stderr,"GT is not present at %s:%"PRId64". (This warning is printed only once.)\n", bcf_seqname(ahdr,arec), (int64_t) arec->pos+1);
+                gt_absent_warned = 1;
+            }
+            continue;
+        }
+        if ( nGTs != 2*nsmpl ) continue;    // not diploid
+        nGTs = bcf_get_genotypes(bhdr, brec, &args->GTb, &args->mGTb);
+        if ( nGTs < 0 )
+        {
+            if ( !gt_absent_warned )
+            {
+                fprintf(bcftools_stderr,"GT is not present at %s:%"PRId64". (This warning is printed only once.)\n", bcf_seqname(bhdr,brec), (int64_t) brec->pos+1);
+                gt_absent_warned = 1;
+            }
+            continue;
+        }
+        if ( nGTs != 2*nsmpl ) continue;    // not diploid
+
+        for (j=0; j<nsmpl; j++)
+        {
+            int *gta = &args->GTa[j*2];
+            int *gtb = &args->GTb[j*2];
+            if ( gta[1]==bcf_int32_vector_end || gtb[1]==bcf_int32_vector_end ) continue;
+            if ( bcf_gt_is_missing(gta[0]) || bcf_gt_is_missing(gta[1]) || bcf_gt_is_missing(gtb[0]) || bcf_gt_is_missing(gtb[1]) ) continue;
+            if ( !bcf_gt_is_phased(gta[1]) || !bcf_gt_is_phased(gtb[1]) ) continue;
+            if ( bcf_gt_allele(gta[0])==bcf_gt_allele(gta[1]) || bcf_gt_allele(gtb[0])==bcf_gt_allele(gtb[1]) ) continue;
+            if ( bcf_gt_allele(gta[0])==bcf_gt_allele(gtb[0]) && bcf_gt_allele(gta[1])==bcf_gt_allele(gtb[1]) )
+            {
+                if ( args->swap_phase[j] ) args->nmism[j]++; else args->nmatch[j]++;
+            }
+            if ( bcf_gt_allele(gta[0])==bcf_gt_allele(gtb[1]) && bcf_gt_allele(gta[1])==bcf_gt_allele(gtb[0]) )
+            {
+                if ( args->swap_phase[j] ) args->nmatch[j]++; else args->nmism[j]++;
+            }
+        }
+    }
+    for (i=0; i<args->nbuf/2; i+=2)
+    {
+        bcf1_t *rec;
+        bcf_hdr_t *hdr;
+        int mask = args->buf_mask[i/2];
+        if ( mask & 1 ) { rec = args->buf[i]; hdr = args->files->readers[0].header; }
+        else { rec = args->buf[i+1]; hdr = args->files->readers[1].header; }
+        bcf_translate(args->out_hdr, hdr, rec);
+        if ( args->nswap && (mask&1) )
+            phase_update(args, args->out_hdr, rec);
+        if ( !args->compact_PS || args->phase_set_changed )
+        {
+            bcf_update_format_int32(args->out_hdr,rec,"PS",args->phase_set,nsmpl);
+            args->phase_set_changed = 0;
+        }
+        if ( bcf_write(args->out_fh, args->out_hdr, rec)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->output_fname);
+
+        if ( rec->pos < args->prev_pos_check ) error("FIXME, disorder: %s:%"PRId64" vs %d  [1]\n", bcf_seqname(hdr,rec),(int64_t)rec->pos+1,args->prev_pos_check+1);
+        args->prev_pos_check = rec->pos;
+    }
+    args->nswap = 0;
+    for (j=0; j<nsmpl; j++)
+    {
+        if ( args->nmatch[j] >= args->nmism[j] )
+            args->swap_phase[j] = 0;
+        else
+        {
+            args->swap_phase[j] = 1;
+            args->nswap++;
+        }
+        if ( args->nmatch[j] && args->nmism[j] )
+        {
+            // Entropy-inspired quality. The factor 0.7 shifts and scales to (0,1)
+            double f = (double)args->nmatch[j]/(args->nmatch[j]+args->nmism[j]);
+            args->phase_qual[j] = 99*(0.7 + f*log(f) + (1-f)*log(1-f))/0.7;
+        }
+        else
+            args->phase_qual[j] = 99;
+        args->nmatch[j] = 0;
+        args->nmism[j]  = 0;
+    }
+    int PQ_printed = 0;
+    for (; i<args->nbuf; i+=2)
+    {
+        bcf1_t *rec;
+        bcf_hdr_t *hdr;
+        int mask = args->buf_mask[i/2];
+        if ( mask & 2 ) { rec = args->buf[i+1]; hdr = args->files->readers[1].header; }
+        else { rec = args->buf[i]; hdr = args->files->readers[0].header; }
+        bcf_translate(args->out_hdr, hdr, rec);
+        if ( !PQ_printed && mask==3 )
+        {
+            bcf_update_format_int32(args->out_hdr,rec,"PQ",args->phase_qual,nsmpl);
+            PQ_printed = 1;
+            for (j=0; j<nsmpl; j++)
+                if ( args->phase_qual[j] < args->min_PQ ) 
+                {
+                    args->phase_set[j] = rec->pos+1;
+                    args->phase_set_changed = 1;
+                }
+                else if ( args->compact_PS ) args->phase_set[j] = bcf_int32_missing;
+        }
+        if ( args->nswap )
+            phase_update(args, args->out_hdr, rec);
+        if ( !args->compact_PS || args->phase_set_changed )
+        {
+            bcf_update_format_int32(args->out_hdr,rec,"PS",args->phase_set,nsmpl);
+            args->phase_set_changed = 0;
+        }
+        if ( bcf_write(args->out_fh, args->out_hdr, rec)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->output_fname);
+
+        if ( rec->pos < args->prev_pos_check ) error("FIXME, disorder: %s:%"PRId64" vs %d  [2]\n", bcf_seqname(hdr,rec),(int64_t)rec->pos+1,args->prev_pos_check+1);
+        args->prev_pos_check = rec->pos;
+    }
+    args->nbuf = 0;
+}
+
+static void phased_push(args_t *args, bcf1_t *arec, bcf1_t *brec, int is_overlap)
+{
+    bcf_hdr_t *ahdr = arec ? bcf_sr_get_header(args->files,0) : NULL;
+    bcf_hdr_t *bhdr = brec ? bcf_sr_get_header(args->files,1) : NULL;
+
+    if ( arec && arec->errcode )
+        error("Parse error at %s:%"PRId64", cannot proceed: %s\n", bcf_seqname(ahdr,arec),(int64_t) arec->pos+1, args->files->readers[0].fname);
+    if ( brec && brec->errcode )
+        error("Parse error at %s:%"PRId64", cannot proceed: %s\n", bcf_seqname(bhdr,brec),(int64_t) brec->pos+1, args->files->readers[1].fname);
+
+    int i, nsmpl = bcf_hdr_nsamples(args->out_hdr);
+    int chr_id = arec ? bcf_hdr_name2id(args->out_hdr,bcf_seqname(ahdr,arec)) : bcf_hdr_name2id(args->out_hdr,bcf_seqname(bhdr,brec));
+    if ( args->prev_chr<0 || args->prev_chr!=chr_id )
+    {
+        if ( args->prev_chr>=0 ) phased_flush(args);
+
+        for (i=0; i<nsmpl; i++)
+            args->phase_set[i] = arec ? arec->pos+1 : brec->pos+1;
+        args->phase_set_changed = 1;
+
+        if ( args->seen_seq[chr_id] ) error("The chromosome block %s is not contiguous\n", arec ? bcf_seqname(ahdr,arec) : bcf_seqname(bhdr,brec));
+        args->seen_seq[chr_id] = 1;
+        args->prev_chr = chr_id;
+        args->prev_pos_check = -1;
+    }
+
+    if ( !is_overlap )
+    {
+        assert(arec);
+
+        bcf_translate(args->out_hdr, ahdr, arec);
+        if ( args->nswap )
+            phase_update(args, args->out_hdr, arec);
+        if ( !args->compact_PS || args->phase_set_changed )
+        {
+            bcf_update_format_int32(args->out_hdr,arec,"PS",args->phase_set,nsmpl);
+            args->phase_set_changed = 0;
+        }
+        if ( bcf_write(args->out_fh, args->out_hdr, arec)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->output_fname);
+
+        if ( arec->pos < args->prev_pos_check )
+            error("FIXME, disorder: %s:%"PRId64" in %s vs %d written  [3]\n", bcf_seqname(ahdr,arec), (int64_t) arec->pos+1,args->files->readers[0].fname, args->prev_pos_check+1);
+        args->prev_pos_check = arec->pos;
+        return;
+    }
+
+    int m = args->mbuf;
+    args->nbuf += 2;
+    hts_expand(bcf1_t*,args->nbuf,args->mbuf,args->buf);
+    if ( m < args->mbuf ) args->buf_mask = (uint8_t*)realloc(args->buf_mask,sizeof(*args->buf_mask)*args->mbuf);
+    for (i=m; i<args->mbuf; i++)
+        args->buf[i] = bcf_init1();
+
+    if ( arec ) SWAP(bcf1_t*, args->files->readers[0].buffer[0], args->buf[args->nbuf-2]);
+    if ( brec ) SWAP(bcf1_t*, args->files->readers[1].buffer[0], args->buf[args->nbuf-1]);
+    args->buf_mask[args->nbuf/2-1] = (arec?1:0) | (brec?2:0);
+}
+
+static int _get_active_index(bcf_srs_t *sr)
+{
+    int i;
+    for (i=0; i<sr->nreaders; i++)
+        if ( bcf_sr_has_line(sr,i) ) return i;
+    return -1;
+}
+
+static void concat(args_t *args)
+{
+    static int site_drop_warned = 0;
+    int i;
+    if ( args->phased_concat )  // phased concat
+    {
+        // keep only two open files at a time
+        while ( args->ifname < args->nfnames )
+        {
+            int new_file = 0;
+            while ( args->files->nreaders < 2 && args->ifname < args->nfnames )
+            {
+                if ( !bcf_sr_add_reader(args->files,args->fnames[args->ifname]) ) error("Failed to open %s: %s\n", args->fnames[args->ifname],bcf_sr_strerror(args->files->errnum));
+                new_file = 1;
+
+                args->ifname++;
+                if ( args->start_pos[args->ifname-1]==-1 ) break;   // new chromosome, start with only one file open
+                if ( args->ifname < args->nfnames && args->start_pos[args->ifname]==-1 ) break; // next file starts on a different chromosome
+            }
+
+            // is there a line from the previous run? Seek the newly opened reader to that position
+            int seek_pos = -1;
+            int seek_chr = -1;
+            if ( bcf_sr_has_line(args->files,0) )
+            {
+                bcf1_t *line = bcf_sr_get_line(args->files,0);
+                bcf_sr_seek(args->files, bcf_seqname(args->files->readers[0].header,line), line->pos);
+                seek_pos = line->pos;
+                seek_chr = bcf_hdr_name2id(args->out_hdr, bcf_seqname(args->files->readers[0].header,line));
+            }
+            else if ( new_file )
+                bcf_sr_seek(args->files,NULL,0);  // set to start
+
+            int nret, ir;
+            while ( (nret = bcf_sr_next_line(args->files)) )
+            {
+                int is_overlap = args->files->nreaders==1 ? 0 : 1;
+                if ( !bcf_sr_has_line(args->files,0) )  // no input from the first reader
+                {
+                    // We are assuming that there is a perfect overlap, sites which are not present in both files are dropped
+                    if ( bcf_sr_region_done(args->files,0) )
+                    {
+                        phased_flush(args);
+                        bcf_sr_remove_reader(args->files, 0);
+                        is_overlap = 0;
+                    }
+                    else if ( args->ligate_warn )
+                    {
+                        if ( !site_drop_warned )
+                        {
+                            ir = _get_active_index(args->files);
+                            fprintf(bcftools_stderr,
+                                "Warning: Dropping the site %s:%"PRId64". The --ligate option is intended for VCFs with perfect\n"
+                                "         overlap, sites in overlapping regions present in one but missing in other are dropped.\n"
+                                "         This warning is printed only once.\n",
+                                bcf_seqname(bcf_sr_get_header(args->files,ir),bcf_sr_get_line(args->files,ir)), (int64_t) bcf_sr_get_line(args->files,ir)->pos+1);
+                            site_drop_warned = 1;
+                        }
+                        continue;
+                    }
+                    else if ( !args->ligate_force )
+                    {
+                        ir = _get_active_index(args->files);
+                        error("Error: The --ligate option is intended for VCFs with perfect overlap, the site %s:%"PRId64" breaks the assumption\n",
+                            bcf_seqname(bcf_sr_get_header(args->files,ir),bcf_sr_get_line(args->files,ir)), (int64_t) bcf_sr_get_line(args->files,ir)->pos+1);
+                    }
+                }
+
+                // Get a line to learn about current position
+                ir = _get_active_index(args->files);
+                bcf1_t *line = bcf_sr_get_line(args->files,ir);
+
+                // This can happen after bcf_sr_seek: indel may start before the coordinate which we seek to.
+                if ( seek_chr>=0 && seek_pos>line->pos && seek_chr==bcf_hdr_name2id(args->out_hdr, bcf_seqname(args->files->readers[ir].header,line)) ) continue;
+                seek_pos = seek_chr = -1;
+
+                //  Check if the position overlaps with the next, yet unopened, reader
+                int must_seek = 0;
+                while ( args->ifname < args->nfnames && args->start_pos[args->ifname]!=-1 && line->pos >= args->start_pos[args->ifname] )
+                {
+                    must_seek = 1;
+                    if ( !bcf_sr_add_reader(args->files,args->fnames[args->ifname]) ) error("Failed to open %s: %s\n", args->fnames[args->ifname],bcf_sr_strerror(args->files->errnum));
+                    args->ifname++;
+                }
+                if ( must_seek )
+                {
+                    bcf_sr_seek(args->files, bcf_seqname(args->files->readers[ir].header,line), line->pos);
+                    seek_pos = line->pos;
+                    seek_chr = bcf_hdr_name2id(args->out_hdr, bcf_seqname(args->files->readers[ir].header,line));
+                    continue;
+                }
+
+                // We are assuming that there is a perfect overlap, sites which are not present in both files are dropped
+                if ( args->files->nreaders>1 && !bcf_sr_has_line(args->files,1) && !bcf_sr_region_done(args->files,1) && !args->ligate_force )
+                {
+                    if ( args->ligate_warn && !site_drop_warned )
+                    {
+                        ir = _get_active_index(args->files);
+                        fprintf(bcftools_stderr,
+                                "Warning: Dropping the site %s:%"PRId64". The --ligate option is intended for VCFs with perfect\n"
+                                "         overlap, sites in overlapping regions present in one but missing in other are dropped.\n"
+                                "         This warning is printed only once.\n",
+                                bcf_seqname(bcf_sr_get_header(args->files,ir),line), (int64_t) line->pos+1);
+                        site_drop_warned = 1;
+                    }
+                    else if ( !args->ligate_warn )
+                    {
+                        ir = _get_active_index(args->files);
+                        error("Error: The --ligate option is intended for VCFs with perfect overlap, the site %s:%"PRId64" breaks the assumption\n",
+                            bcf_seqname(bcf_sr_get_header(args->files,ir),bcf_sr_get_line(args->files,ir)), (int64_t) bcf_sr_get_line(args->files,ir)->pos+1);
+                    }
+                    continue;
+                }
+
+                bcf1_t *line0 = bcf_sr_get_line(args->files,0);
+                bcf1_t *line1 = args->files->nreaders > 1 ? bcf_sr_get_line(args->files,1) : NULL;
+                phased_push(args, line0, line1, is_overlap);
+            }
+
+            if ( args->files->nreaders )
+            {
+                phased_flush(args);
+                while ( args->files->nreaders )
+                    bcf_sr_remove_reader(args->files, 0);
+            }
+        }
+    }
+    else if ( args->files )  // combining overlapping files, using synced reader
+    {
+        while ( bcf_sr_next_line(args->files) )
+        {
+            for (i=0; i<args->files->nreaders; i++)
+            {
+                bcf1_t *line = bcf_sr_get_line(args->files,i);
+                if ( !line ) continue;
+                bcf_translate(args->out_hdr, args->files->readers[i].header, line);
+                if ( bcf_write1(args->out_fh, args->out_hdr, line)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->output_fname);
+                if ( args->remove_dups ) break;
+            }
+        }
+    }
+    else    // concatenating
+    {
+        struct timeval t0, t1;
+        kstring_t tmp = {0,0,0};
+        int prev_chr_id = -1, prev_pos;
+        bcf1_t *line = bcf_init();
+        for (i=0; i<args->nfnames; i++)
+        {
+            if ( args->verbose )
+            {
+                fprintf(bcftools_stderr,"Concatenating %s", args->fnames[i]);
+                gettimeofday(&t0, NULL);
+            }
+            htsFile *fp = hts_open(args->fnames[i], "r"); if ( !fp ) error("\nFailed to open: %s\n", args->fnames[i]);
+            if ( args->n_threads ) hts_set_opt(fp, HTS_OPT_THREAD_POOL, args->tpool);
+            bcf_hdr_t *hdr = bcf_hdr_read(fp); if ( !hdr ) error("\nFailed to parse header: %s\n", args->fnames[i]);
+            if ( !fp->is_bin && args->output_type&FT_VCF )
+            {
+                line->max_unpack = BCF_UN_STR;
+                // if VCF is on both input and output, avoid VCF to BCF conversion
+                while ( hts_getline(fp, KS_SEP_LINE, &fp->line) >=0 )
+                {
+                    char *str = fp->line.s;
+                    while ( *str && *str!='\t' ) str++;
+                    tmp.l = 0;
+                    kputsn(fp->line.s,str-fp->line.s,&tmp);
+                    int chr_id = bcf_hdr_name2id(args->out_hdr, tmp.s);
+                    if ( chr_id<0 ) error("\nThe sequence \"%s\" not defined in the header: %s\n(Quick workaround: index the file.)\n", tmp.s, args->fnames[i]);
+                    if ( prev_chr_id!=chr_id )
+                    {
+                        prev_pos = -1;
+                        if ( args->seen_seq[chr_id] )
+                            error("\nThe chromosome block %s is not contiguous, consider running with -a.\n", tmp.s);
+                    }
+                    char *end;
+                    int pos = strtol(str+1,&end,10) - 1;
+                    if ( end==str+1 ) error("Could not parse line: %s\n", fp->line.s);
+                    if ( prev_pos > pos )
+                        error("\nThe chromosome block %s is not sorted, consider running with -a.\n", tmp.s);
+                    args->seen_seq[chr_id] = 1;
+                    prev_chr_id = chr_id;
+
+                    if ( vcf_write_line(args->out_fh, &fp->line)!=0 ) error("\nFailed to write %"PRIu64" bytes\n", (uint64_t)fp->line.l);
+                }
+            }
+            else
+            {
+                // BCF conversion is required
+                line->max_unpack = 0;
+                while ( bcf_read(fp, hdr, line)==0 )
+                {
+                    bcf_translate(args->out_hdr, hdr, line);
+
+                    if ( prev_chr_id!=line->rid )
+                    {
+                        prev_pos = -1;
+                        if ( args->seen_seq[line->rid] )
+                            error("\nThe chromosome block %s is not contiguous, consider running with -a.\n", bcf_seqname(args->out_hdr, line));
+                    }
+                    if ( prev_pos > line->pos )
+                        error("\nThe chromosome block %s is not sorted, consider running with -a.\n", bcf_seqname(args->out_hdr, line));
+                    args->seen_seq[line->rid] = 1;
+                    prev_chr_id = line->rid;
+
+                    if ( bcf_write(args->out_fh, args->out_hdr, line)!=0 ) error("\nFailed to write\n");
+                }
+            }
+            bcf_hdr_destroy(hdr);
+            hts_close(fp);
+            if ( args->verbose )
+            {
+                gettimeofday(&t1, NULL);
+                double delta = (t1.tv_sec - t0.tv_sec) * 1e6 + (t1.tv_usec - t0.tv_usec);
+                fprintf(bcftools_stderr,"\t%f seconds\n",delta/1e6);
+            }
+        }
+        bcf_destroy(line);
+        free(tmp.s);
+    }
+}
+
+int print_vcf_gz_header(BGZF *fp, BGZF *bgzf_out, int print_header, kstring_t *tmp)
+{
+    char *buffer = (char*) fp->uncompressed_block;
+
+    // Read the header and find the position of the data block
+    if ( buffer[0]!='#' ) error("Could not parse the header, expected '#', found '%c'\n", buffer[0]);
+
+    int nskip = 1;     // end of the header in the current uncompressed block
+    while (1)
+    {
+        if ( buffer[nskip]=='\n' )
+        {
+            nskip++;
+            if ( nskip>=fp->block_length )
+            {
+                kputsn(buffer,nskip,tmp);
+                if ( bgzf_read_block(fp) != 0 ) return -1;
+                if ( !fp->block_length ) break;
+                nskip = 0;
+            }
+            // The header has finished
+            if ( buffer[nskip]!='#' )
+            {
+                kputsn(buffer,nskip,tmp);
+                break;
+            }
+        }
+        nskip++;
+        if ( nskip>=fp->block_length )
+        {
+            kputsn(buffer,fp->block_length,tmp);
+            if ( bgzf_read_block(fp) != 0 ) return -1;
+            if ( !fp->block_length ) break;
+            nskip = 0;
+        }
+    }
+    if ( print_header )
+    {
+        if ( bgzf_write(bgzf_out,tmp->s,tmp->l) != tmp->l ) error("Failed to write %"PRIu64" bytes\n", (uint64_t)tmp->l);
+        tmp->l = 0;
+    }
+    return nskip;
+}
+
+static inline int unpackInt16(const uint8_t *buffer)
+{
+    return buffer[0] | buffer[1] << 8;
+}
+static int check_header(const uint8_t *header)
+{
+    if ( header[0] != 31 || header[1] != 139 || header[2] != 8 ) return -2;
+    return ((header[3] & 4) != 0
+            && unpackInt16((uint8_t*)&header[10]) == 6
+            && header[12] == 'B' && header[13] == 'C'
+            && unpackInt16((uint8_t*)&header[14]) == 2) ? 0 : -1;
+}
+static void _check_hrecs(const bcf_hdr_t *hdr0, const bcf_hdr_t *hdr, char *fname0, char *fname)
+{
+    int j;
+    for (j=0; j<hdr0->nhrec; j++)
+    {
+        bcf_hrec_t *hrec0 = hdr0->hrec[j];
+        if ( hrec0->type!=BCF_HL_FLT && hrec0->type!=BCF_HL_INFO && hrec0->type!=BCF_HL_FMT && hrec0->type!=BCF_HL_CTG ) continue;    // skip fiels w/o IDX
+        int itag = bcf_hrec_find_key(hrec0, "ID");
+        bcf_hrec_t *hrec = bcf_hdr_get_hrec(hdr, hrec0->type, "ID", hrec0->vals[itag], NULL);
+
+        char *type = NULL;
+        if ( hrec0->type==BCF_HL_FLT ) type = "FILTER";
+        if ( hrec0->type==BCF_HL_INFO ) type = "INFO";
+        if ( hrec0->type==BCF_HL_FMT ) type = "FORMAT";
+        if ( hrec0->type==BCF_HL_CTG ) type = "contig";
+
+        if ( !hrec )
+            error("Cannot use --naive, incompatible headers, the tag %s/%s not present in %s\n",type,hrec0->vals[itag],fname);
+
+        int idx0 = bcf_hrec_find_key(hrec0, "IDX");
+        int idx  = bcf_hrec_find_key(hrec,  "IDX");
+        if ( idx0<0 || idx<0 )
+            error("fixme: unexpected IDX<0 for %s/%s in %s or %s\n",type,hrec0->vals[itag],fname0,fname);
+        if ( strcmp(hrec0->vals[idx0],hrec->vals[idx]) )
+            error("Cannot use --naive, use --naive-force instead: different order the tag %s/%s in %s vs %s\n",type,hrec0->vals[itag],fname0,fname);
+    }
+}
+static void naive_concat_check_headers(args_t *args)
+{
+    fprintf(bcftools_stderr,"Checking the headers of %d files.\n",args->nfnames);
+    bcf_hdr_t *hdr0 = NULL;
+    int i,j;
+    for (i=0; i<args->nfnames; i++)
+    {
+        htsFile *fp = hts_open(args->fnames[i], "r"); if ( !fp ) error("Failed to open: %s\n", args->fnames[i]);
+        bcf_hdr_t *hdr = bcf_hdr_read(fp); if ( !hdr ) error("Failed to parse header: %s\n", args->fnames[i]);
+        htsFormat type = *hts_get_format(fp);
+        hts_close(fp);
+
+        if ( i==0 )
+        {
+            hdr0 = hdr;
+            continue;
+        }
+
+        // check the samples
+        if ( bcf_hdr_nsamples(hdr0)!=bcf_hdr_nsamples(hdr) )
+            error("Cannot concatenate, different number of samples: %d vs %d in %s vs %s\n",bcf_hdr_nsamples(hdr0),bcf_hdr_nsamples(hdr),args->fnames[0],args->fnames[i]);
+        for (j=0; j<bcf_hdr_nsamples(hdr0); j++)
+            if ( strcmp(hdr0->samples[j],hdr->samples[j]) )
+                error("Cannot concatenate, different samples in %s vs %s\n",args->fnames[0],args->fnames[i]);
+
+        // if BCF, check if tag IDs are consistent in the dictionary of strings
+        if ( type.compression!=bgzf )
+            error("The --naive option works only for compressed BCFs or VCFs, sorry :-/\n");
+
+        _check_hrecs(hdr0,hdr,args->fnames[0],args->fnames[i]);
+        _check_hrecs(hdr,hdr0,args->fnames[i],args->fnames[0]);
+
+        bcf_hdr_destroy(hdr);
+    }
+    if ( hdr0 ) bcf_hdr_destroy(hdr0);
+    fprintf(bcftools_stderr,"Done, the headers are compatible.\n");
+}
+static void naive_concat(args_t *args)
+{
+    if ( !args->naive_concat_trust_headers )
+        naive_concat_check_headers(args);
+
+    // only compressed BCF atm
+    BGZF *bgzf_out = bgzf_open(args->output_fname,"w");;
+
+    htsFormat output_type;
+    output_type.format = (args->output_type & FT_VCF) ? vcf : bcf;
+    output_type.compression = (args->output_type & FT_GZ) ? bgzf : no_compression;
+
+    struct timeval t0, t1;
+    const size_t page_size = BGZF_MAX_BLOCK_SIZE;
+    uint8_t *buf = (uint8_t*) malloc(page_size);
+    kstring_t tmp = {0,0,0};
+    int i, file_types = 0;
+    for (i=0; i<args->nfnames; i++)
+    {
+        if ( args->verbose )
+        {
+            fprintf(bcftools_stderr,"Concatenating %s", args->fnames[i]);
+            gettimeofday(&t0, NULL);
+        }
+        htsFile *hts_fp = hts_open(args->fnames[i],"r");
+        if ( !hts_fp ) error("\nFailed to open: %s\n", args->fnames[i]);
+        htsFormat type = *hts_get_format(hts_fp);
+
+        if ( type.compression!=bgzf )
+            error("\nThe --naive option works only for compressed BCFs or VCFs\n");
+        file_types |= type.format==vcf ? 1 : 2;
+        if ( file_types==3 )
+            error("\nThe --naive option works only for compressed files of the same type, all BCFs or all VCFs\n");
+        if ( args->explicit_output_type )
+        {
+            if ( output_type.format!=type.format )
+                error("\nThe --naive option works only for the output of the same type, all BCFs or all VCFs\n");
+            if ( output_type.compression!=type.compression )
+                error("\nThe --naive option works only for the output of the same compression type\n");
+        }
+
+        BGZF *fp = hts_get_bgzfp(hts_fp);
+        if ( !fp || bgzf_read_block(fp) != 0 || !fp->block_length )
+            error("\nFailed to read %s: %s\n", args->fnames[i], strerror(errno));
+
+        int nskip;
+        if ( type.format==bcf )
+        {
+            uint8_t magic[5];
+            if ( bgzf_read(fp, magic, 5) != 5 ) error("\nFailed to read the BCF header in %s\n", args->fnames[i]);
+            if (strncmp((char*)magic, "BCF\2\2", 5) != 0) error("\nInvalid BCF magic string in %s\n", args->fnames[i]);
+
+            if ( bgzf_read(fp, &tmp.l, 4) != 4 ) error("\nFailed to read the BCF header in %s\n", args->fnames[i]);
+            hts_expand(char,tmp.l,tmp.m,tmp.s);
+            if ( bgzf_read(fp, tmp.s, tmp.l) != tmp.l ) error("\nFailed to read the BCF header in %s\n", args->fnames[i]);
+
+            // write only the first header
+            if ( i==0 )
+            {
+                if ( bgzf_write(bgzf_out, "BCF\2\2", 5) !=5 ) error("\nFailed to write %d bytes to %s\n", 5,args->output_fname);
+                if ( bgzf_write(bgzf_out, &tmp.l, 4) !=4 ) error("\nFailed to write %d bytes to %s\n", 4,args->output_fname);
+                if ( bgzf_write(bgzf_out, tmp.s, tmp.l) != tmp.l) error("\nFailed to write %"PRId64" bytes to %s\n", (uint64_t)tmp.l,args->output_fname);
+            }
+            nskip = fp->block_offset;
+        }
+        else
+        {
+            nskip = print_vcf_gz_header(fp, bgzf_out, i==0?1:0, &tmp);
+            if ( nskip==-1 ) error("\nError reading %s\n", args->fnames[i]);
+        }
+
+        // Output all non-header data that were read together with the header block
+        if ( fp->block_length - nskip > 0 )
+        {
+            if ( bgzf_write(bgzf_out, (char *)fp->uncompressed_block+nskip, fp->block_length-nskip)<0 ) error("\nError: %d\n",fp->errcode);
+        }
+        if ( bgzf_flush(bgzf_out)<0 ) error("\nError: %d\n",bgzf_out->errcode);
+
+
+        // Stream the rest of the file as it is, without recompressing, but remove BGZF EOF blocks
+        // The final bgzf eof block will be added by bgzf_close.
+        ssize_t nread, nblock, nwr;
+        const int nheader = 18, neof = 28;
+        const uint8_t *eof = (uint8_t*) "\037\213\010\4\0\0\0\0\0\377\6\0\102\103\2\0\033\0\3\0\0\0\0\0\0\0\0\0";
+        while (1)
+        {
+            nread = bgzf_raw_read(fp, buf, nheader);
+            if ( !nread ) break;
+            if ( nread != nheader || check_header(buf)!=0 ) error("\nCould not parse the header of a bgzf block: %s\n",args->fnames[i]);
+            nblock = unpackInt16(buf+16) + 1;
+            assert( nblock <= page_size && nblock >= nheader );
+            nread += bgzf_raw_read(fp, buf+nheader, nblock - nheader);
+            if ( nread!=nblock ) error("\nCould not read %"PRId64" bytes: %s\n",(uint64_t)nblock,args->fnames[i]);
+            if ( nread==neof && !memcmp(buf,eof,neof) ) continue;
+            nwr = bgzf_raw_write(bgzf_out, buf, nread);
+            if ( nwr != nread ) error("\nWrite failed, wrote %"PRId64" instead of %d bytes.\n", (uint64_t)nwr,(int)nread);
+        }
+        if (hts_close(hts_fp)) error("\nClose failed: %s\n",args->fnames[i]);
+        if ( args->verbose )
+        {
+            gettimeofday(&t1, NULL);
+            double delta = (t1.tv_sec - t0.tv_sec) * 1e6 + (t1.tv_usec - t0.tv_usec);
+            fprintf(bcftools_stderr,"\t%f seconds\n",delta/1e6);
+        }
+    }
+    free(buf);
+    free(tmp.s);
+    if (bgzf_close(bgzf_out) < 0) error("Error: %d\n",bgzf_out->errcode);
+}
+
+static void usage(args_t *args)
+{
+    fprintf(bcftools_stderr, "\n");
+    fprintf(bcftools_stderr, "About:   Concatenate or combine VCF/BCF files. All source files must have the same sample\n");
+    fprintf(bcftools_stderr, "         columns appearing in the same order. The program can be used, for example, to\n");
+    fprintf(bcftools_stderr, "         concatenate chromosome VCFs into one VCF, or combine a SNP VCF and an indel\n");
+    fprintf(bcftools_stderr, "         VCF into one. The input files must be sorted by chr and position. The files\n");
+    fprintf(bcftools_stderr, "         must be given in the correct order to produce sorted VCF on output unless\n");
+    fprintf(bcftools_stderr, "         the -a, --allow-overlaps option is specified. With the --naive option, the files\n");
+    fprintf(bcftools_stderr, "         are concatenated without being recompressed, which is very fast.\n");
+    fprintf(bcftools_stderr, "Usage:   bcftools concat [options] <A.vcf.gz> [<B.vcf.gz> [...]]\n");
+    fprintf(bcftools_stderr, "\n");
+    fprintf(bcftools_stderr, "Options:\n");
+    fprintf(bcftools_stderr, "   -a, --allow-overlaps           First coordinate of the next file can precede last record of the current file.\n");
+    fprintf(bcftools_stderr, "   -c, --compact-PS               Do not output PS tag at each site, only at the start of a new phase set block.\n");
+    fprintf(bcftools_stderr, "   -d, --rm-dups STRING           Output duplicate records present in multiple files only once: <snps|indels|both|all|exact>\n");
+    fprintf(bcftools_stderr, "   -D, --remove-duplicates        Alias for -d exact\n");
+    fprintf(bcftools_stderr, "   -f, --file-list FILE           Read the list of files from a file.\n");
+    fprintf(bcftools_stderr, "   -l, --ligate                   Ligate phased VCFs by matching phase at overlapping haplotypes\n");
+    fprintf(bcftools_stderr, "       --ligate-force             Ligate even non-overlapping chunks, keep all sites\n");
+    fprintf(bcftools_stderr, "       --ligate-warn              Drop sites in imperfect overlaps\n");
+    fprintf(bcftools_stderr, "       --no-version               Do not append version and command line to the header\n");
+    fprintf(bcftools_stderr, "   -n, --naive                    Concatenate files without recompression, a header check compatibility is performed\n");
+    fprintf(bcftools_stderr, "       --naive-force              Same as --naive, but header compatibility is not checked. Dangerous, use with caution.\n");
+    fprintf(bcftools_stderr, "   -o, --output FILE              Write output to a file [standard output]\n");
+    fprintf(bcftools_stderr, "   -O, --output-type u|b|v|z[0-9] u/b: un/compressed BCF, v/z: un/compressed VCF, 0-9: compression level [v]\n");
+    fprintf(bcftools_stderr, "   -q, --min-PQ INT               Break phase set if phasing quality is lower than <int> [30]\n");
+    fprintf(bcftools_stderr, "   -r, --regions REGION           Restrict to comma-separated list of regions\n");
+    fprintf(bcftools_stderr, "   -R, --regions-file FILE        Restrict to regions listed in a file\n");
+    fprintf(bcftools_stderr, "       --regions-overlap 0|1|2    Include if POS in the region (0), record overlaps (1), variant overlaps (2) [1]\n");
+    fprintf(bcftools_stderr, "       --threads INT              Use multithreading with <int> worker threads [0]\n");
+    fprintf(bcftools_stderr, "   -v, --verbose 0|1              Set verbosity level [1]\n");
+    fprintf(bcftools_stderr, "\n");
+    bcftools_exit(1);
+}
+
+int main_vcfconcat(int argc, char *argv[])
+{
+    int c;
+    args_t *args  = (args_t*) calloc(1,sizeof(args_t));
+    args->argc    = argc; args->argv = argv;
+    args->output_fname = "-";
+    args->output_type = FT_VCF;
+    args->n_threads = 0;
+    args->record_cmd_line = 1;
+    args->min_PQ  = 30;
+    args->verbose = 1;
+    args->clevel = -1;
+
+    static struct option loptions[] =
+    {
+        {"verbose",required_argument,NULL,'v'},
+        {"naive",no_argument,NULL,'n'},
+        {"naive-force",no_argument,NULL,7},
+        {"compact-PS",no_argument,NULL,'c'},
+        {"regions",required_argument,NULL,'r'},
+        {"regions-file",required_argument,NULL,'R'},
+        {"regions-overlap",required_argument,NULL,12},
+        {"remove-duplicates",no_argument,NULL,'D'},
+        {"rm-dups",required_argument,NULL,'d'},
+        {"allow-overlaps",no_argument,NULL,'a'},
+        {"ligate",no_argument,NULL,'l'},
+        {"ligate-force",no_argument,NULL,10},
+        {"ligate-warn",no_argument,NULL,11},
+        {"output",required_argument,NULL,'o'},
+        {"output-type",required_argument,NULL,'O'},
+        {"threads",required_argument,NULL,9},
+        {"file-list",required_argument,NULL,'f'},
+        {"min-PQ",required_argument,NULL,'q'},
+        {"no-version",no_argument,NULL,8},
+        {NULL,0,NULL,0}
+    };
+    char *tmp;
+    while ((c = getopt_long(argc, argv, "h:?o:O:f:alq:Dd:r:R:cnv:",loptions,NULL)) >= 0)
+    {
+        switch (c) {
+            case 'c': args->compact_PS = 1; break;
+            case 'r': args->regions_list = optarg; break;
+            case 'R': args->regions_list = optarg; args->regions_is_file = 1; break;
+            case 'd': args->remove_dups = optarg; break;
+            case 'D': args->remove_dups = "exact"; break;
+            case 'q': 
+                args->min_PQ = strtol(optarg,&tmp,10);
+                if ( *tmp ) error("Could not parse argument: --min-PQ %s\n", optarg);
+                break;
+            case 'n': args->naive_concat = 1; break;
+            case 'a': args->allow_overlaps = 1; break;
+            case 'l': args->phased_concat = 1; break;
+            case 'f': args->file_list = optarg; break;
+            case 'o': args->output_fname = optarg; break;
+            case 'O':
+                args->explicit_output_type = 1;
+                switch (optarg[0]) {
+                    case 'b': args->output_type = FT_BCF_GZ; break;
+                    case 'u': args->output_type = FT_BCF; break;
+                    case 'z': args->output_type = FT_VCF_GZ; break;
+                    case 'v': args->output_type = FT_VCF; break;
+                    default:
+                    {
+                        args->clevel = strtol(optarg,&tmp,10);
+                        if ( *tmp || args->clevel<0 || args->clevel>9 ) error("The output type \"%s\" not recognised\n", optarg);
+                    }
+                };
+                if ( optarg[1] )
+                {
+                    args->clevel = strtol(optarg+1,&tmp,10);
+                    if ( *tmp || args->clevel<0 || args->clevel>9 ) error("Could not parse argument: --compression-level %s\n", optarg+1);
+                }
+                break;
+            case 10 : args->ligate_force = 1; break;
+            case 11 : args->ligate_warn  = 1; break;
+            case  9 : args->n_threads = strtol(optarg, 0, 0); break;
+            case  8 : args->record_cmd_line = 0; break;
+            case  7 : args->naive_concat = 1; args->naive_concat_trust_headers = 1; break;
+            case 12 :
+                args->regions_overlap = parse_overlap_option(optarg);
+                if ( args->regions_overlap < 0 ) error("Could not parse: --regions-overlap %s\n",optarg);
+                break;
+            case 'v':
+                      args->verbose = strtol(optarg, 0, 0);
+                      error("Error: currently only --verbose 0 or --verbose 1 is supported\n");
+                      break;
+            case 'h':
+            case '?': usage(args); break;
+            default: error("Unknown argument: %s\n", optarg);
+        }
+    }
+    while ( optind<argc )
+    {
+        args->nfnames++;
+        args->fnames = (char **)realloc(args->fnames,sizeof(char*)*args->nfnames);
+        args->fnames[args->nfnames-1] = strdup(argv[optind]);
+        optind++;
+    }
+    if ( args->ligate_force && args->ligate_warn ) error("The options cannot be combined: --ligate-force and --ligate-warn\n");
+    if ( args->allow_overlaps && args->phased_concat ) error("The options -a and -l should not be combined. Please run with -l only.\n");
+    if ( args->compact_PS && !args->phased_concat ) error("The -c option is intended only with -l\n");
+    if ( args->file_list )
+    {
+        if ( args->nfnames ) error("Cannot combine -l with file names on command line.\n");
+        args->fnames = hts_readlines(args->file_list, &args->nfnames);
+        if ( !args->fnames ) error("Could not read the file: %s\n", args->file_list);
+    }
+    if ( !args->nfnames ) usage(args);
+    if ( args->remove_dups && !args->allow_overlaps ) error("The -D option is supported only with -a\n");
+    if ( args->regions_list && !args->allow_overlaps ) error("The -r/-R option is supported only with -a\n");
+    if ( args->naive_concat )
+    {
+        if ( args->allow_overlaps ) error("The option --naive cannot be combined with --allow-overlaps\n");
+        if ( args->phased_concat ) error("The option --naive cannot be combined with --ligate\n");
+        naive_concat(args);
+        destroy_data(args);
+        free(args);
+        return 0;
+    }
+    init_data(args);
+    concat(args);
+    destroy_data(args);
+    free(args);
+    return 0;
+}
diff --git a/bcftools/vcfconvert.c b/bcftools/vcfconvert.c
new file mode 100644
index 0000000..ce5ed99
--- /dev/null
+++ b/bcftools/vcfconvert.c
@@ -0,0 +1,1677 @@
+/*  vcfconvert.c -- convert between VCF/BCF and related formats.
+
+    Copyright (C) 2013-2021 Genome Research Ltd.
+
+    Author: Petr Danecek <pd3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.  */
+
+#include <stdio.h>
+#include <strings.h>
+#include <unistd.h>
+#include <getopt.h>
+#include <ctype.h>
+#include <string.h>
+#include <errno.h>
+#include <sys/stat.h>
+#include <sys/types.h>
+#include <inttypes.h>
+#include <htslib/faidx.h>
+#include <htslib/vcf.h>
+#include <htslib/bgzf.h>
+#include <htslib/synced_bcf_reader.h>
+#include <htslib/vcfutils.h>
+#include <htslib/kseq.h>
+#include "bcftools.h"
+#include "filter.h"
+#include "convert.h"
+#include "tsv2vcf.h"
+
+// Logic of the filters: include or exclude sites which match the filters?
+#define FLT_INCLUDE 1
+#define FLT_EXCLUDE 2
+
+typedef struct _args_t args_t;
+struct _args_t
+{
+    faidx_t *ref;
+    filter_t *filter;
+    char *filter_str;
+    int filter_logic;   // include or exclude sites which match the filters? One of FLT_INCLUDE/FLT_EXCLUDE
+    convert_t *convert;
+    bcf_srs_t *files;
+    bcf_hdr_t *header;
+    void (*convert_func)(struct _args_t *);
+    struct {
+        int total, skipped, hom_rr, het_ra, hom_aa, het_aa, missing; 
+    } n;
+    kstring_t str;
+    int32_t *gts;
+    float *flt;
+    int rev_als, output_vcf_ids, hap2dip, gen_3N6;
+    int nsamples, *samples, sample_is_file, targets_is_file, regions_is_file, output_type;
+    int regions_overlap, targets_overlap;
+    char **argv, *sample_list, *targets_list, *regions_list, *tag, *columns;
+    char *outfname, *infname, *ref_fname, *sex_fname;
+    int argc, n_threads, record_cmd_line, keep_duplicates, clevel;
+};
+
+static void destroy_data(args_t *args)
+{
+    if ( args->ref ) fai_destroy(args->ref);
+    if ( args->convert) convert_destroy(args->convert);
+    if ( args->filter ) filter_destroy(args->filter);
+    free(args->samples);
+    if ( args->files ) bcf_sr_destroy(args->files);
+}
+
+static void open_vcf(args_t *args, const char *format_str)
+{
+    args->files = bcf_sr_init();
+    if ( args->n_threads && bcf_sr_set_threads(args->files, args->n_threads)!=0 )
+        error("Could not initialize --threads %d\n", args->n_threads);
+
+    if ( args->regions_list )
+    {
+        bcf_sr_set_opt(args->files,BCF_SR_REGIONS_OVERLAP,args->regions_overlap);
+        if ( bcf_sr_set_regions(args->files, args->regions_list, args->regions_is_file)<0 )
+            error("Failed to read the regions: %s\n", args->regions_list);
+    }
+    if ( args->targets_list )
+    {
+        bcf_sr_set_opt(args->files,BCF_SR_TARGETS_OVERLAP,args->targets_overlap);
+        if ( bcf_sr_set_targets(args->files, args->targets_list, args->targets_is_file, 0)<0 )
+            error("Failed to read the targets: %s\n", args->targets_list);
+    }
+    if ( !bcf_sr_add_reader(args->files, args->infname) )
+        error("Failed to open %s: %s\n", args->infname,bcf_sr_strerror(args->files->errnum));
+
+    args->header = args->files->readers[0].header;
+
+    if ( args->filter_str )
+        args->filter = filter_init(args->header, args->filter_str);
+
+    int i, nsamples = 0, *samples = NULL;
+    if ( args->sample_list && strcmp("-",args->sample_list) )
+    {
+        for (i=0; i<args->files->nreaders; i++)
+        {
+            int ret = bcf_hdr_set_samples(args->files->readers[i].header,args->sample_list,args->sample_is_file);
+            if ( ret<0 ) error("Error parsing the sample list\n");
+            else if ( ret>0 ) error("Sample name mismatch: sample #%d not found in the header\n", ret);
+        }
+
+        if ( args->sample_list[0]!='^' )
+        {
+            // the sample ordering may be different if not negated
+            int n;
+            char **smpls = hts_readlist(args->sample_list, args->sample_is_file, &n);
+            if ( !smpls ) error("Could not parse %s\n", args->sample_list);
+            if ( n!=bcf_hdr_nsamples(args->files->readers[0].header) )
+                error("The number of samples does not match, perhaps some are present multiple times?\n");
+            nsamples = bcf_hdr_nsamples(args->files->readers[0].header);
+            samples = (int*) malloc(sizeof(int)*nsamples);
+            for (i=0; i<n; i++)
+            {
+                samples[i] = bcf_hdr_id2int(args->files->readers[0].header, BCF_DT_SAMPLE,smpls[i]);
+                free(smpls[i]);
+            }
+            free(smpls);
+        }
+    }
+    if ( format_str ) args->convert = convert_init(args->header, samples, nsamples, format_str);
+    free(samples);
+}
+
+// Try to set CHROM:POS_REF_ALT[_END]. Return 0 on success, -1 on error
+static int _set_chrom_pos_ref_alt(tsv_t *tsv, bcf1_t *rec, void *usr)
+{
+    args_t *args = (args_t*) usr;
+
+    char tmp, *se = tsv->ss, *ss = tsv->ss;
+    while ( se < tsv->se && *se!=':' ) se++;
+    if ( *se!=':' ) return -1;
+    tmp = *se; *se = 0;
+    int rid = bcf_hdr_name2id(args->header,ss);
+    *se = tmp;
+    if ( rid<0 ) return -1;
+
+    // POS
+    hts_pos_t pos = strtol(se+1,&ss,10);
+    if ( ss==se+1 ) return -1;
+    pos--;
+
+    // REF,ALT
+    args->str.l = 0;
+    se = ++ss;
+    while ( se < tsv->se && *se!='_' ) se++; 
+    if ( *se!='_' ) return -1;
+    kputsn(ss,se-ss,&args->str);
+    ss = ++se;
+    while ( se < tsv->se && *se!='_' && isspace(*tsv->se) ) se++;
+    if ( se < tsv->se && *se!='_' && isspace(*tsv->se) ) return -1;
+    kputc(',',&args->str);
+    kputsn(ss,se-ss,&args->str);
+
+    // END - optional
+    if (*se && *se=='_')
+    {
+        long end = strtol(se+1,&ss,10);
+        if ( ss==se+1 ) return -1;
+        bcf_update_info_int32(args->header, rec, "END", &end, 1);
+    }
+
+    rec->rid = rid;
+    rec->pos = pos;
+    bcf_update_alleles_str(args->header, rec, args->str.s);
+
+    return 0;
+}
+static int tsv_setter_chrom_pos_ref_alt_or_chrom(tsv_t *tsv, bcf1_t *rec, void *usr)
+{
+    args_t *args = (args_t*)usr;
+    int ret = _set_chrom_pos_ref_alt(tsv,rec,usr);
+    if ( !ret ) return ret;
+    return tsv_setter_chrom(tsv,rec,args->header);
+}
+static int tsv_setter_chrom_pos_ref_alt(tsv_t *tsv, bcf1_t *rec, void *usr)
+{
+    int ret = _set_chrom_pos_ref_alt(tsv,rec,usr);
+    if ( ret!=0 ) error("Could not parse the CHROM:POS_REF_ALT[_END] string: %s\n", tsv->ss);
+    return ret;
+}
+// This function must be called first, then tsv_setter_chrom_pos_ref_alt_id_or_die.
+// One of them is expected to find the CHROM:POS_REF_ALT[_END] string, if not, die.
+static int tsv_setter_chrom_pos_ref_alt_or_id(tsv_t *tsv, bcf1_t *rec, void *usr)
+{
+    args_t *args = (args_t*)usr;
+    if ( _set_chrom_pos_ref_alt(tsv,rec,usr)==0 )  return 0;
+    rec->pos = -1;  // mark the record as unset
+    if ( !args->output_vcf_ids) return 0;
+    return tsv_setter_id(tsv,rec,usr);
+}
+static int tsv_setter_chrom_pos_ref_alt_id_or_die(tsv_t *tsv, bcf1_t *rec, void *usr)
+{
+    args_t *args = (args_t*)usr;
+    if ( rec->pos!=-1 )
+    {
+        if ( !args->output_vcf_ids ) return 0;
+        return tsv_setter_id(tsv,rec,usr);
+    }
+    return tsv_setter_chrom_pos_ref_alt(tsv,rec,usr);
+}
+static int tsv_setter_verify_pos(tsv_t *tsv, bcf1_t *rec, void *usr)
+{
+    char *se;
+    int pos = strtol(tsv->ss,&se,10);
+    if ( tsv->ss==se ) error("Could not parse POS: %s\n", tsv->ss);
+    if ( rec->pos != pos-1 ) error("POS mismatch: %s\n", tsv->ss);
+    return 0;
+}
+static int tsv_setter_verify_ref_alt(tsv_t *tsv, bcf1_t *rec, void *usr)
+{
+    args_t *args = (args_t*) usr;
+    args->rev_als = 0;
+    char tmp = *tsv->se; *tsv->se = 0;
+    if ( strcmp(tsv->ss,rec->d.allele[0]) )
+    {
+        if ( strcmp(tsv->ss,rec->d.allele[1]) ) { *tsv->se = tmp; error("REF/ALT mismatch: [%s][%s]\n", tsv->ss,rec->d.allele[1]); }
+        args->rev_als = 1;
+    }
+    *tsv->se = tmp;
+    while ( *tsv->se && isspace(*tsv->se) ) tsv->se++;
+    tsv->ss = tsv->se;
+    while ( *tsv->se && !isspace(*tsv->se) ) tsv->se++;
+    tmp = *tsv->se; *tsv->se = 0;
+    if ( !args->rev_als && strcmp(tsv->ss,rec->d.allele[1]) ) { *tsv->se = tmp; error("REF/ALT mismatch: [%s][%s]\n", tsv->ss,rec->d.allele[1]); }
+    else if ( args->rev_als && strcmp(tsv->ss,rec->d.allele[0]) ) { *tsv->se = tmp; error("REF/ALT mismatch: [%s][%s]\n", tsv->ss,rec->d.allele[0]); }
+    *tsv->se = tmp;
+    return 0;
+}
+static int tsv_setter_gt_gp(tsv_t *tsv, bcf1_t *rec, void *usr)
+{
+    args_t *args = (args_t*) usr;
+    int i, nsamples = bcf_hdr_nsamples(args->header);
+    for (i=0; i<nsamples; i++)
+    {
+        float aa,ab,bb;
+        aa = strtod(tsv->ss, &tsv->se);
+        if ( tsv->ss==tsv->se ) { fprintf(stderr,"Could not parse first value of %d-th sample\n", i+1); return -1; }
+        tsv->ss = tsv->se+1;
+        ab = strtod(tsv->ss, &tsv->se);
+        if ( tsv->ss==tsv->se ) { fprintf(stderr,"Could not parse second value of %d-th sample\n", i+1); return -1; }
+        tsv->ss = tsv->se+1;
+        bb = strtod(tsv->ss, &tsv->se);
+        if ( tsv->ss==tsv->se ) { fprintf(stderr,"Could not parse third value of %d-th sample\n", i+1); return -1; }
+        tsv->ss = tsv->se+1;
+
+        if ( args->rev_als ) { float tmp = bb; bb = aa; aa = tmp; }
+        args->flt[3*i+0] = aa;
+        args->flt[3*i+1] = ab;
+        args->flt[3*i+2] = bb;
+
+        if ( aa >= ab )
+        {
+            if ( aa >= bb ) args->gts[2*i+0] = args->gts[2*i+1] = bcf_gt_unphased(0);
+            else args->gts[2*i+0] = args->gts[2*i+1] = bcf_gt_unphased(1); 
+        }
+        else if ( ab >= bb ) 
+        {
+            args->gts[2*i+0] = bcf_gt_unphased(0);
+            args->gts[2*i+1] = bcf_gt_unphased(1); 
+        }
+        else args->gts[2*i+0] = args->gts[2*i+1] = bcf_gt_unphased(1);
+    }
+    if ( *tsv->se ) error("Could not parse: %s\n", tsv->ss);
+    if ( bcf_update_genotypes(args->header,rec,args->gts,nsamples*2) ) error("Could not update GT field\n");
+    if ( bcf_update_format_float(args->header,rec,"GP",args->flt,nsamples*3) ) error("Could not update GP field\n");
+    return 0;
+}
+static int tsv_setter_haps(tsv_t *tsv, bcf1_t *rec, void *usr)
+{
+    args_t *args = (args_t*) usr;
+    int i, nsamples = bcf_hdr_nsamples(args->header);
+
+    int32_t a0, a1;
+    if ( args->rev_als ) { a0 = bcf_gt_phased(1); a1 = bcf_gt_phased(0); }
+    else { a0 = bcf_gt_phased(0); a1 = bcf_gt_phased(1); }
+
+    // up is short for "unphased"
+    int nup = 0; 
+    for (i=0; i<nsamples; i++)
+    {
+        char *ss = tsv->ss + 4*i + nup;
+        int up = 0, all;
+
+        for (all=0; all < 2; all++){
+            // checking for premature ending
+            if ( !ss[0] || !ss[1] || !ss[2] ||
+                 (up && (!ss[3] || !ss[4]) ) )
+            {
+                fprintf(stderr,"Wrong number of fields at %d-th sample ([%c][%c][%c]). ",i+1,ss[0],ss[1],ss[2]);
+                return -1;
+            }
+
+            switch(ss[all*2+up]){
+            case '0':
+                args->gts[2*i+all] = a0;
+                break;
+            case '1' :
+                args->gts[2*i+all] = a1;
+                break;
+            case '?' :
+                // there is no macro to express phased missing allele
+                args->gts[2*i+all] = bcf_gt_phased(-1);
+                break;
+            case '-' :
+                args->gts[2*i+all] = bcf_int32_vector_end;
+                break;
+            default :
+                fprintf(stderr,"Could not parse: [%c][%s]\n", ss[all*2+up],tsv->ss);
+                return -1; 
+            }
+            if( ss[all*2+up+1]=='*' ) up = up + 1;
+        }
+        
+        if(up && up != 2)
+        {
+            fprintf(stderr,"Missing unphased marker '*': [%c][%s]", ss[2+up], tsv->ss);
+            return -1;
+        }
+
+        // change alleles to unphased if the alleles are unphased
+        if ( up )
+        {
+            args->gts[2*i] = bcf_gt_unphased(bcf_gt_allele(args->gts[2*i]));
+            args->gts[2*i+1] = bcf_gt_unphased(bcf_gt_allele(args->gts[2*i+1]));
+        }
+        nup = nup + up;
+    }
+    if ( tsv->ss[(nsamples-1)*4+3+nup] )
+    {
+        fprintf(stderr,"nup: %d", nup);
+        fprintf(stderr,"Wrong number of fields (%d-th column = [%c]). ", nsamples*2,tsv->ss[(nsamples-1)*4+nup]);
+        return -1;
+    }
+
+    if ( bcf_update_genotypes(args->header,rec,args->gts,nsamples*2) ) error("Could not update GT field\n");
+    return 0;
+}
+static void gensample_to_vcf(args_t *args)
+{
+    /*
+     *  Inpute: IMPUTE2 output (indentation changed here for clarity): 
+     *
+     *      20:62116619_C_T 20:62116619     62116619 C T 0.969 0.031 0 ...
+     *      ---             20:62116698_C_A 62116698 C A 1     0     0 ...
+     *
+     *  Second column is expected in the form of CHROM:POS_REF_ALT. We use second
+     *  column because the first can be empty ("--") when filling sites from reference 
+     *  panel. When the option --vcf-ids is given, the first column is used to set the
+     *  VCF ID.
+     *
+     *  Output: VCF with filled GT,GP
+     *
+     */
+    kstring_t line = {0,0,0};
+
+    char *gen_fname = NULL, *sample_fname = NULL;
+    sample_fname = strchr(args->infname,',');
+    if ( !sample_fname )
+    {
+        args->str.l = 0;
+        ksprintf(&args->str,"%s.gen.gz", args->infname);
+        gen_fname = strdup(args->str.s);
+        args->str.l = 0;
+        ksprintf(&args->str,"%s.samples", args->infname);
+        sample_fname = strdup(args->str.s);
+    }
+    else
+    {
+        *sample_fname = 0;
+        gen_fname = strdup(args->infname);
+        sample_fname = strdup(sample_fname+1);
+    }
+    htsFile *gen_fh = hts_open(gen_fname, "r");
+    if ( !gen_fh ) error("Could not read: %s\n", gen_fname);
+    if ( hts_getline(gen_fh, KS_SEP_LINE, &line) <= 0 ) error("Empty file: %s\n", gen_fname);
+
+    // Find out the chromosome name, depending on the format variant (--3N6 or plain) and the ordering
+    // of the columns (CHROM:POS_REF_ALT comes first or second)
+    args->str.l = 0;
+    char *sb = line.s, *se = line.s;
+    while ( *se && !isspace(*se) ) se++;
+    if ( !*se ) error("Could not determine CHROM in %s: %s\n", gen_fname,line.s);
+    if ( args->gen_3N6 )    // first column, just CHROM
+        kputsn(sb, se-sb, &args->str);
+    else                    // first or second column, part of CHROM:POS_REF_ALT
+    {
+        char *sc = strchr(sb,':');
+        if ( !sc || sc > se )
+        {
+            while ( *se && !isspace(*se) ) se++;
+            if ( !*se ) error("Could not determine CHROM in %s: %s\n", gen_fname,line.s);
+            sb = ++se;
+            sc = strchr(sb,':');
+            if ( !sc ) error("Could not determine CHROM in %s: %s\n", gen_fname,line.s);
+        }
+        kputsn(sb, sc-sb, &args->str);
+    }
+
+    // Initialize and print the VCF header, args->str.s contains the chr name
+    args->header = bcf_hdr_init("w");
+    bcf_hdr_append(args->header, "##INFO=<ID=END,Number=1,Type=Integer,Description=\"End position of the variant described in this record\">");
+    bcf_hdr_append(args->header, "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">");
+    bcf_hdr_append(args->header, "##FORMAT=<ID=GP,Number=G,Type=Float,Description=\"Genotype Probabilities\">");
+    bcf_hdr_printf(args->header, "##contig=<ID=%s,length=%d>", args->str.s,0x7fffffff);   // MAX_CSI_COOR
+    if (args->record_cmd_line) bcf_hdr_append_version(args->header, args->argc, args->argv, "bcftools_convert");
+
+    tsv_t *tsv;
+    if ( args->gen_3N6 )
+    {
+        tsv = tsv_init("CHROM,CHROM_POS_REF_ALT,ID,POS,REF_ALT,GT_GP");
+        tsv_register(tsv, "CHROM", tsv_setter_chrom, args->header);
+    }
+    else
+        tsv = tsv_init("CHROM_POS_REF_ALT,ID,POS,REF_ALT,GT_GP");
+    tsv_register(tsv, "CHROM_POS_REF_ALT", tsv_setter_chrom_pos_ref_alt_or_id, args);
+    tsv_register(tsv, "ID", tsv_setter_chrom_pos_ref_alt_id_or_die, args);
+    tsv_register(tsv, "POS", tsv_setter_verify_pos, NULL);
+    tsv_register(tsv, "REF_ALT", tsv_setter_verify_ref_alt, args);
+    tsv_register(tsv, "GT_GP", tsv_setter_gt_gp, args);
+
+    // Find out sample names
+    int i, nsamples;
+    char **samples = hts_readlist(sample_fname, 1, &nsamples);
+    if ( !samples ) error("Could not read %s\n", sample_fname);
+    for (i=2; i<nsamples; i++)
+    {
+        se = samples[i]; while ( *se && !isspace(*se) ) se++;
+        *se = 0;
+        bcf_hdr_add_sample(args->header,samples[i]);
+    }
+    for (i=0; i<nsamples; i++) free(samples[i]);
+    free(samples);
+
+    char wmode[8];
+    set_wmode(wmode,args->output_type,args->outfname,args->clevel);
+    htsFile *out_fh = hts_open(args->outfname ? args->outfname : "-", wmode);
+    if ( out_fh == NULL ) error("Can't write to \"%s\": %s\n", args->outfname, strerror(errno));
+    if ( args->n_threads ) hts_set_threads(out_fh, args->n_threads);
+    if ( bcf_hdr_write(out_fh,args->header)!=0 ) error("[%s] Error: cannot write the header to %s\n", __func__,args->outfname);
+    bcf1_t *rec = bcf_init();
+
+    nsamples -= 2;
+    args->gts = (int32_t *) malloc(sizeof(int32_t)*nsamples*2);
+    args->flt = (float *) malloc(sizeof(float)*nsamples*3);
+
+    do
+    {
+        bcf_clear(rec);
+        args->n.total++;
+        if ( !tsv_parse(tsv, rec, line.s) )
+        {
+            if ( bcf_write(out_fh, args->header, rec)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->outfname);
+        }
+        else
+            error("Error occurred while parsing: %s\n", line.s);
+    }
+    while ( hts_getline(gen_fh, KS_SEP_LINE, &line)>0 );
+
+    if ( hts_close(out_fh) ) error("Close failed: %s\n", args->outfname);
+    if ( hts_close(gen_fh) ) error("Close failed: %s\n", gen_fname);
+    bcf_hdr_destroy(args->header);
+    bcf_destroy(rec);
+    free(sample_fname);
+    free(gen_fname);
+    free(args->str.s);
+    free(line.s);
+    free(args->gts);
+    free(args->flt);
+    tsv_destroy(tsv);
+
+    fprintf(stderr,"Number of processed rows: \t%d\n", args->n.total);
+}
+
+static void haplegendsample_to_vcf(args_t *args)
+{
+    /*
+     *  Convert from IMPUTE2 hap/legend/sample output files to VCF
+     *
+     *      hap:
+     *          0 1 0 1
+     *      legend:
+     *          id position a0 a1
+     *          1:186946386_G_T 186946386 G T
+     *      sample:
+     *          sample population group sex
+     *          sample1 sample1 sample1 2
+     *          sample2 sample2 sample2 2
+     *
+     *  Output: VCF with filled GT
+     */
+    kstring_t line = {0,0,0};
+
+    if ( args->output_vcf_ids )
+        error(
+            "The option --haplegendsample2vcf cannot be combined with --vcf-ids. This is because the\n"
+            "ID column must be formatted as \"CHROM:POS_REF_ALT\" to check sanity of the operation\n");
+
+    char *hap_fname = NULL, *leg_fname = NULL, *sample_fname = NULL;
+    sample_fname = strchr(args->infname,',');
+    if ( !sample_fname )
+    {
+        args->str.l = 0;
+        ksprintf(&args->str,"%s.hap.gz", args->infname);
+        hap_fname = strdup(args->str.s);
+        args->str.l = 0;
+        ksprintf(&args->str,"%s.samples", args->infname);
+        sample_fname = strdup(args->str.s);
+        args->str.l = 0;
+        ksprintf(&args->str,"%s.legend.gz", args->infname);
+        leg_fname = strdup(args->str.s);
+    }
+    else
+    {
+        char *ss = sample_fname, *se = strchr(ss+1,',');
+        if ( !se ) error("Could not parse hap/legend/sample file names: %s\n", args->infname);
+        *ss = 0;
+        *se = 0;
+        hap_fname = strdup(args->infname);
+        leg_fname = strdup(ss+1);
+        sample_fname = strdup(se+1);
+    }
+    htsFile *hap_fh = hts_open(hap_fname, "r");
+    if ( !hap_fh ) error("Could not read: %s\n", hap_fname);
+
+    htsFile *leg_fh = hts_open(leg_fname,"r");
+    if ( !leg_fh ) error("Could not read: %s\n", leg_fname);
+
+    // Eat up first legend line, then determine chromosome name
+    if ( hts_getline(leg_fh, KS_SEP_LINE, &line) <= 0 ) error("Empty file: %s\n", leg_fname);
+    if ( hts_getline(leg_fh, KS_SEP_LINE, &line) <= 0 ) error("Empty file: %s\n", leg_fname);
+
+    // Find out the chromosome name, sample names, init and print the VCF header
+    args->str.l = 0;
+    char *se = strchr(line.s,':');
+    if ( !se ) error("Expected CHROM:POS_REF_ALT in first column of %s\n", leg_fname);
+    kputsn(line.s, se-line.s, &args->str);
+
+    tsv_t *leg_tsv = tsv_init("CHROM_POS_REF_ALT,POS,REF_ALT");
+    tsv_register(leg_tsv, "CHROM_POS_REF_ALT", tsv_setter_chrom_pos_ref_alt, args);
+    tsv_register(leg_tsv, "POS", tsv_setter_verify_pos, NULL);
+    tsv_register(leg_tsv, "REF_ALT", tsv_setter_verify_ref_alt, args);
+    tsv_t *hap_tsv = tsv_init("HAPS");
+    tsv_register(hap_tsv, "HAPS", tsv_setter_haps, args);
+
+    args->header = bcf_hdr_init("w");
+    bcf_hdr_append(args->header, "##INFO=<ID=END,Number=1,Type=Integer,Description=\"End position of the variant described in this record\">");
+    bcf_hdr_append(args->header, "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">");
+    bcf_hdr_printf(args->header, "##contig=<ID=%s,length=%d>", args->str.s,0x7fffffff);   // MAX_CSI_COOR
+    if (args->record_cmd_line) bcf_hdr_append_version(args->header, args->argc, args->argv, "bcftools_convert");
+
+    int i, nrows, nsamples;
+    char **samples = hts_readlist(sample_fname, 1, &nrows);
+    if ( !samples ) error("Could not read %s\n", sample_fname);
+    nsamples = nrows - 1;
+
+    // sample_fname should contain a header line, so need to ignore first row
+    // returned from hts_readlist (i=1, and not i=0)
+    for (i=1; i<nrows; i++)
+    {
+        se = samples[i]; while ( *se && !isspace(*se) ) se++;
+        *se = 0;
+        bcf_hdr_add_sample(args->header,samples[i]);
+    }
+    bcf_hdr_add_sample(args->header,NULL);
+    for (i=0; i<nrows; i++) free(samples[i]);
+    free(samples);
+
+    char wmode[8];
+    set_wmode(wmode,args->output_type,args->outfname,args->clevel);
+    htsFile *out_fh = hts_open(args->outfname ? args->outfname : "-", wmode);
+    if ( out_fh == NULL ) error("Can't write to \"%s\": %s\n", args->outfname, strerror(errno));
+    if ( args->n_threads ) hts_set_threads(out_fh, args->n_threads);
+    if ( bcf_hdr_write(out_fh,args->header)!=0 ) error("[%s] Error: cannot write the header to %s\n", __func__,args->outfname);
+    bcf1_t *rec = bcf_init();
+
+    args->gts = (int32_t *) malloc(sizeof(int32_t)*nsamples*2);
+
+    while (1)
+    {
+        bcf_clear(rec);
+        args->n.total++;
+        if ( tsv_parse(leg_tsv, rec, line.s) )
+            error("Error occurred while parsing %s: %s\n", leg_fname,line.s);
+
+        if ( hts_getline(hap_fh,  KS_SEP_LINE, &line)<=0 )
+            error("Different number of records in %s and %s?\n", leg_fname,hap_fname);
+
+        if ( tsv_parse(hap_tsv, rec, line.s) )
+            error("Error occurred while parsing %s: %s\n", hap_fname,line.s);
+
+        if ( bcf_write(out_fh, args->header, rec)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->outfname);
+
+        if ( hts_getline(leg_fh, KS_SEP_LINE, &line)<=0 )
+        {
+            if ( hts_getline(hap_fh, KS_SEP_LINE, &line)>0 )
+                error("Different number of records in %s and %s?\n", leg_fname,hap_fname);
+            break;
+        }
+    }
+
+    if ( hts_close(out_fh) ) error("Close failed: %s\n", args->outfname);
+    if ( hts_close(hap_fh) ) error("Close failed: %s\n", hap_fname);
+    if ( hts_close(leg_fh) ) error("Close failed: %s\n", leg_fname);
+    bcf_hdr_destroy(args->header);
+    bcf_destroy(rec);
+    free(sample_fname);
+    free(hap_fname);
+    free(leg_fname);
+    free(args->str.s);
+    free(line.s);
+    free(args->gts);
+    tsv_destroy(hap_tsv);
+    tsv_destroy(leg_tsv);
+
+    fprintf(stderr,"Number of processed rows: \t%d\n", args->n.total);
+}
+
+static void hapsample_to_vcf(args_t *args)
+{
+    /*
+     *  Input: SHAPEIT output
+     *
+     *      20:19995888_A_G rsid1 19995888 A G 0 0 0 0 ...
+     *      20 20:19995888_A_G 19995888 A G 0 0 0 0 ...
+     *
+     *  First column is expected in the form of CHROM:POS_REF_ALT
+     *
+     *  Output: VCF with filled GT
+     *
+     */
+    kstring_t line = {0,0,0};
+
+    char *hap_fname = NULL, *sample_fname = NULL;
+    sample_fname = strchr(args->infname,',');
+    if ( !sample_fname )
+    {
+        args->str.l = 0;
+        ksprintf(&args->str,"%s.hap.gz", args->infname);
+        hap_fname = strdup(args->str.s);
+        args->str.l = 0;
+        ksprintf(&args->str,"%s.samples", args->infname);
+        sample_fname = strdup(args->str.s);
+    }
+    else
+    {
+        *sample_fname = 0;
+        hap_fname = strdup(args->infname);
+        sample_fname = strdup(sample_fname+1);
+    }
+    htsFile *hap_fh = hts_open(hap_fname, "r");
+    if ( !hap_fh ) error("Could not read: %s\n", hap_fname);
+    if ( hts_getline(hap_fh, KS_SEP_LINE, &line) <= 0 ) error("Empty file: %s\n", hap_fname);
+
+    // Find out the chromosome name, it can be either in the first or second column
+    args->str.l = 0;
+    char *sb = line.s, *se = line.s;
+    while ( *se && !isspace(*se) ) se++;
+    if ( !*se ) error("Could not determine CHROM in %s: %s\n", hap_fname,line.s);
+    if ( !args->output_vcf_ids )
+    {
+        // first column should be just CHROM, but the second must be CHROM:POS_REF_ALT, use that
+        sb = ++se;
+        while ( *se && !isspace(*se) ) se++;
+        if ( !*se ) error("Could not determine CHROM in %s: %s\n", hap_fname,line.s);
+        if ( !strchr(sb,':') )
+            error("Could not determine CHROM in the second column of %s: %s\n", hap_fname,line.s);
+    }
+    // Parse CHROM:POS_REF_ALT
+    char *sc = strchr(sb,':');
+    if ( !sc || sc > se )
+        error("Could not determine CHROM in %s: %s\n", hap_fname,line.s);
+    kputsn(sb, sc-sb, &args->str);
+
+    // Initialize and print the VCF header, args->str.s contains the chr name
+    args->header = bcf_hdr_init("w");
+    bcf_hdr_append(args->header, "##INFO=<ID=END,Number=1,Type=Integer,Description=\"End position of the variant described in this record\">");
+    bcf_hdr_append(args->header, "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">");
+    bcf_hdr_printf(args->header, "##contig=<ID=%s,length=%d>", args->str.s,0x7fffffff);   // MAX_CSI_COOR
+    if (args->record_cmd_line) bcf_hdr_append_version(args->header, args->argc, args->argv, "bcftools_convert");
+
+    tsv_t *tsv;
+    if ( args->output_vcf_ids )
+    {
+        tsv = tsv_init("CHROM_POS_REF_ALT,ID,POS,REF_ALT,HAPS");
+        tsv_register(tsv, "ID", tsv_setter_id, args);
+    }
+    else
+    {
+        tsv = tsv_init("CHROM,CHROM_POS_REF_ALT,POS,REF_ALT,HAPS");
+        tsv_register(tsv, "CHROM", tsv_setter_chrom_pos_ref_alt_or_chrom, args);
+    }
+    tsv_register(tsv, "CHROM_POS_REF_ALT", tsv_setter_chrom_pos_ref_alt, args);
+    tsv_register(tsv, "POS", tsv_setter_verify_pos, NULL);
+    tsv_register(tsv, "REF_ALT", tsv_setter_verify_ref_alt, args);
+    tsv_register(tsv, "HAPS", tsv_setter_haps, args);
+
+    int i, nsamples;
+    char **samples = hts_readlist(sample_fname, 1, &nsamples);
+    if ( !samples ) error("Could not read %s\n", sample_fname);
+    for (i=2; i<nsamples; i++)
+    {
+        se = samples[i]; while ( *se && !isspace(*se) ) se++;
+        *se = 0;
+        bcf_hdr_add_sample(args->header,samples[i]);
+    }
+    bcf_hdr_add_sample(args->header,NULL);
+    for (i=0; i<nsamples; i++) free(samples[i]);
+    free(samples);
+
+    char wmode[8];
+    set_wmode(wmode,args->output_type,args->outfname,args->clevel);
+    htsFile *out_fh = hts_open(args->outfname ? args->outfname : "-", wmode);
+    if ( out_fh == NULL ) error("Can't write to \"%s\": %s\n", args->outfname, strerror(errno));
+    if ( args->n_threads ) hts_set_threads(out_fh, args->n_threads);
+    if ( bcf_hdr_write(out_fh,args->header)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->outfname);
+    bcf1_t *rec = bcf_init();
+
+    nsamples -= 2;
+    args->gts = (int32_t *) malloc(sizeof(int32_t)*nsamples*2);
+
+    do
+    {
+        bcf_clear(rec);
+        args->n.total++;
+        if ( !tsv_parse(tsv, rec, line.s) )
+        {
+            if ( bcf_write(out_fh, args->header, rec)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->outfname);
+        }
+        else
+            error("Error occurred while parsing: %s\n", line.s);
+    }
+    while ( hts_getline(hap_fh, KS_SEP_LINE, &line)>0 );
+
+    if ( hts_close(out_fh) ) error("Close failed: %s\n", args->outfname);
+    if ( hts_close(hap_fh) ) error("Close failed: %s\n", hap_fname);
+    bcf_hdr_destroy(args->header);
+    bcf_destroy(rec);
+    free(sample_fname);
+    free(hap_fname);
+    free(args->str.s);
+    free(line.s);
+    free(args->gts);
+    tsv_destroy(tsv);
+
+    fprintf(stderr,"Number of processed rows: \t%d\n", args->n.total);
+}
+
+char *init_sample2sex(bcf_hdr_t *hdr, char *sex_fname)
+{
+    int i, nlines;
+    char *sample2sex = (char*) calloc(bcf_hdr_nsamples(hdr),1);
+    char **lines = hts_readlist(sex_fname, 1, &nlines);
+    if ( !lines ) error("Could not read %s\n", sex_fname);
+    for (i=0; i<nlines; i++)
+    {
+        char *se = lines[i]; while ( *se && !isspace(*se) ) se++;
+        char tmp = *se;
+        *se = 0;
+        int id = bcf_hdr_id2int(hdr, BCF_DT_SAMPLE, lines[i]);
+        *se = tmp;
+        if ( id<0 ) continue;
+        while ( *se && isspace(*se) ) se++;
+        if ( *se=='M' ) sample2sex[id] = '1';
+        else if ( *se=='F' ) sample2sex[id] = '2';
+        else error("Could not parse %s: %s\n", sex_fname,lines[i]);
+    }
+    for (i=0; i<nlines; i++) free(lines[i]);
+    free(lines);
+    for (i=0; i<bcf_hdr_nsamples(hdr); i++) 
+        if ( !sample2sex[i] ) error("Missing sex for sample %s in %s\n", bcf_hdr_int2id(hdr, BCF_DT_SAMPLE, i),sex_fname);
+    return sample2sex;
+}
+
+static void vcf_to_gensample(args_t *args)
+{
+    kstring_t str = {0,0,0};
+
+    // insert chrom as first column if needed
+    if ( args->gen_3N6 )
+        kputs("%CHROM ", &str);
+
+    kputs("%CHROM:%POS\\_%REF\\_%FIRST_ALT ", &str);
+
+    // insert rsid as second column if needed
+    if ( args->output_vcf_ids )
+        kputs("%ID ", &str);
+    else
+        kputs("%CHROM:%POS\\_%REF\\_%FIRST_ALT ", &str);
+
+    kputs("%POS %REF %FIRST_ALT", &str);
+    if ( !args->tag || !strcmp(args->tag,"GT") ) kputs("%_GT_TO_PROB3",&str);
+    else if ( !strcmp(args->tag,"PL") ) kputs("%_PL_TO_PROB3",&str);
+    else if ( !strcmp(args->tag,"GP") ) kputs("%_GP_TO_PROB3",&str);
+    else error("todo: --tag %s\n", args->tag);
+    kputs("\n", &str);
+    open_vcf(args,str.s);
+
+    int ret, gen_compressed = 1, sample_compressed = 0;
+    char *gen_fname = NULL, *sample_fname = NULL;
+    str.l = 0;
+    kputs(args->outfname,&str);
+    int n_files = 0, i;
+    char **files = hts_readlist(str.s, 0, &n_files);
+    if ( n_files==1 )
+    {
+        int l = str.l;
+        kputs(".samples",&str);
+        sample_fname = strdup(str.s);
+        str.l = l;
+        kputs(".gen.gz",&str);
+        gen_fname = strdup(str.s);
+    }
+    else if ( n_files==2 )
+    {
+        if (strlen(files[0]) && strcmp(files[0],".")!=0) gen_fname = strdup(files[0]);
+        if (strlen(files[1]) && strcmp(files[1],".")!=0) sample_fname = strdup(files[1]);
+    }
+    else
+    {
+        error("Error parsing --gensample filenames: %s\n", args->outfname);
+    }
+    for (i=0; i<n_files; i++) free(files[i]);
+    free(files);
+
+    if ( gen_fname && (strlen(gen_fname)<3 || strcasecmp(".gz",gen_fname+strlen(gen_fname)-3)) ) gen_compressed = 0;
+    if ( sample_fname && strlen(sample_fname)>3 && strcasecmp(".gz",sample_fname+strlen(sample_fname)-3)==0 ) sample_compressed = 0;
+
+    if (gen_fname) fprintf(stderr, "Gen file: %s\n", gen_fname);
+    if (sample_fname) fprintf(stderr, "Sample file: %s\n", sample_fname);
+
+    // write samples file
+    if (sample_fname) 
+    {
+        char *sample2sex = NULL;
+        if ( args->sex_fname ) sample2sex = init_sample2sex(args->header,args->sex_fname);
+
+        int i;
+        BGZF *sout = bgzf_open(sample_fname, sample_compressed ? "wg" : "wu");
+        str.l = 0;
+        kputs(sample2sex ? "ID_1 ID_2 missing sex\n0 0 0 0\n" : "ID_1 ID_2 missing\n0 0 0\n", &str);
+        ret = bgzf_write(sout, str.s, str.l);
+        if ( ret != str.l ) error("Error writing %s: %s\n", sample_fname, strerror(errno));
+        for (i=0; i<bcf_hdr_nsamples(args->header); i++)
+        {
+            str.l = 0;
+            if ( sample2sex )
+                ksprintf(&str, "%s %s 0 %c\n", args->header->samples[i],args->header->samples[i],sample2sex[i]);
+            else
+                ksprintf(&str, "%s %s 0\n", args->header->samples[i],args->header->samples[i]);
+            ret = bgzf_write(sout, str.s, str.l);
+            if ( ret != str.l ) error("Error writing %s: %s\n", sample_fname, strerror(errno));
+        }
+        if ( bgzf_close(sout)!=0 ) error("Error closing %s: %s\n", sample_fname, strerror(errno));
+        free(sample_fname);
+        free(sample2sex);
+    }
+    if (!gen_fname) {
+        if ( str.m ) free(str.s);
+        return;
+    }
+
+    int prev_rid = -1, prev_pos = -1;
+    int no_alt = 0, non_biallelic = 0, filtered = 0, ndup = 0, nok = 0;
+    BGZF *gout = bgzf_open(gen_fname, gen_compressed ? "wg" : "wu");
+    while ( bcf_sr_next_line(args->files) )
+    {
+        bcf1_t *line = bcf_sr_get_line(args->files,0);
+        if ( args->filter )
+        {
+            int pass = filter_test(args->filter, line, NULL);
+            if ( args->filter_logic & FLT_EXCLUDE ) pass = pass ? 0 : 1;
+            if ( !pass ) { filtered++; continue; }
+        }
+
+        // ALT allele is required
+        if ( line->n_allele<2 ) { no_alt++; continue; }
+
+        // biallelic required
+        if ( line->n_allele>2 ) {
+            if (!non_biallelic)
+                fprintf(stderr, "Warning: non-biallelic records are skipped. Consider splitting multi-allelic records into biallelic records using 'bcftools norm -m-'.\n");
+            non_biallelic++;
+            continue;
+        }
+
+        // skip duplicate lines, or otherwise shapeit complains
+        if ( !args->keep_duplicates && prev_rid==line->rid && prev_pos==line->pos ) { ndup++; continue; }
+        prev_rid = line->rid;
+        prev_pos = line->pos;
+
+        str.l = 0;
+        convert_line(args->convert, line, &str);
+        if ( str.l )
+        {
+            int ret = bgzf_write(gout, str.s, str.l);
+            if ( ret!= str.l ) error("Error writing %s: %s\n", gen_fname,strerror(errno));
+            nok++;
+        }
+    }
+    fprintf(stderr, "%d records written, %d skipped: %d/%d/%d/%d no-ALT/non-biallelic/filtered/duplicated\n", 
+        nok, no_alt+non_biallelic+filtered+ndup, no_alt, non_biallelic, filtered, ndup);
+
+    if ( str.m ) free(str.s);
+    if ( bgzf_close(gout)!=0 ) error("Error closing %s: %s\n", gen_fname,strerror(errno));
+    free(gen_fname);
+}
+
+static void vcf_to_haplegendsample(args_t *args)
+{
+    kstring_t str = {0,0,0};
+    if ( args->hap2dip )
+        kputs("%_GT_TO_HAP2\n", &str);
+    else
+        kputs("%_GT_TO_HAP\n", &str);
+    open_vcf(args,str.s);
+
+    int ret, hap_compressed = 1, legend_compressed = 1, sample_compressed = 0;
+    char *hap_fname = NULL, *legend_fname = NULL, *sample_fname = NULL;
+    str.l = 0;
+    kputs(args->outfname,&str);
+    int n_files = 0, i;
+    char **files = hts_readlist(str.s, 0, &n_files);
+    if ( n_files==1 )
+    {
+        int l = str.l;
+        kputs(".samples",&str);
+        sample_fname = strdup(str.s);
+        str.l = l;
+        kputs(".legend.gz",&str);
+        legend_fname = strdup(str.s);
+        str.l = l;
+        kputs(".hap.gz",&str);
+        hap_fname = strdup(str.s);
+    }
+    else if ( n_files==3 )
+    {
+        if (strlen(files[0]) && strcmp(files[0],".")!=0) hap_fname = strdup(files[0]);
+        if (strlen(files[1]) && strcmp(files[1],".")!=0) legend_fname = strdup(files[1]);
+        if (strlen(files[2]) && strcmp(files[2],".")!=0) sample_fname = strdup(files[2]);
+    }
+    else
+    {
+        error("Error parsing --hapslegendsample filenames: %s\n", args->outfname);
+    }
+    for (i=0; i<n_files; i++) free(files[i]);
+    free(files);
+
+    if ( hap_fname && (strlen(hap_fname)<3 || strcasecmp(".gz",hap_fname+strlen(hap_fname)-3)) ) hap_compressed = 0;
+    if ( legend_fname && (strlen(legend_fname)<3 || strcasecmp(".gz",legend_fname+strlen(legend_fname)-3)) ) legend_compressed = 0;
+    if ( sample_fname && strlen(sample_fname)>3 && strcasecmp(".gz",sample_fname+strlen(sample_fname)-3)==0 ) sample_compressed = 0;
+
+    if (hap_fname) fprintf(stderr, "Hap file: %s\n", hap_fname);
+    if (legend_fname) fprintf(stderr, "Legend file: %s\n", legend_fname);
+    if (sample_fname) fprintf(stderr, "Sample file: %s\n", sample_fname);
+
+    // write samples file
+    if (sample_fname)
+    {
+        char *sample2sex = NULL;
+        if ( args->sex_fname ) sample2sex = init_sample2sex(args->header,args->sex_fname);
+        
+        int i;
+        BGZF *sout = bgzf_open(sample_fname, sample_compressed ? "wg" : "wu");
+        str.l = 0;
+        kputs("sample population group sex\n", &str);
+        ret = bgzf_write(sout, str.s, str.l);
+        if ( ret != str.l ) error("Error writing %s: %s\n", sample_fname, strerror(errno));
+        for (i=0; i<bcf_hdr_nsamples(args->header); i++)
+        {
+            str.l = 0;
+            ksprintf(&str, "%s %s %s %c\n", args->header->samples[i], args->header->samples[i], args->header->samples[i], sample2sex ? sample2sex[i] : '2');
+            ret = bgzf_write(sout, str.s, str.l);
+            if ( ret != str.l ) error("Error writing %s: %s\n", sample_fname, strerror(errno));
+        }
+        if ( bgzf_close(sout)!=0 ) error("Error closing %s: %s\n", sample_fname, strerror(errno));
+        free(sample_fname);
+        free(sample2sex);
+    }
+    if (!hap_fname && !legend_fname) {
+        if ( str.m ) free(str.s);
+        return;
+    }
+
+    // open haps and legend outputs
+    BGZF *hout = hap_fname ? bgzf_open(hap_fname, hap_compressed ? "wg" : "wu") : NULL;
+    if ( hap_compressed && args->n_threads ) bgzf_thread_pool(hout, args->files->p->pool, args->files->p->qsize);
+    BGZF *lout = legend_fname ? bgzf_open(legend_fname, legend_compressed ? "wg" : "wu") : NULL;
+    if (legend_fname) {
+        str.l = 0;
+        kputs("id position a0 a1\n", &str);
+        ret = bgzf_write(lout, str.s, str.l);
+        if ( ret != str.l ) error("Error writing %s: %s\n", legend_fname, strerror(errno));
+    }
+
+    int no_alt = 0, non_biallelic = 0, filtered = 0, nok = 0;
+    while ( bcf_sr_next_line(args->files) )
+    {
+        bcf1_t *line = bcf_sr_get_line(args->files,0);
+        if ( args->filter )
+        {
+            int pass = filter_test(args->filter, line, NULL);
+            if ( args->filter_logic & FLT_EXCLUDE ) pass = pass ? 0 : 1;
+            if ( !pass ) { filtered++; continue; }
+        }
+
+        // ALT allele is required
+        if ( line->n_allele<2 ) { no_alt++; continue; }
+        // biallelic required
+        if ( line->n_allele>2 ) {
+            if (!non_biallelic)
+                fprintf(stderr, "Warning: non-biallelic records are skipped. Consider splitting multi-allelic records into biallelic records using 'bcftools norm -m-'.\n");
+            non_biallelic++;
+            continue;
+        }
+
+        str.l = 0;
+        convert_line(args->convert, line, &str);
+        if ( !str.l ) continue;
+
+        // write haps file
+        if (hap_fname) {
+            ret = bgzf_write(hout, str.s, str.l); // write hap file
+            if ( ret != str.l ) error("Error writing %s: %s\n", hap_fname, strerror(errno));
+        }
+        if (legend_fname) {
+            str.l = 0;
+            if ( args->output_vcf_ids && (line->d.id[0]!='.' || line->d.id[1]!=0) )
+                ksprintf(&str, "%s %"PRId64" %s %s\n", line->d.id, (int64_t) line->pos+1, line->d.allele[0], line->d.allele[1]);
+            else
+                ksprintf(&str, "%s:%"PRId64"_%s_%s %"PRId64" %s %s\n", bcf_seqname(args->header, line), (int64_t) line->pos+1, line->d.allele[0], line->d.allele[1], (int64_t) line->pos+1, line->d.allele[0], line->d.allele[1]);
+
+            // write legend file
+            ret = bgzf_write(lout, str.s, str.l);
+            if ( ret != str.l ) error("Error writing %s: %s\n", legend_fname, strerror(errno));
+        }
+        nok++;
+    }
+    fprintf(stderr, "%d records written, %d skipped: %d/%d/%d no-ALT/non-biallelic/filtered\n", nok,no_alt+non_biallelic+filtered, no_alt, non_biallelic, filtered);
+    if ( str.m ) free(str.s);
+    if ( hout && bgzf_close(hout)!=0 ) error("Error closing %s: %s\n", hap_fname, strerror(errno));
+    if ( lout && bgzf_close(lout)!=0 ) error("Error closing %s: %s\n", legend_fname, strerror(errno));
+    if (hap_fname) free(hap_fname);
+    if (legend_fname) free(legend_fname);
+}
+
+static void vcf_to_hapsample(args_t *args)
+{
+    /*
+     *  WTCCC style haplotypes file
+     *  see https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html#hapsample
+     *
+     *  These are essentially the haplotypes from the impute2 format with some
+     *  legend info tacked on to the first 5 columns
+     *
+     */
+    kstring_t str = {0,0,0};
+
+    // print ID instead of CHROM:POS_REF_ALT1
+    if ( args->output_vcf_ids )
+        kputs("%CHROM:%POS\\_%REF\\_%FIRST_ALT %ID %POS %REF %FIRST_ALT ", &str);
+    else
+        kputs("%CHROM %CHROM:%POS\\_%REF\\_%FIRST_ALT %POS %REF %FIRST_ALT ", &str);
+    
+    if ( args->hap2dip )
+        kputs("%_GT_TO_HAP2\n", &str);
+    else
+        kputs("%_GT_TO_HAP\n", &str);
+    open_vcf(args,str.s);
+
+    int ret, hap_compressed = 1, sample_compressed = 0;
+    char *hap_fname = NULL, *sample_fname = NULL;
+    str.l = 0;
+    kputs(args->outfname,&str);
+    int n_files = 0, i;
+    char **files = hts_readlist(str.s, 0, &n_files);
+    if ( n_files==1 )
+    {
+        int l = str.l;
+        kputs(".samples",&str);
+        sample_fname = strdup(str.s);
+        str.l = l;
+        kputs(".hap.gz",&str);
+        hap_fname = strdup(str.s);
+    }
+    else if ( n_files==2 )
+    {
+        if (strlen(files[0]) && strcmp(files[0],".")!=0) hap_fname = strdup(files[0]);
+        if (strlen(files[1]) && strcmp(files[1],".")!=0) sample_fname = strdup(files[1]);
+    }
+    else
+    {
+        error("Error parsing --hapsample filenames: %s\n", args->outfname);
+    }
+    for (i=0; i<n_files; i++) free(files[i]);
+    free(files);
+
+    if ( hap_fname && (strlen(hap_fname)<3 || strcasecmp(".gz",hap_fname+strlen(hap_fname)-3)) ) hap_compressed = 0;
+    if ( sample_fname && strlen(sample_fname)>3 && strcasecmp(".gz",sample_fname+strlen(sample_fname)-3)==0 ) sample_compressed = 0;
+
+    if (hap_fname) fprintf(stderr, "Hap file: %s\n", hap_fname);
+    if (sample_fname) fprintf(stderr, "Sample file: %s\n", sample_fname);
+
+    // write samples file
+    if (sample_fname)
+    {
+        char *sample2sex = NULL;
+        if ( args->sex_fname ) sample2sex = init_sample2sex(args->header,args->sex_fname);
+
+        int i;
+        BGZF *sout = bgzf_open(sample_fname, sample_compressed ? "wg" : "wu");
+        str.l = 0;
+        kputs(sample2sex ? "ID_1 ID_2 missing sex\n0 0 0 0\n" : "ID_1 ID_2 missing\n0 0 0\n", &str);
+        ret = bgzf_write(sout, str.s, str.l);
+        if ( ret != str.l ) error("Error writing %s: %s\n", sample_fname, strerror(errno));
+        for (i=0; i<bcf_hdr_nsamples(args->header); i++)
+        {
+            str.l = 0;
+            if ( sample2sex )
+                ksprintf(&str, "%s %s 0 %c\n", args->header->samples[i],args->header->samples[i],sample2sex[i]);
+            else
+                ksprintf(&str, "%s %s 0\n", args->header->samples[i],args->header->samples[i]);
+            ret = bgzf_write(sout, str.s, str.l);
+            if ( ret != str.l ) error("Error writing %s: %s\n", sample_fname, strerror(errno));
+        }
+        if ( bgzf_close(sout)!=0 ) error("Error closing %s: %s\n", sample_fname, strerror(errno));
+        free(sample_fname);
+        free(sample2sex);
+    }
+    if (!hap_fname) {
+        if ( str.m ) free(str.s);
+        return;
+    }
+
+    // open haps output
+    BGZF *hout = hap_fname ? bgzf_open(hap_fname, hap_compressed ? "wg" : "wu") : NULL;
+    if ( hap_compressed && args->n_threads ) bgzf_thread_pool(hout, args->files->p->pool, args->files->p->qsize);
+
+    int no_alt = 0, non_biallelic = 0, filtered = 0, nok = 0;
+    while ( bcf_sr_next_line(args->files) )
+    {
+        bcf1_t *line = bcf_sr_get_line(args->files,0);
+        if ( args->filter )
+        {
+            int pass = filter_test(args->filter, line, NULL);
+            if ( args->filter_logic & FLT_EXCLUDE ) pass = pass ? 0 : 1;
+            if ( !pass ) { filtered++; continue; }
+        }
+
+        // ALT allele is required
+        if ( line->n_allele<2 ) { no_alt++; continue; }
+        // biallelic required
+        if ( line->n_allele>2 ) {
+            if (!non_biallelic)
+                fprintf(stderr, "Warning: non-biallelic records are skipped. Consider splitting multi-allelic records into biallelic records using 'bcftools norm -m-'.\n");
+            non_biallelic++;
+            continue;
+        }
+
+        str.l = 0;
+        convert_line(args->convert, line, &str);
+        if ( !str.l ) continue;
+
+        // write haps file
+        if (hap_fname) {
+            ret = bgzf_write(hout, str.s, str.l); // write hap file
+            if ( ret != str.l ) error("Error writing %s: %s\n", hap_fname, strerror(errno));
+        }
+        nok++;
+    }
+    fprintf(stderr, "%d records written, %d skipped: %d/%d/%d no-ALT/non-biallelic/filtered\n", nok, no_alt+non_biallelic+filtered, no_alt, non_biallelic, filtered);
+    if ( str.m ) free(str.s);
+    if ( hout && bgzf_close(hout)!=0 ) error("Error closing %s: %s\n", hap_fname, strerror(errno));
+    if (hap_fname) free(hap_fname);
+}
+
+static void bcf_hdr_set_chrs(bcf_hdr_t *hdr, faidx_t *fai)
+{
+    int i, n = faidx_nseq(fai);
+    for (i=0; i<n; i++)
+    {
+        const char *seq = faidx_iseq(fai,i);
+        int len = faidx_seq_len(fai, seq);
+        bcf_hdr_printf(hdr, "##contig=<ID=%s,length=%d>", seq,len);
+    }
+}
+static inline int acgt_to_5(char base)
+{
+    if ( base=='A' ) return 0;
+    if ( base=='C' ) return 1;
+    if ( base=='G' ) return 2;
+    if ( base=='T' ) return 3;
+    return 4;
+}
+static inline int tsv_setter_aa1(args_t *args, char *ss, char *se, int alleles[], int *nals, int ref, int32_t *gts)
+{
+    if ( se - ss > 2 ) return -1;   // currently only SNPs
+
+    if ( ss[0]=='-' )
+    {
+        // missing GT
+        gts[0] = bcf_gt_missing;
+        gts[1] = bcf_gt_missing;
+        args->n.missing++;
+        return 0;
+    }
+    if ( ss[0]=='I' ) return -2;    // skip insertions/deletions for now
+    if ( ss[0]=='D' ) return -2;
+
+    int a0 = acgt_to_5(toupper(ss[0]));
+    int a1 = ss[1] ? acgt_to_5(toupper(ss[1])) : a0;
+    if ( alleles[a0]<0 ) alleles[a0] = (*nals)++;
+    if ( alleles[a1]<0 ) alleles[a1] = (*nals)++;
+
+    gts[0] = bcf_gt_unphased(alleles[a0]); 
+    gts[1] = ss[1] ? bcf_gt_unphased(alleles[a1]) : bcf_int32_vector_end;
+
+    if ( ref==a0 && ref==a1  ) args->n.hom_rr++;    // hom ref: RR
+    else if ( ref==a0 ) args->n.het_ra++;           // het: RA
+    else if ( ref==a1 ) args->n.het_ra++;           // het: AR
+    else if ( a0==a1 ) args->n.hom_aa++;            // hom-alt: AA
+    else args->n.het_aa++;                          // non-ref het: AA
+
+    return 0;
+}
+static int tsv_setter_aa(tsv_t *tsv, bcf1_t *rec, void *usr)
+{
+    args_t *args = (args_t*) usr;
+
+    int len;
+    char *ref = faidx_fetch_seq(args->ref, (char*)bcf_hdr_id2name(args->header,rec->rid), rec->pos, rec->pos, &len);
+    if ( !ref ) error("faidx_fetch_seq failed at %s:%"PRId64"\n", bcf_hdr_id2name(args->header,rec->rid),(int64_t) rec->pos+1);
+
+    int nals = 1, alleles[5] = { -1, -1, -1, -1, -1 };    // a,c,g,t,n
+    ref[0] = toupper(ref[0]);
+    int iref = acgt_to_5(ref[0]);
+    alleles[iref] = 0;
+
+    rec->n_sample = bcf_hdr_nsamples(args->header);
+
+    int i, ret;
+    for (i=0; i<rec->n_sample; i++)
+    {
+        if ( i>0 )
+        {
+            ret = tsv_next(tsv);
+            if ( ret==-1 ) error("Too few columns for %d samples at %s:%"PRId64"\n", rec->n_sample,bcf_hdr_id2name(args->header,rec->rid),(int64_t) rec->pos+1);
+        }
+        ret = tsv_setter_aa1(args, tsv->ss, tsv->se, alleles, &nals, iref, args->gts+i*2);
+        if ( ret==-1 ) error("Error parsing the site %s:%"PRId64", expected two characters\n", bcf_hdr_id2name(args->header,rec->rid),(int64_t) rec->pos+1);
+        if ( ret==-2 ) 
+        {
+            // something else than a SNP
+            free(ref);
+            return -1;
+        }
+    }
+
+    args->str.l = 0;
+    kputc(ref[0], &args->str);
+    for (i=0; i<5; i++) 
+    {
+        if ( alleles[i]>0 )
+        {
+            kputc(',', &args->str);
+            kputc("ACGTN"[i], &args->str);
+        }
+    }
+    bcf_update_alleles_str(args->header, rec, args->str.s);
+    if ( bcf_update_genotypes(args->header,rec,args->gts,rec->n_sample*2) ) error("Could not update the GT field\n");
+
+    free(ref);
+    return 0;
+}
+
+static void tsv_to_vcf(args_t *args)
+{
+    if ( !args->ref_fname ) error("--tsv2vcf requires the --fasta-ref option\n");
+    if ( !args->sample_list ) error("--tsv2vcf requires the --samples option\n");
+
+    args->ref = fai_load(args->ref_fname);
+    if ( !args->ref ) error("Could not load the reference %s\n", args->ref_fname);
+
+    args->header = bcf_hdr_init("w");
+    bcf_hdr_set_chrs(args->header, args->ref);
+    bcf_hdr_append(args->header, "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">");
+    if (args->record_cmd_line) bcf_hdr_append_version(args->header, args->argc, args->argv, "bcftools_convert");
+
+    int i, n;
+    char **smpls = hts_readlist(args->sample_list, args->sample_is_file, &n);
+    if ( !smpls ) error("Could not parse %s\n", args->sample_list);
+    for (i=0; i<n; i++)
+    {
+        bcf_hdr_add_sample(args->header, smpls[i]);
+        free(smpls[i]);
+    }
+    free(smpls);
+    bcf_hdr_add_sample(args->header, NULL);
+    args->gts = (int32_t *) malloc(sizeof(int32_t)*n*2);
+
+    char wmode[8];
+    set_wmode(wmode,args->output_type,args->outfname,args->clevel);
+    htsFile *out_fh = hts_open(args->outfname ? args->outfname : "-", wmode);
+    if ( out_fh == NULL ) error("Can't write to \"%s\": %s\n", args->outfname, strerror(errno));
+    if ( args->n_threads ) hts_set_threads(out_fh, args->n_threads);
+    if ( bcf_hdr_write(out_fh,args->header)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->outfname);
+
+    tsv_t *tsv = tsv_init(args->columns ? args->columns : "ID,CHROM,POS,AA");
+    if ( tsv_register(tsv, "CHROM", tsv_setter_chrom, args->header) < 0 ) error("Expected CHROM column\n");
+    if ( tsv_register(tsv, "POS", tsv_setter_pos, NULL) < 0 ) error("Expected POS column\n");
+    if ( tsv_register(tsv, "ID", tsv_setter_id, args->header) < 0 && !args->columns ) error("Expected ID column\n");
+    if ( tsv_register(tsv, "AA", tsv_setter_aa, args) < 0 ) error("Expected AA column\n");
+
+    bcf1_t *rec = bcf_init();
+    bcf_float_set_missing(rec->qual);
+
+    kstring_t line = {0,0,0};
+    htsFile *in_fh = hts_open(args->infname, "r");
+    if ( !in_fh ) error("Could not read: %s\n", args->infname);
+    while ( hts_getline(in_fh, KS_SEP_LINE, &line) > 0 )
+    {
+        if ( line.s[0]=='#' ) continue;     // skip comments
+        bcf_clear(rec);
+
+        args->n.total++;
+        if ( !tsv_parse(tsv, rec, line.s) )
+        {
+            if ( bcf_write(out_fh, args->header, rec)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->outfname);
+        }
+        else
+            args->n.skipped++;
+    }
+    if ( hts_close(in_fh) ) error("Close failed: %s\n", args->infname);
+    free(line.s);
+
+    bcf_hdr_destroy(args->header);
+    if ( hts_close(out_fh)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,args->outfname);
+    tsv_destroy(tsv);
+    bcf_destroy(rec);
+    free(args->str.s);
+    free(args->gts);
+
+    fprintf(stderr,"Rows total: \t%d\n", args->n.total);
+    fprintf(stderr,"Rows skipped: \t%d\n", args->n.skipped);
+    fprintf(stderr,"Missing GTs: \t%d\n", args->n.missing);
+    fprintf(stderr,"Hom RR: \t%d\n", args->n.hom_rr);
+    fprintf(stderr,"Het RA: \t%d\n", args->n.het_ra);
+    fprintf(stderr,"Hom AA: \t%d\n", args->n.hom_aa);
+    fprintf(stderr,"Het AA: \t%d\n", args->n.het_aa);
+}
+
+static void vcf_to_vcf(args_t *args)
+{
+    open_vcf(args,NULL);
+    char wmode[8];
+    set_wmode(wmode,args->output_type,args->outfname,args->clevel);
+    htsFile *out_fh = hts_open(args->outfname ? args->outfname : "-", wmode);
+    if ( out_fh == NULL ) error("Can't write to \"%s\": %s\n", args->outfname, strerror(errno));
+    if ( args->n_threads ) hts_set_threads(out_fh, args->n_threads);
+
+    bcf_hdr_t *hdr = bcf_sr_get_header(args->files,0);
+    if ( bcf_hdr_write(out_fh,hdr)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->outfname);
+
+    while ( bcf_sr_next_line(args->files) )
+    {
+        bcf1_t *line = bcf_sr_get_line(args->files,0);
+        if ( args->filter )
+        {
+            int pass = filter_test(args->filter, line, NULL);
+            if ( args->filter_logic & FLT_EXCLUDE ) pass = pass ? 0 : 1;
+            if ( !pass ) continue;
+        }
+        if ( bcf_write(out_fh,hdr,line)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->outfname);
+    }
+    if ( hts_close(out_fh)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,args->outfname);
+}
+
+static void gvcf_to_vcf(args_t *args)
+{
+    if ( !args->ref_fname ) error("--gvcf2vcf requires the --fasta-ref option\n");
+
+    args->ref = fai_load(args->ref_fname);
+    if ( !args->ref ) error("Could not load the fai index for reference %s\n", args->ref_fname);
+
+    open_vcf(args,NULL);
+    char wmode[8];
+    set_wmode(wmode,args->output_type,args->outfname,args->clevel);
+    htsFile *out_fh = hts_open(args->outfname ? args->outfname : "-", wmode);
+    if ( out_fh == NULL ) error("Can't write to \"%s\": %s\n", args->outfname, strerror(errno));
+    if ( args->n_threads ) hts_set_threads(out_fh, args->n_threads);
+
+    bcf_hdr_t *hdr = bcf_sr_get_header(args->files,0);
+    if (args->record_cmd_line) bcf_hdr_append_version(hdr, args->argc, args->argv, "bcftools_convert");
+    if ( bcf_hdr_write(out_fh,hdr)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->outfname);
+
+    int32_t *itmp = NULL, nitmp = 0;
+
+    while ( bcf_sr_next_line(args->files) )
+    {
+        bcf1_t *line = bcf_sr_get_line(args->files,0);
+        if ( args->filter )
+        {
+            int pass = filter_test(args->filter, line, NULL);
+            if ( args->filter_logic & FLT_EXCLUDE ) pass = pass ? 0 : 1;
+            if ( !pass ) 
+            {
+                if ( bcf_write(out_fh,hdr,line)!=0  ) error("[%s] Error: cannot write to %s\n", __func__,args->outfname);
+                continue;
+            }
+        }
+
+        // check if alleles compatible with being a gVCF record
+        // ALT must be one of ., <*>, <X>, <NON_REF>
+        // check for INFO/END is below
+        int i, gallele = -1;
+        if (line->n_allele==1)
+            gallele = 0; // illumina/bcftools-call gvcf (if INFO/END present)
+        else if ( line->d.allele[1][0]=='<' )
+        {
+            for (i=1; i<line->n_allele; i++)
+            {
+                if ( line->d.allele[i][1]=='*' && line->d.allele[i][2]=='>' && line->d.allele[i][3]=='\0' ) { gallele = i; break; } // mpileup/spec compliant gVCF
+                if ( line->d.allele[i][1]=='X' && line->d.allele[i][2]=='>' && line->d.allele[i][3]=='\0' ) { gallele = i; break; } // old mpileup gVCF
+                if ( strcmp(line->d.allele[i],"<NON_REF>")==0 ) { gallele = i; break; }               // GATK gVCF
+            }
+        }
+
+        // no gVCF compatible alleles
+        if (gallele<0)
+        {
+            if ( bcf_write(out_fh,hdr,line)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->outfname);
+            continue;
+        }
+
+        int nend = bcf_get_info_int32(hdr,line,"END",&itmp,&nitmp);
+        if ( nend!=1 )
+        {
+            // No INFO/END => not gVCF record
+            if ( bcf_write(out_fh,hdr,line)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->outfname);
+            continue;
+        }
+        bcf_update_info_int32(hdr,line,"END",NULL,0);
+        int pos, len;
+        for (pos=line->pos; pos<itmp[0]; pos++)
+        {
+            line->pos = pos;
+            char *ref = faidx_fetch_seq(args->ref, (char*)bcf_hdr_id2name(hdr,line->rid), line->pos, line->pos, &len);
+            if ( !ref ) error("faidx_fetch_seq failed at %s:%"PRId64"\n", bcf_hdr_id2name(hdr,line->rid),(int64_t) line->pos+1);
+            strncpy(line->d.allele[0],ref,len);
+            if ( bcf_write(out_fh,hdr,line)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->outfname);
+            free(ref);
+        }
+    }
+    free(itmp);
+    if ( hts_close(out_fh)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,args->outfname);
+}
+
+static void usage(void)
+{
+    fprintf(stderr, "\n");
+    fprintf(stderr, "About:   Converts VCF/BCF to other formats and back. See man page for file\n");
+    fprintf(stderr, "         formats details. When specifying output files explicitly instead\n");
+    fprintf(stderr, "         of with PREFIX, one can use '-' for stdout and '.' to suppress.\n");
+    fprintf(stderr, "Usage:   bcftools convert [OPTIONS] INPUT_FILE\n");
+    fprintf(stderr, "\n");
+    fprintf(stderr, "VCF input options:\n");
+    fprintf(stderr, "   -e, --exclude EXPR             Exclude sites for which the expression is true\n");
+    fprintf(stderr, "   -i, --include EXPR             Select sites for which the expression is true\n");
+    fprintf(stderr, "   -r, --regions REGION           Restrict to comma-separated list of regions\n");
+    fprintf(stderr, "   -R, --regions-file FILE        Restrict to regions listed in a file\n");
+    fprintf(stderr, "       --regions-overlap 0|1|2    Include if POS in the region (0), record overlaps (1), variant overlaps (2) [1]\n");
+    fprintf(stderr, "   -s, --samples LIST             List of samples to include\n");
+    fprintf(stderr, "   -S, --samples-file FILE        File of samples to include\n");
+    fprintf(stderr, "   -t, --targets REGION           Similar to -r but streams rather than index-jumps\n");
+    fprintf(stderr, "   -T, --targets-file FILE        Similar to -R but streams rather than index-jumps\n");
+    fprintf(stderr, "       --targets-overlap 0|1|2    Include if POS in the region (0), record overlaps (1), variant overlaps (2) [0]\n");
+    fprintf(stderr, "\n");
+    fprintf(stderr, "VCF output options:\n");
+    fprintf(stderr, "       --no-version               Do not append version and command line to the header\n");
+    fprintf(stderr, "   -o, --output FILE              Output file name [stdout]\n");
+    fprintf(stderr, "   -O, --output-type u|b|v|z[0-9] u/b: un/compressed BCF, v/z: un/compressed VCF, 0-9: compression level [v]\n");
+    fprintf(stderr, "       --threads INT              Use multithreading with INT worker threads [0]\n");
+    fprintf(stderr, "\n");
+    fprintf(stderr, "GEN/SAMPLE conversion (input/output from IMPUTE2):\n");
+    fprintf(stderr, "   -G, --gensample2vcf ...        <PREFIX>|<GEN-FILE>,<SAMPLE-FILE>\n");
+    fprintf(stderr, "   -g, --gensample ...            <PREFIX>|<GEN-FILE>,<SAMPLE-FILE>\n");
+    fprintf(stderr, "       --3N6                      Use 3*N+6 column format instead of the old 3*N+5 column format\n");
+    fprintf(stderr, "       --tag STRING               Tag to take values for .gen file: GT,PL,GL,GP [GT]\n");
+    fprintf(stderr, "       --chrom                    Output chromosome in first column instead of CHROM:POS_REF_ALT\n");
+    fprintf(stderr, "       --keep-duplicates          Keep duplicate positions\n");
+    fprintf(stderr, "       --sex FILE                 Output sex column in the sample-file, input format is: Sample\\t[MF]\n");
+    fprintf(stderr, "       --vcf-ids                  Output VCF IDs in second column instead of CHROM:POS_REF_ALT\n");
+    fprintf(stderr, "\n");
+    fprintf(stderr, "gVCF conversion:\n");
+    fprintf(stderr, "       --gvcf2vcf                 Expand gVCF reference blocks\n");
+    fprintf(stderr, "   -f, --fasta-ref FILE           Reference sequence in fasta format\n");
+    fprintf(stderr, "\n");
+    fprintf(stderr, "HAP/SAMPLE conversion (output from SHAPEIT):\n");
+    fprintf(stderr, "       --hapsample2vcf ...        <PREFIX>|<HAP-FILE>,<SAMPLE-FILE>\n");
+    fprintf(stderr, "       --hapsample ...            <PREFIX>|<HAP-FILE>,<SAMPLE-FILE>\n");
+    fprintf(stderr, "       --haploid2diploid          Convert haploid genotypes to diploid homozygotes\n");
+    fprintf(stderr, "       --sex FILE                 Output sex column in the sample-file, input format is: Sample\\t[MF]\n");
+    fprintf(stderr, "       --vcf-ids                  Output VCF IDs instead of CHROM:POS_REF_ALT\n");
+    fprintf(stderr, "\n");
+    fprintf(stderr, "HAP/LEGEND/SAMPLE conversion:\n");
+    fprintf(stderr, "   -H, --haplegendsample2vcf ...  <PREFIX>|<HAP-FILE>,<LEGEND-FILE>,<SAMPLE-FILE>\n");
+    fprintf(stderr, "   -h, --haplegendsample ...      <PREFIX>|<HAP-FILE>,<LEGEND-FILE>,<SAMPLE-FILE>\n");
+    fprintf(stderr, "       --haploid2diploid          Convert haploid genotypes to diploid homozygotes\n");
+    fprintf(stderr, "       --sex FILE                 Output sex column in the sample-file, input format is: Sample\\t[MF]\n");
+    fprintf(stderr, "       --vcf-ids                  Output VCF IDs instead of CHROM:POS_REF_ALT\n");
+    fprintf(stderr, "\n");
+    fprintf(stderr, "TSV conversion:\n");
+    fprintf(stderr, "       --tsv2vcf FILE\n");
+    fprintf(stderr, "   -c, --columns STRING           Columns of the input tsv file [ID,CHROM,POS,AA]\n");
+    fprintf(stderr, "   -f, --fasta-ref FILE           Reference sequence in fasta format\n");
+    fprintf(stderr, "   -s, --samples LIST             List of sample names\n");
+    fprintf(stderr, "   -S, --samples-file FILE        File of sample names\n");
+    fprintf(stderr, "\n");
+    // fprintf(stderr, "PLINK options:\n");
+    // fprintf(stderr, "   -p, --plink <prefix>|<ped>,<map>,<fam>|<bed>,<bim>,<fam>|<tped>,<tfam>\n");
+    // fprintf(stderr, "       --tped              make tped file instead\n");
+    // fprintf(stderr, "       --bin               make binary bed/fam/bim files\n");
+    // fprintf(stderr, "\n");
+    // fprintf(stderr, "PBWT options:\n");
+    // fprintf(stderr, "   -b, --pbwt          <prefix> or <pbwt>,<sites>,<sample>,<missing>\n");
+    // fprintf(stderr, "\n");
+    exit(1);
+}
+
+int main_vcfconvert(int argc, char *argv[])
+{
+    int c;
+    args_t *args = (args_t*) calloc(1,sizeof(args_t));
+    args->argc   = argc; args->argv = argv;
+    args->outfname = "-";
+    args->output_type = FT_VCF;
+    args->n_threads = 0;
+    args->record_cmd_line = 1;
+    args->regions_overlap = 1;
+    args->targets_overlap = 0;
+    args->clevel = -1;
+
+    static struct option loptions[] =
+    {
+        {"include",required_argument,NULL,'i'},
+        {"exclude",required_argument,NULL,'e'},
+        {"output",required_argument,NULL,'o'},
+        {"output-type",required_argument,NULL,'O'},
+        {"threads",required_argument,NULL,9},
+        {"regions",required_argument,NULL,'r'},
+        {"regions-file",required_argument,NULL,'R'},
+        {"regions-overlap",required_argument,NULL,13},
+        {"targets",required_argument,NULL,'t'},
+        {"targets-file",required_argument,NULL,'T'},
+        {"targets-overlap",required_argument,NULL,14},
+        {"samples",required_argument,NULL,'s'},
+        {"samples-file",required_argument,NULL,'S'},
+        {"sex",required_argument,NULL,11},
+        {"gensample",required_argument,NULL,'g'},
+        {"gensample2vcf",required_argument,NULL,'G'},
+        {"tag",required_argument,NULL,1},
+        {"chrom",no_argument,NULL,8},
+        {"3N6",no_argument,NULL,15},
+        {"tsv2vcf",required_argument,NULL,2},
+        {"hapsample",required_argument,NULL,7},
+        {"hapsample2vcf",required_argument,NULL,3},
+        {"vcf-ids",no_argument,NULL,4},
+        {"haploid2diploid",no_argument,NULL,5},
+        {"gvcf2vcf",no_argument,NULL,6},
+        {"haplegendsample",required_argument,NULL,'h'},
+        {"haplegendsample2vcf",required_argument,NULL,'H'},
+        {"columns",required_argument,NULL,'c'},
+        {"fasta-ref",required_argument,NULL,'f'},
+        {"no-version",no_argument,NULL,10},
+        {"keep-duplicates",no_argument,NULL,12},
+        {NULL,0,NULL,0}
+    };
+    char *tmp;
+    while ((c = getopt_long(argc, argv, "?h:r:R:s:S:t:T:i:e:g:G:o:O:c:f:H:",loptions,NULL)) >= 0) {
+        switch (c) {
+            case 'e':
+                if ( args->filter_str ) error("Error: only one -i or -e expression can be given, and they cannot be combined\n");
+                args->filter_str = optarg; args->filter_logic |= FLT_EXCLUDE; break;
+            case 'i':
+                if ( args->filter_str ) error("Error: only one -i or -e expression can be given, and they cannot be combined\n");
+                args->filter_str = optarg; args->filter_logic |= FLT_INCLUDE; break;
+            case 'r': args->regions_list = optarg; break;
+            case 'R': args->regions_list = optarg; args->regions_is_file = 1; break;
+            case 't': args->targets_list = optarg; break;
+            case 'T': args->targets_list = optarg; args->targets_is_file = 1; break;
+            case 's': args->sample_list = optarg; break;
+            case 'S': args->sample_list = optarg; args->sample_is_file = 1; break;
+            case 'g': args->convert_func = vcf_to_gensample; args->outfname = optarg; break;
+            case 'G': args->convert_func = gensample_to_vcf; args->infname = optarg; break;
+            case  1 : args->tag = optarg; break;
+            case  2 : args->convert_func = tsv_to_vcf; args->infname = optarg; break;
+            case  3 : args->convert_func = hapsample_to_vcf; args->infname = optarg; break;
+            case  4 : args->output_vcf_ids = 1; break;
+            case  5 : args->hap2dip = 1; break;
+            case  6 : args->convert_func = gvcf_to_vcf; break;
+            case  7 : args->convert_func = vcf_to_hapsample; args->outfname = optarg; break;
+            case  8 : error("The --chrom option has been deprecated, please use --3N6 instead\n"); break;
+            case 15 : args->gen_3N6 = 1; break;
+            case 'H': args->convert_func = haplegendsample_to_vcf; args->infname = optarg; break;
+            case 'f': args->ref_fname = optarg; break;
+            case 'c': args->columns = optarg; break;
+            case 'o': args->outfname = optarg; break;
+            case 'O':
+                switch (optarg[0]) {
+                    case 'b': args->output_type = FT_BCF_GZ; break;
+                    case 'u': args->output_type = FT_BCF; break;
+                    case 'z': args->output_type = FT_VCF_GZ; break;
+                    case 'v': args->output_type = FT_VCF; break;
+                    default:
+                    {
+                        args->clevel = strtol(optarg,&tmp,10);
+                        if ( *tmp || args->clevel<0 || args->clevel>9 ) error("The output type \"%s\" not recognised\n", optarg);
+                    }
+                }
+                if ( optarg[1] )
+                {
+                    args->clevel = strtol(optarg+1,&tmp,10);
+                    if ( *tmp || args->clevel<0 || args->clevel>9 ) error("Could not parse argument: --compression-level %s\n", optarg+1);
+                }
+                break;
+            case 'h': args->convert_func = vcf_to_haplegendsample; args->outfname = optarg; break;
+            case  9 : args->n_threads = strtol(optarg, 0, 0); break;
+            case 10 : args->record_cmd_line = 0; break;
+            case 11 : args->sex_fname = optarg; break;
+            case 12 : args->keep_duplicates = 1; break;
+            case 13 :
+                args->regions_overlap = parse_overlap_option(optarg);
+                if ( args->regions_overlap < 0 ) error("Could not parse: --regions-overlap %s\n",optarg);
+                break;
+            case 14 :
+                args->targets_overlap = parse_overlap_option(optarg);
+                if ( args->targets_overlap < 0 ) error("Could not parse: --targets-overlap %s\n",optarg);
+                break;
+            case '?': usage(); break;
+            default: error("Unknown argument: %s\n", optarg);
+        }
+    }
+
+    if ( !args->infname )
+    {
+        if ( optind>=argc )
+        {
+            if ( !isatty(fileno((FILE *)stdin)) ) args->infname = "-";
+        }
+        else args->infname = argv[optind];
+    }
+    if ( !args->infname ) usage();
+    
+    if ( args->convert_func ) args->convert_func(args);
+    else vcf_to_vcf(args);
+
+    destroy_data(args);
+    free(args);
+    return 0;
+}
diff --git a/bcftools/vcfconvert.c.pysam.c b/bcftools/vcfconvert.c.pysam.c
new file mode 100644
index 0000000..f340171
--- /dev/null
+++ b/bcftools/vcfconvert.c.pysam.c
@@ -0,0 +1,1679 @@
+#include "bcftools.pysam.h"
+
+/*  vcfconvert.c -- convert between VCF/BCF and related formats.
+
+    Copyright (C) 2013-2021 Genome Research Ltd.
+
+    Author: Petr Danecek <pd3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.  */
+
+#include <stdio.h>
+#include <strings.h>
+#include <unistd.h>
+#include <getopt.h>
+#include <ctype.h>
+#include <string.h>
+#include <errno.h>
+#include <sys/stat.h>
+#include <sys/types.h>
+#include <inttypes.h>
+#include <htslib/faidx.h>
+#include <htslib/vcf.h>
+#include <htslib/bgzf.h>
+#include <htslib/synced_bcf_reader.h>
+#include <htslib/vcfutils.h>
+#include <htslib/kseq.h>
+#include "bcftools.h"
+#include "filter.h"
+#include "convert.h"
+#include "tsv2vcf.h"
+
+// Logic of the filters: include or exclude sites which match the filters?
+#define FLT_INCLUDE 1
+#define FLT_EXCLUDE 2
+
+typedef struct _args_t args_t;
+struct _args_t
+{
+    faidx_t *ref;
+    filter_t *filter;
+    char *filter_str;
+    int filter_logic;   // include or exclude sites which match the filters? One of FLT_INCLUDE/FLT_EXCLUDE
+    convert_t *convert;
+    bcf_srs_t *files;
+    bcf_hdr_t *header;
+    void (*convert_func)(struct _args_t *);
+    struct {
+        int total, skipped, hom_rr, het_ra, hom_aa, het_aa, missing; 
+    } n;
+    kstring_t str;
+    int32_t *gts;
+    float *flt;
+    int rev_als, output_vcf_ids, hap2dip, gen_3N6;
+    int nsamples, *samples, sample_is_file, targets_is_file, regions_is_file, output_type;
+    int regions_overlap, targets_overlap;
+    char **argv, *sample_list, *targets_list, *regions_list, *tag, *columns;
+    char *outfname, *infname, *ref_fname, *sex_fname;
+    int argc, n_threads, record_cmd_line, keep_duplicates, clevel;
+};
+
+static void destroy_data(args_t *args)
+{
+    if ( args->ref ) fai_destroy(args->ref);
+    if ( args->convert) convert_destroy(args->convert);
+    if ( args->filter ) filter_destroy(args->filter);
+    free(args->samples);
+    if ( args->files ) bcf_sr_destroy(args->files);
+}
+
+static void open_vcf(args_t *args, const char *format_str)
+{
+    args->files = bcf_sr_init();
+    if ( args->n_threads && bcf_sr_set_threads(args->files, args->n_threads)!=0 )
+        error("Could not initialize --threads %d\n", args->n_threads);
+
+    if ( args->regions_list )
+    {
+        bcf_sr_set_opt(args->files,BCF_SR_REGIONS_OVERLAP,args->regions_overlap);
+        if ( bcf_sr_set_regions(args->files, args->regions_list, args->regions_is_file)<0 )
+            error("Failed to read the regions: %s\n", args->regions_list);
+    }
+    if ( args->targets_list )
+    {
+        bcf_sr_set_opt(args->files,BCF_SR_TARGETS_OVERLAP,args->targets_overlap);
+        if ( bcf_sr_set_targets(args->files, args->targets_list, args->targets_is_file, 0)<0 )
+            error("Failed to read the targets: %s\n", args->targets_list);
+    }
+    if ( !bcf_sr_add_reader(args->files, args->infname) )
+        error("Failed to open %s: %s\n", args->infname,bcf_sr_strerror(args->files->errnum));
+
+    args->header = args->files->readers[0].header;
+
+    if ( args->filter_str )
+        args->filter = filter_init(args->header, args->filter_str);
+
+    int i, nsamples = 0, *samples = NULL;
+    if ( args->sample_list && strcmp("-",args->sample_list) )
+    {
+        for (i=0; i<args->files->nreaders; i++)
+        {
+            int ret = bcf_hdr_set_samples(args->files->readers[i].header,args->sample_list,args->sample_is_file);
+            if ( ret<0 ) error("Error parsing the sample list\n");
+            else if ( ret>0 ) error("Sample name mismatch: sample #%d not found in the header\n", ret);
+        }
+
+        if ( args->sample_list[0]!='^' )
+        {
+            // the sample ordering may be different if not negated
+            int n;
+            char **smpls = hts_readlist(args->sample_list, args->sample_is_file, &n);
+            if ( !smpls ) error("Could not parse %s\n", args->sample_list);
+            if ( n!=bcf_hdr_nsamples(args->files->readers[0].header) )
+                error("The number of samples does not match, perhaps some are present multiple times?\n");
+            nsamples = bcf_hdr_nsamples(args->files->readers[0].header);
+            samples = (int*) malloc(sizeof(int)*nsamples);
+            for (i=0; i<n; i++)
+            {
+                samples[i] = bcf_hdr_id2int(args->files->readers[0].header, BCF_DT_SAMPLE,smpls[i]);
+                free(smpls[i]);
+            }
+            free(smpls);
+        }
+    }
+    if ( format_str ) args->convert = convert_init(args->header, samples, nsamples, format_str);
+    free(samples);
+}
+
+// Try to set CHROM:POS_REF_ALT[_END]. Return 0 on success, -1 on error
+static int _set_chrom_pos_ref_alt(tsv_t *tsv, bcf1_t *rec, void *usr)
+{
+    args_t *args = (args_t*) usr;
+
+    char tmp, *se = tsv->ss, *ss = tsv->ss;
+    while ( se < tsv->se && *se!=':' ) se++;
+    if ( *se!=':' ) return -1;
+    tmp = *se; *se = 0;
+    int rid = bcf_hdr_name2id(args->header,ss);
+    *se = tmp;
+    if ( rid<0 ) return -1;
+
+    // POS
+    hts_pos_t pos = strtol(se+1,&ss,10);
+    if ( ss==se+1 ) return -1;
+    pos--;
+
+    // REF,ALT
+    args->str.l = 0;
+    se = ++ss;
+    while ( se < tsv->se && *se!='_' ) se++; 
+    if ( *se!='_' ) return -1;
+    kputsn(ss,se-ss,&args->str);
+    ss = ++se;
+    while ( se < tsv->se && *se!='_' && isspace(*tsv->se) ) se++;
+    if ( se < tsv->se && *se!='_' && isspace(*tsv->se) ) return -1;
+    kputc(',',&args->str);
+    kputsn(ss,se-ss,&args->str);
+
+    // END - optional
+    if (*se && *se=='_')
+    {
+        long end = strtol(se+1,&ss,10);
+        if ( ss==se+1 ) return -1;
+        bcf_update_info_int32(args->header, rec, "END", &end, 1);
+    }
+
+    rec->rid = rid;
+    rec->pos = pos;
+    bcf_update_alleles_str(args->header, rec, args->str.s);
+
+    return 0;
+}
+static int tsv_setter_chrom_pos_ref_alt_or_chrom(tsv_t *tsv, bcf1_t *rec, void *usr)
+{
+    args_t *args = (args_t*)usr;
+    int ret = _set_chrom_pos_ref_alt(tsv,rec,usr);
+    if ( !ret ) return ret;
+    return tsv_setter_chrom(tsv,rec,args->header);
+}
+static int tsv_setter_chrom_pos_ref_alt(tsv_t *tsv, bcf1_t *rec, void *usr)
+{
+    int ret = _set_chrom_pos_ref_alt(tsv,rec,usr);
+    if ( ret!=0 ) error("Could not parse the CHROM:POS_REF_ALT[_END] string: %s\n", tsv->ss);
+    return ret;
+}
+// This function must be called first, then tsv_setter_chrom_pos_ref_alt_id_or_die.
+// One of them is expected to find the CHROM:POS_REF_ALT[_END] string, if not, die.
+static int tsv_setter_chrom_pos_ref_alt_or_id(tsv_t *tsv, bcf1_t *rec, void *usr)
+{
+    args_t *args = (args_t*)usr;
+    if ( _set_chrom_pos_ref_alt(tsv,rec,usr)==0 )  return 0;
+    rec->pos = -1;  // mark the record as unset
+    if ( !args->output_vcf_ids) return 0;
+    return tsv_setter_id(tsv,rec,usr);
+}
+static int tsv_setter_chrom_pos_ref_alt_id_or_die(tsv_t *tsv, bcf1_t *rec, void *usr)
+{
+    args_t *args = (args_t*)usr;
+    if ( rec->pos!=-1 )
+    {
+        if ( !args->output_vcf_ids ) return 0;
+        return tsv_setter_id(tsv,rec,usr);
+    }
+    return tsv_setter_chrom_pos_ref_alt(tsv,rec,usr);
+}
+static int tsv_setter_verify_pos(tsv_t *tsv, bcf1_t *rec, void *usr)
+{
+    char *se;
+    int pos = strtol(tsv->ss,&se,10);
+    if ( tsv->ss==se ) error("Could not parse POS: %s\n", tsv->ss);
+    if ( rec->pos != pos-1 ) error("POS mismatch: %s\n", tsv->ss);
+    return 0;
+}
+static int tsv_setter_verify_ref_alt(tsv_t *tsv, bcf1_t *rec, void *usr)
+{
+    args_t *args = (args_t*) usr;
+    args->rev_als = 0;
+    char tmp = *tsv->se; *tsv->se = 0;
+    if ( strcmp(tsv->ss,rec->d.allele[0]) )
+    {
+        if ( strcmp(tsv->ss,rec->d.allele[1]) ) { *tsv->se = tmp; error("REF/ALT mismatch: [%s][%s]\n", tsv->ss,rec->d.allele[1]); }
+        args->rev_als = 1;
+    }
+    *tsv->se = tmp;
+    while ( *tsv->se && isspace(*tsv->se) ) tsv->se++;
+    tsv->ss = tsv->se;
+    while ( *tsv->se && !isspace(*tsv->se) ) tsv->se++;
+    tmp = *tsv->se; *tsv->se = 0;
+    if ( !args->rev_als && strcmp(tsv->ss,rec->d.allele[1]) ) { *tsv->se = tmp; error("REF/ALT mismatch: [%s][%s]\n", tsv->ss,rec->d.allele[1]); }
+    else if ( args->rev_als && strcmp(tsv->ss,rec->d.allele[0]) ) { *tsv->se = tmp; error("REF/ALT mismatch: [%s][%s]\n", tsv->ss,rec->d.allele[0]); }
+    *tsv->se = tmp;
+    return 0;
+}
+static int tsv_setter_gt_gp(tsv_t *tsv, bcf1_t *rec, void *usr)
+{
+    args_t *args = (args_t*) usr;
+    int i, nsamples = bcf_hdr_nsamples(args->header);
+    for (i=0; i<nsamples; i++)
+    {
+        float aa,ab,bb;
+        aa = strtod(tsv->ss, &tsv->se);
+        if ( tsv->ss==tsv->se ) { fprintf(bcftools_stderr,"Could not parse first value of %d-th sample\n", i+1); return -1; }
+        tsv->ss = tsv->se+1;
+        ab = strtod(tsv->ss, &tsv->se);
+        if ( tsv->ss==tsv->se ) { fprintf(bcftools_stderr,"Could not parse second value of %d-th sample\n", i+1); return -1; }
+        tsv->ss = tsv->se+1;
+        bb = strtod(tsv->ss, &tsv->se);
+        if ( tsv->ss==tsv->se ) { fprintf(bcftools_stderr,"Could not parse third value of %d-th sample\n", i+1); return -1; }
+        tsv->ss = tsv->se+1;
+
+        if ( args->rev_als ) { float tmp = bb; bb = aa; aa = tmp; }
+        args->flt[3*i+0] = aa;
+        args->flt[3*i+1] = ab;
+        args->flt[3*i+2] = bb;
+
+        if ( aa >= ab )
+        {
+            if ( aa >= bb ) args->gts[2*i+0] = args->gts[2*i+1] = bcf_gt_unphased(0);
+            else args->gts[2*i+0] = args->gts[2*i+1] = bcf_gt_unphased(1); 
+        }
+        else if ( ab >= bb ) 
+        {
+            args->gts[2*i+0] = bcf_gt_unphased(0);
+            args->gts[2*i+1] = bcf_gt_unphased(1); 
+        }
+        else args->gts[2*i+0] = args->gts[2*i+1] = bcf_gt_unphased(1);
+    }
+    if ( *tsv->se ) error("Could not parse: %s\n", tsv->ss);
+    if ( bcf_update_genotypes(args->header,rec,args->gts,nsamples*2) ) error("Could not update GT field\n");
+    if ( bcf_update_format_float(args->header,rec,"GP",args->flt,nsamples*3) ) error("Could not update GP field\n");
+    return 0;
+}
+static int tsv_setter_haps(tsv_t *tsv, bcf1_t *rec, void *usr)
+{
+    args_t *args = (args_t*) usr;
+    int i, nsamples = bcf_hdr_nsamples(args->header);
+
+    int32_t a0, a1;
+    if ( args->rev_als ) { a0 = bcf_gt_phased(1); a1 = bcf_gt_phased(0); }
+    else { a0 = bcf_gt_phased(0); a1 = bcf_gt_phased(1); }
+
+    // up is short for "unphased"
+    int nup = 0; 
+    for (i=0; i<nsamples; i++)
+    {
+        char *ss = tsv->ss + 4*i + nup;
+        int up = 0, all;
+
+        for (all=0; all < 2; all++){
+            // checking for premature ending
+            if ( !ss[0] || !ss[1] || !ss[2] ||
+                 (up && (!ss[3] || !ss[4]) ) )
+            {
+                fprintf(bcftools_stderr,"Wrong number of fields at %d-th sample ([%c][%c][%c]). ",i+1,ss[0],ss[1],ss[2]);
+                return -1;
+            }
+
+            switch(ss[all*2+up]){
+            case '0':
+                args->gts[2*i+all] = a0;
+                break;
+            case '1' :
+                args->gts[2*i+all] = a1;
+                break;
+            case '?' :
+                // there is no macro to express phased missing allele
+                args->gts[2*i+all] = bcf_gt_phased(-1);
+                break;
+            case '-' :
+                args->gts[2*i+all] = bcf_int32_vector_end;
+                break;
+            default :
+                fprintf(bcftools_stderr,"Could not parse: [%c][%s]\n", ss[all*2+up],tsv->ss);
+                return -1; 
+            }
+            if( ss[all*2+up+1]=='*' ) up = up + 1;
+        }
+        
+        if(up && up != 2)
+        {
+            fprintf(bcftools_stderr,"Missing unphased marker '*': [%c][%s]", ss[2+up], tsv->ss);
+            return -1;
+        }
+
+        // change alleles to unphased if the alleles are unphased
+        if ( up )
+        {
+            args->gts[2*i] = bcf_gt_unphased(bcf_gt_allele(args->gts[2*i]));
+            args->gts[2*i+1] = bcf_gt_unphased(bcf_gt_allele(args->gts[2*i+1]));
+        }
+        nup = nup + up;
+    }
+    if ( tsv->ss[(nsamples-1)*4+3+nup] )
+    {
+        fprintf(bcftools_stderr,"nup: %d", nup);
+        fprintf(bcftools_stderr,"Wrong number of fields (%d-th column = [%c]). ", nsamples*2,tsv->ss[(nsamples-1)*4+nup]);
+        return -1;
+    }
+
+    if ( bcf_update_genotypes(args->header,rec,args->gts,nsamples*2) ) error("Could not update GT field\n");
+    return 0;
+}
+static void gensample_to_vcf(args_t *args)
+{
+    /*
+     *  Inpute: IMPUTE2 output (indentation changed here for clarity): 
+     *
+     *      20:62116619_C_T 20:62116619     62116619 C T 0.969 0.031 0 ...
+     *      ---             20:62116698_C_A 62116698 C A 1     0     0 ...
+     *
+     *  Second column is expected in the form of CHROM:POS_REF_ALT. We use second
+     *  column because the first can be empty ("--") when filling sites from reference 
+     *  panel. When the option --vcf-ids is given, the first column is used to set the
+     *  VCF ID.
+     *
+     *  Output: VCF with filled GT,GP
+     *
+     */
+    kstring_t line = {0,0,0};
+
+    char *gen_fname = NULL, *sample_fname = NULL;
+    sample_fname = strchr(args->infname,',');
+    if ( !sample_fname )
+    {
+        args->str.l = 0;
+        ksprintf(&args->str,"%s.gen.gz", args->infname);
+        gen_fname = strdup(args->str.s);
+        args->str.l = 0;
+        ksprintf(&args->str,"%s.samples", args->infname);
+        sample_fname = strdup(args->str.s);
+    }
+    else
+    {
+        *sample_fname = 0;
+        gen_fname = strdup(args->infname);
+        sample_fname = strdup(sample_fname+1);
+    }
+    htsFile *gen_fh = hts_open(gen_fname, "r");
+    if ( !gen_fh ) error("Could not read: %s\n", gen_fname);
+    if ( hts_getline(gen_fh, KS_SEP_LINE, &line) <= 0 ) error("Empty file: %s\n", gen_fname);
+
+    // Find out the chromosome name, depending on the format variant (--3N6 or plain) and the ordering
+    // of the columns (CHROM:POS_REF_ALT comes first or second)
+    args->str.l = 0;
+    char *sb = line.s, *se = line.s;
+    while ( *se && !isspace(*se) ) se++;
+    if ( !*se ) error("Could not determine CHROM in %s: %s\n", gen_fname,line.s);
+    if ( args->gen_3N6 )    // first column, just CHROM
+        kputsn(sb, se-sb, &args->str);
+    else                    // first or second column, part of CHROM:POS_REF_ALT
+    {
+        char *sc = strchr(sb,':');
+        if ( !sc || sc > se )
+        {
+            while ( *se && !isspace(*se) ) se++;
+            if ( !*se ) error("Could not determine CHROM in %s: %s\n", gen_fname,line.s);
+            sb = ++se;
+            sc = strchr(sb,':');
+            if ( !sc ) error("Could not determine CHROM in %s: %s\n", gen_fname,line.s);
+        }
+        kputsn(sb, sc-sb, &args->str);
+    }
+
+    // Initialize and print the VCF header, args->str.s contains the chr name
+    args->header = bcf_hdr_init("w");
+    bcf_hdr_append(args->header, "##INFO=<ID=END,Number=1,Type=Integer,Description=\"End position of the variant described in this record\">");
+    bcf_hdr_append(args->header, "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">");
+    bcf_hdr_append(args->header, "##FORMAT=<ID=GP,Number=G,Type=Float,Description=\"Genotype Probabilities\">");
+    bcf_hdr_printf(args->header, "##contig=<ID=%s,length=%d>", args->str.s,0x7fffffff);   // MAX_CSI_COOR
+    if (args->record_cmd_line) bcf_hdr_append_version(args->header, args->argc, args->argv, "bcftools_convert");
+
+    tsv_t *tsv;
+    if ( args->gen_3N6 )
+    {
+        tsv = tsv_init("CHROM,CHROM_POS_REF_ALT,ID,POS,REF_ALT,GT_GP");
+        tsv_register(tsv, "CHROM", tsv_setter_chrom, args->header);
+    }
+    else
+        tsv = tsv_init("CHROM_POS_REF_ALT,ID,POS,REF_ALT,GT_GP");
+    tsv_register(tsv, "CHROM_POS_REF_ALT", tsv_setter_chrom_pos_ref_alt_or_id, args);
+    tsv_register(tsv, "ID", tsv_setter_chrom_pos_ref_alt_id_or_die, args);
+    tsv_register(tsv, "POS", tsv_setter_verify_pos, NULL);
+    tsv_register(tsv, "REF_ALT", tsv_setter_verify_ref_alt, args);
+    tsv_register(tsv, "GT_GP", tsv_setter_gt_gp, args);
+
+    // Find out sample names
+    int i, nsamples;
+    char **samples = hts_readlist(sample_fname, 1, &nsamples);
+    if ( !samples ) error("Could not read %s\n", sample_fname);
+    for (i=2; i<nsamples; i++)
+    {
+        se = samples[i]; while ( *se && !isspace(*se) ) se++;
+        *se = 0;
+        bcf_hdr_add_sample(args->header,samples[i]);
+    }
+    for (i=0; i<nsamples; i++) free(samples[i]);
+    free(samples);
+
+    char wmode[8];
+    set_wmode(wmode,args->output_type,args->outfname,args->clevel);
+    htsFile *out_fh = hts_open(args->outfname ? args->outfname : "-", wmode);
+    if ( out_fh == NULL ) error("Can't write to \"%s\": %s\n", args->outfname, strerror(errno));
+    if ( args->n_threads ) hts_set_threads(out_fh, args->n_threads);
+    if ( bcf_hdr_write(out_fh,args->header)!=0 ) error("[%s] Error: cannot write the header to %s\n", __func__,args->outfname);
+    bcf1_t *rec = bcf_init();
+
+    nsamples -= 2;
+    args->gts = (int32_t *) malloc(sizeof(int32_t)*nsamples*2);
+    args->flt = (float *) malloc(sizeof(float)*nsamples*3);
+
+    do
+    {
+        bcf_clear(rec);
+        args->n.total++;
+        if ( !tsv_parse(tsv, rec, line.s) )
+        {
+            if ( bcf_write(out_fh, args->header, rec)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->outfname);
+        }
+        else
+            error("Error occurred while parsing: %s\n", line.s);
+    }
+    while ( hts_getline(gen_fh, KS_SEP_LINE, &line)>0 );
+
+    if ( hts_close(out_fh) ) error("Close failed: %s\n", args->outfname);
+    if ( hts_close(gen_fh) ) error("Close failed: %s\n", gen_fname);
+    bcf_hdr_destroy(args->header);
+    bcf_destroy(rec);
+    free(sample_fname);
+    free(gen_fname);
+    free(args->str.s);
+    free(line.s);
+    free(args->gts);
+    free(args->flt);
+    tsv_destroy(tsv);
+
+    fprintf(bcftools_stderr,"Number of processed rows: \t%d\n", args->n.total);
+}
+
+static void haplegendsample_to_vcf(args_t *args)
+{
+    /*
+     *  Convert from IMPUTE2 hap/legend/sample output files to VCF
+     *
+     *      hap:
+     *          0 1 0 1
+     *      legend:
+     *          id position a0 a1
+     *          1:186946386_G_T 186946386 G T
+     *      sample:
+     *          sample population group sex
+     *          sample1 sample1 sample1 2
+     *          sample2 sample2 sample2 2
+     *
+     *  Output: VCF with filled GT
+     */
+    kstring_t line = {0,0,0};
+
+    if ( args->output_vcf_ids )
+        error(
+            "The option --haplegendsample2vcf cannot be combined with --vcf-ids. This is because the\n"
+            "ID column must be formatted as \"CHROM:POS_REF_ALT\" to check sanity of the operation\n");
+
+    char *hap_fname = NULL, *leg_fname = NULL, *sample_fname = NULL;
+    sample_fname = strchr(args->infname,',');
+    if ( !sample_fname )
+    {
+        args->str.l = 0;
+        ksprintf(&args->str,"%s.hap.gz", args->infname);
+        hap_fname = strdup(args->str.s);
+        args->str.l = 0;
+        ksprintf(&args->str,"%s.samples", args->infname);
+        sample_fname = strdup(args->str.s);
+        args->str.l = 0;
+        ksprintf(&args->str,"%s.legend.gz", args->infname);
+        leg_fname = strdup(args->str.s);
+    }
+    else
+    {
+        char *ss = sample_fname, *se = strchr(ss+1,',');
+        if ( !se ) error("Could not parse hap/legend/sample file names: %s\n", args->infname);
+        *ss = 0;
+        *se = 0;
+        hap_fname = strdup(args->infname);
+        leg_fname = strdup(ss+1);
+        sample_fname = strdup(se+1);
+    }
+    htsFile *hap_fh = hts_open(hap_fname, "r");
+    if ( !hap_fh ) error("Could not read: %s\n", hap_fname);
+
+    htsFile *leg_fh = hts_open(leg_fname,"r");
+    if ( !leg_fh ) error("Could not read: %s\n", leg_fname);
+
+    // Eat up first legend line, then determine chromosome name
+    if ( hts_getline(leg_fh, KS_SEP_LINE, &line) <= 0 ) error("Empty file: %s\n", leg_fname);
+    if ( hts_getline(leg_fh, KS_SEP_LINE, &line) <= 0 ) error("Empty file: %s\n", leg_fname);
+
+    // Find out the chromosome name, sample names, init and print the VCF header
+    args->str.l = 0;
+    char *se = strchr(line.s,':');
+    if ( !se ) error("Expected CHROM:POS_REF_ALT in first column of %s\n", leg_fname);
+    kputsn(line.s, se-line.s, &args->str);
+
+    tsv_t *leg_tsv = tsv_init("CHROM_POS_REF_ALT,POS,REF_ALT");
+    tsv_register(leg_tsv, "CHROM_POS_REF_ALT", tsv_setter_chrom_pos_ref_alt, args);
+    tsv_register(leg_tsv, "POS", tsv_setter_verify_pos, NULL);
+    tsv_register(leg_tsv, "REF_ALT", tsv_setter_verify_ref_alt, args);
+    tsv_t *hap_tsv = tsv_init("HAPS");
+    tsv_register(hap_tsv, "HAPS", tsv_setter_haps, args);
+
+    args->header = bcf_hdr_init("w");
+    bcf_hdr_append(args->header, "##INFO=<ID=END,Number=1,Type=Integer,Description=\"End position of the variant described in this record\">");
+    bcf_hdr_append(args->header, "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">");
+    bcf_hdr_printf(args->header, "##contig=<ID=%s,length=%d>", args->str.s,0x7fffffff);   // MAX_CSI_COOR
+    if (args->record_cmd_line) bcf_hdr_append_version(args->header, args->argc, args->argv, "bcftools_convert");
+
+    int i, nrows, nsamples;
+    char **samples = hts_readlist(sample_fname, 1, &nrows);
+    if ( !samples ) error("Could not read %s\n", sample_fname);
+    nsamples = nrows - 1;
+
+    // sample_fname should contain a header line, so need to ignore first row
+    // returned from hts_readlist (i=1, and not i=0)
+    for (i=1; i<nrows; i++)
+    {
+        se = samples[i]; while ( *se && !isspace(*se) ) se++;
+        *se = 0;
+        bcf_hdr_add_sample(args->header,samples[i]);
+    }
+    bcf_hdr_add_sample(args->header,NULL);
+    for (i=0; i<nrows; i++) free(samples[i]);
+    free(samples);
+
+    char wmode[8];
+    set_wmode(wmode,args->output_type,args->outfname,args->clevel);
+    htsFile *out_fh = hts_open(args->outfname ? args->outfname : "-", wmode);
+    if ( out_fh == NULL ) error("Can't write to \"%s\": %s\n", args->outfname, strerror(errno));
+    if ( args->n_threads ) hts_set_threads(out_fh, args->n_threads);
+    if ( bcf_hdr_write(out_fh,args->header)!=0 ) error("[%s] Error: cannot write the header to %s\n", __func__,args->outfname);
+    bcf1_t *rec = bcf_init();
+
+    args->gts = (int32_t *) malloc(sizeof(int32_t)*nsamples*2);
+
+    while (1)
+    {
+        bcf_clear(rec);
+        args->n.total++;
+        if ( tsv_parse(leg_tsv, rec, line.s) )
+            error("Error occurred while parsing %s: %s\n", leg_fname,line.s);
+
+        if ( hts_getline(hap_fh,  KS_SEP_LINE, &line)<=0 )
+            error("Different number of records in %s and %s?\n", leg_fname,hap_fname);
+
+        if ( tsv_parse(hap_tsv, rec, line.s) )
+            error("Error occurred while parsing %s: %s\n", hap_fname,line.s);
+
+        if ( bcf_write(out_fh, args->header, rec)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->outfname);
+
+        if ( hts_getline(leg_fh, KS_SEP_LINE, &line)<=0 )
+        {
+            if ( hts_getline(hap_fh, KS_SEP_LINE, &line)>0 )
+                error("Different number of records in %s and %s?\n", leg_fname,hap_fname);
+            break;
+        }
+    }
+
+    if ( hts_close(out_fh) ) error("Close failed: %s\n", args->outfname);
+    if ( hts_close(hap_fh) ) error("Close failed: %s\n", hap_fname);
+    if ( hts_close(leg_fh) ) error("Close failed: %s\n", leg_fname);
+    bcf_hdr_destroy(args->header);
+    bcf_destroy(rec);
+    free(sample_fname);
+    free(hap_fname);
+    free(leg_fname);
+    free(args->str.s);
+    free(line.s);
+    free(args->gts);
+    tsv_destroy(hap_tsv);
+    tsv_destroy(leg_tsv);
+
+    fprintf(bcftools_stderr,"Number of processed rows: \t%d\n", args->n.total);
+}
+
+static void hapsample_to_vcf(args_t *args)
+{
+    /*
+     *  Input: SHAPEIT output
+     *
+     *      20:19995888_A_G rsid1 19995888 A G 0 0 0 0 ...
+     *      20 20:19995888_A_G 19995888 A G 0 0 0 0 ...
+     *
+     *  First column is expected in the form of CHROM:POS_REF_ALT
+     *
+     *  Output: VCF with filled GT
+     *
+     */
+    kstring_t line = {0,0,0};
+
+    char *hap_fname = NULL, *sample_fname = NULL;
+    sample_fname = strchr(args->infname,',');
+    if ( !sample_fname )
+    {
+        args->str.l = 0;
+        ksprintf(&args->str,"%s.hap.gz", args->infname);
+        hap_fname = strdup(args->str.s);
+        args->str.l = 0;
+        ksprintf(&args->str,"%s.samples", args->infname);
+        sample_fname = strdup(args->str.s);
+    }
+    else
+    {
+        *sample_fname = 0;
+        hap_fname = strdup(args->infname);
+        sample_fname = strdup(sample_fname+1);
+    }
+    htsFile *hap_fh = hts_open(hap_fname, "r");
+    if ( !hap_fh ) error("Could not read: %s\n", hap_fname);
+    if ( hts_getline(hap_fh, KS_SEP_LINE, &line) <= 0 ) error("Empty file: %s\n", hap_fname);
+
+    // Find out the chromosome name, it can be either in the first or second column
+    args->str.l = 0;
+    char *sb = line.s, *se = line.s;
+    while ( *se && !isspace(*se) ) se++;
+    if ( !*se ) error("Could not determine CHROM in %s: %s\n", hap_fname,line.s);
+    if ( !args->output_vcf_ids )
+    {
+        // first column should be just CHROM, but the second must be CHROM:POS_REF_ALT, use that
+        sb = ++se;
+        while ( *se && !isspace(*se) ) se++;
+        if ( !*se ) error("Could not determine CHROM in %s: %s\n", hap_fname,line.s);
+        if ( !strchr(sb,':') )
+            error("Could not determine CHROM in the second column of %s: %s\n", hap_fname,line.s);
+    }
+    // Parse CHROM:POS_REF_ALT
+    char *sc = strchr(sb,':');
+    if ( !sc || sc > se )
+        error("Could not determine CHROM in %s: %s\n", hap_fname,line.s);
+    kputsn(sb, sc-sb, &args->str);
+
+    // Initialize and print the VCF header, args->str.s contains the chr name
+    args->header = bcf_hdr_init("w");
+    bcf_hdr_append(args->header, "##INFO=<ID=END,Number=1,Type=Integer,Description=\"End position of the variant described in this record\">");
+    bcf_hdr_append(args->header, "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">");
+    bcf_hdr_printf(args->header, "##contig=<ID=%s,length=%d>", args->str.s,0x7fffffff);   // MAX_CSI_COOR
+    if (args->record_cmd_line) bcf_hdr_append_version(args->header, args->argc, args->argv, "bcftools_convert");
+
+    tsv_t *tsv;
+    if ( args->output_vcf_ids )
+    {
+        tsv = tsv_init("CHROM_POS_REF_ALT,ID,POS,REF_ALT,HAPS");
+        tsv_register(tsv, "ID", tsv_setter_id, args);
+    }
+    else
+    {
+        tsv = tsv_init("CHROM,CHROM_POS_REF_ALT,POS,REF_ALT,HAPS");
+        tsv_register(tsv, "CHROM", tsv_setter_chrom_pos_ref_alt_or_chrom, args);
+    }
+    tsv_register(tsv, "CHROM_POS_REF_ALT", tsv_setter_chrom_pos_ref_alt, args);
+    tsv_register(tsv, "POS", tsv_setter_verify_pos, NULL);
+    tsv_register(tsv, "REF_ALT", tsv_setter_verify_ref_alt, args);
+    tsv_register(tsv, "HAPS", tsv_setter_haps, args);
+
+    int i, nsamples;
+    char **samples = hts_readlist(sample_fname, 1, &nsamples);
+    if ( !samples ) error("Could not read %s\n", sample_fname);
+    for (i=2; i<nsamples; i++)
+    {
+        se = samples[i]; while ( *se && !isspace(*se) ) se++;
+        *se = 0;
+        bcf_hdr_add_sample(args->header,samples[i]);
+    }
+    bcf_hdr_add_sample(args->header,NULL);
+    for (i=0; i<nsamples; i++) free(samples[i]);
+    free(samples);
+
+    char wmode[8];
+    set_wmode(wmode,args->output_type,args->outfname,args->clevel);
+    htsFile *out_fh = hts_open(args->outfname ? args->outfname : "-", wmode);
+    if ( out_fh == NULL ) error("Can't write to \"%s\": %s\n", args->outfname, strerror(errno));
+    if ( args->n_threads ) hts_set_threads(out_fh, args->n_threads);
+    if ( bcf_hdr_write(out_fh,args->header)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->outfname);
+    bcf1_t *rec = bcf_init();
+
+    nsamples -= 2;
+    args->gts = (int32_t *) malloc(sizeof(int32_t)*nsamples*2);
+
+    do
+    {
+        bcf_clear(rec);
+        args->n.total++;
+        if ( !tsv_parse(tsv, rec, line.s) )
+        {
+            if ( bcf_write(out_fh, args->header, rec)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->outfname);
+        }
+        else
+            error("Error occurred while parsing: %s\n", line.s);
+    }
+    while ( hts_getline(hap_fh, KS_SEP_LINE, &line)>0 );
+
+    if ( hts_close(out_fh) ) error("Close failed: %s\n", args->outfname);
+    if ( hts_close(hap_fh) ) error("Close failed: %s\n", hap_fname);
+    bcf_hdr_destroy(args->header);
+    bcf_destroy(rec);
+    free(sample_fname);
+    free(hap_fname);
+    free(args->str.s);
+    free(line.s);
+    free(args->gts);
+    tsv_destroy(tsv);
+
+    fprintf(bcftools_stderr,"Number of processed rows: \t%d\n", args->n.total);
+}
+
+char *init_sample2sex(bcf_hdr_t *hdr, char *sex_fname)
+{
+    int i, nlines;
+    char *sample2sex = (char*) calloc(bcf_hdr_nsamples(hdr),1);
+    char **lines = hts_readlist(sex_fname, 1, &nlines);
+    if ( !lines ) error("Could not read %s\n", sex_fname);
+    for (i=0; i<nlines; i++)
+    {
+        char *se = lines[i]; while ( *se && !isspace(*se) ) se++;
+        char tmp = *se;
+        *se = 0;
+        int id = bcf_hdr_id2int(hdr, BCF_DT_SAMPLE, lines[i]);
+        *se = tmp;
+        if ( id<0 ) continue;
+        while ( *se && isspace(*se) ) se++;
+        if ( *se=='M' ) sample2sex[id] = '1';
+        else if ( *se=='F' ) sample2sex[id] = '2';
+        else error("Could not parse %s: %s\n", sex_fname,lines[i]);
+    }
+    for (i=0; i<nlines; i++) free(lines[i]);
+    free(lines);
+    for (i=0; i<bcf_hdr_nsamples(hdr); i++) 
+        if ( !sample2sex[i] ) error("Missing sex for sample %s in %s\n", bcf_hdr_int2id(hdr, BCF_DT_SAMPLE, i),sex_fname);
+    return sample2sex;
+}
+
+static void vcf_to_gensample(args_t *args)
+{
+    kstring_t str = {0,0,0};
+
+    // insert chrom as first column if needed
+    if ( args->gen_3N6 )
+        kputs("%CHROM ", &str);
+
+    kputs("%CHROM:%POS\\_%REF\\_%FIRST_ALT ", &str);
+
+    // insert rsid as second column if needed
+    if ( args->output_vcf_ids )
+        kputs("%ID ", &str);
+    else
+        kputs("%CHROM:%POS\\_%REF\\_%FIRST_ALT ", &str);
+
+    kputs("%POS %REF %FIRST_ALT", &str);
+    if ( !args->tag || !strcmp(args->tag,"GT") ) kputs("%_GT_TO_PROB3",&str);
+    else if ( !strcmp(args->tag,"PL") ) kputs("%_PL_TO_PROB3",&str);
+    else if ( !strcmp(args->tag,"GP") ) kputs("%_GP_TO_PROB3",&str);
+    else error("todo: --tag %s\n", args->tag);
+    kputs("\n", &str);
+    open_vcf(args,str.s);
+
+    int ret, gen_compressed = 1, sample_compressed = 0;
+    char *gen_fname = NULL, *sample_fname = NULL;
+    str.l = 0;
+    kputs(args->outfname,&str);
+    int n_files = 0, i;
+    char **files = hts_readlist(str.s, 0, &n_files);
+    if ( n_files==1 )
+    {
+        int l = str.l;
+        kputs(".samples",&str);
+        sample_fname = strdup(str.s);
+        str.l = l;
+        kputs(".gen.gz",&str);
+        gen_fname = strdup(str.s);
+    }
+    else if ( n_files==2 )
+    {
+        if (strlen(files[0]) && strcmp(files[0],".")!=0) gen_fname = strdup(files[0]);
+        if (strlen(files[1]) && strcmp(files[1],".")!=0) sample_fname = strdup(files[1]);
+    }
+    else
+    {
+        error("Error parsing --gensample filenames: %s\n", args->outfname);
+    }
+    for (i=0; i<n_files; i++) free(files[i]);
+    free(files);
+
+    if ( gen_fname && (strlen(gen_fname)<3 || strcasecmp(".gz",gen_fname+strlen(gen_fname)-3)) ) gen_compressed = 0;
+    if ( sample_fname && strlen(sample_fname)>3 && strcasecmp(".gz",sample_fname+strlen(sample_fname)-3)==0 ) sample_compressed = 0;
+
+    if (gen_fname) fprintf(bcftools_stderr, "Gen file: %s\n", gen_fname);
+    if (sample_fname) fprintf(bcftools_stderr, "Sample file: %s\n", sample_fname);
+
+    // write samples file
+    if (sample_fname) 
+    {
+        char *sample2sex = NULL;
+        if ( args->sex_fname ) sample2sex = init_sample2sex(args->header,args->sex_fname);
+
+        int i;
+        BGZF *sout = bgzf_open(sample_fname, sample_compressed ? "wg" : "wu");
+        str.l = 0;
+        kputs(sample2sex ? "ID_1 ID_2 missing sex\n0 0 0 0\n" : "ID_1 ID_2 missing\n0 0 0\n", &str);
+        ret = bgzf_write(sout, str.s, str.l);
+        if ( ret != str.l ) error("Error writing %s: %s\n", sample_fname, strerror(errno));
+        for (i=0; i<bcf_hdr_nsamples(args->header); i++)
+        {
+            str.l = 0;
+            if ( sample2sex )
+                ksprintf(&str, "%s %s 0 %c\n", args->header->samples[i],args->header->samples[i],sample2sex[i]);
+            else
+                ksprintf(&str, "%s %s 0\n", args->header->samples[i],args->header->samples[i]);
+            ret = bgzf_write(sout, str.s, str.l);
+            if ( ret != str.l ) error("Error writing %s: %s\n", sample_fname, strerror(errno));
+        }
+        if ( bgzf_close(sout)!=0 ) error("Error closing %s: %s\n", sample_fname, strerror(errno));
+        free(sample_fname);
+        free(sample2sex);
+    }
+    if (!gen_fname) {
+        if ( str.m ) free(str.s);
+        return;
+    }
+
+    int prev_rid = -1, prev_pos = -1;
+    int no_alt = 0, non_biallelic = 0, filtered = 0, ndup = 0, nok = 0;
+    BGZF *gout = bgzf_open(gen_fname, gen_compressed ? "wg" : "wu");
+    while ( bcf_sr_next_line(args->files) )
+    {
+        bcf1_t *line = bcf_sr_get_line(args->files,0);
+        if ( args->filter )
+        {
+            int pass = filter_test(args->filter, line, NULL);
+            if ( args->filter_logic & FLT_EXCLUDE ) pass = pass ? 0 : 1;
+            if ( !pass ) { filtered++; continue; }
+        }
+
+        // ALT allele is required
+        if ( line->n_allele<2 ) { no_alt++; continue; }
+
+        // biallelic required
+        if ( line->n_allele>2 ) {
+            if (!non_biallelic)
+                fprintf(bcftools_stderr, "Warning: non-biallelic records are skipped. Consider splitting multi-allelic records into biallelic records using 'bcftools norm -m-'.\n");
+            non_biallelic++;
+            continue;
+        }
+
+        // skip duplicate lines, or otherwise shapeit complains
+        if ( !args->keep_duplicates && prev_rid==line->rid && prev_pos==line->pos ) { ndup++; continue; }
+        prev_rid = line->rid;
+        prev_pos = line->pos;
+
+        str.l = 0;
+        convert_line(args->convert, line, &str);
+        if ( str.l )
+        {
+            int ret = bgzf_write(gout, str.s, str.l);
+            if ( ret!= str.l ) error("Error writing %s: %s\n", gen_fname,strerror(errno));
+            nok++;
+        }
+    }
+    fprintf(bcftools_stderr, "%d records written, %d skipped: %d/%d/%d/%d no-ALT/non-biallelic/filtered/duplicated\n", 
+        nok, no_alt+non_biallelic+filtered+ndup, no_alt, non_biallelic, filtered, ndup);
+
+    if ( str.m ) free(str.s);
+    if ( bgzf_close(gout)!=0 ) error("Error closing %s: %s\n", gen_fname,strerror(errno));
+    free(gen_fname);
+}
+
+static void vcf_to_haplegendsample(args_t *args)
+{
+    kstring_t str = {0,0,0};
+    if ( args->hap2dip )
+        kputs("%_GT_TO_HAP2\n", &str);
+    else
+        kputs("%_GT_TO_HAP\n", &str);
+    open_vcf(args,str.s);
+
+    int ret, hap_compressed = 1, legend_compressed = 1, sample_compressed = 0;
+    char *hap_fname = NULL, *legend_fname = NULL, *sample_fname = NULL;
+    str.l = 0;
+    kputs(args->outfname,&str);
+    int n_files = 0, i;
+    char **files = hts_readlist(str.s, 0, &n_files);
+    if ( n_files==1 )
+    {
+        int l = str.l;
+        kputs(".samples",&str);
+        sample_fname = strdup(str.s);
+        str.l = l;
+        kputs(".legend.gz",&str);
+        legend_fname = strdup(str.s);
+        str.l = l;
+        kputs(".hap.gz",&str);
+        hap_fname = strdup(str.s);
+    }
+    else if ( n_files==3 )
+    {
+        if (strlen(files[0]) && strcmp(files[0],".")!=0) hap_fname = strdup(files[0]);
+        if (strlen(files[1]) && strcmp(files[1],".")!=0) legend_fname = strdup(files[1]);
+        if (strlen(files[2]) && strcmp(files[2],".")!=0) sample_fname = strdup(files[2]);
+    }
+    else
+    {
+        error("Error parsing --hapslegendsample filenames: %s\n", args->outfname);
+    }
+    for (i=0; i<n_files; i++) free(files[i]);
+    free(files);
+
+    if ( hap_fname && (strlen(hap_fname)<3 || strcasecmp(".gz",hap_fname+strlen(hap_fname)-3)) ) hap_compressed = 0;
+    if ( legend_fname && (strlen(legend_fname)<3 || strcasecmp(".gz",legend_fname+strlen(legend_fname)-3)) ) legend_compressed = 0;
+    if ( sample_fname && strlen(sample_fname)>3 && strcasecmp(".gz",sample_fname+strlen(sample_fname)-3)==0 ) sample_compressed = 0;
+
+    if (hap_fname) fprintf(bcftools_stderr, "Hap file: %s\n", hap_fname);
+    if (legend_fname) fprintf(bcftools_stderr, "Legend file: %s\n", legend_fname);
+    if (sample_fname) fprintf(bcftools_stderr, "Sample file: %s\n", sample_fname);
+
+    // write samples file
+    if (sample_fname)
+    {
+        char *sample2sex = NULL;
+        if ( args->sex_fname ) sample2sex = init_sample2sex(args->header,args->sex_fname);
+        
+        int i;
+        BGZF *sout = bgzf_open(sample_fname, sample_compressed ? "wg" : "wu");
+        str.l = 0;
+        kputs("sample population group sex\n", &str);
+        ret = bgzf_write(sout, str.s, str.l);
+        if ( ret != str.l ) error("Error writing %s: %s\n", sample_fname, strerror(errno));
+        for (i=0; i<bcf_hdr_nsamples(args->header); i++)
+        {
+            str.l = 0;
+            ksprintf(&str, "%s %s %s %c\n", args->header->samples[i], args->header->samples[i], args->header->samples[i], sample2sex ? sample2sex[i] : '2');
+            ret = bgzf_write(sout, str.s, str.l);
+            if ( ret != str.l ) error("Error writing %s: %s\n", sample_fname, strerror(errno));
+        }
+        if ( bgzf_close(sout)!=0 ) error("Error closing %s: %s\n", sample_fname, strerror(errno));
+        free(sample_fname);
+        free(sample2sex);
+    }
+    if (!hap_fname && !legend_fname) {
+        if ( str.m ) free(str.s);
+        return;
+    }
+
+    // open haps and legend outputs
+    BGZF *hout = hap_fname ? bgzf_open(hap_fname, hap_compressed ? "wg" : "wu") : NULL;
+    if ( hap_compressed && args->n_threads ) bgzf_thread_pool(hout, args->files->p->pool, args->files->p->qsize);
+    BGZF *lout = legend_fname ? bgzf_open(legend_fname, legend_compressed ? "wg" : "wu") : NULL;
+    if (legend_fname) {
+        str.l = 0;
+        kputs("id position a0 a1\n", &str);
+        ret = bgzf_write(lout, str.s, str.l);
+        if ( ret != str.l ) error("Error writing %s: %s\n", legend_fname, strerror(errno));
+    }
+
+    int no_alt = 0, non_biallelic = 0, filtered = 0, nok = 0;
+    while ( bcf_sr_next_line(args->files) )
+    {
+        bcf1_t *line = bcf_sr_get_line(args->files,0);
+        if ( args->filter )
+        {
+            int pass = filter_test(args->filter, line, NULL);
+            if ( args->filter_logic & FLT_EXCLUDE ) pass = pass ? 0 : 1;
+            if ( !pass ) { filtered++; continue; }
+        }
+
+        // ALT allele is required
+        if ( line->n_allele<2 ) { no_alt++; continue; }
+        // biallelic required
+        if ( line->n_allele>2 ) {
+            if (!non_biallelic)
+                fprintf(bcftools_stderr, "Warning: non-biallelic records are skipped. Consider splitting multi-allelic records into biallelic records using 'bcftools norm -m-'.\n");
+            non_biallelic++;
+            continue;
+        }
+
+        str.l = 0;
+        convert_line(args->convert, line, &str);
+        if ( !str.l ) continue;
+
+        // write haps file
+        if (hap_fname) {
+            ret = bgzf_write(hout, str.s, str.l); // write hap file
+            if ( ret != str.l ) error("Error writing %s: %s\n", hap_fname, strerror(errno));
+        }
+        if (legend_fname) {
+            str.l = 0;
+            if ( args->output_vcf_ids && (line->d.id[0]!='.' || line->d.id[1]!=0) )
+                ksprintf(&str, "%s %"PRId64" %s %s\n", line->d.id, (int64_t) line->pos+1, line->d.allele[0], line->d.allele[1]);
+            else
+                ksprintf(&str, "%s:%"PRId64"_%s_%s %"PRId64" %s %s\n", bcf_seqname(args->header, line), (int64_t) line->pos+1, line->d.allele[0], line->d.allele[1], (int64_t) line->pos+1, line->d.allele[0], line->d.allele[1]);
+
+            // write legend file
+            ret = bgzf_write(lout, str.s, str.l);
+            if ( ret != str.l ) error("Error writing %s: %s\n", legend_fname, strerror(errno));
+        }
+        nok++;
+    }
+    fprintf(bcftools_stderr, "%d records written, %d skipped: %d/%d/%d no-ALT/non-biallelic/filtered\n", nok,no_alt+non_biallelic+filtered, no_alt, non_biallelic, filtered);
+    if ( str.m ) free(str.s);
+    if ( hout && bgzf_close(hout)!=0 ) error("Error closing %s: %s\n", hap_fname, strerror(errno));
+    if ( lout && bgzf_close(lout)!=0 ) error("Error closing %s: %s\n", legend_fname, strerror(errno));
+    if (hap_fname) free(hap_fname);
+    if (legend_fname) free(legend_fname);
+}
+
+static void vcf_to_hapsample(args_t *args)
+{
+    /*
+     *  WTCCC style haplotypes file
+     *  see https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html#hapsample
+     *
+     *  These are essentially the haplotypes from the impute2 format with some
+     *  legend info tacked on to the first 5 columns
+     *
+     */
+    kstring_t str = {0,0,0};
+
+    // print ID instead of CHROM:POS_REF_ALT1
+    if ( args->output_vcf_ids )
+        kputs("%CHROM:%POS\\_%REF\\_%FIRST_ALT %ID %POS %REF %FIRST_ALT ", &str);
+    else
+        kputs("%CHROM %CHROM:%POS\\_%REF\\_%FIRST_ALT %POS %REF %FIRST_ALT ", &str);
+    
+    if ( args->hap2dip )
+        kputs("%_GT_TO_HAP2\n", &str);
+    else
+        kputs("%_GT_TO_HAP\n", &str);
+    open_vcf(args,str.s);
+
+    int ret, hap_compressed = 1, sample_compressed = 0;
+    char *hap_fname = NULL, *sample_fname = NULL;
+    str.l = 0;
+    kputs(args->outfname,&str);
+    int n_files = 0, i;
+    char **files = hts_readlist(str.s, 0, &n_files);
+    if ( n_files==1 )
+    {
+        int l = str.l;
+        kputs(".samples",&str);
+        sample_fname = strdup(str.s);
+        str.l = l;
+        kputs(".hap.gz",&str);
+        hap_fname = strdup(str.s);
+    }
+    else if ( n_files==2 )
+    {
+        if (strlen(files[0]) && strcmp(files[0],".")!=0) hap_fname = strdup(files[0]);
+        if (strlen(files[1]) && strcmp(files[1],".")!=0) sample_fname = strdup(files[1]);
+    }
+    else
+    {
+        error("Error parsing --hapsample filenames: %s\n", args->outfname);
+    }
+    for (i=0; i<n_files; i++) free(files[i]);
+    free(files);
+
+    if ( hap_fname && (strlen(hap_fname)<3 || strcasecmp(".gz",hap_fname+strlen(hap_fname)-3)) ) hap_compressed = 0;
+    if ( sample_fname && strlen(sample_fname)>3 && strcasecmp(".gz",sample_fname+strlen(sample_fname)-3)==0 ) sample_compressed = 0;
+
+    if (hap_fname) fprintf(bcftools_stderr, "Hap file: %s\n", hap_fname);
+    if (sample_fname) fprintf(bcftools_stderr, "Sample file: %s\n", sample_fname);
+
+    // write samples file
+    if (sample_fname)
+    {
+        char *sample2sex = NULL;
+        if ( args->sex_fname ) sample2sex = init_sample2sex(args->header,args->sex_fname);
+
+        int i;
+        BGZF *sout = bgzf_open(sample_fname, sample_compressed ? "wg" : "wu");
+        str.l = 0;
+        kputs(sample2sex ? "ID_1 ID_2 missing sex\n0 0 0 0\n" : "ID_1 ID_2 missing\n0 0 0\n", &str);
+        ret = bgzf_write(sout, str.s, str.l);
+        if ( ret != str.l ) error("Error writing %s: %s\n", sample_fname, strerror(errno));
+        for (i=0; i<bcf_hdr_nsamples(args->header); i++)
+        {
+            str.l = 0;
+            if ( sample2sex )
+                ksprintf(&str, "%s %s 0 %c\n", args->header->samples[i],args->header->samples[i],sample2sex[i]);
+            else
+                ksprintf(&str, "%s %s 0\n", args->header->samples[i],args->header->samples[i]);
+            ret = bgzf_write(sout, str.s, str.l);
+            if ( ret != str.l ) error("Error writing %s: %s\n", sample_fname, strerror(errno));
+        }
+        if ( bgzf_close(sout)!=0 ) error("Error closing %s: %s\n", sample_fname, strerror(errno));
+        free(sample_fname);
+        free(sample2sex);
+    }
+    if (!hap_fname) {
+        if ( str.m ) free(str.s);
+        return;
+    }
+
+    // open haps output
+    BGZF *hout = hap_fname ? bgzf_open(hap_fname, hap_compressed ? "wg" : "wu") : NULL;
+    if ( hap_compressed && args->n_threads ) bgzf_thread_pool(hout, args->files->p->pool, args->files->p->qsize);
+
+    int no_alt = 0, non_biallelic = 0, filtered = 0, nok = 0;
+    while ( bcf_sr_next_line(args->files) )
+    {
+        bcf1_t *line = bcf_sr_get_line(args->files,0);
+        if ( args->filter )
+        {
+            int pass = filter_test(args->filter, line, NULL);
+            if ( args->filter_logic & FLT_EXCLUDE ) pass = pass ? 0 : 1;
+            if ( !pass ) { filtered++; continue; }
+        }
+
+        // ALT allele is required
+        if ( line->n_allele<2 ) { no_alt++; continue; }
+        // biallelic required
+        if ( line->n_allele>2 ) {
+            if (!non_biallelic)
+                fprintf(bcftools_stderr, "Warning: non-biallelic records are skipped. Consider splitting multi-allelic records into biallelic records using 'bcftools norm -m-'.\n");
+            non_biallelic++;
+            continue;
+        }
+
+        str.l = 0;
+        convert_line(args->convert, line, &str);
+        if ( !str.l ) continue;
+
+        // write haps file
+        if (hap_fname) {
+            ret = bgzf_write(hout, str.s, str.l); // write hap file
+            if ( ret != str.l ) error("Error writing %s: %s\n", hap_fname, strerror(errno));
+        }
+        nok++;
+    }
+    fprintf(bcftools_stderr, "%d records written, %d skipped: %d/%d/%d no-ALT/non-biallelic/filtered\n", nok, no_alt+non_biallelic+filtered, no_alt, non_biallelic, filtered);
+    if ( str.m ) free(str.s);
+    if ( hout && bgzf_close(hout)!=0 ) error("Error closing %s: %s\n", hap_fname, strerror(errno));
+    if (hap_fname) free(hap_fname);
+}
+
+static void bcf_hdr_set_chrs(bcf_hdr_t *hdr, faidx_t *fai)
+{
+    int i, n = faidx_nseq(fai);
+    for (i=0; i<n; i++)
+    {
+        const char *seq = faidx_iseq(fai,i);
+        int len = faidx_seq_len(fai, seq);
+        bcf_hdr_printf(hdr, "##contig=<ID=%s,length=%d>", seq,len);
+    }
+}
+static inline int acgt_to_5(char base)
+{
+    if ( base=='A' ) return 0;
+    if ( base=='C' ) return 1;
+    if ( base=='G' ) return 2;
+    if ( base=='T' ) return 3;
+    return 4;
+}
+static inline int tsv_setter_aa1(args_t *args, char *ss, char *se, int alleles[], int *nals, int ref, int32_t *gts)
+{
+    if ( se - ss > 2 ) return -1;   // currently only SNPs
+
+    if ( ss[0]=='-' )
+    {
+        // missing GT
+        gts[0] = bcf_gt_missing;
+        gts[1] = bcf_gt_missing;
+        args->n.missing++;
+        return 0;
+    }
+    if ( ss[0]=='I' ) return -2;    // skip insertions/deletions for now
+    if ( ss[0]=='D' ) return -2;
+
+    int a0 = acgt_to_5(toupper(ss[0]));
+    int a1 = ss[1] ? acgt_to_5(toupper(ss[1])) : a0;
+    if ( alleles[a0]<0 ) alleles[a0] = (*nals)++;
+    if ( alleles[a1]<0 ) alleles[a1] = (*nals)++;
+
+    gts[0] = bcf_gt_unphased(alleles[a0]); 
+    gts[1] = ss[1] ? bcf_gt_unphased(alleles[a1]) : bcf_int32_vector_end;
+
+    if ( ref==a0 && ref==a1  ) args->n.hom_rr++;    // hom ref: RR
+    else if ( ref==a0 ) args->n.het_ra++;           // het: RA
+    else if ( ref==a1 ) args->n.het_ra++;           // het: AR
+    else if ( a0==a1 ) args->n.hom_aa++;            // hom-alt: AA
+    else args->n.het_aa++;                          // non-ref het: AA
+
+    return 0;
+}
+static int tsv_setter_aa(tsv_t *tsv, bcf1_t *rec, void *usr)
+{
+    args_t *args = (args_t*) usr;
+
+    int len;
+    char *ref = faidx_fetch_seq(args->ref, (char*)bcf_hdr_id2name(args->header,rec->rid), rec->pos, rec->pos, &len);
+    if ( !ref ) error("faidx_fetch_seq failed at %s:%"PRId64"\n", bcf_hdr_id2name(args->header,rec->rid),(int64_t) rec->pos+1);
+
+    int nals = 1, alleles[5] = { -1, -1, -1, -1, -1 };    // a,c,g,t,n
+    ref[0] = toupper(ref[0]);
+    int iref = acgt_to_5(ref[0]);
+    alleles[iref] = 0;
+
+    rec->n_sample = bcf_hdr_nsamples(args->header);
+
+    int i, ret;
+    for (i=0; i<rec->n_sample; i++)
+    {
+        if ( i>0 )
+        {
+            ret = tsv_next(tsv);
+            if ( ret==-1 ) error("Too few columns for %d samples at %s:%"PRId64"\n", rec->n_sample,bcf_hdr_id2name(args->header,rec->rid),(int64_t) rec->pos+1);
+        }
+        ret = tsv_setter_aa1(args, tsv->ss, tsv->se, alleles, &nals, iref, args->gts+i*2);
+        if ( ret==-1 ) error("Error parsing the site %s:%"PRId64", expected two characters\n", bcf_hdr_id2name(args->header,rec->rid),(int64_t) rec->pos+1);
+        if ( ret==-2 ) 
+        {
+            // something else than a SNP
+            free(ref);
+            return -1;
+        }
+    }
+
+    args->str.l = 0;
+    kputc(ref[0], &args->str);
+    for (i=0; i<5; i++) 
+    {
+        if ( alleles[i]>0 )
+        {
+            kputc(',', &args->str);
+            kputc("ACGTN"[i], &args->str);
+        }
+    }
+    bcf_update_alleles_str(args->header, rec, args->str.s);
+    if ( bcf_update_genotypes(args->header,rec,args->gts,rec->n_sample*2) ) error("Could not update the GT field\n");
+
+    free(ref);
+    return 0;
+}
+
+static void tsv_to_vcf(args_t *args)
+{
+    if ( !args->ref_fname ) error("--tsv2vcf requires the --fasta-ref option\n");
+    if ( !args->sample_list ) error("--tsv2vcf requires the --samples option\n");
+
+    args->ref = fai_load(args->ref_fname);
+    if ( !args->ref ) error("Could not load the reference %s\n", args->ref_fname);
+
+    args->header = bcf_hdr_init("w");
+    bcf_hdr_set_chrs(args->header, args->ref);
+    bcf_hdr_append(args->header, "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">");
+    if (args->record_cmd_line) bcf_hdr_append_version(args->header, args->argc, args->argv, "bcftools_convert");
+
+    int i, n;
+    char **smpls = hts_readlist(args->sample_list, args->sample_is_file, &n);
+    if ( !smpls ) error("Could not parse %s\n", args->sample_list);
+    for (i=0; i<n; i++)
+    {
+        bcf_hdr_add_sample(args->header, smpls[i]);
+        free(smpls[i]);
+    }
+    free(smpls);
+    bcf_hdr_add_sample(args->header, NULL);
+    args->gts = (int32_t *) malloc(sizeof(int32_t)*n*2);
+
+    char wmode[8];
+    set_wmode(wmode,args->output_type,args->outfname,args->clevel);
+    htsFile *out_fh = hts_open(args->outfname ? args->outfname : "-", wmode);
+    if ( out_fh == NULL ) error("Can't write to \"%s\": %s\n", args->outfname, strerror(errno));
+    if ( args->n_threads ) hts_set_threads(out_fh, args->n_threads);
+    if ( bcf_hdr_write(out_fh,args->header)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->outfname);
+
+    tsv_t *tsv = tsv_init(args->columns ? args->columns : "ID,CHROM,POS,AA");
+    if ( tsv_register(tsv, "CHROM", tsv_setter_chrom, args->header) < 0 ) error("Expected CHROM column\n");
+    if ( tsv_register(tsv, "POS", tsv_setter_pos, NULL) < 0 ) error("Expected POS column\n");
+    if ( tsv_register(tsv, "ID", tsv_setter_id, args->header) < 0 && !args->columns ) error("Expected ID column\n");
+    if ( tsv_register(tsv, "AA", tsv_setter_aa, args) < 0 ) error("Expected AA column\n");
+
+    bcf1_t *rec = bcf_init();
+    bcf_float_set_missing(rec->qual);
+
+    kstring_t line = {0,0,0};
+    htsFile *in_fh = hts_open(args->infname, "r");
+    if ( !in_fh ) error("Could not read: %s\n", args->infname);
+    while ( hts_getline(in_fh, KS_SEP_LINE, &line) > 0 )
+    {
+        if ( line.s[0]=='#' ) continue;     // skip comments
+        bcf_clear(rec);
+
+        args->n.total++;
+        if ( !tsv_parse(tsv, rec, line.s) )
+        {
+            if ( bcf_write(out_fh, args->header, rec)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->outfname);
+        }
+        else
+            args->n.skipped++;
+    }
+    if ( hts_close(in_fh) ) error("Close failed: %s\n", args->infname);
+    free(line.s);
+
+    bcf_hdr_destroy(args->header);
+    if ( hts_close(out_fh)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,args->outfname);
+    tsv_destroy(tsv);
+    bcf_destroy(rec);
+    free(args->str.s);
+    free(args->gts);
+
+    fprintf(bcftools_stderr,"Rows total: \t%d\n", args->n.total);
+    fprintf(bcftools_stderr,"Rows skipped: \t%d\n", args->n.skipped);
+    fprintf(bcftools_stderr,"Missing GTs: \t%d\n", args->n.missing);
+    fprintf(bcftools_stderr,"Hom RR: \t%d\n", args->n.hom_rr);
+    fprintf(bcftools_stderr,"Het RA: \t%d\n", args->n.het_ra);
+    fprintf(bcftools_stderr,"Hom AA: \t%d\n", args->n.hom_aa);
+    fprintf(bcftools_stderr,"Het AA: \t%d\n", args->n.het_aa);
+}
+
+static void vcf_to_vcf(args_t *args)
+{
+    open_vcf(args,NULL);
+    char wmode[8];
+    set_wmode(wmode,args->output_type,args->outfname,args->clevel);
+    htsFile *out_fh = hts_open(args->outfname ? args->outfname : "-", wmode);
+    if ( out_fh == NULL ) error("Can't write to \"%s\": %s\n", args->outfname, strerror(errno));
+    if ( args->n_threads ) hts_set_threads(out_fh, args->n_threads);
+
+    bcf_hdr_t *hdr = bcf_sr_get_header(args->files,0);
+    if ( bcf_hdr_write(out_fh,hdr)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->outfname);
+
+    while ( bcf_sr_next_line(args->files) )
+    {
+        bcf1_t *line = bcf_sr_get_line(args->files,0);
+        if ( args->filter )
+        {
+            int pass = filter_test(args->filter, line, NULL);
+            if ( args->filter_logic & FLT_EXCLUDE ) pass = pass ? 0 : 1;
+            if ( !pass ) continue;
+        }
+        if ( bcf_write(out_fh,hdr,line)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->outfname);
+    }
+    if ( hts_close(out_fh)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,args->outfname);
+}
+
+static void gvcf_to_vcf(args_t *args)
+{
+    if ( !args->ref_fname ) error("--gvcf2vcf requires the --fasta-ref option\n");
+
+    args->ref = fai_load(args->ref_fname);
+    if ( !args->ref ) error("Could not load the fai index for reference %s\n", args->ref_fname);
+
+    open_vcf(args,NULL);
+    char wmode[8];
+    set_wmode(wmode,args->output_type,args->outfname,args->clevel);
+    htsFile *out_fh = hts_open(args->outfname ? args->outfname : "-", wmode);
+    if ( out_fh == NULL ) error("Can't write to \"%s\": %s\n", args->outfname, strerror(errno));
+    if ( args->n_threads ) hts_set_threads(out_fh, args->n_threads);
+
+    bcf_hdr_t *hdr = bcf_sr_get_header(args->files,0);
+    if (args->record_cmd_line) bcf_hdr_append_version(hdr, args->argc, args->argv, "bcftools_convert");
+    if ( bcf_hdr_write(out_fh,hdr)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->outfname);
+
+    int32_t *itmp = NULL, nitmp = 0;
+
+    while ( bcf_sr_next_line(args->files) )
+    {
+        bcf1_t *line = bcf_sr_get_line(args->files,0);
+        if ( args->filter )
+        {
+            int pass = filter_test(args->filter, line, NULL);
+            if ( args->filter_logic & FLT_EXCLUDE ) pass = pass ? 0 : 1;
+            if ( !pass ) 
+            {
+                if ( bcf_write(out_fh,hdr,line)!=0  ) error("[%s] Error: cannot write to %s\n", __func__,args->outfname);
+                continue;
+            }
+        }
+
+        // check if alleles compatible with being a gVCF record
+        // ALT must be one of ., <*>, <X>, <NON_REF>
+        // check for INFO/END is below
+        int i, gallele = -1;
+        if (line->n_allele==1)
+            gallele = 0; // illumina/bcftools-call gvcf (if INFO/END present)
+        else if ( line->d.allele[1][0]=='<' )
+        {
+            for (i=1; i<line->n_allele; i++)
+            {
+                if ( line->d.allele[i][1]=='*' && line->d.allele[i][2]=='>' && line->d.allele[i][3]=='\0' ) { gallele = i; break; } // mpileup/spec compliant gVCF
+                if ( line->d.allele[i][1]=='X' && line->d.allele[i][2]=='>' && line->d.allele[i][3]=='\0' ) { gallele = i; break; } // old mpileup gVCF
+                if ( strcmp(line->d.allele[i],"<NON_REF>")==0 ) { gallele = i; break; }               // GATK gVCF
+            }
+        }
+
+        // no gVCF compatible alleles
+        if (gallele<0)
+        {
+            if ( bcf_write(out_fh,hdr,line)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->outfname);
+            continue;
+        }
+
+        int nend = bcf_get_info_int32(hdr,line,"END",&itmp,&nitmp);
+        if ( nend!=1 )
+        {
+            // No INFO/END => not gVCF record
+            if ( bcf_write(out_fh,hdr,line)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->outfname);
+            continue;
+        }
+        bcf_update_info_int32(hdr,line,"END",NULL,0);
+        int pos, len;
+        for (pos=line->pos; pos<itmp[0]; pos++)
+        {
+            line->pos = pos;
+            char *ref = faidx_fetch_seq(args->ref, (char*)bcf_hdr_id2name(hdr,line->rid), line->pos, line->pos, &len);
+            if ( !ref ) error("faidx_fetch_seq failed at %s:%"PRId64"\n", bcf_hdr_id2name(hdr,line->rid),(int64_t) line->pos+1);
+            strncpy(line->d.allele[0],ref,len);
+            if ( bcf_write(out_fh,hdr,line)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->outfname);
+            free(ref);
+        }
+    }
+    free(itmp);
+    if ( hts_close(out_fh)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,args->outfname);
+}
+
+static void usage(void)
+{
+    fprintf(bcftools_stderr, "\n");
+    fprintf(bcftools_stderr, "About:   Converts VCF/BCF to other formats and back. See man page for file\n");
+    fprintf(bcftools_stderr, "         formats details. When specifying output files explicitly instead\n");
+    fprintf(bcftools_stderr, "         of with PREFIX, one can use '-' for bcftools_stdout and '.' to suppress.\n");
+    fprintf(bcftools_stderr, "Usage:   bcftools convert [OPTIONS] INPUT_FILE\n");
+    fprintf(bcftools_stderr, "\n");
+    fprintf(bcftools_stderr, "VCF input options:\n");
+    fprintf(bcftools_stderr, "   -e, --exclude EXPR             Exclude sites for which the expression is true\n");
+    fprintf(bcftools_stderr, "   -i, --include EXPR             Select sites for which the expression is true\n");
+    fprintf(bcftools_stderr, "   -r, --regions REGION           Restrict to comma-separated list of regions\n");
+    fprintf(bcftools_stderr, "   -R, --regions-file FILE        Restrict to regions listed in a file\n");
+    fprintf(bcftools_stderr, "       --regions-overlap 0|1|2    Include if POS in the region (0), record overlaps (1), variant overlaps (2) [1]\n");
+    fprintf(bcftools_stderr, "   -s, --samples LIST             List of samples to include\n");
+    fprintf(bcftools_stderr, "   -S, --samples-file FILE        File of samples to include\n");
+    fprintf(bcftools_stderr, "   -t, --targets REGION           Similar to -r but streams rather than index-jumps\n");
+    fprintf(bcftools_stderr, "   -T, --targets-file FILE        Similar to -R but streams rather than index-jumps\n");
+    fprintf(bcftools_stderr, "       --targets-overlap 0|1|2    Include if POS in the region (0), record overlaps (1), variant overlaps (2) [0]\n");
+    fprintf(bcftools_stderr, "\n");
+    fprintf(bcftools_stderr, "VCF output options:\n");
+    fprintf(bcftools_stderr, "       --no-version               Do not append version and command line to the header\n");
+    fprintf(bcftools_stderr, "   -o, --output FILE              Output file name [bcftools_stdout]\n");
+    fprintf(bcftools_stderr, "   -O, --output-type u|b|v|z[0-9] u/b: un/compressed BCF, v/z: un/compressed VCF, 0-9: compression level [v]\n");
+    fprintf(bcftools_stderr, "       --threads INT              Use multithreading with INT worker threads [0]\n");
+    fprintf(bcftools_stderr, "\n");
+    fprintf(bcftools_stderr, "GEN/SAMPLE conversion (input/output from IMPUTE2):\n");
+    fprintf(bcftools_stderr, "   -G, --gensample2vcf ...        <PREFIX>|<GEN-FILE>,<SAMPLE-FILE>\n");
+    fprintf(bcftools_stderr, "   -g, --gensample ...            <PREFIX>|<GEN-FILE>,<SAMPLE-FILE>\n");
+    fprintf(bcftools_stderr, "       --3N6                      Use 3*N+6 column format instead of the old 3*N+5 column format\n");
+    fprintf(bcftools_stderr, "       --tag STRING               Tag to take values for .gen file: GT,PL,GL,GP [GT]\n");
+    fprintf(bcftools_stderr, "       --chrom                    Output chromosome in first column instead of CHROM:POS_REF_ALT\n");
+    fprintf(bcftools_stderr, "       --keep-duplicates          Keep duplicate positions\n");
+    fprintf(bcftools_stderr, "       --sex FILE                 Output sex column in the sample-file, input format is: Sample\\t[MF]\n");
+    fprintf(bcftools_stderr, "       --vcf-ids                  Output VCF IDs in second column instead of CHROM:POS_REF_ALT\n");
+    fprintf(bcftools_stderr, "\n");
+    fprintf(bcftools_stderr, "gVCF conversion:\n");
+    fprintf(bcftools_stderr, "       --gvcf2vcf                 Expand gVCF reference blocks\n");
+    fprintf(bcftools_stderr, "   -f, --fasta-ref FILE           Reference sequence in fasta format\n");
+    fprintf(bcftools_stderr, "\n");
+    fprintf(bcftools_stderr, "HAP/SAMPLE conversion (output from SHAPEIT):\n");
+    fprintf(bcftools_stderr, "       --hapsample2vcf ...        <PREFIX>|<HAP-FILE>,<SAMPLE-FILE>\n");
+    fprintf(bcftools_stderr, "       --hapsample ...            <PREFIX>|<HAP-FILE>,<SAMPLE-FILE>\n");
+    fprintf(bcftools_stderr, "       --haploid2diploid          Convert haploid genotypes to diploid homozygotes\n");
+    fprintf(bcftools_stderr, "       --sex FILE                 Output sex column in the sample-file, input format is: Sample\\t[MF]\n");
+    fprintf(bcftools_stderr, "       --vcf-ids                  Output VCF IDs instead of CHROM:POS_REF_ALT\n");
+    fprintf(bcftools_stderr, "\n");
+    fprintf(bcftools_stderr, "HAP/LEGEND/SAMPLE conversion:\n");
+    fprintf(bcftools_stderr, "   -H, --haplegendsample2vcf ...  <PREFIX>|<HAP-FILE>,<LEGEND-FILE>,<SAMPLE-FILE>\n");
+    fprintf(bcftools_stderr, "   -h, --haplegendsample ...      <PREFIX>|<HAP-FILE>,<LEGEND-FILE>,<SAMPLE-FILE>\n");
+    fprintf(bcftools_stderr, "       --haploid2diploid          Convert haploid genotypes to diploid homozygotes\n");
+    fprintf(bcftools_stderr, "       --sex FILE                 Output sex column in the sample-file, input format is: Sample\\t[MF]\n");
+    fprintf(bcftools_stderr, "       --vcf-ids                  Output VCF IDs instead of CHROM:POS_REF_ALT\n");
+    fprintf(bcftools_stderr, "\n");
+    fprintf(bcftools_stderr, "TSV conversion:\n");
+    fprintf(bcftools_stderr, "       --tsv2vcf FILE\n");
+    fprintf(bcftools_stderr, "   -c, --columns STRING           Columns of the input tsv file [ID,CHROM,POS,AA]\n");
+    fprintf(bcftools_stderr, "   -f, --fasta-ref FILE           Reference sequence in fasta format\n");
+    fprintf(bcftools_stderr, "   -s, --samples LIST             List of sample names\n");
+    fprintf(bcftools_stderr, "   -S, --samples-file FILE        File of sample names\n");
+    fprintf(bcftools_stderr, "\n");
+    // fprintf(bcftools_stderr, "PLINK options:\n");
+    // fprintf(bcftools_stderr, "   -p, --plink <prefix>|<ped>,<map>,<fam>|<bed>,<bim>,<fam>|<tped>,<tfam>\n");
+    // fprintf(bcftools_stderr, "       --tped              make tped file instead\n");
+    // fprintf(bcftools_stderr, "       --bin               make binary bed/fam/bim files\n");
+    // fprintf(bcftools_stderr, "\n");
+    // fprintf(bcftools_stderr, "PBWT options:\n");
+    // fprintf(bcftools_stderr, "   -b, --pbwt          <prefix> or <pbwt>,<sites>,<sample>,<missing>\n");
+    // fprintf(bcftools_stderr, "\n");
+    bcftools_exit(1);
+}
+
+int main_vcfconvert(int argc, char *argv[])
+{
+    int c;
+    args_t *args = (args_t*) calloc(1,sizeof(args_t));
+    args->argc   = argc; args->argv = argv;
+    args->outfname = "-";
+    args->output_type = FT_VCF;
+    args->n_threads = 0;
+    args->record_cmd_line = 1;
+    args->regions_overlap = 1;
+    args->targets_overlap = 0;
+    args->clevel = -1;
+
+    static struct option loptions[] =
+    {
+        {"include",required_argument,NULL,'i'},
+        {"exclude",required_argument,NULL,'e'},
+        {"output",required_argument,NULL,'o'},
+        {"output-type",required_argument,NULL,'O'},
+        {"threads",required_argument,NULL,9},
+        {"regions",required_argument,NULL,'r'},
+        {"regions-file",required_argument,NULL,'R'},
+        {"regions-overlap",required_argument,NULL,13},
+        {"targets",required_argument,NULL,'t'},
+        {"targets-file",required_argument,NULL,'T'},
+        {"targets-overlap",required_argument,NULL,14},
+        {"samples",required_argument,NULL,'s'},
+        {"samples-file",required_argument,NULL,'S'},
+        {"sex",required_argument,NULL,11},
+        {"gensample",required_argument,NULL,'g'},
+        {"gensample2vcf",required_argument,NULL,'G'},
+        {"tag",required_argument,NULL,1},
+        {"chrom",no_argument,NULL,8},
+        {"3N6",no_argument,NULL,15},
+        {"tsv2vcf",required_argument,NULL,2},
+        {"hapsample",required_argument,NULL,7},
+        {"hapsample2vcf",required_argument,NULL,3},
+        {"vcf-ids",no_argument,NULL,4},
+        {"haploid2diploid",no_argument,NULL,5},
+        {"gvcf2vcf",no_argument,NULL,6},
+        {"haplegendsample",required_argument,NULL,'h'},
+        {"haplegendsample2vcf",required_argument,NULL,'H'},
+        {"columns",required_argument,NULL,'c'},
+        {"fasta-ref",required_argument,NULL,'f'},
+        {"no-version",no_argument,NULL,10},
+        {"keep-duplicates",no_argument,NULL,12},
+        {NULL,0,NULL,0}
+    };
+    char *tmp;
+    while ((c = getopt_long(argc, argv, "?h:r:R:s:S:t:T:i:e:g:G:o:O:c:f:H:",loptions,NULL)) >= 0) {
+        switch (c) {
+            case 'e':
+                if ( args->filter_str ) error("Error: only one -i or -e expression can be given, and they cannot be combined\n");
+                args->filter_str = optarg; args->filter_logic |= FLT_EXCLUDE; break;
+            case 'i':
+                if ( args->filter_str ) error("Error: only one -i or -e expression can be given, and they cannot be combined\n");
+                args->filter_str = optarg; args->filter_logic |= FLT_INCLUDE; break;
+            case 'r': args->regions_list = optarg; break;
+            case 'R': args->regions_list = optarg; args->regions_is_file = 1; break;
+            case 't': args->targets_list = optarg; break;
+            case 'T': args->targets_list = optarg; args->targets_is_file = 1; break;
+            case 's': args->sample_list = optarg; break;
+            case 'S': args->sample_list = optarg; args->sample_is_file = 1; break;
+            case 'g': args->convert_func = vcf_to_gensample; args->outfname = optarg; break;
+            case 'G': args->convert_func = gensample_to_vcf; args->infname = optarg; break;
+            case  1 : args->tag = optarg; break;
+            case  2 : args->convert_func = tsv_to_vcf; args->infname = optarg; break;
+            case  3 : args->convert_func = hapsample_to_vcf; args->infname = optarg; break;
+            case  4 : args->output_vcf_ids = 1; break;
+            case  5 : args->hap2dip = 1; break;
+            case  6 : args->convert_func = gvcf_to_vcf; break;
+            case  7 : args->convert_func = vcf_to_hapsample; args->outfname = optarg; break;
+            case  8 : error("The --chrom option has been deprecated, please use --3N6 instead\n"); break;
+            case 15 : args->gen_3N6 = 1; break;
+            case 'H': args->convert_func = haplegendsample_to_vcf; args->infname = optarg; break;
+            case 'f': args->ref_fname = optarg; break;
+            case 'c': args->columns = optarg; break;
+            case 'o': args->outfname = optarg; break;
+            case 'O':
+                switch (optarg[0]) {
+                    case 'b': args->output_type = FT_BCF_GZ; break;
+                    case 'u': args->output_type = FT_BCF; break;
+                    case 'z': args->output_type = FT_VCF_GZ; break;
+                    case 'v': args->output_type = FT_VCF; break;
+                    default:
+                    {
+                        args->clevel = strtol(optarg,&tmp,10);
+                        if ( *tmp || args->clevel<0 || args->clevel>9 ) error("The output type \"%s\" not recognised\n", optarg);
+                    }
+                }
+                if ( optarg[1] )
+                {
+                    args->clevel = strtol(optarg+1,&tmp,10);
+                    if ( *tmp || args->clevel<0 || args->clevel>9 ) error("Could not parse argument: --compression-level %s\n", optarg+1);
+                }
+                break;
+            case 'h': args->convert_func = vcf_to_haplegendsample; args->outfname = optarg; break;
+            case  9 : args->n_threads = strtol(optarg, 0, 0); break;
+            case 10 : args->record_cmd_line = 0; break;
+            case 11 : args->sex_fname = optarg; break;
+            case 12 : args->keep_duplicates = 1; break;
+            case 13 :
+                args->regions_overlap = parse_overlap_option(optarg);
+                if ( args->regions_overlap < 0 ) error("Could not parse: --regions-overlap %s\n",optarg);
+                break;
+            case 14 :
+                args->targets_overlap = parse_overlap_option(optarg);
+                if ( args->targets_overlap < 0 ) error("Could not parse: --targets-overlap %s\n",optarg);
+                break;
+            case '?': usage(); break;
+            default: error("Unknown argument: %s\n", optarg);
+        }
+    }
+
+    if ( !args->infname )
+    {
+        if ( optind>=argc )
+        {
+            if ( !isatty(fileno((FILE *)stdin)) ) args->infname = "-";
+        }
+        else args->infname = argv[optind];
+    }
+    if ( !args->infname ) usage();
+    
+    if ( args->convert_func ) args->convert_func(args);
+    else vcf_to_vcf(args);
+
+    destroy_data(args);
+    free(args);
+    return 0;
+}
diff --git a/bcftools/vcffilter.c b/bcftools/vcffilter.c
new file mode 100644
index 0000000..68d8672
--- /dev/null
+++ b/bcftools/vcffilter.c
@@ -0,0 +1,722 @@
+/*  vcffilter.c -- Apply fixed-threshold filters.
+
+    Copyright (C) 2013-2022 Genome Research Ltd.
+
+    Author: Petr Danecek <pd3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.  */
+
+#include <stdio.h>
+#include <unistd.h>
+#include <getopt.h>
+#include <assert.h>
+#include <ctype.h>
+#include <string.h>
+#include <strings.h>
+#include <errno.h>
+#include <sys/stat.h>
+#include <sys/types.h>
+#include <math.h>
+#include <htslib/vcf.h>
+#include <htslib/synced_bcf_reader.h>
+#include <htslib/vcfutils.h>
+#include "bcftools.h"
+#include "filter.h"
+#include "rbuf.h"
+#include "regidx.h"
+
+// Logic of the filters: include or exclude sites which match the filters?
+#define FLT_INCLUDE 1
+#define FLT_EXCLUDE 2
+
+// FILTER columns annotation: replace or add to existing FILTERs; set FILTER to PASS at good sites?
+#define ANNOT_ADD   1
+#define ANNOT_RESET 2
+
+// Set genotypes of filtered samples
+#define SET_GTS_MISSING 1
+#define SET_GTS_REF 2
+
+typedef struct _args_t
+{
+    filter_t *filter;
+    char *filter_str;
+    int filter_logic;   // include or exclude sites which match the filters? One of FLT_INCLUDE/FLT_EXCLUDE
+    const uint8_t *smpl_pass;
+    int set_gts;
+    char *soft_filter;  // drop failed sites or annotate FILTER column?
+    int annot_mode;     // add to existing FILTER annotation or replace? Otherwise reset FILTER to PASS or leave as it is?
+    int flt_fail, flt_pass;     // BCF ids of fail and pass filters
+    int snp_gap, snp_gap_type, indel_gap, IndelGap_id, SnpGap_id;
+    char *snp_gap_str;
+    int32_t ntmpi, *tmpi, ntmp_ac, *tmp_ac;
+    rbuf_t rbuf;
+    bcf1_t **rbuf_lines;
+
+    bcf_srs_t *files;
+    bcf_hdr_t *hdr;
+    htsFile *out_fh;
+    int output_type, n_threads, clevel;
+
+    char **argv, *output_fname, *targets_list, *regions_list, *mask_list;
+    int argc, record_cmd_line, mask_is_file, mask_overlap, mask_negate;
+    regidx_t *mask;
+}
+args_t;
+
+static void init_data(args_t *args)
+{
+    char wmode[8];
+    set_wmode(wmode,args->output_type,args->output_fname,args->clevel);
+    args->out_fh = hts_open(args->output_fname ? args->output_fname : "-", wmode);
+    if ( args->out_fh == NULL ) error("Can't write to \"%s\": %s\n", args->output_fname, strerror(errno));
+    if ( args->n_threads ) hts_set_threads(args->out_fh, args->n_threads);
+
+    if ( args->mask_list )
+    {
+        if ( args->mask_list[0]=='^' ) args->mask_negate = 1;
+        if ( args->mask_is_file )
+            args->mask = regidx_init(args->mask_negate?args->mask_list+1:args->mask_list,NULL,NULL,0,NULL);
+        else
+        {
+            char *rmme = strdup(args->mask_negate?args->mask_list+1:args->mask_list), *tmp = rmme;
+            while ( *tmp )
+            {
+                if ( *tmp==',' ) *tmp = '\n';
+                tmp++;
+            }
+            args->mask = regidx_init_string(rmme, regidx_parse_reg, NULL, 0, NULL);
+            free(rmme);
+        }
+        if ( !args->mask )
+            error("Could not initialize the mask: %s\n",args->mask_list);
+    }
+
+    args->hdr = args->files->readers[0].header;
+    args->flt_pass = bcf_hdr_id2int(args->hdr,BCF_DT_ID,"PASS"); assert( !args->flt_pass );  // sanity check: required by BCF spec
+
+    if ( args->soft_filter && (args->filter_logic || args->mask_list) )
+    {
+        kstring_t flt_name = {0,0,0};
+        if ( strcmp(args->soft_filter,"+") )
+            kputs(args->soft_filter, &flt_name);
+        else
+        {
+            // Make up a filter name
+            int i = 0, id = -1;
+            do
+            {
+                ksprintf(&flt_name,"Filter%d", ++i);
+                id = bcf_hdr_id2int(args->hdr,BCF_DT_ID,flt_name.s);
+            }
+            while ( bcf_hdr_idinfo_exists(args->hdr,BCF_HL_FLT,id) );
+        }
+
+        kstring_t tmp = {0,0,0};
+        if ( args->filter_logic )
+        {
+            // -i or -e: append FILTER line
+            ksprintf(&tmp,"Set if %s: ",args->filter_logic & FLT_INCLUDE ? "not true" : "true");
+
+            // escape quotes
+            char *t = args->filter_str;
+            while ( *t )
+            {
+                if ( *t=='"' ) kputc('\\',&tmp);
+                kputc(*t,&tmp);
+                t++;
+            }
+        }
+        else if ( args->mask_list )
+            ksprintf(&tmp,"Record masked by region");
+
+        int ret = bcf_hdr_printf(args->hdr, "##FILTER=<ID=%s,Description=\"%s\">", flt_name.s,tmp.s);
+        if ( ret!=0 )
+            error("Failed to append header line: ##FILTER=<ID=%s,Description=\"%s\">\n", flt_name.s,tmp.s);
+        args->flt_fail = bcf_hdr_id2int(args->hdr,BCF_DT_ID,flt_name.s); assert( args->flt_fail>=0 );
+        free(flt_name.s);
+        free(tmp.s);
+    }
+
+    if ( args->snp_gap || args->indel_gap )
+    {
+        if ( !args->filter_logic && args->soft_filter && strcmp(args->soft_filter,"+") )
+        {
+            kstring_t tmp = {0,0,0};
+            if ( args->snp_gap ) kputs("\"SnpGap\"", &tmp);
+            if ( args->indel_gap )
+            {
+                if ( tmp.s ) kputs(" and ", &tmp);
+                kputs("\"IndelGap\"", &tmp);
+            }
+            if ( strncmp(tmp.s+1,args->soft_filter,tmp.l-2) )
+                fprintf(stderr,"Warning: using %s filter name instead of \"%s\"\n", tmp.s,args->soft_filter);
+            free(tmp.s);
+        }
+
+        rbuf_init(&args->rbuf, 64);
+        args->rbuf_lines = (bcf1_t**) calloc(args->rbuf.m, sizeof(bcf1_t*));
+        if ( args->snp_gap )
+        {
+            bcf_hdr_printf(args->hdr, "##FILTER=<ID=SnpGap,Description=\"SNP within %d bp of %s\">", args->snp_gap,args->snp_gap_str);
+            args->SnpGap_id = bcf_hdr_id2int(args->hdr, BCF_DT_ID, "SnpGap");
+            assert( args->SnpGap_id>=0 );
+        }
+        if ( args->indel_gap )
+        {
+            bcf_hdr_printf(args->hdr, "##FILTER=<ID=IndelGap,Description=\"Indel within %d bp of an indel\">", args->indel_gap);
+            args->IndelGap_id = bcf_hdr_id2int(args->hdr, BCF_DT_ID, "IndelGap");
+            assert( args->IndelGap_id>=0 );
+        }
+    }
+
+    if (args->record_cmd_line) bcf_hdr_append_version(args->hdr, args->argc, args->argv, "bcftools_filter");
+
+    if ( args->filter_str )
+        args->filter = filter_init(args->hdr, args->filter_str);
+}
+
+static void destroy_data(args_t *args)
+{
+    if ( args->rbuf_lines )
+    {
+        int i;
+        for (i=0; i<args->rbuf.m; i++)
+            if ( args->rbuf_lines[i] ) bcf_destroy1(args->rbuf_lines[i]);
+        free(args->rbuf_lines);
+    }
+    if ( args->filter )
+        filter_destroy(args->filter);
+    free(args->tmpi);
+    free(args->tmp_ac);
+    if ( args->mask ) regidx_destroy(args->mask);
+}
+
+static void flush_buffer(args_t *args, int n)
+{
+    int i, j;
+    for (i=0; i<n; i++)
+    {
+        int k = rbuf_shift(&args->rbuf);
+        bcf1_t *rec = args->rbuf_lines[k];
+
+        int pass = 1;
+        if ( !args->soft_filter )
+        {
+            for (j=0; j<rec->d.n_flt; j++)
+            {
+                if ( args->indel_gap && rec->d.flt[j]==args->IndelGap_id ) { pass = 0; break; }
+                if ( args->snp_gap && rec->d.flt[j]==args->SnpGap_id ) { pass = 0; break; }
+            }
+        }
+        if ( pass && bcf_write1(args->out_fh, args->hdr, rec)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->output_fname);
+    }
+}
+
+#define SWAP(type_t, a, b) { type_t t = a; a = b; b = t; }
+static void buffered_filters(args_t *args, bcf1_t *line)
+{
+    /**
+     *  The logic of SnpGap=3. The SNPs at positions 1 and 7 are filtered,
+     *  positions 0 and 8 are not:
+     *           0123456789
+     *      ref  .G.GT..G..
+     *      del  .A.G-..A..
+     *  Here the positions 1 and 6 are filtered, 0 and 7 are not:
+     *           0123-456789
+     *      ref  .G.G-..G..
+     *      ins  .A.GT..A..
+     *
+     *  The logic of IndelGap=2. The second indel is filtered:
+     *           012345678901
+     *      ref  .GT.GT..GT..
+     *      del  .G-.G-..G-..
+     *  And similarly here, the second is filtered:
+     *           01 23 456 78
+     *      ref  .A-.A-..A-..
+     *      ins  .AT.AT..AT..
+     */
+
+    // To avoid additional data structure, we abuse bcf1_t's var and var_type records.
+    const int SnpGap_set     = 1 << (8*sizeof(int)/2);
+    const int IndelGap_set   = 1 << (8*sizeof(int)/2-1);
+    const int IndelGap_flush = 1 << (8*sizeof(int)/2-2);
+
+    int var_type = 0, i;
+    if ( line )
+    {
+        // Still on the same chromosome?
+        int ilast = rbuf_last(&args->rbuf);
+        if ( ilast>=0 && line->rid != args->rbuf_lines[ilast]->rid )
+            flush_buffer(args, args->rbuf.n); // new chromosome, flush everything
+
+        rbuf_expand0(&args->rbuf,bcf1_t*,args->rbuf.n,args->rbuf_lines);
+
+        // Insert the new record in the buffer. The line would be overwritten in
+        // the next bcf_sr_next_line call, therefore we need to swap it with an
+        // unused one
+        ilast = rbuf_append(&args->rbuf);
+        if ( !args->rbuf_lines[ilast] ) args->rbuf_lines[ilast] = bcf_init1();
+        SWAP(bcf1_t*, args->files->readers[0].buffer[0], args->rbuf_lines[ilast]);
+
+        var_type = bcf_get_variant_types(line);
+
+        // Find out the size of an indel. The indel boundaries are based on REF
+        // (POS+1,POS+rlen-1). This is not entirely correct: mpileup likes to
+        // output REF=CAGAGAGAGA, ALT=CAGAGAGAGAGA where REF=C,ALT=CGA could be
+        // used. This filter is therefore more strict and may remove some valid
+        // SNPs.
+        // Set the REF allele's length to max deletion length or to 1 if a SNP or an insertion.
+        line->d.var[0].n = line->rlen;
+    }
+
+    int k_flush = 1;
+    if ( args->indel_gap )
+    {
+        k_flush = 0;
+        // Find indels which are too close to each other
+        int last_to = -1;
+        for (i=-1; rbuf_next(&args->rbuf,&i); )
+        {
+            bcf1_t *rec  = args->rbuf_lines[i];
+            int rec_from = rec->pos;
+            if ( last_to!=-1 && last_to < rec_from ) break;
+
+            k_flush++;
+            if ( !(rec->d.var_type & VCF_INDEL) ) continue;
+
+            rec->d.var_type |= IndelGap_set;
+            last_to = args->indel_gap + rec->pos + rec->d.var[0].n - 1;
+        }
+        if ( i==args->rbuf.f && line && last_to!=-1 ) k_flush = 0;
+        if ( k_flush || !line )
+        {
+            // Select the best indel from the cluster of k_flush indels
+            int k = 0, max_ac = -1, imax_ac = -1, max_qual = -1, imax_qual = -1;
+            for (i=-1; rbuf_next(&args->rbuf,&i) && k<k_flush; )
+            {
+                k++;
+                bcf1_t *rec  = args->rbuf_lines[i];
+                if ( !(rec->d.var_type & IndelGap_set) ) continue;
+                hts_expand(int, rec->n_allele, args->ntmpi, args->tmpi);
+                int ret = bcf_calc_ac(args->hdr, rec, args->tmpi, BCF_UN_ALL);
+                if ( imax_ac==-1 || (ret && max_ac < args->tmpi[1]) ) { max_ac = args->tmpi[1]; imax_ac = i; }
+                if ( imax_qual==-1 || max_qual < rec->qual ) { max_qual = rec->qual; imax_qual = i; }
+            }
+
+            // Filter all but the best indel (with the best QUAL, bigger AC, or take the first if neither QUAL nor AC are available)
+            k = 0;
+            for (i=-1; rbuf_next(&args->rbuf,&i) && k<k_flush; )
+            {
+                k++;
+                bcf1_t *rec = args->rbuf_lines[i];
+                if ( !(rec->d.var_type & IndelGap_set) ) continue;
+                rec->d.var_type |= IndelGap_flush;
+
+                int do_filter = 0;
+                if ( max_qual>0 )
+                {
+                    if ( i!=imax_qual ) do_filter = 1;
+                }
+                else if ( i!=imax_ac ) do_filter = 1;
+                if ( do_filter ) bcf_add_filter(args->hdr, args->rbuf_lines[i], args->IndelGap_id);
+            }
+        }
+    }
+
+    if ( !line )
+    {
+        // Finished: flush everything
+        flush_buffer(args, args->rbuf.n);
+        return;
+    }
+
+    int j_flush = 1;
+    if ( args->snp_gap )
+    {
+        j_flush = 0;
+        int last_from = line->pos;
+        for (i=-1; rbuf_next(&args->rbuf,&i); )
+        {
+            bcf1_t *rec = args->rbuf_lines[i];
+            int rec_to  = rec->pos + rec->d.var[0].n - 1;   // last position affected by the variant
+            if ( rec_to + args->snp_gap < last_from )
+                j_flush++;
+            else if ( (var_type & args->snp_gap_type) && (rec->d.var_type & VCF_SNP) && !(rec->d.var_type & SnpGap_set) )
+            {
+                // this SNP has not been SnpGap-filtered yet
+                rec->d.var_type |= SnpGap_set;
+                bcf_add_filter(args->hdr, rec, args->SnpGap_id);
+            }
+            else if ( (var_type & VCF_SNP) && (rec->d.var_type & args->snp_gap_type) )
+            {
+                // the line which we are adding is a SNP and needs to be filtered
+                line->d.var_type |= SnpGap_set;
+                bcf_add_filter(args->hdr, line, args->SnpGap_id);
+                break;
+            }
+        }
+    }
+    flush_buffer(args, j_flush < k_flush ? j_flush : k_flush);
+}
+
+static void set_genotypes(args_t *args, bcf1_t *line, int pass_site)
+{
+    int i,j;
+    if ( !bcf_hdr_nsamples(args->hdr) ) return;
+    if ( args->smpl_pass )
+    {
+        int npass = 0;
+        for (i=0; i<bcf_hdr_nsamples(args->hdr); i++) npass += args->smpl_pass[i];
+
+        // return if all samples pass
+        if ( npass==bcf_hdr_nsamples(args->hdr) && (args->filter_logic & FLT_INCLUDE) ) return;
+        if ( npass==0 && (args->filter_logic & FLT_EXCLUDE) ) return;
+    }
+    else if ( pass_site ) return;
+
+    int an = 0, has_an = bcf_get_info_int32(args->hdr, line, "AN", &args->tmp_ac, &args->ntmp_ac);
+    if ( has_an==1 ) an = args->tmp_ac[0];
+    else has_an = 0;
+
+    int has_ac = bcf_get_info_int32(args->hdr, line, "AC", &args->tmp_ac, &args->ntmp_ac);
+    has_ac = has_ac==line->n_allele-1 ? 1 : 0;
+
+    int new_gt = 0, ngts = bcf_get_format_int32(args->hdr, line, "GT", &args->tmpi, &args->ntmpi);
+    ngts /= bcf_hdr_nsamples(args->hdr);
+    if ( args->set_gts==SET_GTS_MISSING ) new_gt = bcf_gt_missing;
+    else if ( args->set_gts==SET_GTS_REF ) new_gt = bcf_gt_unphased(0);
+    else error("todo: set_gts=%d\n", args->set_gts);
+    for (i=0; i<bcf_hdr_nsamples(args->hdr); i++)
+    {
+        if ( args->smpl_pass )
+        {
+            int pass = args->smpl_pass[i];
+            if ( args->filter_logic & FLT_EXCLUDE ) pass = pass ? 0 : 1;
+            if ( pass ) continue;
+        }
+        int32_t *gts = args->tmpi + ngts*i;
+        for (j=0; j<ngts; j++)
+        {
+            if ( gts[j]==bcf_int32_vector_end ) break;
+            if ( args->set_gts==SET_GTS_MISSING && !bcf_gt_is_missing(gts[j]) )
+            {
+                int ial = bcf_gt_allele(gts[j]);
+                if ( has_ac && ial>0 && ial<=line->n_allele ) args->tmp_ac[ ial-1 ]--;
+                an--;
+            }
+            else if ( args->set_gts==SET_GTS_REF )
+            {
+                int ial = bcf_gt_allele(gts[j]);
+                if ( bcf_gt_is_missing(gts[j]) ) an++;
+                else if ( has_ac && ial>0 && ial<=line->n_allele ) args->tmp_ac[ ial-1 ]--;
+            }
+            gts[j] = new_gt;
+        }
+    }
+    bcf_update_genotypes(args->hdr,line,args->tmpi,ngts*bcf_hdr_nsamples(args->hdr));
+    if ( has_an ) bcf_update_info_int32(args->hdr,line,"AN",&an,1);
+    if ( has_ac )  bcf_update_info_int32(args->hdr,line,"AC",args->tmp_ac,line->n_allele-1);
+}
+
+static void _set_variant_boundaries(bcf1_t *rec, hts_pos_t *beg, hts_pos_t *end)
+{
+    hts_pos_t off;
+    if ( rec->n_allele )
+    {
+        off = rec->rlen;
+        bcf_unpack(rec, BCF_UN_STR);
+        int i;
+        for (i=1; i<rec->n_allele; i++)
+        {
+            // Make symbolic alleles start at POS, although this is not strictly true for
+            // <DEL>,<INS> where POS should be the position BEFORE the deletion/insertion.
+            // However, since arbitrary symbolic alleles can be defined by the user, we
+            // will simplify the interpretation of --targets-overlap and --region-overlap.
+            int j = 0;
+            char *ref = rec->d.allele[0];
+            char *alt = rec->d.allele[i];
+            while ( ref[j] && alt[j] && ref[j]==alt[j] ) j++;
+            if ( off > j ) off = j;
+            if ( !off ) break;
+        }
+    }
+    else
+        off = 0;
+
+    *beg = rec->pos + off;
+    *end = rec->pos + rec->rlen - 1;
+}
+
+static void usage(args_t *args)
+{
+    fprintf(stderr, "\n");
+    fprintf(stderr, "About:   Apply fixed-threshold filters.\n");
+    fprintf(stderr, "Usage:   bcftools filter [options] <in.vcf.gz>\n");
+    fprintf(stderr, "\n");
+    fprintf(stderr, "Options:\n");
+    fprintf(stderr, "    -e, --exclude EXPR             Exclude sites for which the expression is true (see man page for details)\n");
+    fprintf(stderr, "    -g, --SnpGap INT[:TYPE]        Filter SNPs within <int> base pairs of an indel (the default) or any combination of indel,mnp,bnd,other,overlap\n");
+    fprintf(stderr, "    -G, --IndelGap INT             Filter clusters of indels separated by <int> or fewer base pairs allowing only one to pass\n");
+    fprintf(stderr, "    -i, --include EXPR             Include only sites for which the expression is true (see man page for details\n");
+    fprintf(stderr, "        --mask [^]REGION           Soft filter regions, \"^\" to negate\n");
+    fprintf(stderr, "    -M, --mask-file [^]FILE        Soft filter regions listed in a file, \"^\" to negate\n");
+    fprintf(stderr, "        --mask-overlap 0|1|2       Mask if POS in the region (0), record overlaps (1), variant overlaps (2) [1]\n");
+    fprintf(stderr, "    -m, --mode [+x]                \"+\": do not replace but add to existing FILTER; \"x\": reset filters at sites which pass\n");
+    fprintf(stderr, "        --no-version               Do not append version and command line to the header\n");
+    fprintf(stderr, "    -o, --output FILE              Write output to a file [standard output]\n");
+    fprintf(stderr, "    -O, --output-type u|b|v|z[0-9] u/b: un/compressed BCF, v/z: un/compressed VCF, 0-9: compression level [v]\n");
+    fprintf(stderr, "    -r, --regions REGION           Restrict to comma-separated list of regions\n");
+    fprintf(stderr, "    -R, --regions-file FILE        Restrict to regions listed in a file\n");
+    fprintf(stderr, "        --regions-overlap 0|1|2    Include if POS in the region (0), record overlaps (1), variant overlaps (2) [1]\n");
+    fprintf(stderr, "    -s, --soft-filter STRING       Annotate FILTER column with <string> or unique filter name (\"Filter%%d\") made up by the program (\"+\")\n");
+    fprintf(stderr, "    -S, --set-GTs .|0              Set genotypes of failed samples to missing (.) or ref (0)\n");
+    fprintf(stderr, "    -t, --targets REGION           Similar to -r but streams rather than index-jumps\n");
+    fprintf(stderr, "    -T, --targets-file FILE        Similar to -R but streams rather than index-jumps\n");
+    fprintf(stderr, "        --targets-overlap 0|1|2    Include if POS in the region (0), record overlaps (1), variant overlaps (2) [0]\n");
+    fprintf(stderr, "        --threads INT              Use multithreading with <int> worker threads [0]\n");
+    fprintf(stderr, "\n");
+    exit(1);
+}
+
+int main_vcffilter(int argc, char *argv[])
+{
+    int c;
+    args_t *args  = (args_t*) calloc(1,sizeof(args_t));
+    args->argc    = argc; args->argv = argv;
+    args->files   = bcf_sr_init();
+    args->output_fname = "-";
+    args->output_type = FT_VCF;
+    args->n_threads = 0;
+    args->record_cmd_line = 1;
+    args->clevel = -1;
+    int regions_is_file = 0, targets_is_file = 0;
+    int regions_overlap = 1;
+    int targets_overlap = 0;
+    args->mask_overlap  = 1;
+
+    static struct option loptions[] =
+    {
+        {"set-GTs",required_argument,NULL,'S'},
+        {"mode",required_argument,NULL,'m'},
+        {"mask",required_argument,NULL,10},
+        {"mask-file",required_argument,NULL,'M'},
+        {"mask-overlap",required_argument,NULL,11},
+        {"soft-filter",required_argument,NULL,'s'},
+        {"exclude",required_argument,NULL,'e'},
+        {"include",required_argument,NULL,'i'},
+        {"targets",required_argument,NULL,'t'},
+        {"targets-file",required_argument,NULL,'T'},
+        {"targets-overlap",required_argument,NULL,4},
+        {"regions",required_argument,NULL,'r'},
+        {"regions-file",required_argument,NULL,'R'},
+        {"regions-overlap",required_argument,NULL,3},
+        {"output",required_argument,NULL,'o'},
+        {"output-type",required_argument,NULL,'O'},
+        {"threads",required_argument,NULL,9},
+        {"SnpGap",required_argument,NULL,'g'},
+        {"IndelGap",required_argument,NULL,'G'},
+        {"no-version",no_argument,NULL,8},
+        {NULL,0,NULL,0}
+    };
+    char *tmp;
+    while ((c = getopt_long(argc, argv, "e:i:t:T:r:R:h?s:m:o:O:g:G:S:",loptions,NULL)) >= 0) {
+        switch (c) {
+            case 'g':
+                args->snp_gap = strtol(optarg,&tmp,10); 
+                if ( *tmp && *tmp!=':' ) error("Could not parse argument: --SnpGap %s\n", optarg);
+                if ( *tmp==':' )
+                {
+                    args->snp_gap_str = tmp+1;
+                    int i,n;
+                    char **keys = hts_readlist(tmp+1,0,&n);
+                    for(i=0; i<n; i++)
+                    {
+                        if ( !strcasecmp(keys[i],"indel") ) args->snp_gap_type |= VCF_INDEL;
+                        else if ( !strcasecmp(keys[i],"mnp") ) args->snp_gap_type |= VCF_MNP;
+                        else if ( !strcasecmp(keys[i],"bnd") ) args->snp_gap_type |= VCF_BND;
+                        else if ( !strcasecmp(keys[i],"other") ) args->snp_gap_type |= VCF_OTHER;
+                        else if ( !strcasecmp(keys[i],"overlap") ) args->snp_gap_type |= VCF_OVERLAP;
+                        else error("Could not parse \"%s\" in \"--SnpGap %s\"\n", keys[i], optarg);
+                        free(keys[i]);
+                    }
+                    if ( n ) free(keys);
+                }
+                else
+                {
+                    args->snp_gap_type = VCF_INDEL;
+                    args->snp_gap_str = "indel";
+                }
+                break;
+            case 'G':
+                args->indel_gap = strtol(optarg,&tmp,10);
+                if ( *tmp ) error("Could not parse argument: --IndelGap %s\n", optarg);
+                break;
+            case 'o': args->output_fname = optarg; break;
+            case 'O':
+                switch (optarg[0]) {
+                    case 'b': args->output_type = FT_BCF_GZ; break;
+                    case 'u': args->output_type = FT_BCF; break;
+                    case 'z': args->output_type = FT_VCF_GZ; break;
+                    case 'v': args->output_type = FT_VCF; break;
+                    default:
+                    {
+                        args->clevel = strtol(optarg,&tmp,10);
+                        if ( *tmp || args->clevel<0 || args->clevel>9 ) error("The output type \"%s\" not recognised\n", optarg);
+                    }
+                }
+                if ( optarg[1] )
+                {
+                    args->clevel = strtol(optarg+1,&tmp,10);
+                    if ( *tmp || args->clevel<0 || args->clevel>9 ) error("Could not parse argument: --compression-level %s\n", optarg+1);
+                }
+                break;
+            case 's': args->soft_filter = optarg; break;
+            case 'm':
+                if ( strchr(optarg,'x') ) args->annot_mode |= ANNOT_RESET;
+                if ( strchr(optarg,'+') ) args->annot_mode |= ANNOT_ADD;
+                break;
+            case 't': args->targets_list = optarg; break;
+            case 'T': args->targets_list = optarg; targets_is_file = 1; break;
+            case 'r': args->regions_list = optarg; break;
+            case 'R': args->regions_list = optarg; regions_is_file = 1; break;
+            case 'e':
+                if ( args->filter_str ) error("Error: only one -i or -e expression can be given, and they cannot be combined\n");
+                args->filter_str = optarg; args->filter_logic |= FLT_EXCLUDE; break;
+            case 'i':
+                if ( args->filter_str ) error("Error: only one -i or -e expression can be given, and they cannot be combined\n");
+                args->filter_str = optarg; args->filter_logic |= FLT_INCLUDE; break;
+            case 'S':
+                if ( !strcmp(".",optarg) ) args->set_gts = SET_GTS_MISSING;
+                else if ( !strcmp("0",optarg) ) args->set_gts = SET_GTS_REF;
+                else error("The argument to -S not recognised: %s\n", optarg);
+                break;
+            case  9 : args->n_threads = strtol(optarg, 0, 0); break;
+            case  8 : args->record_cmd_line = 0; break;
+            case  3 :
+                regions_overlap = parse_overlap_option(optarg);
+                if ( regions_overlap < 0 ) error("Could not parse: --regions-overlap %s\n",optarg);
+                break;
+            case  4 :
+                targets_overlap = parse_overlap_option(optarg);
+                if ( targets_overlap < 0 ) error("Could not parse: --targets-overlap %s\n",optarg);
+                break;
+            case  10 : args->mask_list = optarg; break;
+            case 'M' : args->mask_list = optarg; args->mask_is_file = 1; break;
+            case  11 :
+                if ( !strcasecmp(optarg,"0") ) args->mask_overlap = 0;
+                else if ( !strcasecmp(optarg,"1") ) args->mask_overlap = 1;
+                else if ( !strcasecmp(optarg,"2") ) args->mask_overlap = 2;
+                else error("Could not parse: --mask-overlap %s\n",optarg);
+                break;
+            case 'h':
+            case '?': usage(args); break;
+            default: error("Unknown argument: %s\n", optarg);
+        }
+    }
+
+    if ( args->filter_logic == (FLT_EXCLUDE|FLT_INCLUDE) ) error("Only one of -i or -e can be given.\n");
+    char *fname = NULL;
+    if ( optind>=argc )
+    {
+        if ( !isatty(fileno((FILE *)stdin)) ) fname = "-";  // reading from stdin
+        else usage(args);
+    }
+    else fname = argv[optind];
+
+    if ( args->mask_list && !args->soft_filter ) error("The option --soft-filter is required with --mask and --mask-file options\n");
+
+    // read in the regions from the command line
+    if ( args->regions_list )
+    {
+        args->files->require_index = 1;
+        bcf_sr_set_opt(args->files,BCF_SR_REGIONS_OVERLAP,regions_overlap);
+        if ( bcf_sr_set_regions(args->files, args->regions_list, regions_is_file)<0 )
+            error("Failed to read the regions: %s\n", args->regions_list);
+    }
+    else if ( optind+1 < argc )
+    {
+        int i;
+        kstring_t tmp = {0,0,0};
+        kputs(argv[optind+1],&tmp);
+        for (i=optind+2; i<argc; i++) { kputc(',',&tmp); kputs(argv[i],&tmp); }
+        args->files->require_index = 1;
+        bcf_sr_set_opt(args->files,BCF_SR_REGIONS_OVERLAP,regions_overlap);
+        if ( bcf_sr_set_regions(args->files, tmp.s, regions_is_file)<0 )
+            error("Failed to read the regions: %s\n", args->regions_list);
+        free(tmp.s);
+    }
+    if ( args->targets_list )
+    {
+        bcf_sr_set_opt(args->files,BCF_SR_TARGETS_OVERLAP,targets_overlap);
+        if ( bcf_sr_set_targets(args->files, args->targets_list,targets_is_file, 0)<0 )
+            error("Failed to read the targets: %s\n", args->targets_list);
+    }
+    if ( !bcf_sr_add_reader(args->files, fname) ) error("Failed to read from %s: %s\n", !strcmp("-",fname)?"standard input":fname,bcf_sr_strerror(args->files->errnum));
+
+    init_data(args);
+    if ( bcf_hdr_write(args->out_fh, args->hdr)!=0 ) error("[%s] Error: cannot write the header to %s\n", __func__,args->output_fname);
+    while ( bcf_sr_next_line(args->files) )
+    {
+        bcf1_t *line = bcf_sr_get_line(args->files, 0);
+        int pass = 1;
+        if ( args->filter )
+        {
+            pass = filter_test(args->filter, line, &args->smpl_pass);
+            if ( args->filter_logic & FLT_EXCLUDE ) pass = pass ? 0 : 1;
+        }
+        if ( args->mask )
+        {
+            hts_pos_t beg, end;
+            if ( args->mask_overlap==0 ) beg = end = line->pos;
+            else if ( args->mask_overlap==1 ) beg = line->pos, end = line->pos + line->rlen - 1;
+            else _set_variant_boundaries(line,&beg,&end);
+            int mpass = regidx_overlap(args->mask,bcf_seqname(args->hdr,line),beg,end,NULL) ? 0 : 1;
+            if ( args->mask_negate ) mpass = mpass ? 0 : 1;
+            pass &= mpass;
+        }
+        if ( args->soft_filter || args->set_gts || pass )
+        {
+            if ( pass )
+            {
+                bcf_unpack(line,BCF_UN_FLT);
+                if ( args->annot_mode & ANNOT_RESET || !line->d.n_flt ) bcf_add_filter(args->hdr, line, args->flt_pass);
+            }
+            else if ( args->soft_filter )
+            {
+                if ( (args->annot_mode & ANNOT_ADD) ) bcf_add_filter(args->hdr, line, args->flt_fail);
+                else bcf_update_filter(args->hdr, line, &args->flt_fail, 1);
+            }
+            if ( args->set_gts ) set_genotypes(args, line, pass);
+            if ( !args->rbuf_lines )
+            {
+                if ( bcf_write1(args->out_fh, args->hdr, line)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->output_fname);
+            }
+            else
+                buffered_filters(args, line);
+        }
+    }
+    buffered_filters(args, NULL);
+
+    if ( hts_close(args->out_fh)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,args->output_fname);
+    destroy_data(args);
+    bcf_sr_destroy(args->files);
+    free(args);
+    return 0;
+}
diff --git a/bcftools/vcffilter.c.pysam.c b/bcftools/vcffilter.c.pysam.c
new file mode 100644
index 0000000..f998083
--- /dev/null
+++ b/bcftools/vcffilter.c.pysam.c
@@ -0,0 +1,724 @@
+#include "bcftools.pysam.h"
+
+/*  vcffilter.c -- Apply fixed-threshold filters.
+
+    Copyright (C) 2013-2022 Genome Research Ltd.
+
+    Author: Petr Danecek <pd3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.  */
+
+#include <stdio.h>
+#include <unistd.h>
+#include <getopt.h>
+#include <assert.h>
+#include <ctype.h>
+#include <string.h>
+#include <strings.h>
+#include <errno.h>
+#include <sys/stat.h>
+#include <sys/types.h>
+#include <math.h>
+#include <htslib/vcf.h>
+#include <htslib/synced_bcf_reader.h>
+#include <htslib/vcfutils.h>
+#include "bcftools.h"
+#include "filter.h"
+#include "rbuf.h"
+#include "regidx.h"
+
+// Logic of the filters: include or exclude sites which match the filters?
+#define FLT_INCLUDE 1
+#define FLT_EXCLUDE 2
+
+// FILTER columns annotation: replace or add to existing FILTERs; set FILTER to PASS at good sites?
+#define ANNOT_ADD   1
+#define ANNOT_RESET 2
+
+// Set genotypes of filtered samples
+#define SET_GTS_MISSING 1
+#define SET_GTS_REF 2
+
+typedef struct _args_t
+{
+    filter_t *filter;
+    char *filter_str;
+    int filter_logic;   // include or exclude sites which match the filters? One of FLT_INCLUDE/FLT_EXCLUDE
+    const uint8_t *smpl_pass;
+    int set_gts;
+    char *soft_filter;  // drop failed sites or annotate FILTER column?
+    int annot_mode;     // add to existing FILTER annotation or replace? Otherwise reset FILTER to PASS or leave as it is?
+    int flt_fail, flt_pass;     // BCF ids of fail and pass filters
+    int snp_gap, snp_gap_type, indel_gap, IndelGap_id, SnpGap_id;
+    char *snp_gap_str;
+    int32_t ntmpi, *tmpi, ntmp_ac, *tmp_ac;
+    rbuf_t rbuf;
+    bcf1_t **rbuf_lines;
+
+    bcf_srs_t *files;
+    bcf_hdr_t *hdr;
+    htsFile *out_fh;
+    int output_type, n_threads, clevel;
+
+    char **argv, *output_fname, *targets_list, *regions_list, *mask_list;
+    int argc, record_cmd_line, mask_is_file, mask_overlap, mask_negate;
+    regidx_t *mask;
+}
+args_t;
+
+static void init_data(args_t *args)
+{
+    char wmode[8];
+    set_wmode(wmode,args->output_type,args->output_fname,args->clevel);
+    args->out_fh = hts_open(args->output_fname ? args->output_fname : "-", wmode);
+    if ( args->out_fh == NULL ) error("Can't write to \"%s\": %s\n", args->output_fname, strerror(errno));
+    if ( args->n_threads ) hts_set_threads(args->out_fh, args->n_threads);
+
+    if ( args->mask_list )
+    {
+        if ( args->mask_list[0]=='^' ) args->mask_negate = 1;
+        if ( args->mask_is_file )
+            args->mask = regidx_init(args->mask_negate?args->mask_list+1:args->mask_list,NULL,NULL,0,NULL);
+        else
+        {
+            char *rmme = strdup(args->mask_negate?args->mask_list+1:args->mask_list), *tmp = rmme;
+            while ( *tmp )
+            {
+                if ( *tmp==',' ) *tmp = '\n';
+                tmp++;
+            }
+            args->mask = regidx_init_string(rmme, regidx_parse_reg, NULL, 0, NULL);
+            free(rmme);
+        }
+        if ( !args->mask )
+            error("Could not initialize the mask: %s\n",args->mask_list);
+    }
+
+    args->hdr = args->files->readers[0].header;
+    args->flt_pass = bcf_hdr_id2int(args->hdr,BCF_DT_ID,"PASS"); assert( !args->flt_pass );  // sanity check: required by BCF spec
+
+    if ( args->soft_filter && (args->filter_logic || args->mask_list) )
+    {
+        kstring_t flt_name = {0,0,0};
+        if ( strcmp(args->soft_filter,"+") )
+            kputs(args->soft_filter, &flt_name);
+        else
+        {
+            // Make up a filter name
+            int i = 0, id = -1;
+            do
+            {
+                ksprintf(&flt_name,"Filter%d", ++i);
+                id = bcf_hdr_id2int(args->hdr,BCF_DT_ID,flt_name.s);
+            }
+            while ( bcf_hdr_idinfo_exists(args->hdr,BCF_HL_FLT,id) );
+        }
+
+        kstring_t tmp = {0,0,0};
+        if ( args->filter_logic )
+        {
+            // -i or -e: append FILTER line
+            ksprintf(&tmp,"Set if %s: ",args->filter_logic & FLT_INCLUDE ? "not true" : "true");
+
+            // escape quotes
+            char *t = args->filter_str;
+            while ( *t )
+            {
+                if ( *t=='"' ) kputc('\\',&tmp);
+                kputc(*t,&tmp);
+                t++;
+            }
+        }
+        else if ( args->mask_list )
+            ksprintf(&tmp,"Record masked by region");
+
+        int ret = bcf_hdr_printf(args->hdr, "##FILTER=<ID=%s,Description=\"%s\">", flt_name.s,tmp.s);
+        if ( ret!=0 )
+            error("Failed to append header line: ##FILTER=<ID=%s,Description=\"%s\">\n", flt_name.s,tmp.s);
+        args->flt_fail = bcf_hdr_id2int(args->hdr,BCF_DT_ID,flt_name.s); assert( args->flt_fail>=0 );
+        free(flt_name.s);
+        free(tmp.s);
+    }
+
+    if ( args->snp_gap || args->indel_gap )
+    {
+        if ( !args->filter_logic && args->soft_filter && strcmp(args->soft_filter,"+") )
+        {
+            kstring_t tmp = {0,0,0};
+            if ( args->snp_gap ) kputs("\"SnpGap\"", &tmp);
+            if ( args->indel_gap )
+            {
+                if ( tmp.s ) kputs(" and ", &tmp);
+                kputs("\"IndelGap\"", &tmp);
+            }
+            if ( strncmp(tmp.s+1,args->soft_filter,tmp.l-2) )
+                fprintf(bcftools_stderr,"Warning: using %s filter name instead of \"%s\"\n", tmp.s,args->soft_filter);
+            free(tmp.s);
+        }
+
+        rbuf_init(&args->rbuf, 64);
+        args->rbuf_lines = (bcf1_t**) calloc(args->rbuf.m, sizeof(bcf1_t*));
+        if ( args->snp_gap )
+        {
+            bcf_hdr_printf(args->hdr, "##FILTER=<ID=SnpGap,Description=\"SNP within %d bp of %s\">", args->snp_gap,args->snp_gap_str);
+            args->SnpGap_id = bcf_hdr_id2int(args->hdr, BCF_DT_ID, "SnpGap");
+            assert( args->SnpGap_id>=0 );
+        }
+        if ( args->indel_gap )
+        {
+            bcf_hdr_printf(args->hdr, "##FILTER=<ID=IndelGap,Description=\"Indel within %d bp of an indel\">", args->indel_gap);
+            args->IndelGap_id = bcf_hdr_id2int(args->hdr, BCF_DT_ID, "IndelGap");
+            assert( args->IndelGap_id>=0 );
+        }
+    }
+
+    if (args->record_cmd_line) bcf_hdr_append_version(args->hdr, args->argc, args->argv, "bcftools_filter");
+
+    if ( args->filter_str )
+        args->filter = filter_init(args->hdr, args->filter_str);
+}
+
+static void destroy_data(args_t *args)
+{
+    if ( args->rbuf_lines )
+    {
+        int i;
+        for (i=0; i<args->rbuf.m; i++)
+            if ( args->rbuf_lines[i] ) bcf_destroy1(args->rbuf_lines[i]);
+        free(args->rbuf_lines);
+    }
+    if ( args->filter )
+        filter_destroy(args->filter);
+    free(args->tmpi);
+    free(args->tmp_ac);
+    if ( args->mask ) regidx_destroy(args->mask);
+}
+
+static void flush_buffer(args_t *args, int n)
+{
+    int i, j;
+    for (i=0; i<n; i++)
+    {
+        int k = rbuf_shift(&args->rbuf);
+        bcf1_t *rec = args->rbuf_lines[k];
+
+        int pass = 1;
+        if ( !args->soft_filter )
+        {
+            for (j=0; j<rec->d.n_flt; j++)
+            {
+                if ( args->indel_gap && rec->d.flt[j]==args->IndelGap_id ) { pass = 0; break; }
+                if ( args->snp_gap && rec->d.flt[j]==args->SnpGap_id ) { pass = 0; break; }
+            }
+        }
+        if ( pass && bcf_write1(args->out_fh, args->hdr, rec)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->output_fname);
+    }
+}
+
+#define SWAP(type_t, a, b) { type_t t = a; a = b; b = t; }
+static void buffered_filters(args_t *args, bcf1_t *line)
+{
+    /**
+     *  The logic of SnpGap=3. The SNPs at positions 1 and 7 are filtered,
+     *  positions 0 and 8 are not:
+     *           0123456789
+     *      ref  .G.GT..G..
+     *      del  .A.G-..A..
+     *  Here the positions 1 and 6 are filtered, 0 and 7 are not:
+     *           0123-456789
+     *      ref  .G.G-..G..
+     *      ins  .A.GT..A..
+     *
+     *  The logic of IndelGap=2. The second indel is filtered:
+     *           012345678901
+     *      ref  .GT.GT..GT..
+     *      del  .G-.G-..G-..
+     *  And similarly here, the second is filtered:
+     *           01 23 456 78
+     *      ref  .A-.A-..A-..
+     *      ins  .AT.AT..AT..
+     */
+
+    // To avoid additional data structure, we abuse bcf1_t's var and var_type records.
+    const int SnpGap_set     = 1 << (8*sizeof(int)/2);
+    const int IndelGap_set   = 1 << (8*sizeof(int)/2-1);
+    const int IndelGap_flush = 1 << (8*sizeof(int)/2-2);
+
+    int var_type = 0, i;
+    if ( line )
+    {
+        // Still on the same chromosome?
+        int ilast = rbuf_last(&args->rbuf);
+        if ( ilast>=0 && line->rid != args->rbuf_lines[ilast]->rid )
+            flush_buffer(args, args->rbuf.n); // new chromosome, flush everything
+
+        rbuf_expand0(&args->rbuf,bcf1_t*,args->rbuf.n,args->rbuf_lines);
+
+        // Insert the new record in the buffer. The line would be overwritten in
+        // the next bcf_sr_next_line call, therefore we need to swap it with an
+        // unused one
+        ilast = rbuf_append(&args->rbuf);
+        if ( !args->rbuf_lines[ilast] ) args->rbuf_lines[ilast] = bcf_init1();
+        SWAP(bcf1_t*, args->files->readers[0].buffer[0], args->rbuf_lines[ilast]);
+
+        var_type = bcf_get_variant_types(line);
+
+        // Find out the size of an indel. The indel boundaries are based on REF
+        // (POS+1,POS+rlen-1). This is not entirely correct: mpileup likes to
+        // output REF=CAGAGAGAGA, ALT=CAGAGAGAGAGA where REF=C,ALT=CGA could be
+        // used. This filter is therefore more strict and may remove some valid
+        // SNPs.
+        // Set the REF allele's length to max deletion length or to 1 if a SNP or an insertion.
+        line->d.var[0].n = line->rlen;
+    }
+
+    int k_flush = 1;
+    if ( args->indel_gap )
+    {
+        k_flush = 0;
+        // Find indels which are too close to each other
+        int last_to = -1;
+        for (i=-1; rbuf_next(&args->rbuf,&i); )
+        {
+            bcf1_t *rec  = args->rbuf_lines[i];
+            int rec_from = rec->pos;
+            if ( last_to!=-1 && last_to < rec_from ) break;
+
+            k_flush++;
+            if ( !(rec->d.var_type & VCF_INDEL) ) continue;
+
+            rec->d.var_type |= IndelGap_set;
+            last_to = args->indel_gap + rec->pos + rec->d.var[0].n - 1;
+        }
+        if ( i==args->rbuf.f && line && last_to!=-1 ) k_flush = 0;
+        if ( k_flush || !line )
+        {
+            // Select the best indel from the cluster of k_flush indels
+            int k = 0, max_ac = -1, imax_ac = -1, max_qual = -1, imax_qual = -1;
+            for (i=-1; rbuf_next(&args->rbuf,&i) && k<k_flush; )
+            {
+                k++;
+                bcf1_t *rec  = args->rbuf_lines[i];
+                if ( !(rec->d.var_type & IndelGap_set) ) continue;
+                hts_expand(int, rec->n_allele, args->ntmpi, args->tmpi);
+                int ret = bcf_calc_ac(args->hdr, rec, args->tmpi, BCF_UN_ALL);
+                if ( imax_ac==-1 || (ret && max_ac < args->tmpi[1]) ) { max_ac = args->tmpi[1]; imax_ac = i; }
+                if ( imax_qual==-1 || max_qual < rec->qual ) { max_qual = rec->qual; imax_qual = i; }
+            }
+
+            // Filter all but the best indel (with the best QUAL, bigger AC, or take the first if neither QUAL nor AC are available)
+            k = 0;
+            for (i=-1; rbuf_next(&args->rbuf,&i) && k<k_flush; )
+            {
+                k++;
+                bcf1_t *rec = args->rbuf_lines[i];
+                if ( !(rec->d.var_type & IndelGap_set) ) continue;
+                rec->d.var_type |= IndelGap_flush;
+
+                int do_filter = 0;
+                if ( max_qual>0 )
+                {
+                    if ( i!=imax_qual ) do_filter = 1;
+                }
+                else if ( i!=imax_ac ) do_filter = 1;
+                if ( do_filter ) bcf_add_filter(args->hdr, args->rbuf_lines[i], args->IndelGap_id);
+            }
+        }
+    }
+
+    if ( !line )
+    {
+        // Finished: flush everything
+        flush_buffer(args, args->rbuf.n);
+        return;
+    }
+
+    int j_flush = 1;
+    if ( args->snp_gap )
+    {
+        j_flush = 0;
+        int last_from = line->pos;
+        for (i=-1; rbuf_next(&args->rbuf,&i); )
+        {
+            bcf1_t *rec = args->rbuf_lines[i];
+            int rec_to  = rec->pos + rec->d.var[0].n - 1;   // last position affected by the variant
+            if ( rec_to + args->snp_gap < last_from )
+                j_flush++;
+            else if ( (var_type & args->snp_gap_type) && (rec->d.var_type & VCF_SNP) && !(rec->d.var_type & SnpGap_set) )
+            {
+                // this SNP has not been SnpGap-filtered yet
+                rec->d.var_type |= SnpGap_set;
+                bcf_add_filter(args->hdr, rec, args->SnpGap_id);
+            }
+            else if ( (var_type & VCF_SNP) && (rec->d.var_type & args->snp_gap_type) )
+            {
+                // the line which we are adding is a SNP and needs to be filtered
+                line->d.var_type |= SnpGap_set;
+                bcf_add_filter(args->hdr, line, args->SnpGap_id);
+                break;
+            }
+        }
+    }
+    flush_buffer(args, j_flush < k_flush ? j_flush : k_flush);
+}
+
+static void set_genotypes(args_t *args, bcf1_t *line, int pass_site)
+{
+    int i,j;
+    if ( !bcf_hdr_nsamples(args->hdr) ) return;
+    if ( args->smpl_pass )
+    {
+        int npass = 0;
+        for (i=0; i<bcf_hdr_nsamples(args->hdr); i++) npass += args->smpl_pass[i];
+
+        // return if all samples pass
+        if ( npass==bcf_hdr_nsamples(args->hdr) && (args->filter_logic & FLT_INCLUDE) ) return;
+        if ( npass==0 && (args->filter_logic & FLT_EXCLUDE) ) return;
+    }
+    else if ( pass_site ) return;
+
+    int an = 0, has_an = bcf_get_info_int32(args->hdr, line, "AN", &args->tmp_ac, &args->ntmp_ac);
+    if ( has_an==1 ) an = args->tmp_ac[0];
+    else has_an = 0;
+
+    int has_ac = bcf_get_info_int32(args->hdr, line, "AC", &args->tmp_ac, &args->ntmp_ac);
+    has_ac = has_ac==line->n_allele-1 ? 1 : 0;
+
+    int new_gt = 0, ngts = bcf_get_format_int32(args->hdr, line, "GT", &args->tmpi, &args->ntmpi);
+    ngts /= bcf_hdr_nsamples(args->hdr);
+    if ( args->set_gts==SET_GTS_MISSING ) new_gt = bcf_gt_missing;
+    else if ( args->set_gts==SET_GTS_REF ) new_gt = bcf_gt_unphased(0);
+    else error("todo: set_gts=%d\n", args->set_gts);
+    for (i=0; i<bcf_hdr_nsamples(args->hdr); i++)
+    {
+        if ( args->smpl_pass )
+        {
+            int pass = args->smpl_pass[i];
+            if ( args->filter_logic & FLT_EXCLUDE ) pass = pass ? 0 : 1;
+            if ( pass ) continue;
+        }
+        int32_t *gts = args->tmpi + ngts*i;
+        for (j=0; j<ngts; j++)
+        {
+            if ( gts[j]==bcf_int32_vector_end ) break;
+            if ( args->set_gts==SET_GTS_MISSING && !bcf_gt_is_missing(gts[j]) )
+            {
+                int ial = bcf_gt_allele(gts[j]);
+                if ( has_ac && ial>0 && ial<=line->n_allele ) args->tmp_ac[ ial-1 ]--;
+                an--;
+            }
+            else if ( args->set_gts==SET_GTS_REF )
+            {
+                int ial = bcf_gt_allele(gts[j]);
+                if ( bcf_gt_is_missing(gts[j]) ) an++;
+                else if ( has_ac && ial>0 && ial<=line->n_allele ) args->tmp_ac[ ial-1 ]--;
+            }
+            gts[j] = new_gt;
+        }
+    }
+    bcf_update_genotypes(args->hdr,line,args->tmpi,ngts*bcf_hdr_nsamples(args->hdr));
+    if ( has_an ) bcf_update_info_int32(args->hdr,line,"AN",&an,1);
+    if ( has_ac )  bcf_update_info_int32(args->hdr,line,"AC",args->tmp_ac,line->n_allele-1);
+}
+
+static void _set_variant_boundaries(bcf1_t *rec, hts_pos_t *beg, hts_pos_t *end)
+{
+    hts_pos_t off;
+    if ( rec->n_allele )
+    {
+        off = rec->rlen;
+        bcf_unpack(rec, BCF_UN_STR);
+        int i;
+        for (i=1; i<rec->n_allele; i++)
+        {
+            // Make symbolic alleles start at POS, although this is not strictly true for
+            // <DEL>,<INS> where POS should be the position BEFORE the deletion/insertion.
+            // However, since arbitrary symbolic alleles can be defined by the user, we
+            // will simplify the interpretation of --targets-overlap and --region-overlap.
+            int j = 0;
+            char *ref = rec->d.allele[0];
+            char *alt = rec->d.allele[i];
+            while ( ref[j] && alt[j] && ref[j]==alt[j] ) j++;
+            if ( off > j ) off = j;
+            if ( !off ) break;
+        }
+    }
+    else
+        off = 0;
+
+    *beg = rec->pos + off;
+    *end = rec->pos + rec->rlen - 1;
+}
+
+static void usage(args_t *args)
+{
+    fprintf(bcftools_stderr, "\n");
+    fprintf(bcftools_stderr, "About:   Apply fixed-threshold filters.\n");
+    fprintf(bcftools_stderr, "Usage:   bcftools filter [options] <in.vcf.gz>\n");
+    fprintf(bcftools_stderr, "\n");
+    fprintf(bcftools_stderr, "Options:\n");
+    fprintf(bcftools_stderr, "    -e, --exclude EXPR             Exclude sites for which the expression is true (see man page for details)\n");
+    fprintf(bcftools_stderr, "    -g, --SnpGap INT[:TYPE]        Filter SNPs within <int> base pairs of an indel (the default) or any combination of indel,mnp,bnd,other,overlap\n");
+    fprintf(bcftools_stderr, "    -G, --IndelGap INT             Filter clusters of indels separated by <int> or fewer base pairs allowing only one to pass\n");
+    fprintf(bcftools_stderr, "    -i, --include EXPR             Include only sites for which the expression is true (see man page for details\n");
+    fprintf(bcftools_stderr, "        --mask [^]REGION           Soft filter regions, \"^\" to negate\n");
+    fprintf(bcftools_stderr, "    -M, --mask-file [^]FILE        Soft filter regions listed in a file, \"^\" to negate\n");
+    fprintf(bcftools_stderr, "        --mask-overlap 0|1|2       Mask if POS in the region (0), record overlaps (1), variant overlaps (2) [1]\n");
+    fprintf(bcftools_stderr, "    -m, --mode [+x]                \"+\": do not replace but add to existing FILTER; \"x\": reset filters at sites which pass\n");
+    fprintf(bcftools_stderr, "        --no-version               Do not append version and command line to the header\n");
+    fprintf(bcftools_stderr, "    -o, --output FILE              Write output to a file [standard output]\n");
+    fprintf(bcftools_stderr, "    -O, --output-type u|b|v|z[0-9] u/b: un/compressed BCF, v/z: un/compressed VCF, 0-9: compression level [v]\n");
+    fprintf(bcftools_stderr, "    -r, --regions REGION           Restrict to comma-separated list of regions\n");
+    fprintf(bcftools_stderr, "    -R, --regions-file FILE        Restrict to regions listed in a file\n");
+    fprintf(bcftools_stderr, "        --regions-overlap 0|1|2    Include if POS in the region (0), record overlaps (1), variant overlaps (2) [1]\n");
+    fprintf(bcftools_stderr, "    -s, --soft-filter STRING       Annotate FILTER column with <string> or unique filter name (\"Filter%%d\") made up by the program (\"+\")\n");
+    fprintf(bcftools_stderr, "    -S, --set-GTs .|0              Set genotypes of failed samples to missing (.) or ref (0)\n");
+    fprintf(bcftools_stderr, "    -t, --targets REGION           Similar to -r but streams rather than index-jumps\n");
+    fprintf(bcftools_stderr, "    -T, --targets-file FILE        Similar to -R but streams rather than index-jumps\n");
+    fprintf(bcftools_stderr, "        --targets-overlap 0|1|2    Include if POS in the region (0), record overlaps (1), variant overlaps (2) [0]\n");
+    fprintf(bcftools_stderr, "        --threads INT              Use multithreading with <int> worker threads [0]\n");
+    fprintf(bcftools_stderr, "\n");
+    bcftools_exit(1);
+}
+
+int main_vcffilter(int argc, char *argv[])
+{
+    int c;
+    args_t *args  = (args_t*) calloc(1,sizeof(args_t));
+    args->argc    = argc; args->argv = argv;
+    args->files   = bcf_sr_init();
+    args->output_fname = "-";
+    args->output_type = FT_VCF;
+    args->n_threads = 0;
+    args->record_cmd_line = 1;
+    args->clevel = -1;
+    int regions_is_file = 0, targets_is_file = 0;
+    int regions_overlap = 1;
+    int targets_overlap = 0;
+    args->mask_overlap  = 1;
+
+    static struct option loptions[] =
+    {
+        {"set-GTs",required_argument,NULL,'S'},
+        {"mode",required_argument,NULL,'m'},
+        {"mask",required_argument,NULL,10},
+        {"mask-file",required_argument,NULL,'M'},
+        {"mask-overlap",required_argument,NULL,11},
+        {"soft-filter",required_argument,NULL,'s'},
+        {"exclude",required_argument,NULL,'e'},
+        {"include",required_argument,NULL,'i'},
+        {"targets",required_argument,NULL,'t'},
+        {"targets-file",required_argument,NULL,'T'},
+        {"targets-overlap",required_argument,NULL,4},
+        {"regions",required_argument,NULL,'r'},
+        {"regions-file",required_argument,NULL,'R'},
+        {"regions-overlap",required_argument,NULL,3},
+        {"output",required_argument,NULL,'o'},
+        {"output-type",required_argument,NULL,'O'},
+        {"threads",required_argument,NULL,9},
+        {"SnpGap",required_argument,NULL,'g'},
+        {"IndelGap",required_argument,NULL,'G'},
+        {"no-version",no_argument,NULL,8},
+        {NULL,0,NULL,0}
+    };
+    char *tmp;
+    while ((c = getopt_long(argc, argv, "e:i:t:T:r:R:h?s:m:o:O:g:G:S:",loptions,NULL)) >= 0) {
+        switch (c) {
+            case 'g':
+                args->snp_gap = strtol(optarg,&tmp,10); 
+                if ( *tmp && *tmp!=':' ) error("Could not parse argument: --SnpGap %s\n", optarg);
+                if ( *tmp==':' )
+                {
+                    args->snp_gap_str = tmp+1;
+                    int i,n;
+                    char **keys = hts_readlist(tmp+1,0,&n);
+                    for(i=0; i<n; i++)
+                    {
+                        if ( !strcasecmp(keys[i],"indel") ) args->snp_gap_type |= VCF_INDEL;
+                        else if ( !strcasecmp(keys[i],"mnp") ) args->snp_gap_type |= VCF_MNP;
+                        else if ( !strcasecmp(keys[i],"bnd") ) args->snp_gap_type |= VCF_BND;
+                        else if ( !strcasecmp(keys[i],"other") ) args->snp_gap_type |= VCF_OTHER;
+                        else if ( !strcasecmp(keys[i],"overlap") ) args->snp_gap_type |= VCF_OVERLAP;
+                        else error("Could not parse \"%s\" in \"--SnpGap %s\"\n", keys[i], optarg);
+                        free(keys[i]);
+                    }
+                    if ( n ) free(keys);
+                }
+                else
+                {
+                    args->snp_gap_type = VCF_INDEL;
+                    args->snp_gap_str = "indel";
+                }
+                break;
+            case 'G':
+                args->indel_gap = strtol(optarg,&tmp,10);
+                if ( *tmp ) error("Could not parse argument: --IndelGap %s\n", optarg);
+                break;
+            case 'o': args->output_fname = optarg; break;
+            case 'O':
+                switch (optarg[0]) {
+                    case 'b': args->output_type = FT_BCF_GZ; break;
+                    case 'u': args->output_type = FT_BCF; break;
+                    case 'z': args->output_type = FT_VCF_GZ; break;
+                    case 'v': args->output_type = FT_VCF; break;
+                    default:
+                    {
+                        args->clevel = strtol(optarg,&tmp,10);
+                        if ( *tmp || args->clevel<0 || args->clevel>9 ) error("The output type \"%s\" not recognised\n", optarg);
+                    }
+                }
+                if ( optarg[1] )
+                {
+                    args->clevel = strtol(optarg+1,&tmp,10);
+                    if ( *tmp || args->clevel<0 || args->clevel>9 ) error("Could not parse argument: --compression-level %s\n", optarg+1);
+                }
+                break;
+            case 's': args->soft_filter = optarg; break;
+            case 'm':
+                if ( strchr(optarg,'x') ) args->annot_mode |= ANNOT_RESET;
+                if ( strchr(optarg,'+') ) args->annot_mode |= ANNOT_ADD;
+                break;
+            case 't': args->targets_list = optarg; break;
+            case 'T': args->targets_list = optarg; targets_is_file = 1; break;
+            case 'r': args->regions_list = optarg; break;
+            case 'R': args->regions_list = optarg; regions_is_file = 1; break;
+            case 'e':
+                if ( args->filter_str ) error("Error: only one -i or -e expression can be given, and they cannot be combined\n");
+                args->filter_str = optarg; args->filter_logic |= FLT_EXCLUDE; break;
+            case 'i':
+                if ( args->filter_str ) error("Error: only one -i or -e expression can be given, and they cannot be combined\n");
+                args->filter_str = optarg; args->filter_logic |= FLT_INCLUDE; break;
+            case 'S':
+                if ( !strcmp(".",optarg) ) args->set_gts = SET_GTS_MISSING;
+                else if ( !strcmp("0",optarg) ) args->set_gts = SET_GTS_REF;
+                else error("The argument to -S not recognised: %s\n", optarg);
+                break;
+            case  9 : args->n_threads = strtol(optarg, 0, 0); break;
+            case  8 : args->record_cmd_line = 0; break;
+            case  3 :
+                regions_overlap = parse_overlap_option(optarg);
+                if ( regions_overlap < 0 ) error("Could not parse: --regions-overlap %s\n",optarg);
+                break;
+            case  4 :
+                targets_overlap = parse_overlap_option(optarg);
+                if ( targets_overlap < 0 ) error("Could not parse: --targets-overlap %s\n",optarg);
+                break;
+            case  10 : args->mask_list = optarg; break;
+            case 'M' : args->mask_list = optarg; args->mask_is_file = 1; break;
+            case  11 :
+                if ( !strcasecmp(optarg,"0") ) args->mask_overlap = 0;
+                else if ( !strcasecmp(optarg,"1") ) args->mask_overlap = 1;
+                else if ( !strcasecmp(optarg,"2") ) args->mask_overlap = 2;
+                else error("Could not parse: --mask-overlap %s\n",optarg);
+                break;
+            case 'h':
+            case '?': usage(args); break;
+            default: error("Unknown argument: %s\n", optarg);
+        }
+    }
+
+    if ( args->filter_logic == (FLT_EXCLUDE|FLT_INCLUDE) ) error("Only one of -i or -e can be given.\n");
+    char *fname = NULL;
+    if ( optind>=argc )
+    {
+        if ( !isatty(fileno((FILE *)stdin)) ) fname = "-";  // reading from stdin
+        else usage(args);
+    }
+    else fname = argv[optind];
+
+    if ( args->mask_list && !args->soft_filter ) error("The option --soft-filter is required with --mask and --mask-file options\n");
+
+    // read in the regions from the command line
+    if ( args->regions_list )
+    {
+        args->files->require_index = 1;
+        bcf_sr_set_opt(args->files,BCF_SR_REGIONS_OVERLAP,regions_overlap);
+        if ( bcf_sr_set_regions(args->files, args->regions_list, regions_is_file)<0 )
+            error("Failed to read the regions: %s\n", args->regions_list);
+    }
+    else if ( optind+1 < argc )
+    {
+        int i;
+        kstring_t tmp = {0,0,0};
+        kputs(argv[optind+1],&tmp);
+        for (i=optind+2; i<argc; i++) { kputc(',',&tmp); kputs(argv[i],&tmp); }
+        args->files->require_index = 1;
+        bcf_sr_set_opt(args->files,BCF_SR_REGIONS_OVERLAP,regions_overlap);
+        if ( bcf_sr_set_regions(args->files, tmp.s, regions_is_file)<0 )
+            error("Failed to read the regions: %s\n", args->regions_list);
+        free(tmp.s);
+    }
+    if ( args->targets_list )
+    {
+        bcf_sr_set_opt(args->files,BCF_SR_TARGETS_OVERLAP,targets_overlap);
+        if ( bcf_sr_set_targets(args->files, args->targets_list,targets_is_file, 0)<0 )
+            error("Failed to read the targets: %s\n", args->targets_list);
+    }
+    if ( !bcf_sr_add_reader(args->files, fname) ) error("Failed to read from %s: %s\n", !strcmp("-",fname)?"standard input":fname,bcf_sr_strerror(args->files->errnum));
+
+    init_data(args);
+    if ( bcf_hdr_write(args->out_fh, args->hdr)!=0 ) error("[%s] Error: cannot write the header to %s\n", __func__,args->output_fname);
+    while ( bcf_sr_next_line(args->files) )
+    {
+        bcf1_t *line = bcf_sr_get_line(args->files, 0);
+        int pass = 1;
+        if ( args->filter )
+        {
+            pass = filter_test(args->filter, line, &args->smpl_pass);
+            if ( args->filter_logic & FLT_EXCLUDE ) pass = pass ? 0 : 1;
+        }
+        if ( args->mask )
+        {
+            hts_pos_t beg, end;
+            if ( args->mask_overlap==0 ) beg = end = line->pos;
+            else if ( args->mask_overlap==1 ) beg = line->pos, end = line->pos + line->rlen - 1;
+            else _set_variant_boundaries(line,&beg,&end);
+            int mpass = regidx_overlap(args->mask,bcf_seqname(args->hdr,line),beg,end,NULL) ? 0 : 1;
+            if ( args->mask_negate ) mpass = mpass ? 0 : 1;
+            pass &= mpass;
+        }
+        if ( args->soft_filter || args->set_gts || pass )
+        {
+            if ( pass )
+            {
+                bcf_unpack(line,BCF_UN_FLT);
+                if ( args->annot_mode & ANNOT_RESET || !line->d.n_flt ) bcf_add_filter(args->hdr, line, args->flt_pass);
+            }
+            else if ( args->soft_filter )
+            {
+                if ( (args->annot_mode & ANNOT_ADD) ) bcf_add_filter(args->hdr, line, args->flt_fail);
+                else bcf_update_filter(args->hdr, line, &args->flt_fail, 1);
+            }
+            if ( args->set_gts ) set_genotypes(args, line, pass);
+            if ( !args->rbuf_lines )
+            {
+                if ( bcf_write1(args->out_fh, args->hdr, line)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->output_fname);
+            }
+            else
+                buffered_filters(args, line);
+        }
+    }
+    buffered_filters(args, NULL);
+
+    if ( hts_close(args->out_fh)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,args->output_fname);
+    destroy_data(args);
+    bcf_sr_destroy(args->files);
+    free(args);
+    return 0;
+}
diff --git a/bcftools/vcfgtcheck.c b/bcftools/vcfgtcheck.c
new file mode 100644
index 0000000..f646e1f
--- /dev/null
+++ b/bcftools/vcfgtcheck.c
@@ -0,0 +1,1277 @@
+/*  vcfgtcheck.c -- Check sample identity.
+
+    Copyright (C) 2013-2021 Genome Research Ltd.
+
+    Author: Petr Danecek <pd3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.  */
+
+#include <stdio.h>
+#include <stdarg.h>
+#include <unistd.h>
+#include <getopt.h>
+#include <assert.h>
+#include <ctype.h>
+#include <string.h>
+#include <strings.h>
+#include <errno.h>
+#include <sys/stat.h>
+#include <sys/types.h>
+#include <math.h>
+#include <htslib/vcf.h>
+#include <htslib/synced_bcf_reader.h>
+#include <htslib/vcfutils.h>
+#include <htslib/kbitset.h>
+#include <htslib/hts_os.h>
+#include <inttypes.h>
+#include <sys/time.h>
+#include "bcftools.h"
+#include "extsort.h"
+//#include "hclust.h"
+
+typedef struct
+{
+    int iqry, igt;
+}
+pair_t;
+
+typedef struct
+{
+    bcf_srs_t *files;           // first reader is the query VCF - single sample normally or multi-sample for cross-check
+    bcf_hdr_t *gt_hdr, *qry_hdr; // VCF with genotypes to compare against and the query VCF
+    char *cwd, **argv, *gt_samples, *qry_samples, *regions, *targets, *qry_fname, *gt_fname, *pair_samples;
+    int argc, gt_samples_is_file, qry_samples_is_file, regions_is_file, targets_is_file, pair_samples_is_file;
+    int regions_overlap, targets_overlap;
+    int qry_use_GT,gt_use_GT, nqry_smpl,ngt_smpl, *qry_smpl,*gt_smpl;
+    double *pdiff, *qry_prob, *gt_prob;
+    uint32_t *ndiff,*ncnt,ncmp, npairs;
+    int32_t *qry_arr,*gt_arr, nqry_arr,ngt_arr;
+    uint8_t *qry_dsg, *gt_dsg;
+    pair_t *pairs;
+    double *hwe_prob, dsg2prob[8][3], pl2prob[256];
+    double min_inter_err, max_intra_err;
+    int all_sites, hom_only, ntop, cross_check, calc_hwe_prob, sort_by_hwe, dry_run, use_PLs;
+    FILE *fp;
+    unsigned int nskip_no_match, nskip_not_ba, nskip_mono, nskip_no_data, nskip_dip_GT, nskip_dip_PL;
+
+    // for --distinctive-sites
+    double distinctive_sites;
+    kbitset_t *kbs_diff;
+    size_t diff_sites_size;
+    extsort_t *es;
+    char *es_tmp_prefix, *es_max_mem;
+}
+args_t;
+
+static void set_cwd(args_t *args)
+{
+    int i;
+    char *buf;
+    size_t nbuf = 500;
+    args->cwd = (char*) malloc(sizeof(char)*nbuf);
+    for (i=0; i<5; i++)
+    {
+        if ( (buf = getcwd(args->cwd, nbuf)) ) break;
+        nbuf *= 2;
+        args->cwd = (char*) realloc(args->cwd, sizeof(char)*nbuf);
+    }
+    assert(buf);
+}
+static void print_header(args_t *args, FILE *fp)
+{
+    fprintf(fp, "# This file was produced by bcftools (%s+htslib-%s), the command line was:\n", bcftools_version(), hts_version());
+    fprintf(fp, "# \t bcftools %s ", args->argv[0]);
+    int i;
+    for (i=1; i<args->argc; i++)
+        fprintf(fp, " %s",args->argv[i]);
+    fprintf(fp, "\n# and the working directory was:\n");
+    fprintf(fp, "# \t %s\n#\n", args->cwd);
+}
+
+static int cmp_int(const void *_a, const void *_b)
+{
+    int a = *((int*)_a);
+    int b = *((int*)_b);
+    if ( a < b ) return -1;
+    if ( a > b ) return 1;
+    return 0;
+}
+static int cmp_pair(const void *_a, const void *_b)
+{
+    pair_t *a = (pair_t*)_a;
+    pair_t *b = (pair_t*)_b;
+    if ( a->iqry < b->iqry ) return -1;
+    if ( a->iqry > b->iqry ) return 1;
+    if ( a->igt < b->igt ) return -1;
+    if ( a->igt > b->igt ) return 1;
+    return 0;
+}
+
+typedef struct
+{
+    uint32_t ndiff,rid,pos,rand; // rand is to shuffle sites with the same ndiff from across all chromosoms
+    unsigned long kbs_dat[1];
+}
+diff_sites_t;
+#if DBG
+static void diff_sites_debug_print(args_t *args, diff_sites_t *ds)
+{
+    int i;
+    memcpy(args->kbs_diff->b,ds->kbs_dat,args->kbs_diff->n*sizeof(unsigned long));
+    fprintf(stderr,"%s:%d\t%d\t",bcf_hdr_id2name(args->qry_hdr,ds->rid),ds->pos+1,ds->ndiff);
+    for (i=0; i<args->npairs; i++) fprintf(stderr,"%d",kbs_exists(args->kbs_diff,i)?1:0);
+    fprintf(stderr,"\n");
+}
+#endif
+static int diff_sites_cmp(const void *aptr, const void *bptr)
+{
+    diff_sites_t *a = *((diff_sites_t**)aptr);
+    diff_sites_t *b = *((diff_sites_t**)bptr);
+    if ( a->ndiff < b->ndiff ) return 1;        // descending order
+    if ( a->ndiff > b->ndiff ) return -1;
+    if ( a->rand < b->rand ) return -1;
+    if ( a->rand > b->rand ) return 1;
+    return 0;
+}
+static void diff_sites_init(args_t *args)
+{
+    int nsites = args->distinctive_sites<=1 ? args->npairs*args->distinctive_sites : args->distinctive_sites;
+    if ( nsites<=0 ) error("The value for --distinctive-sites was set too low: %d\n",nsites);
+    if ( nsites > args->npairs )
+    {
+        fprintf(stderr,"Warning: The value for --distinctive-sites is bigger than is the number of pairs, all discordant sites be printed.\n");
+        nsites = args->npairs;
+        args->distinctive_sites = args->npairs + 1;
+    }
+    else
+        args->distinctive_sites = nsites;
+    args->kbs_diff = kbs_init(args->npairs);
+    size_t n = (args->npairs + KBS_ELTBITS-1) / KBS_ELTBITS;
+    assert( n==args->kbs_diff->n );
+    args->diff_sites_size = sizeof(diff_sites_t) + (n-1)*sizeof(unsigned long);
+    args->es = extsort_alloc();
+    extsort_set_opt(args->es,size_t,DAT_SIZE,args->diff_sites_size);
+    extsort_set_opt(args->es,const char*,TMP_PREFIX,args->es_tmp_prefix);
+    extsort_set_opt(args->es,const char*,MAX_MEM,args->es_max_mem);
+    extsort_set_opt(args->es,extsort_cmp_f,FUNC_CMP,diff_sites_cmp);
+    extsort_init(args->es);
+}
+static void diff_sites_destroy(args_t *args)
+{
+    kbs_destroy(args->kbs_diff);
+    extsort_destroy(args->es);
+}
+static inline void diff_sites_reset(args_t *args)
+{
+    kbs_clear(args->kbs_diff);
+}
+static inline void diff_sites_push(args_t *args, int ndiff, int rid, int pos)
+{
+    diff_sites_t *dat = (diff_sites_t*) malloc(args->diff_sites_size);
+    memset(dat,0,sizeof(*dat)); // for debugging: prevent warnings about uninitialized memory coming from struct padding (not needed after rand added)
+    dat->ndiff = ndiff;
+    dat->rid  = rid;
+    dat->pos  = pos;
+    dat->rand = hts_lrand48();
+    memcpy(dat->kbs_dat,args->kbs_diff->b,args->kbs_diff->n*sizeof(unsigned long));
+    extsort_push(args->es,dat);
+}
+static inline int diff_sites_shift(args_t *args, int *ndiff, int *rid, int *pos)
+{
+    diff_sites_t *dat = (diff_sites_t*) extsort_shift(args->es);
+    if ( !dat ) return 0;
+    *ndiff = dat->ndiff;
+    *rid   = dat->rid;
+    *pos   = dat->pos;
+    memcpy(args->kbs_diff->b,dat->kbs_dat,args->kbs_diff->n*sizeof(unsigned long));
+    return 1;
+}
+
+static void init_samples(char *list, int list_is_file, int **smpl, int *nsmpl, bcf_hdr_t *hdr, char *vcf_fname)
+{
+    int i;
+    if ( !strcmp(list,"-") )
+    {
+        *nsmpl = bcf_hdr_nsamples(hdr);
+        *smpl  = (int*) malloc(sizeof(**smpl)*(*nsmpl));
+        for (i=0; i<*nsmpl; i++) (*smpl)[i] = i;
+        return;
+    }
+
+    char **tmp = hts_readlist(list, list_is_file, nsmpl);
+    if ( !tmp || !*nsmpl ) error("Failed to parse %s\n", list);
+    *smpl = (int*) malloc(sizeof(**smpl)*(*nsmpl));
+    for (i=0; i<*nsmpl; i++)
+    {
+        int idx = bcf_hdr_id2int(hdr, BCF_DT_SAMPLE, tmp[i]);
+        if ( idx<0 ) error("No such sample in %s: [%s]\n",vcf_fname,tmp[i]);
+        (*smpl)[i] = idx;
+        free(tmp[i]);
+    }
+    free(tmp);
+    qsort(*smpl,*nsmpl,sizeof(**smpl),cmp_int);
+    // check for duplicates
+    for (i=1; i<*nsmpl; i++)
+        if ( (*smpl)[i-1]==(*smpl)[i] )
+            error("Error: the sample \"%s\" is listed twice in %s\n", hdr->samples[(*smpl)[i]],list);
+}
+
+static void init_data(args_t *args)
+{
+    hts_srand48(0);
+
+    args->files = bcf_sr_init();
+    if ( args->regions )
+    {
+        bcf_sr_set_opt(args->files,BCF_SR_REGIONS_OVERLAP,args->regions_overlap);
+        if ( bcf_sr_set_regions(args->files, args->regions, args->regions_is_file)<0 ) error("Failed to read the regions: %s\n", args->regions);
+    }
+    if ( args->targets )
+    {
+        bcf_sr_set_opt(args->files,BCF_SR_TARGETS_OVERLAP,args->targets_overlap);
+        if ( bcf_sr_set_targets(args->files, args->targets, args->targets_is_file, 0)<0 ) error("Failed to read the targets: %s\n", args->targets);
+    }
+
+    if ( args->gt_fname ) bcf_sr_set_opt(args->files, BCF_SR_REQUIRE_IDX);
+    if ( !bcf_sr_add_reader(args->files,args->qry_fname) ) error("Failed to open %s: %s\n", args->qry_fname,bcf_sr_strerror(args->files->errnum));
+    if ( args->gt_fname && !bcf_sr_add_reader(args->files, args->gt_fname) )
+        error("Failed to read from %s: %s\n", !strcmp("-",args->gt_fname)?"standard input":args->gt_fname,bcf_sr_strerror(args->files->errnum));
+
+    args->qry_hdr = bcf_sr_get_header(args->files,0);
+    if ( !bcf_hdr_nsamples(args->qry_hdr) ) error("No samples in %s?\n", args->qry_fname);
+    if ( args->gt_fname )
+    {
+        args->gt_hdr = bcf_sr_get_header(args->files,1);
+        if ( !bcf_hdr_nsamples(args->gt_hdr) ) error("No samples in %s?\n", args->gt_fname);
+    }
+
+    // Determine whether GT or PL will be used
+    if ( args->qry_use_GT==-1 ) // not set by -u, qry uses PL by default
+    {
+        if ( bcf_hdr_id2int(args->qry_hdr,BCF_DT_ID,"PL")>=0 )
+            args->qry_use_GT = 0;
+        else if ( bcf_hdr_id2int(args->qry_hdr,BCF_DT_ID,"GT")>=0 )
+            args->qry_use_GT = 1;
+        else
+            error("[E::%s] Neither PL nor GT tag is present in the header of %s\n", __func__, args->qry_fname);
+    }
+    else if ( args->qry_use_GT==1 )
+    {
+        if ( bcf_hdr_id2int(args->qry_hdr,BCF_DT_ID,"GT")<0 )
+            error("[E::%s] The GT tag is not present in the header of %s\n", __func__, args->qry_fname);
+    }
+    else if ( bcf_hdr_id2int(args->qry_hdr,BCF_DT_ID,"PL")<0 )
+        error("[E::%s] The PL tag is not present in the header of %s\n", __func__, args->qry_fname);
+
+    if ( args->gt_hdr )
+    {
+        if ( args->gt_use_GT==-1 ) // not set by -u, gt uses GT by default
+        {
+            if ( bcf_hdr_id2int(args->gt_hdr,BCF_DT_ID,"GT")>=0 )
+                args->gt_use_GT = 1;
+            else if ( bcf_hdr_id2int(args->gt_hdr,BCF_DT_ID,"PL")>=0 )
+                args->gt_use_GT = 0;
+            else
+                error("[E::%s] Neither PL nor GT tag is present in the header of %s\n", __func__, args->gt_fname);
+        }
+        else if ( args->gt_use_GT==1 )
+        {
+            if ( bcf_hdr_id2int(args->gt_hdr,BCF_DT_ID,"GT")<0 )
+                error("[E::%s] The GT tag is not present in the header of %s\n", __func__, args->gt_fname);
+        }
+        else if ( bcf_hdr_id2int(args->gt_hdr,BCF_DT_ID,"PL")<0 )
+            error("[E::%s] The PL tag is not present in the header of %s\n", __func__, args->gt_fname);
+    }
+    else
+        args->gt_use_GT = args->qry_use_GT;
+
+    // Prepare samples
+    int i,j;
+    args->nqry_smpl = bcf_hdr_nsamples(args->qry_hdr);
+    if ( args->qry_samples )
+    {
+        init_samples(args->qry_samples, args->qry_samples_is_file, &args->qry_smpl, &args->nqry_smpl, args->qry_hdr, args->qry_fname);
+    }
+    if ( args->gt_samples )
+    {   
+        init_samples(args->gt_samples, args->gt_samples_is_file, &args->gt_smpl, &args->ngt_smpl,
+            args->gt_hdr ? args->gt_hdr : args->qry_hdr,
+            args->gt_fname ? args->gt_fname : args->qry_fname);
+    }
+    else if ( args->pair_samples )
+    {
+        int npairs;
+        char **tmp = hts_readlist(args->pair_samples, args->pair_samples_is_file, &npairs);
+        if ( !tmp || !npairs ) error("Failed to parse %s\n", args->pair_samples);
+        if ( !args->pair_samples_is_file && npairs%2 ) error("Expected even number of comma-delimited samples with -p\n");
+        args->npairs = args->pair_samples_is_file ? npairs : npairs/2;
+        args->pairs  = (pair_t*) calloc(args->npairs,sizeof(*args->pairs));
+        if ( !args->pair_samples_is_file )
+        {
+            for (i=0; i<args->npairs; i++)
+            {
+                args->pairs[i].iqry = bcf_hdr_id2int(args->qry_hdr, BCF_DT_SAMPLE, tmp[2*i]);
+                args->pairs[i].igt  = bcf_hdr_id2int(args->gt_hdr?args->gt_hdr:args->qry_hdr, BCF_DT_SAMPLE, tmp[2*i+1]);
+                if ( args->pairs[i].iqry < 0 ) error("No such sample in %s: [%s]\n",args->qry_fname,tmp[2*i]);
+                if ( args->pairs[i].igt  < 0 ) error("No such sample in %s: [%s]\n",args->gt_fname?args->gt_fname:args->qry_fname,tmp[2*i+1]);
+                free(tmp[2*i]);
+                free(tmp[2*i+1]);
+            }
+        }
+        else
+        {
+            for (i=0; i<args->npairs; i++)
+            {
+                char *ptr = tmp[i];
+                while ( *ptr && !isspace(*ptr) ) ptr++;
+                if ( !*ptr ) error("Could not parse %s: %s\n",args->pair_samples,tmp[i]);
+                *ptr = 0;
+                args->pairs[i].iqry = bcf_hdr_id2int(args->qry_hdr, BCF_DT_SAMPLE, tmp[i]);
+                if ( args->pairs[i].iqry < 0 ) error("No such sample in %s: [%s]\n",args->qry_fname,tmp[i]);
+                ptr++;
+                while ( *ptr && isspace(*ptr) ) ptr++;
+                args->pairs[i].igt = bcf_hdr_id2int(args->gt_hdr?args->gt_hdr:args->qry_hdr, BCF_DT_SAMPLE, ptr);
+                if ( args->pairs[i].igt < 0 ) error("No such sample in %s: [%s]\n",args->gt_fname?args->gt_fname:args->qry_fname,ptr);
+                free(tmp[i]);
+            }
+        }
+        free(tmp);
+        qsort(args->pairs,args->npairs,sizeof(*args->pairs),cmp_pair);
+    }
+    else if ( args->gt_hdr )
+        args->ngt_smpl = bcf_hdr_nsamples(args->gt_hdr);
+    if ( !args->ngt_smpl )
+    {
+        args->ngt_smpl = args->nqry_smpl;
+        args->gt_smpl  = args->qry_smpl;
+        args->cross_check = 1;
+    }
+
+    // The data arrays
+    if ( !args->npairs ) args->npairs = args->cross_check ? args->nqry_smpl*(args->nqry_smpl+1)/2 : args->ngt_smpl*args->nqry_smpl;
+    if ( !args->pair_samples )
+    {
+        args->qry_dsg = (uint8_t*) malloc(args->nqry_smpl);
+        args->gt_dsg  = args->cross_check ? args->qry_dsg : (uint8_t*) malloc(args->ngt_smpl);
+    }
+    if ( args->use_PLs )
+    {
+        args->pdiff = (double*) calloc(args->npairs,sizeof(*args->pdiff));      // log probability of pair samples being the same
+        args->qry_prob = (double*) malloc(3*args->nqry_smpl*sizeof(*args->qry_prob));
+        args->gt_prob  = args->cross_check ? args->qry_prob : (double*) malloc(3*args->ngt_smpl*sizeof(*args->gt_prob));
+
+        // dsg2prob: the first index is bitmask of 8 possible dsg combinations (only 1<<0,1<<2,1<<3 are set, accessing
+        // anything else indicated an error, this is just to reuse gt_to_dsg()); the second index are the corresponding 
+        // probabilities of 0/0, 0/1, and 1/1 genotypes
+        for (i=0; i<8; i++)
+            for (j=0; j<3; j++)
+                args->dsg2prob[i][j] = HUGE_VAL;
+        args->dsg2prob[1][0] = -log(1-pow(10,-0.1*args->use_PLs));
+        args->dsg2prob[1][1] = -log(0.5*pow(10,-0.1*args->use_PLs));
+        args->dsg2prob[1][2] = -log(0.5*pow(10,-0.1*args->use_PLs));
+        args->dsg2prob[2][0] = -log(0.5*pow(10,-0.1*args->use_PLs));
+        args->dsg2prob[2][1] = -log(1-pow(10,-0.1*args->use_PLs));
+        args->dsg2prob[2][2] = -log(0.5*pow(10,-0.1*args->use_PLs));
+        args->dsg2prob[4][0] = -log(0.5*pow(10,-0.1*args->use_PLs));
+        args->dsg2prob[4][1] = -log(0.5*pow(10,-0.1*args->use_PLs));
+        args->dsg2prob[4][2] = -log(1-pow(10,-0.1*args->use_PLs));
+
+        // lookup table to avoid exponentiation
+        for (i=0; i<256; i++) args->pl2prob[i] = pow(10,-0.1*i);
+    }
+    else
+        args->ndiff = (uint32_t*) calloc(args->npairs,sizeof(*args->ndiff));    // number of differing genotypes for each pair of samples
+    args->ncnt  = (uint32_t*) calloc(args->npairs,sizeof(*args->ncnt));         // number of comparisons performed (non-missing data)
+    if ( !args->ncnt ) error("Error: failed to allocate %.1f Mb\n", args->npairs*sizeof(*args->ncnt)/1e6);
+    if ( args->calc_hwe_prob )
+    {
+        // prob of the observed sequence of matches given site AFs and HWE
+        args->hwe_prob = (double*) calloc(args->npairs,sizeof(*args->hwe_prob));
+        if ( !args->hwe_prob ) error("Error: failed to allocate %.1f Mb. Run with --no-HWE-prob to save some memory.\n", args->npairs*sizeof(*args->hwe_prob)/1e6);
+    }
+
+    if ( args->distinctive_sites ) diff_sites_init(args);
+
+    args->fp = stdout;
+    print_header(args, args->fp);
+}
+
+static void destroy_data(args_t *args)
+{
+    if ( args->gt_dsg!=args->qry_dsg ) free(args->gt_dsg);
+    free(args->qry_dsg);
+    if ( args->gt_prob!=args->qry_prob ) free(args->gt_prob);
+    free(args->qry_prob);
+    free(args->es_max_mem);
+    fclose(args->fp);
+    if ( args->distinctive_sites ) diff_sites_destroy(args);
+    free(args->hwe_prob);
+    free(args->cwd);
+    free(args->qry_arr);
+    if ( args->gt_hdr ) free(args->gt_arr);
+    free(args->pdiff);
+    free(args->ndiff);
+    free(args->ncnt);
+    free(args->qry_smpl);
+    if ( args->gt_smpl!=args->qry_smpl ) free(args->gt_smpl);
+    free(args->pairs);
+    bcf_sr_destroy(args->files);
+}
+
+static inline uint8_t gt_to_dsg(int32_t *ptr)
+{
+    if ( bcf_gt_is_missing(ptr[0]) || bcf_gt_is_missing(ptr[1]) || ptr[1]==bcf_int32_vector_end ) return 0;
+    uint8_t dsg = (bcf_gt_allele(ptr[0])?1:0) + (bcf_gt_allele(ptr[1])?1:0);
+    return 1<<dsg;
+}
+static inline uint8_t pl_to_dsg(int32_t *ptr)
+{
+    if ( ptr[0]==bcf_int32_missing || ptr[1]==bcf_int32_missing || ptr[2]==bcf_int32_missing ) return 0;
+    if ( ptr[1]==bcf_int32_vector_end || ptr[2]==bcf_int32_vector_end ) return 0;
+    int min_pl = ptr[0]<ptr[1] ? (ptr[0]<ptr[2]?ptr[0]:ptr[2]) : (ptr[1]<ptr[2]?ptr[1]:ptr[2]);
+    uint8_t dsg = 0;
+    if ( ptr[0]==min_pl ) dsg |= 1;
+    if ( ptr[1]==min_pl ) dsg |= 2;
+    if ( ptr[2]==min_pl ) dsg |= 4;
+    return dsg;
+}
+static inline uint8_t gt_to_prob(args_t *args, int32_t *ptr, double *prob)
+{
+    uint8_t dsg = gt_to_dsg(ptr);
+    if ( dsg )
+    {
+        prob[0] = args->dsg2prob[dsg][0];
+        prob[1] = args->dsg2prob[dsg][1];
+        prob[2] = args->dsg2prob[dsg][2];
+    }
+    return dsg;
+}
+static inline uint8_t pl_to_prob(args_t *args, int32_t *ptr, double *prob)
+{
+    uint8_t dsg = pl_to_dsg(ptr);
+    if ( dsg )
+    {
+        prob[0] = (ptr[0]>=0 && ptr[0]<255) ? args->pl2prob[ptr[0]] : args->pl2prob[255];
+        prob[1] = (ptr[1]>=0 && ptr[1]<255) ? args->pl2prob[ptr[1]] : args->pl2prob[255];
+        prob[2] = (ptr[2]>=0 && ptr[2]<255) ? args->pl2prob[ptr[2]] : args->pl2prob[255];
+        double sum = prob[0] + prob[1] + prob[2];
+        prob[0] /= sum;
+        prob[1] /= sum;
+        prob[2] /= sum;
+        prob[0] = -log(prob[0]);
+        prob[1] = -log(prob[1]);
+        prob[2] = -log(prob[2]);
+    }
+    return dsg;
+}
+static int set_data(args_t *args, bcf_hdr_t *hdr, bcf1_t *rec, int32_t **arr, int32_t *narr, int *narr1, int *use_GT)
+{
+    static int warn_dip_GT = 1;
+    static int warn_dip_PL = 1;
+    int i;
+    for (i=0; i<2; i++)
+    {
+        if ( *use_GT )
+        {
+            int ret = bcf_get_genotypes(hdr,rec,arr,narr);
+            if ( ret < 0 )
+            {
+                if ( !i ) { *use_GT = 0; continue; }
+                args->nskip_no_data++;
+                return -1;
+            }
+            if ( ret != 2*bcf_hdr_nsamples(hdr) )
+            {
+                if ( warn_dip_GT )
+                {
+                    fprintf(stderr,"INFO: skipping %s:%"PRIhts_pos", only diploid FORMAT/GT fields supported. (This is printed only once.)\n", bcf_seqname(hdr,rec),rec->pos+1);
+                    warn_dip_GT = 0;
+                }
+                args->nskip_dip_GT++;
+                return -1;
+            }
+            *narr1 = 2;
+            return 0;
+        }
+
+        int ret = bcf_get_format_int32(hdr,rec,"PL",arr,narr);
+        if ( ret < 0 )
+        {
+            if ( !i ) { *use_GT = 1; continue; }
+            args->nskip_no_data++;
+            return -1;
+        }
+        if ( ret != 3*bcf_hdr_nsamples(hdr) )
+        {
+            if ( warn_dip_PL )
+            {
+                fprintf(stderr,"INFO: skipping %s:%"PRIhts_pos", only diploid FORMAT/PL fields supported. (This is printed only once.)\n", bcf_seqname(hdr,rec),rec->pos+1);
+                warn_dip_PL = 0;
+            }
+            args->nskip_dip_PL++;
+            return -1;
+        }
+        *narr1 = 3;
+        return 0;
+    }
+    return -1;  // should never reach
+}
+static void process_line(args_t *args)
+{
+    int i,j,k, nqry1, ngt1, ret;
+
+    bcf1_t *gt_rec = NULL, *qry_rec = bcf_sr_get_line(args->files,0);   // the query file
+    int qry_use_GT = args->qry_use_GT;
+    int gt_use_GT  = args->gt_use_GT;
+
+    ret = set_data(args, args->qry_hdr, qry_rec, &args->qry_arr, &args->nqry_arr, &nqry1, &qry_use_GT);
+    if ( ret<0 ) return;
+
+    if ( args->gt_hdr )
+    {
+        gt_rec = bcf_sr_get_line(args->files,1);
+        ret = set_data(args, args->gt_hdr, gt_rec, &args->gt_arr, &args->ngt_arr, &ngt1, &gt_use_GT);
+        if ( ret<0 ) return;
+    }
+    else
+    {
+        ngt1 = nqry1;
+        args->gt_arr = args->qry_arr;
+    }
+
+    args->ncmp++;
+
+    double af,hwe_dsg[8];
+    if ( args->calc_hwe_prob )
+    {
+        int ac[2];
+        if ( args->gt_hdr )
+        {
+            if ( bcf_calc_ac(args->gt_hdr, gt_rec, ac, BCF_UN_INFO|BCF_UN_FMT)!=1 ) error("todo: bcf_calc_ac() failed\n");
+        }
+        else if ( bcf_calc_ac(args->qry_hdr, qry_rec, ac, BCF_UN_INFO|BCF_UN_FMT)!=1 ) error("todo: bcf_calc_ac() failed\n");
+
+        // hwe indexes correspond to the bitmask of eight dsg combinations to account for PL uncertainty
+        // for in the extreme case we can have uninformative PL=0,0,0. So the values are the minima of e.g.
+        //      hwe[1,2,4] ..  dsg=0,1,2
+        //      hwe[3]     ..  dsg=0 or 1
+        //      hwe[6]     ..  dsg=1 or 2
+
+        double hwe[3];
+        const double min_af = 1e-5;             // cap the AF in case we get unrealistic values
+        af = (double)ac[1]/(ac[0]+ac[1]);
+        hwe[0] = af>min_af ? -log(af*af) : -log(min_af*min_af);
+        hwe[1] = af>min_af && af<1-min_af ? -log(2*af*(1-af)) : -log(2*min_af*(1-min_af));
+        hwe[2] = af<(1-min_af) ? -log((1-af)*(1-af)) : -log(min_af*min_af);
+        hwe_dsg[0] = 0;
+        for (i=1; i<8; i++)
+        {
+            hwe_dsg[i] = HUGE_VAL;
+            for (k=0; k<3; k++)
+            {
+                if ( ((1<<k)&i) && hwe_dsg[i] > hwe[k] ) hwe_dsg[i] = hwe[k];
+            }
+        }
+    }
+
+    // The sample pairs were given explicitly via -p/-P options
+    if ( args->pairs )
+    {
+        if ( !args->use_PLs )
+        {
+            int ndiff = 0;
+            if ( args->kbs_diff ) diff_sites_reset(args);
+
+            for (i=0; i<args->npairs; i++)
+            {
+                int32_t *ptr;
+                uint8_t qry_dsg, gt_dsg;
+
+                ptr = args->gt_arr + args->pairs[i].igt*ngt1;
+                gt_dsg = gt_use_GT ? gt_to_dsg(ptr) : pl_to_dsg(ptr);
+                if ( !gt_dsg ) continue;                        // missing value
+                if ( args->hom_only && !(gt_dsg&5) ) continue;  // not a hom
+
+                ptr = args->qry_arr + args->pairs[i].iqry*nqry1;
+                qry_dsg = qry_use_GT ? gt_to_dsg(ptr) : pl_to_dsg(ptr);
+                if ( !qry_dsg ) continue;                       // missing value
+
+                int match = qry_dsg & gt_dsg;
+                if ( !match )
+                {
+                    args->ndiff[i]++;
+                    if ( args->kbs_diff ) { ndiff++; kbs_insert(args->kbs_diff, i); }
+                }
+                else if ( args->calc_hwe_prob ) args->hwe_prob[i] += hwe_dsg[match];
+                args->ncnt[i]++;
+            }
+
+            if ( ndiff ) diff_sites_push(args, ndiff, qry_rec->rid, qry_rec->pos);
+        }
+        else    // use_PLs set
+        {
+            for (i=0; i<args->npairs; i++)
+            {
+                int32_t *ptr;
+                double qry_prob[3], gt_prob[3];
+                uint8_t qry_dsg, gt_dsg;
+
+                ptr = args->gt_arr + args->pairs[i].igt*ngt1;
+                gt_dsg = gt_use_GT ? gt_to_prob(args,ptr,gt_prob) : pl_to_prob(args,ptr,gt_prob);
+                if ( !gt_dsg ) continue;                        // missing value
+                if ( args->hom_only && !(gt_dsg&5) ) continue;  // not a hom
+               
+                ptr = args->qry_arr + args->pairs[i].iqry*nqry1;
+                qry_dsg = qry_use_GT ? gt_to_prob(args,ptr,qry_prob) : pl_to_prob(args,ptr,qry_prob);
+                if ( !qry_dsg ) continue;                       // missing value
+
+                double min = qry_prob[0] + gt_prob[0];
+                qry_prob[1] += gt_prob[1];
+                if ( min > qry_prob[1] ) min = qry_prob[1];
+                qry_prob[2] += gt_prob[2];
+                if ( min > qry_prob[2] ) min = qry_prob[2];
+                args->pdiff[i] += min;
+
+                if ( args->calc_hwe_prob )
+                {
+                    int match = qry_dsg & gt_dsg;
+                    args->hwe_prob[i] += hwe_dsg[match];
+                }
+                args->ncnt[i]++;
+            }
+        }
+        return;
+    }
+
+    int idx=0;
+    if ( !args->use_PLs )
+    {
+        for (i=0; i<args->nqry_smpl; i++)
+        {
+            int iqry = args->qry_smpl ? args->qry_smpl[i] : i;
+            int32_t *ptr = args->qry_arr + nqry1*iqry;
+            args->qry_dsg[i] = qry_use_GT ? gt_to_dsg(ptr) : pl_to_dsg(ptr);
+        }
+        if ( !args->cross_check )   // in this case gt_dsg points to qry_dsg
+        {
+            for (i=0; i<args->ngt_smpl; i++)
+            {
+                int igt = args->gt_smpl ? args->gt_smpl[i] : i;
+                int32_t *ptr = args->gt_arr + ngt1*igt;
+                args->gt_dsg[i] = gt_use_GT ? gt_to_dsg(ptr) : pl_to_dsg(ptr);
+                if ( args->hom_only && !(args->gt_dsg[i]&5) ) args->gt_dsg[i] = 0;      // not a hom, set to a missing value
+            }
+        }
+        for (i=0; i<args->nqry_smpl; i++)
+        {
+            int ngt = args->cross_check ? i : args->ngt_smpl;       // two files or a sub-diagonal cross-check mode?
+            if ( !args->qry_dsg[i] ) { idx += ngt; continue; }      // missing value
+            for (j=0; j<ngt; j++)
+            {
+                if ( !args->gt_dsg[j] ) { idx++; continue; }        // missing value
+                int match = args->qry_dsg[i] & args->gt_dsg[j];
+                if ( !match ) args->ndiff[idx]++;
+                else if ( args->calc_hwe_prob ) args->hwe_prob[idx] += hwe_dsg[match];
+                args->ncnt[idx]++;
+                idx++;
+            }
+        }
+    }
+    else    // use_PLs set
+    {
+        for (i=0; i<args->nqry_smpl; i++)
+        {
+            int iqry = args->qry_smpl ? args->qry_smpl[i] : i;
+            int32_t *ptr = args->qry_arr + nqry1*iqry;
+            args->qry_dsg[i] = qry_use_GT ? gt_to_prob(args,ptr,args->qry_prob+i*3) : pl_to_prob(args,ptr,args->qry_prob+i*3);
+        }
+        if ( !args->cross_check )   // in this case gt_dsg points to qry_dsg
+        {
+            for (i=0; i<args->ngt_smpl; i++)
+            {
+                int igt = args->gt_smpl ? args->gt_smpl[i] : i;
+                int32_t *ptr = args->gt_arr + ngt1*igt;
+                args->gt_dsg[i] = gt_use_GT ? gt_to_prob(args,ptr,args->gt_prob+i*3) : pl_to_prob(args,ptr,args->gt_prob+i*3);
+                if ( args->hom_only && !(args->gt_dsg[i]&5) ) args->gt_dsg[i] = 0;      // not a hom, set to a missing value
+            }
+        }
+        for (i=0; i<args->nqry_smpl; i++)
+        {
+            int ngt = args->cross_check ? i : args->ngt_smpl;       // two files or a sub-diagonal cross-check mode?
+            if ( !args->qry_dsg[i] ) { idx += ngt; continue; }      // missing value
+            for (j=0; j<ngt; j++)
+            {
+                if ( !args->gt_dsg[j] ) { idx++; continue; }        // missing value
+
+                double min = args->qry_prob[i*3] + args->gt_prob[j*3];
+                if ( min > args->qry_prob[i*3+1] + args->gt_prob[j*3+1] ) min = args->qry_prob[i*3+1] + args->gt_prob[j*3+1];
+                if ( min > args->qry_prob[i*3+2] + args->gt_prob[j*3+2] ) min = args->qry_prob[i*3+2] + args->gt_prob[j*3+2];
+                args->pdiff[idx] += min;
+
+                if ( args->calc_hwe_prob )
+                {
+                    int match = args->qry_dsg[i] & args->gt_dsg[j];
+                    args->hwe_prob[idx] += hwe_dsg[match];
+                }
+                args->ncnt[idx]++;
+                idx++;
+            }
+        }
+    }
+}
+
+
+typedef struct
+{
+    int ism, idx;
+    double val;
+}
+idbl_t;
+static int cmp_idbl(const void *_a, const void *_b)
+{
+    idbl_t *a = (idbl_t*)_a;
+    idbl_t *b = (idbl_t*)_b;
+    if ( a->val < b->val ) return -1;
+    if ( a->val > b->val ) return 1;
+    return 0;
+}
+static void report_distinctive_sites(args_t *args)
+{
+    extsort_sort(args->es);
+
+    fprintf(args->fp,"# DS, distinctive sites:\n");
+    fprintf(args->fp,"#     - chromosome\n");
+    fprintf(args->fp,"#     - position\n");
+    fprintf(args->fp,"#     - cumulative number of pairs distinguished by this block\n");
+    fprintf(args->fp,"#     - block id\n");
+    fprintf(args->fp,"#DS\t[2]Chromosome\t[3]Position\t[4]Cumulative number of distinct pairs\t[5]Block id\n");
+
+    kbitset_t *kbs_blk = kbs_init(args->npairs);
+    kbitset_iter_t itr;
+    int i,ndiff,rid,pos,ndiff_tot = 0, iblock = 0;
+    int ndiff_min = args->distinctive_sites <= args->npairs ? args->distinctive_sites : args->npairs;
+    while ( diff_sites_shift(args,&ndiff,&rid,&pos) )
+    {
+        int ndiff_new = 0, ndiff_dbg = 0;
+        kbs_start(&itr);
+        while ( (i=kbs_next(args->kbs_diff, &itr))>=0 )
+        {
+            ndiff_dbg++;
+            if ( kbs_exists(kbs_blk,i) ) continue;   // already set
+            kbs_insert(kbs_blk,i);
+            ndiff_new++;
+        }
+        if ( ndiff_dbg!=ndiff ) error("Corrupted data, fixme: %d vs %d\n",ndiff_dbg,ndiff);
+        if ( !ndiff_new ) continue;     // no new pair distinguished by this site
+        ndiff_tot += ndiff_new;
+        fprintf(args->fp,"DS\t%s\t%d\t%d\t%d\n",bcf_hdr_id2name(args->qry_hdr,rid),pos+1,ndiff_tot,iblock);
+        if ( ndiff_tot < ndiff_min ) continue;   // fewer than the requested number of pairs can be distinguished at this point
+        iblock++;
+        ndiff_tot = 0;
+        kbs_clear(kbs_blk);
+    }
+    kbs_destroy(kbs_blk);
+}
+static void report(args_t *args)
+{
+    fprintf(args->fp,"INFO\tsites-compared\t%u\n",args->ncmp);
+    fprintf(args->fp,"INFO\tsites-skipped-no-match\t%u\n",args->nskip_no_match);
+    fprintf(args->fp,"INFO\tsites-skipped-multiallelic\t%u\n",args->nskip_not_ba);
+    fprintf(args->fp,"INFO\tsites-skipped-monoallelic\t%u\n",args->nskip_mono);
+    fprintf(args->fp,"INFO\tsites-skipped-no-data\t%u\n",args->nskip_no_data);
+    fprintf(args->fp,"INFO\tsites-skipped-GT-not-diploid\t%u\n",args->nskip_dip_GT);
+    fprintf(args->fp,"INFO\tsites-skipped-PL-not-diploid\t%u\n",args->nskip_dip_PL);
+    fprintf(args->fp,"# DC, discordance:\n");
+    fprintf(args->fp,"#     - query sample\n");
+    fprintf(args->fp,"#     - genotyped sample\n");
+    fprintf(args->fp,"#     - discordance (number of mismatches; smaller is better)\n");
+    fprintf(args->fp,"#     - negative log of HWE probability at matching sites (rare genotypes mataches are more informative, bigger is better)\n");
+    fprintf(args->fp,"#     - number of sites compared (bigger is better)\n");
+    fprintf(args->fp,"#DC\t[2]Query Sample\t[3]Genotyped Sample\t[4]Discordance\t[5]-log P(HWE)\t[6]Number of sites compared\n");
+
+    int trim = args->ntop;
+    if ( !args->pairs )
+    {
+        if ( !args->ngt_smpl && args->nqry_smpl <= args->ntop ) trim = 0;
+        if ( args->ngt_smpl && args->ngt_smpl <= args->ntop  ) trim = 0;
+    }
+
+    if ( args->pairs )
+    {
+        int i;
+        for (i=0; i<args->npairs; i++)
+        {
+            int iqry = args->pairs[i].iqry;
+            int igt  = args->pairs[i].igt;
+            if ( args->ndiff )
+            {
+                fprintf(args->fp,"DC\t%s\t%s\t%u\t%e\t%u\n",
+                        args->qry_hdr->samples[iqry],
+                        args->gt_hdr?args->gt_hdr->samples[igt]:args->qry_hdr->samples[igt],
+                        args->ndiff[i],
+                        args->calc_hwe_prob ? args->hwe_prob[i] : 0,
+                        args->ncnt[i]);
+            }
+            else
+            {
+                fprintf(args->fp,"DC\t%s\t%s\t%e\t%e\t%u\n",
+                        args->qry_hdr->samples[iqry],
+                        args->gt_hdr?args->gt_hdr->samples[igt]:args->qry_hdr->samples[igt],
+                        args->pdiff[i],
+                        args->calc_hwe_prob ? args->hwe_prob[i] : 0,
+                        args->ncnt[i]);
+            }
+        }
+    }
+    else if ( !trim )
+    {
+        int i,j,idx=0;
+        for (i=0; i<args->nqry_smpl; i++)
+        {
+            int iqry = args->qry_smpl ? args->qry_smpl[i] : i;
+            int ngt  = args->cross_check ? i : args->ngt_smpl;
+            for (j=0; j<ngt; j++)
+            {
+                int igt = args->gt_smpl ? args->gt_smpl[j] : j;
+                if ( args->ndiff )
+                {
+                    fprintf(args->fp,"DC\t%s\t%s\t%u\t%e\t%u\n",
+                            args->qry_hdr->samples[iqry],
+                            args->gt_hdr?args->gt_hdr->samples[igt]:args->qry_hdr->samples[igt],
+                            args->ndiff[idx],
+                            args->calc_hwe_prob ? args->hwe_prob[idx] : 0,
+                            args->ncnt[idx]);
+                }
+                else
+                {
+                    fprintf(args->fp,"DC\t%s\t%s\t%e\t%e\t%u\n",
+                            args->qry_hdr->samples[iqry],
+                            args->gt_hdr?args->gt_hdr->samples[igt]:args->qry_hdr->samples[igt],
+                            args->pdiff[idx],
+                            args->calc_hwe_prob ? args->hwe_prob[idx] : 0,
+                            args->ncnt[idx]);
+                }
+                idx++;
+            }
+        }
+    }
+    else if ( !args->cross_check )
+    {
+        idbl_t *arr = (idbl_t*)malloc(sizeof(*arr)*args->ngt_smpl);
+        int i,j;
+        for (i=0; i<args->nqry_smpl; i++)
+        {
+            int idx  = i*args->ngt_smpl;
+            for (j=0; j<args->ngt_smpl; j++)
+            {
+                if ( args->sort_by_hwe )
+                    arr[j].val = -args->hwe_prob[idx];
+                else if ( args->ndiff )
+                    arr[j].val = args->ncnt[idx] ? (double)args->ndiff[idx]/args->ncnt[idx] : 0;
+                else
+                    arr[j].val = args->ncnt[idx] ? args->pdiff[idx]/args->ncnt[idx] : 0;
+                arr[j].ism = j;
+                arr[j].idx = idx;
+                idx++;
+            }
+            qsort(arr, args->ngt_smpl, sizeof(*arr), cmp_idbl);
+            int iqry = args->qry_smpl ? args->qry_smpl[i] : i;
+            for (j=0; j<args->ntop; j++)
+            {
+                int idx = arr[j].idx;
+                int igt = args->gt_smpl ? args->gt_smpl[arr[j].ism] : arr[j].ism;
+                if ( args->ndiff )
+                {
+                    fprintf(args->fp,"DC\t%s\t%s\t%u\t%e\t%u\n",
+                            args->qry_hdr->samples[iqry],
+                            args->gt_hdr?args->gt_hdr->samples[igt]:args->qry_hdr->samples[igt],
+                            args->ndiff[idx],
+                            args->calc_hwe_prob ? args->hwe_prob[idx] : 0,
+                            args->ncnt[idx]);
+                }
+                else
+                {
+                    fprintf(args->fp,"DC\t%s\t%s\t%e\t%e\t%u\n",
+                            args->qry_hdr->samples[iqry],
+                            args->gt_hdr?args->gt_hdr->samples[igt]:args->qry_hdr->samples[igt],
+                            args->pdiff[idx],
+                            args->calc_hwe_prob ? args->hwe_prob[idx] : 0,
+                            args->ncnt[idx]);
+                }
+            }
+        }
+        free(arr);
+    }
+    else
+    {
+        int narr = args->nqry_smpl-1;
+        idbl_t *arr = (idbl_t*)malloc(sizeof(*arr)*narr);
+        int i,j,k,idx;
+        for (i=0; i<args->nqry_smpl; i++)
+        {
+            k = 0, idx = i*(i-1)/2;
+            for (j=0; j<i; j++)
+            {
+                if ( args->sort_by_hwe )
+                    arr[k].val = -args->hwe_prob[idx];
+                else if ( args->ndiff )
+                    arr[k].val = args->ncnt[idx] ? (double)args->ndiff[idx]/args->ncnt[idx] : 0;
+                else
+                    arr[k].val = args->ncnt[idx] ? args->pdiff[idx]/args->ncnt[idx] : 0;
+                arr[k].ism = j;
+                arr[k].idx = idx;
+                idx++;
+                k++;
+            }
+            for (; j<narr; j++)
+            {
+                idx = j*(j+1)/2 + i;
+                if ( args->sort_by_hwe )
+                    arr[k].val = -args->hwe_prob[idx];
+                else if ( args->ndiff )
+                    arr[k].val = args->ncnt[idx] ? (double)args->ndiff[idx]/args->ncnt[idx] : 0;
+                else
+                    arr[k].val = args->ncnt[idx] ? args->pdiff[idx]/args->ncnt[idx] : 0;
+                arr[k].ism = j + 1;
+                arr[k].idx = idx;
+                k++;
+            }
+            qsort(arr, narr, sizeof(*arr), cmp_idbl);
+            int iqry = args->qry_smpl ? args->qry_smpl[i] : i;
+            for (j=0; j<args->ntop; j++)
+            {
+                if ( i <= arr[j].ism ) continue;
+                int idx = arr[j].idx;
+                int igt = args->qry_smpl ? args->qry_smpl[arr[j].ism] : arr[j].ism;
+                if ( args->ndiff )
+                {
+                    fprintf(args->fp,"DC\t%s\t%s\t%u\t%e\t%u\n",
+                            args->qry_hdr->samples[iqry],
+                            args->qry_hdr->samples[igt],
+                            args->ndiff[idx],
+                            args->calc_hwe_prob ? args->hwe_prob[idx] : 0,
+                            args->ncnt[idx]);
+                }
+                else
+                {
+                    fprintf(args->fp,"DC\t%s\t%s\t%e\t%e\t%u\n",
+                            args->qry_hdr->samples[iqry],
+                            args->qry_hdr->samples[igt],
+                            args->pdiff[idx],
+                            args->calc_hwe_prob ? args->hwe_prob[idx] : 0,
+                            args->ncnt[idx]);
+                }
+            }
+        }
+        free(arr);
+    }
+}
+
+static int is_input_okay(args_t *args, int nmatch)
+{
+    int i;
+    const char *msg;
+    bcf_hdr_t *hdr;
+    bcf1_t *rec;
+    if ( args->gt_hdr && nmatch!=2 )
+    {
+        if ( args->nskip_no_match++ ) return 0;
+        for (i=0; i<2; i++)
+        {
+            rec = bcf_sr_get_line(args->files,i);
+            if ( rec ) break;
+        }
+        hdr = bcf_sr_get_header(args->files,i);
+        fprintf(stderr,"INFO: skipping %s:%"PRIhts_pos", no record with matching POS+ALT. (This is printed only once.)\n",
+                bcf_seqname(hdr,rec),rec->pos+1);
+        return 0;
+    }
+    for (i=0; i<2; i++)
+    {
+        hdr = bcf_sr_get_header(args->files,i);
+        rec = bcf_sr_get_line(args->files,i);
+        if ( rec->n_allele>2 )
+        {
+            if ( args->nskip_not_ba++ ) return 0;
+            msg = "not a biallelic site, run `bcftools norm -m -` first";
+            goto not_okay;
+        }
+        if ( bcf_get_variant_types(rec)==VCF_REF )
+        {
+            if ( args->nskip_mono++ ) return 0;
+            msg = "monoallelic site";
+            goto not_okay;
+        }
+        if ( !args->gt_hdr ) break;
+    }
+    return 1;
+
+not_okay:
+    fprintf(stderr,"INFO: skipping %s:%"PRIhts_pos", %s. (This is printed only once.)\n", 
+        bcf_seqname(hdr,rec),rec->pos+1,msg);
+    return 0;
+}
+
+static void usage(void)
+{
+    fprintf(stderr, "\n");
+    fprintf(stderr, "About:   Check sample identity. With no -g BCF given, multi-sample cross-check is performed.\n");
+    fprintf(stderr, "Usage:   bcftools gtcheck [options] [-g <genotypes.vcf.gz>] <query.vcf.gz>\n");
+    fprintf(stderr, "\n");
+    fprintf(stderr, "Options:\n");
+    //fprintf(stderr, "    -a, --all-sites                  Output comparison for all sites\n");
+    //fprintf(stderr, "    -c, --cluster MIN,MAX            Min inter- and max intra-sample error [0.23,-0.3]\n");
+    fprintf(stderr, "        --distinctive-sites            Find sites that can distinguish between at least NUM sample pairs.\n");
+    fprintf(stderr, "                  NUM[,MEM[,TMP]]          If the number is smaller or equal to 1, it is interpreted as the fraction of pairs.\n");
+    fprintf(stderr, "                                           The optional MEM string sets the maximum memory used for in-memory sorting [500M]\n");
+#ifdef _WIN32
+    fprintf(stderr, "                                           and TMP is a prefix of temporary files used by external sorting [/bcftools.XXXXXX]\n");
+#else
+    fprintf(stderr, "                                           and TMP is a prefix of temporary files used by external sorting [/tmp/bcftools.XXXXXX]\n");
+#endif
+    fprintf(stderr, "        --dry-run                      Stop after first record to estimate required time\n");
+    fprintf(stderr, "    -e, --error-probability INT        Phred-scaled probability of genotyping error, 0 for faster but less accurate results [40]\n");
+    fprintf(stderr, "    -g, --genotypes FILE               Genotypes to compare against\n");
+    fprintf(stderr, "    -H, --homs-only                    Homozygous genotypes only, useful with low coverage data (requires -g)\n");
+    fprintf(stderr, "        --n-matches INT                Print only top INT matches for each sample (sorted by average score), 0 for unlimited.\n");
+    fprintf(stderr, "                                           Use negative value to sort by HWE probability rather than by discordance [0]\n");
+    fprintf(stderr, "        --no-HWE-prob                  Disable calculation of HWE probability\n");
+    fprintf(stderr, "    -p, --pairs LIST                   Comma-separated sample pairs to compare (qry,gt[,qry,gt..] with -g or qry,qry[,qry,qry..] w/o)\n");
+    fprintf(stderr, "    -P, --pairs-file FILE              File with tab-delimited sample pairs to compare (qry,gt with -g or qry,qry w/o)\n");
+    fprintf(stderr, "    -r, --regions REGION               Restrict to comma-separated list of regions\n");
+    fprintf(stderr, "    -R, --regions-file FILE            Restrict to regions listed in a file\n");
+    fprintf(stderr, "        --regions-overlap 0|1|2        Include if POS in the region (0), record overlaps (1), variant overlaps (2) [1]\n");
+    fprintf(stderr, "    -s, --samples [qry|gt]:LIST        List of query or -g samples, \"-\" to select all samples (by default all samples are compared)\n");
+    fprintf(stderr, "    -S, --samples-file [qry|gt]:FILE   File with the query or -g samples to compare\n");
+    fprintf(stderr, "    -t, --targets REGION               Similar to -r but streams rather than index-jumps\n");
+    fprintf(stderr, "    -T, --targets-file FILE            Similar to -R but streams rather than index-jumps\n");
+    fprintf(stderr, "        --targets-overlap 0|1|2        Include if POS in the region (0), record overlaps (1), variant overlaps (2) [0]\n");
+    fprintf(stderr, "    -u, --use TAG1[,TAG2]              Which tag to use in the query file (TAG1) and the -g file (TAG2) [PL,GT]\n");
+    fprintf(stderr, "Examples:\n");
+    fprintf(stderr, "   # Check discordance of all samples from B against all sample in A\n");
+    fprintf(stderr, "   bcftools gtcheck -g A.bcf B.bcf\n");
+    fprintf(stderr, "\n");
+    fprintf(stderr, "   # Limit comparisons to the fiven list of samples\n");
+    fprintf(stderr, "   bcftools gtcheck -s gt:a1,a2,a3 -s qry:b1,b2 -g A.bcf B.bcf\n");
+    fprintf(stderr, "\n");
+    fprintf(stderr, "   # Compare only two pairs a1,b1 and a1,b2\n");
+    fprintf(stderr, "   bcftools gtcheck -p a1,b1,a1,b2 -g A.bcf B.bcf\n");
+    fprintf(stderr, "\n");
+    exit(1);
+}
+
+int main_vcfgtcheck(int argc, char *argv[])
+{
+    int c;
+    args_t *args = (args_t*) calloc(1,sizeof(args_t));
+    args->argc   = argc; args->argv = argv; set_cwd(args);
+    args->qry_use_GT = -1;
+    args->gt_use_GT  = -1;
+    args->calc_hwe_prob = 1;
+    args->use_PLs = 40;
+    args->regions_overlap = 1;
+    args->targets_overlap = 0;
+
+    // external sort for --distinctive-sites
+#ifdef _WIN32
+    args->es_tmp_prefix = NULL;
+#else
+    args->es_tmp_prefix = "/tmp/bcftools-gtcheck";
+#endif
+    args->es_max_mem = strdup("500M");
+
+    // In simulated sample swaps the minimum error was 0.3 and maximum intra-sample error was 0.23
+    //    - min_inter: pairs with smaller err value will be considered identical 
+    //    - max_intra: pairs with err value bigger than abs(max_intra_err) will be considered
+    //                  different. If negative, the cutoff may be heuristically lowered
+    args->min_inter_err =  0.23;
+    args->max_intra_err = -0.3;
+
+    static struct option loptions[] =
+    {
+        {"error-probability",1,0,'e'},
+        {"use",1,0,'u'},
+        {"cluster",1,0,'c'},
+        {"GTs-only",1,0,'G'},
+        {"all-sites",0,0,'a'},
+        {"homs-only",0,0,'H'},
+        {"help",0,0,'h'},
+        {"genotypes",1,0,'g'},
+        {"plot",1,0,'p'},
+        {"samples",1,0,'s'},
+        {"samples-file",1,0,'S'},
+        {"n-matches",1,0,2},
+        {"no-HWE-prob",0,0,3},
+        {"target-sample",1,0,4},
+        {"dry-run",0,0,5},
+        {"distinctive-sites",1,0,6},
+        {"regions",1,0,'r'},
+        {"regions-file",1,0,'R'},
+        {"regions-overlap",required_argument,NULL,7},
+        {"targets",1,0,'t'},
+        {"targets-file",1,0,'T'},
+        {"targets-overlap",required_argument,NULL,8},
+        {"pairs",1,0,'p'},
+        {"pairs-file",1,0,'P'},
+        {0,0,0,0}
+    };
+    char *tmp;
+    while ((c = getopt_long(argc, argv, "hg:p:s:S:p:P:Hr:R:at:T:G:c:u:e:",loptions,NULL)) >= 0) {
+        switch (c) {
+            case 'e':
+                args->use_PLs = strtol(optarg,&tmp,10);
+                if ( !tmp || *tmp ) error("Could not parse: --error-probability %s\n", optarg);
+                break;
+            case 'u':
+                {
+                    int i,nlist;
+                    char **list = hts_readlist(optarg, 0, &nlist);
+                    if ( !list || nlist<=0 || nlist>2 ) error("Failed to parse --use %s\n", optarg);
+                    if ( !strcasecmp("GT",list[0]) ) args->qry_use_GT = 1;
+                    else if ( !strcasecmp("PL",list[0]) ) args->qry_use_GT = 0;
+                    else error("Failed to parse --use %s; only GT and PL are supported\n", optarg);
+                    if ( nlist==2 )
+                    {
+                        if ( !strcasecmp("GT",list[1]) ) args->gt_use_GT = 1;
+                        else if ( !strcasecmp("PL",list[1]) ) args->gt_use_GT = 0;
+                        else error("Failed to parse --use %s; only GT and PL are supported\n", optarg);
+                    }
+                    else args->gt_use_GT = args->qry_use_GT;
+                    for (i=0; i<nlist; i++) free(list[i]);
+                    free(list);
+                }
+                break;
+            case 2 :
+                args->ntop = strtol(optarg,&tmp,10);
+                if ( !tmp || *tmp ) error("Could not parse: --n-matches %s\n", optarg);
+                if ( args->ntop < 0 )
+                {
+                    args->sort_by_hwe = 1;
+                    args->ntop *= -1;
+                }
+                break;
+            case 3 : args->calc_hwe_prob = 0; break;
+            case 4 : error("The option -S, --target-sample has been deprecated\n"); break;
+            case 5 : args->dry_run = 1; break;
+            case 6 : 
+                args->distinctive_sites = strtod(optarg,&tmp);
+                if ( *tmp )
+                {
+                    if ( *tmp!=',' ) error("Could not parse: --distinctive-sites %s\n", optarg);
+                    tmp++;
+                    free(args->es_max_mem);
+                    args->es_max_mem = strdup(tmp);
+                    while ( *tmp && *tmp!=',' ) tmp++;
+                    if ( *tmp ) { *tmp = 0; args->es_tmp_prefix = tmp+1; }
+                }
+                args->use_PLs = 0;
+                break;
+            case 'c':
+                error("The -c option is to be implemented, please open an issue on github\n");
+                args->min_inter_err = strtod(optarg,&tmp);
+                if ( *tmp )
+                {
+                    if ( *tmp!=',') error("Could not parse: -c %s\n", optarg);
+                    args->max_intra_err = strtod(tmp+1,&tmp);
+                    if ( *tmp ) error("Could not parse: -c %s\n", optarg);
+                }
+                break;
+            case 'G': error("The option -G, --GTs-only has been deprecated\n"); break;
+            case 'a': args->all_sites = 1; error("The -a option is to be implemented, please open an issue on github\n"); break;
+            case 'H': args->hom_only = 1; break;
+            case 'g': args->gt_fname = optarg; break;
+//            case 'p': args->plot = optarg; break;
+            case 's':
+                if ( !strncasecmp("gt:",optarg,3) ) args->gt_samples = optarg+3;
+                else if ( !strncasecmp("qry:",optarg,4) ) args->qry_samples = optarg+4;
+                else error("Which one? Query samples (qry:%s) or genotype samples (gt:%s)?\n",optarg,optarg);
+                break;
+            case 'S': 
+                if ( !strncasecmp("gt:",optarg,3) ) args->gt_samples = optarg+3, args->gt_samples_is_file = 1;
+                else if ( !strncasecmp("qry:",optarg,4) ) args->qry_samples = optarg+4, args->qry_samples_is_file = 1;
+                else error("Which one? Query samples (qry:%s) or genotype samples (gt:%s)?\n",optarg,optarg);
+                break;
+            case 'p': args->pair_samples = optarg; break;
+            case 'P': args->pair_samples = optarg; args->pair_samples_is_file = 1; break;
+            case 'r': args->regions = optarg; break;
+            case 'R': args->regions = optarg; args->regions_is_file = 1; break;
+            case 't': args->targets = optarg; break;
+            case 'T': args->targets = optarg; args->targets_is_file = 1; break;
+            case  7 :
+                args->regions_overlap = parse_overlap_option(optarg);
+                if ( args->regions_overlap < 0 ) error("Could not parse: --regions-overlap %s\n",optarg);
+                break;
+            case  8 :
+                args->targets_overlap = parse_overlap_option(optarg);
+                if ( args->targets_overlap < 0 ) error("Could not parse: --targets-overlap %s\n",optarg);
+                break;
+            case 'h':
+            case '?': usage(); break;
+            default: error("Unknown argument: %s\n", optarg);
+        }
+    }
+    if ( optind==argc )
+    {
+        if ( !isatty(fileno((FILE *)stdin)) ) args->qry_fname = "-";  // reading from stdin
+        else usage();   // no files given
+    }
+    else args->qry_fname = argv[optind];
+    if ( argc>optind+1 ) error("Error: too many files given, run with -h for help\n");  // too many files given
+    if ( args->pair_samples )
+    {
+        if ( args->gt_samples || args->qry_samples ) error("The -p/-P option cannot be combined with -s/-S\n");
+        if ( args->ntop ) error("The --n-matches option cannot be combined with -p/-P\n");
+    }
+    if ( args->distinctive_sites && !args->pair_samples ) error("The experimental option --distinctive-sites requires -p/-P\n");
+    if ( args->hom_only && !args->gt_fname ) error("The option --homs-only requires --genotypes\n");
+    if ( args->distinctive_sites && args->use_PLs ) error("The option --distinctive-sites cannot be combined with --error-probability\n");
+
+    init_data(args);
+
+    int ret;
+    while ( (ret=bcf_sr_next_line(args->files)) )
+    {
+        if ( !is_input_okay(args,ret) ) continue;
+
+        // time one record to give the user an estimate with very big files
+        struct timeval t0, t1;
+        if ( !args->ncmp )  gettimeofday(&t0, NULL);
+
+        process_line(args);
+
+        if ( args->ncmp==1 )
+        {
+            gettimeofday(&t1, NULL);
+            double delta = (t1.tv_sec - t0.tv_sec) * 1e6 + (t1.tv_usec - t0.tv_usec);
+            fprintf(stderr,"INFO:\tTime required to process one record .. %f seconds\n",delta/1e6);
+            fprintf(args->fp,"INFO\tTime required to process one record .. %f seconds\n",delta/1e6);
+            if ( args->dry_run ) break;
+        }
+    }
+    if ( !args->dry_run )
+    {
+        report(args);
+        if ( args->distinctive_sites ) report_distinctive_sites(args);
+    }
+
+    destroy_data(args);
+    free(args);
+    return 0;
+}
+
diff --git a/bcftools/vcfgtcheck.c.pysam.c b/bcftools/vcfgtcheck.c.pysam.c
new file mode 100644
index 0000000..e0a70ba
--- /dev/null
+++ b/bcftools/vcfgtcheck.c.pysam.c
@@ -0,0 +1,1279 @@
+#include "bcftools.pysam.h"
+
+/*  vcfgtcheck.c -- Check sample identity.
+
+    Copyright (C) 2013-2021 Genome Research Ltd.
+
+    Author: Petr Danecek <pd3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.  */
+
+#include <stdio.h>
+#include <stdarg.h>
+#include <unistd.h>
+#include <getopt.h>
+#include <assert.h>
+#include <ctype.h>
+#include <string.h>
+#include <strings.h>
+#include <errno.h>
+#include <sys/stat.h>
+#include <sys/types.h>
+#include <math.h>
+#include <htslib/vcf.h>
+#include <htslib/synced_bcf_reader.h>
+#include <htslib/vcfutils.h>
+#include <htslib/kbitset.h>
+#include <htslib/hts_os.h>
+#include <inttypes.h>
+#include <sys/time.h>
+#include "bcftools.h"
+#include "extsort.h"
+//#include "hclust.h"
+
+typedef struct
+{
+    int iqry, igt;
+}
+pair_t;
+
+typedef struct
+{
+    bcf_srs_t *files;           // first reader is the query VCF - single sample normally or multi-sample for cross-check
+    bcf_hdr_t *gt_hdr, *qry_hdr; // VCF with genotypes to compare against and the query VCF
+    char *cwd, **argv, *gt_samples, *qry_samples, *regions, *targets, *qry_fname, *gt_fname, *pair_samples;
+    int argc, gt_samples_is_file, qry_samples_is_file, regions_is_file, targets_is_file, pair_samples_is_file;
+    int regions_overlap, targets_overlap;
+    int qry_use_GT,gt_use_GT, nqry_smpl,ngt_smpl, *qry_smpl,*gt_smpl;
+    double *pdiff, *qry_prob, *gt_prob;
+    uint32_t *ndiff,*ncnt,ncmp, npairs;
+    int32_t *qry_arr,*gt_arr, nqry_arr,ngt_arr;
+    uint8_t *qry_dsg, *gt_dsg;
+    pair_t *pairs;
+    double *hwe_prob, dsg2prob[8][3], pl2prob[256];
+    double min_inter_err, max_intra_err;
+    int all_sites, hom_only, ntop, cross_check, calc_hwe_prob, sort_by_hwe, dry_run, use_PLs;
+    FILE *fp;
+    unsigned int nskip_no_match, nskip_not_ba, nskip_mono, nskip_no_data, nskip_dip_GT, nskip_dip_PL;
+
+    // for --distinctive-sites
+    double distinctive_sites;
+    kbitset_t *kbs_diff;
+    size_t diff_sites_size;
+    extsort_t *es;
+    char *es_tmp_prefix, *es_max_mem;
+}
+args_t;
+
+static void set_cwd(args_t *args)
+{
+    int i;
+    char *buf;
+    size_t nbuf = 500;
+    args->cwd = (char*) malloc(sizeof(char)*nbuf);
+    for (i=0; i<5; i++)
+    {
+        if ( (buf = getcwd(args->cwd, nbuf)) ) break;
+        nbuf *= 2;
+        args->cwd = (char*) realloc(args->cwd, sizeof(char)*nbuf);
+    }
+    assert(buf);
+}
+static void print_header(args_t *args, FILE *fp)
+{
+    fprintf(fp, "# This file was produced by bcftools (%s+htslib-%s), the command line was:\n", bcftools_version(), hts_version());
+    fprintf(fp, "# \t bcftools %s ", args->argv[0]);
+    int i;
+    for (i=1; i<args->argc; i++)
+        fprintf(fp, " %s",args->argv[i]);
+    fprintf(fp, "\n# and the working directory was:\n");
+    fprintf(fp, "# \t %s\n#\n", args->cwd);
+}
+
+static int cmp_int(const void *_a, const void *_b)
+{
+    int a = *((int*)_a);
+    int b = *((int*)_b);
+    if ( a < b ) return -1;
+    if ( a > b ) return 1;
+    return 0;
+}
+static int cmp_pair(const void *_a, const void *_b)
+{
+    pair_t *a = (pair_t*)_a;
+    pair_t *b = (pair_t*)_b;
+    if ( a->iqry < b->iqry ) return -1;
+    if ( a->iqry > b->iqry ) return 1;
+    if ( a->igt < b->igt ) return -1;
+    if ( a->igt > b->igt ) return 1;
+    return 0;
+}
+
+typedef struct
+{
+    uint32_t ndiff,rid,pos,rand; // rand is to shuffle sites with the same ndiff from across all chromosoms
+    unsigned long kbs_dat[1];
+}
+diff_sites_t;
+#if DBG
+static void diff_sites_debug_print(args_t *args, diff_sites_t *ds)
+{
+    int i;
+    memcpy(args->kbs_diff->b,ds->kbs_dat,args->kbs_diff->n*sizeof(unsigned long));
+    fprintf(bcftools_stderr,"%s:%d\t%d\t",bcf_hdr_id2name(args->qry_hdr,ds->rid),ds->pos+1,ds->ndiff);
+    for (i=0; i<args->npairs; i++) fprintf(bcftools_stderr,"%d",kbs_exists(args->kbs_diff,i)?1:0);
+    fprintf(bcftools_stderr,"\n");
+}
+#endif
+static int diff_sites_cmp(const void *aptr, const void *bptr)
+{
+    diff_sites_t *a = *((diff_sites_t**)aptr);
+    diff_sites_t *b = *((diff_sites_t**)bptr);
+    if ( a->ndiff < b->ndiff ) return 1;        // descending order
+    if ( a->ndiff > b->ndiff ) return -1;
+    if ( a->rand < b->rand ) return -1;
+    if ( a->rand > b->rand ) return 1;
+    return 0;
+}
+static void diff_sites_init(args_t *args)
+{
+    int nsites = args->distinctive_sites<=1 ? args->npairs*args->distinctive_sites : args->distinctive_sites;
+    if ( nsites<=0 ) error("The value for --distinctive-sites was set too low: %d\n",nsites);
+    if ( nsites > args->npairs )
+    {
+        fprintf(bcftools_stderr,"Warning: The value for --distinctive-sites is bigger than is the number of pairs, all discordant sites be printed.\n");
+        nsites = args->npairs;
+        args->distinctive_sites = args->npairs + 1;
+    }
+    else
+        args->distinctive_sites = nsites;
+    args->kbs_diff = kbs_init(args->npairs);
+    size_t n = (args->npairs + KBS_ELTBITS-1) / KBS_ELTBITS;
+    assert( n==args->kbs_diff->n );
+    args->diff_sites_size = sizeof(diff_sites_t) + (n-1)*sizeof(unsigned long);
+    args->es = extsort_alloc();
+    extsort_set_opt(args->es,size_t,DAT_SIZE,args->diff_sites_size);
+    extsort_set_opt(args->es,const char*,TMP_PREFIX,args->es_tmp_prefix);
+    extsort_set_opt(args->es,const char*,MAX_MEM,args->es_max_mem);
+    extsort_set_opt(args->es,extsort_cmp_f,FUNC_CMP,diff_sites_cmp);
+    extsort_init(args->es);
+}
+static void diff_sites_destroy(args_t *args)
+{
+    kbs_destroy(args->kbs_diff);
+    extsort_destroy(args->es);
+}
+static inline void diff_sites_reset(args_t *args)
+{
+    kbs_clear(args->kbs_diff);
+}
+static inline void diff_sites_push(args_t *args, int ndiff, int rid, int pos)
+{
+    diff_sites_t *dat = (diff_sites_t*) malloc(args->diff_sites_size);
+    memset(dat,0,sizeof(*dat)); // for debugging: prevent warnings about uninitialized memory coming from struct padding (not needed after rand added)
+    dat->ndiff = ndiff;
+    dat->rid  = rid;
+    dat->pos  = pos;
+    dat->rand = hts_lrand48();
+    memcpy(dat->kbs_dat,args->kbs_diff->b,args->kbs_diff->n*sizeof(unsigned long));
+    extsort_push(args->es,dat);
+}
+static inline int diff_sites_shift(args_t *args, int *ndiff, int *rid, int *pos)
+{
+    diff_sites_t *dat = (diff_sites_t*) extsort_shift(args->es);
+    if ( !dat ) return 0;
+    *ndiff = dat->ndiff;
+    *rid   = dat->rid;
+    *pos   = dat->pos;
+    memcpy(args->kbs_diff->b,dat->kbs_dat,args->kbs_diff->n*sizeof(unsigned long));
+    return 1;
+}
+
+static void init_samples(char *list, int list_is_file, int **smpl, int *nsmpl, bcf_hdr_t *hdr, char *vcf_fname)
+{
+    int i;
+    if ( !strcmp(list,"-") )
+    {
+        *nsmpl = bcf_hdr_nsamples(hdr);
+        *smpl  = (int*) malloc(sizeof(**smpl)*(*nsmpl));
+        for (i=0; i<*nsmpl; i++) (*smpl)[i] = i;
+        return;
+    }
+
+    char **tmp = hts_readlist(list, list_is_file, nsmpl);
+    if ( !tmp || !*nsmpl ) error("Failed to parse %s\n", list);
+    *smpl = (int*) malloc(sizeof(**smpl)*(*nsmpl));
+    for (i=0; i<*nsmpl; i++)
+    {
+        int idx = bcf_hdr_id2int(hdr, BCF_DT_SAMPLE, tmp[i]);
+        if ( idx<0 ) error("No such sample in %s: [%s]\n",vcf_fname,tmp[i]);
+        (*smpl)[i] = idx;
+        free(tmp[i]);
+    }
+    free(tmp);
+    qsort(*smpl,*nsmpl,sizeof(**smpl),cmp_int);
+    // check for duplicates
+    for (i=1; i<*nsmpl; i++)
+        if ( (*smpl)[i-1]==(*smpl)[i] )
+            error("Error: the sample \"%s\" is listed twice in %s\n", hdr->samples[(*smpl)[i]],list);
+}
+
+static void init_data(args_t *args)
+{
+    hts_srand48(0);
+
+    args->files = bcf_sr_init();
+    if ( args->regions )
+    {
+        bcf_sr_set_opt(args->files,BCF_SR_REGIONS_OVERLAP,args->regions_overlap);
+        if ( bcf_sr_set_regions(args->files, args->regions, args->regions_is_file)<0 ) error("Failed to read the regions: %s\n", args->regions);
+    }
+    if ( args->targets )
+    {
+        bcf_sr_set_opt(args->files,BCF_SR_TARGETS_OVERLAP,args->targets_overlap);
+        if ( bcf_sr_set_targets(args->files, args->targets, args->targets_is_file, 0)<0 ) error("Failed to read the targets: %s\n", args->targets);
+    }
+
+    if ( args->gt_fname ) bcf_sr_set_opt(args->files, BCF_SR_REQUIRE_IDX);
+    if ( !bcf_sr_add_reader(args->files,args->qry_fname) ) error("Failed to open %s: %s\n", args->qry_fname,bcf_sr_strerror(args->files->errnum));
+    if ( args->gt_fname && !bcf_sr_add_reader(args->files, args->gt_fname) )
+        error("Failed to read from %s: %s\n", !strcmp("-",args->gt_fname)?"standard input":args->gt_fname,bcf_sr_strerror(args->files->errnum));
+
+    args->qry_hdr = bcf_sr_get_header(args->files,0);
+    if ( !bcf_hdr_nsamples(args->qry_hdr) ) error("No samples in %s?\n", args->qry_fname);
+    if ( args->gt_fname )
+    {
+        args->gt_hdr = bcf_sr_get_header(args->files,1);
+        if ( !bcf_hdr_nsamples(args->gt_hdr) ) error("No samples in %s?\n", args->gt_fname);
+    }
+
+    // Determine whether GT or PL will be used
+    if ( args->qry_use_GT==-1 ) // not set by -u, qry uses PL by default
+    {
+        if ( bcf_hdr_id2int(args->qry_hdr,BCF_DT_ID,"PL")>=0 )
+            args->qry_use_GT = 0;
+        else if ( bcf_hdr_id2int(args->qry_hdr,BCF_DT_ID,"GT")>=0 )
+            args->qry_use_GT = 1;
+        else
+            error("[E::%s] Neither PL nor GT tag is present in the header of %s\n", __func__, args->qry_fname);
+    }
+    else if ( args->qry_use_GT==1 )
+    {
+        if ( bcf_hdr_id2int(args->qry_hdr,BCF_DT_ID,"GT")<0 )
+            error("[E::%s] The GT tag is not present in the header of %s\n", __func__, args->qry_fname);
+    }
+    else if ( bcf_hdr_id2int(args->qry_hdr,BCF_DT_ID,"PL")<0 )
+        error("[E::%s] The PL tag is not present in the header of %s\n", __func__, args->qry_fname);
+
+    if ( args->gt_hdr )
+    {
+        if ( args->gt_use_GT==-1 ) // not set by -u, gt uses GT by default
+        {
+            if ( bcf_hdr_id2int(args->gt_hdr,BCF_DT_ID,"GT")>=0 )
+                args->gt_use_GT = 1;
+            else if ( bcf_hdr_id2int(args->gt_hdr,BCF_DT_ID,"PL")>=0 )
+                args->gt_use_GT = 0;
+            else
+                error("[E::%s] Neither PL nor GT tag is present in the header of %s\n", __func__, args->gt_fname);
+        }
+        else if ( args->gt_use_GT==1 )
+        {
+            if ( bcf_hdr_id2int(args->gt_hdr,BCF_DT_ID,"GT")<0 )
+                error("[E::%s] The GT tag is not present in the header of %s\n", __func__, args->gt_fname);
+        }
+        else if ( bcf_hdr_id2int(args->gt_hdr,BCF_DT_ID,"PL")<0 )
+            error("[E::%s] The PL tag is not present in the header of %s\n", __func__, args->gt_fname);
+    }
+    else
+        args->gt_use_GT = args->qry_use_GT;
+
+    // Prepare samples
+    int i,j;
+    args->nqry_smpl = bcf_hdr_nsamples(args->qry_hdr);
+    if ( args->qry_samples )
+    {
+        init_samples(args->qry_samples, args->qry_samples_is_file, &args->qry_smpl, &args->nqry_smpl, args->qry_hdr, args->qry_fname);
+    }
+    if ( args->gt_samples )
+    {   
+        init_samples(args->gt_samples, args->gt_samples_is_file, &args->gt_smpl, &args->ngt_smpl,
+            args->gt_hdr ? args->gt_hdr : args->qry_hdr,
+            args->gt_fname ? args->gt_fname : args->qry_fname);
+    }
+    else if ( args->pair_samples )
+    {
+        int npairs;
+        char **tmp = hts_readlist(args->pair_samples, args->pair_samples_is_file, &npairs);
+        if ( !tmp || !npairs ) error("Failed to parse %s\n", args->pair_samples);
+        if ( !args->pair_samples_is_file && npairs%2 ) error("Expected even number of comma-delimited samples with -p\n");
+        args->npairs = args->pair_samples_is_file ? npairs : npairs/2;
+        args->pairs  = (pair_t*) calloc(args->npairs,sizeof(*args->pairs));
+        if ( !args->pair_samples_is_file )
+        {
+            for (i=0; i<args->npairs; i++)
+            {
+                args->pairs[i].iqry = bcf_hdr_id2int(args->qry_hdr, BCF_DT_SAMPLE, tmp[2*i]);
+                args->pairs[i].igt  = bcf_hdr_id2int(args->gt_hdr?args->gt_hdr:args->qry_hdr, BCF_DT_SAMPLE, tmp[2*i+1]);
+                if ( args->pairs[i].iqry < 0 ) error("No such sample in %s: [%s]\n",args->qry_fname,tmp[2*i]);
+                if ( args->pairs[i].igt  < 0 ) error("No such sample in %s: [%s]\n",args->gt_fname?args->gt_fname:args->qry_fname,tmp[2*i+1]);
+                free(tmp[2*i]);
+                free(tmp[2*i+1]);
+            }
+        }
+        else
+        {
+            for (i=0; i<args->npairs; i++)
+            {
+                char *ptr = tmp[i];
+                while ( *ptr && !isspace(*ptr) ) ptr++;
+                if ( !*ptr ) error("Could not parse %s: %s\n",args->pair_samples,tmp[i]);
+                *ptr = 0;
+                args->pairs[i].iqry = bcf_hdr_id2int(args->qry_hdr, BCF_DT_SAMPLE, tmp[i]);
+                if ( args->pairs[i].iqry < 0 ) error("No such sample in %s: [%s]\n",args->qry_fname,tmp[i]);
+                ptr++;
+                while ( *ptr && isspace(*ptr) ) ptr++;
+                args->pairs[i].igt = bcf_hdr_id2int(args->gt_hdr?args->gt_hdr:args->qry_hdr, BCF_DT_SAMPLE, ptr);
+                if ( args->pairs[i].igt < 0 ) error("No such sample in %s: [%s]\n",args->gt_fname?args->gt_fname:args->qry_fname,ptr);
+                free(tmp[i]);
+            }
+        }
+        free(tmp);
+        qsort(args->pairs,args->npairs,sizeof(*args->pairs),cmp_pair);
+    }
+    else if ( args->gt_hdr )
+        args->ngt_smpl = bcf_hdr_nsamples(args->gt_hdr);
+    if ( !args->ngt_smpl )
+    {
+        args->ngt_smpl = args->nqry_smpl;
+        args->gt_smpl  = args->qry_smpl;
+        args->cross_check = 1;
+    }
+
+    // The data arrays
+    if ( !args->npairs ) args->npairs = args->cross_check ? args->nqry_smpl*(args->nqry_smpl+1)/2 : args->ngt_smpl*args->nqry_smpl;
+    if ( !args->pair_samples )
+    {
+        args->qry_dsg = (uint8_t*) malloc(args->nqry_smpl);
+        args->gt_dsg  = args->cross_check ? args->qry_dsg : (uint8_t*) malloc(args->ngt_smpl);
+    }
+    if ( args->use_PLs )
+    {
+        args->pdiff = (double*) calloc(args->npairs,sizeof(*args->pdiff));      // log probability of pair samples being the same
+        args->qry_prob = (double*) malloc(3*args->nqry_smpl*sizeof(*args->qry_prob));
+        args->gt_prob  = args->cross_check ? args->qry_prob : (double*) malloc(3*args->ngt_smpl*sizeof(*args->gt_prob));
+
+        // dsg2prob: the first index is bitmask of 8 possible dsg combinations (only 1<<0,1<<2,1<<3 are set, accessing
+        // anything else indicated an error, this is just to reuse gt_to_dsg()); the second index are the corresponding 
+        // probabilities of 0/0, 0/1, and 1/1 genotypes
+        for (i=0; i<8; i++)
+            for (j=0; j<3; j++)
+                args->dsg2prob[i][j] = HUGE_VAL;
+        args->dsg2prob[1][0] = -log(1-pow(10,-0.1*args->use_PLs));
+        args->dsg2prob[1][1] = -log(0.5*pow(10,-0.1*args->use_PLs));
+        args->dsg2prob[1][2] = -log(0.5*pow(10,-0.1*args->use_PLs));
+        args->dsg2prob[2][0] = -log(0.5*pow(10,-0.1*args->use_PLs));
+        args->dsg2prob[2][1] = -log(1-pow(10,-0.1*args->use_PLs));
+        args->dsg2prob[2][2] = -log(0.5*pow(10,-0.1*args->use_PLs));
+        args->dsg2prob[4][0] = -log(0.5*pow(10,-0.1*args->use_PLs));
+        args->dsg2prob[4][1] = -log(0.5*pow(10,-0.1*args->use_PLs));
+        args->dsg2prob[4][2] = -log(1-pow(10,-0.1*args->use_PLs));
+
+        // lookup table to avoid exponentiation
+        for (i=0; i<256; i++) args->pl2prob[i] = pow(10,-0.1*i);
+    }
+    else
+        args->ndiff = (uint32_t*) calloc(args->npairs,sizeof(*args->ndiff));    // number of differing genotypes for each pair of samples
+    args->ncnt  = (uint32_t*) calloc(args->npairs,sizeof(*args->ncnt));         // number of comparisons performed (non-missing data)
+    if ( !args->ncnt ) error("Error: failed to allocate %.1f Mb\n", args->npairs*sizeof(*args->ncnt)/1e6);
+    if ( args->calc_hwe_prob )
+    {
+        // prob of the observed sequence of matches given site AFs and HWE
+        args->hwe_prob = (double*) calloc(args->npairs,sizeof(*args->hwe_prob));
+        if ( !args->hwe_prob ) error("Error: failed to allocate %.1f Mb. Run with --no-HWE-prob to save some memory.\n", args->npairs*sizeof(*args->hwe_prob)/1e6);
+    }
+
+    if ( args->distinctive_sites ) diff_sites_init(args);
+
+    args->fp = bcftools_stdout;
+    print_header(args, args->fp);
+}
+
+static void destroy_data(args_t *args)
+{
+    if ( args->gt_dsg!=args->qry_dsg ) free(args->gt_dsg);
+    free(args->qry_dsg);
+    if ( args->gt_prob!=args->qry_prob ) free(args->gt_prob);
+    free(args->qry_prob);
+    free(args->es_max_mem);
+    fclose(args->fp);
+    if ( args->distinctive_sites ) diff_sites_destroy(args);
+    free(args->hwe_prob);
+    free(args->cwd);
+    free(args->qry_arr);
+    if ( args->gt_hdr ) free(args->gt_arr);
+    free(args->pdiff);
+    free(args->ndiff);
+    free(args->ncnt);
+    free(args->qry_smpl);
+    if ( args->gt_smpl!=args->qry_smpl ) free(args->gt_smpl);
+    free(args->pairs);
+    bcf_sr_destroy(args->files);
+}
+
+static inline uint8_t gt_to_dsg(int32_t *ptr)
+{
+    if ( bcf_gt_is_missing(ptr[0]) || bcf_gt_is_missing(ptr[1]) || ptr[1]==bcf_int32_vector_end ) return 0;
+    uint8_t dsg = (bcf_gt_allele(ptr[0])?1:0) + (bcf_gt_allele(ptr[1])?1:0);
+    return 1<<dsg;
+}
+static inline uint8_t pl_to_dsg(int32_t *ptr)
+{
+    if ( ptr[0]==bcf_int32_missing || ptr[1]==bcf_int32_missing || ptr[2]==bcf_int32_missing ) return 0;
+    if ( ptr[1]==bcf_int32_vector_end || ptr[2]==bcf_int32_vector_end ) return 0;
+    int min_pl = ptr[0]<ptr[1] ? (ptr[0]<ptr[2]?ptr[0]:ptr[2]) : (ptr[1]<ptr[2]?ptr[1]:ptr[2]);
+    uint8_t dsg = 0;
+    if ( ptr[0]==min_pl ) dsg |= 1;
+    if ( ptr[1]==min_pl ) dsg |= 2;
+    if ( ptr[2]==min_pl ) dsg |= 4;
+    return dsg;
+}
+static inline uint8_t gt_to_prob(args_t *args, int32_t *ptr, double *prob)
+{
+    uint8_t dsg = gt_to_dsg(ptr);
+    if ( dsg )
+    {
+        prob[0] = args->dsg2prob[dsg][0];
+        prob[1] = args->dsg2prob[dsg][1];
+        prob[2] = args->dsg2prob[dsg][2];
+    }
+    return dsg;
+}
+static inline uint8_t pl_to_prob(args_t *args, int32_t *ptr, double *prob)
+{
+    uint8_t dsg = pl_to_dsg(ptr);
+    if ( dsg )
+    {
+        prob[0] = (ptr[0]>=0 && ptr[0]<255) ? args->pl2prob[ptr[0]] : args->pl2prob[255];
+        prob[1] = (ptr[1]>=0 && ptr[1]<255) ? args->pl2prob[ptr[1]] : args->pl2prob[255];
+        prob[2] = (ptr[2]>=0 && ptr[2]<255) ? args->pl2prob[ptr[2]] : args->pl2prob[255];
+        double sum = prob[0] + prob[1] + prob[2];
+        prob[0] /= sum;
+        prob[1] /= sum;
+        prob[2] /= sum;
+        prob[0] = -log(prob[0]);
+        prob[1] = -log(prob[1]);
+        prob[2] = -log(prob[2]);
+    }
+    return dsg;
+}
+static int set_data(args_t *args, bcf_hdr_t *hdr, bcf1_t *rec, int32_t **arr, int32_t *narr, int *narr1, int *use_GT)
+{
+    static int warn_dip_GT = 1;
+    static int warn_dip_PL = 1;
+    int i;
+    for (i=0; i<2; i++)
+    {
+        if ( *use_GT )
+        {
+            int ret = bcf_get_genotypes(hdr,rec,arr,narr);
+            if ( ret < 0 )
+            {
+                if ( !i ) { *use_GT = 0; continue; }
+                args->nskip_no_data++;
+                return -1;
+            }
+            if ( ret != 2*bcf_hdr_nsamples(hdr) )
+            {
+                if ( warn_dip_GT )
+                {
+                    fprintf(bcftools_stderr,"INFO: skipping %s:%"PRIhts_pos", only diploid FORMAT/GT fields supported. (This is printed only once.)\n", bcf_seqname(hdr,rec),rec->pos+1);
+                    warn_dip_GT = 0;
+                }
+                args->nskip_dip_GT++;
+                return -1;
+            }
+            *narr1 = 2;
+            return 0;
+        }
+
+        int ret = bcf_get_format_int32(hdr,rec,"PL",arr,narr);
+        if ( ret < 0 )
+        {
+            if ( !i ) { *use_GT = 1; continue; }
+            args->nskip_no_data++;
+            return -1;
+        }
+        if ( ret != 3*bcf_hdr_nsamples(hdr) )
+        {
+            if ( warn_dip_PL )
+            {
+                fprintf(bcftools_stderr,"INFO: skipping %s:%"PRIhts_pos", only diploid FORMAT/PL fields supported. (This is printed only once.)\n", bcf_seqname(hdr,rec),rec->pos+1);
+                warn_dip_PL = 0;
+            }
+            args->nskip_dip_PL++;
+            return -1;
+        }
+        *narr1 = 3;
+        return 0;
+    }
+    return -1;  // should never reach
+}
+static void process_line(args_t *args)
+{
+    int i,j,k, nqry1, ngt1, ret;
+
+    bcf1_t *gt_rec = NULL, *qry_rec = bcf_sr_get_line(args->files,0);   // the query file
+    int qry_use_GT = args->qry_use_GT;
+    int gt_use_GT  = args->gt_use_GT;
+
+    ret = set_data(args, args->qry_hdr, qry_rec, &args->qry_arr, &args->nqry_arr, &nqry1, &qry_use_GT);
+    if ( ret<0 ) return;
+
+    if ( args->gt_hdr )
+    {
+        gt_rec = bcf_sr_get_line(args->files,1);
+        ret = set_data(args, args->gt_hdr, gt_rec, &args->gt_arr, &args->ngt_arr, &ngt1, &gt_use_GT);
+        if ( ret<0 ) return;
+    }
+    else
+    {
+        ngt1 = nqry1;
+        args->gt_arr = args->qry_arr;
+    }
+
+    args->ncmp++;
+
+    double af,hwe_dsg[8];
+    if ( args->calc_hwe_prob )
+    {
+        int ac[2];
+        if ( args->gt_hdr )
+        {
+            if ( bcf_calc_ac(args->gt_hdr, gt_rec, ac, BCF_UN_INFO|BCF_UN_FMT)!=1 ) error("todo: bcf_calc_ac() failed\n");
+        }
+        else if ( bcf_calc_ac(args->qry_hdr, qry_rec, ac, BCF_UN_INFO|BCF_UN_FMT)!=1 ) error("todo: bcf_calc_ac() failed\n");
+
+        // hwe indexes correspond to the bitmask of eight dsg combinations to account for PL uncertainty
+        // for in the extreme case we can have uninformative PL=0,0,0. So the values are the minima of e.g.
+        //      hwe[1,2,4] ..  dsg=0,1,2
+        //      hwe[3]     ..  dsg=0 or 1
+        //      hwe[6]     ..  dsg=1 or 2
+
+        double hwe[3];
+        const double min_af = 1e-5;             // cap the AF in case we get unrealistic values
+        af = (double)ac[1]/(ac[0]+ac[1]);
+        hwe[0] = af>min_af ? -log(af*af) : -log(min_af*min_af);
+        hwe[1] = af>min_af && af<1-min_af ? -log(2*af*(1-af)) : -log(2*min_af*(1-min_af));
+        hwe[2] = af<(1-min_af) ? -log((1-af)*(1-af)) : -log(min_af*min_af);
+        hwe_dsg[0] = 0;
+        for (i=1; i<8; i++)
+        {
+            hwe_dsg[i] = HUGE_VAL;
+            for (k=0; k<3; k++)
+            {
+                if ( ((1<<k)&i) && hwe_dsg[i] > hwe[k] ) hwe_dsg[i] = hwe[k];
+            }
+        }
+    }
+
+    // The sample pairs were given explicitly via -p/-P options
+    if ( args->pairs )
+    {
+        if ( !args->use_PLs )
+        {
+            int ndiff = 0;
+            if ( args->kbs_diff ) diff_sites_reset(args);
+
+            for (i=0; i<args->npairs; i++)
+            {
+                int32_t *ptr;
+                uint8_t qry_dsg, gt_dsg;
+
+                ptr = args->gt_arr + args->pairs[i].igt*ngt1;
+                gt_dsg = gt_use_GT ? gt_to_dsg(ptr) : pl_to_dsg(ptr);
+                if ( !gt_dsg ) continue;                        // missing value
+                if ( args->hom_only && !(gt_dsg&5) ) continue;  // not a hom
+
+                ptr = args->qry_arr + args->pairs[i].iqry*nqry1;
+                qry_dsg = qry_use_GT ? gt_to_dsg(ptr) : pl_to_dsg(ptr);
+                if ( !qry_dsg ) continue;                       // missing value
+
+                int match = qry_dsg & gt_dsg;
+                if ( !match )
+                {
+                    args->ndiff[i]++;
+                    if ( args->kbs_diff ) { ndiff++; kbs_insert(args->kbs_diff, i); }
+                }
+                else if ( args->calc_hwe_prob ) args->hwe_prob[i] += hwe_dsg[match];
+                args->ncnt[i]++;
+            }
+
+            if ( ndiff ) diff_sites_push(args, ndiff, qry_rec->rid, qry_rec->pos);
+        }
+        else    // use_PLs set
+        {
+            for (i=0; i<args->npairs; i++)
+            {
+                int32_t *ptr;
+                double qry_prob[3], gt_prob[3];
+                uint8_t qry_dsg, gt_dsg;
+
+                ptr = args->gt_arr + args->pairs[i].igt*ngt1;
+                gt_dsg = gt_use_GT ? gt_to_prob(args,ptr,gt_prob) : pl_to_prob(args,ptr,gt_prob);
+                if ( !gt_dsg ) continue;                        // missing value
+                if ( args->hom_only && !(gt_dsg&5) ) continue;  // not a hom
+               
+                ptr = args->qry_arr + args->pairs[i].iqry*nqry1;
+                qry_dsg = qry_use_GT ? gt_to_prob(args,ptr,qry_prob) : pl_to_prob(args,ptr,qry_prob);
+                if ( !qry_dsg ) continue;                       // missing value
+
+                double min = qry_prob[0] + gt_prob[0];
+                qry_prob[1] += gt_prob[1];
+                if ( min > qry_prob[1] ) min = qry_prob[1];
+                qry_prob[2] += gt_prob[2];
+                if ( min > qry_prob[2] ) min = qry_prob[2];
+                args->pdiff[i] += min;
+
+                if ( args->calc_hwe_prob )
+                {
+                    int match = qry_dsg & gt_dsg;
+                    args->hwe_prob[i] += hwe_dsg[match];
+                }
+                args->ncnt[i]++;
+            }
+        }
+        return;
+    }
+
+    int idx=0;
+    if ( !args->use_PLs )
+    {
+        for (i=0; i<args->nqry_smpl; i++)
+        {
+            int iqry = args->qry_smpl ? args->qry_smpl[i] : i;
+            int32_t *ptr = args->qry_arr + nqry1*iqry;
+            args->qry_dsg[i] = qry_use_GT ? gt_to_dsg(ptr) : pl_to_dsg(ptr);
+        }
+        if ( !args->cross_check )   // in this case gt_dsg points to qry_dsg
+        {
+            for (i=0; i<args->ngt_smpl; i++)
+            {
+                int igt = args->gt_smpl ? args->gt_smpl[i] : i;
+                int32_t *ptr = args->gt_arr + ngt1*igt;
+                args->gt_dsg[i] = gt_use_GT ? gt_to_dsg(ptr) : pl_to_dsg(ptr);
+                if ( args->hom_only && !(args->gt_dsg[i]&5) ) args->gt_dsg[i] = 0;      // not a hom, set to a missing value
+            }
+        }
+        for (i=0; i<args->nqry_smpl; i++)
+        {
+            int ngt = args->cross_check ? i : args->ngt_smpl;       // two files or a sub-diagonal cross-check mode?
+            if ( !args->qry_dsg[i] ) { idx += ngt; continue; }      // missing value
+            for (j=0; j<ngt; j++)
+            {
+                if ( !args->gt_dsg[j] ) { idx++; continue; }        // missing value
+                int match = args->qry_dsg[i] & args->gt_dsg[j];
+                if ( !match ) args->ndiff[idx]++;
+                else if ( args->calc_hwe_prob ) args->hwe_prob[idx] += hwe_dsg[match];
+                args->ncnt[idx]++;
+                idx++;
+            }
+        }
+    }
+    else    // use_PLs set
+    {
+        for (i=0; i<args->nqry_smpl; i++)
+        {
+            int iqry = args->qry_smpl ? args->qry_smpl[i] : i;
+            int32_t *ptr = args->qry_arr + nqry1*iqry;
+            args->qry_dsg[i] = qry_use_GT ? gt_to_prob(args,ptr,args->qry_prob+i*3) : pl_to_prob(args,ptr,args->qry_prob+i*3);
+        }
+        if ( !args->cross_check )   // in this case gt_dsg points to qry_dsg
+        {
+            for (i=0; i<args->ngt_smpl; i++)
+            {
+                int igt = args->gt_smpl ? args->gt_smpl[i] : i;
+                int32_t *ptr = args->gt_arr + ngt1*igt;
+                args->gt_dsg[i] = gt_use_GT ? gt_to_prob(args,ptr,args->gt_prob+i*3) : pl_to_prob(args,ptr,args->gt_prob+i*3);
+                if ( args->hom_only && !(args->gt_dsg[i]&5) ) args->gt_dsg[i] = 0;      // not a hom, set to a missing value
+            }
+        }
+        for (i=0; i<args->nqry_smpl; i++)
+        {
+            int ngt = args->cross_check ? i : args->ngt_smpl;       // two files or a sub-diagonal cross-check mode?
+            if ( !args->qry_dsg[i] ) { idx += ngt; continue; }      // missing value
+            for (j=0; j<ngt; j++)
+            {
+                if ( !args->gt_dsg[j] ) { idx++; continue; }        // missing value
+
+                double min = args->qry_prob[i*3] + args->gt_prob[j*3];
+                if ( min > args->qry_prob[i*3+1] + args->gt_prob[j*3+1] ) min = args->qry_prob[i*3+1] + args->gt_prob[j*3+1];
+                if ( min > args->qry_prob[i*3+2] + args->gt_prob[j*3+2] ) min = args->qry_prob[i*3+2] + args->gt_prob[j*3+2];
+                args->pdiff[idx] += min;
+
+                if ( args->calc_hwe_prob )
+                {
+                    int match = args->qry_dsg[i] & args->gt_dsg[j];
+                    args->hwe_prob[idx] += hwe_dsg[match];
+                }
+                args->ncnt[idx]++;
+                idx++;
+            }
+        }
+    }
+}
+
+
+typedef struct
+{
+    int ism, idx;
+    double val;
+}
+idbl_t;
+static int cmp_idbl(const void *_a, const void *_b)
+{
+    idbl_t *a = (idbl_t*)_a;
+    idbl_t *b = (idbl_t*)_b;
+    if ( a->val < b->val ) return -1;
+    if ( a->val > b->val ) return 1;
+    return 0;
+}
+static void report_distinctive_sites(args_t *args)
+{
+    extsort_sort(args->es);
+
+    fprintf(args->fp,"# DS, distinctive sites:\n");
+    fprintf(args->fp,"#     - chromosome\n");
+    fprintf(args->fp,"#     - position\n");
+    fprintf(args->fp,"#     - cumulative number of pairs distinguished by this block\n");
+    fprintf(args->fp,"#     - block id\n");
+    fprintf(args->fp,"#DS\t[2]Chromosome\t[3]Position\t[4]Cumulative number of distinct pairs\t[5]Block id\n");
+
+    kbitset_t *kbs_blk = kbs_init(args->npairs);
+    kbitset_iter_t itr;
+    int i,ndiff,rid,pos,ndiff_tot = 0, iblock = 0;
+    int ndiff_min = args->distinctive_sites <= args->npairs ? args->distinctive_sites : args->npairs;
+    while ( diff_sites_shift(args,&ndiff,&rid,&pos) )
+    {
+        int ndiff_new = 0, ndiff_dbg = 0;
+        kbs_start(&itr);
+        while ( (i=kbs_next(args->kbs_diff, &itr))>=0 )
+        {
+            ndiff_dbg++;
+            if ( kbs_exists(kbs_blk,i) ) continue;   // already set
+            kbs_insert(kbs_blk,i);
+            ndiff_new++;
+        }
+        if ( ndiff_dbg!=ndiff ) error("Corrupted data, fixme: %d vs %d\n",ndiff_dbg,ndiff);
+        if ( !ndiff_new ) continue;     // no new pair distinguished by this site
+        ndiff_tot += ndiff_new;
+        fprintf(args->fp,"DS\t%s\t%d\t%d\t%d\n",bcf_hdr_id2name(args->qry_hdr,rid),pos+1,ndiff_tot,iblock);
+        if ( ndiff_tot < ndiff_min ) continue;   // fewer than the requested number of pairs can be distinguished at this point
+        iblock++;
+        ndiff_tot = 0;
+        kbs_clear(kbs_blk);
+    }
+    kbs_destroy(kbs_blk);
+}
+static void report(args_t *args)
+{
+    fprintf(args->fp,"INFO\tsites-compared\t%u\n",args->ncmp);
+    fprintf(args->fp,"INFO\tsites-skipped-no-match\t%u\n",args->nskip_no_match);
+    fprintf(args->fp,"INFO\tsites-skipped-multiallelic\t%u\n",args->nskip_not_ba);
+    fprintf(args->fp,"INFO\tsites-skipped-monoallelic\t%u\n",args->nskip_mono);
+    fprintf(args->fp,"INFO\tsites-skipped-no-data\t%u\n",args->nskip_no_data);
+    fprintf(args->fp,"INFO\tsites-skipped-GT-not-diploid\t%u\n",args->nskip_dip_GT);
+    fprintf(args->fp,"INFO\tsites-skipped-PL-not-diploid\t%u\n",args->nskip_dip_PL);
+    fprintf(args->fp,"# DC, discordance:\n");
+    fprintf(args->fp,"#     - query sample\n");
+    fprintf(args->fp,"#     - genotyped sample\n");
+    fprintf(args->fp,"#     - discordance (number of mismatches; smaller is better)\n");
+    fprintf(args->fp,"#     - negative log of HWE probability at matching sites (rare genotypes mataches are more informative, bigger is better)\n");
+    fprintf(args->fp,"#     - number of sites compared (bigger is better)\n");
+    fprintf(args->fp,"#DC\t[2]Query Sample\t[3]Genotyped Sample\t[4]Discordance\t[5]-log P(HWE)\t[6]Number of sites compared\n");
+
+    int trim = args->ntop;
+    if ( !args->pairs )
+    {
+        if ( !args->ngt_smpl && args->nqry_smpl <= args->ntop ) trim = 0;
+        if ( args->ngt_smpl && args->ngt_smpl <= args->ntop  ) trim = 0;
+    }
+
+    if ( args->pairs )
+    {
+        int i;
+        for (i=0; i<args->npairs; i++)
+        {
+            int iqry = args->pairs[i].iqry;
+            int igt  = args->pairs[i].igt;
+            if ( args->ndiff )
+            {
+                fprintf(args->fp,"DC\t%s\t%s\t%u\t%e\t%u\n",
+                        args->qry_hdr->samples[iqry],
+                        args->gt_hdr?args->gt_hdr->samples[igt]:args->qry_hdr->samples[igt],
+                        args->ndiff[i],
+                        args->calc_hwe_prob ? args->hwe_prob[i] : 0,
+                        args->ncnt[i]);
+            }
+            else
+            {
+                fprintf(args->fp,"DC\t%s\t%s\t%e\t%e\t%u\n",
+                        args->qry_hdr->samples[iqry],
+                        args->gt_hdr?args->gt_hdr->samples[igt]:args->qry_hdr->samples[igt],
+                        args->pdiff[i],
+                        args->calc_hwe_prob ? args->hwe_prob[i] : 0,
+                        args->ncnt[i]);
+            }
+        }
+    }
+    else if ( !trim )
+    {
+        int i,j,idx=0;
+        for (i=0; i<args->nqry_smpl; i++)
+        {
+            int iqry = args->qry_smpl ? args->qry_smpl[i] : i;
+            int ngt  = args->cross_check ? i : args->ngt_smpl;
+            for (j=0; j<ngt; j++)
+            {
+                int igt = args->gt_smpl ? args->gt_smpl[j] : j;
+                if ( args->ndiff )
+                {
+                    fprintf(args->fp,"DC\t%s\t%s\t%u\t%e\t%u\n",
+                            args->qry_hdr->samples[iqry],
+                            args->gt_hdr?args->gt_hdr->samples[igt]:args->qry_hdr->samples[igt],
+                            args->ndiff[idx],
+                            args->calc_hwe_prob ? args->hwe_prob[idx] : 0,
+                            args->ncnt[idx]);
+                }
+                else
+                {
+                    fprintf(args->fp,"DC\t%s\t%s\t%e\t%e\t%u\n",
+                            args->qry_hdr->samples[iqry],
+                            args->gt_hdr?args->gt_hdr->samples[igt]:args->qry_hdr->samples[igt],
+                            args->pdiff[idx],
+                            args->calc_hwe_prob ? args->hwe_prob[idx] : 0,
+                            args->ncnt[idx]);
+                }
+                idx++;
+            }
+        }
+    }
+    else if ( !args->cross_check )
+    {
+        idbl_t *arr = (idbl_t*)malloc(sizeof(*arr)*args->ngt_smpl);
+        int i,j;
+        for (i=0; i<args->nqry_smpl; i++)
+        {
+            int idx  = i*args->ngt_smpl;
+            for (j=0; j<args->ngt_smpl; j++)
+            {
+                if ( args->sort_by_hwe )
+                    arr[j].val = -args->hwe_prob[idx];
+                else if ( args->ndiff )
+                    arr[j].val = args->ncnt[idx] ? (double)args->ndiff[idx]/args->ncnt[idx] : 0;
+                else
+                    arr[j].val = args->ncnt[idx] ? args->pdiff[idx]/args->ncnt[idx] : 0;
+                arr[j].ism = j;
+                arr[j].idx = idx;
+                idx++;
+            }
+            qsort(arr, args->ngt_smpl, sizeof(*arr), cmp_idbl);
+            int iqry = args->qry_smpl ? args->qry_smpl[i] : i;
+            for (j=0; j<args->ntop; j++)
+            {
+                int idx = arr[j].idx;
+                int igt = args->gt_smpl ? args->gt_smpl[arr[j].ism] : arr[j].ism;
+                if ( args->ndiff )
+                {
+                    fprintf(args->fp,"DC\t%s\t%s\t%u\t%e\t%u\n",
+                            args->qry_hdr->samples[iqry],
+                            args->gt_hdr?args->gt_hdr->samples[igt]:args->qry_hdr->samples[igt],
+                            args->ndiff[idx],
+                            args->calc_hwe_prob ? args->hwe_prob[idx] : 0,
+                            args->ncnt[idx]);
+                }
+                else
+                {
+                    fprintf(args->fp,"DC\t%s\t%s\t%e\t%e\t%u\n",
+                            args->qry_hdr->samples[iqry],
+                            args->gt_hdr?args->gt_hdr->samples[igt]:args->qry_hdr->samples[igt],
+                            args->pdiff[idx],
+                            args->calc_hwe_prob ? args->hwe_prob[idx] : 0,
+                            args->ncnt[idx]);
+                }
+            }
+        }
+        free(arr);
+    }
+    else
+    {
+        int narr = args->nqry_smpl-1;
+        idbl_t *arr = (idbl_t*)malloc(sizeof(*arr)*narr);
+        int i,j,k,idx;
+        for (i=0; i<args->nqry_smpl; i++)
+        {
+            k = 0, idx = i*(i-1)/2;
+            for (j=0; j<i; j++)
+            {
+                if ( args->sort_by_hwe )
+                    arr[k].val = -args->hwe_prob[idx];
+                else if ( args->ndiff )
+                    arr[k].val = args->ncnt[idx] ? (double)args->ndiff[idx]/args->ncnt[idx] : 0;
+                else
+                    arr[k].val = args->ncnt[idx] ? args->pdiff[idx]/args->ncnt[idx] : 0;
+                arr[k].ism = j;
+                arr[k].idx = idx;
+                idx++;
+                k++;
+            }
+            for (; j<narr; j++)
+            {
+                idx = j*(j+1)/2 + i;
+                if ( args->sort_by_hwe )
+                    arr[k].val = -args->hwe_prob[idx];
+                else if ( args->ndiff )
+                    arr[k].val = args->ncnt[idx] ? (double)args->ndiff[idx]/args->ncnt[idx] : 0;
+                else
+                    arr[k].val = args->ncnt[idx] ? args->pdiff[idx]/args->ncnt[idx] : 0;
+                arr[k].ism = j + 1;
+                arr[k].idx = idx;
+                k++;
+            }
+            qsort(arr, narr, sizeof(*arr), cmp_idbl);
+            int iqry = args->qry_smpl ? args->qry_smpl[i] : i;
+            for (j=0; j<args->ntop; j++)
+            {
+                if ( i <= arr[j].ism ) continue;
+                int idx = arr[j].idx;
+                int igt = args->qry_smpl ? args->qry_smpl[arr[j].ism] : arr[j].ism;
+                if ( args->ndiff )
+                {
+                    fprintf(args->fp,"DC\t%s\t%s\t%u\t%e\t%u\n",
+                            args->qry_hdr->samples[iqry],
+                            args->qry_hdr->samples[igt],
+                            args->ndiff[idx],
+                            args->calc_hwe_prob ? args->hwe_prob[idx] : 0,
+                            args->ncnt[idx]);
+                }
+                else
+                {
+                    fprintf(args->fp,"DC\t%s\t%s\t%e\t%e\t%u\n",
+                            args->qry_hdr->samples[iqry],
+                            args->qry_hdr->samples[igt],
+                            args->pdiff[idx],
+                            args->calc_hwe_prob ? args->hwe_prob[idx] : 0,
+                            args->ncnt[idx]);
+                }
+            }
+        }
+        free(arr);
+    }
+}
+
+static int is_input_okay(args_t *args, int nmatch)
+{
+    int i;
+    const char *msg;
+    bcf_hdr_t *hdr;
+    bcf1_t *rec;
+    if ( args->gt_hdr && nmatch!=2 )
+    {
+        if ( args->nskip_no_match++ ) return 0;
+        for (i=0; i<2; i++)
+        {
+            rec = bcf_sr_get_line(args->files,i);
+            if ( rec ) break;
+        }
+        hdr = bcf_sr_get_header(args->files,i);
+        fprintf(bcftools_stderr,"INFO: skipping %s:%"PRIhts_pos", no record with matching POS+ALT. (This is printed only once.)\n",
+                bcf_seqname(hdr,rec),rec->pos+1);
+        return 0;
+    }
+    for (i=0; i<2; i++)
+    {
+        hdr = bcf_sr_get_header(args->files,i);
+        rec = bcf_sr_get_line(args->files,i);
+        if ( rec->n_allele>2 )
+        {
+            if ( args->nskip_not_ba++ ) return 0;
+            msg = "not a biallelic site, run `bcftools norm -m -` first";
+            goto not_okay;
+        }
+        if ( bcf_get_variant_types(rec)==VCF_REF )
+        {
+            if ( args->nskip_mono++ ) return 0;
+            msg = "monoallelic site";
+            goto not_okay;
+        }
+        if ( !args->gt_hdr ) break;
+    }
+    return 1;
+
+not_okay:
+    fprintf(bcftools_stderr,"INFO: skipping %s:%"PRIhts_pos", %s. (This is printed only once.)\n", 
+        bcf_seqname(hdr,rec),rec->pos+1,msg);
+    return 0;
+}
+
+static void usage(void)
+{
+    fprintf(bcftools_stderr, "\n");
+    fprintf(bcftools_stderr, "About:   Check sample identity. With no -g BCF given, multi-sample cross-check is performed.\n");
+    fprintf(bcftools_stderr, "Usage:   bcftools gtcheck [options] [-g <genotypes.vcf.gz>] <query.vcf.gz>\n");
+    fprintf(bcftools_stderr, "\n");
+    fprintf(bcftools_stderr, "Options:\n");
+    //fprintf(bcftools_stderr, "    -a, --all-sites                  Output comparison for all sites\n");
+    //fprintf(bcftools_stderr, "    -c, --cluster MIN,MAX            Min inter- and max intra-sample error [0.23,-0.3]\n");
+    fprintf(bcftools_stderr, "        --distinctive-sites            Find sites that can distinguish between at least NUM sample pairs.\n");
+    fprintf(bcftools_stderr, "                  NUM[,MEM[,TMP]]          If the number is smaller or equal to 1, it is interpreted as the fraction of pairs.\n");
+    fprintf(bcftools_stderr, "                                           The optional MEM string sets the maximum memory used for in-memory sorting [500M]\n");
+#ifdef _WIN32
+    fprintf(bcftools_stderr, "                                           and TMP is a prefix of temporary files used by external sorting [/bcftools.XXXXXX]\n");
+#else
+    fprintf(bcftools_stderr, "                                           and TMP is a prefix of temporary files used by external sorting [/tmp/bcftools.XXXXXX]\n");
+#endif
+    fprintf(bcftools_stderr, "        --dry-run                      Stop after first record to estimate required time\n");
+    fprintf(bcftools_stderr, "    -e, --error-probability INT        Phred-scaled probability of genotyping error, 0 for faster but less accurate results [40]\n");
+    fprintf(bcftools_stderr, "    -g, --genotypes FILE               Genotypes to compare against\n");
+    fprintf(bcftools_stderr, "    -H, --homs-only                    Homozygous genotypes only, useful with low coverage data (requires -g)\n");
+    fprintf(bcftools_stderr, "        --n-matches INT                Print only top INT matches for each sample (sorted by average score), 0 for unlimited.\n");
+    fprintf(bcftools_stderr, "                                           Use negative value to sort by HWE probability rather than by discordance [0]\n");
+    fprintf(bcftools_stderr, "        --no-HWE-prob                  Disable calculation of HWE probability\n");
+    fprintf(bcftools_stderr, "    -p, --pairs LIST                   Comma-separated sample pairs to compare (qry,gt[,qry,gt..] with -g or qry,qry[,qry,qry..] w/o)\n");
+    fprintf(bcftools_stderr, "    -P, --pairs-file FILE              File with tab-delimited sample pairs to compare (qry,gt with -g or qry,qry w/o)\n");
+    fprintf(bcftools_stderr, "    -r, --regions REGION               Restrict to comma-separated list of regions\n");
+    fprintf(bcftools_stderr, "    -R, --regions-file FILE            Restrict to regions listed in a file\n");
+    fprintf(bcftools_stderr, "        --regions-overlap 0|1|2        Include if POS in the region (0), record overlaps (1), variant overlaps (2) [1]\n");
+    fprintf(bcftools_stderr, "    -s, --samples [qry|gt]:LIST        List of query or -g samples, \"-\" to select all samples (by default all samples are compared)\n");
+    fprintf(bcftools_stderr, "    -S, --samples-file [qry|gt]:FILE   File with the query or -g samples to compare\n");
+    fprintf(bcftools_stderr, "    -t, --targets REGION               Similar to -r but streams rather than index-jumps\n");
+    fprintf(bcftools_stderr, "    -T, --targets-file FILE            Similar to -R but streams rather than index-jumps\n");
+    fprintf(bcftools_stderr, "        --targets-overlap 0|1|2        Include if POS in the region (0), record overlaps (1), variant overlaps (2) [0]\n");
+    fprintf(bcftools_stderr, "    -u, --use TAG1[,TAG2]              Which tag to use in the query file (TAG1) and the -g file (TAG2) [PL,GT]\n");
+    fprintf(bcftools_stderr, "Examples:\n");
+    fprintf(bcftools_stderr, "   # Check discordance of all samples from B against all sample in A\n");
+    fprintf(bcftools_stderr, "   bcftools gtcheck -g A.bcf B.bcf\n");
+    fprintf(bcftools_stderr, "\n");
+    fprintf(bcftools_stderr, "   # Limit comparisons to the fiven list of samples\n");
+    fprintf(bcftools_stderr, "   bcftools gtcheck -s gt:a1,a2,a3 -s qry:b1,b2 -g A.bcf B.bcf\n");
+    fprintf(bcftools_stderr, "\n");
+    fprintf(bcftools_stderr, "   # Compare only two pairs a1,b1 and a1,b2\n");
+    fprintf(bcftools_stderr, "   bcftools gtcheck -p a1,b1,a1,b2 -g A.bcf B.bcf\n");
+    fprintf(bcftools_stderr, "\n");
+    bcftools_exit(1);
+}
+
+int main_vcfgtcheck(int argc, char *argv[])
+{
+    int c;
+    args_t *args = (args_t*) calloc(1,sizeof(args_t));
+    args->argc   = argc; args->argv = argv; set_cwd(args);
+    args->qry_use_GT = -1;
+    args->gt_use_GT  = -1;
+    args->calc_hwe_prob = 1;
+    args->use_PLs = 40;
+    args->regions_overlap = 1;
+    args->targets_overlap = 0;
+
+    // external sort for --distinctive-sites
+#ifdef _WIN32
+    args->es_tmp_prefix = NULL;
+#else
+    args->es_tmp_prefix = "/tmp/bcftools-gtcheck";
+#endif
+    args->es_max_mem = strdup("500M");
+
+    // In simulated sample swaps the minimum error was 0.3 and maximum intra-sample error was 0.23
+    //    - min_inter: pairs with smaller err value will be considered identical 
+    //    - max_intra: pairs with err value bigger than abs(max_intra_err) will be considered
+    //                  different. If negative, the cutoff may be heuristically lowered
+    args->min_inter_err =  0.23;
+    args->max_intra_err = -0.3;
+
+    static struct option loptions[] =
+    {
+        {"error-probability",1,0,'e'},
+        {"use",1,0,'u'},
+        {"cluster",1,0,'c'},
+        {"GTs-only",1,0,'G'},
+        {"all-sites",0,0,'a'},
+        {"homs-only",0,0,'H'},
+        {"help",0,0,'h'},
+        {"genotypes",1,0,'g'},
+        {"plot",1,0,'p'},
+        {"samples",1,0,'s'},
+        {"samples-file",1,0,'S'},
+        {"n-matches",1,0,2},
+        {"no-HWE-prob",0,0,3},
+        {"target-sample",1,0,4},
+        {"dry-run",0,0,5},
+        {"distinctive-sites",1,0,6},
+        {"regions",1,0,'r'},
+        {"regions-file",1,0,'R'},
+        {"regions-overlap",required_argument,NULL,7},
+        {"targets",1,0,'t'},
+        {"targets-file",1,0,'T'},
+        {"targets-overlap",required_argument,NULL,8},
+        {"pairs",1,0,'p'},
+        {"pairs-file",1,0,'P'},
+        {0,0,0,0}
+    };
+    char *tmp;
+    while ((c = getopt_long(argc, argv, "hg:p:s:S:p:P:Hr:R:at:T:G:c:u:e:",loptions,NULL)) >= 0) {
+        switch (c) {
+            case 'e':
+                args->use_PLs = strtol(optarg,&tmp,10);
+                if ( !tmp || *tmp ) error("Could not parse: --error-probability %s\n", optarg);
+                break;
+            case 'u':
+                {
+                    int i,nlist;
+                    char **list = hts_readlist(optarg, 0, &nlist);
+                    if ( !list || nlist<=0 || nlist>2 ) error("Failed to parse --use %s\n", optarg);
+                    if ( !strcasecmp("GT",list[0]) ) args->qry_use_GT = 1;
+                    else if ( !strcasecmp("PL",list[0]) ) args->qry_use_GT = 0;
+                    else error("Failed to parse --use %s; only GT and PL are supported\n", optarg);
+                    if ( nlist==2 )
+                    {
+                        if ( !strcasecmp("GT",list[1]) ) args->gt_use_GT = 1;
+                        else if ( !strcasecmp("PL",list[1]) ) args->gt_use_GT = 0;
+                        else error("Failed to parse --use %s; only GT and PL are supported\n", optarg);
+                    }
+                    else args->gt_use_GT = args->qry_use_GT;
+                    for (i=0; i<nlist; i++) free(list[i]);
+                    free(list);
+                }
+                break;
+            case 2 :
+                args->ntop = strtol(optarg,&tmp,10);
+                if ( !tmp || *tmp ) error("Could not parse: --n-matches %s\n", optarg);
+                if ( args->ntop < 0 )
+                {
+                    args->sort_by_hwe = 1;
+                    args->ntop *= -1;
+                }
+                break;
+            case 3 : args->calc_hwe_prob = 0; break;
+            case 4 : error("The option -S, --target-sample has been deprecated\n"); break;
+            case 5 : args->dry_run = 1; break;
+            case 6 : 
+                args->distinctive_sites = strtod(optarg,&tmp);
+                if ( *tmp )
+                {
+                    if ( *tmp!=',' ) error("Could not parse: --distinctive-sites %s\n", optarg);
+                    tmp++;
+                    free(args->es_max_mem);
+                    args->es_max_mem = strdup(tmp);
+                    while ( *tmp && *tmp!=',' ) tmp++;
+                    if ( *tmp ) { *tmp = 0; args->es_tmp_prefix = tmp+1; }
+                }
+                args->use_PLs = 0;
+                break;
+            case 'c':
+                error("The -c option is to be implemented, please open an issue on github\n");
+                args->min_inter_err = strtod(optarg,&tmp);
+                if ( *tmp )
+                {
+                    if ( *tmp!=',') error("Could not parse: -c %s\n", optarg);
+                    args->max_intra_err = strtod(tmp+1,&tmp);
+                    if ( *tmp ) error("Could not parse: -c %s\n", optarg);
+                }
+                break;
+            case 'G': error("The option -G, --GTs-only has been deprecated\n"); break;
+            case 'a': args->all_sites = 1; error("The -a option is to be implemented, please open an issue on github\n"); break;
+            case 'H': args->hom_only = 1; break;
+            case 'g': args->gt_fname = optarg; break;
+//            case 'p': args->plot = optarg; break;
+            case 's':
+                if ( !strncasecmp("gt:",optarg,3) ) args->gt_samples = optarg+3;
+                else if ( !strncasecmp("qry:",optarg,4) ) args->qry_samples = optarg+4;
+                else error("Which one? Query samples (qry:%s) or genotype samples (gt:%s)?\n",optarg,optarg);
+                break;
+            case 'S': 
+                if ( !strncasecmp("gt:",optarg,3) ) args->gt_samples = optarg+3, args->gt_samples_is_file = 1;
+                else if ( !strncasecmp("qry:",optarg,4) ) args->qry_samples = optarg+4, args->qry_samples_is_file = 1;
+                else error("Which one? Query samples (qry:%s) or genotype samples (gt:%s)?\n",optarg,optarg);
+                break;
+            case 'p': args->pair_samples = optarg; break;
+            case 'P': args->pair_samples = optarg; args->pair_samples_is_file = 1; break;
+            case 'r': args->regions = optarg; break;
+            case 'R': args->regions = optarg; args->regions_is_file = 1; break;
+            case 't': args->targets = optarg; break;
+            case 'T': args->targets = optarg; args->targets_is_file = 1; break;
+            case  7 :
+                args->regions_overlap = parse_overlap_option(optarg);
+                if ( args->regions_overlap < 0 ) error("Could not parse: --regions-overlap %s\n",optarg);
+                break;
+            case  8 :
+                args->targets_overlap = parse_overlap_option(optarg);
+                if ( args->targets_overlap < 0 ) error("Could not parse: --targets-overlap %s\n",optarg);
+                break;
+            case 'h':
+            case '?': usage(); break;
+            default: error("Unknown argument: %s\n", optarg);
+        }
+    }
+    if ( optind==argc )
+    {
+        if ( !isatty(fileno((FILE *)stdin)) ) args->qry_fname = "-";  // reading from stdin
+        else usage();   // no files given
+    }
+    else args->qry_fname = argv[optind];
+    if ( argc>optind+1 ) error("Error: too many files given, run with -h for help\n");  // too many files given
+    if ( args->pair_samples )
+    {
+        if ( args->gt_samples || args->qry_samples ) error("The -p/-P option cannot be combined with -s/-S\n");
+        if ( args->ntop ) error("The --n-matches option cannot be combined with -p/-P\n");
+    }
+    if ( args->distinctive_sites && !args->pair_samples ) error("The experimental option --distinctive-sites requires -p/-P\n");
+    if ( args->hom_only && !args->gt_fname ) error("The option --homs-only requires --genotypes\n");
+    if ( args->distinctive_sites && args->use_PLs ) error("The option --distinctive-sites cannot be combined with --error-probability\n");
+
+    init_data(args);
+
+    int ret;
+    while ( (ret=bcf_sr_next_line(args->files)) )
+    {
+        if ( !is_input_okay(args,ret) ) continue;
+
+        // time one record to give the user an estimate with very big files
+        struct timeval t0, t1;
+        if ( !args->ncmp )  gettimeofday(&t0, NULL);
+
+        process_line(args);
+
+        if ( args->ncmp==1 )
+        {
+            gettimeofday(&t1, NULL);
+            double delta = (t1.tv_sec - t0.tv_sec) * 1e6 + (t1.tv_usec - t0.tv_usec);
+            fprintf(bcftools_stderr,"INFO:\tTime required to process one record .. %f seconds\n",delta/1e6);
+            fprintf(args->fp,"INFO\tTime required to process one record .. %f seconds\n",delta/1e6);
+            if ( args->dry_run ) break;
+        }
+    }
+    if ( !args->dry_run )
+    {
+        report(args);
+        if ( args->distinctive_sites ) report_distinctive_sites(args);
+    }
+
+    destroy_data(args);
+    free(args);
+    return 0;
+}
+
diff --git a/bcftools/vcfhead.c b/bcftools/vcfhead.c
new file mode 100644
index 0000000..20be2a9
--- /dev/null
+++ b/bcftools/vcfhead.c
@@ -0,0 +1,133 @@
+/*  vcfhead.c -- view VCF/BCF file headers.
+
+    Copyright (C) 2021 University of Glasgow.
+
+    Author: John Marshall <jmarshall@hey.com>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.  */
+
+#include <getopt.h>
+#include <inttypes.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <unistd.h>
+
+#include <htslib/kstring.h>
+#include <htslib/vcf.h>
+
+#include "bcftools.h"
+
+int main_vcfhead(int argc, char *argv[])
+{
+    static const char usage[] =
+"\n"
+"About: Displays VCF/BCF headers and optionally the first few variant records\n"
+"Usage: bcftools head [OPTION]... [FILE]\n"
+"\n"
+"Options:\n"
+"  -h, --headers INT   Display INT header lines [all]\n"
+"  -n, --records INT   Display INT variant record lines [none]\n"
+"\n";
+
+    static const struct option loptions[] = {
+        { "headers", required_argument, NULL, 'h' },
+        { "records", required_argument, NULL, 'n' },
+        { NULL, 0, NULL, 0 }
+    };
+
+    int all_headers = 1;
+    uint64_t nheaders = 0;
+    uint64_t nrecords = 0;
+
+    int c, nargs;
+    while ((c = getopt_long(argc, argv, "h:n:", loptions, NULL)) >= 0)
+        switch (c) {
+        case 'h': all_headers = 0; nheaders = strtoull(optarg, NULL, 0); break;
+        case 'n': nrecords = strtoull(optarg, NULL, 0); break;
+        default:
+            fputs(usage, stderr);
+            return EXIT_FAILURE;
+        }
+
+    nargs = argc - optind;
+    if (nargs == 0 && isatty(STDIN_FILENO)) {
+        fputs(usage, stdout);
+        return EXIT_SUCCESS;
+    }
+    else if (nargs > 1) {
+        fputs(usage, stderr);
+        return EXIT_FAILURE;
+    }
+
+    const char *fname = (nargs == 1)? argv[optind] : "-";
+    vcfFile *fp = bcf_open(fname, "r");
+    if (fp == NULL) {
+        if (strcmp(fname, "-") != 0)
+            error_errno("[%s] Can't open \"%s\"", __func__, fname);
+        else
+            error_errno("[%s] Can't open standard input", __func__);
+    }
+
+    bcf_hdr_t *hdr = bcf_hdr_read(fp);
+    if (hdr == NULL) {
+        bcf_close(fp);
+        if (strcmp(fname, "-") != 0)
+            error("[%s] Can't read headers from \"%s\"\n", __func__, fname);
+        else
+            error("[%s] Can't read headers\n", __func__);
+    }
+
+    kstring_t str = KS_INITIALIZE;
+
+    if (all_headers) {
+        bcf_hdr_format(hdr, 0, &str);
+        fputs(ks_str(&str), stdout);
+    }
+    else if (nheaders > 0) {
+        bcf_hdr_format(hdr, 0, &str);
+        char *lim = str.s;
+        uint64_t n;
+        for (n = 0; n < nheaders; n++) {
+            lim = strchr(lim, '\n');
+            if (lim) lim++;
+            else break;
+        }
+        if (lim) *lim = '\0';
+        fputs(ks_str(&str), stdout);
+    }
+
+    if (nrecords > 0) {
+        bcf1_t *rec = bcf_init();
+        uint64_t n;
+        for (n = 0; n < nrecords && bcf_read(fp, hdr, rec) >= 0; n++) {
+            ks_clear(&str);
+            if (vcf_format(hdr, rec, &str) >= 0)
+                fputs(ks_str(&str), stdout);
+            else
+                fprintf(stderr, "[%s] Record #%"PRIu64 " is invalid\n", __func__, n+1);
+        }
+        bcf_destroy(rec);
+    }
+
+    ks_free(&str);
+    bcf_hdr_destroy(hdr);
+    bcf_close(fp);
+
+    return EXIT_SUCCESS;
+}
diff --git a/bcftools/vcfhead.c.pysam.c b/bcftools/vcfhead.c.pysam.c
new file mode 100644
index 0000000..09744f2
--- /dev/null
+++ b/bcftools/vcfhead.c.pysam.c
@@ -0,0 +1,135 @@
+#include "bcftools.pysam.h"
+
+/*  vcfhead.c -- view VCF/BCF file headers.
+
+    Copyright (C) 2021 University of Glasgow.
+
+    Author: John Marshall <jmarshall@hey.com>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.  */
+
+#include <getopt.h>
+#include <inttypes.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <unistd.h>
+
+#include <htslib/kstring.h>
+#include <htslib/vcf.h>
+
+#include "bcftools.h"
+
+int main_vcfhead(int argc, char *argv[])
+{
+    static const char usage[] =
+"\n"
+"About: Displays VCF/BCF headers and optionally the first few variant records\n"
+"Usage: bcftools head [OPTION]... [FILE]\n"
+"\n"
+"Options:\n"
+"  -h, --headers INT   Display INT header lines [all]\n"
+"  -n, --records INT   Display INT variant record lines [none]\n"
+"\n";
+
+    static const struct option loptions[] = {
+        { "headers", required_argument, NULL, 'h' },
+        { "records", required_argument, NULL, 'n' },
+        { NULL, 0, NULL, 0 }
+    };
+
+    int all_headers = 1;
+    uint64_t nheaders = 0;
+    uint64_t nrecords = 0;
+
+    int c, nargs;
+    while ((c = getopt_long(argc, argv, "h:n:", loptions, NULL)) >= 0)
+        switch (c) {
+        case 'h': all_headers = 0; nheaders = strtoull(optarg, NULL, 0); break;
+        case 'n': nrecords = strtoull(optarg, NULL, 0); break;
+        default:
+            fputs(usage, bcftools_stderr);
+            return EXIT_FAILURE;
+        }
+
+    nargs = argc - optind;
+    if (nargs == 0 && isatty(STDIN_FILENO)) {
+        fputs(usage, bcftools_stdout);
+        return EXIT_SUCCESS;
+    }
+    else if (nargs > 1) {
+        fputs(usage, bcftools_stderr);
+        return EXIT_FAILURE;
+    }
+
+    const char *fname = (nargs == 1)? argv[optind] : "-";
+    vcfFile *fp = bcf_open(fname, "r");
+    if (fp == NULL) {
+        if (strcmp(fname, "-") != 0)
+            error_errno("[%s] Can't open \"%s\"", __func__, fname);
+        else
+            error_errno("[%s] Can't open standard input", __func__);
+    }
+
+    bcf_hdr_t *hdr = bcf_hdr_read(fp);
+    if (hdr == NULL) {
+        bcf_close(fp);
+        if (strcmp(fname, "-") != 0)
+            error("[%s] Can't read headers from \"%s\"\n", __func__, fname);
+        else
+            error("[%s] Can't read headers\n", __func__);
+    }
+
+    kstring_t str = KS_INITIALIZE;
+
+    if (all_headers) {
+        bcf_hdr_format(hdr, 0, &str);
+        fputs(ks_str(&str), bcftools_stdout);
+    }
+    else if (nheaders > 0) {
+        bcf_hdr_format(hdr, 0, &str);
+        char *lim = str.s;
+        uint64_t n;
+        for (n = 0; n < nheaders; n++) {
+            lim = strchr(lim, '\n');
+            if (lim) lim++;
+            else break;
+        }
+        if (lim) *lim = '\0';
+        fputs(ks_str(&str), bcftools_stdout);
+    }
+
+    if (nrecords > 0) {
+        bcf1_t *rec = bcf_init();
+        uint64_t n;
+        for (n = 0; n < nrecords && bcf_read(fp, hdr, rec) >= 0; n++) {
+            ks_clear(&str);
+            if (vcf_format(hdr, rec, &str) >= 0)
+                fputs(ks_str(&str), bcftools_stdout);
+            else
+                fprintf(bcftools_stderr, "[%s] Record #%"PRIu64 " is invalid\n", __func__, n+1);
+        }
+        bcf_destroy(rec);
+    }
+
+    ks_free(&str);
+    bcf_hdr_destroy(hdr);
+    bcf_close(fp);
+
+    return EXIT_SUCCESS;
+}
diff --git a/bcftools/vcfindex.c b/bcftools/vcfindex.c
new file mode 100644
index 0000000..1dd960e
--- /dev/null
+++ b/bcftools/vcfindex.c
@@ -0,0 +1,334 @@
+/*  vcfindex.c -- Index bgzip compressed VCF/BCF files for random access.
+
+    Copyright (C) 2014-2021 Genome Research Ltd.
+
+    Author: Shane McCarthy <sm15@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <strings.h>
+#include <unistd.h>
+#include <getopt.h>
+#include <htslib/vcf.h>
+#include <htslib/tbx.h>
+#include <sys/stat.h>
+#define __STDC_FORMAT_MACROS
+#include <inttypes.h>
+#include <htslib/kstring.h>
+#include <htslib/bgzf.h>
+#include "bcftools.h"
+
+#define BCF_LIDX_SHIFT    14
+
+enum {
+    per_contig = 1,
+    all_contigs = 2,
+    total = 4
+};
+
+static void usage(void)
+{
+    fprintf(stderr, "\n");
+    fprintf(stderr, "About:   Index bgzip compressed VCF/BCF files for random access.\n");
+    fprintf(stderr, "Usage:   bcftools index [options] <in.bcf>|<in.vcf.gz>\n");
+    fprintf(stderr, "\n");
+    fprintf(stderr, "Indexing options:\n");
+    fprintf(stderr, "    -c, --csi                generate CSI-format index for VCF/BCF files [default]\n");
+    fprintf(stderr, "    -f, --force              overwrite index if it already exists\n");
+    fprintf(stderr, "    -m, --min-shift INT      set minimal interval size for CSI indices to 2^INT [14]\n");
+    fprintf(stderr, "    -o, --output FILE        optional output index file name\n");
+    fprintf(stderr, "    -t, --tbi                generate TBI-format index for VCF files\n");
+    fprintf(stderr, "        --threads INT        use multithreading with INT worker threads [0]\n");
+    fprintf(stderr, "\n");
+    fprintf(stderr, "Stats options:\n");
+    fprintf(stderr, "    -a, --all            with --stats, print stats for all contigs even when zero\n");
+    fprintf(stderr, "    -n, --nrecords       print number of records based on existing index file\n");
+    fprintf(stderr, "    -s, --stats          print per contig stats based on existing index file\n");
+    fprintf(stderr, "\n");
+    exit(1);
+}
+
+int vcf_index_stats(char *fname, int stats)
+{
+    const char **seq = NULL;
+    int tid, nseq = 0, ret = 0;
+    tbx_t *tbx = NULL;
+    bcf_hdr_t *hdr = NULL;
+    hts_idx_t *idx = NULL;
+    htsFile *fp = NULL;
+    uint64_t sum = 0;
+    char *fntemp = NULL, *fnidx = NULL;
+
+    /*
+     * First, has the user provided an index file? If per contig stats
+     * are requested, open the variant file (together with the index file,
+     * if provided), since the contig names can only be retrieved from its
+     * header. Otherwise, use just the corresponding index file to count
+     * the total number of records.
+     */
+    int len = strlen(fname);
+    int idx_only = 0;
+    if ( (fnidx = strstr(fname, HTS_IDX_DELIM)) != NULL ) {
+        fntemp = strdup(fname);
+        if ( !fntemp ) return 1;
+        fntemp[fnidx-fname] = 0;
+        fname = fntemp;
+        fnidx += strlen(HTS_IDX_DELIM);
+    }
+    else if ( len>4 && (!strcasecmp(".csi",fname+len-4) || !strcasecmp(".tbi",fname+len-4)) )
+    {
+        fnidx  = fname;
+        fntemp = strdup(fname);
+        fname  = fntemp;
+        fname[len-4] = 0;
+        idx_only = 1;
+    }
+
+    if ( stats&per_contig )
+    {
+        if ( idx_only )
+        {
+            struct stat buf;
+            if ( stat(fname, &buf)==0 ) idx_only = 0;
+        }
+
+        enum htsExactFormat fmt;
+        if ( !idx_only )
+        {
+            fp = hts_open(fname,"r");
+            if ( !fp ) {
+                fprintf(stderr,"Could not read %s\n", fname);
+                ret = 1; goto cleanup;
+            }
+            hdr = bcf_hdr_read(fp);
+            if ( !hdr ) {
+                fprintf(stderr,"Could not read the header: %s\n", fname);
+                ret = 1; goto cleanup;
+            }
+            fmt = hts_get_format(fp)->format;
+        }
+        else
+        {
+            int len = strlen(fnidx);
+            if ( !strcasecmp(".tbi",fnidx+len-4) ) fmt = vcf;
+            else fmt = bcf;
+        }
+
+        if ( fmt==vcf )
+        {
+            tbx = tbx_index_load2(fname, fnidx);
+            if ( !tbx ) { fprintf(stderr,"Could not load index for VCF: %s\n", fname); return 1; }
+        }
+        else if ( fmt==bcf )
+        {
+            idx = bcf_index_load2(fname, fnidx);
+            if ( !idx ) { fprintf(stderr,"Could not load index for BCF file: %s\n", fname); return 1; }
+        }
+        else
+        {
+            fprintf(stderr,"Could not detect the file type as VCF or BCF: %s\n", fname);
+            return 1;
+        }
+    }
+    else if ( fnidx )
+    {
+        char *ext = strrchr(fnidx, '.');
+        if ( ext && strcmp(ext, ".tbi") == 0 ) {
+            tbx = tbx_index_load2(fname, fnidx);
+        } else if ( ext && strcmp(ext, ".csi") == 0 ) {
+            idx = bcf_index_load2(fname, fnidx);
+        }
+        if ( !tbx && !idx ) {
+            fprintf(stderr,"Could not load index file '%s'\n", fnidx);
+            ret = 1; goto cleanup;
+        }
+    } else {
+        char *ext = strrchr(fname, '.');
+        if ( ext && strcmp(ext, ".bcf") == 0 ) {
+            idx = bcf_index_load(fname);
+        } else if ( ext && (ext-fname) > 4 && strcmp(ext-4, ".vcf.gz") == 0 ) {
+            tbx = tbx_index_load(fname);
+        }
+    }
+
+    if ( !tbx && !idx ) {
+        fprintf(stderr,"No index file could be found for '%s'. Use 'bcftools index' to create one\n", fname);
+        ret = 1; goto cleanup;
+    }
+
+    if ( tbx ) {
+        seq = tbx_seqnames(tbx, &nseq);
+    } else {
+        nseq = hts_idx_nseq(idx);
+    }
+    if ( !tbx && !hdr ) fprintf(stderr,"Warning: cannot determine contig names given the .csi index alone\n");
+    for (tid=0; tid<nseq; tid++)
+    {
+        uint64_t records, v;
+        int ret = hts_idx_get_stat(tbx ? tbx->idx : idx, tid, &records, &v);
+        sum += records;
+        if ( (stats&total) || (records == 0 && !(stats&all_contigs)) ) continue;
+        const char *ctg_name = tbx ? seq[tid] : hdr ? bcf_hdr_id2name(hdr, tid) : "n/a";
+        bcf_hrec_t *hrec = hdr ? bcf_hdr_get_hrec(hdr, BCF_HL_CTG, "ID", ctg_name, NULL) : NULL;
+        int hkey = hrec ? bcf_hrec_find_key(hrec, "length") : -1;
+        printf("%s\t%s\t", ctg_name, hkey<0?".":hrec->vals[hkey]);
+        if (ret >= 0) printf("%" PRIu64 "\n", records);
+        else printf(".\n");
+    }
+    if ( !sum )
+    {
+        // No counts found.
+        // Is this because index version has no stored count data, or no records?
+        bcf1_t *rec = bcf_init1();
+        if (fp && hdr && rec && bcf_read1(fp, hdr, rec) >= 0) {
+            fprintf(stderr,"index of %s does not contain any count metadata. Please re-index with a newer version of bcftools or tabix.\n", fname);
+            ret = 1;
+        }
+        bcf_destroy1(rec);
+    }
+    if ( (stats&total) && !ret ) {
+        printf("%" PRIu64 "\n", sum);
+    }
+
+cleanup:
+    free(seq);
+    free(fntemp);
+    if ( fp && hts_close(fp)!=0 ) error("[%s] Error: close failed\n", __func__);
+    bcf_hdr_destroy(hdr);
+    if (tbx)
+        tbx_destroy(tbx);
+    if (idx)
+        hts_idx_destroy(idx);
+    return ret;
+}
+
+int main_vcfindex(int argc, char *argv[])
+{
+    int c, force = 0, tbi = 0, stats = 0, n_threads = 0;
+    int min_shift = BCF_LIDX_SHIFT;
+    char *outfn = NULL;
+
+    static struct option loptions[] =
+    {
+        {"all",no_argument,NULL,'a'},
+        {"csi",no_argument,NULL,'c'},
+        {"tbi",no_argument,NULL,'t'},
+        {"force",no_argument,NULL,'f'},
+        {"min-shift",required_argument,NULL,'m'},
+        {"stats",no_argument,NULL,'s'},
+        {"nrecords",no_argument,NULL,'n'},
+        {"threads",required_argument,NULL,9},
+        {"output-file",required_argument,NULL,'o'},
+        {"output",required_argument,NULL,'o'},
+        {NULL, 0, NULL, 0}
+    };
+
+    char *tmp;
+    while ((c = getopt_long(argc, argv, "ctfm:snao:", loptions, NULL)) >= 0)
+    {
+        switch (c)
+        {
+            case 'c': tbi = 0; break;
+            case 't': tbi = 1; min_shift = 0; break;
+            case 'f': force = 1; break;
+            case 'm':
+                min_shift = strtol(optarg,&tmp,10);
+                if ( *tmp ) error("Could not parse argument: --min-shift %s\n", optarg);
+                break;
+            case 's': stats |= per_contig; break;
+            case 'n': stats |= total; break;
+            case 'a': stats |= all_contigs; break;
+            case 9:
+                n_threads = strtol(optarg,&tmp,10);
+                if ( *tmp ) error("Could not parse argument: --threads %s\n", optarg);
+                break;
+            case 'o': outfn = optarg; break;
+            default: usage();
+        }
+    }
+    if (stats > total)
+    {
+        fprintf(stderr, "[E::%s] expected only one of --stats or --nrecords options\n", __func__);
+        return 1;
+    }
+    if (tbi && min_shift>0)
+    {
+        fprintf(stderr, "[E::%s] min-shift option only expected for CSI indices \n", __func__);
+        return 1;
+    }
+    if (min_shift < 0 || min_shift > 30)
+    {
+        fprintf(stderr, "[E::%s] expected min_shift in range [0,30] (%d)\n", __func__, min_shift);
+        return 1;
+    }
+
+    char *fname = NULL;
+    if ( optind>=argc )
+    {
+        if ( !isatty(fileno((FILE *)stdin)) ) fname = "-";  // reading from stdin
+        else usage();
+    }
+    else fname = argv[optind];
+    if (stats) return vcf_index_stats(fname, stats);
+
+    kstring_t idx_fname = {0,0,0};
+    if (outfn)
+        kputs(outfn,&idx_fname);
+    else
+    {
+        if (!strcmp(fname, "-")) { fprintf(stderr, "[E::%s] must specify an output path for index file when reading VCF/BCF from stdin\n", __func__); return 1; }
+        ksprintf(&idx_fname, "%s.%s", fname, tbi ? "tbi" : "csi");
+    }
+    if (!force)
+    {
+        // Before complaining about existing index, check if the VCF file isn't newer.
+        struct stat stat_tbi, stat_file;
+        if ( stat(idx_fname.s, &stat_tbi)==0 )
+        {
+            stat(fname, &stat_file);
+            if ( stat_file.st_mtime <= stat_tbi.st_mtime )
+            {
+                fprintf(stderr,"[E::%s] the index file exists. Please use '-f' to overwrite %s\n", __func__, idx_fname.s);
+                free(idx_fname.s);
+                return 1;
+            }
+        }
+
+        // check for truncated files, allow only with -f
+        BGZF *fp = bgzf_open(fname, "r");
+        if ( !fp ) error("index: failed to open %s\n", fname);
+        if ( bgzf_compression(fp)!=2 ) error("index: the file is not BGZF compressed, cannot index: %s\n", fname);
+        if ( bgzf_check_EOF(fp)!=1 ) error("index: the input is probably truncated, use -f to index anyway: %s\n", fname);
+        if ( bgzf_close(fp)!=0 ) error("index: close failed: %s\n", fname);
+    }
+
+    int ret = bcf_index_build3(fname, idx_fname.s, min_shift, n_threads);
+    free(idx_fname.s);
+    if (ret != 0) {
+        if (ret == -2)
+            error("index: failed to open \"%s\"\n", fname);
+        else if (ret == -3)
+            error("index: \"%s\" is in a format that cannot be usefully indexed\n", fname);
+        else
+            error("index: failed to create index for \"%s\"\n", fname);
+    }
+    return 0;
+}
diff --git a/bcftools/vcfindex.c.pysam.c b/bcftools/vcfindex.c.pysam.c
new file mode 100644
index 0000000..ac9e3ba
--- /dev/null
+++ b/bcftools/vcfindex.c.pysam.c
@@ -0,0 +1,336 @@
+#include "bcftools.pysam.h"
+
+/*  vcfindex.c -- Index bgzip compressed VCF/BCF files for random access.
+
+    Copyright (C) 2014-2021 Genome Research Ltd.
+
+    Author: Shane McCarthy <sm15@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <strings.h>
+#include <unistd.h>
+#include <getopt.h>
+#include <htslib/vcf.h>
+#include <htslib/tbx.h>
+#include <sys/stat.h>
+#define __STDC_FORMAT_MACROS
+#include <inttypes.h>
+#include <htslib/kstring.h>
+#include <htslib/bgzf.h>
+#include "bcftools.h"
+
+#define BCF_LIDX_SHIFT    14
+
+enum {
+    per_contig = 1,
+    all_contigs = 2,
+    total = 4
+};
+
+static void usage(void)
+{
+    fprintf(bcftools_stderr, "\n");
+    fprintf(bcftools_stderr, "About:   Index bgzip compressed VCF/BCF files for random access.\n");
+    fprintf(bcftools_stderr, "Usage:   bcftools index [options] <in.bcf>|<in.vcf.gz>\n");
+    fprintf(bcftools_stderr, "\n");
+    fprintf(bcftools_stderr, "Indexing options:\n");
+    fprintf(bcftools_stderr, "    -c, --csi                generate CSI-format index for VCF/BCF files [default]\n");
+    fprintf(bcftools_stderr, "    -f, --force              overwrite index if it already exists\n");
+    fprintf(bcftools_stderr, "    -m, --min-shift INT      set minimal interval size for CSI indices to 2^INT [14]\n");
+    fprintf(bcftools_stderr, "    -o, --output FILE        optional output index file name\n");
+    fprintf(bcftools_stderr, "    -t, --tbi                generate TBI-format index for VCF files\n");
+    fprintf(bcftools_stderr, "        --threads INT        use multithreading with INT worker threads [0]\n");
+    fprintf(bcftools_stderr, "\n");
+    fprintf(bcftools_stderr, "Stats options:\n");
+    fprintf(bcftools_stderr, "    -a, --all            with --stats, print stats for all contigs even when zero\n");
+    fprintf(bcftools_stderr, "    -n, --nrecords       print number of records based on existing index file\n");
+    fprintf(bcftools_stderr, "    -s, --stats          print per contig stats based on existing index file\n");
+    fprintf(bcftools_stderr, "\n");
+    bcftools_exit(1);
+}
+
+int vcf_index_stats(char *fname, int stats)
+{
+    const char **seq = NULL;
+    int tid, nseq = 0, ret = 0;
+    tbx_t *tbx = NULL;
+    bcf_hdr_t *hdr = NULL;
+    hts_idx_t *idx = NULL;
+    htsFile *fp = NULL;
+    uint64_t sum = 0;
+    char *fntemp = NULL, *fnidx = NULL;
+
+    /*
+     * First, has the user provided an index file? If per contig stats
+     * are requested, open the variant file (together with the index file,
+     * if provided), since the contig names can only be retrieved from its
+     * header. Otherwise, use just the corresponding index file to count
+     * the total number of records.
+     */
+    int len = strlen(fname);
+    int idx_only = 0;
+    if ( (fnidx = strstr(fname, HTS_IDX_DELIM)) != NULL ) {
+        fntemp = strdup(fname);
+        if ( !fntemp ) return 1;
+        fntemp[fnidx-fname] = 0;
+        fname = fntemp;
+        fnidx += strlen(HTS_IDX_DELIM);
+    }
+    else if ( len>4 && (!strcasecmp(".csi",fname+len-4) || !strcasecmp(".tbi",fname+len-4)) )
+    {
+        fnidx  = fname;
+        fntemp = strdup(fname);
+        fname  = fntemp;
+        fname[len-4] = 0;
+        idx_only = 1;
+    }
+
+    if ( stats&per_contig )
+    {
+        if ( idx_only )
+        {
+            struct stat buf;
+            if ( stat(fname, &buf)==0 ) idx_only = 0;
+        }
+
+        enum htsExactFormat fmt;
+        if ( !idx_only )
+        {
+            fp = hts_open(fname,"r");
+            if ( !fp ) {
+                fprintf(bcftools_stderr,"Could not read %s\n", fname);
+                ret = 1; goto cleanup;
+            }
+            hdr = bcf_hdr_read(fp);
+            if ( !hdr ) {
+                fprintf(bcftools_stderr,"Could not read the header: %s\n", fname);
+                ret = 1; goto cleanup;
+            }
+            fmt = hts_get_format(fp)->format;
+        }
+        else
+        {
+            int len = strlen(fnidx);
+            if ( !strcasecmp(".tbi",fnidx+len-4) ) fmt = vcf;
+            else fmt = bcf;
+        }
+
+        if ( fmt==vcf )
+        {
+            tbx = tbx_index_load2(fname, fnidx);
+            if ( !tbx ) { fprintf(bcftools_stderr,"Could not load index for VCF: %s\n", fname); return 1; }
+        }
+        else if ( fmt==bcf )
+        {
+            idx = bcf_index_load2(fname, fnidx);
+            if ( !idx ) { fprintf(bcftools_stderr,"Could not load index for BCF file: %s\n", fname); return 1; }
+        }
+        else
+        {
+            fprintf(bcftools_stderr,"Could not detect the file type as VCF or BCF: %s\n", fname);
+            return 1;
+        }
+    }
+    else if ( fnidx )
+    {
+        char *ext = strrchr(fnidx, '.');
+        if ( ext && strcmp(ext, ".tbi") == 0 ) {
+            tbx = tbx_index_load2(fname, fnidx);
+        } else if ( ext && strcmp(ext, ".csi") == 0 ) {
+            idx = bcf_index_load2(fname, fnidx);
+        }
+        if ( !tbx && !idx ) {
+            fprintf(bcftools_stderr,"Could not load index file '%s'\n", fnidx);
+            ret = 1; goto cleanup;
+        }
+    } else {
+        char *ext = strrchr(fname, '.');
+        if ( ext && strcmp(ext, ".bcf") == 0 ) {
+            idx = bcf_index_load(fname);
+        } else if ( ext && (ext-fname) > 4 && strcmp(ext-4, ".vcf.gz") == 0 ) {
+            tbx = tbx_index_load(fname);
+        }
+    }
+
+    if ( !tbx && !idx ) {
+        fprintf(bcftools_stderr,"No index file could be found for '%s'. Use 'bcftools index' to create one\n", fname);
+        ret = 1; goto cleanup;
+    }
+
+    if ( tbx ) {
+        seq = tbx_seqnames(tbx, &nseq);
+    } else {
+        nseq = hts_idx_nseq(idx);
+    }
+    if ( !tbx && !hdr ) fprintf(bcftools_stderr,"Warning: cannot determine contig names given the .csi index alone\n");
+    for (tid=0; tid<nseq; tid++)
+    {
+        uint64_t records, v;
+        int ret = hts_idx_get_stat(tbx ? tbx->idx : idx, tid, &records, &v);
+        sum += records;
+        if ( (stats&total) || (records == 0 && !(stats&all_contigs)) ) continue;
+        const char *ctg_name = tbx ? seq[tid] : hdr ? bcf_hdr_id2name(hdr, tid) : "n/a";
+        bcf_hrec_t *hrec = hdr ? bcf_hdr_get_hrec(hdr, BCF_HL_CTG, "ID", ctg_name, NULL) : NULL;
+        int hkey = hrec ? bcf_hrec_find_key(hrec, "length") : -1;
+        fprintf(bcftools_stdout, "%s\t%s\t", ctg_name, hkey<0?".":hrec->vals[hkey]);
+        if (ret >= 0) fprintf(bcftools_stdout, "%" PRIu64 "\n", records);
+        else fprintf(bcftools_stdout, ".\n");
+    }
+    if ( !sum )
+    {
+        // No counts found.
+        // Is this because index version has no stored count data, or no records?
+        bcf1_t *rec = bcf_init1();
+        if (fp && hdr && rec && bcf_read1(fp, hdr, rec) >= 0) {
+            fprintf(bcftools_stderr,"index of %s does not contain any count metadata. Please re-index with a newer version of bcftools or tabix.\n", fname);
+            ret = 1;
+        }
+        bcf_destroy1(rec);
+    }
+    if ( (stats&total) && !ret ) {
+        fprintf(bcftools_stdout, "%" PRIu64 "\n", sum);
+    }
+
+cleanup:
+    free(seq);
+    free(fntemp);
+    if ( fp && hts_close(fp)!=0 ) error("[%s] Error: close failed\n", __func__);
+    bcf_hdr_destroy(hdr);
+    if (tbx)
+        tbx_destroy(tbx);
+    if (idx)
+        hts_idx_destroy(idx);
+    return ret;
+}
+
+int main_vcfindex(int argc, char *argv[])
+{
+    int c, force = 0, tbi = 0, stats = 0, n_threads = 0;
+    int min_shift = BCF_LIDX_SHIFT;
+    char *outfn = NULL;
+
+    static struct option loptions[] =
+    {
+        {"all",no_argument,NULL,'a'},
+        {"csi",no_argument,NULL,'c'},
+        {"tbi",no_argument,NULL,'t'},
+        {"force",no_argument,NULL,'f'},
+        {"min-shift",required_argument,NULL,'m'},
+        {"stats",no_argument,NULL,'s'},
+        {"nrecords",no_argument,NULL,'n'},
+        {"threads",required_argument,NULL,9},
+        {"output-file",required_argument,NULL,'o'},
+        {"output",required_argument,NULL,'o'},
+        {NULL, 0, NULL, 0}
+    };
+
+    char *tmp;
+    while ((c = getopt_long(argc, argv, "ctfm:snao:", loptions, NULL)) >= 0)
+    {
+        switch (c)
+        {
+            case 'c': tbi = 0; break;
+            case 't': tbi = 1; min_shift = 0; break;
+            case 'f': force = 1; break;
+            case 'm':
+                min_shift = strtol(optarg,&tmp,10);
+                if ( *tmp ) error("Could not parse argument: --min-shift %s\n", optarg);
+                break;
+            case 's': stats |= per_contig; break;
+            case 'n': stats |= total; break;
+            case 'a': stats |= all_contigs; break;
+            case 9:
+                n_threads = strtol(optarg,&tmp,10);
+                if ( *tmp ) error("Could not parse argument: --threads %s\n", optarg);
+                break;
+            case 'o': outfn = optarg; break;
+            default: usage();
+        }
+    }
+    if (stats > total)
+    {
+        fprintf(bcftools_stderr, "[E::%s] expected only one of --stats or --nrecords options\n", __func__);
+        return 1;
+    }
+    if (tbi && min_shift>0)
+    {
+        fprintf(bcftools_stderr, "[E::%s] min-shift option only expected for CSI indices \n", __func__);
+        return 1;
+    }
+    if (min_shift < 0 || min_shift > 30)
+    {
+        fprintf(bcftools_stderr, "[E::%s] expected min_shift in range [0,30] (%d)\n", __func__, min_shift);
+        return 1;
+    }
+
+    char *fname = NULL;
+    if ( optind>=argc )
+    {
+        if ( !isatty(fileno((FILE *)stdin)) ) fname = "-";  // reading from stdin
+        else usage();
+    }
+    else fname = argv[optind];
+    if (stats) return vcf_index_stats(fname, stats);
+
+    kstring_t idx_fname = {0,0,0};
+    if (outfn)
+        kputs(outfn,&idx_fname);
+    else
+    {
+        if (!strcmp(fname, "-")) { fprintf(bcftools_stderr, "[E::%s] must specify an output path for index file when reading VCF/BCF from stdin\n", __func__); return 1; }
+        ksprintf(&idx_fname, "%s.%s", fname, tbi ? "tbi" : "csi");
+    }
+    if (!force)
+    {
+        // Before complaining about existing index, check if the VCF file isn't newer.
+        struct stat stat_tbi, stat_file;
+        if ( stat(idx_fname.s, &stat_tbi)==0 )
+        {
+            stat(fname, &stat_file);
+            if ( stat_file.st_mtime <= stat_tbi.st_mtime )
+            {
+                fprintf(bcftools_stderr,"[E::%s] the index file exists. Please use '-f' to overwrite %s\n", __func__, idx_fname.s);
+                free(idx_fname.s);
+                return 1;
+            }
+        }
+
+        // check for truncated files, allow only with -f
+        BGZF *fp = bgzf_open(fname, "r");
+        if ( !fp ) error("index: failed to open %s\n", fname);
+        if ( bgzf_compression(fp)!=2 ) error("index: the file is not BGZF compressed, cannot index: %s\n", fname);
+        if ( bgzf_check_EOF(fp)!=1 ) error("index: the input is probably truncated, use -f to index anyway: %s\n", fname);
+        if ( bgzf_close(fp)!=0 ) error("index: close failed: %s\n", fname);
+    }
+
+    int ret = bcf_index_build3(fname, idx_fname.s, min_shift, n_threads);
+    free(idx_fname.s);
+    if (ret != 0) {
+        if (ret == -2)
+            error("index: failed to open \"%s\"\n", fname);
+        else if (ret == -3)
+            error("index: \"%s\" is in a format that cannot be usefully indexed\n", fname);
+        else
+            error("index: failed to create index for \"%s\"\n", fname);
+    }
+    return 0;
+}
diff --git a/bcftools/vcfisec.c b/bcftools/vcfisec.c
new file mode 100644
index 0000000..a755a85
--- /dev/null
+++ b/bcftools/vcfisec.c
@@ -0,0 +1,652 @@
+/*  vcfisec.c -- Create intersections, unions and complements of VCF files.
+
+    Copyright (C) 2012-2022 Genome Research Ltd.
+
+    Author: Petr Danecek <pd3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.  */
+
+#include <stdio.h>
+#include <unistd.h>
+#include <getopt.h>
+#include <ctype.h>
+#include <string.h>
+#include <errno.h>
+#include <sys/stat.h>
+#include <sys/types.h>
+#include <htslib/vcf.h>
+#include <htslib/synced_bcf_reader.h>
+#include <htslib/vcfutils.h>
+#include <htslib/hts_os.h>
+#include "bcftools.h"
+#include "filter.h"
+
+#define OP_PLUS 1
+#define OP_MINUS 2
+#define OP_EQUAL 3
+#define OP_VENN 4
+#define OP_COMPLEMENT 5
+#define OP_EXACT 6
+
+// Logic of the filters: include or exclude sites which match the filters?
+#define FLT_INCLUDE 1
+#define FLT_EXCLUDE 2
+
+typedef struct
+{
+    int isec_op, isec_n, *write, iwrite, nwrite, output_type, n_threads, clevel;
+    int nflt, *flt_logic;
+    filter_t **flt;
+    char **flt_expr;
+    bcf_srs_t *files;
+    FILE *fh_log, *fh_sites;
+    htsFile **fh_out;
+    char **argv, *prefix, *output_fname, **fnames, *write_files, *targets_list, *regions_list;
+    char *isec_exact;
+    int argc, record_cmd_line;
+}
+args_t;
+
+/**
+ *  mkdir_p() - create new directory for a file $fname
+ *  @fname:   the file name to create the directory for, the part after last "/" is ignored
+ */
+void mkdir_p(const char *fmt, ...)
+{
+    va_list ap;
+    va_start(ap, fmt);
+    int n = vsnprintf(NULL, 0, fmt, ap) + 2;
+    va_end(ap);
+
+    char *path = (char*)malloc(n);
+    va_start(ap, fmt);
+    vsnprintf(path, n, fmt, ap);
+    va_end(ap);
+
+    char *tmp = strdup(path), *p = tmp+1;
+    while (*p)
+    {
+        while (*p && *p!='/') p++;
+        if ( !*p ) break;
+        char ctmp = *p;
+        *p = 0;
+        int ret = mkdir(tmp,S_IRWXU | S_IRWXG | S_IROTH | S_IXOTH);
+        if ( ret!=0 && errno!=EEXIST ) error("Error creating directory %s: %s\n", path,strerror(errno));
+        *p = ctmp;
+        while ( *p && *p=='/' ) p++;
+    }
+    free(tmp);
+    free(path);
+}
+
+/**
+ *  open_file() - open new file creating the file name using vsnprintf
+ *  @fname:  if not NULL, on output will point to newly allocated fname string
+ *  @mode:   if NULL, only the file name string will be created
+ *  @fmt:    vsnprintf format and args
+ *
+ *  Returns open file descriptor or NULL if mode is NULL.
+ */
+FILE *open_file(char **fname, const char *mode, const char *fmt, ...)
+{
+    va_list ap;
+    va_start(ap, fmt);
+    int n = vsnprintf(NULL, 0, fmt, ap) + 2;
+    va_end(ap);
+
+    char *str = (char*)malloc(n);
+    va_start(ap, fmt);
+    vsnprintf(str, n, fmt, ap);
+    va_end(ap);
+
+    mkdir_p(str);
+    if ( !mode )
+    {
+        if ( !fname ) error("Uh: expected fname or mode\n");
+        *fname = str;
+        return NULL;
+    }
+
+    FILE *fp = fopen(str,mode);
+    if ( fname ) *fname = str;
+    else free(str);
+    return fp;
+}
+
+void isec_vcf(args_t *args)
+{
+    bcf_srs_t *files = args->files;
+    kstring_t str = {0,0,0};
+    htsFile *out_fh = NULL;
+
+    // When only one VCF is output, print VCF to stdout or -o file
+    int out_std = 0;
+    if ( args->nwrite==1 && !args->prefix ) out_std = 1;
+    if ( args->targets_list && files->nreaders==1 ) out_std = 1;
+    if ( out_std )
+    {
+        char wmode[8];
+        set_wmode(wmode,args->output_type,args->output_fname,args->clevel);
+        out_fh = hts_open(args->output_fname ? args->output_fname : "-", wmode);
+        if ( out_fh == NULL ) error("Can't write to %s: %s\n", args->output_fname? args->output_fname : "standard output", strerror(errno));
+        if ( args->n_threads ) hts_set_threads(out_fh, args->n_threads);
+        if (args->record_cmd_line) bcf_hdr_append_version(files->readers[args->iwrite].header,args->argc,args->argv,"bcftools_isec");
+        if ( bcf_hdr_write(out_fh, files->readers[args->iwrite].header)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->output_fname?args->output_fname:"standard output");
+    }
+    if ( !args->nwrite && !out_std && !args->prefix )
+        fprintf(stderr,"Note: -w option not given, printing list of sites...\n");
+
+    int n;
+    while ( (n=bcf_sr_next_line(files)) )
+    {
+        bcf_sr_t *reader = NULL;
+        bcf1_t *line = NULL;
+        int i, ret = 0;
+        for (i=0; i<files->nreaders; i++)
+        {
+            if ( !bcf_sr_has_line(files,i) ) continue;
+
+            if ( args->nflt && args->flt[i] )
+            {
+                bcf1_t *rec = bcf_sr_get_line(files, i);
+                int pass = filter_test(args->flt[i], rec, NULL);
+                if ( args->flt_logic[i] & FLT_EXCLUDE ) pass = pass ? 0 : 1;
+                if ( !pass )
+                {
+                    files->has_line[i] = 0;
+                    n--;
+                    continue;
+                }
+            }
+
+            if ( !line )
+            {
+                line = files->readers[i].buffer[0];
+                reader = &files->readers[i];
+            }
+            ret |= 1<<i;    // this may overflow for many files, but will be used only with two (OP_VENN)
+        }
+        if ( !line ) continue;  // the site has been filtered in all files
+
+        switch (args->isec_op)
+        {
+            case OP_COMPLEMENT: if ( n!=1 || !bcf_sr_has_line(files,0) ) continue; break;
+            case OP_EQUAL: if ( n != args->isec_n ) continue; break;
+            case OP_PLUS: if ( n < args->isec_n ) continue; break;
+            case OP_MINUS: if ( n > args->isec_n ) continue; break;
+            case OP_EXACT:
+                for (i=0; i<files->nreaders; i++)
+                    if ( files->has_line[i] != args->isec_exact[i] ) break;
+                if ( i<files->nreaders ) continue;
+                break;
+        }
+
+        if ( out_std )
+        {
+            if ( bcf_sr_has_line(files,args->iwrite) && bcf_write1(out_fh, files->readers[args->iwrite].header, files->readers[args->iwrite].buffer[0])!=0 )
+                error("[%s] Error: cannot write to %s\n", __func__, args->output_fname ? args->output_fname : "standard output");
+            continue;
+        }
+        else if ( args->fh_sites )
+        {
+            str.l = 0;
+            kputs(reader->header->id[BCF_DT_CTG][line->rid].key, &str); kputc('\t', &str);
+            kputw(line->pos+1, &str); kputc('\t', &str);
+            if (line->n_allele > 0) kputs(line->d.allele[0], &str);
+            else kputc('.', &str);
+            kputc('\t', &str);
+            if (line->n_allele > 1) kputs(line->d.allele[1], &str);
+            else kputc('.', &str);
+            for (i=2; i<line->n_allele; i++)
+            {
+                kputc(',', &str);
+                kputs(line->d.allele[i], &str);
+            }
+            kputc('\t', &str);
+            for (i=0; i<files->nreaders; i++)
+                kputc(bcf_sr_has_line(files,i)?'1':'0', &str);
+            kputc('\n', &str);
+            if ( fwrite(str.s,sizeof(char),str.l,args->fh_sites)!=str.l )
+                error("[%s] Error: failed to write %d bytes to %s\n", __func__,(int)str.l,args->output_fname ? args->output_fname : "standard output");
+        }
+
+        if ( args->prefix )
+        {
+            if ( args->isec_op==OP_VENN && ret==3 )
+            {
+                if ( !args->nwrite || args->write[0] )
+                {
+                    if ( bcf_write1(args->fh_out[2], bcf_sr_get_header(files,0), bcf_sr_get_line(files,0))!=0 )
+                         error("[%s] Error: cannot write\n", __func__);
+                }
+                if ( !args->nwrite || args->write[1] )
+                {
+                    if ( bcf_write1(args->fh_out[3], bcf_sr_get_header(files,1), bcf_sr_get_line(files,1))!=0 )
+                        error("[%s] Error: cannot write\n", __func__);
+                }
+            }
+            else
+            {
+                for (i=0; i<files->nreaders; i++)
+                {
+                    if ( !bcf_sr_has_line(files,i) ) continue;
+                    if ( args->write && !args->write[i] ) continue;
+                    if ( bcf_write1(args->fh_out[i], files->readers[i].header, files->readers[i].buffer[0])!=0 ) error("[%s] Error: cannot write\n", __func__);
+                }
+            }
+        }
+    }
+    if ( str.s ) free(str.s);
+    if ( out_fh && hts_close(out_fh)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,args->output_fname? args->output_fname : "-");
+}
+
+static void add_filter(args_t *args, char *expr, int logic)
+{
+    args->nflt++;
+    args->flt_expr = (char**) realloc(args->flt_expr,sizeof(char*)*args->nflt);
+    args->flt_logic = (int*) realloc(args->flt_logic,sizeof(int)*args->nflt);
+    args->flt = (filter_t**) realloc(args->flt,sizeof(filter_t*)*args->nflt);
+    if ( expr[0]=='-' && expr[1]==0 )
+    {
+        args->flt_expr[args->nflt-1] = NULL;
+        args->flt[args->nflt-1] = NULL;
+    }
+    else
+        args->flt_expr[args->nflt-1] = expr;
+    args->flt_logic[args->nflt-1] = logic;
+}
+
+static void destroy_data(args_t *args);
+static void init_data(args_t *args)
+{
+    int i;
+    if ( args->nflt )
+    {
+        if ( args->nflt > 1 && args->nflt!=args->files->nreaders )
+            error("Error: expected either one -i/-e option or as many as there are input files\n");
+        if ( args->nflt < args->files->nreaders )
+        {
+            if ( !args->flt_expr[0] ) error("Error: useless use of -i/-e\n");
+            args->nflt = args->files->nreaders;
+            args->flt_expr = (char**) realloc(args->flt_expr,sizeof(char*)*args->nflt);
+            args->flt_logic = (int*) realloc(args->flt_logic,sizeof(int)*args->nflt);
+            args->flt = (filter_t**) realloc(args->flt,sizeof(filter_t*)*args->nflt);
+            for (i=1; i<args->nflt; i++)
+            {
+                args->flt_expr[i]  = args->flt_expr[0];
+                args->flt_logic[i] = args->flt_logic[0];
+                args->flt[i] = filter_init(args->files->readers[i].header,args->flt_expr[i]);
+            }
+            args->flt[0] = filter_init(args->files->readers[0].header,args->flt_expr[0]);
+        }
+        else
+        {
+            for (i=0; i<args->files->nreaders; i++)
+            {
+                if ( !args->flt_expr[i] ) continue;
+                args->flt[i] = filter_init(args->files->readers[i].header,args->flt_expr[i]);
+            }
+        }
+    }
+
+    if ( args->isec_op==OP_EXACT )
+    {
+        if ( strlen(args->isec_exact)!=args->files->nreaders )
+            error("The number of files does not match the bitmask: %d vs %s\n", args->files->nreaders,args->isec_exact);
+        for (i=0; i<args->files->nreaders; i++)
+            if ( args->isec_exact[i]!='0' && args->isec_exact[i]!='1' ) error("Unexpected bitmask: %s\n",args->isec_exact);
+        for (i=0; i<args->files->nreaders; i++)
+            args->isec_exact[i] -= '0';
+    }
+
+    // Which files to write: parse the string passed with -w
+    char *p = args->write_files;
+    while (p && *p)
+    {
+        if ( !args->write ) args->write = (int*) calloc(args->files->nreaders,sizeof(int));
+        if ( sscanf(p,"%d",&i)!=1 ) error("Could not parse --write %s\n", args->write_files);
+        if ( i<=0 || i>args->files->nreaders ) error("The index is out of range: %d (-w %s)\n", i, args->write_files);
+        args->write[i-1] = 1;
+        args->iwrite = i-1;
+        args->nwrite++;
+        while (*p && *p!=',') p++;
+        if ( *p==',' ) p++;
+    }
+    if ( args->nwrite>1 && !args->prefix ) error("Expected -p when multiple output files given: --write %s\n", args->write_files);
+    if ( args->isec_op==OP_COMPLEMENT && args->nwrite )
+    {
+        if ( args->nwrite>1 ) error("Multiple files to -w make no sense with -C\n");
+        if ( !args->write[0] ) error("Only -w1 makes sense with -C\n");
+    }
+
+    if ( args->prefix )
+    {
+        // Init output directory and create the readme file
+        args->fh_log = open_file(NULL,"w","%s/README.txt", args->prefix);
+        if ( !args->fh_log ) error("%s/README.txt: %s\n", args->prefix, strerror(errno));
+
+        fprintf(args->fh_log,"This file was produced by vcfisec.\n");
+        fprintf(args->fh_log,"The command line was:\tbcftools %s ", args->argv[0]);
+        int i;
+        for (i=1; i<args->argc; i++) fprintf(args->fh_log," %s",args->argv[i]);
+        fprintf(args->fh_log,"\n\nUsing the following file names:\n");
+
+        const char *suffix = "vcf";
+        if ( args->output_type & FT_BCF ) suffix = "bcf";
+        else if ( args->output_type & FT_GZ ) suffix = "vcf.gz";
+
+        // Open output files and write the legend
+        if ( args->isec_op==OP_VENN )
+        {
+            args->fh_out = (htsFile**) malloc(sizeof(htsFile*)*4);
+            args->fnames = (char**) calloc(4,sizeof(char*));
+
+            #define OPEN_FILE(i,j) { \
+                open_file(&args->fnames[i], NULL, "%s/%04d.%s", args->prefix, i, suffix); \
+                char wmode[8]; \
+                set_wmode(wmode,args->output_type,args->fnames[i],args->clevel); \
+                args->fh_out[i] = hts_open(args->fnames[i], wmode); \
+                if ( !args->fh_out[i] ) error("Could not open %s\n", args->fnames[i]); \
+                if ( args->n_threads ) hts_set_threads(args->fh_out[i], args->n_threads); \
+                if (args->record_cmd_line) bcf_hdr_append_version(args->files->readers[j].header,args->argc,args->argv,"bcftools_isec"); \
+                if ( bcf_hdr_write(args->fh_out[i], args->files->readers[j].header)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->fnames[i]); \
+            }
+            if ( !args->nwrite || args->write[0] )
+            {
+                OPEN_FILE(0,0);
+                fprintf(args->fh_log,"%s\tfor records private to\t%s\n", args->fnames[0], args->files->readers[0].fname);
+            }
+            if ( !args->nwrite || args->write[1] )
+            {
+                OPEN_FILE(1,1);
+                fprintf(args->fh_log,"%s\tfor records private to\t%s\n", args->fnames[1], args->files->readers[1].fname);
+            }
+            if ( !args->nwrite || args->write[0] )
+            {
+                OPEN_FILE(2,0);
+                fprintf(args->fh_log,"%s\tfor records from %s shared by both\t%s %s\n", args->fnames[2], args->files->readers[0].fname, args->files->readers[0].fname, args->files->readers[1].fname);
+            }
+            if ( !args->nwrite || args->write[1] )
+            {
+                OPEN_FILE(3,1);
+                fprintf(args->fh_log,"%s\tfor records from %s shared by both\t%s %s\n", args->fnames[3], args->files->readers[1].fname, args->files->readers[0].fname, args->files->readers[1].fname);
+            }
+        }
+        else
+        {
+            // Init one output file for each reader
+            args->fh_out = (htsFile**) calloc(args->files->nreaders, sizeof(htsFile*));
+            args->fnames = (char**) calloc(args->files->nreaders, sizeof(char*));
+
+            for (i=0; i<args->files->nreaders; i++)
+            {
+                if ( args->write && !args->write[i] ) continue;
+                if ( args->isec_op==OP_COMPLEMENT && i>0 ) break;
+                OPEN_FILE(i,i);
+                fprintf(args->fh_log,"%s\tfor stripped\t%s\n", args->fnames[i], args->files->readers[i].fname);
+            }
+            #undef OPEN_FILE
+        }
+        args->fh_sites = open_file(NULL, "w", "%s/sites.txt", args->prefix);
+        if ( !args->fh_sites ) error("%s/sites.txt: %s\n", args->prefix, strerror(errno));
+    }
+    else {
+        if (args->output_fname) {
+            args->fh_sites = fopen(args->output_fname, "w");
+            if ( args->fh_sites == NULL ) error("Can't write to \"%s\": %s\n", args->output_fname, strerror(errno));
+        }
+        else
+            args->fh_sites = stdout;
+    }
+}
+
+static void destroy_data(args_t *args)
+{
+    int i;
+    if ( args->nflt )
+    {
+        for (i=0; i<args->nflt; i++)
+        {
+            if ( !args->flt[i] ) continue;
+            filter_destroy(args->flt[i]);
+        }
+        free(args->flt_expr);
+        free(args->flt);
+        free(args->flt_logic);
+    }
+    if ( args->prefix )
+    {
+        fclose(args->fh_log);
+        int n = args->isec_op==OP_VENN ? 4 : args->files->nreaders;
+        for (i=0; i<n; i++)
+        {
+            if ( !args->fnames[i] ) continue;
+            if ( hts_close(args->fh_out[i])!=0 ) error("[%s] Error: close failed .. %s\n", __func__,args->fnames[i]);
+            if ( args->output_type==FT_VCF_GZ )
+            {
+                tbx_conf_t conf = tbx_conf_vcf;
+                tbx_index_build(args->fnames[i], -1, &conf);
+            }
+            else if ( args->output_type==FT_BCF_GZ )
+            {
+                if ( bcf_index_build(args->fnames[i],14) ) error("Could not index %s\n", args->fnames[i]);
+            }
+            free(args->fnames[i]);
+        }
+        free(args->fh_out);
+        free(args->fnames);
+        if ( args->fh_sites ) fclose(args->fh_sites);
+        if ( args->write ) free(args->write);
+    }
+}
+
+static void usage(void)
+{
+    fprintf(stderr, "\n");
+    fprintf(stderr, "About:   Create intersections, unions and complements of VCF files.\n");
+    fprintf(stderr, "Usage:   bcftools isec [options] <A.vcf.gz> <B.vcf.gz> [...]\n");
+    fprintf(stderr, "\n");
+    fprintf(stderr, "Options:\n");
+    fprintf(stderr, "    -c, --collapse STRING          Treat as identical records with <snps|indels|both|all|some|none>, see man page for details [none]\n");
+    fprintf(stderr, "    -C, --complement               Output positions present only in the first file but missing in the others\n");
+    fprintf(stderr, "    -e, --exclude EXPR             Exclude sites for which the expression is true\n");
+    fprintf(stderr, "    -f, --apply-filters LIST       Require at least one of the listed FILTER strings (e.g. \"PASS,.\")\n");
+    fprintf(stderr, "    -i, --include EXPR             Include only sites for which the expression is true\n");
+    fprintf(stderr, "        --no-version               Do not append version and command line to the header\n");
+    fprintf(stderr, "    -n, --nfiles [+-=~]INT         Output positions present in this many (=), this many or more (+), this many or fewer (-), the exact (~) files\n");
+    fprintf(stderr, "    -o, --output FILE              Write output to a file [standard output]\n");
+    fprintf(stderr, "    -O, --output-type u|b|v|z[0-9] u/b: un/compressed BCF, v/z: un/compressed VCF, 0-9: compression level [v]\n");
+    fprintf(stderr, "    -p, --prefix DIR               If given, subset each of the input files accordingly, see also -w\n");
+    fprintf(stderr, "    -r, --regions REGION           Restrict to comma-separated list of regions\n");
+    fprintf(stderr, "    -R, --regions-file FILE        Restrict to regions listed in a file\n");
+    fprintf(stderr, "        --regions-overlap 0|1|2    Include if POS in the region (0), record overlaps (1), variant overlaps (2) [1]\n");
+    fprintf(stderr, "    -t, --targets REGION           Similar to -r but streams rather than index-jumps\n");
+    fprintf(stderr, "    -T, --targets-file FILE        Similar to -R but streams rather than index-jumps\n");
+    fprintf(stderr, "        --targets-overlap 0|1|2    Include if POS in the region (0), record overlaps (1), variant overlaps (2) [0]\n");
+    fprintf(stderr, "        --threads INT              Use multithreading with <int> worker threads [0]\n");
+    fprintf(stderr, "    -w, --write LIST               List of files to write with -p given as 1-based indexes. By default, all files are written\n");
+    fprintf(stderr, "\n");
+    fprintf(stderr, "Examples:\n");
+    fprintf(stderr, "   # Create intersection and complements of two sets saving the output in dir/*\n");
+    fprintf(stderr, "   bcftools isec A.vcf.gz B.vcf.gz -p dir\n");
+    fprintf(stderr, "\n");
+    fprintf(stderr, "   # Filter sites in A and B (but not in C) and create intersection\n");
+    fprintf(stderr, "   bcftools isec -e'MAF<0.01' -i'dbSNP=1' -e - A.vcf.gz B.vcf.gz C.vcf.gz -p dir\n");
+    fprintf(stderr, "\n");
+    fprintf(stderr, "   # Extract and write records from A shared by both A and B using exact allele match\n");
+    fprintf(stderr, "   bcftools isec A.vcf.gz B.vcf.gz -p dir -n =2 -w 1\n");
+    fprintf(stderr, "\n");
+    fprintf(stderr, "   # Extract and write records from C found in A and C but not in B\n");
+    fprintf(stderr, "   bcftools isec A.vcf.gz B.vcf.gz C.vcf.gz -p dir -n~101 -w 3\n");
+    fprintf(stderr, "\n");
+    fprintf(stderr, "   # Extract records private to A or B comparing by position only\n");
+    fprintf(stderr, "   bcftools isec A.vcf.gz B.vcf.gz -p dir -n -1 -c all\n");
+    fprintf(stderr, "\n");
+    exit(1);
+}
+
+int main_vcfisec(int argc, char *argv[])
+{
+    int c;
+    args_t *args = (args_t*) calloc(1,sizeof(args_t));
+    args->files  = bcf_sr_init();
+    args->argc   = argc; args->argv = argv;
+    args->output_fname = NULL;
+    args->output_type = FT_VCF;
+    args->n_threads = 0;
+    args->record_cmd_line = 1;
+    args->clevel = -1;
+    int targets_is_file = 0, regions_is_file = 0;
+    int regions_overlap = 1;
+    int targets_overlap = 0;
+
+    static struct option loptions[] =
+    {
+        {"help",no_argument,NULL,'h'},
+        {"exclude",required_argument,NULL,'e'},
+        {"include",required_argument,NULL,'i'},
+        {"collapse",required_argument,NULL,'c'},
+        {"complement",no_argument,NULL,'C'},
+        {"apply-filters",required_argument,NULL,'f'},
+        {"nfiles",required_argument,NULL,'n'},
+        {"prefix",required_argument,NULL,'p'},
+        {"write",required_argument,NULL,'w'},
+        {"targets",required_argument,NULL,'t'},
+        {"targets-file",required_argument,NULL,'T'},
+        {"targets-overlap",required_argument,NULL,4},
+        {"regions",required_argument,NULL,'r'},
+        {"regions-file",required_argument,NULL,'R'},
+        {"regions-overlap",required_argument,NULL,3},
+        {"output",required_argument,NULL,'o'},
+        {"output-type",required_argument,NULL,'O'},
+        {"threads",required_argument,NULL,9},
+        {"no-version",no_argument,NULL,8},
+        {NULL,0,NULL,0}
+    };
+    char *tmp;
+    while ((c = getopt_long(argc, argv, "hc:r:R:p:n:w:t:T:Cf:o:O:i:e:",loptions,NULL)) >= 0) {
+        switch (c) {
+            case 'o': args->output_fname = optarg; break;
+            case 'O':
+                switch (optarg[0]) {
+                    case 'b': args->output_type = FT_BCF_GZ; break;
+                    case 'u': args->output_type = FT_BCF; break;
+                    case 'z': args->output_type = FT_VCF_GZ; break;
+                    case 'v': args->output_type = FT_VCF; break;
+                    default:
+                    {
+                        args->clevel = strtol(optarg,&tmp,10);
+                        if ( *tmp || args->clevel<0 || args->clevel>9 ) error("The output type \"%s\" not recognised\n", optarg);
+                    }
+                }
+                if ( optarg[1] )
+                {
+                    args->clevel = strtol(optarg+1,&tmp,10);
+                    if ( *tmp || args->clevel<0 || args->clevel>9 ) error("Could not parse argument: --compression-level %s\n", optarg+1);
+                }
+                break;
+            case 'c':
+                if ( !strcmp(optarg,"snps") ) args->files->collapse |= COLLAPSE_SNPS;
+                else if ( !strcmp(optarg,"indels") ) args->files->collapse |= COLLAPSE_INDELS;
+                else if ( !strcmp(optarg,"both") ) args->files->collapse |= COLLAPSE_SNPS | COLLAPSE_INDELS;
+                else if ( !strcmp(optarg,"any") ) args->files->collapse |= COLLAPSE_ANY;
+                else if ( !strcmp(optarg,"all") ) args->files->collapse |= COLLAPSE_ANY;
+                else if ( !strcmp(optarg,"some") ) args->files->collapse |= COLLAPSE_SOME;
+                else if ( !strcmp(optarg,"none") ) args->files->collapse = COLLAPSE_NONE;
+                else error("The --collapse string \"%s\" not recognised.\n", optarg);
+                break;
+            case 'f': args->files->apply_filters = optarg; break;
+            case 'C':
+                if ( args->isec_op!=0 && args->isec_op!=OP_COMPLEMENT ) error("Error: either -C or -n should be given, not both.\n");
+                args->isec_op = OP_COMPLEMENT; break;
+            case 'r': args->regions_list = optarg; break;
+            case 'R': args->regions_list = optarg; regions_is_file = 1; break;
+            case 't': args->targets_list = optarg; break;
+            case 'T': args->targets_list = optarg; targets_is_file = 1; break;
+            case 'p': args->prefix = optarg; break;
+            case 'w': args->write_files = optarg; break;
+            case 'i': add_filter(args, optarg, FLT_INCLUDE); break;
+            case 'e': add_filter(args, optarg, FLT_EXCLUDE); break;
+            case 'n':
+                {
+                    if ( args->isec_op!=0 && args->isec_op==OP_COMPLEMENT ) error("Error: either -C or -n should be given, not both.\n");
+                    if ( args->isec_op!=0 ) error("Error: -n should be given only once.\n");
+                    char *p = optarg;
+                    if ( *p=='-' ) { args->isec_op = OP_MINUS; p++; }
+                    else if ( *p=='+' ) { args->isec_op = OP_PLUS; p++; }
+                    else if ( *p=='=' ) { args->isec_op = OP_EQUAL; p++; }
+                    else if ( *p=='~' ) { args->isec_op = OP_EXACT; p++; }
+                    else if ( isdigit(*p) ) args->isec_op = OP_EQUAL;
+                    else error("Could not parse --nfiles %s\n", optarg);
+                    if ( args->isec_op == OP_EXACT ) args->isec_exact = p;
+                    else if ( sscanf(p,"%d",&args->isec_n)!=1 ) error("Could not parse --nfiles %s\n", optarg);
+                }
+                break;
+            case  3 :
+                regions_overlap = parse_overlap_option(optarg);
+                if ( regions_overlap < 0 ) error("Could not parse: --regions-overlap %s\n",optarg);
+                break;
+            case  4 :
+                targets_overlap = parse_overlap_option(optarg);
+                if ( targets_overlap < 0 ) error("Could not parse: --targets-overlap %s\n",optarg);
+                break;
+            case  9 : args->n_threads = strtol(optarg, 0, 0); break;
+            case  8 : args->record_cmd_line = 0; break;
+            case 'h':
+            case '?': usage(); break;
+            default: error("Unknown argument: %s\n", optarg);
+        }
+    }
+    if ( argc-optind<1 ) usage();   // no file given
+    if ( args->targets_list )
+    {
+        bcf_sr_set_opt(args->files,BCF_SR_TARGETS_OVERLAP,targets_overlap);
+        if ( bcf_sr_set_targets(args->files, args->targets_list, targets_is_file,0)<0 )
+            error("Failed to read the targets: %s\n", args->targets_list);
+    }
+    if ( args->regions_list )
+    {
+        bcf_sr_set_opt(args->files,BCF_SR_REGIONS_OVERLAP,regions_overlap);
+        if ( bcf_sr_set_regions(args->files, args->regions_list, regions_is_file)<0 )
+            error("Failed to read the regions: %s\n", args->regions_list);
+    }
+    if ( argc-optind==2 && !args->isec_op )
+    {
+        args->isec_op = OP_VENN;
+        if ( !args->prefix ) error("Expected the -p option\n");
+    }
+    if ( !args->isec_op )
+    {
+        args->isec_op = OP_PLUS;
+        args->isec_n  = 1;
+    }
+    args->files->require_index = 1;
+    while (optind<argc)
+    {
+        if ( !bcf_sr_add_reader(args->files, argv[optind]) ) error("Failed to open %s: %s\n", argv[optind],bcf_sr_strerror(args->files->errnum));
+        optind++;
+    }
+    init_data(args);
+    isec_vcf(args);
+    destroy_data(args);
+    bcf_sr_destroy(args->files);
+    free(args);
+    return 0;
+}
+
diff --git a/bcftools/vcfisec.c.pysam.c b/bcftools/vcfisec.c.pysam.c
new file mode 100644
index 0000000..50214a6
--- /dev/null
+++ b/bcftools/vcfisec.c.pysam.c
@@ -0,0 +1,654 @@
+#include "bcftools.pysam.h"
+
+/*  vcfisec.c -- Create intersections, unions and complements of VCF files.
+
+    Copyright (C) 2012-2022 Genome Research Ltd.
+
+    Author: Petr Danecek <pd3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.  */
+
+#include <stdio.h>
+#include <unistd.h>
+#include <getopt.h>
+#include <ctype.h>
+#include <string.h>
+#include <errno.h>
+#include <sys/stat.h>
+#include <sys/types.h>
+#include <htslib/vcf.h>
+#include <htslib/synced_bcf_reader.h>
+#include <htslib/vcfutils.h>
+#include <htslib/hts_os.h>
+#include "bcftools.h"
+#include "filter.h"
+
+#define OP_PLUS 1
+#define OP_MINUS 2
+#define OP_EQUAL 3
+#define OP_VENN 4
+#define OP_COMPLEMENT 5
+#define OP_EXACT 6
+
+// Logic of the filters: include or exclude sites which match the filters?
+#define FLT_INCLUDE 1
+#define FLT_EXCLUDE 2
+
+typedef struct
+{
+    int isec_op, isec_n, *write, iwrite, nwrite, output_type, n_threads, clevel;
+    int nflt, *flt_logic;
+    filter_t **flt;
+    char **flt_expr;
+    bcf_srs_t *files;
+    FILE *fh_log, *fh_sites;
+    htsFile **fh_out;
+    char **argv, *prefix, *output_fname, **fnames, *write_files, *targets_list, *regions_list;
+    char *isec_exact;
+    int argc, record_cmd_line;
+}
+args_t;
+
+/**
+ *  mkdir_p() - create new directory for a file $fname
+ *  @fname:   the file name to create the directory for, the part after last "/" is ignored
+ */
+void mkdir_p(const char *fmt, ...)
+{
+    va_list ap;
+    va_start(ap, fmt);
+    int n = vsnprintf(NULL, 0, fmt, ap) + 2;
+    va_end(ap);
+
+    char *path = (char*)malloc(n);
+    va_start(ap, fmt);
+    vsnprintf(path, n, fmt, ap);
+    va_end(ap);
+
+    char *tmp = strdup(path), *p = tmp+1;
+    while (*p)
+    {
+        while (*p && *p!='/') p++;
+        if ( !*p ) break;
+        char ctmp = *p;
+        *p = 0;
+        int ret = mkdir(tmp,S_IRWXU | S_IRWXG | S_IROTH | S_IXOTH);
+        if ( ret!=0 && errno!=EEXIST ) error("Error creating directory %s: %s\n", path,strerror(errno));
+        *p = ctmp;
+        while ( *p && *p=='/' ) p++;
+    }
+    free(tmp);
+    free(path);
+}
+
+/**
+ *  open_file() - open new file creating the file name using vsnprintf
+ *  @fname:  if not NULL, on output will point to newly allocated fname string
+ *  @mode:   if NULL, only the file name string will be created
+ *  @fmt:    vsnprintf format and args
+ *
+ *  Returns open file descriptor or NULL if mode is NULL.
+ */
+FILE *open_file(char **fname, const char *mode, const char *fmt, ...)
+{
+    va_list ap;
+    va_start(ap, fmt);
+    int n = vsnprintf(NULL, 0, fmt, ap) + 2;
+    va_end(ap);
+
+    char *str = (char*)malloc(n);
+    va_start(ap, fmt);
+    vsnprintf(str, n, fmt, ap);
+    va_end(ap);
+
+    mkdir_p(str);
+    if ( !mode )
+    {
+        if ( !fname ) error("Uh: expected fname or mode\n");
+        *fname = str;
+        return NULL;
+    }
+
+    FILE *fp = fopen(str,mode);
+    if ( fname ) *fname = str;
+    else free(str);
+    return fp;
+}
+
+void isec_vcf(args_t *args)
+{
+    bcf_srs_t *files = args->files;
+    kstring_t str = {0,0,0};
+    htsFile *out_fh = NULL;
+
+    // When only one VCF is output, print VCF to bcftools_stdout or -o file
+    int out_std = 0;
+    if ( args->nwrite==1 && !args->prefix ) out_std = 1;
+    if ( args->targets_list && files->nreaders==1 ) out_std = 1;
+    if ( out_std )
+    {
+        char wmode[8];
+        set_wmode(wmode,args->output_type,args->output_fname,args->clevel);
+        out_fh = hts_open(args->output_fname ? args->output_fname : "-", wmode);
+        if ( out_fh == NULL ) error("Can't write to %s: %s\n", args->output_fname? args->output_fname : "standard output", strerror(errno));
+        if ( args->n_threads ) hts_set_threads(out_fh, args->n_threads);
+        if (args->record_cmd_line) bcf_hdr_append_version(files->readers[args->iwrite].header,args->argc,args->argv,"bcftools_isec");
+        if ( bcf_hdr_write(out_fh, files->readers[args->iwrite].header)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->output_fname?args->output_fname:"standard output");
+    }
+    if ( !args->nwrite && !out_std && !args->prefix )
+        fprintf(bcftools_stderr,"Note: -w option not given, printing list of sites...\n");
+
+    int n;
+    while ( (n=bcf_sr_next_line(files)) )
+    {
+        bcf_sr_t *reader = NULL;
+        bcf1_t *line = NULL;
+        int i, ret = 0;
+        for (i=0; i<files->nreaders; i++)
+        {
+            if ( !bcf_sr_has_line(files,i) ) continue;
+
+            if ( args->nflt && args->flt[i] )
+            {
+                bcf1_t *rec = bcf_sr_get_line(files, i);
+                int pass = filter_test(args->flt[i], rec, NULL);
+                if ( args->flt_logic[i] & FLT_EXCLUDE ) pass = pass ? 0 : 1;
+                if ( !pass )
+                {
+                    files->has_line[i] = 0;
+                    n--;
+                    continue;
+                }
+            }
+
+            if ( !line )
+            {
+                line = files->readers[i].buffer[0];
+                reader = &files->readers[i];
+            }
+            ret |= 1<<i;    // this may overflow for many files, but will be used only with two (OP_VENN)
+        }
+        if ( !line ) continue;  // the site has been filtered in all files
+
+        switch (args->isec_op)
+        {
+            case OP_COMPLEMENT: if ( n!=1 || !bcf_sr_has_line(files,0) ) continue; break;
+            case OP_EQUAL: if ( n != args->isec_n ) continue; break;
+            case OP_PLUS: if ( n < args->isec_n ) continue; break;
+            case OP_MINUS: if ( n > args->isec_n ) continue; break;
+            case OP_EXACT:
+                for (i=0; i<files->nreaders; i++)
+                    if ( files->has_line[i] != args->isec_exact[i] ) break;
+                if ( i<files->nreaders ) continue;
+                break;
+        }
+
+        if ( out_std )
+        {
+            if ( bcf_sr_has_line(files,args->iwrite) && bcf_write1(out_fh, files->readers[args->iwrite].header, files->readers[args->iwrite].buffer[0])!=0 )
+                error("[%s] Error: cannot write to %s\n", __func__, args->output_fname ? args->output_fname : "standard output");
+            continue;
+        }
+        else if ( args->fh_sites )
+        {
+            str.l = 0;
+            kputs(reader->header->id[BCF_DT_CTG][line->rid].key, &str); kputc('\t', &str);
+            kputw(line->pos+1, &str); kputc('\t', &str);
+            if (line->n_allele > 0) kputs(line->d.allele[0], &str);
+            else kputc('.', &str);
+            kputc('\t', &str);
+            if (line->n_allele > 1) kputs(line->d.allele[1], &str);
+            else kputc('.', &str);
+            for (i=2; i<line->n_allele; i++)
+            {
+                kputc(',', &str);
+                kputs(line->d.allele[i], &str);
+            }
+            kputc('\t', &str);
+            for (i=0; i<files->nreaders; i++)
+                kputc(bcf_sr_has_line(files,i)?'1':'0', &str);
+            kputc('\n', &str);
+            if ( fwrite(str.s,sizeof(char),str.l,args->fh_sites)!=str.l )
+                error("[%s] Error: failed to write %d bytes to %s\n", __func__,(int)str.l,args->output_fname ? args->output_fname : "standard output");
+        }
+
+        if ( args->prefix )
+        {
+            if ( args->isec_op==OP_VENN && ret==3 )
+            {
+                if ( !args->nwrite || args->write[0] )
+                {
+                    if ( bcf_write1(args->fh_out[2], bcf_sr_get_header(files,0), bcf_sr_get_line(files,0))!=0 )
+                         error("[%s] Error: cannot write\n", __func__);
+                }
+                if ( !args->nwrite || args->write[1] )
+                {
+                    if ( bcf_write1(args->fh_out[3], bcf_sr_get_header(files,1), bcf_sr_get_line(files,1))!=0 )
+                        error("[%s] Error: cannot write\n", __func__);
+                }
+            }
+            else
+            {
+                for (i=0; i<files->nreaders; i++)
+                {
+                    if ( !bcf_sr_has_line(files,i) ) continue;
+                    if ( args->write && !args->write[i] ) continue;
+                    if ( bcf_write1(args->fh_out[i], files->readers[i].header, files->readers[i].buffer[0])!=0 ) error("[%s] Error: cannot write\n", __func__);
+                }
+            }
+        }
+    }
+    if ( str.s ) free(str.s);
+    if ( out_fh && hts_close(out_fh)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,args->output_fname? args->output_fname : "-");
+}
+
+static void add_filter(args_t *args, char *expr, int logic)
+{
+    args->nflt++;
+    args->flt_expr = (char**) realloc(args->flt_expr,sizeof(char*)*args->nflt);
+    args->flt_logic = (int*) realloc(args->flt_logic,sizeof(int)*args->nflt);
+    args->flt = (filter_t**) realloc(args->flt,sizeof(filter_t*)*args->nflt);
+    if ( expr[0]=='-' && expr[1]==0 )
+    {
+        args->flt_expr[args->nflt-1] = NULL;
+        args->flt[args->nflt-1] = NULL;
+    }
+    else
+        args->flt_expr[args->nflt-1] = expr;
+    args->flt_logic[args->nflt-1] = logic;
+}
+
+static void destroy_data(args_t *args);
+static void init_data(args_t *args)
+{
+    int i;
+    if ( args->nflt )
+    {
+        if ( args->nflt > 1 && args->nflt!=args->files->nreaders )
+            error("Error: expected either one -i/-e option or as many as there are input files\n");
+        if ( args->nflt < args->files->nreaders )
+        {
+            if ( !args->flt_expr[0] ) error("Error: useless use of -i/-e\n");
+            args->nflt = args->files->nreaders;
+            args->flt_expr = (char**) realloc(args->flt_expr,sizeof(char*)*args->nflt);
+            args->flt_logic = (int*) realloc(args->flt_logic,sizeof(int)*args->nflt);
+            args->flt = (filter_t**) realloc(args->flt,sizeof(filter_t*)*args->nflt);
+            for (i=1; i<args->nflt; i++)
+            {
+                args->flt_expr[i]  = args->flt_expr[0];
+                args->flt_logic[i] = args->flt_logic[0];
+                args->flt[i] = filter_init(args->files->readers[i].header,args->flt_expr[i]);
+            }
+            args->flt[0] = filter_init(args->files->readers[0].header,args->flt_expr[0]);
+        }
+        else
+        {
+            for (i=0; i<args->files->nreaders; i++)
+            {
+                if ( !args->flt_expr[i] ) continue;
+                args->flt[i] = filter_init(args->files->readers[i].header,args->flt_expr[i]);
+            }
+        }
+    }
+
+    if ( args->isec_op==OP_EXACT )
+    {
+        if ( strlen(args->isec_exact)!=args->files->nreaders )
+            error("The number of files does not match the bitmask: %d vs %s\n", args->files->nreaders,args->isec_exact);
+        for (i=0; i<args->files->nreaders; i++)
+            if ( args->isec_exact[i]!='0' && args->isec_exact[i]!='1' ) error("Unexpected bitmask: %s\n",args->isec_exact);
+        for (i=0; i<args->files->nreaders; i++)
+            args->isec_exact[i] -= '0';
+    }
+
+    // Which files to write: parse the string passed with -w
+    char *p = args->write_files;
+    while (p && *p)
+    {
+        if ( !args->write ) args->write = (int*) calloc(args->files->nreaders,sizeof(int));
+        if ( sscanf(p,"%d",&i)!=1 ) error("Could not parse --write %s\n", args->write_files);
+        if ( i<=0 || i>args->files->nreaders ) error("The index is out of range: %d (-w %s)\n", i, args->write_files);
+        args->write[i-1] = 1;
+        args->iwrite = i-1;
+        args->nwrite++;
+        while (*p && *p!=',') p++;
+        if ( *p==',' ) p++;
+    }
+    if ( args->nwrite>1 && !args->prefix ) error("Expected -p when multiple output files given: --write %s\n", args->write_files);
+    if ( args->isec_op==OP_COMPLEMENT && args->nwrite )
+    {
+        if ( args->nwrite>1 ) error("Multiple files to -w make no sense with -C\n");
+        if ( !args->write[0] ) error("Only -w1 makes sense with -C\n");
+    }
+
+    if ( args->prefix )
+    {
+        // Init output directory and create the readme file
+        args->fh_log = open_file(NULL,"w","%s/README.txt", args->prefix);
+        if ( !args->fh_log ) error("%s/README.txt: %s\n", args->prefix, strerror(errno));
+
+        fprintf(args->fh_log,"This file was produced by vcfisec.\n");
+        fprintf(args->fh_log,"The command line was:\tbcftools %s ", args->argv[0]);
+        int i;
+        for (i=1; i<args->argc; i++) fprintf(args->fh_log," %s",args->argv[i]);
+        fprintf(args->fh_log,"\n\nUsing the following file names:\n");
+
+        const char *suffix = "vcf";
+        if ( args->output_type & FT_BCF ) suffix = "bcf";
+        else if ( args->output_type & FT_GZ ) suffix = "vcf.gz";
+
+        // Open output files and write the legend
+        if ( args->isec_op==OP_VENN )
+        {
+            args->fh_out = (htsFile**) malloc(sizeof(htsFile*)*4);
+            args->fnames = (char**) calloc(4,sizeof(char*));
+
+            #define OPEN_FILE(i,j) { \
+                open_file(&args->fnames[i], NULL, "%s/%04d.%s", args->prefix, i, suffix); \
+                char wmode[8]; \
+                set_wmode(wmode,args->output_type,args->fnames[i],args->clevel); \
+                args->fh_out[i] = hts_open(args->fnames[i], wmode); \
+                if ( !args->fh_out[i] ) error("Could not open %s\n", args->fnames[i]); \
+                if ( args->n_threads ) hts_set_threads(args->fh_out[i], args->n_threads); \
+                if (args->record_cmd_line) bcf_hdr_append_version(args->files->readers[j].header,args->argc,args->argv,"bcftools_isec"); \
+                if ( bcf_hdr_write(args->fh_out[i], args->files->readers[j].header)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->fnames[i]); \
+            }
+            if ( !args->nwrite || args->write[0] )
+            {
+                OPEN_FILE(0,0);
+                fprintf(args->fh_log,"%s\tfor records private to\t%s\n", args->fnames[0], args->files->readers[0].fname);
+            }
+            if ( !args->nwrite || args->write[1] )
+            {
+                OPEN_FILE(1,1);
+                fprintf(args->fh_log,"%s\tfor records private to\t%s\n", args->fnames[1], args->files->readers[1].fname);
+            }
+            if ( !args->nwrite || args->write[0] )
+            {
+                OPEN_FILE(2,0);
+                fprintf(args->fh_log,"%s\tfor records from %s shared by both\t%s %s\n", args->fnames[2], args->files->readers[0].fname, args->files->readers[0].fname, args->files->readers[1].fname);
+            }
+            if ( !args->nwrite || args->write[1] )
+            {
+                OPEN_FILE(3,1);
+                fprintf(args->fh_log,"%s\tfor records from %s shared by both\t%s %s\n", args->fnames[3], args->files->readers[1].fname, args->files->readers[0].fname, args->files->readers[1].fname);
+            }
+        }
+        else
+        {
+            // Init one output file for each reader
+            args->fh_out = (htsFile**) calloc(args->files->nreaders, sizeof(htsFile*));
+            args->fnames = (char**) calloc(args->files->nreaders, sizeof(char*));
+
+            for (i=0; i<args->files->nreaders; i++)
+            {
+                if ( args->write && !args->write[i] ) continue;
+                if ( args->isec_op==OP_COMPLEMENT && i>0 ) break;
+                OPEN_FILE(i,i);
+                fprintf(args->fh_log,"%s\tfor stripped\t%s\n", args->fnames[i], args->files->readers[i].fname);
+            }
+            #undef OPEN_FILE
+        }
+        args->fh_sites = open_file(NULL, "w", "%s/sites.txt", args->prefix);
+        if ( !args->fh_sites ) error("%s/sites.txt: %s\n", args->prefix, strerror(errno));
+    }
+    else {
+        if (args->output_fname) {
+            args->fh_sites = fopen(args->output_fname, "w");
+            if ( args->fh_sites == NULL ) error("Can't write to \"%s\": %s\n", args->output_fname, strerror(errno));
+        }
+        else
+            args->fh_sites = bcftools_stdout;
+    }
+}
+
+static void destroy_data(args_t *args)
+{
+    int i;
+    if ( args->nflt )
+    {
+        for (i=0; i<args->nflt; i++)
+        {
+            if ( !args->flt[i] ) continue;
+            filter_destroy(args->flt[i]);
+        }
+        free(args->flt_expr);
+        free(args->flt);
+        free(args->flt_logic);
+    }
+    if ( args->prefix )
+    {
+        fclose(args->fh_log);
+        int n = args->isec_op==OP_VENN ? 4 : args->files->nreaders;
+        for (i=0; i<n; i++)
+        {
+            if ( !args->fnames[i] ) continue;
+            if ( hts_close(args->fh_out[i])!=0 ) error("[%s] Error: close failed .. %s\n", __func__,args->fnames[i]);
+            if ( args->output_type==FT_VCF_GZ )
+            {
+                tbx_conf_t conf = tbx_conf_vcf;
+                tbx_index_build(args->fnames[i], -1, &conf);
+            }
+            else if ( args->output_type==FT_BCF_GZ )
+            {
+                if ( bcf_index_build(args->fnames[i],14) ) error("Could not index %s\n", args->fnames[i]);
+            }
+            free(args->fnames[i]);
+        }
+        free(args->fh_out);
+        free(args->fnames);
+        if ( args->fh_sites ) fclose(args->fh_sites);
+        if ( args->write ) free(args->write);
+    }
+}
+
+static void usage(void)
+{
+    fprintf(bcftools_stderr, "\n");
+    fprintf(bcftools_stderr, "About:   Create intersections, unions and complements of VCF files.\n");
+    fprintf(bcftools_stderr, "Usage:   bcftools isec [options] <A.vcf.gz> <B.vcf.gz> [...]\n");
+    fprintf(bcftools_stderr, "\n");
+    fprintf(bcftools_stderr, "Options:\n");
+    fprintf(bcftools_stderr, "    -c, --collapse STRING          Treat as identical records with <snps|indels|both|all|some|none>, see man page for details [none]\n");
+    fprintf(bcftools_stderr, "    -C, --complement               Output positions present only in the first file but missing in the others\n");
+    fprintf(bcftools_stderr, "    -e, --exclude EXPR             Exclude sites for which the expression is true\n");
+    fprintf(bcftools_stderr, "    -f, --apply-filters LIST       Require at least one of the listed FILTER strings (e.g. \"PASS,.\")\n");
+    fprintf(bcftools_stderr, "    -i, --include EXPR             Include only sites for which the expression is true\n");
+    fprintf(bcftools_stderr, "        --no-version               Do not append version and command line to the header\n");
+    fprintf(bcftools_stderr, "    -n, --nfiles [+-=~]INT         Output positions present in this many (=), this many or more (+), this many or fewer (-), the exact (~) files\n");
+    fprintf(bcftools_stderr, "    -o, --output FILE              Write output to a file [standard output]\n");
+    fprintf(bcftools_stderr, "    -O, --output-type u|b|v|z[0-9] u/b: un/compressed BCF, v/z: un/compressed VCF, 0-9: compression level [v]\n");
+    fprintf(bcftools_stderr, "    -p, --prefix DIR               If given, subset each of the input files accordingly, see also -w\n");
+    fprintf(bcftools_stderr, "    -r, --regions REGION           Restrict to comma-separated list of regions\n");
+    fprintf(bcftools_stderr, "    -R, --regions-file FILE        Restrict to regions listed in a file\n");
+    fprintf(bcftools_stderr, "        --regions-overlap 0|1|2    Include if POS in the region (0), record overlaps (1), variant overlaps (2) [1]\n");
+    fprintf(bcftools_stderr, "    -t, --targets REGION           Similar to -r but streams rather than index-jumps\n");
+    fprintf(bcftools_stderr, "    -T, --targets-file FILE        Similar to -R but streams rather than index-jumps\n");
+    fprintf(bcftools_stderr, "        --targets-overlap 0|1|2    Include if POS in the region (0), record overlaps (1), variant overlaps (2) [0]\n");
+    fprintf(bcftools_stderr, "        --threads INT              Use multithreading with <int> worker threads [0]\n");
+    fprintf(bcftools_stderr, "    -w, --write LIST               List of files to write with -p given as 1-based indexes. By default, all files are written\n");
+    fprintf(bcftools_stderr, "\n");
+    fprintf(bcftools_stderr, "Examples:\n");
+    fprintf(bcftools_stderr, "   # Create intersection and complements of two sets saving the output in dir/*\n");
+    fprintf(bcftools_stderr, "   bcftools isec A.vcf.gz B.vcf.gz -p dir\n");
+    fprintf(bcftools_stderr, "\n");
+    fprintf(bcftools_stderr, "   # Filter sites in A and B (but not in C) and create intersection\n");
+    fprintf(bcftools_stderr, "   bcftools isec -e'MAF<0.01' -i'dbSNP=1' -e - A.vcf.gz B.vcf.gz C.vcf.gz -p dir\n");
+    fprintf(bcftools_stderr, "\n");
+    fprintf(bcftools_stderr, "   # Extract and write records from A shared by both A and B using exact allele match\n");
+    fprintf(bcftools_stderr, "   bcftools isec A.vcf.gz B.vcf.gz -p dir -n =2 -w 1\n");
+    fprintf(bcftools_stderr, "\n");
+    fprintf(bcftools_stderr, "   # Extract and write records from C found in A and C but not in B\n");
+    fprintf(bcftools_stderr, "   bcftools isec A.vcf.gz B.vcf.gz C.vcf.gz -p dir -n~101 -w 3\n");
+    fprintf(bcftools_stderr, "\n");
+    fprintf(bcftools_stderr, "   # Extract records private to A or B comparing by position only\n");
+    fprintf(bcftools_stderr, "   bcftools isec A.vcf.gz B.vcf.gz -p dir -n -1 -c all\n");
+    fprintf(bcftools_stderr, "\n");
+    bcftools_exit(1);
+}
+
+int main_vcfisec(int argc, char *argv[])
+{
+    int c;
+    args_t *args = (args_t*) calloc(1,sizeof(args_t));
+    args->files  = bcf_sr_init();
+    args->argc   = argc; args->argv = argv;
+    args->output_fname = NULL;
+    args->output_type = FT_VCF;
+    args->n_threads = 0;
+    args->record_cmd_line = 1;
+    args->clevel = -1;
+    int targets_is_file = 0, regions_is_file = 0;
+    int regions_overlap = 1;
+    int targets_overlap = 0;
+
+    static struct option loptions[] =
+    {
+        {"help",no_argument,NULL,'h'},
+        {"exclude",required_argument,NULL,'e'},
+        {"include",required_argument,NULL,'i'},
+        {"collapse",required_argument,NULL,'c'},
+        {"complement",no_argument,NULL,'C'},
+        {"apply-filters",required_argument,NULL,'f'},
+        {"nfiles",required_argument,NULL,'n'},
+        {"prefix",required_argument,NULL,'p'},
+        {"write",required_argument,NULL,'w'},
+        {"targets",required_argument,NULL,'t'},
+        {"targets-file",required_argument,NULL,'T'},
+        {"targets-overlap",required_argument,NULL,4},
+        {"regions",required_argument,NULL,'r'},
+        {"regions-file",required_argument,NULL,'R'},
+        {"regions-overlap",required_argument,NULL,3},
+        {"output",required_argument,NULL,'o'},
+        {"output-type",required_argument,NULL,'O'},
+        {"threads",required_argument,NULL,9},
+        {"no-version",no_argument,NULL,8},
+        {NULL,0,NULL,0}
+    };
+    char *tmp;
+    while ((c = getopt_long(argc, argv, "hc:r:R:p:n:w:t:T:Cf:o:O:i:e:",loptions,NULL)) >= 0) {
+        switch (c) {
+            case 'o': args->output_fname = optarg; break;
+            case 'O':
+                switch (optarg[0]) {
+                    case 'b': args->output_type = FT_BCF_GZ; break;
+                    case 'u': args->output_type = FT_BCF; break;
+                    case 'z': args->output_type = FT_VCF_GZ; break;
+                    case 'v': args->output_type = FT_VCF; break;
+                    default:
+                    {
+                        args->clevel = strtol(optarg,&tmp,10);
+                        if ( *tmp || args->clevel<0 || args->clevel>9 ) error("The output type \"%s\" not recognised\n", optarg);
+                    }
+                }
+                if ( optarg[1] )
+                {
+                    args->clevel = strtol(optarg+1,&tmp,10);
+                    if ( *tmp || args->clevel<0 || args->clevel>9 ) error("Could not parse argument: --compression-level %s\n", optarg+1);
+                }
+                break;
+            case 'c':
+                if ( !strcmp(optarg,"snps") ) args->files->collapse |= COLLAPSE_SNPS;
+                else if ( !strcmp(optarg,"indels") ) args->files->collapse |= COLLAPSE_INDELS;
+                else if ( !strcmp(optarg,"both") ) args->files->collapse |= COLLAPSE_SNPS | COLLAPSE_INDELS;
+                else if ( !strcmp(optarg,"any") ) args->files->collapse |= COLLAPSE_ANY;
+                else if ( !strcmp(optarg,"all") ) args->files->collapse |= COLLAPSE_ANY;
+                else if ( !strcmp(optarg,"some") ) args->files->collapse |= COLLAPSE_SOME;
+                else if ( !strcmp(optarg,"none") ) args->files->collapse = COLLAPSE_NONE;
+                else error("The --collapse string \"%s\" not recognised.\n", optarg);
+                break;
+            case 'f': args->files->apply_filters = optarg; break;
+            case 'C':
+                if ( args->isec_op!=0 && args->isec_op!=OP_COMPLEMENT ) error("Error: either -C or -n should be given, not both.\n");
+                args->isec_op = OP_COMPLEMENT; break;
+            case 'r': args->regions_list = optarg; break;
+            case 'R': args->regions_list = optarg; regions_is_file = 1; break;
+            case 't': args->targets_list = optarg; break;
+            case 'T': args->targets_list = optarg; targets_is_file = 1; break;
+            case 'p': args->prefix = optarg; break;
+            case 'w': args->write_files = optarg; break;
+            case 'i': add_filter(args, optarg, FLT_INCLUDE); break;
+            case 'e': add_filter(args, optarg, FLT_EXCLUDE); break;
+            case 'n':
+                {
+                    if ( args->isec_op!=0 && args->isec_op==OP_COMPLEMENT ) error("Error: either -C or -n should be given, not both.\n");
+                    if ( args->isec_op!=0 ) error("Error: -n should be given only once.\n");
+                    char *p = optarg;
+                    if ( *p=='-' ) { args->isec_op = OP_MINUS; p++; }
+                    else if ( *p=='+' ) { args->isec_op = OP_PLUS; p++; }
+                    else if ( *p=='=' ) { args->isec_op = OP_EQUAL; p++; }
+                    else if ( *p=='~' ) { args->isec_op = OP_EXACT; p++; }
+                    else if ( isdigit(*p) ) args->isec_op = OP_EQUAL;
+                    else error("Could not parse --nfiles %s\n", optarg);
+                    if ( args->isec_op == OP_EXACT ) args->isec_exact = p;
+                    else if ( sscanf(p,"%d",&args->isec_n)!=1 ) error("Could not parse --nfiles %s\n", optarg);
+                }
+                break;
+            case  3 :
+                regions_overlap = parse_overlap_option(optarg);
+                if ( regions_overlap < 0 ) error("Could not parse: --regions-overlap %s\n",optarg);
+                break;
+            case  4 :
+                targets_overlap = parse_overlap_option(optarg);
+                if ( targets_overlap < 0 ) error("Could not parse: --targets-overlap %s\n",optarg);
+                break;
+            case  9 : args->n_threads = strtol(optarg, 0, 0); break;
+            case  8 : args->record_cmd_line = 0; break;
+            case 'h':
+            case '?': usage(); break;
+            default: error("Unknown argument: %s\n", optarg);
+        }
+    }
+    if ( argc-optind<1 ) usage();   // no file given
+    if ( args->targets_list )
+    {
+        bcf_sr_set_opt(args->files,BCF_SR_TARGETS_OVERLAP,targets_overlap);
+        if ( bcf_sr_set_targets(args->files, args->targets_list, targets_is_file,0)<0 )
+            error("Failed to read the targets: %s\n", args->targets_list);
+    }
+    if ( args->regions_list )
+    {
+        bcf_sr_set_opt(args->files,BCF_SR_REGIONS_OVERLAP,regions_overlap);
+        if ( bcf_sr_set_regions(args->files, args->regions_list, regions_is_file)<0 )
+            error("Failed to read the regions: %s\n", args->regions_list);
+    }
+    if ( argc-optind==2 && !args->isec_op )
+    {
+        args->isec_op = OP_VENN;
+        if ( !args->prefix ) error("Expected the -p option\n");
+    }
+    if ( !args->isec_op )
+    {
+        args->isec_op = OP_PLUS;
+        args->isec_n  = 1;
+    }
+    args->files->require_index = 1;
+    while (optind<argc)
+    {
+        if ( !bcf_sr_add_reader(args->files, argv[optind]) ) error("Failed to open %s: %s\n", argv[optind],bcf_sr_strerror(args->files->errnum));
+        optind++;
+    }
+    init_data(args);
+    isec_vcf(args);
+    destroy_data(args);
+    bcf_sr_destroy(args->files);
+    free(args);
+    return 0;
+}
+
diff --git a/bcftools/vcfmerge.c b/bcftools/vcfmerge.c
new file mode 100644
index 0000000..7296a00
--- /dev/null
+++ b/bcftools/vcfmerge.c
@@ -0,0 +1,3330 @@
+/*  vcfmerge.c -- Merge multiple VCF/BCF files to create one multi-sample file.
+
+    Copyright (C) 2012-2022 Genome Research Ltd.
+
+    Author: Petr Danecek <pd3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.  */
+
+#include <stdio.h>
+#include <string.h>
+#include <strings.h>
+#include <assert.h>
+#include <errno.h>
+#include <unistd.h>
+#include <getopt.h>
+#include <inttypes.h>
+#include <htslib/vcf.h>
+#include <htslib/synced_bcf_reader.h>
+#include <htslib/vcfutils.h>
+#include <htslib/faidx.h>
+#include <math.h>
+#include <ctype.h>
+#include <time.h>
+#include "bcftools.h"
+#include "regidx.h"
+#include "vcmp.h"
+
+#define DBG 0
+
+#define COLLAPSE_SNP_INS_DEL (1<<10)
+
+#include <htslib/khash.h>
+KHASH_MAP_INIT_STR(strdict, int)
+typedef khash_t(strdict) strdict_t;
+
+#define FLT_LOGIC_ADD    0
+#define FLT_LOGIC_REMOVE 1
+
+#define SKIP_DONE 1     // the record was processed
+#define SKIP_DIFF 2     // not compatible, merge later
+
+#define IS_VL_G(hdr,id) (bcf_hdr_id2length(hdr,BCF_HL_FMT,id) == BCF_VL_G)
+#define IS_VL_A(hdr,id) (bcf_hdr_id2length(hdr,BCF_HL_FMT,id) == BCF_VL_A)
+#define IS_VL_R(hdr,id) (bcf_hdr_id2length(hdr,BCF_HL_FMT,id) == BCF_VL_R)
+
+#define SWAP(type_t,a,b) { type_t tmp = (a); (a) = (b); (b) = tmp; }
+
+#define PL2PROB_MAX 1024
+
+// For merging INFO Number=A,G,R tags
+typedef struct
+{
+    const char *hdr_tag;
+    int type, nvals;
+    int nbuf, mbuf;
+    uint8_t *buf;
+}
+AGR_info_t;
+
+// Rules for merging arbitrary INFO tags
+typedef struct _info_rule_t
+{
+    char *hdr_tag;
+    void (*merger)(bcf_hdr_t *hdr, bcf1_t *line, struct _info_rule_t *rule);
+    int type;           // one of BCF_HT_*
+    int block_size;     // number of values in a block
+    int type_size;      // size of the corresponding BCF_HT_* type
+    int nblocks;        // number of blocks in nvals (the number of merged files)
+    int nvals, mvals;   // used and total size of vals array
+    void *vals;         // the info tag values
+}
+info_rule_t;
+
+typedef struct
+{
+    bcf1_t *line;
+    int end, active;    // end: 0-based INFO/END
+}
+gvcf_aux_t;
+
+// Auxiliary merge data for selecting the right combination
+//  of buffered records across multiple readers. maux1_t
+//  corresponds to one buffered line.
+typedef struct
+{
+    int skip;
+    int *map;   // mapping from input alleles to the array of output alleles (set by merge_alleles)
+    int mmap;   // size of map array (only buffer[i].n_allele is actually used)
+    int als_differ;
+}
+maux1_t;
+typedef struct
+{
+    int rid;        // current rid
+    int beg,end;    // valid ranges in reader's buffer [beg,end). Maintained by maux_reset and gvcf_flush.
+    int cur;        // current line or -1 if none
+    int mrec;       // allocated size of buf
+    maux1_t *rec;   // buffer to keep reader's lines
+    bcf1_t **lines; // source buffer: either gvcf or readers' buffer
+}
+buffer_t;
+typedef struct
+{
+    int n, pos, var_types;  // number of readers, current position, currently available variant types
+    char *chr;              // current chromosome
+    char **als, **out_als;  // merged alleles (temp, may contain empty records) and merged alleles ready for output
+    int nals, mals, nout_als, mout_als; // size of the output array
+    int *cnt, ncnt; // number of records that refer to the alleles
+    int *smpl_ploidy, *smpl_nGsize; // ploidy and derived number of values in Number=G tags, updated for each line (todo: cache for missing cases)
+    bcf_fmt_t **fmt_map; // i-th output FORMAT field corresponds in j-th reader to i*nreader+j, first row is reserved for GT
+    int nfmt_map;        // number of rows in the fmt_map array
+    int *agr_map, nagr_map, magr_map;   // mapping between Number=AGR element indexes
+    void *tmp_arr;
+    size_t ntmp_arr;
+    buffer_t *buf;
+    AGR_info_t *AGR_info;
+    int nAGR_info, mAGR_info;
+    bcf_srs_t *files;
+    int gvcf_min,       // min buffered gvcf END position (NB: gvcf_min is 1-based) or 0 if no active lines are present
+        gvcf_break;     // 0-based position of a next record which breaks a gVCF block
+    gvcf_aux_t *gvcf;   // buffer of gVCF lines, for each reader one line
+    int nout_smpl;
+    kstring_t *str;
+    int32_t *laa;           // localized alternate alleles given as input-based indexes in per-sample blocks of (args->local_alleles+1) values, 0 is always first
+    int nlaa, laa_dirty;    // number of LAA alleles actually used at this site, and was any L* added?
+    int32_t *tmpi, *k2k;
+    double *tmpd, *pl2prob; // mapping from phred-score likelihoods (PL) to probability
+    int ntmpi, ntmpd, nk2k;
+}
+maux_t;
+
+typedef struct
+{
+    vcmp_t *vcmp;
+    maux_t *maux;
+    regidx_t *regs;    // apply regions only after the blocks are expanded
+    regitr_t *regs_itr;
+    int header_only, collapse, output_type, force_samples, merge_by_id, do_gvcf, filter_logic, missing_to_ref, no_index;
+    char *header_fname, *output_fname, *regions_list, *info_rules, *file_list;
+    faidx_t *gvcf_fai;
+    info_rule_t *rules;
+    int nrules;
+    strdict_t *tmph;
+    kstring_t tmps;
+    bcf_srs_t *files;
+    bcf1_t *out_line;
+    htsFile *out_fh;
+    bcf_hdr_t *out_hdr;
+    char **argv;
+    int argc, n_threads, record_cmd_line, clevel;
+    int local_alleles;    // the value of -L option
+    int keep_AC_AN;
+}
+args_t;
+
+static bcf1_t *maux_get_line(args_t *args, int i)
+{
+    maux_t *ma = args->maux;
+    int ibuf = ma->buf[i].cur;
+    if ( ibuf >= 0 ) return ma->buf[i].lines[ibuf];
+    return NULL;
+}
+
+static void info_rules_merge_sum(bcf_hdr_t *hdr, bcf1_t *line, info_rule_t *rule)
+{
+    if ( !rule->nvals ) return;
+    int i, j, ndim = rule->block_size;
+    #define BRANCH(type_t,is_missing) { \
+        type_t *ptr = (type_t*) rule->vals; \
+        for (i=0; i<rule->nvals; i++) if ( is_missing ) ptr[i] = 0; \
+        for (i=1; i<rule->nblocks; i++) \
+        { \
+            for (j=0; j<ndim; j++) ptr[j] += ptr[j+i*ndim]; \
+        } \
+    }
+    switch (rule->type) {
+        case BCF_HT_INT:  BRANCH(int32_t, ptr[i]==bcf_int32_missing); break;
+        case BCF_HT_REAL: BRANCH(float, bcf_float_is_missing(ptr[i])); break;
+        default: error("TODO: %s:%d .. type=%d\n", __FILE__,__LINE__, rule->type);
+    }
+    #undef BRANCH
+
+    bcf_update_info(hdr,line,rule->hdr_tag,rule->vals,ndim,rule->type);
+}
+static void info_rules_merge_avg(bcf_hdr_t *hdr, bcf1_t *line, info_rule_t *rule)
+{
+    if ( !rule->nvals ) return;
+    int i, j, ndim = rule->block_size;
+    #define BRANCH(type_t,is_missing) { \
+        type_t *ptr = (type_t*) rule->vals; \
+        for (i=0; i<rule->nvals; i++) if ( is_missing ) ptr[i] = 0; \
+        for (j=0; j<ndim; j++) \
+        { \
+            double sum = 0; \
+            for (i=0; i<rule->nblocks; i++) sum += ptr[j+i*ndim]; \
+            ptr[j] = sum / rule->nblocks; \
+        } \
+    }
+    switch (rule->type) {
+        case BCF_HT_INT:  BRANCH(int32_t, ptr[i]==bcf_int32_missing); break;
+        case BCF_HT_REAL: BRANCH(float, bcf_float_is_missing(ptr[i])); break;
+        default: error("TODO: %s:%d .. type=%d\n", __FILE__,__LINE__, rule->type);
+    }
+    #undef BRANCH
+
+    bcf_update_info(hdr,line,rule->hdr_tag,rule->vals,ndim,rule->type);
+}
+static void info_rules_merge_min(bcf_hdr_t *hdr, bcf1_t *line, info_rule_t *rule)
+{
+    if ( !rule->nvals ) return;
+    int i, j, ndim = rule->block_size;
+    #define BRANCH(type_t,is_missing,set_missing,huge_val) { \
+        type_t *ptr = (type_t*) rule->vals; \
+        for (i=0; i<rule->nvals; i++) if ( is_missing ) ptr[i] = huge_val; \
+        for (i=1; i<rule->nblocks; i++) \
+        { \
+            for (j=0; j<ndim; j++) if ( ptr[j] > ptr[j+i*ndim] ) ptr[j] = ptr[j+i*ndim]; \
+        } \
+        for (i=0; i<rule->nvals; i++) if ( ptr[i]==huge_val ) set_missing; \
+    }
+    switch (rule->type) {
+        case BCF_HT_INT:  BRANCH(int32_t, ptr[i]==bcf_int32_missing, ptr[i]=bcf_int32_missing, INT32_MAX); break;
+        case BCF_HT_REAL: BRANCH(float, bcf_float_is_missing(ptr[i]), bcf_float_set_missing(ptr[i]), HUGE_VAL); break;
+        default: error("TODO: %s:%d .. type=%d\n", __FILE__,__LINE__, rule->type);
+    }
+    #undef BRANCH
+
+    bcf_update_info(hdr,line,rule->hdr_tag,rule->vals,ndim,rule->type);
+}
+static void info_rules_merge_max(bcf_hdr_t *hdr, bcf1_t *line, info_rule_t *rule)
+{
+    if ( !rule->nvals ) return;
+    int i, j, ndim = rule->block_size;
+    #define BRANCH(type_t,is_missing,set_missing,huge_val) { \
+        type_t *ptr = (type_t*) rule->vals; \
+        for (i=0; i<rule->nvals; i++) if ( is_missing ) ptr[i] = huge_val; \
+        for (i=1; i<rule->nblocks; i++) \
+        { \
+            for (j=0; j<ndim; j++) if ( ptr[j] < ptr[j+i*ndim] ) ptr[j] = ptr[j+i*ndim]; \
+        } \
+        for (i=0; i<rule->nvals; i++) if ( ptr[i]==huge_val ) set_missing; \
+    }
+    switch (rule->type) {
+        case BCF_HT_INT:  BRANCH(int32_t, ptr[i]==bcf_int32_missing, ptr[i]=bcf_int32_missing, INT32_MIN); break;
+        case BCF_HT_REAL: BRANCH(float, bcf_float_is_missing(ptr[i]), bcf_float_set_missing(ptr[i]), -HUGE_VAL); break;
+        default: error("TODO: %s:%d .. type=%d\n", __FILE__,__LINE__, rule->type);
+    }
+    #undef BRANCH
+
+    bcf_update_info(hdr,line,rule->hdr_tag,rule->vals,ndim,rule->type);
+}
+static void info_rules_merge_join(bcf_hdr_t *hdr, bcf1_t *line, info_rule_t *rule)
+{
+    if ( !rule->nvals ) return;
+    if ( rule->type==BCF_HT_STR )
+    {
+        ((char*)rule->vals)[rule->nvals] = 0;
+        bcf_update_info_string(hdr,line,rule->hdr_tag,rule->vals);
+    }
+    else
+    {
+        int isrc, idst = 0;
+        #define BRANCH(type_t,is_missing,is_vector_end) { \
+            type_t *ptr = (type_t*) rule->vals; \
+            for (isrc=0; isrc<rule->nvals; isrc++) \
+            { \
+                if ( is_vector_end ) break; \
+                if ( is_missing ) continue; \
+                if ( idst!=isrc ) ptr[idst] = ptr[isrc]; \
+                idst++; \
+            } \
+        }
+        switch (rule->type) {
+            case BCF_HT_INT:  BRANCH(int32_t, ptr[isrc]==bcf_int32_missing, ptr[isrc]==bcf_int32_vector_end); break;
+            case BCF_HT_REAL: BRANCH(float, bcf_float_is_missing(ptr[isrc]), bcf_float_is_vector_end(ptr[isrc])); break;
+            default: error("TODO: %s:%d .. type=%d\n", __FILE__,__LINE__, rule->type);
+        }
+        #undef BRANCH
+
+        rule->nvals = idst;
+        bcf_update_info(hdr,line,rule->hdr_tag,rule->vals,rule->nvals,rule->type);
+    }
+}
+
+static int info_rules_comp_key2(const void *a, const void *b)
+{
+    info_rule_t *rule1 = (info_rule_t*) a;
+    info_rule_t *rule2 = (info_rule_t*) b;
+    return strcmp(rule1->hdr_tag, rule2->hdr_tag);
+}
+static int info_rules_comp_key(const void *a, const void *b)
+{
+    char *key = (char*) a;
+    info_rule_t *rule = (info_rule_t*) b;
+    return strcmp(key, rule->hdr_tag);
+}
+static void info_rules_init(args_t *args)
+{
+    if ( args->info_rules && !strcmp("-",args->info_rules) ) return;
+
+    kstring_t str = {0,0,0};
+    if ( !args->info_rules )
+    {
+        if ( bcf_hdr_idinfo_exists(args->out_hdr,BCF_HL_INFO,bcf_hdr_id2int(args->out_hdr, BCF_DT_ID, "DP")) ) kputs("DP:sum",&str);
+        if ( bcf_hdr_idinfo_exists(args->out_hdr,BCF_HL_INFO,bcf_hdr_id2int(args->out_hdr, BCF_DT_ID, "DP4")) )
+        {
+            if ( str.l ) kputc(',',&str);
+            kputs("DP4:sum",&str);
+        }
+        if ( args->do_gvcf && bcf_hdr_idinfo_exists(args->out_hdr,BCF_HL_INFO,bcf_hdr_id2int(args->out_hdr, BCF_DT_ID, "QS")) )
+        {
+            if ( str.l ) kputc(',',&str);
+            kputs("QS:sum",&str);
+        }
+        if ( args->do_gvcf && bcf_hdr_idinfo_exists(args->out_hdr,BCF_HL_INFO,bcf_hdr_id2int(args->out_hdr, BCF_DT_ID, "MinDP")) )
+        {
+            if ( str.l ) kputc(',',&str);
+            kputs("MinDP:min",&str);
+        }
+        if ( args->do_gvcf && bcf_hdr_idinfo_exists(args->out_hdr,BCF_HL_INFO,bcf_hdr_id2int(args->out_hdr, BCF_DT_ID, "I16")) )
+        {
+            if ( str.l ) kputc(',',&str);
+            kputs("I16:sum",&str);
+        }
+        if ( args->do_gvcf && bcf_hdr_idinfo_exists(args->out_hdr,BCF_HL_INFO,bcf_hdr_id2int(args->out_hdr, BCF_DT_ID, "IDV")) )
+        {
+            if ( str.l ) kputc(',',&str);
+            kputs("IDV:max",&str);
+        }
+        if ( args->do_gvcf && bcf_hdr_idinfo_exists(args->out_hdr,BCF_HL_INFO,bcf_hdr_id2int(args->out_hdr, BCF_DT_ID, "IMF")) )
+        {
+            if ( str.l ) kputc(',',&str);
+            kputs("IMF:max",&str);
+        }
+        if ( !bcf_hdr_nsamples(args->out_hdr) )
+        {
+            if ( bcf_hdr_idinfo_exists(args->out_hdr,BCF_HL_INFO,bcf_hdr_id2int(args->out_hdr, BCF_DT_ID, "AN")) )
+            {
+                if ( str.l ) kputc(',',&str);
+                kputs("AN:sum",&str);
+            }
+            if ( bcf_hdr_idinfo_exists(args->out_hdr,BCF_HL_INFO,bcf_hdr_id2int(args->out_hdr, BCF_DT_ID, "AC")) )
+            {
+                if ( str.l ) kputc(',',&str);
+                kputs("AC:sum",&str);
+            }
+        }
+
+        if ( !str.l ) return;
+        args->info_rules = str.s;
+    }
+
+    args->nrules = 1;
+    char *ss = strdup(args->info_rules), *tmp = ss;
+    int n = 0;
+    while ( *ss )
+    {
+        if ( *ss==':' ) { *ss = 0; n++; if ( n%2==0 ) error("Could not parse INFO rules: \"%s\"\n", args->info_rules); }
+        else if ( *ss==',' ) { *ss = 0; args->nrules++; n++; if ( n%2==1 ) error("Could not parse INFO rules: \"%s\"\n", args->info_rules); }
+        ss++;
+    }
+    if ( n%2==0 ) error("Could not parse INFO rules: \"%s\"\n", args->info_rules);
+    args->rules = (info_rule_t*) calloc(args->nrules,sizeof(info_rule_t));
+
+    n = 0;
+    ss = tmp;
+    while ( n < args->nrules )
+    {
+        info_rule_t *rule = &args->rules[n];
+        rule->hdr_tag = strdup(ss);
+        int id = bcf_hdr_id2int(args->out_hdr, BCF_DT_ID, rule->hdr_tag);
+        if ( !bcf_hdr_idinfo_exists(args->out_hdr,BCF_HL_INFO,id) ) error("The INFO tag is not defined in the header: \"%s\"\n", rule->hdr_tag);
+        rule->type = bcf_hdr_id2type(args->out_hdr,BCF_HL_INFO,id);
+        if ( rule->type==BCF_HT_INT ) rule->type_size = sizeof(int32_t);
+        else if ( rule->type==BCF_HT_REAL ) rule->type_size = sizeof(float);
+        else if ( rule->type==BCF_HT_STR ) rule->type_size = sizeof(char);
+        else error("The INFO rule \"%s\" is not supported; the tag \"%s\" type is %d\n", ss,rule->hdr_tag,rule->type);
+
+        if ( !strcmp(rule->hdr_tag,"AC") || !strcmp(rule->hdr_tag,"AN") ) args->keep_AC_AN = 1;
+
+        ss = strchr(ss, '\0'); ss++;
+        if ( !*ss ) error("Could not parse INFO rules, missing logic of \"%s\"\n", rule->hdr_tag);
+
+        int is_join = 0;
+        if ( !strcasecmp(ss,"sum") ) rule->merger = info_rules_merge_sum;
+        else if ( !strcasecmp(ss,"avg") ) rule->merger = info_rules_merge_avg;
+        else if ( !strcasecmp(ss,"min") ) rule->merger = info_rules_merge_min;
+        else if ( !strcasecmp(ss,"max") ) rule->merger = info_rules_merge_max;
+        else if ( !strcasecmp(ss,"join") ) { rule->merger = info_rules_merge_join; is_join = 1; }
+        else error("The rule logic \"%s\" not recognised\n", ss);
+
+        if ( !is_join && rule->type==BCF_HT_STR )
+            error("Numeric operation \"%s\" requested on non-numeric field: %s\n", ss, rule->hdr_tag);
+        if ( bcf_hdr_id2number(args->out_hdr,BCF_HL_INFO,id)==0xfffff )
+        {
+            int is_agr = (
+                    bcf_hdr_id2length(args->out_hdr,BCF_HL_INFO,id)==BCF_VL_A ||
+                    bcf_hdr_id2length(args->out_hdr,BCF_HL_INFO,id)==BCF_VL_G ||
+                    bcf_hdr_id2length(args->out_hdr,BCF_HL_INFO,id)==BCF_VL_R
+                    ) ? 1 : 0;
+            if ( is_join && bcf_hdr_id2length(args->out_hdr,BCF_HL_INFO,id)!=BCF_VL_VAR )
+            {
+                bcf_hrec_t *hrec = bcf_hdr_get_hrec(args->out_hdr, BCF_HL_INFO, "ID", rule->hdr_tag, NULL);
+                hrec = bcf_hrec_dup(hrec);
+                int i = bcf_hrec_find_key(hrec, "Number");
+                if ( i<0 ) error("Uh, could not find the entry Number in the header record of %s\n",rule->hdr_tag);
+                free(hrec->vals[i]);
+                hrec->vals[i] = strdup(".");
+                bcf_hdr_remove(args->out_hdr,BCF_HL_INFO, rule->hdr_tag);
+                bcf_hdr_add_hrec(args->out_hdr, hrec);
+            }
+            if ( !is_join && !is_agr )
+                error("Only fixed-length vectors are supported with -i %s:%s\n", ss, rule->hdr_tag);
+        }
+
+        ss = strchr(ss, '\0'); ss++;
+        n++;
+    }
+    free(str.s);
+    free(tmp);
+
+    qsort(args->rules, args->nrules, sizeof(*args->rules), info_rules_comp_key2);
+}
+static void info_rules_destroy(args_t *args)
+{
+    int i;
+    for (i=0; i<args->nrules; i++)
+    {
+        info_rule_t *rule = &args->rules[i];
+        free(rule->hdr_tag);
+        free(rule->vals);
+    }
+    free(args->rules);
+}
+static void info_rules_reset(args_t *args)
+{
+    int i;
+    for (i=0; i<args->nrules; i++)
+        args->rules[i].nblocks = args->rules[i].nvals = args->rules[i].block_size = 0;
+}
+static int info_rules_add_values(args_t *args, bcf_hdr_t *hdr, bcf1_t *line, info_rule_t *rule, maux1_t *als, int var_len)
+{
+    int msize = args->maux->ntmp_arr / rule->type_size;
+    int ret = bcf_get_info_values(hdr, line, rule->hdr_tag, &args->maux->tmp_arr, &msize, rule->type);
+    if ( ret<=0 ) error("FIXME: error parsing %s at %s:%"PRId64" .. %d\n", rule->hdr_tag,bcf_seqname(hdr,line),(int64_t) line->pos+1,ret);
+    args->maux->ntmp_arr = msize * rule->type_size;
+
+    rule->nblocks++;
+
+    if ( rule->type==BCF_HT_STR )
+    {
+        int need_comma = rule->nblocks==1 ? 0 : 1;
+        hts_expand(char,rule->nvals+ret+need_comma+1,rule->mvals,rule->vals);            // 1 for null-termination
+        char *tmp = (char*) rule->vals + rule->nvals;
+        if ( rule->nvals>0 ) { *tmp = ','; tmp++; }
+        strncpy(tmp,(char*)args->maux->tmp_arr,ret);
+        rule->nvals += ret + need_comma;
+        return 1;
+    }
+
+    int i, j;
+    if ( var_len==BCF_VL_A )
+    {
+        if ( ret!=line->n_allele-1 ) error("Wrong number of %s fields at %s:%"PRId64"\n",rule->hdr_tag,bcf_seqname(hdr,line),(int64_t) line->pos+1);
+        args->maux->nagr_map = ret;
+        hts_expand(int,args->maux->nagr_map,args->maux->magr_map,args->maux->agr_map);
+        // create mapping from source file ALT indexes to dst file indexes
+        for (i=0; i<ret; i++) args->maux->agr_map[i] = als->map[i+1] - 1;
+        rule->block_size = args->maux->nout_als - 1;
+    }
+    else if ( var_len==BCF_VL_R )
+    {
+        if ( ret!=line->n_allele ) error("Wrong number of %s fields at %s:%"PRId64"\n",rule->hdr_tag,bcf_seqname(hdr,line),(int64_t) line->pos+1);
+        args->maux->nagr_map = ret;
+        hts_expand(int,args->maux->nagr_map,args->maux->magr_map,args->maux->agr_map);
+        for (i=0; i<ret; i++) args->maux->agr_map[i] = als->map[i];
+        rule->block_size = args->maux->nout_als;
+    }
+    else if ( var_len==BCF_VL_G )
+    {
+        args->maux->nagr_map = bcf_alleles2gt(line->n_allele-1,line->n_allele-1)+1;
+        assert( ret==line->n_allele || ret==args->maux->nagr_map );
+        if ( ret==line->n_allele ) // haploid
+        {
+            args->maux->nagr_map = line->n_allele;
+            hts_expand(int,args->maux->nagr_map,args->maux->magr_map,args->maux->agr_map);
+            for (i=0; i<ret; i++) args->maux->agr_map[i] = als->map[i];
+            rule->block_size = args->maux->nout_als;
+        }
+        else
+        {
+            hts_expand(int,args->maux->nagr_map,args->maux->magr_map,args->maux->agr_map);
+            int k_src = 0;
+            for (i=0; i<line->n_allele; i++)
+            {
+                for (j=0; j<=i; j++)
+                {
+                    args->maux->agr_map[k_src] = bcf_alleles2gt(als->map[i],als->map[j]);
+                    k_src++;
+                }
+            }
+            rule->block_size = bcf_alleles2gt(args->maux->nout_als-1,args->maux->nout_als-1)+1;
+        }
+    }
+    else
+    {
+        if ( rule->nblocks>1 && ret!=rule->block_size )
+            error("Mismatch in number of values for INFO/%s at %s:%"PRId64"\n", rule->hdr_tag,bcf_seqname(hdr,line),(int64_t) line->pos+1);
+        rule->block_size = ret;
+        args->maux->nagr_map = 0;
+    }
+
+    #define BRANCH(src_type_t,dst_type_t,set_missing) { \
+        src_type_t *src = (src_type_t *) args->maux->tmp_arr; \
+        hts_expand0(dst_type_t,(rule->nvals+rule->block_size),rule->mvals,rule->vals); \
+        dst_type_t *dst = (dst_type_t *) rule->vals + rule->nvals; \
+        rule->nvals += rule->block_size; \
+        if ( !args->maux->nagr_map ) \
+        { \
+            for (i=0; i<ret; i++) dst[i] = src[i]; \
+        } \
+        else \
+        { \
+            for (i=0; i<rule->block_size; i++) set_missing; \
+            for (i=0; i<ret; i++) dst[args->maux->agr_map[i]] = src[i]; \
+        } \
+    }
+    switch (rule->type) {
+        case BCF_HT_INT:  BRANCH(int, int32_t, dst[i] = bcf_int32_missing); break;
+        case BCF_HT_REAL: BRANCH(float, float, bcf_float_set_missing(dst[i])); break;
+        default: error("TODO: %s:%d .. type=%d\n", __FILE__,__LINE__, rule->type);
+    }
+    #undef BRANCH
+
+    return 1;
+}
+
+int bcf_hdr_sync(bcf_hdr_t *h);
+
+void merge_headers(bcf_hdr_t *hw, const bcf_hdr_t *hr, const char *clash_prefix, int force_samples)
+{
+    // header lines
+    hw = bcf_hdr_merge(hw, hr);
+
+    // samples
+    int i;
+    for (i=0; i<bcf_hdr_nsamples(hr); i++)
+    {
+        char *rmme = NULL, *name = hr->samples[i];
+        while ( bcf_hdr_id2int(hw, BCF_DT_SAMPLE, name)!=-1 )
+        {
+            // there is a sample with the same name
+            if ( !force_samples ) error("Error: Duplicate sample names (%s), use --force-samples to proceed anyway.\n", name);
+
+            // Resolve conflicting samples names. For example, replace:
+            //  A + A       with    A,2:A
+            //  A,2:A + A   with    A,2:A,2:2:A
+
+            int len = strlen(name) + strlen(clash_prefix) + 1;
+            char *tmp = (char*) malloc(sizeof(char)*(len+1));
+            sprintf(tmp,"%s:%s",clash_prefix,name);
+            free(rmme);
+            rmme = name = tmp;
+        }
+        bcf_hdr_add_sample(hw,name);
+        free(rmme);
+    }
+}
+
+void debug_als(char **als, int nals)
+{
+    int k; for (k=0; k<nals; k++) fprintf(stderr,"%s ", als[k]);
+    fprintf(stderr,"\n");
+}
+
+/**
+ * normalize_alleles() - create smallest possible representation of the alleles
+ * @als:    alleles to be merged, first is REF (rw)
+ * @nals:   number of $a alleles
+ *
+ * Best explained on an example:
+ *      In:  REF=GTTT  ALT=GTT
+ *      Out: REF=GT    ALT=G
+ *
+ * Note: the als array will be modified
+ */
+void normalize_alleles(char **als, int nals)
+{
+    if ( !als[0][1] ) return;   // ref is 1base long, we're done
+
+    int j, i = 1, done = 0;
+    int *lens = (int*) malloc(sizeof(int)*nals);
+    for (j=0; j<nals; j++) lens[j] = strlen(als[j]);
+
+    while ( i<lens[0] )
+    {
+        for (j=1; j<nals; j++)
+        {
+            if ( i>=lens[j] ) done = 1;
+            if ( als[j][lens[j]-i] != als[0][lens[0]-i] ) { done = 1; break; }
+        }
+        if ( done ) break;
+        i++;
+    }
+    if ( i>1 )
+    {
+        i--;
+        als[0][lens[0]-i] = 0;
+        for (j=1; j<nals; j++) als[j][lens[j]-i] = 0;
+    }
+    free(lens);
+}
+
+ /**
+ * merge_alleles() - merge two REF,ALT records, $a and $b into $b.
+ * @a:      alleles to be merged, first is REF
+ * @na:     number of $a alleles
+ * @map:    map from the original $a indexes to new $b indexes (0-based)
+ * @b:      alleles to be merged, the array will be expanded as required
+ * @nb:     number of $b alleles
+ * @mb:     size of $b
+ *
+ * Returns NULL on error or $b expanded to incorporate $a alleles and sets
+ * $map. Best explained on an example:
+ *      In:     REF   ALT
+ *           a: ACG,  AC,A    (1bp and 2bp deletion)
+ *           b: ACGT, A       (3bp deletion)
+ *      Out:
+ *           b: ACGT, A,ACT,AT (3bp, 1bp and 2bp deletion)
+ *           map: 0,2,3
+ * Here the mapping from the original $a alleles to the new $b alleles is 0->0,
+ * 1->2, and 2->3.
+ */
+char **merge_alleles(char **a, int na, int *map, char **b, int *nb, int *mb)
+{
+    // reference allele never changes
+    map[0] = 0;
+
+    int i,j;
+    int rla = !a[0][1] ? 1 : strlen(a[0]);
+    int rlb = !b[0][1] ? 1 : strlen(b[0]);
+
+    // the most common case: same SNPs
+    if ( na==2 && *nb==2 && rla==1 && rlb==1 && a[1][0]==b[1][0] && !a[1][1] && !b[1][1] )
+    {
+        map[1] = 1;
+        return b;
+    }
+
+    // Sanity check: reference prefixes must be identical
+    if ( strncmp(a[0],b[0],rla<rlb?rla:rlb) )
+    {
+        if ( strncasecmp(a[0],b[0],rla<rlb?rla:rlb) )
+        {
+            fprintf(stderr, "The REF prefixes differ: %s vs %s (%d,%d)\n", a[0],b[0],rla,rlb);
+            return NULL;
+        }
+        // Different case, change to uppercase
+        for (i=0; i<na; i++)
+        {
+            int len = strlen(a[i]);
+            for (j=0; j<len; j++) a[i][j] = toupper(a[i][j]);
+        }
+        for (i=0; i<*nb; i++)
+        {
+            int len = strlen(b[i]);
+            for (j=0; j<len; j++) b[i][j] = toupper(b[i][j]);
+        }
+    }
+
+    int n = *nb + na;
+    hts_expand0(char*,n,*mb,b);
+
+    // $b alleles need expanding
+    if ( rla>rlb )
+    {
+        for (i=0; i<*nb; i++)
+        {
+            if ( b[i][0]=='<' ) continue;   // symbolic allele, do not modify
+            if ( b[i][0]=='*' ) continue;   // overlapping deletion (*), do not modify
+            int l = strlen(b[i]);
+            b[i] = (char*) realloc(b[i],l+rla-rlb+1);
+            memcpy(b[i]+l,a[0]+rlb,rla-rlb+1);
+        }
+    }
+
+    // now check if the $a alleles are present and if not add them
+    for (i=1; i<na; i++)
+    {
+        int const_ai = 1;
+        char *ai;
+        if ( rlb>rla && a[i][0]!='<' && a[i][0]!='*' )  // $a alleles need expanding and not a symbolic allele or *
+        {
+            int l = strlen(a[i]);
+            ai = (char*) malloc(l+rlb-rla+1);
+            memcpy(ai,a[i],l);
+            memcpy(ai+l,b[0]+rla,rlb-rla+1);
+            const_ai = 0;
+        }
+        else
+            ai = a[i];
+
+        for (j=1; j<*nb; j++)
+            if ( !strcasecmp(ai,b[j]) ) break;
+
+        if ( j<*nb ) // $b already has the same allele
+        {
+            map[i] = j;
+            if ( !const_ai ) free(ai);
+            continue;
+        }
+        // new allele
+        map[i] = *nb;
+        b[*nb] = const_ai ? strdup(ai) : ai;
+        (*nb)++;
+    }
+    return b;
+}
+
+maux_t *maux_init(args_t *args)
+{
+    bcf_srs_t *files = args->files;
+    maux_t *ma = (maux_t*) calloc(1,sizeof(maux_t));
+    ma->n      = files->nreaders;
+    ma->files  = files;
+    int i, n_smpl = 0;
+    for (i=0; i<ma->n; i++)
+        n_smpl += bcf_hdr_nsamples(files->readers[i].header);
+    ma->nout_smpl = n_smpl;
+    assert( n_smpl==bcf_hdr_nsamples(args->out_hdr) );
+    if ( args->do_gvcf )
+    {
+        ma->gvcf = (gvcf_aux_t*) calloc(ma->n,sizeof(gvcf_aux_t));  // -Walloc-size-larger-than gives a harmless warning caused by signed integer ma->n
+        for (i=0; i<ma->n; i++)
+            ma->gvcf[i].line = bcf_init1();
+    }
+    ma->smpl_ploidy = (int*) calloc(n_smpl,sizeof(int));
+    ma->smpl_nGsize = (int*) malloc(n_smpl*sizeof(int));
+    ma->buf = (buffer_t*) calloc(ma->n,sizeof(buffer_t));
+    for (i=0; i<ma->n; i++)
+        ma->buf[i].rid = -1;
+    ma->str = (kstring_t*) calloc(n_smpl,sizeof(kstring_t));
+    if ( args->local_alleles )
+    {
+        ma->laa = (int32_t*)malloc(sizeof(*ma->laa)*ma->nout_smpl*(1+args->local_alleles));
+        ma->pl2prob = (double*)malloc(PL2PROB_MAX*sizeof(*ma->pl2prob));
+        for (i=0; i<PL2PROB_MAX; i++)
+            ma->pl2prob[i] = pow(10,-0.1*i);
+    }
+    return ma;
+}
+void maux_destroy(maux_t *ma)
+{
+    int i,j;
+    for (i=0; i<ma->nout_smpl; i++) free(ma->str[i].s);
+    free(ma->str);
+    for (i=0; i<ma->mals; i++)
+    {
+        free(ma->als[i]);
+        ma->als[i] = NULL;
+    }
+    for (i=0; i<ma->n; i++) // for each reader
+    {
+        for (j=0; j<ma->buf[i].mrec; j++)  // for each buffered line
+            free(ma->buf[i].rec[j].map);
+        free(ma->buf[i].rec);
+    }
+    free(ma->buf);
+    if ( ma->gvcf )
+    {
+        for (i=0; i<ma->n; i++) bcf_destroy(ma->gvcf[i].line);
+        free(ma->gvcf);
+    }
+    for (i=0; i<ma->mAGR_info; i++)
+        free(ma->AGR_info[i].buf);
+    free(ma->agr_map);
+    free(ma->AGR_info);
+    if (ma->ntmp_arr) free(ma->tmp_arr);
+    if (ma->nfmt_map) free(ma->fmt_map);
+    // ma->inf freed in bcf_destroy1
+    for (i=0; i<ma->mals; i++) free(ma->als[i]);
+    if (ma->mout_als) free(ma->out_als);
+    free(ma->als);
+    free(ma->cnt);
+    free(ma->smpl_ploidy);
+    free(ma->smpl_nGsize);
+    free(ma->chr);
+    free(ma->laa);
+    free(ma->tmpi);
+    free(ma->k2k);
+    free(ma->tmpd);
+    free(ma->pl2prob);
+    free(ma);
+}
+void maux_expand1(buffer_t *buf, int size)
+{
+    if ( buf->mrec < size )
+    {
+        hts_expand0(maux1_t,size,buf->mrec,buf->rec);
+        buf->mrec = size;
+    }
+}
+void maux_reset(maux_t *ma, int *rid_tab)
+{
+    int i,j;
+    for (i=0; i<ma->n; i++) maux_expand1(&ma->buf[i],ma->files->readers[i].nbuffer+1);
+    for (i=0; i<ma->ncnt; i++) ma->cnt[i] = 0;
+    for (i=0; i<ma->mals; i++)
+    {
+        free(ma->als[i]);
+        ma->als[i] = NULL;
+    }
+    const char *chr = NULL;
+    ma->nals  = 0;
+    ma->pos   = -1;
+    for (i=0; i<ma->n; i++)
+    {
+        if ( !bcf_sr_has_line(ma->files,i) ) continue;
+        bcf1_t *line = bcf_sr_get_line(ma->files,i);
+        bcf_hdr_t *hdr = bcf_sr_get_header(ma->files,i);
+        chr = bcf_seqname(hdr,line);
+        ma->pos = line->pos;
+        break;
+    }
+    int new_chr = 0;
+    if ( chr && (!ma->chr || strcmp(ma->chr,chr)) )
+    {
+        free(ma->chr);
+        ma->chr = strdup(chr);
+        new_chr = 1;
+    }
+    for (i=0; i<ma->n; i++)
+    {
+        bcf_hdr_t *hdr = bcf_sr_get_header(ma->files,i);
+        if (new_chr)
+            rid_tab[i] = bcf_hdr_name2id(hdr,chr);
+
+        ma->buf[i].rid = rid_tab[i];
+        ma->buf[i].beg = bcf_sr_has_line(ma->files,i) ? 0 : 1;
+        for (j=ma->buf[i].beg; j<=ma->files->readers[i].nbuffer; j++)
+        {
+            ma->buf[i].rec[j].skip = 0;
+            bcf1_t *line = ma->files->readers[i].buffer[j];
+            if ( line->rid!=ma->buf[i].rid || line->pos!=ma->pos ) break;
+        }
+        ma->buf[i].end = j;
+        ma->buf[i].cur = -1;
+        if ( ma->buf[i].beg < ma->buf[i].end )
+        {
+            ma->buf[i].lines = ma->files->readers[i].buffer;
+            if ( ma->gvcf ) ma->gvcf[i].active = 0;     // gvcf block cannot overlap with the next record
+        }
+        if ( new_chr && ma->gvcf ) ma->gvcf[i].active = 0;  // make sure to close active gvcf block on new chr
+    }
+}
+void maux_debug(maux_t *ma, int ir, int ib)
+{
+    printf("[%d,%d]\t", ir,ib);
+    int i;
+    for (i=0; i<ma->nals; i++)
+    {
+        printf(" %s [%d]", ma->als[i], ma->cnt[i]);
+    }
+    printf("\n");
+}
+
+void merge_chrom2qual(args_t *args, bcf1_t *out)
+{
+    bcf_srs_t *files = args->files;
+    bcf_hdr_t *out_hdr = args->out_hdr;
+
+    int i, ret;
+    khiter_t kitr;
+    strdict_t *tmph = args->tmph;
+    kh_clear(strdict, tmph);
+    kstring_t *tmps = &args->tmps;
+    tmps->l = 0;
+
+    maux_t *ma = args->maux;
+    int *al_idxs = (int*) calloc(ma->nals,sizeof(int));
+    bcf_float_set_missing(out->qual);
+
+    // CHROM, POS, ID, QUAL
+    out->pos = -1;
+    for (i=0; i<files->nreaders; i++)
+    {
+        bcf1_t *line = maux_get_line(args, i);
+        if ( !line ) continue;
+        bcf_unpack(line, BCF_UN_ALL);
+
+        bcf_sr_t *reader = &files->readers[i];
+        bcf_hdr_t *hdr = reader->header;
+
+        // not all maux alleles are always used, mark the ones we'll need
+        int j;
+        for (j=1; j<line->n_allele; j++)
+        {
+            int irec = ma->buf[i].cur;
+            al_idxs[ ma->buf[i].rec[irec].map[j] ] = 1;
+        }
+
+        // position
+        if ( out->pos==-1 )
+        {
+            const char *chr = hdr->id[BCF_DT_CTG][line->rid].key;
+            out->rid = bcf_hdr_name2id(out_hdr, chr);
+            if ( strcmp(chr,out_hdr->id[BCF_DT_CTG][out->rid].key) ) error("Uh\n");
+            out->pos = line->pos;
+        }
+
+        // ID
+        if ( line->d.id[0]!='.' || line->d.id[1] )
+        {
+            kitr = kh_get(strdict, tmph, line->d.id);
+            if ( kitr == kh_end(tmph) )
+            {
+                if ( tmps->l ) kputc(';', tmps);
+                kputs(line->d.id, tmps);
+                kh_put(strdict, tmph, line->d.id, &ret);
+            }
+        }
+
+        // set QUAL to the max qual value. Not exactly correct, but good enough for now
+        if ( !bcf_float_is_missing(line->qual) )
+        {
+            if ( bcf_float_is_missing(out->qual) || out->qual < line->qual ) out->qual = line->qual;
+        }
+    }
+
+    // set ID
+    if ( !tmps->l ) kputs(".", tmps);
+    bcf_update_id(out_hdr, out, tmps->s);
+
+    // set alleles
+    ma->nout_als = 0;
+    for (i=1; i<ma->nals; i++)
+    {
+        if ( !al_idxs[i] ) continue;
+        ma->nout_als++;
+
+        // Adjust the indexes, the allele map could be created for multiple collapsed records,
+        //  some of which might be unused for this output line
+        int ir, j;
+        for (ir=0; ir<files->nreaders; ir++)
+        {
+            bcf1_t *line = maux_get_line(args,ir);
+            if ( !line ) continue;
+            for (j=1; j<line->n_allele; j++)
+            {
+                int irec = ma->buf[ir].cur;
+                if ( ma->buf[ir].rec[irec].map[j]==i ) ma->buf[ir].rec[irec].map[j] = ma->nout_als;
+            }
+        }
+    }
+    // Expand the arrays and realloc the alleles string. Note that all alleles are in a single allocated block.
+    ma->nout_als++;
+    hts_expand0(char*, ma->nout_als, ma->mout_als, ma->out_als);
+    int k = 0;
+    for (i=0; i<ma->nals; i++)
+        if ( i==0 || al_idxs[i] ) ma->out_als[k++] = strdup(ma->als[i]);
+    assert( k==ma->nout_als );
+    normalize_alleles(ma->out_als, ma->nout_als);
+    bcf_update_alleles(out_hdr, out, (const char**) ma->out_als, ma->nout_als);
+    free(al_idxs);
+    for (i=0; i<ma->nout_als; i++) free(ma->out_als[i]);
+}
+
+void merge_filter(args_t *args, bcf1_t *out)
+{
+    bcf_srs_t *files = args->files;
+    bcf_hdr_t *out_hdr = args->out_hdr;
+
+    int i, ret;
+    if ( args->filter_logic == FLT_LOGIC_REMOVE )
+    {
+        for (i=0; i<files->nreaders; i++)
+        {
+            bcf1_t *line = maux_get_line(args, i);
+            if ( !line ) continue;
+            bcf_sr_t *reader = &files->readers[i];
+            bcf_hdr_t *hdr = reader->header;
+            if ( bcf_has_filter(hdr, line, "PASS") ) break;
+        }
+        if ( i<files->nreaders )
+        {
+            int flt_id = bcf_hdr_id2int(out_hdr, BCF_DT_ID, "PASS");
+            bcf_add_filter(out_hdr, out, flt_id);
+            return;
+        }
+    }
+
+    khiter_t kitr;
+    strdict_t *tmph = args->tmph;
+    kh_clear(strdict, tmph);
+
+    out->d.n_flt = 0;
+    for (i=0; i<files->nreaders; i++)
+    {
+        bcf1_t *line = maux_get_line(args, i);
+        if ( !line ) continue;
+
+        bcf_sr_t *reader = &files->readers[i];
+        bcf_hdr_t *hdr = reader->header;
+
+        int k;
+        for (k=0; k<line->d.n_flt; k++)
+        {
+            const char *flt = hdr->id[BCF_DT_ID][line->d.flt[k]].key;
+            kitr = kh_get(strdict, tmph, flt);
+            if ( kitr == kh_end(tmph) )
+            {
+                int id = bcf_hdr_id2int(out_hdr, BCF_DT_ID, flt);
+                if ( id==-1 ) error("Error: The filter is not defined in the header: %s\n", flt);
+                hts_expand(int,out->d.n_flt+1,out->d.m_flt,out->d.flt);
+                out->d.flt[out->d.n_flt] = id;
+                out->d.n_flt++;
+                kh_put(strdict, tmph, flt, &ret);
+            }
+        }
+    }
+    // Check if PASS is not mixed with other filters
+    if ( out->d.n_flt>1 )
+    {
+        int id = bcf_hdr_id2int(out_hdr, BCF_DT_ID, "PASS");
+        for (i=0; i<out->d.n_flt; i++)
+            if ( out->d.flt[i]==id ) break;
+        if ( i<out->d.n_flt )
+        {
+            out->d.n_flt--;
+            for (; i<out->d.n_flt; i++) out->d.flt[i] = out->d.flt[i+1];
+        }
+    }
+}
+
+static void bcf_info_set_id(bcf1_t *line, bcf_info_t *info, int id, kstring_t *tmp_str)
+{
+    uint8_t *ptr = info->vptr - info->vptr_off;
+    bcf_dec_typed_int1(ptr, &ptr);
+
+    tmp_str->l = 0;
+    bcf_enc_int1(tmp_str, id);
+
+    if ( tmp_str->l == ptr - info->vptr + info->vptr_off )
+    {
+        // the new id is represented with the same number of bytes
+        memcpy(info->vptr - info->vptr_off, tmp_str->s, tmp_str->l);
+        return;
+    }
+
+    kputsn_(ptr, info->vptr - ptr, tmp_str);
+    info->vptr_off = tmp_str->l;
+    kputsn_(info->vptr, info->len << bcf_type_shift[info->type], tmp_str);
+
+    info->vptr = (uint8_t*) tmp_str->s + info->vptr_off;
+    tmp_str->s = NULL;
+    tmp_str->m = 0;
+    tmp_str->l = 0;
+}
+
+/*
+ *  copy_string_field() - copy a comma-separated field
+ *  @param src:     source string
+ *  @param isrc:    index of the field to copy
+ *  @param src_len: length of source string (excluding the terminating \0)
+ *  @param dst:     destination kstring (must be initialized with missing values, e.g. as ".")
+ *  @param idst:    index of the destination field
+ */
+int copy_string_field(char *src, int isrc, int src_len, kstring_t *dst, int idst)
+{
+    int ith_src = 0, start_src = 0;    // i-th field in src string
+    while ( ith_src<isrc && start_src<src_len )
+    {
+        if ( src[start_src]==',' ) { ith_src++; }
+        start_src++;
+    }
+    if ( ith_src!=isrc ) return -1; // requested field not found
+    int end_src = start_src;
+    while ( end_src<src_len && src[end_src] && src[end_src]!=',' ) end_src++;
+
+    int nsrc_cpy = end_src - start_src;     // number of chars to copy (excluding \0)
+    if ( nsrc_cpy==1 && src[start_src]=='.' ) return 0;   // don't write missing values, dst is already initialized
+
+    int ith_dst = 0, start_dst = 0;
+    while ( ith_dst<idst && start_dst<dst->l )
+    {
+        if ( dst->s[start_dst]==',' ) { ith_dst++; }
+        start_dst++;
+    }
+    if ( ith_dst!=idst ) return -2;
+    int end_dst = start_dst;
+    while ( end_dst<dst->l && dst->s[end_dst]!=',' ) end_dst++;
+
+    if ( end_dst - start_dst>1 || dst->s[start_dst]!='.' ) return 0;   // do not overwrite non-empty values
+
+    // Now start_dst and end_dst are indexes to the destination memory area
+    // which needs to be replaced with nsrc_cpy
+    // source bytes, end_dst points just after.
+    int ndst_shift = nsrc_cpy - (end_dst - start_dst);
+    int ndst_move  = dst->l - end_dst + 1;  // how many bytes must be moved (including \0)
+    if ( ndst_shift )
+    {
+        ks_resize(dst, dst->l + ndst_shift + 1);    // plus \0
+        memmove(dst->s+end_dst+ndst_shift, dst->s+end_dst, ndst_move);
+    }
+    memcpy(dst->s+start_dst, src+start_src, nsrc_cpy);
+    dst->l += ndst_shift;
+    return 0;
+}
+
+static void merge_AGR_info_tag(bcf_hdr_t *hdr, bcf1_t *line, bcf_info_t *info, int len, maux1_t *als, AGR_info_t *agr)
+{
+    int i;
+    if ( !agr->nbuf )
+    {
+        if ( info->type==BCF_BT_INT8 || info->type==BCF_BT_INT16 || info->type==BCF_BT_INT32 || info->type==BCF_BT_FLOAT )
+        {
+            agr->nbuf = 4 * agr->nvals;
+            hts_expand(uint8_t,agr->nbuf,agr->mbuf,agr->buf);
+            if ( info->type!=BCF_BT_FLOAT )
+            {
+                int32_t *tmp = (int32_t*) agr->buf;
+                for (i=0; i<agr->nvals; i++) tmp[i] = bcf_int32_missing;
+            }
+            else
+            {
+                float *tmp = (float*) agr->buf;
+                for (i=0; i<agr->nvals; i++) bcf_float_set_missing(tmp[i]);
+            }
+        }
+        else if ( info->type==BCF_BT_CHAR )
+        {
+            kstring_t tmp; tmp.l = 0; tmp.m = agr->mbuf; tmp.s = (char*)agr->buf;
+            kputc('.',&tmp);
+            for (i=1; i<agr->nvals; i++) kputs(",.",&tmp);
+            agr->mbuf = tmp.m; agr->nbuf = tmp.l; agr->buf = (uint8_t*)tmp.s;
+        }
+        else
+            error("Not ready for type [%d]: %s at %"PRId64"\n", info->type,agr->hdr_tag,(int64_t) line->pos+1);
+    }
+
+    if ( info->type==BCF_BT_INT8 || info->type==BCF_BT_INT16 || info->type==BCF_BT_INT32 || info->type==BCF_BT_FLOAT )
+    {
+        if ( len==BCF_VL_A || len==BCF_VL_R )
+        {
+            int ifrom = len==BCF_VL_A ? 1 : 0;
+            #define BRANCH(type_t, is_missing, is_vector_end, out_type_t) { \
+                type_t *src = (type_t *) info->vptr; \
+                out_type_t *tgt = (out_type_t *) agr->buf; \
+                int iori, inew; \
+                for (iori=ifrom; iori<line->n_allele; iori++) \
+                { \
+                    if ( is_vector_end ) break; \
+                    if ( is_missing ) continue; \
+                    inew = als->map[iori] - ifrom; \
+                    tgt[inew] = *src; \
+                    src++; \
+                } \
+            }
+            switch (info->type) {
+                case BCF_BT_INT8:  BRANCH(int8_t,  *src==bcf_int8_missing,  *src==bcf_int8_vector_end,  int); break;
+                case BCF_BT_INT16: BRANCH(int16_t, *src==bcf_int16_missing, *src==bcf_int16_vector_end, int); break;
+                case BCF_BT_INT32: BRANCH(int32_t, *src==bcf_int32_missing, *src==bcf_int32_vector_end, int); break;
+                case BCF_BT_FLOAT: BRANCH(float,   bcf_float_is_missing(*src), bcf_float_is_vector_end(*src), float); break;
+                default: fprintf(stderr,"TODO: %s:%d .. info->type=%d\n", __FILE__,__LINE__, info->type); exit(1);
+            }
+            #undef BRANCH
+        }
+        else
+        {
+            #define BRANCH(type_t, is_missing, is_vector_end, out_type_t) { \
+                type_t *src = (type_t *) info->vptr; \
+                out_type_t *tgt = (out_type_t *) agr->buf; \
+                int iori,jori, inew,jnew; \
+                for (iori=0; iori<line->n_allele; iori++) \
+                { \
+                    inew = als->map[iori]; \
+                    for (jori=0; jori<=iori; jori++) \
+                    { \
+                        jnew = als->map[jori]; \
+                        int kori = iori*(iori+1)/2 + jori; \
+                        if ( is_vector_end ) break; \
+                        if ( is_missing ) continue; \
+                        int knew = inew>jnew ? inew*(inew+1)/2 + jnew : jnew*(jnew+1)/2 + inew; \
+                        tgt[knew] = src[kori]; \
+                    } \
+                    if ( jori<=iori ) break; \
+                } \
+            }
+            switch (info->type) {
+                case BCF_BT_INT8:  BRANCH(int8_t,  src[kori]==bcf_int8_missing,  src[kori]==bcf_int8_vector_end,  int); break;
+                case BCF_BT_INT16: BRANCH(int16_t, src[kori]==bcf_int16_missing, src[kori]==bcf_int16_vector_end, int); break;
+                case BCF_BT_INT32: BRANCH(int32_t, src[kori]==bcf_int32_missing, src[kori]==bcf_int32_vector_end, int); break;
+                case BCF_BT_FLOAT: BRANCH(float,   bcf_float_is_missing(src[kori]), bcf_float_is_vector_end(src[kori]), float); break;
+                default: fprintf(stderr,"TODO: %s:%d .. info->type=%d\n", __FILE__,__LINE__, info->type); exit(1);
+            }
+            #undef BRANCH
+        }
+    }
+    else
+    {
+        kstring_t tmp; tmp.l = agr->nbuf; tmp.m = agr->mbuf; tmp.s = (char*)agr->buf;
+        if ( len==BCF_VL_A || len==BCF_VL_R )
+        {
+            int iori, ifrom = len==BCF_VL_A ? 1 : 0;
+            for (iori=ifrom; iori<line->n_allele; iori++)
+            {
+                int ret = copy_string_field((char*)info->vptr, iori-ifrom, info->len, &tmp, als->map[iori]-ifrom);
+                if ( ret )
+                    error("Error at %s:%"PRId64": wrong number of fields in %s?\n", bcf_seqname(hdr,line),(int64_t) line->pos+1,agr->hdr_tag);
+            }
+        }
+        else
+        {
+            int iori,jori, inew,jnew;
+            for (iori=0; iori<line->n_allele; iori++)
+            {
+                inew = als->map[iori];
+                for (jori=0; jori<=iori; jori++)
+                {
+                    jnew = als->map[jori];
+                    int kori = iori*(iori+1)/2 + jori;
+                    int knew = bcf_alleles2gt(inew,jnew);
+                    int ret  = copy_string_field((char*)info->vptr, kori, info->len, &tmp, knew);
+                    if ( ret )
+                        error("Error at %s:%"PRId64": wrong number of fields in %s?\n", bcf_seqname(hdr,line),(int64_t) line->pos+1,agr->hdr_tag);
+                }
+            }
+        }
+        agr->mbuf = tmp.m; agr->nbuf = tmp.l; agr->buf = (uint8_t*)tmp.s;
+    }
+}
+
+void merge_info(args_t *args, bcf1_t *out)
+{
+    bcf_srs_t *files = args->files;
+    bcf_hdr_t *out_hdr = args->out_hdr;
+
+    int i, j, ret;
+    khiter_t kitr;
+    strdict_t *tmph = args->tmph;
+    kh_clear(strdict, tmph);
+
+    maux_t *ma = args->maux;
+    ma->nAGR_info = 0;
+    out->n_info   = 0;
+    info_rules_reset(args);
+    for (i=0; i<files->nreaders; i++)
+    {
+        bcf1_t *line = maux_get_line(args,i);
+        if ( !line ) continue;
+        int irec = ma->buf[i].cur;
+        bcf_sr_t *reader = &files->readers[i];
+        bcf_hdr_t *hdr = reader->header;
+        for (j=0; j<line->n_info; j++)
+        {
+            bcf_info_t *inf = &line->d.info[j];
+
+            const char *key = hdr->id[BCF_DT_ID][inf->key].key;
+            // AC and AN are done in merge_format() after genotypes are done
+            if (!args->keep_AC_AN &&
+                (key[0] == 'A'
+                  && (key[1] == 'C' || key[1] == 'N')
+                  && key[2] == 0))
+                continue;
+
+            int id = bcf_hdr_id2int(out_hdr, BCF_DT_ID, key);
+            if ( id==-1 ) error("Error: The INFO field is not defined in the header: %s\n", key);
+
+            kitr = kh_get(strdict, tmph, key);  // have we seen the tag in one of the readers?
+            int len = bcf_hdr_id2length(hdr,BCF_HL_INFO,inf->key);
+            if ( args->nrules )
+            {
+                info_rule_t *rule = (info_rule_t*) bsearch(key, args->rules, args->nrules, sizeof(*args->rules), info_rules_comp_key);
+                if ( rule )
+                {
+                    maux1_t *als = ( len==BCF_VL_A || len==BCF_VL_G || len==BCF_VL_R ) ? &ma->buf[i].rec[irec] : NULL;
+                    if ( info_rules_add_values(args, hdr, line, rule, als, len) ) continue;
+                }
+            }
+
+            // Todo: Number=AGR tags should use the newer info_rules_* functions (info_rules_merge_first to be added)
+            // and merge_AGR_info_tag to be made obsolete.
+            if ( len==BCF_VL_A || len==BCF_VL_G || len==BCF_VL_R  ) // Number=R,G,A requires special treatment
+            {
+                if ( kitr == kh_end(tmph) )
+                {
+                    // seeing this key for the first time
+                    ma->nAGR_info++;
+                    hts_expand0(AGR_info_t,ma->nAGR_info,ma->mAGR_info,ma->AGR_info);
+                    kitr = kh_put(strdict, tmph, key, &ret);
+                    kh_val(tmph,kitr) = ma->nAGR_info - 1;
+                    ma->AGR_info[ma->nAGR_info-1].hdr_tag = key;
+                    ma->AGR_info[ma->nAGR_info-1].type  = bcf_hdr_id2type(hdr,BCF_HL_INFO,inf->key);
+                    ma->AGR_info[ma->nAGR_info-1].nbuf  = 0;    // size of the buffer
+                    switch (len)
+                    {
+                        case BCF_VL_A: ma->AGR_info[ma->nAGR_info-1].nvals = ma->nout_als - 1; break;
+                        case BCF_VL_G: ma->AGR_info[ma->nAGR_info-1].nvals = bcf_alleles2gt(ma->nout_als-1,ma->nout_als-1)+1; break;
+                        case BCF_VL_R: ma->AGR_info[ma->nAGR_info-1].nvals = ma->nout_als; break;
+                    }
+                }
+                kitr = kh_get(strdict, tmph, key);
+                int idx = kh_val(tmph, kitr);
+                if ( idx<0 ) error("Error occurred while processing INFO tag \"%s\" at %s:%"PRId64"\n", key,bcf_seqname(hdr,line),(int64_t) line->pos+1);
+                merge_AGR_info_tag(hdr, line,inf,len,&ma->buf[i].rec[irec],&ma->AGR_info[idx]);
+                continue;
+            }
+
+            if ( kitr == kh_end(tmph) )
+            {
+                // Seeing this key for the first time.  Although quite hacky,
+                // this is faster than anything else given the data structures..
+
+                hts_expand0(bcf_info_t,out->n_info+1,out->d.m_info,out->d.info);
+                out->d.info[out->n_info].key  = id;
+                out->d.info[out->n_info].type = inf->type;
+                out->d.info[out->n_info].len  = inf->len;
+                out->d.info[out->n_info].v1.i = inf->v1.i;
+                out->d.info[out->n_info].v1.f = inf->v1.f;
+                out->d.info[out->n_info].vptr_off  = inf->vptr_off;
+                out->d.info[out->n_info].vptr_len  = inf->vptr_len;
+                out->d.info[out->n_info].vptr_free = 1;
+                out->d.info[out->n_info].vptr = (uint8_t*) malloc(inf->vptr_len+inf->vptr_off);
+                memcpy(out->d.info[out->n_info].vptr,inf->vptr-inf->vptr_off, inf->vptr_len+inf->vptr_off);
+                out->d.info[out->n_info].vptr += inf->vptr_off;
+                if ( (args->output_type & FT_BCF) && id!=bcf_hdr_id2int(hdr, BCF_DT_ID, key) )
+                    bcf_info_set_id(out, &out->d.info[out->n_info], id, &args->tmps);
+                out->d.shared_dirty |= BCF1_DIRTY_INF;
+                out->n_info++;
+                kitr = kh_put(strdict, tmph, key, &ret);
+                kh_val(tmph,kitr) = -(out->n_info-1);   // arbitrary negative value
+            }
+        }
+    }
+    for (i=0; i<args->nrules; i++)
+        args->rules[i].merger(args->out_hdr, out, &args->rules[i]);
+    for (i=0; i<ma->nAGR_info; i++)
+    {
+        AGR_info_t *agr = &ma->AGR_info[i];
+        bcf_update_info(out_hdr,out,agr->hdr_tag,agr->buf,agr->nvals,agr->type);
+    }
+}
+
+void update_AN_AC(bcf_hdr_t *hdr, bcf1_t *line)
+{
+    int32_t an = 0, *tmp = (int32_t*) malloc(sizeof(int)*line->n_allele);
+    int ret = bcf_calc_ac(hdr, line, tmp, BCF_UN_FMT);
+    if ( ret>0 )
+    {
+        int i;
+        for (i=0; i<line->n_allele; i++) an += tmp[i];
+        bcf_update_info_int32(hdr, line, "AN", &an, 1);
+        bcf_update_info_int32(hdr, line, "AC", tmp+1, line->n_allele-1);
+    }
+    free(tmp);
+}
+
+static inline int max_used_gt_ploidy(bcf_fmt_t *fmt, int nsmpl)
+{
+    int i,j, max_ploidy = 0;
+
+    #define BRANCH(type_t, vector_end) { \
+        type_t *ptr  = (type_t*) fmt->p; \
+        for (i=0; i<nsmpl; i++) \
+        { \
+            for (j=0; j<fmt->n; j++) \
+                if ( ptr[j]==vector_end ) break; \
+            if ( j==fmt->n ) \
+            { \
+                /* all fields were used */ \
+                if ( max_ploidy < j ) max_ploidy = j; \
+                break; \
+            } \
+            if ( max_ploidy < j ) max_ploidy = j; \
+            ptr += fmt->n; \
+        } \
+    }
+    switch (fmt->type)
+    {
+        case BCF_BT_INT8:  BRANCH(int8_t,   bcf_int8_vector_end); break;
+        case BCF_BT_INT16: BRANCH(int16_t, bcf_int16_vector_end); break;
+        case BCF_BT_INT32: BRANCH(int32_t, bcf_int32_vector_end); break;
+        default: error("Unexpected case: %d\n", fmt->type);
+    }
+    #undef BRANCH
+    return max_ploidy;
+}
+
+// Sets ma->laa to local indexes relevant for each sample or missing/vector_end.
+// The indexes are with respect to the source indexes and must be translated as
+// the very last step.
+void init_local_alleles(args_t *args, bcf1_t *out, int ifmt_PL)
+{
+    bcf_srs_t *files = args->files;
+    maux_t *ma = args->maux;
+    int i,j,k,l, ismpl = 0, nlaa = 0;
+    static int warned = 0;
+
+    hts_expand(double,out->n_allele,ma->ntmpd,ma->tmpd); // allele probabilities
+    hts_expand(int,out->n_allele,ma->ntmpi,ma->tmpi);    // indexes of the sorted probabilities
+
+    // Let map[] be the mapping from src to output idx. Then k2k[] is mapping from src allele idxs to src allele idxs
+    // reordered so that if i<j then map[k2k[i]] < map[k2k[j]]
+    hts_expand(int,out->n_allele,ma->nk2k,ma->k2k);
+
+    // Determine local alleles: either take all that are present in the reader or use PL to determine the best
+    // subset for each sample. The alleles must be listed in the order of the alleles in the output file.
+    for (i=0; i<files->nreaders; i++)
+    {
+        bcf_sr_t *reader = &files->readers[i];
+        bcf_hdr_t *hdr = reader->header;
+        bcf_fmt_t *fmt_ori = ma->fmt_map[files->nreaders*ifmt_PL+i];
+        bcf1_t *line = maux_get_line(args, i);
+        int nsmpl = bcf_hdr_nsamples(hdr);
+        if ( line )
+        {
+            if ( nlaa < line->n_allele - 1 )
+                nlaa = line->n_allele - 1 <= args->local_alleles ? line->n_allele - 1 : args->local_alleles;
+
+            for (j=0; j<line->n_allele; j++) ma->k2k[j] = j;
+
+            if ( line->n_allele <= args->local_alleles + 1 )
+            {
+                // sort to the output order, insertion sort, ascending
+                int *map = ma->buf[i].rec[ma->buf[i].cur].map;
+                int *k2k = ma->k2k;
+                int tmp;
+                for (k=1; k<line->n_allele; k++)
+                    for (l=k; l>0 && map[k2k[l]] < map[k2k[l-1]]; l--)
+                        tmp = k2k[l], k2k[l] = k2k[l-1], k2k[l-1] = tmp;
+
+                // fewer than the allowed number of alleles, use all alleles from this file
+                for (j=0; j<nsmpl; j++)
+                {
+                    int32_t *ptr = ma->laa + (1+args->local_alleles)*ismpl;
+                    for (k=0; k<line->n_allele; k++) ptr[k] = k2k[k];
+                    for (; k<=args->local_alleles; k++) ptr[k] = bcf_int32_vector_end;
+                    ismpl++;
+                }
+                continue;
+            }
+        }
+        if ( !line || !fmt_ori )
+        {
+            // no values, fill in missing values
+            for (j=0; j<nsmpl; j++)
+            {
+                int32_t *ptr = ma->laa + (1+args->local_alleles)*ismpl;
+                ptr[0] = bcf_int32_missing;
+                for (k=1; k<=args->local_alleles; k++) ptr[k] = bcf_int32_vector_end;
+                ismpl++;
+            }
+            continue;
+        }
+
+        // there are more alternate alleles in the input files than is allowed on output, need to subset
+        if ( ifmt_PL==-1 )
+        {
+            if ( !warned )
+                fprintf(stderr,"Warning: local alleles are determined from FORMAT/PL but the tag is missing, cannot apply --local-alleles\n");
+            warned = 1;
+            ma->nlaa = 0;
+            return;
+        }
+
+        if ( !IS_VL_G(hdr, fmt_ori->id) ) error("FORMAT/PL must be defined as Number=G\n");
+        if ( 2*fmt_ori->n != line->n_allele*(line->n_allele+1) ) error("Todo: haploid PL to LPL\n");
+
+        int *map = ma->buf[i].rec[ma->buf[i].cur].map;
+        double *allele_prob = ma->tmpd;
+        int *idx = ma->tmpi;
+        #define BRANCH(src_type_t, src_is_missing, src_is_vector_end, pl2prob_idx) { \
+            src_type_t *src = (src_type_t*) fmt_ori->p; \
+            for (j=0; j<nsmpl; j++) \
+            { \
+                for (k=0; k<line->n_allele; k++) allele_prob[k] = 0; \
+                for (k=0; k<line->n_allele; k++) \
+                    for (l=0; l<=k; l++) \
+                    { \
+                        if ( src_is_missing || src_is_vector_end ) { src++; continue; } \
+                        double prob = ma->pl2prob[pl2prob_idx]; \
+                        allele_prob[k] += prob; \
+                        allele_prob[l] += prob; \
+                        src++; \
+                    } \
+                /* insertion sort by allele probability, descending order, with the twist that REF (idx=0) always comes first */ \
+                allele_prob++; idx[0] = -1; idx++; /* keep REF first */ \
+                int si,sj,tmp; \
+                for (si=0; si<line->n_allele-1; si++) idx[si] = si; \
+                for (si=1; si<line->n_allele-1; si++) \
+                    for (sj=si; sj>0 && allele_prob[idx[sj]] > allele_prob[idx[sj-1]]; sj--) \
+                        tmp = idx[sj], idx[sj] = idx[sj-1], idx[sj-1] = tmp; \
+                /*for debugging only: test order*/ \
+                for (si=1; si<line->n_allele-1; si++) \
+                    assert( allele_prob[idx[si-1]] >= allele_prob[idx[si]] ); \
+                allele_prob--; idx--; /* this was to keep REF first */ \
+                int32_t *ptr = ma->laa + (1+args->local_alleles)*ismpl; \
+                ptr[0] = 0; \
+                for (k=1; k<=args->local_alleles && k<line->n_allele; k++) ptr[k] = idx[k]+1; \
+                int kmax = k; \
+                for (; k<=args->local_alleles; k++) ptr[k] = bcf_int32_vector_end; \
+                /* insertion sort by indexes to the output order, ascending */ \
+                for (k=1; k<kmax; k++) \
+                    for (l=k; l>0 && map[ptr[l]] < map[ptr[l-1]]; l--) \
+                        tmp = ptr[l], ptr[l] = ptr[l-1], ptr[l-1] = tmp; \
+                ismpl++; \
+            } \
+        }
+        switch (fmt_ori->type)
+        {
+            case BCF_BT_INT8:  BRANCH( int8_t, *src==bcf_int8_missing,  *src==bcf_int8_vector_end,  *src); break;
+            case BCF_BT_INT16: BRANCH(int16_t, *src==bcf_int16_missing, *src==bcf_int16_vector_end, *src>=0 && *src<PL2PROB_MAX ? *src : PL2PROB_MAX-1); break;
+            case BCF_BT_INT32: BRANCH(int32_t, *src==bcf_int32_missing, *src==bcf_int32_vector_end, *src>=0 && *src<PL2PROB_MAX ? *src : PL2PROB_MAX-1); break;
+            default: error("Unexpected case: %d, PL\n", fmt_ori->type);
+        }
+        #undef BRANCH
+    }
+    ma->nlaa = nlaa;
+}
+
+void update_local_alleles(args_t *args, bcf1_t *out)
+{
+    bcf_srs_t *files = args->files;
+    maux_t *ma = args->maux;
+    int i,j,k,ismpl=0,nsamples = bcf_hdr_nsamples(args->out_hdr);
+    for (i=0; i<files->nreaders; i++)
+    {
+        int irec = ma->buf[i].cur;
+        bcf_sr_t *reader = &files->readers[i];
+        int nsmpl = bcf_hdr_nsamples(reader->header);
+        for (k=0; k<nsmpl; k++)
+        {
+            int32_t *src = ma->laa + ismpl*(1+args->local_alleles);
+            int32_t *dst = ma->laa + ismpl*ma->nlaa;
+            j = 0;
+            if ( irec>=0 )
+            {
+                for (; j<ma->nlaa; j++)
+                {
+                    if ( src[j+1]==bcf_int32_missing ) dst[j] = bcf_int32_missing;
+                    else if ( src[j+1]==bcf_int32_vector_end ) break;
+                    else
+                        dst[j] = ma->buf[i].rec[irec].map[src[j+1]];
+                }
+            }
+            if ( j==0 ) dst[j++] = bcf_int32_missing;
+            for (; j<ma->nlaa; j++) src[j] = bcf_int32_vector_end;
+            ismpl++;
+        }
+    }
+    bcf_update_format_int32(args->out_hdr, out, "LAA", ma->laa, nsamples*ma->nlaa);
+}
+
+void merge_GT(args_t *args, bcf_fmt_t **fmt_map, bcf1_t *out)
+{
+    bcf_srs_t *files = args->files;
+    bcf_hdr_t *out_hdr = args->out_hdr;
+    maux_t *ma = args->maux;
+    int i, ismpl = 0, nsamples = bcf_hdr_nsamples(out_hdr);
+    static int warned = 0;
+
+    int nsize = 0;
+    for (i=0; i<files->nreaders; i++)
+    {
+        bcf_fmt_t *fmt = fmt_map[i];
+        if ( !fmt ) continue;
+        int pld = max_used_gt_ploidy(fmt_map[i], bcf_hdr_nsamples(bcf_sr_get_header(args->files,i)));
+        if ( nsize < pld ) nsize = pld;
+    }
+    if ( nsize==0 ) nsize = 1;
+
+    size_t msize = sizeof(int32_t)*nsize*nsamples;
+    if ( msize > 2147483647 )
+    {
+        if ( !warned ) fprintf(stderr,"Warning: Too many genotypes at %s:%"PRId64", requires %zu bytes, skipping.\n", bcf_seqname(out_hdr,out),(int64_t) out->pos+1,msize);
+        warned = 1;
+        return;
+    }
+    if ( ma->ntmp_arr < msize )
+    {
+        ma->tmp_arr  = realloc(ma->tmp_arr, msize);
+        if ( !ma->tmp_arr ) error("Could not allocate %zu bytes\n",msize);
+        ma->ntmp_arr = msize;
+    }
+    memset(ma->smpl_ploidy,0,nsamples*sizeof(int));
+
+    int default_gt = args->missing_to_ref ? bcf_gt_unphased(0) : bcf_gt_missing;
+    for (i=0; i<files->nreaders; i++)
+    {
+        bcf_sr_t *reader = &files->readers[i];
+        bcf_hdr_t *hdr = reader->header;
+        bcf_fmt_t *fmt_ori = fmt_map[i];
+        int32_t *tmp  = (int32_t *) ma->tmp_arr + ismpl*nsize;
+        int irec = ma->buf[i].cur;
+
+        int j,k;
+        if ( !fmt_ori )
+        {
+            // missing values: assume maximum ploidy
+            for (j=0; j<bcf_hdr_nsamples(hdr); j++)
+            {
+                for (k=0; k<nsize; k++) { tmp[k] = default_gt; ma->smpl_ploidy[ismpl+j]++; }
+                tmp += nsize;
+            }
+            ismpl += bcf_hdr_nsamples(hdr);
+            continue;
+        }
+
+        #define BRANCH(type_t, vector_end) { \
+            type_t *p_ori  = (type_t*) fmt_ori->p; \
+            if ( !ma->buf[i].rec[irec].als_differ ) \
+            { \
+                /* the allele numbering is unchanged */ \
+                for (j=0; j<bcf_hdr_nsamples(hdr); j++) \
+                { \
+                    for (k=0; k<fmt_ori->n; k++) \
+                    { \
+                        if ( p_ori[k]==vector_end ) break; /* smaller ploidy */ \
+                        ma->smpl_ploidy[ismpl+j]++; \
+                        if ( bcf_gt_is_missing(p_ori[k]) ) tmp[k] = 0; /* missing allele */ \
+                        else tmp[k] = p_ori[k]; \
+                    } \
+                    for (; k<nsize; k++) tmp[k] = bcf_int32_vector_end; \
+                    tmp += nsize; \
+                    p_ori += fmt_ori->n; \
+                } \
+                ismpl += bcf_hdr_nsamples(hdr); \
+                continue; \
+            } \
+            /* allele numbering needs to be changed */ \
+            for (j=0; j<bcf_hdr_nsamples(hdr); j++) \
+            { \
+                for (k=0; k<fmt_ori->n; k++) \
+                { \
+                    if ( p_ori[k]==vector_end ) break; /* smaller ploidy */ \
+                    ma->smpl_ploidy[ismpl+j]++; \
+                    if ( bcf_gt_is_missing(p_ori[k]) ) tmp[k] = 0; /* missing allele */ \
+                    else \
+                    { \
+                        int al = (p_ori[k]>>1) - 1; \
+                        al = al<=0 ? al + 1 : ma->buf[i].rec[irec].map[al] + 1; \
+                        tmp[k] = (al << 1) | ((p_ori[k])&1); \
+                    } \
+                } \
+                for (; k<nsize; k++) tmp[k] = bcf_int32_vector_end; \
+                tmp += nsize; \
+                p_ori += fmt_ori->n; \
+            } \
+            ismpl += bcf_hdr_nsamples(hdr); \
+        }
+        switch (fmt_ori->type)
+        {
+            case BCF_BT_INT8: BRANCH(int8_t,   bcf_int8_vector_end); break;
+            case BCF_BT_INT16: BRANCH(int16_t, bcf_int16_vector_end); break;
+            case BCF_BT_INT32: BRANCH(int32_t, bcf_int32_vector_end); break;
+            default: error("Unexpected case: %d\n", fmt_ori->type);
+        }
+        #undef BRANCH
+    }
+    bcf_update_format_int32(out_hdr, out, "GT", (int32_t*)ma->tmp_arr, nsamples*nsize);
+}
+
+void merge_format_string(args_t *args, const char *key, bcf_fmt_t **fmt_map, bcf1_t *out, int length, int nsize)
+{
+    bcf_srs_t *files = args->files;
+    bcf_hdr_t *out_hdr = args->out_hdr;
+    maux_t *ma = args->maux;
+    int i,j, nsamples = bcf_hdr_nsamples(out_hdr);
+    static int warned = 0;
+
+    // initialize empty strings, a dot for each value, e.g. ".,.,."
+    int nmax = 0;
+    for (i=0; i<nsamples; i++)
+    {
+        kstring_t *str = &ma->str[i];
+        if ( length==BCF_VL_FIXED || length==BCF_VL_VAR )
+        {
+            str->l = 1;
+            ks_resize(str, str->l+1);
+            str->s[0] = '.';
+        }
+        else
+        {
+            str->l = nsize*2 - 1;
+            ks_resize(str, str->l+1);
+            str->s[0] = '.';
+            for (j=1; j<nsize; j++) str->s[j*2-1] = ',', str->s[j*2] = '.';
+        }
+        str->s[str->l] = 0;
+        if ( nmax < str->l ) nmax = str->l;
+    }
+
+    // fill in values for each sample
+    int ismpl = 0;
+    for (i=0; i<files->nreaders; i++)
+    {
+        bcf_sr_t *reader = &files->readers[i];
+        bcf_hdr_t *hdr = reader->header;
+        bcf_fmt_t *fmt_ori = fmt_map[i];
+        if ( !fmt_ori )
+        {
+            // the field is not present in this file
+            ismpl += bcf_hdr_nsamples(hdr);
+            continue;
+        }
+
+        bcf1_t *line = maux_get_line(args, i);
+        int irec = ma->buf[i].cur;
+        char *src = (char*) fmt_ori->p;
+
+        if ( length==BCF_VL_FIXED || length==BCF_VL_VAR || (line->n_allele==out->n_allele && !ma->buf[i].rec[irec].als_differ) )
+        {
+            // alleles unchanged, copy over
+            for (j=0; j<bcf_hdr_nsamples(hdr); j++)
+            {
+                kstring_t *str = &ma->str[ismpl++];
+                str->l = 0;
+                kputsn(src, fmt_ori->n, str);
+                if ( nmax < str->l ) nmax = str->l;
+                src += fmt_ori->n;
+            }
+            continue;
+        }
+        // NB, what is below is not the fastest way, copy_string_field() keeps
+        // finding the indexes repeatedly at multiallelic sites
+        if ( length==BCF_VL_A || length==BCF_VL_R )
+        {
+            int ifrom = length==BCF_VL_A ? 1 : 0;
+            for (j=0; j<bcf_hdr_nsamples(hdr); j++)
+            {
+                kstring_t *str = &ma->str[ismpl++];
+                int iori,inew;
+                for (iori=ifrom; iori<line->n_allele; iori++)
+                {
+                    inew = ma->buf[i].rec[irec].map[iori] - ifrom;
+                    int ret = copy_string_field(src, iori - ifrom, fmt_ori->size, str, inew);
+                    if ( ret<-1 ) error("[E::%s] fixme: internal error at %s:%"PRId64" .. %d\n",__func__,bcf_seqname(hdr,line),(int64_t) line->pos+1,ret);
+                }
+                if ( nmax < str->l ) nmax = str->l;
+                src += fmt_ori->size;
+            }
+            continue;
+        }
+        assert( length==BCF_VL_G );
+        error("[E::%s] Merging of Number=G FORMAT strings (in your case FORMAT/%s) is not supported yet, sorry!\n"
+              "Please open an issue on github if this feature is essential for you. However, note that using FORMAT strings is not\n"
+              "a good idea in general - it is slow to parse and does not compress well, it is better to use integer codes instead.\n"
+              "If you don't really need it, use `bcftools annotate -x` to remove the annotation before merging.\n", __func__,key);
+    }
+    // update the record
+    size_t msize = nsamples*nmax;
+    if ( msize > 2147483647 )
+    {
+        if ( !warned ) fprintf(stderr,"Warning: The row size is too big for FORMAT/%s at %s:%"PRId64", requires %zu bytes, skipping.\n", key,bcf_seqname(out_hdr,out),(int64_t) out->pos+1,msize);
+        warned = 1;
+        return;
+    }
+    if ( ma->ntmp_arr < msize )
+    {
+        ma->tmp_arr  = realloc(ma->tmp_arr, msize);
+        if ( !ma->tmp_arr ) error("Could not allocate %zu bytes\n",msize);
+        ma->ntmp_arr = msize;
+    }
+    char *tgt = (char*) ma->tmp_arr;
+    for (i=0; i<nsamples; i++)
+    {
+        memcpy(tgt, ma->str[i].s, ma->str[i].l);
+        if ( ma->str[i].l < nmax ) memset(tgt + ma->str[i].l, 0, nmax - ma->str[i].l);
+        tgt += nmax;
+    }
+    bcf_update_format_char(out_hdr, out, key, (float*)ma->tmp_arr, nsamples*nmax);
+}
+
+// Note: only diploid Number=G tags only for now
+void merge_localized_numberG_format_field(args_t *args, bcf_fmt_t **fmt_map, bcf1_t *out, int irdr)
+{
+    int i,j,k, nsamples = bcf_hdr_nsamples(args->out_hdr);
+    bcf_srs_t *files = args->files;
+    maux_t *ma = args->maux;
+    bcf_fmt_t *fmt = fmt_map[irdr];
+    const char *key = files->readers[irdr].header->id[BCF_DT_ID][fmt_map[irdr]->id].key;
+    size_t nsize = (ma->nlaa+1)*(ma->nlaa+2)/2;             // max number of Number=G localized fields
+    size_t msize = sizeof(float)>sizeof(int32_t) ? sizeof(float) : sizeof(int32_t);
+    msize *= nsamples*nsize;
+    if ( msize > 2147483647 )
+    {
+        static int warned = 0;
+        if ( !warned ) fprintf(stderr,"Warning: The row size is too big for FORMAT/%s at %s:%"PRId64", requires %zu bytes, skipping.\n", key,bcf_seqname(args->out_hdr,out),(int64_t) out->pos+1,msize);
+        warned = 1;
+        return;
+    }
+    if ( ma->ntmp_arr < msize )
+    {
+        ma->tmp_arr  = realloc(ma->tmp_arr, msize);
+        if ( !ma->tmp_arr ) error("Failed to allocate %zu bytes at %s:%"PRId64" for FORMAT/%s\n", msize,bcf_seqname(args->out_hdr,out),(int64_t) out->pos+1,key);
+        ma->ntmp_arr = msize;
+    }
+    int ismpl = 0;
+    for (i=0; i<files->nreaders; i++)
+    {
+        bcf_sr_t *reader = &files->readers[i];
+        bcf_hdr_t *hdr = reader->header;
+        bcf_fmt_t *fmt_ori = fmt_map[i];
+        bcf1_t *line = maux_get_line(args, i);
+        int nsmpl = bcf_hdr_nsamples(hdr);
+
+        if ( !fmt_ori )
+        {
+            // fill missing values
+            #define BRANCH(tgt_type_t, tgt_set_missing, tgt_set_vector_end) { \
+                for (j=0; j<nsmpl; j++) \
+                { \
+                    tgt_type_t *tgt = (tgt_type_t *) ma->tmp_arr + ismpl*nsize; \
+                    tgt_set_missing; \
+                    for (k=1; k<nsize; k++) { tgt++; tgt_set_vector_end; } \
+                    ismpl++; \
+                } \
+            }
+            switch (fmt->type)
+            {
+                case BCF_BT_INT8:  BRANCH(int32_t, *tgt=bcf_int32_missing, *tgt=bcf_int32_vector_end); break;
+                case BCF_BT_INT16: BRANCH(int32_t, *tgt=bcf_int32_missing, *tgt=bcf_int32_vector_end); break;
+                case BCF_BT_INT32: BRANCH(int32_t, *tgt=bcf_int32_missing, *tgt=bcf_int32_vector_end); break;
+                case BCF_BT_FLOAT: BRANCH(float, bcf_float_set_missing(*tgt), bcf_float_set_vector_end(*tgt)); break;
+                default: error("Unexpected case: %d, %s\n", fmt->type, key);
+            }
+            #undef BRANCH
+            continue;
+        }
+        if ( 2*fmt_ori->n!=line->n_allele*(line->n_allele+1) ) error("Todo: localization of missing or haploid Number=G tags\n");
+
+        // localize
+        #define BRANCH(tgt_type_t, src_type_t, src_is_missing, src_is_vector_end, tgt_set_missing, tgt_set_vector_end) { \
+            for (j=0; j<nsmpl; j++) \
+            { \
+                src_type_t *src = (src_type_t*) fmt_ori->p + j*fmt_ori->n; \
+                tgt_type_t *tgt = (tgt_type_t *) ma->tmp_arr + ismpl*nsize; \
+                int *laa = ma->laa + (1+args->local_alleles)*ismpl; \
+                int ii,ij,tgt_idx = 0; \
+                for (ii=0; ii<=ma->nlaa; ii++) \
+                { \
+                    if ( laa[ii]==bcf_int32_missing || laa[ii]==bcf_int32_vector_end ) break; \
+                    for (ij=0; ij<=ii; ij++) \
+                    { \
+                        int src_idx = bcf_alleles2gt(laa[ii],laa[ij]); \
+                        if ( src_is_missing ) tgt_set_missing; \
+                        else if ( src_is_vector_end ) break; \
+                        else tgt[tgt_idx] = src[src_idx]; \
+                        tgt_idx++; \
+                    } \
+                } \
+                if ( !tgt_idx ) { tgt_set_missing; tgt_idx++; } \
+                for (; tgt_idx<nsize; tgt_idx++) tgt_set_vector_end; \
+                ismpl++; \
+            } \
+        }
+        switch (fmt_ori->type)
+        {
+            case BCF_BT_INT8:  BRANCH(int32_t,  int8_t, src[src_idx]==bcf_int8_missing,  src[src_idx]==bcf_int8_vector_end,  tgt[tgt_idx]=bcf_int32_missing, tgt[tgt_idx]=bcf_int32_vector_end); break;
+            case BCF_BT_INT16: BRANCH(int32_t, int16_t, src[src_idx]==bcf_int16_missing, src[src_idx]==bcf_int16_vector_end, tgt[tgt_idx]=bcf_int32_missing, tgt[tgt_idx]=bcf_int32_vector_end); break;
+            case BCF_BT_INT32: BRANCH(int32_t, int32_t, src[src_idx]==bcf_int32_missing, src[src_idx]==bcf_int32_vector_end, tgt[tgt_idx]=bcf_int32_missing, tgt[tgt_idx]=bcf_int32_vector_end); break;
+            case BCF_BT_FLOAT: BRANCH(float, float, bcf_float_is_missing(src[src_idx]), bcf_float_is_vector_end(src[src_idx]), bcf_float_set_missing(tgt[tgt_idx]), bcf_float_set_vector_end(tgt[tgt_idx])); break;
+            default: error("Unexpected case: %d, %s\n", fmt_ori->type, key);
+        }
+        #undef BRANCH
+    }
+    args->tmps.l = 0;
+    kputc('L',&args->tmps);
+    kputs(key,&args->tmps);
+    if ( fmt_map[irdr]->type==BCF_BT_FLOAT )
+        bcf_update_format_float(args->out_hdr, out, args->tmps.s, (float*)ma->tmp_arr, nsamples*nsize);
+    else
+        bcf_update_format_int32(args->out_hdr, out, args->tmps.s, (int32_t*)ma->tmp_arr, nsamples*nsize);
+    ma->laa_dirty = 1;
+}
+void merge_localized_numberAR_format_field(args_t *args, bcf_fmt_t **fmt_map, bcf1_t *out, int irdr)
+{
+    int i,j,k, nsamples = bcf_hdr_nsamples(args->out_hdr);
+    bcf_srs_t *files = args->files;
+    maux_t *ma = args->maux;
+    bcf_fmt_t *fmt = fmt_map[irdr];
+    const char *key = files->readers[irdr].header->id[BCF_DT_ID][fmt->id].key;
+    size_t nsize = IS_VL_R(files->readers[irdr].header, fmt->id) ? ma->nlaa + 1 : ma->nlaa;
+    size_t msize = sizeof(float)>sizeof(int32_t) ? sizeof(float) : sizeof(int32_t);
+    msize *= nsamples*nsize;
+    if ( msize > 2147483647 )
+    {
+        static int warned = 0;
+        if ( !warned ) fprintf(stderr,"Warning: The row size is too big for FORMAT/%s at %s:%"PRId64", requires %zu bytes, skipping.\n", key,bcf_seqname(args->out_hdr,out),(int64_t) out->pos+1,msize);
+        warned = 1;
+        return;
+    }
+    if ( ma->ntmp_arr < msize )
+    {
+        ma->tmp_arr  = realloc(ma->tmp_arr, msize);
+        if ( !ma->tmp_arr ) error("Failed to allocate %zu bytes at %s:%"PRId64" for FORMAT/%s\n", msize,bcf_seqname(args->out_hdr,out),(int64_t) out->pos+1,key);
+        ma->ntmp_arr = msize;
+    }
+    int ismpl = 0, ibeg = IS_VL_R(files->readers[irdr].header, fmt->id) ? 0 : 1;;
+    for (i=0; i<files->nreaders; i++)
+    {
+        bcf_sr_t *reader = &files->readers[i];
+        bcf_hdr_t *hdr = reader->header;
+        bcf_fmt_t *fmt_ori = fmt_map[i];
+        int nsmpl = bcf_hdr_nsamples(hdr);
+
+        if ( !fmt_ori )
+        {
+            // fill missing values
+            #define BRANCH(tgt_type_t, tgt_set_missing, tgt_set_vector_end) { \
+                for (j=0; j<nsmpl; j++) \
+                { \
+                    tgt_type_t *tgt = (tgt_type_t *) ma->tmp_arr + ismpl*nsize; \
+                    tgt_set_missing; \
+                    for (k=1; k<nsize; k++) { tgt++; tgt_set_vector_end; } \
+                    ismpl++; \
+                } \
+            }
+            switch (fmt->type)
+            {
+                case BCF_BT_INT8:  BRANCH(int32_t, *tgt=bcf_int32_missing, *tgt=bcf_int32_vector_end); break;
+                case BCF_BT_INT16: BRANCH(int32_t, *tgt=bcf_int32_missing, *tgt=bcf_int32_vector_end); break;
+                case BCF_BT_INT32: BRANCH(int32_t, *tgt=bcf_int32_missing, *tgt=bcf_int32_vector_end); break;
+                case BCF_BT_FLOAT: BRANCH(float, bcf_float_set_missing(*tgt), bcf_float_set_vector_end(*tgt)); break;
+                default: error("Unexpected case: %d, %s\n", fmt->type, key);
+            }
+            #undef BRANCH
+            continue;
+        }
+
+        // localize
+        #define BRANCH(tgt_type_t, src_type_t, src_is_missing, src_is_vector_end, tgt_set_missing, tgt_set_vector_end) { \
+            for (j=0; j<nsmpl; j++) \
+            { \
+                src_type_t *src = (src_type_t*) fmt_ori->p + j*fmt_ori->n; \
+                tgt_type_t *tgt = (tgt_type_t *) ma->tmp_arr + ismpl*nsize; \
+                int *laa = ma->laa + (1+args->local_alleles)*ismpl; \
+                int ii,tgt_idx = 0; \
+                for (ii=ibeg; ii<=ma->nlaa; ii++) \
+                { \
+                    if ( laa[ii]==bcf_int32_missing || laa[ii]==bcf_int32_vector_end ) break; \
+                    int src_idx = laa[ii] - ibeg; \
+                    if ( src_is_missing ) tgt_set_missing; \
+                    else if ( src_is_vector_end ) break; \
+                    else tgt[tgt_idx] = src[src_idx]; \
+                    tgt_idx++; \
+                } \
+                if ( !tgt_idx ) { tgt_set_missing; tgt_idx++; } \
+                for (; tgt_idx<nsize; tgt_idx++) tgt_set_vector_end; \
+                ismpl++; \
+            } \
+        }
+        switch (fmt_ori->type)
+        {
+            case BCF_BT_INT8:  BRANCH(int32_t,  int8_t, src[src_idx]==bcf_int8_missing,  src[src_idx]==bcf_int8_vector_end,  tgt[tgt_idx]=bcf_int32_missing, tgt[tgt_idx]=bcf_int32_vector_end); break;
+            case BCF_BT_INT16: BRANCH(int32_t, int16_t, src[src_idx]==bcf_int16_missing, src[src_idx]==bcf_int16_vector_end, tgt[tgt_idx]=bcf_int32_missing, tgt[tgt_idx]=bcf_int32_vector_end); break;
+            case BCF_BT_INT32: BRANCH(int32_t, int32_t, src[src_idx]==bcf_int32_missing, src[src_idx]==bcf_int32_vector_end, tgt[tgt_idx]=bcf_int32_missing, tgt[tgt_idx]=bcf_int32_vector_end); break;
+            case BCF_BT_FLOAT: BRANCH(float, float, bcf_float_is_missing(src[src_idx]), bcf_float_is_vector_end(src[src_idx]), bcf_float_set_missing(tgt[tgt_idx]), bcf_float_set_vector_end(tgt[tgt_idx])); break;
+            default: error("Unexpected case: %d, %s\n", fmt_ori->type, key);
+        }
+        #undef BRANCH
+    }
+    args->tmps.l = 0;
+    kputc('L',&args->tmps);
+    kputs(key,&args->tmps);
+    if ( fmt_map[irdr]->type==BCF_BT_FLOAT )
+        bcf_update_format_float(args->out_hdr, out, args->tmps.s, (float*)ma->tmp_arr, nsamples*nsize);
+    else
+        bcf_update_format_int32(args->out_hdr, out, args->tmps.s, (int32_t*)ma->tmp_arr, nsamples*nsize);
+    ma->laa_dirty = 1;
+}
+void merge_format_field(args_t *args, bcf_fmt_t **fmt_map, bcf1_t *out)
+{
+    bcf_srs_t *files = args->files;
+    bcf_hdr_t *out_hdr = args->out_hdr;
+    maux_t *ma = args->maux;
+    int i, ismpl = 0, nsamples = bcf_hdr_nsamples(out_hdr);
+    static int warned = 0;
+
+    const char *key = NULL;
+    size_t nsize = 0, length = BCF_VL_FIXED;
+    int type = -1;
+    for (i=0; i<files->nreaders; i++)
+    {
+        if ( !maux_get_line(args,i) ) continue;
+        if ( !fmt_map[i] ) continue;
+        if ( !key ) key = files->readers[i].header->id[BCF_DT_ID][fmt_map[i]->id].key;
+        type = fmt_map[i]->type;
+        if ( IS_VL_G(files->readers[i].header, fmt_map[i]->id) )
+        {
+            length = BCF_VL_G;
+            nsize = out->n_allele*(out->n_allele + 1)/2;
+            break;
+        }
+        if ( IS_VL_A(files->readers[i].header, fmt_map[i]->id) )
+        {
+            length = BCF_VL_A;
+            nsize = out->n_allele - 1;
+            break;
+        }
+        if ( IS_VL_R(files->readers[i].header, fmt_map[i]->id) )
+        {
+            length = BCF_VL_R;
+            nsize = out->n_allele;
+            break;
+        }
+        if ( fmt_map[i]->n > nsize ) nsize = fmt_map[i]->n;
+    }
+    if ( ma->nlaa && length!=BCF_VL_FIXED )
+    {
+        if ( length==BCF_VL_G ) merge_localized_numberG_format_field(args,fmt_map,out,i);
+        else if ( length==BCF_VL_A || length==BCF_VL_R ) merge_localized_numberAR_format_field(args,fmt_map,out,i);
+        return;
+    }
+
+    if ( type==BCF_BT_CHAR )
+    {
+        merge_format_string(args, key, fmt_map, out, length, nsize);
+        return;
+    }
+
+    size_t msize = sizeof(float)>sizeof(int32_t) ? sizeof(float) : sizeof(int32_t);
+    msize *= nsamples*nsize;
+    if ( msize > 2147483647 )
+    {
+        if ( !warned ) fprintf(stderr,"Warning: The row size is too big for FORMAT/%s at %s:%"PRId64", requires %zu bytes, skipping.\n", key,bcf_seqname(out_hdr,out),(int64_t) out->pos+1,msize);
+        warned = 1;
+        return;
+    }
+    if ( ma->ntmp_arr < msize )
+    {
+        ma->tmp_arr  = realloc(ma->tmp_arr, msize);
+        if ( !ma->tmp_arr ) error("Failed to allocate %zu bytes at %s:%"PRId64" for FORMAT/%s\n", msize,bcf_seqname(args->out_hdr,out),(int64_t) out->pos+1,key);
+        ma->ntmp_arr = msize;
+    }
+
+    // Fill the temp array for all samples by collecting values from all files
+    for (i=0; i<files->nreaders; i++)
+    {
+        bcf_sr_t *reader = &files->readers[i];
+        bcf_hdr_t *hdr = reader->header;
+        bcf_fmt_t *fmt_ori = fmt_map[i];
+        bcf1_t *line = maux_get_line(args, i);
+        int irec = ma->buf[i].cur;
+
+        if ( fmt_ori )
+        {
+            type = fmt_ori->type;
+            int nals_ori = line->n_allele;
+            if ( length==BCF_VL_G )
+            {
+                // if all fields are missing then n==1 is valid
+                if ( fmt_ori->n!=1 && fmt_ori->n != nals_ori*(nals_ori+1)/2 && fmt_map[i]->n != nals_ori )
+                    error("Incorrect number of FORMAT/%s values at %s:%"PRId64", cannot merge. The tag is defined as Number=G, but found\n"
+                          "%d values and %d alleles. See also http://samtools.github.io/bcftools/howtos/FAQ.html#incorrect-nfields\n",
+                          key,bcf_seqname(args->out_hdr,out),(int64_t) out->pos+1,fmt_ori->n,nals_ori);
+            }
+            else if ( length==BCF_VL_A )
+            {
+                if ( fmt_ori->n!=1 && fmt_ori->n != nals_ori-1 )
+                    error("Incorrect number of FORMAT/%s values at %s:%"PRId64", cannot merge. The tag is defined as Number=A, but found\n"
+                          "%d values and %d alleles. See also http://samtools.github.io/bcftools/howtos/FAQ.html#incorrect-nfields\n",
+                          key,bcf_seqname(args->out_hdr,out),(int64_t) out->pos+1,fmt_ori->n,nals_ori);
+            }
+            else if ( length==BCF_VL_R )
+            {
+                if ( fmt_ori->n!=1 && fmt_ori->n != nals_ori )
+                    error("Incorrect number of FORMAT/%s values at %s:%"PRId64", cannot merge. The tag is defined as Number=R, but found\n"
+                          "%d values and %d alleles. See also http://samtools.github.io/bcftools/howtos/FAQ.html#incorrect-nfields\n",
+                          key,bcf_seqname(args->out_hdr,out),(int64_t) out->pos+1,fmt_ori->n,nals_ori);
+            }
+        }
+
+        // set the values
+        #define BRANCH(tgt_type_t, src_type_t, src_is_missing, src_is_vector_end, tgt_set_missing, tgt_set_vector_end) { \
+            int j, l, k; \
+            tgt_type_t *tgt = (tgt_type_t *) ma->tmp_arr + ismpl*nsize; \
+            if ( !fmt_ori ) \
+            { \
+                /* the field is not present in this file, set missing values */ \
+                for (j=0; j<bcf_hdr_nsamples(hdr); j++) \
+                { \
+                    tgt_set_missing; tgt++; for (l=1; l<nsize; l++) { tgt_set_vector_end; tgt++; } \
+                } \
+                ismpl += bcf_hdr_nsamples(hdr); \
+                continue; \
+            } \
+            src_type_t *src = (src_type_t*) fmt_ori->p; \
+            if ( (length!=BCF_VL_G && length!=BCF_VL_A && length!=BCF_VL_R) || (line->n_allele==out->n_allele && !ma->buf[i].rec[irec].als_differ) ) \
+            { \
+                /* alleles unchanged, copy over */ \
+                for (j=0; j<bcf_hdr_nsamples(hdr); j++) \
+                { \
+                    for (l=0; l<fmt_ori->n; l++) \
+                    { \
+                        if ( src_is_vector_end ) break; \
+                        else if ( src_is_missing ) tgt_set_missing; \
+                        else *tgt = *src; \
+                        tgt++; src++; \
+                    } \
+                    for (k=l; k<nsize; k++) { tgt_set_vector_end; tgt++; } \
+                    src += fmt_ori->n - l; \
+                } \
+                ismpl += bcf_hdr_nsamples(hdr); \
+                continue; \
+            } \
+            /* allele numbering needs to be changed */ \
+            if ( length==BCF_VL_G ) \
+            { \
+                /* Number=G tags */ \
+                for (j=0; j<bcf_hdr_nsamples(hdr); j++) \
+                { \
+                    tgt = (tgt_type_t *) ma->tmp_arr + (ismpl+j)*nsize; \
+                    src = (src_type_t*) fmt_ori->p + j*fmt_ori->n; \
+                    if ( (src_is_missing && fmt_ori->n==1) || (++src && src_is_vector_end) ) \
+                    { \
+                        /* tag with missing value "." */ \
+                        tgt_set_missing; \
+                        for (l=1; l<nsize; l++) { tgt++; tgt_set_vector_end; } \
+                        continue; \
+                    } \
+                    int ngsize = ma->smpl_ploidy[ismpl+j]==1 ? out->n_allele : out->n_allele*(out->n_allele + 1)/2; \
+                    for (l=0; l<ngsize; l++) { tgt_set_missing; tgt++; } \
+                    for (; l<nsize; l++) { tgt_set_vector_end; tgt++; } \
+                    if ( ma->smpl_ploidy[ismpl+j]==1 ) \
+                    { \
+                        /* Haploid */ \
+                        int iori, inew; \
+                        for (iori=0; iori<line->n_allele; iori++) \
+                        { \
+                            inew = ma->buf[i].rec[irec].map[iori]; \
+                            src = (src_type_t*) fmt_ori->p + j*fmt_ori->n + iori; \
+                            tgt = (tgt_type_t *) ma->tmp_arr + (ismpl+j)*nsize + inew; \
+                            if ( src_is_vector_end ) break; \
+                            if ( src_is_missing ) tgt_set_missing; \
+                            else *tgt = *src; \
+                        } \
+                    } \
+                    else \
+                    { \
+                        /* Diploid */ \
+                        int iori,jori, inew,jnew; \
+                        for (iori=0; iori<line->n_allele; iori++) \
+                        { \
+                            inew = ma->buf[i].rec[irec].map[iori]; \
+                            for (jori=0; jori<=iori; jori++) \
+                            { \
+                                jnew = ma->buf[i].rec[irec].map[jori]; \
+                                int kori = iori*(iori+1)/2 + jori; \
+                                int knew = inew>jnew ? inew*(inew+1)/2 + jnew : jnew*(jnew+1)/2 + inew; \
+                                src = (src_type_t*) fmt_ori->p + j*fmt_ori->n + kori; \
+                                tgt = (tgt_type_t *) ma->tmp_arr + (ismpl+j)*nsize + knew; \
+                                if ( src_is_vector_end ) \
+                                { \
+                                    iori = line->n_allele; \
+                                    break; \
+                                } \
+                                if ( src_is_missing ) tgt_set_missing; \
+                                else *tgt = *src; \
+                            } \
+                        } \
+                    } \
+                } \
+            } \
+            else \
+            { \
+                /* Number=A or Number=R tags */ \
+                int ifrom = length==BCF_VL_A ? 1 : 0; \
+                for (j=0; j<bcf_hdr_nsamples(hdr); j++) \
+                { \
+                    tgt = (tgt_type_t *) ma->tmp_arr + (ismpl+j)*nsize; \
+                    src = (src_type_t*) (fmt_ori->p + j*fmt_ori->size); \
+                    if ( (src_is_missing && fmt_ori->n==1) || (++src && src_is_vector_end) ) \
+                    { \
+                        /* tag with missing value "." */ \
+                        tgt_set_missing; \
+                        for (l=1; l<nsize; l++) { tgt++; tgt_set_vector_end; } \
+                        continue; \
+                    } \
+                    src = (src_type_t*) (fmt_ori->p + j*fmt_ori->size); \
+                    for (l=0; l<nsize; l++) { tgt_set_missing; tgt++; } \
+                    int iori,inew; \
+                    for (iori=ifrom; iori<line->n_allele; iori++) \
+                    { \
+                        inew = ma->buf[i].rec[irec].map[iori] - ifrom; \
+                        tgt = (tgt_type_t *) ma->tmp_arr + (ismpl+j)*nsize + inew; \
+                        if ( src_is_vector_end ) break; \
+                        if ( src_is_missing ) tgt_set_missing; \
+                        else *tgt = *src; \
+                        src++; \
+                    } \
+                } \
+            } \
+            ismpl += bcf_hdr_nsamples(hdr); \
+        }
+        switch (type)
+        {
+            case BCF_BT_INT8:  BRANCH(int32_t,  int8_t, *src==bcf_int8_missing,  *src==bcf_int8_vector_end,  *tgt=bcf_int32_missing, *tgt=bcf_int32_vector_end); break;
+            case BCF_BT_INT16: BRANCH(int32_t, int16_t, *src==bcf_int16_missing, *src==bcf_int16_vector_end, *tgt=bcf_int32_missing, *tgt=bcf_int32_vector_end); break;
+            case BCF_BT_INT32: BRANCH(int32_t, int32_t, *src==bcf_int32_missing, *src==bcf_int32_vector_end, *tgt=bcf_int32_missing, *tgt=bcf_int32_vector_end); break;
+            case BCF_BT_FLOAT: BRANCH(float, float, bcf_float_is_missing(*src), bcf_float_is_vector_end(*src), bcf_float_set_missing(*tgt), bcf_float_set_vector_end(*tgt)); break;
+            default: error("Unexpected case: %d, %s\n", type, key);
+        }
+        #undef BRANCH
+    }
+    if ( type==BCF_BT_FLOAT )
+        bcf_update_format_float(out_hdr, out, key, (float*)ma->tmp_arr, nsamples*nsize);
+    else
+        bcf_update_format_int32(out_hdr, out, key, (int32_t*)ma->tmp_arr, nsamples*nsize);
+}
+
+void merge_format(args_t *args, bcf1_t *out)
+{
+    bcf_srs_t *files = args->files;
+    bcf_hdr_t *out_hdr = args->out_hdr;
+    maux_t *ma = args->maux;
+    if ( !ma->nfmt_map )
+    {
+        ma->nfmt_map = 2;
+        ma->fmt_map  = (bcf_fmt_t**) calloc(ma->nfmt_map*files->nreaders, sizeof(bcf_fmt_t*));
+    }
+    else
+        memset(ma->fmt_map, 0, ma->nfmt_map*files->nreaders*sizeof(bcf_fmt_t**));
+
+    khiter_t kitr;
+    strdict_t *tmph = args->tmph;
+    kh_clear(strdict, tmph);
+    int i, j, ret, has_GT = 0, has_PL = -1, max_ifmt = 0; // max fmt index
+    for (i=0; i<files->nreaders; i++)
+    {
+        bcf1_t *line = maux_get_line(args,i);
+        if ( !line ) continue;
+        bcf_sr_t *reader = &files->readers[i];
+        bcf_hdr_t *hdr = reader->header;
+        for (j=0; j<line->n_fmt; j++)
+        {
+            // Wat this tag already seen?
+            bcf_fmt_t *fmt = &line->d.fmt[j];
+            const char *key = hdr->id[BCF_DT_ID][fmt->id].key;
+            kitr = kh_get(strdict, tmph, key);
+
+            int ifmt;
+            if ( kitr != kh_end(tmph) )
+                ifmt = kh_value(tmph, kitr);    // seen
+            else
+            {
+                // new FORMAT tag
+                if ( key[0]=='G' && key[1]=='T' && key[2]==0 ) { has_GT = 1; ifmt = 0; }
+                else
+                {
+                    ifmt = ++max_ifmt;
+                    if ( max_ifmt >= ma->nfmt_map )
+                    {
+                        ma->fmt_map = (bcf_fmt_t**) realloc(ma->fmt_map, sizeof(bcf_fmt_t*)*(max_ifmt+1)*files->nreaders);
+                        memset(ma->fmt_map+ma->nfmt_map*files->nreaders, 0, (max_ifmt-ma->nfmt_map+1)*files->nreaders*sizeof(bcf_fmt_t*));
+                        ma->nfmt_map = max_ifmt+1;
+                    }
+                    if ( key[0]=='P' && key[1]=='L' && key[2]==0  ) { has_PL = ifmt; }
+                }
+                kitr = kh_put(strdict, tmph, key, &ret);
+                kh_value(tmph, kitr) = ifmt;
+            }
+            ma->fmt_map[ifmt*files->nreaders+i] = fmt;
+        }
+        // Check if the allele numbering must be changed
+        int irec = ma->buf[i].cur;
+        for (j=1; j<line->n_allele; j++)
+            if ( ma->buf[i].rec[irec].map[j]!=j ) break;
+        ma->buf[i].rec[irec].als_differ = j==line->n_allele ? 0 : 1;
+    }
+
+    if ( args->local_alleles )
+    {
+        ma->laa_dirty = ma->nlaa = 0;
+        if ( out->n_allele > args->local_alleles + 1 ) init_local_alleles(args, out, has_PL);
+    }
+
+    out->n_sample = bcf_hdr_nsamples(out_hdr);
+    if ( has_GT )
+        merge_GT(args, ma->fmt_map, out);
+    if ( !args->keep_AC_AN )
+        update_AN_AC(out_hdr, out);
+
+    for (i=1; i<=max_ifmt; i++)
+        merge_format_field(args, &ma->fmt_map[i*files->nreaders], out);
+
+    if ( ma->laa_dirty )
+        update_local_alleles(args, out);
+
+    out->d.indiv_dirty = 1;
+}
+
+void gvcf_set_alleles(args_t *args)
+{
+    int i,k;
+    bcf_srs_t *files = args->files;
+    maux_t *maux = args->maux;
+    gvcf_aux_t *gaux = maux->gvcf;
+    for (i=0; i<maux->nals; i++)
+    {
+        free(maux->als[i]);
+        maux->als[i] = NULL;
+    }
+    maux->nals = 0;
+
+    for (i=0; i<files->nreaders; i++)
+    {
+        if ( !gaux[i].active ) continue;
+        bcf1_t *line = maux_get_line(args, i);
+        if ( !line ) continue;
+        int irec = maux->buf[i].cur;
+
+        hts_expand(int, line->n_allele, maux->buf[i].rec[irec].mmap, maux->buf[i].rec[irec].map);
+        if ( !maux->nals )    // first record, copy the alleles to the output
+        {
+            maux->nals = line->n_allele;
+            hts_expand0(char*, maux->nals, maux->mals, maux->als);
+            hts_expand0(int, maux->nals, maux->ncnt, maux->cnt);
+            for (k=0; k<maux->nals; k++)
+            {
+                if ( maux->als[k] ) free(maux->als[k]);
+                maux->als[k] = strdup(line->d.allele[k]);
+                maux->buf[i].rec[irec].map[k] = k;
+            }
+        }
+        else
+        {
+            maux->als = merge_alleles(line->d.allele, line->n_allele, maux->buf[i].rec[irec].map, maux->als, &maux->nals, &maux->mals);
+            if ( !maux->als )
+            {
+                bcf_hdr_t *hdr = bcf_sr_get_header(args->files,i);
+                error("Failed to merge alleles at %s:%"PRId64"\n",bcf_seqname(hdr,line),(int64_t) line->pos+1);
+            }
+        }
+    }
+}
+
+/*
+    Output staged gVCF blocks, end is the last position of the block. Assuming
+    gaux[i].active flags are set and maux_get_line returns correct lines.
+    Both start,end coordinates are 0-based.
+*/
+void gvcf_write_block(args_t *args, int start, int end)
+{
+    int i;
+    maux_t *maux = args->maux;
+    gvcf_aux_t *gaux = maux->gvcf;
+    assert(gaux);
+
+    // Update POS
+    int min = INT_MAX;  // the minimum active gVCF INFO/END (0-based)
+    char ref = 'N';
+    for (i=0; i<args->files->nreaders; i++)
+    {
+        if ( !gaux[i].active ) continue;
+        if ( ref=='N' && gaux[i].line->pos==start ) ref = gaux[i].line->d.allele[0][0];
+        gaux[i].line->pos = start;
+    }
+    for (i=0; i<args->files->nreaders; i++)
+    {
+        if ( !gaux[i].active ) continue;
+        if ( gaux[i].end < start )
+        {
+            gaux[i].active = 0;
+            maux->buf[i].cur = -1;
+            continue;
+        }
+        gaux[i].line->d.allele[0][0] = ref;
+        if ( min > gaux[i].end ) min = gaux[i].end;
+    }
+    // Check for valid gVCF blocks in this region
+    if ( min==INT_MAX ) // this probably should not happen
+    {
+    assert(0);
+        maux->gvcf_min = 0;
+        return;
+    }
+
+    bcf1_t *out = args->out_line;
+
+    gvcf_set_alleles(args);
+
+    // Merge the staged lines
+    merge_chrom2qual(args, out);
+    merge_filter(args, out);
+    merge_info(args, out);
+    merge_format(args, out);
+
+    if ( args->gvcf_fai && out->d.allele[0][0]=='N' )
+    {
+        int slen  = 0;
+        char *seq = faidx_fetch_seq(args->gvcf_fai,maux->chr,out->pos,out->pos,&slen);
+        if (slen)
+        {
+            out->d.allele[0][0] = seq[0];
+            free(seq);
+        }
+    }
+
+    // Update END boundary
+    if ( end > start )
+    {
+        end++;
+        bcf_update_info_int32(args->out_hdr, out, "END", &end, 1);
+    }
+    else
+        bcf_update_info_int32(args->out_hdr, out, "END", NULL, 0);
+    if ( bcf_write1(args->out_fh, args->out_hdr, out)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->output_fname);
+    bcf_clear1(out);
+
+
+    // Inactivate blocks which do not extend beyond END and find new gvcf_min
+    min = INT_MAX;
+    for (i=0; i<args->files->nreaders; i++)
+    {
+        if ( !gaux[i].active ) continue;
+        if ( gaux[i].end < end )
+        {
+            gaux[i].active = 0;
+            maux->buf[i].cur = -1;
+            continue;
+        }
+        // next min END position bigger than the current one
+        if ( maux->gvcf_min < gaux[i].end+1 && min > gaux[i].end+1 ) min = gaux[i].end + 1;
+    }
+    maux->gvcf_min = min==INT_MAX ? 0 : min;
+}
+
+/*
+    Flush staged gVCF blocks. Flush everything if there are no more lines
+    (done=1) or if there is a new chromosome. If still on the same chromosome,
+    all hanging blocks must be ended by creating new records:
+        A
+            1 END=10
+        B
+            3 END=7
+        C
+            3 END=5
+        out
+            1 END=2  A . .
+            3 END=5  A B C
+            6 END=7  A B .
+            8 END=10 A . .
+
+*/
+void gvcf_flush(args_t *args, int done)
+{
+    int i;
+    maux_t *maux = args->maux;
+
+    if ( !maux->chr ) return;   // first time here, nothing to flush
+
+    int flush_until = INT_MAX;
+    if ( !done )
+    {
+        // Get current position and chromosome
+        for (i=0; i<maux->n; i++)
+            if ( bcf_sr_has_line(maux->files,i) ) break;
+        bcf1_t *line = bcf_sr_get_line(maux->files,i);
+        bcf_hdr_t *hdr = bcf_sr_get_header(maux->files,i);
+
+        if ( !strcmp(maux->chr,bcf_seqname(hdr,line)) ) flush_until = line->pos;    // still on the same chr
+    }
+
+    // When called on a region, trim the blocks accordingly
+    int start = maux->gvcf_break>=0 ? maux->gvcf_break + 1 : maux->pos;     // the start of a new gvcf block to output
+    if ( args->regs )
+    {
+        int rstart = -1, rend = -1;
+        if ( regidx_overlap(args->regs,maux->chr,start,flush_until,args->regs_itr) )
+        {
+            // In case there are multiple regions, we treat them as one
+            rstart = args->regs_itr->beg;
+            while ( regitr_overlap(args->regs_itr) ) rend = args->regs_itr->end;
+        }
+        if ( rstart > start ) start = rstart;
+        if ( rend < flush_until ) flush_until = rend+1;
+    }
+
+    // output all finished blocks
+    while ( maux->gvcf_min && start < flush_until )
+    {
+        // does the block end before the new line or is it interrupted?
+        int tmp = maux->gvcf_min < flush_until ? maux->gvcf_min : flush_until;
+        if ( start > tmp-1 ) break;
+        gvcf_write_block(args,start,tmp-1); // gvcf_min is 1-based, passing 0-based coordinates
+        start = tmp;
+    }
+}
+
+static inline int is_gvcf_block(bcf1_t *line)
+{
+    if ( line->rlen<=1 ) return 0;
+    if ( strlen(line->d.allele[0])==line->rlen ) return 0;
+    if ( line->n_allele==1 ) return 1;
+
+    int i;
+    for (i=1; i<line->n_allele; i++)
+    {
+        if ( !strcmp(line->d.allele[i],"<*>") ) return 1;
+        if ( !strcmp(line->d.allele[i],"<NON_REF>") ) return 1;
+        if ( !strcmp(line->d.allele[i],"<X>") ) return 1;
+    }
+    return 0;
+}
+
+// Lines can come with any combination of variant types. We use a subset of types defined in vcf.h
+// but shift by two bits to account for VCF_REF defined as 0 (design flaw in vcf.h, my fault) and
+// to accommodate for VCF_GVCF_REF defined below
+static const int
+    snp_mask = (VCF_SNP<<2)|(VCF_MNP<<2),
+    indel_mask = VCF_INDEL<<2,
+    ins_mask = VCF_INS<<2,
+    del_mask = VCF_DEL<<2,
+    ref_mask = 2;
+
+/*
+    Check incoming lines for new gVCF blocks, set pointer to the current source
+    buffer (gvcf or readers).  In contrast to gvcf_flush, this function can be
+    called only after maux_reset as it relies on updated maux buffers.
+    The coordinate is 0-based
+*/
+void gvcf_stage(args_t *args, int pos)
+{
+    maux_t *maux = args->maux;
+    gvcf_aux_t *gaux = maux->gvcf;
+    bcf_srs_t *files = args->files;
+    int32_t *end = (int32_t*) maux->tmp_arr;
+    int i, nend = maux->ntmp_arr / sizeof(int32_t);
+
+    maux->gvcf_break = -1;
+    maux->gvcf_min = INT_MAX;
+    for (i=0; i<files->nreaders; i++)
+    {
+        if ( gaux[i].active && gaux[i].end < pos ) gaux[i].active = 0;
+        if ( gaux[i].active )
+        {
+            // gvcf block should not overlap with another record
+            if ( maux->gvcf_min > gaux[i].end+1 ) maux->gvcf_min = gaux[i].end + 1;
+            maux->buf[i].beg = 0;
+            maux->buf[i].end = 1;
+            maux->buf[i].cur = 0;
+            continue;
+        }
+
+        // Does any of the lines have END set? It is enough to check only the
+        // first line, there should be no duplicate records with END in gVCF
+
+        if ( maux->buf[i].beg==maux->buf[i].end ) continue; // no new record
+
+        int irec = maux->buf[i].beg;
+        bcf_hdr_t *hdr = bcf_sr_get_header(files, i);
+        bcf1_t *line = args->files->readers[i].buffer[irec];
+        int ret = is_gvcf_block(line) ? bcf_get_info_int32(hdr,line,"END",&end,&nend) : 0;
+        if ( ret==1 )
+        {
+            if ( end[0] == line->pos + 1 )  // POS and INFO/END are identical, treat as if a normal w/o INFO/END
+            {
+                maux->gvcf_break = line->pos;
+                continue;
+            }
+            if ( end[0] <= line->pos ) error("Error: Incorrect END at %s:%"PRId64" .. END=%d\n", bcf_seqname(hdr,line),(int64_t) line->pos+1,end[0]);
+
+            // END is set, this is a new gVCF block. Cache this line in gaux[i] and swap with
+            // an empty record: the gaux line must be kept until we reach its END.
+
+            gaux[i].active = 1;
+            gaux[i].end = end[0] - 1;
+            SWAP(bcf1_t*,args->files->readers[i].buffer[irec],gaux[i].line);
+            gaux[i].line->pos = pos;
+
+            maux->buf[i].lines = &gaux[i].line;
+            maux->buf[i].beg = 0;
+            maux->buf[i].end = 1;
+            maux->buf[i].cur = 0;
+
+            // Set the rid,pos of the swapped line in the buffer or else the
+            // synced reader will have a problem with the next line
+            //
+            args->files->readers[i].buffer[irec]->rid = maux->buf[i].rid;
+            args->files->readers[i].buffer[irec]->pos = maux->pos;
+
+            // Update block offsets
+            if ( maux->gvcf_min > gaux[i].end+1 ) maux->gvcf_min = gaux[i].end + 1;
+        }
+        else
+            maux->gvcf_break = line->pos;   // must break the gvcf block
+    }
+    maux->ntmp_arr = nend * sizeof(int32_t);
+    maux->tmp_arr  = end;
+    if ( maux->gvcf_min==INT_MAX ) maux->gvcf_min = 0;
+}
+
+
+void debug_buffers(FILE *fp, bcf_srs_t *files);
+void debug_buffer(FILE *fp, bcf_srs_t *files, int reader);
+
+/*
+    Flush all buffered and processed records with the same coordinate.
+    Note that synced reader discards buffer[0], so that needs to stay
+    untouched.
+*/
+void clean_buffer(args_t *args)
+{
+    maux_t *ma = args->maux;
+
+    int ir;
+    for (ir=0; ir<ma->n; ir++)
+    {
+        // Invalidate pointer to reader's buffer or else gvcf_flush will attempt
+        // to use the old lines via maux_get_line()
+        if ( ma->gvcf )
+        {
+            if ( ma->gvcf[ir].active )
+            {
+                if ( ma->pos >= ma->gvcf[ir].end )  ma->gvcf[ir].active = 0;
+                else if ( ma->buf[ir].cur==-1 ) ma->buf[ir].cur = ma->buf[ir].beg;  // re-activate interrupted gVCF block
+            }
+            if ( !ma->gvcf[ir].active ) ma->buf[ir].cur = -1;
+        }
+
+        bcf_sr_t *reader = bcf_sr_get_reader(args->files,ir);
+        if ( !reader->nbuffer ) continue;   // nothing to clean
+
+        bcf1_t **buf = reader->buffer;
+        if ( buf[1]->rid!=ma->buf[ir].rid || buf[1]->pos!=ma->pos ) continue;    // nothing to flush
+
+        int a = 1, b = 2;
+        while ( b<=reader->nbuffer && buf[b]->rid==ma->buf[ir].rid && buf[b]->pos==ma->pos ) b++;
+        // b now points to the first line we want to preserve
+        while ( b<=reader->nbuffer )
+        {
+            SWAP(bcf1_t*, buf[a], buf[b]);
+            a++; b++;
+        }
+        reader->nbuffer -= b-a;
+    }
+}
+
+void debug_maux(args_t *args)
+{
+    bcf_srs_t *files = args->files;
+    maux_t *maux = args->maux;
+    int j,k,l;
+
+    fprintf(stderr,"Alleles to merge at %d, nals=%d\n", maux->pos+1,maux->nals);
+    for (j=0; j<files->nreaders; j++)
+    {
+        bcf_sr_t *reader = &files->readers[j];
+        buffer_t *buf = &maux->buf[j];
+        fprintf(stderr," reader %d: ", j);
+        for (k=buf->beg; k<buf->end; k++)
+        {
+            if ( buf->rec[k].skip & SKIP_DONE ) continue;
+            bcf1_t *line = reader->buffer[k];
+            fprintf(stderr,"\t");
+            if ( buf->rec[k].skip ) fprintf(stderr,"[");  // this record will not be merged in this round
+            for (l=0; l<line->n_allele; l++)
+                fprintf(stderr,"%s%s", l==0?"":",", line->d.allele[l]);
+            if ( buf->rec[k].skip ) fprintf(stderr,"]");
+        }
+        fprintf(stderr,"\n");
+    }
+    fprintf(stderr," counts: ");
+    for (j=0; j<maux->nals; j++) fprintf(stderr,"%s   %dx %s", j==0?"":",",maux->cnt[j], maux->als[j]);
+    fprintf(stderr,"\n\n");
+}
+
+void debug_state(args_t *args)
+{
+    maux_t *maux = args->maux;
+    int i,j;
+    for (i=0; i<args->files->nreaders; i++)
+    {
+        fprintf(stderr,"reader %d:\tcur,beg,end=% d,%d,%d", i,maux->buf[i].cur,maux->buf[i].beg,maux->buf[i].end);
+        if ( maux->buf[i].cur >=0 )
+        {
+            bcf_hdr_t *hdr = bcf_sr_get_header(args->files,i);
+            const char *chr = bcf_hdr_id2name(hdr, maux->buf[i].rid);
+            fprintf(stderr,"\t");
+            for (j=maux->buf[i].beg; j<maux->buf[i].end; j++) fprintf(stderr," %s:%"PRId64,chr,(int64_t) maux->buf[i].lines[j]->pos+1);
+        }
+        fprintf(stderr,"\n");
+    }
+    fprintf(stderr,"gvcf_min=%d\n", args->maux->gvcf_min);
+    for (i=0; i<args->files->nreaders; i++)
+    {
+        fprintf(stderr,"reader %d:\tgvcf_active=%d", i,maux->gvcf[i].active);
+        if ( maux->gvcf[i].active ) fprintf(stderr,"\tpos,end=%"PRId64",%"PRId64, (int64_t) maux->gvcf[i].line->pos+1,(int64_t) maux->gvcf[i].end+1);
+        fprintf(stderr,"\n");
+    }
+    fprintf(stderr,"\n");
+}
+
+/*
+   Determine which line should be merged from which reader: go through all
+   readers and all buffered lines, expand REF,ALT and try to match lines with
+   the same ALTs.
+ */
+int can_merge(args_t *args)
+{
+    bcf_srs_t *files = args->files;
+    maux_t *maux = args->maux;
+    gvcf_aux_t *gaux = maux->gvcf;
+    char *id = NULL, ref = 'N';
+    int i,j,k, ntodo = 0;
+
+    for (i=0; i<maux->nals; i++)
+    {
+        free(maux->als[i]);
+        maux->als[i] = NULL;
+    }
+    maux->var_types = maux->nals = 0;
+
+    // this is only for the `-m none -g` mode, ensure that <*> lines come last
+    #define VCF_GVCF_REF 1
+
+    for (i=0; i<files->nreaders; i++)
+    {
+        buffer_t *buf = &maux->buf[i];
+
+        if ( gaux && gaux[i].active )
+        {
+            // skip readers with active gvcf blocks
+            buf->rec[buf->beg].skip = SKIP_DIFF;
+            continue;
+        }
+        for (j=buf->beg; j<buf->end; j++)
+        {
+            if ( buf->rec[j].skip & SKIP_DONE ) continue;
+
+            buf->rec[j].skip = SKIP_DIFF;
+            ntodo++;
+
+            bcf1_t *line = buf->lines[j];
+            if ( args->merge_by_id )
+                id = line->d.id;
+            else
+            {
+                int var_type = bcf_has_variant_types(line, VCF_ANY, bcf_match_overlap);
+                if (var_type < 0) error("bcf_has_variant_types() failed.");
+                if ( args->collapse==COLLAPSE_SNP_INS_DEL )
+                {
+                    // need to distinguish between ins and del so strip the VCF_INDEL flag
+                    var_type &= ~VCF_INDEL;
+                }
+                maux->var_types |= var_type ? var_type<<2 : 2;
+
+                // for the `-m none -g` mode
+                if ( args->collapse==COLLAPSE_NONE && args->do_gvcf && is_gvcf_block(line) )
+                    maux->var_types |= VCF_GVCF_REF;
+            }
+        }
+
+        // for gvcf: find out REF at this position
+        if ( buf->beg < buf->end && ref=='N' )
+            ref = buf->lines[buf->beg]->d.allele[0][0];
+    }
+    if ( !ntodo ) return 0;
+
+    // In this loop we select from each reader compatible candidate lines.
+    // (i.e. SNPs or indels). Go through all files and all lines at this
+    // position and normalize relevant alleles.
+    // REF-only sites may be associated with both SNPs and indels.
+    for (i=0; i<files->nreaders; i++)
+    {
+        bcf_sr_t *reader = &files->readers[i];
+        buffer_t *buf = &maux->buf[i];
+
+        if ( gaux && gaux[i].active )
+        {
+            gaux[i].line->d.allele[0][0] = ref;
+            gaux[i].line->pos = maux->pos;
+        }
+
+        for (j=buf->beg; j<buf->end; j++)
+        {
+            if ( buf->rec[j].skip & SKIP_DONE ) continue;
+
+            bcf1_t *line = buf->lines[j]; // ptr to reader's buffer or gvcf buffer
+
+            int line_type = bcf_has_variant_types(line, VCF_ANY, bcf_match_overlap);
+            if (line_type < 0) error("bcf_has_variant_types() failed.");
+            line_type = line_type ? line_type<<2 : 2;
+
+            // select relevant lines
+            if ( args->merge_by_id )
+            {
+                if ( strcmp(id,line->d.id) ) continue;
+            }
+            else
+            {
+                // when merging gVCF in -m none mode, make sure that gVCF blocks with the same POS as variant
+                // records come last, otherwise infinite loop is created (#1164)
+                if ( args->collapse==COLLAPSE_NONE && args->do_gvcf )
+                {
+                    if ( is_gvcf_block(line) && (maux->var_types & (~(VCF_GVCF_REF|2))) ) continue;
+                }
+                if ( args->collapse==COLLAPSE_NONE && maux->nals )
+                {
+                    // All alleles of the tested record must be present in the
+                    // selected maux record plus variant types must be the same
+                    if ( (maux->var_types & line_type) != line_type ) continue;
+                    if ( vcmp_set_ref(args->vcmp,maux->als[0],line->d.allele[0]) < 0 ) continue;   // refs not compatible
+                    for (k=1; k<line->n_allele; k++)
+                    {
+                        if ( vcmp_find_allele(args->vcmp,maux->als+1,maux->nals-1,line->d.allele[k])>=0 ) break;
+                    }
+                    if ( !(line_type&ref_mask) && k==line->n_allele ) continue;  // not a REF-only site and there is no matching allele
+                }
+                if ( !(args->collapse&COLLAPSE_ANY) )
+                {
+                    // Merge:
+                    //  - SNPs+SNPs+MNPs+REF if -m both,snps
+                    //  - indels+indels+REF  if -m both,indels, REF only if SNPs are not present
+                    //  - SNPs come first
+                    if ( line_type & (indel_mask|ins_mask|del_mask) )
+                    {
+                        if ( !(line_type&snp_mask) && maux->var_types&snp_mask ) continue;  // SNPs come first
+                        if ( args->do_gvcf && maux->var_types&ref_mask ) continue;  // never merge indels with gVCF blocks
+                    }
+                }
+            }
+            buf->rec[j].skip = 0;
+
+            hts_expand(int, line->n_allele, buf->rec[j].mmap, buf->rec[j].map);
+            if ( !maux->nals )    // first record, copy the alleles to the output
+            {
+                maux->nals = line->n_allele;
+                hts_expand0(char*, maux->nals, maux->mals, maux->als);
+                hts_expand0(int, maux->nals, maux->ncnt, maux->cnt);
+                for (k=0; k<maux->nals; k++)
+                {
+                    free(maux->als[k]);
+                    maux->als[k] = strdup(line->d.allele[k]);
+                    buf->rec[j].map[k] = k;
+                    maux->cnt[k] = 1;
+                }
+                continue;
+            }
+            // normalize alleles
+            maux->als = merge_alleles(line->d.allele, line->n_allele, buf->rec[j].map, maux->als, &maux->nals, &maux->mals);
+            if ( !maux->als ) error("Failed to merge alleles at %s:%"PRId64" in %s\n",maux->chr,(int64_t) line->pos+1,reader->fname);
+            hts_expand0(int, maux->nals, maux->ncnt, maux->cnt);
+            for (k=1; k<line->n_allele; k++)
+                maux->cnt[ buf->rec[j].map[k] ]++;    // how many times an allele appears in the files
+            maux->cnt[0]++;
+        }
+    }
+    return 1;
+}
+
+/*
+   Select records that have the same alleles; the input ordering of indels
+   must not matter. Multiple VCF lines can be emitted from this loop.
+   We expect only very few alleles and not many records with the same
+   position in the buffers, therefore the nested loops should not slow us
+   much.
+*/
+void stage_line(args_t *args)
+{
+    bcf_srs_t *files = args->files;
+    maux_t *maux = args->maux;
+
+    // debug_maux(args);
+
+    // take the most frequent allele present in multiple files, REF is skipped
+    int i,j,k,icnt = 1;
+    for (i=2; i<maux->nals; i++)
+        if ( maux->cnt[i] > maux->cnt[icnt] ) icnt = i;
+
+    int nout = 0;
+    for (i=0; i<files->nreaders; i++)
+    {
+        buffer_t *buf = &maux->buf[i];
+        buf->cur = -1;
+        if ( buf->beg >= buf->end ) continue;   // no lines in the buffer
+
+        // find lines with the same allele
+        for (j=buf->beg; j<buf->end; j++)
+        {
+            if ( buf->rec[j].skip ) continue;   // done or not compatible
+            if ( args->merge_by_id ) break;
+            if ( maux->nals==1 && buf->lines[j]->n_allele==1 ) break;   // REF-only record
+
+            for (k=0; k<buf->lines[j]->n_allele; k++)
+                if ( icnt==buf->rec[j].map[k] ) break;
+
+            if ( k<buf->lines[j]->n_allele ) break;
+        }
+        if ( j>=buf->end )
+        {
+            // no matching allele found in this file
+            if ( args->collapse==COLLAPSE_NONE ) continue;
+
+            for (j=buf->beg; j<buf->end; j++)
+            {
+                if ( buf->rec[j].skip ) continue;   // done or not compatible
+                if ( args->collapse&COLLAPSE_ANY ) break;   // anything can be merged
+                int line_type = bcf_has_variant_types(buf->lines[j], VCF_ANY, bcf_match_overlap);
+                if (line_type < 0) error("bcf_has_variant_types() failed.");
+                if ( maux->var_types&snp_mask && line_type&VCF_SNP && (args->collapse&COLLAPSE_SNPS) ) break;
+                if ( maux->var_types&indel_mask && line_type&VCF_INDEL && (args->collapse&COLLAPSE_INDELS) ) break;
+                if ( maux->var_types&ins_mask && line_type&VCF_INS && (args->collapse&COLLAPSE_SNP_INS_DEL) ) break;
+                if ( maux->var_types&del_mask && line_type&VCF_DEL && (args->collapse&COLLAPSE_SNP_INS_DEL) ) break;
+                if ( line_type==VCF_REF )
+                {
+                    if ( maux->var_types&snp_mask && (args->collapse&COLLAPSE_SNPS) ) break;
+                    if ( maux->var_types&indel_mask && (args->collapse&COLLAPSE_INDELS) ) break;
+                    if ( maux->var_types&ins_mask && (args->collapse&COLLAPSE_SNP_INS_DEL) ) break;
+                    if ( maux->var_types&del_mask && (args->collapse&COLLAPSE_SNP_INS_DEL) ) break;
+                    if ( maux->var_types&ref_mask ) break;
+                }
+                else if ( maux->var_types&ref_mask )
+                {
+                    if ( line_type&snp_mask && (args->collapse&COLLAPSE_SNPS) ) break;
+                    if ( line_type&indel_mask && (args->collapse&COLLAPSE_INDELS) ) break;
+                    if ( line_type&ins_mask && (args->collapse&COLLAPSE_SNP_INS_DEL) ) break;
+                    if ( line_type&del_mask && (args->collapse&COLLAPSE_SNP_INS_DEL) ) break;
+                }
+            }
+        }
+        if ( j<buf->end )
+        {
+            // found a suitable line for merging
+            buf->cur = j;
+
+            // mark as finished so that it's ignored next time
+            buf->rec[j].skip  = SKIP_DONE;
+            nout++;
+        }
+    }
+    assert( nout );
+}
+
+void merge_line(args_t *args)
+{
+    bcf1_t *out = args->out_line;
+    merge_chrom2qual(args, out);
+    if ( args->regs && !regidx_overlap(args->regs,args->maux->chr,out->pos,out->pos+out->rlen-1,NULL) ) return;
+    merge_filter(args, out);
+    merge_info(args, out);
+    if ( args->do_gvcf )
+        bcf_update_info_int32(args->out_hdr, out, "END", NULL, 0);
+    merge_format(args, out);
+    if ( bcf_write1(args->out_fh, args->out_hdr, out)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->output_fname);
+    bcf_clear1(out);
+}
+
+void bcf_hdr_append_version(bcf_hdr_t *hdr, int argc, char **argv, const char *cmd)
+{
+    kstring_t str = {0,0,0};
+    int e = 0;
+    if (ksprintf(&str,"##%sVersion=%s+htslib-%s\n", cmd, bcftools_version(), hts_version()) < 0)
+        goto fail;
+    if (bcf_hdr_append(hdr,str.s) < 0)
+        goto fail;
+
+    str.l = 0;
+    e |= ksprintf(&str,"##%sCommand=%s", cmd, argv[0]) < 0;
+    int i;
+    for (i=1; i<argc; i++)
+    {
+        if ( strchr(argv[i],' ') )
+            e |= ksprintf(&str, " '%s'", argv[i]) < 0;
+        else
+            e |= ksprintf(&str, " %s", argv[i]) < 0;
+    }
+    e |= kputs("; Date=", &str) < 0;
+    time_t tm; time(&tm);
+    e |= kputs(ctime(&tm), &str) < 0;
+    e |= kputc('\n', &str) < 0;
+    if (e)
+        goto fail;
+    if (bcf_hdr_append(hdr,str.s) < 0)
+        goto fail;
+    free(ks_release(&str));
+
+    if (bcf_hdr_sync(hdr) < 0)
+        goto fail;
+    return;
+
+ fail:
+    free(str.s);
+    error_errno("[%s] Failed to add program information to header", __func__);
+}
+
+void hdr_add_localized_tags(args_t *args, bcf_hdr_t *hdr)
+{
+    char **str = NULL;
+    int i,j, nstr = 0, mstr = 0;
+    for (i=0; i<hdr->nhrec; i++)
+    {
+        if ( hdr->hrec[i]->type!=BCF_HL_FMT ) continue;
+        j = bcf_hrec_find_key(hdr->hrec[i],"ID");
+        if ( j<0 ) continue;
+        char *key = hdr->hrec[i]->vals[j];
+        int id = bcf_hdr_id2int(hdr, BCF_DT_ID, key);
+        assert( id>=0 );
+        int localize = 0;
+        if ( bcf_hdr_id2length(hdr,BCF_HL_FMT,id) == BCF_VL_G ) localize = 1;
+        if ( bcf_hdr_id2length(hdr,BCF_HL_FMT,id) == BCF_VL_A ) localize = 1;
+        if ( bcf_hdr_id2length(hdr,BCF_HL_FMT,id) == BCF_VL_R ) localize = 1;
+        if ( !localize ) continue;
+        args->tmps.l = 0;
+
+        uint32_t e = 0, nout = 0;
+        e |= ksprintf(&args->tmps, "##%s=<", hdr->hrec[i]->key) < 0;
+        for (j=0; j<hdr->hrec[i]->nkeys; j++)
+        {
+            if ( !strcmp("IDX",hdr->hrec[i]->keys[j]) ) continue;
+            if ( nout ) e |= kputc(',',&args->tmps) < 0;
+            if ( !strcmp("ID",hdr->hrec[i]->keys[j]) )
+                e |= ksprintf(&args->tmps,"%s=L%s", hdr->hrec[i]->keys[j], hdr->hrec[i]->vals[j]) < 0;
+            else if ( !strcmp("Number",hdr->hrec[i]->keys[j]) )
+                e |= ksprintf(&args->tmps,"Number=.") < 0;
+            else if ( !strcmp("Description",hdr->hrec[i]->keys[j]) && hdr->hrec[i]->vals[j][0]=='"' )
+                e |= ksprintf(&args->tmps,"Description=\"Localized field: %s", hdr->hrec[i]->vals[j]+1) < 0;
+            else
+                e |= ksprintf(&args->tmps,"%s=%s", hdr->hrec[i]->keys[j], hdr->hrec[i]->vals[j]) < 0;
+            nout++;
+        }
+        e |= ksprintf(&args->tmps,">\n") < 0;
+        if ( e ) error("Failed to format the header line for %s\n", key);
+        nstr++;
+        hts_expand(char*,nstr,mstr,str);
+        str[nstr-1] = strdup(args->tmps.s);
+    }
+    if ( !nstr ) return;
+    bcf_hdr_append(hdr,"##FORMAT=<ID=LAA,Number=.,Type=Integer,Description=\"Localized alleles: subset of alternate alleles relevant for each sample\">");
+    for (i=0; i<nstr; i++)
+    {
+        bcf_hdr_append(hdr, str[i]);
+        free(str[i]);
+    }
+    free(str);
+}
+void merge_vcf(args_t *args)
+{
+    char wmode[8];
+    set_wmode(wmode,args->output_type,args->output_fname,args->clevel);
+    args->out_fh = hts_open(args->output_fname ? args->output_fname : "-", wmode);
+    if ( args->out_fh == NULL ) error("Can't write to \"%s\": %s\n", args->output_fname, strerror(errno));
+    if ( args->n_threads ) hts_set_opt(args->out_fh, HTS_OPT_THREAD_POOL, args->files->p); //hts_set_threads(args->out_fh, args->n_threads);
+    args->out_hdr = bcf_hdr_init("w");
+
+    if ( args->header_fname )
+    {
+        if ( bcf_hdr_set(args->out_hdr,args->header_fname) ) error("Could not read/parse the header: %s\n", args->header_fname);
+    }
+    else
+    {
+        int i;
+        for (i=0; i<args->files->nreaders; i++)
+        {
+            char buf[24]; snprintf(buf,sizeof buf,"%d",i+1);
+            merge_headers(args->out_hdr, args->files->readers[i].header,buf,args->force_samples);
+        }
+        if ( args->local_alleles ) hdr_add_localized_tags(args, args->out_hdr);
+        if (args->record_cmd_line) bcf_hdr_append_version(args->out_hdr, args->argc, args->argv, "bcftools_merge");
+        if (bcf_hdr_sync(args->out_hdr) < 0)
+            error_errno("[%s] Failed to update header", __func__);
+    }
+    info_rules_init(args);
+
+    bcf_hdr_set_version(args->out_hdr, bcf_hdr_get_version(args->files->readers[0].header));
+    if ( bcf_hdr_write(args->out_fh, args->out_hdr)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->output_fname);
+    if ( args->header_only )
+    {
+        bcf_hdr_destroy(args->out_hdr);
+        if ( hts_close(args->out_fh)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,args->output_fname);
+        return;
+    }
+
+    if ( args->collapse==COLLAPSE_NONE ) args->vcmp = vcmp_init();
+    args->maux = maux_init(args);
+    args->out_line = bcf_init1();
+    args->tmph = kh_init(strdict);
+
+    int *rid_tab = calloc(args->maux->n, sizeof(*rid_tab));
+    if (!rid_tab)
+        error("[%s:%d] Could not allocate %zu bytes\n", __FILE__, __LINE__, args->maux->n*sizeof(*rid_tab));
+
+    while ( bcf_sr_next_line(args->files) )
+    {
+        // output cached gVCF blocks which end before the new record
+        if ( args->do_gvcf )
+            gvcf_flush(args,0);
+
+        maux_reset(args->maux, rid_tab);
+
+        // determine which of the new records are gvcf blocks
+        if ( args->do_gvcf )
+            gvcf_stage(args, args->maux->pos);
+
+        while ( can_merge(args) )
+        {
+            stage_line(args);
+            merge_line(args);
+        }
+        clean_buffer(args);
+        // debug_state(args);
+    }
+    free(rid_tab);
+    if ( args->do_gvcf )
+        gvcf_flush(args,1);
+
+    info_rules_destroy(args);
+    maux_destroy(args->maux);
+    bcf_hdr_destroy(args->out_hdr);
+    if ( hts_close(args->out_fh)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,args->output_fname);
+    bcf_destroy1(args->out_line);
+    kh_destroy(strdict, args->tmph);
+    if ( args->tmps.m ) free(args->tmps.s);
+    if ( args->vcmp ) vcmp_destroy(args->vcmp);
+}
+
+static void usage(void)
+{
+    fprintf(stderr, "\n");
+    fprintf(stderr, "About:   Merge multiple VCF/BCF files from non-overlapping sample sets to create one multi-sample file.\n");
+    fprintf(stderr, "         Note that only records from different files can be merged, never from the same file. For\n");
+    fprintf(stderr, "         \"vertical\" merge take a look at \"bcftools norm\" instead.\n");
+    fprintf(stderr, "Usage:   bcftools merge [options] <A.vcf.gz> <B.vcf.gz> [...]\n");
+    fprintf(stderr, "\n");
+    fprintf(stderr, "Options:\n");
+    fprintf(stderr, "        --force-samples               Resolve duplicate sample names\n");
+    fprintf(stderr, "        --print-header                Print only the merged header and exit\n");
+    fprintf(stderr, "        --use-header FILE             Use the provided header\n");
+    fprintf(stderr, "    -0  --missing-to-ref              Assume genotypes at missing sites are 0/0\n");
+    fprintf(stderr, "    -f, --apply-filters LIST          Require at least one of the listed FILTER strings (e.g. \"PASS,.\")\n");
+    fprintf(stderr, "    -F, --filter-logic x|+            Remove filters if some input is PASS (\"x\"), or apply all filters (\"+\") [+]\n");
+    fprintf(stderr, "    -g, --gvcf -|REF.FA               Merge gVCF blocks, INFO/END tag is expected. Implies -i QS:sum,MinDP:min,I16:sum,IDV:max,IMF:max\n");
+    fprintf(stderr, "    -i, --info-rules TAG:METHOD,..    Rules for merging INFO fields (method is one of sum,avg,min,max,join) or \"-\" to turn off the default [DP:sum,DP4:sum]\n");
+    fprintf(stderr, "    -l, --file-list FILE              Read file names from the file\n");
+    fprintf(stderr, "    -L, --local-alleles INT           EXPERIMENTAL: if more than <int> ALT alleles are encountered, drop FMT/PL and output LAA+LPL instead; 0=unlimited [0]\n");
+    fprintf(stderr, "    -m, --merge STRING                Allow multiallelic records for <snps|indels|both|snp-ins-del|all|none|id>, see man page for details [both]\n");
+    fprintf(stderr, "        --no-index                    Merge unindexed files, the same chromosomal order is required and -r/-R are not allowed\n");
+    fprintf(stderr, "        --no-version                  Do not append version and command line to the header\n");
+    fprintf(stderr, "    -o, --output FILE                 Write output to a file [standard output]\n");
+    fprintf(stderr, "    -O, --output-type u|b|v|z[0-9]    u/b: un/compressed BCF, v/z: un/compressed VCF, 0-9: compression level [v]\n");
+    fprintf(stderr, "    -r, --regions REGION              Restrict to comma-separated list of regions\n");
+    fprintf(stderr, "    -R, --regions-file FILE           Restrict to regions listed in a file\n");
+    fprintf(stderr, "        --regions-overlap 0|1|2       Include if POS in the region (0), record overlaps (1), variant overlaps (2) [1]\n");
+    fprintf(stderr, "        --threads INT                 Use multithreading with <int> worker threads [0]\n");
+    fprintf(stderr, "\n");
+    exit(1);
+}
+
+int main_vcfmerge(int argc, char *argv[])
+{
+    int c;
+    args_t *args = (args_t*) calloc(1,sizeof(args_t));
+    args->files  = bcf_sr_init();
+    args->argc   = argc; args->argv = argv;
+    args->output_fname = "-";
+    args->output_type = FT_VCF;
+    args->n_threads = 0;
+    args->record_cmd_line = 1;
+    args->collapse = COLLAPSE_BOTH;
+    args->clevel = -1;
+    int regions_is_file = 0;
+    int regions_overlap = 1;
+
+    static struct option loptions[] =
+    {
+        {"help",no_argument,NULL,'h'},
+        {"merge",required_argument,NULL,'m'},
+        {"local-alleles",required_argument,NULL,'L'},
+        {"gvcf",required_argument,NULL,'g'},
+        {"file-list",required_argument,NULL,'l'},
+        {"missing-to-ref",no_argument,NULL,'0'},
+        {"apply-filters",required_argument,NULL,'f'},
+        {"use-header",required_argument,NULL,1},
+        {"print-header",no_argument,NULL,2},
+        {"force-samples",no_argument,NULL,3},
+        {"output",required_argument,NULL,'o'},
+        {"output-type",required_argument,NULL,'O'},
+        {"threads",required_argument,NULL,9},
+        {"regions",required_argument,NULL,'r'},
+        {"regions-file",required_argument,NULL,'R'},
+        {"regions-overlap",required_argument,NULL,4},
+        {"info-rules",required_argument,NULL,'i'},
+        {"no-version",no_argument,NULL,8},
+        {"no-index",no_argument,NULL,10},
+        {"filter-logic",required_argument,NULL,'F'},
+        {NULL,0,NULL,0}
+    };
+    char *tmp;
+    while ((c = getopt_long(argc, argv, "hm:f:r:R:o:O:i:l:g:F:0L:",loptions,NULL)) >= 0) {
+        switch (c) {
+            case 'L':
+                args->local_alleles = strtol(optarg,&tmp,10);
+                if ( *tmp ) error("Could not parse argument: --local-alleles %s\n", optarg);
+                if ( args->local_alleles < 1 )
+                    error("Error: \"--local-alleles %s\" makes no sense, expected value bigger or equal than 1\n", optarg);
+                break;
+            case 'F':
+                if ( !strcmp(optarg,"+") ) args->filter_logic = FLT_LOGIC_ADD;
+                else if ( !strcmp(optarg,"x") ) args->filter_logic = FLT_LOGIC_REMOVE;
+                else error("Filter logic not recognised: %s\n", optarg);
+                break;
+            case '0': args->missing_to_ref = 1; break;
+            case 'g':
+                args->do_gvcf = 1;
+                if ( strcmp("-",optarg) )
+                {
+                    args->gvcf_fai = fai_load(optarg);
+                    if ( !args->gvcf_fai ) error("Failed to load the fai index: %s\n", optarg);
+                }
+                break;
+            case 'l': args->file_list = optarg; break;
+            case 'i': args->info_rules = optarg; break;
+            case 'o': args->output_fname = optarg; break;
+            case 'O':
+                switch (optarg[0]) {
+                    case 'b': args->output_type = FT_BCF_GZ; break;
+                    case 'u': args->output_type = FT_BCF; break;
+                    case 'z': args->output_type = FT_VCF_GZ; break;
+                    case 'v': args->output_type = FT_VCF; break;
+                    default:
+                    {
+                        args->clevel = strtol(optarg,&tmp,10);
+                        if ( *tmp || args->clevel<0 || args->clevel>9 ) error("The output type \"%s\" not recognised\n", optarg);
+                    }
+                }
+                if ( optarg[1] )
+                {
+                    args->clevel = strtol(optarg+1,&tmp,10);
+                    if ( *tmp || args->clevel<0 || args->clevel>9 ) error("Could not parse argument: --compression-level %s\n", optarg+1);
+                }
+                break;
+            case 'm':
+                args->collapse = COLLAPSE_NONE;
+                if ( !strcmp(optarg,"snps") ) args->collapse |= COLLAPSE_SNPS;
+                else if ( !strcmp(optarg,"indels") ) args->collapse |= COLLAPSE_INDELS;
+                else if ( !strcmp(optarg,"both") ) args->collapse |= COLLAPSE_BOTH;
+                else if ( !strcmp(optarg,"any") ) args->collapse |= COLLAPSE_ANY;
+                else if ( !strcmp(optarg,"all") ) args->collapse |= COLLAPSE_ANY;
+                else if ( !strcmp(optarg,"none") ) args->collapse = COLLAPSE_NONE;
+                else if ( !strcmp(optarg,"snp-ins-del") ) args->collapse = COLLAPSE_SNP_INS_DEL;
+                else if ( !strcmp(optarg,"id") ) { args->collapse = COLLAPSE_NONE; args->merge_by_id = 1; }
+                else error("The -m type \"%s\" is not recognised.\n", optarg);
+                break;
+            case 'f': args->files->apply_filters = optarg; break;
+            case 'r': args->regions_list = optarg; break;
+            case 'R': args->regions_list = optarg; regions_is_file = 1; break;
+            case  1 : args->header_fname = optarg; break;
+            case  2 : args->header_only = 1; break;
+            case  3 : args->force_samples = 1; break;
+            case  4 :
+                regions_overlap = parse_overlap_option(optarg);
+                if ( regions_overlap < 0 ) error("Could not parse: --regions-overlap %s\n",optarg);
+                break;
+            case  9 : args->n_threads = strtol(optarg, 0, 0); break;
+            case  8 : args->record_cmd_line = 0; break;
+            case 10 : args->no_index = 1; break;
+            case 'h':
+            case '?': usage(); break;
+            default: error("Unknown argument: %s\n", optarg);
+        }
+    }
+    if ( argc==optind && !args->file_list ) usage();
+    if ( argc-optind<2 && !args->file_list ) usage();
+
+    if ( args->no_index )
+    {
+        if ( args->regions_list ) error("Error: cannot combine --no-index with -r/-R\n");
+        bcf_sr_set_opt(args->files,BCF_SR_ALLOW_NO_IDX);
+    }
+    else
+        bcf_sr_set_opt(args->files,BCF_SR_REQUIRE_IDX);
+    if ( args->regions_list )
+    {
+        bcf_sr_set_opt(args->files,BCF_SR_REGIONS_OVERLAP,regions_overlap);
+        if ( bcf_sr_set_regions(args->files, args->regions_list, regions_is_file)<0 )
+            error("Failed to read the regions: %s\n", args->regions_list);
+        if ( regions_is_file )
+            args->regs = regidx_init(args->regions_list,NULL,NULL,sizeof(char*),NULL);
+        else
+        {
+            args->regs = regidx_init(NULL,regidx_parse_reg,NULL,sizeof(char*),NULL);
+            if ( regidx_insert_list(args->regs,args->regions_list,',') !=0 ) error("Could not parse the regions: %s\n", args->regions_list);
+            regidx_insert(args->regs,NULL);
+        }
+        if ( !args->regs ) error("Could not parse the regions: %s\n", args->regions_list);
+        args->regs_itr = regitr_init(args->regs);
+    }
+
+    if ( bcf_sr_set_threads(args->files, args->n_threads)<0 ) error("Failed to create threads\n");
+    while (optind<argc)
+    {
+        if ( !bcf_sr_add_reader(args->files, argv[optind]) ) error("Failed to open %s: %s\n", argv[optind],bcf_sr_strerror(args->files->errnum));
+        optind++;
+    }
+    if ( args->file_list )
+    {
+        int nfiles, i;
+        char **files = hts_readlines(args->file_list, &nfiles);
+        if ( !files ) error("Failed to read from %s\n", args->file_list);
+        for (i=0;i<nfiles; i++)
+            if ( !bcf_sr_add_reader(args->files, files[i]) ) error("Failed to open %s: %s\n", files[i],bcf_sr_strerror(args->files->errnum));
+        for (i=0; i<nfiles; i++) free(files[i]);
+        free(files);
+    }
+    merge_vcf(args);
+    bcf_sr_destroy(args->files);
+    if ( args->regs ) regidx_destroy(args->regs);
+    if ( args->regs_itr ) regitr_destroy(args->regs_itr);
+    if ( args->gvcf_fai ) fai_destroy(args->gvcf_fai);
+    free(args);
+    return 0;
+}
+
diff --git a/bcftools/vcfmerge.c.pysam.c b/bcftools/vcfmerge.c.pysam.c
new file mode 100644
index 0000000..3a26cae
--- /dev/null
+++ b/bcftools/vcfmerge.c.pysam.c
@@ -0,0 +1,3332 @@
+#include "bcftools.pysam.h"
+
+/*  vcfmerge.c -- Merge multiple VCF/BCF files to create one multi-sample file.
+
+    Copyright (C) 2012-2022 Genome Research Ltd.
+
+    Author: Petr Danecek <pd3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.  */
+
+#include <stdio.h>
+#include <string.h>
+#include <strings.h>
+#include <assert.h>
+#include <errno.h>
+#include <unistd.h>
+#include <getopt.h>
+#include <inttypes.h>
+#include <htslib/vcf.h>
+#include <htslib/synced_bcf_reader.h>
+#include <htslib/vcfutils.h>
+#include <htslib/faidx.h>
+#include <math.h>
+#include <ctype.h>
+#include <time.h>
+#include "bcftools.h"
+#include "regidx.h"
+#include "vcmp.h"
+
+#define DBG 0
+
+#define COLLAPSE_SNP_INS_DEL (1<<10)
+
+#include <htslib/khash.h>
+KHASH_MAP_INIT_STR(strdict, int)
+typedef khash_t(strdict) strdict_t;
+
+#define FLT_LOGIC_ADD    0
+#define FLT_LOGIC_REMOVE 1
+
+#define SKIP_DONE 1     // the record was processed
+#define SKIP_DIFF 2     // not compatible, merge later
+
+#define IS_VL_G(hdr,id) (bcf_hdr_id2length(hdr,BCF_HL_FMT,id) == BCF_VL_G)
+#define IS_VL_A(hdr,id) (bcf_hdr_id2length(hdr,BCF_HL_FMT,id) == BCF_VL_A)
+#define IS_VL_R(hdr,id) (bcf_hdr_id2length(hdr,BCF_HL_FMT,id) == BCF_VL_R)
+
+#define SWAP(type_t,a,b) { type_t tmp = (a); (a) = (b); (b) = tmp; }
+
+#define PL2PROB_MAX 1024
+
+// For merging INFO Number=A,G,R tags
+typedef struct
+{
+    const char *hdr_tag;
+    int type, nvals;
+    int nbuf, mbuf;
+    uint8_t *buf;
+}
+AGR_info_t;
+
+// Rules for merging arbitrary INFO tags
+typedef struct _info_rule_t
+{
+    char *hdr_tag;
+    void (*merger)(bcf_hdr_t *hdr, bcf1_t *line, struct _info_rule_t *rule);
+    int type;           // one of BCF_HT_*
+    int block_size;     // number of values in a block
+    int type_size;      // size of the corresponding BCF_HT_* type
+    int nblocks;        // number of blocks in nvals (the number of merged files)
+    int nvals, mvals;   // used and total size of vals array
+    void *vals;         // the info tag values
+}
+info_rule_t;
+
+typedef struct
+{
+    bcf1_t *line;
+    int end, active;    // end: 0-based INFO/END
+}
+gvcf_aux_t;
+
+// Auxiliary merge data for selecting the right combination
+//  of buffered records across multiple readers. maux1_t
+//  corresponds to one buffered line.
+typedef struct
+{
+    int skip;
+    int *map;   // mapping from input alleles to the array of output alleles (set by merge_alleles)
+    int mmap;   // size of map array (only buffer[i].n_allele is actually used)
+    int als_differ;
+}
+maux1_t;
+typedef struct
+{
+    int rid;        // current rid
+    int beg,end;    // valid ranges in reader's buffer [beg,end). Maintained by maux_reset and gvcf_flush.
+    int cur;        // current line or -1 if none
+    int mrec;       // allocated size of buf
+    maux1_t *rec;   // buffer to keep reader's lines
+    bcf1_t **lines; // source buffer: either gvcf or readers' buffer
+}
+buffer_t;
+typedef struct
+{
+    int n, pos, var_types;  // number of readers, current position, currently available variant types
+    char *chr;              // current chromosome
+    char **als, **out_als;  // merged alleles (temp, may contain empty records) and merged alleles ready for output
+    int nals, mals, nout_als, mout_als; // size of the output array
+    int *cnt, ncnt; // number of records that refer to the alleles
+    int *smpl_ploidy, *smpl_nGsize; // ploidy and derived number of values in Number=G tags, updated for each line (todo: cache for missing cases)
+    bcf_fmt_t **fmt_map; // i-th output FORMAT field corresponds in j-th reader to i*nreader+j, first row is reserved for GT
+    int nfmt_map;        // number of rows in the fmt_map array
+    int *agr_map, nagr_map, magr_map;   // mapping between Number=AGR element indexes
+    void *tmp_arr;
+    size_t ntmp_arr;
+    buffer_t *buf;
+    AGR_info_t *AGR_info;
+    int nAGR_info, mAGR_info;
+    bcf_srs_t *files;
+    int gvcf_min,       // min buffered gvcf END position (NB: gvcf_min is 1-based) or 0 if no active lines are present
+        gvcf_break;     // 0-based position of a next record which breaks a gVCF block
+    gvcf_aux_t *gvcf;   // buffer of gVCF lines, for each reader one line
+    int nout_smpl;
+    kstring_t *str;
+    int32_t *laa;           // localized alternate alleles given as input-based indexes in per-sample blocks of (args->local_alleles+1) values, 0 is always first
+    int nlaa, laa_dirty;    // number of LAA alleles actually used at this site, and was any L* added?
+    int32_t *tmpi, *k2k;
+    double *tmpd, *pl2prob; // mapping from phred-score likelihoods (PL) to probability
+    int ntmpi, ntmpd, nk2k;
+}
+maux_t;
+
+typedef struct
+{
+    vcmp_t *vcmp;
+    maux_t *maux;
+    regidx_t *regs;    // apply regions only after the blocks are expanded
+    regitr_t *regs_itr;
+    int header_only, collapse, output_type, force_samples, merge_by_id, do_gvcf, filter_logic, missing_to_ref, no_index;
+    char *header_fname, *output_fname, *regions_list, *info_rules, *file_list;
+    faidx_t *gvcf_fai;
+    info_rule_t *rules;
+    int nrules;
+    strdict_t *tmph;
+    kstring_t tmps;
+    bcf_srs_t *files;
+    bcf1_t *out_line;
+    htsFile *out_fh;
+    bcf_hdr_t *out_hdr;
+    char **argv;
+    int argc, n_threads, record_cmd_line, clevel;
+    int local_alleles;    // the value of -L option
+    int keep_AC_AN;
+}
+args_t;
+
+static bcf1_t *maux_get_line(args_t *args, int i)
+{
+    maux_t *ma = args->maux;
+    int ibuf = ma->buf[i].cur;
+    if ( ibuf >= 0 ) return ma->buf[i].lines[ibuf];
+    return NULL;
+}
+
+static void info_rules_merge_sum(bcf_hdr_t *hdr, bcf1_t *line, info_rule_t *rule)
+{
+    if ( !rule->nvals ) return;
+    int i, j, ndim = rule->block_size;
+    #define BRANCH(type_t,is_missing) { \
+        type_t *ptr = (type_t*) rule->vals; \
+        for (i=0; i<rule->nvals; i++) if ( is_missing ) ptr[i] = 0; \
+        for (i=1; i<rule->nblocks; i++) \
+        { \
+            for (j=0; j<ndim; j++) ptr[j] += ptr[j+i*ndim]; \
+        } \
+    }
+    switch (rule->type) {
+        case BCF_HT_INT:  BRANCH(int32_t, ptr[i]==bcf_int32_missing); break;
+        case BCF_HT_REAL: BRANCH(float, bcf_float_is_missing(ptr[i])); break;
+        default: error("TODO: %s:%d .. type=%d\n", __FILE__,__LINE__, rule->type);
+    }
+    #undef BRANCH
+
+    bcf_update_info(hdr,line,rule->hdr_tag,rule->vals,ndim,rule->type);
+}
+static void info_rules_merge_avg(bcf_hdr_t *hdr, bcf1_t *line, info_rule_t *rule)
+{
+    if ( !rule->nvals ) return;
+    int i, j, ndim = rule->block_size;
+    #define BRANCH(type_t,is_missing) { \
+        type_t *ptr = (type_t*) rule->vals; \
+        for (i=0; i<rule->nvals; i++) if ( is_missing ) ptr[i] = 0; \
+        for (j=0; j<ndim; j++) \
+        { \
+            double sum = 0; \
+            for (i=0; i<rule->nblocks; i++) sum += ptr[j+i*ndim]; \
+            ptr[j] = sum / rule->nblocks; \
+        } \
+    }
+    switch (rule->type) {
+        case BCF_HT_INT:  BRANCH(int32_t, ptr[i]==bcf_int32_missing); break;
+        case BCF_HT_REAL: BRANCH(float, bcf_float_is_missing(ptr[i])); break;
+        default: error("TODO: %s:%d .. type=%d\n", __FILE__,__LINE__, rule->type);
+    }
+    #undef BRANCH
+
+    bcf_update_info(hdr,line,rule->hdr_tag,rule->vals,ndim,rule->type);
+}
+static void info_rules_merge_min(bcf_hdr_t *hdr, bcf1_t *line, info_rule_t *rule)
+{
+    if ( !rule->nvals ) return;
+    int i, j, ndim = rule->block_size;
+    #define BRANCH(type_t,is_missing,set_missing,huge_val) { \
+        type_t *ptr = (type_t*) rule->vals; \
+        for (i=0; i<rule->nvals; i++) if ( is_missing ) ptr[i] = huge_val; \
+        for (i=1; i<rule->nblocks; i++) \
+        { \
+            for (j=0; j<ndim; j++) if ( ptr[j] > ptr[j+i*ndim] ) ptr[j] = ptr[j+i*ndim]; \
+        } \
+        for (i=0; i<rule->nvals; i++) if ( ptr[i]==huge_val ) set_missing; \
+    }
+    switch (rule->type) {
+        case BCF_HT_INT:  BRANCH(int32_t, ptr[i]==bcf_int32_missing, ptr[i]=bcf_int32_missing, INT32_MAX); break;
+        case BCF_HT_REAL: BRANCH(float, bcf_float_is_missing(ptr[i]), bcf_float_set_missing(ptr[i]), HUGE_VAL); break;
+        default: error("TODO: %s:%d .. type=%d\n", __FILE__,__LINE__, rule->type);
+    }
+    #undef BRANCH
+
+    bcf_update_info(hdr,line,rule->hdr_tag,rule->vals,ndim,rule->type);
+}
+static void info_rules_merge_max(bcf_hdr_t *hdr, bcf1_t *line, info_rule_t *rule)
+{
+    if ( !rule->nvals ) return;
+    int i, j, ndim = rule->block_size;
+    #define BRANCH(type_t,is_missing,set_missing,huge_val) { \
+        type_t *ptr = (type_t*) rule->vals; \
+        for (i=0; i<rule->nvals; i++) if ( is_missing ) ptr[i] = huge_val; \
+        for (i=1; i<rule->nblocks; i++) \
+        { \
+            for (j=0; j<ndim; j++) if ( ptr[j] < ptr[j+i*ndim] ) ptr[j] = ptr[j+i*ndim]; \
+        } \
+        for (i=0; i<rule->nvals; i++) if ( ptr[i]==huge_val ) set_missing; \
+    }
+    switch (rule->type) {
+        case BCF_HT_INT:  BRANCH(int32_t, ptr[i]==bcf_int32_missing, ptr[i]=bcf_int32_missing, INT32_MIN); break;
+        case BCF_HT_REAL: BRANCH(float, bcf_float_is_missing(ptr[i]), bcf_float_set_missing(ptr[i]), -HUGE_VAL); break;
+        default: error("TODO: %s:%d .. type=%d\n", __FILE__,__LINE__, rule->type);
+    }
+    #undef BRANCH
+
+    bcf_update_info(hdr,line,rule->hdr_tag,rule->vals,ndim,rule->type);
+}
+static void info_rules_merge_join(bcf_hdr_t *hdr, bcf1_t *line, info_rule_t *rule)
+{
+    if ( !rule->nvals ) return;
+    if ( rule->type==BCF_HT_STR )
+    {
+        ((char*)rule->vals)[rule->nvals] = 0;
+        bcf_update_info_string(hdr,line,rule->hdr_tag,rule->vals);
+    }
+    else
+    {
+        int isrc, idst = 0;
+        #define BRANCH(type_t,is_missing,is_vector_end) { \
+            type_t *ptr = (type_t*) rule->vals; \
+            for (isrc=0; isrc<rule->nvals; isrc++) \
+            { \
+                if ( is_vector_end ) break; \
+                if ( is_missing ) continue; \
+                if ( idst!=isrc ) ptr[idst] = ptr[isrc]; \
+                idst++; \
+            } \
+        }
+        switch (rule->type) {
+            case BCF_HT_INT:  BRANCH(int32_t, ptr[isrc]==bcf_int32_missing, ptr[isrc]==bcf_int32_vector_end); break;
+            case BCF_HT_REAL: BRANCH(float, bcf_float_is_missing(ptr[isrc]), bcf_float_is_vector_end(ptr[isrc])); break;
+            default: error("TODO: %s:%d .. type=%d\n", __FILE__,__LINE__, rule->type);
+        }
+        #undef BRANCH
+
+        rule->nvals = idst;
+        bcf_update_info(hdr,line,rule->hdr_tag,rule->vals,rule->nvals,rule->type);
+    }
+}
+
+static int info_rules_comp_key2(const void *a, const void *b)
+{
+    info_rule_t *rule1 = (info_rule_t*) a;
+    info_rule_t *rule2 = (info_rule_t*) b;
+    return strcmp(rule1->hdr_tag, rule2->hdr_tag);
+}
+static int info_rules_comp_key(const void *a, const void *b)
+{
+    char *key = (char*) a;
+    info_rule_t *rule = (info_rule_t*) b;
+    return strcmp(key, rule->hdr_tag);
+}
+static void info_rules_init(args_t *args)
+{
+    if ( args->info_rules && !strcmp("-",args->info_rules) ) return;
+
+    kstring_t str = {0,0,0};
+    if ( !args->info_rules )
+    {
+        if ( bcf_hdr_idinfo_exists(args->out_hdr,BCF_HL_INFO,bcf_hdr_id2int(args->out_hdr, BCF_DT_ID, "DP")) ) kputs("DP:sum",&str);
+        if ( bcf_hdr_idinfo_exists(args->out_hdr,BCF_HL_INFO,bcf_hdr_id2int(args->out_hdr, BCF_DT_ID, "DP4")) )
+        {
+            if ( str.l ) kputc(',',&str);
+            kputs("DP4:sum",&str);
+        }
+        if ( args->do_gvcf && bcf_hdr_idinfo_exists(args->out_hdr,BCF_HL_INFO,bcf_hdr_id2int(args->out_hdr, BCF_DT_ID, "QS")) )
+        {
+            if ( str.l ) kputc(',',&str);
+            kputs("QS:sum",&str);
+        }
+        if ( args->do_gvcf && bcf_hdr_idinfo_exists(args->out_hdr,BCF_HL_INFO,bcf_hdr_id2int(args->out_hdr, BCF_DT_ID, "MinDP")) )
+        {
+            if ( str.l ) kputc(',',&str);
+            kputs("MinDP:min",&str);
+        }
+        if ( args->do_gvcf && bcf_hdr_idinfo_exists(args->out_hdr,BCF_HL_INFO,bcf_hdr_id2int(args->out_hdr, BCF_DT_ID, "I16")) )
+        {
+            if ( str.l ) kputc(',',&str);
+            kputs("I16:sum",&str);
+        }
+        if ( args->do_gvcf && bcf_hdr_idinfo_exists(args->out_hdr,BCF_HL_INFO,bcf_hdr_id2int(args->out_hdr, BCF_DT_ID, "IDV")) )
+        {
+            if ( str.l ) kputc(',',&str);
+            kputs("IDV:max",&str);
+        }
+        if ( args->do_gvcf && bcf_hdr_idinfo_exists(args->out_hdr,BCF_HL_INFO,bcf_hdr_id2int(args->out_hdr, BCF_DT_ID, "IMF")) )
+        {
+            if ( str.l ) kputc(',',&str);
+            kputs("IMF:max",&str);
+        }
+        if ( !bcf_hdr_nsamples(args->out_hdr) )
+        {
+            if ( bcf_hdr_idinfo_exists(args->out_hdr,BCF_HL_INFO,bcf_hdr_id2int(args->out_hdr, BCF_DT_ID, "AN")) )
+            {
+                if ( str.l ) kputc(',',&str);
+                kputs("AN:sum",&str);
+            }
+            if ( bcf_hdr_idinfo_exists(args->out_hdr,BCF_HL_INFO,bcf_hdr_id2int(args->out_hdr, BCF_DT_ID, "AC")) )
+            {
+                if ( str.l ) kputc(',',&str);
+                kputs("AC:sum",&str);
+            }
+        }
+
+        if ( !str.l ) return;
+        args->info_rules = str.s;
+    }
+
+    args->nrules = 1;
+    char *ss = strdup(args->info_rules), *tmp = ss;
+    int n = 0;
+    while ( *ss )
+    {
+        if ( *ss==':' ) { *ss = 0; n++; if ( n%2==0 ) error("Could not parse INFO rules: \"%s\"\n", args->info_rules); }
+        else if ( *ss==',' ) { *ss = 0; args->nrules++; n++; if ( n%2==1 ) error("Could not parse INFO rules: \"%s\"\n", args->info_rules); }
+        ss++;
+    }
+    if ( n%2==0 ) error("Could not parse INFO rules: \"%s\"\n", args->info_rules);
+    args->rules = (info_rule_t*) calloc(args->nrules,sizeof(info_rule_t));
+
+    n = 0;
+    ss = tmp;
+    while ( n < args->nrules )
+    {
+        info_rule_t *rule = &args->rules[n];
+        rule->hdr_tag = strdup(ss);
+        int id = bcf_hdr_id2int(args->out_hdr, BCF_DT_ID, rule->hdr_tag);
+        if ( !bcf_hdr_idinfo_exists(args->out_hdr,BCF_HL_INFO,id) ) error("The INFO tag is not defined in the header: \"%s\"\n", rule->hdr_tag);
+        rule->type = bcf_hdr_id2type(args->out_hdr,BCF_HL_INFO,id);
+        if ( rule->type==BCF_HT_INT ) rule->type_size = sizeof(int32_t);
+        else if ( rule->type==BCF_HT_REAL ) rule->type_size = sizeof(float);
+        else if ( rule->type==BCF_HT_STR ) rule->type_size = sizeof(char);
+        else error("The INFO rule \"%s\" is not supported; the tag \"%s\" type is %d\n", ss,rule->hdr_tag,rule->type);
+
+        if ( !strcmp(rule->hdr_tag,"AC") || !strcmp(rule->hdr_tag,"AN") ) args->keep_AC_AN = 1;
+
+        ss = strchr(ss, '\0'); ss++;
+        if ( !*ss ) error("Could not parse INFO rules, missing logic of \"%s\"\n", rule->hdr_tag);
+
+        int is_join = 0;
+        if ( !strcasecmp(ss,"sum") ) rule->merger = info_rules_merge_sum;
+        else if ( !strcasecmp(ss,"avg") ) rule->merger = info_rules_merge_avg;
+        else if ( !strcasecmp(ss,"min") ) rule->merger = info_rules_merge_min;
+        else if ( !strcasecmp(ss,"max") ) rule->merger = info_rules_merge_max;
+        else if ( !strcasecmp(ss,"join") ) { rule->merger = info_rules_merge_join; is_join = 1; }
+        else error("The rule logic \"%s\" not recognised\n", ss);
+
+        if ( !is_join && rule->type==BCF_HT_STR )
+            error("Numeric operation \"%s\" requested on non-numeric field: %s\n", ss, rule->hdr_tag);
+        if ( bcf_hdr_id2number(args->out_hdr,BCF_HL_INFO,id)==0xfffff )
+        {
+            int is_agr = (
+                    bcf_hdr_id2length(args->out_hdr,BCF_HL_INFO,id)==BCF_VL_A ||
+                    bcf_hdr_id2length(args->out_hdr,BCF_HL_INFO,id)==BCF_VL_G ||
+                    bcf_hdr_id2length(args->out_hdr,BCF_HL_INFO,id)==BCF_VL_R
+                    ) ? 1 : 0;
+            if ( is_join && bcf_hdr_id2length(args->out_hdr,BCF_HL_INFO,id)!=BCF_VL_VAR )
+            {
+                bcf_hrec_t *hrec = bcf_hdr_get_hrec(args->out_hdr, BCF_HL_INFO, "ID", rule->hdr_tag, NULL);
+                hrec = bcf_hrec_dup(hrec);
+                int i = bcf_hrec_find_key(hrec, "Number");
+                if ( i<0 ) error("Uh, could not find the entry Number in the header record of %s\n",rule->hdr_tag);
+                free(hrec->vals[i]);
+                hrec->vals[i] = strdup(".");
+                bcf_hdr_remove(args->out_hdr,BCF_HL_INFO, rule->hdr_tag);
+                bcf_hdr_add_hrec(args->out_hdr, hrec);
+            }
+            if ( !is_join && !is_agr )
+                error("Only fixed-length vectors are supported with -i %s:%s\n", ss, rule->hdr_tag);
+        }
+
+        ss = strchr(ss, '\0'); ss++;
+        n++;
+    }
+    free(str.s);
+    free(tmp);
+
+    qsort(args->rules, args->nrules, sizeof(*args->rules), info_rules_comp_key2);
+}
+static void info_rules_destroy(args_t *args)
+{
+    int i;
+    for (i=0; i<args->nrules; i++)
+    {
+        info_rule_t *rule = &args->rules[i];
+        free(rule->hdr_tag);
+        free(rule->vals);
+    }
+    free(args->rules);
+}
+static void info_rules_reset(args_t *args)
+{
+    int i;
+    for (i=0; i<args->nrules; i++)
+        args->rules[i].nblocks = args->rules[i].nvals = args->rules[i].block_size = 0;
+}
+static int info_rules_add_values(args_t *args, bcf_hdr_t *hdr, bcf1_t *line, info_rule_t *rule, maux1_t *als, int var_len)
+{
+    int msize = args->maux->ntmp_arr / rule->type_size;
+    int ret = bcf_get_info_values(hdr, line, rule->hdr_tag, &args->maux->tmp_arr, &msize, rule->type);
+    if ( ret<=0 ) error("FIXME: error parsing %s at %s:%"PRId64" .. %d\n", rule->hdr_tag,bcf_seqname(hdr,line),(int64_t) line->pos+1,ret);
+    args->maux->ntmp_arr = msize * rule->type_size;
+
+    rule->nblocks++;
+
+    if ( rule->type==BCF_HT_STR )
+    {
+        int need_comma = rule->nblocks==1 ? 0 : 1;
+        hts_expand(char,rule->nvals+ret+need_comma+1,rule->mvals,rule->vals);            // 1 for null-termination
+        char *tmp = (char*) rule->vals + rule->nvals;
+        if ( rule->nvals>0 ) { *tmp = ','; tmp++; }
+        strncpy(tmp,(char*)args->maux->tmp_arr,ret);
+        rule->nvals += ret + need_comma;
+        return 1;
+    }
+
+    int i, j;
+    if ( var_len==BCF_VL_A )
+    {
+        if ( ret!=line->n_allele-1 ) error("Wrong number of %s fields at %s:%"PRId64"\n",rule->hdr_tag,bcf_seqname(hdr,line),(int64_t) line->pos+1);
+        args->maux->nagr_map = ret;
+        hts_expand(int,args->maux->nagr_map,args->maux->magr_map,args->maux->agr_map);
+        // create mapping from source file ALT indexes to dst file indexes
+        for (i=0; i<ret; i++) args->maux->agr_map[i] = als->map[i+1] - 1;
+        rule->block_size = args->maux->nout_als - 1;
+    }
+    else if ( var_len==BCF_VL_R )
+    {
+        if ( ret!=line->n_allele ) error("Wrong number of %s fields at %s:%"PRId64"\n",rule->hdr_tag,bcf_seqname(hdr,line),(int64_t) line->pos+1);
+        args->maux->nagr_map = ret;
+        hts_expand(int,args->maux->nagr_map,args->maux->magr_map,args->maux->agr_map);
+        for (i=0; i<ret; i++) args->maux->agr_map[i] = als->map[i];
+        rule->block_size = args->maux->nout_als;
+    }
+    else if ( var_len==BCF_VL_G )
+    {
+        args->maux->nagr_map = bcf_alleles2gt(line->n_allele-1,line->n_allele-1)+1;
+        assert( ret==line->n_allele || ret==args->maux->nagr_map );
+        if ( ret==line->n_allele ) // haploid
+        {
+            args->maux->nagr_map = line->n_allele;
+            hts_expand(int,args->maux->nagr_map,args->maux->magr_map,args->maux->agr_map);
+            for (i=0; i<ret; i++) args->maux->agr_map[i] = als->map[i];
+            rule->block_size = args->maux->nout_als;
+        }
+        else
+        {
+            hts_expand(int,args->maux->nagr_map,args->maux->magr_map,args->maux->agr_map);
+            int k_src = 0;
+            for (i=0; i<line->n_allele; i++)
+            {
+                for (j=0; j<=i; j++)
+                {
+                    args->maux->agr_map[k_src] = bcf_alleles2gt(als->map[i],als->map[j]);
+                    k_src++;
+                }
+            }
+            rule->block_size = bcf_alleles2gt(args->maux->nout_als-1,args->maux->nout_als-1)+1;
+        }
+    }
+    else
+    {
+        if ( rule->nblocks>1 && ret!=rule->block_size )
+            error("Mismatch in number of values for INFO/%s at %s:%"PRId64"\n", rule->hdr_tag,bcf_seqname(hdr,line),(int64_t) line->pos+1);
+        rule->block_size = ret;
+        args->maux->nagr_map = 0;
+    }
+
+    #define BRANCH(src_type_t,dst_type_t,set_missing) { \
+        src_type_t *src = (src_type_t *) args->maux->tmp_arr; \
+        hts_expand0(dst_type_t,(rule->nvals+rule->block_size),rule->mvals,rule->vals); \
+        dst_type_t *dst = (dst_type_t *) rule->vals + rule->nvals; \
+        rule->nvals += rule->block_size; \
+        if ( !args->maux->nagr_map ) \
+        { \
+            for (i=0; i<ret; i++) dst[i] = src[i]; \
+        } \
+        else \
+        { \
+            for (i=0; i<rule->block_size; i++) set_missing; \
+            for (i=0; i<ret; i++) dst[args->maux->agr_map[i]] = src[i]; \
+        } \
+    }
+    switch (rule->type) {
+        case BCF_HT_INT:  BRANCH(int, int32_t, dst[i] = bcf_int32_missing); break;
+        case BCF_HT_REAL: BRANCH(float, float, bcf_float_set_missing(dst[i])); break;
+        default: error("TODO: %s:%d .. type=%d\n", __FILE__,__LINE__, rule->type);
+    }
+    #undef BRANCH
+
+    return 1;
+}
+
+int bcf_hdr_sync(bcf_hdr_t *h);
+
+void merge_headers(bcf_hdr_t *hw, const bcf_hdr_t *hr, const char *clash_prefix, int force_samples)
+{
+    // header lines
+    hw = bcf_hdr_merge(hw, hr);
+
+    // samples
+    int i;
+    for (i=0; i<bcf_hdr_nsamples(hr); i++)
+    {
+        char *rmme = NULL, *name = hr->samples[i];
+        while ( bcf_hdr_id2int(hw, BCF_DT_SAMPLE, name)!=-1 )
+        {
+            // there is a sample with the same name
+            if ( !force_samples ) error("Error: Duplicate sample names (%s), use --force-samples to proceed anyway.\n", name);
+
+            // Resolve conflicting samples names. For example, replace:
+            //  A + A       with    A,2:A
+            //  A,2:A + A   with    A,2:A,2:2:A
+
+            int len = strlen(name) + strlen(clash_prefix) + 1;
+            char *tmp = (char*) malloc(sizeof(char)*(len+1));
+            sprintf(tmp,"%s:%s",clash_prefix,name);
+            free(rmme);
+            rmme = name = tmp;
+        }
+        bcf_hdr_add_sample(hw,name);
+        free(rmme);
+    }
+}
+
+void debug_als(char **als, int nals)
+{
+    int k; for (k=0; k<nals; k++) fprintf(bcftools_stderr,"%s ", als[k]);
+    fprintf(bcftools_stderr,"\n");
+}
+
+/**
+ * normalize_alleles() - create smallest possible representation of the alleles
+ * @als:    alleles to be merged, first is REF (rw)
+ * @nals:   number of $a alleles
+ *
+ * Best explained on an example:
+ *      In:  REF=GTTT  ALT=GTT
+ *      Out: REF=GT    ALT=G
+ *
+ * Note: the als array will be modified
+ */
+void normalize_alleles(char **als, int nals)
+{
+    if ( !als[0][1] ) return;   // ref is 1base long, we're done
+
+    int j, i = 1, done = 0;
+    int *lens = (int*) malloc(sizeof(int)*nals);
+    for (j=0; j<nals; j++) lens[j] = strlen(als[j]);
+
+    while ( i<lens[0] )
+    {
+        for (j=1; j<nals; j++)
+        {
+            if ( i>=lens[j] ) done = 1;
+            if ( als[j][lens[j]-i] != als[0][lens[0]-i] ) { done = 1; break; }
+        }
+        if ( done ) break;
+        i++;
+    }
+    if ( i>1 )
+    {
+        i--;
+        als[0][lens[0]-i] = 0;
+        for (j=1; j<nals; j++) als[j][lens[j]-i] = 0;
+    }
+    free(lens);
+}
+
+ /**
+ * merge_alleles() - merge two REF,ALT records, $a and $b into $b.
+ * @a:      alleles to be merged, first is REF
+ * @na:     number of $a alleles
+ * @map:    map from the original $a indexes to new $b indexes (0-based)
+ * @b:      alleles to be merged, the array will be expanded as required
+ * @nb:     number of $b alleles
+ * @mb:     size of $b
+ *
+ * Returns NULL on error or $b expanded to incorporate $a alleles and sets
+ * $map. Best explained on an example:
+ *      In:     REF   ALT
+ *           a: ACG,  AC,A    (1bp and 2bp deletion)
+ *           b: ACGT, A       (3bp deletion)
+ *      Out:
+ *           b: ACGT, A,ACT,AT (3bp, 1bp and 2bp deletion)
+ *           map: 0,2,3
+ * Here the mapping from the original $a alleles to the new $b alleles is 0->0,
+ * 1->2, and 2->3.
+ */
+char **merge_alleles(char **a, int na, int *map, char **b, int *nb, int *mb)
+{
+    // reference allele never changes
+    map[0] = 0;
+
+    int i,j;
+    int rla = !a[0][1] ? 1 : strlen(a[0]);
+    int rlb = !b[0][1] ? 1 : strlen(b[0]);
+
+    // the most common case: same SNPs
+    if ( na==2 && *nb==2 && rla==1 && rlb==1 && a[1][0]==b[1][0] && !a[1][1] && !b[1][1] )
+    {
+        map[1] = 1;
+        return b;
+    }
+
+    // Sanity check: reference prefixes must be identical
+    if ( strncmp(a[0],b[0],rla<rlb?rla:rlb) )
+    {
+        if ( strncasecmp(a[0],b[0],rla<rlb?rla:rlb) )
+        {
+            fprintf(bcftools_stderr, "The REF prefixes differ: %s vs %s (%d,%d)\n", a[0],b[0],rla,rlb);
+            return NULL;
+        }
+        // Different case, change to uppercase
+        for (i=0; i<na; i++)
+        {
+            int len = strlen(a[i]);
+            for (j=0; j<len; j++) a[i][j] = toupper(a[i][j]);
+        }
+        for (i=0; i<*nb; i++)
+        {
+            int len = strlen(b[i]);
+            for (j=0; j<len; j++) b[i][j] = toupper(b[i][j]);
+        }
+    }
+
+    int n = *nb + na;
+    hts_expand0(char*,n,*mb,b);
+
+    // $b alleles need expanding
+    if ( rla>rlb )
+    {
+        for (i=0; i<*nb; i++)
+        {
+            if ( b[i][0]=='<' ) continue;   // symbolic allele, do not modify
+            if ( b[i][0]=='*' ) continue;   // overlapping deletion (*), do not modify
+            int l = strlen(b[i]);
+            b[i] = (char*) realloc(b[i],l+rla-rlb+1);
+            memcpy(b[i]+l,a[0]+rlb,rla-rlb+1);
+        }
+    }
+
+    // now check if the $a alleles are present and if not add them
+    for (i=1; i<na; i++)
+    {
+        int const_ai = 1;
+        char *ai;
+        if ( rlb>rla && a[i][0]!='<' && a[i][0]!='*' )  // $a alleles need expanding and not a symbolic allele or *
+        {
+            int l = strlen(a[i]);
+            ai = (char*) malloc(l+rlb-rla+1);
+            memcpy(ai,a[i],l);
+            memcpy(ai+l,b[0]+rla,rlb-rla+1);
+            const_ai = 0;
+        }
+        else
+            ai = a[i];
+
+        for (j=1; j<*nb; j++)
+            if ( !strcasecmp(ai,b[j]) ) break;
+
+        if ( j<*nb ) // $b already has the same allele
+        {
+            map[i] = j;
+            if ( !const_ai ) free(ai);
+            continue;
+        }
+        // new allele
+        map[i] = *nb;
+        b[*nb] = const_ai ? strdup(ai) : ai;
+        (*nb)++;
+    }
+    return b;
+}
+
+maux_t *maux_init(args_t *args)
+{
+    bcf_srs_t *files = args->files;
+    maux_t *ma = (maux_t*) calloc(1,sizeof(maux_t));
+    ma->n      = files->nreaders;
+    ma->files  = files;
+    int i, n_smpl = 0;
+    for (i=0; i<ma->n; i++)
+        n_smpl += bcf_hdr_nsamples(files->readers[i].header);
+    ma->nout_smpl = n_smpl;
+    assert( n_smpl==bcf_hdr_nsamples(args->out_hdr) );
+    if ( args->do_gvcf )
+    {
+        ma->gvcf = (gvcf_aux_t*) calloc(ma->n,sizeof(gvcf_aux_t));  // -Walloc-size-larger-than gives a harmless warning caused by signed integer ma->n
+        for (i=0; i<ma->n; i++)
+            ma->gvcf[i].line = bcf_init1();
+    }
+    ma->smpl_ploidy = (int*) calloc(n_smpl,sizeof(int));
+    ma->smpl_nGsize = (int*) malloc(n_smpl*sizeof(int));
+    ma->buf = (buffer_t*) calloc(ma->n,sizeof(buffer_t));
+    for (i=0; i<ma->n; i++)
+        ma->buf[i].rid = -1;
+    ma->str = (kstring_t*) calloc(n_smpl,sizeof(kstring_t));
+    if ( args->local_alleles )
+    {
+        ma->laa = (int32_t*)malloc(sizeof(*ma->laa)*ma->nout_smpl*(1+args->local_alleles));
+        ma->pl2prob = (double*)malloc(PL2PROB_MAX*sizeof(*ma->pl2prob));
+        for (i=0; i<PL2PROB_MAX; i++)
+            ma->pl2prob[i] = pow(10,-0.1*i);
+    }
+    return ma;
+}
+void maux_destroy(maux_t *ma)
+{
+    int i,j;
+    for (i=0; i<ma->nout_smpl; i++) free(ma->str[i].s);
+    free(ma->str);
+    for (i=0; i<ma->mals; i++)
+    {
+        free(ma->als[i]);
+        ma->als[i] = NULL;
+    }
+    for (i=0; i<ma->n; i++) // for each reader
+    {
+        for (j=0; j<ma->buf[i].mrec; j++)  // for each buffered line
+            free(ma->buf[i].rec[j].map);
+        free(ma->buf[i].rec);
+    }
+    free(ma->buf);
+    if ( ma->gvcf )
+    {
+        for (i=0; i<ma->n; i++) bcf_destroy(ma->gvcf[i].line);
+        free(ma->gvcf);
+    }
+    for (i=0; i<ma->mAGR_info; i++)
+        free(ma->AGR_info[i].buf);
+    free(ma->agr_map);
+    free(ma->AGR_info);
+    if (ma->ntmp_arr) free(ma->tmp_arr);
+    if (ma->nfmt_map) free(ma->fmt_map);
+    // ma->inf freed in bcf_destroy1
+    for (i=0; i<ma->mals; i++) free(ma->als[i]);
+    if (ma->mout_als) free(ma->out_als);
+    free(ma->als);
+    free(ma->cnt);
+    free(ma->smpl_ploidy);
+    free(ma->smpl_nGsize);
+    free(ma->chr);
+    free(ma->laa);
+    free(ma->tmpi);
+    free(ma->k2k);
+    free(ma->tmpd);
+    free(ma->pl2prob);
+    free(ma);
+}
+void maux_expand1(buffer_t *buf, int size)
+{
+    if ( buf->mrec < size )
+    {
+        hts_expand0(maux1_t,size,buf->mrec,buf->rec);
+        buf->mrec = size;
+    }
+}
+void maux_reset(maux_t *ma, int *rid_tab)
+{
+    int i,j;
+    for (i=0; i<ma->n; i++) maux_expand1(&ma->buf[i],ma->files->readers[i].nbuffer+1);
+    for (i=0; i<ma->ncnt; i++) ma->cnt[i] = 0;
+    for (i=0; i<ma->mals; i++)
+    {
+        free(ma->als[i]);
+        ma->als[i] = NULL;
+    }
+    const char *chr = NULL;
+    ma->nals  = 0;
+    ma->pos   = -1;
+    for (i=0; i<ma->n; i++)
+    {
+        if ( !bcf_sr_has_line(ma->files,i) ) continue;
+        bcf1_t *line = bcf_sr_get_line(ma->files,i);
+        bcf_hdr_t *hdr = bcf_sr_get_header(ma->files,i);
+        chr = bcf_seqname(hdr,line);
+        ma->pos = line->pos;
+        break;
+    }
+    int new_chr = 0;
+    if ( chr && (!ma->chr || strcmp(ma->chr,chr)) )
+    {
+        free(ma->chr);
+        ma->chr = strdup(chr);
+        new_chr = 1;
+    }
+    for (i=0; i<ma->n; i++)
+    {
+        bcf_hdr_t *hdr = bcf_sr_get_header(ma->files,i);
+        if (new_chr)
+            rid_tab[i] = bcf_hdr_name2id(hdr,chr);
+
+        ma->buf[i].rid = rid_tab[i];
+        ma->buf[i].beg = bcf_sr_has_line(ma->files,i) ? 0 : 1;
+        for (j=ma->buf[i].beg; j<=ma->files->readers[i].nbuffer; j++)
+        {
+            ma->buf[i].rec[j].skip = 0;
+            bcf1_t *line = ma->files->readers[i].buffer[j];
+            if ( line->rid!=ma->buf[i].rid || line->pos!=ma->pos ) break;
+        }
+        ma->buf[i].end = j;
+        ma->buf[i].cur = -1;
+        if ( ma->buf[i].beg < ma->buf[i].end )
+        {
+            ma->buf[i].lines = ma->files->readers[i].buffer;
+            if ( ma->gvcf ) ma->gvcf[i].active = 0;     // gvcf block cannot overlap with the next record
+        }
+        if ( new_chr && ma->gvcf ) ma->gvcf[i].active = 0;  // make sure to close active gvcf block on new chr
+    }
+}
+void maux_debug(maux_t *ma, int ir, int ib)
+{
+    fprintf(bcftools_stdout, "[%d,%d]\t", ir,ib);
+    int i;
+    for (i=0; i<ma->nals; i++)
+    {
+        fprintf(bcftools_stdout, " %s [%d]", ma->als[i], ma->cnt[i]);
+    }
+    fprintf(bcftools_stdout, "\n");
+}
+
+void merge_chrom2qual(args_t *args, bcf1_t *out)
+{
+    bcf_srs_t *files = args->files;
+    bcf_hdr_t *out_hdr = args->out_hdr;
+
+    int i, ret;
+    khiter_t kitr;
+    strdict_t *tmph = args->tmph;
+    kh_clear(strdict, tmph);
+    kstring_t *tmps = &args->tmps;
+    tmps->l = 0;
+
+    maux_t *ma = args->maux;
+    int *al_idxs = (int*) calloc(ma->nals,sizeof(int));
+    bcf_float_set_missing(out->qual);
+
+    // CHROM, POS, ID, QUAL
+    out->pos = -1;
+    for (i=0; i<files->nreaders; i++)
+    {
+        bcf1_t *line = maux_get_line(args, i);
+        if ( !line ) continue;
+        bcf_unpack(line, BCF_UN_ALL);
+
+        bcf_sr_t *reader = &files->readers[i];
+        bcf_hdr_t *hdr = reader->header;
+
+        // not all maux alleles are always used, mark the ones we'll need
+        int j;
+        for (j=1; j<line->n_allele; j++)
+        {
+            int irec = ma->buf[i].cur;
+            al_idxs[ ma->buf[i].rec[irec].map[j] ] = 1;
+        }
+
+        // position
+        if ( out->pos==-1 )
+        {
+            const char *chr = hdr->id[BCF_DT_CTG][line->rid].key;
+            out->rid = bcf_hdr_name2id(out_hdr, chr);
+            if ( strcmp(chr,out_hdr->id[BCF_DT_CTG][out->rid].key) ) error("Uh\n");
+            out->pos = line->pos;
+        }
+
+        // ID
+        if ( line->d.id[0]!='.' || line->d.id[1] )
+        {
+            kitr = kh_get(strdict, tmph, line->d.id);
+            if ( kitr == kh_end(tmph) )
+            {
+                if ( tmps->l ) kputc(';', tmps);
+                kputs(line->d.id, tmps);
+                kh_put(strdict, tmph, line->d.id, &ret);
+            }
+        }
+
+        // set QUAL to the max qual value. Not exactly correct, but good enough for now
+        if ( !bcf_float_is_missing(line->qual) )
+        {
+            if ( bcf_float_is_missing(out->qual) || out->qual < line->qual ) out->qual = line->qual;
+        }
+    }
+
+    // set ID
+    if ( !tmps->l ) kputs(".", tmps);
+    bcf_update_id(out_hdr, out, tmps->s);
+
+    // set alleles
+    ma->nout_als = 0;
+    for (i=1; i<ma->nals; i++)
+    {
+        if ( !al_idxs[i] ) continue;
+        ma->nout_als++;
+
+        // Adjust the indexes, the allele map could be created for multiple collapsed records,
+        //  some of which might be unused for this output line
+        int ir, j;
+        for (ir=0; ir<files->nreaders; ir++)
+        {
+            bcf1_t *line = maux_get_line(args,ir);
+            if ( !line ) continue;
+            for (j=1; j<line->n_allele; j++)
+            {
+                int irec = ma->buf[ir].cur;
+                if ( ma->buf[ir].rec[irec].map[j]==i ) ma->buf[ir].rec[irec].map[j] = ma->nout_als;
+            }
+        }
+    }
+    // Expand the arrays and realloc the alleles string. Note that all alleles are in a single allocated block.
+    ma->nout_als++;
+    hts_expand0(char*, ma->nout_als, ma->mout_als, ma->out_als);
+    int k = 0;
+    for (i=0; i<ma->nals; i++)
+        if ( i==0 || al_idxs[i] ) ma->out_als[k++] = strdup(ma->als[i]);
+    assert( k==ma->nout_als );
+    normalize_alleles(ma->out_als, ma->nout_als);
+    bcf_update_alleles(out_hdr, out, (const char**) ma->out_als, ma->nout_als);
+    free(al_idxs);
+    for (i=0; i<ma->nout_als; i++) free(ma->out_als[i]);
+}
+
+void merge_filter(args_t *args, bcf1_t *out)
+{
+    bcf_srs_t *files = args->files;
+    bcf_hdr_t *out_hdr = args->out_hdr;
+
+    int i, ret;
+    if ( args->filter_logic == FLT_LOGIC_REMOVE )
+    {
+        for (i=0; i<files->nreaders; i++)
+        {
+            bcf1_t *line = maux_get_line(args, i);
+            if ( !line ) continue;
+            bcf_sr_t *reader = &files->readers[i];
+            bcf_hdr_t *hdr = reader->header;
+            if ( bcf_has_filter(hdr, line, "PASS") ) break;
+        }
+        if ( i<files->nreaders )
+        {
+            int flt_id = bcf_hdr_id2int(out_hdr, BCF_DT_ID, "PASS");
+            bcf_add_filter(out_hdr, out, flt_id);
+            return;
+        }
+    }
+
+    khiter_t kitr;
+    strdict_t *tmph = args->tmph;
+    kh_clear(strdict, tmph);
+
+    out->d.n_flt = 0;
+    for (i=0; i<files->nreaders; i++)
+    {
+        bcf1_t *line = maux_get_line(args, i);
+        if ( !line ) continue;
+
+        bcf_sr_t *reader = &files->readers[i];
+        bcf_hdr_t *hdr = reader->header;
+
+        int k;
+        for (k=0; k<line->d.n_flt; k++)
+        {
+            const char *flt = hdr->id[BCF_DT_ID][line->d.flt[k]].key;
+            kitr = kh_get(strdict, tmph, flt);
+            if ( kitr == kh_end(tmph) )
+            {
+                int id = bcf_hdr_id2int(out_hdr, BCF_DT_ID, flt);
+                if ( id==-1 ) error("Error: The filter is not defined in the header: %s\n", flt);
+                hts_expand(int,out->d.n_flt+1,out->d.m_flt,out->d.flt);
+                out->d.flt[out->d.n_flt] = id;
+                out->d.n_flt++;
+                kh_put(strdict, tmph, flt, &ret);
+            }
+        }
+    }
+    // Check if PASS is not mixed with other filters
+    if ( out->d.n_flt>1 )
+    {
+        int id = bcf_hdr_id2int(out_hdr, BCF_DT_ID, "PASS");
+        for (i=0; i<out->d.n_flt; i++)
+            if ( out->d.flt[i]==id ) break;
+        if ( i<out->d.n_flt )
+        {
+            out->d.n_flt--;
+            for (; i<out->d.n_flt; i++) out->d.flt[i] = out->d.flt[i+1];
+        }
+    }
+}
+
+static void bcf_info_set_id(bcf1_t *line, bcf_info_t *info, int id, kstring_t *tmp_str)
+{
+    uint8_t *ptr = info->vptr - info->vptr_off;
+    bcf_dec_typed_int1(ptr, &ptr);
+
+    tmp_str->l = 0;
+    bcf_enc_int1(tmp_str, id);
+
+    if ( tmp_str->l == ptr - info->vptr + info->vptr_off )
+    {
+        // the new id is represented with the same number of bytes
+        memcpy(info->vptr - info->vptr_off, tmp_str->s, tmp_str->l);
+        return;
+    }
+
+    kputsn_(ptr, info->vptr - ptr, tmp_str);
+    info->vptr_off = tmp_str->l;
+    kputsn_(info->vptr, info->len << bcf_type_shift[info->type], tmp_str);
+
+    info->vptr = (uint8_t*) tmp_str->s + info->vptr_off;
+    tmp_str->s = NULL;
+    tmp_str->m = 0;
+    tmp_str->l = 0;
+}
+
+/*
+ *  copy_string_field() - copy a comma-separated field
+ *  @param src:     source string
+ *  @param isrc:    index of the field to copy
+ *  @param src_len: length of source string (excluding the terminating \0)
+ *  @param dst:     destination kstring (must be initialized with missing values, e.g. as ".")
+ *  @param idst:    index of the destination field
+ */
+int copy_string_field(char *src, int isrc, int src_len, kstring_t *dst, int idst)
+{
+    int ith_src = 0, start_src = 0;    // i-th field in src string
+    while ( ith_src<isrc && start_src<src_len )
+    {
+        if ( src[start_src]==',' ) { ith_src++; }
+        start_src++;
+    }
+    if ( ith_src!=isrc ) return -1; // requested field not found
+    int end_src = start_src;
+    while ( end_src<src_len && src[end_src] && src[end_src]!=',' ) end_src++;
+
+    int nsrc_cpy = end_src - start_src;     // number of chars to copy (excluding \0)
+    if ( nsrc_cpy==1 && src[start_src]=='.' ) return 0;   // don't write missing values, dst is already initialized
+
+    int ith_dst = 0, start_dst = 0;
+    while ( ith_dst<idst && start_dst<dst->l )
+    {
+        if ( dst->s[start_dst]==',' ) { ith_dst++; }
+        start_dst++;
+    }
+    if ( ith_dst!=idst ) return -2;
+    int end_dst = start_dst;
+    while ( end_dst<dst->l && dst->s[end_dst]!=',' ) end_dst++;
+
+    if ( end_dst - start_dst>1 || dst->s[start_dst]!='.' ) return 0;   // do not overwrite non-empty values
+
+    // Now start_dst and end_dst are indexes to the destination memory area
+    // which needs to be replaced with nsrc_cpy
+    // source bytes, end_dst points just after.
+    int ndst_shift = nsrc_cpy - (end_dst - start_dst);
+    int ndst_move  = dst->l - end_dst + 1;  // how many bytes must be moved (including \0)
+    if ( ndst_shift )
+    {
+        ks_resize(dst, dst->l + ndst_shift + 1);    // plus \0
+        memmove(dst->s+end_dst+ndst_shift, dst->s+end_dst, ndst_move);
+    }
+    memcpy(dst->s+start_dst, src+start_src, nsrc_cpy);
+    dst->l += ndst_shift;
+    return 0;
+}
+
+static void merge_AGR_info_tag(bcf_hdr_t *hdr, bcf1_t *line, bcf_info_t *info, int len, maux1_t *als, AGR_info_t *agr)
+{
+    int i;
+    if ( !agr->nbuf )
+    {
+        if ( info->type==BCF_BT_INT8 || info->type==BCF_BT_INT16 || info->type==BCF_BT_INT32 || info->type==BCF_BT_FLOAT )
+        {
+            agr->nbuf = 4 * agr->nvals;
+            hts_expand(uint8_t,agr->nbuf,agr->mbuf,agr->buf);
+            if ( info->type!=BCF_BT_FLOAT )
+            {
+                int32_t *tmp = (int32_t*) agr->buf;
+                for (i=0; i<agr->nvals; i++) tmp[i] = bcf_int32_missing;
+            }
+            else
+            {
+                float *tmp = (float*) agr->buf;
+                for (i=0; i<agr->nvals; i++) bcf_float_set_missing(tmp[i]);
+            }
+        }
+        else if ( info->type==BCF_BT_CHAR )
+        {
+            kstring_t tmp; tmp.l = 0; tmp.m = agr->mbuf; tmp.s = (char*)agr->buf;
+            kputc('.',&tmp);
+            for (i=1; i<agr->nvals; i++) kputs(",.",&tmp);
+            agr->mbuf = tmp.m; agr->nbuf = tmp.l; agr->buf = (uint8_t*)tmp.s;
+        }
+        else
+            error("Not ready for type [%d]: %s at %"PRId64"\n", info->type,agr->hdr_tag,(int64_t) line->pos+1);
+    }
+
+    if ( info->type==BCF_BT_INT8 || info->type==BCF_BT_INT16 || info->type==BCF_BT_INT32 || info->type==BCF_BT_FLOAT )
+    {
+        if ( len==BCF_VL_A || len==BCF_VL_R )
+        {
+            int ifrom = len==BCF_VL_A ? 1 : 0;
+            #define BRANCH(type_t, is_missing, is_vector_end, out_type_t) { \
+                type_t *src = (type_t *) info->vptr; \
+                out_type_t *tgt = (out_type_t *) agr->buf; \
+                int iori, inew; \
+                for (iori=ifrom; iori<line->n_allele; iori++) \
+                { \
+                    if ( is_vector_end ) break; \
+                    if ( is_missing ) continue; \
+                    inew = als->map[iori] - ifrom; \
+                    tgt[inew] = *src; \
+                    src++; \
+                } \
+            }
+            switch (info->type) {
+                case BCF_BT_INT8:  BRANCH(int8_t,  *src==bcf_int8_missing,  *src==bcf_int8_vector_end,  int); break;
+                case BCF_BT_INT16: BRANCH(int16_t, *src==bcf_int16_missing, *src==bcf_int16_vector_end, int); break;
+                case BCF_BT_INT32: BRANCH(int32_t, *src==bcf_int32_missing, *src==bcf_int32_vector_end, int); break;
+                case BCF_BT_FLOAT: BRANCH(float,   bcf_float_is_missing(*src), bcf_float_is_vector_end(*src), float); break;
+                default: fprintf(bcftools_stderr,"TODO: %s:%d .. info->type=%d\n", __FILE__,__LINE__, info->type); bcftools_exit(1);
+            }
+            #undef BRANCH
+        }
+        else
+        {
+            #define BRANCH(type_t, is_missing, is_vector_end, out_type_t) { \
+                type_t *src = (type_t *) info->vptr; \
+                out_type_t *tgt = (out_type_t *) agr->buf; \
+                int iori,jori, inew,jnew; \
+                for (iori=0; iori<line->n_allele; iori++) \
+                { \
+                    inew = als->map[iori]; \
+                    for (jori=0; jori<=iori; jori++) \
+                    { \
+                        jnew = als->map[jori]; \
+                        int kori = iori*(iori+1)/2 + jori; \
+                        if ( is_vector_end ) break; \
+                        if ( is_missing ) continue; \
+                        int knew = inew>jnew ? inew*(inew+1)/2 + jnew : jnew*(jnew+1)/2 + inew; \
+                        tgt[knew] = src[kori]; \
+                    } \
+                    if ( jori<=iori ) break; \
+                } \
+            }
+            switch (info->type) {
+                case BCF_BT_INT8:  BRANCH(int8_t,  src[kori]==bcf_int8_missing,  src[kori]==bcf_int8_vector_end,  int); break;
+                case BCF_BT_INT16: BRANCH(int16_t, src[kori]==bcf_int16_missing, src[kori]==bcf_int16_vector_end, int); break;
+                case BCF_BT_INT32: BRANCH(int32_t, src[kori]==bcf_int32_missing, src[kori]==bcf_int32_vector_end, int); break;
+                case BCF_BT_FLOAT: BRANCH(float,   bcf_float_is_missing(src[kori]), bcf_float_is_vector_end(src[kori]), float); break;
+                default: fprintf(bcftools_stderr,"TODO: %s:%d .. info->type=%d\n", __FILE__,__LINE__, info->type); bcftools_exit(1);
+            }
+            #undef BRANCH
+        }
+    }
+    else
+    {
+        kstring_t tmp; tmp.l = agr->nbuf; tmp.m = agr->mbuf; tmp.s = (char*)agr->buf;
+        if ( len==BCF_VL_A || len==BCF_VL_R )
+        {
+            int iori, ifrom = len==BCF_VL_A ? 1 : 0;
+            for (iori=ifrom; iori<line->n_allele; iori++)
+            {
+                int ret = copy_string_field((char*)info->vptr, iori-ifrom, info->len, &tmp, als->map[iori]-ifrom);
+                if ( ret )
+                    error("Error at %s:%"PRId64": wrong number of fields in %s?\n", bcf_seqname(hdr,line),(int64_t) line->pos+1,agr->hdr_tag);
+            }
+        }
+        else
+        {
+            int iori,jori, inew,jnew;
+            for (iori=0; iori<line->n_allele; iori++)
+            {
+                inew = als->map[iori];
+                for (jori=0; jori<=iori; jori++)
+                {
+                    jnew = als->map[jori];
+                    int kori = iori*(iori+1)/2 + jori;
+                    int knew = bcf_alleles2gt(inew,jnew);
+                    int ret  = copy_string_field((char*)info->vptr, kori, info->len, &tmp, knew);
+                    if ( ret )
+                        error("Error at %s:%"PRId64": wrong number of fields in %s?\n", bcf_seqname(hdr,line),(int64_t) line->pos+1,agr->hdr_tag);
+                }
+            }
+        }
+        agr->mbuf = tmp.m; agr->nbuf = tmp.l; agr->buf = (uint8_t*)tmp.s;
+    }
+}
+
+void merge_info(args_t *args, bcf1_t *out)
+{
+    bcf_srs_t *files = args->files;
+    bcf_hdr_t *out_hdr = args->out_hdr;
+
+    int i, j, ret;
+    khiter_t kitr;
+    strdict_t *tmph = args->tmph;
+    kh_clear(strdict, tmph);
+
+    maux_t *ma = args->maux;
+    ma->nAGR_info = 0;
+    out->n_info   = 0;
+    info_rules_reset(args);
+    for (i=0; i<files->nreaders; i++)
+    {
+        bcf1_t *line = maux_get_line(args,i);
+        if ( !line ) continue;
+        int irec = ma->buf[i].cur;
+        bcf_sr_t *reader = &files->readers[i];
+        bcf_hdr_t *hdr = reader->header;
+        for (j=0; j<line->n_info; j++)
+        {
+            bcf_info_t *inf = &line->d.info[j];
+
+            const char *key = hdr->id[BCF_DT_ID][inf->key].key;
+            // AC and AN are done in merge_format() after genotypes are done
+            if (!args->keep_AC_AN &&
+                (key[0] == 'A'
+                  && (key[1] == 'C' || key[1] == 'N')
+                  && key[2] == 0))
+                continue;
+
+            int id = bcf_hdr_id2int(out_hdr, BCF_DT_ID, key);
+            if ( id==-1 ) error("Error: The INFO field is not defined in the header: %s\n", key);
+
+            kitr = kh_get(strdict, tmph, key);  // have we seen the tag in one of the readers?
+            int len = bcf_hdr_id2length(hdr,BCF_HL_INFO,inf->key);
+            if ( args->nrules )
+            {
+                info_rule_t *rule = (info_rule_t*) bsearch(key, args->rules, args->nrules, sizeof(*args->rules), info_rules_comp_key);
+                if ( rule )
+                {
+                    maux1_t *als = ( len==BCF_VL_A || len==BCF_VL_G || len==BCF_VL_R ) ? &ma->buf[i].rec[irec] : NULL;
+                    if ( info_rules_add_values(args, hdr, line, rule, als, len) ) continue;
+                }
+            }
+
+            // Todo: Number=AGR tags should use the newer info_rules_* functions (info_rules_merge_first to be added)
+            // and merge_AGR_info_tag to be made obsolete.
+            if ( len==BCF_VL_A || len==BCF_VL_G || len==BCF_VL_R  ) // Number=R,G,A requires special treatment
+            {
+                if ( kitr == kh_end(tmph) )
+                {
+                    // seeing this key for the first time
+                    ma->nAGR_info++;
+                    hts_expand0(AGR_info_t,ma->nAGR_info,ma->mAGR_info,ma->AGR_info);
+                    kitr = kh_put(strdict, tmph, key, &ret);
+                    kh_val(tmph,kitr) = ma->nAGR_info - 1;
+                    ma->AGR_info[ma->nAGR_info-1].hdr_tag = key;
+                    ma->AGR_info[ma->nAGR_info-1].type  = bcf_hdr_id2type(hdr,BCF_HL_INFO,inf->key);
+                    ma->AGR_info[ma->nAGR_info-1].nbuf  = 0;    // size of the buffer
+                    switch (len)
+                    {
+                        case BCF_VL_A: ma->AGR_info[ma->nAGR_info-1].nvals = ma->nout_als - 1; break;
+                        case BCF_VL_G: ma->AGR_info[ma->nAGR_info-1].nvals = bcf_alleles2gt(ma->nout_als-1,ma->nout_als-1)+1; break;
+                        case BCF_VL_R: ma->AGR_info[ma->nAGR_info-1].nvals = ma->nout_als; break;
+                    }
+                }
+                kitr = kh_get(strdict, tmph, key);
+                int idx = kh_val(tmph, kitr);
+                if ( idx<0 ) error("Error occurred while processing INFO tag \"%s\" at %s:%"PRId64"\n", key,bcf_seqname(hdr,line),(int64_t) line->pos+1);
+                merge_AGR_info_tag(hdr, line,inf,len,&ma->buf[i].rec[irec],&ma->AGR_info[idx]);
+                continue;
+            }
+
+            if ( kitr == kh_end(tmph) )
+            {
+                // Seeing this key for the first time.  Although quite hacky,
+                // this is faster than anything else given the data structures..
+
+                hts_expand0(bcf_info_t,out->n_info+1,out->d.m_info,out->d.info);
+                out->d.info[out->n_info].key  = id;
+                out->d.info[out->n_info].type = inf->type;
+                out->d.info[out->n_info].len  = inf->len;
+                out->d.info[out->n_info].v1.i = inf->v1.i;
+                out->d.info[out->n_info].v1.f = inf->v1.f;
+                out->d.info[out->n_info].vptr_off  = inf->vptr_off;
+                out->d.info[out->n_info].vptr_len  = inf->vptr_len;
+                out->d.info[out->n_info].vptr_free = 1;
+                out->d.info[out->n_info].vptr = (uint8_t*) malloc(inf->vptr_len+inf->vptr_off);
+                memcpy(out->d.info[out->n_info].vptr,inf->vptr-inf->vptr_off, inf->vptr_len+inf->vptr_off);
+                out->d.info[out->n_info].vptr += inf->vptr_off;
+                if ( (args->output_type & FT_BCF) && id!=bcf_hdr_id2int(hdr, BCF_DT_ID, key) )
+                    bcf_info_set_id(out, &out->d.info[out->n_info], id, &args->tmps);
+                out->d.shared_dirty |= BCF1_DIRTY_INF;
+                out->n_info++;
+                kitr = kh_put(strdict, tmph, key, &ret);
+                kh_val(tmph,kitr) = -(out->n_info-1);   // arbitrary negative value
+            }
+        }
+    }
+    for (i=0; i<args->nrules; i++)
+        args->rules[i].merger(args->out_hdr, out, &args->rules[i]);
+    for (i=0; i<ma->nAGR_info; i++)
+    {
+        AGR_info_t *agr = &ma->AGR_info[i];
+        bcf_update_info(out_hdr,out,agr->hdr_tag,agr->buf,agr->nvals,agr->type);
+    }
+}
+
+void update_AN_AC(bcf_hdr_t *hdr, bcf1_t *line)
+{
+    int32_t an = 0, *tmp = (int32_t*) malloc(sizeof(int)*line->n_allele);
+    int ret = bcf_calc_ac(hdr, line, tmp, BCF_UN_FMT);
+    if ( ret>0 )
+    {
+        int i;
+        for (i=0; i<line->n_allele; i++) an += tmp[i];
+        bcf_update_info_int32(hdr, line, "AN", &an, 1);
+        bcf_update_info_int32(hdr, line, "AC", tmp+1, line->n_allele-1);
+    }
+    free(tmp);
+}
+
+static inline int max_used_gt_ploidy(bcf_fmt_t *fmt, int nsmpl)
+{
+    int i,j, max_ploidy = 0;
+
+    #define BRANCH(type_t, vector_end) { \
+        type_t *ptr  = (type_t*) fmt->p; \
+        for (i=0; i<nsmpl; i++) \
+        { \
+            for (j=0; j<fmt->n; j++) \
+                if ( ptr[j]==vector_end ) break; \
+            if ( j==fmt->n ) \
+            { \
+                /* all fields were used */ \
+                if ( max_ploidy < j ) max_ploidy = j; \
+                break; \
+            } \
+            if ( max_ploidy < j ) max_ploidy = j; \
+            ptr += fmt->n; \
+        } \
+    }
+    switch (fmt->type)
+    {
+        case BCF_BT_INT8:  BRANCH(int8_t,   bcf_int8_vector_end); break;
+        case BCF_BT_INT16: BRANCH(int16_t, bcf_int16_vector_end); break;
+        case BCF_BT_INT32: BRANCH(int32_t, bcf_int32_vector_end); break;
+        default: error("Unexpected case: %d\n", fmt->type);
+    }
+    #undef BRANCH
+    return max_ploidy;
+}
+
+// Sets ma->laa to local indexes relevant for each sample or missing/vector_end.
+// The indexes are with respect to the source indexes and must be translated as
+// the very last step.
+void init_local_alleles(args_t *args, bcf1_t *out, int ifmt_PL)
+{
+    bcf_srs_t *files = args->files;
+    maux_t *ma = args->maux;
+    int i,j,k,l, ismpl = 0, nlaa = 0;
+    static int warned = 0;
+
+    hts_expand(double,out->n_allele,ma->ntmpd,ma->tmpd); // allele probabilities
+    hts_expand(int,out->n_allele,ma->ntmpi,ma->tmpi);    // indexes of the sorted probabilities
+
+    // Let map[] be the mapping from src to output idx. Then k2k[] is mapping from src allele idxs to src allele idxs
+    // reordered so that if i<j then map[k2k[i]] < map[k2k[j]]
+    hts_expand(int,out->n_allele,ma->nk2k,ma->k2k);
+
+    // Determine local alleles: either take all that are present in the reader or use PL to determine the best
+    // subset for each sample. The alleles must be listed in the order of the alleles in the output file.
+    for (i=0; i<files->nreaders; i++)
+    {
+        bcf_sr_t *reader = &files->readers[i];
+        bcf_hdr_t *hdr = reader->header;
+        bcf_fmt_t *fmt_ori = ma->fmt_map[files->nreaders*ifmt_PL+i];
+        bcf1_t *line = maux_get_line(args, i);
+        int nsmpl = bcf_hdr_nsamples(hdr);
+        if ( line )
+        {
+            if ( nlaa < line->n_allele - 1 )
+                nlaa = line->n_allele - 1 <= args->local_alleles ? line->n_allele - 1 : args->local_alleles;
+
+            for (j=0; j<line->n_allele; j++) ma->k2k[j] = j;
+
+            if ( line->n_allele <= args->local_alleles + 1 )
+            {
+                // sort to the output order, insertion sort, ascending
+                int *map = ma->buf[i].rec[ma->buf[i].cur].map;
+                int *k2k = ma->k2k;
+                int tmp;
+                for (k=1; k<line->n_allele; k++)
+                    for (l=k; l>0 && map[k2k[l]] < map[k2k[l-1]]; l--)
+                        tmp = k2k[l], k2k[l] = k2k[l-1], k2k[l-1] = tmp;
+
+                // fewer than the allowed number of alleles, use all alleles from this file
+                for (j=0; j<nsmpl; j++)
+                {
+                    int32_t *ptr = ma->laa + (1+args->local_alleles)*ismpl;
+                    for (k=0; k<line->n_allele; k++) ptr[k] = k2k[k];
+                    for (; k<=args->local_alleles; k++) ptr[k] = bcf_int32_vector_end;
+                    ismpl++;
+                }
+                continue;
+            }
+        }
+        if ( !line || !fmt_ori )
+        {
+            // no values, fill in missing values
+            for (j=0; j<nsmpl; j++)
+            {
+                int32_t *ptr = ma->laa + (1+args->local_alleles)*ismpl;
+                ptr[0] = bcf_int32_missing;
+                for (k=1; k<=args->local_alleles; k++) ptr[k] = bcf_int32_vector_end;
+                ismpl++;
+            }
+            continue;
+        }
+
+        // there are more alternate alleles in the input files than is allowed on output, need to subset
+        if ( ifmt_PL==-1 )
+        {
+            if ( !warned )
+                fprintf(bcftools_stderr,"Warning: local alleles are determined from FORMAT/PL but the tag is missing, cannot apply --local-alleles\n");
+            warned = 1;
+            ma->nlaa = 0;
+            return;
+        }
+
+        if ( !IS_VL_G(hdr, fmt_ori->id) ) error("FORMAT/PL must be defined as Number=G\n");
+        if ( 2*fmt_ori->n != line->n_allele*(line->n_allele+1) ) error("Todo: haploid PL to LPL\n");
+
+        int *map = ma->buf[i].rec[ma->buf[i].cur].map;
+        double *allele_prob = ma->tmpd;
+        int *idx = ma->tmpi;
+        #define BRANCH(src_type_t, src_is_missing, src_is_vector_end, pl2prob_idx) { \
+            src_type_t *src = (src_type_t*) fmt_ori->p; \
+            for (j=0; j<nsmpl; j++) \
+            { \
+                for (k=0; k<line->n_allele; k++) allele_prob[k] = 0; \
+                for (k=0; k<line->n_allele; k++) \
+                    for (l=0; l<=k; l++) \
+                    { \
+                        if ( src_is_missing || src_is_vector_end ) { src++; continue; } \
+                        double prob = ma->pl2prob[pl2prob_idx]; \
+                        allele_prob[k] += prob; \
+                        allele_prob[l] += prob; \
+                        src++; \
+                    } \
+                /* insertion sort by allele probability, descending order, with the twist that REF (idx=0) always comes first */ \
+                allele_prob++; idx[0] = -1; idx++; /* keep REF first */ \
+                int si,sj,tmp; \
+                for (si=0; si<line->n_allele-1; si++) idx[si] = si; \
+                for (si=1; si<line->n_allele-1; si++) \
+                    for (sj=si; sj>0 && allele_prob[idx[sj]] > allele_prob[idx[sj-1]]; sj--) \
+                        tmp = idx[sj], idx[sj] = idx[sj-1], idx[sj-1] = tmp; \
+                /*for debugging only: test order*/ \
+                for (si=1; si<line->n_allele-1; si++) \
+                    assert( allele_prob[idx[si-1]] >= allele_prob[idx[si]] ); \
+                allele_prob--; idx--; /* this was to keep REF first */ \
+                int32_t *ptr = ma->laa + (1+args->local_alleles)*ismpl; \
+                ptr[0] = 0; \
+                for (k=1; k<=args->local_alleles && k<line->n_allele; k++) ptr[k] = idx[k]+1; \
+                int kmax = k; \
+                for (; k<=args->local_alleles; k++) ptr[k] = bcf_int32_vector_end; \
+                /* insertion sort by indexes to the output order, ascending */ \
+                for (k=1; k<kmax; k++) \
+                    for (l=k; l>0 && map[ptr[l]] < map[ptr[l-1]]; l--) \
+                        tmp = ptr[l], ptr[l] = ptr[l-1], ptr[l-1] = tmp; \
+                ismpl++; \
+            } \
+        }
+        switch (fmt_ori->type)
+        {
+            case BCF_BT_INT8:  BRANCH( int8_t, *src==bcf_int8_missing,  *src==bcf_int8_vector_end,  *src); break;
+            case BCF_BT_INT16: BRANCH(int16_t, *src==bcf_int16_missing, *src==bcf_int16_vector_end, *src>=0 && *src<PL2PROB_MAX ? *src : PL2PROB_MAX-1); break;
+            case BCF_BT_INT32: BRANCH(int32_t, *src==bcf_int32_missing, *src==bcf_int32_vector_end, *src>=0 && *src<PL2PROB_MAX ? *src : PL2PROB_MAX-1); break;
+            default: error("Unexpected case: %d, PL\n", fmt_ori->type);
+        }
+        #undef BRANCH
+    }
+    ma->nlaa = nlaa;
+}
+
+void update_local_alleles(args_t *args, bcf1_t *out)
+{
+    bcf_srs_t *files = args->files;
+    maux_t *ma = args->maux;
+    int i,j,k,ismpl=0,nsamples = bcf_hdr_nsamples(args->out_hdr);
+    for (i=0; i<files->nreaders; i++)
+    {
+        int irec = ma->buf[i].cur;
+        bcf_sr_t *reader = &files->readers[i];
+        int nsmpl = bcf_hdr_nsamples(reader->header);
+        for (k=0; k<nsmpl; k++)
+        {
+            int32_t *src = ma->laa + ismpl*(1+args->local_alleles);
+            int32_t *dst = ma->laa + ismpl*ma->nlaa;
+            j = 0;
+            if ( irec>=0 )
+            {
+                for (; j<ma->nlaa; j++)
+                {
+                    if ( src[j+1]==bcf_int32_missing ) dst[j] = bcf_int32_missing;
+                    else if ( src[j+1]==bcf_int32_vector_end ) break;
+                    else
+                        dst[j] = ma->buf[i].rec[irec].map[src[j+1]];
+                }
+            }
+            if ( j==0 ) dst[j++] = bcf_int32_missing;
+            for (; j<ma->nlaa; j++) src[j] = bcf_int32_vector_end;
+            ismpl++;
+        }
+    }
+    bcf_update_format_int32(args->out_hdr, out, "LAA", ma->laa, nsamples*ma->nlaa);
+}
+
+void merge_GT(args_t *args, bcf_fmt_t **fmt_map, bcf1_t *out)
+{
+    bcf_srs_t *files = args->files;
+    bcf_hdr_t *out_hdr = args->out_hdr;
+    maux_t *ma = args->maux;
+    int i, ismpl = 0, nsamples = bcf_hdr_nsamples(out_hdr);
+    static int warned = 0;
+
+    int nsize = 0;
+    for (i=0; i<files->nreaders; i++)
+    {
+        bcf_fmt_t *fmt = fmt_map[i];
+        if ( !fmt ) continue;
+        int pld = max_used_gt_ploidy(fmt_map[i], bcf_hdr_nsamples(bcf_sr_get_header(args->files,i)));
+        if ( nsize < pld ) nsize = pld;
+    }
+    if ( nsize==0 ) nsize = 1;
+
+    size_t msize = sizeof(int32_t)*nsize*nsamples;
+    if ( msize > 2147483647 )
+    {
+        if ( !warned ) fprintf(bcftools_stderr,"Warning: Too many genotypes at %s:%"PRId64", requires %zu bytes, skipping.\n", bcf_seqname(out_hdr,out),(int64_t) out->pos+1,msize);
+        warned = 1;
+        return;
+    }
+    if ( ma->ntmp_arr < msize )
+    {
+        ma->tmp_arr  = realloc(ma->tmp_arr, msize);
+        if ( !ma->tmp_arr ) error("Could not allocate %zu bytes\n",msize);
+        ma->ntmp_arr = msize;
+    }
+    memset(ma->smpl_ploidy,0,nsamples*sizeof(int));
+
+    int default_gt = args->missing_to_ref ? bcf_gt_unphased(0) : bcf_gt_missing;
+    for (i=0; i<files->nreaders; i++)
+    {
+        bcf_sr_t *reader = &files->readers[i];
+        bcf_hdr_t *hdr = reader->header;
+        bcf_fmt_t *fmt_ori = fmt_map[i];
+        int32_t *tmp  = (int32_t *) ma->tmp_arr + ismpl*nsize;
+        int irec = ma->buf[i].cur;
+
+        int j,k;
+        if ( !fmt_ori )
+        {
+            // missing values: assume maximum ploidy
+            for (j=0; j<bcf_hdr_nsamples(hdr); j++)
+            {
+                for (k=0; k<nsize; k++) { tmp[k] = default_gt; ma->smpl_ploidy[ismpl+j]++; }
+                tmp += nsize;
+            }
+            ismpl += bcf_hdr_nsamples(hdr);
+            continue;
+        }
+
+        #define BRANCH(type_t, vector_end) { \
+            type_t *p_ori  = (type_t*) fmt_ori->p; \
+            if ( !ma->buf[i].rec[irec].als_differ ) \
+            { \
+                /* the allele numbering is unchanged */ \
+                for (j=0; j<bcf_hdr_nsamples(hdr); j++) \
+                { \
+                    for (k=0; k<fmt_ori->n; k++) \
+                    { \
+                        if ( p_ori[k]==vector_end ) break; /* smaller ploidy */ \
+                        ma->smpl_ploidy[ismpl+j]++; \
+                        if ( bcf_gt_is_missing(p_ori[k]) ) tmp[k] = 0; /* missing allele */ \
+                        else tmp[k] = p_ori[k]; \
+                    } \
+                    for (; k<nsize; k++) tmp[k] = bcf_int32_vector_end; \
+                    tmp += nsize; \
+                    p_ori += fmt_ori->n; \
+                } \
+                ismpl += bcf_hdr_nsamples(hdr); \
+                continue; \
+            } \
+            /* allele numbering needs to be changed */ \
+            for (j=0; j<bcf_hdr_nsamples(hdr); j++) \
+            { \
+                for (k=0; k<fmt_ori->n; k++) \
+                { \
+                    if ( p_ori[k]==vector_end ) break; /* smaller ploidy */ \
+                    ma->smpl_ploidy[ismpl+j]++; \
+                    if ( bcf_gt_is_missing(p_ori[k]) ) tmp[k] = 0; /* missing allele */ \
+                    else \
+                    { \
+                        int al = (p_ori[k]>>1) - 1; \
+                        al = al<=0 ? al + 1 : ma->buf[i].rec[irec].map[al] + 1; \
+                        tmp[k] = (al << 1) | ((p_ori[k])&1); \
+                    } \
+                } \
+                for (; k<nsize; k++) tmp[k] = bcf_int32_vector_end; \
+                tmp += nsize; \
+                p_ori += fmt_ori->n; \
+            } \
+            ismpl += bcf_hdr_nsamples(hdr); \
+        }
+        switch (fmt_ori->type)
+        {
+            case BCF_BT_INT8: BRANCH(int8_t,   bcf_int8_vector_end); break;
+            case BCF_BT_INT16: BRANCH(int16_t, bcf_int16_vector_end); break;
+            case BCF_BT_INT32: BRANCH(int32_t, bcf_int32_vector_end); break;
+            default: error("Unexpected case: %d\n", fmt_ori->type);
+        }
+        #undef BRANCH
+    }
+    bcf_update_format_int32(out_hdr, out, "GT", (int32_t*)ma->tmp_arr, nsamples*nsize);
+}
+
+void merge_format_string(args_t *args, const char *key, bcf_fmt_t **fmt_map, bcf1_t *out, int length, int nsize)
+{
+    bcf_srs_t *files = args->files;
+    bcf_hdr_t *out_hdr = args->out_hdr;
+    maux_t *ma = args->maux;
+    int i,j, nsamples = bcf_hdr_nsamples(out_hdr);
+    static int warned = 0;
+
+    // initialize empty strings, a dot for each value, e.g. ".,.,."
+    int nmax = 0;
+    for (i=0; i<nsamples; i++)
+    {
+        kstring_t *str = &ma->str[i];
+        if ( length==BCF_VL_FIXED || length==BCF_VL_VAR )
+        {
+            str->l = 1;
+            ks_resize(str, str->l+1);
+            str->s[0] = '.';
+        }
+        else
+        {
+            str->l = nsize*2 - 1;
+            ks_resize(str, str->l+1);
+            str->s[0] = '.';
+            for (j=1; j<nsize; j++) str->s[j*2-1] = ',', str->s[j*2] = '.';
+        }
+        str->s[str->l] = 0;
+        if ( nmax < str->l ) nmax = str->l;
+    }
+
+    // fill in values for each sample
+    int ismpl = 0;
+    for (i=0; i<files->nreaders; i++)
+    {
+        bcf_sr_t *reader = &files->readers[i];
+        bcf_hdr_t *hdr = reader->header;
+        bcf_fmt_t *fmt_ori = fmt_map[i];
+        if ( !fmt_ori )
+        {
+            // the field is not present in this file
+            ismpl += bcf_hdr_nsamples(hdr);
+            continue;
+        }
+
+        bcf1_t *line = maux_get_line(args, i);
+        int irec = ma->buf[i].cur;
+        char *src = (char*) fmt_ori->p;
+
+        if ( length==BCF_VL_FIXED || length==BCF_VL_VAR || (line->n_allele==out->n_allele && !ma->buf[i].rec[irec].als_differ) )
+        {
+            // alleles unchanged, copy over
+            for (j=0; j<bcf_hdr_nsamples(hdr); j++)
+            {
+                kstring_t *str = &ma->str[ismpl++];
+                str->l = 0;
+                kputsn(src, fmt_ori->n, str);
+                if ( nmax < str->l ) nmax = str->l;
+                src += fmt_ori->n;
+            }
+            continue;
+        }
+        // NB, what is below is not the fastest way, copy_string_field() keeps
+        // finding the indexes repeatedly at multiallelic sites
+        if ( length==BCF_VL_A || length==BCF_VL_R )
+        {
+            int ifrom = length==BCF_VL_A ? 1 : 0;
+            for (j=0; j<bcf_hdr_nsamples(hdr); j++)
+            {
+                kstring_t *str = &ma->str[ismpl++];
+                int iori,inew;
+                for (iori=ifrom; iori<line->n_allele; iori++)
+                {
+                    inew = ma->buf[i].rec[irec].map[iori] - ifrom;
+                    int ret = copy_string_field(src, iori - ifrom, fmt_ori->size, str, inew);
+                    if ( ret<-1 ) error("[E::%s] fixme: internal error at %s:%"PRId64" .. %d\n",__func__,bcf_seqname(hdr,line),(int64_t) line->pos+1,ret);
+                }
+                if ( nmax < str->l ) nmax = str->l;
+                src += fmt_ori->size;
+            }
+            continue;
+        }
+        assert( length==BCF_VL_G );
+        error("[E::%s] Merging of Number=G FORMAT strings (in your case FORMAT/%s) is not supported yet, sorry!\n"
+              "Please open an issue on github if this feature is essential for you. However, note that using FORMAT strings is not\n"
+              "a good idea in general - it is slow to parse and does not compress well, it is better to use integer codes instead.\n"
+              "If you don't really need it, use `bcftools annotate -x` to remove the annotation before merging.\n", __func__,key);
+    }
+    // update the record
+    size_t msize = nsamples*nmax;
+    if ( msize > 2147483647 )
+    {
+        if ( !warned ) fprintf(bcftools_stderr,"Warning: The row size is too big for FORMAT/%s at %s:%"PRId64", requires %zu bytes, skipping.\n", key,bcf_seqname(out_hdr,out),(int64_t) out->pos+1,msize);
+        warned = 1;
+        return;
+    }
+    if ( ma->ntmp_arr < msize )
+    {
+        ma->tmp_arr  = realloc(ma->tmp_arr, msize);
+        if ( !ma->tmp_arr ) error("Could not allocate %zu bytes\n",msize);
+        ma->ntmp_arr = msize;
+    }
+    char *tgt = (char*) ma->tmp_arr;
+    for (i=0; i<nsamples; i++)
+    {
+        memcpy(tgt, ma->str[i].s, ma->str[i].l);
+        if ( ma->str[i].l < nmax ) memset(tgt + ma->str[i].l, 0, nmax - ma->str[i].l);
+        tgt += nmax;
+    }
+    bcf_update_format_char(out_hdr, out, key, (float*)ma->tmp_arr, nsamples*nmax);
+}
+
+// Note: only diploid Number=G tags only for now
+void merge_localized_numberG_format_field(args_t *args, bcf_fmt_t **fmt_map, bcf1_t *out, int irdr)
+{
+    int i,j,k, nsamples = bcf_hdr_nsamples(args->out_hdr);
+    bcf_srs_t *files = args->files;
+    maux_t *ma = args->maux;
+    bcf_fmt_t *fmt = fmt_map[irdr];
+    const char *key = files->readers[irdr].header->id[BCF_DT_ID][fmt_map[irdr]->id].key;
+    size_t nsize = (ma->nlaa+1)*(ma->nlaa+2)/2;             // max number of Number=G localized fields
+    size_t msize = sizeof(float)>sizeof(int32_t) ? sizeof(float) : sizeof(int32_t);
+    msize *= nsamples*nsize;
+    if ( msize > 2147483647 )
+    {
+        static int warned = 0;
+        if ( !warned ) fprintf(bcftools_stderr,"Warning: The row size is too big for FORMAT/%s at %s:%"PRId64", requires %zu bytes, skipping.\n", key,bcf_seqname(args->out_hdr,out),(int64_t) out->pos+1,msize);
+        warned = 1;
+        return;
+    }
+    if ( ma->ntmp_arr < msize )
+    {
+        ma->tmp_arr  = realloc(ma->tmp_arr, msize);
+        if ( !ma->tmp_arr ) error("Failed to allocate %zu bytes at %s:%"PRId64" for FORMAT/%s\n", msize,bcf_seqname(args->out_hdr,out),(int64_t) out->pos+1,key);
+        ma->ntmp_arr = msize;
+    }
+    int ismpl = 0;
+    for (i=0; i<files->nreaders; i++)
+    {
+        bcf_sr_t *reader = &files->readers[i];
+        bcf_hdr_t *hdr = reader->header;
+        bcf_fmt_t *fmt_ori = fmt_map[i];
+        bcf1_t *line = maux_get_line(args, i);
+        int nsmpl = bcf_hdr_nsamples(hdr);
+
+        if ( !fmt_ori )
+        {
+            // fill missing values
+            #define BRANCH(tgt_type_t, tgt_set_missing, tgt_set_vector_end) { \
+                for (j=0; j<nsmpl; j++) \
+                { \
+                    tgt_type_t *tgt = (tgt_type_t *) ma->tmp_arr + ismpl*nsize; \
+                    tgt_set_missing; \
+                    for (k=1; k<nsize; k++) { tgt++; tgt_set_vector_end; } \
+                    ismpl++; \
+                } \
+            }
+            switch (fmt->type)
+            {
+                case BCF_BT_INT8:  BRANCH(int32_t, *tgt=bcf_int32_missing, *tgt=bcf_int32_vector_end); break;
+                case BCF_BT_INT16: BRANCH(int32_t, *tgt=bcf_int32_missing, *tgt=bcf_int32_vector_end); break;
+                case BCF_BT_INT32: BRANCH(int32_t, *tgt=bcf_int32_missing, *tgt=bcf_int32_vector_end); break;
+                case BCF_BT_FLOAT: BRANCH(float, bcf_float_set_missing(*tgt), bcf_float_set_vector_end(*tgt)); break;
+                default: error("Unexpected case: %d, %s\n", fmt->type, key);
+            }
+            #undef BRANCH
+            continue;
+        }
+        if ( 2*fmt_ori->n!=line->n_allele*(line->n_allele+1) ) error("Todo: localization of missing or haploid Number=G tags\n");
+
+        // localize
+        #define BRANCH(tgt_type_t, src_type_t, src_is_missing, src_is_vector_end, tgt_set_missing, tgt_set_vector_end) { \
+            for (j=0; j<nsmpl; j++) \
+            { \
+                src_type_t *src = (src_type_t*) fmt_ori->p + j*fmt_ori->n; \
+                tgt_type_t *tgt = (tgt_type_t *) ma->tmp_arr + ismpl*nsize; \
+                int *laa = ma->laa + (1+args->local_alleles)*ismpl; \
+                int ii,ij,tgt_idx = 0; \
+                for (ii=0; ii<=ma->nlaa; ii++) \
+                { \
+                    if ( laa[ii]==bcf_int32_missing || laa[ii]==bcf_int32_vector_end ) break; \
+                    for (ij=0; ij<=ii; ij++) \
+                    { \
+                        int src_idx = bcf_alleles2gt(laa[ii],laa[ij]); \
+                        if ( src_is_missing ) tgt_set_missing; \
+                        else if ( src_is_vector_end ) break; \
+                        else tgt[tgt_idx] = src[src_idx]; \
+                        tgt_idx++; \
+                    } \
+                } \
+                if ( !tgt_idx ) { tgt_set_missing; tgt_idx++; } \
+                for (; tgt_idx<nsize; tgt_idx++) tgt_set_vector_end; \
+                ismpl++; \
+            } \
+        }
+        switch (fmt_ori->type)
+        {
+            case BCF_BT_INT8:  BRANCH(int32_t,  int8_t, src[src_idx]==bcf_int8_missing,  src[src_idx]==bcf_int8_vector_end,  tgt[tgt_idx]=bcf_int32_missing, tgt[tgt_idx]=bcf_int32_vector_end); break;
+            case BCF_BT_INT16: BRANCH(int32_t, int16_t, src[src_idx]==bcf_int16_missing, src[src_idx]==bcf_int16_vector_end, tgt[tgt_idx]=bcf_int32_missing, tgt[tgt_idx]=bcf_int32_vector_end); break;
+            case BCF_BT_INT32: BRANCH(int32_t, int32_t, src[src_idx]==bcf_int32_missing, src[src_idx]==bcf_int32_vector_end, tgt[tgt_idx]=bcf_int32_missing, tgt[tgt_idx]=bcf_int32_vector_end); break;
+            case BCF_BT_FLOAT: BRANCH(float, float, bcf_float_is_missing(src[src_idx]), bcf_float_is_vector_end(src[src_idx]), bcf_float_set_missing(tgt[tgt_idx]), bcf_float_set_vector_end(tgt[tgt_idx])); break;
+            default: error("Unexpected case: %d, %s\n", fmt_ori->type, key);
+        }
+        #undef BRANCH
+    }
+    args->tmps.l = 0;
+    kputc('L',&args->tmps);
+    kputs(key,&args->tmps);
+    if ( fmt_map[irdr]->type==BCF_BT_FLOAT )
+        bcf_update_format_float(args->out_hdr, out, args->tmps.s, (float*)ma->tmp_arr, nsamples*nsize);
+    else
+        bcf_update_format_int32(args->out_hdr, out, args->tmps.s, (int32_t*)ma->tmp_arr, nsamples*nsize);
+    ma->laa_dirty = 1;
+}
+void merge_localized_numberAR_format_field(args_t *args, bcf_fmt_t **fmt_map, bcf1_t *out, int irdr)
+{
+    int i,j,k, nsamples = bcf_hdr_nsamples(args->out_hdr);
+    bcf_srs_t *files = args->files;
+    maux_t *ma = args->maux;
+    bcf_fmt_t *fmt = fmt_map[irdr];
+    const char *key = files->readers[irdr].header->id[BCF_DT_ID][fmt->id].key;
+    size_t nsize = IS_VL_R(files->readers[irdr].header, fmt->id) ? ma->nlaa + 1 : ma->nlaa;
+    size_t msize = sizeof(float)>sizeof(int32_t) ? sizeof(float) : sizeof(int32_t);
+    msize *= nsamples*nsize;
+    if ( msize > 2147483647 )
+    {
+        static int warned = 0;
+        if ( !warned ) fprintf(bcftools_stderr,"Warning: The row size is too big for FORMAT/%s at %s:%"PRId64", requires %zu bytes, skipping.\n", key,bcf_seqname(args->out_hdr,out),(int64_t) out->pos+1,msize);
+        warned = 1;
+        return;
+    }
+    if ( ma->ntmp_arr < msize )
+    {
+        ma->tmp_arr  = realloc(ma->tmp_arr, msize);
+        if ( !ma->tmp_arr ) error("Failed to allocate %zu bytes at %s:%"PRId64" for FORMAT/%s\n", msize,bcf_seqname(args->out_hdr,out),(int64_t) out->pos+1,key);
+        ma->ntmp_arr = msize;
+    }
+    int ismpl = 0, ibeg = IS_VL_R(files->readers[irdr].header, fmt->id) ? 0 : 1;;
+    for (i=0; i<files->nreaders; i++)
+    {
+        bcf_sr_t *reader = &files->readers[i];
+        bcf_hdr_t *hdr = reader->header;
+        bcf_fmt_t *fmt_ori = fmt_map[i];
+        int nsmpl = bcf_hdr_nsamples(hdr);
+
+        if ( !fmt_ori )
+        {
+            // fill missing values
+            #define BRANCH(tgt_type_t, tgt_set_missing, tgt_set_vector_end) { \
+                for (j=0; j<nsmpl; j++) \
+                { \
+                    tgt_type_t *tgt = (tgt_type_t *) ma->tmp_arr + ismpl*nsize; \
+                    tgt_set_missing; \
+                    for (k=1; k<nsize; k++) { tgt++; tgt_set_vector_end; } \
+                    ismpl++; \
+                } \
+            }
+            switch (fmt->type)
+            {
+                case BCF_BT_INT8:  BRANCH(int32_t, *tgt=bcf_int32_missing, *tgt=bcf_int32_vector_end); break;
+                case BCF_BT_INT16: BRANCH(int32_t, *tgt=bcf_int32_missing, *tgt=bcf_int32_vector_end); break;
+                case BCF_BT_INT32: BRANCH(int32_t, *tgt=bcf_int32_missing, *tgt=bcf_int32_vector_end); break;
+                case BCF_BT_FLOAT: BRANCH(float, bcf_float_set_missing(*tgt), bcf_float_set_vector_end(*tgt)); break;
+                default: error("Unexpected case: %d, %s\n", fmt->type, key);
+            }
+            #undef BRANCH
+            continue;
+        }
+
+        // localize
+        #define BRANCH(tgt_type_t, src_type_t, src_is_missing, src_is_vector_end, tgt_set_missing, tgt_set_vector_end) { \
+            for (j=0; j<nsmpl; j++) \
+            { \
+                src_type_t *src = (src_type_t*) fmt_ori->p + j*fmt_ori->n; \
+                tgt_type_t *tgt = (tgt_type_t *) ma->tmp_arr + ismpl*nsize; \
+                int *laa = ma->laa + (1+args->local_alleles)*ismpl; \
+                int ii,tgt_idx = 0; \
+                for (ii=ibeg; ii<=ma->nlaa; ii++) \
+                { \
+                    if ( laa[ii]==bcf_int32_missing || laa[ii]==bcf_int32_vector_end ) break; \
+                    int src_idx = laa[ii] - ibeg; \
+                    if ( src_is_missing ) tgt_set_missing; \
+                    else if ( src_is_vector_end ) break; \
+                    else tgt[tgt_idx] = src[src_idx]; \
+                    tgt_idx++; \
+                } \
+                if ( !tgt_idx ) { tgt_set_missing; tgt_idx++; } \
+                for (; tgt_idx<nsize; tgt_idx++) tgt_set_vector_end; \
+                ismpl++; \
+            } \
+        }
+        switch (fmt_ori->type)
+        {
+            case BCF_BT_INT8:  BRANCH(int32_t,  int8_t, src[src_idx]==bcf_int8_missing,  src[src_idx]==bcf_int8_vector_end,  tgt[tgt_idx]=bcf_int32_missing, tgt[tgt_idx]=bcf_int32_vector_end); break;
+            case BCF_BT_INT16: BRANCH(int32_t, int16_t, src[src_idx]==bcf_int16_missing, src[src_idx]==bcf_int16_vector_end, tgt[tgt_idx]=bcf_int32_missing, tgt[tgt_idx]=bcf_int32_vector_end); break;
+            case BCF_BT_INT32: BRANCH(int32_t, int32_t, src[src_idx]==bcf_int32_missing, src[src_idx]==bcf_int32_vector_end, tgt[tgt_idx]=bcf_int32_missing, tgt[tgt_idx]=bcf_int32_vector_end); break;
+            case BCF_BT_FLOAT: BRANCH(float, float, bcf_float_is_missing(src[src_idx]), bcf_float_is_vector_end(src[src_idx]), bcf_float_set_missing(tgt[tgt_idx]), bcf_float_set_vector_end(tgt[tgt_idx])); break;
+            default: error("Unexpected case: %d, %s\n", fmt_ori->type, key);
+        }
+        #undef BRANCH
+    }
+    args->tmps.l = 0;
+    kputc('L',&args->tmps);
+    kputs(key,&args->tmps);
+    if ( fmt_map[irdr]->type==BCF_BT_FLOAT )
+        bcf_update_format_float(args->out_hdr, out, args->tmps.s, (float*)ma->tmp_arr, nsamples*nsize);
+    else
+        bcf_update_format_int32(args->out_hdr, out, args->tmps.s, (int32_t*)ma->tmp_arr, nsamples*nsize);
+    ma->laa_dirty = 1;
+}
+void merge_format_field(args_t *args, bcf_fmt_t **fmt_map, bcf1_t *out)
+{
+    bcf_srs_t *files = args->files;
+    bcf_hdr_t *out_hdr = args->out_hdr;
+    maux_t *ma = args->maux;
+    int i, ismpl = 0, nsamples = bcf_hdr_nsamples(out_hdr);
+    static int warned = 0;
+
+    const char *key = NULL;
+    size_t nsize = 0, length = BCF_VL_FIXED;
+    int type = -1;
+    for (i=0; i<files->nreaders; i++)
+    {
+        if ( !maux_get_line(args,i) ) continue;
+        if ( !fmt_map[i] ) continue;
+        if ( !key ) key = files->readers[i].header->id[BCF_DT_ID][fmt_map[i]->id].key;
+        type = fmt_map[i]->type;
+        if ( IS_VL_G(files->readers[i].header, fmt_map[i]->id) )
+        {
+            length = BCF_VL_G;
+            nsize = out->n_allele*(out->n_allele + 1)/2;
+            break;
+        }
+        if ( IS_VL_A(files->readers[i].header, fmt_map[i]->id) )
+        {
+            length = BCF_VL_A;
+            nsize = out->n_allele - 1;
+            break;
+        }
+        if ( IS_VL_R(files->readers[i].header, fmt_map[i]->id) )
+        {
+            length = BCF_VL_R;
+            nsize = out->n_allele;
+            break;
+        }
+        if ( fmt_map[i]->n > nsize ) nsize = fmt_map[i]->n;
+    }
+    if ( ma->nlaa && length!=BCF_VL_FIXED )
+    {
+        if ( length==BCF_VL_G ) merge_localized_numberG_format_field(args,fmt_map,out,i);
+        else if ( length==BCF_VL_A || length==BCF_VL_R ) merge_localized_numberAR_format_field(args,fmt_map,out,i);
+        return;
+    }
+
+    if ( type==BCF_BT_CHAR )
+    {
+        merge_format_string(args, key, fmt_map, out, length, nsize);
+        return;
+    }
+
+    size_t msize = sizeof(float)>sizeof(int32_t) ? sizeof(float) : sizeof(int32_t);
+    msize *= nsamples*nsize;
+    if ( msize > 2147483647 )
+    {
+        if ( !warned ) fprintf(bcftools_stderr,"Warning: The row size is too big for FORMAT/%s at %s:%"PRId64", requires %zu bytes, skipping.\n", key,bcf_seqname(out_hdr,out),(int64_t) out->pos+1,msize);
+        warned = 1;
+        return;
+    }
+    if ( ma->ntmp_arr < msize )
+    {
+        ma->tmp_arr  = realloc(ma->tmp_arr, msize);
+        if ( !ma->tmp_arr ) error("Failed to allocate %zu bytes at %s:%"PRId64" for FORMAT/%s\n", msize,bcf_seqname(args->out_hdr,out),(int64_t) out->pos+1,key);
+        ma->ntmp_arr = msize;
+    }
+
+    // Fill the temp array for all samples by collecting values from all files
+    for (i=0; i<files->nreaders; i++)
+    {
+        bcf_sr_t *reader = &files->readers[i];
+        bcf_hdr_t *hdr = reader->header;
+        bcf_fmt_t *fmt_ori = fmt_map[i];
+        bcf1_t *line = maux_get_line(args, i);
+        int irec = ma->buf[i].cur;
+
+        if ( fmt_ori )
+        {
+            type = fmt_ori->type;
+            int nals_ori = line->n_allele;
+            if ( length==BCF_VL_G )
+            {
+                // if all fields are missing then n==1 is valid
+                if ( fmt_ori->n!=1 && fmt_ori->n != nals_ori*(nals_ori+1)/2 && fmt_map[i]->n != nals_ori )
+                    error("Incorrect number of FORMAT/%s values at %s:%"PRId64", cannot merge. The tag is defined as Number=G, but found\n"
+                          "%d values and %d alleles. See also http://samtools.github.io/bcftools/howtos/FAQ.html#incorrect-nfields\n",
+                          key,bcf_seqname(args->out_hdr,out),(int64_t) out->pos+1,fmt_ori->n,nals_ori);
+            }
+            else if ( length==BCF_VL_A )
+            {
+                if ( fmt_ori->n!=1 && fmt_ori->n != nals_ori-1 )
+                    error("Incorrect number of FORMAT/%s values at %s:%"PRId64", cannot merge. The tag is defined as Number=A, but found\n"
+                          "%d values and %d alleles. See also http://samtools.github.io/bcftools/howtos/FAQ.html#incorrect-nfields\n",
+                          key,bcf_seqname(args->out_hdr,out),(int64_t) out->pos+1,fmt_ori->n,nals_ori);
+            }
+            else if ( length==BCF_VL_R )
+            {
+                if ( fmt_ori->n!=1 && fmt_ori->n != nals_ori )
+                    error("Incorrect number of FORMAT/%s values at %s:%"PRId64", cannot merge. The tag is defined as Number=R, but found\n"
+                          "%d values and %d alleles. See also http://samtools.github.io/bcftools/howtos/FAQ.html#incorrect-nfields\n",
+                          key,bcf_seqname(args->out_hdr,out),(int64_t) out->pos+1,fmt_ori->n,nals_ori);
+            }
+        }
+
+        // set the values
+        #define BRANCH(tgt_type_t, src_type_t, src_is_missing, src_is_vector_end, tgt_set_missing, tgt_set_vector_end) { \
+            int j, l, k; \
+            tgt_type_t *tgt = (tgt_type_t *) ma->tmp_arr + ismpl*nsize; \
+            if ( !fmt_ori ) \
+            { \
+                /* the field is not present in this file, set missing values */ \
+                for (j=0; j<bcf_hdr_nsamples(hdr); j++) \
+                { \
+                    tgt_set_missing; tgt++; for (l=1; l<nsize; l++) { tgt_set_vector_end; tgt++; } \
+                } \
+                ismpl += bcf_hdr_nsamples(hdr); \
+                continue; \
+            } \
+            src_type_t *src = (src_type_t*) fmt_ori->p; \
+            if ( (length!=BCF_VL_G && length!=BCF_VL_A && length!=BCF_VL_R) || (line->n_allele==out->n_allele && !ma->buf[i].rec[irec].als_differ) ) \
+            { \
+                /* alleles unchanged, copy over */ \
+                for (j=0; j<bcf_hdr_nsamples(hdr); j++) \
+                { \
+                    for (l=0; l<fmt_ori->n; l++) \
+                    { \
+                        if ( src_is_vector_end ) break; \
+                        else if ( src_is_missing ) tgt_set_missing; \
+                        else *tgt = *src; \
+                        tgt++; src++; \
+                    } \
+                    for (k=l; k<nsize; k++) { tgt_set_vector_end; tgt++; } \
+                    src += fmt_ori->n - l; \
+                } \
+                ismpl += bcf_hdr_nsamples(hdr); \
+                continue; \
+            } \
+            /* allele numbering needs to be changed */ \
+            if ( length==BCF_VL_G ) \
+            { \
+                /* Number=G tags */ \
+                for (j=0; j<bcf_hdr_nsamples(hdr); j++) \
+                { \
+                    tgt = (tgt_type_t *) ma->tmp_arr + (ismpl+j)*nsize; \
+                    src = (src_type_t*) fmt_ori->p + j*fmt_ori->n; \
+                    if ( (src_is_missing && fmt_ori->n==1) || (++src && src_is_vector_end) ) \
+                    { \
+                        /* tag with missing value "." */ \
+                        tgt_set_missing; \
+                        for (l=1; l<nsize; l++) { tgt++; tgt_set_vector_end; } \
+                        continue; \
+                    } \
+                    int ngsize = ma->smpl_ploidy[ismpl+j]==1 ? out->n_allele : out->n_allele*(out->n_allele + 1)/2; \
+                    for (l=0; l<ngsize; l++) { tgt_set_missing; tgt++; } \
+                    for (; l<nsize; l++) { tgt_set_vector_end; tgt++; } \
+                    if ( ma->smpl_ploidy[ismpl+j]==1 ) \
+                    { \
+                        /* Haploid */ \
+                        int iori, inew; \
+                        for (iori=0; iori<line->n_allele; iori++) \
+                        { \
+                            inew = ma->buf[i].rec[irec].map[iori]; \
+                            src = (src_type_t*) fmt_ori->p + j*fmt_ori->n + iori; \
+                            tgt = (tgt_type_t *) ma->tmp_arr + (ismpl+j)*nsize + inew; \
+                            if ( src_is_vector_end ) break; \
+                            if ( src_is_missing ) tgt_set_missing; \
+                            else *tgt = *src; \
+                        } \
+                    } \
+                    else \
+                    { \
+                        /* Diploid */ \
+                        int iori,jori, inew,jnew; \
+                        for (iori=0; iori<line->n_allele; iori++) \
+                        { \
+                            inew = ma->buf[i].rec[irec].map[iori]; \
+                            for (jori=0; jori<=iori; jori++) \
+                            { \
+                                jnew = ma->buf[i].rec[irec].map[jori]; \
+                                int kori = iori*(iori+1)/2 + jori; \
+                                int knew = inew>jnew ? inew*(inew+1)/2 + jnew : jnew*(jnew+1)/2 + inew; \
+                                src = (src_type_t*) fmt_ori->p + j*fmt_ori->n + kori; \
+                                tgt = (tgt_type_t *) ma->tmp_arr + (ismpl+j)*nsize + knew; \
+                                if ( src_is_vector_end ) \
+                                { \
+                                    iori = line->n_allele; \
+                                    break; \
+                                } \
+                                if ( src_is_missing ) tgt_set_missing; \
+                                else *tgt = *src; \
+                            } \
+                        } \
+                    } \
+                } \
+            } \
+            else \
+            { \
+                /* Number=A or Number=R tags */ \
+                int ifrom = length==BCF_VL_A ? 1 : 0; \
+                for (j=0; j<bcf_hdr_nsamples(hdr); j++) \
+                { \
+                    tgt = (tgt_type_t *) ma->tmp_arr + (ismpl+j)*nsize; \
+                    src = (src_type_t*) (fmt_ori->p + j*fmt_ori->size); \
+                    if ( (src_is_missing && fmt_ori->n==1) || (++src && src_is_vector_end) ) \
+                    { \
+                        /* tag with missing value "." */ \
+                        tgt_set_missing; \
+                        for (l=1; l<nsize; l++) { tgt++; tgt_set_vector_end; } \
+                        continue; \
+                    } \
+                    src = (src_type_t*) (fmt_ori->p + j*fmt_ori->size); \
+                    for (l=0; l<nsize; l++) { tgt_set_missing; tgt++; } \
+                    int iori,inew; \
+                    for (iori=ifrom; iori<line->n_allele; iori++) \
+                    { \
+                        inew = ma->buf[i].rec[irec].map[iori] - ifrom; \
+                        tgt = (tgt_type_t *) ma->tmp_arr + (ismpl+j)*nsize + inew; \
+                        if ( src_is_vector_end ) break; \
+                        if ( src_is_missing ) tgt_set_missing; \
+                        else *tgt = *src; \
+                        src++; \
+                    } \
+                } \
+            } \
+            ismpl += bcf_hdr_nsamples(hdr); \
+        }
+        switch (type)
+        {
+            case BCF_BT_INT8:  BRANCH(int32_t,  int8_t, *src==bcf_int8_missing,  *src==bcf_int8_vector_end,  *tgt=bcf_int32_missing, *tgt=bcf_int32_vector_end); break;
+            case BCF_BT_INT16: BRANCH(int32_t, int16_t, *src==bcf_int16_missing, *src==bcf_int16_vector_end, *tgt=bcf_int32_missing, *tgt=bcf_int32_vector_end); break;
+            case BCF_BT_INT32: BRANCH(int32_t, int32_t, *src==bcf_int32_missing, *src==bcf_int32_vector_end, *tgt=bcf_int32_missing, *tgt=bcf_int32_vector_end); break;
+            case BCF_BT_FLOAT: BRANCH(float, float, bcf_float_is_missing(*src), bcf_float_is_vector_end(*src), bcf_float_set_missing(*tgt), bcf_float_set_vector_end(*tgt)); break;
+            default: error("Unexpected case: %d, %s\n", type, key);
+        }
+        #undef BRANCH
+    }
+    if ( type==BCF_BT_FLOAT )
+        bcf_update_format_float(out_hdr, out, key, (float*)ma->tmp_arr, nsamples*nsize);
+    else
+        bcf_update_format_int32(out_hdr, out, key, (int32_t*)ma->tmp_arr, nsamples*nsize);
+}
+
+void merge_format(args_t *args, bcf1_t *out)
+{
+    bcf_srs_t *files = args->files;
+    bcf_hdr_t *out_hdr = args->out_hdr;
+    maux_t *ma = args->maux;
+    if ( !ma->nfmt_map )
+    {
+        ma->nfmt_map = 2;
+        ma->fmt_map  = (bcf_fmt_t**) calloc(ma->nfmt_map*files->nreaders, sizeof(bcf_fmt_t*));
+    }
+    else
+        memset(ma->fmt_map, 0, ma->nfmt_map*files->nreaders*sizeof(bcf_fmt_t**));
+
+    khiter_t kitr;
+    strdict_t *tmph = args->tmph;
+    kh_clear(strdict, tmph);
+    int i, j, ret, has_GT = 0, has_PL = -1, max_ifmt = 0; // max fmt index
+    for (i=0; i<files->nreaders; i++)
+    {
+        bcf1_t *line = maux_get_line(args,i);
+        if ( !line ) continue;
+        bcf_sr_t *reader = &files->readers[i];
+        bcf_hdr_t *hdr = reader->header;
+        for (j=0; j<line->n_fmt; j++)
+        {
+            // Wat this tag already seen?
+            bcf_fmt_t *fmt = &line->d.fmt[j];
+            const char *key = hdr->id[BCF_DT_ID][fmt->id].key;
+            kitr = kh_get(strdict, tmph, key);
+
+            int ifmt;
+            if ( kitr != kh_end(tmph) )
+                ifmt = kh_value(tmph, kitr);    // seen
+            else
+            {
+                // new FORMAT tag
+                if ( key[0]=='G' && key[1]=='T' && key[2]==0 ) { has_GT = 1; ifmt = 0; }
+                else
+                {
+                    ifmt = ++max_ifmt;
+                    if ( max_ifmt >= ma->nfmt_map )
+                    {
+                        ma->fmt_map = (bcf_fmt_t**) realloc(ma->fmt_map, sizeof(bcf_fmt_t*)*(max_ifmt+1)*files->nreaders);
+                        memset(ma->fmt_map+ma->nfmt_map*files->nreaders, 0, (max_ifmt-ma->nfmt_map+1)*files->nreaders*sizeof(bcf_fmt_t*));
+                        ma->nfmt_map = max_ifmt+1;
+                    }
+                    if ( key[0]=='P' && key[1]=='L' && key[2]==0  ) { has_PL = ifmt; }
+                }
+                kitr = kh_put(strdict, tmph, key, &ret);
+                kh_value(tmph, kitr) = ifmt;
+            }
+            ma->fmt_map[ifmt*files->nreaders+i] = fmt;
+        }
+        // Check if the allele numbering must be changed
+        int irec = ma->buf[i].cur;
+        for (j=1; j<line->n_allele; j++)
+            if ( ma->buf[i].rec[irec].map[j]!=j ) break;
+        ma->buf[i].rec[irec].als_differ = j==line->n_allele ? 0 : 1;
+    }
+
+    if ( args->local_alleles )
+    {
+        ma->laa_dirty = ma->nlaa = 0;
+        if ( out->n_allele > args->local_alleles + 1 ) init_local_alleles(args, out, has_PL);
+    }
+
+    out->n_sample = bcf_hdr_nsamples(out_hdr);
+    if ( has_GT )
+        merge_GT(args, ma->fmt_map, out);
+    if ( !args->keep_AC_AN )
+        update_AN_AC(out_hdr, out);
+
+    for (i=1; i<=max_ifmt; i++)
+        merge_format_field(args, &ma->fmt_map[i*files->nreaders], out);
+
+    if ( ma->laa_dirty )
+        update_local_alleles(args, out);
+
+    out->d.indiv_dirty = 1;
+}
+
+void gvcf_set_alleles(args_t *args)
+{
+    int i,k;
+    bcf_srs_t *files = args->files;
+    maux_t *maux = args->maux;
+    gvcf_aux_t *gaux = maux->gvcf;
+    for (i=0; i<maux->nals; i++)
+    {
+        free(maux->als[i]);
+        maux->als[i] = NULL;
+    }
+    maux->nals = 0;
+
+    for (i=0; i<files->nreaders; i++)
+    {
+        if ( !gaux[i].active ) continue;
+        bcf1_t *line = maux_get_line(args, i);
+        if ( !line ) continue;
+        int irec = maux->buf[i].cur;
+
+        hts_expand(int, line->n_allele, maux->buf[i].rec[irec].mmap, maux->buf[i].rec[irec].map);
+        if ( !maux->nals )    // first record, copy the alleles to the output
+        {
+            maux->nals = line->n_allele;
+            hts_expand0(char*, maux->nals, maux->mals, maux->als);
+            hts_expand0(int, maux->nals, maux->ncnt, maux->cnt);
+            for (k=0; k<maux->nals; k++)
+            {
+                if ( maux->als[k] ) free(maux->als[k]);
+                maux->als[k] = strdup(line->d.allele[k]);
+                maux->buf[i].rec[irec].map[k] = k;
+            }
+        }
+        else
+        {
+            maux->als = merge_alleles(line->d.allele, line->n_allele, maux->buf[i].rec[irec].map, maux->als, &maux->nals, &maux->mals);
+            if ( !maux->als )
+            {
+                bcf_hdr_t *hdr = bcf_sr_get_header(args->files,i);
+                error("Failed to merge alleles at %s:%"PRId64"\n",bcf_seqname(hdr,line),(int64_t) line->pos+1);
+            }
+        }
+    }
+}
+
+/*
+    Output staged gVCF blocks, end is the last position of the block. Assuming
+    gaux[i].active flags are set and maux_get_line returns correct lines.
+    Both start,end coordinates are 0-based.
+*/
+void gvcf_write_block(args_t *args, int start, int end)
+{
+    int i;
+    maux_t *maux = args->maux;
+    gvcf_aux_t *gaux = maux->gvcf;
+    assert(gaux);
+
+    // Update POS
+    int min = INT_MAX;  // the minimum active gVCF INFO/END (0-based)
+    char ref = 'N';
+    for (i=0; i<args->files->nreaders; i++)
+    {
+        if ( !gaux[i].active ) continue;
+        if ( ref=='N' && gaux[i].line->pos==start ) ref = gaux[i].line->d.allele[0][0];
+        gaux[i].line->pos = start;
+    }
+    for (i=0; i<args->files->nreaders; i++)
+    {
+        if ( !gaux[i].active ) continue;
+        if ( gaux[i].end < start )
+        {
+            gaux[i].active = 0;
+            maux->buf[i].cur = -1;
+            continue;
+        }
+        gaux[i].line->d.allele[0][0] = ref;
+        if ( min > gaux[i].end ) min = gaux[i].end;
+    }
+    // Check for valid gVCF blocks in this region
+    if ( min==INT_MAX ) // this probably should not happen
+    {
+    assert(0);
+        maux->gvcf_min = 0;
+        return;
+    }
+
+    bcf1_t *out = args->out_line;
+
+    gvcf_set_alleles(args);
+
+    // Merge the staged lines
+    merge_chrom2qual(args, out);
+    merge_filter(args, out);
+    merge_info(args, out);
+    merge_format(args, out);
+
+    if ( args->gvcf_fai && out->d.allele[0][0]=='N' )
+    {
+        int slen  = 0;
+        char *seq = faidx_fetch_seq(args->gvcf_fai,maux->chr,out->pos,out->pos,&slen);
+        if (slen)
+        {
+            out->d.allele[0][0] = seq[0];
+            free(seq);
+        }
+    }
+
+    // Update END boundary
+    if ( end > start )
+    {
+        end++;
+        bcf_update_info_int32(args->out_hdr, out, "END", &end, 1);
+    }
+    else
+        bcf_update_info_int32(args->out_hdr, out, "END", NULL, 0);
+    if ( bcf_write1(args->out_fh, args->out_hdr, out)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->output_fname);
+    bcf_clear1(out);
+
+
+    // Inactivate blocks which do not extend beyond END and find new gvcf_min
+    min = INT_MAX;
+    for (i=0; i<args->files->nreaders; i++)
+    {
+        if ( !gaux[i].active ) continue;
+        if ( gaux[i].end < end )
+        {
+            gaux[i].active = 0;
+            maux->buf[i].cur = -1;
+            continue;
+        }
+        // next min END position bigger than the current one
+        if ( maux->gvcf_min < gaux[i].end+1 && min > gaux[i].end+1 ) min = gaux[i].end + 1;
+    }
+    maux->gvcf_min = min==INT_MAX ? 0 : min;
+}
+
+/*
+    Flush staged gVCF blocks. Flush everything if there are no more lines
+    (done=1) or if there is a new chromosome. If still on the same chromosome,
+    all hanging blocks must be ended by creating new records:
+        A
+            1 END=10
+        B
+            3 END=7
+        C
+            3 END=5
+        out
+            1 END=2  A . .
+            3 END=5  A B C
+            6 END=7  A B .
+            8 END=10 A . .
+
+*/
+void gvcf_flush(args_t *args, int done)
+{
+    int i;
+    maux_t *maux = args->maux;
+
+    if ( !maux->chr ) return;   // first time here, nothing to flush
+
+    int flush_until = INT_MAX;
+    if ( !done )
+    {
+        // Get current position and chromosome
+        for (i=0; i<maux->n; i++)
+            if ( bcf_sr_has_line(maux->files,i) ) break;
+        bcf1_t *line = bcf_sr_get_line(maux->files,i);
+        bcf_hdr_t *hdr = bcf_sr_get_header(maux->files,i);
+
+        if ( !strcmp(maux->chr,bcf_seqname(hdr,line)) ) flush_until = line->pos;    // still on the same chr
+    }
+
+    // When called on a region, trim the blocks accordingly
+    int start = maux->gvcf_break>=0 ? maux->gvcf_break + 1 : maux->pos;     // the start of a new gvcf block to output
+    if ( args->regs )
+    {
+        int rstart = -1, rend = -1;
+        if ( regidx_overlap(args->regs,maux->chr,start,flush_until,args->regs_itr) )
+        {
+            // In case there are multiple regions, we treat them as one
+            rstart = args->regs_itr->beg;
+            while ( regitr_overlap(args->regs_itr) ) rend = args->regs_itr->end;
+        }
+        if ( rstart > start ) start = rstart;
+        if ( rend < flush_until ) flush_until = rend+1;
+    }
+
+    // output all finished blocks
+    while ( maux->gvcf_min && start < flush_until )
+    {
+        // does the block end before the new line or is it interrupted?
+        int tmp = maux->gvcf_min < flush_until ? maux->gvcf_min : flush_until;
+        if ( start > tmp-1 ) break;
+        gvcf_write_block(args,start,tmp-1); // gvcf_min is 1-based, passing 0-based coordinates
+        start = tmp;
+    }
+}
+
+static inline int is_gvcf_block(bcf1_t *line)
+{
+    if ( line->rlen<=1 ) return 0;
+    if ( strlen(line->d.allele[0])==line->rlen ) return 0;
+    if ( line->n_allele==1 ) return 1;
+
+    int i;
+    for (i=1; i<line->n_allele; i++)
+    {
+        if ( !strcmp(line->d.allele[i],"<*>") ) return 1;
+        if ( !strcmp(line->d.allele[i],"<NON_REF>") ) return 1;
+        if ( !strcmp(line->d.allele[i],"<X>") ) return 1;
+    }
+    return 0;
+}
+
+// Lines can come with any combination of variant types. We use a subset of types defined in vcf.h
+// but shift by two bits to account for VCF_REF defined as 0 (design flaw in vcf.h, my fault) and
+// to accommodate for VCF_GVCF_REF defined below
+static const int
+    snp_mask = (VCF_SNP<<2)|(VCF_MNP<<2),
+    indel_mask = VCF_INDEL<<2,
+    ins_mask = VCF_INS<<2,
+    del_mask = VCF_DEL<<2,
+    ref_mask = 2;
+
+/*
+    Check incoming lines for new gVCF blocks, set pointer to the current source
+    buffer (gvcf or readers).  In contrast to gvcf_flush, this function can be
+    called only after maux_reset as it relies on updated maux buffers.
+    The coordinate is 0-based
+*/
+void gvcf_stage(args_t *args, int pos)
+{
+    maux_t *maux = args->maux;
+    gvcf_aux_t *gaux = maux->gvcf;
+    bcf_srs_t *files = args->files;
+    int32_t *end = (int32_t*) maux->tmp_arr;
+    int i, nend = maux->ntmp_arr / sizeof(int32_t);
+
+    maux->gvcf_break = -1;
+    maux->gvcf_min = INT_MAX;
+    for (i=0; i<files->nreaders; i++)
+    {
+        if ( gaux[i].active && gaux[i].end < pos ) gaux[i].active = 0;
+        if ( gaux[i].active )
+        {
+            // gvcf block should not overlap with another record
+            if ( maux->gvcf_min > gaux[i].end+1 ) maux->gvcf_min = gaux[i].end + 1;
+            maux->buf[i].beg = 0;
+            maux->buf[i].end = 1;
+            maux->buf[i].cur = 0;
+            continue;
+        }
+
+        // Does any of the lines have END set? It is enough to check only the
+        // first line, there should be no duplicate records with END in gVCF
+
+        if ( maux->buf[i].beg==maux->buf[i].end ) continue; // no new record
+
+        int irec = maux->buf[i].beg;
+        bcf_hdr_t *hdr = bcf_sr_get_header(files, i);
+        bcf1_t *line = args->files->readers[i].buffer[irec];
+        int ret = is_gvcf_block(line) ? bcf_get_info_int32(hdr,line,"END",&end,&nend) : 0;
+        if ( ret==1 )
+        {
+            if ( end[0] == line->pos + 1 )  // POS and INFO/END are identical, treat as if a normal w/o INFO/END
+            {
+                maux->gvcf_break = line->pos;
+                continue;
+            }
+            if ( end[0] <= line->pos ) error("Error: Incorrect END at %s:%"PRId64" .. END=%d\n", bcf_seqname(hdr,line),(int64_t) line->pos+1,end[0]);
+
+            // END is set, this is a new gVCF block. Cache this line in gaux[i] and swap with
+            // an empty record: the gaux line must be kept until we reach its END.
+
+            gaux[i].active = 1;
+            gaux[i].end = end[0] - 1;
+            SWAP(bcf1_t*,args->files->readers[i].buffer[irec],gaux[i].line);
+            gaux[i].line->pos = pos;
+
+            maux->buf[i].lines = &gaux[i].line;
+            maux->buf[i].beg = 0;
+            maux->buf[i].end = 1;
+            maux->buf[i].cur = 0;
+
+            // Set the rid,pos of the swapped line in the buffer or else the
+            // synced reader will have a problem with the next line
+            //
+            args->files->readers[i].buffer[irec]->rid = maux->buf[i].rid;
+            args->files->readers[i].buffer[irec]->pos = maux->pos;
+
+            // Update block offsets
+            if ( maux->gvcf_min > gaux[i].end+1 ) maux->gvcf_min = gaux[i].end + 1;
+        }
+        else
+            maux->gvcf_break = line->pos;   // must break the gvcf block
+    }
+    maux->ntmp_arr = nend * sizeof(int32_t);
+    maux->tmp_arr  = end;
+    if ( maux->gvcf_min==INT_MAX ) maux->gvcf_min = 0;
+}
+
+
+void debug_buffers(FILE *fp, bcf_srs_t *files);
+void debug_buffer(FILE *fp, bcf_srs_t *files, int reader);
+
+/*
+    Flush all buffered and processed records with the same coordinate.
+    Note that synced reader discards buffer[0], so that needs to stay
+    untouched.
+*/
+void clean_buffer(args_t *args)
+{
+    maux_t *ma = args->maux;
+
+    int ir;
+    for (ir=0; ir<ma->n; ir++)
+    {
+        // Invalidate pointer to reader's buffer or else gvcf_flush will attempt
+        // to use the old lines via maux_get_line()
+        if ( ma->gvcf )
+        {
+            if ( ma->gvcf[ir].active )
+            {
+                if ( ma->pos >= ma->gvcf[ir].end )  ma->gvcf[ir].active = 0;
+                else if ( ma->buf[ir].cur==-1 ) ma->buf[ir].cur = ma->buf[ir].beg;  // re-activate interrupted gVCF block
+            }
+            if ( !ma->gvcf[ir].active ) ma->buf[ir].cur = -1;
+        }
+
+        bcf_sr_t *reader = bcf_sr_get_reader(args->files,ir);
+        if ( !reader->nbuffer ) continue;   // nothing to clean
+
+        bcf1_t **buf = reader->buffer;
+        if ( buf[1]->rid!=ma->buf[ir].rid || buf[1]->pos!=ma->pos ) continue;    // nothing to flush
+
+        int a = 1, b = 2;
+        while ( b<=reader->nbuffer && buf[b]->rid==ma->buf[ir].rid && buf[b]->pos==ma->pos ) b++;
+        // b now points to the first line we want to preserve
+        while ( b<=reader->nbuffer )
+        {
+            SWAP(bcf1_t*, buf[a], buf[b]);
+            a++; b++;
+        }
+        reader->nbuffer -= b-a;
+    }
+}
+
+void debug_maux(args_t *args)
+{
+    bcf_srs_t *files = args->files;
+    maux_t *maux = args->maux;
+    int j,k,l;
+
+    fprintf(bcftools_stderr,"Alleles to merge at %d, nals=%d\n", maux->pos+1,maux->nals);
+    for (j=0; j<files->nreaders; j++)
+    {
+        bcf_sr_t *reader = &files->readers[j];
+        buffer_t *buf = &maux->buf[j];
+        fprintf(bcftools_stderr," reader %d: ", j);
+        for (k=buf->beg; k<buf->end; k++)
+        {
+            if ( buf->rec[k].skip & SKIP_DONE ) continue;
+            bcf1_t *line = reader->buffer[k];
+            fprintf(bcftools_stderr,"\t");
+            if ( buf->rec[k].skip ) fprintf(bcftools_stderr,"[");  // this record will not be merged in this round
+            for (l=0; l<line->n_allele; l++)
+                fprintf(bcftools_stderr,"%s%s", l==0?"":",", line->d.allele[l]);
+            if ( buf->rec[k].skip ) fprintf(bcftools_stderr,"]");
+        }
+        fprintf(bcftools_stderr,"\n");
+    }
+    fprintf(bcftools_stderr," counts: ");
+    for (j=0; j<maux->nals; j++) fprintf(bcftools_stderr,"%s   %dx %s", j==0?"":",",maux->cnt[j], maux->als[j]);
+    fprintf(bcftools_stderr,"\n\n");
+}
+
+void debug_state(args_t *args)
+{
+    maux_t *maux = args->maux;
+    int i,j;
+    for (i=0; i<args->files->nreaders; i++)
+    {
+        fprintf(bcftools_stderr,"reader %d:\tcur,beg,end=% d,%d,%d", i,maux->buf[i].cur,maux->buf[i].beg,maux->buf[i].end);
+        if ( maux->buf[i].cur >=0 )
+        {
+            bcf_hdr_t *hdr = bcf_sr_get_header(args->files,i);
+            const char *chr = bcf_hdr_id2name(hdr, maux->buf[i].rid);
+            fprintf(bcftools_stderr,"\t");
+            for (j=maux->buf[i].beg; j<maux->buf[i].end; j++) fprintf(bcftools_stderr," %s:%"PRId64,chr,(int64_t) maux->buf[i].lines[j]->pos+1);
+        }
+        fprintf(bcftools_stderr,"\n");
+    }
+    fprintf(bcftools_stderr,"gvcf_min=%d\n", args->maux->gvcf_min);
+    for (i=0; i<args->files->nreaders; i++)
+    {
+        fprintf(bcftools_stderr,"reader %d:\tgvcf_active=%d", i,maux->gvcf[i].active);
+        if ( maux->gvcf[i].active ) fprintf(bcftools_stderr,"\tpos,end=%"PRId64",%"PRId64, (int64_t) maux->gvcf[i].line->pos+1,(int64_t) maux->gvcf[i].end+1);
+        fprintf(bcftools_stderr,"\n");
+    }
+    fprintf(bcftools_stderr,"\n");
+}
+
+/*
+   Determine which line should be merged from which reader: go through all
+   readers and all buffered lines, expand REF,ALT and try to match lines with
+   the same ALTs.
+ */
+int can_merge(args_t *args)
+{
+    bcf_srs_t *files = args->files;
+    maux_t *maux = args->maux;
+    gvcf_aux_t *gaux = maux->gvcf;
+    char *id = NULL, ref = 'N';
+    int i,j,k, ntodo = 0;
+
+    for (i=0; i<maux->nals; i++)
+    {
+        free(maux->als[i]);
+        maux->als[i] = NULL;
+    }
+    maux->var_types = maux->nals = 0;
+
+    // this is only for the `-m none -g` mode, ensure that <*> lines come last
+    #define VCF_GVCF_REF 1
+
+    for (i=0; i<files->nreaders; i++)
+    {
+        buffer_t *buf = &maux->buf[i];
+
+        if ( gaux && gaux[i].active )
+        {
+            // skip readers with active gvcf blocks
+            buf->rec[buf->beg].skip = SKIP_DIFF;
+            continue;
+        }
+        for (j=buf->beg; j<buf->end; j++)
+        {
+            if ( buf->rec[j].skip & SKIP_DONE ) continue;
+
+            buf->rec[j].skip = SKIP_DIFF;
+            ntodo++;
+
+            bcf1_t *line = buf->lines[j];
+            if ( args->merge_by_id )
+                id = line->d.id;
+            else
+            {
+                int var_type = bcf_has_variant_types(line, VCF_ANY, bcf_match_overlap);
+                if (var_type < 0) error("bcf_has_variant_types() failed.");
+                if ( args->collapse==COLLAPSE_SNP_INS_DEL )
+                {
+                    // need to distinguish between ins and del so strip the VCF_INDEL flag
+                    var_type &= ~VCF_INDEL;
+                }
+                maux->var_types |= var_type ? var_type<<2 : 2;
+
+                // for the `-m none -g` mode
+                if ( args->collapse==COLLAPSE_NONE && args->do_gvcf && is_gvcf_block(line) )
+                    maux->var_types |= VCF_GVCF_REF;
+            }
+        }
+
+        // for gvcf: find out REF at this position
+        if ( buf->beg < buf->end && ref=='N' )
+            ref = buf->lines[buf->beg]->d.allele[0][0];
+    }
+    if ( !ntodo ) return 0;
+
+    // In this loop we select from each reader compatible candidate lines.
+    // (i.e. SNPs or indels). Go through all files and all lines at this
+    // position and normalize relevant alleles.
+    // REF-only sites may be associated with both SNPs and indels.
+    for (i=0; i<files->nreaders; i++)
+    {
+        bcf_sr_t *reader = &files->readers[i];
+        buffer_t *buf = &maux->buf[i];
+
+        if ( gaux && gaux[i].active )
+        {
+            gaux[i].line->d.allele[0][0] = ref;
+            gaux[i].line->pos = maux->pos;
+        }
+
+        for (j=buf->beg; j<buf->end; j++)
+        {
+            if ( buf->rec[j].skip & SKIP_DONE ) continue;
+
+            bcf1_t *line = buf->lines[j]; // ptr to reader's buffer or gvcf buffer
+
+            int line_type = bcf_has_variant_types(line, VCF_ANY, bcf_match_overlap);
+            if (line_type < 0) error("bcf_has_variant_types() failed.");
+            line_type = line_type ? line_type<<2 : 2;
+
+            // select relevant lines
+            if ( args->merge_by_id )
+            {
+                if ( strcmp(id,line->d.id) ) continue;
+            }
+            else
+            {
+                // when merging gVCF in -m none mode, make sure that gVCF blocks with the same POS as variant
+                // records come last, otherwise infinite loop is created (#1164)
+                if ( args->collapse==COLLAPSE_NONE && args->do_gvcf )
+                {
+                    if ( is_gvcf_block(line) && (maux->var_types & (~(VCF_GVCF_REF|2))) ) continue;
+                }
+                if ( args->collapse==COLLAPSE_NONE && maux->nals )
+                {
+                    // All alleles of the tested record must be present in the
+                    // selected maux record plus variant types must be the same
+                    if ( (maux->var_types & line_type) != line_type ) continue;
+                    if ( vcmp_set_ref(args->vcmp,maux->als[0],line->d.allele[0]) < 0 ) continue;   // refs not compatible
+                    for (k=1; k<line->n_allele; k++)
+                    {
+                        if ( vcmp_find_allele(args->vcmp,maux->als+1,maux->nals-1,line->d.allele[k])>=0 ) break;
+                    }
+                    if ( !(line_type&ref_mask) && k==line->n_allele ) continue;  // not a REF-only site and there is no matching allele
+                }
+                if ( !(args->collapse&COLLAPSE_ANY) )
+                {
+                    // Merge:
+                    //  - SNPs+SNPs+MNPs+REF if -m both,snps
+                    //  - indels+indels+REF  if -m both,indels, REF only if SNPs are not present
+                    //  - SNPs come first
+                    if ( line_type & (indel_mask|ins_mask|del_mask) )
+                    {
+                        if ( !(line_type&snp_mask) && maux->var_types&snp_mask ) continue;  // SNPs come first
+                        if ( args->do_gvcf && maux->var_types&ref_mask ) continue;  // never merge indels with gVCF blocks
+                    }
+                }
+            }
+            buf->rec[j].skip = 0;
+
+            hts_expand(int, line->n_allele, buf->rec[j].mmap, buf->rec[j].map);
+            if ( !maux->nals )    // first record, copy the alleles to the output
+            {
+                maux->nals = line->n_allele;
+                hts_expand0(char*, maux->nals, maux->mals, maux->als);
+                hts_expand0(int, maux->nals, maux->ncnt, maux->cnt);
+                for (k=0; k<maux->nals; k++)
+                {
+                    free(maux->als[k]);
+                    maux->als[k] = strdup(line->d.allele[k]);
+                    buf->rec[j].map[k] = k;
+                    maux->cnt[k] = 1;
+                }
+                continue;
+            }
+            // normalize alleles
+            maux->als = merge_alleles(line->d.allele, line->n_allele, buf->rec[j].map, maux->als, &maux->nals, &maux->mals);
+            if ( !maux->als ) error("Failed to merge alleles at %s:%"PRId64" in %s\n",maux->chr,(int64_t) line->pos+1,reader->fname);
+            hts_expand0(int, maux->nals, maux->ncnt, maux->cnt);
+            for (k=1; k<line->n_allele; k++)
+                maux->cnt[ buf->rec[j].map[k] ]++;    // how many times an allele appears in the files
+            maux->cnt[0]++;
+        }
+    }
+    return 1;
+}
+
+/*
+   Select records that have the same alleles; the input ordering of indels
+   must not matter. Multiple VCF lines can be emitted from this loop.
+   We expect only very few alleles and not many records with the same
+   position in the buffers, therefore the nested loops should not slow us
+   much.
+*/
+void stage_line(args_t *args)
+{
+    bcf_srs_t *files = args->files;
+    maux_t *maux = args->maux;
+
+    // debug_maux(args);
+
+    // take the most frequent allele present in multiple files, REF is skipped
+    int i,j,k,icnt = 1;
+    for (i=2; i<maux->nals; i++)
+        if ( maux->cnt[i] > maux->cnt[icnt] ) icnt = i;
+
+    int nout = 0;
+    for (i=0; i<files->nreaders; i++)
+    {
+        buffer_t *buf = &maux->buf[i];
+        buf->cur = -1;
+        if ( buf->beg >= buf->end ) continue;   // no lines in the buffer
+
+        // find lines with the same allele
+        for (j=buf->beg; j<buf->end; j++)
+        {
+            if ( buf->rec[j].skip ) continue;   // done or not compatible
+            if ( args->merge_by_id ) break;
+            if ( maux->nals==1 && buf->lines[j]->n_allele==1 ) break;   // REF-only record
+
+            for (k=0; k<buf->lines[j]->n_allele; k++)
+                if ( icnt==buf->rec[j].map[k] ) break;
+
+            if ( k<buf->lines[j]->n_allele ) break;
+        }
+        if ( j>=buf->end )
+        {
+            // no matching allele found in this file
+            if ( args->collapse==COLLAPSE_NONE ) continue;
+
+            for (j=buf->beg; j<buf->end; j++)
+            {
+                if ( buf->rec[j].skip ) continue;   // done or not compatible
+                if ( args->collapse&COLLAPSE_ANY ) break;   // anything can be merged
+                int line_type = bcf_has_variant_types(buf->lines[j], VCF_ANY, bcf_match_overlap);
+                if (line_type < 0) error("bcf_has_variant_types() failed.");
+                if ( maux->var_types&snp_mask && line_type&VCF_SNP && (args->collapse&COLLAPSE_SNPS) ) break;
+                if ( maux->var_types&indel_mask && line_type&VCF_INDEL && (args->collapse&COLLAPSE_INDELS) ) break;
+                if ( maux->var_types&ins_mask && line_type&VCF_INS && (args->collapse&COLLAPSE_SNP_INS_DEL) ) break;
+                if ( maux->var_types&del_mask && line_type&VCF_DEL && (args->collapse&COLLAPSE_SNP_INS_DEL) ) break;
+                if ( line_type==VCF_REF )
+                {
+                    if ( maux->var_types&snp_mask && (args->collapse&COLLAPSE_SNPS) ) break;
+                    if ( maux->var_types&indel_mask && (args->collapse&COLLAPSE_INDELS) ) break;
+                    if ( maux->var_types&ins_mask && (args->collapse&COLLAPSE_SNP_INS_DEL) ) break;
+                    if ( maux->var_types&del_mask && (args->collapse&COLLAPSE_SNP_INS_DEL) ) break;
+                    if ( maux->var_types&ref_mask ) break;
+                }
+                else if ( maux->var_types&ref_mask )
+                {
+                    if ( line_type&snp_mask && (args->collapse&COLLAPSE_SNPS) ) break;
+                    if ( line_type&indel_mask && (args->collapse&COLLAPSE_INDELS) ) break;
+                    if ( line_type&ins_mask && (args->collapse&COLLAPSE_SNP_INS_DEL) ) break;
+                    if ( line_type&del_mask && (args->collapse&COLLAPSE_SNP_INS_DEL) ) break;
+                }
+            }
+        }
+        if ( j<buf->end )
+        {
+            // found a suitable line for merging
+            buf->cur = j;
+
+            // mark as finished so that it's ignored next time
+            buf->rec[j].skip  = SKIP_DONE;
+            nout++;
+        }
+    }
+    assert( nout );
+}
+
+void merge_line(args_t *args)
+{
+    bcf1_t *out = args->out_line;
+    merge_chrom2qual(args, out);
+    if ( args->regs && !regidx_overlap(args->regs,args->maux->chr,out->pos,out->pos+out->rlen-1,NULL) ) return;
+    merge_filter(args, out);
+    merge_info(args, out);
+    if ( args->do_gvcf )
+        bcf_update_info_int32(args->out_hdr, out, "END", NULL, 0);
+    merge_format(args, out);
+    if ( bcf_write1(args->out_fh, args->out_hdr, out)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->output_fname);
+    bcf_clear1(out);
+}
+
+void bcf_hdr_append_version(bcf_hdr_t *hdr, int argc, char **argv, const char *cmd)
+{
+    kstring_t str = {0,0,0};
+    int e = 0;
+    if (ksprintf(&str,"##%sVersion=%s+htslib-%s\n", cmd, bcftools_version(), hts_version()) < 0)
+        goto fail;
+    if (bcf_hdr_append(hdr,str.s) < 0)
+        goto fail;
+
+    str.l = 0;
+    e |= ksprintf(&str,"##%sCommand=%s", cmd, argv[0]) < 0;
+    int i;
+    for (i=1; i<argc; i++)
+    {
+        if ( strchr(argv[i],' ') )
+            e |= ksprintf(&str, " '%s'", argv[i]) < 0;
+        else
+            e |= ksprintf(&str, " %s", argv[i]) < 0;
+    }
+    e |= kputs("; Date=", &str) < 0;
+    time_t tm; time(&tm);
+    e |= kputs(ctime(&tm), &str) < 0;
+    e |= kputc('\n', &str) < 0;
+    if (e)
+        goto fail;
+    if (bcf_hdr_append(hdr,str.s) < 0)
+        goto fail;
+    free(ks_release(&str));
+
+    if (bcf_hdr_sync(hdr) < 0)
+        goto fail;
+    return;
+
+ fail:
+    free(str.s);
+    error_errno("[%s] Failed to add program information to header", __func__);
+}
+
+void hdr_add_localized_tags(args_t *args, bcf_hdr_t *hdr)
+{
+    char **str = NULL;
+    int i,j, nstr = 0, mstr = 0;
+    for (i=0; i<hdr->nhrec; i++)
+    {
+        if ( hdr->hrec[i]->type!=BCF_HL_FMT ) continue;
+        j = bcf_hrec_find_key(hdr->hrec[i],"ID");
+        if ( j<0 ) continue;
+        char *key = hdr->hrec[i]->vals[j];
+        int id = bcf_hdr_id2int(hdr, BCF_DT_ID, key);
+        assert( id>=0 );
+        int localize = 0;
+        if ( bcf_hdr_id2length(hdr,BCF_HL_FMT,id) == BCF_VL_G ) localize = 1;
+        if ( bcf_hdr_id2length(hdr,BCF_HL_FMT,id) == BCF_VL_A ) localize = 1;
+        if ( bcf_hdr_id2length(hdr,BCF_HL_FMT,id) == BCF_VL_R ) localize = 1;
+        if ( !localize ) continue;
+        args->tmps.l = 0;
+
+        uint32_t e = 0, nout = 0;
+        e |= ksprintf(&args->tmps, "##%s=<", hdr->hrec[i]->key) < 0;
+        for (j=0; j<hdr->hrec[i]->nkeys; j++)
+        {
+            if ( !strcmp("IDX",hdr->hrec[i]->keys[j]) ) continue;
+            if ( nout ) e |= kputc(',',&args->tmps) < 0;
+            if ( !strcmp("ID",hdr->hrec[i]->keys[j]) )
+                e |= ksprintf(&args->tmps,"%s=L%s", hdr->hrec[i]->keys[j], hdr->hrec[i]->vals[j]) < 0;
+            else if ( !strcmp("Number",hdr->hrec[i]->keys[j]) )
+                e |= ksprintf(&args->tmps,"Number=.") < 0;
+            else if ( !strcmp("Description",hdr->hrec[i]->keys[j]) && hdr->hrec[i]->vals[j][0]=='"' )
+                e |= ksprintf(&args->tmps,"Description=\"Localized field: %s", hdr->hrec[i]->vals[j]+1) < 0;
+            else
+                e |= ksprintf(&args->tmps,"%s=%s", hdr->hrec[i]->keys[j], hdr->hrec[i]->vals[j]) < 0;
+            nout++;
+        }
+        e |= ksprintf(&args->tmps,">\n") < 0;
+        if ( e ) error("Failed to format the header line for %s\n", key);
+        nstr++;
+        hts_expand(char*,nstr,mstr,str);
+        str[nstr-1] = strdup(args->tmps.s);
+    }
+    if ( !nstr ) return;
+    bcf_hdr_append(hdr,"##FORMAT=<ID=LAA,Number=.,Type=Integer,Description=\"Localized alleles: subset of alternate alleles relevant for each sample\">");
+    for (i=0; i<nstr; i++)
+    {
+        bcf_hdr_append(hdr, str[i]);
+        free(str[i]);
+    }
+    free(str);
+}
+void merge_vcf(args_t *args)
+{
+    char wmode[8];
+    set_wmode(wmode,args->output_type,args->output_fname,args->clevel);
+    args->out_fh = hts_open(args->output_fname ? args->output_fname : "-", wmode);
+    if ( args->out_fh == NULL ) error("Can't write to \"%s\": %s\n", args->output_fname, strerror(errno));
+    if ( args->n_threads ) hts_set_opt(args->out_fh, HTS_OPT_THREAD_POOL, args->files->p); //hts_set_threads(args->out_fh, args->n_threads);
+    args->out_hdr = bcf_hdr_init("w");
+
+    if ( args->header_fname )
+    {
+        if ( bcf_hdr_set(args->out_hdr,args->header_fname) ) error("Could not read/parse the header: %s\n", args->header_fname);
+    }
+    else
+    {
+        int i;
+        for (i=0; i<args->files->nreaders; i++)
+        {
+            char buf[24]; snprintf(buf,sizeof buf,"%d",i+1);
+            merge_headers(args->out_hdr, args->files->readers[i].header,buf,args->force_samples);
+        }
+        if ( args->local_alleles ) hdr_add_localized_tags(args, args->out_hdr);
+        if (args->record_cmd_line) bcf_hdr_append_version(args->out_hdr, args->argc, args->argv, "bcftools_merge");
+        if (bcf_hdr_sync(args->out_hdr) < 0)
+            error_errno("[%s] Failed to update header", __func__);
+    }
+    info_rules_init(args);
+
+    bcf_hdr_set_version(args->out_hdr, bcf_hdr_get_version(args->files->readers[0].header));
+    if ( bcf_hdr_write(args->out_fh, args->out_hdr)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->output_fname);
+    if ( args->header_only )
+    {
+        bcf_hdr_destroy(args->out_hdr);
+        if ( hts_close(args->out_fh)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,args->output_fname);
+        return;
+    }
+
+    if ( args->collapse==COLLAPSE_NONE ) args->vcmp = vcmp_init();
+    args->maux = maux_init(args);
+    args->out_line = bcf_init1();
+    args->tmph = kh_init(strdict);
+
+    int *rid_tab = calloc(args->maux->n, sizeof(*rid_tab));
+    if (!rid_tab)
+        error("[%s:%d] Could not allocate %zu bytes\n", __FILE__, __LINE__, args->maux->n*sizeof(*rid_tab));
+
+    while ( bcf_sr_next_line(args->files) )
+    {
+        // output cached gVCF blocks which end before the new record
+        if ( args->do_gvcf )
+            gvcf_flush(args,0);
+
+        maux_reset(args->maux, rid_tab);
+
+        // determine which of the new records are gvcf blocks
+        if ( args->do_gvcf )
+            gvcf_stage(args, args->maux->pos);
+
+        while ( can_merge(args) )
+        {
+            stage_line(args);
+            merge_line(args);
+        }
+        clean_buffer(args);
+        // debug_state(args);
+    }
+    free(rid_tab);
+    if ( args->do_gvcf )
+        gvcf_flush(args,1);
+
+    info_rules_destroy(args);
+    maux_destroy(args->maux);
+    bcf_hdr_destroy(args->out_hdr);
+    if ( hts_close(args->out_fh)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,args->output_fname);
+    bcf_destroy1(args->out_line);
+    kh_destroy(strdict, args->tmph);
+    if ( args->tmps.m ) free(args->tmps.s);
+    if ( args->vcmp ) vcmp_destroy(args->vcmp);
+}
+
+static void usage(void)
+{
+    fprintf(bcftools_stderr, "\n");
+    fprintf(bcftools_stderr, "About:   Merge multiple VCF/BCF files from non-overlapping sample sets to create one multi-sample file.\n");
+    fprintf(bcftools_stderr, "         Note that only records from different files can be merged, never from the same file. For\n");
+    fprintf(bcftools_stderr, "         \"vertical\" merge take a look at \"bcftools norm\" instead.\n");
+    fprintf(bcftools_stderr, "Usage:   bcftools merge [options] <A.vcf.gz> <B.vcf.gz> [...]\n");
+    fprintf(bcftools_stderr, "\n");
+    fprintf(bcftools_stderr, "Options:\n");
+    fprintf(bcftools_stderr, "        --force-samples               Resolve duplicate sample names\n");
+    fprintf(bcftools_stderr, "        --print-header                Print only the merged header and exit\n");
+    fprintf(bcftools_stderr, "        --use-header FILE             Use the provided header\n");
+    fprintf(bcftools_stderr, "    -0  --missing-to-ref              Assume genotypes at missing sites are 0/0\n");
+    fprintf(bcftools_stderr, "    -f, --apply-filters LIST          Require at least one of the listed FILTER strings (e.g. \"PASS,.\")\n");
+    fprintf(bcftools_stderr, "    -F, --filter-logic x|+            Remove filters if some input is PASS (\"x\"), or apply all filters (\"+\") [+]\n");
+    fprintf(bcftools_stderr, "    -g, --gvcf -|REF.FA               Merge gVCF blocks, INFO/END tag is expected. Implies -i QS:sum,MinDP:min,I16:sum,IDV:max,IMF:max\n");
+    fprintf(bcftools_stderr, "    -i, --info-rules TAG:METHOD,..    Rules for merging INFO fields (method is one of sum,avg,min,max,join) or \"-\" to turn off the default [DP:sum,DP4:sum]\n");
+    fprintf(bcftools_stderr, "    -l, --file-list FILE              Read file names from the file\n");
+    fprintf(bcftools_stderr, "    -L, --local-alleles INT           EXPERIMENTAL: if more than <int> ALT alleles are encountered, drop FMT/PL and output LAA+LPL instead; 0=unlimited [0]\n");
+    fprintf(bcftools_stderr, "    -m, --merge STRING                Allow multiallelic records for <snps|indels|both|snp-ins-del|all|none|id>, see man page for details [both]\n");
+    fprintf(bcftools_stderr, "        --no-index                    Merge unindexed files, the same chromosomal order is required and -r/-R are not allowed\n");
+    fprintf(bcftools_stderr, "        --no-version                  Do not append version and command line to the header\n");
+    fprintf(bcftools_stderr, "    -o, --output FILE                 Write output to a file [standard output]\n");
+    fprintf(bcftools_stderr, "    -O, --output-type u|b|v|z[0-9]    u/b: un/compressed BCF, v/z: un/compressed VCF, 0-9: compression level [v]\n");
+    fprintf(bcftools_stderr, "    -r, --regions REGION              Restrict to comma-separated list of regions\n");
+    fprintf(bcftools_stderr, "    -R, --regions-file FILE           Restrict to regions listed in a file\n");
+    fprintf(bcftools_stderr, "        --regions-overlap 0|1|2       Include if POS in the region (0), record overlaps (1), variant overlaps (2) [1]\n");
+    fprintf(bcftools_stderr, "        --threads INT                 Use multithreading with <int> worker threads [0]\n");
+    fprintf(bcftools_stderr, "\n");
+    bcftools_exit(1);
+}
+
+int main_vcfmerge(int argc, char *argv[])
+{
+    int c;
+    args_t *args = (args_t*) calloc(1,sizeof(args_t));
+    args->files  = bcf_sr_init();
+    args->argc   = argc; args->argv = argv;
+    args->output_fname = "-";
+    args->output_type = FT_VCF;
+    args->n_threads = 0;
+    args->record_cmd_line = 1;
+    args->collapse = COLLAPSE_BOTH;
+    args->clevel = -1;
+    int regions_is_file = 0;
+    int regions_overlap = 1;
+
+    static struct option loptions[] =
+    {
+        {"help",no_argument,NULL,'h'},
+        {"merge",required_argument,NULL,'m'},
+        {"local-alleles",required_argument,NULL,'L'},
+        {"gvcf",required_argument,NULL,'g'},
+        {"file-list",required_argument,NULL,'l'},
+        {"missing-to-ref",no_argument,NULL,'0'},
+        {"apply-filters",required_argument,NULL,'f'},
+        {"use-header",required_argument,NULL,1},
+        {"print-header",no_argument,NULL,2},
+        {"force-samples",no_argument,NULL,3},
+        {"output",required_argument,NULL,'o'},
+        {"output-type",required_argument,NULL,'O'},
+        {"threads",required_argument,NULL,9},
+        {"regions",required_argument,NULL,'r'},
+        {"regions-file",required_argument,NULL,'R'},
+        {"regions-overlap",required_argument,NULL,4},
+        {"info-rules",required_argument,NULL,'i'},
+        {"no-version",no_argument,NULL,8},
+        {"no-index",no_argument,NULL,10},
+        {"filter-logic",required_argument,NULL,'F'},
+        {NULL,0,NULL,0}
+    };
+    char *tmp;
+    while ((c = getopt_long(argc, argv, "hm:f:r:R:o:O:i:l:g:F:0L:",loptions,NULL)) >= 0) {
+        switch (c) {
+            case 'L':
+                args->local_alleles = strtol(optarg,&tmp,10);
+                if ( *tmp ) error("Could not parse argument: --local-alleles %s\n", optarg);
+                if ( args->local_alleles < 1 )
+                    error("Error: \"--local-alleles %s\" makes no sense, expected value bigger or equal than 1\n", optarg);
+                break;
+            case 'F':
+                if ( !strcmp(optarg,"+") ) args->filter_logic = FLT_LOGIC_ADD;
+                else if ( !strcmp(optarg,"x") ) args->filter_logic = FLT_LOGIC_REMOVE;
+                else error("Filter logic not recognised: %s\n", optarg);
+                break;
+            case '0': args->missing_to_ref = 1; break;
+            case 'g':
+                args->do_gvcf = 1;
+                if ( strcmp("-",optarg) )
+                {
+                    args->gvcf_fai = fai_load(optarg);
+                    if ( !args->gvcf_fai ) error("Failed to load the fai index: %s\n", optarg);
+                }
+                break;
+            case 'l': args->file_list = optarg; break;
+            case 'i': args->info_rules = optarg; break;
+            case 'o': args->output_fname = optarg; break;
+            case 'O':
+                switch (optarg[0]) {
+                    case 'b': args->output_type = FT_BCF_GZ; break;
+                    case 'u': args->output_type = FT_BCF; break;
+                    case 'z': args->output_type = FT_VCF_GZ; break;
+                    case 'v': args->output_type = FT_VCF; break;
+                    default:
+                    {
+                        args->clevel = strtol(optarg,&tmp,10);
+                        if ( *tmp || args->clevel<0 || args->clevel>9 ) error("The output type \"%s\" not recognised\n", optarg);
+                    }
+                }
+                if ( optarg[1] )
+                {
+                    args->clevel = strtol(optarg+1,&tmp,10);
+                    if ( *tmp || args->clevel<0 || args->clevel>9 ) error("Could not parse argument: --compression-level %s\n", optarg+1);
+                }
+                break;
+            case 'm':
+                args->collapse = COLLAPSE_NONE;
+                if ( !strcmp(optarg,"snps") ) args->collapse |= COLLAPSE_SNPS;
+                else if ( !strcmp(optarg,"indels") ) args->collapse |= COLLAPSE_INDELS;
+                else if ( !strcmp(optarg,"both") ) args->collapse |= COLLAPSE_BOTH;
+                else if ( !strcmp(optarg,"any") ) args->collapse |= COLLAPSE_ANY;
+                else if ( !strcmp(optarg,"all") ) args->collapse |= COLLAPSE_ANY;
+                else if ( !strcmp(optarg,"none") ) args->collapse = COLLAPSE_NONE;
+                else if ( !strcmp(optarg,"snp-ins-del") ) args->collapse = COLLAPSE_SNP_INS_DEL;
+                else if ( !strcmp(optarg,"id") ) { args->collapse = COLLAPSE_NONE; args->merge_by_id = 1; }
+                else error("The -m type \"%s\" is not recognised.\n", optarg);
+                break;
+            case 'f': args->files->apply_filters = optarg; break;
+            case 'r': args->regions_list = optarg; break;
+            case 'R': args->regions_list = optarg; regions_is_file = 1; break;
+            case  1 : args->header_fname = optarg; break;
+            case  2 : args->header_only = 1; break;
+            case  3 : args->force_samples = 1; break;
+            case  4 :
+                regions_overlap = parse_overlap_option(optarg);
+                if ( regions_overlap < 0 ) error("Could not parse: --regions-overlap %s\n",optarg);
+                break;
+            case  9 : args->n_threads = strtol(optarg, 0, 0); break;
+            case  8 : args->record_cmd_line = 0; break;
+            case 10 : args->no_index = 1; break;
+            case 'h':
+            case '?': usage(); break;
+            default: error("Unknown argument: %s\n", optarg);
+        }
+    }
+    if ( argc==optind && !args->file_list ) usage();
+    if ( argc-optind<2 && !args->file_list ) usage();
+
+    if ( args->no_index )
+    {
+        if ( args->regions_list ) error("Error: cannot combine --no-index with -r/-R\n");
+        bcf_sr_set_opt(args->files,BCF_SR_ALLOW_NO_IDX);
+    }
+    else
+        bcf_sr_set_opt(args->files,BCF_SR_REQUIRE_IDX);
+    if ( args->regions_list )
+    {
+        bcf_sr_set_opt(args->files,BCF_SR_REGIONS_OVERLAP,regions_overlap);
+        if ( bcf_sr_set_regions(args->files, args->regions_list, regions_is_file)<0 )
+            error("Failed to read the regions: %s\n", args->regions_list);
+        if ( regions_is_file )
+            args->regs = regidx_init(args->regions_list,NULL,NULL,sizeof(char*),NULL);
+        else
+        {
+            args->regs = regidx_init(NULL,regidx_parse_reg,NULL,sizeof(char*),NULL);
+            if ( regidx_insert_list(args->regs,args->regions_list,',') !=0 ) error("Could not parse the regions: %s\n", args->regions_list);
+            regidx_insert(args->regs,NULL);
+        }
+        if ( !args->regs ) error("Could not parse the regions: %s\n", args->regions_list);
+        args->regs_itr = regitr_init(args->regs);
+    }
+
+    if ( bcf_sr_set_threads(args->files, args->n_threads)<0 ) error("Failed to create threads\n");
+    while (optind<argc)
+    {
+        if ( !bcf_sr_add_reader(args->files, argv[optind]) ) error("Failed to open %s: %s\n", argv[optind],bcf_sr_strerror(args->files->errnum));
+        optind++;
+    }
+    if ( args->file_list )
+    {
+        int nfiles, i;
+        char **files = hts_readlines(args->file_list, &nfiles);
+        if ( !files ) error("Failed to read from %s\n", args->file_list);
+        for (i=0;i<nfiles; i++)
+            if ( !bcf_sr_add_reader(args->files, files[i]) ) error("Failed to open %s: %s\n", files[i],bcf_sr_strerror(args->files->errnum));
+        for (i=0; i<nfiles; i++) free(files[i]);
+        free(files);
+    }
+    merge_vcf(args);
+    bcf_sr_destroy(args->files);
+    if ( args->regs ) regidx_destroy(args->regs);
+    if ( args->regs_itr ) regitr_destroy(args->regs_itr);
+    if ( args->gvcf_fai ) fai_destroy(args->gvcf_fai);
+    free(args);
+    return 0;
+}
+
diff --git a/bcftools/vcfnorm.c b/bcftools/vcfnorm.c
new file mode 100644
index 0000000..38c5de4
--- /dev/null
+++ b/bcftools/vcfnorm.c
@@ -0,0 +1,2295 @@
+/*  vcfnorm.c -- Left-align and normalize indels.
+
+    Copyright (C) 2013-2021 Genome Research Ltd.
+
+    Author: Petr Danecek <pd3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.  */
+
+#include <stdio.h>
+#include <strings.h>
+#include <unistd.h>
+#include <getopt.h>
+#include <assert.h>
+#include <ctype.h>
+#include <string.h>
+#include <errno.h>
+#include <sys/stat.h>
+#include <sys/types.h>
+#include <inttypes.h>
+#include <htslib/vcf.h>
+#include <htslib/synced_bcf_reader.h>
+#include <htslib/faidx.h>
+#include <htslib/khash_str2int.h>
+#include "bcftools.h"
+#include "rbuf.h"
+#include "abuf.h"
+
+#define CHECK_REF_EXIT 1
+#define CHECK_REF_WARN 2
+#define CHECK_REF_SKIP 4
+#define CHECK_REF_FIX  8
+
+#define MROWS_SPLIT 1
+#define MROWS_MERGE  2
+
+// for -m+, mapping from allele indexes of a single input record
+// to allele indexes of output record
+typedef struct
+{
+    int nals, mals, *map;
+}
+map_t;
+
+// primitive comparison of two records' alleles via hashes; normalized alleles assumed
+typedef struct
+{
+    int n;  // number of alleles
+    char *ref, *alt;
+    void *hash;
+}
+cmpals1_t;
+
+typedef struct
+{
+    cmpals1_t *cmpals;
+    int ncmpals, mcmpals;
+}
+cmpals_t;
+
+typedef struct
+{
+    char *tseq, *seq;
+    int mseq;
+    bcf1_t **lines, **tmp_lines, **alines, **blines, *mrow_out;
+    int ntmp_lines, mtmp_lines, nalines, malines, nblines, mblines;
+    map_t *maps;     // mrow map for each buffered record
+    char **als;
+    int mmaps, nals, mals;
+    uint8_t *tmp_arr1, *tmp_arr2, *diploid;
+    int32_t *int32_arr;
+    int ntmp_arr1, ntmp_arr2, nint32_arr;
+    kstring_t *tmp_str;
+    kstring_t *tmp_als, tmp_kstr;
+    int ntmp_als;
+    rbuf_t rbuf;
+    int buf_win;            // maximum distance between two records to consider
+    int aln_win;            // the realignment window size (maximum repeat size)
+    bcf_srs_t *files;       // using the synced reader only for -r option
+    bcf_hdr_t *hdr, *out_hdr;
+    cmpals_t cmpals_in, cmpals_out;
+    faidx_t *fai;
+    struct { int tot, set, swap; } nref;
+    char **argv, *output_fname, *ref_fname, *vcf_fname, *region, *targets;
+    int argc, rmdup, output_type, n_threads, check_ref, strict_filter, do_indels, clevel;
+    int nchanged, nskipped, nsplit, ntotal, mrows_op, mrows_collapse, parsimonious;
+    int record_cmd_line, force, force_warned, keep_sum_ad;
+    abuf_t *abuf;
+    abuf_opt_t atomize;
+    int use_star_allele;
+    char *old_rec_tag;
+    htsFile *out;
+}
+args_t;
+
+static inline int replace_iupac_codes(char *seq, int nseq)
+{
+    // Replace ambiguity codes with N for now, it awaits to be seen what the VCF spec codifies in the end
+    int i, n = 0;
+    for (i=0; i<nseq; i++)
+    {
+        char c = toupper(seq[i]);
+        if ( c!='A' && c!='C' && c!='G' && c!='T' && c!='N' ) { seq[i] = 'N'; n++; }
+    }
+    return n;
+}
+static inline int has_non_acgtn(char *seq, int nseq)
+{
+    char *end = seq + nseq;
+    while ( *seq && seq<end )
+    {
+        char c = toupper(*seq);
+        if ( c!='A' && c!='C' && c!='G' && c!='T' && c!='N' ) return 1;
+        seq++;
+    }
+    return 0;
+}
+
+static void seq_to_upper(char *seq, int len)
+{
+    int i;
+    if ( len )
+        for (i=0; i<len; i++) seq[i] = nt_to_upper(seq[i]);
+    else
+        for (i=0; seq[i]; i++) seq[i] = nt_to_upper(seq[i]);
+}
+
+static void fix_ref(args_t *args, bcf1_t *line)
+{
+    bcf_unpack(line, BCF_UN_STR);
+    int reflen = strlen(line->d.allele[0]);
+    int i,j, maxlen = reflen, len;
+    for (i=1; i<line->n_allele; i++)
+    {
+        int len = strlen(line->d.allele[i]);
+        if ( maxlen < len ) maxlen = len;
+    }
+
+    char *ref = faidx_fetch_seq(args->fai, (char*)bcf_seqname(args->hdr,line), line->pos, line->pos+maxlen-1, &len);
+    if ( !ref ) error("faidx_fetch_seq failed at %s:%"PRId64"\n", bcf_seqname(args->hdr,line),(int64_t) line->pos+1);
+    replace_iupac_codes(ref,len);
+
+    args->nref.tot++;
+
+    // is the REF different? If not, we are done
+    if ( !strncasecmp(line->d.allele[0],ref,reflen) ) { free(ref); return; }
+
+    // is the REF allele missing?
+    if ( reflen==1 && line->d.allele[0][0]=='.' )
+    {
+        line->d.allele[0][0] = ref[0];
+        args->nref.set++;
+        free(ref);
+        bcf_update_alleles(args->out_hdr,line,(const char**)line->d.allele,line->n_allele);
+        return;
+    }
+
+    // does REF or ALT contain non-standard bases?
+    int has_non_acgtn = 0;
+    for (i=0; i<line->n_allele; i++)
+    {
+        if ( line->d.allele[i][0]=='<' ) continue;
+        has_non_acgtn += replace_iupac_codes(line->d.allele[i],strlen(line->d.allele[i]));
+    }
+    if ( has_non_acgtn )
+    {
+        args->nref.set++;
+        bcf_update_alleles(args->out_hdr,line,(const char**)line->d.allele,line->n_allele);
+        if ( !strncasecmp(line->d.allele[0],ref,reflen) ) { free(ref); return; }
+    }
+
+    // does the REF allele contain N's ?
+    int fix = 0;
+    for (i=0; i<reflen; i++)
+    {
+        if ( line->d.allele[0][i]!='N' ) continue;
+        if ( ref[i]=='N' ) continue;
+        line->d.allele[0][i] = ref[i];
+        fix++;
+        for (j=1; j<line->n_allele; j++)
+        {
+            int len = strlen(line->d.allele[j]);
+            if ( len <= i || line->d.allele[j][i]!='N' ) continue;
+            line->d.allele[j][i] = ref[i];
+            fix++;
+        }
+    }
+    if ( fix )
+    {
+        args->nref.set++;
+        bcf_update_alleles(args->out_hdr,line,(const char**)line->d.allele,line->n_allele);
+        if ( !strncasecmp(line->d.allele[0],ref,reflen) ) { free(ref); return; }
+    }
+
+
+    // is it swapped?
+    for (i=1; i<line->n_allele; i++)
+    {
+        int len = strlen(line->d.allele[i]);
+        if ( !strncasecmp(line->d.allele[i],ref,len) ) break;
+    }
+
+    kstring_t str = {0,0,0};
+    if ( i==line->n_allele )    // none of the alternate alleles matches the reference
+    {
+        args->nref.set++;
+        kputsn(ref,reflen,&str);
+        for (i=1; i<line->n_allele; i++)
+        {
+            kputc(',',&str);
+            kputs(line->d.allele[i],&str);
+        }
+        bcf_update_alleles_str(args->out_hdr,line,str.s);
+        free(ref);
+        free(str.s);
+        return;
+    }
+
+    // one of the alternate alleles matches the reference, assume it's a simple swap
+    kputs(line->d.allele[i],&str);
+    for (j=1; j<line->n_allele; j++)
+    {
+        kputc(',',&str);
+        if ( j==i )
+            kputs(line->d.allele[0],&str);
+        else
+            kputs(line->d.allele[j],&str);
+    }
+    bcf_update_alleles_str(args->out_hdr,line,str.s);
+    args->nref.swap++;
+    free(ref);
+    free(str.s);
+
+    // swap genotypes
+    int ntmp = args->ntmp_arr1 / sizeof(int32_t); // reuse tmp_arr declared as uint8_t
+    int ngts = bcf_get_genotypes(args->hdr, line, &args->tmp_arr1, &ntmp);
+    args->ntmp_arr1 = ntmp * sizeof(int32_t);
+    int32_t *gts = (int32_t*) args->tmp_arr1;
+    int ni = 0;
+    for (j=0; j<ngts; j++)
+    {
+        if ( gts[j]==bcf_gt_unphased(0) ) { gts[j] = bcf_gt_unphased(i); ni++; }
+        else if ( gts[j]==bcf_gt_phased(0) ) { gts[j] = bcf_gt_phased(i); ni++; }
+        else if ( gts[j]==bcf_gt_unphased(i) ) gts[j] = bcf_gt_unphased(0);
+        else if ( gts[j]==bcf_gt_phased(i) ) gts[j] = bcf_gt_phased(0);
+    }
+    bcf_update_genotypes(args->out_hdr,line,gts,ngts);
+
+    // update AC
+    int nac = bcf_get_info_int32(args->hdr, line, "AC", &args->tmp_arr1, &ntmp);
+    args->ntmp_arr1 = ntmp * sizeof(int32_t);
+    if ( i <= nac )
+    {
+        int32_t *ac = (int32_t*)args->tmp_arr1;
+        ac[i-1] = ni;
+        bcf_update_info_int32(args->out_hdr, line, "AC", ac, nac);
+    }
+}
+
+static void fix_dup_alt(args_t *args, bcf1_t *line)
+{
+    // update alleles, create a mapping between old and new indexes
+    hts_expand(uint8_t,line->n_allele,args->ntmp_arr1,args->tmp_arr1);
+    args->tmp_arr1[0] = 0;  // ref always unchanged
+
+    int i, j, nals = line->n_allele, nals_ori = line->n_allele;
+    for (i=1, j=1; i<line->n_allele; i++)
+    {
+        if ( strcasecmp(line->d.allele[0],line->d.allele[i]) )
+        {
+            args->tmp_arr1[i] = j++;
+            continue;
+        }
+        args->tmp_arr1[i] = 0;
+        nals--;
+    }
+    for (i=1, j=1; i<line->n_allele; i++)
+    {
+        if ( !args->tmp_arr1[i] ) continue;
+        line->d.allele[j++] = line->d.allele[i];
+    }
+    bcf_update_alleles(args->out_hdr, line, (const char**)line->d.allele, nals);
+
+
+    // update genotypes
+    int ntmp = args->ntmp_arr2 / sizeof(int32_t); // reuse tmp_arr declared as uint8_t
+    int ngts = bcf_get_genotypes(args->hdr, line, &args->tmp_arr2, &ntmp);
+    args->ntmp_arr2 = ntmp * sizeof(int32_t);
+    int32_t *gts = (int32_t*) args->tmp_arr2;
+    int changed = 0;
+    for (i=0; i<ngts; i++)
+    {
+        if ( bcf_gt_is_missing(gts[i]) || gts[i]==bcf_int32_vector_end ) continue;
+        int ial = bcf_gt_allele(gts[i]);
+        if ( ial<nals_ori && ial==args->tmp_arr1[ial] ) continue;
+        int ial_new = ial<nals_ori ? args->tmp_arr1[ial] : 0;
+        gts[i] = bcf_gt_is_phased(gts[i]) ? bcf_gt_phased(ial_new) : bcf_gt_unphased(ial_new);
+        changed = 1;
+    }
+    if ( changed ) bcf_update_genotypes(args->out_hdr,line,gts,ngts);
+}
+
+static void set_old_rec_tag(args_t *args, bcf1_t *dst, bcf1_t *src, int ialt)
+{
+    if ( !args->old_rec_tag ) return;
+
+    // only update if the tag is not present already, there can be multiple normalization steps
+    int i, id = bcf_hdr_id2int(args->out_hdr, BCF_DT_ID, args->old_rec_tag);
+    bcf_unpack(dst, BCF_UN_INFO);
+    for (i=0; i<dst->n_info; i++)
+    {
+        bcf_info_t *inf = &dst->d.info[i];
+        if ( inf && inf->key == id ) return;
+    }
+
+    args->tmp_kstr.l = 0;
+    ksprintf(&args->tmp_kstr,"%s|%"PRIhts_pos"|%s|",bcf_seqname(args->hdr,src),src->pos+1,src->d.allele[0]);
+    for (i=1; i<src->n_allele; i++)
+    {
+        kputs(src->d.allele[i],&args->tmp_kstr);
+        if ( i+1<src->n_allele ) kputc(',',&args->tmp_kstr);
+    }
+    if ( ialt>0 )
+    {
+        kputc('|',&args->tmp_kstr);
+        kputw(ialt,&args->tmp_kstr);
+    }
+    if ( (bcf_update_info_string(args->out_hdr, dst, args->old_rec_tag, args->tmp_kstr.s))!=0 )
+            error("An error occurred while updating INFO/%s\n",args->old_rec_tag);
+}
+
+#define ERR_DUP_ALLELE       -2
+#define ERR_REF_MISMATCH     -1
+#define ERR_OK                0
+#define ERR_SYMBOLIC          1
+#define ERR_SPANNING_DELETION 2
+
+static int realign(args_t *args, bcf1_t *line)
+{
+    bcf_unpack(line, BCF_UN_STR);
+
+    // Sanity check REF
+    int i, nref, reflen = strlen(line->d.allele[0]);
+    char *ref = faidx_fetch_seq(args->fai, (char*)args->hdr->id[BCF_DT_CTG][line->rid].key, line->pos, line->pos+reflen-1, &nref);
+    if ( !ref ) error("faidx_fetch_seq failed at %s:%"PRId64"\n", args->hdr->id[BCF_DT_CTG][line->rid].key, (int64_t) line->pos+1);
+    seq_to_upper(ref,0);
+    replace_iupac_codes(ref,nref);  // any non-ACGT character in fasta ref is replaced with N
+
+    // does VCF REF contain non-standard bases?
+    if ( has_non_acgtn(line->d.allele[0],reflen) )
+    {
+        if ( args->check_ref==CHECK_REF_EXIT )
+            error("Non-ACGTN reference allele at %s:%"PRId64" .. REF_SEQ:'%s' vs VCF:'%s'\n", bcf_seqname(args->hdr,line),(int64_t) line->pos+1,ref,line->d.allele[0]);
+        if ( args->check_ref & CHECK_REF_WARN )
+            fprintf(stderr,"NON_ACGTN_REF\t%s\t%"PRId64"\t%s\n", bcf_seqname(args->hdr,line),(int64_t) line->pos+1,line->d.allele[0]);
+        free(ref);
+        return ERR_REF_MISMATCH;
+    }
+    if ( strcasecmp(ref,line->d.allele[0]) )
+    {
+        if ( args->check_ref==CHECK_REF_EXIT )
+            error("Reference allele mismatch at %s:%"PRId64" .. REF_SEQ:'%s' vs VCF:'%s'\n", bcf_seqname(args->hdr,line),(int64_t) line->pos+1,ref,line->d.allele[0]);
+        if ( args->check_ref & CHECK_REF_WARN )
+            fprintf(stderr,"REF_MISMATCH\t%s\t%"PRId64"\t%s\t%s\n", bcf_seqname(args->hdr,line),(int64_t) line->pos+1,line->d.allele[0],ref);
+        free(ref);
+        return ERR_REF_MISMATCH;
+    }
+    free(ref);
+    ref = NULL;
+
+    if ( line->n_allele == 1 ) // a REF
+    {
+        if ( line->rlen > 1 )
+        {
+            line->d.allele[0][1] = 0;
+            bcf_update_alleles(args->out_hdr,line,(const char**)line->d.allele,line->n_allele);
+        }
+        return ERR_OK;
+    }
+    if ( bcf_get_variant_types(line)==VCF_BND ) return ERR_SYMBOLIC;   // breakend, not an error
+
+    // make a copy of each allele for trimming
+    hts_expand0(kstring_t,line->n_allele,args->ntmp_als,args->tmp_als);
+    kstring_t *als = args->tmp_als;
+    for (i=0; i<line->n_allele; i++)
+    {
+        if ( line->d.allele[i][0]=='<' ) return ERR_SYMBOLIC;  // symbolic allele
+        if ( line->d.allele[i][0]=='*' ) return ERR_SPANNING_DELETION;  // spanning deletion
+        if ( has_non_acgtn(line->d.allele[i],line->shared.l) )
+        {
+            if ( args->check_ref==CHECK_REF_EXIT )
+                error("Non-ACGTN alternate allele at %s:%"PRId64" .. VCF:'%s'\n", bcf_seqname(args->hdr,line),(int64_t) line->pos+1,line->d.allele[i]);
+            if ( args->check_ref & CHECK_REF_WARN )
+                fprintf(stderr,"NON_ACGTN_ALT\t%s\t%"PRId64"\t%s\n", bcf_seqname(args->hdr,line),(int64_t) line->pos+1,line->d.allele[i]);
+            return ERR_REF_MISMATCH;
+        }
+
+        als[i].l = 0;
+        kputs(line->d.allele[i], &als[i]);
+        seq_to_upper(als[i].s,0);
+
+        if ( i>0 && als[i].l==als[0].l && !strcasecmp(als[0].s,als[i].s) ) return ERR_DUP_ALLELE;
+    }
+
+    // trim from right
+    int new_pos = line->pos;
+    while (1)
+    {
+        // is the rightmost base identical in all alleles?
+        int min_len = als[0].l;
+        for (i=1; i<line->n_allele; i++)
+        {
+            if ( toupper(als[0].s[ als[0].l-1 ])!=toupper(als[i].s[ als[i].l-1 ]) ) break;
+            if ( als[i].l < min_len ) min_len = als[i].l;
+        }
+        if ( i!=line->n_allele ) break; // there are differences, cannot be trimmed
+        if ( min_len<=1 && new_pos==0 ) break;
+
+        int pad_from_left = 0;
+        for (i=0; i<line->n_allele; i++) // trim all alleles
+        {
+            als[i].l--;
+            if ( !als[i].l ) pad_from_left = 1;
+        }
+        if ( pad_from_left )
+        {
+            int npad = new_pos >= args->aln_win ? args->aln_win : new_pos;
+            free(ref);
+            ref = faidx_fetch_seq(args->fai, (char*)args->hdr->id[BCF_DT_CTG][line->rid].key, new_pos-npad, new_pos-1, &nref);
+            if ( !ref ) error("faidx_fetch_seq failed at %s:%"PRId64"\n", args->hdr->id[BCF_DT_CTG][line->rid].key, (int64_t) new_pos-npad+1);
+            replace_iupac_codes(ref,nref);
+            for (i=0; i<line->n_allele; i++)
+            {
+                ks_resize(&als[i], als[i].l + npad);
+                if ( als[i].l ) memmove(als[i].s+npad,als[i].s,als[i].l);
+                memcpy(als[i].s,ref,npad);
+                als[i].l += npad;
+            }
+            new_pos -= npad;
+        }
+    }
+    free(ref);
+
+    // trim from left
+    int ntrim_left = 0;
+    while (1)
+    {
+        // is the first base identical in all alleles?
+        int min_len = als[0].l - ntrim_left;
+        for (i=1; i<line->n_allele; i++)
+        {
+            if ( als[0].s[ntrim_left]!=als[i].s[ntrim_left] ) break;
+            if ( min_len > als[i].l - ntrim_left ) min_len = als[i].l - ntrim_left;
+        }
+        if ( i!=line->n_allele || min_len<=1 ) break; // there are differences, cannot be trimmed
+        ntrim_left++;
+    }
+    if ( ntrim_left )
+    {
+        for (i=0; i<line->n_allele; i++)
+        {
+            memmove(als[i].s,als[i].s+ntrim_left,als[i].l-ntrim_left);
+            als[i].l -= ntrim_left;
+        }
+        new_pos += ntrim_left;
+    }
+
+    // Have the alleles changed?
+    als[0].s[ als[0].l ] = 0;  // in order for strcmp to work
+    if ( new_pos==line->pos && !strcasecmp(line->d.allele[0],als[0].s) ) return ERR_OK;
+
+    set_old_rec_tag(args, line, line, 0);
+
+    // Create new block of alleles and update
+    args->tmp_kstr.l = 0;
+    for (i=0; i<line->n_allele; i++)
+    {
+        if (i>0) kputc(',',&args->tmp_kstr);
+        kputsn(als[i].s,als[i].l,&args->tmp_kstr);
+    }
+    args->tmp_kstr.s[ args->tmp_kstr.l ] = 0;
+    bcf_update_alleles_str(args->out_hdr,line,args->tmp_kstr.s);
+    args->nchanged++;
+
+    // Update INFO/END if necessary
+    int new_reflen = strlen(line->d.allele[0]);
+    if ( (new_pos!=line->pos || reflen!=new_reflen) && bcf_get_info_int32(args->hdr, line, "END", &args->int32_arr, &args->nint32_arr)==1 )
+    {
+        // bcf_update_alleles_str() messed up rlen because line->pos changed. This will be fixed by bcf_update_info_int32()
+        line->pos = new_pos;
+        args->int32_arr[0] = line->pos + new_reflen;
+        bcf_update_info_int32(args->out_hdr, line, "END", args->int32_arr, 1);
+    }
+    line->pos = new_pos;
+
+    return ERR_OK;
+}
+
+static void split_info_numeric(args_t *args, bcf1_t *src, bcf_info_t *info, int ialt, bcf1_t *dst)
+{
+    #define BRANCH_NUMERIC(type,type_t,is_vector_end,is_missing) \
+    { \
+        const char *tag = bcf_hdr_int2id(args->hdr,BCF_DT_ID,info->key); \
+        int ntmp = args->ntmp_arr1 / sizeof(type_t); \
+        int ret = bcf_get_info_##type(args->hdr,src,tag,&args->tmp_arr1,&ntmp); \
+        args->ntmp_arr1 = ntmp * sizeof(type_t); \
+        assert( ret>0 ); \
+        type_t *vals = (type_t*) args->tmp_arr1; \
+        int len = bcf_hdr_id2length(args->hdr,BCF_HL_INFO,info->key); \
+        if ( len==BCF_VL_A ) \
+        { \
+            if ( ret!=src->n_allele-1 ) \
+            { \
+                if ( args->force && !args->force_warned ) \
+                { \
+                    fprintf(stderr, \
+                        "Warning: wrong number of fields in INFO/%s at %s:%"PRId64", expected %d, found %d\n" \
+                        "         (This warning is printed only once.)\n", \
+                        tag,bcf_seqname(args->hdr,src),(int64_t) src->pos+1,src->n_allele-1,ret); \
+                    args->force_warned = 1; \
+                } \
+                if ( args->force ) \
+                { \
+                    bcf_update_info_##type(args->out_hdr,dst,tag,NULL,0); \
+                    return; \
+                } \
+                error("Error: wrong number of fields in INFO/%s at %s:%"PRId64", expected %d, found %d\n", \
+                        tag,bcf_seqname(args->hdr,src),(int64_t) src->pos+1,src->n_allele-1,ret); \
+            } \
+            bcf_update_info_##type(args->out_hdr,dst,tag,vals+ialt,1); \
+        } \
+        else if ( len==BCF_VL_R ) \
+        { \
+            if ( ret!=src->n_allele ) \
+            { \
+                if ( args->force && !args->force_warned ) \
+                { \
+                    fprintf(stderr, \
+                        "Warning: wrong number of fields in INFO/%s at %s:%"PRId64", expected %d, found %d\n" \
+                        "         (This warning is printed only once.)\n", \
+                        tag,bcf_seqname(args->hdr,src),(int64_t) src->pos+1,src->n_allele,ret); \
+                    args->force_warned = 1; \
+                } \
+                if ( args->force ) \
+                { \
+                    bcf_update_info_##type(args->out_hdr,dst,tag,NULL,0); \
+                    return; \
+                } \
+                error("Error: wrong number of fields in INFO/%s at %s:%"PRId64", expected %d, found %d\n", \
+                        tag,bcf_seqname(args->hdr,src),(int64_t) src->pos+1,src->n_allele,ret); \
+            } \
+            if ( args->keep_sum_ad >= 0 && args->keep_sum_ad==info->key ) \
+            { \
+                int j; \
+                for (j=1; j<info->len; j++) \
+                    if ( j!=ialt+1 && !(is_missing) && !(is_vector_end) ) vals[0] += vals[j]; \
+                vals[1] = vals[ialt+1]; \
+            } \
+            else \
+            { \
+                if ( ialt!=0 ) vals[1] = vals[ialt+1]; \
+            } \
+            bcf_update_info_##type(args->out_hdr,dst,tag,vals,2); \
+        } \
+        else if ( len==BCF_VL_G ) \
+        { \
+            if ( ret!=src->n_allele*(src->n_allele+1)/2 ) \
+            { \
+                if ( args->force && !args->force_warned ) \
+                { \
+                    fprintf(stderr, \
+                        "Warning: wrong number of fields in INFO/%s at %s:%"PRId64", expected %d, found %d\n" \
+                        "         (This warning is printed only once.)\n", \
+                        tag,bcf_seqname(args->hdr,src),(int64_t) src->pos+1,src->n_allele*(src->n_allele+1)/2,ret); \
+                    args->force_warned = 1; \
+                } \
+                if ( args->force ) \
+                { \
+                    bcf_update_info_##type(args->out_hdr,dst,tag,NULL,0); \
+                    return; \
+                } \
+                error("Error: wrong number of fields in INFO/%s at %s:%"PRId64", expected %d, found %d\n", \
+                        tag,bcf_seqname(args->hdr,src),(int64_t) src->pos+1,src->n_allele*(src->n_allele+1)/2,ret); \
+            } \
+            if ( ialt!=0 ) \
+            { \
+                vals[1] = vals[bcf_alleles2gt(0,ialt+1)]; \
+                vals[2] = vals[bcf_alleles2gt(ialt+1,ialt+1)]; \
+            } \
+            bcf_update_info_##type(args->out_hdr,dst,tag,vals,3); \
+        } \
+        else \
+            bcf_update_info_##type(args->out_hdr,dst,tag,vals,ret); \
+    }
+    switch (bcf_hdr_id2type(args->hdr,BCF_HL_INFO,info->key))
+    {
+        case BCF_HT_INT:  BRANCH_NUMERIC(int32, int32_t, vals[j]==bcf_int32_vector_end, vals[j]==bcf_int32_missing); break;
+        case BCF_HT_REAL: BRANCH_NUMERIC(float, float, bcf_float_is_vector_end(vals[j]), bcf_float_is_missing(vals[j])); break;
+    }
+    #undef BRANCH_NUMERIC
+}
+// Find n-th field in a comma-separated list and move it to dst.
+// The memory areas may overlap.
+#define STR_MOVE_NTH(dst,src,end,nth,len) \
+{ \
+    char *ss = src, *se = src; \
+    int j = 0; \
+    while ( *se && se<(end) ) \
+    { \
+        if ( *se==',' ) \
+        { \
+            if ( j==nth ) break; \
+            j++; \
+            ss = se+1; \
+        } \
+        se++; \
+    } \
+    if ( j==nth ) \
+    { \
+        int n = se - ss; \
+        memmove((dst),ss,n); \
+        src = se; \
+        len += n; \
+    } \
+    else len = -1; \
+}
+static void split_info_string(args_t *args, bcf1_t *src, bcf_info_t *info, int ialt, bcf1_t *dst)
+{
+    const char *tag = bcf_hdr_int2id(args->hdr,BCF_DT_ID,info->key);
+    int ret = bcf_get_info_string(args->hdr,src,tag,&args->tmp_arr1,&args->ntmp_arr1);
+    assert( ret>0 );
+
+    kstring_t str;
+    str.m = args->ntmp_arr1;
+    str.l = ret;
+    str.s = (char*) args->tmp_arr1;
+
+    int len = bcf_hdr_id2length(args->hdr,BCF_HL_INFO,info->key);
+    if ( len==BCF_VL_A )
+    {
+        char *tmp = str.s;
+        int len = 0;
+        STR_MOVE_NTH(str.s,tmp,str.s+str.l,ialt,len);
+        if ( len<0 ) return;   // wrong number of fields: skip
+        str.s[len] = 0;
+        bcf_update_info_string(args->out_hdr,dst,tag,str.s);
+    }
+    else if ( len==BCF_VL_R )
+    {
+        char *tmp = str.s;
+        int len = 0;
+        STR_MOVE_NTH(str.s,tmp,str.s+str.l,0,len);
+        str.s[len]=','; tmp++; len++;
+        STR_MOVE_NTH(&str.s[len],tmp,str.s+str.l,ialt,len);
+        if ( len<0 ) return;   // wrong number of fields: skip
+        str.s[len] = 0;
+        bcf_update_info_string(args->out_hdr,dst,tag,str.s);
+    }
+    else if ( len==BCF_VL_G )
+    {
+        int i0a = bcf_alleles2gt(0,ialt+1), iaa = bcf_alleles2gt(ialt+1,ialt+1);
+        char *tmp = str.s;
+        int len = 0;
+        STR_MOVE_NTH(str.s,tmp,str.s+str.l,0,len);
+        str.s[len]=','; tmp++; len++;
+        STR_MOVE_NTH(&str.s[len],tmp,str.s+str.l,i0a-1,len);
+        if ( len<0 ) return;   // wrong number of fields: skip
+        str.s[len]=','; tmp++; len++;
+        STR_MOVE_NTH(&str.s[len],tmp,str.s+str.l,iaa-i0a-1,len);
+        if ( len<0 ) return;   // wrong number of fields: skip
+        str.s[len] = 0;
+        bcf_update_info_string(args->out_hdr,dst,tag,str.s);
+    }
+    else
+        bcf_update_info_string(args->out_hdr,dst,tag,str.s);
+}
+static void split_info_flag(args_t *args, bcf1_t *src, bcf_info_t *info, int ialt, bcf1_t *dst)
+{
+    const char *tag = bcf_hdr_int2id(args->hdr,BCF_DT_ID,info->key);
+    int ret = bcf_get_info_flag(args->hdr,src,tag,&args->tmp_arr1,&args->ntmp_arr1);
+    bcf_update_info_flag(args->out_hdr,dst,tag,NULL,ret);
+}
+
+static void split_format_genotype(args_t *args, bcf1_t *src, bcf_fmt_t *fmt, int ialt, bcf1_t *dst)
+{
+    int ntmp = args->ntmp_arr1 / 4;
+    int ngts = bcf_get_genotypes(args->hdr,src,&args->tmp_arr1,&ntmp);
+    args->ntmp_arr1 = ntmp * 4;
+    assert( ngts >0 );
+
+    int32_t *gt = (int32_t*) args->tmp_arr1;
+    int i, j, nsmpl = bcf_hdr_nsamples(args->hdr);
+    ngts /= nsmpl;
+    for (i=0; i<nsmpl; i++)
+    {
+        for (j=0; j<ngts; j++)
+        {
+            if ( gt[j]==bcf_int32_vector_end ) break;
+            if ( bcf_gt_is_missing(gt[j]) || bcf_gt_allele(gt[j])==0 ) continue; // missing allele or ref: leave as is
+            if ( bcf_gt_allele(gt[j])==ialt+1 )
+                gt[j] = bcf_gt_unphased(1) | bcf_gt_is_phased(gt[j]); // set to first ALT
+            else
+                gt[j] = bcf_gt_unphased(0) | bcf_gt_is_phased(gt[j]); // set to REF
+        }
+        gt += ngts;
+    }
+    bcf_update_genotypes(args->out_hdr,dst,args->tmp_arr1,ngts*nsmpl);
+}
+static void split_format_numeric(args_t *args, bcf1_t *src, bcf_fmt_t *fmt, int ialt, bcf1_t *dst)
+{
+    #define BRANCH_NUMERIC(type,type_t,is_vector_end,is_missing,set_vector_end) \
+    { \
+        const char *tag = bcf_hdr_int2id(args->hdr,BCF_DT_ID,fmt->id); \
+        int ntmp = args->ntmp_arr1 / sizeof(type_t); \
+        int nvals = bcf_get_format_##type(args->hdr,src,tag,&args->tmp_arr1,&ntmp); \
+        args->ntmp_arr1 = ntmp * sizeof(type_t); \
+        assert( nvals>0 ); \
+        type_t *vals = (type_t *) args->tmp_arr1; \
+        int len = bcf_hdr_id2length(args->hdr,BCF_HL_FMT,fmt->id); \
+        int i,j, nsmpl = bcf_hdr_nsamples(args->hdr); \
+        if ( nvals==nsmpl ) /* all values are missing */ \
+        { \
+            bcf_update_format_##type(args->out_hdr,dst,tag,vals,nsmpl); \
+            return; \
+        } \
+        if ( len==BCF_VL_A ) \
+        { \
+            if ( nvals!=(src->n_allele-1)*nsmpl ) \
+            { \
+                if ( args->force && !args->force_warned ) \
+                { \
+                    fprintf(stderr, \
+                        "Warning: wrong number of fields in FMT/%s at %s:%"PRId64", expected %d, found %d. Removing the field.\n" \
+                        "         (This warning is printed only once.)\n", \
+                        tag,bcf_seqname(args->hdr,src),(int64_t) src->pos+1,(src->n_allele-1)*nsmpl,nvals); \
+                    args->force_warned = 1; \
+                } \
+                if ( args->force ) \
+                { \
+                    bcf_update_format_##type(args->out_hdr,dst,tag,NULL,0); \
+                    return; \
+                } \
+                error("Error: wrong number of fields in FMT/%s at %s:%"PRId64", expected %d, found %d\n", \
+                    tag,bcf_seqname(args->hdr,src),(int64_t) src->pos+1,(src->n_allele-1)*nsmpl,nvals); \
+            } \
+            nvals /= nsmpl; \
+            type_t *src_vals = vals, *dst_vals = vals; \
+            for (i=0; i<nsmpl; i++) \
+            { \
+                dst_vals[0] = src_vals[ialt]; \
+                dst_vals += 1; \
+                src_vals += nvals; \
+            } \
+            bcf_update_format_##type(args->out_hdr,dst,tag,vals,nsmpl); \
+        } \
+        else if ( len==BCF_VL_R ) \
+        { \
+            if ( nvals!=src->n_allele*nsmpl ) \
+            { \
+                if ( args->force && !args->force_warned ) \
+                { \
+                    fprintf(stderr, \
+                        "Warning: wrong number of fields in FMT/%s at %s:%"PRId64", expected %d, found %d. Removing the field.\n" \
+                        "         (This warning is printed only once.)\n", \
+                        tag,bcf_seqname(args->hdr,src),(int64_t) src->pos+1,(src->n_allele-1)*nsmpl,nvals); \
+                    args->force_warned = 1; \
+                } \
+                if ( args->force ) \
+                { \
+                    bcf_update_format_##type(args->out_hdr,dst,tag,NULL,0); \
+                    return; \
+                } \
+                error("Error: wrong number of fields in FMT/%s at %s:%"PRId64", expected %d, found %d\n", \
+                    tag,bcf_seqname(args->hdr,src),(int64_t) src->pos+1,src->n_allele*nsmpl,nvals); \
+            } \
+            nvals /= nsmpl; \
+            type_t *src_vals = vals, *dst_vals = vals; \
+            if ( args->keep_sum_ad >= 0 && args->keep_sum_ad==fmt->id ) \
+            { \
+                for (i=0; i<nsmpl; i++) \
+                { \
+                    dst_vals[0] = src_vals[0]; \
+                    for (j=1; j<nvals; j++) \
+                        if ( j!=ialt+1 && !(is_missing) && !(is_vector_end) ) dst_vals[0] += src_vals[j]; \
+                    dst_vals[1] = src_vals[ialt+1]; \
+                    dst_vals += 2; \
+                    src_vals += nvals; \
+                } \
+            } \
+            else \
+            { \
+                for (i=0; i<nsmpl; i++) \
+                { \
+                    dst_vals[0] = src_vals[0]; \
+                    dst_vals[1] = src_vals[ialt+1]; \
+                    dst_vals += 2; \
+                    src_vals += nvals; \
+                } \
+            } \
+            bcf_update_format_##type(args->out_hdr,dst,tag,vals,nsmpl*2); \
+        } \
+        else if ( len==BCF_VL_G ) \
+        { \
+            if ( nvals!=src->n_allele*(src->n_allele+1)/2*nsmpl && nvals!=src->n_allele*nsmpl ) \
+            { \
+                if ( args->force && !args->force_warned ) \
+                { \
+                    fprintf(stderr, \
+                        "Warning: wrong number of fields in FMT/%s at %s:%"PRId64", expected %d, found %d. Removing the field.\n" \
+                        "         (This warning is printed only once.)\n", \
+                        tag,bcf_seqname(args->hdr,src),(int64_t) src->pos+1,(src->n_allele-1)*nsmpl,nvals); \
+                    args->force_warned = 1; \
+                } \
+                if ( args->force ) \
+                { \
+                    bcf_update_format_##type(args->out_hdr,dst,tag,NULL,0); \
+                    return; \
+                } \
+                error("Error at %s:%"PRId64", the tag %s has wrong number of fields\n", bcf_seqname(args->hdr,src),(int64_t) src->pos+1,bcf_hdr_int2id(args->hdr,BCF_DT_ID,fmt->id)); \
+            } \
+            nvals /= nsmpl; \
+            int all_haploid = nvals==src->n_allele ? 1 : 0; \
+            type_t *src_vals = vals, *dst_vals = vals; \
+            for (i=0; i<nsmpl; i++) \
+            { \
+                int haploid = all_haploid; \
+                if ( !haploid ) \
+                { \
+                    int j; \
+                    for (j=0; j<nvals; j++) if ( is_vector_end ) break; \
+                    if ( j!=nvals ) haploid = 1; \
+                } \
+                dst_vals[0] = src_vals[0]; \
+                if ( haploid ) \
+                { \
+                    dst_vals[1] = src_vals[ialt+1]; \
+                    if ( !all_haploid ) set_vector_end; \
+                } \
+                else \
+                { \
+                    dst_vals[1] = src_vals[bcf_alleles2gt(0,ialt+1)]; \
+                    dst_vals[2] = src_vals[bcf_alleles2gt(ialt+1,ialt+1)]; \
+                } \
+                dst_vals += all_haploid ? 2 : 3; \
+                src_vals += nvals; \
+            } \
+            bcf_update_format_##type(args->out_hdr,dst,tag,vals,all_haploid ? nsmpl*2 : nsmpl*3); \
+        } \
+        else \
+            bcf_update_format_##type(args->out_hdr,dst,tag,vals,nvals); \
+    }
+    switch (bcf_hdr_id2type(args->hdr,BCF_HL_FMT,fmt->id))
+    {
+        case BCF_HT_INT:  BRANCH_NUMERIC(int32, int32_t, src_vals[j]==bcf_int32_vector_end, src_vals[j]==bcf_int32_missing, dst_vals[2]=bcf_int32_vector_end); break;
+        case BCF_HT_REAL: BRANCH_NUMERIC(float, float, bcf_float_is_vector_end(src_vals[j]), bcf_float_is_missing(src_vals[j]), bcf_float_set_vector_end(dst_vals[2])); break;
+    }
+    #undef BRANCH_NUMERIC
+}
+static void squeeze_format_char(char *str, int src_blen, int dst_blen, int n)
+{
+    int i, isrc = 0, idst = 0;
+    for (i=0; i<n; i++)
+    {
+        memmove(str+idst,str+isrc,dst_blen);
+        idst += dst_blen;
+        isrc += src_blen;
+    }
+}
+static void split_format_string(args_t *args, bcf1_t *src, bcf_fmt_t *fmt, int ialt, bcf1_t *dst)
+{
+    const char *tag = bcf_hdr_int2id(args->hdr,BCF_DT_ID,fmt->id);
+    int ret = bcf_get_format_char(args->hdr,src,tag,&args->tmp_arr1,&args->ntmp_arr1);
+    if ( !ret ) return; // all values can be empty, leave out the tag, no need to panic
+    assert( ret>0 );
+
+    kstring_t str;
+    str.m = args->ntmp_arr1;
+    str.l = ret;
+    str.s = (char*) args->tmp_arr1;
+
+    int nsmpl = bcf_hdr_nsamples(args->hdr);
+    int len = bcf_hdr_id2length(args->hdr,BCF_HL_FMT,fmt->id);
+    if ( len==BCF_VL_A )
+    {
+        int i, blen = ret/nsmpl, maxlen = 0;
+        char *ptr = str.s;
+        for (i=0; i<nsmpl; i++)
+        {
+            char *tmp = ptr;
+            int len = 0;
+            STR_MOVE_NTH(tmp,tmp,ptr+blen,ialt,len);
+            if ( len<0 ) return;   // wrong number of fields: skip
+            if ( maxlen < len ) maxlen = len;
+            ptr += blen;
+        }
+        if ( maxlen<blen ) squeeze_format_char(str.s,blen,maxlen,nsmpl);
+        bcf_update_format_char(args->out_hdr,dst,tag,str.s,nsmpl*maxlen);
+    }
+    else if ( len==BCF_VL_R )
+    {
+        int i, blen = ret/nsmpl, maxlen = 0;
+        char *ptr = str.s;
+        for (i=0; i<nsmpl; i++)
+        {
+            char *tmp = ptr;
+            int len = 0;
+            STR_MOVE_NTH(ptr,tmp,ptr+blen,0,len);
+            ptr[len]=','; tmp++; len++;
+            STR_MOVE_NTH(&ptr[len],tmp,ptr+blen,ialt,len);
+            if ( len<0 ) return;   // wrong number of fields: skip
+            if ( maxlen < len ) maxlen = len;
+            ptr += blen;
+        }
+        if ( maxlen<blen ) squeeze_format_char(str.s,blen,maxlen,nsmpl);
+        bcf_update_format_char(args->out_hdr,dst,tag,str.s,nsmpl*maxlen);
+    }
+    else if ( len==BCF_VL_G )
+    {
+        int i, blen = ret/nsmpl, maxlen = 0, i0a = bcf_alleles2gt(0,ialt+1), iaa = bcf_alleles2gt(ialt+1,ialt+1);
+        char *ptr = str.s;
+        for (i=0; i<nsmpl; i++)
+        {
+            char *se = ptr, *sx = ptr+blen;
+            int nfields = 1;
+            while ( *se && se<sx )
+            {
+                if ( *se==',' ) nfields++;
+                se++;
+            }
+            if ( nfields==1 && se-ptr==1 && *ptr=='.' ) continue;   // missing value
+            if ( nfields!=src->n_allele*(src->n_allele+1)/2 && nfields!=src->n_allele )
+            {
+                if ( args->force && !args->force_warned )
+                {
+                    fprintf(stderr,
+                            "Warning: wrong number of fields in FMT/%s at %s:%"PRId64", expected %d or %d, found %d. Removing the field.\n"
+                            "         (This warning is printed only once.)\n",
+                            tag,bcf_seqname(args->hdr,src),(int64_t)src->pos+1,src->n_allele*(src->n_allele+1)/2,src->n_allele,nfields);
+                    args->force_warned = 1;
+                }
+                if ( args->force )
+                {
+                    bcf_update_format_char(args->out_hdr,dst,tag,NULL,0);
+                    return;
+                }
+                error("Error: wrong number of fields in FMT/%s at %s:%"PRId64", expected %d or %d, found %d\n",
+                        tag,bcf_seqname(args->hdr,src),(int64_t) src->pos+1,src->n_allele*(src->n_allele+1)/2,src->n_allele,nfields);
+            }
+
+            int len = 0;
+            if ( nfields==src->n_allele )   // haploid
+            {
+                char *tmp = ptr;
+                STR_MOVE_NTH(&ptr[len],tmp,ptr+blen,0,len);
+                ptr[len]=','; tmp++; len++;
+                STR_MOVE_NTH(&ptr[len],tmp,ptr+blen,ialt,len);
+                if ( len<0 ) return;   // wrong number of fields: skip
+            }
+            else    // diploid
+            {
+                char *tmp = ptr;
+                STR_MOVE_NTH(&ptr[len],tmp,ptr+blen,0,len);
+                ptr[len]=','; tmp++; len++;
+                STR_MOVE_NTH(&ptr[len],tmp,ptr+blen,i0a-1,len);
+                if ( len<0 ) return;   // wrong number of fields: skip
+                ptr[len]=','; tmp++; len++;
+                STR_MOVE_NTH(&ptr[len],tmp,ptr+blen,iaa-i0a-1,len);
+                if ( len<0 ) return;   // wrong number of fields: skip
+            }
+            if ( maxlen < len ) maxlen = len;
+            ptr += blen;
+        }
+        if ( maxlen<blen ) squeeze_format_char(str.s,blen,maxlen,nsmpl);
+        bcf_update_format_char(args->out_hdr,dst,tag,str.s,nsmpl*maxlen);
+    }
+    else
+        bcf_update_format_char(args->out_hdr,dst,tag,str.s,str.l);
+}
+
+static void split_multiallelic_to_biallelics(args_t *args, bcf1_t *line)
+{
+    int i;
+
+    bcf_unpack(line, BCF_UN_ALL);
+
+    // Init the target biallelic lines
+    args->ntmp_lines = line->n_allele-1;
+    if ( args->mtmp_lines < args->ntmp_lines )
+    {
+        args->tmp_lines = (bcf1_t **)realloc(args->tmp_lines,sizeof(bcf1_t*)*args->ntmp_lines);
+        for (i=args->mtmp_lines; i<args->ntmp_lines; i++)
+            args->tmp_lines[i] = NULL;
+        args->mtmp_lines = args->ntmp_lines;
+    }
+    kstring_t tmp = {0,0,0};
+    kputs(line->d.allele[0], &tmp);
+    kputc(',', &tmp);
+    int rlen  = tmp.l;
+    int gt_id = bcf_hdr_id2int(args->hdr,BCF_DT_ID,"GT");
+    for (i=0; i<args->ntmp_lines; i++)  // for each ALT allele
+    {
+        if ( !args->tmp_lines[i] ) args->tmp_lines[i] = bcf_init1();
+        bcf1_t *dst = args->tmp_lines[i];
+        bcf_clear(dst);
+
+        dst->rid  = line->rid;
+        dst->pos  = line->pos;
+        dst->qual = line->qual;
+
+        // Not quite sure how to handle IDs, they can be assigned to a specific
+        // ALT.  For now we leave the ID unchanged for all.
+        bcf_update_id(args->out_hdr, dst, line->d.id ? line->d.id : ".");
+
+        tmp.l = rlen;
+        kputs(line->d.allele[i+1],&tmp);
+        bcf_update_alleles_str(args->out_hdr,dst,tmp.s);
+
+        if ( line->d.n_flt ) bcf_update_filter(args->hdr, dst, line->d.flt, line->d.n_flt);
+
+        int j;
+        for (j=0; j<line->n_info; j++)
+        {
+            bcf_info_t *info = &line->d.info[j];
+            int type = bcf_hdr_id2type(args->hdr,BCF_HL_INFO,info->key);
+            if ( type==BCF_HT_INT || type==BCF_HT_REAL ) split_info_numeric(args, line, info, i, dst);
+            else if ( type==BCF_HT_FLAG ) split_info_flag(args, line, info, i, dst);
+            else split_info_string(args, line, info, i, dst);
+        }
+        set_old_rec_tag(args, dst, line, i + 1); // 1-based indexes
+
+        dst->n_sample = line->n_sample;
+        for (j=0; j<line->n_fmt; j++)
+        {
+            bcf_fmt_t *fmt = &line->d.fmt[j];
+            int type = bcf_hdr_id2type(args->hdr,BCF_HL_FMT,fmt->id);
+            if ( fmt->id==gt_id ) split_format_genotype(args, line, fmt, i, dst);
+            else if ( type==BCF_HT_INT || type==BCF_HT_REAL ) split_format_numeric(args, line, fmt, i, dst);
+            else split_format_string(args, line, fmt, i, dst);
+        }
+    }
+    free(tmp.s);
+}
+
+// Enlarge FORMAT array containing nsmpl samples each with nals_ori values
+// to accommodate nvals values for each sample, filling the gaps with missing
+// values. Works also for INFO arrays, with nsmpl set to 1.
+#define ENLARGE_ARRAY(type_t,set_missing,arr,narr_bytes,nsmpl,nvals_ori,nvals) \
+{ \
+    int nbytes_new = (nsmpl)*(nvals)*sizeof(type_t); \
+    hts_expand(uint8_t,nbytes_new,narr_bytes,arr); \
+    int ismpl, k; \
+    for (ismpl=nsmpl-1; ismpl>=0; ismpl--) \
+    { \
+        type_t *dst_ptr = ((type_t*)arr) + ismpl*(nvals); \
+        type_t *src_ptr = ((type_t*)arr) + ismpl*nvals_ori; \
+        memmove(dst_ptr,src_ptr,sizeof(type_t)*nvals_ori); \
+        for (k=nvals_ori; k<nvals; k++) set_missing; \
+    } \
+}
+static void merge_info_numeric(args_t *args, bcf1_t **lines, int nlines, bcf_info_t *info, bcf1_t *dst)
+{
+    #define BRANCH_NUMERIC(type,type_t,set_missing,is_vector_end) \
+    { \
+        const char *tag = bcf_hdr_int2id(args->hdr,BCF_DT_ID,info->key); \
+        int ntmp = args->ntmp_arr1 / sizeof(type_t); \
+        int nvals_ori = bcf_get_info_##type(args->hdr,lines[0],tag,&args->tmp_arr1,&ntmp); \
+        args->ntmp_arr1 = ntmp * sizeof(type_t); \
+        assert( nvals_ori>0 ); \
+        type_t *vals = (type_t*) args->tmp_arr1, *vals2; \
+        int i,k,len = bcf_hdr_id2length(args->hdr,BCF_HL_INFO,info->key);  \
+        if ( len==BCF_VL_A ) \
+        { \
+            if (nvals_ori!=lines[0]->n_allele - 1) \
+                error("vcfnorm: number of fields in first record at position %s:%"PRId64" for INFO tag %s not as expected [found: %d vs expected:%d]\n", bcf_seqname(args->hdr,lines[0]),(int64_t) lines[0]->pos+1, tag, nvals_ori, lines[0]->n_allele-1); \
+            int nvals = dst->n_allele - 1; \
+            ENLARGE_ARRAY(type_t,set_missing,args->tmp_arr1,args->ntmp_arr1,1,nvals_ori,nvals); \
+            vals = (type_t*) args->tmp_arr1; \
+            for (i=1; i<nlines; i++) \
+            { \
+                int ntmp2 = args->ntmp_arr2 / sizeof(type_t); \
+                int nvals2 = bcf_get_info_##type(args->hdr,lines[i],tag,&args->tmp_arr2,&ntmp2); \
+                if (nvals2<0) continue; /* info tag does not exist in this record, skip */ \
+                args->ntmp_arr2 = ntmp2 * sizeof(type_t); \
+                if (nvals2!=lines[i]->n_allele-1) \
+                    error("vcfnorm: could not merge INFO tag %s at position %s:%"PRId64"\n", tag, bcf_seqname(args->hdr,lines[i]),(int64_t) lines[i]->pos+1); \
+                vals2 = (type_t*) args->tmp_arr2; \
+                for (k=0; k<nvals2; k++) \
+                { \
+                    if ( is_vector_end ) break; \
+                    vals[ args->maps[i].map[k+1] - 1 ] = vals2[k]; \
+                } \
+            } \
+            bcf_update_info_##type(args->out_hdr,dst,tag,args->tmp_arr1,nvals); \
+        } \
+        else if ( len==BCF_VL_R ) \
+        { \
+            if (nvals_ori!=lines[0]->n_allele) \
+                error("vcfnorm: number of fields in first record at position %s:%"PRId64" for INFO tag %s not as expected [found: %d vs expected:%d]\n", bcf_seqname(args->hdr,lines[0]),(int64_t) lines[0]->pos+1, tag, nvals_ori, lines[0]->n_allele); \
+            int nvals = dst->n_allele; \
+            ENLARGE_ARRAY(type_t,set_missing,args->tmp_arr1,args->ntmp_arr1,1,nvals_ori,nvals); \
+            vals = (type_t*) args->tmp_arr1; \
+            for (i=1; i<nlines; i++) \
+            { \
+                int ntmp2 = args->ntmp_arr2 / sizeof(type_t); \
+                int nvals2 = bcf_get_info_##type(args->hdr,lines[i],tag,&args->tmp_arr2,&ntmp2); \
+                if (nvals2<0) continue; /* info tag does not exist in this record, skip */ \
+                args->ntmp_arr2 = ntmp2 * sizeof(type_t); \
+                if (nvals2!=lines[i]->n_allele) \
+                    error("vcfnorm: could not merge INFO tag %s at position %s:%"PRId64"\n", tag, bcf_seqname(args->hdr,lines[i]),(int64_t) lines[i]->pos+1); \
+                vals2 = (type_t*) args->tmp_arr2; \
+                for (k=0; k<nvals2; k++) \
+                { \
+                    if ( is_vector_end ) break; \
+                    vals[ args->maps[i].map[k] ] = vals2[k]; \
+                } \
+            } \
+            bcf_update_info_##type(args->out_hdr,dst,tag,args->tmp_arr1,nvals); \
+        } \
+        else if ( len==BCF_VL_G ) \
+        { \
+            /* expecting diploid gt in INFO */ \
+            if (nvals_ori!=lines[0]->n_allele*(lines[0]->n_allele+1)/2) { \
+                fprintf(stderr, "todo: merge Number=G INFO fields for haploid sites\n"); \
+                error("vcfnorm: number of fields in first record at position %s:%"PRId64" for INFO tag %s not as expected [found: %d vs expected:%d]\n", bcf_seqname(args->hdr,lines[0]),(int64_t) lines[0]->pos+1, tag, nvals_ori, lines[0]->n_allele*(lines[0]->n_allele+1)/2); \
+            } \
+            int nvals = dst->n_allele*(dst->n_allele+1)/2; \
+            ENLARGE_ARRAY(type_t,set_missing,args->tmp_arr1,args->ntmp_arr1,1,nvals_ori,nvals); \
+            vals = (type_t*) args->tmp_arr1; \
+            for (i=1; i<nlines; i++) \
+            { \
+                int ntmp2 = args->ntmp_arr2 / sizeof(type_t); \
+                int nvals2 = bcf_get_info_##type(args->hdr,lines[i],tag,&args->tmp_arr2,&ntmp2); \
+                if (nvals2<0) continue; /* info tag does not exist in this record, skip */ \
+                args->ntmp_arr2 = ntmp2 * sizeof(type_t); \
+                if (nvals2!=lines[i]->n_allele*(lines[i]->n_allele+1)/2) \
+                    error("vcfnorm: could not merge INFO tag %s at position %s:%"PRId64"\n", tag, bcf_seqname(args->hdr,lines[i]),(int64_t) lines[i]->pos+1); \
+                vals2 = (type_t*) args->tmp_arr2; \
+                int ia,ib; \
+                k = 0; \
+                for (ia=0; ia<lines[i]->n_allele; ia++) \
+                { \
+                    for (ib=0; ib<=ia; ib++) \
+                    { \
+                        if ( is_vector_end ) break; \
+                        int l = bcf_alleles2gt(args->maps[i].map[ia],args->maps[i].map[ib]); \
+                        vals[l] = vals2[k];  \
+                        k++; \
+                    } \
+                } \
+            } \
+            bcf_update_info_##type(args->out_hdr,dst,tag,args->tmp_arr1,nvals); \
+        } \
+        else \
+            bcf_update_info_##type(args->out_hdr,dst,tag,vals,nvals_ori); \
+    }
+    switch (bcf_hdr_id2type(args->hdr,BCF_HL_INFO,info->key))
+    {
+        case BCF_HT_INT:  BRANCH_NUMERIC(int32, int32_t, dst_ptr[k]=bcf_int32_missing, vals2[k]==bcf_int32_vector_end); break;
+        case BCF_HT_REAL: BRANCH_NUMERIC(float, float, bcf_float_set_missing(dst_ptr[k]), bcf_float_is_vector_end(vals2[k])); break;
+    }
+    #undef BRANCH_NUMERIC
+}
+static void merge_info_flag(args_t *args, bcf1_t **lines, int nlines, bcf_info_t *info, bcf1_t *dst)
+{
+    const char *tag = bcf_hdr_int2id(args->hdr,BCF_DT_ID,info->key);
+    int ret = bcf_get_info_flag(args->hdr,lines[0],tag,&args->tmp_arr1,&args->ntmp_arr1);
+    bcf_update_info_flag(args->out_hdr,dst,tag,NULL,ret);
+}
+int copy_string_field(char *src, int isrc, int src_len, kstring_t *dst, int idst); // see vcfmerge.c
+static void merge_info_string(args_t *args, bcf1_t **lines, int nlines, bcf_info_t *info, bcf1_t *dst)
+{
+    const char *tag = bcf_hdr_int2id(args->hdr,BCF_DT_ID,info->key);
+
+    kstring_t str;
+    str.m = args->ntmp_arr1;
+    str.l = 0;
+    str.s = (char*) args->tmp_arr1;
+
+    int i, j, len = bcf_hdr_id2length(args->hdr,BCF_HL_INFO,info->key);
+    if ( len==BCF_VL_A || len==BCF_VL_R )
+    {
+        int jfrom = len==BCF_VL_A ? 1 : 0;
+        kputc('.',&str);
+        for (i=jfrom+1; i<dst->n_allele; i++) kputs(",.",&str);
+        for (i=0; i<nlines; i++)
+        {
+            bcf_info_t *src = bcf_get_info(args->hdr,lines[i],tag);
+            if (!src) continue;
+            for (j=jfrom; j<lines[i]->n_allele; j++)
+                copy_string_field((char*)src->vptr, j-jfrom, src->len, &str, args->maps[i].map[j]-jfrom);
+        }
+        str.s[str.l] = 0;
+        args->tmp_arr1  = (uint8_t*) str.s;
+        args->ntmp_arr1 = str.m;
+        bcf_update_info_string(args->out_hdr,dst,tag,str.s);
+    }
+    else if ( len==BCF_VL_G )
+    {
+        int ngts = dst->n_allele*(dst->n_allele+1)/2;
+        kputc('.',&str);
+        for (i=1; i<ngts; i++) kputs(",.",&str);
+        for (i=0; i<nlines; i++)
+        {
+            bcf_info_t *src = bcf_get_info(args->hdr,lines[i],tag);
+            if (!src) continue;
+            int iori, jori, kori = 0;
+            for (iori=0; iori<lines[i]->n_allele; iori++)
+            {
+                int inew = args->maps[i].map[iori];
+                for (jori=0; jori<=iori; jori++)
+                {
+                    int jnew = args->maps[i].map[jori];
+                    int knew = bcf_alleles2gt(inew,jnew);
+                    copy_string_field((char*)src->vptr,kori,src->len,&str,knew);
+                    kori++;
+                }
+            }
+        }
+        str.s[str.l] = 0;
+        args->tmp_arr1  = (uint8_t*) str.s;
+        args->ntmp_arr1 = str.m;
+        bcf_update_info_string(args->out_hdr,dst,tag,str.s);
+    }
+    else
+    {
+        bcf_get_info_string(args->hdr,lines[0],tag,&args->tmp_arr1,&args->ntmp_arr1);
+        bcf_update_info_string(args->out_hdr,dst,tag,args->tmp_arr1);
+    }
+}
+static void merge_format_genotype(args_t *args, bcf1_t **lines, int nlines, bcf_fmt_t *fmt, bcf1_t *dst)
+{
+    // reusing int8_t arrays as int32_t arrays
+    int ntmp = args->ntmp_arr1 / 4;
+    int ngts = bcf_get_genotypes(args->hdr,lines[0],&args->tmp_arr1,&ntmp);
+    args->ntmp_arr1 = ntmp * 4;
+    assert( ngts >0 );
+
+    int nsmpl = bcf_hdr_nsamples(args->hdr);
+    ngts /= nsmpl;
+
+    int i, j, k,k2;
+    for (i=1; i<nlines; i++)
+    {
+        int ntmp2 = args->ntmp_arr2 / 4;
+        int ngts2 = bcf_get_genotypes(args->hdr,lines[i],&args->tmp_arr2,&ntmp2);
+        args->ntmp_arr2 = ntmp2 * 4;
+        ngts2 /= nsmpl;
+        if ( ngts!=ngts2 ) error("Error at %s:%"PRId64": cannot combine diploid with haploid genotype\n", bcf_seqname(args->hdr,lines[i]),(int64_t) lines[i]->pos+1);
+
+        int32_t *gt  = (int32_t*) args->tmp_arr1;
+        int32_t *gt2 = (int32_t*) args->tmp_arr2;
+        for (j=0; j<nsmpl; j++)
+        {
+            for (k2=0; k2<ngts2; k2++)
+            {
+                if ( gt2[k2]==bcf_int32_vector_end ) break;
+                if ( bcf_gt_is_missing(gt2[k2]) ) continue;
+                int ial2 = bcf_gt_allele(gt2[k2]);
+                if ( ial2==0 ) continue;    // never overwrite with ref
+                if ( ial2>=args->maps[i].nals ) error("Error at %s:%"PRId64": incorrect allele index %d\n",bcf_seqname(args->hdr,lines[i]),(int64_t) lines[i]->pos+1,ial2);
+                int ial = args->maps[i].map[ial2];
+                for (k=0; k<ngts; k++)
+                    if ( gt[k]==bcf_int32_vector_end || bcf_gt_is_missing(gt[k]) || !bcf_gt_allele(gt[k]) ) break;
+                if ( k<ngts )
+                {
+                    gt[k] = bcf_gt_unphased(ial);
+                }
+            }
+            gt  += ngts;
+            gt2 += ngts;
+        }
+    }
+    bcf_update_genotypes(args->out_hdr,dst,args->tmp_arr1,ngts*nsmpl);
+}
+static int diploid_to_haploid(int size, int nsmpl, int nals, uint8_t *vals)
+{
+    int i, dsrc = size*nals*(nals+1)/2, ddst = size*nals;
+    uint8_t *src_ptr = vals + dsrc, *dst_ptr = vals + ddst;
+    for (i=1; i<nsmpl; i++)
+    {
+        memmove(dst_ptr,src_ptr,ddst);
+        dst_ptr += ddst;
+        src_ptr += dsrc;
+    }
+    return nals;
+}
+static void merge_format_numeric(args_t *args, bcf1_t **lines, int nlines, bcf_fmt_t *fmt, bcf1_t *dst)
+{
+    #define BRANCH_NUMERIC(type,type_t,set_missing,is_vector_end,set_vector_end) \
+    { \
+        const char *tag = bcf_hdr_int2id(args->hdr,BCF_DT_ID,fmt->id); \
+        int ntmp = args->ntmp_arr1 / sizeof(type_t); \
+        int nvals_ori = bcf_get_format_##type(args->hdr,lines[0],tag,&args->tmp_arr1,&ntmp); \
+        args->ntmp_arr1 = ntmp * sizeof(type_t); \
+        assert( nvals_ori>0 ); \
+        type_t *vals2, *vals = (type_t *) args->tmp_arr1; \
+        int len = bcf_hdr_id2length(args->hdr,BCF_HL_FMT,fmt->id); \
+        int i, j, k, nsmpl = bcf_hdr_nsamples(args->hdr); \
+        nvals_ori /= nsmpl; \
+        if ( len==BCF_VL_A ) \
+        { \
+            int nvals = dst->n_allele - 1; \
+            ENLARGE_ARRAY(type_t,set_missing,args->tmp_arr1,args->ntmp_arr1,nsmpl,nvals_ori,nvals); \
+            for (i=1; i<nlines; i++) \
+            { \
+                int ntmp2 = args->ntmp_arr2 / sizeof(type_t); \
+                int nvals2 = bcf_get_format_##type(args->hdr,lines[i],tag,&args->tmp_arr2,&ntmp2); \
+                if (nvals2<0) continue; /* format tag does not exist in this record, skip */ \
+                args->ntmp_arr2 = ntmp2 * sizeof(type_t); \
+                nvals2 /= nsmpl; \
+                if (nvals2!=lines[i]->n_allele-1) \
+                    error("vcfnorm: could not merge FORMAT tag %s at position %s:%"PRId64"\n", tag, bcf_seqname(args->hdr,lines[i]),(int64_t) lines[i]->pos+1); \
+                vals  = (type_t*) args->tmp_arr1; \
+                vals2 = (type_t*) args->tmp_arr2; \
+                for (j=0; j<nsmpl; j++) \
+                { \
+                    for (k=0; k<nvals2; k++) \
+                    { \
+                        if ( is_vector_end ) break; \
+                        vals[ args->maps[i].map[k+1] - 1 ] = vals2[k]; \
+                    } \
+                    vals  += nvals; \
+                    vals2 += nvals2; \
+                } \
+            } \
+            bcf_update_format_##type(args->out_hdr,dst,tag,args->tmp_arr1,nvals*nsmpl); \
+        } \
+        else if ( len==BCF_VL_R ) \
+        { \
+            int nvals = dst->n_allele; \
+            ENLARGE_ARRAY(type_t,set_missing,args->tmp_arr1,args->ntmp_arr1,nsmpl,nvals_ori,nvals); \
+            for (i=1; i<nlines; i++) \
+            { \
+                int ntmp2 = args->ntmp_arr2 / sizeof(type_t); \
+                int nvals2 = bcf_get_format_##type(args->hdr,lines[i],tag,&args->tmp_arr2,&ntmp2); \
+                if (nvals2<0) continue; /* format tag does not exist in this record, skip */ \
+                args->ntmp_arr2 = ntmp2 * sizeof(type_t); \
+                nvals2 /= nsmpl; \
+                if (nvals2!=lines[i]->n_allele) \
+                    error("vcfnorm: could not merge FORMAT tag %s at position %s:%"PRId64"\n", tag, bcf_seqname(args->hdr,lines[i]),(int64_t) lines[i]->pos+1); \
+                vals  = (type_t*) args->tmp_arr1; \
+                vals2 = (type_t*) args->tmp_arr2; \
+                for (j=0; j<nsmpl; j++) \
+                { \
+                    for (k=0; k<nvals2; k++) \
+                    { \
+                        if ( is_vector_end ) break; \
+                        vals[ args->maps[i].map[k] ] = vals2[k]; \
+                    } \
+                    vals  += nvals; \
+                    vals2 += nvals2; \
+                } \
+            } \
+            bcf_update_format_##type(args->out_hdr,dst,tag,args->tmp_arr1,nvals*nsmpl); \
+        } \
+        else if ( len==BCF_VL_G ) \
+        { \
+            /* which samples are diploid */ \
+            memset(args->diploid,0,nsmpl); \
+            int all_haploid = 1; \
+            if ( nvals_ori > lines[0]->n_allele ) /* line possibly diploid */ \
+            { \
+                vals2 = (type_t*) args->tmp_arr1; \
+                int ndiploid = lines[0]->n_allele*(lines[0]->n_allele+1)/2; \
+                for (i=0; i<nsmpl; i++) \
+                { \
+                    if ( !args->diploid[i] ) \
+                    { \
+                        for (k=0; k<nvals_ori; k++) if ( is_vector_end ) break; \
+                        if ( k==ndiploid ) { args->diploid[i] = 1; all_haploid = 0; }\
+                    } \
+                    vals2 += nvals_ori; \
+                } \
+            } \
+            int nvals = dst->n_allele*(dst->n_allele+1)/2; \
+            ENLARGE_ARRAY(type_t,set_missing,args->tmp_arr1,args->ntmp_arr1,nsmpl,nvals_ori,nvals); \
+            for (i=1; i<nlines; i++) \
+            { \
+                int ntmp2 = args->ntmp_arr2 / sizeof(type_t); \
+                int nvals2 = bcf_get_format_##type(args->hdr,lines[i],tag,&args->tmp_arr2,&ntmp2); \
+                if (nvals2<0) continue; /* format tag does not exist in this record, skip */ \
+                args->ntmp_arr2 = ntmp2 * sizeof(type_t); \
+                nvals2 /= nsmpl; \
+                int ndiploid = lines[i]->n_allele*(lines[i]->n_allele+1)/2; \
+                int line_diploid = nvals2==ndiploid ? 1 : 0; \
+                if (!(nvals2==1 || nvals2==lines[i]->n_allele || nvals2==lines[i]->n_allele*(lines[i]->n_allele+1)/2)) \
+                    error("vcfnorm: could not merge FORMAT tag %s at position %s:%"PRId64"\n", tag, bcf_seqname(args->hdr,lines[i]),(int64_t) lines[i]->pos+1); \
+                vals  = (type_t*) args->tmp_arr1; \
+                vals2 = (type_t*) args->tmp_arr2; \
+                for (j=0; j<nsmpl; j++) \
+                { \
+                    int smpl_diploid = line_diploid; \
+                    if ( smpl_diploid ) \
+                    { \
+                        for (k=0; k<nvals2; k++) if ( is_vector_end ) break; \
+                        if ( k!=ndiploid ) smpl_diploid = 0; \
+                    } \
+                    if ( smpl_diploid && !args->diploid[j] ) { args->diploid[j] = 1; all_haploid = 0; } \
+                    if ( !smpl_diploid ) \
+                    { \
+                        for (k=0; k<lines[i]->n_allele; k++) vals[args->maps[i].map[k]] = vals2[k]; \
+                    } \
+                    else \
+                    { \
+                        k = 0; \
+                        int ia,ib; \
+                        for (ia=0; ia<lines[i]->n_allele; ia++) \
+                        { \
+                            for (ib=0; ib<=ia; ib++) \
+                            { \
+                                int l = bcf_alleles2gt(args->maps[i].map[ia],args->maps[i].map[ib]); \
+                                vals[l] = vals2[k]; \
+                                k++; \
+                            } \
+                        } \
+                    } \
+                    vals  += nvals; \
+                    vals2 += nvals2; \
+                } \
+            } \
+            if ( all_haploid ) \
+                nvals = diploid_to_haploid(sizeof(type_t),nsmpl,dst->n_allele,args->tmp_arr1); \
+            else \
+            {\
+                k = dst->n_allele;\
+                vals2 = (type_t*) args->tmp_arr1;\
+                for (i=0; i<nsmpl; i++)\
+                {\
+                    if ( !args->diploid[i] ) set_vector_end;\
+                    vals2 += nvals;\
+                }\
+            }\
+            bcf_update_format_##type(args->out_hdr,dst,tag,args->tmp_arr1,nvals*nsmpl); \
+        } \
+        else \
+            bcf_update_format_##type(args->out_hdr,dst,tag,args->tmp_arr1,nvals_ori*nsmpl); \
+    }
+    switch (bcf_hdr_id2type(args->hdr,BCF_HL_FMT,fmt->id))
+    {
+        case BCF_HT_INT:  BRANCH_NUMERIC(int32, int32_t, dst_ptr[k]=bcf_int32_missing, vals2[k]==bcf_int32_vector_end, vals2[k]=bcf_int32_vector_end); break;
+        case BCF_HT_REAL: BRANCH_NUMERIC(float, float, bcf_float_set_missing(dst_ptr[k]), bcf_float_is_vector_end(vals2[k]), bcf_float_set_vector_end(vals2[k])); break;
+    }
+    #undef BRANCH_NUMERIC
+}
+static void merge_format_string(args_t *args, bcf1_t **lines, int nlines, bcf_fmt_t *fmt, bcf1_t *dst)
+{
+    const char *tag = bcf_hdr_int2id(args->hdr,BCF_DT_ID,fmt->id);
+
+    int i, j, k, len = bcf_hdr_id2length(args->hdr,BCF_HL_FMT,fmt->id);
+    if ( len!=BCF_VL_A && len!=BCF_VL_R && len!=BCF_VL_G )
+    {
+        int nret = bcf_get_format_char(args->hdr,lines[0],tag,&args->tmp_arr1,&args->ntmp_arr1);
+        bcf_update_format_char(args->out_hdr,dst,tag,args->tmp_arr1,nret);
+        return;
+    }
+
+    int nsmpl = bcf_hdr_nsamples(args->hdr);
+    for (i=0; i<nsmpl; i++) args->tmp_str[i].l = 0;
+
+    if ( len==BCF_VL_A || len==BCF_VL_R )
+    {
+        int jfrom = len==BCF_VL_A ? 1 : 0;
+        for (i=0; i<nsmpl; i++)
+        {
+            kstring_t *tmp = &args->tmp_str[i];
+            kputc('.',tmp);
+            for (k=jfrom+1; k<dst->n_allele; k++) kputs(",.",tmp);
+        }
+        for (i=0; i<nlines; i++)
+        {
+            int nret = bcf_get_format_char(args->hdr,lines[i],tag,&args->tmp_arr1,&args->ntmp_arr1);
+            if (nret<0) continue; /* format tag does not exist in this record, skip */
+            nret /= nsmpl;
+            for (k=0; k<nsmpl; k++)
+            {
+                kstring_t *tmp = &args->tmp_str[k];
+                char *src = (char*)args->tmp_arr1 + k*nret;
+                for (j=jfrom; j<lines[i]->n_allele; j++)
+                    copy_string_field(src, j-jfrom, nret, tmp, args->maps[i].map[j]-jfrom);
+            }
+        }
+    }
+    else if ( len==BCF_VL_G )
+    {
+        hts_expand(uint8_t,nsmpl,args->ntmp_arr2,args->tmp_arr2);
+        uint8_t *haploid = args->tmp_arr2;
+        int nret = bcf_get_format_char(args->hdr,lines[0],tag,&args->tmp_arr1,&args->ntmp_arr1);
+        nret /= nsmpl;
+        for (i=0; i<nsmpl; i++)
+        {
+            char *ss = (char*)args->tmp_arr1 + i*nret, *se = ss+nret;
+            int nfields = 1;
+            while ( *ss && ss<se )
+            {
+                if ( *ss==',' ) nfields++;
+                ss++;
+            }
+            if ( nfields==lines[0]->n_allele )
+            {
+                haploid[i] = 1;
+                nfields = dst->n_allele;
+            }
+            else if ( nfields==lines[0]->n_allele*(lines[0]->n_allele+1)/2 )
+            {
+                haploid[i] = 0;
+                nfields = dst->n_allele*(dst->n_allele+1)/2;
+            }
+            else error("The field %s at %s:%"PRId64" neither diploid nor haploid?\n", tag,bcf_seqname(args->hdr,dst),(int64_t) dst->pos+1);
+
+            kstring_t *tmp = &args->tmp_str[i];
+            kputc('.',tmp);
+            for (j=1; j<nfields; j++) kputs(",.",tmp);
+        }
+        for (i=0; i<nlines; i++)
+        {
+            if ( i ) // we already have a copy
+            {
+                nret = bcf_get_format_char(args->hdr,lines[i],tag,&args->tmp_arr1,&args->ntmp_arr1);
+                if (nret<0) continue; /* format tag does not exist in this record, skip */
+                nret /= nsmpl;
+            }
+            for (k=0; k<nsmpl; k++)
+            {
+                kstring_t *tmp = &args->tmp_str[k];
+                char *src = (char*)args->tmp_arr1 + k*nret;
+                if ( haploid[k] )
+                {
+                    for (j=0; j<lines[i]->n_allele; j++)
+                        copy_string_field(src,j,nret, tmp, args->maps[i].map[j]);
+                }
+                else
+                {
+                    int iori, jori, kori = 0;
+                    for (iori=0; iori<lines[i]->n_allele; iori++)
+                    {
+                        int inew = args->maps[i].map[iori];
+                        for (jori=0; jori<=iori; jori++)
+                        {
+                            int jnew = args->maps[i].map[jori];
+                            int knew = bcf_alleles2gt(inew,jnew);
+                            copy_string_field(src,kori,nret,tmp,knew);
+                            kori++;
+                        }
+                    }
+                }
+            }
+        }
+    }
+    kstring_t str;
+    str.m = args->ntmp_arr2;
+    str.l = 0;
+    str.s = (char*) args->tmp_arr2;
+
+    int max_len = 0;
+    for (i=0; i<nsmpl; i++)
+        if ( max_len < args->tmp_str[i].l ) max_len = args->tmp_str[i].l;
+    for (i=0; i<nsmpl; i++)
+    {
+        kstring_t *tmp = &args->tmp_str[i];
+        kputsn(tmp->s,tmp->l,&str);
+        for (j=tmp->l; j<max_len; j++) kputc('\0',&str);
+    }
+    args->ntmp_arr2 = str.m;
+    args->tmp_arr2  = (uint8_t*)str.s;
+    bcf_update_format_char(args->out_hdr,dst,tag,str.s,str.l);
+}
+
+char **merge_alleles(char **a, int na, int *map, char **b, int *nb, int *mb);   // see vcfmerge.c
+static void merge_biallelics_to_multiallelic(args_t *args, bcf1_t *dst, bcf1_t **lines, int nlines)
+{
+    int i;
+    for (i=0; i<nlines; i++)
+        bcf_unpack(lines[i], BCF_UN_ALL);
+
+    dst->rid  = lines[0]->rid;
+    dst->pos  = lines[0]->pos;
+
+    // take max for QUAL
+    bcf_float_set_missing(dst->qual);
+    for (i=0; i<nlines; i++) {
+        if (bcf_float_is_missing(lines[i]->qual)) continue;
+        if (bcf_float_is_missing(dst->qual) || dst->qual<lines[i]->qual)
+            dst->qual = lines[i]->qual;
+    }
+
+    bcf_update_id(args->out_hdr, dst, lines[0]->d.id);
+
+    // Merge and set the alleles, create a mapping from source allele indexes to dst idxs
+    hts_expand0(map_t,nlines,args->mmaps,args->maps);   // a mapping for each line
+    args->nals = args->maps[0].nals = lines[0]->n_allele;
+    hts_expand(int,args->maps[0].nals,args->maps[0].mals,args->maps[0].map);
+    hts_expand(char*,args->nals,args->mals,args->als);
+    for (i=0; i<args->maps[0].nals; i++)
+    {
+        args->maps[0].map[i] = i;
+        args->als[i] = strdup(lines[0]->d.allele[i]);
+    }
+    for (i=1; i<nlines; i++)
+    {
+        if (lines[i]->d.id[0]!='.' || lines[i]->d.id[1]) bcf_add_id(args->out_hdr, dst, lines[i]->d.id);
+        args->maps[i].nals = lines[i]->n_allele;
+        hts_expand(int,args->maps[i].nals,args->maps[i].mals,args->maps[i].map);
+        args->als = merge_alleles(lines[i]->d.allele, lines[i]->n_allele, args->maps[i].map, args->als, &args->nals, &args->mals);
+        if ( !args->als ) error("Failed to merge alleles at %s:%"PRId64"\n", bcf_seqname(args->hdr,dst),(int64_t) dst->pos+1);
+    }
+    bcf_update_alleles(args->out_hdr, dst, (const char**)args->als, args->nals);
+    for (i=0; i<args->nals; i++)
+    {
+        free(args->als[i]);
+        args->als[i] = NULL;
+    }
+
+    if ( lines[0]->d.n_flt ) bcf_update_filter(args->out_hdr, dst, lines[0]->d.flt, lines[0]->d.n_flt);
+    for (i=1; i<nlines; i++) {
+        int j;
+        for (j=0; j<lines[i]->d.n_flt; j++) {
+            // if strict_filter, set FILTER to PASS if any site PASS
+            // otherwise accumulate FILTERs
+            if (lines[i]->d.flt[j] == bcf_hdr_id2int(args->hdr, BCF_DT_ID, "PASS")) {
+                if (args->strict_filter) {
+                    bcf_update_filter(args->out_hdr, dst, lines[i]->d.flt, lines[i]->d.n_flt);
+                    break;
+                }
+                else
+                    continue;
+            }
+            bcf_add_filter(args->out_hdr, dst, lines[i]->d.flt[j]);
+        }
+    }
+
+    // merge info
+    for (i=0; i<lines[0]->n_info; i++)
+    {
+        bcf_info_t *info = &lines[0]->d.info[i];
+        int type = bcf_hdr_id2type(args->hdr,BCF_HL_INFO,info->key);
+        if ( type==BCF_HT_INT || type==BCF_HT_REAL ) merge_info_numeric(args, lines, nlines, info, dst);
+        else if ( type==BCF_HT_FLAG ) merge_info_flag(args, lines, nlines, info, dst);
+        else merge_info_string(args, lines, nlines, info, dst);
+    }
+
+    // merge format
+    int gt_id = bcf_hdr_id2int(args->hdr,BCF_DT_ID,"GT");
+    dst->n_sample = lines[0]->n_sample;
+    for (i=0; i<lines[0]->n_fmt; i++)
+    {
+        bcf_fmt_t *fmt = &lines[0]->d.fmt[i];
+        int type = bcf_hdr_id2type(args->hdr,BCF_HL_FMT,fmt->id);
+        if ( fmt->id==gt_id ) merge_format_genotype(args, lines, nlines, fmt, dst);
+        else if ( type==BCF_HT_INT || type==BCF_HT_REAL ) merge_format_numeric(args, lines, nlines, fmt, dst);
+        else merge_format_string(args, lines, nlines, fmt, dst);
+    }
+}
+
+#define SWAP(type_t, a, b) { type_t t = a; a = b; b = t; }
+static void mrows_schedule(args_t *args, bcf1_t **line)
+{
+    int i,m;
+    if ( args->mrows_collapse==COLLAPSE_ANY         // merge all record types together
+        || bcf_get_variant_types(*line)&VCF_SNP     // SNP, put into alines
+        || bcf_get_variant_types(*line)==VCF_REF )  // ref
+    {
+        args->nalines++;
+        m = args->malines;
+        hts_expand(bcf1_t*,args->nalines,args->malines,args->alines);
+        for (i=m; i<args->malines; i++) args->alines[i] = bcf_init1();
+        SWAP(bcf1_t*, args->alines[args->nalines-1], *line);
+    }
+    else
+    {
+        args->nblines++;
+        m = args->mblines;
+        hts_expand(bcf1_t*,args->nblines,args->mblines,args->blines);
+        for (i=m; i<args->mblines; i++) args->blines[i] = bcf_init1();
+        SWAP(bcf1_t*, args->blines[args->nblines-1], *line);
+    }
+}
+static int mrows_ready_to_flush(args_t *args, bcf1_t *line)
+{
+    if ( args->nalines && (args->alines[0]->rid!=line->rid || args->alines[0]->pos!=line->pos) ) return 1;
+    if ( args->nblines && (args->blines[0]->rid!=line->rid || args->blines[0]->pos!=line->pos) ) return 1;
+    return 0;
+}
+static bcf1_t *mrows_flush(args_t *args)
+{
+    if ( args->nblines && args->nalines==1 && bcf_get_variant_types(args->alines[0])==VCF_REF )
+    {
+        // By default, REF lines are merged with SNPs if SNPs and indels are to be kept separately.
+        // However, if there are indels only and a single REF line, merge it with indels.
+        args->nblines++;
+        int i,m = args->mblines;
+        hts_expand(bcf1_t*,args->nblines,args->mblines,args->blines);
+        for (i=m; i<args->mblines; i++) args->blines[i] = bcf_init1();
+        SWAP(bcf1_t*, args->blines[args->nblines-1], args->alines[0]);
+        args->nalines--;
+    }
+    if ( args->nalines )
+    {
+        if ( args->nalines==1 )
+        {
+            args->nalines = 0;
+            return args->alines[0];
+        }
+        bcf_clear(args->mrow_out);
+        merge_biallelics_to_multiallelic(args, args->mrow_out, args->alines, args->nalines);
+        args->nalines = 0;
+        return args->mrow_out;
+    }
+    else if ( args->nblines )
+    {
+        if ( args->nblines==1 )
+        {
+            args->nblines = 0;
+            return args->blines[0];
+        }
+        bcf_clear(args->mrow_out);
+        merge_biallelics_to_multiallelic(args, args->mrow_out, args->blines, args->nblines);
+        args->nblines = 0;
+        return args->mrow_out;
+    }
+    return NULL;
+}
+static void cmpals_add(cmpals_t *ca, bcf1_t *rec)
+{
+    ca->ncmpals++;
+    hts_expand0(cmpals1_t, ca->ncmpals, ca->mcmpals, ca->cmpals);
+    cmpals1_t *cmpals = ca->cmpals + ca->ncmpals - 1;
+    free(cmpals->ref);
+    cmpals->ref = strdup(rec->d.allele[0]);
+    cmpals->n   = rec->n_allele;
+    if ( rec->n_allele==2 )
+    {
+        free(cmpals->alt);
+        cmpals->alt = strdup(rec->d.allele[1]);
+    }
+    else
+    {
+        if ( cmpals->hash ) khash_str2int_destroy_free(cmpals->hash);
+        cmpals->hash = khash_str2int_init();
+        int i;
+        for (i=1; i<rec->n_allele; i++)
+            khash_str2int_inc(cmpals->hash, strdup(rec->d.allele[i]));
+    }
+}
+static int cmpals_match(cmpals_t *ca, bcf1_t *rec)
+{
+    int i, j;
+    for (i=0; i<ca->ncmpals; i++)
+    {
+        cmpals1_t *cmpals = ca->cmpals + i;
+        if ( rec->n_allele != cmpals->n ) continue;
+
+        // NB. assuming both are normalized
+        if ( strcasecmp(rec->d.allele[0], cmpals->ref) ) continue;
+
+        // the most frequent case
+        if ( rec->n_allele==2 )
+        {
+            if ( strcasecmp(rec->d.allele[1], cmpals->alt) ) continue;
+            return 1;
+        }
+
+        khash_t(str2int) *hash = (khash_t(str2int)*) cmpals->hash;
+        for (j=1; j<rec->n_allele; j++)
+            if ( !khash_str2int_has_key(hash, rec->d.allele[j]) ) break;
+        if ( j<rec->n_allele ) continue;
+        return 1;
+    }
+    return 0;
+}
+static void cmpals_reset(cmpals_t *ca) { ca->ncmpals = 0; }
+static void cmpals_destroy(cmpals_t *ca)
+{
+    int i;
+    for (i=0; i<ca->mcmpals; i++)
+    {
+        cmpals1_t *cmpals = ca->cmpals + i;
+        free(cmpals->ref);
+        free(cmpals->alt);
+        if ( cmpals->hash ) khash_str2int_destroy_free(cmpals->hash);
+    }
+    free(ca->cmpals);
+}
+
+static void flush_buffer(args_t *args, htsFile *file, int n)
+{
+    bcf1_t *line;
+    int i, k;
+    int prev_rid = -1, prev_pos = -1, prev_type = 0;
+    for (i=0; i<n; i++)
+    {
+        k = rbuf_shift(&args->rbuf);
+        if ( args->mrows_op==MROWS_MERGE )
+        {
+            if ( mrows_ready_to_flush(args, args->lines[k]) )
+            {
+                while ( (line=mrows_flush(args)) )
+                    if ( bcf_write1(file, args->out_hdr, line)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->output_fname);
+            }
+            int merge = 1;
+            if ( args->mrows_collapse!=COLLAPSE_BOTH && args->mrows_collapse!=COLLAPSE_ANY )
+            {
+                if ( !(bcf_get_variant_types(args->lines[k]) & args->mrows_collapse) ) merge = 0;
+            }
+            if ( merge )
+            {
+                mrows_schedule(args, &args->lines[k]);
+                continue;
+            }
+        }
+        else if ( args->rmdup )
+        {
+            int line_type = bcf_get_variant_types(args->lines[k]);
+            if ( prev_rid>=0 && prev_rid==args->lines[k]->rid && prev_pos==args->lines[k]->pos )
+            {
+                if ( args->rmdup & BCF_SR_PAIR_ANY ) continue;    // rmdup by position only
+                if ( args->rmdup & BCF_SR_PAIR_SNPS && line_type&(VCF_SNP|VCF_MNP) && prev_type&(VCF_SNP|VCF_MNP) ) continue;
+                if ( args->rmdup & BCF_SR_PAIR_INDELS && line_type&(VCF_INDEL) && prev_type&(VCF_INDEL) ) continue;
+                if ( args->rmdup & BCF_SR_PAIR_EXACT && cmpals_match(&args->cmpals_out, args->lines[k]) ) continue;
+            }
+            else
+            {
+                prev_rid  = args->lines[k]->rid;
+                prev_pos  = args->lines[k]->pos;
+                prev_type = 0;
+                if ( args->rmdup & BCF_SR_PAIR_EXACT ) cmpals_reset(&args->cmpals_out);
+            }
+            prev_type |= line_type;
+            if ( args->rmdup & BCF_SR_PAIR_EXACT ) cmpals_add(&args->cmpals_out, args->lines[k]);
+        }
+        if ( bcf_write1(file, args->out_hdr, args->lines[k])!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->output_fname);
+    }
+    if ( args->mrows_op==MROWS_MERGE && !args->rbuf.n )
+    {
+        while ( (line=mrows_flush(args)) )
+            if ( bcf_write1(file, args->out_hdr, line)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->output_fname);
+    }
+}
+
+static void init_data(args_t *args)
+{
+    args->hdr = args->files->readers[0].header;
+    if ( args->keep_sum_ad )
+    {
+        args->keep_sum_ad = bcf_hdr_id2int(args->hdr,BCF_DT_ID,"AD");
+        if ( args->keep_sum_ad < 0 ) error("Error: --keep-sum-ad requested but the tag AD is not present\n");
+    }
+    else
+        args->keep_sum_ad = -1;
+
+    args->out_hdr = bcf_hdr_dup(args->hdr);
+    if ( args->old_rec_tag )
+        bcf_hdr_printf(args->out_hdr,"##INFO=<ID=%s,Number=1,Type=String,Description=\"Original variant. Format: CHR|POS|REF|ALT|USED_ALT_IDX\">",args->old_rec_tag);
+
+    rbuf_init(&args->rbuf, 100);
+    args->lines = (bcf1_t**) calloc(args->rbuf.m, sizeof(bcf1_t*));
+    if ( args->ref_fname )
+    {
+        args->fai = fai_load(args->ref_fname);
+        if ( !args->fai ) error("Failed to load the fai index: %s\n", args->ref_fname);
+    }
+    if ( args->mrows_op==MROWS_MERGE )
+    {
+        args->mrow_out = bcf_init1();
+        args->tmp_str = (kstring_t*) calloc(bcf_hdr_nsamples(args->hdr),sizeof(kstring_t));
+        args->diploid = (uint8_t*) malloc(bcf_hdr_nsamples(args->hdr));
+    }
+    if ( args->atomize==SPLIT )
+    {
+        args->abuf = abuf_init(args->hdr, SPLIT);
+        abuf_set_opt(args->abuf, bcf_hdr_t*, BCF_HDR, args->out_hdr);
+        if ( args->old_rec_tag )
+            abuf_set_opt(args->abuf, const char*, INFO_TAG, args->old_rec_tag);
+        abuf_set_opt(args->abuf, int, STAR_ALLELE, args->use_star_allele);
+    }
+}
+
+static void destroy_data(args_t *args)
+{
+    cmpals_destroy(&args->cmpals_in);
+    cmpals_destroy(&args->cmpals_out);
+    int i;
+    for (i=0; i<args->rbuf.m; i++)
+        if ( args->lines[i] ) bcf_destroy1(args->lines[i]);
+    free(args->lines);
+    for (i=0; i<args->mtmp_lines; i++)
+        if ( args->tmp_lines[i] ) bcf_destroy1(args->tmp_lines[i]);
+    free(args->tmp_lines);
+    for (i=0; i<args->malines; i++)
+        bcf_destroy1(args->alines[i]);
+    free(args->alines);
+    for (i=0; i<args->mblines; i++)
+        bcf_destroy1(args->blines[i]);
+    free(args->blines);
+    for (i=0; i<args->mmaps; i++)
+        free(args->maps[i].map);
+    for (i=0; i<args->ntmp_als; i++)
+        free(args->tmp_als[i].s);
+    free(args->tmp_als);
+    free(args->tmp_kstr.s);
+    if ( args->tmp_str )
+    {
+        for (i=0; i<bcf_hdr_nsamples(args->hdr); i++) free(args->tmp_str[i].s);
+        free(args->tmp_str);
+    }
+    free(args->maps);
+    free(args->als);
+    free(args->int32_arr);
+    free(args->tmp_arr1);
+    free(args->tmp_arr2);
+    free(args->diploid);
+    if ( args->abuf ) abuf_destroy(args->abuf);
+    bcf_hdr_destroy(args->out_hdr);
+    if ( args->mrow_out ) bcf_destroy1(args->mrow_out);
+    if ( args->fai ) fai_destroy(args->fai);
+    if ( args->mseq ) free(args->seq);
+}
+
+
+static void normalize_line(args_t *args, bcf1_t *line)
+{
+    if ( args->fai )
+    {
+        if ( args->check_ref & CHECK_REF_FIX ) fix_ref(args, line);
+        if ( args->do_indels )
+        {
+            int ret = realign(args, line);
+
+            // exclude broken VCF lines
+            if ( ret==ERR_REF_MISMATCH && args->check_ref & CHECK_REF_SKIP )
+            {
+                args->nskipped++;
+                return;
+            }
+            if ( ret==ERR_DUP_ALLELE )
+            {
+                if ( args->check_ref & CHECK_REF_FIX )
+                    fix_dup_alt(args, line);
+                else if ( args->check_ref==CHECK_REF_EXIT )
+                    error("Duplicate alleles at %s:%"PRId64"; run with -cw to turn the error into warning or with -cs to fix.\n", bcf_seqname(args->hdr,line),(int64_t) line->pos+1);
+                else if ( args->check_ref & CHECK_REF_WARN )
+                    fprintf(stderr,"ALT_DUP\t%s\t%"PRId64"\n", bcf_seqname(args->hdr,line),(int64_t) line->pos+1);
+            }
+        }
+    }
+
+    // insert into sorted buffer
+    rbuf_expand0(&args->rbuf,bcf1_t*,args->rbuf.n+1,args->lines);
+    int i,j;
+    i = j = rbuf_append(&args->rbuf);
+    if ( args->lines[i] ) bcf_destroy(args->lines[i]);
+    args->lines[i] = bcf_dup(line);
+    while ( rbuf_prev(&args->rbuf,&i) )
+    {
+        if ( args->lines[i]->pos > args->lines[j]->pos ) SWAP(bcf1_t*, args->lines[i], args->lines[j]);
+        j = i;
+    }
+}
+
+static bcf1_t *next_atomized_line(args_t *args)
+{
+    bcf1_t *rec = NULL;
+    if ( args->atomize==SPLIT )
+    {
+        rec = abuf_flush(args->abuf, 0);
+        if ( rec ) return rec;
+    }
+
+    if ( !bcf_sr_next_line(args->files) ) return NULL;
+
+    if ( args->atomize==SPLIT )
+    {
+        abuf_push(args->abuf,bcf_sr_get_line(args->files,0));
+        return abuf_flush(args->abuf, 0);
+    }
+    return bcf_sr_get_line(args->files,0);
+}
+static void normalize_vcf(args_t *args)
+{
+    char wmode[8];
+    set_wmode(wmode,args->output_type,args->output_fname,args->clevel);
+    args->out = hts_open(args->output_fname ? args->output_fname : "-", wmode);
+    if ( args->out == NULL ) error("Can't write to \"%s\": %s\n", args->output_fname, strerror(errno));
+    if ( args->n_threads )
+        hts_set_opt(args->out, HTS_OPT_THREAD_POOL, args->files->p);
+    if (args->record_cmd_line) bcf_hdr_append_version(args->out_hdr, args->argc, args->argv, "bcftools_norm");
+    if ( bcf_hdr_write(args->out, args->out_hdr)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->output_fname);
+
+    bcf1_t *line;
+    int prev_rid = -1, prev_pos = -1, prev_type = 0;
+    while ( (line = next_atomized_line(args)) )
+    {
+        args->ntotal++;
+        if ( args->rmdup )
+        {
+            int line_type = bcf_get_variant_types(line);
+            if ( prev_rid>=0 && prev_rid==line->rid && prev_pos==line->pos )
+            {
+                if ( args->rmdup & BCF_SR_PAIR_ANY ) continue;    // rmdup by position only
+                if ( args->rmdup & BCF_SR_PAIR_SNPS && line_type&(VCF_SNP|VCF_MNP) && prev_type&(VCF_SNP|VCF_MNP) ) continue;
+                if ( args->rmdup & BCF_SR_PAIR_INDELS && line_type&(VCF_INDEL) && prev_type&(VCF_INDEL) ) continue;
+                if ( args->rmdup & BCF_SR_PAIR_EXACT && cmpals_match(&args->cmpals_in, line) ) continue;
+            }
+            else
+            {
+                prev_rid  = line->rid;
+                prev_pos  = line->pos;
+                prev_type = 0;
+                if ( args->rmdup & BCF_SR_PAIR_EXACT ) cmpals_reset(&args->cmpals_in);
+            }
+            prev_type |= line_type;
+            if ( args->rmdup & BCF_SR_PAIR_EXACT ) cmpals_add(&args->cmpals_in, line);
+        }
+
+        // still on the same chromosome?
+        int i,j,ilast = rbuf_last(&args->rbuf);
+        if ( ilast>=0 && line->rid != args->lines[ilast]->rid ) flush_buffer(args, args->out, args->rbuf.n); // new chromosome
+
+        int split = 0;
+        if ( args->mrows_op==MROWS_SPLIT )
+        {
+            split = 1;
+            if ( args->mrows_collapse!=COLLAPSE_BOTH && args->mrows_collapse!=COLLAPSE_ANY )
+            {
+                if ( !(bcf_get_variant_types(line) & args->mrows_collapse) ) split = 0;
+            }
+            if ( split && line->n_allele>2 )
+            {
+                args->nsplit++;
+                split_multiallelic_to_biallelics(args, line);
+                for (j=0; j<args->ntmp_lines; j++)
+                    normalize_line(args, args->tmp_lines[j]);
+            }
+            else
+                split = 0;
+        }
+        if ( !split )
+            normalize_line(args, line);
+
+        // find out how many sites to flush
+        ilast = rbuf_last(&args->rbuf);
+        j = 0;
+        for (i=-1; rbuf_next(&args->rbuf,&i); )
+        {
+            if ( args->lines[ilast]->pos - args->lines[i]->pos < args->buf_win ) break;
+            j++;
+        }
+        if ( j>0 ) flush_buffer(args, args->out, j);
+    }
+    flush_buffer(args, args->out, args->rbuf.n);
+    if ( hts_close(args->out)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,args->output_fname);
+
+    fprintf(stderr,"Lines   total/split/realigned/skipped:\t%d/%d/%d/%d\n", args->ntotal,args->nsplit,args->nchanged,args->nskipped);
+    if ( args->check_ref & CHECK_REF_FIX )
+        fprintf(stderr,"REF/ALT total/modified/added:  \t%d/%d/%d\n", args->nref.tot,args->nref.swap,args->nref.set);
+}
+
+static void usage(void)
+{
+    fprintf(stderr, "\n");
+    fprintf(stderr, "About:   Left-align and normalize indels; check if REF alleles match the reference;\n");
+    fprintf(stderr, "         split multiallelic sites into multiple rows; recover multiallelics from\n");
+    fprintf(stderr, "         multiple rows.\n");
+    fprintf(stderr, "Usage:   bcftools norm [options] <in.vcf.gz>\n");
+    fprintf(stderr, "\n");
+    fprintf(stderr, "Options:\n");
+    fprintf(stderr, "    -a, --atomize                   Decompose complex variants (e.g. MNVs become consecutive SNVs)\n");
+    fprintf(stderr, "        --atom-overlaps '*'|.       Use the star allele (*) for overlapping alleles or set to missing (.) [*]\n");
+    fprintf(stderr, "    -c, --check-ref e|w|x|s         Check REF alleles and exit (e), warn (w), exclude (x), or set (s) bad sites [e]\n");
+    fprintf(stderr, "    -D, --remove-duplicates         Remove duplicate lines of the same type.\n");
+    fprintf(stderr, "    -d, --rm-dup TYPE               Remove duplicate snps|indels|both|all|exact\n");
+    fprintf(stderr, "    -f, --fasta-ref FILE            Reference sequence\n");
+    fprintf(stderr, "        --force                     Try to proceed even if malformed tags are encountered. Experimental, use at your own risk\n");
+    fprintf(stderr, "        --keep-sum TAG,..           Keep vector sum constant when splitting multiallelics (see github issue #360)\n");
+    fprintf(stderr, "    -m, --multiallelics -|+TYPE     Split multiallelics (-) or join biallelics (+), type: snps|indels|both|any [both]\n");
+    fprintf(stderr, "        --no-version                Do not append version and command line to the header\n");
+    fprintf(stderr, "    -N, --do-not-normalize          Do not normalize indels (with -m or -c s)\n");
+    fprintf(stderr, "        --old-rec-tag STR           Annotate modified records with INFO/STR indicating the original variant\n");
+    fprintf(stderr, "    -o, --output FILE               Write output to a file [standard output]\n");
+    fprintf(stderr, "    -O, --output-type u|b|v|z[0-9]  u/b: un/compressed BCF, v/z: un/compressed VCF, 0-9: compression level [v]\n");
+    fprintf(stderr, "    -r, --regions REGION            Restrict to comma-separated list of regions\n");
+    fprintf(stderr, "    -R, --regions-file FILE         Restrict to regions listed in a file\n");
+    fprintf(stderr, "        --regions-overlap 0|1|2     Include if POS in the region (0), record overlaps (1), variant overlaps (2) [1]\n");
+    fprintf(stderr, "    -s, --strict-filter             When merging (-m+), merged site is PASS only if all sites being merged PASS\n");
+    fprintf(stderr, "    -t, --targets REGION            Similar to -r but streams rather than index-jumps\n");
+    fprintf(stderr, "    -T, --targets-file FILE         Similar to -R but streams rather than index-jumps\n");
+    fprintf(stderr, "        --targets-overlap 0|1|2     Include if POS in the region (0), record overlaps (1), variant overlaps (2) [0]\n");
+    fprintf(stderr, "        --threads INT               Use multithreading with <int> worker threads [0]\n");
+    fprintf(stderr, "    -w, --site-win INT              Buffer for sorting lines which changed position during realignment [1000]\n");
+    fprintf(stderr, "\n");
+    fprintf(stderr, "Examples:\n");
+    fprintf(stderr, "   # normalize and left-align indels\n");
+    fprintf(stderr, "   bcftools norm -f ref.fa in.vcf\n");
+    fprintf(stderr, "\n");
+    fprintf(stderr, "   # split multi-allelic sites\n");
+    fprintf(stderr, "   bcftools norm -m- in.vcf\n");
+    fprintf(stderr, "\n");
+    exit(1);
+}
+
+int main_vcfnorm(int argc, char *argv[])
+{
+    int c;
+    args_t *args  = (args_t*) calloc(1,sizeof(args_t));
+    args->argc    = argc; args->argv = argv;
+    args->files   = bcf_sr_init();
+    args->output_fname = "-";
+    args->output_type = FT_VCF;
+    args->n_threads = 0;
+    args->record_cmd_line = 1;
+    args->aln_win = 100;
+    args->buf_win = 1000;
+    args->mrows_collapse = COLLAPSE_BOTH;
+    args->do_indels = 1;
+    args->clevel = -1;
+    int region_is_file  = 0;
+    int targets_is_file = 0;
+    args->use_star_allele = 1;
+    int regions_overlap = 1;
+    int targets_overlap = 0;
+
+    static struct option loptions[] =
+    {
+        {"help",no_argument,NULL,'h'},
+        {"force",no_argument,NULL,7},
+        {"atomize",no_argument,NULL,'a'},
+        {"atom-overlaps",required_argument,NULL,11},
+        {"old-rec-tag",required_argument,NULL,12},
+        {"keep-sum",required_argument,NULL,10},
+        {"fasta-ref",required_argument,NULL,'f'},
+        {"do-not-normalize",no_argument,NULL,'N'},
+        {"multiallelics",required_argument,NULL,'m'},
+        {"regions",required_argument,NULL,'r'},
+        {"regions-file",required_argument,NULL,'R'},
+        {"regions-overlap",required_argument,NULL,1},
+        {"targets",required_argument,NULL,'t'},
+        {"targets-file",required_argument,NULL,'T'},
+        {"targets-overlap",required_argument,NULL,2},
+        {"site-win",required_argument,NULL,'w'},
+        {"remove-duplicates",no_argument,NULL,'D'},
+        {"rm-dup",required_argument,NULL,'d'},
+        {"output",required_argument,NULL,'o'},
+        {"output-type",required_argument,NULL,'O'},
+        {"threads",required_argument,NULL,9},
+        {"check-ref",required_argument,NULL,'c'},
+        {"strict-filter",no_argument,NULL,'s'},
+        {"no-version",no_argument,NULL,8},
+        {NULL,0,NULL,0}
+    };
+    char *tmp;
+    while ((c = getopt_long(argc, argv, "hr:R:f:w:Dd:o:O:c:m:t:T:sNa",loptions,NULL)) >= 0) {
+        switch (c) {
+            case  10:
+                // possibly generalize this also to INFO/AD and other tags
+                if ( strcasecmp("ad",optarg) )
+                    error("Error: only --keep-sum AD is currently supported. See https://github.com/samtools/bcftools/issues/360 for more.\n");
+                args->keep_sum_ad = 1;  // this will be set to the header id or -1 in init_data
+                break;
+            case 'a': args->atomize = SPLIT; break;
+            case 11 :
+                if ( optarg[0]=='*' ) args->use_star_allele = 1;
+                else if ( optarg[0]=='.' ) args->use_star_allele = 0;
+                else error("Invalid argument to --atom-overlaps. Perhaps you wanted: \"--atom-overlaps '*'\"?\n");
+                break;
+            case 12 : args->old_rec_tag = optarg; break;
+            case 'N': args->do_indels = 0; break;
+            case 'd':
+                if ( !strcmp("snps",optarg) ) args->rmdup = BCF_SR_PAIR_SNPS;
+                else if ( !strcmp("indels",optarg) ) args->rmdup = BCF_SR_PAIR_INDELS;
+                else if ( !strcmp("both",optarg) ) args->rmdup = BCF_SR_PAIR_BOTH;
+                else if ( !strcmp("all",optarg) ) args->rmdup = BCF_SR_PAIR_ANY;
+                else if ( !strcmp("any",optarg) ) args->rmdup = BCF_SR_PAIR_ANY;
+                else if ( !strcmp("none",optarg) ) args->rmdup = BCF_SR_PAIR_EXACT;
+                else if ( !strcmp("exact",optarg) ) args->rmdup = BCF_SR_PAIR_EXACT;
+                else error("The argument to -d not recognised: %s\n", optarg);
+                break;
+            case 'm':
+                if ( optarg[0]=='-' ) args->mrows_op = MROWS_SPLIT;
+                else if ( optarg[0]=='+' ) args->mrows_op = MROWS_MERGE;
+                else error("Expected '+' or '-' with -m\n");
+                if ( optarg[1]!=0 )
+                {
+                    if ( !strcmp("snps",optarg+1) ) args->mrows_collapse = COLLAPSE_SNPS;
+                    else if ( !strcmp("indels",optarg+1) ) args->mrows_collapse = COLLAPSE_INDELS;
+                    else if ( !strcmp("both",optarg+1) ) args->mrows_collapse = COLLAPSE_BOTH;
+                    else if ( !strcmp("any",optarg+1) ) args->mrows_collapse = COLLAPSE_ANY;
+                    else error("The argument to -m not recognised: %s\n", optarg);
+                }
+                break;
+            case 'c':
+                if ( strchr(optarg,'w') ) args->check_ref |= CHECK_REF_WARN;
+                if ( strchr(optarg,'x') ) args->check_ref |= CHECK_REF_SKIP;
+                if ( strchr(optarg,'s') ) args->check_ref |= CHECK_REF_FIX;
+                if ( strchr(optarg,'e') ) args->check_ref = CHECK_REF_EXIT; // overrides the above
+                break;
+            case 'O':
+                switch (optarg[0]) {
+                    case 'b': args->output_type = FT_BCF_GZ; break;
+                    case 'u': args->output_type = FT_BCF; break;
+                    case 'z': args->output_type = FT_VCF_GZ; break;
+                    case 'v': args->output_type = FT_VCF; break;
+                    default:
+                    {
+                        args->clevel = strtol(optarg,&tmp,10);
+                        if ( *tmp || args->clevel<0 || args->clevel>9 ) error("The output type \"%s\" not recognised\n", optarg);
+                    }
+                }
+                if ( optarg[1] )
+                {
+                    args->clevel = strtol(optarg+1,&tmp,10);
+                    if ( *tmp || args->clevel<0 || args->clevel>9 ) error("Could not parse argument: --compression-level %s\n", optarg+1);
+                }
+                break;
+            case 'o': args->output_fname = optarg; break;
+            case 'D':
+                fprintf(stderr,"Warning: `-D` is functional but deprecated, replaced by and alias of `-d none`.\n");
+                args->rmdup = BCF_SR_PAIR_EXACT;
+                break;
+            case 's': args->strict_filter = 1; break;
+            case 'f': args->ref_fname = optarg; break;
+            case 'r': args->region = optarg; break;
+            case 'R': args->region = optarg; region_is_file = 1; break;
+            case 't': args->targets = optarg; break;
+            case 'T': args->targets = optarg; targets_is_file = 1; break;
+            case 'w':
+                args->buf_win = strtol(optarg,&tmp,10);
+                if ( *tmp ) error("Could not parse argument: --site-win %s\n", optarg);
+                break;
+            case  9 : args->n_threads = strtol(optarg, 0, 0); break;
+            case  8 : args->record_cmd_line = 0; break;
+            case  7 : args->force = 1; break;
+            case  1 :
+                regions_overlap = parse_overlap_option(optarg);
+                if ( regions_overlap < 0 ) error("Could not parse: --regions-overlap %s\n",optarg);
+                break;
+            case  2 :
+                targets_overlap = parse_overlap_option(optarg);
+                if ( targets_overlap < 0 ) error("Could not parse: --targets-overlap %s\n",optarg);
+                break;
+            case 'h':
+            case '?': usage(); break;
+            default: error("Unknown argument: %s\n", optarg);
+        }
+    }
+
+    char *fname = NULL;
+    if ( optind>=argc )
+    {
+        if ( !isatty(fileno((FILE *)stdin)) ) fname = "-";  // reading from stdin
+        else usage();
+    }
+    else fname = argv[optind];
+
+    if ( !args->ref_fname && !args->mrows_op && !args->rmdup && args->atomize==NONE ) error("Expected -a, -f, -m, -D or -d option\n");
+    if ( !args->check_ref && args->ref_fname ) args->check_ref = CHECK_REF_EXIT;
+    if ( args->check_ref && !args->ref_fname ) error("Expected --fasta-ref with --check-ref\n");
+
+    if ( args->region )
+    {
+        bcf_sr_set_opt(args->files,BCF_SR_REGIONS_OVERLAP,regions_overlap);
+        if ( bcf_sr_set_regions(args->files, args->region,region_is_file)<0 )
+            error("Failed to read the regions: %s\n", args->region);
+    }
+    if ( args->targets )
+    {
+        bcf_sr_set_opt(args->files,BCF_SR_TARGETS_OVERLAP,targets_overlap);
+        if ( bcf_sr_set_targets(args->files, args->targets,targets_is_file, 0)<0 )
+            error("Failed to read the targets: %s\n", args->targets);
+    }
+
+    if ( bcf_sr_set_threads(args->files, args->n_threads)<0 ) error("Failed to create threads\n");
+    if ( !bcf_sr_add_reader(args->files, fname) ) error("Failed to read from %s: %s\n", !strcmp("-",fname)?"standard input":fname,bcf_sr_strerror(args->files->errnum));
+    if ( args->mrows_op&MROWS_SPLIT && args->rmdup ) error("Cannot combine -D and -m-\n");
+    init_data(args);
+    normalize_vcf(args);
+    destroy_data(args);
+    bcf_sr_destroy(args->files);
+    free(args);
+    return 0;
+}
+
diff --git a/bcftools/vcfnorm.c.pysam.c b/bcftools/vcfnorm.c.pysam.c
new file mode 100644
index 0000000..a292b96
--- /dev/null
+++ b/bcftools/vcfnorm.c.pysam.c
@@ -0,0 +1,2297 @@
+#include "bcftools.pysam.h"
+
+/*  vcfnorm.c -- Left-align and normalize indels.
+
+    Copyright (C) 2013-2021 Genome Research Ltd.
+
+    Author: Petr Danecek <pd3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.  */
+
+#include <stdio.h>
+#include <strings.h>
+#include <unistd.h>
+#include <getopt.h>
+#include <assert.h>
+#include <ctype.h>
+#include <string.h>
+#include <errno.h>
+#include <sys/stat.h>
+#include <sys/types.h>
+#include <inttypes.h>
+#include <htslib/vcf.h>
+#include <htslib/synced_bcf_reader.h>
+#include <htslib/faidx.h>
+#include <htslib/khash_str2int.h>
+#include "bcftools.h"
+#include "rbuf.h"
+#include "abuf.h"
+
+#define CHECK_REF_EXIT 1
+#define CHECK_REF_WARN 2
+#define CHECK_REF_SKIP 4
+#define CHECK_REF_FIX  8
+
+#define MROWS_SPLIT 1
+#define MROWS_MERGE  2
+
+// for -m+, mapping from allele indexes of a single input record
+// to allele indexes of output record
+typedef struct
+{
+    int nals, mals, *map;
+}
+map_t;
+
+// primitive comparison of two records' alleles via hashes; normalized alleles assumed
+typedef struct
+{
+    int n;  // number of alleles
+    char *ref, *alt;
+    void *hash;
+}
+cmpals1_t;
+
+typedef struct
+{
+    cmpals1_t *cmpals;
+    int ncmpals, mcmpals;
+}
+cmpals_t;
+
+typedef struct
+{
+    char *tseq, *seq;
+    int mseq;
+    bcf1_t **lines, **tmp_lines, **alines, **blines, *mrow_out;
+    int ntmp_lines, mtmp_lines, nalines, malines, nblines, mblines;
+    map_t *maps;     // mrow map for each buffered record
+    char **als;
+    int mmaps, nals, mals;
+    uint8_t *tmp_arr1, *tmp_arr2, *diploid;
+    int32_t *int32_arr;
+    int ntmp_arr1, ntmp_arr2, nint32_arr;
+    kstring_t *tmp_str;
+    kstring_t *tmp_als, tmp_kstr;
+    int ntmp_als;
+    rbuf_t rbuf;
+    int buf_win;            // maximum distance between two records to consider
+    int aln_win;            // the realignment window size (maximum repeat size)
+    bcf_srs_t *files;       // using the synced reader only for -r option
+    bcf_hdr_t *hdr, *out_hdr;
+    cmpals_t cmpals_in, cmpals_out;
+    faidx_t *fai;
+    struct { int tot, set, swap; } nref;
+    char **argv, *output_fname, *ref_fname, *vcf_fname, *region, *targets;
+    int argc, rmdup, output_type, n_threads, check_ref, strict_filter, do_indels, clevel;
+    int nchanged, nskipped, nsplit, ntotal, mrows_op, mrows_collapse, parsimonious;
+    int record_cmd_line, force, force_warned, keep_sum_ad;
+    abuf_t *abuf;
+    abuf_opt_t atomize;
+    int use_star_allele;
+    char *old_rec_tag;
+    htsFile *out;
+}
+args_t;
+
+static inline int replace_iupac_codes(char *seq, int nseq)
+{
+    // Replace ambiguity codes with N for now, it awaits to be seen what the VCF spec codifies in the end
+    int i, n = 0;
+    for (i=0; i<nseq; i++)
+    {
+        char c = toupper(seq[i]);
+        if ( c!='A' && c!='C' && c!='G' && c!='T' && c!='N' ) { seq[i] = 'N'; n++; }
+    }
+    return n;
+}
+static inline int has_non_acgtn(char *seq, int nseq)
+{
+    char *end = seq + nseq;
+    while ( *seq && seq<end )
+    {
+        char c = toupper(*seq);
+        if ( c!='A' && c!='C' && c!='G' && c!='T' && c!='N' ) return 1;
+        seq++;
+    }
+    return 0;
+}
+
+static void seq_to_upper(char *seq, int len)
+{
+    int i;
+    if ( len )
+        for (i=0; i<len; i++) seq[i] = nt_to_upper(seq[i]);
+    else
+        for (i=0; seq[i]; i++) seq[i] = nt_to_upper(seq[i]);
+}
+
+static void fix_ref(args_t *args, bcf1_t *line)
+{
+    bcf_unpack(line, BCF_UN_STR);
+    int reflen = strlen(line->d.allele[0]);
+    int i,j, maxlen = reflen, len;
+    for (i=1; i<line->n_allele; i++)
+    {
+        int len = strlen(line->d.allele[i]);
+        if ( maxlen < len ) maxlen = len;
+    }
+
+    char *ref = faidx_fetch_seq(args->fai, (char*)bcf_seqname(args->hdr,line), line->pos, line->pos+maxlen-1, &len);
+    if ( !ref ) error("faidx_fetch_seq failed at %s:%"PRId64"\n", bcf_seqname(args->hdr,line),(int64_t) line->pos+1);
+    replace_iupac_codes(ref,len);
+
+    args->nref.tot++;
+
+    // is the REF different? If not, we are done
+    if ( !strncasecmp(line->d.allele[0],ref,reflen) ) { free(ref); return; }
+
+    // is the REF allele missing?
+    if ( reflen==1 && line->d.allele[0][0]=='.' )
+    {
+        line->d.allele[0][0] = ref[0];
+        args->nref.set++;
+        free(ref);
+        bcf_update_alleles(args->out_hdr,line,(const char**)line->d.allele,line->n_allele);
+        return;
+    }
+
+    // does REF or ALT contain non-standard bases?
+    int has_non_acgtn = 0;
+    for (i=0; i<line->n_allele; i++)
+    {
+        if ( line->d.allele[i][0]=='<' ) continue;
+        has_non_acgtn += replace_iupac_codes(line->d.allele[i],strlen(line->d.allele[i]));
+    }
+    if ( has_non_acgtn )
+    {
+        args->nref.set++;
+        bcf_update_alleles(args->out_hdr,line,(const char**)line->d.allele,line->n_allele);
+        if ( !strncasecmp(line->d.allele[0],ref,reflen) ) { free(ref); return; }
+    }
+
+    // does the REF allele contain N's ?
+    int fix = 0;
+    for (i=0; i<reflen; i++)
+    {
+        if ( line->d.allele[0][i]!='N' ) continue;
+        if ( ref[i]=='N' ) continue;
+        line->d.allele[0][i] = ref[i];
+        fix++;
+        for (j=1; j<line->n_allele; j++)
+        {
+            int len = strlen(line->d.allele[j]);
+            if ( len <= i || line->d.allele[j][i]!='N' ) continue;
+            line->d.allele[j][i] = ref[i];
+            fix++;
+        }
+    }
+    if ( fix )
+    {
+        args->nref.set++;
+        bcf_update_alleles(args->out_hdr,line,(const char**)line->d.allele,line->n_allele);
+        if ( !strncasecmp(line->d.allele[0],ref,reflen) ) { free(ref); return; }
+    }
+
+
+    // is it swapped?
+    for (i=1; i<line->n_allele; i++)
+    {
+        int len = strlen(line->d.allele[i]);
+        if ( !strncasecmp(line->d.allele[i],ref,len) ) break;
+    }
+
+    kstring_t str = {0,0,0};
+    if ( i==line->n_allele )    // none of the alternate alleles matches the reference
+    {
+        args->nref.set++;
+        kputsn(ref,reflen,&str);
+        for (i=1; i<line->n_allele; i++)
+        {
+            kputc(',',&str);
+            kputs(line->d.allele[i],&str);
+        }
+        bcf_update_alleles_str(args->out_hdr,line,str.s);
+        free(ref);
+        free(str.s);
+        return;
+    }
+
+    // one of the alternate alleles matches the reference, assume it's a simple swap
+    kputs(line->d.allele[i],&str);
+    for (j=1; j<line->n_allele; j++)
+    {
+        kputc(',',&str);
+        if ( j==i )
+            kputs(line->d.allele[0],&str);
+        else
+            kputs(line->d.allele[j],&str);
+    }
+    bcf_update_alleles_str(args->out_hdr,line,str.s);
+    args->nref.swap++;
+    free(ref);
+    free(str.s);
+
+    // swap genotypes
+    int ntmp = args->ntmp_arr1 / sizeof(int32_t); // reuse tmp_arr declared as uint8_t
+    int ngts = bcf_get_genotypes(args->hdr, line, &args->tmp_arr1, &ntmp);
+    args->ntmp_arr1 = ntmp * sizeof(int32_t);
+    int32_t *gts = (int32_t*) args->tmp_arr1;
+    int ni = 0;
+    for (j=0; j<ngts; j++)
+    {
+        if ( gts[j]==bcf_gt_unphased(0) ) { gts[j] = bcf_gt_unphased(i); ni++; }
+        else if ( gts[j]==bcf_gt_phased(0) ) { gts[j] = bcf_gt_phased(i); ni++; }
+        else if ( gts[j]==bcf_gt_unphased(i) ) gts[j] = bcf_gt_unphased(0);
+        else if ( gts[j]==bcf_gt_phased(i) ) gts[j] = bcf_gt_phased(0);
+    }
+    bcf_update_genotypes(args->out_hdr,line,gts,ngts);
+
+    // update AC
+    int nac = bcf_get_info_int32(args->hdr, line, "AC", &args->tmp_arr1, &ntmp);
+    args->ntmp_arr1 = ntmp * sizeof(int32_t);
+    if ( i <= nac )
+    {
+        int32_t *ac = (int32_t*)args->tmp_arr1;
+        ac[i-1] = ni;
+        bcf_update_info_int32(args->out_hdr, line, "AC", ac, nac);
+    }
+}
+
+static void fix_dup_alt(args_t *args, bcf1_t *line)
+{
+    // update alleles, create a mapping between old and new indexes
+    hts_expand(uint8_t,line->n_allele,args->ntmp_arr1,args->tmp_arr1);
+    args->tmp_arr1[0] = 0;  // ref always unchanged
+
+    int i, j, nals = line->n_allele, nals_ori = line->n_allele;
+    for (i=1, j=1; i<line->n_allele; i++)
+    {
+        if ( strcasecmp(line->d.allele[0],line->d.allele[i]) )
+        {
+            args->tmp_arr1[i] = j++;
+            continue;
+        }
+        args->tmp_arr1[i] = 0;
+        nals--;
+    }
+    for (i=1, j=1; i<line->n_allele; i++)
+    {
+        if ( !args->tmp_arr1[i] ) continue;
+        line->d.allele[j++] = line->d.allele[i];
+    }
+    bcf_update_alleles(args->out_hdr, line, (const char**)line->d.allele, nals);
+
+
+    // update genotypes
+    int ntmp = args->ntmp_arr2 / sizeof(int32_t); // reuse tmp_arr declared as uint8_t
+    int ngts = bcf_get_genotypes(args->hdr, line, &args->tmp_arr2, &ntmp);
+    args->ntmp_arr2 = ntmp * sizeof(int32_t);
+    int32_t *gts = (int32_t*) args->tmp_arr2;
+    int changed = 0;
+    for (i=0; i<ngts; i++)
+    {
+        if ( bcf_gt_is_missing(gts[i]) || gts[i]==bcf_int32_vector_end ) continue;
+        int ial = bcf_gt_allele(gts[i]);
+        if ( ial<nals_ori && ial==args->tmp_arr1[ial] ) continue;
+        int ial_new = ial<nals_ori ? args->tmp_arr1[ial] : 0;
+        gts[i] = bcf_gt_is_phased(gts[i]) ? bcf_gt_phased(ial_new) : bcf_gt_unphased(ial_new);
+        changed = 1;
+    }
+    if ( changed ) bcf_update_genotypes(args->out_hdr,line,gts,ngts);
+}
+
+static void set_old_rec_tag(args_t *args, bcf1_t *dst, bcf1_t *src, int ialt)
+{
+    if ( !args->old_rec_tag ) return;
+
+    // only update if the tag is not present already, there can be multiple normalization steps
+    int i, id = bcf_hdr_id2int(args->out_hdr, BCF_DT_ID, args->old_rec_tag);
+    bcf_unpack(dst, BCF_UN_INFO);
+    for (i=0; i<dst->n_info; i++)
+    {
+        bcf_info_t *inf = &dst->d.info[i];
+        if ( inf && inf->key == id ) return;
+    }
+
+    args->tmp_kstr.l = 0;
+    ksprintf(&args->tmp_kstr,"%s|%"PRIhts_pos"|%s|",bcf_seqname(args->hdr,src),src->pos+1,src->d.allele[0]);
+    for (i=1; i<src->n_allele; i++)
+    {
+        kputs(src->d.allele[i],&args->tmp_kstr);
+        if ( i+1<src->n_allele ) kputc(',',&args->tmp_kstr);
+    }
+    if ( ialt>0 )
+    {
+        kputc('|',&args->tmp_kstr);
+        kputw(ialt,&args->tmp_kstr);
+    }
+    if ( (bcf_update_info_string(args->out_hdr, dst, args->old_rec_tag, args->tmp_kstr.s))!=0 )
+            error("An error occurred while updating INFO/%s\n",args->old_rec_tag);
+}
+
+#define ERR_DUP_ALLELE       -2
+#define ERR_REF_MISMATCH     -1
+#define ERR_OK                0
+#define ERR_SYMBOLIC          1
+#define ERR_SPANNING_DELETION 2
+
+static int realign(args_t *args, bcf1_t *line)
+{
+    bcf_unpack(line, BCF_UN_STR);
+
+    // Sanity check REF
+    int i, nref, reflen = strlen(line->d.allele[0]);
+    char *ref = faidx_fetch_seq(args->fai, (char*)args->hdr->id[BCF_DT_CTG][line->rid].key, line->pos, line->pos+reflen-1, &nref);
+    if ( !ref ) error("faidx_fetch_seq failed at %s:%"PRId64"\n", args->hdr->id[BCF_DT_CTG][line->rid].key, (int64_t) line->pos+1);
+    seq_to_upper(ref,0);
+    replace_iupac_codes(ref,nref);  // any non-ACGT character in fasta ref is replaced with N
+
+    // does VCF REF contain non-standard bases?
+    if ( has_non_acgtn(line->d.allele[0],reflen) )
+    {
+        if ( args->check_ref==CHECK_REF_EXIT )
+            error("Non-ACGTN reference allele at %s:%"PRId64" .. REF_SEQ:'%s' vs VCF:'%s'\n", bcf_seqname(args->hdr,line),(int64_t) line->pos+1,ref,line->d.allele[0]);
+        if ( args->check_ref & CHECK_REF_WARN )
+            fprintf(bcftools_stderr,"NON_ACGTN_REF\t%s\t%"PRId64"\t%s\n", bcf_seqname(args->hdr,line),(int64_t) line->pos+1,line->d.allele[0]);
+        free(ref);
+        return ERR_REF_MISMATCH;
+    }
+    if ( strcasecmp(ref,line->d.allele[0]) )
+    {
+        if ( args->check_ref==CHECK_REF_EXIT )
+            error("Reference allele mismatch at %s:%"PRId64" .. REF_SEQ:'%s' vs VCF:'%s'\n", bcf_seqname(args->hdr,line),(int64_t) line->pos+1,ref,line->d.allele[0]);
+        if ( args->check_ref & CHECK_REF_WARN )
+            fprintf(bcftools_stderr,"REF_MISMATCH\t%s\t%"PRId64"\t%s\t%s\n", bcf_seqname(args->hdr,line),(int64_t) line->pos+1,line->d.allele[0],ref);
+        free(ref);
+        return ERR_REF_MISMATCH;
+    }
+    free(ref);
+    ref = NULL;
+
+    if ( line->n_allele == 1 ) // a REF
+    {
+        if ( line->rlen > 1 )
+        {
+            line->d.allele[0][1] = 0;
+            bcf_update_alleles(args->out_hdr,line,(const char**)line->d.allele,line->n_allele);
+        }
+        return ERR_OK;
+    }
+    if ( bcf_get_variant_types(line)==VCF_BND ) return ERR_SYMBOLIC;   // breakend, not an error
+
+    // make a copy of each allele for trimming
+    hts_expand0(kstring_t,line->n_allele,args->ntmp_als,args->tmp_als);
+    kstring_t *als = args->tmp_als;
+    for (i=0; i<line->n_allele; i++)
+    {
+        if ( line->d.allele[i][0]=='<' ) return ERR_SYMBOLIC;  // symbolic allele
+        if ( line->d.allele[i][0]=='*' ) return ERR_SPANNING_DELETION;  // spanning deletion
+        if ( has_non_acgtn(line->d.allele[i],line->shared.l) )
+        {
+            if ( args->check_ref==CHECK_REF_EXIT )
+                error("Non-ACGTN alternate allele at %s:%"PRId64" .. VCF:'%s'\n", bcf_seqname(args->hdr,line),(int64_t) line->pos+1,line->d.allele[i]);
+            if ( args->check_ref & CHECK_REF_WARN )
+                fprintf(bcftools_stderr,"NON_ACGTN_ALT\t%s\t%"PRId64"\t%s\n", bcf_seqname(args->hdr,line),(int64_t) line->pos+1,line->d.allele[i]);
+            return ERR_REF_MISMATCH;
+        }
+
+        als[i].l = 0;
+        kputs(line->d.allele[i], &als[i]);
+        seq_to_upper(als[i].s,0);
+
+        if ( i>0 && als[i].l==als[0].l && !strcasecmp(als[0].s,als[i].s) ) return ERR_DUP_ALLELE;
+    }
+
+    // trim from right
+    int new_pos = line->pos;
+    while (1)
+    {
+        // is the rightmost base identical in all alleles?
+        int min_len = als[0].l;
+        for (i=1; i<line->n_allele; i++)
+        {
+            if ( toupper(als[0].s[ als[0].l-1 ])!=toupper(als[i].s[ als[i].l-1 ]) ) break;
+            if ( als[i].l < min_len ) min_len = als[i].l;
+        }
+        if ( i!=line->n_allele ) break; // there are differences, cannot be trimmed
+        if ( min_len<=1 && new_pos==0 ) break;
+
+        int pad_from_left = 0;
+        for (i=0; i<line->n_allele; i++) // trim all alleles
+        {
+            als[i].l--;
+            if ( !als[i].l ) pad_from_left = 1;
+        }
+        if ( pad_from_left )
+        {
+            int npad = new_pos >= args->aln_win ? args->aln_win : new_pos;
+            free(ref);
+            ref = faidx_fetch_seq(args->fai, (char*)args->hdr->id[BCF_DT_CTG][line->rid].key, new_pos-npad, new_pos-1, &nref);
+            if ( !ref ) error("faidx_fetch_seq failed at %s:%"PRId64"\n", args->hdr->id[BCF_DT_CTG][line->rid].key, (int64_t) new_pos-npad+1);
+            replace_iupac_codes(ref,nref);
+            for (i=0; i<line->n_allele; i++)
+            {
+                ks_resize(&als[i], als[i].l + npad);
+                if ( als[i].l ) memmove(als[i].s+npad,als[i].s,als[i].l);
+                memcpy(als[i].s,ref,npad);
+                als[i].l += npad;
+            }
+            new_pos -= npad;
+        }
+    }
+    free(ref);
+
+    // trim from left
+    int ntrim_left = 0;
+    while (1)
+    {
+        // is the first base identical in all alleles?
+        int min_len = als[0].l - ntrim_left;
+        for (i=1; i<line->n_allele; i++)
+        {
+            if ( als[0].s[ntrim_left]!=als[i].s[ntrim_left] ) break;
+            if ( min_len > als[i].l - ntrim_left ) min_len = als[i].l - ntrim_left;
+        }
+        if ( i!=line->n_allele || min_len<=1 ) break; // there are differences, cannot be trimmed
+        ntrim_left++;
+    }
+    if ( ntrim_left )
+    {
+        for (i=0; i<line->n_allele; i++)
+        {
+            memmove(als[i].s,als[i].s+ntrim_left,als[i].l-ntrim_left);
+            als[i].l -= ntrim_left;
+        }
+        new_pos += ntrim_left;
+    }
+
+    // Have the alleles changed?
+    als[0].s[ als[0].l ] = 0;  // in order for strcmp to work
+    if ( new_pos==line->pos && !strcasecmp(line->d.allele[0],als[0].s) ) return ERR_OK;
+
+    set_old_rec_tag(args, line, line, 0);
+
+    // Create new block of alleles and update
+    args->tmp_kstr.l = 0;
+    for (i=0; i<line->n_allele; i++)
+    {
+        if (i>0) kputc(',',&args->tmp_kstr);
+        kputsn(als[i].s,als[i].l,&args->tmp_kstr);
+    }
+    args->tmp_kstr.s[ args->tmp_kstr.l ] = 0;
+    bcf_update_alleles_str(args->out_hdr,line,args->tmp_kstr.s);
+    args->nchanged++;
+
+    // Update INFO/END if necessary
+    int new_reflen = strlen(line->d.allele[0]);
+    if ( (new_pos!=line->pos || reflen!=new_reflen) && bcf_get_info_int32(args->hdr, line, "END", &args->int32_arr, &args->nint32_arr)==1 )
+    {
+        // bcf_update_alleles_str() messed up rlen because line->pos changed. This will be fixed by bcf_update_info_int32()
+        line->pos = new_pos;
+        args->int32_arr[0] = line->pos + new_reflen;
+        bcf_update_info_int32(args->out_hdr, line, "END", args->int32_arr, 1);
+    }
+    line->pos = new_pos;
+
+    return ERR_OK;
+}
+
+static void split_info_numeric(args_t *args, bcf1_t *src, bcf_info_t *info, int ialt, bcf1_t *dst)
+{
+    #define BRANCH_NUMERIC(type,type_t,is_vector_end,is_missing) \
+    { \
+        const char *tag = bcf_hdr_int2id(args->hdr,BCF_DT_ID,info->key); \
+        int ntmp = args->ntmp_arr1 / sizeof(type_t); \
+        int ret = bcf_get_info_##type(args->hdr,src,tag,&args->tmp_arr1,&ntmp); \
+        args->ntmp_arr1 = ntmp * sizeof(type_t); \
+        assert( ret>0 ); \
+        type_t *vals = (type_t*) args->tmp_arr1; \
+        int len = bcf_hdr_id2length(args->hdr,BCF_HL_INFO,info->key); \
+        if ( len==BCF_VL_A ) \
+        { \
+            if ( ret!=src->n_allele-1 ) \
+            { \
+                if ( args->force && !args->force_warned ) \
+                { \
+                    fprintf(bcftools_stderr, \
+                        "Warning: wrong number of fields in INFO/%s at %s:%"PRId64", expected %d, found %d\n" \
+                        "         (This warning is printed only once.)\n", \
+                        tag,bcf_seqname(args->hdr,src),(int64_t) src->pos+1,src->n_allele-1,ret); \
+                    args->force_warned = 1; \
+                } \
+                if ( args->force ) \
+                { \
+                    bcf_update_info_##type(args->out_hdr,dst,tag,NULL,0); \
+                    return; \
+                } \
+                error("Error: wrong number of fields in INFO/%s at %s:%"PRId64", expected %d, found %d\n", \
+                        tag,bcf_seqname(args->hdr,src),(int64_t) src->pos+1,src->n_allele-1,ret); \
+            } \
+            bcf_update_info_##type(args->out_hdr,dst,tag,vals+ialt,1); \
+        } \
+        else if ( len==BCF_VL_R ) \
+        { \
+            if ( ret!=src->n_allele ) \
+            { \
+                if ( args->force && !args->force_warned ) \
+                { \
+                    fprintf(bcftools_stderr, \
+                        "Warning: wrong number of fields in INFO/%s at %s:%"PRId64", expected %d, found %d\n" \
+                        "         (This warning is printed only once.)\n", \
+                        tag,bcf_seqname(args->hdr,src),(int64_t) src->pos+1,src->n_allele,ret); \
+                    args->force_warned = 1; \
+                } \
+                if ( args->force ) \
+                { \
+                    bcf_update_info_##type(args->out_hdr,dst,tag,NULL,0); \
+                    return; \
+                } \
+                error("Error: wrong number of fields in INFO/%s at %s:%"PRId64", expected %d, found %d\n", \
+                        tag,bcf_seqname(args->hdr,src),(int64_t) src->pos+1,src->n_allele,ret); \
+            } \
+            if ( args->keep_sum_ad >= 0 && args->keep_sum_ad==info->key ) \
+            { \
+                int j; \
+                for (j=1; j<info->len; j++) \
+                    if ( j!=ialt+1 && !(is_missing) && !(is_vector_end) ) vals[0] += vals[j]; \
+                vals[1] = vals[ialt+1]; \
+            } \
+            else \
+            { \
+                if ( ialt!=0 ) vals[1] = vals[ialt+1]; \
+            } \
+            bcf_update_info_##type(args->out_hdr,dst,tag,vals,2); \
+        } \
+        else if ( len==BCF_VL_G ) \
+        { \
+            if ( ret!=src->n_allele*(src->n_allele+1)/2 ) \
+            { \
+                if ( args->force && !args->force_warned ) \
+                { \
+                    fprintf(bcftools_stderr, \
+                        "Warning: wrong number of fields in INFO/%s at %s:%"PRId64", expected %d, found %d\n" \
+                        "         (This warning is printed only once.)\n", \
+                        tag,bcf_seqname(args->hdr,src),(int64_t) src->pos+1,src->n_allele*(src->n_allele+1)/2,ret); \
+                    args->force_warned = 1; \
+                } \
+                if ( args->force ) \
+                { \
+                    bcf_update_info_##type(args->out_hdr,dst,tag,NULL,0); \
+                    return; \
+                } \
+                error("Error: wrong number of fields in INFO/%s at %s:%"PRId64", expected %d, found %d\n", \
+                        tag,bcf_seqname(args->hdr,src),(int64_t) src->pos+1,src->n_allele*(src->n_allele+1)/2,ret); \
+            } \
+            if ( ialt!=0 ) \
+            { \
+                vals[1] = vals[bcf_alleles2gt(0,ialt+1)]; \
+                vals[2] = vals[bcf_alleles2gt(ialt+1,ialt+1)]; \
+            } \
+            bcf_update_info_##type(args->out_hdr,dst,tag,vals,3); \
+        } \
+        else \
+            bcf_update_info_##type(args->out_hdr,dst,tag,vals,ret); \
+    }
+    switch (bcf_hdr_id2type(args->hdr,BCF_HL_INFO,info->key))
+    {
+        case BCF_HT_INT:  BRANCH_NUMERIC(int32, int32_t, vals[j]==bcf_int32_vector_end, vals[j]==bcf_int32_missing); break;
+        case BCF_HT_REAL: BRANCH_NUMERIC(float, float, bcf_float_is_vector_end(vals[j]), bcf_float_is_missing(vals[j])); break;
+    }
+    #undef BRANCH_NUMERIC
+}
+// Find n-th field in a comma-separated list and move it to dst.
+// The memory areas may overlap.
+#define STR_MOVE_NTH(dst,src,end,nth,len) \
+{ \
+    char *ss = src, *se = src; \
+    int j = 0; \
+    while ( *se && se<(end) ) \
+    { \
+        if ( *se==',' ) \
+        { \
+            if ( j==nth ) break; \
+            j++; \
+            ss = se+1; \
+        } \
+        se++; \
+    } \
+    if ( j==nth ) \
+    { \
+        int n = se - ss; \
+        memmove((dst),ss,n); \
+        src = se; \
+        len += n; \
+    } \
+    else len = -1; \
+}
+static void split_info_string(args_t *args, bcf1_t *src, bcf_info_t *info, int ialt, bcf1_t *dst)
+{
+    const char *tag = bcf_hdr_int2id(args->hdr,BCF_DT_ID,info->key);
+    int ret = bcf_get_info_string(args->hdr,src,tag,&args->tmp_arr1,&args->ntmp_arr1);
+    assert( ret>0 );
+
+    kstring_t str;
+    str.m = args->ntmp_arr1;
+    str.l = ret;
+    str.s = (char*) args->tmp_arr1;
+
+    int len = bcf_hdr_id2length(args->hdr,BCF_HL_INFO,info->key);
+    if ( len==BCF_VL_A )
+    {
+        char *tmp = str.s;
+        int len = 0;
+        STR_MOVE_NTH(str.s,tmp,str.s+str.l,ialt,len);
+        if ( len<0 ) return;   // wrong number of fields: skip
+        str.s[len] = 0;
+        bcf_update_info_string(args->out_hdr,dst,tag,str.s);
+    }
+    else if ( len==BCF_VL_R )
+    {
+        char *tmp = str.s;
+        int len = 0;
+        STR_MOVE_NTH(str.s,tmp,str.s+str.l,0,len);
+        str.s[len]=','; tmp++; len++;
+        STR_MOVE_NTH(&str.s[len],tmp,str.s+str.l,ialt,len);
+        if ( len<0 ) return;   // wrong number of fields: skip
+        str.s[len] = 0;
+        bcf_update_info_string(args->out_hdr,dst,tag,str.s);
+    }
+    else if ( len==BCF_VL_G )
+    {
+        int i0a = bcf_alleles2gt(0,ialt+1), iaa = bcf_alleles2gt(ialt+1,ialt+1);
+        char *tmp = str.s;
+        int len = 0;
+        STR_MOVE_NTH(str.s,tmp,str.s+str.l,0,len);
+        str.s[len]=','; tmp++; len++;
+        STR_MOVE_NTH(&str.s[len],tmp,str.s+str.l,i0a-1,len);
+        if ( len<0 ) return;   // wrong number of fields: skip
+        str.s[len]=','; tmp++; len++;
+        STR_MOVE_NTH(&str.s[len],tmp,str.s+str.l,iaa-i0a-1,len);
+        if ( len<0 ) return;   // wrong number of fields: skip
+        str.s[len] = 0;
+        bcf_update_info_string(args->out_hdr,dst,tag,str.s);
+    }
+    else
+        bcf_update_info_string(args->out_hdr,dst,tag,str.s);
+}
+static void split_info_flag(args_t *args, bcf1_t *src, bcf_info_t *info, int ialt, bcf1_t *dst)
+{
+    const char *tag = bcf_hdr_int2id(args->hdr,BCF_DT_ID,info->key);
+    int ret = bcf_get_info_flag(args->hdr,src,tag,&args->tmp_arr1,&args->ntmp_arr1);
+    bcf_update_info_flag(args->out_hdr,dst,tag,NULL,ret);
+}
+
+static void split_format_genotype(args_t *args, bcf1_t *src, bcf_fmt_t *fmt, int ialt, bcf1_t *dst)
+{
+    int ntmp = args->ntmp_arr1 / 4;
+    int ngts = bcf_get_genotypes(args->hdr,src,&args->tmp_arr1,&ntmp);
+    args->ntmp_arr1 = ntmp * 4;
+    assert( ngts >0 );
+
+    int32_t *gt = (int32_t*) args->tmp_arr1;
+    int i, j, nsmpl = bcf_hdr_nsamples(args->hdr);
+    ngts /= nsmpl;
+    for (i=0; i<nsmpl; i++)
+    {
+        for (j=0; j<ngts; j++)
+        {
+            if ( gt[j]==bcf_int32_vector_end ) break;
+            if ( bcf_gt_is_missing(gt[j]) || bcf_gt_allele(gt[j])==0 ) continue; // missing allele or ref: leave as is
+            if ( bcf_gt_allele(gt[j])==ialt+1 )
+                gt[j] = bcf_gt_unphased(1) | bcf_gt_is_phased(gt[j]); // set to first ALT
+            else
+                gt[j] = bcf_gt_unphased(0) | bcf_gt_is_phased(gt[j]); // set to REF
+        }
+        gt += ngts;
+    }
+    bcf_update_genotypes(args->out_hdr,dst,args->tmp_arr1,ngts*nsmpl);
+}
+static void split_format_numeric(args_t *args, bcf1_t *src, bcf_fmt_t *fmt, int ialt, bcf1_t *dst)
+{
+    #define BRANCH_NUMERIC(type,type_t,is_vector_end,is_missing,set_vector_end) \
+    { \
+        const char *tag = bcf_hdr_int2id(args->hdr,BCF_DT_ID,fmt->id); \
+        int ntmp = args->ntmp_arr1 / sizeof(type_t); \
+        int nvals = bcf_get_format_##type(args->hdr,src,tag,&args->tmp_arr1,&ntmp); \
+        args->ntmp_arr1 = ntmp * sizeof(type_t); \
+        assert( nvals>0 ); \
+        type_t *vals = (type_t *) args->tmp_arr1; \
+        int len = bcf_hdr_id2length(args->hdr,BCF_HL_FMT,fmt->id); \
+        int i,j, nsmpl = bcf_hdr_nsamples(args->hdr); \
+        if ( nvals==nsmpl ) /* all values are missing */ \
+        { \
+            bcf_update_format_##type(args->out_hdr,dst,tag,vals,nsmpl); \
+            return; \
+        } \
+        if ( len==BCF_VL_A ) \
+        { \
+            if ( nvals!=(src->n_allele-1)*nsmpl ) \
+            { \
+                if ( args->force && !args->force_warned ) \
+                { \
+                    fprintf(bcftools_stderr, \
+                        "Warning: wrong number of fields in FMT/%s at %s:%"PRId64", expected %d, found %d. Removing the field.\n" \
+                        "         (This warning is printed only once.)\n", \
+                        tag,bcf_seqname(args->hdr,src),(int64_t) src->pos+1,(src->n_allele-1)*nsmpl,nvals); \
+                    args->force_warned = 1; \
+                } \
+                if ( args->force ) \
+                { \
+                    bcf_update_format_##type(args->out_hdr,dst,tag,NULL,0); \
+                    return; \
+                } \
+                error("Error: wrong number of fields in FMT/%s at %s:%"PRId64", expected %d, found %d\n", \
+                    tag,bcf_seqname(args->hdr,src),(int64_t) src->pos+1,(src->n_allele-1)*nsmpl,nvals); \
+            } \
+            nvals /= nsmpl; \
+            type_t *src_vals = vals, *dst_vals = vals; \
+            for (i=0; i<nsmpl; i++) \
+            { \
+                dst_vals[0] = src_vals[ialt]; \
+                dst_vals += 1; \
+                src_vals += nvals; \
+            } \
+            bcf_update_format_##type(args->out_hdr,dst,tag,vals,nsmpl); \
+        } \
+        else if ( len==BCF_VL_R ) \
+        { \
+            if ( nvals!=src->n_allele*nsmpl ) \
+            { \
+                if ( args->force && !args->force_warned ) \
+                { \
+                    fprintf(bcftools_stderr, \
+                        "Warning: wrong number of fields in FMT/%s at %s:%"PRId64", expected %d, found %d. Removing the field.\n" \
+                        "         (This warning is printed only once.)\n", \
+                        tag,bcf_seqname(args->hdr,src),(int64_t) src->pos+1,(src->n_allele-1)*nsmpl,nvals); \
+                    args->force_warned = 1; \
+                } \
+                if ( args->force ) \
+                { \
+                    bcf_update_format_##type(args->out_hdr,dst,tag,NULL,0); \
+                    return; \
+                } \
+                error("Error: wrong number of fields in FMT/%s at %s:%"PRId64", expected %d, found %d\n", \
+                    tag,bcf_seqname(args->hdr,src),(int64_t) src->pos+1,src->n_allele*nsmpl,nvals); \
+            } \
+            nvals /= nsmpl; \
+            type_t *src_vals = vals, *dst_vals = vals; \
+            if ( args->keep_sum_ad >= 0 && args->keep_sum_ad==fmt->id ) \
+            { \
+                for (i=0; i<nsmpl; i++) \
+                { \
+                    dst_vals[0] = src_vals[0]; \
+                    for (j=1; j<nvals; j++) \
+                        if ( j!=ialt+1 && !(is_missing) && !(is_vector_end) ) dst_vals[0] += src_vals[j]; \
+                    dst_vals[1] = src_vals[ialt+1]; \
+                    dst_vals += 2; \
+                    src_vals += nvals; \
+                } \
+            } \
+            else \
+            { \
+                for (i=0; i<nsmpl; i++) \
+                { \
+                    dst_vals[0] = src_vals[0]; \
+                    dst_vals[1] = src_vals[ialt+1]; \
+                    dst_vals += 2; \
+                    src_vals += nvals; \
+                } \
+            } \
+            bcf_update_format_##type(args->out_hdr,dst,tag,vals,nsmpl*2); \
+        } \
+        else if ( len==BCF_VL_G ) \
+        { \
+            if ( nvals!=src->n_allele*(src->n_allele+1)/2*nsmpl && nvals!=src->n_allele*nsmpl ) \
+            { \
+                if ( args->force && !args->force_warned ) \
+                { \
+                    fprintf(bcftools_stderr, \
+                        "Warning: wrong number of fields in FMT/%s at %s:%"PRId64", expected %d, found %d. Removing the field.\n" \
+                        "         (This warning is printed only once.)\n", \
+                        tag,bcf_seqname(args->hdr,src),(int64_t) src->pos+1,(src->n_allele-1)*nsmpl,nvals); \
+                    args->force_warned = 1; \
+                } \
+                if ( args->force ) \
+                { \
+                    bcf_update_format_##type(args->out_hdr,dst,tag,NULL,0); \
+                    return; \
+                } \
+                error("Error at %s:%"PRId64", the tag %s has wrong number of fields\n", bcf_seqname(args->hdr,src),(int64_t) src->pos+1,bcf_hdr_int2id(args->hdr,BCF_DT_ID,fmt->id)); \
+            } \
+            nvals /= nsmpl; \
+            int all_haploid = nvals==src->n_allele ? 1 : 0; \
+            type_t *src_vals = vals, *dst_vals = vals; \
+            for (i=0; i<nsmpl; i++) \
+            { \
+                int haploid = all_haploid; \
+                if ( !haploid ) \
+                { \
+                    int j; \
+                    for (j=0; j<nvals; j++) if ( is_vector_end ) break; \
+                    if ( j!=nvals ) haploid = 1; \
+                } \
+                dst_vals[0] = src_vals[0]; \
+                if ( haploid ) \
+                { \
+                    dst_vals[1] = src_vals[ialt+1]; \
+                    if ( !all_haploid ) set_vector_end; \
+                } \
+                else \
+                { \
+                    dst_vals[1] = src_vals[bcf_alleles2gt(0,ialt+1)]; \
+                    dst_vals[2] = src_vals[bcf_alleles2gt(ialt+1,ialt+1)]; \
+                } \
+                dst_vals += all_haploid ? 2 : 3; \
+                src_vals += nvals; \
+            } \
+            bcf_update_format_##type(args->out_hdr,dst,tag,vals,all_haploid ? nsmpl*2 : nsmpl*3); \
+        } \
+        else \
+            bcf_update_format_##type(args->out_hdr,dst,tag,vals,nvals); \
+    }
+    switch (bcf_hdr_id2type(args->hdr,BCF_HL_FMT,fmt->id))
+    {
+        case BCF_HT_INT:  BRANCH_NUMERIC(int32, int32_t, src_vals[j]==bcf_int32_vector_end, src_vals[j]==bcf_int32_missing, dst_vals[2]=bcf_int32_vector_end); break;
+        case BCF_HT_REAL: BRANCH_NUMERIC(float, float, bcf_float_is_vector_end(src_vals[j]), bcf_float_is_missing(src_vals[j]), bcf_float_set_vector_end(dst_vals[2])); break;
+    }
+    #undef BRANCH_NUMERIC
+}
+static void squeeze_format_char(char *str, int src_blen, int dst_blen, int n)
+{
+    int i, isrc = 0, idst = 0;
+    for (i=0; i<n; i++)
+    {
+        memmove(str+idst,str+isrc,dst_blen);
+        idst += dst_blen;
+        isrc += src_blen;
+    }
+}
+static void split_format_string(args_t *args, bcf1_t *src, bcf_fmt_t *fmt, int ialt, bcf1_t *dst)
+{
+    const char *tag = bcf_hdr_int2id(args->hdr,BCF_DT_ID,fmt->id);
+    int ret = bcf_get_format_char(args->hdr,src,tag,&args->tmp_arr1,&args->ntmp_arr1);
+    if ( !ret ) return; // all values can be empty, leave out the tag, no need to panic
+    assert( ret>0 );
+
+    kstring_t str;
+    str.m = args->ntmp_arr1;
+    str.l = ret;
+    str.s = (char*) args->tmp_arr1;
+
+    int nsmpl = bcf_hdr_nsamples(args->hdr);
+    int len = bcf_hdr_id2length(args->hdr,BCF_HL_FMT,fmt->id);
+    if ( len==BCF_VL_A )
+    {
+        int i, blen = ret/nsmpl, maxlen = 0;
+        char *ptr = str.s;
+        for (i=0; i<nsmpl; i++)
+        {
+            char *tmp = ptr;
+            int len = 0;
+            STR_MOVE_NTH(tmp,tmp,ptr+blen,ialt,len);
+            if ( len<0 ) return;   // wrong number of fields: skip
+            if ( maxlen < len ) maxlen = len;
+            ptr += blen;
+        }
+        if ( maxlen<blen ) squeeze_format_char(str.s,blen,maxlen,nsmpl);
+        bcf_update_format_char(args->out_hdr,dst,tag,str.s,nsmpl*maxlen);
+    }
+    else if ( len==BCF_VL_R )
+    {
+        int i, blen = ret/nsmpl, maxlen = 0;
+        char *ptr = str.s;
+        for (i=0; i<nsmpl; i++)
+        {
+            char *tmp = ptr;
+            int len = 0;
+            STR_MOVE_NTH(ptr,tmp,ptr+blen,0,len);
+            ptr[len]=','; tmp++; len++;
+            STR_MOVE_NTH(&ptr[len],tmp,ptr+blen,ialt,len);
+            if ( len<0 ) return;   // wrong number of fields: skip
+            if ( maxlen < len ) maxlen = len;
+            ptr += blen;
+        }
+        if ( maxlen<blen ) squeeze_format_char(str.s,blen,maxlen,nsmpl);
+        bcf_update_format_char(args->out_hdr,dst,tag,str.s,nsmpl*maxlen);
+    }
+    else if ( len==BCF_VL_G )
+    {
+        int i, blen = ret/nsmpl, maxlen = 0, i0a = bcf_alleles2gt(0,ialt+1), iaa = bcf_alleles2gt(ialt+1,ialt+1);
+        char *ptr = str.s;
+        for (i=0; i<nsmpl; i++)
+        {
+            char *se = ptr, *sx = ptr+blen;
+            int nfields = 1;
+            while ( *se && se<sx )
+            {
+                if ( *se==',' ) nfields++;
+                se++;
+            }
+            if ( nfields==1 && se-ptr==1 && *ptr=='.' ) continue;   // missing value
+            if ( nfields!=src->n_allele*(src->n_allele+1)/2 && nfields!=src->n_allele )
+            {
+                if ( args->force && !args->force_warned )
+                {
+                    fprintf(bcftools_stderr,
+                            "Warning: wrong number of fields in FMT/%s at %s:%"PRId64", expected %d or %d, found %d. Removing the field.\n"
+                            "         (This warning is printed only once.)\n",
+                            tag,bcf_seqname(args->hdr,src),(int64_t)src->pos+1,src->n_allele*(src->n_allele+1)/2,src->n_allele,nfields);
+                    args->force_warned = 1;
+                }
+                if ( args->force )
+                {
+                    bcf_update_format_char(args->out_hdr,dst,tag,NULL,0);
+                    return;
+                }
+                error("Error: wrong number of fields in FMT/%s at %s:%"PRId64", expected %d or %d, found %d\n",
+                        tag,bcf_seqname(args->hdr,src),(int64_t) src->pos+1,src->n_allele*(src->n_allele+1)/2,src->n_allele,nfields);
+            }
+
+            int len = 0;
+            if ( nfields==src->n_allele )   // haploid
+            {
+                char *tmp = ptr;
+                STR_MOVE_NTH(&ptr[len],tmp,ptr+blen,0,len);
+                ptr[len]=','; tmp++; len++;
+                STR_MOVE_NTH(&ptr[len],tmp,ptr+blen,ialt,len);
+                if ( len<0 ) return;   // wrong number of fields: skip
+            }
+            else    // diploid
+            {
+                char *tmp = ptr;
+                STR_MOVE_NTH(&ptr[len],tmp,ptr+blen,0,len);
+                ptr[len]=','; tmp++; len++;
+                STR_MOVE_NTH(&ptr[len],tmp,ptr+blen,i0a-1,len);
+                if ( len<0 ) return;   // wrong number of fields: skip
+                ptr[len]=','; tmp++; len++;
+                STR_MOVE_NTH(&ptr[len],tmp,ptr+blen,iaa-i0a-1,len);
+                if ( len<0 ) return;   // wrong number of fields: skip
+            }
+            if ( maxlen < len ) maxlen = len;
+            ptr += blen;
+        }
+        if ( maxlen<blen ) squeeze_format_char(str.s,blen,maxlen,nsmpl);
+        bcf_update_format_char(args->out_hdr,dst,tag,str.s,nsmpl*maxlen);
+    }
+    else
+        bcf_update_format_char(args->out_hdr,dst,tag,str.s,str.l);
+}
+
+static void split_multiallelic_to_biallelics(args_t *args, bcf1_t *line)
+{
+    int i;
+
+    bcf_unpack(line, BCF_UN_ALL);
+
+    // Init the target biallelic lines
+    args->ntmp_lines = line->n_allele-1;
+    if ( args->mtmp_lines < args->ntmp_lines )
+    {
+        args->tmp_lines = (bcf1_t **)realloc(args->tmp_lines,sizeof(bcf1_t*)*args->ntmp_lines);
+        for (i=args->mtmp_lines; i<args->ntmp_lines; i++)
+            args->tmp_lines[i] = NULL;
+        args->mtmp_lines = args->ntmp_lines;
+    }
+    kstring_t tmp = {0,0,0};
+    kputs(line->d.allele[0], &tmp);
+    kputc(',', &tmp);
+    int rlen  = tmp.l;
+    int gt_id = bcf_hdr_id2int(args->hdr,BCF_DT_ID,"GT");
+    for (i=0; i<args->ntmp_lines; i++)  // for each ALT allele
+    {
+        if ( !args->tmp_lines[i] ) args->tmp_lines[i] = bcf_init1();
+        bcf1_t *dst = args->tmp_lines[i];
+        bcf_clear(dst);
+
+        dst->rid  = line->rid;
+        dst->pos  = line->pos;
+        dst->qual = line->qual;
+
+        // Not quite sure how to handle IDs, they can be assigned to a specific
+        // ALT.  For now we leave the ID unchanged for all.
+        bcf_update_id(args->out_hdr, dst, line->d.id ? line->d.id : ".");
+
+        tmp.l = rlen;
+        kputs(line->d.allele[i+1],&tmp);
+        bcf_update_alleles_str(args->out_hdr,dst,tmp.s);
+
+        if ( line->d.n_flt ) bcf_update_filter(args->hdr, dst, line->d.flt, line->d.n_flt);
+
+        int j;
+        for (j=0; j<line->n_info; j++)
+        {
+            bcf_info_t *info = &line->d.info[j];
+            int type = bcf_hdr_id2type(args->hdr,BCF_HL_INFO,info->key);
+            if ( type==BCF_HT_INT || type==BCF_HT_REAL ) split_info_numeric(args, line, info, i, dst);
+            else if ( type==BCF_HT_FLAG ) split_info_flag(args, line, info, i, dst);
+            else split_info_string(args, line, info, i, dst);
+        }
+        set_old_rec_tag(args, dst, line, i + 1); // 1-based indexes
+
+        dst->n_sample = line->n_sample;
+        for (j=0; j<line->n_fmt; j++)
+        {
+            bcf_fmt_t *fmt = &line->d.fmt[j];
+            int type = bcf_hdr_id2type(args->hdr,BCF_HL_FMT,fmt->id);
+            if ( fmt->id==gt_id ) split_format_genotype(args, line, fmt, i, dst);
+            else if ( type==BCF_HT_INT || type==BCF_HT_REAL ) split_format_numeric(args, line, fmt, i, dst);
+            else split_format_string(args, line, fmt, i, dst);
+        }
+    }
+    free(tmp.s);
+}
+
+// Enlarge FORMAT array containing nsmpl samples each with nals_ori values
+// to accommodate nvals values for each sample, filling the gaps with missing
+// values. Works also for INFO arrays, with nsmpl set to 1.
+#define ENLARGE_ARRAY(type_t,set_missing,arr,narr_bytes,nsmpl,nvals_ori,nvals) \
+{ \
+    int nbytes_new = (nsmpl)*(nvals)*sizeof(type_t); \
+    hts_expand(uint8_t,nbytes_new,narr_bytes,arr); \
+    int ismpl, k; \
+    for (ismpl=nsmpl-1; ismpl>=0; ismpl--) \
+    { \
+        type_t *dst_ptr = ((type_t*)arr) + ismpl*(nvals); \
+        type_t *src_ptr = ((type_t*)arr) + ismpl*nvals_ori; \
+        memmove(dst_ptr,src_ptr,sizeof(type_t)*nvals_ori); \
+        for (k=nvals_ori; k<nvals; k++) set_missing; \
+    } \
+}
+static void merge_info_numeric(args_t *args, bcf1_t **lines, int nlines, bcf_info_t *info, bcf1_t *dst)
+{
+    #define BRANCH_NUMERIC(type,type_t,set_missing,is_vector_end) \
+    { \
+        const char *tag = bcf_hdr_int2id(args->hdr,BCF_DT_ID,info->key); \
+        int ntmp = args->ntmp_arr1 / sizeof(type_t); \
+        int nvals_ori = bcf_get_info_##type(args->hdr,lines[0],tag,&args->tmp_arr1,&ntmp); \
+        args->ntmp_arr1 = ntmp * sizeof(type_t); \
+        assert( nvals_ori>0 ); \
+        type_t *vals = (type_t*) args->tmp_arr1, *vals2; \
+        int i,k,len = bcf_hdr_id2length(args->hdr,BCF_HL_INFO,info->key);  \
+        if ( len==BCF_VL_A ) \
+        { \
+            if (nvals_ori!=lines[0]->n_allele - 1) \
+                error("vcfnorm: number of fields in first record at position %s:%"PRId64" for INFO tag %s not as expected [found: %d vs expected:%d]\n", bcf_seqname(args->hdr,lines[0]),(int64_t) lines[0]->pos+1, tag, nvals_ori, lines[0]->n_allele-1); \
+            int nvals = dst->n_allele - 1; \
+            ENLARGE_ARRAY(type_t,set_missing,args->tmp_arr1,args->ntmp_arr1,1,nvals_ori,nvals); \
+            vals = (type_t*) args->tmp_arr1; \
+            for (i=1; i<nlines; i++) \
+            { \
+                int ntmp2 = args->ntmp_arr2 / sizeof(type_t); \
+                int nvals2 = bcf_get_info_##type(args->hdr,lines[i],tag,&args->tmp_arr2,&ntmp2); \
+                if (nvals2<0) continue; /* info tag does not exist in this record, skip */ \
+                args->ntmp_arr2 = ntmp2 * sizeof(type_t); \
+                if (nvals2!=lines[i]->n_allele-1) \
+                    error("vcfnorm: could not merge INFO tag %s at position %s:%"PRId64"\n", tag, bcf_seqname(args->hdr,lines[i]),(int64_t) lines[i]->pos+1); \
+                vals2 = (type_t*) args->tmp_arr2; \
+                for (k=0; k<nvals2; k++) \
+                { \
+                    if ( is_vector_end ) break; \
+                    vals[ args->maps[i].map[k+1] - 1 ] = vals2[k]; \
+                } \
+            } \
+            bcf_update_info_##type(args->out_hdr,dst,tag,args->tmp_arr1,nvals); \
+        } \
+        else if ( len==BCF_VL_R ) \
+        { \
+            if (nvals_ori!=lines[0]->n_allele) \
+                error("vcfnorm: number of fields in first record at position %s:%"PRId64" for INFO tag %s not as expected [found: %d vs expected:%d]\n", bcf_seqname(args->hdr,lines[0]),(int64_t) lines[0]->pos+1, tag, nvals_ori, lines[0]->n_allele); \
+            int nvals = dst->n_allele; \
+            ENLARGE_ARRAY(type_t,set_missing,args->tmp_arr1,args->ntmp_arr1,1,nvals_ori,nvals); \
+            vals = (type_t*) args->tmp_arr1; \
+            for (i=1; i<nlines; i++) \
+            { \
+                int ntmp2 = args->ntmp_arr2 / sizeof(type_t); \
+                int nvals2 = bcf_get_info_##type(args->hdr,lines[i],tag,&args->tmp_arr2,&ntmp2); \
+                if (nvals2<0) continue; /* info tag does not exist in this record, skip */ \
+                args->ntmp_arr2 = ntmp2 * sizeof(type_t); \
+                if (nvals2!=lines[i]->n_allele) \
+                    error("vcfnorm: could not merge INFO tag %s at position %s:%"PRId64"\n", tag, bcf_seqname(args->hdr,lines[i]),(int64_t) lines[i]->pos+1); \
+                vals2 = (type_t*) args->tmp_arr2; \
+                for (k=0; k<nvals2; k++) \
+                { \
+                    if ( is_vector_end ) break; \
+                    vals[ args->maps[i].map[k] ] = vals2[k]; \
+                } \
+            } \
+            bcf_update_info_##type(args->out_hdr,dst,tag,args->tmp_arr1,nvals); \
+        } \
+        else if ( len==BCF_VL_G ) \
+        { \
+            /* expecting diploid gt in INFO */ \
+            if (nvals_ori!=lines[0]->n_allele*(lines[0]->n_allele+1)/2) { \
+                fprintf(bcftools_stderr, "todo: merge Number=G INFO fields for haploid sites\n"); \
+                error("vcfnorm: number of fields in first record at position %s:%"PRId64" for INFO tag %s not as expected [found: %d vs expected:%d]\n", bcf_seqname(args->hdr,lines[0]),(int64_t) lines[0]->pos+1, tag, nvals_ori, lines[0]->n_allele*(lines[0]->n_allele+1)/2); \
+            } \
+            int nvals = dst->n_allele*(dst->n_allele+1)/2; \
+            ENLARGE_ARRAY(type_t,set_missing,args->tmp_arr1,args->ntmp_arr1,1,nvals_ori,nvals); \
+            vals = (type_t*) args->tmp_arr1; \
+            for (i=1; i<nlines; i++) \
+            { \
+                int ntmp2 = args->ntmp_arr2 / sizeof(type_t); \
+                int nvals2 = bcf_get_info_##type(args->hdr,lines[i],tag,&args->tmp_arr2,&ntmp2); \
+                if (nvals2<0) continue; /* info tag does not exist in this record, skip */ \
+                args->ntmp_arr2 = ntmp2 * sizeof(type_t); \
+                if (nvals2!=lines[i]->n_allele*(lines[i]->n_allele+1)/2) \
+                    error("vcfnorm: could not merge INFO tag %s at position %s:%"PRId64"\n", tag, bcf_seqname(args->hdr,lines[i]),(int64_t) lines[i]->pos+1); \
+                vals2 = (type_t*) args->tmp_arr2; \
+                int ia,ib; \
+                k = 0; \
+                for (ia=0; ia<lines[i]->n_allele; ia++) \
+                { \
+                    for (ib=0; ib<=ia; ib++) \
+                    { \
+                        if ( is_vector_end ) break; \
+                        int l = bcf_alleles2gt(args->maps[i].map[ia],args->maps[i].map[ib]); \
+                        vals[l] = vals2[k];  \
+                        k++; \
+                    } \
+                } \
+            } \
+            bcf_update_info_##type(args->out_hdr,dst,tag,args->tmp_arr1,nvals); \
+        } \
+        else \
+            bcf_update_info_##type(args->out_hdr,dst,tag,vals,nvals_ori); \
+    }
+    switch (bcf_hdr_id2type(args->hdr,BCF_HL_INFO,info->key))
+    {
+        case BCF_HT_INT:  BRANCH_NUMERIC(int32, int32_t, dst_ptr[k]=bcf_int32_missing, vals2[k]==bcf_int32_vector_end); break;
+        case BCF_HT_REAL: BRANCH_NUMERIC(float, float, bcf_float_set_missing(dst_ptr[k]), bcf_float_is_vector_end(vals2[k])); break;
+    }
+    #undef BRANCH_NUMERIC
+}
+static void merge_info_flag(args_t *args, bcf1_t **lines, int nlines, bcf_info_t *info, bcf1_t *dst)
+{
+    const char *tag = bcf_hdr_int2id(args->hdr,BCF_DT_ID,info->key);
+    int ret = bcf_get_info_flag(args->hdr,lines[0],tag,&args->tmp_arr1,&args->ntmp_arr1);
+    bcf_update_info_flag(args->out_hdr,dst,tag,NULL,ret);
+}
+int copy_string_field(char *src, int isrc, int src_len, kstring_t *dst, int idst); // see vcfmerge.c
+static void merge_info_string(args_t *args, bcf1_t **lines, int nlines, bcf_info_t *info, bcf1_t *dst)
+{
+    const char *tag = bcf_hdr_int2id(args->hdr,BCF_DT_ID,info->key);
+
+    kstring_t str;
+    str.m = args->ntmp_arr1;
+    str.l = 0;
+    str.s = (char*) args->tmp_arr1;
+
+    int i, j, len = bcf_hdr_id2length(args->hdr,BCF_HL_INFO,info->key);
+    if ( len==BCF_VL_A || len==BCF_VL_R )
+    {
+        int jfrom = len==BCF_VL_A ? 1 : 0;
+        kputc('.',&str);
+        for (i=jfrom+1; i<dst->n_allele; i++) kputs(",.",&str);
+        for (i=0; i<nlines; i++)
+        {
+            bcf_info_t *src = bcf_get_info(args->hdr,lines[i],tag);
+            if (!src) continue;
+            for (j=jfrom; j<lines[i]->n_allele; j++)
+                copy_string_field((char*)src->vptr, j-jfrom, src->len, &str, args->maps[i].map[j]-jfrom);
+        }
+        str.s[str.l] = 0;
+        args->tmp_arr1  = (uint8_t*) str.s;
+        args->ntmp_arr1 = str.m;
+        bcf_update_info_string(args->out_hdr,dst,tag,str.s);
+    }
+    else if ( len==BCF_VL_G )
+    {
+        int ngts = dst->n_allele*(dst->n_allele+1)/2;
+        kputc('.',&str);
+        for (i=1; i<ngts; i++) kputs(",.",&str);
+        for (i=0; i<nlines; i++)
+        {
+            bcf_info_t *src = bcf_get_info(args->hdr,lines[i],tag);
+            if (!src) continue;
+            int iori, jori, kori = 0;
+            for (iori=0; iori<lines[i]->n_allele; iori++)
+            {
+                int inew = args->maps[i].map[iori];
+                for (jori=0; jori<=iori; jori++)
+                {
+                    int jnew = args->maps[i].map[jori];
+                    int knew = bcf_alleles2gt(inew,jnew);
+                    copy_string_field((char*)src->vptr,kori,src->len,&str,knew);
+                    kori++;
+                }
+            }
+        }
+        str.s[str.l] = 0;
+        args->tmp_arr1  = (uint8_t*) str.s;
+        args->ntmp_arr1 = str.m;
+        bcf_update_info_string(args->out_hdr,dst,tag,str.s);
+    }
+    else
+    {
+        bcf_get_info_string(args->hdr,lines[0],tag,&args->tmp_arr1,&args->ntmp_arr1);
+        bcf_update_info_string(args->out_hdr,dst,tag,args->tmp_arr1);
+    }
+}
+static void merge_format_genotype(args_t *args, bcf1_t **lines, int nlines, bcf_fmt_t *fmt, bcf1_t *dst)
+{
+    // reusing int8_t arrays as int32_t arrays
+    int ntmp = args->ntmp_arr1 / 4;
+    int ngts = bcf_get_genotypes(args->hdr,lines[0],&args->tmp_arr1,&ntmp);
+    args->ntmp_arr1 = ntmp * 4;
+    assert( ngts >0 );
+
+    int nsmpl = bcf_hdr_nsamples(args->hdr);
+    ngts /= nsmpl;
+
+    int i, j, k,k2;
+    for (i=1; i<nlines; i++)
+    {
+        int ntmp2 = args->ntmp_arr2 / 4;
+        int ngts2 = bcf_get_genotypes(args->hdr,lines[i],&args->tmp_arr2,&ntmp2);
+        args->ntmp_arr2 = ntmp2 * 4;
+        ngts2 /= nsmpl;
+        if ( ngts!=ngts2 ) error("Error at %s:%"PRId64": cannot combine diploid with haploid genotype\n", bcf_seqname(args->hdr,lines[i]),(int64_t) lines[i]->pos+1);
+
+        int32_t *gt  = (int32_t*) args->tmp_arr1;
+        int32_t *gt2 = (int32_t*) args->tmp_arr2;
+        for (j=0; j<nsmpl; j++)
+        {
+            for (k2=0; k2<ngts2; k2++)
+            {
+                if ( gt2[k2]==bcf_int32_vector_end ) break;
+                if ( bcf_gt_is_missing(gt2[k2]) ) continue;
+                int ial2 = bcf_gt_allele(gt2[k2]);
+                if ( ial2==0 ) continue;    // never overwrite with ref
+                if ( ial2>=args->maps[i].nals ) error("Error at %s:%"PRId64": incorrect allele index %d\n",bcf_seqname(args->hdr,lines[i]),(int64_t) lines[i]->pos+1,ial2);
+                int ial = args->maps[i].map[ial2];
+                for (k=0; k<ngts; k++)
+                    if ( gt[k]==bcf_int32_vector_end || bcf_gt_is_missing(gt[k]) || !bcf_gt_allele(gt[k]) ) break;
+                if ( k<ngts )
+                {
+                    gt[k] = bcf_gt_unphased(ial);
+                }
+            }
+            gt  += ngts;
+            gt2 += ngts;
+        }
+    }
+    bcf_update_genotypes(args->out_hdr,dst,args->tmp_arr1,ngts*nsmpl);
+}
+static int diploid_to_haploid(int size, int nsmpl, int nals, uint8_t *vals)
+{
+    int i, dsrc = size*nals*(nals+1)/2, ddst = size*nals;
+    uint8_t *src_ptr = vals + dsrc, *dst_ptr = vals + ddst;
+    for (i=1; i<nsmpl; i++)
+    {
+        memmove(dst_ptr,src_ptr,ddst);
+        dst_ptr += ddst;
+        src_ptr += dsrc;
+    }
+    return nals;
+}
+static void merge_format_numeric(args_t *args, bcf1_t **lines, int nlines, bcf_fmt_t *fmt, bcf1_t *dst)
+{
+    #define BRANCH_NUMERIC(type,type_t,set_missing,is_vector_end,set_vector_end) \
+    { \
+        const char *tag = bcf_hdr_int2id(args->hdr,BCF_DT_ID,fmt->id); \
+        int ntmp = args->ntmp_arr1 / sizeof(type_t); \
+        int nvals_ori = bcf_get_format_##type(args->hdr,lines[0],tag,&args->tmp_arr1,&ntmp); \
+        args->ntmp_arr1 = ntmp * sizeof(type_t); \
+        assert( nvals_ori>0 ); \
+        type_t *vals2, *vals = (type_t *) args->tmp_arr1; \
+        int len = bcf_hdr_id2length(args->hdr,BCF_HL_FMT,fmt->id); \
+        int i, j, k, nsmpl = bcf_hdr_nsamples(args->hdr); \
+        nvals_ori /= nsmpl; \
+        if ( len==BCF_VL_A ) \
+        { \
+            int nvals = dst->n_allele - 1; \
+            ENLARGE_ARRAY(type_t,set_missing,args->tmp_arr1,args->ntmp_arr1,nsmpl,nvals_ori,nvals); \
+            for (i=1; i<nlines; i++) \
+            { \
+                int ntmp2 = args->ntmp_arr2 / sizeof(type_t); \
+                int nvals2 = bcf_get_format_##type(args->hdr,lines[i],tag,&args->tmp_arr2,&ntmp2); \
+                if (nvals2<0) continue; /* format tag does not exist in this record, skip */ \
+                args->ntmp_arr2 = ntmp2 * sizeof(type_t); \
+                nvals2 /= nsmpl; \
+                if (nvals2!=lines[i]->n_allele-1) \
+                    error("vcfnorm: could not merge FORMAT tag %s at position %s:%"PRId64"\n", tag, bcf_seqname(args->hdr,lines[i]),(int64_t) lines[i]->pos+1); \
+                vals  = (type_t*) args->tmp_arr1; \
+                vals2 = (type_t*) args->tmp_arr2; \
+                for (j=0; j<nsmpl; j++) \
+                { \
+                    for (k=0; k<nvals2; k++) \
+                    { \
+                        if ( is_vector_end ) break; \
+                        vals[ args->maps[i].map[k+1] - 1 ] = vals2[k]; \
+                    } \
+                    vals  += nvals; \
+                    vals2 += nvals2; \
+                } \
+            } \
+            bcf_update_format_##type(args->out_hdr,dst,tag,args->tmp_arr1,nvals*nsmpl); \
+        } \
+        else if ( len==BCF_VL_R ) \
+        { \
+            int nvals = dst->n_allele; \
+            ENLARGE_ARRAY(type_t,set_missing,args->tmp_arr1,args->ntmp_arr1,nsmpl,nvals_ori,nvals); \
+            for (i=1; i<nlines; i++) \
+            { \
+                int ntmp2 = args->ntmp_arr2 / sizeof(type_t); \
+                int nvals2 = bcf_get_format_##type(args->hdr,lines[i],tag,&args->tmp_arr2,&ntmp2); \
+                if (nvals2<0) continue; /* format tag does not exist in this record, skip */ \
+                args->ntmp_arr2 = ntmp2 * sizeof(type_t); \
+                nvals2 /= nsmpl; \
+                if (nvals2!=lines[i]->n_allele) \
+                    error("vcfnorm: could not merge FORMAT tag %s at position %s:%"PRId64"\n", tag, bcf_seqname(args->hdr,lines[i]),(int64_t) lines[i]->pos+1); \
+                vals  = (type_t*) args->tmp_arr1; \
+                vals2 = (type_t*) args->tmp_arr2; \
+                for (j=0; j<nsmpl; j++) \
+                { \
+                    for (k=0; k<nvals2; k++) \
+                    { \
+                        if ( is_vector_end ) break; \
+                        vals[ args->maps[i].map[k] ] = vals2[k]; \
+                    } \
+                    vals  += nvals; \
+                    vals2 += nvals2; \
+                } \
+            } \
+            bcf_update_format_##type(args->out_hdr,dst,tag,args->tmp_arr1,nvals*nsmpl); \
+        } \
+        else if ( len==BCF_VL_G ) \
+        { \
+            /* which samples are diploid */ \
+            memset(args->diploid,0,nsmpl); \
+            int all_haploid = 1; \
+            if ( nvals_ori > lines[0]->n_allele ) /* line possibly diploid */ \
+            { \
+                vals2 = (type_t*) args->tmp_arr1; \
+                int ndiploid = lines[0]->n_allele*(lines[0]->n_allele+1)/2; \
+                for (i=0; i<nsmpl; i++) \
+                { \
+                    if ( !args->diploid[i] ) \
+                    { \
+                        for (k=0; k<nvals_ori; k++) if ( is_vector_end ) break; \
+                        if ( k==ndiploid ) { args->diploid[i] = 1; all_haploid = 0; }\
+                    } \
+                    vals2 += nvals_ori; \
+                } \
+            } \
+            int nvals = dst->n_allele*(dst->n_allele+1)/2; \
+            ENLARGE_ARRAY(type_t,set_missing,args->tmp_arr1,args->ntmp_arr1,nsmpl,nvals_ori,nvals); \
+            for (i=1; i<nlines; i++) \
+            { \
+                int ntmp2 = args->ntmp_arr2 / sizeof(type_t); \
+                int nvals2 = bcf_get_format_##type(args->hdr,lines[i],tag,&args->tmp_arr2,&ntmp2); \
+                if (nvals2<0) continue; /* format tag does not exist in this record, skip */ \
+                args->ntmp_arr2 = ntmp2 * sizeof(type_t); \
+                nvals2 /= nsmpl; \
+                int ndiploid = lines[i]->n_allele*(lines[i]->n_allele+1)/2; \
+                int line_diploid = nvals2==ndiploid ? 1 : 0; \
+                if (!(nvals2==1 || nvals2==lines[i]->n_allele || nvals2==lines[i]->n_allele*(lines[i]->n_allele+1)/2)) \
+                    error("vcfnorm: could not merge FORMAT tag %s at position %s:%"PRId64"\n", tag, bcf_seqname(args->hdr,lines[i]),(int64_t) lines[i]->pos+1); \
+                vals  = (type_t*) args->tmp_arr1; \
+                vals2 = (type_t*) args->tmp_arr2; \
+                for (j=0; j<nsmpl; j++) \
+                { \
+                    int smpl_diploid = line_diploid; \
+                    if ( smpl_diploid ) \
+                    { \
+                        for (k=0; k<nvals2; k++) if ( is_vector_end ) break; \
+                        if ( k!=ndiploid ) smpl_diploid = 0; \
+                    } \
+                    if ( smpl_diploid && !args->diploid[j] ) { args->diploid[j] = 1; all_haploid = 0; } \
+                    if ( !smpl_diploid ) \
+                    { \
+                        for (k=0; k<lines[i]->n_allele; k++) vals[args->maps[i].map[k]] = vals2[k]; \
+                    } \
+                    else \
+                    { \
+                        k = 0; \
+                        int ia,ib; \
+                        for (ia=0; ia<lines[i]->n_allele; ia++) \
+                        { \
+                            for (ib=0; ib<=ia; ib++) \
+                            { \
+                                int l = bcf_alleles2gt(args->maps[i].map[ia],args->maps[i].map[ib]); \
+                                vals[l] = vals2[k]; \
+                                k++; \
+                            } \
+                        } \
+                    } \
+                    vals  += nvals; \
+                    vals2 += nvals2; \
+                } \
+            } \
+            if ( all_haploid ) \
+                nvals = diploid_to_haploid(sizeof(type_t),nsmpl,dst->n_allele,args->tmp_arr1); \
+            else \
+            {\
+                k = dst->n_allele;\
+                vals2 = (type_t*) args->tmp_arr1;\
+                for (i=0; i<nsmpl; i++)\
+                {\
+                    if ( !args->diploid[i] ) set_vector_end;\
+                    vals2 += nvals;\
+                }\
+            }\
+            bcf_update_format_##type(args->out_hdr,dst,tag,args->tmp_arr1,nvals*nsmpl); \
+        } \
+        else \
+            bcf_update_format_##type(args->out_hdr,dst,tag,args->tmp_arr1,nvals_ori*nsmpl); \
+    }
+    switch (bcf_hdr_id2type(args->hdr,BCF_HL_FMT,fmt->id))
+    {
+        case BCF_HT_INT:  BRANCH_NUMERIC(int32, int32_t, dst_ptr[k]=bcf_int32_missing, vals2[k]==bcf_int32_vector_end, vals2[k]=bcf_int32_vector_end); break;
+        case BCF_HT_REAL: BRANCH_NUMERIC(float, float, bcf_float_set_missing(dst_ptr[k]), bcf_float_is_vector_end(vals2[k]), bcf_float_set_vector_end(vals2[k])); break;
+    }
+    #undef BRANCH_NUMERIC
+}
+static void merge_format_string(args_t *args, bcf1_t **lines, int nlines, bcf_fmt_t *fmt, bcf1_t *dst)
+{
+    const char *tag = bcf_hdr_int2id(args->hdr,BCF_DT_ID,fmt->id);
+
+    int i, j, k, len = bcf_hdr_id2length(args->hdr,BCF_HL_FMT,fmt->id);
+    if ( len!=BCF_VL_A && len!=BCF_VL_R && len!=BCF_VL_G )
+    {
+        int nret = bcf_get_format_char(args->hdr,lines[0],tag,&args->tmp_arr1,&args->ntmp_arr1);
+        bcf_update_format_char(args->out_hdr,dst,tag,args->tmp_arr1,nret);
+        return;
+    }
+
+    int nsmpl = bcf_hdr_nsamples(args->hdr);
+    for (i=0; i<nsmpl; i++) args->tmp_str[i].l = 0;
+
+    if ( len==BCF_VL_A || len==BCF_VL_R )
+    {
+        int jfrom = len==BCF_VL_A ? 1 : 0;
+        for (i=0; i<nsmpl; i++)
+        {
+            kstring_t *tmp = &args->tmp_str[i];
+            kputc('.',tmp);
+            for (k=jfrom+1; k<dst->n_allele; k++) kputs(",.",tmp);
+        }
+        for (i=0; i<nlines; i++)
+        {
+            int nret = bcf_get_format_char(args->hdr,lines[i],tag,&args->tmp_arr1,&args->ntmp_arr1);
+            if (nret<0) continue; /* format tag does not exist in this record, skip */
+            nret /= nsmpl;
+            for (k=0; k<nsmpl; k++)
+            {
+                kstring_t *tmp = &args->tmp_str[k];
+                char *src = (char*)args->tmp_arr1 + k*nret;
+                for (j=jfrom; j<lines[i]->n_allele; j++)
+                    copy_string_field(src, j-jfrom, nret, tmp, args->maps[i].map[j]-jfrom);
+            }
+        }
+    }
+    else if ( len==BCF_VL_G )
+    {
+        hts_expand(uint8_t,nsmpl,args->ntmp_arr2,args->tmp_arr2);
+        uint8_t *haploid = args->tmp_arr2;
+        int nret = bcf_get_format_char(args->hdr,lines[0],tag,&args->tmp_arr1,&args->ntmp_arr1);
+        nret /= nsmpl;
+        for (i=0; i<nsmpl; i++)
+        {
+            char *ss = (char*)args->tmp_arr1 + i*nret, *se = ss+nret;
+            int nfields = 1;
+            while ( *ss && ss<se )
+            {
+                if ( *ss==',' ) nfields++;
+                ss++;
+            }
+            if ( nfields==lines[0]->n_allele )
+            {
+                haploid[i] = 1;
+                nfields = dst->n_allele;
+            }
+            else if ( nfields==lines[0]->n_allele*(lines[0]->n_allele+1)/2 )
+            {
+                haploid[i] = 0;
+                nfields = dst->n_allele*(dst->n_allele+1)/2;
+            }
+            else error("The field %s at %s:%"PRId64" neither diploid nor haploid?\n", tag,bcf_seqname(args->hdr,dst),(int64_t) dst->pos+1);
+
+            kstring_t *tmp = &args->tmp_str[i];
+            kputc('.',tmp);
+            for (j=1; j<nfields; j++) kputs(",.",tmp);
+        }
+        for (i=0; i<nlines; i++)
+        {
+            if ( i ) // we already have a copy
+            {
+                nret = bcf_get_format_char(args->hdr,lines[i],tag,&args->tmp_arr1,&args->ntmp_arr1);
+                if (nret<0) continue; /* format tag does not exist in this record, skip */
+                nret /= nsmpl;
+            }
+            for (k=0; k<nsmpl; k++)
+            {
+                kstring_t *tmp = &args->tmp_str[k];
+                char *src = (char*)args->tmp_arr1 + k*nret;
+                if ( haploid[k] )
+                {
+                    for (j=0; j<lines[i]->n_allele; j++)
+                        copy_string_field(src,j,nret, tmp, args->maps[i].map[j]);
+                }
+                else
+                {
+                    int iori, jori, kori = 0;
+                    for (iori=0; iori<lines[i]->n_allele; iori++)
+                    {
+                        int inew = args->maps[i].map[iori];
+                        for (jori=0; jori<=iori; jori++)
+                        {
+                            int jnew = args->maps[i].map[jori];
+                            int knew = bcf_alleles2gt(inew,jnew);
+                            copy_string_field(src,kori,nret,tmp,knew);
+                            kori++;
+                        }
+                    }
+                }
+            }
+        }
+    }
+    kstring_t str;
+    str.m = args->ntmp_arr2;
+    str.l = 0;
+    str.s = (char*) args->tmp_arr2;
+
+    int max_len = 0;
+    for (i=0; i<nsmpl; i++)
+        if ( max_len < args->tmp_str[i].l ) max_len = args->tmp_str[i].l;
+    for (i=0; i<nsmpl; i++)
+    {
+        kstring_t *tmp = &args->tmp_str[i];
+        kputsn(tmp->s,tmp->l,&str);
+        for (j=tmp->l; j<max_len; j++) kputc('\0',&str);
+    }
+    args->ntmp_arr2 = str.m;
+    args->tmp_arr2  = (uint8_t*)str.s;
+    bcf_update_format_char(args->out_hdr,dst,tag,str.s,str.l);
+}
+
+char **merge_alleles(char **a, int na, int *map, char **b, int *nb, int *mb);   // see vcfmerge.c
+static void merge_biallelics_to_multiallelic(args_t *args, bcf1_t *dst, bcf1_t **lines, int nlines)
+{
+    int i;
+    for (i=0; i<nlines; i++)
+        bcf_unpack(lines[i], BCF_UN_ALL);
+
+    dst->rid  = lines[0]->rid;
+    dst->pos  = lines[0]->pos;
+
+    // take max for QUAL
+    bcf_float_set_missing(dst->qual);
+    for (i=0; i<nlines; i++) {
+        if (bcf_float_is_missing(lines[i]->qual)) continue;
+        if (bcf_float_is_missing(dst->qual) || dst->qual<lines[i]->qual)
+            dst->qual = lines[i]->qual;
+    }
+
+    bcf_update_id(args->out_hdr, dst, lines[0]->d.id);
+
+    // Merge and set the alleles, create a mapping from source allele indexes to dst idxs
+    hts_expand0(map_t,nlines,args->mmaps,args->maps);   // a mapping for each line
+    args->nals = args->maps[0].nals = lines[0]->n_allele;
+    hts_expand(int,args->maps[0].nals,args->maps[0].mals,args->maps[0].map);
+    hts_expand(char*,args->nals,args->mals,args->als);
+    for (i=0; i<args->maps[0].nals; i++)
+    {
+        args->maps[0].map[i] = i;
+        args->als[i] = strdup(lines[0]->d.allele[i]);
+    }
+    for (i=1; i<nlines; i++)
+    {
+        if (lines[i]->d.id[0]!='.' || lines[i]->d.id[1]) bcf_add_id(args->out_hdr, dst, lines[i]->d.id);
+        args->maps[i].nals = lines[i]->n_allele;
+        hts_expand(int,args->maps[i].nals,args->maps[i].mals,args->maps[i].map);
+        args->als = merge_alleles(lines[i]->d.allele, lines[i]->n_allele, args->maps[i].map, args->als, &args->nals, &args->mals);
+        if ( !args->als ) error("Failed to merge alleles at %s:%"PRId64"\n", bcf_seqname(args->hdr,dst),(int64_t) dst->pos+1);
+    }
+    bcf_update_alleles(args->out_hdr, dst, (const char**)args->als, args->nals);
+    for (i=0; i<args->nals; i++)
+    {
+        free(args->als[i]);
+        args->als[i] = NULL;
+    }
+
+    if ( lines[0]->d.n_flt ) bcf_update_filter(args->out_hdr, dst, lines[0]->d.flt, lines[0]->d.n_flt);
+    for (i=1; i<nlines; i++) {
+        int j;
+        for (j=0; j<lines[i]->d.n_flt; j++) {
+            // if strict_filter, set FILTER to PASS if any site PASS
+            // otherwise accumulate FILTERs
+            if (lines[i]->d.flt[j] == bcf_hdr_id2int(args->hdr, BCF_DT_ID, "PASS")) {
+                if (args->strict_filter) {
+                    bcf_update_filter(args->out_hdr, dst, lines[i]->d.flt, lines[i]->d.n_flt);
+                    break;
+                }
+                else
+                    continue;
+            }
+            bcf_add_filter(args->out_hdr, dst, lines[i]->d.flt[j]);
+        }
+    }
+
+    // merge info
+    for (i=0; i<lines[0]->n_info; i++)
+    {
+        bcf_info_t *info = &lines[0]->d.info[i];
+        int type = bcf_hdr_id2type(args->hdr,BCF_HL_INFO,info->key);
+        if ( type==BCF_HT_INT || type==BCF_HT_REAL ) merge_info_numeric(args, lines, nlines, info, dst);
+        else if ( type==BCF_HT_FLAG ) merge_info_flag(args, lines, nlines, info, dst);
+        else merge_info_string(args, lines, nlines, info, dst);
+    }
+
+    // merge format
+    int gt_id = bcf_hdr_id2int(args->hdr,BCF_DT_ID,"GT");
+    dst->n_sample = lines[0]->n_sample;
+    for (i=0; i<lines[0]->n_fmt; i++)
+    {
+        bcf_fmt_t *fmt = &lines[0]->d.fmt[i];
+        int type = bcf_hdr_id2type(args->hdr,BCF_HL_FMT,fmt->id);
+        if ( fmt->id==gt_id ) merge_format_genotype(args, lines, nlines, fmt, dst);
+        else if ( type==BCF_HT_INT || type==BCF_HT_REAL ) merge_format_numeric(args, lines, nlines, fmt, dst);
+        else merge_format_string(args, lines, nlines, fmt, dst);
+    }
+}
+
+#define SWAP(type_t, a, b) { type_t t = a; a = b; b = t; }
+static void mrows_schedule(args_t *args, bcf1_t **line)
+{
+    int i,m;
+    if ( args->mrows_collapse==COLLAPSE_ANY         // merge all record types together
+        || bcf_get_variant_types(*line)&VCF_SNP     // SNP, put into alines
+        || bcf_get_variant_types(*line)==VCF_REF )  // ref
+    {
+        args->nalines++;
+        m = args->malines;
+        hts_expand(bcf1_t*,args->nalines,args->malines,args->alines);
+        for (i=m; i<args->malines; i++) args->alines[i] = bcf_init1();
+        SWAP(bcf1_t*, args->alines[args->nalines-1], *line);
+    }
+    else
+    {
+        args->nblines++;
+        m = args->mblines;
+        hts_expand(bcf1_t*,args->nblines,args->mblines,args->blines);
+        for (i=m; i<args->mblines; i++) args->blines[i] = bcf_init1();
+        SWAP(bcf1_t*, args->blines[args->nblines-1], *line);
+    }
+}
+static int mrows_ready_to_flush(args_t *args, bcf1_t *line)
+{
+    if ( args->nalines && (args->alines[0]->rid!=line->rid || args->alines[0]->pos!=line->pos) ) return 1;
+    if ( args->nblines && (args->blines[0]->rid!=line->rid || args->blines[0]->pos!=line->pos) ) return 1;
+    return 0;
+}
+static bcf1_t *mrows_flush(args_t *args)
+{
+    if ( args->nblines && args->nalines==1 && bcf_get_variant_types(args->alines[0])==VCF_REF )
+    {
+        // By default, REF lines are merged with SNPs if SNPs and indels are to be kept separately.
+        // However, if there are indels only and a single REF line, merge it with indels.
+        args->nblines++;
+        int i,m = args->mblines;
+        hts_expand(bcf1_t*,args->nblines,args->mblines,args->blines);
+        for (i=m; i<args->mblines; i++) args->blines[i] = bcf_init1();
+        SWAP(bcf1_t*, args->blines[args->nblines-1], args->alines[0]);
+        args->nalines--;
+    }
+    if ( args->nalines )
+    {
+        if ( args->nalines==1 )
+        {
+            args->nalines = 0;
+            return args->alines[0];
+        }
+        bcf_clear(args->mrow_out);
+        merge_biallelics_to_multiallelic(args, args->mrow_out, args->alines, args->nalines);
+        args->nalines = 0;
+        return args->mrow_out;
+    }
+    else if ( args->nblines )
+    {
+        if ( args->nblines==1 )
+        {
+            args->nblines = 0;
+            return args->blines[0];
+        }
+        bcf_clear(args->mrow_out);
+        merge_biallelics_to_multiallelic(args, args->mrow_out, args->blines, args->nblines);
+        args->nblines = 0;
+        return args->mrow_out;
+    }
+    return NULL;
+}
+static void cmpals_add(cmpals_t *ca, bcf1_t *rec)
+{
+    ca->ncmpals++;
+    hts_expand0(cmpals1_t, ca->ncmpals, ca->mcmpals, ca->cmpals);
+    cmpals1_t *cmpals = ca->cmpals + ca->ncmpals - 1;
+    free(cmpals->ref);
+    cmpals->ref = strdup(rec->d.allele[0]);
+    cmpals->n   = rec->n_allele;
+    if ( rec->n_allele==2 )
+    {
+        free(cmpals->alt);
+        cmpals->alt = strdup(rec->d.allele[1]);
+    }
+    else
+    {
+        if ( cmpals->hash ) khash_str2int_destroy_free(cmpals->hash);
+        cmpals->hash = khash_str2int_init();
+        int i;
+        for (i=1; i<rec->n_allele; i++)
+            khash_str2int_inc(cmpals->hash, strdup(rec->d.allele[i]));
+    }
+}
+static int cmpals_match(cmpals_t *ca, bcf1_t *rec)
+{
+    int i, j;
+    for (i=0; i<ca->ncmpals; i++)
+    {
+        cmpals1_t *cmpals = ca->cmpals + i;
+        if ( rec->n_allele != cmpals->n ) continue;
+
+        // NB. assuming both are normalized
+        if ( strcasecmp(rec->d.allele[0], cmpals->ref) ) continue;
+
+        // the most frequent case
+        if ( rec->n_allele==2 )
+        {
+            if ( strcasecmp(rec->d.allele[1], cmpals->alt) ) continue;
+            return 1;
+        }
+
+        khash_t(str2int) *hash = (khash_t(str2int)*) cmpals->hash;
+        for (j=1; j<rec->n_allele; j++)
+            if ( !khash_str2int_has_key(hash, rec->d.allele[j]) ) break;
+        if ( j<rec->n_allele ) continue;
+        return 1;
+    }
+    return 0;
+}
+static void cmpals_reset(cmpals_t *ca) { ca->ncmpals = 0; }
+static void cmpals_destroy(cmpals_t *ca)
+{
+    int i;
+    for (i=0; i<ca->mcmpals; i++)
+    {
+        cmpals1_t *cmpals = ca->cmpals + i;
+        free(cmpals->ref);
+        free(cmpals->alt);
+        if ( cmpals->hash ) khash_str2int_destroy_free(cmpals->hash);
+    }
+    free(ca->cmpals);
+}
+
+static void flush_buffer(args_t *args, htsFile *file, int n)
+{
+    bcf1_t *line;
+    int i, k;
+    int prev_rid = -1, prev_pos = -1, prev_type = 0;
+    for (i=0; i<n; i++)
+    {
+        k = rbuf_shift(&args->rbuf);
+        if ( args->mrows_op==MROWS_MERGE )
+        {
+            if ( mrows_ready_to_flush(args, args->lines[k]) )
+            {
+                while ( (line=mrows_flush(args)) )
+                    if ( bcf_write1(file, args->out_hdr, line)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->output_fname);
+            }
+            int merge = 1;
+            if ( args->mrows_collapse!=COLLAPSE_BOTH && args->mrows_collapse!=COLLAPSE_ANY )
+            {
+                if ( !(bcf_get_variant_types(args->lines[k]) & args->mrows_collapse) ) merge = 0;
+            }
+            if ( merge )
+            {
+                mrows_schedule(args, &args->lines[k]);
+                continue;
+            }
+        }
+        else if ( args->rmdup )
+        {
+            int line_type = bcf_get_variant_types(args->lines[k]);
+            if ( prev_rid>=0 && prev_rid==args->lines[k]->rid && prev_pos==args->lines[k]->pos )
+            {
+                if ( args->rmdup & BCF_SR_PAIR_ANY ) continue;    // rmdup by position only
+                if ( args->rmdup & BCF_SR_PAIR_SNPS && line_type&(VCF_SNP|VCF_MNP) && prev_type&(VCF_SNP|VCF_MNP) ) continue;
+                if ( args->rmdup & BCF_SR_PAIR_INDELS && line_type&(VCF_INDEL) && prev_type&(VCF_INDEL) ) continue;
+                if ( args->rmdup & BCF_SR_PAIR_EXACT && cmpals_match(&args->cmpals_out, args->lines[k]) ) continue;
+            }
+            else
+            {
+                prev_rid  = args->lines[k]->rid;
+                prev_pos  = args->lines[k]->pos;
+                prev_type = 0;
+                if ( args->rmdup & BCF_SR_PAIR_EXACT ) cmpals_reset(&args->cmpals_out);
+            }
+            prev_type |= line_type;
+            if ( args->rmdup & BCF_SR_PAIR_EXACT ) cmpals_add(&args->cmpals_out, args->lines[k]);
+        }
+        if ( bcf_write1(file, args->out_hdr, args->lines[k])!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->output_fname);
+    }
+    if ( args->mrows_op==MROWS_MERGE && !args->rbuf.n )
+    {
+        while ( (line=mrows_flush(args)) )
+            if ( bcf_write1(file, args->out_hdr, line)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->output_fname);
+    }
+}
+
+static void init_data(args_t *args)
+{
+    args->hdr = args->files->readers[0].header;
+    if ( args->keep_sum_ad )
+    {
+        args->keep_sum_ad = bcf_hdr_id2int(args->hdr,BCF_DT_ID,"AD");
+        if ( args->keep_sum_ad < 0 ) error("Error: --keep-sum-ad requested but the tag AD is not present\n");
+    }
+    else
+        args->keep_sum_ad = -1;
+
+    args->out_hdr = bcf_hdr_dup(args->hdr);
+    if ( args->old_rec_tag )
+        bcf_hdr_printf(args->out_hdr,"##INFO=<ID=%s,Number=1,Type=String,Description=\"Original variant. Format: CHR|POS|REF|ALT|USED_ALT_IDX\">",args->old_rec_tag);
+
+    rbuf_init(&args->rbuf, 100);
+    args->lines = (bcf1_t**) calloc(args->rbuf.m, sizeof(bcf1_t*));
+    if ( args->ref_fname )
+    {
+        args->fai = fai_load(args->ref_fname);
+        if ( !args->fai ) error("Failed to load the fai index: %s\n", args->ref_fname);
+    }
+    if ( args->mrows_op==MROWS_MERGE )
+    {
+        args->mrow_out = bcf_init1();
+        args->tmp_str = (kstring_t*) calloc(bcf_hdr_nsamples(args->hdr),sizeof(kstring_t));
+        args->diploid = (uint8_t*) malloc(bcf_hdr_nsamples(args->hdr));
+    }
+    if ( args->atomize==SPLIT )
+    {
+        args->abuf = abuf_init(args->hdr, SPLIT);
+        abuf_set_opt(args->abuf, bcf_hdr_t*, BCF_HDR, args->out_hdr);
+        if ( args->old_rec_tag )
+            abuf_set_opt(args->abuf, const char*, INFO_TAG, args->old_rec_tag);
+        abuf_set_opt(args->abuf, int, STAR_ALLELE, args->use_star_allele);
+    }
+}
+
+static void destroy_data(args_t *args)
+{
+    cmpals_destroy(&args->cmpals_in);
+    cmpals_destroy(&args->cmpals_out);
+    int i;
+    for (i=0; i<args->rbuf.m; i++)
+        if ( args->lines[i] ) bcf_destroy1(args->lines[i]);
+    free(args->lines);
+    for (i=0; i<args->mtmp_lines; i++)
+        if ( args->tmp_lines[i] ) bcf_destroy1(args->tmp_lines[i]);
+    free(args->tmp_lines);
+    for (i=0; i<args->malines; i++)
+        bcf_destroy1(args->alines[i]);
+    free(args->alines);
+    for (i=0; i<args->mblines; i++)
+        bcf_destroy1(args->blines[i]);
+    free(args->blines);
+    for (i=0; i<args->mmaps; i++)
+        free(args->maps[i].map);
+    for (i=0; i<args->ntmp_als; i++)
+        free(args->tmp_als[i].s);
+    free(args->tmp_als);
+    free(args->tmp_kstr.s);
+    if ( args->tmp_str )
+    {
+        for (i=0; i<bcf_hdr_nsamples(args->hdr); i++) free(args->tmp_str[i].s);
+        free(args->tmp_str);
+    }
+    free(args->maps);
+    free(args->als);
+    free(args->int32_arr);
+    free(args->tmp_arr1);
+    free(args->tmp_arr2);
+    free(args->diploid);
+    if ( args->abuf ) abuf_destroy(args->abuf);
+    bcf_hdr_destroy(args->out_hdr);
+    if ( args->mrow_out ) bcf_destroy1(args->mrow_out);
+    if ( args->fai ) fai_destroy(args->fai);
+    if ( args->mseq ) free(args->seq);
+}
+
+
+static void normalize_line(args_t *args, bcf1_t *line)
+{
+    if ( args->fai )
+    {
+        if ( args->check_ref & CHECK_REF_FIX ) fix_ref(args, line);
+        if ( args->do_indels )
+        {
+            int ret = realign(args, line);
+
+            // exclude broken VCF lines
+            if ( ret==ERR_REF_MISMATCH && args->check_ref & CHECK_REF_SKIP )
+            {
+                args->nskipped++;
+                return;
+            }
+            if ( ret==ERR_DUP_ALLELE )
+            {
+                if ( args->check_ref & CHECK_REF_FIX )
+                    fix_dup_alt(args, line);
+                else if ( args->check_ref==CHECK_REF_EXIT )
+                    error("Duplicate alleles at %s:%"PRId64"; run with -cw to turn the error into warning or with -cs to fix.\n", bcf_seqname(args->hdr,line),(int64_t) line->pos+1);
+                else if ( args->check_ref & CHECK_REF_WARN )
+                    fprintf(bcftools_stderr,"ALT_DUP\t%s\t%"PRId64"\n", bcf_seqname(args->hdr,line),(int64_t) line->pos+1);
+            }
+        }
+    }
+
+    // insert into sorted buffer
+    rbuf_expand0(&args->rbuf,bcf1_t*,args->rbuf.n+1,args->lines);
+    int i,j;
+    i = j = rbuf_append(&args->rbuf);
+    if ( args->lines[i] ) bcf_destroy(args->lines[i]);
+    args->lines[i] = bcf_dup(line);
+    while ( rbuf_prev(&args->rbuf,&i) )
+    {
+        if ( args->lines[i]->pos > args->lines[j]->pos ) SWAP(bcf1_t*, args->lines[i], args->lines[j]);
+        j = i;
+    }
+}
+
+static bcf1_t *next_atomized_line(args_t *args)
+{
+    bcf1_t *rec = NULL;
+    if ( args->atomize==SPLIT )
+    {
+        rec = abuf_flush(args->abuf, 0);
+        if ( rec ) return rec;
+    }
+
+    if ( !bcf_sr_next_line(args->files) ) return NULL;
+
+    if ( args->atomize==SPLIT )
+    {
+        abuf_push(args->abuf,bcf_sr_get_line(args->files,0));
+        return abuf_flush(args->abuf, 0);
+    }
+    return bcf_sr_get_line(args->files,0);
+}
+static void normalize_vcf(args_t *args)
+{
+    char wmode[8];
+    set_wmode(wmode,args->output_type,args->output_fname,args->clevel);
+    args->out = hts_open(args->output_fname ? args->output_fname : "-", wmode);
+    if ( args->out == NULL ) error("Can't write to \"%s\": %s\n", args->output_fname, strerror(errno));
+    if ( args->n_threads )
+        hts_set_opt(args->out, HTS_OPT_THREAD_POOL, args->files->p);
+    if (args->record_cmd_line) bcf_hdr_append_version(args->out_hdr, args->argc, args->argv, "bcftools_norm");
+    if ( bcf_hdr_write(args->out, args->out_hdr)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->output_fname);
+
+    bcf1_t *line;
+    int prev_rid = -1, prev_pos = -1, prev_type = 0;
+    while ( (line = next_atomized_line(args)) )
+    {
+        args->ntotal++;
+        if ( args->rmdup )
+        {
+            int line_type = bcf_get_variant_types(line);
+            if ( prev_rid>=0 && prev_rid==line->rid && prev_pos==line->pos )
+            {
+                if ( args->rmdup & BCF_SR_PAIR_ANY ) continue;    // rmdup by position only
+                if ( args->rmdup & BCF_SR_PAIR_SNPS && line_type&(VCF_SNP|VCF_MNP) && prev_type&(VCF_SNP|VCF_MNP) ) continue;
+                if ( args->rmdup & BCF_SR_PAIR_INDELS && line_type&(VCF_INDEL) && prev_type&(VCF_INDEL) ) continue;
+                if ( args->rmdup & BCF_SR_PAIR_EXACT && cmpals_match(&args->cmpals_in, line) ) continue;
+            }
+            else
+            {
+                prev_rid  = line->rid;
+                prev_pos  = line->pos;
+                prev_type = 0;
+                if ( args->rmdup & BCF_SR_PAIR_EXACT ) cmpals_reset(&args->cmpals_in);
+            }
+            prev_type |= line_type;
+            if ( args->rmdup & BCF_SR_PAIR_EXACT ) cmpals_add(&args->cmpals_in, line);
+        }
+
+        // still on the same chromosome?
+        int i,j,ilast = rbuf_last(&args->rbuf);
+        if ( ilast>=0 && line->rid != args->lines[ilast]->rid ) flush_buffer(args, args->out, args->rbuf.n); // new chromosome
+
+        int split = 0;
+        if ( args->mrows_op==MROWS_SPLIT )
+        {
+            split = 1;
+            if ( args->mrows_collapse!=COLLAPSE_BOTH && args->mrows_collapse!=COLLAPSE_ANY )
+            {
+                if ( !(bcf_get_variant_types(line) & args->mrows_collapse) ) split = 0;
+            }
+            if ( split && line->n_allele>2 )
+            {
+                args->nsplit++;
+                split_multiallelic_to_biallelics(args, line);
+                for (j=0; j<args->ntmp_lines; j++)
+                    normalize_line(args, args->tmp_lines[j]);
+            }
+            else
+                split = 0;
+        }
+        if ( !split )
+            normalize_line(args, line);
+
+        // find out how many sites to flush
+        ilast = rbuf_last(&args->rbuf);
+        j = 0;
+        for (i=-1; rbuf_next(&args->rbuf,&i); )
+        {
+            if ( args->lines[ilast]->pos - args->lines[i]->pos < args->buf_win ) break;
+            j++;
+        }
+        if ( j>0 ) flush_buffer(args, args->out, j);
+    }
+    flush_buffer(args, args->out, args->rbuf.n);
+    if ( hts_close(args->out)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,args->output_fname);
+
+    fprintf(bcftools_stderr,"Lines   total/split/realigned/skipped:\t%d/%d/%d/%d\n", args->ntotal,args->nsplit,args->nchanged,args->nskipped);
+    if ( args->check_ref & CHECK_REF_FIX )
+        fprintf(bcftools_stderr,"REF/ALT total/modified/added:  \t%d/%d/%d\n", args->nref.tot,args->nref.swap,args->nref.set);
+}
+
+static void usage(void)
+{
+    fprintf(bcftools_stderr, "\n");
+    fprintf(bcftools_stderr, "About:   Left-align and normalize indels; check if REF alleles match the reference;\n");
+    fprintf(bcftools_stderr, "         split multiallelic sites into multiple rows; recover multiallelics from\n");
+    fprintf(bcftools_stderr, "         multiple rows.\n");
+    fprintf(bcftools_stderr, "Usage:   bcftools norm [options] <in.vcf.gz>\n");
+    fprintf(bcftools_stderr, "\n");
+    fprintf(bcftools_stderr, "Options:\n");
+    fprintf(bcftools_stderr, "    -a, --atomize                   Decompose complex variants (e.g. MNVs become consecutive SNVs)\n");
+    fprintf(bcftools_stderr, "        --atom-overlaps '*'|.       Use the star allele (*) for overlapping alleles or set to missing (.) [*]\n");
+    fprintf(bcftools_stderr, "    -c, --check-ref e|w|x|s         Check REF alleles and exit (e), warn (w), exclude (x), or set (s) bad sites [e]\n");
+    fprintf(bcftools_stderr, "    -D, --remove-duplicates         Remove duplicate lines of the same type.\n");
+    fprintf(bcftools_stderr, "    -d, --rm-dup TYPE               Remove duplicate snps|indels|both|all|exact\n");
+    fprintf(bcftools_stderr, "    -f, --fasta-ref FILE            Reference sequence\n");
+    fprintf(bcftools_stderr, "        --force                     Try to proceed even if malformed tags are encountered. Experimental, use at your own risk\n");
+    fprintf(bcftools_stderr, "        --keep-sum TAG,..           Keep vector sum constant when splitting multiallelics (see github issue #360)\n");
+    fprintf(bcftools_stderr, "    -m, --multiallelics -|+TYPE     Split multiallelics (-) or join biallelics (+), type: snps|indels|both|any [both]\n");
+    fprintf(bcftools_stderr, "        --no-version                Do not append version and command line to the header\n");
+    fprintf(bcftools_stderr, "    -N, --do-not-normalize          Do not normalize indels (with -m or -c s)\n");
+    fprintf(bcftools_stderr, "        --old-rec-tag STR           Annotate modified records with INFO/STR indicating the original variant\n");
+    fprintf(bcftools_stderr, "    -o, --output FILE               Write output to a file [standard output]\n");
+    fprintf(bcftools_stderr, "    -O, --output-type u|b|v|z[0-9]  u/b: un/compressed BCF, v/z: un/compressed VCF, 0-9: compression level [v]\n");
+    fprintf(bcftools_stderr, "    -r, --regions REGION            Restrict to comma-separated list of regions\n");
+    fprintf(bcftools_stderr, "    -R, --regions-file FILE         Restrict to regions listed in a file\n");
+    fprintf(bcftools_stderr, "        --regions-overlap 0|1|2     Include if POS in the region (0), record overlaps (1), variant overlaps (2) [1]\n");
+    fprintf(bcftools_stderr, "    -s, --strict-filter             When merging (-m+), merged site is PASS only if all sites being merged PASS\n");
+    fprintf(bcftools_stderr, "    -t, --targets REGION            Similar to -r but streams rather than index-jumps\n");
+    fprintf(bcftools_stderr, "    -T, --targets-file FILE         Similar to -R but streams rather than index-jumps\n");
+    fprintf(bcftools_stderr, "        --targets-overlap 0|1|2     Include if POS in the region (0), record overlaps (1), variant overlaps (2) [0]\n");
+    fprintf(bcftools_stderr, "        --threads INT               Use multithreading with <int> worker threads [0]\n");
+    fprintf(bcftools_stderr, "    -w, --site-win INT              Buffer for sorting lines which changed position during realignment [1000]\n");
+    fprintf(bcftools_stderr, "\n");
+    fprintf(bcftools_stderr, "Examples:\n");
+    fprintf(bcftools_stderr, "   # normalize and left-align indels\n");
+    fprintf(bcftools_stderr, "   bcftools norm -f ref.fa in.vcf\n");
+    fprintf(bcftools_stderr, "\n");
+    fprintf(bcftools_stderr, "   # split multi-allelic sites\n");
+    fprintf(bcftools_stderr, "   bcftools norm -m- in.vcf\n");
+    fprintf(bcftools_stderr, "\n");
+    bcftools_exit(1);
+}
+
+int main_vcfnorm(int argc, char *argv[])
+{
+    int c;
+    args_t *args  = (args_t*) calloc(1,sizeof(args_t));
+    args->argc    = argc; args->argv = argv;
+    args->files   = bcf_sr_init();
+    args->output_fname = "-";
+    args->output_type = FT_VCF;
+    args->n_threads = 0;
+    args->record_cmd_line = 1;
+    args->aln_win = 100;
+    args->buf_win = 1000;
+    args->mrows_collapse = COLLAPSE_BOTH;
+    args->do_indels = 1;
+    args->clevel = -1;
+    int region_is_file  = 0;
+    int targets_is_file = 0;
+    args->use_star_allele = 1;
+    int regions_overlap = 1;
+    int targets_overlap = 0;
+
+    static struct option loptions[] =
+    {
+        {"help",no_argument,NULL,'h'},
+        {"force",no_argument,NULL,7},
+        {"atomize",no_argument,NULL,'a'},
+        {"atom-overlaps",required_argument,NULL,11},
+        {"old-rec-tag",required_argument,NULL,12},
+        {"keep-sum",required_argument,NULL,10},
+        {"fasta-ref",required_argument,NULL,'f'},
+        {"do-not-normalize",no_argument,NULL,'N'},
+        {"multiallelics",required_argument,NULL,'m'},
+        {"regions",required_argument,NULL,'r'},
+        {"regions-file",required_argument,NULL,'R'},
+        {"regions-overlap",required_argument,NULL,1},
+        {"targets",required_argument,NULL,'t'},
+        {"targets-file",required_argument,NULL,'T'},
+        {"targets-overlap",required_argument,NULL,2},
+        {"site-win",required_argument,NULL,'w'},
+        {"remove-duplicates",no_argument,NULL,'D'},
+        {"rm-dup",required_argument,NULL,'d'},
+        {"output",required_argument,NULL,'o'},
+        {"output-type",required_argument,NULL,'O'},
+        {"threads",required_argument,NULL,9},
+        {"check-ref",required_argument,NULL,'c'},
+        {"strict-filter",no_argument,NULL,'s'},
+        {"no-version",no_argument,NULL,8},
+        {NULL,0,NULL,0}
+    };
+    char *tmp;
+    while ((c = getopt_long(argc, argv, "hr:R:f:w:Dd:o:O:c:m:t:T:sNa",loptions,NULL)) >= 0) {
+        switch (c) {
+            case  10:
+                // possibly generalize this also to INFO/AD and other tags
+                if ( strcasecmp("ad",optarg) )
+                    error("Error: only --keep-sum AD is currently supported. See https://github.com/samtools/bcftools/issues/360 for more.\n");
+                args->keep_sum_ad = 1;  // this will be set to the header id or -1 in init_data
+                break;
+            case 'a': args->atomize = SPLIT; break;
+            case 11 :
+                if ( optarg[0]=='*' ) args->use_star_allele = 1;
+                else if ( optarg[0]=='.' ) args->use_star_allele = 0;
+                else error("Invalid argument to --atom-overlaps. Perhaps you wanted: \"--atom-overlaps '*'\"?\n");
+                break;
+            case 12 : args->old_rec_tag = optarg; break;
+            case 'N': args->do_indels = 0; break;
+            case 'd':
+                if ( !strcmp("snps",optarg) ) args->rmdup = BCF_SR_PAIR_SNPS;
+                else if ( !strcmp("indels",optarg) ) args->rmdup = BCF_SR_PAIR_INDELS;
+                else if ( !strcmp("both",optarg) ) args->rmdup = BCF_SR_PAIR_BOTH;
+                else if ( !strcmp("all",optarg) ) args->rmdup = BCF_SR_PAIR_ANY;
+                else if ( !strcmp("any",optarg) ) args->rmdup = BCF_SR_PAIR_ANY;
+                else if ( !strcmp("none",optarg) ) args->rmdup = BCF_SR_PAIR_EXACT;
+                else if ( !strcmp("exact",optarg) ) args->rmdup = BCF_SR_PAIR_EXACT;
+                else error("The argument to -d not recognised: %s\n", optarg);
+                break;
+            case 'm':
+                if ( optarg[0]=='-' ) args->mrows_op = MROWS_SPLIT;
+                else if ( optarg[0]=='+' ) args->mrows_op = MROWS_MERGE;
+                else error("Expected '+' or '-' with -m\n");
+                if ( optarg[1]!=0 )
+                {
+                    if ( !strcmp("snps",optarg+1) ) args->mrows_collapse = COLLAPSE_SNPS;
+                    else if ( !strcmp("indels",optarg+1) ) args->mrows_collapse = COLLAPSE_INDELS;
+                    else if ( !strcmp("both",optarg+1) ) args->mrows_collapse = COLLAPSE_BOTH;
+                    else if ( !strcmp("any",optarg+1) ) args->mrows_collapse = COLLAPSE_ANY;
+                    else error("The argument to -m not recognised: %s\n", optarg);
+                }
+                break;
+            case 'c':
+                if ( strchr(optarg,'w') ) args->check_ref |= CHECK_REF_WARN;
+                if ( strchr(optarg,'x') ) args->check_ref |= CHECK_REF_SKIP;
+                if ( strchr(optarg,'s') ) args->check_ref |= CHECK_REF_FIX;
+                if ( strchr(optarg,'e') ) args->check_ref = CHECK_REF_EXIT; // overrides the above
+                break;
+            case 'O':
+                switch (optarg[0]) {
+                    case 'b': args->output_type = FT_BCF_GZ; break;
+                    case 'u': args->output_type = FT_BCF; break;
+                    case 'z': args->output_type = FT_VCF_GZ; break;
+                    case 'v': args->output_type = FT_VCF; break;
+                    default:
+                    {
+                        args->clevel = strtol(optarg,&tmp,10);
+                        if ( *tmp || args->clevel<0 || args->clevel>9 ) error("The output type \"%s\" not recognised\n", optarg);
+                    }
+                }
+                if ( optarg[1] )
+                {
+                    args->clevel = strtol(optarg+1,&tmp,10);
+                    if ( *tmp || args->clevel<0 || args->clevel>9 ) error("Could not parse argument: --compression-level %s\n", optarg+1);
+                }
+                break;
+            case 'o': args->output_fname = optarg; break;
+            case 'D':
+                fprintf(bcftools_stderr,"Warning: `-D` is functional but deprecated, replaced by and alias of `-d none`.\n");
+                args->rmdup = BCF_SR_PAIR_EXACT;
+                break;
+            case 's': args->strict_filter = 1; break;
+            case 'f': args->ref_fname = optarg; break;
+            case 'r': args->region = optarg; break;
+            case 'R': args->region = optarg; region_is_file = 1; break;
+            case 't': args->targets = optarg; break;
+            case 'T': args->targets = optarg; targets_is_file = 1; break;
+            case 'w':
+                args->buf_win = strtol(optarg,&tmp,10);
+                if ( *tmp ) error("Could not parse argument: --site-win %s\n", optarg);
+                break;
+            case  9 : args->n_threads = strtol(optarg, 0, 0); break;
+            case  8 : args->record_cmd_line = 0; break;
+            case  7 : args->force = 1; break;
+            case  1 :
+                regions_overlap = parse_overlap_option(optarg);
+                if ( regions_overlap < 0 ) error("Could not parse: --regions-overlap %s\n",optarg);
+                break;
+            case  2 :
+                targets_overlap = parse_overlap_option(optarg);
+                if ( targets_overlap < 0 ) error("Could not parse: --targets-overlap %s\n",optarg);
+                break;
+            case 'h':
+            case '?': usage(); break;
+            default: error("Unknown argument: %s\n", optarg);
+        }
+    }
+
+    char *fname = NULL;
+    if ( optind>=argc )
+    {
+        if ( !isatty(fileno((FILE *)stdin)) ) fname = "-";  // reading from stdin
+        else usage();
+    }
+    else fname = argv[optind];
+
+    if ( !args->ref_fname && !args->mrows_op && !args->rmdup && args->atomize==NONE ) error("Expected -a, -f, -m, -D or -d option\n");
+    if ( !args->check_ref && args->ref_fname ) args->check_ref = CHECK_REF_EXIT;
+    if ( args->check_ref && !args->ref_fname ) error("Expected --fasta-ref with --check-ref\n");
+
+    if ( args->region )
+    {
+        bcf_sr_set_opt(args->files,BCF_SR_REGIONS_OVERLAP,regions_overlap);
+        if ( bcf_sr_set_regions(args->files, args->region,region_is_file)<0 )
+            error("Failed to read the regions: %s\n", args->region);
+    }
+    if ( args->targets )
+    {
+        bcf_sr_set_opt(args->files,BCF_SR_TARGETS_OVERLAP,targets_overlap);
+        if ( bcf_sr_set_targets(args->files, args->targets,targets_is_file, 0)<0 )
+            error("Failed to read the targets: %s\n", args->targets);
+    }
+
+    if ( bcf_sr_set_threads(args->files, args->n_threads)<0 ) error("Failed to create threads\n");
+    if ( !bcf_sr_add_reader(args->files, fname) ) error("Failed to read from %s: %s\n", !strcmp("-",fname)?"standard input":fname,bcf_sr_strerror(args->files->errnum));
+    if ( args->mrows_op&MROWS_SPLIT && args->rmdup ) error("Cannot combine -D and -m-\n");
+    init_data(args);
+    normalize_vcf(args);
+    destroy_data(args);
+    bcf_sr_destroy(args->files);
+    free(args);
+    return 0;
+}
+
diff --git a/bcftools/vcfplugin.c b/bcftools/vcfplugin.c
new file mode 100644
index 0000000..4568668
--- /dev/null
+++ b/bcftools/vcfplugin.c
@@ -0,0 +1,822 @@
+/*  vcfplugin.c -- plugin modules for operating on VCF/BCF files.
+
+    Copyright (C) 2013-2021 Genome Research Ltd.
+
+    Author: Petr Danecek <pd3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.  */
+
+#include "config.h"
+#include <stdio.h>
+#include <strings.h>
+#include <unistd.h>
+#include <getopt.h>
+#include <ctype.h>
+#include <string.h>
+#include <errno.h>
+#include <sys/stat.h>
+#include <sys/types.h>
+#include <dirent.h>
+#include <math.h>
+#include <htslib/vcf.h>
+#include <htslib/synced_bcf_reader.h>
+#include <htslib/kseq.h>
+#include <htslib/khash_str2int.h>
+#ifdef _WIN32
+#include <windows.h>
+#else
+#include <dlfcn.h>
+#endif
+#include "bcftools.h"
+#include "vcmp.h"
+#include "filter.h"
+
+#ifdef ENABLE_BCF_PLUGINS
+
+typedef struct _plugin_t plugin_t;
+
+/**
+ *   Plugin API:
+ *   ----------
+ *   const char *about(void)
+ *      - short description used by 'bcftools plugin -lv'
+ *
+ *   const char *usage(void)
+ *      - longer description used by 'bcftools +name -h'
+ *
+ *   int run(int argc, char **argv)
+ *      - if implemented, the control is immediately handed over to the plugin,
+ *      none of the init/process/destroy functions is called.  Return 0 on
+ *      success or non-zero value on error.
+ *
+ *   int init(int argc, char **argv, bcf_hdr_t *in_hdr, bcf_hdr_t *out_hdr)
+ *      - called once at startup, allows to initialize local variables.
+ *      Return 1 to suppress normal VCF/BCF header output, -1 on critical
+ *      errors, 0 otherwise.
+ *
+ *   bcf1_t *process(bcf1_t *rec)
+ *      - called for each VCF record, return NULL for no output
+ *
+ *   void destroy(void)
+ *      - called after all lines have been processed to clean up
+ */
+typedef void (*dl_version_f) (const char **, const char **);
+typedef int (*dl_run_f) (int, char **);
+typedef int (*dl_init_f) (int, char **, bcf_hdr_t *, bcf_hdr_t *);
+typedef char* (*dl_about_f) (void);
+typedef char* (*dl_usage_f) (void);
+typedef bcf1_t* (*dl_process_f) (bcf1_t *);
+typedef void (*dl_destroy_f) (void);
+
+struct _plugin_t
+{
+    int argc;
+    char *name, **argv;
+    dl_version_f version;
+    dl_run_f run;
+    dl_init_f init;
+    dl_about_f about;
+    dl_usage_f usage;
+    dl_process_f process;
+    dl_destroy_f destroy;
+    void *handle;
+};
+
+
+struct _args_t;
+
+typedef struct _rm_tag_t
+{
+    char *key;
+    int hdr_id;
+    void (*handler)(struct _args_t *, bcf1_t *, struct _rm_tag_t *);
+}
+rm_tag_t;
+
+typedef struct
+{
+    char **cols;
+    int ncols, mcols;
+    char **als;
+    int nals, mals;
+    kstring_t line;
+    int rid, start, end;
+}
+annot_line_t;
+
+typedef struct _annot_col_t
+{
+    int icol, replace;
+    char *hdr_key;
+    int (*setter)(struct _args_t *, bcf1_t *, struct _annot_col_t *, void*);
+}
+annot_col_t;
+
+// Logic of the filters: include or exclude sites which match the filters?
+#define FLT_INCLUDE 1
+#define FLT_EXCLUDE 2
+
+typedef struct _args_t
+{
+    bcf_srs_t *files;
+    bcf_hdr_t *hdr, *hdr_out;
+    htsFile *out_fh;
+    int output_type, n_threads, clevel;
+
+    filter_t *filter;
+    char *filter_str;
+    int filter_logic;   // include or exclude sites which match the filters? One of FLT_INCLUDE/FLT_EXCLUDE
+
+    plugin_t plugin;
+    int nplugin_paths;
+    char **plugin_paths;
+
+    char **argv, *output_fname, *regions_list, *targets_list;
+    int argc, drop_header, verbose, record_cmd_line, plist_only;
+}
+args_t;
+
+char *msprintf(const char *fmt, ...);
+
+static void add_plugin_paths(args_t *args, const char *path)
+{
+    while (1)
+    {
+        size_t len = strcspn(path, HTS_PATH_SEPARATOR_STR);
+
+        if ( len == 0 )
+        {
+#ifdef PLUGINPATH
+            add_plugin_paths(args, PLUGINPATH);
+#endif
+        }
+        else
+        {
+            char *dir = (char *) malloc(len + 1);
+            strncpy(dir, path, len);
+            dir[len] = '\0';
+
+            struct stat st;
+            if ( stat(dir, &st) == 0 )
+            {
+                args->plugin_paths = (char**) realloc(args->plugin_paths,sizeof(char*)*(args->nplugin_paths+1));
+                args->plugin_paths[args->nplugin_paths] = dir;
+                args->nplugin_paths++;
+                if ( args->verbose > 1 && strcmp(".",dir) ) fprintf(stderr, "plugin directory %s .. ok\n", dir);
+            }
+            else
+            {
+                if ( args->verbose > 1 ) fprintf(stderr, "plugin directory %s .. %s\n", dir, strerror(errno));
+                free(dir);
+            }
+
+        }
+
+        path += len;
+        if ( *path == HTS_PATH_SEPARATOR_CHAR ) path++;
+        else break;
+    }
+}
+
+static void init_plugin_paths(args_t *args)
+{
+    if ( args->nplugin_paths!=-1 ) return;
+
+    args->nplugin_paths = 0;
+    args->plugin_paths = NULL;
+
+    char *path = getenv("BCFTOOLS_PLUGINS");
+    add_plugin_paths(args, path ? path : "");
+}
+
+static void *dlopen_plugin(args_t *args, const char *fname)
+{
+    init_plugin_paths(args);
+
+    void *handle;
+    char *tmp;
+    int is_absolute_path = 0;
+#ifdef _WIN32
+    // Windows accepts both forward slash (/) and backslash (\) as folder separator
+    // and can have any path prefixed by the drive letter and a colon (:).
+    if ( fname[0]=='/' || fname[0]=='\\') is_absolute_path = 1;
+    else if ( fname[0] && fname[1]==':' && (fname[2]=='/' || fname[2]=='\\') ) is_absolute_path = 1;
+#else
+    if ( fname[0]=='/' ) is_absolute_path = 1;
+#endif
+
+    kstring_t err = {0,0,0};
+    if ( !is_absolute_path )
+    {
+        int i;
+        for (i=0; i<args->nplugin_paths; i++)
+        {
+            tmp = msprintf("%s/%s%s", args->plugin_paths[i], fname, PLUGIN_EXT);
+#ifdef _WIN32
+            handle = LoadLibraryA(tmp);
+#else
+            handle = dlopen(tmp, RTLD_NOW); // valgrind complains about unfreed memory, not our problem though
+#endif
+            if ( !handle )
+#ifdef _WIN32
+                ksprintf(&err,"LoadLibraryA   .. %lu\n", GetLastError());
+#else
+                ksprintf(&err,"%s:\n\tdlopen   .. %s\n", tmp,dlerror());
+#endif
+            else if ( args->verbose > 1 )
+                fprintf(stderr,"%s:\n\tplugin open   .. ok\n", tmp);
+            free(tmp);
+            if ( handle ) return handle;
+        }
+    }
+
+#ifdef _WIN32
+    handle = LoadLibraryA(fname);
+#else
+    handle = dlopen(fname, RTLD_NOW);
+#endif
+    if ( !handle )
+#ifdef _WIN32
+        ksprintf(&err,"LoadLibraryA   .. %lu\n", GetLastError());
+#else
+        ksprintf(&err,"%s:\n\tdlopen   .. %s\n", fname,dlerror());
+#endif
+    else if ( args->verbose > 1 )
+        fprintf(stderr,"%s:\n\tplugin open   .. ok\n", fname);
+
+    if ( !handle && (!args->plist_only || args->verbose>1) )
+        fprintf(stderr,"%s",err.s);
+    free(err.s);
+
+    return handle;
+}
+
+static void print_plugin_usage_hint(const char *name)
+{
+    if ( name )
+        fprintf(stderr, "\nThe bcftools plugin \"%s\" was not found or is not functional", name);
+    else
+        fprintf(stderr, "\nNo functional bcftools plugins were found");
+    if ( !getenv("BCFTOOLS_PLUGINS") )
+    {
+        fprintf(stderr,". The environment variable BCFTOOLS_PLUGINS is not set");
+#ifdef PLUGINPATH
+        fprintf(stderr,"\nand no usable plugins were found in %s", PLUGINPATH);
+#endif
+        fprintf(stderr,".\n\n");
+    }
+    else
+    {
+        fprintf(stderr,
+                " in\n\tBCFTOOLS_PLUGINS=\"%s\".\n\n"
+                "- Is the plugin path correct?\n\n"
+                "- Run \"bcftools plugin -l\" or \"bcftools plugin -lvv\" for a list of available plugins.\n"
+                "\n",
+                getenv("BCFTOOLS_PLUGINS")
+               );
+    }
+}
+
+static int load_plugin(args_t *args, const char *fname, int exit_on_error, plugin_t *plugin)
+{
+    plugin->name = strdup(fname);
+
+    plugin->handle = dlopen_plugin(args, fname);
+    if ( !plugin->handle )
+    {
+        if ( exit_on_error )
+        {
+            print_plugin_usage_hint(fname);
+            error("Could not load \"%s\".\n\n", fname);
+        }
+        return -1;
+    }
+
+#ifdef _WIN32
+    plugin->init = (dl_init_f) GetProcAddress(plugin->handle, "init");
+    if ( plugin->init && args->verbose > 1 ) fprintf(stderr,"\tinit     .. ok\n");
+
+    plugin->run = (dl_run_f) GetProcAddress(plugin->handle, "run");
+    if ( plugin->run && args->verbose > 1 ) fprintf(stderr,"\trun     .. ok\n");
+
+    if ( !plugin->init && !plugin->run )
+    {
+        if ( exit_on_error ) error("Could not initialize %s, neither run or init found \n", plugin->name);
+        else if ( args->verbose > 1 ) fprintf(stderr,"\tinit/run .. not found\n");
+        return -1;
+    }
+
+    plugin->version = (dl_version_f) GetProcAddress(plugin->handle, "version");
+    if ( !plugin->version )
+    {
+        if ( exit_on_error ) error("Could not initialize %s: version string not found\n", plugin->name);
+        else if ( args->verbose > 1 ) fprintf(stderr,"\tversion  .. not found\n");
+        return -1;
+    }
+
+    plugin->about = (dl_about_f) GetProcAddress(plugin->handle, "about");
+    if ( !plugin->about )
+    {
+        if ( exit_on_error ) error("Could not initialize %s: about string not found\n", plugin->name);
+        return -1;
+    }
+
+    plugin->usage = (dl_about_f) GetProcAddress(plugin->handle, "usage");
+    if ( !plugin->usage )
+        plugin->usage = plugin->about;
+
+    if ( plugin->run ) return 0;
+
+    plugin->process = (dl_process_f) GetProcAddress(plugin->handle, "process");
+    if ( !plugin->process )
+    {
+        if ( exit_on_error ) error("Could not initialize %s: process method not found\n", plugin->name);
+        return -1;
+    }
+
+    plugin->destroy = (dl_destroy_f) GetProcAddress(plugin->handle, "destroy");
+    if ( !plugin->destroy )
+    {
+        if ( exit_on_error ) error("Could not initialize %s: destroy method not found\n", plugin->name);
+        return -1;
+    }
+#else
+    dlerror();
+    plugin->init = (dl_init_f) dlsym(plugin->handle, "init");
+    char *ret = dlerror();
+    if ( ret )
+        plugin->init = NULL;
+    else
+        if ( args->verbose > 1 ) fprintf(stderr,"\tinit     .. ok\n");
+
+    plugin->run = (dl_run_f) dlsym(plugin->handle, "run");
+    ret = dlerror();
+    if ( ret )
+        plugin->run = NULL;
+    else
+        if ( args->verbose > 1 ) fprintf(stderr,"\trun      .. ok\n");
+
+    if ( !plugin->init && !plugin->run )
+    {
+        if ( exit_on_error ) error("Could not initialize %s, neither run or init found \n", plugin->name);
+        else if ( args->verbose > 1 ) fprintf(stderr,"\tinit/run .. not found\n");
+        return -1;
+    }
+
+    plugin->version = (dl_version_f) dlsym(plugin->handle, "version");
+    ret = dlerror();
+    if ( ret )
+    {
+        if ( exit_on_error ) error("Could not initialize %s, version string not found\n", plugin->name);
+        else if ( args->verbose > 1 ) fprintf(stderr,"\tversion  .. not found\n");
+        return -1;
+    }
+
+    plugin->about = (dl_about_f) dlsym(plugin->handle, "about");
+    ret = dlerror();
+    if ( ret )
+    {
+        if ( exit_on_error ) error("Could not initialize %s: %s\n", plugin->name, ret);
+        return -1;
+    }
+
+    plugin->usage = (dl_about_f) dlsym(plugin->handle, "usage");
+    ret = dlerror();
+    if ( ret )
+        plugin->usage = plugin->about;
+
+    if ( plugin->run ) return 0;
+
+    plugin->process = (dl_process_f) dlsym(plugin->handle, "process");
+    ret = dlerror();
+    if ( ret )
+    {
+        if ( exit_on_error ) error("Could not initialize %s: %s\n", plugin->name, ret);
+        return -1;
+    }
+
+    plugin->destroy = (dl_destroy_f) dlsym(plugin->handle, "destroy");
+    ret = dlerror();
+    if ( ret )
+    {
+        if ( exit_on_error ) error("Could not initialize %s: %s\n", plugin->name, ret);
+        return -1;
+    }
+#endif
+
+    return 0;
+}
+
+static void check_version(args_t *args)
+{
+    static int warned_bcftools = 0, warned_htslib = 0;
+    const char *bver, *hver;
+    args->plugin.version(&bver, &hver);
+    if ( strcmp(bver,bcftools_version()) && !warned_bcftools )
+    {
+        fprintf(stderr,"WARNING: bcftools version mismatch .. bcftools at %s, the plugin \"%s\" at %s\n", bcftools_version(),args->plugin.name,bver);
+        warned_bcftools = 1;
+    }
+    if ( strcmp(hver,hts_version()) && !warned_htslib )
+    {
+        fprintf(stderr,"WARNING: htslib version mismatch .. bcftools at %s, the plugin \"%s\" at %s\n", hts_version(),args->plugin.name,hver);
+        warned_htslib = 1;
+    }
+}
+
+static void init_plugin(args_t *args)
+{
+    int ret = args->plugin.init(args->plugin.argc,args->plugin.argv,args->hdr,args->hdr_out);
+    if ( ret<0 ) error("The plugin exited with an error.\n");
+    check_version(args);
+    args->drop_header += ret;
+}
+
+static int cmp_plugin_name(const void *p1, const void *p2)
+{
+    plugin_t *a = (plugin_t*) p1;
+    plugin_t *b = (plugin_t*) p2;
+    return strcmp(a->name,b->name);
+}
+
+// If args=NULL then returns the number of plugins available. Otherwise prints the
+// plugins on stdout and returns 0 on success.
+static int list_plugins(args_t *args)
+{
+    plugin_t *plugins = NULL;
+    int nplugins = 0, mplugins = 0;
+
+    int count_only = 0;
+    args_t _args;
+    if ( !args )
+    {
+        memset(&_args,0,sizeof(_args));
+        args = &_args;
+        args->nplugin_paths = -1;
+        count_only = 1;
+    }
+    init_plugin_paths(args);
+
+    kstring_t str = {0,0,0};
+    int plugin_ext_len = strlen(PLUGIN_EXT);
+    int i;
+    for (i=0; i<args->nplugin_paths; i++)
+    {
+        DIR *dp = opendir(args->plugin_paths[i]);
+        if ( dp==NULL ) continue;
+
+        struct dirent *ep;
+        while ( (ep=readdir(dp)) )
+        {
+            int len = strlen(ep->d_name);
+            if ( strcasecmp(PLUGIN_EXT,ep->d_name+len-plugin_ext_len) ) continue;
+            str.l = 0;
+            ksprintf(&str,"%s/%s", args->plugin_paths[i],ep->d_name);
+            hts_expand(plugin_t, nplugins+1, mplugins, plugins);
+            if ( load_plugin(args, str.s, 0, &plugins[nplugins]) < 0 ) continue;
+            nplugins++;
+            str.l = 0;
+            kputs(ep->d_name, &str);
+            int l = str.l - 1;
+            while ( l>=0 && str.s[l]!='.' ) l--;
+            if ( l>=0 ) str.s[l] = 0;
+            free(plugins[nplugins-1].name);
+            plugins[nplugins-1].name = strdup(str.s);  // use a short name
+        }
+        closedir(dp);
+    }
+    if ( count_only )
+    {
+        free(str.s);
+        return nplugins;
+    }
+    if ( nplugins )
+    {
+        qsort(plugins, nplugins, sizeof(plugins[0]), cmp_plugin_name);
+
+        for (i=0; i<nplugins; i++)
+        {
+            if ( args->verbose )
+                printf("\n-- %s --\n%s", plugins[i].name, plugins[i].about());
+            else
+                printf("%s\n", plugins[i].name);
+        }
+        if ( args->verbose ) printf("\n");
+    }
+    else
+        print_plugin_usage_hint(NULL);
+    free(str.s);
+    return nplugins ? 0 : 1;
+}
+int count_plugins(void)
+{
+    return list_plugins(NULL);
+}
+
+static void init_data(args_t *args)
+{
+    args->hdr = args->files->readers[0].header;
+    args->hdr_out = bcf_hdr_dup(args->hdr);
+
+    init_plugin(args);
+
+    if ( args->filter_str )
+        args->filter = filter_init(args->hdr, args->filter_str);
+
+    if (args->record_cmd_line) bcf_hdr_append_version(args->hdr_out, args->argc, args->argv, "bcftools_plugin");
+    if ( !args->drop_header )
+    {
+        char wmode[8];
+        set_wmode(wmode,args->output_type,args->output_fname,args->clevel);
+        args->out_fh = hts_open(args->output_fname ? args->output_fname : "-", wmode);
+        if ( args->out_fh == NULL ) error("Can't write to \"%s\": %s\n", args->output_fname, strerror(errno));
+        if ( args->n_threads ) hts_set_threads(args->out_fh, args->n_threads);
+        if ( bcf_hdr_write(args->out_fh, args->hdr_out)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->output_fname);
+    }
+}
+
+static void destroy_data(args_t *args)
+{
+    free(args->plugin.name);
+    if ( args->plugin.destroy ) args->plugin.destroy();
+#ifdef _WIN32
+    FreeLibrary(args->plugin.handle);
+#else
+    dlclose(args->plugin.handle);
+#endif
+    if ( args->hdr_out ) bcf_hdr_destroy(args->hdr_out);
+    if ( args->nplugin_paths>0 )
+    {
+        int i;
+        for (i=0; i<args->nplugin_paths; i++) free(args->plugin_paths[i]);
+        free(args->plugin_paths);
+    }
+    if ( args->filter )
+        filter_destroy(args->filter);
+    if (args->out_fh && hts_close(args->out_fh)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,args->output_fname);
+}
+
+static void usage(args_t *args)
+{
+    fprintf(stderr, "\n");
+    fprintf(stderr, "About:   Run user defined plugin\n");
+    fprintf(stderr, "Usage:   bcftools plugin <name> [OPTIONS] <file> [-- PLUGIN_OPTIONS]\n");
+    fprintf(stderr, "         bcftools +name [OPTIONS] <file>  [-- PLUGIN_OPTIONS]\n");
+    fprintf(stderr, "\n");
+    fprintf(stderr, "VCF input options:\n");
+    fprintf(stderr, "   -e, --exclude EXPR             Exclude sites for which the expression is true\n");
+    fprintf(stderr, "   -i, --include EXPR             Select sites for which the expression is true\n");
+    fprintf(stderr, "   -r, --regions REGION           Restrict to comma-separated list of regions\n");
+    fprintf(stderr, "   -R, --regions-file FILE        Restrict to regions listed in a file\n");
+    fprintf(stderr, "        --regions-overlap 0|1|2   Include if POS in the region (0), record overlaps (1), variant overlaps (2) [1]\n");
+    fprintf(stderr, "   -t, --targets REGION           Similar to -r but streams rather than index-jumps\n");
+    fprintf(stderr, "   -T, --targets-file FILE        Similar to -R but streams rather than index-jumps\n");
+    fprintf(stderr, "        --targets-overlap 0|1|2   Include if POS in the region (0), record overlaps (1), variant overlaps (2) [0]\n");
+    fprintf(stderr, "VCF output options:\n");
+    fprintf(stderr, "       --no-version               Do not append version and command line to the header\n");
+    fprintf(stderr, "   -o, --output FILE              Write output to a file [standard output]\n");
+    fprintf(stderr, "   -O, --output-type u|b|v|z[0-9] u/b: un/compressed BCF, v/z: un/compressed VCF, 0-9: compression level [v]\n");
+    fprintf(stderr, "       --threads INTT             Use multithreading with <int> worker threads [0]\n");
+    fprintf(stderr, "Plugin options:\n");
+    fprintf(stderr, "   -h, --help                     List plugin's options\n");
+    fprintf(stderr, "   -l, --list-plugins             List available plugins. See BCFTOOLS_PLUGINS environment variable and man page for details\n");
+    fprintf(stderr, "   -v, --verbose                  Print verbose information, -vv increases verbosity\n");
+    fprintf(stderr, "   -V, --version                  Print version string and exit\n");
+    fprintf(stderr, "\n");
+    exit(1);
+}
+
+static int is_verbose(int argc, char *argv[])
+{
+    int c, verbose = 0, opterr_ori = opterr;
+    static struct option loptions[] =
+    {
+        {"verbose",no_argument,NULL,'v'},
+        {NULL,0,NULL,0}
+    };
+    opterr = 0;
+    while ((c = getopt_long(argc, argv, "-v",loptions,NULL)) >= 0)
+    {
+        switch (c) {
+            case 'v': verbose++; break;
+            case 1:
+            default: break;
+        }
+    }
+    opterr = opterr_ori;
+    optind = 0;
+    return verbose;
+}
+int main_plugin(int argc, char *argv[])
+{
+    int c;
+    args_t *args  = (args_t*) calloc(1,sizeof(args_t));
+    args->argc    = argc; args->argv = argv;
+    args->output_fname = "-";
+    args->output_type = FT_VCF;
+    args->n_threads = 0;
+    args->record_cmd_line = 1;
+    args->nplugin_paths = -1;
+    args->clevel = -1;
+    int regions_is_file = 0, targets_is_file = 0, usage_only = 0, version_only = 0;
+    int regions_overlap = 1;
+    int targets_overlap = 0;
+
+    if ( argc==1 ) usage(args);
+    char *plugin_name = NULL;
+    if ( argv[1][0]!='-' )
+    {
+        args->verbose = is_verbose(argc, argv);
+        plugin_name = argv[1]; 
+        argc--; 
+        argv++; 
+        load_plugin(args, plugin_name, 1, &args->plugin);
+        if ( args->plugin.run )
+        {
+            check_version(args);
+            int ret = args->plugin.run(argc, argv);
+            destroy_data(args);
+            free(args);
+            return ret;
+        }
+    }
+
+    static struct option loptions[] =
+    {
+        {"version",no_argument,NULL,'V'},
+        {"verbose",no_argument,NULL,'v'},
+        {"help",no_argument,NULL,'h'},
+        {"list-plugins",no_argument,NULL,'l'},
+        {"output",required_argument,NULL,'o'},
+        {"output-type",required_argument,NULL,'O'},
+        {"threads",required_argument,NULL,9},
+        {"include",required_argument,NULL,'i'},
+        {"exclude",required_argument,NULL,'e'},
+        {"regions",required_argument,NULL,'r'},
+        {"regions-file",required_argument,NULL,'R'},
+        {"regions-overlap",required_argument,NULL,1},
+        {"targets",required_argument,NULL,'t'},
+        {"targets-file",required_argument,NULL,'T'},
+        {"targets-overlap",required_argument,NULL,2},
+        {"no-version",no_argument,NULL,8},
+        {NULL,0,NULL,0}
+    };
+    char *tmp;
+    while ((c = getopt_long(argc, argv, "h?o:O:r:R:t:T:li:e:vV",loptions,NULL)) >= 0)
+    {
+        switch (c) {
+            case 'V': version_only = 1; break;
+            case 'v': args->verbose++; break;
+            case 'o': args->output_fname = optarg; break;
+            case 'O':
+                switch (optarg[0]) {
+                    case 'b': args->output_type = FT_BCF_GZ; break;
+                    case 'u': args->output_type = FT_BCF; break;
+                    case 'z': args->output_type = FT_VCF_GZ; break;
+                    case 'v': args->output_type = FT_VCF; break;
+                    default:
+                    {
+                        args->clevel = strtol(optarg,&tmp,10);
+                        if ( *tmp || args->clevel<0 || args->clevel>9 ) error("The output type \"%s\" not recognised\n", optarg);
+                    }
+                };
+                if ( optarg[1] )
+                {
+                    args->clevel = strtol(optarg+1,&tmp,10);
+                    if ( *tmp || args->clevel<0 || args->clevel>9 ) error("Could not parse argument: --compression-level %s\n", optarg+1);
+                }
+                break;
+            case 'e':
+                if ( args->filter_str ) error("Error: only one -i or -e expression can be given, and they cannot be combined\n");
+                args->filter_str = optarg; args->filter_logic |= FLT_EXCLUDE; break;
+            case 'i':
+                if ( args->filter_str ) error("Error: only one -i or -e expression can be given, and they cannot be combined\n");
+                args->filter_str = optarg; args->filter_logic |= FLT_INCLUDE; break;
+            case 'r': args->regions_list = optarg; break;
+            case 'R': args->regions_list = optarg; regions_is_file = 1; break;
+            case 't': args->targets_list = optarg; break;
+            case 'T': args->targets_list = optarg; targets_is_file = 1; break;
+            case 'l': args->plist_only = 1; break;
+            case  1 :
+                regions_overlap = parse_overlap_option(optarg);
+                if ( regions_overlap < 0 ) error("Could not parse: --regions-overlap %s\n",optarg);
+                break;
+            case  2 :
+                targets_overlap = parse_overlap_option(optarg);
+                if ( targets_overlap < 0 ) error("Could not parse: --targets-overlap %s\n",optarg);
+                break;
+            case  9 : args->n_threads = strtol(optarg, 0, 0); break;
+            case  8 : args->record_cmd_line = 0; break;
+            case '?':
+            case 'h': usage_only = 1; break;
+            default: error("Unknown argument: %s\n", optarg);
+        }
+    }
+    if ( args->plist_only )  return list_plugins(args);
+    if ( !plugin_name ) usage(args);
+
+    if ( version_only )
+    {
+        const char *bver, *hver;
+        args->plugin.version(&bver, &hver);
+        printf("bcftools  %s using htslib %s\n", bcftools_version(), hts_version());
+        printf("plugin at %s using htslib %s\n\n", bver, hver);
+        return 0;
+    }
+
+    if ( usage_only )
+    {
+        if ( args->plugin.usage )
+            fprintf(stderr,"%s",args->plugin.usage());
+        else
+            fprintf(stderr,"Usage: bcftools +%s [General Options] -- [Plugin Options]\n",plugin_name);
+        return 0;
+    }
+
+    char *fname = NULL;
+    if ( optind>=argc || (argv[optind][0]=='-' && argv[optind][1]) )
+    {
+        args->plugin.argc = argc - optind + 1;
+        args->plugin.argv = argv + optind - 1;
+
+        if ( !isatty(fileno((FILE *)stdin)) ) fname = "-";  // reading from stdin
+        else if ( optind>=argc ) usage(args);
+        else
+        {
+            optind = 1;
+            init_plugin(args);
+        }
+    }
+    else
+    {
+        fname = argv[optind];
+        args->plugin.argc = argc - optind;
+        args->plugin.argv = argv + optind;
+    }
+    optind = 0;
+
+    args->files = bcf_sr_init();
+    if ( args->regions_list )
+    {
+        bcf_sr_set_opt(args->files,BCF_SR_REGIONS_OVERLAP,regions_overlap);
+        if ( bcf_sr_set_regions(args->files, args->regions_list, regions_is_file)<0 )
+            error("Failed to read the regions: %s\n", args->regions_list);
+    }
+    if ( args->targets_list )
+    {
+        bcf_sr_set_opt(args->files,BCF_SR_TARGETS_OVERLAP,targets_overlap);
+        if ( bcf_sr_set_targets(args->files, args->targets_list, targets_is_file, 0)<0 )
+            error("Failed to read the targets: %s\n", args->targets_list);
+        args->files->collapse |= COLLAPSE_SOME;
+    }
+    if ( !bcf_sr_add_reader(args->files, fname) ) error("Failed to read from %s: %s\n", !strcmp("-",fname)?"standard input":fname,bcf_sr_strerror(args->files->errnum));
+
+    init_data(args);
+    while ( bcf_sr_next_line(args->files) )
+    {
+        bcf1_t *line = bcf_sr_get_line(args->files,0);
+        if ( args->filter )
+        {
+            int pass = filter_test(args->filter, line, NULL);
+            if ( args->filter_logic & FLT_EXCLUDE ) pass = pass ? 0 : 1;
+            if ( !pass ) continue;
+        }
+        line = args->plugin.process(line);
+        if ( line )
+        {
+            if ( line->errcode ) error("[E::main_plugin] Unchecked error (%d), exiting\n",line->errcode);
+            if ( bcf_write1(args->out_fh, args->hdr_out, line)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->output_fname);
+        }
+    }
+    destroy_data(args);
+    bcf_sr_destroy(args->files);
+    free(args);
+    return 0;
+}
+
+#else /* ENABLE_BCF_PLUGINS */
+
+int main_plugin(int argc, char *argv[])
+{
+    fprintf(stderr, "bcftools plugins are disabled.  To use them, you will need to rebuild\n"
+	    "bcftools from the source distribution with plugins enabled.\n");
+    return 1;
+}
+
+#endif /* ENABLE_BCF_PLUGINS */
diff --git a/bcftools/vcfplugin.c.pysam.c b/bcftools/vcfplugin.c.pysam.c
new file mode 100644
index 0000000..b37ac23
--- /dev/null
+++ b/bcftools/vcfplugin.c.pysam.c
@@ -0,0 +1,824 @@
+#include "bcftools.pysam.h"
+
+/*  vcfplugin.c -- plugin modules for operating on VCF/BCF files.
+
+    Copyright (C) 2013-2021 Genome Research Ltd.
+
+    Author: Petr Danecek <pd3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.  */
+
+#include "config.h"
+#include <stdio.h>
+#include <strings.h>
+#include <unistd.h>
+#include <getopt.h>
+#include <ctype.h>
+#include <string.h>
+#include <errno.h>
+#include <sys/stat.h>
+#include <sys/types.h>
+#include <dirent.h>
+#include <math.h>
+#include <htslib/vcf.h>
+#include <htslib/synced_bcf_reader.h>
+#include <htslib/kseq.h>
+#include <htslib/khash_str2int.h>
+#ifdef _WIN32
+#include <windows.h>
+#else
+#include <dlfcn.h>
+#endif
+#include "bcftools.h"
+#include "vcmp.h"
+#include "filter.h"
+
+#ifdef ENABLE_BCF_PLUGINS
+
+typedef struct _plugin_t plugin_t;
+
+/**
+ *   Plugin API:
+ *   ----------
+ *   const char *about(void)
+ *      - short description used by 'bcftools plugin -lv'
+ *
+ *   const char *usage(void)
+ *      - longer description used by 'bcftools +name -h'
+ *
+ *   int run(int argc, char **argv)
+ *      - if implemented, the control is immediately handed over to the plugin,
+ *      none of the init/process/destroy functions is called.  Return 0 on
+ *      success or non-zero value on error.
+ *
+ *   int init(int argc, char **argv, bcf_hdr_t *in_hdr, bcf_hdr_t *out_hdr)
+ *      - called once at startup, allows to initialize local variables.
+ *      Return 1 to suppress normal VCF/BCF header output, -1 on critical
+ *      errors, 0 otherwise.
+ *
+ *   bcf1_t *process(bcf1_t *rec)
+ *      - called for each VCF record, return NULL for no output
+ *
+ *   void destroy(void)
+ *      - called after all lines have been processed to clean up
+ */
+typedef void (*dl_version_f) (const char **, const char **);
+typedef int (*dl_run_f) (int, char **);
+typedef int (*dl_init_f) (int, char **, bcf_hdr_t *, bcf_hdr_t *);
+typedef char* (*dl_about_f) (void);
+typedef char* (*dl_usage_f) (void);
+typedef bcf1_t* (*dl_process_f) (bcf1_t *);
+typedef void (*dl_destroy_f) (void);
+
+struct _plugin_t
+{
+    int argc;
+    char *name, **argv;
+    dl_version_f version;
+    dl_run_f run;
+    dl_init_f init;
+    dl_about_f about;
+    dl_usage_f usage;
+    dl_process_f process;
+    dl_destroy_f destroy;
+    void *handle;
+};
+
+
+struct _args_t;
+
+typedef struct _rm_tag_t
+{
+    char *key;
+    int hdr_id;
+    void (*handler)(struct _args_t *, bcf1_t *, struct _rm_tag_t *);
+}
+rm_tag_t;
+
+typedef struct
+{
+    char **cols;
+    int ncols, mcols;
+    char **als;
+    int nals, mals;
+    kstring_t line;
+    int rid, start, end;
+}
+annot_line_t;
+
+typedef struct _annot_col_t
+{
+    int icol, replace;
+    char *hdr_key;
+    int (*setter)(struct _args_t *, bcf1_t *, struct _annot_col_t *, void*);
+}
+annot_col_t;
+
+// Logic of the filters: include or exclude sites which match the filters?
+#define FLT_INCLUDE 1
+#define FLT_EXCLUDE 2
+
+typedef struct _args_t
+{
+    bcf_srs_t *files;
+    bcf_hdr_t *hdr, *hdr_out;
+    htsFile *out_fh;
+    int output_type, n_threads, clevel;
+
+    filter_t *filter;
+    char *filter_str;
+    int filter_logic;   // include or exclude sites which match the filters? One of FLT_INCLUDE/FLT_EXCLUDE
+
+    plugin_t plugin;
+    int nplugin_paths;
+    char **plugin_paths;
+
+    char **argv, *output_fname, *regions_list, *targets_list;
+    int argc, drop_header, verbose, record_cmd_line, plist_only;
+}
+args_t;
+
+char *msprintf(const char *fmt, ...);
+
+static void add_plugin_paths(args_t *args, const char *path)
+{
+    while (1)
+    {
+        size_t len = strcspn(path, HTS_PATH_SEPARATOR_STR);
+
+        if ( len == 0 )
+        {
+#ifdef PLUGINPATH
+            add_plugin_paths(args, PLUGINPATH);
+#endif
+        }
+        else
+        {
+            char *dir = (char *) malloc(len + 1);
+            strncpy(dir, path, len);
+            dir[len] = '\0';
+
+            struct stat st;
+            if ( stat(dir, &st) == 0 )
+            {
+                args->plugin_paths = (char**) realloc(args->plugin_paths,sizeof(char*)*(args->nplugin_paths+1));
+                args->plugin_paths[args->nplugin_paths] = dir;
+                args->nplugin_paths++;
+                if ( args->verbose > 1 && strcmp(".",dir) ) fprintf(bcftools_stderr, "plugin directory %s .. ok\n", dir);
+            }
+            else
+            {
+                if ( args->verbose > 1 ) fprintf(bcftools_stderr, "plugin directory %s .. %s\n", dir, strerror(errno));
+                free(dir);
+            }
+
+        }
+
+        path += len;
+        if ( *path == HTS_PATH_SEPARATOR_CHAR ) path++;
+        else break;
+    }
+}
+
+static void init_plugin_paths(args_t *args)
+{
+    if ( args->nplugin_paths!=-1 ) return;
+
+    args->nplugin_paths = 0;
+    args->plugin_paths = NULL;
+
+    char *path = getenv("BCFTOOLS_PLUGINS");
+    add_plugin_paths(args, path ? path : "");
+}
+
+static void *dlopen_plugin(args_t *args, const char *fname)
+{
+    init_plugin_paths(args);
+
+    void *handle;
+    char *tmp;
+    int is_absolute_path = 0;
+#ifdef _WIN32
+    // Windows accepts both forward slash (/) and backslash (\) as folder separator
+    // and can have any path prefixed by the drive letter and a colon (:).
+    if ( fname[0]=='/' || fname[0]=='\\') is_absolute_path = 1;
+    else if ( fname[0] && fname[1]==':' && (fname[2]=='/' || fname[2]=='\\') ) is_absolute_path = 1;
+#else
+    if ( fname[0]=='/' ) is_absolute_path = 1;
+#endif
+
+    kstring_t err = {0,0,0};
+    if ( !is_absolute_path )
+    {
+        int i;
+        for (i=0; i<args->nplugin_paths; i++)
+        {
+            tmp = msprintf("%s/%s%s", args->plugin_paths[i], fname, PLUGIN_EXT);
+#ifdef _WIN32
+            handle = LoadLibraryA(tmp);
+#else
+            handle = dlopen(tmp, RTLD_NOW); // valgrind complains about unfreed memory, not our problem though
+#endif
+            if ( !handle )
+#ifdef _WIN32
+                ksprintf(&err,"LoadLibraryA   .. %lu\n", GetLastError());
+#else
+                ksprintf(&err,"%s:\n\tdlopen   .. %s\n", tmp,dlerror());
+#endif
+            else if ( args->verbose > 1 )
+                fprintf(bcftools_stderr,"%s:\n\tplugin open   .. ok\n", tmp);
+            free(tmp);
+            if ( handle ) return handle;
+        }
+    }
+
+#ifdef _WIN32
+    handle = LoadLibraryA(fname);
+#else
+    handle = dlopen(fname, RTLD_NOW);
+#endif
+    if ( !handle )
+#ifdef _WIN32
+        ksprintf(&err,"LoadLibraryA   .. %lu\n", GetLastError());
+#else
+        ksprintf(&err,"%s:\n\tdlopen   .. %s\n", fname,dlerror());
+#endif
+    else if ( args->verbose > 1 )
+        fprintf(bcftools_stderr,"%s:\n\tplugin open   .. ok\n", fname);
+
+    if ( !handle && (!args->plist_only || args->verbose>1) )
+        fprintf(bcftools_stderr,"%s",err.s);
+    free(err.s);
+
+    return handle;
+}
+
+static void print_plugin_usage_hint(const char *name)
+{
+    if ( name )
+        fprintf(bcftools_stderr, "\nThe bcftools plugin \"%s\" was not found or is not functional", name);
+    else
+        fprintf(bcftools_stderr, "\nNo functional bcftools plugins were found");
+    if ( !getenv("BCFTOOLS_PLUGINS") )
+    {
+        fprintf(bcftools_stderr,". The environment variable BCFTOOLS_PLUGINS is not set");
+#ifdef PLUGINPATH
+        fprintf(bcftools_stderr,"\nand no usable plugins were found in %s", PLUGINPATH);
+#endif
+        fprintf(bcftools_stderr,".\n\n");
+    }
+    else
+    {
+        fprintf(bcftools_stderr,
+                " in\n\tBCFTOOLS_PLUGINS=\"%s\".\n\n"
+                "- Is the plugin path correct?\n\n"
+                "- Run \"bcftools plugin -l\" or \"bcftools plugin -lvv\" for a list of available plugins.\n"
+                "\n",
+                getenv("BCFTOOLS_PLUGINS")
+               );
+    }
+}
+
+static int load_plugin(args_t *args, const char *fname, int exit_on_error, plugin_t *plugin)
+{
+    plugin->name = strdup(fname);
+
+    plugin->handle = dlopen_plugin(args, fname);
+    if ( !plugin->handle )
+    {
+        if ( exit_on_error )
+        {
+            print_plugin_usage_hint(fname);
+            error("Could not load \"%s\".\n\n", fname);
+        }
+        return -1;
+    }
+
+#ifdef _WIN32
+    plugin->init = (dl_init_f) GetProcAddress(plugin->handle, "init");
+    if ( plugin->init && args->verbose > 1 ) fprintf(bcftools_stderr,"\tinit     .. ok\n");
+
+    plugin->run = (dl_run_f) GetProcAddress(plugin->handle, "run");
+    if ( plugin->run && args->verbose > 1 ) fprintf(bcftools_stderr,"\trun     .. ok\n");
+
+    if ( !plugin->init && !plugin->run )
+    {
+        if ( exit_on_error ) error("Could not initialize %s, neither run or init found \n", plugin->name);
+        else if ( args->verbose > 1 ) fprintf(bcftools_stderr,"\tinit/run .. not found\n");
+        return -1;
+    }
+
+    plugin->version = (dl_version_f) GetProcAddress(plugin->handle, "version");
+    if ( !plugin->version )
+    {
+        if ( exit_on_error ) error("Could not initialize %s: version string not found\n", plugin->name);
+        else if ( args->verbose > 1 ) fprintf(bcftools_stderr,"\tversion  .. not found\n");
+        return -1;
+    }
+
+    plugin->about = (dl_about_f) GetProcAddress(plugin->handle, "about");
+    if ( !plugin->about )
+    {
+        if ( exit_on_error ) error("Could not initialize %s: about string not found\n", plugin->name);
+        return -1;
+    }
+
+    plugin->usage = (dl_about_f) GetProcAddress(plugin->handle, "usage");
+    if ( !plugin->usage )
+        plugin->usage = plugin->about;
+
+    if ( plugin->run ) return 0;
+
+    plugin->process = (dl_process_f) GetProcAddress(plugin->handle, "process");
+    if ( !plugin->process )
+    {
+        if ( exit_on_error ) error("Could not initialize %s: process method not found\n", plugin->name);
+        return -1;
+    }
+
+    plugin->destroy = (dl_destroy_f) GetProcAddress(plugin->handle, "destroy");
+    if ( !plugin->destroy )
+    {
+        if ( exit_on_error ) error("Could not initialize %s: destroy method not found\n", plugin->name);
+        return -1;
+    }
+#else
+    dlerror();
+    plugin->init = (dl_init_f) dlsym(plugin->handle, "init");
+    char *ret = dlerror();
+    if ( ret )
+        plugin->init = NULL;
+    else
+        if ( args->verbose > 1 ) fprintf(bcftools_stderr,"\tinit     .. ok\n");
+
+    plugin->run = (dl_run_f) dlsym(plugin->handle, "run");
+    ret = dlerror();
+    if ( ret )
+        plugin->run = NULL;
+    else
+        if ( args->verbose > 1 ) fprintf(bcftools_stderr,"\trun      .. ok\n");
+
+    if ( !plugin->init && !plugin->run )
+    {
+        if ( exit_on_error ) error("Could not initialize %s, neither run or init found \n", plugin->name);
+        else if ( args->verbose > 1 ) fprintf(bcftools_stderr,"\tinit/run .. not found\n");
+        return -1;
+    }
+
+    plugin->version = (dl_version_f) dlsym(plugin->handle, "version");
+    ret = dlerror();
+    if ( ret )
+    {
+        if ( exit_on_error ) error("Could not initialize %s, version string not found\n", plugin->name);
+        else if ( args->verbose > 1 ) fprintf(bcftools_stderr,"\tversion  .. not found\n");
+        return -1;
+    }
+
+    plugin->about = (dl_about_f) dlsym(plugin->handle, "about");
+    ret = dlerror();
+    if ( ret )
+    {
+        if ( exit_on_error ) error("Could not initialize %s: %s\n", plugin->name, ret);
+        return -1;
+    }
+
+    plugin->usage = (dl_about_f) dlsym(plugin->handle, "usage");
+    ret = dlerror();
+    if ( ret )
+        plugin->usage = plugin->about;
+
+    if ( plugin->run ) return 0;
+
+    plugin->process = (dl_process_f) dlsym(plugin->handle, "process");
+    ret = dlerror();
+    if ( ret )
+    {
+        if ( exit_on_error ) error("Could not initialize %s: %s\n", plugin->name, ret);
+        return -1;
+    }
+
+    plugin->destroy = (dl_destroy_f) dlsym(plugin->handle, "destroy");
+    ret = dlerror();
+    if ( ret )
+    {
+        if ( exit_on_error ) error("Could not initialize %s: %s\n", plugin->name, ret);
+        return -1;
+    }
+#endif
+
+    return 0;
+}
+
+static void check_version(args_t *args)
+{
+    static int warned_bcftools = 0, warned_htslib = 0;
+    const char *bver, *hver;
+    args->plugin.version(&bver, &hver);
+    if ( strcmp(bver,bcftools_version()) && !warned_bcftools )
+    {
+        fprintf(bcftools_stderr,"WARNING: bcftools version mismatch .. bcftools at %s, the plugin \"%s\" at %s\n", bcftools_version(),args->plugin.name,bver);
+        warned_bcftools = 1;
+    }
+    if ( strcmp(hver,hts_version()) && !warned_htslib )
+    {
+        fprintf(bcftools_stderr,"WARNING: htslib version mismatch .. bcftools at %s, the plugin \"%s\" at %s\n", hts_version(),args->plugin.name,hver);
+        warned_htslib = 1;
+    }
+}
+
+static void init_plugin(args_t *args)
+{
+    int ret = args->plugin.init(args->plugin.argc,args->plugin.argv,args->hdr,args->hdr_out);
+    if ( ret<0 ) error("The plugin exited with an error.\n");
+    check_version(args);
+    args->drop_header += ret;
+}
+
+static int cmp_plugin_name(const void *p1, const void *p2)
+{
+    plugin_t *a = (plugin_t*) p1;
+    plugin_t *b = (plugin_t*) p2;
+    return strcmp(a->name,b->name);
+}
+
+// If args=NULL then returns the number of plugins available. Otherwise prints the
+// plugins on bcftools_stdout and returns 0 on success.
+static int list_plugins(args_t *args)
+{
+    plugin_t *plugins = NULL;
+    int nplugins = 0, mplugins = 0;
+
+    int count_only = 0;
+    args_t _args;
+    if ( !args )
+    {
+        memset(&_args,0,sizeof(_args));
+        args = &_args;
+        args->nplugin_paths = -1;
+        count_only = 1;
+    }
+    init_plugin_paths(args);
+
+    kstring_t str = {0,0,0};
+    int plugin_ext_len = strlen(PLUGIN_EXT);
+    int i;
+    for (i=0; i<args->nplugin_paths; i++)
+    {
+        DIR *dp = opendir(args->plugin_paths[i]);
+        if ( dp==NULL ) continue;
+
+        struct dirent *ep;
+        while ( (ep=readdir(dp)) )
+        {
+            int len = strlen(ep->d_name);
+            if ( strcasecmp(PLUGIN_EXT,ep->d_name+len-plugin_ext_len) ) continue;
+            str.l = 0;
+            ksprintf(&str,"%s/%s", args->plugin_paths[i],ep->d_name);
+            hts_expand(plugin_t, nplugins+1, mplugins, plugins);
+            if ( load_plugin(args, str.s, 0, &plugins[nplugins]) < 0 ) continue;
+            nplugins++;
+            str.l = 0;
+            kputs(ep->d_name, &str);
+            int l = str.l - 1;
+            while ( l>=0 && str.s[l]!='.' ) l--;
+            if ( l>=0 ) str.s[l] = 0;
+            free(plugins[nplugins-1].name);
+            plugins[nplugins-1].name = strdup(str.s);  // use a short name
+        }
+        closedir(dp);
+    }
+    if ( count_only )
+    {
+        free(str.s);
+        return nplugins;
+    }
+    if ( nplugins )
+    {
+        qsort(plugins, nplugins, sizeof(plugins[0]), cmp_plugin_name);
+
+        for (i=0; i<nplugins; i++)
+        {
+            if ( args->verbose )
+                fprintf(bcftools_stdout, "\n-- %s --\n%s", plugins[i].name, plugins[i].about());
+            else
+                fprintf(bcftools_stdout, "%s\n", plugins[i].name);
+        }
+        if ( args->verbose ) fprintf(bcftools_stdout, "\n");
+    }
+    else
+        print_plugin_usage_hint(NULL);
+    free(str.s);
+    return nplugins ? 0 : 1;
+}
+int count_plugins(void)
+{
+    return list_plugins(NULL);
+}
+
+static void init_data(args_t *args)
+{
+    args->hdr = args->files->readers[0].header;
+    args->hdr_out = bcf_hdr_dup(args->hdr);
+
+    init_plugin(args);
+
+    if ( args->filter_str )
+        args->filter = filter_init(args->hdr, args->filter_str);
+
+    if (args->record_cmd_line) bcf_hdr_append_version(args->hdr_out, args->argc, args->argv, "bcftools_plugin");
+    if ( !args->drop_header )
+    {
+        char wmode[8];
+        set_wmode(wmode,args->output_type,args->output_fname,args->clevel);
+        args->out_fh = hts_open(args->output_fname ? args->output_fname : "-", wmode);
+        if ( args->out_fh == NULL ) error("Can't write to \"%s\": %s\n", args->output_fname, strerror(errno));
+        if ( args->n_threads ) hts_set_threads(args->out_fh, args->n_threads);
+        if ( bcf_hdr_write(args->out_fh, args->hdr_out)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->output_fname);
+    }
+}
+
+static void destroy_data(args_t *args)
+{
+    free(args->plugin.name);
+    if ( args->plugin.destroy ) args->plugin.destroy();
+#ifdef _WIN32
+    FreeLibrary(args->plugin.handle);
+#else
+    dlclose(args->plugin.handle);
+#endif
+    if ( args->hdr_out ) bcf_hdr_destroy(args->hdr_out);
+    if ( args->nplugin_paths>0 )
+    {
+        int i;
+        for (i=0; i<args->nplugin_paths; i++) free(args->plugin_paths[i]);
+        free(args->plugin_paths);
+    }
+    if ( args->filter )
+        filter_destroy(args->filter);
+    if (args->out_fh && hts_close(args->out_fh)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,args->output_fname);
+}
+
+static void usage(args_t *args)
+{
+    fprintf(bcftools_stderr, "\n");
+    fprintf(bcftools_stderr, "About:   Run user defined plugin\n");
+    fprintf(bcftools_stderr, "Usage:   bcftools plugin <name> [OPTIONS] <file> [-- PLUGIN_OPTIONS]\n");
+    fprintf(bcftools_stderr, "         bcftools +name [OPTIONS] <file>  [-- PLUGIN_OPTIONS]\n");
+    fprintf(bcftools_stderr, "\n");
+    fprintf(bcftools_stderr, "VCF input options:\n");
+    fprintf(bcftools_stderr, "   -e, --exclude EXPR             Exclude sites for which the expression is true\n");
+    fprintf(bcftools_stderr, "   -i, --include EXPR             Select sites for which the expression is true\n");
+    fprintf(bcftools_stderr, "   -r, --regions REGION           Restrict to comma-separated list of regions\n");
+    fprintf(bcftools_stderr, "   -R, --regions-file FILE        Restrict to regions listed in a file\n");
+    fprintf(bcftools_stderr, "        --regions-overlap 0|1|2   Include if POS in the region (0), record overlaps (1), variant overlaps (2) [1]\n");
+    fprintf(bcftools_stderr, "   -t, --targets REGION           Similar to -r but streams rather than index-jumps\n");
+    fprintf(bcftools_stderr, "   -T, --targets-file FILE        Similar to -R but streams rather than index-jumps\n");
+    fprintf(bcftools_stderr, "        --targets-overlap 0|1|2   Include if POS in the region (0), record overlaps (1), variant overlaps (2) [0]\n");
+    fprintf(bcftools_stderr, "VCF output options:\n");
+    fprintf(bcftools_stderr, "       --no-version               Do not append version and command line to the header\n");
+    fprintf(bcftools_stderr, "   -o, --output FILE              Write output to a file [standard output]\n");
+    fprintf(bcftools_stderr, "   -O, --output-type u|b|v|z[0-9] u/b: un/compressed BCF, v/z: un/compressed VCF, 0-9: compression level [v]\n");
+    fprintf(bcftools_stderr, "       --threads INTT             Use multithreading with <int> worker threads [0]\n");
+    fprintf(bcftools_stderr, "Plugin options:\n");
+    fprintf(bcftools_stderr, "   -h, --help                     List plugin's options\n");
+    fprintf(bcftools_stderr, "   -l, --list-plugins             List available plugins. See BCFTOOLS_PLUGINS environment variable and man page for details\n");
+    fprintf(bcftools_stderr, "   -v, --verbose                  Print verbose information, -vv increases verbosity\n");
+    fprintf(bcftools_stderr, "   -V, --version                  Print version string and exit\n");
+    fprintf(bcftools_stderr, "\n");
+    bcftools_exit(1);
+}
+
+static int is_verbose(int argc, char *argv[])
+{
+    int c, verbose = 0, opterr_ori = opterr;
+    static struct option loptions[] =
+    {
+        {"verbose",no_argument,NULL,'v'},
+        {NULL,0,NULL,0}
+    };
+    opterr = 0;
+    while ((c = getopt_long(argc, argv, "-v",loptions,NULL)) >= 0)
+    {
+        switch (c) {
+            case 'v': verbose++; break;
+            case 1:
+            default: break;
+        }
+    }
+    opterr = opterr_ori;
+    optind = 0;
+    return verbose;
+}
+int main_plugin(int argc, char *argv[])
+{
+    int c;
+    args_t *args  = (args_t*) calloc(1,sizeof(args_t));
+    args->argc    = argc; args->argv = argv;
+    args->output_fname = "-";
+    args->output_type = FT_VCF;
+    args->n_threads = 0;
+    args->record_cmd_line = 1;
+    args->nplugin_paths = -1;
+    args->clevel = -1;
+    int regions_is_file = 0, targets_is_file = 0, usage_only = 0, version_only = 0;
+    int regions_overlap = 1;
+    int targets_overlap = 0;
+
+    if ( argc==1 ) usage(args);
+    char *plugin_name = NULL;
+    if ( argv[1][0]!='-' )
+    {
+        args->verbose = is_verbose(argc, argv);
+        plugin_name = argv[1]; 
+        argc--; 
+        argv++; 
+        load_plugin(args, plugin_name, 1, &args->plugin);
+        if ( args->plugin.run )
+        {
+            check_version(args);
+            int ret = args->plugin.run(argc, argv);
+            destroy_data(args);
+            free(args);
+            return ret;
+        }
+    }
+
+    static struct option loptions[] =
+    {
+        {"version",no_argument,NULL,'V'},
+        {"verbose",no_argument,NULL,'v'},
+        {"help",no_argument,NULL,'h'},
+        {"list-plugins",no_argument,NULL,'l'},
+        {"output",required_argument,NULL,'o'},
+        {"output-type",required_argument,NULL,'O'},
+        {"threads",required_argument,NULL,9},
+        {"include",required_argument,NULL,'i'},
+        {"exclude",required_argument,NULL,'e'},
+        {"regions",required_argument,NULL,'r'},
+        {"regions-file",required_argument,NULL,'R'},
+        {"regions-overlap",required_argument,NULL,1},
+        {"targets",required_argument,NULL,'t'},
+        {"targets-file",required_argument,NULL,'T'},
+        {"targets-overlap",required_argument,NULL,2},
+        {"no-version",no_argument,NULL,8},
+        {NULL,0,NULL,0}
+    };
+    char *tmp;
+    while ((c = getopt_long(argc, argv, "h?o:O:r:R:t:T:li:e:vV",loptions,NULL)) >= 0)
+    {
+        switch (c) {
+            case 'V': version_only = 1; break;
+            case 'v': args->verbose++; break;
+            case 'o': args->output_fname = optarg; break;
+            case 'O':
+                switch (optarg[0]) {
+                    case 'b': args->output_type = FT_BCF_GZ; break;
+                    case 'u': args->output_type = FT_BCF; break;
+                    case 'z': args->output_type = FT_VCF_GZ; break;
+                    case 'v': args->output_type = FT_VCF; break;
+                    default:
+                    {
+                        args->clevel = strtol(optarg,&tmp,10);
+                        if ( *tmp || args->clevel<0 || args->clevel>9 ) error("The output type \"%s\" not recognised\n", optarg);
+                    }
+                };
+                if ( optarg[1] )
+                {
+                    args->clevel = strtol(optarg+1,&tmp,10);
+                    if ( *tmp || args->clevel<0 || args->clevel>9 ) error("Could not parse argument: --compression-level %s\n", optarg+1);
+                }
+                break;
+            case 'e':
+                if ( args->filter_str ) error("Error: only one -i or -e expression can be given, and they cannot be combined\n");
+                args->filter_str = optarg; args->filter_logic |= FLT_EXCLUDE; break;
+            case 'i':
+                if ( args->filter_str ) error("Error: only one -i or -e expression can be given, and they cannot be combined\n");
+                args->filter_str = optarg; args->filter_logic |= FLT_INCLUDE; break;
+            case 'r': args->regions_list = optarg; break;
+            case 'R': args->regions_list = optarg; regions_is_file = 1; break;
+            case 't': args->targets_list = optarg; break;
+            case 'T': args->targets_list = optarg; targets_is_file = 1; break;
+            case 'l': args->plist_only = 1; break;
+            case  1 :
+                regions_overlap = parse_overlap_option(optarg);
+                if ( regions_overlap < 0 ) error("Could not parse: --regions-overlap %s\n",optarg);
+                break;
+            case  2 :
+                targets_overlap = parse_overlap_option(optarg);
+                if ( targets_overlap < 0 ) error("Could not parse: --targets-overlap %s\n",optarg);
+                break;
+            case  9 : args->n_threads = strtol(optarg, 0, 0); break;
+            case  8 : args->record_cmd_line = 0; break;
+            case '?':
+            case 'h': usage_only = 1; break;
+            default: error("Unknown argument: %s\n", optarg);
+        }
+    }
+    if ( args->plist_only )  return list_plugins(args);
+    if ( !plugin_name ) usage(args);
+
+    if ( version_only )
+    {
+        const char *bver, *hver;
+        args->plugin.version(&bver, &hver);
+        fprintf(bcftools_stdout, "bcftools  %s using htslib %s\n", bcftools_version(), hts_version());
+        fprintf(bcftools_stdout, "plugin at %s using htslib %s\n\n", bver, hver);
+        return 0;
+    }
+
+    if ( usage_only )
+    {
+        if ( args->plugin.usage )
+            fprintf(bcftools_stderr,"%s",args->plugin.usage());
+        else
+            fprintf(bcftools_stderr,"Usage: bcftools +%s [General Options] -- [Plugin Options]\n",plugin_name);
+        return 0;
+    }
+
+    char *fname = NULL;
+    if ( optind>=argc || (argv[optind][0]=='-' && argv[optind][1]) )
+    {
+        args->plugin.argc = argc - optind + 1;
+        args->plugin.argv = argv + optind - 1;
+
+        if ( !isatty(fileno((FILE *)stdin)) ) fname = "-";  // reading from stdin
+        else if ( optind>=argc ) usage(args);
+        else
+        {
+            optind = 1;
+            init_plugin(args);
+        }
+    }
+    else
+    {
+        fname = argv[optind];
+        args->plugin.argc = argc - optind;
+        args->plugin.argv = argv + optind;
+    }
+    optind = 0;
+
+    args->files = bcf_sr_init();
+    if ( args->regions_list )
+    {
+        bcf_sr_set_opt(args->files,BCF_SR_REGIONS_OVERLAP,regions_overlap);
+        if ( bcf_sr_set_regions(args->files, args->regions_list, regions_is_file)<0 )
+            error("Failed to read the regions: %s\n", args->regions_list);
+    }
+    if ( args->targets_list )
+    {
+        bcf_sr_set_opt(args->files,BCF_SR_TARGETS_OVERLAP,targets_overlap);
+        if ( bcf_sr_set_targets(args->files, args->targets_list, targets_is_file, 0)<0 )
+            error("Failed to read the targets: %s\n", args->targets_list);
+        args->files->collapse |= COLLAPSE_SOME;
+    }
+    if ( !bcf_sr_add_reader(args->files, fname) ) error("Failed to read from %s: %s\n", !strcmp("-",fname)?"standard input":fname,bcf_sr_strerror(args->files->errnum));
+
+    init_data(args);
+    while ( bcf_sr_next_line(args->files) )
+    {
+        bcf1_t *line = bcf_sr_get_line(args->files,0);
+        if ( args->filter )
+        {
+            int pass = filter_test(args->filter, line, NULL);
+            if ( args->filter_logic & FLT_EXCLUDE ) pass = pass ? 0 : 1;
+            if ( !pass ) continue;
+        }
+        line = args->plugin.process(line);
+        if ( line )
+        {
+            if ( line->errcode ) error("[E::main_plugin] Unchecked error (%d), exiting\n",line->errcode);
+            if ( bcf_write1(args->out_fh, args->hdr_out, line)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->output_fname);
+        }
+    }
+    destroy_data(args);
+    bcf_sr_destroy(args->files);
+    free(args);
+    return 0;
+}
+
+#else /* ENABLE_BCF_PLUGINS */
+
+int main_plugin(int argc, char *argv[])
+{
+    fprintf(bcftools_stderr, "bcftools plugins are disabled.  To use them, you will need to rebuild\n"
+	    "bcftools from the source distribution with plugins enabled.\n");
+    return 1;
+}
+
+#endif /* ENABLE_BCF_PLUGINS */
diff --git a/bcftools/vcfquery.c b/bcftools/vcfquery.c
new file mode 100644
index 0000000..70b5f30
--- /dev/null
+++ b/bcftools/vcfquery.c
@@ -0,0 +1,447 @@
+/*  vcfquery.c -- Extracts fields from VCF/BCF file.
+
+    Copyright (C) 2013-2022 Genome Research Ltd.
+
+    Author: Petr Danecek <pd3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.  */
+
+#include <stdio.h>
+#include <unistd.h>
+#include <getopt.h>
+#include <ctype.h>
+#include <string.h>
+#include <errno.h>
+#include <sys/stat.h>
+#include <sys/types.h>
+#include <htslib/vcf.h>
+#include <htslib/synced_bcf_reader.h>
+#include <htslib/khash_str2int.h>
+#include <htslib/vcfutils.h>
+#include "bcftools.h"
+#include "filter.h"
+#include "convert.h"
+#include "smpl_ilist.h"
+
+
+// Logic of the filters: include or exclude sites which match the filters?
+#define FLT_INCLUDE 1
+#define FLT_EXCLUDE 2
+
+typedef struct
+{
+    filter_t *filter;
+    char *filter_str;
+    int filter_logic;   // include or exclude sites which match the filters? One of FLT_INCLUDE/FLT_EXCLUDE
+    uint8_t *smpl_pass;
+    convert_t *convert;
+    bcf_srs_t *files;
+    bcf_hdr_t *header;
+    int sample_is_file;
+    char **argv, *format_str, *sample_list, *targets_list, *regions_list, *vcf_list, *fn_out;
+    int argc, list_columns, print_header, allow_undef_tags, force_samples;
+    FILE *out;
+}
+args_t;
+
+static void destroy_list(char **list, int n)
+{
+    int i;
+    for (i=0; i<n; i++)
+        free(list[i]);
+    free(list);
+}
+
+static void init_data(args_t *args)
+{
+    args->header = args->files->readers[0].header;
+
+    int i, nsamples = 0, *samples = NULL;
+    if ( args->sample_list && strcmp("-",args->sample_list) )
+    {
+        for (i=0; i<args->files->nreaders; i++)
+        {
+            // This tells htslib to subset samples directly when reading. Also the header is modified to
+            // include only the requested samples
+            int ret = bcf_hdr_set_samples(args->files->readers[i].header,args->sample_list,args->sample_is_file);
+            if ( ret<0 ) error("Error parsing the sample list\n");
+            else if ( ret>0 && !args->force_samples )
+                error("Error: sample #%d not found in the header, user --force-samples to proceed anyway\n", ret);
+        }
+
+        int flags = SMPL_REORDER;
+        smpl_ilist_t *ilist = smpl_ilist_init(args->files->readers[0].header, args->sample_list, args->sample_is_file, flags);
+        nsamples = ilist->n;
+        samples = (int*) malloc(sizeof(int)*nsamples);
+        for (i=0; i<ilist->n; i++)
+            samples[i] = ilist->idx[i];
+        smpl_ilist_destroy(ilist);
+    }
+    args->convert = convert_init(args->header, samples, nsamples, args->format_str);
+    convert_set_option(args->convert, subset_samples, &args->smpl_pass);
+    if ( args->allow_undef_tags ) convert_set_option(args->convert, allow_undef_tags, 1);
+    free(samples);
+
+    int max_unpack = convert_max_unpack(args->convert);
+    if ( args->filter_str )
+    {
+        args->filter = filter_init(args->header, args->filter_str);
+        max_unpack |= filter_max_unpack(args->filter);
+    }
+    args->files->max_unpack = max_unpack;
+}
+
+static void destroy_data(args_t *args)
+{
+    convert_destroy(args->convert);
+    if ( args->filter )
+        filter_destroy(args->filter);
+}
+
+static void query_vcf(args_t *args)
+{
+    kstring_t str = {0,0,0};
+
+    if ( args->print_header )
+    {
+        convert_header(args->convert,&str);
+        if ( fwrite(str.s, str.l, 1, args->out)!=1 ) error("[%s] Error: cannot write to %s\n", __func__,args->fn_out?args->fn_out:"standard output");
+    }
+
+    int i,max_convert_unpack = convert_max_unpack(args->convert);
+    while ( bcf_sr_next_line(args->files) )
+    {
+        if ( !bcf_sr_has_line(args->files,0) ) continue;
+        bcf1_t *line = args->files->readers[0].buffer[0];
+        bcf_unpack(line, args->files->max_unpack);
+
+        if ( args->filter )
+        {
+            int pass = filter_test(args->filter, line, (const uint8_t**) &args->smpl_pass);
+            if ( args->filter_logic & FLT_EXCLUDE )
+            {
+                // This code addresses this problem:
+                //  -i can include a site but exclude a sample
+                //  -e exclude a site but include a sample
+
+                if ( pass )
+                {
+                    if ( !args->smpl_pass ) continue;
+                    if ( !(max_convert_unpack & BCF_UN_FMT) ) continue;
+
+                    pass = 0;
+                    for (i=0; i<line->n_sample; i++)
+                    {
+                        if ( args->smpl_pass[i] ) args->smpl_pass[i] = 0;
+                        else { args->smpl_pass[i] = 1; pass = 1; }
+                    }
+                    if ( !pass ) continue;
+                }
+                else if ( args->smpl_pass )
+                    for (i=0; i<line->n_sample; i++) args->smpl_pass[i] = 1;
+            }
+            else if ( !pass ) continue;
+        }
+
+        str.l = 0;
+        convert_line(args->convert, line, &str);
+        if ( str.l && fwrite(str.s, str.l, 1, args->out)!=1 ) error("[%s] Error: cannot write to %s\n", __func__,args->fn_out?args->fn_out:"standard output");
+    }
+    if ( str.m ) free(str.s);
+}
+
+static void list_columns(args_t *args)
+{
+    int negate = 0;
+    int i;
+    bcf_sr_t *reader = &args->files->readers[0];
+    void *has_sample = NULL;
+    if ( args->sample_list )
+    {
+        if ( args->sample_list[0]=='^' ) negate = 1;
+        has_sample = khash_str2int_init();
+        int i, nsmpl;
+        char **smpl = hts_readlist(negate ? args->sample_list+1 : args->sample_list, args->sample_is_file, &nsmpl);
+        if ( !smpl ) error("Error: failed to read %s\n", negate ? args->sample_list+1 : args->sample_list);
+        for (i=0; i<nsmpl; i++)
+        {
+            if ( bcf_hdr_id2int(reader->header,BCF_DT_SAMPLE,smpl[i])<0 && !args->force_samples )
+                error("Error: sample #%d not found in the header, user --force-samples to proceed anyway\n", i+1);
+            khash_str2int_inc(has_sample, smpl[i]);
+        }
+        free(smpl);
+    }
+
+    for (i=0; i<bcf_hdr_nsamples(reader->header); i++)
+    {
+        int skip = 0;
+        if ( negate )
+        {
+            if ( khash_str2int_has_key(has_sample, reader->header->samples[i]) ) skip = 1;
+        }
+        else if ( has_sample && !khash_str2int_has_key(has_sample, reader->header->samples[i]) ) skip = 1;
+        if ( skip ) continue;
+        printf("%s\n", reader->header->samples[i]);
+    }
+
+    if ( has_sample )
+        khash_str2int_destroy_free(has_sample);
+}
+
+static char **copy_header(bcf_hdr_t *hdr, char **src, int nsrc)
+{
+    char **dst = (char**) malloc(sizeof(char*)*nsrc);
+    int i;
+    for (i=0; i<nsrc; i++) dst[i] = strdup(src[i]);
+    return dst;
+}
+static int compare_header(bcf_hdr_t *hdr, char **a, int na, char **b, int nb)
+{
+    if ( na!=nb ) return na-nb;
+    int i;
+    for (i=0; i<na; i++)
+        if ( strcmp(a[i],b[i]) ) return 1;
+    return 0;
+}
+
+
+static void usage(void)
+{
+    fprintf(stderr, "\n");
+    fprintf(stderr, "About:   Extracts fields from VCF/BCF file and prints them in user-defined format\n");
+    fprintf(stderr, "Usage:   bcftools query [options] <A.vcf.gz> [<B.vcf.gz> [...]]\n");
+    fprintf(stderr, "\n");
+    fprintf(stderr, "Options:\n");
+    fprintf(stderr, "    -e, --exclude EXPR                Exclude sites for which the expression is true (see man page for details)\n");
+    fprintf(stderr, "        --force-samples               Only warn about unknown subset samples\n");
+    fprintf(stderr, "    -f, --format STRING               See man page for details\n");
+    fprintf(stderr, "    -H, --print-header                Print header\n");
+    fprintf(stderr, "    -i, --include EXPR                Select sites for which the expression is true (see man page for details)\n");
+    fprintf(stderr, "    -l, --list-samples                Print the list of samples and exit\n");
+    fprintf(stderr, "    -o, --output FILE                 Output file name [stdout]\n");
+    fprintf(stderr, "    -r, --regions REGION              Restrict to comma-separated list of regions\n");
+    fprintf(stderr, "    -R, --regions-file FILE           Restrict to regions listed in a file\n");
+    fprintf(stderr, "        --regions-overlap 0|1|2       Include if POS in the region (0), record overlaps (1), variant overlaps (2) [1]\n");
+    fprintf(stderr, "    -s, --samples LIST                List of samples to include\n");
+    fprintf(stderr, "    -S, --samples-file FILE           File of samples to include\n");
+    fprintf(stderr, "    -t, --targets REGION              Similar to -r but streams rather than index-jumps\n");
+    fprintf(stderr, "    -T, --targets-file FILE           Similar to -R but streams rather than index-jumps\n");
+    fprintf(stderr, "        --targets-overlap 0|1|2       Include if POS in the region (0), record overlaps (1), variant overlaps (2) [0]\n");
+    fprintf(stderr, "    -u, --allow-undef-tags            Print \".\" for undefined tags\n");
+    fprintf(stderr, "    -v, --vcf-list FILE               Process multiple VCFs listed in the file\n");
+    fprintf(stderr, "\n");
+    fprintf(stderr, "Examples:\n");
+    fprintf(stderr, "\tbcftools query -f '%%CHROM\\t%%POS\\t%%REF\\t%%ALT[\\t%%SAMPLE=%%GT]\\n' file.vcf.gz\n");
+    fprintf(stderr, "\n");
+    exit(1);
+}
+
+int main_vcfquery(int argc, char *argv[])
+{
+    int c, collapse = 0;
+    args_t *args = (args_t*) calloc(1,sizeof(args_t));
+    args->argc   = argc; args->argv = argv;
+    int regions_is_file = 0, targets_is_file = 0;
+    int regions_overlap = 1;
+    int targets_overlap = 0;
+
+    static struct option loptions[] =
+    {
+        {"help",0,0,'h'},
+        {"list-samples",0,0,'l'},
+        {"include",1,0,'i'},
+        {"exclude",1,0,'e'},
+        {"format",1,0,'f'},
+        {"force-samples",0,0,3},
+        {"output-file",1,0,'o'},
+        {"output",1,0,'o'},
+        {"regions",1,0,'r'},
+        {"regions-file",1,0,'R'},
+        {"regions-overlap",required_argument,NULL,1},
+        {"targets",1,0,'t'},
+        {"targets-file",1,0,'T'},
+        {"targets-overlap",required_argument,NULL,2},
+        {"annots",1,0,'a'},
+        {"samples",1,0,'s'},
+        {"samples-file",1,0,'S'},
+        {"print-header",0,0,'H'},
+        {"collapse",1,0,'c'},
+        {"vcf-list",1,0,'v'},
+        {"allow-undef-tags",0,0,'u'},
+        {0,0,0,0}
+    };
+    while ((c = getopt_long(argc, argv, "hlr:R:f:a:s:S:Ht:T:c:v:i:e:o:u",loptions,NULL)) >= 0) {
+        switch (c) {
+            case 'o': args->fn_out = optarg; break;
+            case 'f': args->format_str = strdup(optarg); break;
+            case 'H': args->print_header = 1; break;
+            case 'v': args->vcf_list = optarg; break;
+            case 'c': 
+                error("The --collapse option is obsolete, pipe through `bcftools norm -c` instead.\n");
+                break;
+            case 'a':
+                {
+                    kstring_t str = {0,0,0};
+                    kputs("%CHROM\t%POS\t%MASK\t%REF\t%ALT\t%", &str);
+                    char *p = optarg;
+                    while ( *p )
+                    {
+                        if ( *p==',' )
+                            kputs("\t%", &str);
+                        else
+                            kputc(*p, &str);
+                        p++;
+                    }
+                    kputc('\n', &str);
+                    args->format_str = str.s;
+                    break;
+                }
+            case 'e':
+                if ( args->filter_str ) error("Error: only one -i or -e expression can be given, and they cannot be combined\n");
+                args->filter_str = optarg; args->filter_logic |= FLT_EXCLUDE; break;
+            case 'i':
+                if ( args->filter_str ) error("Error: only one -i or -e expression can be given, and they cannot be combined\n");
+                args->filter_str = optarg; args->filter_logic |= FLT_INCLUDE; break;
+            case 'r': args->regions_list = optarg; break;
+            case 'R': args->regions_list = optarg; regions_is_file = 1; break;
+            case 't': args->targets_list = optarg; break;
+            case 'T': args->targets_list = optarg; targets_is_file = 1; break;
+            case 'l': args->list_columns = 1; break;
+            case 'u': args->allow_undef_tags = 1; break;
+            case 's': args->sample_list = optarg; break;
+            case 'S': args->sample_list = optarg; args->sample_is_file = 1; break;
+            case  1 :
+                regions_overlap = parse_overlap_option(optarg);
+                if ( regions_overlap < 0 ) error("Could not parse: --regions-overlap %s\n",optarg);
+                break;
+            case  2 :
+                targets_overlap = parse_overlap_option(optarg);
+                if ( targets_overlap < 0 ) error("Could not parse: --targets-overlap %s\n",optarg);
+                break;
+            case  3 : args->force_samples = 1; break;
+            case 'h':
+            case '?': usage(); break;
+            default: error("Unknown argument: %s\n", optarg);
+        }
+    }
+
+    char *fname = NULL;
+    if ( optind>=argc )
+    {
+        if ( !isatty(fileno((FILE *)stdin)) ) fname = "-";
+    }
+    else fname = argv[optind];
+
+    if ( args->list_columns )
+    {
+        if ( !fname ) error("Missing the VCF file name\n");
+        args->files = bcf_sr_init();
+        if ( !bcf_sr_add_reader(args->files, fname) ) error("Failed to read from %s: %s\n", !strcmp("-",fname)?"standard input":fname,bcf_sr_strerror(args->files->errnum));
+        list_columns(args);
+        bcf_sr_destroy(args->files);
+        free(args);
+        return 0;
+    }
+
+    if ( !args->format_str )
+    {
+        if ( argc==1 && !fname ) usage();
+        error("Error: Missing the --format option\n");
+    }
+    args->out = args->fn_out ? fopen(args->fn_out, "w") : stdout;
+    if ( !args->out ) error("%s: %s\n", args->fn_out,strerror(errno));
+
+    if ( !args->vcf_list )
+    {
+        if ( !fname ) usage();
+        args->files = bcf_sr_init();
+        if ( optind+1 < argc ) args->files->require_index = 1;
+        if ( args->regions_list )
+        {
+            bcf_sr_set_opt(args->files,BCF_SR_REGIONS_OVERLAP,regions_overlap);
+            if ( bcf_sr_set_regions(args->files, args->regions_list, regions_is_file)<0 )
+                error("Failed to read the regions: %s\n", args->regions_list);
+        }
+        if ( args->targets_list )
+        {
+            bcf_sr_set_opt(args->files,BCF_SR_TARGETS_OVERLAP,targets_overlap);
+            if ( bcf_sr_set_targets(args->files, args->targets_list, targets_is_file, 0)<0 )
+                error("Failed to read the targets: %s\n", args->targets_list);
+        }
+        while ( fname )
+        {
+            if ( !bcf_sr_add_reader(args->files, fname) ) error("Failed to read from %s: %s\n", !strcmp("-",fname)?"standard input":fname,bcf_sr_strerror(args->files->errnum));
+            fname = ++optind < argc ? argv[optind] : NULL;
+        }
+        init_data(args);
+        query_vcf(args);
+        free(args->format_str);
+        destroy_data(args);
+        bcf_sr_destroy(args->files);
+        if ( fclose(args->out)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,args->fn_out);
+        free(args);
+        return 0;
+    }
+
+    // multiple VCFs
+    int i, k, nfiles, prev_nsamples = 0;
+    char **fnames, **prev_samples = NULL;
+    fnames = hts_readlist(args->vcf_list, 1, &nfiles);
+    if ( !fnames ) error("Error: failed to read %s\n", args->vcf_list);
+    if ( !nfiles ) error("No files in %s?\n", args->vcf_list);
+    for (i=0; i<nfiles; i++)
+    {
+        args->files = bcf_sr_init();
+        args->files->collapse = collapse;
+        if ( args->regions_list && bcf_sr_set_regions(args->files, args->regions_list, regions_is_file)<0 )
+            error("Failed to read the regions: %s\n", args->regions_list);
+        if ( optind < argc ) args->files->require_index = 1;
+        if ( args->targets_list )
+        {
+            if ( bcf_sr_set_targets(args->files, args->targets_list,targets_is_file, 0)<0 )
+                error("Failed to read the targets: %s\n", args->targets_list);
+        }
+        if ( !bcf_sr_add_reader(args->files, fnames[i]) ) error("Failed to open %s: %s\n", fnames[i],bcf_sr_strerror(args->files->errnum));
+        for (k=optind; k<argc; k++)
+            if ( !bcf_sr_add_reader(args->files, argv[k]) ) error("Failed to open %s: %s\n", argv[k],bcf_sr_strerror(args->files->errnum));
+        init_data(args);
+        if ( i==0 )
+        {
+            prev_samples = copy_header(args->header, args->files->readers[0].header->samples, bcf_hdr_nsamples(args->files->readers[0].header));
+            prev_nsamples = bcf_hdr_nsamples(args->files->readers[0].header);
+        }
+        else
+        {
+            args->print_header = 0;
+            if ( compare_header(args->header, args->files->readers[0].header->samples, bcf_hdr_nsamples(args->files->readers[0].header), prev_samples, prev_nsamples) )
+                error("Different samples in %s and %s\n", fnames[i-1],fnames[i]);
+        }
+        query_vcf(args);
+        destroy_data(args);
+        bcf_sr_destroy(args->files);
+    }
+    if ( fclose(args->out)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,args->fn_out);;
+    destroy_list(fnames, nfiles);
+    destroy_list(prev_samples, prev_nsamples);
+    free(args->format_str);
+    free(args);
+    return 0;
+}
+
+
diff --git a/bcftools/vcfquery.c.pysam.c b/bcftools/vcfquery.c.pysam.c
new file mode 100644
index 0000000..5ffbd64
--- /dev/null
+++ b/bcftools/vcfquery.c.pysam.c
@@ -0,0 +1,449 @@
+#include "bcftools.pysam.h"
+
+/*  vcfquery.c -- Extracts fields from VCF/BCF file.
+
+    Copyright (C) 2013-2022 Genome Research Ltd.
+
+    Author: Petr Danecek <pd3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.  */
+
+#include <stdio.h>
+#include <unistd.h>
+#include <getopt.h>
+#include <ctype.h>
+#include <string.h>
+#include <errno.h>
+#include <sys/stat.h>
+#include <sys/types.h>
+#include <htslib/vcf.h>
+#include <htslib/synced_bcf_reader.h>
+#include <htslib/khash_str2int.h>
+#include <htslib/vcfutils.h>
+#include "bcftools.h"
+#include "filter.h"
+#include "convert.h"
+#include "smpl_ilist.h"
+
+
+// Logic of the filters: include or exclude sites which match the filters?
+#define FLT_INCLUDE 1
+#define FLT_EXCLUDE 2
+
+typedef struct
+{
+    filter_t *filter;
+    char *filter_str;
+    int filter_logic;   // include or exclude sites which match the filters? One of FLT_INCLUDE/FLT_EXCLUDE
+    uint8_t *smpl_pass;
+    convert_t *convert;
+    bcf_srs_t *files;
+    bcf_hdr_t *header;
+    int sample_is_file;
+    char **argv, *format_str, *sample_list, *targets_list, *regions_list, *vcf_list, *fn_out;
+    int argc, list_columns, print_header, allow_undef_tags, force_samples;
+    FILE *out;
+}
+args_t;
+
+static void destroy_list(char **list, int n)
+{
+    int i;
+    for (i=0; i<n; i++)
+        free(list[i]);
+    free(list);
+}
+
+static void init_data(args_t *args)
+{
+    args->header = args->files->readers[0].header;
+
+    int i, nsamples = 0, *samples = NULL;
+    if ( args->sample_list && strcmp("-",args->sample_list) )
+    {
+        for (i=0; i<args->files->nreaders; i++)
+        {
+            // This tells htslib to subset samples directly when reading. Also the header is modified to
+            // include only the requested samples
+            int ret = bcf_hdr_set_samples(args->files->readers[i].header,args->sample_list,args->sample_is_file);
+            if ( ret<0 ) error("Error parsing the sample list\n");
+            else if ( ret>0 && !args->force_samples )
+                error("Error: sample #%d not found in the header, user --force-samples to proceed anyway\n", ret);
+        }
+
+        int flags = SMPL_REORDER;
+        smpl_ilist_t *ilist = smpl_ilist_init(args->files->readers[0].header, args->sample_list, args->sample_is_file, flags);
+        nsamples = ilist->n;
+        samples = (int*) malloc(sizeof(int)*nsamples);
+        for (i=0; i<ilist->n; i++)
+            samples[i] = ilist->idx[i];
+        smpl_ilist_destroy(ilist);
+    }
+    args->convert = convert_init(args->header, samples, nsamples, args->format_str);
+    convert_set_option(args->convert, subset_samples, &args->smpl_pass);
+    if ( args->allow_undef_tags ) convert_set_option(args->convert, allow_undef_tags, 1);
+    free(samples);
+
+    int max_unpack = convert_max_unpack(args->convert);
+    if ( args->filter_str )
+    {
+        args->filter = filter_init(args->header, args->filter_str);
+        max_unpack |= filter_max_unpack(args->filter);
+    }
+    args->files->max_unpack = max_unpack;
+}
+
+static void destroy_data(args_t *args)
+{
+    convert_destroy(args->convert);
+    if ( args->filter )
+        filter_destroy(args->filter);
+}
+
+static void query_vcf(args_t *args)
+{
+    kstring_t str = {0,0,0};
+
+    if ( args->print_header )
+    {
+        convert_header(args->convert,&str);
+        if ( fwrite(str.s, str.l, 1, args->out)!=1 ) error("[%s] Error: cannot write to %s\n", __func__,args->fn_out?args->fn_out:"standard output");
+    }
+
+    int i,max_convert_unpack = convert_max_unpack(args->convert);
+    while ( bcf_sr_next_line(args->files) )
+    {
+        if ( !bcf_sr_has_line(args->files,0) ) continue;
+        bcf1_t *line = args->files->readers[0].buffer[0];
+        bcf_unpack(line, args->files->max_unpack);
+
+        if ( args->filter )
+        {
+            int pass = filter_test(args->filter, line, (const uint8_t**) &args->smpl_pass);
+            if ( args->filter_logic & FLT_EXCLUDE )
+            {
+                // This code addresses this problem:
+                //  -i can include a site but exclude a sample
+                //  -e exclude a site but include a sample
+
+                if ( pass )
+                {
+                    if ( !args->smpl_pass ) continue;
+                    if ( !(max_convert_unpack & BCF_UN_FMT) ) continue;
+
+                    pass = 0;
+                    for (i=0; i<line->n_sample; i++)
+                    {
+                        if ( args->smpl_pass[i] ) args->smpl_pass[i] = 0;
+                        else { args->smpl_pass[i] = 1; pass = 1; }
+                    }
+                    if ( !pass ) continue;
+                }
+                else if ( args->smpl_pass )
+                    for (i=0; i<line->n_sample; i++) args->smpl_pass[i] = 1;
+            }
+            else if ( !pass ) continue;
+        }
+
+        str.l = 0;
+        convert_line(args->convert, line, &str);
+        if ( str.l && fwrite(str.s, str.l, 1, args->out)!=1 ) error("[%s] Error: cannot write to %s\n", __func__,args->fn_out?args->fn_out:"standard output");
+    }
+    if ( str.m ) free(str.s);
+}
+
+static void list_columns(args_t *args)
+{
+    int negate = 0;
+    int i;
+    bcf_sr_t *reader = &args->files->readers[0];
+    void *has_sample = NULL;
+    if ( args->sample_list )
+    {
+        if ( args->sample_list[0]=='^' ) negate = 1;
+        has_sample = khash_str2int_init();
+        int i, nsmpl;
+        char **smpl = hts_readlist(negate ? args->sample_list+1 : args->sample_list, args->sample_is_file, &nsmpl);
+        if ( !smpl ) error("Error: failed to read %s\n", negate ? args->sample_list+1 : args->sample_list);
+        for (i=0; i<nsmpl; i++)
+        {
+            if ( bcf_hdr_id2int(reader->header,BCF_DT_SAMPLE,smpl[i])<0 && !args->force_samples )
+                error("Error: sample #%d not found in the header, user --force-samples to proceed anyway\n", i+1);
+            khash_str2int_inc(has_sample, smpl[i]);
+        }
+        free(smpl);
+    }
+
+    for (i=0; i<bcf_hdr_nsamples(reader->header); i++)
+    {
+        int skip = 0;
+        if ( negate )
+        {
+            if ( khash_str2int_has_key(has_sample, reader->header->samples[i]) ) skip = 1;
+        }
+        else if ( has_sample && !khash_str2int_has_key(has_sample, reader->header->samples[i]) ) skip = 1;
+        if ( skip ) continue;
+        fprintf(bcftools_stdout, "%s\n", reader->header->samples[i]);
+    }
+
+    if ( has_sample )
+        khash_str2int_destroy_free(has_sample);
+}
+
+static char **copy_header(bcf_hdr_t *hdr, char **src, int nsrc)
+{
+    char **dst = (char**) malloc(sizeof(char*)*nsrc);
+    int i;
+    for (i=0; i<nsrc; i++) dst[i] = strdup(src[i]);
+    return dst;
+}
+static int compare_header(bcf_hdr_t *hdr, char **a, int na, char **b, int nb)
+{
+    if ( na!=nb ) return na-nb;
+    int i;
+    for (i=0; i<na; i++)
+        if ( strcmp(a[i],b[i]) ) return 1;
+    return 0;
+}
+
+
+static void usage(void)
+{
+    fprintf(bcftools_stderr, "\n");
+    fprintf(bcftools_stderr, "About:   Extracts fields from VCF/BCF file and prints them in user-defined format\n");
+    fprintf(bcftools_stderr, "Usage:   bcftools query [options] <A.vcf.gz> [<B.vcf.gz> [...]]\n");
+    fprintf(bcftools_stderr, "\n");
+    fprintf(bcftools_stderr, "Options:\n");
+    fprintf(bcftools_stderr, "    -e, --exclude EXPR                Exclude sites for which the expression is true (see man page for details)\n");
+    fprintf(bcftools_stderr, "        --force-samples               Only warn about unknown subset samples\n");
+    fprintf(bcftools_stderr, "    -f, --format STRING               See man page for details\n");
+    fprintf(bcftools_stderr, "    -H, --print-header                Print header\n");
+    fprintf(bcftools_stderr, "    -i, --include EXPR                Select sites for which the expression is true (see man page for details)\n");
+    fprintf(bcftools_stderr, "    -l, --list-samples                Print the list of samples and exit\n");
+    fprintf(bcftools_stderr, "    -o, --output FILE                 Output file name [bcftools_stdout]\n");
+    fprintf(bcftools_stderr, "    -r, --regions REGION              Restrict to comma-separated list of regions\n");
+    fprintf(bcftools_stderr, "    -R, --regions-file FILE           Restrict to regions listed in a file\n");
+    fprintf(bcftools_stderr, "        --regions-overlap 0|1|2       Include if POS in the region (0), record overlaps (1), variant overlaps (2) [1]\n");
+    fprintf(bcftools_stderr, "    -s, --samples LIST                List of samples to include\n");
+    fprintf(bcftools_stderr, "    -S, --samples-file FILE           File of samples to include\n");
+    fprintf(bcftools_stderr, "    -t, --targets REGION              Similar to -r but streams rather than index-jumps\n");
+    fprintf(bcftools_stderr, "    -T, --targets-file FILE           Similar to -R but streams rather than index-jumps\n");
+    fprintf(bcftools_stderr, "        --targets-overlap 0|1|2       Include if POS in the region (0), record overlaps (1), variant overlaps (2) [0]\n");
+    fprintf(bcftools_stderr, "    -u, --allow-undef-tags            Print \".\" for undefined tags\n");
+    fprintf(bcftools_stderr, "    -v, --vcf-list FILE               Process multiple VCFs listed in the file\n");
+    fprintf(bcftools_stderr, "\n");
+    fprintf(bcftools_stderr, "Examples:\n");
+    fprintf(bcftools_stderr, "\tbcftools query -f '%%CHROM\\t%%POS\\t%%REF\\t%%ALT[\\t%%SAMPLE=%%GT]\\n' file.vcf.gz\n");
+    fprintf(bcftools_stderr, "\n");
+    bcftools_exit(1);
+}
+
+int main_vcfquery(int argc, char *argv[])
+{
+    int c, collapse = 0;
+    args_t *args = (args_t*) calloc(1,sizeof(args_t));
+    args->argc   = argc; args->argv = argv;
+    int regions_is_file = 0, targets_is_file = 0;
+    int regions_overlap = 1;
+    int targets_overlap = 0;
+
+    static struct option loptions[] =
+    {
+        {"help",0,0,'h'},
+        {"list-samples",0,0,'l'},
+        {"include",1,0,'i'},
+        {"exclude",1,0,'e'},
+        {"format",1,0,'f'},
+        {"force-samples",0,0,3},
+        {"output-file",1,0,'o'},
+        {"output",1,0,'o'},
+        {"regions",1,0,'r'},
+        {"regions-file",1,0,'R'},
+        {"regions-overlap",required_argument,NULL,1},
+        {"targets",1,0,'t'},
+        {"targets-file",1,0,'T'},
+        {"targets-overlap",required_argument,NULL,2},
+        {"annots",1,0,'a'},
+        {"samples",1,0,'s'},
+        {"samples-file",1,0,'S'},
+        {"print-header",0,0,'H'},
+        {"collapse",1,0,'c'},
+        {"vcf-list",1,0,'v'},
+        {"allow-undef-tags",0,0,'u'},
+        {0,0,0,0}
+    };
+    while ((c = getopt_long(argc, argv, "hlr:R:f:a:s:S:Ht:T:c:v:i:e:o:u",loptions,NULL)) >= 0) {
+        switch (c) {
+            case 'o': args->fn_out = optarg; break;
+            case 'f': args->format_str = strdup(optarg); break;
+            case 'H': args->print_header = 1; break;
+            case 'v': args->vcf_list = optarg; break;
+            case 'c': 
+                error("The --collapse option is obsolete, pipe through `bcftools norm -c` instead.\n");
+                break;
+            case 'a':
+                {
+                    kstring_t str = {0,0,0};
+                    kputs("%CHROM\t%POS\t%MASK\t%REF\t%ALT\t%", &str);
+                    char *p = optarg;
+                    while ( *p )
+                    {
+                        if ( *p==',' )
+                            kputs("\t%", &str);
+                        else
+                            kputc(*p, &str);
+                        p++;
+                    }
+                    kputc('\n', &str);
+                    args->format_str = str.s;
+                    break;
+                }
+            case 'e':
+                if ( args->filter_str ) error("Error: only one -i or -e expression can be given, and they cannot be combined\n");
+                args->filter_str = optarg; args->filter_logic |= FLT_EXCLUDE; break;
+            case 'i':
+                if ( args->filter_str ) error("Error: only one -i or -e expression can be given, and they cannot be combined\n");
+                args->filter_str = optarg; args->filter_logic |= FLT_INCLUDE; break;
+            case 'r': args->regions_list = optarg; break;
+            case 'R': args->regions_list = optarg; regions_is_file = 1; break;
+            case 't': args->targets_list = optarg; break;
+            case 'T': args->targets_list = optarg; targets_is_file = 1; break;
+            case 'l': args->list_columns = 1; break;
+            case 'u': args->allow_undef_tags = 1; break;
+            case 's': args->sample_list = optarg; break;
+            case 'S': args->sample_list = optarg; args->sample_is_file = 1; break;
+            case  1 :
+                regions_overlap = parse_overlap_option(optarg);
+                if ( regions_overlap < 0 ) error("Could not parse: --regions-overlap %s\n",optarg);
+                break;
+            case  2 :
+                targets_overlap = parse_overlap_option(optarg);
+                if ( targets_overlap < 0 ) error("Could not parse: --targets-overlap %s\n",optarg);
+                break;
+            case  3 : args->force_samples = 1; break;
+            case 'h':
+            case '?': usage(); break;
+            default: error("Unknown argument: %s\n", optarg);
+        }
+    }
+
+    char *fname = NULL;
+    if ( optind>=argc )
+    {
+        if ( !isatty(fileno((FILE *)stdin)) ) fname = "-";
+    }
+    else fname = argv[optind];
+
+    if ( args->list_columns )
+    {
+        if ( !fname ) error("Missing the VCF file name\n");
+        args->files = bcf_sr_init();
+        if ( !bcf_sr_add_reader(args->files, fname) ) error("Failed to read from %s: %s\n", !strcmp("-",fname)?"standard input":fname,bcf_sr_strerror(args->files->errnum));
+        list_columns(args);
+        bcf_sr_destroy(args->files);
+        free(args);
+        return 0;
+    }
+
+    if ( !args->format_str )
+    {
+        if ( argc==1 && !fname ) usage();
+        error("Error: Missing the --format option\n");
+    }
+    args->out = args->fn_out ? fopen(args->fn_out, "w") : bcftools_stdout;
+    if ( !args->out ) error("%s: %s\n", args->fn_out,strerror(errno));
+
+    if ( !args->vcf_list )
+    {
+        if ( !fname ) usage();
+        args->files = bcf_sr_init();
+        if ( optind+1 < argc ) args->files->require_index = 1;
+        if ( args->regions_list )
+        {
+            bcf_sr_set_opt(args->files,BCF_SR_REGIONS_OVERLAP,regions_overlap);
+            if ( bcf_sr_set_regions(args->files, args->regions_list, regions_is_file)<0 )
+                error("Failed to read the regions: %s\n", args->regions_list);
+        }
+        if ( args->targets_list )
+        {
+            bcf_sr_set_opt(args->files,BCF_SR_TARGETS_OVERLAP,targets_overlap);
+            if ( bcf_sr_set_targets(args->files, args->targets_list, targets_is_file, 0)<0 )
+                error("Failed to read the targets: %s\n", args->targets_list);
+        }
+        while ( fname )
+        {
+            if ( !bcf_sr_add_reader(args->files, fname) ) error("Failed to read from %s: %s\n", !strcmp("-",fname)?"standard input":fname,bcf_sr_strerror(args->files->errnum));
+            fname = ++optind < argc ? argv[optind] : NULL;
+        }
+        init_data(args);
+        query_vcf(args);
+        free(args->format_str);
+        destroy_data(args);
+        bcf_sr_destroy(args->files);
+        if ( fclose(args->out)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,args->fn_out);
+        free(args);
+        return 0;
+    }
+
+    // multiple VCFs
+    int i, k, nfiles, prev_nsamples = 0;
+    char **fnames, **prev_samples = NULL;
+    fnames = hts_readlist(args->vcf_list, 1, &nfiles);
+    if ( !fnames ) error("Error: failed to read %s\n", args->vcf_list);
+    if ( !nfiles ) error("No files in %s?\n", args->vcf_list);
+    for (i=0; i<nfiles; i++)
+    {
+        args->files = bcf_sr_init();
+        args->files->collapse = collapse;
+        if ( args->regions_list && bcf_sr_set_regions(args->files, args->regions_list, regions_is_file)<0 )
+            error("Failed to read the regions: %s\n", args->regions_list);
+        if ( optind < argc ) args->files->require_index = 1;
+        if ( args->targets_list )
+        {
+            if ( bcf_sr_set_targets(args->files, args->targets_list,targets_is_file, 0)<0 )
+                error("Failed to read the targets: %s\n", args->targets_list);
+        }
+        if ( !bcf_sr_add_reader(args->files, fnames[i]) ) error("Failed to open %s: %s\n", fnames[i],bcf_sr_strerror(args->files->errnum));
+        for (k=optind; k<argc; k++)
+            if ( !bcf_sr_add_reader(args->files, argv[k]) ) error("Failed to open %s: %s\n", argv[k],bcf_sr_strerror(args->files->errnum));
+        init_data(args);
+        if ( i==0 )
+        {
+            prev_samples = copy_header(args->header, args->files->readers[0].header->samples, bcf_hdr_nsamples(args->files->readers[0].header));
+            prev_nsamples = bcf_hdr_nsamples(args->files->readers[0].header);
+        }
+        else
+        {
+            args->print_header = 0;
+            if ( compare_header(args->header, args->files->readers[0].header->samples, bcf_hdr_nsamples(args->files->readers[0].header), prev_samples, prev_nsamples) )
+                error("Different samples in %s and %s\n", fnames[i-1],fnames[i]);
+        }
+        query_vcf(args);
+        destroy_data(args);
+        bcf_sr_destroy(args->files);
+    }
+    if ( fclose(args->out)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,args->fn_out);;
+    destroy_list(fnames, nfiles);
+    destroy_list(prev_samples, prev_nsamples);
+    free(args->format_str);
+    free(args);
+    return 0;
+}
+
+
diff --git a/bcftools/vcfroh.c b/bcftools/vcfroh.c
new file mode 100644
index 0000000..a0802db
--- /dev/null
+++ b/bcftools/vcfroh.c
@@ -0,0 +1,1301 @@
+/*  vcfroh.c -- HMM model for detecting runs of autozygosity.
+
+    Copyright (C) 2013-2022 Genome Research Ltd.
+
+    Author: Petr Danecek <pd3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.  */
+
+#include <stdio.h>
+#include <unistd.h>
+#include <getopt.h>
+#include <math.h>
+#include <inttypes.h>
+#include <htslib/vcf.h>
+#include <htslib/synced_bcf_reader.h>
+#include <htslib/kstring.h>
+#include <htslib/kseq.h>
+#include <htslib/bgzf.h>
+#include <errno.h>
+#include "bcftools.h"
+#include "HMM.h"
+#include "smpl_ilist.h"
+#include "filter.h"
+
+#define STATE_HW 0        // normal state, follows Hardy-Weinberg allele frequencies
+#define STATE_AZ 1        // autozygous state
+
+#define OUTPUT_ST (1<<1)
+#define OUTPUT_RG (1<<2)
+#define OUTPUT_GZ (1<<3)
+
+// Logic of the filters: include or exclude sites which match the filters?
+#define FLT_INCLUDE 1
+#define FLT_EXCLUDE 2
+
+
+/** Genetic map */
+typedef struct
+{
+    int pos;
+    double rate;
+}
+genmap_t;
+
+/** HMM data for each sample */
+typedef struct
+{
+    double *eprob;      // emission probs [2*nsites,msites]
+    uint32_t *sites;    // positions [nsites,msites]
+    int nsites, msites;
+    int igenmap;        // current position in genmap
+    int nused;          // some stats to detect if things didn't go wrong
+    int nrid, *rid, *rid_off;   // for viterbi training, keep all chromosomes
+    void *snapshot;             // hmm snapshot
+    struct {
+        uint32_t beg,end,nqual;
+        double qual;
+        int rid, state;
+    } rg;
+}
+smpl_t;
+
+typedef struct _args_t
+{
+    bcf_srs_t *files;
+    bcf_hdr_t *hdr;
+    double t2AZ, t2HW;      // P(AZ|HW) and P(HW|AZ) parameters
+    double unseen_PL, dflt_AF;
+
+    char *genmap_fname;
+    genmap_t *genmap;
+    int ngenmap, mgenmap, igenmap;
+    double rec_rate;        // constant recombination rate if > 0
+
+    hmm_t *hmm;
+    double baum_welch_th;
+    int nrids, *rids, *rid_offs;    // multiple chroms with vi_training
+    int nbuf_max, nbuf_olap;
+
+    float *AFs;
+    int32_t *itmp;
+    int mAFs, nitmp, mitmp, pl_hdr_id, gt_hdr_id;
+
+    double pl2p[256], *pdg;
+    int32_t skip_rid, prev_rid, prev_pos;
+
+    int ntot;                   // some stats to detect if things didn't go wrong
+    int nno_af;                 // number of sites rejected because AF could not be determined
+    int nfiltered;              // .. because of filters
+    int nno_alt, nmultiallelic, ndup;
+    smpl_t *smpl;               // HMM data for each sample
+    smpl_ilist_t *af_smpl;      // list of samples to estimate AF from (--estimate-AF)
+    smpl_ilist_t *roh_smpl;     // list of samples to analyze (--samples, --samples-file)
+    char *estimate_AF;          // list of samples for AF estimate and query sample
+    int af_from_PL;             // estimate AF from FMT/PL rather than FMT/GT
+    char **argv, *targets_list, *regions_list, *af_fname, *af_tag, *samples, *buffer_size, *output_fname;
+    int argc, fake_PLs, snps_only, vi_training, samples_is_file, output_type, skip_homref, n_threads;
+    int include_noalt_sites;
+    BGZF *out;
+    kstring_t str;
+
+    int filter_logic;
+    filter_t *filter;
+    char *filter_str;
+}
+args_t;
+
+void set_tprob_genmap(hmm_t *hmm, uint32_t prev_pos, uint32_t pos, void *data, double *tprob);
+void set_tprob_rrate(hmm_t *hmm, uint32_t prev_pos, uint32_t pos, void *data, double *tprob);
+
+void *smalloc(size_t size)
+{
+    void *mem = malloc(size);
+    if ( !mem ) error("malloc: Could not allocate %d bytes\n", (int)size);
+    return mem;
+}
+
+static inline int max255(int i)
+{
+    return i < 256 ? i : 255;
+}
+
+static void init_data(args_t *args)
+{
+    int i;
+
+    args->prev_rid = args->skip_rid = -1;
+    args->hdr = args->files->readers[0].header;
+
+    if ( !bcf_hdr_nsamples(args->hdr) ) error("No samples in the VCF?\n");
+
+    if ( args->filter_str )
+        args->filter = filter_init(args->hdr, args->filter_str);
+
+    if ( !args->fake_PLs )
+    {
+        args->pl_hdr_id = bcf_hdr_id2int(args->hdr, BCF_DT_ID, "PL");
+        if ( !bcf_hdr_idinfo_exists(args->hdr,BCF_HL_FMT,args->pl_hdr_id) )
+            error("Error: The FORMAT/PL tag not found in the header, consider running with -G\n");
+        if ( bcf_hdr_id2type(args->hdr,BCF_HL_FMT,args->pl_hdr_id)!=BCF_HT_INT )
+            error("Error: The FORMAT/PL tag not defined as Integer in the header\n");
+    }
+
+    if ( args->estimate_AF )
+    {
+        if ( !strncmp("GT,",args->estimate_AF,3) ) args->estimate_AF += 3;
+        else if ( !strncmp("PL,",args->estimate_AF,3) ) { args->estimate_AF += 3; args->af_from_PL = 1; }
+        if ( strcmp("-",args->estimate_AF) )
+            args->af_smpl = smpl_ilist_init(args->hdr, args->estimate_AF, 1, SMPL_NONE|SMPL_VERBOSE);
+    }
+
+    if ( args->estimate_AF || args->fake_PLs )
+    {
+        if ( args->af_from_PL )
+        {
+            args->pl_hdr_id = bcf_hdr_id2int(args->hdr, BCF_DT_ID, "PL");
+            if ( !bcf_hdr_idinfo_exists(args->hdr,BCF_HL_FMT,args->pl_hdr_id) )
+                error("Error: The FORMAT/PL tag not found in the header\n");
+        }
+        else
+        {
+            args->gt_hdr_id = bcf_hdr_id2int(args->hdr, BCF_DT_ID, "GT");
+            if ( !bcf_hdr_idinfo_exists(args->hdr,BCF_HL_FMT,args->gt_hdr_id) )
+                error("Error: The FORMAT/GT tag not found in the header\n");
+        }
+    }
+    if ( args->fake_PLs )
+    {
+        args->gt_hdr_id = bcf_hdr_id2int(args->hdr, BCF_DT_ID, "GT");
+        if ( !bcf_hdr_idinfo_exists(args->hdr,BCF_HL_FMT,args->gt_hdr_id) )
+            error("Error: The FORMAT/GT tag not found in the header\n");
+    }
+
+    args->roh_smpl = smpl_ilist_init(args->hdr, args->samples, args->samples_is_file, SMPL_NONE|SMPL_VERBOSE);
+    if ( args->samples )
+    {
+        // we may be able to subset to a few samples, for a text VCF this can be a major speedup
+        if ( (bcf_sr_get_reader(args->files,0))->file->format.format==vcf )
+        {
+            kstring_t str = {0,0,0};
+            smpl_ilist_t *tmp = args->roh_smpl, *rmme = NULL;
+            if ( args->af_smpl )
+            {
+                for (i=0; i<args->roh_smpl->n; i++)
+                {
+                    if ( str.l ) kputc(',', &str);
+                    kputs(args->hdr->samples[args->roh_smpl->idx[i]], &str);
+                }
+                for (i=0; i<args->af_smpl->n; i++)
+                {
+                    kputc(',', &str);
+                    kputs(args->hdr->samples[args->af_smpl->idx[i]], &str);
+                }
+                rmme = tmp = smpl_ilist_init(args->hdr, str.s, 0, SMPL_NONE);
+            }
+            if ( tmp->n < bcf_hdr_nsamples(args->hdr) )
+            {
+                str.l = 0;
+                for (i=0; i<tmp->n; i++)
+                {
+                    if ( str.l ) kputc(',', &str);
+                    kputs(args->hdr->samples[tmp->idx[i]], &str);
+                }
+                int ret = bcf_hdr_set_samples(args->hdr, str.s, 0);
+                if ( ret<0 ) error("Error parsing the list of samples: %s\n", str.s);
+                else if ( ret>0 ) error("The %d-th sample not found in the VCF: %s\n", ret,str.s);
+
+                // update sample ids
+                smpl_ilist_destroy(args->roh_smpl);
+                args->roh_smpl = smpl_ilist_init(args->hdr, args->samples, args->samples_is_file, SMPL_NONE);
+
+                if ( args->af_smpl )
+                {
+                    smpl_ilist_destroy(args->af_smpl);
+                    args->af_smpl = smpl_ilist_init(args->hdr, args->estimate_AF, 1, SMPL_NONE);
+                }
+            }
+            free(str.s);
+            if ( rmme )
+                smpl_ilist_destroy(rmme);
+        }
+    }
+
+    // check whether all samples are in this list. If so, the lookup will not be needed
+    if ( args->af_smpl && args->af_smpl->n == bcf_hdr_nsamples(args->hdr) )
+    {
+        // all samples are in this list
+        smpl_ilist_destroy(args->af_smpl);
+        args->af_smpl = NULL;
+    }
+
+    if ( args->buffer_size )
+    {
+        args->nbuf_olap = -1;
+        char *end;
+        double tmp = strtod(args->buffer_size,&end);
+        if ( *end )
+        {
+            if ( *end!=',') error("Could not parse: --buffer-size %s\n", args->buffer_size);
+            args->nbuf_olap = strtol(end+1,&end,10);
+            if ( *end || args->nbuf_olap<0 ) error("Could not parse: --bufer-size %s\n", args->buffer_size);
+        }
+        if ( tmp<0 )
+            args->nbuf_max = fabs(tmp)*1e6/(4+8*2)/args->roh_smpl->n;
+        else
+            args->nbuf_max = tmp;
+
+        if ( args->nbuf_olap<0 )
+            args->nbuf_olap = args->nbuf_max*0.01;
+    }
+    fprintf(stderr,"Number of target samples: %d\n", args->roh_smpl->n);
+    fprintf(stderr,"Number of --estimate-AF samples: %d\n", args->af_smpl ? args->af_smpl->n : (args->estimate_AF ? bcf_hdr_nsamples(args->hdr) : 0));
+    fprintf(stderr,"Number of sites in the buffer/overlap: ");
+    if ( args->nbuf_max ) fprintf(stderr,"%d/%d\n", args->nbuf_max,args->nbuf_olap);
+    else fprintf(stderr,"unlimited\n");
+
+    args->smpl = (smpl_t*) calloc(args->roh_smpl->n,sizeof(smpl_t));
+
+    for (i=0; i<256; i++) args->pl2p[i] = pow(10., -i/10.);
+
+    // Init transition matrix and HMM
+    double tprob[4];
+    MAT(tprob,2,STATE_HW,STATE_HW) = 1 - args->t2AZ;
+    MAT(tprob,2,STATE_HW,STATE_AZ) = args->t2HW;
+    MAT(tprob,2,STATE_AZ,STATE_HW) = args->t2AZ;
+    MAT(tprob,2,STATE_AZ,STATE_AZ) = 1 - args->t2HW;
+
+    args->hmm = hmm_init(2, tprob, 10000);
+    if ( args->genmap_fname )
+        hmm_set_tprob_func(args->hmm, set_tprob_genmap, args);
+    else if ( args->rec_rate > 0 )
+        hmm_set_tprob_func(args->hmm, set_tprob_rrate, args);
+
+    args->out = bgzf_open(strcmp("stdout",args->output_fname)?args->output_fname:"-", args->output_type&OUTPUT_GZ ? "wg" : "wu");
+    if ( !args->out ) error("Failed to open %s: %s\n", args->output_fname, strerror(errno));
+
+    // print header
+    args->str.l = 0;
+    ksprintf(&args->str, "# This file was produced by: bcftools roh(%s+htslib-%s)\n", bcftools_version(),hts_version());
+    ksprintf(&args->str, "# The command line was:\tbcftools %s", args->argv[0]);
+    for (i=1; i<args->argc; i++)
+        ksprintf(&args->str, " %s",args->argv[i]);
+    ksprintf(&args->str, "\n#\n");
+    if ( args->output_type & OUTPUT_RG )
+    {
+        i = 2;
+        ksprintf(&args->str, "# RG");
+        ksprintf(&args->str, "\t[%d]Sample", i++);
+        ksprintf(&args->str, "\t[%d]Chromosome", i++);
+        ksprintf(&args->str, "\t[%d]Start", i++);
+        ksprintf(&args->str, "\t[%d]End", i++);
+        ksprintf(&args->str, "\t[%d]Length (bp)", i++);
+        ksprintf(&args->str, "\t[%d]Number of markers", i++);
+        ksprintf(&args->str, "\t[%d]Quality (average fwd-bwd phred score)", i++);
+        ksprintf(&args->str, "\n");
+    }
+    if ( args->output_type & OUTPUT_ST )
+    {
+        i = 2;
+        ksprintf(&args->str, "# ST");
+        ksprintf(&args->str, "\t[%d]Sample", i++);
+        ksprintf(&args->str, "\t[%d]Chromosome", i++);
+        ksprintf(&args->str, "\t[%d]Position", i++);
+        ksprintf(&args->str, "\t[%d]State (0:HW, 1:AZ)", i++);
+        ksprintf(&args->str, "\t[%d]Quality (fwd-bwd phred score)", i++);
+        ksprintf(&args->str, "\n");
+    }
+    if ( args->vi_training)
+    {
+        i = 2;
+        ksprintf(&args->str, "# VT, Viterbi Training");
+        ksprintf(&args->str, "\t[%d]Sample", i++);
+        ksprintf(&args->str, "\t[%d]Iteration", i++);
+        ksprintf(&args->str, "\t[%d]dAZ", i++);
+        ksprintf(&args->str, "\t[%d]dHW", i++);
+        ksprintf(&args->str, "\t[%d]1 - P(HW|HW)", i++);
+        ksprintf(&args->str, "\t[%d]P(AZ|HW)", i++);
+        ksprintf(&args->str, "\t[%d]1 - P(AZ|AZ)", i++);
+        ksprintf(&args->str, "\t[%d]P(HW|AZ)", i++);
+        ksprintf(&args->str, "\n");
+    }
+    if ( bgzf_write(args->out, args->str.s, args->str.l) != args->str.l )
+        error("Error writing %s: %s\n", args->output_fname, strerror(errno));
+}
+
+static void destroy_data(args_t *args)
+{
+    if ( args->filter ) filter_destroy(args->filter);
+    if ( bgzf_close(args->out)!=0 ) error("Error: close failed .. %s\n", args->output_fname);
+    int i;
+    for (i=0; i<args->roh_smpl->n; i++)
+    {
+        free(args->smpl[i].eprob);
+        free(args->smpl[i].sites);
+        free(args->smpl[i].rid);
+        free(args->smpl[i].rid_off);
+        free(args->smpl[i].snapshot);
+    }
+    free(args->str.s);
+    free(args->smpl);
+    if ( args->af_smpl ) smpl_ilist_destroy(args->af_smpl);
+    smpl_ilist_destroy(args->roh_smpl);
+    free(args->rids);
+    free(args->rid_offs);
+    hmm_destroy(args->hmm);
+    bcf_sr_destroy(args->files);
+    free(args->AFs); free(args->pdg);
+    free(args->genmap);
+    free(args->itmp);
+    free(args->samples);
+}
+
+static int load_genmap(args_t *args, const char *chr)
+{
+    if ( !args->genmap_fname ) { args->ngenmap = 0; return 0; }
+
+    kstring_t str = {0,0,0};
+    char *fname = strstr(args->genmap_fname,"{CHROM}");
+    if ( fname )
+    {
+        kputsn(args->genmap_fname, fname - args->genmap_fname, &str);
+        kputs(chr, &str);
+        kputs(fname+7,&str);
+        fname = str.s;
+    }
+    else
+        fname = args->genmap_fname;
+
+    htsFile *fp = hts_open(fname, "rb");
+    if ( !fp )
+    {
+        args->ngenmap = 0;
+        return -1;
+    }
+
+    hts_getline(fp, KS_SEP_LINE, &str);
+    if ( strcmp(str.s,"position COMBINED_rate(cM/Mb) Genetic_Map(cM)") )
+        error("Unexpected header in %s, found:\n\t[%s], but expected:\n\t[position COMBINED_rate(cM/Mb) Genetic_Map(cM)]\n", fname, str.s);
+
+    args->ngenmap = args->igenmap = 0;
+    while ( hts_getline(fp, KS_SEP_LINE, &str) > 0 )
+    {
+        args->ngenmap++;
+        hts_expand(genmap_t,args->ngenmap,args->mgenmap,args->genmap);
+        genmap_t *gm = &args->genmap[args->ngenmap-1];
+
+        // position, convert to 0-based
+        char *tmp, *end;
+        gm->pos = strtol(str.s, &tmp, 10);
+        if ( str.s==tmp ) error("Could not parse %s: %s\n", fname, str.s);
+        gm->pos -= 1;
+
+        // skip second column
+        tmp++;
+        while ( *tmp && !isspace(*tmp) ) tmp++;
+
+        // read the genetic map in cM, scale from % to likelihood
+        gm->rate = strtod(tmp+1, &end);
+        if ( tmp+1==end ) error("Could not parse %s: %s\n", fname, str.s);
+        gm->rate *= 0.01;
+    }
+    if ( !args->ngenmap ) error("Genetic map empty?\n");
+    if ( hts_close(fp) ) error("Close failed\n");
+    free(str.s);
+    return 0;
+}
+
+static double get_genmap_rate(args_t *args, int start, int end)
+{
+    // position i to be equal to or smaller than start
+    int i = args->igenmap;
+    if ( args->genmap[i].pos > start )
+    {
+        while ( i>0 && args->genmap[i].pos > start ) i--;
+    }
+    else
+    {
+        while ( i+1<args->ngenmap && args->genmap[i+1].pos < start ) i++;
+    }
+    // position j to be equal or larger than end
+    int j = i;
+    while ( j+1<args->ngenmap && args->genmap[j].pos < end ) j++;
+    if ( i==j )
+    {
+        args->igenmap = i;
+        return 0;
+    }
+
+    if ( start <  args->genmap[i].pos ) start = args->genmap[i].pos;
+    if ( end >  args->genmap[j].pos ) end = args->genmap[j].pos;
+    double rate = (args->genmap[j].rate - args->genmap[i].rate)/(args->genmap[j].pos - args->genmap[i].pos) * (end-start);
+    args->igenmap = j;
+    return rate;
+}
+
+void set_tprob_genmap(hmm_t *hmm, uint32_t prev_pos, uint32_t pos, void *data, double *tprob)
+{
+    args_t *args = (args_t*) data;
+    double ci = get_genmap_rate(args, prev_pos, pos);
+    if ( args->rec_rate ) ci *= args->rec_rate;
+    if ( ci > 1 ) ci = 1;
+    MAT(tprob,2,STATE_HW,STATE_AZ) *= ci;
+    MAT(tprob,2,STATE_AZ,STATE_HW) *= ci;
+    MAT(tprob,2,STATE_AZ,STATE_AZ)  = 1 - MAT(tprob,2,STATE_HW,STATE_AZ);
+    MAT(tprob,2,STATE_HW,STATE_HW)  = 1 - MAT(tprob,2,STATE_AZ,STATE_HW);
+}
+
+void set_tprob_rrate(hmm_t *hmm, uint32_t prev_pos, uint32_t pos, void *data, double *tprob)
+{
+    args_t *args = (args_t*) data;
+    double ci = (pos - prev_pos) * args->rec_rate;
+    if ( ci > 1 ) ci = 1;
+    MAT(tprob,2,STATE_HW,STATE_AZ) *= ci;
+    MAT(tprob,2,STATE_AZ,STATE_HW) *= ci;
+    MAT(tprob,2,STATE_AZ,STATE_AZ)  = 1 - MAT(tprob,2,STATE_HW,STATE_AZ);
+    MAT(tprob,2,STATE_HW,STATE_HW)  = 1 - MAT(tprob,2,STATE_AZ,STATE_HW);
+}
+
+
+/**
+ *  This function implements the HMM model:
+ *    D = Data, AZ = autozygosity, HW = Hardy-Weinberg (non-autozygosity),
+ *    f = non-ref allele frequency
+ *
+ *  Emission probabilities:
+ *    oAZ = P_i(D|AZ) = (1-f)*P(D|RR) + f*P(D|AA)
+ *    oHW = P_i(D|HW) = (1-f)^2 * P(D|RR) + f^2 * P(D|AA) + 2*f*(1-f)*P(D|RA)
+ *
+ *  Transition probabilities:
+ *    tAZ = P(AZ|HW)  .. parameter
+ *    tHW = P(HW|AZ)  .. parameter
+ *
+ *    ci  = P_i(C)    .. probability of cross-over at site i, from genetic map
+ *
+ *    AZi = P_i(AZ)   .. probability of site i being AZ/non-AZ, scaled so that AZi+HWi = 1
+ *    HWi = P_i(HW)
+ *
+ *    P_i(AZ|HW) = P(AZ|HW) * ci * HW{i-1}     = tAZ * ci * (1 - AZ{i-1})
+ *    P_i(HW|AZ) = P(HW|AZ) * ci * AZ{i-1}     = tHW * ci * AZ{i-1}
+ *    P_i(AZ|AZ) = 1 - P_i(HW|AZ)
+ *    P_i(HW|HW) = 1 - P_i(AZ|HW)
+ *
+ */
+
+static void flush_viterbi(args_t *args, int ismpl)
+{
+    smpl_t *smpl = &args->smpl[ismpl];
+    if ( !smpl->nsites ) return;
+
+    const char *name = args->hdr->samples[ args->roh_smpl->idx[ismpl] ];
+
+    int i,j,k;
+
+    if ( !args->vi_training ) // single viterbi pass
+    {
+        hmm_restore(args->hmm, smpl->snapshot);
+        int end = (args->nbuf_max && smpl->nsites >= args->nbuf_max && smpl->nsites > args->nbuf_olap) ? smpl->nsites - args->nbuf_olap : smpl->nsites;
+        if ( end < smpl->nsites )
+            smpl->snapshot = hmm_snapshot(args->hmm, smpl->snapshot, smpl->sites[smpl->nsites - args->nbuf_olap - 1]);
+
+        args->igenmap = smpl->igenmap;
+        hmm_run_viterbi(args->hmm, smpl->nsites, smpl->eprob, smpl->sites);
+        hmm_run_fwd_bwd(args->hmm, smpl->nsites, smpl->eprob, smpl->sites);
+        double *fwd = hmm_get_fwd_bwd_prob(args->hmm);
+
+        const char *chr  = bcf_hdr_id2name(args->hdr,args->prev_rid);
+        uint8_t *vpath   = hmm_get_viterbi_path(args->hmm);
+
+        for (i=0; i<end; i++)
+        {
+            int state = vpath[i*2]==STATE_AZ ? 1 : 0;
+            double qual = phred_score(1.0 - fwd[i*2 + state]);
+            if ( args->output_type & OUTPUT_ST )
+            {
+                args->str.l = 0;
+                ksprintf(&args->str, "ST\t%s\t%s\t%d\t%d\t%.1f\n", name,chr,smpl->sites[i]+1, state, qual);
+                if ( bgzf_write(args->out, args->str.s, args->str.l) != args->str.l ) error("Error writing %s: %s\n", args->output_fname, strerror(errno));
+            }
+
+            if ( args->output_type & OUTPUT_RG )
+            {
+                if ( state!=smpl->rg.state )
+                {
+                    if ( !state )   // the region ends, flush
+                    {
+                        args->str.l = 0;
+                        ksprintf(&args->str, "RG\t%s\t%s\t%d\t%d\t%d\t%d\t%.1f\n",name,bcf_hdr_id2name(args->hdr,smpl->rg.rid),
+                                smpl->rg.beg+1,smpl->rg.end+1,smpl->rg.end-smpl->rg.beg+1,smpl->rg.nqual,smpl->rg.qual/smpl->rg.nqual);
+                        if ( bgzf_write(args->out, args->str.s, args->str.l) != args->str.l ) error("Error writing %s: %s\n", args->output_fname, strerror(errno));
+                        smpl->rg.state = 0;
+                    }
+                    else
+                    {
+                        smpl->rg.state = 1;
+                        smpl->rg.beg = smpl->sites[i];
+                        smpl->rg.end = smpl->sites[i];
+                        smpl->rg.rid = args->prev_rid;
+                        smpl->rg.qual  = qual;
+                        smpl->rg.nqual = 1;
+                    }
+                }
+                else if ( state )
+                {
+                    smpl->rg.nqual++;
+                    smpl->rg.qual += qual;
+                    smpl->rg.end  = smpl->sites[i];
+                }
+            }
+        }
+
+        if ( end < smpl->nsites )
+        {
+            end = smpl->nsites - args->nbuf_olap;
+            memmove(smpl->sites, smpl->sites + end, sizeof(*smpl->sites)*args->nbuf_olap);
+            memmove(smpl->eprob, smpl->eprob + end*2, sizeof(*smpl->eprob)*args->nbuf_olap*2);
+            smpl->nsites  = args->nbuf_olap;
+            smpl->igenmap = args->igenmap;
+        }
+        else
+        {
+            smpl->nsites  = 0;
+            smpl->igenmap = 0;
+
+            if ( smpl->rg.state )
+            {
+                args->str.l = 0;
+                ksprintf(&args->str, "RG\t%s\t%s\t%d\t%d\t%d\t%d\t%.1f\n",name,bcf_hdr_id2name(args->hdr,smpl->rg.rid),
+                        smpl->rg.beg+1,smpl->rg.end+1,smpl->rg.end-smpl->rg.beg+1,smpl->rg.nqual,smpl->rg.qual/smpl->rg.nqual);
+                if ( bgzf_write(args->out, args->str.s, args->str.l) != args->str.l ) error("Error writing %s: %s\n", args->output_fname, strerror(errno));
+                smpl->rg.state = 0;
+            }
+        }
+
+        return;
+    }
+
+
+    // viterbi training, multiple chromosomes
+    double t2az_prev, t2hw_prev;
+    double deltaz, delthw;
+
+    double *tprob_arr = hmm_get_tprob(args->hmm);
+    MAT(tprob_arr,2,STATE_HW,STATE_HW) = 1 - args->t2AZ;
+    MAT(tprob_arr,2,STATE_HW,STATE_AZ) = args->t2HW;
+    MAT(tprob_arr,2,STATE_AZ,STATE_HW) = args->t2AZ;
+    MAT(tprob_arr,2,STATE_AZ,STATE_AZ) = 1 - args->t2HW;
+    hmm_set_tprob(args->hmm, tprob_arr, 10000);
+
+    int niter = 0;
+    do
+    {
+        tprob_arr = hmm_get_tprob(args->hmm);
+        t2az_prev = MAT(tprob_arr,2,STATE_AZ,STATE_HW); //args->t2AZ;
+        t2hw_prev = MAT(tprob_arr,2,STATE_HW,STATE_AZ); //args->t2HW;
+        double tprob_new[] = { 0,0,0,0 };
+        for (i=0; i<smpl->nrid; i++)
+        {
+            int ioff = smpl->rid_off[i];
+            int nsites = (i+1==smpl->nrid ? smpl->nsites : smpl->rid_off[i+1]) - ioff;
+            args->igenmap = 0;
+            tprob_arr = hmm_run_baum_welch(args->hmm, nsites, smpl->eprob+ioff*2, smpl->sites+ioff);
+            for (j=0; j<2; j++)
+                for (k=0; k<2; k++) MAT(tprob_new,2,j,k) += MAT(tprob_arr,2,j,k);
+        }
+        for (j=0; j<2; j++)
+            for (k=0; k<2; k++) MAT(tprob_new,2,j,k) /= smpl->nrid;
+
+        hmm_set_tprob(args->hmm, tprob_new, 10000);
+
+        deltaz = fabs(MAT(tprob_new,2,STATE_AZ,STATE_HW)-t2az_prev);
+        delthw = fabs(MAT(tprob_new,2,STATE_HW,STATE_AZ)-t2hw_prev);
+        niter++;
+        args->str.l = 0;
+        ksprintf(&args->str, "VT\t%s\t%d\t%e\t%e\t%e\t%e\t%e\t%e\n",
+            name,niter,deltaz,delthw,
+            1-MAT(tprob_new,2,STATE_HW,STATE_HW),MAT(tprob_new,2,STATE_AZ,STATE_HW),
+            1-MAT(tprob_new,2,STATE_AZ,STATE_AZ),MAT(tprob_new,2,STATE_HW,STATE_AZ));
+        if ( bgzf_write(args->out, args->str.s, args->str.l) != args->str.l ) error("Error writing %s: %s\n", args->output_fname, strerror(errno));
+    }
+    while ( deltaz > args->baum_welch_th || delthw > args->baum_welch_th );
+
+    // output the results
+    for (i=0; i<smpl->nrid; i++)
+    {
+        int ioff = smpl->rid_off[i];
+        int nsites = (i+1==smpl->nrid ? smpl->nsites : smpl->rid_off[i+1]) - ioff;
+        args->igenmap = 0;
+        hmm_run_viterbi(args->hmm, nsites, smpl->eprob+ioff*2, smpl->sites+ioff);
+        hmm_run_fwd_bwd(args->hmm, nsites, smpl->eprob+ioff*2, smpl->sites+ioff);
+        uint8_t *vpath = hmm_get_viterbi_path(args->hmm);
+        double  *fwd   = hmm_get_fwd_bwd_prob(args->hmm);
+
+        const char *chr = bcf_hdr_id2name(args->hdr,smpl->rid[i]);
+        for (j=0; j<nsites; j++)
+        {
+            int state = vpath[j*2]==STATE_AZ ? 1 : 0;
+            double *pval = fwd + j*2;
+            args->str.l = 0;
+            ksprintf(&args->str, "ROH\t%s\t%s\t%d\t%d\t%.1f\n", name,chr,smpl->sites[ioff+j]+1, state, phred_score(1.0-pval[state]));
+            if ( bgzf_write(args->out, args->str.s, args->str.l) != args->str.l ) error("Error writing %s: %s\n", args->output_fname, strerror(errno));
+        }
+    }
+}
+
+int read_AF(bcf_sr_regions_t *tgt, bcf1_t *line, double *alt_freq)
+{
+    if ( tgt->nals < 2 )
+        error("Expected two comma-separated alleles (REF,ALT) in the third column of %s, found:\n\t%s\n", tgt->fname,tgt->line.s);
+    if ( tgt->nals != line->n_allele ) return -1;    // number of alleles does not match
+
+    int i;
+    for (i=0; i<tgt->nals; i++)
+        if ( strcmp(line->d.allele[i],tgt->als[i]) ) break; // we could be smarter, see vcmp
+    if ( i<tgt->nals ) return -1;
+
+    char *tmp, *str = tgt->line.s;
+    i = 0;
+    while ( *str && i<3 )
+    {
+        if ( *str=='\t' ) i++;
+        str++;
+    }
+    *alt_freq = strtod(str, &tmp);
+    if ( *tmp && !isspace(*tmp) )
+    {
+        if ( str[0]=='.' && (!str[1] || isspace(str[1])) ) return -1; // missing value
+        error("Could not parse: [%s]\n", tgt->line.s);
+    }
+    if ( *alt_freq<0 || *alt_freq>1 ) error("Could not parse AF: [%s]\n", tgt->line.s);
+    return 0;
+}
+
+int8_t *get_GT(args_t *args, bcf1_t *line)
+{
+    int i;
+    for (i=0; i<line->n_fmt; i++)
+        if ( line->d.fmt[i].id==args->gt_hdr_id ) break;
+    if ( i==line->n_fmt ) return NULL;        // the tag is not present in this record
+
+    bcf_fmt_t *fmt = &line->d.fmt[i];
+    if ( fmt->n!=2 ) return NULL;             // not diploid
+
+    if ( fmt->type!=BCF_BT_INT8 ) error("This is unexpected, GT type is %d\n", fmt->type);
+    return (int8_t*) fmt->p;
+}
+
+int estimate_AF_from_GT(args_t *args, int8_t *gt, double *alt_freq)
+{
+    int i, nalt = 0, nref = 0;
+    if ( args->af_smpl )        // subset samples for AF estimate
+    {
+        for (i=0; i<args->af_smpl->n; i++)
+        {
+            int ismpl = args->af_smpl->idx[i];
+            if ( bcf_gt_is_missing(gt[2*ismpl]) || bcf_gt_is_missing(gt[2*ismpl+1]) ) continue;
+
+            if ( bcf_gt_allele(gt[2*ismpl]) ) nalt++;
+            else nref++;
+
+            if ( bcf_gt_allele(gt[2*ismpl+1]) ) nalt++;
+            else nref++;
+        }
+    }
+    else                        // all samples used in AF estimate
+    {
+        int8_t *end = gt + 2*bcf_hdr_nsamples(args->hdr);
+        while ( gt < end )
+        {
+            if ( bcf_gt_is_missing(gt[0]) || bcf_gt_is_missing(gt[1]) )
+            {
+                gt += 2;
+                continue;
+            }
+
+            if ( bcf_gt_allele(gt[0]) ) nalt++;
+            else nref++;
+
+            if ( bcf_gt_allele(gt[1]) ) nalt++;
+            else nref++;
+
+            gt += 2;
+        }
+    }
+    if ( !nalt && !nref ) return -1;
+
+    *alt_freq = (double)nalt / (nalt + nref);
+    return 0;
+}
+
+int estimate_AF_from_PL(args_t *args, bcf_fmt_t *fmt_pl, int ial, double *alt_freq)
+{
+    double af = 0;
+    int i, j, naf = 0;
+
+    int irr = bcf_alleles2gt(0,0), ira = bcf_alleles2gt(0,ial), iaa = bcf_alleles2gt(ial,ial);
+    if ( iaa >= fmt_pl->n ) return -1;  // not diploid or wrong number of fields
+
+    if ( args->af_smpl )        // subset samples for AF estimate
+    {
+        #define BRANCH(type_t) \
+        { \
+            for (i=0; i<args->af_smpl->n; i++) \
+            { \
+                int ismpl = args->af_smpl->idx[i]; \
+                type_t *p = (type_t*)fmt_pl->p + fmt_pl->n*ismpl; \
+                if ( p[irr]<0 || p[ira]<0 || p[iaa]<0 ) continue;    /* missing value */ \
+                if ( p[irr]==p[ira] && p[irr]==p[iaa] ) continue;    /* all values are the same */ \
+                double prob[3], norm = 0; \
+                prob[0] = args->pl2p[ max255(p[irr]) ]; \
+                prob[1] = args->pl2p[ max255(p[ira]) ]; \
+                prob[2] = args->pl2p[ max255(p[iaa]) ]; \
+                for (j=0; j<3; j++) norm += prob[j]; \
+                for (j=0; j<3; j++) prob[j] /= norm; \
+                af += 0.5*prob[1] + prob[2]; \
+                naf++; \
+            } \
+        }
+        switch (fmt_pl->type) {
+            case BCF_BT_INT8:  BRANCH(int8_t); break;
+            case BCF_BT_INT16: BRANCH(int16_t); break;
+            case BCF_BT_INT32: BRANCH(int32_t); break;
+            default: fprintf(stderr,"Unknown format type for PL: %s:%d .. fmt->type=%d\n", __FILE__,__LINE__, fmt_pl->type); exit(1);
+        }
+        #undef BRANCH
+    }
+    else                        // all samples used in AF estimate
+    {
+        int nsmpl = bcf_hdr_nsamples(args->hdr);
+        #define BRANCH(type_t) \
+        { \
+            type_t *p = (type_t*)fmt_pl->p; \
+            p -= fmt_pl->n; \
+            for (i=0; i<nsmpl; i++) \
+            { \
+                p += fmt_pl->n; \
+                if ( p[irr]<0 || p[ira]<0 || p[iaa]<0 ) continue;    /* missing value */ \
+                if ( p[irr]==p[ira] && p[irr]==p[iaa] ) continue;    /* all values are the same */ \
+                double prob[3], norm = 0; \
+                prob[0] = args->pl2p[ max255(p[irr]) ]; \
+                prob[1] = args->pl2p[ max255(p[ira]) ]; \
+                prob[2] = args->pl2p[ max255(p[iaa]) ]; \
+                for (j=0; j<3; j++) norm += prob[j]; \
+                for (j=0; j<3; j++) prob[j] /= norm; \
+                af += 0.5*prob[1] + prob[2]; \
+                naf++; \
+            } \
+        }
+        switch (fmt_pl->type) {
+            case BCF_BT_INT8:  BRANCH(int8_t); break;
+            case BCF_BT_INT16: BRANCH(int16_t); break;
+            case BCF_BT_INT32: BRANCH(int32_t); break;
+            default: fprintf(stderr,"Unknown format type for PL: %s:%d .. fmt->type=%d\n", __FILE__,__LINE__, fmt_pl->type); exit(1);
+        }
+        #undef BRANCH
+    }
+    if ( !naf ) return -1;
+
+    *alt_freq = af / naf;
+    return 0;
+}
+
+bcf_fmt_t *get_PL(args_t *args, bcf1_t *line)
+{
+    int i;
+    for (i=0; i<line->n_fmt; i++)
+        if ( line->d.fmt[i].id==args->pl_hdr_id ) return &line->d.fmt[i];
+    return NULL;
+}
+
+int process_line(args_t *args, bcf1_t *line, int ial)
+{
+    if ( !(line->unpacked & BCF_UN_FMT) ) bcf_unpack(line, BCF_UN_FMT);
+
+    double alt_freq;
+    int8_t *GTs = NULL;
+    bcf_fmt_t *fmt_pl = NULL;
+
+    // Set allele frequency
+    int ret = 0, i,j;
+    if ( args->af_tag )
+    {
+        // Use an INFO tag provided by the user
+        ret = bcf_get_info_float(args->hdr, line, args->af_tag, &args->AFs, &args->mAFs);
+        if ( ret>0 )
+            alt_freq = args->AFs[ial-1];
+        if ( ret==-2 )
+            error("Type mismatch for INFO/%s tag at %s:%"PRId64"\n", args->af_tag, bcf_seqname(args->hdr,line), (int64_t) line->pos+1);
+    }
+    else if ( args->af_fname )
+    {
+        // Read AF from a file
+        ret = read_AF(args->files->targets, line, &alt_freq);
+    }
+    else if ( args->dflt_AF > 0 )
+    {
+        alt_freq = args->dflt_AF;
+    }
+    else if ( args->estimate_AF )
+    {
+        // Estimate AF from GTs or PLs of all samples or samples listed in a file
+        if ( args->af_from_PL )
+        {
+            fmt_pl = get_PL(args, line);
+            if ( !fmt_pl ) return -1;
+            ret = estimate_AF_from_PL(args, fmt_pl, ial, &alt_freq);
+        }
+        else
+        {
+            GTs = get_GT(args, line);
+            if ( !GTs ) return -1;
+            ret = estimate_AF_from_GT(args, GTs, &alt_freq);
+        }
+    }
+    else
+    {
+        // Use AC/AN
+        int AC = -1, AN = 0;
+        ret = bcf_get_info_int32(args->hdr, line, "AN", &args->itmp, &args->mitmp);
+        if ( ret==1 )
+        {
+            AN = args->itmp[0];
+            ret = bcf_get_info_int32(args->hdr, line, "AC", &args->itmp, &args->mitmp);
+            if ( ret>0 )
+                AC = args->itmp[0];
+        }
+        if ( AN<=0 || AC<0 )
+            ret = -1;
+        else
+            alt_freq = (double) AC/AN;
+    }
+
+    if ( args->dflt_AF>0 && (ret<0 || alt_freq==0.0) ) alt_freq = args->dflt_AF;
+    else if ( ret<0 ) { args->nno_af++; return ret; }
+    else if ( alt_freq==0.0 ) { args->nno_af++; return -1; }
+
+    int irr = bcf_alleles2gt(0,0), ira = bcf_alleles2gt(0,ial), iaa = bcf_alleles2gt(ial,ial);
+    if ( args->fake_PLs )
+    {
+        if ( !GTs ) GTs = get_GT(args, line);
+    }
+    else
+    {
+        fmt_pl = get_PL(args, line);
+        if ( !fmt_pl ) return -1;
+        if ( iaa >= fmt_pl->n ) return -1;  // not diploid or wrong number of fields
+    }
+
+    for (i=0; i<args->roh_smpl->n; i++)
+    {
+        int ismpl = args->roh_smpl->idx[i];
+
+        // set P(D|G)
+        double pdg[3];
+        if ( args->fake_PLs )
+        {
+            int8_t *gt = GTs + 2*ismpl;
+            if ( bcf_gt_is_missing(gt[0]) || bcf_gt_is_missing(gt[1]) ) continue;
+
+            int a = bcf_gt_allele(gt[0]);
+            int b = bcf_gt_allele(gt[1]);
+            if ( a!=b )
+            {
+                pdg[0] = pdg[2] = args->unseen_PL;
+                pdg[1] = 1 - 2*args->unseen_PL;
+            }
+            else if ( a==0 )
+            {
+                pdg[0] = 1 - args->unseen_PL - args->unseen_PL*args->unseen_PL;
+                pdg[1] = args->unseen_PL;
+                pdg[2] = args->unseen_PL*args->unseen_PL;
+            }
+            else
+            {
+                pdg[0] = args->unseen_PL*args->unseen_PL;
+                pdg[1] = args->unseen_PL;
+                pdg[2] = 1 - args->unseen_PL - args->unseen_PL*args->unseen_PL;
+            }
+        }
+        else
+        {
+            #define BRANCH(type_t) \
+            { \
+                type_t *p = (type_t*)fmt_pl->p + fmt_pl->n*ismpl; \
+                if ( p[irr]<0 || p[ira]<0 || p[iaa]<0 ) continue;    /* missing value */ \
+                if ( p[irr]==p[ira] && p[irr]==p[iaa] ) continue;    /* all values are the same */ \
+                pdg[0] = args->pl2p[ max255(p[irr]) ]; \
+                pdg[1] = args->pl2p[ max255(p[ira]) ]; \
+                pdg[2] = args->pl2p[ max255(p[iaa]) ]; \
+            }
+            switch (fmt_pl->type) {
+                case BCF_BT_INT8:  BRANCH(int8_t); break;
+                case BCF_BT_INT16: BRANCH(int16_t); break;
+                case BCF_BT_INT32: BRANCH(int32_t); break;
+                default: fprintf(stderr,"Unknown format type for PL: %s:%d .. fmt->type=%d\n", __FILE__,__LINE__, fmt_pl->type); exit(1);
+            }
+            #undef BRANCH
+        }
+
+        double sum = pdg[0] + pdg[1] + pdg[2];
+        if ( !sum ) continue;
+        for (j=0; j<3; j++) pdg[j] /= sum;
+        if ( args->skip_homref && pdg[0]>0.99 ) continue;
+
+        smpl_t *smpl = &args->smpl[i];
+        smpl->nused++;
+
+        if ( smpl->nsites >= smpl->msites )
+        {
+            hts_expand(uint32_t,smpl->nsites+1,smpl->msites,smpl->sites);
+            smpl->eprob = (double*) realloc(smpl->eprob,sizeof(*smpl->eprob)*smpl->msites*2);
+            if ( !smpl->eprob ) error("Error: failed to alloc %"PRIu64" bytes\n", (uint64_t)(sizeof(*smpl->eprob)*smpl->msites*2));
+        }
+
+        // Calculate emission probabilities P(D|AZ) and P(D|HW)
+        double *eprob = &smpl->eprob[2*smpl->nsites];
+        eprob[STATE_AZ] = pdg[0]*(1-alt_freq) + pdg[2]*alt_freq;
+        eprob[STATE_HW] = pdg[0]*(1-alt_freq)*(1-alt_freq) + 2*pdg[1]*(1-alt_freq)*alt_freq + pdg[2]*alt_freq*alt_freq;
+
+        smpl->sites[smpl->nsites] = line->pos;
+        smpl->nsites++;
+
+        if ( args->vi_training )
+        {
+            if ( !smpl->nrid || line->rid!=smpl->rid[smpl->nrid-1] )
+            {
+                smpl->nrid++;
+                smpl->rid = (int*) realloc(smpl->rid,sizeof(*smpl->rid)*smpl->nrid);
+                smpl->rid[smpl->nrid-1] = line->rid;
+                smpl->rid_off = (int*) realloc(smpl->rid_off,sizeof(*smpl->rid_off)*smpl->nrid);
+                smpl->rid_off[smpl->nrid-1] = smpl->nsites - 1;
+            }
+        }
+        else if ( args->nbuf_max && smpl->nsites >= args->nbuf_max ) flush_viterbi(args, i);
+    }
+
+    return 0;
+}
+
+static void vcfroh(args_t *args, bcf1_t *line)
+{
+    int i;
+
+    // Are we done?
+    if ( !line )
+    {
+        for (i=0; i<args->roh_smpl->n; i++) flush_viterbi(args, i);
+        return;
+    }
+
+    // Skip unwanted lines, for simplicity we consider only biallelic sites
+    if ( line->rid == args->skip_rid ) return;
+
+    // This can be raw callable VCF with the symbolic unseen allele <*>
+    int ial = 0, nalt = line->n_allele - 1;
+    for (i=1; i<line->n_allele; i++)
+    {
+        if ( !strcmp("<*>",line->d.allele[i]) || !strcmp("<NON_REF>",line->d.allele[i]) ) nalt--;
+        else if ( !ial ) ial = i;
+    }
+
+    if ( !nalt ) // no ALT allele
+    {
+        args->nno_alt++;
+        if ( !args->include_noalt_sites ) return;
+    }
+    else if ( nalt>1 )
+    {
+        args->nmultiallelic++;
+        return;
+    }
+
+    if ( args->snps_only && !bcf_is_snp(line) ) return;
+
+    // Initialize genetic map
+    int skip_rid = 0;
+    if ( args->prev_rid<0 )
+        skip_rid = load_genmap(args, bcf_seqname(args->hdr,line));
+
+    // New chromosome?
+    if ( args->prev_rid!=line->rid )
+    {
+        if ( !args->vi_training )
+        {
+            for (i=0; i<args->roh_smpl->n; i++)
+            {
+                flush_viterbi(args, i);
+                hmm_reset(args->hmm, args->smpl[i].snapshot);
+            }
+        }
+        args->prev_rid = line->rid;
+        args->prev_pos = line->pos;
+        skip_rid = load_genmap(args, bcf_seqname(args->hdr,line));
+    }
+    else if ( args->prev_pos == line->pos )
+    {
+        args->ndup++;
+        return;     // skip duplicate positions
+    }
+
+    if ( skip_rid )
+    {
+        fprintf(stderr,"Skipping the sequence, no genmap for %s\n", bcf_seqname(args->hdr,line));
+        args->skip_rid = line->rid;
+        return;
+    }
+    if ( args->prev_pos > line->pos ) error("The file is not sorted?!\n");
+
+    args->prev_rid = line->rid;
+    args->prev_pos = line->pos;
+
+
+    // parse the new line
+    process_line(args, line, ial);
+}
+
+static void usage(args_t *args)
+{
+    fprintf(stderr, "\n");
+    fprintf(stderr, "About:   HMM model for detecting runs of autozygosity.\n");
+    fprintf(stderr, "Usage:   bcftools roh [options] <in.vcf.gz>\n");
+    fprintf(stderr, "\n");
+    fprintf(stderr, "General Options:\n");
+    fprintf(stderr, "        --AF-dflt <float>              if AF is not known, use this allele frequency [skip]\n");
+    fprintf(stderr, "        --AF-tag <TAG>                 use TAG for allele frequency\n");
+    fprintf(stderr, "        --AF-file <file>               read allele frequencies from file (CHR\\tPOS\\tREF,ALT\\tAF)\n");
+    fprintf(stderr, "    -b  --buffer-size <int[,int]>      buffer size and the number of overlapping sites, 0 for unlimited [0]\n");
+    fprintf(stderr, "                                           If the first number is negative, it is interpreted as the maximum memory to\n");
+    fprintf(stderr, "                                           use, in MB. The default overlap is set to roughly 1%% of the buffer size.\n");
+    fprintf(stderr, "    -e, --estimate-AF [TAG],<file>     estimate AF from FORMAT/TAG (GT or PL) of all samples (\"-\") or samples listed\n");
+    fprintf(stderr, "                                            in <file>. If TAG is not given, the frequency is estimated from GT by default\n");
+    fprintf(stderr, "        --exclude <expr>               exclude sites for which the expression is true\n");
+    fprintf(stderr, "    -G, --GTs-only <float>             use GTs and ignore PLs, instead using <float> for PL of the two least likely genotypes.\n");
+    fprintf(stderr, "                                           Safe value to use is 30 to account for GT errors.\n");
+    fprintf(stderr, "        --include <expr>               select sites for which the expression is true\n");
+    fprintf(stderr, "    -i, --ignore-homref                skip hom-ref genotypes (0/0)\n");
+    fprintf(stderr, "        --include-noalt                include sites with no ALT allele (ignored by default)\n");
+    fprintf(stderr, "    -I, --skip-indels                  skip indels as their genotypes are enriched for errors\n");
+    fprintf(stderr, "    -m, --genetic-map <file>           genetic map in IMPUTE2 format, single file or mask, where string \"{CHROM}\"\n");
+    fprintf(stderr, "                                           is replaced with chromosome name\n");
+    fprintf(stderr, "    -M, --rec-rate <float>             constant recombination rate per bp\n");
+    fprintf(stderr, "    -o, --output <file>                write output to a file [standard output]\n");
+    fprintf(stderr, "    -O, --output-type [srz]            output s:per-site, r:regions, z:compressed [sr]\n");
+    fprintf(stderr, "    -r, --regions <region>             restrict to comma-separated list of regions\n");
+    fprintf(stderr, "    -R, --regions-file <file>          restrict to regions listed in a file\n");
+    fprintf(stderr, "        --regions-overlap 0|1|2        Include if POS in the region (0), record overlaps (1), variant overlaps (2) [1]\n");
+    fprintf(stderr, "    -s, --samples <list>               list of samples to analyze [all samples]\n");
+    fprintf(stderr, "    -S, --samples-file <file>          file of samples to analyze [all samples]\n");
+    fprintf(stderr, "    -t, --targets <region>             similar to -r but streams rather than index-jumps\n");
+    fprintf(stderr, "    -T, --targets-file <file>          similar to -R but streams rather than index-jumps\n");
+    fprintf(stderr, "        --targets-overlap 0|1|2        Include if POS in the region (0), record overlaps (1), variant overlaps (2) [0]\n");
+    fprintf(stderr, "        --threads <int>                use multithreading with <int> worker threads [0]\n");
+    fprintf(stderr, "\n");
+    fprintf(stderr, "HMM Options:\n");
+    fprintf(stderr, "    -a, --hw-to-az <float>             P(AZ|HW) transition probability from HW (Hardy-Weinberg) to AZ (autozygous) state [6.7e-8]\n");
+    fprintf(stderr, "    -H, --az-to-hw <float>             P(HW|AZ) transition probability from AZ to HW state [5e-9]\n");
+    fprintf(stderr, "    -V, --viterbi-training <float>     estimate HMM parameters, <float> is the convergence threshold, e.g. 1e-10 (experimental)\n");
+    fprintf(stderr, "\n");
+    exit(1);
+}
+
+int main_vcfroh(int argc, char *argv[])
+{
+    int c;
+    args_t *args  = (args_t*) calloc(1,sizeof(args_t));
+    args->argc    = argc; args->argv = argv;
+    args->files   = bcf_sr_init();
+    args->t2AZ    = 6.7e-8;
+    args->t2HW    = 5e-9;
+    args->rec_rate = 0;
+    int regions_is_file = 0, targets_is_file = 0;
+    int regions_overlap = 1;
+    int targets_overlap = 0;
+
+    static struct option loptions[] =
+    {
+        {"AF-tag",1,0,0},
+        {"AF-file",1,0,1},
+        {"AF-dflt",1,0,2},
+        {"include",1,0,3},
+        {"exclude",1,0,4},
+        {"include-noalt",0,0,5},
+        {"buffer-size",1,0,'b'},
+        {"ignore-homref",0,0,'i'},
+        {"estimate-AF",1,0,'e'},
+        {"output",1,0,'o'},
+        {"output-type",1,0,'O'},
+        {"GTs-only",1,0,'G'},
+        {"samples",1,0,'s'},
+        {"samples-file",1,0,'S'},
+        {"hw-to-az",1,0,'a'},
+        {"az-to-hw",1,0,'H'},
+        {"viterbi-training",1,0,'V'},
+        {"targets",1,0,'t'},
+        {"targets-file",1,0,'T'},
+        {"targets-overlap",required_argument,NULL,6},
+        {"regions",1,0,'r'},
+        {"regions-file",1,0,'R'},
+        {"regions-overlap",required_argument,NULL,7},
+        {"genetic-map",1,0,'m'},
+        {"rec-rate",1,0,'M'},
+        {"skip-indels",0,0,'I'},
+        {"threads",1,0,9},
+        {0,0,0,0}
+    };
+
+    int naf_opts = 0;
+    char *tmp;
+    while ((c = getopt_long(argc, argv, "h?r:R:t:T:H:a:s:S:m:M:G:Ia:e:V:b:O:o:i",loptions,NULL)) >= 0) {
+        switch (c) {
+            case 0: args->af_tag = optarg; naf_opts++; break;
+            case 1: args->af_fname = optarg; naf_opts++; break;
+            case 2:
+                args->dflt_AF = strtod(optarg,&tmp);
+                if ( *tmp ) error("Could not parse: --AF-dflt %s\n", optarg);
+                break;
+            case  3 :
+                if ( args->filter_str ) error("Error: only one --include or --exclude expression can be given, and they cannot be combined\n");
+                args->filter_str = optarg; args->filter_logic |= FLT_INCLUDE; break;
+            case  4 :
+                if ( args->filter_str ) error("Error: only one --include or --exclude expression can be given, and they cannot be combined\n");
+                args->filter_str = optarg; args->filter_logic |= FLT_EXCLUDE; break;
+            case 5: args->include_noalt_sites = 1; break;
+            case 'o': args->output_fname = optarg; break;
+            case 'O':
+                if ( strchr(optarg,'s') || strchr(optarg,'S') ) args->output_type |= OUTPUT_ST;
+                if ( strchr(optarg,'r') || strchr(optarg,'R') ) args->output_type |= OUTPUT_RG;
+                if ( strchr(optarg,'z') || strchr(optarg,'z') ) args->output_type |= OUTPUT_GZ;
+                break;
+            case 'e': args->estimate_AF = optarg; naf_opts++; break;
+            case 'b': args->buffer_size = optarg; break;
+            case 'i': args->skip_homref = 1; break;
+            case 'I': args->snps_only = 1; break;
+            case 'G':
+                args->fake_PLs = 1;
+                args->unseen_PL = strtod(optarg,&tmp);
+                if ( *tmp ) error("Could not parse: -G %s\n", optarg);
+                args->unseen_PL = pow(10,-args->unseen_PL/10.);
+                break;
+            case 'm': args->genmap_fname = optarg; break;
+            case 'M':
+                args->rec_rate = strtod(optarg,&tmp);
+                if ( *tmp ) error("Could not parse: -M %s\n", optarg);
+                break;
+            case 's': args->samples = strdup(optarg); break;
+            case 'S': args->samples = strdup(optarg); args->samples_is_file = 1; break;
+            case 'a':
+                args->t2AZ = strtod(optarg,&tmp);
+                if ( *tmp ) error("Could not parse: -a %s\n", optarg);
+                break;
+            case 'H':
+                args->t2HW = strtod(optarg,&tmp);
+                if ( *tmp ) error("Could not parse: -H %s\n", optarg);
+                break;
+            case 't': args->targets_list = optarg; break;
+            case 'T': args->targets_list = optarg; targets_is_file = 1; break;
+            case 'r': args->regions_list = optarg; break;
+            case 'R': args->regions_list = optarg; regions_is_file = 1; break;
+            case  6 :
+                targets_overlap = parse_overlap_option(optarg);
+                if ( targets_overlap < 0 ) error("Could not parse: --targets-overlap %s\n",optarg);
+                break;
+            case  7 :
+                regions_overlap = parse_overlap_option(optarg);
+                if ( regions_overlap < 0 ) error("Could not parse: --regions-overlap %s\n",optarg);
+                break;
+            case  9 : args->n_threads = strtol(optarg, 0, 0); break;
+            case 'V':
+                args->vi_training = 1;
+                args->baum_welch_th = strtod(optarg,&tmp);
+                if ( *tmp ) error("Could not parse: --viterbi-training %s\n", optarg);
+                break;
+            case 'h':
+            case '?': usage(args); break;
+            default: error("Unknown argument: %s\n", optarg);
+        }
+    }
+    if ( !args->output_fname ) args->output_fname = "stdout";
+    if ( !args->output_type || args->output_type==OUTPUT_GZ ) args->output_type |= OUTPUT_ST|OUTPUT_RG;
+    char *fname = NULL;
+    if ( optind==argc )
+    {
+        if ( !isatty(fileno((FILE *)stdin)) ) fname = "-";  // reading from stdin
+        else usage(args);
+    }
+    else fname = argv[optind];
+
+    if ( args->vi_training && args->buffer_size ) error("Error: cannot use -b with -V\n");
+    if ( args->t2AZ<0 || args->t2AZ>1 ) error("Error: The parameter --hw-to-az is not in [0,1] .. %e\n", args->t2AZ);
+    if ( args->t2HW<0 || args->t2HW>1 ) error("Error: The parameter --az-to-hw is not in [0,1] .. %e\n", args->t2HW);
+    if ( naf_opts>1 ) error("Error: The options --AF-tag, --AF-file and -e are mutually exclusive\n");
+    if ( args->af_fname && args->targets_list ) error("Error: The options --AF-file and -t are mutually exclusive\n");
+    if ( args->regions_list )
+    {
+        bcf_sr_set_opt(args->files,BCF_SR_REGIONS_OVERLAP,regions_overlap);
+        if ( bcf_sr_set_regions(args->files, args->regions_list, regions_is_file)<0 )
+            error("Failed to read the regions: %s\n", args->regions_list);
+    }
+    if ( args->targets_list )
+    {
+        bcf_sr_set_opt(args->files,BCF_SR_TARGETS_OVERLAP,targets_overlap);
+        if ( bcf_sr_set_targets(args->files, args->targets_list, targets_is_file, 0)<0 )
+            error("Failed to read the targets: %s\n", args->targets_list);
+    }
+    if ( args->af_fname )
+    {
+        if ( bcf_sr_set_targets(args->files, args->af_fname, 1, 3)<0 )
+            error("Failed to read the targets: %s\n", args->af_fname);
+    }
+    if ( args->n_threads && bcf_sr_set_threads(args->files, args->n_threads)<0)
+        error("Failed to create threads\n");
+    if ( !bcf_sr_add_reader(args->files, fname) ) error("Failed to read from %s: %s\n", !strcmp("-",fname)?"standard input":fname,bcf_sr_strerror(args->files->errnum));
+
+    init_data(args);
+    while ( bcf_sr_next_line(args->files) )
+    {
+        args->ntot++;
+        bcf1_t *line = bcf_sr_get_line(args->files,0);
+        if ( args->filter )
+        {
+            int pass = filter_test(args->filter, line, NULL);
+            if ( args->filter_logic & FLT_EXCLUDE ) pass = pass ? 0 : 1;
+            if ( !pass ) { args->nfiltered++; continue; }
+        }
+        vcfroh(args, line);
+    }
+    vcfroh(args, NULL);
+    int i, nmin = 0;
+    for (i=0; i<args->roh_smpl->n; i++)
+        if ( !i || args->smpl[i].nused < nmin ) nmin = args->smpl[i].nused;
+    if ( args->af_fname )
+        fprintf(stderr,"Number of lines overlapping with --AF-file/processed: %d/%d\n", args->ntot,nmin);
+    else
+        fprintf(stderr,"Number of lines total/processed: %d/%d\n", args->ntot,nmin);
+    fprintf(stderr,"Number of lines filtered/no AF/no alt/multiallelic/dup: %d/%d/%d/%d/%d\n", args->nfiltered,args->nno_af,args->nno_alt,args->nmultiallelic,args->ndup);
+    if ( nmin==0 )
+    {
+        fprintf(stderr,"No usable sites were found.\n");
+        if ( !naf_opts && !args->dflt_AF ) fprintf(stderr, " Consider using one of the AF options.\n");
+    }
+    destroy_data(args);
+    free(args);
+    return 0;
+}
+
+
diff --git a/bcftools/vcfroh.c.pysam.c b/bcftools/vcfroh.c.pysam.c
new file mode 100644
index 0000000..f9b8aab
--- /dev/null
+++ b/bcftools/vcfroh.c.pysam.c
@@ -0,0 +1,1303 @@
+#include "bcftools.pysam.h"
+
+/*  vcfroh.c -- HMM model for detecting runs of autozygosity.
+
+    Copyright (C) 2013-2022 Genome Research Ltd.
+
+    Author: Petr Danecek <pd3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.  */
+
+#include <stdio.h>
+#include <unistd.h>
+#include <getopt.h>
+#include <math.h>
+#include <inttypes.h>
+#include <htslib/vcf.h>
+#include <htslib/synced_bcf_reader.h>
+#include <htslib/kstring.h>
+#include <htslib/kseq.h>
+#include <htslib/bgzf.h>
+#include <errno.h>
+#include "bcftools.h"
+#include "HMM.h"
+#include "smpl_ilist.h"
+#include "filter.h"
+
+#define STATE_HW 0        // normal state, follows Hardy-Weinberg allele frequencies
+#define STATE_AZ 1        // autozygous state
+
+#define OUTPUT_ST (1<<1)
+#define OUTPUT_RG (1<<2)
+#define OUTPUT_GZ (1<<3)
+
+// Logic of the filters: include or exclude sites which match the filters?
+#define FLT_INCLUDE 1
+#define FLT_EXCLUDE 2
+
+
+/** Genetic map */
+typedef struct
+{
+    int pos;
+    double rate;
+}
+genmap_t;
+
+/** HMM data for each sample */
+typedef struct
+{
+    double *eprob;      // emission probs [2*nsites,msites]
+    uint32_t *sites;    // positions [nsites,msites]
+    int nsites, msites;
+    int igenmap;        // current position in genmap
+    int nused;          // some stats to detect if things didn't go wrong
+    int nrid, *rid, *rid_off;   // for viterbi training, keep all chromosomes
+    void *snapshot;             // hmm snapshot
+    struct {
+        uint32_t beg,end,nqual;
+        double qual;
+        int rid, state;
+    } rg;
+}
+smpl_t;
+
+typedef struct _args_t
+{
+    bcf_srs_t *files;
+    bcf_hdr_t *hdr;
+    double t2AZ, t2HW;      // P(AZ|HW) and P(HW|AZ) parameters
+    double unseen_PL, dflt_AF;
+
+    char *genmap_fname;
+    genmap_t *genmap;
+    int ngenmap, mgenmap, igenmap;
+    double rec_rate;        // constant recombination rate if > 0
+
+    hmm_t *hmm;
+    double baum_welch_th;
+    int nrids, *rids, *rid_offs;    // multiple chroms with vi_training
+    int nbuf_max, nbuf_olap;
+
+    float *AFs;
+    int32_t *itmp;
+    int mAFs, nitmp, mitmp, pl_hdr_id, gt_hdr_id;
+
+    double pl2p[256], *pdg;
+    int32_t skip_rid, prev_rid, prev_pos;
+
+    int ntot;                   // some stats to detect if things didn't go wrong
+    int nno_af;                 // number of sites rejected because AF could not be determined
+    int nfiltered;              // .. because of filters
+    int nno_alt, nmultiallelic, ndup;
+    smpl_t *smpl;               // HMM data for each sample
+    smpl_ilist_t *af_smpl;      // list of samples to estimate AF from (--estimate-AF)
+    smpl_ilist_t *roh_smpl;     // list of samples to analyze (--samples, --samples-file)
+    char *estimate_AF;          // list of samples for AF estimate and query sample
+    int af_from_PL;             // estimate AF from FMT/PL rather than FMT/GT
+    char **argv, *targets_list, *regions_list, *af_fname, *af_tag, *samples, *buffer_size, *output_fname;
+    int argc, fake_PLs, snps_only, vi_training, samples_is_file, output_type, skip_homref, n_threads;
+    int include_noalt_sites;
+    BGZF *out;
+    kstring_t str;
+
+    int filter_logic;
+    filter_t *filter;
+    char *filter_str;
+}
+args_t;
+
+void set_tprob_genmap(hmm_t *hmm, uint32_t prev_pos, uint32_t pos, void *data, double *tprob);
+void set_tprob_rrate(hmm_t *hmm, uint32_t prev_pos, uint32_t pos, void *data, double *tprob);
+
+void *smalloc(size_t size)
+{
+    void *mem = malloc(size);
+    if ( !mem ) error("malloc: Could not allocate %d bytes\n", (int)size);
+    return mem;
+}
+
+static inline int max255(int i)
+{
+    return i < 256 ? i : 255;
+}
+
+static void init_data(args_t *args)
+{
+    int i;
+
+    args->prev_rid = args->skip_rid = -1;
+    args->hdr = args->files->readers[0].header;
+
+    if ( !bcf_hdr_nsamples(args->hdr) ) error("No samples in the VCF?\n");
+
+    if ( args->filter_str )
+        args->filter = filter_init(args->hdr, args->filter_str);
+
+    if ( !args->fake_PLs )
+    {
+        args->pl_hdr_id = bcf_hdr_id2int(args->hdr, BCF_DT_ID, "PL");
+        if ( !bcf_hdr_idinfo_exists(args->hdr,BCF_HL_FMT,args->pl_hdr_id) )
+            error("Error: The FORMAT/PL tag not found in the header, consider running with -G\n");
+        if ( bcf_hdr_id2type(args->hdr,BCF_HL_FMT,args->pl_hdr_id)!=BCF_HT_INT )
+            error("Error: The FORMAT/PL tag not defined as Integer in the header\n");
+    }
+
+    if ( args->estimate_AF )
+    {
+        if ( !strncmp("GT,",args->estimate_AF,3) ) args->estimate_AF += 3;
+        else if ( !strncmp("PL,",args->estimate_AF,3) ) { args->estimate_AF += 3; args->af_from_PL = 1; }
+        if ( strcmp("-",args->estimate_AF) )
+            args->af_smpl = smpl_ilist_init(args->hdr, args->estimate_AF, 1, SMPL_NONE|SMPL_VERBOSE);
+    }
+
+    if ( args->estimate_AF || args->fake_PLs )
+    {
+        if ( args->af_from_PL )
+        {
+            args->pl_hdr_id = bcf_hdr_id2int(args->hdr, BCF_DT_ID, "PL");
+            if ( !bcf_hdr_idinfo_exists(args->hdr,BCF_HL_FMT,args->pl_hdr_id) )
+                error("Error: The FORMAT/PL tag not found in the header\n");
+        }
+        else
+        {
+            args->gt_hdr_id = bcf_hdr_id2int(args->hdr, BCF_DT_ID, "GT");
+            if ( !bcf_hdr_idinfo_exists(args->hdr,BCF_HL_FMT,args->gt_hdr_id) )
+                error("Error: The FORMAT/GT tag not found in the header\n");
+        }
+    }
+    if ( args->fake_PLs )
+    {
+        args->gt_hdr_id = bcf_hdr_id2int(args->hdr, BCF_DT_ID, "GT");
+        if ( !bcf_hdr_idinfo_exists(args->hdr,BCF_HL_FMT,args->gt_hdr_id) )
+            error("Error: The FORMAT/GT tag not found in the header\n");
+    }
+
+    args->roh_smpl = smpl_ilist_init(args->hdr, args->samples, args->samples_is_file, SMPL_NONE|SMPL_VERBOSE);
+    if ( args->samples )
+    {
+        // we may be able to subset to a few samples, for a text VCF this can be a major speedup
+        if ( (bcf_sr_get_reader(args->files,0))->file->format.format==vcf )
+        {
+            kstring_t str = {0,0,0};
+            smpl_ilist_t *tmp = args->roh_smpl, *rmme = NULL;
+            if ( args->af_smpl )
+            {
+                for (i=0; i<args->roh_smpl->n; i++)
+                {
+                    if ( str.l ) kputc(',', &str);
+                    kputs(args->hdr->samples[args->roh_smpl->idx[i]], &str);
+                }
+                for (i=0; i<args->af_smpl->n; i++)
+                {
+                    kputc(',', &str);
+                    kputs(args->hdr->samples[args->af_smpl->idx[i]], &str);
+                }
+                rmme = tmp = smpl_ilist_init(args->hdr, str.s, 0, SMPL_NONE);
+            }
+            if ( tmp->n < bcf_hdr_nsamples(args->hdr) )
+            {
+                str.l = 0;
+                for (i=0; i<tmp->n; i++)
+                {
+                    if ( str.l ) kputc(',', &str);
+                    kputs(args->hdr->samples[tmp->idx[i]], &str);
+                }
+                int ret = bcf_hdr_set_samples(args->hdr, str.s, 0);
+                if ( ret<0 ) error("Error parsing the list of samples: %s\n", str.s);
+                else if ( ret>0 ) error("The %d-th sample not found in the VCF: %s\n", ret,str.s);
+
+                // update sample ids
+                smpl_ilist_destroy(args->roh_smpl);
+                args->roh_smpl = smpl_ilist_init(args->hdr, args->samples, args->samples_is_file, SMPL_NONE);
+
+                if ( args->af_smpl )
+                {
+                    smpl_ilist_destroy(args->af_smpl);
+                    args->af_smpl = smpl_ilist_init(args->hdr, args->estimate_AF, 1, SMPL_NONE);
+                }
+            }
+            free(str.s);
+            if ( rmme )
+                smpl_ilist_destroy(rmme);
+        }
+    }
+
+    // check whether all samples are in this list. If so, the lookup will not be needed
+    if ( args->af_smpl && args->af_smpl->n == bcf_hdr_nsamples(args->hdr) )
+    {
+        // all samples are in this list
+        smpl_ilist_destroy(args->af_smpl);
+        args->af_smpl = NULL;
+    }
+
+    if ( args->buffer_size )
+    {
+        args->nbuf_olap = -1;
+        char *end;
+        double tmp = strtod(args->buffer_size,&end);
+        if ( *end )
+        {
+            if ( *end!=',') error("Could not parse: --buffer-size %s\n", args->buffer_size);
+            args->nbuf_olap = strtol(end+1,&end,10);
+            if ( *end || args->nbuf_olap<0 ) error("Could not parse: --bufer-size %s\n", args->buffer_size);
+        }
+        if ( tmp<0 )
+            args->nbuf_max = fabs(tmp)*1e6/(4+8*2)/args->roh_smpl->n;
+        else
+            args->nbuf_max = tmp;
+
+        if ( args->nbuf_olap<0 )
+            args->nbuf_olap = args->nbuf_max*0.01;
+    }
+    fprintf(bcftools_stderr,"Number of target samples: %d\n", args->roh_smpl->n);
+    fprintf(bcftools_stderr,"Number of --estimate-AF samples: %d\n", args->af_smpl ? args->af_smpl->n : (args->estimate_AF ? bcf_hdr_nsamples(args->hdr) : 0));
+    fprintf(bcftools_stderr,"Number of sites in the buffer/overlap: ");
+    if ( args->nbuf_max ) fprintf(bcftools_stderr,"%d/%d\n", args->nbuf_max,args->nbuf_olap);
+    else fprintf(bcftools_stderr,"unlimited\n");
+
+    args->smpl = (smpl_t*) calloc(args->roh_smpl->n,sizeof(smpl_t));
+
+    for (i=0; i<256; i++) args->pl2p[i] = pow(10., -i/10.);
+
+    // Init transition matrix and HMM
+    double tprob[4];
+    MAT(tprob,2,STATE_HW,STATE_HW) = 1 - args->t2AZ;
+    MAT(tprob,2,STATE_HW,STATE_AZ) = args->t2HW;
+    MAT(tprob,2,STATE_AZ,STATE_HW) = args->t2AZ;
+    MAT(tprob,2,STATE_AZ,STATE_AZ) = 1 - args->t2HW;
+
+    args->hmm = hmm_init(2, tprob, 10000);
+    if ( args->genmap_fname )
+        hmm_set_tprob_func(args->hmm, set_tprob_genmap, args);
+    else if ( args->rec_rate > 0 )
+        hmm_set_tprob_func(args->hmm, set_tprob_rrate, args);
+
+    args->out = bgzf_open(strcmp("bcftools_stdout",args->output_fname)?args->output_fname:"-", args->output_type&OUTPUT_GZ ? "wg" : "wu");
+    if ( !args->out ) error("Failed to open %s: %s\n", args->output_fname, strerror(errno));
+
+    // print header
+    args->str.l = 0;
+    ksprintf(&args->str, "# This file was produced by: bcftools roh(%s+htslib-%s)\n", bcftools_version(),hts_version());
+    ksprintf(&args->str, "# The command line was:\tbcftools %s", args->argv[0]);
+    for (i=1; i<args->argc; i++)
+        ksprintf(&args->str, " %s",args->argv[i]);
+    ksprintf(&args->str, "\n#\n");
+    if ( args->output_type & OUTPUT_RG )
+    {
+        i = 2;
+        ksprintf(&args->str, "# RG");
+        ksprintf(&args->str, "\t[%d]Sample", i++);
+        ksprintf(&args->str, "\t[%d]Chromosome", i++);
+        ksprintf(&args->str, "\t[%d]Start", i++);
+        ksprintf(&args->str, "\t[%d]End", i++);
+        ksprintf(&args->str, "\t[%d]Length (bp)", i++);
+        ksprintf(&args->str, "\t[%d]Number of markers", i++);
+        ksprintf(&args->str, "\t[%d]Quality (average fwd-bwd phred score)", i++);
+        ksprintf(&args->str, "\n");
+    }
+    if ( args->output_type & OUTPUT_ST )
+    {
+        i = 2;
+        ksprintf(&args->str, "# ST");
+        ksprintf(&args->str, "\t[%d]Sample", i++);
+        ksprintf(&args->str, "\t[%d]Chromosome", i++);
+        ksprintf(&args->str, "\t[%d]Position", i++);
+        ksprintf(&args->str, "\t[%d]State (0:HW, 1:AZ)", i++);
+        ksprintf(&args->str, "\t[%d]Quality (fwd-bwd phred score)", i++);
+        ksprintf(&args->str, "\n");
+    }
+    if ( args->vi_training)
+    {
+        i = 2;
+        ksprintf(&args->str, "# VT, Viterbi Training");
+        ksprintf(&args->str, "\t[%d]Sample", i++);
+        ksprintf(&args->str, "\t[%d]Iteration", i++);
+        ksprintf(&args->str, "\t[%d]dAZ", i++);
+        ksprintf(&args->str, "\t[%d]dHW", i++);
+        ksprintf(&args->str, "\t[%d]1 - P(HW|HW)", i++);
+        ksprintf(&args->str, "\t[%d]P(AZ|HW)", i++);
+        ksprintf(&args->str, "\t[%d]1 - P(AZ|AZ)", i++);
+        ksprintf(&args->str, "\t[%d]P(HW|AZ)", i++);
+        ksprintf(&args->str, "\n");
+    }
+    if ( bgzf_write(args->out, args->str.s, args->str.l) != args->str.l )
+        error("Error writing %s: %s\n", args->output_fname, strerror(errno));
+}
+
+static void destroy_data(args_t *args)
+{
+    if ( args->filter ) filter_destroy(args->filter);
+    if ( bgzf_close(args->out)!=0 ) error("Error: close failed .. %s\n", args->output_fname);
+    int i;
+    for (i=0; i<args->roh_smpl->n; i++)
+    {
+        free(args->smpl[i].eprob);
+        free(args->smpl[i].sites);
+        free(args->smpl[i].rid);
+        free(args->smpl[i].rid_off);
+        free(args->smpl[i].snapshot);
+    }
+    free(args->str.s);
+    free(args->smpl);
+    if ( args->af_smpl ) smpl_ilist_destroy(args->af_smpl);
+    smpl_ilist_destroy(args->roh_smpl);
+    free(args->rids);
+    free(args->rid_offs);
+    hmm_destroy(args->hmm);
+    bcf_sr_destroy(args->files);
+    free(args->AFs); free(args->pdg);
+    free(args->genmap);
+    free(args->itmp);
+    free(args->samples);
+}
+
+static int load_genmap(args_t *args, const char *chr)
+{
+    if ( !args->genmap_fname ) { args->ngenmap = 0; return 0; }
+
+    kstring_t str = {0,0,0};
+    char *fname = strstr(args->genmap_fname,"{CHROM}");
+    if ( fname )
+    {
+        kputsn(args->genmap_fname, fname - args->genmap_fname, &str);
+        kputs(chr, &str);
+        kputs(fname+7,&str);
+        fname = str.s;
+    }
+    else
+        fname = args->genmap_fname;
+
+    htsFile *fp = hts_open(fname, "rb");
+    if ( !fp )
+    {
+        args->ngenmap = 0;
+        return -1;
+    }
+
+    hts_getline(fp, KS_SEP_LINE, &str);
+    if ( strcmp(str.s,"position COMBINED_rate(cM/Mb) Genetic_Map(cM)") )
+        error("Unexpected header in %s, found:\n\t[%s], but expected:\n\t[position COMBINED_rate(cM/Mb) Genetic_Map(cM)]\n", fname, str.s);
+
+    args->ngenmap = args->igenmap = 0;
+    while ( hts_getline(fp, KS_SEP_LINE, &str) > 0 )
+    {
+        args->ngenmap++;
+        hts_expand(genmap_t,args->ngenmap,args->mgenmap,args->genmap);
+        genmap_t *gm = &args->genmap[args->ngenmap-1];
+
+        // position, convert to 0-based
+        char *tmp, *end;
+        gm->pos = strtol(str.s, &tmp, 10);
+        if ( str.s==tmp ) error("Could not parse %s: %s\n", fname, str.s);
+        gm->pos -= 1;
+
+        // skip second column
+        tmp++;
+        while ( *tmp && !isspace(*tmp) ) tmp++;
+
+        // read the genetic map in cM, scale from % to likelihood
+        gm->rate = strtod(tmp+1, &end);
+        if ( tmp+1==end ) error("Could not parse %s: %s\n", fname, str.s);
+        gm->rate *= 0.01;
+    }
+    if ( !args->ngenmap ) error("Genetic map empty?\n");
+    if ( hts_close(fp) ) error("Close failed\n");
+    free(str.s);
+    return 0;
+}
+
+static double get_genmap_rate(args_t *args, int start, int end)
+{
+    // position i to be equal to or smaller than start
+    int i = args->igenmap;
+    if ( args->genmap[i].pos > start )
+    {
+        while ( i>0 && args->genmap[i].pos > start ) i--;
+    }
+    else
+    {
+        while ( i+1<args->ngenmap && args->genmap[i+1].pos < start ) i++;
+    }
+    // position j to be equal or larger than end
+    int j = i;
+    while ( j+1<args->ngenmap && args->genmap[j].pos < end ) j++;
+    if ( i==j )
+    {
+        args->igenmap = i;
+        return 0;
+    }
+
+    if ( start <  args->genmap[i].pos ) start = args->genmap[i].pos;
+    if ( end >  args->genmap[j].pos ) end = args->genmap[j].pos;
+    double rate = (args->genmap[j].rate - args->genmap[i].rate)/(args->genmap[j].pos - args->genmap[i].pos) * (end-start);
+    args->igenmap = j;
+    return rate;
+}
+
+void set_tprob_genmap(hmm_t *hmm, uint32_t prev_pos, uint32_t pos, void *data, double *tprob)
+{
+    args_t *args = (args_t*) data;
+    double ci = get_genmap_rate(args, prev_pos, pos);
+    if ( args->rec_rate ) ci *= args->rec_rate;
+    if ( ci > 1 ) ci = 1;
+    MAT(tprob,2,STATE_HW,STATE_AZ) *= ci;
+    MAT(tprob,2,STATE_AZ,STATE_HW) *= ci;
+    MAT(tprob,2,STATE_AZ,STATE_AZ)  = 1 - MAT(tprob,2,STATE_HW,STATE_AZ);
+    MAT(tprob,2,STATE_HW,STATE_HW)  = 1 - MAT(tprob,2,STATE_AZ,STATE_HW);
+}
+
+void set_tprob_rrate(hmm_t *hmm, uint32_t prev_pos, uint32_t pos, void *data, double *tprob)
+{
+    args_t *args = (args_t*) data;
+    double ci = (pos - prev_pos) * args->rec_rate;
+    if ( ci > 1 ) ci = 1;
+    MAT(tprob,2,STATE_HW,STATE_AZ) *= ci;
+    MAT(tprob,2,STATE_AZ,STATE_HW) *= ci;
+    MAT(tprob,2,STATE_AZ,STATE_AZ)  = 1 - MAT(tprob,2,STATE_HW,STATE_AZ);
+    MAT(tprob,2,STATE_HW,STATE_HW)  = 1 - MAT(tprob,2,STATE_AZ,STATE_HW);
+}
+
+
+/**
+ *  This function implements the HMM model:
+ *    D = Data, AZ = autozygosity, HW = Hardy-Weinberg (non-autozygosity),
+ *    f = non-ref allele frequency
+ *
+ *  Emission probabilities:
+ *    oAZ = P_i(D|AZ) = (1-f)*P(D|RR) + f*P(D|AA)
+ *    oHW = P_i(D|HW) = (1-f)^2 * P(D|RR) + f^2 * P(D|AA) + 2*f*(1-f)*P(D|RA)
+ *
+ *  Transition probabilities:
+ *    tAZ = P(AZ|HW)  .. parameter
+ *    tHW = P(HW|AZ)  .. parameter
+ *
+ *    ci  = P_i(C)    .. probability of cross-over at site i, from genetic map
+ *
+ *    AZi = P_i(AZ)   .. probability of site i being AZ/non-AZ, scaled so that AZi+HWi = 1
+ *    HWi = P_i(HW)
+ *
+ *    P_i(AZ|HW) = P(AZ|HW) * ci * HW{i-1}     = tAZ * ci * (1 - AZ{i-1})
+ *    P_i(HW|AZ) = P(HW|AZ) * ci * AZ{i-1}     = tHW * ci * AZ{i-1}
+ *    P_i(AZ|AZ) = 1 - P_i(HW|AZ)
+ *    P_i(HW|HW) = 1 - P_i(AZ|HW)
+ *
+ */
+
+static void flush_viterbi(args_t *args, int ismpl)
+{
+    smpl_t *smpl = &args->smpl[ismpl];
+    if ( !smpl->nsites ) return;
+
+    const char *name = args->hdr->samples[ args->roh_smpl->idx[ismpl] ];
+
+    int i,j,k;
+
+    if ( !args->vi_training ) // single viterbi pass
+    {
+        hmm_restore(args->hmm, smpl->snapshot);
+        int end = (args->nbuf_max && smpl->nsites >= args->nbuf_max && smpl->nsites > args->nbuf_olap) ? smpl->nsites - args->nbuf_olap : smpl->nsites;
+        if ( end < smpl->nsites )
+            smpl->snapshot = hmm_snapshot(args->hmm, smpl->snapshot, smpl->sites[smpl->nsites - args->nbuf_olap - 1]);
+
+        args->igenmap = smpl->igenmap;
+        hmm_run_viterbi(args->hmm, smpl->nsites, smpl->eprob, smpl->sites);
+        hmm_run_fwd_bwd(args->hmm, smpl->nsites, smpl->eprob, smpl->sites);
+        double *fwd = hmm_get_fwd_bwd_prob(args->hmm);
+
+        const char *chr  = bcf_hdr_id2name(args->hdr,args->prev_rid);
+        uint8_t *vpath   = hmm_get_viterbi_path(args->hmm);
+
+        for (i=0; i<end; i++)
+        {
+            int state = vpath[i*2]==STATE_AZ ? 1 : 0;
+            double qual = phred_score(1.0 - fwd[i*2 + state]);
+            if ( args->output_type & OUTPUT_ST )
+            {
+                args->str.l = 0;
+                ksprintf(&args->str, "ST\t%s\t%s\t%d\t%d\t%.1f\n", name,chr,smpl->sites[i]+1, state, qual);
+                if ( bgzf_write(args->out, args->str.s, args->str.l) != args->str.l ) error("Error writing %s: %s\n", args->output_fname, strerror(errno));
+            }
+
+            if ( args->output_type & OUTPUT_RG )
+            {
+                if ( state!=smpl->rg.state )
+                {
+                    if ( !state )   // the region ends, flush
+                    {
+                        args->str.l = 0;
+                        ksprintf(&args->str, "RG\t%s\t%s\t%d\t%d\t%d\t%d\t%.1f\n",name,bcf_hdr_id2name(args->hdr,smpl->rg.rid),
+                                smpl->rg.beg+1,smpl->rg.end+1,smpl->rg.end-smpl->rg.beg+1,smpl->rg.nqual,smpl->rg.qual/smpl->rg.nqual);
+                        if ( bgzf_write(args->out, args->str.s, args->str.l) != args->str.l ) error("Error writing %s: %s\n", args->output_fname, strerror(errno));
+                        smpl->rg.state = 0;
+                    }
+                    else
+                    {
+                        smpl->rg.state = 1;
+                        smpl->rg.beg = smpl->sites[i];
+                        smpl->rg.end = smpl->sites[i];
+                        smpl->rg.rid = args->prev_rid;
+                        smpl->rg.qual  = qual;
+                        smpl->rg.nqual = 1;
+                    }
+                }
+                else if ( state )
+                {
+                    smpl->rg.nqual++;
+                    smpl->rg.qual += qual;
+                    smpl->rg.end  = smpl->sites[i];
+                }
+            }
+        }
+
+        if ( end < smpl->nsites )
+        {
+            end = smpl->nsites - args->nbuf_olap;
+            memmove(smpl->sites, smpl->sites + end, sizeof(*smpl->sites)*args->nbuf_olap);
+            memmove(smpl->eprob, smpl->eprob + end*2, sizeof(*smpl->eprob)*args->nbuf_olap*2);
+            smpl->nsites  = args->nbuf_olap;
+            smpl->igenmap = args->igenmap;
+        }
+        else
+        {
+            smpl->nsites  = 0;
+            smpl->igenmap = 0;
+
+            if ( smpl->rg.state )
+            {
+                args->str.l = 0;
+                ksprintf(&args->str, "RG\t%s\t%s\t%d\t%d\t%d\t%d\t%.1f\n",name,bcf_hdr_id2name(args->hdr,smpl->rg.rid),
+                        smpl->rg.beg+1,smpl->rg.end+1,smpl->rg.end-smpl->rg.beg+1,smpl->rg.nqual,smpl->rg.qual/smpl->rg.nqual);
+                if ( bgzf_write(args->out, args->str.s, args->str.l) != args->str.l ) error("Error writing %s: %s\n", args->output_fname, strerror(errno));
+                smpl->rg.state = 0;
+            }
+        }
+
+        return;
+    }
+
+
+    // viterbi training, multiple chromosomes
+    double t2az_prev, t2hw_prev;
+    double deltaz, delthw;
+
+    double *tprob_arr = hmm_get_tprob(args->hmm);
+    MAT(tprob_arr,2,STATE_HW,STATE_HW) = 1 - args->t2AZ;
+    MAT(tprob_arr,2,STATE_HW,STATE_AZ) = args->t2HW;
+    MAT(tprob_arr,2,STATE_AZ,STATE_HW) = args->t2AZ;
+    MAT(tprob_arr,2,STATE_AZ,STATE_AZ) = 1 - args->t2HW;
+    hmm_set_tprob(args->hmm, tprob_arr, 10000);
+
+    int niter = 0;
+    do
+    {
+        tprob_arr = hmm_get_tprob(args->hmm);
+        t2az_prev = MAT(tprob_arr,2,STATE_AZ,STATE_HW); //args->t2AZ;
+        t2hw_prev = MAT(tprob_arr,2,STATE_HW,STATE_AZ); //args->t2HW;
+        double tprob_new[] = { 0,0,0,0 };
+        for (i=0; i<smpl->nrid; i++)
+        {
+            int ioff = smpl->rid_off[i];
+            int nsites = (i+1==smpl->nrid ? smpl->nsites : smpl->rid_off[i+1]) - ioff;
+            args->igenmap = 0;
+            tprob_arr = hmm_run_baum_welch(args->hmm, nsites, smpl->eprob+ioff*2, smpl->sites+ioff);
+            for (j=0; j<2; j++)
+                for (k=0; k<2; k++) MAT(tprob_new,2,j,k) += MAT(tprob_arr,2,j,k);
+        }
+        for (j=0; j<2; j++)
+            for (k=0; k<2; k++) MAT(tprob_new,2,j,k) /= smpl->nrid;
+
+        hmm_set_tprob(args->hmm, tprob_new, 10000);
+
+        deltaz = fabs(MAT(tprob_new,2,STATE_AZ,STATE_HW)-t2az_prev);
+        delthw = fabs(MAT(tprob_new,2,STATE_HW,STATE_AZ)-t2hw_prev);
+        niter++;
+        args->str.l = 0;
+        ksprintf(&args->str, "VT\t%s\t%d\t%e\t%e\t%e\t%e\t%e\t%e\n",
+            name,niter,deltaz,delthw,
+            1-MAT(tprob_new,2,STATE_HW,STATE_HW),MAT(tprob_new,2,STATE_AZ,STATE_HW),
+            1-MAT(tprob_new,2,STATE_AZ,STATE_AZ),MAT(tprob_new,2,STATE_HW,STATE_AZ));
+        if ( bgzf_write(args->out, args->str.s, args->str.l) != args->str.l ) error("Error writing %s: %s\n", args->output_fname, strerror(errno));
+    }
+    while ( deltaz > args->baum_welch_th || delthw > args->baum_welch_th );
+
+    // output the results
+    for (i=0; i<smpl->nrid; i++)
+    {
+        int ioff = smpl->rid_off[i];
+        int nsites = (i+1==smpl->nrid ? smpl->nsites : smpl->rid_off[i+1]) - ioff;
+        args->igenmap = 0;
+        hmm_run_viterbi(args->hmm, nsites, smpl->eprob+ioff*2, smpl->sites+ioff);
+        hmm_run_fwd_bwd(args->hmm, nsites, smpl->eprob+ioff*2, smpl->sites+ioff);
+        uint8_t *vpath = hmm_get_viterbi_path(args->hmm);
+        double  *fwd   = hmm_get_fwd_bwd_prob(args->hmm);
+
+        const char *chr = bcf_hdr_id2name(args->hdr,smpl->rid[i]);
+        for (j=0; j<nsites; j++)
+        {
+            int state = vpath[j*2]==STATE_AZ ? 1 : 0;
+            double *pval = fwd + j*2;
+            args->str.l = 0;
+            ksprintf(&args->str, "ROH\t%s\t%s\t%d\t%d\t%.1f\n", name,chr,smpl->sites[ioff+j]+1, state, phred_score(1.0-pval[state]));
+            if ( bgzf_write(args->out, args->str.s, args->str.l) != args->str.l ) error("Error writing %s: %s\n", args->output_fname, strerror(errno));
+        }
+    }
+}
+
+int read_AF(bcf_sr_regions_t *tgt, bcf1_t *line, double *alt_freq)
+{
+    if ( tgt->nals < 2 )
+        error("Expected two comma-separated alleles (REF,ALT) in the third column of %s, found:\n\t%s\n", tgt->fname,tgt->line.s);
+    if ( tgt->nals != line->n_allele ) return -1;    // number of alleles does not match
+
+    int i;
+    for (i=0; i<tgt->nals; i++)
+        if ( strcmp(line->d.allele[i],tgt->als[i]) ) break; // we could be smarter, see vcmp
+    if ( i<tgt->nals ) return -1;
+
+    char *tmp, *str = tgt->line.s;
+    i = 0;
+    while ( *str && i<3 )
+    {
+        if ( *str=='\t' ) i++;
+        str++;
+    }
+    *alt_freq = strtod(str, &tmp);
+    if ( *tmp && !isspace(*tmp) )
+    {
+        if ( str[0]=='.' && (!str[1] || isspace(str[1])) ) return -1; // missing value
+        error("Could not parse: [%s]\n", tgt->line.s);
+    }
+    if ( *alt_freq<0 || *alt_freq>1 ) error("Could not parse AF: [%s]\n", tgt->line.s);
+    return 0;
+}
+
+int8_t *get_GT(args_t *args, bcf1_t *line)
+{
+    int i;
+    for (i=0; i<line->n_fmt; i++)
+        if ( line->d.fmt[i].id==args->gt_hdr_id ) break;
+    if ( i==line->n_fmt ) return NULL;        // the tag is not present in this record
+
+    bcf_fmt_t *fmt = &line->d.fmt[i];
+    if ( fmt->n!=2 ) return NULL;             // not diploid
+
+    if ( fmt->type!=BCF_BT_INT8 ) error("This is unexpected, GT type is %d\n", fmt->type);
+    return (int8_t*) fmt->p;
+}
+
+int estimate_AF_from_GT(args_t *args, int8_t *gt, double *alt_freq)
+{
+    int i, nalt = 0, nref = 0;
+    if ( args->af_smpl )        // subset samples for AF estimate
+    {
+        for (i=0; i<args->af_smpl->n; i++)
+        {
+            int ismpl = args->af_smpl->idx[i];
+            if ( bcf_gt_is_missing(gt[2*ismpl]) || bcf_gt_is_missing(gt[2*ismpl+1]) ) continue;
+
+            if ( bcf_gt_allele(gt[2*ismpl]) ) nalt++;
+            else nref++;
+
+            if ( bcf_gt_allele(gt[2*ismpl+1]) ) nalt++;
+            else nref++;
+        }
+    }
+    else                        // all samples used in AF estimate
+    {
+        int8_t *end = gt + 2*bcf_hdr_nsamples(args->hdr);
+        while ( gt < end )
+        {
+            if ( bcf_gt_is_missing(gt[0]) || bcf_gt_is_missing(gt[1]) )
+            {
+                gt += 2;
+                continue;
+            }
+
+            if ( bcf_gt_allele(gt[0]) ) nalt++;
+            else nref++;
+
+            if ( bcf_gt_allele(gt[1]) ) nalt++;
+            else nref++;
+
+            gt += 2;
+        }
+    }
+    if ( !nalt && !nref ) return -1;
+
+    *alt_freq = (double)nalt / (nalt + nref);
+    return 0;
+}
+
+int estimate_AF_from_PL(args_t *args, bcf_fmt_t *fmt_pl, int ial, double *alt_freq)
+{
+    double af = 0;
+    int i, j, naf = 0;
+
+    int irr = bcf_alleles2gt(0,0), ira = bcf_alleles2gt(0,ial), iaa = bcf_alleles2gt(ial,ial);
+    if ( iaa >= fmt_pl->n ) return -1;  // not diploid or wrong number of fields
+
+    if ( args->af_smpl )        // subset samples for AF estimate
+    {
+        #define BRANCH(type_t) \
+        { \
+            for (i=0; i<args->af_smpl->n; i++) \
+            { \
+                int ismpl = args->af_smpl->idx[i]; \
+                type_t *p = (type_t*)fmt_pl->p + fmt_pl->n*ismpl; \
+                if ( p[irr]<0 || p[ira]<0 || p[iaa]<0 ) continue;    /* missing value */ \
+                if ( p[irr]==p[ira] && p[irr]==p[iaa] ) continue;    /* all values are the same */ \
+                double prob[3], norm = 0; \
+                prob[0] = args->pl2p[ max255(p[irr]) ]; \
+                prob[1] = args->pl2p[ max255(p[ira]) ]; \
+                prob[2] = args->pl2p[ max255(p[iaa]) ]; \
+                for (j=0; j<3; j++) norm += prob[j]; \
+                for (j=0; j<3; j++) prob[j] /= norm; \
+                af += 0.5*prob[1] + prob[2]; \
+                naf++; \
+            } \
+        }
+        switch (fmt_pl->type) {
+            case BCF_BT_INT8:  BRANCH(int8_t); break;
+            case BCF_BT_INT16: BRANCH(int16_t); break;
+            case BCF_BT_INT32: BRANCH(int32_t); break;
+            default: fprintf(bcftools_stderr,"Unknown format type for PL: %s:%d .. fmt->type=%d\n", __FILE__,__LINE__, fmt_pl->type); bcftools_exit(1);
+        }
+        #undef BRANCH
+    }
+    else                        // all samples used in AF estimate
+    {
+        int nsmpl = bcf_hdr_nsamples(args->hdr);
+        #define BRANCH(type_t) \
+        { \
+            type_t *p = (type_t*)fmt_pl->p; \
+            p -= fmt_pl->n; \
+            for (i=0; i<nsmpl; i++) \
+            { \
+                p += fmt_pl->n; \
+                if ( p[irr]<0 || p[ira]<0 || p[iaa]<0 ) continue;    /* missing value */ \
+                if ( p[irr]==p[ira] && p[irr]==p[iaa] ) continue;    /* all values are the same */ \
+                double prob[3], norm = 0; \
+                prob[0] = args->pl2p[ max255(p[irr]) ]; \
+                prob[1] = args->pl2p[ max255(p[ira]) ]; \
+                prob[2] = args->pl2p[ max255(p[iaa]) ]; \
+                for (j=0; j<3; j++) norm += prob[j]; \
+                for (j=0; j<3; j++) prob[j] /= norm; \
+                af += 0.5*prob[1] + prob[2]; \
+                naf++; \
+            } \
+        }
+        switch (fmt_pl->type) {
+            case BCF_BT_INT8:  BRANCH(int8_t); break;
+            case BCF_BT_INT16: BRANCH(int16_t); break;
+            case BCF_BT_INT32: BRANCH(int32_t); break;
+            default: fprintf(bcftools_stderr,"Unknown format type for PL: %s:%d .. fmt->type=%d\n", __FILE__,__LINE__, fmt_pl->type); bcftools_exit(1);
+        }
+        #undef BRANCH
+    }
+    if ( !naf ) return -1;
+
+    *alt_freq = af / naf;
+    return 0;
+}
+
+bcf_fmt_t *get_PL(args_t *args, bcf1_t *line)
+{
+    int i;
+    for (i=0; i<line->n_fmt; i++)
+        if ( line->d.fmt[i].id==args->pl_hdr_id ) return &line->d.fmt[i];
+    return NULL;
+}
+
+int process_line(args_t *args, bcf1_t *line, int ial)
+{
+    if ( !(line->unpacked & BCF_UN_FMT) ) bcf_unpack(line, BCF_UN_FMT);
+
+    double alt_freq;
+    int8_t *GTs = NULL;
+    bcf_fmt_t *fmt_pl = NULL;
+
+    // Set allele frequency
+    int ret = 0, i,j;
+    if ( args->af_tag )
+    {
+        // Use an INFO tag provided by the user
+        ret = bcf_get_info_float(args->hdr, line, args->af_tag, &args->AFs, &args->mAFs);
+        if ( ret>0 )
+            alt_freq = args->AFs[ial-1];
+        if ( ret==-2 )
+            error("Type mismatch for INFO/%s tag at %s:%"PRId64"\n", args->af_tag, bcf_seqname(args->hdr,line), (int64_t) line->pos+1);
+    }
+    else if ( args->af_fname )
+    {
+        // Read AF from a file
+        ret = read_AF(args->files->targets, line, &alt_freq);
+    }
+    else if ( args->dflt_AF > 0 )
+    {
+        alt_freq = args->dflt_AF;
+    }
+    else if ( args->estimate_AF )
+    {
+        // Estimate AF from GTs or PLs of all samples or samples listed in a file
+        if ( args->af_from_PL )
+        {
+            fmt_pl = get_PL(args, line);
+            if ( !fmt_pl ) return -1;
+            ret = estimate_AF_from_PL(args, fmt_pl, ial, &alt_freq);
+        }
+        else
+        {
+            GTs = get_GT(args, line);
+            if ( !GTs ) return -1;
+            ret = estimate_AF_from_GT(args, GTs, &alt_freq);
+        }
+    }
+    else
+    {
+        // Use AC/AN
+        int AC = -1, AN = 0;
+        ret = bcf_get_info_int32(args->hdr, line, "AN", &args->itmp, &args->mitmp);
+        if ( ret==1 )
+        {
+            AN = args->itmp[0];
+            ret = bcf_get_info_int32(args->hdr, line, "AC", &args->itmp, &args->mitmp);
+            if ( ret>0 )
+                AC = args->itmp[0];
+        }
+        if ( AN<=0 || AC<0 )
+            ret = -1;
+        else
+            alt_freq = (double) AC/AN;
+    }
+
+    if ( args->dflt_AF>0 && (ret<0 || alt_freq==0.0) ) alt_freq = args->dflt_AF;
+    else if ( ret<0 ) { args->nno_af++; return ret; }
+    else if ( alt_freq==0.0 ) { args->nno_af++; return -1; }
+
+    int irr = bcf_alleles2gt(0,0), ira = bcf_alleles2gt(0,ial), iaa = bcf_alleles2gt(ial,ial);
+    if ( args->fake_PLs )
+    {
+        if ( !GTs ) GTs = get_GT(args, line);
+    }
+    else
+    {
+        fmt_pl = get_PL(args, line);
+        if ( !fmt_pl ) return -1;
+        if ( iaa >= fmt_pl->n ) return -1;  // not diploid or wrong number of fields
+    }
+
+    for (i=0; i<args->roh_smpl->n; i++)
+    {
+        int ismpl = args->roh_smpl->idx[i];
+
+        // set P(D|G)
+        double pdg[3];
+        if ( args->fake_PLs )
+        {
+            int8_t *gt = GTs + 2*ismpl;
+            if ( bcf_gt_is_missing(gt[0]) || bcf_gt_is_missing(gt[1]) ) continue;
+
+            int a = bcf_gt_allele(gt[0]);
+            int b = bcf_gt_allele(gt[1]);
+            if ( a!=b )
+            {
+                pdg[0] = pdg[2] = args->unseen_PL;
+                pdg[1] = 1 - 2*args->unseen_PL;
+            }
+            else if ( a==0 )
+            {
+                pdg[0] = 1 - args->unseen_PL - args->unseen_PL*args->unseen_PL;
+                pdg[1] = args->unseen_PL;
+                pdg[2] = args->unseen_PL*args->unseen_PL;
+            }
+            else
+            {
+                pdg[0] = args->unseen_PL*args->unseen_PL;
+                pdg[1] = args->unseen_PL;
+                pdg[2] = 1 - args->unseen_PL - args->unseen_PL*args->unseen_PL;
+            }
+        }
+        else
+        {
+            #define BRANCH(type_t) \
+            { \
+                type_t *p = (type_t*)fmt_pl->p + fmt_pl->n*ismpl; \
+                if ( p[irr]<0 || p[ira]<0 || p[iaa]<0 ) continue;    /* missing value */ \
+                if ( p[irr]==p[ira] && p[irr]==p[iaa] ) continue;    /* all values are the same */ \
+                pdg[0] = args->pl2p[ max255(p[irr]) ]; \
+                pdg[1] = args->pl2p[ max255(p[ira]) ]; \
+                pdg[2] = args->pl2p[ max255(p[iaa]) ]; \
+            }
+            switch (fmt_pl->type) {
+                case BCF_BT_INT8:  BRANCH(int8_t); break;
+                case BCF_BT_INT16: BRANCH(int16_t); break;
+                case BCF_BT_INT32: BRANCH(int32_t); break;
+                default: fprintf(bcftools_stderr,"Unknown format type for PL: %s:%d .. fmt->type=%d\n", __FILE__,__LINE__, fmt_pl->type); bcftools_exit(1);
+            }
+            #undef BRANCH
+        }
+
+        double sum = pdg[0] + pdg[1] + pdg[2];
+        if ( !sum ) continue;
+        for (j=0; j<3; j++) pdg[j] /= sum;
+        if ( args->skip_homref && pdg[0]>0.99 ) continue;
+
+        smpl_t *smpl = &args->smpl[i];
+        smpl->nused++;
+
+        if ( smpl->nsites >= smpl->msites )
+        {
+            hts_expand(uint32_t,smpl->nsites+1,smpl->msites,smpl->sites);
+            smpl->eprob = (double*) realloc(smpl->eprob,sizeof(*smpl->eprob)*smpl->msites*2);
+            if ( !smpl->eprob ) error("Error: failed to alloc %"PRIu64" bytes\n", (uint64_t)(sizeof(*smpl->eprob)*smpl->msites*2));
+        }
+
+        // Calculate emission probabilities P(D|AZ) and P(D|HW)
+        double *eprob = &smpl->eprob[2*smpl->nsites];
+        eprob[STATE_AZ] = pdg[0]*(1-alt_freq) + pdg[2]*alt_freq;
+        eprob[STATE_HW] = pdg[0]*(1-alt_freq)*(1-alt_freq) + 2*pdg[1]*(1-alt_freq)*alt_freq + pdg[2]*alt_freq*alt_freq;
+
+        smpl->sites[smpl->nsites] = line->pos;
+        smpl->nsites++;
+
+        if ( args->vi_training )
+        {
+            if ( !smpl->nrid || line->rid!=smpl->rid[smpl->nrid-1] )
+            {
+                smpl->nrid++;
+                smpl->rid = (int*) realloc(smpl->rid,sizeof(*smpl->rid)*smpl->nrid);
+                smpl->rid[smpl->nrid-1] = line->rid;
+                smpl->rid_off = (int*) realloc(smpl->rid_off,sizeof(*smpl->rid_off)*smpl->nrid);
+                smpl->rid_off[smpl->nrid-1] = smpl->nsites - 1;
+            }
+        }
+        else if ( args->nbuf_max && smpl->nsites >= args->nbuf_max ) flush_viterbi(args, i);
+    }
+
+    return 0;
+}
+
+static void vcfroh(args_t *args, bcf1_t *line)
+{
+    int i;
+
+    // Are we done?
+    if ( !line )
+    {
+        for (i=0; i<args->roh_smpl->n; i++) flush_viterbi(args, i);
+        return;
+    }
+
+    // Skip unwanted lines, for simplicity we consider only biallelic sites
+    if ( line->rid == args->skip_rid ) return;
+
+    // This can be raw callable VCF with the symbolic unseen allele <*>
+    int ial = 0, nalt = line->n_allele - 1;
+    for (i=1; i<line->n_allele; i++)
+    {
+        if ( !strcmp("<*>",line->d.allele[i]) || !strcmp("<NON_REF>",line->d.allele[i]) ) nalt--;
+        else if ( !ial ) ial = i;
+    }
+
+    if ( !nalt ) // no ALT allele
+    {
+        args->nno_alt++;
+        if ( !args->include_noalt_sites ) return;
+    }
+    else if ( nalt>1 )
+    {
+        args->nmultiallelic++;
+        return;
+    }
+
+    if ( args->snps_only && !bcf_is_snp(line) ) return;
+
+    // Initialize genetic map
+    int skip_rid = 0;
+    if ( args->prev_rid<0 )
+        skip_rid = load_genmap(args, bcf_seqname(args->hdr,line));
+
+    // New chromosome?
+    if ( args->prev_rid!=line->rid )
+    {
+        if ( !args->vi_training )
+        {
+            for (i=0; i<args->roh_smpl->n; i++)
+            {
+                flush_viterbi(args, i);
+                hmm_reset(args->hmm, args->smpl[i].snapshot);
+            }
+        }
+        args->prev_rid = line->rid;
+        args->prev_pos = line->pos;
+        skip_rid = load_genmap(args, bcf_seqname(args->hdr,line));
+    }
+    else if ( args->prev_pos == line->pos )
+    {
+        args->ndup++;
+        return;     // skip duplicate positions
+    }
+
+    if ( skip_rid )
+    {
+        fprintf(bcftools_stderr,"Skipping the sequence, no genmap for %s\n", bcf_seqname(args->hdr,line));
+        args->skip_rid = line->rid;
+        return;
+    }
+    if ( args->prev_pos > line->pos ) error("The file is not sorted?!\n");
+
+    args->prev_rid = line->rid;
+    args->prev_pos = line->pos;
+
+
+    // parse the new line
+    process_line(args, line, ial);
+}
+
+static void usage(args_t *args)
+{
+    fprintf(bcftools_stderr, "\n");
+    fprintf(bcftools_stderr, "About:   HMM model for detecting runs of autozygosity.\n");
+    fprintf(bcftools_stderr, "Usage:   bcftools roh [options] <in.vcf.gz>\n");
+    fprintf(bcftools_stderr, "\n");
+    fprintf(bcftools_stderr, "General Options:\n");
+    fprintf(bcftools_stderr, "        --AF-dflt <float>              if AF is not known, use this allele frequency [skip]\n");
+    fprintf(bcftools_stderr, "        --AF-tag <TAG>                 use TAG for allele frequency\n");
+    fprintf(bcftools_stderr, "        --AF-file <file>               read allele frequencies from file (CHR\\tPOS\\tREF,ALT\\tAF)\n");
+    fprintf(bcftools_stderr, "    -b  --buffer-size <int[,int]>      buffer size and the number of overlapping sites, 0 for unlimited [0]\n");
+    fprintf(bcftools_stderr, "                                           If the first number is negative, it is interpreted as the maximum memory to\n");
+    fprintf(bcftools_stderr, "                                           use, in MB. The default overlap is set to roughly 1%% of the buffer size.\n");
+    fprintf(bcftools_stderr, "    -e, --estimate-AF [TAG],<file>     estimate AF from FORMAT/TAG (GT or PL) of all samples (\"-\") or samples listed\n");
+    fprintf(bcftools_stderr, "                                            in <file>. If TAG is not given, the frequency is estimated from GT by default\n");
+    fprintf(bcftools_stderr, "        --exclude <expr>               exclude sites for which the expression is true\n");
+    fprintf(bcftools_stderr, "    -G, --GTs-only <float>             use GTs and ignore PLs, instead using <float> for PL of the two least likely genotypes.\n");
+    fprintf(bcftools_stderr, "                                           Safe value to use is 30 to account for GT errors.\n");
+    fprintf(bcftools_stderr, "        --include <expr>               select sites for which the expression is true\n");
+    fprintf(bcftools_stderr, "    -i, --ignore-homref                skip hom-ref genotypes (0/0)\n");
+    fprintf(bcftools_stderr, "        --include-noalt                include sites with no ALT allele (ignored by default)\n");
+    fprintf(bcftools_stderr, "    -I, --skip-indels                  skip indels as their genotypes are enriched for errors\n");
+    fprintf(bcftools_stderr, "    -m, --genetic-map <file>           genetic map in IMPUTE2 format, single file or mask, where string \"{CHROM}\"\n");
+    fprintf(bcftools_stderr, "                                           is replaced with chromosome name\n");
+    fprintf(bcftools_stderr, "    -M, --rec-rate <float>             constant recombination rate per bp\n");
+    fprintf(bcftools_stderr, "    -o, --output <file>                write output to a file [standard output]\n");
+    fprintf(bcftools_stderr, "    -O, --output-type [srz]            output s:per-site, r:regions, z:compressed [sr]\n");
+    fprintf(bcftools_stderr, "    -r, --regions <region>             restrict to comma-separated list of regions\n");
+    fprintf(bcftools_stderr, "    -R, --regions-file <file>          restrict to regions listed in a file\n");
+    fprintf(bcftools_stderr, "        --regions-overlap 0|1|2        Include if POS in the region (0), record overlaps (1), variant overlaps (2) [1]\n");
+    fprintf(bcftools_stderr, "    -s, --samples <list>               list of samples to analyze [all samples]\n");
+    fprintf(bcftools_stderr, "    -S, --samples-file <file>          file of samples to analyze [all samples]\n");
+    fprintf(bcftools_stderr, "    -t, --targets <region>             similar to -r but streams rather than index-jumps\n");
+    fprintf(bcftools_stderr, "    -T, --targets-file <file>          similar to -R but streams rather than index-jumps\n");
+    fprintf(bcftools_stderr, "        --targets-overlap 0|1|2        Include if POS in the region (0), record overlaps (1), variant overlaps (2) [0]\n");
+    fprintf(bcftools_stderr, "        --threads <int>                use multithreading with <int> worker threads [0]\n");
+    fprintf(bcftools_stderr, "\n");
+    fprintf(bcftools_stderr, "HMM Options:\n");
+    fprintf(bcftools_stderr, "    -a, --hw-to-az <float>             P(AZ|HW) transition probability from HW (Hardy-Weinberg) to AZ (autozygous) state [6.7e-8]\n");
+    fprintf(bcftools_stderr, "    -H, --az-to-hw <float>             P(HW|AZ) transition probability from AZ to HW state [5e-9]\n");
+    fprintf(bcftools_stderr, "    -V, --viterbi-training <float>     estimate HMM parameters, <float> is the convergence threshold, e.g. 1e-10 (experimental)\n");
+    fprintf(bcftools_stderr, "\n");
+    bcftools_exit(1);
+}
+
+int main_vcfroh(int argc, char *argv[])
+{
+    int c;
+    args_t *args  = (args_t*) calloc(1,sizeof(args_t));
+    args->argc    = argc; args->argv = argv;
+    args->files   = bcf_sr_init();
+    args->t2AZ    = 6.7e-8;
+    args->t2HW    = 5e-9;
+    args->rec_rate = 0;
+    int regions_is_file = 0, targets_is_file = 0;
+    int regions_overlap = 1;
+    int targets_overlap = 0;
+
+    static struct option loptions[] =
+    {
+        {"AF-tag",1,0,0},
+        {"AF-file",1,0,1},
+        {"AF-dflt",1,0,2},
+        {"include",1,0,3},
+        {"exclude",1,0,4},
+        {"include-noalt",0,0,5},
+        {"buffer-size",1,0,'b'},
+        {"ignore-homref",0,0,'i'},
+        {"estimate-AF",1,0,'e'},
+        {"output",1,0,'o'},
+        {"output-type",1,0,'O'},
+        {"GTs-only",1,0,'G'},
+        {"samples",1,0,'s'},
+        {"samples-file",1,0,'S'},
+        {"hw-to-az",1,0,'a'},
+        {"az-to-hw",1,0,'H'},
+        {"viterbi-training",1,0,'V'},
+        {"targets",1,0,'t'},
+        {"targets-file",1,0,'T'},
+        {"targets-overlap",required_argument,NULL,6},
+        {"regions",1,0,'r'},
+        {"regions-file",1,0,'R'},
+        {"regions-overlap",required_argument,NULL,7},
+        {"genetic-map",1,0,'m'},
+        {"rec-rate",1,0,'M'},
+        {"skip-indels",0,0,'I'},
+        {"threads",1,0,9},
+        {0,0,0,0}
+    };
+
+    int naf_opts = 0;
+    char *tmp;
+    while ((c = getopt_long(argc, argv, "h?r:R:t:T:H:a:s:S:m:M:G:Ia:e:V:b:O:o:i",loptions,NULL)) >= 0) {
+        switch (c) {
+            case 0: args->af_tag = optarg; naf_opts++; break;
+            case 1: args->af_fname = optarg; naf_opts++; break;
+            case 2:
+                args->dflt_AF = strtod(optarg,&tmp);
+                if ( *tmp ) error("Could not parse: --AF-dflt %s\n", optarg);
+                break;
+            case  3 :
+                if ( args->filter_str ) error("Error: only one --include or --exclude expression can be given, and they cannot be combined\n");
+                args->filter_str = optarg; args->filter_logic |= FLT_INCLUDE; break;
+            case  4 :
+                if ( args->filter_str ) error("Error: only one --include or --exclude expression can be given, and they cannot be combined\n");
+                args->filter_str = optarg; args->filter_logic |= FLT_EXCLUDE; break;
+            case 5: args->include_noalt_sites = 1; break;
+            case 'o': args->output_fname = optarg; break;
+            case 'O':
+                if ( strchr(optarg,'s') || strchr(optarg,'S') ) args->output_type |= OUTPUT_ST;
+                if ( strchr(optarg,'r') || strchr(optarg,'R') ) args->output_type |= OUTPUT_RG;
+                if ( strchr(optarg,'z') || strchr(optarg,'z') ) args->output_type |= OUTPUT_GZ;
+                break;
+            case 'e': args->estimate_AF = optarg; naf_opts++; break;
+            case 'b': args->buffer_size = optarg; break;
+            case 'i': args->skip_homref = 1; break;
+            case 'I': args->snps_only = 1; break;
+            case 'G':
+                args->fake_PLs = 1;
+                args->unseen_PL = strtod(optarg,&tmp);
+                if ( *tmp ) error("Could not parse: -G %s\n", optarg);
+                args->unseen_PL = pow(10,-args->unseen_PL/10.);
+                break;
+            case 'm': args->genmap_fname = optarg; break;
+            case 'M':
+                args->rec_rate = strtod(optarg,&tmp);
+                if ( *tmp ) error("Could not parse: -M %s\n", optarg);
+                break;
+            case 's': args->samples = strdup(optarg); break;
+            case 'S': args->samples = strdup(optarg); args->samples_is_file = 1; break;
+            case 'a':
+                args->t2AZ = strtod(optarg,&tmp);
+                if ( *tmp ) error("Could not parse: -a %s\n", optarg);
+                break;
+            case 'H':
+                args->t2HW = strtod(optarg,&tmp);
+                if ( *tmp ) error("Could not parse: -H %s\n", optarg);
+                break;
+            case 't': args->targets_list = optarg; break;
+            case 'T': args->targets_list = optarg; targets_is_file = 1; break;
+            case 'r': args->regions_list = optarg; break;
+            case 'R': args->regions_list = optarg; regions_is_file = 1; break;
+            case  6 :
+                targets_overlap = parse_overlap_option(optarg);
+                if ( targets_overlap < 0 ) error("Could not parse: --targets-overlap %s\n",optarg);
+                break;
+            case  7 :
+                regions_overlap = parse_overlap_option(optarg);
+                if ( regions_overlap < 0 ) error("Could not parse: --regions-overlap %s\n",optarg);
+                break;
+            case  9 : args->n_threads = strtol(optarg, 0, 0); break;
+            case 'V':
+                args->vi_training = 1;
+                args->baum_welch_th = strtod(optarg,&tmp);
+                if ( *tmp ) error("Could not parse: --viterbi-training %s\n", optarg);
+                break;
+            case 'h':
+            case '?': usage(args); break;
+            default: error("Unknown argument: %s\n", optarg);
+        }
+    }
+    if ( !args->output_fname ) args->output_fname = "bcftools_stdout";
+    if ( !args->output_type || args->output_type==OUTPUT_GZ ) args->output_type |= OUTPUT_ST|OUTPUT_RG;
+    char *fname = NULL;
+    if ( optind==argc )
+    {
+        if ( !isatty(fileno((FILE *)stdin)) ) fname = "-";  // reading from stdin
+        else usage(args);
+    }
+    else fname = argv[optind];
+
+    if ( args->vi_training && args->buffer_size ) error("Error: cannot use -b with -V\n");
+    if ( args->t2AZ<0 || args->t2AZ>1 ) error("Error: The parameter --hw-to-az is not in [0,1] .. %e\n", args->t2AZ);
+    if ( args->t2HW<0 || args->t2HW>1 ) error("Error: The parameter --az-to-hw is not in [0,1] .. %e\n", args->t2HW);
+    if ( naf_opts>1 ) error("Error: The options --AF-tag, --AF-file and -e are mutually exclusive\n");
+    if ( args->af_fname && args->targets_list ) error("Error: The options --AF-file and -t are mutually exclusive\n");
+    if ( args->regions_list )
+    {
+        bcf_sr_set_opt(args->files,BCF_SR_REGIONS_OVERLAP,regions_overlap);
+        if ( bcf_sr_set_regions(args->files, args->regions_list, regions_is_file)<0 )
+            error("Failed to read the regions: %s\n", args->regions_list);
+    }
+    if ( args->targets_list )
+    {
+        bcf_sr_set_opt(args->files,BCF_SR_TARGETS_OVERLAP,targets_overlap);
+        if ( bcf_sr_set_targets(args->files, args->targets_list, targets_is_file, 0)<0 )
+            error("Failed to read the targets: %s\n", args->targets_list);
+    }
+    if ( args->af_fname )
+    {
+        if ( bcf_sr_set_targets(args->files, args->af_fname, 1, 3)<0 )
+            error("Failed to read the targets: %s\n", args->af_fname);
+    }
+    if ( args->n_threads && bcf_sr_set_threads(args->files, args->n_threads)<0)
+        error("Failed to create threads\n");
+    if ( !bcf_sr_add_reader(args->files, fname) ) error("Failed to read from %s: %s\n", !strcmp("-",fname)?"standard input":fname,bcf_sr_strerror(args->files->errnum));
+
+    init_data(args);
+    while ( bcf_sr_next_line(args->files) )
+    {
+        args->ntot++;
+        bcf1_t *line = bcf_sr_get_line(args->files,0);
+        if ( args->filter )
+        {
+            int pass = filter_test(args->filter, line, NULL);
+            if ( args->filter_logic & FLT_EXCLUDE ) pass = pass ? 0 : 1;
+            if ( !pass ) { args->nfiltered++; continue; }
+        }
+        vcfroh(args, line);
+    }
+    vcfroh(args, NULL);
+    int i, nmin = 0;
+    for (i=0; i<args->roh_smpl->n; i++)
+        if ( !i || args->smpl[i].nused < nmin ) nmin = args->smpl[i].nused;
+    if ( args->af_fname )
+        fprintf(bcftools_stderr,"Number of lines overlapping with --AF-file/processed: %d/%d\n", args->ntot,nmin);
+    else
+        fprintf(bcftools_stderr,"Number of lines total/processed: %d/%d\n", args->ntot,nmin);
+    fprintf(bcftools_stderr,"Number of lines filtered/no AF/no alt/multiallelic/dup: %d/%d/%d/%d/%d\n", args->nfiltered,args->nno_af,args->nno_alt,args->nmultiallelic,args->ndup);
+    if ( nmin==0 )
+    {
+        fprintf(bcftools_stderr,"No usable sites were found.\n");
+        if ( !naf_opts && !args->dflt_AF ) fprintf(bcftools_stderr, " Consider using one of the AF options.\n");
+    }
+    destroy_data(args);
+    free(args);
+    return 0;
+}
+
+
diff --git a/bcftools/vcfsom.c b/bcftools/vcfsom.c
new file mode 100644
index 0000000..db01d24
--- /dev/null
+++ b/bcftools/vcfsom.c
@@ -0,0 +1,718 @@
+/*  vcfsom.c -- SOM (Self-Organizing Map) filtering.
+
+    Copyright (C) 2013-2014, 2020 Genome Research Ltd.
+
+    Author: Petr Danecek <pd3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.  */
+
+#include <stdio.h>
+#include <unistd.h>
+#include <getopt.h>
+#include <assert.h>
+#include <ctype.h>
+#include <string.h>
+#include <errno.h>
+#include <sys/stat.h>
+#include <sys/types.h>
+#include <math.h>
+#include <time.h>
+#include <htslib/vcf.h>
+#include <htslib/synced_bcf_reader.h>
+#include <htslib/vcfutils.h>
+#include <htslib/hts_os.h>
+#include <inttypes.h>
+#include "bcftools.h"
+
+#define SOM_TRAIN    1
+#define SOM_CLASSIFY 2
+
+typedef struct
+{
+    int ndim;       // dimension of the map (2D, 3D, ...)
+    int nbin;       // number of bins in th map
+    int size;       // pow(nbin,ndim)
+    int kdim;       // dimension of the input vectors
+    int nt, t;      // total number of learning cycles and the current cycle
+    double *w, *c;  // weights and counts (sum of learning influence)
+    double learn;   // learning rate
+    double bmu_th;  // best-matching unit threshold
+    int *a_idx, *b_idx; // temp arrays for traversing variable number of nested loops
+    double *div;        // dtto
+}
+som_t;
+
+typedef struct
+{
+    // SOM parameters
+    double bmu_th, learn;
+    int ndim, nbin, ntrain, t;
+    int nfold;                  // n-fold cross validation = the number of SOMs
+    som_t **som;
+
+    // annots reader's data
+    htsFile *file;              // reader
+    kstring_t str;              // temporary string for the reader
+    int dclass, mvals;
+    double *vals;
+
+    // training data
+    double *train_dat;
+    int *train_class, mtrain_class, mtrain_dat;
+
+    int rand_seed, good_class, bad_class;
+    char **argv, *fname, *prefix;
+    int argc, action, train_bad, merge;
+}
+args_t;
+
+static void usage(void);
+FILE *open_file(char **fname, const char *mode, const char *fmt, ...);
+void mkdir_p(const char *fmt, ...);
+
+char *msprintf(const char *fmt, ...)
+{
+    va_list ap;
+    va_start(ap, fmt);
+    int n = vsnprintf(NULL, 0, fmt, ap) + 2;
+    va_end(ap);
+
+    char *str = (char*)malloc(n);
+    va_start(ap, fmt);
+    vsnprintf(str, n, fmt, ap);
+    va_end(ap);
+
+    return str;
+}
+
+/*
+ *  char *t, *p = str;
+ *  t = column_next(p, '\t');
+ *  if ( strlen("<something>")==t-p && !strncmp(p,"<something>",t-p) ) printf("found!\n");
+ *
+ *  char *t;
+ *  t = column_next(str, '\t'); if ( !*t ) error("expected field\n", str);
+ *  t = column_next(t+1, '\t'); if ( !*t ) error("expected field\n", str);
+ */
+static inline char *column_next(char *start, char delim)
+{
+    char *end = start;
+    while (*end && *end!=delim) end++;
+    return end;
+}
+/**
+ *  annots_reader_next() - reads next line from annots.tab.gz and sets: class, vals
+ *   Returns 1 on successful read or 0 if no further record could be read.
+ */
+int annots_reader_next(args_t *args)
+{
+    args->str.l = 0;
+    if ( hts_getline(args->file,'\n',&args->str)<=0 ) return 0;
+
+    char *t, *line = args->str.s;
+
+    if ( !args->mvals )
+    {
+        t = line;
+        while ( *t )
+        {
+            if ( *t=='\t' ) args->mvals++;
+            t++;
+        }
+        args->vals = (double*) malloc(args->mvals*sizeof(double));
+    }
+
+    // class
+    args->dclass = atoi(line);
+    t = column_next(line, '\t');
+
+    // values
+    int i;
+    for (i=0; i<args->mvals; i++)
+    {
+        if ( !*t ) error("Could not parse %d-th data field: is the line truncated?\nThe line was: [%s]\n",i+2,line);
+        args->vals[i] = atof(++t);
+        t = column_next(t,'\t');
+    }
+    return 1;
+}
+void annots_reader_reset(args_t *args)
+{
+    if ( args->file ) hts_close(args->file);
+    if ( !args->fname ) error("annots_reader_reset: no fname\n");
+    args->file = hts_open(args->fname, "r");
+}
+void annots_reader_close(args_t *args)
+{
+    hts_close(args->file);
+}
+
+static void som_write_map(char *prefix, som_t **som, int nsom)
+{
+    FILE *fp = open_file(NULL,"w","%s.som",prefix);
+    size_t nw;
+    if ( (nw=fwrite("SOMv1",5,1,fp))!=5 ) error("Failed to write 5 bytes\n");
+    if ( (nw=fwrite(&nsom,sizeof(int),1,fp))!=sizeof(int) ) error("Failed to write %zu bytes\n",sizeof(int));
+    int i;
+    for (i=0; i<nsom; i++)
+    {
+        if ( (nw=fwrite(&som[i]->size,sizeof(int),1,fp))!=sizeof(int) ) error("Failed to write %zu bytes\n",sizeof(int));
+        if ( (nw=fwrite(&som[i]->kdim,sizeof(int),1,fp))!=sizeof(int) ) error("Failed to write %zu bytes\n",sizeof(int));
+        if ( (nw=fwrite(som[i]->w,sizeof(double),som[i]->size*som[i]->kdim,fp))!=sizeof(double)*som[i]->size*som[i]->kdim ) error("Failed to write %zu bytes\n",sizeof(double)*som[i]->size*som[i]->kdim);
+        if ( (nw=fwrite(som[i]->c,sizeof(double),som[i]->size,fp))!=sizeof(double)*som[i]->size ) error("Failed to write %zu bytes\n",sizeof(double)*som[i]->size);
+    }
+    if ( fclose(fp) ) error("%s.som: fclose failed\n",prefix);
+}
+static som_t** som_load_map(char *prefix, int *nsom)
+{
+    FILE *fp = open_file(NULL,"r","%s.som",prefix);
+    char buf[5];
+    if ( fread(buf,5,1,fp)!=1 || strncmp(buf,"SOMv1",5) ) error("Could not parse %s.som\n", prefix);
+
+    if ( fread(nsom,sizeof(int),1,fp)!=1 ) error("Could not read %s.som\n", prefix);
+    som_t **som = (som_t**)malloc(*nsom*sizeof(som_t*));
+
+    int i;
+    for (i=0; i<*nsom; i++)
+    {
+        som[i] = (som_t*) calloc(1,sizeof(som_t));
+        if ( fread(&som[i]->size,sizeof(int),1,fp) != 1 ) error("Could not read %s.som\n", prefix);
+        if ( fread(&som[i]->kdim,sizeof(int),1,fp) != 1 ) error("Could not read %s.som\n", prefix);
+        som[i]->w = (double*) malloc(sizeof(double)*som[i]->size*som[i]->kdim);
+        som[i]->c = (double*) malloc(sizeof(double)*som[i]->size);
+        if ( fread(som[i]->w,sizeof(double),som[i]->size*som[i]->kdim,fp) != som[i]->size*som[i]->kdim ) error("Could not read from %s.som\n", prefix);
+        if ( fread(som[i]->c,sizeof(double),som[i]->size,fp) != som[i]->size ) error("Could not read from %s.som\n", prefix);
+    }
+    if ( fclose(fp) ) error("%s.som: fclose failed\n",prefix);
+    return som;
+}
+static void som_create_plot(som_t *som, char *prefix)
+{
+    if ( som->ndim!=2 ) return;
+
+    char *fname;
+    FILE *fp = open_file(&fname,"w","%s.py",prefix);
+    fprintf(fp,
+            "import matplotlib as mpl\n"
+            "mpl.use('Agg')\n"
+            "import matplotlib.pyplot as plt\n"
+            "\n"
+            "dat = [\n"
+           );
+    int i,j;
+    double *val = som->c;
+    for (i=0; i<som->nbin; i++)
+    {
+        fprintf(fp,"[");
+        for (j=0; j<som->nbin; j++)
+        {
+            if ( j>0 ) fprintf(fp,",");
+            fprintf(fp,"%e", *val);
+            val++;
+        }
+        fprintf(fp,"],\n");
+    }
+    fprintf(fp,
+            "]\n"
+            "fig = plt.figure()\n"
+            "ax1 = plt.subplot(111)\n"
+            "im1 = ax1.imshow(dat)\n"
+            "fig.colorbar(im1)\n"
+            "plt.savefig('%s.png')\n"
+            "plt.close()\n"
+            "\n", prefix
+           );
+    fclose(fp);
+    free(fname);
+}
+// Find the best matching unit: the node with minimum distance from the input vector
+static inline int som_find_bmu(som_t *som, double *vec, double *dist)
+{
+    double *ptr = som->w;
+    double min_dist = HUGE_VAL;
+    int min_idx = 0;
+
+    int i, k;
+    for (i=0; i<som->size; i++)
+    {
+        double dist = 0;
+        for (k=0; k<som->kdim; k++)
+            dist += (vec[k] - ptr[k]) * (vec[k] - ptr[k]);
+        if ( dist < min_dist )
+        {
+            min_dist = dist;
+            min_idx  = i;
+        }
+        ptr += som->kdim;
+    }
+
+    if ( dist ) *dist = min_dist;
+    return min_idx;
+}
+static inline double som_get_score(som_t *som, double *vec, double bmu_th)
+{
+    double *ptr = som->w;
+    double min_dist = HUGE_VAL;
+
+    int i, k;
+    for (i=0; i<som->size; i++)
+    {
+        if ( som->c[i] >= bmu_th )
+        {
+            double dist = 0;
+            for (k=0; k<som->kdim; k++)
+                dist += (vec[k] - ptr[k]) * (vec[k] - ptr[k]);
+            if ( dist < min_dist ) min_dist = dist;
+        }
+        ptr += som->kdim;
+    }
+    return sqrt(min_dist);
+}
+// Convert flat index to that of a k-dimensional cube
+static inline void som_idx_to_ndim(som_t *som, int idx, int *ndim)
+{
+    int i;
+    double sub = 0;
+
+    ndim[0] = idx/som->div[0];
+    for (i=1; i<som->ndim; i++)
+    {
+        sub += ndim[i-1] * som->div[i-1];
+        ndim[i] = (idx - sub)/som->div[i];
+    }
+}
+static void som_train_site(som_t *som, double *vec, int update_counts)
+{
+    // update learning rate and learning radius
+    som->t++;
+    double dt = exp(-som->t/som->nt);
+    double learning_rate = som->learn * dt;
+    double radius = som->nbin * dt; radius *= radius;
+
+    // find the best matching unit and its indexes
+    int min_idx = som_find_bmu(som, vec, NULL);
+    som_idx_to_ndim(som, min_idx, som->a_idx);
+
+    // update the weights: traverse the map and make all nodes within the
+    // radius more similar to the input vector
+    double *ptr = som->w;
+    double *cnt = som->c;
+    int i, j, k;
+    for (i=0; i<som->size; i++)
+    {
+        som_idx_to_ndim(som, i, som->b_idx);
+        double dist = 0;
+        for (j=0; j<som->ndim; j++)
+            dist += (som->a_idx[j] - som->b_idx[j]) * (som->a_idx[j] - som->b_idx[j]);
+        if ( dist <= radius )
+        {
+            double influence = exp(-dist*dist*0.5/radius) * learning_rate;
+            for (k=0; k<som->kdim; k++)
+                ptr[k] += influence * (vec[k] - ptr[k]);
+
+            // Bad sites may help to shape the map, but only nodes with big enough
+            // influence will be used for classification.
+            if ( update_counts ) *cnt += influence;
+        }
+        ptr += som->kdim;
+        cnt++;
+    }
+}
+static void som_norm_counts(som_t *som)
+{
+    int i;
+    double max = 0;
+    for (i=0; i<som->size; i++)
+        if ( max < som->c[i] ) max = som->c[i];
+    for (i=0; i<som->size; i++)
+        som->c[i] /= max;
+}
+static som_t *som_init(args_t *args)
+{
+    som_t *som  = (som_t*) calloc(1,sizeof(som_t));
+    som->ndim   = args->ndim;
+    som->nbin   = args->nbin;
+    som->kdim   = args->mvals;
+    som->nt     = args->ntrain;
+    som->learn  = args->learn;
+    som->bmu_th = args->bmu_th;
+    som->size   = pow(som->nbin,som->ndim);
+    som->w = (double*) malloc(sizeof(double)*som->size*som->kdim);
+    if ( !som->w ) error("Could not alloc %"PRIu64" bytes [nbin=%d ndim=%d kdim=%d]\n", (uint64_t)(sizeof(double)*som->size*som->kdim),som->nbin,som->ndim,som->kdim);
+    som->c = (double*) calloc(som->size,sizeof(double));
+    if ( !som->w ) error("Could not alloc %"PRIu64" bytes [nbin=%d ndim=%d]\n", (uint64_t)(sizeof(double)*som->size),som->nbin,som->ndim);
+    int i;
+    for (i=0; i<som->size*som->kdim; i++)
+        som->w[i] = random();
+    som->a_idx = (int*) malloc(sizeof(int)*som->ndim);
+    som->b_idx = (int*) malloc(sizeof(int)*som->ndim);
+    som->div   = (double*) malloc(sizeof(double)*som->ndim);
+    for (i=0; i<som->ndim; i++)
+        som->div[i] = pow(som->nbin,som->ndim-i-1);
+    return som;
+}
+static void som_destroy(som_t *som)
+{
+    free(som->a_idx); free(som->b_idx); free(som->div);
+    free(som->w); free(som->c);
+    free(som);
+}
+
+static void init_data(args_t *args)
+{
+    // Get first line to learn the vector size
+    annots_reader_reset(args);
+    annots_reader_next(args);
+
+    if ( args->action==SOM_CLASSIFY )
+        args->som = som_load_map(args->prefix,&args->nfold);
+}
+static void destroy_data(args_t *args)
+{
+    int i;
+    if ( args->som )
+    {
+        for (i=0; i<args->nfold; i++) som_destroy(args->som[i]);
+    }
+    free(args->train_dat);
+    free(args->train_class);
+    free(args->som);
+    free(args->vals);
+    free(args->str.s);
+}
+
+#define MERGE_MIN 0
+#define MERGE_MAX 1
+#define MERGE_AVG 2
+static double get_min_score(args_t *args, int iskip)
+{
+    int i;
+    double score, min_score = HUGE_VAL;
+    for (i=0; i<args->nfold; i++)
+    {
+        if ( i==iskip ) continue;
+        score = som_get_score(args->som[i], args->vals, args->bmu_th);
+        if ( i==0 || score < min_score ) min_score = score;
+    }
+    return min_score;
+}
+static double get_max_score(args_t *args, int iskip)
+{
+    int i;
+    double score, max_score = -HUGE_VAL;
+    for (i=0; i<args->nfold; i++)
+    {
+        if ( i==iskip ) continue;
+        score = som_get_score(args->som[i], args->vals, args->bmu_th);
+        if ( i==0 || max_score < score ) max_score = score;
+    }
+    return max_score;
+}
+static double get_avg_score(args_t *args, int iskip)
+{
+    int i, n = 0;
+    double score = 0;
+    for (i=0; i<args->nfold; i++)
+    {
+        if ( i==iskip ) continue;
+        score += som_get_score(args->som[i], args->vals, args->bmu_th);
+        n++;
+    }
+    return score/n;
+}
+static int cmpfloat_desc(const void *a, const void *b)
+{
+    float fa = *((float*)a);
+    float fb = *((float*)b);
+    if ( fa<fb ) return 1;
+    if ( fa>fb ) return -1;
+    return 0;
+}
+
+static void create_eval_plot(args_t *args)
+{
+    FILE *fp = open_file(NULL,"w","%s.eval.py", args->prefix);
+    fprintf(fp,
+            "import matplotlib as mpl\n"
+            "mpl.use('Agg')\n"
+            "import matplotlib.pyplot as plt\n"
+            "\n"
+            "import csv\n"
+            "csv.register_dialect('tab', delimiter='\\t', quoting=csv.QUOTE_NONE)\n"
+            "dat = []\n"
+            "with open('%s.eval', 'r') as f:\n"
+            "\treader = csv.reader(f, 'tab')\n"
+            "\tfor row in reader:\n"
+            "\t\tif row[0][0]!='#': dat.append(row)\n"
+            "\n"
+            "fig = plt.figure()\n"
+            "ax1 = plt.subplot(111)\n"
+            "ax1.plot([x[0] for x in dat],[x[1] for x in dat],'g',label='Good')\n"
+            "ax1.plot([x[0] for x in dat],[x[2] for x in dat],'r',label='Bad')\n"
+            "ax1.set_xlabel('SOM score')\n"
+            "ax1.set_ylabel('Number of training sites')\n"
+            "ax1.legend(loc='best',prop={'size':8},frameon=False)\n"
+            "plt.savefig('%s.eval.png')\n"
+            "plt.close()\n"
+            "\n", args->prefix,args->prefix
+           );
+    fclose(fp);
+}
+
+static void do_train(args_t *args)
+{
+    // read training sites
+    int i, igood = 0, ibad = 0, ngood = 0, nbad = 0, ntrain = 0;
+    annots_reader_reset(args);
+    while ( annots_reader_next(args) )
+    {
+        // determine which of the nfold's SOMs to train
+        int isom = 0;
+        if ( args->dclass == args->good_class )
+        {
+            if ( ++igood >= args->nfold ) igood = 0;
+            isom = igood;
+            ngood++;
+        }
+        else if ( args->dclass == args->bad_class )
+        {
+            if ( ++ibad >= args->nfold ) ibad = 0;
+            isom = ibad;
+            nbad++;
+        }
+        else
+            error("Could not determine the class: %d (vs %d and %d)\n", args->dclass,args->good_class,args->bad_class);
+
+        // save the values for evaluation
+        ntrain++;
+        hts_expand(double, ntrain*args->mvals, args->mtrain_dat, args->train_dat);
+        hts_expand(int, ntrain, args->mtrain_class, args->train_class);
+        memcpy(args->train_dat+(ntrain-1)*args->mvals, args->vals, args->mvals*sizeof(double));
+        args->train_class[ntrain-1] = (args->dclass==args->good_class ? 1 : 0) | isom<<1;  // store class + chunk used for training
+    }
+    annots_reader_close(args);
+
+    // init maps
+    if ( !args->ntrain ) args->ntrain = ngood/args->nfold;
+    srandom(args->rand_seed);
+    args->som = (som_t**) malloc(sizeof(som_t*)*args->nfold);
+    for (i=0; i<args->nfold; i++) args->som[i] = som_init(args);
+
+    // train
+    for (i=0; i<ntrain; i++)
+    {
+        int is_good = args->train_class[i] & 1;
+        int isom    = args->train_class[i] >> 1;
+        if ( is_good || args->train_bad )
+            som_train_site(args->som[isom], args->train_dat+i*args->mvals, is_good);
+    }
+
+    // norm and create plots
+    for (i=0; i<args->nfold; i++)
+    {
+        som_norm_counts(args->som[i]);
+        if ( args->prefix )
+        {
+            char *bname = msprintf("%s.som.%d", args->prefix,i);
+            som_create_plot(args->som[i], bname);
+            free(bname);
+        }
+    }
+
+    // evaluate
+    float *good = (float*) malloc(sizeof(float)*ngood); assert(good);
+    float *bad  = (float*) malloc(sizeof(float)*nbad); assert(bad);
+    igood = ibad = 0;
+    double max_score = sqrt(args->som[0]->kdim);
+    for (i=0; i<ntrain; i++)
+    {
+        double score = 0;
+        int is_good = args->train_class[i] & 1;
+        int isom    = args->train_class[i] >> 1;    // this vector was used for training isom-th SOM, skip
+        if ( args->nfold==1 ) isom = -1;
+        memcpy(args->vals, args->train_dat+i*args->mvals, args->mvals*sizeof(double));
+        switch (args->merge)
+        {
+            case MERGE_MIN: score = get_min_score(args, isom); break;
+            case MERGE_MAX: score = get_max_score(args, isom); break;
+            case MERGE_AVG: score = get_avg_score(args, isom); break;
+        }
+        score = 1.0 - score/max_score;
+        if ( is_good )
+            good[igood++] = score;
+        else
+            bad[ibad++] = score;
+    }
+    qsort(good, ngood, sizeof(float), cmpfloat_desc);
+    qsort(bad, nbad, sizeof(float), cmpfloat_desc);
+    FILE *fp = NULL;
+    if ( args->prefix ) fp = open_file(NULL,"w","%s.eval", args->prefix);
+    igood = 0;
+    ibad  = 0;
+    float prev_score = good[0]>bad[0] ? good[0] : bad[0];
+    int printed = 0;
+    while ( igood<ngood || ibad<nbad )
+    {
+        if ( igood<ngood && good[igood]==prev_score ) { igood++; continue; }
+        if ( ibad<nbad && bad[ibad]==prev_score ) { ibad++; continue; }
+        if ( fp )
+            fprintf(fp,"%e\t%f\t%f\n", prev_score, (float)igood/ngood, (float)ibad/nbad);
+        if ( !printed && (float)igood/ngood > 0.9 )
+        {
+            printf("%.2f\t%.2f\t%e\t# %% of bad [1] and good [2] sites at a cutoff [3]\n", 100.*ibad/nbad,100.*igood/ngood,prev_score);
+            printed = 1;
+        }
+
+        if ( igood<ngood && ibad<nbad ) prev_score = good[igood]>bad[ibad] ? good[igood] : bad[ibad];
+        else if ( igood<ngood ) prev_score = good[igood];
+        else prev_score = bad[ibad];
+    }
+    if ( !printed ) printf("%.2f\t%.2f\t%e\t# %% of bad [1] and good [2] sites at a cutoff [3]\n", 100.*ibad/nbad,100.*igood/ngood,prev_score);
+    if ( fp )
+    {
+        if ( fclose(fp) ) error("%s.eval: fclose failed: %s\n",args->prefix,strerror(errno));
+        create_eval_plot(args);
+        som_write_map(args->prefix, args->som, args->nfold);
+    }
+
+    free(good);
+    free(bad);
+}
+
+static void do_classify(args_t *args)
+{
+    annots_reader_reset(args);
+    double max_score = sqrt(args->som[0]->kdim);
+    while ( annots_reader_next(args) )
+    {
+        double score = 0;
+        switch (args->merge)
+        {
+            case MERGE_MIN: score = get_min_score(args, -1); break;
+            case MERGE_MAX: score = get_max_score(args, -1); break;
+            case MERGE_AVG: score = get_avg_score(args, -1); break;
+        }
+        printf("%e\n", 1.0 - score/max_score);
+    }
+    annots_reader_close(args);
+}
+
+static void usage(void)
+{
+    fprintf(stderr, "\n");
+    fprintf(stderr, "About:   SOM (Self-Organizing Map) filtering.\n");
+    fprintf(stderr, "Usage:   bcftools som --train    [options] <annots.tab.gz>\n");
+    fprintf(stderr, "         bcftools som --classify [options]\n");
+    fprintf(stderr, "\n");
+    fprintf(stderr, "Model training options:\n");
+    fprintf(stderr, "    -f, --nfold <int>                  n-fold cross-validation (number of maps) [5]\n");
+    fprintf(stderr, "    -p, --prefix <string>              prefix of output files\n");
+    fprintf(stderr, "    -s, --size <int>                   map size [20]\n");
+    fprintf(stderr, "    -t, --train                        \n");
+    fprintf(stderr, "\n");
+    fprintf(stderr, "Classifying options:\n");
+    fprintf(stderr, "    -c, --classify                     \n");
+    fprintf(stderr, "\n");
+    fprintf(stderr, "Experimental training options (no reason to change):\n");
+    fprintf(stderr, "    -b, --bmu-threshold <float>        threshold for selection of best-matching unit [0.9]\n");
+    fprintf(stderr, "    -d, --som-dimension <int>          SOM dimension [2]\n");
+    fprintf(stderr, "    -e, --exclude-bad                  exclude bad sites from training, use for evaluation only\n");
+    fprintf(stderr, "    -l, --learning-rate <float>        learning rate [1.0]\n");
+    fprintf(stderr, "    -m, --merge <min|max|avg>          -f merge algorithm [avg]\n");
+    fprintf(stderr, "    -n, --ntrain-sites <int>           effective number of training sites [number of good sites]\n");
+    fprintf(stderr, "    -r, --random-seed <int>            random seed, 0 for time() [1]\n");
+    fprintf(stderr, "\n");
+    exit(1);
+}
+
+int main_vcfsom(int argc, char *argv[])
+{
+    int c;
+    args_t *args     = (args_t*) calloc(1,sizeof(args_t));
+    args->argc       = argc; args->argv = argv;
+    args->nbin       = 20;
+    args->learn      = 1.0;
+    args->bmu_th     = 0.9;
+    args->nfold      = 5;
+    args->rand_seed  = 1;
+    args->ndim       = 2;
+    args->bad_class  = 1;
+    args->good_class = 2;
+    args->merge      = MERGE_AVG;
+    args->train_bad  = 1;
+
+    static struct option loptions[] =
+    {
+        {"help",0,0,'h'},
+        {"prefix",1,0,'p'},
+        {"ntrain-sites",1,0,'n'},
+        {"random-seed",1,0,'r'},
+        {"bmu-threshold",1,0,'b'},
+        {"exclude-bad",0,0,'e'},
+        {"learning-rate",1,0,'l'},
+        {"size",1,0,'s'},
+        {"som-dimension",1,0,'d'},
+        {"nfold",1,0,'f'},
+        {"merge",1,0,'m'},
+        {"train",0,0,'t'},
+        {"classify",0,0,'c'},
+        {0,0,0,0}
+    };
+    while ((c = getopt_long(argc, argv, "htcp:n:r:b:l:s:f:d:m:e",loptions,NULL)) >= 0) {
+        switch (c) {
+            case 'e': args->train_bad = 0; break;
+            case 'm':
+                if ( !strcmp(optarg,"min") ) args->merge = MERGE_MIN;
+                else if ( !strcmp(optarg,"max") ) args->merge = MERGE_MAX;
+                else if ( !strcmp(optarg,"avg") ) args->merge = MERGE_AVG;
+                else error("The -m method not recognised: %s\n", optarg);
+                break;
+            case 'p': args->prefix = optarg; break;
+            case 'n': args->ntrain = atoi(optarg); break;
+            case 'r': args->rand_seed = atoi(optarg); break;
+            case 'b': args->bmu_th = atof(optarg); break;
+            case 'l': args->learn = atof(optarg); break;
+            case 's': args->nbin = atoi(optarg); break;
+            case 'f': args->nfold = atoi(optarg); break;
+            case 'd':
+                args->ndim = atoi(optarg);
+                if ( args->ndim<2 ) error("Expected -d >=2, got %d\n", args->ndim);
+                if ( args->ndim>3 ) fprintf(stderr,"Warning: This will take a long time and is not going to make the results better: -d %d\n", args->ndim);
+                break;
+            case 't': args->action = SOM_TRAIN; break;
+            case 'c': args->action = SOM_CLASSIFY; break;
+            case 'h':
+            case '?': usage(); break;
+            default: error("Unknown argument: %s\n", optarg);
+        }
+    }
+
+    if ( !args->rand_seed ) args->rand_seed = time(NULL);
+    if ( argc!=optind+1 ) usage();
+    args->fname = argv[optind];
+    init_data(args);
+
+    if ( args->action == SOM_TRAIN ) do_train(args);
+    else if ( args->action == SOM_CLASSIFY ) do_classify(args);
+
+    destroy_data(args);
+    free(args);
+    return 0;
+}
+
diff --git a/bcftools/vcfsom.c.pysam.c b/bcftools/vcfsom.c.pysam.c
new file mode 100644
index 0000000..effd352
--- /dev/null
+++ b/bcftools/vcfsom.c.pysam.c
@@ -0,0 +1,720 @@
+#include "bcftools.pysam.h"
+
+/*  vcfsom.c -- SOM (Self-Organizing Map) filtering.
+
+    Copyright (C) 2013-2014, 2020 Genome Research Ltd.
+
+    Author: Petr Danecek <pd3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.  */
+
+#include <stdio.h>
+#include <unistd.h>
+#include <getopt.h>
+#include <assert.h>
+#include <ctype.h>
+#include <string.h>
+#include <errno.h>
+#include <sys/stat.h>
+#include <sys/types.h>
+#include <math.h>
+#include <time.h>
+#include <htslib/vcf.h>
+#include <htslib/synced_bcf_reader.h>
+#include <htslib/vcfutils.h>
+#include <htslib/hts_os.h>
+#include <inttypes.h>
+#include "bcftools.h"
+
+#define SOM_TRAIN    1
+#define SOM_CLASSIFY 2
+
+typedef struct
+{
+    int ndim;       // dimension of the map (2D, 3D, ...)
+    int nbin;       // number of bins in th map
+    int size;       // pow(nbin,ndim)
+    int kdim;       // dimension of the input vectors
+    int nt, t;      // total number of learning cycles and the current cycle
+    double *w, *c;  // weights and counts (sum of learning influence)
+    double learn;   // learning rate
+    double bmu_th;  // best-matching unit threshold
+    int *a_idx, *b_idx; // temp arrays for traversing variable number of nested loops
+    double *div;        // dtto
+}
+som_t;
+
+typedef struct
+{
+    // SOM parameters
+    double bmu_th, learn;
+    int ndim, nbin, ntrain, t;
+    int nfold;                  // n-fold cross validation = the number of SOMs
+    som_t **som;
+
+    // annots reader's data
+    htsFile *file;              // reader
+    kstring_t str;              // temporary string for the reader
+    int dclass, mvals;
+    double *vals;
+
+    // training data
+    double *train_dat;
+    int *train_class, mtrain_class, mtrain_dat;
+
+    int rand_seed, good_class, bad_class;
+    char **argv, *fname, *prefix;
+    int argc, action, train_bad, merge;
+}
+args_t;
+
+static void usage(void);
+FILE *open_file(char **fname, const char *mode, const char *fmt, ...);
+void mkdir_p(const char *fmt, ...);
+
+char *msprintf(const char *fmt, ...)
+{
+    va_list ap;
+    va_start(ap, fmt);
+    int n = vsnprintf(NULL, 0, fmt, ap) + 2;
+    va_end(ap);
+
+    char *str = (char*)malloc(n);
+    va_start(ap, fmt);
+    vsnprintf(str, n, fmt, ap);
+    va_end(ap);
+
+    return str;
+}
+
+/*
+ *  char *t, *p = str;
+ *  t = column_next(p, '\t');
+ *  if ( strlen("<something>")==t-p && !strncmp(p,"<something>",t-p) ) fprintf(bcftools_stdout, "found!\n");
+ *
+ *  char *t;
+ *  t = column_next(str, '\t'); if ( !*t ) error("expected field\n", str);
+ *  t = column_next(t+1, '\t'); if ( !*t ) error("expected field\n", str);
+ */
+static inline char *column_next(char *start, char delim)
+{
+    char *end = start;
+    while (*end && *end!=delim) end++;
+    return end;
+}
+/**
+ *  annots_reader_next() - reads next line from annots.tab.gz and sets: class, vals
+ *   Returns 1 on successful read or 0 if no further record could be read.
+ */
+int annots_reader_next(args_t *args)
+{
+    args->str.l = 0;
+    if ( hts_getline(args->file,'\n',&args->str)<=0 ) return 0;
+
+    char *t, *line = args->str.s;
+
+    if ( !args->mvals )
+    {
+        t = line;
+        while ( *t )
+        {
+            if ( *t=='\t' ) args->mvals++;
+            t++;
+        }
+        args->vals = (double*) malloc(args->mvals*sizeof(double));
+    }
+
+    // class
+    args->dclass = atoi(line);
+    t = column_next(line, '\t');
+
+    // values
+    int i;
+    for (i=0; i<args->mvals; i++)
+    {
+        if ( !*t ) error("Could not parse %d-th data field: is the line truncated?\nThe line was: [%s]\n",i+2,line);
+        args->vals[i] = atof(++t);
+        t = column_next(t,'\t');
+    }
+    return 1;
+}
+void annots_reader_reset(args_t *args)
+{
+    if ( args->file ) hts_close(args->file);
+    if ( !args->fname ) error("annots_reader_reset: no fname\n");
+    args->file = hts_open(args->fname, "r");
+}
+void annots_reader_close(args_t *args)
+{
+    hts_close(args->file);
+}
+
+static void som_write_map(char *prefix, som_t **som, int nsom)
+{
+    FILE *fp = open_file(NULL,"w","%s.som",prefix);
+    size_t nw;
+    if ( (nw=fwrite("SOMv1",5,1,fp))!=5 ) error("Failed to write 5 bytes\n");
+    if ( (nw=fwrite(&nsom,sizeof(int),1,fp))!=sizeof(int) ) error("Failed to write %zu bytes\n",sizeof(int));
+    int i;
+    for (i=0; i<nsom; i++)
+    {
+        if ( (nw=fwrite(&som[i]->size,sizeof(int),1,fp))!=sizeof(int) ) error("Failed to write %zu bytes\n",sizeof(int));
+        if ( (nw=fwrite(&som[i]->kdim,sizeof(int),1,fp))!=sizeof(int) ) error("Failed to write %zu bytes\n",sizeof(int));
+        if ( (nw=fwrite(som[i]->w,sizeof(double),som[i]->size*som[i]->kdim,fp))!=sizeof(double)*som[i]->size*som[i]->kdim ) error("Failed to write %zu bytes\n",sizeof(double)*som[i]->size*som[i]->kdim);
+        if ( (nw=fwrite(som[i]->c,sizeof(double),som[i]->size,fp))!=sizeof(double)*som[i]->size ) error("Failed to write %zu bytes\n",sizeof(double)*som[i]->size);
+    }
+    if ( fclose(fp) ) error("%s.som: fclose failed\n",prefix);
+}
+static som_t** som_load_map(char *prefix, int *nsom)
+{
+    FILE *fp = open_file(NULL,"r","%s.som",prefix);
+    char buf[5];
+    if ( fread(buf,5,1,fp)!=1 || strncmp(buf,"SOMv1",5) ) error("Could not parse %s.som\n", prefix);
+
+    if ( fread(nsom,sizeof(int),1,fp)!=1 ) error("Could not read %s.som\n", prefix);
+    som_t **som = (som_t**)malloc(*nsom*sizeof(som_t*));
+
+    int i;
+    for (i=0; i<*nsom; i++)
+    {
+        som[i] = (som_t*) calloc(1,sizeof(som_t));
+        if ( fread(&som[i]->size,sizeof(int),1,fp) != 1 ) error("Could not read %s.som\n", prefix);
+        if ( fread(&som[i]->kdim,sizeof(int),1,fp) != 1 ) error("Could not read %s.som\n", prefix);
+        som[i]->w = (double*) malloc(sizeof(double)*som[i]->size*som[i]->kdim);
+        som[i]->c = (double*) malloc(sizeof(double)*som[i]->size);
+        if ( fread(som[i]->w,sizeof(double),som[i]->size*som[i]->kdim,fp) != som[i]->size*som[i]->kdim ) error("Could not read from %s.som\n", prefix);
+        if ( fread(som[i]->c,sizeof(double),som[i]->size,fp) != som[i]->size ) error("Could not read from %s.som\n", prefix);
+    }
+    if ( fclose(fp) ) error("%s.som: fclose failed\n",prefix);
+    return som;
+}
+static void som_create_plot(som_t *som, char *prefix)
+{
+    if ( som->ndim!=2 ) return;
+
+    char *fname;
+    FILE *fp = open_file(&fname,"w","%s.py",prefix);
+    fprintf(fp,
+            "import matplotlib as mpl\n"
+            "mpl.use('Agg')\n"
+            "import matplotlib.pyplot as plt\n"
+            "\n"
+            "dat = [\n"
+           );
+    int i,j;
+    double *val = som->c;
+    for (i=0; i<som->nbin; i++)
+    {
+        fprintf(fp,"[");
+        for (j=0; j<som->nbin; j++)
+        {
+            if ( j>0 ) fprintf(fp,",");
+            fprintf(fp,"%e", *val);
+            val++;
+        }
+        fprintf(fp,"],\n");
+    }
+    fprintf(fp,
+            "]\n"
+            "fig = plt.figure()\n"
+            "ax1 = plt.subplot(111)\n"
+            "im1 = ax1.imshow(dat)\n"
+            "fig.colorbar(im1)\n"
+            "plt.savefig('%s.png')\n"
+            "plt.close()\n"
+            "\n", prefix
+           );
+    fclose(fp);
+    free(fname);
+}
+// Find the best matching unit: the node with minimum distance from the input vector
+static inline int som_find_bmu(som_t *som, double *vec, double *dist)
+{
+    double *ptr = som->w;
+    double min_dist = HUGE_VAL;
+    int min_idx = 0;
+
+    int i, k;
+    for (i=0; i<som->size; i++)
+    {
+        double dist = 0;
+        for (k=0; k<som->kdim; k++)
+            dist += (vec[k] - ptr[k]) * (vec[k] - ptr[k]);
+        if ( dist < min_dist )
+        {
+            min_dist = dist;
+            min_idx  = i;
+        }
+        ptr += som->kdim;
+    }
+
+    if ( dist ) *dist = min_dist;
+    return min_idx;
+}
+static inline double som_get_score(som_t *som, double *vec, double bmu_th)
+{
+    double *ptr = som->w;
+    double min_dist = HUGE_VAL;
+
+    int i, k;
+    for (i=0; i<som->size; i++)
+    {
+        if ( som->c[i] >= bmu_th )
+        {
+            double dist = 0;
+            for (k=0; k<som->kdim; k++)
+                dist += (vec[k] - ptr[k]) * (vec[k] - ptr[k]);
+            if ( dist < min_dist ) min_dist = dist;
+        }
+        ptr += som->kdim;
+    }
+    return sqrt(min_dist);
+}
+// Convert flat index to that of a k-dimensional cube
+static inline void som_idx_to_ndim(som_t *som, int idx, int *ndim)
+{
+    int i;
+    double sub = 0;
+
+    ndim[0] = idx/som->div[0];
+    for (i=1; i<som->ndim; i++)
+    {
+        sub += ndim[i-1] * som->div[i-1];
+        ndim[i] = (idx - sub)/som->div[i];
+    }
+}
+static void som_train_site(som_t *som, double *vec, int update_counts)
+{
+    // update learning rate and learning radius
+    som->t++;
+    double dt = exp(-som->t/som->nt);
+    double learning_rate = som->learn * dt;
+    double radius = som->nbin * dt; radius *= radius;
+
+    // find the best matching unit and its indexes
+    int min_idx = som_find_bmu(som, vec, NULL);
+    som_idx_to_ndim(som, min_idx, som->a_idx);
+
+    // update the weights: traverse the map and make all nodes within the
+    // radius more similar to the input vector
+    double *ptr = som->w;
+    double *cnt = som->c;
+    int i, j, k;
+    for (i=0; i<som->size; i++)
+    {
+        som_idx_to_ndim(som, i, som->b_idx);
+        double dist = 0;
+        for (j=0; j<som->ndim; j++)
+            dist += (som->a_idx[j] - som->b_idx[j]) * (som->a_idx[j] - som->b_idx[j]);
+        if ( dist <= radius )
+        {
+            double influence = exp(-dist*dist*0.5/radius) * learning_rate;
+            for (k=0; k<som->kdim; k++)
+                ptr[k] += influence * (vec[k] - ptr[k]);
+
+            // Bad sites may help to shape the map, but only nodes with big enough
+            // influence will be used for classification.
+            if ( update_counts ) *cnt += influence;
+        }
+        ptr += som->kdim;
+        cnt++;
+    }
+}
+static void som_norm_counts(som_t *som)
+{
+    int i;
+    double max = 0;
+    for (i=0; i<som->size; i++)
+        if ( max < som->c[i] ) max = som->c[i];
+    for (i=0; i<som->size; i++)
+        som->c[i] /= max;
+}
+static som_t *som_init(args_t *args)
+{
+    som_t *som  = (som_t*) calloc(1,sizeof(som_t));
+    som->ndim   = args->ndim;
+    som->nbin   = args->nbin;
+    som->kdim   = args->mvals;
+    som->nt     = args->ntrain;
+    som->learn  = args->learn;
+    som->bmu_th = args->bmu_th;
+    som->size   = pow(som->nbin,som->ndim);
+    som->w = (double*) malloc(sizeof(double)*som->size*som->kdim);
+    if ( !som->w ) error("Could not alloc %"PRIu64" bytes [nbin=%d ndim=%d kdim=%d]\n", (uint64_t)(sizeof(double)*som->size*som->kdim),som->nbin,som->ndim,som->kdim);
+    som->c = (double*) calloc(som->size,sizeof(double));
+    if ( !som->w ) error("Could not alloc %"PRIu64" bytes [nbin=%d ndim=%d]\n", (uint64_t)(sizeof(double)*som->size),som->nbin,som->ndim);
+    int i;
+    for (i=0; i<som->size*som->kdim; i++)
+        som->w[i] = random();
+    som->a_idx = (int*) malloc(sizeof(int)*som->ndim);
+    som->b_idx = (int*) malloc(sizeof(int)*som->ndim);
+    som->div   = (double*) malloc(sizeof(double)*som->ndim);
+    for (i=0; i<som->ndim; i++)
+        som->div[i] = pow(som->nbin,som->ndim-i-1);
+    return som;
+}
+static void som_destroy(som_t *som)
+{
+    free(som->a_idx); free(som->b_idx); free(som->div);
+    free(som->w); free(som->c);
+    free(som);
+}
+
+static void init_data(args_t *args)
+{
+    // Get first line to learn the vector size
+    annots_reader_reset(args);
+    annots_reader_next(args);
+
+    if ( args->action==SOM_CLASSIFY )
+        args->som = som_load_map(args->prefix,&args->nfold);
+}
+static void destroy_data(args_t *args)
+{
+    int i;
+    if ( args->som )
+    {
+        for (i=0; i<args->nfold; i++) som_destroy(args->som[i]);
+    }
+    free(args->train_dat);
+    free(args->train_class);
+    free(args->som);
+    free(args->vals);
+    free(args->str.s);
+}
+
+#define MERGE_MIN 0
+#define MERGE_MAX 1
+#define MERGE_AVG 2
+static double get_min_score(args_t *args, int iskip)
+{
+    int i;
+    double score, min_score = HUGE_VAL;
+    for (i=0; i<args->nfold; i++)
+    {
+        if ( i==iskip ) continue;
+        score = som_get_score(args->som[i], args->vals, args->bmu_th);
+        if ( i==0 || score < min_score ) min_score = score;
+    }
+    return min_score;
+}
+static double get_max_score(args_t *args, int iskip)
+{
+    int i;
+    double score, max_score = -HUGE_VAL;
+    for (i=0; i<args->nfold; i++)
+    {
+        if ( i==iskip ) continue;
+        score = som_get_score(args->som[i], args->vals, args->bmu_th);
+        if ( i==0 || max_score < score ) max_score = score;
+    }
+    return max_score;
+}
+static double get_avg_score(args_t *args, int iskip)
+{
+    int i, n = 0;
+    double score = 0;
+    for (i=0; i<args->nfold; i++)
+    {
+        if ( i==iskip ) continue;
+        score += som_get_score(args->som[i], args->vals, args->bmu_th);
+        n++;
+    }
+    return score/n;
+}
+static int cmpfloat_desc(const void *a, const void *b)
+{
+    float fa = *((float*)a);
+    float fb = *((float*)b);
+    if ( fa<fb ) return 1;
+    if ( fa>fb ) return -1;
+    return 0;
+}
+
+static void create_eval_plot(args_t *args)
+{
+    FILE *fp = open_file(NULL,"w","%s.eval.py", args->prefix);
+    fprintf(fp,
+            "import matplotlib as mpl\n"
+            "mpl.use('Agg')\n"
+            "import matplotlib.pyplot as plt\n"
+            "\n"
+            "import csv\n"
+            "csv.register_dialect('tab', delimiter='\\t', quoting=csv.QUOTE_NONE)\n"
+            "dat = []\n"
+            "with open('%s.eval', 'r') as f:\n"
+            "\treader = csv.reader(f, 'tab')\n"
+            "\tfor row in reader:\n"
+            "\t\tif row[0][0]!='#': dat.append(row)\n"
+            "\n"
+            "fig = plt.figure()\n"
+            "ax1 = plt.subplot(111)\n"
+            "ax1.plot([x[0] for x in dat],[x[1] for x in dat],'g',label='Good')\n"
+            "ax1.plot([x[0] for x in dat],[x[2] for x in dat],'r',label='Bad')\n"
+            "ax1.set_xlabel('SOM score')\n"
+            "ax1.set_ylabel('Number of training sites')\n"
+            "ax1.legend(loc='best',prop={'size':8},frameon=False)\n"
+            "plt.savefig('%s.eval.png')\n"
+            "plt.close()\n"
+            "\n", args->prefix,args->prefix
+           );
+    fclose(fp);
+}
+
+static void do_train(args_t *args)
+{
+    // read training sites
+    int i, igood = 0, ibad = 0, ngood = 0, nbad = 0, ntrain = 0;
+    annots_reader_reset(args);
+    while ( annots_reader_next(args) )
+    {
+        // determine which of the nfold's SOMs to train
+        int isom = 0;
+        if ( args->dclass == args->good_class )
+        {
+            if ( ++igood >= args->nfold ) igood = 0;
+            isom = igood;
+            ngood++;
+        }
+        else if ( args->dclass == args->bad_class )
+        {
+            if ( ++ibad >= args->nfold ) ibad = 0;
+            isom = ibad;
+            nbad++;
+        }
+        else
+            error("Could not determine the class: %d (vs %d and %d)\n", args->dclass,args->good_class,args->bad_class);
+
+        // save the values for evaluation
+        ntrain++;
+        hts_expand(double, ntrain*args->mvals, args->mtrain_dat, args->train_dat);
+        hts_expand(int, ntrain, args->mtrain_class, args->train_class);
+        memcpy(args->train_dat+(ntrain-1)*args->mvals, args->vals, args->mvals*sizeof(double));
+        args->train_class[ntrain-1] = (args->dclass==args->good_class ? 1 : 0) | isom<<1;  // store class + chunk used for training
+    }
+    annots_reader_close(args);
+
+    // init maps
+    if ( !args->ntrain ) args->ntrain = ngood/args->nfold;
+    srandom(args->rand_seed);
+    args->som = (som_t**) malloc(sizeof(som_t*)*args->nfold);
+    for (i=0; i<args->nfold; i++) args->som[i] = som_init(args);
+
+    // train
+    for (i=0; i<ntrain; i++)
+    {
+        int is_good = args->train_class[i] & 1;
+        int isom    = args->train_class[i] >> 1;
+        if ( is_good || args->train_bad )
+            som_train_site(args->som[isom], args->train_dat+i*args->mvals, is_good);
+    }
+
+    // norm and create plots
+    for (i=0; i<args->nfold; i++)
+    {
+        som_norm_counts(args->som[i]);
+        if ( args->prefix )
+        {
+            char *bname = msprintf("%s.som.%d", args->prefix,i);
+            som_create_plot(args->som[i], bname);
+            free(bname);
+        }
+    }
+
+    // evaluate
+    float *good = (float*) malloc(sizeof(float)*ngood); assert(good);
+    float *bad  = (float*) malloc(sizeof(float)*nbad); assert(bad);
+    igood = ibad = 0;
+    double max_score = sqrt(args->som[0]->kdim);
+    for (i=0; i<ntrain; i++)
+    {
+        double score = 0;
+        int is_good = args->train_class[i] & 1;
+        int isom    = args->train_class[i] >> 1;    // this vector was used for training isom-th SOM, skip
+        if ( args->nfold==1 ) isom = -1;
+        memcpy(args->vals, args->train_dat+i*args->mvals, args->mvals*sizeof(double));
+        switch (args->merge)
+        {
+            case MERGE_MIN: score = get_min_score(args, isom); break;
+            case MERGE_MAX: score = get_max_score(args, isom); break;
+            case MERGE_AVG: score = get_avg_score(args, isom); break;
+        }
+        score = 1.0 - score/max_score;
+        if ( is_good )
+            good[igood++] = score;
+        else
+            bad[ibad++] = score;
+    }
+    qsort(good, ngood, sizeof(float), cmpfloat_desc);
+    qsort(bad, nbad, sizeof(float), cmpfloat_desc);
+    FILE *fp = NULL;
+    if ( args->prefix ) fp = open_file(NULL,"w","%s.eval", args->prefix);
+    igood = 0;
+    ibad  = 0;
+    float prev_score = good[0]>bad[0] ? good[0] : bad[0];
+    int printed = 0;
+    while ( igood<ngood || ibad<nbad )
+    {
+        if ( igood<ngood && good[igood]==prev_score ) { igood++; continue; }
+        if ( ibad<nbad && bad[ibad]==prev_score ) { ibad++; continue; }
+        if ( fp )
+            fprintf(fp,"%e\t%f\t%f\n", prev_score, (float)igood/ngood, (float)ibad/nbad);
+        if ( !printed && (float)igood/ngood > 0.9 )
+        {
+            fprintf(bcftools_stdout, "%.2f\t%.2f\t%e\t# %% of bad [1] and good [2] sites at a cutoff [3]\n", 100.*ibad/nbad,100.*igood/ngood,prev_score);
+            printed = 1;
+        }
+
+        if ( igood<ngood && ibad<nbad ) prev_score = good[igood]>bad[ibad] ? good[igood] : bad[ibad];
+        else if ( igood<ngood ) prev_score = good[igood];
+        else prev_score = bad[ibad];
+    }
+    if ( !printed ) fprintf(bcftools_stdout, "%.2f\t%.2f\t%e\t# %% of bad [1] and good [2] sites at a cutoff [3]\n", 100.*ibad/nbad,100.*igood/ngood,prev_score);
+    if ( fp )
+    {
+        if ( fclose(fp) ) error("%s.eval: fclose failed: %s\n",args->prefix,strerror(errno));
+        create_eval_plot(args);
+        som_write_map(args->prefix, args->som, args->nfold);
+    }
+
+    free(good);
+    free(bad);
+}
+
+static void do_classify(args_t *args)
+{
+    annots_reader_reset(args);
+    double max_score = sqrt(args->som[0]->kdim);
+    while ( annots_reader_next(args) )
+    {
+        double score = 0;
+        switch (args->merge)
+        {
+            case MERGE_MIN: score = get_min_score(args, -1); break;
+            case MERGE_MAX: score = get_max_score(args, -1); break;
+            case MERGE_AVG: score = get_avg_score(args, -1); break;
+        }
+        fprintf(bcftools_stdout, "%e\n", 1.0 - score/max_score);
+    }
+    annots_reader_close(args);
+}
+
+static void usage(void)
+{
+    fprintf(bcftools_stderr, "\n");
+    fprintf(bcftools_stderr, "About:   SOM (Self-Organizing Map) filtering.\n");
+    fprintf(bcftools_stderr, "Usage:   bcftools som --train    [options] <annots.tab.gz>\n");
+    fprintf(bcftools_stderr, "         bcftools som --classify [options]\n");
+    fprintf(bcftools_stderr, "\n");
+    fprintf(bcftools_stderr, "Model training options:\n");
+    fprintf(bcftools_stderr, "    -f, --nfold <int>                  n-fold cross-validation (number of maps) [5]\n");
+    fprintf(bcftools_stderr, "    -p, --prefix <string>              prefix of output files\n");
+    fprintf(bcftools_stderr, "    -s, --size <int>                   map size [20]\n");
+    fprintf(bcftools_stderr, "    -t, --train                        \n");
+    fprintf(bcftools_stderr, "\n");
+    fprintf(bcftools_stderr, "Classifying options:\n");
+    fprintf(bcftools_stderr, "    -c, --classify                     \n");
+    fprintf(bcftools_stderr, "\n");
+    fprintf(bcftools_stderr, "Experimental training options (no reason to change):\n");
+    fprintf(bcftools_stderr, "    -b, --bmu-threshold <float>        threshold for selection of best-matching unit [0.9]\n");
+    fprintf(bcftools_stderr, "    -d, --som-dimension <int>          SOM dimension [2]\n");
+    fprintf(bcftools_stderr, "    -e, --exclude-bad                  exclude bad sites from training, use for evaluation only\n");
+    fprintf(bcftools_stderr, "    -l, --learning-rate <float>        learning rate [1.0]\n");
+    fprintf(bcftools_stderr, "    -m, --merge <min|max|avg>          -f merge algorithm [avg]\n");
+    fprintf(bcftools_stderr, "    -n, --ntrain-sites <int>           effective number of training sites [number of good sites]\n");
+    fprintf(bcftools_stderr, "    -r, --random-seed <int>            random seed, 0 for time() [1]\n");
+    fprintf(bcftools_stderr, "\n");
+    bcftools_exit(1);
+}
+
+int main_vcfsom(int argc, char *argv[])
+{
+    int c;
+    args_t *args     = (args_t*) calloc(1,sizeof(args_t));
+    args->argc       = argc; args->argv = argv;
+    args->nbin       = 20;
+    args->learn      = 1.0;
+    args->bmu_th     = 0.9;
+    args->nfold      = 5;
+    args->rand_seed  = 1;
+    args->ndim       = 2;
+    args->bad_class  = 1;
+    args->good_class = 2;
+    args->merge      = MERGE_AVG;
+    args->train_bad  = 1;
+
+    static struct option loptions[] =
+    {
+        {"help",0,0,'h'},
+        {"prefix",1,0,'p'},
+        {"ntrain-sites",1,0,'n'},
+        {"random-seed",1,0,'r'},
+        {"bmu-threshold",1,0,'b'},
+        {"exclude-bad",0,0,'e'},
+        {"learning-rate",1,0,'l'},
+        {"size",1,0,'s'},
+        {"som-dimension",1,0,'d'},
+        {"nfold",1,0,'f'},
+        {"merge",1,0,'m'},
+        {"train",0,0,'t'},
+        {"classify",0,0,'c'},
+        {0,0,0,0}
+    };
+    while ((c = getopt_long(argc, argv, "htcp:n:r:b:l:s:f:d:m:e",loptions,NULL)) >= 0) {
+        switch (c) {
+            case 'e': args->train_bad = 0; break;
+            case 'm':
+                if ( !strcmp(optarg,"min") ) args->merge = MERGE_MIN;
+                else if ( !strcmp(optarg,"max") ) args->merge = MERGE_MAX;
+                else if ( !strcmp(optarg,"avg") ) args->merge = MERGE_AVG;
+                else error("The -m method not recognised: %s\n", optarg);
+                break;
+            case 'p': args->prefix = optarg; break;
+            case 'n': args->ntrain = atoi(optarg); break;
+            case 'r': args->rand_seed = atoi(optarg); break;
+            case 'b': args->bmu_th = atof(optarg); break;
+            case 'l': args->learn = atof(optarg); break;
+            case 's': args->nbin = atoi(optarg); break;
+            case 'f': args->nfold = atoi(optarg); break;
+            case 'd':
+                args->ndim = atoi(optarg);
+                if ( args->ndim<2 ) error("Expected -d >=2, got %d\n", args->ndim);
+                if ( args->ndim>3 ) fprintf(bcftools_stderr,"Warning: This will take a long time and is not going to make the results better: -d %d\n", args->ndim);
+                break;
+            case 't': args->action = SOM_TRAIN; break;
+            case 'c': args->action = SOM_CLASSIFY; break;
+            case 'h':
+            case '?': usage(); break;
+            default: error("Unknown argument: %s\n", optarg);
+        }
+    }
+
+    if ( !args->rand_seed ) args->rand_seed = time(NULL);
+    if ( argc!=optind+1 ) usage();
+    args->fname = argv[optind];
+    init_data(args);
+
+    if ( args->action == SOM_TRAIN ) do_train(args);
+    else if ( args->action == SOM_CLASSIFY ) do_classify(args);
+
+    destroy_data(args);
+    free(args);
+    return 0;
+}
+
diff --git a/bcftools/vcfsort.c b/bcftools/vcfsort.c
new file mode 100644
index 0000000..a8052d0
--- /dev/null
+++ b/bcftools/vcfsort.c
@@ -0,0 +1,443 @@
+/*  vcfsort.c -- sort subcommand
+
+   Copyright (C) 2017-2021 Genome Research Ltd.
+
+   Author: Petr Danecek <pd3@sanger.ac.uk>
+   
+   Permission is hereby granted, free of charge, to any person obtaining a copy
+   of this software and associated documentation files (the "Software"), to deal
+   in the Software without restriction, including without limitation the rights
+   to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+   copies of the Software, and to permit persons to whom the Software is
+   furnished to do so, subject to the following conditions:
+   
+   The above copyright notice and this permission notice shall be included in
+   all copies or substantial portions of the Software.
+   
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+   IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+   FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+   AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+   LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+   OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+   THE SOFTWARE.
+
+ */
+
+#include <stdio.h>
+#include <unistd.h>
+#include <getopt.h>
+#include <ctype.h>
+#include <string.h>
+#include <strings.h>
+#include <errno.h>
+#include <sys/stat.h>
+#include <sys/types.h>
+#include <fcntl.h>
+#include <math.h>
+#ifdef _WIN32
+#include <windows.h>
+#endif
+#include <htslib/vcf.h>
+#include <htslib/kstring.h>
+#include <htslib/hts_os.h>
+#include "kheap.h"
+#include "bcftools.h"
+
+typedef struct
+{
+    char *fname;
+    htsFile *fh;
+    bcf1_t *rec;
+}
+blk_t;
+
+typedef struct _args_t
+{
+    bcf_hdr_t *hdr;
+    char **argv, *fname, *output_fname, *tmp_dir;
+    int argc, output_type, clevel;
+    size_t max_mem, mem;
+    bcf1_t **buf;
+    uint8_t *mem_block;
+    size_t nbuf, mbuf, nblk;
+    blk_t *blk;
+}
+args_t;
+
+void clean_files(args_t *args)
+{
+    int i;
+    fprintf(stderr,"Cleaning\n");
+    for (i=0; i<args->nblk; i++)
+    {
+        blk_t *blk = args->blk + i;
+        if ( blk->fname )
+        {
+            unlink(blk->fname);
+            free(blk->fname);
+        }
+        if ( blk->rec ) 
+            bcf_destroy(blk->rec);
+    }
+    rmdir(args->tmp_dir);
+}
+void clean_files_and_throw(args_t *args, const char *format, ...)
+{
+    va_list ap;
+    va_start(ap, format);
+    vfprintf(stderr, format, ap);
+    va_end(ap);
+    clean_files(args);
+    exit(-1);
+}
+
+int cmp_bcf_pos(const void *aptr, const void *bptr)
+{
+    bcf1_t *a = *((bcf1_t**)aptr);
+    bcf1_t *b = *((bcf1_t**)bptr);
+    if ( a->rid < b->rid ) return -1;
+    if ( a->rid > b->rid ) return 1;
+    if ( a->pos < b->pos ) return -1;
+    if ( a->pos > b->pos ) return 1;
+
+    // Sort the same chr:pos records lexicographically by ref,alt.
+    // This will be called rarely so should not slow the sorting down
+    // noticeably.
+
+    int i;
+    for (i=0; i<a->n_allele; i++)
+    { 
+        if ( i >= b->n_allele ) return 1;
+        int ret = strcasecmp(a->d.allele[i],b->d.allele[i]);
+        if ( ret ) return ret;
+    }
+    if ( a->n_allele < b->n_allele ) return -1;
+    return 0;
+}
+
+void buf_flush(args_t *args)
+{
+    if ( !args->nbuf ) return;
+
+    qsort(args->buf, args->nbuf, sizeof(*args->buf), cmp_bcf_pos);
+
+    args->nblk++;
+    args->blk = (blk_t*) realloc(args->blk, sizeof(blk_t)*args->nblk);
+    blk_t *blk = args->blk + args->nblk - 1;
+
+    kstring_t str = {0,0,0};
+    ksprintf(&str, "%s/%05d.bcf", args->tmp_dir, (int)args->nblk);
+    blk->fname = str.s;
+    blk->rec   = NULL;
+    blk->fh    = NULL;
+
+    htsFile *fh = hts_open(blk->fname, "wbu");
+    if ( fh == NULL ) clean_files_and_throw(args, "Cannot write %s: %s\n", blk->fname, strerror(errno));
+    if ( bcf_hdr_write(fh, args->hdr)!=0 ) clean_files_and_throw(args, "[%s] Error: cannot write to %s\n", __func__,blk->fname);
+    
+    int i;
+    for (i=0; i<args->nbuf; i++)
+    {
+        if ( bcf_write(fh, args->hdr, args->buf[i])!=0 ) clean_files_and_throw(args, "[%s] Error: cannot write to %s\n", __func__,blk->fname);
+    }
+    if ( hts_close(fh)!=0 ) clean_files_and_throw(args, "[%s] Error: close failed .. %s\n", __func__,blk->fname);
+
+    args->nbuf = 0;
+    args->mem  = 0;
+}
+
+
+static inline uint8_t *_align_up(uint8_t *ptr)
+{
+    return (uint8_t*)(((size_t)ptr + 8 - 1) & ~((size_t)(8 - 1)));
+}
+
+void buf_push(args_t *args, bcf1_t *rec)
+{
+    size_t delta = sizeof(bcf1_t) + rec->shared.l + rec->indiv.l + rec->unpack_size[0] + rec->unpack_size[1]
+        + sizeof(*rec->d.allele)*rec->d.m_allele
+        + sizeof(bcf1_t*)       // args->buf
+        + 8;                    // the number of _align_up() calls
+
+    if ( delta > args->max_mem - args->mem )
+    {
+        args->nbuf++;
+        hts_expand(bcf1_t*, args->nbuf, args->mbuf, args->buf);
+        args->buf[args->nbuf-1] = rec;
+        buf_flush(args);
+        bcf_destroy(rec);
+        return;
+    }
+
+    // make sure nothing has changed in htslib
+    assert( rec->unpacked==BCF_UN_STR && !rec->d.flt && !rec->d.info && !rec->d.fmt && !rec->d.var );
+
+    uint8_t *ptr_beg = args->mem_block + args->mem;
+    uint8_t *ptr = _align_up(ptr_beg);
+    bcf1_t *new_rec = (bcf1_t*)ptr;
+    memcpy(new_rec,rec,sizeof(*rec));
+    ptr += sizeof(*rec);
+
+    // The array of allele pointers does not need alignment as bcf1_t is already padded to the biggest
+    // data type in the structure
+    char **allele = (char**)ptr;
+    ptr += rec->n_allele*sizeof(*allele);
+
+    // This is just to prevent valgrind from complaining about memcpy, unpack_size is a high-water mark
+    // and the end may be uninitialized
+    delta = rec->d.allele[rec->n_allele-1] - rec->d.allele[0];
+    while ( delta < rec->unpack_size[1] ) if ( !rec->d.als[delta++] ) break;
+    memcpy(ptr,rec->d.als,delta);
+    new_rec->d.als = (char*)ptr;
+    ptr = ptr + delta;
+
+    int i;
+    for (i=0; i<rec->n_allele; i++) allele[i] = new_rec->d.als + (ptrdiff_t)(rec->d.allele[i] - rec->d.allele[0]);
+    new_rec->d.allele = allele;
+
+    memcpy(ptr,rec->shared.s,rec->shared.l);
+    new_rec->shared.s = (char*)ptr;
+    new_rec->shared.m = rec->shared.l;
+    ptr += rec->shared.l;
+
+    memcpy(ptr,rec->indiv.s,rec->indiv.l);
+    new_rec->indiv.s = (char*)ptr;
+    new_rec->indiv.m = rec->indiv.l;
+    ptr += rec->indiv.l;
+
+    // This is just to prevent valgrind from complaining about memcpy, unpack_size is a high-water mark
+    // and the end may be uninitialized
+    i = 0;
+    while ( i < rec->unpack_size[0] ) if ( !rec->d.id[i++] ) break;
+    memcpy(ptr,rec->d.id,i);
+    new_rec->d.id = (char*)ptr;
+    ptr += i;
+
+    args->nbuf++;
+    hts_expand(bcf1_t*, args->nbuf, args->mbuf, args->buf);
+    args->buf[args->nbuf-1] = new_rec;
+
+    delta = ptr - ptr_beg;
+    args->mem += delta;
+
+    assert( args->mem <= args->max_mem );
+
+    bcf_destroy(rec);
+}
+
+void sort_blocks(args_t *args) 
+{
+    htsFile *in = hts_open(args->fname, "r");
+    if ( !in ) clean_files_and_throw(args, "Could not read %s\n", args->fname);
+    args->hdr = bcf_hdr_read(in);
+    if ( !args->hdr) clean_files_and_throw(args, "Could not read VCF/BCF headers from %s\n", args->fname);
+
+    while ( 1 )
+    {
+        bcf1_t *rec = bcf_init();
+        int ret = bcf_read1(in, args->hdr, rec);
+        if ( ret < -1 ) clean_files_and_throw(args,"Error encountered while parsing the input\n");
+        if ( ret == -1 )
+        {
+            bcf_destroy(rec);
+            break;
+        }
+        if ( rec->errcode ) clean_files_and_throw(args,"Error encountered while parsing the input at %s:%d\n",bcf_seqname(args->hdr,rec),rec->pos+1);
+        bcf_unpack(rec, BCF_UN_STR);
+        buf_push(args, rec);
+    }
+    buf_flush(args);
+    free(args->buf);
+
+    if ( hts_close(in)!=0 ) clean_files_and_throw(args,"Close failed: %s\n", args->fname);
+}
+
+static inline int blk_is_smaller(blk_t **aptr, blk_t **bptr)
+{
+    blk_t *a = *aptr;
+    blk_t *b = *bptr;
+    int ret = cmp_bcf_pos(&a->rec, &b->rec);
+    if ( ret < 0 ) return 1;
+    return 0;
+}
+KHEAP_INIT(blk, blk_t*, blk_is_smaller)
+
+void blk_read(args_t *args, khp_blk_t *bhp, bcf_hdr_t *hdr, blk_t *blk)
+{
+    if ( !blk->fh ) return;
+    int ret = bcf_read(blk->fh, hdr, blk->rec);
+    if ( ret < -1 ) clean_files_and_throw(args, "Error reading %s\n", blk->fname);
+    if ( ret == -1 )
+    {
+        if ( hts_close(blk->fh)!=0 ) clean_files_and_throw(args, "Close failed: %s\n", blk->fname);
+        blk->fh = 0;
+        return;
+    }
+    bcf_unpack(blk->rec, BCF_UN_STR);
+    khp_insert(blk, bhp, &blk);
+}
+
+void merge_blocks(args_t *args) 
+{
+    fprintf(stderr,"Merging %d temporary files\n", (int)args->nblk);
+    khp_blk_t *bhp = khp_init(blk);
+
+    int i;
+    for (i=0; i<args->nblk; i++)
+    {
+        blk_t *blk = args->blk + i;
+        blk->fh = hts_open(blk->fname, "r");
+        if ( !blk->fh ) clean_files_and_throw(args, "Could not read %s: %s\n", blk->fname, strerror(errno));
+        bcf_hdr_t *hdr = bcf_hdr_read(blk->fh);
+        bcf_hdr_destroy(hdr);
+        blk->rec = bcf_init();
+        blk_read(args, bhp, args->hdr, blk);
+    }
+
+    char wmode[8];
+    set_wmode(wmode,args->output_type,args->output_fname,args->clevel);
+    htsFile *out = hts_open(args->output_fname ? args->output_fname : "-", wmode);
+    if ( bcf_hdr_write(out, args->hdr)!=0 ) clean_files_and_throw(args, "[%s] Error: cannot write to %s\n", __func__,args->output_fname);
+    while ( bhp->ndat )
+    {
+        blk_t *blk = bhp->dat[0];
+        if ( bcf_write(out, args->hdr, blk->rec)!=0 ) clean_files_and_throw(args, "[%s] Error: cannot write to %s\n", __func__,args->output_fname);
+        khp_delete(blk, bhp);
+        blk_read(args, bhp, args->hdr, blk);
+    }
+    if ( hts_close(out)!=0 ) clean_files_and_throw(args, "Close failed: %s\n", args->output_fname);
+
+    clean_files(args);
+
+    free(args->blk);
+    khp_destroy(blk, bhp);
+    fprintf(stderr,"Done\n");
+}
+
+static void usage(args_t *args)
+{
+    fprintf(stderr, "\n");
+    fprintf(stderr, "About:   Sort VCF/BCF file.\n");
+    fprintf(stderr, "Usage:   bcftools sort [OPTIONS] <FILE.vcf>\n");
+    fprintf(stderr, "\n");
+    fprintf(stderr, "Options:\n");
+    fprintf(stderr, "    -m, --max-mem FLOAT[kMG]       maximum memory to use [768M]\n");    // using metric units, 1M=1e6
+    fprintf(stderr, "    -o, --output FILE              output file name [stdout]\n");
+    fprintf(stderr, "    -O, --output-type b|u|z|v      b: compressed BCF, u: uncompressed BCF, z: compressed VCF, v: uncompressed VCF [v]\n");
+    fprintf(stderr, "    -O, --output-type u|b|v|z[0-9] u/b: un/compressed BCF, v/z: un/compressed VCF, 0-9: compression level [v]\n");
+
+#ifdef _WIN32
+    fprintf(stderr, "    -T, --temp-dir DIR             temporary files [/bcftools.XXXXXX]\n");
+#else
+    fprintf(stderr, "    -T, --temp-dir DIR             temporary files [/tmp/bcftools.XXXXXX]\n");
+#endif
+    fprintf(stderr, "\n");
+    exit(1);
+}
+
+size_t parse_mem_string(const char *str) 
+{
+    char *tmp;
+    double mem = strtod(str, &tmp);
+    if ( tmp==str ) error("Could not parse the memory string: \"%s\"\n", str);
+    if ( !strcasecmp("k",tmp) ) mem *= 1000;
+    else if ( !strcasecmp("m",tmp) ) mem *= 1000*1000;
+    else if ( !strcasecmp("g",tmp) ) mem *= 1000*1000*1000;
+    return mem;
+}
+
+void mkdir_p(const char *fmt, ...);
+static void init(args_t *args)
+{
+    args->max_mem *= 0.9;
+    args->mem_block = malloc(args->max_mem);
+    args->mem = 0;
+
+    args->tmp_dir = init_tmp_prefix(args->tmp_dir);
+
+#ifdef _WIN32
+        int ret = mkdir(mktemp(args->tmp_dir), 0700);
+        if ( ret ) error("mkdir(%s) failed: %s\n", args->tmp_dir,strerror(errno));
+#else
+        char *tmp = mkdtemp(args->tmp_dir);
+        if ( !tmp ) error("mkdtemp(%s) failed: %s\n",  args->tmp_dir,strerror(errno));
+        int ret = chmod(tmp, S_IRUSR|S_IWUSR|S_IXUSR);
+        if ( ret ) error("chmod(%s,S_IRUSR|S_IWUSR|S_IXUSR) failed: %s\n", args->tmp_dir,strerror(errno));
+#endif
+
+    fprintf(stderr,"Writing to %s\n", args->tmp_dir);
+}
+static void destroy(args_t *args)
+{
+    bcf_hdr_destroy(args->hdr);
+    free(args->mem_block);
+    free(args->tmp_dir);
+    free(args);
+}
+
+int main_sort(int argc, char *argv[])
+{
+    int c;
+    args_t *args  = (args_t*) calloc(1,sizeof(args_t));
+    args->argc    = argc; args->argv = argv;
+    args->max_mem = 768*1000*1000;
+    args->output_fname = "-";
+    args->clevel = -1;
+
+    static struct option loptions[] =
+    {
+        {"max-mem",required_argument,NULL,'m'},
+        {"temp-dir",required_argument,NULL,'T'},
+        {"output-type",required_argument,NULL,'O'},
+        {"output-file",required_argument,NULL,'o'},
+        {"output",required_argument,NULL,'o'},
+        {"help",no_argument,NULL,'h'},
+        {0,0,0,0}
+    };
+    char *tmp;
+    while ((c = getopt_long(argc, argv, "m:T:O:o:h?",loptions,NULL)) >= 0)
+    {
+        switch (c)
+        {
+            case 'm': args->max_mem = parse_mem_string(optarg); break;
+            case 'T': args->tmp_dir = optarg; break;
+            case 'o': args->output_fname = optarg; break;
+            case 'O':
+                      switch (optarg[0]) {
+                          case 'b': args->output_type = FT_BCF_GZ; break;
+                          case 'u': args->output_type = FT_BCF; break;
+                          case 'z': args->output_type = FT_VCF_GZ; break;
+                          case 'v': args->output_type = FT_VCF; break;
+                          default:
+                          {
+                              args->clevel = strtol(optarg,&tmp,10);
+                              if ( *tmp || args->clevel<0 || args->clevel>9 ) error("The output type \"%s\" not recognised\n", optarg);
+                          }
+                      };
+                      if ( optarg[1] )
+                      {
+                          args->clevel = strtol(optarg+1,&tmp,10);
+                          if ( *tmp || args->clevel<0 || args->clevel>9 ) error("Could not parse argument: --compression-level %s\n", optarg+1);
+                      }
+                      break;
+            case 'h':
+            case '?': usage(args); break;
+            default: error("Unknown argument: %s\n", optarg);
+        }
+    }
+
+    if ( optind>=argc )
+    {
+        if ( !isatty(fileno((FILE *)stdin)) ) args->fname = "-";  // reading from stdin
+        else usage(args);
+    }
+    else args->fname = argv[optind];
+
+    init(args);
+    sort_blocks(args);
+    merge_blocks(args);
+    destroy(args);
+
+    return 0;
+}
diff --git a/bcftools/vcfsort.c.pysam.c b/bcftools/vcfsort.c.pysam.c
new file mode 100644
index 0000000..d3eb6b7
--- /dev/null
+++ b/bcftools/vcfsort.c.pysam.c
@@ -0,0 +1,445 @@
+#include "bcftools.pysam.h"
+
+/*  vcfsort.c -- sort subcommand
+
+   Copyright (C) 2017-2021 Genome Research Ltd.
+
+   Author: Petr Danecek <pd3@sanger.ac.uk>
+   
+   Permission is hereby granted, free of charge, to any person obtaining a copy
+   of this software and associated documentation files (the "Software"), to deal
+   in the Software without restriction, including without limitation the rights
+   to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+   copies of the Software, and to permit persons to whom the Software is
+   furnished to do so, subject to the following conditions:
+   
+   The above copyright notice and this permission notice shall be included in
+   all copies or substantial portions of the Software.
+   
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+   IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+   FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+   AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+   LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+   OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+   THE SOFTWARE.
+
+ */
+
+#include <stdio.h>
+#include <unistd.h>
+#include <getopt.h>
+#include <ctype.h>
+#include <string.h>
+#include <strings.h>
+#include <errno.h>
+#include <sys/stat.h>
+#include <sys/types.h>
+#include <fcntl.h>
+#include <math.h>
+#ifdef _WIN32
+#include <windows.h>
+#endif
+#include <htslib/vcf.h>
+#include <htslib/kstring.h>
+#include <htslib/hts_os.h>
+#include "kheap.h"
+#include "bcftools.h"
+
+typedef struct
+{
+    char *fname;
+    htsFile *fh;
+    bcf1_t *rec;
+}
+blk_t;
+
+typedef struct _args_t
+{
+    bcf_hdr_t *hdr;
+    char **argv, *fname, *output_fname, *tmp_dir;
+    int argc, output_type, clevel;
+    size_t max_mem, mem;
+    bcf1_t **buf;
+    uint8_t *mem_block;
+    size_t nbuf, mbuf, nblk;
+    blk_t *blk;
+}
+args_t;
+
+void clean_files(args_t *args)
+{
+    int i;
+    fprintf(bcftools_stderr,"Cleaning\n");
+    for (i=0; i<args->nblk; i++)
+    {
+        blk_t *blk = args->blk + i;
+        if ( blk->fname )
+        {
+            unlink(blk->fname);
+            free(blk->fname);
+        }
+        if ( blk->rec ) 
+            bcf_destroy(blk->rec);
+    }
+    rmdir(args->tmp_dir);
+}
+void clean_files_and_throw(args_t *args, const char *format, ...)
+{
+    va_list ap;
+    va_start(ap, format);
+    vfprintf(bcftools_stderr, format, ap);
+    va_end(ap);
+    clean_files(args);
+    bcftools_exit(-1);
+}
+
+int cmp_bcf_pos(const void *aptr, const void *bptr)
+{
+    bcf1_t *a = *((bcf1_t**)aptr);
+    bcf1_t *b = *((bcf1_t**)bptr);
+    if ( a->rid < b->rid ) return -1;
+    if ( a->rid > b->rid ) return 1;
+    if ( a->pos < b->pos ) return -1;
+    if ( a->pos > b->pos ) return 1;
+
+    // Sort the same chr:pos records lexicographically by ref,alt.
+    // This will be called rarely so should not slow the sorting down
+    // noticeably.
+
+    int i;
+    for (i=0; i<a->n_allele; i++)
+    { 
+        if ( i >= b->n_allele ) return 1;
+        int ret = strcasecmp(a->d.allele[i],b->d.allele[i]);
+        if ( ret ) return ret;
+    }
+    if ( a->n_allele < b->n_allele ) return -1;
+    return 0;
+}
+
+void buf_flush(args_t *args)
+{
+    if ( !args->nbuf ) return;
+
+    qsort(args->buf, args->nbuf, sizeof(*args->buf), cmp_bcf_pos);
+
+    args->nblk++;
+    args->blk = (blk_t*) realloc(args->blk, sizeof(blk_t)*args->nblk);
+    blk_t *blk = args->blk + args->nblk - 1;
+
+    kstring_t str = {0,0,0};
+    ksprintf(&str, "%s/%05d.bcf", args->tmp_dir, (int)args->nblk);
+    blk->fname = str.s;
+    blk->rec   = NULL;
+    blk->fh    = NULL;
+
+    htsFile *fh = hts_open(blk->fname, "wbu");
+    if ( fh == NULL ) clean_files_and_throw(args, "Cannot write %s: %s\n", blk->fname, strerror(errno));
+    if ( bcf_hdr_write(fh, args->hdr)!=0 ) clean_files_and_throw(args, "[%s] Error: cannot write to %s\n", __func__,blk->fname);
+    
+    int i;
+    for (i=0; i<args->nbuf; i++)
+    {
+        if ( bcf_write(fh, args->hdr, args->buf[i])!=0 ) clean_files_and_throw(args, "[%s] Error: cannot write to %s\n", __func__,blk->fname);
+    }
+    if ( hts_close(fh)!=0 ) clean_files_and_throw(args, "[%s] Error: close failed .. %s\n", __func__,blk->fname);
+
+    args->nbuf = 0;
+    args->mem  = 0;
+}
+
+
+static inline uint8_t *_align_up(uint8_t *ptr)
+{
+    return (uint8_t*)(((size_t)ptr + 8 - 1) & ~((size_t)(8 - 1)));
+}
+
+void buf_push(args_t *args, bcf1_t *rec)
+{
+    size_t delta = sizeof(bcf1_t) + rec->shared.l + rec->indiv.l + rec->unpack_size[0] + rec->unpack_size[1]
+        + sizeof(*rec->d.allele)*rec->d.m_allele
+        + sizeof(bcf1_t*)       // args->buf
+        + 8;                    // the number of _align_up() calls
+
+    if ( delta > args->max_mem - args->mem )
+    {
+        args->nbuf++;
+        hts_expand(bcf1_t*, args->nbuf, args->mbuf, args->buf);
+        args->buf[args->nbuf-1] = rec;
+        buf_flush(args);
+        bcf_destroy(rec);
+        return;
+    }
+
+    // make sure nothing has changed in htslib
+    assert( rec->unpacked==BCF_UN_STR && !rec->d.flt && !rec->d.info && !rec->d.fmt && !rec->d.var );
+
+    uint8_t *ptr_beg = args->mem_block + args->mem;
+    uint8_t *ptr = _align_up(ptr_beg);
+    bcf1_t *new_rec = (bcf1_t*)ptr;
+    memcpy(new_rec,rec,sizeof(*rec));
+    ptr += sizeof(*rec);
+
+    // The array of allele pointers does not need alignment as bcf1_t is already padded to the biggest
+    // data type in the structure
+    char **allele = (char**)ptr;
+    ptr += rec->n_allele*sizeof(*allele);
+
+    // This is just to prevent valgrind from complaining about memcpy, unpack_size is a high-water mark
+    // and the end may be uninitialized
+    delta = rec->d.allele[rec->n_allele-1] - rec->d.allele[0];
+    while ( delta < rec->unpack_size[1] ) if ( !rec->d.als[delta++] ) break;
+    memcpy(ptr,rec->d.als,delta);
+    new_rec->d.als = (char*)ptr;
+    ptr = ptr + delta;
+
+    int i;
+    for (i=0; i<rec->n_allele; i++) allele[i] = new_rec->d.als + (ptrdiff_t)(rec->d.allele[i] - rec->d.allele[0]);
+    new_rec->d.allele = allele;
+
+    memcpy(ptr,rec->shared.s,rec->shared.l);
+    new_rec->shared.s = (char*)ptr;
+    new_rec->shared.m = rec->shared.l;
+    ptr += rec->shared.l;
+
+    memcpy(ptr,rec->indiv.s,rec->indiv.l);
+    new_rec->indiv.s = (char*)ptr;
+    new_rec->indiv.m = rec->indiv.l;
+    ptr += rec->indiv.l;
+
+    // This is just to prevent valgrind from complaining about memcpy, unpack_size is a high-water mark
+    // and the end may be uninitialized
+    i = 0;
+    while ( i < rec->unpack_size[0] ) if ( !rec->d.id[i++] ) break;
+    memcpy(ptr,rec->d.id,i);
+    new_rec->d.id = (char*)ptr;
+    ptr += i;
+
+    args->nbuf++;
+    hts_expand(bcf1_t*, args->nbuf, args->mbuf, args->buf);
+    args->buf[args->nbuf-1] = new_rec;
+
+    delta = ptr - ptr_beg;
+    args->mem += delta;
+
+    assert( args->mem <= args->max_mem );
+
+    bcf_destroy(rec);
+}
+
+void sort_blocks(args_t *args) 
+{
+    htsFile *in = hts_open(args->fname, "r");
+    if ( !in ) clean_files_and_throw(args, "Could not read %s\n", args->fname);
+    args->hdr = bcf_hdr_read(in);
+    if ( !args->hdr) clean_files_and_throw(args, "Could not read VCF/BCF headers from %s\n", args->fname);
+
+    while ( 1 )
+    {
+        bcf1_t *rec = bcf_init();
+        int ret = bcf_read1(in, args->hdr, rec);
+        if ( ret < -1 ) clean_files_and_throw(args,"Error encountered while parsing the input\n");
+        if ( ret == -1 )
+        {
+            bcf_destroy(rec);
+            break;
+        }
+        if ( rec->errcode ) clean_files_and_throw(args,"Error encountered while parsing the input at %s:%d\n",bcf_seqname(args->hdr,rec),rec->pos+1);
+        bcf_unpack(rec, BCF_UN_STR);
+        buf_push(args, rec);
+    }
+    buf_flush(args);
+    free(args->buf);
+
+    if ( hts_close(in)!=0 ) clean_files_and_throw(args,"Close failed: %s\n", args->fname);
+}
+
+static inline int blk_is_smaller(blk_t **aptr, blk_t **bptr)
+{
+    blk_t *a = *aptr;
+    blk_t *b = *bptr;
+    int ret = cmp_bcf_pos(&a->rec, &b->rec);
+    if ( ret < 0 ) return 1;
+    return 0;
+}
+KHEAP_INIT(blk, blk_t*, blk_is_smaller)
+
+void blk_read(args_t *args, khp_blk_t *bhp, bcf_hdr_t *hdr, blk_t *blk)
+{
+    if ( !blk->fh ) return;
+    int ret = bcf_read(blk->fh, hdr, blk->rec);
+    if ( ret < -1 ) clean_files_and_throw(args, "Error reading %s\n", blk->fname);
+    if ( ret == -1 )
+    {
+        if ( hts_close(blk->fh)!=0 ) clean_files_and_throw(args, "Close failed: %s\n", blk->fname);
+        blk->fh = 0;
+        return;
+    }
+    bcf_unpack(blk->rec, BCF_UN_STR);
+    khp_insert(blk, bhp, &blk);
+}
+
+void merge_blocks(args_t *args) 
+{
+    fprintf(bcftools_stderr,"Merging %d temporary files\n", (int)args->nblk);
+    khp_blk_t *bhp = khp_init(blk);
+
+    int i;
+    for (i=0; i<args->nblk; i++)
+    {
+        blk_t *blk = args->blk + i;
+        blk->fh = hts_open(blk->fname, "r");
+        if ( !blk->fh ) clean_files_and_throw(args, "Could not read %s: %s\n", blk->fname, strerror(errno));
+        bcf_hdr_t *hdr = bcf_hdr_read(blk->fh);
+        bcf_hdr_destroy(hdr);
+        blk->rec = bcf_init();
+        blk_read(args, bhp, args->hdr, blk);
+    }
+
+    char wmode[8];
+    set_wmode(wmode,args->output_type,args->output_fname,args->clevel);
+    htsFile *out = hts_open(args->output_fname ? args->output_fname : "-", wmode);
+    if ( bcf_hdr_write(out, args->hdr)!=0 ) clean_files_and_throw(args, "[%s] Error: cannot write to %s\n", __func__,args->output_fname);
+    while ( bhp->ndat )
+    {
+        blk_t *blk = bhp->dat[0];
+        if ( bcf_write(out, args->hdr, blk->rec)!=0 ) clean_files_and_throw(args, "[%s] Error: cannot write to %s\n", __func__,args->output_fname);
+        khp_delete(blk, bhp);
+        blk_read(args, bhp, args->hdr, blk);
+    }
+    if ( hts_close(out)!=0 ) clean_files_and_throw(args, "Close failed: %s\n", args->output_fname);
+
+    clean_files(args);
+
+    free(args->blk);
+    khp_destroy(blk, bhp);
+    fprintf(bcftools_stderr,"Done\n");
+}
+
+static void usage(args_t *args)
+{
+    fprintf(bcftools_stderr, "\n");
+    fprintf(bcftools_stderr, "About:   Sort VCF/BCF file.\n");
+    fprintf(bcftools_stderr, "Usage:   bcftools sort [OPTIONS] <FILE.vcf>\n");
+    fprintf(bcftools_stderr, "\n");
+    fprintf(bcftools_stderr, "Options:\n");
+    fprintf(bcftools_stderr, "    -m, --max-mem FLOAT[kMG]       maximum memory to use [768M]\n");    // using metric units, 1M=1e6
+    fprintf(bcftools_stderr, "    -o, --output FILE              output file name [bcftools_stdout]\n");
+    fprintf(bcftools_stderr, "    -O, --output-type b|u|z|v      b: compressed BCF, u: uncompressed BCF, z: compressed VCF, v: uncompressed VCF [v]\n");
+    fprintf(bcftools_stderr, "    -O, --output-type u|b|v|z[0-9] u/b: un/compressed BCF, v/z: un/compressed VCF, 0-9: compression level [v]\n");
+
+#ifdef _WIN32
+    fprintf(bcftools_stderr, "    -T, --temp-dir DIR             temporary files [/bcftools.XXXXXX]\n");
+#else
+    fprintf(bcftools_stderr, "    -T, --temp-dir DIR             temporary files [/tmp/bcftools.XXXXXX]\n");
+#endif
+    fprintf(bcftools_stderr, "\n");
+    bcftools_exit(1);
+}
+
+size_t parse_mem_string(const char *str) 
+{
+    char *tmp;
+    double mem = strtod(str, &tmp);
+    if ( tmp==str ) error("Could not parse the memory string: \"%s\"\n", str);
+    if ( !strcasecmp("k",tmp) ) mem *= 1000;
+    else if ( !strcasecmp("m",tmp) ) mem *= 1000*1000;
+    else if ( !strcasecmp("g",tmp) ) mem *= 1000*1000*1000;
+    return mem;
+}
+
+void mkdir_p(const char *fmt, ...);
+static void init(args_t *args)
+{
+    args->max_mem *= 0.9;
+    args->mem_block = malloc(args->max_mem);
+    args->mem = 0;
+
+    args->tmp_dir = init_tmp_prefix(args->tmp_dir);
+
+#ifdef _WIN32
+        int ret = mkdir(mktemp(args->tmp_dir), 0700);
+        if ( ret ) error("mkdir(%s) failed: %s\n", args->tmp_dir,strerror(errno));
+#else
+        char *tmp = mkdtemp(args->tmp_dir);
+        if ( !tmp ) error("mkdtemp(%s) failed: %s\n",  args->tmp_dir,strerror(errno));
+        int ret = chmod(tmp, S_IRUSR|S_IWUSR|S_IXUSR);
+        if ( ret ) error("chmod(%s,S_IRUSR|S_IWUSR|S_IXUSR) failed: %s\n", args->tmp_dir,strerror(errno));
+#endif
+
+    fprintf(bcftools_stderr,"Writing to %s\n", args->tmp_dir);
+}
+static void destroy(args_t *args)
+{
+    bcf_hdr_destroy(args->hdr);
+    free(args->mem_block);
+    free(args->tmp_dir);
+    free(args);
+}
+
+int main_sort(int argc, char *argv[])
+{
+    int c;
+    args_t *args  = (args_t*) calloc(1,sizeof(args_t));
+    args->argc    = argc; args->argv = argv;
+    args->max_mem = 768*1000*1000;
+    args->output_fname = "-";
+    args->clevel = -1;
+
+    static struct option loptions[] =
+    {
+        {"max-mem",required_argument,NULL,'m'},
+        {"temp-dir",required_argument,NULL,'T'},
+        {"output-type",required_argument,NULL,'O'},
+        {"output-file",required_argument,NULL,'o'},
+        {"output",required_argument,NULL,'o'},
+        {"help",no_argument,NULL,'h'},
+        {0,0,0,0}
+    };
+    char *tmp;
+    while ((c = getopt_long(argc, argv, "m:T:O:o:h?",loptions,NULL)) >= 0)
+    {
+        switch (c)
+        {
+            case 'm': args->max_mem = parse_mem_string(optarg); break;
+            case 'T': args->tmp_dir = optarg; break;
+            case 'o': args->output_fname = optarg; break;
+            case 'O':
+                      switch (optarg[0]) {
+                          case 'b': args->output_type = FT_BCF_GZ; break;
+                          case 'u': args->output_type = FT_BCF; break;
+                          case 'z': args->output_type = FT_VCF_GZ; break;
+                          case 'v': args->output_type = FT_VCF; break;
+                          default:
+                          {
+                              args->clevel = strtol(optarg,&tmp,10);
+                              if ( *tmp || args->clevel<0 || args->clevel>9 ) error("The output type \"%s\" not recognised\n", optarg);
+                          }
+                      };
+                      if ( optarg[1] )
+                      {
+                          args->clevel = strtol(optarg+1,&tmp,10);
+                          if ( *tmp || args->clevel<0 || args->clevel>9 ) error("Could not parse argument: --compression-level %s\n", optarg+1);
+                      }
+                      break;
+            case 'h':
+            case '?': usage(args); break;
+            default: error("Unknown argument: %s\n", optarg);
+        }
+    }
+
+    if ( optind>=argc )
+    {
+        if ( !isatty(fileno((FILE *)stdin)) ) args->fname = "-";  // reading from stdin
+        else usage(args);
+    }
+    else args->fname = argv[optind];
+
+    init(args);
+    sort_blocks(args);
+    merge_blocks(args);
+    destroy(args);
+
+    return 0;
+}
diff --git a/bcftools/vcfstats.c b/bcftools/vcfstats.c
new file mode 100644
index 0000000..6a7272f
--- /dev/null
+++ b/bcftools/vcfstats.c
@@ -0,0 +1,1915 @@
+/*  vcfstats.c -- Produces stats which can be plotted using plot-vcfstats.
+
+    Copyright (C) 2012-2022 Genome Research Ltd.
+
+    Author: Petr Danecek <pd3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.  */
+
+/*
+    Notes and known issues:
+        - SN ts/tv calculation includes all non-ref alleles listed in ALT while per-sample ts/tv
+        takes the first non-ref allele only, something to consider with many non-ref HETs.
+*/
+#include <stdio.h>
+#include <stdarg.h>
+#include <unistd.h>
+#include <getopt.h>
+#include <assert.h>
+#include <math.h>
+#include <htslib/vcf.h>
+#include <htslib/synced_bcf_reader.h>
+#include <htslib/vcfutils.h>
+#include <htslib/faidx.h>
+#include <inttypes.h>
+#include "bcftools.h"
+#include "filter.h"
+#include "bin.h"
+#include "dist.h"
+
+// Logic of the filters: include or exclude sites which match the filters?
+#define FLT_INCLUDE 1
+#define FLT_EXCLUDE 2
+
+#define HWE_STATS 1
+#define QUAL_STATS 1
+#define IRC_STATS 1
+#define IRC_RLEN 10
+#define NA_STRING "0"
+
+typedef struct
+{
+    char *tag;
+    float min, max;
+    uint64_t *vals_ts, *vals_tv;
+    void *val;
+    int nbins, type, m_val, idx;
+}
+user_stats_t;
+
+typedef struct
+{
+    int min, max, step, m_vals;
+    uint64_t *vals;
+}
+idist_t;
+
+typedef struct
+{
+    uint64_t n_snps, n_indels, n_mnps, n_others, n_mals, n_snp_mals, n_records, n_noalts;
+    int *af_ts, *af_tv, *af_snps;   // first bin of af_* stats are singletons
+    #if HWE_STATS
+        int *af_hwe;
+    #endif
+    #if IRC_STATS
+        int n_repeat[IRC_RLEN][4], n_repeat_na;    // number of indels which are repeat-consistent, repeat-inconsistent (dels and ins), and not applicable
+        int *af_repeats[3];
+    #endif
+    int ts_alt1, tv_alt1;
+    #if QUAL_STATS
+        // Values are rounded to one significant digit and 1 is added (Q*10+1); missing and negative values go in the first bin
+        // Only SNPs that are the 1st alternate allele are counted
+        dist_t *qual_ts, *qual_tv, *qual_indels;
+    #endif
+    int *insertions, *deletions, m_indel;   // maximum indel length
+    int in_frame, out_frame, na_frame, in_frame_alt1, out_frame_alt1, na_frame_alt1;
+    int subst[15];
+    int *smpl_hets, *smpl_homRR, *smpl_homAA, *smpl_ts, *smpl_tv, *smpl_indels, *smpl_ndp, *smpl_sngl;
+    int *smpl_hapRef, *smpl_hapAlt, *smpl_missing;
+    int *smpl_ins_hets, *smpl_del_hets, *smpl_ins_homs, *smpl_del_homs;
+    int *smpl_frm_shifts; // not-applicable, in-frame, out-frame
+    unsigned long int *smpl_dp;
+    idist_t dp, dp_sites;
+    int nusr;
+    user_stats_t *usr;
+    double *dvaf;   // distribution of the mean indel-allele frequency by length: -m_indel,-(m_indel-1),...-1,0,1,..,m_indel
+    uint32_t *nvaf;
+}
+stats_t;
+
+typedef struct
+{
+    uint64_t gt2gt[5][5];   // number of RR->RR, RR->RA, etc. matches/mismatches; see type2stats
+    /*
+        Pearson's R^2 is used for aggregate R^2
+        y, yy .. sum of dosage and squared dosage in the query VCF (second file)
+        x, xx .. sum of squared dosage in the truth VCF (first file)
+        n     .. number of genotypes
+     */
+    double y, yy, x, xx, yx, n;
+}
+gtcmp_t;
+
+typedef struct
+{
+    char *seq;
+    int pos, cnt, len;
+}
+_idc1_t;
+typedef struct
+{
+    faidx_t *ref;
+    _idc1_t *dat;
+    int ndat, mdat;
+}
+indel_ctx_t;
+
+typedef struct
+{
+    // stats
+    stats_t stats[3];
+    int *tmp_iaf, ntmp_iaf, m_af, m_qual, naf_hwe, mtmp_frm;
+    uint8_t *tmp_frm;
+    int dp_min, dp_max, dp_step;
+    gtcmp_t *smpl_gts_snps, *smpl_gts_indels;
+    gtcmp_t *af_gts_snps, *af_gts_indels; // first bin of af_* stats are singletons
+    bin_t *af_bins;
+    float *farr;
+    int mfarr;
+
+    // indel context
+    indel_ctx_t *indel_ctx;
+    char *ref_fname;
+
+    // user stats
+    int nusr;
+    user_stats_t *usr;
+
+    // other
+    bcf_srs_t *files;
+    bcf_sr_regions_t *exons;
+    char **argv, *exons_fname, *regions_list, *samples_list, *targets_list, *af_bins_list, *af_tag;
+    int argc, verbose_sites, first_allele_only, samples_is_file;
+    int split_by_id, nstats;
+
+    filter_t *filter[2];
+    char *filter_str;
+    int filter_logic;   // include or exclude sites which match the filters? One of FLT_INCLUDE/FLT_EXCLUDE
+    int n_threads;
+}
+args_t;
+
+static int type2dosage[6], type2ploidy[6], type2stats[7];
+
+static void idist_init(idist_t *d, int min, int max, int step)
+{
+    d->min = min; d->max = max; d->step = step;
+    d->m_vals = 4 + (d->max - d->min)/d->step;
+    d->vals = (uint64_t*) calloc(d->m_vals,sizeof(uint64_t));
+}
+static void idist_destroy(idist_t *d)
+{
+    if ( d->vals ) free(d->vals);
+}
+static inline uint64_t *idist(idist_t *d, int val)
+{
+    if ( val < d->min ) return &d->vals[0];
+    if ( val > d->max ) return &d->vals[d->m_vals-1];
+    return &d->vals[1 + (val - d->min) / d->step];
+}
+static inline int idist_i2bin(idist_t *d, int i)
+{
+    if ( i<=0 ) return d->min;
+    if ( i>= d->m_vals ) return d->max;
+    return i-1+d->min;
+}
+
+#define IC_DBG 0
+#if IC_DBG
+static void _indel_ctx_print1(_idc1_t *idc)
+{
+    int i;
+    fprintf(stdout, "%d\t", idc->cnt);
+    for (i=0; i<idc->len; i++)
+        fputc(idc->seq[i], stdout);
+    fputc('\n', stdout);
+}
+static void _indel_ctx_print(indel_ctx_t *ctx)
+{
+    int i;
+    for (i=0; i<ctx->ndat; i++)
+        _indel_ctx_print1(&ctx->dat[i]);
+    fputc('\n',stdout);
+}
+#endif
+static int _indel_ctx_lookup(indel_ctx_t *ctx, char *seq, int seq_len, int *hit)
+{
+    // binary search
+    int min = 0, max = ctx->ndat - 1;
+    while ( min<=max )
+    {
+        int i = (min+max)/2;
+        int cmp = strncmp(seq, ctx->dat[i].seq, seq_len);
+        if ( cmp<0 ) max = i - 1;
+        else if ( cmp>0 ) min = i + 1;
+        else
+        {
+            if ( seq_len==ctx->dat[i].len )
+            {
+                *hit = 1;
+                return i;
+            }
+            else if ( seq_len<ctx->dat[i].len ) max = i - 1;
+            else min = i + 1;
+        }
+    }
+    *hit = 0;
+    return max;
+}
+static void _indel_ctx_insert(indel_ctx_t *ctx, char *seq, int seq_len, int pos)
+{
+    int idat, hit, i;
+    idat = _indel_ctx_lookup(ctx, seq, seq_len, &hit);
+    if ( !hit )
+    {
+        if ( pos>0 ) return;
+        idat++;
+        ctx->ndat++;
+        hts_expand(_idc1_t, ctx->ndat+1, ctx->mdat, ctx->dat);
+        if ( idat<ctx->ndat && ctx->ndat>1 )
+            memmove(&ctx->dat[idat+1], &ctx->dat[idat], (ctx->ndat - idat - 1)*sizeof(_idc1_t));
+        ctx->dat[idat].len = seq_len;
+        ctx->dat[idat].cnt = 1;
+        ctx->dat[idat].pos = pos;
+        ctx->dat[idat].seq = (char*) malloc(sizeof(char)*(seq_len+1));
+        for (i=0; i<seq_len; i++) ctx->dat[idat].seq[i] = seq[i];
+        ctx->dat[idat].seq[i] = 0;
+        return;
+    }
+    if ( ctx->dat[idat].pos + seq_len == pos )
+    {
+        ctx->dat[idat].cnt++;
+        ctx->dat[idat].pos = pos;
+    }
+}
+indel_ctx_t *indel_ctx_init(char *fa_ref_fname)
+{
+    indel_ctx_t *ctx = (indel_ctx_t *) calloc(1,sizeof(indel_ctx_t));
+    ctx->ref = fai_load(fa_ref_fname);
+    if ( !ctx->ref )
+    {
+        free(ctx);
+        return NULL;
+    }
+    return ctx;
+}
+void indel_ctx_destroy(indel_ctx_t *ctx)
+{
+    fai_destroy(ctx->ref);
+    if ( ctx->mdat ) free(ctx->dat);
+    free(ctx);
+}
+/**
+ * indel_ctx_type() - determine indel context type
+ * @ctx:
+ * @chr:    chromosome name
+ * @pos:    position of the first @ref base, 1-based
+ * @ref:    reference allele
+ * @alt:    alternate allele. Only first of multiple comma-separated alleles is
+ *          considered
+ * @nrep:   number of repeated elements (w)
+ * @nlen:   length of a single repeat element (w)
+ *
+ * Returns the INDEL length, negative for deletions, positive for insertions
+ */
+int indel_ctx_type(indel_ctx_t *ctx, char *chr, int pos, char *ref, char *alt, int *nrep, int *nlen)
+{
+    const int win_size = 50;             // hard-wired for now
+    const int rep_len  = IRC_RLEN;       // hard-wired for now
+
+    int ref_len = strlen(ref);
+    int alt_len = 0;
+    while ( alt[alt_len] && alt[alt_len]!=',' ) alt_len++;
+
+    int i, fai_ref_len;
+    char *fai_ref = faidx_fetch_seq(ctx->ref, chr, pos-1, pos+win_size, &fai_ref_len);
+    for (i=0; i<fai_ref_len; i++)
+        if ( (int)fai_ref[i]>96 ) fai_ref[i] -= 32;
+
+    // Sanity check: the reference sequence must match the REF allele
+    for (i=0; i<fai_ref_len && i<ref_len; i++)
+        if ( ref[i] != fai_ref[i] && ref[i] - 32 != fai_ref[i] && !iupac_consistent(fai_ref[i], ref[i]) )
+            error("\nSanity check failed, the reference sequence differs: %s:%d+%d .. %c vs %c\n", chr, pos, i, ref[i],fai_ref[i]);
+
+    // Count occurrences of all possible kmers
+    ctx->ndat = 0;
+    for (i=0; i<win_size; i++)
+    {
+        int k, kmax = rep_len <= i ? rep_len : i+1;
+        for (k=0; k<kmax; k++)
+            _indel_ctx_insert(ctx, &fai_ref[i-k+1], k+1, i-k);
+    }
+
+    #if IC_DBG
+    fprintf(stdout,"ref: %s\n", ref);
+    fprintf(stdout,"alt: %s\n", alt);
+    fprintf(stdout,"ctx: %s\n", fai_ref);
+    _indel_ctx_print(ctx);
+    #endif
+
+    int max_cnt = 0, max_len = 0;
+    for (i=0; i<ctx->ndat; i++)
+    {
+        if ( max_cnt < ctx->dat[i].cnt || (max_cnt==ctx->dat[i].cnt && max_len < ctx->dat[i].len) )
+        {
+            max_cnt = ctx->dat[i].cnt;
+            max_len = ctx->dat[i].len;
+        }
+        free(ctx->dat[i].seq);
+    }
+    free(fai_ref);
+
+    *nrep = max_cnt;
+    *nlen = max_len;
+    return alt_len - ref_len;
+}
+
+static void add_user_stats(args_t *args, char *str)
+{
+    args->nusr++;
+    args->usr = (user_stats_t*) realloc(args->usr,sizeof(user_stats_t)*args->nusr);
+    user_stats_t *usr = &args->usr[args->nusr-1];
+    memset(usr,0,sizeof(*usr));
+    usr->min   = 0;
+    usr->max   = 1;
+    usr->nbins = 100;
+    usr->idx   = 0;
+
+    char *tmp = str;
+    while ( *tmp && *tmp!=':' ) tmp++;
+
+    // Tag with an index or just tag? (e.g. PV4[1] vs DP)
+    if ( tmp > str && tmp[-1]==']' )
+    {
+        char *ptr = tmp;
+        while ( ptr>str && *ptr!='[' ) ptr--;
+        if ( *ptr=='[' )
+        {
+            char *ptr2;
+            usr->idx = strtol(ptr+1, &ptr2, 10);
+            if ( ptr+1==ptr2 || ptr2 != tmp-1 ) error("Could not parse the index in \"%s\" (ptr=%s;ptr2=%s(%p),tmp=%s(%p),idx=%d)\n", str,ptr,ptr2,ptr2,tmp,tmp,usr->idx);
+            if ( usr->idx<0 ) error("Error: negative index is not allowed: \"%s\"\n", str);
+            *ptr = 0;
+        }
+    }
+
+    usr->tag = (char*)calloc(tmp-str+2,sizeof(char));
+    memcpy(usr->tag,str,tmp-str);
+
+    if ( *tmp )
+    {
+        char *ptr = ++tmp;
+        usr->min = strtod(tmp, &ptr);
+        if ( tmp==ptr ) error("Could not parse %s\n", str);
+        tmp = ptr+1;
+    }
+    if ( *tmp )
+    {
+        char *ptr = tmp;
+        usr->max = strtod(tmp, &ptr);
+        if ( tmp==ptr ) error("Could not parse %s\n", str);
+        tmp = ptr+1;
+    }
+    if ( *tmp )
+    {
+        char *ptr = tmp;
+        usr->nbins = strtol(tmp, &ptr, 10);
+        if ( tmp==ptr ) error("Could not parse %s\n", str);
+        if ( usr->nbins<=0 ) error("Number of bins does not make sense (%d): %s.\n", usr->nbins, str);
+    }
+}
+static void init_user_stats(args_t *args, bcf_hdr_t *hdr, stats_t *stats)
+{
+    stats->nusr = args->nusr;
+    stats->usr = (user_stats_t*)malloc(sizeof(user_stats_t)*args->nusr);
+    memcpy(stats->usr,args->usr,args->nusr*sizeof(user_stats_t));
+    int i;
+    for (i=0; i<stats->nusr; i++)
+    {
+        user_stats_t *usr = &stats->usr[i];
+        usr->vals_ts = (uint64_t*)calloc(usr->nbins,sizeof(uint64_t));
+        usr->vals_tv = (uint64_t*)calloc(usr->nbins,sizeof(uint64_t));
+        int id = bcf_hdr_id2int(hdr,BCF_DT_ID,usr->tag);
+        if ( !bcf_hdr_idinfo_exists(hdr,BCF_HL_INFO,id) ) error("The INFO tag \"%s\" is not defined in the header\n", usr->tag);
+        usr->type = bcf_hdr_id2type(hdr,BCF_HL_INFO,id);
+        if ( usr->type!=BCF_HT_REAL && usr->type!=BCF_HT_INT ) error("The INFO tag \"%s\" is not of Float or Integer type (%d)\n", usr->tag, usr->type);
+    }
+}
+static void init_stats(args_t *args)
+{
+    int i;
+    args->nstats = args->files->nreaders==1 ? 1 : 3;
+    if ( args->split_by_id ) args->nstats = 2;
+
+    if ( args->filter_str )
+    {
+        args->filter[0] = filter_init(bcf_sr_get_header(args->files,0), args->filter_str);
+        if ( args->files->nreaders==2 )
+            args->filter[1] = filter_init(bcf_sr_get_header(args->files,1), args->filter_str);
+        args->files->max_unpack |= filter_max_unpack(args->filter[0]);
+    }
+
+    // AF corresponds to AC but is more robust to mixtures of haploid and diploid GTs
+    if ( !args->af_bins_list )
+    {
+        args->m_af = 101;
+        for (i=0; i<args->files->nreaders; i++)
+            if ( bcf_hdr_nsamples(args->files->readers[i].header) + 1> args->m_af )
+                args->m_af = bcf_hdr_nsamples(args->files->readers[i].header) + 1;
+    }
+    else
+    {
+        args->af_bins = bin_init(args->af_bins_list,0,1);
+
+        // m_af is used also for other af arrays, where the first bin is for
+        // singletons. However, since the last element is unused in af_bins
+        // (n boundaries form n-1 intervals), the m_af count is good for both.
+        args->m_af = bin_get_size(args->af_bins);
+    }
+
+    bcf_hdr_t *hdr = bcf_sr_get_header(args->files,0);
+    if ( args->af_tag && !bcf_hdr_idinfo_exists(hdr,BCF_HL_INFO,bcf_hdr_id2int(hdr,BCF_DT_ID,args->af_tag)) )
+        error("No such INFO tag: %s\n", args->af_tag);
+
+    #if QUAL_STATS
+        args->m_qual = 999;
+    #endif
+    #if HWE_STATS
+        args->naf_hwe = 100;
+    #endif
+
+    if ( args->samples_list )
+    {
+        if ( !bcf_sr_set_samples(args->files,args->samples_list,args->samples_is_file) )
+        {
+            if ( !bcf_hdr_nsamples(args->files->readers[0].header) )
+                error("No sample columns in %s\n", args->files->readers[0].fname);
+            error("Unable to parse the samples: \"%s\"\n", args->samples_list);
+        }
+        args->af_gts_snps     = (gtcmp_t *) calloc(args->m_af,sizeof(gtcmp_t));
+        args->af_gts_indels   = (gtcmp_t *) calloc(args->m_af,sizeof(gtcmp_t));
+        args->smpl_gts_snps   = (gtcmp_t *) calloc(args->files->n_smpl,sizeof(gtcmp_t));
+        args->smpl_gts_indels = (gtcmp_t *) calloc(args->files->n_smpl,sizeof(gtcmp_t));
+    }
+    for (i=0; i<args->nstats; i++)
+    {
+        stats_t *stats = &args->stats[i];
+        stats->m_indel     = 60;
+        stats->insertions  = (int*) calloc(stats->m_indel,sizeof(int));
+        stats->deletions   = (int*) calloc(stats->m_indel,sizeof(int));
+        stats->af_ts       = (int*) calloc(args->m_af,sizeof(int));
+        stats->af_tv       = (int*) calloc(args->m_af,sizeof(int));
+        stats->af_snps     = (int*) calloc(args->m_af,sizeof(int));
+        int j;
+        for (j=0; j<3; j++) stats->af_repeats[j] = (int*) calloc(args->m_af,sizeof(int));
+        #if QUAL_STATS
+            stats->qual_ts     = dist_init(5);
+            stats->qual_tv     = dist_init(5);
+            stats->qual_indels = dist_init(5);
+        #endif
+        if ( args->files->n_smpl )
+        {
+            stats->smpl_missing = (int *) calloc(args->files->n_smpl,sizeof(int));
+            stats->smpl_hets   = (int *) calloc(args->files->n_smpl,sizeof(int));
+            stats->smpl_homAA  = (int *) calloc(args->files->n_smpl,sizeof(int));
+            stats->smpl_homRR  = (int *) calloc(args->files->n_smpl,sizeof(int));
+            stats->smpl_hapRef = (int *) calloc(args->files->n_smpl,sizeof(int));
+            stats->smpl_hapAlt = (int *) calloc(args->files->n_smpl,sizeof(int));
+            stats->smpl_ins_hets = (int *) calloc(args->files->n_smpl,sizeof(int));
+            stats->smpl_del_hets = (int *) calloc(args->files->n_smpl,sizeof(int));
+            stats->smpl_ins_homs = (int *) calloc(args->files->n_smpl,sizeof(int));
+            stats->smpl_del_homs = (int *) calloc(args->files->n_smpl,sizeof(int));
+            stats->smpl_ts     = (int *) calloc(args->files->n_smpl,sizeof(int));
+            stats->smpl_tv     = (int *) calloc(args->files->n_smpl,sizeof(int));
+            stats->smpl_indels = (int *) calloc(args->files->n_smpl,sizeof(int));
+            stats->smpl_dp     = (unsigned long int *) calloc(args->files->n_smpl,sizeof(unsigned long int));
+            stats->smpl_ndp    = (int *) calloc(args->files->n_smpl,sizeof(int));
+            stats->smpl_sngl   = (int *) calloc(args->files->n_smpl,sizeof(int));
+            #if HWE_STATS
+                stats->af_hwe  = (int*) calloc(args->m_af*args->naf_hwe,sizeof(int));
+            #endif
+            if ( args->exons_fname )
+                stats->smpl_frm_shifts = (int*) calloc(args->files->n_smpl*3,sizeof(int));
+            stats->nvaf = (uint32_t*) calloc(stats->m_indel*2+1,sizeof(*stats->nvaf));
+            stats->dvaf = (double*) calloc(stats->m_indel*2+1,sizeof(*stats->dvaf));
+        }
+        idist_init(&stats->dp, args->dp_min,args->dp_max,args->dp_step);
+        idist_init(&stats->dp_sites, args->dp_min,args->dp_max,args->dp_step);
+        init_user_stats(args, i!=1 ? args->files->readers[0].header : args->files->readers[1].header, stats);
+    }
+
+    if ( args->exons_fname )
+    {
+        args->exons = bcf_sr_regions_init(args->exons_fname,1,0,1,2);
+        if ( !args->exons )
+            error("Error occurred while reading, was the file compressed with bgzip: %s?\n", args->exons_fname);
+    }
+
+    #if IRC_STATS
+    if ( args->ref_fname )
+        args->indel_ctx = indel_ctx_init(args->ref_fname);
+    #endif
+
+    type2dosage[GT_HOM_RR] = 0;
+    type2dosage[GT_HET_RA] = 1;
+    type2dosage[GT_HOM_AA] = 2;
+    type2dosage[GT_HET_AA] = 2;
+    type2dosage[GT_HAPL_R] = 0;
+    type2dosage[GT_HAPL_A] = 1;
+
+    type2ploidy[GT_HOM_RR] = 1;
+    type2ploidy[GT_HET_RA] = 1;
+    type2ploidy[GT_HOM_AA] = 1;
+    type2ploidy[GT_HET_AA] = 1;
+    type2ploidy[GT_HAPL_R] = -1;
+    type2ploidy[GT_HAPL_A] = -1;
+
+    type2stats[GT_HOM_RR] = 0;
+    type2stats[GT_HET_RA] = 1;
+    type2stats[GT_HOM_AA] = 2;
+    type2stats[GT_HET_AA] = 3;
+    type2stats[GT_HAPL_R] = 0;
+    type2stats[GT_HAPL_A] = 2;
+    type2stats[GT_UNKN]   = 4;
+
+}
+static void destroy_stats(args_t *args)
+{
+    int id, j;
+    for (id=0; id<args->nstats; id++)
+    {
+        stats_t *stats = &args->stats[id];
+        if (stats->af_ts) free(stats->af_ts);
+        if (stats->af_tv) free(stats->af_tv);
+        if (stats->af_snps) free(stats->af_snps);
+        for (j=0; j<3; j++)
+            if (stats->af_repeats[j]) free(stats->af_repeats[j]);
+        #if QUAL_STATS
+            if (stats->qual_ts) dist_destroy(stats->qual_ts);
+            if (stats->qual_tv) dist_destroy(stats->qual_tv);
+            if (stats->qual_indels) dist_destroy(stats->qual_indels);
+        #endif
+        #if HWE_STATS
+            free(stats->af_hwe);
+        #endif
+        free(stats->insertions);
+        free(stats->deletions);
+        free(stats->smpl_missing);
+        free(stats->smpl_hets);
+        free(stats->smpl_homAA);
+        free(stats->smpl_homRR);
+        free(stats->smpl_hapRef);
+        free(stats->smpl_hapAlt);
+        free(stats->smpl_ins_homs);
+        free(stats->smpl_del_homs);
+        free(stats->smpl_ins_hets);
+        free(stats->smpl_del_hets);
+        free(stats->smpl_ts);
+        free(stats->smpl_tv);
+        free(stats->smpl_indels);
+        free(stats->smpl_dp);
+        free(stats->smpl_ndp);
+        free(stats->smpl_sngl);
+        idist_destroy(&stats->dp);
+        idist_destroy(&stats->dp_sites);
+        for (j=0; j<stats->nusr; j++)
+        {
+            free(stats->usr[j].vals_ts);
+            free(stats->usr[j].vals_tv);
+            free(stats->usr[j].val);
+        }
+        free(stats->usr);
+        if ( args->exons ) free(stats->smpl_frm_shifts);
+        free(stats->nvaf);
+        free(stats->dvaf);
+    }
+    for (j=0; j<args->nusr; j++) free(args->usr[j].tag);
+    if ( args->af_bins ) bin_destroy(args->af_bins);
+    free(args->farr);
+    free(args->usr);
+    free(args->tmp_frm);
+    free(args->tmp_iaf);
+    if (args->exons) bcf_sr_regions_destroy(args->exons);
+    free(args->af_gts_snps);
+    free(args->af_gts_indels);
+    free(args->smpl_gts_snps);
+    free(args->smpl_gts_indels);
+    if (args->indel_ctx) indel_ctx_destroy(args->indel_ctx);
+    if (args->filter[0]) filter_destroy(args->filter[0]);
+    if (args->filter[1]) filter_destroy(args->filter[1]);
+}
+
+static void init_iaf(args_t *args, bcf_sr_t *reader)
+{
+    bcf1_t *line = reader->buffer[0];
+    hts_expand(int32_t,line->n_allele,args->ntmp_iaf,args->tmp_iaf);
+
+    int i, ret;
+    if ( args->af_tag )
+    {
+        ret = bcf_get_info_float(reader->header, line, args->af_tag, &args->farr, &args->mfarr);
+        if ( ret<=0 || ret!=line->n_allele-1 )
+        {
+            // the AF tag is not present or wrong number of values, put in the singletons/unknown bin
+            for (i=0; i<line->n_allele; i++) args->tmp_iaf[i] = 0;
+            return;
+        }
+        args->tmp_iaf[0] = 0;
+        for (i=1; i<line->n_allele; i++)
+        {
+            float af = args->farr[i-1];
+            if ( af<0 ) af = 0;
+            else if ( af>1 ) af = 1;
+            int iaf = args->af_bins ? bin_get_idx(args->af_bins,af) : af*(args->m_af-2);
+            args->tmp_iaf[i] = iaf + 1;     // the first tmp_iaf bin is reserved for singletons
+        }
+        return;
+    }
+
+    // tmp_iaf is first filled with AC counts in calc_ac and then transformed to
+    //  an index to af_gts_snps
+    ret = bcf_calc_ac(reader->header, line, args->tmp_iaf, args->samples_list ? BCF_UN_INFO|BCF_UN_FMT : BCF_UN_INFO);
+    if ( !ret )
+    {
+        for (i=0; i<line->n_allele; i++) args->tmp_iaf[i] = 0;      // singletons/unknown bin
+        return;
+    }
+
+    int an = 0;
+    for (i=0; i<line->n_allele; i++)
+        an += args->tmp_iaf[i];
+
+    args->tmp_iaf[0] = 0;
+    for (i=1; i<line->n_allele; i++)
+    {
+        if ( args->tmp_iaf[i]==1 )
+            args->tmp_iaf[i] = 0;   // singletons into the first bin
+        else if ( !an )
+            args->tmp_iaf[i] = 1;   // no genotype at all, put to the AF=0 bin
+        else
+        {
+            float af = (float) args->tmp_iaf[i] / an;
+            if ( af<0 ) af = 0;
+            else if ( af>1 ) af = 1;
+            int iaf = args->af_bins ? bin_get_idx(args->af_bins,af) : af*(args->m_af-2);
+            args->tmp_iaf[i] = iaf + 1;
+        }
+    }
+}
+
+static inline void do_mnp_stats(args_t *args, stats_t *stats, bcf_sr_t *reader)
+{
+    stats->n_mnps++;
+}
+
+static inline void do_other_stats(args_t *args, stats_t *stats, bcf_sr_t *reader)
+{
+    stats->n_others++;
+}
+
+static void do_indel_stats(args_t *args, stats_t *stats, bcf_sr_t *reader)
+{
+    stats->n_indels++;
+
+    bcf1_t *line = reader->buffer[0];
+
+    #if QUAL_STATS
+        int iqual = (isnan(line->qual) || line->qual<0) ? 0 : 1 + (int)(line->qual*10);
+        dist_insert(stats->qual_indels, iqual);
+    #endif
+
+    // Check if the indel is near an exon for the frameshift statistics
+    int i, exon_overlap = 0;
+    if ( args->exons )
+    {
+        if ( !bcf_sr_regions_overlap(args->exons, bcf_seqname(reader->header,line),line->pos,line->pos) ) exon_overlap = 1;
+        hts_expand(uint8_t,line->n_allele,args->mtmp_frm,args->tmp_frm);
+        for (i=0; i<line->n_allele; i++) args->tmp_frm[i] = 0;
+    }
+
+    for (i=1; i<line->n_allele; i++)
+    {
+        if ( args->first_allele_only && i>1 ) break;
+        int is_indel = bcf_has_variant_type(line,i,VCF_INDEL);
+        if (is_indel < 0) error("bcf_has_variant_type() failed.");
+        if ( !is_indel ) continue;
+        int len = bcf_variant_length(line, i);
+
+        #if IRC_STATS
+        // Indel repeat consistency
+        if ( args->indel_ctx )
+        {
+            int nrep, nlen, ndel;
+            ndel = indel_ctx_type(args->indel_ctx, (char*)reader->header->id[BCF_DT_CTG][line->rid].key, line->pos+1, line->d.allele[0], line->d.allele[i], &nrep, &nlen);
+            if ( nlen<=1 || nrep<=1 )
+            {
+                // not a repeat or a single base repeat
+                stats->n_repeat_na++;
+                stats->af_repeats[2][ args->tmp_iaf[i] ]++;
+            }
+            else
+            {
+                if ( abs(ndel) % nlen )
+                {
+                    // the length of the inserted/deleted sequence is not consistent with the repeat element
+                    stats->n_repeat[nlen-1][ndel<0 ? 1 : 3]++;
+                    stats->af_repeats[1][ args->tmp_iaf[i] ]++;
+                }
+                else
+                {
+                    // the length consistent with the repeat
+                    stats->n_repeat[nlen-1][ndel<0 ? 0 : 2]++;
+                    stats->af_repeats[0][ args->tmp_iaf[i] ]++;
+                }
+            }
+        }
+        else
+            stats->af_repeats[2][ args->tmp_iaf[i] ]++;
+        #endif
+
+        // Check the frameshifts
+        int tlen = 0;
+        if ( args->exons && exon_overlap )   // there is an exon
+        {
+            if ( len>0 )
+            {
+                // insertion
+                if ( args->exons->start <= line->pos && args->exons->end > line->pos ) tlen = abs(len);
+            }
+            else if ( args->exons->start <= line->pos + abs(len) )
+            {
+                // deletion
+                tlen = abs(len);
+                if ( line->pos < args->exons->start )              // trim the beginning
+                    tlen -= args->exons->start - line->pos + 1;
+                if ( args->exons->end < line->pos + abs(len) )     // trim the end
+                    tlen -= line->pos + abs(len) - args->exons->end;
+            }
+        }
+        if ( tlen )     // there are some deleted/inserted bases in the exon
+        {
+            if ( tlen%3 ) { stats->out_frame++; args->tmp_frm[i] = 2; }
+            else { stats->in_frame++; args->tmp_frm[i] = 1; }
+
+            if ( i==1 )
+            {
+                if ( tlen%3 ) stats->out_frame_alt1++;
+                else stats->in_frame_alt1++;
+            }
+        }
+        else            // no exon affected
+        {
+            if ( i==1 ) stats->na_frame_alt1++;
+            stats->na_frame++;
+        }
+
+
+        // Indel length distribution
+        int *ptr = stats->insertions;
+        if ( len<0 )
+        {
+            len *= -1;
+            ptr = stats->deletions;
+        }
+        if ( --len >= stats->m_indel ) len = stats->m_indel-1;
+        ptr[len]++;
+    }
+}
+
+static void do_user_stats(stats_t *stats, bcf_sr_t *reader, int is_ts)
+{
+    int i, nval;
+    for (i=0; i<stats->nusr; i++)
+    {
+        user_stats_t *usr = &stats->usr[i];
+        uint64_t *vals = is_ts ? usr->vals_ts : usr->vals_tv;
+        float val;
+        if ( usr->type==BCF_HT_REAL )
+        {
+            if ( (nval=bcf_get_info_float(reader->header,reader->buffer[0],usr->tag,&usr->val,&usr->m_val))<=0 ) continue;
+            if ( usr->idx >= nval ) continue;
+            val = ((float*)usr->val)[usr->idx];
+        }
+        else
+        {
+            if ( (nval=bcf_get_info_int32(reader->header,reader->buffer[0],usr->tag,&usr->val,&usr->m_val))<=0 ) continue;
+            if ( usr->idx >= nval ) continue;
+            val = ((int32_t*)usr->val)[usr->idx];
+        }
+        int idx;
+        if ( val<=usr->min ) idx = 0;
+        else if ( val>=usr->max ) idx = usr->nbins - 1;
+        else idx = (val - usr->min)/(usr->max - usr->min) * (usr->nbins-1);
+        vals[idx]++;
+    }
+}
+
+static void do_snp_stats(args_t *args, stats_t *stats, bcf_sr_t *reader)
+{
+    stats->n_snps++;
+
+    bcf1_t *line = reader->buffer[0];
+    int ref = bcf_acgt2int(*line->d.allele[0]);
+    if ( ref<0 ) return;
+
+    #if QUAL_STATS
+        int iqual = (isnan(line->qual) || line->qual<0) ? 0 : 1 + (int)(line->qual*10);
+    #endif
+
+    int i;
+    for (i=1; i<line->n_allele; i++)
+    {
+        if ( args->first_allele_only && i>1 ) break;
+        if ( !(bcf_get_variant_type(line,i)&VCF_SNP) ) continue;
+        int alt = bcf_acgt2int(*line->d.allele[i]);
+        if ( alt<0 || ref==alt ) continue;
+        stats->subst[ref<<2|alt]++;
+        int iaf = args->tmp_iaf[i];
+        stats->af_snps[iaf]++;
+        if ( abs(ref-alt)==2 )
+        {
+            if (i==1)
+            {
+                stats->ts_alt1++;
+                #if QUAL_STATS
+                    dist_insert(stats->qual_ts,iqual);
+                #endif
+                do_user_stats(stats, reader, 1);
+            }
+            stats->af_ts[iaf]++;
+        }
+        else
+        {
+            if (i==1)
+            {
+                stats->tv_alt1++;
+                #if QUAL_STATS
+                    dist_insert(stats->qual_tv,iqual);
+                #endif
+                do_user_stats(stats, reader, 0);
+            }
+            stats->af_tv[iaf]++;
+        }
+    }
+}
+
+static inline void update_dvaf(stats_t *stats, bcf1_t *line, bcf_fmt_t *fmt, int ismpl, int ial, int jal)
+{
+    if ( !fmt ) return;
+
+    float dvaf;
+    #define BRANCH_INT(type_t,missing,vector_end) { \
+        type_t *p = (type_t *) (fmt->p + fmt->size*ismpl); \
+        if ( p[ial]==vector_end || p[jal]==vector_end ) return; \
+        if ( p[ial]==missing || p[jal]==missing ) return; \
+        if ( !p[ial] && !p[jal] ) return; \
+        dvaf = (float)p[ial]/(p[ial]+p[jal]); \
+    }
+    switch (fmt->type) {
+        case BCF_BT_INT8:  BRANCH_INT(int8_t,  bcf_int8_missing, bcf_int8_vector_end); break;
+        case BCF_BT_INT16: BRANCH_INT(int16_t, bcf_int16_missing, bcf_int16_vector_end); break;
+        case BCF_BT_INT32: BRANCH_INT(int32_t, bcf_int32_missing, bcf_int32_vector_end); break;
+        default: fprintf(stderr, "[E::%s] todo: %d\n", __func__, fmt->type); exit(1); break;
+    }
+    #undef BRANCH_INT
+
+    int len = line->d.var[ial].n;
+    if ( len < -stats->m_indel ) len = -stats->m_indel;
+    else if ( len > stats->m_indel ) len = stats->m_indel;
+    int bin = stats->m_indel + len;
+    stats->nvaf[bin]++;
+    stats->dvaf[bin] += dvaf;
+}
+
+static void do_sample_stats(args_t *args, stats_t *stats, bcf_sr_t *reader, int matched)
+{
+    bcf_srs_t *files = args->files;
+    bcf1_t *line = reader->buffer[0];
+    bcf_fmt_t *fmt_ptr;
+    int nref_tot = 0, nhet_tot = 0, nalt_tot = 0;
+    int line_type = bcf_get_variant_types(line);
+
+    if ( (fmt_ptr = bcf_get_fmt(reader->header,reader->buffer[0],"GT")) )
+    {
+        bcf_fmt_t *ad_fmt_ptr = bcf_get_variant_types(line)&VCF_INDEL ? bcf_get_fmt(reader->header,reader->buffer[0],"AD") : NULL;
+
+        int ref = bcf_acgt2int(*line->d.allele[0]);
+        int is, n_nref = 0, i_nref = 0;
+        for (is=0; is<args->files->n_smpl; is++)
+        {
+            int ial, jal;
+            int gt = bcf_gt_type(fmt_ptr, reader->samples[is], &ial, &jal);
+            if ( gt==GT_UNKN )
+            {
+                stats->smpl_missing[is]++;
+                continue;
+            }
+            if ( gt==GT_HAPL_R || gt==GT_HAPL_A )
+            {
+                if ( line_type&VCF_INDEL && stats->smpl_frm_shifts )
+                {
+                    assert( ial<line->n_allele );
+                    stats->smpl_frm_shifts[is*3 + args->tmp_frm[ial]]++;
+                }
+                if ( gt == GT_HAPL_R ) stats->smpl_hapRef[is]++;
+                if ( gt == GT_HAPL_A ) stats->smpl_hapAlt[is]++;
+                continue;
+            }
+            if ( gt != GT_HOM_RR ) { n_nref++; i_nref = is; }
+            #if HWE_STATS
+                switch (gt)
+                {
+                    case GT_HOM_RR: nref_tot++; break;
+                    case GT_HET_RA: nhet_tot++; break;
+                    case GT_HET_AA:
+                    case GT_HOM_AA: nalt_tot++; break;
+                }
+            #endif
+            int var_type = 0;
+            if ( ial>0 ) var_type |= bcf_get_variant_type(line,ial);
+            if ( jal>0 ) var_type |= bcf_get_variant_type(line,jal);
+            if ( var_type&VCF_SNP || var_type==VCF_REF )  // count ALT=. as SNP
+            {
+                if ( gt == GT_HET_RA ) stats->smpl_hets[is]++;
+                else if ( gt == GT_HET_AA ) stats->smpl_hets[is]++;
+                else if ( gt == GT_HOM_RR ) stats->smpl_homRR[is]++;
+                else if ( gt == GT_HOM_AA ) stats->smpl_homAA[is]++;
+                if ( gt != GT_HOM_RR && line->d.var[ial].type&VCF_SNP ) // this is safe, bcf_get_variant_types has been already called
+                {
+                    int alt = bcf_acgt2int(*line->d.allele[ial]);
+                    if ( alt<0 ) continue;
+                    if ( abs(ref-alt)==2 )
+                        stats->smpl_ts[is]++;
+                    else
+                        stats->smpl_tv[is]++;
+                }
+            }
+            if ( var_type&VCF_INDEL )
+            {
+                if ( gt != GT_HOM_RR )
+                {
+                    stats->smpl_indels[is]++;
+
+                    if ( gt==GT_HET_RA || gt==GT_HET_AA )
+                    {
+                        int is_ins = 0, is_del = 0;
+                        if ( bcf_get_variant_type(line,ial)&VCF_INDEL )
+                        {
+                            if ( line->d.var[ial].n < 0 ) is_del = 1;
+                            else is_ins = 1;
+                            update_dvaf(stats,line,ad_fmt_ptr,is,ial,jal);
+                        }
+                        if ( bcf_get_variant_type(line,jal)&VCF_INDEL )
+                        {
+                            if ( line->d.var[jal].n < 0 ) is_del = 1;
+                            else is_ins = 1;
+                            update_dvaf(stats,line,ad_fmt_ptr,is,jal,ial);
+                        }
+                        // Note that alt-het genotypes with both ins and del allele are counted twice!!
+                        if ( is_del ) stats->smpl_del_hets[is]++;
+                        if ( is_ins ) stats->smpl_ins_hets[is]++;
+                    }
+                    else if ( gt==GT_HOM_AA )
+                    {
+                        if ( line->d.var[ial].n < 0 ) stats->smpl_del_homs[is]++;
+                        else stats->smpl_ins_homs[is]++;
+                    }
+                }
+                if ( stats->smpl_frm_shifts )
+                {
+                    assert( ial<line->n_allele && jal<line->n_allele );
+                    stats->smpl_frm_shifts[is*3 + args->tmp_frm[ial]]++;
+                    stats->smpl_frm_shifts[is*3 + args->tmp_frm[jal]]++;
+                }
+            }
+        }
+        if ( n_nref==1 ) stats->smpl_sngl[i_nref]++;
+    }
+
+    #if HWE_STATS
+        if ( nhet_tot + nref_tot + nalt_tot )
+        {
+            float het_frac = (float)nhet_tot/(nhet_tot + nref_tot + nalt_tot);
+            int idx = het_frac*(args->naf_hwe - 1);
+//check me: what is this?
+            if ( line->n_allele>1 ) idx += args->naf_hwe*args->tmp_iaf[1];
+            stats->af_hwe[idx]++;
+        }
+    #endif
+
+    if ( (fmt_ptr = bcf_get_fmt(reader->header,reader->buffer[0],"DP")) )
+    {
+        #define BRANCH_INT(type_t,missing,vector_end) { \
+            int is; \
+            for (is=0; is<args->files->n_smpl; is++) \
+            { \
+                type_t *p = (type_t *) (fmt_ptr->p + fmt_ptr->size*is); \
+                if ( *p==vector_end ) continue; \
+                if ( *p!=missing ) \
+                { \
+                    (*idist(&stats->dp, *p))++; \
+                    stats->smpl_ndp[is]++; \
+                    stats->smpl_dp[is] += *p; \
+                } \
+            } \
+        }
+        switch (fmt_ptr->type) {
+            case BCF_BT_INT8:  BRANCH_INT(int8_t,  bcf_int8_missing, bcf_int8_vector_end); break;
+            case BCF_BT_INT16: BRANCH_INT(int16_t, bcf_int16_missing, bcf_int16_vector_end); break;
+            case BCF_BT_INT32: BRANCH_INT(int32_t, bcf_int32_missing, bcf_int32_vector_end); break;
+            default: fprintf(stderr, "[E::%s] todo: %d\n", __func__, fmt_ptr->type); exit(1); break;
+        }
+        #undef BRANCH_INT
+    }
+    else if ( (fmt_ptr = bcf_get_fmt(reader->header,reader->buffer[0],"AD")) )
+    {
+        #define BRANCH_INT(type_t,missing,vector_end) { \
+            int is,iv; \
+            for (is=0; is<args->files->n_smpl; is++) \
+            { \
+                type_t *p = (type_t *) (fmt_ptr->p + fmt_ptr->size*is); \
+                int dp = 0, has_value = 0; \
+                for (iv=0; iv<fmt_ptr->n; iv++) \
+                { \
+                    if ( p[iv]==vector_end ) break; \
+                    if ( p[iv]==missing ) continue; \
+                    has_value = 1; \
+                    dp += p[iv]; \
+                } \
+                if ( has_value ) \
+                { \
+                    (*idist(&stats->dp, dp))++; \
+                    stats->smpl_ndp[is]++; \
+                    stats->smpl_dp[is] += dp; \
+                } \
+            } \
+        }
+        switch (fmt_ptr->type) {
+            case BCF_BT_INT8:  BRANCH_INT(int8_t,  bcf_int8_missing, bcf_int8_vector_end); break;
+            case BCF_BT_INT16: BRANCH_INT(int16_t, bcf_int16_missing, bcf_int16_vector_end); break;
+            case BCF_BT_INT32: BRANCH_INT(int32_t, bcf_int32_missing, bcf_int32_vector_end); break;
+            default: fprintf(stderr, "[E::%s] todo: %d\n", __func__, fmt_ptr->type); exit(1); break;
+        }
+        #undef BRANCH_INT
+    }
+
+    if ( matched==3 )
+    {
+        int is;
+        bcf_fmt_t *fmt0, *fmt1;
+        fmt0 = bcf_get_fmt(files->readers[0].header,files->readers[0].buffer[0],"GT"); if ( !fmt0 ) return;
+        fmt1 = bcf_get_fmt(files->readers[1].header,files->readers[1].buffer[0],"GT"); if ( !fmt1 ) return;
+
+        // only the first ALT allele is considered
+        if (args->ntmp_iaf <= 1) return; // Do not consider invariate sites
+        int iaf = args->tmp_iaf[1];
+        int line_type = bcf_get_variant_types(files->readers[0].buffer[0]);
+        gtcmp_t *af_stats = line_type&VCF_SNP ? args->af_gts_snps : args->af_gts_indels;
+        gtcmp_t *smpl_stats = line_type&VCF_SNP ? args->smpl_gts_snps : args->smpl_gts_indels;
+
+        for (is=0; is<files->n_smpl; is++)
+        {
+            // Simplified comparison: only 0/0, 0/1, 1/1 is looked at as the identity of
+            //  actual alleles can be enforced by running without the -c option.
+            int gt0 = bcf_gt_type(fmt0, files->readers[0].samples[is], NULL, NULL);
+            int gt1 = bcf_gt_type(fmt1, files->readers[1].samples[is], NULL, NULL);
+
+            int idx0 = type2stats[gt0];
+            int idx1 = type2stats[gt1];
+            af_stats[iaf].gt2gt[idx0][idx1]++;
+            smpl_stats[is].gt2gt[idx0][idx1]++;
+
+            if ( gt0 == GT_UNKN || gt1 == GT_UNKN ) continue;
+            if ( type2ploidy[gt0]*type2ploidy[gt1] == -1 ) continue;   // cannot compare diploid and haploid genotypes
+
+            float y = type2dosage[gt0];
+            float x = type2dosage[gt1];
+
+            smpl_stats[is].yx += y*x;
+            smpl_stats[is].x  += x;
+            smpl_stats[is].xx += x*x;
+            smpl_stats[is].y  += y;
+            smpl_stats[is].yy += y*y;
+            smpl_stats[is].n  += 1;
+
+            af_stats[iaf].yx += y*x;
+            af_stats[iaf].x  += x;
+            af_stats[iaf].xx += x*x;
+            af_stats[iaf].y  += y;
+            af_stats[iaf].yy += y*y;
+            af_stats[iaf].n  += 1;
+        }
+
+        if ( args->verbose_sites )
+        {
+            int nm = 0, nmm = 0, nrefm = 0;
+            for (is=0; is<files->n_smpl; is++)
+            {
+                int gt = bcf_gt_type(fmt0, files->readers[0].samples[is], NULL, NULL);
+                if ( gt == GT_UNKN ) continue;
+                int gt2 = bcf_gt_type(fmt1, files->readers[1].samples[is], NULL, NULL);
+                if ( gt2 == GT_UNKN ) continue;
+                if ( gt != gt2 )
+                {
+                    nmm++;
+                    bcf_sr_t *reader = &files->readers[0];
+                    printf("DBG\t%s\t%"PRId64"\t%s\t%d\t%d\n",reader->header->id[BCF_DT_CTG][reader->buffer[0]->rid].key,(int64_t) reader->buffer[0]->pos+1,files->samples[is],gt,gt2);
+                }
+                else
+                {
+                    if ( gt!=GT_HOM_RR ) nrefm++;
+                    nm++;
+                }
+            }
+            float nrd = nrefm+nmm ? 100.*nmm/(nrefm+nmm) : 0;
+            printf("PSD\t%s\t%"PRId64"\t%d\t%d\t%f\n", reader->header->id[BCF_DT_CTG][reader->buffer[0]->rid].key,(int64_t) reader->buffer[0]->pos+1,nm,nmm,nrd);
+        }
+    }
+}
+
+static void do_vcf_stats(args_t *args)
+{
+    bcf_srs_t *files = args->files;
+    assert( sizeof(int)>files->nreaders );
+    while ( bcf_sr_next_line(files) )
+    {
+        bcf_sr_t *reader = NULL;
+        bcf1_t *line = NULL;
+        int ret = 0, i, pass = 1;
+        for (i=0; i<files->nreaders; i++)
+        {
+            if ( !bcf_sr_has_line(files,i) ) continue;
+            if ( args->filter[i] )
+            {
+                int is_ok = filter_test(args->filter[i], bcf_sr_get_line(files,i), NULL);
+                if ( args->filter_logic & FLT_EXCLUDE ) is_ok = is_ok ? 0 : 1;
+                if ( !is_ok ) { pass = 0; break; }
+            }
+            ret |= 1<<i;
+            if ( !reader )
+            {
+                reader = &files->readers[i];
+                line = bcf_sr_get_line(files,i);
+            }
+
+        }
+        if ( !pass ) continue;
+
+        int line_type = bcf_get_variant_types(line);
+        init_iaf(args, reader);
+
+        stats_t *stats = &args->stats[ret-1];
+        if ( args->split_by_id && line->d.id[0]=='.' && !line->d.id[1] )
+            stats = &args->stats[1];
+
+        stats->n_records++;
+
+        if ( line_type==VCF_REF )
+            stats->n_noalts++;
+        if ( line_type&VCF_SNP )
+            do_snp_stats(args, stats, reader);
+        if ( line_type&VCF_INDEL )
+            do_indel_stats(args, stats, reader);
+        if ( line_type&VCF_MNP )
+            do_mnp_stats(args, stats, reader);
+        if ( line_type&VCF_OTHER )
+            do_other_stats(args, stats, reader);
+
+        if ( line->n_allele>2 )
+        {
+            stats->n_mals++;
+            if ( line_type == VCF_SNP ) stats->n_snp_mals++;    // note: this will be fooled by C>C,T
+        }
+
+        if ( files->n_smpl )
+            do_sample_stats(args, stats, reader, ret);
+
+        if ( bcf_get_info_int32(reader->header,line,"DP",&args->tmp_iaf,&args->ntmp_iaf)==1 )
+            (*idist(&stats->dp_sites, args->tmp_iaf[0]))++;
+    }
+}
+
+static void print_header(args_t *args)
+{
+    int i;
+    printf("# This file was produced by bcftools stats (%s+htslib-%s) and can be plotted using plot-vcfstats.\n", bcftools_version(),hts_version());
+    printf("# The command line was:\tbcftools %s ", args->argv[0]);
+    for (i=1; i<args->argc; i++)
+        printf(" %s",args->argv[i]);
+    printf("\n#\n");
+
+    printf("# Definition of sets:\n# ID\t[2]id\t[3]tab-separated file names\n");
+    if ( args->files->nreaders==1 )
+    {
+        const char *fname = strcmp("-",args->files->readers[0].fname) ? args->files->readers[0].fname : "<STDIN>";
+        if ( args->split_by_id )
+        {
+            printf("ID\t0\t%s:known (sites with ID different from \".\")\n", fname);
+            printf("ID\t1\t%s:novel (sites where ID column is \".\")\n", fname);
+        }
+        else
+            printf("ID\t0\t%s\n", fname);
+    }
+    else
+    {
+        const char *fname0 = strcmp("-",args->files->readers[0].fname) ? args->files->readers[0].fname : "<STDIN>";
+        const char *fname1 = strcmp("-",args->files->readers[1].fname) ? args->files->readers[1].fname : "<STDIN>";
+        printf("ID\t0\t%s\n", fname0);
+        printf("ID\t1\t%s\n", fname1);
+        printf("ID\t2\t%s\t%s\n", fname0,fname1);
+
+        if ( args->verbose_sites )
+        {
+            printf(
+                    "# Verbose per-site discordance output.\n"
+                    "# PSD\t[2]CHROM\t[3]POS\t[4]Number of matches\t[5]Number of mismatches\t[6]NRD\n");
+            printf(
+                    "# Verbose per-site and per-sample output. Genotype codes: %d:HomRefRef, %d:HomAltAlt, %d:HetAltRef, %d:HetAltAlt, %d:haploidRef, %d:haploidAlt\n"
+                    "# DBG\t[2]CHROM\t[3]POS\t[4]Sample\t[5]GT in %s\t[6]GT in %s\n",
+                    GT_HOM_RR, GT_HOM_AA, GT_HET_RA, GT_HET_AA, GT_HAPL_R, GT_HAPL_A, fname0,fname1);
+        }
+    }
+}
+
+#define T2S(x) type2stats[x]
+static void print_stats(args_t *args)
+{
+    int i, j,k, id;
+    printf("# SN, Summary numbers:\n");
+    printf("#   number of records   .. number of data rows in the VCF\n");
+    printf("#   number of no-ALTs   .. reference-only sites, ALT is either \".\" or identical to REF\n");
+    printf("#   number of SNPs      .. number of rows with a SNP\n");
+    printf("#   number of MNPs      .. number of rows with a MNP, such as CC>TT\n");
+    printf("#   number of indels    .. number of rows with an indel\n");
+    printf("#   number of others    .. number of rows with other type, for example a symbolic allele or\n");
+    printf("#                          a complex substitution, such as ACT>TCGA\n");
+    printf("#   number of multiallelic sites     .. number of rows with multiple alternate alleles\n");
+    printf("#   number of multiallelic SNP sites .. number of rows with multiple alternate alleles, all SNPs\n");
+    printf("# \n");
+    printf("#   Note that rows containing multiple types will be counted multiple times, in each\n");
+    printf("#   counter. For example, a row with a SNP and an indel increments both the SNP and\n");
+    printf("#   the indel counter.\n");
+    printf("# \n");
+    printf("# SN\t[2]id\t[3]key\t[4]value\n");
+    for (id=0; id<args->files->nreaders; id++)
+        printf("SN\t%d\tnumber of samples:\t%d\n", id, bcf_hdr_nsamples(args->files->readers[id].header));
+    for (id=0; id<args->nstats; id++)
+    {
+        stats_t *stats = &args->stats[id];
+        printf("SN\t%d\tnumber of records:\t%"PRIu64"\n", id, stats->n_records);
+        printf("SN\t%d\tnumber of no-ALTs:\t%"PRIu64"\n", id, stats->n_noalts);
+        printf("SN\t%d\tnumber of SNPs:\t%"PRIu64"\n", id, stats->n_snps);
+        printf("SN\t%d\tnumber of MNPs:\t%"PRIu64"\n", id, stats->n_mnps);
+        printf("SN\t%d\tnumber of indels:\t%"PRIu64"\n", id, stats->n_indels);
+        printf("SN\t%d\tnumber of others:\t%"PRIu64"\n", id, stats->n_others);
+        printf("SN\t%d\tnumber of multiallelic sites:\t%"PRIu64"\n", id, stats->n_mals);
+        printf("SN\t%d\tnumber of multiallelic SNP sites:\t%"PRIu64"\n", id, stats->n_snp_mals);
+    }
+    printf("# TSTV, transitions/transversions:\n# TSTV\t[2]id\t[3]ts\t[4]tv\t[5]ts/tv\t[6]ts (1st ALT)\t[7]tv (1st ALT)\t[8]ts/tv (1st ALT)\n");
+    for (id=0; id<args->nstats; id++)
+    {
+        stats_t *stats = &args->stats[id];
+        int ts=0,tv=0;
+        for (i=0; i<args->m_af; i++) { ts += stats->af_ts[i]; tv += stats->af_tv[i];  }
+        printf("TSTV\t%d\t%d\t%d\t%.2f\t%d\t%d\t%.2f\n", id,ts,tv,tv?(float)ts/tv:0, stats->ts_alt1,stats->tv_alt1,stats->tv_alt1?(float)stats->ts_alt1/stats->tv_alt1:0);
+    }
+    if ( args->exons_fname )
+    {
+        printf("# FS, Indel frameshifts:\n# FS\t[2]id\t[3]in-frame\t[4]out-frame\t[5]not applicable\t[6]out/(in+out) ratio\t[7]in-frame (1st ALT)\t[8]out-frame (1st ALT)\t[9]not applicable (1st ALT)\t[10]out/(in+out) ratio (1st ALT)\n");
+        for (id=0; id<args->nstats; id++)
+        {
+            int in=args->stats[id].in_frame, out=args->stats[id].out_frame, na=args->stats[id].na_frame;
+            int in1=args->stats[id].in_frame_alt1, out1=args->stats[id].out_frame_alt1, na1=args->stats[id].na_frame_alt1;
+            printf("FS\t%d\t%d\t%d\t%d\t%.2f\t%d\t%d\t%d\t%.2f\n", id, in,out,na,out?(float)out/(in+out):0,in1,out1,na1,out1?(float)out1/(in1+out1):0);
+        }
+    }
+    if ( args->indel_ctx )
+    {
+        printf("# ICS, Indel context summary:\n# ICS\t[2]id\t[3]repeat-consistent\t[4]repeat-inconsistent\t[5]not applicable\t[6]c/(c+i) ratio\n");
+        for (id=0; id<args->nstats; id++)
+        {
+            int nc = 0, ni = 0, na = args->stats[id].n_repeat_na;
+            for (i=0; i<IRC_RLEN; i++)
+            {
+                nc += args->stats[id].n_repeat[i][0] + args->stats[id].n_repeat[i][2];
+                ni += args->stats[id].n_repeat[i][1] + args->stats[id].n_repeat[i][3];
+            }
+            printf("ICS\t%d\t%d\t%d\t%d\t%.4f\n", id, nc,ni,na,nc+ni ? (float)nc/(nc+ni) : 0.0);
+        }
+        printf("# ICL, Indel context by length:\n# ICL\t[2]id\t[3]length of repeat element\t[4]repeat-consistent deletions)\t[5]repeat-inconsistent deletions\t[6]consistent insertions\t[7]inconsistent insertions\t[8]c/(c+i) ratio\n");
+        for (id=0; id<args->nstats; id++)
+        {
+            for (i=1; i<IRC_RLEN; i++)
+            {
+                int nc = args->stats[id].n_repeat[i][0]+args->stats[id].n_repeat[i][2], ni = args->stats[id].n_repeat[i][1]+args->stats[id].n_repeat[i][3];
+                printf("ICL\t%d\t%d\t%d\t%d\t%d\t%d\t%.4f\n", id, i+1,
+                    args->stats[id].n_repeat[i][0],args->stats[id].n_repeat[i][1],args->stats[id].n_repeat[i][2],args->stats[id].n_repeat[i][3],
+                    nc+ni ? (float)nc/(nc+ni) : 0.0);
+            }
+        }
+    }
+    printf("# SiS, Singleton stats:\n# SiS\t[2]id\t[3]allele count\t[4]number of SNPs\t[5]number of transitions\t[6]number of transversions\t[7]number of indels\t[8]repeat-consistent\t[9]repeat-inconsistent\t[10]not applicable\n");
+    for (id=0; id<args->nstats; id++)
+    {
+        stats_t *stats = &args->stats[id];
+        printf("SiS\t%d\t%d\t%d\t%d\t%d\t%d\t%d\t%d\t%d\n", id,1,stats->af_snps[0],stats->af_ts[0],stats->af_tv[0],
+            stats->af_repeats[0][0]+stats->af_repeats[1][0]+stats->af_repeats[2][0],stats->af_repeats[0][0],stats->af_repeats[1][0],stats->af_repeats[2][0]);
+        // put the singletons stats into the first AF bin, note that not all of the stats is transferred (i.e. nrd mismatches)
+        stats->af_snps[1]       += stats->af_snps[0];
+        stats->af_ts[1]         += stats->af_ts[0];
+        stats->af_tv[1]         += stats->af_tv[0];
+        stats->af_repeats[0][1] += stats->af_repeats[0][0];
+        stats->af_repeats[1][1] += stats->af_repeats[1][0];
+        stats->af_repeats[2][1] += stats->af_repeats[2][0];
+    }
+    // move the singletons stats into the first AF bin, singleton stats was collected separately because of init_iaf
+    if ( args->af_gts_snps )
+    {
+        args->af_gts_snps[1].y    += args->af_gts_snps[0].y;
+        args->af_gts_snps[1].yy   += args->af_gts_snps[0].yy;
+        args->af_gts_snps[1].xx   += args->af_gts_snps[0].xx;
+        args->af_gts_snps[1].yx   += args->af_gts_snps[0].yx;
+        args->af_gts_snps[1].n    += args->af_gts_snps[0].n;
+    }
+    if ( args->af_gts_indels )
+    {
+        args->af_gts_indels[1].y  += args->af_gts_indels[0].y;
+        args->af_gts_indels[1].yy += args->af_gts_indels[0].yy;
+        args->af_gts_indels[1].xx += args->af_gts_indels[0].xx;
+        args->af_gts_indels[1].yx += args->af_gts_indels[0].yx;
+        args->af_gts_indels[1].n  += args->af_gts_indels[0].n;
+    }
+
+    printf("# AF, Stats by non-reference allele frequency:\n# AF\t[2]id\t[3]allele frequency\t[4]number of SNPs\t[5]number of transitions\t[6]number of transversions\t[7]number of indels\t[8]repeat-consistent\t[9]repeat-inconsistent\t[10]not applicable\n");
+    for (id=0; id<args->nstats; id++)
+    {
+        stats_t *stats = &args->stats[id];
+        for (i=1; i<args->m_af; i++) // note that af[1] now contains also af[0], see SiS stats output above
+        {
+            if ( stats->af_snps[i]+stats->af_ts[i]+stats->af_tv[i]+stats->af_repeats[0][i]+stats->af_repeats[1][i]+stats->af_repeats[2][i] == 0  ) continue;
+            double af = args->af_bins ? (bin_get_value(args->af_bins,i)+bin_get_value(args->af_bins,i-1))*0.5 : (double)(i-1)/(args->m_af-1);
+            printf("AF\t%d\t%f\t%d\t%d\t%d\t%d\t%d\t%d\t%d\n", id,af,stats->af_snps[i],stats->af_ts[i],stats->af_tv[i],
+                stats->af_repeats[0][i]+stats->af_repeats[1][i]+stats->af_repeats[2][i],stats->af_repeats[0][i],stats->af_repeats[1][i],stats->af_repeats[2][i]);
+        }
+    }
+    #if QUAL_STATS
+        printf("# QUAL, Stats by quality\n# QUAL\t[2]id\t[3]Quality\t[4]number of SNPs\t[5]number of transitions (1st ALT)\t[6]number of transversions (1st ALT)\t[7]number of indels\n");
+        for (id=0; id<args->nstats; id++)
+        {
+            stats_t *stats = &args->stats[id];
+            int ndist_ts = dist_nbins(stats->qual_ts);
+            int ndist_tv = dist_nbins(stats->qual_tv);
+            int ndist_in = dist_nbins(stats->qual_indels);
+            int ndist_max = ndist_ts;
+            if ( ndist_max < ndist_tv ) ndist_max = ndist_tv;
+            if ( ndist_max < ndist_in ) ndist_max = ndist_in;
+            uint32_t beg, end;
+            uint32_t nts, ntv, nin;
+            for (i=0; i<ndist_max; i++)
+            {
+                nts = ntv = nin = 0;
+                float qval = -1;
+                if ( i < ndist_ts )
+                {
+                    nts = dist_get(stats->qual_ts, i, &beg, &end);
+                    qval = beg>0 ? 0.1*(beg - 1) : -1;
+                }
+                if ( i < ndist_tv )
+                {
+                    ntv = dist_get(stats->qual_tv, i, &beg, &end);
+                    if ( qval==-1 ) qval = beg > 0 ? 0.1*(beg - 1) : -1;
+                }
+                if ( i < ndist_in )
+                {
+                    nin = dist_get(stats->qual_indels, i, &beg, &end);
+                    if ( qval==-1 ) qval = beg > 0 ? 0.1*(beg - 1) : -1;
+                }
+                if ( nts+ntv+nin==0 ) continue;
+
+                printf("QUAL\t%d\t",id);
+                if ( qval==-1 ) printf(".");
+                else printf("%.1f",qval);
+                printf("\t%d\t%d\t%d\t%d\n",nts+ntv,nts,ntv,nin);
+            }
+        }
+    #endif
+    for (i=0; i<args->nusr; i++)
+    {
+        printf("# USR:%s/%d\t[2]id\t[3]%s/%d\t[4]number of SNPs\t[5]number of transitions (1st ALT)\t[6]number of transversions (1st ALT)\n",
+            args->usr[i].tag,args->usr[i].idx,args->usr[i].tag,args->usr[i].idx);
+        for (id=0; id<args->nstats; id++)
+        {
+            user_stats_t *usr = &args->stats[id].usr[i];
+            int j;
+            for (j=0; j<usr->nbins; j++)
+            {
+                if ( usr->vals_ts[j]+usr->vals_tv[j] == 0 ) continue;   // skip empty bins
+                float val = usr->min + (usr->max - usr->min)*j/(usr->nbins-1);
+                const char *fmt = usr->type==BCF_HT_REAL ? "USR:%s/%d\t%d\t%e\t%"PRIu64"\t%"PRIu64"\t%"PRIu64"\n" : "USR:%s/%d\t%d\t%.0f\t%"PRIu64"\t%"PRIu64"\t%"PRIu64"\n";
+                printf(fmt,usr->tag,usr->idx,id,val,usr->vals_ts[j]+usr->vals_tv[j],usr->vals_ts[j],usr->vals_tv[j]);
+            }
+        }
+    }
+    printf("# IDD, InDel distribution:\n# IDD\t[2]id\t[3]length (deletions negative)\t[4]number of sites\t[5]number of genotypes\t[6]mean VAF\n");
+    for (id=0; id<args->nstats; id++)
+    {
+        stats_t *stats = &args->stats[id];
+        for (i=stats->m_indel-1; i>=0; i--)
+        {
+            if ( !stats->deletions[i] ) continue;
+            // whops, differently organized arrow, dels are together with ins
+            int bin = stats->m_indel - i - 1;
+            printf("IDD\t%d\t%d\t%d\t", id,-i-1,stats->deletions[i]);
+            if ( stats->nvaf && stats->nvaf[bin] )
+                printf("%u\t%.2f",stats->nvaf[bin],stats->dvaf[bin]/stats->nvaf[bin]);
+            else
+                printf("0\t.");
+            printf("\n");
+        }
+        for (i=0; i<stats->m_indel; i++)
+        {
+            if ( !stats->insertions[i] ) continue;
+            int bin = stats->m_indel + i + 1;
+            printf("IDD\t%d\t%d\t%d\t", id,i+1,stats->insertions[i]);
+            if ( stats->nvaf && stats->nvaf[bin] )
+                printf("%u\t%.2f",stats->nvaf[bin],stats->dvaf[bin]/stats->nvaf[bin]);
+            else
+                printf("0\t.");
+            printf("\n");
+        }
+    }
+    printf("# ST, Substitution types:\n# ST\t[2]id\t[3]type\t[4]count\n");
+    for (id=0; id<args->nstats; id++)
+    {
+        int t;
+        for (t=0; t<15; t++)
+        {
+            if ( t>>2 == (t&3) ) continue;
+            printf("ST\t%d\t%c>%c\t%d\n", id, bcf_int2acgt(t>>2),bcf_int2acgt(t&3),args->stats[id].subst[t]);
+        }
+    }
+    if ( args->files->nreaders>1 && args->files->n_smpl )
+    {
+        printf("SN\t%d\tnumber of samples:\t%d\n", 2, args->files->n_smpl);
+
+        int x;
+        for (x=0; x<2; x++)     // x=0: snps, x=1: indels
+        {
+            gtcmp_t *stats;
+            if ( x==0 )
+            {
+                printf("# GCsAF, Genotype concordance by non-reference allele frequency (SNPs)\n# GCsAF\t[2]id\t[3]allele frequency\t[4]RR Hom matches\t[5]RA Het matches\t[6]AA Hom matches\t[7]RR Hom mismatches\t[8]RA Het mismatches\t[9]AA Hom mismatches\t[10]dosage r-squared\t[11]number of genotypes\n");
+                stats = args->af_gts_snps;
+            }
+            else
+            {
+                printf("# GCiAF, Genotype concordance by non-reference allele frequency (indels)\n# GCiAF\t[2]id\t[3]allele frequency\t[4]RR Hom matches\t[5]RA Het matches\t[6]AA Hom matches\t[7]RR Hom mismatches\t[8]RA Het mismatches\t[9]AA Hom mismatches\t[10]dosage r-squared\t[11]number of genotypes\n");
+                stats = args->af_gts_indels;
+            }
+            uint64_t nrd_m[4] = {0,0,0,0}, nrd_mm[4] = {0,0,0,0};   // across all bins
+            for (i=0; i<args->m_af; i++)
+            {
+                int n = 0;
+                uint64_t m[4] = {0,0,0,0}, mm[4] = {0,0,0,0};    // in i-th AF bin
+                for (j=0; j<4; j++)     // rr, ra, aa hom, aa het, ./.
+                    for (k=0; k<4; k++)
+                    {
+                        n += stats[i].gt2gt[j][k];
+                        if ( j==k )
+                        {
+                            nrd_m[j] += stats[i].gt2gt[j][k];
+                            m[j]     += stats[i].gt2gt[j][k];
+                        }
+                        else
+                        {
+                            nrd_mm[j] += stats[i].gt2gt[j][k];
+                            mm[j]     += stats[i].gt2gt[j][k];
+                        }
+                    }
+                if ( !i || !n ) continue;   // skip singleton stats and empty bins
+
+                // Pearson's r2
+                double r2 = 0;
+                if ( stats[i].n )
+                {
+                    r2  = (stats[i].yx - stats[i].x*stats[i].y/stats[i].n);
+                    r2 /= sqrt((stats[i].xx - stats[i].x*stats[i].x/stats[i].n) * (stats[i].yy - stats[i].y*stats[i].y/stats[i].n));
+                    r2 *= r2;
+                }
+                double af = args->af_bins ? (bin_get_value(args->af_bins,i)+bin_get_value(args->af_bins,i-1))*0.5 : (double)(i-1)/(args->m_af-1);
+                printf("GC%cAF\t2\t%f", x==0 ? 's' : 'i', af);
+                printf("\t%"PRIu64"\t%"PRIu64"\t%"PRIu64"", m[T2S(GT_HOM_RR)],m[T2S(GT_HET_RA)],m[T2S(GT_HOM_AA)]);
+                printf("\t%"PRIu64"\t%"PRIu64"\t%"PRIu64"", mm[T2S(GT_HOM_RR)],mm[T2S(GT_HET_RA)],mm[T2S(GT_HOM_AA)]);
+                if ( stats[i].n && !isnan(r2) ) printf("\t%f", r2);
+                else printf("\t"NA_STRING);
+                printf("\t%.0f\n", stats[i].n);
+            }
+
+            if ( x==0 )
+            {
+                printf("# NRD and discordance is calculated as follows:\n");
+                printf("#   m .. number of matches\n");
+                printf("#   x .. number of mismatches\n");
+                printf("#   NRD = 100 * (xRR + xRA + xAA) / (xRR + xRA + xAA + mRA + mAA)\n");
+                printf("#   RR discordance = 100 * xRR / (xRR + mRR)\n");
+                printf("#   RA discordance = 100 * xRA / (xRA + mRA)\n");
+                printf("#   AA discordance = 100 * xAA / (xAA + mAA)\n");
+                printf("# Non-Reference Discordance (NRD), SNPs\n# NRDs\t[2]id\t[3]NRD\t[4]Ref/Ref discordance\t[5]Ref/Alt discordance\t[6]Alt/Alt discordance\n");
+            }
+            else
+                printf("# Non-Reference Discordance (NRD), indels\n# NRDi\t[2]id\t[3]NRD\t[4]Ref/Ref discordance\t[5]Ref/Alt discordance\t[6]Alt/Alt discordance\n");
+            uint64_t m  = nrd_m[T2S(GT_HET_RA)] + nrd_m[T2S(GT_HOM_AA)] + nrd_m[T2S(GT_HET_AA)];
+            uint64_t mm = nrd_mm[T2S(GT_HOM_RR)] + nrd_mm[T2S(GT_HET_RA)] + nrd_mm[T2S(GT_HOM_AA)] + nrd_mm[T2S(GT_HET_AA)];
+            printf("NRD%c\t2\t%f\t%f\t%f\t%f\n", x==0 ? 's' : 'i',
+                    m+mm ? mm*100.0/(m+mm) : 0,
+                    nrd_m[T2S(GT_HOM_RR)]+nrd_mm[T2S(GT_HOM_RR)] ? nrd_mm[T2S(GT_HOM_RR)]*100.0/(nrd_m[T2S(GT_HOM_RR)]+nrd_mm[T2S(GT_HOM_RR)]) : 0,
+                    nrd_m[T2S(GT_HET_RA)]+nrd_mm[T2S(GT_HET_RA)] ? nrd_mm[T2S(GT_HET_RA)]*100.0/(nrd_m[T2S(GT_HET_RA)]+nrd_mm[T2S(GT_HET_RA)]) : 0,
+                    nrd_m[T2S(GT_HOM_AA)]+nrd_mm[T2S(GT_HOM_AA)] ? nrd_mm[T2S(GT_HOM_AA)]*100.0/(nrd_m[T2S(GT_HOM_AA)]+nrd_mm[T2S(GT_HOM_AA)]) : 0
+                  );
+        }
+
+        for (x=0; x<2; x++) // x=0: snps, x=1: indels
+        {
+            gtcmp_t *stats;
+            if ( x==0 )
+            {
+                printf("# GCsS, Genotype concordance by sample (SNPs)\n# GCsS\t[2]id\t[3]sample\t[4]non-reference discordance rate\t[5]RR Hom matches\t[6]RA Het matches\t[7]AA Hom matches\t[8]RR Hom mismatches\t[9]RA Het mismatches\t[10]AA Hom mismatches\t[11]dosage r-squared\n");
+                stats = args->smpl_gts_snps;
+            }
+            else
+            {
+                printf("# GCiS, Genotype concordance by sample (indels)\n# GCiS\t[2]id\t[3]sample\t[4]non-reference discordance rate\t[5]RR Hom matches\t[6]RA Het matches\t[7]AA Hom matches\t[8]RR Hom mismatches\t[9]RA Het mismatches\t[10]AA Hom mismatches\t[11]dosage r-squared\n");
+                stats = args->smpl_gts_indels;
+            }
+            for (i=0; i<args->files->n_smpl; i++)
+            {
+                uint64_t mm = 0, m = stats[i].gt2gt[T2S(GT_HET_RA)][T2S(GT_HET_RA)] + stats[i].gt2gt[T2S(GT_HOM_AA)][T2S(GT_HOM_AA)];
+                for (j=0; j<3; j++)
+                    for (k=0; k<3; k++)
+                        if ( j!=k ) mm += stats[i].gt2gt[j][k];
+
+                // Pearson's r2
+                double r2 = 0;
+                if ( stats[i].n )
+                {
+                    r2  = (stats[i].yx - stats[i].x*stats[i].y/stats[i].n);
+                    r2 /= sqrt((stats[i].xx - stats[i].x*stats[i].x/stats[i].n) * (stats[i].yy - stats[i].y*stats[i].y/stats[i].n));
+                    r2 *= r2;
+                }
+                printf("GC%cS\t2\t%s\t%.3f",  x==0 ? 's' : 'i', args->files->samples[i], m+mm ? mm*100.0/(m+mm) : 0);
+                printf("\t%"PRIu64"\t%"PRIu64"\t%"PRIu64"",
+                    stats[i].gt2gt[T2S(GT_HOM_RR)][T2S(GT_HOM_RR)],
+                    stats[i].gt2gt[T2S(GT_HET_RA)][T2S(GT_HET_RA)],
+                    stats[i].gt2gt[T2S(GT_HOM_AA)][T2S(GT_HOM_AA)]);
+                printf("\t%"PRIu64"\t%"PRIu64"\t%"PRIu64"",
+                    stats[i].gt2gt[T2S(GT_HOM_RR)][T2S(GT_HET_RA)] + stats[i].gt2gt[T2S(GT_HOM_RR)][T2S(GT_HOM_AA)],
+                    stats[i].gt2gt[T2S(GT_HET_RA)][T2S(GT_HOM_RR)] + stats[i].gt2gt[T2S(GT_HET_RA)][T2S(GT_HOM_AA)],
+                    stats[i].gt2gt[T2S(GT_HOM_AA)][T2S(GT_HOM_RR)] + stats[i].gt2gt[T2S(GT_HOM_AA)][T2S(GT_HET_RA)]);
+                if ( stats[i].n && !isnan(r2) ) printf("\t%f\n", r2);
+                else printf("\t"NA_STRING"\n");
+            }
+        }
+        for (x=0; x<2; x++) // x=0: snps, x=1: indels
+        {
+                //printf("# GCiS, Genotype concordance by sample (indels)\n# GCiS\t[2]id\t[3]sample\t[4]non-reference discordance rate\t[5]RR Hom matches\t[6]RA Het matches\t[7]AA Hom matches\t[8]RR Hom mismatches\t[9]RA Het mismatches\t[10]AA Hom mismatches\t[11]dosage r-squared\n");
+
+            gtcmp_t *stats;
+            if ( x==0 )
+            {
+                printf("# GCTs, Genotype concordance table (SNPs)\n# GCTs");
+                stats = args->smpl_gts_snps;
+            }
+            else
+            {
+                printf("# GCTi, Genotype concordance table (indels)\n# GCTi");
+                stats = args->smpl_gts_indels;
+            }
+            i = 1;
+            printf("\t[%d]sample", ++i);
+            printf("\t[%d]RR Hom -> RR Hom", ++i);
+            printf("\t[%d]RR Hom -> RA Het", ++i);
+            printf("\t[%d]RR Hom -> AA Hom", ++i);
+            printf("\t[%d]RR Hom -> AA Het", ++i);
+            printf("\t[%d]RR Hom -> missing", ++i);
+            printf("\t[%d]RA Het -> RR Hom", ++i);
+            printf("\t[%d]RA Het -> RA Het", ++i);
+            printf("\t[%d]RA Het -> AA Hom", ++i);
+            printf("\t[%d]RA Het -> AA Het", ++i);
+            printf("\t[%d]RA Het -> missing", ++i);
+            printf("\t[%d]AA Hom -> RR Hom", ++i);
+            printf("\t[%d]AA Hom -> RA Het", ++i);
+            printf("\t[%d]AA Hom -> AA Hom", ++i);
+            printf("\t[%d]AA Hom -> AA Het", ++i);
+            printf("\t[%d]AA Hom -> missing", ++i);
+            printf("\t[%d]AA Het -> RR Hom", ++i);
+            printf("\t[%d]AA Het -> RA Het", ++i);
+            printf("\t[%d]AA Het -> AA Hom", ++i);
+            printf("\t[%d]AA Het -> AA Het", ++i);
+            printf("\t[%d]AA Het -> missing", ++i);
+            printf("\t[%d]missing -> RR Hom", ++i);
+            printf("\t[%d]missing -> RA Het", ++i);
+            printf("\t[%d]missing -> AA Hom", ++i);
+            printf("\t[%d]missing -> AA Het", ++i);
+            printf("\t[%d]missing -> missing\n", ++i);
+
+            for (i=0; i<args->files->n_smpl; i++)
+            {
+                printf("GCT%c\t%s",  x==0 ? 's' : 'i', args->files->samples[i]);
+                for (j=0; j<5; j++)
+                    for (k=0; k<5; k++)
+                        printf("\t%"PRIu64, stats[i].gt2gt[j][k]);
+                printf("\n");
+            }
+        }
+    }
+
+    printf("# DP, Depth distribution\n# DP\t[2]id\t[3]bin\t[4]number of genotypes\t[5]fraction of genotypes (%%)\t[6]number of sites\t[7]fraction of sites (%%)\n");
+    for (id=0; id<args->nstats; id++)
+    {
+        stats_t *stats = &args->stats[id];
+        long unsigned int sum = 0, sum_sites = 0;
+        for (i=0; i<stats->dp.m_vals; i++) { sum += stats->dp.vals[i]; sum_sites += stats->dp_sites.vals[i]; }
+        for (i=0; i<stats->dp.m_vals; i++)
+        {
+            if ( stats->dp.vals[i]==0 && stats->dp_sites.vals[i]==0 ) continue;
+            printf("DP\t%d\t", id);
+            if ( i==0 ) printf("<%d", stats->dp.min);
+            else if ( i+1==stats->dp.m_vals ) printf(">%d", stats->dp.max);
+            else printf("%d", idist_i2bin(&stats->dp,i));
+            printf("\t%"PRIu64"\t%f", stats->dp.vals[i], sum ? stats->dp.vals[i]*100./sum : 0);
+            printf("\t%"PRIu64"\t%f\n", stats->dp_sites.vals[i], sum_sites ? stats->dp_sites.vals[i]*100./sum_sites : 0);
+        }
+    }
+
+    if ( args->files->n_smpl )
+    {
+        printf("# PSC, Per-sample counts. Note that the ref/het/hom counts include only SNPs, for indels see PSI. The rest include both SNPs and indels.\n");
+        printf("# PSC\t[2]id\t[3]sample\t[4]nRefHom\t[5]nNonRefHom\t[6]nHets\t[7]nTransitions\t[8]nTransversions\t[9]nIndels\t[10]average depth\t[11]nSingletons"
+            "\t[12]nHapRef\t[13]nHapAlt\t[14]nMissing\n");
+        for (id=0; id<args->nstats; id++)
+        {
+            stats_t *stats = &args->stats[id];
+            for (i=0; i<args->files->n_smpl; i++)
+            {
+                float dp = stats->smpl_ndp[i] ? stats->smpl_dp[i]/(float)stats->smpl_ndp[i] : 0;
+                printf("PSC\t%d\t%s\t%d\t%d\t%d\t%d\t%d\t%d\t%.1f\t%d\t%d\t%d\t%d\n", id,args->files->samples[i],
+                    stats->smpl_homRR[i], stats->smpl_homAA[i], stats->smpl_hets[i], stats->smpl_ts[i],
+                    stats->smpl_tv[i], stats->smpl_indels[i],dp, stats->smpl_sngl[i], stats->smpl_hapRef[i],
+                    stats->smpl_hapAlt[i], stats->smpl_missing[i]);
+            }
+        }
+
+        printf("# PSI, Per-Sample Indels. Note that alt-het genotypes with both ins and del allele are counted twice, in both nInsHets and nDelHets.\n");
+        printf("# PSI\t[2]id\t[3]sample\t[4]in-frame\t[5]out-frame\t[6]not applicable\t[7]out/(in+out) ratio\t[8]nInsHets\t[9]nDelHets\t[10]nInsAltHoms\t[11]nDelAltHoms\n");
+        for (id=0; id<args->nstats; id++)
+        {
+            stats_t *stats = &args->stats[id];
+            for (i=0; i<args->files->n_smpl; i++)
+            {
+                int na = 0, in = 0, out = 0;
+                if ( args->exons )
+                {
+                    na  = stats->smpl_frm_shifts[i*3 + 0];
+                    in  = stats->smpl_frm_shifts[i*3 + 1];
+                    out = stats->smpl_frm_shifts[i*3 + 2];
+                }
+                printf("PSI\t%d\t%s\t%d\t%d\t%d\t%.2f\t%d\t%d\t%d\t%d\n", id,args->files->samples[i], in,out,na,in+out?1.0*out/(in+out):0,
+                    stats->smpl_ins_hets[i],stats->smpl_del_hets[i],stats->smpl_ins_homs[i],stats->smpl_del_homs[i]);
+            }
+        }
+
+        #ifdef HWE_STATS
+        printf("# HWE\n# HWE\t[2]id\t[3]1st ALT allele frequency\t[4]Number of observations\t[5]25th percentile\t[6]median\t[7]75th percentile\n");
+        for (id=0; id<args->nstats; id++)
+        {
+            stats_t *stats = &args->stats[id];
+            for (i=0; i<args->naf_hwe; i++) stats->af_hwe[i+args->naf_hwe] += stats->af_hwe[i]; // singletons
+            for (i=1; i<args->m_af; i++)
+            {
+                unsigned int sum_tot = 0, sum_tmp = 0;
+                int j, *ptr = &stats->af_hwe[i*args->naf_hwe];
+                for (j=0; j<args->naf_hwe; j++) sum_tot += ptr[j];
+                if ( !sum_tot ) continue;
+
+                double af = args->af_bins ? (bin_get_value(args->af_bins,i)+bin_get_value(args->af_bins,i-1))*0.5 : (double)(i-1)/(args->m_af-1);
+
+                int nprn = 3;
+                printf("HWE\t%d\t%f\t%d",id,af,sum_tot);
+                for (j=0; j<args->naf_hwe; j++)
+                {
+                    sum_tmp += ptr[j];
+                    float frac = (float)sum_tmp/sum_tot;
+                    if ( frac >= 0.75 )
+                    {
+                        while (nprn>0) { printf("\t%f", (float)j/args->naf_hwe); nprn--; }
+                        break;
+                    }
+                    if ( frac >= 0.5 )
+                    {
+                        while (nprn>1) { printf("\t%f", (float)j/args->naf_hwe); nprn--; }
+                        continue;
+                    }
+                    if ( frac >= 0.25 )
+                    {
+                        while (nprn>2) { printf("\t%f", (float)j/args->naf_hwe); nprn--; }
+                    }
+                }
+                assert(nprn==0);
+                printf("\n");
+            }
+        }
+        #endif
+    }
+}
+
+static void usage(void)
+{
+    fprintf(stderr, "\n");
+    fprintf(stderr, "About:   Parses VCF or BCF and produces stats which can be plotted using plot-vcfstats.\n");
+    fprintf(stderr, "         When two files are given, the program generates separate stats for intersection\n");
+    fprintf(stderr, "         and the complements. By default only sites are compared, -s/-S must given to include\n");
+    fprintf(stderr, "         also sample columns.\n");
+    fprintf(stderr, "Usage:   bcftools stats [options] <A.vcf.gz> [<B.vcf.gz>]\n");
+    fprintf(stderr, "\n");
+    fprintf(stderr, "Options:\n");
+    fprintf(stderr, "        --af-bins LIST               Allele frequency bins, a list (0.1,0.5,1) or a file (0.1\\n0.5\\n1)\n");
+    fprintf(stderr, "        --af-tag STRING              Allele frequency tag to use, by default estimated from AN,AC or GT\n");
+    fprintf(stderr, "    -1, --1st-allele-only            Include only 1st allele at multiallelic sites\n");
+    fprintf(stderr, "    -c, --collapse STRING            Treat as identical records with <snps|indels|both|all|some|none>, see man page for details [none]\n");
+    fprintf(stderr, "    -d, --depth INT,INT,INT          Depth distribution: min,max,bin size [0,500,1]\n");
+    fprintf(stderr, "    -e, --exclude EXPR               Exclude sites for which the expression is true (see man page for details)\n");
+    fprintf(stderr, "    -E, --exons FILE.gz              Tab-delimited file with exons for indel frameshifts (chr,beg,end; 1-based, inclusive, bgzip compressed)\n");
+    fprintf(stderr, "    -f, --apply-filters LIST         Require at least one of the listed FILTER strings (e.g. \"PASS,.\")\n");
+    fprintf(stderr, "    -F, --fasta-ref FILE             Faidx indexed reference sequence file to determine INDEL context\n");
+    fprintf(stderr, "    -i, --include EXPR               Select sites for which the expression is true (see man page for details)\n");
+    fprintf(stderr, "    -I, --split-by-ID                Collect stats for sites with ID separately (known vs novel)\n");
+    fprintf(stderr, "    -r, --regions REGION             Restrict to comma-separated list of regions\n");
+    fprintf(stderr, "    -R, --regions-file FILE          Restrict to regions listed in a file\n");
+    fprintf(stderr, "        --regions-overlap 0|1|2      Include if POS in the region (0), record overlaps (1), variant overlaps (2) [1]\n");
+    fprintf(stderr, "    -s, --samples LIST               List of samples for sample stats, \"-\" to include all samples\n");
+    fprintf(stderr, "    -S, --samples-file FILE          File of samples to include\n");
+    fprintf(stderr, "    -t, --targets REGION             Similar to -r but streams rather than index-jumps\n");
+    fprintf(stderr, "    -T, --targets-file FILE          Similar to -R but streams rather than index-jumps\n");
+    fprintf(stderr, "        --targets-overlap 0|1|2      Include if POS in the region (0), record overlaps (1), variant overlaps (2) [0]\n");
+    fprintf(stderr, "    -u, --user-tstv TAG[:min:max:n]  Collect Ts/Tv stats for any tag using the given binning [0:1:100]\n");
+    fprintf(stderr, "                                       A subfield can be selected as e.g. 'PV4[0]', here the first value of the PV4 tag\n");
+    fprintf(stderr, "        --threads INT                Use multithreading with <int> worker threads [0]\n");
+    fprintf(stderr, "    -v, --verbose                    Produce verbose per-site and per-sample output\n");
+    fprintf(stderr, "\n");
+    exit(1);
+}
+
+int main_vcfstats(int argc, char *argv[])
+{
+    int c;
+    args_t *args = (args_t*) calloc(1,sizeof(args_t));
+    args->files  = bcf_sr_init();
+    args->argc   = argc; args->argv = argv;
+    args->dp_min = 0; args->dp_max = 500; args->dp_step = 1;
+    int regions_is_file = 0, targets_is_file = 0;
+    int regions_overlap = 1;
+    int targets_overlap = 0;
+
+    static struct option loptions[] =
+    {
+        {"af-bins",1,0,1},
+        {"af-tag",1,0,2},
+        {"1st-allele-only",0,0,'1'},
+        {"include",1,0,'i'},
+        {"exclude",1,0,'e'},
+        {"help",0,0,'h'},
+        {"collapse",1,0,'c'},
+        {"regions",1,0,'r'},
+        {"regions-file",1,0,'R'},
+        {"regions-overlap",required_argument,NULL,3},
+        {"verbose",0,0,'v'},
+        {"depth",1,0,'d'},
+        {"apply-filters",1,0,'f'},
+        {"exons",1,0,'E'},
+        {"samples",1,0,'s'},
+        {"samples-file",1,0,'S'},
+        {"split-by-ID",0,0,'I'},
+        {"targets",1,0,'t'},
+        {"targets-file",1,0,'T'},
+        {"targets-overlap",required_argument,NULL,4},
+        {"fasta-ref",1,0,'F'},
+        {"user-tstv",1,0,'u'},
+        {"threads",1,0,9},
+        {0,0,0,0}
+    };
+    while ((c = getopt_long(argc, argv, "hc:r:R:e:s:S:d:i:t:T:F:f:1u:vIE:",loptions,NULL)) >= 0) {
+        switch (c) {
+            case  1 : args->af_bins_list = optarg; break;
+            case  2 : args->af_tag = optarg; break;
+            case 'u': add_user_stats(args,optarg); break;
+            case '1': args->first_allele_only = 1; break;
+            case 'F': args->ref_fname = optarg; break;
+            case 't': args->targets_list = optarg; break;
+            case 'T': args->targets_list = optarg; targets_is_file = 1; break;
+            case 'c':
+                if ( !strcmp(optarg,"snps") ) args->files->collapse |= COLLAPSE_SNPS;
+                else if ( !strcmp(optarg,"indels") ) args->files->collapse |= COLLAPSE_INDELS;
+                else if ( !strcmp(optarg,"both") ) args->files->collapse |= COLLAPSE_SNPS | COLLAPSE_INDELS;
+                else if ( !strcmp(optarg,"any") ) args->files->collapse |= COLLAPSE_ANY;
+                else if ( !strcmp(optarg,"all") ) args->files->collapse |= COLLAPSE_ANY;
+                else if ( !strcmp(optarg,"some") ) args->files->collapse |= COLLAPSE_SOME;
+                else if ( !strcmp(optarg,"none") ) args->files->collapse = COLLAPSE_NONE;
+                else error("The --collapse string \"%s\" not recognised.\n", optarg);
+                break;
+            case 'v': args->verbose_sites = 1; break;
+            case 'd':
+                if ( sscanf(optarg,"%d,%d,%d",&args->dp_min,&args->dp_max,&args->dp_step)!=3 )
+                    error("Could not parse --depth %s\n", optarg);
+                if ( args->dp_min<0 || args->dp_min >= args->dp_max || args->dp_step > args->dp_max - args->dp_min + 1 )
+                    error("Is this a typo? --depth %s\n", optarg);
+                break;
+            case 'f': args->files->apply_filters = optarg; break;
+            case 'r': args->regions_list = optarg; break;
+            case 'R': args->regions_list = optarg; regions_is_file = 1; break;
+            case 'E': args->exons_fname = optarg; break;
+            case 's': args->samples_list = optarg; break;
+            case 'S': args->samples_list = optarg; args->samples_is_file = 1; break;
+            case 'I': args->split_by_id = 1; break;
+            case 'e':
+                if ( args->filter_str ) error("Error: only one -i or -e expression can be given, and they cannot be combined\n");
+                args->filter_str = optarg; args->filter_logic |= FLT_EXCLUDE; break;
+            case 'i':
+                if ( args->filter_str ) error("Error: only one -i or -e expression can be given, and they cannot be combined\n");
+                args->filter_str = optarg; args->filter_logic |= FLT_INCLUDE; break;
+            case  3 :
+                regions_overlap = parse_overlap_option(optarg);
+                if ( regions_overlap < 0 ) error("Could not parse: --regions-overlap %s\n",optarg);
+                break;
+            case  4 :
+                targets_overlap = parse_overlap_option(optarg);
+                if ( targets_overlap < 0 ) error("Could not parse: --targets-overlap %s\n",optarg);
+                break;
+            case  9 : args->n_threads = strtol(optarg, 0, 0); break;
+            case 'h':
+            case '?': usage(); break;
+            default: error("Unknown argument: %s\n", optarg);
+        }
+    }
+    char *fname = NULL;
+    if ( optind==argc )
+    {
+        if ( !isatty(fileno((FILE *)stdin)) ) fname = "-";  // reading from stdin
+        else usage();
+    }
+    else fname = argv[optind];
+
+    if ( argc-optind>2 ) usage();
+    if ( argc-optind>1 )
+    {
+        args->files->require_index = 1;
+        if ( args->split_by_id ) error("Only one file can be given with -i.\n");
+    }
+    if ( !args->samples_list ) args->files->max_unpack = BCF_UN_INFO;
+    if ( args->targets_list )
+    {
+        bcf_sr_set_opt(args->files,BCF_SR_TARGETS_OVERLAP,targets_overlap);
+        if ( bcf_sr_set_targets(args->files, args->targets_list, targets_is_file, 0)<0 )
+            error("Failed to read the targets: %s\n", args->targets_list);
+    }
+    if ( args->regions_list)
+    {
+        bcf_sr_set_opt(args->files,BCF_SR_REGIONS_OVERLAP,regions_overlap);
+        if ( bcf_sr_set_regions(args->files, args->regions_list, regions_is_file)<0 )
+            error("Failed to read the regions: %s\n", args->regions_list);
+    }
+    if ( args->n_threads && bcf_sr_set_threads(args->files, args->n_threads)<0)
+        error("Failed to create threads\n");
+
+    while (fname)
+    {
+        if ( !bcf_sr_add_reader(args->files, fname) )
+            error("Failed to read from %s: %s\n", !strcmp("-",fname)?"standard input":fname,bcf_sr_strerror(args->files->errnum));
+        fname = ++optind < argc ? argv[optind] : NULL;
+    }
+
+    init_stats(args);
+    print_header(args);
+    do_vcf_stats(args);
+    print_stats(args);
+    destroy_stats(args);
+    bcf_sr_destroy(args->files);
+    free(args);
+    return 0;
+}
+
diff --git a/bcftools/vcfstats.c.pysam.c b/bcftools/vcfstats.c.pysam.c
new file mode 100644
index 0000000..7b5c485
--- /dev/null
+++ b/bcftools/vcfstats.c.pysam.c
@@ -0,0 +1,1917 @@
+#include "bcftools.pysam.h"
+
+/*  vcfstats.c -- Produces stats which can be plotted using plot-vcfstats.
+
+    Copyright (C) 2012-2022 Genome Research Ltd.
+
+    Author: Petr Danecek <pd3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.  */
+
+/*
+    Notes and known issues:
+        - SN ts/tv calculation includes all non-ref alleles listed in ALT while per-sample ts/tv
+        takes the first non-ref allele only, something to consider with many non-ref HETs.
+*/
+#include <stdio.h>
+#include <stdarg.h>
+#include <unistd.h>
+#include <getopt.h>
+#include <assert.h>
+#include <math.h>
+#include <htslib/vcf.h>
+#include <htslib/synced_bcf_reader.h>
+#include <htslib/vcfutils.h>
+#include <htslib/faidx.h>
+#include <inttypes.h>
+#include "bcftools.h"
+#include "filter.h"
+#include "bin.h"
+#include "dist.h"
+
+// Logic of the filters: include or exclude sites which match the filters?
+#define FLT_INCLUDE 1
+#define FLT_EXCLUDE 2
+
+#define HWE_STATS 1
+#define QUAL_STATS 1
+#define IRC_STATS 1
+#define IRC_RLEN 10
+#define NA_STRING "0"
+
+typedef struct
+{
+    char *tag;
+    float min, max;
+    uint64_t *vals_ts, *vals_tv;
+    void *val;
+    int nbins, type, m_val, idx;
+}
+user_stats_t;
+
+typedef struct
+{
+    int min, max, step, m_vals;
+    uint64_t *vals;
+}
+idist_t;
+
+typedef struct
+{
+    uint64_t n_snps, n_indels, n_mnps, n_others, n_mals, n_snp_mals, n_records, n_noalts;
+    int *af_ts, *af_tv, *af_snps;   // first bin of af_* stats are singletons
+    #if HWE_STATS
+        int *af_hwe;
+    #endif
+    #if IRC_STATS
+        int n_repeat[IRC_RLEN][4], n_repeat_na;    // number of indels which are repeat-consistent, repeat-inconsistent (dels and ins), and not applicable
+        int *af_repeats[3];
+    #endif
+    int ts_alt1, tv_alt1;
+    #if QUAL_STATS
+        // Values are rounded to one significant digit and 1 is added (Q*10+1); missing and negative values go in the first bin
+        // Only SNPs that are the 1st alternate allele are counted
+        dist_t *qual_ts, *qual_tv, *qual_indels;
+    #endif
+    int *insertions, *deletions, m_indel;   // maximum indel length
+    int in_frame, out_frame, na_frame, in_frame_alt1, out_frame_alt1, na_frame_alt1;
+    int subst[15];
+    int *smpl_hets, *smpl_homRR, *smpl_homAA, *smpl_ts, *smpl_tv, *smpl_indels, *smpl_ndp, *smpl_sngl;
+    int *smpl_hapRef, *smpl_hapAlt, *smpl_missing;
+    int *smpl_ins_hets, *smpl_del_hets, *smpl_ins_homs, *smpl_del_homs;
+    int *smpl_frm_shifts; // not-applicable, in-frame, out-frame
+    unsigned long int *smpl_dp;
+    idist_t dp, dp_sites;
+    int nusr;
+    user_stats_t *usr;
+    double *dvaf;   // distribution of the mean indel-allele frequency by length: -m_indel,-(m_indel-1),...-1,0,1,..,m_indel
+    uint32_t *nvaf;
+}
+stats_t;
+
+typedef struct
+{
+    uint64_t gt2gt[5][5];   // number of RR->RR, RR->RA, etc. matches/mismatches; see type2stats
+    /*
+        Pearson's R^2 is used for aggregate R^2
+        y, yy .. sum of dosage and squared dosage in the query VCF (second file)
+        x, xx .. sum of squared dosage in the truth VCF (first file)
+        n     .. number of genotypes
+     */
+    double y, yy, x, xx, yx, n;
+}
+gtcmp_t;
+
+typedef struct
+{
+    char *seq;
+    int pos, cnt, len;
+}
+_idc1_t;
+typedef struct
+{
+    faidx_t *ref;
+    _idc1_t *dat;
+    int ndat, mdat;
+}
+indel_ctx_t;
+
+typedef struct
+{
+    // stats
+    stats_t stats[3];
+    int *tmp_iaf, ntmp_iaf, m_af, m_qual, naf_hwe, mtmp_frm;
+    uint8_t *tmp_frm;
+    int dp_min, dp_max, dp_step;
+    gtcmp_t *smpl_gts_snps, *smpl_gts_indels;
+    gtcmp_t *af_gts_snps, *af_gts_indels; // first bin of af_* stats are singletons
+    bin_t *af_bins;
+    float *farr;
+    int mfarr;
+
+    // indel context
+    indel_ctx_t *indel_ctx;
+    char *ref_fname;
+
+    // user stats
+    int nusr;
+    user_stats_t *usr;
+
+    // other
+    bcf_srs_t *files;
+    bcf_sr_regions_t *exons;
+    char **argv, *exons_fname, *regions_list, *samples_list, *targets_list, *af_bins_list, *af_tag;
+    int argc, verbose_sites, first_allele_only, samples_is_file;
+    int split_by_id, nstats;
+
+    filter_t *filter[2];
+    char *filter_str;
+    int filter_logic;   // include or exclude sites which match the filters? One of FLT_INCLUDE/FLT_EXCLUDE
+    int n_threads;
+}
+args_t;
+
+static int type2dosage[6], type2ploidy[6], type2stats[7];
+
+static void idist_init(idist_t *d, int min, int max, int step)
+{
+    d->min = min; d->max = max; d->step = step;
+    d->m_vals = 4 + (d->max - d->min)/d->step;
+    d->vals = (uint64_t*) calloc(d->m_vals,sizeof(uint64_t));
+}
+static void idist_destroy(idist_t *d)
+{
+    if ( d->vals ) free(d->vals);
+}
+static inline uint64_t *idist(idist_t *d, int val)
+{
+    if ( val < d->min ) return &d->vals[0];
+    if ( val > d->max ) return &d->vals[d->m_vals-1];
+    return &d->vals[1 + (val - d->min) / d->step];
+}
+static inline int idist_i2bin(idist_t *d, int i)
+{
+    if ( i<=0 ) return d->min;
+    if ( i>= d->m_vals ) return d->max;
+    return i-1+d->min;
+}
+
+#define IC_DBG 0
+#if IC_DBG
+static void _indel_ctx_print1(_idc1_t *idc)
+{
+    int i;
+    fprintf(bcftools_stdout, "%d\t", idc->cnt);
+    for (i=0; i<idc->len; i++)
+        fputc(idc->seq[i], bcftools_stdout);
+    fputc('\n', bcftools_stdout);
+}
+static void _indel_ctx_print(indel_ctx_t *ctx)
+{
+    int i;
+    for (i=0; i<ctx->ndat; i++)
+        _indel_ctx_print1(&ctx->dat[i]);
+    fputc('\n',bcftools_stdout);
+}
+#endif
+static int _indel_ctx_lookup(indel_ctx_t *ctx, char *seq, int seq_len, int *hit)
+{
+    // binary search
+    int min = 0, max = ctx->ndat - 1;
+    while ( min<=max )
+    {
+        int i = (min+max)/2;
+        int cmp = strncmp(seq, ctx->dat[i].seq, seq_len);
+        if ( cmp<0 ) max = i - 1;
+        else if ( cmp>0 ) min = i + 1;
+        else
+        {
+            if ( seq_len==ctx->dat[i].len )
+            {
+                *hit = 1;
+                return i;
+            }
+            else if ( seq_len<ctx->dat[i].len ) max = i - 1;
+            else min = i + 1;
+        }
+    }
+    *hit = 0;
+    return max;
+}
+static void _indel_ctx_insert(indel_ctx_t *ctx, char *seq, int seq_len, int pos)
+{
+    int idat, hit, i;
+    idat = _indel_ctx_lookup(ctx, seq, seq_len, &hit);
+    if ( !hit )
+    {
+        if ( pos>0 ) return;
+        idat++;
+        ctx->ndat++;
+        hts_expand(_idc1_t, ctx->ndat+1, ctx->mdat, ctx->dat);
+        if ( idat<ctx->ndat && ctx->ndat>1 )
+            memmove(&ctx->dat[idat+1], &ctx->dat[idat], (ctx->ndat - idat - 1)*sizeof(_idc1_t));
+        ctx->dat[idat].len = seq_len;
+        ctx->dat[idat].cnt = 1;
+        ctx->dat[idat].pos = pos;
+        ctx->dat[idat].seq = (char*) malloc(sizeof(char)*(seq_len+1));
+        for (i=0; i<seq_len; i++) ctx->dat[idat].seq[i] = seq[i];
+        ctx->dat[idat].seq[i] = 0;
+        return;
+    }
+    if ( ctx->dat[idat].pos + seq_len == pos )
+    {
+        ctx->dat[idat].cnt++;
+        ctx->dat[idat].pos = pos;
+    }
+}
+indel_ctx_t *indel_ctx_init(char *fa_ref_fname)
+{
+    indel_ctx_t *ctx = (indel_ctx_t *) calloc(1,sizeof(indel_ctx_t));
+    ctx->ref = fai_load(fa_ref_fname);
+    if ( !ctx->ref )
+    {
+        free(ctx);
+        return NULL;
+    }
+    return ctx;
+}
+void indel_ctx_destroy(indel_ctx_t *ctx)
+{
+    fai_destroy(ctx->ref);
+    if ( ctx->mdat ) free(ctx->dat);
+    free(ctx);
+}
+/**
+ * indel_ctx_type() - determine indel context type
+ * @ctx:
+ * @chr:    chromosome name
+ * @pos:    position of the first @ref base, 1-based
+ * @ref:    reference allele
+ * @alt:    alternate allele. Only first of multiple comma-separated alleles is
+ *          considered
+ * @nrep:   number of repeated elements (w)
+ * @nlen:   length of a single repeat element (w)
+ *
+ * Returns the INDEL length, negative for deletions, positive for insertions
+ */
+int indel_ctx_type(indel_ctx_t *ctx, char *chr, int pos, char *ref, char *alt, int *nrep, int *nlen)
+{
+    const int win_size = 50;             // hard-wired for now
+    const int rep_len  = IRC_RLEN;       // hard-wired for now
+
+    int ref_len = strlen(ref);
+    int alt_len = 0;
+    while ( alt[alt_len] && alt[alt_len]!=',' ) alt_len++;
+
+    int i, fai_ref_len;
+    char *fai_ref = faidx_fetch_seq(ctx->ref, chr, pos-1, pos+win_size, &fai_ref_len);
+    for (i=0; i<fai_ref_len; i++)
+        if ( (int)fai_ref[i]>96 ) fai_ref[i] -= 32;
+
+    // Sanity check: the reference sequence must match the REF allele
+    for (i=0; i<fai_ref_len && i<ref_len; i++)
+        if ( ref[i] != fai_ref[i] && ref[i] - 32 != fai_ref[i] && !iupac_consistent(fai_ref[i], ref[i]) )
+            error("\nSanity check failed, the reference sequence differs: %s:%d+%d .. %c vs %c\n", chr, pos, i, ref[i],fai_ref[i]);
+
+    // Count occurrences of all possible kmers
+    ctx->ndat = 0;
+    for (i=0; i<win_size; i++)
+    {
+        int k, kmax = rep_len <= i ? rep_len : i+1;
+        for (k=0; k<kmax; k++)
+            _indel_ctx_insert(ctx, &fai_ref[i-k+1], k+1, i-k);
+    }
+
+    #if IC_DBG
+    fprintf(bcftools_stdout,"ref: %s\n", ref);
+    fprintf(bcftools_stdout,"alt: %s\n", alt);
+    fprintf(bcftools_stdout,"ctx: %s\n", fai_ref);
+    _indel_ctx_print(ctx);
+    #endif
+
+    int max_cnt = 0, max_len = 0;
+    for (i=0; i<ctx->ndat; i++)
+    {
+        if ( max_cnt < ctx->dat[i].cnt || (max_cnt==ctx->dat[i].cnt && max_len < ctx->dat[i].len) )
+        {
+            max_cnt = ctx->dat[i].cnt;
+            max_len = ctx->dat[i].len;
+        }
+        free(ctx->dat[i].seq);
+    }
+    free(fai_ref);
+
+    *nrep = max_cnt;
+    *nlen = max_len;
+    return alt_len - ref_len;
+}
+
+static void add_user_stats(args_t *args, char *str)
+{
+    args->nusr++;
+    args->usr = (user_stats_t*) realloc(args->usr,sizeof(user_stats_t)*args->nusr);
+    user_stats_t *usr = &args->usr[args->nusr-1];
+    memset(usr,0,sizeof(*usr));
+    usr->min   = 0;
+    usr->max   = 1;
+    usr->nbins = 100;
+    usr->idx   = 0;
+
+    char *tmp = str;
+    while ( *tmp && *tmp!=':' ) tmp++;
+
+    // Tag with an index or just tag? (e.g. PV4[1] vs DP)
+    if ( tmp > str && tmp[-1]==']' )
+    {
+        char *ptr = tmp;
+        while ( ptr>str && *ptr!='[' ) ptr--;
+        if ( *ptr=='[' )
+        {
+            char *ptr2;
+            usr->idx = strtol(ptr+1, &ptr2, 10);
+            if ( ptr+1==ptr2 || ptr2 != tmp-1 ) error("Could not parse the index in \"%s\" (ptr=%s;ptr2=%s(%p),tmp=%s(%p),idx=%d)\n", str,ptr,ptr2,ptr2,tmp,tmp,usr->idx);
+            if ( usr->idx<0 ) error("Error: negative index is not allowed: \"%s\"\n", str);
+            *ptr = 0;
+        }
+    }
+
+    usr->tag = (char*)calloc(tmp-str+2,sizeof(char));
+    memcpy(usr->tag,str,tmp-str);
+
+    if ( *tmp )
+    {
+        char *ptr = ++tmp;
+        usr->min = strtod(tmp, &ptr);
+        if ( tmp==ptr ) error("Could not parse %s\n", str);
+        tmp = ptr+1;
+    }
+    if ( *tmp )
+    {
+        char *ptr = tmp;
+        usr->max = strtod(tmp, &ptr);
+        if ( tmp==ptr ) error("Could not parse %s\n", str);
+        tmp = ptr+1;
+    }
+    if ( *tmp )
+    {
+        char *ptr = tmp;
+        usr->nbins = strtol(tmp, &ptr, 10);
+        if ( tmp==ptr ) error("Could not parse %s\n", str);
+        if ( usr->nbins<=0 ) error("Number of bins does not make sense (%d): %s.\n", usr->nbins, str);
+    }
+}
+static void init_user_stats(args_t *args, bcf_hdr_t *hdr, stats_t *stats)
+{
+    stats->nusr = args->nusr;
+    stats->usr = (user_stats_t*)malloc(sizeof(user_stats_t)*args->nusr);
+    memcpy(stats->usr,args->usr,args->nusr*sizeof(user_stats_t));
+    int i;
+    for (i=0; i<stats->nusr; i++)
+    {
+        user_stats_t *usr = &stats->usr[i];
+        usr->vals_ts = (uint64_t*)calloc(usr->nbins,sizeof(uint64_t));
+        usr->vals_tv = (uint64_t*)calloc(usr->nbins,sizeof(uint64_t));
+        int id = bcf_hdr_id2int(hdr,BCF_DT_ID,usr->tag);
+        if ( !bcf_hdr_idinfo_exists(hdr,BCF_HL_INFO,id) ) error("The INFO tag \"%s\" is not defined in the header\n", usr->tag);
+        usr->type = bcf_hdr_id2type(hdr,BCF_HL_INFO,id);
+        if ( usr->type!=BCF_HT_REAL && usr->type!=BCF_HT_INT ) error("The INFO tag \"%s\" is not of Float or Integer type (%d)\n", usr->tag, usr->type);
+    }
+}
+static void init_stats(args_t *args)
+{
+    int i;
+    args->nstats = args->files->nreaders==1 ? 1 : 3;
+    if ( args->split_by_id ) args->nstats = 2;
+
+    if ( args->filter_str )
+    {
+        args->filter[0] = filter_init(bcf_sr_get_header(args->files,0), args->filter_str);
+        if ( args->files->nreaders==2 )
+            args->filter[1] = filter_init(bcf_sr_get_header(args->files,1), args->filter_str);
+        args->files->max_unpack |= filter_max_unpack(args->filter[0]);
+    }
+
+    // AF corresponds to AC but is more robust to mixtures of haploid and diploid GTs
+    if ( !args->af_bins_list )
+    {
+        args->m_af = 101;
+        for (i=0; i<args->files->nreaders; i++)
+            if ( bcf_hdr_nsamples(args->files->readers[i].header) + 1> args->m_af )
+                args->m_af = bcf_hdr_nsamples(args->files->readers[i].header) + 1;
+    }
+    else
+    {
+        args->af_bins = bin_init(args->af_bins_list,0,1);
+
+        // m_af is used also for other af arrays, where the first bin is for
+        // singletons. However, since the last element is unused in af_bins
+        // (n boundaries form n-1 intervals), the m_af count is good for both.
+        args->m_af = bin_get_size(args->af_bins);
+    }
+
+    bcf_hdr_t *hdr = bcf_sr_get_header(args->files,0);
+    if ( args->af_tag && !bcf_hdr_idinfo_exists(hdr,BCF_HL_INFO,bcf_hdr_id2int(hdr,BCF_DT_ID,args->af_tag)) )
+        error("No such INFO tag: %s\n", args->af_tag);
+
+    #if QUAL_STATS
+        args->m_qual = 999;
+    #endif
+    #if HWE_STATS
+        args->naf_hwe = 100;
+    #endif
+
+    if ( args->samples_list )
+    {
+        if ( !bcf_sr_set_samples(args->files,args->samples_list,args->samples_is_file) )
+        {
+            if ( !bcf_hdr_nsamples(args->files->readers[0].header) )
+                error("No sample columns in %s\n", args->files->readers[0].fname);
+            error("Unable to parse the samples: \"%s\"\n", args->samples_list);
+        }
+        args->af_gts_snps     = (gtcmp_t *) calloc(args->m_af,sizeof(gtcmp_t));
+        args->af_gts_indels   = (gtcmp_t *) calloc(args->m_af,sizeof(gtcmp_t));
+        args->smpl_gts_snps   = (gtcmp_t *) calloc(args->files->n_smpl,sizeof(gtcmp_t));
+        args->smpl_gts_indels = (gtcmp_t *) calloc(args->files->n_smpl,sizeof(gtcmp_t));
+    }
+    for (i=0; i<args->nstats; i++)
+    {
+        stats_t *stats = &args->stats[i];
+        stats->m_indel     = 60;
+        stats->insertions  = (int*) calloc(stats->m_indel,sizeof(int));
+        stats->deletions   = (int*) calloc(stats->m_indel,sizeof(int));
+        stats->af_ts       = (int*) calloc(args->m_af,sizeof(int));
+        stats->af_tv       = (int*) calloc(args->m_af,sizeof(int));
+        stats->af_snps     = (int*) calloc(args->m_af,sizeof(int));
+        int j;
+        for (j=0; j<3; j++) stats->af_repeats[j] = (int*) calloc(args->m_af,sizeof(int));
+        #if QUAL_STATS
+            stats->qual_ts     = dist_init(5);
+            stats->qual_tv     = dist_init(5);
+            stats->qual_indels = dist_init(5);
+        #endif
+        if ( args->files->n_smpl )
+        {
+            stats->smpl_missing = (int *) calloc(args->files->n_smpl,sizeof(int));
+            stats->smpl_hets   = (int *) calloc(args->files->n_smpl,sizeof(int));
+            stats->smpl_homAA  = (int *) calloc(args->files->n_smpl,sizeof(int));
+            stats->smpl_homRR  = (int *) calloc(args->files->n_smpl,sizeof(int));
+            stats->smpl_hapRef = (int *) calloc(args->files->n_smpl,sizeof(int));
+            stats->smpl_hapAlt = (int *) calloc(args->files->n_smpl,sizeof(int));
+            stats->smpl_ins_hets = (int *) calloc(args->files->n_smpl,sizeof(int));
+            stats->smpl_del_hets = (int *) calloc(args->files->n_smpl,sizeof(int));
+            stats->smpl_ins_homs = (int *) calloc(args->files->n_smpl,sizeof(int));
+            stats->smpl_del_homs = (int *) calloc(args->files->n_smpl,sizeof(int));
+            stats->smpl_ts     = (int *) calloc(args->files->n_smpl,sizeof(int));
+            stats->smpl_tv     = (int *) calloc(args->files->n_smpl,sizeof(int));
+            stats->smpl_indels = (int *) calloc(args->files->n_smpl,sizeof(int));
+            stats->smpl_dp     = (unsigned long int *) calloc(args->files->n_smpl,sizeof(unsigned long int));
+            stats->smpl_ndp    = (int *) calloc(args->files->n_smpl,sizeof(int));
+            stats->smpl_sngl   = (int *) calloc(args->files->n_smpl,sizeof(int));
+            #if HWE_STATS
+                stats->af_hwe  = (int*) calloc(args->m_af*args->naf_hwe,sizeof(int));
+            #endif
+            if ( args->exons_fname )
+                stats->smpl_frm_shifts = (int*) calloc(args->files->n_smpl*3,sizeof(int));
+            stats->nvaf = (uint32_t*) calloc(stats->m_indel*2+1,sizeof(*stats->nvaf));
+            stats->dvaf = (double*) calloc(stats->m_indel*2+1,sizeof(*stats->dvaf));
+        }
+        idist_init(&stats->dp, args->dp_min,args->dp_max,args->dp_step);
+        idist_init(&stats->dp_sites, args->dp_min,args->dp_max,args->dp_step);
+        init_user_stats(args, i!=1 ? args->files->readers[0].header : args->files->readers[1].header, stats);
+    }
+
+    if ( args->exons_fname )
+    {
+        args->exons = bcf_sr_regions_init(args->exons_fname,1,0,1,2);
+        if ( !args->exons )
+            error("Error occurred while reading, was the file compressed with bgzip: %s?\n", args->exons_fname);
+    }
+
+    #if IRC_STATS
+    if ( args->ref_fname )
+        args->indel_ctx = indel_ctx_init(args->ref_fname);
+    #endif
+
+    type2dosage[GT_HOM_RR] = 0;
+    type2dosage[GT_HET_RA] = 1;
+    type2dosage[GT_HOM_AA] = 2;
+    type2dosage[GT_HET_AA] = 2;
+    type2dosage[GT_HAPL_R] = 0;
+    type2dosage[GT_HAPL_A] = 1;
+
+    type2ploidy[GT_HOM_RR] = 1;
+    type2ploidy[GT_HET_RA] = 1;
+    type2ploidy[GT_HOM_AA] = 1;
+    type2ploidy[GT_HET_AA] = 1;
+    type2ploidy[GT_HAPL_R] = -1;
+    type2ploidy[GT_HAPL_A] = -1;
+
+    type2stats[GT_HOM_RR] = 0;
+    type2stats[GT_HET_RA] = 1;
+    type2stats[GT_HOM_AA] = 2;
+    type2stats[GT_HET_AA] = 3;
+    type2stats[GT_HAPL_R] = 0;
+    type2stats[GT_HAPL_A] = 2;
+    type2stats[GT_UNKN]   = 4;
+
+}
+static void destroy_stats(args_t *args)
+{
+    int id, j;
+    for (id=0; id<args->nstats; id++)
+    {
+        stats_t *stats = &args->stats[id];
+        if (stats->af_ts) free(stats->af_ts);
+        if (stats->af_tv) free(stats->af_tv);
+        if (stats->af_snps) free(stats->af_snps);
+        for (j=0; j<3; j++)
+            if (stats->af_repeats[j]) free(stats->af_repeats[j]);
+        #if QUAL_STATS
+            if (stats->qual_ts) dist_destroy(stats->qual_ts);
+            if (stats->qual_tv) dist_destroy(stats->qual_tv);
+            if (stats->qual_indels) dist_destroy(stats->qual_indels);
+        #endif
+        #if HWE_STATS
+            free(stats->af_hwe);
+        #endif
+        free(stats->insertions);
+        free(stats->deletions);
+        free(stats->smpl_missing);
+        free(stats->smpl_hets);
+        free(stats->smpl_homAA);
+        free(stats->smpl_homRR);
+        free(stats->smpl_hapRef);
+        free(stats->smpl_hapAlt);
+        free(stats->smpl_ins_homs);
+        free(stats->smpl_del_homs);
+        free(stats->smpl_ins_hets);
+        free(stats->smpl_del_hets);
+        free(stats->smpl_ts);
+        free(stats->smpl_tv);
+        free(stats->smpl_indels);
+        free(stats->smpl_dp);
+        free(stats->smpl_ndp);
+        free(stats->smpl_sngl);
+        idist_destroy(&stats->dp);
+        idist_destroy(&stats->dp_sites);
+        for (j=0; j<stats->nusr; j++)
+        {
+            free(stats->usr[j].vals_ts);
+            free(stats->usr[j].vals_tv);
+            free(stats->usr[j].val);
+        }
+        free(stats->usr);
+        if ( args->exons ) free(stats->smpl_frm_shifts);
+        free(stats->nvaf);
+        free(stats->dvaf);
+    }
+    for (j=0; j<args->nusr; j++) free(args->usr[j].tag);
+    if ( args->af_bins ) bin_destroy(args->af_bins);
+    free(args->farr);
+    free(args->usr);
+    free(args->tmp_frm);
+    free(args->tmp_iaf);
+    if (args->exons) bcf_sr_regions_destroy(args->exons);
+    free(args->af_gts_snps);
+    free(args->af_gts_indels);
+    free(args->smpl_gts_snps);
+    free(args->smpl_gts_indels);
+    if (args->indel_ctx) indel_ctx_destroy(args->indel_ctx);
+    if (args->filter[0]) filter_destroy(args->filter[0]);
+    if (args->filter[1]) filter_destroy(args->filter[1]);
+}
+
+static void init_iaf(args_t *args, bcf_sr_t *reader)
+{
+    bcf1_t *line = reader->buffer[0];
+    hts_expand(int32_t,line->n_allele,args->ntmp_iaf,args->tmp_iaf);
+
+    int i, ret;
+    if ( args->af_tag )
+    {
+        ret = bcf_get_info_float(reader->header, line, args->af_tag, &args->farr, &args->mfarr);
+        if ( ret<=0 || ret!=line->n_allele-1 )
+        {
+            // the AF tag is not present or wrong number of values, put in the singletons/unknown bin
+            for (i=0; i<line->n_allele; i++) args->tmp_iaf[i] = 0;
+            return;
+        }
+        args->tmp_iaf[0] = 0;
+        for (i=1; i<line->n_allele; i++)
+        {
+            float af = args->farr[i-1];
+            if ( af<0 ) af = 0;
+            else if ( af>1 ) af = 1;
+            int iaf = args->af_bins ? bin_get_idx(args->af_bins,af) : af*(args->m_af-2);
+            args->tmp_iaf[i] = iaf + 1;     // the first tmp_iaf bin is reserved for singletons
+        }
+        return;
+    }
+
+    // tmp_iaf is first filled with AC counts in calc_ac and then transformed to
+    //  an index to af_gts_snps
+    ret = bcf_calc_ac(reader->header, line, args->tmp_iaf, args->samples_list ? BCF_UN_INFO|BCF_UN_FMT : BCF_UN_INFO);
+    if ( !ret )
+    {
+        for (i=0; i<line->n_allele; i++) args->tmp_iaf[i] = 0;      // singletons/unknown bin
+        return;
+    }
+
+    int an = 0;
+    for (i=0; i<line->n_allele; i++)
+        an += args->tmp_iaf[i];
+
+    args->tmp_iaf[0] = 0;
+    for (i=1; i<line->n_allele; i++)
+    {
+        if ( args->tmp_iaf[i]==1 )
+            args->tmp_iaf[i] = 0;   // singletons into the first bin
+        else if ( !an )
+            args->tmp_iaf[i] = 1;   // no genotype at all, put to the AF=0 bin
+        else
+        {
+            float af = (float) args->tmp_iaf[i] / an;
+            if ( af<0 ) af = 0;
+            else if ( af>1 ) af = 1;
+            int iaf = args->af_bins ? bin_get_idx(args->af_bins,af) : af*(args->m_af-2);
+            args->tmp_iaf[i] = iaf + 1;
+        }
+    }
+}
+
+static inline void do_mnp_stats(args_t *args, stats_t *stats, bcf_sr_t *reader)
+{
+    stats->n_mnps++;
+}
+
+static inline void do_other_stats(args_t *args, stats_t *stats, bcf_sr_t *reader)
+{
+    stats->n_others++;
+}
+
+static void do_indel_stats(args_t *args, stats_t *stats, bcf_sr_t *reader)
+{
+    stats->n_indels++;
+
+    bcf1_t *line = reader->buffer[0];
+
+    #if QUAL_STATS
+        int iqual = (isnan(line->qual) || line->qual<0) ? 0 : 1 + (int)(line->qual*10);
+        dist_insert(stats->qual_indels, iqual);
+    #endif
+
+    // Check if the indel is near an exon for the frameshift statistics
+    int i, exon_overlap = 0;
+    if ( args->exons )
+    {
+        if ( !bcf_sr_regions_overlap(args->exons, bcf_seqname(reader->header,line),line->pos,line->pos) ) exon_overlap = 1;
+        hts_expand(uint8_t,line->n_allele,args->mtmp_frm,args->tmp_frm);
+        for (i=0; i<line->n_allele; i++) args->tmp_frm[i] = 0;
+    }
+
+    for (i=1; i<line->n_allele; i++)
+    {
+        if ( args->first_allele_only && i>1 ) break;
+        int is_indel = bcf_has_variant_type(line,i,VCF_INDEL);
+        if (is_indel < 0) error("bcf_has_variant_type() failed.");
+        if ( !is_indel ) continue;
+        int len = bcf_variant_length(line, i);
+
+        #if IRC_STATS
+        // Indel repeat consistency
+        if ( args->indel_ctx )
+        {
+            int nrep, nlen, ndel;
+            ndel = indel_ctx_type(args->indel_ctx, (char*)reader->header->id[BCF_DT_CTG][line->rid].key, line->pos+1, line->d.allele[0], line->d.allele[i], &nrep, &nlen);
+            if ( nlen<=1 || nrep<=1 )
+            {
+                // not a repeat or a single base repeat
+                stats->n_repeat_na++;
+                stats->af_repeats[2][ args->tmp_iaf[i] ]++;
+            }
+            else
+            {
+                if ( abs(ndel) % nlen )
+                {
+                    // the length of the inserted/deleted sequence is not consistent with the repeat element
+                    stats->n_repeat[nlen-1][ndel<0 ? 1 : 3]++;
+                    stats->af_repeats[1][ args->tmp_iaf[i] ]++;
+                }
+                else
+                {
+                    // the length consistent with the repeat
+                    stats->n_repeat[nlen-1][ndel<0 ? 0 : 2]++;
+                    stats->af_repeats[0][ args->tmp_iaf[i] ]++;
+                }
+            }
+        }
+        else
+            stats->af_repeats[2][ args->tmp_iaf[i] ]++;
+        #endif
+
+        // Check the frameshifts
+        int tlen = 0;
+        if ( args->exons && exon_overlap )   // there is an exon
+        {
+            if ( len>0 )
+            {
+                // insertion
+                if ( args->exons->start <= line->pos && args->exons->end > line->pos ) tlen = abs(len);
+            }
+            else if ( args->exons->start <= line->pos + abs(len) )
+            {
+                // deletion
+                tlen = abs(len);
+                if ( line->pos < args->exons->start )              // trim the beginning
+                    tlen -= args->exons->start - line->pos + 1;
+                if ( args->exons->end < line->pos + abs(len) )     // trim the end
+                    tlen -= line->pos + abs(len) - args->exons->end;
+            }
+        }
+        if ( tlen )     // there are some deleted/inserted bases in the exon
+        {
+            if ( tlen%3 ) { stats->out_frame++; args->tmp_frm[i] = 2; }
+            else { stats->in_frame++; args->tmp_frm[i] = 1; }
+
+            if ( i==1 )
+            {
+                if ( tlen%3 ) stats->out_frame_alt1++;
+                else stats->in_frame_alt1++;
+            }
+        }
+        else            // no exon affected
+        {
+            if ( i==1 ) stats->na_frame_alt1++;
+            stats->na_frame++;
+        }
+
+
+        // Indel length distribution
+        int *ptr = stats->insertions;
+        if ( len<0 )
+        {
+            len *= -1;
+            ptr = stats->deletions;
+        }
+        if ( --len >= stats->m_indel ) len = stats->m_indel-1;
+        ptr[len]++;
+    }
+}
+
+static void do_user_stats(stats_t *stats, bcf_sr_t *reader, int is_ts)
+{
+    int i, nval;
+    for (i=0; i<stats->nusr; i++)
+    {
+        user_stats_t *usr = &stats->usr[i];
+        uint64_t *vals = is_ts ? usr->vals_ts : usr->vals_tv;
+        float val;
+        if ( usr->type==BCF_HT_REAL )
+        {
+            if ( (nval=bcf_get_info_float(reader->header,reader->buffer[0],usr->tag,&usr->val,&usr->m_val))<=0 ) continue;
+            if ( usr->idx >= nval ) continue;
+            val = ((float*)usr->val)[usr->idx];
+        }
+        else
+        {
+            if ( (nval=bcf_get_info_int32(reader->header,reader->buffer[0],usr->tag,&usr->val,&usr->m_val))<=0 ) continue;
+            if ( usr->idx >= nval ) continue;
+            val = ((int32_t*)usr->val)[usr->idx];
+        }
+        int idx;
+        if ( val<=usr->min ) idx = 0;
+        else if ( val>=usr->max ) idx = usr->nbins - 1;
+        else idx = (val - usr->min)/(usr->max - usr->min) * (usr->nbins-1);
+        vals[idx]++;
+    }
+}
+
+static void do_snp_stats(args_t *args, stats_t *stats, bcf_sr_t *reader)
+{
+    stats->n_snps++;
+
+    bcf1_t *line = reader->buffer[0];
+    int ref = bcf_acgt2int(*line->d.allele[0]);
+    if ( ref<0 ) return;
+
+    #if QUAL_STATS
+        int iqual = (isnan(line->qual) || line->qual<0) ? 0 : 1 + (int)(line->qual*10);
+    #endif
+
+    int i;
+    for (i=1; i<line->n_allele; i++)
+    {
+        if ( args->first_allele_only && i>1 ) break;
+        if ( !(bcf_get_variant_type(line,i)&VCF_SNP) ) continue;
+        int alt = bcf_acgt2int(*line->d.allele[i]);
+        if ( alt<0 || ref==alt ) continue;
+        stats->subst[ref<<2|alt]++;
+        int iaf = args->tmp_iaf[i];
+        stats->af_snps[iaf]++;
+        if ( abs(ref-alt)==2 )
+        {
+            if (i==1)
+            {
+                stats->ts_alt1++;
+                #if QUAL_STATS
+                    dist_insert(stats->qual_ts,iqual);
+                #endif
+                do_user_stats(stats, reader, 1);
+            }
+            stats->af_ts[iaf]++;
+        }
+        else
+        {
+            if (i==1)
+            {
+                stats->tv_alt1++;
+                #if QUAL_STATS
+                    dist_insert(stats->qual_tv,iqual);
+                #endif
+                do_user_stats(stats, reader, 0);
+            }
+            stats->af_tv[iaf]++;
+        }
+    }
+}
+
+static inline void update_dvaf(stats_t *stats, bcf1_t *line, bcf_fmt_t *fmt, int ismpl, int ial, int jal)
+{
+    if ( !fmt ) return;
+
+    float dvaf;
+    #define BRANCH_INT(type_t,missing,vector_end) { \
+        type_t *p = (type_t *) (fmt->p + fmt->size*ismpl); \
+        if ( p[ial]==vector_end || p[jal]==vector_end ) return; \
+        if ( p[ial]==missing || p[jal]==missing ) return; \
+        if ( !p[ial] && !p[jal] ) return; \
+        dvaf = (float)p[ial]/(p[ial]+p[jal]); \
+    }
+    switch (fmt->type) {
+        case BCF_BT_INT8:  BRANCH_INT(int8_t,  bcf_int8_missing, bcf_int8_vector_end); break;
+        case BCF_BT_INT16: BRANCH_INT(int16_t, bcf_int16_missing, bcf_int16_vector_end); break;
+        case BCF_BT_INT32: BRANCH_INT(int32_t, bcf_int32_missing, bcf_int32_vector_end); break;
+        default: fprintf(bcftools_stderr, "[E::%s] todo: %d\n", __func__, fmt->type); bcftools_exit(1); break;
+    }
+    #undef BRANCH_INT
+
+    int len = line->d.var[ial].n;
+    if ( len < -stats->m_indel ) len = -stats->m_indel;
+    else if ( len > stats->m_indel ) len = stats->m_indel;
+    int bin = stats->m_indel + len;
+    stats->nvaf[bin]++;
+    stats->dvaf[bin] += dvaf;
+}
+
+static void do_sample_stats(args_t *args, stats_t *stats, bcf_sr_t *reader, int matched)
+{
+    bcf_srs_t *files = args->files;
+    bcf1_t *line = reader->buffer[0];
+    bcf_fmt_t *fmt_ptr;
+    int nref_tot = 0, nhet_tot = 0, nalt_tot = 0;
+    int line_type = bcf_get_variant_types(line);
+
+    if ( (fmt_ptr = bcf_get_fmt(reader->header,reader->buffer[0],"GT")) )
+    {
+        bcf_fmt_t *ad_fmt_ptr = bcf_get_variant_types(line)&VCF_INDEL ? bcf_get_fmt(reader->header,reader->buffer[0],"AD") : NULL;
+
+        int ref = bcf_acgt2int(*line->d.allele[0]);
+        int is, n_nref = 0, i_nref = 0;
+        for (is=0; is<args->files->n_smpl; is++)
+        {
+            int ial, jal;
+            int gt = bcf_gt_type(fmt_ptr, reader->samples[is], &ial, &jal);
+            if ( gt==GT_UNKN )
+            {
+                stats->smpl_missing[is]++;
+                continue;
+            }
+            if ( gt==GT_HAPL_R || gt==GT_HAPL_A )
+            {
+                if ( line_type&VCF_INDEL && stats->smpl_frm_shifts )
+                {
+                    assert( ial<line->n_allele );
+                    stats->smpl_frm_shifts[is*3 + args->tmp_frm[ial]]++;
+                }
+                if ( gt == GT_HAPL_R ) stats->smpl_hapRef[is]++;
+                if ( gt == GT_HAPL_A ) stats->smpl_hapAlt[is]++;
+                continue;
+            }
+            if ( gt != GT_HOM_RR ) { n_nref++; i_nref = is; }
+            #if HWE_STATS
+                switch (gt)
+                {
+                    case GT_HOM_RR: nref_tot++; break;
+                    case GT_HET_RA: nhet_tot++; break;
+                    case GT_HET_AA:
+                    case GT_HOM_AA: nalt_tot++; break;
+                }
+            #endif
+            int var_type = 0;
+            if ( ial>0 ) var_type |= bcf_get_variant_type(line,ial);
+            if ( jal>0 ) var_type |= bcf_get_variant_type(line,jal);
+            if ( var_type&VCF_SNP || var_type==VCF_REF )  // count ALT=. as SNP
+            {
+                if ( gt == GT_HET_RA ) stats->smpl_hets[is]++;
+                else if ( gt == GT_HET_AA ) stats->smpl_hets[is]++;
+                else if ( gt == GT_HOM_RR ) stats->smpl_homRR[is]++;
+                else if ( gt == GT_HOM_AA ) stats->smpl_homAA[is]++;
+                if ( gt != GT_HOM_RR && line->d.var[ial].type&VCF_SNP ) // this is safe, bcf_get_variant_types has been already called
+                {
+                    int alt = bcf_acgt2int(*line->d.allele[ial]);
+                    if ( alt<0 ) continue;
+                    if ( abs(ref-alt)==2 )
+                        stats->smpl_ts[is]++;
+                    else
+                        stats->smpl_tv[is]++;
+                }
+            }
+            if ( var_type&VCF_INDEL )
+            {
+                if ( gt != GT_HOM_RR )
+                {
+                    stats->smpl_indels[is]++;
+
+                    if ( gt==GT_HET_RA || gt==GT_HET_AA )
+                    {
+                        int is_ins = 0, is_del = 0;
+                        if ( bcf_get_variant_type(line,ial)&VCF_INDEL )
+                        {
+                            if ( line->d.var[ial].n < 0 ) is_del = 1;
+                            else is_ins = 1;
+                            update_dvaf(stats,line,ad_fmt_ptr,is,ial,jal);
+                        }
+                        if ( bcf_get_variant_type(line,jal)&VCF_INDEL )
+                        {
+                            if ( line->d.var[jal].n < 0 ) is_del = 1;
+                            else is_ins = 1;
+                            update_dvaf(stats,line,ad_fmt_ptr,is,jal,ial);
+                        }
+                        // Note that alt-het genotypes with both ins and del allele are counted twice!!
+                        if ( is_del ) stats->smpl_del_hets[is]++;
+                        if ( is_ins ) stats->smpl_ins_hets[is]++;
+                    }
+                    else if ( gt==GT_HOM_AA )
+                    {
+                        if ( line->d.var[ial].n < 0 ) stats->smpl_del_homs[is]++;
+                        else stats->smpl_ins_homs[is]++;
+                    }
+                }
+                if ( stats->smpl_frm_shifts )
+                {
+                    assert( ial<line->n_allele && jal<line->n_allele );
+                    stats->smpl_frm_shifts[is*3 + args->tmp_frm[ial]]++;
+                    stats->smpl_frm_shifts[is*3 + args->tmp_frm[jal]]++;
+                }
+            }
+        }
+        if ( n_nref==1 ) stats->smpl_sngl[i_nref]++;
+    }
+
+    #if HWE_STATS
+        if ( nhet_tot + nref_tot + nalt_tot )
+        {
+            float het_frac = (float)nhet_tot/(nhet_tot + nref_tot + nalt_tot);
+            int idx = het_frac*(args->naf_hwe - 1);
+//check me: what is this?
+            if ( line->n_allele>1 ) idx += args->naf_hwe*args->tmp_iaf[1];
+            stats->af_hwe[idx]++;
+        }
+    #endif
+
+    if ( (fmt_ptr = bcf_get_fmt(reader->header,reader->buffer[0],"DP")) )
+    {
+        #define BRANCH_INT(type_t,missing,vector_end) { \
+            int is; \
+            for (is=0; is<args->files->n_smpl; is++) \
+            { \
+                type_t *p = (type_t *) (fmt_ptr->p + fmt_ptr->size*is); \
+                if ( *p==vector_end ) continue; \
+                if ( *p!=missing ) \
+                { \
+                    (*idist(&stats->dp, *p))++; \
+                    stats->smpl_ndp[is]++; \
+                    stats->smpl_dp[is] += *p; \
+                } \
+            } \
+        }
+        switch (fmt_ptr->type) {
+            case BCF_BT_INT8:  BRANCH_INT(int8_t,  bcf_int8_missing, bcf_int8_vector_end); break;
+            case BCF_BT_INT16: BRANCH_INT(int16_t, bcf_int16_missing, bcf_int16_vector_end); break;
+            case BCF_BT_INT32: BRANCH_INT(int32_t, bcf_int32_missing, bcf_int32_vector_end); break;
+            default: fprintf(bcftools_stderr, "[E::%s] todo: %d\n", __func__, fmt_ptr->type); bcftools_exit(1); break;
+        }
+        #undef BRANCH_INT
+    }
+    else if ( (fmt_ptr = bcf_get_fmt(reader->header,reader->buffer[0],"AD")) )
+    {
+        #define BRANCH_INT(type_t,missing,vector_end) { \
+            int is,iv; \
+            for (is=0; is<args->files->n_smpl; is++) \
+            { \
+                type_t *p = (type_t *) (fmt_ptr->p + fmt_ptr->size*is); \
+                int dp = 0, has_value = 0; \
+                for (iv=0; iv<fmt_ptr->n; iv++) \
+                { \
+                    if ( p[iv]==vector_end ) break; \
+                    if ( p[iv]==missing ) continue; \
+                    has_value = 1; \
+                    dp += p[iv]; \
+                } \
+                if ( has_value ) \
+                { \
+                    (*idist(&stats->dp, dp))++; \
+                    stats->smpl_ndp[is]++; \
+                    stats->smpl_dp[is] += dp; \
+                } \
+            } \
+        }
+        switch (fmt_ptr->type) {
+            case BCF_BT_INT8:  BRANCH_INT(int8_t,  bcf_int8_missing, bcf_int8_vector_end); break;
+            case BCF_BT_INT16: BRANCH_INT(int16_t, bcf_int16_missing, bcf_int16_vector_end); break;
+            case BCF_BT_INT32: BRANCH_INT(int32_t, bcf_int32_missing, bcf_int32_vector_end); break;
+            default: fprintf(bcftools_stderr, "[E::%s] todo: %d\n", __func__, fmt_ptr->type); bcftools_exit(1); break;
+        }
+        #undef BRANCH_INT
+    }
+
+    if ( matched==3 )
+    {
+        int is;
+        bcf_fmt_t *fmt0, *fmt1;
+        fmt0 = bcf_get_fmt(files->readers[0].header,files->readers[0].buffer[0],"GT"); if ( !fmt0 ) return;
+        fmt1 = bcf_get_fmt(files->readers[1].header,files->readers[1].buffer[0],"GT"); if ( !fmt1 ) return;
+
+        // only the first ALT allele is considered
+        if (args->ntmp_iaf <= 1) return; // Do not consider invariate sites
+        int iaf = args->tmp_iaf[1];
+        int line_type = bcf_get_variant_types(files->readers[0].buffer[0]);
+        gtcmp_t *af_stats = line_type&VCF_SNP ? args->af_gts_snps : args->af_gts_indels;
+        gtcmp_t *smpl_stats = line_type&VCF_SNP ? args->smpl_gts_snps : args->smpl_gts_indels;
+
+        for (is=0; is<files->n_smpl; is++)
+        {
+            // Simplified comparison: only 0/0, 0/1, 1/1 is looked at as the identity of
+            //  actual alleles can be enforced by running without the -c option.
+            int gt0 = bcf_gt_type(fmt0, files->readers[0].samples[is], NULL, NULL);
+            int gt1 = bcf_gt_type(fmt1, files->readers[1].samples[is], NULL, NULL);
+
+            int idx0 = type2stats[gt0];
+            int idx1 = type2stats[gt1];
+            af_stats[iaf].gt2gt[idx0][idx1]++;
+            smpl_stats[is].gt2gt[idx0][idx1]++;
+
+            if ( gt0 == GT_UNKN || gt1 == GT_UNKN ) continue;
+            if ( type2ploidy[gt0]*type2ploidy[gt1] == -1 ) continue;   // cannot compare diploid and haploid genotypes
+
+            float y = type2dosage[gt0];
+            float x = type2dosage[gt1];
+
+            smpl_stats[is].yx += y*x;
+            smpl_stats[is].x  += x;
+            smpl_stats[is].xx += x*x;
+            smpl_stats[is].y  += y;
+            smpl_stats[is].yy += y*y;
+            smpl_stats[is].n  += 1;
+
+            af_stats[iaf].yx += y*x;
+            af_stats[iaf].x  += x;
+            af_stats[iaf].xx += x*x;
+            af_stats[iaf].y  += y;
+            af_stats[iaf].yy += y*y;
+            af_stats[iaf].n  += 1;
+        }
+
+        if ( args->verbose_sites )
+        {
+            int nm = 0, nmm = 0, nrefm = 0;
+            for (is=0; is<files->n_smpl; is++)
+            {
+                int gt = bcf_gt_type(fmt0, files->readers[0].samples[is], NULL, NULL);
+                if ( gt == GT_UNKN ) continue;
+                int gt2 = bcf_gt_type(fmt1, files->readers[1].samples[is], NULL, NULL);
+                if ( gt2 == GT_UNKN ) continue;
+                if ( gt != gt2 )
+                {
+                    nmm++;
+                    bcf_sr_t *reader = &files->readers[0];
+                    fprintf(bcftools_stdout, "DBG\t%s\t%"PRId64"\t%s\t%d\t%d\n",reader->header->id[BCF_DT_CTG][reader->buffer[0]->rid].key,(int64_t) reader->buffer[0]->pos+1,files->samples[is],gt,gt2);
+                }
+                else
+                {
+                    if ( gt!=GT_HOM_RR ) nrefm++;
+                    nm++;
+                }
+            }
+            float nrd = nrefm+nmm ? 100.*nmm/(nrefm+nmm) : 0;
+            fprintf(bcftools_stdout, "PSD\t%s\t%"PRId64"\t%d\t%d\t%f\n", reader->header->id[BCF_DT_CTG][reader->buffer[0]->rid].key,(int64_t) reader->buffer[0]->pos+1,nm,nmm,nrd);
+        }
+    }
+}
+
+static void do_vcf_stats(args_t *args)
+{
+    bcf_srs_t *files = args->files;
+    assert( sizeof(int)>files->nreaders );
+    while ( bcf_sr_next_line(files) )
+    {
+        bcf_sr_t *reader = NULL;
+        bcf1_t *line = NULL;
+        int ret = 0, i, pass = 1;
+        for (i=0; i<files->nreaders; i++)
+        {
+            if ( !bcf_sr_has_line(files,i) ) continue;
+            if ( args->filter[i] )
+            {
+                int is_ok = filter_test(args->filter[i], bcf_sr_get_line(files,i), NULL);
+                if ( args->filter_logic & FLT_EXCLUDE ) is_ok = is_ok ? 0 : 1;
+                if ( !is_ok ) { pass = 0; break; }
+            }
+            ret |= 1<<i;
+            if ( !reader )
+            {
+                reader = &files->readers[i];
+                line = bcf_sr_get_line(files,i);
+            }
+
+        }
+        if ( !pass ) continue;
+
+        int line_type = bcf_get_variant_types(line);
+        init_iaf(args, reader);
+
+        stats_t *stats = &args->stats[ret-1];
+        if ( args->split_by_id && line->d.id[0]=='.' && !line->d.id[1] )
+            stats = &args->stats[1];
+
+        stats->n_records++;
+
+        if ( line_type==VCF_REF )
+            stats->n_noalts++;
+        if ( line_type&VCF_SNP )
+            do_snp_stats(args, stats, reader);
+        if ( line_type&VCF_INDEL )
+            do_indel_stats(args, stats, reader);
+        if ( line_type&VCF_MNP )
+            do_mnp_stats(args, stats, reader);
+        if ( line_type&VCF_OTHER )
+            do_other_stats(args, stats, reader);
+
+        if ( line->n_allele>2 )
+        {
+            stats->n_mals++;
+            if ( line_type == VCF_SNP ) stats->n_snp_mals++;    // note: this will be fooled by C>C,T
+        }
+
+        if ( files->n_smpl )
+            do_sample_stats(args, stats, reader, ret);
+
+        if ( bcf_get_info_int32(reader->header,line,"DP",&args->tmp_iaf,&args->ntmp_iaf)==1 )
+            (*idist(&stats->dp_sites, args->tmp_iaf[0]))++;
+    }
+}
+
+static void print_header(args_t *args)
+{
+    int i;
+    fprintf(bcftools_stdout, "# This file was produced by bcftools stats (%s+htslib-%s) and can be plotted using plot-vcfstats.\n", bcftools_version(),hts_version());
+    fprintf(bcftools_stdout, "# The command line was:\tbcftools %s ", args->argv[0]);
+    for (i=1; i<args->argc; i++)
+        fprintf(bcftools_stdout, " %s",args->argv[i]);
+    fprintf(bcftools_stdout, "\n#\n");
+
+    fprintf(bcftools_stdout, "# Definition of sets:\n# ID\t[2]id\t[3]tab-separated file names\n");
+    if ( args->files->nreaders==1 )
+    {
+        const char *fname = strcmp("-",args->files->readers[0].fname) ? args->files->readers[0].fname : "<STDIN>";
+        if ( args->split_by_id )
+        {
+            fprintf(bcftools_stdout, "ID\t0\t%s:known (sites with ID different from \".\")\n", fname);
+            fprintf(bcftools_stdout, "ID\t1\t%s:novel (sites where ID column is \".\")\n", fname);
+        }
+        else
+            fprintf(bcftools_stdout, "ID\t0\t%s\n", fname);
+    }
+    else
+    {
+        const char *fname0 = strcmp("-",args->files->readers[0].fname) ? args->files->readers[0].fname : "<STDIN>";
+        const char *fname1 = strcmp("-",args->files->readers[1].fname) ? args->files->readers[1].fname : "<STDIN>";
+        fprintf(bcftools_stdout, "ID\t0\t%s\n", fname0);
+        fprintf(bcftools_stdout, "ID\t1\t%s\n", fname1);
+        fprintf(bcftools_stdout, "ID\t2\t%s\t%s\n", fname0,fname1);
+
+        if ( args->verbose_sites )
+        {
+            fprintf(bcftools_stdout, 
+                    "# Verbose per-site discordance output.\n"
+                    "# PSD\t[2]CHROM\t[3]POS\t[4]Number of matches\t[5]Number of mismatches\t[6]NRD\n");
+            fprintf(bcftools_stdout, 
+                    "# Verbose per-site and per-sample output. Genotype codes: %d:HomRefRef, %d:HomAltAlt, %d:HetAltRef, %d:HetAltAlt, %d:haploidRef, %d:haploidAlt\n"
+                    "# DBG\t[2]CHROM\t[3]POS\t[4]Sample\t[5]GT in %s\t[6]GT in %s\n",
+                    GT_HOM_RR, GT_HOM_AA, GT_HET_RA, GT_HET_AA, GT_HAPL_R, GT_HAPL_A, fname0,fname1);
+        }
+    }
+}
+
+#define T2S(x) type2stats[x]
+static void print_stats(args_t *args)
+{
+    int i, j,k, id;
+    fprintf(bcftools_stdout, "# SN, Summary numbers:\n");
+    fprintf(bcftools_stdout, "#   number of records   .. number of data rows in the VCF\n");
+    fprintf(bcftools_stdout, "#   number of no-ALTs   .. reference-only sites, ALT is either \".\" or identical to REF\n");
+    fprintf(bcftools_stdout, "#   number of SNPs      .. number of rows with a SNP\n");
+    fprintf(bcftools_stdout, "#   number of MNPs      .. number of rows with a MNP, such as CC>TT\n");
+    fprintf(bcftools_stdout, "#   number of indels    .. number of rows with an indel\n");
+    fprintf(bcftools_stdout, "#   number of others    .. number of rows with other type, for example a symbolic allele or\n");
+    fprintf(bcftools_stdout, "#                          a complex substitution, such as ACT>TCGA\n");
+    fprintf(bcftools_stdout, "#   number of multiallelic sites     .. number of rows with multiple alternate alleles\n");
+    fprintf(bcftools_stdout, "#   number of multiallelic SNP sites .. number of rows with multiple alternate alleles, all SNPs\n");
+    fprintf(bcftools_stdout, "# \n");
+    fprintf(bcftools_stdout, "#   Note that rows containing multiple types will be counted multiple times, in each\n");
+    fprintf(bcftools_stdout, "#   counter. For example, a row with a SNP and an indel increments both the SNP and\n");
+    fprintf(bcftools_stdout, "#   the indel counter.\n");
+    fprintf(bcftools_stdout, "# \n");
+    fprintf(bcftools_stdout, "# SN\t[2]id\t[3]key\t[4]value\n");
+    for (id=0; id<args->files->nreaders; id++)
+        fprintf(bcftools_stdout, "SN\t%d\tnumber of samples:\t%d\n", id, bcf_hdr_nsamples(args->files->readers[id].header));
+    for (id=0; id<args->nstats; id++)
+    {
+        stats_t *stats = &args->stats[id];
+        fprintf(bcftools_stdout, "SN\t%d\tnumber of records:\t%"PRIu64"\n", id, stats->n_records);
+        fprintf(bcftools_stdout, "SN\t%d\tnumber of no-ALTs:\t%"PRIu64"\n", id, stats->n_noalts);
+        fprintf(bcftools_stdout, "SN\t%d\tnumber of SNPs:\t%"PRIu64"\n", id, stats->n_snps);
+        fprintf(bcftools_stdout, "SN\t%d\tnumber of MNPs:\t%"PRIu64"\n", id, stats->n_mnps);
+        fprintf(bcftools_stdout, "SN\t%d\tnumber of indels:\t%"PRIu64"\n", id, stats->n_indels);
+        fprintf(bcftools_stdout, "SN\t%d\tnumber of others:\t%"PRIu64"\n", id, stats->n_others);
+        fprintf(bcftools_stdout, "SN\t%d\tnumber of multiallelic sites:\t%"PRIu64"\n", id, stats->n_mals);
+        fprintf(bcftools_stdout, "SN\t%d\tnumber of multiallelic SNP sites:\t%"PRIu64"\n", id, stats->n_snp_mals);
+    }
+    fprintf(bcftools_stdout, "# TSTV, transitions/transversions:\n# TSTV\t[2]id\t[3]ts\t[4]tv\t[5]ts/tv\t[6]ts (1st ALT)\t[7]tv (1st ALT)\t[8]ts/tv (1st ALT)\n");
+    for (id=0; id<args->nstats; id++)
+    {
+        stats_t *stats = &args->stats[id];
+        int ts=0,tv=0;
+        for (i=0; i<args->m_af; i++) { ts += stats->af_ts[i]; tv += stats->af_tv[i];  }
+        fprintf(bcftools_stdout, "TSTV\t%d\t%d\t%d\t%.2f\t%d\t%d\t%.2f\n", id,ts,tv,tv?(float)ts/tv:0, stats->ts_alt1,stats->tv_alt1,stats->tv_alt1?(float)stats->ts_alt1/stats->tv_alt1:0);
+    }
+    if ( args->exons_fname )
+    {
+        fprintf(bcftools_stdout, "# FS, Indel frameshifts:\n# FS\t[2]id\t[3]in-frame\t[4]out-frame\t[5]not applicable\t[6]out/(in+out) ratio\t[7]in-frame (1st ALT)\t[8]out-frame (1st ALT)\t[9]not applicable (1st ALT)\t[10]out/(in+out) ratio (1st ALT)\n");
+        for (id=0; id<args->nstats; id++)
+        {
+            int in=args->stats[id].in_frame, out=args->stats[id].out_frame, na=args->stats[id].na_frame;
+            int in1=args->stats[id].in_frame_alt1, out1=args->stats[id].out_frame_alt1, na1=args->stats[id].na_frame_alt1;
+            fprintf(bcftools_stdout, "FS\t%d\t%d\t%d\t%d\t%.2f\t%d\t%d\t%d\t%.2f\n", id, in,out,na,out?(float)out/(in+out):0,in1,out1,na1,out1?(float)out1/(in1+out1):0);
+        }
+    }
+    if ( args->indel_ctx )
+    {
+        fprintf(bcftools_stdout, "# ICS, Indel context summary:\n# ICS\t[2]id\t[3]repeat-consistent\t[4]repeat-inconsistent\t[5]not applicable\t[6]c/(c+i) ratio\n");
+        for (id=0; id<args->nstats; id++)
+        {
+            int nc = 0, ni = 0, na = args->stats[id].n_repeat_na;
+            for (i=0; i<IRC_RLEN; i++)
+            {
+                nc += args->stats[id].n_repeat[i][0] + args->stats[id].n_repeat[i][2];
+                ni += args->stats[id].n_repeat[i][1] + args->stats[id].n_repeat[i][3];
+            }
+            fprintf(bcftools_stdout, "ICS\t%d\t%d\t%d\t%d\t%.4f\n", id, nc,ni,na,nc+ni ? (float)nc/(nc+ni) : 0.0);
+        }
+        fprintf(bcftools_stdout, "# ICL, Indel context by length:\n# ICL\t[2]id\t[3]length of repeat element\t[4]repeat-consistent deletions)\t[5]repeat-inconsistent deletions\t[6]consistent insertions\t[7]inconsistent insertions\t[8]c/(c+i) ratio\n");
+        for (id=0; id<args->nstats; id++)
+        {
+            for (i=1; i<IRC_RLEN; i++)
+            {
+                int nc = args->stats[id].n_repeat[i][0]+args->stats[id].n_repeat[i][2], ni = args->stats[id].n_repeat[i][1]+args->stats[id].n_repeat[i][3];
+                fprintf(bcftools_stdout, "ICL\t%d\t%d\t%d\t%d\t%d\t%d\t%.4f\n", id, i+1,
+                    args->stats[id].n_repeat[i][0],args->stats[id].n_repeat[i][1],args->stats[id].n_repeat[i][2],args->stats[id].n_repeat[i][3],
+                    nc+ni ? (float)nc/(nc+ni) : 0.0);
+            }
+        }
+    }
+    fprintf(bcftools_stdout, "# SiS, Singleton stats:\n# SiS\t[2]id\t[3]allele count\t[4]number of SNPs\t[5]number of transitions\t[6]number of transversions\t[7]number of indels\t[8]repeat-consistent\t[9]repeat-inconsistent\t[10]not applicable\n");
+    for (id=0; id<args->nstats; id++)
+    {
+        stats_t *stats = &args->stats[id];
+        fprintf(bcftools_stdout, "SiS\t%d\t%d\t%d\t%d\t%d\t%d\t%d\t%d\t%d\n", id,1,stats->af_snps[0],stats->af_ts[0],stats->af_tv[0],
+            stats->af_repeats[0][0]+stats->af_repeats[1][0]+stats->af_repeats[2][0],stats->af_repeats[0][0],stats->af_repeats[1][0],stats->af_repeats[2][0]);
+        // put the singletons stats into the first AF bin, note that not all of the stats is transferred (i.e. nrd mismatches)
+        stats->af_snps[1]       += stats->af_snps[0];
+        stats->af_ts[1]         += stats->af_ts[0];
+        stats->af_tv[1]         += stats->af_tv[0];
+        stats->af_repeats[0][1] += stats->af_repeats[0][0];
+        stats->af_repeats[1][1] += stats->af_repeats[1][0];
+        stats->af_repeats[2][1] += stats->af_repeats[2][0];
+    }
+    // move the singletons stats into the first AF bin, singleton stats was collected separately because of init_iaf
+    if ( args->af_gts_snps )
+    {
+        args->af_gts_snps[1].y    += args->af_gts_snps[0].y;
+        args->af_gts_snps[1].yy   += args->af_gts_snps[0].yy;
+        args->af_gts_snps[1].xx   += args->af_gts_snps[0].xx;
+        args->af_gts_snps[1].yx   += args->af_gts_snps[0].yx;
+        args->af_gts_snps[1].n    += args->af_gts_snps[0].n;
+    }
+    if ( args->af_gts_indels )
+    {
+        args->af_gts_indels[1].y  += args->af_gts_indels[0].y;
+        args->af_gts_indels[1].yy += args->af_gts_indels[0].yy;
+        args->af_gts_indels[1].xx += args->af_gts_indels[0].xx;
+        args->af_gts_indels[1].yx += args->af_gts_indels[0].yx;
+        args->af_gts_indels[1].n  += args->af_gts_indels[0].n;
+    }
+
+    fprintf(bcftools_stdout, "# AF, Stats by non-reference allele frequency:\n# AF\t[2]id\t[3]allele frequency\t[4]number of SNPs\t[5]number of transitions\t[6]number of transversions\t[7]number of indels\t[8]repeat-consistent\t[9]repeat-inconsistent\t[10]not applicable\n");
+    for (id=0; id<args->nstats; id++)
+    {
+        stats_t *stats = &args->stats[id];
+        for (i=1; i<args->m_af; i++) // note that af[1] now contains also af[0], see SiS stats output above
+        {
+            if ( stats->af_snps[i]+stats->af_ts[i]+stats->af_tv[i]+stats->af_repeats[0][i]+stats->af_repeats[1][i]+stats->af_repeats[2][i] == 0  ) continue;
+            double af = args->af_bins ? (bin_get_value(args->af_bins,i)+bin_get_value(args->af_bins,i-1))*0.5 : (double)(i-1)/(args->m_af-1);
+            fprintf(bcftools_stdout, "AF\t%d\t%f\t%d\t%d\t%d\t%d\t%d\t%d\t%d\n", id,af,stats->af_snps[i],stats->af_ts[i],stats->af_tv[i],
+                stats->af_repeats[0][i]+stats->af_repeats[1][i]+stats->af_repeats[2][i],stats->af_repeats[0][i],stats->af_repeats[1][i],stats->af_repeats[2][i]);
+        }
+    }
+    #if QUAL_STATS
+        fprintf(bcftools_stdout, "# QUAL, Stats by quality\n# QUAL\t[2]id\t[3]Quality\t[4]number of SNPs\t[5]number of transitions (1st ALT)\t[6]number of transversions (1st ALT)\t[7]number of indels\n");
+        for (id=0; id<args->nstats; id++)
+        {
+            stats_t *stats = &args->stats[id];
+            int ndist_ts = dist_nbins(stats->qual_ts);
+            int ndist_tv = dist_nbins(stats->qual_tv);
+            int ndist_in = dist_nbins(stats->qual_indels);
+            int ndist_max = ndist_ts;
+            if ( ndist_max < ndist_tv ) ndist_max = ndist_tv;
+            if ( ndist_max < ndist_in ) ndist_max = ndist_in;
+            uint32_t beg, end;
+            uint32_t nts, ntv, nin;
+            for (i=0; i<ndist_max; i++)
+            {
+                nts = ntv = nin = 0;
+                float qval = -1;
+                if ( i < ndist_ts )
+                {
+                    nts = dist_get(stats->qual_ts, i, &beg, &end);
+                    qval = beg>0 ? 0.1*(beg - 1) : -1;
+                }
+                if ( i < ndist_tv )
+                {
+                    ntv = dist_get(stats->qual_tv, i, &beg, &end);
+                    if ( qval==-1 ) qval = beg > 0 ? 0.1*(beg - 1) : -1;
+                }
+                if ( i < ndist_in )
+                {
+                    nin = dist_get(stats->qual_indels, i, &beg, &end);
+                    if ( qval==-1 ) qval = beg > 0 ? 0.1*(beg - 1) : -1;
+                }
+                if ( nts+ntv+nin==0 ) continue;
+
+                fprintf(bcftools_stdout, "QUAL\t%d\t",id);
+                if ( qval==-1 ) fprintf(bcftools_stdout, ".");
+                else fprintf(bcftools_stdout, "%.1f",qval);
+                fprintf(bcftools_stdout, "\t%d\t%d\t%d\t%d\n",nts+ntv,nts,ntv,nin);
+            }
+        }
+    #endif
+    for (i=0; i<args->nusr; i++)
+    {
+        fprintf(bcftools_stdout, "# USR:%s/%d\t[2]id\t[3]%s/%d\t[4]number of SNPs\t[5]number of transitions (1st ALT)\t[6]number of transversions (1st ALT)\n",
+            args->usr[i].tag,args->usr[i].idx,args->usr[i].tag,args->usr[i].idx);
+        for (id=0; id<args->nstats; id++)
+        {
+            user_stats_t *usr = &args->stats[id].usr[i];
+            int j;
+            for (j=0; j<usr->nbins; j++)
+            {
+                if ( usr->vals_ts[j]+usr->vals_tv[j] == 0 ) continue;   // skip empty bins
+                float val = usr->min + (usr->max - usr->min)*j/(usr->nbins-1);
+                const char *fmt = usr->type==BCF_HT_REAL ? "USR:%s/%d\t%d\t%e\t%"PRIu64"\t%"PRIu64"\t%"PRIu64"\n" : "USR:%s/%d\t%d\t%.0f\t%"PRIu64"\t%"PRIu64"\t%"PRIu64"\n";
+                fprintf(bcftools_stdout, fmt,usr->tag,usr->idx,id,val,usr->vals_ts[j]+usr->vals_tv[j],usr->vals_ts[j],usr->vals_tv[j]);
+            }
+        }
+    }
+    fprintf(bcftools_stdout, "# IDD, InDel distribution:\n# IDD\t[2]id\t[3]length (deletions negative)\t[4]number of sites\t[5]number of genotypes\t[6]mean VAF\n");
+    for (id=0; id<args->nstats; id++)
+    {
+        stats_t *stats = &args->stats[id];
+        for (i=stats->m_indel-1; i>=0; i--)
+        {
+            if ( !stats->deletions[i] ) continue;
+            // whops, differently organized arrow, dels are together with ins
+            int bin = stats->m_indel - i - 1;
+            fprintf(bcftools_stdout, "IDD\t%d\t%d\t%d\t", id,-i-1,stats->deletions[i]);
+            if ( stats->nvaf && stats->nvaf[bin] )
+                fprintf(bcftools_stdout, "%u\t%.2f",stats->nvaf[bin],stats->dvaf[bin]/stats->nvaf[bin]);
+            else
+                fprintf(bcftools_stdout, "0\t.");
+            fprintf(bcftools_stdout, "\n");
+        }
+        for (i=0; i<stats->m_indel; i++)
+        {
+            if ( !stats->insertions[i] ) continue;
+            int bin = stats->m_indel + i + 1;
+            fprintf(bcftools_stdout, "IDD\t%d\t%d\t%d\t", id,i+1,stats->insertions[i]);
+            if ( stats->nvaf && stats->nvaf[bin] )
+                fprintf(bcftools_stdout, "%u\t%.2f",stats->nvaf[bin],stats->dvaf[bin]/stats->nvaf[bin]);
+            else
+                fprintf(bcftools_stdout, "0\t.");
+            fprintf(bcftools_stdout, "\n");
+        }
+    }
+    fprintf(bcftools_stdout, "# ST, Substitution types:\n# ST\t[2]id\t[3]type\t[4]count\n");
+    for (id=0; id<args->nstats; id++)
+    {
+        int t;
+        for (t=0; t<15; t++)
+        {
+            if ( t>>2 == (t&3) ) continue;
+            fprintf(bcftools_stdout, "ST\t%d\t%c>%c\t%d\n", id, bcf_int2acgt(t>>2),bcf_int2acgt(t&3),args->stats[id].subst[t]);
+        }
+    }
+    if ( args->files->nreaders>1 && args->files->n_smpl )
+    {
+        fprintf(bcftools_stdout, "SN\t%d\tnumber of samples:\t%d\n", 2, args->files->n_smpl);
+
+        int x;
+        for (x=0; x<2; x++)     // x=0: snps, x=1: indels
+        {
+            gtcmp_t *stats;
+            if ( x==0 )
+            {
+                fprintf(bcftools_stdout, "# GCsAF, Genotype concordance by non-reference allele frequency (SNPs)\n# GCsAF\t[2]id\t[3]allele frequency\t[4]RR Hom matches\t[5]RA Het matches\t[6]AA Hom matches\t[7]RR Hom mismatches\t[8]RA Het mismatches\t[9]AA Hom mismatches\t[10]dosage r-squared\t[11]number of genotypes\n");
+                stats = args->af_gts_snps;
+            }
+            else
+            {
+                fprintf(bcftools_stdout, "# GCiAF, Genotype concordance by non-reference allele frequency (indels)\n# GCiAF\t[2]id\t[3]allele frequency\t[4]RR Hom matches\t[5]RA Het matches\t[6]AA Hom matches\t[7]RR Hom mismatches\t[8]RA Het mismatches\t[9]AA Hom mismatches\t[10]dosage r-squared\t[11]number of genotypes\n");
+                stats = args->af_gts_indels;
+            }
+            uint64_t nrd_m[4] = {0,0,0,0}, nrd_mm[4] = {0,0,0,0};   // across all bins
+            for (i=0; i<args->m_af; i++)
+            {
+                int n = 0;
+                uint64_t m[4] = {0,0,0,0}, mm[4] = {0,0,0,0};    // in i-th AF bin
+                for (j=0; j<4; j++)     // rr, ra, aa hom, aa het, ./.
+                    for (k=0; k<4; k++)
+                    {
+                        n += stats[i].gt2gt[j][k];
+                        if ( j==k )
+                        {
+                            nrd_m[j] += stats[i].gt2gt[j][k];
+                            m[j]     += stats[i].gt2gt[j][k];
+                        }
+                        else
+                        {
+                            nrd_mm[j] += stats[i].gt2gt[j][k];
+                            mm[j]     += stats[i].gt2gt[j][k];
+                        }
+                    }
+                if ( !i || !n ) continue;   // skip singleton stats and empty bins
+
+                // Pearson's r2
+                double r2 = 0;
+                if ( stats[i].n )
+                {
+                    r2  = (stats[i].yx - stats[i].x*stats[i].y/stats[i].n);
+                    r2 /= sqrt((stats[i].xx - stats[i].x*stats[i].x/stats[i].n) * (stats[i].yy - stats[i].y*stats[i].y/stats[i].n));
+                    r2 *= r2;
+                }
+                double af = args->af_bins ? (bin_get_value(args->af_bins,i)+bin_get_value(args->af_bins,i-1))*0.5 : (double)(i-1)/(args->m_af-1);
+                fprintf(bcftools_stdout, "GC%cAF\t2\t%f", x==0 ? 's' : 'i', af);
+                fprintf(bcftools_stdout, "\t%"PRIu64"\t%"PRIu64"\t%"PRIu64"", m[T2S(GT_HOM_RR)],m[T2S(GT_HET_RA)],m[T2S(GT_HOM_AA)]);
+                fprintf(bcftools_stdout, "\t%"PRIu64"\t%"PRIu64"\t%"PRIu64"", mm[T2S(GT_HOM_RR)],mm[T2S(GT_HET_RA)],mm[T2S(GT_HOM_AA)]);
+                if ( stats[i].n && !isnan(r2) ) fprintf(bcftools_stdout, "\t%f", r2);
+                else fprintf(bcftools_stdout, "\t"NA_STRING);
+                fprintf(bcftools_stdout, "\t%.0f\n", stats[i].n);
+            }
+
+            if ( x==0 )
+            {
+                fprintf(bcftools_stdout, "# NRD and discordance is calculated as follows:\n");
+                fprintf(bcftools_stdout, "#   m .. number of matches\n");
+                fprintf(bcftools_stdout, "#   x .. number of mismatches\n");
+                fprintf(bcftools_stdout, "#   NRD = 100 * (xRR + xRA + xAA) / (xRR + xRA + xAA + mRA + mAA)\n");
+                fprintf(bcftools_stdout, "#   RR discordance = 100 * xRR / (xRR + mRR)\n");
+                fprintf(bcftools_stdout, "#   RA discordance = 100 * xRA / (xRA + mRA)\n");
+                fprintf(bcftools_stdout, "#   AA discordance = 100 * xAA / (xAA + mAA)\n");
+                fprintf(bcftools_stdout, "# Non-Reference Discordance (NRD), SNPs\n# NRDs\t[2]id\t[3]NRD\t[4]Ref/Ref discordance\t[5]Ref/Alt discordance\t[6]Alt/Alt discordance\n");
+            }
+            else
+                fprintf(bcftools_stdout, "# Non-Reference Discordance (NRD), indels\n# NRDi\t[2]id\t[3]NRD\t[4]Ref/Ref discordance\t[5]Ref/Alt discordance\t[6]Alt/Alt discordance\n");
+            uint64_t m  = nrd_m[T2S(GT_HET_RA)] + nrd_m[T2S(GT_HOM_AA)] + nrd_m[T2S(GT_HET_AA)];
+            uint64_t mm = nrd_mm[T2S(GT_HOM_RR)] + nrd_mm[T2S(GT_HET_RA)] + nrd_mm[T2S(GT_HOM_AA)] + nrd_mm[T2S(GT_HET_AA)];
+            fprintf(bcftools_stdout, "NRD%c\t2\t%f\t%f\t%f\t%f\n", x==0 ? 's' : 'i',
+                    m+mm ? mm*100.0/(m+mm) : 0,
+                    nrd_m[T2S(GT_HOM_RR)]+nrd_mm[T2S(GT_HOM_RR)] ? nrd_mm[T2S(GT_HOM_RR)]*100.0/(nrd_m[T2S(GT_HOM_RR)]+nrd_mm[T2S(GT_HOM_RR)]) : 0,
+                    nrd_m[T2S(GT_HET_RA)]+nrd_mm[T2S(GT_HET_RA)] ? nrd_mm[T2S(GT_HET_RA)]*100.0/(nrd_m[T2S(GT_HET_RA)]+nrd_mm[T2S(GT_HET_RA)]) : 0,
+                    nrd_m[T2S(GT_HOM_AA)]+nrd_mm[T2S(GT_HOM_AA)] ? nrd_mm[T2S(GT_HOM_AA)]*100.0/(nrd_m[T2S(GT_HOM_AA)]+nrd_mm[T2S(GT_HOM_AA)]) : 0
+                  );
+        }
+
+        for (x=0; x<2; x++) // x=0: snps, x=1: indels
+        {
+            gtcmp_t *stats;
+            if ( x==0 )
+            {
+                fprintf(bcftools_stdout, "# GCsS, Genotype concordance by sample (SNPs)\n# GCsS\t[2]id\t[3]sample\t[4]non-reference discordance rate\t[5]RR Hom matches\t[6]RA Het matches\t[7]AA Hom matches\t[8]RR Hom mismatches\t[9]RA Het mismatches\t[10]AA Hom mismatches\t[11]dosage r-squared\n");
+                stats = args->smpl_gts_snps;
+            }
+            else
+            {
+                fprintf(bcftools_stdout, "# GCiS, Genotype concordance by sample (indels)\n# GCiS\t[2]id\t[3]sample\t[4]non-reference discordance rate\t[5]RR Hom matches\t[6]RA Het matches\t[7]AA Hom matches\t[8]RR Hom mismatches\t[9]RA Het mismatches\t[10]AA Hom mismatches\t[11]dosage r-squared\n");
+                stats = args->smpl_gts_indels;
+            }
+            for (i=0; i<args->files->n_smpl; i++)
+            {
+                uint64_t mm = 0, m = stats[i].gt2gt[T2S(GT_HET_RA)][T2S(GT_HET_RA)] + stats[i].gt2gt[T2S(GT_HOM_AA)][T2S(GT_HOM_AA)];
+                for (j=0; j<3; j++)
+                    for (k=0; k<3; k++)
+                        if ( j!=k ) mm += stats[i].gt2gt[j][k];
+
+                // Pearson's r2
+                double r2 = 0;
+                if ( stats[i].n )
+                {
+                    r2  = (stats[i].yx - stats[i].x*stats[i].y/stats[i].n);
+                    r2 /= sqrt((stats[i].xx - stats[i].x*stats[i].x/stats[i].n) * (stats[i].yy - stats[i].y*stats[i].y/stats[i].n));
+                    r2 *= r2;
+                }
+                fprintf(bcftools_stdout, "GC%cS\t2\t%s\t%.3f",  x==0 ? 's' : 'i', args->files->samples[i], m+mm ? mm*100.0/(m+mm) : 0);
+                fprintf(bcftools_stdout, "\t%"PRIu64"\t%"PRIu64"\t%"PRIu64"",
+                    stats[i].gt2gt[T2S(GT_HOM_RR)][T2S(GT_HOM_RR)],
+                    stats[i].gt2gt[T2S(GT_HET_RA)][T2S(GT_HET_RA)],
+                    stats[i].gt2gt[T2S(GT_HOM_AA)][T2S(GT_HOM_AA)]);
+                fprintf(bcftools_stdout, "\t%"PRIu64"\t%"PRIu64"\t%"PRIu64"",
+                    stats[i].gt2gt[T2S(GT_HOM_RR)][T2S(GT_HET_RA)] + stats[i].gt2gt[T2S(GT_HOM_RR)][T2S(GT_HOM_AA)],
+                    stats[i].gt2gt[T2S(GT_HET_RA)][T2S(GT_HOM_RR)] + stats[i].gt2gt[T2S(GT_HET_RA)][T2S(GT_HOM_AA)],
+                    stats[i].gt2gt[T2S(GT_HOM_AA)][T2S(GT_HOM_RR)] + stats[i].gt2gt[T2S(GT_HOM_AA)][T2S(GT_HET_RA)]);
+                if ( stats[i].n && !isnan(r2) ) fprintf(bcftools_stdout, "\t%f\n", r2);
+                else fprintf(bcftools_stdout, "\t"NA_STRING"\n");
+            }
+        }
+        for (x=0; x<2; x++) // x=0: snps, x=1: indels
+        {
+                //printf("# GCiS, Genotype concordance by sample (indels)\n# GCiS\t[2]id\t[3]sample\t[4]non-reference discordance rate\t[5]RR Hom matches\t[6]RA Het matches\t[7]AA Hom matches\t[8]RR Hom mismatches\t[9]RA Het mismatches\t[10]AA Hom mismatches\t[11]dosage r-squared\n");
+
+            gtcmp_t *stats;
+            if ( x==0 )
+            {
+                fprintf(bcftools_stdout, "# GCTs, Genotype concordance table (SNPs)\n# GCTs");
+                stats = args->smpl_gts_snps;
+            }
+            else
+            {
+                fprintf(bcftools_stdout, "# GCTi, Genotype concordance table (indels)\n# GCTi");
+                stats = args->smpl_gts_indels;
+            }
+            i = 1;
+            fprintf(bcftools_stdout, "\t[%d]sample", ++i);
+            fprintf(bcftools_stdout, "\t[%d]RR Hom -> RR Hom", ++i);
+            fprintf(bcftools_stdout, "\t[%d]RR Hom -> RA Het", ++i);
+            fprintf(bcftools_stdout, "\t[%d]RR Hom -> AA Hom", ++i);
+            fprintf(bcftools_stdout, "\t[%d]RR Hom -> AA Het", ++i);
+            fprintf(bcftools_stdout, "\t[%d]RR Hom -> missing", ++i);
+            fprintf(bcftools_stdout, "\t[%d]RA Het -> RR Hom", ++i);
+            fprintf(bcftools_stdout, "\t[%d]RA Het -> RA Het", ++i);
+            fprintf(bcftools_stdout, "\t[%d]RA Het -> AA Hom", ++i);
+            fprintf(bcftools_stdout, "\t[%d]RA Het -> AA Het", ++i);
+            fprintf(bcftools_stdout, "\t[%d]RA Het -> missing", ++i);
+            fprintf(bcftools_stdout, "\t[%d]AA Hom -> RR Hom", ++i);
+            fprintf(bcftools_stdout, "\t[%d]AA Hom -> RA Het", ++i);
+            fprintf(bcftools_stdout, "\t[%d]AA Hom -> AA Hom", ++i);
+            fprintf(bcftools_stdout, "\t[%d]AA Hom -> AA Het", ++i);
+            fprintf(bcftools_stdout, "\t[%d]AA Hom -> missing", ++i);
+            fprintf(bcftools_stdout, "\t[%d]AA Het -> RR Hom", ++i);
+            fprintf(bcftools_stdout, "\t[%d]AA Het -> RA Het", ++i);
+            fprintf(bcftools_stdout, "\t[%d]AA Het -> AA Hom", ++i);
+            fprintf(bcftools_stdout, "\t[%d]AA Het -> AA Het", ++i);
+            fprintf(bcftools_stdout, "\t[%d]AA Het -> missing", ++i);
+            fprintf(bcftools_stdout, "\t[%d]missing -> RR Hom", ++i);
+            fprintf(bcftools_stdout, "\t[%d]missing -> RA Het", ++i);
+            fprintf(bcftools_stdout, "\t[%d]missing -> AA Hom", ++i);
+            fprintf(bcftools_stdout, "\t[%d]missing -> AA Het", ++i);
+            fprintf(bcftools_stdout, "\t[%d]missing -> missing\n", ++i);
+
+            for (i=0; i<args->files->n_smpl; i++)
+            {
+                fprintf(bcftools_stdout, "GCT%c\t%s",  x==0 ? 's' : 'i', args->files->samples[i]);
+                for (j=0; j<5; j++)
+                    for (k=0; k<5; k++)
+                        fprintf(bcftools_stdout, "\t%"PRIu64, stats[i].gt2gt[j][k]);
+                fprintf(bcftools_stdout, "\n");
+            }
+        }
+    }
+
+    fprintf(bcftools_stdout, "# DP, Depth distribution\n# DP\t[2]id\t[3]bin\t[4]number of genotypes\t[5]fraction of genotypes (%%)\t[6]number of sites\t[7]fraction of sites (%%)\n");
+    for (id=0; id<args->nstats; id++)
+    {
+        stats_t *stats = &args->stats[id];
+        long unsigned int sum = 0, sum_sites = 0;
+        for (i=0; i<stats->dp.m_vals; i++) { sum += stats->dp.vals[i]; sum_sites += stats->dp_sites.vals[i]; }
+        for (i=0; i<stats->dp.m_vals; i++)
+        {
+            if ( stats->dp.vals[i]==0 && stats->dp_sites.vals[i]==0 ) continue;
+            fprintf(bcftools_stdout, "DP\t%d\t", id);
+            if ( i==0 ) fprintf(bcftools_stdout, "<%d", stats->dp.min);
+            else if ( i+1==stats->dp.m_vals ) fprintf(bcftools_stdout, ">%d", stats->dp.max);
+            else fprintf(bcftools_stdout, "%d", idist_i2bin(&stats->dp,i));
+            fprintf(bcftools_stdout, "\t%"PRIu64"\t%f", stats->dp.vals[i], sum ? stats->dp.vals[i]*100./sum : 0);
+            fprintf(bcftools_stdout, "\t%"PRIu64"\t%f\n", stats->dp_sites.vals[i], sum_sites ? stats->dp_sites.vals[i]*100./sum_sites : 0);
+        }
+    }
+
+    if ( args->files->n_smpl )
+    {
+        fprintf(bcftools_stdout, "# PSC, Per-sample counts. Note that the ref/het/hom counts include only SNPs, for indels see PSI. The rest include both SNPs and indels.\n");
+        fprintf(bcftools_stdout, "# PSC\t[2]id\t[3]sample\t[4]nRefHom\t[5]nNonRefHom\t[6]nHets\t[7]nTransitions\t[8]nTransversions\t[9]nIndels\t[10]average depth\t[11]nSingletons"
+            "\t[12]nHapRef\t[13]nHapAlt\t[14]nMissing\n");
+        for (id=0; id<args->nstats; id++)
+        {
+            stats_t *stats = &args->stats[id];
+            for (i=0; i<args->files->n_smpl; i++)
+            {
+                float dp = stats->smpl_ndp[i] ? stats->smpl_dp[i]/(float)stats->smpl_ndp[i] : 0;
+                fprintf(bcftools_stdout, "PSC\t%d\t%s\t%d\t%d\t%d\t%d\t%d\t%d\t%.1f\t%d\t%d\t%d\t%d\n", id,args->files->samples[i],
+                    stats->smpl_homRR[i], stats->smpl_homAA[i], stats->smpl_hets[i], stats->smpl_ts[i],
+                    stats->smpl_tv[i], stats->smpl_indels[i],dp, stats->smpl_sngl[i], stats->smpl_hapRef[i],
+                    stats->smpl_hapAlt[i], stats->smpl_missing[i]);
+            }
+        }
+
+        fprintf(bcftools_stdout, "# PSI, Per-Sample Indels. Note that alt-het genotypes with both ins and del allele are counted twice, in both nInsHets and nDelHets.\n");
+        fprintf(bcftools_stdout, "# PSI\t[2]id\t[3]sample\t[4]in-frame\t[5]out-frame\t[6]not applicable\t[7]out/(in+out) ratio\t[8]nInsHets\t[9]nDelHets\t[10]nInsAltHoms\t[11]nDelAltHoms\n");
+        for (id=0; id<args->nstats; id++)
+        {
+            stats_t *stats = &args->stats[id];
+            for (i=0; i<args->files->n_smpl; i++)
+            {
+                int na = 0, in = 0, out = 0;
+                if ( args->exons )
+                {
+                    na  = stats->smpl_frm_shifts[i*3 + 0];
+                    in  = stats->smpl_frm_shifts[i*3 + 1];
+                    out = stats->smpl_frm_shifts[i*3 + 2];
+                }
+                fprintf(bcftools_stdout, "PSI\t%d\t%s\t%d\t%d\t%d\t%.2f\t%d\t%d\t%d\t%d\n", id,args->files->samples[i], in,out,na,in+out?1.0*out/(in+out):0,
+                    stats->smpl_ins_hets[i],stats->smpl_del_hets[i],stats->smpl_ins_homs[i],stats->smpl_del_homs[i]);
+            }
+        }
+
+        #ifdef HWE_STATS
+        fprintf(bcftools_stdout, "# HWE\n# HWE\t[2]id\t[3]1st ALT allele frequency\t[4]Number of observations\t[5]25th percentile\t[6]median\t[7]75th percentile\n");
+        for (id=0; id<args->nstats; id++)
+        {
+            stats_t *stats = &args->stats[id];
+            for (i=0; i<args->naf_hwe; i++) stats->af_hwe[i+args->naf_hwe] += stats->af_hwe[i]; // singletons
+            for (i=1; i<args->m_af; i++)
+            {
+                unsigned int sum_tot = 0, sum_tmp = 0;
+                int j, *ptr = &stats->af_hwe[i*args->naf_hwe];
+                for (j=0; j<args->naf_hwe; j++) sum_tot += ptr[j];
+                if ( !sum_tot ) continue;
+
+                double af = args->af_bins ? (bin_get_value(args->af_bins,i)+bin_get_value(args->af_bins,i-1))*0.5 : (double)(i-1)/(args->m_af-1);
+
+                int nprn = 3;
+                fprintf(bcftools_stdout, "HWE\t%d\t%f\t%d",id,af,sum_tot);
+                for (j=0; j<args->naf_hwe; j++)
+                {
+                    sum_tmp += ptr[j];
+                    float frac = (float)sum_tmp/sum_tot;
+                    if ( frac >= 0.75 )
+                    {
+                        while (nprn>0) { fprintf(bcftools_stdout, "\t%f", (float)j/args->naf_hwe); nprn--; }
+                        break;
+                    }
+                    if ( frac >= 0.5 )
+                    {
+                        while (nprn>1) { fprintf(bcftools_stdout, "\t%f", (float)j/args->naf_hwe); nprn--; }
+                        continue;
+                    }
+                    if ( frac >= 0.25 )
+                    {
+                        while (nprn>2) { fprintf(bcftools_stdout, "\t%f", (float)j/args->naf_hwe); nprn--; }
+                    }
+                }
+                assert(nprn==0);
+                fprintf(bcftools_stdout, "\n");
+            }
+        }
+        #endif
+    }
+}
+
+static void usage(void)
+{
+    fprintf(bcftools_stderr, "\n");
+    fprintf(bcftools_stderr, "About:   Parses VCF or BCF and produces stats which can be plotted using plot-vcfstats.\n");
+    fprintf(bcftools_stderr, "         When two files are given, the program generates separate stats for intersection\n");
+    fprintf(bcftools_stderr, "         and the complements. By default only sites are compared, -s/-S must given to include\n");
+    fprintf(bcftools_stderr, "         also sample columns.\n");
+    fprintf(bcftools_stderr, "Usage:   bcftools stats [options] <A.vcf.gz> [<B.vcf.gz>]\n");
+    fprintf(bcftools_stderr, "\n");
+    fprintf(bcftools_stderr, "Options:\n");
+    fprintf(bcftools_stderr, "        --af-bins LIST               Allele frequency bins, a list (0.1,0.5,1) or a file (0.1\\n0.5\\n1)\n");
+    fprintf(bcftools_stderr, "        --af-tag STRING              Allele frequency tag to use, by default estimated from AN,AC or GT\n");
+    fprintf(bcftools_stderr, "    -1, --1st-allele-only            Include only 1st allele at multiallelic sites\n");
+    fprintf(bcftools_stderr, "    -c, --collapse STRING            Treat as identical records with <snps|indels|both|all|some|none>, see man page for details [none]\n");
+    fprintf(bcftools_stderr, "    -d, --depth INT,INT,INT          Depth distribution: min,max,bin size [0,500,1]\n");
+    fprintf(bcftools_stderr, "    -e, --exclude EXPR               Exclude sites for which the expression is true (see man page for details)\n");
+    fprintf(bcftools_stderr, "    -E, --exons FILE.gz              Tab-delimited file with exons for indel frameshifts (chr,beg,end; 1-based, inclusive, bgzip compressed)\n");
+    fprintf(bcftools_stderr, "    -f, --apply-filters LIST         Require at least one of the listed FILTER strings (e.g. \"PASS,.\")\n");
+    fprintf(bcftools_stderr, "    -F, --fasta-ref FILE             Faidx indexed reference sequence file to determine INDEL context\n");
+    fprintf(bcftools_stderr, "    -i, --include EXPR               Select sites for which the expression is true (see man page for details)\n");
+    fprintf(bcftools_stderr, "    -I, --split-by-ID                Collect stats for sites with ID separately (known vs novel)\n");
+    fprintf(bcftools_stderr, "    -r, --regions REGION             Restrict to comma-separated list of regions\n");
+    fprintf(bcftools_stderr, "    -R, --regions-file FILE          Restrict to regions listed in a file\n");
+    fprintf(bcftools_stderr, "        --regions-overlap 0|1|2      Include if POS in the region (0), record overlaps (1), variant overlaps (2) [1]\n");
+    fprintf(bcftools_stderr, "    -s, --samples LIST               List of samples for sample stats, \"-\" to include all samples\n");
+    fprintf(bcftools_stderr, "    -S, --samples-file FILE          File of samples to include\n");
+    fprintf(bcftools_stderr, "    -t, --targets REGION             Similar to -r but streams rather than index-jumps\n");
+    fprintf(bcftools_stderr, "    -T, --targets-file FILE          Similar to -R but streams rather than index-jumps\n");
+    fprintf(bcftools_stderr, "        --targets-overlap 0|1|2      Include if POS in the region (0), record overlaps (1), variant overlaps (2) [0]\n");
+    fprintf(bcftools_stderr, "    -u, --user-tstv TAG[:min:max:n]  Collect Ts/Tv stats for any tag using the given binning [0:1:100]\n");
+    fprintf(bcftools_stderr, "                                       A subfield can be selected as e.g. 'PV4[0]', here the first value of the PV4 tag\n");
+    fprintf(bcftools_stderr, "        --threads INT                Use multithreading with <int> worker threads [0]\n");
+    fprintf(bcftools_stderr, "    -v, --verbose                    Produce verbose per-site and per-sample output\n");
+    fprintf(bcftools_stderr, "\n");
+    bcftools_exit(1);
+}
+
+int main_vcfstats(int argc, char *argv[])
+{
+    int c;
+    args_t *args = (args_t*) calloc(1,sizeof(args_t));
+    args->files  = bcf_sr_init();
+    args->argc   = argc; args->argv = argv;
+    args->dp_min = 0; args->dp_max = 500; args->dp_step = 1;
+    int regions_is_file = 0, targets_is_file = 0;
+    int regions_overlap = 1;
+    int targets_overlap = 0;
+
+    static struct option loptions[] =
+    {
+        {"af-bins",1,0,1},
+        {"af-tag",1,0,2},
+        {"1st-allele-only",0,0,'1'},
+        {"include",1,0,'i'},
+        {"exclude",1,0,'e'},
+        {"help",0,0,'h'},
+        {"collapse",1,0,'c'},
+        {"regions",1,0,'r'},
+        {"regions-file",1,0,'R'},
+        {"regions-overlap",required_argument,NULL,3},
+        {"verbose",0,0,'v'},
+        {"depth",1,0,'d'},
+        {"apply-filters",1,0,'f'},
+        {"exons",1,0,'E'},
+        {"samples",1,0,'s'},
+        {"samples-file",1,0,'S'},
+        {"split-by-ID",0,0,'I'},
+        {"targets",1,0,'t'},
+        {"targets-file",1,0,'T'},
+        {"targets-overlap",required_argument,NULL,4},
+        {"fasta-ref",1,0,'F'},
+        {"user-tstv",1,0,'u'},
+        {"threads",1,0,9},
+        {0,0,0,0}
+    };
+    while ((c = getopt_long(argc, argv, "hc:r:R:e:s:S:d:i:t:T:F:f:1u:vIE:",loptions,NULL)) >= 0) {
+        switch (c) {
+            case  1 : args->af_bins_list = optarg; break;
+            case  2 : args->af_tag = optarg; break;
+            case 'u': add_user_stats(args,optarg); break;
+            case '1': args->first_allele_only = 1; break;
+            case 'F': args->ref_fname = optarg; break;
+            case 't': args->targets_list = optarg; break;
+            case 'T': args->targets_list = optarg; targets_is_file = 1; break;
+            case 'c':
+                if ( !strcmp(optarg,"snps") ) args->files->collapse |= COLLAPSE_SNPS;
+                else if ( !strcmp(optarg,"indels") ) args->files->collapse |= COLLAPSE_INDELS;
+                else if ( !strcmp(optarg,"both") ) args->files->collapse |= COLLAPSE_SNPS | COLLAPSE_INDELS;
+                else if ( !strcmp(optarg,"any") ) args->files->collapse |= COLLAPSE_ANY;
+                else if ( !strcmp(optarg,"all") ) args->files->collapse |= COLLAPSE_ANY;
+                else if ( !strcmp(optarg,"some") ) args->files->collapse |= COLLAPSE_SOME;
+                else if ( !strcmp(optarg,"none") ) args->files->collapse = COLLAPSE_NONE;
+                else error("The --collapse string \"%s\" not recognised.\n", optarg);
+                break;
+            case 'v': args->verbose_sites = 1; break;
+            case 'd':
+                if ( sscanf(optarg,"%d,%d,%d",&args->dp_min,&args->dp_max,&args->dp_step)!=3 )
+                    error("Could not parse --depth %s\n", optarg);
+                if ( args->dp_min<0 || args->dp_min >= args->dp_max || args->dp_step > args->dp_max - args->dp_min + 1 )
+                    error("Is this a typo? --depth %s\n", optarg);
+                break;
+            case 'f': args->files->apply_filters = optarg; break;
+            case 'r': args->regions_list = optarg; break;
+            case 'R': args->regions_list = optarg; regions_is_file = 1; break;
+            case 'E': args->exons_fname = optarg; break;
+            case 's': args->samples_list = optarg; break;
+            case 'S': args->samples_list = optarg; args->samples_is_file = 1; break;
+            case 'I': args->split_by_id = 1; break;
+            case 'e':
+                if ( args->filter_str ) error("Error: only one -i or -e expression can be given, and they cannot be combined\n");
+                args->filter_str = optarg; args->filter_logic |= FLT_EXCLUDE; break;
+            case 'i':
+                if ( args->filter_str ) error("Error: only one -i or -e expression can be given, and they cannot be combined\n");
+                args->filter_str = optarg; args->filter_logic |= FLT_INCLUDE; break;
+            case  3 :
+                regions_overlap = parse_overlap_option(optarg);
+                if ( regions_overlap < 0 ) error("Could not parse: --regions-overlap %s\n",optarg);
+                break;
+            case  4 :
+                targets_overlap = parse_overlap_option(optarg);
+                if ( targets_overlap < 0 ) error("Could not parse: --targets-overlap %s\n",optarg);
+                break;
+            case  9 : args->n_threads = strtol(optarg, 0, 0); break;
+            case 'h':
+            case '?': usage(); break;
+            default: error("Unknown argument: %s\n", optarg);
+        }
+    }
+    char *fname = NULL;
+    if ( optind==argc )
+    {
+        if ( !isatty(fileno((FILE *)stdin)) ) fname = "-";  // reading from stdin
+        else usage();
+    }
+    else fname = argv[optind];
+
+    if ( argc-optind>2 ) usage();
+    if ( argc-optind>1 )
+    {
+        args->files->require_index = 1;
+        if ( args->split_by_id ) error("Only one file can be given with -i.\n");
+    }
+    if ( !args->samples_list ) args->files->max_unpack = BCF_UN_INFO;
+    if ( args->targets_list )
+    {
+        bcf_sr_set_opt(args->files,BCF_SR_TARGETS_OVERLAP,targets_overlap);
+        if ( bcf_sr_set_targets(args->files, args->targets_list, targets_is_file, 0)<0 )
+            error("Failed to read the targets: %s\n", args->targets_list);
+    }
+    if ( args->regions_list)
+    {
+        bcf_sr_set_opt(args->files,BCF_SR_REGIONS_OVERLAP,regions_overlap);
+        if ( bcf_sr_set_regions(args->files, args->regions_list, regions_is_file)<0 )
+            error("Failed to read the regions: %s\n", args->regions_list);
+    }
+    if ( args->n_threads && bcf_sr_set_threads(args->files, args->n_threads)<0)
+        error("Failed to create threads\n");
+
+    while (fname)
+    {
+        if ( !bcf_sr_add_reader(args->files, fname) )
+            error("Failed to read from %s: %s\n", !strcmp("-",fname)?"standard input":fname,bcf_sr_strerror(args->files->errnum));
+        fname = ++optind < argc ? argv[optind] : NULL;
+    }
+
+    init_stats(args);
+    print_header(args);
+    do_vcf_stats(args);
+    print_stats(args);
+    destroy_stats(args);
+    bcf_sr_destroy(args->files);
+    free(args);
+    return 0;
+}
+
diff --git a/bcftools/vcfview.c b/bcftools/vcfview.c
new file mode 100644
index 0000000..cc02058
--- /dev/null
+++ b/bcftools/vcfview.c
@@ -0,0 +1,801 @@
+/*  vcfview.c -- VCF/BCF conversion, view, subset and filter VCF/BCF files.
+
+    Copyright (C) 2013-2021 Genome Research Ltd.
+
+    Author: Shane McCarthy <sm15@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.  */
+
+#include <stdio.h>
+#include <strings.h>
+#include <unistd.h>
+#include <getopt.h>
+#include <ctype.h>
+#include <string.h>
+#include <errno.h>
+#include <sys/stat.h>
+#include <sys/types.h>
+#include <math.h>
+#include <inttypes.h>
+#include <htslib/vcf.h>
+#include <htslib/synced_bcf_reader.h>
+#include <htslib/vcfutils.h>
+#include "bcftools.h"
+#include "filter.h"
+#include "htslib/khash_str2int.h"
+
+#define FLT_INCLUDE 1
+#define FLT_EXCLUDE 2
+
+#define ALLELE_NONREF 1
+#define ALLELE_MINOR 2
+#define ALLELE_ALT1 3
+#define ALLELE_MAJOR 4
+#define ALLELE_NONMAJOR 5
+
+#define GT_NEED_HOM 1
+#define GT_NEED_HET 2
+#define GT_NO_HOM   3
+#define GT_NO_HET   4
+#define GT_NEED_MISSING 5
+#define GT_NO_MISSING 6
+
+typedef struct _args_t
+{
+    filter_t *filter;
+    char *filter_str;
+    int filter_logic;   // one of FLT_INCLUDE/FLT_EXCLUDE (-i or -e)
+
+    bcf_srs_t *files;
+    bcf_hdr_t *hdr, *hnull, *hsub; // original header, sites-only header, subset header
+    char **argv, *format, *sample_names, *subset_fname, *targets_list, *regions_list;
+    int regions_overlap, targets_overlap;
+    int argc, clevel, n_threads, output_type, print_header, update_info, header_only, n_samples, *imap, calc_ac;
+    int trim_alts, sites_only, known, novel, min_alleles, max_alleles, private_vars, uncalled, phased;
+    int min_ac, min_ac_type, max_ac, max_ac_type, min_af_type, max_af_type, gt_type;
+    int *ac, mac;
+    float min_af, max_af;
+    char *fn_ref, *fn_out, **samples;
+    int sample_is_file, force_samples;
+    char *include_types, *exclude_types;
+    int include, exclude;
+    int record_cmd_line;
+    htsFile *out;
+}
+args_t;
+
+static void init_data(args_t *args)
+{
+    int i;
+    args->hdr = args->files->readers[0].header;
+
+    if (args->calc_ac && args->update_info)
+    {
+        if (bcf_hdr_append(args->hdr,"##INFO=<ID=AC,Number=A,Type=Integer,Description=\"Allele count in genotypes\">") < 0)
+            error_errno("[%s] Failed to add \"AC\" INFO header", __func__);
+        if (bcf_hdr_append(args->hdr,"##INFO=<ID=AN,Number=1,Type=Integer,Description=\"Total number of alleles in called genotypes\">") < 0)
+            error_errno("[%s] Failed to add \"AN\" INFO header", __func__);
+    }
+    if (args->record_cmd_line) bcf_hdr_append_version(args->hdr, args->argc, args->argv, "bcftools_view");
+    else if (bcf_hdr_sync(args->hdr) < 0)
+        error_errno("[%s] Failed to update header", __func__);
+
+    // setup sample data
+    if (args->sample_names)
+    {
+        void *hdr_samples = khash_str2int_init();
+        for (i=0; i<bcf_hdr_nsamples(args->hdr); i++)
+            khash_str2int_inc(hdr_samples, bcf_hdr_int2id(args->hdr,BCF_DT_SAMPLE,i));
+
+        void *exclude = (args->sample_names[0]=='^') ? khash_str2int_init() : NULL;
+        int nsmpl;
+        char **smpl = NULL;
+        args->samples = NULL; args->n_samples = 0;
+        smpl = hts_readlist(exclude ? &args->sample_names[1] : args->sample_names, args->sample_is_file, &nsmpl);
+        if ( !smpl )
+        {
+            error("Could not read the list: \"%s\"\n", exclude ? &args->sample_names[1] : args->sample_names);
+        }
+
+        if ( exclude )
+        {
+            for (i=0; i<nsmpl; i++) {
+                if (!khash_str2int_has_key(hdr_samples,smpl[i])) {
+                    if (args->force_samples) {
+                        fprintf(stderr, "Warn: exclude called for sample that does not exist in header: \"%s\"... skipping\n", smpl[i]);
+                    } else {
+                        error("Error: exclude called for sample that does not exist in header: \"%s\". Use \"--force-samples\" to ignore this error.\n", smpl[i]);
+                    }
+                }
+                khash_str2int_inc(exclude, smpl[i]);
+            }
+
+            for (i=0; i<bcf_hdr_nsamples(args->hdr); i++)
+            {
+                if ( exclude && khash_str2int_has_key(exclude,bcf_hdr_int2id(args->hdr,BCF_DT_SAMPLE,i))  ) continue;
+                args->samples = (char**) realloc(args->samples, (args->n_samples+1)*sizeof(const char*));
+                args->samples[args->n_samples++] = strdup(bcf_hdr_int2id(args->hdr,BCF_DT_SAMPLE,i));
+            }
+            khash_str2int_destroy(exclude);
+        }
+        else
+        {
+            for (i=0; i<nsmpl; i++) {
+                if (!khash_str2int_has_key(hdr_samples,smpl[i])) {
+                    if (args->force_samples) {
+                        fprintf(stderr, "Warn: subset called for sample that does not exist in header: \"%s\"... skipping\n", smpl[i]);
+                        continue;
+                    } else {
+                        error("Error: subset called for sample that does not exist in header: \"%s\". Use \"--force-samples\" to ignore this error.\n", smpl[i]);
+                    }
+                }
+                args->samples = (char**) realloc(args->samples, (args->n_samples+1)*sizeof(const char*));
+                args->samples[args->n_samples++] = strdup(smpl[i]);
+            }
+        }
+        for (i=0; i<nsmpl; i++) free(smpl[i]);
+        free(smpl);
+        khash_str2int_destroy(hdr_samples);
+        if (args->n_samples == 0) {
+            fprintf(stderr, "Warn: subsetting has removed all samples\n");
+            args->sites_only = 1;
+        }
+    }
+
+    if (args->n_samples)
+        args->imap = (int*)malloc(args->n_samples * sizeof(int));
+
+    // determine variant types to include/exclude
+    if (args->include_types || args->exclude_types) {
+        if (args->include_types && args->exclude_types) {
+            fprintf(stderr, "Error: only supply one of --include-types, --exclude-types options\n");
+            exit(1);
+        }
+        char **type_list = 0;
+        int m = 0, n = 0;
+        const char *q, *p;
+        for (q = p = args->include_types ? args->include_types : args->exclude_types;; ++p) {
+            if (*p == ',' || *p == 0) {
+                if (m == n) {
+                    m = m? m<<1 : 16;
+                    type_list = (char**)realloc(type_list, m * sizeof(char*));
+                }
+                type_list[n] = (char*)calloc(p - q + 1, 1);
+                strncpy(type_list[n++], q, p - q);
+                q = p + 1;
+                if (*p == 0) break;
+            }
+        }
+        type_list = (char**)realloc(type_list, n * sizeof(char*));
+
+        if (args->include_types) {
+            args->include = 0;
+            for (i = 0; i < n; ++i) {
+                if (strcmp(type_list[i], "snps") == 0) args->include |= VCF_SNP<<1;
+                else if (strcmp(type_list[i], "indels") == 0) args->include |= VCF_INDEL<<1;
+                else if (strcmp(type_list[i], "mnps") == 0) args->include |= VCF_MNP<<1;
+                else if (strcmp(type_list[i], "other") == 0) args->include |= VCF_OTHER<<1;
+                else if (strcmp(type_list[i], "ref") == 0) args->include |= VCF_OTHER<<1;
+                else if (strcmp(type_list[i], "bnd") == 0) args->include |= VCF_BND<<1;
+                else {
+                    fprintf(stderr, "[E::%s] unknown type\n", type_list[i]);
+                    fprintf(stderr, "Accepted types are snps, indels, mnps, other\n");
+                    exit(1);
+                }
+            }
+        }
+        if (args->exclude_types) {
+            args->exclude = 0;
+            for (i = 0; i < n; ++i) {
+                if (strcmp(type_list[i], "snps") == 0) args->exclude |= VCF_SNP<<1;
+                else if (strcmp(type_list[i], "indels") == 0) args->exclude |= VCF_INDEL<<1;
+                else if (strcmp(type_list[i], "mnps") == 0) args->exclude |= VCF_MNP<<1;
+                else if (strcmp(type_list[i], "other") == 0) args->exclude |= VCF_OTHER<<1;
+                else if (strcmp(type_list[i], "ref") == 0) args->exclude |= VCF_OTHER<<1;
+                else if (strcmp(type_list[i], "bnd") == 0) args->exclude |= VCF_BND<<1;
+                else {
+                    fprintf(stderr, "[E::%s] unknown type\n", type_list[i]);
+                    fprintf(stderr, "Accepted types are snps, indels, mnps, other\n");
+                    exit(1);
+                }
+            }
+        }
+        for (i = 0; i < n; ++i)
+            free(type_list[i]);
+        free(type_list);
+    }
+
+    char wmode[8];
+    set_wmode(wmode,args->output_type,args->fn_out,args->clevel);
+    args->out = hts_open(args->fn_out ? args->fn_out : "-", wmode);
+    if ( !args->out ) error("%s: %s\n", args->fn_out,strerror(errno));
+    if ( args->n_threads > 0)
+        hts_set_opt(args->out, HTS_OPT_THREAD_POOL, args->files->p);
+
+    // headers: hdr=full header, hsub=subset header, hnull=sites only header
+    if (args->sites_only){
+        args->hnull = bcf_hdr_subset(args->hdr, 0, 0, 0);
+        bcf_hdr_remove(args->hnull, BCF_HL_FMT, NULL);
+    }
+    if (args->n_samples > 0)
+    {
+        args->hsub = bcf_hdr_subset(args->hdr, args->n_samples, args->samples, args->imap);
+        if ( !args->hsub ) error("Error occurred while subsetting samples\n");
+        if ( args->n_samples != bcf_hdr_nsamples(args->hsub) )
+        {
+            int i;
+            for (i=0; i<args->n_samples; i++)
+                if ( args->imap[i]<0 ) error("Error: No such sample: \"%s\"\n", args->samples[i]);
+        }
+    }
+
+    if ( args->filter_str )
+        args->filter = filter_init(args->hdr, args->filter_str);
+}
+
+static void destroy_data(args_t *args)
+{
+    int i;
+    if ( args->imap ) {
+        for (i = 0; i < args->n_samples; ++i)
+            free(args->samples[i]);
+        free(args->samples);
+        free(args->imap);
+    }
+    if (args->hnull) bcf_hdr_destroy(args->hnull);
+    if (args->hsub) bcf_hdr_destroy(args->hsub);
+    if ( args->filter )
+        filter_destroy(args->filter);
+    free(args->ac);
+}
+
+// true if all samples are phased.
+// haploid genotypes are considered phased
+// ./. => not phased, .|. => phased
+int bcf_all_phased(const bcf_hdr_t *header, bcf1_t *line)
+{
+    bcf_unpack(line, BCF_UN_FMT);
+    bcf_fmt_t *fmt_ptr = bcf_get_fmt(header, line, "GT");
+    int all_phased = 1;
+    if ( fmt_ptr )
+    {
+        int i, isample;
+        for (isample=0; isample<line->n_sample; isample++)
+        {
+            int sample_phased = 0;
+            #define BRANCH_INT(type_t,vector_end) { \
+                type_t *p = (type_t*) (fmt_ptr->p + isample*fmt_ptr->size); \
+                for (i=0; i<fmt_ptr->n; i++) \
+                { \
+                    if (fmt_ptr->n == 1 || (p[i] == vector_end && i == 1)) { sample_phased = 1; break; } /* haploid phased by definition */ \
+                    if ( p[i] == vector_end ) { break; }; /* smaller ploidy */ \
+                    if ( bcf_gt_is_missing(p[i]) ) continue; /* missing allele */ \
+                    if ((p[i])&1) { \
+                        sample_phased = 1; \
+                        break; \
+                    } \
+                } \
+            }
+            switch (fmt_ptr->type) {
+                case BCF_BT_INT8:  BRANCH_INT(int8_t,  bcf_int8_vector_end); break;
+                case BCF_BT_INT16: BRANCH_INT(int16_t, bcf_int16_vector_end); break;
+                case BCF_BT_INT32: BRANCH_INT(int32_t, bcf_int32_vector_end); break;
+                default: fprintf(stderr, "[E::%s] todo: fmt_type %d\n", __func__, fmt_ptr->type); exit(1); break;
+            }
+            #undef BRANCH_INT
+            if (!sample_phased) {
+                all_phased = 0;
+                break;
+            }
+        }
+    }
+    return all_phased;
+}
+
+int subset_vcf(args_t *args, bcf1_t *line)
+{
+    if ( args->min_alleles && line->n_allele < args->min_alleles ) return 0; // min alleles
+    if ( args->max_alleles && line->n_allele > args->max_alleles ) return 0; // max alleles
+    if (args->novel || args->known)
+    {
+        if ( args->novel && (line->d.id[0]!='.' || line->d.id[1]!=0) ) return 0; // skip sites which are known, ID != '.'
+        if ( args->known && line->d.id[0]=='.' && line->d.id[1]==0 ) return 0;  // skip sites which are novel, ID == '.'
+    }
+
+    if (args->include || args->exclude)
+    {
+        int line_type = bcf_get_variant_types(line);
+        if ( args->include && !((line_type<<1) & args->include) ) return 0; // include only given variant types
+        if ( args->exclude &&   (line_type<<1) & args->exclude  ) return 0; // exclude given variant types
+    }
+
+    if ( args->filter )
+    {
+        int ret = filter_test(args->filter, line, NULL);
+        if ( args->filter_logic==FLT_INCLUDE ) { if ( !ret ) return 0; }
+        else if ( ret ) return 0;
+    }
+
+    hts_expand(int, line->n_allele, args->mac, args->ac);
+    int i, an = 0, non_ref_ac = 0;
+    if (args->calc_ac) {
+        bcf_calc_ac(args->hdr, line, args->ac, BCF_UN_INFO|BCF_UN_FMT); // get original AC and AN values from INFO field if available, otherwise calculate
+        for (i=1; i<line->n_allele; i++)
+            non_ref_ac += args->ac[i];
+        for (i=0; i<line->n_allele; i++)
+            an += args->ac[i];
+    }
+
+    int update_ac = args->calc_ac;
+    if (args->n_samples)
+    {
+        int non_ref_ac_sub = 0, *ac_sub = (int*) calloc(line->n_allele,sizeof(int));
+        bcf_subset(args->hdr, line, args->n_samples, args->imap);
+        if ( args->calc_ac && !bcf_get_fmt(args->hdr,line,"GT") ) update_ac = 0;
+        if ( update_ac )
+        {
+            bcf_calc_ac(args->hsub, line, ac_sub, BCF_UN_FMT); // recalculate AC and AN
+            an = 0;
+            for (i=0; i<line->n_allele; i++) {
+                args->ac[i] = ac_sub[i];
+                an += ac_sub[i];
+            }
+            for (i=1; i<line->n_allele; i++)
+                non_ref_ac_sub += ac_sub[i];
+            if (args->private_vars) {
+                if (args->private_vars == FLT_INCLUDE && !(non_ref_ac_sub > 0 && non_ref_ac == non_ref_ac_sub)) { free(ac_sub); return 0; } // select private sites
+                if (args->private_vars == FLT_EXCLUDE && non_ref_ac_sub > 0 && non_ref_ac == non_ref_ac_sub) { free(ac_sub); return 0; } // exclude private sites
+            }
+            non_ref_ac = non_ref_ac_sub;
+        }
+        free(ac_sub);
+    }
+
+    bcf_fmt_t *gt_fmt;
+    if ( args->gt_type && (gt_fmt=bcf_get_fmt(args->hdr,line,"GT")) )
+    {
+        int nhet = 0, nhom = 0, nmiss = 0;
+        for (i=0; i<bcf_hdr_nsamples(args->hdr); i++)
+        {
+            int type = bcf_gt_type(gt_fmt,i,NULL,NULL);
+            if ( type==GT_HET_RA || type==GT_HET_AA )
+            {
+                if ( args->gt_type==GT_NO_HET ) return 0;
+                nhet = 1;
+            }
+            else if ( type==GT_UNKN )
+            {
+                if ( args->gt_type==GT_NO_MISSING ) return 0;
+                nmiss = 1;
+            }
+            else
+            {
+                if ( args->gt_type==GT_NO_HOM ) return 0;
+                nhom = 1;
+            }
+        }
+        if ( args->gt_type==GT_NEED_HOM && !nhom ) return 0;
+        else if ( args->gt_type==GT_NEED_HET && !nhet ) return 0;
+        else if ( args->gt_type==GT_NEED_MISSING && !nmiss ) return 0;
+    }
+
+    int minor_ac = 0;
+    int major_ac = 0;
+    if ( args->calc_ac )
+    {
+        minor_ac = args->ac[0];
+        major_ac = args->ac[0];
+        for (i=1; i<line->n_allele; i++){
+            if (args->ac[i] < minor_ac) { minor_ac = args->ac[i]; }
+            if (args->ac[i] > major_ac) { major_ac = args->ac[i]; }
+        }
+    }
+
+    if (args->min_ac!=-1)
+    {
+        if (args->min_ac_type == ALLELE_NONREF && args->min_ac>non_ref_ac) return 0; // min AC
+        else if (args->min_ac_type == ALLELE_MINOR && args->min_ac>minor_ac) return 0; // min minor AC
+        else if (args->min_ac_type == ALLELE_ALT1 && args->min_ac>args->ac[1]) return 0; // min 1st alternate AC
+        else if (args->min_ac_type == ALLELE_MAJOR && args->min_ac > major_ac) return 0; // min major AC
+        else if (args->min_ac_type == ALLELE_NONMAJOR && args->min_ac > an-major_ac) return 0; // min non-major AC
+    }
+    if (args->max_ac!=-1)
+    {
+        if (args->max_ac_type == ALLELE_NONREF && args->max_ac<non_ref_ac) return 0; // max AC
+        else if (args->max_ac_type == ALLELE_MINOR && args->max_ac<minor_ac) return 0; // max minor AC
+        else if (args->max_ac_type == ALLELE_ALT1 && args->max_ac<args->ac[1]) return 0; // max 1st alternate AC
+        else if (args->max_ac_type == ALLELE_MAJOR && args->max_ac < major_ac) return 0; // max major AC
+        else if (args->max_ac_type == ALLELE_NONMAJOR && args->max_ac < an-major_ac) return 0; // max non-major AC
+    }
+    if (args->min_af!=-1)
+    {
+        if (an == 0) return 0; // freq not defined, skip site
+        if (args->min_af_type == ALLELE_NONREF && args->min_af>non_ref_ac/(double)an) return 0; // min AF
+        else if (args->min_af_type == ALLELE_MINOR && args->min_af>minor_ac/(double)an) return 0; // min minor AF
+        else if (args->min_af_type == ALLELE_ALT1 && args->min_af>args->ac[1]/(double)an) return 0; // min 1st alternate AF
+        else if (args->min_af_type == ALLELE_MAJOR && args->min_af > major_ac/(double)an) return 0; // min major AF
+        else if (args->min_af_type == ALLELE_NONMAJOR && args->min_af > (an-major_ac)/(double)an) return 0; // min non-major AF
+    }
+    if (args->max_af!=-1)
+    {
+        if (an == 0) return 0; // freq not defined, skip site
+        if (args->max_af_type == ALLELE_NONREF && args->max_af<non_ref_ac/(double)an) return 0; // max AF
+        else if (args->max_af_type == ALLELE_MINOR && args->max_af<minor_ac/(double)an) return 0; // max minor AF
+        else if (args->max_af_type == ALLELE_ALT1 && args->max_af<args->ac[1]/(double)an) return 0; // max 1st alternate AF
+        else if (args->max_af_type == ALLELE_MAJOR && args->max_af < major_ac/(double)an) return 0; // max major AF
+        else if (args->max_af_type == ALLELE_NONMAJOR && args->max_af < (an-major_ac)/(double)an) return 0; // max non-major AF
+    }
+    if (args->uncalled) {
+        if (args->uncalled == FLT_INCLUDE && an > 0) return 0; // select uncalled
+        if (args->uncalled == FLT_EXCLUDE && an == 0) return 0; // skip if uncalled
+    }
+    if (update_ac && args->update_info) {
+        bcf_update_info_int32(args->hdr, line, "AC", &args->ac[1], line->n_allele-1);
+        bcf_update_info_int32(args->hdr, line, "AN", &an, 1);
+    }
+    if (args->trim_alts)
+    {
+        int ret = bcf_trim_alleles(args->hsub ? args->hsub : args->hdr, line);
+        if ( ret<0 ) error("Error: Could not trim alleles at %s:%"PRId64"\n", bcf_seqname(args->hsub ? args->hsub : args->hdr, line), (int64_t) line->pos+1);
+    }
+    if (args->phased) {
+        int phased = bcf_all_phased(args->hdr, line);
+        if (args->phased == FLT_INCLUDE && !phased) { return 0; } // skip unphased
+        if (args->phased == FLT_EXCLUDE && phased) { return 0; } // skip phased
+    }
+    if (args->sites_only) bcf_subset(args->hsub ? args->hsub : args->hdr, line, 0, 0);
+    return 1;
+}
+
+void set_allele_type (int *atype, char *atype_string)
+{
+    *atype = ALLELE_NONREF;
+    if (strcmp(atype_string, "minor") == 0) {
+        *atype = ALLELE_MINOR;
+    }
+    else if (strcmp(atype_string, "alt1") == 0) {
+        *atype = ALLELE_ALT1;
+    }
+    else if (strcmp(atype_string, "nref") == 0) {
+        *atype = ALLELE_NONREF;
+    }
+    else if (strcmp(atype_string, "major") == 0) {
+        *atype = ALLELE_MAJOR;
+    }
+    else if (strcmp(atype_string, "nonmajor") == 0) {
+        *atype = ALLELE_NONMAJOR;
+    }
+    else {
+        error("Error: allele type not recognised. Expected one of nref|alt1|minor|major|nonmajor, got \"%s\".\n", atype_string);
+    }
+}
+
+static void usage(args_t *args)
+{
+    fprintf(stderr, "\n");
+    fprintf(stderr, "About:   VCF/BCF conversion, view, subset and filter VCF/BCF files.\n");
+    fprintf(stderr, "Usage:   bcftools view [options] <in.vcf.gz> [region1 [...]]\n");
+    fprintf(stderr, "\n");
+    fprintf(stderr, "Output options:\n");
+    fprintf(stderr, "    -G, --drop-genotypes              Drop individual genotype information (after subsetting if -s option set)\n");
+    fprintf(stderr, "    -h, --header-only                 Print only the header in VCF output (equivalent to bcftools head)\n");
+    fprintf(stderr, "    -H, --no-header                   Suppress the header in VCF output\n");
+    fprintf(stderr, "        --with-header                 Print both header and records in VCF output [default]\n");
+    fprintf(stderr, "    -l, --compression-level [0-9]     Compression level: 0 uncompressed, 1 best speed, 9 best compression [%d]\n", args->clevel);
+    fprintf(stderr, "        --no-version                  Do not append version and command line to the header\n");
+    fprintf(stderr, "    -o, --output FILE                 Output file name [stdout]\n");
+    fprintf(stderr, "    -O, --output-type u|b|v|z[0-9]    u/b: un/compressed BCF, v/z: un/compressed VCF, 0-9: compression level [v]\n");
+    fprintf(stderr, "    -r, --regions REGION              Restrict to comma-separated list of regions\n");
+    fprintf(stderr, "    -R, --regions-file FILE           Restrict to regions listed in FILE\n");
+    fprintf(stderr, "        --regions-overlap 0|1|2       Include if POS in the region (0), record overlaps (1), variant overlaps (2) [1]\n");
+    fprintf(stderr, "    -t, --targets [^]REGION           Similar to -r but streams rather than index-jumps. Exclude regions with \"^\" prefix\n");
+    fprintf(stderr, "    -T, --targets-file [^]FILE        Similar to -R but streams rather than index-jumps. Exclude regions with \"^\" prefix\n");
+    fprintf(stderr, "        --targets-overlap 0|1|2       Include if POS in the region (0), record overlaps (1), variant overlaps (2) [0]\n");
+    fprintf(stderr, "        --threads INT                 Use multithreading with INT worker threads [0]\n");
+    fprintf(stderr, "\n");
+    fprintf(stderr, "Subset options:\n");
+    fprintf(stderr, "    -a, --trim-alt-alleles            Trim ALT alleles not seen in the genotype fields (or their subset with -s/-S)\n");
+    fprintf(stderr, "    -I, --no-update                   Do not (re)calculate INFO fields for the subset (currently INFO/AC and INFO/AN)\n");
+    fprintf(stderr, "    -s, --samples [^]LIST             Comma separated list of samples to include (or exclude with \"^\" prefix)\n");
+    fprintf(stderr, "    -S, --samples-file [^]FILE        File of samples to include (or exclude with \"^\" prefix)\n");
+    fprintf(stderr, "        --force-samples               Only warn about unknown subset samples\n");
+    fprintf(stderr, "\n");
+    fprintf(stderr, "Filter options:\n");
+    fprintf(stderr, "    -c/C, --min-ac/--max-ac INT[:TYPE]     Minimum/maximum count for non-reference (nref), 1st alternate (alt1), least frequent\n");
+    fprintf(stderr, "                                               (minor), most frequent (major) or sum of all but most frequent (nonmajor) alleles [nref]\n");
+    fprintf(stderr, "    -f,   --apply-filters LIST             Require at least one of the listed FILTER strings (e.g. \"PASS,.\")\n");
+    fprintf(stderr, "    -g,   --genotype [^]hom|het|miss       Require one or more hom/het/missing genotype or, if prefixed with \"^\", exclude such sites\n");
+    fprintf(stderr, "    -i/e, --include/--exclude EXPR         Select/exclude sites for which the expression is true (see man page for details)\n");
+    fprintf(stderr, "    -k/n, --known/--novel                  Select known/novel sites only (ID is not/is '.')\n");
+    fprintf(stderr, "    -m/M, --min-alleles/--max-alleles INT  Minimum/maximum number of alleles listed in REF and ALT (e.g. -m2 -M2 for biallelic sites)\n");
+    fprintf(stderr, "    -p/P, --phased/--exclude-phased        Select/exclude sites where all samples are phased\n");
+    fprintf(stderr, "    -q/Q, --min-af/--max-af FLOAT[:TYPE]   Minimum/maximum frequency for non-reference (nref), 1st alternate (alt1), least frequent\n");
+    fprintf(stderr, "                                               (minor), most frequent (major) or sum of all but most frequent (nonmajor) alleles [nref]\n");
+    fprintf(stderr, "    -u/U, --uncalled/--exclude-uncalled    Select/exclude sites without a called genotype\n");
+    fprintf(stderr, "    -v/V, --types/--exclude-types LIST     Select/exclude comma-separated list of variant types: snps,indels,mnps,ref,bnd,other [null]\n");
+    fprintf(stderr, "    -x/X, --private/--exclude-private      Select/exclude sites where the non-reference alleles are exclusive (private) to the subset samples\n");
+    fprintf(stderr, "\n");
+    exit(1);
+}
+
+int main_vcfview(int argc, char *argv[])
+{
+    int c;
+    args_t *args  = (args_t*) calloc(1,sizeof(args_t));
+    args->argc    = argc; args->argv = argv;
+    args->files   = bcf_sr_init();
+    args->clevel  = -1;
+    args->print_header = 1;
+    args->update_info = 1;
+    args->output_type = FT_VCF;
+    args->n_threads = 0;
+    args->record_cmd_line = 1;
+    args->min_ac = args->max_ac = args->min_af = args->max_af = -1;
+    args->regions_overlap = 1;
+    args->targets_overlap = 0;
+    int targets_is_file = 0, regions_is_file = 0;
+
+    static struct option loptions[] =
+    {
+        {"genotype",required_argument,NULL,'g'},
+        {"compression-level",required_argument,NULL,'l'},
+        {"threads",required_argument,NULL,9},
+        {"header-only",no_argument,NULL,'h'},
+        {"no-header",no_argument,NULL,'H'},
+        {"with-header",no_argument,NULL,4},
+        {"exclude",required_argument,NULL,'e'},
+        {"include",required_argument,NULL,'i'},
+        {"trim-alt-alleles",no_argument,NULL,'a'},
+        {"no-update",no_argument,NULL,'I'},
+        {"drop-genotypes",no_argument,NULL,'G'},
+        {"private",no_argument,NULL,'x'},
+        {"exclude-private",no_argument,NULL,'X'},
+        {"uncalled",no_argument,NULL,'u'},
+        {"exclude-uncalled",no_argument,NULL,'U'},
+        {"apply-filters",required_argument,NULL,'f'},
+        {"known",no_argument,NULL,'k'},
+        {"novel",no_argument,NULL,'n'},
+        {"min-alleles",required_argument,NULL,'m'},
+        {"max-alleles",required_argument,NULL,'M'},
+        {"samples",required_argument,NULL,'s'},
+        {"samples-file",required_argument,NULL,'S'},
+        {"force-samples",no_argument,NULL,1},
+        {"output-type",required_argument,NULL,'O'},
+        {"output-file",required_argument,NULL,'o'},
+        {"output",required_argument,NULL,'o'},
+        {"types",required_argument,NULL,'v'},
+        {"exclude-types",required_argument,NULL,'V'},
+        {"targets",required_argument,NULL,'t'},
+        {"targets-file",required_argument,NULL,'T'},
+        {"targets-overlap",required_argument,NULL,2},
+        {"regions",required_argument,NULL,'r'},
+        {"regions-file",required_argument,NULL,'R'},
+        {"regions-overlap",required_argument,NULL,3},
+        {"min-ac",required_argument,NULL,'c'},
+        {"max-ac",required_argument,NULL,'C'},
+        {"min-af",required_argument,NULL,'q'},
+        {"max-af",required_argument,NULL,'Q'},
+        {"phased",no_argument,NULL,'p'},
+        {"exclude-phased",no_argument,NULL,'P'},
+        {"no-version",no_argument,NULL,8},
+        {NULL,0,NULL,0}
+    };
+    char *tmp;
+    while ((c = getopt_long(argc, argv, "l:t:T:r:R:o:O:s:S:Gf:knv:V:m:M:auUhHc:C:Ii:e:xXpPq:Q:g:",loptions,NULL)) >= 0)
+    {
+        char allele_type[9] = "nref";
+        switch (c)
+        {
+            case 'O':
+                switch (optarg[0]) {
+                    case 'b': args->output_type = FT_BCF_GZ; break;
+                    case 'u': args->output_type = FT_BCF; break;
+                    case 'z': args->output_type = FT_VCF_GZ; break;
+                    case 'v': args->output_type = FT_VCF; break;
+                    default:
+                    {
+                        args->clevel = strtol(optarg,&tmp,10);
+                        if ( *tmp || args->clevel<0 || args->clevel>9 ) error("The output type \"%s\" not recognised\n", optarg);
+                    }
+                };
+                if ( optarg[1] )
+                {
+                    args->clevel = strtol(optarg+1,&tmp,10);
+                    if ( *tmp || args->clevel<0 || args->clevel>9 ) error("Could not parse argument: --compression-level %s\n", optarg+1);
+                }
+                break;
+            case 'l':
+                args->clevel = strtol(optarg,&tmp,10);
+                if ( *tmp ) error("Could not parse argument: --compression-level %s\n", optarg);
+                args->output_type |= FT_GZ; 
+                break;
+            case 'o': args->fn_out = optarg; break;
+            case 'H': args->print_header = 0; break;
+            case 'h': args->header_only = 1; break;
+            case  4 : args->print_header = 1; args->header_only = 0; break;
+
+            case 't': args->targets_list = optarg; break;
+            case 'T': args->targets_list = optarg; targets_is_file = 1; break;
+            case 'r': args->regions_list = optarg; break;
+            case 'R': args->regions_list = optarg; regions_is_file = 1; break;
+
+            case 's': args->sample_names = optarg; break;
+            case 'S': args->sample_names = optarg; args->sample_is_file = 1; break;
+            case  1 : args->force_samples = 1; break;
+            case 'a': args->trim_alts = 1; args->calc_ac = 1; break;
+            case 'I': args->update_info = 0; break;
+            case 'G': args->sites_only = 1; break;
+
+            case 'f': args->files->apply_filters = optarg; break;
+            case 'k': args->known = 1; break;
+            case 'n': args->novel = 1; break;
+            case 'm':
+                args->min_alleles = strtol(optarg,&tmp,10);
+                if ( *tmp ) error("Could not parse argument: --min-alleles %s\n", optarg);
+                break;
+            case 'M': 
+                args->max_alleles = strtol(optarg,&tmp,10);
+                if ( *tmp ) error("Could not parse argument: --max-alleles %s\n", optarg);
+                break;
+            case 'v': args->include_types = optarg; break;
+            case 'V': args->exclude_types = optarg; break;
+            case 'e':
+                if ( args->filter_str ) error("Error: only one -i or -e expression can be given, and they cannot be combined\n");
+                args->filter_str = optarg; args->filter_logic |= FLT_EXCLUDE; break;
+            case 'i':
+                if ( args->filter_str ) error("Error: only one -i or -e expression can be given, and they cannot be combined\n");
+                args->filter_str = optarg; args->filter_logic |= FLT_INCLUDE; break;
+            case 'c':
+            {
+                args->min_ac_type = ALLELE_NONREF;
+                if ( sscanf(optarg,"%d:%8s",&args->min_ac, allele_type)!=2 && sscanf(optarg,"%d",&args->min_ac)!=1 )
+                    error("Error: Could not parse --min-ac %s\n", optarg);
+                set_allele_type(&args->min_ac_type, allele_type);
+                args->calc_ac = 1;
+                break;
+            }
+            case 'C':
+            {
+                args->max_ac_type = ALLELE_NONREF;
+                if ( sscanf(optarg,"%d:%8s",&args->max_ac, allele_type)!=2 && sscanf(optarg,"%d",&args->max_ac)!=1 )
+                    error("Error: Could not parse --max-ac %s\n", optarg);
+                set_allele_type(&args->max_ac_type, allele_type);
+                args->calc_ac = 1;
+                break;
+            }
+            case 'q':
+            {
+                args->min_af_type = ALLELE_NONREF;
+                if ( sscanf(optarg,"%f:%8s",&args->min_af, allele_type)!=2 && sscanf(optarg,"%f",&args->min_af)!=1 )
+                    error("Error: Could not parse --min-af %s\n", optarg);
+                set_allele_type(&args->min_af_type, allele_type);
+                args->calc_ac = 1;
+                break;
+            }
+            case 'Q':
+            {
+                args->max_af_type = ALLELE_NONREF;
+                if ( sscanf(optarg,"%f:%8s",&args->max_af, allele_type)!=2 && sscanf(optarg,"%f",&args->max_af)!=1 )
+                    error("Error: Could not parse --max-af %s\n", optarg);
+                set_allele_type(&args->max_af_type, allele_type);
+                args->calc_ac = 1;
+                break;
+            }
+
+            case 'x': args->private_vars |= FLT_INCLUDE; args->calc_ac = 1; break;
+            case 'X': args->private_vars |= FLT_EXCLUDE; args->calc_ac = 1; break;
+            case 'u': args->uncalled |= FLT_INCLUDE; args->calc_ac = 1; break;
+            case 'U': args->uncalled |= FLT_EXCLUDE; args->calc_ac = 1; break;
+            case 'p': args->phased |= FLT_INCLUDE; break; // phased
+            case 'P': args->phased |= FLT_EXCLUDE; break; // exclude-phased
+            case 'g':
+            {
+                if ( !strcasecmp(optarg,"hom") ) args->gt_type = GT_NEED_HOM;
+                else if ( !strcasecmp(optarg,"het") ) args->gt_type = GT_NEED_HET;
+                else if ( !strcasecmp(optarg,"miss") ) args->gt_type = GT_NEED_MISSING;
+                else if ( !strcasecmp(optarg,"^hom") ) args->gt_type = GT_NO_HOM;
+                else if ( !strcasecmp(optarg,"^het") ) args->gt_type = GT_NO_HET;
+                else if ( !strcasecmp(optarg,"^miss") ) args->gt_type = GT_NO_MISSING;
+                else error("The argument to -g not recognised. Expected one of hom/het/miss/^hom/^het/^miss, got \"%s\".\n", optarg);
+                break;
+            }
+            case  2 :
+                args->targets_overlap = parse_overlap_option(optarg);
+                if ( args->targets_overlap < 0 ) error("Could not parse: --targets-overlap %s\n",optarg);
+                break;
+            case  3 :
+                args->regions_overlap = parse_overlap_option(optarg);
+                if ( args->regions_overlap < 0 ) error("Could not parse: --regions-overlap %s\n",optarg);
+                break;
+            case  9 : args->n_threads = strtol(optarg, 0, 0); break;
+            case  8 : args->record_cmd_line = 0; break;
+            case '?': usage(args); break;
+            default: error("Unknown argument: %s\n", optarg);
+        }
+    }
+
+    if ( args->filter_logic == (FLT_EXCLUDE|FLT_INCLUDE) ) error("Only one of -i or -e can be given.\n");
+    if ( args->private_vars > FLT_EXCLUDE ) error("Only one of -x or -X can be given.\n");
+    if ( args->uncalled > FLT_EXCLUDE ) error("Only one of -u or -U can be given.\n");
+    if ( args->phased > FLT_EXCLUDE ) error("Only one of -p or -P can be given.\n");
+
+    if ( args->sample_names && args->update_info) args->calc_ac = 1;
+
+    char *fname = NULL;
+    if ( optind>=argc )
+    {
+        if ( !isatty(fileno((FILE *)stdin)) ) fname = "-";  // reading from stdin
+        else usage(args);
+    }
+    else fname = argv[optind];
+
+    // read in the regions from the command line
+    if ( args->regions_list )
+    {
+        bcf_sr_set_opt(args->files,BCF_SR_REGIONS_OVERLAP,args->regions_overlap);
+        if ( bcf_sr_set_regions(args->files, args->regions_list, regions_is_file)<0 )
+            error("Failed to read the regions: %s\n", args->regions_list);
+    }
+    else if ( optind+1 < argc )
+    {
+        int i;
+        kstring_t tmp = {0,0,0};
+        kputs(argv[optind+1],&tmp);
+        for (i=optind+2; i<argc; i++) { kputc(',',&tmp); kputs(argv[i],&tmp); }
+        if ( bcf_sr_set_regions(args->files, tmp.s, 0)<0 )
+            error("Failed to read the regions: %s\n", tmp.s);
+        free(tmp.s);
+    }
+    if ( args->targets_list )
+    {
+        bcf_sr_set_opt(args->files,BCF_SR_TARGETS_OVERLAP,args->targets_overlap);
+        if ( bcf_sr_set_targets(args->files, args->targets_list, targets_is_file, 0)<0 )
+            error("Failed to read the targets: %s\n", args->targets_list);
+    }
+
+    if ( bcf_sr_set_threads(args->files, args->n_threads)<0 ) error("Failed to create threads\n");
+    if ( !bcf_sr_add_reader(args->files, fname) ) error("Failed to read from %s: %s\n", !strcmp("-",fname)?"standard input":fname,bcf_sr_strerror(args->files->errnum));
+
+    init_data(args);
+    bcf_hdr_t *out_hdr = args->hnull ? args->hnull : (args->hsub ? args->hsub : args->hdr);
+    if (args->print_header)
+    {
+        if ( bcf_hdr_write(args->out, out_hdr)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->fn_out);
+    }
+    else if ( args->output_type & FT_BCF )
+        error("BCF output requires header, cannot proceed with -H\n");
+
+    int ret = 0;
+    if (!args->header_only)
+    {
+        while ( bcf_sr_next_line(args->files) )
+        {
+            bcf1_t *line = args->files->readers[0].buffer[0];
+            if ( line->errcode && out_hdr!=args->hdr ) error("Undefined tags in the header, cannot proceed in the sample subset mode.\n");
+            if ( subset_vcf(args, line) && bcf_write1(args->out, out_hdr, line)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->fn_out);
+        }
+        ret = args->files->errnum;
+        if ( ret ) fprintf(stderr,"Error: %s\n", bcf_sr_strerror(args->files->errnum));
+    }
+    hts_close(args->out);
+    destroy_data(args);
+    bcf_sr_destroy(args->files);
+    free(args);
+    return ret;
+}
diff --git a/bcftools/vcfview.c.pysam.c b/bcftools/vcfview.c.pysam.c
new file mode 100644
index 0000000..4bbbefb
--- /dev/null
+++ b/bcftools/vcfview.c.pysam.c
@@ -0,0 +1,803 @@
+#include "bcftools.pysam.h"
+
+/*  vcfview.c -- VCF/BCF conversion, view, subset and filter VCF/BCF files.
+
+    Copyright (C) 2013-2021 Genome Research Ltd.
+
+    Author: Shane McCarthy <sm15@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.  */
+
+#include <stdio.h>
+#include <strings.h>
+#include <unistd.h>
+#include <getopt.h>
+#include <ctype.h>
+#include <string.h>
+#include <errno.h>
+#include <sys/stat.h>
+#include <sys/types.h>
+#include <math.h>
+#include <inttypes.h>
+#include <htslib/vcf.h>
+#include <htslib/synced_bcf_reader.h>
+#include <htslib/vcfutils.h>
+#include "bcftools.h"
+#include "filter.h"
+#include "htslib/khash_str2int.h"
+
+#define FLT_INCLUDE 1
+#define FLT_EXCLUDE 2
+
+#define ALLELE_NONREF 1
+#define ALLELE_MINOR 2
+#define ALLELE_ALT1 3
+#define ALLELE_MAJOR 4
+#define ALLELE_NONMAJOR 5
+
+#define GT_NEED_HOM 1
+#define GT_NEED_HET 2
+#define GT_NO_HOM   3
+#define GT_NO_HET   4
+#define GT_NEED_MISSING 5
+#define GT_NO_MISSING 6
+
+typedef struct _args_t
+{
+    filter_t *filter;
+    char *filter_str;
+    int filter_logic;   // one of FLT_INCLUDE/FLT_EXCLUDE (-i or -e)
+
+    bcf_srs_t *files;
+    bcf_hdr_t *hdr, *hnull, *hsub; // original header, sites-only header, subset header
+    char **argv, *format, *sample_names, *subset_fname, *targets_list, *regions_list;
+    int regions_overlap, targets_overlap;
+    int argc, clevel, n_threads, output_type, print_header, update_info, header_only, n_samples, *imap, calc_ac;
+    int trim_alts, sites_only, known, novel, min_alleles, max_alleles, private_vars, uncalled, phased;
+    int min_ac, min_ac_type, max_ac, max_ac_type, min_af_type, max_af_type, gt_type;
+    int *ac, mac;
+    float min_af, max_af;
+    char *fn_ref, *fn_out, **samples;
+    int sample_is_file, force_samples;
+    char *include_types, *exclude_types;
+    int include, exclude;
+    int record_cmd_line;
+    htsFile *out;
+}
+args_t;
+
+static void init_data(args_t *args)
+{
+    int i;
+    args->hdr = args->files->readers[0].header;
+
+    if (args->calc_ac && args->update_info)
+    {
+        if (bcf_hdr_append(args->hdr,"##INFO=<ID=AC,Number=A,Type=Integer,Description=\"Allele count in genotypes\">") < 0)
+            error_errno("[%s] Failed to add \"AC\" INFO header", __func__);
+        if (bcf_hdr_append(args->hdr,"##INFO=<ID=AN,Number=1,Type=Integer,Description=\"Total number of alleles in called genotypes\">") < 0)
+            error_errno("[%s] Failed to add \"AN\" INFO header", __func__);
+    }
+    if (args->record_cmd_line) bcf_hdr_append_version(args->hdr, args->argc, args->argv, "bcftools_view");
+    else if (bcf_hdr_sync(args->hdr) < 0)
+        error_errno("[%s] Failed to update header", __func__);
+
+    // setup sample data
+    if (args->sample_names)
+    {
+        void *hdr_samples = khash_str2int_init();
+        for (i=0; i<bcf_hdr_nsamples(args->hdr); i++)
+            khash_str2int_inc(hdr_samples, bcf_hdr_int2id(args->hdr,BCF_DT_SAMPLE,i));
+
+        void *exclude = (args->sample_names[0]=='^') ? khash_str2int_init() : NULL;
+        int nsmpl;
+        char **smpl = NULL;
+        args->samples = NULL; args->n_samples = 0;
+        smpl = hts_readlist(exclude ? &args->sample_names[1] : args->sample_names, args->sample_is_file, &nsmpl);
+        if ( !smpl )
+        {
+            error("Could not read the list: \"%s\"\n", exclude ? &args->sample_names[1] : args->sample_names);
+        }
+
+        if ( exclude )
+        {
+            for (i=0; i<nsmpl; i++) {
+                if (!khash_str2int_has_key(hdr_samples,smpl[i])) {
+                    if (args->force_samples) {
+                        fprintf(bcftools_stderr, "Warn: exclude called for sample that does not exist in header: \"%s\"... skipping\n", smpl[i]);
+                    } else {
+                        error("Error: exclude called for sample that does not exist in header: \"%s\". Use \"--force-samples\" to ignore this error.\n", smpl[i]);
+                    }
+                }
+                khash_str2int_inc(exclude, smpl[i]);
+            }
+
+            for (i=0; i<bcf_hdr_nsamples(args->hdr); i++)
+            {
+                if ( exclude && khash_str2int_has_key(exclude,bcf_hdr_int2id(args->hdr,BCF_DT_SAMPLE,i))  ) continue;
+                args->samples = (char**) realloc(args->samples, (args->n_samples+1)*sizeof(const char*));
+                args->samples[args->n_samples++] = strdup(bcf_hdr_int2id(args->hdr,BCF_DT_SAMPLE,i));
+            }
+            khash_str2int_destroy(exclude);
+        }
+        else
+        {
+            for (i=0; i<nsmpl; i++) {
+                if (!khash_str2int_has_key(hdr_samples,smpl[i])) {
+                    if (args->force_samples) {
+                        fprintf(bcftools_stderr, "Warn: subset called for sample that does not exist in header: \"%s\"... skipping\n", smpl[i]);
+                        continue;
+                    } else {
+                        error("Error: subset called for sample that does not exist in header: \"%s\". Use \"--force-samples\" to ignore this error.\n", smpl[i]);
+                    }
+                }
+                args->samples = (char**) realloc(args->samples, (args->n_samples+1)*sizeof(const char*));
+                args->samples[args->n_samples++] = strdup(smpl[i]);
+            }
+        }
+        for (i=0; i<nsmpl; i++) free(smpl[i]);
+        free(smpl);
+        khash_str2int_destroy(hdr_samples);
+        if (args->n_samples == 0) {
+            fprintf(bcftools_stderr, "Warn: subsetting has removed all samples\n");
+            args->sites_only = 1;
+        }
+    }
+
+    if (args->n_samples)
+        args->imap = (int*)malloc(args->n_samples * sizeof(int));
+
+    // determine variant types to include/exclude
+    if (args->include_types || args->exclude_types) {
+        if (args->include_types && args->exclude_types) {
+            fprintf(bcftools_stderr, "Error: only supply one of --include-types, --exclude-types options\n");
+            bcftools_exit(1);
+        }
+        char **type_list = 0;
+        int m = 0, n = 0;
+        const char *q, *p;
+        for (q = p = args->include_types ? args->include_types : args->exclude_types;; ++p) {
+            if (*p == ',' || *p == 0) {
+                if (m == n) {
+                    m = m? m<<1 : 16;
+                    type_list = (char**)realloc(type_list, m * sizeof(char*));
+                }
+                type_list[n] = (char*)calloc(p - q + 1, 1);
+                strncpy(type_list[n++], q, p - q);
+                q = p + 1;
+                if (*p == 0) break;
+            }
+        }
+        type_list = (char**)realloc(type_list, n * sizeof(char*));
+
+        if (args->include_types) {
+            args->include = 0;
+            for (i = 0; i < n; ++i) {
+                if (strcmp(type_list[i], "snps") == 0) args->include |= VCF_SNP<<1;
+                else if (strcmp(type_list[i], "indels") == 0) args->include |= VCF_INDEL<<1;
+                else if (strcmp(type_list[i], "mnps") == 0) args->include |= VCF_MNP<<1;
+                else if (strcmp(type_list[i], "other") == 0) args->include |= VCF_OTHER<<1;
+                else if (strcmp(type_list[i], "ref") == 0) args->include |= VCF_OTHER<<1;
+                else if (strcmp(type_list[i], "bnd") == 0) args->include |= VCF_BND<<1;
+                else {
+                    fprintf(bcftools_stderr, "[E::%s] unknown type\n", type_list[i]);
+                    fprintf(bcftools_stderr, "Accepted types are snps, indels, mnps, other\n");
+                    bcftools_exit(1);
+                }
+            }
+        }
+        if (args->exclude_types) {
+            args->exclude = 0;
+            for (i = 0; i < n; ++i) {
+                if (strcmp(type_list[i], "snps") == 0) args->exclude |= VCF_SNP<<1;
+                else if (strcmp(type_list[i], "indels") == 0) args->exclude |= VCF_INDEL<<1;
+                else if (strcmp(type_list[i], "mnps") == 0) args->exclude |= VCF_MNP<<1;
+                else if (strcmp(type_list[i], "other") == 0) args->exclude |= VCF_OTHER<<1;
+                else if (strcmp(type_list[i], "ref") == 0) args->exclude |= VCF_OTHER<<1;
+                else if (strcmp(type_list[i], "bnd") == 0) args->exclude |= VCF_BND<<1;
+                else {
+                    fprintf(bcftools_stderr, "[E::%s] unknown type\n", type_list[i]);
+                    fprintf(bcftools_stderr, "Accepted types are snps, indels, mnps, other\n");
+                    bcftools_exit(1);
+                }
+            }
+        }
+        for (i = 0; i < n; ++i)
+            free(type_list[i]);
+        free(type_list);
+    }
+
+    char wmode[8];
+    set_wmode(wmode,args->output_type,args->fn_out,args->clevel);
+    args->out = hts_open(args->fn_out ? args->fn_out : "-", wmode);
+    if ( !args->out ) error("%s: %s\n", args->fn_out,strerror(errno));
+    if ( args->n_threads > 0)
+        hts_set_opt(args->out, HTS_OPT_THREAD_POOL, args->files->p);
+
+    // headers: hdr=full header, hsub=subset header, hnull=sites only header
+    if (args->sites_only){
+        args->hnull = bcf_hdr_subset(args->hdr, 0, 0, 0);
+        bcf_hdr_remove(args->hnull, BCF_HL_FMT, NULL);
+    }
+    if (args->n_samples > 0)
+    {
+        args->hsub = bcf_hdr_subset(args->hdr, args->n_samples, args->samples, args->imap);
+        if ( !args->hsub ) error("Error occurred while subsetting samples\n");
+        if ( args->n_samples != bcf_hdr_nsamples(args->hsub) )
+        {
+            int i;
+            for (i=0; i<args->n_samples; i++)
+                if ( args->imap[i]<0 ) error("Error: No such sample: \"%s\"\n", args->samples[i]);
+        }
+    }
+
+    if ( args->filter_str )
+        args->filter = filter_init(args->hdr, args->filter_str);
+}
+
+static void destroy_data(args_t *args)
+{
+    int i;
+    if ( args->imap ) {
+        for (i = 0; i < args->n_samples; ++i)
+            free(args->samples[i]);
+        free(args->samples);
+        free(args->imap);
+    }
+    if (args->hnull) bcf_hdr_destroy(args->hnull);
+    if (args->hsub) bcf_hdr_destroy(args->hsub);
+    if ( args->filter )
+        filter_destroy(args->filter);
+    free(args->ac);
+}
+
+// true if all samples are phased.
+// haploid genotypes are considered phased
+// ./. => not phased, .|. => phased
+int bcf_all_phased(const bcf_hdr_t *header, bcf1_t *line)
+{
+    bcf_unpack(line, BCF_UN_FMT);
+    bcf_fmt_t *fmt_ptr = bcf_get_fmt(header, line, "GT");
+    int all_phased = 1;
+    if ( fmt_ptr )
+    {
+        int i, isample;
+        for (isample=0; isample<line->n_sample; isample++)
+        {
+            int sample_phased = 0;
+            #define BRANCH_INT(type_t,vector_end) { \
+                type_t *p = (type_t*) (fmt_ptr->p + isample*fmt_ptr->size); \
+                for (i=0; i<fmt_ptr->n; i++) \
+                { \
+                    if (fmt_ptr->n == 1 || (p[i] == vector_end && i == 1)) { sample_phased = 1; break; } /* haploid phased by definition */ \
+                    if ( p[i] == vector_end ) { break; }; /* smaller ploidy */ \
+                    if ( bcf_gt_is_missing(p[i]) ) continue; /* missing allele */ \
+                    if ((p[i])&1) { \
+                        sample_phased = 1; \
+                        break; \
+                    } \
+                } \
+            }
+            switch (fmt_ptr->type) {
+                case BCF_BT_INT8:  BRANCH_INT(int8_t,  bcf_int8_vector_end); break;
+                case BCF_BT_INT16: BRANCH_INT(int16_t, bcf_int16_vector_end); break;
+                case BCF_BT_INT32: BRANCH_INT(int32_t, bcf_int32_vector_end); break;
+                default: fprintf(bcftools_stderr, "[E::%s] todo: fmt_type %d\n", __func__, fmt_ptr->type); bcftools_exit(1); break;
+            }
+            #undef BRANCH_INT
+            if (!sample_phased) {
+                all_phased = 0;
+                break;
+            }
+        }
+    }
+    return all_phased;
+}
+
+int subset_vcf(args_t *args, bcf1_t *line)
+{
+    if ( args->min_alleles && line->n_allele < args->min_alleles ) return 0; // min alleles
+    if ( args->max_alleles && line->n_allele > args->max_alleles ) return 0; // max alleles
+    if (args->novel || args->known)
+    {
+        if ( args->novel && (line->d.id[0]!='.' || line->d.id[1]!=0) ) return 0; // skip sites which are known, ID != '.'
+        if ( args->known && line->d.id[0]=='.' && line->d.id[1]==0 ) return 0;  // skip sites which are novel, ID == '.'
+    }
+
+    if (args->include || args->exclude)
+    {
+        int line_type = bcf_get_variant_types(line);
+        if ( args->include && !((line_type<<1) & args->include) ) return 0; // include only given variant types
+        if ( args->exclude &&   (line_type<<1) & args->exclude  ) return 0; // exclude given variant types
+    }
+
+    if ( args->filter )
+    {
+        int ret = filter_test(args->filter, line, NULL);
+        if ( args->filter_logic==FLT_INCLUDE ) { if ( !ret ) return 0; }
+        else if ( ret ) return 0;
+    }
+
+    hts_expand(int, line->n_allele, args->mac, args->ac);
+    int i, an = 0, non_ref_ac = 0;
+    if (args->calc_ac) {
+        bcf_calc_ac(args->hdr, line, args->ac, BCF_UN_INFO|BCF_UN_FMT); // get original AC and AN values from INFO field if available, otherwise calculate
+        for (i=1; i<line->n_allele; i++)
+            non_ref_ac += args->ac[i];
+        for (i=0; i<line->n_allele; i++)
+            an += args->ac[i];
+    }
+
+    int update_ac = args->calc_ac;
+    if (args->n_samples)
+    {
+        int non_ref_ac_sub = 0, *ac_sub = (int*) calloc(line->n_allele,sizeof(int));
+        bcf_subset(args->hdr, line, args->n_samples, args->imap);
+        if ( args->calc_ac && !bcf_get_fmt(args->hdr,line,"GT") ) update_ac = 0;
+        if ( update_ac )
+        {
+            bcf_calc_ac(args->hsub, line, ac_sub, BCF_UN_FMT); // recalculate AC and AN
+            an = 0;
+            for (i=0; i<line->n_allele; i++) {
+                args->ac[i] = ac_sub[i];
+                an += ac_sub[i];
+            }
+            for (i=1; i<line->n_allele; i++)
+                non_ref_ac_sub += ac_sub[i];
+            if (args->private_vars) {
+                if (args->private_vars == FLT_INCLUDE && !(non_ref_ac_sub > 0 && non_ref_ac == non_ref_ac_sub)) { free(ac_sub); return 0; } // select private sites
+                if (args->private_vars == FLT_EXCLUDE && non_ref_ac_sub > 0 && non_ref_ac == non_ref_ac_sub) { free(ac_sub); return 0; } // exclude private sites
+            }
+            non_ref_ac = non_ref_ac_sub;
+        }
+        free(ac_sub);
+    }
+
+    bcf_fmt_t *gt_fmt;
+    if ( args->gt_type && (gt_fmt=bcf_get_fmt(args->hdr,line,"GT")) )
+    {
+        int nhet = 0, nhom = 0, nmiss = 0;
+        for (i=0; i<bcf_hdr_nsamples(args->hdr); i++)
+        {
+            int type = bcf_gt_type(gt_fmt,i,NULL,NULL);
+            if ( type==GT_HET_RA || type==GT_HET_AA )
+            {
+                if ( args->gt_type==GT_NO_HET ) return 0;
+                nhet = 1;
+            }
+            else if ( type==GT_UNKN )
+            {
+                if ( args->gt_type==GT_NO_MISSING ) return 0;
+                nmiss = 1;
+            }
+            else
+            {
+                if ( args->gt_type==GT_NO_HOM ) return 0;
+                nhom = 1;
+            }
+        }
+        if ( args->gt_type==GT_NEED_HOM && !nhom ) return 0;
+        else if ( args->gt_type==GT_NEED_HET && !nhet ) return 0;
+        else if ( args->gt_type==GT_NEED_MISSING && !nmiss ) return 0;
+    }
+
+    int minor_ac = 0;
+    int major_ac = 0;
+    if ( args->calc_ac )
+    {
+        minor_ac = args->ac[0];
+        major_ac = args->ac[0];
+        for (i=1; i<line->n_allele; i++){
+            if (args->ac[i] < minor_ac) { minor_ac = args->ac[i]; }
+            if (args->ac[i] > major_ac) { major_ac = args->ac[i]; }
+        }
+    }
+
+    if (args->min_ac!=-1)
+    {
+        if (args->min_ac_type == ALLELE_NONREF && args->min_ac>non_ref_ac) return 0; // min AC
+        else if (args->min_ac_type == ALLELE_MINOR && args->min_ac>minor_ac) return 0; // min minor AC
+        else if (args->min_ac_type == ALLELE_ALT1 && args->min_ac>args->ac[1]) return 0; // min 1st alternate AC
+        else if (args->min_ac_type == ALLELE_MAJOR && args->min_ac > major_ac) return 0; // min major AC
+        else if (args->min_ac_type == ALLELE_NONMAJOR && args->min_ac > an-major_ac) return 0; // min non-major AC
+    }
+    if (args->max_ac!=-1)
+    {
+        if (args->max_ac_type == ALLELE_NONREF && args->max_ac<non_ref_ac) return 0; // max AC
+        else if (args->max_ac_type == ALLELE_MINOR && args->max_ac<minor_ac) return 0; // max minor AC
+        else if (args->max_ac_type == ALLELE_ALT1 && args->max_ac<args->ac[1]) return 0; // max 1st alternate AC
+        else if (args->max_ac_type == ALLELE_MAJOR && args->max_ac < major_ac) return 0; // max major AC
+        else if (args->max_ac_type == ALLELE_NONMAJOR && args->max_ac < an-major_ac) return 0; // max non-major AC
+    }
+    if (args->min_af!=-1)
+    {
+        if (an == 0) return 0; // freq not defined, skip site
+        if (args->min_af_type == ALLELE_NONREF && args->min_af>non_ref_ac/(double)an) return 0; // min AF
+        else if (args->min_af_type == ALLELE_MINOR && args->min_af>minor_ac/(double)an) return 0; // min minor AF
+        else if (args->min_af_type == ALLELE_ALT1 && args->min_af>args->ac[1]/(double)an) return 0; // min 1st alternate AF
+        else if (args->min_af_type == ALLELE_MAJOR && args->min_af > major_ac/(double)an) return 0; // min major AF
+        else if (args->min_af_type == ALLELE_NONMAJOR && args->min_af > (an-major_ac)/(double)an) return 0; // min non-major AF
+    }
+    if (args->max_af!=-1)
+    {
+        if (an == 0) return 0; // freq not defined, skip site
+        if (args->max_af_type == ALLELE_NONREF && args->max_af<non_ref_ac/(double)an) return 0; // max AF
+        else if (args->max_af_type == ALLELE_MINOR && args->max_af<minor_ac/(double)an) return 0; // max minor AF
+        else if (args->max_af_type == ALLELE_ALT1 && args->max_af<args->ac[1]/(double)an) return 0; // max 1st alternate AF
+        else if (args->max_af_type == ALLELE_MAJOR && args->max_af < major_ac/(double)an) return 0; // max major AF
+        else if (args->max_af_type == ALLELE_NONMAJOR && args->max_af < (an-major_ac)/(double)an) return 0; // max non-major AF
+    }
+    if (args->uncalled) {
+        if (args->uncalled == FLT_INCLUDE && an > 0) return 0; // select uncalled
+        if (args->uncalled == FLT_EXCLUDE && an == 0) return 0; // skip if uncalled
+    }
+    if (update_ac && args->update_info) {
+        bcf_update_info_int32(args->hdr, line, "AC", &args->ac[1], line->n_allele-1);
+        bcf_update_info_int32(args->hdr, line, "AN", &an, 1);
+    }
+    if (args->trim_alts)
+    {
+        int ret = bcf_trim_alleles(args->hsub ? args->hsub : args->hdr, line);
+        if ( ret<0 ) error("Error: Could not trim alleles at %s:%"PRId64"\n", bcf_seqname(args->hsub ? args->hsub : args->hdr, line), (int64_t) line->pos+1);
+    }
+    if (args->phased) {
+        int phased = bcf_all_phased(args->hdr, line);
+        if (args->phased == FLT_INCLUDE && !phased) { return 0; } // skip unphased
+        if (args->phased == FLT_EXCLUDE && phased) { return 0; } // skip phased
+    }
+    if (args->sites_only) bcf_subset(args->hsub ? args->hsub : args->hdr, line, 0, 0);
+    return 1;
+}
+
+void set_allele_type (int *atype, char *atype_string)
+{
+    *atype = ALLELE_NONREF;
+    if (strcmp(atype_string, "minor") == 0) {
+        *atype = ALLELE_MINOR;
+    }
+    else if (strcmp(atype_string, "alt1") == 0) {
+        *atype = ALLELE_ALT1;
+    }
+    else if (strcmp(atype_string, "nref") == 0) {
+        *atype = ALLELE_NONREF;
+    }
+    else if (strcmp(atype_string, "major") == 0) {
+        *atype = ALLELE_MAJOR;
+    }
+    else if (strcmp(atype_string, "nonmajor") == 0) {
+        *atype = ALLELE_NONMAJOR;
+    }
+    else {
+        error("Error: allele type not recognised. Expected one of nref|alt1|minor|major|nonmajor, got \"%s\".\n", atype_string);
+    }
+}
+
+static void usage(args_t *args)
+{
+    fprintf(bcftools_stderr, "\n");
+    fprintf(bcftools_stderr, "About:   VCF/BCF conversion, view, subset and filter VCF/BCF files.\n");
+    fprintf(bcftools_stderr, "Usage:   bcftools view [options] <in.vcf.gz> [region1 [...]]\n");
+    fprintf(bcftools_stderr, "\n");
+    fprintf(bcftools_stderr, "Output options:\n");
+    fprintf(bcftools_stderr, "    -G, --drop-genotypes              Drop individual genotype information (after subsetting if -s option set)\n");
+    fprintf(bcftools_stderr, "    -h, --header-only                 Print only the header in VCF output (equivalent to bcftools head)\n");
+    fprintf(bcftools_stderr, "    -H, --no-header                   Suppress the header in VCF output\n");
+    fprintf(bcftools_stderr, "        --with-header                 Print both header and records in VCF output [default]\n");
+    fprintf(bcftools_stderr, "    -l, --compression-level [0-9]     Compression level: 0 uncompressed, 1 best speed, 9 best compression [%d]\n", args->clevel);
+    fprintf(bcftools_stderr, "        --no-version                  Do not append version and command line to the header\n");
+    fprintf(bcftools_stderr, "    -o, --output FILE                 Output file name [bcftools_stdout]\n");
+    fprintf(bcftools_stderr, "    -O, --output-type u|b|v|z[0-9]    u/b: un/compressed BCF, v/z: un/compressed VCF, 0-9: compression level [v]\n");
+    fprintf(bcftools_stderr, "    -r, --regions REGION              Restrict to comma-separated list of regions\n");
+    fprintf(bcftools_stderr, "    -R, --regions-file FILE           Restrict to regions listed in FILE\n");
+    fprintf(bcftools_stderr, "        --regions-overlap 0|1|2       Include if POS in the region (0), record overlaps (1), variant overlaps (2) [1]\n");
+    fprintf(bcftools_stderr, "    -t, --targets [^]REGION           Similar to -r but streams rather than index-jumps. Exclude regions with \"^\" prefix\n");
+    fprintf(bcftools_stderr, "    -T, --targets-file [^]FILE        Similar to -R but streams rather than index-jumps. Exclude regions with \"^\" prefix\n");
+    fprintf(bcftools_stderr, "        --targets-overlap 0|1|2       Include if POS in the region (0), record overlaps (1), variant overlaps (2) [0]\n");
+    fprintf(bcftools_stderr, "        --threads INT                 Use multithreading with INT worker threads [0]\n");
+    fprintf(bcftools_stderr, "\n");
+    fprintf(bcftools_stderr, "Subset options:\n");
+    fprintf(bcftools_stderr, "    -a, --trim-alt-alleles            Trim ALT alleles not seen in the genotype fields (or their subset with -s/-S)\n");
+    fprintf(bcftools_stderr, "    -I, --no-update                   Do not (re)calculate INFO fields for the subset (currently INFO/AC and INFO/AN)\n");
+    fprintf(bcftools_stderr, "    -s, --samples [^]LIST             Comma separated list of samples to include (or exclude with \"^\" prefix)\n");
+    fprintf(bcftools_stderr, "    -S, --samples-file [^]FILE        File of samples to include (or exclude with \"^\" prefix)\n");
+    fprintf(bcftools_stderr, "        --force-samples               Only warn about unknown subset samples\n");
+    fprintf(bcftools_stderr, "\n");
+    fprintf(bcftools_stderr, "Filter options:\n");
+    fprintf(bcftools_stderr, "    -c/C, --min-ac/--max-ac INT[:TYPE]     Minimum/maximum count for non-reference (nref), 1st alternate (alt1), least frequent\n");
+    fprintf(bcftools_stderr, "                                               (minor), most frequent (major) or sum of all but most frequent (nonmajor) alleles [nref]\n");
+    fprintf(bcftools_stderr, "    -f,   --apply-filters LIST             Require at least one of the listed FILTER strings (e.g. \"PASS,.\")\n");
+    fprintf(bcftools_stderr, "    -g,   --genotype [^]hom|het|miss       Require one or more hom/het/missing genotype or, if prefixed with \"^\", exclude such sites\n");
+    fprintf(bcftools_stderr, "    -i/e, --include/--exclude EXPR         Select/exclude sites for which the expression is true (see man page for details)\n");
+    fprintf(bcftools_stderr, "    -k/n, --known/--novel                  Select known/novel sites only (ID is not/is '.')\n");
+    fprintf(bcftools_stderr, "    -m/M, --min-alleles/--max-alleles INT  Minimum/maximum number of alleles listed in REF and ALT (e.g. -m2 -M2 for biallelic sites)\n");
+    fprintf(bcftools_stderr, "    -p/P, --phased/--exclude-phased        Select/exclude sites where all samples are phased\n");
+    fprintf(bcftools_stderr, "    -q/Q, --min-af/--max-af FLOAT[:TYPE]   Minimum/maximum frequency for non-reference (nref), 1st alternate (alt1), least frequent\n");
+    fprintf(bcftools_stderr, "                                               (minor), most frequent (major) or sum of all but most frequent (nonmajor) alleles [nref]\n");
+    fprintf(bcftools_stderr, "    -u/U, --uncalled/--exclude-uncalled    Select/exclude sites without a called genotype\n");
+    fprintf(bcftools_stderr, "    -v/V, --types/--exclude-types LIST     Select/exclude comma-separated list of variant types: snps,indels,mnps,ref,bnd,other [null]\n");
+    fprintf(bcftools_stderr, "    -x/X, --private/--exclude-private      Select/exclude sites where the non-reference alleles are exclusive (private) to the subset samples\n");
+    fprintf(bcftools_stderr, "\n");
+    bcftools_exit(1);
+}
+
+int main_vcfview(int argc, char *argv[])
+{
+    int c;
+    args_t *args  = (args_t*) calloc(1,sizeof(args_t));
+    args->argc    = argc; args->argv = argv;
+    args->files   = bcf_sr_init();
+    args->clevel  = -1;
+    args->print_header = 1;
+    args->update_info = 1;
+    args->output_type = FT_VCF;
+    args->n_threads = 0;
+    args->record_cmd_line = 1;
+    args->min_ac = args->max_ac = args->min_af = args->max_af = -1;
+    args->regions_overlap = 1;
+    args->targets_overlap = 0;
+    int targets_is_file = 0, regions_is_file = 0;
+
+    static struct option loptions[] =
+    {
+        {"genotype",required_argument,NULL,'g'},
+        {"compression-level",required_argument,NULL,'l'},
+        {"threads",required_argument,NULL,9},
+        {"header-only",no_argument,NULL,'h'},
+        {"no-header",no_argument,NULL,'H'},
+        {"with-header",no_argument,NULL,4},
+        {"exclude",required_argument,NULL,'e'},
+        {"include",required_argument,NULL,'i'},
+        {"trim-alt-alleles",no_argument,NULL,'a'},
+        {"no-update",no_argument,NULL,'I'},
+        {"drop-genotypes",no_argument,NULL,'G'},
+        {"private",no_argument,NULL,'x'},
+        {"exclude-private",no_argument,NULL,'X'},
+        {"uncalled",no_argument,NULL,'u'},
+        {"exclude-uncalled",no_argument,NULL,'U'},
+        {"apply-filters",required_argument,NULL,'f'},
+        {"known",no_argument,NULL,'k'},
+        {"novel",no_argument,NULL,'n'},
+        {"min-alleles",required_argument,NULL,'m'},
+        {"max-alleles",required_argument,NULL,'M'},
+        {"samples",required_argument,NULL,'s'},
+        {"samples-file",required_argument,NULL,'S'},
+        {"force-samples",no_argument,NULL,1},
+        {"output-type",required_argument,NULL,'O'},
+        {"output-file",required_argument,NULL,'o'},
+        {"output",required_argument,NULL,'o'},
+        {"types",required_argument,NULL,'v'},
+        {"exclude-types",required_argument,NULL,'V'},
+        {"targets",required_argument,NULL,'t'},
+        {"targets-file",required_argument,NULL,'T'},
+        {"targets-overlap",required_argument,NULL,2},
+        {"regions",required_argument,NULL,'r'},
+        {"regions-file",required_argument,NULL,'R'},
+        {"regions-overlap",required_argument,NULL,3},
+        {"min-ac",required_argument,NULL,'c'},
+        {"max-ac",required_argument,NULL,'C'},
+        {"min-af",required_argument,NULL,'q'},
+        {"max-af",required_argument,NULL,'Q'},
+        {"phased",no_argument,NULL,'p'},
+        {"exclude-phased",no_argument,NULL,'P'},
+        {"no-version",no_argument,NULL,8},
+        {NULL,0,NULL,0}
+    };
+    char *tmp;
+    while ((c = getopt_long(argc, argv, "l:t:T:r:R:o:O:s:S:Gf:knv:V:m:M:auUhHc:C:Ii:e:xXpPq:Q:g:",loptions,NULL)) >= 0)
+    {
+        char allele_type[9] = "nref";
+        switch (c)
+        {
+            case 'O':
+                switch (optarg[0]) {
+                    case 'b': args->output_type = FT_BCF_GZ; break;
+                    case 'u': args->output_type = FT_BCF; break;
+                    case 'z': args->output_type = FT_VCF_GZ; break;
+                    case 'v': args->output_type = FT_VCF; break;
+                    default:
+                    {
+                        args->clevel = strtol(optarg,&tmp,10);
+                        if ( *tmp || args->clevel<0 || args->clevel>9 ) error("The output type \"%s\" not recognised\n", optarg);
+                    }
+                };
+                if ( optarg[1] )
+                {
+                    args->clevel = strtol(optarg+1,&tmp,10);
+                    if ( *tmp || args->clevel<0 || args->clevel>9 ) error("Could not parse argument: --compression-level %s\n", optarg+1);
+                }
+                break;
+            case 'l':
+                args->clevel = strtol(optarg,&tmp,10);
+                if ( *tmp ) error("Could not parse argument: --compression-level %s\n", optarg);
+                args->output_type |= FT_GZ; 
+                break;
+            case 'o': args->fn_out = optarg; break;
+            case 'H': args->print_header = 0; break;
+            case 'h': args->header_only = 1; break;
+            case  4 : args->print_header = 1; args->header_only = 0; break;
+
+            case 't': args->targets_list = optarg; break;
+            case 'T': args->targets_list = optarg; targets_is_file = 1; break;
+            case 'r': args->regions_list = optarg; break;
+            case 'R': args->regions_list = optarg; regions_is_file = 1; break;
+
+            case 's': args->sample_names = optarg; break;
+            case 'S': args->sample_names = optarg; args->sample_is_file = 1; break;
+            case  1 : args->force_samples = 1; break;
+            case 'a': args->trim_alts = 1; args->calc_ac = 1; break;
+            case 'I': args->update_info = 0; break;
+            case 'G': args->sites_only = 1; break;
+
+            case 'f': args->files->apply_filters = optarg; break;
+            case 'k': args->known = 1; break;
+            case 'n': args->novel = 1; break;
+            case 'm':
+                args->min_alleles = strtol(optarg,&tmp,10);
+                if ( *tmp ) error("Could not parse argument: --min-alleles %s\n", optarg);
+                break;
+            case 'M': 
+                args->max_alleles = strtol(optarg,&tmp,10);
+                if ( *tmp ) error("Could not parse argument: --max-alleles %s\n", optarg);
+                break;
+            case 'v': args->include_types = optarg; break;
+            case 'V': args->exclude_types = optarg; break;
+            case 'e':
+                if ( args->filter_str ) error("Error: only one -i or -e expression can be given, and they cannot be combined\n");
+                args->filter_str = optarg; args->filter_logic |= FLT_EXCLUDE; break;
+            case 'i':
+                if ( args->filter_str ) error("Error: only one -i or -e expression can be given, and they cannot be combined\n");
+                args->filter_str = optarg; args->filter_logic |= FLT_INCLUDE; break;
+            case 'c':
+            {
+                args->min_ac_type = ALLELE_NONREF;
+                if ( sscanf(optarg,"%d:%8s",&args->min_ac, allele_type)!=2 && sscanf(optarg,"%d",&args->min_ac)!=1 )
+                    error("Error: Could not parse --min-ac %s\n", optarg);
+                set_allele_type(&args->min_ac_type, allele_type);
+                args->calc_ac = 1;
+                break;
+            }
+            case 'C':
+            {
+                args->max_ac_type = ALLELE_NONREF;
+                if ( sscanf(optarg,"%d:%8s",&args->max_ac, allele_type)!=2 && sscanf(optarg,"%d",&args->max_ac)!=1 )
+                    error("Error: Could not parse --max-ac %s\n", optarg);
+                set_allele_type(&args->max_ac_type, allele_type);
+                args->calc_ac = 1;
+                break;
+            }
+            case 'q':
+            {
+                args->min_af_type = ALLELE_NONREF;
+                if ( sscanf(optarg,"%f:%8s",&args->min_af, allele_type)!=2 && sscanf(optarg,"%f",&args->min_af)!=1 )
+                    error("Error: Could not parse --min-af %s\n", optarg);
+                set_allele_type(&args->min_af_type, allele_type);
+                args->calc_ac = 1;
+                break;
+            }
+            case 'Q':
+            {
+                args->max_af_type = ALLELE_NONREF;
+                if ( sscanf(optarg,"%f:%8s",&args->max_af, allele_type)!=2 && sscanf(optarg,"%f",&args->max_af)!=1 )
+                    error("Error: Could not parse --max-af %s\n", optarg);
+                set_allele_type(&args->max_af_type, allele_type);
+                args->calc_ac = 1;
+                break;
+            }
+
+            case 'x': args->private_vars |= FLT_INCLUDE; args->calc_ac = 1; break;
+            case 'X': args->private_vars |= FLT_EXCLUDE; args->calc_ac = 1; break;
+            case 'u': args->uncalled |= FLT_INCLUDE; args->calc_ac = 1; break;
+            case 'U': args->uncalled |= FLT_EXCLUDE; args->calc_ac = 1; break;
+            case 'p': args->phased |= FLT_INCLUDE; break; // phased
+            case 'P': args->phased |= FLT_EXCLUDE; break; // exclude-phased
+            case 'g':
+            {
+                if ( !strcasecmp(optarg,"hom") ) args->gt_type = GT_NEED_HOM;
+                else if ( !strcasecmp(optarg,"het") ) args->gt_type = GT_NEED_HET;
+                else if ( !strcasecmp(optarg,"miss") ) args->gt_type = GT_NEED_MISSING;
+                else if ( !strcasecmp(optarg,"^hom") ) args->gt_type = GT_NO_HOM;
+                else if ( !strcasecmp(optarg,"^het") ) args->gt_type = GT_NO_HET;
+                else if ( !strcasecmp(optarg,"^miss") ) args->gt_type = GT_NO_MISSING;
+                else error("The argument to -g not recognised. Expected one of hom/het/miss/^hom/^het/^miss, got \"%s\".\n", optarg);
+                break;
+            }
+            case  2 :
+                args->targets_overlap = parse_overlap_option(optarg);
+                if ( args->targets_overlap < 0 ) error("Could not parse: --targets-overlap %s\n",optarg);
+                break;
+            case  3 :
+                args->regions_overlap = parse_overlap_option(optarg);
+                if ( args->regions_overlap < 0 ) error("Could not parse: --regions-overlap %s\n",optarg);
+                break;
+            case  9 : args->n_threads = strtol(optarg, 0, 0); break;
+            case  8 : args->record_cmd_line = 0; break;
+            case '?': usage(args); break;
+            default: error("Unknown argument: %s\n", optarg);
+        }
+    }
+
+    if ( args->filter_logic == (FLT_EXCLUDE|FLT_INCLUDE) ) error("Only one of -i or -e can be given.\n");
+    if ( args->private_vars > FLT_EXCLUDE ) error("Only one of -x or -X can be given.\n");
+    if ( args->uncalled > FLT_EXCLUDE ) error("Only one of -u or -U can be given.\n");
+    if ( args->phased > FLT_EXCLUDE ) error("Only one of -p or -P can be given.\n");
+
+    if ( args->sample_names && args->update_info) args->calc_ac = 1;
+
+    char *fname = NULL;
+    if ( optind>=argc )
+    {
+        if ( !isatty(fileno((FILE *)stdin)) ) fname = "-";  // reading from stdin
+        else usage(args);
+    }
+    else fname = argv[optind];
+
+    // read in the regions from the command line
+    if ( args->regions_list )
+    {
+        bcf_sr_set_opt(args->files,BCF_SR_REGIONS_OVERLAP,args->regions_overlap);
+        if ( bcf_sr_set_regions(args->files, args->regions_list, regions_is_file)<0 )
+            error("Failed to read the regions: %s\n", args->regions_list);
+    }
+    else if ( optind+1 < argc )
+    {
+        int i;
+        kstring_t tmp = {0,0,0};
+        kputs(argv[optind+1],&tmp);
+        for (i=optind+2; i<argc; i++) { kputc(',',&tmp); kputs(argv[i],&tmp); }
+        if ( bcf_sr_set_regions(args->files, tmp.s, 0)<0 )
+            error("Failed to read the regions: %s\n", tmp.s);
+        free(tmp.s);
+    }
+    if ( args->targets_list )
+    {
+        bcf_sr_set_opt(args->files,BCF_SR_TARGETS_OVERLAP,args->targets_overlap);
+        if ( bcf_sr_set_targets(args->files, args->targets_list, targets_is_file, 0)<0 )
+            error("Failed to read the targets: %s\n", args->targets_list);
+    }
+
+    if ( bcf_sr_set_threads(args->files, args->n_threads)<0 ) error("Failed to create threads\n");
+    if ( !bcf_sr_add_reader(args->files, fname) ) error("Failed to read from %s: %s\n", !strcmp("-",fname)?"standard input":fname,bcf_sr_strerror(args->files->errnum));
+
+    init_data(args);
+    bcf_hdr_t *out_hdr = args->hnull ? args->hnull : (args->hsub ? args->hsub : args->hdr);
+    if (args->print_header)
+    {
+        if ( bcf_hdr_write(args->out, out_hdr)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->fn_out);
+    }
+    else if ( args->output_type & FT_BCF )
+        error("BCF output requires header, cannot proceed with -H\n");
+
+    int ret = 0;
+    if (!args->header_only)
+    {
+        while ( bcf_sr_next_line(args->files) )
+        {
+            bcf1_t *line = args->files->readers[0].buffer[0];
+            if ( line->errcode && out_hdr!=args->hdr ) error("Undefined tags in the header, cannot proceed in the sample subset mode.\n");
+            if ( subset_vcf(args, line) && bcf_write1(args->out, out_hdr, line)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->fn_out);
+        }
+        ret = args->files->errnum;
+        if ( ret ) fprintf(bcftools_stderr,"Error: %s\n", bcf_sr_strerror(args->files->errnum));
+    }
+    hts_close(args->out);
+    destroy_data(args);
+    bcf_sr_destroy(args->files);
+    free(args);
+    return ret;
+}
diff --git a/bcftools/vcmp.c b/bcftools/vcmp.c
new file mode 100644
index 0000000..dbdc4b7
--- /dev/null
+++ b/bcftools/vcmp.c
@@ -0,0 +1,155 @@
+/*  vcmp.c -- reference allele utility functions.
+
+    Copyright (C) 2013-2015, 2018 Genome Research Ltd.
+
+    Author: Petr Danecek <pd3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.  */
+
+#include <stdio.h>
+#include <string.h>
+#include <stdlib.h>
+#include <htslib/hts.h>
+#include <htslib/vcf.h>
+#include <ctype.h>
+#include "vcmp.h"
+
+struct _vcmp_t
+{
+    char *dref;
+    int ndref, mdref;   // ndref: positive when ref1 longer, negative when ref2 is longer
+    int nmatch;
+    int *map, mmap, nmap;
+    int *map_dip, mmap_dip, nmap_dip;
+};
+
+vcmp_t *vcmp_init()
+{
+    return (vcmp_t*)calloc(1,sizeof(vcmp_t));
+}
+
+void vcmp_destroy(vcmp_t *vcmp)
+{
+    free(vcmp->map_dip);
+    free(vcmp->map);
+    free(vcmp->dref);
+    free(vcmp);
+}
+
+int vcmp_set_ref(vcmp_t *vcmp, char *ref1, char *ref2)
+{
+    vcmp->ndref = 0;
+
+    char *a = ref1, *b = ref2;
+    while ( *a && *b && toupper(*a)==toupper(*b) ) { a++; b++; }
+    if ( !*a && !*b ) return 0;
+    if ( *a && *b ) return -1;  // refs not compatible
+
+    int i;
+    if ( *a )   // ref1 is longer
+    {
+        vcmp->nmatch = b-ref2;
+        while ( *a ) a++;
+        vcmp->ndref = (a-ref1) - vcmp->nmatch;
+        hts_expand(char,vcmp->ndref+1,vcmp->mdref,vcmp->dref);
+        for (i=0; i<vcmp->ndref; i++) vcmp->dref[i] = toupper(ref1[vcmp->nmatch+i]);
+        vcmp->dref[vcmp->ndref] = 0;
+        return 0;
+    }
+
+    // ref2 is longer
+    vcmp->nmatch = a-ref1;
+    while ( *b ) b++;
+    vcmp->ndref = (b-ref2) - vcmp->nmatch;
+    hts_expand(char,vcmp->ndref+1,vcmp->mdref,vcmp->dref);
+    for (i=0; i<vcmp->ndref; i++) vcmp->dref[i] = toupper(ref2[vcmp->nmatch+i]);
+    vcmp->dref[vcmp->ndref] = 0;
+    vcmp->ndref *= -1;
+    return 0;
+}
+
+int vcmp_find_allele(vcmp_t *vcmp, char **als1, int nals1, char *al2)
+{
+    int i, j;
+    for (i=0; i<nals1; i++)
+    {
+        char *a = als1[i], *b = al2;
+        while ( *a && *b && toupper(*a)==toupper(*b) ) { a++; b++; }
+        if ( *a && *b ) continue;   // mismatch
+        if ( !vcmp->ndref )
+        {
+            if ( !*a && !*b ) break;    // found
+            continue;
+        }
+
+        // the prefixes match
+        if ( *a )
+        {
+            if ( vcmp->ndref<0 ) continue;
+            for (j=0; j<vcmp->ndref; j++)
+                if ( !a[j] || toupper(a[j])!=vcmp->dref[j] ) break;
+            if ( j!=vcmp->ndref || a[j] ) continue;
+            break;  // found
+        }
+
+        if ( vcmp->ndref>0 ) continue;
+        for (j=0; j<-vcmp->ndref; j++)
+            if ( !b[j] || toupper(b[j])!=vcmp->dref[j] ) break;
+        if ( j!=-vcmp->ndref || b[j] ) continue;
+        break;  // found
+    }
+    if (i==nals1) return -1;
+    return i;
+}
+
+
+int *vcmp_map_ARvalues(vcmp_t *vcmp, int n, int nals1, char **als1, int nals2, char **als2)
+{
+    if ( vcmp_set_ref(vcmp,als1[0],als2[0]) < 0 ) return NULL;
+
+    vcmp->nmap = n;
+    hts_expand(int, vcmp->nmap, vcmp->mmap, vcmp->map);
+
+    int i, ifrom = n==nals2 ? 0 : 1;
+    for (i=ifrom; i<nals2; i++)
+    {
+        vcmp->map[i-ifrom] = vcmp_find_allele(vcmp, als1+ifrom, nals1-ifrom, als2[i]);
+    }
+    return vcmp->map;
+}
+
+int *vcmp_map_dipGvalues(vcmp_t *vcmp, int *nmap)
+{
+    vcmp->nmap_dip = vcmp->nmap*(vcmp->nmap+1)/2;
+    hts_expand(int, vcmp->nmap_dip, vcmp->mmap_dip, vcmp->map_dip);
+
+    int i, j, k = 0;
+    for (i=0; i<vcmp->nmap; i++)
+    {
+        for (j=0; j<=i; j++)
+        {
+            vcmp->map_dip[k] = vcmp->map[i]>=0 && vcmp->map[j]>=0 ? bcf_alleles2gt(vcmp->map[i],vcmp->map[j]) : -1;
+            k++;
+        }
+    }
+    *nmap = k;
+    return vcmp->map_dip;
+}
+
+
diff --git a/bcftools/vcmp.c.pysam.c b/bcftools/vcmp.c.pysam.c
new file mode 100644
index 0000000..18a6813
--- /dev/null
+++ b/bcftools/vcmp.c.pysam.c
@@ -0,0 +1,157 @@
+#include "bcftools.pysam.h"
+
+/*  vcmp.c -- reference allele utility functions.
+
+    Copyright (C) 2013-2015, 2018 Genome Research Ltd.
+
+    Author: Petr Danecek <pd3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.  */
+
+#include <stdio.h>
+#include <string.h>
+#include <stdlib.h>
+#include <htslib/hts.h>
+#include <htslib/vcf.h>
+#include <ctype.h>
+#include "vcmp.h"
+
+struct _vcmp_t
+{
+    char *dref;
+    int ndref, mdref;   // ndref: positive when ref1 longer, negative when ref2 is longer
+    int nmatch;
+    int *map, mmap, nmap;
+    int *map_dip, mmap_dip, nmap_dip;
+};
+
+vcmp_t *vcmp_init()
+{
+    return (vcmp_t*)calloc(1,sizeof(vcmp_t));
+}
+
+void vcmp_destroy(vcmp_t *vcmp)
+{
+    free(vcmp->map_dip);
+    free(vcmp->map);
+    free(vcmp->dref);
+    free(vcmp);
+}
+
+int vcmp_set_ref(vcmp_t *vcmp, char *ref1, char *ref2)
+{
+    vcmp->ndref = 0;
+
+    char *a = ref1, *b = ref2;
+    while ( *a && *b && toupper(*a)==toupper(*b) ) { a++; b++; }
+    if ( !*a && !*b ) return 0;
+    if ( *a && *b ) return -1;  // refs not compatible
+
+    int i;
+    if ( *a )   // ref1 is longer
+    {
+        vcmp->nmatch = b-ref2;
+        while ( *a ) a++;
+        vcmp->ndref = (a-ref1) - vcmp->nmatch;
+        hts_expand(char,vcmp->ndref+1,vcmp->mdref,vcmp->dref);
+        for (i=0; i<vcmp->ndref; i++) vcmp->dref[i] = toupper(ref1[vcmp->nmatch+i]);
+        vcmp->dref[vcmp->ndref] = 0;
+        return 0;
+    }
+
+    // ref2 is longer
+    vcmp->nmatch = a-ref1;
+    while ( *b ) b++;
+    vcmp->ndref = (b-ref2) - vcmp->nmatch;
+    hts_expand(char,vcmp->ndref+1,vcmp->mdref,vcmp->dref);
+    for (i=0; i<vcmp->ndref; i++) vcmp->dref[i] = toupper(ref2[vcmp->nmatch+i]);
+    vcmp->dref[vcmp->ndref] = 0;
+    vcmp->ndref *= -1;
+    return 0;
+}
+
+int vcmp_find_allele(vcmp_t *vcmp, char **als1, int nals1, char *al2)
+{
+    int i, j;
+    for (i=0; i<nals1; i++)
+    {
+        char *a = als1[i], *b = al2;
+        while ( *a && *b && toupper(*a)==toupper(*b) ) { a++; b++; }
+        if ( *a && *b ) continue;   // mismatch
+        if ( !vcmp->ndref )
+        {
+            if ( !*a && !*b ) break;    // found
+            continue;
+        }
+
+        // the prefixes match
+        if ( *a )
+        {
+            if ( vcmp->ndref<0 ) continue;
+            for (j=0; j<vcmp->ndref; j++)
+                if ( !a[j] || toupper(a[j])!=vcmp->dref[j] ) break;
+            if ( j!=vcmp->ndref || a[j] ) continue;
+            break;  // found
+        }
+
+        if ( vcmp->ndref>0 ) continue;
+        for (j=0; j<-vcmp->ndref; j++)
+            if ( !b[j] || toupper(b[j])!=vcmp->dref[j] ) break;
+        if ( j!=-vcmp->ndref || b[j] ) continue;
+        break;  // found
+    }
+    if (i==nals1) return -1;
+    return i;
+}
+
+
+int *vcmp_map_ARvalues(vcmp_t *vcmp, int n, int nals1, char **als1, int nals2, char **als2)
+{
+    if ( vcmp_set_ref(vcmp,als1[0],als2[0]) < 0 ) return NULL;
+
+    vcmp->nmap = n;
+    hts_expand(int, vcmp->nmap, vcmp->mmap, vcmp->map);
+
+    int i, ifrom = n==nals2 ? 0 : 1;
+    for (i=ifrom; i<nals2; i++)
+    {
+        vcmp->map[i-ifrom] = vcmp_find_allele(vcmp, als1+ifrom, nals1-ifrom, als2[i]);
+    }
+    return vcmp->map;
+}
+
+int *vcmp_map_dipGvalues(vcmp_t *vcmp, int *nmap)
+{
+    vcmp->nmap_dip = vcmp->nmap*(vcmp->nmap+1)/2;
+    hts_expand(int, vcmp->nmap_dip, vcmp->mmap_dip, vcmp->map_dip);
+
+    int i, j, k = 0;
+    for (i=0; i<vcmp->nmap; i++)
+    {
+        for (j=0; j<=i; j++)
+        {
+            vcmp->map_dip[k] = vcmp->map[i]>=0 && vcmp->map[j]>=0 ? bcf_alleles2gt(vcmp->map[i],vcmp->map[j]) : -1;
+            k++;
+        }
+    }
+    *nmap = k;
+    return vcmp->map_dip;
+}
+
+
diff --git a/bcftools/vcmp.h b/bcftools/vcmp.h
new file mode 100644
index 0000000..03234b4
--- /dev/null
+++ b/bcftools/vcmp.h
@@ -0,0 +1,63 @@
+/*  vcmp.h -- reference allele utility functions.
+
+    Copyright (C) 2013-2015 Genome Research Ltd.
+
+    Author: Petr Danecek <pd3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.  */
+
+#ifndef __VCMP_H__
+#define __VCMP_H__
+
+typedef struct _vcmp_t vcmp_t;
+
+vcmp_t *vcmp_init(void);
+void vcmp_destroy(vcmp_t *vcmp);
+
+/*
+ *  vcmp_set_ref() - sets and compares reference alleles
+ *  Returns 0 on success or -1 if alleles not compatible
+ */
+int vcmp_set_ref(vcmp_t *vcmp, char *ref1, char *ref2);
+
+/*
+ *  vcmp_find_allele()
+ *  @param als1:  alternate alleles to ref1 above
+ *  @param al2:   alternate allele to ref2 above
+ *  Returns -1 if not found or 0-based index to als1 of matching allele
+ */
+int vcmp_find_allele(vcmp_t *vcmp, char **als1, int nals1, char *al2);
+
+/*
+ *  vcmp_map_ARvalues() - Create mapping for Number=A,R tag values
+ *  @param number:  nals2 for Number=R, nals2-1 for Number=A
+ *  @param nals1:   number of alleles
+ *  @param als1:    alleles
+ *
+ *  Returns pointer to an array of size nals2 with mapping from als2
+ *  to als1 or NULL if REFs (als1[0] and als2[0]) are not compatible.
+ *  If i is the index of an allele in als2, ret[i] is the index of matching
+ *  allele in als1 or -1 if als2 does not have a matching allele.
+ *  The caller must not free the array.
+ */
+int *vcmp_map_ARvalues(vcmp_t *vcmp, int number, int nals1, char **als1, int nals2, char **als2);
+
+int *vcmp_map_dipGvalues(vcmp_t *vcmp, int *nmap);
+
+#endif
diff --git a/bcftools/version.c b/bcftools/version.c
new file mode 100644
index 0000000..4306d40
--- /dev/null
+++ b/bcftools/version.c
@@ -0,0 +1,109 @@
+/*  version.c -- report version numbers for plugins.
+
+    Copyright (C) 2014-2021 Genome Research Ltd.
+
+    Author: Petr Danecek <pd3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <stdarg.h>
+#include <stdlib.h>
+#include <stdio.h>
+#include <strings.h>
+#include <errno.h>
+#include <htslib/hts.h>
+#include "bcftools.h"
+#include "version.h"
+
+void version(const char **bcftools_version, const char **htslib_version)
+{
+    *bcftools_version = BCFTOOLS_VERSION;
+    *htslib_version = hts_version();
+}
+
+void error(const char *format, ...)
+{
+    va_list ap;
+    va_start(ap, format);
+    vfprintf(stderr, format, ap);
+    va_end(ap);
+    exit(-1);
+}
+
+void error_errno(const char *format, ...)
+{
+    va_list ap;
+    int e = errno;
+    va_start(ap, format);
+    vfprintf(stderr, format, ap);
+    va_end(ap);
+    if (e) {
+        fprintf(stderr, ": %s\n", strerror(e));
+    } else {
+        fprintf(stderr, "\n");
+    }
+    exit(-1);
+}
+
+const char *hts_bcf_wmode(int file_type)
+{
+    if ( file_type == FT_BCF ) return "wbu";    // uncompressed BCF
+    if ( file_type & FT_BCF ) return "wb";      // compressed BCF
+    if ( file_type & FT_GZ ) return "wz";       // compressed VCF
+    return "w";                                 // uncompressed VCF
+}
+
+const char *hts_bcf_wmode2(int file_type, const char *fname)
+{
+    if ( !fname ) return hts_bcf_wmode(file_type);
+    int len = strlen(fname);
+    if ( len >= 4 && !strcasecmp(".bcf",fname+len-4) ) return hts_bcf_wmode(FT_BCF|FT_GZ);
+    if ( len >= 4 && !strcasecmp(".vcf",fname+len-4) ) return hts_bcf_wmode(FT_VCF);
+    if ( len >= 7 && !strcasecmp(".vcf.gz",fname+len-7) ) return hts_bcf_wmode(FT_VCF|FT_GZ);
+    if ( len >= 8 && !strcasecmp(".vcf.bgz",fname+len-8) ) return hts_bcf_wmode(FT_VCF|FT_GZ);
+    return hts_bcf_wmode(file_type);
+}
+
+void set_wmode(char dst[8], int file_type, const char *fname, int clevel)
+{
+    const char *ret = NULL;
+    int len = fname ? strlen(fname) : 0;
+    if ( len >= 4 && !strcasecmp(".bcf",fname+len-4) ) ret = hts_bcf_wmode(FT_BCF|FT_GZ);
+    else if ( len >= 4 && !strcasecmp(".vcf",fname+len-4) ) ret = hts_bcf_wmode(FT_VCF);
+    else if ( len >= 7 && !strcasecmp(".vcf.gz",fname+len-7) ) ret = hts_bcf_wmode(FT_VCF|FT_GZ);
+    else if ( len >= 8 && !strcasecmp(".vcf.bgz",fname+len-8) ) ret = hts_bcf_wmode(FT_VCF|FT_GZ);
+    else ret = hts_bcf_wmode(file_type);
+    if ( clevel>=0 && clevel<=9 )
+    {
+        if ( strchr(ret,'v') || strchr(ret,'u') ) error("Error: compression level (%d) cannot be set on uncompressed streams (%s)\n",clevel,fname);
+        len = strlen(ret);
+        if ( len>6 ) error("Fixme: %s\n", ret);
+        sprintf(dst, "%s%d", ret, clevel);
+    }
+    else
+        strcpy(dst, ret);
+}
+
+int parse_overlap_option(const char *arg)
+{
+    if ( strcasecmp(arg, "pos") == 0 || strcmp(arg, "0") == 0 ) return 0;
+    else if ( strcasecmp(arg, "record") == 0 || strcmp(arg, "1") == 0 ) return 1;
+    else if ( strcasecmp(arg, "variant") == 0 || strcmp(arg, "2") == 0 ) return 2;
+    else return -1;
+}
diff --git a/bcftools/version.c.pysam.c b/bcftools/version.c.pysam.c
new file mode 100644
index 0000000..df12fc4
--- /dev/null
+++ b/bcftools/version.c.pysam.c
@@ -0,0 +1,111 @@
+#include "bcftools.pysam.h"
+
+/*  version.c -- report version numbers for plugins.
+
+    Copyright (C) 2014-2021 Genome Research Ltd.
+
+    Author: Petr Danecek <pd3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <stdarg.h>
+#include <stdlib.h>
+#include <stdio.h>
+#include <strings.h>
+#include <errno.h>
+#include <htslib/hts.h>
+#include "bcftools.h"
+#include "version.h"
+
+void version(const char **bcftools_version, const char **htslib_version)
+{
+    *bcftools_version = BCFTOOLS_VERSION;
+    *htslib_version = hts_version();
+}
+
+void error(const char *format, ...)
+{
+    va_list ap;
+    va_start(ap, format);
+    vfprintf(bcftools_stderr, format, ap);
+    va_end(ap);
+    bcftools_exit(-1);
+}
+
+void error_errno(const char *format, ...)
+{
+    va_list ap;
+    int e = errno;
+    va_start(ap, format);
+    vfprintf(bcftools_stderr, format, ap);
+    va_end(ap);
+    if (e) {
+        fprintf(bcftools_stderr, ": %s\n", strerror(e));
+    } else {
+        fprintf(bcftools_stderr, "\n");
+    }
+    bcftools_exit(-1);
+}
+
+const char *hts_bcf_wmode(int file_type)
+{
+    if ( file_type == FT_BCF ) return "wbu";    // uncompressed BCF
+    if ( file_type & FT_BCF ) return "wb";      // compressed BCF
+    if ( file_type & FT_GZ ) return "wz";       // compressed VCF
+    return "w";                                 // uncompressed VCF
+}
+
+const char *hts_bcf_wmode2(int file_type, const char *fname)
+{
+    if ( !fname ) return hts_bcf_wmode(file_type);
+    int len = strlen(fname);
+    if ( len >= 4 && !strcasecmp(".bcf",fname+len-4) ) return hts_bcf_wmode(FT_BCF|FT_GZ);
+    if ( len >= 4 && !strcasecmp(".vcf",fname+len-4) ) return hts_bcf_wmode(FT_VCF);
+    if ( len >= 7 && !strcasecmp(".vcf.gz",fname+len-7) ) return hts_bcf_wmode(FT_VCF|FT_GZ);
+    if ( len >= 8 && !strcasecmp(".vcf.bgz",fname+len-8) ) return hts_bcf_wmode(FT_VCF|FT_GZ);
+    return hts_bcf_wmode(file_type);
+}
+
+void set_wmode(char dst[8], int file_type, const char *fname, int clevel)
+{
+    const char *ret = NULL;
+    int len = fname ? strlen(fname) : 0;
+    if ( len >= 4 && !strcasecmp(".bcf",fname+len-4) ) ret = hts_bcf_wmode(FT_BCF|FT_GZ);
+    else if ( len >= 4 && !strcasecmp(".vcf",fname+len-4) ) ret = hts_bcf_wmode(FT_VCF);
+    else if ( len >= 7 && !strcasecmp(".vcf.gz",fname+len-7) ) ret = hts_bcf_wmode(FT_VCF|FT_GZ);
+    else if ( len >= 8 && !strcasecmp(".vcf.bgz",fname+len-8) ) ret = hts_bcf_wmode(FT_VCF|FT_GZ);
+    else ret = hts_bcf_wmode(file_type);
+    if ( clevel>=0 && clevel<=9 )
+    {
+        if ( strchr(ret,'v') || strchr(ret,'u') ) error("Error: compression level (%d) cannot be set on uncompressed streams (%s)\n",clevel,fname);
+        len = strlen(ret);
+        if ( len>6 ) error("Fixme: %s\n", ret);
+        sprintf(dst, "%s%d", ret, clevel);
+    }
+    else
+        strcpy(dst, ret);
+}
+
+int parse_overlap_option(const char *arg)
+{
+    if ( strcasecmp(arg, "pos") == 0 || strcmp(arg, "0") == 0 ) return 0;
+    else if ( strcasecmp(arg, "record") == 0 || strcmp(arg, "1") == 0 ) return 1;
+    else if ( strcasecmp(arg, "variant") == 0 || strcmp(arg, "2") == 0 ) return 2;
+    else return -1;
+}
diff --git a/bcftools/version.sh b/bcftools/version.sh
new file mode 100755
index 0000000..5fbf8df
--- /dev/null
+++ b/bcftools/version.sh
@@ -0,0 +1,36 @@
+#!/bin/sh
+# version.sh 
+#
+#     Author : Petr Danecek <pd3@sanger.ac.uk>
+#
+#     Copyright (C) 2018-2021 Genome Research Ltd.
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+# THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+# DEALINGS IN THE SOFTWARE.
+
+# Master version, for use in tarballs or non-git source copies
+VERSION=1.16
+
+# If we have a git clone, then check against the current tag
+if [ -e .git ]
+then
+    # If we ever get to 10.x this will need to be more liberal
+    VERSION=`git describe --match '[0-9].[0-9]*' --dirty --always`
+fi
+
+echo $VERSION
diff --git a/cy_build.py b/cy_build.py
new file mode 100644
index 0000000..2726e94
--- /dev/null
+++ b/cy_build.py
@@ -0,0 +1,90 @@
+import os
+import re
+import sys
+
+try:
+    from Cython.Distutils import build_ext
+except ImportError:
+    from setuptools.command.build_ext import build_ext
+
+from distutils.extension import Extension
+from distutils.sysconfig import get_config_vars, get_python_version
+from pkg_resources import Distribution
+
+
+if sys.platform == 'darwin':
+    config_vars = get_config_vars()
+    config_vars['LDSHARED'] = config_vars['LDSHARED'].replace('-bundle', '')
+    config_vars['SHLIB_EXT'] = '.so'
+
+
+def is_pip_install():
+    if "_" in os.environ and os.environ["_"].endswith("pip"):
+        return True
+    if "pip-egg-info" in sys.argv:
+        return True
+    if re.search("/pip-.*-build/", __file__):
+        return True
+    return False
+
+
+class CyExtension(Extension):
+    def __init__(self, *args, **kwargs):
+        self._init_func = kwargs.pop("init_func", None)
+        self._prebuild_func = kwargs.pop("prebuild_func", None)
+        Extension.__init__(self, *args, **kwargs)
+
+    def extend_includes(self, includes):
+        self.include_dirs.extend(includes)
+
+    def extend_macros(self, macros):
+        self.define_macros.extend(macros)
+
+    def extend_extra_objects(self, objs):
+        self.extra_objects.extend(objs)
+
+
+class cy_build_ext(build_ext):
+
+    def _get_egg_name(self):
+        ei_cmd = self.get_finalized_command("egg_info")
+        return Distribution(
+            None, None, ei_cmd.egg_name, ei_cmd.egg_version, get_python_version(),
+            self.distribution.has_ext_modules() and self.plat_name).egg_name()
+
+    def build_extension(self, ext):
+
+        if isinstance(ext, CyExtension) and ext._init_func:
+            ext._init_func(ext)
+
+        if not self.inplace:
+            ext.library_dirs.append(os.path.join(self.build_lib, "pysam"))
+
+        if sys.platform == 'darwin':
+            # The idea is to give shared libraries an install name of the form
+            # `@rpath/<library-name.so>`, and to set the rpath equal to
+            # @loader_path. This will allow Python packages to find the library
+            # in the expected place, while still giving enough flexibility to
+            # external applications to link against the library.
+            relative_module_path = ext.name.replace(".", os.sep) + get_config_vars()["SO"]
+            library_path = os.path.join(
+                "@rpath", os.path.basename(relative_module_path)
+            )
+
+            if not ext.extra_link_args:
+                ext.extra_link_args = []
+            ext.extra_link_args += ['-dynamiclib',
+                                    '-rpath', '@loader_path',
+                                    '-Wl,-headerpad_max_install_names',
+                                    '-Wl,-install_name,%s' % library_path,
+                                    '-Wl,-x']
+        else:
+            if not ext.extra_link_args:
+                ext.extra_link_args = []
+
+            ext.extra_link_args += ['-Wl,-rpath,$ORIGIN']
+
+        if isinstance(ext, CyExtension) and ext._prebuild_func:
+            ext._prebuild_func(ext, self.force)
+
+        build_ext.build_extension(self, ext)
diff --git a/devtools/buildwheels.sh b/devtools/buildwheels.sh
new file mode 100755
index 0000000..4d12566
--- /dev/null
+++ b/devtools/buildwheels.sh
@@ -0,0 +1,73 @@
+#!/bin/bash
+#
+# Build manylinux1 wheels for pysam. Based on the example at
+# <https://github.com/pypa/python-manylinux-demo>
+#
+# It is best to run this in a fresh clone of the repository!
+#
+# Before running, make sure to update image:
+#
+#   docker pull quay.io/pypa/manylinux1_x86_64
+#
+# Run this within the repository root:
+#   docker run --rm -v $(pwd):/io quay.io/pypa/manylinux1_x86_64 /io/buildwheels.sh
+#
+# The wheels will be put into the wheelhouse/ subdirectory.
+#
+# For interactive tests:
+#   docker run -it -v $(pwd):/io quay.io/pypa/manylinux1_x86_64 /bin/bash
+
+set -xeuo pipefail
+
+# For convenience, if this script is called from outside of a docker container,
+# it starts a container and runs itself inside of it.
+if ! grep -q docker /proc/1/cgroup; then
+  # We are not inside a container
+  exec docker run --rm -v $(pwd):/io quay.io/pypa/manylinux1_x86_64 /io/$0
+fi
+
+yum install -y zlib-devel bzip2-devel xz-devel
+
+# Without libcurl support, htslib can open files from HTTP and FTP URLs.
+# With libcurl support, it also supports HTTPS and S3 URLs, but libcurl needs a
+# current version of OpenSSL, and we do not want to be responsible for
+# updating the wheels as soon as there are any security issues. So disable
+# libcurl for now.
+# See also <https://github.com/pypa/manylinux/issues/74>.
+#
+export HTSLIB_CONFIGURE_OPTIONS="--disable-libcurl"
+
+PYBINS="/opt/python/*/bin"
+echo $PYBINS
+
+for PYBIN in ${PYBINS}; do
+    ${PYBIN}/pip install -r /io/requirements.txt
+    ${PYBIN}/pip wheel /io/ -w wheelhouse/
+done
+
+# Bundle external shared libraries into the wheels
+#
+# The '-L ""' option is a workaround. By default, auditwheel puts all external
+# libraries (.so files) into a .libs directory and sets the RUNPATH to $ORIGIN/.libs.
+# When HTSLIB_MODE is 'shared' (now the default), then all so libraries part of
+# pysam require that RUNPATH is set to $ORIGIN (without the .libs). It seems
+# auditwheel overwrites $ORIGIN with $ORIGIN/.libs. This workaround makes
+# auditwheel keeps the RUNPATH at "$ORIGIN" and put all the external libraries into
+# the pysam directory.
+for whl in wheelhouse/*.whl; do
+    auditwheel repair -L "" $whl -w /io/wheelhouse/
+done
+
+# mkdir -p /io/wheelhouse
+# cp wheelhouse/*.whl /io/wheelhouse
+
+# Created files are owned by root, so fix permissions.
+chown -R --reference=/io/setup.py /io/wheelhouse/
+
+# TODO Install packages and test them
+for PYBIN in ${PYBINS}; do
+   ${PYBIN}/pip install pysam --no-index -f /io/wheelhouse
+   # smoketest
+   (cd $HOME; ${PYBIN}/python -c 'import pysam')
+   # todo: add more tests
+done
diff --git a/devtools/conda-recipe/build.sh b/devtools/conda-recipe/build.sh
new file mode 100644
index 0000000..32b67db
--- /dev/null
+++ b/devtools/conda-recipe/build.sh
@@ -0,0 +1,8 @@
+#!/bin/bash
+
+# Use internal htslib
+chmod a+x ./htslib/configure
+export CFLAGS="-I${PREFIX}/include/curl/ -I${PREFIX}/include -L${PREFIX}/lib"
+export HTSLIB_CONFIGURE_OPTIONS="--disable-libcurl"
+
+$PYTHON setup.py install
diff --git a/devtools/conda-recipe/meta.yaml b/devtools/conda-recipe/meta.yaml
new file mode 100644
index 0000000..4e57895
--- /dev/null
+++ b/devtools/conda-recipe/meta.yaml
@@ -0,0 +1,29 @@
+package:
+  name: pysam
+  version: 0.8.5
+
+source:
+  path: ../../
+
+build:
+  number: 0
+
+requirements:
+  build:
+    - python
+    - setuptools
+    - zlib
+    - cython
+
+  run:
+    - python
+    - zlib
+
+test:
+  imports:
+    - pysam
+
+about:
+  home: https://github.com/pysam-developers/pysam
+  license: MIT
+  summary: Pysam is a python module for reading and manipulating Samfiles. It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix.
diff --git a/devtools/import.py b/devtools/import.py
new file mode 100644
index 0000000..90194d0
--- /dev/null
+++ b/devtools/import.py
@@ -0,0 +1,262 @@
+#################################################################
+# Importing samtools, bcftools, and htslib
+#
+# For each package PKG:
+#
+# rm -rf PKG
+# python import.py PKG path/to/download/PKG-X.Y
+
+import fnmatch
+import os
+import re
+import itertools
+import shutil
+import sys
+import hashlib
+
+
+EXCLUDE = {
+    "samtools": (
+        "test", "misc",
+        "bgzip.c",
+        "main.c",
+        "calDepth.c",
+        "bam2bed.c",
+        "bam_tview.c",
+        "bam_tview.h",
+        "bam_tview_html.c",
+        "bam_tview_curses.c",
+        "bam2bcf.c",
+        "bam2bcf.h",
+        "vcf-miniview.c",
+    ),
+    "bcftools": (
+        "test", "plugins", "peakfit.c",
+        "peakfit.h",
+        "polysomy.c"),
+    "htslib": (
+        'htslib/tabix.c', 'htslib/bgzip.c',
+        'htslib/htsfile.c',
+        "test", "tests"),
+}
+
+
+MAIN = {
+    "samtools": "bamtk",
+    "bcftools": "main"
+}
+
+
+C_VERSION = {
+    "htslib":   "HTS_VERSION_TEXT",
+    "samtools": "SAMTOOLS_VERSION",
+    "bcftools": "BCFTOOLS_VERSION"
+}
+
+
+def locate(pattern, root=os.curdir, exclude=[], exclude_htslib=False):
+    '''Locate all files matching supplied filename pattern (but not listed
+    in exclude) in and below the supplied root directory. Omit any files under
+    directories listed in exclude or (if exclude_htslib=True) matching /htslib-*/.
+    '''
+    for path, dirs, files in os.walk(os.path.abspath(root)):
+        for filename in fnmatch.filter(files, pattern):
+            if filename not in exclude:
+                yield os.path.join(path, filename)
+
+        for dirname in exclude:
+            if dirname in dirs: dirs.remove(dirname)
+        if exclude_htslib:
+            for dirname in [d for d in dirs if re.match(r"htslib-", d)]:
+                dirs.remove(dirname)
+
+
+def _update_pysam_files(cf, destdir):
+    '''update pysam files applying redirection of ouput'''
+    basename = os.path.basename(destdir)
+    for filename in cf:
+        if not filename:
+            continue
+        dest = filename + ".pysam.c"
+        with open(filename, encoding="utf-8") as infile:
+            lines = "".join(infile.readlines())
+
+            with open(dest, "w", encoding="utf-8") as outfile:
+                outfile.write('#include "{}.pysam.h"\n\n'.format(basename))
+                subname, _ = os.path.splitext(os.path.basename(filename))
+                if subname in MAIN.get(basename, []):
+                    lines = re.sub(r"int main\(", "int {}_main(".format(
+                        basename), lines)
+                else:
+                    lines = re.sub(r"int main\(", "int {}_{}_main(".format(
+                        basename, subname), lines)
+                lines = re.sub(r"\b({}_stdout)\b".format(basename), r"\1_internal", lines)
+                lines = re.sub(r"\bexit\(", "{}_exit(".format(basename), lines)
+                lines = re.sub(r"\bstderr\b", "{}_stderr".format(basename), lines)
+                lines = re.sub(r"\bstdout\b", "{}_stdout".format(basename), lines)
+                lines = re.sub(r" printf\(", " fprintf({}_stdout, ".format(basename), lines)
+                lines = re.sub(r"([^kf])puts\(", r"\1{}_puts(".format(basename), lines)
+                lines = re.sub(r"putchar\(([^)]+)\)",
+                               r"fputc(\1, {}_stdout)".format(basename), lines)
+
+                fn = os.path.basename(filename)
+                # some specific fixes:
+                SPECIFIC_SUBSTITUTIONS = {
+                    "bam_md.c": (
+                        'sam_open_format("-", mode_w',
+                        'sam_open_format({}_stdout_fn, mode_w'.format(basename)),
+                    "phase.c": (
+                        'putc("ACGT"[f->seq[j] == 1? (c&3, {}_stdout) : (c>>16&3)]);'.format(basename),
+                        'putc("ACGT"[f->seq[j] == 1? (c&3) : (c>>16&3)], {}_stdout);'.format(basename)),
+                    "cut_target.c": (
+                        'putc(33 + (cns[j]>>8>>2, {}_stdout));'.format(basename),
+                        'putc(33 + (cns[j]>>8>>2), {}_stdout);'.format(basename))
+                    }
+                if fn in SPECIFIC_SUBSTITUTIONS:
+                    lines = lines.replace(
+                        SPECIFIC_SUBSTITUTIONS[fn][0],
+                        SPECIFIC_SUBSTITUTIONS[fn][1])
+                if fn == "bamtk.c":
+                    lines = re.sub(r'(#include "version.h")', r'\1\n#include "samtools_config_vars.h"', lines)
+                    lines = re.sub(r'(else if.*"tview")', r'//\1', lines)
+
+                outfile.write(lines)
+
+    with open(os.path.join("import", "pysam.h")) as inf, \
+         open(os.path.join(destdir, "{}.pysam.h".format(basename)), "w") as outf:
+        outf.write(re.sub("@pysam@", basename, inf.read()))
+
+    with open(os.path.join("import", "pysam.c")) as inf, \
+         open(os.path.join(destdir, "{}.pysam.c".format(basename)), "w") as outf:
+        outf.write(re.sub("@pysam@", basename, inf.read()))
+
+
+if len(sys.argv) >= 1:
+    if len(sys.argv) != 3:
+        raise ValueError("import requires dest src")
+
+    dest, srcdir = sys.argv[1:3]
+    if dest not in EXCLUDE:
+        raise ValueError("import expected one of %s" %
+                         ",".join(EXCLUDE.keys()))
+    exclude = EXCLUDE[dest]
+    destdir = os.path.abspath(dest)
+    srcdir = os.path.abspath(srcdir)
+    if not os.path.exists(srcdir):
+        raise IOError(
+            "source directory `%s` does not exist." % srcdir)
+
+    cfiles = locate("*.c", srcdir, exclude=exclude, exclude_htslib=True)
+    hfiles = locate("*.h", srcdir, exclude=exclude, exclude_htslib=True)
+    mfiles = itertools.chain(locate("README", srcdir), locate("LICENSE", srcdir),
+                             locate("version.sh", srcdir, exclude_htslib=True))
+
+    if dest == "htslib":
+        # Add build files, including *.ac *.in *.mk *.m4 *.sh
+        mfiles = itertools.chain(mfiles, locate("Makefile", srcdir),
+                                 locate("configure", srcdir),
+                                 locate("*.[aims][cnk4h]", srcdir, exclude))
+
+    ncopied = 0
+
+    def _compareAndCopy(src, srcdir, destdir, exclude):
+
+        d, f = os.path.split(src)
+        common_prefix = os.path.commonprefix((d, srcdir))
+        subdir = re.sub(common_prefix, "", d)[1:]
+        targetdir = os.path.join(destdir, subdir)
+        if not os.path.exists(targetdir):
+            os.makedirs(targetdir)
+        old_file = os.path.join(targetdir, f)
+        if os.path.exists(old_file):
+            md5_old = hashlib.md5(
+                "".join(open(old_file, "r", encoding="utf-8").readlines()).encode()).digest()
+            md5_new = hashlib.md5(
+                "".join(open(src, "r", encoding="utf-8").readlines()).encode()).digest()
+            if md5_old != md5_new:
+                raise ValueError(
+                    "incompatible files for %s and %s" %
+                    (old_file, src))
+
+        shutil.copy(src, targetdir)
+        return old_file
+
+    for src_file in hfiles:
+        _compareAndCopy(src_file, srcdir, destdir, exclude)
+        ncopied += 1
+
+    for src_file in mfiles:
+        _compareAndCopy(src_file, srcdir, destdir, exclude)
+        ncopied += 1
+
+    cf = []
+    for src_file in cfiles:
+        cf.append(_compareAndCopy(src_file,
+                                  srcdir,
+                                  destdir,
+                                  exclude))
+        ncopied += 1
+
+    sys.stdout.write(
+        "installed latest source code from %s: "
+        "%i files copied\n" % (srcdir, ncopied))
+
+    if dest in MAIN:
+        # redirect stderr to pysamerr and replace bam.h with a stub.
+        sys.stdout.write("applying stderr redirection\n")
+
+        _update_pysam_files(cf, destdir)
+
+    def _getVersion(srcdir):
+        with open(os.path.join(srcdir, "version.sh"), encoding="utf-8") as inf:
+            for line in inf:
+                m = re.match(r"VERSION=(\S+)", line)
+                if m: return m.group(1)
+            raise ValueError("no VERSION line in version.sh")
+
+    def _update_version_file(key, value, filename):
+        tmpfilename = filename + ".tmp"
+        with open(filename, encoding="utf-8") as inf:
+            with open(tmpfilename, "w", encoding="utf-8") as outf:
+                for line in inf:
+                    if key in line:
+                        line = re.sub(r'"[^"]*"', '"{}"'.format(value), line)
+                    outf.write(line)
+        os.rename(tmpfilename, filename)
+
+    def _update_version_doc_file(dest, value, filename):
+        tmpfilename = filename + ".tmp"
+        with open(filename, encoding="utf-8") as inf:
+            with open(tmpfilename, "w", encoding="utf-8") as outf:
+                for line in inf:
+                    if " wraps " in line:
+                        # hide the sentence's fullstop from the main regexp
+                        line = re.sub(r'\.$', ',DOT', line)
+                        line = re.sub(r'{}-[^*,]*'.format(dest),
+                                      '{}-{}'.format(dest, value), line)
+                        line = re.sub(',DOT', '.', line)
+                    outf.write(line)
+        os.rename(tmpfilename, filename)
+
+    version = _getVersion(srcdir)
+    _update_version_file("__{}_version__".format(dest), version, "pysam/version.py")
+    _update_version_file(C_VERSION[dest], version + " (pysam)", "pysam/version.h")
+    _update_version_doc_file(dest, version, "README.rst")
+    _update_version_doc_file(dest, version, "doc/index.rst")
+
+    sys.exit(0)
+
+
+# if len(sys.argv) >= 2 and sys.argv[1] == "refresh":
+#     sys.stdout.write("refreshing latest source code from .c to .pysam.c")
+#     # redirect stderr to pysamerr and replace bam.h with a stub.
+#     sys.stdout.write("applying stderr redirection")
+#     for destdir in ('samtools', ):
+#         pysamcfiles = locate("*.pysam.c", destdir)
+#         for f in pysamcfiles:
+#             os.remove(f)
+#         cfiles = locate("*.c", destdir)
+#         _update_pysam_files(cfiles, destdir)
+
+#     sys.exit(0)
+
diff --git a/devtools/install-CGAT-tools.sh b/devtools/install-CGAT-tools.sh
new file mode 100755
index 0000000..e45d391
--- /dev/null
+++ b/devtools/install-CGAT-tools.sh
@@ -0,0 +1,282 @@
+#!/usr/bin/env bash
+
+# function to detect the Operating System
+detect_os(){
+
+if [ -f /etc/os-release ]; then
+
+   OS=$(cat /etc/os-release | awk '/VERSION_ID/ {sub("="," "); print $2;}' | sed 's/\"//g' | awk '{sub("\\."," "); print $1;}')
+   if [ "$OS" != "12" ] ; then
+
+      echo       
+      echo " Ubuntu version not supported "
+      echo
+      echo " Only Ubuntu 12.x has been tested so far "
+      echo 
+      exit 1;
+
+   fi
+
+   OS="ubuntu"
+
+elif [ -f /etc/system-release ]; then
+
+   OS=$(cat /etc/system-release | awk ' {print $4;}' | awk '{sub("\\."," "); print $1;}')
+   if [ "$OS" != "6" ] ; then
+      echo
+      echo " Scientific Linux version not supported "
+      echo
+      echo " Only 6.x Scientific Linux has been tested so far "
+      echo
+      exit 1;
+   fi
+
+   OS="sl"
+
+else
+
+   echo
+   echo " Operating system not supported "
+   echo
+   echo " Exiting installation "
+   echo
+   exit 1;
+
+fi
+} # detect_os
+
+# message to display when the OS is not correct
+sanity_check_os() {
+   echo
+   echo " Unsupported operating system: $OS "
+   echo " Installation aborted "
+   echo
+   exit 1;
+} # sanity_check_os
+
+# function to install operating system dependencies
+install_os_packages() {
+
+if [ "$OS" == "ubuntu" -o "$OS" == "travis" ] ; then
+
+   echo
+   echo " Installing packages for Ubuntu "
+   echo
+
+   apt-get install -y gcc g++
+
+elif [ "$OS" == "sl" ] ; then
+
+   echo 
+   echo " Installing packages for Scientific Linux "
+   echo
+
+   yum -y install gcc zlib-devel gcc-c++
+
+else
+
+   sanity_check_os
+
+fi # if-OS
+} # install_os_packages
+
+# function to install Python dependencies
+install_python_deps() {
+
+if [ "$OS" == "ubuntu" -o "$OS" == "sl" ] ; then
+
+   echo
+   echo " Installing Python dependencies for $1 "
+   echo
+
+   # Create virtual environment
+   cd
+   mkdir CGAT
+   cd CGAT
+   wget --no-check-certificate https://pypi.python.org/packages/source/v/virtualenv/virtualenv-1.10.1.tar.gz
+   tar xvfz virtualenv-1.10.1.tar.gz
+   rm virtualenv-1.10.1.tar.gz
+   cd virtualenv-1.10.1
+   python virtualenv.py cgat-venv
+   source cgat-venv/bin/activate
+
+   # Install Python prerequisites
+   pip install cython
+
+elif [ "$OS" == "travis" ] ; then
+   # Travis-CI provides a virtualenv with Python 2.7
+   echo 
+   echo " Installing Python dependencies in travis "
+   echo
+
+   # Install Python prerequisites
+   pip install cython
+   pip install nose
+
+else
+
+   sanity_check_os
+
+fi # if-OS
+} # install_python_deps
+
+# common set of tasks to prepare external dependencies
+nosetests_external_deps() {
+echo
+echo " Running nosetests for $1 "
+echo
+
+pushd .
+
+# create a new folder to store external tools
+mkdir -p $HOME/CGAT/external-tools
+
+# install samtools
+cd $HOME/CGAT/external-tools
+curl -L http://downloads.sourceforge.net/project/samtools/samtools/1.3/samtools-1.3.tar.bz2 > samtools-1.3.tar.bz2
+tar xjf samtools-1.3.tar.bz2 
+cd samtools-1.3
+make
+PATH=$PATH:$HOME/CGAT/external-tools/samtools-1.3
+
+echo "installed samtools"
+samtools --version
+
+if [ $? != 0 ]; then
+    exit 1
+fi
+
+# install bcftools
+cd $HOME/CGAT/external-tools
+curl -L https://github.com/samtools/bcftools/releases/download/1.3/bcftools-1.3.tar.bz2 > bcftools-1.3.tar.bz2
+tar xjf bcftools-1.3.tar.bz2
+cd bcftools-1.3
+make
+PATH=$PATH:$HOME/CGAT/external-tools/bcftools-1.3
+
+echo "installed bcftools"
+bcftools --version
+
+if [ $? != 0 ]; then
+    exit 1
+fi
+
+popd
+
+} # nosetests_external_deps
+
+
+# function to run nosetests
+run_nosetests() {
+
+echo
+echo " Running nosetests for $1 "
+echo
+
+# prepare external dependencies
+nosetests_external_deps $OS
+
+# install code
+python setup.py install
+
+# change into tests directory. Otherwise,
+# 'import pysam' will import the repository,
+# not the installed version. This causes
+# problems in the compilation test.
+cd tests
+
+# create auxiliary data
+echo
+echo 'building test data'
+echo 
+make -C pysam_data all
+make -C cbcf_data all
+make -C tabix_data all
+
+# run nosetests
+# -s: do not capture stdout, conflicts with pysam.dispatch
+# -v: verbose output
+nosetests -s -v 
+
+} # run_nosetests
+
+# function to display help message
+help_message() {
+echo
+echo " Use this script as follows: "
+echo
+echo " 1) Become root and install the operating system* packages: "
+echo " ./install-CGAT-tools.sh --install-os-packages"
+echo
+echo " 2) Now, as a normal user (non root), install the Python dependencies**: "
+echo " ./install-CGAT-tools.sh --install-python-deps"
+echo
+echo " At this stage the CGAT Code Collection is ready to go and you do not need further steps. Please type the following for more information:"
+echo " source $HOME/CGAT/virtualenv-1.10.1/cgat-venv/bin/activate"
+echo " cgat --help "
+echo
+echo " The CGAT Code Collection tests the software with nosetests. If you are interested in running those, please continue with the following steps:"
+echo
+echo " 3) Become root to install external tools and set up the environment: "
+echo " ./install-CGAT-tools.sh --install-nosetests-deps"
+echo
+echo " 4) Then, back as a normal user (non root), run nosetests as follows:"
+echo " ./install-CGAT-tools.sh --run-nosetests"
+echo 
+echo " NOTES: "
+echo " * Supported operating systems: Ubuntu 12.x and Scientific Linux 6.x "
+echo " ** An isolated virtual environment will be created to install Python dependencies "
+echo
+exit 1;
+}
+
+
+# the main script starts here
+
+if [ $# -eq 0 -o $# -gt 1 ] ; then
+
+   help_message
+
+else
+
+   if [ "$1" == "--help" ] ; then
+
+      help_message
+
+   elif [ "$1" == "--travis" ] ; then
+
+      OS="travis"
+      install_os_packages
+      install_python_deps
+      run_nosetests
+
+   elif [ "$1" == "--install-os-packages" ] ; then
+
+      detect_os
+      install_os_packages
+
+   elif [ "$1" == "--install-python-deps" ] ; then
+
+      detect_os
+      install_python_deps
+
+   elif [ "$1" == "--install-nosetests-deps" ] ; then
+
+      detect_os
+      install_nosetests_deps
+
+   elif [ "$1" == "--run-nosetests" ] ; then
+
+      detect_os
+      run_nosetests
+
+   else 
+
+      echo 
+      echo " Incorrect input parameter: $1 "
+      help_message
+
+   fi # if argument 1
+
+fi # if number of input parameters
+
diff --git a/devtools/run_tests_travis.sh b/devtools/run_tests_travis.sh
new file mode 100755
index 0000000..1f14fc3
--- /dev/null
+++ b/devtools/run_tests_travis.sh
@@ -0,0 +1,126 @@
+#!/usr/bin/env bash
+
+# test script for pysam.
+# The script performs the following tasks:
+# 1. Setup a conda environment and install dependencies via conda
+# 2. Build pysam via the conda recipe
+# 3. Build pysam via setup.py from repository
+# 4. Run tests on the setup.py version
+# 5. Additional build tests
+# 5.1 pip install with cython
+# 5.2 pip install without cython
+# 5.3 pip install without cython and without configure options
+
+pushd .
+
+WORKDIR=`pwd`
+
+#Install miniconda python
+if [ $TRAVIS_OS_NAME == "osx" ]; then
+	wget -q https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -O Miniconda3.sh
+else
+	wget -q https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O Miniconda3.sh --no-check-certificate  # Default OS versions are old and have SSL / CERT issues
+fi
+
+bash Miniconda3.sh -b
+
+# Create a new conda environment with the target python version
+~/miniconda3/bin/conda install conda-build -y
+~/miniconda3/bin/conda create -q -y --name testenv python=$CONDA_PY cython numpy pytest psutil pip
+
+# activate testenv environment
+source ~/miniconda3/bin/activate testenv
+
+conda config --add channels defaults
+conda config --add channels bioconda
+conda config --add channels conda-forge
+
+# pin versions, so that tests do not fail when pysam/htslib out of step
+# add htslib dependencies
+# NB: force conda-forge:blas due to conda/conda#7548
+conda install -y "samtools>=1.11" "bcftools>=1.11" "htslib>=1.11" xz curl bzip2 "conda-forge::blas=*=openblas"
+
+# As HTSLIB_MODE is (defaulted to) 'shared', ensure we don't pick up
+# the external headers from the Conda-installed htslib package.
+mv $CONDA_PREFIX/include/htslib $CONDA_PREFIX/include/htslib-disable
+
+export HTSLIB_CONFIGURE_OPTIONS="--disable-libcurl"
+
+echo "show samtools, htslib, and bcftools versions"
+samtools --version
+htsfile --version
+bcftools --version
+
+# Try building conda recipe first
+~/miniconda3/bin/conda-build devtools/conda-recipe/ --python=$CONDA_PY
+
+# install code from the repository via setup.py
+echo
+echo "============ installing via setup.py from repository ============"
+echo
+python setup.py install || exit
+
+# create auxiliary data
+echo
+echo 'building test data'
+echo
+make -C tests/pysam_data
+make -C tests/cbcf_data
+make -C tests/tabix_data
+
+# echo any limits that are in place
+ulimit -a
+
+# run tests
+pytest
+
+if [ $? != 0 ]; then
+    exit 1
+fi
+
+# build source tar-ball. Make sure to run 'build' target so that .pyx
+# files are cythonized.
+python setup.py build sdist
+
+if [ $? != 0 ]; then
+    exit 1
+fi
+
+# check for presence of config.h files
+echo "checking for presence of config.h files in tar-ball"
+tar -tvzf dist/pysam-*.tar.gz | grep "config.h$"
+
+if [ $? != 1 ]; then
+    echo "ERROR: found config.h in tar-ball"
+    tar -tvzf dist/pysam-*.tar.gz | grep "config.h%"
+    exit 1
+fi
+
+# test pip installation from tar-ball with cython
+echo "pip installing with cython"
+pip install --verbose --no-deps --no-binary=:all: dist/pysam-*.tar.gz
+
+if [ $? != 0 ]; then
+    exit 1
+fi
+
+# attempt pip installation without cython
+echo "pip installing without cython"
+~/miniconda3/bin/conda remove -y cython
+~/miniconda3/bin/conda list
+echo "python is" `which python`
+pip install --verbose --no-deps --no-binary=:all: --force-reinstall --upgrade dist/pysam-*.tar.gz
+
+if [ $? != 0 ]; then
+    exit 1
+fi
+
+# attempt pip installation without cython and without
+# command line options
+echo "pip installing without cython and no configure options"
+export HTSLIB_CONFIGURE_OPTIONS=""
+pip install --verbose --no-deps --no-binary=:all: --force-reinstall --upgrade dist/pysam-*.tar.gz
+
+if [ $? != 0 ]; then
+    exit 1
+fi
diff --git a/doc/Makefile b/doc/Makefile
new file mode 100644
index 0000000..69e4e3a
--- /dev/null
+++ b/doc/Makefile
@@ -0,0 +1,96 @@
+# Makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+PAPER         =
+
+# Internal variables.
+PAPEROPT_a4     = -D latex_paper_size=a4
+PAPEROPT_letter = -D latex_paper_size=letter
+ALLSPHINXOPTS   = -d _build/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
+
+DIR_PUBLISH=/ifs/home/andreas/public_html/documentation/pysam
+
+.PHONY: help clean html dirhtml pickle json htmlhelp qthelp latex changes linkcheck doctest
+
+help:
+	@echo "Please use \`make <target>' where <target> is one of"
+	@echo "  html      to make standalone HTML files"
+	@echo "  dirhtml   to make HTML files named index.html in directories"
+	@echo "  pickle    to make pickle files"
+	@echo "  json      to make JSON files"
+	@echo "  htmlhelp  to make HTML files and a HTML help project"
+	@echo "  qthelp    to make HTML files and a qthelp project"
+	@echo "  latex     to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
+	@echo "  changes   to make an overview of all changed/added/deprecated items"
+	@echo "  linkcheck to check all external links for integrity"
+	@echo "  doctest   to run all doctests embedded in the documentation (if enabled)"
+	@echo "  publish   to copy the HTML documentation to the server."
+
+clean:
+	-rm -rf _build/*
+
+html:
+	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) _build/html
+	@echo
+	@echo "Build finished. The HTML pages are in _build/html."
+
+dirhtml:
+	$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) _build/dirhtml
+	@echo
+	@echo "Build finished. The HTML pages are in _build/dirhtml."
+
+pickle:
+	$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) _build/pickle
+	@echo
+	@echo "Build finished; now you can process the pickle files."
+
+json:
+	$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) _build/json
+	@echo
+	@echo "Build finished; now you can process the JSON files."
+
+htmlhelp:
+	$(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) _build/htmlhelp
+	@echo
+	@echo "Build finished; now you can run HTML Help Workshop with the" \
+	      ".hhp project file in _build/htmlhelp."
+
+qthelp:
+	$(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) _build/qthelp
+	@echo
+	@echo "Build finished; now you can run "qcollectiongenerator" with the" \
+	      ".qhcp project file in _build/qthelp, like this:"
+	@echo "# qcollectiongenerator _build/qthelp/samtools.qhcp"
+	@echo "To view the help file:"
+	@echo "# assistant -collectionFile _build/qthelp/samtools.qhc"
+
+latex:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) _build/latex
+	@echo
+	@echo "Build finished; the LaTeX files are in _build/latex."
+	@echo "Run \`make all-pdf' or \`make all-ps' in that directory to" \
+	      "run these through (pdf)latex."
+
+changes:
+	$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) _build/changes
+	@echo
+	@echo "The overview file is in _build/changes."
+
+linkcheck:
+	$(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) _build/linkcheck
+	@echo
+	@echo "Link check complete; look for any errors in the above output " \
+	      "or in _build/linkcheck/output.txt."
+
+doctest:
+	$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) _build/doctest
+	@echo "Testing of doctests in the sources finished, look at the " \
+	      "results in _build/doctest/output.txt."
+
+publish:
+	rm -rf $(DIR_PUBLISH)
+	mkdir -p $(DIR_PUBLISH)
+	cp -r _build/html/* $(DIR_PUBLISH)
diff --git a/doc/api.rst b/doc/api.rst
new file mode 100644
index 0000000..47fe314
--- /dev/null
+++ b/doc/api.rst
@@ -0,0 +1,230 @@
+============
+Introduction
+============
+
+Pysam is a python module that makes it easy to read and manipulate
+mapped short read sequence data stored in SAM/BAM files.  It is a
+lightweight wrapper of the htslib_ C-API.
+
+This page provides a quick introduction in using pysam followed by the
+API. See :ref:`usage` for more detailed usage instructions.
+
+To use the module to read a file in BAM format, create a
+:class:`~pysam.AlignmentFile` object::
+
+   import pysam
+   samfile = pysam.AlignmentFile("ex1.bam", "rb")
+
+Once a file is opened you can iterate over all of the read mapping to
+a specified region using :meth:`~pysam.AlignmentFile.fetch`.  Each
+iteration returns a :class:`~pysam.AlignedSegment` object which
+represents a single read along with its fields and optional tags::
+
+   for read in samfile.fetch('chr1', 100, 120):
+       print(read)
+
+   samfile.close()
+
+To give::
+
+    EAS56_57:6:190:289:82	0	99	<<<7<<<;<<<<<<<<8;;<7;4<;<;;;;;94<;	69	CTCAAGGTTGTTGCAAGGGGGTCTATGTGAACAAA	0	192	1
+    EAS56_57:6:190:289:82	0	99	<<<<<<;<<<<<<<<<<;<<;<<<<;8<6;9;;2;	137	AGGGGTGCAGAGCCGAGTCACGGGGTTGCCAGCAC	73	64	1
+    EAS51_64:3:190:727:308	0	102	<<<<<<<<<<<<<<<<<<<<<<<<<<<::<<<844	99	GGTGCAGAGCCGAGTCACGGGGTTGCCAGCACAGG	99	18	1
+    ...
+
+You can also write to a :class:`~pysam.AlignmentFile`::
+
+   import pysam
+   samfile = pysam.AlignmentFile("ex1.bam", "rb")
+   pairedreads = pysam.AlignmentFile("allpaired.bam", "wb", template=samfile)
+   for read in samfile.fetch():
+       if read.is_paired:
+           pairedreads.write(read)
+
+   pairedreads.close()
+   samfile.close()
+
+An alternative way of accessing the data in a SAM file is by iterating
+over each base of a specified region using the
+:meth:`~pysam.AlignmentFile.pileup` method. Each iteration returns a
+:class:`~pysam.PileupColumn` which represents all the reads in the SAM
+file that map to a single base in the reference sequence. The list of
+reads are represented as :class:`~pysam.PileupRead` objects in the
+:attr:`PileupColumn.pileups <pysam.PileupColumn.pileups>` property::
+
+    import pysam
+    samfile = pysam.AlignmentFile("ex1.bam", "rb" )
+    for pileupcolumn in samfile.pileup("chr1", 100, 120):
+        print("\ncoverage at base %s = %s" % (pileupcolumn.pos, pileupcolumn.n))
+        for pileupread in pileupcolumn.pileups:
+            if not pileupread.is_del and not pileupread.is_refskip:
+                # query position is None if is_del or is_refskip is set.
+                print('\tbase in read %s = %s' %
+                      (pileupread.alignment.query_name,
+                       pileupread.alignment.query_sequence[pileupread.query_position]))
+
+    samfile.close()
+
+The above code outputs::
+
+    coverage at base 99 = 1
+        base in read EAS56_57:6:190:289:82 = A
+
+    coverage at base 100 = 1
+        base in read EAS56_57:6:190:289:82 = G
+
+    coverage at base 101 = 1
+        base in read EAS56_57:6:190:289:82 = G
+
+    coverage at base 102 = 2
+        base in read EAS56_57:6:190:289:82 = G
+        base in read EAS51_64:3:190:727:308 = G
+    ...
+
+Commands available in `samtools`_ are available as simple
+function calls. For example::
+
+   pysam.sort("-o", "output.bam", "ex1.bam")
+
+corresponds to the command line::
+
+   samtools sort -o output.bam ex1.bam 
+
+Analogous to :class:`~pysam.AlignmentFile`, a
+:class:`~pysam.TabixFile` allows fast random access to compressed and
+tabix indexed tab-separated file formats with genomic data::
+
+   import pysam
+   tabixfile = pysam.TabixFile("example.gtf.gz")
+
+   for gtf in tabixfile.fetch("chr1", 1000, 2000):
+       print(gtf.contig, gtf.start, gtf.end, gtf.gene_id)
+
+:class:`~pysam.TabixFile` implements lazy parsing in order to iterate
+over large tables efficiently.
+
+More detailed usage instructions is at :ref:`usage`.
+
+.. note::
+
+   Coordinates in pysam are always 0-based (following the python
+   convention). SAM text files use 1-based coordinates.
+
+.. note::
+
+   The above examples can be run in the :file:`tests` directory of the
+    installation directory. Type 'make' before running them.
+
+.. seealso::
+
+   https://github.com/pysam-developers/pysam
+
+       The pysam code repository, containing source code and download
+       instructions
+
+   http://pysam.readthedocs.org/en/latest/
+
+       The pysam website containing documentation
+
+===
+API
+===
+
+SAM/BAM/CRAM files
+==================
+
+Objects of type :class:`~pysam.AlignmentFile` allow working with
+BAM/SAM formatted files.
+
+.. autoclass:: pysam.AlignmentFile
+   :members:
+
+.. autoclass:: pysam.AlignmentHeader
+   :members:
+
+An :class:`~pysam.AlignedSegment` represents an aligned segment within
+a SAM/BAM file.
+
+.. autoclass:: pysam.AlignedSegment
+   :members:
+
+.. autoclass:: pysam.PileupColumn
+   :members:
+
+.. autoclass:: pysam.PileupRead
+   :members:
+
+.. autoclass:: pysam.IndexedReads
+   :members:
+
+
+Tabix files
+===========
+
+:class:`~pysam.TabixFile` opens tabular files that have been
+indexed with tabix_.
+
+.. autoclass:: pysam.TabixFile
+   :members:
+
+To iterate over tabix files, use :func:`~pysam.tabix_iterator`:
+
+.. autofunction:: pysam.tabix_iterator
+
+.. autofunction:: pysam.tabix_compress
+
+.. autofunction:: pysam.tabix_index
+
+.. autoclass:: pysam.asTuple
+   :members:
+
+.. autoclass:: pysam.asVCF
+   :members:
+
+.. autoclass:: pysam.asBed
+   :members:
+
+.. autoclass:: pysam.asGTF
+   :members:
+
+
+FASTA files
+===========
+
+.. autoclass:: pysam.FastaFile
+   :members:
+
+FASTQ files
+===========
+
+.. autoclass:: pysam.FastxFile
+   :members:
+
+
+.. autoclass:: pysam.FastqProxy
+   :members:
+
+
+VCF/BCF files
+=============
+
+.. autoclass:: pysam.VariantFile
+   :members:
+
+.. autoclass:: pysam.VariantHeader
+   :members:
+
+.. autoclass:: pysam.VariantRecord
+   :members:
+
+.. autoclass:: pysam.VariantHeaderRecord
+   :members:
+
+HTSFile
+=======
+
+HTSFile is the base class for :class:`pysam.AlignmentFile` and
+:class:`pysam.VariantFile`.
+
+.. autoclass:: pysam.HTSFile
+   :members:
diff --git a/doc/benchmarking.rst b/doc/benchmarking.rst
new file mode 100644
index 0000000..8fc054a
--- /dev/null
+++ b/doc/benchmarking.rst
@@ -0,0 +1,70 @@
+.. _Benchmarking:
+
+============
+Benchmarking
+============
+
+Latest benchmarking results::
+
+    ------------------------------------------------------------------------------------------------------------------------ benchmark: 57 tests ------------------------------------------------------------------------------------------------------------------------
+    Name (time in us)                                                              Min                     Max                    Mean                StdDev                  Median                   IQR            Outliers          OPS            Rounds  Iterations
+    ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+    test_set_binary_tag                                                        93.8382 (1.0)          199.8786 (1.0)           96.1554 (1.0)          2.6241 (1.0)           95.7036 (1.0)          1.2442 (1.0)       276;303  10,399.8372 (1.0)        3170           1
+    test_fasta_iteration_long_sequences_without_persistence                   145.3292 (1.55)         296.4940 (1.48)         176.5367 (1.84)        30.0896 (11.47)        167.2544 (1.75)        25.1532 (20.22)     840;579   5,664.5438 (0.54)       4972           1
+    test_fasta_iteration_long_sequences_as_file                               149.0638 (1.59)         312.6319 (1.56)         177.2990 (1.84)        30.5218 (11.63)        168.6383 (1.76)        27.7516 (22.30)     669;510   5,640.1883 (0.54)       4493           1
+    test_fasta_iteration_long_sequences                                       150.3211 (1.60)         429.9153 (2.15)         176.7384 (1.84)        30.7021 (11.70)        167.5002 (1.75)        21.7482 (17.48)     682;647   5,658.0803 (0.54)       4845           1
+    test_fasta_iteration_short_sequences_as_file                              190.6604 (2.03)         395.8736 (1.98)         216.6984 (2.25)        32.8710 (12.53)        208.9385 (2.18)        16.8057 (13.51)     291;326   4,614.7086 (0.44)       3205           1
+    test_read_python_uncompressed                                             214.1297 (2.28)         450.2051 (2.25)         234.6956 (2.44)        33.3642 (12.71)        223.4913 (2.34)        15.0129 (12.07)     140;221   4,260.8375 (0.41)       2043           1
+    test_fastq_iteration_short_sequences_as_file                              217.5961 (2.32)         420.1643 (2.10)         238.0264 (2.48)        30.4469 (11.60)        228.8874 (2.39)        15.5573 (12.50)     209;235   4,201.2146 (0.40)       2877           1
+    test_iterate_file_uncompressed                                            225.5719 (2.40)         481.0989 (2.41)         249.7603 (2.60)        40.7266 (15.52)        239.5548 (2.50)        15.9908 (12.85)     209;327   4,003.8387 (0.38)       3627           1
+    test_iterate_file_compressed                                              257.5517 (2.74)         576.6843 (2.89)         287.2536 (2.99)        49.8803 (19.01)        277.4149 (2.90)        14.3824 (11.56)     126;248   3,481.2446 (0.33)       3023           1
+    test_iterate_generic_uncompressed                                         344.8855 (3.68)         712.5959 (3.57)         370.9369 (3.86)        46.2477 (17.62)        365.0384 (3.81)        15.7915 (12.69)       54;83   2,695.8763 (0.26)       2240           1
+    test_iterate_parsed_uncompressed                                          349.3819 (3.72)         765.3460 (3.83)         378.1446 (3.93)        54.2199 (20.66)        369.5488 (3.86)        15.4320 (12.40)       48;69   2,644.4910 (0.25)       1638           1
+    test_read_python_compressed                                               462.0645 (4.92)         836.2234 (4.18)         493.6158 (5.13)        51.2946 (19.55)        485.5469 (5.07)        11.4385 (9.19)        28;46   2,025.8670 (0.19)        906           1
+    test_iterate_parsed_compressed                                            586.5730 (6.25)       1,050.1631 (5.25)         632.5464 (6.58)        82.6438 (31.49)        608.1080 (6.35)        20.1799 (16.22)     115;143   1,580.9117 (0.15)       1474           1
+    test_iterate_generic_compressed                                           587.7707 (6.26)       1,093.4286 (5.47)         639.6830 (6.65)        85.2593 (32.49)        612.6408 (6.40)        19.9433 (16.03)     105;144   1,563.2743 (0.15)       1260           1
+    test_fasta_iteration_short_sequences_without_persistence                  725.2563 (7.73)       1,091.6069 (5.46)         774.6549 (8.06)        53.0901 (20.23)        751.8455 (7.86)        45.0788 (36.23)     172;110   1,290.8974 (0.12)       1276           1
+    test_read_binary_tag                                                      817.2598 (8.71)       1,232.0559 (6.16)         902.7002 (9.39)        87.7807 (33.45)        871.5261 (9.11)        17.4227 (14.00)       39;55   1,107.7875 (0.11)        331           1
+    test_fastq_iteration_short_sequences_without_persistence                  840.3640 (8.96)       1,201.5756 (6.01)         870.9679 (9.06)        35.8709 (13.67)        866.1682 (9.05)        15.9768 (12.84)       53;85   1,148.1480 (0.11)       1124           1
+    test_count_number_lines_from_sam_with_pysam                             2,755.6140 (29.37)      9,656.9806 (48.31)      2,963.2206 (30.82)      729.0077 (277.81)     2,814.3115 (29.41)      106.2388 (85.38)        8;14     337.4707 (0.03)        281           1
+    test_fasta_iteration_short_sequences                                    2,905.5942 (30.96)      3,674.1439 (18.38)      2,982.3892 (31.02)       90.9585 (34.66)      2,941.2108 (30.73)       96.1348 (77.26)        27;7     335.3016 (0.03)        302           1
+    test_fastq_iteration_short_sequences                                    3,601.3145 (38.38)      4,065.5769 (20.34)      3,671.8361 (38.19)       71.5348 (27.26)      3,635.1625 (37.98)       81.5415 (65.53)       43;10     272.3433 (0.03)        243           1
+    test_count_number_lines_from_bam_with_pysam                             4,178.8872 (44.53)     12,063.5536 (60.35)      4,395.9713 (45.72)      794.3991 (302.73)     4,240.1757 (44.31)       67.0198 (53.86)        6;19     227.4810 (0.02)        205           1
+    test_build_depth_from_bam_with_pysam                                    6,290.2980 (67.03)      6,788.0806 (33.96)      6,420.3862 (66.77)      126.5447 (48.22)      6,357.6270 (66.43)       94.3104 (75.80)       35;29     155.7539 (0.01)        145           1
+    test_build_depth_with_filter_from_bam_with_pysam                        6,935.8926 (73.91)      8,309.5767 (41.57)      7,085.6801 (73.69)      221.5069 (84.41)      7,005.6170 (73.20)       74.4388 (59.83)       14;27     141.1297 (0.01)        139           1
+    test_build_query_positions_from_bam_with_pysam                          8,729.2437 (93.02)     16,836.6525 (84.23)      9,173.2902 (95.40)    1,057.4321 (402.97)     8,885.4395 (92.84)      264.7634 (212.79)        3;9     109.0121 (0.01)        103           1
+    test_build_mapping_qualities_from_bam_with_pysam                        8,805.0570 (93.83)     15,829.8910 (79.20)      9,274.7475 (96.46)      964.6925 (367.63)     9,004.7438 (94.09)      354.9103 (285.24)        4;9     107.8196 (0.01)        106           1
+    test_build_query_qualities_from_bam_with_pysam                          8,947.6798 (95.35)     16,756.8158 (83.83)      9,272.9117 (96.44)    1,008.7759 (384.43)     9,017.0493 (94.22)      217.2068 (174.57)        3;5     107.8410 (0.01)         94           1
+    test_build_query_bases_from_bam_with_samtoolspysam                      9,149.0448 (97.50)      9,776.0092 (48.91)      9,208.3405 (95.77)       86.1889 (32.85)      9,190.2809 (96.03)       34.1963 (27.48)         5;7     108.5972 (0.01)         84           1
+    test_count_number_lines_from_bam_with_samtoolspipe                     10,431.4052 (111.16)    13,431.7447 (67.20)     11,052.2360 (114.94)     445.8241 (169.90)    11,014.8042 (115.09)     492.6044 (395.91)       17;3      90.4794 (0.01)         90           1
+    test_count_number_lines_from_bam_with_samtools                         12,057.8520 (128.50)    13,537.5429 (67.73)     12,595.0708 (130.99)     381.1799 (145.26)    12,499.5783 (130.61)     457.8107 (367.94)       25;1      79.3961 (0.01)         73           1
+    test_count_number_lines_from_sam_with_samtoolspipe                     12,434.8756 (132.51)    14,234.1983 (71.21)     13,034.1032 (135.55)     371.0373 (141.40)    13,049.9089 (136.36)     464.8147 (373.57)       21;3      76.7218 (0.01)         72           1
+    test_build_query_bases_from_bam_with_pysam                             12,811.6887 (136.53)    19,972.7099 (99.92)     13,268.7908 (137.99)   1,103.9459 (420.70)    13,023.1632 (136.08)     202.3596 (162.64)        4;6      75.3648 (0.01)         76           1
+    test_build_pileup_from_bam_with_samtoolspipe                           13,480.7490 (143.66)    15,413.4836 (77.11)     13,968.3817 (145.27)     362.1282 (138.00)    13,917.4843 (145.42)     447.9736 (360.04)       12;3      71.5903 (0.01)         66           1
+    test_count_number_lines_from_sam_with_samtools                         13,963.2300 (148.80)    15,936.2238 (79.73)     14,442.5627 (150.20)     340.4846 (129.75)    14,395.4996 (150.42)     339.3036 (272.70)       12;2      69.2398 (0.01)         59           1
+    test_build_pileup_from_bam_with_samtoolsshell                          15,140.2969 (161.34)    16,469.8567 (82.40)     15,525.9034 (161.47)     256.0741 (97.59)     15,526.7641 (162.24)     318.5044 (255.98)       13;2      64.4085 (0.01)         51           1
+    test_build_depth_from_bam_with_samtoolsshell                           15,291.4841 (162.96)    16,387.9916 (81.99)     15,656.5365 (162.83)     217.2420 (82.79)     15,609.9945 (163.11)     258.9412 (208.11)       16;2      63.8711 (0.01)         57           1
+    test_build_query_bases_from_bam_with_samtoolspipe                      15,478.0652 (164.94)    17,068.8462 (85.40)     16,072.5749 (167.15)     327.6668 (124.87)    16,040.5049 (167.61)     428.1597 (344.11)       18;2      62.2178 (0.01)         60           1
+    test_build_query_bases_from_bam_with_samtoolsshell                     15,765.5794 (168.01)    17,102.8059 (85.57)     16,305.4955 (169.57)     367.6865 (140.12)    16,256.2486 (169.86)     593.9230 (477.34)       20;0      61.3290 (0.01)         57           1
+    test_build_depth_from_bam_with_samtoolspipe                            16,024.7944 (170.77)    25,804.2309 (129.10)    17,041.3497 (177.23)   1,522.0046 (580.01)    16,726.8887 (174.78)     767.1015 (616.52)        1;1      58.6808 (0.01)         40           1
+    test_build_query_qualities_from_bam_with_samtoolspipe                  16,275.7467 (173.44)    18,501.0433 (92.56)     17,262.6517 (179.53)     642.2656 (244.76)    17,255.3696 (180.30)   1,060.3429 (852.20)       20;0      57.9285 (0.01)         51           1
+    test_build_pileup_from_bam_with_pysam                                  16,632.5681 (177.25)    19,306.6560 (96.59)     17,037.7162 (177.19)     531.0751 (202.38)    16,870.8330 (176.28)     279.1677 (224.37)        3;4      58.6933 (0.01)         32           1
+    test_build_mapping_qualities_from_bam_with_samtoolspipe                17,398.3518 (185.41)    18,481.6569 (92.46)     17,832.1261 (185.45)     294.9103 (112.39)    17,837.8206 (186.39)     511.8400 (411.37)       21;0      56.0786 (0.01)         52           1
+    test_build_query_names_from_bam_with_pysam                             31,534.0199 (336.05)    38,316.2647 (191.70)    32,677.2804 (339.84)   1,371.6101 (522.70)    32,179.0325 (336.24)   1,392.1391 (>1000.0)       3;1      30.6023 (0.00)         30           1
+    test_fetch_plain                                                       43,747.1233 (466.20)    48,690.7829 (243.60)    44,573.8085 (463.56)   1,170.8588 (446.20)    44,067.5411 (460.46)   1,436.5837 (>1000.0)       3;1      22.4347 (0.00)         22           1
+    test_build_query_positions_from_bam_with_samtoolspipe                  46,316.5548 (493.58)    53,700.3577 (268.66)    48,235.6640 (501.64)   1,861.0317 (709.21)    47,625.2194 (497.63)   2,603.7074 (>1000.0)       6;1      20.7315 (0.00)         21           1
+    test_build_query_bases_with_reference_from_bam_with_samtoolspysam      51,565.1479 (549.51)    53,523.1121 (267.78)    51,778.6650 (538.49)     424.4621 (161.76)    51,656.8925 (539.76)     110.5051 (88.81)         1;4      19.3130 (0.00)         20           1
+    test_build_query_bases_with_reference_from_bam_with_pysam              58,850.6740 (627.15)    62,164.5451 (311.01)    60,161.6779 (625.67)   1,120.6101 (427.05)    59,595.2785 (622.71)   1,995.0196 (>1000.0)       7;0      16.6219 (0.00)         16           1
+    test_iterate_file_large_uncompressed                                   59,419.9076 (633.22)    69,053.0874 (345.48)    62,825.7126 (653.38)   3,805.1150 (>1000.0)   60,805.1391 (635.35)   6,407.6949 (>1000.0)       3;0      15.9170 (0.00)         14           1
+    test_iterate_file_large_compressed                                     63,986.9571 (681.89)    74,156.9120 (371.01)    68,370.8835 (711.05)   3,254.6200 (>1000.0)   67,221.2075 (702.39)   4,770.3525 (>1000.0)       5;0      14.6261 (0.00)         16           1
+    test_read_python_large_uncompressed                                    67,611.8080 (720.51)    89,112.1533 (445.83)    73,631.8916 (765.76)   5,978.7052 (>1000.0)   71,702.4822 (749.21)   7,856.0165 (>1000.0)       2;1      13.5811 (0.00)         13           1
+    test_fetch_parsed                                                      72,237.5344 (769.81)    81,976.9856 (410.13)    74,540.4099 (775.21)   2,326.3668 (886.54)    74,016.3419 (773.39)   1,579.0667 (>1000.0)       1;1      13.4155 (0.00)         14           1
+    test_build_query_bases_from_bam_with_pysam_pileups                     75,841.3766 (808.21)    87,975.1425 (440.14)    79,393.9784 (825.68)   3,516.2458 (>1000.0)   79,346.7313 (829.09)   5,217.5033 (>1000.0)       2;0      12.5954 (0.00)         13           1
+    test_build_query_bases_with_reference_from_bam_with_samtoolspipe      131,162.9396 (>1000.0)  132,858.8147 (664.70)   131,838.0199 (>1000.0)    595.6090 (226.98)   131,801.5633 (>1000.0)    956.9665 (769.11)        2;0       7.5851 (0.00)          8           1
+    test_iterate_parsed_large_uncompressed                                132,991.8914 (>1000.0)  140,153.4099 (701.19)   134,101.5892 (>1000.0)  2,452.3161 (934.54)   133,218.1590 (>1000.0)    396.3616 (318.56)        1;1       7.4570 (0.00)          8           1
+    test_iterate_generic_large_uncompressed                               134,743.7277 (>1000.0)  142,329.4526 (712.08)   138,167.4954 (>1000.0)  3,346.7773 (>1000.0)  136,839.1849 (>1000.0)  6,541.1879 (>1000.0)       4;0       7.2376 (0.00)          8           1
+    test_read_python_large_compressed                                     175,127.6311 (>1000.0)  190,855.1529 (954.86)   181,702.9339 (>1000.0)  5,756.2207 (>1000.0)  181,221.0185 (>1000.0)  8,577.6616 (>1000.0)       2;0       5.5035 (0.00)          6           1
+    test_iterate_parsed_large_compressed                                  231,405.7611 (>1000.0)  243,728.8519 (>1000.0)  239,037.8296 (>1000.0)  5,212.7778 (>1000.0)  241,544.3324 (>1000.0)  8,062.6113 (>1000.0)       1;0       4.1834 (0.00)          5           1
+    test_iterate_generic_large_compressed                                 235,042.3876 (>1000.0)  256,518.8371 (>1000.0)  242,535.5468 (>1000.0)  8,272.5197 (>1000.0)  240,163.0748 (>1000.0)  8,360.1568 (>1000.0)       1;0       4.1231 (0.00)          5           1
+    ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+
diff --git a/doc/conf.py b/doc/conf.py
new file mode 100644
index 0000000..aaf1d35
--- /dev/null
+++ b/doc/conf.py
@@ -0,0 +1,228 @@
+# -*- coding: utf-8 -*-
+#
+# samtools documentation build configuration file, created by
+# sphinx-quickstart on Wed Aug 12 14:43:42 2009.
+#
+# This file is execfile()d with the current directory set to its containing dir.
+#
+# Note that not all possible configuration values are present in this
+# autogenerated file.
+#
+# All configuration values have a default; values that are commented out
+# serve to show the default.
+
+import sys, os, setuptools
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+_build_obj = setuptools.dist.Distribution().get_command_obj('build')
+_build_obj.ensure_finalized()
+
+_libdir = os.path.join('..', _build_obj.build_platlib)
+if os.path.exists(_libdir):
+    sys.path.insert(0, os.path.abspath(_libdir))
+
+# -- General configuration -----------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be extensions
+# coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
+extensions = ['sphinx.ext.autodoc',
+              'sphinx.ext.autosummary',
+              'sphinx.ext.todo', 
+              'sphinx.ext.ifconfig',
+              'sphinx.ext.intersphinx',
+              'sphinx.ext.napoleon']
+
+intersphinx_mapping = {'python': ('https://docs.python.org/%d.%d' % sys.version_info[:2], None)}
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The suffix of source filenames.
+source_suffix = '.rst'
+
+# The encoding of source files.
+#source_encoding = 'utf-8'
+
+# The master toctree document.
+master_doc = 'index'
+
+# General information about the project.
+project = u'pysam'
+copyright = u'2009–2021, Andreas Heger, Kevin Jacobs, et al'
+
+# Included at the end of each rst file
+rst_epilog = '''
+.. _CGAT Training Programme: http://www.cgat.org
+.. _pysam: https://github.com/pysam-developers/pysam
+.. _samtools: http://samtools.sourceforge.net/
+.. _bcftools: https://samtools.github.io/bcftools/bcftools.html
+.. _htslib: http://www.htslib.org/
+.. _tabix: http://www.htslib.org/doc/tabix.html
+.. _Galaxy: https://main.g2.bx.psu.edu/
+.. _cython: https://cython.org/
+.. _python: https://www.python.org/
+.. _pypi: https://pypi.org/
+.. _pip: https://pip.pypa.io/
+.. _pyximport: https://github.com/cython/cython/tree/master/pyximport
+.. _conda: https://conda.io/docs/
+.. _bioconda: https://bioconda.github.io/
+.. _sphinx: https://www.sphinx-doc.org/en/master/usage/installation.html
+'''
+
+autosummary_generate = True
+
+# The version info for the project you're documenting, acts as replacement for
+# |version| and |release|, also used in various other places throughout the
+# built documents.
+#
+import pysam.version
+# The short X.Y version.
+version = pysam.version.__version__
+# The full version, including alpha/beta/rc tags.
+release = version
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+# language = None
+
+# There are two options for replacing |today|: either, you set today to some
+# non-false value, then it is used:
+# today = ''
+# Else, today_fmt is used as the format for a strftime call.
+# today_fmt = '%B %d, %Y'
+
+# List of documents that shouldn't be included in the build.
+# unused_docs = []
+
+# List of directories, relative to source directory, that shouldn't be searched
+# for source files.
+exclude_trees = ['_build']
+
+# The reST default role (used for this markup: `text`) to use for all documents.
+# default_role = None
+
+# If true, '()' will be appended to :func: etc. cross-reference text.
+# add_function_parentheses = True
+
+# If true, the current module name will be prepended to all description
+# unit titles (such as .. function::).
+# add_module_names = True
+
+# If true, sectionauthor and moduleauthor directives will be shown in the
+# output. They are ignored by default.
+# show_authors = False
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+# A list of ignored prefixes for module index sorting.
+#modindex_common_prefix = []
+
+
+# -- Options for HTML output ---------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  Major themes that come with
+# Sphinx are currently 'default' and 'sphinxdoc'.
+html_theme = 'default'
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further.  For a list of options available for each theme, see the
+# documentation.
+# html_theme_options = {}
+
+# Add any paths that contain custom themes here, relative to this directory.
+# html_theme_path = []
+
+# The name for this set of Sphinx documents.  If None, it defaults to
+# "<project> v<release> documentation".
+# html_title = None
+
+# A shorter title for the navigation bar.  Default is the same as html_title.
+# html_short_title = None
+
+# The name of an image file (relative to this directory) to place at the top
+# of the sidebar.
+# html_logo = None
+
+# The name of an image file (within the static path) to use as favicon of the
+# docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
+# pixels large.
+# html_favicon = None
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = []
+
+# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
+# using the given strftime format.
+# html_last_updated_fmt = '%b %d, %Y'
+
+# If true, SmartyPants will be used to convert quotes and dashes to
+# typographically correct entities.
+# html_use_smartypants = True
+
+# Custom sidebar templates, maps document names to template names.
+# html_sidebars = {}
+
+# Additional templates that should be rendered to pages, maps page names to
+# template names.
+# html_additional_pages = {}
+
+# If false, no module index is generated.
+# html_use_modindex = True
+
+# If false, no index is generated.
+# html_use_index = True
+
+# If true, the index is split into individual pages for each letter.
+# html_split_index = False
+
+# If true, links to the reST sources are added to the pages.
+# html_show_sourcelink = True
+
+# If true, an OpenSearch description file will be output, and all pages will
+# contain a <link> tag referring to it.  The value of this option must be the
+# base URL from which the finished HTML is served.
+# html_use_opensearch = ''
+
+# If nonempty, this is the file name suffix for HTML files (e.g. ".xhtml").
+# html_file_suffix = ''
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'samtoolsdoc'
+
+
+# -- Options for LaTeX output --------------------------------------------------
+
+# The paper size ('letter' or 'a4').
+# latex_paper_size = 'letter'
+
+# The font size ('10pt', '11pt' or '12pt').
+# latex_font_size = '10pt'
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title, author, documentclass [howto/manual]).
+latex_documents = [
+    ('index', 'pysam.tex', u'pysam documentation',
+     u'Andreas Heger, Kevin Jacobs, et al.', 'manual'),
+]
+
+# The name of an image file (relative to this directory) to place at the top of
+# the title page.
+# latex_logo = None
+
+# For "manual" documents, if this is true, then toplevel headings are parts,
+# not chapters.
+# latex_use_parts = False
+
+# Additional stuff for the LaTeX preamble.
+# latex_preamble = ''
+
+# Documents to append as an appendix to all manuals.
+# latex_appendices = []
+
+# If false, no module index is generated.
+# latex_use_modindex = True
diff --git a/doc/developer.rst b/doc/developer.rst
new file mode 100644
index 0000000..5bc3066
--- /dev/null
+++ b/doc/developer.rst
@@ -0,0 +1,80 @@
+=================
+Developer's guide
+=================
+
+Code organization
+=================
+
+The top level directory is organized in the following 
+directories:
+
+:file:`pysam`
+   Code specific to pysam.
+
+:file:`doc`
+   The documentation. To build the latest documentation, first install 
+   `Sphinx`_ and then type::
+
+       make -C doc html
+
+:file:`tests`
+   Code and data for testing and benchmarking.
+
+:file:`htslib`
+   Source code from `htslib`_ shipped with pysam. See
+   :file:`import.py` about importing.
+
+:file:`samtools`
+   Source code from `samtools`_ shipped with pysam. See
+   :file:`import.py` about importing.
+
+:file:`bcftools`
+   Source code from `bcftools`_ shipped with pysam. See
+   :file:`import.py` about importing.
+
+
+Importing new versions of htslib and samtools
+=============================================
+
+See instructions in :file:`import.py` to import the latest
+versions of `htslib`_, `samtools`_ and `bcftools`_.
+
+Unit testing
+============
+
+Unit tests are in the :file:`tests` directory. To run all unit tests,
+run::
+
+   pytest tests
+
+Most tests use test data from the :file:`tests/*_data` directories.
+Some of these test data files are generated from other files in these
+directories, which is done by running ``make`` in each directory::
+
+   make -C tests/pysam_data
+   # etc
+
+Alternatively if any :file:`tests/*_data/all.stamp` file is not already
+present, running the unit tests should generate that directory's data
+files automatically.
+
+Benchmarking
+============
+
+To run the benchmarking suite, make sure that `pytest-benchmark
+<https://github.com/ionelmc/pytest-benchmark>`_ is installed. To run
+all benchmarks, type::
+
+   pytest tests/*_bench.py
+
+See :ref:`Benchmarking` for more on this topic.
+
+Contributors
+============
+
+Please see Github for a list of all contributors:
+
+https://github.com/pysam-developers/pysam/graphs/contributors
+
+Many thanks to all contributors for helping in making pysam
+useful.
diff --git a/doc/faq.rst b/doc/faq.rst
new file mode 100644
index 0000000..e2352eb
--- /dev/null
+++ b/doc/faq.rst
@@ -0,0 +1,278 @@
+===
+FAQ
+===
+
+How should I cite pysam
+=======================
+
+Pysam has not been published in print. When referring to pysam, please
+use the github URL: https://github.com/pysam-developers/pysam. 
+As pysam is a wrapper around htslib and the samtools package, I
+suggest citing [Li.2009]_, [Bonfield.2021]_, and/or [Danecek.2021]_,
+as appropriate.
+
+Is pysam thread-safe?
+=====================
+
+Pysam is a mix of python and C code. Instructions within python are
+generally made thread-safe through python's `global interpreter lock`_
+(:dfn:`GIL`). This ensures that python data structures will always be in a
+consistent state. 
+
+If an external function outside python is called, the programmer has a
+choice to keep the GIL in place or to release it. Keeping the GIL in
+place will make sure that all python threads wait until the external
+function has completed. This is a safe option and ensures
+thread-safety.
+
+Alternatively, the GIL can be released while the external function is
+called. This will allow other threads to run concurrently. This can be
+beneficial if the external function is expected to halt, for example
+when waiting for data to read or write. However, to achieve
+thread-safety, the external function needs to be implemented with
+thread-safety in mind. This means that there can be no shared state
+between threads, or if there is shared, it needs to be controlled to
+prevent any access conflicts.
+
+Pysam generally uses the latter option and aims to release the GIL for
+I/O intensive tasks. This is generally fine, but thread-safety of all
+parts have not been fully tested. 
+
+A related issue is when different threads read from the same file
+object - or the same thread uses two iterators over a file. There is
+only a single file-position for each opened file. To prevent this from
+happening, use the option ``multiple_iterators=True`` when calling
+a fetch() method. This will return an iterator on a newly opened
+file.
+
+pysam coordinates are wrong
+===========================
+
+pysam uses 0-based coordinates and the half-open notation for ranges
+as does python. Coordinates and intervals reported from pysam always
+follow that convention.
+
+Confusion might arise as different file formats might have different
+conventions. For example, the SAM format is 1-based while the BAM
+format is 0-based. It is important to remember that pysam will always
+conform to the python convention and translate to/from the file format
+automatically.
+
+The only exception is the :term:`region` string in the
+:meth:`~pysam.AlignmentFile.fetch` and
+:meth:`~pysam.AlignmentFile.pileup` methods. This string follows the
+convention of the samtools command line utilities. The same is true
+for any coordinates passed to the samtools command utilities directly,
+such as :meth:`pysam.mpileup`.
+
+Calling pysam.fetch() confuses existing iterators
+=================================================
+
+The following code will cause unexpected behaviour::
+
+   samfile = pysam.AlignmentFile("pysam_ex1.bam", "rb")
+
+   iter1 = samfile.fetch("chr1")
+   print(next(iter1).reference_id)
+   iter2 = samfile.fetch("chr2")
+   print(next(iter2).reference_id)
+   print(next(iter1).reference_id)
+
+This will give the following output::
+
+    0
+    1
+    Traceback (most recent call last):
+      File "xx.py", line 8, in <module>
+        print(next(iter1).reference_id)
+      File "libcalignmentfile.pyx", line 2103,
+      in pysam.libcalignmentfile.IteratorRowRegion.__next__
+    StopIteration
+
+Note how the second iterator stops as the file pointer has moved to
+chr2. The correct way to work with multiple iterators is::
+
+   samfile = pysam.AlignmentFile("pysam_ex1.bam", "rb")
+
+   iter1 = samfile.fetch("chr1", multiple_iterators=True)
+   print(next(iter1).reference_id)
+   iter2 = samfile.fetch("chr2")
+   print(next(iter2).reference_id)
+   print(next(iter1).reference_id)
+
+Here, the output is::
+
+   0
+   1
+   0
+
+The reason for this behaviour is that every iterator needs to keep
+track of its current position in the file. Within pysam, each opened
+file can only keep track of one file position and hence there can only
+be one iterator per file. Using the option ``multiple_iterators=True``
+will return an iterator within a newly opened file. This iterator will
+not interfere with existing iterators as it has its own file handle
+associated with it.
+
+Note that re-opening files incurs a performance penalty which can
+become severe when calling :meth:`~pysam.AlignmentFile.fetch` often.
+Thus, ``multiple_iterators`` is set to ``False`` by default.
+
+AlignmentFile.fetch does not show unmapped reads
+================================================
+
+:meth:`~pysam.AlignmentFile.fetch` will only iterate over alignments
+in the SAM/BAM file. The following thus always works::
+
+    bf = pysam.AlignmentFile(fname, "rb")
+    for r in bf.fetch():
+        assert not r.is_unmapped
+
+If the SAM/BAM file contains unaligned reads, they can be included
+in the iteration by adding the ``until_eof=True`` flag::
+
+    bf = pysam.AlignmentFile(fname, "rb")
+    for r in bf.fetch(until_eof=True):
+        if r.is_unmapped:
+	    print("read is unmapped")
+
+I can't call AlignmentFile.fetch on a file without an index
+===========================================================
+
+:meth:`~pysam.AlignmentFile.fetch` requires an index when
+iterating over a SAM/BAM file. To iterate over a file without an
+index, use ``until_eof=True``::
+
+    bf = pysam.AlignmentFile(fname, "rb")
+    for r in bf.fetch(until_eof=True):
+        print(r)
+
+	
+BAM files with a large number of reference sequences are slow
+=============================================================
+
+If you have many reference sequences in a BAM file, the following
+might be slow::
+
+      track = pysam.AlignmentFile(fname, "rb")
+      for aln in track.fetch():
+      	  pass
+	  
+The reason is that track.fetch() will iterate through the BAM file
+for each reference sequence in the order as it is defined in the
+header. This might require a lot of jumping around in the file. To
+avoid this, use::
+
+      track = pysam.AlignmentFile(fname, "rb")
+      for aln in track.fetch(until_eof=True):
+      	  pass
+ 
+This will iterate through reads as they appear in the file.
+
+Weirdness with spliced reads in samfile.pileup(chr,start,end) given spliced alignments from an RNA-seq bam file
+===============================================================================================================
+
+Spliced reads are reported within samfile.pileup. To ignore these
+in your analysis, test the flags ``is_del == True and indel == 0``
+in the :class:`~.PileupRead` object.
+
+I can't edit quality scores in place
+====================================
+
+Editing reads in-place generally works, though there is one
+quirk to be aware of. Assigning to AlignedSegment.query_sequence will invalidate 
+any quality scores in AlignedSegment.query_qualities. The reason is that samtools
+manages the memory of the sequence and quality scores together 
+and thus requires them to always be of the same length or 0.
+
+Thus, to in-place edit the sequence and quality scores, copies of
+the quality scores need to be taken. Consider trimming for example::
+
+    quals = read.query_qualities
+    read.query_sequence = read.query_sequence[5:10]
+    read.query_qualities = quals[5:10]
+ 
+Why is there no SNPCaller class anymore?
+=========================================
+
+SNP calling is highly complex and heavily parameterized. There was a
+danger that the pysam implementations might show different behaviour from the
+samtools implementation, which would have caused a lot of confusion.
+
+The best way to use samtools SNP calling from python is to use the 
+:meth:`pysam.mpileup` command and parse the output directly.
+
+I get an error 'PileupProxy accessed after iterator finished'
+=============================================================
+
+Pysam works by providing proxy objects to objects defined within
+the C-samtools package. Thus, some attention must be paid to the
+lifetime of objects. The following to code snippets will cause an
+error::
+
+    s = AlignmentFile('ex1.bam')
+    for p in s.pileup('chr1', 1000,1010):
+        pass
+    
+    for pp in p.pileups:
+        print(pp)
+
+The iteration has finished, thus the contents of ``p`` are invalid. Another
+variation of this::
+
+    p = next(AlignmentFile('ex1.bam').pileup('chr1', 1000, 1010))
+    for pp in p.pileups:
+        print(pp)
+
+Again, the iteration finishes as the temporary iterator created
+by pileup goes out of scope. The solution is to keep a handle
+to the iterator that remains alive::
+
+    i = AlignmentFile('ex1.bam').pileup('chr1', 1000, 1010)
+    p = next(i)
+    for pp in p.pileups:
+        print(pp)
+
+Pysam won't compile
+===================
+
+Compiling pysam can be tricky as there are numerous variables that
+differ between build environments such as OS, version, python version,
+and compiler. It is difficult to build software that builds cleanly
+on all systems and the process might fail. Please see the 
+`pysam user group
+<https://groups.google.com/forum/#!forum/pysam-user-group>`_
+for common issues.
+
+If there is a build issue, read the generated output carefully -
+generally the cause of the problem is among the first errors to be
+reported. For example, you will need to have the development version
+of python installed that includes the header files such as
+:file:`Python.h`. If that file is missing, the compiler will report
+this at the very top of its error messages but will follow it 
+with any unknown function or variable definition it encounters later
+on.
+
+General advice is to always use the latest version on python_ and
+cython_ when building pysam. There are some known incompatibilities:
+
+* Python 3.4 requires cython 0.20.2 or later (see `here
+  <https://github.com/pysam-developers/pysam/issues/37>`_)
+
+.. _global interpreter lock: https://en.wikipedia.org/wiki/Global_interpreter_lock
+
+ImportError: cannot import name csamtools
+=========================================
+
+In version 0.10.0 and onwards, all pysam extension modules contain a
+``lib``-prefix. This facilates linking against pysam extension modules
+with compilers that require to start with ``lib``. As a consequence,
+all code using pysam extension modules directly will need to be
+adapted. For example,::
+
+   cimport pysam.csamtools
+
+will become::
+
+   cimport pysam.libcsamtools
+
diff --git a/doc/glossary.rst b/doc/glossary.rst
new file mode 100644
index 0000000..b67e2f4
--- /dev/null
+++ b/doc/glossary.rst
@@ -0,0 +1,144 @@
+========
+Glossary
+========
+
+.. glossary::
+   :sorted:
+
+   cigar
+      Stands for Compact Idiosyncratic Gapped Alignment Report and
+      represents a compressed (run-length encoded) pairwise alignment
+      format.  It was first defined by the Exonerate Aligner, but was alter
+      adapted and adopted as part of the :term:`SAM` standard and many other
+      aligners.  In the Python API, the cigar alignment is presented as a
+      list of tuples ``(operation,length)``.  For example, the tuple ``[
+      (0,3), (1,5), (0,2) ]`` refers to an alignment with 3 matches, 5
+      insertions and another 2 matches.
+
+   region
+      A genomic region, stated relative to a :term:`reference` sequence. A
+      region consists of reference name ('chr1'), start (15000), and
+      end (20000). Start and end can be omitted for regions spanning
+      a whole chromosome. If ``end`` is missing, the region will span from
+      ``start`` to the end of the chromosome. Within pysam, coordinates
+      are 0-based half-open intervals, i.e., the first base of the
+      reference sequence is numbered zero; and the base at position
+      ``start`` is part of the interval, but the base at ``end`` is not.
+
+      When a region is written as a single string using
+      `samtools`_-compatible notation, e.g., 'chr1:15001-20000',
+      the string's coordinates instead represent a 1-based closed interval,
+      i.e., both (1-based) positions 15,001 and 20,000 are part of the
+      interval. (This example denotes the same 5,000-base region as the
+      example in the previous paragraph.)
+
+   genotype
+      An individual's collection of genes. It can also refer to the two alleles
+	  inherited for a particular gene.
+
+   column
+      The portion of reads aligned to a single base in the 
+	  :term:`reference` sequence.
+
+   tid
+      The :term:`target` id. The target id is 0 or a positive integer mapping to
+      entries within the sequence dictionary in the header section of
+      a :term:`TAM` file or :term:`BAM` file.
+
+   contig
+      The sequence that a :term:`tid` refers to. For example ``chr1``, ``contig123``.
+
+   reference
+      Synonym for contig.
+
+   BED
+      Browser Extensible Data format. A text file format used to store genomic
+      :term:`regions<region>` as coordinates and associated notations.
+
+   GTF
+      The Gene Transfer Format is a file format used to hold information
+	  about gene structure.
+
+   SAM
+       A textual format for storing genomic alignment information.
+
+   BAM
+       Binary SAM format. BAM files are binary formatted, indexed and
+       allow random access.
+
+   CRAM
+       CRAM is a binary format representing the same sequence alignment
+       information as SAM and BAM, but offering significantly better
+       lossless compression than BAM.
+
+   TAM
+       Text SAM file. TAM files are human readable files of
+       tab-separated fields. TAM files do not allow random access.
+
+   sam file
+       A file containing aligned reads. The :term:`sam file` can either
+       be a :term:`BAM` file or a :term:`TAM` file.
+
+   pileup
+      Pileup
+
+   fetching
+      Retrieving all mapped reads mapped to a :term:`region`.
+
+   target
+      The sequence that a read has been aligned to. Target
+      sequences have bot a numerical identifier (:term:`tid`)
+      and an alphanumeric name (:term:`Reference`).
+
+   tabix file
+      A sorted, compressed and indexed tab-separated file created
+      by the command line tool :file:`tabix` or the commands
+      :meth:`tabix_compress` and :meth:`tabix_index`. The file
+      is indexed by chromosomal coordinates.
+
+   tabix row
+      A row in a :term:`tabix file`. Fields within a row are
+      tab-separated.
+
+   soft clipping
+   soft clipped
+
+      In alignments with soft clipping part of the query sequence
+      are not aligned. The unaligned query sequence is still part
+      of the alignment record. This is in difference to
+      :term:`hard clipped` reads.
+
+   hard clipping
+   hard clipped
+
+      In hard clipped reads, part of the sequence has been removed
+      prior to alignment. That only a subsequence is aligend might be
+      recorded in the :term:`cigar` alignment, but the removed
+      sequence will not be part of the alignment record, in contrast
+      to :term:`soft clipped` reads.
+
+   VCF
+      Variant Call Format.
+
+   BCF
+      Binary :term:`VCF`.
+
+   FASTA
+      Simple text format containing sequence data, with only the bare
+      minimum of metadata. Typically used for reference sequence data.
+
+   FASTQ
+      Simple text format containing sequence data and associated base
+      qualities.
+
+   tabix
+      Utility in the htslib package to index :term:`bgzip` compressed
+      files.
+
+   faidx
+      Utility in the `samtools`_ package to index :term:`fasta` formatted
+      files.
+
+   bgzip
+      Utility in the htslib package to block compress genomic data
+      files.
diff --git a/doc/index.rst b/doc/index.rst
new file mode 100644
index 0000000..6bff551
--- /dev/null
+++ b/doc/index.rst
@@ -0,0 +1,84 @@
+pysam: htslib interface for python
+==================================
+
+:Author: Andreas Heger, Kevin Jacobs and contributors
+:Date: |today|
+:Version: |version|
+
+Pysam is a python module for reading, manipulating and writing
+genomic data sets.
+
+Pysam is a wrapper of the htslib_ C-API and provides facilities to
+read and write SAM/BAM/VCF/BCF/BED/GFF/GTF/FASTA/FASTQ files as well
+as access to the command line functionality of the samtools_ and
+bcftools_ packages. The module supports compression and random access
+through indexing.
+
+This module provides a low-level wrapper around the htslib_ C-API as
+using cython and a high-level, pythonic API for convenient access to
+the data within genomic file formats. 
+
+The current version wraps *htslib-1.16*, *samtools-1.16.1*, and *bcftools-1.16*.
+
+To install the latest release, type::
+
+    pip install pysam
+
+See the :ref:`Installation notes <installation>` for details.
+
+Contents
+--------
+
+.. toctree::
+   :maxdepth: 2
+
+   api.rst
+   usage.rst
+   installation.rst
+   faq.rst
+   developer.rst
+   release.rst
+   benchmarking.rst
+   glossary.rst
+
+Indices and tables
+------------------
+
+Contents:
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
+
+References
+----------
+
+.. [Li.2009] *The Sequence Alignment/Map format and SAMtools.*
+   Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup.
+   Bioinformatics. 2009 Aug 15;25(16):2078-9.
+   Epub 2009 Jun 8 `btp352 <https://doi.org/10.1093/bioinformatics/btp352>`_.
+   PMID: `19505943 <https://pubmed.ncbi.nlm.nih.gov/19505943>`_.
+
+.. [Bonfield.2021] *HTSlib: C library for reading/writing high-throughput sequencing data.*
+   Bonfield JK, Marshall J, Danecek P, Li H, Ohan V, Whitwham A, Keane T, Davies RM.
+   GigaScience (2021) 10(2) `giab007 <https://doi.org/10.1093/gigascience/giab007>`_.
+   PMID: `33594436 <https://pubmed.ncbi.nlm.nih.gov/33594436>`_.
+
+.. [Danecek.2021] *Twelve years of SAMtools and BCFtools.*
+   Danecek P, Bonfield JK, Liddle J, Marshall J, Ohan V, Pollard MO, Whitwham A, Keane T, McCarthy SA, Davies RM, Li H.
+   GigaScience (2021) 10(2) `giab008 <https://doi.org/10.1093/gigascience/giab008>`_.
+   PMID: `33590861 <https://pubmed.ncbi.nlm.nih.gov/33590861>`_.
+
+.. seealso::
+ 
+   Information about htslib
+      http://www.htslib.org
+
+   The samtools homepage
+      http://samtools.sourceforge.net
+   
+   The cython C-extensions for python
+      https://cython.org/
+
+   The python language
+      https://www.python.org
diff --git a/doc/installation.rst b/doc/installation.rst
new file mode 100644
index 0000000..a286c27
--- /dev/null
+++ b/doc/installation.rst
@@ -0,0 +1,108 @@
+.. _installation:
+
+================
+Installing pysam
+================
+
+Pysam can be installed through conda_, pypi_ and from the repository.
+The recommended way to install pysam is through conda/bioconda.
+
+Conda installation
+==================
+
+To install pysam in your current conda_ environment, type::
+
+   conda config --add channels r
+   conda config --add channels bioconda
+   conda install pysam
+
+This will install pysam from the bioconda_ channel and automatically
+makes sure that dependencies are installed. Also, compilation flags
+will be set automatically, which will potentially save a lot of
+trouble on OS X.
+
+Pypi installation
+=================
+
+Pysam provides a python interface to the functionality contained
+within the htslib_ C library. There are two ways that these two
+can be combined, ``builtin`` and ``external``.
+
+Builtin
+-------
+
+The typical installation will be through pypi_::
+
+   pip install pysam
+
+This will compile the ``builtin`` htslib source code within pysam.
+
+htslib_ can be configured at compilation to turn on additional
+features such support using encrypted configurations, enable plugins,
+and more. See the htslib_ project for more information on these.
+
+Pysam will attempt to configure htslib_ to turn on some advanced
+features. If these fail, for example due to missing library
+dependencies (`libcurl`, `libcrypto`), it will fall back to
+conservative defaults.
+
+Options can be passed to the configure script explicitly by
+setting the environment variable `HTSLIB_CONFIGURE_OPTIONS`.
+For example::
+
+  export HTSLIB_CONFIGURE_OPTIONS=--enable-plugins
+  pip install pysam
+
+External
+--------
+
+pysam can be combined with an externally installed htslib_
+library. This is a good way to avoid duplication of libraries. To link
+against an externally installed library, set the environment variables
+`HTSLIB_LIBRARY_DIR` and `HTSLIB_INCLUDE_DIR` before installing::
+
+   export HTSLIB_LIBRARY_DIR=/usr/local/lib
+   export HTSLIB_INCLUDE_DIR=/usr/local/include
+   pip install pysam
+
+Note that the location of the file :file:`libhts.so` needs to be known
+to the linker once you run pysam, for example by setting the
+environment-varirable `LD_LIBRARY_PATH`.
+
+Note that generally the pysam and htslib version need to be
+compatible. See the release notes for more information.
+
+Installation from repository
+============================
+
+pysam depends on cython_ to provide the connectivity to the htslib_ C
+library. The installation of the source tarball (:file:`.tar.gz`)
+contains pre-built C-files and cython needs not be present
+during installation. However, when installing from the repository,
+cython needs to be installed beforehand.
+
+To install from repository, type::
+
+    python setup.py install
+
+For compilation options, see the section on Pypi installation above.
+
+Requirements
+============
+
+Depending on the installation method, requirements for building pysam differ.
+
+When installing through conda_, dependencies will be resolved by the
+package manager. The pip_ installation and installation from source
+require a C compiler and its standard libraries as well as all
+requirements for building htslib. Htslib requirements are listed in
+the htslib/INSTALL file.
+
+Installing from the repository will require cython_ to be installed.
+
+
+
+
+
+
+
diff --git a/doc/make.bat b/doc/make.bat
new file mode 100644
index 0000000..caca799
--- /dev/null
+++ b/doc/make.bat
@@ -0,0 +1,112 @@
+@ECHO OFF
+
+REM Command file for Sphinx documentation
+
+set SPHINXBUILD=sphinx-build
+set ALLSPHINXOPTS=-d _build/doctrees %SPHINXOPTS% .
+if NOT "%PAPER%" == "" (
+	set ALLSPHINXOPTS=-D latex_paper_size=%PAPER% %ALLSPHINXOPTS%
+)
+
+if "%1" == "" goto help
+
+if "%1" == "help" (
+	:help
+	echo.Please use `make ^<target^>` where ^<target^> is one of
+	echo.  html      to make standalone HTML files
+	echo.  dirhtml   to make HTML files named index.html in directories
+	echo.  pickle    to make pickle files
+	echo.  json      to make JSON files
+	echo.  htmlhelp  to make HTML files and a HTML help project
+	echo.  qthelp    to make HTML files and a qthelp project
+	echo.  latex     to make LaTeX files, you can set PAPER=a4 or PAPER=letter
+	echo.  changes   to make an overview over all changed/added/deprecated items
+	echo.  linkcheck to check all external links for integrity
+	echo.  doctest   to run all doctests embedded in the documentation if enabled
+	goto end
+)
+
+if "%1" == "clean" (
+	for /d %%i in (_build\*) do rmdir /q /s %%i
+	del /q /s _build\*
+	goto end
+)
+
+if "%1" == "html" (
+	%SPHINXBUILD% -b html %ALLSPHINXOPTS% _build/html
+	echo.
+	echo.Build finished. The HTML pages are in _build/html.
+	goto end
+)
+
+if "%1" == "dirhtml" (
+	%SPHINXBUILD% -b dirhtml %ALLSPHINXOPTS% _build/dirhtml
+	echo.
+	echo.Build finished. The HTML pages are in _build/dirhtml.
+	goto end
+)
+
+if "%1" == "pickle" (
+	%SPHINXBUILD% -b pickle %ALLSPHINXOPTS% _build/pickle
+	echo.
+	echo.Build finished; now you can process the pickle files.
+	goto end
+)
+
+if "%1" == "json" (
+	%SPHINXBUILD% -b json %ALLSPHINXOPTS% _build/json
+	echo.
+	echo.Build finished; now you can process the JSON files.
+	goto end
+)
+
+if "%1" == "htmlhelp" (
+	%SPHINXBUILD% -b htmlhelp %ALLSPHINXOPTS% _build/htmlhelp
+	echo.
+	echo.Build finished; now you can run HTML Help Workshop with the ^
+.hhp project file in _build/htmlhelp.
+	goto end
+)
+
+if "%1" == "qthelp" (
+	%SPHINXBUILD% -b qthelp %ALLSPHINXOPTS% _build/qthelp
+	echo.
+	echo.Build finished; now you can run "qcollectiongenerator" with the ^
+.qhcp project file in _build/qthelp, like this:
+	echo.^> qcollectiongenerator _build\qthelp\samtools.qhcp
+	echo.To view the help file:
+	echo.^> assistant -collectionFile _build\qthelp\samtools.ghc
+	goto end
+)
+
+if "%1" == "latex" (
+	%SPHINXBUILD% -b latex %ALLSPHINXOPTS% _build/latex
+	echo.
+	echo.Build finished; the LaTeX files are in _build/latex.
+	goto end
+)
+
+if "%1" == "changes" (
+	%SPHINXBUILD% -b changes %ALLSPHINXOPTS% _build/changes
+	echo.
+	echo.The overview file is in _build/changes.
+	goto end
+)
+
+if "%1" == "linkcheck" (
+	%SPHINXBUILD% -b linkcheck %ALLSPHINXOPTS% _build/linkcheck
+	echo.
+	echo.Link check complete; look for any errors in the above output ^
+or in _build/linkcheck/output.txt.
+	goto end
+)
+
+if "%1" == "doctest" (
+	%SPHINXBUILD% -b doctest %ALLSPHINXOPTS% _build/doctest
+	echo.
+	echo.Testing of doctests in the sources finished, look at the ^
+results in _build/doctest/output.txt.
+	goto end
+)
+
+:end
diff --git a/doc/release.rst b/doc/release.rst
new file mode 100644
index 0000000..d731c36
--- /dev/null
+++ b/doc/release.rst
@@ -0,0 +1,841 @@
+=============
+Release notes
+=============
+
+Release 0.19.1
+==============
+
+This release wraps htslib/samtools/bcftools version 1.15.1.
+
+* [#1104] add an add_samples() method to quickly add multiple samples
+  to VCF.
+
+Release 0.19.0
+==============
+
+This release wraps htslib/samtools/bcftools version 1.15.
+
+* [#1085] Improve getopt()/getopt_long() resetting when running samtools/bcftools commands
+
+* [#1078] Support BAM_CPAD in get_aligned_pairs
+
+* [#1063] Run flake8 and fix some linting issues
+
+* [#1088] Add AlignedSegment is_mapped/mate_is_mapped/is_forward/mate_is_forward properties
+
+* Write an absent AlignedSegment.qual as all-bytes-0xff
+
+* Fix BGZFile.read() behaviour near or at EOF
+
+* First API for the htslib modified bases interface
+  
+Release 0.18.0
+==============
+
+This release wraps htslib/samtools/bcftools version 1.14.
+
+* [#1048] and [#1060], clarify documentation of index statistics with CRAM files
+* Prevent "retval may be used uninitialised" warning.
+* Add new "samples" subcommand to pysam/samtools.py
+* Introduce TupleProxyIterator iterator object class
+
+Release 0.17.0
+==============
+
+This release wraps htslib/samtools/bcftools version 1.13. Corresponding
+to new samtools commands, `pysam.samtools` now has additional functions
+`ampliconclip`, `ampliconstats`, `fqimport`, and `version`.
+
+Bugs fixed:
+
+* [#447] The maximum QNAME length is fully restored to 254
+* [#506, #958, #1000] Don't crash the Python interpreter on ``pysam.bcftools.*()`` errors
+* [#603] count_coverage: ignore reads that have no SEQ field
+* [#928] Fix ``pysam.bcftools.mpileup()`` segmentation fault
+* [#983] Add win32/\*.[ch] to MANIFEST.in
+* [#994] Raise exception in ``get_tid()`` if header could not be parsed
+* [#995] Choose TBI/CSI in ``tabix_index()`` via both min_shift and csi
+* [#996] ``AlignmentFile.fetch()`` now works with large chromosomes longer than 2\ :sup:`29` bases
+* [#1019] Fix Sphinx documentation generation by avoiding Python 2 ``ur'string'`` syntax
+* [#1035] Improved handling of file iteration errors
+* [#1038] ``tabix_index()`` no longer leaks file descriptors
+* [#1040] ``print(aligned_segment)`` now prints the correct TLEN value
+  (it also now prints RNAME/RNEXT more clearly and prints POS/PNEXT 1-based)
+* *setup.py* longer uses ``setup(use_2to3)`` for compatibility with setuptools >= v58.0.0
+
+New facilities:
+
+* [PR #963] Additional VCF classes are exposed to pysam programmers
+* [#998, PR #1001] Add ``get/set_encoding_error_handler()`` to control UTF-8 conversion
+* [PR #1012] Running ``python setup.py sdist`` now automatically runs cythonize
+* Running tests with ``pytest`` now automatically runs ``make`` to generate test data
+
+Documentation improvements:
+
+* [#726] Clarify get_forward_sequence/get_forward_qualities documentation
+* [#865] Improved example
+* [#968] ``get_index_statstics`` parameters
+* [#986] Clarify ``VariantFile.fetch`` start/stop region parameters are 0-based and half-open.
+* [#990] Corrected ``PileupColumn.get_query_sequences`` documentation
+* [#999] Fix documentation for ``AlignmentFile.get_reference_length()``
+* [#1002] Document the default min_base_quality for ``pileup()``
+
+
+Release 0.16.0
+==============
+
+This release wraps htslib/bcftools version 1.10.2 and samtools version
+1.10. The following bugs reported against pysam are fixed due to this:
+
+* [#447] Writing out QNAME longer than 251 characters corrupts BAM
+* [#640, #734, #843] Setting VariantRecord pos or stop raises error
+* [#738, #919] FastxFile truncates concatenated plain gzip compressed files
+
+Additional bugfixes:
+
+* [#840] Pileup doesn't work on python3 when `index_filename` is used
+* [#886] FastqProxy raises ValueError when instantiated from python
+* [#904] VariantFile.fetch() throws ValueError on files with no records
+* [#909] Fix incorrect quoting in VariantFile contig records
+* [#915, #916] Implement pileup() for unindexed files and/or SAM files
+
+Backwards incompatible changes:
+
+* The `samtools import` command was removed in samtools 1.10, so pysam
+  no longer exports a `samimport` function. Use `pysam.view()` instead.
+
+
+Release 0.15.4
+==============
+
+Bugfix release. Principal reason for release is to update cython
+version in order to fix pip install pysam with python 3.8.
+
+* [#879] Fix add_meta function in libcbcf.pyx, so meta-information
+  lines in header added with this function have double-quoting rules
+  in accordance to rules specified in VCF4.2 and VCF4.3 specifications
+* [#863] Force arg to bytes to support non-ASCII encoding
+* [#875] Bump minimum Cython version
+* [#868] Prevent segfault on Python 2.7 AlignedSegment.compare(other=None)
+* [#867] Fix wheel building on TravisCI
+* [#863] Force arg to bytes to support non-ASCII encoding
+* [#799] disambiguate interpretation of bcf_read return code
+* [#841] Fix silent truncation of FASTQ with bad q strings
+* [#846] Prevent segmentation fault on ID, when handling malformed records
+* [#829] Run configure with the correct CC/CFLAGS/LDFLAGS env vars
+
+
+Release 0.15.3
+==============
+
+Bugfix release.
+
+* [#824] allow reading of UTF-8 encoded text in VCF/BCF files.
+* [#780] close all filehandles before opening new ones in pysam_dispatch
+* [#773] do not cache VariantRecord.id to avoid memory leak
+* [#781] default of multiple_iterators=True is changed to False for
+  CRAM files.
+* [#825] fix collections.abc import
+* [#825] use bcf_hdr_format instead of bcf_hdr_fmt_text, fix memcpy
+  bug when setting FORMAT fields.
+* [#804] Use HTSlib's kstring_t, which reallocates and enlarges its
+  memory as needed, rather than a fixed-size char buffer.
+* [#814] Build wheels and upload them to PyPI
+* [#755] Allow passing flags and arguments to index methods
+* [#763] Strip \0 in header check
+* [#761] Test Tabix index contents, not the compression
+
+Release 0.15.2
+==============
+
+Bugfix release.
+
+* [#746] catch pileup itorator out-of-scope segfaults
+* [#747] fix faixd fetch with region
+* [#748] increase max_pos to (1<<31)-1
+* [#645] Add missing macOS stub files in `MANIFEST.in`, @SoapZA
+* [#737] Fix bug in get_aligned_pairs, @bkohrn
+
+Release 0.15.1
+==============
+
+Bugfix release.
+
+* [#716] raise ValueError if tid is out of range when writing
+* [#697] release version using cython 0.28.5 for python 3.7
+  compatibility
+
+Release 0.15.0
+==============
+
+This release wraps htslib/samtools/bcftools version 1.9.0.
+
+* [#673] permit dash in chromosome name of region string
+* [#656] Support `text` when opening a SAM file for writing
+* [#658] return None in get_forward_sequence if sequence not in record
+* [#683] allow lower case bases in MD tags
+* Ensure that = and X CIGAR ops are treated the same as M
+
+Release 0.14.1
+==============
+
+This is mostly a bugfix release, though bcftools has now also been
+upgraded to 1.7.0.
+
+* [#621] Add a warning to count_coverage when an alignment has an
+  empty QUAL field
+* [#635] Speed-up of AlignedSegment.find_intro()
+* treat border case of all bases in pileup column below quality score
+* [#634] Fix access to pileup reference_sequence
+
+
+Release 0.14.0
+==============
+
+This release wraps htslib/samtools versions 1.7.0.
+
+* SAM/BAM/CRAM headers are now managed by a separate AlignmentHeader
+  class.
+* AlignmentFile.header.as_dict() returns an ordered dictionary.
+* Use "stop" instead of "end" to ensure consistency to
+  VariantFile. The end designations have been kept for backwards
+  compatibility.
+
+* [#611] and [#293] CRAM repeated fetch now works, each iterator
+  reloads index if multiple_iterators=True
+* [#608] pysam now wraps htslib 1.7 and samtools 1.7.
+* [#580] reference_name and next_reference_name can now be set to "*"
+  (will be converted to None to indicate an unmapped location)
+* [#302] providing no coordinate to count_coverage will not count from
+  start/end of contig.
+* [#325] @SQ records will be automatically added to header if they are
+  absent from text section of header.
+* [#529] add get_forward_sequence() and get_forward_qualities()
+  methods
+* [#577] add from_string() and to_dict()/from_dict() methods to
+  AlignedSegment. Rename tostring() to to_string() throughout for
+  consistency
+* [#589] return None from build_alignment_sequence if no MD tag is set
+* [#528] add PileupColumn.__len__ method
+
+Backwards incompatible changes:
+
+* AlignmentFile.header now returns an AlignmentHeader object. Use
+  AlignmentFile.header.to_dict() to get the dictionary as
+  previously. Most dictionary accessor methods (keys(), values(),
+  __getitem__, ...) have been implemented to ensure some level of
+  backwards compatibility when only reading.
+
+  The rationale for this change is to have consistency between
+  AlignmentFile and VariantFile.
+
+* AlignmentFile and FastaFile now raise IOError instead of OSError
+
+Medium term we plan to have a 1.0 release. The pysam
+interface has grown over the years and the API is cluttered with
+deprecated names (Samfile, getrname(), gettid(), ...). To work towards
+this, the next release (0.15.0) will yield DeprecationWarnings 
+for any parts of the API that are considered obsolete and will not be
+in 1.0. Once 1.0 has been reached, we will use semantic versioning.
+
+Release 0.13.0
+===============
+
+This release wraps htslib/samtools/bcftools versions 1.6.0 and
+contains a series of bugfixes.
+
+* [#544] reading header from remote TabixFiles now works.
+* [#531] add missing tag types H and A. A python float will now be
+  added as 'f' type instead of 'd' type.
+* [#543] use FastaFile instead of Fastafile in pileup.
+* [#546] set is_modified flag in setAttribute so updated attributes
+  are output.
+* [#537] allow tabix index files to be created in a custom location.
+* [#530] add get_index_statistics() method
+
+
+Release 0.12.0.1
+================
+
+Bugfix release to solve compilation issue due to missinge
+bcftools/config.h file.
+
+Release 0.12.0
+==============
+
+This release wraps htslib/samtools/bcftools versions 1.5.0 and
+contains a series of bugfixes.
+
+* [#473] A new FastxRecord class that can be instantiated from class and
+  modified in-place. Replaces PersistentFastqProxy.
+* [#521] In AligmentFile, Simplify file detection logic and allow remote index files
+
+  * Removed attempts to guess data and index file names; this is magic left
+    to htslib.
+  * Removed file existence check prior to opening files with htslib
+  * Better error checking after opening files that raise the appropriate
+    error (IOError for when errno is set, ValueError otherwise for backward
+    compatibility).
+  * Report IO errors when loading an index by name.
+  * Allow remote indices (tested using S3 signed URLs).
+  * Document filepath_index and make it an alias for index_filename.
+  * Added a require_index parameter to AlignmentFile
+
+* [#526] handle unset ref when creating new records
+* [#513] fix bcf_translate to skip deleted FORMAT fields to avoid
+  segfaults
+* [#516] expose IO errors via IOError exceptions
+* [#487] add tabix line_skip, remove 'pileup' preset
+* add FastxRecord, replaces PersistentFastqProxy (still present for
+  backwards compatibility)
+* [#496] upgrade to htslib/samtools/bcftools versions 1.5
+* add start/stop to AlignmentFile.fetch() to be consistent with
+  VariantFile.fetch(). "end" is kept for backwards compatibility.
+* [#512] add get_index_statistics() method to AlignmentFile.
+
+Upcoming changes:
+
+In the next release we are plannig to separate the header information
+from AlignmentFile into a separate class AlignmentHeader. This layout
+is similar to VariantFile/VariantHeader. With this change we will
+ensure that an AlignedSegment record will be linked to a header so
+that chromosome names can be automatically translated from the numeric
+representation. As a consequence, the way new AlignedSegment records
+are created will need to change as the constructor requires a header::
+
+    header = pysam.AlignmentHeader(
+        reference_names=["chr1", "chr2"],
+        reference_lengths=[1000, 1000])
+
+    read = pysam.AlignedSegment(header)
+
+This will affect all code that instantiates AlignedSegment objects
+directly. We have not yet merged to allow users to provide feed-back.
+The pull-request is here: https://github.com/pysam-developers/pysam/pull/518
+Please comment on github.
+
+Release 0.11.2.2
+================
+
+Bugfix release to address two issues:
+
+* Changes in 0.11.2.1 broke the GTF/GFF3 parser. Corrected and
+  more tests have been added.
+* [#479] Correct VariantRecord edge cases described in issue
+
+Release 0.11.2.1
+================
+
+Release to fix release tar-ball containing 0.11.1 pre-compiled
+C-files.
+
+Release 0.11.2
+==============
+
+This release wraps htslib/samtools/bcfools versions 1.4.1 in response
+to a security fix in these libraries. Additionally the following
+issues have been fixed:
+
+* [#452] add GFF3 support for tabix parsers
+* [#461] Multiple fixes related to VariantRecordInfo and handling of INFO/END
+* [#447] limit query name to 251 characters (only partially addresses issue)
+
+VariantFile and related object fixes
+
+* Restore VariantFile.\_\_dealloc\_\_
+* Correct handling of bcf_str_missing in bcf_array_to_object and
+  bcf_object_to_array
+* Added update() and pop() methods to some dict-like proxy objects
+* scalar INFO entries could not be set again after being deleted
+* VariantRecordInfo.__delitem__ now allows unset flags to be deleted without
+  raising a KeyError
+* Multiple other fixes for VariantRecordInfo methods
+* INFO/END is now accessible only via VariantRecord.stop and
+  VariantRecord.rlen.  Even if present behind the scenes, it is no longer
+  accessible via VariantRecordInfo.
+* Add argument to issue a warning instead of an exception if input appears
+  to be truncated
+
+Other features and fixes:
+
+* Make AlignmentFile \_\_dealloc\_\_ and close more
+  stringent
+* Add argument AlignmentFile to issue a warning instead of an
+  exception if input appears to be truncated
+
+Release 0.11.1
+==============
+
+Bugfix release
+
+* [#440] add deprecated 'always' option to infer_query_length for backwards compatibility.
+
+Release 0.11.0
+==============
+
+This release wraps the latest versions of htslib/samtools/bcftools and
+implements a few bugfixes.
+
+* [#413] Wrap HTSlib/Samtools/BCFtools 1.4 
+* [#422] Fix missing pysam.sort.usage() message
+* [#411] Fix BGZfile initialization bug
+* [#412] Add seek support for BGZFile
+* [#395] Make BGZfile iterable
+* [#433] Correct getQueryEnd
+* [#419] Export SAM enums such as pysam.CMATCH
+* [#415] Fix access by tid in AlignmentFile.fetch()
+* [#405] Writing SAM now outputs a header by default.
+* [#332] split infer_query_length(always) into infer_query_length and infer_read_length
+
+Release 0.10.0
+==============
+
+This release implements further functionality in the VariantFile API
+and includes several bugfixes:
+
+* treat special case -c option in samtools view outputs to stdout even
+  if -o given, fixes #315
+* permit reading BAM files with CSI index, closes #370
+* raise Error if query name exceeds maximum length, fixes #373
+* new method to compute hash value for AlignedSegment
+* AlignmentFile, VariantFile and TabixFile all inherit from HTSFile
+* Avoid segfault by detecting out of range reference_id and
+  next_reference in AlignedSegment.tostring
+* Issue #355: Implement streams using file descriptors for VariantFile
+* upgrade to htslib 1.3.2
+* fix compilation with musl libc
+* Issue #316, #360: Rename all Cython modules to have lib as a prefix
+* Issue #332, hardclipped bases in cigar included by
+  pysam.AlignedSegment.infer_query_length()
+* Added support for Python 3.6 filename encoding protocol
+* Issue #371, fix incorrect parsing of scalar INFO and FORMAT fields in VariantRecord
+* Issue #331, fix failure in VariantFile.reset() method
+* Issue #314, add VariantHeader.new_record(), VariantFile.new_record() and
+  VariantRecord.copy() methods to create new VariantRecord objects
+* Added VariantRecordFilter.add() method to allow setting new VariantRecord filters
+* Preliminary (potentially unsafe) support for removing and altering header metadata
+* Many minor fixes and improvements to VariantFile and related objects
+
+Please note that all internal cython extensions now have a lib prefix
+to facilitate linking against pysam extension modules. Any user cython
+extensions using cimport to import pysam definitions will need
+changes, for example::
+
+   cimport pysam.csamtools
+
+will become::
+
+   cimport pysam.libcsamtools
+
+Release 0.9.1
+=============
+
+This is a bugfix release addressing some installation problems
+in pysam 0.9.0, in particular:
+
+* patch included htslib to work with older libcurl versions, fixes #262.
+* do not require cython for python 3 install, fixes #260
+* FastaFile does not accept filepath_index any more, see #270
+* add AlignedSegment.get_cigar_stats method.
+* py3 bugfix in VariantFile.subset_samples, fixes #272
+* add missing sysconfig import, fixes #278
+* do not redirect stdout, but instead write to a separately
+  created file. This should resolve issues when pysam is used
+  in notebooks or other environments that redirect stdout.
+* wrap htslib-1.3.1, samtools-1.3.1 and bcftools-1.3.1
+* use bgzf throughout instead of gzip
+* allow specifying a fasta reference for CRAM file when opening
+  for both read and write, fixes #280
+
+Release 0.9.0
+=============
+
+Overview
+--------
+
+The 0.9.0 release upgrades htslib to htslib 1.3 and numerous other
+enhancements and bugfixes. See below for a detailed list.
+
+`Htslib 1.3 <https://github.com/samtools/htslib/releases/tag/1.3>`_
+comes with additional capabilities for remote file access which depend
+on the presence of optional system libraries. As a consequence, the
+installation script :file:`setup.py` has become more complex. For an
+overview, see :ref:`installation`.  We have tested installation on
+linux and OS X, but could not capture all variations. It is possible
+that a 0.9.1 release might follow soon addressing installation issues.
+
+The :py:class:`~.pysam.VariantFile` class provides access to
+:term:`vcf` and :term:`bcf` formatted files. The class is certainly
+usable and interface is reaching completion, but the API and the
+functionality is subject to change.
+
+Detailed release notes
+----------------------
+
+* upgrade to htslib 1.3
+* python 3 compatibility tested throughout.
+* added a first set of bcftools commands in the pysam.bcftools
+  submodule.
+* samtools commands are now in the pysam.samtools module. For
+  backwards compatibility they are still imported into the pysam
+  namespace.
+* samtools/bcftools return stdout as a single (byte) string. As output
+  can be binary (VCF.gz, BAM) this is necessary to ensure py2/py3
+  compatibility. To replicate the previous behaviour in py2.7, use::
+
+     pysam.samtools.view(self.filename).splitlines(True)
+
+* get_tags() returns the tag type as a character, not an integer (#214)
+* TabixFile now raises ValueError on indices created by tabix <1.0 (#206)
+* improve OSX installation and develop mode
+* FastxIterator now handles empty sequences (#204)
+* TabixFile.isremote is not TabixFile.is_remote in line with AlignmentFile
+* AlignmentFile.count() has extra optional argument read_callback
+* setup.py has been changed to:
+   * install a single builtin htslib library. Previously, each pysam
+     module contained its own version. This reduces compilation time
+     and code bloat.
+   * run configure for the builtin htslib library in order to detect
+     optional libraries such as libcurl. Configure behaviour can be
+     controlled by setting the environment variable
+     HTSLIB_CONFIGURE_OPTIONS.
+* get_reference_sequence() now returns the reference sequence and not
+  something looking like it. This bug had effects on
+  get_aligned_pairs(with_seq=True), see #225. If you have relied on on
+  get_aligned_pairs(with_seq=True) in pysam-0.8.4, please check your
+  results.
+* improved autodetection of file formats in AlignmentFile and VariantFile.
+
+Release 0.8.4
+=============
+
+This release contains numerous bugfixes and a first implementation of
+a pythonic interface to VCF/BCF files. Note that this code is still
+incomplete and preliminary, but does offer a nearly complete immutable
+Pythonic interface to VCF/BCF metadata and data with reading and
+writing capability.
+
+Potential isses when upgrading from v0.8.3:
+
+* binary tags are now returned as python arrays
+
+* renamed several methods for pep8 compatibility, old names still retained for	
+  backwards compatibility, but should be considered deprecated.
+
+   * gettid() is now get_tid()
+   * getrname() is now get_reference_name()
+   * parseRegion() is now parse_region()
+
+* some methods have changed for pep8 compatibility without the old
+  names being present:
+
+   * fromQualityString() is now qualitystring_to_array()
+   * toQualityString() is now qualities_to_qualitystring()
+
+* faidx now returns strings and not binary strings in py3.
+
+* The cython components have been broken up into smaller files with
+  more specific content. This will affect users using the cython
+  interfaces.
+
+Edited list of commit log changes:
+
+*    fixes AlignmentFile.check_index to return True
+*    add RG/PM header tag - closes #179
+*    add with_seq option to get_aligned_pairs
+*    use char * inside reconsituteReferenceSequence
+*    add soft clipping for get_reference_sequence
+*    add get_reference_sequence
+*    queryEnd now computes length from cigar string if no sequence present, closes #176
+*    tolerate missing space at end of gtf files, closes #162
+*    do not raise Error when receiving output on stderr
+*    add docu about fetching without index, closes #170
+*    FastaFile and FastxFile now return strings in python3, closes #173
+*    py3 compat: relative -> absolute imports.
+*    add reference_name and next_reference_name attributes to AlignedSegment
+*    add function signatures to cvcf cython.  Added note about other VCF code.
+*    add context manager functions to FastaFile
+*    add reference_name and next_reference_name attributes to AlignedSegment
+*    PileupColumn also gets a reference_name attribute.
+*    add context manager functions to FastaFile
+*    TabixFile.header for remote files raises AttributeError, fixes #157
+*    add context manager interface to TabixFile, closes #165
+*    change ctypedef enum to typedef enum for cython 0.23
+*    add function signatures to cvcf cython, also added note about other VCF code
+*    remove exception for custom upper-case header record tags.
+*    rename VALID_HEADER_FIELDS to KNOWN_HEADER_FIELDS
+*    fix header record tag parsing for custom tags.
+*    use cython.str in count_coverage, fixes #141
+*    avoid maketrans (issues with python3)
+*    refactoring: AlignedSegment now in separate module
+*    do not execute remote tests if URL not available
+*    fix the unmapped count, incl reads with no SQ group
+*    add raw output to tags
+*    added write access for binary tags
+*    bugfix in call to resize
+*    implemented writing of binary tags from arrays
+*    implemented convert_binary_tag to use arrays
+*    add special cases for reads that are unmapped or whose mates are unmapped.
+*    rename TabProxies to ctabixproxies
+*    remove underscores from utility functions
+*    move utility methods into cutils
+*    remove callback argument to fetch - closes #128
+*    avoid calling close in dealloc
+*    add unit tests for File object opening
+*    change AlignmentFile.open to filepath_or_object
+*    implement copy.copy, close #65
+*    add chaching of array attributes in AlignedSegment, closes #121
+*    add export of Fastafile
+*    remove superfluous pysam_dispatch
+*    use persist option in FastqFile
+*    get_tag: expose tag type if requested with `with_value_type`
+*    fix to allow reading vcf record info via tabix-based vcf reader
+*    add pFastqProxy and pFastqFile objects to make it possible to work with multiple fastq records per file handle, unlike FastqProxy/FastqFile.
+*    release GIL around htslib IO operations
+*    More work on read/write support, API improvements
+*    add `phased` property on `VariantRecordSample`
+*    add mutable properties to VariantRecord
+*    BCF fixes and start of read/write support
+*    VariantHeaderRecord objects now act like mappings for attributes.
+*    add VariantHeader.alts dict from alt ID->Record.
+*    Bug fix to strong representation of structured header records.
+*    VariantHeader is now mutable
+
+
+Release 0.8.3
+=============
+
+* samtools command now accept the "catch_stdout" option.
+
+* get_aligned_pairs now works for soft-clipped reads.
+
+* query_position is now None when a PileupRead is not aligned
+  to a particular position.
+
+* AlignedSegments are now comparable and hashable.
+
+Release 0.8.2.1
+===============
+
+* Installation bugfix release.
+
+Release 0.8.2
+=============
+
+* Pysam now wraps htslib 1.2.1 and samtools version 1.2.
+
+* Added CRAM file support to pysam.
+
+* New alignment info interface.
+   * opt() and setTag are deprecated, use get_tag() and set_tag()
+     instead.
+   * added has_tag()
+   * tags is deprecated, use get_tags() and set_tags() instead.
+
+* FastqFile is now FastxFile to reflect that the latter permits
+  iteration over both fastq- and fasta-formatted files.
+
+* A Cython wrapper for htslib VCF/BCF reader/writer. The wrapper
+  provides a nearly complete Pythonic interface to VCF/BCF metadata
+  with reading and writing capability. However, the interface is still
+  incomplete and preliminary and lacks capability to mutate the
+  resulting data.
+
+Release 0.8.1
+=============
+
+* Pysam now wraps htslib and samtools versions 1.1.
+
+* Bugfixes, most notable:
+  * issue #43: uncompressed BAM output
+  * issue #42: skip tests requiring network if none available
+  * issue #19: multiple iterators can now be made to work on the same tabix file
+  * issue #24: All strings returned from/passed to the pysam API are now unicode in python 3
+  * issue #5:  type guessing for lists of integers fixed    
+
+* API changes for consistency. The old API is still present,
+  but deprecated.
+  In particular:
+
+  * Tabixfile -> TabixFile
+  * Fastafile -> FastaFile
+  * Fastqfile -> FastqFile
+  * Samfile -> AlignmentFile
+  * AlignedRead -> AlignedSegment
+     * qname -> query_name
+     * tid -> reference_id
+     * pos -> reference_start
+     * mapq -> mapping_quality
+     * rnext -> next_reference_id
+     * pnext -> next_reference_start
+     * cigar -> cigartuples
+     * cigarstring -> cigarstring
+     * tlen -> template_length
+     * seq -> query_sequence
+     * qual -> query_qualities, now returns array
+     * qqual -> query_alignment_qualities, now returns array
+     * tags -> tags
+     * alen -> reference_length, reference is always "alignment", so removed
+     * aend -> reference_end
+     * rlen -> query_length
+     * query -> query_alignment_sequence
+     * qstart -> query_alignment_start
+     * qend -> query_alignment_end
+     * qlen -> query_alignment_length
+     * mrnm -> next_reference_id   
+     * mpos -> next_reference_start
+     * rname -> reference_id
+     * isize -> template_length
+     * blocks -> get_blocks()
+     * aligned_pairs -> get_aligned_pairs()
+     * inferred_length -> infer_query_length()
+     * positions -> get_reference_positions()
+     * overlap() -> get_overlap()
+
+  * All strings are now passed to or received from the pysam API
+    as strings, no more bytes.
+
+Other changes:
+   * AlignmentFile.fetch(reopen) option is now multiple_iterators. The
+     default changed to not reopen a file unless requested by the user.
+   * FastaFile.getReferenceLength is now FastaFile.get_reference_length
+
+Backwards incompatible changes
+
+* Empty cigarstring now returns None (instead of '')
+* Empty cigar now returns None (instead of [])
+* When using the extension classes in cython modules, AlignedRead
+  needs to be substituted with AlignedSegment. 
+* fancy_str() has been removed
+* qual, qqual now return arrays
+
+Release 0.8.0
+=============
+
+* Disabled features
+   * IteratorColumn.setMask() disabled as htslib does not implement
+     this functionality?
+
+* Not implemented yet:
+   * reading SAM files without header
+
+Tabix files between version 0.7.8 and 0.8.0 are
+not compatible and need to be re-indexed.
+
+While version 0.7.8 and 0.8.0 should be mostly
+compatible, there are some notable exceptions:
+
+* tabix iterators will fail if there are comments
+  in the middle or the end of a file.
+
+* tabix raises always ValueError for invalid intervals.
+  Previously, different types of errors were raised
+  (KeyError, IndexError, ValueError) depending on
+  the type of invalid intervals (missing chromosome,
+  out-of-range, malformatted interval).
+
+
+Release 0.7.8
+=============
+
+* added AlignedRead.setTag method
+* added AlignedRead.blocks
+* unsetting CIGAR strings is now possible
+* empty CIGAR string returns empty list
+* added reopen flag to Samfile.fetch()
+* various bugfixes
+
+Release 0.7.7
+=============
+
+* added Fastafile.references, .nreferences and .lengths
+* tabix_iterator now uses kseq.h for python 2.7
+
+Release 0.7.6
+=============
+
+* added inferred_length property
+* issue 122: MACOSX getline missing, now it works?
+* seq and qual can be set None
+* added Fastqfile
+
+Release 0.7.5
+=============
+
+* switch to samtools 0.1.19
+* issue 122: MACOSX getline missing
+* issue 130: clean up tempfiles
+* various other bugfixes
+
+Release 0.7.4
+=============
+
+* further bugfixes to setup.py and package layout
+
+Release 0.7.3
+=============
+
+* further bugfixes to setup.py
+* upgraded distribute_setup.py to 0.6.34
+
+Release 0.7.2
+=============
+
+* bugfix in installer - failed when cython not present
+* changed installation locations of shared libraries
+
+Release 0.7.1
+=============
+
+* bugfix: missing PP tag PG records in header
+* added pre-built .c files to distribution
+
+Release 0.7
+===========
+
+* switch to tabix 0.2.6
+* added cigarstring field
+* python3 compatibility
+* added B tag handling
+* added check_sq and check_header options to Samfile.__init__
+* added lazy GTF parsing to tabix
+* reworked support for VCF format parsing
+* bugfixes
+
+Release 0.6
+===========
+
+* switch to samtools 0.1.18
+* various bugfixes
+* removed references to deprecated 'samtools pileup' functionality
+* AlignedRead.tags now returns an empty list if there are no tags.
+* added pnext, rnext and tlen
+
+Release 0.5
+===========
+
+* switch to samtools 0.1.16 and tabix 0.2.5
+* improved tabix parsing, added vcf support
+* re-organized code to permit linking against pysam
+* various bugfixes
+* added Samfile.positions and Samfile.overlap
+
+Release 0.4
+===========
+
+* switch to samtools 0.1.12a and tabix 0.2.3
+* added snp and indel calling.
+* switch from pyrex to cython
+* changed handling of samtools stderr
+* various bugfixes
+* added Samfile.count and Samfile.mate
+* deprecated AlignedRead.rname, added AlignedRead.tid
+
+Release 0.3
+===========
+
+* switch to samtools 0.1.8
+* added support for tabix files
+* numerous bugfixes including
+* permit simultaneous iterators on the same file
+* working access to remote files
diff --git a/doc/usage.rst b/doc/usage.rst
new file mode 100644
index 0000000..3c8ab04
--- /dev/null
+++ b/doc/usage.rst
@@ -0,0 +1,423 @@
+.. _Usage: 
+
+=========================================
+Working with BAM/CRAM/SAM-formatted files
+=========================================
+
+Opening a file
+==============
+
+To begin with, import the pysam module and open a
+:class:`pysam.AlignmentFile`::
+
+   import pysam
+   samfile = pysam.AlignmentFile("ex1.bam", "rb")
+
+The above command opens the file :file:`ex1.bam` for reading.
+The ``b`` qualifier indicates that this is a :term:`BAM` file. 
+To open a :term:`SAM` file, type::
+
+   import pysam
+   samfile = pysam.AlignmentFile("ex1.sam", "r")
+
+:term:`CRAM` files are identified by a ``c`` qualifier::
+
+   import pysam
+   samfile = pysam.AlignmentFile("ex1.cram", "rc")
+
+Fetching reads mapped to a :term:`region`
+=========================================
+
+Reads are obtained through a call to the
+:meth:`pysam.AlignmentFile.fetch` method which returns an iterator.
+Each call to the iterator will returns a :class:`pysam.AlignedSegment`
+object::
+
+   iter = samfile.fetch("seq1", 10, 20)
+   for x in iter:
+       print(str(x))
+
+:meth:`pysam.AlignmentFile.fetch` returns all reads overlapping a
+region sorted by the first aligned base in the :term:`reference`
+sequence.  Note that it will also return reads that are only partially
+overlapping with the :term:`region`. Thus the reads returned might
+span a region that is larger than the one queried.
+
+Using the pileup-engine
+=======================
+
+In contrast to :term:`fetching`, the :term:`pileup` engine returns for
+each base in the :term:`reference` sequence the reads that map to that
+particular position. In the typical view of reads stacking vertically
+on top of the reference sequence similar to a multiple alignment,
+:term:`fetching` iterates over the rows of this implied multiple
+alignment while a :term:`pileup` iterates over the :term:`columns<column>`.
+
+Calling :meth:`~pysam.AlignmentFile.pileup` will return an iterator
+over each :term:`column` (reference base) of a specified
+:term:`region`. Each call to the iterator returns an object of the
+type :class:`pysam.PileupColumn` that provides access to all the
+reads aligned to that particular reference position as well as
+some additional information::
+
+   iter = samfile.pileup('seq1', 10, 20)
+   for x in iter:
+      print(str(x))
+ 
+
+Creating BAM/CRAM/SAM files from scratch
+========================================
+
+The following example shows how a new :term:`BAM` file is constructed
+from scratch.  The important part here is that the
+:class:`pysam.AlignmentFile` class needs to receive the sequence
+identifiers. These can be given either as a dictionary in a header
+structure, as lists of names and sizes, or from a template file.
+Here, we use a header dictionary::
+
+   header = { 'HD': {'VN': '1.0'},
+               'SQ': [{'LN': 1575, 'SN': 'chr1'}, 
+                      {'LN': 1584, 'SN': 'chr2'}] }
+
+   with pysam.AlignmentFile(tmpfilename, "wb", header=header) as outf:
+       a = pysam.AlignedSegment()
+       a.query_name = "read_28833_29006_6945"
+       a.query_sequence="AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG"
+       a.flag = 99
+       a.reference_id = 0
+       a.reference_start = 32
+       a.mapping_quality = 20
+       a.cigar = ((0,10), (2,1), (0,25))
+       a.next_reference_id = 0
+       a.next_reference_start=199
+       a.template_length=167
+       a.query_qualities = pysam.qualitystring_to_array("<<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<<")
+       a.tags = (("NM", 1),
+		 ("RG", "L1"))
+       outf.write(a)
+
+Using streams
+=============
+
+Pysam does not support reading and writing from true python file
+objects, but it does support reading and writing from stdin and
+stdout. The following example reads from stdin and writes to stdout::
+
+   infile = pysam.AlignmentFile("-", "r")
+   outfile = pysam.AlignmentFile("-", "w", template=infile)
+   for s in infile:
+       outfile.write(s)
+
+It will also work with :term:`BAM` files. The following script
+converts a :term:`BAM` formatted file on stdin to a :term:`SAM`
+formatted file on stdout::
+
+   infile = pysam.AlignmentFile("-", "rb")
+   outfile = pysam.AlignmentFile("-", "w", template=infile)
+   for s in infile:
+       outfile.write(s)
+
+Note that the file open mode needs to changed from ``r`` to ``rb``.
+
+=====================================
+Using samtools commands within python
+=====================================
+
+Commands available in `samtools`_ are available as simple
+function calls. Command line options are provided as arguments. For
+example::
+
+   pysam.sort("-o", "output.bam", "ex1.bam")
+
+corresponds to the command line::
+
+   samtools sort -o output.bam ex1.bam
+
+Or for example::
+
+   pysam.sort("-m", "1000000", "-o", "output.bam", "ex1.bam")
+
+In order to get usage information, try::
+
+   print(pysam.sort.usage())
+
+Argument errors raise a :class:`pysam.SamtoolsError`::
+
+   pysam.sort()
+
+   Traceback (most recent call last):
+   File "x.py", line 12, in <module>
+     pysam.sort()
+   File "/build/lib.linux-x86_64-2.6/pysam/__init__.py", line 37, in __call__
+     if retval: raise SamtoolsError( "\n".join( stderr ) )
+   pysam.SamtoolsError: 'Usage: samtools sort [-n] [-m <maxMem>] <in.bam> <out.prefix>\n'
+
+Messages from `samtools`_ on stderr are captured and are
+available using the :meth:`getMessages` method::
+
+   pysam.sort.getMessage()
+
+Note that only the output from the last invocation of a command is
+stored.
+
+In order for pysam to make the output of samtools commands accessible
+the stdout stream needs to be redirected. This is the default
+behaviour, but can cause problems in environments such as the ipython
+notebook. A solution is to pass the ``catch_stdout`` keyword
+argument::
+
+   pysam.sort(catch_stdout=False)
+
+Note that this means that output from commands which produce output on
+stdout will not be available. The only solution is to run samtools
+commands through subprocess.
+
+================================
+Working with tabix-indexed files
+================================
+
+To open a tabular file that has been indexed with tabix_, use
+:class:`~pysam.TabixFile`::
+
+    import pysam
+    tbx = pysam.TabixFile("example.bed.gz")
+
+Similar to :class:`~pysam.AlignmentFile.fetch`, intervals within a
+region can be retrieved by calling :meth:`~pysam.TabixFile.fetch()`::
+
+    for row in tbx.fetch("chr1", 1000, 2000):
+         print(str(row))
+
+This will return a tuple-like data structure in which columns can
+be retrieved by numeric index::
+
+    for row in tbx.fetch("chr1", 1000, 2000):
+         print("chromosome is", row[0])
+
+By providing a parser to :class:`~pysam.AlignmentFile.fetch`
+or :class:`~pysam.TabixFile`, the data will we presented in parsed
+form::
+
+    for row in tbx.fetch("chr1", 1000, 2000, parser=pysam.asTuple()):
+         print("chromosome is", row.contig)
+         print("first field (chrom)=", row[0])
+
+Pre-built parsers are available for :term:`bed`
+(:class:`~pysam.asBed`) formatted files and :term:`gtf`
+(:class:`~pysam.asGTF`) formatted files. Thus, additional fields
+become available through named access, for example::
+
+    for row in tbx.fetch("chr1", 1000, 2000, parser=pysam.asBed()):
+         print("name is", row.name)
+
+
+.. Currently inactivated as pileup deprecated
+.. Using the samtools SNP caller
+.. -----------------------------
+
+.. There are two ways to access the samtools SNP caller. The :class:`pysam.IteratorSNPCalls`
+.. is appropriate when calling many consecutive SNPs, while :class:`pysam.SNPCaller` is
+.. best when calling SNPs at non-consecutive genomic positions. Each snp caller returns objects of
+.. type :class:`pysam.SNPCall`.
+
+.. To use :class:`pysam.IteratorSNPCalls`, associate it with a :class:`pysam.IteratorColumn`::
+
+..     samfile = pysam.AlignmentFile( "ex1.bam", "rb")  
+..     fastafile = pysam.Fastafile( "ex1.fa" )
+..     pileup_iter = samfile.pileup( stepper = "samtools", fastafile = fastafile )
+..     sncpall_iter = pysam.IteratorSNPCalls(pileup_iter)
+..     for call in snpcall_iter:
+..         print(str(call))
+
+.. Usage of :class:`pysam.SNPCaller` is similar::
+
+..     samfile = pysam.AlignmentFile( "ex1.bam", "rb")  
+..     fastafile = pysam.Fastafile( "ex1.fa" )
+..     pileup_iter = samfile.pileup( stepper = "samtools", fastafile = fastafile )
+..     snpcaller = pysam.SNPCaller.call(pileup_iter)
+..     print(snpcaller( "chr1", 100 ))
+
+.. Note the use of the option *stepper* to control which reads are included in the 
+.. in the :term:`pileup`. The ``samtools`` stepper implements the same read selection
+.. and processing as in the samtools pileup command.
+
+.. Calling indels works along the same lines, using the :class:`pysam.IteratorIndelCalls`
+.. and :class:`pysam.IteratorIndelCaller`.
+
+
+====================================
+Working with VCF/BCF formatted files
+====================================
+
+To iterate through a VCF/BCF formatted file use
+:class:`~pysam.VariantFile`::
+
+   from pysam import VariantFile
+
+   bcf_in = VariantFile("test.bcf")  # auto-detect input format
+   bcf_out = VariantFile('-', 'w', header=bcf_in.header)
+   
+   for rec in bcf_in.fetch('chr1', 100000, 200000):
+       bcf_out.write(rec)
+
+:meth:`_pysam.VariantFile.fetch()` iterates over
+:class:`~pysam.VariantRecord` objects which provides access to
+simple variant attributes such as :class:`~pysam.VariantRecord.contig`,
+:class:`~pysam.VariantRecord.pos`, :class:`~pysam.VariantRecord.ref`::
+
+   for rec in bcf_in.fetch():
+       print(rec.pos)
+
+but also to complex attributes such as the contents to the
+:class:`~pysam.VariantRecord.info`, :class:`~pysam.VariantRecord.format`
+and :term:`genotype` columns. These
+complex attributes are views on the underlying htslib data structures
+and provide dictionary-like access to the data::
+
+   for rec in bcf_in.fetch():
+       print(rec.info)
+       print(rec.info.keys())
+       print(rec.info["DP"])
+
+The :py:attr:`~pysam.VariantFile.header` attribute
+(:class:`~pysam.VariantHeader`) provides access information
+stored in the :term:`vcf` header. The complete header can be printed::
+
+   >>> print(bcf_in.header)
+   ##fileformat=VCFv4.2
+   ##FILTER=<ID=PASS,Description="All filters passed">
+   ##fileDate=20090805
+   ##source=myImputationProgramV3.1
+   ##reference=1000GenomesPilot-NCBI36
+   ##phasing=partial
+   ##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples
+   With Data">
+   ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
+   ##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency">
+   ##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele">
+   ##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build
+   129">
+   ##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership">
+   ##FILTER=<ID=q10,Description="Quality below 10">
+   ##FILTER=<ID=s50,Description="Less than 50% of samples have data">
+   ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+   ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+   ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
+   ##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
+   ##contig=<ID=M>
+   ##contig=<ID=17>
+   ##contig=<ID=20>
+   ##bcftools_viewVersion=1.3+htslib-1.3
+   ##bcftools_viewCommand=view -O b -o example_vcf42.bcf
+   example_vcf42.vcf.gz
+   #CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO   FORMAT    NA00001 NA00002 NA0000
+  
+Individual contents such as contigs, info fields, samples, formats can
+be retrieved as attributes from :py:attr:`~pysam.VariantFile.header`::
+
+   >>> print(bcf_in.header.contigs)
+   <pysam.cbcf.VariantHeaderContigs object at 0xf250f8>
+
+To convert these views to native python types, iterate through the views::
+
+   >>> print(list((bcf_in.header.contigs)))
+   ['M', '17', '20']
+   >>> print(list((bcf_in.header.filters)))
+   ['PASS', 'q10', 's50']
+   >>> print(list((bcf_in.header.info)))
+   ['NS', 'DP', 'AF', 'AA', 'DB', 'H2']
+   >>> print(list((bcf_in.header.samples)))
+   ['NA00001', 'NA00002', 'NA00003']
+
+Alternatively, it is possible to iterate through all records in the
+header returning objects of type :py:class:`~pysam.VariantHeaderRecord`:: ::
+
+   >>> for x in bcf_in.header.records:
+   >>>    print(x)
+   >>>    print(x.type, x.key)
+   GENERIC fileformat
+   FILTER FILTER
+   GENERIC fileDate
+   GENERIC source
+   GENERIC reference
+   GENERIC phasing
+   INFO INFO
+   INFO INFO
+   INFO INFO
+   INFO INFO
+   INFO INFO
+   INFO INFO
+   FILTER FILTER
+   FILTER FILTER
+   FORMAT FORMAT
+   FORMAT FORMAT
+   FORMAT FORMAT
+   FORMAT FORMAT
+   CONTIG contig
+   CONTIG contig
+   CONTIG contig
+   GENERIC bcftools_viewVersion
+   GENERIC bcftools_viewCommand
+
+===============
+Extending pysam
+===============
+
+Using pyximport_, it is (relatively) straight-forward to access pysam
+internals and the underlying `samtools`_ library. An example is provided
+in the :file:`tests` directory. The example emulates the samtools
+flagstat command and consists of three files:
+
+1. The main script :file:`pysam_flagstat.py`. The important lines in
+   this script are::
+
+      import pyximport
+      pyximport.install()
+      import _pysam_flagstat
+
+      ...
+   
+      flag_counts = _pysam_flagstat.count(pysam_in)
+
+   The first part imports, sets up pyximport_ and imports the cython
+   module :file:`_pysam_flagstat`.  The second part calls the
+   ``count`` method in :file:`_pysam_flagstat`.
+ 
+2. The cython implementation :file:`_pysam_flagstat.pyx`. This script
+   imports the pysam API via::
+
+      from pysam.libcalignmentfile cimport AlignmentFile, AlignedSegment
+
+   This statement imports, amongst others, :class:`AlignedSegment`
+   into the namespace. Speed can be gained from declaring
+   variables. For example, to efficiently iterate over a file, an
+   :class:`AlignedSegment` object is declared::
+
+      # loop over samfile
+      cdef AlignedSegment read
+      for read in samfile:
+          ...
+
+3. A :file:`pyxbld` providing pyximport_ with build information.
+   Required are the locations of the samtools and pysam header
+   libraries of a source installation of pysam plus the
+   :file:`csamtools.so` shared library. For example::
+
+     def make_ext(modname, pyxfilename):
+	 from distutils.extension import Extension
+	 import pysam
+	 return Extension(name=modname,
+               sources=[pyxfilename],
+               extra_link_args=pysam.get_libraries(),
+	       include_dirs=pysam.get_include(),
+	       define_macros=pysam.get_defines())
+
+If the script :file:`pysam_flagstat.py` is called the first time,
+pyximport_ will compile the cython_ extension
+:file:`_pysam_flagstat.pyx` and make it available to the
+script. Compilation requires a working compiler and cython_
+installation.  Each time :file:`_pysam_flagstat.pyx` is modified, a
+new compilation will take place.
+
+pyximport_ comes with cython_.
+
diff --git a/import/pysam.c b/import/pysam.c
new file mode 100644
index 0000000..168255c
--- /dev/null
+++ b/import/pysam.c
@@ -0,0 +1,83 @@
+#include <getopt.h>
+#include <unistd.h>
+#include <setjmp.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+
+#include "@pysam@.pysam.h"
+
+FILE * @pysam@_stderr = NULL;
+FILE * @pysam@_stdout = NULL;
+const char * @pysam@_stdout_fn = NULL;
+
+
+FILE * @pysam@_set_stderr(int fd)
+{
+  if (@pysam@_stderr != NULL)
+    fclose(@pysam@_stderr);
+  @pysam@_stderr = fdopen(fd, "w");
+  return @pysam@_stderr;
+}
+
+void @pysam@_close_stderr(void)
+{
+  fclose(@pysam@_stderr);
+  @pysam@_stderr = NULL;
+}
+
+FILE * @pysam@_set_stdout(int fd)
+{
+  if (@pysam@_stdout != NULL)
+    fclose(@pysam@_stdout);
+  @pysam@_stdout = fdopen(fd, "w");
+  if (@pysam@_stdout == NULL)
+    {
+      fprintf(@pysam@_stderr, "could not set stdout to fd %i", fd);
+    }
+  return @pysam@_stdout;
+}
+
+void @pysam@_set_stdout_fn(const char *fn)
+{
+  @pysam@_stdout_fn = fn;
+}
+
+void @pysam@_close_stdout(void)
+{
+  fclose(@pysam@_stdout);
+  @pysam@_stdout = NULL;
+}
+
+int @pysam@_puts(const char *s)
+{
+  if (fputs(s, @pysam@_stdout) == EOF) return EOF;
+  return putc('\n', @pysam@_stdout);
+}
+
+
+static jmp_buf @pysam@_jmpbuf;
+static int @pysam@_status = 0;
+
+int @pysam@_dispatch(int argc, char *argv[])
+{
+  /* Reset getopt()/getopt_long() processing. */
+#if defined __GLIBC__
+  optind = 0;
+#elif defined _OPTRESET || defined _OPTRESET_DECLARED
+  optreset = optind = 1;
+#else
+  optind = 1;
+#endif
+
+  if (setjmp(@pysam@_jmpbuf) == 0)
+    return @pysam@_main(argc, argv);
+  else
+    return @pysam@_status;
+}
+
+void @pysam@_exit(int status)
+{
+  @pysam@_status = status;
+  longjmp(@pysam@_jmpbuf, 1);
+}
diff --git a/import/pysam.h b/import/pysam.h
new file mode 100644
index 0000000..da07281
--- /dev/null
+++ b/import/pysam.h
@@ -0,0 +1,74 @@
+#ifndef @pysam@_PYSAM_H
+#define @pysam@_PYSAM_H
+
+#include <stdio.h>
+
+#ifndef __has_attribute
+#define __has_attribute(attribute) 0
+#endif
+#ifndef PYSAM_NORETURN
+#if __has_attribute(__noreturn__) || __GNUC__ >= 3
+#define PYSAM_NORETURN __attribute__((__noreturn__))
+#else
+#define PYSAM_NORETURN
+#endif
+#endif
+
+extern FILE * @pysam@_stderr;
+
+extern FILE * @pysam@_stdout;
+
+extern const char * @pysam@_stdout_fn;
+
+/*! set pysam standard error to point to file descriptor
+
+  Setting the stderr will close the previous stderr.
+ */
+FILE * @pysam@_set_stderr(int fd);
+
+/*! set pysam standard output to point to file descriptor
+
+  Setting the stdout will close the previous stdout.
+ */
+FILE * @pysam@_set_stdout(int fd);
+
+/*! set pysam standard output to point to filename
+
+ */
+void @pysam@_set_stdout_fn(const char * fn);
+
+/*! close pysam standard error and set to NULL
+  
+ */
+void @pysam@_close_stderr(void);
+
+/*! close pysam standard output and set to NULL
+  
+ */
+void @pysam@_close_stdout(void);
+
+int @pysam@_puts(const char *s);
+
+int @pysam@_dispatch(int argc, char *argv[]);
+
+void PYSAM_NORETURN @pysam@_exit(int status);
+
+extern int @pysam@_main(int argc, char *argv[]);
+
+/* Define these only in samtools/bcftools C source, not Cython code. */
+#if !(defined CYTHON_ABI || defined CYTHON_HEX_VERSION)
+
+/*! Several non-static function names are used in both samtools and bcftools.
+    Both libcsamtools.so and libcbcftools.so are loaded simultaneously, leading
+    to collisions and wrong functions being called. #define these names so the
+    actual symbol names include distinct prefixes to avoid collisions.
+ */
+#define main_consensus @pysam@_main_consensus
+#define main_reheader @pysam@_main_reheader
+#define bam_smpl_init @pysam@_bam_smpl_init
+#define bam_smpl_destroy @pysam@_bam_smpl_destroy
+#define read_file_list @pysam@_read_file_list
+
+#endif
+
+#endif
diff --git a/linker_tests/link_pre_489/PysamTestModule_link_pre_489/BuildRead.pyx b/linker_tests/link_pre_489/PysamTestModule_link_pre_489/BuildRead.pyx
new file mode 100644
index 0000000..9c51e8f
--- /dev/null
+++ b/linker_tests/link_pre_489/PysamTestModule_link_pre_489/BuildRead.pyx
@@ -0,0 +1,24 @@
+from __future__ import absolute_import
+
+from pysam.libchtslib         cimport bam1_t, bam_endpos
+from pysam.libcsamfile        cimport aux_type2size
+from pysam.libcalignedsegment cimport AlignedSegment
+
+import pysam
+
+
+cpdef build_read():
+    cdef AlignedSegment read = pysam.AlignedSegment()
+    read.query_name = "hello"
+    read.query_sequence = "ACGT"
+    read.reference_start = 10
+    read.cigarstring = "4M"
+
+    # Test calling htslib function
+    cdef bam1_t *calign = read._delegate
+    print(bam_endpos(calign))
+
+    # Test calling pysam htslib_util function
+    print(aux_type2size(12))
+
+    return read
diff --git a/linker_tests/link_pre_489/PysamTestModule_link_pre_489/__init__.py b/linker_tests/link_pre_489/PysamTestModule_link_pre_489/__init__.py
new file mode 100644
index 0000000..e441021
--- /dev/null
+++ b/linker_tests/link_pre_489/PysamTestModule_link_pre_489/__init__.py
@@ -0,0 +1,3 @@
+from PysamTestModule_link_pre_489.BuildRead import build_read
+
+all = ["build_read"]
diff --git a/linker_tests/link_pre_489/cy_build.py b/linker_tests/link_pre_489/cy_build.py
new file mode 100644
index 0000000..fae7055
--- /dev/null
+++ b/linker_tests/link_pre_489/cy_build.py
@@ -0,0 +1,86 @@
+import os
+import re
+import sys
+
+try:
+    from Cython.Distutils import build_ext
+except ImportError:
+    from setuptools.command.build_ext import build_ext
+
+from distutils.extension import Extension
+from distutils.sysconfig import get_config_vars, get_python_lib, get_python_version
+from pkg_resources import Distribution
+
+
+if sys.platform == 'darwin':
+    config_vars = get_config_vars()
+    config_vars['LDSHARED'] = config_vars['LDSHARED'].replace('-bundle', '')
+    config_vars['SHLIB_EXT'] = '.so'
+
+
+def is_pip_install():
+    if "_" in os.environ and os.environ["_"].endswith("pip"):
+        return True
+    if "pip-egg-info" in sys.argv:
+        return True
+    if re.search("/pip-.*-build/", __file__):
+        return True
+    return False
+
+
+class CyExtension(Extension):
+    def __init__(self, *args, **kwargs):
+        self._init_func = kwargs.pop("init_func", None)
+        Extension.__init__(self, *args, **kwargs)
+
+    def extend_includes(self, includes):
+        self.include_dirs.extend(includes)
+
+    def extend_macros(self, macros):
+        self.define_macros.extend(macros)
+
+    def extend_extra_objects(self, objs):
+        self.extra_objects.extend(objs)
+
+
+class cy_build_ext(build_ext):
+
+    def _get_egg_name(self):
+        ei_cmd = self.get_finalized_command("egg_info")
+        return Distribution(
+            None, None, ei_cmd.egg_name, ei_cmd.egg_version, get_python_version(),
+            self.distribution.has_ext_modules() and self.plat_name).egg_name()
+
+    def build_extension(self, ext):
+
+        if isinstance(ext, CyExtension) and ext._init_func:
+            ext._init_func(ext)
+
+        if not self.inplace:
+            ext.library_dirs.append(os.path.join(self.build_lib, "pysam"))
+
+        if sys.platform == 'darwin':
+            # The idea is to give shared libraries an install name of the form
+            # `@rpath/<library-name.so>`, and to set the rpath equal to
+            # @loader_path. This will allow Python packages to find the library
+            # in the expected place, while still giving enough flexibility to
+            # external applications to link against the library.
+            relative_module_path = ext.name.replace(".", os.sep) + get_config_vars()["SO"]
+            library_path = os.path.join(
+                "@rpath", os.path.basename(relative_module_path)
+            )
+
+            if not ext.extra_link_args:
+                ext.extra_link_args = []
+            ext.extra_link_args += ['-dynamiclib',
+                                    '-rpath', '@loader_path',
+                                    '-Wl,-headerpad_max_install_names',
+                                    '-Wl,-install_name,%s' % library_path,
+                                    '-Wl,-x']
+        else:
+            if not ext.extra_link_args:
+                ext.extra_link_args = []
+
+            ext.extra_link_args += ['-Wl,-rpath,$ORIGIN']
+                                    
+        build_ext.build_extension(self, ext)
diff --git a/linker_tests/link_pre_489/setup.py b/linker_tests/link_pre_489/setup.py
new file mode 100644
index 0000000..5fc75d5
--- /dev/null
+++ b/linker_tests/link_pre_489/setup.py
@@ -0,0 +1,28 @@
+import glob
+import sys
+import os
+
+from setuptools import setup, find_packages, Extension
+from cy_build import CyExtension as Extension, cy_build_ext as build_ext
+
+import pysam
+
+test_module_suffix = os.path.dirname(os.path.abspath(__file__)).split(os.sep)[-1]
+test_module_name = "PysamTestModule_{}".format(test_module_suffix)
+
+TestModule = Extension(
+    "{}.BuildRead".format(test_module_name),
+    ["{}/BuildRead.pyx".format(test_module_name)],
+    include_dirs=pysam.get_include(),
+    extra_link_args=pysam.get_libraries(),
+    define_macros=pysam.get_defines(),
+)
+
+setup(
+    name=test_module_name,
+    version='0.1',
+    packages=find_packages(),
+    package_dir={test_module_name: test_module_name},
+    ext_modules=[TestModule],
+    cmdclass={'build_ext': build_ext},
+)
diff --git a/linker_tests/link_pre_489/tests/test_module.py b/linker_tests/link_pre_489/tests/test_module.py
new file mode 100644
index 0000000..46ba27a
--- /dev/null
+++ b/linker_tests/link_pre_489/tests/test_module.py
@@ -0,0 +1,15 @@
+import unittest
+
+from PysamTestModule_link_pre_489 import build_read
+
+        
+class TestModule(unittest.TestCase):
+
+    def test_pass_if_module_can_be_called(self):
+        read = build_read()
+        self.assertEqual(read.query_name, "hello")
+        self.assertEqual(read.query_sequence, "ACGT")
+        
+
+if __name__ == "__main__":
+    unittest.main()
diff --git a/linker_tests/link_with_rpath/PysamTestModule_link_with_rpath/BuildRead.pyx b/linker_tests/link_with_rpath/PysamTestModule_link_with_rpath/BuildRead.pyx
new file mode 100644
index 0000000..9c51e8f
--- /dev/null
+++ b/linker_tests/link_with_rpath/PysamTestModule_link_with_rpath/BuildRead.pyx
@@ -0,0 +1,24 @@
+from __future__ import absolute_import
+
+from pysam.libchtslib         cimport bam1_t, bam_endpos
+from pysam.libcsamfile        cimport aux_type2size
+from pysam.libcalignedsegment cimport AlignedSegment
+
+import pysam
+
+
+cpdef build_read():
+    cdef AlignedSegment read = pysam.AlignedSegment()
+    read.query_name = "hello"
+    read.query_sequence = "ACGT"
+    read.reference_start = 10
+    read.cigarstring = "4M"
+
+    # Test calling htslib function
+    cdef bam1_t *calign = read._delegate
+    print(bam_endpos(calign))
+
+    # Test calling pysam htslib_util function
+    print(aux_type2size(12))
+
+    return read
diff --git a/linker_tests/link_with_rpath/PysamTestModule_link_with_rpath/__init__.py b/linker_tests/link_with_rpath/PysamTestModule_link_with_rpath/__init__.py
new file mode 100644
index 0000000..c4b1a09
--- /dev/null
+++ b/linker_tests/link_with_rpath/PysamTestModule_link_with_rpath/__init__.py
@@ -0,0 +1,3 @@
+from PysamTestModule_link_with_rpath.BuildRead import build_read
+
+all = ["build_read"]
diff --git a/linker_tests/link_with_rpath/setup.py b/linker_tests/link_with_rpath/setup.py
new file mode 100644
index 0000000..2e5a8af
--- /dev/null
+++ b/linker_tests/link_with_rpath/setup.py
@@ -0,0 +1,36 @@
+import glob
+import sys
+import os
+
+from setuptools import setup, find_packages, Extension
+from Cython.Distutils import build_ext
+
+import pysam
+
+test_module_suffix = os.path.dirname(os.path.abspath(__file__)).split(os.sep)[-1]
+test_module_name = "PysamTestModule_{}".format(test_module_suffix)
+
+pysam_libraries = pysam.get_libraries()
+pysam_libdirs, pysam_libs = zip(*[os.path.split(x) for x in pysam_libraries])
+pysam_libdir = pysam_libdirs[0]
+# remove lib and .so
+pysam_libs = [x[3:-3] for x in pysam_libs]
+
+TestModule = Extension(
+    "{}.BuildRead".format(test_module_name),
+    ["{}/BuildRead.pyx".format(test_module_name)],
+    include_dirs=pysam.get_include(),
+    library_dirs=[pysam_libdir],
+    libraries=pysam_libs,
+    extra_link_args=['-Wl,-rpath,{}'.format(pysam_libdir)],
+    language="C",
+)
+
+setup(
+    name=test_module_name,
+    version='0.1',
+    packages=find_packages(),
+    package_dir={test_module_name: test_module_name},
+    ext_modules=[TestModule],
+    cmdclass={'build_ext': build_ext},
+)
diff --git a/linker_tests/link_with_rpath/tests/test_module.py b/linker_tests/link_with_rpath/tests/test_module.py
new file mode 100644
index 0000000..f8621b4
--- /dev/null
+++ b/linker_tests/link_with_rpath/tests/test_module.py
@@ -0,0 +1,15 @@
+import unittest
+
+from PysamTestModule_link_with_rpath import build_read
+
+        
+class TestModule(unittest.TestCase):
+
+    def test_pass_if_module_can_be_called(self):
+        read = build_read()
+        self.assertEqual(read.query_name, "hello")
+        self.assertEqual(read.query_sequence, "ACGT")
+        
+
+if __name__ == "__main__":
+    unittest.main()
diff --git a/linker_tests/link_without_rpath/PysamTestModule_link_without_rpath/BuildRead.pyx b/linker_tests/link_without_rpath/PysamTestModule_link_without_rpath/BuildRead.pyx
new file mode 100644
index 0000000..9c51e8f
--- /dev/null
+++ b/linker_tests/link_without_rpath/PysamTestModule_link_without_rpath/BuildRead.pyx
@@ -0,0 +1,24 @@
+from __future__ import absolute_import
+
+from pysam.libchtslib         cimport bam1_t, bam_endpos
+from pysam.libcsamfile        cimport aux_type2size
+from pysam.libcalignedsegment cimport AlignedSegment
+
+import pysam
+
+
+cpdef build_read():
+    cdef AlignedSegment read = pysam.AlignedSegment()
+    read.query_name = "hello"
+    read.query_sequence = "ACGT"
+    read.reference_start = 10
+    read.cigarstring = "4M"
+
+    # Test calling htslib function
+    cdef bam1_t *calign = read._delegate
+    print(bam_endpos(calign))
+
+    # Test calling pysam htslib_util function
+    print(aux_type2size(12))
+
+    return read
diff --git a/linker_tests/link_without_rpath/PysamTestModule_link_without_rpath/__init__.py b/linker_tests/link_without_rpath/PysamTestModule_link_without_rpath/__init__.py
new file mode 100644
index 0000000..722c5d0
--- /dev/null
+++ b/linker_tests/link_without_rpath/PysamTestModule_link_without_rpath/__init__.py
@@ -0,0 +1,3 @@
+from PysamTestModule_link_without_rpath.BuildRead import build_read
+
+all = ["build_read"]
diff --git a/linker_tests/link_without_rpath/setup.py b/linker_tests/link_without_rpath/setup.py
new file mode 100644
index 0000000..7846e4b
--- /dev/null
+++ b/linker_tests/link_without_rpath/setup.py
@@ -0,0 +1,35 @@
+import glob
+import sys
+import os
+
+from setuptools import setup, find_packages, Extension
+from Cython.Distutils import build_ext
+
+import pysam
+
+test_module_suffix = os.path.dirname(os.path.abspath(__file__)).split(os.sep)[-1]
+test_module_name = "PysamTestModule_{}".format(test_module_suffix)
+
+pysam_libraries = pysam.get_libraries()
+pysam_libdirs, pysam_libs = zip(*[os.path.split(x) for x in pysam_libraries])
+pysam_libdir = pysam_libdirs[0]
+# remove lib and .so
+pysam_libs = [x[3:-3] for x in pysam_libs]
+
+TestModule = Extension(
+    "{}.BuildRead".format(test_module_name),
+    ["{}/BuildRead.pyx".format(test_module_name)],
+    include_dirs=pysam.get_include(),
+    library_dirs=[pysam_libdir],
+    libraries=pysam_libs,
+    language="C",
+)
+
+setup(
+    name=test_module_name,
+    version='0.1',
+    packages=find_packages(),
+    package_dir={test_module_name: test_module_name},
+    ext_modules=[TestModule],
+    cmdclass={'build_ext': build_ext},
+)
diff --git a/linker_tests/link_without_rpath/tests/test_module.py b/linker_tests/link_without_rpath/tests/test_module.py
new file mode 100644
index 0000000..1da5bbc
--- /dev/null
+++ b/linker_tests/link_without_rpath/tests/test_module.py
@@ -0,0 +1,15 @@
+import unittest
+
+from PysamTestModule_link_without_rpath import build_read
+
+        
+class TestModule(unittest.TestCase):
+
+    def test_pass_if_module_can_be_called(self):
+        read = build_read()
+        self.assertEqual(read.query_name, "hello")
+        self.assertEqual(read.query_sequence, "ACGT")
+        
+
+if __name__ == "__main__":
+    unittest.main()
diff --git a/pysam/Pileup.py b/pysam/Pileup.py
new file mode 100644
index 0000000..2d05e3a
--- /dev/null
+++ b/pysam/Pileup.py
@@ -0,0 +1,282 @@
+'''Tools for working with files in the samtools pileup -c format.'''
+import collections
+import pysam
+
+PileupSubstitution = collections.namedtuple("PileupSubstitution",
+                                            (
+                                                "chromosome",
+                                                "pos",
+                                                "reference_base",
+                                                "genotype",
+                                                "consensus_quality",
+                                                "snp_quality",
+                                                "mapping_quality",
+                                                "coverage",
+                                                "read_bases",
+                                                "base_qualities"))
+
+PileupIndel = collections.namedtuple("PileupIndel",
+                                     (
+                                         "chromosome",
+                                         "pos",
+                                         "reference_base",
+                                         "genotype",
+                                         "consensus_quality",
+                                         "snp_quality",
+                                         "mapping_quality",
+                                         "coverage",
+                                         "first_allele",
+                                         "second_allele",
+                                         "reads_first",
+                                         "reads_second",
+                                         "reads_diff"))
+
+
+def iterate(infile):
+    '''iterate over ``samtools pileup -c`` formatted file.
+
+    *infile* can be any iterator over a lines.
+
+    The function yields named tuples of the type :class:`pysam.Pileup.PileupSubstitution`
+    or :class:`pysam.Pileup.PileupIndel`.
+
+    .. note::
+
+       The parser converts to 0-based coordinates
+    '''
+
+    conv_subst = (str, lambda x: int(x) - 1, str,
+                  str, int, int, int, int, str, str)
+    conv_indel = (str, lambda x: int(x) - 1, str, str, int,
+                  int, int, int, str, str, int, int, int)
+
+    for line in infile:
+        d = line[:-1].split()
+        if d[2] == "*":
+            try:
+                yield PileupIndel(*[x(y) for x, y in zip(conv_indel, d)])
+            except TypeError:
+                raise pysam.SamtoolsError("parsing error in line: `%s`" % line)
+        else:
+            try:
+                yield PileupSubstitution(*[x(y) for x, y in zip(conv_subst, d)])
+            except TypeError:
+                raise pysam.SamtoolsError("parsing error in line: `%s`" % line)
+
+
+ENCODE_GENOTYPE = {
+    'A': 'A', 'C': 'C', 'G': 'G', 'T': 'T',
+    'AA': 'A', 'CC': 'C', 'GG': 'G', 'TT': 'T', 'UU': 'U',
+    'AG': 'r', 'GA': 'R',
+    'CT': 'y', 'TC': 'Y',
+    'AC': 'm', 'CA': 'M',
+    'GT': 'k', 'TG': 'K',
+    'CG': 's', 'GC': 'S',
+    'AT': 'w', 'TA': 'W',
+}
+
+DECODE_GENOTYPE = {
+    'A': 'AA',
+    'C': 'CC',
+    'G': 'GG',
+    'T': 'TT',
+    'r': 'AG', 'R': 'AG',
+    'y': 'CT', 'Y': 'CT',
+    'm': 'AC', 'M': 'AC',
+    'k': 'GT', 'K': 'GT',
+    's': 'CG', 'S': 'CG',
+    'w': 'AT', 'W': 'AT',
+}
+
+# ------------------------------------------------------------
+
+
+def encodeGenotype(code):
+    '''encode genotypes like GG, GA into a one-letter code.
+    The returned code is lower case if code[0] < code[1], otherwise
+    it is uppercase.
+    '''
+    return ENCODE_GENOTYPE[code.upper()]
+
+
+def decodeGenotype(code):
+    '''decode single letter genotypes like m, M into two letters.
+    This is the reverse operation to :meth:`encodeGenotype`.
+    '''
+    return DECODE_GENOTYPE[code]
+
+
+def translateIndelGenotypeFromVCF(vcf_genotypes, ref):
+    '''translate indel from vcf to pileup format.'''
+
+    # indels
+    def getPrefix(s1, s2):
+        '''get common prefix of strings s1 and s2.'''
+        n = min(len(s1), len(s2))
+        for x in range(n):
+            if s1[x] != s2[x]:
+                return s1[:x]
+        return s1[:n]
+
+    def getSuffix(s1, s2):
+        '''get common sufix of strings s1 and s2.'''
+        n = min(len(s1), len(s2))
+        if s1[-1] != s2[-1]:
+            return ""
+        for x in range(-2, -n - 1, -1):
+            if s1[x] != s2[x]:
+                return s1[x + 1:]
+        return s1[-n:]
+
+    def getGenotype(variant, ref):
+
+        if variant == ref:
+            return "*", 0
+
+        if len(ref) > len(variant):
+            # is a deletion
+            if ref.startswith(variant):
+                return "-%s" % ref[len(variant):], len(variant) - 1
+            elif ref.endswith(variant):
+                return "-%s" % ref[:-len(variant)], -1
+            else:
+                prefix = getPrefix(ref, variant)
+                suffix = getSuffix(ref, variant)
+                shared = len(prefix) + len(suffix) - len(variant)
+                # print "-", prefix, suffix, ref, variant, shared, len(prefix), len(suffix), len(ref)
+                if shared < 0:
+                    raise ValueError()
+                return "-%s" % ref[len(prefix):-(len(suffix) - shared)], len(prefix) - 1
+
+        elif len(ref) < len(variant):
+            # is an insertion
+            if variant.startswith(ref):
+                return "+%s" % variant[len(ref):], len(ref) - 1
+            elif variant.endswith(ref):
+                return "+%s" % variant[:len(ref)], 0
+            else:
+                prefix = getPrefix(ref, variant)
+                suffix = getSuffix(ref, variant)
+                shared = len(prefix) + len(suffix) - len(ref)
+                if shared < 0:
+                    raise ValueError()
+
+                return "+%s" % variant[len(prefix):-(len(suffix) - shared)], len(prefix)
+        else:
+            assert 0, "snp?"
+
+    # in pileup, the position refers to the base
+    # after the coordinate, hence subtract 1
+    # pos -= 1
+
+    genotypes, offsets = [], []
+    is_error = True
+
+    for variant in vcf_genotypes:
+        try:
+            g, offset = getGenotype(variant, ref)
+        except ValueError:
+            break
+
+        genotypes.append(g)
+        if g != "*":
+            offsets.append(offset)
+
+    else:
+        is_error = False
+
+    if is_error:
+        raise ValueError()
+
+    assert len(set(offsets)) == 1, "multiple offsets for indel"
+    offset = offsets[0]
+
+    genotypes = "/".join(genotypes)
+    return genotypes, offset
+
+
+def vcf2pileup(vcf, sample):
+    '''convert vcf record to pileup record.'''
+
+    chromosome = vcf.contig
+    pos = vcf.pos
+    reference = vcf.ref
+    allelles = [reference] + vcf.alt
+
+    data = vcf[sample]
+
+    # get genotype
+    genotypes = data["GT"]
+    if len(genotypes) > 1:
+        raise ValueError("only single genotype per position, %s" % (str(vcf)))
+
+    genotypes = genotypes[0]
+
+    # not a variant
+    if genotypes[0] == ".":
+        return None
+
+    genotypes = [allelles[int(x)] for x in genotypes if x != "/"]
+
+    # snp_quality is "genotype quality"
+    snp_quality = consensus_quality = data.get("GQ", [0])[0]
+    mapping_quality = vcf.info.get("MQ", [0])[0]
+    coverage = data.get("DP", 0)
+
+    if len(reference) > 1 or max([len(x) for x in vcf.alt]) > 1:
+        # indel
+        genotype, offset = translateIndelGenotypeFromVCF(genotypes, reference)
+
+        return PileupIndel(chromosome,
+                           pos + offset,
+                           "*",
+                           genotype,
+                           consensus_quality,
+                           snp_quality,
+                           mapping_quality,
+                           coverage,
+                           genotype,
+                           "<" * len(genotype),
+                           0,
+                           0,
+                           0)
+
+    else:
+        genotype = encodeGenotype("".join(genotypes))
+        read_bases = ""
+        base_qualities = ""
+
+        return PileupSubstitution(chromosome, pos, reference,
+                                  genotype, consensus_quality,
+                                  snp_quality, mapping_quality,
+                                  coverage, read_bases,
+                                  base_qualities)
+
+
+def iterate_from_vcf(infile, sample):
+    '''iterate over a vcf-formatted file.
+
+    *infile* can be any iterator over a lines.
+
+    The function yields named tuples of the type
+    :class:`pysam.Pileup.PileupSubstitution` or
+    :class:`pysam.Pileup.PileupIndel`.
+
+    Positions without a snp will be skipped.
+
+    This method is wasteful and written to support same legacy code
+    that expects samtools pileup output.
+
+    Better use the vcf parser directly.
+
+    '''
+    vcf = pysam.VCF()
+    vcf.connect(infile)
+
+    if sample not in vcf.getsamples():
+        raise KeyError("sample %s not vcf file")
+
+    for row in vcf.fetch():
+        result = vcf2pileup(row, sample)
+        if result:
+            yield result
diff --git a/pysam/VCF.py.obsolete b/pysam/VCF.py.obsolete
new file mode 100644
index 0000000..78e6220
--- /dev/null
+++ b/pysam/VCF.py.obsolete
@@ -0,0 +1,1087 @@
+#
+# Code to read, write and edit VCF files
+#
+# VCF lines are encoded as a dictionary with these keys (note: all lowercase):
+# 'chrom':  string
+# 'pos':    integer
+# 'id':     string
+# 'ref':    string
+# 'alt':    list of strings
+# 'qual':   integer
+# 'filter': None (missing value), or list of keys (strings); empty list parsed as ["PASS"]
+# 'info':   dictionary of values (see below)
+# 'format': list of keys (strings)
+# sample keys: dictionary of values (see below)
+#
+# The sample keys are accessible through vcf.getsamples()
+#
+# A dictionary of values contains value keys (defined in ##INFO or ##FORMAT lines) which map
+# to a list, containign integers, floats, strings, or characters.  Missing values are replaced 
+# by a particular value, often -1 or .
+#
+# Genotypes are not stored as a string, but as a list of 1 or 3 elements (for haploid and diploid samples),
+# the first (and last) the integer representing an allele, and the second the separation character.
+# Note that there is just one genotype per sample, but for consistency the single element is stored in a list.
+#
+# Header lines other than ##INFO, ##FORMAT and ##FILTER are stored as (key, value) pairs and are accessible
+# through getheader()
+#
+# The VCF class can be instantiated with a 'regions' variable consisting of tuples (chrom,start,end) encoding
+# 0-based half-open segments.  Only variants with a position inside the segment will be parsed.  A regions
+# parser is available under parse_regions.
+#
+# When instantiated, a reference can be passed to the VCF class.  This may be any class that supports a
+# fetch(chrom, start, end) method.
+#
+#
+#
+# NOTE: the position that is returned to Python is 0-based, NOT 1-based as in the VCF file.
+#
+#
+#
+# TODO:
+#  only v4.0 writing is complete; alleles are not converted to v3.3 format
+#
+
+from collections import namedtuple, defaultdict
+from operator import itemgetter
+import sys, re, copy, bisect
+
+import pysam
+
+gtsRegEx = re.compile("[|/\\\\]")
+alleleRegEx = re.compile('^[ACGTN]+$')
+
+# Utility function.  Uses 0-based coordinates
+def get_sequence(chrom, start, end, fa):
+    # obtain sequence from .fa file, without truncation
+    if end<=start: return ""
+    if not fa: return "N"*(end-start)
+    if start<0: return "N"*(-start) + get_sequence(chrom, 0, end, fa).upper()
+    sequence = fa.fetch(chrom, start, end).upper()
+    if len(sequence) < end-start: sequence += "N"*(end-start-len(sequence))
+    return sequence
+
+# Utility function.  Parses a region string
+def parse_regions( string ):
+    result = []
+    for r in string.split(','):
+        elts = r.split(':')
+        chrom, start, end = elts[0], 0, 3000000000
+        if len(elts)==1: pass
+        elif len(elts)==2:
+            if len(elts[1])>0:
+                ielts = elts[1].split('-')
+                if len(ielts) != 2: ValueError("Don't understand region string '%s'" % r)
+                try:    start, end = int(ielts[0])-1, int(ielts[1])
+                except: raise ValueError("Don't understand region string '%s'" % r)
+        else:
+            raise ValueError("Don't understand region string '%s'" % r)
+        result.append( (chrom,start,end) )
+    return result
+            
+
+FORMAT = namedtuple('FORMAT','id numbertype number type description missingvalue')
+
+###########################################################################################################
+# 
+# New class
+# 
+###########################################################################################################
+
+class VCFRecord(object):
+    '''vcf record.
+
+    initialized from data and vcf meta 
+    '''
+    
+    data = None
+    vcf = None
+
+    def __init__(self, data, vcf):
+        self.data, self.vcf = data, vcf
+
+        if len(data) != len(self.vcf._samples):
+            self.error(str(data),
+                       self.BAD_NUMBER_OF_COLUMNS, 
+                       "expected %s for %s samples (%s), got %s" % \
+                           (len(self.vcf._samples), 
+                            len(self.vcf._samples), 
+                            self.vcf._samples, 
+                            len(data)))
+        
+    property contig:
+        def __get__( self ): return self.data[0]
+
+    property pos:
+        def __get__( self ): 
+            return self.data.pos
+        
+    property id:
+        def __get__( self ): return self.data[2]
+
+    property ref:
+        def __get__(self ): 
+            # note: gerton substitutes reference if it can be fixed.
+            return self.data[3].upper()
+
+    property alt:
+        def __get__(self):
+            # convert v3.3 to v4.0 alleles below
+            alt = self.data[4] 
+            if alt == ".": alt = []
+            else: alt = alt.upper().split(',')
+            return alt
+
+    property qual:
+        def __get__(self):
+            qual = self.data[5]
+            if qual == ".": qual = -1
+            else: 
+                try:    qual = float(qual)
+                except: self.error(line,self.QUAL_NOT_NUMERICAL)
+
+    property filter:
+        def __get__(self):
+            # postpone checking that filters exist.  Encode missing filter or no filtering as empty list
+            if cols[6] == "." or cols[6] == "PASS" or cols[6] == "0": filter = []
+            else: filter = cols[6].split(';')
+
+            return filter
+
+    property info:
+        def __get__(self):
+            col = self.data[7]
+            # dictionary of keys, and list of values
+            info = {}
+            if col != ".":
+                for blurp in col.split(';'):
+                    elts = blurp.split('=')
+                    if len(elts) == 1: v = None
+                    elif len(elts) == 2: v = elts[1]
+                    else: self.error(str(self.data),self.ERROR_INFO_STRING)
+                    info[elts[0]] = self.parse_formatdata(elts[0], v, self.vcf._info, line)
+            return info
+
+    property format:
+         def __get__(self):
+             return self.data[8].split(':')
+
+    def __getitem__(self, key):
+        
+        # parse sample columns
+        values = self.data[self.vcf._sample2column[key]].split(':')
+        alt = self.alt
+        format = self.format
+
+        if len(values) > len(format):
+            self.error(line,self.BAD_NUMBER_OF_VALUES,"(found %s values in element %s; expected %s)" % (len(values),sample,len(format)))
+
+        result = {}
+        for idx in range(len(format)):
+            expected = self.vcf.get_expected(format[idx], self.vcf._format, alt)
+            if idx < len(values): value = values[idx]
+            else:
+                if expected == -1: value = "."
+                else: value = ",".join(["."]*expected)
+
+            result[format[idx]] = self.vcf.parse_formatdata(format[idx], value, self.vcf._format, line)
+            if expected != -1 and len(result[format[idx]]) != expected:
+                self.error(str(self.data),self.BAD_NUMBER_OF_PARAMETERS,
+                           "id=%s, expected %s parameters, got %s" % (format[idx],expected,result[format[idx]]))
+                if len(result[format[idx]] ) < expected: result[format[idx]] += [result[format[idx]][-1]]*(expected-len(result[format[idx]]))
+                result[format[idx]] = result[format[idx]][:expected]
+
+        return result
+ 
+    def __str__(self):
+        return str(self.data)
+
+class VCF:
+
+    # types
+    NT_UNKNOWN = 0
+    NT_NUMBER = 1
+    NT_ALLELES = 2
+    NT_NR_ALLELES = 3
+    NT_GENOTYPES = 4
+    NT_PHASED_GENOTYPES = 5
+
+    _errors = { 0:"UNKNOWN_FORMAT_STRING:Unknown file format identifier",
+                1:"BADLY_FORMATTED_FORMAT_STRING:Formatting error in the format string",
+                2:"BADLY_FORMATTED_HEADING:Did not find 9 required headings (CHROM, POS, ..., FORMAT) %s",
+                3:"BAD_NUMBER_OF_COLUMNS:Wrong number of columns found (%s)",
+                4:"POS_NOT_NUMERICAL:Position column is not numerical",
+                5:"UNKNOWN_CHAR_IN_REF:Unknown character in reference field",
+                6:"V33_BAD_REF:Reference should be single-character in v3.3 VCF",
+                7:"V33_BAD_ALLELE:Cannot interpret allele for v3.3 VCF",
+                8:"POS_NOT_POSITIVE:Position field must be >0",
+                9:"QUAL_NOT_NUMERICAL:Quality field must be numerical, or '.'",
+               10:"ERROR_INFO_STRING:Error while parsing info field",
+               11:"ERROR_UNKNOWN_KEY:Unknown key (%s) found in formatted field (info; format; or filter)",
+               12:"ERROR_FORMAT_NOT_NUMERICAL:Expected integer or float in formatted field; got %s",
+               13:"ERROR_FORMAT_NOT_CHAR:Eexpected character in formatted field; got string",
+               14:"FILTER_NOT_DEFINED:Identifier (%s) in filter found which was not defined in header",
+               15:"FORMAT_NOT_DEFINED:Identifier (%s) in format found which was not defined in header",
+               16:"BAD_NUMBER_OF_VALUES:Found too many of values in sample column (%s)",
+               17:"BAD_NUMBER_OF_PARAMETERS:Found unexpected number of parameters (%s)",
+               18:"BAD_GENOTYPE:Cannot parse genotype (%s)",
+               19:"V40_BAD_ALLELE:Bad allele found for v4.0 VCF (%s)",
+               20:"MISSING_REF:Reference allele missing",
+               21:"V33_UNMATCHED_DELETION:Deleted sequence does not match reference (%s)",
+               22:"V40_MISSING_ANGLE_BRACKETS:Format definition is not deliminted by angular brackets",
+               23:"FORMAT_MISSING_QUOTES:Description field in format definition is not surrounded by quotes",
+               24:"V40_FORMAT_MUST_HAVE_NAMED_FIELDS:Fields in v4.0 VCF format definition must have named fields",
+               25:"HEADING_NOT_SEPARATED_BY_TABS:Heading line appears separated by spaces, not tabs",
+               26:"WRONG_REF:Wrong reference %s",
+               27:"ERROR_TRAILING_DATA:Numerical field ('%s') has semicolon-separated trailing data",
+               28:"BAD_CHR_TAG:Error calculating chr tag for %s",
+               29:"ZERO_LENGTH_ALLELE:Found zero-length allele",
+               30:"MISSING_INDEL_ALLELE_REF_BASE:Indel alleles must begin with single reference base"
+                }
+
+    # tag-value pairs; tags are not unique; does not include fileformat, INFO, FILTER or FORMAT fields
+    _header = []
+
+    # version number; 33=v3.3; 40=v4.0
+    _version = 40
+
+    # info, filter and format data
+    _info = {}
+    _filter = {}
+    _format = {}
+
+    # header; and required columns
+    _required = ["CHROM","POS","ID","REF","ALT","QUAL","FILTER","INFO","FORMAT"]
+    _samples = []
+
+    # control behaviour
+    _ignored_errors = set([11])   # ERROR_UNKNOWN_KEY
+    _warn_errors = set([])
+    _leftalign = False
+
+    # reference sequence
+    _reference = None
+
+    # regions to include; None includes everything
+    _regions = None
+
+    # statefull stuff
+    _lineno = -1
+    _line = None
+    _lines = None
+
+    def __init__(self, _copy=None, reference=None, regions=None, lines=None, leftalign=False):
+        # make error identifiers accessible by name
+        for id in self._errors.keys(): self.__dict__[self._errors[id].split(':')[0]] = id
+        if _copy != None:
+            self._leftalign = _copy._leftalign
+            self._header = _copy._header[:]
+            self._version = _copy._version
+            self._info = copy.deepcopy(_copy._info)
+            self._filter = copy.deepcopy(_copy._filter)
+            self._format = copy.deepcopy(_copy._format)
+            self._samples = _copy._samples[:]
+            self._sample2column = copy.deepcopy(_copy._sample2column)
+            self._ignored_errors = copy.deepcopy(_copy._ignored_errors)
+            self._warn_errors = copy.deepcopy(_copy._warn_errors)
+            self._reference = _copy._reference
+            self._regions = _copy._regions
+        if reference: self._reference = reference
+        if regions: self._regions = regions
+        if leftalign: self._leftalign = leftalign
+        self._lines = lines
+
+    def error(self,line,error,opt=None):
+        if error in self._ignored_errors: return
+        errorlabel, errorstring = self._errors[error].split(':')
+        if opt: errorstring = errorstring % opt
+        errwarn = ["Error","Warning"][error in self._warn_errors]
+        sys.stderr.write("Line %s: '%s'\n%s %s: %s\n" % (self._lineno,line,errwarn,errorlabel,errorstring))
+        if error in self._warn_errors: return
+        raise ValueError(errorstring)
+
+    def parse_format(self,line,format,filter=False):
+        if self._version >= 40:
+            if not format.startswith('<'): 
+                self.error(line,self.V40_MISSING_ANGLE_BRACKETS)
+                format = "<"+format
+            if not format.endswith('>'): 
+                self.error(line,self.V40_MISSING_ANGLE_BRACKETS)
+                format += ">"
+            format = format[1:-1]
+        data = {'id':None,'number':None,'type':None,'descr':None}
+        idx = 0
+        while len(format.strip())>0:
+            elts = format.strip().split(',')
+            first, rest = elts[0], ','.join(elts[1:])
+            if first.find('=') == -1 or (first.find('"')>=0 and first.find('=') > first.find('"')):
+                if self._version >= 40: self.error(line,self.V40_FORMAT_MUST_HAVE_NAMED_FIELDS)
+                if idx == 4: self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
+                first = ["ID=","Number=","Type=","Description="][idx] + first
+            if first.startswith('ID='):            data['id'] = first.split('=')[1]
+            elif first.startswith('Number='):      data['number'] = first.split('=')[1]
+            elif first.startswith('Type='):        data['type'] = first.split('=')[1]
+            elif first.startswith('Description='):
+                elts = format.split('"')
+                if len(elts)<3: 
+                    self.error(line,self.FORMAT_MISSING_QUOTES)
+                    elts = first.split('=') + [rest] 
+                data['descr'] = elts[1]
+                rest = '"'.join(elts[2:])
+                if rest.startswith(','): rest = rest[1:]
+            else:
+                self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
+            format = rest
+            idx += 1
+            if filter and idx==1: idx=3  # skip number and type fields for FILTER format strings
+        if not data['id']: self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
+        if not data['descr']: 
+            self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
+            data['descr'] = '<none>'
+        if not data['type'] and not data['number']:
+            # fine, ##filter format
+            return FORMAT(data['id'],self.NT_NUMBER,0,"Flag",data['descr'],'.')
+        if not data['type'] in ["Integer","Float","Character","String","Flag"]:
+            self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
+        # I would like a missing-value field, but it isn't there
+        if data['type'] in ['Integer','Float']: data['missing'] = None    # Do NOT use arbitrary int/float as missing value
+        else:                                   data['missing'] = '.'
+        if not data['number']: self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
+        try:
+            n = int(data['number'])
+            t = self.NT_NUMBER
+        except ValueError:
+            n = -1
+            if data['number'] == '.':                   t = self.NT_UNKNOWN
+            elif data['number'] == '#alleles':          t = self.NT_ALLELES
+            elif data['number'] == '#nonref_alleles':   t = self.NT_NR_ALLELES
+            elif data['number'] == '#genotypes':        t = self.NT_GENOTYPES
+            elif data['number'] == '#phased_genotypes': t = self.NT_PHASED_GENOTYPES
+            else:
+                self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
+        return FORMAT(data['id'],t,n,data['type'],data['descr'],data['missing'])
+    
+
+    def format_format( self, fmt, filter=False ):
+        values = [('ID',fmt.id)]
+        if fmt.number != None and not filter:
+            if fmt.numbertype == self.NT_UNKNOWN: nmb = "."
+            elif fmt.numbertype == self.NT_NUMBER: nmb = str(fmt.number)
+            elif fmt.numbertype == self.NT_ALLELES: nmb = "#alleles"
+            elif fmt.numbertype == self.NT_NR_ALLELES: nmb = "#nonref_alleles"
+            elif fmt.numbertype == self.NT_GENOTYPES: nmb = "#genotypes"
+            elif fmt.numbertype == self.NT_PHASED_GENOTYPES: nmb = "#phased_genotypes"
+            else:
+                raise ValueError("Unknown number type encountered: %s" % fmt.numbertype)
+            values.append( ('Number',nmb) )
+            values.append( ('Type', fmt.type) )
+        values.append( ('Description', '"' + fmt.description + '"') )
+        if self._version == 33:
+            format = ",".join(v for k,v in values)
+        else:
+            format = "<" + (",".join( "%s=%s" % (k,v) for (k,v) in values )) + ">"
+        return format
+
+    def get_expected(self, format, formatdict, alt):
+        fmt = formatdict[format]
+        if fmt.numbertype == self.NT_UNKNOWN: return -1
+        if fmt.numbertype == self.NT_NUMBER: return fmt.number
+        if fmt.numbertype == self.NT_ALLELES: return len(alt)+1
+        if fmt.numbertype == self.NT_NR_ALLELES: return len(alt)
+        if fmt.numbertype == self.NT_GENOTYPES: return ((len(alt)+1)*(len(alt)+2)) // 2
+        if fmt.numbertype == self.NT_PHASED_GENOTYPES: return (len(alt)+1)*(len(alt)+1)
+        return 0
+
+
+    def _add_definition(self, formatdict, key, data, line ):
+        if key in formatdict: return
+        self.error(line,self.ERROR_UNKNOWN_KEY,key)
+        if data == None:
+            formatdict[key] = FORMAT(key,self.NT_NUMBER,0,"Flag","(Undefined tag)",".")
+            return
+        if data == []: data = [""]             # unsure what type -- say string
+        if type(data[0]) == type(0.0):
+            formatdict[key] = FORMAT(key,self.NT_UNKNOWN,-1,"Float","(Undefined tag)",None)
+            return
+        if type(data[0]) == type(0):
+            formatdict[key] = FORMAT(key,self.NT_UNKNOWN,-1,"Integer","(Undefined tag)",None)
+            return
+        formatdict[key] = FORMAT(key,self.NT_UNKNOWN,-1,"String","(Undefined tag)",".")
+
+
+    # todo: trim trailing missing values
+    def format_formatdata( self, data, format, key=True, value=True, separator=":" ):
+        output, sdata = [], []
+        if type(data) == type([]): # for FORMAT field, make data with dummy values
+            d = {}
+            for k in data: d[k] = []
+            data = d
+        # convert missing values; and silently add definitions if required
+        for k in data:
+            self._add_definition( format, k, data[k], "(output)" )
+            for idx,v in enumerate(data[k]):
+                if v == format[k].missingvalue: data[k][idx] = "."
+        # make sure GT comes first; and ensure fixed ordering; also convert GT data back to string
+        for k in data: 
+            if k != 'GT': sdata.append( (k,data[k]) )
+        sdata.sort()
+        if 'GT' in data:
+            sdata = [('GT',map(self.convertGTback,data['GT']))] + sdata
+        for k,v in sdata:
+            if v == []: v = None
+            if key and value:
+                if v != None: output.append( k+"="+','.join(map(str,v)) )
+                else: output.append( k )
+            elif key: output.append(k)
+            elif value:
+                if v != None: output.append( ','.join(map(str,v)) )
+                else: output.append( "." )                    # should not happen
+        # snip off trailing missing data
+        while len(output) > 1:
+            last = output[-1].replace(',','').replace('.','')
+            if len(last)>0: break
+            output = output[:-1]
+        return separator.join(output)
+
+
+    def enter_default_format(self):
+        for f in [FORMAT('GT',self.NT_NUMBER,1,'String','Genotype','.'),
+                  FORMAT('GQ',self.NT_NUMBER,1,'Integer','Genotype Quality',-1),
+                  FORMAT('DP',self.NT_NUMBER,1,'Integer','Read depth at this position for this sample',-1),
+                  FORMAT('HQ',self.NT_UNKNOWN,-1,'Integer','Haplotype Quality',-1),    # unknown number, since may be haploid
+                  FORMAT('FT',self.NT_NUMBER,1,'String','Sample Genotype Filter','.')]:
+            if f.id not in self._format:
+                self._format[f.id] = f
+
+    def parse_header( self, line ):
+        assert line.startswith('##')
+        elts = line[2:].split('=')
+        key = elts[0].strip()
+        value = '='.join(elts[1:]).strip()
+        if key == "fileformat":
+            if value == "VCFv3.3":
+                self._version = 33
+            elif value == "VCFv4.0":
+                self._version = 40
+            elif value == "VCFv4.1":
+                self._version = 41
+            else:
+                self.error(line,self.UNKNOWN_FORMAT_STRING)
+        elif key == "INFO":
+            f = self.parse_format(line, value)
+            self._info[ f.id ] = f
+        elif key == "FILTER":
+            f = self.parse_format(line, value, filter=True)
+            self._filter[ f.id ] = f
+        elif key == "FORMAT":
+            f = self.parse_format(line, value)
+            self._format[ f.id ] = f
+        else:
+            # keep other keys in the header field
+            self._header.append( (key,value) )
+
+
+    def write_header( self, stream ):
+        stream.write("##fileformat=VCFv%s.%s\n" % (self._version // 10, self._version % 10))
+        for key,value in self._header: stream.write("##%s=%s\n" % (key,value))
+        for var,label in [(self._info,"INFO"),(self._filter,"FILTER"),(self._format,"FORMAT")]:
+            for f in var.itervalues(): stream.write("##%s=%s\n" % (label,self.format_format(f,filter=(label=="FILTER"))))
+        
+
+    def parse_heading( self, line ):
+        assert line.startswith('#')
+        assert not line.startswith('##')
+        headings = line[1:].split('\t')
+        if len(headings)==1 and len(line[1:].split()) >= 9:
+            self.error(line,self.HEADING_NOT_SEPARATED_BY_TABS)
+            headings = line[1:].split()
+
+        for i,s in enumerate(self._required):
+
+            if len(headings)<=i or headings[i] != s:
+
+                if len(headings) <= i: 
+                    err = "(%sth entry not found)" % (i+1)
+                else:
+                    err = "(found %s, expected %s)" % (headings[i],s)
+
+                #self.error(line,self.BADLY_FORMATTED_HEADING,err)
+
+                # allow FORMAT column to be absent
+                if len(headings) == 8:
+                    headings.append("FORMAT")
+                else:
+                    self.error(line,self.BADLY_FORMATTED_HEADING,err)
+
+        self._samples = headings[9:]
+        self._sample2column = dict( [(y,x) for x,y in enumerate( self._samples ) ] )
+                           
+    def write_heading( self, stream ):
+        stream.write("#" + "\t".join(self._required + self._samples) + "\n")
+
+    def convertGT(self, GTstring):
+        if GTstring == ".": return ["."]
+        try:
+            gts = gtsRegEx.split(GTstring)
+            if len(gts) == 1: return [int(gts[0])]
+            if len(gts) != 2: raise ValueError()
+            if gts[0] == "." and gts[1] == ".": return [gts[0],GTstring[len(gts[0]):-len(gts[1])],gts[1]]
+            return [int(gts[0]),GTstring[len(gts[0]):-len(gts[1])],int(gts[1])]
+        except ValueError:
+            self.error(self._line,self.BAD_GENOTYPE,GTstring)
+            return [".","|","."]
+
+
+    def convertGTback(self, GTdata):
+        return ''.join(map(str,GTdata))
+
+    def parse_formatdata( self, key, value, formatdict, line ):
+        # To do: check that the right number of values is present
+        f = formatdict.get(key,None)
+        if f == None:
+            self._add_definition(formatdict, key, value, line )
+            f = formatdict[key]
+        if f.type == "Flag":
+            if value is not None: self.error(line,self.ERROR_FLAG_HAS_VALUE)
+            return []
+        values = value.split(',')
+        # deal with trailing data in some early VCF files
+        if f.type in ["Float","Integer"] and len(values)>0 and values[-1].find(';') > -1:
+            self.error(line,self.ERROR_TRAILING_DATA,values[-1])
+            values[-1] = values[-1].split(';')[0]
+        if f.type == "Integer": 
+            for idx,v in enumerate(values):
+                try:
+                    if v == ".": values[idx] = f.missingvalue
+                    else:        values[idx] = int(v)
+                except: 
+                    self.error(line,self.ERROR_FORMAT_NOT_NUMERICAL,values)
+                    return [0] * len(values)
+            return values
+        elif f.type == "String":
+            self._line = line
+            if f.id == "GT": values = map( self.convertGT, values )
+            return values
+        elif f.type == "Character":
+            for v in values: 
+                if len(v) != 1: self.error(line,self.ERROR_FORMAT_NOT_CHAR)
+            return values
+        elif f.type == "Float":
+            for idx,v in enumerate(values):
+                if v == ".": values[idx] = f.missingvalue
+            try: return map(float,values)
+            except:
+                self.error(line,self.ERROR_FORMAT_NOT_NUMERICAL,values)
+                return [0.0] * len(values)
+        else:
+            # can't happen
+            self.error(line,self.ERROR_INFO_STRING)
+
+
+    def inregion(self, chrom, pos):
+        if not self._regions: return True
+        for r in self._regions:
+            if r[0] == chrom and r[1] <= pos < r[2]: return True
+        return False
+        
+
+    def parse_data( self, line, lineparse=False ):
+        cols = line.split('\t')
+        if len(cols) != len(self._samples)+9:
+            # gracefully deal with absent FORMAT column
+            if len(cols) == 8 and len(self._samples)==0:
+                cols.append("")
+            else:
+                self.error(line,
+                           self.BAD_NUMBER_OF_COLUMNS, 
+                           "expected %s for %s samples (%s), got %s" % (len(self._samples)+9, len(self._samples), self._samples, len(cols)))
+
+        chrom = cols[0]
+
+        # get 0-based position
+        try:    pos = int(cols[1])-1
+        except: self.error(line,self.POS_NOT_NUMERICAL)
+        if pos < 0: self.error(line,self.POS_NOT_POSITIVE)
+
+        # implement filtering
+        if not self.inregion(chrom,pos): return None
+
+        # end of first-pass parse for sortedVCF
+        if lineparse: return chrom, pos, line
+        
+        id = cols[2]
+
+        ref = cols[3].upper()
+        if ref == ".":
+            self.error(line,self.MISSING_REF)
+            if self._version == 33: ref = get_sequence(chrom,pos,pos+1,self._reference)
+            else:                   ref = ""
+        else:
+            for c in ref:
+                if c not in "ACGTN": self.error(line,self.UNKNOWN_CHAR_IN_REF)
+            if "N" in ref: ref = get_sequence(chrom,pos,pos+len(ref),self._reference)
+
+        # make sure reference is sane
+        if self._reference:
+            left = max(0,pos-100)
+            faref_leftflank = get_sequence(chrom,left,pos+len(ref),self._reference)
+            faref = faref_leftflank[pos-left:]
+            if faref != ref: self.error(line,self.WRONG_REF,"(reference is %s, VCF says %s)" % (faref,ref))
+            ref = faref
+
+        # convert v3.3 to v4.0 alleles below
+        if cols[4] == ".": alt = []
+        else: alt = cols[4].upper().split(',')
+
+        if cols[5] == ".": qual = -1
+        else: 
+            try:    qual = float(cols[5])
+            except: self.error(line,self.QUAL_NOT_NUMERICAL)
+
+        # postpone checking that filters exist.  Encode missing filter or no filtering as empty list
+        if cols[6] == "." or cols[6] == "PASS" or cols[6] == "0": filter = []
+        else: filter = cols[6].split(';')
+
+        # dictionary of keys, and list of values
+        info = {}
+        if cols[7] != ".":
+            for blurp in cols[7].split(';'):
+                elts = blurp.split('=')
+                if len(elts) == 1: v = None
+                elif len(elts) == 2: v = elts[1]
+                else: self.error(line,self.ERROR_INFO_STRING)
+                info[elts[0]] = self.parse_formatdata(elts[0], v, self._info, line)
+
+        # Gracefully deal with absent FORMAT column
+        if cols[8] == "": format = []
+        else: format = cols[8].split(':')
+
+        # check: all filters are defined
+        for f in filter:
+            if f not in self._filter: self.error(line,self.FILTER_NOT_DEFINED, f)
+            
+        # check: format fields are defined
+        for f in format:
+            if f not in self._format: self.error(line,self.FORMAT_NOT_DEFINED, f)
+
+        # convert v3.3 alleles
+        if self._version == 33:
+            if len(ref) != 1: self.error(line,self.V33_BAD_REF)
+            newalts = []
+            have_deletions = False
+            for a in alt:
+                if len(a) == 1: a = a + ref[1:]                       # SNP; add trailing reference
+                elif a.startswith('I'): a = ref[0] + a[1:] + ref[1:]  # insertion just beyond pos; add first and trailing reference
+                elif a.startswith('D'): # allow D<seq> and D<num>
+                    have_deletions = True
+                    try:
+                        l = int(a[1:])          # throws ValueError if sequence
+                        if len(ref) < l:        # add to reference if necessary
+                            addns = get_sequence(chrom,pos+len(ref),pos+l,self._reference)
+                            ref += addns
+                            for i,na in enumerate(newalts): newalts[i] = na+addns
+                        a = ref[l:]             # new deletion, deleting pos...pos+l
+                    except ValueError:
+                        s = a[1:]
+                        if len(ref) < len(s):   # add Ns to reference if necessary
+                            addns = get_sequence(chrom,pos+len(ref),pos+len(s),self._reference)
+                            if not s.endswith(addns) and addns != 'N'*len(addns):
+                                self.error(line,self.V33_UNMATCHED_DELETION,
+                                           "(deletion is %s, reference is %s)" % (a,get_sequence(chrom,pos,pos+len(s),self._reference)))
+                            ref += addns
+                            for i,na in enumerate(newalts): newalts[i] = na+addns
+                        a = ref[len(s):]        # new deletion, deleting from pos
+                else:
+                    self.error(line,self.V33_BAD_ALLELE)
+                newalts.append(a)
+            alt = newalts
+            # deletion alleles exist, add dummy 1st reference allele, and account for leading base
+            if have_deletions:
+                if pos == 0:
+                    # Petr Danacek's: we can't have a leading nucleotide at (1-based) position 1
+                    addn = get_sequence(chrom,pos+len(ref),pos+len(ref)+1,self._reference)
+                    ref += addn
+                    alt = [allele+addn for allele in alt]
+                else:
+                    addn = get_sequence(chrom,pos-1,pos,self._reference)
+                    ref = addn + ref
+                    alt = [addn + allele for allele in alt]
+                    pos -= 1
+        else:
+            # format v4.0 -- just check for nucleotides
+            for allele in alt:
+                if not alleleRegEx.match(allele):
+                    self.error(line,self.V40_BAD_ALLELE,allele)
+
+        # check for leading nucleotide in indel calls
+        for allele in alt:
+            if len(allele) != len(ref):
+                if len(allele) == 0: self.error(line,self.ZERO_LENGTH_ALLELE)
+                if ref[0].upper() != allele[0].upper() and "N" not in (ref[0]+allele[0]).upper():
+                    self.error(line,self.MISSING_INDEL_ALLELE_REF_BASE)
+
+        # trim trailing bases in alleles
+        for i in range(1,min(len(ref),min(map(len,alt)))):
+            if len(set(allele[-1].upper() for allele in alt)) > 1 or ref[-1].upper() != alt[0][-1].upper():
+                break
+            ref, alt = ref[:-1], [allele[:-1] for allele in alt]
+
+        # left-align alleles, if a reference is available
+        if self._leftalign and self._reference:
+            while left < pos:
+                movable = True
+                for allele in alt:
+                    if len(allele) > len(ref):
+                        longest, shortest = allele, ref
+                    else:
+                        longest, shortest = ref, allele
+                    if len(longest) == len(shortest) or longest[:len(shortest)].upper() != shortest.upper():
+                        movable = False
+                    if longest[-1].upper() != longest[len(shortest)-1].upper():
+                        movable = False
+                if not movable:
+                    break
+                ref = ref[:-1]
+                alt = [allele[:-1] for allele in alt]
+                if min(len(allele) for allele in alt) == 0 or len(ref) == 0:
+                    ref = faref_leftflank[pos-left-1] + ref
+                    alt = [faref_leftflank[pos-left-1] + allele for allele in alt]
+                    pos -= 1
+
+        # parse sample columns
+        samples = []
+        for sample in cols[9:]:
+            dict = {}
+            values = sample.split(':')
+            if len(values) > len(format):
+                self.error(line,self.BAD_NUMBER_OF_VALUES,"(found %s values in element %s; expected %s)" % (len(values),sample,len(format)))
+            for idx in range(len(format)):
+                expected = self.get_expected(format[idx], self._format, alt)
+                if idx < len(values): value = values[idx]
+                else:
+                    if expected == -1: value = "."
+                    else: value = ",".join(["."]*expected)
+                dict[format[idx]] = self.parse_formatdata(format[idx], value, self._format, line)
+                if expected != -1 and len(dict[format[idx]]) != expected:
+                    self.error(line,self.BAD_NUMBER_OF_PARAMETERS,
+                               "id=%s, expected %s parameters, got %s" % (format[idx],expected,dict[format[idx]]))
+                    if len(dict[format[idx]] ) < expected: dict[format[idx]] += [dict[format[idx]][-1]]*(expected-len(dict[format[idx]]))
+                    dict[format[idx]] = dict[format[idx]][:expected]
+            samples.append( dict )
+
+        # done
+        d = {'chrom':chrom,
+             'pos':pos,      # return 0-based position
+             'id':id,
+             'ref':ref,
+             'alt':alt,
+             'qual':qual,
+             'filter':filter,
+             'info':info,
+             'format':format}
+        for key,value in zip(self._samples,samples):
+            d[key] = value
+        
+        return d
+
+
+    def write_data(self, stream, data):
+        required = ['chrom','pos','id','ref','alt','qual','filter','info','format'] + self._samples
+        for k in required:
+            if k not in data: raise ValueError("Required key %s not found in data" % str(k))
+        if data['alt'] == []: alt = "."
+        else: alt = ",".join(data['alt'])
+        if data['filter'] == None: filter = "."
+        elif data['filter'] == []: 
+            if self._version == 33: filter = "0"
+            else: filter = "PASS"
+        else: filter = ';'.join(data['filter'])
+        if data['qual'] == -1: qual = "."
+        else: qual = str(data['qual'])
+
+        output = [data['chrom'], 
+                  str(data['pos']+1),   # change to 1-based position
+                  data['id'],
+                  data['ref'],
+                  alt,
+                  qual,
+                  filter,
+                  self.format_formatdata( data['info'], self._info, separator=";" ),
+                  self.format_formatdata( data['format'], self._format, value=False ) ]
+        
+        for s in self._samples:
+            output.append( self.format_formatdata( data[s], self._format, key=False ) )
+        
+        stream.write( "\t".join(output) + "\n" )
+
+    def _parse_header(self, stream):
+        self._lineno = 0
+        for line in stream:
+            self._lineno += 1
+            if line.startswith('##'):
+                self.parse_header( line.strip() )
+            elif line.startswith('#'):
+                self.parse_heading( line.strip() )
+                self.enter_default_format()
+            else:
+                break
+        return line
+
+    def _parse(self, line, stream):
+        if len(line.strip()) > 0:
+            d = self.parse_data( line.strip() )
+            if d: yield d
+        for line in stream:
+            self._lineno += 1
+            if self._lines and self._lineno > self._lines: raise StopIteration
+            d = self.parse_data( line.strip() )
+            if d: yield d
+
+    ######################################################################################################
+    #
+    # API follows
+    #
+    ######################################################################################################
+
+    def getsamples(self):
+        """ List of samples in VCF file """
+        return self._samples
+
+    def setsamples(self,samples):
+        """ List of samples in VCF file """
+        self._samples = samples
+
+    def getheader(self):
+        """ List of header key-value pairs (strings) """
+        return self._header
+
+    def setheader(self,header):
+        """ List of header key-value pairs (strings) """
+        self._header = header
+
+    def getinfo(self):
+        """ Dictionary of ##INFO tags, as VCF.FORMAT values """
+        return self._info
+
+    def setinfo(self,info):
+        """ Dictionary of ##INFO tags, as VCF.FORMAT values """
+        self._info = info
+
+    def getformat(self):
+        """ Dictionary of ##FORMAT tags, as VCF.FORMAT values """
+        return self._format
+
+    def setformat(self,format):
+        """ Dictionary of ##FORMAT tags, as VCF.FORMAT values """
+        self._format = format
+
+    def getfilter(self):
+        """ Dictionary of ##FILTER tags, as VCF.FORMAT values """
+        return self._filter
+
+    def setfilter(self,filter):
+        """ Dictionary of ##FILTER tags, as VCF.FORMAT values """
+        self._filter = filter
+
+    def setversion(self, version):
+        if version not in [33,40,41]: raise ValueError("Can only handle v3.3, v4.0 and v4.1 VCF files")
+        self._version = version
+
+    def setregions(self, regions):
+        self._regions = regions
+
+    def setreference(self, ref):
+        """ Provide a reference sequence; a Python class supporting a fetch(chromosome, start, end) method, e.g. PySam.FastaFile """
+        self._reference = ref
+
+    def ignoreerror(self, errorstring):
+        try:             self._ignored_errors.add(self.__dict__[errorstring])
+        except KeyError: raise ValueError("Invalid error string: %s" % errorstring)
+
+    def warnerror(self, errorstring):
+        try:             self._warn_errors.add(self.__dict__[errorstring])
+        except KeyError: raise ValueError("Invalid error string: %s" % errorstring)
+
+    def parse(self, stream):
+        """ Parse a stream of VCF-formatted lines.  Initializes class instance and return generator """
+        last_line = self._parse_header(stream)
+        # now return a generator that does the actual work.  In this way the pre-processing is done
+        # before the first piece of data is yielded
+        return self._parse(last_line, stream)
+
+    def write(self, stream, datagenerator):
+        """ Writes a VCF file to a stream, using a data generator (or list) """
+        self.write_header(stream)
+        self.write_heading(stream)
+        for data in datagenerator: self.write_data(stream,data)
+
+    def writeheader(self, stream):
+        """ Writes a VCF header """
+        self.write_header(stream)
+        self.write_heading(stream)
+
+    def compare_calls(self, pos1, ref1, alt1, pos2, ref2, alt2):
+        """ Utility function: compares two calls for equality """
+        # a variant should always be assigned to a unique position, one base before
+        # the leftmost position of the alignment gap.  If this rule is implemented
+        # correctly, the two positions must be equal for the calls to be identical.
+        if pos1 != pos2: return False
+        # from both calls, trim rightmost bases when identical.  Do this safely, i.e.
+        # only when the reference bases are not Ns
+        while len(ref1)>0 and len(alt1)>0 and ref1[-1] == alt1[-1]:
+            ref1 = ref1[:-1]
+            alt1 = alt1[:-1]
+        while len(ref2)>0 and len(alt2)>0 and ref2[-1] == alt2[-1]:
+            ref2 = ref2[:-1]
+            alt2 = alt2[:-1]
+        # now, the alternative alleles must be identical
+        return alt1 == alt2
+
+###########################################################################################################
+###########################################################################################################
+## API functions added by Andreas
+###########################################################################################################
+
+    def connect( self, filename ):
+        '''connect to tabix file.'''
+        self.tabixfile = pysam.Tabixfile( filename )
+        self._parse_header(self.tabixfile.header)
+        
+    def fetch(self,
+              reference = None,
+              start = None, 
+              end = None, 
+              region = None ):
+        """ Parse a stream of VCF-formatted lines.  Initializes class instance and return generator """
+
+        iter = self.tabixfile.fetch( reference, start, end, region, parser = pysam.asVCF() )
+        for x in iter:
+            yield VCFRecord( x, self )
+
+    def validate( self, record ):
+        '''validate vcf record.
+
+        returns a validated record.
+        '''
+
+        chrom, pos = record.chrom, record.pos
+
+        # check reference
+        ref = record.ref
+        if ref == ".":
+            self.error(str(record),self.MISSING_REF)
+            if self._version == 33: ref = get_sequence(chrom,pos,pos+1,self._reference)
+            else:                   ref = ""
+        else:
+            for c in ref:
+                if c not in "ACGTN": self.error(str(record),self.UNKNOWN_CHAR_IN_REF)
+                if "N" in ref: ref = get_sequence(chrom,
+                                                  pos,
+                                                  pos+len(ref),
+                                                  self._reference)
+
+        # make sure reference is sane
+        if self._reference:
+            left = max(0,self.pos-100)
+            faref_leftflank = get_sequence(chrom,left,self.pos+len(ref),self._reference)
+            faref = faref_leftflank[pos-left:]
+            if faref != ref: self.error(line,self.WRONG_REF,"(reference is %s, VCF says %s)" % (faref,ref))
+            ref = faref
+            
+        # check: format fields are defined
+        for f in record.format:
+            if f not in self._format: self.error(str(record),self.FORMAT_NOT_DEFINED, f)
+            
+        # check: all filters are defined
+        for f in record.filter:
+            if f not in self._filter: self.error(str(record),self.FILTER_NOT_DEFINED, f)
+
+        # convert v3.3 alleles
+        if self._version == 33:
+            if len(ref) != 1: self.error(line,self.V33_BAD_REF)
+            newalts = []
+            have_deletions = False
+            for a in alt:
+                if len(a) == 1: a = a + ref[1:]                       # SNP; add trailing reference
+                elif a.startswith('I'): a = ref[0] + a[1:] + ref[1:]  # insertion just beyond pos; add first and trailing reference
+                elif a.startswith('D'): # allow D<seq> and D<num>
+                    have_deletions = True
+                    try:
+                        l = int(a[1:])          # throws ValueError if sequence
+                        if len(ref) < l:        # add to reference if necessary
+                            addns = get_sequence(chrom,pos+len(ref),pos+l,self._reference)
+                            ref += addns
+                            for i,na in enumerate(newalts): newalts[i] = na+addns
+                        a = ref[l:]             # new deletion, deleting pos...pos+l
+                    except ValueError:
+                        s = a[1:]
+                        if len(ref) < len(s):   # add Ns to reference if necessary
+                            addns = get_sequence(chrom,pos+len(ref),pos+len(s),self._reference)
+                            if not s.endswith(addns) and addns != 'N'*len(addns):
+                                self.error(line,self.V33_UNMATCHED_DELETION,
+                                           "(deletion is %s, reference is %s)" % (a,get_sequence(chrom,pos,pos+len(s),self._reference)))
+                            ref += addns
+                            for i,na in enumerate(newalts): newalts[i] = na+addns
+                        a = ref[len(s):]        # new deletion, deleting from pos
+                else:
+                    self.error(line,self.V33_BAD_ALLELE)
+                newalts.append(a)
+            alt = newalts
+            # deletion alleles exist, add dummy 1st reference allele, and account for leading base
+            if have_deletions:
+                if pos == 0:
+                    # Petr Danacek's: we can't have a leading nucleotide at (1-based) position 1
+                    addn = get_sequence(chrom,pos+len(ref),pos+len(ref)+1,self._reference)
+                    ref += addn
+                    alt = [allele+addn for allele in alt]
+                else:
+                    addn = get_sequence(chrom,pos-1,pos,self._reference)
+                    ref = addn + ref
+                    alt = [addn + allele for allele in alt]
+                    pos -= 1
+        else:
+            # format v4.0 -- just check for nucleotides
+            for allele in alt:
+                if not alleleRegEx.match(allele):
+                    self.error(line,self.V40_BAD_ALLELE,allele)
+                    
+
+        # check for leading nucleotide in indel calls
+        for allele in alt:
+            if len(allele) != len(ref):
+                if len(allele) == 0: self.error(line,self.ZERO_LENGTH_ALLELE)
+                if ref[0].upper() != allele[0].upper() and "N" not in (ref[0]+allele[0]).upper():
+                    self.error(line,self.MISSING_INDEL_ALLELE_REF_BASE)
+
+        # trim trailing bases in alleles
+        for i in range(1,min(len(ref),min(map(len,alt)))):
+            if len(set(allele[-1].upper() for allele in alt)) > 1 or ref[-1].upper() != alt[0][-1].upper():
+                break
+            ref, alt = ref[:-1], [allele[:-1] for allele in alt]
+
+        # left-align alleles, if a reference is available
+        if self._leftalign and self._reference:
+            while left < pos:
+                movable = True
+                for allele in alt:
+                    if len(allele) > len(ref):
+                        longest, shortest = allele, ref
+                    else:
+                        longest, shortest = ref, allele
+                    if len(longest) == len(shortest) or longest[:len(shortest)].upper() != shortest.upper():
+                        movable = False
+                    if longest[-1].upper() != longest[len(shortest)-1].upper():
+                        movable = False
+                if not movable:
+                    break
+                ref = ref[:-1]
+                alt = [allele[:-1] for allele in alt]
+                if min(len(allele) for allele in alt) == 0 or len(ref) == 0:
+                    ref = faref_leftflank[pos-left-1] + ref
+                    alt = [faref_leftflank[pos-left-1] + allele for allele in alt]
+                    pos -= 1
+
+
+
+
diff --git a/pysam/__init__.py b/pysam/__init__.py
new file mode 100644
index 0000000..ec52d94
--- /dev/null
+++ b/pysam/__init__.py
@@ -0,0 +1,100 @@
+import os
+import sysconfig
+
+from pysam.libchtslib import *
+import pysam.libchtslib as libchtslib
+from pysam.libcsamtools import *
+from pysam.libcbcftools import *
+from pysam.libcutils import *
+import pysam.libcutils as libcutils
+import pysam.libcfaidx as libcfaidx
+from pysam.libcfaidx import *
+import pysam.libctabix as libctabix
+from pysam.libctabix import *
+import pysam.libctabixproxies as libctabixproxies
+from pysam.libctabixproxies import *
+import pysam.libcsamfile as libcsamfile
+from pysam.libcsamfile import *
+import pysam.libcalignmentfile as libcalignmentfile
+from pysam.libcalignmentfile import *
+import pysam.libcalignedsegment as libcalignedsegment
+from pysam.libcalignedsegment import *
+import pysam.libcvcf as libcvcf
+from pysam.libcvcf import *
+import pysam.libcbcf as libcbcf
+from pysam.libcbcf import *
+import pysam.libcbgzf as libcbgzf
+from pysam.libcbgzf import *
+from pysam.utils import SamtoolsError
+import pysam.Pileup as Pileup
+from pysam.samtools import *
+import pysam.config
+
+
+# export all the symbols from separate modules
+__all__ = (
+    libchtslib.__all__ +  # type: ignore
+    libcutils.__all__ +  # type: ignore
+    libctabix.__all__ +  # type: ignore
+    libcvcf.__all__ +  # type: ignore
+    libcbcf.__all__ +  # type: ignore
+    libcbgzf.__all__ +  # type: ignore
+    libcfaidx.__all__ +  # type: ignore
+    libctabixproxies.__all__ +  # type: ignore
+    libcalignmentfile.__all__ +  # type: ignore
+    libcalignedsegment.__all__ +  # type: ignore
+    libcsamfile.__all__ +  # type: ignore
+    ["SamtoolsError"] +
+    ["Pileup"]
+)
+from pysam.version import __version__, __samtools_version__
+
+
+def get_include():
+    '''return a list of include directories.'''
+    dirname = os.path.abspath(os.path.join(os.path.dirname(__file__)))
+
+    #
+    # Header files may be stored in different relative locations
+    # depending on installation mode (e.g., `python setup.py install`,
+    # `python setup.py develop`. The first entry in each list is
+    # where develop-mode headers can be found.
+    #
+    htslib_possibilities = [os.path.join(dirname, '..', 'htslib'),
+                            os.path.join(dirname, 'include', 'htslib')]
+    samtool_possibilities = [os.path.join(dirname, '..', 'samtools'),
+                             os.path.join(dirname, 'include', 'samtools')]
+
+    includes = [dirname]
+    for header_locations in [htslib_possibilities, samtool_possibilities]:
+        for header_location in header_locations:
+            if os.path.exists(header_location):
+                includes.append(os.path.abspath(header_location))
+                break
+
+    return includes
+
+
+def get_defines():
+    '''return a list of defined compilation parameters.'''
+    # ('_FILE_OFFSET_BITS', '64'),
+    # ('_USE_KNETFILE', '')]
+    return []
+
+
+def get_libraries():
+    '''return a list of libraries to link against.'''
+    # Note that this list does not include libcsamtools.so as there are
+    # numerous name conflicts with libchtslib.so.
+    dirname = os.path.abspath(os.path.join(os.path.dirname(__file__)))
+    pysam_libs = ['libctabixproxies',
+                  'libcfaidx',
+                  'libcsamfile',
+                  'libcvcf',
+                  'libcbcf',
+                  'libctabix']
+    if pysam.config.HTSLIB == "builtin":
+        pysam_libs.append('libchtslib')
+
+    so = sysconfig.get_config_var('SO')
+    return [os.path.join(dirname, x + so) for x in pysam_libs]
diff --git a/pysam/alternatives.py.obsolete b/pysam/alternatives.py.obsolete
new file mode 100644
index 0000000..fd76802
--- /dev/null
+++ b/pysam/alternatives.py.obsolete
@@ -0,0 +1,82 @@
+# This file contains an alternative implementation
+# to call samtools functions. These are direct calls.
+# Plus: less overhead
+# Minus: more trouble in maintaining
+
+#in csamtools.pxd
+    # samtools toolkit functions
+    ctypedef int (*pysam_samtools_f)(int argc, char *argv[])
+
+    int bam_taf2baf(int argc, char *argv[])
+    int bam_pileup(int argc, char *argv[])
+    int bam_merge(int argc, char *argv[])
+    int bam_index(int argc, char *argv[])
+    int bam_sort(int argc, char *argv[])
+    int bam_tview_main(int argc, char *argv[])
+    int bam_mating(int argc, char *argv[])
+    int bam_rmdup(int argc, char *argv[])
+    int bam_rmdupse(int argc, char *argv[])
+    int bam_flagstat(int argc, char *argv[])
+    int bam_fillmd(int argc, char *argv[])
+    int main_samview(int argc, char *argv[])
+    int main_import(int argc, char *argv[])
+    int faidx_main(int argc, char *argv[])
+    int glf3_view_main(int argc, char *argv[])
+
+
+## Alternative code in csamtools.pyx
+cdef class SamtoolsWrapper:
+    '''generic wrapper around samtools functions'''
+    cdef pysam_samtools_f f 
+
+    def __init__(self): self.f = NULL
+
+    def call(self, *args ):
+
+        if self.f == NULL: raise NotImplementedError("invalid call to base class" )
+
+        cdef char ** cargs
+        cdef int i, n, retval
+        n = len(args)
+        # allocate one more for first (dummy) argument (contains command)
+        cargs = <char**>calloc( n+1, sizeof( char *) )
+        cargs[0] = "method"
+        for i from 0 <= i < n:
+            cargs[i+1] = args[i]
+        for i from 0 <= i < n+1:
+            print cargs[i]
+        retval = self.f(n+1, cargs)
+        free( cargs )
+        return retval
+
+cdef class SamtoolsWrapperImport( SamtoolsWrapper ):
+    def __init__(self): self.f = main_import
+cdef class SamtoolsWrapperPileup( SamtoolsWrapper ):
+    def __init__(self): self.f = bam_pileup
+cdef class SamtoolsWrapperMerge( SamtoolsWrapper ):
+    def __init__(self): self.f = bam_merge
+cdef class SamtoolsWrapperSort( SamtoolsWrapper ):
+    def __init__(self): self.f = bam_sort
+cdef class SamtoolsWrapperIndex( SamtoolsWrapper ):
+    def __init__(self): self.f = bam_index
+cdef class SamtoolsWrapperFaidx( SamtoolsWrapper ):
+    def __init__(self): self.f = faidx_main
+cdef class SamtoolsWrapperFixMate( SamtoolsWrapper ):
+    def __init__(self): self.f = bam_mating
+cdef class SamtoolsWrapperRmDup( SamtoolsWrapper ):
+    def __init__(self): self.f = bam_rmdup
+cdef class SamtoolsWrapperRmDupSe( SamtoolsWrapper ):
+    def __init__(self): self.f = bam_rmdupse
+cdef class SamtoolsWrapperGlf3Viwen( SamtoolsWrapper ):
+    def __init__(self): self.f = glf3_view_main
+cdef class SamtoolsWrapperFlagStat( SamtoolsWrapper ):
+    def __init__(self): self.f = bam_flagstat
+cdef class SamtoolsWrapperFillMd( SamtoolsWrapper ):
+    def __init__(self): self.f = bam_fillmd
+cdef class SamtoolsWrapperCalMd( SamtoolsWrapper ):
+    def __init__(self): self.f = bam_fillmd
+
+automatic creation of these functions does not work 
+due to pyrex/cython
+
+def sort( *args, **kwargs ): return SamtoolsWrapperSort().call(*args, **kwargs)
diff --git a/pysam/bcftools.py b/pysam/bcftools.py
new file mode 100644
index 0000000..4cbe82f
--- /dev/null
+++ b/pysam/bcftools.py
@@ -0,0 +1,29 @@
+from pysam.utils import PysamDispatcher
+
+BCFTOOLS_DISPATCH = [
+    "index",
+    "annotate",
+    "concat",
+    "convert",
+    "isec",
+    "merge",
+    "norm",
+    "plugin",
+    "query",
+    "reheader",
+    "sort",
+    "view",
+    "head",
+    "call",
+    "consensus",
+    "cnv",
+    "csq",
+    "filter",
+    "gtcheck",
+    "mpileup",
+    "roh",
+    "stats"]
+
+# instantiate bcftools commands as python functions
+for cmd in BCFTOOLS_DISPATCH:
+    globals()[cmd] = PysamDispatcher("bcftools", cmd, None)
diff --git a/pysam/cbcftools_util.h b/pysam/cbcftools_util.h
new file mode 100644
index 0000000..4a9f2e9
--- /dev/null
+++ b/pysam/cbcftools_util.h
@@ -0,0 +1,6 @@
+#ifndef CBCFTOOLS_UTIL_H
+#define CBCFTOOLS_UTIL_H
+
+int bcftools_main(int argc, char *argv[]);
+
+#endif
diff --git a/pysam/csamtools_util.h b/pysam/csamtools_util.h
new file mode 100644
index 0000000..0a03c13
--- /dev/null
+++ b/pysam/csamtools_util.h
@@ -0,0 +1,6 @@
+#ifndef CSAMTOOLS_UTIL_H
+#define CSAMTOOLS_UTIL_H
+
+int samtools_main(int argc, char *argv[]);
+
+#endif
diff --git a/pysam/htslib_util.c b/pysam/htslib_util.c
new file mode 100644
index 0000000..0830900
--- /dev/null
+++ b/pysam/htslib_util.c
@@ -0,0 +1,159 @@
+#include <ctype.h>
+#include <assert.h>
+#include "htslib/khash.h"
+#include "htslib/ksort.h"
+#include "htslib/sam.h"
+#include "htslib/hts.h"
+#include "htslib/knetfile.h"
+#include "htslib/kseq.h"
+#include "htslib_util.h"
+#include <stdio.h>
+
+#ifndef inline
+#define inline __inline
+#endif
+
+// set htslib verbosity level
+extern int hts_verbose;
+int hts_set_verbosity(int verbosity)
+{
+  int old_verbosity = hts_verbose;
+  hts_verbose = verbosity;
+  return old_verbosity;
+}
+
+int hts_get_verbosity(void)
+{
+  return hts_verbose;
+}
+
+
+// taken from samtools/bam_import.c
+static inline uint8_t * alloc_data(bam1_t *b, size_t size)
+{
+  if (b->m_data < size)
+    {
+      b->m_data = size;
+      kroundup32(b->m_data);
+      b->data = (uint8_t*)realloc(b->data, b->m_data);
+    }
+  return b->data;
+}
+
+// update the variable length data within a bam1_t entry.
+// Adds *nbytes_new* - *nbytes_old* into the variable length data of *src* at *pos*.
+// Data within the bam1_t entry is moved so that it is
+// consistent with the data field lengths.
+// Return NULL on error (memory allocation)
+bam1_t * pysam_bam_update(bam1_t * b,
+			  const size_t nbytes_old,
+			  const size_t nbytes_new, 
+			  uint8_t * field_start)
+{
+  int d = nbytes_new - nbytes_old;
+  int new_size;
+  size_t nbytes_before;
+  uint8_t * retval = NULL;
+    
+  // no change
+  if (d == 0)
+    return b;
+
+  // new size of total data
+  new_size = d + b->l_data;
+  
+  // fields before field in data
+  nbytes_before = field_start - b->data;
+
+  if (b->l_data != 0)
+    {
+      assert(nbytes_before >= 0);
+      assert(nbytes_before <= b->l_data);
+    }
+
+  // increase memory if required
+  if (d > 0)
+    {
+      retval = alloc_data(b, new_size);
+      if (retval == NULL)
+	return NULL;
+      field_start = b->data + nbytes_before;
+    }
+  
+  // move data after field to new location
+  memmove(field_start + nbytes_new,
+	  field_start + nbytes_old,
+	  b->l_data - (nbytes_before + nbytes_old));
+
+  // adjust l_data
+  b->l_data = new_size;
+      
+  return b;
+}
+
+// translate a nucleotide character to binary code
+unsigned char pysam_translate_sequence(const unsigned char s)
+{
+  return seq_nt16_table[s];
+}
+
+// Auxiliary functions for B support
+void bam_aux_appendB(bam1_t *b,
+		     const char tag[2],
+		     char type,
+		     char subtype,
+		     int len,
+		     uint8_t *data)
+{
+
+  int ori_len;
+  int l_data;
+
+  // check that type is 'B'
+  if('B' != type) return;
+
+  ori_len = b->l_data;
+
+  l_data = len * aux_type2size(subtype);
+  // infer the data length from the sub-type
+  b->l_data += 8 + l_data;
+
+  // htslib: obsolete?
+  // b->l_aux += 8 + l_data;
+  if (b->m_data < b->l_data) 
+    {
+      b->m_data = b->l_data;
+      kroundup32(b->m_data);
+      b->data = (uint8_t*)realloc(b->data, b->m_data);
+    }
+
+  b->data[ori_len] = tag[0];
+  b->data[ori_len + 1] = tag[1];
+  // tag
+  b->data[ori_len + 2] = type;
+  // type
+  b->data[ori_len + 3] = subtype;
+  // subtype
+  (*(int32_t*)(b->data + ori_len + 4)) = len;
+  // size
+  memcpy(b->data + ori_len + 8, data, l_data);
+  // data
+}
+
+int aux_type2size(uint8_t type)
+{
+	switch (type) {
+	case 'A': case 'c': case 'C':
+		return 1;
+	case 's': case 'S':
+		return 2;
+	case 'i': case 'I': case 'f':
+		return 4;
+	case 'd':
+		return 8;
+	case 'Z': case 'H': case 'B':
+		return type;
+	default:
+		return 0;
+	}
+}
diff --git a/pysam/htslib_util.h b/pysam/htslib_util.h
new file mode 100644
index 0000000..63fdaaa
--- /dev/null
+++ b/pysam/htslib_util.h
@@ -0,0 +1,97 @@
+#ifndef HTSLIB_UTIL_H
+#define HTSLIB_UTIL_H
+
+#include "htslib/sam.h"
+#include "htslib/vcf.h"
+#include "htslib/khash.h"
+
+int hts_set_verbosity(int verbosity);
+int hts_get_verbosity(void);
+
+
+KHASH_MAP_INIT_STR(vdict, bcf_idinfo_t)
+typedef khash_t(vdict) vdict_t;
+
+KHASH_DECLARE(s2i, kh_cstr_t, int64_t)
+typedef khash_t(s2i) s2i_t;
+		     
+//////////////////////////////////////////////////////////////////
+//////////////////////////////////////////////////////////////////
+//////////////////////////////////////////////////////////////////
+// various helper functions
+//
+
+/*!
+  @abstract Update the variable length data within a bam1_t entry
+
+  Old data is deleted and the data within b are re-arranged to 
+  make place for new data.
+  
+  @discussion Return NULL on error, otherwise b is returned.
+
+  @param  b           bam1_t data
+  @param  nbytes_old  size of old data
+  @param  nbytes_new  size of new data
+  @param  pos         position of data
+*/
+bam1_t * pysam_bam_update(bam1_t * b,
+			  const size_t nbytes_old,
+			  const size_t nbytes_new,
+			  uint8_t * pos);
+
+// translate a nucleotide character to binary code
+unsigned char pysam_translate_sequence(const unsigned char s);
+
+// return byte size of type
+int aux_type2size(uint8_t type);
+
+
+//-------------------------------------------------------
+// Wrapping accessor macros in sam.h
+static inline int pysam_bam_is_rev(bam1_t * b) {
+  return bam_is_rev(b);};
+
+static inline int pysam_bam_is_mrev(bam1_t * b) {
+  return bam_is_mrev(b);}
+
+static inline char * pysam_bam_get_qname(bam1_t * b) {
+  return bam_get_qname(b);}
+
+static inline uint32_t * pysam_bam_get_cigar(bam1_t * b) {
+  return bam_get_cigar(b);}
+
+static inline uint8_t * pysam_bam_get_seq(bam1_t * b) {
+  return bam_get_seq(b);}
+
+static inline uint8_t * pysam_bam_get_qual(bam1_t * b) {
+  return bam_get_qual(b);}
+
+static inline uint8_t * pysam_bam_get_aux(bam1_t * b) {
+  return bam_get_aux(b);}
+
+static inline int pysam_bam_get_l_aux(bam1_t * b) {
+  return bam_get_l_aux(b); }
+
+static inline char pysam_bam_seqi(uint8_t * s, int i) {
+  return bam_seqi(s,i);}
+
+static inline uint8_t pysam_get_qual(bam1_t * b) {
+  return b->core.qual;}
+
+static inline uint32_t pysam_get_n_cigar(bam1_t * b) {
+  return b->core.n_cigar;}
+
+static inline void pysam_set_qual(bam1_t * b, uint8_t v) {
+  b->core.qual=v;}
+
+static inline void pysam_set_n_cigar(bam1_t * b, uint32_t v) {
+  b->core.n_cigar=v;}
+
+static inline void pysam_update_flag(bam1_t * b, uint16_t v, uint16_t flag) {
+  if (v)
+    b->core.flag |= flag;
+  else
+    b->core.flag &= ~flag;
+}
+
+#endif
diff --git a/pysam/include/__init__.py b/pysam/include/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/pysam/libcalignedsegment.pxd b/pysam/libcalignedsegment.pxd
new file mode 100644
index 0000000..32e2c97
--- /dev/null
+++ b/pysam/libcalignedsegment.pxd
@@ -0,0 +1,102 @@
+from pysam.libchtslib cimport *
+
+cdef extern from "htslib_util.h":
+
+    # add *nbytes* into the variable length data of *src* at *pos*
+    bam1_t * pysam_bam_update(bam1_t * b,
+           	         size_t nbytes_old,
+                         size_t nbytes_new,
+                         uint8_t * pos)
+
+    # now: static
+    int aux_type2size(int)
+
+    char * pysam_bam_get_qname(bam1_t * b)
+    uint32_t * pysam_bam_get_cigar(bam1_t * b)
+    uint8_t * pysam_bam_get_seq(bam1_t * b)
+    uint8_t * pysam_bam_get_qual(bam1_t * b)
+    uint8_t * pysam_bam_get_aux(bam1_t * b)
+    int pysam_bam_get_l_aux(bam1_t * b)
+    char pysam_bam_seqi(uint8_t * s, int i)
+
+    uint8_t pysam_get_qual(bam1_t * b)
+    uint32_t pysam_get_n_cigar(bam1_t * b)
+    void pysam_set_qual(bam1_t * b, uint8_t v)
+    void pysam_set_n_cigar(bam1_t * b, uint32_t v)
+    void pysam_update_flag(bam1_t * b, uint16_t v, uint16_t flag)
+
+
+from pysam.libcalignmentfile cimport AlignmentFile, AlignmentHeader
+ctypedef AlignmentFile AlignmentFile_t
+
+
+# Note: need to declare all C fields and methods here
+cdef class AlignedSegment:
+
+    # object that this AlignedSegment represents
+    cdef bam1_t * _delegate
+
+    # the header that a read is associated with
+    cdef readonly AlignmentHeader header
+
+    # caching of array properties for quick access
+    cdef object cache_query_qualities
+    cdef object cache_query_alignment_qualities
+    cdef object cache_query_sequence
+    cdef object cache_query_alignment_sequence
+
+    # add an alignment tag with value to the AlignedSegment
+    # an existing tag of the same name will be replaced.
+    cpdef set_tag(self, tag, value, value_type=?, replace=?)
+
+    # get an alignment tag from the AlignedSegment
+    cpdef get_tag(self, tag, with_value_type=?)
+
+    # return true if tag exists
+    cpdef has_tag(self, tag)
+
+    # returns a valid sam alignment string
+    cpdef to_string(self)
+
+    # returns a valid sam alignment string (deprecated)
+    cpdef tostring(self, htsfile=*)
+
+
+cdef class PileupColumn:
+    cdef const bam_pileup1_t ** plp
+    cdef int tid
+    cdef int pos
+    cdef int n_pu
+    cdef AlignmentHeader header
+    cdef uint32_t min_base_quality
+    cdef kstring_t buf
+    cdef char * reference_sequence
+
+cdef class PileupRead:
+    cdef int32_t  _qpos
+    cdef AlignedSegment _alignment
+    cdef int _indel
+    cdef int _level
+    cdef uint32_t _is_del
+    cdef uint32_t _is_head
+    cdef uint32_t _is_tail
+    cdef uint32_t _is_refskip
+
+# factory methods
+cdef AlignedSegment makeAlignedSegment(
+    bam1_t * src,
+    AlignmentHeader header)
+
+cdef PileupColumn makePileupColumn(
+    const bam_pileup1_t ** plp,
+    int tid,
+    int pos,
+    int n_pu,
+    uint32_t min_base_quality,
+    char * reference_sequence,
+    AlignmentHeader header)
+
+cdef PileupRead makePileupRead(const bam_pileup1_t * src,
+		               AlignmentHeader header)
+
+cdef uint32_t get_alignment_length(bam1_t * src)
diff --git a/pysam/libcalignedsegment.pyi b/pysam/libcalignedsegment.pyi
new file mode 100644
index 0000000..4e4b1d6
--- /dev/null
+++ b/pysam/libcalignedsegment.pyi
@@ -0,0 +1,222 @@
+import enum
+import re
+import sys
+from array import array
+from typing import Any, List, Optional, Dict, Tuple, Union, overload
+
+if sys.version_info < (3, 8):
+    from typing_extensions import Literal
+else:
+    from typing import Literal
+
+from pysam import AlignmentHeader  # type: ignore
+
+CMATCH: int
+CINS: int
+CDEL: int
+CREF_SKIP: int
+CSOFT_CLIP: int
+CHARD_CLIP: int
+CPAD: int
+CEQUAL: int
+CDIFF: int
+CBACK: int
+
+FPAIRED: int
+FPROPER_PAIR: int
+FUNMAP: int
+FMUNMAP: int
+FREVERSE: int
+FMREVERSE: int
+FREAD1: int
+FREAD2: int
+FSECONDARY: int
+FQCFAIL: int
+FDUP: int
+FSUPPLEMENTARY: int
+
+CIGAR2CODE: Dict[int, str]
+CIGAR_REGEX: re.Pattern
+DATATYPE2FORMAT: Dict[int, Tuple[str, int]]
+KEY_NAMES: List[str]
+
+TagValue = Union[str, int, float, array]
+
+class CIGAR_OPS(enum.IntEnum):
+    CBACK: int
+    CDEL: int
+    CDIFF: int
+    CEQUAL: int
+    CHARD_CLIP: int
+    CINS: int
+    CMATCH: int
+    CPAD: int
+    CREF_SKIP: int
+    CSOFT_CLIP: int
+
+class SAM_FLAGS(enum.IntEnum):
+    FDUP: int
+    FMREVERSE: int
+    FMUNMAP: int
+    FPAIRED: int
+    FPROPER_PAIR: int
+    FQCFAIL: int
+    FREAD1: int
+    FREAD2: int
+    FREVERSE: int
+    FSECONDARY: int
+    FSUPPLEMENTARY: int
+    FUNMAP: int
+
+class AlignedSegment:
+    header: AlignmentHeader
+    query_name: Optional[str]
+    flag: int
+    reference_name: Optional[str]
+    reference_id: int
+    reference_start: int
+    mapping_quality: int
+    cigarstring: Optional[str]
+    next_reference_id: int
+    next_reference_name: Optional[str]
+    next_reference_start: int
+    template_length: int
+    query_sequence: Optional[str]
+    query_qualities: Optional[array]
+    bin: int
+    is_paired: bool
+    is_proper_pair: bool
+    is_unmapped: bool
+    mate_is_unmapped: bool
+    is_reverse: bool
+    mate_is_reverse: bool
+    is_read1: bool
+    is_read2: bool
+    is_secondary: bool
+    is_qcfail: bool
+    is_duplicate: bool
+    is_supplementary: bool
+    cigartuples: Optional[List[Tuple[int, int]]]
+    def __init__(self, header: Optional[AlignmentHeader] = ...) -> None: ...
+    def compare(self, other: Any) -> int: ...
+    def to_string(self) -> str: ...
+    @classmethod
+    def fromstring(cls, sam: str, header: AlignmentHeader) -> AlignedSegment: ...
+    def to_dict(self) -> Dict: ...
+    @classmethod
+    def from_dict(cls, sam_dict: Dict[str, Any], header: AlignmentHeader) -> Any: ...
+    def get_reference_positions(self, full_length: bool = ...) -> List[int]: ...
+    @property
+    def query_length(self) -> int: ...
+    @property
+    def reference_end(self) -> Optional[int]: ...
+    @property
+    def reference_length(self) -> Optional[int]: ...
+    @property
+    def query_alignment_sequence(self) -> Optional[str]: ...
+    @property
+    def query_alignment_qualities(self) -> Optional[array]: ...
+    @property
+    def query_alignment_start(self) -> int: ...
+    @property
+    def query_alignment_end(self) -> int: ...
+    @property
+    def query_alignment_length(self) -> int: ...
+    def infer_query_length(self) -> Optional[int]: ...
+    def infer_read_length(self) -> Optional[int]: ...
+    def get_reference_sequence(self) -> str: ...
+    def get_forward_sequence(self) -> Optional[str]: ...
+    def get_forward_qualities(self) -> Optional[array]: ...
+    def get_aligned_pairs(
+        self, matches_only: bool = ..., with_seq: bool = ...
+    ) -> List[Tuple[int, int]]: ...
+    def get_blocks(self) -> List[Tuple[int, int]]: ...
+    def get_overlap(self, start: int, end: int) -> Optional[int]: ...
+    def get_cigar_stats(self) -> Tuple[array, array]: ...
+    def set_tag(
+        self,
+        tag: str,
+        value: Union[int, float, str, bytes, array, List, Tuple, None],
+        value_type: Optional[
+            Literal["A", "i", "f", "Z", "H", "B", "c", "C", "s", "S", "I"]
+        ] = ...,
+        replace: bool = ...,
+    ) -> None: ...
+    def has_tag(self, tag: str) -> bool: ...
+    @overload
+    def get_tag(self, tag: str, with_value_type: Literal[False] = ...) -> TagValue: ...
+    @overload
+    def get_tag(
+        self, tag: str, with_value_type: Literal[True]
+    ) -> Tuple[TagValue, str]: ...
+    @overload
+    def get_tag(
+        self, tag: str, with_value_type: bool
+    ) -> Union[TagValue, Tuple[TagValue, str]]: ...
+    @overload
+    def get_tags(
+        self, with_value_type: Literal[False] = ...
+    ) -> List[Tuple[str, TagValue]]: ...
+    @overload
+    def get_tags(
+        self, with_value_type: Literal[True]
+    ) -> List[Tuple[str, TagValue, str]]: ...
+    @overload
+    def get_tags(
+        self, with_value_type: bool
+    ) -> Union[List[Tuple[str, TagValue]], List[Tuple[str, TagValue, str]]]: ...
+    @overload
+    def get_tags(
+        self, with_value_type: bool = ...
+    ) -> Union[List[Tuple[str, TagValue, str]], List[Tuple[str, TagValue]]]: ...
+    def set_tags(self, tags: Any) -> None: ...
+    def __eq__(self, other): ...
+    def __ge__(self, other): ...
+    def __gt__(self, other): ...
+    def __le__(self, other): ...
+    def __lt__(self, other): ...
+    def __ne__(self, other): ...
+
+class PileupRead:
+    @property
+    def alignment(self) -> AlignedSegment: ...
+    @property
+    def query_position(self) -> Optional[int]: ...
+    @property
+    def query_position_or_next(self) -> int: ...
+    @property
+    def indel(self) -> int: ...
+    @property
+    def level(self) -> int: ...
+    @property
+    def is_del(self) -> int: ...
+    @property
+    def is_head(self) -> int: ...
+    @property
+    def is_tail(self) -> int: ...
+    @property
+    def is_refskip(self) -> int: ...
+
+class PileupColumn:
+    nsegments: int
+    def set_min_base_quality(self, min_base_quality: int) -> None: ...
+    def __len__(self) -> int: ...
+    @property
+    def reference_id(self) -> int: ...
+    @property
+    def reference_name(self) -> Optional[str]: ...
+    @property
+    def reference_pos(self) -> int: ...
+    @property
+    def pileups(self) -> List[PileupRead]: ...
+    def get_num_aligned(self) -> int: ...
+    def get_query_sequences(
+        self,
+        mark_matches: bool = ...,
+        mark_ends: bool = ...,
+        add_indels: bool = ...,
+    ) -> List[str]: ...
+    def get_query_qualities(self) -> List[int]: ...
+    def get_mapping_qualities(self) -> List[int]: ...
+    def get_query_positions(self) -> List[int]: ...
+    def get_query_names(self) -> List[str]: ...
diff --git a/pysam/libcalignedsegment.pyx b/pysam/libcalignedsegment.pyx
new file mode 100644
index 0000000..810a861
--- /dev/null
+++ b/pysam/libcalignedsegment.pyx
@@ -0,0 +1,3409 @@
+# cython: embedsignature=True
+# cython: profile=True
+###############################################################################
+###############################################################################
+# Cython wrapper for SAM/BAM/CRAM files based on htslib
+###############################################################################
+# The principal classes defined in this module are:
+#
+# class AlignedSegment  an aligned segment (read)
+#
+# class PileupColumn    a collection of segments (PileupRead) aligned to
+#                       a particular genomic position.
+#
+# class PileupRead      an AlignedSegment aligned to a particular genomic
+#                       position. Contains additional attributes with respect
+#                       to this.
+#
+# Additionally this module defines numerous additional classes that are part
+# of the internal API. These are:
+#
+# Various iterator classes to iterate over alignments in sequential (IteratorRow)
+# or in a stacked fashion (IteratorColumn):
+#
+# class IteratorRow
+# class IteratorRowRegion
+# class IteratorRowHead
+# class IteratorRowAll
+# class IteratorRowAllRefs
+# class IteratorRowSelection
+#
+###############################################################################
+#
+# The MIT License
+#
+# Copyright (c) 2015 Andreas Heger
+#
+# Permission is hereby granted, free of charge, to any person obtaining a
+# copy of this software and associated documentation files (the "Software"),
+# to deal in the Software without restriction, including without limitation
+# the rights to use, copy, modify, merge, publish, distribute, sublicense,
+# and/or sell copies of the Software, and to permit persons to whom the
+# Software is furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.  IN NO EVENT SHALL
+# THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+# DEALINGS IN THE SOFTWARE.
+#
+###############################################################################
+import re
+import array
+import json
+import string
+import ctypes
+import struct
+
+cimport cython
+from cpython cimport array as c_array
+from cpython.version cimport PY_MAJOR_VERSION
+from cpython cimport PyBytes_FromStringAndSize
+from libc.string cimport memset, strchr
+from cpython cimport array as c_array
+from libc.stdint cimport INT8_MIN, INT16_MIN, INT32_MIN, \
+    INT8_MAX, INT16_MAX, INT32_MAX, \
+    UINT8_MAX, UINT16_MAX, UINT32_MAX
+
+from pysam.libchtslib cimport HTS_IDX_NOCOOR
+from pysam.libcutils cimport force_bytes, force_str, \
+    charptr_to_str, charptr_to_bytes
+from pysam.libcutils cimport qualities_to_qualitystring, qualitystring_to_array, \
+    array_to_qualitystring
+
+# Constants for binary tag conversion
+cdef char * htslib_types = 'cCsSiIf'
+cdef char * parray_types = 'bBhHiIf'
+
+cdef bint IS_PYTHON3 = PY_MAJOR_VERSION >= 3
+
+# translation tables
+
+# cigar code to character and vice versa
+cdef char* CODE2CIGAR= "MIDNSHP=XB"
+cdef int NCIGAR_CODES = 10
+
+if IS_PYTHON3:
+    CIGAR2CODE = dict([y, x] for x, y in enumerate(CODE2CIGAR))
+    maketrans = str.maketrans
+else:
+    CIGAR2CODE = dict([ord(y), x] for x, y in enumerate(CODE2CIGAR))
+    maketrans = string.maketrans
+
+CIGAR_REGEX = re.compile("(\d+)([MIDNSHP=XB])")
+
+# names for keys in dictionary representation of an AlignedSegment
+KEY_NAMES = ["name", "flag", "ref_name", "ref_pos", "map_quality", "cigar",
+             "next_ref_name", "next_ref_pos", "length", "seq", "qual", "tags"]
+
+#####################################################################
+# C multiplication with wrapping around
+cdef inline uint32_t c_mul(uint32_t a, uint32_t b):
+    return (a * b) & 0xffffffff
+
+
+cdef inline uint8_t tolower(uint8_t ch):
+    if ch >= 65 and ch <= 90:
+        return ch + 32
+    else:
+        return ch
+
+
+cdef inline uint8_t toupper(uint8_t ch):
+    if ch >= 97 and ch <= 122:
+        return ch - 32
+    else:
+        return ch
+
+
+cdef inline uint8_t strand_mark_char(uint8_t ch, bam1_t *b):
+    if ch == '=':
+        if bam_is_rev(b):
+            return ','
+        else:
+            return '.'
+    else:
+        if bam_is_rev(b):
+            return tolower(ch)
+        else:
+            return toupper(ch)
+
+
+cdef inline bint pileup_base_qual_skip(const bam_pileup1_t * p, uint32_t threshold):
+    cdef uint32_t c
+    if p.qpos < p.b.core.l_qseq:
+        c = bam_get_qual(p.b)[p.qpos]
+    else:
+        c = 0
+    if c < threshold:
+        return True
+    return False
+
+
+cdef inline char map_typecode_htslib_to_python(uint8_t s):
+    """map an htslib typecode to the corresponding python typecode
+    to be used in the struct or array modules."""
+
+    # map type from htslib to python array
+    cdef char * f = strchr(htslib_types, s)
+
+    if f == NULL:
+        return 0
+    return parray_types[f - htslib_types]
+
+
+cdef inline uint8_t map_typecode_python_to_htslib(char s):
+    """determine value type from type code of array"""
+    cdef char * f = strchr(parray_types, s)
+    if f == NULL:
+        return 0
+    return htslib_types[f - parray_types]
+
+
+cdef inline void update_bin(bam1_t * src):
+    if src.core.flag & BAM_FUNMAP:
+        # treat alignment as length of 1 for unmapped reads
+        src.core.bin = hts_reg2bin(
+            src.core.pos,
+            src.core.pos + 1,
+            14,
+            5)
+    elif pysam_get_n_cigar(src):
+        src.core.bin = hts_reg2bin(
+            src.core.pos,
+            bam_endpos(src),
+            14,
+            5)
+    else:
+        src.core.bin = hts_reg2bin(
+            src.core.pos,
+            src.core.pos + 1,
+            14,
+            5)
+
+
+# optional tag data manipulation
+cdef convert_binary_tag(uint8_t * tag):
+    """return bytesize, number of values and array of values
+    in aux_data memory location pointed to by tag."""
+    cdef uint8_t auxtype
+    cdef uint8_t byte_size
+    cdef int32_t nvalues
+    # get byte size
+    auxtype = tag[0]
+    byte_size = aux_type2size(auxtype)
+    tag += 1
+    # get number of values in array
+    nvalues = (<int32_t*>tag)[0]
+    tag += 4
+
+    # define python array
+    cdef c_array.array c_values = array.array(
+        chr(map_typecode_htslib_to_python(auxtype)))
+    c_array.resize(c_values, nvalues)
+
+    # copy data
+    memcpy(c_values.data.as_voidptr, <uint8_t*>tag, nvalues * byte_size)
+
+    # no need to check for endian-ness as bam1_core_t fields
+    # and aux_data are in host endian-ness. See sam.c and calls
+    # to swap_data
+    return byte_size, nvalues, c_values
+
+
+cdef inline uint8_t get_tag_typecode(value, value_type=None):
+    """guess type code for a *value*. If *value_type* is None, the type
+    code will be inferred based on the Python type of *value*
+
+    """
+    # 0 is unknown typecode
+    cdef char typecode = 0
+
+    if value_type is None:
+        if isinstance(value, int):
+            if value < 0:
+                if value >= INT8_MIN:
+                    typecode = 'c'
+                elif value >= INT16_MIN:
+                    typecode = 's'
+                elif value >= INT32_MIN:
+                    typecode = 'i'
+            # unsigned ints
+            else:
+                if value <= UINT8_MAX:
+                    typecode = 'C'
+                elif value <= UINT16_MAX:
+                    typecode = 'S'
+                elif value <= UINT32_MAX:
+                    typecode = 'I'
+        elif isinstance(value, float):
+            typecode = 'f'
+        elif isinstance(value, str):
+            typecode = 'Z'
+        elif isinstance(value, bytes):
+            typecode = 'Z'
+        elif isinstance(value, array.array) or \
+                isinstance(value, list) or \
+                isinstance(value, tuple):
+            typecode = 'B'
+    else:
+        if value_type in 'aAsSIcCZidfH':
+            typecode = force_bytes(value_type)[0]
+
+    return typecode
+
+
+cdef inline uint8_t get_btag_typecode(value, min_value=None, max_value=None):
+    '''returns the value typecode of a value.
+
+    If max is specified, the appropriate type is returned for a range
+    where value is the minimum.
+
+    Note that this method returns types from the extended BAM alphabet
+    of types that includes tags that are not part of the SAM
+    specification.
+    '''
+
+
+    cdef uint8_t typecode
+
+    t = type(value)
+
+    if t is float:
+        typecode = 'f'
+    elif t is int:
+        if max_value is None:
+            max_value = value
+        if min_value is None:
+            min_value = value
+        # signed ints
+        if min_value < 0:
+            if min_value >= INT8_MIN and max_value <= INT8_MAX:
+                typecode = 'c'
+            elif min_value >= INT16_MIN and max_value <= INT16_MAX:
+                typecode = 's'
+            elif min_value >= INT32_MIN or max_value <= INT32_MAX:
+                typecode = 'i'
+            else:
+                raise ValueError(
+                    "at least one signed integer out of range of "
+                    "BAM/SAM specification")
+        # unsigned ints
+        else:
+            if max_value <= UINT8_MAX:
+                typecode = 'C'
+            elif max_value <= UINT16_MAX:
+                typecode = 'S'
+            elif max_value <= UINT32_MAX:
+                typecode = 'I'
+            else:
+                raise ValueError(
+                    "at least one integer out of range of BAM/SAM specification")
+    else:
+        # Note: hex strings (H) are not supported yet
+        if t is not bytes:
+            value = value.encode('ascii')
+        if len(value) == 1:
+            typecode = 'A'
+        else:
+            typecode = 'Z'
+
+    return typecode
+
+
+# mapping python array.array and htslib typecodes to struct typecodes
+DATATYPE2FORMAT = {
+    ord('c'): ('b', 1),
+    ord('C'): ('B', 1),
+    ord('s'): ('h', 2),
+    ord('S'): ('H', 2),
+    ord('i'): ('i', 4),
+    ord('I'): ('I', 4),
+    ord('f'): ('f', 4),
+    ord('d'): ('d', 8),
+    ord('A'): ('c', 1),
+    ord('a'): ('c', 1)}
+
+
+cdef inline pack_tags(tags):
+    """pack a list of tags. Each tag is a tuple of (tag, tuple).
+
+    Values are packed into the most space efficient data structure
+    possible unless the tag contains a third field with the typecode.
+
+    Returns a format string and the associated list of arguments to be
+    used in a call to struct.pack_into.
+    """
+    fmts, args = ["<"], []
+
+    # htslib typecode
+    cdef uint8_t typecode
+    for tag in tags:
+
+        if len(tag) == 2:
+            pytag, value = tag
+            valuetype = None
+        elif len(tag) == 3:
+            pytag, value, valuetype = tag
+        else:
+            raise ValueError("malformatted tag: %s" % str(tag))
+
+        if valuetype is None:
+            typecode = 0
+        else:
+            # only first character in valuecode matters
+            if IS_PYTHON3:
+                typecode = force_bytes(valuetype)[0]
+            else:
+                typecode = ord(valuetype[0])
+
+        pytag = force_bytes(pytag)
+        pytype = type(value)
+
+        if pytype is tuple or pytype is list:
+            # binary tags from tuples or lists
+            if not typecode:
+                # automatically determine value type - first value
+                # determines type. If there is a mix of types, the
+                # result is undefined.
+                typecode = get_btag_typecode(min(value),
+                                             min_value=min(value),
+                                             max_value=max(value))
+
+            if typecode not in DATATYPE2FORMAT:
+                raise ValueError("invalid value type '{}'".format(chr(typecode)))
+
+            datafmt = "2sBBI%i%s" % (len(value), DATATYPE2FORMAT[typecode][0])
+            args.extend([pytag[:2],
+                         ord("B"),
+                         typecode,
+                         len(value)] + list(value))
+
+        elif isinstance(value, array.array):
+            # binary tags from arrays
+            if typecode == 0:
+                typecode = map_typecode_python_to_htslib(ord(value.typecode))
+
+                if typecode == 0:
+                    raise ValueError("unsupported type code '{}'".format(value.typecode))
+
+            if typecode not in DATATYPE2FORMAT:
+                raise ValueError("invalid value type '{}' ({})".format(chr(typecode), array.typecode))
+
+            # use array.tostring() to retrieve byte representation and
+            # save as bytes
+            datafmt = "2sBBI%is" % (len(value) * DATATYPE2FORMAT[typecode][1])
+            if IS_PYTHON3:
+                args.extend([pytag[:2],
+                             ord("B"),
+                             typecode,
+                             len(value),
+                             value.tobytes()])
+            else:
+                args.extend([pytag[:2],
+                             ord("B"),
+                             typecode,
+                             len(value),
+                             force_bytes(value.tostring())])
+
+        else:
+            if typecode == 0:
+                typecode = get_tag_typecode(value)
+                if typecode == 0:
+                    raise ValueError("could not deduce typecode for value {}".format(value))
+
+            if typecode == 'a' or typecode == 'A' or typecode == 'Z' or typecode == 'H':
+                value = force_bytes(value)
+
+            if typecode == "a":
+                typecode = 'A'
+
+            if typecode == 'Z' or typecode == 'H':
+                datafmt = "2sB%is" % (len(value)+1)
+            else:
+                datafmt = "2sB%s" % DATATYPE2FORMAT[typecode][0]
+
+            args.extend([pytag[:2],
+                         typecode,
+                         value])
+
+        fmts.append(datafmt)
+
+    return "".join(fmts), args
+
+
+cdef inline int32_t calculateQueryLengthWithoutHardClipping(bam1_t * src):
+    """return query length computed from CIGAR alignment.
+
+    Length ignores hard-clipped bases.
+
+    Return 0 if there is no CIGAR alignment.
+    """
+
+    cdef uint32_t * cigar_p = pysam_bam_get_cigar(src)
+
+    if cigar_p == NULL:
+        return 0
+
+    cdef uint32_t k, qpos
+    cdef int op
+    qpos = 0
+
+    for k from 0 <= k < pysam_get_n_cigar(src):
+        op = cigar_p[k] & BAM_CIGAR_MASK
+
+        if op == BAM_CMATCH or \
+           op == BAM_CINS or \
+           op == BAM_CSOFT_CLIP or \
+           op == BAM_CEQUAL or \
+           op == BAM_CDIFF:
+            qpos += cigar_p[k] >> BAM_CIGAR_SHIFT
+
+    return qpos
+
+
+cdef inline int32_t calculateQueryLengthWithHardClipping(bam1_t * src):
+    """return query length computed from CIGAR alignment.
+
+    Length includes hard-clipped bases.
+
+    Return 0 if there is no CIGAR alignment.
+    """
+
+    cdef uint32_t * cigar_p = pysam_bam_get_cigar(src)
+
+    if cigar_p == NULL:
+        return 0
+
+    cdef uint32_t k, qpos
+    cdef int op
+    qpos = 0
+
+    for k from 0 <= k < pysam_get_n_cigar(src):
+        op = cigar_p[k] & BAM_CIGAR_MASK
+
+        if op == BAM_CMATCH or \
+           op == BAM_CINS or \
+           op == BAM_CSOFT_CLIP or \
+           op == BAM_CHARD_CLIP or \
+           op == BAM_CEQUAL or \
+           op == BAM_CDIFF:
+            qpos += cigar_p[k] >> BAM_CIGAR_SHIFT
+
+    return qpos
+
+
+cdef inline int32_t getQueryStart(bam1_t *src) except -1:
+    cdef uint32_t * cigar_p
+    cdef uint32_t start_offset = 0
+    cdef uint32_t k, op
+
+    cigar_p = pysam_bam_get_cigar(src);
+    for k from 0 <= k < pysam_get_n_cigar(src):
+        op = cigar_p[k] & BAM_CIGAR_MASK
+        if op == BAM_CHARD_CLIP:
+            if start_offset != 0 and start_offset != src.core.l_qseq:
+                raise ValueError('Invalid clipping in CIGAR string')
+        elif op == BAM_CSOFT_CLIP:
+            start_offset += cigar_p[k] >> BAM_CIGAR_SHIFT
+        else:
+            break
+
+    return start_offset
+
+
+cdef inline int32_t getQueryEnd(bam1_t *src) except -1:
+    cdef uint32_t * cigar_p = pysam_bam_get_cigar(src)
+    cdef uint32_t end_offset = src.core.l_qseq
+    cdef uint32_t k, op
+
+    # if there is no sequence, compute length from cigar string
+    if end_offset == 0:
+        for k from 0 <= k < pysam_get_n_cigar(src):
+            op = cigar_p[k] & BAM_CIGAR_MASK
+            if op == BAM_CMATCH or \
+               op == BAM_CINS or \
+               op == BAM_CEQUAL or \
+               op == BAM_CDIFF or \
+              (op == BAM_CSOFT_CLIP and end_offset == 0):
+                end_offset += cigar_p[k] >> BAM_CIGAR_SHIFT
+    else:
+        # walk backwards in cigar string
+        for k from pysam_get_n_cigar(src) > k >= 1:
+            op = cigar_p[k] & BAM_CIGAR_MASK
+            if op == BAM_CHARD_CLIP:
+                if end_offset != src.core.l_qseq:
+                    raise ValueError('Invalid clipping in CIGAR string')
+            elif op == BAM_CSOFT_CLIP:
+                end_offset -= cigar_p[k] >> BAM_CIGAR_SHIFT
+            else:
+                break
+
+    return end_offset
+
+
+cdef inline bytes getSequenceInRange(bam1_t *src,
+                                     uint32_t start,
+                                     uint32_t end):
+    """return python string of the sequence in a bam1_t object.
+    """
+
+    cdef uint8_t * p
+    cdef uint32_t k
+    cdef char * s
+
+    if not src.core.l_qseq:
+        return None
+
+    seq = PyBytes_FromStringAndSize(NULL, end - start)
+    s   = <char*>seq
+    p   = pysam_bam_get_seq(src)
+
+    for k from start <= k < end:
+        # equivalent to seq_nt16_str[bam1_seqi(s, i)] (see bam.c)
+        # note: do not use string literal as it will be a python string
+        s[k-start] = seq_nt16_str[p[k/2] >> 4 * (1 - k%2) & 0xf]
+
+    return charptr_to_bytes(seq)
+
+
+cdef inline object getQualitiesInRange(bam1_t *src,
+                                       uint32_t start,
+                                       uint32_t end):
+    """return python array of quality values from a bam1_t object"""
+
+    cdef uint8_t * p
+    cdef uint32_t k
+
+    p = pysam_bam_get_qual(src)
+    if p[0] == 0xff:
+        return None
+
+    # 'B': unsigned char
+    cdef c_array.array result = array.array('B', [0])
+    c_array.resize(result, end - start)
+
+    # copy data
+    memcpy(result.data.as_voidptr, <void*>&p[start], end - start)
+
+    return result
+
+
+#####################################################################
+## factory methods for instantiating extension classes
+cdef class AlignedSegment
+cdef AlignedSegment makeAlignedSegment(bam1_t *src,
+                                       AlignmentHeader header):
+    '''return an AlignedSegment object constructed from `src`'''
+    # note that the following does not call __init__
+    cdef AlignedSegment dest = AlignedSegment.__new__(AlignedSegment)
+    dest._delegate = bam_dup1(src)
+    dest.header = header
+    return dest
+
+
+cdef class PileupColumn
+cdef PileupColumn makePileupColumn(const bam_pileup1_t ** plp,
+                      int tid,
+                      int pos,
+                      int n_pu,
+                      uint32_t min_base_quality,
+                      char * reference_sequence,
+                      AlignmentHeader header):
+    '''return a PileupColumn object constructed from pileup in `plp` and
+    setting additional attributes.
+
+    '''
+    # note that the following does not call __init__
+    cdef PileupColumn dest = PileupColumn.__new__(PileupColumn)
+    dest.header = header
+    dest.plp = plp
+    dest.tid = tid
+    dest.pos = pos
+    dest.n_pu = n_pu
+    dest.min_base_quality = min_base_quality
+    dest.reference_sequence = reference_sequence
+    dest.buf.l = dest.buf.m = 0
+    dest.buf.s = NULL
+
+    return dest
+
+
+cdef class PileupRead
+cdef PileupRead makePileupRead(const bam_pileup1_t *src,
+                               AlignmentHeader header):
+    '''return a PileupRead object construted from a bam_pileup1_t * object.'''
+    # note that the following does not call __init__
+    cdef PileupRead dest = PileupRead.__new__(PileupRead)
+    dest._alignment = makeAlignedSegment(src.b, header)
+    dest._qpos = src.qpos
+    dest._indel = src.indel
+    dest._level = src.level
+    dest._is_del = src.is_del
+    dest._is_head = src.is_head
+    dest._is_tail = src.is_tail
+    dest._is_refskip = src.is_refskip
+    return dest
+
+
+cdef inline uint32_t get_alignment_length(bam1_t *src):
+    cdef uint32_t k = 0
+    cdef uint32_t l = 0
+    if src == NULL:
+        return 0
+    cdef uint32_t * cigar_p = bam_get_cigar(src)
+    if cigar_p == NULL:
+        return 0
+    cdef int op
+    cdef uint32_t n = pysam_get_n_cigar(src)
+    for k from 0 <= k < n:
+        op = cigar_p[k] & BAM_CIGAR_MASK
+        if op == BAM_CSOFT_CLIP or op == BAM_CHARD_CLIP:
+            continue
+        l += cigar_p[k] >> BAM_CIGAR_SHIFT
+    return l
+
+
+cdef inline uint32_t get_md_reference_length(char * md_tag):
+    cdef int l = 0
+    cdef int md_idx = 0
+    cdef int nmatches = 0
+
+    while md_tag[md_idx] != 0:
+        if md_tag[md_idx] >= 48 and md_tag[md_idx] <= 57:
+            nmatches *= 10
+            nmatches += md_tag[md_idx] - 48
+            md_idx += 1
+            continue
+        else:
+            l += nmatches
+            nmatches = 0
+            if md_tag[md_idx] == '^':
+                md_idx += 1
+                while md_tag[md_idx] >= 65 and md_tag[md_idx] <= 90:
+                    md_idx += 1
+                    l += 1
+            else:
+                md_idx += 1
+                l += 1
+
+    l += nmatches
+    return l
+
+# TODO: avoid string copying for getSequenceInRange, reconstituneSequenceFromMD, ...
+cdef inline bytes build_alignment_sequence(bam1_t * src):
+    """return expanded sequence from MD tag.
+
+    The sequence includes substitutions and both insertions in the
+    reference as well as deletions to the reference sequence. Combine
+    with the cigar string to reconstitute the query or the reference
+    sequence.
+
+    Positions corresponding to `N` (skipped region from the reference)
+    or `P` (padding (silent deletion from padded reference)) in the CIGAR
+    string will not appear in the returned sequence. The MD should
+    correspondingly not contain these. Thus proper tags are::
+
+       Deletion from the reference:    cigar=5M1D5M    MD=5^C5
+       Skipped region from reference:  cigar=5M1N5M    MD=10
+       Padded region in the reference: cigar=5M1P5M    MD=10
+
+    Returns
+    -------
+
+    None, if no MD tag is present.
+
+    """
+    if src == NULL:
+        return None
+
+    cdef uint8_t * md_tag_ptr = bam_aux_get(src, "MD")
+    if md_tag_ptr == NULL:
+        return None
+
+    cdef uint32_t start = getQueryStart(src)
+    cdef uint32_t end = getQueryEnd(src)
+    # get read sequence, taking into account soft-clipping
+    r = getSequenceInRange(src, start, end)
+    cdef char * read_sequence = r
+    cdef uint32_t * cigar_p = pysam_bam_get_cigar(src)
+    if cigar_p == NULL:
+        return None
+
+    cdef uint32_t r_idx = 0
+    cdef int op
+    cdef uint32_t k, i, l, x
+    cdef int nmatches = 0
+    cdef int s_idx = 0
+
+    cdef uint32_t max_len = get_alignment_length(src)
+    if max_len == 0:
+        raise ValueError("could not determine alignment length")
+
+    cdef char * s = <char*>calloc(max_len + 1, sizeof(char))
+    if s == NULL:
+        raise ValueError(
+            "could not allocate sequence of length %i" % max_len)
+
+    for k from 0 <= k < pysam_get_n_cigar(src):
+        op = cigar_p[k] & BAM_CIGAR_MASK
+        l = cigar_p[k] >> BAM_CIGAR_SHIFT
+        if op == BAM_CMATCH or op == BAM_CEQUAL or op == BAM_CDIFF:
+            for i from 0 <= i < l:
+                s[s_idx] = read_sequence[r_idx]
+                r_idx += 1
+                s_idx += 1
+        elif op == BAM_CDEL:
+            for i from 0 <= i < l:
+                s[s_idx] = '-'
+                s_idx += 1
+        elif op == BAM_CREF_SKIP:
+            pass
+        elif op == BAM_CINS or op == BAM_CPAD:
+            for i from 0 <= i < l:
+                # encode insertions into reference as lowercase
+                s[s_idx] = read_sequence[r_idx] + 32
+                r_idx += 1
+                s_idx += 1
+        elif op == BAM_CSOFT_CLIP:
+            pass
+        elif op == BAM_CHARD_CLIP:
+            pass # advances neither
+
+    cdef char * md_tag = <char*>bam_aux2Z(md_tag_ptr)
+    cdef int md_idx = 0
+    cdef char c
+    s_idx = 0
+
+    # Check if MD tag is valid by matching CIGAR length to MD tag defined length
+    # Insertions would be in addition to what is described by MD, so we calculate
+    # the number of insertions separately.
+    cdef int insertions = 0
+
+    while s[s_idx] != 0:
+        if s[s_idx] >= 'a':
+            insertions += 1
+        s_idx += 1
+    s_idx = 0
+
+    cdef uint32_t md_len = get_md_reference_length(md_tag)
+    if md_len + insertions > max_len:
+        free(s)
+        raise AssertionError(
+            "Invalid MD tag: MD length {} mismatch with CIGAR length {} and {} insertions".format(
+            md_len, max_len, insertions))
+
+    while md_tag[md_idx] != 0:
+        # c is numerical
+        if md_tag[md_idx] >= 48 and md_tag[md_idx] <= 57:
+            nmatches *= 10
+            nmatches += md_tag[md_idx] - 48
+            md_idx += 1
+            continue
+        else:
+            # save matches up to this point, skipping insertions
+            for x from 0 <= x < nmatches:
+                while s[s_idx] >= 'a':
+                    s_idx += 1
+                s_idx += 1
+            while s[s_idx] >= 'a':
+                s_idx += 1
+
+            r_idx += nmatches
+            nmatches = 0
+            if md_tag[md_idx] == '^':
+                md_idx += 1
+                while md_tag[md_idx] >= 65 and md_tag[md_idx] <= 90:
+                    # assert s[s_idx] == '-'
+                    s[s_idx] = md_tag[md_idx]
+                    s_idx += 1
+                    md_idx += 1
+            else:
+                # save mismatch
+                # enforce lower case
+                c = md_tag[md_idx]
+                if c <= 90:
+                    c += 32
+                s[s_idx] = c
+                s_idx += 1
+                r_idx += 1
+                md_idx += 1
+
+    # save matches up to this point, skipping insertions
+    for x from 0 <= x < nmatches:
+        while s[s_idx] >= 'a':
+            s_idx += 1
+        s_idx += 1
+    while s[s_idx] >= 'a':
+        s_idx += 1
+
+    seq = PyBytes_FromStringAndSize(s, s_idx)
+    free(s)
+
+    return seq
+
+
+cdef inline bytes build_reference_sequence(bam1_t * src):
+    """return the reference sequence in the region that is covered by the
+    alignment of the read to the reference.
+
+    This method requires the MD tag to be set.
+
+    """
+    cdef uint32_t k, i, l
+    cdef int op
+    cdef int s_idx = 0
+    ref_seq = build_alignment_sequence(src)
+    if ref_seq is None:
+        raise ValueError("MD tag not present")
+
+    cdef char * s = <char*>calloc(len(ref_seq) + 1, sizeof(char))
+    if s == NULL:
+        raise ValueError(
+            "could not allocate sequence of length %i" % len(ref_seq))
+
+    cdef char * cref_seq = ref_seq
+    cdef uint32_t * cigar_p = pysam_bam_get_cigar(src)
+    cdef uint32_t r_idx = 0
+    for k from 0 <= k < pysam_get_n_cigar(src):
+        op = cigar_p[k] & BAM_CIGAR_MASK
+        l = cigar_p[k] >> BAM_CIGAR_SHIFT
+        if op == BAM_CMATCH or op == BAM_CEQUAL or op == BAM_CDIFF:
+            for i from 0 <= i < l:
+                s[s_idx] = cref_seq[r_idx]
+                r_idx += 1
+                s_idx += 1
+        elif op == BAM_CDEL:
+            for i from 0 <= i < l:
+                s[s_idx] = cref_seq[r_idx]
+                r_idx += 1
+                s_idx += 1
+        elif op == BAM_CREF_SKIP:
+            pass
+        elif op == BAM_CINS or op == BAM_CPAD:
+            r_idx += l
+        elif op == BAM_CSOFT_CLIP:
+            pass
+        elif op == BAM_CHARD_CLIP:
+            pass # advances neither
+
+    seq = PyBytes_FromStringAndSize(s, s_idx)
+    free(s)
+
+    return seq
+
+
+cdef class AlignedSegment:
+    '''Class representing an aligned segment.
+
+    This class stores a handle to the samtools C-structure representing
+    an aligned read. Member read access is forwarded to the C-structure
+    and converted into python objects. This implementation should be fast,
+    as only the data needed is converted.
+
+    For write access, the C-structure is updated in-place. This is
+    not the most efficient way to build BAM entries, as the variable
+    length data is concatenated and thus needs to be resized if
+    a field is updated. Furthermore, the BAM entry might be
+    in an inconsistent state.
+
+    One issue to look out for is that the sequence should always
+    be set *before* the quality scores. Setting the sequence will
+    also erase any quality scores that were set previously.
+
+    Parameters
+    ----------
+
+    header:
+         :class:`~pysam.AlignmentHeader` object to map numerical
+         identifiers to chromosome names. If not given, an empty
+         header is created.
+    '''
+
+    # Now only called when instances are created from Python
+    def __init__(self, AlignmentHeader header=None):
+        # see bam_init1
+        self._delegate = <bam1_t*>calloc(1, sizeof(bam1_t))
+        if self._delegate == NULL:
+            raise MemoryError("could not allocated memory of {} bytes".format(sizeof(bam1_t)))
+        # allocate some memory. If size is 0, calloc does not return a
+        # pointer that can be passed to free() so allocate 40 bytes
+        # for a new read
+        self._delegate.m_data = 40
+        self._delegate.data = <uint8_t *>calloc(
+            self._delegate.m_data, 1)
+        if self._delegate.data == NULL:
+            raise MemoryError("could not allocate memory of {} bytes".format(self._delegate.m_data))
+        self._delegate.l_data = 0
+        # set some data to make read approximately legit.
+        # Note, SAM writing fails with q_name of length 0
+        self._delegate.core.l_qname = 0
+        self._delegate.core.tid = -1
+        self._delegate.core.pos = -1
+        self._delegate.core.mtid = -1
+        self._delegate.core.mpos = -1
+
+        # caching for selected fields
+        self.cache_query_qualities = None
+        self.cache_query_alignment_qualities = None
+        self.cache_query_sequence = None
+        self.cache_query_alignment_sequence = None
+
+        self.header = header
+
+    def __dealloc__(self):
+        bam_destroy1(self._delegate)
+
+    def __str__(self):
+        """return string representation of alignment.
+
+        The representation is an approximate :term:`SAM` format, because
+        an aligned read might not be associated with a :term:`AlignmentFile`.
+        As a result :term:`tid` is shown instead of the reference name.
+        Similarly, the tags field is returned in its parsed state.
+
+        To get a valid SAM record, use :meth:`to_string`.
+        """
+        # sam-parsing is done in sam.c/bam_format1_core which
+        # requires a valid header.
+        return "\t".join(map(str, (self.query_name,
+                                   self.flag,
+                                   "#%d" % self.reference_id if self.reference_id >= 0 else "*",
+                                   self.reference_start + 1,
+                                   self.mapping_quality,
+                                   self.cigarstring,
+                                   "#%d" % self.next_reference_id if self.next_reference_id >= 0 else "*",
+                                   self.next_reference_start + 1,
+                                   self.template_length,
+                                   self.query_sequence,
+                                   self.query_qualities,
+                                   self.tags)))
+
+    def __copy__(self):
+        return makeAlignedSegment(self._delegate, self.header)
+
+    def __deepcopy__(self, memo):
+        return makeAlignedSegment(self._delegate, self.header)
+
+    def compare(self, AlignedSegment other):
+        '''return -1,0,1, if contents in this are binary
+        <,=,> to *other*
+        '''
+
+        # avoid segfault when other equals None
+        if other is None:
+            return -1
+
+        cdef int retval, x
+        cdef bam1_t *t
+        cdef bam1_t *o
+
+        t = self._delegate
+        o = other._delegate
+
+        # uncomment for debugging purposes
+        # cdef unsigned char * oo, * tt
+        # tt = <unsigned char*>(&t.core)
+        # oo = <unsigned char*>(&o.core)
+        # for x from 0 <= x < sizeof( bam1_core_t): print x, tt[x], oo[x]
+        # tt = <unsigned char*>(t.data)
+        # oo = <unsigned char*>(o.data)
+        # for x from 0 <= x < max(t.l_data, o.l_data): print x, tt[x], oo[x], chr(tt[x]), chr(oo[x])
+
+        # Fast-path test for object identity
+        if t == o:
+            return 0
+
+        cdef uint8_t *a = <uint8_t*>&t.core
+        cdef uint8_t *b = <uint8_t*>&o.core
+
+        retval = memcmp(&t.core, &o.core, sizeof(bam1_core_t))
+        if retval:
+            return retval
+
+        # cmp(t.l_data, o.l_data)
+        retval = (t.l_data > o.l_data) - (t.l_data < o.l_data)
+        if retval:
+            return retval
+        return memcmp(t.data, o.data, t.l_data)
+
+    def __richcmp__(self, AlignedSegment other, int op):
+        if op == 2:  # == operator
+            return self.compare(other) == 0
+        elif op == 3:  # != operator
+            return self.compare(other) != 0
+        else:
+            return NotImplemented
+
+    def __hash__(self):
+        cdef bam1_t * src = self._delegate
+        cdef int x
+
+        # see http://effbot.org/zone/python-hash.htm
+        cdef uint8_t * c = <uint8_t *>&src.core
+        cdef uint32_t hash_value = c[0]
+        for x from 1 <= x < sizeof(bam1_core_t):
+            hash_value = c_mul(hash_value, 1000003) ^ c[x]
+        c = <uint8_t *>src.data
+        for x from 0 <= x < src.l_data:
+            hash_value = c_mul(hash_value, 1000003) ^ c[x]
+
+        return hash_value
+
+    cpdef to_string(self):
+        """returns a string representation of the aligned segment.
+
+        The output format is valid SAM format if a header is associated
+        with the AlignedSegment.
+        """
+        cdef kstring_t line
+        line.l = line.m = 0
+        line.s = NULL
+
+        if self.header:
+            if sam_format1(self.header.ptr, self._delegate, &line) < 0:
+                if line.m:
+                    free(line.s)
+                raise ValueError('sam_format failed')
+        else:
+            raise NotImplementedError("todo")
+
+        ret = force_str(line.s[:line.l])
+
+        if line.m:
+            free(line.s)
+
+        return ret
+
+    @classmethod
+    def fromstring(cls, sam, AlignmentHeader header):
+        """parses a string representation of the aligned segment.
+
+        The input format should be valid SAM format.
+
+        Parameters
+        ----------
+        sam:
+            :term:`SAM` formatted string
+
+        """
+        cdef AlignedSegment dest = cls.__new__(cls)
+        dest._delegate = <bam1_t*>calloc(1, sizeof(bam1_t))
+        dest.header = header
+
+        cdef kstring_t line
+        line.l = line.m = len(sam)
+        _sam = force_bytes(sam)
+        line.s = _sam
+
+        sam_parse1(&line, dest.header.ptr, dest._delegate)
+
+        return dest
+
+    cpdef tostring(self, htsfile=None):
+        """deprecated, use :meth:`to_string()` instead.
+
+        Parameters
+        ----------
+
+        htsfile:
+            (deprecated) AlignmentFile object to map numerical
+            identifiers to chromosome names. This parameter is present
+            for backwards compatibility and ignored.
+        """
+
+        return self.to_string()
+
+    def to_dict(self):
+        """returns a json representation of the aligned segment.
+
+        Field names are abbreviated versions of the class attributes.
+        """
+        # let htslib do the string conversions, but treat optional field properly as list
+        vals = self.to_string().split("\t")
+        n = len(KEY_NAMES) - 1
+        return dict(list(zip(KEY_NAMES[:-1], vals[:n])) + [(KEY_NAMES[-1], vals[n:])])
+
+    @classmethod
+    def from_dict(cls, sam_dict, AlignmentHeader header):
+        """parses a dictionary representation of the aligned segment.
+
+        Parameters
+        ----------
+        sam_dict:
+            dictionary of alignment values, keys corresponding to output from
+            :meth:`todict()`.
+
+        """
+        # let htslib do the parsing
+        # the tags field can be missing
+        return cls.fromstring(
+            "\t".join((sam_dict[x] for x in KEY_NAMES[:-1])) +
+            "\t" +
+            "\t".join(sam_dict.get(KEY_NAMES[-1], [])), header)
+
+    ########################################################
+    ## Basic attributes in order of appearance in SAM format
+    property query_name:
+        """the query template name (None if not present)"""
+        def __get__(self):
+
+            cdef bam1_t * src = self._delegate
+            if src.core.l_qname == 0:
+                return None
+
+            return charptr_to_str(<char *>pysam_bam_get_qname(src))
+
+        def __set__(self, qname):
+
+            if qname is None or len(qname) == 0:
+                return
+
+            if len(qname) > 254:
+                raise ValueError("query length out of range {} > 254".format(
+                    len(qname)))
+
+            qname = force_bytes(qname)
+            cdef bam1_t * src = self._delegate
+            # the qname is \0 terminated
+            cdef uint8_t l = len(qname) + 1
+
+            cdef char * p = pysam_bam_get_qname(src)
+            cdef uint8_t l_extranul = 0
+
+            if l % 4 != 0:
+                l_extranul = 4 - l % 4
+
+            cdef bam1_t * retval = pysam_bam_update(src,
+                                                    src.core.l_qname,
+                                                    l + l_extranul,
+                                                    <uint8_t*>p)
+            if retval == NULL:
+                raise MemoryError("could not allocate memory")
+
+            src.core.l_extranul = l_extranul
+            src.core.l_qname = l + l_extranul
+
+            # re-acquire pointer to location in memory
+            # as it might have moved
+            p = pysam_bam_get_qname(src)
+
+            strncpy(p, qname, l)
+            # x might be > 255
+            cdef uint16_t x = 0
+
+            for x from l <= x < l + l_extranul:
+                p[x] = '\0'
+
+    property flag:
+        """properties flag"""
+        def __get__(self):
+            return self._delegate.core.flag
+        def __set__(self, flag):
+            self._delegate.core.flag = flag
+
+    property reference_name:
+        """:term:`reference` name"""
+        def __get__(self):
+            if self._delegate.core.tid == -1:
+                return None
+            if self.header:
+                return self.header.get_reference_name(self._delegate.core.tid)
+            else:
+                raise ValueError("reference_name unknown if no header associated with record")
+        def __set__(self, reference):
+            cdef int tid
+            if reference is None or reference == "*":
+                self._delegate.core.tid = -1
+            elif self.header:
+                tid = self.header.get_tid(reference)
+                if tid < 0:
+                    raise ValueError("reference {} does not exist in header".format(
+                        reference))
+                self._delegate.core.tid = tid
+            else:
+                raise ValueError("reference_name can not be set if no header associated with record")
+
+    property reference_id:
+        """:term:`reference` ID
+
+        .. note::
+
+            This field contains the index of the reference sequence in
+            the sequence dictionary. To obtain the name of the
+            reference sequence, use :meth:`get_reference_name()`
+
+        """
+        def __get__(self):
+            return self._delegate.core.tid
+        def __set__(self, tid):
+            if tid != -1 and self.header and not self.header.is_valid_tid(tid):
+                raise ValueError("reference id {} does not exist in header".format(
+                    tid))
+            self._delegate.core.tid = tid
+
+    property reference_start:
+        """0-based leftmost coordinate"""
+        def __get__(self):
+            return self._delegate.core.pos
+        def __set__(self, pos):
+            ## setting the position requires updating the "bin" attribute
+            cdef bam1_t * src
+            src = self._delegate
+            src.core.pos = pos
+            update_bin(src)
+
+    property mapping_quality:
+        """mapping quality"""
+        def __get__(self):
+            return pysam_get_qual(self._delegate)
+        def __set__(self, qual):
+            pysam_set_qual(self._delegate, qual)
+
+    property cigarstring:
+        '''the :term:`cigar` alignment as a string.
+
+        The cigar string is a string of alternating integers
+        and characters denoting the length and the type of
+        an operation.
+
+        .. note::
+            The order length,operation is specified in the
+            SAM format. It is different from the order of
+            the :attr:`cigar` property.
+
+        Returns None if not present.
+
+        To unset the cigarstring, assign None or the
+        empty string.
+        '''
+        def __get__(self):
+            c = self.cigartuples
+            if c is None:
+                return None
+            # reverse order
+            else:
+                return "".join([ "%i%c" % (y,CODE2CIGAR[x]) for x,y in c])
+
+        def __set__(self, cigar):
+            if cigar is None or len(cigar) == 0:
+                self.cigartuples = []
+            else:
+                parts = CIGAR_REGEX.findall(cigar)
+                # reverse order
+                self.cigartuples = [(CIGAR2CODE[ord(y)], int(x)) for x,y in parts]
+
+    # TODO
+    # property cigar:
+    #     """the cigar alignment"""
+
+    property next_reference_id:
+        """the :term:`reference` id of the mate/next read."""
+        def __get__(self):
+            return self._delegate.core.mtid
+        def __set__(self, mtid):
+            if mtid != -1 and self.header and not self.header.is_valid_tid(mtid):
+                raise ValueError("reference id {} does not exist in header".format(
+                    mtid))
+            self._delegate.core.mtid = mtid
+
+    property next_reference_name:
+        """:term:`reference` name of the mate/next read (None if no
+        AlignmentFile is associated)"""
+        def __get__(self):
+            if self._delegate.core.mtid == -1:
+                return None
+            if self.header:
+                return self.header.get_reference_name(self._delegate.core.mtid)
+            else:
+                raise ValueError("next_reference_name unknown if no header associated with record")
+
+        def __set__(self, reference):
+            cdef int mtid
+            if reference is None or reference == "*":
+                self._delegate.core.mtid = -1
+            elif reference == "=":
+                self._delegate.core.mtid = self._delegate.core.tid
+            elif self.header:
+                mtid = self.header.get_tid(reference)
+                if mtid < 0:
+                    raise ValueError("reference {} does not exist in header".format(
+                        reference))
+                self._delegate.core.mtid = mtid
+            else:
+                raise ValueError("next_reference_name can not be set if no header associated with record")
+
+    property next_reference_start:
+        """the position of the mate/next read."""
+        def __get__(self):
+            return self._delegate.core.mpos
+        def __set__(self, mpos):
+            self._delegate.core.mpos = mpos
+
+    property query_length:
+        """the length of the query/read.
+
+        This value corresponds to the length of the sequence supplied
+        in the BAM/SAM file. The length of a query is 0 if there is no
+        sequence in the BAM/SAM file. In those cases, the read length
+        can be inferred from the CIGAR alignment, see
+        :meth:`pysam.AlignedSegment.infer_query_length`.
+
+        The length includes soft-clipped bases and is equal to
+        ``len(query_sequence)``.
+
+        This property is read-only but is updated when a new query
+        sequence is assigned to this AlignedSegment.
+
+        Returns 0 if not available.
+
+        """
+        def __get__(self):
+            return self._delegate.core.l_qseq
+
+    property template_length:
+        """the observed query template length"""
+        def __get__(self):
+            return self._delegate.core.isize
+        def __set__(self, isize):
+            self._delegate.core.isize = isize
+
+    property query_sequence:
+        """read sequence bases, including :term:`soft clipped` bases
+        (None if not present).
+
+        Assigning to this attribute will invalidate any quality scores.
+        Thus, to in-place edit the sequence and quality scores, copies of
+        the quality scores need to be taken. Consider trimming for example::
+
+           q = read.query_qualities
+           read.query_sequence = read.query_sequence[5:10]
+           read.query_qualities = q[5:10]
+
+        The sequence is returned as it is stored in the BAM file. (This will
+        be the reverse complement of the original read sequence if the mapper
+        has aligned the read to the reverse strand.)
+        """
+        def __get__(self):
+            if self.cache_query_sequence:
+                return self.cache_query_sequence
+
+            cdef bam1_t * src
+            cdef char * s
+            src = self._delegate
+
+            if src.core.l_qseq == 0:
+                return None
+
+            self.cache_query_sequence = force_str(getSequenceInRange(
+                src, 0, src.core.l_qseq))
+            return self.cache_query_sequence
+
+        def __set__(self, seq):
+            # samtools manages sequence and quality length memory together
+            # if no quality information is present, the first byte says 0xff.
+            cdef bam1_t * src
+            cdef uint8_t * p
+            cdef char * s
+            cdef int l, k
+            cdef Py_ssize_t nbytes_new, nbytes_old
+
+            if seq == None:
+                l = 0
+            else:
+                l = len(seq)
+                seq = force_bytes(seq)
+
+            src = self._delegate
+
+            # as the sequence is stored in half-bytes, the total length (sequence
+            # plus quality scores) is (l+1)/2 + l
+            nbytes_new = (l + 1) / 2 + l
+            nbytes_old = (src.core.l_qseq + 1) / 2 + src.core.l_qseq
+
+            # acquire pointer to location in memory
+            p = pysam_bam_get_seq(src)
+            src.core.l_qseq = l
+
+            # change length of data field
+            cdef bam1_t * retval = pysam_bam_update(src,
+                                                    nbytes_old,
+                                                    nbytes_new,
+                                                    p)
+
+            if retval == NULL:
+                raise MemoryError("could not allocate memory")
+
+            if l > 0:
+                # re-acquire pointer to location in memory
+                # as it might have moved
+                p = pysam_bam_get_seq(src)
+                for k from 0 <= k < nbytes_new:
+                    p[k] = 0
+                # convert to C string
+                s = seq
+                for k from 0 <= k < l:
+                    p[k/2] |= seq_nt16_table[<unsigned char>s[k]] << 4 * (1 - k % 2)
+
+                # erase qualities
+                p = pysam_bam_get_qual(src)
+                memset(p, 0xff, l)
+
+            self.cache_query_sequence = force_str(seq)
+
+            # clear cached values for quality values
+            self.cache_query_qualities = None
+            self.cache_query_alignment_qualities = None
+
+    property query_qualities:
+        """read sequence base qualities, including :term:`soft clipped` bases 
+        (None if not present).
+
+        Quality scores are returned as a python array of unsigned
+        chars. Note that this is not the ASCII-encoded value typically
+        seen in FASTQ or SAM formatted files. Thus, no offset of 33
+        needs to be subtracted.
+
+        Note that to set quality scores the sequence has to be set
+        beforehand as this will determine the expected length of the
+        quality score array.
+
+        This method raises a ValueError if the length of the
+        quality scores and the sequence are not the same.
+
+        """
+        def __get__(self):
+
+            if self.cache_query_qualities:
+                return self.cache_query_qualities
+
+            cdef bam1_t * src
+            cdef char * q
+
+            src = self._delegate
+
+            if src.core.l_qseq == 0:
+                return None
+
+            self.cache_query_qualities = getQualitiesInRange(src, 0, src.core.l_qseq)
+            return self.cache_query_qualities
+
+        def __set__(self, qual):
+
+            # note that memory is already allocated via setting the sequence
+            # hence length match of sequence and quality needs is checked.
+            cdef bam1_t * src
+            cdef uint8_t * p
+            cdef int l
+
+            src = self._delegate
+            p = pysam_bam_get_qual(src)
+            if qual is None or len(qual) == 0:
+                # if absent and there is a sequence: set to 0xff
+                memset(p, 0xff, src.core.l_qseq)
+                return
+
+            # check for length match
+            l = len(qual)
+            if src.core.l_qseq != l:
+                raise ValueError(
+                    "quality and sequence mismatch: %i != %i" %
+                    (l, src.core.l_qseq))
+
+            # create a python array object filling it
+            # with the quality scores
+
+            # NB: should avoid this copying if qual is
+            # already of the correct type.
+            cdef c_array.array result = c_array.array('B', qual)
+
+            # copy data
+            memcpy(p, result.data.as_voidptr, l)
+
+            # save in cache
+            self.cache_query_qualities = qual
+
+    property bin:
+        """properties bin"""
+        def __get__(self):
+            return self._delegate.core.bin
+        def __set__(self, bin):
+            self._delegate.core.bin = bin
+
+
+    ##########################################################
+    # Derived simple attributes. These are simple attributes of
+    # AlignedSegment getting and setting values.
+    ##########################################################
+    # 1. Flags
+    ##########################################################
+    property is_paired:
+        """true if read is paired in sequencing"""
+        def __get__(self):
+            return (self.flag & BAM_FPAIRED) != 0
+        def __set__(self,val):
+            pysam_update_flag(self._delegate, val, BAM_FPAIRED)
+
+    property is_proper_pair:
+        """true if read is mapped in a proper pair"""
+        def __get__(self):
+            return (self.flag & BAM_FPROPER_PAIR) != 0
+        def __set__(self,val):
+            pysam_update_flag(self._delegate, val, BAM_FPROPER_PAIR)
+
+    property is_unmapped:
+        """true if read itself is unmapped"""
+        def __get__(self):
+            return (self.flag & BAM_FUNMAP) != 0
+        def __set__(self, val):
+            pysam_update_flag(self._delegate, val, BAM_FUNMAP)
+            # setting the unmapped flag requires recalculation of
+            # bin as alignment length is now implicitly 1
+            update_bin(self._delegate)
+
+    property is_mapped:
+        """true if read itself is mapped
+        (implemented in terms of :attr:`is_unmapped`)"""
+        def __get__(self):
+            return (self.flag & BAM_FUNMAP) == 0
+        def __set__(self, val):
+            pysam_update_flag(self._delegate, not val, BAM_FUNMAP)
+            update_bin(self._delegate)
+
+    property mate_is_unmapped:
+        """true if the mate is unmapped"""
+        def __get__(self):
+            return (self.flag & BAM_FMUNMAP) != 0
+        def __set__(self,val):
+            pysam_update_flag(self._delegate, val, BAM_FMUNMAP)
+
+    property mate_is_mapped:
+        """true if the mate is mapped
+        (implemented in terms of :attr:`mate_is_unmapped`)"""
+        def __get__(self):
+            return (self.flag & BAM_FMUNMAP) == 0
+        def __set__(self,val):
+            pysam_update_flag(self._delegate, not val, BAM_FMUNMAP)
+
+    property is_reverse:
+        """true if read is mapped to reverse strand"""
+        def __get__(self):
+            return (self.flag & BAM_FREVERSE) != 0
+        def __set__(self,val):
+            pysam_update_flag(self._delegate, val, BAM_FREVERSE)
+
+    property is_forward:
+        """true if read is mapped to forward strand
+        (implemented in terms of :attr:`is_reverse`)"""
+        def __get__(self):
+            return (self.flag & BAM_FREVERSE) == 0
+        def __set__(self,val):
+            pysam_update_flag(self._delegate, not val, BAM_FREVERSE)
+
+    property mate_is_reverse:
+        """true if the mate is mapped to reverse strand"""
+        def __get__(self):
+            return (self.flag & BAM_FMREVERSE) != 0
+        def __set__(self,val):
+            pysam_update_flag(self._delegate, val, BAM_FMREVERSE)
+
+    property mate_is_forward:
+        """true if the mate is mapped to forward strand
+        (implemented in terms of :attr:`mate_is_reverse`)"""
+        def __get__(self):
+            return (self.flag & BAM_FMREVERSE) == 0
+        def __set__(self,val):
+            pysam_update_flag(self._delegate, not val, BAM_FMREVERSE)
+
+    property is_read1:
+        """true if this is read1"""
+        def __get__(self):
+            return (self.flag & BAM_FREAD1) != 0
+        def __set__(self,val):
+            pysam_update_flag(self._delegate, val, BAM_FREAD1)
+    property is_read2:
+        """true if this is read2"""
+        def __get__(self):
+            return (self.flag & BAM_FREAD2) != 0
+        def __set__(self, val):
+            pysam_update_flag(self._delegate, val, BAM_FREAD2)
+    property is_secondary:
+        """true if not primary alignment"""
+        def __get__(self):
+            return (self.flag & BAM_FSECONDARY) != 0
+        def __set__(self, val):
+            pysam_update_flag(self._delegate, val, BAM_FSECONDARY)
+    property is_qcfail:
+        """true if QC failure"""
+        def __get__(self):
+            return (self.flag & BAM_FQCFAIL) != 0
+        def __set__(self, val):
+            pysam_update_flag(self._delegate, val, BAM_FQCFAIL)
+    property is_duplicate:
+        """true if optical or PCR duplicate"""
+        def __get__(self):
+            return (self.flag & BAM_FDUP) != 0
+        def __set__(self, val):
+            pysam_update_flag(self._delegate, val, BAM_FDUP)
+    property is_supplementary:
+        """true if this is a supplementary alignment"""
+        def __get__(self):
+            return (self.flag & BAM_FSUPPLEMENTARY) != 0
+        def __set__(self, val):
+            pysam_update_flag(self._delegate, val, BAM_FSUPPLEMENTARY)
+
+    # 2. Coordinates and lengths
+    property reference_end:
+        '''aligned reference position of the read on the reference genome.
+
+        reference_end points to one past the last aligned residue.
+        Returns None if not available (read is unmapped or no cigar
+        alignment present).
+
+        '''
+        def __get__(self):
+            cdef bam1_t * src
+            src = self._delegate
+            if (self.flag & BAM_FUNMAP) or pysam_get_n_cigar(src) == 0:
+                return None
+            return bam_endpos(src)
+
+    property reference_length:
+        '''aligned length of the read on the reference genome.
+
+        This is equal to `reference_end - reference_start`. 
+        Returns None if not available.
+        '''
+        def __get__(self):
+            cdef bam1_t * src
+            src = self._delegate
+            if (self.flag & BAM_FUNMAP) or pysam_get_n_cigar(src) == 0:
+                return None
+            return bam_endpos(src) - \
+                self._delegate.core.pos
+
+    property query_alignment_sequence:
+        """aligned portion of the read.
+
+        This is a substring of :attr:`query_sequence` that excludes flanking
+        bases that were :term:`soft clipped` (None if not present). It
+        is equal to ``query_sequence[query_alignment_start:query_alignment_end]``.
+
+        SAM/BAM files may include extra flanking bases that are not
+        part of the alignment.  These bases may be the result of the
+        Smith-Waterman or other algorithms, which may not require
+        alignments that begin at the first residue or end at the last.
+        In addition, extra sequencing adapters, multiplex identifiers,
+        and low-quality bases that were not considered for alignment
+        may have been retained.
+
+        """
+
+        def __get__(self):
+            if self.cache_query_alignment_sequence:
+                return self.cache_query_alignment_sequence
+
+            cdef bam1_t * src
+            cdef uint32_t start, end
+
+            src = self._delegate
+
+            if src.core.l_qseq == 0:
+                return None
+
+            start = getQueryStart(src)
+            end   = getQueryEnd(src)
+
+            self.cache_query_alignment_sequence = force_str(
+                getSequenceInRange(src, start, end))
+            return self.cache_query_alignment_sequence
+
+    property query_alignment_qualities:
+        """aligned query sequence quality values (None if not present). These
+        are the quality values that correspond to 
+        :attr:`query_alignment_sequence`, that is, they exclude qualities of 
+        :term:`soft clipped` bases. This is equal to 
+        ``query_qualities[query_alignment_start:query_alignment_end]``.
+
+        Quality scores are returned as a python array of unsigned
+        chars. Note that this is not the ASCII-encoded value typically
+        seen in FASTQ or SAM formatted files. Thus, no offset of 33
+        needs to be subtracted.
+
+        This property is read-only.
+
+        """
+        def __get__(self):
+
+            if self.cache_query_alignment_qualities:
+                return self.cache_query_alignment_qualities
+
+            cdef bam1_t * src
+            cdef uint32_t start, end
+
+            src = self._delegate
+
+            if src.core.l_qseq == 0:
+                return None
+
+            start = getQueryStart(src)
+            end   = getQueryEnd(src)
+            self.cache_query_alignment_qualities = \
+                getQualitiesInRange(src, start, end)
+            return self.cache_query_alignment_qualities
+
+    property query_alignment_start:
+        """start index of the aligned query portion of the sequence (0-based,
+        inclusive).
+
+        This the index of the first base in :attr:`query_sequence` 
+        that is not soft-clipped.
+        """
+        def __get__(self):
+            return getQueryStart(self._delegate)
+
+    property query_alignment_end:
+        """end index of the aligned query portion of the sequence (0-based,
+        exclusive)
+
+        This the index just past the last base in :attr:`query_sequence` 
+        that is not soft-clipped.
+        """
+        def __get__(self):
+            return getQueryEnd(self._delegate)
+
+    property modified_bases:
+        """Modified bases annotations from Ml/Mm tags. The output is
+        Dict[(canonical base, strand, modification)] -> [ (pos,qual), ...]
+        with qual being (256*probability), or -1 if unknown.
+        Strand==0 for forward and 1 for reverse strand modification
+        """
+        def __get__(self):
+            cdef bam1_t * src
+            cdef hts_base_mod_state *m = hts_base_mod_state_alloc()
+            cdef hts_base_mod mods[5]
+            cdef int pos
+
+            ret = {}
+            src = self._delegate
+            
+            if bam_parse_basemod(src, m) < 0:        
+                return None
+            
+            n = bam_next_basemod(src, m, mods, 5, &pos)
+
+            while n>0:
+                for i in range(n):
+                    mod_code = chr(mods[i].modified_base) if mods[i].modified_base>0 else -mods[i].modified_base
+                    mod_strand = mods[i].strand
+                    if self.is_reverse:
+                        mod_strand = 1 - mod_strand
+                    key = (chr(mods[i].canonical_base), 
+                            mod_strand,
+                            mod_code )
+                    ret.setdefault(key,[]).append((pos,mods[i].qual))
+                    
+                n = bam_next_basemod(src, m, mods, 5, &pos)
+
+            if n<0:
+                return None
+
+            hts_base_mod_state_free(m)
+            return ret
+
+    property modified_bases_forward:
+        """Modified bases annotations from Ml/Mm tags. The output is
+        Dict[(canonical base, strand, modification)] -> [ (pos,qual), ...]
+        with qual being (256*probability), or -1 if unknown.
+        Strand==0 for forward and 1 for reverse strand modification.
+        The positions are with respect to the original sequence from get_forward_sequence()
+        """
+        def __get__(self):
+            pmods = self.modified_bases
+            if pmods and self.is_reverse:                
+                rmod = {}
+
+                # Try to find the length of the original sequence
+                rlen = self.infer_read_length()
+                if rlen is None and self.query_sequence is None:
+                    return rmod
+                else:
+                    rlen = len(self.query_sequence)
+                    
+                for k,mods in pmods.items():
+                    nk = k[0],1 - k[1],k[2]
+                    for i in range(len(mods)):
+                        
+                        mods[i] = (rlen - 1 -mods[i][0], mods[i][1])
+                    rmod[nk] = mods
+                return rmod
+            
+            return pmods
+
+ 
+    property query_alignment_length:
+        """length of the aligned query sequence.
+
+        This is equal to :attr:`query_alignment_end` - 
+        :attr:`query_alignment_start`
+        """
+        def __get__(self):
+            cdef bam1_t * src
+            src = self._delegate
+            return getQueryEnd(src) - getQueryStart(src)
+
+    #####################################################
+    # Computed properties
+
+    def get_reference_positions(self, full_length=False):
+        """a list of reference positions that this read aligns to.
+
+        By default, this method only returns positions in the
+        reference that are within the alignment. If *full_length* is
+        set, None values will be included for any soft-clipped or
+        unaligned positions within the read. The returned list will
+        thus be of the same length as the read.
+
+        """
+        cdef uint32_t k, i, l, pos
+        cdef int op
+        cdef uint32_t * cigar_p
+        cdef bam1_t * src
+        cdef bint _full = full_length
+
+        src = self._delegate
+        if pysam_get_n_cigar(src) == 0:
+            return []
+
+        result = []
+        pos = src.core.pos
+        cigar_p = pysam_bam_get_cigar(src)
+
+        for k from 0 <= k < pysam_get_n_cigar(src):
+            op = cigar_p[k] & BAM_CIGAR_MASK
+            l = cigar_p[k] >> BAM_CIGAR_SHIFT
+
+            if op == BAM_CSOFT_CLIP or op == BAM_CINS:
+                if _full:
+                    for i from 0 <= i < l:
+                        result.append(None)
+            elif op == BAM_CMATCH or op == BAM_CEQUAL or op == BAM_CDIFF:
+                for i from pos <= i < pos + l:
+                    result.append(i)
+                pos += l
+            elif op == BAM_CDEL or op == BAM_CREF_SKIP:
+                pos += l
+
+        return result
+
+    def infer_query_length(self, always=False):
+        """infer query length from CIGAR alignment.
+
+        This method deduces the query length from the CIGAR alignment
+        but does not include hard-clipped bases.
+
+        Returns None if CIGAR alignment is not present.
+
+        If *always* is set to True, `infer_read_length` is used instead.
+        This is deprecated and only present for backward compatibility.
+        """
+        if always is True:
+            return self.infer_read_length()
+        cdef int32_t l = calculateQueryLengthWithoutHardClipping(self._delegate)
+        if l > 0:
+            return l
+        else:
+            return None
+
+    def infer_read_length(self):
+        """infer read length from CIGAR alignment.
+
+        This method deduces the read length from the CIGAR alignment
+        including hard-clipped bases.
+
+        Returns None if CIGAR alignment is not present.
+        """
+        cdef int32_t l = calculateQueryLengthWithHardClipping(self._delegate)
+        if l > 0:
+            return l
+        else:
+            return None
+
+    def get_reference_sequence(self):
+        """return the reference sequence in the region that is covered by the
+        alignment of the read to the reference.
+
+        This method requires the MD tag to be set.
+
+        """
+        return force_str(build_reference_sequence(self._delegate))
+
+    def get_forward_sequence(self):
+        """return the original read sequence.
+
+        Reads mapped to the reverse strand are stored reverse complemented in
+        the BAM file. This method returns such reads reverse complemented back
+        to their original orientation.
+
+        Returns None if the record has no query sequence.
+        """
+        if self.query_sequence is None:
+            return None
+        s = force_str(self.query_sequence)
+        if self.is_reverse:
+            s = s.translate(maketrans("ACGTacgtNnXx", "TGCAtgcaNnXx"))[::-1]
+        return s
+
+    def get_forward_qualities(self):
+        """return the original base qualities of the read sequence,
+        in the same format as the :attr:`query_qualities` property.
+
+        Reads mapped to the reverse strand have their base qualities stored
+        reversed in the BAM file. This method returns such reads' base qualities
+        reversed back to their original orientation.
+        """
+        if self.is_reverse:
+            return self.query_qualities[::-1]
+        else:
+            return self.query_qualities
+
+
+    def get_aligned_pairs(self, matches_only=False, with_seq=False):
+        """a list of aligned read (query) and reference positions.
+
+        For inserts, deletions, skipping either query or reference
+        position may be None.
+
+        For padding in the reference, the reference position will
+        always be None.
+
+        Parameters
+        ----------
+
+        matches_only : bool
+          If True, only matched bases are returned - no None on either
+          side.
+        with_seq : bool
+          If True, return a third element in the tuple containing the
+          reference sequence. For CIGAR 'P' (padding in the reference)
+          operations, the third tuple element will be None. Substitutions
+          are lower-case. This option requires an MD tag to be present.
+
+        Returns
+        -------
+
+        aligned_pairs : list of tuples
+
+        """
+        cdef uint32_t k, i, pos, qpos, r_idx, l
+        cdef int op
+        cdef uint32_t * cigar_p
+        cdef bam1_t * src = self._delegate
+        cdef bint _matches_only = bool(matches_only)
+        cdef bint _with_seq = bool(with_seq)
+
+        # TODO: this method performs no checking and assumes that
+        # read sequence, cigar and MD tag are consistent.
+
+        if _with_seq:
+            # force_str required for py2/py3 compatibility
+            ref_seq = force_str(build_reference_sequence(src))
+            if ref_seq is None:
+                raise ValueError("MD tag not present")
+
+        r_idx = 0
+
+        if pysam_get_n_cigar(src) == 0:
+            return []
+
+        result = []
+        pos = src.core.pos
+        qpos = 0
+        cigar_p = pysam_bam_get_cigar(src)
+        for k from 0 <= k < pysam_get_n_cigar(src):
+            op = cigar_p[k] & BAM_CIGAR_MASK
+            l = cigar_p[k] >> BAM_CIGAR_SHIFT
+
+            if op == BAM_CMATCH or op == BAM_CEQUAL or op == BAM_CDIFF:
+                if _with_seq:
+                    for i from pos <= i < pos + l:
+                        result.append((qpos, i, ref_seq[r_idx]))
+                        r_idx += 1
+                        qpos += 1
+                else:
+                    for i from pos <= i < pos + l:
+                        result.append((qpos, i))
+                        qpos += 1
+                pos += l
+
+            elif op == BAM_CINS or op == BAM_CSOFT_CLIP or op == BAM_CPAD:
+                if not _matches_only:
+                    if _with_seq:
+                        for i from pos <= i < pos + l:
+                            result.append((qpos, None, None))
+                            qpos += 1
+                    else:
+                        for i from pos <= i < pos + l:
+                            result.append((qpos, None))
+                            qpos += 1
+                else:
+                    qpos += l
+
+            elif op == BAM_CDEL:
+                if not _matches_only:
+                    if _with_seq:
+                        for i from pos <= i < pos + l:
+                            result.append((None, i, ref_seq[r_idx]))
+                            r_idx += 1
+                    else:
+                        for i from pos <= i < pos + l:
+                            result.append((None, i))
+                else:
+                    r_idx += l
+                pos += l
+
+            elif op == BAM_CHARD_CLIP:
+                pass # advances neither
+
+            elif op == BAM_CREF_SKIP:
+                if not _matches_only:
+                    if _with_seq:
+                        for i from pos <= i < pos + l:
+                            result.append((None, i, None))
+                    else:
+                        for i from pos <= i < pos + l:
+                            result.append((None, i))
+
+                pos += l
+
+        return result
+
+    def get_blocks(self):
+        """ a list of start and end positions of
+        aligned gapless blocks.
+
+        The start and end positions are in genomic
+        coordinates.
+
+        Blocks are not normalized, i.e. two blocks
+        might be directly adjacent. This happens if
+        the two blocks are separated by an insertion
+        in the read.
+        """
+
+        cdef uint32_t k, pos, l
+        cdef int op
+        cdef uint32_t * cigar_p
+        cdef bam1_t * src
+
+        src = self._delegate
+        if pysam_get_n_cigar(src) == 0:
+            return []
+
+        result = []
+        pos = src.core.pos
+        cigar_p = pysam_bam_get_cigar(src)
+        l = 0
+
+        for k from 0 <= k < pysam_get_n_cigar(src):
+            op = cigar_p[k] & BAM_CIGAR_MASK
+            l = cigar_p[k] >> BAM_CIGAR_SHIFT
+            if op == BAM_CMATCH or op == BAM_CEQUAL or op == BAM_CDIFF:
+                result.append((pos, pos + l))
+                pos += l
+            elif op == BAM_CDEL or op == BAM_CREF_SKIP:
+                pos += l
+
+        return result
+
+    def get_overlap(self, uint32_t start, uint32_t end):
+        """return number of aligned bases of read overlapping the interval
+        *start* and *end* on the reference sequence.
+
+        Return None if cigar alignment is not available.
+        """
+        cdef uint32_t k, i, pos, overlap
+        cdef int op, o
+        cdef uint32_t * cigar_p
+        cdef bam1_t * src
+
+        overlap = 0
+
+        src = self._delegate
+        if pysam_get_n_cigar(src) == 0:
+            return None
+        pos = src.core.pos
+        o = 0
+
+        cigar_p = pysam_bam_get_cigar(src)
+        for k from 0 <= k < pysam_get_n_cigar(src):
+            op = cigar_p[k] & BAM_CIGAR_MASK
+            l = cigar_p[k] >> BAM_CIGAR_SHIFT
+
+            if op == BAM_CMATCH or op == BAM_CEQUAL or op == BAM_CDIFF:
+                o = min( pos + l, end) - max( pos, start )
+                if o > 0: overlap += o
+
+            if op == BAM_CMATCH or op == BAM_CDEL or op == BAM_CREF_SKIP or op == BAM_CEQUAL or op == BAM_CDIFF:
+                pos += l
+
+        return overlap
+
+    def get_cigar_stats(self):
+        """summary of operations in cigar string.
+
+        The output order in the array is "MIDNSHP=X" followed by a
+        field for the NM tag. If the NM tag is not present, this
+        field will always be 0.
+
+        +-----+--------------+-----+
+        |M    |BAM_CMATCH    |0    |
+        +-----+--------------+-----+
+        |I    |BAM_CINS      |1    |
+        +-----+--------------+-----+
+        |D    |BAM_CDEL      |2    |
+        +-----+--------------+-----+
+        |N    |BAM_CREF_SKIP |3    |
+        +-----+--------------+-----+
+        |S    |BAM_CSOFT_CLIP|4    |
+        +-----+--------------+-----+
+        |H    |BAM_CHARD_CLIP|5    |
+        +-----+--------------+-----+
+        |P    |BAM_CPAD      |6    |
+        +-----+--------------+-----+
+        |=    |BAM_CEQUAL    |7    |
+        +-----+--------------+-----+
+        |X    |BAM_CDIFF     |8    |
+        +-----+--------------+-----+
+        |B    |BAM_CBACK     |9    |
+        +-----+--------------+-----+
+        |NM   |NM tag        |10   |
+        +-----+--------------+-----+
+
+        If no cigar string is present, empty arrays will be returned.
+
+        Returns:
+            arrays :
+                two arrays. The first contains the nucleotide counts within
+                each cigar operation, the second contains the number of blocks
+                for each cigar operation.
+
+        """
+
+        cdef int nfields = NCIGAR_CODES + 1
+
+        cdef c_array.array base_counts = array.array(
+            "I",
+            [0] * nfields)
+        cdef uint32_t [:] base_view = base_counts
+        cdef c_array.array block_counts = array.array(
+            "I",
+            [0] * nfields)
+        cdef uint32_t [:] block_view = block_counts
+
+        cdef bam1_t * src = self._delegate
+        cdef int op
+        cdef uint32_t l
+        cdef int32_t k
+        cdef uint32_t * cigar_p = pysam_bam_get_cigar(src)
+
+        if cigar_p == NULL:
+            return None
+
+        for k from 0 <= k < pysam_get_n_cigar(src):
+            op = cigar_p[k] & BAM_CIGAR_MASK
+            l = cigar_p[k] >> BAM_CIGAR_SHIFT
+            base_view[op] += l
+            block_view[op] += 1
+
+        cdef uint8_t * v = bam_aux_get(src, 'NM')
+        if v != NULL:
+            base_view[nfields - 1] = <int32_t>bam_aux2i(v)
+
+        return base_counts, block_counts
+
+    #####################################################
+    ## Unsorted as yet
+    # TODO: capture in CIGAR object
+    property cigartuples:
+        """the :term:`cigar` alignment. The alignment
+        is returned as a list of tuples of (operation, length).
+
+        If the alignment is not present, None is returned.
+
+        The operations are:
+
+        +-----+--------------+-----+
+        |M    |BAM_CMATCH    |0    |
+        +-----+--------------+-----+
+        |I    |BAM_CINS      |1    |
+        +-----+--------------+-----+
+        |D    |BAM_CDEL      |2    |
+        +-----+--------------+-----+
+        |N    |BAM_CREF_SKIP |3    |
+        +-----+--------------+-----+
+        |S    |BAM_CSOFT_CLIP|4    |
+        +-----+--------------+-----+
+        |H    |BAM_CHARD_CLIP|5    |
+        +-----+--------------+-----+
+        |P    |BAM_CPAD      |6    |
+        +-----+--------------+-----+
+        |=    |BAM_CEQUAL    |7    |
+        +-----+--------------+-----+
+        |X    |BAM_CDIFF     |8    |
+        +-----+--------------+-----+
+        |B    |BAM_CBACK     |9    |
+        +-----+--------------+-----+
+
+        .. note::
+            The output is a list of (operation, length) tuples, such as
+            ``[(0, 30)]``.
+            This is different from the SAM specification and
+            the :attr:`cigarstring` property, which uses a
+            (length, operation) order, for example: ``30M``.
+
+        To unset the cigar property, assign an empty list
+        or None.
+        """
+        def __get__(self):
+            cdef uint32_t * cigar_p
+            cdef bam1_t * src
+            cdef uint32_t op, l
+            cdef uint32_t k
+
+            src = self._delegate
+            if pysam_get_n_cigar(src) == 0:
+                return None
+
+            cigar = []
+
+            cigar_p = pysam_bam_get_cigar(src);
+            for k from 0 <= k < pysam_get_n_cigar(src):
+                op = cigar_p[k] & BAM_CIGAR_MASK
+                l = cigar_p[k] >> BAM_CIGAR_SHIFT
+                cigar.append((op, l))
+            return cigar
+
+        def __set__(self, values):
+            cdef uint32_t * p
+            cdef bam1_t * src
+            cdef op, l
+            cdef int k
+
+            k = 0
+
+            src = self._delegate
+
+            # get location of cigar string
+            p = pysam_bam_get_cigar(src)
+
+            # empty values for cigar string
+            if values is None:
+                values = []
+
+            cdef uint32_t ncigar = len(values)
+
+            cdef bam1_t * retval = pysam_bam_update(src,
+                                                    pysam_get_n_cigar(src) * 4,
+                                                    ncigar * 4,
+                                                    <uint8_t*>p)
+
+            if retval == NULL:
+                raise MemoryError("could not allocate memory")
+
+            # length is number of cigar operations, not bytes
+            pysam_set_n_cigar(src, ncigar)
+
+            # re-acquire pointer to location in memory
+            # as it might have moved
+            p = pysam_bam_get_cigar(src)
+
+            # insert cigar operations
+            for op, l in values:
+                p[k] = l << BAM_CIGAR_SHIFT | op
+                k += 1
+
+            ## setting the cigar string requires updating the bin
+            update_bin(src)
+
+    cpdef set_tag(self,
+                  tag,
+                  value,
+                  value_type=None,
+                  replace=True):
+        """sets a particular field *tag* to *value* in the optional alignment
+        section.
+
+        *value_type* describes the type of *value* that is to entered
+        into the alignment record. It can be set explicitly to one of
+        the valid one-letter type codes. If unset, an appropriate type
+        will be chosen automatically based on the python type of
+        *value*.
+
+        An existing value of the same *tag* will be overwritten unless
+        *replace* is set to False. This is usually not recommended as a
+        tag may only appear once in the optional alignment section.
+
+        If *value* is `None`, the tag will be deleted.
+
+        This method accepts valid SAM specification value types, which
+        are::
+
+           A: printable char
+           i: signed int
+           f: float
+           Z: printable string
+           H: Byte array in hex format
+           B: Integer or numeric array
+
+        Additionally, it will accept the integer BAM types ('cCsSI')
+
+        For htslib compatibility, 'a' is synonymous with 'A' and the
+        method accepts a 'd' type code for a double precision float.
+
+        When deducing the type code by the python type of *value*, the
+        following mapping is applied::
+
+            i: python int
+            f: python float
+            Z: python str or bytes
+            B: python array.array, list or tuple
+
+        Note that a single character string will be output as 'Z' and
+        not 'A' as the former is the more general type.
+        """
+
+        cdef int value_size
+        cdef uint8_t tc
+        cdef uint8_t * value_ptr
+        cdef uint8_t *existing_ptr
+        cdef float float_value
+        cdef double double_value
+        cdef int32_t int32_t_value
+        cdef uint32_t uint32_t_value
+        cdef int16_t int16_t_value
+        cdef uint16_t uint16_t_value
+        cdef int8_t int8_t_value
+        cdef uint8_t uint8_t_value
+        cdef bam1_t * src = self._delegate
+        cdef char * _value_type
+        cdef c_array.array array_value
+        cdef object buffer
+
+        if len(tag) != 2:
+            raise ValueError('Invalid tag: %s' % tag)
+
+        tag = force_bytes(tag)
+        if replace:
+            existing_ptr = bam_aux_get(src, tag)
+            if existing_ptr:
+                bam_aux_del(src, existing_ptr)
+
+        # setting value to None deletes a tag
+        if value is None:
+            return
+
+        cdef uint8_t typecode = get_tag_typecode(value, value_type)
+        if typecode == 0:
+            raise ValueError("can't guess type or invalid type code specified: {} {}".format(
+                value, value_type))
+
+        # sam_format1 for typecasting
+        if typecode == 'Z':
+            value = force_bytes(value)
+            value_ptr = <uint8_t*><char*>value
+            value_size = len(value)+1
+        elif typecode == 'H':
+            # Note that hex tags are stored the very same
+            # way as Z string.s
+            value = force_bytes(value)
+            value_ptr = <uint8_t*><char*>value
+            value_size = len(value)+1
+        elif typecode == 'A' or typecode == 'a':
+            value = force_bytes(value)
+            value_ptr = <uint8_t*><char*>value
+            value_size = sizeof(char)
+            typecode = 'A'
+        elif typecode == 'i':
+            int32_t_value = value
+            value_ptr = <uint8_t*>&int32_t_value
+            value_size = sizeof(int32_t)
+        elif typecode == 'I':
+            uint32_t_value = value
+            value_ptr = <uint8_t*>&uint32_t_value
+            value_size = sizeof(uint32_t)
+        elif typecode == 's':
+            int16_t_value = value
+            value_ptr = <uint8_t*>&int16_t_value
+            value_size = sizeof(int16_t)
+        elif typecode == 'S':
+            uint16_t_value = value
+            value_ptr = <uint8_t*>&uint16_t_value
+            value_size = sizeof(uint16_t)
+        elif typecode == 'c':
+            int8_t_value = value
+            value_ptr = <uint8_t*>&int8_t_value
+            value_size = sizeof(int8_t)
+        elif typecode == 'C':
+            uint8_t_value = value
+            value_ptr = <uint8_t*>&uint8_t_value
+            value_size = sizeof(uint8_t)
+        elif typecode == 'd':
+            double_value = value
+            value_ptr = <uint8_t*>&double_value
+            value_size = sizeof(double)
+        elif typecode == 'f':
+            float_value  = value
+            value_ptr = <uint8_t*>&float_value
+            value_size = sizeof(float)
+        elif typecode == 'B':
+            # the following goes through python, needs to be cleaned up
+            # pack array using struct
+            fmt, args = pack_tags([(tag, value, value_type)])
+
+            # remove tag and type code as set by bam_aux_append
+            # first four chars of format (<2sB)
+            fmt = '<' + fmt[4:]
+            # first two values to pack
+            args = args[2:]
+            value_size = struct.calcsize(fmt)
+            # buffer will be freed when object goes out of scope
+            buffer = ctypes.create_string_buffer(value_size)
+            struct.pack_into(fmt, buffer, 0, *args)
+            # bam_aux_append copies data from value_ptr
+            bam_aux_append(src,
+                           tag,
+                           typecode,
+                           value_size,
+                           <uint8_t*>buffer.raw)
+            return
+        else:
+            raise ValueError('unsupported value_type {} in set_option'.format(typecode))
+
+        bam_aux_append(src,
+                       tag,
+                       typecode,
+                       value_size,
+                       value_ptr)
+
+    cpdef has_tag(self, tag):
+        """returns true if the optional alignment section
+        contains a given *tag*."""
+        cdef uint8_t * v
+        cdef int nvalues
+        btag = force_bytes(tag)
+        v = bam_aux_get(self._delegate, btag)
+        return v != NULL
+
+    cpdef get_tag(self, tag, with_value_type=False):
+        """
+        retrieves data from the optional alignment section
+        given a two-letter *tag* denoting the field.
+
+        The returned value is cast into an appropriate python type.
+
+        This method is the fastest way to access the optional
+        alignment section if only few tags need to be retrieved.
+
+        Possible value types are "AcCsSiIfZHB" (see BAM format
+        specification) as well as additional value type 'd' as
+        implemented in htslib.
+
+        Parameters:
+
+            tag :
+                data tag.
+
+            with_value_type : Optional[bool]
+                if set to True, the return value is a tuple of (tag value, type
+                code). (default False)
+
+        Returns:
+
+            A python object with the value of the `tag`. The type of the
+            object depends on the data type in the data record.
+
+        Raises:
+
+            KeyError
+                If `tag` is not present, a KeyError is raised.
+
+        """
+        cdef uint8_t * v
+        cdef int nvalues
+        btag = force_bytes(tag)
+        v = bam_aux_get(self._delegate, btag)
+        if v == NULL:
+            raise KeyError("tag '%s' not present" % tag)
+        if chr(v[0]) == "B":
+            auxtype = chr(v[0]) + chr(v[1])
+        else:
+            auxtype = chr(v[0])
+
+        if auxtype in "iIcCsS":
+            value = bam_aux2i(v)
+        elif auxtype == 'f' or auxtype == 'F':
+            value = bam_aux2f(v)
+        elif auxtype == 'd' or auxtype == 'D':
+            value = bam_aux2f(v)
+        elif auxtype == 'A' or auxtype == 'a':
+            # force A to a
+            v[0] = 'A'
+            # there might a more efficient way
+            # to convert a char into a string
+            value = '%c' % <char>bam_aux2A(v)
+        elif auxtype == 'Z' or auxtype == 'H':
+            # Z and H are treated equally as strings in htslib
+            value = charptr_to_str(<char*>bam_aux2Z(v))
+        elif auxtype[0] == 'B':
+            bytesize, nvalues, values = convert_binary_tag(v + 1)
+            value = values
+        else:
+            raise ValueError("unknown auxiliary type '%s'" % auxtype)
+
+        if with_value_type:
+            return (value, auxtype)
+        else:
+            return value
+
+    def get_tags(self, with_value_type=False):
+        """the fields in the optional alignment section.
+
+        Returns a list of all fields in the optional
+        alignment section. Values are converted to appropriate python
+        values. For example: ``[(NM, 2), (RG, "GJP00TM04")]``
+
+        If *with_value_type* is set, the value type as encode in
+        the AlignedSegment record will be returned as well:
+
+        [(NM, 2, "i"), (RG, "GJP00TM04", "Z")]
+
+        This method will convert all values in the optional alignment
+        section. When getting only one or few tags, please see
+        :meth:`get_tag` for a quicker way to achieve this.
+
+        """
+
+        cdef char * ctag
+        cdef bam1_t * src
+        cdef uint8_t * s
+        cdef char auxtag[3]
+        cdef char auxtype
+        cdef uint8_t byte_size
+        cdef int32_t nvalues
+
+        src = self._delegate
+        if src.l_data == 0:
+            return []
+        s = pysam_bam_get_aux(src)
+        result = []
+        auxtag[2] = 0
+        while s < (src.data + src.l_data):
+            # get tag
+            auxtag[0] = s[0]
+            auxtag[1] = s[1]
+            s += 2
+            auxtype = s[0]
+            if auxtype in ('c', 'C'):
+                value = <int>bam_aux2i(s)
+                s += 1
+            elif auxtype in ('s', 'S'):
+                value = <int>bam_aux2i(s)
+                s += 2
+            elif auxtype in ('i', 'I'):
+                value = <int32_t>bam_aux2i(s)
+                s += 4
+            elif auxtype == 'f':
+                value = <float>bam_aux2f(s)
+                s += 4
+            elif auxtype == 'd':
+                value = <double>bam_aux2f(s)
+                s += 8
+            elif auxtype in ('A', 'a'):
+                value = "%c" % <char>bam_aux2A(s)
+                s += 1
+            elif auxtype in ('Z', 'H'):
+                value = charptr_to_str(<char*>bam_aux2Z(s))
+                # +1 for NULL terminated string
+                s += len(value) + 1
+            elif auxtype == 'B':
+                s += 1
+                byte_size, nvalues, value = convert_binary_tag(s)
+                # 5 for 1 char and 1 int
+                s += 5 + (nvalues * byte_size) - 1
+            else:
+                raise KeyError("unknown type '%s'" % auxtype)
+
+            s += 1
+
+            if with_value_type:
+                result.append((charptr_to_str(auxtag), value, chr(auxtype)))
+            else:
+                result.append((charptr_to_str(auxtag), value))
+
+        return result
+
+    def set_tags(self, tags):
+        """sets the fields in the optional alignment section with
+        a list of (tag, value) tuples.
+
+        The value type of the values is determined from the
+        python type. Optionally, a type may be given explicitly as
+        a third value in the tuple, For example:
+
+        x.set_tags([(NM, 2, "i"), (RG, "GJP00TM04", "Z")]
+
+        This method will not enforce the rule that the same tag may appear
+        only once in the optional alignment section.
+        """
+
+        cdef bam1_t * src
+        cdef uint8_t * s
+        cdef char * temp
+        cdef int new_size = 0
+        cdef int old_size
+        src = self._delegate
+
+        # convert and pack the data
+        if tags is not None and len(tags) > 0:
+            fmt, args = pack_tags(tags)
+            new_size = struct.calcsize(fmt)
+            buffer = ctypes.create_string_buffer(new_size)
+            struct.pack_into(fmt,
+                             buffer,
+                             0,
+                             *args)
+
+
+        # delete the old data and allocate new space.
+        # If total_size == 0, the aux field will be
+        # empty
+        old_size = pysam_bam_get_l_aux(src)
+        cdef bam1_t * retval = pysam_bam_update(src,
+                                                old_size,
+                                                new_size,
+                                                pysam_bam_get_aux(src))
+        if retval == NULL:
+            raise MemoryError("could not allocate memory")
+
+        # copy data only if there is any
+        if new_size > 0:
+
+            # get location of new data
+            s = pysam_bam_get_aux(src)
+
+            # check if there is direct path from buffer.raw to tmp
+            p = buffer.raw
+            # create handle to make sure buffer stays alive long
+            # enough for memcpy, see issue 129
+            temp = p
+            memcpy(s, temp, new_size)
+
+
+    ########################################################
+    # Compatibility Accessors
+    # Functions, properties for compatibility with pysam < 0.8
+    #
+    # Several options
+    #     change the factory functions according to API
+    #         * requires code changes throughout, incl passing
+    #           handles to factory functions
+    #     subclass functions and add attributes at runtime
+    #         e.g.: AlignedSegments.qname = AlignedSegments.query_name
+    #         * will slow down the default interface
+    #     explicit declaration of getters/setters
+    ########################################################
+    property qname:
+        """deprecated, use :attr:`query_name` instead."""
+        def __get__(self): return self.query_name
+        def __set__(self, v): self.query_name = v
+    property tid:
+        """deprecated, use :attr:`reference_id` instead."""
+        def __get__(self): return self.reference_id
+        def __set__(self, v): self.reference_id = v
+    property pos:
+        """deprecated, use :attr:`reference_start` instead."""
+        def __get__(self): return self.reference_start
+        def __set__(self, v): self.reference_start = v
+    property mapq:
+        """deprecated, use :attr:`mapping_quality` instead."""
+        def __get__(self): return self.mapping_quality
+        def __set__(self, v): self.mapping_quality = v
+    property rnext:
+        """deprecated, use :attr:`next_reference_id` instead."""
+        def __get__(self): return self.next_reference_id
+        def __set__(self, v): self.next_reference_id = v
+    property pnext:
+        """deprecated, use :attr:`next_reference_start` instead."""
+        def __get__(self):
+            return self.next_reference_start
+        def __set__(self, v):
+            self.next_reference_start = v
+    property cigar:
+        """deprecated, use :attr:`cigarstring` or :attr:`cigartuples` instead."""
+        def __get__(self):
+            r = self.cigartuples
+            if r is None:
+                r = []
+            return r
+        def __set__(self, v): self.cigartuples = v
+    property tlen:
+        """deprecated, use :attr:`template_length` instead."""
+        def __get__(self):
+            return self.template_length
+        def __set__(self, v):
+            self.template_length = v
+    property seq:
+        """deprecated, use :attr:`query_sequence` instead."""
+        def __get__(self):
+            return self.query_sequence
+        def __set__(self, v):
+            self.query_sequence = v
+    property qual:
+        """deprecated, use :attr:`query_qualities` instead."""
+        def __get__(self):
+            return array_to_qualitystring(self.query_qualities)
+        def __set__(self, v):
+            self.query_qualities = qualitystring_to_array(v)
+    property alen:
+        """deprecated, use :attr:`reference_length` instead."""
+        def __get__(self):
+            return self.reference_length
+        def __set__(self, v):
+            self.reference_length = v
+    property aend:
+        """deprecated, use :attr:`reference_end` instead."""
+        def __get__(self):
+            return self.reference_end
+        def __set__(self, v):
+            self.reference_end = v
+    property rlen:
+        """deprecated, use :attr:`query_length` instead."""
+        def __get__(self):
+            return self.query_length
+        def __set__(self, v):
+            self.query_length = v
+    property query:
+        """deprecated, use :attr:`query_alignment_sequence` 
+        instead."""
+        def __get__(self):
+            return self.query_alignment_sequence
+        def __set__(self, v):
+            self.query_alignment_sequence = v
+    property qqual:
+        """deprecated, use :attr:`query_alignment_qualities` 
+        instead."""
+        def __get__(self):
+            return array_to_qualitystring(self.query_alignment_qualities)
+        def __set__(self, v):
+            self.query_alignment_qualities = qualitystring_to_array(v)
+    property qstart:
+        """deprecated, use :attr:`query_alignment_start` instead."""
+        def __get__(self):
+            return self.query_alignment_start
+        def __set__(self, v):
+            self.query_alignment_start = v
+    property qend:
+        """deprecated, use :attr:`query_alignment_end` instead."""
+        def __get__(self):
+            return self.query_alignment_end
+        def __set__(self, v):
+            self.query_alignment_end = v
+    property qlen:
+        """deprecated, use :attr:`query_alignment_length` 
+        instead."""
+        def __get__(self):
+            return self.query_alignment_length
+        def __set__(self, v):
+            self.query_alignment_length = v
+    property mrnm:
+        """deprecated, use :attr:`next_reference_id` instead."""
+        def __get__(self):
+            return self.next_reference_id
+        def __set__(self, v):
+            self.next_reference_id = v
+    property mpos:
+        """deprecated, use :attr:`next_reference_start` 
+        instead."""
+        def __get__(self):
+            return self.next_reference_start
+        def __set__(self, v):
+            self.next_reference_start = v
+    property rname:
+        """deprecated, use :attr:`reference_id` instead."""
+        def __get__(self):
+            return self.reference_id
+        def __set__(self, v):
+            self.reference_id = v
+    property isize:
+        """deprecated, use :attr:`template_length` instead."""
+        def __get__(self):
+            return self.template_length
+        def __set__(self, v):
+            self.template_length = v
+    property blocks:
+        """deprecated, use :meth:`get_blocks()` instead."""
+        def __get__(self):
+            return self.get_blocks()
+    property aligned_pairs:
+        """deprecated, use :meth:`get_aligned_pairs()` instead."""
+        def __get__(self):
+            return self.get_aligned_pairs()
+    property inferred_length:
+        """deprecated, use :meth:`infer_query_length()` instead."""
+        def __get__(self):
+            return self.infer_query_length()
+    property positions:
+        """deprecated, use :meth:`get_reference_positions()` instead."""
+        def __get__(self):
+            return self.get_reference_positions()
+    property tags:
+        """deprecated, use :meth:`get_tags()` instead."""
+        def __get__(self):
+            return self.get_tags()
+        def __set__(self, tags):
+            self.set_tags(tags)
+    def overlap(self):
+        """deprecated, use :meth:`get_overlap()` instead."""
+        return self.get_overlap()
+    def opt(self, tag):
+        """deprecated, use :meth:`get_tag()` instead."""
+        return self.get_tag(tag)
+    def setTag(self, tag, value, value_type=None, replace=True):
+        """deprecated, use :meth:`set_tag()` instead."""
+        return self.set_tag(tag, value, value_type, replace)
+
+
+cdef class PileupColumn:
+    '''A pileup of reads at a particular reference sequence position
+    (:term:`column`). A pileup column contains all the reads that map
+    to a certain target base.
+
+    This class is a proxy for results returned by the samtools pileup
+    engine.  If the underlying engine iterator advances, the results
+    of this column will change.
+    '''
+    def __init__(self):
+        raise TypeError("this class cannot be instantiated from Python")
+
+    def __str__(self):
+        return "\t".join(map(str,
+                              (self.reference_id,
+                               self.reference_pos,
+                               self.nsegments))) +\
+            "\n" +\
+            "\n".join(map(str, self.pileups))
+
+    def __dealloc__(self):
+        free(self.buf.s)
+
+    def set_min_base_quality(self, min_base_quality):
+        """set the minimum base quality for this pileup column.
+        """
+        self.min_base_quality = min_base_quality
+
+    def __len__(self):
+        """return number of reads aligned to this column.
+
+        see :meth:`get_num_aligned`
+        """
+        return self.get_num_aligned()
+
+    property reference_id:
+        '''the reference sequence number as defined in the header'''
+        def __get__(self):
+            return self.tid
+
+    property reference_name:
+        """:term:`reference` name (None if no AlignmentFile is associated)"""
+        def __get__(self):
+            if self.header is not None:
+                return self.header.get_reference_name(self.tid)
+            return None
+
+    property nsegments:
+        '''number of reads mapping to this column.
+
+        Note that this number ignores the base quality filter.'''
+        def __get__(self):
+            return self.n_pu
+        def __set__(self, n):
+            self.n_pu = n
+
+    property reference_pos:
+        '''the position in the reference sequence (0-based).'''
+        def __get__(self):
+            return self.pos
+
+    property pileups:
+        '''list of reads (:class:`pysam.PileupRead`) aligned to this column'''
+        def __get__(self):
+            if self.plp == NULL or self.plp[0] == NULL:
+                raise ValueError("PileupColumn accessed after iterator finished")
+
+            cdef int x
+            cdef const bam_pileup1_t * p = NULL
+            pileups = []
+
+            # warning: there could be problems if self.n and self.buf are
+            # out of sync.
+            for x from 0 <= x < self.n_pu:
+                p = &(self.plp[0][x])
+                if p == NULL:
+                    raise ValueError(
+                        "pileup buffer out of sync - most likely use of iterator "
+                        "outside loop")
+                if pileup_base_qual_skip(p, self.min_base_quality):
+                    continue
+                pileups.append(makePileupRead(p, self.header))
+            return pileups
+
+    ########################################################
+    # Compatibility Accessors
+    # Functions, properties for compatibility with pysam < 0.8
+    ########################################################
+    property pos:
+        """deprecated, use :attr:`reference_pos` instead."""
+        def __get__(self):
+            return self.reference_pos
+        def __set__(self, v):
+            self.reference_pos = v
+
+    property tid:
+        """deprecated, use :attr:`reference_id` instead."""
+        def __get__(self):
+            return self.reference_id
+        def __set__(self, v):
+            self.reference_id = v
+
+    property n:
+        """deprecated, use :attr:`nsegments` instead."""
+        def __get__(self):
+            return self.nsegments
+        def __set__(self, v):
+            self.nsegments = v
+
+    def get_num_aligned(self):
+        """return number of aligned bases at pileup column position.
+
+        This method applies a base quality filter and the number is
+        equal to the size of :meth:`get_query_sequences`,
+        :meth:`get_mapping_qualities`, etc.
+
+        """
+        cdef uint32_t x = 0
+        cdef uint32_t c = 0
+        cdef uint32_t cnt = 0
+        cdef const bam_pileup1_t * p = NULL
+        if self.plp == NULL or self.plp[0] == NULL:
+            raise ValueError("PileupColumn accessed after iterator finished")
+
+        for x from 0 <= x < self.n_pu:
+            p = &(self.plp[0][x])
+            if p == NULL:
+                raise ValueError(
+                    "pileup buffer out of sync - most likely use of iterator "
+                    "outside loop")
+            if pileup_base_qual_skip(p, self.min_base_quality):
+                continue
+            cnt += 1
+        return cnt
+
+    def get_query_sequences(self, bint mark_matches=False, bint mark_ends=False, bint add_indels=False):
+        """query bases/sequences at pileup column position.
+
+        Optionally, the bases/sequences can be annotated according to the samtools
+        mpileup format. This is the format description from the samtools mpileup tool::
+
+           Information on match, mismatch, indel, strand, mapping
+           quality and start and end of a read are all encoded at the
+           read base column. At this column, a dot stands for a match
+           to the reference base on the forward strand, a comma for a
+           match on the reverse strand, a '>' or '<' for a reference
+           skip, `ACGTN' for a mismatch on the forward strand and
+           `acgtn' for a mismatch on the reverse strand. A pattern
+           `\\+[0-9]+[ACGTNacgtn]+' indicates there is an insertion
+           between this reference position and the next reference
+           position. The length of the insertion is given by the
+           integer in the pattern, followed by the inserted
+           sequence. Similarly, a pattern `-[0-9]+[ACGTNacgtn]+'
+           represents a deletion from the reference. The deleted bases
+           will be presented as `*' in the following lines. Also at
+           the read base column, a symbol `^' marks the start of a
+           read. The ASCII of the character following `^' minus 33
+           gives the mapping quality. A symbol `$' marks the end of a
+           read segment
+
+        To reproduce samtools mpileup format, set all of mark_matches,
+        mark_ends and add_indels to True.
+
+        Parameters
+        ----------
+
+        mark_matches: bool
+
+          If True, output bases matching the reference as "." or ","
+          for forward and reverse strand, respectively. This mark
+          requires the reference sequence. If no reference is
+          present, this option is ignored.
+
+        mark_ends : bool
+
+          If True, add markers "^" and "$" for read start and end, respectively.
+
+        add_indels : bool
+
+          If True, add bases for bases inserted into or skipped from the
+          reference. The latter requires a reference sequence file to have
+          been given, e.g. via `pileup(fastafile = ...)`. If no reference
+          sequence is available, skipped bases are represented as 'N's.
+
+        Returns
+        -------
+
+        a list of bases/sequences per read at pileup column position. : list
+
+        """
+        cdef uint32_t x = 0
+        cdef uint32_t j = 0
+        cdef uint32_t c = 0
+        cdef uint8_t cc = 0
+        cdef uint8_t rb = 0
+        cdef kstring_t * buf = &self.buf
+        cdef const bam_pileup1_t * p = NULL
+
+        if self.plp == NULL or self.plp[0] == NULL:
+            raise ValueError("PileupColumn accessed after iterator finished")
+
+        buf.l = 0
+
+        # todo: reference sequence to count matches/mismatches
+        # todo: convert assertions to exceptions
+        for x from 0 <= x < self.n_pu:
+            p = &(self.plp[0][x])
+            if p == NULL:
+                raise ValueError(
+                    "pileup buffer out of sync - most likely use of iterator "
+                    "outside loop")
+            if pileup_base_qual_skip(p, self.min_base_quality):
+                continue
+            # see samtools pileup_seq
+            if mark_ends and p.is_head:
+                kputc('^', buf)
+
+                if p.b.core.qual > 93:
+                    kputc(126, buf)
+                else:
+                    kputc(p.b.core.qual + 33, buf)
+            if not p.is_del:
+                if p.qpos < p.b.core.l_qseq:
+                    cc = <uint8_t>seq_nt16_str[bam_seqi(bam_get_seq(p.b), p.qpos)]
+                else:
+                    cc = 'N'
+
+                if mark_matches and self.reference_sequence != NULL:
+                    rb = self.reference_sequence[self.reference_pos]
+                    if seq_nt16_table[cc] == seq_nt16_table[rb]:
+                        cc = "="
+                kputc(strand_mark_char(cc, p.b), buf)
+            elif add_indels:
+                if p.is_refskip:
+                    if bam_is_rev(p.b):
+                        kputc('<', buf)
+                    else:
+                        kputc('>', buf)
+                else:
+                    kputc('*', buf)
+            if add_indels:
+                if p.indel > 0:
+                    kputc('+', buf)
+                    kputw(p.indel, buf)
+                    for j from 1 <= j <= p.indel:
+                        cc = seq_nt16_str[bam_seqi(bam_get_seq(p.b), p.qpos + j)]
+                        kputc(strand_mark_char(cc, p.b), buf)
+                elif p.indel < 0:
+                    kputc('-', buf)
+                    kputw(-p.indel, buf)
+                    for j from 1 <= j <= -p.indel:
+                        # TODO: out-of-range check here?
+                        if self.reference_sequence == NULL:
+                            cc = 'N'
+                        else:
+                            cc = self.reference_sequence[self.reference_pos + j]
+                        kputc(strand_mark_char(cc, p.b), buf)
+            if mark_ends and p.is_tail:
+                kputc('$', buf)
+
+            kputc(':', buf)
+
+        if buf.l == 0:
+            # could be zero if all qualities are too low
+            return ""
+        else:
+            # quicker to ensemble all and split than to encode all separately.
+            # ignore last ":"
+            return force_str(PyBytes_FromStringAndSize(buf.s, buf.l-1)).split(":")
+
+    def get_query_qualities(self):
+        """query base quality scores at pileup column position.
+
+        Returns
+        -------
+
+        a list of quality scores : list
+        """
+        cdef uint32_t x = 0
+        cdef const bam_pileup1_t * p = NULL
+        cdef uint32_t c = 0
+        result = []
+        for x from 0 <= x < self.n_pu:
+            p = &(self.plp[0][x])
+            if p == NULL:
+                raise ValueError(
+                    "pileup buffer out of sync - most likely use of iterator "
+                    "outside loop")
+
+            if p.qpos < p.b.core.l_qseq:
+                c = bam_get_qual(p.b)[p.qpos]
+            else:
+                c = 0
+            if c < self.min_base_quality:
+                continue
+            result.append(c)
+        return result
+
+    def get_mapping_qualities(self):
+        """query mapping quality scores at pileup column position.
+
+        Returns
+        -------
+
+        a list of quality scores : list
+        """
+        if self.plp == NULL or self.plp[0] == NULL:
+            raise ValueError("PileupColumn accessed after iterator finished")
+
+        cdef uint32_t x = 0
+        cdef const bam_pileup1_t * p = NULL
+        result = []
+        for x from 0 <= x < self.n_pu:
+            p = &(self.plp[0][x])
+            if p == NULL:
+                raise ValueError(
+                    "pileup buffer out of sync - most likely use of iterator "
+                    "outside loop")
+
+            if pileup_base_qual_skip(p, self.min_base_quality):
+                continue
+            result.append(p.b.core.qual)
+        return result
+
+    def get_query_positions(self):
+        """positions in read at pileup column position.
+
+        Returns
+        -------
+
+        a list of read positions : list
+        """
+        if self.plp == NULL or self.plp[0] == NULL:
+            raise ValueError("PileupColumn accessed after iterator finished")
+
+        cdef uint32_t x = 0
+        cdef const bam_pileup1_t * p = NULL
+        result = []
+        for x from 0 <= x < self.n_pu:
+            p = &(self.plp[0][x])
+            if p == NULL:
+                raise ValueError(
+                    "pileup buffer out of sync - most likely use of iterator "
+                    "outside loop")
+
+            if pileup_base_qual_skip(p, self.min_base_quality):
+                continue
+            result.append(p.qpos)
+        return result
+
+    def get_query_names(self):
+        """query/read names aligned at pileup column position.
+
+        Returns
+        -------
+
+        a list of query names at pileup column position. : list
+        """
+        if self.plp == NULL or self.plp[0] == NULL:
+            raise ValueError("PileupColumn accessed after iterator finished")
+
+        cdef uint32_t x = 0
+        cdef const bam_pileup1_t * p = NULL
+        result = []
+        for x from 0 <= x < self.n_pu:
+            p = &(self.plp[0][x])
+            if p == NULL:
+                raise ValueError(
+                    "pileup buffer out of sync - most likely use of iterator "
+                    "outside loop")
+
+            if pileup_base_qual_skip(p, self.min_base_quality):
+                continue
+            result.append(charptr_to_str(pysam_bam_get_qname(p.b)))
+        return result
+
+
+cdef class PileupRead:
+    '''Representation of a read aligned to a particular position in the
+    reference sequence.
+
+    '''
+
+    def __init__(self):
+        raise TypeError(
+            "this class cannot be instantiated from Python")
+
+    def __str__(self):
+        return "\t".join(
+            map(str,
+                (self.alignment, self.query_position,
+                 self.indel, self.level,
+                 self.is_del, self.is_head,
+                 self.is_tail, self.is_refskip)))
+
+    property alignment:
+        """a :class:`pysam.AlignedSegment` object of the aligned read"""
+        def __get__(self):
+            return self._alignment
+
+    property query_position:
+        """position of the read base at the pileup site, 0-based.
+        None if :attr:`is_del` or :attr:`is_refskip` is set.
+
+        """
+        def __get__(self):
+            if self.is_del or self.is_refskip:
+                return None
+            else:
+                return self._qpos
+
+    property query_position_or_next:
+        """position of the read base at the pileup site, 0-based.
+
+        If the current position is a deletion, returns the next
+        aligned base.
+
+        """
+        def __get__(self):
+            return self._qpos
+
+    property indel:
+        """indel length for the position following the current pileup site.
+
+        This quantity peeks ahead to the next cigar operation in this
+        alignment. If the next operation is an insertion, indel will
+        be positive. If the next operation is a deletion, it will be
+        negation. 0 if the next operation is not an indel.
+
+        """
+        def __get__(self):
+            return self._indel
+
+    property level:
+        """the level of the read in the "viewer" mode. Note that this value
+        is currently not computed."""
+        def __get__(self):
+            return self._level
+
+    property is_del:
+        """1 iff the base on the padded read is a deletion"""
+        def __get__(self):
+            return self._is_del
+
+    property is_head:
+        """1 iff the base on the padded read is the left-most base."""
+        def __get__(self):
+            return self._is_head
+
+    property is_tail:
+        """1 iff the base on the padded read is the right-most base."""
+        def __get__(self):
+            return self._is_tail
+
+    property is_refskip:
+        """1 iff the base on the padded read is part of CIGAR N op."""
+        def __get__(self):
+            return self._is_refskip
+
+
+
+cpdef enum CIGAR_OPS:
+    CMATCH = 0
+    CINS = 1
+    CDEL = 2
+    CREF_SKIP = 3
+    CSOFT_CLIP = 4
+    CHARD_CLIP = 5
+    CPAD = 6
+    CEQUAL = 7
+    CDIFF = 8
+    CBACK = 9
+
+
+cpdef enum SAM_FLAGS:
+    # the read is paired in sequencing, no matter whether it is mapped in a pair
+    FPAIRED = 1
+    # the read is mapped in a proper pair
+    FPROPER_PAIR = 2
+    # the read itself is unmapped; conflictive with FPROPER_PAIR
+    FUNMAP = 4
+    # the mate is unmapped
+    FMUNMAP = 8
+    # the read is mapped to the reverse strand
+    FREVERSE = 16
+    # the mate is mapped to the reverse strand
+    FMREVERSE = 32
+    # this is read1
+    FREAD1 = 64
+    # this is read2
+    FREAD2 = 128
+    # not primary alignment
+    FSECONDARY = 256
+    # QC failure
+    FQCFAIL = 512
+    # optical or PCR duplicate
+    FDUP = 1024
+    # supplementary alignment
+    FSUPPLEMENTARY = 2048
+
+
+__all__ = [
+    "AlignedSegment",
+    "PileupColumn",
+    "PileupRead",
+    "CMATCH",
+    "CINS",
+    "CDEL",
+    "CREF_SKIP",
+    "CSOFT_CLIP",
+    "CHARD_CLIP",
+    "CPAD",
+    "CEQUAL",
+    "CDIFF",
+    "CBACK",
+    "FPAIRED",
+    "FPROPER_PAIR",
+    "FUNMAP",
+    "FMUNMAP",
+    "FREVERSE",
+    "FMREVERSE",
+    "FREAD1",
+    "FREAD2",
+    "FSECONDARY",
+    "FQCFAIL",
+    "FDUP",
+    "FSUPPLEMENTARY",
+    "KEY_NAMES"]
diff --git a/pysam/libcalignmentfile.pxd b/pysam/libcalignmentfile.pxd
new file mode 100644
index 0000000..2a17fbe
--- /dev/null
+++ b/pysam/libcalignmentfile.pxd
@@ -0,0 +1,152 @@
+from libc.stdint cimport int8_t, int16_t, int32_t, int64_t
+from libc.stdint cimport uint8_t, uint16_t, uint32_t, uint64_t
+from libc.stdlib cimport malloc, calloc, realloc, free
+from libc.string cimport memcpy, memcmp, strncpy, strlen, strdup
+from libc.stdio cimport FILE, printf
+
+from pysam.libcfaidx cimport faidx_t, FastaFile
+from pysam.libcalignedsegment cimport AlignedSegment
+from pysam.libchtslib cimport *
+
+from cpython cimport array
+cimport cython
+
+cdef extern from *:
+    ctypedef char* const_char_ptr "const char*"
+
+cdef extern from "htslib_util.h":
+
+    char * pysam_bam_get_qname(bam1_t * b)
+
+####################################################################
+# Utility types
+
+ctypedef struct __iterdata:
+    htsFile * htsfile
+    bam_hdr_t * header
+    hts_itr_t * iter
+    faidx_t * fastafile
+    int tid
+    char * seq
+    int seq_len
+    int min_mapping_quality
+    int flag_require
+    int flag_filter
+    bint compute_baq
+    bint redo_baq
+    bint ignore_orphans
+    int adjust_capq_threshold
+
+
+cdef class AlignmentHeader(object):
+    cdef bam_hdr_t *ptr
+
+cdef class AlignmentFile(HTSFile):
+    cdef readonly object reference_filename
+    cdef readonly AlignmentHeader header
+
+    # pointer to index
+    cdef hts_idx_t *index
+
+    # current read within iteration
+    cdef bam1_t * b
+
+    cdef bam1_t * getCurrent(self)
+    cdef int cnext(self)
+
+    # write an aligned read
+    cpdef int write(self, AlignedSegment read) except -1
+
+
+cdef class IteratorRow:
+    cdef int retval
+    cdef bam1_t * b
+    cdef AlignmentFile samfile
+    cdef htsFile * htsfile
+    cdef hts_idx_t * index
+    cdef AlignmentHeader header
+    cdef int owns_samfile
+
+
+cdef class IteratorRowRegion(IteratorRow):
+    cdef hts_itr_t * iter
+    cdef bam1_t * getCurrent(self)
+    cdef int cnext(self)
+
+
+cdef class IteratorRowHead(IteratorRow):
+    cdef int max_rows
+    cdef int current_row
+    cdef bam1_t * getCurrent(self)
+    cdef int cnext(self)
+
+
+cdef class IteratorRowAll(IteratorRow):
+    cdef bam1_t * getCurrent(self)
+    cdef int cnext(self)
+
+
+cdef class IteratorRowAllRefs(IteratorRow):
+    cdef int         tid
+    cdef IteratorRowRegion rowiter
+
+
+cdef class IteratorRowSelection(IteratorRow):
+    cdef int current_pos
+    cdef positions
+    cdef bam1_t * getCurrent(self)
+    cdef int cnext(self)
+
+
+cdef class IteratorColumn:
+
+    # result of the last plbuf_push
+    cdef IteratorRowRegion iter
+    cdef int tid
+    cdef int pos
+    cdef int n_plp
+    cdef uint32_t min_base_quality
+    cdef const bam_pileup1_t * plp
+    cdef bam_mplp_t pileup_iter
+    cdef __iterdata iterdata
+    cdef AlignmentFile samfile
+    cdef FastaFile fastafile
+    cdef stepper
+    cdef int max_depth
+    cdef bint ignore_overlaps
+
+    cdef int cnext(self)
+    cdef char * get_sequence(self)
+    cdef _setup_iterator(self,
+                         int tid,
+                         int start,
+                         int stop,
+                         int multiple_iterators=?)
+    cdef _setup_raw_rest_iterator(self)
+
+    cdef reset(self, tid, start, stop)
+    cdef _free_pileup_iter(self)
+    # backwards compatibility
+    cdef char * getSequence(self)
+
+
+cdef class IteratorColumnRegion(IteratorColumn):
+    cdef int start
+    cdef int stop
+    cdef int truncate
+
+
+cdef class IteratorColumnAllRefs(IteratorColumn):
+    pass
+
+
+cdef class IteratorColumnAll(IteratorColumn):
+    pass
+
+
+cdef class IndexedReads:
+    cdef AlignmentFile samfile
+    cdef htsFile * htsfile
+    cdef object index
+    cdef int owns_samfile
+    cdef AlignmentHeader header
diff --git a/pysam/libcalignmentfile.pyi b/pysam/libcalignmentfile.pyi
new file mode 100644
index 0000000..75c1fa4
--- /dev/null
+++ b/pysam/libcalignmentfile.pyi
@@ -0,0 +1,237 @@
+import array
+import sys
+from typing import (
+    Any,
+    Dict,
+    Type,
+    NamedTuple,
+    Tuple,
+    Optional,
+    Sequence,
+    Union,
+    Callable,
+    List,
+    Iterable,
+)
+
+if sys.version_info < (3, 8):
+    from typing_extensions import Literal
+else:
+    from typing import Literal
+
+from pysam.libchtslib import HTSFile, _HasFileNo
+from pysam.libcalignedsegment import AlignedSegment
+from pysam.libcfaidx import FastaFile
+
+class IndexStats(NamedTuple):
+    contig: str
+    mapped: int
+    unmapped: int
+    total: int
+
+VALID_HEADER_TYPES: Dict[str, Type]
+VALID_HEADERS: Tuple[str]
+KNOWN_HEADER_FIELDS: Dict[str, Dict[str, Type]]
+VALID_HEADER_ORDER: Dict[str, Tuple[str]]
+
+def build_header_line(fields: Dict[str, str], record: str) -> str: ...
+
+class AlignmentHeader:
+    def __init__(self) -> None: ...
+    @classmethod
+    def _from_text_and_lengths(
+        cls,
+        text: Optional[str],
+        reference_names: Optional[Sequence[str]],
+        reference_lengths: Optional[Sequence[int]],
+    ) -> AlignmentHeader: ...
+    @classmethod
+    def from_text(cls, text: str) -> AlignmentHeader: ...
+    @classmethod
+    def from_dict(cls, header_dict: Dict) -> AlignmentHeader: ...
+    @classmethod
+    def from_references(
+        cls,
+        reference_names: Sequence[str],
+        reference_lengths: Sequence[int],
+        text: Optional[str] = ...,
+        add_sq_text: bool = ...,
+    ) -> AlignmentHeader: ...
+    def __bool__(self) -> bool: ...
+    def copy(self) -> AlignmentHeader: ...
+    @property
+    def nreferences(self) -> int: ...
+    @property
+    def references(self) -> Tuple[str]: ...
+    @property
+    def lengths(self) -> Tuple[int]: ...
+    def to_dict(self) -> Dict: ...
+    def get_reference_name(self, tid: int) -> Optional[str]: ...
+    def get_reference_length(self, reference: int) -> int: ...
+    def is_valid_tid(self, tid: int) -> bool: ...
+    def get_tid(self, reference: int) -> int: ...
+
+class AlignmentFile(HTSFile):
+    def __init__(
+        self,
+        filename: Union[str, bytes, int, _HasFileNo],
+        mode: Optional[
+            Literal["r", "w", "wh", "rb", "wb", "wbu", "wb0", "rc", "wc"]
+        ] = ...,
+        template: Optional[AlignmentFile] = ...,
+        reference_names: Optional[Sequence[str]] = ...,
+        reference_lengths: Optional[Sequence[int]] = ...,
+        reference_filename: Optional[str] = ...,
+        text: Optional[str] = ...,
+        header: Union[None, Dict, AlignmentHeader] = ...,
+        add_sq_text: bool = ...,
+        add_sam_header: bool = ...,
+        check_sq: bool = ...,
+        index_filename: Optional[str] = ...,
+        filepath_index: Optional[str] = ...,
+        require_index: bool = ...,
+        duplicate_filehandle: bool = ...,
+        ignore_truncation: bool = ...,
+        format_options: Optional[Sequence[str]] = ...,
+        threads: int = ...,
+    ) -> None: ...
+    def has_index(self) -> bool: ...
+    def check_index(self) -> bool: ...
+    def fetch(
+        self,
+        contig: Optional[str] = ...,
+        start: Optional[int] = ...,
+        stop: Optional[int] = ...,
+        region: Optional[str] = ...,
+        tid: Optional[int] = ...,
+        until_eof: bool = ...,
+        multiple_iterators: bool = ...,
+        reference: Optional[str] = ...,
+        end: int = ...,
+    ) -> IteratorRow: ...
+    def head(self, n: int, multiple_iterators: bool = ...) -> IteratorRow: ...
+    def mate(self, read: AlignedSegment) -> AlignedSegment: ...
+    def pileup(
+        self,
+        contig: Optional[str] = ...,
+        start: Optional[int] = ...,
+        stop: Optional[int] = ...,
+        region: Optional[str] = ...,
+        reference: Optional[str] = ...,
+        end: Optional[int] = ...,
+        truncate: bool = ...,
+        max_depth: int = ...,
+        stepper: str = ...,
+        fastafile: Optional[FastaFile] = ...,
+        ignore_overlaps: bool = ...,
+        flag_filter: int = ...,
+        flag_require: int = ...,
+        ignore_orphans: bool = ...,
+        min_base_quality: int = ...,
+        adjust_capq_threshold: int = ...,
+        min_mapping_quality: int = ...,
+        compute_baq: bool = ...,
+        redo_baq: bool = ...,
+    ) -> IteratorColumn: ...
+    def count(
+        self,
+        contig: Optional[str] = ...,
+        start: Optional[int] = ...,
+        stop: Optional[int] = ...,
+        region: Optional[str] = ...,
+        until_eof: bool = ...,
+        read_callback: Union[str, Callable[[AlignedSegment], bool]] = ...,
+        reference: Optional[str] = ...,
+        end: Optional[int] = ...,
+    ) -> int: ...
+    def count_coverage(
+        self,
+        contig: Optional[str] = ...,
+        start: Optional[int] = ...,
+        stop: Optional[int] = ...,
+        region: Optional[str] = ...,
+        quality_threshold: int = ...,
+        read_callback: Union[str, Callable[[AlignedSegment], bool]] = ...,
+        reference: Optional[str] = ...,
+        end: Optional[int] = ...,
+    ) -> Tuple[array.array, array.array, array.array, array.array]: ...
+    def find_introns_slow(
+        self, read_iterator: Iterable[AlignedSegment]
+    ) -> Dict[Tuple[int, int], int]: ...
+    def find_introns(
+        self, read_iterator: Iterable[AlignedSegment]
+    ) -> Dict[Tuple[int, int], int]: ...
+    def close(self) -> None: ...
+    def write(self, read: AlignedSegment) -> int: ...
+    def __enter__(self) -> AlignmentFile: ...
+    def __exit__(self, exc_type, exc_value, traceback): ...
+    @property
+    def mapped(self) -> int: ...
+    @property
+    def unmapped(self) -> int: ...
+    @property
+    def nocoordinate(self) -> int: ...
+    def get_index_statistics(self) -> List[IndexStats]: ...
+    def __iter__(self) -> Any: ...
+    def __next__(self) -> Any: ...
+    def is_valid_tid(self, tid: int) -> bool: ...
+    def get_tid(self, reference: str) -> int: ...
+    def get_reference_name(self, tid: int) -> str: ...
+    def get_reference_length(self, reference: str) -> int: ...
+    @property
+    def nreferences(self) -> int: ...
+    @property
+    def references(self) -> Tuple[str, ...]: ...
+    @property
+    def lengths(self) -> Tuple[int, ...]: ...
+    @property
+    def reference_filename(self) -> Optional[str]: ...
+    @property
+    def header(self) -> AlignmentHeader: ...
+
+class IteratorRow:
+    def __iter__(self) -> IteratorRow: ...
+    def __next__(self) -> PileupColumn: ...
+
+class IteratorRowAll(IteratorRow): ...
+class IteratorRowAllRefs(IteratorRow): ...
+class IteratorRowHead(IteratorRow): ...
+class IteratorRowRegion(IteratorRow): ...
+class IteratorRowSelection(IteratorRow): ...
+
+class IteratorColumn:
+    def __iter__(self) -> IteratorRow: ...
+    def __next__(self) -> PileupColumn: ...
+    @property
+    def seq_len(self) -> int: ...
+    def add_reference(self, fastafile: FastaFile) -> None: ...
+    def has_reference(self) -> bool: ...
+
+class IteratorColumnAll(IteratorColumn): ...
+class IteratorColumnAllRefs(IteratorColumn): ...
+class IteratorColumnRegion(IteratorColumn): ...
+
+class SNPCall:
+    @property
+    def tid(self) -> int: ...
+    @property
+    def pos(self) -> int: ...
+    @property
+    def reference_base(self) -> str: ...
+    @property
+    def genotype(self) -> str: ...
+    @property
+    def consensus_quality(self) -> int: ...
+    @property
+    def snp_quality(self) -> int: ...
+    @property
+    def mapping_quality(self) -> int: ...
+    @property
+    def coverage(self) -> int: ...
+
+class IndexedReads:
+    def __init__(
+        self, samfile: AlignmentFile, multiple_iterators: bool = ...
+    ) -> None: ...
+    def build(self) -> None: ...
+    def find(self, query_name: str) -> IteratorRow: ...
diff --git a/pysam/libcalignmentfile.pyx b/pysam/libcalignmentfile.pyx
new file mode 100644
index 0000000..799258a
--- /dev/null
+++ b/pysam/libcalignmentfile.pyx
@@ -0,0 +1,2988 @@
+# cython: embedsignature=True
+# cython: profile=True
+########################################################
+########################################################
+# Cython wrapper for SAM/BAM/CRAM files based on htslib
+########################################################
+# The principal classes defined in this module are:
+#
+# class AlignmentFile   read/write access to SAM/BAM/CRAM formatted files
+#
+# class AlignmentHeader manage SAM/BAM/CRAM header data
+#
+# class IndexedReads    index a SAM/BAM/CRAM file by query name while keeping
+#                       the original sort order intact
+#
+# Additionally this module defines numerous additional classes that
+# are part of the internal API. These are:
+#
+# Various iterator classes to iterate over alignments in sequential
+# (IteratorRow) or in a stacked fashion (IteratorColumn):
+#
+# class IteratorRow
+# class IteratorRowRegion
+# class IteratorRowHead
+# class IteratorRowAll
+# class IteratorRowAllRefs
+# class IteratorRowSelection
+# class IteratorColumn
+# class IteratorColumnRegion
+# class IteratorColumnAll
+# class IteratorColumnAllRefs
+#
+########################################################
+#
+# The MIT License
+#
+# Copyright (c) 2015 Andreas Heger
+#
+# Permission is hereby granted, free of charge, to any person obtaining a
+# copy of this software and associated documentation files (the "Software"),
+# to deal in the Software without restriction, including without limitation
+# the rights to use, copy, modify, merge, publish, distribute, sublicense,
+# and/or sell copies of the Software, and to permit persons to whom the
+# Software is furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.  IN NO EVENT SHALL
+# THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+# DEALINGS IN THE SOFTWARE.
+#
+########################################################
+import os
+import collections
+try:
+    from collections.abc import Sequence, Mapping  # noqa
+except ImportError:
+    from collections import Sequence, Mapping  # noqa
+import re
+import warnings
+import array
+from libc.errno  cimport errno, EPIPE
+from libc.string cimport strcmp, strpbrk, strerror
+from libc.stdint cimport INT32_MAX
+
+from cpython cimport array as c_array
+from cpython.version cimport PY_MAJOR_VERSION
+
+from pysam.libcutils cimport force_bytes, force_str, charptr_to_str
+from pysam.libcutils cimport encode_filename, from_string_and_size
+from pysam.libcalignedsegment cimport makeAlignedSegment, makePileupColumn
+from pysam.libchtslib cimport HTSFile, hisremote
+
+if PY_MAJOR_VERSION >= 3:
+    from io import StringIO
+else:
+    from StringIO import StringIO
+
+cimport cython
+
+
+__all__ = [
+    "AlignmentFile",
+    "AlignmentHeader",
+    "IteratorRow",
+    "IteratorColumn",
+    "IndexedReads"]
+
+IndexStats = collections.namedtuple("IndexStats",
+                                    ("contig",
+                                     "mapped",
+                                     "unmapped",
+                                     "total"))
+
+########################################################
+## global variables
+# maximum genomic coordinace
+# for some reason, using 'int' causes overflow
+cdef int MAX_POS = (1 << 31) - 1
+
+# valid types for SAM headers
+VALID_HEADER_TYPES = {"HD" : Mapping,
+                      "SQ" : Sequence,
+                      "RG" : Sequence,
+                      "PG" : Sequence,
+                      "CO" : Sequence}
+
+# order of records within SAM headers
+VALID_HEADERS = ("HD", "SQ", "RG", "PG", "CO")
+
+# default type conversions within SAM header records
+KNOWN_HEADER_FIELDS = {"HD" : {"VN" : str, "SO" : str, "GO" : str},
+                       "SQ" : {"SN" : str, "LN" : int, "AS" : str,
+                               "M5" : str, "SP" : str, "UR" : str,
+                               "AH" : str,},
+                       "RG" : {"ID" : str, "CN" : str, "DS" : str,
+                               "DT" : str, "FO" : str, "KS" : str,
+                               "LB" : str, "PG" : str, "PI" : str,
+                               "PL" : str, "PM" : str, "PU" : str,
+                               "SM" : str,},
+                       "PG" : {"ID" : str, "PN" : str, "CL" : str,
+                               "PP" : str, "DS" : str, "VN" : str,},}
+
+# output order of fields within records. Ensure that CL is at
+# the end as parsing a CL will ignore any subsequent records.
+VALID_HEADER_ORDER = {"HD" : ("VN", "SO", "GO"),
+                      "SQ" : ("SN", "LN", "AS", "M5",
+                               "UR", "SP", "AH"),
+                      "RG" : ("ID", "CN", "SM", "LB",
+                              "PU", "PI", "DT", "DS",
+                              "PL", "FO", "KS", "PG",
+                              "PM"),
+                      "PG" : ("PN", "ID", "VN", "PP",
+                              "DS", "CL"),}
+
+
+def build_header_line(fields, record):
+    '''build a header line from `fields` dictionary for `record`'''
+
+    # TODO: add checking for field and sort order
+    line = ["@%s" % record]
+        # comment
+    if record == "CO":
+        line.append(fields)
+    # user tags
+    elif record.islower():
+        for key in sorted(fields):
+            line.append("%s:%s" % (key, str(fields[key])))
+    # defined tags
+    else:
+        # write fields of the specification
+        for key in VALID_HEADER_ORDER[record]:
+            if key in fields:
+                line.append("%s:%s" % (key, str(fields[key])))
+        # write user fields
+        for key in fields:
+            if not key.isupper():
+                line.append("%s:%s" % (key, str(fields[key])))
+
+    return "\t".join(line)
+
+
+cdef AlignmentHeader makeAlignmentHeader(bam_hdr_t *hdr):
+    if not hdr:
+        raise ValueError('cannot create AlignmentHeader, received NULL pointer')
+
+    # check: is AlignmetHeader.__cinit__ called?
+    cdef AlignmentHeader header = AlignmentHeader.__new__(AlignmentHeader)
+    header.ptr = hdr
+
+    return header
+
+def read_failure_reason(code):
+    if code == -2:
+        return 'truncated file'
+    else:
+        return "error {} while reading file".format(code)
+
+
+# the following should be class-method for VariantHeader, but cdef @classmethods
+# are not implemented in cython.
+cdef int fill_AlignmentHeader_from_list(bam_hdr_t *dest,
+                                        reference_names,
+                                        reference_lengths,
+                                        add_sq_text=True,
+                                        text=None) except -1:
+    """build header from list of reference names and lengths.
+    """
+
+cdef class AlignmentHeader(object):
+    """header information for a :class:`AlignmentFile` object
+
+    Parameters
+    ----------
+    header_dict : dict
+        build header from a multi-level dictionary. The
+        first level are the four types ('HD', 'SQ', ...). The second
+        level are a list of lines, with each line being a list of
+        tag-value pairs. The header is constructed first from all the
+        defined fields, followed by user tags in alphabetical
+        order. Alternatively, an :class:`~pysam.AlignmentHeader`
+        object can be passed directly.
+
+    text : string
+        use the string provided as the header
+
+    reference_names : list
+        see reference_lengths
+
+    reference_lengths : list
+        build header from list of chromosome names and lengths.  By
+        default, 'SQ' and 'LN' tags will be added to the header
+        text. This option can be changed by unsetting the flag
+        `add_sq_text`.
+
+    add_sq_text : bool
+        do not add 'SQ' and 'LN' tags to header. This option permits
+        construction :term:`SAM` formatted files without a header.
+
+    """
+
+    # See makeVariantHeader for C constructor
+    def __cinit__(self):
+        self.ptr = NULL
+
+    # Python constructor
+    def __init__(self):
+        self.ptr = bam_hdr_init()
+        if self.ptr is NULL:
+            raise MemoryError("could not create header")
+
+    @classmethod
+    def _from_text_and_lengths(cls, text, reference_names, reference_lengths):
+
+        cdef AlignmentHeader self = AlignmentHeader()
+        cdef char *ctext
+        cdef int l_text
+        cdef int n, x
+        if text is not None:
+            btext = force_bytes(text)
+            ctext = btext
+            l_text = len(btext)
+            self.ptr.text = <char*>calloc(l_text + 1, sizeof(char))
+            if self.ptr.text == NULL:
+                raise MemoryError("could not allocate {} bytes".format(l_text + 1), sizeof(char))
+            self.ptr.l_text = l_text
+            memcpy(self.ptr.text, ctext, l_text + 1)
+
+        if reference_names and reference_lengths:
+            reference_names = [force_bytes(ref) for ref in reference_names]
+
+            self.ptr.n_targets = len(reference_names)
+
+            n = sum([len(reference_names) + 1])
+            self.ptr.target_name = <char**>calloc(n, sizeof(char*))
+            if self.ptr.target_name == NULL:
+                raise MemoryError("could not allocate {} bytes".format(n, sizeof(char *)))
+
+            self.ptr.target_len = <uint32_t*>calloc(n, sizeof(uint32_t))
+            if self.ptr.target_len == NULL:
+                raise MemoryError("could not allocate {} bytes".format(n, sizeof(uint32_t)))
+
+            for x from 0 <= x < self.ptr.n_targets:
+                self.ptr.target_len[x] = reference_lengths[x]
+                name = reference_names[x]
+                self.ptr.target_name[x] = <char*>calloc(len(name) + 1, sizeof(char))
+                if self.ptr.target_name[x] == NULL:
+                    raise MemoryError("could not allocate {} bytes".format(len(name) + 1, sizeof(char)))
+                strncpy(self.ptr.target_name[x], name, len(name))
+
+        return self
+
+    @classmethod
+    def from_text(cls, text):
+
+        reference_names, reference_lengths = [], []
+        for line in text.splitlines():
+            if line.startswith("@SQ"):
+                fields = dict([x.split(":", 1) for x in line.split("\t")[1:]])
+                try:
+                    reference_names.append(fields["SN"])
+                    reference_lengths.append(int(fields["LN"]))
+                except KeyError:
+                    raise KeyError("incomplete sequence information in '%s'" % str(fields))
+                except ValueError:
+                    raise ValueError("wrong sequence information in '%s'" % str(fields))
+
+        return cls._from_text_and_lengths(text, reference_names, reference_lengths)
+
+    @classmethod
+    def from_dict(cls, header_dict):
+
+        cdef list lines = []
+        # first: defined tags
+        for record in VALID_HEADERS:
+            if record in header_dict:
+                data = header_dict[record]
+                if not isinstance(data, VALID_HEADER_TYPES[record]):
+                    raise ValueError(
+                        "invalid type for record %s: %s, expected %s".format(
+                            record, type(data), VALID_HEADER_TYPES[record]))
+                if isinstance(data, Mapping):
+                    lines.append(build_header_line(data, record))
+                else:
+                    for fields in header_dict[record]:
+                        lines.append(build_header_line(fields, record))
+
+        # then: user tags (lower case), sorted alphabetically
+        for record, data in sorted(header_dict.items()):
+            if record in VALID_HEADERS:
+                continue
+            if isinstance(data, Mapping):
+                lines.append(build_header_line(data, record))
+            else:
+                for fields in header_dict[record]:
+                    lines.append(build_header_line(fields, record))
+
+        text = "\n".join(lines) + "\n"
+
+        reference_names, reference_lengths = [], []
+        if "SQ" in header_dict:
+            for fields in header_dict["SQ"]:
+                try:
+                    reference_names.append(fields["SN"])
+                    reference_lengths.append(fields["LN"])
+                except KeyError:
+                    raise KeyError("incomplete sequence information in '%s'" % str(fields))
+
+        return cls._from_text_and_lengths(text, reference_names, reference_lengths)
+
+    @classmethod
+    def from_references(cls, reference_names, reference_lengths, text=None, add_sq_text=True):
+
+        if len(reference_names) != len(reference_lengths):
+            raise ValueError("number of reference names and lengths do not match")
+
+        # optionally, if there is no text, add a SAM compatible header to output file.
+        if text is None and add_sq_text:
+            text = "".join(["@SQ\tSN:{}\tLN:{}\n".format(x, y) for x, y in zip(
+                reference_names, reference_lengths)])
+
+        return cls._from_text_and_lengths(text, reference_names, reference_lengths)
+
+    def __dealloc__(self):
+        bam_hdr_destroy(self.ptr)
+        self.ptr = NULL
+
+    def __bool__(self):
+        return self.ptr != NULL
+
+    def copy(self):
+        return makeAlignmentHeader(bam_hdr_dup(self.ptr))
+
+    property nreferences:
+        """int with the number of :term:`reference` sequences in the file.
+
+        This is a read-only attribute."""
+        def __get__(self):
+            return self.ptr.n_targets
+
+    property references:
+        """tuple with the names of :term:`reference` sequences. This is a
+        read-only attribute"""
+        def __get__(self):
+            t = []
+            cdef int x
+            for x in range(self.ptr.n_targets):
+                t.append(charptr_to_str(self.ptr.target_name[x]))
+            return tuple(t)
+
+    property lengths:
+        """tuple of the lengths of the :term:`reference` sequences. This is a
+        read-only attribute. The lengths are in the same order as
+        :attr:`pysam.AlignmentFile.references`
+        """
+        def __get__(self):
+            t = []
+            cdef int x
+            for x in range(self.ptr.n_targets):
+                t.append(self.ptr.target_len[x])
+            return tuple(t)
+
+    def _build_sequence_section(self):
+        """return sequence section of header.
+
+        The sequence section is built from the list of reference names and
+        lengths stored in the BAM-file and not from any @SQ entries that
+        are part of the header's text section.
+        """
+
+        cdef int x
+        text = []
+        for x in range(self.ptr.n_targets):
+            text.append("@SQ\tSN:{}\tLN:{}\n".format(
+                force_str(self.ptr.target_name[x]),
+                self.ptr.target_len[x]))
+        return "".join(text)
+
+    def to_dict(self):
+        """return two-level dictionary with header information from the file.
+
+        The first level contains the record (``HD``, ``SQ``, etc) and
+        the second level contains the fields (``VN``, ``LN``, etc).
+
+        The parser is validating and will raise an AssertionError if
+        if encounters any record or field tags that are not part of
+        the SAM specification. Use the
+        :attr:`pysam.AlignmentFile.text` attribute to get the unparsed
+        header.
+
+        The parsing follows the SAM format specification with the
+        exception of the ``CL`` field. This option will consume the
+        rest of a header line irrespective of any additional fields.
+        This behaviour has been added to accommodate command line
+        options that contain characters that are not valid field
+        separators.
+
+        If no @SQ entries are within the text section of the header,
+        this will be automatically added from the reference names and
+        lengths stored in the binary part of the header.
+        """
+        result = collections.OrderedDict()
+
+        # convert to python string
+        t = self.__str__()
+        for line in t.split("\n"):
+            line = line.strip(' \0')
+            if not line:
+                continue
+            assert line.startswith("@"), \
+                "header line without '@': '%s'" % line
+            fields = line[1:].split("\t")
+            record = fields[0]
+            assert record in VALID_HEADER_TYPES, \
+                "header line with invalid type '%s': '%s'" % (record, line)
+
+            # treat comments
+            if record == "CO":
+                if record not in result:
+                    result[record] = []
+                result[record].append("\t".join( fields[1:]))
+                continue
+            # the following is clumsy as generators do not work?
+            x = {}
+
+            for idx, field in enumerate(fields[1:]):
+                if ":" not in field:
+                    raise ValueError("malformatted header: no ':' in field" )
+                key, value = field.split(":", 1)
+                if key in ("CL",):
+                    # special treatment for command line
+                    # statements (CL). These might contain
+                    # characters that are non-conformant with
+                    # the valid field separators in the SAM
+                    # header. Thus, in contravention to the
+                    # SAM API, consume the rest of the line.
+                    key, value = "\t".join(fields[idx+1:]).split(":", 1)
+                    x[key] = KNOWN_HEADER_FIELDS[record][key](value)
+                    break
+
+                # interpret type of known header record tags, default to str
+                x[key] = KNOWN_HEADER_FIELDS[record].get(key, str)(value)
+
+            if VALID_HEADER_TYPES[record] == Mapping:
+                if record in result:
+                    raise ValueError(
+                        "multiple '%s' lines are not permitted" % record)
+
+                result[record] = x
+            elif VALID_HEADER_TYPES[record] == Sequence:
+                if record not in result: result[record] = []
+                result[record].append(x)
+
+        # if there are no SQ lines in the header, add the
+        # reference names from the information in the bam
+        # file.
+        #
+        # Background: c-samtools keeps the textual part of the
+        # header separate from the list of reference names and
+        # lengths. Thus, if a header contains only SQ lines,
+        # the SQ information is not part of the textual header
+        # and thus are missing from the output. See issue 84.
+        if "SQ" not in result:
+            sq = []
+            for ref, length in zip(self.references, self.lengths):
+                sq.append({'LN': length, 'SN': ref })
+            result["SQ"] = sq
+
+        return result
+
+    def as_dict(self):
+        """deprecated, use :meth:`to_dict()` instead"""
+        return self.to_dict()
+
+    def get_reference_name(self, tid):
+        if tid == -1:
+            return None
+        if not 0 <= tid < self.ptr.n_targets:
+            raise ValueError("reference_id %i out of range 0<=tid<%i" %
+                             (tid, self.ptr.n_targets))
+        return charptr_to_str(self.ptr.target_name[tid])
+
+    def get_reference_length(self, reference):
+        cdef int tid = self.get_tid(reference)
+        if tid < 0:
+            raise KeyError("unknown reference {}".format(reference))
+        else:
+            return self.ptr.target_len[tid]
+
+    def is_valid_tid(self, int tid):
+        """
+        return True if the numerical :term:`tid` is valid; False otherwise.
+
+        Note that the unmapped tid code (-1) counts as an invalid.
+        """
+        return 0 <= tid < self.ptr.n_targets
+
+    def get_tid(self, reference):
+        """
+        return the numerical :term:`tid` corresponding to
+        :term:`reference`
+
+        returns -1 if reference is not known.
+        """
+        reference = force_bytes(reference)
+        tid = bam_name2id(self.ptr, reference)
+        if tid < -1:
+            raise ValueError('could not parse header')
+        return tid
+
+    def __str__(self):
+        '''string with the full contents of the :term:`sam file` header as a
+        string.
+
+        If no @SQ entries are within the text section of the header,
+        this will be automatically added from the reference names and
+        lengths stored in the binary part of the header.
+
+        See :attr:`pysam.AlignmentFile.header.to_dict()` to get a parsed
+        representation of the header.
+        '''
+        text = from_string_and_size(self.ptr.text, self.ptr.l_text)
+        if "@SQ" not in text:
+            text += "\n" + self._build_sequence_section()
+        return text
+
+    # dictionary access methods, for backwards compatibility.
+    def __setitem__(self, key, value):
+        raise TypeError("AlignmentHeader does not support item assignment (use header.to_dict()")
+
+    def __getitem__(self, key):
+        return self.to_dict().__getitem__(key)
+
+    def items(self):
+        return self.to_dict().items()
+
+    # PY2 compatibility
+    def iteritems(self):
+        return self.to_dict().items()
+
+    def keys(self):
+        return self.to_dict().keys()
+
+    def values(self):
+        return self.to_dict().values()
+
+    def get(self, *args):
+        return self.to_dict().get(*args)
+
+    def __len__(self):
+        return self.to_dict().__len__()
+
+    def __contains__(self, key):
+        return self.to_dict().__contains__(key)
+
+
+cdef class AlignmentFile(HTSFile):
+    """AlignmentFile(filepath_or_object, mode=None, template=None,
+    reference_names=None, reference_lengths=None, text=NULL,
+    header=None, add_sq_text=False, check_header=True, check_sq=True,
+    reference_filename=None, filename=None, index_filename=None,
+    filepath_index=None, require_index=False, duplicate_filehandle=True,
+    ignore_truncation=False, threads=1)
+
+    A :term:`SAM`/:term:`BAM`/:term:`CRAM` formatted file.
+
+    If `filepath_or_object` is a string, the file is automatically
+    opened. If `filepath_or_object` is a python File object, the
+    already opened file will be used.
+
+    If the file is opened for reading and an index exists (if file is BAM, a
+    .bai file or if CRAM a .crai file), it will be opened automatically.
+    `index_filename` may be specified explicitly. If the index is not named
+    in the standard manner, not located in the same directory as the
+    BAM/CRAM file, or is remote.  Without an index, random access via
+    :meth:`~pysam.AlignmentFile.fetch` and :meth:`~pysam.AlignmentFile.pileup`
+    is disabled.
+
+    For writing, the header of a :term:`SAM` file/:term:`BAM` file can
+    be constituted from several sources (see also the samtools format
+    specification):
+
+        1. If `template` is given, the header is copied from another
+           `AlignmentFile` (`template` must be a
+           :class:`~pysam.AlignmentFile`).
+
+        2. If `header` is given, the header is built from a
+           multi-level dictionary.
+
+        3. If `text` is given, new header text is copied from raw
+           text.
+
+        4. The names (`reference_names`) and lengths
+           (`reference_lengths`) are supplied directly as lists.
+
+    When reading or writing a CRAM file, the filename of a FASTA-formatted
+    reference can be specified with `reference_filename`.
+
+    By default, if a file is opened in mode 'r', it is checked
+    for a valid header (`check_header` = True) and a definition of
+    chromosome names (`check_sq` = True).
+
+    Parameters
+    ----------
+    mode : string
+        `mode` should be ``r`` for reading or ``w`` for writing. The
+        default is text mode (:term:`SAM`). For binary (:term:`BAM`)
+        I/O you should append ``b`` for compressed or ``u`` for
+        uncompressed :term:`BAM` output.  Use ``h`` to output header
+        information in text (:term:`TAM`) mode. Use ``c`` for
+        :term:`CRAM` formatted files.
+
+        If ``b`` is present, it must immediately follow ``r`` or
+        ``w``.  Valid modes are ``r``, ``w``, ``wh``, ``rb``, ``wb``,
+        ``wbu``, ``wb0``, ``rc`` and ``wc``. For instance, to open a
+        :term:`BAM` formatted file for reading, type::
+
+           f = pysam.AlignmentFile('ex1.bam','rb')
+
+        If mode is not specified, the method will try to auto-detect
+        in the order 'rb', 'r', thus both the following should work::
+
+            f1 = pysam.AlignmentFile('ex1.bam')
+            f2 = pysam.AlignmentFile('ex1.sam')
+
+    template : AlignmentFile
+        when writing, copy header from file `template`.
+
+    header :  dict or AlignmentHeader
+        when writing, build header from a multi-level dictionary. The
+        first level are the four types ('HD', 'SQ', ...). The second
+        level are a list of lines, with each line being a list of
+        tag-value pairs. The header is constructed first from all the
+        defined fields, followed by user tags in alphabetical
+        order. Alternatively, an :class:`~pysam.AlignmentHeader`
+        object can be passed directly.
+
+    text : string
+        when writing, use the string provided as the header
+
+    reference_names : list
+        see reference_lengths
+
+    reference_lengths : list
+        when writing or opening a SAM file without header build header
+        from list of chromosome names and lengths.  By default, 'SQ'
+        and 'LN' tags will be added to the header text. This option
+        can be changed by unsetting the flag `add_sq_text`.
+
+    add_sq_text : bool
+        do not add 'SQ' and 'LN' tags to header. This option permits
+        construction :term:`SAM` formatted files without a header.
+
+    add_sam_header : bool
+        when outputting SAM the default is to output a header. This is
+        equivalent to opening the file in 'wh' mode. If this option is
+        set to False, no header will be output. To read such a file,
+        set `check_header=False`.
+
+    check_header : bool
+        obsolete: when reading a SAM file, check if header is present
+        (default=True)
+
+    check_sq : bool
+        when reading, check if SQ entries are present in header
+        (default=True)
+
+    reference_filename : string
+        Path to a FASTA-formatted reference file. Valid only for CRAM files.
+        When reading a CRAM file, this overrides both ``$REF_PATH`` and the URL
+        specified in the header (``UR`` tag), which are normally used to find
+        the reference.
+
+    index_filename : string
+        Explicit path to the index file.  Only needed if the index is not
+        named in the standard manner, not located in the same directory as
+        the BAM/CRAM file, or is remote.  An IOError is raised if the index
+        cannot be found or is invalid.
+
+    filepath_index : string
+        Alias for `index_filename`.
+
+    require_index : bool
+        When reading, require that an index file is present and is valid or
+        raise an IOError.  (default=False)
+
+    filename : string
+        Alternative to filepath_or_object. Filename of the file
+        to be opened.
+
+    duplicate_filehandle: bool
+        By default, file handles passed either directly or through
+        File-like objects will be duplicated before passing them to
+        htslib. The duplication prevents issues where the same stream
+        will be closed by htslib and through destruction of the
+        high-level python object. Set to False to turn off
+        duplication.
+
+    ignore_truncation: bool
+        Issue a warning, instead of raising an error if the current file
+        appears to be truncated due to a missing EOF marker.  Only applies
+        to bgzipped formats. (Default=False)
+
+    format_options: list
+        A list of key=value strings, as accepted by --input-fmt-option and
+        --output-fmt-option in samtools.
+    threads: integer
+        Number of threads to use for compressing/decompressing BAM/CRAM files.
+        Setting threads to > 1 cannot be combined with `ignore_truncation`.
+        (Default=1)
+    """
+
+    def __cinit__(self, *args, **kwargs):
+        self.htsfile = NULL
+        self.filename = None
+        self.mode = None
+        self.threads = 1
+        self.is_stream = False
+        self.is_remote = False
+        self.index = NULL
+
+        if "filename" in kwargs:
+            args = [kwargs["filename"]]
+            del kwargs["filename"]
+
+        self._open(*args, **kwargs)
+
+        # allocate memory for iterator
+        self.b = <bam1_t*>calloc(1, sizeof(bam1_t))
+        if self.b == NULL:
+            raise MemoryError("could not allocate memory of size {}".format(sizeof(bam1_t)))
+
+    def has_index(self):
+        """return true if htsfile has an existing (and opened) index.
+        """
+        return self.index != NULL
+
+    def check_index(self):
+        """return True if index is present.
+
+        Raises
+        ------
+
+        AttributeError
+            if htsfile is :term:`SAM` formatted and thus has no index.
+
+        ValueError
+            if htsfile is closed or index could not be opened.
+        """
+
+        if not self.is_open:
+            raise ValueError("I/O operation on closed file")
+        if not self.is_bam and not self.is_cram:
+            raise AttributeError(
+                "AlignmentFile.mapped only available in bam files")
+        if self.index == NULL:
+            raise ValueError(
+                "mapping information not recorded in index "
+                "or index not available")
+        return True
+
+    def _open(self,
+              filepath_or_object,
+              mode=None,
+              AlignmentFile template=None,
+              reference_names=None,
+              reference_lengths=None,
+              reference_filename=None,
+              text=None,
+              header=None,
+              port=None,
+              add_sq_text=True,
+              add_sam_header=True,
+              check_header=True,
+              check_sq=True,
+              index_filename=None,
+              filepath_index=None,
+              require_index=False,
+              referencenames=None,
+              referencelengths=None,
+              duplicate_filehandle=True,
+              ignore_truncation=False,
+              format_options=None,
+              threads=1):
+        '''open a sam, bam or cram formatted file.
+
+        If _open is called on an existing file, the current file
+        will be closed and a new file will be opened.
+
+        '''
+        cdef char *cfilename = NULL
+        cdef char *creference_filename = NULL
+        cdef char *cindexname = NULL
+        cdef char *cmode = NULL
+        cdef bam_hdr_t * hdr = NULL
+
+        if threads > 1 and ignore_truncation:
+           # This won't raise errors if reaching a truncated alignment,
+           # because bgzf_mt_reader in htslib does not deal with
+           # bgzf_mt_read_block returning non-zero values, contrary
+           # to bgzf_read (https://github.com/samtools/htslib/blob/1.7/bgzf.c#L888)
+           # Better to avoid this (for now) than to produce seemingly correct results.
+           raise ValueError('Cannot add extra threads when "ignore_truncation" is True')
+        self.threads = threads
+
+        # for backwards compatibility:
+        if referencenames is not None:
+            reference_names = referencenames
+        if referencelengths is not None:
+            reference_lengths = referencelengths
+
+        # close a previously opened file
+        if self.is_open:
+            self.close()
+
+        # autodetection for read
+        if mode is None:
+            mode = "r"
+
+        if add_sam_header and mode == "w":
+            mode = "wh"
+
+        assert mode in ("r", "w", "rb", "wb", "wh",
+                        "wbu", "rU", "wb0",
+                        "rc", "wc"), \
+            "invalid file opening mode `%s`" % mode
+
+        self.duplicate_filehandle = duplicate_filehandle
+
+        # StringIO not supported
+        if isinstance(filepath_or_object, StringIO):
+            raise NotImplementedError(
+                "access from StringIO objects not supported")
+        # reading from a file descriptor
+        elif isinstance(filepath_or_object, int):
+            self.filename = filepath_or_object
+            filename = None
+            self.is_remote = False
+            self.is_stream = True
+        # reading from a File object or other object with fileno
+        elif hasattr(filepath_or_object, "fileno"):
+            if filepath_or_object.closed:
+                raise ValueError('I/O operation on closed file')
+            self.filename = filepath_or_object
+            # .name can be TextIOWrapper
+            try:
+                filename = encode_filename(str(filepath_or_object.name))
+                cfilename = filename
+            except AttributeError:
+                filename = None
+            self.is_remote = False
+            self.is_stream = True
+        # what remains is a filename
+        else:
+            self.filename = filename = encode_filename(filepath_or_object)
+            cfilename = filename
+            self.is_remote = hisremote(cfilename)
+            self.is_stream = self.filename == b'-'
+
+        # for htslib, wbu seems to not work
+        if mode == "wbu":
+            mode = "wb0"
+
+        self.mode = force_bytes(mode)
+        self.reference_filename = reference_filename = encode_filename(
+            reference_filename)
+
+        if mode[0] == 'w':
+            # open file for writing
+
+            if not (template or header or text or (reference_names and reference_lengths)):
+                raise ValueError(
+                    "either supply options `template`, `header`, `text` or  both `reference_names` "
+                    "and `reference_lengths` for writing")
+
+            if template:
+                # header is copied, though at the moment not strictly
+                # necessary as AlignmentHeader is immutable.
+                self.header = template.header.copy()
+            elif isinstance(header, AlignmentHeader):
+                self.header = header.copy()
+            elif isinstance(header, Mapping):
+                self.header = AlignmentHeader.from_dict(header)
+            elif reference_names and reference_lengths:
+                self.header = AlignmentHeader.from_references(
+                    reference_names,
+                    reference_lengths,
+                    add_sq_text=add_sq_text,
+                    text=text)
+            elif text:
+                self.header = AlignmentHeader.from_text(text)
+            else:
+                raise ValueError("not enough information to construct header. Please provide template, "
+                                 "header, text or reference_names/reference_lengths")
+            self.htsfile = self._open_htsfile()
+
+            if self.htsfile == NULL:
+                if errno:
+                    raise IOError(errno, "could not open alignment file `{}`: {}".format(
+                        force_str(filename),
+                        force_str(strerror(errno))))
+                else:
+                    raise ValueError("could not open alignment file `{}`".format(force_str(filename)))
+            if format_options and len(format_options):
+                self.add_hts_options(format_options)
+            # set filename with reference sequences. If no filename
+            # is given, the CRAM reference arrays will be built from
+            # the @SQ header in the header
+            if "c" in mode and reference_filename:
+                if (hts_set_fai_filename(self.htsfile, self.reference_filename) != 0):
+                    raise ValueError("failure when setting reference filename")
+
+            # write header to htsfile
+            if "b" in mode or "c" in mode or "h" in mode:
+                hdr = self.header.ptr
+                with nogil:
+                    sam_hdr_write(self.htsfile, hdr)
+
+        elif mode[0] == "r":
+            # open file for reading
+            self.htsfile = self._open_htsfile()
+
+            if self.htsfile == NULL:
+                if errno:
+                    raise IOError(errno, "could not open alignment file `{}`: {}".format(force_str(filename),
+                                  force_str(strerror(errno))))
+                else:
+                    raise ValueError("could not open alignment file `{}`".format(force_str(filename)))
+
+            if self.htsfile.format.category != sequence_data:
+                raise ValueError("file does not contain alignment data")
+
+            if format_options and len(format_options):
+                self.add_hts_options(format_options)
+
+            self.check_truncation(ignore_truncation)
+
+            # bam/cram files require a valid header
+            if self.is_bam or self.is_cram:
+                with nogil:
+                    hdr = sam_hdr_read(self.htsfile)
+                if hdr == NULL:
+                    raise ValueError(
+                        "file does not have a valid header (mode='%s') "
+                        "- is it BAM/CRAM format?" % mode)
+                self.header = makeAlignmentHeader(hdr)
+            else:
+                # in sam files a header is optional. If not given,
+                # user may provide reference names and lengths to built
+                # an on-the-fly header.
+                if reference_names and reference_lengths:
+                    # build header from a target names and lengths
+                    self.header = AlignmentHeader.from_references(
+                        reference_names=reference_names,
+                        reference_lengths=reference_lengths,
+                        add_sq_text=add_sq_text,
+                        text=text)
+                else:
+                    with nogil:
+                        hdr = sam_hdr_read(self.htsfile)
+                    if hdr == NULL:
+                        raise ValueError(
+                            "SAM? file does not have a valid header (mode='%s'), "
+                            "please provide reference_names and reference_lengths")
+                    self.header = makeAlignmentHeader(hdr)
+
+            # set filename with reference sequences
+            if self.is_cram and reference_filename:
+                creference_filename = self.reference_filename
+                hts_set_opt(self.htsfile,
+                            CRAM_OPT_REFERENCE,
+                            creference_filename)
+
+            if check_sq and self.header.nreferences == 0:
+                raise ValueError(
+                    ("file has no sequences defined (mode='%s') - "
+                     "is it SAM/BAM format? Consider opening with "
+                     "check_sq=False") % mode)
+
+            if self.is_bam or self.is_cram:
+                self.index_filename = index_filename or filepath_index
+                if self.index_filename:
+                    cindexname = bfile_name = encode_filename(self.index_filename)
+
+                if cfilename or cindexname:
+                    with nogil:
+                        self.index = sam_index_load2(self.htsfile, cfilename, cindexname)
+
+                    if not self.index and (cindexname or require_index):
+                        if errno:
+                            raise IOError(errno, force_str(strerror(errno)))
+                        else:
+                            raise IOError('unable to open index file `%s`' % self.index_filename)
+
+                elif require_index:
+                    raise IOError('unable to open index file')
+
+                # save start of data section
+                if not self.is_stream:
+                    self.start_offset = self.tell()
+
+    def fetch(self,
+              contig=None,
+              start=None,
+              stop=None,
+              region=None,
+              tid=None,
+              until_eof=False,
+              multiple_iterators=False,
+              reference=None,
+              end=None):
+        """fetch reads aligned in a :term:`region`.
+
+        See :meth:`~pysam.HTSFile.parse_region` for more information
+        on how genomic regions can be specified. :term:`reference` and
+        `end` are also accepted for backward compatibility as synonyms
+        for :term:`contig` and `stop`, respectively.
+
+        Without a `contig` or `region` all mapped reads in the file
+        will be fetched. The reads will be returned ordered by reference
+        sequence, which will not necessarily be the order within the
+        file. This mode of iteration still requires an index. If there is
+        no index, use `until_eof=True`.
+
+        If only `contig` is set, all reads aligned to `contig`
+        will be fetched.
+
+        A :term:`SAM` file does not allow random access. If `region`
+        or `contig` are given, an exception is raised.
+
+        Parameters
+        ----------
+
+        until_eof : bool
+
+           If `until_eof` is True, all reads from the current file
+           position will be returned in order as they are within the
+           file. Using this option will also fetch unmapped reads.
+
+        multiple_iterators : bool
+
+           If `multiple_iterators` is True, multiple
+           iterators on the same file can be used at the same time. The
+           iterator returned will receive its own copy of a filehandle to
+           the file effectively re-opening the file. Re-opening a file
+           creates some overhead, so beware.
+
+        Returns
+        -------
+
+		An iterator over a collection of reads. : IteratorRow
+
+        Raises
+        ------
+
+        ValueError
+            if the genomic coordinates are out of range or invalid or the
+            file does not permit random access to genomic coordinates.
+
+        """
+        cdef int rtid, rstart, rstop, has_coord
+
+        if not self.is_open:
+            raise ValueError( "I/O operation on closed file" )
+
+        has_coord, rtid, rstart, rstop = self.parse_region(
+            contig, start, stop, region, tid,
+            end=end, reference=reference)
+
+       # Turn of re-opening if htsfile is a stream
+        if self.is_stream:
+            multiple_iterators = False
+
+        if self.is_bam or self.is_cram:
+            if not until_eof and not self.is_remote:
+                if not self.has_index():
+                    raise ValueError(
+                        "fetch called on bamfile without index")
+
+            if has_coord:
+                return IteratorRowRegion(
+                    self, rtid, rstart, rstop,
+                    multiple_iterators=multiple_iterators)
+            else:
+                if until_eof:
+                    return IteratorRowAll(
+                        self,
+                        multiple_iterators=multiple_iterators)
+                else:
+                    # AH: check - reason why no multiple_iterators for
+                    # AllRefs?
+                    return IteratorRowAllRefs(
+                        self,
+                        multiple_iterators=multiple_iterators)
+        else:
+            if has_coord:
+                raise ValueError(
+                    "fetching by region is not available for SAM files")
+
+            if multiple_iterators == True:
+                raise ValueError(
+                    "multiple iterators not implemented for SAM files")
+
+            return IteratorRowAll(self,
+                                  multiple_iterators=multiple_iterators)
+
+    def head(self, n, multiple_iterators=True):
+        '''return an iterator over the first n alignments.
+
+        This iterator is is useful for inspecting the bam-file.
+
+        Parameters
+        ----------
+
+        multiple_iterators : bool
+
+            is set to True by default in order to
+            avoid changing the current file position.
+
+        Returns
+        -------
+
+		an iterator over a collection of reads : IteratorRowHead
+
+        '''
+        return IteratorRowHead(self, n,
+                               multiple_iterators=multiple_iterators)
+
+    def mate(self, AlignedSegment read):
+        '''return the mate of :class:`pysam.AlignedSegment` `read`.
+
+        .. note::
+
+            Calling this method will change the file position.
+            This might interfere with any iterators that have
+            not re-opened the file.
+
+        .. note::
+
+           This method is too slow for high-throughput processing.
+           If a read needs to be processed with its mate, work
+           from a read name sorted file or, better, cache reads.
+
+        Returns
+        -------
+
+        the mate : AlignedSegment
+
+        Raises
+        ------
+
+        ValueError
+            if the read is unpaired or the mate is unmapped
+
+        '''
+        cdef uint32_t flag = read._delegate.core.flag
+
+        if flag & BAM_FPAIRED == 0:
+            raise ValueError("read %s: is unpaired" %
+                             (read.query_name))
+        if flag & BAM_FMUNMAP != 0:
+            raise ValueError("mate %s: is unmapped" %
+                             (read.query_name))
+
+        # xor flags to get the other mate
+        cdef int x = BAM_FREAD1 + BAM_FREAD2
+        flag = (flag ^ x) & x
+
+        # Make sure to use a separate file to jump around
+        # to mate as otherwise the original file position
+        # will be lost
+        # The following code is not using the C API and
+        # could thus be made much quicker, for example
+        # by using tell and seek.
+        for mate in self.fetch(
+                read._delegate.core.mpos,
+                read._delegate.core.mpos + 1,
+                tid=read._delegate.core.mtid,
+                multiple_iterators=True):
+            if mate.flag & flag != 0 and \
+               mate.query_name == read.query_name:
+                break
+        else:
+            raise ValueError("mate not found")
+
+        return mate
+
+    def pileup(self,
+               contig=None,
+               start=None,
+               stop=None,
+               region=None,
+               reference=None,
+               end=None,
+               **kwargs):
+        """perform a :term:`pileup` within a :term:`region`. The region is
+        specified by :term:`contig`, `start` and `stop` (using
+        0-based indexing).  :term:`reference` and `end` are also accepted for
+        backward compatibility as synonyms for :term:`contig` and `stop`,
+        respectively.  Alternatively, a samtools 'region' string
+        can be supplied.
+
+        Without 'contig' or 'region' all reads will be used for the
+        pileup. The reads will be returned ordered by
+        :term:`contig` sequence, which will not necessarily be the
+        order within the file.
+
+        Note that :term:`SAM` formatted files do not allow random
+        access.  In these files, if a 'region' or 'contig' are
+        given an exception is raised.
+
+        .. note::
+
+            'all' reads which overlap the region are returned. The
+            first base returned will be the first base of the first
+            read 'not' necessarily the first base of the region used
+            in the query.
+
+        Parameters
+        ----------
+
+        truncate : bool
+
+           By default, the samtools pileup engine outputs all reads
+           overlapping a region. If truncate is True and a region is
+           given, only columns in the exact region specified are
+           returned.
+
+        max_depth : int
+           Maximum read depth permitted. The default limit is '8000'.
+
+        stepper : string
+           The stepper controls how the iterator advances.
+           Possible options for the stepper are
+
+           ``all``
+              skip reads in which any of the following flags are set:
+              BAM_FUNMAP, BAM_FSECONDARY, BAM_FQCFAIL, BAM_FDUP
+
+           ``nofilter``
+              uses every single read turning off any filtering.
+
+           ``samtools``
+              same filter and read processing as in samtools
+              pileup. For full compatibility, this requires a
+              'fastafile' to be given. The following options all pertain
+              to filtering of the ``samtools`` stepper.
+
+        fastafile : :class:`~pysam.FastaFile` object.
+
+           This is required for some of the steppers.
+
+        ignore_overlaps: bool
+
+           If set to True, detect if read pairs overlap and only take
+           the higher quality base. This is the default.
+
+        flag_filter : int
+
+           ignore reads where any of the bits in the flag are set. The default is
+           BAM_FUNMAP | BAM_FSECONDARY | BAM_FQCFAIL | BAM_FDUP.
+
+        flag_require : int
+
+           only use reads where certain flags are set. The default is 0.
+
+        ignore_orphans: bool
+
+            ignore orphans (paired reads that are not in a proper pair).
+            The default is to ignore orphans.
+
+        min_base_quality: int
+
+           Minimum base quality. Bases below the minimum quality will
+           not be output. The default is 13.
+
+        adjust_capq_threshold: int
+
+           adjust mapping quality. The default is 0 for no
+           adjustment. The recommended value for adjustment is 50.
+
+        min_mapping_quality : int
+
+           only use reads above a minimum mapping quality. The default is 0.
+
+        compute_baq: bool
+
+           re-alignment computing per-Base Alignment Qualities (BAQ). The
+           default is to do re-alignment. Realignment requires a reference
+           sequence. If none is present, no realignment will be performed.
+
+        redo_baq: bool
+
+           recompute per-Base Alignment Quality on the fly ignoring
+           existing base qualities. The default is False (use existing
+           base qualities).
+
+        Returns
+        -------
+
+        an iterator over genomic positions. : IteratorColumn
+
+        """
+        cdef int rtid, has_coord
+        cdef int32_t rstart, rstop
+
+        if not self.is_open:
+            raise ValueError("I/O operation on closed file")
+
+        has_coord, rtid, rstart, rstop = self.parse_region(
+            contig, start, stop, region, reference=reference, end=end)
+
+        if has_coord:
+            if not self.has_index():
+                raise ValueError("no index available for pileup")
+
+            return IteratorColumnRegion(self,
+                                        tid=rtid,
+                                        start=rstart,
+                                        stop=rstop,
+                                        **kwargs)
+        else:
+            if self.has_index():
+                return IteratorColumnAllRefs(self, **kwargs)
+            else:
+                return IteratorColumnAll(self, **kwargs)
+
+    def count(self,
+              contig=None,
+              start=None,
+              stop=None,
+              region=None,
+              until_eof=False,
+              read_callback="nofilter",
+              reference=None,
+              end=None):
+        '''count the number of reads in :term:`region`
+
+        The region is specified by :term:`contig`, `start` and `stop`.
+        :term:`reference` and `end` are also accepted for backward
+        compatibility as synonyms for :term:`contig` and `stop`,
+        respectively.  Alternatively, a `samtools`_ :term:`region`
+        string can be supplied.
+
+        A :term:`SAM` file does not allow random access and if
+        `region` or `contig` are given, an exception is raised.
+
+        Parameters
+        ----------
+
+        contig : string
+            reference_name of the genomic region (chromosome)
+
+        start : int
+            start of the genomic region (0-based inclusive)
+
+        stop : int
+            end of the genomic region (0-based exclusive)
+
+        region : string
+            a region string in samtools format.
+
+        until_eof : bool
+            count until the end of the file, possibly including
+            unmapped reads as well.
+
+        read_callback: string or function
+
+            select a call-back to ignore reads when counting. It can
+            be either a string with the following values:
+
+            ``all``
+                skip reads in which any of the following
+                flags are set: BAM_FUNMAP, BAM_FSECONDARY, BAM_FQCFAIL,
+                BAM_FDUP
+
+            ``nofilter``
+                uses every single read
+
+            Alternatively, `read_callback` can be a function
+            ``check_read(read)`` that should return True only for
+            those reads that shall be included in the counting.
+
+        reference : string
+            backward compatible synonym for `contig`
+
+        end : int
+            backward compatible synonym for `stop`
+
+        Raises
+        ------
+
+        ValueError
+            if the genomic coordinates are out of range or invalid.
+
+        '''
+        cdef AlignedSegment read
+        cdef long counter = 0
+
+        if not self.is_open:
+            raise ValueError("I/O operation on closed file")
+
+        cdef int filter_method = 0
+        if read_callback == "all":
+            filter_method = 1
+        elif read_callback == "nofilter":
+            filter_method = 2
+
+        for read in self.fetch(contig=contig,
+                               start=start,
+                               stop=stop,
+                               reference=reference,
+                               end=end,
+                               region=region,
+                               until_eof=until_eof):
+            # apply filter
+            if filter_method == 1:
+                # filter = "all"
+                if (read.flag & (0x4 | 0x100 | 0x200 | 0x400)):
+                    continue
+            elif filter_method == 2:
+                # filter = "nofilter"
+                pass
+            else:
+                if not read_callback(read):
+                    continue
+            counter += 1
+
+        return counter
+
+    @cython.boundscheck(False)  # we do manual bounds checking
+    def count_coverage(self,
+                       contig,
+                       start=None,
+                       stop=None,
+                       region=None,
+                       quality_threshold=15,
+                       read_callback='all',
+                       reference=None,
+                       end=None):
+        """count the coverage of genomic positions by reads in :term:`region`.
+
+        The region is specified by :term:`contig`, `start` and `stop`.
+        :term:`reference` and `end` are also accepted for backward
+        compatibility as synonyms for :term:`contig` and `stop`,
+        respectively.  Alternatively, a `samtools`_ :term:`region`
+        string can be supplied.  The coverage is computed per-base [ACGT].
+
+        Parameters
+        ----------
+
+        contig : string
+            reference_name of the genomic region (chromosome)
+
+        start : int
+            start of the genomic region (0-based inclusive). If not
+            given, count from the start of the chromosome.
+
+        stop : int
+            end of the genomic region (0-based exclusive). If not given,
+            count to the end of the chromosome.
+
+        region : string
+            a region string.
+
+        quality_threshold : int
+            quality_threshold is the minimum quality score (in phred) a
+            base has to reach to be counted.
+
+        read_callback: string or function
+
+            select a call-back to ignore reads when counting. It can
+            be either a string with the following values:
+
+            ``all``
+                skip reads in which any of the following
+                flags are set: BAM_FUNMAP, BAM_FSECONDARY, BAM_FQCFAIL,
+                BAM_FDUP
+
+            ``nofilter``
+                uses every single read
+
+            Alternatively, `read_callback` can be a function
+            ``check_read(read)`` that should return True only for
+            those reads that shall be included in the counting.
+
+        reference : string
+            backward compatible synonym for `contig`
+
+        end : int
+            backward compatible synonym for `stop`
+
+        Raises
+        ------
+
+        ValueError
+            if the genomic coordinates are out of range or invalid.
+
+        Returns
+        -------
+
+        four array.arrays of the same length in order A C G T : tuple
+
+        """
+
+        cdef uint32_t contig_length = self.get_reference_length(contig)
+        cdef int _start = start if start is not None else 0
+        cdef int _stop = stop if stop is not None else contig_length
+        _stop = _stop if _stop < contig_length else contig_length
+
+        if _stop == _start:
+            raise ValueError("interval of size 0")
+        if _stop < _start:
+            raise ValueError("interval of size less than 0")
+
+        cdef int length = _stop - _start
+        cdef c_array.array int_array_template = array.array('L', [])
+        cdef c_array.array count_a
+        cdef c_array.array count_c
+        cdef c_array.array count_g
+        cdef c_array.array count_t
+        count_a = c_array.clone(int_array_template, length, zero=True)
+        count_c = c_array.clone(int_array_template, length, zero=True)
+        count_g = c_array.clone(int_array_template, length, zero=True)
+        count_t = c_array.clone(int_array_template, length, zero=True)
+
+        cdef AlignedSegment read
+        cdef cython.str seq
+        cdef c_array.array quality
+        cdef int qpos
+        cdef int refpos
+        cdef int c = 0
+        cdef int filter_method = 0
+
+
+        if read_callback == "all":
+            filter_method = 1
+        elif read_callback == "nofilter":
+            filter_method = 2
+
+        cdef int _threshold = quality_threshold or 0
+        for read in self.fetch(contig=contig,
+                               reference=reference,
+                               start=start,
+                               stop=stop,
+                               end=end,
+                               region=region):
+            # apply filter
+            if filter_method == 1:
+                # filter = "all"
+                if (read.flag & (0x4 | 0x100 | 0x200 | 0x400)):
+                    continue
+            elif filter_method == 2:
+                # filter = "nofilter"
+                pass
+            else:
+                if not read_callback(read):
+                    continue
+
+            # count
+            seq = read.seq
+            if seq is None:
+                continue
+            quality = read.query_qualities
+
+            for qpos, refpos in read.get_aligned_pairs(True):
+                if qpos is not None and refpos is not None and \
+                   _start <= refpos < _stop:
+
+                    # only check base quality if _threshold > 0
+                    if (_threshold and quality and quality[qpos] >= _threshold) or not _threshold:
+                        if seq[qpos] == 'A':
+                            count_a.data.as_ulongs[refpos - _start] += 1
+                        if seq[qpos] == 'C':
+                            count_c.data.as_ulongs[refpos - _start] += 1
+                        if seq[qpos] == 'G':
+                            count_g.data.as_ulongs[refpos - _start] += 1
+                        if seq[qpos] == 'T':
+                            count_t.data.as_ulongs[refpos - _start] += 1
+
+        return count_a, count_c, count_g, count_t
+
+    def find_introns_slow(self, read_iterator):
+        """Return a dictionary {(start, stop): count}
+        Listing the intronic sites in the reads (identified by 'N' in the cigar strings),
+        and their support ( = number of reads ).
+
+        read_iterator can be the result of a .fetch(...) call.
+        Or it can be a generator filtering such reads. Example
+        samfile.find_introns((read for read in samfile.fetch(...) if read.is_reverse)
+        """
+        res = collections.Counter()
+        for r in read_iterator:
+            if 'N' in r.cigarstring:
+                last_read_pos = False
+                for read_loc, genome_loc in r.get_aligned_pairs():
+                    if read_loc is None and last_read_pos:
+                        start = genome_loc
+                    elif read_loc and last_read_pos is None:
+                        stop = genome_loc  # we are right exclusive ,so this is correct
+                        res[(start, stop)] += 1
+                        del start
+                        del stop
+                    last_read_pos = read_loc
+        return res
+
+    def find_introns(self, read_iterator):
+        """Return a dictionary {(start, stop): count}
+        Listing the intronic sites in the reads (identified by 'N' in the cigar strings),
+        and their support ( = number of reads ).
+
+        read_iterator can be the result of a .fetch(...) call.
+        Or it can be a generator filtering such reads. Example
+        samfile.find_introns((read for read in samfile.fetch(...) if read.is_reverse)
+        """
+        cdef:
+            uint32_t base_position, junc_start, nt
+            int op
+            AlignedSegment r
+            int BAM_CREF_SKIP = 3 #BAM_CREF_SKIP
+
+        res = collections.Counter()
+
+        match_or_deletion = {0, 2, 7, 8} # only M/=/X (0/7/8) and D (2) are related to genome position
+        for r in read_iterator:
+            base_position = r.pos
+
+            for op, nt in r.cigartuples:
+                if op in match_or_deletion:
+                    base_position += nt
+                elif op == BAM_CREF_SKIP:
+                    junc_start = base_position
+                    base_position += nt
+                    res[(junc_start, base_position)] += 1
+        return res
+
+
+    def close(self):
+        '''closes the :class:`pysam.AlignmentFile`.'''
+
+        if self.htsfile == NULL:
+            return
+
+        cdef int ret = hts_close(self.htsfile)
+        self.htsfile = NULL
+
+        if self.index != NULL:
+            hts_idx_destroy(self.index)
+            self.index = NULL
+
+        self.header = None
+
+        if ret < 0:
+            global errno
+            if errno == EPIPE:
+                errno = 0
+            else:
+                raise IOError(errno, force_str(strerror(errno)))
+
+    def __dealloc__(self):
+        cdef int ret = 0
+
+        if self.htsfile != NULL:
+            ret = hts_close(self.htsfile)
+            self.htsfile = NULL
+
+        if self.index != NULL:
+            hts_idx_destroy(self.index)
+            self.index = NULL
+
+        self.header = None
+
+        if self.b:
+            bam_destroy1(self.b)
+            self.b = NULL
+
+        if ret < 0:
+            global errno
+            if errno == EPIPE:
+                errno = 0
+            else:
+                raise IOError(errno, force_str(strerror(errno)))
+
+    cpdef int write(self, AlignedSegment read) except -1:
+        '''
+        write a single :class:`pysam.AlignedSegment` to disk.
+
+        Raises:
+            ValueError
+                if the writing failed
+
+        Returns:
+            int :
+                the number of bytes written. If the file is closed,
+                this will be 0.
+        '''
+        if not self.is_open:
+            return 0
+
+        if self.header.ptr.n_targets <= read._delegate.core.tid:
+            raise ValueError(
+                "AlignedSegment refers to reference number {} that "
+                "is larger than the number of references ({}) in the header".format(
+                    read._delegate.core.tid, self.header.ptr.n_targets))
+
+        cdef int ret
+        with nogil:
+            ret = sam_write1(self.htsfile,
+                             self.header.ptr,
+                             read._delegate)
+
+        # kbj: Still need to raise an exception with except -1. Otherwise
+        #      when ret == -1 we get a "SystemError: error return without
+        #      exception set".
+        if ret < 0:
+            raise IOError(
+            "sam_write1 failed with error code {}".format(ret))
+
+        return ret
+
+    # context manager interface
+    def __enter__(self):
+        return self
+
+    def __exit__(self, exc_type, exc_value, traceback):
+        self.close()
+        return False
+
+    ###############################################################
+    ###############################################################
+    ###############################################################
+    ## properties
+    ###############################################################
+    property mapped:
+        """int with total number of mapped alignments according to the
+        statistics recorded in the index. This is a read-only
+        attribute.
+        (This will be 0 for a CRAM file indexed by a .crai index, as that
+        index format does not record these statistics.)
+        """
+        def __get__(self):
+            self.check_index()
+            cdef int tid
+            cdef uint64_t total = 0
+            cdef uint64_t mapped, unmapped
+            for tid from 0 <= tid < self.header.nreferences:
+                with nogil:
+                    hts_idx_get_stat(self.index, tid, &mapped, &unmapped)
+                total += mapped
+            return total
+
+    property unmapped:
+        """int with total number of unmapped reads according to the statistics
+        recorded in the index. This number of reads includes the number of reads
+        without coordinates. This is a read-only attribute.
+        (This will be 0 for a CRAM file indexed by a .crai index, as that
+        index format does not record these statistics.)
+        """
+        def __get__(self):
+            self.check_index()
+            cdef int tid
+            cdef uint64_t total = hts_idx_get_n_no_coor(self.index)
+            cdef uint64_t mapped, unmapped
+            for tid from 0 <= tid < self.header.nreferences:
+                with nogil:
+                    hts_idx_get_stat(self.index, tid, &mapped, &unmapped)
+                total += unmapped
+            return total
+
+    property nocoordinate:
+        """int with total number of reads without coordinates according to the
+        statistics recorded in the index, i.e., the statistic printed for "*"
+        by the ``samtools idxstats`` command. This is a read-only attribute.
+        (This will be 0 for a CRAM file indexed by a .crai index, as that
+        index format does not record these statistics.)
+        """
+        def __get__(self):
+            self.check_index()
+            cdef uint64_t n
+            with nogil:
+                n = hts_idx_get_n_no_coor(self.index)
+            return n
+
+    def get_index_statistics(self):
+        """return statistics about mapped/unmapped reads per chromosome as
+        they are stored in the index, similarly to the statistics printed
+        by the ``samtools idxstats`` command.
+
+        CRAI indexes do not record these statistics, so for a CRAM file
+        with a .crai index the returned statistics will all be 0.
+
+        Returns:
+            list :
+                a list of records for each chromosome. Each record has the
+                attributes 'contig', 'mapped', 'unmapped' and 'total'.
+        """
+
+        self.check_index()
+        cdef int tid
+        cdef uint64_t mapped, unmapped
+        results = []
+        # TODO: use header
+        for tid from 0 <= tid < self.nreferences:
+            with nogil:
+                hts_idx_get_stat(self.index, tid, &mapped, &unmapped)
+            results.append(
+                IndexStats._make((
+                    self.get_reference_name(tid),
+                    mapped,
+                    unmapped,
+                    mapped + unmapped)))
+
+        return results
+
+    ###############################################################
+    ## file-object like iterator access
+    ## note: concurrent access will cause errors (see IteratorRow
+    ## and multiple_iterators)
+    ## Possible solutions: deprecate or open new file handle
+    def __iter__(self):
+        if not self.is_open:
+            raise ValueError("I/O operation on closed file")
+
+        if not self.is_bam and self.header.nreferences == 0:
+            raise NotImplementedError(
+                "can not iterate over samfile without header")
+        return self
+
+    cdef bam1_t * getCurrent(self):
+        return self.b
+
+    cdef int cnext(self):
+        '''
+        cversion of iterator. Used by :class:`pysam.AlignmentFile.IteratorColumn`.
+        '''
+        cdef int ret
+        cdef bam_hdr_t * hdr = self.header.ptr
+        with nogil:
+            ret = sam_read1(self.htsfile,
+                            hdr,
+                            self.b)
+        return ret
+
+    def __next__(self):
+        cdef int ret = self.cnext()
+        if ret >= 0:
+            return makeAlignedSegment(self.b, self.header)
+        elif ret == -1:
+            raise StopIteration
+        else:
+            raise IOError(read_failure_reason(ret))
+
+    ###########################################
+    # methods/properties referencing the header
+    def is_valid_tid(self, int tid):
+        """
+        return True if the numerical :term:`tid` is valid; False otherwise.
+
+        Note that the unmapped tid code (-1) counts as an invalid.
+        """
+        if self.header is None:
+            raise ValueError("header not available in closed files")
+        return self.header.is_valid_tid(tid)
+
+    def get_tid(self, reference):
+        """
+        return the numerical :term:`tid` corresponding to
+        :term:`reference`
+
+        returns -1 if reference is not known.
+        """
+        if self.header is None:
+            raise ValueError("header not available in closed files")
+        return self.header.get_tid(reference)
+
+    def get_reference_name(self, tid):
+        """
+        return :term:`reference` name corresponding to numerical :term:`tid`
+        """
+        if self.header is None:
+            raise ValueError("header not available in closed files")
+        return self.header.get_reference_name(tid)
+
+    def get_reference_length(self, reference):
+        """
+        return :term:`reference` length corresponding to numerical :term:`tid`
+        """
+        if self.header is None:
+            raise ValueError("header not available in closed files")
+        return self.header.get_reference_length(reference)
+
+    property nreferences:
+        """int with the number of :term:`reference` sequences in the file.
+        This is a read-only attribute."""
+        def __get__(self):
+            if self.header:
+                return self.header.nreferences
+            else:
+                raise ValueError("header not available in closed files")
+
+    property references:
+        """tuple with the names of :term:`reference` sequences. This is a
+        read-only attribute"""
+        def __get__(self):
+            if self.header:
+                return self.header.references
+            else:
+                raise ValueError("header not available in closed files")
+
+    property lengths:
+        """tuple of the lengths of the :term:`reference` sequences. This is a
+        read-only attribute. The lengths are in the same order as
+        :attr:`pysam.AlignmentFile.references`
+
+        """
+        def __get__(self):
+            if self.header:
+                return self.header.lengths
+            else:
+                raise ValueError("header not available in closed files")
+
+    # Compatibility functions for pysam < 0.14
+    property text:
+        """deprecated, use :attr:`references` and :attr:`lengths` instead"""
+        def __get__(self):
+            if self.header:
+                return self.header.__str__()
+            else:
+                raise ValueError("header not available in closed files")
+
+    # Compatibility functions for pysam < 0.8.3
+    def gettid(self, reference):
+        """deprecated, use :meth:`get_tid` instead"""
+        return self.get_tid(reference)
+
+    def getrname(self, tid):
+        """deprecated, use :meth:`get_reference_name` instead"""
+        return self.get_reference_name(tid)
+
+
+cdef class IteratorRow:
+    '''abstract base class for iterators over mapped reads.
+
+    Various iterators implement different behaviours for wrapping around
+    contig boundaries. Examples include:
+
+    :class:`pysam.IteratorRowRegion`
+        iterate within a single contig and a defined region.
+
+    :class:`pysam.IteratorRowAll`
+        iterate until EOF. This iterator will also include unmapped reads.
+
+    :class:`pysam.IteratorRowAllRefs`
+        iterate over all reads in all reference sequences.
+
+    The method :meth:`AlignmentFile.fetch` returns an IteratorRow.
+
+    .. note::
+
+        It is usually not necessary to create an object of this class
+        explicitly. It is returned as a result of call to a
+        :meth:`AlignmentFile.fetch`.
+
+    '''
+
+    def __init__(self, AlignmentFile samfile, int multiple_iterators=False):
+        cdef char *cfilename
+        cdef char *creference_filename
+        cdef char *cindexname = NULL
+
+        if not samfile.is_open:
+            raise ValueError("I/O operation on closed file")
+
+        # makes sure that samfile stays alive as long as the
+        # iterator is alive
+        self.samfile = samfile
+
+        # reopen the file - note that this makes the iterator
+        # slow and causes pileup to slow down significantly.
+        if multiple_iterators:
+
+            cfilename = samfile.filename
+            with nogil:
+                self.htsfile = hts_open(cfilename, 'r')
+            assert self.htsfile != NULL
+
+            if samfile.has_index():
+                if samfile.index_filename:
+                    cindexname = bindex_filename = encode_filename(samfile.index_filename)
+                with nogil:
+                    self.index = sam_index_load2(self.htsfile, cfilename, cindexname)
+            else:
+                self.index = NULL
+
+            # need to advance in newly opened file to position after header
+            # better: use seek/tell?
+            with nogil:
+                hdr = sam_hdr_read(self.htsfile)
+            if hdr is NULL:
+                raise IOError("unable to read header information")
+            self.header = makeAlignmentHeader(hdr)
+
+            self.owns_samfile = True
+
+            # options specific to CRAM files
+            if samfile.is_cram and samfile.reference_filename:
+                creference_filename = samfile.reference_filename
+                hts_set_opt(self.htsfile,
+                            CRAM_OPT_REFERENCE,
+                            creference_filename)
+
+        else:
+            self.htsfile = samfile.htsfile
+            self.index = samfile.index
+            self.owns_samfile = False
+            self.header = samfile.header
+
+        self.retval = 0
+
+        self.b = bam_init1()
+
+    def __dealloc__(self):
+        bam_destroy1(self.b)
+        if self.owns_samfile:
+            hts_close(self.htsfile)
+            hts_idx_destroy(self.index)
+
+
+cdef class IteratorRowRegion(IteratorRow):
+    """*(AlignmentFile samfile, int tid, int beg, int stop,
+    int multiple_iterators=False)*
+
+    iterate over mapped reads in a region.
+
+    .. note::
+
+        It is usually not necessary to create an object of this class
+        explicitly. It is returned as a result of call to a
+        :meth:`AlignmentFile.fetch`.
+
+    """
+
+    def __init__(self, AlignmentFile samfile,
+                 int tid, int beg, int stop,
+                 int multiple_iterators=False):
+
+        if not samfile.has_index():
+            raise ValueError("no index available for iteration")
+
+        IteratorRow.__init__(self, samfile,
+                             multiple_iterators=multiple_iterators)
+        with nogil:
+            self.iter = sam_itr_queryi(
+                self.index,
+                tid,
+                beg,
+                stop)
+
+    def __iter__(self):
+        return self
+
+    cdef bam1_t * getCurrent(self):
+        return self.b
+
+    cdef int cnext(self):
+        '''cversion of iterator. Used by IteratorColumn'''
+        with nogil:
+            self.retval = hts_itr_next(hts_get_bgzfp(self.htsfile),
+                                       self.iter,
+                                       self.b,
+                                       self.htsfile)
+
+    def __next__(self):
+        self.cnext()
+        if self.retval >= 0:
+            return makeAlignedSegment(self.b, self.header)
+        elif self.retval == -1:
+            raise StopIteration
+        elif self.retval == -2:
+            # Note: it is currently not the case that hts_iter_next
+            # returns -2 for a truncated file.
+            # See https://github.com/pysam-developers/pysam/pull/50#issuecomment-64928625
+            raise IOError('truncated file')
+        else:
+            raise IOError("error while reading file {}: {}".format(self.samfile.filename, self.retval))
+
+    def __dealloc__(self):
+        hts_itr_destroy(self.iter)
+
+
+cdef class IteratorRowHead(IteratorRow):
+    """*(AlignmentFile samfile, n, int multiple_iterators=False)*
+
+    iterate over first n reads in `samfile`
+
+    .. note::
+        It is usually not necessary to create an object of this class
+        explicitly. It is returned as a result of call to a
+        :meth:`AlignmentFile.head`.
+
+    """
+
+    def __init__(self,
+                 AlignmentFile samfile,
+                 int n,
+                 int multiple_iterators=False):
+
+        IteratorRow.__init__(self, samfile,
+                             multiple_iterators=multiple_iterators)
+
+        self.max_rows = n
+        self.current_row = 0
+
+    def __iter__(self):
+        return self
+
+    cdef bam1_t * getCurrent(self):
+        return self.b
+
+    cdef int cnext(self):
+        '''cversion of iterator. Used by IteratorColumn'''
+        cdef int ret
+        cdef bam_hdr_t * hdr = self.header.ptr
+        with nogil:
+            ret = sam_read1(self.htsfile,
+                            hdr,
+                            self.b)
+        return ret
+
+    def __next__(self):
+        if self.current_row >= self.max_rows:
+            raise StopIteration
+
+        cdef int ret = self.cnext()
+        if ret >= 0:
+            self.current_row += 1
+            return makeAlignedSegment(self.b, self.header)
+        elif ret == -1:
+            raise StopIteration
+        else:
+            raise IOError(read_failure_reason(ret))
+
+
+cdef class IteratorRowAll(IteratorRow):
+    """*(AlignmentFile samfile, int multiple_iterators=False)*
+
+    iterate over all reads in `samfile`
+
+    .. note::
+
+        It is usually not necessary to create an object of this class
+        explicitly. It is returned as a result of call to a
+        :meth:`AlignmentFile.fetch`.
+
+    """
+
+    def __init__(self, AlignmentFile samfile,
+                 int multiple_iterators=False):
+
+        IteratorRow.__init__(self, samfile,
+                             multiple_iterators=multiple_iterators)
+
+    def __iter__(self):
+        return self
+
+    cdef bam1_t * getCurrent(self):
+        return self.b
+
+    cdef int cnext(self):
+        '''cversion of iterator. Used by IteratorColumn'''
+        cdef int ret
+        cdef bam_hdr_t * hdr = self.header.ptr
+        with nogil:
+            ret = sam_read1(self.htsfile,
+                            hdr,
+                            self.b)
+        return ret
+
+    def __next__(self):
+        cdef int ret = self.cnext()
+        if ret >= 0:
+            return makeAlignedSegment(self.b, self.header)
+        elif ret == -1:
+            raise StopIteration
+        else:
+            raise IOError(read_failure_reason(ret))
+
+
+cdef class IteratorRowAllRefs(IteratorRow):
+    """iterates over all mapped reads by chaining iterators over each
+    reference
+
+    .. note::
+        It is usually not necessary to create an object of this class
+        explicitly. It is returned as a result of call to a
+        :meth:`AlignmentFile.fetch`.
+
+    """
+
+    def __init__(self, AlignmentFile samfile,
+                 multiple_iterators=False):
+
+        IteratorRow.__init__(self, samfile,
+                             multiple_iterators=multiple_iterators)
+
+        if not samfile.has_index():
+            raise ValueError("no index available for fetch")
+
+        self.tid = -1
+
+    def nextiter(self):
+        # get a new iterator for a chromosome. The file
+        # will not be re-opened.
+        self.rowiter = IteratorRowRegion(self.samfile,
+                                         self.tid,
+                                         0,
+                                         MAX_POS)
+        # set htsfile and header of the rowiter
+        # to the values in this iterator to reflect multiple_iterators
+        self.rowiter.htsfile = self.htsfile
+        self.rowiter.header = self.header
+
+        # make sure the iterator understand that IteratorRowAllRefs
+        # has ownership
+        self.rowiter.owns_samfile = False
+
+    def __iter__(self):
+        return self
+
+    def __next__(self):
+        # Create an initial iterator
+        if self.tid == -1:
+            if not self.samfile.nreferences:
+                raise StopIteration
+            self.tid = 0
+            self.nextiter()
+
+        while 1:
+            self.rowiter.cnext()
+
+            # If current iterator is not exhausted, return aligned read
+            if self.rowiter.retval > 0:
+                return makeAlignedSegment(self.rowiter.b, self.header)
+
+            self.tid += 1
+
+            # Otherwise, proceed to next reference or stop
+            if self.tid < self.samfile.nreferences:
+                self.nextiter()
+            else:
+                raise StopIteration
+
+
+cdef class IteratorRowSelection(IteratorRow):
+    """*(AlignmentFile samfile)*
+
+    iterate over reads in `samfile` at a given list of file positions.
+
+    .. note::
+        It is usually not necessary to create an object of this class
+        explicitly. It is returned as a result of call to a :meth:`AlignmentFile.fetch`.
+    """
+
+    def __init__(self, AlignmentFile samfile, positions, int multiple_iterators=True):
+
+        IteratorRow.__init__(self, samfile, multiple_iterators=multiple_iterators)
+
+        self.positions = positions
+        self.current_pos = 0
+
+    def __iter__(self):
+        return self
+
+    cdef bam1_t * getCurrent(self):
+        return self.b
+
+    cdef int cnext(self):
+        '''cversion of iterator'''
+        # end iteration if out of positions
+        if self.current_pos >= len(self.positions): return -1
+
+        cdef uint64_t pos = self.positions[self.current_pos]
+        with nogil:
+            bgzf_seek(hts_get_bgzfp(self.htsfile),
+                      pos,
+                      0)
+        self.current_pos += 1
+
+        cdef int ret
+        cdef bam_hdr_t * hdr = self.header.ptr
+        with nogil:
+            ret = sam_read1(self.htsfile,
+                            hdr,
+                            self.b)
+        return ret
+
+    def __next__(self):
+        cdef int ret = self.cnext()
+        if ret >= 0:
+            return makeAlignedSegment(self.b, self.header)
+        elif ret == -1:
+            raise StopIteration
+        else:
+            raise IOError(read_failure_reason(ret))
+
+
+cdef int __advance_nofilter(void *data, bam1_t *b):
+    '''advance without any read filtering.
+    '''
+    cdef __iterdata * d = <__iterdata*>data
+    cdef int ret
+    with nogil:
+        ret = sam_itr_next(d.htsfile, d.iter, b)
+    return ret
+
+
+cdef int __advance_raw_nofilter(void *data, bam1_t *b):
+    '''advance (without iterator) without any read filtering.
+    '''
+    cdef __iterdata * d = <__iterdata*>data
+    cdef int ret
+    with nogil:
+        ret = sam_read1(d.htsfile, d.header, b)
+    return ret
+
+
+cdef int __advance_all(void *data, bam1_t *b):
+    '''only use reads for pileup passing basic filters such as
+
+    BAM_FUNMAP, BAM_FSECONDARY, BAM_FQCFAIL, BAM_FDUP
+    '''
+
+    cdef __iterdata * d = <__iterdata*>data
+    cdef mask = BAM_FUNMAP | BAM_FSECONDARY | BAM_FQCFAIL | BAM_FDUP
+    cdef int ret
+    while 1:
+        with nogil:
+            ret = sam_itr_next(d.htsfile, d.iter, b)
+        if ret < 0:
+            break
+        if b.core.flag & d.flag_filter:
+            continue
+        break
+    return ret
+
+
+cdef int __advance_raw_all(void *data, bam1_t *b):
+    '''only use reads for pileup passing basic filters such as
+
+    BAM_FUNMAP, BAM_FSECONDARY, BAM_FQCFAIL, BAM_FDUP
+    '''
+
+    cdef __iterdata * d = <__iterdata*>data
+    cdef int ret
+    while 1:
+        with nogil:
+            ret = sam_read1(d.htsfile, d.header, b)
+        if ret < 0:
+            break
+        if b.core.flag & d.flag_filter:
+            continue
+        break
+    return ret
+
+
+cdef int __advance_samtools(void * data, bam1_t * b):
+    '''advance using same filter and read processing as in
+    the samtools pileup.
+    '''
+    cdef __iterdata * d = <__iterdata*>data
+    cdef int ret
+    cdef int q
+
+    while 1:
+        with nogil:
+            ret = sam_itr_next(d.htsfile, d.iter, b) if d.iter else sam_read1(d.htsfile, d.header, b)
+        if ret < 0:
+            break
+        if b.core.flag & d.flag_filter:
+            continue
+        if d.flag_require and not (b.core.flag & d.flag_require):
+            continue
+
+        # reload sequence
+        if d.fastafile != NULL and b.core.tid != d.tid:
+            if d.seq != NULL:
+                free(d.seq)
+            d.tid = b.core.tid
+            with nogil:
+                d.seq = faidx_fetch_seq(
+                    d.fastafile,
+                    d.header.target_name[d.tid],
+                    0, MAX_POS,
+                    &d.seq_len)
+
+            if d.seq == NULL:
+                raise ValueError(
+                    "reference sequence for '{}' (tid={}) not found".format(
+                        d.header.target_name[d.tid], d.tid))
+
+        # realign read - changes base qualities
+        if d.seq != NULL and d.compute_baq:
+            # 4th option to realign is flag:
+            # apply_baq = flag&1, extend_baq = flag&2, redo_baq = flag&4
+            if d.redo_baq:
+                sam_prob_realn(b, d.seq, d.seq_len, 7)
+            else:
+                sam_prob_realn(b, d.seq, d.seq_len, 3)
+
+        if d.seq != NULL and d.adjust_capq_threshold > 10:
+            q = sam_cap_mapq(b, d.seq, d.seq_len, d.adjust_capq_threshold)
+            if q < 0:
+                continue
+            elif b.core.qual > q:
+                b.core.qual = q
+
+        if b.core.qual < d.min_mapping_quality:
+            continue
+        if d.ignore_orphans and b.core.flag & BAM_FPAIRED and not (b.core.flag & BAM_FPROPER_PAIR):
+            continue
+
+        break
+
+    return ret
+
+
+cdef class IteratorColumn:
+    '''abstract base class for iterators over columns.
+
+    IteratorColumn objects wrap the pileup functionality of samtools.
+
+    For reasons of efficiency, the iterator points to the current
+    pileup buffer. The pileup buffer is updated at every iteration.
+    This might cause some unexpected behaviour. For example,
+    consider the conversion to a list::
+
+       f = AlignmentFile("file.bam", "rb")
+       result = list(f.pileup())
+
+    Here, ``result`` will contain ``n`` objects of type
+    :class:`~pysam.PileupColumn` for ``n`` columns, but each object in
+    ``result`` will contain the same information.
+
+    The desired behaviour can be achieved by list comprehension::
+
+       result = [x.pileups() for x in f.pileup()]
+
+    ``result`` will be a list of ``n`` lists of objects of type
+    :class:`~pysam.PileupRead`.
+
+    If the iterator is associated with a :class:`~pysam.Fastafile`
+    using the :meth:`add_reference` method, then the iterator will
+    export the current sequence via the methods :meth:`get_sequence`
+    and :meth:`seq_len`.
+
+    See :class:`~AlignmentFile.pileup` for kwargs to the iterator.
+    '''
+
+    def __cinit__( self, AlignmentFile samfile, **kwargs):
+        self.samfile = samfile
+        self.fastafile = kwargs.get("fastafile", None)
+        self.stepper = kwargs.get("stepper", "samtools")
+        self.max_depth = kwargs.get("max_depth", 8000)
+        self.ignore_overlaps = kwargs.get("ignore_overlaps", True)
+        self.min_base_quality = kwargs.get("min_base_quality", 13)
+        self.iterdata.seq = NULL
+        self.iterdata.min_mapping_quality = kwargs.get("min_mapping_quality", 0)
+        self.iterdata.flag_require = kwargs.get("flag_require", 0)
+        self.iterdata.flag_filter = kwargs.get("flag_filter", BAM_FUNMAP | BAM_FSECONDARY | BAM_FQCFAIL | BAM_FDUP)
+        self.iterdata.adjust_capq_threshold = kwargs.get("adjust_capq_threshold", 0)
+        self.iterdata.compute_baq = kwargs.get("compute_baq", True)
+        self.iterdata.redo_baq = kwargs.get("redo_baq", False)
+        self.iterdata.ignore_orphans = kwargs.get("ignore_orphans", True)
+
+        self.tid = 0
+        self.pos = 0
+        self.n_plp = 0
+        self.plp = NULL
+        self.pileup_iter = <bam_mplp_t>NULL
+
+    def __iter__(self):
+        return self
+
+    cdef int cnext(self):
+        '''perform next iteration.
+        '''
+        # do not release gil here because of call-backs
+        cdef int ret = bam_mplp_auto(self.pileup_iter,
+                                     &self.tid,
+                                     &self.pos,
+                                     &self.n_plp,
+                                     &self.plp)
+        return ret
+
+    cdef char * get_sequence(self):
+        '''return current reference sequence underlying the iterator.
+        '''
+        return self.iterdata.seq
+
+    property seq_len:
+        '''current sequence length.'''
+        def __get__(self):
+            return self.iterdata.seq_len
+
+    def add_reference(self, FastaFile fastafile):
+       '''
+       add reference sequences in `fastafile` to iterator.'''
+       self.fastafile = fastafile
+       if self.iterdata.seq != NULL:
+           free(self.iterdata.seq)
+       self.iterdata.tid = -1
+       self.iterdata.fastafile = self.fastafile.fastafile
+
+    def has_reference(self):
+        '''
+        return true if iterator is associated with a reference'''
+        return self.fastafile
+
+    cdef _setup_iterator(self,
+                         int tid,
+                         int start,
+                         int stop,
+                         int multiple_iterators=0):
+        '''setup the iterator structure'''
+
+        self.iter = IteratorRowRegion(self.samfile, tid, start, stop, multiple_iterators)
+        self.iterdata.htsfile = self.samfile.htsfile
+        self.iterdata.iter = self.iter.iter
+        self.iterdata.seq = NULL
+        self.iterdata.tid = -1
+        self.iterdata.header = self.samfile.header.ptr
+
+        if self.fastafile is not None:
+            self.iterdata.fastafile = self.fastafile.fastafile
+        else:
+            self.iterdata.fastafile = NULL
+
+        # Free any previously allocated memory before reassigning
+        # pileup_iter
+        self._free_pileup_iter()
+
+        cdef void * data[1]
+        data[0] = <void*>&self.iterdata
+
+        if self.stepper is None or self.stepper == "all":
+            with nogil:
+                self.pileup_iter = bam_mplp_init(1,
+                                                 <bam_plp_auto_f>&__advance_all,
+                                                 data)
+        elif self.stepper == "nofilter":
+            with nogil:
+                self.pileup_iter = bam_mplp_init(1,
+                                                 <bam_plp_auto_f>&__advance_nofilter,
+                                                 data)
+        elif self.stepper == "samtools":
+            with nogil:
+                self.pileup_iter = bam_mplp_init(1,
+                                                 <bam_plp_auto_f>&__advance_samtools,
+                                                 data)
+        else:
+            raise ValueError(
+                "unknown stepper option `%s` in IteratorColumn" % self.stepper)
+
+        if self.max_depth:
+            with nogil:
+                bam_mplp_set_maxcnt(self.pileup_iter, self.max_depth)
+
+        if self.ignore_overlaps:
+            with nogil:
+                bam_mplp_init_overlaps(self.pileup_iter)
+
+    cdef _setup_raw_rest_iterator(self):
+        '''set up an "iterator" that just uses sam_read1(), similar to HTS_IDX_REST'''
+
+        self.iter = None
+        self.iterdata.iter = NULL
+        self.iterdata.htsfile = self.samfile.htsfile
+        self.iterdata.seq = NULL
+        self.iterdata.tid = -1
+        self.iterdata.header = self.samfile.header.ptr
+
+        if self.fastafile is not None:
+            self.iterdata.fastafile = self.fastafile.fastafile
+        else:
+            self.iterdata.fastafile = NULL
+
+        # Free any previously allocated memory before reassigning
+        # pileup_iter
+        self._free_pileup_iter()
+
+        cdef void * data[1]
+        data[0] = <void*>&self.iterdata
+
+        if self.stepper is None or self.stepper == "all":
+            with nogil:
+                self.pileup_iter = bam_mplp_init(1,
+                                                 <bam_plp_auto_f>&__advance_raw_all,
+                                                 data)
+        elif self.stepper == "nofilter":
+            with nogil:
+                self.pileup_iter = bam_mplp_init(1,
+                                                 <bam_plp_auto_f>&__advance_raw_nofilter,
+                                                 data)
+        elif self.stepper == "samtools":
+            with nogil:
+                self.pileup_iter = bam_mplp_init(1,
+                                                 <bam_plp_auto_f>&__advance_samtools,
+                                                 data)
+        else:
+            raise ValueError(
+                "unknown stepper option `%s` in IteratorColumn" % self.stepper)
+
+        if self.max_depth:
+            with nogil:
+                bam_mplp_set_maxcnt(self.pileup_iter, self.max_depth)
+
+        if self.ignore_overlaps:
+            with nogil:
+                bam_mplp_init_overlaps(self.pileup_iter)
+
+    cdef reset(self, tid, start, stop):
+        '''reset iterator position.
+
+        This permits using the iterator multiple times without
+        having to incur the full set-up costs.
+        '''
+        if self.iter is None:
+            raise TypeError("Raw iterator set up without region cannot be reset")
+
+        self.iter = IteratorRowRegion(self.samfile, tid, start, stop, multiple_iterators=0)
+        self.iterdata.iter = self.iter.iter
+
+        # invalidate sequence if different tid
+        if self.tid != tid:
+            if self.iterdata.seq != NULL:
+                free(self.iterdata.seq)
+            self.iterdata.seq = NULL
+            self.iterdata.tid = -1
+
+        # self.pileup_iter = bam_mplp_init(1
+        #                                  &__advancepileup,
+        #                                  &self.iterdata)
+        with nogil:
+            bam_mplp_reset(self.pileup_iter)
+
+    cdef _free_pileup_iter(self):
+        '''free the memory alloc'd by bam_plp_init.
+
+        This is needed before setup_iterator allocates another
+        pileup_iter, or else memory will be lost.  '''
+        if self.pileup_iter != <bam_mplp_t>NULL:
+            with nogil:
+                bam_mplp_reset(self.pileup_iter)
+                bam_mplp_destroy(self.pileup_iter)
+                self.pileup_iter = <bam_mplp_t>NULL
+
+    def __dealloc__(self):
+        # reset in order to avoid memory leak messages for iterators
+        # that have not been fully consumed
+        self._free_pileup_iter()
+        self.plp = <const bam_pileup1_t*>NULL
+
+        if self.iterdata.seq != NULL:
+            free(self.iterdata.seq)
+            self.iterdata.seq = NULL
+
+    # backwards compatibility
+
+    def hasReference(self):
+        return self.has_reference()
+    cdef char * getSequence(self):
+        return self.get_sequence()
+    def addReference(self, FastaFile fastafile):
+        return self.add_reference(fastafile)
+
+
+cdef class IteratorColumnRegion(IteratorColumn):
+    '''iterates over a region only.
+    '''
+    def __cinit__(self,
+                  AlignmentFile samfile,
+                  int tid = 0,
+                  int start = 0,
+                  int stop = MAX_POS,
+                  int truncate = False,
+                  int multiple_iterators = True,
+                  **kwargs ):
+
+        # initialize iterator. Multiple iterators not available
+        # for CRAM.
+        if multiple_iterators and samfile.is_cram:
+            warnings.warn("multiple_iterators not implemented for CRAM")
+            multiple_iterators = False
+
+        self._setup_iterator(tid, start, stop, multiple_iterators)
+        self.start = start
+        self.stop = stop
+        self.truncate = truncate
+
+    def __next__(self):
+
+        cdef int n
+
+        while 1:
+            n = self.cnext()
+            if n < 0:
+                raise ValueError("error during iteration" )
+
+            if n == 0:
+                raise StopIteration
+
+            if self.truncate:
+                if self.start > self.pos:
+                    continue
+                if self.pos >= self.stop:
+                    raise StopIteration
+
+            return makePileupColumn(&self.plp,
+                                    self.tid,
+                                    self.pos,
+                                    self.n_plp,
+                                    self.min_base_quality,
+                                    self.iterdata.seq,
+                                    self.samfile.header)
+
+
+cdef class IteratorColumnAllRefs(IteratorColumn):
+    """iterates over all columns by chaining iterators over each reference
+    """
+
+    def __cinit__(self,
+                  AlignmentFile samfile,
+                  **kwargs):
+
+        # no iteration over empty files
+        if not samfile.nreferences:
+            raise StopIteration
+
+        # initialize iterator
+        self._setup_iterator(self.tid, 0, MAX_POS, 1)
+
+    def __next__(self):
+
+        cdef int n
+        while 1:
+            n = self.cnext()
+            if n < 0:
+                raise ValueError("error during iteration")
+
+            # proceed to next reference or stop
+            if n == 0:
+                self.tid += 1
+                if self.tid < self.samfile.nreferences:
+                    self._setup_iterator(self.tid, 0, MAX_POS, 0)
+                else:
+                    raise StopIteration
+                continue
+
+            # return result, if within same reference
+            return makePileupColumn(&self.plp,
+                                    self.tid,
+                                    self.pos,
+                                    self.n_plp,
+                                    self.min_base_quality,
+                                    self.iterdata.seq,
+                                    self.samfile.header)
+
+
+cdef class IteratorColumnAll(IteratorColumn):
+    """iterates over all columns, without using an index
+    """
+
+    def __cinit__(self,
+                  AlignmentFile samfile,
+                  **kwargs):
+
+        self._setup_raw_rest_iterator()
+
+    def __next__(self):
+
+        cdef int n
+        n = self.cnext()
+        if n < 0:
+            raise ValueError("error during iteration")
+
+        if n == 0:
+            raise StopIteration
+
+        return makePileupColumn(&self.plp,
+                                self.tid,
+                                self.pos,
+                                self.n_plp,
+                                self.min_base_quality,
+                                self.iterdata.seq,
+                                self.samfile.header)
+
+
+cdef class SNPCall:
+    '''the results of a SNP call.'''
+    cdef int _tid
+    cdef int _pos
+    cdef char _reference_base
+    cdef char _genotype
+    cdef int _consensus_quality
+    cdef int _snp_quality
+    cdef int _rms_mapping_quality
+    cdef int _coverage
+
+    property tid:
+        '''the chromosome ID as is defined in the header'''
+        def __get__(self):
+            return self._tid
+
+    property pos:
+       '''nucleotide position of SNP.'''
+       def __get__(self): return self._pos
+
+    property reference_base:
+       '''reference base at pos. ``N`` if no reference sequence supplied.'''
+       def __get__(self): return from_string_and_size( &self._reference_base, 1 )
+
+    property genotype:
+       '''the genotype called.'''
+       def __get__(self): return from_string_and_size( &self._genotype, 1 )
+
+    property consensus_quality:
+       '''the genotype quality (Phred-scaled).'''
+       def __get__(self): return self._consensus_quality
+
+    property snp_quality:
+       '''the snp quality (Phred scaled) - probability of consensus being
+       identical to reference sequence.'''
+       def __get__(self): return self._snp_quality
+
+    property mapping_quality:
+       '''the root mean square (rms) of the mapping quality of all reads
+       involved in the call.'''
+       def __get__(self): return self._rms_mapping_quality
+
+    property coverage:
+       '''coverage or read depth - the number of reads involved in the call.'''
+       def __get__(self): return self._coverage
+
+    def __str__(self):
+
+        return "\t".join( map(str, (
+                    self.tid,
+                    self.pos,
+                    self.reference_base,
+                    self.genotype,
+                    self.consensus_quality,
+                    self.snp_quality,
+                    self.mapping_quality,
+                    self.coverage ) ) )
+
+
+cdef class IndexedReads:
+    """Index a Sam/BAM-file by query name while keeping the
+    original sort order intact.
+
+    The index is kept in memory and can be substantial.
+
+    By default, the file is re-opened to avoid conflicts if multiple
+    operators work on the same file. Set `multiple_iterators` = False
+    to not re-open `samfile`.
+
+    Parameters
+    ----------
+
+    samfile : AlignmentFile
+        File to be indexed.
+
+    multiple_iterators : bool
+        Flag indicating whether the file should be reopened. Reopening prevents
+        existing iterators being affected by the indexing.
+
+    """
+
+    def __init__(self, AlignmentFile samfile, int multiple_iterators=True):
+        cdef char *cfilename
+
+        # makes sure that samfile stays alive as long as this
+        # object is alive.
+        self.samfile = samfile
+        cdef bam_hdr_t * hdr = NULL
+        assert samfile.is_bam, "can only apply IndexReads on bam files"
+
+        # multiple_iterators the file - note that this makes the iterator
+        # slow and causes pileup to slow down significantly.
+        if multiple_iterators:
+            cfilename = samfile.filename
+            with nogil:
+                self.htsfile = hts_open(cfilename, 'r')
+            if self.htsfile == NULL:
+                raise OSError("unable to reopen htsfile")
+
+            # need to advance in newly opened file to position after header
+            # better: use seek/tell?
+            with nogil:
+                hdr = sam_hdr_read(self.htsfile)
+            if hdr == NULL:
+                raise OSError("unable to read header information")
+            self.header = makeAlignmentHeader(hdr)
+            self.owns_samfile = True
+        else:
+            self.htsfile = self.samfile.htsfile
+            self.header = samfile.header
+            self.owns_samfile = False
+
+    def build(self):
+        '''build the index.'''
+
+        self.index = collections.defaultdict(list)
+
+        # this method will start indexing from the current file position
+        cdef int ret = 1
+        cdef bam1_t * b = <bam1_t*>calloc(1, sizeof( bam1_t))
+        if b == NULL:
+            raise MemoryError("could not allocate {} bytes".format(sizeof(bam1_t)))
+
+        cdef uint64_t pos
+        cdef bam_hdr_t * hdr = self.header.ptr
+
+        while ret > 0:
+            with nogil:
+                pos = bgzf_tell(hts_get_bgzfp(self.htsfile))
+                ret = sam_read1(self.htsfile,
+                                hdr,
+                                b)
+
+            if ret > 0:
+                qname = charptr_to_str(pysam_bam_get_qname(b))
+                self.index[qname].append(pos)
+
+        bam_destroy1(b)
+
+    def find(self, query_name):
+        '''find `query_name` in index.
+
+        Returns
+        -------
+
+        IteratorRowSelection
+            Returns an iterator over all reads with query_name.
+
+        Raises
+        ------
+
+        KeyError
+            if the `query_name` is not in the index.
+
+        '''
+        if query_name in self.index:
+            return IteratorRowSelection(
+                self.samfile,
+                self.index[query_name],
+                multiple_iterators = False)
+        else:
+            raise KeyError("read %s not found" % query_name)
+
+    def __dealloc__(self):
+        if self.owns_samfile:
+            hts_close(self.htsfile)
diff --git a/pysam/libcbcf.pxd b/pysam/libcbcf.pxd
new file mode 100644
index 0000000..6508994
--- /dev/null
+++ b/pysam/libcbcf.pxd
@@ -0,0 +1,143 @@
+###############################################################################
+###############################################################################
+## Cython wrapper for htslib VCF/BCF reader/writer
+###############################################################################
+#
+# The MIT License
+#
+# Copyright (c) 2015, 2016 Kevin Jacobs (jacobs@bioinformed.com)
+#
+# Permission is hereby granted, free of charge, to any person obtaining a
+# copy of this software and associated documentation files (the "Software"),
+# to deal in the Software without restriction, including without limitation
+# the rights to use, copy, modify, merge, publish, distribute, sublicense,
+# and/or sell copies of the Software, and to permit persons to whom the
+# Software is furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.  IN NO EVENT SHALL
+# THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+# DEALINGS IN THE SOFTWARE.
+#
+###############################################################################
+
+from libc.stdint cimport int8_t, int16_t, int32_t, int64_t
+from libc.stdint cimport uint8_t, uint16_t, uint32_t, uint64_t
+from libc.stdlib cimport malloc, calloc, realloc, free
+from libc.string cimport memcpy, memcmp, memmove, strncpy, strlen, strdup
+
+from pysam.libchtslib cimport *
+
+
+cdef class VariantHeader(object):
+    cdef bcf_hdr_t *ptr
+
+    cdef _add_sample(self, name)
+    cdef _hdr_sync(self)
+    cdef _subset_samples(self, include_samples)
+
+
+cdef class VariantHeaderRecord(object):
+    cdef readonly VariantHeader header
+    cdef bcf_hrec_t *ptr
+
+
+cdef class VariantHeaderRecords(object):
+    cdef readonly VariantHeader header
+
+
+cdef class VariantHeaderContigs(object):
+    cdef readonly VariantHeader header
+
+
+cdef class VariantHeaderSamples(object):
+    cdef readonly VariantHeader header
+
+
+cdef class VariantContig(object):
+    cdef readonly VariantHeader header
+    cdef int id
+
+
+cdef class VariantMetadata(object):
+    cdef readonly VariantHeader header
+    cdef int type
+    cdef int id
+
+
+cdef class VariantHeaderMetadata(object):
+    cdef readonly VariantHeader header
+    cdef int32_t type
+
+
+cdef class VariantRecord(object):
+    cdef readonly VariantHeader header
+    cdef bcf1_t *ptr
+
+
+cdef class VariantRecordFilter(object):
+    cdef VariantRecord record
+
+
+cdef class VariantRecordFormat(object):
+    cdef VariantRecord record
+
+
+cdef class VariantRecordInfo(object):
+    cdef VariantRecord record
+
+
+cdef class VariantRecordSamples(object):
+    cdef VariantRecord record
+
+
+cdef class VariantRecordSample(object):
+    cdef VariantRecord record
+    cdef readonly int32_t index
+
+
+cdef class BaseIndex(object):
+    cdef tuple refs
+    cdef dict refmap
+
+
+cdef class BCFIndex(BaseIndex):
+    cdef readonly VariantHeader header
+    cdef hts_idx_t *ptr
+
+
+cdef class TabixIndex(BaseIndex):
+    cdef tbx_t *ptr
+
+
+cdef class BaseIterator(object):
+    cdef VariantFile bcf
+    cdef hts_itr_t  *iter
+
+
+cdef class BCFIterator(BaseIterator):
+    cdef BCFIndex index
+
+
+cdef class TabixIterator(BaseIterator):
+    cdef TabixIndex index
+    cdef kstring_t line_buffer
+
+
+cdef class VariantFile(HTSFile):
+    cdef readonly VariantHeader  header
+    cdef readonly BaseIndex      index
+
+    cdef readonly bint           drop_samples  # true if sample information is to be ignored
+
+    # FIXME: Temporary, use htsFormat when it is available
+    cdef readonly bint       is_reading     # true if file has begun reading records
+    cdef readonly bint       header_written # true if header has already been written
+
+    cpdef int write(self, VariantRecord record) except -1
diff --git a/pysam/libcbcf.pyi b/pysam/libcbcf.pyi
new file mode 100644
index 0000000..bb875dd
--- /dev/null
+++ b/pysam/libcbcf.pyi
@@ -0,0 +1,369 @@
+import sys
+from typing import (
+    Optional,
+    Union,
+    Any,
+    Sequence,
+    Tuple,
+    Iterator,
+    List,
+    Iterable,
+    Dict,
+    overload,
+    TypeVar,
+    Mapping,
+    Generic,
+)
+
+if sys.version_info < (3, 8):
+    from typing_extensions import Literal
+else:
+    from typing import Literal
+
+from .libchtslib import HTSFile, _HasFileNo
+
+_D = TypeVar("_D")
+_K = TypeVar("_K", str, Union[int, str])
+_V = TypeVar("_V")
+
+class _Mapping(Generic[_K, _V]):
+    def __len__(self) -> int: ...
+    def __contains__(self, key: _K) -> bool: ...
+    def __iter__(self) -> Iterator[_K]: ...
+    def iterkeys(self) -> Iterator[_K]: ...
+    def itervalues(self) -> Iterator[_V]: ...
+    def iteritems(self) -> Iterator[Tuple[_K, _V]]: ...
+    def keys(self) -> List[_K]: ...
+    def items(self) -> List[Tuple[_K, _V]]: ...
+    def values(self) -> List[_V]: ...
+    def __bool__(self) -> bool: ...
+    def __getitem__(self, key: _K) -> _V: ...
+    def get(self, key: _K, default: _D = ...) -> Union[_D, _V]: ...
+
+class VariantHeaderRecord(_Mapping[str, str]):
+    @property
+    def header(self) -> VariantHeader: ...
+    @property
+    def type(self) -> Optional[str]: ...
+    @property
+    def key(self) -> Optional[str]: ...
+    @property
+    def value(self) -> Optional[str]: ...
+    @property
+    def attrs(self) -> Sequence[Tuple[str, str]]: ...
+    def update(self, items: Union[Iterable, Dict] = ..., **kwargs) -> None: ...
+    def pop(self, key: str, default: str = ...) -> str: ...
+    def remove(self) -> None: ...  # crashes
+
+class VariantHeaderRecords:
+    @property
+    def header(self) -> VariantHeader: ...
+    def __len__(self) -> int: ...
+    def __bool__(self) -> bool: ...
+    def __getitem__(self, index) -> VariantHeaderRecord: ...
+    def __iter__(self) -> Iterator[VariantHeaderRecord]: ...
+
+class VariantMetadata:
+    @property
+    def header(self) -> VariantHeader: ...
+    @property
+    def name(self) -> str: ...
+    # @property  # should this be exposed?
+    # def id(self) -> int: ...
+    @property
+    def number(self) -> Optional[str]: ...
+    @property
+    def type(self) -> Optional[str]: ...
+    @property
+    def description(self) -> Optional[str]: ...
+    @property
+    def record(self) -> Optional[VariantHeaderRecord]: ...
+    def remove_header(self) -> None: ...
+
+class VariantHeaderMetadata(_Mapping[str, VariantMetadata]):
+    @property
+    def header(self) -> VariantHeader: ...
+    def add(
+        self,
+        id: str,
+        number: Optional[Union[int, str]],
+        type: Optional[str],
+        description: str,
+        **kwargs
+    ) -> None: ...
+    def remove_header(self, key: str) -> None: ...
+    def clear_header(self) -> None: ...
+
+class VariantContig:
+    @property
+    def header(self) -> VariantHeader: ...
+    @property
+    def name(self) -> str: ...
+    @property
+    def id(self) -> int: ...
+    @property
+    def length(self) -> Optional[int]: ...
+    @property
+    def header_record(self) -> VariantHeaderRecord: ...
+    def remove_header(self) -> None: ...
+
+class VariantHeaderContigs(_Mapping[Union[int, str], VariantContig]):
+    @property
+    def header(self) -> VariantHeader: ...
+    def remove_header(self, key: Union[int, str]) -> None: ...
+    def clear_header(self) -> None: ...
+    def add(self, id: str, length: Optional[int] = ..., **kwargs) -> None: ...
+
+class VariantHeaderSamples:
+    @property
+    def header(self) -> VariantHeader: ...
+    def __len__(self) -> int: ...
+    def __bool__(self) -> bool: ...
+    def __getitem__(self, index: int) -> str: ...
+    def __iter__(self) -> Iterator[str]: ...
+    def __contains__(self, key: str) -> bool: ...
+    def add(self, name: str) -> None: ...
+
+class VariantHeader:
+    def __init__(self) -> None: ...
+    def __bool__(self) -> bool: ...
+    def copy(self) -> VariantHeader: ...
+    def merge(self, header: VariantHeader) -> None: ...
+    @property
+    def version(self) -> str: ...
+    @property
+    def samples(self) -> VariantHeaderSamples: ...
+    @property
+    def records(self) -> VariantHeaderRecords: ...
+    @property
+    def contigs(self) -> VariantHeaderContigs: ...
+    @property
+    def filters(self) -> VariantHeaderMetadata: ...
+    @property
+    def info(self) -> VariantHeaderMetadata: ...
+    @property
+    def formats(self) -> VariantHeaderMetadata: ...
+    @property
+    def alts(self) -> Dict[str, VariantHeaderRecord]: ...
+    def new_record(
+        self,
+        contig: Optional[str] = ...,
+        start: int = ...,
+        stop: int = ...,
+        alleles: Optional[Tuple[str, ...]] = ...,
+        id: Optional[str] = ...,
+        qual: Optional[int] = ...,
+        filter: Optional[Any] = ...,
+        info: Optional[Mapping[str, _InfoValue]] = ...,
+        samples: Optional[Iterable[Optional[Mapping[str, _FormatValue]]]] = ...,
+        **kwargs
+    ) -> VariantRecord: ...
+    def add_record(self, record: VariantHeaderRecord) -> None: ...
+    def add_line(self, line: str) -> None: ...
+    @overload
+    def add_meta(
+        self, key: str, value: None = ..., items: Iterable[Tuple[str, str]] = ...
+    ) -> None: ...
+    @overload
+    def add_meta(self, key: str, value: str = ..., items: None = ...) -> None: ...
+    def add_sample(self, name: str) -> None: ...
+    def add_samples(self, *args: Union[str, Iterable[str]]) -> None: ...
+
+class VariantRecordFilter(_Mapping[Union[int, str], VariantMetadata]):
+    def add(self, key: str) -> None: ...
+    def __delitem__(self, key: Union[int, str]) -> None: ...
+    def clear(self) -> None: ...
+    def __eq__(self, other) -> bool: ...
+    def __ne__(self, other) -> bool: ...
+
+class VariantRecordFormat(_Mapping[str, VariantMetadata]):
+    def __delitem__(self, key: str) -> None: ...
+    def clear(self) -> None: ...
+
+_InfoValue = Any  # TODO see bcf_info_get_value
+
+class VariantRecordInfo(_Mapping[str, _InfoValue]):
+    def __setitem__(self, key: str, object: _InfoValue) -> None: ...
+    def __delitem__(self, key: str) -> None: ...
+    def clear(self) -> None: ...
+    def update(
+        self, items: Optional[_Mapping[str, _InfoValue]] = ..., **kwargs
+    ) -> None: ...
+    def pop(self, key: str, default: _D = ...) -> Union[_D, _InfoValue]: ...
+    def __eq__(self, other) -> bool: ...
+    def __ne__(self, other) -> bool: ...
+
+class VariantRecordSamples(_Mapping[Union[str, int], "VariantRecordSample"]):
+    def __eq__(self, other) -> bool: ...
+    def __ne__(self, other) -> bool: ...
+    # TODO Do these work? Isn’t the container read only?
+    def update(
+        self,
+        items: Optional[Mapping[Union[str, int], VariantRecordSample]] = ...,
+        **kwargs
+    ) -> None: ...
+    def pop(
+        self, key: Union[str, int], default: _D = ...
+    ) -> Union[_D, VariantRecordSample]: ...
+
+class VariantRecord:
+    @property
+    def header(self) -> VariantHeader: ...
+    def copy(self) -> VariantRecord: ...
+    def translate(self, dst_header: VariantHeader) -> None: ...
+    rid: int
+    chrom: str
+    contig: str
+    pos: int
+    start: int
+    stop: int
+    rlen: int
+    qual: Optional[int]
+    id: Optional[str]
+    ref: Optional[str]
+    alleles: Optional[Tuple[str, ...]]
+    alts: Optional[Tuple[str, ...]]
+    @property
+    def filter(self) -> VariantRecordFilter: ...
+    @property
+    def info(self) -> VariantRecordInfo: ...
+    @property
+    def format(self) -> VariantRecordFormat: ...
+    @property
+    def samples(self) -> VariantRecordSamples: ...
+    def __eq__(self, other) -> bool: ...
+    def __ne__(self, other) -> bool: ...
+
+_FormatValue = Any  # TODO see bcf_format_get_value
+
+class VariantRecordSample(_Mapping[str, _FormatValue]):
+    @property
+    def index(self) -> int: ...
+    @property
+    def name(self) -> str: ...
+    allele_indices: Optional[Tuple[Optional[int, ...]]]
+    alleles: Optional[Tuple[Optional[str, ...]]]
+    phased: bool
+    def __setitem__(self, key: str, value: _FormatValue) -> None: ...
+    def __delitem__(self, key: str) -> None: ...
+    def clear(self) -> None: ...
+    def update(
+        self, items: Optional[Mapping[str, _FormatValue]] = ..., **kwargs
+    ) -> None: ...
+    def pop(self, key: str, default: _D = ...) -> Union[_D, _FormatValue]: ...
+    def __eq__(self, other) -> Any: ...
+    def __ne__(self, other) -> Any: ...
+
+class BaseIndex(_Mapping[Union[int, str], str]):
+    refs: Sequence[str]
+    refmap: Dict[str, str]
+    def __init__(self) -> None: ...
+    # TODO Do these work? Isn’t the container read only?
+    def update(self, items: Optional[Mapping[str, str]] = ..., **kwargs) -> None: ...
+    def pop(self, key: str, default: _D = ...) -> Union[_D, str]: ...
+
+class BCFIndex(BaseIndex):
+    @property
+    def header(self) -> VariantHeader: ...
+    def __init__(self) -> None: ...
+    def fetch(
+        self,
+        bcf: VariantFile,
+        contig: str,
+        start: Optional[int],
+        stop: Optional[int],
+        reopen: bool,
+    ) -> BCFIterator: ...
+
+class TabixIndex(BaseIndex):
+    def __init__(self) -> None: ...
+    def fetch(
+        self,
+        bcf: VariantFile,
+        contig: str,
+        start: Optional[int],
+        stop: Optional[int],
+        reopen: bool,
+    ) -> TabixIterator: ...
+
+class BaseIterator:
+    def __init__(self) -> None: ...
+
+class BCFIterator(BaseIterator):
+    def __init__(
+        self,
+        bcf: VariantFile,
+        contig: str,
+        start: Optional[int] = ...,
+        stop: Optional[int] = ...,
+        reopen: bool = ...,
+    ) -> None: ...
+    def __iter__(self) -> BCFIterator: ...
+    def __next__(self) -> VariantRecord: ...
+
+class TabixIterator(BaseIterator):
+    def __init__(
+        self,
+        bcf: VariantFile,
+        contig: str,
+        start: Optional[int] = ...,
+        stop: Optional[int] = ...,
+        reopen: bool = ...,
+    ) -> None: ...
+    def __iter__(self) -> TabixIterator: ...
+    def __next__(self) -> VariantRecord: ...
+
+class VariantFile(HTSFile):
+    @property
+    def header(self) -> VariantHeader: ...
+    @property
+    def index(self) -> BaseIndex: ...
+    @property
+    def drop_samples(self) -> bool: ...
+    @property
+    def is_reading(self) -> bool: ...
+    @property
+    def header_written(self) -> bool: ...
+    def __init__(
+        self,
+        filename: Union[str, bytes, int, _HasFileNo],
+        mode: Optional[Literal["r", "w", "wh", "rb", "wb", "wbu", "wb0"]] = ...,
+        index_filename: Optional[str] = ...,
+        header: Optional[VariantHeader] = ...,
+        drop_samples: bool = ...,
+        duplicate_filehandle: bool = ...,
+        ignore_truncation: bool = ...,
+        threads: int = ...,
+    ) -> None: ...
+    def close(self) -> None: ...
+    def __iter__(self) -> VariantFile: ...
+    def __next__(self) -> VariantRecord: ...
+    def copy(self) -> VariantFile: ...
+    def open(
+        self,
+        filename: Union[str, bytes, int, _HasFileNo],
+        mode: Optional[Literal["r", "w", "wh", "rb", "wb", "wbu", "wb0"]] = ...,
+        index_filename: Optional[str] = ...,
+        header: Optional[VariantHeader] = ...,
+        drop_samples: bool = ...,
+        duplicate_filehandle: bool = ...,
+        ignore_truncation: bool = ...,
+        threads: int = ...,
+    ) -> None: ...
+    def reset(self) -> None: ...
+    def is_valid_tid(self, tid: int) -> bool: ...
+    def get_tid(self, reference: str) -> int: ...
+    def get_reference_name(self, tid: int) -> str: ...
+    def fetch(
+        self,
+        contig: Optional[str] = ...,
+        start: Optional[int] = ...,
+        stop: Optional[int] = ...,
+        region: Optional[str] = ...,
+        reopen: bool = ...,
+        end: Optional[int] = ...,
+        reference: Optional[str] = ...,
+    ) -> Iterator[VariantRecord]: ...
+    def new_record(self, *args, **kwargs) -> Any: ...
+    def write(self, record: VariantRecord) -> int: ...
+    def subset_samples(self, include_samples: Iterable[str]) -> None: ...
diff --git a/pysam/libcbcf.pyx b/pysam/libcbcf.pyx
new file mode 100644
index 0000000..c3cf8cf
--- /dev/null
+++ b/pysam/libcbcf.pyx
@@ -0,0 +1,4544 @@
+# cython: embedsignature=True
+# cython: profile=True
+###############################################################################
+###############################################################################
+## Cython wrapper for htslib VCF/BCF reader/writer
+###############################################################################
+#
+# NOTICE: This code is incomplete and preliminary.  It offers a nearly
+#         complete Pythonic interface to VCF/BCF metadata and data with
+#         reading and writing capability.  Documentation and a unit test suite
+#         are in the works.  The code is best tested under Python 2, but
+#         should also work with Python 3.  Please report any remaining
+#         str/bytes issues on the github site when using Python 3 and I'll
+#         fix them promptly.
+#
+# Here is a minimal example of how to use the API:
+#
+#     $ cat bcfview.py
+#     import sys
+#     from pysam import VariantFile
+#
+#     bcf_in = VariantFile(sys.argv[1]) # auto-detect input format
+#     bcf_out = VariantFile('-', 'w', header=bcf_in.header)
+#
+#     for rec in bcf_in:
+#         bcf_out.write(rec)
+#
+# Performance is fairly close to that of bcftools view.  Here is an example
+# using some 1k Genomes data:
+#
+#     $ time python bcfview.py ALL.chr22.phase3_shapeit2_mvncall_integrated_v5.20130502.genotypes.bcf |wc -l
+#      1103799
+#
+#     real	0m56.114s
+#     user	1m4.489s
+#     sys	0m3.102s
+#
+#     $ time bcftools view ALL.chr22.phase3_shapeit2_mvncall_integrated_v5.20130502.genotypes.bcf |wc -l
+#      1103800  # bcftools adds an extra header
+#
+#     real	0m55.126s
+#     user	1m3.502s
+#     sys	0m3.459s
+#
+###############################################################################
+#
+# TODO list:
+#
+#   * more genotype methods
+#   * unit test suite (perhaps py.test based)
+#   * documentation
+#   * pickle support
+#   * left/right locus normalization
+#   * fix reopen to re-use fd
+#
+###############################################################################
+#
+# The MIT License
+#
+# Copyright (c) 2015,2016 Kevin Jacobs (jacobs@bioinformed.com)
+#
+# Permission is hereby granted, free of charge, to any person obtaining a
+# copy of this software and associated documentation files (the "Software"),
+# to deal in the Software without restriction, including without limitation
+# the rights to use, copy, modify, merge, publish, distribute, sublicense,
+# and/or sell copies of the Software, and to permit persons to whom the
+# Software is furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.  IN NO EVENT SHALL
+# THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+# DEALINGS IN THE SOFTWARE.
+#
+###############################################################################
+
+from __future__ import division, print_function
+
+import os
+import sys
+
+from libc.errno  cimport errno, EPIPE
+from libc.string cimport strcmp, strpbrk, strerror
+from libc.stdint cimport INT8_MAX, INT16_MAX, INT32_MAX
+
+cimport cython
+
+from cpython.object  cimport PyObject
+from cpython.ref     cimport Py_INCREF
+from cpython.dict    cimport PyDict_GetItemString, PyDict_SetItemString
+from cpython.tuple   cimport PyTuple_New, PyTuple_SET_ITEM
+from cpython.bytes   cimport PyBytes_FromStringAndSize
+from cpython.unicode cimport PyUnicode_DecodeUTF8
+from cpython.version cimport PY_MAJOR_VERSION
+
+from pysam.libchtslib cimport HTSFile, hisremote
+
+from pysam.utils import unquoted_str
+
+
+__all__ = ['VariantFile',
+           'VariantHeader',
+           'VariantHeaderRecord',
+           'VariantHeaderRecords',
+           'VariantMetadata',
+           'VariantHeaderMetadata',
+           'VariantContig',
+           'VariantHeaderContigs',
+           'VariantHeaderSamples',
+           'VariantRecordFilter',
+           'VariantRecordFormat',
+           'VariantRecordInfo',
+           'VariantRecordSamples',
+           'VariantRecord',
+           'VariantRecordSample',
+           'BaseIndex',
+           'BCFIndex',
+           'TabixIndex',
+           'BaseIterator',
+           'BCFIterator',
+           'TabixIterator',
+           'VariantRecord']
+
+########################################################################
+########################################################################
+## Constants
+########################################################################
+
+cdef int MAX_POS = (1 << 31) - 1
+cdef tuple VALUE_TYPES = ('Flag', 'Integer', 'Float', 'String')
+cdef tuple METADATA_TYPES = ('FILTER', 'INFO', 'FORMAT', 'CONTIG', 'STRUCTURED', 'GENERIC')
+cdef tuple METADATA_LENGTHS = ('FIXED', 'VARIABLE', 'A', 'G', 'R')
+
+
+########################################################################
+########################################################################
+## Python 3 compatibility functions
+########################################################################
+
+from pysam.libcutils cimport force_bytes, force_str, charptr_to_str, charptr_to_str_w_len
+from pysam.libcutils cimport encode_filename, from_string_and_size, decode_bytes
+
+
+########################################################################
+########################################################################
+## Sentinel object
+########################################################################
+
+cdef object _nothing = object()
+
+########################################################################
+########################################################################
+## VCF/BCF string intern system
+########################################################################
+
+cdef dict bcf_str_cache = {}
+
+cdef inline bcf_str_cache_get_charptr(const char* s):
+    if s == NULL:
+        return None
+
+    cdef PyObject *pystr = PyDict_GetItemString(bcf_str_cache, s)
+    if pystr:
+        return <object>pystr
+
+    if PY_MAJOR_VERSION < 3:
+        val = s
+    else:
+        val = PyUnicode_DecodeUTF8(s, strlen(s), NULL)
+
+    PyDict_SetItemString(bcf_str_cache, s, val)
+
+    return val
+
+
+########################################################################
+########################################################################
+## Genotype math
+########################################################################
+
+cdef int comb(int n, int k) except -1:
+    """Return binomial coefficient: n choose k
+
+    >>> comb(5, 1)
+    5
+    >>> comb(5, 2)
+    10
+    >>> comb(2, 2)
+    1
+    >>> comb(100, 2)
+    4950
+    """
+    if k > n:
+        return 0
+    elif k == n:
+        return 1
+    elif k > n // 2:
+        k = n - k
+
+    cdef d, result
+
+    d = result = n - k + 1
+    for i in range(2, k + 1):
+        d += 1
+        result  *= d
+        result //= i
+    return result
+
+
+cdef inline int bcf_geno_combinations(int ploidy, int alleles) except -1:
+    """Return the count of genotypes expected for the given ploidy and number of alleles.
+
+    >>> bcf_geno_combinations(1, 2)
+    2
+    >>> bcf_geno_combinations(2, 2)
+    3
+    >>> bcf_geno_combinations(2, 3)
+    6
+    >>> bcf_geno_combinations(3, 2)
+    4
+    """
+    return comb(alleles + ploidy - 1, ploidy)
+
+
+########################################################################
+########################################################################
+## Low level type conversion helpers
+########################################################################
+
+
+cdef inline bint check_header_id(bcf_hdr_t *hdr, int hl_type, int id):
+    return id >= 0 and id < hdr.n[BCF_DT_ID] and bcf_hdr_idinfo_exists(hdr, hl_type, id)
+
+
+cdef inline int is_gt_fmt(bcf_hdr_t *hdr, int fmt_id):
+    return strcmp(bcf_hdr_int2id(hdr, BCF_DT_ID, fmt_id), 'GT') == 0
+
+
+cdef inline int bcf_genotype_count(bcf_hdr_t *hdr, bcf1_t *rec, int sample) except -1:
+
+    if sample < 0:
+        raise ValueError('genotype is only valid as a format field')
+
+    cdef int32_t *gt_arr = NULL
+    cdef int ngt = 0
+    ngt = bcf_get_genotypes(hdr, rec, &gt_arr, &ngt)
+
+    if ngt <= 0 or not gt_arr:
+        return 0
+
+    assert ngt % rec.n_sample == 0
+    cdef int max_ploidy = ngt // rec.n_sample
+    cdef int32_t *gt = gt_arr + sample * max_ploidy
+    cdef int ploidy = 0
+
+    while ploidy < max_ploidy and gt[0] != bcf_int32_vector_end:
+        gt += 1
+        ploidy += 1
+
+    free(<void*>gt_arr)
+
+    return bcf_geno_combinations(ploidy, rec.n_allele)
+
+
+cdef tuple char_array_to_tuple(const char **a, ssize_t n, int free_after=0):
+    if not a:
+        return None
+    try:
+         return tuple(charptr_to_str(a[i]) for i in range(n))
+    finally:
+        if free_after and a:
+            free(a)
+
+
+cdef bcf_array_to_object(void *data, int type, ssize_t n, ssize_t count, int scalar):
+    cdef char    *datac
+    cdef int8_t  *data8
+    cdef int16_t *data16
+    cdef int32_t *data32
+    cdef float   *dataf
+    cdef int      i
+    cdef bytes    b
+
+    if not data or n <= 0:
+        return None
+
+    if type == BCF_BT_CHAR:
+        datac = <char *>data
+
+        if not n:
+            value = ()
+        else:
+            # Check if at least one null terminator is present
+            if datac[n-1] == bcf_str_vector_end:
+                # If so, create a string up to the first null terminator
+                b = datac
+            else:
+                # Otherwise, copy the entire block
+                b = datac[:n]
+            value = tuple(decode_bytes(v, 'utf-8') if v and v != bcf_str_missing else None for v in b.split(b','))
+    else:
+        value = []
+        if type == BCF_BT_INT8:
+            data8 = <int8_t *>data
+            for i in range(n):
+                if data8[i] == bcf_int8_vector_end:
+                    break
+                value.append(data8[i] if data8[i] != bcf_int8_missing else None)
+        elif type == BCF_BT_INT16:
+            data16 = <int16_t *>data
+            for i in range(n):
+                if data16[i] == bcf_int16_vector_end:
+                    break
+                value.append(data16[i] if data16[i] != bcf_int16_missing else None)
+        elif type == BCF_BT_INT32:
+            data32 = <int32_t *>data
+            for i in range(n):
+                if data32[i] == bcf_int32_vector_end:
+                    break
+                value.append(data32[i] if data32[i] != bcf_int32_missing else None)
+        elif type == BCF_BT_FLOAT:
+            dataf = <float *>data
+            for i in range(n):
+                if bcf_float_is_vector_end(dataf[i]):
+                    break
+                value.append(dataf[i] if not bcf_float_is_missing(dataf[i]) else None)
+        else:
+            raise TypeError('unsupported info type code')
+
+    # FIXME: Need to know length?  Report errors?  Pad with missing values?  Not clear what to do.
+    if not value:
+        if scalar:
+            value = None
+        elif count <= 0:
+            value = ()
+        else:
+            value = (None,)*count
+    elif scalar and len(value) == 1:
+        value = value[0]
+    else:
+        value = tuple(value)
+
+    return value
+
+
+cdef bcf_object_to_array(values, void *data, int bt_type, ssize_t n, int vlen):
+    cdef char    *datac
+    cdef int8_t  *data8
+    cdef int16_t *data16
+    cdef int32_t *data32
+    cdef float   *dataf
+    cdef ssize_t  i, value_count = len(values)
+
+    assert value_count <= n
+
+    if bt_type == BCF_BT_CHAR:
+        if not isinstance(values, (str, bytes)):
+            values = b','.join(force_bytes(v) if v else bcf_str_missing for v in values)
+            value_count = len(values)
+        assert value_count <= n
+        datac = <char *>data
+        memcpy(datac, <char *>values, value_count)
+        for i in range(value_count, n):
+            datac[i] = 0
+    elif bt_type == BCF_BT_INT8:
+        datai8 = <int8_t *>data
+        for i in range(value_count):
+            val = values[i]
+            datai8[i] = val if val is not None else bcf_int8_missing
+        for i in range(value_count, n):
+            datai8[i] = bcf_int8_vector_end
+    elif bt_type == BCF_BT_INT16:
+        datai16 = <int16_t *>data
+        for i in range(value_count):
+            val = values[i]
+            datai16[i] = val if val is not None else bcf_int16_missing
+        for i in range(value_count, n):
+            datai16[i] = bcf_int16_vector_end
+    elif bt_type == BCF_BT_INT32:
+        datai32 = <int32_t *>data
+        for i in range(value_count):
+            val = values[i]
+            datai32[i] = val if val is not None else bcf_int32_missing
+        for i in range(value_count, n):
+            datai32[i] = bcf_int32_vector_end
+    elif bt_type == BCF_BT_FLOAT:
+        dataf = <float *>data
+        for i in range(value_count):
+            val = values[i]
+            if val is None:
+                bcf_float_set(dataf + i, bcf_float_missing)
+            else:
+                dataf[i] = val
+        for i in range(value_count, n):
+            bcf_float_set(dataf + i, bcf_float_vector_end)
+    else:
+        raise TypeError('unsupported type')
+
+
+cdef bcf_empty_array(int type, ssize_t n, int vlen):
+    cdef char    *datac
+    cdef int32_t *data32
+    cdef float   *dataf
+    cdef int      i
+
+    if n <= 0:
+        raise ValueError('Cannot create empty array')
+
+    if type == BCF_HT_STR:
+        value = PyBytes_FromStringAndSize(NULL, sizeof(char)*n)
+        datac = <char *>value
+        for i in range(n):
+            datac[i] = bcf_str_missing if not vlen else bcf_str_vector_end
+    elif type == BCF_HT_INT:
+        value = PyBytes_FromStringAndSize(NULL, sizeof(int32_t)*n)
+        data32 = <int32_t *><char *>value
+        for i in range(n):
+            data32[i] = bcf_int32_missing if not vlen else bcf_int32_vector_end
+    elif type == BCF_HT_REAL:
+        value = PyBytes_FromStringAndSize(NULL, sizeof(float)*n)
+        dataf = <float *><char *>value
+        for i in range(n):
+            bcf_float_set(dataf + i, bcf_float_missing if not vlen else bcf_float_vector_end)
+    else:
+        raise TypeError('unsupported header type code')
+
+    return value
+
+
+cdef bcf_copy_expand_array(void *src_data, int src_type, size_t src_values,
+                           void *dst_data, int dst_type, size_t dst_values,
+                           int vlen):
+    """copy data from src to dest where the size of the elements (src_type/dst_type) differ
+    as well as the number of elements (src_values/dst_values).
+    """
+
+    cdef char    *src_datac
+    cdef char    *dst_datac
+    cdef int8_t  *src_datai8
+    cdef int16_t *src_datai16
+    cdef int32_t *src_datai32
+    cdef int32_t *dst_datai
+    cdef float   *src_dataf
+    cdef float   *dst_dataf
+    cdef ssize_t src_size, dst_size, i, j
+    cdef int val
+
+    if src_values > dst_values:
+        raise ValueError('Cannot copy arrays with src_values={} > dst_values={}'.format(src_values, dst_values))
+
+    if src_type == dst_type == BCF_BT_CHAR:
+        src_datac = <char *>src_data
+        dst_datac = <char *>dst_data
+        memcpy(dst_datac, src_datac, src_values)
+        for i in range(src_values, dst_values):
+            dst_datac[i] = 0
+    elif src_type == BCF_BT_INT8 and dst_type == BCF_BT_INT32:
+        src_datai8 = <int8_t *>src_data
+        dst_datai  = <int32_t *>dst_data
+        for i in range(src_values):
+            val = src_datai8[i]
+            if val == bcf_int8_missing:
+                val = bcf_int32_missing
+            elif val == bcf_int8_vector_end:
+                val = bcf_int32_vector_end
+            dst_datai[i] = val
+        for i in range(src_values, dst_values):
+            dst_datai[i] = bcf_int32_missing if not vlen else bcf_int32_vector_end
+    elif src_type == BCF_BT_INT16 and dst_type == BCF_BT_INT32:
+        src_datai16 = <int16_t *>src_data
+        dst_datai   = <int32_t *>dst_data
+        for i in range(src_values):
+            val = src_datai16[i]
+            if val == bcf_int16_missing:
+                val = bcf_int32_missing
+            elif val == bcf_int16_vector_end:
+                val = bcf_int32_vector_end
+            dst_datai[i] = val
+        for i in range(src_values, dst_values):
+            dst_datai[i] = bcf_int32_missing if not vlen else bcf_int32_vector_end
+    elif src_type == BCF_BT_INT32 and dst_type == BCF_BT_INT32:
+        src_datai32 = <int32_t *>src_data
+        dst_datai   = <int32_t *>dst_data
+        for i in range(src_values):
+            dst_datai[i] = src_datai32[i]
+        for i in range(src_values, dst_values):
+            dst_datai[i] = bcf_int32_missing if not vlen else bcf_int32_vector_end
+    elif src_type == BCF_BT_FLOAT and dst_type == BCF_BT_FLOAT:
+        src_dataf = <float *>src_data
+        dst_dataf = <float *>dst_data
+        for i in range(src_values):
+            dst_dataf[i] = src_dataf[i]
+        for i in range(src_values, dst_values):
+            bcf_float_set(dst_dataf + i, bcf_float_missing if not vlen else bcf_float_vector_end)
+    else:
+        raise TypeError('unsupported types')
+
+
+cdef bcf_get_value_count(VariantRecord record, int hl_type, int id, ssize_t *count, int *scalar, int sample):
+    if record is None:
+        raise ValueError('record must not be None')
+
+    cdef bcf_hdr_t *hdr = record.header.ptr
+    cdef bcf1_t *r = record.ptr
+
+    if not check_header_id(hdr, hl_type, id):
+        raise ValueError('Invalid header')
+
+    cdef int length = bcf_hdr_id2length(hdr, hl_type, id)
+    cdef int number = bcf_hdr_id2number(hdr, hl_type, id)
+
+    scalar[0] = 0
+
+    if hl_type == BCF_HL_FMT and is_gt_fmt(hdr, id):
+        count[0] = number
+    elif length == BCF_VL_FIXED:
+        if number == 1:
+            scalar[0] = 1
+        count[0] = number
+    elif length == BCF_VL_R:
+        count[0] = r.n_allele
+    elif length == BCF_VL_A:
+        count[0] = r.n_allele - 1
+    elif length == BCF_VL_G:
+        count[0] = bcf_genotype_count(hdr, r, sample)
+    elif length == BCF_VL_VAR:
+        count[0] = -1
+    else:
+        raise ValueError('Unknown format length')
+
+
+cdef object bcf_info_get_value(VariantRecord record, const bcf_info_t *z):
+    if record is None:
+        raise ValueError('record must not be None')
+
+    cdef bcf_hdr_t *hdr = record.header.ptr
+
+    cdef char *s
+    cdef ssize_t count
+    cdef int scalar
+
+    bcf_get_value_count(record, BCF_HL_INFO, z.key, &count, &scalar, -1)
+
+    if z.len == 0:
+        if  bcf_hdr_id2type(hdr, BCF_HL_INFO, z.key) == BCF_HT_FLAG:
+            value = True
+        elif scalar:
+            value = None
+        else:
+            value = ()
+    elif z.len == 1:
+        if z.type == BCF_BT_INT8:
+            value = z.v1.i if z.v1.i != bcf_int8_missing else None
+        elif z.type == BCF_BT_INT16:
+            value = z.v1.i if z.v1.i != bcf_int16_missing else None
+        elif z.type == BCF_BT_INT32:
+            value = z.v1.i if z.v1.i != bcf_int32_missing else None
+        elif z.type == BCF_BT_FLOAT:
+            value = z.v1.f if not bcf_float_is_missing(z.v1.f) else None
+        elif z.type == BCF_BT_CHAR:
+            value = force_str(chr(z.v1.i))
+        else:
+            raise TypeError('unsupported info type code')
+
+        if not scalar and value != ():
+            value = (value,)
+    else:
+        value = bcf_array_to_object(z.vptr, z.type, z.len, count, scalar)
+
+    return value
+
+
+cdef object bcf_check_values(VariantRecord record, value, int sample,
+                             int hl_type, int ht_type,
+                             int id, int bt_type, ssize_t bt_len,
+                             ssize_t *value_count, int *scalar, int *realloc):
+
+    if record is None:
+        raise ValueError('record must not be None')
+
+    bcf_get_value_count(record, hl_type, id, value_count, scalar, sample)
+
+    # Validate values now that we know the type and size
+    values = (value,) if not isinstance(value, (list, tuple)) else value
+
+    # Validate values now that we know the type and size
+    if ht_type == BCF_HT_FLAG:
+        value_count[0] = 1
+    elif hl_type == BCF_HL_FMT and is_gt_fmt(record.header.ptr, id):
+        # KBJ: htslib lies about the cardinality of GT fields-- they're really VLEN (-1)
+        value_count[0] = -1
+
+    cdef int given = len(values)
+    if value_count[0] != -1 and value_count[0] != given:
+        if scalar[0]:
+            raise TypeError('value expected to be scalar, given len={}'.format(given))
+        else:
+            raise TypeError('values expected to be {}-tuple, given len={}'.format(value_count[0], given))
+
+    if ht_type == BCF_HT_REAL:
+        for v in values:
+            if not(v is None or isinstance(v, (float, int))):
+                raise TypeError('invalid value for Float format')
+    elif ht_type == BCF_HT_INT:
+        for v in values:
+            if not(v is None or (isinstance(v, (float, int)) and int(v) == v)):
+                raise TypeError('invalid value for Integer format')
+        for v in values:
+            if not(v is None or bcf_int32_missing < v <= INT32_MAX):
+                raise ValueError('Integer value too small/large to store in VCF/BCF')
+    elif ht_type == BCF_HT_STR:
+        values = b','.join(force_bytes(v) if v is not None else b'' for v in values)
+    elif ht_type == BCF_HT_FLAG:
+        if values[0] not in (True, False, None, 1, 0):
+            raise ValueError('Flag values must be: True, False, None, 1, 0')
+    else:
+        raise TypeError('unsupported type')
+
+    realloc[0] = 0
+    if len(values) <= 1 and hl_type == BCF_HL_INFO:
+        realloc[0] = 0
+    elif len(values) > bt_len:
+        realloc[0] = 1
+    elif bt_type == BCF_BT_INT8:
+        for v in values:
+            if v is not None and not(bcf_int8_missing < v <= INT8_MAX):
+                realloc[0] = 1
+                break
+    elif bt_type == BCF_BT_INT16:
+        for v in values:
+            if v is not None and not(bcf_int16_missing < v <= INT16_MAX):
+                realloc[0] = 1
+                break
+
+    return values
+
+
+cdef bcf_encode_alleles(VariantRecord record, values):
+    if record is None:
+        raise ValueError('record must not be None')
+
+    cdef bcf1_t *r = record.ptr
+    cdef int32_t nalleles = r.n_allele
+    cdef list gt_values = []
+    cdef char *s
+    cdef int i
+
+    if values is None:
+        return ()
+
+    if not isinstance(values, (list, tuple)):
+        values = (values,)
+
+    for value in values:
+        if value is None:
+            gt_values.append(bcf_gt_missing)
+        elif isinstance(value, (str, bytes)):
+            bvalue = force_bytes(value)
+            s = bvalue
+            for i in range(r.n_allele):
+                if strcmp(r.d.allele[i], s) != 0:
+                    gt_values.append(bcf_gt_unphased(i))
+                    break
+            else:
+                raise ValueError('Unknown allele')
+        else:
+            i = value
+            if not (0 <= i < nalleles):
+                raise ValueError('Invalid allele index')
+            gt_values.append(bcf_gt_unphased(i))
+
+    return gt_values
+
+
+cdef bcf_info_set_value(VariantRecord record, key, value):
+    if record is None:
+        raise ValueError('record must not be None')
+
+    cdef bcf_hdr_t *hdr = record.header.ptr
+    cdef bcf1_t *r = record.ptr
+    cdef int info_id, info_type, scalar, dst_type, realloc, vlen = 0
+    cdef ssize_t i, value_count, alloc_len, alloc_size, dst_size
+
+    if bcf_unpack(r, BCF_UN_INFO) < 0:
+        raise ValueError('Error unpacking VariantRecord')
+
+    cdef bytes bkey = force_bytes(key)
+    cdef bcf_info_t *info = bcf_get_info(hdr, r, bkey)
+
+    if info:
+        info_id = info.key
+    else:
+        info_id = bcf_header_get_info_id(hdr, bkey)
+
+    if info_id < 0:
+        raise KeyError('unknown INFO: {}'.format(key))
+
+    if not check_header_id(hdr, BCF_HL_INFO, info_id):
+        raise ValueError('Invalid header')
+
+    info_type = bcf_hdr_id2type(hdr, BCF_HL_INFO, info_id)
+    values = bcf_check_values(record, value, -1,
+                              BCF_HL_INFO, info_type, info_id,
+                              info.type if info else -1,
+                              info.len  if info else -1,
+                              &value_count, &scalar, &realloc)
+
+    if info_type == BCF_HT_FLAG:
+        if bcf_update_info(hdr, r, bkey, NULL, bool(values[0]), info_type) < 0:
+            raise ValueError('Unable to update INFO values')
+        return
+
+    vlen = value_count < 0
+    value_count = len(values)
+
+    # DISABLED DUE TO ISSUES WITH THE CRAZY POINTERS
+    # If we can, write updated values to existing allocated storage
+    if 0 and info and not realloc:
+        r.d.shared_dirty |= BCF1_DIRTY_INF
+
+        if value_count == 0:
+            info.len = 0
+            if not info.vptr:
+                info.vptr = <uint8_t *>&info.v1.i
+
+        elif value_count == 1:
+            # FIXME: Check if need to free vptr if info.len > 0?
+            if info.type == BCF_BT_INT8 or info.type == BCF_BT_INT16 or info.type == BCF_BT_INT32:
+                bcf_object_to_array(values, &info.v1.i, BCF_BT_INT32, 1, vlen)
+            elif info.type == BCF_BT_FLOAT:
+                bcf_object_to_array(values, &info.v1.f, BCF_BT_FLOAT, 1, vlen)
+            else:
+                raise TypeError('unsupported info type code')
+
+            info.len = 1
+            if not info.vptr:
+                info.vptr = <uint8_t *>&info.v1.i
+        else:
+            bcf_object_to_array(values, info.vptr, info.type, info.len, vlen)
+
+        return
+
+    alloc_len = max(1, value_count)
+    if info and info.len > alloc_len:
+        alloc_len = info.len
+
+    new_values = bcf_empty_array(info_type, alloc_len, vlen)
+    cdef char *valp = <char *>new_values
+
+    if info_type == BCF_HT_INT:
+        dst_type = BCF_BT_INT32
+    elif info_type == BCF_HT_REAL:
+        dst_type = BCF_BT_FLOAT
+    elif info_type == BCF_HT_STR:
+        dst_type = BCF_BT_CHAR
+    else:
+        raise ValueError('Unsupported INFO type')
+
+    bcf_object_to_array(values, valp, dst_type, alloc_len, vlen)
+
+    if bcf_update_info(hdr, r, bkey, valp, <int>alloc_len, info_type) < 0:
+        raise ValueError('Unable to update INFO values')
+
+
+cdef bcf_info_del_value(VariantRecord record, key):
+    if record is None:
+        raise ValueError('record must not be None')
+
+    cdef bcf_hdr_t *hdr = record.header.ptr
+    cdef bcf1_t *r = record.ptr
+    cdef ssize_t value_count
+    cdef int scalar
+
+    if bcf_unpack(r, BCF_UN_INFO) < 0:
+        raise ValueError('Error unpacking VariantRecord')
+
+    cdef bytes bkey = force_bytes(key)
+    cdef bcf_info_t *info = bcf_get_info(hdr, r, bkey)
+
+    if not info:
+        raise KeyError(key)
+
+    bcf_get_value_count(record, BCF_HL_INFO, info.key, &value_count, &scalar, -1)
+
+    if value_count <= 0:
+        null_value = ()
+    elif scalar:
+        null_value = None
+    else:
+        null_value = (None,)*value_count
+
+    bcf_info_set_value(record, bkey, null_value)
+
+
+cdef bcf_format_get_value(VariantRecordSample sample, key):
+    if sample is None:
+        raise ValueError('sample must not be None')
+
+    cdef bcf_hdr_t *hdr = sample.record.header.ptr
+    cdef bcf1_t *r = sample.record.ptr
+    cdef ssize_t count
+    cdef int scalar
+
+    if bcf_unpack(r, BCF_UN_ALL) < 0:
+        raise ValueError('Error unpacking VariantRecord')
+
+    cdef bytes bkey = force_bytes(key)
+    cdef bcf_fmt_t *fmt = bcf_get_fmt(hdr, r, bkey)
+
+    if not fmt or not fmt.p:
+        raise KeyError('invalid FORMAT: {}'.format(key))
+
+    if is_gt_fmt(hdr, fmt.id):
+        return bcf_format_get_allele_indices(sample)
+
+    bcf_get_value_count(sample.record, BCF_HL_FMT, fmt.id, &count, &scalar, sample.index)
+
+    if fmt.p and fmt.n and fmt.size:
+        return bcf_array_to_object(fmt.p + sample.index * fmt.size, fmt.type, fmt.n, count, scalar)
+    elif scalar:
+        return None
+    elif count <= 0:
+        return ()
+    else:
+        return (None,)*count
+
+
+cdef bcf_format_set_value(VariantRecordSample sample, key, value):
+    if sample is None:
+        raise ValueError('sample must not be None')
+
+    if key == 'phased':
+        sample.phased = bool(value)
+        return
+
+    cdef bcf_hdr_t *hdr = sample.record.header.ptr
+    cdef bcf1_t *r = sample.record.ptr
+    cdef int fmt_id
+    cdef vdict_t *d
+    cdef khiter_t k
+    cdef int fmt_type, scalar, realloc, dst_type, vlen = 0
+    cdef ssize_t i, nsamples, value_count, alloc_size, alloc_len, dst_size
+
+    if bcf_unpack(r, BCF_UN_ALL) < 0:
+        raise ValueError('Error unpacking VariantRecord')
+
+    cdef bytes bkey = force_bytes(key)
+    cdef bcf_fmt_t *fmt = bcf_get_fmt(hdr, r, bkey)
+
+    if fmt:
+        fmt_id = fmt.id
+    else:
+        d = <vdict_t *>hdr.dict[BCF_DT_ID]
+        k = kh_get_vdict(d, bkey)
+
+        if k == kh_end(d) or kh_val_vdict(d, k).info[BCF_HL_FMT] & 0xF == 0xF:
+            raise KeyError('unknown format: {}'.format(key))
+
+        fmt_id = kh_val_vdict(d, k).id
+
+    if not check_header_id(hdr, BCF_HL_FMT, fmt_id):
+        raise ValueError('Invalid header')
+
+    fmt_type = bcf_hdr_id2type(hdr, BCF_HL_FMT, fmt_id)
+
+    if fmt_type == BCF_HT_FLAG:
+        raise ValueError('Flag types are not allowed on FORMATs')
+
+    if is_gt_fmt(hdr, fmt_id):
+        value = bcf_encode_alleles(sample.record, value)
+        # KBJ: GT field is considered to be a string by the VCF header but BCF represents it as INT.
+        fmt_type = BCF_HT_INT
+
+    values = bcf_check_values(sample.record, value, sample.index,
+                              BCF_HL_FMT, fmt_type, fmt_id,
+                              fmt.type if fmt else -1,
+                              fmt.n    if fmt else -1,
+                              &value_count, &scalar, &realloc)
+    vlen = value_count < 0
+    value_count = len(values)
+
+    # If we can, write updated values to existing allocated storage.
+    if fmt and not realloc:
+        r.d.indiv_dirty = 1
+        bcf_object_to_array(values, fmt.p + sample.index * fmt.size, fmt.type, fmt.n, vlen)
+        return
+
+    alloc_len = max(1, value_count)
+    if fmt and fmt.n > alloc_len:
+        alloc_len = fmt.n
+
+    nsamples = r.n_sample
+    new_values = bcf_empty_array(fmt_type, nsamples * alloc_len, vlen)
+    cdef char *new_values_p = <char *>new_values
+
+    if fmt_type == BCF_HT_INT:
+        dst_type = BCF_BT_INT32
+        dst_size = sizeof(int32_t) * alloc_len
+    elif fmt_type == BCF_HT_REAL:
+        dst_type = BCF_BT_FLOAT
+        dst_size = sizeof(float) * alloc_len
+    elif fmt_type == BCF_HT_STR:
+        dst_type = BCF_BT_CHAR
+        dst_size = sizeof(char) * alloc_len
+    else:
+        raise ValueError('Unsupported FORMAT type')
+
+    if fmt and nsamples > 1:
+        for i in range(nsamples):
+            bcf_copy_expand_array(fmt.p + i * fmt.size, fmt.type, fmt.n,
+                                  new_values_p  + i * dst_size, dst_type, alloc_len,
+                                  vlen)
+
+    bcf_object_to_array(values, new_values_p + sample.index * dst_size, dst_type, alloc_len, vlen)
+
+    if bcf_update_format(hdr, r, bkey, new_values_p, <int>(nsamples * alloc_len), fmt_type) < 0:
+        raise ValueError('Unable to update format values')
+
+
+cdef bcf_format_del_value(VariantRecordSample sample, key):
+    if sample is None:
+        raise ValueError('sample must not be None')
+
+    cdef bcf_hdr_t *hdr = sample.record.header.ptr
+    cdef bcf1_t *r = sample.record.ptr
+    cdef ssize_t value_count
+    cdef int scalar
+
+    if bcf_unpack(r, BCF_UN_ALL) < 0:
+        raise ValueError('Error unpacking VariantRecord')
+
+    cdef bytes bkey = force_bytes(key)
+    cdef bcf_fmt_t *fmt = bcf_get_fmt(hdr, r, bkey)
+
+    if not fmt or not fmt.p:
+        raise KeyError(key)
+
+    bcf_get_value_count(sample.record, BCF_HL_FMT, fmt.id, &value_count, &scalar, sample.index)
+
+    if value_count <= 0:
+        null_value = ()
+    elif scalar:
+        null_value = None
+    else:
+        null_value = (None,)*value_count
+
+    bcf_format_set_value(sample, bkey, null_value)
+
+
+cdef bcf_format_get_allele_indices(VariantRecordSample sample):
+    if sample is None:
+        raise ValueError('sample must not be None')
+
+    cdef bcf_hdr_t *hdr = sample.record.header.ptr
+    cdef bcf1_t *r = sample.record.ptr
+    cdef int32_t n = r.n_sample
+
+    if bcf_unpack(r, BCF_UN_ALL) < 0:
+        raise ValueError('Error unpacking VariantRecord')
+
+    if sample.index < 0 or sample.index >= n or not r.n_fmt:
+        return ()
+
+    cdef bcf_fmt_t *fmt0 = r.d.fmt
+    cdef int gt0 = is_gt_fmt(hdr, fmt0.id)
+
+    if not gt0 or not fmt0.n:
+        return ()
+
+    cdef int8_t  *data8
+    cdef int16_t *data16
+    cdef int32_t *data32
+    cdef int32_t a, nalleles = r.n_allele
+    cdef list alleles = []
+
+    if fmt0.type == BCF_BT_INT8:
+        data8 = <int8_t *>(fmt0.p + sample.index * fmt0.size)
+        for i in range(fmt0.n):
+            if data8[i] == bcf_int8_vector_end:
+                break
+            elif data8[i] == bcf_gt_missing:
+                a = -1
+            else:
+                a = bcf_gt_allele(data8[i])
+            alleles.append(a if 0 <= a < nalleles else None)
+    elif fmt0.type == BCF_BT_INT16:
+        data16 = <int16_t *>(fmt0.p + sample.index * fmt0.size)
+        for i in range(fmt0.n):
+            if data16[i] == bcf_int16_vector_end:
+                break
+            elif data16[i] == bcf_gt_missing:
+                a = -1
+            else:
+                a = bcf_gt_allele(data16[i])
+            alleles.append(a if 0 <= a < nalleles else None)
+    elif fmt0.type == BCF_BT_INT32:
+        data32 = <int32_t *>(fmt0.p + sample.index * fmt0.size)
+        for i in range(fmt0.n):
+            if data32[i] == bcf_int32_vector_end:
+                break
+            elif data32[i] == bcf_gt_missing:
+                a = -1
+            else:
+                a = bcf_gt_allele(data32[i])
+            alleles.append(a if 0 <= a < nalleles else None)
+
+    return tuple(alleles)
+
+
+cdef bcf_format_get_alleles(VariantRecordSample sample):
+    if sample is None:
+        raise ValueError('sample must not be None')
+
+    cdef bcf_hdr_t *hdr = sample.record.header.ptr
+    cdef bcf1_t *r = sample.record.ptr
+    cdef int32_t nsamples = r.n_sample
+
+    if bcf_unpack(r, BCF_UN_ALL) < 0:
+        raise ValueError('Error unpacking VariantRecord')
+
+    cdef int32_t nalleles = r.n_allele
+
+    if sample.index < 0 or sample.index >= nsamples or not r.n_fmt:
+        return ()
+
+    cdef bcf_fmt_t *fmt0 = r.d.fmt
+    cdef int gt0 = is_gt_fmt(hdr, fmt0.id)
+
+    if not gt0 or not fmt0.n:
+        return ()
+
+    cdef int32_t  a
+    cdef int8_t  *data8
+    cdef int16_t *data16
+    cdef int32_t *data32
+    alleles = []
+    if fmt0.type == BCF_BT_INT8:
+        data8 = <int8_t *>(fmt0.p + sample.index * fmt0.size)
+        for i in range(fmt0.n):
+            if data8[i] == bcf_int8_vector_end:
+                break
+            a = bcf_gt_allele(data8[i])
+            alleles.append(charptr_to_str(r.d.allele[a]) if 0 <= a < nalleles else None)
+    elif fmt0.type == BCF_BT_INT16:
+        data16 = <int16_t *>(fmt0.p + sample.index * fmt0.size)
+        for i in range(fmt0.n):
+            if data16[i] == bcf_int16_vector_end:
+                break
+            a = bcf_gt_allele(data16[i])
+            alleles.append(charptr_to_str(r.d.allele[a]) if 0 <= a < nalleles else None)
+    elif fmt0.type == BCF_BT_INT32:
+        data32 = <int32_t *>(fmt0.p + sample.index * fmt0.size)
+        for i in range(fmt0.n):
+            if data32[i] == bcf_int32_vector_end:
+                break
+            a = bcf_gt_allele(data32[i])
+            alleles.append(charptr_to_str(r.d.allele[a]) if 0 <= a < nalleles else None)
+    return tuple(alleles)
+
+
+cdef bint bcf_sample_get_phased(VariantRecordSample sample):
+    if sample is None:
+        raise ValueError('sample must not be None')
+
+    cdef bcf_hdr_t *hdr = sample.record.header.ptr
+    cdef bcf1_t *r = sample.record.ptr
+    cdef int32_t n = r.n_sample
+
+    if bcf_unpack(r, BCF_UN_ALL) < 0:
+        raise ValueError('Error unpacking VariantRecord')
+
+    if sample.index < 0 or sample.index >= n or not r.n_fmt:
+        return False
+
+    cdef bcf_fmt_t *fmt0 = r.d.fmt
+    cdef int gt0 = is_gt_fmt(hdr, fmt0.id)
+
+    if not gt0 or not fmt0.n:
+        return False
+
+    cdef int8_t  *data8
+    cdef int16_t *data16
+    cdef int32_t *data32
+
+    cdef bint phased = False
+
+    if fmt0.type == BCF_BT_INT8:
+        data8 = <int8_t *>(fmt0.p + sample.index * fmt0.size)
+        for i in range(fmt0.n):
+            if data8[i] == bcf_int8_vector_end:
+                break
+            elif data8[i] == bcf_int8_missing:
+                continue
+            elif i and not bcf_gt_is_phased(data8[i]):
+                return False
+            else:
+                phased = True
+    elif fmt0.type == BCF_BT_INT16:
+        data16 = <int16_t *>(fmt0.p + sample.index * fmt0.size)
+        for i in range(fmt0.n):
+            if data16[i] == bcf_int16_vector_end:
+                break
+            elif data16[i] == bcf_int16_missing:
+                continue
+            elif i and not bcf_gt_is_phased(data16[i]):
+                return False
+            else:
+                phased = True
+    elif fmt0.type == BCF_BT_INT32:
+        data32 = <int32_t *>(fmt0.p + sample.index * fmt0.size)
+        for i in range(fmt0.n):
+            if data32[i] == bcf_int32_vector_end:
+                break
+            elif data32[i] == bcf_int32_missing:
+                continue
+            elif i and not bcf_gt_is_phased(data32[i]):
+                return False
+            else:
+                phased = True
+
+    return phased
+
+
+cdef bcf_sample_set_phased(VariantRecordSample sample, bint phased):
+    if sample is None:
+        raise ValueError('sample must not be None')
+
+    cdef bcf_hdr_t *hdr = sample.record.header.ptr
+    cdef bcf1_t *r = sample.record.ptr
+    cdef int32_t n = r.n_sample
+
+    if bcf_unpack(r, BCF_UN_ALL) < 0:
+        raise ValueError('Error unpacking VariantRecord')
+
+    if sample.index < 0 or sample.index >= n or not r.n_fmt:
+        return
+
+    cdef bcf_fmt_t *fmt0 = r.d.fmt
+    cdef int gt0 = is_gt_fmt(hdr, fmt0.id)
+
+    if not gt0 or not fmt0.n:
+        raise ValueError('Cannot set phased before genotype is set')
+
+    cdef int8_t  *data8
+    cdef int16_t *data16
+    cdef int32_t *data32
+
+    if fmt0.type == BCF_BT_INT8:
+        data8 = <int8_t *>(fmt0.p + sample.index * fmt0.size)
+        for i in range(fmt0.n):
+            if data8[i] == bcf_int8_vector_end:
+                break
+            elif data8[i] == bcf_int8_missing:
+                continue
+            elif i:
+                data8[i] = (data8[i] & 0xFE) | phased
+    elif fmt0.type == BCF_BT_INT16:
+        data16 = <int16_t *>(fmt0.p + sample.index * fmt0.size)
+        for i in range(fmt0.n):
+            if data16[i] == bcf_int16_vector_end:
+                break
+            elif data16[i] == bcf_int16_missing:
+                continue
+            elif i:
+                data16[i] = (data16[i] & 0xFFFE) | phased
+    elif fmt0.type == BCF_BT_INT32:
+        data32 = <int32_t *>(fmt0.p + sample.index * fmt0.size)
+        for i in range(fmt0.n):
+            if data32[i] == bcf_int32_vector_end:
+                break
+            elif data32[i] == bcf_int32_missing:
+                continue
+            elif i:
+                data32[i] = (data32[i] & 0xFFFFFFFE) | phased
+
+
+cdef inline bcf_sync_end(VariantRecord record):
+    cdef bcf_hdr_t *hdr = record.header.ptr
+    cdef bcf_info_t *info
+    cdef int end_id = bcf_header_get_info_id(record.header.ptr, b'END')
+    cdef int ref_len
+
+    # allow missing ref when instantiating a new record
+    if record.ref is not None:
+        ref_len = len(record.ref)
+    else:
+        ref_len = 0
+
+    # Delete INFO/END if no alleles are present or if rlen is equal to len(ref)
+    # Always keep END for symbolic alleles
+    if not has_symbolic_allele(record) and (not record.ptr.n_allele or record.ptr.rlen == ref_len):
+        # If INFO/END is not defined in the header, it doesn't exist in the record
+        if end_id >= 0:
+            info = bcf_get_info(hdr, record.ptr, b'END')
+            if info and info.vptr:
+                if bcf_update_info(hdr, record.ptr, b'END', NULL, 0, info.type) < 0:
+                    raise ValueError('Unable to delete END')
+    else:
+        # Create END header, if not present
+        if end_id < 0:
+            record.header.info.add('END', number=1, type='Integer', description='Stop position of the interval')
+
+        # Update to reflect stop position
+        bcf_info_set_value(record, b'END', record.ptr.pos + record.ptr.rlen)
+
+
+cdef inline int has_symbolic_allele(VariantRecord record):
+    """Return index of first symbolic allele. 0 if no symbolic alleles."""
+
+    for i in range(1, record.ptr.n_allele):
+        alt = record.ptr.d.allele[i]
+        if alt[0] == b'<' and alt[len(alt) - 1] == b'>':
+            return i
+
+    return 0
+
+
+########################################################################
+########################################################################
+## Variant Header objects
+########################################################################
+
+
+cdef bcf_header_remove_hrec(VariantHeader header, int i):
+    if header is None:
+        raise ValueError('header must not be None')
+
+    cdef bcf_hdr_t *hdr = header.ptr
+
+    if i < 0 or i >= hdr.nhrec:
+        raise ValueError('Invalid header record index')
+
+    cdef bcf_hrec_t *hrec = hdr.hrec[i]
+    hdr.nhrec -= 1
+
+    if i < hdr.nhrec:
+        memmove(&hdr.hrec[i], &hdr.hrec[i+1], (hdr.nhrec-i)*sizeof(bcf_hrec_t*))
+
+    bcf_hrec_destroy(hrec)
+    hdr.hrec[hdr.nhrec] = NULL
+    hdr.dirty = 1
+
+
+#FIXME: implement a full mapping interface
+#FIXME: passing bcf_hrec_t* is not safe, since we cannot control the
+#       object lifetime.
+cdef class VariantHeaderRecord(object):
+    """header record from a :class:`VariantHeader` object"""
+    def __init__(self, *args, **kwargs):
+        raise TypeError('this class cannot be instantiated from Python')
+
+    @property
+    def type(self):
+        """header type: FILTER, INFO, FORMAT, CONTIG, STRUCTURED, or GENERIC"""
+        cdef bcf_hrec_t *r = self.ptr
+        if not r:
+            return None
+        return METADATA_TYPES[r.type]
+
+    @property
+    def key(self):
+        """header key (the part before '=', in FILTER/INFO/FORMAT/contig/fileformat etc.)"""
+        cdef bcf_hrec_t *r = self.ptr
+        return bcf_str_cache_get_charptr(r.key) if r and r.key else None
+
+    @property
+    def value(self):
+        """header value.  Set only for generic lines, None for FILTER/INFO, etc."""
+        cdef bcf_hrec_t *r = self.ptr
+        return charptr_to_str(r.value) if r and r.value else None
+
+    @property
+    def attrs(self):
+        """sequence of additional header attributes"""
+        cdef bcf_hrec_t *r = self.ptr
+        if not r:
+            return ()
+        cdef int i
+        return tuple((bcf_str_cache_get_charptr(r.keys[i]) if r.keys[i] else None,
+                      charptr_to_str(r.vals[i]) if r.vals[i] else None)
+                     for i in range(r.nkeys))
+
+    def __len__(self):
+        cdef bcf_hrec_t *r = self.ptr
+        return r.nkeys if r else 0
+
+    def __bool__(self):
+        cdef bcf_hrec_t *r = self.ptr
+        return r != NULL and r.nkeys != 0
+
+    def __getitem__(self, key):
+        """get attribute value"""
+        cdef bcf_hrec_t *r = self.ptr
+        cdef int i
+        if r:
+            bkey = force_bytes(key)
+            for i in range(r.nkeys):
+                if r.keys[i] and r.keys[i] == bkey:
+                    return charptr_to_str(r.vals[i]) if r.vals[i] else None
+        raise KeyError('cannot find metadata key')
+
+    def __iter__(self):
+        cdef bcf_hrec_t *r = self.ptr
+        if not r:
+            return
+        cdef int i
+        for i in range(r.nkeys):
+            if r.keys[i]:
+                yield bcf_str_cache_get_charptr(r.keys[i])
+
+    def get(self, key, default=None):
+        """D.get(k[,d]) -> D[k] if k in D, else d.  d defaults to None."""
+        try:
+            return self[key]
+        except KeyError:
+            return default
+
+    def __contains__(self, key):
+        try:
+            self[key]
+        except KeyError:
+            return False
+        else:
+            return True
+
+    def iterkeys(self):
+        """D.iterkeys() -> an iterator over the keys of D"""
+        return iter(self)
+
+    def itervalues(self):
+        """D.itervalues() -> an iterator over the values of D"""
+        cdef bcf_hrec_t *r = self.ptr
+        if not r:
+            return
+        cdef int i
+        for i in range(r.nkeys):
+            if r.keys[i]:
+                yield charptr_to_str(r.vals[i]) if r.vals[i] else None
+
+    def iteritems(self):
+        """D.iteritems() -> an iterator over the (key, value) items of D"""
+        cdef bcf_hrec_t *r = self.ptr
+        if not r:
+            return
+        cdef int i
+        for i in range(r.nkeys):
+            if r.keys[i]:
+                yield (bcf_str_cache_get_charptr(r.keys[i]), charptr_to_str(r.vals[i]) if r.vals[i] else None)
+
+    def keys(self):
+        """D.keys() -> list of D's keys"""
+        return list(self)
+
+    def items(self):
+        """D.items() -> list of D's (key, value) pairs, as 2-tuples"""
+        return list(self.iteritems())
+
+    def values(self):
+        """D.values() -> list of D's values"""
+        return list(self.itervalues())
+
+    def update(self, items=None, **kwargs):
+        """D.update([E, ]**F) -> None.
+
+        Update D from dict/iterable E and F.
+        """
+        for k, v in items.items():
+            self[k] = v
+
+        if kwargs:
+            for k, v in kwargs.items():
+                self[k] = v
+
+    def pop(self, key, default=_nothing):
+        try:
+            value = self[key]
+            del self[key]
+            return value
+        except KeyError:
+            if default is not _nothing:
+                return default
+            raise
+
+    # Mappings are not hashable by default, but subclasses can change this
+    __hash__ = None
+
+    #TODO: implement __richcmp__
+
+    def __str__(self):
+        cdef bcf_hrec_t *r = self.ptr
+
+        if not r:
+            raise ValueError('cannot convert deleted record to str')
+
+        cdef kstring_t hrec_str
+        hrec_str.l = hrec_str.m = 0
+        hrec_str.s = NULL
+
+        bcf_hrec_format(r, &hrec_str)
+
+        ret = charptr_to_str_w_len(hrec_str.s, hrec_str.l)
+
+        if hrec_str.m:
+            free(hrec_str.s)
+
+        return ret
+
+    # FIXME: Not safe -- causes trivial segfaults at the moment
+    def remove(self):
+        cdef bcf_hdr_t *hdr = self.header.ptr
+        cdef bcf_hrec_t *r = self.ptr
+        if not r:
+            return
+        assert r.key
+        cdef char *key = r.key if r.type == BCF_HL_GEN else r.value
+        bcf_hdr_remove(hdr, r.type, key)
+        self.ptr = NULL
+
+
+cdef VariantHeaderRecord makeVariantHeaderRecord(VariantHeader header, bcf_hrec_t *hdr):
+    if not header:
+        raise ValueError('invalid VariantHeader')
+
+    if not hdr:
+        return None
+
+    cdef VariantHeaderRecord record = VariantHeaderRecord.__new__(VariantHeaderRecord)
+    record.header = header
+    record.ptr = hdr
+
+    return record
+
+
+cdef class VariantHeaderRecords(object):
+    """sequence of :class:`VariantHeaderRecord` object from a :class:`VariantHeader` object"""
+    def __init__(self, *args, **kwargs):
+        raise TypeError('this class cannot be instantiated from Python')
+
+    def __len__(self):
+        return self.header.ptr.nhrec
+
+    def __bool__(self):
+        return self.header.ptr.nhrec != 0
+
+    def __getitem__(self, index):
+        cdef int32_t i = index
+        if i < 0 or i >= self.header.ptr.nhrec:
+            raise IndexError('invalid header record index')
+        return makeVariantHeaderRecord(self.header, self.header.ptr.hrec[i])
+
+    def __iter__(self):
+        cdef int32_t i
+        for i in range(self.header.ptr.nhrec):
+            yield makeVariantHeaderRecord(self.header, self.header.ptr.hrec[i])
+
+    __hash__ = None
+
+
+cdef VariantHeaderRecords makeVariantHeaderRecords(VariantHeader header):
+    if not header:
+        raise ValueError('invalid VariantHeader')
+
+    cdef VariantHeaderRecords records = VariantHeaderRecords.__new__(VariantHeaderRecords)
+    records.header = header
+    return records
+
+
+cdef class VariantMetadata(object):
+    """filter, info or format metadata record from a :class:`VariantHeader` object"""
+    def __init__(self, *args, **kwargs):
+        raise TypeError('this class cannot be instantiated from Python')
+
+    @property
+    def name(self):
+        """metadata name"""
+        cdef bcf_hdr_t *hdr = self.header.ptr
+        return bcf_str_cache_get_charptr(hdr.id[BCF_DT_ID][self.id].key)
+
+    # Q: Should this be exposed?
+    @property
+    def id(self):
+        """metadata internal header id number"""
+        return self.id
+
+    @property
+    def number(self):
+        """metadata number (i.e. cardinality)"""
+        cdef bcf_hdr_t *hdr = self.header.ptr
+
+        if not check_header_id(hdr, self.type, self.id):
+            raise ValueError('Invalid header id')
+
+        if self.type == BCF_HL_FLT:
+            return None
+
+        cdef int l = bcf_hdr_id2length(hdr, self.type, self.id)
+        if l == BCF_VL_FIXED:
+            return bcf_hdr_id2number(hdr, self.type, self.id)
+        elif l == BCF_VL_VAR:
+            return '.'
+        else:
+            return METADATA_LENGTHS[l]
+
+    @property
+    def type(self):
+        """metadata value type"""
+        cdef bcf_hdr_t *hdr = self.header.ptr
+        if not check_header_id(hdr, self.type, self.id):
+            raise ValueError('Invalid header id')
+
+        if self.type == BCF_HL_FLT:
+            return None
+        return VALUE_TYPES[bcf_hdr_id2type(hdr, self.type, self.id)]
+
+    @property
+    def description(self):
+        """metadata description (or None if not set)"""
+        descr = self.record.get('Description')
+        if descr:
+            descr = descr.strip('"')
+        return force_str(descr)
+
+    @property
+    def record(self):
+        """:class:`VariantHeaderRecord` associated with this :class:`VariantMetadata` object"""
+        cdef bcf_hdr_t *hdr = self.header.ptr
+        if not check_header_id(hdr, self.type, self.id):
+            raise ValueError('Invalid header id')
+        cdef bcf_hrec_t *hrec = hdr.id[BCF_DT_ID][self.id].val.hrec[self.type]
+        if not hrec:
+            return None
+        return makeVariantHeaderRecord(self.header, hrec)
+
+    def remove_header(self):
+        cdef bcf_hdr_t *hdr = self.header.ptr
+        cdef const char *key = hdr.id[BCF_DT_ID][self.id].key
+        bcf_hdr_remove(hdr, self.type, key)
+
+
+cdef VariantMetadata makeVariantMetadata(VariantHeader header, int type, int id):
+    if not header:
+        raise ValueError('invalid VariantHeader')
+
+    if type != BCF_HL_FLT and type != BCF_HL_INFO and type != BCF_HL_FMT:
+        raise ValueError('invalid metadata type')
+
+    if id < 0 or id >= header.ptr.n[BCF_DT_ID]:
+        raise ValueError('invalid metadata id')
+
+    cdef VariantMetadata meta = VariantMetadata.__new__(VariantMetadata)
+    meta.header = header
+    meta.type = type
+    meta.id = id
+
+    return meta
+
+
+cdef class VariantHeaderMetadata(object):
+    """mapping from filter, info or format name to :class:`VariantMetadata` object"""
+    def __init__(self, *args, **kwargs):
+        raise TypeError('this class cannot be instantiated from Python')
+
+    def add(self, id, number, type, description, **kwargs):
+        """Add a new filter, info or format record"""
+        if id in self:
+            raise ValueError('Header already exists for id={}'.format(id))
+
+        if self.type == BCF_HL_FLT:
+            if number is not None:
+                raise ValueError('Number must be None when adding a filter')
+            if type is not None:
+                raise ValueError('Type must be None when adding a filter')
+
+            items = [('ID', unquoted_str(id)), ('Description', description)]
+        else:
+            if type not in VALUE_TYPES:
+                raise ValueError('unknown type specified: {}'.format(type))
+            if number is None:
+                number = '.'
+
+            items = [('ID', unquoted_str(id)),
+                     ('Number', unquoted_str(number)),
+                     ('Type', unquoted_str(type)),
+                     ('Description', description)]
+
+        items += kwargs.items()
+        self.header.add_meta(METADATA_TYPES[self.type], items=items)
+
+    def __len__(self):
+        cdef bcf_hdr_t *hdr = self.header.ptr
+        cdef bcf_idpair_t *idpair
+        cdef int32_t i, n = 0
+
+        for i in range(hdr.n[BCF_DT_ID]):
+            idpair = hdr.id[BCF_DT_ID] + i
+            if idpair.key and idpair.val and idpair.val.info[self.type] & 0xF != 0xF:
+                n += 1
+        return n
+
+    def __bool__(self):
+        cdef bcf_hdr_t *hdr = self.header.ptr
+        cdef bcf_idpair_t *idpair
+        cdef int32_t i
+
+        for i in range(hdr.n[BCF_DT_ID]):
+            idpair = hdr.id[BCF_DT_ID] + i
+            if idpair.key and idpair.val and idpair.val.info[self.type] & 0xF != 0xF:
+                return True
+        return False
+
+    def __getitem__(self, key):
+        cdef bcf_hdr_t *hdr = self.header.ptr
+        cdef vdict_t *d = <vdict_t *>hdr.dict[BCF_DT_ID]
+
+        cdef bytes bkey = force_bytes(key)
+        cdef khiter_t k = kh_get_vdict(d, bkey)
+
+        if k == kh_end(d) or kh_val_vdict(d, k).info[self.type] & 0xF == 0xF:
+            raise KeyError('invalid key: {}'.format(key))
+
+        return makeVariantMetadata(self.header, self.type, kh_val_vdict(d, k).id)
+
+    def remove_header(self, key):
+        cdef bcf_hdr_t *hdr = self.header.ptr
+        cdef vdict_t *d = <vdict_t *>hdr.dict[BCF_DT_ID]
+
+        cdef bytes bkey = force_bytes(key)
+        cdef khiter_t k = kh_get_vdict(d, bkey)
+
+        if k == kh_end(d) or kh_val_vdict(d, k).info[self.type] & 0xF == 0xF:
+            raise KeyError('invalid key: {}'.format(key))
+
+        bcf_hdr_remove(hdr, self.type, bkey)
+        #bcf_hdr_sync(hdr)
+
+    def clear_header(self):
+        cdef bcf_hdr_t *hdr = self.header.ptr
+        bcf_hdr_remove(hdr, self.type, NULL)
+        #bcf_hdr_sync(hdr)
+
+    def __iter__(self):
+        cdef bcf_hdr_t *hdr = self.header.ptr
+        cdef bcf_idpair_t *idpair
+        cdef int32_t i
+
+        for i in range(hdr.n[BCF_DT_ID]):
+            idpair = hdr.id[BCF_DT_ID] + i
+            if idpair.key and idpair.val and idpair.val.info[self.type] & 0xF != 0xF:
+                yield bcf_str_cache_get_charptr(idpair.key)
+
+    def get(self, key, default=None):
+        """D.get(k[,d]) -> D[k] if k in D, else d.  d defaults to None."""
+        try:
+            return self[key]
+        except KeyError:
+            return default
+
+    def __contains__(self, key):
+        try:
+            self[key]
+        except KeyError:
+            return False
+        else:
+            return True
+
+    def iterkeys(self):
+        """D.iterkeys() -> an iterator over the keys of D"""
+        return iter(self)
+
+    def itervalues(self):
+        """D.itervalues() -> an iterator over the values of D"""
+        for key in self:
+            yield self[key]
+
+    def iteritems(self):
+        """D.iteritems() -> an iterator over the (key, value) items of D"""
+        for key in self:
+            yield (key, self[key])
+
+    def keys(self):
+        """D.keys() -> list of D's keys"""
+        return list(self)
+
+    def items(self):
+        """D.items() -> list of D's (key, value) pairs, as 2-tuples"""
+        return list(self.iteritems())
+
+    def values(self):
+        """D.values() -> list of D's values"""
+        return list(self.itervalues())
+
+    # Mappings are not hashable by default, but subclasses can change this
+    __hash__ = None
+
+    #TODO: implement __richcmp__
+
+
+cdef VariantHeaderMetadata makeVariantHeaderMetadata(VariantHeader header, int32_t type):
+    if not header:
+        raise ValueError('invalid VariantHeader')
+
+    cdef VariantHeaderMetadata meta = VariantHeaderMetadata.__new__(VariantHeaderMetadata)
+    meta.header = header
+    meta.type = type
+
+    return meta
+
+
+cdef class VariantContig(object):
+    """contig metadata from a :class:`VariantHeader`"""
+    def __init__(self, *args, **kwargs):
+        raise TypeError('this class cannot be instantiated from Python')
+
+    @property
+    def name(self):
+        """contig name"""
+        cdef bcf_hdr_t *hdr = self.header.ptr
+        return bcf_str_cache_get_charptr(hdr.id[BCF_DT_CTG][self.id].key)
+
+    @property
+    def id(self):
+        """contig internal id number"""
+        return self.id
+
+    @property
+    def length(self):
+        """contig length or None if not available"""
+        cdef bcf_hdr_t *hdr = self.header.ptr
+        cdef uint32_t length = hdr.id[BCF_DT_CTG][self.id].val.info[0]
+        return length if length else None
+
+    @property
+    def header_record(self):
+        """:class:`VariantHeaderRecord` associated with this :class:`VariantContig` object"""
+        cdef bcf_hdr_t *hdr = self.header.ptr
+        cdef bcf_hrec_t *hrec = hdr.id[BCF_DT_CTG][self.id].val.hrec[0]
+        return makeVariantHeaderRecord(self.header, hrec)
+
+    def remove_header(self):
+        cdef bcf_hdr_t *hdr = self.header.ptr
+        cdef const char *key = hdr.id[BCF_DT_CTG][self.id].key
+        bcf_hdr_remove(hdr, BCF_HL_CTG, key)
+
+
+cdef VariantContig makeVariantContig(VariantHeader header, int id):
+    if not header:
+        raise ValueError('invalid VariantHeader')
+
+    if id < 0 or id >= header.ptr.n[BCF_DT_CTG]:
+        raise ValueError('invalid contig id')
+
+    cdef VariantContig contig = VariantContig.__new__(VariantContig)
+    contig.header = header
+    contig.id = id
+
+    return contig
+
+
+cdef class VariantHeaderContigs(object):
+    """mapping from contig name or index to :class:`VariantContig` object."""
+    def __init__(self, *args, **kwargs):
+        raise TypeError('this class cannot be instantiated from Python')
+
+    def __len__(self):
+        cdef bcf_hdr_t *hdr = self.header.ptr
+        assert kh_size(<vdict_t *>hdr.dict[BCF_DT_CTG]) == hdr.n[BCF_DT_CTG]
+        return hdr.n[BCF_DT_CTG]
+
+    def __bool__(self):
+        cdef bcf_hdr_t *hdr = self.header.ptr
+        assert kh_size(<vdict_t *>hdr.dict[BCF_DT_CTG]) == hdr.n[BCF_DT_CTG]
+        return hdr.n[BCF_DT_CTG] != 0
+
+    def __getitem__(self, key):
+        cdef bcf_hdr_t *hdr = self.header.ptr
+        cdef int index
+
+        if isinstance(key, int):
+            index = key
+            if index < 0 or index >= hdr.n[BCF_DT_CTG]:
+                raise IndexError('invalid contig index')
+            return makeVariantContig(self.header, index)
+
+        cdef vdict_t *d = <vdict_t *>hdr.dict[BCF_DT_CTG]
+        cdef bytes bkey = force_bytes(key)
+        cdef khiter_t k = kh_get_vdict(d, bkey)
+
+        if k == kh_end(d):
+            raise KeyError('invalid contig: {}'.format(key))
+
+        cdef int id = kh_val_vdict(d, k).id
+
+        return makeVariantContig(self.header, id)
+
+    def remove_header(self, key):
+        cdef bcf_hdr_t *hdr = self.header.ptr
+        cdef int index
+        cdef const char *ckey
+        cdef vdict_t *d
+        cdef khiter_t k
+
+        if isinstance(key, int):
+            index = key
+            if index < 0 or index >= hdr.n[BCF_DT_CTG]:
+                raise IndexError('invalid contig index')
+            ckey = hdr.id[BCF_DT_CTG][self.id].key
+        else:
+            d = <vdict_t *>hdr.dict[BCF_DT_CTG]
+            key = force_bytes(key)
+            if kh_get_vdict(d, key) == kh_end(d):
+                raise KeyError('invalid contig: {}'.format(key))
+            ckey = key
+
+        bcf_hdr_remove(hdr, BCF_HL_CTG, ckey)
+
+    def clear_header(self):
+        cdef bcf_hdr_t *hdr = self.header.ptr
+        bcf_hdr_remove(hdr, BCF_HL_CTG, NULL)
+        #bcf_hdr_sync(hdr)
+
+    def __iter__(self):
+        cdef bcf_hdr_t *hdr = self.header.ptr
+        cdef vdict_t *d = <vdict_t *>hdr.dict[BCF_DT_CTG]
+        cdef uint32_t n = kh_size(d)
+
+        assert n == hdr.n[BCF_DT_CTG]
+
+        for i in range(n):
+            yield bcf_str_cache_get_charptr(bcf_hdr_id2name(hdr, i))
+
+    def get(self, key, default=None):
+        """D.get(k[,d]) -> D[k] if k in D, else d.  d defaults to None."""
+        try:
+            return self[key]
+        except KeyError:
+            return default
+
+    def __contains__(self, key):
+        try:
+            self[key]
+        except KeyError:
+            return False
+        else:
+            return True
+
+    def iterkeys(self):
+        """D.iterkeys() -> an iterator over the keys of D"""
+        return iter(self)
+
+    def itervalues(self):
+        """D.itervalues() -> an iterator over the values of D"""
+        for key in self:
+            yield self[key]
+
+    def iteritems(self):
+        """D.iteritems() -> an iterator over the (key, value) items of D"""
+        for key in self:
+            yield (key, self[key])
+
+    def keys(self):
+        """D.keys() -> list of D's keys"""
+        return list(self)
+
+    def items(self):
+        """D.items() -> list of D's (key, value) pairs, as 2-tuples"""
+        return list(self.iteritems())
+
+    def values(self):
+        """D.values() -> list of D's values"""
+        return list(self.itervalues())
+
+    # Mappings are not hashable by default, but subclasses can change this
+    __hash__ = None
+
+    #TODO: implement __richcmp__
+
+    def add(self, id, length=None, **kwargs):
+        """Add a new contig record"""
+        if id in self:
+            raise ValueError('Header already exists for contig {}'.format(id))
+
+        items = [('ID', unquoted_str(id))]
+        if length is not None:
+            items.append(("length", unquoted_str(length)))
+        items += kwargs.items()
+        self.header.add_meta('contig', items=items)
+
+
+cdef VariantHeaderContigs makeVariantHeaderContigs(VariantHeader header):
+    if not header:
+        raise ValueError('invalid VariantHeader')
+
+    cdef VariantHeaderContigs contigs = VariantHeaderContigs.__new__(VariantHeaderContigs)
+    contigs.header = header
+
+    return contigs
+
+
+cdef class VariantHeaderSamples(object):
+    """sequence of sample names from a :class:`VariantHeader` object"""
+    def __init__(self, *args, **kwargs):
+        raise TypeError('this class cannot be instantiated from Python')
+
+    def __len__(self):
+        return bcf_hdr_nsamples(self.header.ptr)
+
+    def __bool__(self):
+        return bcf_hdr_nsamples(self.header.ptr) != 0
+
+    def __getitem__(self, index):
+        cdef bcf_hdr_t *hdr = self.header.ptr
+        cdef int32_t n = bcf_hdr_nsamples(hdr)
+        cdef int32_t i = index
+
+        if i < 0 or i >= n:
+            raise IndexError('invalid sample index')
+
+        return charptr_to_str(hdr.samples[i])
+
+    def __iter__(self):
+        cdef bcf_hdr_t *hdr = self.header.ptr
+        cdef int32_t i, n = bcf_hdr_nsamples(hdr)
+
+        for i in range(n):
+            yield charptr_to_str(hdr.samples[i])
+
+    def __contains__(self, key):
+        cdef bcf_hdr_t *hdr = self.header.ptr
+        cdef vdict_t *d = <vdict_t *>hdr.dict[BCF_DT_SAMPLE]
+        cdef bytes bkey = force_bytes(key)
+        cdef khiter_t k = kh_get_vdict(d, bkey)
+
+        return k != kh_end(d)
+
+    # Mappings are not hashable by default, but subclasses can change this
+    __hash__ = None
+
+    #TODO: implement __richcmp__
+
+    def add(self, name):
+        """Add a new sample"""
+        self.header.add_sample(name)
+
+
+cdef VariantHeaderSamples makeVariantHeaderSamples(VariantHeader header):
+    if not header:
+        raise ValueError('invalid VariantHeader')
+
+    cdef VariantHeaderSamples samples = VariantHeaderSamples.__new__(VariantHeaderSamples)
+    samples.header = header
+
+    return samples
+
+
+cdef class VariantHeader(object):
+    """header information for a :class:`VariantFile` object"""
+    #FIXME: Add structured proxy
+    #FIXME: Add generic proxy
+    #FIXME: Add mutable methods
+
+    # See makeVariantHeader for C constructor
+    def __cinit__(self):
+        self.ptr = NULL
+
+    # Python constructor
+    def __init__(self):
+        self.ptr = bcf_hdr_init(b'w')
+        if not self.ptr:
+            raise ValueError('cannot create VariantHeader')
+
+    def __dealloc__(self):
+        if self.ptr:
+            bcf_hdr_destroy(self.ptr)
+            self.ptr = NULL
+
+    def __bool__(self):
+        return self.ptr != NULL
+
+    def copy(self):
+        return makeVariantHeader(bcf_hdr_dup(self.ptr))
+
+    def merge(self, VariantHeader header):
+        if header is None:
+            raise ValueError('header must not be None')
+        bcf_hdr_merge(self.ptr, header.ptr)
+
+    @property
+    def version(self):
+        """VCF version"""
+        return force_str(bcf_hdr_get_version(self.ptr))
+
+    @property
+    def samples(self):
+        """samples (:class:`VariantHeaderSamples`)"""
+        return makeVariantHeaderSamples(self)
+
+    @property
+    def records(self):
+        """header records (:class:`VariantHeaderRecords`)"""
+        return makeVariantHeaderRecords(self)
+
+    @property
+    def contigs(self):
+        """contig information (:class:`VariantHeaderContigs`)"""
+        return makeVariantHeaderContigs(self)
+
+    @property
+    def filters(self):
+        """filter metadata (:class:`VariantHeaderMetadata`)"""
+        return makeVariantHeaderMetadata(self, BCF_HL_FLT)
+
+    @property
+    def info(self):
+        """info metadata (:class:`VariantHeaderMetadata`)"""
+        return makeVariantHeaderMetadata(self, BCF_HL_INFO)
+
+    @property
+    def formats(self):
+        """format metadata (:class:`VariantHeaderMetadata`)"""
+        return makeVariantHeaderMetadata(self, BCF_HL_FMT)
+
+    @property
+    def alts(self):
+        """alt metadata (:class:`dict` ID->record).
+
+        The data returned just a snapshot of alt records, is created
+        every time the property is requested, and modifications will
+        not be reflected in the header metadata and vice versa.
+
+        i.e. it is just a dict that reflects the state of alt records
+        at the time it is created.
+        """
+        return {record['ID']:record for record in self.records
+                if record.key.upper() == 'ALT' }
+
+    # only safe to do when opening an htsfile
+    cdef _subset_samples(self, include_samples):
+        keep_samples    = set(self.samples)
+        include_samples = set(include_samples)
+        missing_samples = include_samples - keep_samples
+        keep_samples   &= include_samples
+
+        if missing_samples:
+            # FIXME: add specialized exception with payload
+            raise ValueError(
+                'missing {:d} requested samples'.format(
+                    len(missing_samples)))
+
+        keep_samples = force_bytes(','.join(keep_samples))
+        cdef char *keep = <char *>keep_samples if keep_samples else NULL
+        cdef ret = bcf_hdr_set_samples(self.ptr, keep, 0)
+
+        if ret != 0:
+            raise ValueError(
+                'bcf_hdr_set_samples failed: ret = {}'.format(ret))
+
+    def __str__(self):
+        cdef int hlen
+        cdef kstring_t line
+        line.l = line.m = 0
+        line.s = NULL
+
+        if bcf_hdr_format(self.ptr, 0, &line) < 0:
+            if line.m:
+                free(line.s)
+            raise ValueError('bcf_hdr_format failed')
+
+        ret = charptr_to_str_w_len(line.s, line.l)
+
+        if line.m:
+            free(line.s)
+        return ret
+
+    def new_record(self, contig=None, start=0, stop=0, alleles=None,
+                         id=None, qual=None, filter=None, info=None, samples=None,
+                         **kwargs):
+        """Create a new empty VariantRecord.
+
+        Arguments are currently experimental.  Use with caution and expect
+        changes in upcoming releases.
+
+        """
+        rec = makeVariantRecord(self, bcf_init())
+
+        if not rec:
+            raise MemoryError('unable to allocate BCF record')
+
+        rec.ptr.n_sample = bcf_hdr_nsamples(self.ptr)
+
+        if contig is not None:
+            rec.contig  = contig
+        if alleles is not None:
+            rec.alleles = alleles
+
+        rec.start = start
+        rec.stop  = stop
+        rec.id    = id
+        rec.qual  = qual
+
+        if filter is not None:
+            if isinstance(filter, (list, tuple, VariantRecordFilter)):
+                for f in filter:
+                    rec.filter.add(f)
+            else:
+                rec.filter.add(filter)
+
+        if info:
+            rec.info.update(info)
+
+        if kwargs:
+            if 'GT' in kwargs:
+                rec.samples[0]['GT'] = kwargs.pop('GT')
+            rec.samples[0].update(kwargs)
+
+        if samples:
+            for i, sample in enumerate(samples):
+                if 'GT' in sample:
+                    rec.samples[i]['GT'] = sample.pop('GT')
+                rec.samples[i].update(sample)
+
+        return rec
+
+    def add_record(self, VariantHeaderRecord record):
+        """Add an existing :class:`VariantHeaderRecord` to this header"""
+        if record is None:
+            raise ValueError('record must not be None')
+
+        cdef bcf_hrec_t *hrec = bcf_hrec_dup(record.ptr)
+
+        bcf_hdr_add_hrec(self.ptr, hrec)
+
+        self._hdr_sync()
+
+    def add_line(self, line):
+        """Add a metadata line to this header"""
+        bline = force_bytes(line)
+        if bcf_hdr_append(self.ptr, bline) < 0:
+            raise ValueError('invalid header line')
+
+        self._hdr_sync()
+
+
+    def add_meta(self, key, value=None, items=None):
+        """Add metadata to this header"""
+        if not ((value is not None) ^ (items is not None)):
+            raise ValueError('either value or items must be specified')
+
+        cdef bcf_hrec_t *hrec = <bcf_hrec_t*>calloc(1, sizeof(bcf_hrec_t))
+        cdef int quoted
+
+        try:
+            key = force_bytes(key)
+            hrec.key = strdup(key)
+
+            if value is not None:
+                hrec.value = strdup(force_bytes(value))
+            else:
+                for key, value in items:
+                    quoted = not isinstance(value, unquoted_str) and key not in ("ID", "Number", "Type")
+
+                    key = force_bytes(key)
+                    bcf_hrec_add_key(hrec, key, <int>len(key))
+
+                    value = force_bytes(str(value))
+                    bcf_hrec_set_val(hrec, hrec.nkeys-1, value, <int>len(value), quoted)
+        except:
+            bcf_hrec_destroy(hrec)
+            raise
+
+        bcf_hdr_add_hrec(self.ptr, hrec)
+
+        self._hdr_sync()
+
+    cdef _add_sample(self, name):
+        bname = force_bytes(name)
+        if bcf_hdr_add_sample(self.ptr, bname) < 0:
+            raise ValueError('Duplicated sample name: {}'.format(name))
+
+    cdef _hdr_sync(self):
+        cdef bcf_hdr_t *hdr = self.ptr
+        if hdr.dirty:
+            if bcf_hdr_sync(hdr) < 0:
+                raise MemoryError('unable to reallocate VariantHeader')
+
+    def add_sample(self, name):
+        """Add a new sample to this header"""
+        self._add_sample(name)
+        self._hdr_sync()
+
+    def add_samples(self, *args):
+        """Add several new samples to this header.
+        This function takes multiple arguments, each of which may
+        be either a sample name or an iterable returning sample names
+        (e.g., a list of sample names).
+        """
+        for arg in args:
+            if isinstance(arg, str):
+                self._add_sample(arg)
+            else:
+                for name in arg:
+                    self._add_sample(name)
+        self._hdr_sync()
+
+
+cdef VariantHeader makeVariantHeader(bcf_hdr_t *hdr):
+    if not hdr:
+        raise ValueError('cannot create VariantHeader')
+
+    cdef VariantHeader header = VariantHeader.__new__(VariantHeader)
+    header.ptr = hdr
+
+    return header
+
+
+cdef inline int bcf_header_get_info_id(bcf_hdr_t *hdr, key) except? -2:
+    cdef vdict_t *d
+    cdef khiter_t k
+    cdef int info_id
+
+    if isinstance(key, str):
+        key = force_bytes(key)
+
+    d = <vdict_t *>hdr.dict[BCF_DT_ID]
+    k = kh_get_vdict(d, key)
+
+    if k == kh_end(d) or kh_val_vdict(d, k).info[BCF_HL_INFO] & 0xF == 0xF:
+        return -1
+
+    return kh_val_vdict(d, k).id
+
+
+########################################################################
+########################################################################
+## Variant Record objects
+########################################################################
+
+cdef class VariantRecordFilter(object):
+    """Filters set on a :class:`VariantRecord` object, presented as a mapping from
+       filter index or name to :class:`VariantMetadata` object"""
+    def __init__(self, *args, **kwargs):
+        raise TypeError('this class cannot be instantiated from Python')
+
+    def __len__(self):
+        return self.record.ptr.d.n_flt
+
+    def __bool__(self):
+        return self.record.ptr.d.n_flt != 0
+
+    def __getitem__(self, key):
+        cdef bcf_hdr_t *hdr = self.record.header.ptr
+        cdef bcf1_t *r = self.record.ptr
+        cdef int index, id
+        cdef int n = r.d.n_flt
+
+        if isinstance(key, int):
+            index = key
+
+            if index < 0 or index >= n:
+                raise IndexError('invalid filter index')
+
+            id = r.d.flt[index]
+        else:
+            if key == '.':
+                key = 'PASS'
+
+            bkey = force_bytes(key)
+            id = bcf_hdr_id2int(hdr, BCF_DT_ID, bkey)
+
+            if not check_header_id(hdr, BCF_HL_FLT, id) or not bcf_has_filter(hdr, r, bkey):
+                raise KeyError('Invalid filter: {}'.format(key))
+
+        return makeVariantMetadata(self.record.header, BCF_HL_FLT, id)
+
+    def add(self, key):
+        """Add a new filter"""
+        cdef bcf_hdr_t *hdr = self.record.header.ptr
+        cdef bcf1_t *r = self.record.ptr
+        cdef int id
+
+        if key == '.':
+            key = 'PASS'
+
+        cdef bytes bkey = force_bytes(key)
+        id = bcf_hdr_id2int(hdr, BCF_DT_ID, bkey)
+
+        if not check_header_id(hdr, BCF_HL_FLT, id):
+            raise KeyError('Invalid filter: {}'.format(key))
+
+        bcf_add_filter(hdr, r, id)
+
+    def __delitem__(self, key):
+        cdef bcf_hdr_t *hdr = self.record.header.ptr
+        cdef bcf1_t *r = self.record.ptr
+        cdef int index, id
+        cdef int n = r.d.n_flt
+
+        if isinstance(key, int):
+            index = key
+
+            if index < 0 or index >= n:
+                raise IndexError('invalid filter index')
+
+            id = r.d.flt[index]
+        else:
+            if key == '.':
+                key = 'PASS'
+
+            bkey = force_bytes(key)
+            id = bcf_hdr_id2int(hdr, BCF_DT_ID, bkey)
+
+            if not check_header_id(hdr, BCF_HL_FLT, id) or not bcf_has_filter(hdr, r, bkey):
+                raise KeyError('Invalid filter: {}'.format(key))
+
+        bcf_remove_filter(hdr, r, id, 0)
+
+    def clear(self):
+        """Clear all filters"""
+        cdef bcf1_t *r = self.record.ptr
+        r.d.shared_dirty |= BCF1_DIRTY_FLT
+        r.d.n_flt = 0
+
+    def __iter__(self):
+        cdef bcf_hdr_t *hdr = self.record.header.ptr
+        cdef bcf1_t *r = self.record.ptr
+        cdef int i
+
+        for i in range(r.d.n_flt):
+            yield bcf_str_cache_get_charptr(bcf_hdr_int2id(hdr, BCF_DT_ID, r.d.flt[i]))
+
+    def get(self, key, default=None):
+        """D.get(k[,d]) -> D[k] if k in D, else d.  d defaults to None."""
+        try:
+            return self[key]
+        except KeyError:
+            return default
+
+    def __contains__(self, key):
+        cdef bcf_hdr_t *hdr = self.record.header.ptr
+        cdef bcf1_t *r = self.record.ptr
+        cdef bytes bkey = force_bytes(key)
+        return bcf_has_filter(hdr, r, bkey) == 1
+
+    def iterkeys(self):
+        """D.iterkeys() -> an iterator over the keys of D"""
+        return iter(self)
+
+    def itervalues(self):
+        """D.itervalues() -> an iterator over the values of D"""
+        for key in self:
+            yield self[key]
+
+    def iteritems(self):
+        """D.iteritems() -> an iterator over the (key, value) items of D"""
+        for key in self:
+            yield (key, self[key])
+
+    def keys(self):
+        """D.keys() -> list of D's keys"""
+        return list(self)
+
+    def items(self):
+        """D.items() -> list of D's (key, value) pairs, as 2-tuples"""
+        return list(self.iteritems())
+
+    def values(self):
+        """D.values() -> list of D's values"""
+        return list(self.itervalues())
+
+    def __richcmp__(VariantRecordFilter self not None, VariantRecordFilter other not None, int op):
+        if op != 2 and op != 3:
+            return NotImplemented
+
+        cdef bcf1_t *s = self.record.ptr
+        cdef bcf1_t *o = other.record.ptr
+
+        cdef bint cmp = (s.d.n_flt == o.d.n_flt and list(self) == list(other))
+
+        if op == 3:
+            cmp = not cmp
+
+        return cmp
+
+    # Mappings are not hashable by default, but subclasses can change this
+    __hash__ = None
+
+    #TODO: implement __richcmp__
+
+
+cdef VariantRecordFilter makeVariantRecordFilter(VariantRecord record):
+    if not record:
+        raise ValueError('invalid VariantRecord')
+
+    cdef VariantRecordFilter filter = VariantRecordFilter.__new__(VariantRecordFilter)
+    filter.record = record
+
+    return filter
+
+
+cdef class VariantRecordFormat(object):
+    """Format data present for each sample in a :class:`VariantRecord` object,
+       presented as mapping from format name to :class:`VariantMetadata` object."""
+    def __init__(self, *args, **kwargs):
+        raise TypeError('this class cannot be instantiated from Python')
+
+    def __len__(self):
+        cdef bcf_hdr_t *hdr = self.record.header.ptr
+        cdef bcf1_t *r = self.record.ptr
+        cdef int i, n = 0
+
+        for i in range(r.n_fmt):
+            if r.d.fmt[i].p:
+                n += 1
+        return n
+
+    def __bool__(self):
+        cdef bcf_hdr_t *hdr = self.record.header.ptr
+        cdef bcf1_t *r = self.record.ptr
+        cdef int i
+
+        for i in range(r.n_fmt):
+            if r.d.fmt[i].p:
+                return True
+        return False
+
+    def __getitem__(self, key):
+        cdef bcf_hdr_t *hdr = self.record.header.ptr
+        cdef bcf1_t *r = self.record.ptr
+
+        cdef bytes bkey = force_bytes(key)
+        cdef bcf_fmt_t *fmt = bcf_get_fmt(hdr, r, bkey)
+
+        if not fmt or not fmt.p:
+            raise KeyError('unknown format: {}'.format(key))
+
+        return makeVariantMetadata(self.record.header, BCF_HL_FMT, fmt.id)
+
+    def __delitem__(self, key):
+        cdef bcf_hdr_t *hdr = self.record.header.ptr
+        cdef bcf1_t *r = self.record.ptr
+
+        cdef bytes bkey = force_bytes(key)
+        cdef bcf_fmt_t *fmt = bcf_get_fmt(hdr, r, bkey)
+
+        if not fmt or not fmt.p:
+            raise KeyError('unknown format: {}'.format(key))
+
+        if bcf_update_format(hdr, r, bkey, fmt.p, 0, fmt.type) < 0:
+            raise ValueError('Unable to delete FORMAT')
+
+    def clear(self):
+        """Clear all formats for all samples within the associated
+           :class:`VariantRecord` instance"""
+        cdef bcf_hdr_t *hdr = self.record.header.ptr
+        cdef bcf1_t *r = self.record.ptr
+        cdef bcf_fmt_t *fmt
+        cdef const char *key
+        cdef int i
+
+        for i in reversed(range(r.n_fmt)):
+            fmt = &r.d.fmt[i]
+            if fmt.p:
+                key = bcf_hdr_int2id(hdr, BCF_DT_ID, fmt.id)
+                if bcf_update_format(hdr, r, key, fmt.p, 0, fmt.type) < 0:
+                    raise ValueError('Unable to delete FORMAT')
+
+    def __iter__(self):
+        cdef bcf_hdr_t *hdr = self.record.header.ptr
+        cdef bcf1_t *r = self.record.ptr
+        cdef bcf_fmt_t *fmt
+        cdef int i
+
+        for i in range(r.n_fmt):
+            fmt = &r.d.fmt[i]
+            if fmt.p:
+                yield bcf_str_cache_get_charptr(bcf_hdr_int2id(hdr, BCF_DT_ID, fmt.id))
+
+    def get(self, key, default=None):
+        """D.get(k[,d]) -> D[k] if k in D, else d.  d defaults to None."""
+        try:
+            return self[key]
+        except KeyError:
+            return default
+
+    def __contains__(self, key):
+        cdef bcf_hdr_t *hdr = self.record.header.ptr
+        cdef bcf1_t *r = self.record.ptr
+        cdef bytes bkey = force_bytes(key)
+        cdef bcf_fmt_t *fmt = bcf_get_fmt(hdr, r, bkey)
+        return fmt != NULL and fmt.p != NULL
+
+    def iterkeys(self):
+        """D.iterkeys() -> an iterator over the keys of D"""
+        return iter(self)
+
+    def itervalues(self):
+        """D.itervalues() -> an iterator over the values of D"""
+        for key in self:
+            yield self[key]
+
+    def iteritems(self):
+        """D.iteritems() -> an iterator over the (key, value) items of D"""
+        for key in self:
+            yield (key, self[key])
+
+    def keys(self):
+        """D.keys() -> list of D's keys"""
+        return list(self)
+
+    def items(self):
+        """D.items() -> list of D's (key, value) pairs, as 2-tuples"""
+        return list(self.iteritems())
+
+    def values(self):
+        """D.values() -> list of D's values"""
+        return list(self.itervalues())
+
+    # Mappings are not hashable by default, but subclasses can change this
+    __hash__ = None
+
+    #TODO: implement __richcmp__
+
+
+cdef VariantRecordFormat makeVariantRecordFormat(VariantRecord record):
+    if not record:
+        raise ValueError('invalid VariantRecord')
+
+    cdef VariantRecordFormat format = VariantRecordFormat.__new__(VariantRecordFormat)
+    format.record = record
+
+    return format
+
+
+#TODO: Add a getmeta method to return the corresponding VariantMetadata?
+cdef class VariantRecordInfo(object):
+    """Info data stored in a :class:`VariantRecord` object, presented as a
+       mapping from info metadata name to value."""
+
+    def __init__(self, *args, **kwargs):
+        raise TypeError('this class cannot be instantiated from Python')
+
+    def __len__(self):
+        cdef bcf_hdr_t *hdr = self.record.header.ptr
+        cdef bcf1_t *r = self.record.ptr
+        cdef bcf_info_t *info
+        cdef const char *key
+        cdef int i, count = 0
+
+        if bcf_unpack(r, BCF_UN_INFO) < 0:
+            raise ValueError('Error unpacking VariantRecord')
+
+        for i in range(r.n_info):
+            info = &r.d.info[i]
+            key = bcf_hdr_int2id(hdr, BCF_DT_ID, info.key)
+            if info != NULL and info.vptr != NULL and strcmp(key, b'END') != 0:
+                count += 1
+
+        return count
+
+    def __bool__(self):
+        cdef bcf_hdr_t *hdr = self.record.header.ptr
+        cdef bcf1_t *r = self.record.ptr
+        cdef bcf_info_t *info
+        cdef const char *key
+        cdef int i
+
+        if bcf_unpack(r, BCF_UN_INFO) < 0:
+            raise ValueError('Error unpacking VariantRecord')
+
+        for i in range(r.n_info):
+            info = &r.d.info[i]
+            key = bcf_hdr_int2id(hdr, BCF_DT_ID, info.key)
+            if info != NULL and info.vptr != NULL and strcmp(key, b'END') != 0:
+                return True
+
+        return False
+
+    def __getitem__(self, key):
+        cdef bcf_hdr_t *hdr = self.record.header.ptr
+        cdef bcf1_t *r = self.record.ptr
+
+        if bcf_unpack(r, BCF_UN_INFO) < 0:
+            raise ValueError('Error unpacking VariantRecord')
+
+        cdef bytes bkey = force_bytes(key)
+
+        if strcmp(bkey, b'END') == 0:
+            raise KeyError('END is a reserved attribute; access is via record.stop')
+
+        cdef bcf_info_t *info = bcf_get_info(hdr, r, bkey)
+
+        # Cannot stop here if info == NULL, since flags must return False
+        cdef int info_id = bcf_header_get_info_id(hdr, bkey) if not info else info.key
+
+        if info_id < 0:
+            raise KeyError('Unknown INFO field: {}'.format(key))
+
+        if not check_header_id(hdr, BCF_HL_INFO, info_id):
+            raise ValueError('Invalid header')
+
+        # Handle type=Flag values
+        if bcf_hdr_id2type(hdr, BCF_HL_INFO, info_id) == BCF_HT_FLAG:
+            return info != NULL and info.vptr != NULL
+
+        if not info or not info.vptr:
+            raise KeyError('Invalid INFO field: {}'.format(key))
+
+        return bcf_info_get_value(self.record, info)
+
+    def __setitem__(self, key, value):
+        cdef bytes bkey = force_bytes(key)
+
+        if strcmp(bkey, b'END') == 0:
+            raise KeyError('END is a reserved attribute; access is via record.stop')
+
+        if bcf_unpack(self.record.ptr, BCF_UN_INFO) < 0:
+            raise ValueError('Error unpacking VariantRecord')
+
+        bcf_info_set_value(self.record, key, value)
+
+    def __delitem__(self, key):
+        cdef bcf_hdr_t *hdr = self.record.header.ptr
+        cdef bcf1_t *r = self.record.ptr
+
+        cdef bytes bkey = force_bytes(key)
+        if strcmp(bkey, b'END') == 0:
+            raise KeyError('END is a reserved attribute; access is via record.stop')
+
+        if bcf_unpack(r, BCF_UN_INFO) < 0:
+            raise ValueError('Error unpacking VariantRecord')
+
+        cdef bcf_info_t *info = bcf_get_info(hdr, r, bkey)
+
+        # Cannot stop here if info == NULL, since flags must return False
+        cdef int info_id = bcf_header_get_info_id(hdr, bkey) if not info else info.key
+
+        if info_id < 0:
+            raise KeyError('Unknown INFO field: {}'.format(key))
+
+        if not check_header_id(hdr, BCF_HL_INFO, info_id):
+            raise ValueError('Invalid header')
+
+        # Handle flags
+        if bcf_hdr_id2type(hdr, BCF_HL_INFO, info_id) == BCF_HT_FLAG and (not info or not info.vptr):
+            return
+
+        if not info or not info.vptr:
+            raise KeyError('Unknown INFO field: {}'.format(key))
+
+        if bcf_update_info(hdr, r, bkey, NULL, 0, info.type) < 0:
+            raise ValueError('Unable to delete INFO')
+
+    def clear(self):
+        """Clear all info data"""
+        cdef bcf_hdr_t *hdr = self.record.header.ptr
+        cdef bcf1_t *r = self.record.ptr
+        cdef bcf_info_t *info
+        cdef const char *key
+        cdef int i
+
+        if bcf_unpack(r, BCF_UN_INFO) < 0:
+            raise ValueError('Error unpacking VariantRecord')
+
+        for i in range(r.n_info):
+            info = &r.d.info[i]
+            if info and info.vptr:
+                key = bcf_hdr_int2id(hdr, BCF_DT_ID, info.key)
+                if strcmp(key, b'END') == 0:
+                    continue
+                if bcf_update_info(hdr, r, key, NULL, 0, info.type) < 0:
+                    raise ValueError('Unable to delete INFO')
+
+    def __iter__(self):
+        cdef bcf_hdr_t *hdr = self.record.header.ptr
+        cdef bcf1_t *r = self.record.ptr
+        cdef bcf_info_t *info
+        cdef const char *key
+        cdef int i
+
+        if bcf_unpack(r, BCF_UN_INFO) < 0:
+            raise ValueError('Error unpacking VariantRecord')
+
+        for i in range(r.n_info):
+            info = &r.d.info[i]
+            if info and info.vptr:
+                key = bcf_hdr_int2id(hdr, BCF_DT_ID, info.key)
+                if strcmp(key, b'END') != 0:
+                    yield bcf_str_cache_get_charptr(key)
+
+    def get(self, key, default=None):
+        """D.get(k[,d]) -> D[k] if k in D, else d.  d defaults to None."""
+        cdef bcf_hdr_t *hdr = self.record.header.ptr
+        cdef bcf1_t *r = self.record.ptr
+
+        if bcf_unpack(r, BCF_UN_INFO) < 0:
+            raise ValueError('Error unpacking VariantRecord')
+
+        cdef bytes bkey = force_bytes(key)
+
+        if strcmp(bkey, b'END') == 0:
+            return default
+
+        cdef bcf_info_t *info = bcf_get_info(hdr, r, bkey)
+
+        # Cannot stop here if info == NULL, since flags must return False
+        cdef int info_id = bcf_header_get_info_id(hdr, bkey) if not info else info.key
+
+        if not check_header_id(hdr, BCF_HL_INFO, info_id):
+            raise ValueError('Invalid header')
+
+        # Handle flags
+        if bcf_hdr_id2type(hdr, BCF_HL_INFO, info_id) == BCF_HT_FLAG:
+            return info != NULL and info.vptr != NULL
+
+        if not info or not info.vptr:
+            return default
+
+        return bcf_info_get_value(self.record, info)
+
+    def __contains__(self, key):
+        cdef bcf_hdr_t *hdr = self.record.header.ptr
+        cdef bcf1_t *r = self.record.ptr
+
+        if bcf_unpack(r, BCF_UN_INFO) < 0:
+            raise ValueError('Error unpacking VariantRecord')
+
+        cdef bytes bkey = force_bytes(key)
+
+        if strcmp(bkey, b'END') == 0:
+            return False
+
+        cdef bcf_info_t *info = bcf_get_info(hdr, r, bkey)
+
+        return info != NULL and info.vptr != NULL
+
+    def iterkeys(self):
+        """D.iterkeys() -> an iterator over the keys of D"""
+        return iter(self)
+
+    def itervalues(self):
+        """D.itervalues() -> an iterator over the values of D"""
+        cdef bcf_hdr_t *hdr = self.record.header.ptr
+        cdef bcf1_t *r = self.record.ptr
+        cdef bcf_info_t *info
+        cdef const char *key
+        cdef int i
+
+        if bcf_unpack(r, BCF_UN_INFO) < 0:
+            raise ValueError('Error unpacking VariantRecord')
+
+        for i in range(r.n_info):
+            info = &r.d.info[i]
+            if info and info.vptr:
+                key = bcf_hdr_int2id(hdr, BCF_DT_ID, info.key)
+                if strcmp(key, b'END') != 0:
+                    yield bcf_info_get_value(self.record, info)
+
+    def iteritems(self):
+        """D.iteritems() -> an iterator over the (key, value) items of D"""
+        cdef bcf_hdr_t *hdr = self.record.header.ptr
+        cdef bcf1_t *r = self.record.ptr
+        cdef bcf_info_t *info
+        cdef const char *key
+        cdef int i
+
+        if bcf_unpack(r, BCF_UN_INFO) < 0:
+            raise ValueError('Error unpacking VariantRecord')
+
+        for i in range(r.n_info):
+            info = &r.d.info[i]
+            if info and info.vptr:
+                key = bcf_hdr_int2id(hdr, BCF_DT_ID, info.key)
+                if strcmp(key, b'END') != 0:
+                    value = bcf_info_get_value(self.record, info)
+                    yield bcf_str_cache_get_charptr(key), value
+
+    def keys(self):
+        """D.keys() -> list of D's keys"""
+        return list(self)
+
+    def items(self):
+        """D.items() -> list of D's (key, value) pairs, as 2-tuples"""
+        return list(self.iteritems())
+
+    def values(self):
+        """D.values() -> list of D's values"""
+        return list(self.itervalues())
+
+    def update(self, items=None, **kwargs):
+        """D.update([E, ]**F) -> None.
+
+        Update D from dict/iterable E and F.
+        """
+        for k, v in items.items():
+            if k != 'END':
+                self[k] = v
+
+        if kwargs:
+            kwargs.pop('END', None)
+            for k, v in kwargs.items():
+                self[k] = v
+
+    def pop(self, key, default=_nothing):
+        cdef bcf_hdr_t *hdr = self.record.header.ptr
+        cdef bcf1_t *r = self.record.ptr
+
+        if bcf_unpack(r, BCF_UN_INFO) < 0:
+            raise ValueError('Error unpacking VariantRecord')
+
+        cdef bytes bkey = force_bytes(key)
+        cdef bcf_info_t *info = bcf_get_info(hdr, r, bkey)
+
+        # Cannot stop here if info == NULL, since flags must return False
+        cdef int info_id = bcf_header_get_info_id(hdr, bkey) if not info else info.key
+
+        if info_id < 0:
+            if default is _nothing:
+                raise KeyError('Unknown INFO field: {}'.format(key))
+            return default
+
+        if not check_header_id(hdr, BCF_HL_INFO, info_id):
+            raise ValueError('Invalid header')
+
+        # Handle flags
+        if bcf_hdr_id2type(hdr, BCF_HL_INFO, info_id) == BCF_HT_FLAG and (not info or not info.vptr):
+            return
+
+        if not info or not info.vptr:
+            if default is _nothing:
+                raise KeyError('Unknown INFO field: {}'.format(key))
+            return default
+
+        value = bcf_info_get_value(self.record, info)
+
+        if bcf_update_info(hdr, r, bkey, NULL, 0, info.type) < 0:
+            raise ValueError('Unable to delete INFO')
+
+        return value
+
+    def __richcmp__(VariantRecordInfo self not None, VariantRecordInfo other not None, int op):
+        if op != 2 and op != 3:
+            return NotImplemented
+
+        cdef bcf1_t *s = self.record.ptr
+        cdef bcf1_t *o = other.record.ptr
+
+        # Cannot use n_info as shortcut logic, since null values may remain
+        cdef bint cmp = dict(self) == dict(other)
+
+        if op == 3:
+            cmp = not cmp
+
+        return cmp
+
+    # Mappings are not hashable by default, but subclasses can change this
+    __hash__ = None
+
+
+cdef VariantRecordInfo makeVariantRecordInfo(VariantRecord record):
+    if not record:
+        raise ValueError('invalid VariantRecord')
+
+    cdef VariantRecordInfo info = VariantRecordInfo.__new__(VariantRecordInfo)
+    info.record = record
+
+    return info
+
+
+cdef class VariantRecordSamples(object):
+    """mapping from sample index or name to :class:`VariantRecordSample` object."""
+    def __init__(self, *args, **kwargs):
+        raise TypeError('this class cannot be instantiated from Python')
+
+    def __len__(self):
+        return self.record.ptr.n_sample  # bcf_hdr_nsamples(self.record.header.ptr)
+
+    def __bool__(self):
+        return self.record.ptr.n_sample != 0  # bcf_hdr_nsamples(self.record.header.ptr) != 0
+
+    def __getitem__(self, key):
+        cdef bcf_hdr_t *hdr = self.record.header.ptr
+        cdef bcf1_t *r = self.record.ptr
+        cdef int n = self.record.ptr.n_sample
+        cdef int sample_index
+        cdef vdict_t *d
+        cdef khiter_t k
+
+        if isinstance(key, int):
+            sample_index = key
+        else:
+            bkey = force_bytes(key)
+            sample_index = bcf_hdr_id2int(hdr, BCF_DT_SAMPLE, bkey)
+            if sample_index < 0:
+                raise KeyError('invalid sample name: {}'.format(key))
+
+        if sample_index < 0 or sample_index >= n:
+            raise IndexError('invalid sample index')
+
+        return makeVariantRecordSample(self.record, sample_index)
+
+    def __iter__(self):
+        cdef bcf_hdr_t *hdr = self.record.header.ptr
+        cdef bcf1_t *r = self.record.ptr
+        cdef int32_t i, n = self.record.ptr.n_sample
+
+        for i in range(n):
+            yield charptr_to_str(hdr.samples[i])
+
+    def get(self, key, default=None):
+        """D.get(k[,d]) -> D[k] if k in D, else d.  d defaults to None."""
+        try:
+            return self[key]
+        except KeyError:
+            return default
+
+    def __contains__(self, key):
+        cdef bcf_hdr_t *hdr = self.record.header.ptr
+        cdef bcf1_t *r = self.record.ptr
+        cdef int n = self.record.ptr.n_sample
+        cdef int sample_index
+        cdef vdict_t *d
+        cdef khiter_t k
+
+        if isinstance(key, int):
+            sample_index = key
+        else:
+            bkey = force_bytes(key)
+            sample_index = bcf_hdr_id2int(hdr, BCF_DT_SAMPLE, bkey)
+            if sample_index < 0:
+                raise KeyError('invalid sample name: {}'.format(key))
+
+        return 0 <= sample_index < n
+
+    def iterkeys(self):
+        """D.iterkeys() -> an iterator over the keys of D"""
+        return iter(self)
+
+    def itervalues(self):
+        """D.itervalues() -> an iterator over the values of D"""
+        cdef bcf_hdr_t *hdr = self.record.header.ptr
+        cdef bcf1_t *r = self.record.ptr
+        cdef int32_t i, n = self.record.ptr.n_sample
+
+        for i in range(n):
+            yield makeVariantRecordSample(self.record, i)
+
+    def iteritems(self):
+        """D.iteritems() -> an iterator over the (key, value) items of D"""
+        cdef bcf_hdr_t *hdr = self.record.header.ptr
+        cdef bcf1_t *r = self.record.ptr
+        cdef int32_t i, n = self.record.ptr.n_sample
+
+        for i in range(n):
+            yield (charptr_to_str(hdr.samples[i]), makeVariantRecordSample(self.record, i))
+
+    def keys(self):
+        """D.keys() -> list of D's keys"""
+        return list(self)
+
+    def items(self):
+        """D.items() -> list of D's (key, value) pairs, as 2-tuples"""
+        return list(self.iteritems())
+
+    def values(self):
+        """D.values() -> list of D's values"""
+        return list(self.itervalues())
+
+    def update(self, items=None, **kwargs):
+        """D.update([E, ]**F) -> None.
+
+        Update D from dict/iterable E and F.
+        """
+        for k, v in items.items():
+            self[k] = v
+
+        if kwargs:
+            for k, v in kwargs.items():
+                self[k] = v
+
+    def pop(self, key, default=_nothing):
+        try:
+            value = self[key]
+            del self[key]
+            return value
+        except KeyError:
+            if default is not _nothing:
+                return default
+            raise
+
+    def __richcmp__(VariantRecordSamples self not None, VariantRecordSamples other not None, int op):
+        if op != 2 and op != 3:
+            return NotImplemented
+
+        cdef bcf1_t *s = self.record.ptr
+        cdef bcf1_t *o = other.record.ptr
+
+        cdef bint cmp = (s.n_sample == o.n_sample and self.values() == other.values())
+
+        if op == 3:
+            cmp = not cmp
+
+        return cmp
+
+    # Mappings are not hashable by default, but subclasses can change this
+    __hash__ = None
+
+
+cdef VariantRecordSamples makeVariantRecordSamples(VariantRecord record):
+    if not record:
+        raise ValueError('invalid VariantRecord')
+
+    cdef VariantRecordSamples samples = VariantRecordSamples.__new__(
+        VariantRecordSamples)
+    samples.record = record
+
+    return samples
+
+
+cdef class VariantRecord(object):
+    """Variant record"""
+    def __init__(self, *args, **kwargs):
+        raise TypeError('this class cannot be instantiated from Python')
+
+    def __dealloc__(self):
+        if self.ptr:
+            bcf_destroy1(self.ptr)
+            self.ptr = NULL
+
+    def copy(self):
+        """return a copy of this VariantRecord object"""
+        return makeVariantRecord(self.header, bcf_dup(self.ptr))
+
+    def translate(self, VariantHeader dst_header):
+        if dst_header is None:
+            raise ValueError('dst_header must not be None')
+
+        cdef bcf_hdr_t *src_hdr = self.header.ptr
+        cdef bcf_hdr_t *dst_hdr = dst_header.ptr
+
+        if src_hdr != dst_hdr:
+            if self.ptr.n_sample != bcf_hdr_nsamples(dst_hdr):
+                msg = 'Cannot translate record.  Number of samples does not match header ({} vs {})'
+                raise ValueError(msg.format(self.ptr.n_sample, bcf_hdr_nsamples(dst_hdr)))
+
+            bcf_translate(dst_hdr, src_hdr, self.ptr)
+            self.header = dst_header
+
+    @property
+    def rid(self):
+        """internal reference id number"""
+        return self.ptr.rid
+
+    @rid.setter
+    def rid(self, value):
+        cdef bcf_hdr_t *hdr = self.header.ptr
+        cdef int r = value
+        if r < 0 or r >= hdr.n[BCF_DT_CTG] or not hdr.id[BCF_DT_CTG][r].val:
+            raise ValueError('invalid reference id')
+        self.ptr.rid = r
+
+    @property
+    def chrom(self):
+        """chromosome/contig name"""
+        cdef bcf_hdr_t *hdr = self.header.ptr
+        cdef int rid = self.ptr.rid
+        if rid < 0 or rid >= hdr.n[BCF_DT_CTG]:
+            raise ValueError('Invalid header')
+        return bcf_str_cache_get_charptr(bcf_hdr_id2name(hdr, rid))
+
+    @chrom.setter
+    def chrom(self, value):
+        cdef vdict_t *d = <vdict_t*>self.header.ptr.dict[BCF_DT_CTG]
+        bchrom = force_bytes(value)
+        cdef khint_t k = kh_get_vdict(d, bchrom)
+        if k == kh_end(d):
+            raise ValueError('Invalid chromosome/contig')
+        self.ptr.rid = kh_val_vdict(d, k).id
+
+    @property
+    def contig(self):
+        """chromosome/contig name"""
+        cdef bcf_hdr_t *hdr = self.header.ptr
+        cdef int rid = self.ptr.rid
+        if rid < 0 or rid >= hdr.n[BCF_DT_CTG]:
+            raise ValueError('Invalid header')
+        return bcf_str_cache_get_charptr(bcf_hdr_id2name(hdr, rid))
+
+    @contig.setter
+    def contig(self, value):
+        cdef vdict_t *d = <vdict_t*>self.header.ptr.dict[BCF_DT_CTG]
+        bchrom = force_bytes(value)
+        cdef khint_t k = kh_get_vdict(d, bchrom)
+        if k == kh_end(d):
+            raise ValueError('Invalid chromosome/contig')
+        self.ptr.rid = kh_val_vdict(d, k).id
+
+    @property
+    def pos(self):
+        """record start position on chrom/contig (1-based inclusive)"""
+        return self.ptr.pos + 1
+
+    @pos.setter
+    def pos(self, value):
+        cdef int p = value
+        if p < 1:
+            raise ValueError('Position must be positive')
+        self.ptr.pos = p - 1
+        bcf_sync_end(self)
+
+    @property
+    def start(self):
+        """record start position on chrom/contig (0-based inclusive)"""
+        return self.ptr.pos
+
+    @start.setter
+    def start(self, value):
+        cdef int s = value
+        if s < 0:
+            raise ValueError('Start coordinate must be non-negative')
+        self.ptr.pos = s
+        bcf_sync_end(self)
+
+    @property
+    def stop(self):
+        """record stop position on chrom/contig (0-based exclusive)"""
+        return self.ptr.pos + self.ptr.rlen
+
+    @stop.setter
+    def stop(self, value):
+        cdef int s = value
+        if s < 0:
+            raise ValueError('Stop coordinate must be non-negative')
+        self.ptr.rlen = s - self.ptr.pos
+        bcf_sync_end(self)
+
+    @property
+    def rlen(self):
+        """record length on chrom/contig (aka rec.stop - rec.start)"""
+        return self.ptr.rlen
+
+    @rlen.setter
+    def rlen(self, value):
+        cdef int r = value
+        self.ptr.rlen = r
+        bcf_sync_end(self)
+
+    @property
+    def qual(self):
+        """phred scaled quality score or None if not available"""
+        return self.ptr.qual if not bcf_float_is_missing(self.ptr.qual) else None
+
+    @qual.setter
+    def qual(self, value):
+        if value is not None:
+            self.ptr.qual = value
+        else:
+            bcf_float_set(&self.ptr.qual, bcf_float_missing)
+
+
+#   @property
+#   def n_allele(self):
+#       return self.ptr.n_allele
+
+#   @property
+#   def n_sample(self):
+#       return self.ptr.n_sample
+
+    @property
+    def id(self):
+        """record identifier or None if not available"""
+        cdef bcf1_t *r = self.ptr
+        if bcf_unpack(r, BCF_UN_STR) < 0:
+            raise ValueError('Error unpacking VariantRecord')
+        # causes a memory leak https://github.com/pysam-developers/pysam/issues/773
+        # return bcf_str_cache_get_charptr(r.d.id) if r.d.id != b'.' else None
+        if (r.d.m_id == 0):
+            raise ValueError('Error extracting ID')
+        return charptr_to_str(r.d.id) if r.d.id != b'.' else None
+
+    @id.setter
+    def id(self, value):
+        cdef bcf1_t *r = self.ptr
+        if bcf_unpack(r, BCF_UN_STR) < 0:
+            raise ValueError('Error unpacking VariantRecord')
+        cdef char *idstr = NULL
+        if value is not None:
+            bid = force_bytes(value)
+            idstr = bid
+        if bcf_update_id(self.header.ptr, self.ptr, idstr) < 0:
+            raise ValueError('Error updating id')
+
+    @property
+    def ref(self):
+        """reference allele"""
+        cdef bcf1_t *r = self.ptr
+        if bcf_unpack(r, BCF_UN_STR) < 0:
+            raise ValueError('Error unpacking VariantRecord')
+        return charptr_to_str(r.d.allele[0]) if r.d.allele else None
+
+    @ref.setter
+    def ref(self, value):
+        cdef bcf1_t *r = self.ptr
+        if bcf_unpack(r, BCF_UN_STR) < 0:
+            raise ValueError('Error unpacking VariantRecord')
+        #FIXME: Set alleles directly -- this is stupid
+        if not value:
+            raise ValueError('ref allele must not be null')
+        value = force_bytes(value)
+        if r.d.allele and r.n_allele:
+            alleles = [r.d.allele[i] for i in range(r.n_allele)]
+            alleles[0] = value
+        else:
+            alleles = [value, '<NON_REF>']
+        self.alleles = alleles
+        bcf_sync_end(self)
+
+    @property
+    def alleles(self):
+        """tuple of reference allele followed by alt alleles"""
+        cdef bcf1_t *r = self.ptr
+        if bcf_unpack(r, BCF_UN_STR) < 0:
+            raise ValueError('Error unpacking VariantRecord')
+        if not r.d.allele:
+            return None
+        cdef tuple res = PyTuple_New(r.n_allele)
+        for i in range(r.n_allele):
+            a = charptr_to_str(r.d.allele[i])
+            PyTuple_SET_ITEM(res, i, a)
+            Py_INCREF(a)
+        return res
+
+    @alleles.setter
+    def alleles(self, values):
+        cdef bcf1_t *r = self.ptr
+
+        # Cache rlen of symbolic alleles before call to bcf_update_alleles_str
+        cdef int rlen = r.rlen
+
+        if bcf_unpack(r, BCF_UN_STR) < 0:
+            raise ValueError('Error unpacking VariantRecord')
+
+        values = [force_bytes(v) for v in values]
+
+        if len(values) < 2:
+            raise ValueError('must set at least 2 alleles')
+
+        if b'' in values:
+            raise ValueError('cannot set null allele')
+
+        value = b','.join(values)
+
+        if bcf_update_alleles_str(self.header.ptr, r, value) < 0:
+            raise ValueError('Error updating alleles')
+
+        # Reset rlen if alternate allele isn't symbolic, otherwise used cached
+        if has_symbolic_allele(self):
+            self.ptr.rlen = rlen
+        else:
+            self.ptr.rlen = len(values[0])
+        r.d.var_type = -1
+        bcf_sync_end(self)
+
+    @property
+    def alts(self):
+        """tuple of alt alleles"""
+        cdef bcf1_t *r = self.ptr
+        if bcf_unpack(r, BCF_UN_STR) < 0:
+            raise ValueError('Error unpacking VariantRecord')
+        if r.n_allele < 2 or not r.d.allele:
+            return None
+        cdef tuple res = PyTuple_New(r.n_allele - 1)
+        for i in range(1, r.n_allele):
+            a = charptr_to_str(r.d.allele[i])
+            PyTuple_SET_ITEM(res, i - 1, a)
+            Py_INCREF(a)
+        return res
+
+    @alts.setter
+    def alts(self, value):
+        #FIXME: Set alleles directly -- this is stupid
+        cdef bcf1_t *r = self.ptr
+        if bcf_unpack(r, BCF_UN_STR) < 0:
+            raise ValueError('Error unpacking VariantRecord')
+        value = [force_bytes(v) for v in value]
+        if b'' in value:
+            raise ValueError('cannot set null alt allele')
+        ref  = [r.d.allele[0] if r.d.allele and r.n_allele else b'.']
+        self.alleles = ref + value
+        r.d.var_type = -1
+
+    @property
+    def filter(self):
+        """filter information (see :class:`VariantRecordFilter`)"""
+        if bcf_unpack(self.ptr, BCF_UN_FLT) < 0:
+            raise ValueError('Error unpacking VariantRecord')
+        return makeVariantRecordFilter(self)
+
+    @property
+    def info(self):
+        """info data (see :class:`VariantRecordInfo`)"""
+        if bcf_unpack(self.ptr, BCF_UN_INFO) < 0:
+            raise ValueError('Error unpacking VariantRecord')
+        return makeVariantRecordInfo(self)
+
+    @property
+    def format(self):
+        """sample format metadata (see :class:`VariantRecordFormat`)"""
+        if bcf_unpack(self.ptr, BCF_UN_FMT) < 0:
+            raise ValueError('Error unpacking VariantRecord')
+        return makeVariantRecordFormat(self)
+
+    @property
+    def samples(self):
+        """sample data (see :class:`VariantRecordSamples`)"""
+        if bcf_unpack(self.ptr, BCF_UN_ALL) < 0:
+            raise ValueError('Error unpacking VariantRecord')
+        return makeVariantRecordSamples(self)
+
+    property alleles_variant_types:
+        def __get__(self):
+            cdef bcf1_t *r = self.ptr
+            cdef tuple result = PyTuple_New(r.n_allele)
+
+            for i in range(r.n_allele):
+                tp = bcf_get_variant_type(r, i)
+
+                if tp == VCF_REF:
+                    v_type = "REF"
+                elif tp == VCF_SNP:
+                    v_type = "SNP"
+                elif tp == VCF_MNP:
+                    v_type = "MNP"
+                elif tp == VCF_INDEL:
+                    v_type = "INDEL"
+                elif tp == VCF_BND:
+                    v_type = "BND"
+                elif tp == VCF_OVERLAP:
+                    v_type = "OVERLAP"
+                else:
+                    v_type = "OTHER"
+
+                PyTuple_SET_ITEM(result, i, v_type)
+                Py_INCREF(v_type)
+
+            return result
+
+    def __richcmp__(VariantRecord self not None, VariantRecord other not None, int op):
+        if op != 2 and op != 3:
+            return NotImplemented
+
+        cdef bcf1_t *s = self.ptr
+        cdef bcf1_t *o = other.ptr
+
+        cdef bint cmp = self is other or (
+                             s.pos        == o.pos
+                        and  s.rlen       == o.rlen
+                        and ((bcf_float_is_missing(s.qual) and bcf_float_is_missing(o.qual))
+                          or s.qual       == o.qual)
+                        and  s.n_sample   == o.n_sample
+                        and  s.n_allele   == o.n_allele
+                        and  self.contig  == other.contig
+                        and  self.alleles == other.alleles
+                        and  self.id      == other.id
+                        and  self.info    == other.info
+                        and  self.filter  == other.filter
+                        and  self.samples == other.samples)
+
+        if op == 3:
+            cmp = not cmp
+
+        return cmp
+
+    def __str__(self):
+        cdef kstring_t line
+        cdef char c
+
+        line.l = line.m = 0
+        line.s = NULL
+
+        if vcf_format(self.header.ptr, self.ptr, &line) < 0:
+            if line.m:
+                free(line.s)
+            raise ValueError('vcf_format failed')
+
+        # Strip CR/LF?
+        #while line.l:
+        #    c = line.s[line.l - 1]
+        #    if c != b'\n' and c != b'\r':
+        #        break
+        #    line.l -= 1
+
+        ret = charptr_to_str_w_len(line.s, line.l)
+
+        if line.m:
+            free(line.s)
+
+        return ret
+
+
+cdef VariantRecord makeVariantRecord(VariantHeader header, bcf1_t *r):
+    if not header:
+        raise ValueError('invalid VariantHeader')
+
+    if not r:
+        raise ValueError('cannot create VariantRecord')
+
+    if r.errcode:
+        msg = []
+        #if r.errcode & BCF_ERR_CTG_UNDEF:
+        #    msg.append('undefined contig')
+        #if r.errcode & BCF_ERR_TAG_UNDEF:
+        #    msg.append('undefined tag')
+        if r.errcode & BCF_ERR_NCOLS:
+            msg.append('invalid number of columns')
+        if r.errcode & BCF_ERR_LIMITS:
+            msg.append('limits violated')
+        if r.errcode & BCF_ERR_CHAR:
+            msg.append('invalid character found')
+        if r.errcode & BCF_ERR_CTG_INVALID:
+            msg.append('invalid contig')
+        if r.errcode & BCF_ERR_TAG_INVALID:
+            msg.append('invalid tag')
+
+        if msg:
+            msg = ', '.join(msg)
+            raise ValueError('Error(s) reading record: {}'.format(msg))
+
+    cdef VariantRecord record = VariantRecord.__new__(VariantRecord)
+    record.header = header
+    record.ptr = r
+
+    return record
+
+
+########################################################################
+########################################################################
+## Variant Sampletype object
+########################################################################
+
+
+cdef class VariantRecordSample(object):
+    """Data for a single sample from a :class:`VariantRecord` object.
+       Provides data accessors for genotypes and a mapping interface
+       from format name to values.
+    """
+    def __init__(self, *args, **kwargs):
+        raise TypeError('this class cannot be instantiated from Python')
+
+    @property
+    def name(self):
+        """sample name"""
+        cdef bcf_hdr_t *hdr = self.record.header.ptr
+        cdef bcf1_t *r = self.record.ptr
+        cdef int32_t n = r.n_sample
+
+        if self.index < 0 or self.index >= n:
+            raise ValueError('invalid sample index')
+
+        return charptr_to_str(hdr.samples[self.index])
+
+    @property
+    def allele_indices(self):
+        """allele indices for called genotype, if present.  Otherwise None"""
+        return bcf_format_get_allele_indices(self)
+
+    @allele_indices.setter
+    def allele_indices(self, value):
+        self['GT'] = value
+
+    @allele_indices.deleter
+    def allele_indices(self):
+        self['GT'] = ()
+
+    @property
+    def alleles(self):
+        """alleles for called genotype, if present.  Otherwise None"""
+        return bcf_format_get_alleles(self)
+
+    @alleles.setter
+    def alleles(self, value: tuple):
+        # Sets the genotype, supply a tuple of alleles to set.
+        # The supplied alleles need to be defined in the correspoding pysam.libcbcf.VariantRecord
+        # The genotype is reset when an empty tuple, None or (None,) is supplied
+
+        if value==(None,) or value==tuple() or value is None:
+            self['GT'] = ()
+            return
+
+        if any((type(x) == int for x in value)):
+            raise ValueError('Use .allele_indices to set integer allele indices')
+
+        # determine and set allele indices:    
+        try:
+            self['GT'] = tuple( (self.record.alleles.index(allele) for allele in value) )
+        except ValueError:
+            raise ValueError("One or more of the supplied sample alleles are not defined as alleles of the corresponding pysam.libcbcf.VariantRecord."
+                             "First set the .alleles of this record to define the alleles")
+
+    @alleles.deleter
+    def alleles(self):
+        self['GT'] = ()
+
+    @property
+    def phased(self):
+        """False if genotype is missing or any allele is unphased.  Otherwise True."""
+        return bcf_sample_get_phased(self)
+
+    @phased.setter
+    def phased(self, value):
+        bcf_sample_set_phased(self, value)
+
+    def __len__(self):
+        cdef bcf_hdr_t *hdr = self.record.header.ptr
+        cdef bcf1_t *r = self.record.ptr
+        cdef int i, n = 0
+
+        if bcf_unpack(r, BCF_UN_FMT) < 0:
+            raise ValueError('Error unpacking VariantRecord')
+
+        for i in range(r.n_fmt):
+            if r.d.fmt[i].p:
+                n += 1
+        return n
+
+    def __bool__(self):
+        cdef bcf_hdr_t *hdr = self.record.header.ptr
+        cdef bcf1_t *r = self.record.ptr
+        cdef int i
+
+        if bcf_unpack(r, BCF_UN_FMT) < 0:
+            raise ValueError('Error unpacking VariantRecord')
+
+        for i in range(r.n_fmt):
+            if r.d.fmt[i].p:
+                return True
+        return False
+
+    def __getitem__(self, key):
+        return bcf_format_get_value(self, key)
+
+    def __setitem__(self, key, value):
+        bcf_format_set_value(self, key, value)
+
+    def __delitem__(self, key):
+        bcf_format_del_value(self, key)
+
+    def clear(self):
+        """Clear all format data (including genotype) for this sample"""
+        cdef bcf_hdr_t *hdr = self.record.header.ptr
+        cdef bcf1_t *r = self.record.ptr
+        cdef bcf_fmt_t *fmt
+        cdef int i
+
+        for i in range(r.n_fmt):
+            fmt = &r.d.fmt[i]
+            if fmt.p:
+                bcf_format_del_value(self, bcf_hdr_int2id(hdr, BCF_DT_ID, fmt.id))
+
+    def __iter__(self):
+        cdef bcf_hdr_t *hdr = self.record.header.ptr
+        cdef bcf1_t *r = self.record.ptr
+        cdef bcf_fmt_t *fmt
+        cdef int i
+
+        for i in range(r.n_fmt):
+            fmt = &r.d.fmt[i]
+            if r.d.fmt[i].p:
+                yield bcf_str_cache_get_charptr(bcf_hdr_int2id(hdr, BCF_DT_ID, fmt.id))
+
+    def get(self, key, default=None):
+        """D.get(k[,d]) -> D[k] if k in D, else d.  d defaults to None."""
+        try:
+            return self[key]
+        except KeyError:
+            return default
+
+    def __contains__(self, key):
+        cdef bcf_hdr_t *hdr = self.record.header.ptr
+        cdef bcf1_t *r = self.record.ptr
+        cdef bytes bkey = force_bytes(key)
+        cdef bcf_fmt_t *fmt = bcf_get_fmt(hdr, r, bkey)
+        return fmt != NULL and fmt.p != NULL
+
+    def iterkeys(self):
+        """D.iterkeys() -> an iterator over the keys of D"""
+        return iter(self)
+
+    def itervalues(self):
+        """D.itervalues() -> an iterator over the values of D"""
+        for key in self:
+            yield self[key]
+
+    def iteritems(self):
+        """D.iteritems() -> an iterator over the (key, value) items of D"""
+        for key in self:
+            yield (key, self[key])
+
+    def keys(self):
+        """D.keys() -> list of D's keys"""
+        return list(self)
+
+    def items(self):
+        """D.items() -> list of D's (key, value) pairs, as 2-tuples"""
+        return list(self.iteritems())
+
+    def values(self):
+        """D.values() -> list of D's values"""
+        return list(self.itervalues())
+
+    def update(self, items=None, **kwargs):
+        """D.update([E, ]**F) -> None.
+
+        Update D from dict/iterable E and F.
+        """
+        for k, v in items.items():
+            self[k] = v
+
+        if kwargs:
+            for k, v in kwargs.items():
+                self[k] = v
+
+    def pop(self, key, default=_nothing):
+        try:
+            value = self[key]
+            del self[key]
+            return value
+        except KeyError:
+            if default is not _nothing:
+                return default
+            raise
+
+    def __richcmp__(VariantRecordSample self not None, VariantRecordSample other not None, int op):
+        if op != 2 and op != 3:
+            return NotImplemented
+
+        cdef bint cmp = dict(self) == dict(other)
+
+        if op == 3:
+            cmp = not cmp
+
+        return cmp
+
+    # Mappings are not hashable by default, but subclasses can change this
+    __hash__ = None
+
+
+cdef VariantRecordSample makeVariantRecordSample(VariantRecord record, int32_t sample_index):
+    if not record or sample_index < 0:
+        raise ValueError('cannot create VariantRecordSample')
+
+    cdef VariantRecordSample sample = VariantRecordSample.__new__(VariantRecordSample)
+    sample.record = record
+    sample.index = sample_index
+
+    return sample
+
+
+########################################################################
+########################################################################
+## Index objects
+########################################################################
+
+
+cdef class BaseIndex(object):
+    def __init__(self):
+        self.refs = ()
+        self.remap = {}
+
+    def __len__(self):
+        return len(self.refs)
+
+    def __bool__(self):
+        return len(self.refs) != 0
+
+    def __getitem__(self, key):
+        if isinstance(key, int):
+            return self.refs[key]
+        else:
+            return self.refmap[key]
+
+    def __iter__(self):
+        return iter(self.refs)
+
+    def get(self, key, default=None):
+        """D.get(k[,d]) -> D[k] if k in D, else d.  d defaults to None."""
+        try:
+            return self[key]
+        except KeyError:
+            return default
+
+    def __contains__(self, key):
+        try:
+            self[key]
+        except KeyError:
+            return False
+        else:
+            return True
+
+    def iterkeys(self):
+        """D.iterkeys() -> an iterator over the keys of D"""
+        return iter(self)
+
+    def itervalues(self):
+        """D.itervalues() -> an iterator over the values of D"""
+        for key in self:
+            yield self[key]
+
+    def iteritems(self):
+        """D.iteritems() -> an iterator over the (key, value) items of D"""
+        for key in self:
+            yield (key, self[key])
+
+    def keys(self):
+        """D.keys() -> list of D's keys"""
+        return list(self)
+
+    def items(self):
+        """D.items() -> list of D's (key, value) pairs, as 2-tuples"""
+        return list(self.iteritems())
+
+    def values(self):
+        """D.values() -> list of D's values"""
+        return list(self.itervalues())
+
+    def update(self, items=None, **kwargs):
+        """D.update([E, ]**F) -> None.
+
+        Update D from dict/iterable E and F.
+        """
+        for k, v in items.items():
+            self[k] = v
+
+        if kwargs:
+            for k, v in kwargs.items():
+                self[k] = v
+
+    def pop(self, key, default=_nothing):
+        try:
+            value = self[key]
+            del self[key]
+            return value
+        except KeyError:
+            if default is not _nothing:
+                return default
+            raise
+
+    # Mappings are not hashable by default, but subclasses can change this
+    __hash__ = None
+
+    #TODO: implement __richcmp__
+
+
+cdef class BCFIndex(object):
+    """CSI index data structure for BCF files"""
+    def __init__(self):
+        self.refs = ()
+        self.refmap = {}
+
+        if not self.ptr:
+            raise ValueError('Invalid index object')
+
+        cdef int n
+        cdef const char **refs = bcf_index_seqnames(self.ptr, self.header.ptr, &n)
+
+        self.refs = char_array_to_tuple(refs, n, free_after=1) if refs else ()
+        self.refmap = { r:i for i,r in enumerate(self.refs) }
+
+    def __dealloc__(self):
+        if self.ptr:
+            hts_idx_destroy(self.ptr)
+            self.ptr = NULL
+
+    def fetch(self, bcf, contig, start, stop, reopen):
+        return BCFIterator(bcf, contig, start, stop, reopen)
+
+
+cdef BCFIndex makeBCFIndex(VariantHeader header, hts_idx_t *idx):
+    if not idx:
+        return None
+
+    if not header:
+        raise ValueError('invalid VariantHeader')
+
+    cdef BCFIndex index = BCFIndex.__new__(BCFIndex)
+    index.header = header
+    index.ptr = idx
+    index.__init__()
+
+    return index
+
+
+cdef class TabixIndex(BaseIndex):
+    """Tabix index data structure for VCF files"""
+    def __init__(self):
+        self.refs = ()
+        self.refmap = {}
+
+        if not self.ptr:
+            raise ValueError('Invalid index object')
+
+        cdef int n
+        cdef const char **refs = tbx_seqnames(self.ptr, &n)
+
+        self.refs = char_array_to_tuple(refs, n, free_after=1) if refs else ()
+        self.refmap = { r:i for i,r in enumerate(self.refs) }
+
+    def __dealloc__(self):
+        if self.ptr:
+            tbx_destroy(self.ptr)
+            self.ptr = NULL
+
+    def fetch(self, bcf, contig, start, stop, reopen):
+        return TabixIterator(bcf, contig, start, stop, reopen)
+
+
+cdef TabixIndex makeTabixIndex(tbx_t *idx):
+    if not idx:
+        return None
+
+    cdef TabixIndex index = TabixIndex.__new__(TabixIndex)
+    index.ptr = idx
+    index.__init__()
+
+    return index
+
+
+########################################################################
+########################################################################
+## Iterators
+########################################################################
+
+
+cdef class BaseIterator(object):
+    pass
+
+
+# Internal function to clean up after iteration stop or failure.
+# This would be a nested function if it weren't a cdef function.
+cdef void _stop_BCFIterator(BCFIterator self, bcf1_t *record):
+    bcf_destroy1(record)
+
+    # destroy iter so future calls to __next__ raise StopIteration
+    bcf_itr_destroy(self.iter)
+    self.iter = NULL
+
+
+cdef class BCFIterator(BaseIterator):
+    def __init__(self, VariantFile bcf, contig=None, start=None, stop=None, reopen=True):
+        if bcf is None:
+            raise ValueError('bcf must not be None')
+
+        if contig is None:
+            raise ValueError('contig must be specified')
+
+        if not isinstance(bcf.index, BCFIndex):
+            raise ValueError('bcf index required')
+
+        cdef BCFIndex index = bcf.index
+
+        self.bcf = bcf
+        self.index = index
+
+        cdef int rid, cstart, cstop
+
+        try:
+            rid = index.refmap[contig]
+        except KeyError:
+            # A query for a non-existent contig yields an empty iterator, does not raise an error
+            self.iter = NULL
+            return
+
+        if reopen:
+            self.bcf = self.bcf.copy()
+
+        cstart = start if start is not None else 0
+        cstop  = stop  if stop  is not None else MAX_POS
+
+        with nogil:
+            self.iter = bcf_itr_queryi(index.ptr, rid, cstart, cstop)
+
+        if not self.iter:
+            if errno:
+                raise IOError(errno, strerror(errno))
+            else:
+                raise IOError('unable to fetch {}:{}-{}'.format(contig, start+1, stop))
+
+    def __dealloc__(self):
+        if self.iter:
+            bcf_itr_destroy(self.iter)
+            self.iter = NULL
+
+    def __iter__(self):
+        return self
+
+    def __next__(self):
+        if not self.iter:
+            raise StopIteration
+
+        cdef bcf1_t *record = bcf_init1()
+
+        if not record:
+            raise MemoryError('unable to allocate BCF record')
+
+        record.pos = -1
+        if self.bcf.drop_samples:
+            record.max_unpack = BCF_UN_SHR
+
+        cdef int ret
+
+        with nogil:
+            ret = bcf_itr_next(self.bcf.htsfile, self.iter, record)
+
+        if ret < 0:
+            _stop_BCFIterator(self, record)
+            if ret == -1:
+                raise StopIteration
+            elif ret == -2:
+                raise IOError('truncated file')
+            elif errno:
+                raise IOError(errno, strerror(errno))
+            else:
+                raise IOError('unable to fetch next record')
+
+        ret = bcf_subset_format(self.bcf.header.ptr, record)
+
+        if ret < 0:
+            _stop_BCFIterator(self, record)
+            raise ValueError('error in bcf_subset_format')
+
+        return makeVariantRecord(self.bcf.header, record)
+
+
+cdef class TabixIterator(BaseIterator):
+    def __cinit__(self, *args, **kwargs):
+        self.line_buffer.l = 0
+        self.line_buffer.m = 0
+        self.line_buffer.s = NULL
+
+    def __init__(self, VariantFile bcf, contig=None, start=None, stop=None, reopen=True):
+        if bcf is None:
+            raise ValueError('bcf must not be None')
+
+        if not isinstance(bcf.index, TabixIndex):
+            raise ValueError('tabix index required')
+
+        cdef TabixIndex index = bcf.index
+
+        self.bcf = bcf
+        self.index = index
+
+        cdef int rid, cstart, cstop
+
+        try:
+            rid = index.refmap[contig]
+        except KeyError:
+            # A query for a non-existent contig yields an empty iterator, does not raise an error
+            self.iter = NULL
+            return
+
+        if reopen:
+            self.bcf = self.bcf.copy()
+
+        cstart = start if start is not None else 0
+        cstop  = stop  if stop  is not None else MAX_POS
+
+        self.iter = tbx_itr_queryi(index.ptr, rid, start, stop)
+
+        if not self.iter:
+            if errno:
+                raise IOError(errno, strerror(errno))
+            else:
+                raise IOError('unable to fetch {}:{}-{}'.format(contig, start+1, stop))
+
+    def __dealloc__(self):
+        if self.iter:
+            tbx_itr_destroy(self.iter)
+            self.iter = NULL
+
+        if self.line_buffer.m:
+            free(self.line_buffer.s)
+
+        self.line_buffer.l = 0
+        self.line_buffer.m = 0
+        self.line_buffer.s = NULL
+
+    def __iter__(self):
+        return self
+
+    def __next__(self):
+        if not self.iter:
+            raise StopIteration
+
+        cdef int ret
+
+        with nogil:
+            ret = tbx_itr_next(self.bcf.htsfile, self.index.ptr, self.iter, &self.line_buffer)
+
+        if ret < 0:
+            tbx_itr_destroy(self.iter)
+            self.iter = NULL
+            if ret == -1:
+                raise StopIteration
+            elif ret == -2:
+                raise IOError('truncated file')
+            elif errno:
+                raise IOError(errno, strerror(errno))
+            else:
+                raise IOError('unable to fetch next record')
+
+        cdef bcf1_t *record = bcf_init1()
+
+        if not record:
+            raise MemoryError('unable to allocate BCF record')
+
+        record.pos = -1
+        if self.bcf.drop_samples:
+            record.max_unpack = BCF_UN_SHR
+
+        ret = vcf_parse1(&self.line_buffer, self.bcf.header.ptr, record)
+
+        # FIXME: stop iteration on parse failure?
+        if ret < 0:
+            bcf_destroy1(record)
+            raise ValueError('error in vcf_parse')
+
+        return makeVariantRecord(self.bcf.header, record)
+
+
+########################################################################
+########################################################################
+## Variant File
+########################################################################
+
+
+cdef class VariantFile(HTSFile):
+    """*(filename, mode=None, index_filename=None, header=None, drop_samples=False,
+    duplicate_filehandle=True, ignore_truncation=False, threads=1)*
+
+    A :term:`VCF`/:term:`BCF` formatted file. The file is automatically
+    opened.
+
+    If an index for a variant file exists (.csi or .tbi), it will be
+    opened automatically.  Without an index random access to records
+    via :meth:`fetch` is disabled.
+
+    For writing, a :class:`VariantHeader` object must be provided,
+    typically obtained from another :term:`VCF` file/:term:`BCF`
+    file.
+
+    Parameters
+    ----------
+    mode : string
+        *mode* should be ``r`` for reading or ``w`` for writing. The default is
+        text mode (:term:`VCF`).  For binary (:term:`BCF`) I/O you should append
+        ``b`` for compressed or ``u`` for uncompressed :term:`BCF` output.
+
+        If ``b`` is present, it must immediately follow ``r`` or ``w``.  Valid
+        modes are ``r``, ``w``, ``wh``, ``rb``, ``wb``, ``wbu`` and ``wb0``.
+        For instance, to open a :term:`BCF` formatted file for reading, type::
+
+            f = pysam.VariantFile('ex1.bcf','r')
+
+        If mode is not specified, we will try to auto-detect the file type.  All
+        of the following should work::
+
+            f1 = pysam.VariantFile('ex1.bcf')
+            f2 = pysam.VariantFile('ex1.vcf')
+            f3 = pysam.VariantFile('ex1.vcf.gz')
+
+    index_filename : string
+        Explicit path to an index file.
+
+    header : VariantHeader
+        :class:`VariantHeader` object required for writing.
+
+    drop_samples: bool
+        Ignore sample information when reading.
+
+    duplicate_filehandle: bool
+        By default, file handles passed either directly or through
+        File-like objects will be duplicated before passing them to
+        htslib. The duplication prevents issues where the same stream
+        will be closed by htslib and through destruction of the
+        high-level python object. Set to False to turn off
+        duplication.
+
+    ignore_truncation: bool
+        Issue a warning, instead of raising an error if the current file
+        appears to be truncated due to a missing EOF marker.  Only applies
+        to bgzipped formats. (Default=False)
+
+    threads: integer
+        Number of threads to use for compressing/decompressing VCF/BCF files.
+        Setting threads to > 1 cannot be combined with `ignore_truncation`.
+        (Default=1)
+
+    """
+    def __cinit__(self, *args, **kwargs):
+        self.htsfile = NULL
+
+    def __init__(self, *args, **kwargs):
+        self.header         = None
+        self.index          = None
+        self.filename       = None
+        self.mode           = None
+        self.threads        = 1
+        self.index_filename = None
+        self.is_stream      = False
+        self.is_remote      = False
+        self.is_reading     = False
+        self.drop_samples   = False
+        self.header_written = False
+        self.start_offset   = -1
+
+        self.open(*args, **kwargs)
+
+    def __dealloc__(self):
+        if not self.htsfile or not self.header:
+            return
+
+        # Write header if no records were written
+        if self.htsfile.is_write and not self.header_written:
+            with nogil:
+                bcf_hdr_write(self.htsfile, self.header.ptr)
+
+        cdef int ret = hts_close(self.htsfile)
+        self.htsfile = NULL
+        self.header = self.index = None
+
+        if ret < 0:
+            global errno
+            if errno == EPIPE:
+                errno = 0
+            else:
+                raise IOError(errno, force_str(strerror(errno)))
+
+    def close(self):
+        """closes the :class:`pysam.VariantFile`."""
+        if not self.htsfile:
+            return
+
+        # Write header if no records were written
+        if self.htsfile.is_write and not self.header_written:
+            with nogil:
+                bcf_hdr_write(self.htsfile, self.header.ptr)
+
+        cdef int ret = hts_close(self.htsfile)
+        self.htsfile = NULL
+        self.header = self.index = None
+
+        if ret < 0:
+            global errno
+            if errno == EPIPE:
+                errno = 0
+            else:
+                raise IOError(errno, force_str(strerror(errno)))
+
+    def __iter__(self):
+        if not self.is_open:
+            raise ValueError('I/O operation on closed file')
+
+        if self.htsfile.is_write:
+            raise ValueError('cannot iterate over Variantfile opened for writing')
+
+        self.is_reading = 1
+        return self
+
+    def __next__(self):
+        cdef int ret
+        cdef int errcode
+        cdef bcf1_t *record = bcf_init1()
+
+        if not record:
+            raise MemoryError('unable to allocate BCF record')
+
+        record.pos = -1
+        if self.drop_samples:
+            record.max_unpack = BCF_UN_SHR
+
+        with nogil:
+            ret = bcf_read1(self.htsfile, self.header.ptr, record)
+
+        if ret < 0:
+            errcode = record.errcode
+            bcf_destroy1(record)
+            if errcode:
+                raise IOError('unable to parse next record')
+            if ret == -1:
+                raise StopIteration
+            elif ret == -2:
+                raise IOError('truncated file')
+            elif errno:
+                raise IOError(errno, strerror(errno))
+            else:
+                raise IOError('unable to fetch next record')
+
+        return makeVariantRecord(self.header, record)
+
+    def copy(self):
+        if not self.is_open:
+            raise ValueError
+
+        cdef VariantFile vars = VariantFile.__new__(VariantFile)
+        cdef bcf_hdr_t *hdr
+
+        # FIXME: re-open using fd or else header and index could be invalid
+        vars.htsfile = self._open_htsfile()
+
+        if not vars.htsfile:
+            raise ValueError('Cannot re-open htsfile')
+
+        # minimize overhead by re-using header and index.  This approach is
+        # currently risky, but see above for how this can be mitigated.
+        vars.header         = self.header
+        vars.index          = self.index
+
+        vars.filename       = self.filename
+        vars.mode           = self.mode
+        vars.threads        = self.threads
+        vars.index_filename = self.index_filename
+        vars.drop_samples   = self.drop_samples
+        vars.is_stream      = self.is_stream
+        vars.is_remote      = self.is_remote
+        vars.is_reading     = self.is_reading
+        vars.start_offset   = self.start_offset
+        vars.header_written = self.header_written
+
+        if self.htsfile.is_bin:
+            vars.seek(self.tell())
+        else:
+            with nogil:
+                hdr = bcf_hdr_read(vars.htsfile)
+            makeVariantHeader(hdr)
+
+        return vars
+
+    def open(self, filename, mode='r',
+             index_filename=None,
+             VariantHeader header=None,
+             drop_samples=False,
+             duplicate_filehandle=True,
+             ignore_truncation=False,
+             threads=1):
+        """open a vcf/bcf file.
+
+        If open is called on an existing VariantFile, the current file will be
+        closed and a new file will be opened.
+        """
+        cdef bcf_hdr_t *hdr
+        cdef BGZF *bgzfp
+        cdef hts_idx_t *idx
+        cdef tbx_t *tidx
+        cdef char *cfilename
+        cdef char *cindex_filename = NULL
+        cdef char *cmode
+
+        if threads > 1 and ignore_truncation:
+            # This won't raise errors if reaching a truncated alignment,
+            # because bgzf_mt_reader in htslib does not deal with
+            # bgzf_mt_read_block returning non-zero values, contrary
+            # to bgzf_read (https://github.com/samtools/htslib/blob/1.7/bgzf.c#L888)
+            # Better to avoid this (for now) than to produce seemingly correct results.
+            raise ValueError('Cannot add extra threads when "ignore_truncation" is True')
+        self.threads = threads
+
+        # close a previously opened file
+        if self.is_open:
+            self.close()
+
+        if not mode or mode[0] not in 'rwa':
+            raise ValueError('mode must begin with r, w or a')
+
+        self.duplicate_filehandle = duplicate_filehandle
+
+        format_modes = [m for m in mode[1:] if m in 'bcguz']
+        if len(format_modes) > 1:
+            raise ValueError('mode contains conflicting format specifiers: {}'.format(''.join(format_modes)))
+
+        invalid_modes = [m for m in mode[1:] if m not in 'bcguz0123456789ex']
+        if invalid_modes:
+            raise ValueError('invalid mode options: {}'.format(''.join(invalid_modes)))
+
+        # Autodetect mode from filename
+        if mode == 'w' and isinstance(filename, str):
+            if filename.endswith('.gz'):
+                mode = 'wz'
+            elif filename.endswith('.bcf'):
+                mode = 'wb'
+
+        # for htslib, wbu seems to not work
+        if mode == 'wbu':
+            mode = 'wb0'
+
+        self.mode = mode = force_bytes(mode)
+        try:
+            filename = encode_filename(filename)
+            self.is_remote = hisremote(filename)
+            self.is_stream = filename == b'-'
+        except TypeError:
+            filename = filename
+            self.is_remote = False
+            self.is_stream = True
+
+        self.filename = filename
+
+        if index_filename is not None:
+            self.index_filename = index_filename = encode_filename(index_filename)
+        else:
+            self.index_filename = None
+
+        self.drop_samples = bool(drop_samples)
+        self.header = None
+
+        self.header_written = False
+
+        if mode.startswith(b'w'):
+            # open file for writing
+            if index_filename is not None:
+                raise ValueError('Cannot specify an index filename when writing a VCF/BCF file')
+
+            # header structure (used for writing)
+            if header:
+                self.header = header.copy()
+            else:
+                self.header = VariantHeader()
+                #raise ValueError('a VariantHeader must be specified')
+
+            # Header is not written until the first write or on close
+            self.htsfile = self._open_htsfile()
+
+            if not self.htsfile:
+                raise ValueError("could not open file `{}` (mode='{}')".format(filename, mode))
+
+        elif mode.startswith(b'r'):
+            # open file for reading
+            self.htsfile = self._open_htsfile()
+
+            if not self.htsfile:
+                if errno:
+                    raise IOError(errno, 'could not open variant file `{}`: {}'.format(filename, force_str(strerror(errno))))
+                else:
+                    raise ValueError('could not open variant file `{}`'.format(filename))
+
+            if self.htsfile.format.format not in (bcf, vcf):
+                raise ValueError('invalid file `{}` (mode=`{}`) - is it VCF/BCF format?'.format(filename, mode))
+
+            self.check_truncation(ignore_truncation)
+
+            with nogil:
+                hdr = bcf_hdr_read(self.htsfile)
+
+            try:
+                self.header = makeVariantHeader(hdr)
+            except ValueError:
+                raise ValueError('file `{}` does not have valid header (mode=`{}`) - is it VCF/BCF format?'.format(filename, mode))
+
+            if isinstance(self.filename, bytes):
+                cfilename = self.filename
+            else:
+                cfilename = NULL
+
+            # check for index and open if present
+            if self.htsfile.format.format == bcf and cfilename:
+                if index_filename is not None:
+                    cindex_filename = index_filename
+                with nogil:
+                    idx = bcf_index_load2(cfilename, cindex_filename)
+                self.index = makeBCFIndex(self.header, idx)
+
+            elif self.htsfile.format.compression == bgzf and cfilename:
+                if index_filename is not None:
+                    cindex_filename = index_filename
+                with nogil:
+                    tidx = tbx_index_load2(cfilename, cindex_filename)
+                self.index = makeTabixIndex(tidx)
+
+            if not self.is_stream:
+                self.start_offset = self.tell()
+        else:
+            raise ValueError('unknown mode {}'.format(mode))
+
+    def reset(self):
+        """reset file position to beginning of file just after the header."""
+        return self.seek(self.start_offset)
+
+    def is_valid_tid(self, tid):
+        """
+        return True if the numerical :term:`tid` is valid; False otherwise.
+
+        returns -1 if reference is not known.
+        """
+        if not self.is_open:
+            raise ValueError('I/O operation on closed file')
+
+        cdef bcf_hdr_t *hdr = self.header.ptr
+        cdef int rid = tid
+        return 0 <= rid < hdr.n[BCF_DT_CTG]
+
+    def get_tid(self, reference):
+        """
+        return the numerical :term:`tid` corresponding to
+        :term:`reference`
+
+        returns -1 if reference is not known.
+        """
+        if not self.is_open:
+            raise ValueError('I/O operation on closed file')
+
+        cdef vdict_t *d = <vdict_t*>self.header.ptr.dict[BCF_DT_CTG]
+        reference = force_bytes(reference)
+        cdef khint_t k = kh_get_vdict(d, reference)
+        return kh_val_vdict(d, k).id if k != kh_end(d) else -1
+
+    def get_reference_name(self, tid):
+        """
+        return :term:`reference` name corresponding to numerical :term:`tid`
+        """
+        if not self.is_open:
+            raise ValueError('I/O operation on closed file')
+
+        cdef bcf_hdr_t *hdr = self.header.ptr
+        cdef int rid = tid
+        if rid < 0 or rid >= hdr.n[BCF_DT_CTG]:
+            raise ValueError('Invalid tid')
+        return bcf_str_cache_get_charptr(bcf_hdr_id2name(hdr, rid))
+
+    def fetch(self, contig=None, start=None, stop=None, region=None, reopen=False, end=None, reference=None):
+        """fetch records in a :term:`region`, specified either by
+        :term:`contig`, *start*, and *end* (which are 0-based, half-open);
+        or alternatively by a samtools :term:`region` string (which is
+        1-based inclusive).
+
+        Without *contig* or *region* all mapped records will be fetched.  The
+        records will be returned ordered by contig, which will not necessarily
+        be the order within the file.
+
+        Set *reopen* to true if you will be using multiple iterators on the
+        same file at the same time.  The iterator returned will receive its
+        own copy of a filehandle to the file effectively re-opening the
+        file.  Re-opening a file incurrs some overhead, so use with care.
+
+        If only *contig* is set, all records on *contig* will be fetched.
+        If both *region* and *contig* are given, an exception is raised.
+
+        Note that a bgzipped :term:`VCF`.gz file without a tabix/CSI index
+        (.tbi/.csi) or a :term:`BCF` file without a CSI index can only be
+        read sequentially.
+        """
+        if not self.is_open:
+            raise ValueError('I/O operation on closed file')
+
+        if self.htsfile.is_write:
+            raise ValueError('cannot fetch from Variantfile opened for writing')
+
+        if contig is None and region is None:
+            self.is_reading = 1
+            bcf = self.copy() if reopen else self
+            bcf.seek(self.start_offset)
+            return iter(bcf)
+
+        if self.index is None:
+            raise ValueError('fetch requires an index')
+
+        _, tid, start, stop = self.parse_region(contig, start, stop, region,
+                                                None, end=end, reference=reference)
+
+        if contig is None:
+            contig = self.get_reference_name(tid)
+
+        self.is_reading = 1
+        return self.index.fetch(self, contig, start, stop, reopen)
+
+    def new_record(self, *args, **kwargs):
+        """Create a new empty :class:`VariantRecord`.
+
+        See :meth:`VariantHeader.new_record`
+        """
+        return self.header.new_record(*args, **kwargs)
+
+    cpdef int write(self, VariantRecord record) except -1:
+        """
+        write a single :class:`pysam.VariantRecord` to disk.
+
+        returns the number of bytes written.
+        """
+        if record is None:
+            raise ValueError('record must not be None')
+
+        if not self.is_open:
+            return ValueError('I/O operation on closed file')
+
+        if not self.htsfile.is_write:
+            raise ValueError('cannot write to a Variantfile opened for reading')
+
+        if not self.header_written:
+            self.header_written = True
+            with nogil:
+                bcf_hdr_write(self.htsfile, self.header.ptr)
+
+        #if record.header is not self.header:
+        #    record.translate(self.header)
+        #    raise ValueError('Writing records from a different VariantFile is not yet supported')
+
+        if record.ptr.n_sample != bcf_hdr_nsamples(self.header.ptr):
+            msg = 'Invalid VariantRecord.  Number of samples does not match header ({} vs {})'
+            raise ValueError(msg.format(record.ptr.n_sample, bcf_hdr_nsamples(self.header.ptr)))
+
+        # Sync END annotation before writing
+        bcf_sync_end(record)
+
+        cdef int ret
+
+        with nogil:
+            ret = bcf_write1(self.htsfile, self.header.ptr, record.ptr)
+
+        if ret < 0:
+            raise IOError(errno, strerror(errno))
+
+        return ret
+
+    def subset_samples(self, include_samples):
+        """
+        Read only a subset of samples to reduce processing time and memory.
+        Must be called prior to retrieving records.
+        """
+        if not self.is_open:
+            raise ValueError('I/O operation on closed file')
+
+        if self.htsfile.is_write:
+            raise ValueError('cannot subset samples from Variantfile opened for writing')
+
+        if self.is_reading:
+            raise ValueError('cannot subset samples after fetching records')
+
+        self.header._subset_samples(include_samples)
+
+        # potentially unnecessary optimization that also sets max_unpack
+        if not include_samples:
+            self.drop_samples = True
+
diff --git a/pysam/libcbcftools.pxd b/pysam/libcbcftools.pxd
new file mode 100644
index 0000000..f8892ed
--- /dev/null
+++ b/pysam/libcbcftools.pxd
@@ -0,0 +1,8 @@
+cdef extern from "bcftools.pysam.h":
+
+    int bcftools_dispatch(int argc, char *argv[])
+    void bcftools_set_stderr(int fd)
+    void bcftools_close_stderr()
+    void bcftools_set_stdout(int fd)
+    void bcftools_set_stdout_fn(const char *)
+    void bcftools_close_stdout()
diff --git a/pysam/libcbcftools.pyi b/pysam/libcbcftools.pyi
new file mode 100644
index 0000000..242b931
--- /dev/null
+++ b/pysam/libcbcftools.pyi
@@ -0,0 +1 @@
+def py_bcftools() -> None: ...
diff --git a/pysam/libcbcftools.pyx b/pysam/libcbcftools.pyx
new file mode 100644
index 0000000..8e90388
--- /dev/null
+++ b/pysam/libcbcftools.pyx
@@ -0,0 +1,2 @@
+def py_bcftools():
+    pass
diff --git a/pysam/libcbgzf.pyi b/pysam/libcbgzf.pyi
new file mode 100644
index 0000000..4d64e8d
--- /dev/null
+++ b/pysam/libcbgzf.pyi
@@ -0,0 +1,40 @@
+import sys
+
+from typing import Optional, Union, Any, NoReturn
+
+if sys.version_info < (3, 8):
+    from typing_extensions import Literal
+else:
+    from typing import Literal
+
+BUFFER_SIZE: int
+
+class BGZFile:
+    def __init__(
+        self,
+        filename: str,
+        mode: Optional[Literal["r", "rb", "a", "ab", "w", "wb", "x", "xb"]],
+        index: Optional[str],
+    ) -> None: ...
+    @property
+    def name(self) -> str: ...
+    @property
+    def index(self) -> Optional[str]: ...
+    def write(self, data: Union[bytes, bytearray, memoryview]) -> int: ...
+    def read(self, size: int = ...) -> bytes: ...
+    @property
+    def closed(self) -> bool: ...
+    def close(self) -> None: ...
+    def __enter__(self) -> BGZFile: ...
+    def __exit__(self, type, value, traceback) -> Any: ...
+    def flush(self) -> None: ...
+    def fileno(self) -> NoReturn: ...
+    def rewind(self) -> None: ...
+    def readable(self) -> bool: ...
+    def writable(self) -> bool: ...
+    def seekable(self) -> bool: ...
+    def tell(self) -> int: ...
+    def seek(self, offset: int, whence: int = ...) -> int: ...
+    def readline(self, size: int = ...) -> bytes: ...
+    def __iter__(self) -> BGZFile: ...
+    def __next__(self) -> bytes: ...
diff --git a/pysam/libcbgzf.pyx b/pysam/libcbgzf.pyx
new file mode 100644
index 0000000..ede6463
--- /dev/null
+++ b/pysam/libcbgzf.pyx
@@ -0,0 +1,238 @@
+"""Functions that read and write block gzipped files.
+
+The user of the file doesn't have to worry about the compression
+and random access is allowed if an index file is present."""
+
+# based on Python 3.5's gzip module
+
+import io
+
+from libc.stdint cimport int8_t, int16_t, int32_t, int64_t
+from libc.stdint cimport uint8_t, uint16_t, uint32_t, uint64_t
+from libc.stdlib cimport malloc, calloc, realloc, free
+
+from cpython.object cimport PyObject
+from cpython.bytes  cimport PyBytes_FromStringAndSize, _PyBytes_Resize
+
+from pysam.libcutils   cimport force_bytes, encode_filename
+from pysam.libchtslib  cimport bgzf_open, bgzf_index_build_init, bgzf_write, bgzf_read, \
+                               bgzf_flush, bgzf_index_dump, bgzf_close, bgzf_seek, \
+                               bgzf_tell, bgzf_getline, kstring_t, SEEK_SET, BGZF
+
+__all__ = ["BGZFile"]
+
+
+BUFFER_SIZE = io.DEFAULT_BUFFER_SIZE
+
+
+cdef class BGZFile(object):
+    """The BGZFile class simulates most of the methods of a file object with
+    the exception of the truncate() method.
+
+    This class only supports opening files in binary mode. If you need to open a
+    compressed file in text mode, use the gzip.open() function.
+    """
+    cdef BGZF* bgzf
+    cdef readonly object name, index
+
+    def __init__(self, filename, mode=None, index=None):
+        """Constructor for the BGZFile class.
+
+        The mode argument can be any of 'r', 'rb', 'a', 'ab', 'w', 'wb', 'x', or
+        'xb' depending on whether the file will be read or written.  The default
+        is the mode of fileobj if discernible; otherwise, the default is 'rb'.
+        A mode of 'r' is equivalent to one of 'rb', and similarly for 'w' and
+        'wb', 'a' and 'ab', and 'x' and 'xb'.
+        """
+        if mode and ('t' in mode or 'U' in mode):
+            raise ValueError("Invalid mode: {!r}".format(mode))
+        if not mode:
+            mode = 'rb'
+        elif mode and 'b' not in mode:
+            mode += 'b'
+
+        mode = force_bytes(mode)
+
+        self.name = encode_filename(filename)
+        self.index = encode_filename(index) if index is not None else None
+
+        self.bgzf = bgzf_open(self.name, mode)
+
+        if self.bgzf.is_write and index is not None and bgzf_index_build_init(self.bgzf) < 0:
+            raise IOError('Error building bgzf index')
+
+    def __dealloc__(self):
+        self.close()
+
+    def write(self, data):
+        if not self.bgzf:
+            raise ValueError("write() on closed BGZFile object")
+
+        if not self.bgzf.is_write:
+            import errno
+            raise IOError(errno.EBADF, "write() on read-only BGZFile object")
+
+        if isinstance(data, bytes):
+            length = len(data)
+        else:
+            # accept any data that supports the buffer protocol
+            data = memoryview(data)
+            length = data.nbytes
+
+        if length > 0 and bgzf_write(self.bgzf, <char *>data, length) < 0:
+            raise IOError('BGZFile write failed')
+
+        return length
+
+    def read(self, size=-1):
+        cdef ssize_t read_size
+
+        if not self.bgzf:
+            raise ValueError("read() on closed BGZFile object")
+
+        if self.bgzf.is_write:
+            import errno
+            raise IOError(errno.EBADF, "read() on write-only BGZFile object")
+
+        if size < 0:
+            chunks = []
+            while 1:
+                chunk = PyBytes_FromStringAndSize(NULL, BUFFER_SIZE)
+                cdata = <bytes>chunk
+                read_size = bgzf_read(self.bgzf, <char *>chunk, BUFFER_SIZE)
+                if read_size < 0:
+                    raise IOError('Error reading from BGZFile')
+                elif not read_size:
+                    break
+                elif read_size < BUFFER_SIZE:
+                    chunk = chunk[:read_size]
+                chunks.append(chunk)
+            return b''.join(chunks)
+
+        elif size > 0:
+            chunk = PyBytes_FromStringAndSize(NULL, size)
+            read_size = bgzf_read(self.bgzf, <char *>chunk, size)
+            if read_size < 0:
+                raise IOError('Error reading from BGZFile')
+            elif read_size < size:
+                chunk = chunk[:read_size]
+            return chunk
+        else:
+            return b''
+
+    @property
+    def closed(self):
+        return self.bgzf == NULL
+
+    def close(self):
+        if not self.bgzf:
+            return
+
+        if self.bgzf.is_write and bgzf_flush(self.bgzf) < 0:
+            raise IOError('Error flushing BGZFile object')
+
+        if self.index and bgzf_index_dump(self.bgzf, self.index, NULL) < 0:
+            raise IOError('Cannot write index')
+
+        cdef ret = bgzf_close(self.bgzf)
+        self.bgzf = NULL
+
+        if ret < 0:
+            raise IOError('Error closing BGZFile object')
+
+    def __enter__(self):
+        return self
+
+    def __exit__(self, type, value, tb):
+        self.close()
+
+    def flush(self):
+        if not self.bgzf:
+            return
+
+        if self.bgzf.is_write and bgzf_flush(self.bgzf) < 0:
+            raise IOError('Error flushing BGZFile object')
+
+    def fileno(self):
+        """Invoke the underlying file object's fileno() method.
+
+        This will raise AttributeError if the underlying file object
+        doesn't support fileno().
+        """
+        raise AttributeError('fileno')
+
+    def rewind(self):
+        '''Return the uncompressed stream file position indicator to the
+        beginning of the file'''
+        if not self.bgzf:
+            raise ValueError("rewind() on closed BGZFile object")
+        if not self.bgzf.is_write:
+            raise IOError("Can't rewind in write mode")
+        if bgzf_seek(self.bgzf, 0, SEEK_SET) < 0:
+            raise IOError('Error seeking BGZFFile object')
+
+    def readable(self):
+        if not self.bgzf:
+            raise ValueError("readable() on closed BGZFile object")
+        return self.bgzf != NULL and not self.bgzf.is_write
+
+    def writable(self):
+        return self.bgzf != NULL and self.bgzf.is_write
+
+    def seekable(self):
+        return True
+
+    def tell(self):
+        if not self.bgzf:
+            raise ValueError("seek() on closed BGZFile object")
+        cdef int64_t off = bgzf_tell(self.bgzf)
+        if off < 0:
+            raise IOError('Error in tell on BGZFFile object')
+
+        return off
+
+    def seek(self, offset, whence=io.SEEK_SET):
+        if not self.bgzf:
+            raise ValueError("seek() on closed BGZFile object")
+        if whence is not io.SEEK_SET:
+            raise ValueError('Seek from end not supported')
+
+        cdef int64_t off = bgzf_seek(self.bgzf, offset, SEEK_SET)
+        if off < 0:
+            raise IOError('Error seeking BGZFFile object')
+
+        return off
+
+    def readline(self, size=-1):
+        if not self.bgzf:
+            raise ValueError("readline() on closed BGZFile object")
+
+        cdef kstring_t line
+        cdef char c
+
+        line.l = line.m = 0
+        line.s = NULL
+
+        cdef int ret = bgzf_getline(self.bgzf, '\n', &line)
+        if ret == -1:
+            s = b''
+        elif ret == -2:
+            if line.m:
+                free(line.s)
+            raise IOError('Error reading line in BGZFFile object')
+        else:
+            s = line.s[:line.l]
+
+        if line.m:
+            free(line.s)
+
+        return s
+
+    def __iter__(self):
+        return self
+
+    def __next__(self):
+        line = self.readline()
+        if not line:
+            raise StopIteration()
+        return line
diff --git a/pysam/libcfaidx.pxd b/pysam/libcfaidx.pxd
new file mode 100644
index 0000000..53ad767
--- /dev/null
+++ b/pysam/libcfaidx.pxd
@@ -0,0 +1,80 @@
+from libc.stdint cimport int8_t, int16_t, int32_t, int64_t
+from libc.stdint cimport uint8_t, uint16_t, uint32_t, uint64_t
+from libc.stdlib cimport malloc, calloc, realloc, free
+from libc.string cimport memcpy, memcmp, strncpy, strlen, strdup
+from libc.stdio cimport FILE, printf
+cimport cython
+
+from cpython cimport array
+from pysam.libchtslib cimport faidx_t, kstring_t, BGZF
+
+# These functions are put here and not in chtslib.pxd in order
+# to avoid warnings for unused functions.
+cdef extern from "pysam_stream.h" nogil:
+
+    ctypedef struct kstream_t:
+        pass
+
+    ctypedef struct kseq_t:
+        kstring_t name
+        kstring_t comment
+        kstring_t seq
+        kstring_t qual
+
+    kseq_t *kseq_init(BGZF *)
+    int kseq_read(kseq_t *)
+    void kseq_destroy(kseq_t *)
+    kstream_t *ks_init(BGZF *)
+    void ks_destroy(kstream_t *)
+
+    # Retrieve characters from stream until delimiter
+    # is reached placing results in str.
+    int ks_getuntil(kstream_t *,
+                    int delimiter,
+                    kstring_t * str,
+                    int * dret)
+
+cdef class FastaFile:
+    cdef bint is_remote
+    cdef object _filename, _references, _lengths, reference2length
+    cdef faidx_t* fastafile
+    cdef char* _fetch(self, char* reference,
+                      int start, int end, int* length) except? NULL
+
+
+cdef class FastqProxy:
+    cdef kseq_t * _delegate
+    cdef cython.str to_string(self)
+    cdef cython.str tostring(self)
+    cpdef array.array get_quality_array(self, int offset=*)
+
+
+cdef class FastxRecord:
+    """
+    Python container for pysam.libcfaidx.FastqProxy with persistence.
+    """
+    cdef public str comment, quality, sequence, name
+    cdef cython.str to_string(self)
+    cdef cython.str tostring(self)
+    cpdef array.array get_quality_array(self, int offset=*)
+
+cdef class FastxFile:
+    cdef object _filename
+    cdef BGZF * fastqfile
+    cdef kseq_t * entry
+    cdef bint persist
+    cdef bint is_remote
+
+    cdef kseq_t * getCurrent(self)
+    cdef int cnext(self)
+
+
+# Compatibility Layer for pysam 0.8.1
+cdef class FastqFile(FastxFile):
+    pass
+
+
+# Compatibility Layer for pysam < 0.8
+cdef class Fastafile(FastaFile):
+    pass
+
diff --git a/pysam/libcfaidx.pyi b/pysam/libcfaidx.pyi
new file mode 100644
index 0000000..5865701
--- /dev/null
+++ b/pysam/libcfaidx.pyi
@@ -0,0 +1,68 @@
+import array
+from typing import Optional, Any, Sequence, Iterator
+
+class FastaFile:
+    def __init__(
+        self,
+        filename: str,
+        filepath_index: Optional[str] = ...,
+        filepath_index_compressed: Optional[str] = ...,
+    ) -> None: ...
+    def is_open(self) -> bool: ...
+    def __len__(self) -> int: ...
+    def close(self) -> None: ...
+    def __enter__(self) -> FastaFile: ...
+    def __exit__(self, type, value, traceback) -> Any: ...
+    @property
+    def closed(self) -> bool: ...
+    @property
+    def filename(self) -> str: ...
+    @property
+    def references(self) -> Sequence[str]: ...
+    @property
+    def nreferences(self) -> Optional[int]: ...
+    @property
+    def lengths(self) -> Sequence[int]: ...
+    def fetch(
+        self,
+        reference: Optional[str] = ...,
+        start: Optional[int] = ...,
+        end: Optional[int] = ...,
+        region: Optional[str] = ...,
+    ) -> str: ...
+    def get_reference_length(self, reference: str) -> int: ...
+    def __getitem__(self, reference: str) -> str: ...
+    def __contains__(self, reference: str) -> bool: ...
+
+class FastxRecord:
+    comment: str = ...
+    quality: str = ...
+    sequence: str = ...
+    name: str = ...
+    def __init__(
+        self,
+        name: Optional[str] = ...,
+        comment: Optional[str] = ...,
+        sequence: Optional[str] = ...,
+        quality: Optional[str] = ...,
+    ) -> None: ...
+    def set_name(self, name: str) -> None: ...
+    def set_comment(self, comment: str) -> None: ...
+    def set_sequence(self, sequence: str, quality: Optional[str] = ...) -> None: ...
+    def get_quality_array(self, offset: int = ...) -> array.array: ...
+
+class FastxFile:
+    def __init__(self, filename: str, persist: bool = ...) -> None: ...
+    def is_open(self) -> bool: ...
+    def close(self) -> None: ...
+    def __enter__(self) -> FastxFile: ...
+    def __exit__(self, type, value, traceback) -> Any: ...
+    @property
+    def closed(self) -> bool: ...
+    @property
+    def filename(self) -> str: ...
+    def __iter__(self) -> Iterator[FastxRecord]: ...
+    def __next__(self) -> FastxRecord: ...
+
+# deprecated
+class FastqFile(FastxFile): ...
diff --git a/pysam/libcfaidx.pyx b/pysam/libcfaidx.pyx
new file mode 100644
index 0000000..e73adf9
--- /dev/null
+++ b/pysam/libcfaidx.pyx
@@ -0,0 +1,674 @@
+# cython: embedsignature=True
+# cython: profile=True
+###############################################################################
+###############################################################################
+# Cython wrapper for SAM/BAM/CRAM files based on htslib
+###############################################################################
+# The principal classes defined in this module are:
+#
+# class FastaFile   random read read/write access to faidx indexd files
+# class FastxFile   streamed read/write access to fasta/fastq files
+#
+# Additionally this module defines several additional classes that are part
+# of the internal API. These are:
+#
+# class FastqProxy
+# class FastxRecord
+#
+# For backwards compatibility, the following classes are also defined:
+#
+# class Fastafile   equivalent to FastaFile
+# class FastqFile   equivalent to FastxFile
+#
+###############################################################################
+#
+# The MIT License
+#
+# Copyright (c) 2015 Andreas Heger
+#
+# Permission is hereby granted, free of charge, to any person obtaining a
+# copy of this software and associated documentation files (the "Software"),
+# to deal in the Software without restriction, including without limitation
+# the rights to use, copy, modify, merge, publish, distribute, sublicense,
+# and/or sell copies of the Software, and to permit persons to whom the
+# Software is furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.  IN NO EVENT SHALL
+# THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+# DEALINGS IN THE SOFTWARE.
+#
+###############################################################################
+import sys
+import os
+import re
+
+
+from libc.errno  cimport errno
+from libc.string cimport strerror
+
+from cpython cimport array
+
+from cpython cimport PyErr_SetString, \
+    PyBytes_Check, \
+    PyUnicode_Check, \
+    PyBytes_FromStringAndSize
+
+from cpython.version cimport PY_MAJOR_VERSION
+
+from pysam.libchtslib cimport \
+    faidx_nseq, fai_load, fai_load3, fai_destroy, fai_fetch, \
+    faidx_seq_len, faidx_iseq, faidx_seq_len, \
+    faidx_fetch_seq, hisremote, \
+    bgzf_open, bgzf_close
+
+from pysam.libcutils cimport force_bytes, force_str, charptr_to_str
+from pysam.libcutils cimport encode_filename, from_string_and_size
+from pysam.libcutils cimport qualitystring_to_array, parse_region
+
+cdef class FastqProxy
+cdef makeFastqProxy(kseq_t * src):
+    '''enter src into AlignedRead.'''
+    cdef FastqProxy dest = FastqProxy.__new__(FastqProxy)
+    dest._delegate = src
+    return dest
+
+## TODO:
+##        add automatic indexing.
+##        add function to get sequence names.
+cdef class FastaFile:
+    """Random access to fasta formatted files that
+    have been indexed by :term:`faidx`.
+
+    The file is automatically opened. The index file of file
+    ``<filename>`` is expected to be called ``<filename>.fai``.
+
+    Parameters
+    ----------
+
+    filename : string
+        Filename of fasta file to be opened.
+
+    filepath_index : string
+        Optional, filename of the index. By default this is
+        the filename + ".fai".
+
+    filepath_index_compressed : string
+        Optional, filename of the index if fasta file is. By default this is
+        the filename + ".gzi".
+
+    Raises
+    ------
+
+    ValueError
+        if index file is missing
+
+    IOError
+        if file could not be opened
+
+    """
+
+    def __cinit__(self, *args, **kwargs):
+        self.fastafile = NULL
+        self._filename = None
+        self._references = None
+        self._lengths = None
+        self.reference2length = None
+        self._open(*args, **kwargs)
+
+    def is_open(self):
+        '''return true if samfile has been opened.'''
+        return self.fastafile != NULL
+
+    def __len__(self):
+        if self.fastafile == NULL:
+            raise ValueError("calling len() on closed file")
+
+        return faidx_nseq(self.fastafile)
+
+    def _open(self, filename, filepath_index=None, filepath_index_compressed=None):
+        '''open an indexed fasta file.
+
+        This method expects an indexed fasta file.
+        '''
+
+        # close a previously opened file
+        if self.fastafile != NULL:
+            self.close()
+
+        self._filename = encode_filename(filename)
+        cdef char *cfilename = self._filename
+        cdef char *cindexname = NULL
+        cdef char *cindexname_compressed = NULL
+        self.is_remote = hisremote(cfilename)
+        
+        # open file for reading
+        if (self._filename != b"-"
+            and not self.is_remote
+            and not os.path.exists(filename)):
+            raise IOError("file `%s` not found" % filename)
+
+        # 3 modes to open:
+        # compressed fa: fai_load3 with filename, index_fai and index_gzi
+        # uncompressed fa: fai_load3 with filename and index_fai
+        # uncompressed fa: fai_load with default index name
+        if filepath_index:
+            # when opening, set flags to 0 - do not automatically
+            # build index if it does not exist.
+
+            if not os.path.exists(filepath_index):
+                raise IOError("filename {} does not exist".format(filepath_index))
+            cindexname = bindex_filename = encode_filename(filepath_index)
+            
+            if filepath_index_compressed:
+                if not os.path.exists(filepath_index_compressed):
+                    raise IOError("filename {} does not exist".format(filepath_index_compressed))
+                cindexname_compressed = bindex_filename_compressed = encode_filename(filepath_index_compressed)
+                with nogil:
+                    self.fastafile = fai_load3(cfilename, cindexname, cindexname_compressed, 0)
+            else:
+                with nogil:
+                    self.fastafile = fai_load3(cfilename, cindexname, NULL, 0)
+        else:
+            with nogil:
+                self.fastafile = fai_load(cfilename)
+
+        if self.fastafile == NULL:
+            raise IOError("error when opening file `%s`" % filename)
+
+        cdef int nreferences = faidx_nseq(self.fastafile)
+        cdef int x
+        cdef const char * s
+        self._references = []
+        self._lengths = []
+        for x from 0 <= x < nreferences:
+            s = faidx_iseq(self.fastafile, x)
+            ss = force_str(s)
+            self._references.append(ss)
+            self._lengths.append(faidx_seq_len(self.fastafile, s))
+        self.reference2length = dict(zip(self._references, self._lengths))
+
+    def close(self):
+        """close the file."""
+        if self.fastafile != NULL:
+            fai_destroy(self.fastafile)
+            self.fastafile = NULL
+
+    def __dealloc__(self):
+        if self.fastafile != NULL:
+            fai_destroy(self.fastafile)
+            self.fastafile = NULL
+
+    # context manager interface
+    def __enter__(self):
+        return self
+
+    def __exit__(self, exc_type, exc_value, traceback):
+        self.close()
+        return False
+
+    property closed:
+        """bool indicating the current state of the file object.
+        This is a read-only attribute; the close() method changes the value.
+        """
+        def __get__(self):
+            return not self.is_open()
+
+    property filename:
+        """filename associated with this object. This is a read-only attribute."""
+        def __get__(self):
+            return self._filename
+
+    property references:
+        '''tuple with the names of :term:`reference` sequences.'''
+        def __get__(self):
+            return self._references
+
+    property nreferences:
+        """int with the number of :term:`reference` sequences in the file.
+        This is a read-only attribute."""
+        def __get__(self):
+            return len(self._references) if self.references else None
+
+    property lengths:
+        """tuple with the lengths of :term:`reference` sequences."""
+        def __get__(self):
+            return self._lengths
+
+    def fetch(self,
+              reference=None,
+              start=None,
+              end=None,
+              region=None):
+        """fetch sequences in a :term:`region`.
+
+        A region can
+        either be specified by :term:`reference`, `start` and
+        `end`. `start` and `end` denote 0-based, half-open
+        intervals.
+
+        Alternatively, a samtools :term:`region` string can be
+        supplied.
+
+        If any of the coordinates are missing they will be replaced by the
+        minimum (`start`) or maximum (`end`) coordinate.
+
+        Note that region strings are 1-based, while `start` and `end` denote
+        an interval in python coordinates.
+        The region is specified by :term:`reference`, `start` and `end`.
+
+        Returns
+        -------
+
+        string : a string with the sequence specified by the region.
+
+        Raises
+        ------
+
+        IndexError
+            if the coordinates are out of range
+
+        ValueError
+            if the region is invalid
+
+        """
+
+        if not self.is_open():
+            raise ValueError("I/O operation on closed file" )
+
+        cdef int length
+        cdef char *seq
+        cdef char *ref
+        cdef int rstart, rend
+
+        contig, rstart, rend = parse_region(reference, start, end, region)
+
+        if contig is None:
+            raise ValueError("no sequence/region supplied.")
+
+        if rstart == rend:
+            return ""
+
+        contig_b = force_bytes(contig)
+        ref = contig_b
+        with nogil:
+            length = faidx_seq_len(self.fastafile, ref)
+        if length == -1:
+            raise KeyError("sequence '%s' not present" % contig)
+        if rstart >= length:
+            return ""
+
+        # fai_fetch adds a '\0' at the end
+        with nogil:
+            seq = faidx_fetch_seq(self.fastafile,
+                                  ref,
+                                  rstart,
+                                  rend-1,
+                                  &length)
+
+        if not seq:
+            if errno:
+                raise IOError(errno, strerror(errno))
+            else:
+                raise ValueError("failure when retrieving sequence on '%s'" % contig)
+
+        try:
+            return charptr_to_str(seq)
+        finally:
+            free(seq)
+
+    cdef char *_fetch(self, char *reference, int start, int end, int *length) except? NULL:
+        '''fetch sequence for reference, start and end'''
+
+        cdef char *seq
+        with nogil:
+            seq = faidx_fetch_seq(self.fastafile,
+                                  reference,
+                                  start,
+                                  end-1,
+                                  length)
+
+        if not seq:
+            if errno:
+                raise IOError(errno, strerror(errno))
+            else:
+                raise ValueError("failure when retrieving sequence on '%s'" % reference)
+
+        return seq
+
+    def get_reference_length(self, reference):
+        '''return the length of reference.'''
+        return self.reference2length[reference]
+
+    def __getitem__(self, reference):
+        return self.fetch(reference)
+
+    def __contains__(self, reference):
+        '''return true if reference in fasta file.'''
+        return reference in self.reference2length
+
+
+cdef class FastqProxy:
+    """A single entry in a fastq file."""
+    def __init__(self):
+        raise ValueError("do not instantiate FastqProxy directly")
+
+    property name:
+        """The name of each entry in the fastq file."""
+        def __get__(self):
+            return charptr_to_str(self._delegate.name.s)
+
+    property sequence:
+        """The sequence of each entry in the fastq file."""
+        def __get__(self):
+            return charptr_to_str(self._delegate.seq.s)
+
+    property comment:
+        def __get__(self):
+            if self._delegate.comment.l:
+                return charptr_to_str(self._delegate.comment.s)
+            else:
+                return None
+
+    property quality:
+        """The quality score of each entry in the fastq file, represented as a string."""
+        def __get__(self):
+            if self._delegate.qual.l:
+                return charptr_to_str(self._delegate.qual.s)
+            else:
+                return None
+
+    cdef cython.str to_string(self):
+        if self.comment is None:
+            comment = ""
+        else:
+            comment = " %s" % self.comment
+
+        if self.quality is None:
+            return ">%s%s\n%s" % (self.name, comment, self.sequence)
+        else:
+            return "@%s%s\n%s\n+\n%s" % (self.name, comment,
+                                         self.sequence, self.quality)
+    
+    cdef cython.str tostring(self):
+        """deprecated : use :meth:`to_string`"""
+        return self.to_string()
+    
+    def __str__(self):
+        return self.to_string()
+
+    cpdef array.array get_quality_array(self, int offset=33):
+        '''return quality values as integer array after subtracting offset.'''
+        if self.quality is None:
+            return None
+        return qualitystring_to_array(force_bytes(self.quality),
+                                      offset=offset)
+
+cdef class FastxRecord:
+    """A fasta/fastq record.
+
+    A record must contain a name and a sequence. If either of them are
+    None, a ValueError is raised on writing.
+
+    """
+    def __init__(self,
+                 name=None,
+                 comment=None,
+                 sequence=None,
+                 quality=None,
+                 FastqProxy proxy=None):
+        if proxy is not None:
+            self.comment = proxy.comment
+            self.quality = proxy.quality
+            self.sequence = proxy.sequence
+            self.name = proxy.name
+        else:
+            self.comment = comment
+            self.quality = quality
+            self.sequence = sequence
+            self.name = name
+
+    def __copy__(self):
+        return FastxRecord(self.name, self.comment, self.sequence, self.quality)
+
+    def __deepcopy__(self, memo):
+        return FastxRecord(self.name, self.comment, self.sequence, self.quality)
+
+    cdef cython.str to_string(self):
+        if self.name is None:
+            raise ValueError("can not write record without name")
+
+        if self.sequence is None:
+            raise ValueError("can not write record without a sequence")
+        
+        if self.comment is None:
+            comment = ""
+        else:
+            comment = " %s" % self.comment
+
+        if self.quality is None:
+            return ">%s%s\n%s" % (self.name, comment, self.sequence)
+        else:
+            return "@%s%s\n%s\n+\n%s" % (self.name, comment,
+                                         self.sequence, self.quality)
+        
+    cdef cython.str tostring(self):
+        """deprecated : use :meth:`to_string`"""
+        return self.to_string()
+
+    def set_name(self, name):
+        if name is None:
+            raise ValueError("FastxRecord must have a name and not None")
+        self.name = name
+
+    def set_comment(self, comment):
+        self.comment = comment    
+        
+    def set_sequence(self, sequence, quality=None):
+        """set sequence of this record.
+
+        """
+        self.sequence = sequence
+        if quality is not None:
+            if len(sequence) != len(quality):
+                raise ValueError("sequence and quality length do not match: {} vs {}".format(
+                    len(sequence), len(quality)))
+
+            self.quality = quality
+        else:
+            self.quality = None
+
+    def __str__(self):
+        return self.to_string()
+
+    cpdef array.array get_quality_array(self, int offset=33):
+        '''return quality values as array after subtracting offset.'''
+        if self.quality is None:
+            return None
+        return qualitystring_to_array(force_bytes(self.quality),
+                                      offset=offset)
+
+
+cdef class FastxFile:
+    r"""Stream access to :term:`fasta` or :term:`fastq` formatted files.
+
+    The file is automatically opened.
+
+    Entries in the file can be both fastq or fasta formatted or even a
+    mixture of the two.
+
+    This file object permits iterating over all entries in the
+    file. Random access is not implemented. The iteration returns
+    objects of type :class:`FastqProxy`
+
+    Parameters
+    ----------
+
+    filename : string
+        Filename of fasta/fastq file to be opened.
+
+    persist : bool
+
+        If True (default) make a copy of the entry in the file during
+        iteration. If set to False, no copy will be made. This will
+        permit much faster iteration, but an entry will not persist
+        when the iteration continues and an entry is read-only.
+
+    Notes
+    -----
+    Prior to version 0.8.2, this class was called FastqFile.
+
+    Raises
+    ------
+
+    IOError
+        if file could not be opened
+
+
+    Examples
+    --------
+    >>> with pysam.FastxFile(filename) as fh:
+    ...    for entry in fh:
+    ...        print(entry.name)
+    ...        print(entry.sequence)
+    ...        print(entry.comment)
+    ...        print(entry.quality)
+    >>> with pysam.FastxFile(filename) as fin, open(out_filename, mode='w') as fout:
+    ...    for entry in fin:
+    ...        fout.write(str(entry) + '\n')
+
+    """
+    def __cinit__(self, *args, **kwargs):
+        # self.fastqfile = <gzFile*>NULL
+        self._filename = None
+        self.entry = NULL
+        self._open(*args, **kwargs)
+
+    def is_open(self):
+        '''return true if samfile has been opened.'''
+        return self.entry != NULL
+
+    def _open(self, filename, persist=True):
+        '''open a fastq/fasta file in *filename*
+
+        Paramentes
+        ----------
+
+        persist : bool
+
+            if True return a copy of the underlying data (default
+            True).  The copy will persist even if the iteration
+            on the file continues.
+
+        '''
+        if self.fastqfile != NULL:
+            self.close()
+
+        self._filename = encode_filename(filename)
+        cdef char *cfilename = self._filename
+        self.is_remote = hisremote(cfilename)
+
+        # open file for reading
+        if (self._filename != b"-"
+            and not self.is_remote
+            and not os.path.exists(filename)):
+            raise IOError("file `%s` not found" % filename)
+
+        self.persist = persist
+
+        with nogil:
+            self.fastqfile = bgzf_open(cfilename, "r")
+            self.entry = kseq_init(self.fastqfile)
+        self._filename = filename
+
+    def close(self):
+        '''close the file.'''
+        if self.fastqfile != NULL:
+            bgzf_close(self.fastqfile)
+            self.fastqfile = NULL
+        if self.entry != NULL:
+            kseq_destroy(self.entry)
+            self.entry = NULL
+
+    def __dealloc__(self):
+        if self.fastqfile != NULL:
+            bgzf_close(self.fastqfile)
+        if self.entry:
+            kseq_destroy(self.entry)
+
+    # context manager interface
+    def __enter__(self):
+        return self
+
+    def __exit__(self, exc_type, exc_value, traceback):
+        self.close()
+        return False
+
+    property closed:
+        """bool indicating the current state of the file object.
+        This is a read-only attribute; the close() method changes the value.
+        """
+        def __get__(self):
+            return not self.is_open()
+
+    property filename:
+        """string with the filename associated with this object."""
+        def __get__(self):
+            return self._filename
+
+    def __iter__(self):
+        if not self.is_open():
+            raise ValueError("I/O operation on closed file")
+        return self
+
+    cdef kseq_t * getCurrent(self):
+        return self.entry
+
+    cdef int cnext(self):
+        '''C version of iterator
+        '''
+        with nogil:
+            return kseq_read(self.entry)
+
+    def __next__(self):
+        """
+        python version of next().
+        """
+        cdef int l
+        with nogil:
+            l = kseq_read(self.entry)
+        if (l >= 0):
+            if self.persist:
+                return FastxRecord(proxy=makeFastqProxy(self.entry))
+            return makeFastqProxy(self.entry)
+        elif (l == -1):
+            raise StopIteration
+        elif (l == -2):
+            raise ValueError('truncated quality string in {0}'
+                             .format(self._filename))
+        else:
+            raise ValueError('unknown problem parsing {0}'
+                             .format(self._filename))
+
+# Compatibility Layer for pysam 0.8.1
+cdef class FastqFile(FastxFile):
+    """FastqFile is deprecated: use FastxFile instead"""
+    pass
+
+# Compatibility Layer for pysam < 0.8
+cdef class Fastafile(FastaFile):
+    """Fastafile is deprecated: use FastaFile instead"""
+    pass
+
+__all__ = ["FastaFile",
+           "FastqFile",
+           "FastxFile",
+           "Fastafile",
+           "FastxRecord",
+           "FastqProxy"]
diff --git a/pysam/libchtslib.pxd b/pysam/libchtslib.pxd
new file mode 100644
index 0000000..ed3ca92
--- /dev/null
+++ b/pysam/libchtslib.pxd
@@ -0,0 +1,2693 @@
+from libc.stdint cimport int8_t, int16_t, int32_t, int64_t
+from libc.stdint cimport uint8_t, uint16_t, uint32_t, uint64_t
+from libc.stdlib cimport malloc, calloc, realloc, free
+from libc.string cimport memcpy, memcmp, strncpy, strlen, strdup
+from libc.stdio cimport FILE, printf
+from posix.types cimport off_t
+
+cdef extern from "Python.h":
+   FILE* PyFile_AsFile(object)
+
+
+# cython does not wrap stdarg
+cdef extern from "stdarg.h":
+    ctypedef struct va_list:
+        pass
+
+   
+cdef extern from "htslib/kstring.h" nogil:
+    ctypedef struct kstring_t:
+        size_t l, m
+        char *s
+
+    int kputc(int c, kstring_t *s)
+    int kputw(int c, kstring_t *s)
+    int kputl(long c, kstring_t *s)
+    int ksprintf(kstring_t *s, const char *fmt, ...)
+
+
+cdef extern from "htslib_util.h" nogil:
+    int hts_set_verbosity(int verbosity)
+    int hts_get_verbosity()
+
+    ctypedef uint32_t khint32_t
+    ctypedef uint32_t khint_t
+    ctypedef khint_t  khiter_t
+
+    # Used to manage BCF Header info
+    ctypedef struct vdict_t:
+        khint_t n_buckets, size, n_occupied, upper_bound
+        khint32_t *flags
+        const char *keys
+        bcf_idinfo_t *vals
+
+    # Used to manage indexed contigs in Tabix
+    ctypedef struct s2i_t:
+        khint_t n_buckets, size, n_occupied, upper_bound
+        khint32_t *flags
+        const char *keys
+        int64_t *vals
+
+    # Generic khash methods
+    khint_t kh_size(void *d)
+    khint_t kh_begin(void *d)
+    khint_t kh_end(void *d)
+    int kh_exist(void *d, khiter_t i)
+
+    # Specialized khash methods for vdict
+    khint_t kh_get_vdict(vdict_t *d, const char *key)
+    const char *kh_key_vdict "kh_key" (vdict_t *d, khint_t i)
+    bcf_idinfo_t kh_val_vdict "kh_val" (vdict_t *d, khint_t i)
+
+
+cdef extern from "htslib/hfile.h" nogil:
+    ctypedef struct hFILE
+
+    # @abstract  Open the named file or URL as a stream
+    # @return    An hFILE pointer, or NULL (with errno set) if an error occurred.
+    hFILE *hopen(const char *filename, const char *mode, ...)
+
+    # @abstract  Associate a stream with an existing open file descriptor
+    # @return    An hFILE pointer, or NULL (with errno set) if an error occurred.
+    # @notes     For socket descriptors (on Windows), mode should contain 's'.
+    hFILE *hdopen(int fd, const char *mode)
+
+    # @abstract  Report whether the file name or URL denotes remote storage
+    # @return    0 if local, 1 if remote.
+    # @notes     "Remote" means involving e.g. explicit network access, with the
+    #   implication that callers may wish to cache such files' contents locally.
+    int hisremote(const char *filename)
+
+    # @abstract  Flush (for output streams) and close the stream
+    # @return    0 if successful, or EOF (with errno set) if an error occurred.
+    int hclose(hFILE *fp)
+
+    # @abstract  Close the stream, without flushing or propagating errors
+    # @notes     For use while cleaning up after an error only.  Preserves errno.
+    void hclose_abruptly(hFILE *fp)
+
+    # @abstract  Return the stream's error indicator
+    # @return    Non-zero (in fact, an errno value) if an error has occurred.
+    # @notes     This would be called herror() and return true/false to parallel
+    #   ferror(3), but a networking-related herror(3) function already exists.  */
+    int herrno(hFILE *fp)
+
+    # @abstract  Clear the stream's error indicator
+    void hclearerr(hFILE *fp)
+
+    # @abstract  Reposition the read/write stream offset
+    # @return    The resulting offset within the stream (as per lseek(2)),
+    #   or negative if an error occurred.
+    off_t hseek(hFILE *fp, off_t offset, int whence)
+
+    # @abstract  Report the current stream offset
+    # @return    The offset within the stream, starting from zero.
+    off_t htell(hFILE *fp)
+
+    # @abstract  Read one character from the stream
+    # @return    The character read, or EOF on end-of-file or error
+    int hgetc(hFILE *fp)
+
+    # Read from the stream until the delimiter, up to a maximum length
+    #    @param buffer  The buffer into which bytes will be written
+    #    @param size    The size of the buffer
+    #    @param delim   The delimiter (interpreted as an `unsigned char`)
+    #    @param fp      The file stream
+    #    @return  The number of bytes read, or negative on error.
+    #    @since   1.4
+    #
+    # Bytes will be read into the buffer up to and including a delimiter, until
+    # EOF is reached, or _size-1_ bytes have been written, whichever comes first.
+    # The string will then be terminated with a NUL byte (`\0`).
+    ssize_t hgetdelim(char *buffer, size_t size, int delim, hFILE *fp)
+
+    # Read a line from the stream, up to a maximum length
+    #    @param buffer  The buffer into which bytes will be written
+    #    @param size    The size of the buffer
+    #    @param fp      The file stream
+    #    @return  The number of bytes read, or negative on error.
+    #    @since   1.4
+    #
+    # Specialization of hgetdelim() for a `\n` delimiter.
+    ssize_t hgetln(char *buffer, size_t size, hFILE *fp)
+
+    # Read a line from the stream, up to a maximum length
+    #    @param buffer  The buffer into which bytes will be written
+    #    @param size    The size of the buffer (must be > 1 to be useful)
+    #    @param fp      The file stream
+    #    @return  _buffer_ on success, or `NULL` if an error occurred.
+    #    @since   1.4
+    #
+    # This function can be used as a replacement for `fgets(3)`, or together with
+    # kstring's `kgetline()` to read arbitrarily-long lines into a _kstring_t_.
+    char *hgets(char *buffer, int size, hFILE *fp)
+
+    # @abstract  Peek at characters to be read without removing them from buffers
+    # @param fp      The file stream
+    # @param buffer  The buffer to which the peeked bytes will be written
+    # @param nbytes  The number of bytes to peek at; limited by the size of the
+    #   internal buffer, which could be as small as 4K.
+    # @return    The number of bytes peeked, which may be less than nbytes if EOF
+    #   is encountered; or negative, if there was an I/O error.
+    # @notes  The characters peeked at remain in the stream's internal buffer,
+    #   and will be returned by later hread() etc calls.
+    ssize_t hpeek(hFILE *fp, void *buffer, size_t nbytes)
+
+    # @abstract  Read a block of characters from the file
+    # @return    The number of bytes read, or negative if an error occurred.
+    # @notes     The full nbytes requested will be returned, except as limited
+    #   by EOF or I/O errors.
+    ssize_t hread(hFILE *fp, void *buffer, size_t nbytes)
+
+    # @abstract  Write a character to the stream
+    # @return    The character written, or EOF if an error occurred.
+    int hputc(int c, hFILE *fp)
+
+    # @abstract  Write a string to the stream
+    # @return    0 if successful, or EOF if an error occurred.
+    int hputs(const char *text, hFILE *fp)
+
+    # @abstract  Write a block of characters to the file
+    # @return    Either nbytes, or negative if an error occurred.
+    # @notes     In the absence of I/O errors, the full nbytes will be written.
+    ssize_t hwrite(hFILE *fp, const void *buffer, size_t nbytes)
+
+    # @abstract  For writing streams, flush buffered output to the underlying stream
+    # @return    0 if successful, or EOF if an error occurred.
+    int hflush(hFILE *fp)
+
+
+cdef extern from "htslib/bgzf.h" nogil:
+    ctypedef struct bgzf_mtaux_t
+    ctypedef struct bgzidx_t
+    ctypedef struct z_stream
+
+    ctypedef struct BGZF:
+        unsigned           errcode
+        unsigned           is_write
+        int           is_be
+        int           compress_level
+        int           is_compressed
+        int           is_gzip
+        int           cache_size
+        int64_t       block_address
+        int64_t       uncompressed_address
+        void         *uncompressed_block
+        void         *compressed_block
+        void         *cache
+        hFILE        *fp
+        bgzf_mtaux_t *mt
+        bgzidx_t     *idx
+        int           idx_build_otf
+        z_stream     *gz_stream
+
+    #*****************
+    #  Basic routines *
+    # *****************/
+
+    #  Open an existing file descriptor for reading or writing.
+    #
+    #  @param fd    file descriptor
+    #  @param mode  mode matching /[rwag][u0-9]+/: 'r' for reading, 'w' for
+    #               writing, 'a' for appending, 'g' for gzip rather than BGZF
+    #               compression (with 'w' only), and digit specifies the zlib
+    #               compression level.
+    #               Note that there is a distinction between 'u' and '0': the
+    #               first yields plain uncompressed output whereas the latter
+    #               outputs uncompressed data wrapped in the zlib format.
+    #  @return      BGZF file handler; 0 on error
+
+    BGZF* bgzf_dopen(int fd, const char *mode)
+    BGZF* bgzf_fdopen(int fd, const char *mode) # for backward compatibility
+
+    #  Open the specified file for reading or writing.
+    BGZF* bgzf_open(const char* path, const char *mode)
+
+    #  Open an existing hFILE stream for reading or writing.
+    BGZF* bgzf_hopen(hFILE *fp, const char *mode)
+
+    #  Close the BGZF and free all associated resources.
+    #
+    #  @param fp    BGZF file handler
+    #  @return      0 on success and -1 on error
+    int bgzf_close(BGZF *fp)
+
+    #  Read up to _length_ bytes from the file storing into _data_.
+    #
+    #  @param fp     BGZF file handler
+    #  @param data   data array to read into
+    #  @param length size of data to read
+    #  @return       number of bytes actually read; 0 on end-of-file and -1 on error
+    ssize_t bgzf_read(BGZF *fp, void *data, size_t length)
+
+    #  Write _length_ bytes from _data_ to the file.  If no I/O errors occur,
+    #  the complete _length_ bytes will be written (or queued for writing).
+    #
+    #  @param fp     BGZF file handler
+    #  @param data   data array to write
+    #  @param length size of data to write
+    #  @return       number of bytes written (i.e., _length_); negative on error
+    ssize_t bgzf_write(BGZF *fp, const void *data, size_t length)
+
+    #  Read up to _length_ bytes directly from the underlying stream without
+    #  decompressing.  Bypasses BGZF blocking, so must be used with care in
+    #  specialised circumstances only.
+    #
+    #  @param fp     BGZF file handler
+    #  @param data   data array to read into
+    #  @param length number of raw bytes to read
+    #  @return       number of bytes actually read; 0 on end-of-file and -1 on error
+    ssize_t bgzf_raw_read(BGZF *fp, void *data, size_t length)
+
+    #  Write _length_ bytes directly to the underlying stream without
+    #  compressing.  Bypasses BGZF blocking, so must be used with care
+    #  in specialised circumstances only.
+    #
+    #  @param fp     BGZF file handler
+    #  @param data   data array to write
+    #  @param length number of raw bytes to write
+    #  @return       number of bytes actually written; -1 on error
+    ssize_t bgzf_raw_write(BGZF *fp, const void *data, size_t length)
+
+    #  Write the data in the buffer to the file.
+    int bgzf_flush(BGZF *fp)
+
+    int SEEK_SET
+
+    #  Return a virtual file pointer to the current location in the file.
+    #  No interpretation of the value should be made, other than a subsequent
+    #  call to bgzf_seek can be used to position the file at the same point.
+    #  Return value is non-negative on success.
+    int64_t bgzf_tell(BGZF *fp)
+
+    #  Set the file to read from the location specified by _pos_.
+    #
+    #  @param fp     BGZF file handler
+    #  @param pos    virtual file offset returned by bgzf_tell()
+    #  @param whence must be SEEK_SET
+    #  @return       0 on success and -1 on error
+    # /
+    int64_t bgzf_seek(BGZF *fp, int64_t pos, int whence)
+
+    #  Check if the BGZF end-of-file (EOF) marker is present
+    #
+    #  @param fp    BGZF file handler opened for reading
+    #  @return      1 if the EOF marker is present and correct
+    #               2 if it can't be checked, e.g., because fp isn't seekable
+    #               0 if the EOF marker is absent
+    #               -1 (with errno set) on error
+    int bgzf_check_EOF(BGZF *fp)
+
+    #  Check if a file is in the BGZF format
+    #
+    #  @param fn    file name
+    #  @return      1 if _fn_ is BGZF; 0 if not or on I/O error
+    int bgzf_is_bgzf(const char *fn)
+
+    #*********************
+    #  Advanced routines *
+    #*********************
+
+    #  Set the cache size. Only effective when compiled with -DBGZF_CACHE.
+    #
+    #  @param fp    BGZF file handler
+    #  @param size  size of cache in bytes; 0 to disable caching (default)
+    void bgzf_set_cache_size(BGZF *fp, int size)
+
+    #  Flush the file if the remaining buffer size is smaller than _size_
+    #  @return      0 if flushing succeeded or was not needed; negative on error
+    int bgzf_flush_try(BGZF *fp, ssize_t size)
+
+    #  Read one byte from a BGZF file. It is faster than bgzf_read()
+    #  @param fp     BGZF file handler
+    #  @return       byte read; -1 on end-of-file or error
+    int bgzf_getc(BGZF *fp)
+
+    #  Read one line from a BGZF file. It is faster than bgzf_getc()
+    #
+    #  @param fp     BGZF file handler
+    #  @param delim  delimiter
+    #  @param str    string to write to; must be initialized
+    #  @return       length of the string; 0 on end-of-file; negative on error
+    int bgzf_getline(BGZF *fp, int delim, kstring_t *str)
+
+    #  Read the next BGZF block.
+    int bgzf_read_block(BGZF *fp)
+
+    #  Enable multi-threading (only effective on writing and when the
+    #  library was compiled with -DBGZF_MT)
+    #
+    #  @param fp          BGZF file handler; must be opened for writing
+    #  @param n_threads   #threads used for writing
+    #  @param n_sub_blks  #blocks processed by each thread; a value 64-256 is recommended
+    int bgzf_mt(BGZF *fp, int n_threads, int n_sub_blks)
+
+
+    # Compress a single BGZF block.
+    #
+    # @param dst    output buffer (must have size >= BGZF_MAX_BLOCK_SIZE)
+    # @param dlen   size of output buffer; updated on return to the number
+    #               of bytes actually written to dst
+    # @param src    buffer to be compressed
+    # @param slen   size of data to compress (must be <= BGZF_BLOCK_SIZE)
+    # @param level  compression level
+    # @return       0 on success and negative on error
+    #
+    int bgzf_compress(void *dst, size_t *dlen, const void *src, size_t slen, int level)
+
+    #*******************
+    #  bgzidx routines *
+    #   BGZF at the uncompressed offset
+    #
+    #   @param fp           BGZF file handler; must be opened for reading
+    #   @param uoffset      file offset in the uncompressed data
+    #   @param where        SEEK_SET supported atm
+    #
+    #   Returns 0 on success and -1 on error.
+    int bgzf_useek(BGZF *fp, long uoffset, int where)
+
+    #   Position in uncompressed BGZF
+    #
+    #   @param fp           BGZF file handler; must be opened for reading
+    #
+    #   Returns the current offset on success and -1 on error.
+    long bgzf_utell(BGZF *fp)
+
+    #  Tell BGZF to build index while compressing.
+    #
+    #  @param fp          BGZF file handler; can be opened for reading or writing.
+    #
+    #  Returns 0 on success and -1 on error.
+    int bgzf_index_build_init(BGZF *fp)
+
+    #  Load BGZF index
+    #
+    #  @param fp          BGZF file handler
+    #  @param bname       base name
+    #  @param suffix      suffix to add to bname (can be NULL)
+    #
+    #  Returns 0 on success and -1 on error.
+    int bgzf_index_load(BGZF *fp, const char *bname, const char *suffix)
+
+    #  Save BGZF index
+    #
+    #  @param fp          BGZF file handler
+    #  @param bname       base name
+    #  @param suffix      suffix to add to bname (can be NULL)
+    #
+    #  Returns 0 on success and -1 on error.
+    int bgzf_index_dump(BGZF *fp, const char *bname, const char *suffix)
+
+
+cdef extern from "htslib/hts.h" nogil:
+    uint32_t kroundup32(uint32_t x)
+
+    ctypedef struct cram_fd
+
+    union FilePointerUnion:
+        BGZF    *bgzf
+        cram_fd *cram
+        hFILE   *hfile
+        void    *voidp
+
+    enum htsFormatCategory:
+        unknown_category
+        sequence_data    # Sequence data -- SAM, BAM, CRAM, etc
+        variant_data     # Variant calling data -- VCF, BCF, etc
+        index_file       # Index file associated with some data file
+        region_list      # Coordinate intervals or regions -- BED, etc
+        category_maximum
+
+    enum htsExactFormat:
+        unknown_format
+        binary_format
+        text_format
+        sam, bam, bai, cram, crai, vcf, bcf, csi, gzi, tbi, bed
+        format_maximum
+
+    enum htsCompression:
+        no_compression, gzip, bgzf, custom
+        compression_maximum
+
+    cdef enum hts_fmt_option:
+        CRAM_OPT_DECODE_MD,
+        CRAM_OPT_PREFIX,
+        CRAM_OPT_VERBOSITY,
+        CRAM_OPT_SEQS_PER_SLICE,
+        CRAM_OPT_SLICES_PER_CONTAINER,
+        CRAM_OPT_RANGE,
+        CRAM_OPT_VERSION,
+        CRAM_OPT_EMBED_REF,
+        CRAM_OPT_IGNORE_MD5,
+        CRAM_OPT_REFERENCE,
+        CRAM_OPT_MULTI_SEQ_PER_SLICE,
+        CRAM_OPT_NO_REF,
+        CRAM_OPT_USE_BZIP2,
+        CRAM_OPT_SHARED_REF,
+        CRAM_OPT_NTHREADS,
+        CRAM_OPT_THREAD_POOL,
+        CRAM_OPT_USE_LZMA,
+        CRAM_OPT_USE_RANS,
+        CRAM_OPT_REQUIRED_FIELDS,
+        HTS_OPT_COMPRESSION_LEVEL,
+        HTS_OPT_NTHREADS,
+
+    ctypedef struct htsVersion:
+        short major, minor
+
+    ctypedef struct htsFormat:
+        htsFormatCategory category
+        htsExactFormat    format
+        htsVersion        version
+        htsCompression    compression
+        short             compression_level
+        void              *specific  
+
+    ctypedef struct htsFile:
+        uint8_t  is_bin
+        uint8_t  is_write
+        uint8_t  is_be
+        uint8_t  is_cram
+        int64_t lineno
+        kstring_t line
+        char *fn
+        char *fn_aux
+        FilePointerUnion fp
+        htsFormat format
+
+    int hts_verbose
+
+    cdef union hts_opt_val_union:
+        int i
+        char *s
+
+    ctypedef struct hts_opt:
+        char *arg
+        hts_fmt_option opt
+        hts_opt_val_union val
+        void *next
+
+    # @abstract Parses arg and appends it to the option list.
+    # @return   0 on success and -1 on failure
+    int hts_opt_add(hts_opt **opts, const char *c_arg)
+
+    # @abstract Applies an hts_opt option list to a given htsFile.
+    # @return   0 on success and -1 on failure
+    int hts_opt_apply(htsFile *fp, hts_opt *opts)
+
+    # @abstract Frees an hts_opt list.
+    void hts_opt_free(hts_opt *opts)
+
+    # @abstract Table for converting a nucleotide character to 4-bit encoding.
+    # The input character may be either an IUPAC ambiguity code, '=' for 0, or
+    # '0'/'1'/'2'/'3' for a result of 1/2/4/8.  The result is encoded as 1/2/4/8
+    # for A/C/G/T or combinations of these bits for ambiguous bases.
+    const unsigned char *seq_nt16_table
+
+    # @abstract Table for converting a 4-bit encoded nucleotide to an IUPAC
+    # ambiguity code letter (or '=' when given 0).
+    const char *seq_nt16_str
+
+    # @abstract Table for converting a 4-bit encoded nucleotide to about 2 bits.
+    # Returns 0/1/2/3 for 1/2/4/8 (i.e., A/C/G/T), or 4 otherwise (0 or ambiguous).
+    const int *seq_nt16_int
+
+    # @abstract  Get the htslib version number
+    # @return    For released versions, a string like "N.N[.N]"; or git describe
+    # output if using a library built within a Git repository.
+    const char *hts_version()
+
+    # @abstract    Determine format by peeking at the start of a file
+    # @param fp    File opened for reading, positioned at the beginning
+    # @param fmt   Format structure that will be filled out on return
+    # @return      0 for success, or negative if an error occurred.
+    int hts_detect_format(hFILE *fp, htsFormat *fmt)
+
+    # @abstract    Get a human-readable description of the file format
+    # @return      Description string, to be freed by the caller after use.
+    char *hts_format_description(const htsFormat *format)
+
+    # @abstract       Open a SAM/BAM/CRAM/VCF/BCF/etc file
+    # @param fn       The file name or "-" for stdin/stdout
+    # @param mode     Mode matching / [rwa][bceguxz0-9]* /
+    # @discussion
+    #     With 'r' opens for reading; any further format mode letters are ignored
+    #     as the format is detected by checking the first few bytes or BGZF blocks
+    #     of the file.  With 'w' or 'a' opens for writing or appending, with format
+    #     specifier letters:
+    #       b  binary format (BAM, BCF, etc) rather than text (SAM, VCF, etc)
+    #       c  CRAM format
+    #       g  gzip compressed
+    #       u  uncompressed
+    #       z  bgzf compressed
+    #       [0-9]  zlib compression level
+    #     and with non-format option letters (for any of 'r'/'w'/'a'):
+    #       e  close the file on exec(2) (opens with O_CLOEXEC, where supported)
+    #       x  create the file exclusively (opens with O_EXCL, where supported)
+    #     Note that there is a distinction between 'u' and '0': the first yields
+    #     plain uncompressed output whereas the latter outputs uncompressed data
+    #     wrapped in the zlib format.
+    # @example
+    #     [rw]b  .. compressed BCF, BAM, FAI
+    #     [rw]bu .. uncompressed BCF
+    #     [rw]z  .. compressed VCF
+    #     [rw]   .. uncompressed VCF
+    htsFile *hts_open(const char *fn, const char *mode)
+
+    # @abstract       Open a SAM/BAM/CRAM/VCF/BCF/etc file
+    # @param fn       The file name or "-" for stdin/stdout
+    # @param mode     Open mode, as per hts_open()
+    # @param fmt      Optional format specific parameters
+    # @discussion
+    #     See hts_open() for description of fn and mode.
+    #     // TODO Update documentation for s/opts/fmt/
+    #     Opts contains a format string (sam, bam, cram, vcf, bcf) which will,
+    #     if defined, override mode.  Opts also contains a linked list of hts_opt
+    #     structures to apply to the open file handle.  These can contain things
+    #     like pointers to the reference or information on compression levels,
+    #     block sizes, etc.
+    htsFile *hts_open_format(const char *fn, const char *mode, const htsFormat *fmt)
+
+    # @abstract       Open an existing stream as a SAM/BAM/CRAM/VCF/BCF/etc file
+    # @param fp       The already-open file handle
+    # @param fn       The file name or "-" for stdin/stdout
+    # @param mode     Open mode, as per hts_open()
+    htsFile *hts_hopen(hFILE *fp, const char *fn, const char *mode)
+
+    # @abstract  Close a file handle, flushing buffered data for output streams
+    # @param fp  The file handle to be closed
+    # @return    0 for success, or negative if an error occurred.
+    int hts_close(htsFile *fp)
+
+    # @abstract  Returns the file's format information
+    # @param fp  The file handle
+    # @return    Read-only pointer to the file's htsFormat.
+    const htsFormat *hts_get_format(htsFile *fp)
+
+    # @ abstract      Returns a string containing the file format extension.
+    # @ param format  Format structure containing the file type.
+    # @ return        A string ("sam", "bam", etc) or "?" for unknown formats.
+    const char *hts_format_file_extension(const htsFormat *format)
+
+    # @abstract  Sets a specified CRAM option on the open file handle.
+    # @param fp  The file handle open the open file.
+    # @param opt The CRAM_OPT_* option.
+    # @param ... Optional arguments, dependent on the option used.
+    # @return    0 for success, or negative if an error occurred.
+    int hts_set_opt(htsFile *fp, hts_fmt_option opt, ...)
+
+    int hts_getline(htsFile *fp, int delimiter, kstring_t *str)
+    char **hts_readlines(const char *fn, int *_n)
+
+    #   @abstract       Parse comma-separated list or read list from a file
+    #   @param list     File name or comma-separated list
+    #   @param is_file
+    #   @param _n       Size of the output array (number of items read)
+    #   @return         NULL on failure or pointer to newly allocated array of
+    #                   strings
+    char **hts_readlist(const char *fn, int is_file, int *_n)
+
+    # @abstract  Create extra threads to aid compress/decompression for this file
+    # @param fp  The file handle
+    # @param n   The number of worker threads to create
+    # @return    0 for success, or negative if an error occurred.
+    # @notes     THIS THREADING API IS LIKELY TO CHANGE IN FUTURE.
+    int hts_set_threads(htsFile *fp, int n)
+
+    # @abstract  Set .fai filename for a file opened for reading
+    # @return    0 for success, negative on failure
+    # @discussion
+    #     Called before *_hdr_read(), this provides the name of a .fai file
+    #     used to provide a reference list if the htsFile contains no @SQ headers.
+    int hts_set_fai_filename(htsFile *fp, const char *fn_aux)
+
+    int8_t HTS_IDX_NOCOOR
+    int8_t HTS_IDX_START
+    int8_t HTS_IDX_REST
+    int8_t HTS_IDX_NONE
+
+    int8_t HTS_FMT_CSI
+    int8_t HTS_FMT_BAI
+    int8_t HTS_FMT_TBI
+    int8_t HTS_FMT_CRAI
+
+    BGZF *hts_get_bgzfp(htsFile *fp)
+
+    ctypedef struct hts_idx_t
+
+    ctypedef struct hts_pair64_t:
+        uint64_t u, v
+
+    ctypedef int hts_readrec_func(BGZF *fp, void *data, void *r, int *tid, int *beg, int *end)
+
+    ctypedef struct hts_bins_t:
+        int n, m
+        int *a
+
+    ctypedef struct hts_itr_t:
+        uint32_t read_rest
+        uint32_t finished
+        int tid, bed, end, n_off, i
+        int curr_tid, curr_beg, curr_end
+        uint64_t curr_off
+        hts_pair64_t *off
+        hts_readrec_func *readfunc
+        hts_bins_t bins
+
+    hts_idx_t *hts_idx_init(int n, int fmt, uint64_t offset0, int min_shift, int n_lvls)
+    void hts_idx_destroy(hts_idx_t *idx)
+    int hts_idx_push(hts_idx_t *idx, int tid, int beg, int end, uint64_t offset, int is_mapped)
+    void hts_idx_finish(hts_idx_t *idx, uint64_t final_offset)
+
+    #### Save an index to a file
+    #    @param idx  Index to be written
+    #    @param fn   Input BAM/BCF/etc filename, to which .bai/.csi/etc will be added
+    #    @param fmt  One of the HTS_FMT_* index formats
+    #    @return  0 if successful, or negative if an error occurred.
+    int hts_idx_save(const hts_idx_t *idx, const char *fn, int fmt)
+
+    #### Save an index to a specific file
+    #    @param idx    Index to be written
+    #    @param fn     Input BAM/BCF/etc filename
+    #    @param fnidx  Output filename, or NULL to add .bai/.csi/etc to @a fn
+    #    @param fmt    One of the HTS_FMT_* index formats
+    #    @return  0 if successful, or negative if an error occurred.
+    int hts_idx_save_as(const hts_idx_t *idx, const char *fn, const char *fnidx, int fmt)
+
+    #### Load an index file
+    #    @param fn   BAM/BCF/etc filename, to which .bai/.csi/etc will be added or
+    #                the extension substituted, to search for an existing index file
+    #    @param fmt  One of the HTS_FMT_* index formats
+    #    @return  The index, or NULL if an error occurred.
+    hts_idx_t *hts_idx_load(const char *fn, int fmt)
+
+    #### Load a specific index file
+    #    @param fn     Input BAM/BCF/etc filename
+    #    @param fnidx  The input index filename
+    #    @return  The index, or NULL if an error occurred.
+    hts_idx_t *hts_idx_load2(const char *fn, const char *fnidx)
+
+    uint8_t *hts_idx_get_meta(hts_idx_t *idx, uint32_t *l_meta)
+    void hts_idx_set_meta(hts_idx_t *idx, int l_meta, uint8_t *meta, int is_copy)
+
+    int hts_idx_get_stat(const hts_idx_t* idx, int tid,
+                         uint64_t* mapped, uint64_t* unmapped)
+
+    uint64_t hts_idx_get_n_no_coor(const hts_idx_t* idx)
+
+    int HTS_PARSE_THOUSANDS_SEP  # Ignore ',' separators within numbers
+
+    # Parse a numeric string
+    #    The number may be expressed in scientific notation, and optionally may
+    #    contain commas in the integer part (before any decimal point or E notation).
+    #    @param str     String to be parsed
+    #    @param strend  If non-NULL, set on return to point to the first character
+    #                   in @a str after those forming the parsed number
+    #    @param flags   Or'ed-together combination of HTS_PARSE_* flags
+    #    @return  Converted value of the parsed number.
+    #
+    #    When @a strend is NULL, a warning will be printed (if hts_verbose is 2
+    #    or more) if there are any trailing characters after the number.
+    long long hts_parse_decimal(const char *str, char **strend, int flags)
+
+    # Parse a "CHR:START-END"-style region string
+    #    @param str  String to be parsed
+    #    @param beg  Set on return to the 0-based start of the region
+    #    @param end  Set on return to the 1-based end of the region
+    #    @return  Pointer to the colon or '\0' after the reference sequence name,
+    #             or NULL if @a str could not be parsed.
+    const char *hts_parse_reg(const char *str, int *beg, int *end)
+
+    hts_itr_t *hts_itr_query(const hts_idx_t *idx, int tid, int beg, int end, hts_readrec_func *readrec)
+    void hts_itr_destroy(hts_itr_t *iter)
+
+    ctypedef int (*hts_name2id_f)(void*, const char*)
+    ctypedef const char *(*hts_id2name_f)(void*, int)
+    ctypedef hts_itr_t *hts_itr_query_func(
+        const hts_idx_t *idx,
+        int tid,
+        int beg,
+        int end,
+        hts_readrec_func *readrec)
+
+    hts_itr_t *hts_itr_querys(
+        const hts_idx_t *idx,
+        const char *reg,
+        hts_name2id_f getid,
+        void *hdr,
+        hts_itr_query_func *itr_query,
+        hts_readrec_func *readrec)
+
+    int hts_itr_next(BGZF *fp, hts_itr_t *iter, void *r, void *data)
+    const char **hts_idx_seqnames(const hts_idx_t *idx, int *n, hts_id2name_f getid, void *hdr)  # free only the array, not the values
+
+    # hts_file_type() - Convenience function to determine file type
+    # @fname: the file name
+    #
+    # Returns one of the FT_* defines.
+    #
+    # DEPRECATED:  This function has been replaced by hts_detect_format().
+    # It and these FT_* macros will be removed in a future HTSlib release.
+    int FT_UNKN
+    int FT_GZ
+    int FT_VCF
+    int FT_VCF_GZ
+    int FT_BCF
+    int FT_BCF_GZ
+    int FT_STDIN
+
+    int hts_file_type(const char *fname)
+
+    # /***************************
+    #  * Revised MAQ error model *
+    #  ***************************/
+
+    ctypedef struct errmod_t
+
+    errmod_t *errmod_init(double depcorr)
+    void errmod_destroy(errmod_t *em)
+
+    # /*
+    #     n: number of bases
+    #     m: maximum base
+    #     bases[i]: qual:6, strand:1, base:4
+    #     q[i*m+j]: phred-scaled likelihood of (i,j)
+    #  */
+    int errmod_cal(const errmod_t *em, int n, int m, uint16_t *bases, float *Probabilistic)
+
+    # /*****************************************
+    #  * q banded glocal alignment *
+    #  *****************************************/
+
+    ctypedef struct probaln_par_t:
+        float d, e
+        int bw
+
+    int probaln_glocal(const uint8_t *ref,
+                       int l_ref,
+                       const uint8_t *query,
+                       int l_query, const uint8_t *iqual,
+                       const probaln_par_t *c,
+                       int *state, uint8_t *q)
+
+    # /**********************
+    #  * MD5 implementation *
+    #  **********************/
+
+    ctypedef struct hts_md5_context
+
+    # /*! @abstract   Initialises an MD5 context.
+    #  *  @discussion
+    #  *    The expected use is to allocate an hts_md5_context using
+    #  *    hts_md5_init().  This pointer is then passed into one or more calls
+    #  *    of hts_md5_update() to compute successive internal portions of the
+    #  *    MD5 sum, which can then be externalised as a full 16-byte MD5sum
+    #  *    calculation by calling hts_md5_final().  This can then be turned
+    #  *    into ASCII via hts_md5_hex().
+    #  *
+    #  *    To dealloate any resources created by hts_md5_init() call the
+    #  *    hts_md5_destroy() function.
+    #  *
+    #  *  @return     hts_md5_context pointer on success, NULL otherwise.
+    #  */
+    hts_md5_context *hts_md5_init()
+
+    # /*! @abstract Updates the context with the MD5 of the data. */
+    void hts_md5_update(hts_md5_context *ctx, const void *data, unsigned long size)
+
+    # /*! @abstract Computes the final 128-bit MD5 hash from the given context */
+    void hts_md5_final(unsigned char *digest, hts_md5_context *ctx)
+
+    # /*! @abstract Resets an md5_context to the initial state, as returned
+    #  *            by hts_md5_init().
+    #  */
+    void hts_md5_reset(hts_md5_context *ctx)
+
+    # /*! @abstract Converts a 128-bit MD5 hash into a 33-byte nul-termninated
+    #  *            hex string.
+    #  */
+    void hts_md5_hex(char *hex, const unsigned char *digest)
+
+    # /*! @abstract Deallocates any memory allocated by hts_md5_init. */
+    void hts_md5_destroy(hts_md5_context *ctx)
+
+    int hts_reg2bin(int64_t beg, int64_t end, int min_shift, int n_lvls)
+    int hts_bin_bot(int bin, int n_lvls)
+
+    # * Endianness *
+    int ed_is_big()
+    uint16_t ed_swap_2(uint16_t v)
+    void *ed_swap_2p(void *x)
+    uint32_t ed_swap_4(uint32_t v)
+    void *ed_swap_4p(void *x)
+    uint64_t ed_swap_8(uint64_t v)
+    void *ed_swap_8p(void *x)
+
+
+cdef extern from "htslib/sam.h" nogil:
+    #**********************
+    #*** SAM/BAM header ***
+    #**********************
+
+    # @abstract Structure for the alignment header.
+    # @field n_targets   number of reference sequences
+    # @field l_text      length of the plain text in the header
+    # @field target_len  lengths of the reference sequences
+    # @field target_name names of the reference sequences
+    # @field text        plain text
+    # @field sdict       header dictionary
+
+    ctypedef struct bam_hdr_t:
+         int32_t n_targets, ignore_sam_err
+         uint32_t l_text
+         uint32_t *target_len
+         uint8_t *cigar_tab
+         char **target_name
+         char *text
+         void *sdict
+
+    #****************************
+    #*** CIGAR related macros ***
+    #****************************
+
+    int BAM_CMATCH
+    int BAM_CINS
+    int BAM_CDEL
+    int BAM_CREF_SKIP
+    int BAM_CSOFT_CLIP
+    int BAM_CHARD_CLIP
+    int BAM_CPAD
+    int BAM_CEQUAL
+    int BAM_CDIFF
+    int BAM_CBACK
+
+    char    *BAM_CIGAR_STR
+    int      BAM_CIGAR_SHIFT
+    uint32_t BAM_CIGAR_MASK
+    uint32_t BAM_CIGAR_TYPE
+
+    char bam_cigar_op(uint32_t c)
+    uint32_t bam_cigar_oplen(uint32_t c)
+    char bam_cigar_opchr(uint32_t)
+    uint32_t bam_cigar_gen(char, uint32_t)
+    int bam_cigar_type(char o)
+
+    # @abstract the read is paired in sequencing, no matter whether it is mapped in a pair
+    int BAM_FPAIRED
+    # @abstract the read is mapped in a proper pair
+    int BAM_FPROPER_PAIR
+    # @abstract the read itself is unmapped; conflictive with BAM_FPROPER_PAIR
+    int BAM_FUNMAP
+    # @abstract the mate is unmapped
+    int BAM_FMUNMAP
+    # @abstract the read is mapped to the reverse strand
+    int BAM_FREVERSE
+    # @abstract the mate is mapped to the reverse strand
+    int BAM_FMREVERSE
+    # @abstract this is read1
+    int BAM_FREAD1
+    # @abstract this is read2
+    int BAM_FREAD2
+    # @abstract not primary alignment
+    int BAM_FSECONDARY
+    # @abstract QC failure
+    int BAM_FQCFAIL
+    # @abstract optical or PCR duplicate
+    int BAM_FDUP
+    # @abstract supplementary alignment
+    int BAM_FSUPPLEMENTARY
+
+    #*************************
+    #*** Alignment records ***
+    #*************************
+
+    # @abstract Structure for core alignment information.
+    # @field  tid     chromosome ID, defined by bam_hdr_t
+    # @field  pos     0-based leftmost coordinate
+    # @field  bin     bin calculated by bam_reg2bin()
+    # @field  qual    mapping quality
+    # @field  l_qname length of the query name
+    # @field  flag    bitwise flag
+    # @field  n_cigar number of CIGAR operations
+    # @field  l_qseq  length of the query sequence (read)
+    # @field  mtid    chromosome ID of next read in template, defined by bam_hdr_t
+    # @field  mpos    0-based leftmost coordinate of next read in template
+
+    ctypedef struct bam1_core_t:
+        int32_t tid
+        int32_t pos
+        uint16_t bin
+        uint8_t qual
+        uint8_t l_qname
+        uint16_t flag
+        uint8_t unused1
+        uint8_t l_extranul
+        uint32_t n_cigar
+        int32_t l_qseq
+        int32_t mtid
+        int32_t mpos
+        int32_t isize
+
+    # @abstract Structure for one alignment.
+    # @field  core       core information about the alignment
+    # @field  l_data     current length of bam1_t::data
+    # @field  m_data     maximum length of bam1_t::data
+    # @field  data       all variable-length data, concatenated; structure: qname-cigar-seq-qual-aux
+    #
+    # @discussion Notes:
+    #
+    # 1. qname is zero tailing and core.l_qname includes the tailing '\0'.
+    # 2. l_qseq is calculated from the total length of an alignment block
+    # on reading or from CIGAR.
+    # 3. cigar data is encoded 4 bytes per CIGAR operation.
+    # 4. seq is nybble-encoded according to seq_nt16_table.
+    ctypedef struct bam1_t:
+        bam1_core_t core
+        int l_data
+        uint32_t m_data
+        uint8_t *data
+        uint64_t id
+
+    # @abstract  Get whether the query is on the reverse strand
+    # @param  b  pointer to an alignment
+    # @return    boolean true if query is on the reverse strand
+    int bam_is_rev(bam1_t *b)
+
+    # @abstract  Get whether the query's mate is on the reverse strand
+    # @param  b  pointer to an alignment
+    # @return    boolean true if query's mate on the reverse strand
+    int bam_is_mrev(bam1_t *b)
+
+    # @abstract  Get the name of the query
+    # @param  b  pointer to an alignment
+    # @return    pointer to the name string, null terminated
+    char *bam_get_qname(bam1_t *b)
+
+    # @abstract  Get the CIGAR array
+    # @param  b  pointer to an alignment
+    # @return    pointer to the CIGAR array
+    #
+    # @discussion In the CIGAR array, each element is a 32-bit integer. The
+    # lower 4 bits gives a CIGAR operation and the higher 28 bits keep the
+    # length of a CIGAR.
+    uint32_t *bam_get_cigar(bam1_t *b)
+
+    # @abstract  Get query sequence
+    # @param  b  pointer to an alignment
+    # @return    pointer to sequence
+    #
+    # @discussion Each base is encoded in 4 bits: 1 for A, 2 for C, 4 for G,
+    # 8 for T and 15 for N. Two bases are packed in one byte with the base
+    # at the higher 4 bits having smaller coordinate on the read. It is
+    # recommended to use bam_seqi() macro to get the base.
+    char *bam_get_seq(bam1_t *b)
+
+    # @abstract  Get query quality
+    # @param  b  pointer to an alignment
+    # @return    pointer to quality string
+    uint8_t *bam_get_qual(bam1_t *b)
+
+    # @abstract  Get auxiliary data
+    # @param  b  pointer to an alignment
+    # @return    pointer to the concatenated auxiliary data
+    uint8_t *bam_get_aux(bam1_t *b)
+
+    # @abstract  Get length of auxiliary data
+    # @param  b  pointer to an alignment
+    # @return    length of the concatenated auxiliary data
+    int bam_get_l_aux(bam1_t *b)
+
+    # @abstract  Get a base on read
+    # @param  s  Query sequence returned by bam1_seq()
+    # @param  i  The i-th position, 0-based
+    # @return    4-bit integer representing the base.
+    char bam_seqi(char *s, int i)
+
+    #**************************
+    #*** Exported functions ***
+    #**************************
+
+    #***************
+    #*** BAM I/O ***
+    #***************
+
+    bam_hdr_t *bam_hdr_init()
+    bam_hdr_t *bam_hdr_read(BGZF *fp)
+    int bam_hdr_write(BGZF *fp, const bam_hdr_t *h)
+    void bam_hdr_destroy(bam_hdr_t *h)
+    int bam_name2id(bam_hdr_t *h, const char *ref)
+    bam_hdr_t* bam_hdr_dup(const bam_hdr_t *h0)
+
+    bam1_t *bam_init1()
+    void bam_destroy1(bam1_t *b)
+    int bam_read1(BGZF *fp, bam1_t *b)
+    int bam_write1(BGZF *fp, const bam1_t *b)
+    bam1_t *bam_copy1(bam1_t *bdst, const bam1_t *bsrc)
+    bam1_t *bam_dup1(const bam1_t *bsrc)
+
+    int bam_cigar2qlen(int n_cigar, const uint32_t *cigar)
+    int bam_cigar2rlen(int n_cigar, const uint32_t *cigar)
+
+    # @abstract Calculate the rightmost base position of an alignment on the
+    # reference genome.
+
+    # @param  b  pointer to an alignment
+    # @return    the coordinate of the first base after the alignment, 0-based
+
+    # @discussion For a mapped read, this is just b->core.pos + bam_cigar2rlen.
+    # For an unmapped read (either according to its flags or if it has no cigar
+    # string), we return b->core.pos + 1 by convention.
+    int32_t bam_endpos(const bam1_t *b)
+
+    int   bam_str2flag(const char *str)  # returns negative value on error
+    char *bam_flag2str(int flag)         # The string must be freed by the user
+
+    #*************************
+    #*** BAM/CRAM indexing ***
+    #*************************
+
+    # These BAM iterator functions work only on BAM files.  To work with either
+    # BAM or CRAM files use the sam_index_load() & sam_itr_*() functions.
+    void bam_itr_destroy(hts_itr_t *iter)
+    hts_itr_t *bam_itr_queryi(const hts_idx_t *idx, int tid, int beg, int end)
+    hts_itr_t *bam_itr_querys(const hts_idx_t *idx, bam_hdr_t *hdr, const char *region)
+    int bam_itr_next(htsFile *htsfp, hts_itr_t *itr, void *r)
+
+    # Load/build .csi or .bai BAM index file.  Does not work with CRAM.
+    # It is recommended to use the sam_index_* functions below instead.
+    hts_idx_t *bam_index_load(const char *fn)
+    int bam_index_build(const char *fn, int min_shift)
+
+    # Load a BAM (.csi or .bai) or CRAM (.crai) index file
+    # @param fp  File handle of the data file whose index is being opened
+    # @param fn  BAM/CRAM/etc filename to search alongside for the index file
+    # @return  The index, or NULL if an error occurred.
+    hts_idx_t *sam_index_load(htsFile *fp, const char *fn)
+
+    # Load a specific BAM (.csi or .bai) or CRAM (.crai) index file
+    # @param fp     File handle of the data file whose index is being opened
+    # @param fn     BAM/CRAM/etc data file filename
+    # @param fnidx  Index filename, or NULL to search alongside @a fn
+    # @return  The index, or NULL if an error occurred.
+    hts_idx_t *sam_index_load2(htsFile *fp, const char *fn, const char *fnidx)
+
+    # Generate and save an index file
+    # @param fn        Input BAM/etc filename, to which .csi/etc will be added
+    # @param min_shift Positive to generate CSI, or 0 to generate BAI
+    # @return  0 if successful, or negative if an error occurred (usually -1; or
+    #         -2: opening fn failed; -3: format not indexable)
+    int sam_index_build(const char *fn, int min_shift)
+
+    # Generate and save an index to a specific file
+    # @param fn        Input BAM/CRAM/etc filename
+    # @param fnidx     Output filename, or NULL to add .bai/.csi/etc to @a fn
+    # @param min_shift Positive to generate CSI, or 0 to generate BAI
+    # @return  0 if successful, or negative if an error occurred.
+    int sam_index_build2(const char *fn, const char *fnidx, int min_shift)
+
+    void sam_itr_destroy(hts_itr_t *iter)
+    hts_itr_t *sam_itr_queryi(const hts_idx_t *idx, int tid, int beg, int end)
+    hts_itr_t *sam_itr_querys(const hts_idx_t *idx, bam_hdr_t *hdr, const char *region)
+    int sam_itr_next(htsFile *htsfp, hts_itr_t *itr, void *r)
+
+    #***************
+    #*** SAM I/O ***
+    #***************
+
+    htsFile *sam_open(const char *fn, const char *mode)
+    htsFile *sam_open_format(const char *fn, const char *mode, const htsFormat *fmt)
+    int sam_close(htsFile *fp)
+
+    int sam_open_mode(char *mode, const char *fn, const char *format)
+
+    # A version of sam_open_mode that can handle ,key=value options.
+    # The format string is allocated and returned, to be freed by the caller.
+    # Prefix should be "r" or "w",
+    char *sam_open_mode_opts(const char *fn, const char *mode, const char *format)
+
+    bam_hdr_t *sam_hdr_parse(int l_text, const char *text)
+    bam_hdr_t *sam_hdr_read(htsFile *fp)
+    int sam_hdr_write(htsFile *fp, const bam_hdr_t *h)
+
+    int sam_parse1(kstring_t *s, bam_hdr_t *h, bam1_t *b)
+    int sam_format1(const bam_hdr_t *h, const bam1_t *b, kstring_t *str)
+    int sam_read1(htsFile *fp, bam_hdr_t *h, bam1_t *b)
+    int sam_write1(htsFile *fp, const bam_hdr_t *h, const bam1_t *b)
+
+    #*************************************
+    #*** Manipulating auxiliary fields ***
+    #*************************************
+
+    uint8_t *bam_aux_get(const bam1_t *b, const char *tag)
+    int64_t  bam_aux2i(const uint8_t *s)
+    double   bam_aux2f(const uint8_t *s)
+    char     bam_aux2A(const uint8_t *s)
+    char    *bam_aux2Z(const uint8_t *s)
+
+    void bam_aux_append(bam1_t *b, const char *tag, char type, int len, uint8_t *data)
+    int bam_aux_del(bam1_t *b, uint8_t *s)
+
+    #**************************
+    #*** Pileup and Mpileup ***
+    #**************************
+
+    #  @abstract Generic pileup 'client data'.
+    #  @discussion The pileup iterator allows setting a constructor and
+    #  destructor function, which will be called every time a sequence is
+    #  fetched and discarded.  This permits caching of per-sequence data in
+    #  a tidy manner during the pileup process.  This union is the cached
+    #  data to be manipulated by the "client" (the caller of pileup).
+    # 
+    union bam_pileup_cd:
+        void *p
+        int64_t i
+        double f
+
+    # @abstract Structure for one alignment covering the pileup position.
+    # @field  b          pointer to the alignment
+    # @field  qpos       position of the read base at the pileup site, 0-based
+    # @field  indel      indel length; 0 for no indel, positive for ins and negative for del
+    # @field  level      the level of the read in the "viewer" mode
+    # @field  is_del     1 iff the base on the padded read is a deletion
+    # @field  is_head    ???
+    # @field  is_tail    ???
+    # @field  is_refskip ???
+    # @field  aux        ???
+    #
+    # @discussion See also bam_plbuf_push() and bam_lplbuf_push(). The
+    # difference between the two functions is that the former does not
+    # set bam_pileup1_t::level, while the later does. Level helps the
+    # implementation of alignment viewers, but calculating this has some
+    # overhead.
+    #
+    # is_del, is_head, etc are a bit field, declaring as below should
+    # work as expected, see
+    # https://groups.google.com/forum/#!msg/cython-users/24tD1kwRY7A/pmoPuSmanM0J
+
+    ctypedef struct bam_pileup1_t:
+        bam1_t *b
+        int32_t qpos
+        int indel, level
+        uint32_t is_del
+        uint32_t is_head
+        uint32_t is_tail
+        uint32_t is_refskip
+        uint32_t aux
+        bam_pileup_cd cd
+
+    ctypedef int (*bam_plp_auto_f)(void *data, bam1_t *b)
+    ctypedef int (*bam_test_f)()
+
+    ctypedef struct __bam_plp_t
+    ctypedef __bam_plp_t *bam_plp_t
+
+    ctypedef struct __bam_mplp_t
+    ctypedef __bam_mplp_t *bam_mplp_t
+
+    # bam_plp_init() - sets an iterator over multiple
+    # @func:      see mplp_func in bam_plcmd.c in samtools for an example. Expected return
+    #             status: 0 on success, -1 on end, < -1 on non-recoverable errors
+    # @data:      user data to pass to @func
+    bam_plp_t bam_plp_init(bam_plp_auto_f func, void *data)
+    void bam_plp_destroy(bam_plp_t iter)
+    int bam_plp_push(bam_plp_t iter, const bam1_t *b)
+    const bam_pileup1_t *bam_plp_next(bam_plp_t iter, int *_tid, int *_pos, int *_n_plp)
+    const bam_pileup1_t *bam_plp_auto(bam_plp_t iter, int *_tid, int *_pos, int *_n_plp)
+    void bam_plp_set_maxcnt(bam_plp_t iter, int maxcnt)
+    void bam_plp_reset(bam_plp_t iter)
+
+    bam_mplp_t bam_mplp_init(int n, bam_plp_auto_f func, void **data)
+
+    # bam_mplp_init_overlaps() - if called, mpileup will detect overlapping
+    # read pairs and for each base pair set the base quality of the
+    # lower-quality base to zero, thus effectively discarding it from
+    # calling. If the two bases are identical, the quality of the other base
+    # is increased to the sum of their qualities (capped at 200), otherwise
+    # it is multiplied by 0.8.
+    void bam_mplp_init_overlaps(bam_mplp_t iter)
+    void bam_mplp_destroy(bam_mplp_t iter)
+    void bam_mplp_set_maxcnt(bam_mplp_t iter, int maxcnt)
+    int bam_mplp_auto(bam_mplp_t iter, int *_tid, int *_pos, int *n_plp, const bam_pileup1_t **plp)
+    void bam_mplp_reset(bam_mplp_t iter)
+    void bam_mplp_constructor(bam_mplp_t iter,
+          		      int (*func)(void *data, const bam1_t *b, bam_pileup_cd *cd))
+    void bam_mplp_destructor(bam_mplp_t iter,
+			     int (*func)(void *data, const bam1_t *b, bam_pileup_cd *cd))
+    
+    # Added by AH
+    # ctypedef bam_pileup1_t * const_bam_pileup1_t_ptr "const bam_pileup1_t *"
+
+
+
+
+    # // ---------------------------
+    # // Base modification retrieval
+
+    # /*! @typedef
+    #  @abstract Holds a single base modification.
+    #  @field modified_base     The short base code (m, h, etc) or -ChEBI (negative)
+    #  @field canonical_base    The canonical base referred to in the MM tag.
+    #                           One of A, C, G, T or N.  Note this may not be the
+    #                           explicit base recorded in the SEQ column (esp. if N).
+    #  @field strand            0 or 1, indicating + or - strand from MM tag.
+    #  @field qual              Quality code (256*probability), or -1 if unknown
+
+    #  @discussion
+    #  Note this doesn't hold any location data or information on which other
+    #  modifications may be possible at this site.
+    ctypedef struct hts_base_mod:
+        int modified_base
+        int canonical_base
+        int strand
+        int qual
+
+    # /// Allocates an hts_base_mode_state.
+    # /**
+    # * @return An hts_base_mode_state pointer on success,
+    # *         NULL on failure.
+    # *
+    # * This just allocates the memory.  The initialisation of the contents is
+    # * done using bam_parse_basemod.  Successive calls may be made to that
+    # * without the need to free and allocate a new state.
+    # *
+    # * The state be destroyed using the hts_base_mode_state_free function.
+    # */
+    ctypedef struct hts_base_mod_state 
+    hts_base_mod_state *hts_base_mod_state_alloc()
+
+
+    # /// Destroys an  hts_base_mode_state.
+    # /**
+    # * @param state    The base modification state pointer.
+    # *
+    # * The should have previously been created by hts_base_mode_state_alloc.
+    # */
+    void hts_base_mod_state_free(hts_base_mod_state *state)
+
+    # /// Parses the Mm and Ml tags out of a bam record.
+    # /**
+    # * @param b        BAM alignment record
+    # * @param state    The base modification state pointer.
+    # * @return 0 on success,
+    # *         -1 on failure.
+    # *
+    # * This fills out the contents of the modification state, resetting the
+    # * iterator location to the first sequence base.
+    # */
+    int bam_parse_basemod(const bam1_t *b, hts_base_mod_state *state)
+
+    # /// Finds the next location containing base modifications and returns them
+    # /**
+    # * @param b        BAM alignment record
+    # * @param state    The base modification state pointer.
+    # * @param mods     A supplied array for returning base modifications
+    # * @param n_mods   The size of the mods array
+    # * @return The number of modifications found on success,
+    # *         0 if no more modifications are present,
+    # *         -1 on failure.
+    # *
+    # * Unlike bam_mods_at_next_pos this skips ahead to the next site
+    # * with modifications.
+    # *
+    # * If more than n_mods modifications are found, the total found is returned.
+    # * Note this means the caller needs to check whether this is higher than
+    # * n_mods.
+    # */
+
+    int bam_next_basemod(const bam1_t *b, hts_base_mod_state *state,hts_base_mod *mods, int n_mods, int *pos)
+
+    # ***********************************
+    # * BAQ calculation and realignment *
+    # ***********************************/
+    int sam_cap_mapq(bam1_t *b, const char *ref, int ref_len, int thres)
+    int sam_prob_realn(bam1_t *b, const char *ref, int ref_len, int flag)
+
+
+cdef extern from "htslib/faidx.h" nogil:
+
+    ctypedef struct faidx_t:
+       pass
+
+    # /// Build index for a FASTA or bgzip-compressed FASTA file.
+    # /**  @param  fn  FASTA file name
+    # @param  fnfai Name of .fai file to build.
+    # @param  fngzi Name of .gzi file to build (if fn is bgzip-compressed).
+    # @return     0 on success; or -1 on failure
+
+    # If fnfai is NULL, ".fai" will be appended to fn to make the FAI file name.
+    # If fngzi is NULL, ".gzi" will be appended to fn for the GZI file.  The GZI
+    # file will only be built if fn is bgzip-compressed.
+    # */
+    int fai_build3(const char *fn,
+                   const char *fnfai,
+                   const char *fngzi)
+
+    # /// Build index for a FASTA or bgzip-compressed FASTA file.
+    # /** @param  fn  FASTA file name
+    # @return     0 on success; or -1 on failure
+    #
+    # File "fn.fai" will be generated.  This function is equivalent to
+    # fai_build3(fn, NULL, NULL);
+    # */
+    int fai_build(char *fn)
+
+    # /// Destroy a faidx_t struct
+    void fai_destroy(faidx_t *fai)
+
+    # /// Load FASTA indexes.
+    # /** @param  fn  File name of the FASTA file (can be compressed with bgzip).
+    #     @param  fnfai File name of the FASTA index.
+    #     @param  fngzi File name of the bgzip index.
+    #     @param  flags Option flags to control index file caching and creation.
+    #     @return Pointer to a faidx_t struct on success, NULL on failure.
+    
+    # If fnfai is NULL, ".fai" will be appended to fn to make the FAI file name.
+    # If fngzi is NULL, ".gzi" will be appended to fn for the bgzip index name.
+    # The bgzip index is only needed if fn is compressed.
+    
+    # If (flags & FAI_CREATE) is true, the index files will be built using
+    # fai_build3() if they are not already present.
+    # */
+    faidx_t *fai_load3(const char *fn,
+                       const char *fnfai,
+                       const char *fngzi,
+                       int flags)
+
+    # /// Load index from "fn.fai".
+    # /** @param  fn  File name of the FASTA file
+    #     @return Pointer to a faidx_t struct on success, NULL on failure.
+    # This function is equivalent to fai_load3(fn, NULL, NULL, FAI_CREATE|FAI_CACHE);
+    # */
+    faidx_t *fai_load(char *fn)
+
+    # /// Fetch the sequence in a region
+    # /** @param  fai  Pointer to the faidx_t struct
+    #     @param  reg  Region in the format "chr2:20,000-30,000"
+    #     @param  len  Length of the region; -2 if seq not present, -1 general error
+    #     @return      Pointer to the sequence; `NULL` on failure
+    # The returned sequence is allocated by `malloc()` family and should be destroyed
+    # by end users by calling `free()` on it.
+    # */
+    char *fai_fetch(faidx_t *fai,
+                    char *reg,
+                    int *len)
+
+    # /// Fetch the sequence in a region
+    # /** @param  fai  Pointer to the faidx_t struct
+    #     @param  c_name Region name
+    #     @param  p_beg_i  Beginning position number (zero-based)
+    #     @param  p_end_i  End position number (zero-based)
+    #     @param  len  Length of the region; -2 if c_name not present, -1 general error
+    #     @return      Pointer to the sequence; null on failure
+    # The returned sequence is allocated by `malloc()` family and should be destroyed
+    # by end users by calling `free()` on it.
+    # */
+    char *faidx_fetch_seq(faidx_t *fai,
+                         char *c_name,
+                         int p_beg_i,
+                         int p_end_i,
+                         int *len)
+
+    # /// Query if sequence is present
+    # /**   @param  fai  Pointer to the faidx_t struct
+    #   @param  seq  Sequence name
+    #   @return      1 if present or 0 if absent
+    #   */
+    int faidx_has_seq(faidx_t *fai, const char *seq)
+
+    # /// Fetch the number of sequences
+    # /** @param  fai  Pointer to the faidx_t struct
+    # @return      The number of sequences
+    # */
+    int faidx_nseq(const faidx_t *fai)
+
+    # /// Return name of i-th sequence
+    const char *faidx_iseq(const faidx_t *fai, int i)
+
+    # /// Return sequence length, -1 if not present
+    int faidx_seq_len(faidx_t *fai, const char *seq)
+
+# tabix support
+cdef extern from "htslib/tbx.h" nogil:
+
+    # tbx.h definitions
+    int8_t TBX_MAX_SHIFT
+    int32_t TBX_GENERIC
+    int32_t TBX_SAM
+    int32_t TBX_VCF
+    int32_t TBX_UCSC
+
+    ctypedef struct tbx_conf_t:
+        int32_t preset
+        int32_t sc, bc, ec   # seq col., beg col. and end col.
+        int32_t meta_char, line_skip
+
+    ctypedef struct tbx_t:
+        tbx_conf_t conf
+        hts_idx_t *idx
+        void * dict
+
+    tbx_conf_t tbx_conf_gff
+    tbx_conf_t tbx_conf_bed
+    tbx_conf_t tbx_conf_psltbl
+    tbx_conf_t tbx_conf_sam
+    tbx_conf_t tbx_conf_vcf
+
+    void tbx_itr_destroy(hts_itr_t * iter)
+    hts_itr_t * tbx_itr_queryi(tbx_t * t, int tid, int bed, int end)
+    hts_itr_t * tbx_itr_querys(tbx_t * t, char * s)
+    int tbx_itr_next(htsFile * fp, tbx_t * t, hts_itr_t * iter, void * data)
+
+    int tbx_name2id(tbx_t *tbx, char *ss)
+
+    int tbx_index_build(char *fn, int min_shift, tbx_conf_t *conf)
+    int tbx_index_build2(const char *fn, const char *fnidx, int min_shift, const tbx_conf_t *conf)
+
+    tbx_t * tbx_index_load(char *fn)
+    tbx_t *tbx_index_load2(const char *fn, const char *fnidx)
+
+    # free the array but not the values
+    char **tbx_seqnames(tbx_t *tbx, int *n)
+
+    void tbx_destroy(tbx_t *tbx)
+
+
+# VCF/BCF API
+cdef extern from "htslib/vcf.h" nogil:
+
+    # Header struct
+
+    uint8_t BCF_HL_FLT   # header line
+    uint8_t BCF_HL_INFO
+    uint8_t BCF_HL_FMT
+    uint8_t BCF_HL_CTG
+    uint8_t BCF_HL_STR   # structured header line TAG=<A=..,B=..>
+    uint8_t BCF_HL_GEN   # generic header line
+
+    uint8_t BCF_HT_FLAG  # header type
+    uint8_t BCF_HT_INT
+    uint8_t BCF_HT_REAL
+    uint8_t BCF_HT_STR
+
+    uint8_t BCF_VL_FIXED # variable length
+    uint8_t BCF_VL_VAR
+    uint8_t BCF_VL_A
+    uint8_t BCF_VL_G
+    uint8_t BCF_VL_R
+
+    # === Dictionary ===
+    #
+    # The header keeps three dictionaries. The first keeps IDs in the
+    # "FILTER/INFO/FORMAT" lines, the second keeps the sequence names and lengths
+    # in the "contig" lines and the last keeps the sample names. bcf_hdr_t::dict[]
+    # is the actual hash table, which is opaque to the end users. In the hash
+    # table, the key is the ID or sample name as a C string and the value is a
+    # bcf_idinfo_t struct. bcf_hdr_t::id[] points to key-value pairs in the hash
+    # table in the order that they appear in the VCF header. bcf_hdr_t::n[] is the
+    # size of the hash table or, equivalently, the length of the id[] arrays.
+
+    uint8_t BCF_DT_ID       # dictionary type
+    uint8_t BCF_DT_CTG
+    uint8_t BCF_DT_SAMPLE
+
+    # Complete textual representation of a header line
+    ctypedef struct bcf_hrec_t:
+        int type            # One of the BCF_HL_* type
+        char *key           # The part before '=', i.e. FILTER/INFO/FORMAT/contig/fileformat etc.
+        char *value         # Set only for generic lines, NULL for FILTER/INFO, etc.
+        int nkeys           # Number of structured fields
+        char **keys         # The key=value pairs
+        char **vals
+
+    ctypedef struct bcf_idinfo_t:
+        uint32_t info[3]     # stores Number:20, var:4, Type:4, ColType:4 in info[0..2]
+        bcf_hrec_t *hrec[3]  # for BCF_HL_FLT,INFO,FMT and contig length in info[0] for BCF_HL_CTG
+        int id
+
+    ctypedef struct bcf_idpair_t:
+        const char *key
+        const bcf_idinfo_t *val
+
+    ctypedef struct bcf_hdr_t:
+        int32_t n[3]                # n:the size of the dictionary block in use, (allocated size, m, is below to preserve ABI)
+        bcf_idpair_t *id[3]
+        void *dict[3]               # ID dictionary, contig dict and sample dict
+        char **samples
+        bcf_hrec_t **hrec
+        int nhrec, dirty
+        int ntransl
+        int *transl[2]              # for bcf_translate()
+        int nsamples_ori            # for bcf_hdr_set_samples()
+        uint8_t *keep_samples
+        kstring_t mem
+        int32_t m[3]                # m: allocated size of the dictionary block in use (see n above)
+
+    uint8_t bcf_type_shift[]
+
+    # * VCF record *
+
+    uint8_t BCF_BT_NULL
+    uint8_t BCF_BT_INT8
+    uint8_t BCF_BT_INT16
+    uint8_t BCF_BT_INT32
+    uint8_t BCF_BT_FLOAT
+    uint8_t BCF_BT_CHAR
+
+    uint8_t VCF_REF
+    uint8_t VCF_SNP
+    uint8_t VCF_MNP
+    uint8_t VCF_INDEL
+    uint8_t VCF_OTHER
+    uint8_t VCF_BND
+    uint8_t VCF_OVERLAP
+
+
+    ctypedef struct variant_t:
+        int type, n     # variant type and the number of bases affected, negative for deletions
+
+    ctypedef struct bcf_fmt_t:
+        int id             # id: numeric tag id, the corresponding string is bcf_hdr_t::id[BCF_DT_ID][$id].key
+        int n, size, type  # n: number of values per-sample; size: number of bytes per-sample; type: one of BCF_BT_* types
+        uint8_t *p         # same as vptr and vptr_* in bcf_info_t below
+        uint32_t p_len
+        uint32_t p_off
+        uint8_t p_free
+
+    union bcf_info_union_t:
+        int32_t i      # integer value
+        float f        # float value
+
+    ctypedef struct bcf_info_t:
+        int key        # key: numeric tag id, the corresponding string is bcf_hdr_t::id[BCF_DT_ID][$key].key
+        int type, len  # type: one of BCF_BT_* types; len: vector length, 1 for scalars
+
+        # v1 union only set if $len==1; for easier access
+        bcf_info_union_t v1
+        uint8_t *vptr           # pointer to data array in bcf1_t->shared.s, excluding the size+type and tag id bytes
+        uint32_t vptr_len       # length of the vptr block or, when set, of the vptr_mod block, excluding offset
+        uint32_t vptr_off       # vptr offset, i.e., the size of the INFO key plus size+type bytes
+        uint8_t  vptr_free      # indicates that vptr-vptr_off must be freed; set only when modified and the new
+                                # data block is bigger than the original
+
+    uint8_t BCF1_DIRTY_ID
+    uint8_t BCF1_DIRTY_ALS
+    uint8_t BCF1_DIRTY_FLT
+    uint8_t BCF1_DIRTY_INF
+
+    ctypedef struct bcf_dec_t:
+        int m_fmt, m_info, m_id, m_als, m_allele, m_flt  # allocated size (high-water mark); do not change
+        int n_flt           # Number of FILTER fields
+        int *flt            # FILTER keys in the dictionary
+        char *id            # ID
+        char *als           # REF+ALT block (\0-seperated)
+        char **allele       # allele[0] is the REF (allele[] pointers to the als block); all null terminated
+        bcf_info_t *info    # INFO
+        bcf_fmt_t *fmt      # FORMAT and individual sample
+        variant_t *var      # $var and $var_type set only when set_variant_types called
+        int n_var, var_type
+        int shared_dirty    # if set, shared.s must be recreated on BCF output
+        int indiv_dirty     # if set, indiv.s must be recreated on BCF output
+
+    uint8_t BCF_ERR_CTG_UNDEF
+    uint8_t BCF_ERR_TAG_UNDEF
+    uint8_t BCF_ERR_NCOLS
+    uint8_t BCF_ERR_LIMITS
+    uint8_t BCF_ERR_CHAR
+    uint8_t BCF_ERR_CTG_INVALID
+    uint8_t BCF_ERR_TAG_INVALID
+
+    # The bcf1_t structure corresponds to one VCF/BCF line. Reading from VCF file
+    # is slower because the string is first to be parsed, packed into BCF line
+    # (done in vcf_parse), then unpacked into internal bcf1_t structure. If it
+    # is known in advance that some of the fields will not be required (notably
+    # the sample columns), parsing of these can be skipped by setting max_unpack
+    # appropriately.
+    # Similarly, it is fast to output a BCF line because the columns (kept in
+    # shared.s, indiv.s, etc.) are written directly by bcf_write, whereas a VCF
+    # line must be formatted in vcf_format.
+
+    ctypedef struct bcf1_t:
+        int32_t rid               # CHROM
+        int32_t pos               # POS
+        int32_t rlen              # length of REF
+        float qual                # QUAL
+        uint32_t n_info, n_allele
+        uint32_t n_fmt, n_sample
+        kstring_t shared, indiv
+        bcf_dec_t d               # lazy evaluation: $d is not generated by bcf_read(), but by explicitly calling bcf_unpack()
+        int max_unpack            # Set to BCF_UN_STR, BCF_UN_FLT, or BCF_UN_INFO to boost performance of vcf_parse when some of the fields won't be needed
+        int unpacked              # remember what has been unpacked to allow calling bcf_unpack() repeatedly without redoing the work
+        int unpack_size[3]        # the original block size of ID, REF+ALT and FILTER
+        int errcode               # one of BCF_ERR_* codes
+
+    ####### API #######
+
+    # BCF and VCF I/O
+    #
+    # A note about naming conventions: htslib internally represents VCF
+    # records as bcf1_t data structures, therefore most functions are
+    # prefixed with bcf_. There are a few exceptions where the functions must
+    # be aware of both BCF and VCF worlds, such as bcf_parse vs vcf_parse. In
+    # these cases, functions prefixed with bcf_ are more general and work
+    # with both BCF and VCF.
+
+    # bcf_hdr_init() - create an empty BCF header.
+    # @param mode    "r" or "w"
+    #
+    # When opened for writing, the mandatory fileFormat and
+    # FILTER=PASS lines are added automatically.
+    bcf_hdr_t *bcf_hdr_init(const char *mode)
+
+    # Destroy a BCF header struct
+    void bcf_hdr_destroy(bcf_hdr_t *h)
+
+    # Initialize a bcf1_t object; equivalent to calloc(1, sizeof(bcf1_t))
+    bcf1_t *bcf_init()
+
+    # Deallocate a bcf1_t object
+    void bcf_destroy(bcf1_t *v)
+
+    # Same as bcf_destroy() but frees only the memory allocated by bcf1_t,
+    # not the bcf1_t object itself.
+    void bcf_empty(bcf1_t *v)
+
+    # Make the bcf1_t object ready for next read. Intended mostly for
+    # internal use, the user should rarely need to call this function
+    # directly.
+    void bcf_clear(bcf1_t *v)
+
+    # Reads VCF or BCF header
+    bcf_hdr_t *bcf_hdr_read(htsFile *fp)
+
+    # bcf_hdr_set_samples() - for more efficient VCF parsing when only one/few samples are needed
+    # @samples: samples to include or exclude from file or as a comma-separated string.
+    #             LIST|FILE   .. select samples in list/file
+    #             ^LIST|FILE  .. exclude samples from list/file
+    #             -           .. include all samples
+    #             NULL        .. exclude all samples
+    # @is_file: @samples is a file (1) or a comma-separated list (0)
+    #
+    # The bottleneck of VCF reading is parsing of genotype fields. If the
+    # reader knows in advance that only subset of samples is needed (possibly
+    # no samples at all), the performance of bcf_read() can be significantly
+    # improved by calling bcf_hdr_set_samples after bcf_hdr_read().
+    # The function bcf_read() will subset the VCF/BCF records automatically
+    # with the notable exception when reading records via bcf_itr_next().
+    # In this case, bcf_subset_format() must be called explicitly, because
+    # bcf_readrec() does not see the header.
+    #
+    # Returns 0 on success, -1 on error or a positive integer if the list
+    # contains samples not present in the VCF header. In such a case, the
+    # return value is the index of the offending sample.
+    #
+    int bcf_hdr_set_samples(bcf_hdr_t *hdr, const char *samples, int is_file)
+    int bcf_subset_format(const bcf_hdr_t *hdr, bcf1_t *rec)
+
+    # Writes VCF or BCF header
+    int bcf_hdr_write(htsFile *fp, bcf_hdr_t *h)
+
+    # Parse VCF line contained in kstring and populate the bcf1_t struct
+    int vcf_parse(kstring_t *s, const bcf_hdr_t *h, bcf1_t *v)
+
+    # The opposite of vcf_parse. It should rarely be called directly, see vcf_write
+    int vcf_format(const bcf_hdr_t *h, const bcf1_t *v, kstring_t *s)
+
+    # bcf_read() - read next VCF or BCF record
+    #
+    # Returns -1 on critical errors, 0 otherwise. On errors which are not
+    # critical for reading, such as missing header definitions, v->errcode is
+    # set to one of BCF_ERR* code and must be checked before calling
+    # vcf_write().
+    int bcf_read(htsFile *fp, const bcf_hdr_t *h, bcf1_t *v)
+
+    # bcf_unpack() - unpack/decode a BCF record (fills the bcf1_t::d field)
+    #
+    # Note that bcf_unpack() must be called even when reading VCF. It is safe
+    # to call the function repeatedly, it will not unpack the same field
+    # twice.
+    uint8_t BCF_UN_STR        # up to ALT inclusive
+    uint8_t BCF_UN_FLT        # up to FILTER
+    uint8_t BCF_UN_INFO       # up to INFO
+    uint8_t BCF_UN_SHR        # all shared information
+    uint8_t BCF_UN_FMT        # unpack format and each sample
+    uint8_t BCF_UN_IND        # a synonymo of BCF_UN_FMT
+    uint8_t BCF_UN_ALL        # everything
+
+    int bcf_unpack(bcf1_t *b, int which)
+
+    # bcf_dup() - create a copy of BCF record.
+    #
+    # Note that bcf_unpack() must be called on the returned copy as if it was
+    # obtained from bcf_read(). Also note that bcf_dup() calls bcf_sync1(src)
+    # internally to reflect any changes made by bcf_update_* functions.
+    bcf1_t *bcf_dup(bcf1_t *src)
+    bcf1_t *bcf_copy(bcf1_t *dst, bcf1_t *src)
+
+    # bcf_write() - write one VCF or BCF record. The type is determined at the open() call.
+    int bcf_write(htsFile *fp, bcf_hdr_t *h, bcf1_t *v)
+
+    # The following functions work only with VCFs and should rarely be called
+    # directly. Usually one wants to use their bcf_* alternatives, which work
+    # transparently with both VCFs and BCFs.
+    bcf_hdr_t *vcf_hdr_read(htsFile *fp)
+    int vcf_hdr_write(htsFile *fp, const bcf_hdr_t *h)
+    int vcf_read(htsFile *fp, const bcf_hdr_t *h, bcf1_t *v)
+    int vcf_write(htsFile *fp, const bcf_hdr_t *h, bcf1_t *v)
+
+    #************************************************************************
+    # Header querying and manipulation routines
+    #************************************************************************
+
+    # Create a new header using the supplied template
+    bcf_hdr_t *bcf_hdr_dup(const bcf_hdr_t *hdr)
+
+    # Copy header lines from src to dst if not already present in dst. See also bcf_translate().
+    # Returns 0 on success or sets a bit on error:
+    #     1 .. conflicting definitions of tag length
+    #     # todo
+    int bcf_hdr_combine(bcf_hdr_t *dst, const bcf_hdr_t *src)
+
+    # bcf_hdr_merge() - copy header lines from src to dst, see also bcf_translate()
+    # @param dst: the destination header to be merged into, NULL on the first pass
+    # @param src: the source header
+    #
+    # Notes:
+    #     - use as:
+    #         bcf_hdr_t *dst = NULL;
+    #         for (i=0; i<nsrc; i++) dst = bcf_hdr_merge(dst,src[i]);
+    #
+    #     - bcf_hdr_merge() replaces bcf_hdr_combine() which had a problem when
+    #     combining multiple BCF headers. The current bcf_hdr_combine()
+    #     does not have this problem, but became slow when used for many files.
+    bcf_hdr_t *bcf_hdr_merge(bcf_hdr_t *dst, const bcf_hdr_t *src)
+
+    # bcf_hdr_add_sample() - add a new sample.
+    # @param sample:  sample name to be added
+    int bcf_hdr_add_sample(bcf_hdr_t *hdr, const char *sample)
+
+    # Read VCF header from a file and update the header
+    int bcf_hdr_set(bcf_hdr_t *hdr, const char *fname)
+
+    # Appends formatted header text to _str_.
+    # If _is_bcf_ is zero, `IDX` fields are discarded.
+    #  @return 0 if successful, or negative if an error occurred
+    #  @since 1.4
+    int bcf_hdr_format(const bcf_hdr_t *hdr, int is_bcf, kstring_t *str);
+    
+    # Returns formatted header (newly allocated string) and its length,
+    # excluding the terminating \0. If is_bcf parameter is unset, IDX
+    # fields are discarded.
+    char *bcf_hdr_fmt_text(const bcf_hdr_t *hdr, int is_bcf, int *len)
+
+    # Append new VCF header line, returns 0 on success
+    int bcf_hdr_append(bcf_hdr_t *h, const char *line)
+    int bcf_hdr_printf(bcf_hdr_t *h, const char *format, ...)
+
+    # VCF version, e.g. VCFv4.2
+    const char *bcf_hdr_get_version(const bcf_hdr_t *hdr)
+    void bcf_hdr_set_version(bcf_hdr_t *hdr, const char *version)
+
+    # bcf_hdr_remove() - remove VCF header tag
+    # @param type:      one of BCF_HL_*
+    # @param key:       tag name or NULL to remove all tags of the given type
+    void bcf_hdr_remove(bcf_hdr_t *h, int type, const char *key)
+
+    # bcf_hdr_subset() - creates a new copy of the header removing unwanted samples
+    # @param n:        number of samples to keep
+    # @param samples:  names of the samples to keep
+    # @param imap:     mapping from index in @samples to the sample index in the original file
+    #
+    # Sample names not present in h0 are ignored. The number of unmatched samples can be checked
+    # by comparing n and bcf_hdr_nsamples(out_hdr).
+    # This function can be used to reorder samples.
+    # See also bcf_subset() which subsets individual records.
+    #
+    bcf_hdr_t *bcf_hdr_subset(const bcf_hdr_t *h0, int n, char *const* samples, int *imap)
+
+    # Creates a list of sequence names. It is up to the caller to free the list (but not the sequence names)
+    const char **bcf_hdr_seqnames(const bcf_hdr_t *h, int *nseqs)
+
+    # Get number of samples
+    int32_t bcf_hdr_nsamples(const bcf_hdr_t *h)
+
+    # The following functions are for internal use and should rarely be called directly
+    int bcf_hdr_parse(bcf_hdr_t *hdr, char *htxt)
+    int bcf_hdr_sync(bcf_hdr_t *h)
+    bcf_hrec_t *bcf_hdr_parse_line(const bcf_hdr_t *h, const char *line, int *len)
+    void bcf_hrec_format(const bcf_hrec_t *hrec, kstring_t *str)
+    int bcf_hdr_add_hrec(bcf_hdr_t *hdr, bcf_hrec_t *hrec)
+
+    # bcf_hdr_get_hrec() - get header line info
+    # @param type:  one of the BCF_HL_* types: FLT,INFO,FMT,CTG,STR,GEN
+    # @param key:   the header key for generic lines (e.g. "fileformat"), any field
+    #                 for structured lines, typically "ID".
+    # @param value: the value which pairs with key. Can be be NULL for BCF_HL_GEN
+    # @param str_class: the class of BCF_HL_STR line (e.g. "ALT" or "SAMPLE"), otherwise NULL
+    #
+    bcf_hrec_t *bcf_hdr_get_hrec(const bcf_hdr_t *hdr, int type, const char *key, const char *value, const char *str_class)
+    bcf_hrec_t *bcf_hrec_dup(bcf_hrec_t *hrec)
+    void bcf_hrec_add_key(bcf_hrec_t *hrec, const char *str, int len)
+    void bcf_hrec_set_val(bcf_hrec_t *hrec, int i, const char *str, int len, int is_quoted)
+    int bcf_hrec_find_key(bcf_hrec_t *hrec, const char *key)
+    void hrec_add_idx(bcf_hrec_t *hrec, int idx)
+    void bcf_hrec_destroy(bcf_hrec_t *hrec)
+
+    #************************************************************************
+    # Individual record querying and manipulation routines
+    #************************************************************************
+
+    # See the description of bcf_hdr_subset()
+    int bcf_subset(const bcf_hdr_t *h, bcf1_t *v, int n, int *imap)
+
+    # bcf_translate() - translate tags ids to be consistent with different header. This function
+    #                   is useful when lines from multiple VCF need to be combined.
+    # @dst_hdr:   the destination header, to be used in bcf_write(), see also bcf_hdr_combine()
+    # @src_hdr:   the source header, used in bcf_read()
+    # @src_line:  line obtained by bcf_read()
+    int bcf_translate(const bcf_hdr_t *dst_hdr, bcf_hdr_t *src_hdr, bcf1_t *src_line)
+
+    # bcf_get_variant_type[s]()  - returns one of VCF_REF, VCF_SNP, etc
+    int bcf_get_variant_types(bcf1_t *rec)
+    int bcf_get_variant_type(bcf1_t *rec, int ith_allele)
+    int bcf_is_snp(bcf1_t *v)
+
+    # bcf_update_filter() - sets the FILTER column
+    # @flt_ids:  The filter IDs to set, numeric IDs returned by bcf_hdr_id2int(hdr, BCF_DT_ID, "PASS")
+    # @n:        Number of filters. If n==0, all filters are removed
+    int bcf_update_filter(const bcf_hdr_t *hdr, bcf1_t *line, int *flt_ids, int n)
+
+    # bcf_add_filter() - adds to the FILTER column
+    # @flt_id:   The filter IDs to add, numeric IDs returned by bcf_hdr_id2int(hdr, BCF_DT_ID, "PASS")
+    #
+    # If flt_id is PASS, all existing filters are removed first. If other than PASS, existing PASS is removed.
+    int bcf_add_filter(const bcf_hdr_t *hdr, bcf1_t *line, int flt_id)
+
+    # bcf_remove_filter() - removes from the FILTER column
+    # @flt_id:   filter ID to remove, numeric ID returned by bcf_hdr_id2int(hdr, BCF_DT_ID, "PASS")
+    # @pass:     when set to 1 and no filters are present, set to PASS
+    int bcf_remove_filter(const bcf_hdr_t *hdr, bcf1_t *line, int flt_id, int set_pass)
+
+    # Returns 1 if present, 0 if absent, or -1 if filter does not exist. "PASS" and "." can be used interchangeably.
+    int bcf_has_filter(const bcf_hdr_t *hdr, bcf1_t *line, char *filter)
+
+    # bcf_update_alleles() and bcf_update_alleles_str() - update REF and ALT column
+    # @alleles:           Array of alleles
+    # @nals:              Number of alleles
+    # @alleles_string:    Comma-separated alleles, starting with the REF allele
+    int bcf_update_alleles(const bcf_hdr_t *hdr, bcf1_t *line, const char **alleles, int nals)
+    int bcf_update_alleles_str(const bcf_hdr_t *hdr, bcf1_t *line, const char *alleles_string)
+
+    # bcf_update_id() - sets new ID string
+    # bcf_add_id() - adds to the ID string checking for duplicates
+    int bcf_update_id(const bcf_hdr_t *hdr, bcf1_t *line, const char *id)
+    int bcf_add_id(const bcf_hdr_t *hdr, bcf1_t *line, const char *id)
+
+    # bcf_update_info_*() - functions for updating INFO fields
+    # @hdr:       the BCF header
+    # @line:      VCF line to be edited
+    # @key:       the INFO tag to be updated
+    # @values:    pointer to the array of values. Pass NULL to remove the tag.
+    # @n:         number of values in the array. When set to 0, the INFO tag is removed
+    #
+    # The @string in bcf_update_info_flag() is optional, @n indicates whether
+    # the flag is set or removed.
+    #
+    # Returns 0 on success or negative value on error.
+    #
+    int bcf_update_info_int32(const bcf_hdr_t *hdr, bcf1_t *line, const char *key, const int32_t *values, int n)
+    int bcf_update_info_float(const bcf_hdr_t *hdr, bcf1_t *line, const char *key, const float *values, int n)
+    int bcf_update_info_flag(const bcf_hdr_t *hdr, bcf1_t *line, const char *key, const char *values, int n)
+    int bcf_update_info_string(const bcf_hdr_t *hdr, bcf1_t *line, const char *key, const char *values, int n)
+    int bcf_update_info(const bcf_hdr_t *hdr, bcf1_t *line, const char *key, const void *values, int n, int type)
+
+    # bcf_update_format_*() - functions for updating FORMAT fields
+    # @values:    pointer to the array of values, the same number of elements
+    #             is expected for each sample. Missing values must be padded
+    #             with bcf_*_missing or bcf_*_vector_end values.
+    # @n:         number of values in the array. If n==0, existing tag is removed.
+    #
+    # The function bcf_update_format_string() is a higher-level (slower) variant of
+    # bcf_update_format_char(). The former accepts array of \0-terminated strings
+    # whereas the latter requires that the strings are collapsed into a single array
+    # of fixed-length strings. In case of strings with variable length, shorter strings
+    # can be \0-padded. Note that the collapsed strings passed to bcf_update_format_char()
+    # are not \0-terminated.
+    #
+    # Returns 0 on success or negative value on error.
+    #
+    int bcf_update_format_int32(const bcf_hdr_t *hdr, bcf1_t *line, const char *key, const int32_t *values, int n)
+    int bcf_update_format_float(const bcf_hdr_t *hdr, bcf1_t *line, const char *key, const float *values, int n)
+    int bcf_update_format_char(const bcf_hdr_t *hdr, bcf1_t *line, const char *key, const char *values, int n)
+    int bcf_update_genotypes(const bcf_hdr_t *hdr, bcf1_t *line, const int32_t *values, int n)
+    int bcf_update_format_string(const bcf_hdr_t *hdr, bcf1_t *line, const char *key, const char **values, int n)
+    int bcf_update_format(const bcf_hdr_t *hdr, bcf1_t *line, const char *key, const void *values, int n, int type)
+
+    # Macros for setting genotypes correctly, for use with bcf_update_genotypes only; idx corresponds
+    # to VCF's GT (1-based index to ALT or 0 for the reference allele) and val is the opposite, obtained
+    # from bcf_get_genotypes() below.
+    uint32_t bcf_gt_phased(uint32_t idx)
+    uint32_t bcf_gt_unphased(uint32_t idx)
+    uint32_t bcf_gt_missing
+    uint32_t bcf_gt_is_missing(uint32_t val)
+    uint32_t bcf_gt_is_phased(uint32_t idx)
+    uint32_t bcf_gt_allele(uint32_t val)
+
+    # Conversion between alleles indexes to Number=G genotype index (assuming diploid, all 0-based)
+    uint32_t bcf_alleles2gt(uint32_t a, uint32_t b)
+    void bcf_gt2alleles(int igt, int *a, int *b)
+
+    # bcf_get_fmt() - returns pointer to FORMAT's field data
+    # @header: for access to BCF_DT_ID dictionary
+    # @line:   VCF line obtained from vcf_parse1
+    # @fmt:    one of GT,PL,...
+    #
+    # Returns bcf_fmt_t* if the call succeeded, or returns NULL when the field
+    # is not available.
+    #
+    bcf_fmt_t *bcf_get_fmt(const bcf_hdr_t *hdr, bcf1_t *line, const char *key)
+    bcf_info_t *bcf_get_info(const bcf_hdr_t *hdr, bcf1_t *line, const char *key)
+
+    # bcf_get_*_id() - returns pointer to FORMAT/INFO field data given the header index instead of the string ID
+    # @line: VCF line obtained from vcf_parse1
+    # @id:  The header index for the tag, obtained from bcf_hdr_id2int()
+    #
+    # Returns bcf_fmt_t* / bcf_info_t*. These functions do not check if the index is valid
+    # as their goal is to avoid the header lookup.
+    #
+    bcf_fmt_t *bcf_get_fmt_id(bcf1_t *line, const int id)
+    bcf_info_t *bcf_get_info_id(bcf1_t *line, const int id)
+
+    # bcf_get_info_*() - get INFO values, integers or floats
+    # @hdr:       BCF header
+    # @line:      BCF record
+    # @tag:       INFO tag to retrieve
+    # @dst:       *dst is pointer to a memory location, can point to NULL
+    # @ndst:      pointer to the size of allocated memory
+    #
+    # Returns negative value on error or the number of written values on
+    # success. bcf_get_info_string() returns on success the number of
+    # characters written excluding the null-terminating byte. bcf_get_info_flag()
+    # returns 1 when flag is set or 0 if not.
+    #
+    # List of return codes:
+    #     -1 .. no such INFO tag defined in the header
+    #     -2 .. clash between types defined in the header and encountered in the VCF record
+    #     -3 .. tag is not present in the VCF record
+    #
+    int bcf_get_info_int32(const bcf_hdr_t *hdr, bcf1_t *line, const char *tag, int32_t **dst, int *ndst)
+    int bcf_get_info_float(const bcf_hdr_t *hdr, bcf1_t *line, const char *tag, float **dst, int *ndst)
+    int bcf_get_info_string(const bcf_hdr_t *hdr, bcf1_t *line, const char *tag, char **dst, int *ndst)
+    int bcf_get_info_flag(const bcf_hdr_t *hdr, bcf1_t *line, const char *tag, int **dst, int *ndst)
+    int bcf_get_info_values(const bcf_hdr_t *hdr, bcf1_t *line, const char *tag, void **dst, int *ndst, int type)
+
+    # bcf_get_format_*() - same as bcf_get_info*() above
+    #
+    # The function bcf_get_format_string() is a higher-level (slower) variant of bcf_get_format_char().
+    # see the description of bcf_update_format_string() and bcf_update_format_char() above.
+    # Unlike other bcf_get_format__*() functions, bcf_get_format_string() allocates two arrays:
+    # a single block of \0-terminated strings collapsed into a single array and an array of pointers
+    # to these strings. Both arrays must be cleaned by the user.
+    #
+    # Returns negative value on error or the number of written values on success.
+    #
+    # Example:
+    #     int ndst = 0; char **dst = NULL
+    #     if ( bcf_get_format_string(hdr, line, "XX", &dst, &ndst) > 0 )
+    #         for (i=0; i<bcf_hdr_nsamples(hdr); i++) printf("%s\n", dst[i])
+    #     free(dst[0]); free(dst)
+    #
+    # Example:
+    #     int ngt, *gt_arr = NULL, ngt_arr = 0
+    #     ngt = bcf_get_genotypes(hdr, line, &gt_arr, &ngt_arr)
+    #
+    int bcf_get_format_int32(const bcf_hdr_t *hdr, bcf1_t *line, const char *tag, int32_t **dst, int *ndst)
+    int bcf_get_format_float(const bcf_hdr_t *hdr, bcf1_t *line, const char *tag, float **dst, int *ndst)
+    int bcf_get_format_char(const bcf_hdr_t *hdr, bcf1_t *line, const char *tag, char **dst, int *ndst)
+    int bcf_get_genotypes(const bcf_hdr_t *hdr, bcf1_t *line, int32_t **dst, int *ndst)
+    int bcf_get_format_string(const bcf_hdr_t *hdr, bcf1_t *line, const char *tag, char ***dst, int *ndst)
+    int bcf_get_format_values(const bcf_hdr_t *hdr, bcf1_t *line, const char *tag, void **dst, int *ndst, int type)
+
+    #************************************************************************
+    # Helper functions
+    #************************************************************************
+
+    #
+    # bcf_hdr_id2int() - Translates string into numeric ID
+    # bcf_hdr_int2id() - Translates numeric ID into string
+    # @type:     one of BCF_DT_ID, BCF_DT_CTG, BCF_DT_SAMPLE
+    # @id:       tag name, such as: PL, DP, GT, etc.
+    #
+    # Returns -1 if string is not in dictionary, otherwise numeric ID which identifies
+    # fields in BCF records.
+    #
+    int bcf_hdr_id2int(const bcf_hdr_t *hdr, int type, const char *id)
+    const char *bcf_hdr_int2id(const bcf_hdr_t *hdr, int type, int int_id)
+
+    # bcf_hdr_name2id() - Translates sequence names (chromosomes) into numeric ID
+    # bcf_hdr_id2name() - Translates numeric ID to sequence name
+    #
+    int bcf_hdr_name2id(const bcf_hdr_t *hdr, const char *id)
+    const char *bcf_hdr_id2name(const bcf_hdr_t *hdr, int rid)
+    const char *bcf_seqname(const bcf_hdr_t *hdr, bcf1_t *rec)
+
+    #
+    # bcf_hdr_id2*() - Macros for accessing bcf_idinfo_t
+    # @type:      one of BCF_HL_FLT, BCF_HL_INFO, BCF_HL_FMT
+    # @int_id:    return value of bcf_hdr_id2int, must be >=0
+    #
+    # The returned values are:
+    #    bcf_hdr_id2length   ..  whether the number of values is fixed or variable, one of BCF_VL_*
+    #    bcf_hdr_id2number   ..  the number of values, 0xfffff for variable length fields
+    #    bcf_hdr_id2type     ..  the field type, one of BCF_HT_*
+    #    bcf_hdr_id2coltype  ..  the column type, one of BCF_HL_*
+    #
+    # Notes: Prior to using the macros, the presence of the info should be
+    # tested with bcf_hdr_idinfo_exists().
+    #
+    int bcf_hdr_id2length(const bcf_hdr_t *hdr, int type, int int_id)
+    int bcf_hdr_id2number(const bcf_hdr_t *hdr, int type, int int_id)
+    int bcf_hdr_id2type(const bcf_hdr_t *hdr, int type, int int_id)
+    int bcf_hdr_id2coltype(const bcf_hdr_t *hdr, int type, int int_id)
+    int bcf_hdr_idinfo_exists(const bcf_hdr_t *hdr, int type, int int_id)
+    bcf_hrec_t *bcf_hdr_id2hrec(const bcf_hdr_t *hdr, int type, int col_type, int int_id)
+
+    void bcf_fmt_array(kstring_t *s, int n, int type, void *data)
+    uint8_t *bcf_fmt_sized_array(kstring_t *s, uint8_t *ptr)
+
+    void bcf_enc_vchar(kstring_t *s, int l, const char *a)
+    void bcf_enc_vint(kstring_t *s, int n, int32_t *a, int wsize)
+    void bcf_enc_vfloat(kstring_t *s, int n, float *a)
+
+    #************************************************************************
+    # BCF index
+    #
+    # Note that these functions work with BCFs only. See synced_bcf_reader.h
+    # which provides (amongst other things) an API to work transparently with
+    # both indexed BCFs and VCFs.
+    #************************************************************************
+
+    hts_idx_t *bcf_index_load2(const char *fn, const char *fnidx)
+    int bcf_index_build(const char *fn, int min_shift)
+    int bcf_index_build2(const char *fn, const char *fnidx, int min_shift)
+
+    #*******************
+    # Typed value I/O *
+    #******************
+
+    # Note that in contrast with BCFv2.1 specification, HTSlib implementation
+    # allows missing values in vectors. For integer types, the values 0x80,
+    # 0x8000, 0x80000000 are interpreted as missing values and 0x81, 0x8001,
+    # 0x80000001 as end-of-vector indicators.  Similarly for floats, the value of
+    # 0x7F800001 is interpreted as a missing value and 0x7F800002 as an
+    # end-of-vector indicator.
+    # Note that the end-of-vector byte is not part of the vector.
+
+    # This trial BCF version (v2.2) is compatible with the VCF specification and
+    # enables to handle correctly vectors with different ploidy in presence of
+    # missing values.
+
+    int32_t bcf_int8_vector_end
+    int32_t bcf_int16_vector_end
+    int32_t bcf_int32_vector_end
+    int32_t bcf_str_vector_end
+    int32_t bcf_int8_missing
+    int32_t bcf_int16_missing
+    int32_t bcf_int32_missing
+    int32_t bcf_str_missing
+
+    uint32_t bcf_float_vector_end
+    uint32_t bcf_float_missing
+
+    void bcf_float_set(float *ptr, uint32_t value)
+    void bcf_float_set_vector_end(float *x)
+    void bcf_float_set_missing(float *x)
+
+    int bcf_float_is_missing(float f)
+    int bcf_float_is_vector_end(float f)
+    void bcf_format_gt(bcf_fmt_t *fmt, int isample, kstring_t *str)
+    void bcf_enc_size(kstring_t *s, int size, int type)
+    int bcf_enc_inttype(long x)
+    void bcf_enc_int1(kstring_t *s, int32_t x)
+    int32_t bcf_dec_int1(const uint8_t *p, int type, uint8_t **q)
+    int32_t bcf_dec_typed_int1(const uint8_t *p, uint8_t **q)
+    int32_t bcf_dec_size(const uint8_t *p, uint8_t **q, int *type)
+
+    # These trivial wrappers are defined only for consistency with other parts of htslib
+    bcf1_t *bcf_init1()
+    int bcf_read1(htsFile *fp, const bcf_hdr_t *h, bcf1_t *v)
+    int vcf_read1(htsFile *fp, const bcf_hdr_t *h, bcf1_t *v)
+    int bcf_write1(htsFile *fp, const bcf_hdr_t *h, bcf1_t *v)
+    int vcf_write1(htsFile *fp, const bcf_hdr_t *h, bcf1_t *v)
+    void bcf_destroy1(bcf1_t *v)
+    void bcf_empty1(bcf1_t *v)
+    int vcf_parse1(kstring_t *s, const bcf_hdr_t *h, bcf1_t *v)
+    void bcf_clear1(bcf1_t *v)
+    int vcf_format1(const bcf_hdr_t *h, const bcf1_t *v, kstring_t *s)
+
+    # Other nice wrappers
+    void bcf_itr_destroy(hts_itr_t *iter)
+    hts_itr_t *bcf_itr_queryi(const hts_idx_t *idx, int tid, int beg, int end)
+    hts_itr_t *bcf_itr_querys(const hts_idx_t *idx, const bcf_hdr_t *hdr, char *s)
+    int bcf_itr_next(htsFile *fp, hts_itr_t *iter, void *r)
+    hts_idx_t *bcf_index_load(const char *fn)
+    const char **bcf_index_seqnames(const hts_idx_t *idx, const bcf_hdr_t *hdr, int *nptr)
+
+
+# VCF/BCF utility functions
+cdef extern from "htslib/vcfutils.h" nogil:
+    struct kbitset_t
+
+    # bcf_trim_alleles() - remove ALT alleles unused in genotype fields
+    # @header:  for access to BCF_DT_ID dictionary
+    # @line:    VCF line obtain from vcf_parse1
+    #
+    # Returns the number of removed alleles on success or negative
+    # on error:
+    #     -1 .. some allele index is out of bounds
+    int bcf_trim_alleles(const bcf_hdr_t *header, bcf1_t *line)
+
+    # bcf_remove_alleles() - remove ALT alleles according to bitmask @mask
+    # @header:  for access to BCF_DT_ID dictionary
+    # @line:    VCF line obtained from vcf_parse1
+    # @mask:    alleles to remove
+    #
+    # If you have more than 31 alleles, then the integer bit mask will
+    # overflow, so use bcf_remove_allele_set instead
+    void bcf_remove_alleles(const bcf_hdr_t *header, bcf1_t *line, int mask)
+
+    # bcf_remove_allele_set() - remove ALT alleles according to bitset @rm_set
+    # @header:  for access to BCF_DT_ID dictionary
+    # @line:    VCF line obtained from vcf_parse1
+    # @rm_set:  pointer to kbitset_t object with bits set for allele
+    #           indexes to remove
+    #
+    # Number=A,R,G INFO and FORMAT fields will be updated accordingly.
+    void bcf_remove_allele_set(const bcf_hdr_t *header, bcf1_t *line, kbitset_t *rm_set)
+
+    # bcf_calc_ac() - calculate the number of REF and ALT alleles
+    # @header:  for access to BCF_DT_ID dictionary
+    # @line:    VCF line obtained from vcf_parse1
+    # @ac:      array of length line->n_allele
+    # @which:   determine if INFO/AN,AC and indv fields be used
+    #
+    # Returns 1 if the call succeeded, or 0 if the value could not
+    # be determined.
+    #
+    # The value of @which determines if existing INFO/AC,AN can be
+    # used (BCF_UN_INFO) and and if indv fields can be split (BCF_UN_FMT).
+    int bcf_calc_ac(const bcf_hdr_t *header, bcf1_t *line, int *ac, int which)
+
+    # bcf_gt_type() - determines type of the genotype
+    # @fmt_ptr:  the GT format field as set for example by set_fmt_ptr
+    # @isample:  sample index (starting from 0)
+    # @ial:      index of the 1st non-reference allele (starting from 1)
+    # @jal:      index of the 2nd non-reference allele (starting from 1)
+    #
+    # Returns the type of the genotype (one of GT_HOM_RR, GT_HET_RA,
+    # GT_HOM_AA, GT_HET_AA, GT_HAPL_R, GT_HAPL_A or GT_UNKN). If $ial
+    # is not NULL and the genotype has one or more non-reference
+    # alleles, $ial will be set. In case of GT_HET_AA, $ial is the
+    # position of the allele which appeared first in ALT. If $jal is
+    # not null and the genotype is GT_HET_AA, $jal will be set and is
+    # the position of the second allele in ALT.
+    uint8_t GT_HOM_RR    # note: the actual value of GT_* matters, used in dosage r2 calculation
+    uint8_t GT_HOM_AA
+    uint8_t GT_HET_RA
+    uint8_t GT_HET_AA
+    uint8_t GT_HAPL_R
+    uint8_t GT_HAPL_A
+    uint8_t GT_UNKN
+    int bcf_gt_type(bcf_fmt_t *fmt_ptr, int isample, int *ial, int *jal)
+
+    int bcf_acgt2int(char c)
+    char bcf_int2acgt(int i)
+
+    # bcf_ij2G() - common task: allele indexes to Number=G index (diploid)
+    # @i,j:  allele indexes, 0-based, i<=j
+    # Returns index to the Number=G diploid array
+    uint32_t bcf_ij2G(uint32_t i, uint32_t j)
+
+
+cdef extern from "htslib/cram.h" nogil:
+
+    enum cram_block_method:
+        ERROR
+        RAW
+        GZIP
+        BZIP2
+        LZMA
+        RANS
+        RANS0
+        RANS1
+        GZIP_RLE
+
+    enum cram_content_type:
+        CT_ERROR
+        FILE_HEADER
+        COMPRESSION_HEADER
+        MAPPED_SLICE
+        UNMAPPED_SLICE
+        EXTERNAL
+        CORE
+
+    # Opaque data types, see cram_structs for the fully fledged versions.
+    ctypedef struct SAM_hdr
+    ctypedef struct cram_file_def
+    ctypedef struct cram_fd
+    ctypedef struct cram_container
+    ctypedef struct cram_block
+    ctypedef struct cram_slice
+    ctypedef struct cram_metrics
+    ctypedef struct cram_block_slice_hdr
+    ctypedef struct cram_block_compression_hdr
+    ctypedef struct refs_t
+
+    # Accessor functions
+
+    #
+    #-----------------------------------------------------------------------------
+    # cram_fd
+    #
+    SAM_hdr *cram_fd_get_header(cram_fd *fd)
+    void cram_fd_set_header(cram_fd *fd, SAM_hdr *hdr)
+
+    int cram_fd_get_version(cram_fd *fd)
+    void cram_fd_set_version(cram_fd *fd, int vers)
+
+    int cram_major_vers(cram_fd *fd)
+    int cram_minor_vers(cram_fd *fd)
+
+    hFILE *cram_fd_get_fp(cram_fd *fd)
+    void cram_fd_set_fp(cram_fd *fd, hFILE *fp)
+
+    #
+    #-----------------------------------------------------------------------------
+    # cram_container
+    #
+    int32_t cram_container_get_length(cram_container *c)
+    void cram_container_set_length(cram_container *c, int32_t length)
+    int32_t cram_container_get_num_blocks(cram_container *c)
+    void cram_container_set_num_blocks(cram_container *c, int32_t num_blocks)
+    int32_t *cram_container_get_landmarks(cram_container *c, int32_t *num_landmarks)
+    void cram_container_set_landmarks(cram_container *c, int32_t num_landmarks,
+				      int32_t *landmarks)
+
+    # Returns true if the container is empty (EOF marker) */
+    int cram_container_is_empty(cram_fd *fd)
+
+
+    #
+    #-----------------------------------------------------------------------------
+    # cram_block
+    #
+    int32_t cram_block_get_content_id(cram_block *b)
+    int32_t cram_block_get_comp_size(cram_block *b)
+    int32_t cram_block_get_uncomp_size(cram_block *b)
+    int32_t cram_block_get_crc32(cram_block *b)
+    void *  cram_block_get_data(cram_block *b)
+
+    cram_content_type cram_block_get_content_type(cram_block *b)
+
+    void cram_block_set_content_id(cram_block *b, int32_t id)
+    void cram_block_set_comp_size(cram_block *b, int32_t size)
+    void cram_block_set_uncomp_size(cram_block *b, int32_t size)
+    void cram_block_set_crc32(cram_block *b, int32_t crc)
+    void cram_block_set_data(cram_block *b, void *data)
+
+    int cram_block_append(cram_block *b, void *data, int size)
+    void cram_block_update_size(cram_block *b)
+
+    # Offset is known as "size" internally, but it can be confusing.
+    size_t cram_block_get_offset(cram_block *b)
+    void cram_block_set_offset(cram_block *b, size_t offset)
+
+    #
+    # Computes the size of a cram block, including the block
+    # header itself.
+    #
+    uint32_t cram_block_size(cram_block *b)
+
+    #
+    # Renumbers RG numbers in a cram compression header.
+    #
+    # CRAM stores RG as the Nth number in the header, rather than a
+    # string holding the ID: tag.  This is smaller in space, but means
+    # "samtools cat" to join files together that contain single but
+    # different RG lines needs a way of renumbering them.
+    #
+    # The file descriptor is expected to be immediately after the
+    # cram_container structure (ie before the cram compression header).
+    # Due to the nature of the CRAM format, this needs to read and write
+    # the blocks itself.  Note that there may be multiple slices within
+    # the container, meaning multiple compression headers to manipulate.
+    # Changing RG may change the size of the compression header and
+    # therefore the length field in the container.  Hence we rewrite all
+    # blocks just in case and also emit the adjusted container.
+    #
+    # The current implementation can only cope with renumbering a single
+    # RG (and only then if it is using HUFFMAN or BETA codecs).  In
+    # theory it *may* be possible to renumber multiple RGs if they use
+    # HUFFMAN to the CORE block or use an external block unshared by any
+    # other data series.  So we have an API that can be upgraded to
+    # support this, but do not implement it for now.  An example
+    # implementation of RG as an EXTERNAL block would be to find that
+    # block and rewrite it, returning the number of blocks consumed.
+    #
+    # Returns 0 on success;
+    #        -1 if unable to edit;
+    #        -2 on other errors (eg I/O).
+    #
+    int cram_transcode_rg(cram_fd *input, cram_fd *output,
+    			  cram_container *c,
+			  int nrg, int *in_rg, int *out_rg)
+
+    #
+    # Copies the blocks representing the next num_slice slices from a
+    # container from 'in' to 'out'.  It is expected that the file pointer
+    # is just after the read of the cram_container and cram compression
+    # header.
+    #
+    # Returns 0 on success
+    #        -1 on failure
+    #
+    int cram_copy_slice(cram_fd *input, cram_fd *output, int32_t num_slice)
+
+    #
+    #-----------------------------------------------------------------------------
+    # SAM_hdr
+    #
+
+    # Tokenises a SAM header into a hash table.
+    #
+    # Also extracts a few bits on specific data types, such as @RG lines.
+    #
+    # @return
+    # Returns a SAM_hdr struct on success (free with sam_hdr_free())
+    #         NULL on failure
+    #
+    SAM_hdr *sam_hdr_parse_(const char *hdr, int len)
+
+
+    #
+    #-----------------------------------------------------------------------------
+    # cram_io basics
+    #
+
+    # CRAM blocks - the dynamically growable data block. We have code to
+    # create, update, (un)compress and read/write.
+    #
+    # These are derived from the deflate_interlaced.c blocks, but with the
+    # CRAM extension of content types and IDs.
+    #
+
+    # Allocates a new cram_block structure with a specified content_type and
+    # id.
+    #
+    # @return
+    # Returns block pointer on success;
+    #         NULL on failure
+    #
+    cram_block *cram_new_block(cram_content_type content_type,
+			       int content_id)
+
+    # Reads a block from a cram file.
+    #
+    # @return
+    # Returns cram_block pointer on success;
+    #         NULL on failure
+    #
+    cram_block *cram_read_block(cram_fd *fd)
+
+    # Writes a CRAM block.
+    #
+    # @return
+    # Returns 0 on success;
+    #        -1 on failure
+    #
+    int cram_write_block(cram_fd *fd, cram_block *b)
+
+    # Frees a CRAM block, deallocating internal data too.
+    #
+    void cram_free_block(cram_block *b)
+
+    # Uncompresses a CRAM block, if compressed.
+    #
+    # @return
+    # Returns 0 on success;
+    #        -1 on failure
+    #
+    int cram_uncompress_block(cram_block *b)
+
+    # Compresses a block.
+    #
+    # Compresses a block using one of two different zlib strategies. If we only
+    # want one choice set strat2 to be -1.
+    #
+    # The logic here is that sometimes Z_RLE does a better job than Z_FILTERED
+    # or Z_DEFAULT_STRATEGY on quality data. If so, we'd rather use it as it is
+    # significantly faster.
+    #
+    # @return
+    # Returns 0 on success;
+    #        -1 on failure
+    #
+    int cram_compress_block(cram_fd *fd, cram_block *b, cram_metrics *metrics,
+			    int method, int level)
+
+    # Containers
+    #
+
+    # Creates a new container, specifying the maximum number of slices
+    # and records permitted.
+    #
+    # @return
+    # Returns cram_container ptr on success;
+    #         NULL on failure
+    #
+    cram_container *cram_new_container(int nrec, int nslice)
+    void cram_free_container(cram_container *c)
+
+    # Reads a container header.
+    #
+    # @return
+    # Returns cram_container on success;
+    #         NULL on failure or no container left (fd->err == 0).
+    #
+    cram_container *cram_read_container(cram_fd *fd)
+
+    # Writes a container structure.
+    #
+    # @return
+    # Returns 0 on success;
+    #        -1 on failure
+    #
+    int cram_write_container(cram_fd *fd, cram_container *h)
+
+    #
+    # Stores the container structure in dat and returns *size as the
+    # number of bytes written to dat[].  The input size of dat is also
+    # held in *size and should be initialised to cram_container_size(c).
+    #
+    # Returns 0 on success;
+    #        -1 on failure
+    #
+    int cram_store_container(cram_fd *fd, cram_container *c, char *dat, int *size)
+
+    int cram_container_size(cram_container *c)
+
+    # The top-level cram opening, closing and option handling
+    #
+
+    # Opens a CRAM file for read (mode "rb") or write ("wb").
+    #
+    # The filename may be "-" to indicate stdin or stdout.
+    #
+    # @return
+    # Returns file handle on success;
+    #         NULL on failure.
+    #
+    cram_fd *cram_open(const char *filename, const char *mode)
+
+    # Opens an existing stream for reading or writing.
+    #
+    # @return
+    # Returns file handle on success;
+    #         NULL on failure.
+    #
+    cram_fd *cram_dopen(hFILE *fp, const char *filename, const char *mode)
+
+    # Closes a CRAM file.
+    #
+    # @return
+    # Returns 0 on success;
+    #        -1 on failure
+    #
+    int cram_close(cram_fd *fd)
+
+    #
+    # Seek within a CRAM file.
+    #
+    # Returns 0 on success
+    #        -1 on failure
+    #
+    int cram_seek(cram_fd *fd, off_t offset, int whence)
+
+    #
+    # Flushes a CRAM file.
+    # Useful for when writing to stdout without wishing to close the stream.
+    #
+    # Returns 0 on success
+    #        -1 on failure
+    #
+    int cram_flush(cram_fd *fd)
+
+    # Checks for end of file on a cram_fd stream.
+    #
+    # @return
+    # Returns 0 if not at end of file
+    #         1 if we hit an expected EOF (end of range or EOF block)
+    #         2 for other EOF (end of stream without EOF block)
+    #
+    int cram_eof(cram_fd *fd)
+
+    # Sets options on the cram_fd.
+    #
+    # See CRAM_OPT_* definitions in hts.h.
+    # Use this immediately after opening.
+    #
+    # @return
+    # Returns 0 on success;
+    #        -1 on failure
+    #
+    int cram_set_option(cram_fd *fd, hts_fmt_option opt, ...)
+
+    # Sets options on the cram_fd.
+    #
+    # See CRAM_OPT_* definitions in hts.h.
+    # Use this immediately after opening.
+    #
+    # @return
+    # Returns 0 on success;
+    #        -1 on failure
+    #
+    int cram_set_voption(cram_fd *fd, hts_fmt_option opt, va_list args)
+
+    #
+    # Attaches a header to a cram_fd.
+    #
+    # This should be used when creating a new cram_fd for writing where
+    # we have an SAM_hdr already constructed (eg from a file we've read
+    # in).
+    #
+    # @return
+    # Returns 0 on success;
+    #        -1 on failure
+    #
+    int cram_set_header(cram_fd *fd, SAM_hdr *hdr)
+
+    # Check if this file has a proper EOF block
+    #
+    # @return
+    # Returns 3 if the file is a version of CRAM that does not contain EOF blocks
+    #         2 if the file is a stream and thus unseekable
+    #         1 if the file contains an EOF block
+    #         0 if the file does not contain an EOF block
+    #        -1 if an error occurred whilst reading the file or we could not seek back to where we were
+    #
+    #
+    int cram_check_EOF(cram_fd *fd)
+
+    # As int32_decoded/encode, but from/to blocks instead of cram_fd */
+    int int32_put_blk(cram_block *b, int32_t val)
+
+    # Deallocates all storage used by a SAM_hdr struct.
+    #
+    # This also decrements the header reference count. If after decrementing
+    # it is still non-zero then the header is assumed to be in use by another
+    # caller and the free is not done.
+    #
+    # This is a synonym for sam_hdr_dec_ref().
+    #
+    void sam_hdr_free(SAM_hdr *hdr)
+
+    # Returns the current length of the SAM_hdr in text form.
+    #
+    # Call sam_hdr_rebuild() first if editing has taken place.
+    #
+    int sam_hdr_length(SAM_hdr *hdr)
+
+    # Returns the string form of the SAM_hdr.
+    #
+    # Call sam_hdr_rebuild() first if editing has taken place.
+    #
+    char *sam_hdr_str(SAM_hdr *hdr)
+
+    # Appends a formatted line to an existing SAM header.
+    #
+    # Line is a full SAM header record, eg "@SQ\tSN:foo\tLN:100", with
+    # optional new-line. If it contains more than 1 line then multiple lines
+    # will be added in order.
+    #
+    # Len is the length of the text data, or 0 if unknown (in which case
+    # it should be null terminated).
+    #
+    # @return
+    # Returns 0 on success;
+    #        -1 on failure
+    #
+
+    # Add an @PG line.
+    #
+    # If we wish complete control over this use sam_hdr_add() directly. This
+    # function uses that, but attempts to do a lot of tedious house work for
+    # you too.
+    #
+    # - It will generate a suitable ID if the supplied one clashes.
+    # - It will generate multiple @PG records if we have multiple PG chains.
+    #
+    # Call it as per sam_hdr_add() with a series of key,value pairs ending
+    # in NULL.
+    #
+    # @return
+    # Returns 0 on success;
+    #        -1 on failure
+    #
+    int sam_hdr_add_PG(SAM_hdr *sh, const char *name, ...)
+
+    #
+    # A function to help with construction of CL tags in @PG records.
+    # Takes an argc, argv pair and returns a single space-separated string.
+    # This string should be deallocated by the calling function.
+    #
+    # @return
+    # Returns malloced char * on success;
+    #         NULL on failure
+    #
+    char *stringify_argv(int argc, char *argv[])
+
+    #
+    # Returns the refs_t structure used by a cram file handle.
+    #
+    # This may be used in conjunction with option CRAM_OPT_SHARED_REF to
+    # share reference memory between multiple file handles.
+    #
+    # @return
+    # Returns NULL if none exists or the file handle is not a CRAM file.
+    #
+    refs_t *cram_get_refs(htsFile *fd)
+
+
+cdef class HTSFile(object):
+    cdef          htsFile *htsfile       # pointer to htsFile structure
+    cdef          int64_t start_offset   # BGZF offset of first record
+
+    cdef readonly object  filename       # filename as supplied by user
+    cdef readonly object  mode           # file opening mode
+    cdef readonly object  threads        # number of threads to use
+    cdef readonly object  index_filename # filename of index, if supplied by user
+
+    cdef readonly bint    is_stream      # Is htsfile a non-seekable stream
+    cdef readonly bint    is_remote      # Is htsfile a remote stream
+    cdef readonly bint	  duplicate_filehandle   # Duplicate filehandle when opening via fh
+
+    cdef htsFile *_open_htsfile(self) except? NULL
diff --git a/pysam/libchtslib.pyi b/pysam/libchtslib.pyi
new file mode 100644
index 0000000..925828b
--- /dev/null
+++ b/pysam/libchtslib.pyi
@@ -0,0 +1,115 @@
+import sys
+from typing import List, Union, NoReturn, Iterable, Any, Tuple, Optional, TypeVar
+
+if sys.version_info < (3, 8):
+    from typing_extensions import Protocol
+else:
+    from typing import Protocol
+
+class _HasFileNo(Protocol):
+    def fileno(self) -> int: ...
+
+def get_verbosity() -> int: ...
+def set_verbosity(level: int): ...
+
+THFile = TypeVar("THFile", bound="HFile")
+
+class HFile:
+    def __init__(self, name: Union[int, str], mode: str = ...) -> None: ...
+    def __enter__(self: THFile) -> THFile: ...
+    def __exit__(self, type, value, tb): ...
+    def __iter__(self) -> Any: ...
+    def __next__(self) -> str: ...
+    @property
+    def closed(self) -> bool: ...
+    @property
+    def mode(self) -> str: ...
+    @property
+    def name(self) -> Union[int, str]: ...
+    def close(self) -> None: ...
+    def fileno(self) -> int: ...
+    def flush(self) -> None: ...
+    def isatty(self) -> bool: ...
+    def readable(self) -> bool: ...
+    def read(self, size: int = ...) -> bytes: ...
+    def readall(self) -> bytes: ...
+    def readinto(self, buf: Any) -> bytes: ...
+    def readline(self, size: int = ...) -> bytes: ...
+    def readlines(self) -> List[bytes]: ...
+    def seek(self, offset: int, whence: int = ...) -> int: ...
+    def seekable(self) -> bool: ...
+    def tell(self) -> int: ...
+    def truncate(self, *args) -> NoReturn: ...
+    def writable(self) -> bool: ...
+    def write(self, b: bytes) -> int: ...
+    def writelines(self, lines: Iterable[bytes]) -> None: ...
+
+THTSFile = TypeVar("THTSFile", bound="HTSFile")
+
+class HTSFile:
+    def __enter__(self: THTSFile) -> THTSFile: ...
+    def __exit__(self, type, value, traceback) -> Any: ...
+    @property
+    def filename(self) -> Any: ...
+    @property
+    def mode(self) -> str: ...
+    @property
+    def threads(self) -> int: ...
+    @property
+    def index_filename(self) -> Optional[str]: ...
+    @property
+    def is_stream(self) -> bool: ...
+    @property
+    def is_remote(self) -> bool: ...
+    @property
+    def duplicate_filehandle(self) -> bool: ...
+    def close(self) -> None: ...
+    def check_truncation(self, ignore_truncation: bool = ...) -> None: ...
+    @property
+    def category(self) -> str: ...
+    @property
+    def format(self) -> str: ...
+    @property
+    def version(self) -> Tuple[int, int]: ...
+    @property
+    def compression(self) -> str: ...
+    @property
+    def description(self) -> str: ...
+    @property
+    def is_open(self) -> bool: ...
+    @property
+    def is_closed(self) -> bool: ...
+    @property
+    def closed(self) -> bool: ...
+    @property
+    def is_write(self) -> bool: ...
+    @property
+    def is_read(self) -> bool: ...
+    @property
+    def is_sam(self) -> bool: ...
+    @property
+    def is_bam(self) -> bool: ...
+    @property
+    def is_cram(self) -> bool: ...
+    @property
+    def is_vcf(self) -> bool: ...
+    @property
+    def is_bcf(self) -> bool: ...
+    def reset(self) -> None: ...
+    def seek(self, offset: int) -> int: ...
+    def tell(self) -> int: ...
+    def add_hts_options(self, format_options: Optional[List[str]] = ...) -> None: ...
+    def parse_region(
+        self,
+        contig: Optional[str] = ...,
+        start: Optional[int] = ...,
+        stop: Optional[int] = ...,
+        region: Optional[str] = ...,
+        tid: Optional[int] = ...,
+        reference: Optional[str] = ...,
+        end: Optional[int] = ...,
+    ) -> Tuple[int, int, int, int]: ...
+    def is_valid_tid(self, tid: int) -> bool: ...
+    def is_valid_reference_name(self, contig: str) -> bool: ...
+    def get_tid(self, contig: str) -> int: ...
+    def get_reference_name(self, tid: int) -> Optional[str]: ...
diff --git a/pysam/libchtslib.pyx b/pysam/libchtslib.pyx
new file mode 100644
index 0000000..3a9bbd2
--- /dev/null
+++ b/pysam/libchtslib.pyx
@@ -0,0 +1,723 @@
+# cython: embedsignature=True
+# cython: profile=True
+# adds doc-strings for sphinx
+
+########################################################################
+########################################################################
+## Cython cimports
+########################################################################
+
+from posix.unistd cimport dup
+from libc.errno  cimport errno
+from libc.stdint cimport INT32_MAX
+from cpython cimport PyBytes_FromStringAndSize
+from pysam.libchtslib cimport *
+from pysam.libcutils cimport force_bytes, force_str, charptr_to_str, charptr_to_str_w_len
+from pysam.libcutils cimport encode_filename, from_string_and_size
+
+
+########################################################################
+########################################################################
+## Python imports
+########################################################################
+
+import os
+import io
+import re
+from warnings import warn
+
+
+########################################################################
+########################################################################
+## Constants
+########################################################################
+
+__all__ = ['get_verbosity', 'set_verbosity', 'HFile', 'HTSFile']
+
+# defines imported from samtools
+DEF SEEK_SET = 0
+DEF SEEK_CUR = 1
+DEF SEEK_END = 2
+
+# maximum genomic coordinace
+cdef int MAX_POS = (1 << 31) - 1
+
+cdef tuple FORMAT_CATEGORIES = ('UNKNOWN', 'ALIGNMENTS', 'VARIANTS', 'INDEX', 'REGIONS')
+cdef tuple FORMATS = ('UNKNOWN', 'BINARY_FORMAT', 'TEXT_FORMAT', 'SAM', 'BAM', 'BAI', 'CRAM', 'CRAI',
+                      'VCF', 'BCF', 'CSI', 'GZI', 'TBI', 'BED')
+cdef tuple COMPRESSION = ('NONE', 'GZIP', 'BGZF', 'CUSTOM')
+
+
+########################################################################
+########################################################################
+## Verbosity functions
+########################################################################
+
+
+cpdef set_verbosity(int verbosity):
+    """Set htslib's hts_verbose global variable to the specified value."""
+    return hts_set_verbosity(verbosity)
+
+cpdef get_verbosity():
+    """Return the value of htslib's hts_verbose global variable."""
+    return hts_get_verbosity()
+
+
+########################################################################
+########################################################################
+## HFile wrapper class
+########################################################################
+
+cdef class HFile(object):
+    cdef hFILE *fp
+    cdef readonly object name, mode
+
+    def __init__(self, name, mode='r', closefd=True):
+        self._open(name, mode, closefd=True)
+
+    def __dealloc__(self):
+        self.close()
+
+    @property
+    def closed(self):
+        return self.fp == NULL
+
+    cdef _open(self, name, mode, closefd=True):
+        self.name = name
+        self.mode = mode
+
+        mode = force_bytes(mode)
+
+        if isinstance(name, int):
+            if self.fp != NULL:
+                name = dup(name)
+            self.fp = hdopen(name, mode)
+        else:
+            name = encode_filename(name)
+            self.fp = hopen(name, mode)
+
+        if not self.fp:
+            raise IOError(errno, 'failed to open HFile', self.name)
+
+    def close(self):
+        if self.fp == NULL:
+            return
+
+        cdef hFILE *fp = self.fp
+        self.fp = NULL
+
+        if hclose(fp) != 0:
+            raise IOError(herrno(self.fp), 'failed to close HFile', self.name)
+
+    def fileno(self):
+        if self.fp == NULL:
+            raise IOError('operation on closed HFile')
+        if isinstance(self.name, int):
+            return self.name
+        else:
+            raise AttributeError('fileno not available')
+
+    def __enter__(self):
+        return self
+
+    def __exit__(self, type, value, tb):
+        self.close()
+
+    def __iter__(self):
+        return self
+
+    def __next__(self):
+        line = self.readline()
+        if not line:
+            raise StopIteration()
+        return line
+
+    def flush(self):
+        if self.fp == NULL:
+            raise IOError('operation on closed HFile')
+        if hflush(self.fp) != 0:
+            raise IOError(herrno(self.fp), 'failed to flush HFile', self.name)
+
+    def isatty(self):
+        if self.fp == NULL:
+            raise IOError('operation on closed HFile')
+        return False
+
+    def readable(self):
+        return self.fp != NULL and 'r' in self.mode
+
+    def read(self, Py_ssize_t size=-1):
+        if self.fp == NULL:
+            raise IOError('operation on closed HFile')
+
+        if size == 0:
+            return b''
+
+        cdef list parts = []
+        cdef bytes part
+        cdef Py_ssize_t chunk_size, ret, bytes_read = 0
+        cdef char *cpart
+
+        while size == -1 or bytes_read < size:
+            chunk_size = 4096
+            if size != -1:
+                chunk_size = min(chunk_size, size - bytes_read)
+
+            part = PyBytes_FromStringAndSize(NULL, chunk_size)
+            cpart = <char *>part
+            ret = hread(self.fp, <void *>cpart, chunk_size)
+
+            if ret < 0:
+                IOError(herrno(self.fp), 'failed to read HFile', self.name)
+            elif not ret:
+                break
+
+            bytes_read += ret
+
+            if ret < chunk_size:
+                part = cpart[:ret]
+
+            parts.append(part)
+
+        return b''.join(parts)
+
+    def readall(self):
+        return self.read()
+
+    def readinto(self, buf):
+        if self.fp == NULL:
+            raise IOError('operation on closed HFile')
+
+        size = len(buf)
+
+        if size == 0:
+            return size
+
+        mv = memoryview(buf)
+        ret = hread(self.fp, <void *>mv, size)
+
+        if ret < 0:
+            IOError(herrno(self.fp), 'failed to read HFile', self.name)
+
+        return ret
+
+    def readline(self, Py_ssize_t size=-1):
+        if self.fp == NULL:
+            raise IOError('operation on closed HFile')
+
+        if size == 0:
+            return b''
+
+        cdef list parts = []
+        cdef bytes part
+        cdef Py_ssize_t chunk_size, ret, bytes_read = 0
+        cdef char *cpart
+
+        while size == -1 or bytes_read < size:
+            chunk_size = 4096
+            if size != -1:
+                chunk_size = min(chunk_size, size - bytes_read)
+
+            part = PyBytes_FromStringAndSize(NULL, chunk_size)
+            cpart = <char *>part
+
+            # Python bytes objects allocate an extra byte for a null terminator
+            ret = hgetln(cpart, chunk_size+1, self.fp)
+
+            if ret < 0:
+                IOError(herrno(self.fp), 'failed to read HFile', self.name)
+            elif not ret:
+                break
+
+            bytes_read += ret
+
+            if ret < chunk_size:
+                part = cpart[:ret]
+                cpart = <char *>part
+
+            parts.append(part)
+
+            if cpart[ret-1] == b'\n':
+               break
+
+        return b''.join(parts)
+
+    def readlines(self):
+        return list(self)
+
+    def seek(self, Py_ssize_t offset, int whence=SEEK_SET):
+        if self.fp == NULL:
+            raise IOError('operation on closed HFile')
+
+        cdef Py_ssize_t off = hseek(self.fp, offset, whence)
+
+        if off < 0:
+            raise IOError(herrno(self.fp), 'seek failed on HFile', self.name)
+
+        return off
+
+    def tell(self):
+        if self.fp == NULL:
+            raise IOError('operation on closed HFile')
+
+        ret = htell(self.fp)
+
+        if ret < 0:
+            raise IOError(herrno(self.fp), 'tell failed on HFile', self.name)
+
+        return ret
+
+    def seekable(self):
+        return self.fp != NULL
+
+    def truncate(self, size=None):
+        raise NotImplementedError()
+
+    def writable(self):
+        return self.fp != NULL and 'w' in self.mode
+
+    def write(self, bytes b):
+        if self.fp == NULL:
+            raise IOError('operation on closed HFile')
+
+        got = hwrite(self.fp, <void *>b, len(b))
+
+        if got < 0:
+            raise IOError(herrno(self.fp), 'write failed on HFile', self.name)
+
+        return got
+
+    def writelines(self, lines):
+        for line in lines:
+            self.write(line)
+
+
+########################################################################
+########################################################################
+## Helpers for backward compatibility to hide the difference between
+## boolean properties and methods
+########################################################################
+
+class CallableValue(object):
+    def __init__(self, value):
+        self.value = value
+    def __call__(self):
+        return self.value
+    def __bool__(self):
+        return self.value
+    def __nonzero__(self):
+        return self.value
+    def __eq__(self, other):
+        return self.value == other
+    def __ne__(self, other):
+        return self.value != other
+
+
+CTrue = CallableValue(True)
+CFalse = CallableValue(False)
+
+
+########################################################################
+########################################################################
+## HTSFile wrapper class (base class for AlignmentFile and VariantFile)
+########################################################################
+
+cdef class HTSFile(object):
+    """
+    Base class for HTS file types
+    """
+
+    def __cinit__(self, *args, **kwargs):
+        self.htsfile = NULL
+        self.threads = 1
+        self.duplicate_filehandle = True
+
+    def close(self):
+        if self.htsfile:
+            hts_close(self.htsfile)
+            self.htsfile = NULL
+
+    def __dealloc__(self):
+        if self.htsfile:
+            hts_close(self.htsfile)
+            self.htsfile = NULL
+
+    def check_truncation(self, ignore_truncation=False):
+        """Check if file is truncated."""
+        if not self.htsfile:
+            return
+
+        if self.htsfile.format.compression != bgzf:
+            return
+
+        cdef BGZF *bgzfp = hts_get_bgzfp(self.htsfile)
+        if not bgzfp:
+            return
+
+        cdef int ret = bgzf_check_EOF(bgzfp)
+        if ret < 0:
+            raise IOError(errno, 'error checking for EOF marker')
+        elif ret == 0:
+            msg = 'no BGZF EOF marker; file may be truncated'.format(self.filename)
+            if ignore_truncation:
+                warn(msg)
+            else:
+                raise IOError(msg)
+
+    def __enter__(self):
+        return self
+
+    def __exit__(self, exc_type, exc_value, traceback):
+        self.close()
+        return False
+
+    @property
+    def category(self):
+        """General file format category.  One of UNKNOWN, ALIGNMENTS,
+        VARIANTS, INDEX, REGIONS"""
+        if not self.htsfile:
+            raise ValueError('metadata not available on closed file')
+        return FORMAT_CATEGORIES[self.htsfile.format.category]
+
+    @property
+    def format(self):
+        """File format.
+
+        One of UNKNOWN, BINARY_FORMAT, TEXT_FORMAT, SAM, BAM,
+        BAI, CRAM, CRAI, VCF, BCF, CSI, GZI, TBI, BED.
+        """
+        if not self.htsfile:
+            raise ValueError('metadata not available on closed file')
+        return FORMATS[self.htsfile.format.format]
+
+    @property
+    def version(self):
+        """Tuple of file format version numbers (major, minor)"""
+        if not self.htsfile:
+            raise ValueError('metadata not available on closed file')
+        return self.htsfile.format.version.major, self.htsfile.format.version.minor
+
+    @property
+    def compression(self):
+        """File compression.
+
+        One of NONE, GZIP, BGZF, CUSTOM."""
+        if not self.htsfile:
+            raise ValueError('metadata not available on closed file')
+        return COMPRESSION[self.htsfile.format.compression]
+
+    @property
+    def description(self):
+        """Vaguely human readable description of the file format"""
+        if not self.htsfile:
+            raise ValueError('metadata not available on closed file')
+        cdef char *desc = hts_format_description(&self.htsfile.format)
+        try:
+            return charptr_to_str(desc)
+        finally:
+            free(desc)
+
+    @property
+    def is_open(self):
+        """return True if HTSFile is open and in a valid state."""
+        return CTrue if self.htsfile != NULL else CFalse
+
+    @property
+    def is_closed(self):
+        """return True if HTSFile is closed."""
+        return self.htsfile == NULL
+
+    @property
+    def closed(self):
+        """return True if HTSFile is closed."""
+        return self.htsfile == NULL
+
+    @property
+    def is_write(self):
+        """return True if HTSFile is open for writing"""
+        return self.htsfile != NULL and self.htsfile.is_write != 0
+
+    @property
+    def is_read(self):
+        """return True if HTSFile is open for reading"""
+        return self.htsfile != NULL and self.htsfile.is_write == 0
+
+    @property
+    def is_sam(self):
+        """return True if HTSFile is reading or writing a SAM alignment file"""
+        return self.htsfile != NULL and self.htsfile.format.format == sam
+
+    @property
+    def is_bam(self):
+        """return True if HTSFile is reading or writing a BAM alignment file"""
+        return self.htsfile != NULL and self.htsfile.format.format == bam
+
+    @property
+    def is_cram(self):
+        """return True if HTSFile is reading or writing a BAM alignment file"""
+        return self.htsfile != NULL and self.htsfile.format.format == cram
+
+    @property
+    def is_vcf(self):
+        """return True if HTSFile is reading or writing a VCF variant file"""
+        return self.htsfile != NULL and self.htsfile.format.format == vcf
+
+    @property
+    def is_bcf(self):
+        """return True if HTSFile is reading or writing a BCF variant file"""
+        return self.htsfile != NULL and self.htsfile.format.format == bcf
+
+    def reset(self):
+        """reset file position to beginning of file just after the header.
+
+        Returns
+        -------
+
+        The file position after moving the file pointer. : pointer
+
+        """
+        return self.seek(self.start_offset)
+
+    def seek(self, uint64_t offset):
+        """move file pointer to position *offset*, see :meth:`pysam.HTSFile.tell`."""
+        if not self.is_open:
+            raise ValueError('I/O operation on closed file')
+        if self.is_stream:
+            raise IOError('seek not available in streams')
+
+        cdef int64_t ret
+        if self.htsfile.format.compression == bgzf:
+            with nogil:
+                ret = bgzf_seek(hts_get_bgzfp(self.htsfile), offset, SEEK_SET)
+        elif self.htsfile.format.compression == no_compression:
+            ret = 0 if (hseek(self.htsfile.fp.hfile, offset, SEEK_SET) >= 0) else -1
+        else:
+            raise NotImplementedError("seek not implemented in files compressed by method {}".format(
+                self.htsfile.format.compression))
+        return ret
+
+    def tell(self):
+        """return current file position, see :meth:`pysam.HTSFile.seek`."""
+        if not self.is_open:
+            raise ValueError('I/O operation on closed file')
+        if self.is_stream:
+            raise IOError('tell not available in streams')
+
+        cdef int64_t ret
+        if self.htsfile.format.compression == bgzf:
+            with nogil:
+                ret = bgzf_tell(hts_get_bgzfp(self.htsfile))
+        elif self.htsfile.format.compression == no_compression:
+            ret = htell(self.htsfile.fp.hfile)
+        elif self.htsfile.format.format == cram:
+            with nogil:
+                ret = htell(cram_fd_get_fp(self.htsfile.fp.cram))
+        else:
+            raise NotImplementedError("seek not implemented in files compressed by method {}".format(
+                self.htsfile.format.compression))
+
+        return ret
+
+    cdef htsFile *_open_htsfile(self) except? NULL:
+        cdef char *cfilename
+        cdef char *cmode = self.mode
+        cdef int fd, dup_fd, threads
+
+        threads = self.threads - 1
+        if isinstance(self.filename, bytes):
+            cfilename = self.filename
+            with nogil:
+                htsfile = hts_open(cfilename, cmode)
+                if htsfile != NULL:
+                    hts_set_threads(htsfile, threads)
+                return htsfile
+        else:
+            if isinstance(self.filename, int):
+                fd = self.filename
+            else:
+                fd = self.filename.fileno()
+
+            if self.duplicate_filehandle:
+                dup_fd = dup(fd)
+            else:
+                dup_fd = fd
+
+            # Replicate mode normalization done in hts_open_format
+            smode = self.mode.replace(b'b', b'').replace(b'c', b'')
+            if b'b' in self.mode:
+                smode += b'b'
+            elif b'c' in self.mode:
+                smode += b'c'
+            cmode = smode
+
+            hfile = hdopen(dup_fd, cmode)
+            if hfile == NULL:
+                raise IOError('Cannot create hfile')
+
+            try:
+                # filename.name can be an int
+                filename = str(self.filename.name)
+            except AttributeError:
+                filename = '<fd:{}>'.format(fd)
+
+            filename = encode_filename(filename)
+            cfilename = filename
+            with nogil:
+                htsfile = hts_hopen(hfile, cfilename, cmode)
+                if htsfile != NULL:
+                    hts_set_threads(htsfile, threads)
+                return htsfile
+
+    def add_hts_options(self, format_options=None):
+        """Given a list of key=value format option strings, add them to an open htsFile
+        """
+        cdef int rval
+        cdef hts_opt *opts = NULL
+
+        if format_options:
+            for format_option in format_options:
+                rval = hts_opt_add(&opts, format_option)
+                if rval != 0:
+                    if opts != NULL:
+                        hts_opt_free(opts)
+                    raise RuntimeError('Invalid format option ({}) specified'.format(format_option))
+            if opts != NULL:
+                rval = hts_opt_apply(self.htsfile, opts)
+                if rval != 0:
+                    hts_opt_free(opts)
+                    raise RuntimeError('An error occurred while applying the requested format options')
+                hts_opt_free(opts)
+
+    def parse_region(self, contig=None, start=None, stop=None,
+                     region=None, tid=None,
+                     reference=None, end=None):
+        """parse alternative ways to specify a genomic region. A region can
+        either be specified by :term:`contig`, `start` and
+        `stop`. `start` and `stop` denote 0-based, half-open
+        intervals. :term:`reference` and `end` are also accepted for
+        backward compatibility as synonyms for :term:`contig` and
+        `stop`, respectively.
+
+        Alternatively, a samtools :term:`region` string can be
+        supplied.
+
+        If any of the coordinates are missing they will be replaced by
+        the minimum (`start`) or maximum (`stop`) coordinate.
+
+        Note that region strings are 1-based inclusive, while `start`
+        and `stop` denote an interval in 0-based, half-open
+        coordinates (like BED files and Python slices).
+
+        If `contig` or `region` or are ``*``, unmapped reads at the end
+        of a BAM file will be returned. Setting either to ``.`` will
+        iterate from the beginning of the file.
+
+        Returns
+        -------
+
+        tuple :
+            a tuple of `flag`, :term:`tid`, `start` and
+            `stop`. The flag indicates whether no coordinates were
+            supplied and the genomic region is the complete genomic space.
+
+        Raises
+        ------
+
+        ValueError
+           for invalid or out of bounds regions.
+
+        """
+        cdef int rtid
+        cdef int32_t rstart
+        cdef int32_t rstop
+
+        if reference is not None:
+            if contig is not None:
+                raise ValueError('contig and reference should not both be specified')
+            contig = reference
+
+        if end is not None:
+            if stop is not None:
+                raise ValueError('stop and end should not both be specified')
+            stop = end
+
+        if contig is None and tid is None and region is None:
+            return 0, 0, 0, MAX_POS
+
+        rtid = -1
+        rstart = 0
+        rstop = MAX_POS
+        if start is not None:
+            try:
+                rstart = start
+            except OverflowError:
+                raise ValueError('start out of range (%i)' % start)
+
+        if stop is not None:
+            try:
+                rstop = stop
+            except OverflowError:
+                raise ValueError('stop out of range (%i)' % stop)
+
+        if region:
+            region = force_str(region)
+            if ":" in region:
+                contig, coord = region.split(":")
+                parts = coord.split("-")
+                rstart = int(parts[0]) - 1
+                if len(parts) >= 1:
+                    rstop = int(parts[1])
+            else:
+                contig = region
+
+        if tid is not None:
+            if not self.is_valid_tid(tid):
+                raise IndexError('invalid tid')
+            rtid = tid
+        else:
+            if contig == "*":
+                rtid = HTS_IDX_NOCOOR
+            elif contig == ".":
+                rtid = HTS_IDX_START
+            else:
+                rtid = self.get_tid(contig)
+                if rtid < 0:
+                    raise ValueError('invalid contig `%s`' % contig)
+
+        if rstart > rstop:
+            raise ValueError('invalid coordinates: start (%i) > stop (%i)' % (rstart, rstop))
+        if not 0 <= rstart < MAX_POS:
+            raise ValueError('start out of range (%i)' % rstart)
+        if not 0 <= rstop <= MAX_POS:
+            raise ValueError('stop out of range (%i)' % rstop)
+
+        return 1, rtid, rstart, rstop
+
+    def is_valid_tid(self, tid):
+        """
+        return True if the numerical :term:`tid` is valid; False otherwise.
+
+        returns -1 if contig is not known.
+        """
+        raise NotImplementedError()
+
+    def is_valid_reference_name(self, contig):
+        """
+        return True if the contig name :term:`contig` is valid; False otherwise.
+        """
+        return self.get_tid(contig) != -1
+
+    def get_tid(self, contig):
+        """
+        return the numerical :term:`tid` corresponding to
+        :term:`contig`
+
+        returns -1 if contig is not known.
+        """
+        raise NotImplementedError()
+
+    def get_reference_name(self, tid):
+        """
+        return :term:`contig` name corresponding to numerical :term:`tid`
+        """
+        raise NotImplementedError()
diff --git a/pysam/libcsamfile.pxd b/pysam/libcsamfile.pxd
new file mode 100644
index 0000000..dff1345
--- /dev/null
+++ b/pysam/libcsamfile.pxd
@@ -0,0 +1,45 @@
+from pysam.libcalignmentfile cimport AlignedSegment, AlignmentFile
+
+#################################################
+# Compatibility Layer for pysam < 0.8
+
+# import all declarations from htslib
+from pysam.libchtslib cimport *
+
+cdef class AlignedRead(AlignedSegment):
+    pass
+
+cdef class Samfile(AlignmentFile):
+    pass
+
+# import the conversion functions
+cdef extern from "htslib_util.h":
+
+    # add *nbytes* into the variable length data of *src* at *pos*
+    bam1_t * pysam_bam_update(bam1_t * b,
+                              size_t nbytes_old,
+                              size_t nbytes_new,
+                              uint8_t * pos)
+
+    # now: static
+    int aux_type2size(int)
+
+    char * pysam_bam_get_qname(bam1_t * b)
+    uint32_t * pysam_bam_get_cigar(bam1_t * b)
+    uint8_t * pysam_bam_get_seq(bam1_t * b)
+    uint8_t * pysam_bam_get_qual(bam1_t * b)
+    uint8_t * pysam_bam_get_aux(bam1_t * b)
+    int pysam_bam_get_l_aux(bam1_t * b)
+    char pysam_bam_seqi(uint8_t * s, int i)
+
+    uint16_t pysam_get_bin(bam1_t * b)
+    uint8_t pysam_get_qual(bam1_t * b)
+    uint8_t pysam_get_l_qname(bam1_t * b)
+    uint16_t pysam_get_flag(bam1_t * b)
+    uint32_t pysam_get_n_cigar(bam1_t * b)
+    void pysam_set_bin(bam1_t * b, uint16_t v)
+    void pysam_set_qual(bam1_t * b, uint8_t v)
+    void pysam_set_l_qname(bam1_t * b, uint8_t v)
+    void pysam_set_flag(bam1_t * b, uint16_t v)
+    void pysam_set_n_cigar(bam1_t * b, uint32_t v)
+    void pysam_update_flag(bam1_t * b, uint16_t v, uint16_t flag)
diff --git a/pysam/libcsamfile.pyi b/pysam/libcsamfile.pyi
new file mode 100644
index 0000000..e9b5a25
--- /dev/null
+++ b/pysam/libcsamfile.pyi
@@ -0,0 +1,5 @@
+from pysam.libcalignedsegment import AlignedSegment
+from pysam.libcalignmentfile import AlignmentFile
+
+class AlignedRead(AlignedSegment): ...
+class Samfile(AlignmentFile): ...
diff --git a/pysam/libcsamfile.pyx b/pysam/libcsamfile.pyx
new file mode 100644
index 0000000..bde93d8
--- /dev/null
+++ b/pysam/libcsamfile.pyx
@@ -0,0 +1,43 @@
+# cython: embedsignature=True
+# cython: profile=True
+# adds doc-strings for sphinx
+import tempfile
+import os
+import sys
+import types
+import itertools
+import struct
+import ctypes
+import collections
+import re
+import platform
+import warnings
+from cpython cimport PyErr_SetString, \
+    PyBytes_Check, \
+    PyUnicode_Check, \
+    PyBytes_FromStringAndSize
+
+from cpython.version cimport PY_MAJOR_VERSION
+
+from pysam.libcalignmentfile cimport AlignmentFile, AlignedSegment
+
+
+cdef class Samfile(AlignmentFile):
+    '''Deprecated alternative for :class:`~pysam.AlignmentFile`
+
+    Added for backwards compatibility with pysam <= 0.8.0
+    '''
+    pass
+
+
+cdef class AlignedRead(AlignedSegment):
+    '''Deprecated alternative for :class:`~pysam.AlignedSegment`
+
+    Added for backwards compatibility with pysam <= 0.8.0
+    '''
+    pass
+
+
+__all__ = ['Samfile', 'AlignedRead']
+
+
diff --git a/pysam/libcsamtools.pxd b/pysam/libcsamtools.pxd
new file mode 100644
index 0000000..628d9a5
--- /dev/null
+++ b/pysam/libcsamtools.pxd
@@ -0,0 +1,8 @@
+cdef extern from "samtools.pysam.h":
+
+    int samtools_dispatch(int argc, char *argv[])
+    void samtools_set_stderr(int fd)
+    void samtools_close_stderr()
+    void samtools_set_stdout(int fd)
+    void samtools_set_stdout_fn(const char *)
+    void samtools_close_stdout()
diff --git a/pysam/libcsamtools.pyi b/pysam/libcsamtools.pyi
new file mode 100644
index 0000000..fe158dd
--- /dev/null
+++ b/pysam/libcsamtools.pyi
@@ -0,0 +1 @@
+def py_samtools() -> None: ...
diff --git a/pysam/libcsamtools.pyx b/pysam/libcsamtools.pyx
new file mode 100644
index 0000000..cc60ace
--- /dev/null
+++ b/pysam/libcsamtools.pyx
@@ -0,0 +1,2 @@
+def py_samtools():
+    pass
diff --git a/pysam/libctabix.pxd b/pysam/libctabix.pxd
new file mode 100644
index 0000000..c986f03
--- /dev/null
+++ b/pysam/libctabix.pxd
@@ -0,0 +1,127 @@
+from libc.stdint cimport int8_t, int16_t, int32_t, int64_t
+from libc.stdint cimport uint8_t, uint16_t, uint32_t, uint64_t
+from libc.stdlib cimport malloc, calloc, realloc, free
+from libc.string cimport memcpy, memcmp, strncpy, strlen, strdup
+from libc.stdio cimport FILE, printf
+
+# Note: this replaces python "open"!
+cdef extern from "fcntl.h":
+    int open(char *pathname, int flags)
+
+cdef extern from "unistd.h" nogil:
+    ctypedef int ssize_t
+    ssize_t read(int fd, void *buf, size_t count)
+    int close(int fd)
+
+from pysam.libchtslib cimport hts_idx_t, hts_itr_t, htsFile, \
+    tbx_t, kstring_t, BGZF, HTSFile
+
+
+# These functions are put here and not in chtslib.pxd in order
+# to avoid warnings for unused functions.
+cdef extern from "pysam_stream.h" nogil:
+
+    ctypedef struct kstream_t:
+        pass
+
+    ctypedef struct kseq_t:
+        kstring_t name
+        kstring_t comment
+        kstring_t seq
+        kstring_t qual
+
+    kseq_t *kseq_init(BGZF *)
+    int kseq_read(kseq_t *)
+    void kseq_destroy(kseq_t *)
+    kstream_t *ks_init(BGZF *)
+    void ks_destroy(kstream_t *)
+
+    # Retrieve characters from stream until delimiter
+    # is reached placing results in str.
+    int ks_getuntil(kstream_t *,
+                    int delimiter,
+                    kstring_t * str,
+                    int * dret)
+
+
+cdef class tabix_file_iterator:
+    cdef BGZF * fh
+    cdef kstream_t * kstream
+    cdef kstring_t buffer
+    cdef size_t size
+    cdef Parser parser
+    cdef int fd
+    cdef int duplicated_fd
+    cdef infile
+
+    cdef __cnext__(self)
+
+
+cdef class TabixFile(HTSFile):
+    # pointer to index structure
+    cdef tbx_t * index
+
+    cdef readonly object filename_index
+
+    cdef Parser parser
+
+    cdef encoding    
+
+
+cdef class Parser:
+    cdef encoding
+    cdef parse(self, char * buffer, int len)
+
+
+cdef class asTuple(Parser):
+    cdef parse(self, char * buffer, int len)
+
+
+cdef class asGTF(Parser):
+    pass
+
+
+cdef class asGFF3(Parser):
+    pass
+
+
+cdef class asBed(Parser):
+    pass
+
+
+cdef class asVCF(Parser):
+    pass
+
+
+cdef class TabixIterator:
+    cdef hts_itr_t * iterator
+    cdef TabixFile tabixfile
+    cdef kstring_t buffer
+    cdef encoding
+    cdef int __cnext__(self)
+
+
+cdef class TabixIteratorParsed(TabixIterator):
+    cdef Parser parser
+
+
+cdef class GZIterator:
+    cdef object _filename
+    cdef BGZF * gzipfile
+    cdef kstream_t * kstream
+    cdef kstring_t buffer
+    cdef int __cnext__(self)
+    cdef encoding
+
+
+cdef class GZIteratorHead(GZIterator):
+    pass
+
+
+cdef class GZIteratorParsed(GZIterator):
+    cdef Parser parser
+
+
+# Compatibility Layer for pysam < 0.8
+cdef class Tabixfile(TabixFile):
+    pass
diff --git a/pysam/libctabix.pyi b/pysam/libctabix.pyi
new file mode 100644
index 0000000..e1ba211
--- /dev/null
+++ b/pysam/libctabix.pyi
@@ -0,0 +1,103 @@
+from typing import Optional, Literal, List, Any
+
+from pysam.libchtslib import HTSFile
+
+_ParseResult = Any
+
+class Parser:
+    def __init__(self, encoding: str = ...) -> None: ...
+    def get_encoding(self) -> str: ...
+    def set_encoding(self, encoding: str) -> None: ...
+    def __call__(self, buffer: str, length: int) -> _ParseResult: ...
+
+class asTuple(Parser): ...
+class asGFF3(Parser): ...
+class asGTF(Parser): ...
+class asBed(Parser): ...
+class asVCF(Parser): ...
+
+class TabixFile(HTSFile):
+    filename_index: bytes = ...
+    @property
+    def header(self) -> List[str]: ...
+    @property
+    def contigs(self) -> List[str]: ...
+    def __init__(
+        self,
+        filename: str,
+        mode: str = ...,
+        parser: Parser = ...,
+        index: Optional[str] = ...,
+        encoding: str = ...,
+        threads: int = ...,
+        *args,
+        **kwargs
+    ) -> None: ...
+    def fetch(
+        self,
+        reference: Optional[str] = ...,
+        start: Optional[int] = ...,
+        end: Optional[int] = ...,
+        region: Optional[str] = ...,
+        parser: Optional[Parser] = ...,
+        multiple_iterators: bool = ...,
+    ) -> Any: ...
+    def close(self) -> None: ...
+
+class TabixIterator:
+    def __init__(self, encoding: str = ...) -> None: ...
+    def __iter__(self) -> TabixIterator: ...
+    def __next__(self) -> str: ...
+
+class EmptyIterator:
+    def __iter__(self) -> Any: ...
+    def __next__(self) -> Any: ...
+
+class TabixIteratorParsed(TabixIterator):
+    def __init__(self, parser: Parser) -> None: ...
+    def __next__(self) -> Any: ...
+
+class GZIterator:
+    def __init__(
+        self, filename: str, bufer_size: int = ..., encoding: str = ...
+    ) -> None: ...
+    def __iter__(self) -> GZIterator: ...
+    def __next__(self) -> str: ...
+
+class GZIteratorHead(GZIterator): ...
+
+class GZIteratorParsed(GZIterator):
+    def __init__(self, parser: Parser) -> None: ...
+    def __next__(self) -> _ParseResult: ...
+
+def tabix_compress(filename_in: str, filename_out: str, force: bool = ...) -> None: ...
+def tabix_index(
+    filename: str,
+    force: bool = ...,
+    seq_col: Optional[int] = ...,
+    start_col: Optional[int] = ...,
+    end_col: Optional[int] = ...,
+    preset: Optional[Literal["gff", "bed", "sam", "vcf", "psltbl", "pileup"]] = ...,
+    meta_char: str = ...,
+    line_skip: int = ...,
+    zerobased: bool = ...,
+    min_shift: int = ...,
+    index: Optional[str] = ...,
+    keep_original: bool = ...,
+    csi: bool = ...,
+) -> str: ...
+
+class tabix_file_iterator:
+    def __init__(self, infile: str, parser: Parser, buffer_size: int = ...) -> None: ...
+    def __iter__(self) -> tabix_file_iterator: ...
+    def __next__(self) -> _ParseResult: ...
+
+class tabix_generic_iterator:
+    def __init__(self, infile: str, parser: Parser) -> None: ...
+    def __iter__(self) -> tabix_generic_iterator: ...
+    def __next__(self) -> _ParseResult: ...
+
+def tabix_iterator(infile: str, parser: Optional[Parser]) -> _ParseResult: ...
+
+# backwards compatibility
+class Tabixfile(TabixFile): ...
diff --git a/pysam/libctabix.pyx b/pysam/libctabix.pyx
new file mode 100644
index 0000000..4436420
--- /dev/null
+++ b/pysam/libctabix.pyx
@@ -0,0 +1,1302 @@
+# cython: embedsignature=True
+# cython: profile=True
+###############################################################################
+###############################################################################
+# Cython wrapper for access to tabix indexed files in bgzf format
+###############################################################################
+# The principal classes and functions defined in this module are:
+#
+# class TabixFile  class wrapping tabix indexed files in bgzf format
+#
+# class asTuple  Parser class for tuples
+# class asGTF    Parser class for GTF formatted rows
+# class asGFF3   Parser class for GFF3 formatted rows
+# class asBed    Parser class for Bed formatted rows
+# class asVCF    Parser class for VCF formatted rows
+#
+# class tabix_generic_iterator  Streamed iterator of bgzf formatted files
+#
+# Additionally this module defines several additional classes that are part
+# of the internal API. These are:
+#
+# class Parser                base class for parsers of tab-separated rows
+# class tabix_file_iterator
+# class TabixIterator         iterator class over rows in bgzf file
+# class EmptyIterator
+#
+# For backwards compatibility, the following classes are also defined:
+#
+# class Tabixfile   equivalent to TabixFile
+#
+###############################################################################
+#
+# The MIT License
+#
+# Copyright (c) 2015 Andreas Heger
+#
+# Permission is hereby granted, free of charge, to any person obtaining a
+# copy of this software and associated documentation files (the "Software"),
+# to deal in the Software without restriction, including without limitation
+# the rights to use, copy, modify, merge, publish, distribute, sublicense,
+# and/or sell copies of the Software, and to permit persons to whom the
+# Software is furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.  IN NO EVENT SHALL
+# THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+# DEALINGS IN THE SOFTWARE.
+#
+###############################################################################
+import os
+import sys
+
+from libc.stdio cimport printf, fprintf, stderr
+from libc.string cimport strerror
+from libc.errno cimport errno
+from posix.unistd cimport dup
+
+from cpython cimport PyErr_SetString, PyBytes_Check, \
+    PyUnicode_Check, PyBytes_FromStringAndSize, \
+    PyObject_AsFileDescriptor
+
+from cpython.version cimport PY_MAJOR_VERSION
+
+cimport pysam.libctabixproxies as ctabixproxies
+
+from pysam.libchtslib cimport htsFile, hts_open, hts_close, HTS_IDX_START,\
+    BGZF, bgzf_open, bgzf_dopen, bgzf_close, bgzf_write, \
+    tbx_index_build2, tbx_index_load2, tbx_itr_queryi, tbx_itr_querys, \
+    tbx_conf_t, tbx_seqnames, tbx_itr_next, tbx_itr_destroy, \
+    tbx_destroy, hisremote, region_list, hts_getline, \
+    TBX_GENERIC, TBX_SAM, TBX_VCF, TBX_UCSC, hts_get_format, htsFormat, \
+    no_compression, bcf, bcf_index_build2
+
+from pysam.libcutils cimport force_bytes, force_str, charptr_to_str
+from pysam.libcutils cimport encode_filename, from_string_and_size
+
+cdef class Parser:
+
+    def __init__(self, encoding="ascii"):
+        self.encoding = encoding
+
+    def set_encoding(self, encoding):
+        self.encoding = encoding
+
+    def get_encoding(self):
+        return self.encoding
+
+    cdef parse(self, char * buffer, int length):
+        raise NotImplementedError(
+            'parse method of %s not implemented' % str(self))
+
+    def __call__(self, char * buffer, int length):
+        return self.parse(buffer, length)
+
+
+cdef class asTuple(Parser):
+    '''converts a :term:`tabix row` into a python tuple.
+
+    A field in a row is accessed by numeric index.
+    ''' 
+    cdef parse(self, char * buffer, int len):
+        cdef ctabixproxies.TupleProxy r
+        r = ctabixproxies.TupleProxy(self.encoding)
+        # need to copy - there were some
+        # persistence issues with "present"
+        r.copy(buffer, len)
+        return r
+
+
+cdef class asGFF3(Parser):
+    '''converts a :term:`tabix row` into a GFF record with the following
+    fields:
+   
+    +----------+----------+-------------------------------+
+    |*Column*  |*Name*    |*Content*                      |
+    +----------+----------+-------------------------------+
+    |1         |contig    |the chromosome name            |
+    +----------+----------+-------------------------------+
+    |2         |feature   |The feature type               |
+    +----------+----------+-------------------------------+
+    |3         |source    |The feature source             |
+    +----------+----------+-------------------------------+
+    |4         |start     |genomic start coordinate       |
+    |          |          |(0-based)                      |
+    +----------+----------+-------------------------------+
+    |5         |end       |genomic end coordinate         |
+    |          |          |(0-based)                      |
+    +----------+----------+-------------------------------+
+    |6         |score     |feature score                  |
+    +----------+----------+-------------------------------+
+    |7         |strand    |strand                         |
+    +----------+----------+-------------------------------+
+    |8         |frame     |frame                          |
+    +----------+----------+-------------------------------+
+    |9         |attributes|the attribute field            |
+    +----------+----------+-------------------------------+
+
+    ''' 
+    cdef parse(self, char * buffer, int len):
+        cdef ctabixproxies.GFF3Proxy r
+        r = ctabixproxies.GFF3Proxy(self.encoding)
+        r.copy(buffer, len)
+        return r
+
+
+cdef class asGTF(Parser):
+    '''converts a :term:`tabix row` into a GTF record with the following
+    fields:
+   
+    +----------+----------+-------------------------------+
+    |*Column*  |*Name*    |*Content*                      |
+    +----------+----------+-------------------------------+
+    |1         |contig    |the chromosome name            |
+    +----------+----------+-------------------------------+
+    |2         |feature   |The feature type               |
+    +----------+----------+-------------------------------+
+    |3         |source    |The feature source             |
+    +----------+----------+-------------------------------+
+    |4         |start     |genomic start coordinate       |
+    |          |          |(0-based)                      |
+    +----------+----------+-------------------------------+
+    |5         |end       |genomic end coordinate         |
+    |          |          |(0-based)                      |
+    +----------+----------+-------------------------------+
+    |6         |score     |feature score                  |
+    +----------+----------+-------------------------------+
+    |7         |strand    |strand                         |
+    +----------+----------+-------------------------------+
+    |8         |frame     |frame                          |
+    +----------+----------+-------------------------------+
+    |9         |attributes|the attribute field            |
+    +----------+----------+-------------------------------+
+
+    GTF formatted entries also define the following fields that
+    are derived from the attributes field:
+
+    +--------------------+------------------------------+
+    |*Name*              |*Content*                     |
+    +--------------------+------------------------------+
+    |gene_id             |the gene identifier           |
+    +--------------------+------------------------------+
+    |transcript_id       |the transcript identifier     |
+    +--------------------+------------------------------+
+
+    ''' 
+    cdef parse(self, char * buffer, int len):
+        cdef ctabixproxies.GTFProxy r
+        r = ctabixproxies.GTFProxy(self.encoding)
+        r.copy(buffer, len)
+        return r
+    
+
+cdef class asBed(Parser):
+    '''converts a :term:`tabix row` into a bed record
+    with the following fields:
+
+    +-----------+-----------+------------------------------------------+
+    |*Column*   |*Field*    |*Contents*                                |
+    |           |           |                                          |
+    +-----------+-----------+------------------------------------------+
+    |1          |contig     |contig                                    |
+    |           |           |                                          |
+    +-----------+-----------+------------------------------------------+
+    |2          |start      |genomic start coordinate (zero-based)     |
+    +-----------+-----------+------------------------------------------+
+    |3          |end        |genomic end coordinate plus one           |
+    |           |           |(zero-based)                              |
+    +-----------+-----------+------------------------------------------+
+    |4          |name       |name of feature.                          |
+    +-----------+-----------+------------------------------------------+
+    |5          |score      |score of feature                          |
+    +-----------+-----------+------------------------------------------+
+    |6          |strand     |strand of feature                         |
+    +-----------+-----------+------------------------------------------+
+    |7          |thickStart |thickStart                                |
+    +-----------+-----------+------------------------------------------+
+    |8          |thickEnd   |thickEnd                                  |
+    +-----------+-----------+------------------------------------------+
+    |9          |itemRGB    |itemRGB                                   |
+    +-----------+-----------+------------------------------------------+
+    |10         |blockCount |number of bocks                           |
+    +-----------+-----------+------------------------------------------+
+    |11         |blockSizes |',' separated string of block sizes       |
+    +-----------+-----------+------------------------------------------+
+    |12         |blockStarts|',' separated string of block genomic     |
+    |           |           |start positions                           |
+    +-----------+-----------+------------------------------------------+
+
+    Only the first three fields are required. Additional
+    fields are optional, but if one is defined, all the preceding
+    need to be defined as well.
+
+    ''' 
+    cdef parse(self, char * buffer, int len):
+        cdef ctabixproxies.BedProxy r
+        r = ctabixproxies.BedProxy(self.encoding)
+        r.copy(buffer, len)
+        return r
+
+
+cdef class asVCF(Parser): 
+    '''converts a :term:`tabix row` into a VCF record with
+    the following fields:
+    
+    +----------+---------+------------------------------------+
+    |*Column*  |*Field*  |*Contents*                          |
+    |          |         |                                    |
+    +----------+---------+------------------------------------+
+    |1         |contig   |chromosome                          |
+    +----------+---------+------------------------------------+
+    |2         |pos      |chromosomal position, zero-based    |
+    +----------+---------+------------------------------------+
+    |3         |id       |id                                  |
+    +----------+---------+------------------------------------+
+    |4         |ref      |reference allele                    |
+    +----------+---------+------------------------------------+
+    |5         |alt      |alternate alleles                   |
+    +----------+---------+------------------------------------+
+    |6         |qual     |quality                             |
+    +----------+---------+------------------------------------+
+    |7         |filter   |filter                              |
+    +----------+---------+------------------------------------+
+    |8         |info     |info                                |
+    +----------+---------+------------------------------------+
+    |9         |format   |format specifier.                   |
+    +----------+---------+------------------------------------+
+
+    Access to genotypes is via index::
+
+        contig = vcf.contig
+        first_sample_genotype = vcf[0]
+        second_sample_genotype = vcf[1]
+
+    '''
+    cdef parse(self, char * buffer, int len):
+        cdef ctabixproxies.VCFProxy r
+        r = ctabixproxies.VCFProxy(self.encoding)
+        r.copy(buffer, len)
+        return r
+
+
+cdef class TabixFile:
+    """Random access to bgzf formatted files that
+    have been indexed by :term:`tabix`.
+
+    The file is automatically opened. The index file of file
+    ``<filename>`` is expected to be called ``<filename>.tbi``
+    by default (see parameter `index`).
+    
+    Parameters
+    ----------
+    
+    filename : string
+        Filename of bgzf file to be opened.
+
+    index : string
+        The filename of the index. If not set, the default is to
+        assume that the index is called ``filename.tbi``
+
+    mode : char
+        The file opening mode. Currently, only ``r`` is permitted.
+        
+    parser : :class:`pysam.Parser`
+    
+        sets the default parser for this tabix file. If `parser`
+        is None, the results are returned as an unparsed string.
+        Otherwise, `parser` is assumed to be a functor that will return
+        parsed data (see for example :class:`~pysam.asTuple` and
+        :class:`~pysam.asGTF`).
+
+    encoding : string
+
+        The encoding passed to the parser
+
+    threads: integer
+        Number of threads to use for decompressing Tabix files.
+        (Default=1)
+
+
+    Raises
+    ------
+    
+    ValueError
+        if index file is missing.
+
+    IOError
+        if file could not be opened
+    """
+    def __cinit__(self,
+                  filename,
+                  mode='r',
+                  parser=None,
+                  index=None,
+                  encoding="ascii",
+                  threads=1,
+                  *args,
+                  **kwargs ):
+
+        self.htsfile = NULL
+        self.is_remote = False
+        self.is_stream = False
+        self.parser = parser
+        self.threads = threads
+        self._open(filename, mode, index, *args, **kwargs)
+        self.encoding = encoding
+
+    def _open( self,
+               filename,
+               mode='r',
+               index=None,
+               threads=1,
+              ):
+        '''open a :term:`tabix file` for reading.'''
+
+        if mode != 'r':
+            raise ValueError("invalid file opening mode `%s`" % mode)
+
+        if self.htsfile != NULL:
+            self.close()
+        self.htsfile = NULL
+        self.threads=threads
+
+        filename_index = index or (filename + ".tbi")
+        # encode all the strings to pass to tabix
+        self.filename = encode_filename(filename)
+        self.filename_index = encode_filename(filename_index)
+
+        self.is_stream = self.filename == b'-'
+        self.is_remote = hisremote(self.filename)
+
+        if not self.is_remote:
+            if not os.path.exists(filename):
+                raise IOError("file `%s` not found" % filename)
+
+            if not os.path.exists(filename_index):
+                raise IOError("index `%s` not found" % filename_index)
+
+        # open file
+        cdef char *cfilename = self.filename
+        cdef char *cfilename_index = self.filename_index
+        with nogil:
+            self.htsfile = hts_open(cfilename, 'r')
+
+        if self.htsfile == NULL:
+            raise IOError("could not open file `%s`" % filename)
+        
+        #if self.htsfile.format.category != region_list:
+        #    raise ValueError("file does not contain region data")
+
+        with nogil:
+            self.index = tbx_index_load2(cfilename, cfilename_index)
+
+        if self.index == NULL:
+            raise IOError("could not open index for `%s`" % filename)
+
+        if not self.is_stream:
+            self.start_offset = self.tell()
+
+    def _dup(self):
+        '''return a copy of this tabix file.
+        
+        The file is being re-opened.
+        '''
+        return TabixFile(self.filename,
+                         mode="r",
+                         threads=self.threads,
+                         parser=self.parser,
+                         index=self.filename_index,
+                         encoding=self.encoding)
+
+    def fetch(self, 
+              reference=None,
+              start=None, 
+              end=None, 
+              region=None,
+              parser=None,
+              multiple_iterators=False):
+        '''fetch one or more rows in a :term:`region` using 0-based
+        indexing. The region is specified by :term:`reference`,
+        *start* and *end*. Alternatively, a samtools :term:`region`
+        string can be supplied.
+
+        Without *reference* or *region* all entries will be fetched. 
+        
+        If only *reference* is set, all reads matching on *reference*
+        will be fetched.
+
+        If *parser* is None, the default parser will be used for
+        parsing.
+        
+        Set *multiple_iterators* to true if you will be using multiple
+        iterators on the same file at the same time. The iterator
+        returned will receive its own copy of a filehandle to the file
+        effectively re-opening the file. Re-opening a file creates
+        some overhead, so beware.
+
+        '''
+        if not self.is_open():
+            raise ValueError("I/O operation on closed file")
+
+        # convert coordinates to region string, which is one-based
+        if reference:
+            if end is not None:
+                if end < 0:
+                    raise ValueError("end out of range (%i)" % end)
+                if start is None:
+                    start = 0
+                    
+                if start < 0:
+                    raise ValueError("start out of range (%i)" % end)
+                elif start > end:
+                    raise ValueError(
+                        'start (%i) >= end (%i)' % (start, end))
+                elif start == end:
+                    return EmptyIterator()
+                else:
+                    region = '%s:%i-%i' % (reference, start + 1, end)
+            elif start is not None:
+                if start < 0:
+                    raise ValueError("start out of range (%i)" % end)
+                region = '%s:%i' % (reference, start + 1)
+            else:
+                region = reference
+
+        # get iterator
+        cdef hts_itr_t * itr
+        cdef char *cstr
+        cdef TabixFile fileobj
+
+        # reopen the same file if necessary
+        if multiple_iterators:
+            fileobj = self._dup()
+        else:
+            fileobj = self
+
+        if region is None:
+            # without region or reference - iterate from start
+            with nogil:
+                itr = tbx_itr_queryi(fileobj.index,
+                                     HTS_IDX_START,
+                                     0,
+                                     0)
+        else:
+            s = force_bytes(region, encoding=fileobj.encoding)
+            cstr = s
+            with nogil:
+                itr = tbx_itr_querys(fileobj.index, cstr)
+
+        if itr == NULL:
+            if region is None:
+                if len(self.contigs) > 0:
+                    # when accessing a tabix file created prior tabix 1.0
+                    # the full-file iterator is empty.
+                    raise ValueError(
+                        "could not create iterator, possible "
+                        "tabix version mismatch")
+                else:
+                    # possible reason is that the file is empty -
+                    # return an empty iterator
+                    return EmptyIterator()
+            else:
+                raise ValueError(
+                    "could not create iterator for region '%s'" %
+                    region)
+            
+        # use default parser if no parser is specified
+        if parser is None:
+            parser = fileobj.parser
+
+        cdef TabixIterator a
+        if parser is None: 
+            a = TabixIterator(encoding=fileobj.encoding)
+        else:
+            parser.set_encoding(fileobj.encoding)
+            a = TabixIteratorParsed(parser)
+
+        a.tabixfile = fileobj
+        a.iterator = itr
+
+        return a
+
+    ###############################################################
+    ###############################################################
+    ###############################################################
+    ## properties
+    ###############################################################
+    property header:
+        '''the file header.
+
+        The file header consists of the lines at the beginning of a
+        file that are prefixed by the comment character ``#``.
+       
+        .. note::
+            The header is returned as an iterator presenting lines
+            without the newline character.
+        '''
+        
+        def __get__(self):
+
+            cdef char *cfilename = self.filename
+            cdef char *cfilename_index = self.filename_index
+            
+            cdef kstring_t buffer
+            buffer.l = buffer.m = 0
+            buffer.s = NULL
+            
+            cdef htsFile * fp = NULL
+            cdef int KS_SEP_LINE = 2
+            cdef tbx_t * tbx = NULL
+            lines = []
+            with nogil:
+                fp = hts_open(cfilename, 'r')
+                
+            if fp == NULL:
+                raise OSError("could not open {} for reading header".format(self.filename))
+
+            with nogil:
+                tbx = tbx_index_load2(cfilename, cfilename_index)
+                
+            if tbx == NULL:
+                raise OSError("could not load .tbi/.csi index of {}".format(self.filename))
+
+            while hts_getline(fp, KS_SEP_LINE, &buffer) >= 0:
+                if not buffer.l or buffer.s[0] != tbx.conf.meta_char:
+                    break
+                lines.append(force_str(buffer.s, self.encoding))
+
+            with nogil:
+                hts_close(fp)
+                free(buffer.s)
+
+            return lines
+
+    property contigs:
+        '''list of chromosome names'''
+        def __get__(self):
+            cdef const char ** sequences
+            cdef int nsequences
+            
+            with nogil:
+                sequences = tbx_seqnames(self.index, &nsequences)
+            cdef int x
+            result = []
+            for x from 0 <= x < nsequences:
+                result.append(force_str(sequences[x]))
+            
+            # htslib instructions:
+            # only free container, not the sequences themselves
+            free(sequences)
+
+            return result
+            
+    def close(self):
+        '''
+        closes the :class:`pysam.TabixFile`.'''
+        if self.htsfile != NULL:
+            hts_close(self.htsfile)
+            self.htsfile = NULL
+        if self.index != NULL:
+            tbx_destroy(self.index)
+            self.index = NULL
+
+    def __dealloc__( self ):
+        # remember: dealloc cannot call other python methods
+        # note: no doc string
+        # note: __del__ is not called.
+        if self.htsfile != NULL:
+            hts_close(self.htsfile)
+            self.htsfile = NULL
+        if self.index != NULL:
+            tbx_destroy(self.index)
+
+
+cdef class TabixIterator:
+    """iterates over rows in *tabixfile* in region
+    given by *tid*, *start* and *end*.
+    """
+
+    def __init__(self, encoding="ascii"):
+        self.encoding = encoding
+    
+    def __iter__(self):
+        self.buffer.s = NULL
+        self.buffer.l = 0
+        self.buffer.m = 0
+
+        return self 
+
+    cdef int __cnext__(self):
+        '''iterate to next element.
+        
+        Return -5 if file has been closed when this function
+        was called.
+        '''
+        if self.tabixfile.htsfile == NULL:
+            return -5
+
+        cdef int retval
+
+        while 1:
+            with nogil:
+                retval = tbx_itr_next(
+                    self.tabixfile.htsfile,
+                    self.tabixfile.index,
+                    self.iterator,
+                    &self.buffer)
+
+            if retval < 0:
+                break
+
+            if self.buffer.s[0] != '#':
+                break
+
+        return retval
+
+    def __next__(self): 
+        """python version of next().
+
+        pyrex uses this non-standard name instead of next()
+        """
+        
+        cdef int retval = self.__cnext__()
+        if retval == -5:
+            raise IOError("iteration on closed file")
+        elif retval < 0:
+            raise StopIteration
+
+        return charptr_to_str(self.buffer.s, self.encoding)
+
+    def next(self):
+        return self.__next__()
+
+    def __dealloc__(self):
+        if <void*>self.iterator != NULL:
+            tbx_itr_destroy(self.iterator)
+        if self.buffer.s != NULL:
+            free(self.buffer.s)
+
+
+class EmptyIterator:
+    '''empty iterator'''
+
+    def __iter__(self):
+        return self
+
+    def next(self):
+        raise StopIteration()
+
+    def __next__(self):
+        raise StopIteration()
+
+
+cdef class TabixIteratorParsed(TabixIterator):
+    """iterates over mapped reads in a region.
+
+    The *parser* determines the encoding.
+
+    Returns parsed data.
+    """
+
+    def __init__(self, 
+                 Parser parser):
+        
+        TabixIterator.__init__(self)
+        self.parser = parser
+
+    def __next__(self): 
+        """python version of next().
+
+        pyrex uses this non-standard name instead of next()
+        """
+        
+        cdef int retval = self.__cnext__()
+        if retval == -5:
+            raise IOError("iteration on closed file")
+        elif retval < 0:
+            raise StopIteration
+
+        return self.parser.parse(self.buffer.s,
+                                 self.buffer.l)
+
+
+cdef class GZIterator:
+    def __init__(self, filename, int buffer_size=65536, encoding="ascii"):
+        '''iterate line-by-line through gzip (or bgzip)
+        compressed file.
+        '''
+        if not os.path.exists(filename):
+            raise IOError("No such file or directory: %s" % filename)
+
+        filename = encode_filename(filename)
+        cdef char *cfilename = filename
+        with nogil:
+            self.gzipfile = bgzf_open(cfilename, "r")
+        self._filename = filename
+        self.kstream = ks_init(self.gzipfile)
+        self.encoding = encoding
+
+        self.buffer.l = 0
+        self.buffer.m = 0
+        self.buffer.s = <char*>malloc(buffer_size)
+
+    def __dealloc__(self):
+        '''close file.'''
+        if self.gzipfile != NULL:
+            bgzf_close(self.gzipfile)
+            self.gzipfile = NULL
+        if self.buffer.s != NULL:
+            free(self.buffer.s)
+        if self.kstream != NULL:
+            ks_destroy(self.kstream)
+
+    def __iter__(self):
+        return self
+
+    cdef int __cnext__(self):
+        cdef int dret = 0
+        cdef int retval = 0
+        while 1:
+            with nogil:
+                retval = ks_getuntil(self.kstream, '\n', &self.buffer, &dret)
+            
+            if retval < 0: 
+                break
+
+            return dret
+        return -1
+
+    def __next__(self):
+        """python version of next().
+        """
+        cdef int retval = self.__cnext__()
+        if retval < 0:
+            raise StopIteration
+        return force_str(self.buffer.s, self.encoding)
+
+
+cdef class GZIteratorHead(GZIterator):
+    '''iterate line-by-line through gzip (or bgzip)
+    compressed file returning comments at top of file.
+    '''
+
+    def __next__(self):
+        """python version of next().
+        """
+        cdef int retval = self.__cnext__()
+        if retval < 0:
+            raise StopIteration
+        if self.buffer.s[0] == '#':
+            return self.buffer.s
+        else:
+            raise StopIteration
+
+
+cdef class GZIteratorParsed(GZIterator):
+    '''iterate line-by-line through gzip (or bgzip)
+    compressed file returning comments at top of file.
+    '''
+
+    def __init__(self, parser):
+        self.parser = parser
+
+    def __next__(self):
+        """python version of next().
+        """
+        cdef int retval = self.__cnext__()
+        if retval < 0:
+            raise StopIteration
+
+        return self.parser.parse(self.buffer.s,
+                                 self.buffer.l)
+
+
+def tabix_compress(filename_in, 
+                   filename_out,
+                   force=False):
+    '''compress *filename_in* writing the output to *filename_out*.
+    
+    Raise an IOError if *filename_out* already exists, unless *force*
+    is set.
+    '''
+
+    if not force and os.path.exists(filename_out):
+        raise IOError(
+            "Filename '%s' already exists, use *force* to "
+            "overwrite" % filename_out)
+
+    cdef int WINDOW_SIZE
+    cdef int c, r
+    cdef void * buffer
+    cdef BGZF * fp
+    cdef int fd_src
+    cdef bint is_empty = True
+    cdef int O_RDONLY
+    O_RDONLY = os.O_RDONLY
+
+    WINDOW_SIZE = 64 * 1024
+
+    fn = encode_filename(filename_out)
+    cdef char *cfn = fn
+    with nogil:
+        fp = bgzf_open(cfn, "w")
+    if fp == NULL:
+        raise IOError("could not open '%s' for writing" % filename_out)
+
+    fn = encode_filename(filename_in)
+    fd_src = open(fn, O_RDONLY)
+    if fd_src == 0:
+        raise IOError("could not open '%s' for reading" % filename_in)
+
+    buffer = malloc(WINDOW_SIZE)
+    c = 1
+    
+    while c > 0:
+        with nogil:
+            c = read(fd_src, buffer, WINDOW_SIZE)
+            if c > 0:
+                is_empty = False
+            r = bgzf_write(fp, buffer, c)
+        if r < 0:
+            free(buffer)
+            raise IOError("writing failed")
+        
+    free(buffer)
+    r = bgzf_close(fp)
+    if r < 0:
+        raise IOError("error %i when writing to file %s" % (r, filename_out))
+
+    r = close(fd_src)
+    # an empty file will return with -1, thus ignore this.
+    if r < 0:
+        if not (r == -1 and is_empty):
+            raise IOError("error %i when closing file %s" % (r, filename_in))
+
+
+def tabix_index(filename,
+                force=False,
+                seq_col=None,
+                start_col=None,
+                end_col=None,
+                preset=None,
+                meta_char="#",
+                int line_skip=0,
+                zerobased=False,
+                int min_shift=-1,
+                index=None,
+                keep_original=False,
+                csi=False,
+                ):
+    '''index tab-separated *filename* using tabix.
+
+    An existing index will not be overwritten unless *force* is set.
+
+    The index will be built from coordinates in columns *seq_col*,
+    *start_col* and *end_col*.
+
+    The contents of *filename* have to be sorted by contig and
+    position - the method does not check if the file is sorted.
+
+    Column indices are 0-based. Note that this is different from the
+    tabix command line utility where column indices start at 1.
+    
+    Coordinates in the file are assumed to be 1-based unless
+    *zerobased* is set.
+
+    If *preset* is provided, the column coordinates are taken from a
+    preset. Valid values for preset are "gff", "bed", "sam", "vcf",
+    psltbl", "pileup".
+    
+    Lines beginning with *meta_char* and the first *line_skip* lines
+    will be skipped.
+
+    If *filename* is not detected as a gzip file it will be automatically
+    compressed. The original file will be removed and only the compressed
+    file will be retained.
+
+    By default or when *min_shift* is 0, creates a TBI index. If *min_shift*
+    is greater than zero and/or *csi* is True, creates a CSI index with a
+    minimal interval size of 1<<*min_shift* (1<<14 if only *csi* is set).
+
+    *index* controls the filename which should be used for creating the index.
+    If not set, the default is to append ``.tbi`` to *filename*.
+
+    When automatically compressing files, if *keep_original* is set the
+    uncompressed file will not be deleted.
+
+    returns the filename of the compressed data
+
+    '''
+    
+    if preset is None and \
+       (seq_col is None or start_col is None or end_col is None):
+        raise ValueError(
+            "neither preset nor seq_col,start_col and end_col given")
+
+    fn = encode_filename(filename)
+    cdef char *cfn = fn
+
+    cdef htsFile *fp = hts_open(cfn, "r")
+    if fp == NULL:
+        raise IOError("Could not open file '%s': %s" % (filename, force_str(strerror(errno))))
+
+    cdef htsFormat fmt = hts_get_format(fp)[0]
+    hts_close(fp)
+
+    if fmt.compression == no_compression:
+        tabix_compress(filename, filename + ".gz", force=force)
+        if not keep_original:
+            os.unlink(filename)
+        filename += ".gz"
+        fn = encode_filename(filename)
+        cfn = fn
+
+    # columns (1-based):
+    #   preset-code, contig, start, end, metachar for
+    #     comments, lines to ignore at beginning
+    # 0 is a missing column
+    preset2conf = {
+        'gff' : (TBX_GENERIC, 1, 4, 5, ord('#'), 0),
+        'bed' : (TBX_UCSC, 1, 2, 3, ord('#'), 0),
+        'psltbl' : (TBX_UCSC, 15, 17, 18, ord('#'), 0),
+        'sam' : (TBX_SAM, 3, 4, 0, ord('@'), 0),
+        'vcf' : (TBX_VCF, 1, 2, 0, ord('#'), 0),
+        }
+    
+    conf_data = None
+    if preset == "bcf" or fmt.format == bcf:
+        csi = True
+    elif preset:
+        try:
+            conf_data = preset2conf[preset]
+        except KeyError:
+            raise KeyError(
+                "unknown preset '%s', valid presets are '%s'" %
+                (preset, ",".join(preset2conf.keys())))
+    else:
+        if end_col is None:
+            end_col = -1
+            
+        preset = 0
+        # tabix internally works with 0-based coordinates and
+        # open/closed intervals.  When using a preset, conversion is
+        # automatically taken care of.  Otherwise, the coordinates are
+        # assumed to be 1-based closed intervals and -1 is subtracted
+        # from the start coordinate. To avoid doing this, set the
+        # TI_FLAG_UCSC=0x10000 flag:
+        if zerobased:
+            preset = preset | TBX_UCSC
+
+        conf_data = (preset, seq_col + 1, start_col + 1, end_col + 1, ord(meta_char), line_skip)
+
+    cdef tbx_conf_t conf
+    if conf_data:
+        conf.preset, conf.sc, conf.bc, conf.ec, conf.meta_char, conf.line_skip = conf_data
+
+    if csi or min_shift > 0:
+        suffix = ".csi"
+        if min_shift <= 0: min_shift = 14
+    else:
+        suffix = ".tbi"
+        min_shift = 0
+
+    index = index or filename + suffix    
+    fn_index = encode_filename(index)
+
+    if not force and os.path.exists(index):
+        raise IOError(
+            "filename '%s' already exists, use *force* to overwrite" % index)
+    
+    cdef char *fnidx = fn_index
+    cdef int retval = 0
+
+    if csi and fmt.format == bcf:
+        with nogil:
+            retval = bcf_index_build2(cfn, fnidx, min_shift)
+    else:
+        with nogil:
+            retval = tbx_index_build2(cfn, fnidx, min_shift, &conf)
+            
+    if retval != 0:
+        raise OSError("building of index for {} failed".format(filename))
+    
+    return filename
+
+# #########################################################
+# cdef class tabix_file_iterator_old:
+#     '''iterate over ``infile``.
+
+#     This iterator is not safe. If the :meth:`__next__()` method is called 
+#     after ``infile`` is closed, the result is undefined (see ``fclose()``).
+
+#     The iterator might either raise a StopIteration or segfault.
+#     '''
+
+
+#     def __cinit__(self, 
+#                   infile, 
+#                   Parser parser,
+#                   int buffer_size = 65536 ):
+
+#         cdef int fd = PyObject_AsFileDescriptor( infile )
+#         if fd == -1: raise ValueError( "I/O operation on closed file." )
+#         self.infile = fdopen( fd, 'r')
+
+#         if self.infile == NULL: raise ValueError( "I/O operation on closed file." )
+
+#         self.buffer = <char*>malloc( buffer_size )        
+#         self.size = buffer_size
+#         self.parser = parser
+
+#     def __iter__(self):
+#         return self
+
+#     cdef __cnext__(self):
+
+#         cdef char * b
+#         cdef size_t nbytes
+#         b = self.buffer
+
+#         while not feof( self.infile ):
+#             nbytes = getline( &b, &self.size, self.infile)
+
+#             # stop at first error or eof
+#             if (nbytes == -1): break
+#             # skip comments
+#             if (b[0] == '#'): continue
+
+#             # skip empty lines
+#             if b[0] == '\0' or b[0] == '\n' or b[0] == '\r': continue
+
+#             # make sure that entry is complete
+#             if b[nbytes-1] != '\n' and b[nbytes-1] != '\r':
+#                 result = b
+#                 raise ValueError( "incomplete line at %s" % result )
+
+#             # make sure that this goes fully through C
+#             # otherwise buffer is copied to/from a
+#             # Python object causing segfaults as
+#             # the wrong memory is freed
+#             return self.parser.parse( b, nbytes )
+
+#         raise StopIteration
+
+#     def __dealloc__(self):
+#         free(self.buffer)
+
+#     def __next__(self):
+#         return self.__cnext__()
+
+#########################################################
+#########################################################
+#########################################################
+## Iterators for parsing through unindexed files.
+#########################################################
+# cdef buildGzipError(void *gzfp):
+#     cdef int errnum = 0
+#     cdef char *s = gzerror(gzfp, &errnum)
+#     return "error (%d): %s (%d: %s)" % (errno, strerror(errno), errnum, s)
+
+
+cdef class tabix_file_iterator:
+    '''iterate over a compressed or uncompressed ``infile``.
+    '''
+
+    def __cinit__(self, 
+                  infile, 
+                  Parser parser,
+                  int buffer_size=65536):
+
+        if infile.closed:
+            raise ValueError("I/O operation on closed file.")
+
+        self.infile = infile
+
+        cdef int fd = PyObject_AsFileDescriptor(infile)
+        if fd == -1:
+            raise ValueError("I/O operation on closed file.")
+
+        self.duplicated_fd = dup(fd)
+
+        # From the manual:
+        # gzopen can be used to read a file which is not in gzip format; 
+        # in this case gzread will directly read from the file without decompression. 
+        # When reading, this will be detected automatically by looking 
+        # for the magic two-byte gzip header. 
+        self.fh = bgzf_dopen(self.duplicated_fd, 'r')
+
+        if self.fh == NULL: 
+            raise IOError('%s' % strerror(errno))
+
+        self.kstream = ks_init(self.fh) 
+        
+        self.buffer.s = <char*>malloc(buffer_size)
+        #if self.buffer == NULL:
+        #    raise MemoryError( "tabix_file_iterator: could not allocate %i bytes" % buffer_size)
+        #self.size = buffer_size
+        self.parser = parser
+
+    def __iter__(self):
+        return self
+
+    cdef __cnext__(self):
+
+        cdef char * b
+        cdef int dret = 0
+        cdef int retval = 0
+        while 1:
+            with nogil:
+                retval = ks_getuntil(self.kstream, '\n', &self.buffer, &dret)
+            
+            if retval < 0: 
+                break
+                #raise IOError('gzip error: %s' % buildGzipError( self.fh ))
+
+            b = self.buffer.s
+            
+            # skip comments
+            if (b[0] == '#'):
+                continue
+
+            # skip empty lines
+            if b[0] == '\0' or b[0] == '\n' or b[0] == '\r':
+                continue
+
+            # gzgets terminates at \n, no need to test
+
+            # parser creates a copy
+            return self.parser.parse(b, self.buffer.l)
+
+        raise StopIteration
+
+    def __dealloc__(self):
+        free(self.buffer.s)
+        ks_destroy(self.kstream)
+        bgzf_close(self.fh)
+        
+    def __next__(self):
+        return self.__cnext__()
+
+    def next(self):
+        return self.__cnext__()
+    
+
+class tabix_generic_iterator:
+    '''iterate over ``infile``.
+    
+    Permits the use of file-like objects for example from the gzip module.
+    '''
+    def __init__(self, infile, parser):
+
+        self.infile = infile
+        if self.infile.closed:
+            raise ValueError("I/O operation on closed file.")
+        self.parser = parser
+
+    def __iter__(self):
+        return self
+
+    # cython version - required for python 3
+    def __next__(self):
+        
+        cdef char * b
+        cdef char * cpy
+        cdef size_t nbytes
+
+        encoding = self.parser.get_encoding()
+
+        # note that GzipFile.close() does not close the file
+        # reading is still possible.
+        if self.infile.closed:
+            raise ValueError("I/O operation on closed file.")
+
+        while 1:
+
+            line = self.infile.readline()
+            if not line:
+                break
+            
+            s = force_bytes(line, encoding)
+            b = s
+            nbytes = len(line)
+            assert b[nbytes] == '\0'
+
+            # skip comments
+            if b[0] == '#':
+                continue
+
+            # skip empty lines
+            if b[0] == '\0' or b[0] == '\n' or b[0] == '\r':
+                continue
+            
+            # make sure that entry is complete
+            if b[nbytes-1] != '\n' and b[nbytes-1] != '\r':
+                raise ValueError("incomplete line at %s" % line)
+            
+            bytes_cpy = <bytes> b
+            cpy = <char *> bytes_cpy
+
+            return self.parser(cpy, nbytes)            
+
+        raise StopIteration
+
+    # python version - required for python 2.7
+    def next(self):
+        return self.__next__()
+    
+
+def tabix_iterator(infile, parser):
+    """return an iterator over all entries in a file.
+    
+    Results are returned parsed as specified by the *parser*. If
+    *parser* is None, the results are returned as an unparsed string.
+    Otherwise, *parser* is assumed to be a functor that will return
+    parsed data (see for example :class:`~pysam.asTuple` and
+    :class:`~pysam.asGTF`).
+
+    """
+    if PY_MAJOR_VERSION >= 3:
+        return tabix_generic_iterator(infile, parser)
+    else:
+        return tabix_file_iterator(infile, parser)
+        
+    # file objects can use C stdio
+    # used to be: isinstance( infile, file):
+    # if PY_MAJOR_VERSION >= 3:
+    #     if isinstance( infile, io.IOBase ):
+    #         return tabix_copy_iterator( infile, parser )
+    #     else:
+    #         return tabix_generic_iterator( infile, parser )
+    # else:
+#        if isinstance( infile, file ):
+#            return tabix_copy_iterator( infile, parser )
+#        else:
+#            return tabix_generic_iterator( infile, parser )
+    
+cdef class Tabixfile(TabixFile):
+    """Tabixfile is deprecated: use TabixFile instead"""
+    pass
+
+
+__all__ = [
+    "tabix_index", 
+    "tabix_compress",
+    "TabixFile",
+    "Tabixfile",
+    "asTuple",
+    "asGTF",
+    "asGFF3",
+    "asVCF",
+    "asBed",
+    "GZIterator",
+    "GZIteratorHead",
+    "tabix_iterator", 
+    "tabix_generic_iterator", 
+    "tabix_file_iterator", 
+]
diff --git a/pysam/libctabixproxies.pxd b/pysam/libctabixproxies.pxd
new file mode 100644
index 0000000..907b40d
--- /dev/null
+++ b/pysam/libctabixproxies.pxd
@@ -0,0 +1,65 @@
+#cdef extern from "Python.h":
+#    ctypedef struct FILE
+
+from libc.stdint cimport uint8_t, int32_t, uint32_t, int64_t, uint64_t
+
+cdef class TupleProxy:
+
+    cdef:
+        char * data
+        char ** fields
+        int nfields
+        int nbytes
+        int offset
+        bint is_modified
+
+    cdef encoding
+
+    cpdef int getMaxFields(self)
+    cpdef int getMinFields(self)
+#    cdef char * _getindex(self, int idx)
+
+    cdef take(self, char * buffer, size_t nbytes)
+    cdef present(self, char * buffer, size_t nbytes)
+    cdef copy(self, char * buffer, size_t nbytes, bint reset=*)
+    cdef update(self, char * buffer, size_t nbytes)
+
+
+cdef class TupleProxyIterator:
+    cdef TupleProxy proxy
+    cdef int index
+
+
+cdef class NamedTupleProxy(TupleProxy):
+    pass
+
+
+cdef class GTFProxy(NamedTupleProxy):
+    cdef object attribute_dict
+    cpdef int getMaxFields(self)
+    cpdef int getMinFields(self)
+
+
+cdef class GFF3Proxy(GTFProxy):
+    pass
+
+
+cdef class BedProxy(NamedTupleProxy):
+
+    cdef:
+        char * contig
+        uint32_t start
+        uint32_t end
+        int bedfields
+
+    cpdef int getMaxFields(self)
+    cpdef int getMinFields(self)
+    cdef update(self, char * buffer, size_t nbytes)
+
+cdef class VCFProxy(NamedTupleProxy) :
+
+    cdef:
+        char * contig
+        uint32_t pos
+
+    cdef update(self, char * buffer, size_t nbytes)
diff --git a/pysam/libctabixproxies.pyi b/pysam/libctabixproxies.pyi
new file mode 100644
index 0000000..f720c7e
--- /dev/null
+++ b/pysam/libctabixproxies.pyi
@@ -0,0 +1,62 @@
+from typing import (
+    Optional,
+    overload,
+    List,
+    Dict,
+    OrderedDict,
+    Tuple,
+    Iterable,
+    KeysView,
+    Any,
+)
+
+class TupleProxyIterator:
+    def __init__(self, proxy: Any): ...
+    def __iter__(self) -> TupleProxyIterator: ...
+    def __next__(self) -> Optional[str]: ...
+
+class TupleProxy:
+    def __init__(self, encoding: str = ...) -> None: ...
+    def __copy__(self) -> TupleProxy: ...
+    def compare(self, other: TupleProxy) -> int: ...
+    def getMinFields(self) -> int: ...
+    def getMaxFields(self) -> int: ...
+    def _getindex(self, index: int) -> str: ...
+    @overload
+    def __getitem__(self, key: slice) -> List[str]: ...
+    @overload
+    def __getitem__(self, key: int) -> Any: ...
+    def _setindex(self, index: int, value: Optional[str]) -> None: ...
+    def __setitem__(self, index: int, value: Optional[str]) -> None: ...
+    def __len__(self) -> int: ...
+    def __iter__(self) -> TupleProxyIterator: ...
+
+class NamedTupleProxy(TupleProxy):
+    def __setattr__(self, key: str, value: str) -> None: ...
+    def __getattr__(self, key: str) -> str: ...
+
+class GTFProxy(NamedTupleProxy):
+    def to_dict(self) -> Dict[str, Any]: ...
+    def from_dict(self, d: Dict[str, Any]) -> None: ...
+    def invert(self, lcontig: int) -> None: ...
+    def keys(self) -> KeysView[str]: ...
+    def setAttribute(self, key: str, value: Any) -> None: ...
+    def attribute_string2dict(self, s: str) -> OrderedDict[str, Any]: ...
+    def dict2attribute_string(self, d: Dict[str, Any]) -> str: ...
+    def attribute_string2iterator(self, s: str) -> Iterable[Tuple[str, Any]]: ...
+    def __getattr__(self, key: str) -> Any: ...
+    def __setattr__(self, key: str, value: Any) -> None: ...
+    # deprecated:
+    # def asDict(self) -> Any: ...
+    # def as_dict(self) -> Any: ...
+    # def fromDict(self, *args, **kwargs) -> Any: ...
+
+class GFF3Proxy(GTFProxy): ...
+
+class BedProxy(NamedTupleProxy):
+    def __setattr__(self, key: str, value: Any) -> None: ...
+
+class VCFProxy(NamedTupleProxy):
+    @property
+    def pos(self) -> int: ...
+    def __setattr__(self, key: str, value: Any) -> None: ...
diff --git a/pysam/libctabixproxies.pyx b/pysam/libctabixproxies.pyx
new file mode 100644
index 0000000..10b3e5a
--- /dev/null
+++ b/pysam/libctabixproxies.pyx
@@ -0,0 +1,836 @@
+from cpython cimport PyBytes_FromStringAndSize
+
+from libc.stdio cimport printf, feof, fgets
+from libc.string cimport strcpy, strlen, memcmp, memcpy, memchr, strstr, strchr
+from libc.stdlib cimport free, malloc, calloc, realloc
+from libc.stdlib cimport atoi, atol, atof
+
+from pysam.libcutils cimport force_bytes, force_str, charptr_to_str
+from pysam.libcutils cimport encode_filename, from_string_and_size
+
+import collections
+import copy
+
+
+cdef char *StrOrEmpty(char * buffer):
+     if buffer == NULL:
+         return ""
+     else: return buffer
+
+
+cdef int isNew(char * p, char * buffer, size_t nbytes):
+    """return True if `p` is located within `buffer` of size
+    `nbytes`
+    """
+    if p == NULL:
+        return 0
+    
+    return not (buffer <= p <= buffer + nbytes)
+
+
+cdef class TupleProxy:
+    '''Proxy class for access to parsed row as a tuple.
+
+    This class represents a table row for fast read-access.
+
+    Access to individual fields is via the [] operator.
+    
+    Only read-only access is implemented.
+
+    '''
+
+    def __cinit__(self, encoding="ascii"): 
+        self.data = NULL
+        self.fields = NULL
+        self.nbytes = 0
+        self.is_modified = 0
+        self.nfields = 0
+        # start counting at field offset
+        self.offset = 0
+        self.encoding = encoding
+
+    def __dealloc__(self):
+        cdef int x
+        if self.is_modified:
+            for x from 0 <= x < self.nfields:
+                if isNew(self.fields[x], self.data, self.nbytes):
+                    free(self.fields[x])
+                    self.fields[x] = NULL
+
+        if self.data != NULL:
+            free(self.data)
+        if self.fields != NULL:
+            free(self.fields)
+
+    def __copy__(self):
+        if self.is_modified:
+            raise NotImplementedError(
+                "copying modified tuples is not implemented")
+        cdef TupleProxy n = type(self)()
+        n.copy(self.data, self.nbytes, reset=True)
+        return n
+
+    def compare(self, TupleProxy other):
+        '''return -1,0,1, if contents in this are binary
+        <,=,> to *other*
+
+        '''
+        if self.is_modified or other.is_modified:
+            raise NotImplementedError(
+                'comparison of modified TupleProxies is not implemented')
+        if self.data == other.data:
+            return 0
+
+        if self.nbytes < other.nbytes:
+            return -1
+        elif self.nbytes > other.nbytes:
+            return 1
+        return memcmp(self.data, other.data, self.nbytes)
+
+    def __richcmp__(self, TupleProxy other, int op):
+        if op == 2:  # == operator
+            return self.compare(other) == 0
+        elif op == 3:  # != operator
+            return self.compare(other) != 0
+        else:
+            err_msg = "op {0} isn't implemented yet".format(op)
+            raise NotImplementedError(err_msg)
+
+    cdef take(self, char * buffer, size_t nbytes):
+        '''start presenting buffer.
+
+        Take ownership of the pointer.
+        '''
+        self.data = buffer
+        self.nbytes = nbytes
+        self.update(buffer, nbytes)
+
+    cdef present(self, char * buffer, size_t nbytes):
+        '''start presenting buffer.
+
+        Do not take ownership of the pointer.
+        '''
+        self.update(buffer, nbytes)
+
+    cdef copy(self, char * buffer, size_t nbytes, bint reset=False):
+        '''start presenting buffer of size *nbytes*.
+
+        Buffer is a '\0'-terminated string without the '\n'.
+
+        Take a copy of buffer.
+        '''
+        # +1 for '\0'
+        cdef int s = sizeof(char) *  (nbytes + 1)
+        self.data = <char*>malloc(s)
+        if self.data == NULL:
+            raise ValueError("out of memory in TupleProxy.copy()")
+        memcpy(<char*>self.data, buffer, s)
+
+        if reset:
+            for x from 0 <= x < nbytes:
+                if self.data[x] == '\0':
+                    self.data[x] = '\t'
+
+        self.update(self.data, nbytes)
+
+    cpdef int getMinFields(self):
+        '''return minimum number of fields.'''
+        # 1 is not a valid tabix entry, but TupleProxy
+        # could be more generic.
+        return 1
+
+    cpdef int getMaxFields(self):
+        '''return maximum number of fields. Return 
+        0 for unknown length.'''
+        return 0
+
+    cdef update(self, char * buffer, size_t nbytes):
+        '''update internal data.
+
+        *buffer* is a \0 terminated string.
+
+        *nbytes* is the number of bytes in buffer (excluding
+        the \0)
+
+        Update starts work in buffer, thus can be used
+        to collect any number of fields until nbytes
+        is exhausted.
+
+        If max_fields is set, the number of fields is initialized to
+        max_fields.
+
+        '''
+        cdef char * pos
+        cdef char * old_pos
+        cdef int field
+        cdef int max_fields, min_fields, x
+
+        assert strlen(buffer) == nbytes, \
+            "length of buffer (%i) != number of bytes (%i)" % (
+            strlen(buffer), nbytes)
+
+        if buffer[nbytes] != 0:
+            raise ValueError("incomplete line at %s" % buffer)
+
+        #################################
+        # remove line breaks and feeds and update number of bytes
+        x = nbytes - 1
+        while x > 0 and (buffer[x] == '\n' or buffer[x] == '\r'): 
+            buffer[x] = '\0'
+            x -= 1
+        self.nbytes = x + 1
+
+        #################################
+        # clear data
+        if self.fields != NULL:
+            free(self.fields)
+ 
+        for field from 0 <= field < self.nfields:
+            if isNew(self.fields[field], self.data, self.nbytes):
+                free(self.fields[field])
+                
+        self.is_modified = self.nfields = 0
+
+        #################################
+        # allocate new
+        max_fields = self.getMaxFields()
+        # pre-count fields - better would be
+        # to guess or dynamically grow
+        if max_fields == 0:
+            for x from 0 <= x < nbytes:
+                if buffer[x] == '\t':
+                    max_fields += 1
+            max_fields += 1
+
+        self.fields = <char **>calloc(max_fields, sizeof(char *)) 
+        if self.fields == NULL:
+            raise ValueError("out of memory in TupleProxy.update()")
+
+        #################################
+        # start filling
+        field = 0
+        self.fields[field] = pos = buffer
+        field += 1
+        old_pos = pos
+        while 1:
+            
+            pos = <char*>memchr(pos, '\t', nbytes)
+            if pos == NULL:
+                break
+            if field >= max_fields:
+                raise ValueError(
+                    "parsing error: more than %i fields in line: %s" %
+                    (max_fields, buffer))
+
+            pos[0] = '\0'
+            pos += 1
+            self.fields[field] = pos
+            field += 1
+            nbytes -= pos - old_pos
+            if nbytes < 0:
+                break
+            old_pos = pos
+        self.nfields = field
+        if self.nfields < self.getMinFields():
+            raise ValueError(
+                "parsing error: fewer than %i fields in line: %s" %
+                (self.getMinFields(), buffer))
+
+    def _getindex(self, int index):
+        '''return item at idx index'''
+        cdef int i = index
+        if i < 0:
+            i += self.nfields
+        if i < 0:
+            raise IndexError("list index out of range")
+        # apply offset - separating a fixed number 
+        # of fields from a variable number such as in VCF
+        i += self.offset
+        if i >= self.nfields:
+            raise IndexError(
+                "list index out of range %i >= %i" %
+                (i, self.nfields))
+        return force_str(self.fields[i], self.encoding)
+
+    def __getitem__(self, key):
+        if type(key) == int:
+            return self._getindex(key)
+        # slice object
+        start, end, step = key.indices(self.nfields)
+        result = []
+        for index in range(start, end, step):
+            result.append(self._getindex(index))
+        return result
+
+    def _setindex(self, index, value):
+        '''set item at idx index.'''
+        cdef int idx = index
+        if idx < 0:
+            raise IndexError("list index out of range")
+        if idx >= self.nfields:
+            raise IndexError("list index out of range")
+
+        if isNew(self.fields[idx], self.data, self.nbytes):
+            free(self.fields[idx])
+
+        self.is_modified = 1
+
+        if value is None:
+            self.fields[idx] = NULL
+            return
+
+        # conversion with error checking
+        value = force_bytes(value)
+        cdef char * tmp = <char*>value
+        self.fields[idx] = <char*>malloc((strlen( tmp ) + 1) * sizeof(char))
+        if self.fields[idx] == NULL:
+            raise ValueError("out of memory" )
+        strcpy(self.fields[idx], tmp)
+
+    def __setitem__(self, index, value):
+        '''set item at *index* to *value*'''
+        cdef int i = index
+        if i < 0:
+            i += self.nfields
+        i += self.offset
+        
+        self._setindex(i, value)
+
+    def __len__(self):
+        return self.nfields
+
+    def __iter__(self):
+        return TupleProxyIterator(self)
+
+    def __str__(self):
+        '''return original data'''
+        # copy and replace \0 bytes with \t characters
+        cdef char * cpy
+        if self.is_modified:
+            # todo: treat NULL values
+            result = []
+            for x in xrange(0, self.nfields):
+                result.append(StrOrEmpty(self.fields[x]).decode(self.encoding))
+            return "\t".join(result)
+        else:
+            cpy = <char*>calloc(sizeof(char), self.nbytes+1)
+            if cpy == NULL:
+                raise ValueError("out of memory")
+            memcpy(cpy, self.data, self.nbytes+1)
+            for x from 0 <= x < self.nbytes:
+                if cpy[x] == '\0':
+                    cpy[x] = '\t'
+            result = cpy[:self.nbytes]
+            free(cpy)
+            r = result.decode(self.encoding)
+            return r
+
+
+cdef class TupleProxyIterator:
+    def __init__(self, proxy):
+        self.proxy = proxy
+        self.index = 0
+
+    def __iter__(self):
+        return self
+
+    def __next__(self):
+        if self.index >= self.proxy.nfields:
+            raise StopIteration
+        cdef char *retval = self.proxy.fields[self.index]
+        self.index += 1
+        return force_str(retval, self.proxy.encoding) if retval != NULL else None
+
+
+def toDot(v):
+    '''convert value to '.' if None'''
+    if v is None:
+        return "." 
+    else:
+        return str(v)
+
+def quote(v):
+    '''return a quoted attribute.'''
+    if isinstance(v, str):
+        return '"%s"' % v
+    else: 
+        return str(v)
+
+
+cdef class NamedTupleProxy(TupleProxy):
+
+    map_key2field = {}
+
+    def __setattr__(self, key, value):
+        '''set attribute.'''
+        cdef int idx
+        idx, f = self.map_key2field[key]
+        if self.nfields < idx:
+            raise KeyError("field %s not set" % key)
+        TupleProxy.__setitem__(self, idx, str(value))
+
+    def __getattr__(self, key):
+        cdef int idx
+        idx, f = self.map_key2field[key]
+        if self.nfields < idx:
+            raise KeyError("field %s not set" % key)
+        if f == str:
+            return force_str(self.fields[idx],
+                              self.encoding)
+        return f(self.fields[idx])
+
+
+cdef dot_or_float(v):
+    if v == "" or v == b".":
+        return None
+    else:
+        try:
+            return int(v)
+        except ValueError:
+            return float(v)
+
+
+cdef dot_or_int(v):
+    if v == "" or v == b".":
+        return None
+    else:
+        return int(v)
+
+
+cdef dot_or_str(v):
+    if v == "" or v == b".":
+        return None
+    else:
+        return force_str(v)
+
+
+cdef int from1based(v):
+    return atoi(v) - 1
+
+
+cdef str to1based(int v):
+    return str(v + 1)
+
+
+cdef class GTFProxy(NamedTupleProxy):
+    '''Proxy class for access to GTF fields.
+
+    This class represents a GTF entry for fast read-access.
+    Write-access has been added as well, though some care must
+    be taken. If any of the string fields (contig, source, ...)
+    are set, the new value is tied to the lifetime of the
+    argument that was supplied.
+
+    The only exception is the attributes field when set from
+    a dictionary - this field will manage its own memory.
+
+    '''
+    separator = "; "
+
+    # first value is field index, the tuple contains conversion
+    # functions for getting (converting internal string representation
+    # to pythonic value) and setting (converting pythonic value to
+    # interval string representation)
+    map_key2field = {
+        'contig' : (0, (str, str)),
+        'source' : (1, (dot_or_str, str)),
+        'feature': (2, (dot_or_str, str)),
+        'start' : (3, (from1based, to1based)),
+        'end' : (4, (int, int)),
+        'score' : (5, (dot_or_float, toDot)),
+        'strand' : (6, (dot_or_str, str)),
+        'frame' : (7, (dot_or_int, toDot)),
+        'attributes': (8, (str, str))}
+    
+    def __cinit__(self): 
+        # automatically calls TupleProxy.__cinit__
+        self.attribute_dict = None
+        
+    cpdef int getMinFields(self):
+        '''return minimum number of fields.'''
+        return 9
+
+    cpdef int getMaxFields(self):
+        '''return max number of fields.'''
+        return 9
+
+    def to_dict(self):
+        """parse attributes - return as dict
+
+        The dictionary can be modified to update attributes.
+        """
+        if not self.attribute_dict:
+            self.attribute_dict = self.attribute_string2dict(
+                self.attributes)
+            self.is_modified = True
+        return self.attribute_dict
+
+    def as_dict(self):
+        """deprecated: use :meth:`to_dict`
+        """
+        return self.to_dict()
+
+    def from_dict(self, d):
+        '''set attributes from a dictionary.'''
+        self.attribute_dict = None
+        attribute_string = force_bytes(
+            self.attribute_dict2string(d),
+            self.encoding)
+        self._setindex(8, attribute_string)
+
+    def __str__(self):
+        cdef char * cpy
+        cdef int x
+
+        if self.is_modified:
+            return "\t".join( 
+                (self.contig, 
+                 toDot(self.source), 
+                 toDot(self.feature), 
+                 str(self.start + 1),
+                 str(self.end),
+                 toDot(self.score),
+                 toDot(self.strand),
+                 toDot(self.frame),
+                 self.attributes))
+        else: 
+            return TupleProxy.__str__(self)
+
+    def invert(self, int lcontig):
+        '''invert coordinates to negative strand coordinates
+        
+        This method will only act if the feature is on the
+        negative strand.'''
+
+        if self.strand[0] == '-':
+            start = min(self.start, self.end)
+            end = max(self.start, self.end)
+            self.start, self.end = lcontig - end, lcontig - start
+
+    def keys(self):
+        '''return a list of attributes defined in this entry.'''
+        if not self.attribute_dict:
+            self.attribute_dict = self.attribute_string2dict(
+                self.attributes)
+        return self.attribute_dict.keys()
+
+    def __getitem__(self, key):
+        return self.__getattr__(key)
+
+    def setAttribute(self, name, value):
+        '''convenience method to set an attribute.
+        '''
+        if not self.attribute_dict:
+            self.attribute_dict = self.attribute_string2dict(
+                self.attributes)
+        self.attribute_dict[name] = value
+        self.is_modified = True
+
+    def attribute_string2dict(self, s):
+        return collections.OrderedDict(
+            self.attribute_string2iterator(s))
+    
+    def __cmp__(self, other):
+        return (self.contig, self.strand, self.start) < \
+            (other.contig, other.strand, other.start)
+
+    # python 3 compatibility
+    def __richcmp__(GTFProxy self, GTFProxy other, int op):
+        if op == 0:
+            return (self.contig, self.strand, self.start) < \
+                (other.contig, other.strand, other.start)
+        elif op == 1:
+            return (self.contig, self.strand, self.start) <= \
+                (other.contig, other.strand, other.start)
+        elif op == 2:
+            return self.compare(other) == 0
+        elif op == 3:
+            return self.compare(other) != 0
+        else:
+            err_msg = "op {0} isn't implemented yet".format(op)
+            raise NotImplementedError(err_msg)
+
+    def dict2attribute_string(self, d):
+        """convert dictionary to attribute string in GTF format.
+
+        """
+        aa = []
+        for k, v in d.items():
+            if isinstance(v, str):
+                aa.append('{} "{}"'.format(k, v))
+            else:
+                aa.append("{} {}".format(k, str(v)))
+
+        return self.separator.join(aa) + ";"
+
+    def attribute_string2iterator(self, s):
+        """convert attribute string in GTF format to records
+        and iterate over key, value pairs.
+        """
+        
+        # remove comments
+        attributes = force_str(s, encoding=self.encoding)
+
+        # separate into fields
+        # Fields might contain a ";", for example in ENSEMBL GTF file
+        # for mouse, v78:
+        # ...; transcript_name "TXNRD2;-001"; ....
+        # The current heuristic is to split on a semicolon followed by a
+        # space, see also http://mblab.wustl.edu/GTF22.html
+
+        # Remove white space to prevent a last empty field.
+        fields = [x.strip() for x in attributes.strip().split("; ")]
+        for f in fields:
+
+            # strip semicolon (GTF files without a space after the last semicolon)
+            if f.endswith(";"):
+                f = f[:-1]
+
+            # split at most once in order to avoid separating
+            # multi-word values
+            d = [x.strip() for x in f.split(" ", 1)]
+
+            n, v = d[0], d[1]
+            if len(d) > 2:
+                v = d[1:]
+
+            if v[0] == '"' and v[-1] == '"':
+                v = v[1:-1]
+            else:
+                ## try to convert to a value
+                try:
+                    v = float(v)
+                    v = int(v)
+                except ValueError:
+                    pass
+                except TypeError:
+                    pass
+                
+            yield n, v
+       
+    def __getattr__(self, key):
+        """Generic lookup of attribute from GFF/GTF attributes 
+        """
+
+        # Only called if there *isn't* an attribute with this name
+        cdef int idx
+        idx, f = self.map_key2field.get(key, (-1, None))
+        if idx >= 0:
+            # deal with known attributes (fields 0-8)
+            if idx == 8:
+                # flush attributes if requested
+                if self.is_modified and self.attribute_dict is not None:
+                    s = self.dict2attribute_string(self.attribute_dict)
+                    TupleProxy._setindex(self, idx, s)
+                    self.attribute_dict = None
+                    return s
+                                         
+            if f[0] == str:
+                return force_str(self.fields[idx],
+                                 self.encoding)
+            else:
+                return f[0](self.fields[idx])
+        else:
+            # deal with generic attributes (gene_id, ...)
+            if self.attribute_dict is None:
+                self.attribute_dict = self.attribute_string2dict(
+                    self.attributes)
+            return self.attribute_dict[key]
+
+    def __setattr__(self, key, value):
+        '''set attribute.'''
+
+        # Note that __setattr__ is called before properties, so __setattr__ and
+        # properties don't mix well. This is different from __getattr__ which is
+        # called after any properties have been resolved.
+        cdef int idx
+        idx, f = self.map_key2field.get(key, (-1, None))
+
+        if idx >= 0:
+            if value is None:
+                s = "."
+            elif f[1] == str:
+                s = force_bytes(value,
+                                self.encoding)
+            else:
+                s = str(f[1](value))
+            TupleProxy._setindex(self, idx, s)
+        else:
+            if self.attribute_dict is None:
+                self.attribute_dict = self.attribute_string2dict(
+                    self.attributes)
+            self.attribute_dict[key] = value
+            self.is_modified = True
+
+    # for backwards compatibility
+    def asDict(self, *args, **kwargs):
+        return self.to_dict(*args, **kwargs)
+
+    def fromDict(self, *args, **kwargs):
+        return self.from_dict(*args, **kwargs)
+    
+
+cdef class GFF3Proxy(GTFProxy):
+
+    def dict2attribute_string(self, d):
+        """convert dictionary to attribute string."""
+        return ";".join(["{}={}".format(k, v) for k, v in d.items()])
+        
+    def attribute_string2iterator(self, s):
+        """convert attribute string in GFF3 format to records
+        and iterate over key, value pairs.
+        """
+        
+        for f in (x.strip() for x in s.split(";")):
+            if not f:
+                continue
+
+            key, value = f.split("=", 1)
+            value = value.strip()
+            
+            ## try to convert to a value
+            try:
+                value = float(value)
+                value = int(value)
+            except ValueError:
+                pass
+            except TypeError:
+                pass
+                
+            yield key.strip(), value
+   
+
+cdef class BedProxy(NamedTupleProxy):
+    '''Proxy class for access to Bed fields.
+
+    This class represents a BED entry for fast read-access.
+    '''
+    map_key2field = {
+        'contig' : (0, str),
+        'start' : (1, int),
+        'end' : (2, int),
+        'name' : (3, str),
+        'score' : (4, float),
+        'strand' : (5, str),
+        'thickStart' : (6, int),
+        'thickEnd' : (7, int),
+        'itemRGB' : (8, str),
+        'blockCount': (9, int),
+        'blockSizes': (10, str),
+        'blockStarts': (11, str), } 
+
+    cpdef int getMinFields(self):
+        '''return minimum number of fields.'''
+        return 3
+
+    cpdef int getMaxFields(self):
+        '''return max number of fields.'''
+        return 12
+
+    cdef update(self, char * buffer, size_t nbytes):
+        '''update internal data.
+
+        nbytes does not include the terminal '\0'.
+        '''
+        TupleProxy.update(self, buffer, nbytes)
+
+        if self.nfields < 3:
+            raise ValueError(
+                "bed format requires at least three columns")
+
+        # determines bed format
+        self.bedfields = self.nfields
+
+        # do automatic conversion
+        self.contig = self.fields[0]
+        self.start = atoi(self.fields[1]) 
+        self.end = atoi(self.fields[2])
+
+    # __setattr__ in base class seems to take precedence
+    # hence implement setters in __setattr__
+    #property start:
+    #    def __get__( self ): return self.start
+    #property end:
+    #    def __get__( self ): return self.end
+
+    def __str__(self):
+
+        cdef int save_fields = self.nfields
+        # ensure fields to use correct format
+        self.nfields = self.bedfields
+        retval = TupleProxy.__str__(self)
+        self.nfields = save_fields
+        return retval
+
+    def __setattr__(self, key, value):
+        '''set attribute.'''
+        if key == "start":
+            self.start = value
+        elif key == "end":
+            self.end = value
+
+        cdef int idx
+        idx, f = self.map_key2field[key]
+        TupleProxy._setindex(self, idx, str(value))
+        
+
+cdef class VCFProxy(NamedTupleProxy):
+    '''Proxy class for access to VCF fields.
+
+    The genotypes are accessed via a numeric index.
+    Sample headers are not available.
+    '''
+    map_key2field = { 
+        'contig' : (0, str),
+        'pos' : (1, int),
+        'id' : (2, str),
+        'ref' : (3, str),
+        'alt' : (4, str),
+        'qual' : (5, str),
+        'filter' : (6, str),
+        'info' : (7, str),
+        'format' : (8, str) }
+
+    def __cinit__(self): 
+        # automatically calls TupleProxy.__cinit__
+        # start indexed access at genotypes
+        self.offset = 9
+
+    cdef update(self, char * buffer, size_t nbytes):
+        '''update internal data.
+        
+        nbytes does not include the terminal '\0'.
+        '''
+        TupleProxy.update(self, buffer, nbytes)
+
+        self.contig = self.fields[0]
+        # vcf counts from 1 - correct here
+        self.pos = atoi(self.fields[1]) - 1
+                             
+    def __len__(self):
+        '''return number of genotype fields.'''
+        return max(0, self.nfields - 9)
+
+    property pos:
+       '''feature end (in 0-based open/closed coordinates).'''
+       def __get__(self): 
+           return self.pos
+
+    def __setattr__(self, key, value):
+        '''set attribute.'''
+        if key == "pos": 
+            self.pos = value
+            value += 1
+
+        cdef int idx
+        idx, f = self.map_key2field[key]
+        TupleProxy._setindex(self, idx, str(value))
+
+
+__all__ = [
+    "TupleProxy",
+    "NamedTupleProxy",
+    "GTFProxy",
+    "GFF3Proxy",
+    "BedProxy",
+    "VCFProxy"]
diff --git a/pysam/libcutils.pxd b/pysam/libcutils.pxd
new file mode 100644
index 0000000..d78b706
--- /dev/null
+++ b/pysam/libcutils.pxd
@@ -0,0 +1,34 @@
+#########################################################################
+# Utility functions used across pysam
+#########################################################################
+cimport cython
+from cpython cimport array as c_array
+
+cpdef parse_region(contig=*, start=*, stop=*, region=*, reference=*, end=*)
+
+#########################################################################
+# Utility functions for quality string conversions
+
+cpdef c_array.array qualitystring_to_array(input_str, int offset=*)
+cpdef array_to_qualitystring(c_array.array arr, int offset=*)
+cpdef qualities_to_qualitystring(qualities, int offset=*)
+
+########################################################################
+## String encoding configuration facilities
+########################################################################
+
+cpdef get_encoding_error_handler()
+cpdef set_encoding_error_handler(name)
+
+########################################################################
+## Python 3 compatibility functions
+########################################################################
+cdef charptr_to_str(const char *s, encoding=*, errors=*)
+cdef bytes charptr_to_bytes(const char *s, encoding=*, errors=*)
+cdef charptr_to_str_w_len(const char* s, size_t n, encoding=*, errors=*)
+cdef force_str(object s, encoding=*, errors=*)
+cdef bytes force_bytes(object s, encoding=*, errors=*)
+cdef decode_bytes(bytes s, encoding=*, errors=*)
+cdef bytes encode_filename(object filename)
+cdef from_string_and_size(const char *s, size_t length)
+
diff --git a/pysam/libcutils.pyi b/pysam/libcutils.pyi
new file mode 100644
index 0000000..c82d2a6
--- /dev/null
+++ b/pysam/libcutils.pyi
@@ -0,0 +1,28 @@
+from array import array
+from typing import Iterable, Optional, Tuple, Union
+
+def get_encoding_error_handler() -> str: ...
+def set_encoding_error_handler(name: str) -> str: ...
+def _pysam_dispatch(
+    collection: str,
+    method: str,
+    args: Optional[Iterable[str]],
+    catch_stdout: bool = ...,
+    is_usage: bool = ...,
+    save_stdout: Optional[str] = ...,
+) -> Tuple[int, Union[bytes, str], Union[bytes, str]]: ...
+def parse_region(
+    contig: Optional[str] = ...,
+    start: Optional[int] = ...,
+    stop: Optional[int] = ...,
+    region: Optional[str] = ...,
+    reference: Optional[str] = ...,
+    end: Optional[int] = ...,
+) -> Tuple[str, int, int]: ...
+def qualitystring_to_array(
+    input_str: Optional[str], offset: int = ...
+) -> Optional[array]: ...
+def array_to_qualitystring(qualities: array, offset: int = ...) -> Optional[str]: ...
+def qualities_to_qualitystring(
+    qualities: Union[array, Iterable[str]], offset: int = ...
+) -> Optional[str]: ...
diff --git a/pysam/libcutils.pyx b/pysam/libcutils.pyx
new file mode 100644
index 0000000..81a19d3
--- /dev/null
+++ b/pysam/libcutils.pyx
@@ -0,0 +1,457 @@
+import types
+import sys
+import string
+import re
+import tempfile
+import os
+import io
+from contextlib import contextmanager
+from codecs import register_error
+
+from cpython.version cimport PY_MAJOR_VERSION, PY_MINOR_VERSION
+from cpython cimport PyBytes_Check, PyUnicode_Check
+from cpython cimport array as c_array
+from libc.stdlib cimport calloc, free
+from libc.string cimport strncpy
+from libc.stdint cimport INT32_MAX, int32_t
+from libc.stdio cimport fprintf, stderr, fflush
+from libc.stdio cimport stdout as c_stdout
+from posix.fcntl cimport open as c_open, O_WRONLY
+
+from libcsamtools cimport samtools_dispatch, samtools_set_stdout, samtools_set_stderr, \
+    samtools_close_stdout, samtools_close_stderr, samtools_set_stdout_fn
+
+from libcbcftools cimport bcftools_dispatch, bcftools_set_stdout, bcftools_set_stderr, \
+    bcftools_close_stdout, bcftools_close_stderr, bcftools_set_stdout_fn
+
+#####################################################################
+# hard-coded constants
+cdef int MAX_POS = (1 << 31) - 1
+
+#################################################################
+# Utility functions for quality string conversions
+cpdef c_array.array qualitystring_to_array(input_str, int offset=33):
+    """convert a qualitystring to an array of quality values."""
+    if input_str is None:
+        return None
+    qs = force_bytes(input_str)
+    cdef char i
+    return c_array.array('B', [i - offset for i in qs])
+
+
+cpdef array_to_qualitystring(c_array.array qualities, int offset=33):
+    """convert an array of quality values to a string."""
+    if qualities is None:
+        return None
+    cdef int x
+
+    cdef c_array.array result
+    result = c_array.clone(qualities, len(qualities), zero=False)
+
+    for x from 0 <= x < len(qualities):
+        result[x] = qualities[x] + offset
+    if IS_PYTHON3:
+        return force_str(result.tobytes())
+    else:
+        return result.tostring()
+
+
+cpdef qualities_to_qualitystring(qualities, int offset=33):
+    """convert a list or array of quality scores to the string
+    representation used in the SAM format.
+
+    Parameters
+    ----------
+    offset : int
+        offset to be added to the quality scores to arrive at
+        the characters of the quality string (default=33).
+
+    Returns
+    -------
+    string
+         a quality string
+
+    """
+    cdef char x
+    if qualities is None:
+        return None
+    elif isinstance(qualities, c_array.array):
+        return array_to_qualitystring(qualities, offset=offset)
+    else:
+        # tuples and lists
+        return force_str("".join([chr(x + offset) for x in qualities]))
+
+
+########################################################################
+## String encoding configuration facilities
+########################################################################
+
+# Codec error handler that just interprets each bad byte as ISO-8859-1.
+def latin1_replace(exception):
+    return (chr(exception.object[exception.start]), exception.end)
+
+register_error('pysam.latin1replace', latin1_replace)
+
+
+cdef str ERROR_HANDLER = 'strict'
+
+cpdef get_encoding_error_handler():
+    return ERROR_HANDLER
+
+cpdef set_encoding_error_handler(name):
+    global ERROR_HANDLER
+    previous = ERROR_HANDLER
+    ERROR_HANDLER = name
+    return previous
+
+########################################################################
+## Python 3 compatibility functions
+########################################################################
+
+cdef bint IS_PYTHON3 = PY_MAJOR_VERSION >= 3
+
+cdef from_string_and_size(const char* s, size_t length):
+    if IS_PYTHON3:
+        return s[:length].decode('utf-8', ERROR_HANDLER)
+    else:
+        return s[:length]
+
+
+# filename encoding (adapted from lxml.etree.pyx)
+cdef str FILENAME_ENCODING = sys.getfilesystemencoding() or sys.getdefaultencoding() or 'ascii'
+cdef str TEXT_ENCODING = 'utf-8'
+
+cdef bytes encode_filename(object filename):
+    """Make sure a filename is 8-bit encoded (or None)."""
+    if filename is None:
+        return None
+    elif PY_MAJOR_VERSION >= 3 and PY_MINOR_VERSION >= 2:
+        # Added to support path-like objects
+        return os.fsencode(filename)
+    elif PyBytes_Check(filename):
+        return filename
+    elif PyUnicode_Check(filename):
+        return filename.encode(FILENAME_ENCODING)
+    else:
+        raise TypeError("Argument must be string or unicode.")
+
+
+cdef bytes force_bytes(object s, encoding=None, errors=None):
+    """convert string or unicode object to bytes, assuming
+    utf8 encoding.
+    """
+    if s is None:
+        return None
+    elif PyBytes_Check(s):
+        return s
+    elif PyUnicode_Check(s):
+        return s.encode(encoding or TEXT_ENCODING, errors or ERROR_HANDLER)
+    else:
+        raise TypeError("Argument must be string, bytes or unicode.")
+
+
+cdef charptr_to_str(const char* s, encoding=None, errors=None):
+    if s == NULL:
+        return None
+    if PY_MAJOR_VERSION < 3:
+        return s
+    else:
+        return s.decode(encoding or TEXT_ENCODING, errors or ERROR_HANDLER)
+
+
+cdef charptr_to_str_w_len(const char* s, size_t n, encoding=None, errors=None):
+    if s == NULL:
+        return None
+    if PY_MAJOR_VERSION < 3:
+        return s[:n]
+    else:
+        return s[:n].decode(encoding or TEXT_ENCODING, errors or ERROR_HANDLER)
+
+
+cdef bytes charptr_to_bytes(const char* s, encoding=None, errors=None):
+    if s == NULL:
+        return None
+    else:
+        return s
+
+
+cdef force_str(object s, encoding=None, errors=None):
+    """Return s converted to str type of current Python
+    (bytes in Py2, unicode in Py3)"""
+    if s is None:
+        return None
+    if PY_MAJOR_VERSION < 3:
+        return s
+    elif PyBytes_Check(s):
+        return s.decode(encoding or TEXT_ENCODING, errors or ERROR_HANDLER)
+    else:
+        # assume unicode
+        return s
+
+
+cdef decode_bytes(bytes s, encoding=None, errors=None):
+    """Return s converted to current Python's str type,
+    always decoding even in Python 2"""
+    if s is None:
+        return None
+    else:
+        return s.decode(encoding or TEXT_ENCODING, errors or ERROR_HANDLER)
+
+
+cpdef parse_region(contig=None,
+                   start=None,
+                   stop=None,
+                   region=None,
+                   reference=None,
+                   end=None):
+    """parse alternative ways to specify a genomic region. A region can
+    either be specified by :term:`reference`, `start` and
+    `end`. `start` and `end` denote 0-based, half-open intervals.
+    
+    :term:`reference` and `end` are also accepted for backward
+    compatibility as synonyms for :term:`contig` and `stop`,
+    respectively.
+
+    Alternatively, a samtools :term:`region` string can be supplied.
+
+    If any of the coordinates are missing they will be replaced by the
+    minimum (`start`) or maximum (`end`) coordinate.
+
+    Note that region strings are 1-based, while `start` and `end`
+    denote an interval in python coordinates.
+
+    Returns
+    -------
+
+    tuple :  a tuple of `reference`, `start` and `end`.
+
+    Raises
+    ------
+
+    ValueError
+       for invalid or out of bounds regions.
+
+    """
+    cdef int32_t rstart
+    cdef int32_t rstop
+
+    
+    if reference is not None:
+        if contig is not None:
+           raise ValueError('contig and reference should not both be specified')
+        contig = reference
+
+    if contig is not None and region is not None:
+        raise ValueError('contig/reference and region should not both be specified')
+        
+    if end is not None:
+        if stop is not None:
+            raise ValueError('stop and end should not both be specified')
+        stop = end
+
+    if contig is None and region is None:
+        raise ValueError("neither contig nor region are given")
+
+    rstart = 0
+    rstop = MAX_POS
+    if start is not None:
+        try:
+            rstart = start
+        except OverflowError:
+            raise ValueError('start out of range (%i)' % start)
+
+    if stop is not None:
+        try:
+            rstop = stop
+        except OverflowError:
+            raise ValueError('stop out of range (%i)' % stop)
+
+    if region:
+        if ":" in region:
+            contig, coord = region.split(":")
+            parts = coord.split("-")
+            rstart = int(parts[0]) - 1
+            if len(parts) >= 1:
+                rstop = int(parts[1])
+        else:
+            contig = region
+
+    if rstart > rstop:
+        raise ValueError('invalid coordinates: start (%i) > stop (%i)' % (rstart, rstop))
+    if not 0 <= rstart < MAX_POS:
+        raise ValueError('start out of range (%i)' % rstart)
+    if not 0 <= rstop <= MAX_POS:
+        raise ValueError('stop out of range (%i)' % rstop)
+
+    return contig, rstart, rstop
+
+
+def _pysam_dispatch(collection,
+                    method,
+                    args=None,
+                    catch_stdout=True,
+                    is_usage=False,
+                    save_stdout=None):
+    '''call ``method`` in samtools/bcftools providing arguments in args.
+    
+    By default, stdout is redirected to a temporary file using the patched
+    C sources except for a few commands that have an explicit output option
+    (typically: -o). In these commands (such as samtools view), this explicit
+    option is used. If *is_usage* is True, then these explicit output options
+    will not be used.
+
+    Catching of stdout can be turned off by setting *catch_stdout* to
+    False.
+    '''
+
+    if method == "index" and args:
+        # We make sure that at least 1 input file exists,
+        # and if it doesn't we raise an IOError.
+        SIMPLE_FLAGS = ['-c', '--csi', '-f', '--force', '-t', '--tbi', '-n', '--nstats', '-s', '--stats']
+        ARGUMENTS = ['-m', '--min-shift', '-o', '--output-file', '--threads', '-@']
+        skip_next = False
+        for arg in args:
+            if skip_next:
+                skip_next = False
+                continue
+            if arg in SIMPLE_FLAGS or (len(arg) > 2 and force_bytes(arg).startswith(b'-@')):
+                continue
+            if arg in ARGUMENTS:
+                skip_next = True
+                continue
+            if not os.path.exists(arg):
+                raise IOError("No such file or directory: '%s'" % arg)
+            else:
+                break
+            
+    if args is None:
+        args = []
+    else:
+        args = list(args)
+
+    # redirect stderr to file
+    stderr_h, stderr_f = tempfile.mkstemp()
+        
+    # redirect stdout to file
+    if save_stdout:
+        stdout_f = save_stdout
+        stdout_h = c_open(force_bytes(stdout_f),
+                          O_WRONLY)
+        if stdout_h == -1:
+            raise IOError("error while opening {} for writing".format(stdout_f))
+
+        samtools_set_stdout_fn(force_bytes(stdout_f))
+        bcftools_set_stdout_fn(force_bytes(stdout_f))
+            
+    elif catch_stdout:
+        stdout_h, stdout_f = tempfile.mkstemp()
+        MAP_STDOUT_OPTIONS = {
+        "samtools": {
+            "view": "-o {}",
+            "mpileup": "-o {}",
+            "depad": "-o {}",
+            "calmd": "",  # uses pysam_stdout_fn
+        },
+            "bcftools": {}
+        }
+        
+        stdout_option = None
+        if collection == "bcftools":
+            # in bcftools, most methods accept -o, the exceptions
+            # are below:
+            if method not in ("index", "roh", "stats"):
+                stdout_option = "-o {}"
+        elif method in MAP_STDOUT_OPTIONS[collection]:
+            # special case - samtools view -c outputs on stdout
+            if not(method == "view" and "-c" in args):
+                stdout_option = MAP_STDOUT_OPTIONS[collection][method]
+
+        if stdout_option is not None and not is_usage:
+            os.close(stdout_h)
+            samtools_set_stdout_fn(force_bytes(stdout_f))
+            bcftools_set_stdout_fn(force_bytes(stdout_f))
+            args.extend(stdout_option.format(stdout_f).split(" "))
+            stdout_h = c_open(b"/dev/null", O_WRONLY)
+    else:
+        samtools_set_stdout_fn("-")
+        bcftools_set_stdout_fn("-")
+        stdout_h = c_open(b"/dev/null", O_WRONLY)
+
+    # setup the function call to samtools/bcftools main
+    cdef char ** cargs
+    cdef int i, n, retval, l
+    n = len(args)
+    method = force_bytes(method)
+    collection = force_bytes(collection)
+    args = [force_bytes(a) for a in args]
+
+    # allocate two more for first (dummy) argument (contains command)
+    cdef int extra_args = 0
+    if method == b"index":
+        extra_args = 1
+    # add extra arguments for commands accepting optional arguments
+    # such as 'samtools index x.bam [out.index]'
+    cargs = <char**>calloc(n + 2 + extra_args, sizeof(char *))
+    cargs[0] = collection
+    cargs[1] = method
+
+    # create copies of strings - getopt for long options permutes
+    # arguments
+    for i from 0 <= i < n:
+        l = len(args[i])
+        cargs[i + 2] = <char *>calloc(l + 1, sizeof(char))
+        strncpy(cargs[i + 2], args[i], l)
+
+    # call samtools/bcftools
+    if collection == b"samtools":
+        samtools_set_stdout(stdout_h)
+        samtools_set_stderr(stderr_h)
+        retval = samtools_dispatch(n + 2, cargs)
+        samtools_close_stdout()
+        samtools_close_stderr()
+    elif collection == b"bcftools":
+        bcftools_set_stdout(stdout_h)
+        bcftools_set_stderr(stderr_h)
+        retval = bcftools_dispatch(n + 2, cargs)
+        bcftools_close_stdout()
+        bcftools_close_stderr()
+    else:
+        # unknown -- just return a Unix shell's "command not found" exit status
+        retval = 127
+
+    for i from 0 <= i < n:
+        free(cargs[i + 2])
+    free(cargs)
+
+    # get error messages
+    def _collect(fn):
+        out = []
+        try:
+            with open(fn, "r") as inf:
+                out = inf.read()
+        except UnicodeDecodeError:
+            with open(fn, "rb") as inf:
+                # read binary output
+                out = inf.read()
+        finally:
+            os.remove(fn)
+        return out
+
+    out_stderr = _collect(stderr_f)
+    if save_stdout:
+        out_stdout = None
+    elif catch_stdout:
+        out_stdout = _collect(stdout_f)
+    else:
+        out_stdout = None
+        
+    return retval, out_stderr, out_stdout
+
+
+__all__ = [
+    "qualitystring_to_array",
+    "array_to_qualitystring",
+    "qualities_to_qualitystring",
+    "get_encoding_error_handler",
+    "set_encoding_error_handler",
+]
diff --git a/pysam/libcvcf.pxd b/pysam/libcvcf.pxd
new file mode 100644
index 0000000..139597f
--- /dev/null
+++ b/pysam/libcvcf.pxd
@@ -0,0 +1,2 @@
+
+
diff --git a/pysam/libcvcf.pyi b/pysam/libcvcf.pyi
new file mode 100644
index 0000000..e69de29
diff --git a/pysam/libcvcf.pyx b/pysam/libcvcf.pyx
new file mode 100644
index 0000000..956f8a5
--- /dev/null
+++ b/pysam/libcvcf.pyx
@@ -0,0 +1,1203 @@
+# cython: embedsignature=True
+#
+# Code to read, write and edit VCF files
+#
+# VCF lines are encoded as a dictionary with these keys (note: all lowercase):
+# 'chrom':  string
+# 'pos':    integer
+# 'id':     string
+# 'ref':    string
+# 'alt':    list of strings
+# 'qual':   integer
+# 'filter': None (missing value), or list of keys (strings); empty list parsed as ["PASS"]
+# 'info':   dictionary of values (see below)
+# 'format': list of keys (strings)
+# sample keys: dictionary of values (see below)
+#
+# The sample keys are accessible through vcf.getsamples()
+#
+# A dictionary of values contains value keys (defined in ##INFO or
+# ##FORMAT lines) which map to a list, containing integers, floats,
+# strings, or characters.  Missing values are replaced by a particular
+# value, often -1 or .
+#
+# Genotypes are not stored as a string, but as a list of 1 or 3
+# elements (for haploid and diploid samples), the first (and last) the
+# integer representing an allele, and the second the separation
+# character.  Note that there is just one genotype per sample, but for
+# consistency the single element is stored in a list.
+#
+# Header lines other than ##INFO, ##FORMAT and ##FILTER are stored as
+# (key, value) pairs and are accessible through getheader()
+#
+# The VCF class can be instantiated with a 'regions' variable
+# consisting of tuples (chrom,start,end) encoding 0-based half-open
+# segments.  Only variants with a position inside the segment will be
+# parsed.  A regions parser is available under parse_regions.
+#
+# When instantiated, a reference can be passed to the VCF class.  This
+# may be any class that supports a fetch(chrom, start, end) method.
+#
+# NOTE: the position that is returned to Python is 0-based, NOT
+# 1-based as in the VCF file.
+# NOTE: There is also preliminary VCF functionality in the VariantFile class.
+#
+# TODO:
+#  only v4.0 writing is complete; alleles are not converted to v3.3 format
+#
+
+from collections import namedtuple, defaultdict
+from operator import itemgetter
+import sys, re, copy, bisect
+
+from libc.stdlib cimport atoi
+from libc.stdint cimport int8_t, int16_t, int32_t, int64_t
+from libc.stdint cimport uint8_t, uint16_t, uint32_t, uint64_t
+
+cimport pysam.libctabix as libctabix
+cimport pysam.libctabixproxies as libctabixproxies
+
+from pysam.libcutils cimport force_str
+
+import pysam
+
+gtsRegEx = re.compile("[|/\\\\]")
+alleleRegEx = re.compile('^[ACGTN]+$')
+
+# Utility function.  Uses 0-based coordinates
+def get_sequence(chrom, start, end, fa):
+    # obtain sequence from .fa file, without truncation
+    if end<=start: return ""
+    if not fa: return "N"*(end-start)
+    if start<0: return "N"*(-start) + get_sequence(chrom, 0, end, fa).upper()
+    sequence = fa.fetch(chrom, start, end).upper()
+    if len(sequence) < end-start: sequence += "N"*(end-start-len(sequence))
+    return sequence
+
+# Utility function.  Parses a region string
+def parse_regions( string ):
+    result = []
+    for r in string.split(','):
+        elts = r.split(':')
+        chrom, start, end = elts[0], 0, 3000000000
+        if len(elts)==1: pass
+        elif len(elts)==2:
+            if len(elts[1])>0:
+                ielts = elts[1].split('-')
+                if len(ielts) != 2: ValueError("Don't understand region string '%s'" % r)
+                try:    start, end = int(ielts[0])-1, int(ielts[1])
+                except: raise ValueError("Don't understand region string '%s'" % r)
+        else:
+            raise ValueError("Don't understand region string '%s'" % r)
+        result.append( (chrom,start,end) )
+    return result
+
+
+FORMAT = namedtuple('FORMAT','id numbertype number type description missingvalue')
+
+###########################################################################################################
+#
+# New class
+#
+###########################################################################################################
+
+cdef class VCFRecord(libctabixproxies.TupleProxy):
+    '''vcf record.
+
+    initialized from data and vcf meta
+    '''
+
+    cdef vcf
+    cdef char * contig
+    cdef uint32_t pos
+
+    def __init__(self, vcf):
+        self.vcf = vcf
+        self.encoding = vcf.encoding
+
+        # if len(data) != len(self.vcf._samples):
+        #     self.vcf.error(str(data),
+        #                self.BAD_NUMBER_OF_COLUMNS,
+        #                "expected %s for %s samples (%s), got %s" % \
+        #                    (len(self.vcf._samples),
+        #                     len(self.vcf._samples),
+        #                     self.vcf._samples,
+        #                     len(data)))
+
+    def __cinit__(self, vcf):
+        # start indexed access at genotypes
+        self.offset = 9
+
+        self.vcf = vcf
+        self.encoding = vcf.encoding
+
+    def error(self, line, error, opt=None):
+        '''raise error.'''
+        # pass to vcf file for error handling
+        return self.vcf.error(line, error, opt)
+
+    cdef update(self, char * buffer, size_t nbytes):
+        '''update internal data.
+
+        nbytes does not include the terminal '\0'.
+        '''
+        libctabixproxies.TupleProxy.update(self, buffer, nbytes)
+
+        self.contig = self.fields[0]
+        # vcf counts from 1 - correct here
+        self.pos = atoi(self.fields[1]) - 1
+
+    def __len__(self):
+        return max(0, self.nfields - 9)
+
+    property contig:
+        def __get__(self): return self.contig
+
+    property pos:
+        def __get__(self): return self.pos
+
+    property id:
+        def __get__(self): return self.fields[2]
+
+    property ref:
+        def __get__(self):
+            return self.fields[3]
+
+    property alt:
+        def __get__(self):
+            # convert v3.3 to v4.0 alleles below
+            alt = self.fields[4]
+            if alt == ".": alt = []
+            else: alt = alt.upper().split(',')
+            return alt
+
+    property qual:
+        def __get__(self):
+            qual = self.fields[5]
+            if qual == b".": qual = -1
+            else:
+                try:    qual = float(qual)
+                except: self.vcf.error(str(self),self.QUAL_NOT_NUMERICAL)
+            return qual
+
+    property filter:
+        def __get__(self):
+            f = self.fields[6]
+            # postpone checking that filters exist.  Encode missing filter or no filtering as empty list
+            if f == b"." or f == b"PASS" or f == b"0": return []
+            else: return f.split(';')
+
+    property info:
+        def __get__(self):
+            col = self.fields[7]
+            # dictionary of keys, and list of values
+            info = {}
+            if col != b".":
+                for blurp in col.split(';'):
+                    elts = blurp.split('=')
+                    if len(elts) == 1: v = None
+                    elif len(elts) == 2: v = elts[1]
+                    else: self.vcf.error(str(self),self.ERROR_INFO_STRING)
+                    info[elts[0]] = self.vcf.parse_formatdata(elts[0], v, self.vcf._info, str(self.vcf))
+            return info
+
+    property format:
+         def __get__(self):
+             return self.fields[8].split(':')
+
+    property samples:
+        def __get__(self):
+            return self.vcf._samples
+
+    def __getitem__(self, key):
+
+        # parse sample columns
+        values = self.fields[self.vcf._sample2column[key]].split(':')
+        alt = self.alt
+        format = self.format
+
+        if len(values) > len(format):
+            self.vcf.error(str(self.line),self.BAD_NUMBER_OF_VALUES,"(found %s values in element %s; expected %s)" %\
+                           (len(values),key,len(format)))
+
+        result = {}
+        for idx in range(len(format)):
+            expected = self.vcf.get_expected(format[idx], self.vcf._format, alt)
+            if idx < len(values): value = values[idx]
+            else:
+                if expected == -1: value = "."
+                else: value = ",".join(["."]*expected)
+
+            result[format[idx]] = self.vcf.parse_formatdata(format[idx], value, self.vcf._format, str(self.data))
+            if expected != -1 and len(result[format[idx]]) != expected:
+                self.vcf.error(str(self.data),self.BAD_NUMBER_OF_PARAMETERS,
+                               "id=%s, expected %s parameters, got %s" % (format[idx],expected,result[format[idx]]))
+                if len(result[format[idx]] ) < expected: result[format[idx]] += [result[format[idx]][-1]]*(expected-len(result[format[idx]]))
+                result[format[idx]] = result[format[idx]][:expected]
+
+        return result
+
+
+cdef class asVCFRecord(libctabix.Parser):
+    '''converts a :term:`tabix row` into a VCF record.'''
+    cdef vcffile
+    def __init__(self, vcffile):
+        self.vcffile = vcffile
+
+    cdef parse(self, char * buffer, int len):
+        cdef VCFRecord r
+        r = VCFRecord(self.vcffile)
+        r.copy(buffer, len)
+        return r
+
+class VCF(object):
+
+    # types
+    NT_UNKNOWN = 0
+    NT_NUMBER = 1
+    NT_ALLELES = 2
+    NT_NR_ALLELES = 3
+    NT_GENOTYPES = 4
+    NT_PHASED_GENOTYPES = 5
+
+    _errors = { 0:"UNKNOWN_FORMAT_STRING:Unknown file format identifier",
+                1:"BADLY_FORMATTED_FORMAT_STRING:Formatting error in the format string",
+                2:"BADLY_FORMATTED_HEADING:Did not find 9 required headings (CHROM, POS, ..., FORMAT) %s",
+                3:"BAD_NUMBER_OF_COLUMNS:Wrong number of columns found (%s)",
+                4:"POS_NOT_NUMERICAL:Position column is not numerical",
+                5:"UNKNOWN_CHAR_IN_REF:Unknown character in reference field",
+                6:"V33_BAD_REF:Reference should be single-character in v3.3 VCF",
+                7:"V33_BAD_ALLELE:Cannot interpret allele for v3.3 VCF",
+                8:"POS_NOT_POSITIVE:Position field must be >0",
+                9:"QUAL_NOT_NUMERICAL:Quality field must be numerical, or '.'",
+               10:"ERROR_INFO_STRING:Error while parsing info field",
+               11:"ERROR_UNKNOWN_KEY:Unknown key (%s) found in formatted field (info; format; or filter)",
+               12:"ERROR_FORMAT_NOT_NUMERICAL:Expected integer or float in formatted field; got %s",
+               13:"ERROR_FORMAT_NOT_CHAR:Eexpected character in formatted field; got string",
+               14:"FILTER_NOT_DEFINED:Identifier (%s) in filter found which was not defined in header",
+               15:"FORMAT_NOT_DEFINED:Identifier (%s) in format found which was not defined in header",
+               16:"BAD_NUMBER_OF_VALUES:Found too many of values in sample column (%s)",
+               17:"BAD_NUMBER_OF_PARAMETERS:Found unexpected number of parameters (%s)",
+               18:"BAD_GENOTYPE:Cannot parse genotype (%s)",
+               19:"V40_BAD_ALLELE:Bad allele found for v4.0 VCF (%s)",
+               20:"MISSING_REF:Reference allele missing",
+               21:"V33_UNMATCHED_DELETION:Deleted sequence does not match reference (%s)",
+               22:"V40_MISSING_ANGLE_BRACKETS:Format definition is not deliminted by angular brackets",
+               23:"FORMAT_MISSING_QUOTES:Description field in format definition is not surrounded by quotes",
+               24:"V40_FORMAT_MUST_HAVE_NAMED_FIELDS:Fields in v4.0 VCF format definition must have named fields",
+               25:"HEADING_NOT_SEPARATED_BY_TABS:Heading line appears separated by spaces, not tabs",
+               26:"WRONG_REF:Wrong reference %s",
+               27:"ERROR_TRAILING_DATA:Numerical field ('%s') has semicolon-separated trailing data",
+               28:"BAD_CHR_TAG:Error calculating chr tag for %s",
+               29:"ZERO_LENGTH_ALLELE:Found zero-length allele",
+               30:"MISSING_INDEL_ALLELE_REF_BASE:Indel alleles must begin with single reference base",
+               31:"ZERO_FOR_NON_FLAG_FIELD: number set to 0, but type is not 'FLAG'",
+               32:"ERROR_FORMAT_NOT_INTEGER:Expected integer in formatted field; got %s",
+               33:"ERROR_FLAG_HAS_VALUE:Flag fields should not have a value",
+                }
+
+    # tag-value pairs; tags are not unique; does not include fileformat, INFO, FILTER or FORMAT fields
+    _header = []
+
+    # version number; 33=v3.3; 40=v4.0
+    _version = 40
+
+    # info, filter and format data
+    _info = {}
+    _filter = {}
+    _format = {}
+
+    # header; and required columns
+    _required = ["CHROM","POS","ID","REF","ALT","QUAL","FILTER","INFO","FORMAT"]
+    _samples = []
+
+    # control behaviour
+    _ignored_errors = set([11,31])   # ERROR_UNKNOWN_KEY, ERROR_ZERO_FOR_NON_FLAG_FIELD
+    _warn_errors = set([])
+    _leftalign = False
+
+    # reference sequence
+    _reference = None
+
+    # regions to include; None includes everything
+    _regions = None
+
+    # statefull stuff
+    _lineno = -1
+    _line = None
+    _lines = None
+
+    def __init__(self, _copy=None, reference=None, regions=None,
+                 lines=None, leftalign=False):
+        # make error identifiers accessible by name
+        for id in self._errors.keys():
+            self.__dict__[self._errors[id].split(':')[0]] = id
+        if _copy != None:
+            self._leftalign = _copy._leftalign
+            self._header = _copy._header[:]
+            self._version = _copy._version
+            self._info = copy.deepcopy(_copy._info)
+            self._filter = copy.deepcopy(_copy._filter)
+            self._format = copy.deepcopy(_copy._format)
+            self._samples = _copy._samples[:]
+            self._sample2column = copy.deepcopy(_copy._sample2column)
+            self._ignored_errors = copy.deepcopy(_copy._ignored_errors)
+            self._warn_errors = copy.deepcopy(_copy._warn_errors)
+            self._reference = _copy._reference
+            self._regions = _copy._regions
+        if reference: self._reference = reference
+        if regions: self._regions = regions
+        if leftalign: self._leftalign = leftalign
+        self._lines = lines
+        self.encoding = "ascii"
+        self.tabixfile = None
+
+    def error(self,line,error,opt=None):
+        if error in self._ignored_errors: return
+        errorlabel, errorstring = self._errors[error].split(':')
+        if opt: errorstring = errorstring % opt
+        errwarn = ["Error","Warning"][error in self._warn_errors]
+        errorstring += " in line %s: '%s'\n%s %s: %s\n" % (self._lineno,line,errwarn,errorlabel,errorstring)
+        if error in self._warn_errors: return
+        raise ValueError(errorstring)
+
+    def parse_format(self,line,format,filter=False):
+        if self._version == 40:
+            if not format.startswith('<'):
+                self.error(line,self.V40_MISSING_ANGLE_BRACKETS)
+                format = "<"+format
+            if not format.endswith('>'):
+                self.error(line,self.V40_MISSING_ANGLE_BRACKETS)
+                format += ">"
+            format = format[1:-1]
+        data = {'id':None,'number':None,'type':None,'descr':None}
+        idx = 0
+        while len(format.strip())>0:
+            elts = format.strip().split(',')
+            first, rest = elts[0], ','.join(elts[1:])
+            if first.find('=') == -1 or (first.find('"')>=0 and first.find('=') > first.find('"')):
+                if self._version == 40: self.error(line,self.V40_FORMAT_MUST_HAVE_NAMED_FIELDS)
+                if idx == 4: self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
+                first = ["ID=","Number=","Type=","Description="][idx] + first
+            if first.startswith('ID='):            data['id'] = first.split('=')[1]
+            elif first.startswith('Number='):      data['number'] = first.split('=')[1]
+            elif first.startswith('Type='):        data['type'] = first.split('=')[1]
+            elif first.startswith('Description='):
+                elts = format.split('"')
+                if len(elts)<3:
+                    self.error(line,self.FORMAT_MISSING_QUOTES)
+                    elts = first.split('=') + [rest]
+                data['descr'] = elts[1]
+                rest = '"'.join(elts[2:])
+                if rest.startswith(','): rest = rest[1:]
+            else:
+                self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
+            format = rest
+            idx += 1
+            if filter and idx==1: idx=3  # skip number and type fields for FILTER format strings
+        if not data['id']: self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
+        if 'descr' not in data:
+            # missing description
+            self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
+            data['descr'] = ""
+        if not data['type'] and not data['number']:
+            # fine, ##filter format
+            return FORMAT(data['id'],self.NT_NUMBER,0,"Flag",data['descr'],'.')
+        if not data['type'] in ["Integer","Float","Character","String","Flag"]:
+            self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
+        # I would like a missing-value field, but it isn't there
+        if data['type'] in ['Integer','Float']: data['missing'] = None    # Do NOT use arbitrary int/float as missing value
+        else:                                   data['missing'] = '.'
+        if not data['number']: self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
+        try:
+            n = int(data['number'])
+            t = self.NT_NUMBER
+        except ValueError:
+            n = -1
+            if data['number'] == '.':                   t = self.NT_UNKNOWN
+            elif data['number'] == '#alleles':          t = self.NT_ALLELES
+            elif data['number'] == '#nonref_alleles':   t = self.NT_NR_ALLELES
+            elif data['number'] == '#genotypes':        t = self.NT_GENOTYPES
+            elif data['number'] == '#phased_genotypes': t = self.NT_PHASED_GENOTYPES
+            elif data['number'] == '#phased_genotypes': t = self.NT_PHASED_GENOTYPES
+            # abbreviations added in VCF version v4.1
+            elif data['number'] == 'A': t = self.NT_ALLELES
+            elif data['number'] == 'G': t = self.NT_GENOTYPES
+            else:
+                self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
+        # if number is 0 - type must be Flag
+        if n == 0 and data['type'] != 'Flag':
+            self.error( line, self.ZERO_FOR_NON_FLAG_FIELD)
+            # force type 'Flag' if no number
+            data['type'] = 'Flag'
+
+        return FORMAT(data['id'],t,n,data['type'],data['descr'],data['missing'])
+
+    def format_format( self, fmt, filter=False ):
+        values = [('ID',fmt.id)]
+        if fmt.number != None and not filter:
+            if fmt.numbertype == self.NT_UNKNOWN: nmb = "."
+            elif fmt.numbertype == self.NT_NUMBER: nmb = str(fmt.number)
+            elif fmt.numbertype == self.NT_ALLELES: nmb = "#alleles"
+            elif fmt.numbertype == self.NT_NR_ALLELES: nmb = "#nonref_alleles"
+            elif fmt.numbertype == self.NT_GENOTYPES: nmb = "#genotypes"
+            elif fmt.numbertype == self.NT_PHASED_GENOTYPES: nmb = "#phased_genotypes"
+            else:
+                raise ValueError("Unknown number type encountered: %s" % fmt.numbertype)
+            values.append( ('Number',nmb) )
+            values.append( ('Type', fmt.type) )
+        values.append( ('Description', '"' + fmt.description + '"') )
+        if self._version == 33:
+            format = ",".join([v for k,v in values])
+        else:
+            format = "<" + (",".join( ["%s=%s" % (k,v) for (k,v) in values] )) + ">"
+        return format
+
+    def get_expected(self, format, formatdict, alt):
+        fmt = formatdict[format]
+        if fmt.numbertype == self.NT_UNKNOWN: return -1
+        if fmt.numbertype == self.NT_NUMBER: return fmt.number
+        if fmt.numbertype == self.NT_ALLELES: return len(alt)+1
+        if fmt.numbertype == self.NT_NR_ALLELES: return len(alt)
+        if fmt.numbertype == self.NT_GENOTYPES: return ((len(alt)+1)*(len(alt)+2)) // 2
+        if fmt.numbertype == self.NT_PHASED_GENOTYPES: return (len(alt)+1)*(len(alt)+1)
+        return 0
+
+
+    def _add_definition(self, formatdict, key, data, line ):
+        if key in formatdict: return
+        self.error(line,self.ERROR_UNKNOWN_KEY,key)
+        if data == None:
+            formatdict[key] = FORMAT(key,self.NT_NUMBER,0,"Flag","(Undefined tag)",".")
+            return
+        if data == []: data = [""]             # unsure what type -- say string
+        if type(data[0]) == type(0.0):
+            formatdict[key] = FORMAT(key,self.NT_UNKNOWN,-1,"Float","(Undefined tag)",None)
+            return
+        if type(data[0]) == type(0):
+            formatdict[key] = FORMAT(key,self.NT_UNKNOWN,-1,"Integer","(Undefined tag)",None)
+            return
+        formatdict[key] = FORMAT(key,self.NT_UNKNOWN,-1,"String","(Undefined tag)",".")
+
+
+    # todo: trim trailing missing values
+    def format_formatdata( self, data, format, key=True, value=True, separator=":" ):
+        output, sdata = [], []
+        if type(data) == type([]): # for FORMAT field, make data with dummy values
+            d = {}
+            for k in data: d[k] = []
+            data = d
+        # convert missing values; and silently add definitions if required
+        for k in data:
+            self._add_definition( format, k, data[k], "(output)" )
+            for idx,v in enumerate(data[k]):
+                if v == format[k].missingvalue: data[k][idx] = "."
+        # make sure GT comes first; and ensure fixed ordering; also convert GT data back to string
+        for k in data:
+            if k != 'GT': sdata.append( (k,data[k]) )
+        sdata.sort()
+        if 'GT' in data:
+            sdata = [('GT',map(self.convertGTback,data['GT']))] + sdata
+        for k,v in sdata:
+            if v == []: v = None
+            if key and value:
+                if v != None: output.append( k+"="+','.join(map(str,v)) )
+                else: output.append( k )
+            elif key: output.append(k)
+            elif value:
+                if v != None: output.append( ','.join(map(str,v)) )
+                else: output.append( "." )                    # should not happen
+        # snip off trailing missing data
+        while len(output) > 1:
+            last = output[-1].replace(',','').replace('.','')
+            if len(last)>0: break
+            output = output[:-1]
+        return separator.join(output)
+
+
+    def enter_default_format(self):
+        for f in [FORMAT('GT',self.NT_NUMBER,1,'String','Genotype','.'),
+                  FORMAT('DP',self.NT_NUMBER,1,'Integer','Read depth at this position for this sample',-1),
+                  FORMAT('FT',self.NT_NUMBER,1,'String','Sample Genotype Filter','.'),
+                  FORMAT('GL',self.NT_UNKNOWN,-1,'Float','Genotype likelihoods','.'),
+                  FORMAT('GLE',self.NT_UNKNOWN,-1,'Float','Genotype likelihoods','.'),
+                  FORMAT('GQ',self.NT_NUMBER,1,'Integer','Genotype Quality',-1),
+                  FORMAT('PL',self.NT_GENOTYPES,-1,'Integer','Phred-scaled genotype likelihoods', '.'),
+                  FORMAT('GP',self.NT_GENOTYPES,-1,'Float','Genotype posterior probabilities','.'),
+                  FORMAT('GQ',self.NT_GENOTYPES,-1,'Integer','Conditional genotype quality','.'),
+                  FORMAT('HQ',self.NT_UNKNOWN,-1,'Integer','Haplotype Quality',-1),    # unknown number, since may be haploid
+                  FORMAT('PS',self.NT_UNKNOWN,-1,'Integer','Phase set','.'),
+                  FORMAT('PQ',self.NT_NUMBER,1,'Integer','Phasing quality',-1),
+                  FORMAT('EC',self.NT_ALLELES,1,'Integer','Expected alternate allel counts',-1),
+                  FORMAT('MQ',self.NT_NUMBER,1,'Integer','RMS mapping quality',-1),
+                  ]:
+            if f.id not in self._format:
+                self._format[f.id] = f
+
+    def parse_header(self, line):
+
+        assert line.startswith('##')
+        elts = line[2:].split('=')
+        key = elts[0].strip()
+        value = '='.join(elts[1:]).strip()
+        if key == "fileformat":
+            if value == "VCFv3.3":
+                self._version = 33
+            elif value == "VCFv4.0":
+                self._version = 40
+            elif value == "VCFv4.1":
+                # AH - for testing
+                self._version = 40
+            elif value == "VCFv4.2":
+                # AH - for testing
+                self._version = 40
+            else:
+                self.error(line,self.UNKNOWN_FORMAT_STRING)
+        elif key == "INFO":
+            f = self.parse_format(line, value)
+            self._info[ f.id ] = f
+        elif key == "FILTER":
+            f = self.parse_format(line, value, filter=True)
+            self._filter[ f.id ] = f
+        elif key == "FORMAT":
+            f = self.parse_format(line, value)
+            self._format[ f.id ] = f
+        else:
+            # keep other keys in the header field
+            self._header.append( (key,value) )
+
+
+    def write_header( self, stream ):
+        stream.write("##fileformat=VCFv%s.%s\n" % (self._version // 10, self._version % 10))
+        for key,value in self._header: stream.write("##%s=%s\n" % (key,value))
+        for var,label in [(self._info,"INFO"),(self._filter,"FILTER"),(self._format,"FORMAT")]:
+            for f in var.itervalues(): stream.write("##%s=%s\n" % (label,self.format_format(f,filter=(label=="FILTER"))))
+
+
+    def parse_heading( self, line ):
+        assert line.startswith('#')
+        assert not line.startswith('##')
+        headings = line[1:].split('\t')
+        # test for 8, as FORMAT field might be missing
+        if len(headings)==1 and len(line[1:].split()) >= 8:
+            self.error(line,self.HEADING_NOT_SEPARATED_BY_TABS)
+            headings = line[1:].split()
+
+        for i,s in enumerate(self._required):
+
+            if len(headings)<=i or headings[i] != s:
+
+                if len(headings) <= i:
+                    err = "(%sth entry not found)" % (i+1)
+                else:
+                    err = "(found %s, expected %s)" % (headings[i],s)
+
+                #self.error(line,self.BADLY_FORMATTED_HEADING,err)
+                # allow FORMAT column to be absent
+                if len(headings) == 8:
+                    headings.append("FORMAT")
+                else:
+                    self.error(line,self.BADLY_FORMATTED_HEADING,err)
+
+        self._samples = headings[9:]
+        self._sample2column = dict( [(y,x+9) for x,y in enumerate( self._samples ) ] )
+
+    def write_heading( self, stream ):
+        stream.write("#" + "\t".join(self._required + self._samples) + "\n")
+
+    def convertGT(self, GTstring):
+        if GTstring == ".": return ["."]
+        try:
+            gts = gtsRegEx.split(GTstring)
+            if len(gts) == 1: return [int(gts[0])]
+            if len(gts) != 2: raise ValueError()
+            if gts[0] == "." and gts[1] == ".": return [gts[0],GTstring[len(gts[0]):-len(gts[1])],gts[1]]
+            return [int(gts[0]),GTstring[len(gts[0]):-len(gts[1])],int(gts[1])]
+        except ValueError:
+            self.error(self._line,self.BAD_GENOTYPE,GTstring)
+            return [".","|","."]
+
+    def convertGTback(self, GTdata):
+        return ''.join(map(str,GTdata))
+
+    def parse_formatdata( self, key, value, formatdict, line ):
+        # To do: check that the right number of values is present
+        f = formatdict.get(key,None)
+        if f == None:
+            self._add_definition(formatdict, key, value, line )
+            f = formatdict[key]
+        if f.type == "Flag":
+            if value is not None: self.error(line,self.ERROR_FLAG_HAS_VALUE)
+            return []
+        values = value.split(',')
+        # deal with trailing data in some early VCF files
+        if f.type in ["Float","Integer"] and len(values)>0 and values[-1].find(';') > -1:
+            self.error(line,self.ERROR_TRAILING_DATA,values[-1])
+            values[-1] = values[-1].split(';')[0]
+        if f.type == "Integer":
+            for idx,v in enumerate(values):
+                try:
+                    if v == ".": values[idx] = f.missingvalue
+                    else:        values[idx] = int(v)
+                except:
+                    self.error(line,self.ERROR_FORMAT_NOT_INTEGER,"%s=%s" % (key, str(values)))
+                    return [0] * len(values)
+            return values
+        elif f.type == "String":
+            self._line = line
+            if f.id == "GT": values = list(map( self.convertGT, values ))
+            return values
+        elif f.type == "Character":
+            for v in values:
+                if len(v) != 1: self.error(line,self.ERROR_FORMAT_NOT_CHAR)
+            return values
+        elif f.type == "Float":
+            for idx,v in enumerate(values):
+                if v == ".": values[idx] = f.missingvalue
+            try: return list(map(float,values))
+            except:
+                self.error(line,self.ERROR_FORMAT_NOT_NUMERICAL,"%s=%s" % (key, str(values)))
+                return [0.0] * len(values)
+        else:
+            # can't happen
+            self.error(line,self.ERROR_INFO_STRING)
+
+    def inregion(self, chrom, pos):
+        if not self._regions: return True
+        for r in self._regions:
+            if r[0] == chrom and r[1] <= pos < r[2]: return True
+        return False
+
+    def parse_data( self, line, lineparse=False ):
+        cols = line.split('\t')
+        if len(cols) != len(self._samples)+9:
+            # gracefully deal with absent FORMAT column
+            # and those missing samples
+            if len(cols) == 8:
+                cols.append("")
+            else:
+                self.error(line,
+                           self.BAD_NUMBER_OF_COLUMNS,
+                           "expected %s for %s samples (%s), got %s" % (len(self._samples)+9, len(self._samples), self._samples, len(cols)))
+
+        chrom = cols[0]
+
+        # get 0-based position
+        try:    pos = int(cols[1])-1
+        except: self.error(line,self.POS_NOT_NUMERICAL)
+        if pos < 0: self.error(line,self.POS_NOT_POSITIVE)
+
+        # implement filtering
+        if not self.inregion(chrom,pos): return None
+
+        # end of first-pass parse for sortedVCF
+        if lineparse: return chrom, pos, line
+
+        id = cols[2]
+
+        ref = cols[3].upper()
+        if ref == ".":
+            self.error(line,self.MISSING_REF)
+            if self._version == 33: ref = get_sequence(chrom,pos,pos+1,self._reference)
+            else:                   ref = ""
+        else:
+            for c in ref:
+                if c not in "ACGTN": self.error(line,self.UNKNOWN_CHAR_IN_REF)
+            if "N" in ref: ref = get_sequence(chrom,pos,pos+len(ref),self._reference)
+
+        # make sure reference is sane
+        if self._reference:
+            left = max(0,pos-100)
+            faref_leftflank = get_sequence(chrom,left,pos+len(ref),self._reference)
+            faref = faref_leftflank[pos-left:]
+            if faref != ref: self.error(line,self.WRONG_REF,"(reference is %s, VCF says %s)" % (faref,ref))
+            ref = faref
+
+        # convert v3.3 to v4.0 alleles below
+        if cols[4] == ".": alt = []
+        else: alt = cols[4].upper().split(',')
+
+        if cols[5] == ".": qual = -1
+        else:
+            try:    qual = float(cols[5])
+            except: self.error(line,self.QUAL_NOT_NUMERICAL)
+
+        # postpone checking that filters exist.  Encode missing filter or no filtering as empty list
+        if cols[6] == "." or cols[6] == "PASS" or cols[6] == "0": filter = []
+        else: filter = cols[6].split(';')
+
+        # dictionary of keys, and list of values
+        info = {}
+        if cols[7] != ".":
+            for blurp in cols[7].split(';'):
+                elts = blurp.split('=')
+                if len(elts) == 1: v = None
+                elif len(elts) == 2: v = elts[1]
+                else: self.error(line,self.ERROR_INFO_STRING)
+                info[elts[0]] = self.parse_formatdata(elts[0],
+                                                      v,
+                                                      self._info,
+                                                      line)
+
+        # Gracefully deal with absent FORMAT column
+        if cols[8] == "": format = []
+        else: format = cols[8].split(':')
+
+        # check: all filters are defined
+        for f in filter:
+            if f not in self._filter: self.error(line,self.FILTER_NOT_DEFINED, f)
+
+        # check: format fields are defined
+        if self._format:
+            for f in format:
+                if f not in self._format: self.error(line,self.FORMAT_NOT_DEFINED, f)
+
+        # convert v3.3 alleles
+        if self._version == 33:
+            if len(ref) != 1: self.error(line,self.V33_BAD_REF)
+            newalts = []
+            have_deletions = False
+            for a in alt:
+                if len(a) == 1: a = a + ref[1:]                       # SNP; add trailing reference
+                elif a.startswith('I'): a = ref[0] + a[1:] + ref[1:]  # insertion just beyond pos; add first and trailing reference
+                elif a.startswith('D'): # allow D<seq> and D<num>
+                    have_deletions = True
+                    try:
+                        l = int(a[1:])          # throws ValueError if sequence
+                        if len(ref) < l:        # add to reference if necessary
+                            addns = get_sequence(chrom,pos+len(ref),pos+l,self._reference)
+                            ref += addns
+                            for i,na in enumerate(newalts): newalts[i] = na+addns
+                        a = ref[l:]             # new deletion, deleting pos...pos+l
+                    except ValueError:
+                        s = a[1:]
+                        if len(ref) < len(s):   # add Ns to reference if necessary
+                            addns = get_sequence(chrom,pos+len(ref),pos+len(s),self._reference)
+                            if not s.endswith(addns) and addns != 'N'*len(addns):
+                                self.error(line,self.V33_UNMATCHED_DELETION,
+                                           "(deletion is %s, reference is %s)" % (a,get_sequence(chrom,pos,pos+len(s),self._reference)))
+                            ref += addns
+                            for i,na in enumerate(newalts): newalts[i] = na+addns
+                        a = ref[len(s):]        # new deletion, deleting from pos
+                else:
+                    self.error(line,self.V33_BAD_ALLELE)
+                newalts.append(a)
+            alt = newalts
+            # deletion alleles exist, add dummy 1st reference allele, and account for leading base
+            if have_deletions:
+                if pos == 0:
+                    # Petr Danacek's: we can't have a leading nucleotide at (1-based) position 1
+                    addn = get_sequence(chrom,pos+len(ref),pos+len(ref)+1,self._reference)
+                    ref += addn
+                    alt = [allele+addn for allele in alt]
+                else:
+                    addn = get_sequence(chrom,pos-1,pos,self._reference)
+                    ref = addn + ref
+                    alt = [addn + allele for allele in alt]
+                    pos -= 1
+        else:
+            # format v4.0 -- just check for nucleotides
+            for allele in alt:
+                if not alleleRegEx.match(allele):
+                    self.error(line,self.V40_BAD_ALLELE,allele)
+
+        # check for leading nucleotide in indel calls
+        for allele in alt:
+            if len(allele) != len(ref):
+                if len(allele) == 0: self.error(line,self.ZERO_LENGTH_ALLELE)
+                if ref[0].upper() != allele[0].upper() and "N" not in (ref[0]+allele[0]).upper():
+                    self.error(line,self.MISSING_INDEL_ALLELE_REF_BASE)
+
+        # trim trailing bases in alleles
+        # AH: not certain why trimming this needs to be added
+        #     disabled now for unit testing
+        # if alt:
+        #     for i in range(1,min(len(ref),min(map(len,alt)))):
+        #         if len(set(allele[-1].upper() for allele in alt)) > 1 or ref[-1].upper() != alt[0][-1].upper():
+        #             break
+        #         ref, alt = ref[:-1], [allele[:-1] for allele in alt]
+
+        # left-align alleles, if a reference is available
+        if self._leftalign and self._reference:
+            while left < pos:
+                movable = True
+                for allele in alt:
+                    if len(allele) > len(ref):
+                        longest, shortest = allele, ref
+                    else:
+                        longest, shortest = ref, allele
+                    if len(longest) == len(shortest) or longest[:len(shortest)].upper() != shortest.upper():
+                        movable = False
+                    if longest[-1].upper() != longest[len(shortest)-1].upper():
+                        movable = False
+                if not movable:
+                    break
+                ref = ref[:-1]
+                alt = [allele[:-1] for allele in alt]
+                if min([len(allele) for allele in alt]) == 0 or len(ref) == 0:
+                    ref = faref_leftflank[pos-left-1] + ref
+                    alt = [faref_leftflank[pos-left-1] + allele for allele in alt]
+                    pos -= 1
+
+        # parse sample columns
+        samples = []
+        for sample in cols[9:]:
+            dict = {}
+            values = sample.split(':')
+            if len(values) > len(format):
+                self.error(line,self.BAD_NUMBER_OF_VALUES,"(found %s values in element %s; expected %s)" % (len(values),sample,len(format)))
+            for idx in range(len(format)):
+                expected = self.get_expected(format[idx], self._format, alt)
+                if idx < len(values): value = values[idx]
+                else:
+                    if expected == -1: value = "."
+                    else: value = ",".join(["."]*expected)
+
+                dict[format[idx]] = self.parse_formatdata(format[idx],
+                                                          value,
+                                                          self._format,
+                                                          line)
+                if expected != -1 and len(dict[format[idx]]) != expected:
+                    self.error(line,self.BAD_NUMBER_OF_PARAMETERS,
+                               "id=%s, expected %s parameters, got %s" % (format[idx],expected,dict[format[idx]]))
+                    if len(dict[format[idx]] ) < expected: dict[format[idx]] += [dict[format[idx]][-1]]*(expected-len(dict[format[idx]]))
+                    dict[format[idx]] = dict[format[idx]][:expected]
+            samples.append( dict )
+
+        # done
+        d = {'chrom':chrom,
+             'pos':pos,      # return 0-based position
+             'id':id,
+             'ref':ref,
+             'alt':alt,
+             'qual':qual,
+             'filter':filter,
+             'info':info,
+             'format':format}
+        for key,value in zip(self._samples,samples):
+            d[key] = value
+
+        return d
+
+
+    def write_data(self, stream, data):
+        required = ['chrom','pos','id','ref','alt','qual','filter','info','format'] + self._samples
+        for k in required:
+            if k not in data: raise ValueError("Required key %s not found in data" % str(k))
+        if data['alt'] == []: alt = "."
+        else: alt = ",".join(data['alt'])
+        if data['filter'] == None: filter = "."
+        elif data['filter'] == []:
+            if self._version == 33: filter = "0"
+            else: filter = "PASS"
+        else: filter = ';'.join(data['filter'])
+        if data['qual'] == -1: qual = "."
+        else: qual = str(data['qual'])
+
+        output = [data['chrom'],
+                  str(data['pos']+1),   # change to 1-based position
+                  data['id'],
+                  data['ref'],
+                  alt,
+                  qual,
+                  filter,
+                  self.format_formatdata(
+                      data['info'], self._info, separator=";"),
+                  self.format_formatdata(
+                      data['format'], self._format, value=False)]
+
+        for s in self._samples:
+            output.append(self.format_formatdata(
+                data[s], self._format, key=False))
+
+        stream.write( "\t".join(output) + "\n" )
+
+    def _parse_header(self, stream):
+        self._lineno = 0
+        for line in stream:
+            line = force_str(line, self.encoding)
+            self._lineno += 1
+            if line.startswith('##'):
+                self.parse_header(line.strip())
+            elif line.startswith('#'):
+                self.parse_heading(line.strip())
+                self.enter_default_format()
+            else:
+                break
+        return line
+
+    def _parse(self, line, stream):
+        # deal with files with header only
+        if line.startswith("##"): return
+        if len(line.strip()) > 0:
+            d = self.parse_data( line.strip() )
+            if d: yield d
+        for line in stream:
+            self._lineno += 1
+            if self._lines and self._lineno > self._lines: raise StopIteration
+            d = self.parse_data( line.strip() )
+            if d: yield d
+
+    ######################################################################################################
+    #
+    # API follows
+    #
+    ######################################################################################################
+
+    def getsamples(self):
+        """ List of samples in VCF file """
+        return self._samples
+
+    def setsamples(self,samples):
+        """ List of samples in VCF file """
+        self._samples = samples
+
+    def getheader(self):
+        """ List of header key-value pairs (strings) """
+        return self._header
+
+    def setheader(self,header):
+        """ List of header key-value pairs (strings) """
+        self._header = header
+
+    def getinfo(self):
+        """ Dictionary of ##INFO tags, as VCF.FORMAT values """
+        return self._info
+
+    def setinfo(self,info):
+        """ Dictionary of ##INFO tags, as VCF.FORMAT values """
+        self._info = info
+
+    def getformat(self):
+        """ Dictionary of ##FORMAT tags, as VCF.FORMAT values """
+        return self._format
+
+    def setformat(self,format):
+        """ Dictionary of ##FORMAT tags, as VCF.FORMAT values """
+        self._format = format
+
+    def getfilter(self):
+        """ Dictionary of ##FILTER tags, as VCF.FORMAT values """
+        return self._filter
+
+    def setfilter(self,filter):
+        """ Dictionary of ##FILTER tags, as VCF.FORMAT values """
+        self._filter = filter
+
+    def setversion(self, version):
+        if version != 33 and version != 40: raise ValueError("Can only handle v3.3 and v4.0 VCF files")
+        self._version = version
+
+    def setregions(self, regions):
+        self._regions = regions
+
+    def setreference(self, ref):
+        """ Provide a reference sequence; a Python class supporting a fetch(chromosome, start, end) method, e.g. PySam.FastaFile """
+        self._reference = ref
+
+    def ignoreerror(self, errorstring):
+        try:             self._ignored_errors.add(self.__dict__[errorstring])
+        except KeyError: raise ValueError("Invalid error string: %s" % errorstring)
+
+    def warnerror(self, errorstring):
+        try:             self._warn_errors.add(self.__dict__[errorstring])
+        except KeyError: raise ValueError("Invalid error string: %s" % errorstring)
+
+    def parse(self, stream):
+        """ Parse a stream of VCF-formatted lines.  Initializes class instance and return generator """
+        last_line = self._parse_header(stream)
+        # now return a generator that does the actual work.  In this way the pre-processing is done
+        # before the first piece of data is yielded
+        return self._parse(last_line, stream)
+
+    def write(self, stream, datagenerator):
+        """ Writes a VCF file to a stream, using a data generator (or list) """
+        self.write_header(stream)
+        self.write_heading(stream)
+        for data in datagenerator: self.write_data(stream,data)
+
+    def writeheader(self, stream):
+        """ Writes a VCF header """
+        self.write_header(stream)
+        self.write_heading(stream)
+
+    def compare_calls(self, pos1, ref1, alt1, pos2, ref2, alt2):
+        """ Utility function: compares two calls for equality """
+        # a variant should always be assigned to a unique position, one base before
+        # the leftmost position of the alignment gap.  If this rule is implemented
+        # correctly, the two positions must be equal for the calls to be identical.
+        if pos1 != pos2: return False
+        # from both calls, trim rightmost bases when identical.  Do this safely, i.e.
+        # only when the reference bases are not Ns
+        while len(ref1)>0 and len(alt1)>0 and ref1[-1] == alt1[-1]:
+            ref1 = ref1[:-1]
+            alt1 = alt1[:-1]
+        while len(ref2)>0 and len(alt2)>0 and ref2[-1] == alt2[-1]:
+            ref2 = ref2[:-1]
+            alt2 = alt2[:-1]
+        # now, the alternative alleles must be identical
+        return alt1 == alt2
+
+###########################################################################################################
+###########################################################################################################
+## API functions added by Andreas
+###########################################################################################################
+
+    def connect(self, filename, encoding="ascii"):
+        '''connect to tabix file.'''
+        self.encoding=encoding
+        self.tabixfile = pysam.Tabixfile(filename, encoding=encoding)
+        self._parse_header(self.tabixfile.header)
+
+    def __del__(self):
+        self.close()
+        self.tabixfile = None
+
+    def close(self):
+        if self.tabixfile:
+            self.tabixfile.close()
+            self.tabixfile = None
+
+    def fetch(self,
+              reference=None,
+              start=None,
+              end=None,
+              region=None ):
+        """ Parse a stream of VCF-formatted lines.
+        Initializes class instance and return generator """
+        return self.tabixfile.fetch(
+            reference,
+            start,
+            end,
+            region,
+            parser = asVCFRecord(self))
+
+    def validate(self, record):
+        '''validate vcf record.
+
+        returns a validated record.
+        '''
+
+        raise NotImplementedError("needs to be checked")
+
+        chrom, pos = record.chrom, record.pos
+
+        # check reference
+        ref = record.ref
+        if ref == ".":
+            self.error(str(record),self.MISSING_REF)
+            if self._version == 33: ref = get_sequence(chrom,pos,pos+1,self._reference)
+            else:                   ref = ""
+        else:
+            for c in ref:
+                if c not in "ACGTN": self.error(str(record),self.UNKNOWN_CHAR_IN_REF)
+                if "N" in ref: ref = get_sequence(chrom,
+                                                  pos,
+                                                  pos+len(ref),
+                                                  self._reference)
+
+        # make sure reference is sane
+        if self._reference:
+            left = max(0,self.pos-100)
+            faref_leftflank = get_sequence(chrom,left,self.pos+len(ref),self._reference)
+            faref = faref_leftflank[pos-left:]
+            if faref != ref: self.error(str(record),self.WRONG_REF,"(reference is %s, VCF says %s)" % (faref,ref))
+            ref = faref
+
+        # check: format fields are defined
+        for f in record.format:
+            if f not in self._format: self.error(str(record),self.FORMAT_NOT_DEFINED, f)
+
+        # check: all filters are defined
+        for f in record.filter:
+            if f not in self._filter: self.error(str(record),self.FILTER_NOT_DEFINED, f)
+
+        # convert v3.3 alleles
+        if self._version == 33:
+            if len(ref) != 1: self.error(str(record),self.V33_BAD_REF)
+            newalts = []
+            have_deletions = False
+            for a in alt:
+                if len(a) == 1: a = a + ref[1:]                       # SNP; add trailing reference
+                elif a.startswith('I'): a = ref[0] + a[1:] + ref[1:]  # insertion just beyond pos; add first and trailing reference
+                elif a.startswith('D'): # allow D<seq> and D<num>
+                    have_deletions = True
+                    try:
+                        l = int(a[1:])          # throws ValueError if sequence
+                        if len(ref) < l:        # add to reference if necessary
+                            addns = get_sequence(chrom,pos+len(ref),pos+l,self._reference)
+                            ref += addns
+                            for i,na in enumerate(newalts): newalts[i] = na+addns
+                        a = ref[l:]             # new deletion, deleting pos...pos+l
+                    except ValueError:
+                        s = a[1:]
+                        if len(ref) < len(s):   # add Ns to reference if necessary
+                            addns = get_sequence(chrom,pos+len(ref),pos+len(s),self._reference)
+                            if not s.endswith(addns) and addns != 'N'*len(addns):
+                                self.error(str(record),self.V33_UNMATCHED_DELETION,
+                                           "(deletion is %s, reference is %s)" % (a,get_sequence(chrom,pos,pos+len(s),self._reference)))
+                            ref += addns
+                            for i,na in enumerate(newalts): newalts[i] = na+addns
+                        a = ref[len(s):]        # new deletion, deleting from pos
+                else:
+                    self.error(str(record),self.V33_BAD_ALLELE)
+                newalts.append(a)
+            alt = newalts
+            # deletion alleles exist, add dummy 1st reference allele, and account for leading base
+            if have_deletions:
+                if pos == 0:
+                    # Petr Danacek's: we can't have a leading nucleotide at (1-based) position 1
+                    addn = get_sequence(chrom,pos+len(ref),pos+len(ref)+1,self._reference)
+                    ref += addn
+                    alt = [allele+addn for allele in alt]
+                else:
+                    addn = get_sequence(chrom,pos-1,pos,self._reference)
+                    ref = addn + ref
+                    alt = [addn + allele for allele in alt]
+                    pos -= 1
+        else:
+            # format v4.0 -- just check for nucleotides
+            for allele in alt:
+                if not alleleRegEx.match(allele):
+                    self.error(str(record),self.V40_BAD_ALLELE,allele)
+
+
+        # check for leading nucleotide in indel calls
+        for allele in alt:
+            if len(allele) != len(ref):
+                if len(allele) == 0: self.error(str(record),self.ZERO_LENGTH_ALLELE)
+                if ref[0].upper() != allele[0].upper() and "N" not in (ref[0]+allele[0]).upper():
+                    self.error(str(record),self.MISSING_INDEL_ALLELE_REF_BASE)
+
+        # trim trailing bases in alleles
+        # AH: not certain why trimming this needs to be added
+        #     disabled now for unit testing
+        # for i in range(1,min(len(ref),min(map(len,alt)))):
+        #     if len(set(allele[-1].upper() for allele in alt)) > 1 or ref[-1].upper() != alt[0][-1].upper():
+        #         break
+        #     ref, alt = ref[:-1], [allele[:-1] for allele in alt]
+
+        # left-align alleles, if a reference is available
+        if self._leftalign and self._reference:
+            while left < pos:
+                movable = True
+                for allele in alt:
+                    if len(allele) > len(ref):
+                        longest, shortest = allele, ref
+                    else:
+                        longest, shortest = ref, allele
+                    if len(longest) == len(shortest) or longest[:len(shortest)].upper() != shortest.upper():
+                        movable = False
+                    if longest[-1].upper() != longest[len(shortest)-1].upper():
+                        movable = False
+                if not movable:
+                    break
+                ref = ref[:-1]
+                alt = [allele[:-1] for allele in alt]
+                if min([len(allele) for allele in alt]) == 0 or len(ref) == 0:
+                    ref = faref_leftflank[pos-left-1] + ref
+                    alt = [faref_leftflank[pos-left-1] + allele for allele in alt]
+                    pos -= 1
+
+__all__ = [
+    "VCF", "VCFRecord", ]
diff --git a/pysam/py.typed b/pysam/py.typed
new file mode 100644
index 0000000..e69de29
diff --git a/pysam/pysam_stream.h b/pysam/pysam_stream.h
new file mode 100644
index 0000000..3a4eb16
--- /dev/null
+++ b/pysam/pysam_stream.h
@@ -0,0 +1,13 @@
+#ifndef PYSAM_STREAM_H
+#define PYSAM_STREAM_H
+
+#include "htslib/kseq.h"
+
+// #######################################################
+// fastq parsing
+// KSEQ_INIT(gzFile, gzread)
+KSEQ_INIT(BGZF *, bgzf_read)
+
+//KSTREAM_INIT( gzFile, gzread, 16384)
+
+#endif
diff --git a/pysam/pysam_util.c b/pysam/pysam_util.c
new file mode 100644
index 0000000..349af44
--- /dev/null
+++ b/pysam/pysam_util.c
@@ -0,0 +1,36 @@
+#include <ctype.h>
+#include <assert.h>
+#include <unistd.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+
+#include "htslib/khash.h"
+#include "htslib/ksort.h"
+#include "htslib/knetfile.h"
+
+#if !(_POSIX_C_SOURCE >= 200809L || _XOPEN_SOURCE >= 700)
+/*
+ * A rudimentary emulation of getline() for systems that dont support it
+ * natively.  Since this is used for PPD file reading, it assumes (possibly
+ * falsely) that BUFSIZ is big enough.
+ */
+ssize_t
+getline(char **line, size_t *linelen, FILE *fp)
+{
+  if (*linelen == 0) 
+    {
+      *linelen = BUFSIZ;
+      *line = malloc(*linelen);
+    }
+
+  memset(*line, 0, *linelen);
+  fgets(*line, *linelen, fp);
+
+  return (strlen(*line));
+
+}
+#endif
+
+
+
diff --git a/pysam/pysam_util.h b/pysam/pysam_util.h
new file mode 100644
index 0000000..789e9d0
--- /dev/null
+++ b/pysam/pysam_util.h
@@ -0,0 +1,5 @@
+#ifndef PYSAM_UTIL_H
+#define PYSAM_UTIL_H
+
+
+#endif
diff --git a/pysam/samtools.py b/pysam/samtools.py
new file mode 100644
index 0000000..a90d32c
--- /dev/null
+++ b/pysam/samtools.py
@@ -0,0 +1,55 @@
+from pysam.utils import PysamDispatcher
+
+# samtools command line options to export in python
+SAMTOOLS_DISPATCH = {
+    # samtools 'documented' commands
+    "view": ("view", None),
+    "head": ("head", None),
+    "sort": ("sort", None),
+    "mpileup": ("mpileup", None),
+    "consensus": ("consensus", None),
+    "depth": ("depth", None),
+    "faidx": ("faidx", None),
+    "fqidx": ("fqidx", None),
+    "tview": ("tview", None),
+    "index": ("index", None),
+    "idxstats": ("idxstats", None),
+    "fixmate": ("fixmate", None),
+    "flagstat": ("flagstat", None),
+    "calmd": ("calmd", None),
+    "merge": ("merge", None),
+    "markdup": ("markdup", None),
+    "rmdup": ("rmdup", None),
+    "reference": ("reference", None),
+    "reheader": ("reheader", None),
+    "cat": ("cat", None),
+    "targetcut": ("targetcut", None),
+    "phase": ("phase", None),
+    "bam2fq": ("bam2fq", None),
+    "dict": ("dict", None),
+    "addreplacerg": ("addreplacerg", None),
+    "pad2unpad": ("pad2unpad", None),
+    "depad": ("pad2unpad", None),
+    "bedcov": ("bedcov", None),
+    "coverage": ("coverage", None),
+    "bamshuf": ("bamshuf", None),
+    "collate": ("collate", None),
+    "stats": ("stats", None),
+    "fasta": ("fasta", None),
+    "fastq": ("fastq", None),
+    "quickcheck": ("quickcheck", None),
+    "split": ("split", None),
+    "flags": ("flags", None),
+    "ampliconclip": ("ampliconclip", None),
+    "ampliconstats": ("ampliconstats", None),
+    "version": ("version", None),
+    "fqimport": ("import", None),
+    "samples": ("samples", None),
+}
+
+# instantiate samtools commands as python functions
+for key, options in SAMTOOLS_DISPATCH.items():
+    cmd, parser = options
+    globals()[key] = PysamDispatcher("samtools", cmd, parser)
+
+__all__ = list(SAMTOOLS_DISPATCH)
diff --git a/pysam/utils.py b/pysam/utils.py
new file mode 100644
index 0000000..fcc4434
--- /dev/null
+++ b/pysam/utils.py
@@ -0,0 +1,111 @@
+from pysam.libcutils import _pysam_dispatch
+
+
+class SamtoolsError(Exception):
+    '''exception raised in case of an error incurred in the samtools
+    library.'''
+
+    def __init__(self, value):
+        self.value = value
+
+    def __str__(self):
+        return repr(self.value)
+
+
+class PysamDispatcher(object):
+    '''The dispatcher emulates the samtools/bctools command line.
+
+    Captures stdout and stderr.
+
+    Raises a :class:`pysam.SamtoolsError` exception in case samtools
+    exits with an error code other than 0.
+
+    Some command line options are associated with parsers.  For
+    example, the samtools command "pileup -c" creates a tab-separated
+    table on standard output. In order to associate parsers with
+    options, an optional list of parsers can be supplied. The list
+    will be processed in order checking for the presence of each
+    option.
+
+    If no parser is given or no appropriate parser is found, the
+    stdout output of samtools/bcftools commands will be returned.
+
+    '''
+
+    dispatch = None
+    parsers = None
+    collection = None
+
+    def __init__(self, collection, dispatch, parsers):
+        self.collection = collection
+        self.dispatch = dispatch
+        self.parsers = parsers
+        self.stderr = []
+
+    def __call__(self, *args, **kwargs):
+        '''execute a samtools command.
+
+        Keyword arguments:
+        catch_stdout -- redirect stdout from the samtools command and
+            return as variable (default True)
+        save_stdout -- redirect stdout to a filename.
+        raw -- ignore any parsers associated with this samtools command.
+        split_lines -- return stdout (if catch_stdout is True and stderr
+                       as a list of strings.
+        '''
+        retval, stderr, stdout = _pysam_dispatch(
+            self.collection,
+            self.dispatch,
+            args,
+            catch_stdout=kwargs.get("catch_stdout", True),
+            save_stdout=kwargs.get("save_stdout", None))
+
+        if kwargs.get("split_lines", False):
+            stdout = stdout.splitlines()
+            if stderr:
+                stderr = stderr.splitlines()
+
+        if retval:
+            raise SamtoolsError(
+                "%s returned with error %i: "
+                "stdout=%s, stderr=%s" %
+                (self.collection,
+                 retval,
+                 stdout,
+                 stderr))
+
+        self.stderr = stderr
+
+        # call parser for stdout:
+        if not kwargs.get("raw") and stdout and self.parsers:
+            for options, parser in self.parsers:
+                for option in options:
+                    if option not in args:
+                        break
+                else:
+                    return parser(stdout)
+
+        return stdout
+
+    def get_messages(self):
+        return self.stderr
+
+    def usage(self):
+        '''return the samtools usage information for this command'''
+        retval, stderr, stdout = _pysam_dispatch(
+            self.collection,
+            self.dispatch,
+            is_usage=True,
+            catch_stdout=True)
+        # some tools write usage to stderr, such as mpileup
+        if stderr:
+            return stderr
+        else:
+            return stdout
+
+
+class unquoted_str(str):
+    '''Tag a value as an unquoted string. Meta-information in the VCF
+    header takes the form of key=value pairs. By default, pysam will
+    enclose the value in quotation marks. Tagging that value with
+    unquoted_str will prevent this quoting.'''
diff --git a/pysam/version.h b/pysam/version.h
new file mode 100644
index 0000000..dddd49c
--- /dev/null
+++ b/pysam/version.h
@@ -0,0 +1,5 @@
+// Version information used while compiling samtools, bcftools, and htslib
+
+#define SAMTOOLS_VERSION "1.16.1 (pysam)"
+#define BCFTOOLS_VERSION "1.16 (pysam)"
+#define HTS_VERSION_TEXT "1.16 (pysam)"
diff --git a/pysam/version.py b/pysam/version.py
new file mode 100644
index 0000000..b6aede0
--- /dev/null
+++ b/pysam/version.py
@@ -0,0 +1,6 @@
+# pysam versioning information
+__version__ = "0.20.0"
+
+__samtools_version__ = "1.16.1"
+__bcftools_version__ = "1.16"
+__htslib_version__ = "1.16"
diff --git a/pysam/version.pyi b/pysam/version.pyi
new file mode 100644
index 0000000..9d52128
--- /dev/null
+++ b/pysam/version.pyi
@@ -0,0 +1,4 @@
+__version__: str
+__samtools_version__: str
+__bcftools_version__: str
+__htslib_version__: str
diff --git a/requirements.txt b/requirements.txt
new file mode 100644
index 0000000..f937d1c
--- /dev/null
+++ b/requirements.txt
@@ -0,0 +1 @@
+cython>=0.29.12
diff --git a/samtools/LICENSE b/samtools/LICENSE
new file mode 100644
index 0000000..a14e403
--- /dev/null
+++ b/samtools/LICENSE
@@ -0,0 +1,33 @@
+The MIT/Expat License
+
+Copyright (C) 2008-2022 Genome Research Ltd.
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.
+
+
+[The use of a range of years within a copyright notice in this distribution
+should be interpreted as being equivalent to a list of years including the
+first and last year specified and all consecutive years between them.
+
+For example, a copyright notice that reads "Copyright (C) 2005, 2007-2009,
+2011-2012" should be interpreted as being identical to a notice that reads
+"Copyright (C) 2005, 2007, 2008, 2009, 2011, 2012" and a copyright notice
+that reads "Copyright (C) 2005-2012" should be interpreted as being identical
+to a notice that reads "Copyright (C) 2005, 2006, 2007, 2008, 2009, 2010,
+2011, 2012".]
diff --git a/samtools/README b/samtools/README
new file mode 100644
index 0000000..7be5383
--- /dev/null
+++ b/samtools/README
@@ -0,0 +1,126 @@
+Samtools implements various utilities for post-processing alignments in the
+SAM, BAM, and CRAM formats, including indexing, variant calling (in conjunction
+with bcftools), and a simple alignment viewer.
+
+
+Building samtools
+=================
+
+The typical simple case of building Samtools using the HTSlib bundled within
+this Samtools release tarball is done as follows:
+
+    cd .../samtools-1.16.1 # Within the unpacked release directory
+    ./configure
+    make
+
+You may wish to copy the resulting samtools executable into somewhere on your
+$PATH, or run it where it is.
+
+Rather than running-in-place like that, the next simplest typical case is to
+install samtools etc properly into a directory of your choosing.  Building for
+installation using the HTSlib bundled within this Samtools release tarball,
+and building the various HTSlib utilities such as bgzip is done as follows:
+
+    cd .../samtools-1.16.1 # Within the unpacked release directory
+    ./configure --prefix=/path/to/location
+    make all all-htslib
+    make install install-htslib
+
+You will likely wish to add /path/to/location/bin to your $PATH.
+
+See INSTALL for full building and installation instructions and details.
+
+Building with HTSlib plug-in support
+====================================
+
+Enabling plug-ins causes some parts of HTSlib to be built as separate modules.
+There are two advantages to this:
+
+ * The static library libhts.a has fewer dependencies, which makes linking
+   third-party code against it easier.
+
+ * It is possible to build extra plug-ins in addition to the ones that are
+   bundled with HTSlib.  For example, the hts-plugins repository
+   <https://github.com/samtools/htslib-plugins> includes a module that
+   allows direct access to files stored in an iRODS data management
+   repository (see <https://irods.org/>).
+
+To build with plug-ins, you need to use the --enable-plugins configure option
+as follows:
+
+    cd .../samtools-1.16.1 # Within the unpacked release directory
+    ./configure --enable-plugins --prefix=/path/to/location
+    make all all-htslib
+    make install install-htslib
+
+There are two other configure options that affect plug-ins.  These are:
+   --with-plugin-dir=DIR     plug-in installation location
+   --with-plugin-path=PATH   default plug-in search path
+
+The default for --with-plugin-dir is <prefix>/libexec/htslib.
+--with-plugin-path sets the built-in search path used to find the plug-ins.  By
+default this is the directory set by the --with-plugin-dir option.  Multiple
+directories should be separated by colons.
+
+Setting --with-plugin-path is useful if you want to run directly from
+the source distribution instead of installing the package.  In that case
+you can use:
+
+    cd .../samtools-1.16.1 # Within the unpacked release directory
+    ./configure --enable-plugins --with-plugin-path=$PWD/htslib-1.16
+    make all all-htslib
+
+It is possible to override the built-in search path using the HTS_PATH
+environment variable.  Directories should be separated by colons.  To
+include the built-in path, add an empty entry to HTS_PATH:
+
+   export HTS_PATH=:/my/path            # Search built-in path first
+   export HTS_PATH=/my/path:            # Search built-in path last
+   export HTS_PATH=/my/path1::/my/path2 # Search built-in path between others
+
+Using an optimised zlib library
+===============================
+
+Samtools has been minimally tested against both the Intel-optimised and
+CloudFlare-optimised zlibs and shown to work.
+
+They can be downloaded from:
+
+    https://github.com/jtkukunas/zlib     # Intel
+    https://github.com/cloudflare/zlib    # CloudFlare
+
+Neither Samtools nor HTSlib needs recompiling to use these optimised libraries,
+but the LD_LIBRARY_PATH environment variable should be set to a directory
+containing the libz.so.1 file.
+
+Benchmarks comparing the various zlibs are available at:
+
+    http://www.htslib.org/benchmarks/zlib.html
+
+It is recommended that you perform your own rigorous tests for an entire
+pipeline if you wish to switch to one of the optimised zlib implementations.
+
+Citing
+======
+
+Please cite this paper when using SAMtools for your publications:
+
+Twelve years of SAMtools and BCFtools
+Petr Danecek, James K Bonfield, Jennifer Liddle, John Marshall, Valeriu Ohan, Martin O Pollard, Andrew Whitwham, Thomas Keane, Shane A McCarthy, Robert M Davies, Heng Li
+GigaScience, Volume 10, Issue 2, February 2021, giab008, https://doi.org/10.1093/gigascience/giab008
+
+@article{10.1093/gigascience/giab008,
+    author = {Danecek, Petr and Bonfield, James K and Liddle, Jennifer and Marshall, John and Ohan, Valeriu and Pollard, Martin O and Whitwham, Andrew and Keane, Thomas and McCarthy, Shane A and Davies, Robert M and Li, Heng},
+    title = "{Twelve years of SAMtools and BCFtools}",
+    journal = {GigaScience},
+    volume = {10},
+    number = {2},
+    year = {2021},
+    month = {02},
+    abstract = "{SAMtools and BCFtools are widely used programs for processing and analysing high-throughput sequencing data. They include tools for file format conversion and manipulation, sorting, querying, statistics, variant calling, and effect analysis amongst other methods.The first version appeared online 12 years ago and has been maintained and further developed ever since, with many new features and improvements added over the years. The SAMtools and BCFtools packages represent a unique collection of tools that have been used in numerous other software projects and countless genomic pipelines.Both SAMtools and BCFtools are freely available on GitHub under the permissive MIT licence, free for both non-commercial and commercial use. Both packages have been installed \\&gt;1 million times via Bioconda. The source code and documentation are available from https://www.htslib.org.}",
+    issn = {2047-217X},
+    doi = {10.1093/gigascience/giab008},
+    url = {https://doi.org/10.1093/gigascience/giab008},
+    note = {giab008},
+    eprint = {https://academic.oup.com/gigascience/article-pdf/10/2/giab008/36332246/giab008.pdf},
+}
diff --git a/samtools/amplicon_stats.c b/samtools/amplicon_stats.c
new file mode 100644
index 0000000..62bb15c
--- /dev/null
+++ b/samtools/amplicon_stats.c
@@ -0,0 +1,1754 @@
+/*  stats.c -- This is the former bamcheck integrated into samtools/htslib.
+
+    Copyright (C) 2020-2021 Genome Research Ltd.
+
+    Author: James Bonfield <jkb@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+/*
+ * This tool is designed to give "samtools stats" style output, but dedicated
+ * to small amplicon sequencing projects.  It gathers stats on the
+ * distribution of reads across amplicons.
+ */
+
+/*
+ * TODO:
+ * - Cope with multiple references.  What do we do here?  Just request one?
+ * - Permit regions rather than consuming whole file (maybe solves above).
+ */
+
+#include <config.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <inttypes.h>
+#include <getopt.h>
+#include <unistd.h>
+#include <math.h>
+
+#include <htslib/sam.h>
+#include <htslib/khash.h>
+
+#include "samtools.h"
+#include "sam_opts.h"
+#include "bam_ampliconclip.h"
+
+KHASH_MAP_INIT_INT64(tcoord, int64_t)
+KHASH_MAP_INIT_STR(qname, int64_t)
+
+#ifndef MIN
+#define MIN(a,b) ((a)<(b)?(a):(b))
+#endif
+
+#ifndef MAX
+#define MAX(a,b) ((a)>(b)?(a):(b))
+#endif
+
+#ifndef ABS
+#define ABS(a) ((a)>=0?(a):-(a))
+#endif
+
+#define TCOORD_MIN_COUNT   10
+#define MAX_AMP 1000       // Default maximum number of amplicons
+#define MAX_AMP_LEN 1000   // Default maximum length of any single amplicon
+#define MAX_PRIMER_PER_AMPLICON 4  // Max primers per LEFT/RIGHT
+#define MAX_DEPTH 5        // Number of different depths permitted
+
+typedef struct {
+    sam_global_args ga;
+    uint32_t flag_require;
+    uint32_t flag_filter;
+    int max_delta;   // Used for matching read to amplicon primer loc
+    int min_depth[MAX_DEPTH]; // Used for coverage; must be >= min_depth deep
+    int use_sample_name;
+    int max_amp;     // Total number of amplicons
+    int max_amp_len; // Maximum length of an individual amplicon
+    double depth_bin;// aggregate depth within this fraction
+    int tlen_adj;    // Adjust tlen by this amount, due to clip but no fixmate
+    FILE *out_fp;
+    char *argv;
+    int tcoord_min_count;
+    int tcoord_bin;
+    int multi_ref;
+} astats_args_t;
+
+typedef struct {
+    int nseq;       // total sequence count
+    int nfiltered;  // sequence filtered
+    int nfailprimer;// count of sequences not matching the primer locations
+
+    // Sizes of memory allocated below, to permit reset
+    int max_amp, max_amp_len, max_len;
+
+    // Summary across all samples, sum(x) plus sum(x^2) for s.d. calc
+    int64_t *nreads, *nreads2;          // [max_amp]
+    double  *nfull_reads;               // [max_amp]; 0.5/read if paired.
+    double  *nrperc, *nrperc2;          // [max_amp]
+    int64_t *nbases, *nbases2;          // [max_amp]
+    int64_t *coverage;                  // [max_amp][max_amp_len]
+    double  (*covered_perc)[MAX_DEPTH]; // [max_amp][MAX_DEPTH]
+    double  (*covered_perc2)[MAX_DEPTH];// [max_amp][MAX_DEPTH];
+    khash_t(tcoord) **tcoord;           // [max_amp+1]
+
+    // 0 is correct pair, 1 is incorrect pair, 2 is unidentified
+    int     (*amp_dist)[3];             // [MAX_AMP][3];
+
+    int *depth_valid; // [max_len]
+    int *depth_all;   // [max_len]
+    khash_t(qname) *qend;  // queryname end, for overlap removal
+} astats_t;
+
+// We can have multiple primers for LEFT / RIGHT, so this
+// permits detection by any compatible combination.
+// One reference:
+typedef struct {
+    int64_t left[MAX_PRIMER_PER_AMPLICON];
+    int nleft;
+    int64_t right[MAX_PRIMER_PER_AMPLICON];
+    int nright;
+    int64_t max_left, min_right; // inner dimensions
+    int64_t min_left, max_right; // outer dimensions
+} amplicon_t;
+
+// Multiple references, we have an array of amplicons_t - one per used ref.
+// We have per reference local and global stats here, as some of the stats
+// are coordinate based.  However we report them combined together as a single
+// list across all references.
+// "namp" is the number of amplicons in this reference, but they're
+// numbered first_amp to first_amp+namp-1 inclusively.
+typedef struct {
+    int tid, namp;
+    int64_t len;
+    bed_entry_list_t *sites;
+    amplicon_t *amp;
+    astats_t *lstats, *gstats; // local (1 file) and global (all file) stats
+    const char *ref;           // ref name (pointer to the bed hash table key)
+    int first_amp;             // first amplicon number for this ref
+} amplicons_t;
+
+// Reinitialised for each new reference/chromosome.
+// Counts from 1 to namp, -1 for no match and 0 for ?.
+static int *pos2start = NULL;
+static int *pos2end = NULL;
+static int pos2size = 0; // allocated size of pos2start/end
+
+// Lookup table to go from position to amplicon based on
+// read start / end.
+static int initialise_amp_pos_lookup(astats_args_t *args,
+                                     amplicons_t *amps,
+                                     int ref) {
+    int64_t i, j;
+    amplicon_t *amp = amps[ref].amp;
+    int64_t max_len = amps[ref].len;
+    int namp = amps[ref].namp;
+
+    if (max_len+1 > pos2size) {
+        if (!(pos2start = realloc(pos2start, (max_len+1)*sizeof(*pos2start))))
+            return -1;
+        if (!(pos2end   = realloc(pos2end,   (max_len+1)*sizeof(*pos2end))))
+            return -1;
+        pos2size = max_len;
+    }
+    for (i = 0; i < max_len; i++)
+        pos2start[i] = pos2end[i] = -1;
+
+    for (i = 0; i < namp; i++) {
+        for (j = 0; j < amp[i].nleft; j++) {
+            int64_t p;
+            for (p = amp[i].left[j] - args->max_delta;
+                 p <= amp[i].left[j] + args->max_delta; p++) {
+                if (p < 1 || p > max_len)
+                    continue;
+                pos2start[p-1] = i;
+            }
+        }
+        for (j = 0; j < amp[i].nright; j++) {
+            int64_t p;
+            for (p = amp[i].right[j] - args->max_delta;
+                 p <= amp[i].right[j] + args->max_delta; p++) {
+                if (p < 1 || p > max_len)
+                    continue;
+                pos2end[p-1] = i;
+            }
+        }
+    }
+
+    return 0;
+}
+
+// Counts amplicons.
+// Assumption: input BED file alternates between LEFT and RIGHT primers
+// per amplicon, thus we can count the number based on the switching
+// orientation.
+static int count_amplicon(bed_entry_list_t *sites) {
+    int i, namp, last_rev = 0;
+    for (i = namp = 0; i < sites->length; i++) {
+        if (sites->bp[i].rev == 0 && last_rev)
+            namp++;
+        last_rev = sites->bp[i].rev;
+    }
+
+    return ++namp;
+}
+
+// We're only interest in the internal part of the amplicon.
+// Our bed file has LEFT start/end followed by RIGHT start/end,
+// so collapse these to LEFT end / RIGHT start.
+//
+// Returns right most amplicon position on success,
+//         < 0 on error
+static int64_t bed2amplicon(astats_args_t *args, bed_entry_list_t *sites,
+                            amplicon_t *amp, int *namp, int do_title,
+                            const char *ref, int first_amp) {
+    int i, j;
+    int64_t max_right = 0;
+    FILE *ofp = args->out_fp;
+
+    *namp = 0;
+
+    // Assume all primers for the same amplicon are adjacent in BED
+    // with all + followed by all -.  Thus - to + signifies next primer set.
+    int last_rev = 0;
+    amp[0].max_left = 0;
+    amp[0].min_right = INT64_MAX;
+    amp[0].min_left = INT64_MAX;
+    amp[0].max_right = 0;
+    if (do_title) {
+        fprintf(ofp, "# Amplicon locations from BED file.\n");
+        fprintf(ofp, "# LEFT/RIGHT are <start>-<end> format and "
+                "comma-separated for alt-primers.\n");
+        if (args->multi_ref)
+            fprintf(ofp, "#\n# AMPLICON\tREF\tNUMBER\tLEFT\tRIGHT\n");
+        else
+            fprintf(ofp, "#\n# AMPLICON\tNUMBER\tLEFT\tRIGHT\n");
+    }
+    for (i = j = 0; i < sites->length; i++) {
+        if (i == 0 && sites->bp[i].rev != 0) {
+            fprintf(stderr, "[ampliconstats] error: BED file should start"
+                    " with the + strand primer\n");
+            return -1;
+        }
+        if (sites->bp[i].rev == 0 && last_rev) {
+            j++;
+            if (j >= args->max_amp) {
+                fprintf(stderr, "[ampliconstats] error: too many amplicons"
+                        " (%d). Use -a option to raise this.\n", j);
+                return -1;
+            }
+            amp[j].max_left = 0;
+            amp[j].min_right = INT64_MAX;
+            amp[j].min_left = INT64_MAX;
+            amp[j].max_right = 0;
+        }
+        if (sites->bp[i].rev == 0) {
+            if (i == 0 || last_rev) {
+                if (j>0) fprintf(ofp, "\n");
+                if (args->multi_ref)
+                    fprintf(ofp, "AMPLICON\t%s\t%d", ref, j+1 + first_amp);
+                else
+                    fprintf(ofp, "AMPLICON\t%d", j+1);
+            }
+            if (amp[j].nleft >= MAX_PRIMER_PER_AMPLICON) {
+                print_error_errno("ampliconstats",
+                                  "too many primers per amplicon (%d).\n",
+                                  MAX_PRIMER_PER_AMPLICON);
+                return -1;
+            }
+            amp[j].left[amp[j].nleft++] = sites->bp[i].right;
+            if (amp[j].max_left < sites->bp[i].right+1)
+                amp[j].max_left = sites->bp[i].right+1;
+            if (amp[j].min_left > sites->bp[i].right+1)
+                amp[j].min_left = sites->bp[i].right+1;
+            // BED file, so left+1 as zero based. right(+1-1) as
+            // BED goes one beyond end (and we want inclusive range).
+            fprintf(ofp, "%c%"PRId64"-%"PRId64, "\t,"[amp[j].nleft > 1],
+                    sites->bp[i].left+1, sites->bp[i].right);
+        } else {
+            if (amp[j].nright >= MAX_PRIMER_PER_AMPLICON) {
+                print_error_errno("ampliconstats",
+                                  "too many primers per amplicon (%d)",
+                                  MAX_PRIMER_PER_AMPLICON);
+                return -1;
+            }
+            amp[j].right[amp[j].nright++] = sites->bp[i].left;
+            if (amp[j].min_right > sites->bp[i].left-1)
+                amp[j].min_right = sites->bp[i].left-1;
+            if (amp[j].max_right < sites->bp[i].left-1) {
+                amp[j].max_right = sites->bp[i].left-1;
+                if (amp[j].max_right - amp[j].min_left + 1 >=
+                    args->max_amp_len) {
+                    fprintf(stderr, "[ampliconstats] error: amplicon "
+                            "longer (%d) than max_amp_len option (%d)\n",
+                            (int)(amp[j].max_right - amp[j].min_left + 2),
+                            args->max_amp_len);
+                    return -1;
+                }
+                if (max_right < amp[j].max_right)
+                    max_right = amp[j].max_right;
+            }
+            fprintf(ofp, "%c%"PRId64"-%"PRId64, "\t,"[amp[j].nright > 1],
+                    sites->bp[i].left+1, sites->bp[i].right);
+        }
+        last_rev = sites->bp[i].rev;
+    }
+    if (last_rev != 1) {
+        fprintf(ofp, "\n"); // useful if going to stdout
+        fprintf(stderr, "[ampliconstats] error: bed file does not end on"
+                " a reverse strand primer.\n");
+        return -1;
+    }
+    *namp = ++j;
+    if (j) fprintf(ofp, "\n");
+
+    if (j >= args->max_amp) {
+        fprintf(stderr, "[ampliconstats] error: "
+                "too many amplicons (%d). Use -a option to raise this.", j);
+        return -1;
+    }
+
+//    for (i = 0; i < *namp; i++) {
+//      printf("%d\t%ld", i, amp[i].length);
+//      for (j = 0; j < amp[i].nleft; j++)
+//          printf("%c%ld", "\t,"[j>0], amp[i].left[j]);
+//      for (j = 0; j < amp[i].nright; j++)
+//          printf("%c%ld", "\t,"[j>0], amp[i].right[j]);
+//      printf("\n");
+//    }
+
+    return max_right;
+}
+
+void stats_free(astats_t *st) {
+    if (!st)
+        return;
+
+    free(st->nreads);
+    free(st->nreads2);
+    free(st->nfull_reads);
+    free(st->nrperc);
+    free(st->nrperc2);
+    free(st->nbases);
+    free(st->nbases2);
+    free(st->coverage);
+    free(st->covered_perc);
+    free(st->covered_perc2);
+    free(st->amp_dist);
+
+    free(st->depth_valid);
+    free(st->depth_all);
+
+    if (st->tcoord) {
+        int i;
+        for (i = 0; i <= st->max_amp; i++) {
+            if (st->tcoord[i])
+                kh_destroy(tcoord, st->tcoord[i]);
+        }
+        free(st->tcoord);
+    }
+
+    khiter_t k;
+    for (k = kh_begin(st->qend); k != kh_end(st->qend); k++)
+        if (kh_exist(st->qend, k))
+            free((void *)kh_key(st->qend, k));
+    kh_destroy(qname, st->qend);
+
+    free(st);
+}
+
+astats_t *stats_alloc(int64_t max_len, int max_amp, int max_amp_len) {
+    astats_t *st = calloc(1, sizeof(*st));
+    if (!st)
+        return NULL;
+
+    st->max_amp = max_amp;
+    st->max_amp_len = max_amp_len;
+    st->max_len = max_len;
+
+    if (!(st->nreads  = calloc(max_amp, sizeof(*st->nreads))))  goto err;
+    if (!(st->nreads2 = calloc(max_amp, sizeof(*st->nreads2)))) goto err;
+    if (!(st->nrperc  = calloc(max_amp, sizeof(*st->nrperc))))  goto err;
+    if (!(st->nrperc2 = calloc(max_amp, sizeof(*st->nrperc2)))) goto err;
+    if (!(st->nbases  = calloc(max_amp, sizeof(*st->nbases))))  goto err;
+    if (!(st->nbases2 = calloc(max_amp, sizeof(*st->nbases2)))) goto err;
+
+    if (!(st->nfull_reads = calloc(max_amp, sizeof(*st->nfull_reads))))
+        goto err;
+
+    if (!(st->coverage = calloc(max_amp*max_amp_len, sizeof(*st->coverage))))
+        goto err;
+
+    if (!(st->covered_perc  = calloc(max_amp, sizeof(*st->covered_perc))))
+        goto err;
+    if (!(st->covered_perc2 = calloc(max_amp, sizeof(*st->covered_perc2))))
+        goto err;
+
+    if (!(st->tcoord = calloc(max_amp+1, sizeof(*st->tcoord)))) goto err;
+    int i;
+    for (i = 0; i <= st->max_amp; i++)
+        if (!(st->tcoord[i] = kh_init(tcoord)))
+            goto err;
+
+    if (!(st->qend = kh_init(qname)))
+        goto err;
+
+    if (!(st->depth_valid = calloc(max_len, sizeof(*st->depth_valid))))
+        goto err;
+    if (!(st->depth_all   = calloc(max_len, sizeof(*st->depth_all))))
+        goto err;
+
+    if (!(st->amp_dist  = calloc(max_amp, sizeof(*st->amp_dist))))  goto err;
+
+    return st;
+
+ err:
+    stats_free(st);
+    return NULL;
+}
+
+static void stats_reset(astats_t *st) {
+    st->nseq = 0;
+    st->nfiltered = 0;
+    st->nfailprimer = 0;
+
+    memset(st->nreads,  0, st->max_amp * sizeof(*st->nreads));
+    memset(st->nreads2, 0, st->max_amp * sizeof(*st->nreads2));
+    memset(st->nfull_reads, 0, st->max_amp * sizeof(*st->nfull_reads));
+
+    memset(st->nrperc,  0, st->max_amp * sizeof(*st->nrperc));
+    memset(st->nrperc2, 0, st->max_amp * sizeof(*st->nrperc2));
+
+    memset(st->nbases,  0, st->max_amp * sizeof(*st->nbases));
+    memset(st->nbases2, 0, st->max_amp * sizeof(*st->nbases2));
+
+    memset(st->coverage, 0, st->max_amp * st->max_amp_len
+           * sizeof(*st->coverage));
+    memset(st->covered_perc,  0, st->max_amp * sizeof(*st->covered_perc));
+    memset(st->covered_perc2, 0, st->max_amp * sizeof(*st->covered_perc2));
+
+    // Keep the allocated entries as it's likely all files will share
+    // the same keys.  Instead we reset counters to zero for common ones
+    // and delete rare ones.
+    int i;
+    for (i = 0; i <= st->max_amp; i++) {
+        khiter_t k;
+        for (k = kh_begin(st->tcoord[i]);
+             k != kh_end(st->tcoord[i]); k++)
+            if (kh_exist(st->tcoord[i], k)) {
+                if (kh_value(st->tcoord[i], k) < 5)
+                    kh_del(tcoord, st->tcoord[i], k);
+                else
+                    kh_value(st->tcoord[i], k) = 0;
+            }
+    }
+
+    khiter_t k;
+    for (k = kh_begin(st->qend); k != kh_end(st->qend); k++)
+        if (kh_exist(st->qend, k))
+            free((void *)kh_key(st->qend, k));
+    kh_clear(qname, st->qend);
+
+    memset(st->depth_valid, 0, st->max_len * sizeof(*st->depth_valid));
+    memset(st->depth_all,   0, st->max_len * sizeof(*st->depth_all));
+    memset(st->amp_dist,  0, st->max_amp * sizeof(*st->amp_dist));
+}
+
+static void amp_stats_reset(amplicons_t *amps, int nref) {
+    int i;
+    for (i = 0; i < nref; i++) {
+        if (!amps[i].sites)
+            continue;
+        stats_reset(amps[i].lstats);
+    }
+}
+
+static int accumulate_stats(astats_args_t *args, amplicons_t *amps,
+                            bam1_t *b) {
+    int ref = b->core.tid;
+    amplicon_t *amp = amps[ref].amp;
+    astats_t *stats = amps[ref].lstats;
+    int len = amps[ref].len;
+
+    if (!stats)
+        return 0;
+
+    stats->nseq++;
+    if ((b->core.flag & args->flag_require) != args->flag_require ||
+        (b->core.flag & args->flag_filter)  != 0) {
+        stats->nfiltered++;
+        return 0;
+    }
+
+    int64_t start = b->core.pos, mstart = start; // modified start
+    int64_t end = bam_endpos(b), i;
+
+    // Compute all-template-depth and valid-template-depth.
+    // We track current end location per read name so we can remove overlaps.
+    // Potentially we could use this data for a better amplicon-depth
+    // count too, but for now it's purely for the per-base plots.
+    int ret;
+    khiter_t k;
+    int prev_start = 0, prev_end = 0;
+    if ((b->core.flag & BAM_FPAIRED)
+        && !(b->core.flag & (BAM_FSUPPLEMENTARY | BAM_FSECONDARY))) {
+        k = kh_put(qname, stats->qend, bam_get_qname(b), &ret);
+        if (ret == 0) {
+            prev_start = kh_value(stats->qend, k) & 0xffffffff;
+            prev_end = kh_value(stats->qend, k)>>32;
+            mstart = MAX(mstart, prev_end);
+            // Ideally we'd reuse strings so we don't thrash free/malloc.
+            // However let's see if the official way of doing that (malloc
+            // itself) is fast enough first.
+            free((void *)kh_key(stats->qend, k));
+            kh_del(qname, stats->qend, k);
+            //fprintf(stderr, "remove overlap %d to %d\n", (int)start, (int)mstart);
+        } else {
+            if (!(kh_key(stats->qend, k) = strdup(bam_get_qname(b))))
+                return -1;
+
+            kh_value(stats->qend, k) = start | (end << 32);
+        }
+    }
+    for (i = mstart; i < end && i < len; i++)
+        stats->depth_all[i]++;
+    if (i < end) {
+        print_error("ampliconstats", "record %s overhangs end of reference",
+                    bam_get_qname(b));
+        // But keep going, as it's harmless.
+    }
+
+    // On single ended runs, eg ONT or PacBio, we just use the start/end
+    // of the template to assign.
+    int anum = (b->core.flag & BAM_FREVERSE) || !(b->core.flag & BAM_FPAIRED)
+        ? (end-1 >= 0 && end-1 < len ? pos2end[end-1] : -1)
+        : (start >= 0 && start < len ? pos2start[start] : -1);
+
+    // ivar sometimes soft-clips 100% of the bases.
+    // This is essentially unmapped
+    if (end == start && (args->flag_filter & BAM_FUNMAP)) {
+        stats->nfiltered++;
+        return 0;
+    }
+
+    if (anum == -1)
+        stats->nfailprimer++;
+
+    if (anum >= 0) {
+        int64_t c = MIN(end,amp[anum].min_right+1) - MAX(start,amp[anum].max_left);
+        if (c > 0) {
+            stats->nreads[anum]++;
+            // NB: ref bases rather than read bases
+            stats->nbases[anum] += c;
+
+            int64_t i;
+            if (start < 0) start = 0;
+            if (end > len) end = len;
+
+            int64_t ostart = MAX(start, amp[anum].min_left-1);
+            int64_t oend = MIN(end, amp[anum].max_right);
+            int64_t offset = amp[anum].min_left-1;
+            for (i = ostart; i < oend; i++)
+                stats->coverage[anum*stats->max_amp_len + i-offset]++;
+        } else {
+            stats->nfailprimer++;
+        }
+    }
+
+    // Template length in terms of amplicon number to amplicon number.
+    // We expect left to right of same amplicon (len 0), but it may go
+    // to next amplicon (len 1) or prev (len -1), etc.
+    int64_t t_end;
+    int oth_anum = -1;
+
+    if (b->core.flag & BAM_FPAIRED) {
+        t_end = (b->core.flag & BAM_FREVERSE ? end : start)
+            + b->core.isize;
+
+        // If we've clipped the primers but not followed up with a fixmates
+        // then our start+TLEN will take us to a location which is
+        // length(LEFT_PRIMER) + length(RIGHT_PRIMER) too far away.
+        //
+        // The correct solution is to run samtools fixmate so TLEN is correct.
+        // The hacky solution is to fudge the expected tlen by double the
+        // average primer length (e.g. 50).
+        t_end += b->core.isize > 0 ? -args->tlen_adj : +args->tlen_adj;
+
+        if (t_end > 0 && t_end < len && b->core.isize != 0)
+            oth_anum = (b->core.flag & BAM_FREVERSE)
+                ? pos2start[t_end]
+                : pos2end[t_end];
+    } else {
+        // Not paired (see int anum = (REV || !PAIR) ?en :st expr above)
+        oth_anum = pos2start[start];
+        t_end = end;
+    }
+
+    // We don't want to count our pairs twice.
+    // If both left/right are known, count it on left only.
+    // If only one is known, we'll only get to this code once
+    // so we can also count it.
+    int astatus = 2;
+    if (anum != -1 && oth_anum != -1) {
+        astatus = oth_anum == anum ? 0 : 1;
+        if (start <= t_end)
+            stats->amp_dist[anum][astatus]++;
+    } else if (anum >= 0) {
+        stats->amp_dist[anum][astatus = 2]++;
+    }
+
+    if (astatus == 0 && !(b->core.flag & (BAM_FUNMAP | BAM_FMUNMAP))) {
+        if (prev_end && mstart > prev_end) {
+            // 2nd read with gap to 1st; undo previous increment.
+            for (i = prev_start; i < prev_end; i++)
+                stats->depth_valid[i]--;
+            stats->nfull_reads[anum] -= (b->core.flag & BAM_FPAIRED) ? 0.5 : 1;
+        } else {
+            // 1st read, or 2nd read that overlaps 1st
+            for (i = mstart; i < end; i++)
+                stats->depth_valid[i]++;
+            stats->nfull_reads[anum] += (b->core.flag & BAM_FPAIRED) ? 0.5 : 1;
+        }
+    }
+
+    // Track template start,end frequencies, so we can give stats on
+    // amplicon primer usage.
+    if ((b->core.flag & BAM_FPAIRED) && b->core.isize <= 0)
+        // left to right only, so we don't double count template positions.
+        return 0;
+
+    start = b->core.pos;
+    t_end = b->core.flag & BAM_FPAIRED
+        ? start + b->core.isize-1
+        : end;
+    uint64_t tcoord = MIN(start+1, UINT32_MAX) | (MIN(t_end+1, UINT32_MAX)<<32);
+    k = kh_put(tcoord, stats->tcoord[anum+1], tcoord, &ret);
+    if (ret < 0)
+        return -1;
+    if (ret == 0)
+        kh_value(stats->tcoord[anum+1], k)++;
+    else
+        kh_value(stats->tcoord[anum+1], k)=1;
+    kh_value(stats->tcoord[anum+1], k) |= ((int64_t)astatus<<32);
+
+    return 0;
+}
+
+// Append file local stats to global stats
+int append_lstats(astats_t *lstats, astats_t *gstats, int namp, int all_nseq) {
+    gstats->nseq += lstats->nseq;
+    gstats->nfiltered += lstats->nfiltered;
+    gstats->nfailprimer += lstats->nfailprimer;
+
+    int a;
+    for (a = -1; a < namp; a++) {
+        // Add khash local (kl) to khash global (kg)
+        khiter_t kl, kg;
+        for (kl = kh_begin(lstats->tcoord[a+1]);
+             kl != kh_end(lstats->tcoord[a+1]); kl++) {
+            if (!kh_exist(lstats->tcoord[a+1], kl) ||
+                kh_value(lstats->tcoord[a+1], kl) == 0)
+                continue;
+
+            int ret;
+            kg = kh_put(tcoord, gstats->tcoord[a+1],
+                        kh_key(lstats->tcoord[a+1], kl),
+                        &ret);
+            if (ret < 0)
+                return -1;
+
+            kh_value(gstats->tcoord[a+1], kg) =
+                (ret == 0
+                 ? (kh_value(gstats->tcoord[a+1], kg) & 0xFFFFFFFF)
+                 : 0)
+                + kh_value(lstats->tcoord[a+1], kl);
+        }
+        if (a == -1) continue;
+
+        gstats->nreads[a]  += lstats->nreads[a];
+        gstats->nreads2[a] += lstats->nreads[a] * lstats->nreads[a];
+        gstats->nfull_reads[a] += lstats->nfull_reads[a];
+
+        // To get mean & sd for amplicon read percentage, we need
+        // to do the divisions here as nseq differs for each sample.
+        double nrperc = all_nseq ? 100.0 * lstats->nreads[a] / all_nseq : 0;
+        gstats->nrperc[a]  += nrperc;
+        gstats->nrperc2[a] += nrperc*nrperc;
+
+        gstats->nbases[a]  += lstats->nbases[a];
+        gstats->nbases2[a] += lstats->nbases[a] * lstats->nbases[a];
+
+        int d;
+        for (d = 0; d < MAX_DEPTH; d++) {
+            gstats->covered_perc[a][d]  += lstats->covered_perc[a][d];
+            gstats->covered_perc2[a][d] += lstats->covered_perc[a][d]
+                                         * lstats->covered_perc[a][d];
+        }
+
+        for (d = 0; d < 3; d++)
+            gstats->amp_dist[a][d] += lstats->amp_dist[a][d];
+    }
+
+    for (a = 0; a < lstats->max_len; a++) {
+        gstats->depth_valid[a] += lstats->depth_valid[a];
+        gstats->depth_all[a]   += lstats->depth_all[a];
+    }
+
+    return 0;
+}
+
+int append_stats(amplicons_t *amps, int nref) {
+    int i, r, all_nseq = 0;
+    for (r = 0; r < nref; r++) {
+        if (!amps[r].sites)
+            continue;
+        astats_t *stats = amps[r].lstats;
+        all_nseq  += stats->nseq - stats->nfiltered - stats->nfailprimer;
+    }
+
+    for (i = 0; i < nref; i++) {
+        if (!amps[i].sites)
+            continue;
+        if (append_lstats(amps[i].lstats, amps[i].gstats, amps[i].namp,
+                          all_nseq) < 0)
+            return -1;
+    }
+
+    return 0;
+}
+
+typedef struct {
+    int32_t start, end;
+    uint32_t freq;
+    uint32_t status;
+} tcoord_t;
+
+// Sort tcoord by descending frequency and then ascending start and  end.
+static int tcoord_freq_sort(const void *vp1, const void *vp2) {
+    const tcoord_t *t1 = (const tcoord_t *)vp1;
+    const tcoord_t *t2 = (const tcoord_t *)vp2;
+
+    if (t1->freq != t2->freq)
+        return t2->freq - t1->freq;
+
+    if (t1->start != t2->start)
+        return t1->start - t2->start;
+
+    return t1->end - t2->end;
+}
+
+
+/*
+ * Merges tcoord start,end,freq,status tuples if their coordinates are
+ * close together.  We aim to keep the start,end for the most frequent
+ * value and assume that is the correct coordinate and all others are
+ * minor fluctuations due to errors or variants.
+ *
+ * We sort by frequency first and then merge later items in the list into
+ * the earlier more frequent ones.  It's O(N^2), but sufficient for now
+ * given current scale of projects.
+ *
+ * If we ever need to resolve that then consider sorting by start
+ * coordinate and scanning the list to find all items within X, find
+ * the most frequent of those, and then cluster that way.  (I'd have
+ * done that had I thought of it at the time!)
+ */
+static void aggregate_tcoord(astats_args_t *args, tcoord_t *tpos, size_t *np){
+    size_t n = *np, j, j2, j3, k;
+
+    // Sort by frequency and cluster infrequent coords into frequent
+    // ones provided they're close by.
+    // This is O(N^2), but we've already binned by tcoord_bin/2 so
+    // the list isn't intended to be vast at this point.
+    qsort(tpos, n, sizeof(*tpos), tcoord_freq_sort);
+
+    // For frequency ties, find mid start coord, and then find mid end
+    // coord of those matching start.
+    // We make that the first item so we merge into that mid point.
+    for (j = 0; j < n; j++) {
+        for (j2 = j+1; j2 < n; j2++) {
+            if (tpos[j].freq != tpos[j2].freq)
+                break;
+            if (tpos[j2].start - tpos[j].start >= args->tcoord_bin)
+                break;
+        }
+
+        // j to j2 all within bin of a common start,
+        // m is the mid start.
+        if (j2-1 > j) {
+            size_t m = (j2-1 + j)/2;
+
+            // Find mid end for this same start
+            while (m > 1 && tpos[m].start == tpos[m-1].start)
+                m--;
+            for (j3 = m+1; j3 < j2; j3++) {
+                if (tpos[m].start != tpos[j3].start)
+                    break;
+                if (tpos[m].end - tpos[j3].end >= args->tcoord_bin)
+                    break;
+            }
+            if (j3-1 > m)
+                m = (j3-1 + m)/2;
+
+            // Swap with first item.
+            tcoord_t tmp = tpos[j];
+            tpos[j] = tpos[m];
+            tpos[m] = tmp;
+            j = j2-1;
+        }
+    }
+
+    // Now merge in coordinates.
+    // This bit is O(N^2), so consider binning first to reduce the
+    // size of the list if we have excessive positional variation.
+    for (k = j = 0; j < n; j++) {
+        if (!tpos[j].freq)
+            continue;
+
+        if (k < j)
+            tpos[k] = tpos[j];
+
+        for (j2 = j+1; j2 < n; j2++) {
+            if (ABS(tpos[j].start-tpos[j2].start) < args->tcoord_bin/2 &&
+                ABS(tpos[j].end  -tpos[j2].end)  < args->tcoord_bin/2 &&
+                tpos[j].status == tpos[j2].status) {
+                tpos[k].freq += tpos[j2].freq;
+                tpos[j2].freq = 0;
+            }
+        }
+        k++;
+    }
+
+    *np = k;
+}
+
+int dump_stats(astats_args_t *args, char type, char *name, int nfile,
+               amplicons_t *amps, int nref, int local) {
+    int i, r;
+    FILE *ofp = args->out_fp;
+    tcoord_t *tpos = NULL;
+    size_t ntcoord = 0;
+
+    // summary stats for this sample (or for all samples)
+    fprintf(ofp, "# Summary stats.\n");
+    fprintf(ofp, "# Use 'grep ^%cSS | cut -f 2-' to extract this part.\n", type);
+
+    for (r = 0; r < nref; r++) {
+        if (!amps[r].sites)
+            continue;
+        astats_t *stats = local ? amps[r].lstats : amps[r].gstats;
+        int nmatch = stats->nseq - stats->nfiltered - stats->nfailprimer;
+        char *name_ref = malloc(strlen(name) + strlen(amps[r].ref) + 2);
+        if (!name_ref)
+            return -1;
+        if (args->multi_ref)
+            sprintf(name_ref, "%s\t%s", name, amps[r].ref);
+        else
+            sprintf(name_ref, "%s", name);
+        fprintf(ofp, "%cSS\t%s\traw total sequences:\t%d\n",
+                type, name_ref, stats->nseq);
+        fprintf(ofp, "%cSS\t%s\tfiltered sequences:\t%d\n",
+                type, name_ref, stats->nfiltered);
+        fprintf(ofp, "%cSS\t%s\tfailed primer match:\t%d\n",
+                type, name_ref, stats->nfailprimer);
+        fprintf(ofp, "%cSS\t%s\tmatching sequences:\t%d\n",
+                type, name_ref, nmatch);
+
+        int d = 0;
+        do {
+            // From first to last amplicon only, so not entire consensus.
+            // If contig length is known, maybe we want to add the missing
+            // count to < DEPTH figures?
+            int64_t start = 0, covered = 0, total = 0;
+            amplicon_t *amp = amps[r].amp;
+            for (i = 0; i < amps[r].namp; i++) {
+                int64_t j, offset = amp[i].min_left-1;
+                if (amp[i].min_right - amp[i].min_left > stats->max_amp_len) {
+                    fprintf(stderr, "[ampliconstats] error: "
+                            "Maximum amplicon length (%d) exceeded for '%s'\n",
+                            stats->max_amp, name);
+                    return -1;
+                }
+                for (j = MAX(start, amp[i].max_left-1);
+                     j < MAX(start, amp[i].min_right); j++) {
+                    if (stats->coverage[i*stats->max_amp_len + j-offset]
+                        >= args->min_depth[d])
+                        covered++;
+                    total++;
+                }
+                start = MAX(start, amp[i].min_right);
+            }
+            fprintf(ofp, "%cSS\t%s\tconsensus depth count < %d and >= %d:\t%"
+                    PRId64"\t%"PRId64"\n", type, name_ref,
+                    args->min_depth[d], args->min_depth[d],
+                    total-covered, covered);
+        } while (++d < MAX_DEPTH && args->min_depth[d]);
+
+        free(name_ref);
+    }
+
+    // Read count
+    fprintf(ofp, "# Absolute matching read counts per amplicon.\n");
+    fprintf(ofp, "# Use 'grep ^%cREADS | cut -f 2-' to extract this part.\n", type);
+    fprintf(ofp, "%cREADS\t%s", type, name);
+    for (r = 0; r < nref; r++) {
+        if (!amps[r].sites)
+            continue;
+        astats_t *stats = local ? amps[r].lstats : amps[r].gstats;
+        for (i = 0; i < amps[r].namp; i++) {
+            fprintf(ofp, "\t%"PRId64, stats->nreads[i]);
+        }
+    }
+    fprintf(ofp, "\n");
+
+    // Valid depth is the number of full length reads (already divided
+    // by the number we expect to cover), so +0.5 per read in pair.
+    // A.k.a "usable depth" in the plots.
+    fprintf(ofp, "%cVDEPTH\t%s", type, name);
+    for (r = 0; r < nref; r++) {
+        if (!amps[r].sites)
+            continue;
+        astats_t *stats = local ? amps[r].lstats : amps[r].gstats;
+        for (i = 0; i < amps[r].namp; i++)
+            fprintf(ofp, "\t%d", (int)stats->nfull_reads[i]);
+    }
+    fprintf(ofp, "\n");
+
+    if (type == 'C') {
+        // For combined we can compute mean & standard deviation too
+        fprintf(ofp, "CREADS\tMEAN");
+        for (r = 0; r < nref; r++) {
+            if (!amps[r].sites)
+                continue;
+            astats_t *stats = local ? amps[r].lstats : amps[r].gstats;
+            for (i = 0; i < amps[r].namp; i++) {
+                fprintf(ofp, "\t%.1f", stats->nreads[i] / (double)nfile);
+            }
+        }
+        fprintf(ofp, "\n");
+
+        fprintf(ofp, "CREADS\tSTDDEV");
+        for (r = 0; r < nref; r++) {
+            if (!amps[r].sites)
+                continue;
+            astats_t *stats = local ? amps[r].lstats : amps[r].gstats;
+            for (i = 0; i < amps[r].namp; i++) {
+                double n1 = stats->nreads[i];
+                fprintf(ofp, "\t%.1f", nfile > 1 && stats->nreads2[i] > 0
+                        ? sqrt(stats->nreads2[i]/(double)nfile
+                               - (n1/nfile)*(n1/nfile))
+                        : 0);
+            }
+        }
+        fprintf(ofp, "\n");
+    }
+
+    fprintf(ofp, "# Read percentage of distribution between amplicons.\n");
+    fprintf(ofp, "# Use 'grep ^%cRPERC | cut -f 2-' to extract this part.\n", type);
+    fprintf(ofp, "%cRPERC\t%s", type, name);
+    int all_nseq = 0;
+    for (r = 0; r < nref; r++) {
+        if (!amps[r].sites)
+            continue;
+        astats_t *stats = local ? amps[r].lstats : amps[r].gstats;
+        all_nseq  += stats->nseq - stats->nfiltered - stats->nfailprimer;
+    }
+    for (r = 0; r < nref; r++) {
+        if (!amps[r].sites)
+            continue;
+        astats_t *stats = local ? amps[r].lstats : amps[r].gstats;
+        for (i = 0; i < amps[r].namp; i++) {
+            if (type == 'C') {
+                fprintf(ofp, "\t%.3f", (double)stats->nrperc[i] / nfile);
+            } else {
+                fprintf(ofp, "\t%.3f",
+                        all_nseq ? 100.0 * stats->nreads[i] / all_nseq : 0);
+            }
+        }
+    }
+    fprintf(ofp, "\n");
+
+    if (type == 'C') {
+        // For combined we compute mean and standard deviation too
+        fprintf(ofp, "CRPERC\tMEAN");
+        for (r = 0; r < nref; r++) {
+            if (!amps[r].sites)
+                continue;
+            astats_t *stats = local ? amps[r].lstats : amps[r].gstats;
+            for (i = 0; i < amps[r].namp; i++) {
+                fprintf(ofp, "\t%.3f", stats->nrperc[i] / nfile);
+            }
+        }
+        fprintf(ofp, "\n");
+
+        fprintf(ofp, "CRPERC\tSTDDEV");
+        for (r = 0; r < nref; r++) {
+            if (!amps[r].sites)
+                continue;
+            astats_t *stats = local ? amps[r].lstats : amps[r].gstats;
+            for (i = 0; i < amps[r].namp; i++) {
+                // variance = SUM(X^2) - ((SUM(X)^2) / N)
+                double n1 = stats->nrperc[i];
+                double v = stats->nrperc2[i]/nfile - (n1/nfile)*(n1/nfile);
+                fprintf(ofp, "\t%.3f", v>0?sqrt(v):0);
+            }
+        }
+        fprintf(ofp, "\n");
+    }
+
+    // Base depth
+    fprintf(ofp, "# Read depth per amplicon.\n");
+    fprintf(ofp, "# Use 'grep ^%cDEPTH | cut -f 2-' to extract this part.\n", type);
+    fprintf(ofp, "%cDEPTH\t%s", type, name);
+    for (r = 0; r < nref; r++) {
+        if (!amps[r].sites)
+            continue;
+        astats_t *stats = local ? amps[r].lstats : amps[r].gstats;
+        amplicon_t *amp = amps[r].amp;
+        for (i = 0; i < amps[r].namp; i++) {
+            int nseq = stats->nseq - stats->nfiltered - stats->nfailprimer;
+            int64_t alen = amp[i].min_right - amp[i].max_left+1;
+            fprintf(ofp, "\t%.1f", nseq ? stats->nbases[i] / (double)alen : 0);
+        }
+    }
+    fprintf(ofp, "\n");
+
+    if (type == 'C') {
+        // For combined we can compute mean & standard deviation too
+        fprintf(ofp, "CDEPTH\tMEAN");
+        for (r = 0; r < nref; r++) {
+            if (!amps[r].sites)
+                continue;
+            astats_t *stats = local ? amps[r].lstats : amps[r].gstats;
+            amplicon_t *amp = amps[r].amp;
+            int nseq = stats->nseq - stats->nfiltered - stats->nfailprimer;
+            for (i = 0; i < amps[r].namp; i++) {
+                int64_t alen = amp[i].min_right - amp[i].max_left+1;
+                fprintf(ofp, "\t%.1f", nseq ? stats->nbases[i] / (double)alen / nfile : 0);
+            }
+        }
+        fprintf(ofp, "\n");
+
+        fprintf(ofp, "CDEPTH\tSTDDEV");
+        for (r = 0; r < nref; r++) {
+            if (!amps[r].sites)
+                continue;
+            astats_t *stats = local ? amps[r].lstats : amps[r].gstats;
+            amplicon_t *amp = amps[r].amp;
+            for (i = 0; i < amps[r].namp; i++) {
+                double alen = amp[i].min_right - amp[i].max_left+1;
+                double n1 = stats->nbases[i] / alen;
+                double v = stats->nbases2[i] / (alen*alen) /nfile
+                    - (n1/nfile)*(n1/nfile);
+                fprintf(ofp, "\t%.1f", v>0?sqrt(v):0);
+            }
+        }
+        fprintf(ofp, "\n");
+    }
+
+    // Percent Coverage
+    if (type == 'F') {
+        fprintf(ofp, "# Percentage coverage per amplicon\n");
+        fprintf(ofp, "# Use 'grep ^%cPCOV | cut -f 2-' to extract this part.\n", type);
+        int d = 0;
+        do {
+            fprintf(ofp, "%cPCOV-%d\t%s", type, args->min_depth[d], name);
+
+            for (r = 0; r < nref; r++) {
+                if (!amps[r].sites)
+                    continue;
+                astats_t *stats = local ? amps[r].lstats : amps[r].gstats;
+                amplicon_t *amp = amps[r].amp;
+                for (i = 0; i < amps[r].namp; i++) {
+                    int covered = 0;
+                    if (amp[i].min_right - amp[i].min_left > stats->max_amp_len) {
+                        fprintf(stderr, "[ampliconstats] error: "
+                                "Maximum amplicon length (%d) exceeded for '%s'\n",
+                                stats->max_amp, name);
+                        return -1;
+                    }
+                    int64_t j, offset = amp[i].min_left-1;
+                    for (j = amp[i].max_left-1; j < amp[i].min_right; j++) {
+                        int apos = i*stats->max_amp_len + j-offset;
+                        if (stats->coverage[apos] >= args->min_depth[d])
+                            covered++;
+                    }
+                    int64_t alen = amp[i].min_right - amp[i].max_left+1;
+                    stats->covered_perc[i][d] = 100.0 * covered / alen;
+                    fprintf(ofp, "\t%.2f", 100.0 * covered / alen);
+                }
+            }
+            fprintf(ofp, "\n");
+        } while (++d < MAX_DEPTH && args->min_depth[d]);
+
+    } else if (type == 'C') {
+        // For combined we can compute mean & standard deviation too
+        int d = 0;
+        do {
+            fprintf(ofp, "CPCOV-%d\tMEAN", args->min_depth[d]);
+            for (r = 0; r < nref; r++) {
+                if (!amps[r].sites)
+                    continue;
+                astats_t *stats = local ? amps[r].lstats : amps[r].gstats;
+                for (i = 0; i < amps[r].namp; i++) {
+                    fprintf(ofp, "\t%.1f", stats->covered_perc[i][d] / nfile);
+                }
+            }
+            fprintf(ofp, "\n");
+
+            fprintf(ofp, "CPCOV-%d\tSTDDEV", args->min_depth[d]);
+            for (r = 0; r < nref; r++) {
+                if (!amps[r].sites)
+                    continue;
+                astats_t *stats = local ? amps[r].lstats : amps[r].gstats;
+                for (i = 0; i < amps[r].namp; i++) {
+                    double n1 = stats->covered_perc[i][d] / nfile;
+                    double v = stats->covered_perc2[i][d] / nfile - n1*n1;
+                    fprintf(ofp, "\t%.1f", v>0?sqrt(v):0);
+                }
+            }
+            fprintf(ofp, "\n");
+        } while (++d < MAX_DEPTH && args->min_depth[d]);
+    }
+
+    // Plus base depth for all reads, irrespective of amplicon.
+    // This is post overlap removal, if reads in the read-pair overlap.
+    fprintf(ofp, "# Depth per reference base for ALL data.\n");
+    fprintf(ofp, "# Use 'grep ^%cDP_ALL | cut -f 2-' to extract this part.\n",
+            type);
+    for (r = 0; r < nref; r++) {
+        if (!amps[r].sites)
+            continue;
+        astats_t *stats = local ? amps[r].lstats : amps[r].gstats;
+        if (args->multi_ref)
+            fprintf(ofp, "%cDP_ALL\t%s\t%s", type, name, amps[r].ref);
+        else
+            fprintf(ofp, "%cDP_ALL\t%s", type, name);
+
+        for (i = 0; i < amps[r].len; i++) {
+            // Basic run-length encoding provided all values are within
+            // +- depth_bin fraction of the mid-point.
+            int dmin = stats->depth_all[i], dmax = stats->depth_all[i], j;
+            double dmid = (dmin + dmax)/2.0;
+            double low  = dmid*(1-args->depth_bin);
+            double high = dmid*(1+args->depth_bin);
+            for (j = i+1; j < amps[r].len; j++) {
+                int d = stats->depth_all[j];
+                if (d < low || d > high)
+                    break;
+                if (dmin > d) {
+                    dmin = d;
+                    dmid = (dmin + dmax)/2.0;
+                    low  = dmid*(1-args->depth_bin);
+                    high = dmid*(1+args->depth_bin);
+                } else if (dmax < d) {
+                    dmax = d;
+                    dmid = (dmin + dmax)/2.0;
+                    low  = dmid*(1-args->depth_bin);
+                    high = dmid*(1+args->depth_bin);
+                }
+            }
+            fprintf(ofp, "\t%d,%d", (int)dmid, j-i);
+            i = j-1;
+        }
+        fprintf(ofp, "\n");
+    }
+
+    // And depth for only reads matching to a single amplicon for full
+    // length.  This is post read overlap removal.
+    fprintf(ofp, "# Depth per reference base for full-length valid amplicon data.\n");
+    fprintf(ofp, "# Use 'grep ^%cDP_VALID | cut -f 2-' to extract this "
+            "part.\n", type);
+    for (r = 0; r < nref; r++) {
+        if (!amps[r].sites)
+            continue;
+        astats_t *stats = local ? amps[r].lstats : amps[r].gstats;
+        if (args->multi_ref)
+            fprintf(ofp, "%cDP_VALID\t%s\t%s", type, name, amps[r].ref);
+        else
+            fprintf(ofp, "%cDP_VALID\t%s", type, name);
+
+        for (i = 0; i < amps[r].len; i++) {
+            int dmin = stats->depth_valid[i], dmax = stats->depth_valid[i], j;
+            double dmid = (dmin + dmax)/2.0;
+            double low  = dmid*(1-args->depth_bin);
+            double high = dmid*(1+args->depth_bin);
+            for (j = i+1; j < amps[r].len; j++) {
+                int d = stats->depth_valid[j];
+                if (d < low || d > high)
+                    break;
+                if (dmin > d) {
+                    dmin = d;
+                    dmid = (dmin + dmax)/2.0;
+                    low  = dmid*(1-args->depth_bin);
+                    high = dmid*(1+args->depth_bin);
+                } else if (dmax < d) {
+                    dmax = d;
+                    dmid = (dmin + dmax)/2.0;
+                    low  = dmid*(1-args->depth_bin);
+                    high = dmid*(1+args->depth_bin);
+                }
+            }
+            fprintf(ofp, "\t%d,%d", (int)dmid, j-i);
+            i = j-1;
+        }
+        fprintf(ofp, "\n");
+    }
+
+    // TCOORD (start to end) distribution
+    fprintf(ofp, "# Distribution of aligned template coordinates.\n");
+    fprintf(ofp, "# Use 'grep ^%cTCOORD | cut -f 2-' to extract this part.\n", type);
+    for (r = 0; r < nref; r++) {
+        if (!amps[r].sites)
+            continue;
+        astats_t *stats = local ? amps[r].lstats : amps[r].gstats;
+        for (i = 0 - (nref==1); i < amps[r].namp; i++) {
+            if (ntcoord < kh_size(stats->tcoord[i+1])) {
+                ntcoord = kh_size(stats->tcoord[i+1]);
+                tcoord_t *tmp = realloc(tpos, ntcoord * sizeof(*tmp));
+                if (!tmp) {
+                    free(tpos);
+                    return -1;
+                }
+                tpos = tmp;
+            }
+
+            khiter_t k;
+            size_t n = 0, j;
+            for (k = kh_begin(stats->tcoord[i+1]);
+                 k != kh_end(stats->tcoord[i+1]); k++) {
+                if (!kh_exist(stats->tcoord[i+1], k) ||
+                    (kh_value(stats->tcoord[i+1], k) & 0xFFFFFFFF) == 0)
+                    continue;
+                // Key is start,end in 32-bit quantities.
+                // Yes this limits us to 4Gb references, but just how
+                // many primers are we planning on making?  Not that many
+                // I hope.
+                tpos[n].start = kh_key(stats->tcoord[i+1], k)&0xffffffff;
+                tpos[n].end   = kh_key(stats->tcoord[i+1], k)>>32;
+
+                // Value is frequency (top 32-bits) and status (bottom 32).
+                tpos[n].freq   = kh_value(stats->tcoord[i+1], k)&0xffffffff;
+                tpos[n].status = kh_value(stats->tcoord[i+1], k)>>32;
+                n++;
+            }
+
+            if (args->tcoord_bin > 1)
+                aggregate_tcoord(args, tpos, &n);
+
+            fprintf(ofp, "%cTCOORD\t%s\t%d", type, name,
+                    i+1+amps[r].first_amp); // per amplicon
+            for (j = 0; j < n; j++) {
+                if (tpos[j].freq < args->tcoord_min_count)
+                    continue;
+                fprintf(ofp, "\t%d,%d,%u,%u",
+                        tpos[j].start,
+                        tpos[j].end,
+                        tpos[j].freq,
+                        tpos[j].status);
+            }
+            fprintf(ofp, "\n");
+        }
+    }
+
+
+    // AMP length distribution.
+    // 0 = both ends in this amplicon
+    // 1 = ends in different amplicons
+    // 2 = other end matching an unknown amplicon site
+    //     (see tcoord for further analysis of where)
+    fprintf(ofp, "# Classification of amplicon status.  Columns are\n");
+    fprintf(ofp, "# number with both primers from this amplicon, number with\n");
+    fprintf(ofp, "# primers from different amplicon, and number with a position\n");
+    fprintf(ofp, "# not matching any valid amplicon primer site\n");
+    fprintf(ofp, "# Use 'grep ^%cAMP | cut -f 2-' to extract this part.\n", type);
+
+    fprintf(ofp, "%cAMP\t%s\t0", type, name); // all merged
+    int amp_dist[3] = {0};
+    for (r = 0; r < nref; r++) {
+        if (!amps[r].sites)
+            continue;
+        astats_t *stats = local ? amps[r].lstats : amps[r].gstats;
+        for (i = 0; i < amps[r].namp; i++) { // accumulate for all amps
+            amp_dist[0] += stats->amp_dist[i][0];
+            amp_dist[1] += stats->amp_dist[i][1];
+            amp_dist[2] += stats->amp_dist[i][2];
+        }
+    }
+    fprintf(ofp, "\t%d\t%d\t%d\n", amp_dist[0], amp_dist[1], amp_dist[2]);
+
+    for (r = 0; r < nref; r++) {
+        if (!amps[r].sites)
+            continue;
+        astats_t *stats = local ? amps[r].lstats : amps[r].gstats;
+        for (i = 0; i < amps[r].namp; i++) {
+            // per amplicon
+            fprintf(ofp, "%cAMP\t%s\t%d", type, name, i+1+amps[r].first_amp);
+            fprintf(ofp, "\t%d\t%d\t%d\n", stats->amp_dist[i][0],
+                    stats->amp_dist[i][1], stats->amp_dist[i][2]);
+        }
+    }
+
+    free(tpos);
+    return 0;
+}
+
+int dump_lstats(astats_args_t *args, char type, char *name, int nfile,
+               amplicons_t *amps, int nref) {
+    return dump_stats(args, type, name, nfile, amps, nref, 1);
+}
+
+int dump_gstats(astats_args_t *args, char type, char *name, int nfile,
+               amplicons_t *amps, int nref) {
+    return dump_stats(args, type, name, nfile, amps, nref, 0);
+}
+
+char const *get_sample_name(sam_hdr_t *header, char *RG) {
+    kstring_t ks = {0};
+    sam_hdr_find_tag_id(header, "RG", RG?"ID":NULL, RG, "SM", &ks);
+    return ks.s;
+}
+
+// Return maximum reference length (SQ is NULL) or the length
+// of the specified reference in SQ.
+int64_t get_ref_len(sam_hdr_t *header, const char *SQ) {
+    if (SQ) {
+        int tid = SQ ? sam_hdr_name2tid(header, SQ) : 0;
+        return tid >= 0 ? sam_hdr_tid2len(header, tid) : -1;
+    } else {
+        int nref = sam_hdr_nref(header), tid;;
+        int64_t len = 0;
+        for (tid = 0; tid < nref; tid++) {
+            int64_t rl = sam_hdr_tid2len(header, tid);
+            if (len < rl)
+                len = rl;
+        }
+        return len;
+    }
+}
+
+static int amplicon_stats(astats_args_t *args,
+                          khash_t(bed_list_hash) *bed_hash,
+                          char **filev, int filec) {
+    int i, ref = -1, ref_tid = -1, ret = -1, nref = 0;
+    samFile *fp = NULL;
+    sam_hdr_t *header = NULL;
+    bam1_t *b = bam_init1();
+    FILE *ofp = args->out_fp;
+    char sname_[8192], *sname = NULL;
+    amplicons_t *amps = NULL;
+
+    // Report initial SS header.  We gather data from the bed_hash entries
+    // as well as from the first SAM header (with the requirement that all
+    // headers should be compatible).
+    if (filec) {
+        if (!(fp = sam_open_format(filev[0], "r", &args->ga.in))) {
+            print_error_errno("ampliconstats",
+                              "Cannot open input file \"%s\"",
+                              filev[0]);
+            goto err;
+        }
+        if (!(header = sam_hdr_read(fp)))
+            goto err;
+
+        if (!amps) {
+            amps = calloc(nref=sam_hdr_nref(header), sizeof(*amps));
+            if (!amps)
+                goto err;
+            fprintf(ofp, "# Summary statistics, used for scaling the plots.\n");
+            fprintf(ofp, "SS\tSamtools version: %s\n", samtools_version());
+            fprintf(ofp, "SS\tCommand line: %s\n", args->argv);
+            fprintf(ofp, "SS\tNumber of files:\t%d\n", filec);
+
+            // Note: order of hash entries will be different to order of
+            // BED file which may also differ to order of SQ headers.
+            // SQ header is canonical ordering (pos sorted file).
+            khiter_t k;
+            int bam_nref = sam_hdr_nref(header);
+            for (i = 0; i < bam_nref; i++) {
+                k = kh_get(bed_list_hash, bed_hash,
+                           sam_hdr_tid2name(header, i));
+                if (!kh_exist(bed_hash, k))
+                    continue;
+
+                bed_entry_list_t *sites = &kh_value(bed_hash, k);
+
+                ref = i;
+                amps[ref].ref = kh_key(bed_hash, k);
+                amps[ref].sites = sites;
+                amps[ref].namp = count_amplicon(sites);
+                amps[ref].amp  = calloc(sites->length,
+                                        sizeof(*amps[ref].amp));
+                if (!amps[ref].amp)
+                    goto err;
+                if (args->multi_ref)
+                    fprintf(ofp, "SS\tNumber of amplicons:\t%s\t%d\n",
+                            kh_key(bed_hash, k), amps[ref].namp);
+                else
+                    fprintf(ofp, "SS\tNumber of amplicons:\t%d\n",
+                            amps[ref].namp);
+
+                amps[ref].tid = ref;
+                if (ref_tid == -1)
+                    ref_tid = ref;
+
+                int64_t len = get_ref_len(header, kh_key(bed_hash, k));
+                amps[ref].len = len;
+                if (args->multi_ref)
+                    fprintf(ofp, "SS\tReference length:\t%s\t%"PRId64"\n",
+                            kh_key(bed_hash, k), len);
+                else
+                    fprintf(ofp, "SS\tReference length:\t%"PRId64"\n",
+                            len);
+
+                amps[ref].lstats = stats_alloc(len, args->max_amp,
+                                               args->max_amp_len);
+                amps[ref].gstats = stats_alloc(len, args->max_amp,
+                                               args->max_amp_len);
+                if (!amps[ref].lstats || !amps[ref].gstats)
+                    goto err;
+            }
+        }
+
+        sam_hdr_destroy(header);
+        header = NULL;
+        if (sam_close(fp) < 0) {
+            fp = NULL;
+            goto err;
+        }
+        fp = NULL;
+    }
+    fprintf(ofp, "SS\tEnd of summary\n");
+
+    // Extract the bits of amplicon data we need from bed hash and turn
+    // it into a position-to-amplicon lookup table.
+    int offset = 0;
+    for (i = 0; i < nref; i++) {
+        if (!amps[i].sites)
+            continue;
+
+        amps[i].first_amp = offset;
+        if (bed2amplicon(args, amps[i].sites, amps[i].amp,
+                         &amps[i].namp, i==0, amps[i].ref, offset) < 0)
+            goto err;
+
+        offset += amps[i].namp; // cumulative amplicon number across refs
+    }
+
+    // Now iterate over file contents, one at a time.
+    for (i = 0; i < filec; i++) {
+        char *nstart = filev[i];
+
+        fp = sam_open_format(filev[i], "r", &args->ga.in);
+        if (!fp) {
+            print_error_errno("ampliconstats",
+                              "Cannot open input file \"%s\"",
+                              filev[i]);
+            goto err;
+        }
+
+        if (args->ga.nthreads > 0)
+            hts_set_threads(fp, args->ga.nthreads);
+
+        if (!(header = sam_hdr_read(fp)))
+            goto err;
+
+        if (nref != sam_hdr_nref(header)) {
+            print_error_errno("ampliconstats",
+                              "SAM headers are not consistent across input files");
+            goto err;
+        }
+        int r;
+        for (r = 0; r < nref; r++) {
+            if (!amps[r].ref ||
+                strcmp(amps[r].ref, sam_hdr_tid2name(header, r)) != 0 ||
+                amps[r].len != sam_hdr_tid2len(header, r)) {
+                print_error_errno("ampliconstats",
+                                  "SAM headers are not consistent across "
+                                  "input files");
+                goto err;
+            }
+        }
+
+        if (args->use_sample_name)
+            sname = (char *)get_sample_name(header, NULL);
+
+        if (!sname) {
+            sname = sname_;
+            char *nend = filev[i] + strlen(filev[i]), *cp;
+            if ((cp = strrchr(filev[i], '/')))
+                nstart = cp+1;
+            if ((cp = strrchr(nstart, '.')) &&
+                (strcmp(cp, ".bam") == 0 ||
+                 strcmp(cp, ".sam") == 0 ||
+                 strcmp(cp, ".cram") == 0))
+                nend = cp;
+            if (nend - nstart >= 8192) nend = nstart+8191;
+            memcpy(sname, nstart, nend-nstart);
+            sname[nend-nstart] = 0;
+        }
+
+        // Stats local to this sample only
+        amp_stats_reset(amps, nref);
+
+        int last_ref = -9;
+        while ((r = sam_read1(fp, header, b)) >= 0) {
+            // Other filter options useful here?
+            if (b->core.tid < 0)
+                continue;
+
+            if (last_ref != b->core.tid) {
+                last_ref  = b->core.tid;
+                if (initialise_amp_pos_lookup(args, amps, last_ref) < 0)
+                    goto err;
+            }
+
+            if (accumulate_stats(args, amps, b) < 0)
+                goto err;
+        }
+
+        if (r < -1) {
+            print_error_errno("ampliconstats", "Fail reading record");
+            goto err;
+        }
+
+        sam_hdr_destroy(header);
+        if (sam_close(fp) < 0) {
+            fp = NULL;
+            goto err;
+        }
+
+        fp = NULL;
+        header = NULL;
+
+        if (dump_lstats(args, 'F', sname, filec, amps, nref) < 0)
+            goto err;
+
+        if (append_stats(amps, nref) < 0)
+            goto err;
+
+        if (sname && sname != sname_)
+            free(sname);
+        sname = NULL;
+    }
+
+    if (dump_gstats(args, 'C', "COMBINED", filec, amps, nref) < 0)
+        goto err;
+
+    ret = 0;
+ err:
+    bam_destroy1(b);
+    if (ret) {
+        if (header)
+            sam_hdr_destroy(header);
+        if (fp)
+            sam_close(fp);
+    }
+    for (i = 0; i < nref; i++) {
+        stats_free(amps[i].lstats);
+        stats_free(amps[i].gstats);
+        free(amps[i].amp);
+    }
+    free(amps);
+    free(pos2start);
+    free(pos2end);
+    if (ret) {
+        if (sname && sname != sname_)
+            free(sname);
+    }
+
+    return ret;
+}
+
+static int usage(astats_args_t *args, FILE *fp, int exit_status) {
+    fprintf(fp,
+"\n"
+"Usage: samtools ampliconstats [options] primers.bed *.bam > astats.txt\n"
+"\n"
+"Options:\n");
+    fprintf(fp, "  -f, --required-flag STR|INT\n"
+            "               Only include reads with all of the FLAGs present [0x%X]\n",args->flag_require);
+    fprintf(fp, "  -F, --filter-flag STR|INT\n"
+            "               Only include reads with none of the FLAGs present [0x%X]\n",args->flag_filter & 0xffff);
+    fprintf(fp, "  -a, --max-amplicons INT\n"
+            "               Change the maximum number of amplicons permitted [%d]\n", MAX_AMP);
+    fprintf(fp, "  -l, --max-amplicon-length INT\n"
+            "               Change the maximum length of an individual amplicon [%d]\n", MAX_AMP_LEN);
+    fprintf(fp, "  -d, --min-depth INT[,INT]...\n"
+            "               Minimum base depth(s) to consider position covered [%d]\n", args->min_depth[0]);
+    fprintf(fp, "  -m, --pos-margin INT\n"
+            "               Margin of error for matching primer positions [%d]\n", args->max_delta);
+    fprintf(fp, "  -o, --output FILE\n"
+            "               Specify output file [stdout if unset]\n");
+    fprintf(fp, "  -s, --use-sample-name\n"
+            "               Use the sample name from the first @RG header line\n");
+    fprintf(fp, "  -t, --tlen-adjust INT\n"
+            "               Add/subtract from TLEN; use when clipping but no fixmate step\n");
+    fprintf(fp, "  -b, --tcoord-bin INT\n"
+            "               Bin template start,end positions into multiples of INT[1]\n");
+    fprintf(fp, "  -c, --tcoord-min-count INT\n"
+            "               Minimum template start,end frequency for recording [%d]\n", TCOORD_MIN_COUNT);
+    fprintf(fp, "  -D, --depth-bin FRACTION\n"
+            "               Merge FDP values within +/- FRACTION together\n");
+    fprintf(fp, "  -S, --single-ref\n"
+            "               Force single-ref (<=1.12) output format\n");
+    sam_global_opt_help(fp, "I.--.@");
+
+    return exit_status;
+}
+
+int main_ampliconstats(int argc, char **argv) {
+    astats_args_t args = {
+        .ga = SAM_GLOBAL_ARGS_INIT,
+        .flag_require = 0,
+        .flag_filter = 0x10B04,
+        //.sites = BED_LIST_INIT,
+        .max_delta = 30, // large enough to cope with alt primers
+        .min_depth = {1},
+        .use_sample_name = 0,
+        .max_amp = MAX_AMP,
+        .max_amp_len = MAX_AMP_LEN,
+        .tlen_adj = 0,
+        .out_fp = stdout,
+        .tcoord_min_count = TCOORD_MIN_COUNT,
+        .tcoord_bin = 1,
+        .depth_bin = 0.01,
+        .multi_ref = 1
+    }, oargs = args;
+
+    static const struct option loptions[] =
+    {
+        SAM_OPT_GLOBAL_OPTIONS('I', 0, '-', '-', 0, '@'),
+        {"help", no_argument, NULL, 'h'},
+        {"flag-require", required_argument, NULL, 'f'},
+        {"flag-filter", required_argument, NULL, 'F'},
+        {"min-depth", required_argument, NULL, 'd'},
+        {"output", required_argument, NULL, 'o'},
+        {"pos-margin", required_argument, NULL, 'm'},
+        {"use-sample-name", no_argument, NULL, 's'},
+        {"max-amplicons", required_argument, NULL, 'a'},
+        {"max-amplicon-length", required_argument, NULL, 'l'},
+        {"tlen-adjust", required_argument, NULL, 't'},
+        {"tcoord-min-count", required_argument, NULL, 'c'},
+        {"tcoord-bin", required_argument, NULL, 'b'},
+        {"depth-bin", required_argument, NULL, 'D'},
+        {"single-ref", no_argument, NULL, 'S'},
+        {NULL, 0, NULL, 0}
+    };
+    int opt;
+
+    while ( (opt=getopt_long(argc,argv,"?hf:F:@:p:m:d:sa:l:t:o:c:b:D:S",loptions,NULL))>0 ) {
+        switch (opt) {
+        case 'f': args.flag_require = bam_str2flag(optarg); break;
+        case 'F':
+            if (args.flag_filter & 0x10000)
+                args.flag_filter = 0; // strip default on first -F usage
+            args.flag_filter |= bam_str2flag(optarg); break;
+
+        case 'm': args.max_delta = atoi(optarg); break; // margin
+        case 'D': args.depth_bin = atof(optarg); break; // depth bin fraction
+        case 'd': {
+            int d = 0;
+            char *cp = optarg, *ep;
+            do {
+                long n = strtol(cp, &ep, 10);
+                args.min_depth[d++] = n;
+                if (*ep != ',')
+                    break;
+                cp = ep+1;
+            } while (d < MAX_DEPTH);
+            break;
+        }
+
+        case 'a': args.max_amp = atoi(optarg)+1;break;
+        case 'l': args.max_amp_len = atoi(optarg)+1;break;
+
+        case 'c': args.tcoord_min_count = atoi(optarg);break;
+        case 'b':
+            args.tcoord_bin = atoi(optarg);
+            if (args.tcoord_bin < 1)
+                args.tcoord_bin = 1;
+            break;
+
+        case 't': args.tlen_adj = atoi(optarg);break;
+
+        case 's': args.use_sample_name = 1;break;
+
+        case 'o':
+            if (!(args.out_fp = fopen(optarg, "w"))) {
+                perror(optarg);
+                return 1;
+            }
+            break;
+
+        case 'S':
+            args.multi_ref = 0;
+            break;
+
+        case '?': return usage(&oargs, stderr, EXIT_FAILURE);
+        case 'h': return usage(&oargs, stdout, EXIT_SUCCESS);
+
+        default:
+            if (parse_sam_global_opt(opt, optarg, loptions, &args.ga) != 0)
+                usage(&oargs,stderr, EXIT_FAILURE);
+            break;
+        }
+    }
+
+    if (argc <= optind)
+        return usage(&oargs, stdout, EXIT_SUCCESS);
+    if (argc <= optind+1 && isatty(STDIN_FILENO))
+        return usage(&oargs, stderr, EXIT_FAILURE);
+
+    khash_t(bed_list_hash) *bed_hash = kh_init(bed_list_hash);
+    if (load_bed_file_multi_ref(argv[optind], 1, 0, bed_hash)) {
+        print_error_errno("ampliconstats",
+                          "Could not read file \"%s\"", argv[optind]);
+        return 1;
+
+    }
+
+    khiter_t k, ref_count = 0;
+    for (k = kh_begin(bed_hash); k != kh_end(bed_hash); k++) {
+        if (!kh_exist(bed_hash, k))
+            continue;
+        ref_count++;
+    }
+    if (ref_count == 0)
+        return 1;
+    if (ref_count > 1 && args.multi_ref == 0) {
+        print_error("ampliconstats",
+                    "Single-ref mode is not permitted for BED files\n"
+                    "containing more than one reference.");
+        return 1;
+    }
+
+    args.argv = stringify_argv(argc, argv);
+    int ret;
+    if (argc == ++optind) {
+        char *av = "-";
+        ret = amplicon_stats(&args, bed_hash, &av, 1);
+    } else {
+        ret = amplicon_stats(&args, bed_hash, &argv[optind], argc-optind);
+    }
+
+    free(args.argv);
+    destroy_bed_hash(bed_hash);
+
+    return ret;
+}
diff --git a/samtools/amplicon_stats.c.pysam.c b/samtools/amplicon_stats.c.pysam.c
new file mode 100644
index 0000000..aa09459
--- /dev/null
+++ b/samtools/amplicon_stats.c.pysam.c
@@ -0,0 +1,1756 @@
+#include "samtools.pysam.h"
+
+/*  stats.c -- This is the former bamcheck integrated into samtools/htslib.
+
+    Copyright (C) 2020-2021 Genome Research Ltd.
+
+    Author: James Bonfield <jkb@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+/*
+ * This tool is designed to give "samtools stats" style output, but dedicated
+ * to small amplicon sequencing projects.  It gathers stats on the
+ * distribution of reads across amplicons.
+ */
+
+/*
+ * TODO:
+ * - Cope with multiple references.  What do we do here?  Just request one?
+ * - Permit regions rather than consuming whole file (maybe solves above).
+ */
+
+#include <config.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <inttypes.h>
+#include <getopt.h>
+#include <unistd.h>
+#include <math.h>
+
+#include <htslib/sam.h>
+#include <htslib/khash.h>
+
+#include "samtools.h"
+#include "sam_opts.h"
+#include "bam_ampliconclip.h"
+
+KHASH_MAP_INIT_INT64(tcoord, int64_t)
+KHASH_MAP_INIT_STR(qname, int64_t)
+
+#ifndef MIN
+#define MIN(a,b) ((a)<(b)?(a):(b))
+#endif
+
+#ifndef MAX
+#define MAX(a,b) ((a)>(b)?(a):(b))
+#endif
+
+#ifndef ABS
+#define ABS(a) ((a)>=0?(a):-(a))
+#endif
+
+#define TCOORD_MIN_COUNT   10
+#define MAX_AMP 1000       // Default maximum number of amplicons
+#define MAX_AMP_LEN 1000   // Default maximum length of any single amplicon
+#define MAX_PRIMER_PER_AMPLICON 4  // Max primers per LEFT/RIGHT
+#define MAX_DEPTH 5        // Number of different depths permitted
+
+typedef struct {
+    sam_global_args ga;
+    uint32_t flag_require;
+    uint32_t flag_filter;
+    int max_delta;   // Used for matching read to amplicon primer loc
+    int min_depth[MAX_DEPTH]; // Used for coverage; must be >= min_depth deep
+    int use_sample_name;
+    int max_amp;     // Total number of amplicons
+    int max_amp_len; // Maximum length of an individual amplicon
+    double depth_bin;// aggregate depth within this fraction
+    int tlen_adj;    // Adjust tlen by this amount, due to clip but no fixmate
+    FILE *out_fp;
+    char *argv;
+    int tcoord_min_count;
+    int tcoord_bin;
+    int multi_ref;
+} astats_args_t;
+
+typedef struct {
+    int nseq;       // total sequence count
+    int nfiltered;  // sequence filtered
+    int nfailprimer;// count of sequences not matching the primer locations
+
+    // Sizes of memory allocated below, to permit reset
+    int max_amp, max_amp_len, max_len;
+
+    // Summary across all samples, sum(x) plus sum(x^2) for s.d. calc
+    int64_t *nreads, *nreads2;          // [max_amp]
+    double  *nfull_reads;               // [max_amp]; 0.5/read if paired.
+    double  *nrperc, *nrperc2;          // [max_amp]
+    int64_t *nbases, *nbases2;          // [max_amp]
+    int64_t *coverage;                  // [max_amp][max_amp_len]
+    double  (*covered_perc)[MAX_DEPTH]; // [max_amp][MAX_DEPTH]
+    double  (*covered_perc2)[MAX_DEPTH];// [max_amp][MAX_DEPTH];
+    khash_t(tcoord) **tcoord;           // [max_amp+1]
+
+    // 0 is correct pair, 1 is incorrect pair, 2 is unidentified
+    int     (*amp_dist)[3];             // [MAX_AMP][3];
+
+    int *depth_valid; // [max_len]
+    int *depth_all;   // [max_len]
+    khash_t(qname) *qend;  // queryname end, for overlap removal
+} astats_t;
+
+// We can have multiple primers for LEFT / RIGHT, so this
+// permits detection by any compatible combination.
+// One reference:
+typedef struct {
+    int64_t left[MAX_PRIMER_PER_AMPLICON];
+    int nleft;
+    int64_t right[MAX_PRIMER_PER_AMPLICON];
+    int nright;
+    int64_t max_left, min_right; // inner dimensions
+    int64_t min_left, max_right; // outer dimensions
+} amplicon_t;
+
+// Multiple references, we have an array of amplicons_t - one per used ref.
+// We have per reference local and global stats here, as some of the stats
+// are coordinate based.  However we report them combined together as a single
+// list across all references.
+// "namp" is the number of amplicons in this reference, but they're
+// numbered first_amp to first_amp+namp-1 inclusively.
+typedef struct {
+    int tid, namp;
+    int64_t len;
+    bed_entry_list_t *sites;
+    amplicon_t *amp;
+    astats_t *lstats, *gstats; // local (1 file) and global (all file) stats
+    const char *ref;           // ref name (pointer to the bed hash table key)
+    int first_amp;             // first amplicon number for this ref
+} amplicons_t;
+
+// Reinitialised for each new reference/chromosome.
+// Counts from 1 to namp, -1 for no match and 0 for ?.
+static int *pos2start = NULL;
+static int *pos2end = NULL;
+static int pos2size = 0; // allocated size of pos2start/end
+
+// Lookup table to go from position to amplicon based on
+// read start / end.
+static int initialise_amp_pos_lookup(astats_args_t *args,
+                                     amplicons_t *amps,
+                                     int ref) {
+    int64_t i, j;
+    amplicon_t *amp = amps[ref].amp;
+    int64_t max_len = amps[ref].len;
+    int namp = amps[ref].namp;
+
+    if (max_len+1 > pos2size) {
+        if (!(pos2start = realloc(pos2start, (max_len+1)*sizeof(*pos2start))))
+            return -1;
+        if (!(pos2end   = realloc(pos2end,   (max_len+1)*sizeof(*pos2end))))
+            return -1;
+        pos2size = max_len;
+    }
+    for (i = 0; i < max_len; i++)
+        pos2start[i] = pos2end[i] = -1;
+
+    for (i = 0; i < namp; i++) {
+        for (j = 0; j < amp[i].nleft; j++) {
+            int64_t p;
+            for (p = amp[i].left[j] - args->max_delta;
+                 p <= amp[i].left[j] + args->max_delta; p++) {
+                if (p < 1 || p > max_len)
+                    continue;
+                pos2start[p-1] = i;
+            }
+        }
+        for (j = 0; j < amp[i].nright; j++) {
+            int64_t p;
+            for (p = amp[i].right[j] - args->max_delta;
+                 p <= amp[i].right[j] + args->max_delta; p++) {
+                if (p < 1 || p > max_len)
+                    continue;
+                pos2end[p-1] = i;
+            }
+        }
+    }
+
+    return 0;
+}
+
+// Counts amplicons.
+// Assumption: input BED file alternates between LEFT and RIGHT primers
+// per amplicon, thus we can count the number based on the switching
+// orientation.
+static int count_amplicon(bed_entry_list_t *sites) {
+    int i, namp, last_rev = 0;
+    for (i = namp = 0; i < sites->length; i++) {
+        if (sites->bp[i].rev == 0 && last_rev)
+            namp++;
+        last_rev = sites->bp[i].rev;
+    }
+
+    return ++namp;
+}
+
+// We're only interest in the internal part of the amplicon.
+// Our bed file has LEFT start/end followed by RIGHT start/end,
+// so collapse these to LEFT end / RIGHT start.
+//
+// Returns right most amplicon position on success,
+//         < 0 on error
+static int64_t bed2amplicon(astats_args_t *args, bed_entry_list_t *sites,
+                            amplicon_t *amp, int *namp, int do_title,
+                            const char *ref, int first_amp) {
+    int i, j;
+    int64_t max_right = 0;
+    FILE *ofp = args->out_fp;
+
+    *namp = 0;
+
+    // Assume all primers for the same amplicon are adjacent in BED
+    // with all + followed by all -.  Thus - to + signifies next primer set.
+    int last_rev = 0;
+    amp[0].max_left = 0;
+    amp[0].min_right = INT64_MAX;
+    amp[0].min_left = INT64_MAX;
+    amp[0].max_right = 0;
+    if (do_title) {
+        fprintf(ofp, "# Amplicon locations from BED file.\n");
+        fprintf(ofp, "# LEFT/RIGHT are <start>-<end> format and "
+                "comma-separated for alt-primers.\n");
+        if (args->multi_ref)
+            fprintf(ofp, "#\n# AMPLICON\tREF\tNUMBER\tLEFT\tRIGHT\n");
+        else
+            fprintf(ofp, "#\n# AMPLICON\tNUMBER\tLEFT\tRIGHT\n");
+    }
+    for (i = j = 0; i < sites->length; i++) {
+        if (i == 0 && sites->bp[i].rev != 0) {
+            fprintf(samtools_stderr, "[ampliconstats] error: BED file should start"
+                    " with the + strand primer\n");
+            return -1;
+        }
+        if (sites->bp[i].rev == 0 && last_rev) {
+            j++;
+            if (j >= args->max_amp) {
+                fprintf(samtools_stderr, "[ampliconstats] error: too many amplicons"
+                        " (%d). Use -a option to raise this.\n", j);
+                return -1;
+            }
+            amp[j].max_left = 0;
+            amp[j].min_right = INT64_MAX;
+            amp[j].min_left = INT64_MAX;
+            amp[j].max_right = 0;
+        }
+        if (sites->bp[i].rev == 0) {
+            if (i == 0 || last_rev) {
+                if (j>0) fprintf(ofp, "\n");
+                if (args->multi_ref)
+                    fprintf(ofp, "AMPLICON\t%s\t%d", ref, j+1 + first_amp);
+                else
+                    fprintf(ofp, "AMPLICON\t%d", j+1);
+            }
+            if (amp[j].nleft >= MAX_PRIMER_PER_AMPLICON) {
+                print_error_errno("ampliconstats",
+                                  "too many primers per amplicon (%d).\n",
+                                  MAX_PRIMER_PER_AMPLICON);
+                return -1;
+            }
+            amp[j].left[amp[j].nleft++] = sites->bp[i].right;
+            if (amp[j].max_left < sites->bp[i].right+1)
+                amp[j].max_left = sites->bp[i].right+1;
+            if (amp[j].min_left > sites->bp[i].right+1)
+                amp[j].min_left = sites->bp[i].right+1;
+            // BED file, so left+1 as zero based. right(+1-1) as
+            // BED goes one beyond end (and we want inclusive range).
+            fprintf(ofp, "%c%"PRId64"-%"PRId64, "\t,"[amp[j].nleft > 1],
+                    sites->bp[i].left+1, sites->bp[i].right);
+        } else {
+            if (amp[j].nright >= MAX_PRIMER_PER_AMPLICON) {
+                print_error_errno("ampliconstats",
+                                  "too many primers per amplicon (%d)",
+                                  MAX_PRIMER_PER_AMPLICON);
+                return -1;
+            }
+            amp[j].right[amp[j].nright++] = sites->bp[i].left;
+            if (amp[j].min_right > sites->bp[i].left-1)
+                amp[j].min_right = sites->bp[i].left-1;
+            if (amp[j].max_right < sites->bp[i].left-1) {
+                amp[j].max_right = sites->bp[i].left-1;
+                if (amp[j].max_right - amp[j].min_left + 1 >=
+                    args->max_amp_len) {
+                    fprintf(samtools_stderr, "[ampliconstats] error: amplicon "
+                            "longer (%d) than max_amp_len option (%d)\n",
+                            (int)(amp[j].max_right - amp[j].min_left + 2),
+                            args->max_amp_len);
+                    return -1;
+                }
+                if (max_right < amp[j].max_right)
+                    max_right = amp[j].max_right;
+            }
+            fprintf(ofp, "%c%"PRId64"-%"PRId64, "\t,"[amp[j].nright > 1],
+                    sites->bp[i].left+1, sites->bp[i].right);
+        }
+        last_rev = sites->bp[i].rev;
+    }
+    if (last_rev != 1) {
+        fprintf(ofp, "\n"); // useful if going to samtools_stdout
+        fprintf(samtools_stderr, "[ampliconstats] error: bed file does not end on"
+                " a reverse strand primer.\n");
+        return -1;
+    }
+    *namp = ++j;
+    if (j) fprintf(ofp, "\n");
+
+    if (j >= args->max_amp) {
+        fprintf(samtools_stderr, "[ampliconstats] error: "
+                "too many amplicons (%d). Use -a option to raise this.", j);
+        return -1;
+    }
+
+//    for (i = 0; i < *namp; i++) {
+//      fprintf(samtools_stdout, "%d\t%ld", i, amp[i].length);
+//      for (j = 0; j < amp[i].nleft; j++)
+//          fprintf(samtools_stdout, "%c%ld", "\t,"[j>0], amp[i].left[j]);
+//      for (j = 0; j < amp[i].nright; j++)
+//          fprintf(samtools_stdout, "%c%ld", "\t,"[j>0], amp[i].right[j]);
+//      fprintf(samtools_stdout, "\n");
+//    }
+
+    return max_right;
+}
+
+void stats_free(astats_t *st) {
+    if (!st)
+        return;
+
+    free(st->nreads);
+    free(st->nreads2);
+    free(st->nfull_reads);
+    free(st->nrperc);
+    free(st->nrperc2);
+    free(st->nbases);
+    free(st->nbases2);
+    free(st->coverage);
+    free(st->covered_perc);
+    free(st->covered_perc2);
+    free(st->amp_dist);
+
+    free(st->depth_valid);
+    free(st->depth_all);
+
+    if (st->tcoord) {
+        int i;
+        for (i = 0; i <= st->max_amp; i++) {
+            if (st->tcoord[i])
+                kh_destroy(tcoord, st->tcoord[i]);
+        }
+        free(st->tcoord);
+    }
+
+    khiter_t k;
+    for (k = kh_begin(st->qend); k != kh_end(st->qend); k++)
+        if (kh_exist(st->qend, k))
+            free((void *)kh_key(st->qend, k));
+    kh_destroy(qname, st->qend);
+
+    free(st);
+}
+
+astats_t *stats_alloc(int64_t max_len, int max_amp, int max_amp_len) {
+    astats_t *st = calloc(1, sizeof(*st));
+    if (!st)
+        return NULL;
+
+    st->max_amp = max_amp;
+    st->max_amp_len = max_amp_len;
+    st->max_len = max_len;
+
+    if (!(st->nreads  = calloc(max_amp, sizeof(*st->nreads))))  goto err;
+    if (!(st->nreads2 = calloc(max_amp, sizeof(*st->nreads2)))) goto err;
+    if (!(st->nrperc  = calloc(max_amp, sizeof(*st->nrperc))))  goto err;
+    if (!(st->nrperc2 = calloc(max_amp, sizeof(*st->nrperc2)))) goto err;
+    if (!(st->nbases  = calloc(max_amp, sizeof(*st->nbases))))  goto err;
+    if (!(st->nbases2 = calloc(max_amp, sizeof(*st->nbases2)))) goto err;
+
+    if (!(st->nfull_reads = calloc(max_amp, sizeof(*st->nfull_reads))))
+        goto err;
+
+    if (!(st->coverage = calloc(max_amp*max_amp_len, sizeof(*st->coverage))))
+        goto err;
+
+    if (!(st->covered_perc  = calloc(max_amp, sizeof(*st->covered_perc))))
+        goto err;
+    if (!(st->covered_perc2 = calloc(max_amp, sizeof(*st->covered_perc2))))
+        goto err;
+
+    if (!(st->tcoord = calloc(max_amp+1, sizeof(*st->tcoord)))) goto err;
+    int i;
+    for (i = 0; i <= st->max_amp; i++)
+        if (!(st->tcoord[i] = kh_init(tcoord)))
+            goto err;
+
+    if (!(st->qend = kh_init(qname)))
+        goto err;
+
+    if (!(st->depth_valid = calloc(max_len, sizeof(*st->depth_valid))))
+        goto err;
+    if (!(st->depth_all   = calloc(max_len, sizeof(*st->depth_all))))
+        goto err;
+
+    if (!(st->amp_dist  = calloc(max_amp, sizeof(*st->amp_dist))))  goto err;
+
+    return st;
+
+ err:
+    stats_free(st);
+    return NULL;
+}
+
+static void stats_reset(astats_t *st) {
+    st->nseq = 0;
+    st->nfiltered = 0;
+    st->nfailprimer = 0;
+
+    memset(st->nreads,  0, st->max_amp * sizeof(*st->nreads));
+    memset(st->nreads2, 0, st->max_amp * sizeof(*st->nreads2));
+    memset(st->nfull_reads, 0, st->max_amp * sizeof(*st->nfull_reads));
+
+    memset(st->nrperc,  0, st->max_amp * sizeof(*st->nrperc));
+    memset(st->nrperc2, 0, st->max_amp * sizeof(*st->nrperc2));
+
+    memset(st->nbases,  0, st->max_amp * sizeof(*st->nbases));
+    memset(st->nbases2, 0, st->max_amp * sizeof(*st->nbases2));
+
+    memset(st->coverage, 0, st->max_amp * st->max_amp_len
+           * sizeof(*st->coverage));
+    memset(st->covered_perc,  0, st->max_amp * sizeof(*st->covered_perc));
+    memset(st->covered_perc2, 0, st->max_amp * sizeof(*st->covered_perc2));
+
+    // Keep the allocated entries as it's likely all files will share
+    // the same keys.  Instead we reset counters to zero for common ones
+    // and delete rare ones.
+    int i;
+    for (i = 0; i <= st->max_amp; i++) {
+        khiter_t k;
+        for (k = kh_begin(st->tcoord[i]);
+             k != kh_end(st->tcoord[i]); k++)
+            if (kh_exist(st->tcoord[i], k)) {
+                if (kh_value(st->tcoord[i], k) < 5)
+                    kh_del(tcoord, st->tcoord[i], k);
+                else
+                    kh_value(st->tcoord[i], k) = 0;
+            }
+    }
+
+    khiter_t k;
+    for (k = kh_begin(st->qend); k != kh_end(st->qend); k++)
+        if (kh_exist(st->qend, k))
+            free((void *)kh_key(st->qend, k));
+    kh_clear(qname, st->qend);
+
+    memset(st->depth_valid, 0, st->max_len * sizeof(*st->depth_valid));
+    memset(st->depth_all,   0, st->max_len * sizeof(*st->depth_all));
+    memset(st->amp_dist,  0, st->max_amp * sizeof(*st->amp_dist));
+}
+
+static void amp_stats_reset(amplicons_t *amps, int nref) {
+    int i;
+    for (i = 0; i < nref; i++) {
+        if (!amps[i].sites)
+            continue;
+        stats_reset(amps[i].lstats);
+    }
+}
+
+static int accumulate_stats(astats_args_t *args, amplicons_t *amps,
+                            bam1_t *b) {
+    int ref = b->core.tid;
+    amplicon_t *amp = amps[ref].amp;
+    astats_t *stats = amps[ref].lstats;
+    int len = amps[ref].len;
+
+    if (!stats)
+        return 0;
+
+    stats->nseq++;
+    if ((b->core.flag & args->flag_require) != args->flag_require ||
+        (b->core.flag & args->flag_filter)  != 0) {
+        stats->nfiltered++;
+        return 0;
+    }
+
+    int64_t start = b->core.pos, mstart = start; // modified start
+    int64_t end = bam_endpos(b), i;
+
+    // Compute all-template-depth and valid-template-depth.
+    // We track current end location per read name so we can remove overlaps.
+    // Potentially we could use this data for a better amplicon-depth
+    // count too, but for now it's purely for the per-base plots.
+    int ret;
+    khiter_t k;
+    int prev_start = 0, prev_end = 0;
+    if ((b->core.flag & BAM_FPAIRED)
+        && !(b->core.flag & (BAM_FSUPPLEMENTARY | BAM_FSECONDARY))) {
+        k = kh_put(qname, stats->qend, bam_get_qname(b), &ret);
+        if (ret == 0) {
+            prev_start = kh_value(stats->qend, k) & 0xffffffff;
+            prev_end = kh_value(stats->qend, k)>>32;
+            mstart = MAX(mstart, prev_end);
+            // Ideally we'd reuse strings so we don't thrash free/malloc.
+            // However let's see if the official way of doing that (malloc
+            // itself) is fast enough first.
+            free((void *)kh_key(stats->qend, k));
+            kh_del(qname, stats->qend, k);
+            //fprintf(samtools_stderr, "remove overlap %d to %d\n", (int)start, (int)mstart);
+        } else {
+            if (!(kh_key(stats->qend, k) = strdup(bam_get_qname(b))))
+                return -1;
+
+            kh_value(stats->qend, k) = start | (end << 32);
+        }
+    }
+    for (i = mstart; i < end && i < len; i++)
+        stats->depth_all[i]++;
+    if (i < end) {
+        print_error("ampliconstats", "record %s overhangs end of reference",
+                    bam_get_qname(b));
+        // But keep going, as it's harmless.
+    }
+
+    // On single ended runs, eg ONT or PacBio, we just use the start/end
+    // of the template to assign.
+    int anum = (b->core.flag & BAM_FREVERSE) || !(b->core.flag & BAM_FPAIRED)
+        ? (end-1 >= 0 && end-1 < len ? pos2end[end-1] : -1)
+        : (start >= 0 && start < len ? pos2start[start] : -1);
+
+    // ivar sometimes soft-clips 100% of the bases.
+    // This is essentially unmapped
+    if (end == start && (args->flag_filter & BAM_FUNMAP)) {
+        stats->nfiltered++;
+        return 0;
+    }
+
+    if (anum == -1)
+        stats->nfailprimer++;
+
+    if (anum >= 0) {
+        int64_t c = MIN(end,amp[anum].min_right+1) - MAX(start,amp[anum].max_left);
+        if (c > 0) {
+            stats->nreads[anum]++;
+            // NB: ref bases rather than read bases
+            stats->nbases[anum] += c;
+
+            int64_t i;
+            if (start < 0) start = 0;
+            if (end > len) end = len;
+
+            int64_t ostart = MAX(start, amp[anum].min_left-1);
+            int64_t oend = MIN(end, amp[anum].max_right);
+            int64_t offset = amp[anum].min_left-1;
+            for (i = ostart; i < oend; i++)
+                stats->coverage[anum*stats->max_amp_len + i-offset]++;
+        } else {
+            stats->nfailprimer++;
+        }
+    }
+
+    // Template length in terms of amplicon number to amplicon number.
+    // We expect left to right of same amplicon (len 0), but it may go
+    // to next amplicon (len 1) or prev (len -1), etc.
+    int64_t t_end;
+    int oth_anum = -1;
+
+    if (b->core.flag & BAM_FPAIRED) {
+        t_end = (b->core.flag & BAM_FREVERSE ? end : start)
+            + b->core.isize;
+
+        // If we've clipped the primers but not followed up with a fixmates
+        // then our start+TLEN will take us to a location which is
+        // length(LEFT_PRIMER) + length(RIGHT_PRIMER) too far away.
+        //
+        // The correct solution is to run samtools fixmate so TLEN is correct.
+        // The hacky solution is to fudge the expected tlen by double the
+        // average primer length (e.g. 50).
+        t_end += b->core.isize > 0 ? -args->tlen_adj : +args->tlen_adj;
+
+        if (t_end > 0 && t_end < len && b->core.isize != 0)
+            oth_anum = (b->core.flag & BAM_FREVERSE)
+                ? pos2start[t_end]
+                : pos2end[t_end];
+    } else {
+        // Not paired (see int anum = (REV || !PAIR) ?en :st expr above)
+        oth_anum = pos2start[start];
+        t_end = end;
+    }
+
+    // We don't want to count our pairs twice.
+    // If both left/right are known, count it on left only.
+    // If only one is known, we'll only get to this code once
+    // so we can also count it.
+    int astatus = 2;
+    if (anum != -1 && oth_anum != -1) {
+        astatus = oth_anum == anum ? 0 : 1;
+        if (start <= t_end)
+            stats->amp_dist[anum][astatus]++;
+    } else if (anum >= 0) {
+        stats->amp_dist[anum][astatus = 2]++;
+    }
+
+    if (astatus == 0 && !(b->core.flag & (BAM_FUNMAP | BAM_FMUNMAP))) {
+        if (prev_end && mstart > prev_end) {
+            // 2nd read with gap to 1st; undo previous increment.
+            for (i = prev_start; i < prev_end; i++)
+                stats->depth_valid[i]--;
+            stats->nfull_reads[anum] -= (b->core.flag & BAM_FPAIRED) ? 0.5 : 1;
+        } else {
+            // 1st read, or 2nd read that overlaps 1st
+            for (i = mstart; i < end; i++)
+                stats->depth_valid[i]++;
+            stats->nfull_reads[anum] += (b->core.flag & BAM_FPAIRED) ? 0.5 : 1;
+        }
+    }
+
+    // Track template start,end frequencies, so we can give stats on
+    // amplicon primer usage.
+    if ((b->core.flag & BAM_FPAIRED) && b->core.isize <= 0)
+        // left to right only, so we don't double count template positions.
+        return 0;
+
+    start = b->core.pos;
+    t_end = b->core.flag & BAM_FPAIRED
+        ? start + b->core.isize-1
+        : end;
+    uint64_t tcoord = MIN(start+1, UINT32_MAX) | (MIN(t_end+1, UINT32_MAX)<<32);
+    k = kh_put(tcoord, stats->tcoord[anum+1], tcoord, &ret);
+    if (ret < 0)
+        return -1;
+    if (ret == 0)
+        kh_value(stats->tcoord[anum+1], k)++;
+    else
+        kh_value(stats->tcoord[anum+1], k)=1;
+    kh_value(stats->tcoord[anum+1], k) |= ((int64_t)astatus<<32);
+
+    return 0;
+}
+
+// Append file local stats to global stats
+int append_lstats(astats_t *lstats, astats_t *gstats, int namp, int all_nseq) {
+    gstats->nseq += lstats->nseq;
+    gstats->nfiltered += lstats->nfiltered;
+    gstats->nfailprimer += lstats->nfailprimer;
+
+    int a;
+    for (a = -1; a < namp; a++) {
+        // Add khash local (kl) to khash global (kg)
+        khiter_t kl, kg;
+        for (kl = kh_begin(lstats->tcoord[a+1]);
+             kl != kh_end(lstats->tcoord[a+1]); kl++) {
+            if (!kh_exist(lstats->tcoord[a+1], kl) ||
+                kh_value(lstats->tcoord[a+1], kl) == 0)
+                continue;
+
+            int ret;
+            kg = kh_put(tcoord, gstats->tcoord[a+1],
+                        kh_key(lstats->tcoord[a+1], kl),
+                        &ret);
+            if (ret < 0)
+                return -1;
+
+            kh_value(gstats->tcoord[a+1], kg) =
+                (ret == 0
+                 ? (kh_value(gstats->tcoord[a+1], kg) & 0xFFFFFFFF)
+                 : 0)
+                + kh_value(lstats->tcoord[a+1], kl);
+        }
+        if (a == -1) continue;
+
+        gstats->nreads[a]  += lstats->nreads[a];
+        gstats->nreads2[a] += lstats->nreads[a] * lstats->nreads[a];
+        gstats->nfull_reads[a] += lstats->nfull_reads[a];
+
+        // To get mean & sd for amplicon read percentage, we need
+        // to do the divisions here as nseq differs for each sample.
+        double nrperc = all_nseq ? 100.0 * lstats->nreads[a] / all_nseq : 0;
+        gstats->nrperc[a]  += nrperc;
+        gstats->nrperc2[a] += nrperc*nrperc;
+
+        gstats->nbases[a]  += lstats->nbases[a];
+        gstats->nbases2[a] += lstats->nbases[a] * lstats->nbases[a];
+
+        int d;
+        for (d = 0; d < MAX_DEPTH; d++) {
+            gstats->covered_perc[a][d]  += lstats->covered_perc[a][d];
+            gstats->covered_perc2[a][d] += lstats->covered_perc[a][d]
+                                         * lstats->covered_perc[a][d];
+        }
+
+        for (d = 0; d < 3; d++)
+            gstats->amp_dist[a][d] += lstats->amp_dist[a][d];
+    }
+
+    for (a = 0; a < lstats->max_len; a++) {
+        gstats->depth_valid[a] += lstats->depth_valid[a];
+        gstats->depth_all[a]   += lstats->depth_all[a];
+    }
+
+    return 0;
+}
+
+int append_stats(amplicons_t *amps, int nref) {
+    int i, r, all_nseq = 0;
+    for (r = 0; r < nref; r++) {
+        if (!amps[r].sites)
+            continue;
+        astats_t *stats = amps[r].lstats;
+        all_nseq  += stats->nseq - stats->nfiltered - stats->nfailprimer;
+    }
+
+    for (i = 0; i < nref; i++) {
+        if (!amps[i].sites)
+            continue;
+        if (append_lstats(amps[i].lstats, amps[i].gstats, amps[i].namp,
+                          all_nseq) < 0)
+            return -1;
+    }
+
+    return 0;
+}
+
+typedef struct {
+    int32_t start, end;
+    uint32_t freq;
+    uint32_t status;
+} tcoord_t;
+
+// Sort tcoord by descending frequency and then ascending start and  end.
+static int tcoord_freq_sort(const void *vp1, const void *vp2) {
+    const tcoord_t *t1 = (const tcoord_t *)vp1;
+    const tcoord_t *t2 = (const tcoord_t *)vp2;
+
+    if (t1->freq != t2->freq)
+        return t2->freq - t1->freq;
+
+    if (t1->start != t2->start)
+        return t1->start - t2->start;
+
+    return t1->end - t2->end;
+}
+
+
+/*
+ * Merges tcoord start,end,freq,status tuples if their coordinates are
+ * close together.  We aim to keep the start,end for the most frequent
+ * value and assume that is the correct coordinate and all others are
+ * minor fluctuations due to errors or variants.
+ *
+ * We sort by frequency first and then merge later items in the list into
+ * the earlier more frequent ones.  It's O(N^2), but sufficient for now
+ * given current scale of projects.
+ *
+ * If we ever need to resolve that then consider sorting by start
+ * coordinate and scanning the list to find all items within X, find
+ * the most frequent of those, and then cluster that way.  (I'd have
+ * done that had I thought of it at the time!)
+ */
+static void aggregate_tcoord(astats_args_t *args, tcoord_t *tpos, size_t *np){
+    size_t n = *np, j, j2, j3, k;
+
+    // Sort by frequency and cluster infrequent coords into frequent
+    // ones provided they're close by.
+    // This is O(N^2), but we've already binned by tcoord_bin/2 so
+    // the list isn't intended to be vast at this point.
+    qsort(tpos, n, sizeof(*tpos), tcoord_freq_sort);
+
+    // For frequency ties, find mid start coord, and then find mid end
+    // coord of those matching start.
+    // We make that the first item so we merge into that mid point.
+    for (j = 0; j < n; j++) {
+        for (j2 = j+1; j2 < n; j2++) {
+            if (tpos[j].freq != tpos[j2].freq)
+                break;
+            if (tpos[j2].start - tpos[j].start >= args->tcoord_bin)
+                break;
+        }
+
+        // j to j2 all within bin of a common start,
+        // m is the mid start.
+        if (j2-1 > j) {
+            size_t m = (j2-1 + j)/2;
+
+            // Find mid end for this same start
+            while (m > 1 && tpos[m].start == tpos[m-1].start)
+                m--;
+            for (j3 = m+1; j3 < j2; j3++) {
+                if (tpos[m].start != tpos[j3].start)
+                    break;
+                if (tpos[m].end - tpos[j3].end >= args->tcoord_bin)
+                    break;
+            }
+            if (j3-1 > m)
+                m = (j3-1 + m)/2;
+
+            // Swap with first item.
+            tcoord_t tmp = tpos[j];
+            tpos[j] = tpos[m];
+            tpos[m] = tmp;
+            j = j2-1;
+        }
+    }
+
+    // Now merge in coordinates.
+    // This bit is O(N^2), so consider binning first to reduce the
+    // size of the list if we have excessive positional variation.
+    for (k = j = 0; j < n; j++) {
+        if (!tpos[j].freq)
+            continue;
+
+        if (k < j)
+            tpos[k] = tpos[j];
+
+        for (j2 = j+1; j2 < n; j2++) {
+            if (ABS(tpos[j].start-tpos[j2].start) < args->tcoord_bin/2 &&
+                ABS(tpos[j].end  -tpos[j2].end)  < args->tcoord_bin/2 &&
+                tpos[j].status == tpos[j2].status) {
+                tpos[k].freq += tpos[j2].freq;
+                tpos[j2].freq = 0;
+            }
+        }
+        k++;
+    }
+
+    *np = k;
+}
+
+int dump_stats(astats_args_t *args, char type, char *name, int nfile,
+               amplicons_t *amps, int nref, int local) {
+    int i, r;
+    FILE *ofp = args->out_fp;
+    tcoord_t *tpos = NULL;
+    size_t ntcoord = 0;
+
+    // summary stats for this sample (or for all samples)
+    fprintf(ofp, "# Summary stats.\n");
+    fprintf(ofp, "# Use 'grep ^%cSS | cut -f 2-' to extract this part.\n", type);
+
+    for (r = 0; r < nref; r++) {
+        if (!amps[r].sites)
+            continue;
+        astats_t *stats = local ? amps[r].lstats : amps[r].gstats;
+        int nmatch = stats->nseq - stats->nfiltered - stats->nfailprimer;
+        char *name_ref = malloc(strlen(name) + strlen(amps[r].ref) + 2);
+        if (!name_ref)
+            return -1;
+        if (args->multi_ref)
+            sprintf(name_ref, "%s\t%s", name, amps[r].ref);
+        else
+            sprintf(name_ref, "%s", name);
+        fprintf(ofp, "%cSS\t%s\traw total sequences:\t%d\n",
+                type, name_ref, stats->nseq);
+        fprintf(ofp, "%cSS\t%s\tfiltered sequences:\t%d\n",
+                type, name_ref, stats->nfiltered);
+        fprintf(ofp, "%cSS\t%s\tfailed primer match:\t%d\n",
+                type, name_ref, stats->nfailprimer);
+        fprintf(ofp, "%cSS\t%s\tmatching sequences:\t%d\n",
+                type, name_ref, nmatch);
+
+        int d = 0;
+        do {
+            // From first to last amplicon only, so not entire consensus.
+            // If contig length is known, maybe we want to add the missing
+            // count to < DEPTH figures?
+            int64_t start = 0, covered = 0, total = 0;
+            amplicon_t *amp = amps[r].amp;
+            for (i = 0; i < amps[r].namp; i++) {
+                int64_t j, offset = amp[i].min_left-1;
+                if (amp[i].min_right - amp[i].min_left > stats->max_amp_len) {
+                    fprintf(samtools_stderr, "[ampliconstats] error: "
+                            "Maximum amplicon length (%d) exceeded for '%s'\n",
+                            stats->max_amp, name);
+                    return -1;
+                }
+                for (j = MAX(start, amp[i].max_left-1);
+                     j < MAX(start, amp[i].min_right); j++) {
+                    if (stats->coverage[i*stats->max_amp_len + j-offset]
+                        >= args->min_depth[d])
+                        covered++;
+                    total++;
+                }
+                start = MAX(start, amp[i].min_right);
+            }
+            fprintf(ofp, "%cSS\t%s\tconsensus depth count < %d and >= %d:\t%"
+                    PRId64"\t%"PRId64"\n", type, name_ref,
+                    args->min_depth[d], args->min_depth[d],
+                    total-covered, covered);
+        } while (++d < MAX_DEPTH && args->min_depth[d]);
+
+        free(name_ref);
+    }
+
+    // Read count
+    fprintf(ofp, "# Absolute matching read counts per amplicon.\n");
+    fprintf(ofp, "# Use 'grep ^%cREADS | cut -f 2-' to extract this part.\n", type);
+    fprintf(ofp, "%cREADS\t%s", type, name);
+    for (r = 0; r < nref; r++) {
+        if (!amps[r].sites)
+            continue;
+        astats_t *stats = local ? amps[r].lstats : amps[r].gstats;
+        for (i = 0; i < amps[r].namp; i++) {
+            fprintf(ofp, "\t%"PRId64, stats->nreads[i]);
+        }
+    }
+    fprintf(ofp, "\n");
+
+    // Valid depth is the number of full length reads (already divided
+    // by the number we expect to cover), so +0.5 per read in pair.
+    // A.k.a "usable depth" in the plots.
+    fprintf(ofp, "%cVDEPTH\t%s", type, name);
+    for (r = 0; r < nref; r++) {
+        if (!amps[r].sites)
+            continue;
+        astats_t *stats = local ? amps[r].lstats : amps[r].gstats;
+        for (i = 0; i < amps[r].namp; i++)
+            fprintf(ofp, "\t%d", (int)stats->nfull_reads[i]);
+    }
+    fprintf(ofp, "\n");
+
+    if (type == 'C') {
+        // For combined we can compute mean & standard deviation too
+        fprintf(ofp, "CREADS\tMEAN");
+        for (r = 0; r < nref; r++) {
+            if (!amps[r].sites)
+                continue;
+            astats_t *stats = local ? amps[r].lstats : amps[r].gstats;
+            for (i = 0; i < amps[r].namp; i++) {
+                fprintf(ofp, "\t%.1f", stats->nreads[i] / (double)nfile);
+            }
+        }
+        fprintf(ofp, "\n");
+
+        fprintf(ofp, "CREADS\tSTDDEV");
+        for (r = 0; r < nref; r++) {
+            if (!amps[r].sites)
+                continue;
+            astats_t *stats = local ? amps[r].lstats : amps[r].gstats;
+            for (i = 0; i < amps[r].namp; i++) {
+                double n1 = stats->nreads[i];
+                fprintf(ofp, "\t%.1f", nfile > 1 && stats->nreads2[i] > 0
+                        ? sqrt(stats->nreads2[i]/(double)nfile
+                               - (n1/nfile)*(n1/nfile))
+                        : 0);
+            }
+        }
+        fprintf(ofp, "\n");
+    }
+
+    fprintf(ofp, "# Read percentage of distribution between amplicons.\n");
+    fprintf(ofp, "# Use 'grep ^%cRPERC | cut -f 2-' to extract this part.\n", type);
+    fprintf(ofp, "%cRPERC\t%s", type, name);
+    int all_nseq = 0;
+    for (r = 0; r < nref; r++) {
+        if (!amps[r].sites)
+            continue;
+        astats_t *stats = local ? amps[r].lstats : amps[r].gstats;
+        all_nseq  += stats->nseq - stats->nfiltered - stats->nfailprimer;
+    }
+    for (r = 0; r < nref; r++) {
+        if (!amps[r].sites)
+            continue;
+        astats_t *stats = local ? amps[r].lstats : amps[r].gstats;
+        for (i = 0; i < amps[r].namp; i++) {
+            if (type == 'C') {
+                fprintf(ofp, "\t%.3f", (double)stats->nrperc[i] / nfile);
+            } else {
+                fprintf(ofp, "\t%.3f",
+                        all_nseq ? 100.0 * stats->nreads[i] / all_nseq : 0);
+            }
+        }
+    }
+    fprintf(ofp, "\n");
+
+    if (type == 'C') {
+        // For combined we compute mean and standard deviation too
+        fprintf(ofp, "CRPERC\tMEAN");
+        for (r = 0; r < nref; r++) {
+            if (!amps[r].sites)
+                continue;
+            astats_t *stats = local ? amps[r].lstats : amps[r].gstats;
+            for (i = 0; i < amps[r].namp; i++) {
+                fprintf(ofp, "\t%.3f", stats->nrperc[i] / nfile);
+            }
+        }
+        fprintf(ofp, "\n");
+
+        fprintf(ofp, "CRPERC\tSTDDEV");
+        for (r = 0; r < nref; r++) {
+            if (!amps[r].sites)
+                continue;
+            astats_t *stats = local ? amps[r].lstats : amps[r].gstats;
+            for (i = 0; i < amps[r].namp; i++) {
+                // variance = SUM(X^2) - ((SUM(X)^2) / N)
+                double n1 = stats->nrperc[i];
+                double v = stats->nrperc2[i]/nfile - (n1/nfile)*(n1/nfile);
+                fprintf(ofp, "\t%.3f", v>0?sqrt(v):0);
+            }
+        }
+        fprintf(ofp, "\n");
+    }
+
+    // Base depth
+    fprintf(ofp, "# Read depth per amplicon.\n");
+    fprintf(ofp, "# Use 'grep ^%cDEPTH | cut -f 2-' to extract this part.\n", type);
+    fprintf(ofp, "%cDEPTH\t%s", type, name);
+    for (r = 0; r < nref; r++) {
+        if (!amps[r].sites)
+            continue;
+        astats_t *stats = local ? amps[r].lstats : amps[r].gstats;
+        amplicon_t *amp = amps[r].amp;
+        for (i = 0; i < amps[r].namp; i++) {
+            int nseq = stats->nseq - stats->nfiltered - stats->nfailprimer;
+            int64_t alen = amp[i].min_right - amp[i].max_left+1;
+            fprintf(ofp, "\t%.1f", nseq ? stats->nbases[i] / (double)alen : 0);
+        }
+    }
+    fprintf(ofp, "\n");
+
+    if (type == 'C') {
+        // For combined we can compute mean & standard deviation too
+        fprintf(ofp, "CDEPTH\tMEAN");
+        for (r = 0; r < nref; r++) {
+            if (!amps[r].sites)
+                continue;
+            astats_t *stats = local ? amps[r].lstats : amps[r].gstats;
+            amplicon_t *amp = amps[r].amp;
+            int nseq = stats->nseq - stats->nfiltered - stats->nfailprimer;
+            for (i = 0; i < amps[r].namp; i++) {
+                int64_t alen = amp[i].min_right - amp[i].max_left+1;
+                fprintf(ofp, "\t%.1f", nseq ? stats->nbases[i] / (double)alen / nfile : 0);
+            }
+        }
+        fprintf(ofp, "\n");
+
+        fprintf(ofp, "CDEPTH\tSTDDEV");
+        for (r = 0; r < nref; r++) {
+            if (!amps[r].sites)
+                continue;
+            astats_t *stats = local ? amps[r].lstats : amps[r].gstats;
+            amplicon_t *amp = amps[r].amp;
+            for (i = 0; i < amps[r].namp; i++) {
+                double alen = amp[i].min_right - amp[i].max_left+1;
+                double n1 = stats->nbases[i] / alen;
+                double v = stats->nbases2[i] / (alen*alen) /nfile
+                    - (n1/nfile)*(n1/nfile);
+                fprintf(ofp, "\t%.1f", v>0?sqrt(v):0);
+            }
+        }
+        fprintf(ofp, "\n");
+    }
+
+    // Percent Coverage
+    if (type == 'F') {
+        fprintf(ofp, "# Percentage coverage per amplicon\n");
+        fprintf(ofp, "# Use 'grep ^%cPCOV | cut -f 2-' to extract this part.\n", type);
+        int d = 0;
+        do {
+            fprintf(ofp, "%cPCOV-%d\t%s", type, args->min_depth[d], name);
+
+            for (r = 0; r < nref; r++) {
+                if (!amps[r].sites)
+                    continue;
+                astats_t *stats = local ? amps[r].lstats : amps[r].gstats;
+                amplicon_t *amp = amps[r].amp;
+                for (i = 0; i < amps[r].namp; i++) {
+                    int covered = 0;
+                    if (amp[i].min_right - amp[i].min_left > stats->max_amp_len) {
+                        fprintf(samtools_stderr, "[ampliconstats] error: "
+                                "Maximum amplicon length (%d) exceeded for '%s'\n",
+                                stats->max_amp, name);
+                        return -1;
+                    }
+                    int64_t j, offset = amp[i].min_left-1;
+                    for (j = amp[i].max_left-1; j < amp[i].min_right; j++) {
+                        int apos = i*stats->max_amp_len + j-offset;
+                        if (stats->coverage[apos] >= args->min_depth[d])
+                            covered++;
+                    }
+                    int64_t alen = amp[i].min_right - amp[i].max_left+1;
+                    stats->covered_perc[i][d] = 100.0 * covered / alen;
+                    fprintf(ofp, "\t%.2f", 100.0 * covered / alen);
+                }
+            }
+            fprintf(ofp, "\n");
+        } while (++d < MAX_DEPTH && args->min_depth[d]);
+
+    } else if (type == 'C') {
+        // For combined we can compute mean & standard deviation too
+        int d = 0;
+        do {
+            fprintf(ofp, "CPCOV-%d\tMEAN", args->min_depth[d]);
+            for (r = 0; r < nref; r++) {
+                if (!amps[r].sites)
+                    continue;
+                astats_t *stats = local ? amps[r].lstats : amps[r].gstats;
+                for (i = 0; i < amps[r].namp; i++) {
+                    fprintf(ofp, "\t%.1f", stats->covered_perc[i][d] / nfile);
+                }
+            }
+            fprintf(ofp, "\n");
+
+            fprintf(ofp, "CPCOV-%d\tSTDDEV", args->min_depth[d]);
+            for (r = 0; r < nref; r++) {
+                if (!amps[r].sites)
+                    continue;
+                astats_t *stats = local ? amps[r].lstats : amps[r].gstats;
+                for (i = 0; i < amps[r].namp; i++) {
+                    double n1 = stats->covered_perc[i][d] / nfile;
+                    double v = stats->covered_perc2[i][d] / nfile - n1*n1;
+                    fprintf(ofp, "\t%.1f", v>0?sqrt(v):0);
+                }
+            }
+            fprintf(ofp, "\n");
+        } while (++d < MAX_DEPTH && args->min_depth[d]);
+    }
+
+    // Plus base depth for all reads, irrespective of amplicon.
+    // This is post overlap removal, if reads in the read-pair overlap.
+    fprintf(ofp, "# Depth per reference base for ALL data.\n");
+    fprintf(ofp, "# Use 'grep ^%cDP_ALL | cut -f 2-' to extract this part.\n",
+            type);
+    for (r = 0; r < nref; r++) {
+        if (!amps[r].sites)
+            continue;
+        astats_t *stats = local ? amps[r].lstats : amps[r].gstats;
+        if (args->multi_ref)
+            fprintf(ofp, "%cDP_ALL\t%s\t%s", type, name, amps[r].ref);
+        else
+            fprintf(ofp, "%cDP_ALL\t%s", type, name);
+
+        for (i = 0; i < amps[r].len; i++) {
+            // Basic run-length encoding provided all values are within
+            // +- depth_bin fraction of the mid-point.
+            int dmin = stats->depth_all[i], dmax = stats->depth_all[i], j;
+            double dmid = (dmin + dmax)/2.0;
+            double low  = dmid*(1-args->depth_bin);
+            double high = dmid*(1+args->depth_bin);
+            for (j = i+1; j < amps[r].len; j++) {
+                int d = stats->depth_all[j];
+                if (d < low || d > high)
+                    break;
+                if (dmin > d) {
+                    dmin = d;
+                    dmid = (dmin + dmax)/2.0;
+                    low  = dmid*(1-args->depth_bin);
+                    high = dmid*(1+args->depth_bin);
+                } else if (dmax < d) {
+                    dmax = d;
+                    dmid = (dmin + dmax)/2.0;
+                    low  = dmid*(1-args->depth_bin);
+                    high = dmid*(1+args->depth_bin);
+                }
+            }
+            fprintf(ofp, "\t%d,%d", (int)dmid, j-i);
+            i = j-1;
+        }
+        fprintf(ofp, "\n");
+    }
+
+    // And depth for only reads matching to a single amplicon for full
+    // length.  This is post read overlap removal.
+    fprintf(ofp, "# Depth per reference base for full-length valid amplicon data.\n");
+    fprintf(ofp, "# Use 'grep ^%cDP_VALID | cut -f 2-' to extract this "
+            "part.\n", type);
+    for (r = 0; r < nref; r++) {
+        if (!amps[r].sites)
+            continue;
+        astats_t *stats = local ? amps[r].lstats : amps[r].gstats;
+        if (args->multi_ref)
+            fprintf(ofp, "%cDP_VALID\t%s\t%s", type, name, amps[r].ref);
+        else
+            fprintf(ofp, "%cDP_VALID\t%s", type, name);
+
+        for (i = 0; i < amps[r].len; i++) {
+            int dmin = stats->depth_valid[i], dmax = stats->depth_valid[i], j;
+            double dmid = (dmin + dmax)/2.0;
+            double low  = dmid*(1-args->depth_bin);
+            double high = dmid*(1+args->depth_bin);
+            for (j = i+1; j < amps[r].len; j++) {
+                int d = stats->depth_valid[j];
+                if (d < low || d > high)
+                    break;
+                if (dmin > d) {
+                    dmin = d;
+                    dmid = (dmin + dmax)/2.0;
+                    low  = dmid*(1-args->depth_bin);
+                    high = dmid*(1+args->depth_bin);
+                } else if (dmax < d) {
+                    dmax = d;
+                    dmid = (dmin + dmax)/2.0;
+                    low  = dmid*(1-args->depth_bin);
+                    high = dmid*(1+args->depth_bin);
+                }
+            }
+            fprintf(ofp, "\t%d,%d", (int)dmid, j-i);
+            i = j-1;
+        }
+        fprintf(ofp, "\n");
+    }
+
+    // TCOORD (start to end) distribution
+    fprintf(ofp, "# Distribution of aligned template coordinates.\n");
+    fprintf(ofp, "# Use 'grep ^%cTCOORD | cut -f 2-' to extract this part.\n", type);
+    for (r = 0; r < nref; r++) {
+        if (!amps[r].sites)
+            continue;
+        astats_t *stats = local ? amps[r].lstats : amps[r].gstats;
+        for (i = 0 - (nref==1); i < amps[r].namp; i++) {
+            if (ntcoord < kh_size(stats->tcoord[i+1])) {
+                ntcoord = kh_size(stats->tcoord[i+1]);
+                tcoord_t *tmp = realloc(tpos, ntcoord * sizeof(*tmp));
+                if (!tmp) {
+                    free(tpos);
+                    return -1;
+                }
+                tpos = tmp;
+            }
+
+            khiter_t k;
+            size_t n = 0, j;
+            for (k = kh_begin(stats->tcoord[i+1]);
+                 k != kh_end(stats->tcoord[i+1]); k++) {
+                if (!kh_exist(stats->tcoord[i+1], k) ||
+                    (kh_value(stats->tcoord[i+1], k) & 0xFFFFFFFF) == 0)
+                    continue;
+                // Key is start,end in 32-bit quantities.
+                // Yes this limits us to 4Gb references, but just how
+                // many primers are we planning on making?  Not that many
+                // I hope.
+                tpos[n].start = kh_key(stats->tcoord[i+1], k)&0xffffffff;
+                tpos[n].end   = kh_key(stats->tcoord[i+1], k)>>32;
+
+                // Value is frequency (top 32-bits) and status (bottom 32).
+                tpos[n].freq   = kh_value(stats->tcoord[i+1], k)&0xffffffff;
+                tpos[n].status = kh_value(stats->tcoord[i+1], k)>>32;
+                n++;
+            }
+
+            if (args->tcoord_bin > 1)
+                aggregate_tcoord(args, tpos, &n);
+
+            fprintf(ofp, "%cTCOORD\t%s\t%d", type, name,
+                    i+1+amps[r].first_amp); // per amplicon
+            for (j = 0; j < n; j++) {
+                if (tpos[j].freq < args->tcoord_min_count)
+                    continue;
+                fprintf(ofp, "\t%d,%d,%u,%u",
+                        tpos[j].start,
+                        tpos[j].end,
+                        tpos[j].freq,
+                        tpos[j].status);
+            }
+            fprintf(ofp, "\n");
+        }
+    }
+
+
+    // AMP length distribution.
+    // 0 = both ends in this amplicon
+    // 1 = ends in different amplicons
+    // 2 = other end matching an unknown amplicon site
+    //     (see tcoord for further analysis of where)
+    fprintf(ofp, "# Classification of amplicon status.  Columns are\n");
+    fprintf(ofp, "# number with both primers from this amplicon, number with\n");
+    fprintf(ofp, "# primers from different amplicon, and number with a position\n");
+    fprintf(ofp, "# not matching any valid amplicon primer site\n");
+    fprintf(ofp, "# Use 'grep ^%cAMP | cut -f 2-' to extract this part.\n", type);
+
+    fprintf(ofp, "%cAMP\t%s\t0", type, name); // all merged
+    int amp_dist[3] = {0};
+    for (r = 0; r < nref; r++) {
+        if (!amps[r].sites)
+            continue;
+        astats_t *stats = local ? amps[r].lstats : amps[r].gstats;
+        for (i = 0; i < amps[r].namp; i++) { // accumulate for all amps
+            amp_dist[0] += stats->amp_dist[i][0];
+            amp_dist[1] += stats->amp_dist[i][1];
+            amp_dist[2] += stats->amp_dist[i][2];
+        }
+    }
+    fprintf(ofp, "\t%d\t%d\t%d\n", amp_dist[0], amp_dist[1], amp_dist[2]);
+
+    for (r = 0; r < nref; r++) {
+        if (!amps[r].sites)
+            continue;
+        astats_t *stats = local ? amps[r].lstats : amps[r].gstats;
+        for (i = 0; i < amps[r].namp; i++) {
+            // per amplicon
+            fprintf(ofp, "%cAMP\t%s\t%d", type, name, i+1+amps[r].first_amp);
+            fprintf(ofp, "\t%d\t%d\t%d\n", stats->amp_dist[i][0],
+                    stats->amp_dist[i][1], stats->amp_dist[i][2]);
+        }
+    }
+
+    free(tpos);
+    return 0;
+}
+
+int dump_lstats(astats_args_t *args, char type, char *name, int nfile,
+               amplicons_t *amps, int nref) {
+    return dump_stats(args, type, name, nfile, amps, nref, 1);
+}
+
+int dump_gstats(astats_args_t *args, char type, char *name, int nfile,
+               amplicons_t *amps, int nref) {
+    return dump_stats(args, type, name, nfile, amps, nref, 0);
+}
+
+char const *get_sample_name(sam_hdr_t *header, char *RG) {
+    kstring_t ks = {0};
+    sam_hdr_find_tag_id(header, "RG", RG?"ID":NULL, RG, "SM", &ks);
+    return ks.s;
+}
+
+// Return maximum reference length (SQ is NULL) or the length
+// of the specified reference in SQ.
+int64_t get_ref_len(sam_hdr_t *header, const char *SQ) {
+    if (SQ) {
+        int tid = SQ ? sam_hdr_name2tid(header, SQ) : 0;
+        return tid >= 0 ? sam_hdr_tid2len(header, tid) : -1;
+    } else {
+        int nref = sam_hdr_nref(header), tid;;
+        int64_t len = 0;
+        for (tid = 0; tid < nref; tid++) {
+            int64_t rl = sam_hdr_tid2len(header, tid);
+            if (len < rl)
+                len = rl;
+        }
+        return len;
+    }
+}
+
+static int amplicon_stats(astats_args_t *args,
+                          khash_t(bed_list_hash) *bed_hash,
+                          char **filev, int filec) {
+    int i, ref = -1, ref_tid = -1, ret = -1, nref = 0;
+    samFile *fp = NULL;
+    sam_hdr_t *header = NULL;
+    bam1_t *b = bam_init1();
+    FILE *ofp = args->out_fp;
+    char sname_[8192], *sname = NULL;
+    amplicons_t *amps = NULL;
+
+    // Report initial SS header.  We gather data from the bed_hash entries
+    // as well as from the first SAM header (with the requirement that all
+    // headers should be compatible).
+    if (filec) {
+        if (!(fp = sam_open_format(filev[0], "r", &args->ga.in))) {
+            print_error_errno("ampliconstats",
+                              "Cannot open input file \"%s\"",
+                              filev[0]);
+            goto err;
+        }
+        if (!(header = sam_hdr_read(fp)))
+            goto err;
+
+        if (!amps) {
+            amps = calloc(nref=sam_hdr_nref(header), sizeof(*amps));
+            if (!amps)
+                goto err;
+            fprintf(ofp, "# Summary statistics, used for scaling the plots.\n");
+            fprintf(ofp, "SS\tSamtools version: %s\n", samtools_version());
+            fprintf(ofp, "SS\tCommand line: %s\n", args->argv);
+            fprintf(ofp, "SS\tNumber of files:\t%d\n", filec);
+
+            // Note: order of hash entries will be different to order of
+            // BED file which may also differ to order of SQ headers.
+            // SQ header is canonical ordering (pos sorted file).
+            khiter_t k;
+            int bam_nref = sam_hdr_nref(header);
+            for (i = 0; i < bam_nref; i++) {
+                k = kh_get(bed_list_hash, bed_hash,
+                           sam_hdr_tid2name(header, i));
+                if (!kh_exist(bed_hash, k))
+                    continue;
+
+                bed_entry_list_t *sites = &kh_value(bed_hash, k);
+
+                ref = i;
+                amps[ref].ref = kh_key(bed_hash, k);
+                amps[ref].sites = sites;
+                amps[ref].namp = count_amplicon(sites);
+                amps[ref].amp  = calloc(sites->length,
+                                        sizeof(*amps[ref].amp));
+                if (!amps[ref].amp)
+                    goto err;
+                if (args->multi_ref)
+                    fprintf(ofp, "SS\tNumber of amplicons:\t%s\t%d\n",
+                            kh_key(bed_hash, k), amps[ref].namp);
+                else
+                    fprintf(ofp, "SS\tNumber of amplicons:\t%d\n",
+                            amps[ref].namp);
+
+                amps[ref].tid = ref;
+                if (ref_tid == -1)
+                    ref_tid = ref;
+
+                int64_t len = get_ref_len(header, kh_key(bed_hash, k));
+                amps[ref].len = len;
+                if (args->multi_ref)
+                    fprintf(ofp, "SS\tReference length:\t%s\t%"PRId64"\n",
+                            kh_key(bed_hash, k), len);
+                else
+                    fprintf(ofp, "SS\tReference length:\t%"PRId64"\n",
+                            len);
+
+                amps[ref].lstats = stats_alloc(len, args->max_amp,
+                                               args->max_amp_len);
+                amps[ref].gstats = stats_alloc(len, args->max_amp,
+                                               args->max_amp_len);
+                if (!amps[ref].lstats || !amps[ref].gstats)
+                    goto err;
+            }
+        }
+
+        sam_hdr_destroy(header);
+        header = NULL;
+        if (sam_close(fp) < 0) {
+            fp = NULL;
+            goto err;
+        }
+        fp = NULL;
+    }
+    fprintf(ofp, "SS\tEnd of summary\n");
+
+    // Extract the bits of amplicon data we need from bed hash and turn
+    // it into a position-to-amplicon lookup table.
+    int offset = 0;
+    for (i = 0; i < nref; i++) {
+        if (!amps[i].sites)
+            continue;
+
+        amps[i].first_amp = offset;
+        if (bed2amplicon(args, amps[i].sites, amps[i].amp,
+                         &amps[i].namp, i==0, amps[i].ref, offset) < 0)
+            goto err;
+
+        offset += amps[i].namp; // cumulative amplicon number across refs
+    }
+
+    // Now iterate over file contents, one at a time.
+    for (i = 0; i < filec; i++) {
+        char *nstart = filev[i];
+
+        fp = sam_open_format(filev[i], "r", &args->ga.in);
+        if (!fp) {
+            print_error_errno("ampliconstats",
+                              "Cannot open input file \"%s\"",
+                              filev[i]);
+            goto err;
+        }
+
+        if (args->ga.nthreads > 0)
+            hts_set_threads(fp, args->ga.nthreads);
+
+        if (!(header = sam_hdr_read(fp)))
+            goto err;
+
+        if (nref != sam_hdr_nref(header)) {
+            print_error_errno("ampliconstats",
+                              "SAM headers are not consistent across input files");
+            goto err;
+        }
+        int r;
+        for (r = 0; r < nref; r++) {
+            if (!amps[r].ref ||
+                strcmp(amps[r].ref, sam_hdr_tid2name(header, r)) != 0 ||
+                amps[r].len != sam_hdr_tid2len(header, r)) {
+                print_error_errno("ampliconstats",
+                                  "SAM headers are not consistent across "
+                                  "input files");
+                goto err;
+            }
+        }
+
+        if (args->use_sample_name)
+            sname = (char *)get_sample_name(header, NULL);
+
+        if (!sname) {
+            sname = sname_;
+            char *nend = filev[i] + strlen(filev[i]), *cp;
+            if ((cp = strrchr(filev[i], '/')))
+                nstart = cp+1;
+            if ((cp = strrchr(nstart, '.')) &&
+                (strcmp(cp, ".bam") == 0 ||
+                 strcmp(cp, ".sam") == 0 ||
+                 strcmp(cp, ".cram") == 0))
+                nend = cp;
+            if (nend - nstart >= 8192) nend = nstart+8191;
+            memcpy(sname, nstart, nend-nstart);
+            sname[nend-nstart] = 0;
+        }
+
+        // Stats local to this sample only
+        amp_stats_reset(amps, nref);
+
+        int last_ref = -9;
+        while ((r = sam_read1(fp, header, b)) >= 0) {
+            // Other filter options useful here?
+            if (b->core.tid < 0)
+                continue;
+
+            if (last_ref != b->core.tid) {
+                last_ref  = b->core.tid;
+                if (initialise_amp_pos_lookup(args, amps, last_ref) < 0)
+                    goto err;
+            }
+
+            if (accumulate_stats(args, amps, b) < 0)
+                goto err;
+        }
+
+        if (r < -1) {
+            print_error_errno("ampliconstats", "Fail reading record");
+            goto err;
+        }
+
+        sam_hdr_destroy(header);
+        if (sam_close(fp) < 0) {
+            fp = NULL;
+            goto err;
+        }
+
+        fp = NULL;
+        header = NULL;
+
+        if (dump_lstats(args, 'F', sname, filec, amps, nref) < 0)
+            goto err;
+
+        if (append_stats(amps, nref) < 0)
+            goto err;
+
+        if (sname && sname != sname_)
+            free(sname);
+        sname = NULL;
+    }
+
+    if (dump_gstats(args, 'C', "COMBINED", filec, amps, nref) < 0)
+        goto err;
+
+    ret = 0;
+ err:
+    bam_destroy1(b);
+    if (ret) {
+        if (header)
+            sam_hdr_destroy(header);
+        if (fp)
+            sam_close(fp);
+    }
+    for (i = 0; i < nref; i++) {
+        stats_free(amps[i].lstats);
+        stats_free(amps[i].gstats);
+        free(amps[i].amp);
+    }
+    free(amps);
+    free(pos2start);
+    free(pos2end);
+    if (ret) {
+        if (sname && sname != sname_)
+            free(sname);
+    }
+
+    return ret;
+}
+
+static int usage(astats_args_t *args, FILE *fp, int exit_status) {
+    fprintf(fp,
+"\n"
+"Usage: samtools ampliconstats [options] primers.bed *.bam > astats.txt\n"
+"\n"
+"Options:\n");
+    fprintf(fp, "  -f, --required-flag STR|INT\n"
+            "               Only include reads with all of the FLAGs present [0x%X]\n",args->flag_require);
+    fprintf(fp, "  -F, --filter-flag STR|INT\n"
+            "               Only include reads with none of the FLAGs present [0x%X]\n",args->flag_filter & 0xffff);
+    fprintf(fp, "  -a, --max-amplicons INT\n"
+            "               Change the maximum number of amplicons permitted [%d]\n", MAX_AMP);
+    fprintf(fp, "  -l, --max-amplicon-length INT\n"
+            "               Change the maximum length of an individual amplicon [%d]\n", MAX_AMP_LEN);
+    fprintf(fp, "  -d, --min-depth INT[,INT]...\n"
+            "               Minimum base depth(s) to consider position covered [%d]\n", args->min_depth[0]);
+    fprintf(fp, "  -m, --pos-margin INT\n"
+            "               Margin of error for matching primer positions [%d]\n", args->max_delta);
+    fprintf(fp, "  -o, --output FILE\n"
+            "               Specify output file [samtools_stdout if unset]\n");
+    fprintf(fp, "  -s, --use-sample-name\n"
+            "               Use the sample name from the first @RG header line\n");
+    fprintf(fp, "  -t, --tlen-adjust INT\n"
+            "               Add/subtract from TLEN; use when clipping but no fixmate step\n");
+    fprintf(fp, "  -b, --tcoord-bin INT\n"
+            "               Bin template start,end positions into multiples of INT[1]\n");
+    fprintf(fp, "  -c, --tcoord-min-count INT\n"
+            "               Minimum template start,end frequency for recording [%d]\n", TCOORD_MIN_COUNT);
+    fprintf(fp, "  -D, --depth-bin FRACTION\n"
+            "               Merge FDP values within +/- FRACTION together\n");
+    fprintf(fp, "  -S, --single-ref\n"
+            "               Force single-ref (<=1.12) output format\n");
+    sam_global_opt_help(fp, "I.--.@");
+
+    return exit_status;
+}
+
+int main_ampliconstats(int argc, char **argv) {
+    astats_args_t args = {
+        .ga = SAM_GLOBAL_ARGS_INIT,
+        .flag_require = 0,
+        .flag_filter = 0x10B04,
+        //.sites = BED_LIST_INIT,
+        .max_delta = 30, // large enough to cope with alt primers
+        .min_depth = {1},
+        .use_sample_name = 0,
+        .max_amp = MAX_AMP,
+        .max_amp_len = MAX_AMP_LEN,
+        .tlen_adj = 0,
+        .out_fp = samtools_stdout,
+        .tcoord_min_count = TCOORD_MIN_COUNT,
+        .tcoord_bin = 1,
+        .depth_bin = 0.01,
+        .multi_ref = 1
+    }, oargs = args;
+
+    static const struct option loptions[] =
+    {
+        SAM_OPT_GLOBAL_OPTIONS('I', 0, '-', '-', 0, '@'),
+        {"help", no_argument, NULL, 'h'},
+        {"flag-require", required_argument, NULL, 'f'},
+        {"flag-filter", required_argument, NULL, 'F'},
+        {"min-depth", required_argument, NULL, 'd'},
+        {"output", required_argument, NULL, 'o'},
+        {"pos-margin", required_argument, NULL, 'm'},
+        {"use-sample-name", no_argument, NULL, 's'},
+        {"max-amplicons", required_argument, NULL, 'a'},
+        {"max-amplicon-length", required_argument, NULL, 'l'},
+        {"tlen-adjust", required_argument, NULL, 't'},
+        {"tcoord-min-count", required_argument, NULL, 'c'},
+        {"tcoord-bin", required_argument, NULL, 'b'},
+        {"depth-bin", required_argument, NULL, 'D'},
+        {"single-ref", no_argument, NULL, 'S'},
+        {NULL, 0, NULL, 0}
+    };
+    int opt;
+
+    while ( (opt=getopt_long(argc,argv,"?hf:F:@:p:m:d:sa:l:t:o:c:b:D:S",loptions,NULL))>0 ) {
+        switch (opt) {
+        case 'f': args.flag_require = bam_str2flag(optarg); break;
+        case 'F':
+            if (args.flag_filter & 0x10000)
+                args.flag_filter = 0; // strip default on first -F usage
+            args.flag_filter |= bam_str2flag(optarg); break;
+
+        case 'm': args.max_delta = atoi(optarg); break; // margin
+        case 'D': args.depth_bin = atof(optarg); break; // depth bin fraction
+        case 'd': {
+            int d = 0;
+            char *cp = optarg, *ep;
+            do {
+                long n = strtol(cp, &ep, 10);
+                args.min_depth[d++] = n;
+                if (*ep != ',')
+                    break;
+                cp = ep+1;
+            } while (d < MAX_DEPTH);
+            break;
+        }
+
+        case 'a': args.max_amp = atoi(optarg)+1;break;
+        case 'l': args.max_amp_len = atoi(optarg)+1;break;
+
+        case 'c': args.tcoord_min_count = atoi(optarg);break;
+        case 'b':
+            args.tcoord_bin = atoi(optarg);
+            if (args.tcoord_bin < 1)
+                args.tcoord_bin = 1;
+            break;
+
+        case 't': args.tlen_adj = atoi(optarg);break;
+
+        case 's': args.use_sample_name = 1;break;
+
+        case 'o':
+            if (!(args.out_fp = fopen(optarg, "w"))) {
+                perror(optarg);
+                return 1;
+            }
+            break;
+
+        case 'S':
+            args.multi_ref = 0;
+            break;
+
+        case '?': return usage(&oargs, samtools_stderr, EXIT_FAILURE);
+        case 'h': return usage(&oargs, samtools_stdout, EXIT_SUCCESS);
+
+        default:
+            if (parse_sam_global_opt(opt, optarg, loptions, &args.ga) != 0)
+                usage(&oargs,samtools_stderr, EXIT_FAILURE);
+            break;
+        }
+    }
+
+    if (argc <= optind)
+        return usage(&oargs, samtools_stdout, EXIT_SUCCESS);
+    if (argc <= optind+1 && isatty(STDIN_FILENO))
+        return usage(&oargs, samtools_stderr, EXIT_FAILURE);
+
+    khash_t(bed_list_hash) *bed_hash = kh_init(bed_list_hash);
+    if (load_bed_file_multi_ref(argv[optind], 1, 0, bed_hash)) {
+        print_error_errno("ampliconstats",
+                          "Could not read file \"%s\"", argv[optind]);
+        return 1;
+
+    }
+
+    khiter_t k, ref_count = 0;
+    for (k = kh_begin(bed_hash); k != kh_end(bed_hash); k++) {
+        if (!kh_exist(bed_hash, k))
+            continue;
+        ref_count++;
+    }
+    if (ref_count == 0)
+        return 1;
+    if (ref_count > 1 && args.multi_ref == 0) {
+        print_error("ampliconstats",
+                    "Single-ref mode is not permitted for BED files\n"
+                    "containing more than one reference.");
+        return 1;
+    }
+
+    args.argv = stringify_argv(argc, argv);
+    int ret;
+    if (argc == ++optind) {
+        char *av = "-";
+        ret = amplicon_stats(&args, bed_hash, &av, 1);
+    } else {
+        ret = amplicon_stats(&args, bed_hash, &argv[optind], argc-optind);
+    }
+
+    free(args.argv);
+    destroy_bed_hash(bed_hash);
+
+    return ret;
+}
diff --git a/samtools/bam.c b/samtools/bam.c
new file mode 100644
index 0000000..f847f89
--- /dev/null
+++ b/samtools/bam.c
@@ -0,0 +1,267 @@
+/*  bam.c -- miscellaneous BAM functions.
+
+    Copyright (C) 2008-2013, 2015, 2019-2020, 2022 Genome Research Ltd.
+    Portions copyright (C) 2009-2012 Broad Institute.
+
+    Author: Heng Li <lh3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <config.h>
+
+#include <stdio.h>
+#include <ctype.h>
+#include <errno.h>
+#include "bam.h"
+#include "htslib/kstring.h"
+
+// FIXME: we should also check the LB tag associated with each alignment
+const char *bam_get_library(sam_hdr_t *h, const bam1_t *b)
+{
+    const char *rg;
+    kstring_t lib = { 0, 0, NULL };
+    rg = (char *)bam_aux_get(b, "RG");
+
+    if (!rg)
+        return NULL;
+    else
+        rg++;
+
+    if (sam_hdr_find_tag_id(h, "RG", "ID", rg, "LB", &lib)  < 0)
+        return NULL;
+
+    static char LB_text[1024];
+    int len = lib.l < sizeof(LB_text) - 1 ? lib.l : sizeof(LB_text) - 1;
+
+    memcpy(LB_text, lib.s, len);
+    LB_text[len] = 0;
+
+    free(lib.s);
+
+    return LB_text;
+}
+
+/************
+ * Remove B *
+ ************/
+
+#define bam1_seq_seti(s, i, c) ( (s)[(i)>>1] = ((s)[(i)>>1] & 0xf<<(((i)&1)<<2)) | (c)<<((~(i)&1)<<2) )
+
+int bam_remove_B(bam1_t *b)
+{
+    int i, j, end_j, k, l, no_qual;
+    uint32_t *cigar, *new_cigar;
+    uint8_t *seq, *qual, *p;
+    // test if removal is necessary
+    if (b->core.flag & BAM_FUNMAP) return 0; // unmapped; do nothing
+    cigar = bam_get_cigar(b);
+    for (k = 0; k < b->core.n_cigar; ++k)
+        if (bam_cigar_op(cigar[k]) == BAM_CBACK) break;
+    if (k == b->core.n_cigar) return 0; // no 'B'
+    if (bam_cigar_op(cigar[0]) == BAM_CBACK) goto rmB_err; // cannot be removed
+    // allocate memory for the new CIGAR
+    if (b->l_data + (b->core.n_cigar + 1) * 4 > b->m_data) { // not enough memory
+        b->m_data = b->l_data + b->core.n_cigar * 4;
+        kroundup32(b->m_data);
+        b->data = (uint8_t*)realloc(b->data, b->m_data);
+        cigar = bam_get_cigar(b); // after realloc, cigar may be changed
+    }
+    new_cigar = (uint32_t*)(b->data + (b->m_data - b->core.n_cigar * 4)); // from the end of b->data
+    // the core loop
+    seq = bam_get_seq(b); qual = bam_get_qual(b);
+    no_qual = (qual[0] == 0xff); // test whether base quality is available
+    i = j = 0; end_j = -1;
+    for (k = l = 0; k < b->core.n_cigar; ++k) {
+        int op  = bam_cigar_op(cigar[k]);
+        int len = bam_cigar_oplen(cigar[k]);
+        if (op == BAM_CBACK) { // the backward operation
+            int t, u;
+            if (k == b->core.n_cigar - 1) break; // ignore 'B' at the end of CIGAR
+            if (len > j) goto rmB_err; // an excessively long backward
+            for (t = l - 1, u = 0; t >= 0; --t) { // look back
+                int op1  = bam_cigar_op(new_cigar[t]);
+                int len1 = bam_cigar_oplen(new_cigar[t]);
+                if (bam_cigar_type(op1)&1) { // consume the query
+                    if (u + len1 >= len) { // stop
+                        new_cigar[t] -= (len - u) << BAM_CIGAR_SHIFT;
+                        break;
+                    } else u += len1;
+                }
+            }
+            if (bam_cigar_oplen(new_cigar[t]) == 0) --t; // squeeze out the zero-length operation
+            l = t + 1;
+            end_j = j; j -= len;
+        } else { // other CIGAR operations
+            new_cigar[l++] = cigar[k];
+            if (bam_cigar_type(op)&1) { // consume the query
+                if (i != j) { // no need to copy if i == j
+                    int u, c, c0;
+                    for (u = 0; u < len; ++u) { // construct the consensus
+                        c = bam_seqi(seq, i+u);
+                        if (j + u < end_j) { // in an overlap
+                            c0 = bam_seqi(seq, j+u);
+                            if (c != c0) { // a mismatch; choose the better base
+                                if (qual[j+u] < qual[i+u]) { // the base in the 2nd segment is better
+                                    bam1_seq_seti(seq, j+u, c);
+                                    qual[j+u] = qual[i+u] - qual[j+u];
+                                } else qual[j+u] -= qual[i+u]; // the 1st is better; reduce base quality
+                            } else qual[j+u] = qual[j+u] > qual[i+u]? qual[j+u] : qual[i+u];
+                        } else { // not in an overlap; copy over
+                            bam1_seq_seti(seq, j+u, c);
+                            qual[j+u] = qual[i+u];
+                        }
+                    }
+                }
+                i += len, j += len;
+            }
+        }
+    }
+    if (no_qual) qual[0] = 0xff; // in very rare cases, this may be modified
+    // merge adjacent operations if possible
+    for (k = 1; k < l; ++k)
+        if (bam_cigar_op(new_cigar[k]) == bam_cigar_op(new_cigar[k-1]))
+            new_cigar[k] += new_cigar[k-1] >> BAM_CIGAR_SHIFT << BAM_CIGAR_SHIFT, new_cigar[k-1] &= 0xf;
+    // kill zero length operations
+    for (k = i = 0; k < l; ++k)
+        if (new_cigar[k] >> BAM_CIGAR_SHIFT)
+            new_cigar[i++] = new_cigar[k];
+    l = i;
+    // update b
+    memcpy(cigar, new_cigar, l * 4); // set CIGAR
+    p = b->data + b->core.l_qname + l * 4;
+    memmove(p, seq, (j+1)>>1); p += (j+1)>>1; // set SEQ
+    memmove(p, qual, j); p += j; // set QUAL
+    memmove(p, bam_get_aux(b), bam_get_l_aux(b)); p += bam_get_l_aux(b); // set optional fields
+    b->core.n_cigar = l, b->core.l_qseq = j; // update CIGAR length and query length
+    b->l_data = p - b->data; // update record length
+    return 0;
+
+rmB_err:
+    b->core.flag |= BAM_FUNMAP;
+    return -1;
+}
+
+/* Calculate the current read's start based on the stored cigar string. */
+hts_pos_t unclipped_start(bam1_t *b) {
+    uint32_t *cigar = bam_get_cigar(b);
+    int64_t clipped = 0;
+    uint32_t i;
+
+    for (i = 0; i < b->core.n_cigar; i++) {
+        char c = bam_cigar_opchr(cigar[i]);
+
+        if (c == 'S' || c == 'H') { // clips
+            clipped += bam_cigar_oplen(cigar[i]);
+        } else {
+            break;
+        }
+    }
+
+    return b->core.pos - clipped + 1;
+}
+
+/* Calculate the mate's unclipped start based on position and cigar string from MC tag. */
+hts_pos_t unclipped_other_start(hts_pos_t op, char *cigar) {
+    char *c = cigar;
+    int64_t clipped = 0;
+
+    while (*c && *c != '*') {
+        long num = 0;
+
+        if (isdigit((int)*c)) {
+            num = strtol(c, &c, 10);
+        } else {
+            num = 1;
+        }
+
+        if (*c == 'S' || *c == 'H') { // clips
+            clipped += num;
+        } else {
+            break;
+        }
+
+        c++;
+    }
+
+    return op - clipped + 1;
+}
+
+/* Calculate the current read's end based on the stored cigar string. */
+hts_pos_t unclipped_end(bam1_t *b) {
+    uint32_t *cigar = bam_get_cigar(b);
+    hts_pos_t end_pos, clipped = 0;
+    int32_t i;
+
+    end_pos = bam_endpos(b);
+
+    // now get the clipped end bases (if any)
+    // if we get to the beginning of the cigar string
+    // without hitting a non-clip then the results are meaningless
+    for (i = b->core.n_cigar - 1; i >= 0; i--) {
+        char c = bam_cigar_opchr(cigar[i]);
+
+        if (c == 'S' || c == 'H') { // clips
+            clipped += bam_cigar_oplen(cigar[i]);
+        } else {
+            break;
+        }
+    }
+
+    return end_pos + clipped;
+}
+
+
+/* Calculate the mate's unclipped end based on start position and cigar string from MC tag.*/
+hts_pos_t unclipped_other_end(int64_t op, char *cigar) {
+    char *c = cigar;
+    int64_t refpos = 0;
+    int skip = 1;
+
+    while (*c && *c != '*') {
+        long num = 0;
+
+        if (isdigit((int)*c)) {
+            num = strtol(c, &c, 10);
+        } else {
+            num = 1;
+        }
+
+        switch (*c) {
+            case 'M':
+            case 'D':
+            case 'N':
+            case '=':
+            case 'X':
+                refpos += num;
+                skip = 0; // ignore initial clips
+            break;
+
+            case 'S':
+            case 'H':
+                if (!skip) {
+                refpos += num;
+            }
+            break;
+        }
+
+        c++;
+   }
+
+    return  op + refpos;
+}
diff --git a/samtools/bam.c.pysam.c b/samtools/bam.c.pysam.c
new file mode 100644
index 0000000..4f235ed
--- /dev/null
+++ b/samtools/bam.c.pysam.c
@@ -0,0 +1,269 @@
+#include "samtools.pysam.h"
+
+/*  bam.c -- miscellaneous BAM functions.
+
+    Copyright (C) 2008-2013, 2015, 2019-2020, 2022 Genome Research Ltd.
+    Portions copyright (C) 2009-2012 Broad Institute.
+
+    Author: Heng Li <lh3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <config.h>
+
+#include <stdio.h>
+#include <ctype.h>
+#include <errno.h>
+#include "bam.h"
+#include "htslib/kstring.h"
+
+// FIXME: we should also check the LB tag associated with each alignment
+const char *bam_get_library(sam_hdr_t *h, const bam1_t *b)
+{
+    const char *rg;
+    kstring_t lib = { 0, 0, NULL };
+    rg = (char *)bam_aux_get(b, "RG");
+
+    if (!rg)
+        return NULL;
+    else
+        rg++;
+
+    if (sam_hdr_find_tag_id(h, "RG", "ID", rg, "LB", &lib)  < 0)
+        return NULL;
+
+    static char LB_text[1024];
+    int len = lib.l < sizeof(LB_text) - 1 ? lib.l : sizeof(LB_text) - 1;
+
+    memcpy(LB_text, lib.s, len);
+    LB_text[len] = 0;
+
+    free(lib.s);
+
+    return LB_text;
+}
+
+/************
+ * Remove B *
+ ************/
+
+#define bam1_seq_seti(s, i, c) ( (s)[(i)>>1] = ((s)[(i)>>1] & 0xf<<(((i)&1)<<2)) | (c)<<((~(i)&1)<<2) )
+
+int bam_remove_B(bam1_t *b)
+{
+    int i, j, end_j, k, l, no_qual;
+    uint32_t *cigar, *new_cigar;
+    uint8_t *seq, *qual, *p;
+    // test if removal is necessary
+    if (b->core.flag & BAM_FUNMAP) return 0; // unmapped; do nothing
+    cigar = bam_get_cigar(b);
+    for (k = 0; k < b->core.n_cigar; ++k)
+        if (bam_cigar_op(cigar[k]) == BAM_CBACK) break;
+    if (k == b->core.n_cigar) return 0; // no 'B'
+    if (bam_cigar_op(cigar[0]) == BAM_CBACK) goto rmB_err; // cannot be removed
+    // allocate memory for the new CIGAR
+    if (b->l_data + (b->core.n_cigar + 1) * 4 > b->m_data) { // not enough memory
+        b->m_data = b->l_data + b->core.n_cigar * 4;
+        kroundup32(b->m_data);
+        b->data = (uint8_t*)realloc(b->data, b->m_data);
+        cigar = bam_get_cigar(b); // after realloc, cigar may be changed
+    }
+    new_cigar = (uint32_t*)(b->data + (b->m_data - b->core.n_cigar * 4)); // from the end of b->data
+    // the core loop
+    seq = bam_get_seq(b); qual = bam_get_qual(b);
+    no_qual = (qual[0] == 0xff); // test whether base quality is available
+    i = j = 0; end_j = -1;
+    for (k = l = 0; k < b->core.n_cigar; ++k) {
+        int op  = bam_cigar_op(cigar[k]);
+        int len = bam_cigar_oplen(cigar[k]);
+        if (op == BAM_CBACK) { // the backward operation
+            int t, u;
+            if (k == b->core.n_cigar - 1) break; // ignore 'B' at the end of CIGAR
+            if (len > j) goto rmB_err; // an excessively long backward
+            for (t = l - 1, u = 0; t >= 0; --t) { // look back
+                int op1  = bam_cigar_op(new_cigar[t]);
+                int len1 = bam_cigar_oplen(new_cigar[t]);
+                if (bam_cigar_type(op1)&1) { // consume the query
+                    if (u + len1 >= len) { // stop
+                        new_cigar[t] -= (len - u) << BAM_CIGAR_SHIFT;
+                        break;
+                    } else u += len1;
+                }
+            }
+            if (bam_cigar_oplen(new_cigar[t]) == 0) --t; // squeeze out the zero-length operation
+            l = t + 1;
+            end_j = j; j -= len;
+        } else { // other CIGAR operations
+            new_cigar[l++] = cigar[k];
+            if (bam_cigar_type(op)&1) { // consume the query
+                if (i != j) { // no need to copy if i == j
+                    int u, c, c0;
+                    for (u = 0; u < len; ++u) { // construct the consensus
+                        c = bam_seqi(seq, i+u);
+                        if (j + u < end_j) { // in an overlap
+                            c0 = bam_seqi(seq, j+u);
+                            if (c != c0) { // a mismatch; choose the better base
+                                if (qual[j+u] < qual[i+u]) { // the base in the 2nd segment is better
+                                    bam1_seq_seti(seq, j+u, c);
+                                    qual[j+u] = qual[i+u] - qual[j+u];
+                                } else qual[j+u] -= qual[i+u]; // the 1st is better; reduce base quality
+                            } else qual[j+u] = qual[j+u] > qual[i+u]? qual[j+u] : qual[i+u];
+                        } else { // not in an overlap; copy over
+                            bam1_seq_seti(seq, j+u, c);
+                            qual[j+u] = qual[i+u];
+                        }
+                    }
+                }
+                i += len, j += len;
+            }
+        }
+    }
+    if (no_qual) qual[0] = 0xff; // in very rare cases, this may be modified
+    // merge adjacent operations if possible
+    for (k = 1; k < l; ++k)
+        if (bam_cigar_op(new_cigar[k]) == bam_cigar_op(new_cigar[k-1]))
+            new_cigar[k] += new_cigar[k-1] >> BAM_CIGAR_SHIFT << BAM_CIGAR_SHIFT, new_cigar[k-1] &= 0xf;
+    // kill zero length operations
+    for (k = i = 0; k < l; ++k)
+        if (new_cigar[k] >> BAM_CIGAR_SHIFT)
+            new_cigar[i++] = new_cigar[k];
+    l = i;
+    // update b
+    memcpy(cigar, new_cigar, l * 4); // set CIGAR
+    p = b->data + b->core.l_qname + l * 4;
+    memmove(p, seq, (j+1)>>1); p += (j+1)>>1; // set SEQ
+    memmove(p, qual, j); p += j; // set QUAL
+    memmove(p, bam_get_aux(b), bam_get_l_aux(b)); p += bam_get_l_aux(b); // set optional fields
+    b->core.n_cigar = l, b->core.l_qseq = j; // update CIGAR length and query length
+    b->l_data = p - b->data; // update record length
+    return 0;
+
+rmB_err:
+    b->core.flag |= BAM_FUNMAP;
+    return -1;
+}
+
+/* Calculate the current read's start based on the stored cigar string. */
+hts_pos_t unclipped_start(bam1_t *b) {
+    uint32_t *cigar = bam_get_cigar(b);
+    int64_t clipped = 0;
+    uint32_t i;
+
+    for (i = 0; i < b->core.n_cigar; i++) {
+        char c = bam_cigar_opchr(cigar[i]);
+
+        if (c == 'S' || c == 'H') { // clips
+            clipped += bam_cigar_oplen(cigar[i]);
+        } else {
+            break;
+        }
+    }
+
+    return b->core.pos - clipped + 1;
+}
+
+/* Calculate the mate's unclipped start based on position and cigar string from MC tag. */
+hts_pos_t unclipped_other_start(hts_pos_t op, char *cigar) {
+    char *c = cigar;
+    int64_t clipped = 0;
+
+    while (*c && *c != '*') {
+        long num = 0;
+
+        if (isdigit((int)*c)) {
+            num = strtol(c, &c, 10);
+        } else {
+            num = 1;
+        }
+
+        if (*c == 'S' || *c == 'H') { // clips
+            clipped += num;
+        } else {
+            break;
+        }
+
+        c++;
+    }
+
+    return op - clipped + 1;
+}
+
+/* Calculate the current read's end based on the stored cigar string. */
+hts_pos_t unclipped_end(bam1_t *b) {
+    uint32_t *cigar = bam_get_cigar(b);
+    hts_pos_t end_pos, clipped = 0;
+    int32_t i;
+
+    end_pos = bam_endpos(b);
+
+    // now get the clipped end bases (if any)
+    // if we get to the beginning of the cigar string
+    // without hitting a non-clip then the results are meaningless
+    for (i = b->core.n_cigar - 1; i >= 0; i--) {
+        char c = bam_cigar_opchr(cigar[i]);
+
+        if (c == 'S' || c == 'H') { // clips
+            clipped += bam_cigar_oplen(cigar[i]);
+        } else {
+            break;
+        }
+    }
+
+    return end_pos + clipped;
+}
+
+
+/* Calculate the mate's unclipped end based on start position and cigar string from MC tag.*/
+hts_pos_t unclipped_other_end(int64_t op, char *cigar) {
+    char *c = cigar;
+    int64_t refpos = 0;
+    int skip = 1;
+
+    while (*c && *c != '*') {
+        long num = 0;
+
+        if (isdigit((int)*c)) {
+            num = strtol(c, &c, 10);
+        } else {
+            num = 1;
+        }
+
+        switch (*c) {
+            case 'M':
+            case 'D':
+            case 'N':
+            case '=':
+            case 'X':
+                refpos += num;
+                skip = 0; // ignore initial clips
+            break;
+
+            case 'S':
+            case 'H':
+                if (!skip) {
+                refpos += num;
+            }
+            break;
+        }
+
+        c++;
+   }
+
+    return  op + refpos;
+}
diff --git a/samtools/bam.h b/samtools/bam.h
new file mode 100644
index 0000000..c0b43d5
--- /dev/null
+++ b/samtools/bam.h
@@ -0,0 +1,39 @@
+/*  bam.h -- miscellaneous BAM functions.
+
+    Copyright (C) 2008-2014, 2019 Genome Research Ltd.
+
+    Author: Heng Li <lh3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#ifndef BAM_BAM_H
+#define BAM_BAM_H
+
+#include "htslib/sam.h"
+
+int bam_remove_B(bam1_t *b);
+
+const char *bam_get_library(sam_hdr_t *header, const bam1_t *b);
+
+hts_pos_t unclipped_start(bam1_t *b);
+hts_pos_t unclipped_other_start(hts_pos_t op, char *cigar);
+hts_pos_t unclipped_end(bam1_t *b);
+hts_pos_t unclipped_other_end(int64_t op, char *cigar);
+
+#endif
diff --git a/samtools/bam2depth.c b/samtools/bam2depth.c
new file mode 100644
index 0000000..098d3ae
--- /dev/null
+++ b/samtools/bam2depth.c
@@ -0,0 +1,973 @@
+/*  bam2depth.c -- depth subcommand.
+
+    Copyright (C) 2011, 2012 Broad Institute.
+    Copyright (C) 2012-2016, 2018, 2019-2022 Genome Research Ltd.
+
+    Author: Heng Li <lh3@sanger.ac.uk> (to 2020)
+    Author: James Bonfield <jkb@sanger.ac.uk> (2021 rewrite)
+
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+/* This program demonstrates how to generate pileup from multiple BAMs
+ * simultaneously, to achieve random access and to use the BED interface.
+ * To compile this program separately, you may:
+ *
+ *   gcc -g -O2 -Wall -o bam2depth -D_MAIN_BAM2DEPTH bam2depth.c -lhts -lz
+ */
+
+#include <config.h>
+
+#include <stdlib.h>
+#include <string.h>
+#include <stdio.h>
+#include <limits.h>
+#include <unistd.h>
+#include "htslib/sam.h"
+#include "samtools.h"
+#include "bedidx.h"
+#include "sam_opts.h"
+#include "htslib/khash.h"
+
+// From bam_plcmd.c
+int read_file_list(const char *file_list, int *n, char **argv[]);
+
+// We accumulate to hist[pos & (size-1)].  This is a ring-buffer.
+// We track where we last got to in output and what the biggest value
+// we've written to so far (in absolute unmasked coordinates) in
+// "last_output" and "end_pos" respectively.
+// For each new record we just flush anything we haven't written yet
+// already, between "last_output" and this read's start position, and
+// initialise any newly seen positions between "end_pos" and this read's
+// end position.
+typedef struct {
+    size_t size;
+    int **hist;         // hist[nfiles][size]
+    hts_pos_t *end_pos; // end_pos[nfiles]
+    hts_pos_t last_output;
+    int last_ref;
+    int nfiles;
+    const char *ref;
+    kstring_t ks;
+    hts_pos_t beg, end; // limit to region
+    int tid;
+} depth_hist;
+
+typedef struct {
+    int header;
+    int flag;
+    int min_qual;
+    int min_mqual;
+    int min_len;
+    int skip_del;
+    int all_pos;
+    int remove_overlaps;
+    FILE *out;
+    char *reg;
+    void *bed;
+} depth_opt;
+
+static void zero_region(depth_opt *opt, depth_hist *dh,
+                        const char *name, hts_pos_t start, hts_pos_t end) {
+    hts_pos_t i;
+    kstring_t *ks = &dh->ks;
+
+    kputs(name, ks_clear(ks));
+    kputc('\t', ks);
+    size_t cur_l = ks->l;
+    if (dh->beg >= 0 && start < dh->beg)
+        start = dh->beg;
+    if (dh->end >= 0 && end > dh->end)
+        end = dh->end;
+
+    for (i = start; i < end; i++) {
+        // Could be optimised, but needs better API to skip to next
+        // bed region.
+        if (opt->bed && bed_overlap(opt->bed, name, i, i+1) == 0)
+            continue;
+
+        ks->l = cur_l;
+        kputll(i+1,  ks);
+        int n;
+        for (n = 0; n < dh->nfiles; n++) {
+            kputc_('\t', ks);
+            kputc_('0',  ks);
+        }
+        kputc('\n',  ks);
+        fputs(ks->s, opt->out);
+    }
+    ks->l = cur_l;
+}
+
+// A variation of bam_cigar2qlen which doesn't count soft-clips in to the
+// equation.  Basically it's the number of bases in query that are aligned
+// in some way to the reference (including insertions, which are considered
+// to be aligned by dint of being anchored either side).
+hts_pos_t qlen_used(bam1_t *b) {
+    int n_cigar = b->core.n_cigar;
+    const uint32_t *cigar = bam_get_cigar(b);
+
+    hts_pos_t l;
+
+    if (b->core.l_qseq) {
+        // Known SEQ permits of short cut of l_qseq minus CSOFT_CLIPs.
+        // Full scan not needed, which helps on excessively long CIGARs.
+        l = b->core.l_qseq;
+        int kl, kr;
+        for (kl = 0; kl < n_cigar; kl++)
+            if (bam_cigar_op(cigar[kl]) == BAM_CSOFT_CLIP)
+                l -= bam_cigar_oplen(cigar[kl]);
+            else
+                break;
+
+        for (kr = n_cigar-1; kr > kl; kr--)
+            if (bam_cigar_op(cigar[kr]) == BAM_CSOFT_CLIP)
+                l -= bam_cigar_oplen(cigar[kr]);
+            else
+                break;
+    } else {
+        // Unknown SEQ ("*") needs a full scan through the CIGAR string.
+        static int query[16] = {
+          //M I D N  S H P =  X B ? ?  ? ? ? ?
+            1,1,0,0, 0,0,0,1, 1,0,0,0, 0,0,0,0
+        };
+        int k;
+        for (k = l = 0; k < n_cigar; k++)
+            if (query[bam_cigar_op(cigar[k])])
+                l += bam_cigar_oplen(cigar[k]);
+    }
+    return l;
+
+}
+
+// Adds the depth for a single read to a depth_hist struct.
+// For just one file, this is easy.  We just have a circular buffer
+// where we increment values for bits that overlap existing data
+// and initialise values for coordinates which we're seeing for the first
+// time.  This is tracked by "end_pos" to know where we've got to.
+//
+// As the input is sorted, we can flush output from "last_output" to
+// b->core.pos.
+//
+// With multiple files, we must feed data in sorted order as if all files
+// are merged, but track depth per file.  This also means "end_pos" is per
+// file too, but "last_output" is global as it corresponds to rows printed.
+static int add_depth(depth_opt *opt, depth_hist *dh, sam_hdr_t *h, bam1_t *b,
+                     int overlap_clip, int file) {
+    hts_pos_t i;
+    size_t hmask = dh->size-1;
+    int n;
+
+    if (!b || b->core.tid != dh->last_ref) {
+        // New ref
+        if (dh->last_ref >= 0) {
+            // do end
+            size_t cur_l = dh->ks.l;
+            int nf = dh->nfiles;
+            i = dh->last_output;
+            for (i = dh->last_output; nf; i++) {
+                nf = 0;
+                for (n = 0; n < dh->nfiles; n++) {
+                    if (i < dh->end_pos[n])
+                        nf++;
+                }
+                if (!nf)
+                    break;
+
+                if (opt->bed && bed_overlap(opt->bed, dh->ref, i, i+1) == 0)
+                    continue;
+
+                dh->ks.l = cur_l;
+                kputll(i+1, &dh->ks);
+                for (n = 0; n < dh->nfiles; n++) {
+                    kputc_('\t', &dh->ks);
+                    int d = i < dh->end_pos[n]
+                        ? dh->hist[n][i & hmask]
+                        : 0;
+                    kputuw(d, &dh->ks);
+                }
+                kputc('\n', &dh->ks);
+                fputs(dh->ks.s, opt->out);
+            }
+            if (opt->all_pos) {
+                // End of last ref
+                zero_region(opt, dh,
+                            sam_hdr_tid2name(h, dh->last_ref),
+                            i, sam_hdr_tid2len(h, dh->last_ref));
+            }
+            dh->ks.l = cur_l;
+        }
+
+        if (opt->all_pos > 1 && !opt->reg) {
+            // Any previous unused refs
+            int lr = dh->last_ref < 0 ? 0 : dh->last_ref+1;
+            int rr = b ? b->core.tid : sam_hdr_nref(h), r;
+            for (r = lr; r < rr; r++)
+                zero_region(opt, dh,
+                            sam_hdr_tid2name(h, r),
+                            0, sam_hdr_tid2len(h, r));
+        }
+
+        if (!b) {
+            // we're just flushing to end of file
+            if (opt->all_pos && opt->reg && dh->last_ref < 0)
+                // -a or -aa without a single read being output yet
+                zero_region(opt, dh, sam_hdr_tid2name(h, dh->tid), dh->beg,
+                            MIN(dh->end, sam_hdr_tid2len(h, dh->tid)));
+
+            return 0;
+        }
+
+        for (n = 0; dh->end_pos && n < dh->nfiles; n++)
+            dh->end_pos[n] = 0;
+        dh->last_output = dh->beg >= 0
+            ? MAX(b->core.pos, dh->beg)
+            : b->core.pos;
+        dh->last_ref = b->core.tid;
+        dh->ref = sam_hdr_tid2name(h, b->core.tid);
+        kputs(dh->ref, ks_clear(&dh->ks));
+        kputc('\t', &dh->ks);
+
+        if (opt->all_pos)
+            // Start of ref
+            zero_region(opt, dh, dh->ref, 0, b->core.pos);
+    } else {
+        if (dh->last_output < b->core.pos) {
+            // Flush any depth outputs up to start of new read
+            size_t cur_l = dh->ks.l;
+            int nf = dh->nfiles;
+            for (i = dh->last_output; i < b->core.pos; i++) {
+                nf = 0;
+                for (n = 0; n < dh->nfiles; n++) {
+                    if (i < dh->end_pos[n])
+                        nf++;
+                }
+                if (!nf)
+                    break;
+
+                if (opt->bed && bed_overlap(opt->bed, dh->ref, i, i+1) == 0)
+                    continue;
+
+                dh->ks.l = cur_l;
+                kputll(i+1, &dh->ks);
+                for (n = 0; n < dh->nfiles; n++) {
+                    kputc_('\t', &dh->ks);
+                    int d = i < dh->end_pos[n]
+                        ? dh->hist[n][i & hmask]
+                        : 0;
+                    kputuw(d, &dh->ks);
+                }
+                kputc('\n', &dh->ks);
+                fputs(dh->ks.s, opt->out);
+            }
+            if (opt->all_pos && i < b->core.pos)
+                // Hole in middle of ref
+                zero_region(opt, dh, dh->ref, i, b->core.pos);
+
+            dh->ks.l = cur_l;
+            dh->last_output = b->core.pos;
+        }
+    }
+
+    hts_pos_t end_pos = bam_endpos(b); // 0 based, 1 past end.
+    //printf("%d %d\n", (int)b->core.pos+1, (int)end_pos);
+
+    if (b->core.tid < dh->last_ref ||
+        (dh->last_ref == b->core.tid && end_pos < dh->last_output)) {
+        print_error_errno("depth", "Data is not position sorted");
+        return -1;
+    }
+
+    // If needed, grow the circular buffer.
+    if (end_pos+1 - b->core.pos >= dh->size) {
+        size_t old_size = dh->size;
+        size_t old_hmask = hmask;
+        while (end_pos+1 - b->core.pos >= dh->size)
+            dh->size = dh->size ? 2*dh->size : 2048;
+        hmask = dh->size-1;
+        if (!dh->hist) {
+            dh->hist = calloc(dh->nfiles, sizeof(*dh->hist));
+            dh->end_pos = calloc(dh->nfiles, sizeof(*dh->end_pos));
+            if (!dh->hist || !dh->end_pos)
+                return -1;
+        }
+        for (n = 0; n < dh->nfiles; n++) {
+            int *hist = calloc(dh->size, sizeof(*dh->hist[n]));
+            if (!hist)
+                return -1;
+
+            // Simple approach for now; copy over old histogram verbatim.
+            for (i = dh->last_output; i < dh->last_output + old_size; i++)
+                hist[i & hmask] = dh->hist[n][i & old_hmask];
+            free(dh->hist[n]);
+            dh->hist[n] = hist;
+        }
+    }
+
+    // Accumulate depth, based on CIGAR
+    uint32_t *cig = bam_get_cigar(b);
+    int ncig = b->core.n_cigar, j, k, spos = 0;
+
+    // Zero new (previously unseen) coordinates so increment works later.
+    hts_pos_t end = MAX(dh->end_pos[file], b->core.pos);
+    if (end_pos > end && (end & hmask) < (end_pos & hmask)) {
+        memset(&dh->hist[file][end & hmask], 0,
+               sizeof(**dh->hist) * (end_pos - end));
+    } else {
+        for (i = end; i < end_pos; i++)
+            dh->hist[file][i & hmask] = 0;
+    }
+
+    i = b->core.pos;
+    uint8_t *qual = bam_get_qual(b);
+    int min_qual = opt->min_qual;
+    for (j = 0; j < ncig; j++) {
+        int op    = bam_cigar_op(cig[j]);
+        int oplen = bam_cigar_oplen(cig[j]);
+
+        switch (op) {
+        case BAM_CDEL:
+        case BAM_CREF_SKIP:
+            if (op != BAM_CDEL || opt->skip_del) {
+                // don't increment reference location
+                if (i + oplen >= dh->end_pos[file]) {
+                    for (k = 0; k < oplen; k++, i++) {
+                        if (i >= dh->end_pos[file])
+                            // redundant due to zero new elements above?
+                            dh->hist[file][i & hmask] = 0;
+                    }
+                } else {
+                    i += oplen;
+                }
+            } else { // op == BAM_CDEL and we count them (-J option),
+                // We don't incr spos here, but we still use qual.
+                // This doesn't make much sense, but it's for compatibility
+                // with the old code.  Arguably DEL shouldn't have a min
+                // qual and should always pass (as we've explicitly asked to
+                // include them).
+                int *hist = dh->hist[file];
+                k = 0;
+                if (overlap_clip) {
+                    if (i+oplen < overlap_clip) {
+                        i += oplen;
+                        break;
+                    } else if (i < overlap_clip) {
+                        k = overlap_clip - i;
+                        i = overlap_clip;
+                    }
+                }
+
+                // Question: should we even check quality values for DEL?
+                // We've explicitly asked to include them, and the quality
+                // is wrong anyway (it's the neighbouring base).  We do this
+                // for now for compatibility with the old depth command.
+
+                if (spos < b->core.l_qseq)
+                    for (; k < oplen; k++, i++)
+                        hist[i & hmask]+=qual[spos]>=min_qual;
+                else
+                    for (; k < oplen; k++, i++)
+                        hist[i & hmask]++;
+            }
+            break;
+
+        case BAM_CMATCH:
+        case BAM_CEQUAL:
+        case BAM_CDIFF:
+            if ((i & hmask) < ((i+oplen) & hmask)) {
+                // Optimisation when not wrapping around
+
+                // Unrolling doesn't help clang, but helps gcc,
+                // especially when not using -O3.
+                int *hist = &dh->hist[file][i & hmask];
+                if (min_qual || overlap_clip) {
+                    k = 0;
+                    if (overlap_clip) {
+                        if (i+oplen < overlap_clip) {
+                            i += oplen;
+                            spos += oplen;
+                            break;
+                        } else if (i < overlap_clip) {
+                            oplen -= overlap_clip - i;
+                            spos += overlap_clip - i;
+                            hist += overlap_clip - i;
+                            i = overlap_clip;
+                        }
+                    }
+
+                    // approx 50% of this func cpu time in this loop
+                    for (; k < (oplen & ~7); k+=8) {
+                        hist[k+0]+=qual[spos+0]>=min_qual;
+                        hist[k+1]+=qual[spos+1]>=min_qual;
+                        hist[k+2]+=qual[spos+2]>=min_qual;
+                        hist[k+3]+=qual[spos+3]>=min_qual;
+                        hist[k+4]+=qual[spos+4]>=min_qual;
+                        hist[k+5]+=qual[spos+5]>=min_qual;
+                        hist[k+6]+=qual[spos+6]>=min_qual;
+                        hist[k+7]+=qual[spos+7]>=min_qual;
+                        spos += 8;
+                    }
+                } else {
+                    // easier to vectorize when no min_qual
+                    for (k = 0; k < (oplen & ~7); k+=8) {
+                        hist[k+0]++;
+                        hist[k+1]++;
+                        hist[k+2]++;
+                        hist[k+3]++;
+                        hist[k+4]++;
+                        hist[k+5]++;
+                        hist[k+6]++;
+                        hist[k+7]++;
+                    }
+                    spos += k;
+                }
+                for (; k < oplen && spos < b->core.l_qseq; k++, spos++)
+                    hist[k]+=qual[spos]>=min_qual;
+                for (; k < oplen; k++, spos++)
+                    hist[k]++;
+                i += oplen;
+            } else {
+                // Simple to understand case, but slower.
+                // We use this only for reads with wrap-around.
+                int *hist = dh->hist[file];
+                k = 0;
+                if (overlap_clip) {
+                    if (i+oplen < overlap_clip) {
+                        i += oplen;
+                        break;
+                    } else if (i < overlap_clip) {
+                        oplen -= overlap_clip - i;
+                        spos += overlap_clip - i;
+                        i = overlap_clip;
+                    }
+                }
+                for (; k < oplen && spos < b->core.l_qseq; k++, i++, spos++)
+                    hist[i & hmask]+=qual[spos]>=min_qual;
+                for (; k < oplen; k++, i++, spos++)
+                    hist[i & hmask]++;
+            }
+            break;
+
+        case BAM_CINS:
+        case BAM_CSOFT_CLIP:
+            spos += oplen;
+            break;
+
+        case BAM_CPAD:
+        case BAM_CHARD_CLIP:
+            // ignore
+            break;
+
+        default:
+            print_error("depth", "Unsupported cigar op '%d'", op);
+            return -1;
+        }
+    }
+
+    if (dh->end >= 0 && end_pos > dh->end)
+        end_pos = dh->end;
+    if (dh->end_pos[file] < end_pos)
+        dh->end_pos[file] = end_pos;
+
+    return 0;
+}
+
+// Hash on name -> alignment end pos. This permits a naive overlap removal.
+// Note it cannot analyse the overlapping sequence and qualities, so the
+// interaction of basecalls/qualities and the -Q parameter cannot be
+// applied here (unlike the full mpileup algorithm).
+KHASH_MAP_INIT_STR(olap_hash, hts_pos_t)
+typedef khash_t(olap_hash) olap_hash_t;
+
+static int fastdepth_core(depth_opt *opt, uint32_t nfiles, char **fn,
+                          samFile **fp, hts_itr_t **itr, sam_hdr_t **h) {
+    int ret = -1, err = 1, i;
+    olap_hash_t **overlaps = NULL;
+    depth_hist dh = {0};
+
+    // An array of bam structs, one per input file, to hold the next entry
+    bam1_t **b = calloc(nfiles, sizeof(*b));
+    int *finished = calloc(nfiles, sizeof(*finished)), to_go = nfiles;
+    if (!b || !finished)
+        goto err;
+
+    for (i = 0; i < nfiles; i++)
+        if (!(b[i] = bam_init1()))
+            goto err;
+
+    // Do we need one overlap hash per file? Or shared?
+    if (opt->remove_overlaps) {
+        if (!(overlaps = calloc(nfiles, sizeof(*overlaps))))
+            return -1;
+        for (i = 0; i < nfiles; i++) {
+            if (!(overlaps[i] = kh_init(olap_hash)))
+                return -1;
+        }
+    }
+
+    // Create the initial histogram
+    dh.nfiles = nfiles;
+    dh.size = 0;
+    dh.hist = NULL;
+    dh.last_ref = -99;
+    dh.end_pos = NULL;
+    dh.last_output = itr && itr[0] ? itr[0]->beg : 0;
+    ks_initialize(&dh.ks);
+
+    // Clip results to region if specified
+    dh.beg = -1;
+    dh.end = -1;
+    dh.tid = 0;
+    if (itr && itr[0]) {
+        dh.tid = itr[0]->tid;
+        dh.beg = itr[0]->beg;
+        dh.end = itr[0]->end;
+    }
+
+    if (opt->header) {
+        fprintf(opt->out, "#CHROM\tPOS");
+        for (i = 0; i < nfiles; i++)
+            fprintf(opt->out, "\t%s", fn[i]);
+        fputc('\n', opt->out);
+    }
+
+    // Populate first record per file
+    for (i = 0; i < nfiles; i++) {
+        for(;;) {
+            ret = itr && itr[i]
+                ? sam_itr_next(fp[i], itr[i], b[i])
+                : sam_read1(fp[i], h[i], b[i]);
+            if (ret < -1)
+                goto err;
+            if (ret == -1) {
+                to_go--;
+                finished[i] = 1;
+                break;
+            }
+
+            if (b[i]->core.tid < 0)
+                continue;
+            if (b[i]->core.flag & opt->flag)
+                continue;
+            if (b[i]->core.qual < opt->min_mqual)
+                continue;
+
+            // Original samtools depth used the total sequence (l_qseq)
+            // including soft-clips.  This doesn't feel like a useful metric
+            // to be filtering on.  We now only count sequence bases that
+            // form the used part of the alignment.
+            if (opt->min_len) {
+                if (qlen_used(b[i]) < opt->min_len)
+                    continue;
+            }
+
+            break;
+        }
+    }
+
+    // Loop through input files, merging in order so we're
+    // always adding the next record in sequence
+    while (to_go) {
+        // Find next record in file list
+        int best_tid = INT_MAX, best_file = 0;
+        hts_pos_t best_pos = HTS_POS_MAX;
+
+        for (i = 0; i < nfiles; i++) {
+            if (finished[i])
+                continue;
+            if (best_tid > b[i]->core.tid) {
+                best_tid = b[i]->core.tid;
+                best_pos = b[i]->core.pos;
+                best_file = i;
+            } else if (best_tid == b[i]->core.tid &&
+                       best_pos > b[i]->core.pos) {
+                best_pos = b[i]->core.pos;
+                best_file = i;
+            }
+        }
+        i = best_file;
+
+        hts_pos_t clip = 0;
+        if (overlaps && (b[i]->core.flag & BAM_FPAIRED) &&
+            !(b[i]->core.flag & BAM_FMUNMAP)) {
+            khiter_t k = kh_get(olap_hash, overlaps[i], bam_get_qname(b[i]));
+            if (k == kh_end(overlaps[i])) {
+                // not seen before
+                hts_pos_t endpos = bam_endpos(b[i]);
+
+                // Don't add if mate location is known and can't overlap.
+                if (b[i]->core.mpos == -1 ||
+                    (b[i]->core.tid == b[i]->core.mtid &&
+                     b[i]->core.mpos <= endpos)) {
+                    k = kh_put(olap_hash, overlaps[i], bam_get_qname(b[i]),
+                               &ret);
+                    if (ret < 0)
+                        return -1;
+                    kh_key(overlaps[i], k) = strdup(bam_get_qname(b[i]));
+                    kh_value(overlaps[i], k) = endpos;
+                }
+            } else {
+                // seen before
+                clip = kh_value(overlaps[i], k);
+                free((char *)kh_key(overlaps[i], k));
+                kh_del(olap_hash, overlaps[i], k);
+            }
+        }
+
+        // Add the next merged BAM record to the depth plot
+        if ((ret = add_depth(opt, &dh, h[i], b[i], clip, i)) < 0) {
+            ret = -1;
+            goto err;
+        }
+
+        // Populate next record from this file
+        for(;!finished[i];) {
+            ret = itr && itr[i]
+                ? sam_itr_next(fp[i], itr[i], b[i])
+                : sam_read1(fp[i], h[i], b[i]);
+            if (ret < -1) {
+                ret = -1;
+                goto err;
+            }
+            if (ret == -1) {
+                to_go--;
+                finished[i] = 1;
+                break;
+            }
+
+            if (b[i]->core.tid < 0)
+                continue;
+            if (b[i]->core.flag & opt->flag)
+                continue;
+            if (b[i]->core.qual < opt->min_mqual)
+                continue;
+
+            if (opt->min_len) {
+                if (qlen_used(b[i]) < opt->min_len)
+                    continue;
+            }
+
+            break;
+        }
+    }
+
+    // Tidy up end.
+    ret = add_depth(opt, &dh, h[0], NULL, 0, 0);
+    err = 0;
+
+ err:
+    if (ret == 0 && err)
+        ret = -1;
+
+    for (i = 0; i < nfiles; i++) {
+        if (b[i])
+            bam_destroy1(b[i]);
+        if (dh.hist && dh.hist[i])
+            free(dh.hist[i]);
+    }
+    free(b);
+    free(finished);
+    ks_free(&dh.ks);
+    free(dh.hist);
+    free(dh.end_pos);
+    if (overlaps) {
+        khiter_t k;
+        for (i = 0; i < nfiles; i++) {
+            if (!overlaps[i])
+                continue;
+            for (k = kh_begin(overlaps[i]); k < kh_end(overlaps[i]); k++)
+                if (kh_exist(overlaps[i], k))
+                    free((char *)kh_key(overlaps[i], k));
+            kh_destroy(olap_hash, overlaps[i]);
+        }
+        free(overlaps);
+    }
+
+    return ret;
+}
+
+static void usage_exit(FILE *fp, int exit_status)
+{
+    fprintf(fp, "Usage: samtools depth [options] in.bam [in.bam ...]\n");
+    fprintf(fp, "\nOptions:\n");
+    fprintf(fp, "  -a           Output all positions (including zero depth)\n");
+    fprintf(fp, "  -a -a, -aa   Output absolutely all positions, including unused ref seqs\n");
+    fprintf(fp, "  -r REG       Specify a region in chr or chr:from-to syntax\n");
+    fprintf(fp, "  -b FILE      Use bed FILE for list of regions\n");
+    fprintf(fp, "  -f FILE      Specify list of input BAM/SAM/CRAM filenames\n");
+    fprintf(fp, "  -X           Use custom index files (in -X *.bam *.bam.bai order)\n");
+    fprintf(fp, "  -g INT       Remove specified flags from default flag filter\n");
+    fprintf(fp, "  -G INT       Add specified flags to the default flag filter\n");
+    fprintf(fp, "  -H           Print a file header line\n");
+    fprintf(fp, "  -l INT       Minimum read length [0]\n");
+    fprintf(fp, "  -o FILE      Write output to FILE [stdout]\n");
+    fprintf(fp, "  -q, --min-BQ INT\n"
+                "               Filter bases with base quality smaller than INT [0]\n");
+    fprintf(fp, "  -Q, --min-MQ INT\n"
+                "               Filter alignments with mapping quality smaller than INT [0]\n");
+    fprintf(fp, "  -H           Print a file header\n");
+    fprintf(fp, "  -J           Include reads with deletions in depth computation\n");
+    fprintf(fp, "  -s           Do not count overlapping reads within a template\n");
+    sam_global_opt_help(fp, "-.--.@-.");
+    exit(exit_status);
+}
+
+int main_depth(int argc, char *argv[])
+{
+    int nfiles, i;
+    samFile **fp;
+    sam_hdr_t **header;
+    int c, has_index_file = 0;
+    char *file_list = NULL, **fn = NULL;
+    char *out_file = NULL;
+    depth_opt opt = {
+        .flag = BAM_FUNMAP | BAM_FSECONDARY | BAM_FDUP | BAM_FQCFAIL,
+        .min_qual = 0,
+        .min_mqual = 0,
+        .skip_del = 1,
+        .header = 0,
+        .min_len = 0,
+        .out = stdout,
+        .all_pos = 0,
+        .remove_overlaps = 0,
+        .reg = NULL,
+        .bed = NULL,
+    };
+
+    sam_global_args ga = SAM_GLOBAL_ARGS_INIT;
+    static const struct option lopts[] = {
+        {"min-MQ", required_argument, NULL, 'Q'},
+        {"min-mq", required_argument, NULL, 'Q'},
+        {"min-BQ", required_argument, NULL, 'q'},
+        {"min-bq", required_argument, NULL, 'q'},
+        SAM_OPT_GLOBAL_OPTIONS('-', 0, '-', '-', 0, '@'),
+        {NULL, 0, NULL, 0}
+    };
+
+    while ((c = getopt_long(argc, argv, "@:q:Q:JHd:m:l:g:G:o:ar:Xf:b:s",
+                            lopts, NULL)) >= 0) {
+        switch (c) {
+        case 'a':
+            opt.all_pos++;
+            break;
+
+        case 'b':
+            opt.bed = bed_read(optarg);
+            if (!opt.bed) {
+                print_error_errno("depth", "Could not read file \"%s\"",
+                                  optarg);
+                return 1;
+            }
+            break;
+
+        case 'f':
+            file_list = optarg;
+            break;
+
+        case 'd':
+        case 'm':
+            // depth limit - now ignored
+            break;
+
+        case 'g':
+            opt.flag &= ~bam_str2flag(optarg);
+            break;
+        case 'G':
+            opt.flag |= bam_str2flag(optarg);
+            break;
+
+        case 'l':
+            opt.min_len = atoi(optarg);
+            break;
+
+        case 'H':
+            opt.header = 1;
+            break;
+
+        case 'q':
+            opt.min_qual = atoi(optarg);
+            break;
+        case 'Q':
+            opt.min_mqual = atoi(optarg);
+            break;
+
+        case 'J':
+            opt.skip_del = 0;
+            break;
+
+        case 'o':
+            if (opt.out != stdout)
+                break;
+            opt.out = fopen(out_file = optarg, "w");
+            if (!opt.out) {
+                print_error_errno("depth", "Cannot open \"%s\" for writing.",
+                                  optarg);
+                return EXIT_FAILURE;
+            }
+            break;
+
+        case 'r':
+            opt.reg = optarg;
+            break;
+
+        case 's':
+            opt.remove_overlaps = 1;
+            break;
+
+        case 'X':
+            has_index_file = 1;
+            break;
+
+        default:  if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break;
+            /* else fall-through */
+        case '?':
+            usage_exit(stderr, EXIT_FAILURE);
+        }
+    }
+
+    if (argc < optind+1 && !file_list) {
+        if (argc == optind)
+            usage_exit(stdout, EXIT_SUCCESS);
+        else
+            usage_exit(stderr, EXIT_FAILURE);
+    }
+
+    if (file_list) {
+        if (has_index_file) {
+            print_error("depth", "The -f option cannot be combined with -X");
+            return 1;
+        }
+        if (read_file_list(file_list, &nfiles, &fn))
+            return 1;
+        argv = fn;
+        argc = nfiles;
+        optind = 0;
+    } else {
+        nfiles = argc - optind;
+    }
+
+    if (has_index_file) {
+        if (nfiles%1) {
+            print_error("depth", "-X needs one index specified per bam file");
+            return 1;
+        }
+        nfiles /= 2;
+    }
+    fp = malloc(nfiles * sizeof(*fp));
+    header = malloc(nfiles * sizeof(*header));
+    if (!fp || !header) {
+        print_error_errno("depth", "Out of memory");
+        return 1;
+    }
+
+    hts_itr_t **itr = NULL;
+    if (opt.reg) {
+        itr = calloc(nfiles, sizeof(*itr));
+        if (!itr)
+            return 1;
+    }
+
+    for (i = 0; i < nfiles; i++, optind++) {
+        fp[i] = sam_open_format(argv[optind], "r", &ga.in);
+        if (fp[i] == NULL) {
+            print_error_errno("depth",
+                              "Cannot open input file \"%s\"", argv[optind]);
+            return 1;
+        }
+
+        if (ga.nthreads > 0)
+            hts_set_threads(fp[i], ga.nthreads);
+
+        if (hts_set_opt(fp[i], CRAM_OPT_REQUIRED_FIELDS,
+                        SAM_FLAG | SAM_RNAME | SAM_POS | SAM_CIGAR
+                        | (opt.remove_overlaps ? SAM_QNAME|SAM_RNEXT|SAM_PNEXT
+                                               : 0)
+                        | (opt.min_mqual       ? SAM_MAPQ  : 0)
+                        | (opt.min_len         ? SAM_SEQ   : 0)
+                        | (opt.min_qual        ? SAM_QUAL  : 0))) {
+            fprintf(stderr, "Failed to set CRAM_OPT_REQUIRED_FIELDS value\n");
+            return 1;
+        }
+
+        if (hts_set_opt(fp[i], CRAM_OPT_DECODE_MD, 0)) {
+            fprintf(stderr, "Failed to set CRAM_OPT_DECODE_MD value\n");
+            return 1;
+        }
+
+        // FIXME: what if headers differ?
+        header[i] = sam_hdr_read(fp[i]);
+        if (header == NULL) {
+            fprintf(stderr, "Failed to read header for \"%s\"\n",
+                    argv[optind]);
+            return 1;
+        }
+
+        if (opt.reg) {
+            hts_idx_t *idx = has_index_file
+                ? sam_index_load2(fp[i], argv[optind], argv[optind+nfiles])
+                : sam_index_load(fp[i], argv[optind]);
+            if (!idx) {
+                print_error("depth", "cannot load index for \"%s\"",
+                            argv[optind]);
+                return 1;
+            }
+            if (!(itr[i] = sam_itr_querys(idx, header[i], opt.reg))) {
+                print_error("depth", "cannot parse region \"%s\"", opt.reg);
+                return 1;
+            }
+            hts_idx_destroy(idx);
+        }
+    }
+
+    int ret = fastdepth_core(&opt, nfiles, &argv[argc-nfiles], fp, itr, header)
+        ? 1 : 0;
+
+    for (i = 0; i < nfiles; i++) {
+        sam_hdr_destroy(header[i]);
+        sam_close(fp[i]);
+        if (itr && itr[i])
+            hts_itr_destroy(itr[i]);
+    }
+    free(header);
+    free(fp);
+    free(itr);
+    if (file_list) {
+        for (i=0; i<nfiles; i++)
+            free(fn[i]);
+        free(fn);
+    }
+    if (opt.bed)
+        bed_destroy(opt.bed);
+    sam_global_args_free(&ga);
+    if (opt.out != stdout) {
+        if (fclose(opt.out) != 0 && ret == 0) {
+            print_error_errno("depth", "error on closing \"%s\"", out_file);
+            ret = 1;
+        }
+    }
+
+    return ret;
+}
+
+#ifdef _MAIN_BAM2DEPTH
+int main(int argc, char *argv[])
+{
+    return main_depth(argc, argv);
+}
+#endif
diff --git a/samtools/bam2depth.c.pysam.c b/samtools/bam2depth.c.pysam.c
new file mode 100644
index 0000000..e713822
--- /dev/null
+++ b/samtools/bam2depth.c.pysam.c
@@ -0,0 +1,975 @@
+#include "samtools.pysam.h"
+
+/*  bam2depth.c -- depth subcommand.
+
+    Copyright (C) 2011, 2012 Broad Institute.
+    Copyright (C) 2012-2016, 2018, 2019-2022 Genome Research Ltd.
+
+    Author: Heng Li <lh3@sanger.ac.uk> (to 2020)
+    Author: James Bonfield <jkb@sanger.ac.uk> (2021 rewrite)
+
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+/* This program demonstrates how to generate pileup from multiple BAMs
+ * simultaneously, to achieve random access and to use the BED interface.
+ * To compile this program separately, you may:
+ *
+ *   gcc -g -O2 -Wall -o bam2depth -D_MAIN_BAM2DEPTH bam2depth.c -lhts -lz
+ */
+
+#include <config.h>
+
+#include <stdlib.h>
+#include <string.h>
+#include <stdio.h>
+#include <limits.h>
+#include <unistd.h>
+#include "htslib/sam.h"
+#include "samtools.h"
+#include "bedidx.h"
+#include "sam_opts.h"
+#include "htslib/khash.h"
+
+// From bam_plcmd.c
+int read_file_list(const char *file_list, int *n, char **argv[]);
+
+// We accumulate to hist[pos & (size-1)].  This is a ring-buffer.
+// We track where we last got to in output and what the biggest value
+// we've written to so far (in absolute unmasked coordinates) in
+// "last_output" and "end_pos" respectively.
+// For each new record we just flush anything we haven't written yet
+// already, between "last_output" and this read's start position, and
+// initialise any newly seen positions between "end_pos" and this read's
+// end position.
+typedef struct {
+    size_t size;
+    int **hist;         // hist[nfiles][size]
+    hts_pos_t *end_pos; // end_pos[nfiles]
+    hts_pos_t last_output;
+    int last_ref;
+    int nfiles;
+    const char *ref;
+    kstring_t ks;
+    hts_pos_t beg, end; // limit to region
+    int tid;
+} depth_hist;
+
+typedef struct {
+    int header;
+    int flag;
+    int min_qual;
+    int min_mqual;
+    int min_len;
+    int skip_del;
+    int all_pos;
+    int remove_overlaps;
+    FILE *out;
+    char *reg;
+    void *bed;
+} depth_opt;
+
+static void zero_region(depth_opt *opt, depth_hist *dh,
+                        const char *name, hts_pos_t start, hts_pos_t end) {
+    hts_pos_t i;
+    kstring_t *ks = &dh->ks;
+
+    kputs(name, ks_clear(ks));
+    kputc('\t', ks);
+    size_t cur_l = ks->l;
+    if (dh->beg >= 0 && start < dh->beg)
+        start = dh->beg;
+    if (dh->end >= 0 && end > dh->end)
+        end = dh->end;
+
+    for (i = start; i < end; i++) {
+        // Could be optimised, but needs better API to skip to next
+        // bed region.
+        if (opt->bed && bed_overlap(opt->bed, name, i, i+1) == 0)
+            continue;
+
+        ks->l = cur_l;
+        kputll(i+1,  ks);
+        int n;
+        for (n = 0; n < dh->nfiles; n++) {
+            kputc_('\t', ks);
+            kputc_('0',  ks);
+        }
+        kputc('\n',  ks);
+        fputs(ks->s, opt->out);
+    }
+    ks->l = cur_l;
+}
+
+// A variation of bam_cigar2qlen which doesn't count soft-clips in to the
+// equation.  Basically it's the number of bases in query that are aligned
+// in some way to the reference (including insertions, which are considered
+// to be aligned by dint of being anchored either side).
+hts_pos_t qlen_used(bam1_t *b) {
+    int n_cigar = b->core.n_cigar;
+    const uint32_t *cigar = bam_get_cigar(b);
+
+    hts_pos_t l;
+
+    if (b->core.l_qseq) {
+        // Known SEQ permits of short cut of l_qseq minus CSOFT_CLIPs.
+        // Full scan not needed, which helps on excessively long CIGARs.
+        l = b->core.l_qseq;
+        int kl, kr;
+        for (kl = 0; kl < n_cigar; kl++)
+            if (bam_cigar_op(cigar[kl]) == BAM_CSOFT_CLIP)
+                l -= bam_cigar_oplen(cigar[kl]);
+            else
+                break;
+
+        for (kr = n_cigar-1; kr > kl; kr--)
+            if (bam_cigar_op(cigar[kr]) == BAM_CSOFT_CLIP)
+                l -= bam_cigar_oplen(cigar[kr]);
+            else
+                break;
+    } else {
+        // Unknown SEQ ("*") needs a full scan through the CIGAR string.
+        static int query[16] = {
+          //M I D N  S H P =  X B ? ?  ? ? ? ?
+            1,1,0,0, 0,0,0,1, 1,0,0,0, 0,0,0,0
+        };
+        int k;
+        for (k = l = 0; k < n_cigar; k++)
+            if (query[bam_cigar_op(cigar[k])])
+                l += bam_cigar_oplen(cigar[k]);
+    }
+    return l;
+
+}
+
+// Adds the depth for a single read to a depth_hist struct.
+// For just one file, this is easy.  We just have a circular buffer
+// where we increment values for bits that overlap existing data
+// and initialise values for coordinates which we're seeing for the first
+// time.  This is tracked by "end_pos" to know where we've got to.
+//
+// As the input is sorted, we can flush output from "last_output" to
+// b->core.pos.
+//
+// With multiple files, we must feed data in sorted order as if all files
+// are merged, but track depth per file.  This also means "end_pos" is per
+// file too, but "last_output" is global as it corresponds to rows printed.
+static int add_depth(depth_opt *opt, depth_hist *dh, sam_hdr_t *h, bam1_t *b,
+                     int overlap_clip, int file) {
+    hts_pos_t i;
+    size_t hmask = dh->size-1;
+    int n;
+
+    if (!b || b->core.tid != dh->last_ref) {
+        // New ref
+        if (dh->last_ref >= 0) {
+            // do end
+            size_t cur_l = dh->ks.l;
+            int nf = dh->nfiles;
+            i = dh->last_output;
+            for (i = dh->last_output; nf; i++) {
+                nf = 0;
+                for (n = 0; n < dh->nfiles; n++) {
+                    if (i < dh->end_pos[n])
+                        nf++;
+                }
+                if (!nf)
+                    break;
+
+                if (opt->bed && bed_overlap(opt->bed, dh->ref, i, i+1) == 0)
+                    continue;
+
+                dh->ks.l = cur_l;
+                kputll(i+1, &dh->ks);
+                for (n = 0; n < dh->nfiles; n++) {
+                    kputc_('\t', &dh->ks);
+                    int d = i < dh->end_pos[n]
+                        ? dh->hist[n][i & hmask]
+                        : 0;
+                    kputuw(d, &dh->ks);
+                }
+                kputc('\n', &dh->ks);
+                fputs(dh->ks.s, opt->out);
+            }
+            if (opt->all_pos) {
+                // End of last ref
+                zero_region(opt, dh,
+                            sam_hdr_tid2name(h, dh->last_ref),
+                            i, sam_hdr_tid2len(h, dh->last_ref));
+            }
+            dh->ks.l = cur_l;
+        }
+
+        if (opt->all_pos > 1 && !opt->reg) {
+            // Any previous unused refs
+            int lr = dh->last_ref < 0 ? 0 : dh->last_ref+1;
+            int rr = b ? b->core.tid : sam_hdr_nref(h), r;
+            for (r = lr; r < rr; r++)
+                zero_region(opt, dh,
+                            sam_hdr_tid2name(h, r),
+                            0, sam_hdr_tid2len(h, r));
+        }
+
+        if (!b) {
+            // we're just flushing to end of file
+            if (opt->all_pos && opt->reg && dh->last_ref < 0)
+                // -a or -aa without a single read being output yet
+                zero_region(opt, dh, sam_hdr_tid2name(h, dh->tid), dh->beg,
+                            MIN(dh->end, sam_hdr_tid2len(h, dh->tid)));
+
+            return 0;
+        }
+
+        for (n = 0; dh->end_pos && n < dh->nfiles; n++)
+            dh->end_pos[n] = 0;
+        dh->last_output = dh->beg >= 0
+            ? MAX(b->core.pos, dh->beg)
+            : b->core.pos;
+        dh->last_ref = b->core.tid;
+        dh->ref = sam_hdr_tid2name(h, b->core.tid);
+        kputs(dh->ref, ks_clear(&dh->ks));
+        kputc('\t', &dh->ks);
+
+        if (opt->all_pos)
+            // Start of ref
+            zero_region(opt, dh, dh->ref, 0, b->core.pos);
+    } else {
+        if (dh->last_output < b->core.pos) {
+            // Flush any depth outputs up to start of new read
+            size_t cur_l = dh->ks.l;
+            int nf = dh->nfiles;
+            for (i = dh->last_output; i < b->core.pos; i++) {
+                nf = 0;
+                for (n = 0; n < dh->nfiles; n++) {
+                    if (i < dh->end_pos[n])
+                        nf++;
+                }
+                if (!nf)
+                    break;
+
+                if (opt->bed && bed_overlap(opt->bed, dh->ref, i, i+1) == 0)
+                    continue;
+
+                dh->ks.l = cur_l;
+                kputll(i+1, &dh->ks);
+                for (n = 0; n < dh->nfiles; n++) {
+                    kputc_('\t', &dh->ks);
+                    int d = i < dh->end_pos[n]
+                        ? dh->hist[n][i & hmask]
+                        : 0;
+                    kputuw(d, &dh->ks);
+                }
+                kputc('\n', &dh->ks);
+                fputs(dh->ks.s, opt->out);
+            }
+            if (opt->all_pos && i < b->core.pos)
+                // Hole in middle of ref
+                zero_region(opt, dh, dh->ref, i, b->core.pos);
+
+            dh->ks.l = cur_l;
+            dh->last_output = b->core.pos;
+        }
+    }
+
+    hts_pos_t end_pos = bam_endpos(b); // 0 based, 1 past end.
+    //printf("%d %d\n", (int)b->core.pos+1, (int)end_pos);
+
+    if (b->core.tid < dh->last_ref ||
+        (dh->last_ref == b->core.tid && end_pos < dh->last_output)) {
+        print_error_errno("depth", "Data is not position sorted");
+        return -1;
+    }
+
+    // If needed, grow the circular buffer.
+    if (end_pos+1 - b->core.pos >= dh->size) {
+        size_t old_size = dh->size;
+        size_t old_hmask = hmask;
+        while (end_pos+1 - b->core.pos >= dh->size)
+            dh->size = dh->size ? 2*dh->size : 2048;
+        hmask = dh->size-1;
+        if (!dh->hist) {
+            dh->hist = calloc(dh->nfiles, sizeof(*dh->hist));
+            dh->end_pos = calloc(dh->nfiles, sizeof(*dh->end_pos));
+            if (!dh->hist || !dh->end_pos)
+                return -1;
+        }
+        for (n = 0; n < dh->nfiles; n++) {
+            int *hist = calloc(dh->size, sizeof(*dh->hist[n]));
+            if (!hist)
+                return -1;
+
+            // Simple approach for now; copy over old histogram verbatim.
+            for (i = dh->last_output; i < dh->last_output + old_size; i++)
+                hist[i & hmask] = dh->hist[n][i & old_hmask];
+            free(dh->hist[n]);
+            dh->hist[n] = hist;
+        }
+    }
+
+    // Accumulate depth, based on CIGAR
+    uint32_t *cig = bam_get_cigar(b);
+    int ncig = b->core.n_cigar, j, k, spos = 0;
+
+    // Zero new (previously unseen) coordinates so increment works later.
+    hts_pos_t end = MAX(dh->end_pos[file], b->core.pos);
+    if (end_pos > end && (end & hmask) < (end_pos & hmask)) {
+        memset(&dh->hist[file][end & hmask], 0,
+               sizeof(**dh->hist) * (end_pos - end));
+    } else {
+        for (i = end; i < end_pos; i++)
+            dh->hist[file][i & hmask] = 0;
+    }
+
+    i = b->core.pos;
+    uint8_t *qual = bam_get_qual(b);
+    int min_qual = opt->min_qual;
+    for (j = 0; j < ncig; j++) {
+        int op    = bam_cigar_op(cig[j]);
+        int oplen = bam_cigar_oplen(cig[j]);
+
+        switch (op) {
+        case BAM_CDEL:
+        case BAM_CREF_SKIP:
+            if (op != BAM_CDEL || opt->skip_del) {
+                // don't increment reference location
+                if (i + oplen >= dh->end_pos[file]) {
+                    for (k = 0; k < oplen; k++, i++) {
+                        if (i >= dh->end_pos[file])
+                            // redundant due to zero new elements above?
+                            dh->hist[file][i & hmask] = 0;
+                    }
+                } else {
+                    i += oplen;
+                }
+            } else { // op == BAM_CDEL and we count them (-J option),
+                // We don't incr spos here, but we still use qual.
+                // This doesn't make much sense, but it's for compatibility
+                // with the old code.  Arguably DEL shouldn't have a min
+                // qual and should always pass (as we've explicitly asked to
+                // include them).
+                int *hist = dh->hist[file];
+                k = 0;
+                if (overlap_clip) {
+                    if (i+oplen < overlap_clip) {
+                        i += oplen;
+                        break;
+                    } else if (i < overlap_clip) {
+                        k = overlap_clip - i;
+                        i = overlap_clip;
+                    }
+                }
+
+                // Question: should we even check quality values for DEL?
+                // We've explicitly asked to include them, and the quality
+                // is wrong anyway (it's the neighbouring base).  We do this
+                // for now for compatibility with the old depth command.
+
+                if (spos < b->core.l_qseq)
+                    for (; k < oplen; k++, i++)
+                        hist[i & hmask]+=qual[spos]>=min_qual;
+                else
+                    for (; k < oplen; k++, i++)
+                        hist[i & hmask]++;
+            }
+            break;
+
+        case BAM_CMATCH:
+        case BAM_CEQUAL:
+        case BAM_CDIFF:
+            if ((i & hmask) < ((i+oplen) & hmask)) {
+                // Optimisation when not wrapping around
+
+                // Unrolling doesn't help clang, but helps gcc,
+                // especially when not using -O3.
+                int *hist = &dh->hist[file][i & hmask];
+                if (min_qual || overlap_clip) {
+                    k = 0;
+                    if (overlap_clip) {
+                        if (i+oplen < overlap_clip) {
+                            i += oplen;
+                            spos += oplen;
+                            break;
+                        } else if (i < overlap_clip) {
+                            oplen -= overlap_clip - i;
+                            spos += overlap_clip - i;
+                            hist += overlap_clip - i;
+                            i = overlap_clip;
+                        }
+                    }
+
+                    // approx 50% of this func cpu time in this loop
+                    for (; k < (oplen & ~7); k+=8) {
+                        hist[k+0]+=qual[spos+0]>=min_qual;
+                        hist[k+1]+=qual[spos+1]>=min_qual;
+                        hist[k+2]+=qual[spos+2]>=min_qual;
+                        hist[k+3]+=qual[spos+3]>=min_qual;
+                        hist[k+4]+=qual[spos+4]>=min_qual;
+                        hist[k+5]+=qual[spos+5]>=min_qual;
+                        hist[k+6]+=qual[spos+6]>=min_qual;
+                        hist[k+7]+=qual[spos+7]>=min_qual;
+                        spos += 8;
+                    }
+                } else {
+                    // easier to vectorize when no min_qual
+                    for (k = 0; k < (oplen & ~7); k+=8) {
+                        hist[k+0]++;
+                        hist[k+1]++;
+                        hist[k+2]++;
+                        hist[k+3]++;
+                        hist[k+4]++;
+                        hist[k+5]++;
+                        hist[k+6]++;
+                        hist[k+7]++;
+                    }
+                    spos += k;
+                }
+                for (; k < oplen && spos < b->core.l_qseq; k++, spos++)
+                    hist[k]+=qual[spos]>=min_qual;
+                for (; k < oplen; k++, spos++)
+                    hist[k]++;
+                i += oplen;
+            } else {
+                // Simple to understand case, but slower.
+                // We use this only for reads with wrap-around.
+                int *hist = dh->hist[file];
+                k = 0;
+                if (overlap_clip) {
+                    if (i+oplen < overlap_clip) {
+                        i += oplen;
+                        break;
+                    } else if (i < overlap_clip) {
+                        oplen -= overlap_clip - i;
+                        spos += overlap_clip - i;
+                        i = overlap_clip;
+                    }
+                }
+                for (; k < oplen && spos < b->core.l_qseq; k++, i++, spos++)
+                    hist[i & hmask]+=qual[spos]>=min_qual;
+                for (; k < oplen; k++, i++, spos++)
+                    hist[i & hmask]++;
+            }
+            break;
+
+        case BAM_CINS:
+        case BAM_CSOFT_CLIP:
+            spos += oplen;
+            break;
+
+        case BAM_CPAD:
+        case BAM_CHARD_CLIP:
+            // ignore
+            break;
+
+        default:
+            print_error("depth", "Unsupported cigar op '%d'", op);
+            return -1;
+        }
+    }
+
+    if (dh->end >= 0 && end_pos > dh->end)
+        end_pos = dh->end;
+    if (dh->end_pos[file] < end_pos)
+        dh->end_pos[file] = end_pos;
+
+    return 0;
+}
+
+// Hash on name -> alignment end pos. This permits a naive overlap removal.
+// Note it cannot analyse the overlapping sequence and qualities, so the
+// interaction of basecalls/qualities and the -Q parameter cannot be
+// applied here (unlike the full mpileup algorithm).
+KHASH_MAP_INIT_STR(olap_hash, hts_pos_t)
+typedef khash_t(olap_hash) olap_hash_t;
+
+static int fastdepth_core(depth_opt *opt, uint32_t nfiles, char **fn,
+                          samFile **fp, hts_itr_t **itr, sam_hdr_t **h) {
+    int ret = -1, err = 1, i;
+    olap_hash_t **overlaps = NULL;
+    depth_hist dh = {0};
+
+    // An array of bam structs, one per input file, to hold the next entry
+    bam1_t **b = calloc(nfiles, sizeof(*b));
+    int *finished = calloc(nfiles, sizeof(*finished)), to_go = nfiles;
+    if (!b || !finished)
+        goto err;
+
+    for (i = 0; i < nfiles; i++)
+        if (!(b[i] = bam_init1()))
+            goto err;
+
+    // Do we need one overlap hash per file? Or shared?
+    if (opt->remove_overlaps) {
+        if (!(overlaps = calloc(nfiles, sizeof(*overlaps))))
+            return -1;
+        for (i = 0; i < nfiles; i++) {
+            if (!(overlaps[i] = kh_init(olap_hash)))
+                return -1;
+        }
+    }
+
+    // Create the initial histogram
+    dh.nfiles = nfiles;
+    dh.size = 0;
+    dh.hist = NULL;
+    dh.last_ref = -99;
+    dh.end_pos = NULL;
+    dh.last_output = itr && itr[0] ? itr[0]->beg : 0;
+    ks_initialize(&dh.ks);
+
+    // Clip results to region if specified
+    dh.beg = -1;
+    dh.end = -1;
+    dh.tid = 0;
+    if (itr && itr[0]) {
+        dh.tid = itr[0]->tid;
+        dh.beg = itr[0]->beg;
+        dh.end = itr[0]->end;
+    }
+
+    if (opt->header) {
+        fprintf(opt->out, "#CHROM\tPOS");
+        for (i = 0; i < nfiles; i++)
+            fprintf(opt->out, "\t%s", fn[i]);
+        fputc('\n', opt->out);
+    }
+
+    // Populate first record per file
+    for (i = 0; i < nfiles; i++) {
+        for(;;) {
+            ret = itr && itr[i]
+                ? sam_itr_next(fp[i], itr[i], b[i])
+                : sam_read1(fp[i], h[i], b[i]);
+            if (ret < -1)
+                goto err;
+            if (ret == -1) {
+                to_go--;
+                finished[i] = 1;
+                break;
+            }
+
+            if (b[i]->core.tid < 0)
+                continue;
+            if (b[i]->core.flag & opt->flag)
+                continue;
+            if (b[i]->core.qual < opt->min_mqual)
+                continue;
+
+            // Original samtools depth used the total sequence (l_qseq)
+            // including soft-clips.  This doesn't feel like a useful metric
+            // to be filtering on.  We now only count sequence bases that
+            // form the used part of the alignment.
+            if (opt->min_len) {
+                if (qlen_used(b[i]) < opt->min_len)
+                    continue;
+            }
+
+            break;
+        }
+    }
+
+    // Loop through input files, merging in order so we're
+    // always adding the next record in sequence
+    while (to_go) {
+        // Find next record in file list
+        int best_tid = INT_MAX, best_file = 0;
+        hts_pos_t best_pos = HTS_POS_MAX;
+
+        for (i = 0; i < nfiles; i++) {
+            if (finished[i])
+                continue;
+            if (best_tid > b[i]->core.tid) {
+                best_tid = b[i]->core.tid;
+                best_pos = b[i]->core.pos;
+                best_file = i;
+            } else if (best_tid == b[i]->core.tid &&
+                       best_pos > b[i]->core.pos) {
+                best_pos = b[i]->core.pos;
+                best_file = i;
+            }
+        }
+        i = best_file;
+
+        hts_pos_t clip = 0;
+        if (overlaps && (b[i]->core.flag & BAM_FPAIRED) &&
+            !(b[i]->core.flag & BAM_FMUNMAP)) {
+            khiter_t k = kh_get(olap_hash, overlaps[i], bam_get_qname(b[i]));
+            if (k == kh_end(overlaps[i])) {
+                // not seen before
+                hts_pos_t endpos = bam_endpos(b[i]);
+
+                // Don't add if mate location is known and can't overlap.
+                if (b[i]->core.mpos == -1 ||
+                    (b[i]->core.tid == b[i]->core.mtid &&
+                     b[i]->core.mpos <= endpos)) {
+                    k = kh_put(olap_hash, overlaps[i], bam_get_qname(b[i]),
+                               &ret);
+                    if (ret < 0)
+                        return -1;
+                    kh_key(overlaps[i], k) = strdup(bam_get_qname(b[i]));
+                    kh_value(overlaps[i], k) = endpos;
+                }
+            } else {
+                // seen before
+                clip = kh_value(overlaps[i], k);
+                free((char *)kh_key(overlaps[i], k));
+                kh_del(olap_hash, overlaps[i], k);
+            }
+        }
+
+        // Add the next merged BAM record to the depth plot
+        if ((ret = add_depth(opt, &dh, h[i], b[i], clip, i)) < 0) {
+            ret = -1;
+            goto err;
+        }
+
+        // Populate next record from this file
+        for(;!finished[i];) {
+            ret = itr && itr[i]
+                ? sam_itr_next(fp[i], itr[i], b[i])
+                : sam_read1(fp[i], h[i], b[i]);
+            if (ret < -1) {
+                ret = -1;
+                goto err;
+            }
+            if (ret == -1) {
+                to_go--;
+                finished[i] = 1;
+                break;
+            }
+
+            if (b[i]->core.tid < 0)
+                continue;
+            if (b[i]->core.flag & opt->flag)
+                continue;
+            if (b[i]->core.qual < opt->min_mqual)
+                continue;
+
+            if (opt->min_len) {
+                if (qlen_used(b[i]) < opt->min_len)
+                    continue;
+            }
+
+            break;
+        }
+    }
+
+    // Tidy up end.
+    ret = add_depth(opt, &dh, h[0], NULL, 0, 0);
+    err = 0;
+
+ err:
+    if (ret == 0 && err)
+        ret = -1;
+
+    for (i = 0; i < nfiles; i++) {
+        if (b[i])
+            bam_destroy1(b[i]);
+        if (dh.hist && dh.hist[i])
+            free(dh.hist[i]);
+    }
+    free(b);
+    free(finished);
+    ks_free(&dh.ks);
+    free(dh.hist);
+    free(dh.end_pos);
+    if (overlaps) {
+        khiter_t k;
+        for (i = 0; i < nfiles; i++) {
+            if (!overlaps[i])
+                continue;
+            for (k = kh_begin(overlaps[i]); k < kh_end(overlaps[i]); k++)
+                if (kh_exist(overlaps[i], k))
+                    free((char *)kh_key(overlaps[i], k));
+            kh_destroy(olap_hash, overlaps[i]);
+        }
+        free(overlaps);
+    }
+
+    return ret;
+}
+
+static void usage_exit(FILE *fp, int exit_status)
+{
+    fprintf(fp, "Usage: samtools depth [options] in.bam [in.bam ...]\n");
+    fprintf(fp, "\nOptions:\n");
+    fprintf(fp, "  -a           Output all positions (including zero depth)\n");
+    fprintf(fp, "  -a -a, -aa   Output absolutely all positions, including unused ref seqs\n");
+    fprintf(fp, "  -r REG       Specify a region in chr or chr:from-to syntax\n");
+    fprintf(fp, "  -b FILE      Use bed FILE for list of regions\n");
+    fprintf(fp, "  -f FILE      Specify list of input BAM/SAM/CRAM filenames\n");
+    fprintf(fp, "  -X           Use custom index files (in -X *.bam *.bam.bai order)\n");
+    fprintf(fp, "  -g INT       Remove specified flags from default flag filter\n");
+    fprintf(fp, "  -G INT       Add specified flags to the default flag filter\n");
+    fprintf(fp, "  -H           Print a file header line\n");
+    fprintf(fp, "  -l INT       Minimum read length [0]\n");
+    fprintf(fp, "  -o FILE      Write output to FILE [samtools_stdout]\n");
+    fprintf(fp, "  -q, --min-BQ INT\n"
+                "               Filter bases with base quality smaller than INT [0]\n");
+    fprintf(fp, "  -Q, --min-MQ INT\n"
+                "               Filter alignments with mapping quality smaller than INT [0]\n");
+    fprintf(fp, "  -H           Print a file header\n");
+    fprintf(fp, "  -J           Include reads with deletions in depth computation\n");
+    fprintf(fp, "  -s           Do not count overlapping reads within a template\n");
+    sam_global_opt_help(fp, "-.--.@-.");
+    samtools_exit(exit_status);
+}
+
+int main_depth(int argc, char *argv[])
+{
+    int nfiles, i;
+    samFile **fp;
+    sam_hdr_t **header;
+    int c, has_index_file = 0;
+    char *file_list = NULL, **fn = NULL;
+    char *out_file = NULL;
+    depth_opt opt = {
+        .flag = BAM_FUNMAP | BAM_FSECONDARY | BAM_FDUP | BAM_FQCFAIL,
+        .min_qual = 0,
+        .min_mqual = 0,
+        .skip_del = 1,
+        .header = 0,
+        .min_len = 0,
+        .out = samtools_stdout,
+        .all_pos = 0,
+        .remove_overlaps = 0,
+        .reg = NULL,
+        .bed = NULL,
+    };
+
+    sam_global_args ga = SAM_GLOBAL_ARGS_INIT;
+    static const struct option lopts[] = {
+        {"min-MQ", required_argument, NULL, 'Q'},
+        {"min-mq", required_argument, NULL, 'Q'},
+        {"min-BQ", required_argument, NULL, 'q'},
+        {"min-bq", required_argument, NULL, 'q'},
+        SAM_OPT_GLOBAL_OPTIONS('-', 0, '-', '-', 0, '@'),
+        {NULL, 0, NULL, 0}
+    };
+
+    while ((c = getopt_long(argc, argv, "@:q:Q:JHd:m:l:g:G:o:ar:Xf:b:s",
+                            lopts, NULL)) >= 0) {
+        switch (c) {
+        case 'a':
+            opt.all_pos++;
+            break;
+
+        case 'b':
+            opt.bed = bed_read(optarg);
+            if (!opt.bed) {
+                print_error_errno("depth", "Could not read file \"%s\"",
+                                  optarg);
+                return 1;
+            }
+            break;
+
+        case 'f':
+            file_list = optarg;
+            break;
+
+        case 'd':
+        case 'm':
+            // depth limit - now ignored
+            break;
+
+        case 'g':
+            opt.flag &= ~bam_str2flag(optarg);
+            break;
+        case 'G':
+            opt.flag |= bam_str2flag(optarg);
+            break;
+
+        case 'l':
+            opt.min_len = atoi(optarg);
+            break;
+
+        case 'H':
+            opt.header = 1;
+            break;
+
+        case 'q':
+            opt.min_qual = atoi(optarg);
+            break;
+        case 'Q':
+            opt.min_mqual = atoi(optarg);
+            break;
+
+        case 'J':
+            opt.skip_del = 0;
+            break;
+
+        case 'o':
+            if (opt.out != samtools_stdout)
+                break;
+            opt.out = fopen(out_file = optarg, "w");
+            if (!opt.out) {
+                print_error_errno("depth", "Cannot open \"%s\" for writing.",
+                                  optarg);
+                return EXIT_FAILURE;
+            }
+            break;
+
+        case 'r':
+            opt.reg = optarg;
+            break;
+
+        case 's':
+            opt.remove_overlaps = 1;
+            break;
+
+        case 'X':
+            has_index_file = 1;
+            break;
+
+        default:  if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break;
+            /* else fall-through */
+        case '?':
+            usage_exit(samtools_stderr, EXIT_FAILURE);
+        }
+    }
+
+    if (argc < optind+1 && !file_list) {
+        if (argc == optind)
+            usage_exit(samtools_stdout, EXIT_SUCCESS);
+        else
+            usage_exit(samtools_stderr, EXIT_FAILURE);
+    }
+
+    if (file_list) {
+        if (has_index_file) {
+            print_error("depth", "The -f option cannot be combined with -X");
+            return 1;
+        }
+        if (read_file_list(file_list, &nfiles, &fn))
+            return 1;
+        argv = fn;
+        argc = nfiles;
+        optind = 0;
+    } else {
+        nfiles = argc - optind;
+    }
+
+    if (has_index_file) {
+        if (nfiles%1) {
+            print_error("depth", "-X needs one index specified per bam file");
+            return 1;
+        }
+        nfiles /= 2;
+    }
+    fp = malloc(nfiles * sizeof(*fp));
+    header = malloc(nfiles * sizeof(*header));
+    if (!fp || !header) {
+        print_error_errno("depth", "Out of memory");
+        return 1;
+    }
+
+    hts_itr_t **itr = NULL;
+    if (opt.reg) {
+        itr = calloc(nfiles, sizeof(*itr));
+        if (!itr)
+            return 1;
+    }
+
+    for (i = 0; i < nfiles; i++, optind++) {
+        fp[i] = sam_open_format(argv[optind], "r", &ga.in);
+        if (fp[i] == NULL) {
+            print_error_errno("depth",
+                              "Cannot open input file \"%s\"", argv[optind]);
+            return 1;
+        }
+
+        if (ga.nthreads > 0)
+            hts_set_threads(fp[i], ga.nthreads);
+
+        if (hts_set_opt(fp[i], CRAM_OPT_REQUIRED_FIELDS,
+                        SAM_FLAG | SAM_RNAME | SAM_POS | SAM_CIGAR
+                        | (opt.remove_overlaps ? SAM_QNAME|SAM_RNEXT|SAM_PNEXT
+                                               : 0)
+                        | (opt.min_mqual       ? SAM_MAPQ  : 0)
+                        | (opt.min_len         ? SAM_SEQ   : 0)
+                        | (opt.min_qual        ? SAM_QUAL  : 0))) {
+            fprintf(samtools_stderr, "Failed to set CRAM_OPT_REQUIRED_FIELDS value\n");
+            return 1;
+        }
+
+        if (hts_set_opt(fp[i], CRAM_OPT_DECODE_MD, 0)) {
+            fprintf(samtools_stderr, "Failed to set CRAM_OPT_DECODE_MD value\n");
+            return 1;
+        }
+
+        // FIXME: what if headers differ?
+        header[i] = sam_hdr_read(fp[i]);
+        if (header == NULL) {
+            fprintf(samtools_stderr, "Failed to read header for \"%s\"\n",
+                    argv[optind]);
+            return 1;
+        }
+
+        if (opt.reg) {
+            hts_idx_t *idx = has_index_file
+                ? sam_index_load2(fp[i], argv[optind], argv[optind+nfiles])
+                : sam_index_load(fp[i], argv[optind]);
+            if (!idx) {
+                print_error("depth", "cannot load index for \"%s\"",
+                            argv[optind]);
+                return 1;
+            }
+            if (!(itr[i] = sam_itr_querys(idx, header[i], opt.reg))) {
+                print_error("depth", "cannot parse region \"%s\"", opt.reg);
+                return 1;
+            }
+            hts_idx_destroy(idx);
+        }
+    }
+
+    int ret = fastdepth_core(&opt, nfiles, &argv[argc-nfiles], fp, itr, header)
+        ? 1 : 0;
+
+    for (i = 0; i < nfiles; i++) {
+        sam_hdr_destroy(header[i]);
+        sam_close(fp[i]);
+        if (itr && itr[i])
+            hts_itr_destroy(itr[i]);
+    }
+    free(header);
+    free(fp);
+    free(itr);
+    if (file_list) {
+        for (i=0; i<nfiles; i++)
+            free(fn[i]);
+        free(fn);
+    }
+    if (opt.bed)
+        bed_destroy(opt.bed);
+    sam_global_args_free(&ga);
+    if (opt.out != samtools_stdout) {
+        if (fclose(opt.out) != 0 && ret == 0) {
+            print_error_errno("depth", "error on closing \"%s\"", out_file);
+            ret = 1;
+        }
+    }
+
+    return ret;
+}
+
+#ifdef _MAIN_BAM2DEPTH
+int samtools_bam2depth_main(int argc, char *argv[])
+{
+    return main_depth(argc, argv);
+}
+#endif
diff --git a/samtools/bam_addrprg.c b/samtools/bam_addrprg.c
new file mode 100644
index 0000000..06c3147
--- /dev/null
+++ b/samtools/bam_addrprg.c
@@ -0,0 +1,499 @@
+/* bam_addrprg.c -- samtools command to add or replace readgroups.
+
+   Copyright (c) 2013, 2015-2017, 2019-2021 Genome Research Limited.
+
+   Author: Martin O. Pollard <mp15@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <config.h>
+
+#include <htslib/sam.h>
+#include <htslib/kstring.h>
+#include "samtools.h"
+#include "htslib/thread_pool.h"
+#include "sam_opts.h"
+#include <string.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <stdbool.h>
+#include <limits.h>
+#include <assert.h>
+#include <unistd.h>
+
+typedef enum {
+    overwrite_all,
+    orphan_only,
+} rg_mode;
+
+struct parsed_opts {
+    char* input_name;
+    char* output_name;
+    char* rg_id;
+    char* rg_line;
+    int no_pg;
+    rg_mode mode;
+    sam_global_args ga;
+    htsThreadPool p;
+    int uncompressed;
+    int overwrite_hdr_rg;
+};
+
+struct state;
+typedef struct parsed_opts parsed_opts_t;
+typedef struct state state_t;
+
+struct state {
+    samFile* input_file;
+    sam_hdr_t* input_header;
+    samFile* output_file;
+    sam_hdr_t* output_header;
+    char* rg_id;
+    void (*mode_func)(const state_t*, bam1_t*);
+};
+
+static void cleanup_opts(parsed_opts_t* opts)
+{
+    if (!opts) return;
+    free(opts->rg_id);
+    free(opts->output_name);
+    free(opts->input_name);
+    free(opts->rg_line);
+    if (opts->p.pool) hts_tpool_destroy(opts->p.pool);
+    sam_global_args_free(&opts->ga);
+    free(opts);
+}
+
+static void cleanup_state(state_t* state)
+{
+    if (!state) return;
+    free(state->rg_id);
+    if (state->output_file) sam_close(state->output_file);
+    sam_hdr_destroy(state->output_header);
+    if (state->input_file) sam_close(state->input_file);
+    sam_hdr_destroy(state->input_header);
+    free(state);
+}
+
+// Converts \t and \n into real tabs and newlines
+static char* basic_unescape(const char* in)
+{
+    assert(in);
+    char *ptr, *out;
+    out = ptr = malloc(strlen(in)+1);
+    size_t size = 0;
+    while (*in) {
+        if (*in == '\\') {
+            ++in;
+            if (*in == '\0') {
+                fprintf(stderr, "[%s] Unterminated escape sequence.\n", __func__);
+                free(out);
+                return NULL;
+            }
+            switch (*in) {
+            case '\\':
+                *ptr = '\\';
+                break;
+            case 't':
+                *ptr = '\t';
+                break;
+            case 'n':
+                fprintf(stderr, "[%s] \\n in escape sequence is not supported.\n", __func__);
+                free(out);
+                return NULL;
+            default:
+                fprintf(stderr, "[%s] Unsupported escape sequence.\n", __func__);
+                free(out);
+                return NULL;
+            }
+        } else {
+            *ptr = *in;
+        }
+        ++in;
+        ++ptr;
+        ++size;
+    }
+    *ptr = '\0';
+    ++size;
+    char* tmp = (char*)realloc(out, size);
+    if (!tmp) {
+        free(out);
+    }
+    return tmp;
+}
+
+// Malloc a string containing [s,slim) or to the end of s if slim is NULL.
+// If lenp is non-NULL, stores the length of the resulting string there.
+static char *dup_substring(const char *s, const char *slim, size_t *lenp)
+{
+    size_t len = slim? (slim - s) : strlen(s);
+    char *ns = malloc(len+1);
+    if (ns == NULL) return NULL;
+    memcpy(ns, s, len);
+    ns[len] = '\0';
+    if (lenp) *lenp = len;
+    return ns;
+}
+
+
+// Given a @RG line return the id
+static char* get_rg_id(const char *line)
+{
+    const char *id = strstr(line, "\tID:");
+    if (! id) return NULL;
+
+    id += 4;
+    return dup_substring(id, strchr(id, '\t'), NULL);
+}
+
+
+static void usage(FILE *fp)
+{
+    fprintf(fp,
+            "Usage: samtools addreplacerg [options] [-r <@RG line> | -R <existing id>] [-m orphan_only|overwrite_all] [-o <output.bam>] <input.bam>\n"
+            "\n"
+            "Options:\n"
+            "  -m MODE   Set the mode of operation from one of overwrite_all, orphan_only [overwrite_all]\n"
+            "  -o FILE   Where to write output to [stdout]\n"
+            "  -r STRING @RG line text\n"
+            "  -R STRING ID of @RG line in existing header to use\n"
+            "  -u        Output uncompressed data\n"
+            "  -w        Overwrite an existing @RG line\n"
+            "  --no-PG   Do not add a PG line\n"
+            );
+    sam_global_opt_help(fp, "..O..@..");
+}
+
+static bool parse_args(int argc, char** argv, parsed_opts_t** opts)
+{
+    *opts = NULL;
+    int n;
+
+    if (argc == 1) { usage(stdout); return true; }
+
+    parsed_opts_t* retval = calloc(1, sizeof(parsed_opts_t));
+    if (! retval ) {
+        fprintf(stderr, "[%s] Out of memory allocating parsed_opts_t\n", __func__);
+        return false;
+    }
+    // Set defaults
+    retval->mode = overwrite_all;
+    sam_global_args_init(&retval->ga);
+    static const struct option lopts[] = {
+        SAM_OPT_GLOBAL_OPTIONS(0, 0, 'O', 0, 0, '@'),
+        {"no-PG", no_argument, NULL, 1},
+        { NULL, 0, NULL, 0 }
+    };
+    kstring_t rg_line = {0,0,NULL};
+
+    while ((n = getopt_long(argc, argv, "r:R:m:o:O:h@:uw", lopts, NULL)) >= 0) {
+        switch (n) {
+            case 'r':
+                // Are we adding to existing rg line?
+                if (ks_len(&rg_line) == 0) {
+                    if (strlen(optarg)<3 || (optarg[0] != '@' && optarg[1] != 'R' && optarg[2] != 'G')) {
+                        kputs("@RG\t", &rg_line);
+                    }
+                } else {
+                    kputs("\t", &rg_line);
+                }
+                kputs(optarg, &rg_line);
+                break;
+            case 'R':
+                retval->rg_id = strdup(optarg);
+                break;
+            case 'm': {
+                if (strcmp(optarg, "overwrite_all") == 0) {
+                    retval->mode = overwrite_all;
+                } else if (strcmp(optarg, "orphan_only") == 0) {
+                    retval->mode = orphan_only;
+                } else {
+                    usage(stderr);
+                    return false;
+                }
+                break;
+            }
+            case 'o':
+                retval->output_name = strdup(optarg);
+                break;
+            case 'h':
+                usage(stdout);
+                free(retval);
+                return true;
+            case 1:
+                retval->no_pg = 1;
+                break;
+            case 'u':
+                retval->uncompressed = 1;
+                break;
+            case 'w':
+                retval->overwrite_hdr_rg = 1;
+                break;
+            case '?':
+                usage(stderr);
+                free(retval);
+                return false;
+            case 'O':
+            default:
+                if (parse_sam_global_opt(n, optarg, lopts, &retval->ga) == 0) break;
+                usage(stderr);
+                free(retval);
+                return false;
+        }
+    }
+    retval->rg_line = ks_release(&rg_line);
+
+    if (argc-optind < 1) {
+        fprintf(stderr, "You must specify an input file.\n");
+        usage(stderr);
+        cleanup_opts(retval);
+        return false;
+    }
+    if (retval->rg_id && retval->rg_line) {
+        fprintf(stderr, "The options -r and -R are mutually exclusive.\n");
+        cleanup_opts(retval);
+        return false;
+    }
+
+    if (retval->rg_line)
+    {
+        char* tmp = basic_unescape(retval->rg_line);
+
+        if ((retval->rg_id = get_rg_id(tmp)) == NULL) {
+            fprintf(stderr, "[%s] The supplied RG line lacks an ID tag.\n", __func__);
+            free(tmp);
+            cleanup_opts(retval);
+            return false;
+        }
+        free(retval->rg_line);
+        retval->rg_line = tmp;
+    }
+    retval->input_name = strdup(argv[optind+0]);
+
+    if (retval->ga.nthreads > 0) {
+        if (!(retval->p.pool = hts_tpool_init(retval->ga.nthreads))) {
+            fprintf(stderr, "Error creating thread pool\n");
+            return false;
+        }
+    }
+
+    *opts = retval;
+    return true;
+}
+
+static void overwrite_all_func(const state_t* state, bam1_t* file_read)
+{
+    uint8_t* data = (uint8_t*)strdup(state->rg_id);
+    int len = strlen(state->rg_id)+1;
+    // If the old exists delete it
+    uint8_t* old = bam_aux_get(file_read, "RG");
+    if (old != NULL) {
+        bam_aux_del(file_read, old);
+    }
+
+    bam_aux_append(file_read, "RG", 'Z', len, data);
+    free(data);
+}
+
+static void orphan_only_func(const state_t* state, bam1_t* file_read)
+{
+    uint8_t* data = (uint8_t*)strdup(state->rg_id);
+    int len = strlen(state->rg_id)+1;
+    // If the old exists don't do anything
+    uint8_t* old = bam_aux_get(file_read, "RG");
+    if (old == NULL) {
+        bam_aux_append(file_read, "RG",'Z',len,data);
+    }
+    free(data);
+}
+
+static bool init(const parsed_opts_t* opts, state_t** state_out) {
+    char output_mode[9] = "w";
+    state_t* retval = (state_t*) calloc(1, sizeof(state_t));
+
+    if (retval == NULL) {
+        fprintf(stderr, "[init] Out of memory allocating state struct.\n");
+        return false;
+    }
+    *state_out = retval;
+
+    // Open files
+    retval->input_file = sam_open_format(opts->input_name, "r", &opts->ga.in);
+    if (retval->input_file == NULL) {
+        print_error_errno("addreplacerg", "could not open \"%s\"", opts->input_name);
+        return false;
+    }
+    retval->input_header = sam_hdr_read(retval->input_file);
+
+    retval->output_header = sam_hdr_dup(retval->input_header);
+
+    if (opts->uncompressed)
+        strcat(output_mode, "0");
+    if (opts->output_name) // File format auto-detection
+        sam_open_mode(output_mode + strlen(output_mode),
+                      opts->output_name, NULL);
+    retval->output_file = sam_open_format(opts->output_name == NULL?"-":opts->output_name, output_mode, &opts->ga.out);
+
+    if (retval->output_file == NULL) {
+        print_error_errno("addreplacerg", "could not create \"%s\"", opts->output_name);
+        return false;
+    }
+
+    if (opts->p.pool) {
+        hts_set_opt(retval->input_file,  HTS_OPT_THREAD_POOL, &opts->p);
+        hts_set_opt(retval->output_file, HTS_OPT_THREAD_POOL, &opts->p);
+    }
+
+    if (opts->rg_line) {
+        // Append new RG line to header.
+        // Check does not already exist
+        kstring_t hdr_line = { 0, 0, NULL };
+        if (sam_hdr_find_line_id(retval->output_header, "RG", "ID", opts->rg_id, &hdr_line) == 0) {
+            if (opts->overwrite_hdr_rg) {
+                if(-1 == sam_hdr_remove_line_id(retval->output_header, "RG", "ID", opts->rg_id)) {
+                    fprintf(stderr, "[init] Error removing the RG line with ID:%s from the output header.\n", opts->rg_id);
+                    ks_free(&hdr_line);
+                    return false;
+                }
+            } else {
+                fprintf(stderr, "[init] RG line with ID:%s already present in the header. Use -w to overwrite.\n", opts->rg_id);
+                ks_free(&hdr_line);
+                return false;
+            }
+        }
+        ks_free(&hdr_line);
+
+        if (-1 == sam_hdr_add_lines(retval->output_header, opts->rg_line, strlen(opts->rg_line))) {
+            fprintf(stderr, "[init] Error adding RG line with ID:%s to the output header.\n", opts->rg_id);
+            return false;
+        }
+        if (opts->mode == overwrite_all &&
+            -1 == sam_hdr_remove_except(retval->output_header, "RG", "ID", opts->rg_id)) {
+            fprintf(stderr, "[init] Error removing the old RG lines from the output header.\n");
+            return false;
+        }
+        retval->rg_id = strdup(opts->rg_id);
+    } else {
+        if (opts->rg_id) {
+            // Confirm what has been supplied exists
+            kstring_t hdr_line = { 0, 0, NULL };
+            if (sam_hdr_find_line_id(retval->output_header, "RG", "ID", opts->rg_id, &hdr_line) < 0) {
+                fprintf(stderr, "RG ID supplied does not exist in header. Supply full @RG line with -r instead?\n");
+                return false;
+            }
+            retval->rg_id = strdup(opts->rg_id);
+            ks_free(&hdr_line);
+        } else {
+            kstring_t rg_id = { 0, 0, NULL };
+            if (sam_hdr_find_tag_id(retval->output_header, "RG", NULL, NULL, "ID", &rg_id) < 0) {
+                fprintf(stderr, "No RG specified on command line or in existing header.\n");
+                return false;
+            }
+            retval->rg_id = ks_release(&rg_id);
+        }
+    }
+
+    switch (opts->mode) {
+        case overwrite_all:
+            retval->mode_func = &overwrite_all_func;
+            break;
+        case orphan_only:
+            retval->mode_func = &orphan_only_func;
+            break;
+    }
+
+    return true;
+}
+
+static bool readgroupise(parsed_opts_t *opts, state_t* state, char *arg_list)
+{
+    if (!opts->no_pg && sam_hdr_add_pg(state->output_header, "samtools",
+                                       "VN", samtools_version(),
+                                       arg_list ? "CL": NULL,
+                                       arg_list ? arg_list : NULL,
+                                       NULL))
+        return false;
+
+    if (sam_hdr_write(state->output_file, state->output_header) != 0) {
+        print_error_errno("addreplacerg", "[%s] Could not write header to output file", __func__);
+        return false;
+    }
+    char *idx_fn = NULL;
+    if (opts->ga.write_index) {
+        if (!(idx_fn = auto_index(state->output_file, opts->output_name, state->output_header)))
+            return false;
+    }
+
+    bam1_t* file_read = bam_init1();
+    int ret;
+    while ((ret = sam_read1(state->input_file, state->input_header, file_read)) >= 0) {
+        state->mode_func(state, file_read);
+
+        if (sam_write1(state->output_file, state->output_header, file_read) < 0) {
+            print_error_errno("addreplacerg", "[%s] Could not write read to output file", __func__);
+            bam_destroy1(file_read);
+            free(idx_fn);
+            return false;
+        }
+    }
+    bam_destroy1(file_read);
+    if (ret != -1) {
+        print_error_errno("addreplacerg", "[%s] Error reading from input file", __func__);
+        free(idx_fn);
+        return false;
+    } else {
+
+        if (opts->ga.write_index) {
+            if (sam_idx_save(state->output_file) < 0) {
+                print_error_errno("addreplacerg", "[%s] Writing index failed", __func__);
+                free(idx_fn);
+                return false;
+            }
+        }
+        free(idx_fn);
+        return true;
+    }
+}
+
+int main_addreplacerg(int argc, char** argv)
+{
+    parsed_opts_t* opts = NULL;
+    state_t* state = NULL;
+    char *arg_list = stringify_argv(argc+1, argv-1);
+    if (!arg_list)
+        return EXIT_FAILURE;
+
+    if (!parse_args(argc, argv, &opts)) goto error;
+    if (opts) { // Not an error but user doesn't want us to proceed
+        if (!init(opts, &state) || !readgroupise(opts, state, arg_list))
+            goto error;
+    }
+
+    cleanup_state(state);
+    cleanup_opts(opts);
+    free(arg_list);
+
+    return EXIT_SUCCESS;
+error:
+    cleanup_state(state);
+    cleanup_opts(opts);
+    free(arg_list);
+
+    return EXIT_FAILURE;
+}
diff --git a/samtools/bam_addrprg.c.pysam.c b/samtools/bam_addrprg.c.pysam.c
new file mode 100644
index 0000000..88ce7e3
--- /dev/null
+++ b/samtools/bam_addrprg.c.pysam.c
@@ -0,0 +1,501 @@
+#include "samtools.pysam.h"
+
+/* bam_addrprg.c -- samtools command to add or replace readgroups.
+
+   Copyright (c) 2013, 2015-2017, 2019-2021 Genome Research Limited.
+
+   Author: Martin O. Pollard <mp15@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <config.h>
+
+#include <htslib/sam.h>
+#include <htslib/kstring.h>
+#include "samtools.h"
+#include "htslib/thread_pool.h"
+#include "sam_opts.h"
+#include <string.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <stdbool.h>
+#include <limits.h>
+#include <assert.h>
+#include <unistd.h>
+
+typedef enum {
+    overwrite_all,
+    orphan_only,
+} rg_mode;
+
+struct parsed_opts {
+    char* input_name;
+    char* output_name;
+    char* rg_id;
+    char* rg_line;
+    int no_pg;
+    rg_mode mode;
+    sam_global_args ga;
+    htsThreadPool p;
+    int uncompressed;
+    int overwrite_hdr_rg;
+};
+
+struct state;
+typedef struct parsed_opts parsed_opts_t;
+typedef struct state state_t;
+
+struct state {
+    samFile* input_file;
+    sam_hdr_t* input_header;
+    samFile* output_file;
+    sam_hdr_t* output_header;
+    char* rg_id;
+    void (*mode_func)(const state_t*, bam1_t*);
+};
+
+static void cleanup_opts(parsed_opts_t* opts)
+{
+    if (!opts) return;
+    free(opts->rg_id);
+    free(opts->output_name);
+    free(opts->input_name);
+    free(opts->rg_line);
+    if (opts->p.pool) hts_tpool_destroy(opts->p.pool);
+    sam_global_args_free(&opts->ga);
+    free(opts);
+}
+
+static void cleanup_state(state_t* state)
+{
+    if (!state) return;
+    free(state->rg_id);
+    if (state->output_file) sam_close(state->output_file);
+    sam_hdr_destroy(state->output_header);
+    if (state->input_file) sam_close(state->input_file);
+    sam_hdr_destroy(state->input_header);
+    free(state);
+}
+
+// Converts \t and \n into real tabs and newlines
+static char* basic_unescape(const char* in)
+{
+    assert(in);
+    char *ptr, *out;
+    out = ptr = malloc(strlen(in)+1);
+    size_t size = 0;
+    while (*in) {
+        if (*in == '\\') {
+            ++in;
+            if (*in == '\0') {
+                fprintf(samtools_stderr, "[%s] Unterminated escape sequence.\n", __func__);
+                free(out);
+                return NULL;
+            }
+            switch (*in) {
+            case '\\':
+                *ptr = '\\';
+                break;
+            case 't':
+                *ptr = '\t';
+                break;
+            case 'n':
+                fprintf(samtools_stderr, "[%s] \\n in escape sequence is not supported.\n", __func__);
+                free(out);
+                return NULL;
+            default:
+                fprintf(samtools_stderr, "[%s] Unsupported escape sequence.\n", __func__);
+                free(out);
+                return NULL;
+            }
+        } else {
+            *ptr = *in;
+        }
+        ++in;
+        ++ptr;
+        ++size;
+    }
+    *ptr = '\0';
+    ++size;
+    char* tmp = (char*)realloc(out, size);
+    if (!tmp) {
+        free(out);
+    }
+    return tmp;
+}
+
+// Malloc a string containing [s,slim) or to the end of s if slim is NULL.
+// If lenp is non-NULL, stores the length of the resulting string there.
+static char *dup_substring(const char *s, const char *slim, size_t *lenp)
+{
+    size_t len = slim? (slim - s) : strlen(s);
+    char *ns = malloc(len+1);
+    if (ns == NULL) return NULL;
+    memcpy(ns, s, len);
+    ns[len] = '\0';
+    if (lenp) *lenp = len;
+    return ns;
+}
+
+
+// Given a @RG line return the id
+static char* get_rg_id(const char *line)
+{
+    const char *id = strstr(line, "\tID:");
+    if (! id) return NULL;
+
+    id += 4;
+    return dup_substring(id, strchr(id, '\t'), NULL);
+}
+
+
+static void usage(FILE *fp)
+{
+    fprintf(fp,
+            "Usage: samtools addreplacerg [options] [-r <@RG line> | -R <existing id>] [-m orphan_only|overwrite_all] [-o <output.bam>] <input.bam>\n"
+            "\n"
+            "Options:\n"
+            "  -m MODE   Set the mode of operation from one of overwrite_all, orphan_only [overwrite_all]\n"
+            "  -o FILE   Where to write output to [samtools_stdout]\n"
+            "  -r STRING @RG line text\n"
+            "  -R STRING ID of @RG line in existing header to use\n"
+            "  -u        Output uncompressed data\n"
+            "  -w        Overwrite an existing @RG line\n"
+            "  --no-PG   Do not add a PG line\n"
+            );
+    sam_global_opt_help(fp, "..O..@..");
+}
+
+static bool parse_args(int argc, char** argv, parsed_opts_t** opts)
+{
+    *opts = NULL;
+    int n;
+
+    if (argc == 1) { usage(samtools_stdout); return true; }
+
+    parsed_opts_t* retval = calloc(1, sizeof(parsed_opts_t));
+    if (! retval ) {
+        fprintf(samtools_stderr, "[%s] Out of memory allocating parsed_opts_t\n", __func__);
+        return false;
+    }
+    // Set defaults
+    retval->mode = overwrite_all;
+    sam_global_args_init(&retval->ga);
+    static const struct option lopts[] = {
+        SAM_OPT_GLOBAL_OPTIONS(0, 0, 'O', 0, 0, '@'),
+        {"no-PG", no_argument, NULL, 1},
+        { NULL, 0, NULL, 0 }
+    };
+    kstring_t rg_line = {0,0,NULL};
+
+    while ((n = getopt_long(argc, argv, "r:R:m:o:O:h@:uw", lopts, NULL)) >= 0) {
+        switch (n) {
+            case 'r':
+                // Are we adding to existing rg line?
+                if (ks_len(&rg_line) == 0) {
+                    if (strlen(optarg)<3 || (optarg[0] != '@' && optarg[1] != 'R' && optarg[2] != 'G')) {
+                        kputs("@RG\t", &rg_line);
+                    }
+                } else {
+                    kputs("\t", &rg_line);
+                }
+                kputs(optarg, &rg_line);
+                break;
+            case 'R':
+                retval->rg_id = strdup(optarg);
+                break;
+            case 'm': {
+                if (strcmp(optarg, "overwrite_all") == 0) {
+                    retval->mode = overwrite_all;
+                } else if (strcmp(optarg, "orphan_only") == 0) {
+                    retval->mode = orphan_only;
+                } else {
+                    usage(samtools_stderr);
+                    return false;
+                }
+                break;
+            }
+            case 'o':
+                retval->output_name = strdup(optarg);
+                break;
+            case 'h':
+                usage(samtools_stdout);
+                free(retval);
+                return true;
+            case 1:
+                retval->no_pg = 1;
+                break;
+            case 'u':
+                retval->uncompressed = 1;
+                break;
+            case 'w':
+                retval->overwrite_hdr_rg = 1;
+                break;
+            case '?':
+                usage(samtools_stderr);
+                free(retval);
+                return false;
+            case 'O':
+            default:
+                if (parse_sam_global_opt(n, optarg, lopts, &retval->ga) == 0) break;
+                usage(samtools_stderr);
+                free(retval);
+                return false;
+        }
+    }
+    retval->rg_line = ks_release(&rg_line);
+
+    if (argc-optind < 1) {
+        fprintf(samtools_stderr, "You must specify an input file.\n");
+        usage(samtools_stderr);
+        cleanup_opts(retval);
+        return false;
+    }
+    if (retval->rg_id && retval->rg_line) {
+        fprintf(samtools_stderr, "The options -r and -R are mutually exclusive.\n");
+        cleanup_opts(retval);
+        return false;
+    }
+
+    if (retval->rg_line)
+    {
+        char* tmp = basic_unescape(retval->rg_line);
+
+        if ((retval->rg_id = get_rg_id(tmp)) == NULL) {
+            fprintf(samtools_stderr, "[%s] The supplied RG line lacks an ID tag.\n", __func__);
+            free(tmp);
+            cleanup_opts(retval);
+            return false;
+        }
+        free(retval->rg_line);
+        retval->rg_line = tmp;
+    }
+    retval->input_name = strdup(argv[optind+0]);
+
+    if (retval->ga.nthreads > 0) {
+        if (!(retval->p.pool = hts_tpool_init(retval->ga.nthreads))) {
+            fprintf(samtools_stderr, "Error creating thread pool\n");
+            return false;
+        }
+    }
+
+    *opts = retval;
+    return true;
+}
+
+static void overwrite_all_func(const state_t* state, bam1_t* file_read)
+{
+    uint8_t* data = (uint8_t*)strdup(state->rg_id);
+    int len = strlen(state->rg_id)+1;
+    // If the old exists delete it
+    uint8_t* old = bam_aux_get(file_read, "RG");
+    if (old != NULL) {
+        bam_aux_del(file_read, old);
+    }
+
+    bam_aux_append(file_read, "RG", 'Z', len, data);
+    free(data);
+}
+
+static void orphan_only_func(const state_t* state, bam1_t* file_read)
+{
+    uint8_t* data = (uint8_t*)strdup(state->rg_id);
+    int len = strlen(state->rg_id)+1;
+    // If the old exists don't do anything
+    uint8_t* old = bam_aux_get(file_read, "RG");
+    if (old == NULL) {
+        bam_aux_append(file_read, "RG",'Z',len,data);
+    }
+    free(data);
+}
+
+static bool init(const parsed_opts_t* opts, state_t** state_out) {
+    char output_mode[9] = "w";
+    state_t* retval = (state_t*) calloc(1, sizeof(state_t));
+
+    if (retval == NULL) {
+        fprintf(samtools_stderr, "[init] Out of memory allocating state struct.\n");
+        return false;
+    }
+    *state_out = retval;
+
+    // Open files
+    retval->input_file = sam_open_format(opts->input_name, "r", &opts->ga.in);
+    if (retval->input_file == NULL) {
+        print_error_errno("addreplacerg", "could not open \"%s\"", opts->input_name);
+        return false;
+    }
+    retval->input_header = sam_hdr_read(retval->input_file);
+
+    retval->output_header = sam_hdr_dup(retval->input_header);
+
+    if (opts->uncompressed)
+        strcat(output_mode, "0");
+    if (opts->output_name) // File format auto-detection
+        sam_open_mode(output_mode + strlen(output_mode),
+                      opts->output_name, NULL);
+    retval->output_file = sam_open_format(opts->output_name == NULL?"-":opts->output_name, output_mode, &opts->ga.out);
+
+    if (retval->output_file == NULL) {
+        print_error_errno("addreplacerg", "could not create \"%s\"", opts->output_name);
+        return false;
+    }
+
+    if (opts->p.pool) {
+        hts_set_opt(retval->input_file,  HTS_OPT_THREAD_POOL, &opts->p);
+        hts_set_opt(retval->output_file, HTS_OPT_THREAD_POOL, &opts->p);
+    }
+
+    if (opts->rg_line) {
+        // Append new RG line to header.
+        // Check does not already exist
+        kstring_t hdr_line = { 0, 0, NULL };
+        if (sam_hdr_find_line_id(retval->output_header, "RG", "ID", opts->rg_id, &hdr_line) == 0) {
+            if (opts->overwrite_hdr_rg) {
+                if(-1 == sam_hdr_remove_line_id(retval->output_header, "RG", "ID", opts->rg_id)) {
+                    fprintf(samtools_stderr, "[init] Error removing the RG line with ID:%s from the output header.\n", opts->rg_id);
+                    ks_free(&hdr_line);
+                    return false;
+                }
+            } else {
+                fprintf(samtools_stderr, "[init] RG line with ID:%s already present in the header. Use -w to overwrite.\n", opts->rg_id);
+                ks_free(&hdr_line);
+                return false;
+            }
+        }
+        ks_free(&hdr_line);
+
+        if (-1 == sam_hdr_add_lines(retval->output_header, opts->rg_line, strlen(opts->rg_line))) {
+            fprintf(samtools_stderr, "[init] Error adding RG line with ID:%s to the output header.\n", opts->rg_id);
+            return false;
+        }
+        if (opts->mode == overwrite_all &&
+            -1 == sam_hdr_remove_except(retval->output_header, "RG", "ID", opts->rg_id)) {
+            fprintf(samtools_stderr, "[init] Error removing the old RG lines from the output header.\n");
+            return false;
+        }
+        retval->rg_id = strdup(opts->rg_id);
+    } else {
+        if (opts->rg_id) {
+            // Confirm what has been supplied exists
+            kstring_t hdr_line = { 0, 0, NULL };
+            if (sam_hdr_find_line_id(retval->output_header, "RG", "ID", opts->rg_id, &hdr_line) < 0) {
+                fprintf(samtools_stderr, "RG ID supplied does not exist in header. Supply full @RG line with -r instead?\n");
+                return false;
+            }
+            retval->rg_id = strdup(opts->rg_id);
+            ks_free(&hdr_line);
+        } else {
+            kstring_t rg_id = { 0, 0, NULL };
+            if (sam_hdr_find_tag_id(retval->output_header, "RG", NULL, NULL, "ID", &rg_id) < 0) {
+                fprintf(samtools_stderr, "No RG specified on command line or in existing header.\n");
+                return false;
+            }
+            retval->rg_id = ks_release(&rg_id);
+        }
+    }
+
+    switch (opts->mode) {
+        case overwrite_all:
+            retval->mode_func = &overwrite_all_func;
+            break;
+        case orphan_only:
+            retval->mode_func = &orphan_only_func;
+            break;
+    }
+
+    return true;
+}
+
+static bool readgroupise(parsed_opts_t *opts, state_t* state, char *arg_list)
+{
+    if (!opts->no_pg && sam_hdr_add_pg(state->output_header, "samtools",
+                                       "VN", samtools_version(),
+                                       arg_list ? "CL": NULL,
+                                       arg_list ? arg_list : NULL,
+                                       NULL))
+        return false;
+
+    if (sam_hdr_write(state->output_file, state->output_header) != 0) {
+        print_error_errno("addreplacerg", "[%s] Could not write header to output file", __func__);
+        return false;
+    }
+    char *idx_fn = NULL;
+    if (opts->ga.write_index) {
+        if (!(idx_fn = auto_index(state->output_file, opts->output_name, state->output_header)))
+            return false;
+    }
+
+    bam1_t* file_read = bam_init1();
+    int ret;
+    while ((ret = sam_read1(state->input_file, state->input_header, file_read)) >= 0) {
+        state->mode_func(state, file_read);
+
+        if (sam_write1(state->output_file, state->output_header, file_read) < 0) {
+            print_error_errno("addreplacerg", "[%s] Could not write read to output file", __func__);
+            bam_destroy1(file_read);
+            free(idx_fn);
+            return false;
+        }
+    }
+    bam_destroy1(file_read);
+    if (ret != -1) {
+        print_error_errno("addreplacerg", "[%s] Error reading from input file", __func__);
+        free(idx_fn);
+        return false;
+    } else {
+
+        if (opts->ga.write_index) {
+            if (sam_idx_save(state->output_file) < 0) {
+                print_error_errno("addreplacerg", "[%s] Writing index failed", __func__);
+                free(idx_fn);
+                return false;
+            }
+        }
+        free(idx_fn);
+        return true;
+    }
+}
+
+int main_addreplacerg(int argc, char** argv)
+{
+    parsed_opts_t* opts = NULL;
+    state_t* state = NULL;
+    char *arg_list = stringify_argv(argc+1, argv-1);
+    if (!arg_list)
+        return EXIT_FAILURE;
+
+    if (!parse_args(argc, argv, &opts)) goto error;
+    if (opts) { // Not an error but user doesn't want us to proceed
+        if (!init(opts, &state) || !readgroupise(opts, state, arg_list))
+            goto error;
+    }
+
+    cleanup_state(state);
+    cleanup_opts(opts);
+    free(arg_list);
+
+    return EXIT_SUCCESS;
+error:
+    cleanup_state(state);
+    cleanup_opts(opts);
+    free(arg_list);
+
+    return EXIT_FAILURE;
+}
diff --git a/samtools/bam_ampliconclip.c b/samtools/bam_ampliconclip.c
new file mode 100644
index 0000000..2cf1ac1
--- /dev/null
+++ b/samtools/bam_ampliconclip.c
@@ -0,0 +1,1078 @@
+/*  bam_ampliconclip.c -- loads amplicon primers from a BED file and cuts reads
+                          from the 5' end.
+
+    Copyright (C) 2020-2021 Genome Research Ltd.
+
+    Authors: Andrew Whitwham <aw7@sanger.ac.uk>
+             Rob Davies <rmd+git@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE
+*/
+
+#include <config.h>
+
+#include <assert.h>
+#include <stdbool.h>
+#include <stdlib.h>
+#include <string.h>
+#include <unistd.h>
+#include <errno.h>
+#include "htslib/thread_pool.h"
+#include "sam_opts.h"
+#include <htslib/hts.h>
+#include "htslib/hfile.h"
+#include "htslib/kstring.h"
+#include "htslib/sam.h"
+#include "samtools.h"
+#include "bam_ampliconclip.h"
+
+typedef enum {
+    soft_clip,
+    hard_clip
+} clipping_type;
+
+typedef struct {
+    int add_pg;
+    int use_strand;
+    int write_clipped;
+    int mark_fail;
+    int both;
+    int fail_len;
+    int filter_len;
+    int unmapped;
+    int oa_tag;
+    int del_tag;
+    int tol;
+    char *arg_list;
+    char *stats_file;
+    char *rejects_file;
+} cl_param_t;
+
+
+static int bed_entry_sort(const void *av, const void *bv) {
+    bed_entry_t *a = (bed_entry_t *) av;
+    bed_entry_t *b = (bed_entry_t *) bv;
+    return a->right < b->right ? -1 : (a->right == b->right ? 0 : 1);
+}
+
+
+int load_bed_file_multi_ref(char *infile, int get_strand, int sort_by_pos, khash_t(bed_list_hash) *bed_lists) {
+    hFILE *fp;
+    int line_count = 0, ret;
+    int64_t left, right;
+    kstring_t line = KS_INITIALIZE;
+    bed_entry_list_t *list;
+    khiter_t bed_itr;
+
+    if ((fp = hopen(infile, "r")) == NULL) {
+        print_error_errno("amplicon", "unable to open file %s.", infile);
+        return 1;
+    }
+
+    char ref[1024];
+
+    while (line.l = 0, kgetline(&line, (kgets_func *)hgets, fp) >= 0) {
+        line_count++;
+        int hret;
+        char strand;
+
+        if (line.l == 0 || *line.s == '#') continue;
+        if (strncmp(line.s, "track ", 6) == 0) continue;
+        if (strncmp(line.s, "browser ", 8) == 0) continue;
+
+        if (get_strand) {
+            if (sscanf(line.s, "%1023s %"SCNd64" %"SCNd64" %*s %*s %c",
+                       ref, &left, &right, &strand) != 4) {
+                fprintf(stderr, "[amplicon] error: bad bed file format in line %d of %s.\n"
+                                "(N.B. ref/chrom name limited to 1023 characters.)\n",
+                                    line_count, infile);
+                ret = 1;
+                goto error;
+            }
+        } else {
+            if (sscanf(line.s, "%1023s %"SCNd64" %"SCNd64,
+                       ref, &left, &right) != 3) {
+                fprintf(stderr, "[amplicon] error: bad bed file format in line %d of %s\n"
+                                "(N.B. ref/chrom name limited to 1023 characters.)\n",
+                                    line_count, infile);
+                ret = 1;
+                goto error;
+            }
+        }
+
+        bed_itr = kh_get(bed_list_hash, bed_lists, ref);
+
+        if (bed_itr == kh_end(bed_lists)) { // new ref entry
+            char *ref_name = strdup(ref); // need a copy for the hash key
+
+            if (!ref_name) {
+                fprintf(stderr, "[amplicon] error: unable to allocate memory for ref name.\n");
+                ret = 1;
+                goto error;
+            }
+
+            bed_itr = kh_put(bed_list_hash, bed_lists, ref_name, &hret);
+
+            if (hret > 0) {
+                list = &kh_val(bed_lists, bed_itr);
+
+                // initialise the new hash entry
+                list->longest = 0;
+                list->size = 0;
+                list->length = 0;
+                list->bp = NULL;
+            } else {
+                fprintf(stderr, "[amplicon] error: ref hashing failure.\n");
+                ret = 1;
+                goto error;
+            }
+        } else { // existing ref
+            list = &kh_val(bed_lists, bed_itr);
+        }
+
+        if (list->length == list->size) {
+           bed_entry_t *tmp;
+
+           list->size += list->size / 2 + 256;
+
+           if ((tmp = realloc(list->bp, list->size * sizeof(bed_entry_t))) == NULL) {
+               fprintf(stderr, "[amplicon] error: unable to allocate more memory for bed data.\n");
+               ret = 1;
+               goto error;
+           }
+
+           list->bp = tmp;
+        }
+
+        list->bp[list->length].left  = left;
+        list->bp[list->length].right = right;
+
+        if (get_strand) {
+            if (strand == '+') {
+                list->bp[list->length].rev = 0;
+            } else if (strand == '-') {
+                list->bp[list->length].rev = 1;
+            } else {
+                fprintf(stderr, "[amplicon] error: bad strand value in line %d, expecting '+' or '-', found '%c'.\n",
+                            line_count, strand);
+                ret = 1;
+                goto error;
+            }
+        }
+
+        if (right - left > list->longest)
+            list->longest = right - left;
+
+        list->length++;
+    }
+
+    if (sort_by_pos) {
+        for (bed_itr = kh_begin(bed_lists); bed_itr != kh_end(bed_lists); ++bed_itr) {
+            if (kh_exist(bed_lists, bed_itr)) {
+                list = &kh_val(bed_lists, bed_itr);
+                qsort(list->bp, list->length, sizeof(list->bp[0]), bed_entry_sort);
+            }
+        }
+    }
+
+    if (kh_size(bed_lists) > 0) {// any entries
+        ret = 0;
+    } else {
+        ret = 1;
+    }
+
+error:
+    ks_free(&line);
+
+    if (hclose(fp) != 0) {
+        fprintf(stderr, "[amplicon] warning: failed to close %s", infile);
+    }
+
+    return ret;
+}
+
+
+void destroy_bed_hash(khash_t(bed_list_hash) *hash) {
+    khiter_t itr;
+
+    for (itr = kh_begin(hash); itr != kh_end(hash); ++itr) {
+       if (kh_exist(hash, itr)) {
+           free(kh_val(hash, itr).bp);
+           free((char *)kh_key(hash, itr));
+           kh_key(hash, itr) = NULL;
+        }
+    }
+
+    kh_destroy(bed_list_hash, hash);
+}
+
+
+static int matching_clip_site(bed_entry_list_t *sites, hts_pos_t pos,
+                              int is_rev, int use_strand, int64_t longest,
+                              cl_param_t *param) {
+    int i, size;  // may need this to be variable
+    int tol = param->tol;
+    int l = 0, mid = sites->length / 2, r = sites->length;
+    int pos_tol = is_rev ? (pos > tol ? pos - tol : 0) : pos;
+
+    while (r - l > 1) {
+        if (sites->bp[mid].right <= pos_tol) {
+            l = mid;
+        } else {
+            r = mid;
+        }
+        mid = (l + r) / 2;
+    }
+
+    size = 0;
+
+    for (i = l; i < sites->length; i++) {
+        hts_pos_t mod_left, mod_right;
+
+        if (use_strand && is_rev != sites->bp[i].rev)
+            continue;
+
+        if (is_rev) {
+            mod_left = sites->bp[i].left;
+            mod_right = sites->bp[i].right + tol;
+        } else {
+            if (sites->bp[i].left > tol) {
+                mod_left = sites->bp[i].left - tol;
+            } else {
+                mod_left = 0;
+            }
+            mod_right = sites->bp[i].right;
+        }
+
+        if (pos + longest + tol < mod_right)
+            break;
+
+        if (pos >= mod_left && pos <= mod_right) {
+            if (is_rev) {
+                if (size < pos - sites->bp[i].left) {
+                    size = pos - sites->bp[i].left;
+                }
+            } else {
+                if (size < sites->bp[i].right - pos) {
+                    size = sites->bp[i].right - pos;
+                }
+            }
+        }
+    }
+
+    return size;
+}
+
+
+static int bam_trim_left(bam1_t *rec, bam1_t *rec_out, uint32_t bases,
+                         clipping_type clipping) {
+    uint32_t *orig_cigar = bam_get_cigar(rec);
+    uint8_t *orig_seq = bam_get_seq(rec);
+    uint8_t *orig_qual = bam_get_qual(rec);
+    uint8_t *orig_aux = bam_get_aux(rec);
+    uint32_t *new_cigar;
+    uint8_t *new_qual;
+    size_t orig_l_aux = bam_get_l_aux(rec);
+    uint32_t i, j;
+    uint32_t ref_remove = bases, qry_removed = 0, hardclip = 0;
+    hts_pos_t new_pos = rec->core.pos;
+    uint32_t cig_type, cig_op;
+
+    if (rec->l_data + 8 > rec_out->m_data) {
+        uint8_t *new_data = realloc(rec_out->data, rec->l_data + 8);
+        if (!new_data) {
+            fprintf(stderr, "[ampliconclip] error: could not allocate memoy for new bam record\n");
+            return 1;
+        }
+        rec_out->data = new_data;
+        rec_out->m_data = rec->l_data + 8;
+    }
+
+    // Copy core data & name
+    memcpy(&rec_out->core, &rec->core, sizeof(rec->core));
+    memcpy(rec_out->data, rec->data, rec->core.l_qname);
+
+    if (clipping == hard_clip && bases >= rec->core.l_qseq) {
+        rec_out->core.l_qseq = 0;
+        rec_out->core.n_cigar = 0;
+
+        if (orig_l_aux)
+            memcpy(bam_get_aux(rec_out), orig_aux, orig_l_aux);
+
+        rec_out->l_data = bam_get_aux(rec_out) - rec_out->data + orig_l_aux;
+
+        return 0;
+    }
+
+    // Modify CIGAR
+    new_cigar = bam_get_cigar(rec_out);
+
+    for (i = 0;  i < rec->core.n_cigar; i++) {
+        cig_op = bam_cigar_op(orig_cigar[i]);
+        cig_type = bam_cigar_type(cig_op);
+
+        if (cig_op == BAM_CHARD_CLIP) {
+            hardclip += bam_cigar_oplen(orig_cigar[i]);
+        } else {
+            if (cig_type & 2) {
+                if (bam_cigar_oplen(orig_cigar[i]) <= ref_remove) {
+                    ref_remove -= bam_cigar_oplen(orig_cigar[i]);
+                } else {
+                    break;
+                }
+                new_pos += bam_cigar_oplen(orig_cigar[i]);
+            }
+            if (cig_type & 1) {
+                qry_removed += bam_cigar_oplen(orig_cigar[i]);
+            }
+        }
+    }
+
+    if (i < rec->core.n_cigar) {
+        cig_type = bam_cigar_type(bam_cigar_op(orig_cigar[i]));
+
+        // account for the last operation
+        if (cig_type & 2) {
+            new_pos += ref_remove;
+        }
+        if (cig_type & 1) {
+            qry_removed += ref_remove;
+        }
+    } else {
+        qry_removed = rec->core.l_qseq;
+    }
+
+    j = 0;
+    if (clipping == hard_clip && hardclip + qry_removed > 0) {
+        new_cigar[j++] = bam_cigar_gen(hardclip + qry_removed, BAM_CHARD_CLIP);
+    }
+    if (clipping == soft_clip) {
+        if (hardclip > 0) {
+            new_cigar[j++] = bam_cigar_gen(hardclip, BAM_CHARD_CLIP);
+        }
+        if (qry_removed > 0) {
+            new_cigar[j++] = bam_cigar_gen(qry_removed, BAM_CSOFT_CLIP);
+        }
+    }
+
+    if (i < rec->core.n_cigar
+        && bam_cigar_oplen(orig_cigar[i]) > ref_remove) {
+        new_cigar[j++] = bam_cigar_gen(bam_cigar_oplen(orig_cigar[i]) - ref_remove, bam_cigar_op(orig_cigar[i]));
+
+        // fill in the rest of the cigar
+        i++;
+
+        for (; i < rec->core.n_cigar; i++) {
+            new_cigar[j++] = orig_cigar[i];
+        }
+    }
+
+    rec_out->core.n_cigar = j;
+
+    if (clipping == soft_clip) {
+        qry_removed = 0; // Copy all the sequence and confidence values
+    }
+
+    new_qual = bam_get_seq(rec_out) + (rec->core.l_qseq - qry_removed + 1) / 2;
+    // Copy remaining SEQ
+    if ((qry_removed & 1) == 0) {
+        memcpy(bam_get_seq(rec_out), orig_seq + (qry_removed / 2),
+                (rec->core.l_qseq - qry_removed + 1) / 2); // +1 to account for odd numbers
+    } else {
+        uint8_t *in = orig_seq + qry_removed / 2;
+        uint8_t *out = bam_get_seq(rec_out);
+        uint32_t i;
+        for (i = qry_removed; i < rec->core.l_qseq - 1; i += 2) {
+            *out++ = ((in[0] & 0x0f) << 4) | ((in[1] & 0xf0) >> 4);
+            in++;
+        }
+        if (i < rec->core.l_qseq) {
+            *out++ = (in[0] & 0x0f) << 4;
+        }
+        assert(out == new_qual);
+    }
+
+    // Copy remaining QUAL
+    memmove(new_qual, orig_qual, rec->core.l_qseq - qry_removed);
+
+    // Set new l_qseq
+    rec_out->core.l_qseq -= qry_removed;
+
+    // Move AUX
+    if (orig_l_aux)
+        memcpy(bam_get_aux(rec_out), orig_aux, orig_l_aux);
+
+    // Set new l_data
+    rec_out->l_data = bam_get_aux(rec_out) - rec_out->data + orig_l_aux;
+
+    // put in new pos
+    rec_out->core.pos = new_pos;
+
+    return 0;
+}
+
+
+static int bam_trim_right(bam1_t *rec, bam1_t *rec_out, uint32_t bases,
+                          clipping_type clipping) {
+    uint32_t *orig_cigar = bam_get_cigar(rec);
+    uint8_t *orig_seq = bam_get_seq(rec);
+    uint8_t *orig_qual = bam_get_qual(rec);
+    uint8_t *orig_aux = bam_get_aux(rec);
+    uint32_t *new_cigar;
+    uint32_t new_n_cigar = 0;
+    uint8_t *new_qual;
+    size_t orig_l_aux = bam_get_l_aux(rec);
+    int32_t i;
+    int32_t j;
+    uint32_t ref_remove = bases, qry_removed = 0, hardclip = 0;
+    uint32_t cig_type, cig_op;
+
+    if (rec->l_data + 8 > rec_out->m_data) {
+        uint8_t *new_data = realloc(rec_out->data, rec->l_data + 8);
+        if (!new_data) {
+            fprintf(stderr, "[ampliconclip] error: could not allocate memoy for new bam record\n");
+            return 1;
+        }
+        rec_out->data = new_data;
+        rec_out->m_data = rec->l_data + 8;
+    }
+
+    // Copy core data & name
+    memcpy(&rec_out->core, &rec->core, sizeof(rec->core));
+    memcpy(rec_out->data, rec->data, rec->core.l_qname);
+
+    if (clipping == hard_clip && bases >= rec->core.l_qseq) {
+        rec_out->core.l_qseq = 0;
+        rec_out->core.n_cigar = 0;
+
+        if (orig_l_aux)
+            memcpy(bam_get_aux(rec_out), orig_aux, orig_l_aux);
+
+        rec_out->l_data = bam_get_aux(rec_out) - rec_out->data + orig_l_aux;
+        return 0;
+    }
+
+    // Modify CIGAR here
+    new_cigar = bam_get_cigar(rec_out);
+
+    for (i = rec->core.n_cigar - 1;  i >= 0; --i) {
+        cig_op = bam_cigar_op(orig_cigar[i]);
+        cig_type = bam_cigar_type(cig_op);
+
+        if (cig_op == BAM_CHARD_CLIP) {
+            hardclip += bam_cigar_oplen(orig_cigar[i]);
+        } else {
+            if (cig_type & 2) {
+                if (bam_cigar_oplen(orig_cigar[i]) <= ref_remove) {
+                    ref_remove -= bam_cigar_oplen(orig_cigar[i]);
+                } else {
+                    break;
+                }
+            }
+            if (cig_type & 1) {
+                qry_removed += bam_cigar_oplen(orig_cigar[i]);
+            }
+        }
+    }
+
+    if (i >= 0) {
+        cig_type = bam_cigar_type(bam_cigar_op(orig_cigar[i]));
+        if (cig_type & 1) {
+            qry_removed += ref_remove;
+        }
+        j = i;
+        if (qry_removed > 0) j++;
+        if (hardclip > 0 && (clipping == soft_clip || qry_removed == 0)) j++;
+    } else {
+        qry_removed = rec->core.l_qseq;
+        j = 0;
+        if (hardclip > 0 && clipping == soft_clip) j++;
+    }
+
+    if (clipping == hard_clip && hardclip + qry_removed > 0) {
+        new_cigar[j] = bam_cigar_gen(hardclip + qry_removed, BAM_CHARD_CLIP);
+        new_n_cigar++;
+    }
+    if (clipping == soft_clip) {
+        if (hardclip > 0) {
+            new_cigar[j] = bam_cigar_gen(hardclip, BAM_CHARD_CLIP);
+            new_n_cigar++;
+            if (qry_removed > 0) --j;
+        }
+        if (qry_removed > 0) {
+            new_cigar[j] = bam_cigar_gen(qry_removed, BAM_CSOFT_CLIP);
+            new_n_cigar++;
+        }
+    }
+
+    if (j > 0) {
+        new_cigar[--j] = bam_cigar_gen(bam_cigar_oplen(orig_cigar[i]) - ref_remove, bam_cigar_op(orig_cigar[i]));
+        new_n_cigar++;
+    }
+
+    // fill in the rest of the cigar
+    while (j > 0) {
+        new_cigar[--j] = orig_cigar[--i];
+        new_n_cigar++;
+    }
+
+    rec_out->core.n_cigar = new_n_cigar;
+
+    if (clipping == soft_clip)
+        qry_removed = 0; // Copy all the sequence and confidence values
+
+    new_qual = bam_get_seq(rec_out) + (rec->core.l_qseq - qry_removed + 1) / 2;
+    // Copy remaining SEQ
+    memcpy(bam_get_seq(rec_out), orig_seq, (rec->core.l_qseq - qry_removed + 1) / 2);
+
+    // Copy remaining QUAL
+    memcpy(new_qual, orig_qual, rec->core.l_qseq - qry_removed);
+
+    // Set new l_qseq
+    rec_out->core.l_qseq -= qry_removed;
+
+    // Copy AUX
+    if (orig_l_aux)
+        memcpy(bam_get_aux(rec_out), orig_aux, orig_l_aux);
+
+    // Set new l_data
+    rec_out->l_data = bam_get_aux(rec_out) - rec_out->data + orig_l_aux;
+
+    return 0;
+}
+
+
+static hts_pos_t active_query_len(bam1_t *b) {
+    uint32_t *cigar = bam_get_cigar(b);
+    uint32_t cig_type, cig_op;
+    hts_pos_t len = 0;
+    int i;
+
+    for (i = 0; i < b->core.n_cigar; i++) {
+        cig_op =  bam_cigar_op(cigar[i]);
+        cig_type = bam_cigar_type(cig_op);
+
+        if ((cig_type & 1) && (cig_op != BAM_CSOFT_CLIP)) {
+            len += bam_cigar_oplen(cigar[i]);
+        }
+    }
+
+    return len;
+}
+
+
+static inline void swap_bams(bam1_t **a, bam1_t **b) {
+    bam1_t *tmp = *a;
+    *a = *b;
+    *b = tmp;
+}
+
+
+// Format OA:Z:(RNAME,POS,strand,CIGAR,MAPQ,NM;
+static inline int tag_original_data(bam1_t *orig, kstring_t *oa_tag) {
+    char strand;
+    uint8_t *nm_tag, *old_oa_tag;
+    uint32_t *cigar;
+    int64_t nm = 0;
+    int i, res = 0;
+
+    ks_clear(oa_tag);
+
+    // if there is an existing OA tag the new one gets appended to it
+    if ((old_oa_tag = bam_aux_get(orig, "OA"))) {
+        res |= ksprintf(oa_tag, "%s", bam_aux2Z(old_oa_tag)) < 0;
+    }
+
+    if (orig->core.flag & BAM_FREVERSE)
+        strand = '-';
+    else
+        strand = '+';
+
+    if ((nm_tag = bam_aux_get(orig, "NM"))) {
+        nm = bam_aux2i(nm_tag);
+    }
+
+    res |= ksprintf(oa_tag, "%s,%"PRIhts_pos",%c,", bam_get_qname(orig), orig->core.pos + 1, strand) < 0;
+
+    for (i = 0, cigar = bam_get_cigar(orig); i < orig->core.n_cigar && res == 0; ++i) {
+        res |= kputw(bam_cigar_oplen(cigar[i]), oa_tag) < 0;
+        res |= kputc(bam_cigar_opchr(cigar[i]), oa_tag) < 0;
+    }
+
+    if (nm_tag) {
+        res |= ksprintf(oa_tag, ",%d,%"PRId64";", orig->core.qual, nm) < 0;
+    } else {
+        res |= ksprintf(oa_tag, "%d,;", orig->core.qual) < 0;
+    }
+
+    return res;
+}
+
+
+static int bam_clip(samFile *in, samFile *out, samFile *reject, char *bedfile,
+                    clipping_type clipping, cl_param_t *param) {
+    int ret = 1, r, file_open = 0;
+
+    bam_hdr_t *header = NULL;
+    bam1_t *b = NULL, *b_tmp = NULL;
+    long f_count = 0, r_count = 0, n_count = 0, l_count = 0, l_exclude = 0, b_count = 0;
+    long filtered = 0, written = 0, failed = 0;
+    kstring_t str = KS_INITIALIZE;
+    kstring_t oat = KS_INITIALIZE;
+    bed_entry_list_t *sites;
+    FILE *stats_fp = stderr;
+    khash_t(bed_list_hash) *bed_hash = kh_init(bed_list_hash);
+
+    if (load_bed_file_multi_ref(bedfile, param->use_strand, 1, bed_hash)) {
+        fprintf(stderr, "[ampliconclip] error: unable to load bed file.\n");
+        goto fail;
+    }
+
+    if ((header = sam_hdr_read(in)) == NULL) {
+        fprintf(stderr, "[ampliconclip] error: could not read header\n");
+        goto fail;
+    }
+
+    // changing pos can ruin coordinate sort order
+    if (sam_hdr_find_tag_hd(header, "SO", &str) == 0 && str.s && strcmp(str.s, "coordinate") == 0) {
+        const char *new_order = "unknown";
+
+        if (sam_hdr_update_hd(header, "SO", new_order) == -1) {
+            fprintf(stderr, "[ampliconclip] error: unable to change sort order to 'SO:%s'\n", new_order);
+            goto fail;
+        }
+    }
+
+    ks_free(&str);
+
+    if (param->add_pg && sam_hdr_add_pg(header, "samtools", "VN", samtools_version(),
+                        param->arg_list ? "CL" : NULL,
+                        param->arg_list ? param->arg_list : NULL,
+                        NULL) != 0) {
+        fprintf(stderr, "[ampliconclip] warning: unable to add @PG line to header.\n");
+    }
+    if (sam_hdr_write(out, header) < 0) {
+        fprintf(stderr, "[ampliconclip] error: could not write header.\n");
+        goto fail;
+    }
+
+    if (reject) {
+       if (sam_hdr_write(reject, header) < 0) {
+           fprintf(stderr, "[ampliconclip] error: could not write header to rejects file.\n");
+           goto fail;
+       }
+    }
+
+    b = bam_init1();
+    b_tmp = bam_init1();
+    if (!b || !b_tmp) {
+        fprintf(stderr, "[ampliconclip] error: out of memory when trying to create record.\n");
+        goto fail;
+    }
+
+    int32_t last_tid = -1;
+    int ref_found = 0;
+
+    while ((r = sam_read1(in, header, b)) >= 0) {
+        hts_pos_t pos;
+        int is_rev;
+        int p_size;
+        int been_clipped  = 0, filter = 0;
+        int exclude = (BAM_FUNMAP | BAM_FQCFAIL);
+        khiter_t itr;
+
+        l_count++;
+
+        if (b->core.tid != last_tid) {
+            const char *ref_name;
+
+            ref_found = 0;
+            last_tid = b->core.tid;
+
+            if ((ref_name = sam_hdr_tid2name(header, b->core.tid)) != NULL) {
+                itr = kh_get(bed_list_hash, bed_hash, ref_name);
+
+                if (itr != kh_end(bed_hash)) {
+                    sites = &kh_val(bed_hash, itr);
+                    ref_found = 1;
+                }
+            }
+        }
+
+        if (!(b->core.flag & exclude) && ref_found) {
+            if (param->oa_tag)
+                if (tag_original_data(b, &oat))
+                    goto fail;
+
+            if (!param->both) {
+                if (bam_is_rev(b)) {
+                    pos = bam_endpos(b);
+                    is_rev = 1;
+                } else {
+                    pos = b->core.pos;
+                    is_rev = 0;
+                }
+
+                if ((p_size = matching_clip_site(sites, pos, is_rev, param->use_strand, sites->longest, param))) {
+                    if (is_rev) {
+                        if (bam_trim_right(b, b_tmp, p_size, clipping) != 0)
+                            goto fail;
+
+                        swap_bams(&b, &b_tmp);
+                        r_count++;
+                    } else {
+                        if (bam_trim_left(b, b_tmp, p_size, clipping) != 0)
+                            goto fail;
+
+                        swap_bams(&b, &b_tmp);
+                        f_count++;
+                    }
+
+                    if (param->oa_tag) {
+                        if (bam_aux_update_str(b, "OA", oat.l + 1, (const char *)oat.s))
+                            goto fail;
+                    }
+
+                    if (param->del_tag) {
+                        uint8_t *tag;
+
+                        if ((tag = bam_aux_get(b, "NM")))
+                            bam_aux_del(b, tag);
+
+                        if ((tag = bam_aux_get(b, "MD")))
+                            bam_aux_del(b, tag);
+                    }
+
+                    been_clipped = 1;
+                } else {
+                    if (param->mark_fail) {
+                        b->core.flag |= BAM_FQCFAIL;
+                    }
+
+                    n_count++;
+                }
+            } else {
+                int left = 0, right = 0;
+
+                // left first
+                pos = b->core.pos;
+                is_rev = 0;
+
+                if ((p_size = matching_clip_site(sites, pos, is_rev, param->use_strand, sites->longest, param))) {
+                    if (bam_trim_left(b, b_tmp, p_size, clipping) != 0)
+                        goto fail;
+
+                    swap_bams(&b, &b_tmp);
+                    f_count++;
+                    left = 1;
+                    been_clipped = 1;
+                }
+
+                // the right
+                pos = bam_endpos(b);
+                is_rev = 1;
+
+                if ((p_size = matching_clip_site(sites, pos, is_rev, param->use_strand, sites->longest, param))) {
+                    if (bam_trim_right(b, b_tmp, p_size, clipping) != 0)
+                        goto fail;
+
+                    swap_bams(&b, &b_tmp);
+                    r_count++;
+                    right = 1;
+                    been_clipped = 1;
+                }
+
+                if (left || right) {
+                    uint8_t *tag;
+
+                    if (param->oa_tag) {
+                        if (bam_aux_update_str(b, "OA", oat.l + 1, (const char *)oat.s))
+                            goto fail;
+                    }
+
+                    if (param->del_tag) {
+                        if ((tag = bam_aux_get(b, "NM")))
+                            bam_aux_del(b, tag);
+
+                        if ((tag = bam_aux_get(b, "MD")))
+                            bam_aux_del(b, tag);
+                    }
+                }
+
+                if (left && right) {
+                    b_count++;
+                } else if (!left && !right) {
+                    if (param->mark_fail) {
+                        b->core.flag |= BAM_FQCFAIL;
+                    }
+
+                    n_count++;
+                }
+            }
+
+            if (param->fail_len >= 0 || param->filter_len >= 0) {
+               hts_pos_t aql = active_query_len(b);
+
+               if (param->fail_len >= 0 && aql <= param->fail_len) {
+                   b->core.flag |= BAM_FQCFAIL;
+               }
+
+               if (param->filter_len >= 0 && aql <= param->filter_len) {
+                   filter = 1;
+               }
+           }
+
+           if (b->core.flag & BAM_FQCFAIL) {
+               failed++;
+           }
+
+           if (param->write_clipped && !been_clipped) {
+               filter = 1;
+           }
+
+        } else {
+            l_exclude++;
+
+            if (param->unmapped) {
+                filter = 1;
+            }
+        }
+
+        if (!filter) {
+            if (sam_write1(out, header, b) < 0) {
+                fprintf(stderr, "[ampliconclip] error: could not write line %ld.\n", l_count);
+                goto fail;
+            }
+
+            written++;
+        } else {
+            if (reject) {
+                if (sam_write1(reject, header, b) < 0) {
+                    fprintf(stderr, "[ampliconclip] error: could not write to reject file %s\n",
+                            param->rejects_file);
+                    goto fail;
+                }
+            }
+
+            filtered++;
+        }
+    }
+
+    if (r < -1) {
+        fprintf(stderr, "[ampliconclip] error: failed to read input.\n");
+        goto fail;
+    }
+
+    if (param->stats_file) {
+        if ((stats_fp = fopen(param->stats_file, "w")) == NULL) {
+            fprintf(stderr, "[ampliconclip] warning: cannot write stats to %s.\n", param->stats_file);
+        } else {
+            file_open = 1;
+        }
+    }
+
+    fprintf(stats_fp, "COMMAND: %s\n"
+                    "TOTAL READS: %ld\n"
+                    "TOTAL CLIPPED: %ld\n"
+                    "FORWARD CLIPPED: %ld\n"
+                    "REVERSE CLIPPED: %ld\n"
+                    "BOTH CLIPPED: %ld\n"
+                    "NOT CLIPPED: %ld\n"
+                    "EXCLUDED: %ld\n"
+                    "FILTERED: %ld\n"
+                    "FAILED: %ld\n"
+                    "WRITTEN: %ld\n", param->arg_list, l_count, f_count + r_count,
+                                    f_count, r_count, b_count, n_count, l_exclude,
+                                    filtered, failed, written);
+
+    if (file_open) {
+        fclose(stats_fp);
+    }
+
+    ret = 0;
+
+fail:
+    destroy_bed_hash(bed_hash);
+    ks_free(&oat);
+    sam_hdr_destroy(header);
+    bam_destroy1(b);
+    bam_destroy1(b_tmp);
+    return ret;
+}
+
+
+static void usage(void) {
+    fprintf(stderr, "Usage: samtools ampliconclip -b BED file <input.bam> -o <output.bam>\n\n");
+    fprintf(stderr, "Option: \n");
+    fprintf(stderr, " -b  FILE            BED file of regions (eg amplicon primers) to be removed.\n");
+    fprintf(stderr, " -o  FILE            output file name (default stdout).\n");
+    fprintf(stderr, " -f  FILE            write stats to file name (default stderr)\n");
+    fprintf(stderr, " -u                  Output uncompressed data\n");
+    fprintf(stderr, " --soft-clip         soft clip amplicon primers from reads (default)\n");
+    fprintf(stderr, " --hard-clip         hard clip amplicon primers from reads.\n");
+    fprintf(stderr, " --both-ends         clip on both 5' and 3' ends.\n");
+    fprintf(stderr, " --strand            use strand data from BED file to match read direction.\n");
+    fprintf(stderr, " --clipped           only output clipped reads.\n");
+    fprintf(stderr, " --fail              mark unclipped, mapped reads as QCFAIL.\n");
+    fprintf(stderr, " --filter-len INT    do not output reads INT size or shorter.\n");
+    fprintf(stderr, " --fail-len   INT    mark as QCFAIL reads INT size or shorter.\n");
+    fprintf(stderr, " --no-excluded       do not write excluded reads (unmapped or QCFAIL).\n");
+    fprintf(stderr, " --rejects-file FILE file to write filtered reads.\n");
+    fprintf(stderr, " --original          for clipped entries add an OA tag with original data.\n");
+    fprintf(stderr, " --keep-tag          for clipped entries keep the old NM and MD tags.\n");
+    fprintf(stderr, " --tolerance         match region within this number of bases, default 5.\n");
+    fprintf(stderr, " --no-PG             do not add an @PG line.\n");
+    sam_global_opt_help(stderr, "-.O..@-.");
+    fprintf(stderr, "\nAbout: Soft clips read alignments where they match BED file defined regions.\n"
+                    "Default clipping is only on the 5' end.\n\n");
+}
+
+
+int amplicon_clip_main(int argc, char **argv) {
+    int c, ret;
+    char wmode[4] = {'w', 'b', 0, 0};
+    char *bedfile = NULL, *fnout = "-";
+    sam_global_args ga = SAM_GLOBAL_ARGS_INIT;
+    htsThreadPool p = {NULL, 0};
+    samFile *in = NULL, *out = NULL, *reject = NULL;
+    clipping_type clipping = soft_clip;
+    cl_param_t param = {1, 0, 0, 0, 0, -1, -1, 0, 0, 1, 5, NULL, NULL, NULL};
+
+    static const struct option lopts[] = {
+        SAM_OPT_GLOBAL_OPTIONS('-', 0, 'O', 0, 0, '@'),
+        {"no-PG", no_argument, NULL, 1002},
+        {"soft-clip", no_argument, NULL, 1003},
+        {"hard-clip", no_argument, NULL, 1004},
+        {"strand", no_argument, NULL, 1005},
+        {"clipped", no_argument, NULL, 1006},
+        {"fail", no_argument, NULL, 1007},
+        {"both-ends", no_argument, NULL, 1008},
+        {"filter-len", required_argument, NULL, 1009},
+        {"fail-len", required_argument, NULL, 1010},
+        {"no-excluded", no_argument, NULL, 1011},
+        {"rejects-file", required_argument, NULL, 1012},
+        {"original", no_argument, NULL, 1013},
+        {"keep-tag", no_argument, NULL, 1014},
+        {"tolerance", required_argument, NULL, 1015},
+        {NULL, 0, NULL, 0}
+    };
+
+    while ((c = getopt_long(argc, argv, "b:@:o:O:f:u", lopts, NULL)) >= 0) {
+        switch (c) {
+            case 'b': bedfile = optarg; break;
+            case 'o': fnout = optarg; break;
+            case 'f': param.stats_file = optarg; break;
+            case 'u': wmode[2] = '0'; break;
+            case 1002: param.add_pg = 0; break;
+            case 1003: clipping = soft_clip; break;
+            case 1004: clipping = hard_clip; break;
+            case 1005: param.use_strand = 1; break;
+            case 1006: param.write_clipped = 1; break;
+            case 1007: param.mark_fail = 1; break;
+            case 1008: param.both = 1; break;
+            case 1009: param.filter_len = atoi(optarg); break;
+            case 1010: param.fail_len = atoi(optarg); break;
+            case 1011: param.unmapped = 1; break;
+            case 1012: param.rejects_file = optarg; break;
+            case 1013: param.oa_tag = 1; break;
+            case 1014: param.del_tag = 0; break;
+            case 1015: param.tol = atoi(optarg); break;
+            default:  if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break;
+                      /* else fall-through */
+            case '?': usage(); exit(1);
+        }
+    }
+
+    if (!bedfile) {
+        usage();
+        return 1;
+    }
+
+    if (optind + 1 > argc) {
+        usage();
+        return 1;
+    }
+
+    if (param.tol < 0) {
+        fprintf(stderr, "[ampliconclip] warning: invalid tolerance of %d,"
+                        " reseting tolerance to default of 5.\n", param.tol);
+        param.tol = 5;
+    }
+
+    if ((in = sam_open_format(argv[optind], "rb", &ga.in)) == NULL) {
+        print_error_errno("ampliconclip", "cannot open input file");
+        return 1;
+    }
+
+    sam_open_mode(wmode+1, fnout, NULL);
+
+    if ((out = sam_open_format(fnout, wmode, &ga.out)) == NULL) {
+        print_error_errno("ampliconclip", "cannot open output file");
+        return 1;
+    }
+
+    if (param.rejects_file) {
+        sam_open_mode(wmode+1, param.rejects_file, NULL);
+
+        if ((reject = sam_open_format(param.rejects_file, wmode, &ga.out)) == NULL) {
+            print_error_errno("ampliconclip", "cannot open rejects file");
+            return 1;
+        }
+    }
+
+    if (ga.nthreads > 0) {
+        if (!(p.pool = hts_tpool_init(ga.nthreads))) {
+            fprintf(stderr, "[ampliconclip] error: cannot create thread pool.\n");
+            return 1;
+        }
+        hts_set_opt(in,  HTS_OPT_THREAD_POOL, &p);
+        hts_set_opt(out, HTS_OPT_THREAD_POOL, &p);
+
+        if (reject) {
+           hts_set_opt(reject,  HTS_OPT_THREAD_POOL, &p);
+        }
+    }
+
+    param.arg_list = stringify_argv(argc + 1, argv - 1);
+
+    ret = bam_clip(in, out, reject, bedfile, clipping, &param);
+
+    // cleanup
+    sam_close(in);
+
+    if (sam_close(out) < 0) {
+        fprintf(stderr, "[ampliconclip] error: error while closing output file %s.\n", argv[optind+1]);
+        ret = 1;
+    }
+
+    if (reject) {
+        if (sam_close(reject) < 0) {
+            fprintf(stderr, "[ampliconclip] error: error while closing reject file %s.\n", param.rejects_file);
+            ret = 1;
+        }
+    }
+
+    if (p.pool) hts_tpool_destroy(p.pool);
+
+    sam_global_args_free(&ga);
+    free(param.arg_list);
+
+    return ret;
+}
+
diff --git a/samtools/bam_ampliconclip.c.pysam.c b/samtools/bam_ampliconclip.c.pysam.c
new file mode 100644
index 0000000..1feda1d
--- /dev/null
+++ b/samtools/bam_ampliconclip.c.pysam.c
@@ -0,0 +1,1080 @@
+#include "samtools.pysam.h"
+
+/*  bam_ampliconclip.c -- loads amplicon primers from a BED file and cuts reads
+                          from the 5' end.
+
+    Copyright (C) 2020-2021 Genome Research Ltd.
+
+    Authors: Andrew Whitwham <aw7@sanger.ac.uk>
+             Rob Davies <rmd+git@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE
+*/
+
+#include <config.h>
+
+#include <assert.h>
+#include <stdbool.h>
+#include <stdlib.h>
+#include <string.h>
+#include <unistd.h>
+#include <errno.h>
+#include "htslib/thread_pool.h"
+#include "sam_opts.h"
+#include <htslib/hts.h>
+#include "htslib/hfile.h"
+#include "htslib/kstring.h"
+#include "htslib/sam.h"
+#include "samtools.h"
+#include "bam_ampliconclip.h"
+
+typedef enum {
+    soft_clip,
+    hard_clip
+} clipping_type;
+
+typedef struct {
+    int add_pg;
+    int use_strand;
+    int write_clipped;
+    int mark_fail;
+    int both;
+    int fail_len;
+    int filter_len;
+    int unmapped;
+    int oa_tag;
+    int del_tag;
+    int tol;
+    char *arg_list;
+    char *stats_file;
+    char *rejects_file;
+} cl_param_t;
+
+
+static int bed_entry_sort(const void *av, const void *bv) {
+    bed_entry_t *a = (bed_entry_t *) av;
+    bed_entry_t *b = (bed_entry_t *) bv;
+    return a->right < b->right ? -1 : (a->right == b->right ? 0 : 1);
+}
+
+
+int load_bed_file_multi_ref(char *infile, int get_strand, int sort_by_pos, khash_t(bed_list_hash) *bed_lists) {
+    hFILE *fp;
+    int line_count = 0, ret;
+    int64_t left, right;
+    kstring_t line = KS_INITIALIZE;
+    bed_entry_list_t *list;
+    khiter_t bed_itr;
+
+    if ((fp = hopen(infile, "r")) == NULL) {
+        print_error_errno("amplicon", "unable to open file %s.", infile);
+        return 1;
+    }
+
+    char ref[1024];
+
+    while (line.l = 0, kgetline(&line, (kgets_func *)hgets, fp) >= 0) {
+        line_count++;
+        int hret;
+        char strand;
+
+        if (line.l == 0 || *line.s == '#') continue;
+        if (strncmp(line.s, "track ", 6) == 0) continue;
+        if (strncmp(line.s, "browser ", 8) == 0) continue;
+
+        if (get_strand) {
+            if (sscanf(line.s, "%1023s %"SCNd64" %"SCNd64" %*s %*s %c",
+                       ref, &left, &right, &strand) != 4) {
+                fprintf(samtools_stderr, "[amplicon] error: bad bed file format in line %d of %s.\n"
+                                "(N.B. ref/chrom name limited to 1023 characters.)\n",
+                                    line_count, infile);
+                ret = 1;
+                goto error;
+            }
+        } else {
+            if (sscanf(line.s, "%1023s %"SCNd64" %"SCNd64,
+                       ref, &left, &right) != 3) {
+                fprintf(samtools_stderr, "[amplicon] error: bad bed file format in line %d of %s\n"
+                                "(N.B. ref/chrom name limited to 1023 characters.)\n",
+                                    line_count, infile);
+                ret = 1;
+                goto error;
+            }
+        }
+
+        bed_itr = kh_get(bed_list_hash, bed_lists, ref);
+
+        if (bed_itr == kh_end(bed_lists)) { // new ref entry
+            char *ref_name = strdup(ref); // need a copy for the hash key
+
+            if (!ref_name) {
+                fprintf(samtools_stderr, "[amplicon] error: unable to allocate memory for ref name.\n");
+                ret = 1;
+                goto error;
+            }
+
+            bed_itr = kh_put(bed_list_hash, bed_lists, ref_name, &hret);
+
+            if (hret > 0) {
+                list = &kh_val(bed_lists, bed_itr);
+
+                // initialise the new hash entry
+                list->longest = 0;
+                list->size = 0;
+                list->length = 0;
+                list->bp = NULL;
+            } else {
+                fprintf(samtools_stderr, "[amplicon] error: ref hashing failure.\n");
+                ret = 1;
+                goto error;
+            }
+        } else { // existing ref
+            list = &kh_val(bed_lists, bed_itr);
+        }
+
+        if (list->length == list->size) {
+           bed_entry_t *tmp;
+
+           list->size += list->size / 2 + 256;
+
+           if ((tmp = realloc(list->bp, list->size * sizeof(bed_entry_t))) == NULL) {
+               fprintf(samtools_stderr, "[amplicon] error: unable to allocate more memory for bed data.\n");
+               ret = 1;
+               goto error;
+           }
+
+           list->bp = tmp;
+        }
+
+        list->bp[list->length].left  = left;
+        list->bp[list->length].right = right;
+
+        if (get_strand) {
+            if (strand == '+') {
+                list->bp[list->length].rev = 0;
+            } else if (strand == '-') {
+                list->bp[list->length].rev = 1;
+            } else {
+                fprintf(samtools_stderr, "[amplicon] error: bad strand value in line %d, expecting '+' or '-', found '%c'.\n",
+                            line_count, strand);
+                ret = 1;
+                goto error;
+            }
+        }
+
+        if (right - left > list->longest)
+            list->longest = right - left;
+
+        list->length++;
+    }
+
+    if (sort_by_pos) {
+        for (bed_itr = kh_begin(bed_lists); bed_itr != kh_end(bed_lists); ++bed_itr) {
+            if (kh_exist(bed_lists, bed_itr)) {
+                list = &kh_val(bed_lists, bed_itr);
+                qsort(list->bp, list->length, sizeof(list->bp[0]), bed_entry_sort);
+            }
+        }
+    }
+
+    if (kh_size(bed_lists) > 0) {// any entries
+        ret = 0;
+    } else {
+        ret = 1;
+    }
+
+error:
+    ks_free(&line);
+
+    if (hclose(fp) != 0) {
+        fprintf(samtools_stderr, "[amplicon] warning: failed to close %s", infile);
+    }
+
+    return ret;
+}
+
+
+void destroy_bed_hash(khash_t(bed_list_hash) *hash) {
+    khiter_t itr;
+
+    for (itr = kh_begin(hash); itr != kh_end(hash); ++itr) {
+       if (kh_exist(hash, itr)) {
+           free(kh_val(hash, itr).bp);
+           free((char *)kh_key(hash, itr));
+           kh_key(hash, itr) = NULL;
+        }
+    }
+
+    kh_destroy(bed_list_hash, hash);
+}
+
+
+static int matching_clip_site(bed_entry_list_t *sites, hts_pos_t pos,
+                              int is_rev, int use_strand, int64_t longest,
+                              cl_param_t *param) {
+    int i, size;  // may need this to be variable
+    int tol = param->tol;
+    int l = 0, mid = sites->length / 2, r = sites->length;
+    int pos_tol = is_rev ? (pos > tol ? pos - tol : 0) : pos;
+
+    while (r - l > 1) {
+        if (sites->bp[mid].right <= pos_tol) {
+            l = mid;
+        } else {
+            r = mid;
+        }
+        mid = (l + r) / 2;
+    }
+
+    size = 0;
+
+    for (i = l; i < sites->length; i++) {
+        hts_pos_t mod_left, mod_right;
+
+        if (use_strand && is_rev != sites->bp[i].rev)
+            continue;
+
+        if (is_rev) {
+            mod_left = sites->bp[i].left;
+            mod_right = sites->bp[i].right + tol;
+        } else {
+            if (sites->bp[i].left > tol) {
+                mod_left = sites->bp[i].left - tol;
+            } else {
+                mod_left = 0;
+            }
+            mod_right = sites->bp[i].right;
+        }
+
+        if (pos + longest + tol < mod_right)
+            break;
+
+        if (pos >= mod_left && pos <= mod_right) {
+            if (is_rev) {
+                if (size < pos - sites->bp[i].left) {
+                    size = pos - sites->bp[i].left;
+                }
+            } else {
+                if (size < sites->bp[i].right - pos) {
+                    size = sites->bp[i].right - pos;
+                }
+            }
+        }
+    }
+
+    return size;
+}
+
+
+static int bam_trim_left(bam1_t *rec, bam1_t *rec_out, uint32_t bases,
+                         clipping_type clipping) {
+    uint32_t *orig_cigar = bam_get_cigar(rec);
+    uint8_t *orig_seq = bam_get_seq(rec);
+    uint8_t *orig_qual = bam_get_qual(rec);
+    uint8_t *orig_aux = bam_get_aux(rec);
+    uint32_t *new_cigar;
+    uint8_t *new_qual;
+    size_t orig_l_aux = bam_get_l_aux(rec);
+    uint32_t i, j;
+    uint32_t ref_remove = bases, qry_removed = 0, hardclip = 0;
+    hts_pos_t new_pos = rec->core.pos;
+    uint32_t cig_type, cig_op;
+
+    if (rec->l_data + 8 > rec_out->m_data) {
+        uint8_t *new_data = realloc(rec_out->data, rec->l_data + 8);
+        if (!new_data) {
+            fprintf(samtools_stderr, "[ampliconclip] error: could not allocate memoy for new bam record\n");
+            return 1;
+        }
+        rec_out->data = new_data;
+        rec_out->m_data = rec->l_data + 8;
+    }
+
+    // Copy core data & name
+    memcpy(&rec_out->core, &rec->core, sizeof(rec->core));
+    memcpy(rec_out->data, rec->data, rec->core.l_qname);
+
+    if (clipping == hard_clip && bases >= rec->core.l_qseq) {
+        rec_out->core.l_qseq = 0;
+        rec_out->core.n_cigar = 0;
+
+        if (orig_l_aux)
+            memcpy(bam_get_aux(rec_out), orig_aux, orig_l_aux);
+
+        rec_out->l_data = bam_get_aux(rec_out) - rec_out->data + orig_l_aux;
+
+        return 0;
+    }
+
+    // Modify CIGAR
+    new_cigar = bam_get_cigar(rec_out);
+
+    for (i = 0;  i < rec->core.n_cigar; i++) {
+        cig_op = bam_cigar_op(orig_cigar[i]);
+        cig_type = bam_cigar_type(cig_op);
+
+        if (cig_op == BAM_CHARD_CLIP) {
+            hardclip += bam_cigar_oplen(orig_cigar[i]);
+        } else {
+            if (cig_type & 2) {
+                if (bam_cigar_oplen(orig_cigar[i]) <= ref_remove) {
+                    ref_remove -= bam_cigar_oplen(orig_cigar[i]);
+                } else {
+                    break;
+                }
+                new_pos += bam_cigar_oplen(orig_cigar[i]);
+            }
+            if (cig_type & 1) {
+                qry_removed += bam_cigar_oplen(orig_cigar[i]);
+            }
+        }
+    }
+
+    if (i < rec->core.n_cigar) {
+        cig_type = bam_cigar_type(bam_cigar_op(orig_cigar[i]));
+
+        // account for the last operation
+        if (cig_type & 2) {
+            new_pos += ref_remove;
+        }
+        if (cig_type & 1) {
+            qry_removed += ref_remove;
+        }
+    } else {
+        qry_removed = rec->core.l_qseq;
+    }
+
+    j = 0;
+    if (clipping == hard_clip && hardclip + qry_removed > 0) {
+        new_cigar[j++] = bam_cigar_gen(hardclip + qry_removed, BAM_CHARD_CLIP);
+    }
+    if (clipping == soft_clip) {
+        if (hardclip > 0) {
+            new_cigar[j++] = bam_cigar_gen(hardclip, BAM_CHARD_CLIP);
+        }
+        if (qry_removed > 0) {
+            new_cigar[j++] = bam_cigar_gen(qry_removed, BAM_CSOFT_CLIP);
+        }
+    }
+
+    if (i < rec->core.n_cigar
+        && bam_cigar_oplen(orig_cigar[i]) > ref_remove) {
+        new_cigar[j++] = bam_cigar_gen(bam_cigar_oplen(orig_cigar[i]) - ref_remove, bam_cigar_op(orig_cigar[i]));
+
+        // fill in the rest of the cigar
+        i++;
+
+        for (; i < rec->core.n_cigar; i++) {
+            new_cigar[j++] = orig_cigar[i];
+        }
+    }
+
+    rec_out->core.n_cigar = j;
+
+    if (clipping == soft_clip) {
+        qry_removed = 0; // Copy all the sequence and confidence values
+    }
+
+    new_qual = bam_get_seq(rec_out) + (rec->core.l_qseq - qry_removed + 1) / 2;
+    // Copy remaining SEQ
+    if ((qry_removed & 1) == 0) {
+        memcpy(bam_get_seq(rec_out), orig_seq + (qry_removed / 2),
+                (rec->core.l_qseq - qry_removed + 1) / 2); // +1 to account for odd numbers
+    } else {
+        uint8_t *in = orig_seq + qry_removed / 2;
+        uint8_t *out = bam_get_seq(rec_out);
+        uint32_t i;
+        for (i = qry_removed; i < rec->core.l_qseq - 1; i += 2) {
+            *out++ = ((in[0] & 0x0f) << 4) | ((in[1] & 0xf0) >> 4);
+            in++;
+        }
+        if (i < rec->core.l_qseq) {
+            *out++ = (in[0] & 0x0f) << 4;
+        }
+        assert(out == new_qual);
+    }
+
+    // Copy remaining QUAL
+    memmove(new_qual, orig_qual, rec->core.l_qseq - qry_removed);
+
+    // Set new l_qseq
+    rec_out->core.l_qseq -= qry_removed;
+
+    // Move AUX
+    if (orig_l_aux)
+        memcpy(bam_get_aux(rec_out), orig_aux, orig_l_aux);
+
+    // Set new l_data
+    rec_out->l_data = bam_get_aux(rec_out) - rec_out->data + orig_l_aux;
+
+    // put in new pos
+    rec_out->core.pos = new_pos;
+
+    return 0;
+}
+
+
+static int bam_trim_right(bam1_t *rec, bam1_t *rec_out, uint32_t bases,
+                          clipping_type clipping) {
+    uint32_t *orig_cigar = bam_get_cigar(rec);
+    uint8_t *orig_seq = bam_get_seq(rec);
+    uint8_t *orig_qual = bam_get_qual(rec);
+    uint8_t *orig_aux = bam_get_aux(rec);
+    uint32_t *new_cigar;
+    uint32_t new_n_cigar = 0;
+    uint8_t *new_qual;
+    size_t orig_l_aux = bam_get_l_aux(rec);
+    int32_t i;
+    int32_t j;
+    uint32_t ref_remove = bases, qry_removed = 0, hardclip = 0;
+    uint32_t cig_type, cig_op;
+
+    if (rec->l_data + 8 > rec_out->m_data) {
+        uint8_t *new_data = realloc(rec_out->data, rec->l_data + 8);
+        if (!new_data) {
+            fprintf(samtools_stderr, "[ampliconclip] error: could not allocate memoy for new bam record\n");
+            return 1;
+        }
+        rec_out->data = new_data;
+        rec_out->m_data = rec->l_data + 8;
+    }
+
+    // Copy core data & name
+    memcpy(&rec_out->core, &rec->core, sizeof(rec->core));
+    memcpy(rec_out->data, rec->data, rec->core.l_qname);
+
+    if (clipping == hard_clip && bases >= rec->core.l_qseq) {
+        rec_out->core.l_qseq = 0;
+        rec_out->core.n_cigar = 0;
+
+        if (orig_l_aux)
+            memcpy(bam_get_aux(rec_out), orig_aux, orig_l_aux);
+
+        rec_out->l_data = bam_get_aux(rec_out) - rec_out->data + orig_l_aux;
+        return 0;
+    }
+
+    // Modify CIGAR here
+    new_cigar = bam_get_cigar(rec_out);
+
+    for (i = rec->core.n_cigar - 1;  i >= 0; --i) {
+        cig_op = bam_cigar_op(orig_cigar[i]);
+        cig_type = bam_cigar_type(cig_op);
+
+        if (cig_op == BAM_CHARD_CLIP) {
+            hardclip += bam_cigar_oplen(orig_cigar[i]);
+        } else {
+            if (cig_type & 2) {
+                if (bam_cigar_oplen(orig_cigar[i]) <= ref_remove) {
+                    ref_remove -= bam_cigar_oplen(orig_cigar[i]);
+                } else {
+                    break;
+                }
+            }
+            if (cig_type & 1) {
+                qry_removed += bam_cigar_oplen(orig_cigar[i]);
+            }
+        }
+    }
+
+    if (i >= 0) {
+        cig_type = bam_cigar_type(bam_cigar_op(orig_cigar[i]));
+        if (cig_type & 1) {
+            qry_removed += ref_remove;
+        }
+        j = i;
+        if (qry_removed > 0) j++;
+        if (hardclip > 0 && (clipping == soft_clip || qry_removed == 0)) j++;
+    } else {
+        qry_removed = rec->core.l_qseq;
+        j = 0;
+        if (hardclip > 0 && clipping == soft_clip) j++;
+    }
+
+    if (clipping == hard_clip && hardclip + qry_removed > 0) {
+        new_cigar[j] = bam_cigar_gen(hardclip + qry_removed, BAM_CHARD_CLIP);
+        new_n_cigar++;
+    }
+    if (clipping == soft_clip) {
+        if (hardclip > 0) {
+            new_cigar[j] = bam_cigar_gen(hardclip, BAM_CHARD_CLIP);
+            new_n_cigar++;
+            if (qry_removed > 0) --j;
+        }
+        if (qry_removed > 0) {
+            new_cigar[j] = bam_cigar_gen(qry_removed, BAM_CSOFT_CLIP);
+            new_n_cigar++;
+        }
+    }
+
+    if (j > 0) {
+        new_cigar[--j] = bam_cigar_gen(bam_cigar_oplen(orig_cigar[i]) - ref_remove, bam_cigar_op(orig_cigar[i]));
+        new_n_cigar++;
+    }
+
+    // fill in the rest of the cigar
+    while (j > 0) {
+        new_cigar[--j] = orig_cigar[--i];
+        new_n_cigar++;
+    }
+
+    rec_out->core.n_cigar = new_n_cigar;
+
+    if (clipping == soft_clip)
+        qry_removed = 0; // Copy all the sequence and confidence values
+
+    new_qual = bam_get_seq(rec_out) + (rec->core.l_qseq - qry_removed + 1) / 2;
+    // Copy remaining SEQ
+    memcpy(bam_get_seq(rec_out), orig_seq, (rec->core.l_qseq - qry_removed + 1) / 2);
+
+    // Copy remaining QUAL
+    memcpy(new_qual, orig_qual, rec->core.l_qseq - qry_removed);
+
+    // Set new l_qseq
+    rec_out->core.l_qseq -= qry_removed;
+
+    // Copy AUX
+    if (orig_l_aux)
+        memcpy(bam_get_aux(rec_out), orig_aux, orig_l_aux);
+
+    // Set new l_data
+    rec_out->l_data = bam_get_aux(rec_out) - rec_out->data + orig_l_aux;
+
+    return 0;
+}
+
+
+static hts_pos_t active_query_len(bam1_t *b) {
+    uint32_t *cigar = bam_get_cigar(b);
+    uint32_t cig_type, cig_op;
+    hts_pos_t len = 0;
+    int i;
+
+    for (i = 0; i < b->core.n_cigar; i++) {
+        cig_op =  bam_cigar_op(cigar[i]);
+        cig_type = bam_cigar_type(cig_op);
+
+        if ((cig_type & 1) && (cig_op != BAM_CSOFT_CLIP)) {
+            len += bam_cigar_oplen(cigar[i]);
+        }
+    }
+
+    return len;
+}
+
+
+static inline void swap_bams(bam1_t **a, bam1_t **b) {
+    bam1_t *tmp = *a;
+    *a = *b;
+    *b = tmp;
+}
+
+
+// Format OA:Z:(RNAME,POS,strand,CIGAR,MAPQ,NM;
+static inline int tag_original_data(bam1_t *orig, kstring_t *oa_tag) {
+    char strand;
+    uint8_t *nm_tag, *old_oa_tag;
+    uint32_t *cigar;
+    int64_t nm = 0;
+    int i, res = 0;
+
+    ks_clear(oa_tag);
+
+    // if there is an existing OA tag the new one gets appended to it
+    if ((old_oa_tag = bam_aux_get(orig, "OA"))) {
+        res |= ksprintf(oa_tag, "%s", bam_aux2Z(old_oa_tag)) < 0;
+    }
+
+    if (orig->core.flag & BAM_FREVERSE)
+        strand = '-';
+    else
+        strand = '+';
+
+    if ((nm_tag = bam_aux_get(orig, "NM"))) {
+        nm = bam_aux2i(nm_tag);
+    }
+
+    res |= ksprintf(oa_tag, "%s,%"PRIhts_pos",%c,", bam_get_qname(orig), orig->core.pos + 1, strand) < 0;
+
+    for (i = 0, cigar = bam_get_cigar(orig); i < orig->core.n_cigar && res == 0; ++i) {
+        res |= kputw(bam_cigar_oplen(cigar[i]), oa_tag) < 0;
+        res |= kputc(bam_cigar_opchr(cigar[i]), oa_tag) < 0;
+    }
+
+    if (nm_tag) {
+        res |= ksprintf(oa_tag, ",%d,%"PRId64";", orig->core.qual, nm) < 0;
+    } else {
+        res |= ksprintf(oa_tag, "%d,;", orig->core.qual) < 0;
+    }
+
+    return res;
+}
+
+
+static int bam_clip(samFile *in, samFile *out, samFile *reject, char *bedfile,
+                    clipping_type clipping, cl_param_t *param) {
+    int ret = 1, r, file_open = 0;
+
+    bam_hdr_t *header = NULL;
+    bam1_t *b = NULL, *b_tmp = NULL;
+    long f_count = 0, r_count = 0, n_count = 0, l_count = 0, l_exclude = 0, b_count = 0;
+    long filtered = 0, written = 0, failed = 0;
+    kstring_t str = KS_INITIALIZE;
+    kstring_t oat = KS_INITIALIZE;
+    bed_entry_list_t *sites;
+    FILE *stats_fp = samtools_stderr;
+    khash_t(bed_list_hash) *bed_hash = kh_init(bed_list_hash);
+
+    if (load_bed_file_multi_ref(bedfile, param->use_strand, 1, bed_hash)) {
+        fprintf(samtools_stderr, "[ampliconclip] error: unable to load bed file.\n");
+        goto fail;
+    }
+
+    if ((header = sam_hdr_read(in)) == NULL) {
+        fprintf(samtools_stderr, "[ampliconclip] error: could not read header\n");
+        goto fail;
+    }
+
+    // changing pos can ruin coordinate sort order
+    if (sam_hdr_find_tag_hd(header, "SO", &str) == 0 && str.s && strcmp(str.s, "coordinate") == 0) {
+        const char *new_order = "unknown";
+
+        if (sam_hdr_update_hd(header, "SO", new_order) == -1) {
+            fprintf(samtools_stderr, "[ampliconclip] error: unable to change sort order to 'SO:%s'\n", new_order);
+            goto fail;
+        }
+    }
+
+    ks_free(&str);
+
+    if (param->add_pg && sam_hdr_add_pg(header, "samtools", "VN", samtools_version(),
+                        param->arg_list ? "CL" : NULL,
+                        param->arg_list ? param->arg_list : NULL,
+                        NULL) != 0) {
+        fprintf(samtools_stderr, "[ampliconclip] warning: unable to add @PG line to header.\n");
+    }
+    if (sam_hdr_write(out, header) < 0) {
+        fprintf(samtools_stderr, "[ampliconclip] error: could not write header.\n");
+        goto fail;
+    }
+
+    if (reject) {
+       if (sam_hdr_write(reject, header) < 0) {
+           fprintf(samtools_stderr, "[ampliconclip] error: could not write header to rejects file.\n");
+           goto fail;
+       }
+    }
+
+    b = bam_init1();
+    b_tmp = bam_init1();
+    if (!b || !b_tmp) {
+        fprintf(samtools_stderr, "[ampliconclip] error: out of memory when trying to create record.\n");
+        goto fail;
+    }
+
+    int32_t last_tid = -1;
+    int ref_found = 0;
+
+    while ((r = sam_read1(in, header, b)) >= 0) {
+        hts_pos_t pos;
+        int is_rev;
+        int p_size;
+        int been_clipped  = 0, filter = 0;
+        int exclude = (BAM_FUNMAP | BAM_FQCFAIL);
+        khiter_t itr;
+
+        l_count++;
+
+        if (b->core.tid != last_tid) {
+            const char *ref_name;
+
+            ref_found = 0;
+            last_tid = b->core.tid;
+
+            if ((ref_name = sam_hdr_tid2name(header, b->core.tid)) != NULL) {
+                itr = kh_get(bed_list_hash, bed_hash, ref_name);
+
+                if (itr != kh_end(bed_hash)) {
+                    sites = &kh_val(bed_hash, itr);
+                    ref_found = 1;
+                }
+            }
+        }
+
+        if (!(b->core.flag & exclude) && ref_found) {
+            if (param->oa_tag)
+                if (tag_original_data(b, &oat))
+                    goto fail;
+
+            if (!param->both) {
+                if (bam_is_rev(b)) {
+                    pos = bam_endpos(b);
+                    is_rev = 1;
+                } else {
+                    pos = b->core.pos;
+                    is_rev = 0;
+                }
+
+                if ((p_size = matching_clip_site(sites, pos, is_rev, param->use_strand, sites->longest, param))) {
+                    if (is_rev) {
+                        if (bam_trim_right(b, b_tmp, p_size, clipping) != 0)
+                            goto fail;
+
+                        swap_bams(&b, &b_tmp);
+                        r_count++;
+                    } else {
+                        if (bam_trim_left(b, b_tmp, p_size, clipping) != 0)
+                            goto fail;
+
+                        swap_bams(&b, &b_tmp);
+                        f_count++;
+                    }
+
+                    if (param->oa_tag) {
+                        if (bam_aux_update_str(b, "OA", oat.l + 1, (const char *)oat.s))
+                            goto fail;
+                    }
+
+                    if (param->del_tag) {
+                        uint8_t *tag;
+
+                        if ((tag = bam_aux_get(b, "NM")))
+                            bam_aux_del(b, tag);
+
+                        if ((tag = bam_aux_get(b, "MD")))
+                            bam_aux_del(b, tag);
+                    }
+
+                    been_clipped = 1;
+                } else {
+                    if (param->mark_fail) {
+                        b->core.flag |= BAM_FQCFAIL;
+                    }
+
+                    n_count++;
+                }
+            } else {
+                int left = 0, right = 0;
+
+                // left first
+                pos = b->core.pos;
+                is_rev = 0;
+
+                if ((p_size = matching_clip_site(sites, pos, is_rev, param->use_strand, sites->longest, param))) {
+                    if (bam_trim_left(b, b_tmp, p_size, clipping) != 0)
+                        goto fail;
+
+                    swap_bams(&b, &b_tmp);
+                    f_count++;
+                    left = 1;
+                    been_clipped = 1;
+                }
+
+                // the right
+                pos = bam_endpos(b);
+                is_rev = 1;
+
+                if ((p_size = matching_clip_site(sites, pos, is_rev, param->use_strand, sites->longest, param))) {
+                    if (bam_trim_right(b, b_tmp, p_size, clipping) != 0)
+                        goto fail;
+
+                    swap_bams(&b, &b_tmp);
+                    r_count++;
+                    right = 1;
+                    been_clipped = 1;
+                }
+
+                if (left || right) {
+                    uint8_t *tag;
+
+                    if (param->oa_tag) {
+                        if (bam_aux_update_str(b, "OA", oat.l + 1, (const char *)oat.s))
+                            goto fail;
+                    }
+
+                    if (param->del_tag) {
+                        if ((tag = bam_aux_get(b, "NM")))
+                            bam_aux_del(b, tag);
+
+                        if ((tag = bam_aux_get(b, "MD")))
+                            bam_aux_del(b, tag);
+                    }
+                }
+
+                if (left && right) {
+                    b_count++;
+                } else if (!left && !right) {
+                    if (param->mark_fail) {
+                        b->core.flag |= BAM_FQCFAIL;
+                    }
+
+                    n_count++;
+                }
+            }
+
+            if (param->fail_len >= 0 || param->filter_len >= 0) {
+               hts_pos_t aql = active_query_len(b);
+
+               if (param->fail_len >= 0 && aql <= param->fail_len) {
+                   b->core.flag |= BAM_FQCFAIL;
+               }
+
+               if (param->filter_len >= 0 && aql <= param->filter_len) {
+                   filter = 1;
+               }
+           }
+
+           if (b->core.flag & BAM_FQCFAIL) {
+               failed++;
+           }
+
+           if (param->write_clipped && !been_clipped) {
+               filter = 1;
+           }
+
+        } else {
+            l_exclude++;
+
+            if (param->unmapped) {
+                filter = 1;
+            }
+        }
+
+        if (!filter) {
+            if (sam_write1(out, header, b) < 0) {
+                fprintf(samtools_stderr, "[ampliconclip] error: could not write line %ld.\n", l_count);
+                goto fail;
+            }
+
+            written++;
+        } else {
+            if (reject) {
+                if (sam_write1(reject, header, b) < 0) {
+                    fprintf(samtools_stderr, "[ampliconclip] error: could not write to reject file %s\n",
+                            param->rejects_file);
+                    goto fail;
+                }
+            }
+
+            filtered++;
+        }
+    }
+
+    if (r < -1) {
+        fprintf(samtools_stderr, "[ampliconclip] error: failed to read input.\n");
+        goto fail;
+    }
+
+    if (param->stats_file) {
+        if ((stats_fp = fopen(param->stats_file, "w")) == NULL) {
+            fprintf(samtools_stderr, "[ampliconclip] warning: cannot write stats to %s.\n", param->stats_file);
+        } else {
+            file_open = 1;
+        }
+    }
+
+    fprintf(stats_fp, "COMMAND: %s\n"
+                    "TOTAL READS: %ld\n"
+                    "TOTAL CLIPPED: %ld\n"
+                    "FORWARD CLIPPED: %ld\n"
+                    "REVERSE CLIPPED: %ld\n"
+                    "BOTH CLIPPED: %ld\n"
+                    "NOT CLIPPED: %ld\n"
+                    "EXCLUDED: %ld\n"
+                    "FILTERED: %ld\n"
+                    "FAILED: %ld\n"
+                    "WRITTEN: %ld\n", param->arg_list, l_count, f_count + r_count,
+                                    f_count, r_count, b_count, n_count, l_exclude,
+                                    filtered, failed, written);
+
+    if (file_open) {
+        fclose(stats_fp);
+    }
+
+    ret = 0;
+
+fail:
+    destroy_bed_hash(bed_hash);
+    ks_free(&oat);
+    sam_hdr_destroy(header);
+    bam_destroy1(b);
+    bam_destroy1(b_tmp);
+    return ret;
+}
+
+
+static void usage(void) {
+    fprintf(samtools_stderr, "Usage: samtools ampliconclip -b BED file <input.bam> -o <output.bam>\n\n");
+    fprintf(samtools_stderr, "Option: \n");
+    fprintf(samtools_stderr, " -b  FILE            BED file of regions (eg amplicon primers) to be removed.\n");
+    fprintf(samtools_stderr, " -o  FILE            output file name (default samtools_stdout).\n");
+    fprintf(samtools_stderr, " -f  FILE            write stats to file name (default samtools_stderr)\n");
+    fprintf(samtools_stderr, " -u                  Output uncompressed data\n");
+    fprintf(samtools_stderr, " --soft-clip         soft clip amplicon primers from reads (default)\n");
+    fprintf(samtools_stderr, " --hard-clip         hard clip amplicon primers from reads.\n");
+    fprintf(samtools_stderr, " --both-ends         clip on both 5' and 3' ends.\n");
+    fprintf(samtools_stderr, " --strand            use strand data from BED file to match read direction.\n");
+    fprintf(samtools_stderr, " --clipped           only output clipped reads.\n");
+    fprintf(samtools_stderr, " --fail              mark unclipped, mapped reads as QCFAIL.\n");
+    fprintf(samtools_stderr, " --filter-len INT    do not output reads INT size or shorter.\n");
+    fprintf(samtools_stderr, " --fail-len   INT    mark as QCFAIL reads INT size or shorter.\n");
+    fprintf(samtools_stderr, " --no-excluded       do not write excluded reads (unmapped or QCFAIL).\n");
+    fprintf(samtools_stderr, " --rejects-file FILE file to write filtered reads.\n");
+    fprintf(samtools_stderr, " --original          for clipped entries add an OA tag with original data.\n");
+    fprintf(samtools_stderr, " --keep-tag          for clipped entries keep the old NM and MD tags.\n");
+    fprintf(samtools_stderr, " --tolerance         match region within this number of bases, default 5.\n");
+    fprintf(samtools_stderr, " --no-PG             do not add an @PG line.\n");
+    sam_global_opt_help(samtools_stderr, "-.O..@-.");
+    fprintf(samtools_stderr, "\nAbout: Soft clips read alignments where they match BED file defined regions.\n"
+                    "Default clipping is only on the 5' end.\n\n");
+}
+
+
+int amplicon_clip_main(int argc, char **argv) {
+    int c, ret;
+    char wmode[4] = {'w', 'b', 0, 0};
+    char *bedfile = NULL, *fnout = "-";
+    sam_global_args ga = SAM_GLOBAL_ARGS_INIT;
+    htsThreadPool p = {NULL, 0};
+    samFile *in = NULL, *out = NULL, *reject = NULL;
+    clipping_type clipping = soft_clip;
+    cl_param_t param = {1, 0, 0, 0, 0, -1, -1, 0, 0, 1, 5, NULL, NULL, NULL};
+
+    static const struct option lopts[] = {
+        SAM_OPT_GLOBAL_OPTIONS('-', 0, 'O', 0, 0, '@'),
+        {"no-PG", no_argument, NULL, 1002},
+        {"soft-clip", no_argument, NULL, 1003},
+        {"hard-clip", no_argument, NULL, 1004},
+        {"strand", no_argument, NULL, 1005},
+        {"clipped", no_argument, NULL, 1006},
+        {"fail", no_argument, NULL, 1007},
+        {"both-ends", no_argument, NULL, 1008},
+        {"filter-len", required_argument, NULL, 1009},
+        {"fail-len", required_argument, NULL, 1010},
+        {"no-excluded", no_argument, NULL, 1011},
+        {"rejects-file", required_argument, NULL, 1012},
+        {"original", no_argument, NULL, 1013},
+        {"keep-tag", no_argument, NULL, 1014},
+        {"tolerance", required_argument, NULL, 1015},
+        {NULL, 0, NULL, 0}
+    };
+
+    while ((c = getopt_long(argc, argv, "b:@:o:O:f:u", lopts, NULL)) >= 0) {
+        switch (c) {
+            case 'b': bedfile = optarg; break;
+            case 'o': fnout = optarg; break;
+            case 'f': param.stats_file = optarg; break;
+            case 'u': wmode[2] = '0'; break;
+            case 1002: param.add_pg = 0; break;
+            case 1003: clipping = soft_clip; break;
+            case 1004: clipping = hard_clip; break;
+            case 1005: param.use_strand = 1; break;
+            case 1006: param.write_clipped = 1; break;
+            case 1007: param.mark_fail = 1; break;
+            case 1008: param.both = 1; break;
+            case 1009: param.filter_len = atoi(optarg); break;
+            case 1010: param.fail_len = atoi(optarg); break;
+            case 1011: param.unmapped = 1; break;
+            case 1012: param.rejects_file = optarg; break;
+            case 1013: param.oa_tag = 1; break;
+            case 1014: param.del_tag = 0; break;
+            case 1015: param.tol = atoi(optarg); break;
+            default:  if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break;
+                      /* else fall-through */
+            case '?': usage(); samtools_exit(1);
+        }
+    }
+
+    if (!bedfile) {
+        usage();
+        return 1;
+    }
+
+    if (optind + 1 > argc) {
+        usage();
+        return 1;
+    }
+
+    if (param.tol < 0) {
+        fprintf(samtools_stderr, "[ampliconclip] warning: invalid tolerance of %d,"
+                        " reseting tolerance to default of 5.\n", param.tol);
+        param.tol = 5;
+    }
+
+    if ((in = sam_open_format(argv[optind], "rb", &ga.in)) == NULL) {
+        print_error_errno("ampliconclip", "cannot open input file");
+        return 1;
+    }
+
+    sam_open_mode(wmode+1, fnout, NULL);
+
+    if ((out = sam_open_format(fnout, wmode, &ga.out)) == NULL) {
+        print_error_errno("ampliconclip", "cannot open output file");
+        return 1;
+    }
+
+    if (param.rejects_file) {
+        sam_open_mode(wmode+1, param.rejects_file, NULL);
+
+        if ((reject = sam_open_format(param.rejects_file, wmode, &ga.out)) == NULL) {
+            print_error_errno("ampliconclip", "cannot open rejects file");
+            return 1;
+        }
+    }
+
+    if (ga.nthreads > 0) {
+        if (!(p.pool = hts_tpool_init(ga.nthreads))) {
+            fprintf(samtools_stderr, "[ampliconclip] error: cannot create thread pool.\n");
+            return 1;
+        }
+        hts_set_opt(in,  HTS_OPT_THREAD_POOL, &p);
+        hts_set_opt(out, HTS_OPT_THREAD_POOL, &p);
+
+        if (reject) {
+           hts_set_opt(reject,  HTS_OPT_THREAD_POOL, &p);
+        }
+    }
+
+    param.arg_list = stringify_argv(argc + 1, argv - 1);
+
+    ret = bam_clip(in, out, reject, bedfile, clipping, &param);
+
+    // cleanup
+    sam_close(in);
+
+    if (sam_close(out) < 0) {
+        fprintf(samtools_stderr, "[ampliconclip] error: error while closing output file %s.\n", argv[optind+1]);
+        ret = 1;
+    }
+
+    if (reject) {
+        if (sam_close(reject) < 0) {
+            fprintf(samtools_stderr, "[ampliconclip] error: error while closing reject file %s.\n", param.rejects_file);
+            ret = 1;
+        }
+    }
+
+    if (p.pool) hts_tpool_destroy(p.pool);
+
+    sam_global_args_free(&ga);
+    free(param.arg_list);
+
+    return ret;
+}
+
diff --git a/samtools/bam_ampliconclip.h b/samtools/bam_ampliconclip.h
new file mode 100644
index 0000000..ef35357
--- /dev/null
+++ b/samtools/bam_ampliconclip.h
@@ -0,0 +1,54 @@
+/*  bam_ampliconclip.h -- shared functions between amplicon clip/stats
+
+    Copyright (C) 2020-2021 Genome Research Ltd.
+
+    Author: James Bonfield <jkb@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#ifndef BAM_AMPLICONCLIP_H
+#define BAM_AMPLICONCLIP_H
+
+#include "htslib/khash.h"
+
+typedef struct {
+    int64_t left;
+    int64_t right;
+    int rev;
+} bed_entry_t;
+
+typedef struct {
+    bed_entry_t *bp;
+    int64_t longest;
+    int length;
+    int size;
+} bed_entry_list_t;
+
+KHASH_MAP_INIT_STR(bed_list_hash, bed_entry_list_t);
+
+#define BED_LIST_INIT {NULL, 0, 0, 0, {0}}
+
+
+int load_bed_file_multi_ref(char *infile, int get_strand,
+                        int sort_by_pos, khash_t(bed_list_hash) *bed_lists);
+
+void destroy_bed_hash(khash_t(bed_list_hash) *hash);
+
+
+#endif /* BAM_AMPLICONCLIP_H */
diff --git a/samtools/bam_aux.c b/samtools/bam_aux.c
new file mode 100644
index 0000000..d11ee6e
--- /dev/null
+++ b/samtools/bam_aux.c
@@ -0,0 +1,61 @@
+/*  bam_aux.c -- remaining aux field handling.
+
+    Copyright (C) 2008-2010, 2013, 2015, 2019 Genome Research Ltd.
+    Portions copyright (C) 2011 Broad Institute.
+
+    Author: Heng Li <lh3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <config.h>
+
+#include <ctype.h>
+#include "htslib/sam.h"
+
+static inline int bam_aux_type2size(int x)
+{
+    if (x == 'C' || x == 'c' || x == 'A') return 1;
+    else if (x == 'S' || x == 's') return 2;
+    else if (x == 'I' || x == 'i' || x == 'f' || x == 'F') return 4;
+    else return 0;
+}
+
+#define __skip_tag(s) do { \
+        int type = toupper(*(s)); \
+        ++(s); \
+        if (type == 'Z' || type == 'H') { while (*(s)) ++(s); ++(s); } \
+        else if (type == 'B') (s) += 5 + bam_aux_type2size(*(s)) * (*(int32_t*)((s)+1)); \
+        else (s) += bam_aux_type2size(type); \
+    } while(0)
+
+
+int bam_aux_drop_other(bam1_t *b, uint8_t *s)
+{
+    if (s) {
+        uint8_t *p, *aux;
+        aux = bam_get_aux(b);
+        p = s - 2;
+        __skip_tag(s);
+        memmove(aux, p, s - p);
+        b->l_data -= bam_get_l_aux(b) - (s - p);
+    } else {
+        b->l_data -= bam_get_l_aux(b);
+    }
+    return 0;
+}
diff --git a/samtools/bam_aux.c.pysam.c b/samtools/bam_aux.c.pysam.c
new file mode 100644
index 0000000..621589d
--- /dev/null
+++ b/samtools/bam_aux.c.pysam.c
@@ -0,0 +1,63 @@
+#include "samtools.pysam.h"
+
+/*  bam_aux.c -- remaining aux field handling.
+
+    Copyright (C) 2008-2010, 2013, 2015, 2019 Genome Research Ltd.
+    Portions copyright (C) 2011 Broad Institute.
+
+    Author: Heng Li <lh3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <config.h>
+
+#include <ctype.h>
+#include "htslib/sam.h"
+
+static inline int bam_aux_type2size(int x)
+{
+    if (x == 'C' || x == 'c' || x == 'A') return 1;
+    else if (x == 'S' || x == 's') return 2;
+    else if (x == 'I' || x == 'i' || x == 'f' || x == 'F') return 4;
+    else return 0;
+}
+
+#define __skip_tag(s) do { \
+        int type = toupper(*(s)); \
+        ++(s); \
+        if (type == 'Z' || type == 'H') { while (*(s)) ++(s); ++(s); } \
+        else if (type == 'B') (s) += 5 + bam_aux_type2size(*(s)) * (*(int32_t*)((s)+1)); \
+        else (s) += bam_aux_type2size(type); \
+    } while(0)
+
+
+int bam_aux_drop_other(bam1_t *b, uint8_t *s)
+{
+    if (s) {
+        uint8_t *p, *aux;
+        aux = bam_get_aux(b);
+        p = s - 2;
+        __skip_tag(s);
+        memmove(aux, p, s - p);
+        b->l_data -= bam_get_l_aux(b) - (s - p);
+    } else {
+        b->l_data -= bam_get_l_aux(b);
+    }
+    return 0;
+}
diff --git a/samtools/bam_cat.c b/samtools/bam_cat.c
new file mode 100644
index 0000000..ed8cf58
--- /dev/null
+++ b/samtools/bam_cat.c
@@ -0,0 +1,587 @@
+/*  bam_cat.c -- efficiently concatenates bam files.
+
+    Copyright (C) 2008-2009, 2011-2013, 2015-2017, 2019, 2021 Genome Research Ltd.
+    Modified SAMtools work copyright (C) 2010 Illumina, Inc.
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notices and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+/*
+bam_cat can be used to concatenate BAM files. Under special
+circumstances, it can be used as an alternative to 'samtools merge' to
+concatenate multiple sorted files into a single sorted file. For this
+to work each file must be sorted, and the sorted files must be given
+as command line arguments in order such that the final read in file i
+is less than or equal to the first read in file i+1.
+
+This code is derived from the bam_reheader function in samtools 0.1.8
+and modified to perform concatenation by Chris Saunders on behalf of
+Illumina.
+*/
+
+#include <config.h>
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <unistd.h>
+#include <string.h>
+#include <strings.h>
+
+#include "htslib/bgzf.h"
+#include "htslib/sam.h"
+#include "htslib/cram.h"
+#include "htslib/kstring.h"
+#include "samtools.h"
+#include "sam_opts.h"
+
+/*
+ * Check the files are consistent and capable of being concatenated.
+ * Also fills out the version numbers and produces a new sam_hdr_t
+ * structure with merged RG lines.
+ * Note it is only a simple merge.
+ *
+ * Returns updated header on success;
+ *        NULL on failure.
+ */
+static sam_hdr_t *cram_cat_check_hdr(int nfn, char * const *fn, const sam_hdr_t *h,
+                                     int *vers_maj_p, int *vers_min_p) {
+    int i, vers_maj = -1, vers_min = -1;
+    sam_hdr_t *new_h = NULL, *old_h = NULL;
+    samFile *in = NULL;
+    kstring_t ks = KS_INITIALIZE;
+
+    if (h) {
+        new_h = sam_hdr_dup(h);
+        if (!new_h) {
+            fprintf(stderr, "[%s] ERROR: header duplication failed.\n",
+                    __func__);
+            goto fail;
+        }
+    }
+
+    for (i = 0; i < nfn; ++i) {
+        cram_fd *in_c;
+        int ki;
+
+        in = sam_open(fn[i], "rc");
+        if (in == 0) {
+            print_error_errno("cat", "fail to open file '%s'", fn[i]);
+            goto fail;
+        }
+        in_c = in->fp.cram;
+
+        int vmaj = cram_major_vers(in_c);
+        int vmin = cram_minor_vers(in_c);
+        if ((vers_maj != -1 && vers_maj != vmaj) ||
+            (vers_min != -1 && vers_min != vmin)) {
+            fprintf(stderr, "[%s] ERROR: input files have differing version numbers.\n",
+                    __func__);
+            goto fail;
+        }
+        vers_maj = vmaj;
+        vers_min = vmin;
+
+        old_h = sam_hdr_read(in);
+        if (!old_h) {
+            fprintf(stderr, "[%s] ERROR: header reading for file '%s' filed.\n",
+                    __func__, fn[i]);
+            goto fail;
+        }
+
+        if (!new_h) {
+            new_h = sam_hdr_dup(old_h);
+            if (!new_h) {
+                fprintf(stderr, "[%s] ERROR: header duplication for file '%s' failed.\n",
+                        __func__, fn[i]);
+                goto fail;
+            }
+            sam_hdr_destroy(old_h);
+            sam_close(in);
+            continue;
+        }
+
+        int old_count = sam_hdr_count_lines(old_h, "RG");
+        for (ki = 0; ki < old_count; ki++) {
+            const char *old_name = sam_hdr_line_name(old_h, "RG", ki);
+            if (old_name) {
+                int new_i = sam_hdr_line_index(new_h, "RG", old_name);
+                if (-1 == new_i) { // line does not exist in the new header
+                    if (sam_hdr_find_line_pos(old_h, "RG", ki, &ks) ||
+                        !ks.s || sam_hdr_add_lines(new_h, ks.s, ks.l)) {
+                        fprintf(stderr, "[%s] ERROR: failed to add @RG line 'ID:%s' from file '%s'\n",
+                                __func__, old_name, fn[i]);
+                        goto fail;
+                    }
+                    ks_free(&ks);
+                }
+            } else {
+                fprintf(stderr, "[%s] ERROR: failed to read %d @RG line from file '%s'\n",
+                        __func__, ki, fn[i]);
+                goto fail;
+            }
+        }
+
+        if (old_count > 1 && sam_hdr_count_lines(new_h, "RG") == old_count) {
+            for (ki = 0; ki < old_count; ki++) {
+                const char *old_name = sam_hdr_line_name(old_h, "RG", ki);
+                const char *new_name = sam_hdr_line_name(new_h, "RG", ki);
+                if (!old_name || !new_name || strcmp(old_name, new_name)) {
+                    fprintf(stderr, "[%s] ERROR: Same size @RG lists but differing order / contents\n",
+                            __func__);
+                    goto fail;
+                }
+            }
+        }
+
+        sam_hdr_destroy(old_h);
+        sam_close(in);
+    }
+
+    ks_free(&ks);
+
+    *vers_maj_p = vers_maj;
+    *vers_min_p = vers_min;
+
+    return new_h;
+
+fail:
+    ks_free(&ks);
+    if (old_h) sam_hdr_destroy(old_h);
+    if (new_h) sam_hdr_destroy(new_h);
+    if (in) sam_close(in);
+
+    return NULL;
+}
+
+
+/*
+ * CRAM files don't store the RG:Z:ID per read in the aux field.
+ * Instead they have a numerical data series (RG) to point each read
+ * back to the Nth @RG line in the file.  This means that we may need
+ * to edit the RG data series (if the files were produced from
+ * "samtools split" for example).
+ *
+ * The encoding method is stored in the compression header. Typical
+ * examples:
+ *
+ * RG => EXTERNAL {18}           # Block content-id 18 holds RG values
+ *                               # as a series of ITF8 encoded values
+ *
+ * RG => HUFFMAN {1, 255, 255, 255, 255, 255, 1, 0}
+ *                               # One RG value #-1.  (No RG)
+ *
+ * RG => HUFFMAN {1, 0, 1, 0}    # One RG value #0 (always first RG)
+ *
+ * RG => HUFFMAN {2, 0, 1, 2, 1, 1}
+ *                               # Two RG values, #0 and #1, written
+ *                               # to the CORE block and possibly
+ *                               # mixed with other data series.
+ *
+ * A single value can (but may not be) implemented as a zero bit
+ * huffman code.  In this situation we can change the meta-data in the
+ * compression header to renumber an RG value..
+ */
+int cram_cat(int nfn, char * const *fn, const sam_hdr_t *h, const char* outcram, sam_global_args *ga, char *arg_list, int no_pg)
+{
+    samFile *out;
+    cram_fd *out_c;
+    int i, vers_maj, vers_min;
+    sam_hdr_t *new_h = NULL;
+
+    /* Check consistent versioning and compatible headers */
+    if (!(new_h = cram_cat_check_hdr(nfn, fn, h, &vers_maj, &vers_min)))
+        return -1;
+
+    /* Open the file with cram_vers */
+    char vers[100];
+    sprintf(vers, "%d.%d", vers_maj, vers_min);
+    out = sam_open_format(outcram, "wc", &ga->out);
+    if (out == 0) {
+        print_error_errno("cat", "fail to open output file '%s'", outcram);
+        return -1;
+    }
+    out_c = out->fp.cram;
+    cram_set_option(out_c, CRAM_OPT_VERSION, vers);
+    //fprintf(stderr, "Creating cram vers %s\n", vers);
+
+    if (!no_pg && sam_hdr_add_pg(new_h, "samtools",
+                                 "VN", samtools_version(),
+                                 arg_list ? "CL": NULL,
+                                 arg_list ? arg_list : NULL,
+                                 NULL))
+        return -1;
+
+    if (sam_hdr_write(out, new_h) < 0) {
+        print_error_errno("cat", "Couldn't write header");
+        return -1;
+    }
+
+    for (i = 0; i < nfn; ++i) {
+        samFile *in;
+        cram_fd *in_c;
+        cram_container *c;
+        sam_hdr_t *old_h;
+        int new_rg = -1;
+
+        in = sam_open(fn[i], "rc");
+        if (in == 0) {
+            print_error_errno("cat", "fail to open file '%s'", fn[i]);
+            return -1;
+        }
+        in_c = in->fp.cram;
+
+        old_h = sam_hdr_read(in);
+        if (!old_h) {
+            print_error("cat", "fail to read the header of file '%s'", fn[i]);
+            return -1;
+        }
+
+        // Compute RG mapping if suitable for changing.
+        if (sam_hdr_count_lines(old_h, "RG") == 1) {
+            const char *old_name = sam_hdr_line_name(old_h, "RG", 0);
+            if (old_name) {
+                new_rg = sam_hdr_line_index(new_h, "RG", old_name);
+                if (new_rg < 0) {
+                    print_error("cat", "fail to find @RG line '%s' in the new header", old_name);
+                    return -1;
+                }
+            } else {
+                print_error("cat", "fail to find @RG line in file '%s'", fn[i]);
+                return -1;
+            }
+        } else {
+            new_rg = 0;
+        }
+
+        // Copy contains and blocks within them
+        while ((c = cram_read_container(in_c))) {
+            if (cram_container_is_empty(in_c)) {
+                cram_block *blk;
+                // Container compression header
+                if (!(blk = cram_read_block(in_c)))
+                    return -1;
+                cram_free_block(blk);
+                cram_free_container(c);
+                continue;
+            }
+
+            // If we have just one RG key and new_rg != 0 then
+            // we need to edit the compression header. IF WE CAN.
+            if (new_rg) {
+                int zero = 0;
+                //fprintf(stderr, "Transcode RG %d to %d\n", 0, new_rg);
+                cram_transcode_rg(in_c, out_c, c, 1, &zero, &new_rg);
+            } else {
+                int32_t num_slices;
+                cram_block *blk;
+
+                // Not switching rg so do the usual read/write loop
+                if (cram_write_container(out_c, c) != 0)
+                    return -1;
+
+                // Container compression header
+                if (!(blk = cram_read_block(in_c)))
+                    return -1;
+                if (cram_write_block(out_c, blk) != 0) {
+                    cram_free_block(blk);
+                    return -1;
+                }
+                cram_free_block(blk);
+
+
+                // Container num_blocks can be invalid, due to a bug.
+                // Instead we iterate in slice context instead.
+                (void)cram_container_get_landmarks(c, &num_slices);
+                cram_copy_slice(in_c, out_c, num_slices);
+            }
+
+            cram_free_container(c);
+        }
+
+        sam_hdr_destroy(old_h);
+        sam_close(in);
+    }
+    sam_close(out);
+    sam_hdr_destroy(new_h);
+
+    return 0;
+}
+
+
+#define BUF_SIZE 0x10000
+
+#define GZIPID1 31
+#define GZIPID2 139
+
+#define BGZF_EMPTY_BLOCK_SIZE 28
+
+int bam_cat(int nfn, char * const *fn, sam_hdr_t *h, const char* outbam, char *arg_list, int no_pg)
+{
+    BGZF *fp, *in = NULL;
+    uint8_t *buf = NULL;
+    uint8_t ebuf[BGZF_EMPTY_BLOCK_SIZE];
+    const int es=BGZF_EMPTY_BLOCK_SIZE;
+    int i;
+
+    fp = strcmp(outbam, "-")? bgzf_open(outbam, "w") : bgzf_fdopen(fileno(stdout), "w");
+    if (fp == 0) {
+        print_error_errno("cat", "fail to open output file '%s'", outbam);
+        return -1;
+    }
+    if (h) {
+        if (!no_pg && sam_hdr_add_pg(h, "samtools",
+                                     "VN", samtools_version(),
+                                     arg_list ? "CL": NULL,
+                                     arg_list ? arg_list : NULL,
+                                     NULL))
+            goto fail;
+
+        if (bam_hdr_write(fp, h) < 0) {
+            print_error_errno("cat", "Couldn't write header");
+            goto fail;
+        }
+    }
+
+    buf = (uint8_t*) malloc(BUF_SIZE);
+    if (!buf) {
+        fprintf(stderr, "[%s] Couldn't allocate buffer\n", __func__);
+        goto fail;
+    }
+    for(i = 0; i < nfn; ++i){
+        sam_hdr_t *old;
+        int len,j;
+
+        in = strcmp(fn[i], "-")? bgzf_open(fn[i], "r") : bgzf_fdopen(fileno(stdin), "r");
+        if (in == 0) {
+            print_error_errno("cat", "fail to open file '%s'", fn[i]);
+            goto fail;
+        }
+        if (in->is_write) return -1;
+
+        old = bam_hdr_read(in);
+        if (old == NULL) {
+            fprintf(stderr, "[%s] ERROR: couldn't read header for '%s'.\n",
+                    __func__, fn[i]);
+            goto fail;
+        }
+        if (h == 0 && i == 0) {
+            if (!no_pg && sam_hdr_add_pg(old, "samtools",
+                                         "VN", samtools_version(),
+                                         arg_list ? "CL": NULL,
+                                         arg_list ? arg_list : NULL,
+                                         NULL))
+                goto fail;
+
+            if (bam_hdr_write(fp, old) < 0) {
+                print_error_errno("cat", "Couldn't write header");
+                goto fail;
+            }
+        }
+
+        if (in->block_offset < in->block_length) {
+            if (bgzf_write(fp, (char *)in->uncompressed_block + in->block_offset, in->block_length - in->block_offset) < 0) goto write_fail;
+            if (bgzf_flush(fp) != 0) goto write_fail;
+        }
+
+        j=0;
+        while ((len = bgzf_raw_read(in, buf, BUF_SIZE)) > 0) {
+            if(len<es){
+                int diff=es-len;
+                if(j==0) {
+                    fprintf(stderr, "[%s] ERROR: truncated file?: '%s'.\n", __func__, fn[i]);
+                    goto fail;
+                }
+                if (bgzf_raw_write(fp, ebuf, len) < 0) goto write_fail;
+
+                memcpy(ebuf,ebuf+len,diff);
+                memcpy(ebuf+diff,buf,len);
+            } else {
+                if(j!=0) {
+                    if (bgzf_raw_write(fp, ebuf, es) < 0) goto write_fail;
+                }
+                len-= es;
+                memcpy(ebuf,buf+len,es);
+                if (bgzf_raw_write(fp, buf, len) < 0) goto write_fail;
+            }
+            j=1;
+        }
+
+        /* check final gzip block */
+        {
+            const uint8_t gzip1=ebuf[0];
+            const uint8_t gzip2=ebuf[1];
+            const uint32_t isize=*((uint32_t*)(ebuf+es-4));
+            if(((gzip1!=GZIPID1) || (gzip2!=GZIPID2)) || (isize!=0)) {
+                fprintf(stderr, "[%s] WARNING: Unexpected block structure in file '%s'.", __func__, fn[i]);
+                fprintf(stderr, " Possible output corruption.\n");
+                if (bgzf_raw_write(fp, ebuf, es) < 0) goto write_fail;
+            }
+        }
+        sam_hdr_destroy(old);
+        bgzf_close(in);
+        in = NULL;
+    }
+    free(buf);
+    if (bgzf_close(fp) < 0) {
+        fprintf(stderr, "[%s] Error on closing '%s'.\n", __func__, outbam);
+        return -1;
+    }
+    return 0;
+
+ write_fail:
+    fprintf(stderr, "[%s] Error writing to '%s'.\n", __func__, outbam);
+ fail:
+    if (in) bgzf_close(in);
+    if (fp) bgzf_close(fp);
+    free(buf);
+    return -1;
+}
+
+
+int main_cat(int argc, char *argv[])
+{
+    sam_hdr_t *h = 0;
+    char *outfn = 0;
+    char **infns = NULL; // files to concatenate
+    int infns_size = 0;
+    int c, ret = 0, no_pg = 0, usage = 0;
+    samFile *in;
+    sam_global_args ga;
+
+    static const struct option lopts[] = {
+        SAM_OPT_GLOBAL_OPTIONS('-', '-', '-', 0, '-', '@'),
+        {"no-PG", no_argument, NULL, 1},
+        { NULL, 0, NULL, 0 }
+    };
+
+    char *arg_list = NULL;
+
+    sam_global_args_init(&ga);
+
+    while ((c = getopt_long(argc, argv, "h:o:b:@:", lopts, NULL)) >= 0) {
+        switch (c) {
+            case 'h': {
+                samFile *fph = sam_open(optarg, "r");
+                if (fph == 0) {
+                    fprintf(stderr, "[%s] ERROR: fail to read the header from '%s'.\n", __func__, optarg);
+                    return 1;
+                }
+                h = sam_hdr_read(fph);
+                if (h == NULL) {
+                    fprintf(stderr,
+                            "[%s] ERROR: failed to read the header from '%s'.\n",
+                            __func__, optarg);
+                    return 1;
+                }
+                sam_close(fph);
+                break;
+            }
+            case 'o': outfn = strdup(optarg); break;
+            case 'b': {
+                // add file names in "optarg" to the list
+                // of files to concatenate
+                int nfns;
+                char **fns_read = hts_readlines(optarg, &nfns);
+                if (fns_read) {
+                    infns = realloc(infns, (infns_size + nfns) * sizeof(char*));
+                    if (infns == NULL) { ret = 1; goto end; }
+                    memcpy(infns+infns_size, fns_read, nfns * sizeof(char*));
+                    infns_size += nfns;
+                    free(fns_read);
+                } else {
+                    print_error("cat", "Invalid file list \"%s\"", optarg);
+                    ret = 1;
+                }
+                break;
+            }
+            case 1:
+                no_pg = 1;
+                break;
+            default:
+                if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break;
+                /* else fall-through */
+            case '?': usage=1; break;
+        }
+    }
+
+    if (!no_pg && !(arg_list = stringify_argv(argc+1, argv-1))) {
+        print_error("cat", "failed to create arg_list");
+        return 1;
+    }
+
+    // Append files specified in argv to the list.
+    int nargv_fns = argc - optind;
+    if (nargv_fns > 0) {
+        infns = realloc(infns, (infns_size + nargv_fns) * sizeof(char*));
+        if (infns == NULL) { ret = 1; goto end; }
+        memcpy(infns + infns_size, argv + optind, nargv_fns * sizeof(char*));
+    }
+
+    // Require at least one input file
+    if (infns_size + nargv_fns == 0 || usage) {
+        fprintf(stderr, "Usage: samtools cat [options] <in1.bam>  [... <inN.bam>]\n");
+        fprintf(stderr, "       samtools cat [options] <in1.cram> [... <inN.cram>]\n\n");
+        fprintf(stderr, "Concatenate BAM or CRAM files, first those in <bamlist.fofn>, then those\non the command line.\n\n");
+        fprintf(stderr, "Options: -b FILE  list of input BAM/CRAM file names, one per line\n");
+        fprintf(stderr, "         -h FILE  copy the header from FILE [default is 1st input file]\n");
+        fprintf(stderr, "         -o FILE  output BAM/CRAM\n");
+        fprintf(stderr, "         --no-PG  do not add a PG line\n");
+        sam_global_opt_help(stderr, "--..-@-.");
+        return 1;
+    }
+
+    in = sam_open(infns[0], "r");
+    if (!in) {
+        print_error_errno("cat", "failed to open file '%s'", infns[0]);
+        return 1;
+    }
+
+    switch (hts_get_format(in)->format) {
+    case bam:
+        sam_close(in);
+        if (bam_cat(infns_size+nargv_fns, infns, h, outfn? outfn : "-", arg_list, no_pg) < 0)
+            ret = 1;
+        break;
+
+    case cram:
+        sam_close(in);
+        if (cram_cat(infns_size+nargv_fns, infns, h, outfn? outfn : "-", &ga, arg_list, no_pg) < 0)
+            ret = 1;
+        break;
+
+    default:
+        sam_close(in);
+        fprintf(stderr, "[%s] ERROR: input is not BAM or CRAM\n", __func__);
+        return 1;
+    }
+
+ end:
+    if (infns_size > 0) {
+        int i;
+        for (i=0; i<infns_size; i++)
+            free(infns[i]);
+    }
+
+    free(outfn);
+    free(infns);
+    free(arg_list);
+    if (h)
+        sam_hdr_destroy(h);
+
+    return ret;
+}
diff --git a/samtools/bam_cat.c.pysam.c b/samtools/bam_cat.c.pysam.c
new file mode 100644
index 0000000..ef2199c
--- /dev/null
+++ b/samtools/bam_cat.c.pysam.c
@@ -0,0 +1,589 @@
+#include "samtools.pysam.h"
+
+/*  bam_cat.c -- efficiently concatenates bam files.
+
+    Copyright (C) 2008-2009, 2011-2013, 2015-2017, 2019, 2021 Genome Research Ltd.
+    Modified SAMtools work copyright (C) 2010 Illumina, Inc.
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notices and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+/*
+bam_cat can be used to concatenate BAM files. Under special
+circumstances, it can be used as an alternative to 'samtools merge' to
+concatenate multiple sorted files into a single sorted file. For this
+to work each file must be sorted, and the sorted files must be given
+as command line arguments in order such that the final read in file i
+is less than or equal to the first read in file i+1.
+
+This code is derived from the bam_reheader function in samtools 0.1.8
+and modified to perform concatenation by Chris Saunders on behalf of
+Illumina.
+*/
+
+#include <config.h>
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <unistd.h>
+#include <string.h>
+#include <strings.h>
+
+#include "htslib/bgzf.h"
+#include "htslib/sam.h"
+#include "htslib/cram.h"
+#include "htslib/kstring.h"
+#include "samtools.h"
+#include "sam_opts.h"
+
+/*
+ * Check the files are consistent and capable of being concatenated.
+ * Also fills out the version numbers and produces a new sam_hdr_t
+ * structure with merged RG lines.
+ * Note it is only a simple merge.
+ *
+ * Returns updated header on success;
+ *        NULL on failure.
+ */
+static sam_hdr_t *cram_cat_check_hdr(int nfn, char * const *fn, const sam_hdr_t *h,
+                                     int *vers_maj_p, int *vers_min_p) {
+    int i, vers_maj = -1, vers_min = -1;
+    sam_hdr_t *new_h = NULL, *old_h = NULL;
+    samFile *in = NULL;
+    kstring_t ks = KS_INITIALIZE;
+
+    if (h) {
+        new_h = sam_hdr_dup(h);
+        if (!new_h) {
+            fprintf(samtools_stderr, "[%s] ERROR: header duplication failed.\n",
+                    __func__);
+            goto fail;
+        }
+    }
+
+    for (i = 0; i < nfn; ++i) {
+        cram_fd *in_c;
+        int ki;
+
+        in = sam_open(fn[i], "rc");
+        if (in == 0) {
+            print_error_errno("cat", "fail to open file '%s'", fn[i]);
+            goto fail;
+        }
+        in_c = in->fp.cram;
+
+        int vmaj = cram_major_vers(in_c);
+        int vmin = cram_minor_vers(in_c);
+        if ((vers_maj != -1 && vers_maj != vmaj) ||
+            (vers_min != -1 && vers_min != vmin)) {
+            fprintf(samtools_stderr, "[%s] ERROR: input files have differing version numbers.\n",
+                    __func__);
+            goto fail;
+        }
+        vers_maj = vmaj;
+        vers_min = vmin;
+
+        old_h = sam_hdr_read(in);
+        if (!old_h) {
+            fprintf(samtools_stderr, "[%s] ERROR: header reading for file '%s' filed.\n",
+                    __func__, fn[i]);
+            goto fail;
+        }
+
+        if (!new_h) {
+            new_h = sam_hdr_dup(old_h);
+            if (!new_h) {
+                fprintf(samtools_stderr, "[%s] ERROR: header duplication for file '%s' failed.\n",
+                        __func__, fn[i]);
+                goto fail;
+            }
+            sam_hdr_destroy(old_h);
+            sam_close(in);
+            continue;
+        }
+
+        int old_count = sam_hdr_count_lines(old_h, "RG");
+        for (ki = 0; ki < old_count; ki++) {
+            const char *old_name = sam_hdr_line_name(old_h, "RG", ki);
+            if (old_name) {
+                int new_i = sam_hdr_line_index(new_h, "RG", old_name);
+                if (-1 == new_i) { // line does not exist in the new header
+                    if (sam_hdr_find_line_pos(old_h, "RG", ki, &ks) ||
+                        !ks.s || sam_hdr_add_lines(new_h, ks.s, ks.l)) {
+                        fprintf(samtools_stderr, "[%s] ERROR: failed to add @RG line 'ID:%s' from file '%s'\n",
+                                __func__, old_name, fn[i]);
+                        goto fail;
+                    }
+                    ks_free(&ks);
+                }
+            } else {
+                fprintf(samtools_stderr, "[%s] ERROR: failed to read %d @RG line from file '%s'\n",
+                        __func__, ki, fn[i]);
+                goto fail;
+            }
+        }
+
+        if (old_count > 1 && sam_hdr_count_lines(new_h, "RG") == old_count) {
+            for (ki = 0; ki < old_count; ki++) {
+                const char *old_name = sam_hdr_line_name(old_h, "RG", ki);
+                const char *new_name = sam_hdr_line_name(new_h, "RG", ki);
+                if (!old_name || !new_name || strcmp(old_name, new_name)) {
+                    fprintf(samtools_stderr, "[%s] ERROR: Same size @RG lists but differing order / contents\n",
+                            __func__);
+                    goto fail;
+                }
+            }
+        }
+
+        sam_hdr_destroy(old_h);
+        sam_close(in);
+    }
+
+    ks_free(&ks);
+
+    *vers_maj_p = vers_maj;
+    *vers_min_p = vers_min;
+
+    return new_h;
+
+fail:
+    ks_free(&ks);
+    if (old_h) sam_hdr_destroy(old_h);
+    if (new_h) sam_hdr_destroy(new_h);
+    if (in) sam_close(in);
+
+    return NULL;
+}
+
+
+/*
+ * CRAM files don't store the RG:Z:ID per read in the aux field.
+ * Instead they have a numerical data series (RG) to point each read
+ * back to the Nth @RG line in the file.  This means that we may need
+ * to edit the RG data series (if the files were produced from
+ * "samtools split" for example).
+ *
+ * The encoding method is stored in the compression header. Typical
+ * examples:
+ *
+ * RG => EXTERNAL {18}           # Block content-id 18 holds RG values
+ *                               # as a series of ITF8 encoded values
+ *
+ * RG => HUFFMAN {1, 255, 255, 255, 255, 255, 1, 0}
+ *                               # One RG value #-1.  (No RG)
+ *
+ * RG => HUFFMAN {1, 0, 1, 0}    # One RG value #0 (always first RG)
+ *
+ * RG => HUFFMAN {2, 0, 1, 2, 1, 1}
+ *                               # Two RG values, #0 and #1, written
+ *                               # to the CORE block and possibly
+ *                               # mixed with other data series.
+ *
+ * A single value can (but may not be) implemented as a zero bit
+ * huffman code.  In this situation we can change the meta-data in the
+ * compression header to renumber an RG value..
+ */
+int cram_cat(int nfn, char * const *fn, const sam_hdr_t *h, const char* outcram, sam_global_args *ga, char *arg_list, int no_pg)
+{
+    samFile *out;
+    cram_fd *out_c;
+    int i, vers_maj, vers_min;
+    sam_hdr_t *new_h = NULL;
+
+    /* Check consistent versioning and compatible headers */
+    if (!(new_h = cram_cat_check_hdr(nfn, fn, h, &vers_maj, &vers_min)))
+        return -1;
+
+    /* Open the file with cram_vers */
+    char vers[100];
+    sprintf(vers, "%d.%d", vers_maj, vers_min);
+    out = sam_open_format(outcram, "wc", &ga->out);
+    if (out == 0) {
+        print_error_errno("cat", "fail to open output file '%s'", outcram);
+        return -1;
+    }
+    out_c = out->fp.cram;
+    cram_set_option(out_c, CRAM_OPT_VERSION, vers);
+    //fprintf(samtools_stderr, "Creating cram vers %s\n", vers);
+
+    if (!no_pg && sam_hdr_add_pg(new_h, "samtools",
+                                 "VN", samtools_version(),
+                                 arg_list ? "CL": NULL,
+                                 arg_list ? arg_list : NULL,
+                                 NULL))
+        return -1;
+
+    if (sam_hdr_write(out, new_h) < 0) {
+        print_error_errno("cat", "Couldn't write header");
+        return -1;
+    }
+
+    for (i = 0; i < nfn; ++i) {
+        samFile *in;
+        cram_fd *in_c;
+        cram_container *c;
+        sam_hdr_t *old_h;
+        int new_rg = -1;
+
+        in = sam_open(fn[i], "rc");
+        if (in == 0) {
+            print_error_errno("cat", "fail to open file '%s'", fn[i]);
+            return -1;
+        }
+        in_c = in->fp.cram;
+
+        old_h = sam_hdr_read(in);
+        if (!old_h) {
+            print_error("cat", "fail to read the header of file '%s'", fn[i]);
+            return -1;
+        }
+
+        // Compute RG mapping if suitable for changing.
+        if (sam_hdr_count_lines(old_h, "RG") == 1) {
+            const char *old_name = sam_hdr_line_name(old_h, "RG", 0);
+            if (old_name) {
+                new_rg = sam_hdr_line_index(new_h, "RG", old_name);
+                if (new_rg < 0) {
+                    print_error("cat", "fail to find @RG line '%s' in the new header", old_name);
+                    return -1;
+                }
+            } else {
+                print_error("cat", "fail to find @RG line in file '%s'", fn[i]);
+                return -1;
+            }
+        } else {
+            new_rg = 0;
+        }
+
+        // Copy contains and blocks within them
+        while ((c = cram_read_container(in_c))) {
+            if (cram_container_is_empty(in_c)) {
+                cram_block *blk;
+                // Container compression header
+                if (!(blk = cram_read_block(in_c)))
+                    return -1;
+                cram_free_block(blk);
+                cram_free_container(c);
+                continue;
+            }
+
+            // If we have just one RG key and new_rg != 0 then
+            // we need to edit the compression header. IF WE CAN.
+            if (new_rg) {
+                int zero = 0;
+                //fprintf(samtools_stderr, "Transcode RG %d to %d\n", 0, new_rg);
+                cram_transcode_rg(in_c, out_c, c, 1, &zero, &new_rg);
+            } else {
+                int32_t num_slices;
+                cram_block *blk;
+
+                // Not switching rg so do the usual read/write loop
+                if (cram_write_container(out_c, c) != 0)
+                    return -1;
+
+                // Container compression header
+                if (!(blk = cram_read_block(in_c)))
+                    return -1;
+                if (cram_write_block(out_c, blk) != 0) {
+                    cram_free_block(blk);
+                    return -1;
+                }
+                cram_free_block(blk);
+
+
+                // Container num_blocks can be invalid, due to a bug.
+                // Instead we iterate in slice context instead.
+                (void)cram_container_get_landmarks(c, &num_slices);
+                cram_copy_slice(in_c, out_c, num_slices);
+            }
+
+            cram_free_container(c);
+        }
+
+        sam_hdr_destroy(old_h);
+        sam_close(in);
+    }
+    sam_close(out);
+    sam_hdr_destroy(new_h);
+
+    return 0;
+}
+
+
+#define BUF_SIZE 0x10000
+
+#define GZIPID1 31
+#define GZIPID2 139
+
+#define BGZF_EMPTY_BLOCK_SIZE 28
+
+int bam_cat(int nfn, char * const *fn, sam_hdr_t *h, const char* outbam, char *arg_list, int no_pg)
+{
+    BGZF *fp, *in = NULL;
+    uint8_t *buf = NULL;
+    uint8_t ebuf[BGZF_EMPTY_BLOCK_SIZE];
+    const int es=BGZF_EMPTY_BLOCK_SIZE;
+    int i;
+
+    fp = strcmp(outbam, "-")? bgzf_open(outbam, "w") : bgzf_fdopen(fileno(samtools_stdout), "w");
+    if (fp == 0) {
+        print_error_errno("cat", "fail to open output file '%s'", outbam);
+        return -1;
+    }
+    if (h) {
+        if (!no_pg && sam_hdr_add_pg(h, "samtools",
+                                     "VN", samtools_version(),
+                                     arg_list ? "CL": NULL,
+                                     arg_list ? arg_list : NULL,
+                                     NULL))
+            goto fail;
+
+        if (bam_hdr_write(fp, h) < 0) {
+            print_error_errno("cat", "Couldn't write header");
+            goto fail;
+        }
+    }
+
+    buf = (uint8_t*) malloc(BUF_SIZE);
+    if (!buf) {
+        fprintf(samtools_stderr, "[%s] Couldn't allocate buffer\n", __func__);
+        goto fail;
+    }
+    for(i = 0; i < nfn; ++i){
+        sam_hdr_t *old;
+        int len,j;
+
+        in = strcmp(fn[i], "-")? bgzf_open(fn[i], "r") : bgzf_fdopen(fileno(stdin), "r");
+        if (in == 0) {
+            print_error_errno("cat", "fail to open file '%s'", fn[i]);
+            goto fail;
+        }
+        if (in->is_write) return -1;
+
+        old = bam_hdr_read(in);
+        if (old == NULL) {
+            fprintf(samtools_stderr, "[%s] ERROR: couldn't read header for '%s'.\n",
+                    __func__, fn[i]);
+            goto fail;
+        }
+        if (h == 0 && i == 0) {
+            if (!no_pg && sam_hdr_add_pg(old, "samtools",
+                                         "VN", samtools_version(),
+                                         arg_list ? "CL": NULL,
+                                         arg_list ? arg_list : NULL,
+                                         NULL))
+                goto fail;
+
+            if (bam_hdr_write(fp, old) < 0) {
+                print_error_errno("cat", "Couldn't write header");
+                goto fail;
+            }
+        }
+
+        if (in->block_offset < in->block_length) {
+            if (bgzf_write(fp, (char *)in->uncompressed_block + in->block_offset, in->block_length - in->block_offset) < 0) goto write_fail;
+            if (bgzf_flush(fp) != 0) goto write_fail;
+        }
+
+        j=0;
+        while ((len = bgzf_raw_read(in, buf, BUF_SIZE)) > 0) {
+            if(len<es){
+                int diff=es-len;
+                if(j==0) {
+                    fprintf(samtools_stderr, "[%s] ERROR: truncated file?: '%s'.\n", __func__, fn[i]);
+                    goto fail;
+                }
+                if (bgzf_raw_write(fp, ebuf, len) < 0) goto write_fail;
+
+                memcpy(ebuf,ebuf+len,diff);
+                memcpy(ebuf+diff,buf,len);
+            } else {
+                if(j!=0) {
+                    if (bgzf_raw_write(fp, ebuf, es) < 0) goto write_fail;
+                }
+                len-= es;
+                memcpy(ebuf,buf+len,es);
+                if (bgzf_raw_write(fp, buf, len) < 0) goto write_fail;
+            }
+            j=1;
+        }
+
+        /* check final gzip block */
+        {
+            const uint8_t gzip1=ebuf[0];
+            const uint8_t gzip2=ebuf[1];
+            const uint32_t isize=*((uint32_t*)(ebuf+es-4));
+            if(((gzip1!=GZIPID1) || (gzip2!=GZIPID2)) || (isize!=0)) {
+                fprintf(samtools_stderr, "[%s] WARNING: Unexpected block structure in file '%s'.", __func__, fn[i]);
+                fprintf(samtools_stderr, " Possible output corruption.\n");
+                if (bgzf_raw_write(fp, ebuf, es) < 0) goto write_fail;
+            }
+        }
+        sam_hdr_destroy(old);
+        bgzf_close(in);
+        in = NULL;
+    }
+    free(buf);
+    if (bgzf_close(fp) < 0) {
+        fprintf(samtools_stderr, "[%s] Error on closing '%s'.\n", __func__, outbam);
+        return -1;
+    }
+    return 0;
+
+ write_fail:
+    fprintf(samtools_stderr, "[%s] Error writing to '%s'.\n", __func__, outbam);
+ fail:
+    if (in) bgzf_close(in);
+    if (fp) bgzf_close(fp);
+    free(buf);
+    return -1;
+}
+
+
+int main_cat(int argc, char *argv[])
+{
+    sam_hdr_t *h = 0;
+    char *outfn = 0;
+    char **infns = NULL; // files to concatenate
+    int infns_size = 0;
+    int c, ret = 0, no_pg = 0, usage = 0;
+    samFile *in;
+    sam_global_args ga;
+
+    static const struct option lopts[] = {
+        SAM_OPT_GLOBAL_OPTIONS('-', '-', '-', 0, '-', '@'),
+        {"no-PG", no_argument, NULL, 1},
+        { NULL, 0, NULL, 0 }
+    };
+
+    char *arg_list = NULL;
+
+    sam_global_args_init(&ga);
+
+    while ((c = getopt_long(argc, argv, "h:o:b:@:", lopts, NULL)) >= 0) {
+        switch (c) {
+            case 'h': {
+                samFile *fph = sam_open(optarg, "r");
+                if (fph == 0) {
+                    fprintf(samtools_stderr, "[%s] ERROR: fail to read the header from '%s'.\n", __func__, optarg);
+                    return 1;
+                }
+                h = sam_hdr_read(fph);
+                if (h == NULL) {
+                    fprintf(samtools_stderr,
+                            "[%s] ERROR: failed to read the header from '%s'.\n",
+                            __func__, optarg);
+                    return 1;
+                }
+                sam_close(fph);
+                break;
+            }
+            case 'o': outfn = strdup(optarg); break;
+            case 'b': {
+                // add file names in "optarg" to the list
+                // of files to concatenate
+                int nfns;
+                char **fns_read = hts_readlines(optarg, &nfns);
+                if (fns_read) {
+                    infns = realloc(infns, (infns_size + nfns) * sizeof(char*));
+                    if (infns == NULL) { ret = 1; goto end; }
+                    memcpy(infns+infns_size, fns_read, nfns * sizeof(char*));
+                    infns_size += nfns;
+                    free(fns_read);
+                } else {
+                    print_error("cat", "Invalid file list \"%s\"", optarg);
+                    ret = 1;
+                }
+                break;
+            }
+            case 1:
+                no_pg = 1;
+                break;
+            default:
+                if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break;
+                /* else fall-through */
+            case '?': usage=1; break;
+        }
+    }
+
+    if (!no_pg && !(arg_list = stringify_argv(argc+1, argv-1))) {
+        print_error("cat", "failed to create arg_list");
+        return 1;
+    }
+
+    // Append files specified in argv to the list.
+    int nargv_fns = argc - optind;
+    if (nargv_fns > 0) {
+        infns = realloc(infns, (infns_size + nargv_fns) * sizeof(char*));
+        if (infns == NULL) { ret = 1; goto end; }
+        memcpy(infns + infns_size, argv + optind, nargv_fns * sizeof(char*));
+    }
+
+    // Require at least one input file
+    if (infns_size + nargv_fns == 0 || usage) {
+        fprintf(samtools_stderr, "Usage: samtools cat [options] <in1.bam>  [... <inN.bam>]\n");
+        fprintf(samtools_stderr, "       samtools cat [options] <in1.cram> [... <inN.cram>]\n\n");
+        fprintf(samtools_stderr, "Concatenate BAM or CRAM files, first those in <bamlist.fofn>, then those\non the command line.\n\n");
+        fprintf(samtools_stderr, "Options: -b FILE  list of input BAM/CRAM file names, one per line\n");
+        fprintf(samtools_stderr, "         -h FILE  copy the header from FILE [default is 1st input file]\n");
+        fprintf(samtools_stderr, "         -o FILE  output BAM/CRAM\n");
+        fprintf(samtools_stderr, "         --no-PG  do not add a PG line\n");
+        sam_global_opt_help(samtools_stderr, "--..-@-.");
+        return 1;
+    }
+
+    in = sam_open(infns[0], "r");
+    if (!in) {
+        print_error_errno("cat", "failed to open file '%s'", infns[0]);
+        return 1;
+    }
+
+    switch (hts_get_format(in)->format) {
+    case bam:
+        sam_close(in);
+        if (bam_cat(infns_size+nargv_fns, infns, h, outfn? outfn : "-", arg_list, no_pg) < 0)
+            ret = 1;
+        break;
+
+    case cram:
+        sam_close(in);
+        if (cram_cat(infns_size+nargv_fns, infns, h, outfn? outfn : "-", &ga, arg_list, no_pg) < 0)
+            ret = 1;
+        break;
+
+    default:
+        sam_close(in);
+        fprintf(samtools_stderr, "[%s] ERROR: input is not BAM or CRAM\n", __func__);
+        return 1;
+    }
+
+ end:
+    if (infns_size > 0) {
+        int i;
+        for (i=0; i<infns_size; i++)
+            free(infns[i]);
+    }
+
+    free(outfn);
+    free(infns);
+    free(arg_list);
+    if (h)
+        sam_hdr_destroy(h);
+
+    return ret;
+}
diff --git a/samtools/bam_color.c b/samtools/bam_color.c
new file mode 100644
index 0000000..6decbc1
--- /dev/null
+++ b/samtools/bam_color.c
@@ -0,0 +1,173 @@
+/*  bam_color.c -- color-space support.
+
+    Copyright (C) 2009, 2012 University of California - Los Angeles.
+
+    Author: Nils Homer <nilshomer@gmail.com>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <config.h>
+
+#include <ctype.h>
+#include <string.h>
+
+#include "htslib/sam.h"
+
+/*!
+ @abstract     Get the color encoding the previous and current base
+ @param b      pointer to an alignment
+ @param i      The i-th position, 0-based
+ @return       color
+
+ @discussion   Returns 0 no color information is found.
+ */
+char bam_aux_getCSi(bam1_t *b, int i)
+{
+    uint8_t *c = bam_aux_get(b, "CS");
+    char *cs = NULL;
+
+    // return the base if the tag was not found
+    if(0 == c) return 0;
+
+    cs = bam_aux2Z(c);
+    // adjust for strandedness and leading adaptor
+    if(bam_is_rev(b)) {
+        i = strlen(cs) - 1 - i;
+        // adjust for leading hard clip
+        uint32_t cigar = bam_get_cigar(b)[0];
+        if((cigar & BAM_CIGAR_MASK) == BAM_CHARD_CLIP) {
+        i -= cigar >> BAM_CIGAR_SHIFT;
+        }
+    } else { i++; }
+    return cs[i];
+}
+
+/*!
+ @abstract     Get the color quality of the color encoding the previous and current base
+ @param b      pointer to an alignment
+ @param i      The i-th position, 0-based
+ @return       color quality
+
+ @discussion   Returns 0 no color information is found.
+ */
+char bam_aux_getCQi(bam1_t *b, int i)
+{
+    uint8_t *c = bam_aux_get(b, "CQ");
+    char *cq = NULL;
+
+    // return the base if the tag was not found
+    if(0 == c) return 0;
+
+    cq = bam_aux2Z(c);
+    // adjust for strandedness
+    if(bam_is_rev(b)) {
+        i = strlen(cq) - 1 - i;
+        // adjust for leading hard clip
+        uint32_t cigar = bam_get_cigar(b)[0];
+        if((cigar & BAM_CIGAR_MASK) == BAM_CHARD_CLIP) {
+        i -= (cigar >> BAM_CIGAR_SHIFT);
+        }
+    }
+    return cq[i];
+}
+
+char bam_aux_nt2int(char a)
+{
+    switch(toupper(a)) {
+        case 'A':
+            return 0;
+            break;
+        case 'C':
+            return 1;
+            break;
+        case 'G':
+            return 2;
+            break;
+        case 'T':
+            return 3;
+            break;
+        default:
+            return 4;
+            break;
+    }
+}
+
+char bam_aux_ntnt2cs(char a, char b)
+{
+    a = bam_aux_nt2int(a);
+    b = bam_aux_nt2int(b);
+    if(4 == a || 4 == b) return '4';
+    return "0123"[(int)(a ^ b)];
+}
+
+/*!
+ @abstract     Get the color error profile at the give position
+ @param b      pointer to an alignment
+ @return       the original color if the color was an error, '-' (dash) otherwise
+
+ @discussion   Returns 0 no color information is found.
+ */
+char bam_aux_getCEi(bam1_t *b, int i)
+{
+    int cs_i;
+    uint8_t *c = bam_aux_get(b, "CS");
+    char *cs = NULL;
+    char prev_b, cur_b;
+    char cur_color, cor_color;
+
+    // return the base if the tag was not found
+    if(0 == c) return 0;
+
+    cs = bam_aux2Z(c);
+
+    // adjust for strandedness and leading adaptor
+    if(bam_is_rev(b)) { //reverse strand
+        cs_i = strlen(cs) - 1 - i;
+        // adjust for leading hard clip
+        uint32_t cigar = bam_get_cigar(b)[0];
+        if((cigar & BAM_CIGAR_MASK) == BAM_CHARD_CLIP) {
+            cs_i -= cigar >> BAM_CIGAR_SHIFT;
+        }
+        // get current color
+        cur_color = cs[cs_i];
+        // get previous base.  Note: must rc adaptor
+        prev_b = (cs_i == 1) ? "TGCAN"[(int)bam_aux_nt2int(cs[0])] : seq_nt16_str[bam_seqi(bam_get_seq(b), i+1)];
+        // get current base
+        cur_b = seq_nt16_str[bam_seqi(bam_get_seq(b), i)];
+    }
+    else {
+        cs_i=i+1;
+        // get current color
+        cur_color = cs[cs_i];
+        // get previous base
+        prev_b = (0 == i) ? cs[0] : seq_nt16_str[bam_seqi(bam_get_seq(b), i-1)];
+        // get current base
+        cur_b = seq_nt16_str[bam_seqi(bam_get_seq(b), i)];
+    }
+
+    // corrected color
+    cor_color = bam_aux_ntnt2cs(prev_b, cur_b);
+
+    if(cur_color == cor_color) {
+        return '-';
+    }
+    else {
+        return cur_color;
+    }
+}
diff --git a/samtools/bam_color.c.pysam.c b/samtools/bam_color.c.pysam.c
new file mode 100644
index 0000000..105cc33
--- /dev/null
+++ b/samtools/bam_color.c.pysam.c
@@ -0,0 +1,175 @@
+#include "samtools.pysam.h"
+
+/*  bam_color.c -- color-space support.
+
+    Copyright (C) 2009, 2012 University of California - Los Angeles.
+
+    Author: Nils Homer <nilshomer@gmail.com>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <config.h>
+
+#include <ctype.h>
+#include <string.h>
+
+#include "htslib/sam.h"
+
+/*!
+ @abstract     Get the color encoding the previous and current base
+ @param b      pointer to an alignment
+ @param i      The i-th position, 0-based
+ @return       color
+
+ @discussion   Returns 0 no color information is found.
+ */
+char bam_aux_getCSi(bam1_t *b, int i)
+{
+    uint8_t *c = bam_aux_get(b, "CS");
+    char *cs = NULL;
+
+    // return the base if the tag was not found
+    if(0 == c) return 0;
+
+    cs = bam_aux2Z(c);
+    // adjust for strandedness and leading adaptor
+    if(bam_is_rev(b)) {
+        i = strlen(cs) - 1 - i;
+        // adjust for leading hard clip
+        uint32_t cigar = bam_get_cigar(b)[0];
+        if((cigar & BAM_CIGAR_MASK) == BAM_CHARD_CLIP) {
+        i -= cigar >> BAM_CIGAR_SHIFT;
+        }
+    } else { i++; }
+    return cs[i];
+}
+
+/*!
+ @abstract     Get the color quality of the color encoding the previous and current base
+ @param b      pointer to an alignment
+ @param i      The i-th position, 0-based
+ @return       color quality
+
+ @discussion   Returns 0 no color information is found.
+ */
+char bam_aux_getCQi(bam1_t *b, int i)
+{
+    uint8_t *c = bam_aux_get(b, "CQ");
+    char *cq = NULL;
+
+    // return the base if the tag was not found
+    if(0 == c) return 0;
+
+    cq = bam_aux2Z(c);
+    // adjust for strandedness
+    if(bam_is_rev(b)) {
+        i = strlen(cq) - 1 - i;
+        // adjust for leading hard clip
+        uint32_t cigar = bam_get_cigar(b)[0];
+        if((cigar & BAM_CIGAR_MASK) == BAM_CHARD_CLIP) {
+        i -= (cigar >> BAM_CIGAR_SHIFT);
+        }
+    }
+    return cq[i];
+}
+
+char bam_aux_nt2int(char a)
+{
+    switch(toupper(a)) {
+        case 'A':
+            return 0;
+            break;
+        case 'C':
+            return 1;
+            break;
+        case 'G':
+            return 2;
+            break;
+        case 'T':
+            return 3;
+            break;
+        default:
+            return 4;
+            break;
+    }
+}
+
+char bam_aux_ntnt2cs(char a, char b)
+{
+    a = bam_aux_nt2int(a);
+    b = bam_aux_nt2int(b);
+    if(4 == a || 4 == b) return '4';
+    return "0123"[(int)(a ^ b)];
+}
+
+/*!
+ @abstract     Get the color error profile at the give position
+ @param b      pointer to an alignment
+ @return       the original color if the color was an error, '-' (dash) otherwise
+
+ @discussion   Returns 0 no color information is found.
+ */
+char bam_aux_getCEi(bam1_t *b, int i)
+{
+    int cs_i;
+    uint8_t *c = bam_aux_get(b, "CS");
+    char *cs = NULL;
+    char prev_b, cur_b;
+    char cur_color, cor_color;
+
+    // return the base if the tag was not found
+    if(0 == c) return 0;
+
+    cs = bam_aux2Z(c);
+
+    // adjust for strandedness and leading adaptor
+    if(bam_is_rev(b)) { //reverse strand
+        cs_i = strlen(cs) - 1 - i;
+        // adjust for leading hard clip
+        uint32_t cigar = bam_get_cigar(b)[0];
+        if((cigar & BAM_CIGAR_MASK) == BAM_CHARD_CLIP) {
+            cs_i -= cigar >> BAM_CIGAR_SHIFT;
+        }
+        // get current color
+        cur_color = cs[cs_i];
+        // get previous base.  Note: must rc adaptor
+        prev_b = (cs_i == 1) ? "TGCAN"[(int)bam_aux_nt2int(cs[0])] : seq_nt16_str[bam_seqi(bam_get_seq(b), i+1)];
+        // get current base
+        cur_b = seq_nt16_str[bam_seqi(bam_get_seq(b), i)];
+    }
+    else {
+        cs_i=i+1;
+        // get current color
+        cur_color = cs[cs_i];
+        // get previous base
+        prev_b = (0 == i) ? cs[0] : seq_nt16_str[bam_seqi(bam_get_seq(b), i-1)];
+        // get current base
+        cur_b = seq_nt16_str[bam_seqi(bam_get_seq(b), i)];
+    }
+
+    // corrected color
+    cor_color = bam_aux_ntnt2cs(prev_b, cur_b);
+
+    if(cur_color == cor_color) {
+        return '-';
+    }
+    else {
+        return cur_color;
+    }
+}
diff --git a/samtools/bam_consensus.c b/samtools/bam_consensus.c
new file mode 100644
index 0000000..072dcd3
--- /dev/null
+++ b/samtools/bam_consensus.c
@@ -0,0 +1,1712 @@
+/*  bam_consensus.c -- consensus subcommand.
+
+    Copyright (C) 1998-2001,2003 Medical Research Council (Gap4/5 source)
+    Copyright (C) 2003-2005,2007-2022 Genome Research Ltd.
+
+    Author: James Bonfield <jkb@sanger.ac.uk>
+
+The primary work here is GRL since 2021, under an MIT license.
+Sections derived from Gap5, which include calculate_consensus_gap5()
+associated functions, are mostly copyright Genome Research Limited from
+2003 onwards.  These were originally under a BSD license, but as GRL is
+copyright holder these portions can be considered to also be under the
+same MIT license below:
+
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+/*
+ * The Gap5 consensus algorithm was in turn derived from the earlier Gap4
+ * tool, developed by the Medical Research Council as part of the
+ * Staden Package.  It is unsure how much of this source code is still
+ * extant, without deep review, but the license used was a compatible
+ * modified BSD license, included below.
+ */
+
+/*
+Modified BSD license for any legacy components from the Staden Package:
+
+Copyright (c) 2003 MEDICAL RESEARCH COUNCIL
+All rights reserved
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+   . Redistributions of source code must retain the above copyright notice,
+this list of conditions and the following disclaimer.
+
+   . Redistributions in binary form must reproduce the above copyright notice,
+this list of conditions and the following disclaimer in the documentation
+and/or other materials provided with the distribution.
+
+   . Neither the name of the MEDICAL RESEARCH COUNCIL, THE LABORATORY OF
+MOLECULAR BIOLOGY nor the names of its contributors may be used to endorse or
+promote products derived from this software without specific prior written
+permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
+ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
+ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+*/
+
+
+// FIXME: also use strand to spot possible basecalling errors.
+//        Specifically het calls where mods are predominantly on one
+//        strand.  So maybe require + and - calls and check concordance
+//        before calling a het as confident.  (Still call, but low qual?)
+
+// TODO: call by kmers rather than individual bases?  Or use kmers to skew
+// quality at least.  It can identify variants that are low quality due to
+// neighbouring edits that aren't consistently correlated.
+
+// TODO: pileup callback ought to know when it's the last in the region /
+// chromosome.  This means the caller code doesn't have to handle the
+// termination phase and deduplicates the code.  (Changing from
+// one chr to the next is the same as ending the last.)
+//
+// TODO: track which reads contribute to multiple confirmed (HQ) differences
+// vs which contribute to only one (LQ) difference.  Correlated changes
+// are more likely to be real.  Ie consensus more of a path than solely
+// isolated columns.
+//
+// Either that or a dummy "end of data" call is made to signify end to
+// permit tidying up.  Maybe add a "start of data" call too?
+
+// Eg 50T 20A seems T/A het,
+// but 30T+ 20T- 18A+ 2A- seems like a consistent A miscall on one strand
+// only, while T is spread evenly across both strands.
+
+#include <config.h>
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <strings.h>
+#include <math.h>
+#include <limits.h>
+#include <float.h>
+#include <ctype.h>
+
+#include <htslib/sam.h>
+
+#include "samtools.h"
+#include "sam_opts.h"
+#include "bam_plbuf.h"
+#include "consensus_pileup.h"
+
+#ifdef __SSE__
+#   include <xmmintrin.h>
+#else
+#   define _mm_prefetch(a,b)
+#endif
+
+#ifndef MIN
+#  define MIN(a,b) ((a)<(b)?(a):(b))
+#endif
+#ifndef MAX
+#  define MAX(a,b) ((a)>(b)?(a):(b))
+#endif
+
+// Minimum cutoff for storing mod data; => at least 10% chance
+#define MOD_CUTOFF 0.46
+
+enum format {
+    FASTQ,
+    FASTA,
+    PILEUP
+};
+
+typedef unsigned char uc;
+
+typedef struct {
+    // User options
+    char *reg;
+    int use_qual;
+    int min_qual;
+    int adj_qual;
+    int use_mqual;
+    double scale_mqual;
+    int nm_adjust;
+    int nm_halo;
+    int sc_cost;
+    int low_mqual;
+    int high_mqual;
+    int min_depth;
+    double call_fract;
+    double het_fract;
+    int gap5;
+    enum format fmt;
+    int cons_cutoff;
+    int ambig;
+    int line_len;
+    int default_qual;
+    int het_only;
+    int all_bases;
+    int show_del;
+    int show_ins;
+    int excl_flags;
+    int incl_flags;
+    int min_mqual;
+    double P_het;
+
+    // Internal state
+    samFile *fp;
+    FILE *fp_out;
+    sam_hdr_t *h;
+    hts_idx_t *idx;
+    hts_itr_t *iter;
+    kstring_t ks_line;
+    kstring_t ks_ins_seq;
+    kstring_t ks_ins_qual;
+    int last_tid;
+    hts_pos_t last_pos;
+} consensus_opts;
+
+/* --------------------------------------------------------------------------
+ * A bayesian consensus algorithm that analyses the data to work out
+ * which hypothesis of pure A/C/G/T/absent and all combinations of two
+ * such bases meets the observations.
+ *
+ * This has its origins in Gap4 (homozygous) -> Gap5 (heterozygous)
+ * -> Crumble (tidied up to use htslib's pileup) -> here.
+ *
+ */
+
+#define CONS_DISCREP    4
+#define CONS_ALL        15
+
+#define CONS_MQUAL      16
+
+typedef struct {
+    /* the most likely base call - we never call N here */
+    /* A=0, C=1, G=2, T=3, *=4 */
+    int call;
+
+    /* The most likely heterozygous base call */
+    /* Use "ACGT*"[het / 5] vs "ACGT*"[het % 5] for the combination */
+    int het_call;
+
+    /* Log-odds for het_call */
+    int het_logodd;
+
+    /* Single phred style call */
+    int phred;
+
+    /* Sequence depth */
+    int depth;
+
+    /* Discrepancy search score */
+    float discrep;
+} consensus_t;
+
+#define P_HET 1e-4
+
+#define LOG10            2.30258509299404568401
+#define TENOVERLOG10     4.34294481903251827652
+#define TENLOG2OVERLOG10 3.0103
+
+#ifdef __GNUC__
+#define ALIGNED(x) __attribute((aligned(x)))
+#else
+#define ALIGNED(x)
+#endif
+
+static double prior[25]    ALIGNED(16);  /* Sum to 1.0 */
+static double lprior15[15] ALIGNED(16);  /* 15 combinations of {ACGT*} */
+
+/* Precomputed matrices for the consensus algorithm */
+static double pMM[101] ALIGNED(16);
+static double p__[101] ALIGNED(16);
+static double p_M[101] ALIGNED(16);
+
+static double e_tab_a[1002]  ALIGNED(16);
+static double *e_tab = &e_tab_a[500];
+static double e_tab2_a[1002] ALIGNED(16);
+static double *e_tab2 = &e_tab2_a[500];
+static double e_log[501]     ALIGNED(16);
+
+/*
+ * Lots of confusing matrix terms here, so some definitions will help.
+ *
+ * M = match base
+ * m = match pad
+ * _ = mismatch
+ * o = overcall
+ * u = undercall
+ *
+ * We need to distinguish between homozygous columns and heterozygous columns,
+ * done using a flat prior.  This is implemented by treating every observation
+ * as coming from one of two alleles, giving us a 2D matrix of possibilities
+ * (the hypotheses) for each and every call (the observation).
+ *
+ * So pMM[] is the chance that given a call 'x' that it came from the
+ * x/x allele combination.  Similarly p_o[] is the chance that call
+ * 'x' came from a mismatch (non-x) / overcall (consensus=*) combination.
+ *
+ * Examples with observation (call) C and * follows
+ *
+ *  C | A  C  G  T  *          * | A  C  G  T  *
+ *  -----------------          -----------------
+ *  A | __ _M __ __ o_         A | uu uu uu uu um
+ *  C | _M MM _M _M oM         C | uu uu uu uu um
+ *  G | __ _M __ __ o_         G | uu uu uu uu um
+ *  T | __ _M __ __ o_         T | uu uu uu uu um
+ *  * | o_ oM o_ o_ oo         * | um um um um mm
+ *
+ * In calculation terms, the _M is half __ and half MM, similarly o_ and um.
+ *
+ * Relative weights of substitution vs overcall vs undercall are governed on a
+ * per base basis using the P_OVER and P_UNDER scores (subst is
+ * 1-P_OVER-P_UNDER).
+ *
+ * The heterozygosity weight though is a per column calculation as we're
+ * trying to model whether the column is pure or mixed. Hence this is done
+ * once via a prior and has no affect on the individual matrix cells.
+ */
+
+static void consensus_init(double p_het) {
+    int i;
+
+    for (i = -500; i <= 500; i++)
+        e_tab[i] = exp(i);
+    for (i = -500; i <= 500; i++)
+        e_tab2[i] = exp(i/10.);
+    for (i = 0; i <= 500; i++)
+        e_log[i] = log(i);
+
+    // Heterozygous locations
+    for (i = 0; i < 25; i++)
+        prior[i] = p_het / 20;
+    prior[0] = prior[6] = prior[12] = prior[18] = prior[24] = (1-p_het)/5;
+
+    lprior15[0]  = log(prior[0]);
+    lprior15[1]  = log(prior[1]*2);
+    lprior15[2]  = log(prior[2]*2);
+    lprior15[3]  = log(prior[3]*2);
+    lprior15[4]  = log(prior[4]*2);
+    lprior15[5]  = log(prior[6]);
+    lprior15[6]  = log(prior[7]*2);
+    lprior15[7]  = log(prior[8]*2);
+    lprior15[8]  = log(prior[9]*2);
+    lprior15[9]  = log(prior[12]);
+    lprior15[10] = log(prior[13]*2);
+    lprior15[11] = log(prior[14]*2);
+    lprior15[12] = log(prior[18]);
+    lprior15[13] = log(prior[19]*2);
+    lprior15[14] = log(prior[24]);
+
+
+    // Rewrite as new form
+    for (i = 1; i < 101; i++) {
+        double prob = 1 - pow(10, -i / 10.0);
+
+        // May want to multiply all these by 5 so pMM[i] becomes close
+        // to -0 for most data. This makes the sums increment very slowly,
+        // keeping bit precision in the accumulator.
+        pMM[i] = log(prob/5);
+        p__[i] = log((1-prob)/20);
+        p_M[i] = log((exp(pMM[i]) + exp(p__[i]))/2);
+    }
+
+    pMM[0] = pMM[1];
+    p__[0] = p__[1];
+    p_M[0] = p_M[1];
+}
+
+static inline double fast_exp(double y) {
+    if (y >= -50 && y <= 50)
+        return e_tab2[(int)(y*10)];
+
+    if (y < -500)
+        y = -500;
+    if (y > 500)
+        y = 500;
+
+    return e_tab[(int)y];
+}
+
+/* Taylor (deg 3) implementation of the log */
+static inline double fast_log2(double val)
+{
+    // FP representation is exponent & mantissa, where
+    // value = 2^E * M.
+    // Hence log2(value) = log2(2^E * M)
+    //                   = log2(2^E)+ log2(M)
+    //                   =        E + log2(M)
+    union { double d; uint64_t x; } u = {val};
+    const int E = ((u.x >> 52) & 2047) - 1024; // exponent E
+    // Initial log2(M) based on mantissa
+    u.x &= ~(2047LL << 52);
+    u.x +=   1023LL << 52;
+
+    val = ((-1/3.) * u.d + 2) * u.d - 2/3.;
+
+    return E + val;
+}
+
+#define ph_log(x) (-TENLOG2OVERLOG10*fast_log2((x)))
+
+
+int nins(const bam1_t *b){
+    int i, indel = 0;
+    uint32_t *cig = bam_get_cigar(b);
+    for (i = 0; i < b->core.n_cigar; i++) {
+        int op = bam_cigar_op(cig[i]);
+        if (op == BAM_CINS || op == BAM_CDEL)
+            indel += bam_cigar_oplen(cig[i]);
+    }
+    return indel;
+}
+
+// Return the local NM figure within halo (+/- HALO) of pos.
+// This local NM is used as a way to modify MAPQ to get a localised MAPQ
+// score via an adhoc fashion.
+double nm_local(const pileup_t *p, const bam1_t *b, hts_pos_t pos) {
+    int *nm = (int *)p->cd;
+    if (!nm)
+        return 0;
+    pos -= b->core.pos;
+    if (pos < 0)
+        return nm[0];
+    if (pos >= b->core.l_qseq)
+        return nm[b->core.l_qseq-1];
+
+    return nm[pos] / 10.0;
+}
+
+/*
+ * Initialise a new sequence appearing in the pileup.  We use this to
+ * precompute some metrics that we'll repeatedly use in the consensus
+ * caller; the localised NM score.
+ *
+ * We also directly amend the BAM record (which will be discarded later
+ * anyway) to modify qualities to account for local quality minima.
+ *
+ * Returns 0 (discard) or 1 (keep) on success, -1 on failure.
+ */
+int nm_init(void *client_data, samFile *fp, sam_hdr_t *h, pileup_t *p) {
+    consensus_opts *opts = (consensus_opts *)client_data;
+    if (!opts->use_mqual)
+        return 1;
+
+    const bam1_t *b = &p->b;
+    int qlen = b->core.l_qseq, i;
+    int *local_nm = calloc(qlen, sizeof(*local_nm));
+    if (!local_nm)
+        return -1;
+    p->cd = local_nm;
+
+    if (opts->adj_qual) {
+#if 0
+        // Tweak by localised quality.
+        // Quality is reduced by a significant portion of the minimum quality
+        // in neighbouring bases, on the pretext that if the region is bad, then
+        // this base is bad even if it claims otherwise.
+        uint8_t *qual = bam_get_qual(b);
+        const int qhalo = 8; // 2?
+        int qmin = 50; // effectively caps PacBio qual too
+        for (i = 0; i < qlen && i < qhalo; i++) {
+            local_nm[i] = qual[i];
+            if (qmin > qual[i])
+                qmin = qual[i];
+        }
+        for (;i < qlen-qhalo; i++) {
+            //int t = (qual[i]*1   + 3*qmin)/4; // good on 60x
+            int t = (qual[i]   + 5*qmin)/4; // good on 15x
+            local_nm[i] = t < qual[i] ? t : qual[i];
+            if (qmin > qual[i+qhalo])
+                qmin = qual[i+qhalo];
+            else if (qmin <= qual[i-qhalo]) {
+                int j;
+                qmin = 50;
+                for (j = i-qhalo+1; j <= i+qhalo; j++)
+                    if (qmin > qual[j])
+                        qmin = qual[j];
+            }
+        }
+        for (; i < qlen; i++) {
+            local_nm[i] = qual[i];
+            local_nm[i] = (local_nm[i] + 6*qmin)/4;
+        }
+
+        for (i = 0; i < qlen; i++) {
+            qual[i] = local_nm[i];
+
+            // Plus overall rescale.
+            // Lower becomes lower, very high becomes a little higher.
+            // Helps deep GIAB, but detrimental elsewhere.  (What this really
+            // indicates is quality calibration differs per data set.)
+            // It's probably something best accounted for somewhere else.
+
+            //qual[i] = qual[i]*qual[i]/40+1;
+        }
+        memset(local_nm, 0, qlen * sizeof(*local_nm));
+#else
+        // Skew local NM by qual vs min-qual delta
+        uint8_t *qual = bam_get_qual(b);
+        const int qhalo = 8; // 4
+        int qmin = 99;
+        for (i = 0; i < qlen && i < qhalo; i++) {
+            if (qmin > qual[i])
+                qmin = qual[i];
+        }
+        for (;i < qlen-qhalo; i++) {
+            int t = (qual[i]   + 5*qmin)/4; // good on 15x
+            local_nm[i] += t < qual[i] ? (qual[i]-t) : 0;
+            if (qmin > qual[i+qhalo])
+                qmin = qual[i+qhalo];
+            else if (qmin <= qual[i-qhalo]) {
+                int j;
+                qmin = 99;
+                for (j = i-qhalo+1; j <= i+qhalo; j++)
+                    if (qmin > qual[j])
+                        qmin = qual[j];
+            }
+        }
+        for (; i < qlen; i++) {
+            int t = (qual[i]   + 5*qmin)/4; // good on 15x
+            local_nm[i] += t < qual[i] ? (qual[i]-t) : 0;
+        }
+#endif
+    }
+
+    // Adjust local_nm array by the number of edits within
+    // a defined region (pos +/- halo).
+    const int halo = opts->nm_halo;
+    const uint8_t *md = bam_aux_get(b, "MD");
+    if (!md)
+        return 1;
+    md = (const uint8_t *)bam_aux2Z(md);
+
+    // Handle cost of being near a soft-clip
+    uint32_t *cig = bam_get_cigar(b);
+    int ncig = b->core.n_cigar;
+
+    if ( (cig[0] & BAM_CIGAR_MASK) == BAM_CSOFT_CLIP ||
+        ((cig[0] & BAM_CIGAR_MASK) == BAM_CHARD_CLIP && ncig > 1 &&
+         (cig[1] & BAM_CIGAR_MASK) == BAM_CSOFT_CLIP)) {
+        for (i = 0; i < halo && i < qlen; i++)
+            local_nm[i]+=opts->sc_cost;
+        for (; i < halo*2 && i < qlen; i++)
+            local_nm[i]+=opts->sc_cost>>1;
+    }
+    if ( (cig[ncig-1] & BAM_CIGAR_MASK) == BAM_CSOFT_CLIP ||
+        ((cig[ncig-1] & BAM_CIGAR_MASK) == BAM_CHARD_CLIP && ncig > 1 &&
+         (cig[ncig-2] & BAM_CIGAR_MASK) == BAM_CSOFT_CLIP)) {
+        for (i = qlen-1; i >= qlen-halo && i >= 0; i--)
+            local_nm[i]+=opts->sc_cost;
+        for (; i >= qlen-halo*2 && i >= 0; i--)
+            local_nm[i]+=opts->sc_cost>>1;
+    }
+
+    // Now iterate over MD tag
+    int pos = 0;
+    while (*md) {
+        if (isdigit(*md)) {
+            uint8_t *endptr;
+            long i = strtol((char *)md, (char **)&endptr, 10);
+            md = endptr;
+            pos += i;
+            continue;
+        }
+
+        // deletion.
+        // Should we bump local_nm here too?  Maybe
+        if (*md == '^') {
+            while (*++md && !isdigit(*md))
+                continue;
+            continue;
+        }
+
+        // substitution
+        for (i = pos-halo*2 >= 0 ? pos-halo*2 : 0; i < pos-halo; i++)
+            local_nm[i]+=5;
+        for (; i < pos+halo && i < qlen; i++)
+            local_nm[i]+=10;
+        for (; i < pos+halo*2 && i < qlen; i++)
+            local_nm[i]+=5;
+        md++;
+    }
+
+    return 1;
+}
+
+
+static
+int calculate_consensus_gap5(hts_pos_t pos, int flags, int depth,
+                             pileup_t *plp, consensus_opts *opts,
+                             consensus_t *cons, int default_qual) {
+    int i, j;
+    static int init_done =0;
+    static double q2p[101], mqual_pow[256];
+    double min_e_exp = DBL_MIN_EXP * log(2) + 1;
+
+    double S[15] ALIGNED(16) = {0,0,0,0,0,0,0,0,0,0,0,0,0,0,0};
+    double sumsC[6] = {0,0,0,0,0,0}; // A C G T * N
+
+    // Small hash on seq to check for uniqueness of surrounding bases.
+    // If it's frequent, then it's more likely to be correctly called than
+    // if it's rare.
+    // Helps a bit on deep data, especially with K2=3, but detrimental on
+    // shallow and (currently) quite a slow down.
+
+//#define K2 2
+#ifdef K2
+    int hashN[1<<(K2*4+2)] = {0};
+    int hash1[1<<2] = {0};
+#endif
+
+    /* Map the 15 possible combinations to 1-base or 2-base encodings */
+    static int map_sing[15] ALIGNED(16) =
+        {0, 5, 5, 5, 5,
+            1, 5, 5, 5,
+               2, 5, 5,
+                  3, 5,
+                     4};
+    static int map_het[15] ALIGNED(16) =
+        {0,  1,  2,  3,  4,
+             6,  7,  8,  9,
+                12, 13, 14,
+                    18, 19,
+                        24};
+
+    if (!init_done) {
+        init_done = 1;
+        consensus_init(opts->P_het);
+
+        for (i = 0; i <= 100; i++) {
+            q2p[i] = pow(10, -i/10.0);
+        }
+
+        for (i = 0; i < 255; i++) {
+            //mqual_pow[i] = 1-pow(10, -(i+.01)/10.0);
+            mqual_pow[i] = 1-pow(10, -(i*.9)/10.0);
+            //mqual_pow[i] = 1-pow(10, -(i/3+.1)/10.0);
+            //mqual_pow[i] = 1-pow(10, -(i/2+.05)/10.0);
+        }
+        // unknown mqual
+        mqual_pow[255] = mqual_pow[10];
+    }
+
+    /* Initialise */
+    int counts[6] = {0};
+
+    /* Accumulate */
+
+#ifdef K2
+    const pileup_t *ptmp = plp;
+    for (; ptmp; ptmp = ptmp->next) {
+        const pileup_t *p = ptmp;
+        if (p->qual < opts->min_qual)
+            continue;
+
+        int hb = 0;
+#define _ 0
+        static int X[16] = {_,0,1,_,2,_,_,_,3,_,_,_,_,_,_,_};
+#undef _
+        uint8_t *seq = bam_get_seq(&p->b);
+        int i, base1 = X[p->base4];
+        hash1[base1]++;
+        for (i = p->seq_offset-K2; i <= p->seq_offset+K2; i++) {
+            int base = i >= 0 && i < p->b.core.l_qseq ? X[bam_seqi(seq,i)] : _;
+            hb = (hb<<2)|base;
+        }
+        hashN[hb]++;
+    }
+#endif
+
+    int td = depth; // original depth
+    depth = 0;
+    for (; plp; plp = plp->next) {
+        pileup_t *p = plp;
+
+        if (p->next)
+            _mm_prefetch(p->next, _MM_HINT_T0);
+
+        if (p->qual < opts->min_qual)
+            continue;
+
+        if (p->ref_skip)
+            continue;
+
+#ifdef K2
+        int hb = 0;
+#define _ 0
+        static int X[16] = {_,0,1,_,2,_,_,_,3,_,_,_,_,_,_,_};
+        int i, base1 = X[p->base4];
+        for (i = p->seq_offset-K2; i <= p->seq_offset+K2; i++) {
+            int base = i >= 0 && i < p->b.core.l_qseq ? X[bam_seqi(seq,i)] : _;
+            hb = (hb<<2)|base;
+        }
+        //        fprintf(stderr, "%c: %d %d of %d\t%d %d\n", p->base, hashN[hb], hash1[base1], td, p->qual, p->qual * hashN[hb] / hash1[base1]);
+#undef _
+#endif
+
+        const bam1_t *b = &p->b;
+        uint8_t base = p->base4;
+        uint8_t *qual_arr = bam_get_qual(b);
+        uint8_t qual = p->qual;
+        //qual = qual*qual/40+1;
+        if (qual == 255 || (qual == 0 && *qual_arr == 255))
+            qual = default_qual;
+
+#ifdef K2
+        //qual = qual * hashN[hb] / hash1[base1];
+        qual -= -TENOVERLOG10*log(hashN[hb] / (hash1[base1]+.1));
+        if (qual < 1)
+            qual = 1;
+#endif
+
+        // =ACM GRSV TWYH KDBN *
+        static int L[32] = {
+            5,0,1,5, 2,5,5,5, 3,5,5,5, 5,5,5,5,
+            4,4,4,4, 4,4,4,4, 4,4,4,4, 4,4,4,4,
+        };
+
+        // convert from sam base to acgt*n order.
+        base = L[base];
+
+        double MM, __, _M, qe;
+
+        // Correction for mapping quality.  Maybe speed up via lookups?
+        // Cannot nullify mapping quality completely.  Lots of (true)
+        // SNPs means low mapping quality.  (Ideally need to know
+        // hamming distance to next best location.)
+
+        if (flags & CONS_MQUAL) {
+            int mqual = b->core.qual;
+            if (opts->nm_adjust) {
+                mqual /= (nm_local(p, b, pos)+1);
+                mqual *= 1 + 2*(0.5-(td>30?30:td)/60.0); // depth fudge
+            }
+
+            // higher => call more; +FP, -FN
+            // lower  => call less; -FP, +FN
+            mqual *= opts->scale_mqual;
+
+            // Drop these?  They don't seem to ever help.
+            if (mqual < opts->low_mqual)
+                mqual = opts->low_mqual;
+            if (mqual > opts->high_mqual)
+                mqual = opts->high_mqual;
+
+            double _p = 1-q2p[qual];
+            double _m = mqual_pow[mqual];
+            qual = ph_log(1-(_m * _p + (1 - _m)/4)); // CURRENT
+            //qual = ph_log(1-_p*_m); // testing
+            //qual *= 6/sqrt(td);
+        }
+
+        /* Quality 0 should never be permitted as it breaks the maths */
+        if (qual < 1)
+            qual = 1;
+
+        __ = p__[qual];       // neither match
+        MM = pMM[qual] - __;  // both match
+        _M = p_M[qual] - __;  // one allele only (half match)
+
+        if (flags & CONS_DISCREP) {
+            qe = q2p[qual];
+            sumsC[base] += 1 - qe;
+        }
+
+        counts[base]++;
+
+        switch (base) {
+        case 0: // A
+            S[0] += MM;
+            S[1] += _M;
+            S[2] += _M;
+            S[3] += _M;
+            S[4] += _M;
+            break;
+
+        case 1: // C
+            S[1] += _M;
+            S[5] += MM;
+            S[6] += _M;
+            S[7] += _M;
+            S[8] += _M;
+            break;
+
+        case 2: // G
+            S[ 2] += _M;
+            S[ 6] += _M;
+            S[ 9] += MM;
+            S[10] += _M;
+            S[11] += _M;
+            break;
+
+        case 3: // T
+            S[ 3] += _M;
+            S[ 7] += _M;
+            S[10] += _M;
+            S[12] += MM;
+            S[13] += _M;
+
+            break;
+
+        case 4: // *
+            S[ 4] += _M;
+            S[ 8] += _M;
+            S[11] += _M;
+            S[13] += _M;
+            S[14] += MM;
+            break;
+
+        case 5: /* N => equal weight to all A,C,G,T but not a pad */
+            S[ 0] += MM;
+            S[ 1] += MM;
+            S[ 2] += MM;
+            S[ 3] += MM;
+            S[ 4] += _M;
+
+            S[ 5] += MM;
+            S[ 6] += MM;
+            S[ 7] += MM;
+            S[ 8] += _M;
+
+            S[ 9] += MM;
+            S[10] += MM;
+            S[11] += _M;
+
+            S[12] += MM;
+            S[13] += _M;
+            break;
+        }
+
+        depth++;
+
+        if (p->eof && p->cd) {
+            free(p->cd);
+            p->cd = NULL;
+        }
+    }
+
+    /* We've accumulated stats, so now we speculate on the consensus call */
+    double shift, max, max_het, norm[15];
+    int call = 0, het_call = 0;
+    double tot1 = 0, tot2 = 0;
+
+    /*
+     * Scale numbers so the maximum score is 0. This shift is essentially
+     * a multiplication in non-log scale to both numerator and denominator,
+     * so it cancels out. We do this to avoid calling exp(-large_num) and
+     * ending up with norm == 0 and hence a 0/0 error.
+     *
+     * Can also generate the base-call here too.
+     */
+    shift = -DBL_MAX;
+    max = -DBL_MAX;
+    max_het = -DBL_MAX;
+
+    for (j = 0; j < 15; j++) {
+        S[j] += lprior15[j];
+        if (shift < S[j])
+            shift = S[j];
+
+        /* Only call pure AA, CC, GG, TT, ** for now */
+        if (j != 0 && j != 5 && j != 9 && j != 12 && j != 14) {
+            if (max_het < S[j]) {
+                max_het = S[j];
+                het_call = j;
+            }
+            continue;
+        }
+
+        if (max < S[j]) {
+            max = S[j];
+            call = j;
+        }
+    }
+
+    /*
+     * Shift and normalise.
+     * If call is, say, b we want p = b/(a+b+c+...+n), but then we do
+     * p/(1-p) later on and this has exceptions when p is very close
+     * to 1.
+     *
+     * Hence we compute b/(a+b+c+...+n - b) and
+     * rearrange (p/norm) / (1 - (p/norm)) to be p/norm2.
+     */
+    for (j = 0; j < 15; j++) {
+        S[j] -= shift;
+        double e = fast_exp(S[j]);
+        S[j] = (S[j] > min_e_exp) ? e : DBL_MIN;
+        norm[j] = 0;
+    }
+
+    for (j = 0; j < 15; j++) {
+        norm[j]    += tot1;
+        norm[14-j] += tot2;
+        tot1 += S[j];
+        tot2 += S[14-j];
+    }
+
+    /* And store result */
+    if (!depth || depth == counts[5] /* all N */) {
+        cons->call = 4; /* N */
+        cons->het_call = 0;
+        cons->het_logodd = 0;
+        cons->phred = 0;
+        cons->depth = 0;
+        cons->discrep = 0;
+        return 0;
+    }
+
+    cons->depth = depth;
+
+    /* Call */
+    if (norm[call] == 0) norm[call] = DBL_MIN;
+    // Approximation of phred for when S[call] ~= 1 and norm[call]
+    // is small.  Otherwise we need the full calculation.
+    int ph;
+    if (S[call] == 1 && norm[call] < .01)
+        ph = ph_log(norm[call]) + .5;
+    else
+        ph = ph_log(1-S[call]/(norm[call]+S[call])) + .5;
+
+    cons->call     = map_sing[call];
+    cons->phred = ph < 0 ? 0 : ph;
+
+    if (norm[het_call] == 0) norm[het_call] = DBL_MIN;
+    ph = TENLOG2OVERLOG10 * (fast_log2(S[het_call])
+                             - fast_log2(norm[het_call])) + .5;
+
+    cons->het_call = map_het[het_call];
+    cons->het_logodd = ph;
+
+    /* Compute discrepancy score */
+    if (flags & CONS_DISCREP) {
+        double m = sumsC[0]+sumsC[1]+sumsC[2]+sumsC[3]+sumsC[4];
+        double c;
+        if (cons->het_logodd > 0)
+            c = sumsC[cons->het_call%5] + sumsC[cons->het_call/5];
+        else
+            c = sumsC[cons->call];
+        cons->discrep = (m-c)/sqrt(m);
+    }
+
+    return 0;
+}
+
+
+/* --------------------------------------------------------------------------
+ * Main processing logic
+ */
+
+static void dump_fastq(consensus_opts *opts,
+                       const char *name,
+                       const char *seq, size_t seq_l,
+                       const char *qual, size_t qual_l) {
+    enum format fmt = opts->fmt;
+    int line_len = opts->line_len;
+    FILE *fp = opts->fp_out;
+
+    fprintf(fp, "%c%s\n", ">@"[fmt==FASTQ], name);
+    size_t i;
+    for (i = 0; i < seq_l; i += line_len)
+        fprintf(fp, "%.*s\n", (int)MIN(line_len, seq_l - i), seq+i);
+
+    if (fmt == FASTQ) {
+        fprintf(fp, "+\n");
+        for (i = 0; i < seq_l; i += line_len)
+            fprintf(fp, "%.*s\n", (int)MIN(line_len, seq_l - i), qual+i);
+    }
+}
+
+//---------------------------------------------------------------------------
+
+/*
+ * Reads a single alignment record, using either the iterator
+ * or a direct sam_read1 call.
+ */
+static int readaln2(void *dat, samFile *fp, sam_hdr_t *h, bam1_t *b) {
+    consensus_opts *opts = (consensus_opts *)dat;
+
+    for (;;) {
+        int ret = opts->iter
+            ? sam_itr_next(fp, opts->iter, b)
+            : sam_read1(fp, h, b);
+        if (ret < 0)
+            return ret;
+
+        // Apply hard filters
+        if (opts->incl_flags && !(b->core.flag & opts->incl_flags))
+            continue;
+        if (opts->excl_flags &&  (b->core.flag & opts->excl_flags))
+            continue;
+        if (b->core.qual < opts->min_mqual)
+            continue;
+
+        return ret;
+    }
+}
+
+/* --------------------------------------------------------------------------
+ * A simple summing algorithm, either pure base frequency, or by
+ * weighting them according to their quality values.
+ *
+ * This is crude, but easy to understand and fits with several
+ * standard pileup criteria (eg COG-UK / CLIMB Covid-19 seq project).
+ *
+ *
+ * call1 / score1 / depth1 is the highest scoring allele.
+ * call2 / score2 / depth2 is the second highest scoring allele.
+ *
+ * Het_fract:  score2/score1
+ * Call_fract: score1 or score1+score2 over total score
+ * Min_depth:  minimum total depth of utilised bases (depth1+depth2)
+ * Min_score:  minimum total score of utilised bases (score1+score2)
+ *
+ * Eg het_fract 0.66, call_fract 0.75 and min_depth 10.
+ * 11A, 2C, 2G (14 total depth) is A.
+ * 9A, 2C, 2G  (12 total depth) is N as depth(A) < 10.
+ * 11A, 5C, 5G (21 total depth) is N as 11/21 < 0.75 (call_fract)
+ *
+ *
+ * 6A, 5G, 1C  (12 total depth) is AG het as depth(A)+depth(G) >= 10
+ *                              and 5/6 >= 0.66 and 11/12 >= 0.75.
+ *
+ * 6A, 5G, 4C  (15 total depth) is N as (6+5)/15 < 0.75 (call_fract).
+ *
+ *
+ * Note for the purpose of deletions, a base/del has an ambiguity
+ * code of lower-case base (otherwise it is uppercase).
+ */
+static int calculate_consensus_simple(const pileup_t *plp,
+                                      consensus_opts *opts, int *qual) {
+    int i, min_qual = opts->min_qual;
+
+    // Map "seqi" nt16 to A,C,G,T compatibility with weights on pure bases.
+    // where seqi is A | (C<<1) | (G<<2) | (T<<3)
+    //                        * A C M  G R S V  T W Y H  K D B N
+    static int seqi2A[16] = { 0,8,0,4, 0,4,0,2, 0,4,0,2, 0,2,0,1 };
+    static int seqi2C[16] = { 0,0,8,4, 0,0,4,2, 0,0,4,2, 0,0,2,1 };
+    static int seqi2G[16] = { 0,0,0,0, 8,4,4,1, 0,0,0,0, 4,2,2,1 };
+    static int seqi2T[16] = { 0,0,0,0, 0,0,0,0, 8,4,4,2, 8,2,2,1 };
+
+    // Ignore ambiguous bases in seq for now, so we don't treat R, Y, etc
+    // as part of one base and part another.  Based on BAM seqi values.
+    // We also use freq[16] as "*" for gap.
+    int freq[17] = {0};  // base frequency, aka depth
+    int score[17] = {0}; // summation of base qualities
+
+    // Accumulate
+    for (; plp; plp = plp->next) {
+        const pileup_t *p = plp;
+        if (p->next)
+            _mm_prefetch(p->next, _MM_HINT_T0);
+
+        int q = p->qual;
+        if (q < min_qual)
+            // Should we still record these in freq[] somewhere so
+            // we can use them in the fracts?
+            // Difference between >= X% of high-qual bases calling Y
+            // and >= X% of all bases are high-quality Y calls.
+            continue;
+
+        //int b = p->is_del ? 16 : bam_seqi(bam_get_seq(&p->b), p->seq_offset);
+        int b = p->base4;
+
+        // Map ambiguity codes to one or more component bases.
+        if (b < 16) {
+            int Q = seqi2A[b] * (opts->use_qual ? q : 1);
+            freq[1]  += Q?1:0;
+            score[1] += Q?Q:0;
+            Q = seqi2C[b] * (opts->use_qual ? q : 1);
+            freq[2]  += Q?1:0;
+            score[2] += Q?Q:0;
+            Q = seqi2G[b] * (opts->use_qual ? q : 1);
+            freq[4]  += Q?1:0;
+            score[4] += Q?Q:0;
+            Q = seqi2T[b] * (opts->use_qual ? q : 1);
+            freq[8]  += Q?1:0;
+            score[8] += Q?Q:0;
+        } else { /* * */
+            freq[16] ++;
+            score[16]+=8 * (opts->use_qual ? q : 1);
+        }
+    }
+
+    // Total usable depth
+    int tscore = 0;
+    for (i = 0; i < 5; i++)
+        tscore += score[1<<i];
+
+    // Best and second best potential calls
+    int call1  = 15, call2 = 15;
+    int depth1 = 0,  depth2 = 0;
+    int score1 = 0,  score2 = 0;
+    for (i = 0; i < 5; i++) {
+        int c = 1<<i; // A C G T *
+        if (score1 < score[c]) {
+            depth2 = depth1;
+            score2 = score1;
+            call2  = call1;
+            depth1 = freq[c];
+            score1 = score[c];
+            call1  = c;
+        } else if (score2 < score[c]) {
+            depth2 = freq[c];
+            score2 = score[c];
+            call2  = c;
+        }
+    }
+
+    // Work out which best and second best are usable as a call
+    int used_score = score1;
+    int used_depth = depth1;
+    int used_base  = call1;
+    if (score2 >= opts->het_fract * score1 && opts->ambig) {
+        used_base  |= call2;
+        used_score += score2;
+        used_depth += depth2;
+    }
+
+    // N is too shallow, or insufficient proportion of total
+    if (used_depth < opts->min_depth ||
+        used_score < opts->call_fract * tscore) {
+        used_depth = 0;
+        // But note shallow gaps are still called gaps, not N, as
+        // we're still more confident there is no base than it is
+        // A, C, G or T.
+        used_base = call1 == 16 /*&& depth1 >= call_fract * depth*/
+            ? 16 : 0; // * or N
+    }
+
+    // Our final call.  "?" shouldn't be possible to generate
+    const char *het =
+        "NACMGRSVTWYHKDBN"
+        "*ac?g???t???????";
+
+    //printf("%c %d\n", het[used_base], used_depth);
+    if (qual)
+        *qual = used_base ? 100.0 * used_score / tscore : 0;
+
+    return het[used_base];
+}
+
+static int empty_pileup2(consensus_opts *opts, sam_hdr_t *h, int tid,
+                         hts_pos_t start, hts_pos_t end) {
+    const char *name = sam_hdr_tid2name(h, tid);
+    hts_pos_t i;
+
+    int err = 0;
+    for (i = start; i < end; i++)
+        err |= fprintf(opts->fp_out, "%s\t%"PRIhts_pos"\t0\t0\tN\t0\t*\t*\n", name, i+1) < 0;
+
+    return err ? -1 : 0;
+}
+
+/*
+ * Returns 0 on success
+ *        -1 on failure
+ */
+static int basic_pileup(void *cd, samFile *fp, sam_hdr_t *h, pileup_t *p,
+                        int depth, hts_pos_t pos, int nth, int is_insert) {
+    unsigned char *qp, *cp;
+    char *rp;
+    int ref, cb, cq;
+    consensus_opts *opts = (consensus_opts *)cd;
+    int tid = p->b.core.tid;
+
+//    opts->show_ins=0;
+//    opts->show_del=1;
+    if (!opts->show_ins && nth)
+        return 0;
+
+    if (opts->iter) {
+        if (opts->iter->beg >= pos || opts->iter->end < pos)
+            return 0;
+    }
+
+    if (opts->all_bases) {
+        if (tid != opts->last_tid && opts->last_tid >= 0) {
+            hts_pos_t len = sam_hdr_tid2len(opts->h, opts->last_tid);
+            if (opts->iter)
+                len =  MIN(opts->iter->end, len);
+            if (empty_pileup2(opts, opts->h, opts->last_tid, opts->last_pos,
+                              len) < 0)
+                return -1;
+            if (tid >= 0) {
+                if (empty_pileup2(opts, opts->h, tid,
+                                  opts->iter ? opts->iter->beg : 0,
+                                  pos-1) < 0)
+                    return -1;
+            }
+        }
+        if (opts->last_pos >= 0 && pos > opts->last_pos+1) {
+            if (empty_pileup2(opts, opts->h, p->b.core.tid, opts->last_pos,
+                              pos-1) < 0)
+                return -1;
+        } else if (opts->last_pos < 0) {
+            if (empty_pileup2(opts, opts->h, p->b.core.tid,
+                              opts->iter ? opts->iter->beg : 0, pos-1) < 0)
+                return -1;
+        }
+    }
+
+    if (opts->gap5) {
+        consensus_t cons;
+        calculate_consensus_gap5(pos, opts->use_mqual ? CONS_MQUAL : 0,
+                                 depth, p, opts, &cons, opts->default_qual);
+        if (cons.het_logodd > 0 && opts->ambig) {
+            cb = "AMRWa" // 5x5 matrix with ACGT* per row / col
+                 "MCSYc"
+                 "RSGKg"
+                 "WYKTt"
+                 "acgt*"[cons.het_call];
+            cq = cons.het_logodd;
+        } else{
+            cb = "ACGT*"[cons.call];
+            cq = cons.phred;
+        }
+        if (cq < opts->cons_cutoff && cb != '*') {
+            cb = 'N';
+            cq = 0;
+        }
+    } else {
+        cb = calculate_consensus_simple(p, opts, &cq);
+    }
+    if (cb < 0)
+        return -1;
+
+    if (!p)
+        return 0;
+
+    if (!opts->show_del && cb == '*')
+        return 0;
+
+    /* Ref, pos, nth, score, seq, qual */
+    kstring_t *ks = &opts->ks_line;
+    ks->l = 0;
+    ref = p->b.core.tid;
+    rp = (char *)sam_hdr_tid2name(h, ref);
+
+    int err = 0;
+    err |= kputs(rp, ks)    < 0;
+    err |= kputc_('\t', ks) < 0;
+    err |= kputw(pos, ks)   < 0;
+    err |= kputc_('\t', ks) < 0;
+    err |= kputw(nth, ks)   < 0;
+    err |= kputc_('\t', ks) < 0;
+    err |= kputw(depth, ks) < 0;
+    err |= kputc_('\t', ks) < 0;
+    err |= kputc_(cb, ks)   < 0;
+    err |= kputc_('\t', ks) < 0;
+    err |= kputw(cq, ks)    < 0;
+    err |= kputc_('\t', ks) < 0;
+    if (err)
+        return -1;
+
+    /* Seq + qual at predetermined offsets */
+    if (ks_resize(ks, ks->l + depth*2 + 2) < 0)
+        return -1;
+
+    cp = (unsigned char *)ks->s + ks->l;
+    ks->l += depth*2 + 2;
+    qp = cp+depth+1;
+    for (; p; p = p->next) {
+        // Too tight a loop to help much, but some benefit still
+        if (p->next && p->next->next)
+            _mm_prefetch(p->next->next, _MM_HINT_T0);
+        if (p->b_is_rev) {
+            *cp++ = p->base == '*' ? '#' : tolower(p->base);
+        } else {
+            *cp++ = p->base;
+        }
+        *qp++ = MIN(p->qual,93) + '!';
+    }
+    *cp++ = '\t';
+    *qp++ = '\n';
+    if (fwrite(ks->s, 1, ks->l, opts->fp_out) != ks->l)
+        return -1;
+
+    opts->last_pos = pos;
+    opts->last_tid = tid;
+
+    return 0;
+}
+
+static int basic_fasta(void *cd, samFile *fp, sam_hdr_t *h, pileup_t *p,
+                       int depth, hts_pos_t pos, int nth, int is_insert) {
+    int cb, cq;
+    consensus_opts *opts = (consensus_opts *)cd;
+    int tid = p->b.core.tid;
+    kstring_t *seq  = &opts->ks_ins_seq;
+    kstring_t *qual = &opts->ks_ins_qual;
+
+    if (!opts->show_ins && nth)
+        return 0;
+
+    if (opts->iter) {
+        if (opts->iter->beg >= pos || opts->iter->end < pos)
+            return 0;
+    }
+
+    if (tid != opts->last_tid) {
+        if (opts->last_tid != -1) {
+            if (opts->all_bases) {
+                int i, N;
+                if (opts->iter) {
+                    opts->last_pos = MAX(opts->last_pos, opts->iter->beg-1);
+                    N = opts->iter->end;
+                } else {
+                    N = INT_MAX;
+                }
+                N = MIN(N, sam_hdr_tid2len(opts->h, opts->last_tid))
+                    - opts->last_pos;
+                if (N > 0) {
+                    if (ks_expand(seq, N+1) < 0)
+                        return -1;
+                    if (ks_expand(qual, N+1) < 0)
+                        return -1;
+                    for (i = 0; i < N; i++) {
+                        seq->s[seq->l++] = 'N';
+                        qual->s[qual->l++] = '!';
+                    }
+                    seq->s[seq->l] = 0;
+                    qual->s[qual->l] = 0;
+                }
+            }
+            dump_fastq(opts, sam_hdr_tid2name(opts->h, opts->last_tid),
+                       seq->s, seq->l, qual->s, qual->l);
+        }
+
+        seq->l = 0; qual->l = 0;
+        opts->last_tid = tid;
+//        if (opts->all_bases)
+//            opts->last_pos = 0;
+        if (opts->iter)
+            opts->last_pos = opts->iter->beg;
+        else
+            opts->last_pos = opts->all_bases ? 0 : pos-1;
+    }
+
+    // share this with basic_pileup
+    if (opts->gap5) {
+        consensus_t cons;
+        calculate_consensus_gap5(pos, opts->use_mqual ? CONS_MQUAL : 0,
+                                 depth, p, opts, &cons, opts->default_qual);
+        if (cons.het_logodd > 0 && opts->ambig) {
+            cb = "AMRWa" // 5x5 matrix with ACGT* per row / col
+                 "MCSYc"
+                 "RSGKg"
+                 "WYKTt"
+                 "acgt*"[cons.het_call];
+            cq = cons.het_logodd;
+        } else{
+            cb = "ACGT*"[cons.call];
+            cq = cons.phred;
+        }
+        if (cq < opts->cons_cutoff && cb != '*' &&
+            cons.het_call % 5 != 4 && cons.het_call / 5 != 4) {
+            // het base/* keeps base or * as most likely pure call, else N.
+            // This is because we don't have a traditional way of representing
+            // base or not-base ambiguity.
+            cb = 'N';
+            cq = 0;
+        }
+    } else {
+        cb = calculate_consensus_simple(p, opts, &cq);
+    }
+    if (cb < 0)
+        return -1;
+
+    if (!p)
+        return 0;
+
+    if (!opts->show_del && cb == '*') {
+        opts->last_pos = pos;
+        opts->last_tid = tid;
+        return 0;
+    }
+    // end of share
+
+    // Append consensus base/qual to seqs
+    if (pos > opts->last_pos) {
+        if (opts->last_pos >= 0 || opts->all_bases) {
+            // FIXME: don't expand qual if fasta
+            if (ks_expand(seq,  pos - opts->last_pos) < 0 ||
+                ks_expand(qual, pos - opts->last_pos) < 0)
+                return -1;
+            memset(seq->s  + seq->l,  'N', pos - (opts->last_pos+1));
+            memset(qual->s + qual->l, '!', pos - (opts->last_pos+1));
+            seq->l  += pos - (opts->last_pos+1);
+            qual->l += pos - (opts->last_pos+1);
+        }
+    }
+    if ((nth && opts->show_ins && cb != '*')
+        || cb != '*' || (pos > opts->last_pos && opts->show_del)) {
+        int err = 0;
+        err |= kputc(cb, seq) < 0;
+        err |= kputc(MIN(cq, '~'-'!')+'!', qual) < 0;
+        if (err)
+            return -1;
+    }
+
+    opts->last_pos = pos;
+    opts->last_tid = tid;
+
+    return 0;
+}
+// END OF NEW PILEUP
+//---------------------------------------------------------------------------
+
+static void usage_exit(FILE *fp, int exit_status) {
+    fprintf(fp, "Usage: samtools consensus [options] <in.bam>\n");
+    fprintf(fp, "\nOptions:\n");
+    fprintf(fp, "  -r, --region REG      Limit query to REG. Requires an index\n");
+    fprintf(fp, "  -f, --format FMT      Output in format FASTA, FASTQ or PILEUP [FASTA]\n");
+    fprintf(fp, "  -l, --line-len INT    Wrap FASTA/Q at line length INT [70]\n");
+    fprintf(fp, "  -o, --output FILE     Output consensus to FILE\n");
+    fprintf(fp, "  -m, --mode STR        Switch consensus mode to \"simple\"/\"bayesian\" [bayesian]\n");
+    fprintf(fp, "  -a                    Output all bases (start/end of reference)\n");
+    fprintf(fp, "  --rf, --incl-flags STR|INT\n");
+    fprintf(fp, "                        Only include reads with any flag bit set [0]\n");
+    fprintf(fp, "  --ff, --excl-flags STR|INT\n");
+    fprintf(fp, "                        Exclude reads with any flag bit set\n");
+    fprintf(fp, "                        [UNMAP,SECONDARY,QCFAIL,DUP]\n");
+    fprintf(fp, "  --min-MQ INT          Exclude reads with mapping quality below INT [0]\n");
+    fprintf(fp, "  --show-del yes/no     Whether to show deletion as \"*\" [no]\n");
+    fprintf(fp, "  --show-ins yes/no     Whether to show insertions [yes]\n");
+    fprintf(fp, "  -A, --ambig           Enable IUPAC ambiguity codes [off]\n");
+    fprintf(fp, "\nFor simple consensus mode:\n");
+    fprintf(fp, "  -q, --(no-)use-qual   Use quality values in calculation [off]\n");
+    fprintf(fp, "  -c, --call-fract INT  At least INT portion of bases must agree [0.75]\n");
+    fprintf(fp, "  -d, --min-depth INT   Minimum depth of INT [1]\n");
+    fprintf(fp, "  -H, --het-fract INT   Minimum fraction of 2nd-most to most common base [0.5]\n");
+    fprintf(fp, "\nFor default \"Bayesian\" consensus mode:\n");
+    fprintf(fp, "  -C, --cutoff C        Consensus cutoff quality C [10]\n");
+    fprintf(fp, "      --(no-)adj-qual   Modify quality with local minima [on]\n");
+    fprintf(fp, "      --(no-)use-MQ     Use mapping quality in calculation [on]\n");
+    fprintf(fp, "      --(no-)adj-MQ     Modify mapping quality by local NM [on]\n");
+    fprintf(fp, "      --NM-halo INT     Size of window for NM count in --adj-MQ [50]\n");
+    fprintf(fp, "      --scale-MQ FLOAT  Scale mapping quality by FLOAT [1.00]\n");
+    fprintf(fp, "      --low-MQ  INT     Cap minimum mapping quality [1]\n");
+    fprintf(fp, "      --high-MQ INT     Cap maximum mapping quality [60]\n");
+    fprintf(fp, "      --P-het FLOAT     Probability of heterozygous site[%.1e]\n",
+            P_HET);
+
+    fprintf(fp, "\nGlobal options:\n");
+    sam_global_opt_help(fp, "-.---@-.");
+    exit(exit_status);
+}
+
+int main_consensus(int argc, char **argv) {
+    int c, ret = 1;
+
+    consensus_opts opts = {
+        // User options
+        .gap5         = 1,
+        .use_qual     = 0,
+        .min_qual     = 0,
+        .adj_qual     = 1,
+        .use_mqual    = 1,
+        .scale_mqual  = 1.00,
+        .nm_adjust    = 1,
+        .nm_halo      = 50,
+        .sc_cost      = 60,
+        .low_mqual    = 1,
+        .high_mqual   = 60,
+        .min_depth    = 1,
+        .call_fract   = 0.75,
+        .het_fract    = 0.5,
+        .het_only     = 0,
+        .fmt          = FASTA,
+        .cons_cutoff  = 10,
+        .ambig        = 0,
+        .line_len     = 70,
+        .default_qual = 10,
+        .all_bases    = 0,
+        .show_del     = 0,
+        .show_ins     = 1,
+        .incl_flags   = 0,
+        .excl_flags   = BAM_FUNMAP | BAM_FSECONDARY | BAM_FQCFAIL | BAM_FDUP,
+        .min_mqual    = 0,
+        .P_het        = P_HET,
+
+        // Internal state
+        .ks_line      = {0,0},
+        .ks_ins_seq   = {0,0},
+        .ks_ins_qual  = {0,0},
+        .fp           = NULL,
+        .fp_out       = stdout,
+        .iter         = NULL,
+        .idx          = NULL,
+        .last_tid     = -1,
+        .last_pos     = -1,
+    };
+
+    sam_global_args ga = SAM_GLOBAL_ARGS_INIT;
+    static const struct option lopts[] = {
+        SAM_OPT_GLOBAL_OPTIONS('-', 0, 'O', '-', '-', '@'),
+        {"use-qual",           no_argument,       NULL, 'q'},
+        {"no-use-qual",        no_argument,       NULL, 'q'+1000},
+        {"adj-qual",           no_argument,       NULL, 'q'+100},
+        {"no-adj-qual",        no_argument,       NULL, 'q'+101},
+        {"use-MQ",             no_argument,       NULL, 'm'+1000},
+        {"no-use-MQ",          no_argument,       NULL, 'm'+1001},
+        {"adj-MQ",             no_argument,       NULL, 'm'+100},
+        {"no-adj-MQ",          no_argument,       NULL, 'm'+101},
+        {"NM-halo",            required_argument, NULL, 'h'+100},
+        {"SC-cost",            required_argument, NULL, 'h'+101},
+        {"scale-MQ",           required_argument, NULL, 14},
+        {"low-MQ"   ,          required_argument, NULL,  9},
+        {"high-MQ",            required_argument, NULL, 10},
+        {"min-depth",          required_argument, NULL, 'd'},
+        {"call-fract",         required_argument, NULL, 'c'},
+        {"het-fract",          required_argument, NULL, 'H'},
+        {"region",             required_argument, NULL, 'r'},
+        {"format",             required_argument, NULL, 'f'},
+        {"cutoff",             required_argument, NULL, 'C'},
+        {"ambig",              no_argument,       NULL, 'A'},
+        {"line-len",           required_argument, NULL, 'l'},
+        {"default-qual",       required_argument, NULL, 1},
+        {"het-only",           no_argument,       NULL, 6},
+        {"show-del",           required_argument, NULL, 7},
+        {"show-ins",           required_argument, NULL, 8},
+        {"output",             required_argument, NULL, 'o'},
+        {"incl-flags",         required_argument, NULL, 11},
+        {"rf",                 required_argument, NULL, 11},
+        {"excl-flags",         required_argument, NULL, 12},
+        {"ff",                 required_argument, NULL, 12},
+        {"min-MQ",             required_argument, NULL, 13},
+        {"P-het",              required_argument, NULL, 15},
+        {"mode",               required_argument, NULL, 'm'},
+        {NULL, 0, NULL, 0}
+    };
+
+    while ((c = getopt_long(argc, argv, "@:qd:c:H:r:5f:C:aAl:o:m:",
+                            lopts, NULL)) >= 0) {
+        switch (c) {
+        case 'a': opts.all_bases++; break;
+        case 'q': opts.use_qual=1; break;
+        case 'q'+1000: opts.use_qual=0; break;
+        case 'm'+1000: opts.use_mqual=1; break;
+        case 'm'+1001: opts.use_mqual=0; break;
+        case 14:  opts.scale_mqual = atof(optarg); break;
+        case  9:  opts.low_mqual = atoi(optarg); break;
+        case 10:  opts.high_mqual = atoi(optarg); break;
+        case 'd': opts.min_depth = atoi(optarg); break;
+        case 'c': opts.call_fract = atof(optarg); break;
+        case 'H': opts.het_fract = atof(optarg); break;
+        case 'r': opts.reg = optarg; break;
+        case 'C': opts.cons_cutoff = atoi(optarg); break;
+        case 'A': opts.ambig = 1; break;
+        case 1:   opts.default_qual = atoi(optarg); break;
+        case 6:   opts.het_only = 1; break;
+        case 7:   opts.show_del = (*optarg == 'y' || *optarg == 'Y'); break;
+        case 8:   opts.show_ins = (*optarg == 'y' || *optarg == 'Y'); break;
+        case 13:  opts.min_mqual = atoi(optarg); break;
+        case 15:  opts.P_het = atof(optarg); break;
+        case 'q'+100: opts.adj_qual = 1; break;
+        case 'q'+101: opts.adj_qual = 0; break;
+        case 'm'+100: opts.nm_adjust = 1; break;
+        case 'm'+101: opts.nm_adjust = 0; break;
+        case 'h'+100: opts.nm_halo = atoi(optarg); break;
+        case 'h'+101: opts.sc_cost = atoi(optarg); break;
+
+        case 'm': // mode
+            if (strcasecmp(optarg, "simple") == 0) {
+                opts.gap5 = 0;
+            } else if (strcasecmp(optarg, "bayesian") == 0) {
+                opts.gap5 = 1;
+            } else {
+                fprintf(stderr, "Unknown mode %s\n", optarg);
+                return 1;
+            }
+            break;
+
+        case 'l':
+            if ((opts.line_len = atoi(optarg)) <= 0)
+                opts.line_len = INT_MAX;
+            break;
+
+        case 'f':
+            if (strcasecmp(optarg, "fasta") == 0) {
+                opts.fmt = FASTA;
+            } else if (strcasecmp(optarg, "fastq") == 0) {
+                opts.fmt = FASTQ;
+            } else if (strcasecmp(optarg, "pileup") == 0) {
+                opts.fmt = PILEUP;
+            } else {
+                fprintf(stderr, "Unknown format %s\n", optarg);
+                return 1;
+            }
+            break;
+
+        case 'o':
+            if (!(opts.fp_out = fopen(optarg, "w"))) {
+                perror(optarg);
+                return 1;
+            }
+            break;
+
+        case 11:
+            if ((opts.incl_flags = bam_str2flag(optarg)) < 0) {
+                print_error("consensus", "could not parse --rf %s", optarg);
+                return 1;
+            }
+            break;
+        case 12:
+            if ((opts.excl_flags = bam_str2flag(optarg)) < 0) {
+                print_error("consensus", "could not parse --ff %s", optarg);
+                return 1;
+            }
+            break;
+
+         default:  if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break;
+            /* else fall-through */
+        case '?':
+            usage_exit(stderr, EXIT_FAILURE);
+        }
+    }
+
+    if (argc != optind+1) {
+        if (argc == optind) usage_exit(stdout, EXIT_SUCCESS);
+        else usage_exit(stderr, EXIT_FAILURE);
+    }
+    opts.fp = sam_open_format(argv[optind], "r", &ga.in);
+    if (opts.fp == NULL) {
+        print_error_errno("consensus", "Cannot open input file \"%s\"",
+                          argv[optind]);
+        goto err;
+    }
+    if (ga.nthreads > 0)
+        hts_set_threads(opts.fp, ga.nthreads);
+
+    if (hts_set_opt(opts.fp, CRAM_OPT_DECODE_MD, 0)) {
+        fprintf(stderr, "Failed to set CRAM_OPT_DECODE_MD value\n");
+        goto err;
+    }
+
+    if (!(opts.h = sam_hdr_read(opts.fp))) {
+        fprintf(stderr, "Failed to read header for \"%s\"\n", argv[optind]);
+        goto err;
+    }
+
+    if (opts.reg) {
+        opts.idx = sam_index_load(opts.fp, argv[optind]);
+        if (!opts.idx) {
+            print_error("consensus", "Cannot load index for input file \"%s\"",
+                        argv[optind]);
+            goto err;
+        }
+        opts.iter = sam_itr_querys(opts.idx, opts.h, opts.reg);
+        if (!opts.iter) {
+            print_error("consensus", "Failed to parse region \"%s\"",
+                        opts.reg);
+            goto err;
+        }
+    }
+
+    if (opts.fmt == PILEUP) {
+        if (pileup_loop(opts.fp, opts.h, readaln2, opts.gap5 ? nm_init : NULL,
+                        basic_pileup, &opts) < 0)
+            goto err;
+
+        if (opts.all_bases) {
+            int tid = opts.iter ? opts.iter->tid : opts.last_tid;
+            int len = sam_hdr_tid2len(opts.h, tid);
+            int pos = opts.last_pos;
+            if (opts.iter) {
+                len = MIN(opts.iter->end, len);
+                pos = MAX(opts.iter->beg, pos);
+            }
+            if (empty_pileup2(&opts, opts.h, tid, pos, len) < 0)
+                goto err;
+        }
+    } else {
+        if (pileup_loop(opts.fp, opts.h, readaln2, opts.gap5 ? nm_init : NULL,
+                        basic_fasta,
+                        &opts) < 0)
+            goto err;
+        if (opts.all_bases) {
+            // fill out terminator
+            int tid = opts.iter ? opts.iter->tid : opts.last_tid;
+            int len = sam_hdr_tid2len(opts.h, tid);
+            int pos = opts.last_pos;
+            if (opts.iter) {
+                len = MIN(opts.iter->end, len);
+                pos = MAX(opts.iter->beg, pos);
+                opts.last_tid = opts.iter->tid;
+            }
+            if (pos < len) {
+                if (ks_expand(&opts.ks_ins_seq,  len-pos+1) < 0)
+                    goto err;
+                if (ks_expand(&opts.ks_ins_qual, len-pos+1) < 0)
+                    goto err;
+                while (pos++ < len) {
+                    opts.ks_ins_seq.s [opts.ks_ins_seq.l++] = 'N';
+                    opts.ks_ins_qual.s[opts.ks_ins_qual.l++] = '!';
+                }
+                opts.ks_ins_seq.s [opts.ks_ins_seq.l] = 0;
+                opts.ks_ins_qual.s[opts.ks_ins_qual.l] = 0;
+            }
+        }
+        if (opts.last_tid >= 0)
+            dump_fastq(&opts, sam_hdr_tid2name(opts.h, opts.last_tid),
+                       opts.ks_ins_seq.s,  opts.ks_ins_seq.l,
+                       opts.ks_ins_qual.s, opts.ks_ins_qual.l);
+//        if (consensus_loop(&opts) < 0) {
+//            print_error_errno("consensus", "Failed");
+//            goto err;
+//        }
+    }
+
+    ret = 0;
+
+ err:
+    if (opts.iter)
+        hts_itr_destroy(opts.iter);
+    if (opts.idx)
+        hts_idx_destroy(opts.idx);
+
+    if (opts.fp && sam_close(opts.fp) < 0) {
+        print_error_errno("consensus", "Closing input file \"%s\"",
+                          argv[optind]);
+        ret = 1;
+    }
+
+    if (opts.h)
+        sam_hdr_destroy(opts.h);
+    sam_global_args_free(&ga);
+
+    if (opts.fp_out && opts.fp_out != stdout)
+        ret |= fclose(opts.fp_out) != 0;
+    else
+        ret |= fflush(stdout) != 0;
+
+    ks_free(&opts.ks_line);
+    ks_free(&opts.ks_ins_seq);
+    ks_free(&opts.ks_ins_qual);
+
+    if (ret)
+        print_error("consensus", "failed");
+
+    return ret;
+}
diff --git a/samtools/bam_consensus.c.pysam.c b/samtools/bam_consensus.c.pysam.c
new file mode 100644
index 0000000..08536c6
--- /dev/null
+++ b/samtools/bam_consensus.c.pysam.c
@@ -0,0 +1,1714 @@
+#include "samtools.pysam.h"
+
+/*  bam_consensus.c -- consensus subcommand.
+
+    Copyright (C) 1998-2001,2003 Medical Research Council (Gap4/5 source)
+    Copyright (C) 2003-2005,2007-2022 Genome Research Ltd.
+
+    Author: James Bonfield <jkb@sanger.ac.uk>
+
+The primary work here is GRL since 2021, under an MIT license.
+Sections derived from Gap5, which include calculate_consensus_gap5()
+associated functions, are mostly copyright Genome Research Limited from
+2003 onwards.  These were originally under a BSD license, but as GRL is
+copyright holder these portions can be considered to also be under the
+same MIT license below:
+
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+/*
+ * The Gap5 consensus algorithm was in turn derived from the earlier Gap4
+ * tool, developed by the Medical Research Council as part of the
+ * Staden Package.  It is unsure how much of this source code is still
+ * extant, without deep review, but the license used was a compatible
+ * modified BSD license, included below.
+ */
+
+/*
+Modified BSD license for any legacy components from the Staden Package:
+
+Copyright (c) 2003 MEDICAL RESEARCH COUNCIL
+All rights reserved
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+   . Redistributions of source code must retain the above copyright notice,
+this list of conditions and the following disclaimer.
+
+   . Redistributions in binary form must reproduce the above copyright notice,
+this list of conditions and the following disclaimer in the documentation
+and/or other materials provided with the distribution.
+
+   . Neither the name of the MEDICAL RESEARCH COUNCIL, THE LABORATORY OF
+MOLECULAR BIOLOGY nor the names of its contributors may be used to endorse or
+promote products derived from this software without specific prior written
+permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
+ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
+ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+*/
+
+
+// FIXME: also use strand to spot possible basecalling errors.
+//        Specifically het calls where mods are predominantly on one
+//        strand.  So maybe require + and - calls and check concordance
+//        before calling a het as confident.  (Still call, but low qual?)
+
+// TODO: call by kmers rather than individual bases?  Or use kmers to skew
+// quality at least.  It can identify variants that are low quality due to
+// neighbouring edits that aren't consistently correlated.
+
+// TODO: pileup callback ought to know when it's the last in the region /
+// chromosome.  This means the caller code doesn't have to handle the
+// termination phase and deduplicates the code.  (Changing from
+// one chr to the next is the same as ending the last.)
+//
+// TODO: track which reads contribute to multiple confirmed (HQ) differences
+// vs which contribute to only one (LQ) difference.  Correlated changes
+// are more likely to be real.  Ie consensus more of a path than solely
+// isolated columns.
+//
+// Either that or a dummy "end of data" call is made to signify end to
+// permit tidying up.  Maybe add a "start of data" call too?
+
+// Eg 50T 20A seems T/A het,
+// but 30T+ 20T- 18A+ 2A- seems like a consistent A miscall on one strand
+// only, while T is spread evenly across both strands.
+
+#include <config.h>
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <strings.h>
+#include <math.h>
+#include <limits.h>
+#include <float.h>
+#include <ctype.h>
+
+#include <htslib/sam.h>
+
+#include "samtools.h"
+#include "sam_opts.h"
+#include "bam_plbuf.h"
+#include "consensus_pileup.h"
+
+#ifdef __SSE__
+#   include <xmmintrin.h>
+#else
+#   define _mm_prefetch(a,b)
+#endif
+
+#ifndef MIN
+#  define MIN(a,b) ((a)<(b)?(a):(b))
+#endif
+#ifndef MAX
+#  define MAX(a,b) ((a)>(b)?(a):(b))
+#endif
+
+// Minimum cutoff for storing mod data; => at least 10% chance
+#define MOD_CUTOFF 0.46
+
+enum format {
+    FASTQ,
+    FASTA,
+    PILEUP
+};
+
+typedef unsigned char uc;
+
+typedef struct {
+    // User options
+    char *reg;
+    int use_qual;
+    int min_qual;
+    int adj_qual;
+    int use_mqual;
+    double scale_mqual;
+    int nm_adjust;
+    int nm_halo;
+    int sc_cost;
+    int low_mqual;
+    int high_mqual;
+    int min_depth;
+    double call_fract;
+    double het_fract;
+    int gap5;
+    enum format fmt;
+    int cons_cutoff;
+    int ambig;
+    int line_len;
+    int default_qual;
+    int het_only;
+    int all_bases;
+    int show_del;
+    int show_ins;
+    int excl_flags;
+    int incl_flags;
+    int min_mqual;
+    double P_het;
+
+    // Internal state
+    samFile *fp;
+    FILE *fp_out;
+    sam_hdr_t *h;
+    hts_idx_t *idx;
+    hts_itr_t *iter;
+    kstring_t ks_line;
+    kstring_t ks_ins_seq;
+    kstring_t ks_ins_qual;
+    int last_tid;
+    hts_pos_t last_pos;
+} consensus_opts;
+
+/* --------------------------------------------------------------------------
+ * A bayesian consensus algorithm that analyses the data to work out
+ * which hypothesis of pure A/C/G/T/absent and all combinations of two
+ * such bases meets the observations.
+ *
+ * This has its origins in Gap4 (homozygous) -> Gap5 (heterozygous)
+ * -> Crumble (tidied up to use htslib's pileup) -> here.
+ *
+ */
+
+#define CONS_DISCREP    4
+#define CONS_ALL        15
+
+#define CONS_MQUAL      16
+
+typedef struct {
+    /* the most likely base call - we never call N here */
+    /* A=0, C=1, G=2, T=3, *=4 */
+    int call;
+
+    /* The most likely heterozygous base call */
+    /* Use "ACGT*"[het / 5] vs "ACGT*"[het % 5] for the combination */
+    int het_call;
+
+    /* Log-odds for het_call */
+    int het_logodd;
+
+    /* Single phred style call */
+    int phred;
+
+    /* Sequence depth */
+    int depth;
+
+    /* Discrepancy search score */
+    float discrep;
+} consensus_t;
+
+#define P_HET 1e-4
+
+#define LOG10            2.30258509299404568401
+#define TENOVERLOG10     4.34294481903251827652
+#define TENLOG2OVERLOG10 3.0103
+
+#ifdef __GNUC__
+#define ALIGNED(x) __attribute((aligned(x)))
+#else
+#define ALIGNED(x)
+#endif
+
+static double prior[25]    ALIGNED(16);  /* Sum to 1.0 */
+static double lprior15[15] ALIGNED(16);  /* 15 combinations of {ACGT*} */
+
+/* Precomputed matrices for the consensus algorithm */
+static double pMM[101] ALIGNED(16);
+static double p__[101] ALIGNED(16);
+static double p_M[101] ALIGNED(16);
+
+static double e_tab_a[1002]  ALIGNED(16);
+static double *e_tab = &e_tab_a[500];
+static double e_tab2_a[1002] ALIGNED(16);
+static double *e_tab2 = &e_tab2_a[500];
+static double e_log[501]     ALIGNED(16);
+
+/*
+ * Lots of confusing matrix terms here, so some definitions will help.
+ *
+ * M = match base
+ * m = match pad
+ * _ = mismatch
+ * o = overcall
+ * u = undercall
+ *
+ * We need to distinguish between homozygous columns and heterozygous columns,
+ * done using a flat prior.  This is implemented by treating every observation
+ * as coming from one of two alleles, giving us a 2D matrix of possibilities
+ * (the hypotheses) for each and every call (the observation).
+ *
+ * So pMM[] is the chance that given a call 'x' that it came from the
+ * x/x allele combination.  Similarly p_o[] is the chance that call
+ * 'x' came from a mismatch (non-x) / overcall (consensus=*) combination.
+ *
+ * Examples with observation (call) C and * follows
+ *
+ *  C | A  C  G  T  *          * | A  C  G  T  *
+ *  -----------------          -----------------
+ *  A | __ _M __ __ o_         A | uu uu uu uu um
+ *  C | _M MM _M _M oM         C | uu uu uu uu um
+ *  G | __ _M __ __ o_         G | uu uu uu uu um
+ *  T | __ _M __ __ o_         T | uu uu uu uu um
+ *  * | o_ oM o_ o_ oo         * | um um um um mm
+ *
+ * In calculation terms, the _M is half __ and half MM, similarly o_ and um.
+ *
+ * Relative weights of substitution vs overcall vs undercall are governed on a
+ * per base basis using the P_OVER and P_UNDER scores (subst is
+ * 1-P_OVER-P_UNDER).
+ *
+ * The heterozygosity weight though is a per column calculation as we're
+ * trying to model whether the column is pure or mixed. Hence this is done
+ * once via a prior and has no affect on the individual matrix cells.
+ */
+
+static void consensus_init(double p_het) {
+    int i;
+
+    for (i = -500; i <= 500; i++)
+        e_tab[i] = exp(i);
+    for (i = -500; i <= 500; i++)
+        e_tab2[i] = exp(i/10.);
+    for (i = 0; i <= 500; i++)
+        e_log[i] = log(i);
+
+    // Heterozygous locations
+    for (i = 0; i < 25; i++)
+        prior[i] = p_het / 20;
+    prior[0] = prior[6] = prior[12] = prior[18] = prior[24] = (1-p_het)/5;
+
+    lprior15[0]  = log(prior[0]);
+    lprior15[1]  = log(prior[1]*2);
+    lprior15[2]  = log(prior[2]*2);
+    lprior15[3]  = log(prior[3]*2);
+    lprior15[4]  = log(prior[4]*2);
+    lprior15[5]  = log(prior[6]);
+    lprior15[6]  = log(prior[7]*2);
+    lprior15[7]  = log(prior[8]*2);
+    lprior15[8]  = log(prior[9]*2);
+    lprior15[9]  = log(prior[12]);
+    lprior15[10] = log(prior[13]*2);
+    lprior15[11] = log(prior[14]*2);
+    lprior15[12] = log(prior[18]);
+    lprior15[13] = log(prior[19]*2);
+    lprior15[14] = log(prior[24]);
+
+
+    // Rewrite as new form
+    for (i = 1; i < 101; i++) {
+        double prob = 1 - pow(10, -i / 10.0);
+
+        // May want to multiply all these by 5 so pMM[i] becomes close
+        // to -0 for most data. This makes the sums increment very slowly,
+        // keeping bit precision in the accumulator.
+        pMM[i] = log(prob/5);
+        p__[i] = log((1-prob)/20);
+        p_M[i] = log((exp(pMM[i]) + exp(p__[i]))/2);
+    }
+
+    pMM[0] = pMM[1];
+    p__[0] = p__[1];
+    p_M[0] = p_M[1];
+}
+
+static inline double fast_exp(double y) {
+    if (y >= -50 && y <= 50)
+        return e_tab2[(int)(y*10)];
+
+    if (y < -500)
+        y = -500;
+    if (y > 500)
+        y = 500;
+
+    return e_tab[(int)y];
+}
+
+/* Taylor (deg 3) implementation of the log */
+static inline double fast_log2(double val)
+{
+    // FP representation is exponent & mantissa, where
+    // value = 2^E * M.
+    // Hence log2(value) = log2(2^E * M)
+    //                   = log2(2^E)+ log2(M)
+    //                   =        E + log2(M)
+    union { double d; uint64_t x; } u = {val};
+    const int E = ((u.x >> 52) & 2047) - 1024; // exponent E
+    // Initial log2(M) based on mantissa
+    u.x &= ~(2047LL << 52);
+    u.x +=   1023LL << 52;
+
+    val = ((-1/3.) * u.d + 2) * u.d - 2/3.;
+
+    return E + val;
+}
+
+#define ph_log(x) (-TENLOG2OVERLOG10*fast_log2((x)))
+
+
+int nins(const bam1_t *b){
+    int i, indel = 0;
+    uint32_t *cig = bam_get_cigar(b);
+    for (i = 0; i < b->core.n_cigar; i++) {
+        int op = bam_cigar_op(cig[i]);
+        if (op == BAM_CINS || op == BAM_CDEL)
+            indel += bam_cigar_oplen(cig[i]);
+    }
+    return indel;
+}
+
+// Return the local NM figure within halo (+/- HALO) of pos.
+// This local NM is used as a way to modify MAPQ to get a localised MAPQ
+// score via an adhoc fashion.
+double nm_local(const pileup_t *p, const bam1_t *b, hts_pos_t pos) {
+    int *nm = (int *)p->cd;
+    if (!nm)
+        return 0;
+    pos -= b->core.pos;
+    if (pos < 0)
+        return nm[0];
+    if (pos >= b->core.l_qseq)
+        return nm[b->core.l_qseq-1];
+
+    return nm[pos] / 10.0;
+}
+
+/*
+ * Initialise a new sequence appearing in the pileup.  We use this to
+ * precompute some metrics that we'll repeatedly use in the consensus
+ * caller; the localised NM score.
+ *
+ * We also directly amend the BAM record (which will be discarded later
+ * anyway) to modify qualities to account for local quality minima.
+ *
+ * Returns 0 (discard) or 1 (keep) on success, -1 on failure.
+ */
+int nm_init(void *client_data, samFile *fp, sam_hdr_t *h, pileup_t *p) {
+    consensus_opts *opts = (consensus_opts *)client_data;
+    if (!opts->use_mqual)
+        return 1;
+
+    const bam1_t *b = &p->b;
+    int qlen = b->core.l_qseq, i;
+    int *local_nm = calloc(qlen, sizeof(*local_nm));
+    if (!local_nm)
+        return -1;
+    p->cd = local_nm;
+
+    if (opts->adj_qual) {
+#if 0
+        // Tweak by localised quality.
+        // Quality is reduced by a significant portion of the minimum quality
+        // in neighbouring bases, on the pretext that if the region is bad, then
+        // this base is bad even if it claims otherwise.
+        uint8_t *qual = bam_get_qual(b);
+        const int qhalo = 8; // 2?
+        int qmin = 50; // effectively caps PacBio qual too
+        for (i = 0; i < qlen && i < qhalo; i++) {
+            local_nm[i] = qual[i];
+            if (qmin > qual[i])
+                qmin = qual[i];
+        }
+        for (;i < qlen-qhalo; i++) {
+            //int t = (qual[i]*1   + 3*qmin)/4; // good on 60x
+            int t = (qual[i]   + 5*qmin)/4; // good on 15x
+            local_nm[i] = t < qual[i] ? t : qual[i];
+            if (qmin > qual[i+qhalo])
+                qmin = qual[i+qhalo];
+            else if (qmin <= qual[i-qhalo]) {
+                int j;
+                qmin = 50;
+                for (j = i-qhalo+1; j <= i+qhalo; j++)
+                    if (qmin > qual[j])
+                        qmin = qual[j];
+            }
+        }
+        for (; i < qlen; i++) {
+            local_nm[i] = qual[i];
+            local_nm[i] = (local_nm[i] + 6*qmin)/4;
+        }
+
+        for (i = 0; i < qlen; i++) {
+            qual[i] = local_nm[i];
+
+            // Plus overall rescale.
+            // Lower becomes lower, very high becomes a little higher.
+            // Helps deep GIAB, but detrimental elsewhere.  (What this really
+            // indicates is quality calibration differs per data set.)
+            // It's probably something best accounted for somewhere else.
+
+            //qual[i] = qual[i]*qual[i]/40+1;
+        }
+        memset(local_nm, 0, qlen * sizeof(*local_nm));
+#else
+        // Skew local NM by qual vs min-qual delta
+        uint8_t *qual = bam_get_qual(b);
+        const int qhalo = 8; // 4
+        int qmin = 99;
+        for (i = 0; i < qlen && i < qhalo; i++) {
+            if (qmin > qual[i])
+                qmin = qual[i];
+        }
+        for (;i < qlen-qhalo; i++) {
+            int t = (qual[i]   + 5*qmin)/4; // good on 15x
+            local_nm[i] += t < qual[i] ? (qual[i]-t) : 0;
+            if (qmin > qual[i+qhalo])
+                qmin = qual[i+qhalo];
+            else if (qmin <= qual[i-qhalo]) {
+                int j;
+                qmin = 99;
+                for (j = i-qhalo+1; j <= i+qhalo; j++)
+                    if (qmin > qual[j])
+                        qmin = qual[j];
+            }
+        }
+        for (; i < qlen; i++) {
+            int t = (qual[i]   + 5*qmin)/4; // good on 15x
+            local_nm[i] += t < qual[i] ? (qual[i]-t) : 0;
+        }
+#endif
+    }
+
+    // Adjust local_nm array by the number of edits within
+    // a defined region (pos +/- halo).
+    const int halo = opts->nm_halo;
+    const uint8_t *md = bam_aux_get(b, "MD");
+    if (!md)
+        return 1;
+    md = (const uint8_t *)bam_aux2Z(md);
+
+    // Handle cost of being near a soft-clip
+    uint32_t *cig = bam_get_cigar(b);
+    int ncig = b->core.n_cigar;
+
+    if ( (cig[0] & BAM_CIGAR_MASK) == BAM_CSOFT_CLIP ||
+        ((cig[0] & BAM_CIGAR_MASK) == BAM_CHARD_CLIP && ncig > 1 &&
+         (cig[1] & BAM_CIGAR_MASK) == BAM_CSOFT_CLIP)) {
+        for (i = 0; i < halo && i < qlen; i++)
+            local_nm[i]+=opts->sc_cost;
+        for (; i < halo*2 && i < qlen; i++)
+            local_nm[i]+=opts->sc_cost>>1;
+    }
+    if ( (cig[ncig-1] & BAM_CIGAR_MASK) == BAM_CSOFT_CLIP ||
+        ((cig[ncig-1] & BAM_CIGAR_MASK) == BAM_CHARD_CLIP && ncig > 1 &&
+         (cig[ncig-2] & BAM_CIGAR_MASK) == BAM_CSOFT_CLIP)) {
+        for (i = qlen-1; i >= qlen-halo && i >= 0; i--)
+            local_nm[i]+=opts->sc_cost;
+        for (; i >= qlen-halo*2 && i >= 0; i--)
+            local_nm[i]+=opts->sc_cost>>1;
+    }
+
+    // Now iterate over MD tag
+    int pos = 0;
+    while (*md) {
+        if (isdigit(*md)) {
+            uint8_t *endptr;
+            long i = strtol((char *)md, (char **)&endptr, 10);
+            md = endptr;
+            pos += i;
+            continue;
+        }
+
+        // deletion.
+        // Should we bump local_nm here too?  Maybe
+        if (*md == '^') {
+            while (*++md && !isdigit(*md))
+                continue;
+            continue;
+        }
+
+        // substitution
+        for (i = pos-halo*2 >= 0 ? pos-halo*2 : 0; i < pos-halo; i++)
+            local_nm[i]+=5;
+        for (; i < pos+halo && i < qlen; i++)
+            local_nm[i]+=10;
+        for (; i < pos+halo*2 && i < qlen; i++)
+            local_nm[i]+=5;
+        md++;
+    }
+
+    return 1;
+}
+
+
+static
+int calculate_consensus_gap5(hts_pos_t pos, int flags, int depth,
+                             pileup_t *plp, consensus_opts *opts,
+                             consensus_t *cons, int default_qual) {
+    int i, j;
+    static int init_done =0;
+    static double q2p[101], mqual_pow[256];
+    double min_e_exp = DBL_MIN_EXP * log(2) + 1;
+
+    double S[15] ALIGNED(16) = {0,0,0,0,0,0,0,0,0,0,0,0,0,0,0};
+    double sumsC[6] = {0,0,0,0,0,0}; // A C G T * N
+
+    // Small hash on seq to check for uniqueness of surrounding bases.
+    // If it's frequent, then it's more likely to be correctly called than
+    // if it's rare.
+    // Helps a bit on deep data, especially with K2=3, but detrimental on
+    // shallow and (currently) quite a slow down.
+
+//#define K2 2
+#ifdef K2
+    int hashN[1<<(K2*4+2)] = {0};
+    int hash1[1<<2] = {0};
+#endif
+
+    /* Map the 15 possible combinations to 1-base or 2-base encodings */
+    static int map_sing[15] ALIGNED(16) =
+        {0, 5, 5, 5, 5,
+            1, 5, 5, 5,
+               2, 5, 5,
+                  3, 5,
+                     4};
+    static int map_het[15] ALIGNED(16) =
+        {0,  1,  2,  3,  4,
+             6,  7,  8,  9,
+                12, 13, 14,
+                    18, 19,
+                        24};
+
+    if (!init_done) {
+        init_done = 1;
+        consensus_init(opts->P_het);
+
+        for (i = 0; i <= 100; i++) {
+            q2p[i] = pow(10, -i/10.0);
+        }
+
+        for (i = 0; i < 255; i++) {
+            //mqual_pow[i] = 1-pow(10, -(i+.01)/10.0);
+            mqual_pow[i] = 1-pow(10, -(i*.9)/10.0);
+            //mqual_pow[i] = 1-pow(10, -(i/3+.1)/10.0);
+            //mqual_pow[i] = 1-pow(10, -(i/2+.05)/10.0);
+        }
+        // unknown mqual
+        mqual_pow[255] = mqual_pow[10];
+    }
+
+    /* Initialise */
+    int counts[6] = {0};
+
+    /* Accumulate */
+
+#ifdef K2
+    const pileup_t *ptmp = plp;
+    for (; ptmp; ptmp = ptmp->next) {
+        const pileup_t *p = ptmp;
+        if (p->qual < opts->min_qual)
+            continue;
+
+        int hb = 0;
+#define _ 0
+        static int X[16] = {_,0,1,_,2,_,_,_,3,_,_,_,_,_,_,_};
+#undef _
+        uint8_t *seq = bam_get_seq(&p->b);
+        int i, base1 = X[p->base4];
+        hash1[base1]++;
+        for (i = p->seq_offset-K2; i <= p->seq_offset+K2; i++) {
+            int base = i >= 0 && i < p->b.core.l_qseq ? X[bam_seqi(seq,i)] : _;
+            hb = (hb<<2)|base;
+        }
+        hashN[hb]++;
+    }
+#endif
+
+    int td = depth; // original depth
+    depth = 0;
+    for (; plp; plp = plp->next) {
+        pileup_t *p = plp;
+
+        if (p->next)
+            _mm_prefetch(p->next, _MM_HINT_T0);
+
+        if (p->qual < opts->min_qual)
+            continue;
+
+        if (p->ref_skip)
+            continue;
+
+#ifdef K2
+        int hb = 0;
+#define _ 0
+        static int X[16] = {_,0,1,_,2,_,_,_,3,_,_,_,_,_,_,_};
+        int i, base1 = X[p->base4];
+        for (i = p->seq_offset-K2; i <= p->seq_offset+K2; i++) {
+            int base = i >= 0 && i < p->b.core.l_qseq ? X[bam_seqi(seq,i)] : _;
+            hb = (hb<<2)|base;
+        }
+        //        fprintf(samtools_stderr, "%c: %d %d of %d\t%d %d\n", p->base, hashN[hb], hash1[base1], td, p->qual, p->qual * hashN[hb] / hash1[base1]);
+#undef _
+#endif
+
+        const bam1_t *b = &p->b;
+        uint8_t base = p->base4;
+        uint8_t *qual_arr = bam_get_qual(b);
+        uint8_t qual = p->qual;
+        //qual = qual*qual/40+1;
+        if (qual == 255 || (qual == 0 && *qual_arr == 255))
+            qual = default_qual;
+
+#ifdef K2
+        //qual = qual * hashN[hb] / hash1[base1];
+        qual -= -TENOVERLOG10*log(hashN[hb] / (hash1[base1]+.1));
+        if (qual < 1)
+            qual = 1;
+#endif
+
+        // =ACM GRSV TWYH KDBN *
+        static int L[32] = {
+            5,0,1,5, 2,5,5,5, 3,5,5,5, 5,5,5,5,
+            4,4,4,4, 4,4,4,4, 4,4,4,4, 4,4,4,4,
+        };
+
+        // convert from sam base to acgt*n order.
+        base = L[base];
+
+        double MM, __, _M, qe;
+
+        // Correction for mapping quality.  Maybe speed up via lookups?
+        // Cannot nullify mapping quality completely.  Lots of (true)
+        // SNPs means low mapping quality.  (Ideally need to know
+        // hamming distance to next best location.)
+
+        if (flags & CONS_MQUAL) {
+            int mqual = b->core.qual;
+            if (opts->nm_adjust) {
+                mqual /= (nm_local(p, b, pos)+1);
+                mqual *= 1 + 2*(0.5-(td>30?30:td)/60.0); // depth fudge
+            }
+
+            // higher => call more; +FP, -FN
+            // lower  => call less; -FP, +FN
+            mqual *= opts->scale_mqual;
+
+            // Drop these?  They don't seem to ever help.
+            if (mqual < opts->low_mqual)
+                mqual = opts->low_mqual;
+            if (mqual > opts->high_mqual)
+                mqual = opts->high_mqual;
+
+            double _p = 1-q2p[qual];
+            double _m = mqual_pow[mqual];
+            qual = ph_log(1-(_m * _p + (1 - _m)/4)); // CURRENT
+            //qual = ph_log(1-_p*_m); // testing
+            //qual *= 6/sqrt(td);
+        }
+
+        /* Quality 0 should never be permitted as it breaks the maths */
+        if (qual < 1)
+            qual = 1;
+
+        __ = p__[qual];       // neither match
+        MM = pMM[qual] - __;  // both match
+        _M = p_M[qual] - __;  // one allele only (half match)
+
+        if (flags & CONS_DISCREP) {
+            qe = q2p[qual];
+            sumsC[base] += 1 - qe;
+        }
+
+        counts[base]++;
+
+        switch (base) {
+        case 0: // A
+            S[0] += MM;
+            S[1] += _M;
+            S[2] += _M;
+            S[3] += _M;
+            S[4] += _M;
+            break;
+
+        case 1: // C
+            S[1] += _M;
+            S[5] += MM;
+            S[6] += _M;
+            S[7] += _M;
+            S[8] += _M;
+            break;
+
+        case 2: // G
+            S[ 2] += _M;
+            S[ 6] += _M;
+            S[ 9] += MM;
+            S[10] += _M;
+            S[11] += _M;
+            break;
+
+        case 3: // T
+            S[ 3] += _M;
+            S[ 7] += _M;
+            S[10] += _M;
+            S[12] += MM;
+            S[13] += _M;
+
+            break;
+
+        case 4: // *
+            S[ 4] += _M;
+            S[ 8] += _M;
+            S[11] += _M;
+            S[13] += _M;
+            S[14] += MM;
+            break;
+
+        case 5: /* N => equal weight to all A,C,G,T but not a pad */
+            S[ 0] += MM;
+            S[ 1] += MM;
+            S[ 2] += MM;
+            S[ 3] += MM;
+            S[ 4] += _M;
+
+            S[ 5] += MM;
+            S[ 6] += MM;
+            S[ 7] += MM;
+            S[ 8] += _M;
+
+            S[ 9] += MM;
+            S[10] += MM;
+            S[11] += _M;
+
+            S[12] += MM;
+            S[13] += _M;
+            break;
+        }
+
+        depth++;
+
+        if (p->eof && p->cd) {
+            free(p->cd);
+            p->cd = NULL;
+        }
+    }
+
+    /* We've accumulated stats, so now we speculate on the consensus call */
+    double shift, max, max_het, norm[15];
+    int call = 0, het_call = 0;
+    double tot1 = 0, tot2 = 0;
+
+    /*
+     * Scale numbers so the maximum score is 0. This shift is essentially
+     * a multiplication in non-log scale to both numerator and denominator,
+     * so it cancels out. We do this to avoid calling exp(-large_num) and
+     * ending up with norm == 0 and hence a 0/0 error.
+     *
+     * Can also generate the base-call here too.
+     */
+    shift = -DBL_MAX;
+    max = -DBL_MAX;
+    max_het = -DBL_MAX;
+
+    for (j = 0; j < 15; j++) {
+        S[j] += lprior15[j];
+        if (shift < S[j])
+            shift = S[j];
+
+        /* Only call pure AA, CC, GG, TT, ** for now */
+        if (j != 0 && j != 5 && j != 9 && j != 12 && j != 14) {
+            if (max_het < S[j]) {
+                max_het = S[j];
+                het_call = j;
+            }
+            continue;
+        }
+
+        if (max < S[j]) {
+            max = S[j];
+            call = j;
+        }
+    }
+
+    /*
+     * Shift and normalise.
+     * If call is, say, b we want p = b/(a+b+c+...+n), but then we do
+     * p/(1-p) later on and this has exceptions when p is very close
+     * to 1.
+     *
+     * Hence we compute b/(a+b+c+...+n - b) and
+     * rearrange (p/norm) / (1 - (p/norm)) to be p/norm2.
+     */
+    for (j = 0; j < 15; j++) {
+        S[j] -= shift;
+        double e = fast_exp(S[j]);
+        S[j] = (S[j] > min_e_exp) ? e : DBL_MIN;
+        norm[j] = 0;
+    }
+
+    for (j = 0; j < 15; j++) {
+        norm[j]    += tot1;
+        norm[14-j] += tot2;
+        tot1 += S[j];
+        tot2 += S[14-j];
+    }
+
+    /* And store result */
+    if (!depth || depth == counts[5] /* all N */) {
+        cons->call = 4; /* N */
+        cons->het_call = 0;
+        cons->het_logodd = 0;
+        cons->phred = 0;
+        cons->depth = 0;
+        cons->discrep = 0;
+        return 0;
+    }
+
+    cons->depth = depth;
+
+    /* Call */
+    if (norm[call] == 0) norm[call] = DBL_MIN;
+    // Approximation of phred for when S[call] ~= 1 and norm[call]
+    // is small.  Otherwise we need the full calculation.
+    int ph;
+    if (S[call] == 1 && norm[call] < .01)
+        ph = ph_log(norm[call]) + .5;
+    else
+        ph = ph_log(1-S[call]/(norm[call]+S[call])) + .5;
+
+    cons->call     = map_sing[call];
+    cons->phred = ph < 0 ? 0 : ph;
+
+    if (norm[het_call] == 0) norm[het_call] = DBL_MIN;
+    ph = TENLOG2OVERLOG10 * (fast_log2(S[het_call])
+                             - fast_log2(norm[het_call])) + .5;
+
+    cons->het_call = map_het[het_call];
+    cons->het_logodd = ph;
+
+    /* Compute discrepancy score */
+    if (flags & CONS_DISCREP) {
+        double m = sumsC[0]+sumsC[1]+sumsC[2]+sumsC[3]+sumsC[4];
+        double c;
+        if (cons->het_logodd > 0)
+            c = sumsC[cons->het_call%5] + sumsC[cons->het_call/5];
+        else
+            c = sumsC[cons->call];
+        cons->discrep = (m-c)/sqrt(m);
+    }
+
+    return 0;
+}
+
+
+/* --------------------------------------------------------------------------
+ * Main processing logic
+ */
+
+static void dump_fastq(consensus_opts *opts,
+                       const char *name,
+                       const char *seq, size_t seq_l,
+                       const char *qual, size_t qual_l) {
+    enum format fmt = opts->fmt;
+    int line_len = opts->line_len;
+    FILE *fp = opts->fp_out;
+
+    fprintf(fp, "%c%s\n", ">@"[fmt==FASTQ], name);
+    size_t i;
+    for (i = 0; i < seq_l; i += line_len)
+        fprintf(fp, "%.*s\n", (int)MIN(line_len, seq_l - i), seq+i);
+
+    if (fmt == FASTQ) {
+        fprintf(fp, "+\n");
+        for (i = 0; i < seq_l; i += line_len)
+            fprintf(fp, "%.*s\n", (int)MIN(line_len, seq_l - i), qual+i);
+    }
+}
+
+//---------------------------------------------------------------------------
+
+/*
+ * Reads a single alignment record, using either the iterator
+ * or a direct sam_read1 call.
+ */
+static int readaln2(void *dat, samFile *fp, sam_hdr_t *h, bam1_t *b) {
+    consensus_opts *opts = (consensus_opts *)dat;
+
+    for (;;) {
+        int ret = opts->iter
+            ? sam_itr_next(fp, opts->iter, b)
+            : sam_read1(fp, h, b);
+        if (ret < 0)
+            return ret;
+
+        // Apply hard filters
+        if (opts->incl_flags && !(b->core.flag & opts->incl_flags))
+            continue;
+        if (opts->excl_flags &&  (b->core.flag & opts->excl_flags))
+            continue;
+        if (b->core.qual < opts->min_mqual)
+            continue;
+
+        return ret;
+    }
+}
+
+/* --------------------------------------------------------------------------
+ * A simple summing algorithm, either pure base frequency, or by
+ * weighting them according to their quality values.
+ *
+ * This is crude, but easy to understand and fits with several
+ * standard pileup criteria (eg COG-UK / CLIMB Covid-19 seq project).
+ *
+ *
+ * call1 / score1 / depth1 is the highest scoring allele.
+ * call2 / score2 / depth2 is the second highest scoring allele.
+ *
+ * Het_fract:  score2/score1
+ * Call_fract: score1 or score1+score2 over total score
+ * Min_depth:  minimum total depth of utilised bases (depth1+depth2)
+ * Min_score:  minimum total score of utilised bases (score1+score2)
+ *
+ * Eg het_fract 0.66, call_fract 0.75 and min_depth 10.
+ * 11A, 2C, 2G (14 total depth) is A.
+ * 9A, 2C, 2G  (12 total depth) is N as depth(A) < 10.
+ * 11A, 5C, 5G (21 total depth) is N as 11/21 < 0.75 (call_fract)
+ *
+ *
+ * 6A, 5G, 1C  (12 total depth) is AG het as depth(A)+depth(G) >= 10
+ *                              and 5/6 >= 0.66 and 11/12 >= 0.75.
+ *
+ * 6A, 5G, 4C  (15 total depth) is N as (6+5)/15 < 0.75 (call_fract).
+ *
+ *
+ * Note for the purpose of deletions, a base/del has an ambiguity
+ * code of lower-case base (otherwise it is uppercase).
+ */
+static int calculate_consensus_simple(const pileup_t *plp,
+                                      consensus_opts *opts, int *qual) {
+    int i, min_qual = opts->min_qual;
+
+    // Map "seqi" nt16 to A,C,G,T compatibility with weights on pure bases.
+    // where seqi is A | (C<<1) | (G<<2) | (T<<3)
+    //                        * A C M  G R S V  T W Y H  K D B N
+    static int seqi2A[16] = { 0,8,0,4, 0,4,0,2, 0,4,0,2, 0,2,0,1 };
+    static int seqi2C[16] = { 0,0,8,4, 0,0,4,2, 0,0,4,2, 0,0,2,1 };
+    static int seqi2G[16] = { 0,0,0,0, 8,4,4,1, 0,0,0,0, 4,2,2,1 };
+    static int seqi2T[16] = { 0,0,0,0, 0,0,0,0, 8,4,4,2, 8,2,2,1 };
+
+    // Ignore ambiguous bases in seq for now, so we don't treat R, Y, etc
+    // as part of one base and part another.  Based on BAM seqi values.
+    // We also use freq[16] as "*" for gap.
+    int freq[17] = {0};  // base frequency, aka depth
+    int score[17] = {0}; // summation of base qualities
+
+    // Accumulate
+    for (; plp; plp = plp->next) {
+        const pileup_t *p = plp;
+        if (p->next)
+            _mm_prefetch(p->next, _MM_HINT_T0);
+
+        int q = p->qual;
+        if (q < min_qual)
+            // Should we still record these in freq[] somewhere so
+            // we can use them in the fracts?
+            // Difference between >= X% of high-qual bases calling Y
+            // and >= X% of all bases are high-quality Y calls.
+            continue;
+
+        //int b = p->is_del ? 16 : bam_seqi(bam_get_seq(&p->b), p->seq_offset);
+        int b = p->base4;
+
+        // Map ambiguity codes to one or more component bases.
+        if (b < 16) {
+            int Q = seqi2A[b] * (opts->use_qual ? q : 1);
+            freq[1]  += Q?1:0;
+            score[1] += Q?Q:0;
+            Q = seqi2C[b] * (opts->use_qual ? q : 1);
+            freq[2]  += Q?1:0;
+            score[2] += Q?Q:0;
+            Q = seqi2G[b] * (opts->use_qual ? q : 1);
+            freq[4]  += Q?1:0;
+            score[4] += Q?Q:0;
+            Q = seqi2T[b] * (opts->use_qual ? q : 1);
+            freq[8]  += Q?1:0;
+            score[8] += Q?Q:0;
+        } else { /* * */
+            freq[16] ++;
+            score[16]+=8 * (opts->use_qual ? q : 1);
+        }
+    }
+
+    // Total usable depth
+    int tscore = 0;
+    for (i = 0; i < 5; i++)
+        tscore += score[1<<i];
+
+    // Best and second best potential calls
+    int call1  = 15, call2 = 15;
+    int depth1 = 0,  depth2 = 0;
+    int score1 = 0,  score2 = 0;
+    for (i = 0; i < 5; i++) {
+        int c = 1<<i; // A C G T *
+        if (score1 < score[c]) {
+            depth2 = depth1;
+            score2 = score1;
+            call2  = call1;
+            depth1 = freq[c];
+            score1 = score[c];
+            call1  = c;
+        } else if (score2 < score[c]) {
+            depth2 = freq[c];
+            score2 = score[c];
+            call2  = c;
+        }
+    }
+
+    // Work out which best and second best are usable as a call
+    int used_score = score1;
+    int used_depth = depth1;
+    int used_base  = call1;
+    if (score2 >= opts->het_fract * score1 && opts->ambig) {
+        used_base  |= call2;
+        used_score += score2;
+        used_depth += depth2;
+    }
+
+    // N is too shallow, or insufficient proportion of total
+    if (used_depth < opts->min_depth ||
+        used_score < opts->call_fract * tscore) {
+        used_depth = 0;
+        // But note shallow gaps are still called gaps, not N, as
+        // we're still more confident there is no base than it is
+        // A, C, G or T.
+        used_base = call1 == 16 /*&& depth1 >= call_fract * depth*/
+            ? 16 : 0; // * or N
+    }
+
+    // Our final call.  "?" shouldn't be possible to generate
+    const char *het =
+        "NACMGRSVTWYHKDBN"
+        "*ac?g???t???????";
+
+    //printf("%c %d\n", het[used_base], used_depth);
+    if (qual)
+        *qual = used_base ? 100.0 * used_score / tscore : 0;
+
+    return het[used_base];
+}
+
+static int empty_pileup2(consensus_opts *opts, sam_hdr_t *h, int tid,
+                         hts_pos_t start, hts_pos_t end) {
+    const char *name = sam_hdr_tid2name(h, tid);
+    hts_pos_t i;
+
+    int err = 0;
+    for (i = start; i < end; i++)
+        err |= fprintf(opts->fp_out, "%s\t%"PRIhts_pos"\t0\t0\tN\t0\t*\t*\n", name, i+1) < 0;
+
+    return err ? -1 : 0;
+}
+
+/*
+ * Returns 0 on success
+ *        -1 on failure
+ */
+static int basic_pileup(void *cd, samFile *fp, sam_hdr_t *h, pileup_t *p,
+                        int depth, hts_pos_t pos, int nth, int is_insert) {
+    unsigned char *qp, *cp;
+    char *rp;
+    int ref, cb, cq;
+    consensus_opts *opts = (consensus_opts *)cd;
+    int tid = p->b.core.tid;
+
+//    opts->show_ins=0;
+//    opts->show_del=1;
+    if (!opts->show_ins && nth)
+        return 0;
+
+    if (opts->iter) {
+        if (opts->iter->beg >= pos || opts->iter->end < pos)
+            return 0;
+    }
+
+    if (opts->all_bases) {
+        if (tid != opts->last_tid && opts->last_tid >= 0) {
+            hts_pos_t len = sam_hdr_tid2len(opts->h, opts->last_tid);
+            if (opts->iter)
+                len =  MIN(opts->iter->end, len);
+            if (empty_pileup2(opts, opts->h, opts->last_tid, opts->last_pos,
+                              len) < 0)
+                return -1;
+            if (tid >= 0) {
+                if (empty_pileup2(opts, opts->h, tid,
+                                  opts->iter ? opts->iter->beg : 0,
+                                  pos-1) < 0)
+                    return -1;
+            }
+        }
+        if (opts->last_pos >= 0 && pos > opts->last_pos+1) {
+            if (empty_pileup2(opts, opts->h, p->b.core.tid, opts->last_pos,
+                              pos-1) < 0)
+                return -1;
+        } else if (opts->last_pos < 0) {
+            if (empty_pileup2(opts, opts->h, p->b.core.tid,
+                              opts->iter ? opts->iter->beg : 0, pos-1) < 0)
+                return -1;
+        }
+    }
+
+    if (opts->gap5) {
+        consensus_t cons;
+        calculate_consensus_gap5(pos, opts->use_mqual ? CONS_MQUAL : 0,
+                                 depth, p, opts, &cons, opts->default_qual);
+        if (cons.het_logodd > 0 && opts->ambig) {
+            cb = "AMRWa" // 5x5 matrix with ACGT* per row / col
+                 "MCSYc"
+                 "RSGKg"
+                 "WYKTt"
+                 "acgt*"[cons.het_call];
+            cq = cons.het_logodd;
+        } else{
+            cb = "ACGT*"[cons.call];
+            cq = cons.phred;
+        }
+        if (cq < opts->cons_cutoff && cb != '*') {
+            cb = 'N';
+            cq = 0;
+        }
+    } else {
+        cb = calculate_consensus_simple(p, opts, &cq);
+    }
+    if (cb < 0)
+        return -1;
+
+    if (!p)
+        return 0;
+
+    if (!opts->show_del && cb == '*')
+        return 0;
+
+    /* Ref, pos, nth, score, seq, qual */
+    kstring_t *ks = &opts->ks_line;
+    ks->l = 0;
+    ref = p->b.core.tid;
+    rp = (char *)sam_hdr_tid2name(h, ref);
+
+    int err = 0;
+    err |= kputs(rp, ks)    < 0;
+    err |= kputc_('\t', ks) < 0;
+    err |= kputw(pos, ks)   < 0;
+    err |= kputc_('\t', ks) < 0;
+    err |= kputw(nth, ks)   < 0;
+    err |= kputc_('\t', ks) < 0;
+    err |= kputw(depth, ks) < 0;
+    err |= kputc_('\t', ks) < 0;
+    err |= kputc_(cb, ks)   < 0;
+    err |= kputc_('\t', ks) < 0;
+    err |= kputw(cq, ks)    < 0;
+    err |= kputc_('\t', ks) < 0;
+    if (err)
+        return -1;
+
+    /* Seq + qual at predetermined offsets */
+    if (ks_resize(ks, ks->l + depth*2 + 2) < 0)
+        return -1;
+
+    cp = (unsigned char *)ks->s + ks->l;
+    ks->l += depth*2 + 2;
+    qp = cp+depth+1;
+    for (; p; p = p->next) {
+        // Too tight a loop to help much, but some benefit still
+        if (p->next && p->next->next)
+            _mm_prefetch(p->next->next, _MM_HINT_T0);
+        if (p->b_is_rev) {
+            *cp++ = p->base == '*' ? '#' : tolower(p->base);
+        } else {
+            *cp++ = p->base;
+        }
+        *qp++ = MIN(p->qual,93) + '!';
+    }
+    *cp++ = '\t';
+    *qp++ = '\n';
+    if (fwrite(ks->s, 1, ks->l, opts->fp_out) != ks->l)
+        return -1;
+
+    opts->last_pos = pos;
+    opts->last_tid = tid;
+
+    return 0;
+}
+
+static int basic_fasta(void *cd, samFile *fp, sam_hdr_t *h, pileup_t *p,
+                       int depth, hts_pos_t pos, int nth, int is_insert) {
+    int cb, cq;
+    consensus_opts *opts = (consensus_opts *)cd;
+    int tid = p->b.core.tid;
+    kstring_t *seq  = &opts->ks_ins_seq;
+    kstring_t *qual = &opts->ks_ins_qual;
+
+    if (!opts->show_ins && nth)
+        return 0;
+
+    if (opts->iter) {
+        if (opts->iter->beg >= pos || opts->iter->end < pos)
+            return 0;
+    }
+
+    if (tid != opts->last_tid) {
+        if (opts->last_tid != -1) {
+            if (opts->all_bases) {
+                int i, N;
+                if (opts->iter) {
+                    opts->last_pos = MAX(opts->last_pos, opts->iter->beg-1);
+                    N = opts->iter->end;
+                } else {
+                    N = INT_MAX;
+                }
+                N = MIN(N, sam_hdr_tid2len(opts->h, opts->last_tid))
+                    - opts->last_pos;
+                if (N > 0) {
+                    if (ks_expand(seq, N+1) < 0)
+                        return -1;
+                    if (ks_expand(qual, N+1) < 0)
+                        return -1;
+                    for (i = 0; i < N; i++) {
+                        seq->s[seq->l++] = 'N';
+                        qual->s[qual->l++] = '!';
+                    }
+                    seq->s[seq->l] = 0;
+                    qual->s[qual->l] = 0;
+                }
+            }
+            dump_fastq(opts, sam_hdr_tid2name(opts->h, opts->last_tid),
+                       seq->s, seq->l, qual->s, qual->l);
+        }
+
+        seq->l = 0; qual->l = 0;
+        opts->last_tid = tid;
+//        if (opts->all_bases)
+//            opts->last_pos = 0;
+        if (opts->iter)
+            opts->last_pos = opts->iter->beg;
+        else
+            opts->last_pos = opts->all_bases ? 0 : pos-1;
+    }
+
+    // share this with basic_pileup
+    if (opts->gap5) {
+        consensus_t cons;
+        calculate_consensus_gap5(pos, opts->use_mqual ? CONS_MQUAL : 0,
+                                 depth, p, opts, &cons, opts->default_qual);
+        if (cons.het_logodd > 0 && opts->ambig) {
+            cb = "AMRWa" // 5x5 matrix with ACGT* per row / col
+                 "MCSYc"
+                 "RSGKg"
+                 "WYKTt"
+                 "acgt*"[cons.het_call];
+            cq = cons.het_logodd;
+        } else{
+            cb = "ACGT*"[cons.call];
+            cq = cons.phred;
+        }
+        if (cq < opts->cons_cutoff && cb != '*' &&
+            cons.het_call % 5 != 4 && cons.het_call / 5 != 4) {
+            // het base/* keeps base or * as most likely pure call, else N.
+            // This is because we don't have a traditional way of representing
+            // base or not-base ambiguity.
+            cb = 'N';
+            cq = 0;
+        }
+    } else {
+        cb = calculate_consensus_simple(p, opts, &cq);
+    }
+    if (cb < 0)
+        return -1;
+
+    if (!p)
+        return 0;
+
+    if (!opts->show_del && cb == '*') {
+        opts->last_pos = pos;
+        opts->last_tid = tid;
+        return 0;
+    }
+    // end of share
+
+    // Append consensus base/qual to seqs
+    if (pos > opts->last_pos) {
+        if (opts->last_pos >= 0 || opts->all_bases) {
+            // FIXME: don't expand qual if fasta
+            if (ks_expand(seq,  pos - opts->last_pos) < 0 ||
+                ks_expand(qual, pos - opts->last_pos) < 0)
+                return -1;
+            memset(seq->s  + seq->l,  'N', pos - (opts->last_pos+1));
+            memset(qual->s + qual->l, '!', pos - (opts->last_pos+1));
+            seq->l  += pos - (opts->last_pos+1);
+            qual->l += pos - (opts->last_pos+1);
+        }
+    }
+    if ((nth && opts->show_ins && cb != '*')
+        || cb != '*' || (pos > opts->last_pos && opts->show_del)) {
+        int err = 0;
+        err |= kputc(cb, seq) < 0;
+        err |= kputc(MIN(cq, '~'-'!')+'!', qual) < 0;
+        if (err)
+            return -1;
+    }
+
+    opts->last_pos = pos;
+    opts->last_tid = tid;
+
+    return 0;
+}
+// END OF NEW PILEUP
+//---------------------------------------------------------------------------
+
+static void usage_exit(FILE *fp, int exit_status) {
+    fprintf(fp, "Usage: samtools consensus [options] <in.bam>\n");
+    fprintf(fp, "\nOptions:\n");
+    fprintf(fp, "  -r, --region REG      Limit query to REG. Requires an index\n");
+    fprintf(fp, "  -f, --format FMT      Output in format FASTA, FASTQ or PILEUP [FASTA]\n");
+    fprintf(fp, "  -l, --line-len INT    Wrap FASTA/Q at line length INT [70]\n");
+    fprintf(fp, "  -o, --output FILE     Output consensus to FILE\n");
+    fprintf(fp, "  -m, --mode STR        Switch consensus mode to \"simple\"/\"bayesian\" [bayesian]\n");
+    fprintf(fp, "  -a                    Output all bases (start/end of reference)\n");
+    fprintf(fp, "  --rf, --incl-flags STR|INT\n");
+    fprintf(fp, "                        Only include reads with any flag bit set [0]\n");
+    fprintf(fp, "  --ff, --excl-flags STR|INT\n");
+    fprintf(fp, "                        Exclude reads with any flag bit set\n");
+    fprintf(fp, "                        [UNMAP,SECONDARY,QCFAIL,DUP]\n");
+    fprintf(fp, "  --min-MQ INT          Exclude reads with mapping quality below INT [0]\n");
+    fprintf(fp, "  --show-del yes/no     Whether to show deletion as \"*\" [no]\n");
+    fprintf(fp, "  --show-ins yes/no     Whether to show insertions [yes]\n");
+    fprintf(fp, "  -A, --ambig           Enable IUPAC ambiguity codes [off]\n");
+    fprintf(fp, "\nFor simple consensus mode:\n");
+    fprintf(fp, "  -q, --(no-)use-qual   Use quality values in calculation [off]\n");
+    fprintf(fp, "  -c, --call-fract INT  At least INT portion of bases must agree [0.75]\n");
+    fprintf(fp, "  -d, --min-depth INT   Minimum depth of INT [1]\n");
+    fprintf(fp, "  -H, --het-fract INT   Minimum fraction of 2nd-most to most common base [0.5]\n");
+    fprintf(fp, "\nFor default \"Bayesian\" consensus mode:\n");
+    fprintf(fp, "  -C, --cutoff C        Consensus cutoff quality C [10]\n");
+    fprintf(fp, "      --(no-)adj-qual   Modify quality with local minima [on]\n");
+    fprintf(fp, "      --(no-)use-MQ     Use mapping quality in calculation [on]\n");
+    fprintf(fp, "      --(no-)adj-MQ     Modify mapping quality by local NM [on]\n");
+    fprintf(fp, "      --NM-halo INT     Size of window for NM count in --adj-MQ [50]\n");
+    fprintf(fp, "      --scale-MQ FLOAT  Scale mapping quality by FLOAT [1.00]\n");
+    fprintf(fp, "      --low-MQ  INT     Cap minimum mapping quality [1]\n");
+    fprintf(fp, "      --high-MQ INT     Cap maximum mapping quality [60]\n");
+    fprintf(fp, "      --P-het FLOAT     Probability of heterozygous site[%.1e]\n",
+            P_HET);
+
+    fprintf(fp, "\nGlobal options:\n");
+    sam_global_opt_help(fp, "-.---@-.");
+    samtools_exit(exit_status);
+}
+
+int main_consensus(int argc, char **argv) {
+    int c, ret = 1;
+
+    consensus_opts opts = {
+        // User options
+        .gap5         = 1,
+        .use_qual     = 0,
+        .min_qual     = 0,
+        .adj_qual     = 1,
+        .use_mqual    = 1,
+        .scale_mqual  = 1.00,
+        .nm_adjust    = 1,
+        .nm_halo      = 50,
+        .sc_cost      = 60,
+        .low_mqual    = 1,
+        .high_mqual   = 60,
+        .min_depth    = 1,
+        .call_fract   = 0.75,
+        .het_fract    = 0.5,
+        .het_only     = 0,
+        .fmt          = FASTA,
+        .cons_cutoff  = 10,
+        .ambig        = 0,
+        .line_len     = 70,
+        .default_qual = 10,
+        .all_bases    = 0,
+        .show_del     = 0,
+        .show_ins     = 1,
+        .incl_flags   = 0,
+        .excl_flags   = BAM_FUNMAP | BAM_FSECONDARY | BAM_FQCFAIL | BAM_FDUP,
+        .min_mqual    = 0,
+        .P_het        = P_HET,
+
+        // Internal state
+        .ks_line      = {0,0},
+        .ks_ins_seq   = {0,0},
+        .ks_ins_qual  = {0,0},
+        .fp           = NULL,
+        .fp_out       = samtools_stdout,
+        .iter         = NULL,
+        .idx          = NULL,
+        .last_tid     = -1,
+        .last_pos     = -1,
+    };
+
+    sam_global_args ga = SAM_GLOBAL_ARGS_INIT;
+    static const struct option lopts[] = {
+        SAM_OPT_GLOBAL_OPTIONS('-', 0, 'O', '-', '-', '@'),
+        {"use-qual",           no_argument,       NULL, 'q'},
+        {"no-use-qual",        no_argument,       NULL, 'q'+1000},
+        {"adj-qual",           no_argument,       NULL, 'q'+100},
+        {"no-adj-qual",        no_argument,       NULL, 'q'+101},
+        {"use-MQ",             no_argument,       NULL, 'm'+1000},
+        {"no-use-MQ",          no_argument,       NULL, 'm'+1001},
+        {"adj-MQ",             no_argument,       NULL, 'm'+100},
+        {"no-adj-MQ",          no_argument,       NULL, 'm'+101},
+        {"NM-halo",            required_argument, NULL, 'h'+100},
+        {"SC-cost",            required_argument, NULL, 'h'+101},
+        {"scale-MQ",           required_argument, NULL, 14},
+        {"low-MQ"   ,          required_argument, NULL,  9},
+        {"high-MQ",            required_argument, NULL, 10},
+        {"min-depth",          required_argument, NULL, 'd'},
+        {"call-fract",         required_argument, NULL, 'c'},
+        {"het-fract",          required_argument, NULL, 'H'},
+        {"region",             required_argument, NULL, 'r'},
+        {"format",             required_argument, NULL, 'f'},
+        {"cutoff",             required_argument, NULL, 'C'},
+        {"ambig",              no_argument,       NULL, 'A'},
+        {"line-len",           required_argument, NULL, 'l'},
+        {"default-qual",       required_argument, NULL, 1},
+        {"het-only",           no_argument,       NULL, 6},
+        {"show-del",           required_argument, NULL, 7},
+        {"show-ins",           required_argument, NULL, 8},
+        {"output",             required_argument, NULL, 'o'},
+        {"incl-flags",         required_argument, NULL, 11},
+        {"rf",                 required_argument, NULL, 11},
+        {"excl-flags",         required_argument, NULL, 12},
+        {"ff",                 required_argument, NULL, 12},
+        {"min-MQ",             required_argument, NULL, 13},
+        {"P-het",              required_argument, NULL, 15},
+        {"mode",               required_argument, NULL, 'm'},
+        {NULL, 0, NULL, 0}
+    };
+
+    while ((c = getopt_long(argc, argv, "@:qd:c:H:r:5f:C:aAl:o:m:",
+                            lopts, NULL)) >= 0) {
+        switch (c) {
+        case 'a': opts.all_bases++; break;
+        case 'q': opts.use_qual=1; break;
+        case 'q'+1000: opts.use_qual=0; break;
+        case 'm'+1000: opts.use_mqual=1; break;
+        case 'm'+1001: opts.use_mqual=0; break;
+        case 14:  opts.scale_mqual = atof(optarg); break;
+        case  9:  opts.low_mqual = atoi(optarg); break;
+        case 10:  opts.high_mqual = atoi(optarg); break;
+        case 'd': opts.min_depth = atoi(optarg); break;
+        case 'c': opts.call_fract = atof(optarg); break;
+        case 'H': opts.het_fract = atof(optarg); break;
+        case 'r': opts.reg = optarg; break;
+        case 'C': opts.cons_cutoff = atoi(optarg); break;
+        case 'A': opts.ambig = 1; break;
+        case 1:   opts.default_qual = atoi(optarg); break;
+        case 6:   opts.het_only = 1; break;
+        case 7:   opts.show_del = (*optarg == 'y' || *optarg == 'Y'); break;
+        case 8:   opts.show_ins = (*optarg == 'y' || *optarg == 'Y'); break;
+        case 13:  opts.min_mqual = atoi(optarg); break;
+        case 15:  opts.P_het = atof(optarg); break;
+        case 'q'+100: opts.adj_qual = 1; break;
+        case 'q'+101: opts.adj_qual = 0; break;
+        case 'm'+100: opts.nm_adjust = 1; break;
+        case 'm'+101: opts.nm_adjust = 0; break;
+        case 'h'+100: opts.nm_halo = atoi(optarg); break;
+        case 'h'+101: opts.sc_cost = atoi(optarg); break;
+
+        case 'm': // mode
+            if (strcasecmp(optarg, "simple") == 0) {
+                opts.gap5 = 0;
+            } else if (strcasecmp(optarg, "bayesian") == 0) {
+                opts.gap5 = 1;
+            } else {
+                fprintf(samtools_stderr, "Unknown mode %s\n", optarg);
+                return 1;
+            }
+            break;
+
+        case 'l':
+            if ((opts.line_len = atoi(optarg)) <= 0)
+                opts.line_len = INT_MAX;
+            break;
+
+        case 'f':
+            if (strcasecmp(optarg, "fasta") == 0) {
+                opts.fmt = FASTA;
+            } else if (strcasecmp(optarg, "fastq") == 0) {
+                opts.fmt = FASTQ;
+            } else if (strcasecmp(optarg, "pileup") == 0) {
+                opts.fmt = PILEUP;
+            } else {
+                fprintf(samtools_stderr, "Unknown format %s\n", optarg);
+                return 1;
+            }
+            break;
+
+        case 'o':
+            if (!(opts.fp_out = fopen(optarg, "w"))) {
+                perror(optarg);
+                return 1;
+            }
+            break;
+
+        case 11:
+            if ((opts.incl_flags = bam_str2flag(optarg)) < 0) {
+                print_error("consensus", "could not parse --rf %s", optarg);
+                return 1;
+            }
+            break;
+        case 12:
+            if ((opts.excl_flags = bam_str2flag(optarg)) < 0) {
+                print_error("consensus", "could not parse --ff %s", optarg);
+                return 1;
+            }
+            break;
+
+         default:  if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break;
+            /* else fall-through */
+        case '?':
+            usage_exit(samtools_stderr, EXIT_FAILURE);
+        }
+    }
+
+    if (argc != optind+1) {
+        if (argc == optind) usage_exit(samtools_stdout, EXIT_SUCCESS);
+        else usage_exit(samtools_stderr, EXIT_FAILURE);
+    }
+    opts.fp = sam_open_format(argv[optind], "r", &ga.in);
+    if (opts.fp == NULL) {
+        print_error_errno("consensus", "Cannot open input file \"%s\"",
+                          argv[optind]);
+        goto err;
+    }
+    if (ga.nthreads > 0)
+        hts_set_threads(opts.fp, ga.nthreads);
+
+    if (hts_set_opt(opts.fp, CRAM_OPT_DECODE_MD, 0)) {
+        fprintf(samtools_stderr, "Failed to set CRAM_OPT_DECODE_MD value\n");
+        goto err;
+    }
+
+    if (!(opts.h = sam_hdr_read(opts.fp))) {
+        fprintf(samtools_stderr, "Failed to read header for \"%s\"\n", argv[optind]);
+        goto err;
+    }
+
+    if (opts.reg) {
+        opts.idx = sam_index_load(opts.fp, argv[optind]);
+        if (!opts.idx) {
+            print_error("consensus", "Cannot load index for input file \"%s\"",
+                        argv[optind]);
+            goto err;
+        }
+        opts.iter = sam_itr_querys(opts.idx, opts.h, opts.reg);
+        if (!opts.iter) {
+            print_error("consensus", "Failed to parse region \"%s\"",
+                        opts.reg);
+            goto err;
+        }
+    }
+
+    if (opts.fmt == PILEUP) {
+        if (pileup_loop(opts.fp, opts.h, readaln2, opts.gap5 ? nm_init : NULL,
+                        basic_pileup, &opts) < 0)
+            goto err;
+
+        if (opts.all_bases) {
+            int tid = opts.iter ? opts.iter->tid : opts.last_tid;
+            int len = sam_hdr_tid2len(opts.h, tid);
+            int pos = opts.last_pos;
+            if (opts.iter) {
+                len = MIN(opts.iter->end, len);
+                pos = MAX(opts.iter->beg, pos);
+            }
+            if (empty_pileup2(&opts, opts.h, tid, pos, len) < 0)
+                goto err;
+        }
+    } else {
+        if (pileup_loop(opts.fp, opts.h, readaln2, opts.gap5 ? nm_init : NULL,
+                        basic_fasta,
+                        &opts) < 0)
+            goto err;
+        if (opts.all_bases) {
+            // fill out terminator
+            int tid = opts.iter ? opts.iter->tid : opts.last_tid;
+            int len = sam_hdr_tid2len(opts.h, tid);
+            int pos = opts.last_pos;
+            if (opts.iter) {
+                len = MIN(opts.iter->end, len);
+                pos = MAX(opts.iter->beg, pos);
+                opts.last_tid = opts.iter->tid;
+            }
+            if (pos < len) {
+                if (ks_expand(&opts.ks_ins_seq,  len-pos+1) < 0)
+                    goto err;
+                if (ks_expand(&opts.ks_ins_qual, len-pos+1) < 0)
+                    goto err;
+                while (pos++ < len) {
+                    opts.ks_ins_seq.s [opts.ks_ins_seq.l++] = 'N';
+                    opts.ks_ins_qual.s[opts.ks_ins_qual.l++] = '!';
+                }
+                opts.ks_ins_seq.s [opts.ks_ins_seq.l] = 0;
+                opts.ks_ins_qual.s[opts.ks_ins_qual.l] = 0;
+            }
+        }
+        if (opts.last_tid >= 0)
+            dump_fastq(&opts, sam_hdr_tid2name(opts.h, opts.last_tid),
+                       opts.ks_ins_seq.s,  opts.ks_ins_seq.l,
+                       opts.ks_ins_qual.s, opts.ks_ins_qual.l);
+//        if (consensus_loop(&opts) < 0) {
+//            print_error_errno("consensus", "Failed");
+//            goto err;
+//        }
+    }
+
+    ret = 0;
+
+ err:
+    if (opts.iter)
+        hts_itr_destroy(opts.iter);
+    if (opts.idx)
+        hts_idx_destroy(opts.idx);
+
+    if (opts.fp && sam_close(opts.fp) < 0) {
+        print_error_errno("consensus", "Closing input file \"%s\"",
+                          argv[optind]);
+        ret = 1;
+    }
+
+    if (opts.h)
+        sam_hdr_destroy(opts.h);
+    sam_global_args_free(&ga);
+
+    if (opts.fp_out && opts.fp_out != samtools_stdout)
+        ret |= fclose(opts.fp_out) != 0;
+    else
+        ret |= fflush(samtools_stdout) != 0;
+
+    ks_free(&opts.ks_line);
+    ks_free(&opts.ks_ins_seq);
+    ks_free(&opts.ks_ins_qual);
+
+    if (ret)
+        print_error("consensus", "failed");
+
+    return ret;
+}
diff --git a/samtools/bam_fastq.c b/samtools/bam_fastq.c
new file mode 100644
index 0000000..c17821d
--- /dev/null
+++ b/samtools/bam_fastq.c
@@ -0,0 +1,885 @@
+/*  bam_fastq.c -- FASTA and FASTQ file generation
+
+    Copyright (C) 2009-2017, 2019-2020 Genome Research Ltd.
+    Portions copyright (C) 2009, 2011, 2012 Broad Institute.
+
+    Author: Heng Li <lh3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notices and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <config.h>
+
+#include <stdlib.h>
+#include <string.h>
+#include <strings.h>
+#include <stdbool.h>
+#include <ctype.h>
+#include <assert.h>
+#include <inttypes.h>
+#include <unistd.h>
+
+#include "htslib/sam.h"
+#include "htslib/klist.h"
+#include "htslib/kstring.h"
+#include "htslib/bgzf.h"
+#include "htslib/thread_pool.h"
+#include "samtools.h"
+#include "sam_opts.h"
+
+#define DEFAULT_BARCODE_TAG "BC"
+#define DEFAULT_QUALITY_TAG "QT"
+#define INDEX_SEPARATOR "+"
+
+int8_t seq_comp_table[16] = { 0, 8, 4, 12, 2, 10, 6, 14, 1, 9, 5, 13, 3, 11, 7, 15 };
+static void bam2fq_usage(FILE *to, const char *command)
+{
+    int fq = strcasecmp("fastq", command) == 0 || strcasecmp("bam2fq", command) == 0;
+    fprintf(to,
+"Usage: samtools %s [options...] <in.bam>\n", command);
+    fprintf(to,
+"\n"
+"Description:\n"
+"Converts a SAM, BAM or CRAM to %s format.\n"
+"\n"
+"Options:\n"
+"  -0 FILE      write reads designated READ_OTHER to FILE\n"
+"  -1 FILE      write reads designated READ1 to FILE\n"
+"  -2 FILE      write reads designated READ2 to FILE\n"
+"  -o FILE      write reads designated READ1 or READ2 to FILE\n"
+"               note: if a singleton file is specified with -s, only\n"
+"               paired reads will be written to the -1 and -2 files.\n"
+"  -f INT       only include reads with all  of the FLAGs in INT present [0]\n"       //   F&x == x
+"  -F INT       only include reads with none of the FLAGS in INT present [0x900]\n"       //   F&x == 0
+"  -G INT       only EXCLUDE reads with all  of the FLAGs in INT present [0]\n"       // !(F&x == x)
+"  -n           don't append /1 and /2 to the read name\n"
+"  -N           always append /1 and /2 to the read name\n",
+    fq ? "FASTQ" : "FASTA");
+    if (fq) fprintf(to,
+"  -O           output quality in the OQ tag if present\n");
+    fprintf(to,
+"  -s FILE      write singleton reads designated READ1 or READ2 to FILE\n"
+"  -t           copy RG, BC and QT tags to the %s header line\n",
+    fq ? "FASTQ" : "FASTA");
+    fprintf(to,
+"  -T TAGLIST   copy arbitrary tags to the %s header line, '*' for all\n",
+    fq ? "FASTQ" : "FASTA");
+    if (fq) fprintf(to,
+"  -v INT       default quality score if not given in file [1]\n"
+"  -i           add Illumina Casava 1.8 format entry to header (eg 1:N:0:ATCACG)\n"
+"  -c INT       compression level [0..9] to use when writing bgzf files [1]\n"
+"  --i1 FILE    write first index reads to FILE\n"
+"  --i2 FILE    write second index reads to FILE\n"
+"  --barcode-tag TAG\n"
+"               Barcode tag [" DEFAULT_BARCODE_TAG "]\n"
+"  --quality-tag TAG\n"
+"               Quality tag [" DEFAULT_QUALITY_TAG "]\n"
+"  --index-format STR\n"
+"               How to parse barcode and quality tags\n\n");
+    sam_global_opt_help(to, "-.--.@-.");
+    fprintf(to,
+"\n"
+"The files will be automatically compressed if the file names have a .gz\n"
+"or .bgzf extension.  The input to this program must be collated by name.\n"
+"Run 'samtools collate' or 'samtools sort -n' to achieve this.\n"
+"\n"
+"Reads are designated READ1 if FLAG READ1 is set and READ2 is not set.\n"
+"Reads are designated READ2 if FLAG READ1 is not set and READ2 is set.\n"
+"Otherwise reads are designated READ_OTHER (both flags set or both flags unset).\n"
+"Run 'samtools flags' for more information on flag codes and meanings.\n");
+    fprintf(to,
+"\n"
+"The index-format string describes how to parse the barcode and quality tags.\n"
+"It is made up of 'i' or 'n' followed by a length or '*'.  For example:\n"
+"   i14i8       The first 14 characters are index 1, the next 8 are index 2\n"
+"   n8i14       Ignore the first 8 characters, and use the next 14 for index 1\n\n"
+"If the tag contains a separator, then the numeric part can be replaced with\n"
+"'*' to mean 'read until the separator or end of tag', for example:\n"
+"   i*i*        Break the tag at the separator into index 1 and index 2\n"
+"   n*i*        Ignore the left part of the tag until the separator,\n"
+"               then use the second part of the tag as index 1\n");
+    fprintf(to,
+"\n"
+"Examples:\n"
+"To get just the paired reads in separate files, use:\n"
+"   samtools %s -1 pair1.%s -2 pair2.%s -0 /dev/null -s /dev/null -n in.bam\n"
+"\nTo get all non-supplementary/secondary reads in a single file, redirect\n"
+"the output:\n"
+"   samtools %s in.bam > all_reads.%s\n",
+            command, fq ? "fq" : "fa", fq ? "fq" : "fa",
+            command, fq ? "fq" : "fa");
+}
+
+typedef enum { READ_UNKNOWN = 0, READ_1 = 1, READ_2 = 2 } readpart;
+typedef enum { FASTA, FASTQ } fastfile;
+typedef struct bam2fq_opts {
+    char *fnse;
+    char *fnr[3];
+    char *fn_input; // pointer to input filename in argv do not free
+    bool has12, has12always, use_oq, copy_tags, illumina_tag;
+    int flag_on, flag_off, flag_alloff;
+    sam_global_args ga;
+    fastfile filetype;
+    int def_qual;
+    char *barcode_tag;
+    char *quality_tag;
+    char *index_file[2];
+    char *index_format;
+    char *extra_tags;
+    char compression_level;
+} bam2fq_opts_t;
+
+typedef struct bam2fq_state {
+    samFile *fp;
+    samFile *fpse;
+    samFile *fpr[3];
+    samFile *fpi[3];
+    samFile *hstdout;
+    sam_hdr_t *h;
+    bool has12, use_oq, copy_tags, illumina_tag;
+    int flag_on, flag_off, flag_alloff;
+    fastfile filetype;
+    int def_qual;
+    char *index_sequence;
+    char compression_level;
+    htsThreadPool p;
+} bam2fq_state_t;
+
+static readpart which_readpart(const bam1_t *b)
+{
+    if ((b->core.flag & BAM_FREAD1) && !(b->core.flag & BAM_FREAD2)) {
+        return READ_1;
+    } else if ((b->core.flag & BAM_FREAD2) && !(b->core.flag & BAM_FREAD1)) {
+        return READ_2;
+    } else {
+        return READ_UNKNOWN;
+    }
+}
+
+static void free_opts(bam2fq_opts_t *opts)
+{
+    free(opts);
+}
+
+// return true if valid
+static bool parse_opts(int argc, char *argv[], bam2fq_opts_t** opts_out)
+{
+    // Parse args
+    bam2fq_opts_t* opts = calloc(1, sizeof(bam2fq_opts_t));
+    opts->has12 = true;
+    opts->has12always = false;
+    opts->filetype = FASTQ;
+    opts->def_qual = 1;
+    opts->barcode_tag = NULL;
+    opts->quality_tag = NULL;
+    opts->index_format = NULL;
+    opts->index_file[0] = NULL;
+    opts->index_file[1] = NULL;
+    opts->extra_tags = NULL;
+    opts->compression_level = 1;
+    opts->flag_off = BAM_FSECONDARY|BAM_FSUPPLEMENTARY;
+    int flag_off_set = 0;
+
+    int c;
+    sam_global_args_init(&opts->ga);
+    static const struct option lopts[] = {
+        SAM_OPT_GLOBAL_OPTIONS('-', 0, '-', '-', 0, '@'),
+        {"i1", required_argument, NULL, 1},
+        {"I1", required_argument, NULL, 1},
+        {"i2", required_argument, NULL, 2},
+        {"I2", required_argument, NULL, 2},
+        {"if", required_argument, NULL, 3},
+        {"IF", required_argument, NULL, 3},
+        {"index-format", required_argument, NULL, 3},
+        {"barcode-tag", required_argument, NULL, 'b'},
+        {"quality-tag", required_argument, NULL, 'q'},
+        { NULL, 0, NULL, 0 }
+    };
+    while ((c = getopt_long(argc, argv, "0:1:2:o:f:F:G:niNOs:c:tT:v:@:",
+                            lopts, NULL)) > 0) {
+        switch (c) {
+            case 'b': opts->barcode_tag = optarg; break;
+            case 'q': opts->quality_tag = optarg; break;
+            case  1 : opts->index_file[0] = optarg; break;
+            case  2 : opts->index_file[1] = optarg; break;
+            case  3 : opts->index_format = optarg; break;
+            case '0': opts->fnr[0] = optarg; break;
+            case '1': opts->fnr[1] = optarg; break;
+            case '2': opts->fnr[2] = optarg; break;
+            case 'o': opts->fnr[1] = optarg; opts->fnr[2] = optarg; break;
+            case 'f': opts->flag_on |= strtol(optarg, 0, 0); break;
+            case 'F':
+                if (!flag_off_set) {
+                    flag_off_set = 1;
+                    opts->flag_off = 0;
+                }
+                opts->flag_off |= strtol(optarg, 0, 0);
+                break;
+            case 'G': opts->flag_alloff |= strtol(optarg, 0, 0); break;
+            case 'n': opts->has12 = false; break;
+            case 'N': opts->has12always = true; break;
+            case 'O': opts->use_oq = true; break;
+            case 's': opts->fnse = optarg; break;
+            case 't': opts->copy_tags = true; break;
+            case 'i': opts->illumina_tag = true; break;
+            case 'c':
+                opts->compression_level = atoi(optarg);
+                if (opts->compression_level < 0)
+                    opts->compression_level = 0;
+                if (opts->compression_level > 9)
+                    opts->compression_level = 9;
+                break;
+            case 'T': opts->extra_tags = optarg; break;
+            case 'v': opts->def_qual = atoi(optarg); break;
+
+            case '?':
+                bam2fq_usage(stderr, argv[0]);
+                free_opts(opts);
+                return false;
+            default:
+                if (parse_sam_global_opt(c, optarg, lopts, &opts->ga) != 0) {
+                    bam2fq_usage(stderr, argv[0]);
+                    free_opts(opts);
+                    return false;
+                }
+                break;
+        }
+    }
+
+    if (opts->fnr[1] || opts->fnr[2]) opts->has12 = false;
+    if (opts->has12always) opts->has12 = true;
+
+    if (!opts->barcode_tag) opts->barcode_tag = DEFAULT_BARCODE_TAG;
+    if (!opts->quality_tag) opts->quality_tag = DEFAULT_QUALITY_TAG;
+
+    int nIndex = 0;
+    if (opts->index_format) {
+        char *s;
+        for (s = opts->index_format; *s; s++) {
+            if (*s == 'i') nIndex++;
+        }
+    }
+    if (nIndex>2) {
+        fprintf(stderr,"Invalid index format: more than 2 indexes\n");
+        bam2fq_usage(stderr, argv[0]);
+        free_opts(opts);
+        return false;
+    }
+
+    if (opts->index_file[1] && !opts->index_file[0]) {
+        fprintf(stderr, "Index one specified, but index two not given\n");
+        bam2fq_usage(stderr, argv[0]);
+        free_opts(opts);
+        return false;
+    }
+
+    if (opts->illumina_tag && !nIndex) {
+        fprintf(stderr, "You must specify an index format (--index-format) with the Illumina Casava (-i) option\n");
+        bam2fq_usage(stderr, argv[0]);
+        free_opts(opts);
+        return false;
+    }
+
+    if (nIndex==0 && opts->index_file[0]) {
+        fprintf(stderr, "index_format not specified, but index file given\n");
+        bam2fq_usage(stderr, argv[0]);
+        free_opts(opts);
+        return false;
+    }
+
+    if (opts->def_qual < 0 || 93 < opts->def_qual) {
+        fprintf(stderr, "Invalid -v default quality %i, allowed range 0 to 93\n", opts->def_qual);
+        bam2fq_usage(stderr, argv[0]);
+        free_opts(opts);
+        return false;
+    }
+
+    const char* type_str = argv[0];
+    if (strcasecmp("fastq", type_str) == 0 ||
+        strcasecmp("bam2fq", type_str) == 0) {
+        opts->filetype = FASTQ;
+    } else if (strcasecmp("fasta", type_str) == 0) {
+        opts->filetype = FASTA;
+    } else {
+        print_error("bam2fq", "Unrecognised type call \"%s\", this should be impossible... but you managed it!", type_str);
+        bam2fq_usage(stderr, argv[0]);
+        free_opts(opts);
+        return false;
+    }
+
+    if (argc == optind && isatty(STDIN_FILENO)) {
+        bam2fq_usage(stdout, argv[0]);
+        free_opts(opts);
+        return true;
+    }
+
+    if (argc - optind > 1) {
+        fprintf(stderr, "Too many arguments.\n");
+        bam2fq_usage(stderr, argv[0]);
+        free_opts(opts);
+        return false;
+    }
+    opts->fn_input = argc > optind ? argv[optind] : "-";
+    *opts_out = opts;
+    return true;
+}
+
+void set_sam_opts(samFile *fp, bam2fq_state_t *state,
+                  const bam2fq_opts_t *opts) {
+    if (state->has12)
+        hts_set_opt(fp, FASTQ_OPT_RNUM, 1);
+
+    if (state->illumina_tag)
+        hts_set_opt(fp, FASTQ_OPT_CASAVA, 1);
+
+    hts_set_opt(fp, FASTQ_OPT_BARCODE, opts->barcode_tag);
+
+    if (opts->extra_tags && (*opts->extra_tags == '*' || *opts->extra_tags == '\0'))
+        hts_set_opt(fp, FASTQ_OPT_AUX, NULL);
+    else {
+        kstring_t tag_list = {0,0};
+        if (state->copy_tags)
+            kputs("RG,BC,QT", &tag_list);
+        if (opts->extra_tags) {
+            if (tag_list.l)
+                kputc(',', &tag_list);
+            kputs(opts->extra_tags, &tag_list);
+        }
+        if (tag_list.l)
+            hts_set_opt(fp, FASTQ_OPT_AUX, tag_list.s);
+        ks_free(&tag_list);
+    }
+}
+
+// Open a file as normal or gzipped based on filename.
+// Note we always use bgzf and don't bother to attempt non-blocked
+// gzip streams.  This is a departure from the old fastq code.
+static samFile *sam_open_z(char *fn, char *mode, bam2fq_state_t *state) {
+    char modez[6];
+    strcpy(modez, mode);
+
+    size_t l = strlen(fn);
+    if ((l > 3 && strcmp(fn+l-3, ".gz") == 0) ||
+        (l > 4 && strcmp(fn+l-4, ".bgz") == 0) ||
+        (l > 5 && strcmp(fn+l-5, ".bgzf") == 0)) {
+        char m[3] = {'z', state->compression_level+'0', '\0'};
+        strcat(modez, m);
+    }
+
+    samFile *fp = sam_open(fn, modez);
+    if (!fp)
+        return NULL;
+
+    if (state->p.pool)
+        hts_set_thread_pool(fp, &state->p);
+
+    return fp;
+}
+
+static bool init_state(const bam2fq_opts_t* opts, bam2fq_state_t** state_out)
+{
+    char *mode = opts->filetype == FASTA ? "wF" : "wf";
+
+    bam2fq_state_t* state = calloc(1, sizeof(bam2fq_state_t));
+    if (!state)
+        return false;
+    state->flag_on = opts->flag_on;
+    state->flag_off = opts->flag_off;
+    state->flag_alloff = opts->flag_alloff;
+    state->has12 = opts->has12;
+    state->use_oq = opts->use_oq;
+    state->illumina_tag = opts->illumina_tag;
+    state->copy_tags = opts->copy_tags;
+    state->filetype = opts->filetype;
+    state->def_qual = opts->def_qual;
+    state->index_sequence = NULL;
+    state->hstdout = NULL;
+    state->compression_level = opts->compression_level;
+
+    state->fp = sam_open(opts->fn_input, "r");
+    if (state->fp == NULL) {
+        print_error_errno("bam2fq","Cannot read file \"%s\"", opts->fn_input);
+        free(state);
+        return false;
+    }
+
+    state->p.pool = NULL;
+    if (opts->ga.nthreads > 0) {
+        if (!(state->p.pool = hts_tpool_init(opts->ga.nthreads))) {
+            fprintf(stderr, "Failed to create thread pool\n");
+            free(state);
+            return false;
+        }
+        state->p.qsize = opts->ga.nthreads*2;
+        hts_set_thread_pool(state->fp, &state->p);
+    }
+
+    uint32_t rf = SAM_QNAME | SAM_FLAG | SAM_SEQ | SAM_QUAL;
+    if (opts->use_oq || opts->extra_tags || opts->index_file[0]) rf |= SAM_AUX;
+    if (hts_set_opt(state->fp, CRAM_OPT_REQUIRED_FIELDS, rf)) {
+        fprintf(stderr, "Failed to set CRAM_OPT_REQUIRED_FIELDS value\n");
+        free(state);
+        return false;
+    }
+    if (hts_set_opt(state->fp, CRAM_OPT_DECODE_MD, 0)) {
+        fprintf(stderr, "Failed to set CRAM_OPT_DECODE_MD value\n");
+        free(state);
+        return false;
+    }
+    if (opts->fnse) {
+        if (!(state->fpse = sam_open_z(opts->fnse, mode, state))) {
+            print_error_errno("bam2fq", "Cannot open singleton file \"%s\"", opts->fnse);
+            free(state);
+            return false;
+        }
+        set_sam_opts(state->fpse, state, opts);
+    }
+
+    if (opts->ga.reference) {
+        if (hts_set_fai_filename(state->fp, opts->ga.reference) != 0) {
+            print_error_errno("bam2fq", "cannot load reference \"%s\"", opts->ga.reference);
+            free(state);
+            return false;
+        }
+    }
+
+    // single, read1, read2
+    int i, j;
+    for (i = 0; i < 3; ++i) {
+        if (opts->fnr[i]) {
+            for (j = 0; j < i; j++)
+                if (opts->fnr[j] && strcmp(opts->fnr[j], opts->fnr[i]) == 0)
+                    break;
+            if (j == i) {
+                if (!(state->fpr[i] = sam_open_z(opts->fnr[i], mode, state))) {
+                    print_error_errno("bam2fq", "Cannot open r%d file \"%s\"",
+                                      i, opts->fnr[i]);
+                    free(state);
+                    return false;
+                }
+                set_sam_opts(state->fpr[i], state, opts);
+            } else {
+                state->fpr[i] = state->fpr[j];
+            }
+        } else {
+            if (!state->hstdout) {
+                if (!(state->hstdout = sam_open_z("-", mode, state))) {
+                    print_error_errno("bam2fq", "Cannot open STDOUT");
+                    free(state);
+                    return false;
+                }
+                set_sam_opts(state->hstdout, state, opts);
+                autoflush_if_stdout(state->hstdout, "-");
+            }
+            state->fpr[i] = state->hstdout;
+        }
+    }
+
+    // index 1, index 2
+    for (i = 0; i < 2; i++) {
+        state->fpi[i] = NULL;
+        if (opts->index_file[i]) {
+            for (j = 0; j < 3; j++)
+                if (opts->fnr[j] && strcmp(opts->fnr[j], opts->index_file[i]) == 0)
+                    break;
+            for (j -= 3; j >= 0 && j < i; j++)
+                if (opts->index_file[j] && strcmp(opts->index_file[j], opts->index_file[i]) == 0)
+                    break;
+            if (i == j) {
+                if (!(state->fpi[i] = sam_open_z(opts->index_file[i], mode,
+                                                 state))) {
+                    print_error_errno("bam2fq", "Cannot open i%d file \"%s\"",
+                                      i+1, opts->index_file[i]);
+                    free(state);
+                    return false;
+                }
+                set_sam_opts(state->fpi[i], state, opts);
+            } else if (j < 0) {
+                state->fpi[i] = state->fpr[j+3];
+            } else {
+                state->fpi[i] = state->fpi[j];
+            }
+        }
+    }
+
+    state->h = sam_hdr_read(state->fp);
+    if (state->h == NULL) {
+        fprintf(stderr, "Failed to read header for \"%s\"\n", opts->fn_input);
+        free(state);
+        return false;
+    }
+
+    *state_out = state;
+    return true;
+}
+
+static bool destroy_state(const bam2fq_opts_t *opts, bam2fq_state_t *state, int* status)
+{
+    bool valid = true;
+    sam_hdr_destroy(state->h);
+    check_sam_close("bam2fq", state->fp, opts->fn_input, "file", status);
+    if (state->fpse && sam_close(state->fpse) < 0) {
+        print_error_errno("bam2fq", "Error closing singleton file \"%s\"", opts->fnse);
+        valid = false;
+    }
+
+    int i, j;
+    for (i = 0; i < 3; ++i) {
+        if (state->fpr[i] != state->hstdout) {
+            for (j = 0; j < i; j++)
+                if (state->fpr[i] == state->fpr[j])
+                    break;
+            if (j == i && sam_close(state->fpr[i])) {
+                print_error_errno("bam2fq", "Error closing r%d file \"%s\"", i, opts->fnr[i]);
+                valid = false;
+            }
+        }
+    }
+    if (state->hstdout) {
+        release_autoflush(state->hstdout);
+        if (sam_close(state->hstdout) < 0) {
+            print_error_errno("bam2fq", "Error closing STDOUT");
+            valid = false;
+        }
+    }
+    for (i = 0; i < 2; i++) {
+        for (j = 0; j < 3; j++)
+            if (state->fpi[i] == state->fpr[j])
+                break;
+        for (j -= 3; j >= 0 && j < i; j++)
+            if (state->fpi[i] == state->fpi[j])
+                break;
+        if (j == i && state->fpi[i] && sam_close(state->fpi[i]) < 0) {
+            print_error_errno("bam2fq", "Error closing i%d file \"%s\"", i+1, opts->index_file[i]);
+            valid = false;
+        }
+    }
+    free(state->index_sequence);
+    if (state->p.pool)
+        hts_tpool_destroy(state->p.pool);
+    free(state);
+    return valid;
+}
+
+static inline bool filter_it_out(const bam1_t *b, const bam2fq_state_t *state)
+{
+    return ((b->core.flag&(state->flag_on)) != state->flag_on // or reads indicated by filter flags
+        ||  (b->core.flag&(state->flag_off)) != 0
+        ||  (b->core.flag&(state->flag_alloff) && (b->core.flag&(state->flag_alloff)) == state->flag_alloff));
+
+}
+
+int write_index_rec(samFile *fp, bam1_t *b, bam2fq_state_t *state,
+                    bam2fq_opts_t* opts, char *seq, int seq_len,
+                    char *qual, int qual_len) {
+    if (!fp || !b || !seq_len)
+        return 0;
+
+    int ret = -1;
+    bam1_t *b2 = bam_init1(); // FIXME: reuse
+    if (!b2)
+        return -1;
+
+    size_t aux_len = b->data + b->l_data - bam_get_aux(b);
+    if (bam_set1(b2, b->core.l_qname, bam_get_qname(b),
+                 (b->core.flag | BAM_FUNMAP) & ~BAM_FREVERSE,
+                 -1, -1, 0,    // refid, pos, mapq
+                 0, NULL,      // cigar
+                 -1, -1, 0,    // rnext, pnext, tlen
+                 seq_len, seq, qual,
+                 aux_len) < 0)
+        goto err;
+
+    uint8_t *q = bam_get_qual(b2);
+    if (qual) {
+        int i;
+        for (i = 0; i < seq_len; i++)
+            q[i] -= '!';
+    } else {
+        memset(q, opts->def_qual, seq_len);
+    }
+
+    memcpy(bam_get_aux(b2), bam_get_aux(b), aux_len);
+    b2->l_data += aux_len;
+    if (sam_write1(fp, state->h, b2) < 0)
+        goto err;
+
+    ret = 0;
+ err:
+    if (b2)
+        bam_destroy1(b2);
+    return ret;
+}
+
+int output_index(bam1_t *b1, bam1_t *b2, bam2fq_state_t *state,
+                 bam2fq_opts_t* opts) {
+    bam1_t *b = b1 ? b1 : b2;
+
+    char *ifmt = opts->index_format;
+    if (!ifmt)
+        ifmt = "i*i*";
+
+    // Get seq / qual elements
+    char *bc = NULL, *qt = NULL;
+    if (b1)
+        bc = (char *)bam_aux_get(b1, opts->barcode_tag);
+    if (b2 && !bc)
+        bc = (char *)bam_aux_get(b2, opts->barcode_tag);
+    if (!bc)
+        return 0;
+    else
+        bc++; // skip Z
+
+    if (b1)
+        qt = (char *)bam_aux_get(b1, opts->quality_tag);
+    if (b2 && !qt)
+        qt = (char *)bam_aux_get(b2, opts->quality_tag);
+    if (qt && strlen(bc) != strlen(qt)-1)
+        qt = NULL;
+    else if (qt)
+        qt++;
+
+    int inum = 0;
+    while (inum < 2) {
+        char fc = *ifmt++;
+        if (!fc)
+            break; // ran out of index-format
+
+        long len, rem = 0;
+        if (isdigit(*ifmt)) {
+            rem = len = strtol(ifmt, &ifmt, 10);
+        } else {
+            ifmt++;
+            len = 0;
+        }
+
+        char *bc_end = bc, *qt_end = qt;
+        while (len ? *bc_end && rem-- : isalpha(*bc_end))
+            bc_end++, qt_end += qt != NULL;
+
+        switch (fc) {
+        case 'n':
+            // skip
+            bc = bc_end + (len==0);
+            if (qt)
+                qt = qt_end + (len==0);
+            break;
+
+        case 'i':
+            if (write_index_rec(state->fpi[inum], b, state, opts,
+                                bc, bc_end-bc, qt, qt_end-qt) < 0)
+                return -1;
+            bc = bc_end + (len==0);
+            if (qt)
+                qt = qt_end + (len==0);
+            inum++;
+            break;
+
+        default:
+            fprintf(stderr, "Unknown index-format code\n");
+            return -1;
+        }
+    }
+
+    return 0;
+}
+
+static int flush_rec(bam2fq_state_t *state, bam2fq_opts_t* opts,
+                     bam1_t *b[4], int score[3], int best[3],
+                     int64_t *n_singletons) {
+    // Paired data, with 1 or 2 ends present.
+    if (score[1] > 0 && score[2] > 0) {
+        // If CASAVA tag is required and barcode is only on R1,
+        // copy it to R2
+        if (state->illumina_tag) {
+            char *tag;
+            if ((tag = (char *)bam_aux_get(b[best[1]],
+                                           opts->barcode_tag)))
+                if (bam_aux_update_str(b[best[2]],
+                                       opts->barcode_tag,
+                                       strlen(tag), tag+1) < 0)
+                    goto err;
+            if ((tag = (char *)bam_aux_get(b[best[1]],
+                                           opts->quality_tag)))
+                if (bam_aux_update_str(b[best[2]],
+                                       opts->quality_tag,
+                                       strlen(tag), tag+1) < 0)
+                    goto err;
+
+        }
+        if (sam_write1(state->fpr[1], state->h, b[best[1]]) < 0)
+            goto err;
+        if (sam_write1(state->fpr[2], state->h, b[best[2]]) < 0)
+            goto err;
+
+        if (output_index(b[best[1]], b[best[2]], state, opts) < 0)
+            goto err;
+    } else if (score[1] > 0 || score[2] > 0) {
+        if (state->fpse) {
+            // print whichever one exists to fpse
+            if (score[1] > 0) {
+                if (sam_write1(state->fpse, state->h, b[best[1]]) < 0)
+                    goto err;
+            } else {
+                if (sam_write1(state->fpse, state->h, b[best[2]]) < 0)
+                    goto err;
+            }
+            ++(*n_singletons);
+        } else {
+            if (score[1] > 0) {
+                if (sam_write1(state->fpr[1], state->h, b[best[1]]) < 0)
+                    goto err;
+            } else {
+                if (sam_write1(state->fpr[2], state->h, b[best[2]]) < 0)
+                    goto err;
+            }
+        }
+
+        if (output_index(score[1] > 0 ? b[best[1]] : NULL,
+                         score[2] > 0 ? b[best[2]] : NULL,
+                         state, opts) < 0)
+            goto err;
+    }
+
+    if (score[0]) { // single ended data (neither READ1 nor READ2)
+        if (sam_write1(state->fpr[0], state->h, b[best[0]]) < 0)
+            goto err;
+
+        if (output_index(b[best[0]], NULL, state, opts) < 0)
+            goto err;
+    }
+
+    return 0;
+
+ err:
+    return -1;
+}
+
+static bool bam2fq_mainloop(bam2fq_state_t *state, bam2fq_opts_t* opts)
+{
+    int n;
+    char *current_qname = NULL;
+    int64_t n_reads = 0, n_singletons = 0; // Statistics
+    int score[3];
+    int at_eof;
+    bool valid = false;
+    int best[3] = {-1, -1, -1}; // map R0, R1, single to b[] indices;
+                                // indexed by [readpart]
+    bam1_t *b[4];               // 3 readparts, plus current record
+
+    for (n = 0; n < 4; n++) {
+        if (!(b[n] = bam_init1())) {
+            perror("[bam2fq_mainloop] Malloc error for bam record buffer.");
+            return false;
+        }
+    }
+
+    n = 0;
+    while (true) {
+        int res = sam_read1(state->fp, state->h, b[n]);
+        if (res < -1) {
+            print_error("bam2fq", "Failed to read bam record");
+            goto err;
+        }
+        at_eof = res < 0;
+
+        if (!at_eof && filter_it_out(b[n], state))
+            continue;
+        if (!at_eof) {
+            ++n_reads;
+
+            // Handle -O option: use OQ for qual
+            uint8_t *oq;
+            if (state->use_oq && (oq = bam_aux_get(b[n],"OQ")) && *oq == 'Z') {
+                int i, l = strlen((char *)++oq);
+                uint8_t *qual = bam_get_qual(b[n]);
+                for (i = 0; i < l && i < b[n]->core.l_qseq; i++)
+                    qual[i] = oq[i] - '!';
+            }
+        }
+
+        if (at_eof
+            || !current_qname
+            || (strcmp(current_qname, bam_get_qname(b[n])) != 0)) {
+            // New name, so flush best examples of previous name.
+            if (current_qname)
+                if (flush_rec(state, opts, b, score, best, &n_singletons) < 0)
+                    goto err;
+
+            current_qname = bam_get_qname(b[n]);
+            score[0] = score[1] = score[2] = 0;
+
+            if (at_eof) { break; }
+        }
+
+        // Prefer a copy of the read that has base qualities
+        int b_score = bam_get_qual(b[n])[0] != 0xff? 2 : 1;
+        readpart rp = which_readpart(b[n]);
+        if (score[rp] < b_score) {
+            score[rp] = b_score;
+            // Record b[n] slot for best copy of readpair and find a new
+            // slot for next bam read
+            best[rp] = n;
+            int used_slot[4] = {0}, i;
+            for (i = 0; i < 3; i++)
+                if (best[i] >= 0)
+                    used_slot[best[i]] = 1;
+            for (i = 0; i < 4 && used_slot[i]; i++)
+                ;
+            n = i;
+        }
+    }
+
+    valid = true;
+ err:
+    if (!valid)
+        print_error_errno("bam2fq", "Error writing to FASTx files.");
+
+    for (n = 0; n < 4; n++)
+        bam_destroy1(b[n]);
+
+    fprintf(stderr, "[M::%s] discarded %" PRId64 " singletons\n",
+            __func__, n_singletons);
+    fprintf(stderr, "[M::%s] processed %" PRId64 " reads\n",
+            __func__, n_reads);
+
+    return valid;
+}
+
+int main_bam2fq(int argc, char *argv[])
+{
+    int status = EXIT_FAILURE;
+    bam2fq_opts_t* opts = NULL;
+    bam2fq_state_t* state = NULL;
+
+    bool valid = parse_opts(argc, argv, &opts);
+    if (!valid || opts == NULL) return valid ? EXIT_SUCCESS : EXIT_FAILURE;
+
+    if (!init_state(opts, &state)) goto err;
+
+    if (!bam2fq_mainloop(state,opts)) goto err;
+
+    if (!destroy_state(opts, state, &status)) goto err;
+
+    status = EXIT_SUCCESS;
+ err:
+    sam_global_args_free(&opts->ga);
+    free_opts(opts);
+
+    return status;
+}
diff --git a/samtools/bam_fastq.c.pysam.c b/samtools/bam_fastq.c.pysam.c
new file mode 100644
index 0000000..fbe65fb
--- /dev/null
+++ b/samtools/bam_fastq.c.pysam.c
@@ -0,0 +1,887 @@
+#include "samtools.pysam.h"
+
+/*  bam_fastq.c -- FASTA and FASTQ file generation
+
+    Copyright (C) 2009-2017, 2019-2020 Genome Research Ltd.
+    Portions copyright (C) 2009, 2011, 2012 Broad Institute.
+
+    Author: Heng Li <lh3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notices and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <config.h>
+
+#include <stdlib.h>
+#include <string.h>
+#include <strings.h>
+#include <stdbool.h>
+#include <ctype.h>
+#include <assert.h>
+#include <inttypes.h>
+#include <unistd.h>
+
+#include "htslib/sam.h"
+#include "htslib/klist.h"
+#include "htslib/kstring.h"
+#include "htslib/bgzf.h"
+#include "htslib/thread_pool.h"
+#include "samtools.h"
+#include "sam_opts.h"
+
+#define DEFAULT_BARCODE_TAG "BC"
+#define DEFAULT_QUALITY_TAG "QT"
+#define INDEX_SEPARATOR "+"
+
+int8_t seq_comp_table[16] = { 0, 8, 4, 12, 2, 10, 6, 14, 1, 9, 5, 13, 3, 11, 7, 15 };
+static void bam2fq_usage(FILE *to, const char *command)
+{
+    int fq = strcasecmp("fastq", command) == 0 || strcasecmp("bam2fq", command) == 0;
+    fprintf(to,
+"Usage: samtools %s [options...] <in.bam>\n", command);
+    fprintf(to,
+"\n"
+"Description:\n"
+"Converts a SAM, BAM or CRAM to %s format.\n"
+"\n"
+"Options:\n"
+"  -0 FILE      write reads designated READ_OTHER to FILE\n"
+"  -1 FILE      write reads designated READ1 to FILE\n"
+"  -2 FILE      write reads designated READ2 to FILE\n"
+"  -o FILE      write reads designated READ1 or READ2 to FILE\n"
+"               note: if a singleton file is specified with -s, only\n"
+"               paired reads will be written to the -1 and -2 files.\n"
+"  -f INT       only include reads with all  of the FLAGs in INT present [0]\n"       //   F&x == x
+"  -F INT       only include reads with none of the FLAGS in INT present [0x900]\n"       //   F&x == 0
+"  -G INT       only EXCLUDE reads with all  of the FLAGs in INT present [0]\n"       // !(F&x == x)
+"  -n           don't append /1 and /2 to the read name\n"
+"  -N           always append /1 and /2 to the read name\n",
+    fq ? "FASTQ" : "FASTA");
+    if (fq) fprintf(to,
+"  -O           output quality in the OQ tag if present\n");
+    fprintf(to,
+"  -s FILE      write singleton reads designated READ1 or READ2 to FILE\n"
+"  -t           copy RG, BC and QT tags to the %s header line\n",
+    fq ? "FASTQ" : "FASTA");
+    fprintf(to,
+"  -T TAGLIST   copy arbitrary tags to the %s header line, '*' for all\n",
+    fq ? "FASTQ" : "FASTA");
+    if (fq) fprintf(to,
+"  -v INT       default quality score if not given in file [1]\n"
+"  -i           add Illumina Casava 1.8 format entry to header (eg 1:N:0:ATCACG)\n"
+"  -c INT       compression level [0..9] to use when writing bgzf files [1]\n"
+"  --i1 FILE    write first index reads to FILE\n"
+"  --i2 FILE    write second index reads to FILE\n"
+"  --barcode-tag TAG\n"
+"               Barcode tag [" DEFAULT_BARCODE_TAG "]\n"
+"  --quality-tag TAG\n"
+"               Quality tag [" DEFAULT_QUALITY_TAG "]\n"
+"  --index-format STR\n"
+"               How to parse barcode and quality tags\n\n");
+    sam_global_opt_help(to, "-.--.@-.");
+    fprintf(to,
+"\n"
+"The files will be automatically compressed if the file names have a .gz\n"
+"or .bgzf extension.  The input to this program must be collated by name.\n"
+"Run 'samtools collate' or 'samtools sort -n' to achieve this.\n"
+"\n"
+"Reads are designated READ1 if FLAG READ1 is set and READ2 is not set.\n"
+"Reads are designated READ2 if FLAG READ1 is not set and READ2 is set.\n"
+"Otherwise reads are designated READ_OTHER (both flags set or both flags unset).\n"
+"Run 'samtools flags' for more information on flag codes and meanings.\n");
+    fprintf(to,
+"\n"
+"The index-format string describes how to parse the barcode and quality tags.\n"
+"It is made up of 'i' or 'n' followed by a length or '*'.  For example:\n"
+"   i14i8       The first 14 characters are index 1, the next 8 are index 2\n"
+"   n8i14       Ignore the first 8 characters, and use the next 14 for index 1\n\n"
+"If the tag contains a separator, then the numeric part can be replaced with\n"
+"'*' to mean 'read until the separator or end of tag', for example:\n"
+"   i*i*        Break the tag at the separator into index 1 and index 2\n"
+"   n*i*        Ignore the left part of the tag until the separator,\n"
+"               then use the second part of the tag as index 1\n");
+    fprintf(to,
+"\n"
+"Examples:\n"
+"To get just the paired reads in separate files, use:\n"
+"   samtools %s -1 pair1.%s -2 pair2.%s -0 /dev/null -s /dev/null -n in.bam\n"
+"\nTo get all non-supplementary/secondary reads in a single file, redirect\n"
+"the output:\n"
+"   samtools %s in.bam > all_reads.%s\n",
+            command, fq ? "fq" : "fa", fq ? "fq" : "fa",
+            command, fq ? "fq" : "fa");
+}
+
+typedef enum { READ_UNKNOWN = 0, READ_1 = 1, READ_2 = 2 } readpart;
+typedef enum { FASTA, FASTQ } fastfile;
+typedef struct bam2fq_opts {
+    char *fnse;
+    char *fnr[3];
+    char *fn_input; // pointer to input filename in argv do not free
+    bool has12, has12always, use_oq, copy_tags, illumina_tag;
+    int flag_on, flag_off, flag_alloff;
+    sam_global_args ga;
+    fastfile filetype;
+    int def_qual;
+    char *barcode_tag;
+    char *quality_tag;
+    char *index_file[2];
+    char *index_format;
+    char *extra_tags;
+    char compression_level;
+} bam2fq_opts_t;
+
+typedef struct bam2fq_state {
+    samFile *fp;
+    samFile *fpse;
+    samFile *fpr[3];
+    samFile *fpi[3];
+    samFile *hstdout;
+    sam_hdr_t *h;
+    bool has12, use_oq, copy_tags, illumina_tag;
+    int flag_on, flag_off, flag_alloff;
+    fastfile filetype;
+    int def_qual;
+    char *index_sequence;
+    char compression_level;
+    htsThreadPool p;
+} bam2fq_state_t;
+
+static readpart which_readpart(const bam1_t *b)
+{
+    if ((b->core.flag & BAM_FREAD1) && !(b->core.flag & BAM_FREAD2)) {
+        return READ_1;
+    } else if ((b->core.flag & BAM_FREAD2) && !(b->core.flag & BAM_FREAD1)) {
+        return READ_2;
+    } else {
+        return READ_UNKNOWN;
+    }
+}
+
+static void free_opts(bam2fq_opts_t *opts)
+{
+    free(opts);
+}
+
+// return true if valid
+static bool parse_opts(int argc, char *argv[], bam2fq_opts_t** opts_out)
+{
+    // Parse args
+    bam2fq_opts_t* opts = calloc(1, sizeof(bam2fq_opts_t));
+    opts->has12 = true;
+    opts->has12always = false;
+    opts->filetype = FASTQ;
+    opts->def_qual = 1;
+    opts->barcode_tag = NULL;
+    opts->quality_tag = NULL;
+    opts->index_format = NULL;
+    opts->index_file[0] = NULL;
+    opts->index_file[1] = NULL;
+    opts->extra_tags = NULL;
+    opts->compression_level = 1;
+    opts->flag_off = BAM_FSECONDARY|BAM_FSUPPLEMENTARY;
+    int flag_off_set = 0;
+
+    int c;
+    sam_global_args_init(&opts->ga);
+    static const struct option lopts[] = {
+        SAM_OPT_GLOBAL_OPTIONS('-', 0, '-', '-', 0, '@'),
+        {"i1", required_argument, NULL, 1},
+        {"I1", required_argument, NULL, 1},
+        {"i2", required_argument, NULL, 2},
+        {"I2", required_argument, NULL, 2},
+        {"if", required_argument, NULL, 3},
+        {"IF", required_argument, NULL, 3},
+        {"index-format", required_argument, NULL, 3},
+        {"barcode-tag", required_argument, NULL, 'b'},
+        {"quality-tag", required_argument, NULL, 'q'},
+        { NULL, 0, NULL, 0 }
+    };
+    while ((c = getopt_long(argc, argv, "0:1:2:o:f:F:G:niNOs:c:tT:v:@:",
+                            lopts, NULL)) > 0) {
+        switch (c) {
+            case 'b': opts->barcode_tag = optarg; break;
+            case 'q': opts->quality_tag = optarg; break;
+            case  1 : opts->index_file[0] = optarg; break;
+            case  2 : opts->index_file[1] = optarg; break;
+            case  3 : opts->index_format = optarg; break;
+            case '0': opts->fnr[0] = optarg; break;
+            case '1': opts->fnr[1] = optarg; break;
+            case '2': opts->fnr[2] = optarg; break;
+            case 'o': opts->fnr[1] = optarg; opts->fnr[2] = optarg; break;
+            case 'f': opts->flag_on |= strtol(optarg, 0, 0); break;
+            case 'F':
+                if (!flag_off_set) {
+                    flag_off_set = 1;
+                    opts->flag_off = 0;
+                }
+                opts->flag_off |= strtol(optarg, 0, 0);
+                break;
+            case 'G': opts->flag_alloff |= strtol(optarg, 0, 0); break;
+            case 'n': opts->has12 = false; break;
+            case 'N': opts->has12always = true; break;
+            case 'O': opts->use_oq = true; break;
+            case 's': opts->fnse = optarg; break;
+            case 't': opts->copy_tags = true; break;
+            case 'i': opts->illumina_tag = true; break;
+            case 'c':
+                opts->compression_level = atoi(optarg);
+                if (opts->compression_level < 0)
+                    opts->compression_level = 0;
+                if (opts->compression_level > 9)
+                    opts->compression_level = 9;
+                break;
+            case 'T': opts->extra_tags = optarg; break;
+            case 'v': opts->def_qual = atoi(optarg); break;
+
+            case '?':
+                bam2fq_usage(samtools_stderr, argv[0]);
+                free_opts(opts);
+                return false;
+            default:
+                if (parse_sam_global_opt(c, optarg, lopts, &opts->ga) != 0) {
+                    bam2fq_usage(samtools_stderr, argv[0]);
+                    free_opts(opts);
+                    return false;
+                }
+                break;
+        }
+    }
+
+    if (opts->fnr[1] || opts->fnr[2]) opts->has12 = false;
+    if (opts->has12always) opts->has12 = true;
+
+    if (!opts->barcode_tag) opts->barcode_tag = DEFAULT_BARCODE_TAG;
+    if (!opts->quality_tag) opts->quality_tag = DEFAULT_QUALITY_TAG;
+
+    int nIndex = 0;
+    if (opts->index_format) {
+        char *s;
+        for (s = opts->index_format; *s; s++) {
+            if (*s == 'i') nIndex++;
+        }
+    }
+    if (nIndex>2) {
+        fprintf(samtools_stderr,"Invalid index format: more than 2 indexes\n");
+        bam2fq_usage(samtools_stderr, argv[0]);
+        free_opts(opts);
+        return false;
+    }
+
+    if (opts->index_file[1] && !opts->index_file[0]) {
+        fprintf(samtools_stderr, "Index one specified, but index two not given\n");
+        bam2fq_usage(samtools_stderr, argv[0]);
+        free_opts(opts);
+        return false;
+    }
+
+    if (opts->illumina_tag && !nIndex) {
+        fprintf(samtools_stderr, "You must specify an index format (--index-format) with the Illumina Casava (-i) option\n");
+        bam2fq_usage(samtools_stderr, argv[0]);
+        free_opts(opts);
+        return false;
+    }
+
+    if (nIndex==0 && opts->index_file[0]) {
+        fprintf(samtools_stderr, "index_format not specified, but index file given\n");
+        bam2fq_usage(samtools_stderr, argv[0]);
+        free_opts(opts);
+        return false;
+    }
+
+    if (opts->def_qual < 0 || 93 < opts->def_qual) {
+        fprintf(samtools_stderr, "Invalid -v default quality %i, allowed range 0 to 93\n", opts->def_qual);
+        bam2fq_usage(samtools_stderr, argv[0]);
+        free_opts(opts);
+        return false;
+    }
+
+    const char* type_str = argv[0];
+    if (strcasecmp("fastq", type_str) == 0 ||
+        strcasecmp("bam2fq", type_str) == 0) {
+        opts->filetype = FASTQ;
+    } else if (strcasecmp("fasta", type_str) == 0) {
+        opts->filetype = FASTA;
+    } else {
+        print_error("bam2fq", "Unrecognised type call \"%s\", this should be impossible... but you managed it!", type_str);
+        bam2fq_usage(samtools_stderr, argv[0]);
+        free_opts(opts);
+        return false;
+    }
+
+    if (argc == optind && isatty(STDIN_FILENO)) {
+        bam2fq_usage(samtools_stdout, argv[0]);
+        free_opts(opts);
+        return true;
+    }
+
+    if (argc - optind > 1) {
+        fprintf(samtools_stderr, "Too many arguments.\n");
+        bam2fq_usage(samtools_stderr, argv[0]);
+        free_opts(opts);
+        return false;
+    }
+    opts->fn_input = argc > optind ? argv[optind] : "-";
+    *opts_out = opts;
+    return true;
+}
+
+void set_sam_opts(samFile *fp, bam2fq_state_t *state,
+                  const bam2fq_opts_t *opts) {
+    if (state->has12)
+        hts_set_opt(fp, FASTQ_OPT_RNUM, 1);
+
+    if (state->illumina_tag)
+        hts_set_opt(fp, FASTQ_OPT_CASAVA, 1);
+
+    hts_set_opt(fp, FASTQ_OPT_BARCODE, opts->barcode_tag);
+
+    if (opts->extra_tags && (*opts->extra_tags == '*' || *opts->extra_tags == '\0'))
+        hts_set_opt(fp, FASTQ_OPT_AUX, NULL);
+    else {
+        kstring_t tag_list = {0,0};
+        if (state->copy_tags)
+            kputs("RG,BC,QT", &tag_list);
+        if (opts->extra_tags) {
+            if (tag_list.l)
+                kputc(',', &tag_list);
+            kputs(opts->extra_tags, &tag_list);
+        }
+        if (tag_list.l)
+            hts_set_opt(fp, FASTQ_OPT_AUX, tag_list.s);
+        ks_free(&tag_list);
+    }
+}
+
+// Open a file as normal or gzipped based on filename.
+// Note we always use bgzf and don't bother to attempt non-blocked
+// gzip streams.  This is a departure from the old fastq code.
+static samFile *sam_open_z(char *fn, char *mode, bam2fq_state_t *state) {
+    char modez[6];
+    strcpy(modez, mode);
+
+    size_t l = strlen(fn);
+    if ((l > 3 && strcmp(fn+l-3, ".gz") == 0) ||
+        (l > 4 && strcmp(fn+l-4, ".bgz") == 0) ||
+        (l > 5 && strcmp(fn+l-5, ".bgzf") == 0)) {
+        char m[3] = {'z', state->compression_level+'0', '\0'};
+        strcat(modez, m);
+    }
+
+    samFile *fp = sam_open(fn, modez);
+    if (!fp)
+        return NULL;
+
+    if (state->p.pool)
+        hts_set_thread_pool(fp, &state->p);
+
+    return fp;
+}
+
+static bool init_state(const bam2fq_opts_t* opts, bam2fq_state_t** state_out)
+{
+    char *mode = opts->filetype == FASTA ? "wF" : "wf";
+
+    bam2fq_state_t* state = calloc(1, sizeof(bam2fq_state_t));
+    if (!state)
+        return false;
+    state->flag_on = opts->flag_on;
+    state->flag_off = opts->flag_off;
+    state->flag_alloff = opts->flag_alloff;
+    state->has12 = opts->has12;
+    state->use_oq = opts->use_oq;
+    state->illumina_tag = opts->illumina_tag;
+    state->copy_tags = opts->copy_tags;
+    state->filetype = opts->filetype;
+    state->def_qual = opts->def_qual;
+    state->index_sequence = NULL;
+    state->hstdout = NULL;
+    state->compression_level = opts->compression_level;
+
+    state->fp = sam_open(opts->fn_input, "r");
+    if (state->fp == NULL) {
+        print_error_errno("bam2fq","Cannot read file \"%s\"", opts->fn_input);
+        free(state);
+        return false;
+    }
+
+    state->p.pool = NULL;
+    if (opts->ga.nthreads > 0) {
+        if (!(state->p.pool = hts_tpool_init(opts->ga.nthreads))) {
+            fprintf(samtools_stderr, "Failed to create thread pool\n");
+            free(state);
+            return false;
+        }
+        state->p.qsize = opts->ga.nthreads*2;
+        hts_set_thread_pool(state->fp, &state->p);
+    }
+
+    uint32_t rf = SAM_QNAME | SAM_FLAG | SAM_SEQ | SAM_QUAL;
+    if (opts->use_oq || opts->extra_tags || opts->index_file[0]) rf |= SAM_AUX;
+    if (hts_set_opt(state->fp, CRAM_OPT_REQUIRED_FIELDS, rf)) {
+        fprintf(samtools_stderr, "Failed to set CRAM_OPT_REQUIRED_FIELDS value\n");
+        free(state);
+        return false;
+    }
+    if (hts_set_opt(state->fp, CRAM_OPT_DECODE_MD, 0)) {
+        fprintf(samtools_stderr, "Failed to set CRAM_OPT_DECODE_MD value\n");
+        free(state);
+        return false;
+    }
+    if (opts->fnse) {
+        if (!(state->fpse = sam_open_z(opts->fnse, mode, state))) {
+            print_error_errno("bam2fq", "Cannot open singleton file \"%s\"", opts->fnse);
+            free(state);
+            return false;
+        }
+        set_sam_opts(state->fpse, state, opts);
+    }
+
+    if (opts->ga.reference) {
+        if (hts_set_fai_filename(state->fp, opts->ga.reference) != 0) {
+            print_error_errno("bam2fq", "cannot load reference \"%s\"", opts->ga.reference);
+            free(state);
+            return false;
+        }
+    }
+
+    // single, read1, read2
+    int i, j;
+    for (i = 0; i < 3; ++i) {
+        if (opts->fnr[i]) {
+            for (j = 0; j < i; j++)
+                if (opts->fnr[j] && strcmp(opts->fnr[j], opts->fnr[i]) == 0)
+                    break;
+            if (j == i) {
+                if (!(state->fpr[i] = sam_open_z(opts->fnr[i], mode, state))) {
+                    print_error_errno("bam2fq", "Cannot open r%d file \"%s\"",
+                                      i, opts->fnr[i]);
+                    free(state);
+                    return false;
+                }
+                set_sam_opts(state->fpr[i], state, opts);
+            } else {
+                state->fpr[i] = state->fpr[j];
+            }
+        } else {
+            if (!state->hstdout) {
+                if (!(state->hstdout = sam_open_z("-", mode, state))) {
+                    print_error_errno("bam2fq", "Cannot open STDOUT");
+                    free(state);
+                    return false;
+                }
+                set_sam_opts(state->hstdout, state, opts);
+                autoflush_if_stdout(state->hstdout, "-");
+            }
+            state->fpr[i] = state->hstdout;
+        }
+    }
+
+    // index 1, index 2
+    for (i = 0; i < 2; i++) {
+        state->fpi[i] = NULL;
+        if (opts->index_file[i]) {
+            for (j = 0; j < 3; j++)
+                if (opts->fnr[j] && strcmp(opts->fnr[j], opts->index_file[i]) == 0)
+                    break;
+            for (j -= 3; j >= 0 && j < i; j++)
+                if (opts->index_file[j] && strcmp(opts->index_file[j], opts->index_file[i]) == 0)
+                    break;
+            if (i == j) {
+                if (!(state->fpi[i] = sam_open_z(opts->index_file[i], mode,
+                                                 state))) {
+                    print_error_errno("bam2fq", "Cannot open i%d file \"%s\"",
+                                      i+1, opts->index_file[i]);
+                    free(state);
+                    return false;
+                }
+                set_sam_opts(state->fpi[i], state, opts);
+            } else if (j < 0) {
+                state->fpi[i] = state->fpr[j+3];
+            } else {
+                state->fpi[i] = state->fpi[j];
+            }
+        }
+    }
+
+    state->h = sam_hdr_read(state->fp);
+    if (state->h == NULL) {
+        fprintf(samtools_stderr, "Failed to read header for \"%s\"\n", opts->fn_input);
+        free(state);
+        return false;
+    }
+
+    *state_out = state;
+    return true;
+}
+
+static bool destroy_state(const bam2fq_opts_t *opts, bam2fq_state_t *state, int* status)
+{
+    bool valid = true;
+    sam_hdr_destroy(state->h);
+    check_sam_close("bam2fq", state->fp, opts->fn_input, "file", status);
+    if (state->fpse && sam_close(state->fpse) < 0) {
+        print_error_errno("bam2fq", "Error closing singleton file \"%s\"", opts->fnse);
+        valid = false;
+    }
+
+    int i, j;
+    for (i = 0; i < 3; ++i) {
+        if (state->fpr[i] != state->hstdout) {
+            for (j = 0; j < i; j++)
+                if (state->fpr[i] == state->fpr[j])
+                    break;
+            if (j == i && sam_close(state->fpr[i])) {
+                print_error_errno("bam2fq", "Error closing r%d file \"%s\"", i, opts->fnr[i]);
+                valid = false;
+            }
+        }
+    }
+    if (state->hstdout) {
+        release_autoflush(state->hstdout);
+        if (sam_close(state->hstdout) < 0) {
+            print_error_errno("bam2fq", "Error closing STDOUT");
+            valid = false;
+        }
+    }
+    for (i = 0; i < 2; i++) {
+        for (j = 0; j < 3; j++)
+            if (state->fpi[i] == state->fpr[j])
+                break;
+        for (j -= 3; j >= 0 && j < i; j++)
+            if (state->fpi[i] == state->fpi[j])
+                break;
+        if (j == i && state->fpi[i] && sam_close(state->fpi[i]) < 0) {
+            print_error_errno("bam2fq", "Error closing i%d file \"%s\"", i+1, opts->index_file[i]);
+            valid = false;
+        }
+    }
+    free(state->index_sequence);
+    if (state->p.pool)
+        hts_tpool_destroy(state->p.pool);
+    free(state);
+    return valid;
+}
+
+static inline bool filter_it_out(const bam1_t *b, const bam2fq_state_t *state)
+{
+    return ((b->core.flag&(state->flag_on)) != state->flag_on // or reads indicated by filter flags
+        ||  (b->core.flag&(state->flag_off)) != 0
+        ||  (b->core.flag&(state->flag_alloff) && (b->core.flag&(state->flag_alloff)) == state->flag_alloff));
+
+}
+
+int write_index_rec(samFile *fp, bam1_t *b, bam2fq_state_t *state,
+                    bam2fq_opts_t* opts, char *seq, int seq_len,
+                    char *qual, int qual_len) {
+    if (!fp || !b || !seq_len)
+        return 0;
+
+    int ret = -1;
+    bam1_t *b2 = bam_init1(); // FIXME: reuse
+    if (!b2)
+        return -1;
+
+    size_t aux_len = b->data + b->l_data - bam_get_aux(b);
+    if (bam_set1(b2, b->core.l_qname, bam_get_qname(b),
+                 (b->core.flag | BAM_FUNMAP) & ~BAM_FREVERSE,
+                 -1, -1, 0,    // refid, pos, mapq
+                 0, NULL,      // cigar
+                 -1, -1, 0,    // rnext, pnext, tlen
+                 seq_len, seq, qual,
+                 aux_len) < 0)
+        goto err;
+
+    uint8_t *q = bam_get_qual(b2);
+    if (qual) {
+        int i;
+        for (i = 0; i < seq_len; i++)
+            q[i] -= '!';
+    } else {
+        memset(q, opts->def_qual, seq_len);
+    }
+
+    memcpy(bam_get_aux(b2), bam_get_aux(b), aux_len);
+    b2->l_data += aux_len;
+    if (sam_write1(fp, state->h, b2) < 0)
+        goto err;
+
+    ret = 0;
+ err:
+    if (b2)
+        bam_destroy1(b2);
+    return ret;
+}
+
+int output_index(bam1_t *b1, bam1_t *b2, bam2fq_state_t *state,
+                 bam2fq_opts_t* opts) {
+    bam1_t *b = b1 ? b1 : b2;
+
+    char *ifmt = opts->index_format;
+    if (!ifmt)
+        ifmt = "i*i*";
+
+    // Get seq / qual elements
+    char *bc = NULL, *qt = NULL;
+    if (b1)
+        bc = (char *)bam_aux_get(b1, opts->barcode_tag);
+    if (b2 && !bc)
+        bc = (char *)bam_aux_get(b2, opts->barcode_tag);
+    if (!bc)
+        return 0;
+    else
+        bc++; // skip Z
+
+    if (b1)
+        qt = (char *)bam_aux_get(b1, opts->quality_tag);
+    if (b2 && !qt)
+        qt = (char *)bam_aux_get(b2, opts->quality_tag);
+    if (qt && strlen(bc) != strlen(qt)-1)
+        qt = NULL;
+    else if (qt)
+        qt++;
+
+    int inum = 0;
+    while (inum < 2) {
+        char fc = *ifmt++;
+        if (!fc)
+            break; // ran out of index-format
+
+        long len, rem = 0;
+        if (isdigit(*ifmt)) {
+            rem = len = strtol(ifmt, &ifmt, 10);
+        } else {
+            ifmt++;
+            len = 0;
+        }
+
+        char *bc_end = bc, *qt_end = qt;
+        while (len ? *bc_end && rem-- : isalpha(*bc_end))
+            bc_end++, qt_end += qt != NULL;
+
+        switch (fc) {
+        case 'n':
+            // skip
+            bc = bc_end + (len==0);
+            if (qt)
+                qt = qt_end + (len==0);
+            break;
+
+        case 'i':
+            if (write_index_rec(state->fpi[inum], b, state, opts,
+                                bc, bc_end-bc, qt, qt_end-qt) < 0)
+                return -1;
+            bc = bc_end + (len==0);
+            if (qt)
+                qt = qt_end + (len==0);
+            inum++;
+            break;
+
+        default:
+            fprintf(samtools_stderr, "Unknown index-format code\n");
+            return -1;
+        }
+    }
+
+    return 0;
+}
+
+static int flush_rec(bam2fq_state_t *state, bam2fq_opts_t* opts,
+                     bam1_t *b[4], int score[3], int best[3],
+                     int64_t *n_singletons) {
+    // Paired data, with 1 or 2 ends present.
+    if (score[1] > 0 && score[2] > 0) {
+        // If CASAVA tag is required and barcode is only on R1,
+        // copy it to R2
+        if (state->illumina_tag) {
+            char *tag;
+            if ((tag = (char *)bam_aux_get(b[best[1]],
+                                           opts->barcode_tag)))
+                if (bam_aux_update_str(b[best[2]],
+                                       opts->barcode_tag,
+                                       strlen(tag), tag+1) < 0)
+                    goto err;
+            if ((tag = (char *)bam_aux_get(b[best[1]],
+                                           opts->quality_tag)))
+                if (bam_aux_update_str(b[best[2]],
+                                       opts->quality_tag,
+                                       strlen(tag), tag+1) < 0)
+                    goto err;
+
+        }
+        if (sam_write1(state->fpr[1], state->h, b[best[1]]) < 0)
+            goto err;
+        if (sam_write1(state->fpr[2], state->h, b[best[2]]) < 0)
+            goto err;
+
+        if (output_index(b[best[1]], b[best[2]], state, opts) < 0)
+            goto err;
+    } else if (score[1] > 0 || score[2] > 0) {
+        if (state->fpse) {
+            // print whichever one exists to fpse
+            if (score[1] > 0) {
+                if (sam_write1(state->fpse, state->h, b[best[1]]) < 0)
+                    goto err;
+            } else {
+                if (sam_write1(state->fpse, state->h, b[best[2]]) < 0)
+                    goto err;
+            }
+            ++(*n_singletons);
+        } else {
+            if (score[1] > 0) {
+                if (sam_write1(state->fpr[1], state->h, b[best[1]]) < 0)
+                    goto err;
+            } else {
+                if (sam_write1(state->fpr[2], state->h, b[best[2]]) < 0)
+                    goto err;
+            }
+        }
+
+        if (output_index(score[1] > 0 ? b[best[1]] : NULL,
+                         score[2] > 0 ? b[best[2]] : NULL,
+                         state, opts) < 0)
+            goto err;
+    }
+
+    if (score[0]) { // single ended data (neither READ1 nor READ2)
+        if (sam_write1(state->fpr[0], state->h, b[best[0]]) < 0)
+            goto err;
+
+        if (output_index(b[best[0]], NULL, state, opts) < 0)
+            goto err;
+    }
+
+    return 0;
+
+ err:
+    return -1;
+}
+
+static bool bam2fq_mainloop(bam2fq_state_t *state, bam2fq_opts_t* opts)
+{
+    int n;
+    char *current_qname = NULL;
+    int64_t n_reads = 0, n_singletons = 0; // Statistics
+    int score[3];
+    int at_eof;
+    bool valid = false;
+    int best[3] = {-1, -1, -1}; // map R0, R1, single to b[] indices;
+                                // indexed by [readpart]
+    bam1_t *b[4];               // 3 readparts, plus current record
+
+    for (n = 0; n < 4; n++) {
+        if (!(b[n] = bam_init1())) {
+            perror("[bam2fq_mainloop] Malloc error for bam record buffer.");
+            return false;
+        }
+    }
+
+    n = 0;
+    while (true) {
+        int res = sam_read1(state->fp, state->h, b[n]);
+        if (res < -1) {
+            print_error("bam2fq", "Failed to read bam record");
+            goto err;
+        }
+        at_eof = res < 0;
+
+        if (!at_eof && filter_it_out(b[n], state))
+            continue;
+        if (!at_eof) {
+            ++n_reads;
+
+            // Handle -O option: use OQ for qual
+            uint8_t *oq;
+            if (state->use_oq && (oq = bam_aux_get(b[n],"OQ")) && *oq == 'Z') {
+                int i, l = strlen((char *)++oq);
+                uint8_t *qual = bam_get_qual(b[n]);
+                for (i = 0; i < l && i < b[n]->core.l_qseq; i++)
+                    qual[i] = oq[i] - '!';
+            }
+        }
+
+        if (at_eof
+            || !current_qname
+            || (strcmp(current_qname, bam_get_qname(b[n])) != 0)) {
+            // New name, so flush best examples of previous name.
+            if (current_qname)
+                if (flush_rec(state, opts, b, score, best, &n_singletons) < 0)
+                    goto err;
+
+            current_qname = bam_get_qname(b[n]);
+            score[0] = score[1] = score[2] = 0;
+
+            if (at_eof) { break; }
+        }
+
+        // Prefer a copy of the read that has base qualities
+        int b_score = bam_get_qual(b[n])[0] != 0xff? 2 : 1;
+        readpart rp = which_readpart(b[n]);
+        if (score[rp] < b_score) {
+            score[rp] = b_score;
+            // Record b[n] slot for best copy of readpair and find a new
+            // slot for next bam read
+            best[rp] = n;
+            int used_slot[4] = {0}, i;
+            for (i = 0; i < 3; i++)
+                if (best[i] >= 0)
+                    used_slot[best[i]] = 1;
+            for (i = 0; i < 4 && used_slot[i]; i++)
+                ;
+            n = i;
+        }
+    }
+
+    valid = true;
+ err:
+    if (!valid)
+        print_error_errno("bam2fq", "Error writing to FASTx files.");
+
+    for (n = 0; n < 4; n++)
+        bam_destroy1(b[n]);
+
+    fprintf(samtools_stderr, "[M::%s] discarded %" PRId64 " singletons\n",
+            __func__, n_singletons);
+    fprintf(samtools_stderr, "[M::%s] processed %" PRId64 " reads\n",
+            __func__, n_reads);
+
+    return valid;
+}
+
+int main_bam2fq(int argc, char *argv[])
+{
+    int status = EXIT_FAILURE;
+    bam2fq_opts_t* opts = NULL;
+    bam2fq_state_t* state = NULL;
+
+    bool valid = parse_opts(argc, argv, &opts);
+    if (!valid || opts == NULL) return valid ? EXIT_SUCCESS : EXIT_FAILURE;
+
+    if (!init_state(opts, &state)) goto err;
+
+    if (!bam2fq_mainloop(state,opts)) goto err;
+
+    if (!destroy_state(opts, state, &status)) goto err;
+
+    status = EXIT_SUCCESS;
+ err:
+    sam_global_args_free(&opts->ga);
+    free_opts(opts);
+
+    return status;
+}
diff --git a/samtools/bam_flags.c b/samtools/bam_flags.c
new file mode 100644
index 0000000..78312ee
--- /dev/null
+++ b/samtools/bam_flags.c
@@ -0,0 +1,86 @@
+/*  bam_flags.c -- flags subcommand.
+
+    Copyright (C) 2013-2014, 2021 Genome Research Ltd.
+
+    Author: Petr Danecek <pd3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <config.h>
+
+#include <ctype.h>
+#include <string.h>
+#include <stdlib.h>
+#include <stdio.h>
+#include <stdint.h>
+#include <unistd.h>
+#include <stdarg.h>
+#include <htslib/sam.h>
+#include "samtools.h"
+
+static void usage(FILE *fp)
+{
+    static const struct { int bit; const char *desc; } *fl, flags[] = {
+        { BAM_FPAIRED, "paired-end / multiple-segment sequencing technology" },
+        { BAM_FPROPER_PAIR, "each segment properly aligned according to aligner" },
+        { BAM_FUNMAP, "segment unmapped" },
+        { BAM_FMUNMAP, "next segment in the template unmapped" },
+        { BAM_FREVERSE, "SEQ is reverse complemented" },
+        { BAM_FMREVERSE, "SEQ of next segment in template is rev.complemented" },
+        { BAM_FREAD1, "the first segment in the template" },
+        { BAM_FREAD2, "the last segment in the template" },
+        { BAM_FSECONDARY, "secondary alignment" },
+        { BAM_FQCFAIL, "not passing quality controls or other filters" },
+        { BAM_FDUP, "PCR or optical duplicate" },
+        { BAM_FSUPPLEMENTARY, "supplementary alignment" },
+        { 0, NULL }
+    };
+
+    fprintf(fp,
+"About: Convert between textual and numeric flag representation\n"
+"Usage: samtools flags FLAGS...\n"
+"\n"
+"Each FLAGS argument is either an INT (in decimal/hexadecimal/octal) representing\n"
+"a combination of the following numeric flag values, or a comma-separated string\n"
+"NAME,...,NAME representing a combination of the following flag names:\n"
+"\n");
+    for (fl = flags; fl->desc; fl++) {
+        char *name = bam_flag2str(fl->bit);
+        fprintf(fp, "%#6x %5d  %-15s%s\n", fl->bit, fl->bit, name, fl->desc);
+        free(name);
+    }
+}
+
+
+int main_flags(int argc, char *argv[])
+{
+    if ( argc < 2 ) { usage(stdout); return 0; }
+
+    int i;
+    for (i = 1; i < argc; i++)
+    {
+        int mask = bam_str2flag(argv[i]);
+        if ( mask<0 ) { print_error("flags", "Could not parse \"%s\"", argv[i]); usage(stderr); return 1; }
+        char *str = bam_flag2str(mask);
+        printf("0x%x\t%d\t%s\n", mask, mask, str);
+        free(str);
+    }
+    return 0;
+}
+
diff --git a/samtools/bam_flags.c.pysam.c b/samtools/bam_flags.c.pysam.c
new file mode 100644
index 0000000..b3a9d29
--- /dev/null
+++ b/samtools/bam_flags.c.pysam.c
@@ -0,0 +1,88 @@
+#include "samtools.pysam.h"
+
+/*  bam_flags.c -- flags subcommand.
+
+    Copyright (C) 2013-2014, 2021 Genome Research Ltd.
+
+    Author: Petr Danecek <pd3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <config.h>
+
+#include <ctype.h>
+#include <string.h>
+#include <stdlib.h>
+#include <stdio.h>
+#include <stdint.h>
+#include <unistd.h>
+#include <stdarg.h>
+#include <htslib/sam.h>
+#include "samtools.h"
+
+static void usage(FILE *fp)
+{
+    static const struct { int bit; const char *desc; } *fl, flags[] = {
+        { BAM_FPAIRED, "paired-end / multiple-segment sequencing technology" },
+        { BAM_FPROPER_PAIR, "each segment properly aligned according to aligner" },
+        { BAM_FUNMAP, "segment unmapped" },
+        { BAM_FMUNMAP, "next segment in the template unmapped" },
+        { BAM_FREVERSE, "SEQ is reverse complemented" },
+        { BAM_FMREVERSE, "SEQ of next segment in template is rev.complemented" },
+        { BAM_FREAD1, "the first segment in the template" },
+        { BAM_FREAD2, "the last segment in the template" },
+        { BAM_FSECONDARY, "secondary alignment" },
+        { BAM_FQCFAIL, "not passing quality controls or other filters" },
+        { BAM_FDUP, "PCR or optical duplicate" },
+        { BAM_FSUPPLEMENTARY, "supplementary alignment" },
+        { 0, NULL }
+    };
+
+    fprintf(fp,
+"About: Convert between textual and numeric flag representation\n"
+"Usage: samtools flags FLAGS...\n"
+"\n"
+"Each FLAGS argument is either an INT (in decimal/hexadecimal/octal) representing\n"
+"a combination of the following numeric flag values, or a comma-separated string\n"
+"NAME,...,NAME representing a combination of the following flag names:\n"
+"\n");
+    for (fl = flags; fl->desc; fl++) {
+        char *name = bam_flag2str(fl->bit);
+        fprintf(fp, "%#6x %5d  %-15s%s\n", fl->bit, fl->bit, name, fl->desc);
+        free(name);
+    }
+}
+
+
+int main_flags(int argc, char *argv[])
+{
+    if ( argc < 2 ) { usage(samtools_stdout); return 0; }
+
+    int i;
+    for (i = 1; i < argc; i++)
+    {
+        int mask = bam_str2flag(argv[i]);
+        if ( mask<0 ) { print_error("flags", "Could not parse \"%s\"", argv[i]); usage(samtools_stderr); return 1; }
+        char *str = bam_flag2str(mask);
+        fprintf(samtools_stdout, "0x%x\t%d\t%s\n", mask, mask, str);
+        free(str);
+    }
+    return 0;
+}
+
diff --git a/samtools/bam_import.c b/samtools/bam_import.c
new file mode 100644
index 0000000..47cb125
--- /dev/null
+++ b/samtools/bam_import.c
@@ -0,0 +1,503 @@
+/* bam_import -- Import of FASTQ files.
+ *
+ *   samtools import -1 a_1.fq -2 a_2.fq --i1 a_i1.fq --i2 a_i2.fq
+ *   samtools import a_1.fq a_2.fq
+ *   samtools import a_interleaved.fq
+ *
+ * Copyright (C) 2020 Genome Research Ltd.
+ *
+ * Author: James Bonfield <jkb@sanger.ac.uk>
+ */
+
+/*
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notices and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.
+*/
+
+// TODO: Store other non-aux comments; in new sam tag?
+
+#include <config.h>
+#include <ctype.h>
+
+#include "htslib/sam.h"
+#include "htslib/thread_pool.h"
+
+#include "samtools.h"
+#include "sam_opts.h"
+
+static int usage(FILE *fp, int exit_status) {
+    fprintf(fp, "Usage: samtools import [options] [file.fastq ...]\n");
+    fprintf(fp, "\n");
+    fprintf(fp, "Options:\n");
+    fprintf(fp, "  -s FILE      Read paired-ended data from single FILE\n");
+    fprintf(fp, "  -0 FILE      Read single-ended data from FILE\n");
+    fprintf(fp, "  -1 FILE      Read-1 from FILE\n");
+    fprintf(fp, "  -2 FILE      Read-2 from FILE\n");
+    fprintf(fp, "  --i1 FILE    Index-1 from FILE\n");
+    fprintf(fp, "  --i2 FILE    Index-2 from FILE\n");
+    fprintf(fp, "  -i           Parse CASAVA identifier\n");
+    fprintf(fp, "  --barcode-tag TAG\n");
+    fprintf(fp, "               Tag to use with barcode sequences [BC]\n");
+    fprintf(fp, "  --quality-tag TAG\n");
+    fprintf(fp, "               Tag to use with barcode qualities [QT]\n");
+    fprintf(fp, "  -N, --name2  Use 2nd field as read name (SRA format)\n");
+    fprintf(fp, "  -r STRING    Build up a complete @RG line\n");
+    fprintf(fp, "  -R STRING    Add a simple RG line of \"@RG\\tID:STRING\"\n");
+    fprintf(fp, "  -T TAGLIST   Parse tags in SAM format; list of '*' for all\n");
+    fprintf(fp, "  -o FILE      Output to FILE instead of stdout\n");
+    fprintf(fp, "  -u           Uncompressed output\n");
+    fprintf(fp, "  --order TAG  Store Nth record count in TAG\n");
+    fprintf(fp, "\n");
+    sam_global_opt_help(fp, "-.O.-@--");
+
+    fprintf(fp, "\nA single fastq file will be interpreted as -s, -0 or -1 depending on\n");
+    fprintf(fp, "file contents, and a pair of fastq files as \"-1 FILE1 -2 FILE2\".\n");
+
+    return exit_status;
+}
+
+// Order matters here as we want to read index elements before main
+// sequences so on reading the seqs we can emit a fully annotated record.
+enum fileno {
+    FQ_I1, FQ_I2, // index seqs for R1 and R2
+    FQ_R0,        // single file and unpaired data (singled-ended tech).
+    FQ_R1, FQ_R2, // separate read1 and read2 files
+    FQ_SINGLE,    // single file, but with read1 and/or read2 present.
+    FQ_END
+};
+
+typedef struct {
+    sam_global_args ga;
+    int no_pg;
+    char *fn[FQ_END], *fn_out;
+    int idx_both;      // add index to READ2 too, not just READ1
+    int casava;
+    char *barcode_seq;
+    char *barcode_qual;
+    char *aux;
+    char *rg;
+    char *rg_line;
+    char *order;
+    int compress_level;
+    htsThreadPool p;
+    int name2;
+} opts_t;
+
+// Append a sequence and quality string from a BAM record to a BC:Z and
+// QT:Z style aux tag string.
+static int append_index(kstring_t *s, kstring_t *q, bam1_t *b) {
+    char *sp, *qp;
+    if (ks_resize(s, s->l + b->core.l_qseq+1 +1) < 0)
+        return -1;
+    if (ks_resize(q, q->l + b->core.l_qseq+1 +1) < 0)
+        return -1;
+
+    sp = s->s + s->l - (s->l > 0);
+    qp = q->s + q->l - (q->l > 0);
+
+    if (s->l)
+        *sp++ = '-';
+
+    if (q->l)
+        *qp++ = ' ';
+
+    int i;
+    uint8_t *seq = bam_get_seq(b);
+    uint8_t *qual = bam_get_qual(b);
+    for (i = 0; i < b->core.l_qseq; i++) {
+        *sp++ = seq_nt16_str[bam_seqi(seq, i)];
+        *qp++ = qual[i] + '!';
+    }
+    *sp++ = 0;
+    *qp++ = 0;
+
+    s->l = sp - s->s;
+    q->l = qp - q->s;
+
+    return 0;
+}
+
+static int import_fastq(int argc, char **argv, opts_t *opts) {
+    int i, n, ret = 0;
+    samFile *fp_in[FQ_END] = {NULL};
+    bam1_t *b = bam_init1();
+    int ids[FQ_END];
+    samFile *fp_out = NULL;
+    sam_hdr_t *hdr_out = NULL;
+    kstring_t index_str = {0,0};
+    kstring_t read_str = {0,0};
+    char *rg = opts->rg;
+    kstring_t rg_line = {0,0};
+    uint64_t read_num = 0;
+    kstring_t idx_seq  = {0};
+    kstring_t idx_qual = {0};
+
+    // Any additional arguments are assumed to be r1 r2, as a
+    // short cut. We support reading index tags out of those too (eg
+    // Illumina CASAVA format), but if we do that we lack the barcode
+    // quality string.
+    //
+    // We also consider a read name ending in /1 or /2 to be a single
+    // file containing interleaved fastq records for both ends.
+    // These will be labeled as fn[FQ_R1] but adjusted during reading.
+    if (argc == 1)
+        opts->fn[FQ_SINGLE] = argv[0];
+    else
+        for (i = 0; i < 4; i++)
+            if (argc > i)
+                opts->fn[FQ_R1+i] = argv[i];
+
+    // Open all files
+    for (i = n = 0; i < FQ_END; i++) {
+        if (!opts->fn[i])
+            continue;
+        fp_in[i] = sam_open_format(opts->fn[i], "r", &opts->ga.in);
+        if (!fp_in[i]) {
+            perror(opts->fn[i]);
+            ret = -1;
+            goto err;
+        }
+        if (opts->p.pool)
+            hts_set_thread_pool(fp_in[i], &opts->p);
+        ids[n++] = i;
+
+        if (opts->name2)
+            hts_set_opt(fp_in[i], FASTQ_OPT_NAME2, 1);
+        if (opts->casava)
+            hts_set_opt(fp_in[i], FASTQ_OPT_CASAVA, 1);
+        if (opts->barcode_seq) // for auto-CASAVA parsing
+            hts_set_opt(fp_in[i], FASTQ_OPT_BARCODE, opts->barcode_seq);
+        if (opts->aux)
+            hts_set_opt(fp_in[i], FASTQ_OPT_AUX,
+                        *opts->aux == '*' || *opts->aux == '\0'
+                        ? NULL : opts->aux);
+
+        switch (i) {
+        case FQ_I1:
+            kputs("--i1 I1.fastq ", &read_str);
+            kputs("i*", &index_str);
+            break;
+        case FQ_I2:
+            kputs("--i2 I2.fastq ", &read_str);
+            kputs("i*", &index_str);
+            break;
+
+        case FQ_R0:
+            kputs("-0 unpaired.fastq ", &read_str);
+            break;
+
+        case FQ_R1:
+            kputs("-1 R1.fastq ", &read_str);
+            break;
+
+        case FQ_R2:
+            kputs("-2 R2.fastq ", &read_str);
+            break;
+
+        case FQ_SINGLE:
+            kputs("-N -o paired.fastq ", &read_str);
+            break;
+
+        default:
+            ks_clear(&read_str); // not reversible
+            kputs("", &read_str);
+        }
+    }
+    if (n == 0) {
+        bam_destroy1(b);
+        return usage(stdout, EXIT_SUCCESS);
+    }
+
+    char out_mode[10] = {'w', 0, 0};
+    if (opts->compress_level != -1)
+        out_mode[1] = '0' + opts->compress_level;
+    sam_open_mode(out_mode+strlen(out_mode), opts->fn_out, NULL);
+    fp_out = sam_open_format(opts->fn_out, out_mode, &opts->ga.out);
+    if (!fp_out) {
+        perror(opts->fn_out);
+        goto err;
+    }
+    autoflush_if_stdout(fp_out, opts->fn_out);
+    if (opts->p.pool)
+        hts_set_thread_pool(fp_out, &opts->p);
+
+    // Create header
+    if (ks_len(&read_str)) {
+        char CO[2100];
+        if (ks_len(&index_str))
+            snprintf(CO, sizeof(CO), "@CO\tReverse with: samtools fastq %s "
+                    "--index-format=\"%s\"\n",
+                    ks_str(&read_str), ks_str(&index_str));
+        else
+            snprintf(CO, sizeof(CO), "@CO\tReverse with: samtools fastq %s\n",
+                    ks_str(&read_str));
+
+        hdr_out = sam_hdr_parse(strlen(CO), CO);
+    } else {
+        hdr_out = sam_hdr_init();
+    }
+
+    // Add a version line with the sort order to the output header
+    if (sam_hdr_add_line(hdr_out, "HD", "VN", SAM_FORMAT_VERSION, "SO", "unsorted", "GO", "query", NULL) < 0) {
+        fprintf(stderr, "Could not set SO and GO in the header.\n");
+        goto err;
+    }
+
+    // Read group
+    if (opts->rg_line) {
+        if (*opts->rg_line != '@')
+            ksprintf(&rg_line, "@RG\t%s", opts->rg_line);
+        else
+            kputs(opts->rg_line, &rg_line);
+    } else if (opts->rg) {
+        ksprintf(&rg_line, "@RG\tID:%s", opts->rg);
+    }
+
+    if (ks_len(&rg_line)) {
+        if (sam_hdr_add_lines(hdr_out, ks_str(&rg_line), 0) < 0)
+            goto err;
+        rg = strstr(ks_str(&rg_line), "\tID:");
+        if (!rg) {
+            fprintf(stderr, "\"-r RG-LINE\" option contained no ID field\n");
+            goto err;
+        }
+        rg += 4;
+
+        i = 0;
+        while (rg[i] != '\t' && rg[i] != '\0')
+            i++;
+        rg[i] = 0;
+    }
+
+    if ((ret = sam_hdr_write(fp_out, hdr_out)) < 0)
+        goto err;
+
+
+    // Interleave / combine from n files (ids[0..n-1]).
+    int res;
+    int eof = 0;
+    do {
+        idx_seq.l = idx_qual.l = 0;
+        for (i = 0; i < n; i++) {
+            if ((res = sam_read1(fp_in[ids[i]], NULL, b)) < 0) {
+                if (res == -1) {
+                    eof++;
+                    continue;
+                } else
+                    break;
+            }
+
+            // index
+            if (ids[i] == FQ_I1 || ids[i] == FQ_I2) {
+                if (append_index(&idx_seq, &idx_qual, b) < 0) {
+                    res = -1;
+                    break;
+                }
+                continue;
+            }
+
+            // full read
+            if (idx_seq.l) {
+                if (opts->idx_both || ids[i] == FQ_SINGLE ||
+                    ids[i] == FQ_R0 || ids[i] == FQ_R1) {
+                    if (bam_aux_append(b, opts->barcode_seq, 'Z', idx_seq.l,
+                                       (uint8_t *)idx_seq.s) ||
+                        bam_aux_append(b, opts->barcode_qual, 'Z', idx_qual.l,
+                                       (uint8_t *)idx_qual.s)) {
+                        res = -1;
+                        break;
+                    }
+                }
+            }
+
+            switch(ids[i]) {
+            case FQ_R0:
+                // unpaired; no flags to declare
+                break;
+            case FQ_SINGLE:
+                // paired (but don't know if R1 or R2) or unpaired.
+                // We rely on the /1 and /2 read suffix parsing in htslib
+                // to distinguish the two cases, or CASAVA tags if
+                // explicitly enabled.
+                break;
+            case FQ_R1:
+                if ((b->core.flag & (BAM_FREAD1 | BAM_FREAD2)) == 0)
+                    b->core.flag |= BAM_FREAD1;
+                b->core.flag |= BAM_FPAIRED;
+                if (i+1 < n && ids[i+1] == FQ_R2)
+                    b->core.flag |= BAM_FMUNMAP;
+                break;
+            case FQ_R2:
+                b->core.flag |= BAM_FPAIRED | BAM_FREAD2;
+                if (i > 0 && ids[i-1] == FQ_R1)
+                    b->core.flag |= BAM_FMUNMAP;
+                break;
+            }
+
+            if (rg) {
+                if (bam_aux_append(b, "RG", 'Z', strlen(rg)+1,
+                                   (uint8_t *)rg) < 0) {
+                    ret = -1;
+                    goto err;
+                }
+            }
+
+            if (opts->order) {
+                if (bam_aux_update_int(b, opts->order, read_num++) < 0) {
+                    ret = -1;
+                    goto err;
+                }
+            }
+
+            res = sam_write1(fp_out, hdr_out, b);
+        }
+    } while (res >= 0);
+
+    if (res != -1) {
+        print_error("import", "truncated file. Aborting");
+        ret = res;
+        goto err;
+    }
+
+    if (eof != n) {
+        print_error("import", "input files with differing number of records");
+        ret = -1;
+        goto err;
+    }
+
+    // Close and return
+    ret = 0;
+err:
+    bam_destroy1(b);
+    sam_hdr_destroy(hdr_out);
+    ks_free(&rg_line);
+    ks_free(&index_str);
+    ks_free(&read_str);
+    if (fp_out) {
+        release_autoflush(fp_out);
+        if (sam_close(fp_out) < 0) {
+            perror(opts->fn_out);
+            ret |= -1;
+        }
+    }
+    for (i = 0; i < FQ_END; i++) {
+        if (fp_in[i] && sam_close(fp_in[i]) < 0) {
+            perror(opts->fn[i]);
+            ret |= -1;
+        }
+    }
+    ks_free(&idx_seq);
+    ks_free(&idx_qual);
+
+    return ret;
+}
+
+int main_import(int argc, char *argv[]) {
+    int c;
+    opts_t opts = {
+        .no_pg = 0,
+        .ga = SAM_GLOBAL_ARGS_INIT,
+        .fn = {NULL},
+        .fn_out = "-",
+        .casava = 0,
+        .barcode_seq = "BC",
+        .barcode_qual = "QT",
+        .aux = NULL,
+        .rg = NULL,
+        .rg_line = NULL,
+        .order = NULL,
+        .compress_level = -1,
+        .name2 = 0,
+    };
+    kstring_t rg = {0};
+
+    static const struct option lopts[] = {
+        SAM_OPT_GLOBAL_OPTIONS('-', 0, 'O', 0, '-', '@'),
+        {"no-PG", no_argument, NULL, 9},
+        {"i1", required_argument, NULL, 1},
+        {"i2", required_argument, NULL, 2},
+        {"r1", required_argument, NULL, '1'},
+        {"r2", required_argument, NULL, '2'},
+        {"rg", required_argument, NULL, 'R'},
+        {"rg-line", required_argument, NULL, 'r'},
+        {"order", required_argument, NULL, 3},
+        {"barcode-tag", required_argument, NULL, 4},
+        {"quality-tag", required_argument, NULL, 5},
+        {"name2", no_argument, NULL, 'N'},
+        { NULL, 0, NULL, 0 }
+    };
+
+    while ((c = getopt_long(argc, argv, "1:2:s:0:bhiT:r:R:o:O:u@:N", lopts, NULL)) >= 0) {
+        switch (c) {
+        case 'b': opts.idx_both = 1; break;
+        case '0': opts.fn[FQ_R0] = optarg; break;
+        case '1': opts.fn[FQ_R1] = optarg; break;
+        case '2': opts.fn[FQ_R2] = optarg; break;
+        case  1:  opts.fn[FQ_I1] = optarg; break;
+        case  2:  opts.fn[FQ_I2] = optarg; break;
+        case 's': opts.fn[FQ_SINGLE] = optarg; break;
+        case 'o': opts.fn_out = optarg; break;
+        case 'i': opts.casava = 1; break;
+        case  4:  opts.barcode_seq = optarg; break;
+        case  5:  opts.barcode_qual = optarg; break;
+        case 'T': opts.aux = optarg; break;
+        case 'u': opts.compress_level = 0; break;
+        case 'R': opts.rg = optarg; break;
+        case 'r':
+            if (*optarg != '@' && ks_len(&rg) == 0)
+                kputs("@RG", &rg);
+            if (ks_len(&rg))
+                kputc_('\t', &rg);
+            kputs(optarg, &rg);
+            opts.rg_line = rg.s;
+            break;
+
+        case 'N': opts.name2 = 1; break;
+
+        case 9: opts.no_pg = 1; break;
+        case 3: opts.order = optarg; break;
+
+        case 'h': return usage(stdout, EXIT_SUCCESS);
+        case '?': return usage(stderr, EXIT_FAILURE);
+
+        default:
+            if (parse_sam_global_opt(c, optarg, lopts, &opts.ga) != 0)
+                return usage(stderr, EXIT_FAILURE);
+            break;
+        }
+    }
+
+    if (opts.ga.nthreads > 0) {
+        if (!(opts.p.pool = hts_tpool_init(opts.ga.nthreads))) {
+            fprintf(stderr, "Failed to create thread pool\n");
+            if (rg.s)
+                free(rg.s);
+            return -1;;
+        }
+    }
+
+    int ret = import_fastq(argc-optind, argv+optind, &opts) ? 1 : 0;
+
+    if (rg.s)
+        free(rg.s);
+
+    if (opts.p.pool)
+        hts_tpool_destroy(opts.p.pool);
+
+    return ret;
+}
diff --git a/samtools/bam_import.c.pysam.c b/samtools/bam_import.c.pysam.c
new file mode 100644
index 0000000..76b61a4
--- /dev/null
+++ b/samtools/bam_import.c.pysam.c
@@ -0,0 +1,505 @@
+#include "samtools.pysam.h"
+
+/* bam_import -- Import of FASTQ files.
+ *
+ *   samtools import -1 a_1.fq -2 a_2.fq --i1 a_i1.fq --i2 a_i2.fq
+ *   samtools import a_1.fq a_2.fq
+ *   samtools import a_interleaved.fq
+ *
+ * Copyright (C) 2020 Genome Research Ltd.
+ *
+ * Author: James Bonfield <jkb@sanger.ac.uk>
+ */
+
+/*
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notices and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.
+*/
+
+// TODO: Store other non-aux comments; in new sam tag?
+
+#include <config.h>
+#include <ctype.h>
+
+#include "htslib/sam.h"
+#include "htslib/thread_pool.h"
+
+#include "samtools.h"
+#include "sam_opts.h"
+
+static int usage(FILE *fp, int exit_status) {
+    fprintf(fp, "Usage: samtools import [options] [file.fastq ...]\n");
+    fprintf(fp, "\n");
+    fprintf(fp, "Options:\n");
+    fprintf(fp, "  -s FILE      Read paired-ended data from single FILE\n");
+    fprintf(fp, "  -0 FILE      Read single-ended data from FILE\n");
+    fprintf(fp, "  -1 FILE      Read-1 from FILE\n");
+    fprintf(fp, "  -2 FILE      Read-2 from FILE\n");
+    fprintf(fp, "  --i1 FILE    Index-1 from FILE\n");
+    fprintf(fp, "  --i2 FILE    Index-2 from FILE\n");
+    fprintf(fp, "  -i           Parse CASAVA identifier\n");
+    fprintf(fp, "  --barcode-tag TAG\n");
+    fprintf(fp, "               Tag to use with barcode sequences [BC]\n");
+    fprintf(fp, "  --quality-tag TAG\n");
+    fprintf(fp, "               Tag to use with barcode qualities [QT]\n");
+    fprintf(fp, "  -N, --name2  Use 2nd field as read name (SRA format)\n");
+    fprintf(fp, "  -r STRING    Build up a complete @RG line\n");
+    fprintf(fp, "  -R STRING    Add a simple RG line of \"@RG\\tID:STRING\"\n");
+    fprintf(fp, "  -T TAGLIST   Parse tags in SAM format; list of '*' for all\n");
+    fprintf(fp, "  -o FILE      Output to FILE instead of samtools_stdout\n");
+    fprintf(fp, "  -u           Uncompressed output\n");
+    fprintf(fp, "  --order TAG  Store Nth record count in TAG\n");
+    fprintf(fp, "\n");
+    sam_global_opt_help(fp, "-.O.-@--");
+
+    fprintf(fp, "\nA single fastq file will be interpreted as -s, -0 or -1 depending on\n");
+    fprintf(fp, "file contents, and a pair of fastq files as \"-1 FILE1 -2 FILE2\".\n");
+
+    return exit_status;
+}
+
+// Order matters here as we want to read index elements before main
+// sequences so on reading the seqs we can emit a fully annotated record.
+enum fileno {
+    FQ_I1, FQ_I2, // index seqs for R1 and R2
+    FQ_R0,        // single file and unpaired data (singled-ended tech).
+    FQ_R1, FQ_R2, // separate read1 and read2 files
+    FQ_SINGLE,    // single file, but with read1 and/or read2 present.
+    FQ_END
+};
+
+typedef struct {
+    sam_global_args ga;
+    int no_pg;
+    char *fn[FQ_END], *fn_out;
+    int idx_both;      // add index to READ2 too, not just READ1
+    int casava;
+    char *barcode_seq;
+    char *barcode_qual;
+    char *aux;
+    char *rg;
+    char *rg_line;
+    char *order;
+    int compress_level;
+    htsThreadPool p;
+    int name2;
+} opts_t;
+
+// Append a sequence and quality string from a BAM record to a BC:Z and
+// QT:Z style aux tag string.
+static int append_index(kstring_t *s, kstring_t *q, bam1_t *b) {
+    char *sp, *qp;
+    if (ks_resize(s, s->l + b->core.l_qseq+1 +1) < 0)
+        return -1;
+    if (ks_resize(q, q->l + b->core.l_qseq+1 +1) < 0)
+        return -1;
+
+    sp = s->s + s->l - (s->l > 0);
+    qp = q->s + q->l - (q->l > 0);
+
+    if (s->l)
+        *sp++ = '-';
+
+    if (q->l)
+        *qp++ = ' ';
+
+    int i;
+    uint8_t *seq = bam_get_seq(b);
+    uint8_t *qual = bam_get_qual(b);
+    for (i = 0; i < b->core.l_qseq; i++) {
+        *sp++ = seq_nt16_str[bam_seqi(seq, i)];
+        *qp++ = qual[i] + '!';
+    }
+    *sp++ = 0;
+    *qp++ = 0;
+
+    s->l = sp - s->s;
+    q->l = qp - q->s;
+
+    return 0;
+}
+
+static int import_fastq(int argc, char **argv, opts_t *opts) {
+    int i, n, ret = 0;
+    samFile *fp_in[FQ_END] = {NULL};
+    bam1_t *b = bam_init1();
+    int ids[FQ_END];
+    samFile *fp_out = NULL;
+    sam_hdr_t *hdr_out = NULL;
+    kstring_t index_str = {0,0};
+    kstring_t read_str = {0,0};
+    char *rg = opts->rg;
+    kstring_t rg_line = {0,0};
+    uint64_t read_num = 0;
+    kstring_t idx_seq  = {0};
+    kstring_t idx_qual = {0};
+
+    // Any additional arguments are assumed to be r1 r2, as a
+    // short cut. We support reading index tags out of those too (eg
+    // Illumina CASAVA format), but if we do that we lack the barcode
+    // quality string.
+    //
+    // We also consider a read name ending in /1 or /2 to be a single
+    // file containing interleaved fastq records for both ends.
+    // These will be labeled as fn[FQ_R1] but adjusted during reading.
+    if (argc == 1)
+        opts->fn[FQ_SINGLE] = argv[0];
+    else
+        for (i = 0; i < 4; i++)
+            if (argc > i)
+                opts->fn[FQ_R1+i] = argv[i];
+
+    // Open all files
+    for (i = n = 0; i < FQ_END; i++) {
+        if (!opts->fn[i])
+            continue;
+        fp_in[i] = sam_open_format(opts->fn[i], "r", &opts->ga.in);
+        if (!fp_in[i]) {
+            perror(opts->fn[i]);
+            ret = -1;
+            goto err;
+        }
+        if (opts->p.pool)
+            hts_set_thread_pool(fp_in[i], &opts->p);
+        ids[n++] = i;
+
+        if (opts->name2)
+            hts_set_opt(fp_in[i], FASTQ_OPT_NAME2, 1);
+        if (opts->casava)
+            hts_set_opt(fp_in[i], FASTQ_OPT_CASAVA, 1);
+        if (opts->barcode_seq) // for auto-CASAVA parsing
+            hts_set_opt(fp_in[i], FASTQ_OPT_BARCODE, opts->barcode_seq);
+        if (opts->aux)
+            hts_set_opt(fp_in[i], FASTQ_OPT_AUX,
+                        *opts->aux == '*' || *opts->aux == '\0'
+                        ? NULL : opts->aux);
+
+        switch (i) {
+        case FQ_I1:
+            kputs("--i1 I1.fastq ", &read_str);
+            kputs("i*", &index_str);
+            break;
+        case FQ_I2:
+            kputs("--i2 I2.fastq ", &read_str);
+            kputs("i*", &index_str);
+            break;
+
+        case FQ_R0:
+            kputs("-0 unpaired.fastq ", &read_str);
+            break;
+
+        case FQ_R1:
+            kputs("-1 R1.fastq ", &read_str);
+            break;
+
+        case FQ_R2:
+            kputs("-2 R2.fastq ", &read_str);
+            break;
+
+        case FQ_SINGLE:
+            kputs("-N -o paired.fastq ", &read_str);
+            break;
+
+        default:
+            ks_clear(&read_str); // not reversible
+            kputs("", &read_str);
+        }
+    }
+    if (n == 0) {
+        bam_destroy1(b);
+        return usage(samtools_stdout, EXIT_SUCCESS);
+    }
+
+    char out_mode[10] = {'w', 0, 0};
+    if (opts->compress_level != -1)
+        out_mode[1] = '0' + opts->compress_level;
+    sam_open_mode(out_mode+strlen(out_mode), opts->fn_out, NULL);
+    fp_out = sam_open_format(opts->fn_out, out_mode, &opts->ga.out);
+    if (!fp_out) {
+        perror(opts->fn_out);
+        goto err;
+    }
+    autoflush_if_stdout(fp_out, opts->fn_out);
+    if (opts->p.pool)
+        hts_set_thread_pool(fp_out, &opts->p);
+
+    // Create header
+    if (ks_len(&read_str)) {
+        char CO[2100];
+        if (ks_len(&index_str))
+            snprintf(CO, sizeof(CO), "@CO\tReverse with: samtools fastq %s "
+                    "--index-format=\"%s\"\n",
+                    ks_str(&read_str), ks_str(&index_str));
+        else
+            snprintf(CO, sizeof(CO), "@CO\tReverse with: samtools fastq %s\n",
+                    ks_str(&read_str));
+
+        hdr_out = sam_hdr_parse(strlen(CO), CO);
+    } else {
+        hdr_out = sam_hdr_init();
+    }
+
+    // Add a version line with the sort order to the output header
+    if (sam_hdr_add_line(hdr_out, "HD", "VN", SAM_FORMAT_VERSION, "SO", "unsorted", "GO", "query", NULL) < 0) {
+        fprintf(samtools_stderr, "Could not set SO and GO in the header.\n");
+        goto err;
+    }
+
+    // Read group
+    if (opts->rg_line) {
+        if (*opts->rg_line != '@')
+            ksprintf(&rg_line, "@RG\t%s", opts->rg_line);
+        else
+            kputs(opts->rg_line, &rg_line);
+    } else if (opts->rg) {
+        ksprintf(&rg_line, "@RG\tID:%s", opts->rg);
+    }
+
+    if (ks_len(&rg_line)) {
+        if (sam_hdr_add_lines(hdr_out, ks_str(&rg_line), 0) < 0)
+            goto err;
+        rg = strstr(ks_str(&rg_line), "\tID:");
+        if (!rg) {
+            fprintf(samtools_stderr, "\"-r RG-LINE\" option contained no ID field\n");
+            goto err;
+        }
+        rg += 4;
+
+        i = 0;
+        while (rg[i] != '\t' && rg[i] != '\0')
+            i++;
+        rg[i] = 0;
+    }
+
+    if ((ret = sam_hdr_write(fp_out, hdr_out)) < 0)
+        goto err;
+
+
+    // Interleave / combine from n files (ids[0..n-1]).
+    int res;
+    int eof = 0;
+    do {
+        idx_seq.l = idx_qual.l = 0;
+        for (i = 0; i < n; i++) {
+            if ((res = sam_read1(fp_in[ids[i]], NULL, b)) < 0) {
+                if (res == -1) {
+                    eof++;
+                    continue;
+                } else
+                    break;
+            }
+
+            // index
+            if (ids[i] == FQ_I1 || ids[i] == FQ_I2) {
+                if (append_index(&idx_seq, &idx_qual, b) < 0) {
+                    res = -1;
+                    break;
+                }
+                continue;
+            }
+
+            // full read
+            if (idx_seq.l) {
+                if (opts->idx_both || ids[i] == FQ_SINGLE ||
+                    ids[i] == FQ_R0 || ids[i] == FQ_R1) {
+                    if (bam_aux_append(b, opts->barcode_seq, 'Z', idx_seq.l,
+                                       (uint8_t *)idx_seq.s) ||
+                        bam_aux_append(b, opts->barcode_qual, 'Z', idx_qual.l,
+                                       (uint8_t *)idx_qual.s)) {
+                        res = -1;
+                        break;
+                    }
+                }
+            }
+
+            switch(ids[i]) {
+            case FQ_R0:
+                // unpaired; no flags to declare
+                break;
+            case FQ_SINGLE:
+                // paired (but don't know if R1 or R2) or unpaired.
+                // We rely on the /1 and /2 read suffix parsing in htslib
+                // to distinguish the two cases, or CASAVA tags if
+                // explicitly enabled.
+                break;
+            case FQ_R1:
+                if ((b->core.flag & (BAM_FREAD1 | BAM_FREAD2)) == 0)
+                    b->core.flag |= BAM_FREAD1;
+                b->core.flag |= BAM_FPAIRED;
+                if (i+1 < n && ids[i+1] == FQ_R2)
+                    b->core.flag |= BAM_FMUNMAP;
+                break;
+            case FQ_R2:
+                b->core.flag |= BAM_FPAIRED | BAM_FREAD2;
+                if (i > 0 && ids[i-1] == FQ_R1)
+                    b->core.flag |= BAM_FMUNMAP;
+                break;
+            }
+
+            if (rg) {
+                if (bam_aux_append(b, "RG", 'Z', strlen(rg)+1,
+                                   (uint8_t *)rg) < 0) {
+                    ret = -1;
+                    goto err;
+                }
+            }
+
+            if (opts->order) {
+                if (bam_aux_update_int(b, opts->order, read_num++) < 0) {
+                    ret = -1;
+                    goto err;
+                }
+            }
+
+            res = sam_write1(fp_out, hdr_out, b);
+        }
+    } while (res >= 0);
+
+    if (res != -1) {
+        print_error("import", "truncated file. Aborting");
+        ret = res;
+        goto err;
+    }
+
+    if (eof != n) {
+        print_error("import", "input files with differing number of records");
+        ret = -1;
+        goto err;
+    }
+
+    // Close and return
+    ret = 0;
+err:
+    bam_destroy1(b);
+    sam_hdr_destroy(hdr_out);
+    ks_free(&rg_line);
+    ks_free(&index_str);
+    ks_free(&read_str);
+    if (fp_out) {
+        release_autoflush(fp_out);
+        if (sam_close(fp_out) < 0) {
+            perror(opts->fn_out);
+            ret |= -1;
+        }
+    }
+    for (i = 0; i < FQ_END; i++) {
+        if (fp_in[i] && sam_close(fp_in[i]) < 0) {
+            perror(opts->fn[i]);
+            ret |= -1;
+        }
+    }
+    ks_free(&idx_seq);
+    ks_free(&idx_qual);
+
+    return ret;
+}
+
+int main_import(int argc, char *argv[]) {
+    int c;
+    opts_t opts = {
+        .no_pg = 0,
+        .ga = SAM_GLOBAL_ARGS_INIT,
+        .fn = {NULL},
+        .fn_out = "-",
+        .casava = 0,
+        .barcode_seq = "BC",
+        .barcode_qual = "QT",
+        .aux = NULL,
+        .rg = NULL,
+        .rg_line = NULL,
+        .order = NULL,
+        .compress_level = -1,
+        .name2 = 0,
+    };
+    kstring_t rg = {0};
+
+    static const struct option lopts[] = {
+        SAM_OPT_GLOBAL_OPTIONS('-', 0, 'O', 0, '-', '@'),
+        {"no-PG", no_argument, NULL, 9},
+        {"i1", required_argument, NULL, 1},
+        {"i2", required_argument, NULL, 2},
+        {"r1", required_argument, NULL, '1'},
+        {"r2", required_argument, NULL, '2'},
+        {"rg", required_argument, NULL, 'R'},
+        {"rg-line", required_argument, NULL, 'r'},
+        {"order", required_argument, NULL, 3},
+        {"barcode-tag", required_argument, NULL, 4},
+        {"quality-tag", required_argument, NULL, 5},
+        {"name2", no_argument, NULL, 'N'},
+        { NULL, 0, NULL, 0 }
+    };
+
+    while ((c = getopt_long(argc, argv, "1:2:s:0:bhiT:r:R:o:O:u@:N", lopts, NULL)) >= 0) {
+        switch (c) {
+        case 'b': opts.idx_both = 1; break;
+        case '0': opts.fn[FQ_R0] = optarg; break;
+        case '1': opts.fn[FQ_R1] = optarg; break;
+        case '2': opts.fn[FQ_R2] = optarg; break;
+        case  1:  opts.fn[FQ_I1] = optarg; break;
+        case  2:  opts.fn[FQ_I2] = optarg; break;
+        case 's': opts.fn[FQ_SINGLE] = optarg; break;
+        case 'o': opts.fn_out = optarg; break;
+        case 'i': opts.casava = 1; break;
+        case  4:  opts.barcode_seq = optarg; break;
+        case  5:  opts.barcode_qual = optarg; break;
+        case 'T': opts.aux = optarg; break;
+        case 'u': opts.compress_level = 0; break;
+        case 'R': opts.rg = optarg; break;
+        case 'r':
+            if (*optarg != '@' && ks_len(&rg) == 0)
+                kputs("@RG", &rg);
+            if (ks_len(&rg))
+                kputc_('\t', &rg);
+            kputs(optarg, &rg);
+            opts.rg_line = rg.s;
+            break;
+
+        case 'N': opts.name2 = 1; break;
+
+        case 9: opts.no_pg = 1; break;
+        case 3: opts.order = optarg; break;
+
+        case 'h': return usage(samtools_stdout, EXIT_SUCCESS);
+        case '?': return usage(samtools_stderr, EXIT_FAILURE);
+
+        default:
+            if (parse_sam_global_opt(c, optarg, lopts, &opts.ga) != 0)
+                return usage(samtools_stderr, EXIT_FAILURE);
+            break;
+        }
+    }
+
+    if (opts.ga.nthreads > 0) {
+        if (!(opts.p.pool = hts_tpool_init(opts.ga.nthreads))) {
+            fprintf(samtools_stderr, "Failed to create thread pool\n");
+            if (rg.s)
+                free(rg.s);
+            return -1;;
+        }
+    }
+
+    int ret = import_fastq(argc-optind, argv+optind, &opts) ? 1 : 0;
+
+    if (rg.s)
+        free(rg.s);
+
+    if (opts.p.pool)
+        hts_tpool_destroy(opts.p.pool);
+
+    return ret;
+}
diff --git a/samtools/bam_index.c b/samtools/bam_index.c
new file mode 100644
index 0000000..f7c3358
--- /dev/null
+++ b/samtools/bam_index.c
@@ -0,0 +1,280 @@
+/*  bam_index.c -- index and idxstats subcommands.
+
+    Copyright (C) 2008-2011, 2013-2016, 2018, 2019  Genome Research Ltd.
+    Portions copyright (C) 2010 Broad Institute.
+    Portions copyright (C) 2013 Peter Cock, The James Hutton Institute.
+
+    Author: Heng Li <lh3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notices and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <config.h>
+
+#include <htslib/hts.h>
+#include <htslib/sam.h>
+#include <htslib/hfile.h>
+#include <htslib/khash.h>
+#include <stdlib.h>
+#include <stdio.h>
+#include <inttypes.h>
+#include <unistd.h>
+#include <getopt.h>
+
+#include "samtools.h"
+#include "sam_opts.h"
+
+#define BAM_LIDX_SHIFT    14
+
+static void index_usage(FILE *fp)
+{
+    fprintf(fp,
+"Usage: samtools index -M [-bc] [-m INT] <in1.bam> <in2.bam>...\n"
+"   or: samtools index [-bc] [-m INT] <in.bam> [out.index]\n"
+"Options:\n"
+"  -b       Generate BAI-format index for BAM files [default]\n"
+"  -c       Generate CSI-format index for BAM files\n"
+"  -m INT   Set minimum interval size for CSI indices to 2^INT [%d]\n"
+"  -M       Interpret all filename arguments as files to be indexed\n"
+"  -o FILE  Write index to FILE [alternative to <out.index> as an argument]\n"
+"  -@ INT   Sets the number of threads [none]\n", BAM_LIDX_SHIFT);
+}
+
+// Returns 1 if the file does not exist or can be positively
+// identified as an index file.
+static int nonexistent_or_index(const char *fn)
+{
+    int ret1, ret2;
+    htsFormat fmt;
+    hFILE *fp = hopen(fn, "r");
+    if (fp == NULL) return 1;
+
+    ret1 = hts_detect_format2(fp, fn, &fmt);
+    ret2 = hclose(fp);
+    if (ret1 < 0 || ret2 < 0) return 0;
+
+    return fmt.category == index_file;
+}
+
+int bam_index(int argc, char *argv[])
+{
+    int csi = 0;
+    int min_shift = BAM_LIDX_SHIFT;
+    int multiple = 0;
+    int n_threads = 0;
+    int n_files, c, i, ret;
+    const char *fn_idx = NULL;
+
+    while ((c = getopt(argc, argv, "bcm:Mo:@:")) >= 0)
+        switch (c) {
+        case 'b': csi = 0; break;
+        case 'c': csi = 1; break;
+        case 'm': csi = 1; min_shift = atoi(optarg); break;
+        case 'M': multiple = 1; break;
+        case 'o': fn_idx = optarg; break;
+        case '@': n_threads = atoi(optarg); break;
+        default:
+            index_usage(stderr);
+            return 1;
+        }
+
+    n_files = argc - optind;
+
+    if (n_files == 0) {
+        index_usage(stdout);
+        return 0;
+    }
+
+    // Handle legacy synopsis
+    if (n_files == 2 && !fn_idx && nonexistent_or_index(argv[optind+1])) {
+        n_files = 1;
+        fn_idx = argv[optind+1];
+    }
+
+    if (n_files > 1 && !multiple) {
+        print_error("index", "use -M to enable indexing more than one alignment file");
+        return EXIT_FAILURE;
+    }
+
+    if (fn_idx && n_files > 1) {
+        // TODO In future we may allow %* placeholders or similar
+        print_error("index", "can't use -o with multiple input alignment files");
+        return EXIT_FAILURE;
+    }
+
+    for (i = optind; i < optind + n_files; i++) {
+        ret = sam_index_build3(argv[i], fn_idx, csi? min_shift : 0, n_threads);
+        if (ret < 0) {
+            if (ret == -2)
+                print_error_errno("index", "failed to open \"%s\"", argv[i]);
+            else if (ret == -3)
+                print_error("index", "\"%s\" is in a format that cannot be usefully indexed", argv[i]);
+            else if (ret == -4 && fn_idx)
+                print_error("index", "failed to create or write index \"%s\"", fn_idx);
+            else if (ret == -4)
+                print_error("index", "failed to create or write index");
+            else
+                print_error_errno("index", "failed to create index for \"%s\"", argv[i]);
+            return EXIT_FAILURE;
+        }
+    }
+
+    return EXIT_SUCCESS;
+}
+
+/*
+ * Cram indices do not contain mapped/unmapped record counts, so we have to
+ * decode each record and count.  However we can speed this up as much as
+ * possible by using the required fields parameter.
+ *
+ * This prints the stats to stdout in the same manner than the BAM function
+ * does.
+ *
+ * Returns 0 on success,
+ *        -1 on failure.
+ */
+int slow_idxstats(samFile *fp, sam_hdr_t *header) {
+    int ret, last_tid = -2;
+    bam1_t *b = bam_init1();
+
+    if (hts_set_opt(fp, CRAM_OPT_REQUIRED_FIELDS, SAM_RNAME | SAM_FLAG))
+        return -1;
+
+    uint64_t (*count0)[2] = calloc(sam_hdr_nref(header)+1, sizeof(*count0));
+    uint64_t (*counts)[2] = count0+1;
+    if (!count0)
+        return -1;
+
+    while ((ret = sam_read1(fp, header, b)) >= 0) {
+        if (b->core.tid >= sam_hdr_nref(header) || b->core.tid < -1) {
+            free(count0);
+            return -1;
+        }
+
+        if (b->core.tid != last_tid) {
+            if (last_tid >= -1) {
+                if (counts[b->core.tid][0] + counts[b->core.tid][1]) {
+                    print_error("idxstats", "file is not position sorted");
+                    free(count0);
+                    return -1;
+                }
+            }
+            last_tid = b->core.tid;
+        }
+
+        counts[b->core.tid][(b->core.flag & BAM_FUNMAP) ? 1 : 0]++;
+    }
+
+    if (ret == -1) {
+        int i;
+        for (i = 0; i < sam_hdr_nref(header); i++) {
+            printf("%s\t%"PRId64"\t%"PRIu64"\t%"PRIu64"\n",
+                   sam_hdr_tid2name(header, i),
+                   (int64_t) sam_hdr_tid2len(header, i),
+                   counts[i][0], counts[i][1]);
+        }
+        printf("*\t0\t%"PRIu64"\t%"PRIu64"\n", counts[-1][0], counts[-1][1]);
+    }
+
+    free(count0);
+
+    bam_destroy1(b);
+
+    return (ret == -1) ? 0 : -1;
+}
+
+static void usage_exit(FILE *fp, int exit_status)
+{
+    fprintf(fp, "Usage: samtools idxstats [options] <in.bam>\n");
+    sam_global_opt_help(fp, "-.---@-.");
+    exit(exit_status);
+}
+
+int bam_idxstats(int argc, char *argv[])
+{
+    hts_idx_t* idx;
+    sam_hdr_t* header;
+    samFile* fp;
+    int c;
+
+    sam_global_args ga = SAM_GLOBAL_ARGS_INIT;
+    static const struct option lopts[] = {
+        SAM_OPT_GLOBAL_OPTIONS('-', 0, '-', '-', '-', '@'),
+        {NULL, 0, NULL, 0}
+    };
+
+    while ((c = getopt_long(argc, argv, "@:", lopts, NULL)) >= 0) {
+        switch (c) {
+        default:  if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break;
+            /* else fall-through */
+        case '?':
+            usage_exit(stderr, EXIT_FAILURE);
+        }
+    }
+
+    if (argc != optind+1) {
+        if (argc == optind) usage_exit(stdout, EXIT_SUCCESS);
+        else usage_exit(stderr, EXIT_FAILURE);
+    }
+
+    fp = sam_open_format(argv[optind], "r", &ga.in);
+    if (fp == NULL) {
+        print_error_errno("idxstats", "failed to open \"%s\"", argv[optind]);
+        return 1;
+    }
+    header = sam_hdr_read(fp);
+    if (header == NULL) {
+        print_error("idxstats", "failed to read header for \"%s\"", argv[optind]);
+        return 1;
+    }
+
+    if (hts_get_format(fp)->format != bam) {
+    slow_method:
+        if (ga.nthreads)
+            hts_set_threads(fp, ga.nthreads);
+
+        if (slow_idxstats(fp, header) < 0) {
+            print_error("idxstats", "failed to process \"%s\"", argv[optind]);
+            return 1;
+        }
+    } else {
+        idx = sam_index_load(fp, argv[optind]);
+        if (idx == NULL) {
+            print_error("idxstats", "fail to load index for \"%s\", "
+                        "reverting to slow method", argv[optind]);
+            goto slow_method;
+        }
+
+        int i;
+        for (i = 0; i < sam_hdr_nref(header); ++i) {
+            // Print out contig name and length
+            printf("%s\t%"PRId64, sam_hdr_tid2name(header, i), (int64_t) sam_hdr_tid2len(header, i));
+            // Now fetch info about it from the meta bin
+            uint64_t u, v;
+            hts_idx_get_stat(idx, i, &u, &v);
+            printf("\t%" PRIu64 "\t%" PRIu64 "\n", u, v);
+        }
+        // Dump information about unmapped reads
+        printf("*\t0\t0\t%" PRIu64 "\n", hts_idx_get_n_no_coor(idx));
+        hts_idx_destroy(idx);
+    }
+
+    sam_hdr_destroy(header);
+    sam_close(fp);
+    return 0;
+}
diff --git a/samtools/bam_index.c.pysam.c b/samtools/bam_index.c.pysam.c
new file mode 100644
index 0000000..6627cfa
--- /dev/null
+++ b/samtools/bam_index.c.pysam.c
@@ -0,0 +1,282 @@
+#include "samtools.pysam.h"
+
+/*  bam_index.c -- index and idxstats subcommands.
+
+    Copyright (C) 2008-2011, 2013-2016, 2018, 2019  Genome Research Ltd.
+    Portions copyright (C) 2010 Broad Institute.
+    Portions copyright (C) 2013 Peter Cock, The James Hutton Institute.
+
+    Author: Heng Li <lh3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notices and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <config.h>
+
+#include <htslib/hts.h>
+#include <htslib/sam.h>
+#include <htslib/hfile.h>
+#include <htslib/khash.h>
+#include <stdlib.h>
+#include <stdio.h>
+#include <inttypes.h>
+#include <unistd.h>
+#include <getopt.h>
+
+#include "samtools.h"
+#include "sam_opts.h"
+
+#define BAM_LIDX_SHIFT    14
+
+static void index_usage(FILE *fp)
+{
+    fprintf(fp,
+"Usage: samtools index -M [-bc] [-m INT] <in1.bam> <in2.bam>...\n"
+"   or: samtools index [-bc] [-m INT] <in.bam> [out.index]\n"
+"Options:\n"
+"  -b       Generate BAI-format index for BAM files [default]\n"
+"  -c       Generate CSI-format index for BAM files\n"
+"  -m INT   Set minimum interval size for CSI indices to 2^INT [%d]\n"
+"  -M       Interpret all filename arguments as files to be indexed\n"
+"  -o FILE  Write index to FILE [alternative to <out.index> as an argument]\n"
+"  -@ INT   Sets the number of threads [none]\n", BAM_LIDX_SHIFT);
+}
+
+// Returns 1 if the file does not exist or can be positively
+// identified as an index file.
+static int nonexistent_or_index(const char *fn)
+{
+    int ret1, ret2;
+    htsFormat fmt;
+    hFILE *fp = hopen(fn, "r");
+    if (fp == NULL) return 1;
+
+    ret1 = hts_detect_format2(fp, fn, &fmt);
+    ret2 = hclose(fp);
+    if (ret1 < 0 || ret2 < 0) return 0;
+
+    return fmt.category == index_file;
+}
+
+int bam_index(int argc, char *argv[])
+{
+    int csi = 0;
+    int min_shift = BAM_LIDX_SHIFT;
+    int multiple = 0;
+    int n_threads = 0;
+    int n_files, c, i, ret;
+    const char *fn_idx = NULL;
+
+    while ((c = getopt(argc, argv, "bcm:Mo:@:")) >= 0)
+        switch (c) {
+        case 'b': csi = 0; break;
+        case 'c': csi = 1; break;
+        case 'm': csi = 1; min_shift = atoi(optarg); break;
+        case 'M': multiple = 1; break;
+        case 'o': fn_idx = optarg; break;
+        case '@': n_threads = atoi(optarg); break;
+        default:
+            index_usage(samtools_stderr);
+            return 1;
+        }
+
+    n_files = argc - optind;
+
+    if (n_files == 0) {
+        index_usage(samtools_stdout);
+        return 0;
+    }
+
+    // Handle legacy synopsis
+    if (n_files == 2 && !fn_idx && nonexistent_or_index(argv[optind+1])) {
+        n_files = 1;
+        fn_idx = argv[optind+1];
+    }
+
+    if (n_files > 1 && !multiple) {
+        print_error("index", "use -M to enable indexing more than one alignment file");
+        return EXIT_FAILURE;
+    }
+
+    if (fn_idx && n_files > 1) {
+        // TODO In future we may allow %* placeholders or similar
+        print_error("index", "can't use -o with multiple input alignment files");
+        return EXIT_FAILURE;
+    }
+
+    for (i = optind; i < optind + n_files; i++) {
+        ret = sam_index_build3(argv[i], fn_idx, csi? min_shift : 0, n_threads);
+        if (ret < 0) {
+            if (ret == -2)
+                print_error_errno("index", "failed to open \"%s\"", argv[i]);
+            else if (ret == -3)
+                print_error("index", "\"%s\" is in a format that cannot be usefully indexed", argv[i]);
+            else if (ret == -4 && fn_idx)
+                print_error("index", "failed to create or write index \"%s\"", fn_idx);
+            else if (ret == -4)
+                print_error("index", "failed to create or write index");
+            else
+                print_error_errno("index", "failed to create index for \"%s\"", argv[i]);
+            return EXIT_FAILURE;
+        }
+    }
+
+    return EXIT_SUCCESS;
+}
+
+/*
+ * Cram indices do not contain mapped/unmapped record counts, so we have to
+ * decode each record and count.  However we can speed this up as much as
+ * possible by using the required fields parameter.
+ *
+ * This prints the stats to samtools_stdout in the same manner than the BAM function
+ * does.
+ *
+ * Returns 0 on success,
+ *        -1 on failure.
+ */
+int slow_idxstats(samFile *fp, sam_hdr_t *header) {
+    int ret, last_tid = -2;
+    bam1_t *b = bam_init1();
+
+    if (hts_set_opt(fp, CRAM_OPT_REQUIRED_FIELDS, SAM_RNAME | SAM_FLAG))
+        return -1;
+
+    uint64_t (*count0)[2] = calloc(sam_hdr_nref(header)+1, sizeof(*count0));
+    uint64_t (*counts)[2] = count0+1;
+    if (!count0)
+        return -1;
+
+    while ((ret = sam_read1(fp, header, b)) >= 0) {
+        if (b->core.tid >= sam_hdr_nref(header) || b->core.tid < -1) {
+            free(count0);
+            return -1;
+        }
+
+        if (b->core.tid != last_tid) {
+            if (last_tid >= -1) {
+                if (counts[b->core.tid][0] + counts[b->core.tid][1]) {
+                    print_error("idxstats", "file is not position sorted");
+                    free(count0);
+                    return -1;
+                }
+            }
+            last_tid = b->core.tid;
+        }
+
+        counts[b->core.tid][(b->core.flag & BAM_FUNMAP) ? 1 : 0]++;
+    }
+
+    if (ret == -1) {
+        int i;
+        for (i = 0; i < sam_hdr_nref(header); i++) {
+            fprintf(samtools_stdout, "%s\t%"PRId64"\t%"PRIu64"\t%"PRIu64"\n",
+                   sam_hdr_tid2name(header, i),
+                   (int64_t) sam_hdr_tid2len(header, i),
+                   counts[i][0], counts[i][1]);
+        }
+        fprintf(samtools_stdout, "*\t0\t%"PRIu64"\t%"PRIu64"\n", counts[-1][0], counts[-1][1]);
+    }
+
+    free(count0);
+
+    bam_destroy1(b);
+
+    return (ret == -1) ? 0 : -1;
+}
+
+static void usage_exit(FILE *fp, int exit_status)
+{
+    fprintf(fp, "Usage: samtools idxstats [options] <in.bam>\n");
+    sam_global_opt_help(fp, "-.---@-.");
+    samtools_exit(exit_status);
+}
+
+int bam_idxstats(int argc, char *argv[])
+{
+    hts_idx_t* idx;
+    sam_hdr_t* header;
+    samFile* fp;
+    int c;
+
+    sam_global_args ga = SAM_GLOBAL_ARGS_INIT;
+    static const struct option lopts[] = {
+        SAM_OPT_GLOBAL_OPTIONS('-', 0, '-', '-', '-', '@'),
+        {NULL, 0, NULL, 0}
+    };
+
+    while ((c = getopt_long(argc, argv, "@:", lopts, NULL)) >= 0) {
+        switch (c) {
+        default:  if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break;
+            /* else fall-through */
+        case '?':
+            usage_exit(samtools_stderr, EXIT_FAILURE);
+        }
+    }
+
+    if (argc != optind+1) {
+        if (argc == optind) usage_exit(samtools_stdout, EXIT_SUCCESS);
+        else usage_exit(samtools_stderr, EXIT_FAILURE);
+    }
+
+    fp = sam_open_format(argv[optind], "r", &ga.in);
+    if (fp == NULL) {
+        print_error_errno("idxstats", "failed to open \"%s\"", argv[optind]);
+        return 1;
+    }
+    header = sam_hdr_read(fp);
+    if (header == NULL) {
+        print_error("idxstats", "failed to read header for \"%s\"", argv[optind]);
+        return 1;
+    }
+
+    if (hts_get_format(fp)->format != bam) {
+    slow_method:
+        if (ga.nthreads)
+            hts_set_threads(fp, ga.nthreads);
+
+        if (slow_idxstats(fp, header) < 0) {
+            print_error("idxstats", "failed to process \"%s\"", argv[optind]);
+            return 1;
+        }
+    } else {
+        idx = sam_index_load(fp, argv[optind]);
+        if (idx == NULL) {
+            print_error("idxstats", "fail to load index for \"%s\", "
+                        "reverting to slow method", argv[optind]);
+            goto slow_method;
+        }
+
+        int i;
+        for (i = 0; i < sam_hdr_nref(header); ++i) {
+            // Print out contig name and length
+            fprintf(samtools_stdout, "%s\t%"PRId64, sam_hdr_tid2name(header, i), (int64_t) sam_hdr_tid2len(header, i));
+            // Now fetch info about it from the meta bin
+            uint64_t u, v;
+            hts_idx_get_stat(idx, i, &u, &v);
+            fprintf(samtools_stdout, "\t%" PRIu64 "\t%" PRIu64 "\n", u, v);
+        }
+        // Dump information about unmapped reads
+        fprintf(samtools_stdout, "*\t0\t0\t%" PRIu64 "\n", hts_idx_get_n_no_coor(idx));
+        hts_idx_destroy(idx);
+    }
+
+    sam_hdr_destroy(header);
+    sam_close(fp);
+    return 0;
+}
diff --git a/samtools/bam_lpileup.c b/samtools/bam_lpileup.c
new file mode 100644
index 0000000..58c428f
--- /dev/null
+++ b/samtools/bam_lpileup.c
@@ -0,0 +1,225 @@
+/*  bam_lpileup.c -- lplbuf routines.
+
+    Copyright (C) 2008, 2009, 2013 Genome Research Ltd.
+
+    Author: Heng Li <lh3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <config.h>
+
+#include <stdlib.h>
+#include <stdio.h>
+#include <assert.h>
+#include "bam_plbuf.h"
+#include "bam_lpileup.h"
+#include "splaysort.h"
+
+#define TV_GAP 2
+
+typedef struct __freenode_t {
+    uint32_t level:28, cnt:4;
+    struct __freenode_t *next;
+} freenode_t, *freenode_p;
+
+#define freenode_lt(a,b) ((a)->cnt < (b)->cnt || ((a)->cnt == (b)->cnt && (a)->level < (b)->level))
+SPLAYSORT_INIT(node, freenode_p, freenode_lt)
+
+/* Memory pool, similar to the one in bam_pileup.c */
+typedef struct {
+    int cnt, n, max;
+    freenode_t **buf;
+} mempool_t;
+
+static mempool_t *mp_init(void)
+{
+    return (mempool_t*)calloc(1, sizeof(mempool_t));
+}
+static void mp_destroy(mempool_t *mp)
+{
+    int k;
+    for (k = 0; k < mp->n; ++k) free(mp->buf[k]);
+    free(mp->buf); free(mp);
+}
+static inline freenode_t *mp_alloc(mempool_t *mp)
+{
+    ++mp->cnt;
+    if (mp->n == 0) return (freenode_t*)calloc(1, sizeof(freenode_t));
+    else return mp->buf[--mp->n];
+}
+static inline void mp_free(mempool_t *mp, freenode_t *p)
+{
+    --mp->cnt; p->next = 0; p->cnt = TV_GAP;
+    if (mp->n == mp->max) {
+        mp->max = mp->max? mp->max<<1 : 256;
+        mp->buf = (freenode_t**)realloc(mp->buf, sizeof(freenode_t*) * mp->max);
+    }
+    mp->buf[mp->n++] = p;
+}
+
+/* core part */
+struct __bam_lplbuf_t {
+    int max, n_cur, n_pre;
+    int max_level, *cur_level, *pre_level;
+    mempool_t *mp;
+    freenode_t **aux, *head, *tail;
+    int n_nodes, m_aux;
+    bam_pileup_f func;
+    void *user_data;
+    bam_plbuf_t *plbuf;
+};
+
+void bam_lplbuf_reset(bam_lplbuf_t *buf)
+{
+    freenode_t *p, *q;
+    bam_plbuf_reset(buf->plbuf);
+    for (p = buf->head; p->next;) {
+        q = p->next;
+        mp_free(buf->mp, p);
+        p = q;
+    }
+    buf->head = buf->tail;
+    buf->max_level = 0;
+    buf->n_cur = buf->n_pre = 0;
+    buf->n_nodes = 0;
+}
+
+static int tview_func(uint32_t tid, hts_pos_t pos, int n, const bam_pileup1_t *pl, void *data)
+{
+    bam_lplbuf_t *tv = (bam_lplbuf_t*)data;
+    freenode_t *p;
+    int i, l, max_level;
+    // allocate memory if necessary
+    if (tv->max < n) { // enlarge
+        tv->max = n;
+        kroundup32(tv->max);
+        tv->cur_level = (int*)realloc(tv->cur_level, sizeof(int) * tv->max);
+        tv->pre_level = (int*)realloc(tv->pre_level, sizeof(int) * tv->max);
+    }
+    tv->n_cur = n;
+    // update cnt
+    for (p = tv->head; p->next; p = p->next)
+        if (p->cnt > 0) --p->cnt;
+    // calculate cur_level[]
+    max_level = 0;
+    for (i = l = 0; i < n; ++i) {
+        const bam_pileup1_t *p = pl + i;
+        if (p->is_head) {
+            if (tv->head->next && tv->head->cnt == 0) { // then take a free slot
+                freenode_t *p = tv->head->next;
+                tv->cur_level[i] = tv->head->level;
+                mp_free(tv->mp, tv->head);
+                tv->head = p;
+                --tv->n_nodes;
+            } else tv->cur_level[i] = ++tv->max_level;
+        } else {
+            tv->cur_level[i] = tv->pre_level[l++];
+            if (p->is_tail) { // then return a free slot
+                tv->tail->level = tv->cur_level[i];
+                tv->tail->next = mp_alloc(tv->mp);
+                tv->tail = tv->tail->next;
+                ++tv->n_nodes;
+            }
+        }
+        if (tv->cur_level[i] > max_level) max_level = tv->cur_level[i];
+        ((bam_pileup1_t*)p)->level = tv->cur_level[i];
+    }
+    assert(l == tv->n_pre);
+    tv->func(tid, pos, n, pl, tv->user_data);
+    // sort the linked list
+    if (tv->n_nodes) {
+        freenode_t *q;
+        if (tv->n_nodes + 1 > tv->m_aux) { // enlarge
+            tv->m_aux = tv->n_nodes + 1;
+            kroundup32(tv->m_aux);
+            tv->aux = (freenode_t**)realloc(tv->aux, sizeof(freenode_t*) * tv->m_aux);
+        }
+        for (p = tv->head, i = l = 0; p->next;) {
+            if (p->level > max_level) { // then discard this entry
+                q = p->next;
+                mp_free(tv->mp, p);
+                p = q;
+            } else {
+                tv->aux[i++] = p;
+                p = p->next;
+            }
+        }
+        tv->aux[i] = tv->tail; // add a proper tail for the loop below
+        tv->n_nodes = i;
+        if (tv->n_nodes) {
+            splaysort(node, tv->n_nodes, tv->aux);
+            for (i = 0; i < tv->n_nodes; ++i) tv->aux[i]->next = tv->aux[i+1];
+            tv->head = tv->aux[0];
+        } else tv->head = tv->tail;
+    }
+    // clean up
+    tv->max_level = max_level;
+    memcpy(tv->pre_level, tv->cur_level, tv->n_cur * 4);
+    // squeeze out terminated levels
+    for (i = l = 0; i < n; ++i) {
+        const bam_pileup1_t *p = pl + i;
+        if (!p->is_tail)
+            tv->pre_level[l++] = tv->pre_level[i];
+    }
+    tv->n_pre = l;
+/*
+    fprintf(stderr, "%d\t", pos+1);
+    for (i = 0; i < n; ++i) {
+        const bam_pileup1_t *p = pl + i;
+        if (p->is_head) fprintf(stderr, "^");
+        if (p->is_tail) fprintf(stderr, "$");
+        fprintf(stderr, "%d,", p->level);
+    }
+    fprintf(stderr, "\n");
+*/
+    return 0;
+}
+
+bam_lplbuf_t *bam_lplbuf_init(bam_pileup_f func, void *data)
+{
+    bam_lplbuf_t *tv;
+    tv = (bam_lplbuf_t*)calloc(1, sizeof(bam_lplbuf_t));
+    tv->mp = mp_init();
+    tv->head = tv->tail = mp_alloc(tv->mp);
+    tv->func = func;
+    tv->user_data = data;
+    tv->plbuf = bam_plbuf_init(tview_func, tv);
+    return (bam_lplbuf_t*)tv;
+}
+
+void bam_lplbuf_destroy(bam_lplbuf_t *tv)
+{
+    freenode_t *p, *q;
+    free(tv->cur_level); free(tv->pre_level);
+    bam_plbuf_destroy(tv->plbuf);
+    free(tv->aux);
+    for (p = tv->head; p->next;) {
+        q = p->next;
+        mp_free(tv->mp, p); p = q;
+    }
+    mp_free(tv->mp, p);
+    assert(tv->mp->cnt == 0);
+    mp_destroy(tv->mp);
+    free(tv);
+}
+
+int bam_lplbuf_push(const bam1_t *b, bam_lplbuf_t *tv)
+{
+    return bam_plbuf_push(b, tv->plbuf);
+}
diff --git a/samtools/bam_lpileup.c.pysam.c b/samtools/bam_lpileup.c.pysam.c
new file mode 100644
index 0000000..ea76417
--- /dev/null
+++ b/samtools/bam_lpileup.c.pysam.c
@@ -0,0 +1,227 @@
+#include "samtools.pysam.h"
+
+/*  bam_lpileup.c -- lplbuf routines.
+
+    Copyright (C) 2008, 2009, 2013 Genome Research Ltd.
+
+    Author: Heng Li <lh3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <config.h>
+
+#include <stdlib.h>
+#include <stdio.h>
+#include <assert.h>
+#include "bam_plbuf.h"
+#include "bam_lpileup.h"
+#include "splaysort.h"
+
+#define TV_GAP 2
+
+typedef struct __freenode_t {
+    uint32_t level:28, cnt:4;
+    struct __freenode_t *next;
+} freenode_t, *freenode_p;
+
+#define freenode_lt(a,b) ((a)->cnt < (b)->cnt || ((a)->cnt == (b)->cnt && (a)->level < (b)->level))
+SPLAYSORT_INIT(node, freenode_p, freenode_lt)
+
+/* Memory pool, similar to the one in bam_pileup.c */
+typedef struct {
+    int cnt, n, max;
+    freenode_t **buf;
+} mempool_t;
+
+static mempool_t *mp_init(void)
+{
+    return (mempool_t*)calloc(1, sizeof(mempool_t));
+}
+static void mp_destroy(mempool_t *mp)
+{
+    int k;
+    for (k = 0; k < mp->n; ++k) free(mp->buf[k]);
+    free(mp->buf); free(mp);
+}
+static inline freenode_t *mp_alloc(mempool_t *mp)
+{
+    ++mp->cnt;
+    if (mp->n == 0) return (freenode_t*)calloc(1, sizeof(freenode_t));
+    else return mp->buf[--mp->n];
+}
+static inline void mp_free(mempool_t *mp, freenode_t *p)
+{
+    --mp->cnt; p->next = 0; p->cnt = TV_GAP;
+    if (mp->n == mp->max) {
+        mp->max = mp->max? mp->max<<1 : 256;
+        mp->buf = (freenode_t**)realloc(mp->buf, sizeof(freenode_t*) * mp->max);
+    }
+    mp->buf[mp->n++] = p;
+}
+
+/* core part */
+struct __bam_lplbuf_t {
+    int max, n_cur, n_pre;
+    int max_level, *cur_level, *pre_level;
+    mempool_t *mp;
+    freenode_t **aux, *head, *tail;
+    int n_nodes, m_aux;
+    bam_pileup_f func;
+    void *user_data;
+    bam_plbuf_t *plbuf;
+};
+
+void bam_lplbuf_reset(bam_lplbuf_t *buf)
+{
+    freenode_t *p, *q;
+    bam_plbuf_reset(buf->plbuf);
+    for (p = buf->head; p->next;) {
+        q = p->next;
+        mp_free(buf->mp, p);
+        p = q;
+    }
+    buf->head = buf->tail;
+    buf->max_level = 0;
+    buf->n_cur = buf->n_pre = 0;
+    buf->n_nodes = 0;
+}
+
+static int tview_func(uint32_t tid, hts_pos_t pos, int n, const bam_pileup1_t *pl, void *data)
+{
+    bam_lplbuf_t *tv = (bam_lplbuf_t*)data;
+    freenode_t *p;
+    int i, l, max_level;
+    // allocate memory if necessary
+    if (tv->max < n) { // enlarge
+        tv->max = n;
+        kroundup32(tv->max);
+        tv->cur_level = (int*)realloc(tv->cur_level, sizeof(int) * tv->max);
+        tv->pre_level = (int*)realloc(tv->pre_level, sizeof(int) * tv->max);
+    }
+    tv->n_cur = n;
+    // update cnt
+    for (p = tv->head; p->next; p = p->next)
+        if (p->cnt > 0) --p->cnt;
+    // calculate cur_level[]
+    max_level = 0;
+    for (i = l = 0; i < n; ++i) {
+        const bam_pileup1_t *p = pl + i;
+        if (p->is_head) {
+            if (tv->head->next && tv->head->cnt == 0) { // then take a free slot
+                freenode_t *p = tv->head->next;
+                tv->cur_level[i] = tv->head->level;
+                mp_free(tv->mp, tv->head);
+                tv->head = p;
+                --tv->n_nodes;
+            } else tv->cur_level[i] = ++tv->max_level;
+        } else {
+            tv->cur_level[i] = tv->pre_level[l++];
+            if (p->is_tail) { // then return a free slot
+                tv->tail->level = tv->cur_level[i];
+                tv->tail->next = mp_alloc(tv->mp);
+                tv->tail = tv->tail->next;
+                ++tv->n_nodes;
+            }
+        }
+        if (tv->cur_level[i] > max_level) max_level = tv->cur_level[i];
+        ((bam_pileup1_t*)p)->level = tv->cur_level[i];
+    }
+    assert(l == tv->n_pre);
+    tv->func(tid, pos, n, pl, tv->user_data);
+    // sort the linked list
+    if (tv->n_nodes) {
+        freenode_t *q;
+        if (tv->n_nodes + 1 > tv->m_aux) { // enlarge
+            tv->m_aux = tv->n_nodes + 1;
+            kroundup32(tv->m_aux);
+            tv->aux = (freenode_t**)realloc(tv->aux, sizeof(freenode_t*) * tv->m_aux);
+        }
+        for (p = tv->head, i = l = 0; p->next;) {
+            if (p->level > max_level) { // then discard this entry
+                q = p->next;
+                mp_free(tv->mp, p);
+                p = q;
+            } else {
+                tv->aux[i++] = p;
+                p = p->next;
+            }
+        }
+        tv->aux[i] = tv->tail; // add a proper tail for the loop below
+        tv->n_nodes = i;
+        if (tv->n_nodes) {
+            splaysort(node, tv->n_nodes, tv->aux);
+            for (i = 0; i < tv->n_nodes; ++i) tv->aux[i]->next = tv->aux[i+1];
+            tv->head = tv->aux[0];
+        } else tv->head = tv->tail;
+    }
+    // clean up
+    tv->max_level = max_level;
+    memcpy(tv->pre_level, tv->cur_level, tv->n_cur * 4);
+    // squeeze out terminated levels
+    for (i = l = 0; i < n; ++i) {
+        const bam_pileup1_t *p = pl + i;
+        if (!p->is_tail)
+            tv->pre_level[l++] = tv->pre_level[i];
+    }
+    tv->n_pre = l;
+/*
+    fprintf(samtools_stderr, "%d\t", pos+1);
+    for (i = 0; i < n; ++i) {
+        const bam_pileup1_t *p = pl + i;
+        if (p->is_head) fprintf(samtools_stderr, "^");
+        if (p->is_tail) fprintf(samtools_stderr, "$");
+        fprintf(samtools_stderr, "%d,", p->level);
+    }
+    fprintf(samtools_stderr, "\n");
+*/
+    return 0;
+}
+
+bam_lplbuf_t *bam_lplbuf_init(bam_pileup_f func, void *data)
+{
+    bam_lplbuf_t *tv;
+    tv = (bam_lplbuf_t*)calloc(1, sizeof(bam_lplbuf_t));
+    tv->mp = mp_init();
+    tv->head = tv->tail = mp_alloc(tv->mp);
+    tv->func = func;
+    tv->user_data = data;
+    tv->plbuf = bam_plbuf_init(tview_func, tv);
+    return (bam_lplbuf_t*)tv;
+}
+
+void bam_lplbuf_destroy(bam_lplbuf_t *tv)
+{
+    freenode_t *p, *q;
+    free(tv->cur_level); free(tv->pre_level);
+    bam_plbuf_destroy(tv->plbuf);
+    free(tv->aux);
+    for (p = tv->head; p->next;) {
+        q = p->next;
+        mp_free(tv->mp, p); p = q;
+    }
+    mp_free(tv->mp, p);
+    assert(tv->mp->cnt == 0);
+    mp_destroy(tv->mp);
+    free(tv);
+}
+
+int bam_lplbuf_push(const bam1_t *b, bam_lplbuf_t *tv)
+{
+    return bam_plbuf_push(b, tv->plbuf);
+}
diff --git a/samtools/bam_lpileup.h b/samtools/bam_lpileup.h
new file mode 100644
index 0000000..97c7324
--- /dev/null
+++ b/samtools/bam_lpileup.h
@@ -0,0 +1,57 @@
+/*  bam_lpileup.h -- lplbuf routines (declarations copied from bam.h).
+
+    Copyright (C) 2008, 2013 Genome Research Ltd.
+
+    Author: Heng Li <lh3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#ifndef BAM_LPILEUP_H
+#define BAM_LPILEUP_H
+
+
+#include <htslib/sam.h>
+
+struct __bam_lplbuf_t;
+typedef struct __bam_lplbuf_t bam_lplbuf_t;
+
+#ifndef BAM_PILEUP_F_DEFINED
+#define BAM_PILEUP_F_DEFINED
+typedef int (*bam_pileup_f)(uint32_t tid, hts_pos_t pos, int n, const bam_pileup1_t *pl, void *data);
+#endif //BAM_PILEUP_F_DEFINED
+
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+    void bam_lplbuf_reset(bam_lplbuf_t *buf);
+
+    /*! @abstract  bam_plbuf_init() equivalent with level calculated. */
+    bam_lplbuf_t *bam_lplbuf_init(bam_pileup_f func, void *data);
+
+    /*! @abstract  bam_plbuf_destroy() equivalent with level calculated. */
+    void bam_lplbuf_destroy(bam_lplbuf_t *tv);
+
+    /*! @abstract  bam_plbuf_push() equivalent with level calculated. */
+    int bam_lplbuf_push(const bam1_t *b, bam_lplbuf_t *buf);
+#ifdef __cplusplus
+}
+#endif
+
+#endif // BAM_LPILEUP_H
diff --git a/samtools/bam_markdup.c b/samtools/bam_markdup.c
new file mode 100644
index 0000000..be9b195
--- /dev/null
+++ b/samtools/bam_markdup.c
@@ -0,0 +1,2280 @@
+/*  bam_markdup.c -- Mark duplicates from a coord sorted file that has gone
+                     through fixmates with the mate scoring option on.
+
+    Copyright (C) 2017-2022 Genome Research Ltd.
+
+    Author: Andrew Whitwham <aw7@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE
+
+Estimate library size derived from Picard DuplicationMetrics.java
+Copyright (c) 2009,2018 The Broad Institute.  MIT license.
+*/
+
+#include <config.h>
+
+#include <stdlib.h>
+#include <string.h>
+#include <stdio.h>
+#include <unistd.h>
+#include <ctype.h>
+#include <time.h>
+#include <sys/stat.h>
+#include <math.h>
+#include <regex.h>
+#include "htslib/thread_pool.h"
+#include "htslib/sam.h"
+#include "sam_opts.h"
+#include "samtools.h"
+#include "htslib/khash.h"
+#include "htslib/klist.h"
+#include "htslib/kstring.h"
+#include "tmp_file.h"
+#include "bam.h"
+
+
+typedef struct {
+    samFile *in;
+    samFile *out;
+    char *prefix;
+    int remove_dups;
+    int32_t max_length;
+    int do_stats;
+    int supp;
+    int tag;
+    int opt_dist;
+    int no_pg;
+    int clear;
+    int mode;
+    int write_index;
+    int include_fails;
+    int check_chain;
+    char *stats_file;
+    char *arg_list;
+    char *out_fn;
+    regex_t *rgx;
+    int rgx_x;
+    int rgx_y;
+    int rgx_t;
+    char *barcode;
+    regex_t *bc_rgx;
+} md_param_t;
+
+typedef struct {
+    hts_pos_t this_coord;
+    hts_pos_t other_coord;
+    int32_t this_ref;
+    int32_t other_ref;
+    int32_t barcode;
+    int8_t single;
+    int8_t leftmost;
+    int8_t orientation;
+} key_data_t;
+
+typedef struct read_queue_s {
+    key_data_t pair_key;
+    key_data_t single_key;
+    bam1_t *b;
+    struct read_queue_s *duplicate;
+    hts_pos_t pos;
+    int dup_checked;
+} read_queue_t;
+
+typedef struct {
+    read_queue_t *p;
+} in_hash_t;
+
+typedef struct {
+    char *name;
+    char type;
+} dup_map_t;
+
+typedef struct {
+    bam1_t *b;
+    int64_t score;
+    int64_t mate_score;
+    long x;
+    long y;
+    int opt;
+    int beg;
+    int end;
+} check_t;
+
+
+typedef struct {
+    check_t *c;
+    size_t size;
+    size_t length;
+} check_list_t;
+
+static khint32_t do_hash(unsigned char *key, khint32_t len);
+
+static khint_t hash_key(key_data_t key) {
+    int i = 0;
+    khint_t hash;
+
+    if (key.single) {
+        unsigned char sig[17];
+
+        memcpy(sig + i, &key.this_ref, 4);      i += 4;
+        memcpy(sig + i, &key.this_coord, 8);    i += 8;
+        memcpy(sig + i, &key.orientation, 1);   i += 1;
+        memcpy(sig + i, &key.barcode, 4);       i += 4;
+
+        hash = do_hash(sig, i);
+    } else {
+        unsigned char sig[30];
+
+        memcpy(sig + i, &key.this_ref, 4);      i += 4;
+        memcpy(sig + i, &key.this_coord, 8);    i += 8;
+        memcpy(sig + i, &key.other_ref, 4);     i += 4;
+        memcpy(sig + i, &key.other_coord, 8);   i += 8;
+        memcpy(sig + i, &key.leftmost, 1);      i += 1;
+        memcpy(sig + i, &key.orientation, 1);   i += 1;
+        memcpy(sig + i, &key.barcode, 4);       i += 4;
+
+        hash = do_hash(sig, i);
+    }
+
+    return hash;
+}
+
+
+static int key_equal(key_data_t a, key_data_t b) {
+    int match = 1;
+
+    if (a.this_coord != b.this_coord)
+        match = 0;
+    else if (a.orientation != b.orientation)
+        match = 0;
+    else if (a.this_ref != b.this_ref)
+        match = 0;
+    else if (a.single != b.single)
+        match = 0;
+    else if (a.barcode != b.barcode)
+        match = 0;
+
+    if (!a.single) {
+        if (a.other_coord != b.other_coord)
+            match = 0;
+        else if (a.leftmost != b.leftmost)
+            match = 0;
+        else if (a.other_ref != b.other_ref)
+            match = 0;
+    }
+
+    return match;
+}
+
+
+#define __free_queue_element(p)
+
+// Orientations (prime numbers to feed to hashing algorithm)
+#define O_FF 2
+#define O_RR 3
+#define O_FR 5
+#define O_RF 7
+
+// Left or rightmost
+#define R_LE 11
+#define R_RI 13
+
+#define BMD_WARNING_MAX 10
+
+#define MD_MIN_QUALITY 15
+
+// Duplicate finding mode
+#define MD_MODE_TEMPLATE 0
+#define MD_MODE_SEQUENCE 1
+
+KHASH_INIT(reads, key_data_t, in_hash_t, 1, hash_key, key_equal) // read map hash
+KLIST_INIT(read_queue, read_queue_t, __free_queue_element) // the reads buffer
+KHASH_MAP_INIT_STR(duplicates, dup_map_t) // map of duplicates for supplementary dup id
+
+/* The Bob Jenkins one_at_a_time hash to reduce the key to a 32 bit value. */
+
+static khint32_t do_hash(unsigned char *key, khint32_t len) {
+    khint32_t   hash, i;
+
+    for (hash = 0, i = 0; i < len; ++i) {
+        hash += key[i];
+        hash += (hash << 10);
+        hash ^= (hash >> 6);
+    }
+
+    hash += (hash << 3);
+    hash ^= (hash >> 11);
+    hash += (hash << 15);
+
+    return hash;
+}
+
+
+/* Get mate score from tag. */
+
+static int64_t get_mate_score(bam1_t *b) {
+    uint8_t *data;
+    int64_t score;
+
+    if ((data = bam_aux_get(b, "ms"))) {
+        score = bam_aux2i(data);
+    } else {
+        fprintf(stderr, "[markdup] error: no ms score tag. Please run samtools fixmate on file first.\n");
+        return -1;
+    }
+
+    return score;
+}
+
+
+/* Calc current score from quality. */
+
+static int64_t calc_score(bam1_t *b)
+{
+    int64_t score = 0;
+    uint8_t  *qual = bam_get_qual(b);
+    int i;
+
+    for (i = 0; i < b->core.l_qseq; i++) {
+        if (qual[i] >= MD_MIN_QUALITY) score += qual[i];
+    }
+
+    return score;
+}
+
+
+/* Create a signature hash of the current read and its pair.
+   Uses the unclipped start (or end depending on orientation),
+   the reference id, orientation and whether the current
+   read is leftmost of the pair. */
+
+
+static int make_pair_key(md_param_t *param, key_data_t *key, bam1_t *bam, long *warnings) {
+     hts_pos_t this_coord, this_end, other_coord, other_end, leftmost;
+    int32_t this_ref, other_ref, barcode = 0;
+    int8_t orientation, left_read;
+    uint8_t *data;
+    char *cig, *bar;
+    long incoming_warnings = *warnings;
+
+    this_ref    = bam->core.tid + 1; // avoid a 0 being put into the hash
+    other_ref   = bam->core.mtid + 1;
+
+    this_coord = unclipped_start(bam);
+    this_end   = unclipped_end(bam);
+
+    if ((data = bam_aux_get(bam, "MC"))) {
+        if (!(cig = bam_aux2Z(data))) {
+            fprintf(stderr, "[markdup] error: MC tag wrong type. Please use the MC tag provided by samtools fixmate.\n");
+            return 1;
+        }
+
+        other_end   = unclipped_other_end(bam->core.mpos, cig);
+        other_coord = unclipped_other_start(bam->core.mpos, cig);
+    } else {
+        fprintf(stderr, "[markdup] error: no MC tag. Please run samtools fixmate on file first.\n");
+        return 1;
+    }
+
+    // work out orientations
+    if (param->mode == MD_MODE_TEMPLATE) {
+
+        if (this_ref != other_ref) {
+            leftmost = this_ref < other_ref;
+        } else {
+            if (bam_is_rev(bam) == bam_is_mrev(bam)) {
+                if (!bam_is_rev(bam)) {
+                    leftmost = this_coord <= other_coord;
+                } else {
+                    leftmost = this_end <= other_end;
+                }
+            } else {
+                if (bam_is_rev(bam)) {
+                    leftmost = this_end <= other_coord;
+                } else {
+                    leftmost = this_coord <= other_end;
+                }
+            }
+        }
+
+        // pair orientation
+        if (leftmost) {
+            if (bam_is_rev(bam) == bam_is_mrev(bam)) {
+                other_coord = other_end;
+
+                if (!bam_is_rev(bam)) {
+                    if (bam->core.flag & BAM_FREAD1) {
+                        orientation = O_FF;
+                    } else {
+                        orientation = O_RR;
+                    }
+                } else {
+                    if (bam->core.flag & BAM_FREAD1) {
+                        orientation = O_RR;
+                    } else {
+                        orientation = O_FF;
+                    }
+                }
+            } else {
+                if (!bam_is_rev(bam)) {
+                    orientation = O_FR;
+                    other_coord = other_end;
+                } else {
+                    orientation = O_RF;
+                    this_coord = this_end;
+                }
+            }
+        } else {
+            if (bam_is_rev(bam) == bam_is_mrev(bam)) {
+                this_coord = this_end;
+
+                if (!bam_is_rev(bam)) {
+                    if (bam->core.flag & BAM_FREAD1) {
+                        orientation = O_RR;
+                    } else {
+                        orientation = O_FF;
+                    }
+                } else {
+                    if (bam->core.flag & BAM_FREAD1) {
+                        orientation = O_FF;
+                    } else {
+                        orientation = O_RR;
+                    }
+                }
+            } else {
+                if (!bam_is_rev(bam)) {
+                    orientation = O_RF;
+                    other_coord = other_end;
+                } else {
+                    orientation = O_FR;
+                    this_coord = this_end;
+                }
+            }
+        }
+    } else { // MD_MODE_SEQUENCE
+
+        if (this_ref != other_ref) {
+            leftmost = this_ref - other_ref;
+        } else {
+            if (bam_is_rev(bam) == bam_is_mrev(bam)) {
+                if (!bam_is_rev(bam)) {
+                    leftmost = this_coord - other_coord;
+                } else {
+                    leftmost = this_end - other_end;
+                }
+            } else {
+                if (bam_is_rev(bam)) {
+                    leftmost = this_end - other_coord;
+                } else {
+                    leftmost = this_coord - other_end;
+                }
+            }
+        }
+
+        if (leftmost < 0) {
+            leftmost = 1;
+        } else if (leftmost > 0) {
+            leftmost = 0;
+        } else {
+            // tie breaks
+
+            if (bam->core.pos == bam->core.mpos) {
+                if (bam->core.flag & BAM_FREAD1) {
+                    leftmost = 1;
+                } else {
+                    leftmost = 0;
+                }
+            } else if (bam->core.pos < bam->core.mpos) {
+                leftmost = 1;
+            } else {
+                leftmost = 0;
+            }
+        }
+
+        // pair orientation
+        if (leftmost) {
+            if (bam_is_rev(bam) == bam_is_mrev(bam)) {
+
+                if (!bam_is_rev(bam)) {
+                        orientation = O_FF;
+                } else {
+                        orientation = O_RR;
+                }
+            } else {
+                if (!bam_is_rev(bam)) {
+                    orientation = O_FR;
+                } else {
+                    orientation = O_RF;
+                }
+            }
+        } else {
+            if (bam_is_rev(bam) == bam_is_mrev(bam)) {
+
+                if (!bam_is_rev(bam)) {
+                        orientation = O_RR;
+                } else {
+                        orientation = O_FF;
+                }
+            } else {
+                if (!bam_is_rev(bam)) {
+                    orientation = O_RF;
+                } else {
+                    orientation = O_FR;
+                }
+            }
+        }
+
+        if (!bam_is_rev(bam)) {
+            this_coord = unclipped_start(bam);
+        } else {
+            this_coord = unclipped_end(bam);
+        }
+
+        if (!bam_is_mrev(bam)) {
+            other_coord = unclipped_other_start(bam->core.mpos, cig);
+        } else {
+            other_coord = unclipped_other_end(bam->core.mpos, cig);
+        }
+    }
+
+    if (!leftmost)
+        left_read = R_RI;
+    else
+        left_read = R_LE;
+
+    if (param->barcode) {
+        if ((data = bam_aux_get(bam, param->barcode))) {
+            if (!(bar = bam_aux2Z(data))) {
+                (*warnings)++;
+
+                if (*warnings <= BMD_WARNING_MAX) {
+                    fprintf(stderr, "[markdup] warning: %s tag wrong type. Aux tag needs to be a string type.\n", param->barcode);
+                }
+            } else {
+                barcode = do_hash((unsigned char *)bar, strlen(bar));
+            }
+        }
+    } else if (param->bc_rgx) {
+        int result;
+        regmatch_t matches[3];
+        size_t max_matches = 2;
+        char *qname = bam_get_qname(bam);
+
+        if ((result = regexec(param->bc_rgx, qname, max_matches, matches, 0)) == 0) {
+            int bc_start, bc_end;
+
+            bc_start = matches[1].rm_so;
+            bc_end   = matches[1].rm_eo;
+
+            if (bc_start != -1) {
+                barcode = do_hash((unsigned char *)qname + bc_start, bc_end - bc_start);
+            } else {
+                (*warnings)++;
+
+                if (*warnings <= BMD_WARNING_MAX) {
+                    fprintf(stderr, "[markdup] warning: barcode regex unable to match substring on %s.\n", qname);
+                }
+            }
+        } else {
+            (*warnings)++;
+
+            if (*warnings <= BMD_WARNING_MAX) {
+                char warn_msg[256];
+
+                regerror(result, param->bc_rgx, warn_msg, 256);
+                fprintf(stderr, "[markdup] warning: barcode regex match error \"%s\" on %s.\n", warn_msg, qname);
+            }
+        }
+    }
+
+    if ((*warnings == BMD_WARNING_MAX) && (incoming_warnings != *warnings)) {
+        fprintf(stderr, "[markdup] warning: %ld barcode read warnings.  New warnings will not be reported.\n",
+                        *warnings);
+    }
+
+    key->single        = 0;
+    key->this_ref      = this_ref;
+    key->this_coord    = this_coord;
+    key->other_ref     = other_ref;
+    key->other_coord   = other_coord;
+    key->leftmost      = left_read;
+    key->orientation   = orientation;
+    key->barcode       = barcode;
+
+    return 0;
+}
+
+
+/* Create a signature hash of single read (or read with an unmatched pair).
+   Uses unclipped start (or end depending on orientation), reference id,
+   and orientation. */
+
+static void make_single_key(md_param_t *param, key_data_t *key, bam1_t *bam, long *warnings) {
+    hts_pos_t this_coord;
+    int32_t this_ref, barcode = 0;
+    int8_t orientation;
+    uint8_t *data;
+    char *bar;
+    long incoming_warnings = *warnings;
+
+    this_ref = bam->core.tid + 1; // avoid a 0 being put into the hash
+
+    if (bam_is_rev(bam)) {
+        this_coord = unclipped_end(bam);
+        orientation = O_RR;
+    } else {
+        this_coord = unclipped_start(bam);
+        orientation = O_FF;
+    }
+
+    if (param->barcode) {
+        if ((data = bam_aux_get(bam, param->barcode))) {
+            if (!(bar = bam_aux2Z(data))) {
+                (*warnings)++;
+
+                if (*warnings <= BMD_WARNING_MAX) {
+                    fprintf(stderr, "[markdup] warning: %s tag wrong type. Aux tag needs to be a string type.\n", param->barcode);
+                }
+            } else {
+                barcode = do_hash((unsigned char *)bar, strlen(bar));
+            }
+        }
+    } else if (param->bc_rgx) {
+        int result;
+        regmatch_t matches[3];
+        size_t max_matches = 2;
+        char *qname = bam_get_qname(bam);
+
+        if ((result = regexec(param->bc_rgx, qname, max_matches, matches, 0)) == 0) {
+            int bc_start, bc_end;
+
+            bc_start = matches[1].rm_so;
+            bc_end   = matches[1].rm_eo;
+
+            if (bc_start != -1) {
+                barcode = do_hash((unsigned char *)qname + bc_start, bc_end - bc_start);
+            } else {
+                (*warnings)++;
+
+                if (*warnings <= BMD_WARNING_MAX) {
+                    fprintf(stderr, "[markdup] warning: barcode regex unable to match substring on %s.\n", qname);
+                }
+            }
+        } else {
+            (*warnings)++;
+
+            if (*warnings <= BMD_WARNING_MAX) {
+                char warn_msg[256];
+
+                regerror(result, param->bc_rgx, warn_msg, 256);
+                fprintf(stderr, "[markdup] warning: barcode regex match error \"%s\" on %s.\n", warn_msg, qname);
+            }
+        }
+    }
+
+    if ((*warnings == BMD_WARNING_MAX) && (incoming_warnings != *warnings)) {
+        fprintf(stderr, "[markdup] warning: %ld barcode read warnings.  New warnings will not be reported.\n",
+                        *warnings);
+    }
+
+    key->single        = 1;
+    key->this_ref      = this_ref;
+    key->this_coord    = this_coord;
+    key->orientation   = orientation;
+    key->barcode       = barcode;
+}
+
+
+/* Add the duplicate name to a hash if it does not exist. */
+
+static int add_duplicate(khash_t(duplicates) *d_hash, bam1_t *dupe, char *orig_name, char type) {
+    khiter_t d;
+    int ret;
+
+    d = kh_get(duplicates, d_hash, bam_get_qname(dupe));
+
+    if (d == kh_end(d_hash)) {
+        char *name = strdup(bam_get_qname(dupe));
+        if (name) {
+            d = kh_put(duplicates, d_hash, name, &ret);
+        } else {
+            ret = -1;
+        }
+
+        if (ret >= 0) {
+            if (orig_name) {
+                if (ret == 0) {
+                    // replace old name
+                    free(kh_value(d_hash, d).name);
+                    free(name);
+                }
+
+                kh_value(d_hash, d).name = strdup(orig_name);
+
+                if (kh_value(d_hash, d).name == NULL) {
+                    fprintf(stderr, "[markdup] error: unable to allocate memory for duplicate original name.\n");
+                    return 1;
+                }
+            } else {
+                kh_value(d_hash, d).name = NULL;
+            }
+
+            kh_value(d_hash, d).type = type;
+        } else {
+            fprintf(stderr, "[markdup] error: unable to store supplementary duplicates.\n");
+            free(name);
+            return 1;
+        }
+    }
+
+    return 0;
+}
+
+
+/* Get coordinates from the standard Illumina style read names.
+   Returned values are of the x and y coordinates and a section of
+   the read name to test (t) for string equality e.g. lane and tile part. */
+
+static int get_coordinates_colons(md_param_t *param, const char *qname, int *t_beg, int *t_end, long *x_coord, long *y_coord, long *warnings) {
+    int sep = 0;
+    int pos = 0;
+    int xpos = 0, ypos = 0;
+    char *end;
+
+    while (qname[pos]) {
+        if (qname[pos] == ':') {
+            sep++;
+
+            if (sep == 2) {
+                xpos = pos + 1;
+            } else if (sep == 3) {
+                ypos = pos + 1;
+            } else if (sep == 4) { // HiSeq style names
+                xpos = ypos;
+                ypos = pos + 1;
+            } else if (sep == 5) { // Newer Illumina format
+                xpos = pos + 1;
+            } else if (sep == 6) {
+                ypos = pos + 1;
+            }
+        }
+
+        pos++;
+    }
+
+    /* The most current Illumina read format at time of writing is:
+       @machine:run:flowcell:lane:tile:x:y:UMI or
+       @machine:run:flowcell:lane:tile:x:y
+
+       Counting the separating colons gives us a quick format check.
+       Older name formats have fewer elements.
+    */
+
+    if (!(sep == 3 || sep == 4 || sep == 6 || sep == 7)) {
+        (*warnings)++;
+
+        if (*warnings <= BMD_WARNING_MAX) {
+            fprintf(stderr, "[markdup] warning: cannot decipher read name %s for optical duplicate marking.\n", qname);
+        }
+
+        return 1;
+    } else {
+        *x_coord = strtol(qname + xpos, &end, 10);
+
+        if ((qname + xpos) == end) {
+            (*warnings)++;
+
+            if (*warnings <= BMD_WARNING_MAX) {
+                fprintf(stderr, "[markdup] warning: cannot decipher x coordinate in %s .\n", qname);
+            }
+
+            return 1;
+        }
+
+        *y_coord = strtol(qname + ypos, &end, 10);
+
+        if ((qname + ypos) == end) {
+            (*warnings)++;
+
+            if (*warnings <= BMD_WARNING_MAX) {
+                fprintf(stderr, "[markdup] warning: cannot decipher y coordinate in %s .\n", qname);
+            }
+
+            return 1;
+        }
+
+        *t_beg = 0;
+        *t_end = xpos;
+    }
+
+    return 0;
+}
+
+/* Get the coordinates from the read name.
+   Returned values are of the x and y coordinates and an optional section of
+   the read name to test (t) for string equality e.g. lane and tile part. */
+
+static inline int get_coordinates_regex(md_param_t *param, const char *qname, int *t_beg, int *t_end, long *x_coord, long *y_coord, long *warnings) {
+    regmatch_t matches[5];
+    size_t max_matches = 5;
+    int xpos, ypos, xend, yend, xlen, ylen;
+    char coord[255];
+    char *end;
+
+    if (!param->rgx_t)
+        max_matches = 4;
+
+    if (regexec(param->rgx, qname, max_matches, matches, 0))
+        return -1;
+
+    xpos = matches[param->rgx_x].rm_so;
+    ypos = matches[param->rgx_y].rm_so;
+
+    if (param->rgx_t) {
+        *t_beg = matches[param->rgx_t].rm_so;
+        *t_end = matches[param->rgx_t].rm_eo;
+    } else {
+        *t_beg = *t_end = 0;
+    }
+
+    if (xpos == -1 || ypos == -1 || *t_beg == -1)
+        return -1;
+
+    xend = matches[param->rgx_x].rm_eo;
+    yend = matches[param->rgx_y].rm_eo;
+
+    if ((xlen = xend - xpos) > 254) {
+        (*warnings)++;
+
+        if (*warnings <= BMD_WARNING_MAX) {
+            fprintf(stderr, "[markdup] warning: x coordinate string longer than allowed qname length in %s (%d long).\n", qname, xlen);
+        }
+
+        return 1;
+    }
+
+    strncpy(coord, qname + xpos, xlen);
+    coord[xlen] = '\0';
+    *x_coord = strtol(coord, &end, 10);
+
+    if (coord == end) {
+        (*warnings)++;
+
+        if (*warnings <= BMD_WARNING_MAX) {
+            fprintf(stderr, "[markdup] warning: cannot decipher x coordinate in %s (%s).\n", qname, coord);
+        }
+
+        return 1;
+    }
+
+    if ((ylen = yend - ypos) > 254) {
+        (*warnings)++;
+
+        if (*warnings <= BMD_WARNING_MAX) {
+            fprintf(stderr, "[markdup] warning: y coordinate string longer than allowed qname length in %s (%d long).\n", qname, ylen);
+        }
+
+        return 1;
+    }
+
+    strncpy(coord, qname + ypos, ylen);
+    coord[ylen] = '\0';
+    *y_coord = strtol(coord, &end, 10);
+
+    if (coord == end) {
+        (*warnings)++;
+
+        if (*warnings <= BMD_WARNING_MAX) {
+            fprintf(stderr, "[markdup] warning: cannot decipher y coordinate in %s (%s).\n", qname, coord);
+        }
+
+        return 1;
+    }
+
+    return 0;
+}
+
+
+static int get_coordinates(md_param_t *param, const char *name, int *t_beg, int *t_end, long *x_coord, long *y_coord, long *warnings) {
+    int ret = 1;
+
+    if (param->rgx == NULL) {
+        ret = get_coordinates_colons(param, name, t_beg, t_end, x_coord, y_coord, warnings);
+    } else {
+        ret = get_coordinates_regex(param, name, t_beg, t_end, x_coord, y_coord, warnings);
+    }
+
+    return ret;
+}
+
+
+/* Using the coordinates from the read name, see whether the duplicated read is
+   close enough (set by max_dist) to the original to be counted as optical.*/
+
+static int is_optical_duplicate(md_param_t *param, bam1_t *ori, bam1_t *dup, long max_dist, long *warnings) {
+    int ret = 0;
+    char *original, *duplicate;
+    long ox, oy, dx, dy;
+    int o_beg = 0, o_end = 0, d_beg = 0, d_end = 0;
+
+    original  = bam_get_qname(ori);
+    duplicate = bam_get_qname(dup);
+
+    if (get_coordinates(param, original, &o_beg, &o_end, &ox, &oy, warnings)) {
+        return ret;
+    }
+
+    if (get_coordinates(param, duplicate, &d_beg, &d_end, &dx, &dy, warnings)) {
+        return ret;
+    }
+
+    if (strncmp(original + o_beg, duplicate + d_beg, o_end - o_beg) == 0) {
+        long xdiff, ydiff;
+
+        if (ox > dx) {
+            xdiff = ox - dx;
+        } else {
+            xdiff = dx - ox;
+        }
+
+        if (xdiff <= max_dist) {
+            // still might be optical
+
+            if (oy > dy) {
+                ydiff = oy - dy;
+            } else {
+                ydiff = dy - oy;
+            }
+
+            if (ydiff <= max_dist) ret = 1;
+        }
+    }
+
+    return ret;
+}
+
+
+/* Using the coordinates from the Illumina read name, see whether the duplicated read is
+   close enough (set by max_dist) to the original to be counted as optical.
+
+   This function needs the values from the first read to be already calculated. */
+
+static int optical_duplicate_partial(md_param_t *param, const char *name, const int o_beg, const int o_end, const long ox, const long oy, bam1_t *dup, check_t *c, long max_dist, long *warnings) {
+    int ret = 0;
+    char *duplicate;
+    int d_beg = 0, d_end = 0;
+    long dx, dy;
+
+    duplicate = bam_get_qname(dup);
+
+    if (get_coordinates(param, duplicate, &d_beg, &d_end, &dx, &dy, warnings)) {
+        return ret;
+    }
+
+    if (strncmp(name + o_beg, duplicate + d_beg, o_end - o_beg) == 0) {
+        // the initial parts match, look at the numbers
+        long xdiff, ydiff;
+
+        if (ox > dx) {
+            xdiff = ox - dx;
+        } else {
+            xdiff = dx - ox;
+        }
+
+        if (xdiff <= max_dist) {
+            // still might be optical
+
+            if (oy > dy) {
+                ydiff = oy - dy;
+            } else {
+                ydiff = dy - oy;
+            }
+
+            if (ydiff <= max_dist) ret = 1;
+        }
+    }
+
+    c->x = dx;
+    c->y = dy;
+    c->beg = d_beg;
+    c->end = d_end;
+
+    return ret;
+}
+
+
+/* Mark the read as a duplicate and update the duplicate hash (if needed) */
+static int mark_duplicates(md_param_t *param, khash_t(duplicates) *dup_hash, bam1_t *ori, bam1_t *dup,
+                           long *optical, long *warn) {
+    char dup_type = 0;
+    long incoming_warnings = *warn;
+
+    dup->core.flag |= BAM_FDUP;
+
+    if (param->tag) {
+        if (bam_aux_update_str(dup, "do", strlen(bam_get_qname(ori)) + 1, bam_get_qname(ori))) {
+            fprintf(stderr, "[markdup] error: unable to append 'do' tag.\n");
+            return -1;
+        }
+    }
+
+    if (param->opt_dist) { // mark optical duplicates
+        if (is_optical_duplicate(param, ori, dup, param->opt_dist, warn)) {
+            bam_aux_update_str(dup, "dt", 3, "SQ");
+            dup_type = 'O';
+            (*optical)++;
+        } else {
+            // not an optical duplicate
+            bam_aux_update_str(dup, "dt", 3, "LB");
+        }
+    }
+
+    if ((*warn == BMD_WARNING_MAX) && (incoming_warnings != *warn)) {
+        fprintf(stderr, "[markdup] warning: %ld decipher read name warnings.  New warnings will not be reported.\n",
+                        *warn);
+    }
+
+    if (param->supp) {
+        if (bam_aux_get(dup, "SA") || (dup->core.flag & BAM_FMUNMAP) || bam_aux_get(dup, "XA")) {
+            char *original = NULL;
+
+            if (param->tag) {
+                original = bam_get_qname(ori);
+            }
+
+            if (add_duplicate(dup_hash, dup, original, dup_type))
+                return -1;
+        }
+    }
+
+    return 0;
+}
+
+
+/* If the duplicate type has changed to optical then retag and duplicate hash. */
+static inline int optical_retag(md_param_t *param, khash_t(duplicates) *dup_hash, bam1_t *b, int paired, long *optical_single, long *optical_pair) {
+    int ret = 0;
+
+    if (bam_aux_update_str(b, "dt", 3, "SQ")) {
+        fprintf(stderr, "[markdup] error: unable to update 'dt' tag.\n");
+        ret = -1;
+    }
+
+    if (paired) {
+        (*optical_pair)++;
+    } else {
+        (*optical_single)++;
+    }
+
+    if (param->supp) {
+        // Change the duplicate type
+
+        if (bam_aux_get(b, "SA") || (b->core.flag & BAM_FMUNMAP)
+            || bam_aux_get(b, "XA")) {
+            khiter_t d;
+
+            d = kh_get(duplicates, dup_hash, bam_get_qname(b));
+
+            if (d == kh_end(dup_hash)) {
+                // error, name should already be in dup hash
+                fprintf(stderr, "[markdup] error: duplicate name %s not found in hash.\n",
+                    bam_get_qname(b));
+                ret = -1;
+            } else {
+                kh_value(dup_hash, d).type = 'O';
+            }
+        }
+    }
+
+    return ret;
+}
+
+
+/* Check all duplicates of the highest quality read (the "original") for consistancy.  Also
+   pre-calculate any values for use in check_duplicate_chain later.
+   Returns 0 on success, >0 on coordinate reading error (program can continue) or
+   <0 on an error (program should not continue. */
+static int check_chain_against_original(md_param_t *param, khash_t(duplicates) *dup_hash, read_queue_t *ori,
+             check_list_t *list, long *warn, long *optical_single, long *optical_pair) {
+
+    int ret = 0, coord_fail = 0;
+    char *ori_name = bam_get_qname(ori->b);
+    read_queue_t *current = ori->duplicate;
+    int t_beg = 0, t_end = 0;
+    long x, y;
+
+    if (param->opt_dist) {
+        coord_fail = get_coordinates(param, ori_name, &t_beg, &t_end, &x, &y, warn);
+    }
+
+    list->length = 0;
+
+    while (current) {
+        check_t *c;
+
+        if (list->length >= list->size) {
+            check_t *tmp;
+
+            list->size *= 2;
+
+            if (!(tmp = realloc(list->c, list->size * sizeof(check_t)))) {
+                fprintf(stderr, "[markdup] error: Unable to expand opt check list.\n");
+                return -1;
+            }
+
+            list->c = tmp;
+        }
+
+        c = &list->c[list->length];
+
+        c->b = current->b;
+        c->x = -1;
+        c->y = -1;
+        c->opt = 0;
+        c->score = 0;
+        c->mate_score = 0;
+        current->dup_checked = 1;
+
+        if (param->tag) {
+            uint8_t *data;
+
+            // at this stage all duplicates should have a do tag
+            if ((data = bam_aux_get(current->b, "do")) != NULL) {
+                // see if we need to change the tag
+                char *old_name = bam_aux2Z(data);
+
+                if (old_name) {
+                    if (strcmp(old_name, ori_name) != 0) {
+                        if (bam_aux_update_str(current->b, "do", strlen(ori_name) + 1, (const char *)ori_name)) {
+                            fprintf(stderr, "[markdup] error: unable to update 'do' tag.\n");
+                            ret =  -1;
+                            break;
+                        }
+                    }
+                } else {
+                    fprintf(stderr, "[markdup] error: 'do' tag has wrong type for read %s.\n", bam_get_qname(current->b));
+                    ret = -1;
+                    break;
+                }
+            }
+        }
+
+        if (param->opt_dist && !coord_fail) {
+            uint8_t *data;
+            char *dup_type;
+            int is_opt = 0;
+            int current_paired = (current->b->core.flag & BAM_FPAIRED) && !(current->b->core.flag & BAM_FMUNMAP);
+
+            if ((data = bam_aux_get(current->b, "dt"))) {
+                if ((dup_type = bam_aux2Z(data))) {
+                    if (strcmp(dup_type, "SQ") == 0) {
+                        c->opt = 1;
+                    }
+                }
+            }
+
+            // need to run this to get the duplicates x and y scores
+            is_opt = optical_duplicate_partial(param, ori_name, t_beg, t_end, x, y, current->b, c, param->opt_dist, warn);
+
+            if (!c->opt && is_opt) {
+                if (optical_retag(param, dup_hash, current->b, current_paired, optical_single, optical_pair)) {
+                    ret = -1;
+                    break;
+                }
+
+                c->opt = 1;
+            }
+
+            c->score = calc_score(current->b);
+
+            if (current_paired) {
+                if ((c->mate_score = get_mate_score(current->b)) == -1) {
+                     fprintf(stderr, "[markdup] error: no ms score tag. Please run samtools fixmate on file first.\n");
+                     ret = -1;
+                     break;
+                }
+            }
+        }
+
+        current = current->duplicate;
+        list->length++;
+    }
+
+    if (!ret && coord_fail)
+        ret = coord_fail;
+
+    return ret;
+}
+
+
+static int xcoord_sort(const void *a, const void *b) {
+    check_t *ac = (check_t *) a;
+    check_t *bc = (check_t *) b;
+
+    return (ac->x - bc->x);
+}
+
+
+/* Check all the duplicates against each other to see if they are optical duplicates. */
+static int check_duplicate_chain(md_param_t *param, khash_t(duplicates) *dup_hash, check_list_t *list,
+             long *warn, long *optical_single, long *optical_pair) {
+    int ret = 0;
+    size_t curr = 0;
+
+    qsort(list->c, list->length, sizeof(list->c[0]), xcoord_sort);
+
+    while (curr < list->length - 1) {
+        check_t *current = &list->c[curr];
+        size_t count = curr;
+        char *cur_name = bam_get_qname(current->b);
+        int current_paired = (current->b->core.flag & BAM_FPAIRED) && !(current->b->core.flag & BAM_FMUNMAP);
+
+        while (++count < list->length && (list->c[count].x - current->x <= param->opt_dist)) {
+            // while close enough along the x coordinate
+            check_t *chk = &list->c[count];
+
+            if (current->opt && chk->opt)
+                continue;
+
+            // if both are already optical duplicates there is no need to check again, otherwise...
+
+            long ydiff;
+
+            if (current->y > chk->y) {
+                ydiff = current->y - chk->y;
+            } else {
+                ydiff = chk->y - current->y;
+            }
+
+            if (ydiff > param->opt_dist)
+                continue;
+
+            // the number are right, check the names
+            if (strncmp(cur_name + current->beg, bam_get_qname(chk->b) + chk->beg, current->end - current->beg) != 0)
+                continue;
+
+            // optical duplicates
+            int chk_dup = 0;
+            int chk_paired = (chk->b->core.flag & BAM_FPAIRED) && !(chk->b->core.flag & BAM_FMUNMAP);
+
+            if (current_paired != chk_paired) {
+                if (!chk_paired) {
+                    // chk is single vs pair, this is a dup.
+                    chk_dup = 1;
+                }
+            } else {
+                // do it by scores
+                int64_t cur_score, chk_score;
+
+                if ((current->b->core.flag & BAM_FQCFAIL) != (chk->b->core.flag & BAM_FQCFAIL)) {
+                    if (current->b->core.flag & BAM_FQCFAIL) {
+                        cur_score = 0;
+                        chk_score = 1;
+                    } else {
+                        cur_score = 1;
+                        chk_score = 0;
+                    }
+                } else {
+                    cur_score = current->score;
+                    chk_score = chk->score;
+
+                    if (current_paired) {
+                        // they are pairs so add mate scores.
+                        chk_score += chk->mate_score;
+                        cur_score += current->mate_score;
+                    }
+                }
+
+                if (cur_score == chk_score) {
+                    if (strcmp(bam_get_qname(chk->b), cur_name) < 0) {
+                        chk_score++;
+                    } else {
+                        chk_score--;
+                    }
+                }
+
+                if (cur_score > chk_score) {
+                    chk_dup = 1;
+                }
+            }
+
+            if (chk_dup) {
+                // the duplicate is the optical duplicate
+                if (!chk->opt) { // only change if not already an optical duplicate
+                    if (optical_retag(param, dup_hash, chk->b, chk_paired, optical_single, optical_pair)) {
+                        ret = -1;
+                        goto fail;
+                    }
+
+                    chk->opt = 1;
+                }
+            } else {
+                if (!current->opt) {
+                    if (optical_retag(param, dup_hash, current->b, current_paired, optical_single, optical_pair)) {
+                        ret = -1;
+                        goto fail;
+                    }
+
+                    current->opt = 1;
+                }
+            }
+        }
+
+        curr++;
+    }
+
+ fail:
+    return ret;
+}
+
+
+/* Where there is more than one duplicate go down the list and check for optical duplicates and change
+   do tags (where used) to point to original (non-duplicate) read. */
+static int find_duplicate_chains(md_param_t *param, klist_t(read_queue) *read_buffer, khash_t(duplicates) *dup_hash, check_list_t *dup_list,
+                                const hts_pos_t prev_coord, const int32_t prev_tid, long *warn, long *optical_single,
+                                long *optical_pair, const int check_range) {
+    int ret = 0;
+    kliter_t(read_queue) *rq;
+
+    rq = kl_begin(read_buffer);
+
+    while (rq != kl_end(read_buffer)) {
+        read_queue_t *in_read = &kl_val(rq);
+
+        if (check_range) {
+            /* Just check against the moving window of reads based on coordinates and max read length. */
+            if (in_read->pos + param->max_length > prev_coord && in_read->b->core.tid == prev_tid && (prev_tid != -1 || prev_coord != -1)) {
+                break;
+            }
+        } else {
+            // this is the last set of results and the end entry will be blank
+            if (!bam_get_qname(in_read->b)) {
+                break;
+            }
+        }
+
+        if (!(in_read->b->core.flag & BAM_FDUP) && in_read->duplicate) { // is the head of a duplicate chain
+
+            // check against the original for tagging and optical duplication
+            if ((ret = check_chain_against_original(param, dup_hash, in_read, dup_list, warn, optical_single, optical_pair))) {
+                if (ret < 0) { // real error
+                    ret = -1;
+                    break;
+                } else { // coordinate decoding error
+                    ret = 0;
+                    in_read->duplicate = NULL;
+                    continue;
+                }
+            }
+
+            // check the rest of the duplicates against each other for optical duplication
+            if (param->opt_dist && check_duplicate_chain(param, dup_hash, dup_list, warn, optical_single, optical_pair)) {
+                ret = -1;
+                break;
+            }
+
+            in_read->duplicate = NULL;
+        }
+
+        rq = kl_next(rq);
+    }
+
+    return ret;
+}
+
+
+/*
+  Function to use when estimating library size.
+
+  This is based on an approximate formula for the coverage of a set
+  obtained after sampling it a given number of times with replacement.
+
+  x = number of items in the set (the number of unique fragments in the library)
+
+  c = number of unique items (unique read pairs observed)
+
+  n = number of items samples (total number of read pairs)
+
+  c and n are known; x is unknown.
+
+  As n -> infinity, the coverage (c/x) can be given as:
+
+  c / x = 1 - exp(-n / x)  (see https://math.stackexchange.com/questions/32800)
+
+  This needs to be solved for x, so it is rearranged to put both terms on the
+  left side and estimate_library_size() finds a value of x which gives a
+  result of zero (or as close as it can get).
+ */
+static inline double coverage_equation(double x, double c, double n) {
+    return c / x - 1 + exp(-n / x);
+}
+
+
+/* estimate the library size, based on the Picard code in DuplicationMetrics.java*/
+static unsigned long estimate_library_size(unsigned long paired_reads, unsigned long paired_duplicate_reads, unsigned long optical) {
+    unsigned long estimated_size = 0;
+    unsigned long non_optical_pairs = (paired_reads - optical) / 2;
+    unsigned long unique_pairs = (paired_reads - paired_duplicate_reads) / 2;
+    unsigned long duplicate_pairs = (paired_duplicate_reads - optical) / 2;
+
+    if ((non_optical_pairs && duplicate_pairs && unique_pairs) && (non_optical_pairs > duplicate_pairs)) {
+        double m = 1;
+        double M = 100;
+        int i;
+
+        if (coverage_equation(m * (double)unique_pairs, (double)unique_pairs, (double)non_optical_pairs) < 0) {
+            fprintf(stderr, "[markdup] warning: unable to calculate estimated library size.\n");
+            return  estimated_size;
+        }
+
+        while (coverage_equation(M * (double)unique_pairs, (double)unique_pairs, (double)non_optical_pairs) > 0) {
+            M *= 10;
+        }
+
+        for (i = 0; i < 40; i++) {
+            double r = (m + M) / 2;
+            double u = coverage_equation(r * (double)unique_pairs, (double)unique_pairs, (double)non_optical_pairs);
+
+            if (u > 0) {
+                m = r;
+            } else if (u < 0) {
+                M = r;
+            } else {
+                break;
+            }
+        }
+
+        estimated_size = (unsigned long)(unique_pairs * (m + M) / 2);
+    } else {
+        fprintf(stderr, "[markdup] warning: unable to calculate estimated library size."
+                        " Read pairs %ld should be greater than duplicate pairs %ld,"
+                        " which should both be non zero.\n",
+                        non_optical_pairs, duplicate_pairs);
+    }
+
+    return estimated_size;
+}
+
+
+/* Compare the reads near each other (coordinate sorted) and try to spot the duplicates.
+   Generally the highest quality scoring is chosen as the original and all others the duplicates.
+   The score is based on the sum of the quality values (<= 15) of the read and its mate (if any).
+   While single reads are compared to only one read of a pair, the pair will chosen as the original.
+   The comparison is done on position and orientation, see above for details.
+
+   Marking the supplementary reads of a duplicate as also duplicates takes an extra file read/write
+   step.  This is because the duplicate can occur before the primary read.*/
+
+static int bam_mark_duplicates(md_param_t *param) {
+    bam_hdr_t *header = NULL;
+    khiter_t k;
+    khash_t(reads) *pair_hash        = kh_init(reads);
+    khash_t(reads) *single_hash      = kh_init(reads);
+    klist_t(read_queue) *read_buffer = kl_init(read_queue);
+    kliter_t(read_queue) *rq;
+    khash_t(duplicates) *dup_hash    = kh_init(duplicates);
+    int32_t prev_tid;
+    hts_pos_t prev_coord;
+    read_queue_t *in_read;
+    int ret;
+    long reading, writing, excluded, duplicate, single, pair, single_dup, examined, optical, single_optical;
+    long np_duplicate, np_opt_duplicate;
+    long opt_warnings = 0, bc_warnings = 0;
+    tmp_file_t temp;
+    char *idx_fn = NULL;
+    int exclude = 0;
+    check_list_t dup_list = {NULL, 0, 0};
+
+    if (!pair_hash || !single_hash || !read_buffer || !dup_hash) {
+        fprintf(stderr, "[markdup] out of memory\n");
+        goto fail;
+    }
+
+    if ((header = sam_hdr_read(param->in)) == NULL) {
+        fprintf(stderr, "[markdup] error reading header\n");
+        goto fail;
+    }
+
+    // accept unknown, unsorted or coordinate sort order, but error on queryname sorted.
+    // only really works on coordinate sorted files.
+    kstring_t str = KS_INITIALIZE;
+    if (!sam_hdr_find_tag_hd(header, "SO", &str) && str.s && !strcmp(str.s, "queryname")) {
+        fprintf(stderr, "[markdup] error: queryname sorted, must be sorted by coordinate.\n");
+        ks_free(&str);
+        goto fail;
+    }
+    ks_free(&str);
+
+    if (!param->no_pg && sam_hdr_add_pg(header, "samtools", "VN", samtools_version(),
+                        param->arg_list ? "CL" : NULL,
+                        param->arg_list ? param->arg_list : NULL,
+                        NULL) != 0) {
+        fprintf(stderr, "[markdup] warning: unable to add @PG line to header.\n");
+    }
+
+    if (sam_hdr_write(param->out, header) < 0) {
+        fprintf(stderr, "[markdup] error writing header.\n");
+        goto fail;
+    }
+    if (param->write_index) {
+        if (!(idx_fn = auto_index(param->out, param->out_fn, header)))
+            goto fail;
+    }
+
+    // used for coordinate order checks
+    prev_tid = prev_coord = 0;
+
+    // get the buffer going
+    in_read = kl_pushp(read_queue, read_buffer);
+    if (!in_read) {
+        fprintf(stderr, "[markdup] out of memory\n");
+        goto fail;
+    }
+
+    // handling supplementary reads needs a temporary file
+    if (param->supp) {
+        if (tmp_file_open_write(&temp, param->prefix, 1)) {
+            fprintf(stderr, "[markdup] error: unable to open tmp file %s.\n", param->prefix);
+            goto fail;
+        }
+    }
+
+    if ((in_read->b = bam_init1()) == NULL) {
+        fprintf(stderr, "[markdup] error: unable to allocate memory for alignment.\n");
+        goto fail;
+    }
+
+    if (param->check_chain && !(param->tag || param->opt_dist))
+        param->check_chain = 0;
+
+    if (param->check_chain) {
+        dup_list.size = 128;
+        dup_list.c = NULL;
+
+        if ((dup_list.c = malloc(dup_list.size * sizeof(check_t))) == NULL) {
+            fprintf(stderr, "[markdup] error: unable to allocate memory for dup_list.\n");
+            goto fail;
+        }
+    }
+
+    reading = writing = excluded = single_dup = duplicate = examined = pair = single = optical = single_optical = 0;
+    np_duplicate = np_opt_duplicate = 0;
+
+    while ((ret = sam_read1(param->in, header, in_read->b)) >= 0) {
+        int dup_checked = 0;
+
+        // do some basic coordinate order checks
+        if (in_read->b->core.tid >= 0) { // -1 for unmapped reads
+            if (in_read->b->core.tid < prev_tid ||
+               ((in_read->b->core.tid == prev_tid) && (in_read->b->core.pos < prev_coord))) {
+                fprintf(stderr, "[markdup] error: not in coordinate sorted order.\n");
+                goto fail;
+            }
+        }
+
+        prev_coord = in_read->pos = in_read->b->core.pos;
+        prev_tid   =  in_read->b->core.tid;
+        in_read->pair_key.single   = 1;
+        in_read->single_key.single = 0;
+        in_read->duplicate = NULL;
+        in_read->dup_checked = 0;
+
+        reading++;
+
+        if (param->clear && (in_read->b->core.flag & BAM_FDUP)) {
+            uint8_t *data;
+
+            in_read->b->core.flag ^= BAM_FDUP;
+
+            if ((data = bam_aux_get(in_read->b, "dt")) != NULL) {
+                bam_aux_del(in_read->b, data);
+            }
+
+            if ((data = bam_aux_get(in_read->b, "do")) != NULL) {
+                bam_aux_del(in_read->b, data);
+            }
+        }
+
+        if (param->include_fails) {
+            exclude |= (BAM_FSECONDARY | BAM_FSUPPLEMENTARY | BAM_FUNMAP);
+        } else {
+            exclude |= (BAM_FSECONDARY | BAM_FSUPPLEMENTARY | BAM_FUNMAP | BAM_FQCFAIL);
+        }
+
+        // read must not be secondary, supplementary, unmapped or (possibly) failed QC
+        if (!(in_read->b->core.flag & exclude)) {
+            examined++;
+
+
+            // look at the pairs first
+            if ((in_read->b->core.flag & BAM_FPAIRED) && !(in_read->b->core.flag & BAM_FMUNMAP)) {
+                int ret, mate_tmp;
+                key_data_t pair_key;
+                key_data_t single_key;
+                in_hash_t *bp;
+
+                if (make_pair_key(param, &pair_key, in_read->b, &bc_warnings)) {
+                    fprintf(stderr, "[markdup] error: unable to assign pair hash key.\n");
+                    goto fail;
+                }
+
+                make_single_key(param, &single_key, in_read->b, &bc_warnings);
+
+                pair++;
+                in_read->pos = single_key.this_coord; // cigar/orientation modified pos
+
+                // put in singles hash for checking against non paired reads
+                k = kh_put(reads, single_hash, single_key, &ret);
+
+                if (ret > 0) { // new
+                    // add to single duplicate hash
+                    bp = &kh_val(single_hash, k);
+                    bp->p = in_read;
+                    in_read->single_key = single_key;
+                } else if (ret == 0) { // exists
+                    // look at singles only for duplication marking
+                    bp = &kh_val(single_hash, k);
+
+                    if (!(bp->p->b->core.flag & BAM_FPAIRED) || (bp->p->b->core.flag & BAM_FMUNMAP)) {
+                       // singleton will always be marked duplicate even if
+                       // scores more than one read of the pair
+                        bam1_t *dup = bp->p->b;
+
+                        if (param->check_chain)
+                            in_read->duplicate = bp->p;
+
+                        bp->p = in_read;
+
+                        if (mark_duplicates(param, dup_hash, bp->p->b, dup, &single_optical, &opt_warnings))
+                            goto fail;
+
+                        single_dup++;
+                    }
+                } else {
+                    fprintf(stderr, "[markdup] error: single hashing failure.\n");
+                    goto fail;
+                }
+
+                // now do the pair
+                k = kh_put(reads, pair_hash, pair_key, &ret);
+
+                if (ret > 0) { // new
+                    // add to the pair hash
+                    bp = &kh_val(pair_hash, k);
+                    bp->p = in_read;
+                    in_read->pair_key = pair_key;
+                } else if (ret == 0) {
+                    int64_t old_score, new_score, tie_add = 0;
+                    bam1_t *dup = NULL;
+
+                    bp = &kh_val(pair_hash, k);
+
+                    if ((bp->p->b->core.flag & BAM_FQCFAIL) != (in_read->b->core.flag & BAM_FQCFAIL)) {
+                        if (bp->p->b->core.flag & BAM_FQCFAIL) {
+                            old_score = 0;
+                            new_score = 1;
+                        } else {
+                            old_score = 1;
+                            new_score = 0;
+                        }
+                    } else {
+                        if ((mate_tmp = get_mate_score(bp->p->b)) == -1) {
+                            fprintf(stderr, "[markdup] error: no ms score tag. Please run samtools fixmate on file first.\n");
+                            goto fail;
+                        } else {
+                            old_score = calc_score(bp->p->b) + mate_tmp;
+                        }
+
+                        if ((mate_tmp = get_mate_score(in_read->b)) == -1) {
+                            fprintf(stderr, "[markdup] error: no ms score tag. Please run samtools fixmate on file first.\n");
+                            goto fail;
+                        } else {
+                            new_score = calc_score(in_read->b) + mate_tmp;
+                        }
+                    }
+
+                    // choose the highest score as the original
+                    // and add it to the pair hash, mark the other as duplicate
+
+                    if (new_score == old_score) {
+                        if (strcmp(bam_get_qname(in_read->b), bam_get_qname(bp->p->b)) < 0) {
+                            tie_add = 1;
+                        } else {
+                            tie_add = -1;
+                        }
+                    }
+
+                    if (new_score + tie_add > old_score) { // swap reads
+                        dup = bp->p->b;
+
+                        if (param->check_chain) {
+
+                            if (in_read->duplicate) {
+                                read_queue_t *current = in_read->duplicate;
+
+                                while (current->duplicate) {
+                                    current = current->duplicate;
+                                }
+
+                                current->duplicate = bp->p;
+                            } else {
+                                in_read->duplicate = bp->p;
+                            }
+                        }
+
+                        bp->p = in_read;
+                    } else {
+                        if (param->check_chain) {
+                            if (bp->p->duplicate) {
+                                if (in_read->duplicate) {
+                                    read_queue_t *current = bp->p->duplicate;
+
+                                    while (current->duplicate) {
+                                        current = current->duplicate;
+                                    }
+
+                                    current->duplicate = in_read->duplicate;
+                                }
+
+                                in_read->duplicate = bp->p->duplicate;
+                            }
+
+                            bp->p->duplicate = in_read;
+                        }
+
+                        dup = in_read->b;
+                    }
+
+                    if (mark_duplicates(param, dup_hash, bp->p->b, dup, &optical, &opt_warnings))
+                        goto fail;
+
+                    duplicate++;
+                } else {
+                    fprintf(stderr, "[markdup] error: pair hashing failure.\n");
+                    goto fail;
+                }
+            } else { // do the single (or effectively single) reads
+                int ret;
+                key_data_t single_key;
+                in_hash_t *bp;
+
+                make_single_key(param, &single_key, in_read->b, &bc_warnings);
+
+                single++;
+                in_read->pos = single_key.this_coord; // cigar/orientation modified pos
+
+                k = kh_put(reads, single_hash, single_key, &ret);
+
+                if (ret > 0) { // new
+                    bp = &kh_val(single_hash, k);
+                    bp->p = in_read;
+                    in_read->single_key = single_key;
+                } else if (ret == 0) { // exists
+                    bp = &kh_val(single_hash, k);
+
+                    if ((bp->p->b->core.flag & BAM_FPAIRED) && !(bp->p->b->core.flag & BAM_FMUNMAP)) {
+                        // if matched against one of a pair just mark as duplicate
+
+                        if (param->check_chain) {
+                            if (bp->p->duplicate) {
+                                in_read->duplicate = bp->p->duplicate;
+                            }
+
+                            bp->p->duplicate = in_read;
+                        }
+
+                        if (mark_duplicates(param, dup_hash, bp->p->b, in_read->b, &single_optical, &opt_warnings))
+                            goto fail;
+
+                    } else {
+                        int64_t old_score, new_score;
+                        bam1_t *dup = NULL;
+
+                        old_score = calc_score(bp->p->b);
+                        new_score = calc_score(in_read->b);
+
+                        // choose the highest score as the original, add it
+                        // to the single hash and mark the other as duplicate
+                        if (new_score > old_score) { // swap reads
+                            dup = bp->p->b;
+
+                            if (param->check_chain)
+                                in_read->duplicate = bp->p;
+
+                            bp->p = in_read;
+                        } else {
+                            if (param->check_chain) {
+                                if (bp->p->duplicate) {
+                                    in_read->duplicate = bp->p->duplicate;
+                                }
+
+                                bp->p->duplicate = in_read;
+                            }
+
+                            dup = in_read->b;
+                        }
+
+                        if (mark_duplicates(param, dup_hash, bp->p->b, dup, &single_optical, &opt_warnings))
+                            goto fail;
+                    }
+
+                    single_dup++;
+                } else {
+                    fprintf(stderr, "[markdup] error: single hashing failure.\n");
+                    goto fail;
+                }
+            }
+        } else {
+            excluded++;
+        }
+
+        // loop through the stored reads and write out those we
+        // no longer need
+        rq = kl_begin(read_buffer);
+        while (rq != kl_end(read_buffer)) {
+            in_read = &kl_val(rq);
+
+            /* keep a moving window of reads based on coordinates and max read length.  Any unaligned reads
+               should just be written as they cannot be matched as duplicates. */
+            if (in_read->pos + param->max_length > prev_coord && in_read->b->core.tid == prev_tid && (prev_tid != -1 || prev_coord != -1)) {
+                break;
+            }
+
+            if (!dup_checked && param->check_chain) {
+                // check for multiple optical duplicates of the same original read
+
+                if (find_duplicate_chains(param, read_buffer, dup_hash, &dup_list, prev_coord, prev_tid, &opt_warnings, &single_optical, &optical, 1)) {
+                    fprintf(stderr, "[markdup] error: duplicate checking failed.\n");
+                    goto fail;
+                }
+
+                dup_checked = 1;
+            }
+
+
+            if (param->check_chain && (in_read->b->core.flag & BAM_FDUP) && !in_read->dup_checked && !(in_read->b->core.flag & exclude)) {
+                break;
+            }
+
+            if (!param->remove_dups || !(in_read->b->core.flag & BAM_FDUP)) {
+                if (param->supp) {
+                    if (tmp_file_write(&temp, in_read->b)) {
+                        fprintf(stderr, "[markdup] error: writing temp output failed.\n");
+                        goto fail;
+                    }
+                } else {
+                    if (sam_write1(param->out, header, in_read->b) < 0) {
+                        fprintf(stderr, "[markdup] error: writing output failed.\n");
+                        goto fail;
+                    }
+                }
+
+                writing++;
+            }
+
+            // remove from hash
+            if (in_read->pair_key.single == 0) {
+                k = kh_get(reads, pair_hash, in_read->pair_key);
+                kh_del(reads, pair_hash, k);
+            }
+
+            if (in_read->single_key.single == 1) {
+                k = kh_get(reads, single_hash, in_read->single_key);
+                kh_del(reads, single_hash, k);
+            }
+
+            kl_shift(read_queue, read_buffer, NULL);
+            bam_destroy1(in_read->b);
+            rq = kl_begin(read_buffer);
+        }
+
+        // set the next one up for reading
+        in_read = kl_pushp(read_queue, read_buffer);
+        if (!in_read) {
+            fprintf(stderr, "[markdup] out of memory\n");
+            goto fail;
+        }
+
+        if ((in_read->b = bam_init1()) == NULL) {
+            fprintf(stderr, "[markdup] error: unable to allocate memory for alignment.\n");
+            goto fail;
+        }
+    }
+
+    if (ret < -1) {
+        fprintf(stderr, "[markdup] error: truncated input file.\n");
+        goto fail;
+    }
+
+    // one last check
+    if (param->tag || param->opt_dist) {
+        if (find_duplicate_chains(param, read_buffer, dup_hash, &dup_list, prev_coord, prev_tid, &opt_warnings, &single_optical, &optical, 0)) {
+            fprintf(stderr, "[markdup] error: duplicate checking failed.\n");
+            goto fail;
+        }
+    }
+
+    // write out the end of the list
+    rq = kl_begin(read_buffer);
+    while (rq != kl_end(read_buffer)) {
+        in_read = &kl_val(rq);
+
+        if (bam_get_qname(in_read->b)) { // last entry will be blank
+            if (!param->remove_dups || !(in_read->b->core.flag & BAM_FDUP)) {
+                if (param->supp) {
+                    if (tmp_file_write(&temp, in_read->b)) {
+                        fprintf(stderr, "[markdup] error: writing temp output failed.\n");
+                        goto fail;
+                    }
+                } else {
+                    if (sam_write1(param->out, header, in_read->b) < 0) {
+                        fprintf(stderr, "[markdup] error: writing output failed.\n");
+                        goto fail;
+                    }
+                }
+
+                writing++;
+            }
+        }
+
+        kl_shift(read_queue, read_buffer, NULL);
+        bam_destroy1(in_read->b);
+        rq = kl_begin(read_buffer);
+    }
+
+    if (param->supp) {
+        bam1_t *b;
+
+        if (tmp_file_end_write(&temp)) {
+            fprintf(stderr, "[markdup] error: unable to end tmp writing.\n");
+            goto fail;
+        }
+
+        // read data from temp file and mark duplicate supplementary alignments
+
+        if (tmp_file_begin_read(&temp)) {
+            goto fail;
+        }
+
+        b = bam_init1();
+
+        while ((ret = tmp_file_read(&temp, b)) > 0) {
+
+            if ((b->core.flag & BAM_FSUPPLEMENTARY) || (b->core.flag & BAM_FUNMAP) || (b->core.flag & BAM_FSECONDARY)) {
+
+                k = kh_get(duplicates, dup_hash, bam_get_qname(b));
+
+                if (k != kh_end(dup_hash)) {
+
+                    b->core.flag  |= BAM_FDUP;
+                    np_duplicate++;
+
+                    if (param->tag && kh_val(dup_hash, k).name) {
+                        if (bam_aux_update_str(b, "do", strlen(kh_val(dup_hash, k).name) + 1, (char*)kh_val(dup_hash, k).name)) {
+                            fprintf(stderr, "[markdup] error: unable to append supplementary 'do' tag.\n");
+                            goto fail;
+                        }
+                    }
+
+                    if (param->opt_dist) {
+                        if (kh_val(dup_hash, k).type) {
+                            bam_aux_update_str(b, "dt", 3, "SQ");
+                            np_opt_duplicate++;
+                        } else {
+                            bam_aux_update_str(b, "dt", 3, "LB");
+                        }
+                    }
+                }
+            }
+
+            if (!param->remove_dups || !(b->core.flag & BAM_FDUP)) {
+                if (sam_write1(param->out, header, b) < 0) {
+                    fprintf(stderr, "[markdup] error: writing final output failed.\n");
+                    goto fail;
+                }
+            }
+        }
+
+        if (ret == -1) {
+            fprintf(stderr, "[markdup] error: failed to read tmp file.\n");
+            goto fail;
+        }
+
+        for (k = kh_begin(dup_hash); k != kh_end(dup_hash); ++k) {
+            if (kh_exist(dup_hash, k)) {
+                free(kh_val(dup_hash, k).name);
+                free((char *)kh_key(dup_hash, k));
+                kh_key(dup_hash, k) = NULL;
+            }
+        }
+
+        tmp_file_destroy(&temp);
+        bam_destroy1(b);
+    }
+
+    if (opt_warnings) {
+        fprintf(stderr, "[markdup] warning: number of failed attempts to get coordinates from read names = %ld\n",
+                        opt_warnings);
+    }
+
+    if (bc_warnings) {
+        fprintf(stderr, "[markdup] warning: number of failed attempts to get barcodes = %ld\n", bc_warnings);
+    }
+
+    if (param->do_stats) {
+        FILE *fp;
+        int file_open = 0;
+        unsigned long els;
+
+        if (param->stats_file) {
+            if (NULL == (fp = fopen(param->stats_file, "w"))) {
+                fprintf(stderr, "[markdup] warning: cannot write stats to %s.\n", param->stats_file);
+                fp = stderr;
+            } else {
+                file_open = 1;
+            }
+        } else {
+            fp = stderr;
+        }
+
+        els = estimate_library_size(pair, duplicate, optical);
+
+        fprintf(fp,
+                "COMMAND: %s\n"
+                "READ: %ld\n"
+                "WRITTEN: %ld\n"
+                "EXCLUDED: %ld\n"
+                "EXAMINED: %ld\n"
+                "PAIRED: %ld\n"
+                "SINGLE: %ld\n"
+                "DUPLICATE PAIR: %ld\n"
+                "DUPLICATE SINGLE: %ld\n"
+                "DUPLICATE PAIR OPTICAL: %ld\n"
+                "DUPLICATE SINGLE OPTICAL: %ld\n"
+                "DUPLICATE NON PRIMARY: %ld\n"
+                "DUPLICATE NON PRIMARY OPTICAL: %ld\n"
+                "DUPLICATE PRIMARY TOTAL: %ld\n"
+                "DUPLICATE TOTAL: %ld\n"
+                "ESTIMATED_LIBRARY_SIZE: %ld\n", param->arg_list, reading, writing, excluded, examined, pair, single,
+                                duplicate, single_dup, optical, single_optical, np_duplicate, np_opt_duplicate,
+                                single_dup + duplicate, single_dup + duplicate + np_duplicate, els);
+
+        if (file_open) {
+            fclose(fp);
+        }
+    }
+
+    if (param->write_index) {
+        if (sam_idx_save(param->out) < 0) {
+            print_error_errno("markdup", "writing index failed");
+            goto fail;
+        }
+    }
+
+    if (param->check_chain && (param->tag || param->opt_dist))
+        free(dup_list.c);
+
+    kh_destroy(reads, pair_hash);
+    kh_destroy(reads, single_hash);
+    kl_destroy(read_queue, read_buffer);
+    kh_destroy(duplicates, dup_hash);
+    sam_hdr_destroy(header);
+
+    return 0;
+
+ fail:
+    for (rq = kl_begin(read_buffer); rq != kl_end(read_buffer); rq = kl_next(rq))
+        bam_destroy1(kl_val(rq).b);
+    kl_destroy(read_queue, read_buffer);
+
+    for (k = kh_begin(dup_hash); k != kh_end(dup_hash); ++k) {
+        if (kh_exist(dup_hash, k)) {
+            free((char *)kh_key(dup_hash, k));
+        }
+    }
+    kh_destroy(duplicates, dup_hash);
+
+    if (param->check_chain && (param->tag || param->opt_dist))
+        free(dup_list.c);
+
+    kh_destroy(reads, pair_hash);
+    kh_destroy(reads, single_hash);
+    sam_hdr_destroy(header);
+    return 1;
+}
+
+
+static int markdup_usage(void) {
+    fprintf(stderr, "\n");
+    fprintf(stderr, "Usage:  samtools markdup <input.bam> <output.bam>\n\n");
+    fprintf(stderr, "Option: \n");
+    fprintf(stderr, "  -r                 Remove duplicate reads\n");
+    fprintf(stderr, "  -l INT             Max read length (default 300 bases)\n");
+    fprintf(stderr, "  -S                 Mark supplementary alignments of duplicates as duplicates (slower).\n");
+    fprintf(stderr, "  -s                 Report stats.\n");
+    fprintf(stderr, "  -f NAME            Write stats to named file.  Implies -s.\n");
+    fprintf(stderr, "  -T PREFIX          Write temporary files to PREFIX.samtools.nnnn.nnnn.tmp.\n");
+    fprintf(stderr, "  -d INT             Optical distance (if set, marks with dt tag)\n");
+    fprintf(stderr, "  -c                 Clear previous duplicate settings and tags.\n");
+    fprintf(stderr, "  -m --mode TYPE     Duplicate decision method for paired reads.\n"
+                    "                     TYPE = t measure positions based on template start/end (default).\n"
+                    "                            s measure positions based on sequence start.\n");
+    fprintf(stderr, "  -u                 Output uncompressed data\n");
+    fprintf(stderr, "  --include-fails    Include quality check failed reads.\n");
+    fprintf(stderr, "  --no-PG            Do not add a PG line\n");
+    fprintf(stderr, "  --no-multi-dup     Reduced duplicates of duplicates checking.\n");
+    fprintf(stderr, "  --read-coords STR  Regex for coords from read name.\n");
+    fprintf(stderr, "  --coords-order STR Order of regex elements. txy (default).  With t being a part of\n"
+                    "                     the read names that must be equal and x/y being coordinates.\n");
+    fprintf(stderr, "  --barcode-tag STR  Use barcode a tag that duplicates much match.\n");
+    fprintf(stderr, "  --barcode-name     Use the UMI/barcode in the read name (eigth colon delimited part).\n");
+    fprintf(stderr, "  --barcode-rgx STR  Regex for barcode in the readname (alternative to --barcode-name).\n");
+    fprintf(stderr, "  -t                 Mark primary duplicates with the name of the original in a \'do\' tag."
+                                        " Mainly for information and debugging.\n");
+
+    sam_global_opt_help(stderr, "-.O..@..");
+
+    fprintf(stderr, "\nThe input file must be coordinate sorted and must have gone"
+                     " through fixmates with the mate scoring option on.\n");
+
+    return 1;
+}
+
+
+int bam_markdup(int argc, char **argv) {
+    int c, ret, bc_name = 0;
+    char wmode[4] = {'w', 'b', 0, 0};
+    sam_global_args ga = SAM_GLOBAL_ARGS_INIT;
+    htsThreadPool p = {NULL, 0};
+    kstring_t tmpprefix = {0, 0, NULL};
+    struct stat st;
+    unsigned int t;
+    char *regex = NULL, *bc_regex = NULL;
+    char *regex_order = "txy";
+    md_param_t param = {NULL, NULL, NULL, 0, 300, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+                        1, NULL, NULL, NULL, NULL, 0, 0, 0, NULL, NULL};
+
+    static const struct option lopts[] = {
+        SAM_OPT_GLOBAL_OPTIONS('-', 0, 'O', 0, 0, '@'),
+        {"include-fails", no_argument, NULL, 1001},
+        {"no-PG", no_argument, NULL, 1002},
+        {"mode", required_argument, NULL, 'm'},
+        {"no-multi-dup", no_argument, NULL, 1003},
+        {"read-coords", required_argument, NULL, 1004},
+        {"coords-order", required_argument, NULL, 1005},
+        {"barcode-tag", required_argument, NULL, 1006},
+        {"barcode-name", no_argument, NULL, 1007},
+        {"barcode-rgx", required_argument, NULL, 1008},
+        {NULL, 0, NULL, 0}
+    };
+
+    while ((c = getopt_long(argc, argv, "rsl:StT:O:@:f:d:cm:u", lopts, NULL)) >= 0) {
+        switch (c) {
+            case 'r': param.remove_dups = 1; break;
+            case 'l': param.max_length = atoi(optarg); break;
+            case 's': param.do_stats = 1; break;
+            case 'T': kputs(optarg, &tmpprefix); break;
+            case 'S': param.supp = 1; break;
+            case 't': param.tag = 1; break;
+            case 'f': param.stats_file = optarg; param.do_stats = 1; break;
+            case 'd': param.opt_dist = atoi(optarg); break;
+            case 'c': param.clear = 1; break;
+            case 'm':
+                if (strcmp(optarg, "t") == 0) {
+                    param.mode = MD_MODE_TEMPLATE;
+                } else if (strcmp(optarg, "s") == 0) {
+                    param.mode = MD_MODE_SEQUENCE;
+                } else {
+                    fprintf(stderr, "[markdup] error: unknown mode '%s'.\n", optarg);
+                    return markdup_usage();
+                }
+
+                break;
+            case 'u': wmode[2] = '0'; break;
+            case 1001: param.include_fails = 1; break;
+            case 1002: param.no_pg = 1; break;
+            case 1003: param.check_chain = 0; break;
+            case 1004: regex = optarg; break;
+            case 1005: regex_order = optarg; break;
+            case 1006: param.barcode = optarg; break;
+            case 1007: bc_name = 1; break;
+            case 1008: bc_name = 1, bc_regex = optarg; break;
+            default: if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break;
+            /* else fall-through */
+            case '?': return markdup_usage();
+        }
+    }
+
+    if (optind + 2 > argc)
+        return markdup_usage();
+
+    if (param.barcode && bc_name) {
+        fprintf(stderr, "[markdup] Error: cannot specify --barcode-tag and "
+                        "--barcode-name (or --barcode-rgx) at same time.\n");
+        return 1;
+    }
+
+    if (param.opt_dist < 0) param.opt_dist = 0;
+    if (param.max_length < 0) param.max_length = 300;
+
+    if (regex) {
+        int result;
+
+        // set the order the elements of the regex are assigned to.
+        // x and y being coordinates, t being any other important part of the read
+        // e.g. tile and lane
+        // x and y order does not matter as long as it is consistent
+
+        if ((strncmp(regex_order, "txy", 3) == 0) || (strncmp(regex_order, "tyx", 3) == 0)) {
+            param.rgx_t = 1;
+            param.rgx_x = 2;
+            param.rgx_y = 3;
+        } else if ((strncmp(regex_order, "xyt", 3) == 0) || (strncmp(regex_order, "yxt", 3) == 0)) {
+            param.rgx_x = 1;
+            param.rgx_y = 2;
+            param.rgx_t = 3;
+        } else if ((strncmp(regex_order, "xty", 3) == 0) || (strncmp(regex_order, "ytx", 3) == 0)) {
+            param.rgx_x = 1;
+            param.rgx_t = 2;
+            param.rgx_y = 3;
+        } else if ((strncmp(regex_order, "xy", 2) == 0) || (strncmp(regex_order, "yx", 2) == 0)) {
+            param.rgx_x = 1;
+            param.rgx_y = 2;
+            param.rgx_t = 0;
+        } else {
+            fprintf(stderr, "[markdup] error:  could not recognise regex coordinate order \"%s\".\n", regex_order);
+            return 1;
+        }
+
+        if ((param.rgx = malloc(sizeof(regex_t))) == NULL) {
+            fprintf(stderr, "[markdup] error:  could not allocate memory for regex.\n");
+            return 1;
+        }
+
+        if ((result = regcomp(param.rgx, regex, REG_EXTENDED))) {
+            char err_msg[256];
+
+            regerror(result, param.rgx, err_msg, 256);
+            fprintf(stderr, "[markdup] error: regex error \"%s\"\n", err_msg);
+            free(param.rgx);
+            return 1;
+        }
+    }
+
+    if (bc_name) {
+        int result;
+
+        /* From Illumina UMI documentation: "The UMI sequence is located in the
+           eighth colon-delimited field of the read name (QNAME)". */
+        char *rgx = "[0-9A-Za-z]+:[0-9]+:[0-9]+:[0-9]+:[0-9]+:[0-9]+:[0-9]+:([!-?A-~]+)";
+
+        if ((param.bc_rgx = malloc(sizeof(regex_t))) == NULL) {
+            fprintf(stderr, "[markdup] error:  could not allocate memory for barcode regex.\n");
+            return 1;
+        }
+
+        if (bc_regex) {
+            rgx = bc_regex;
+        }
+
+        if ((result = regcomp(param.bc_rgx, rgx, REG_EXTENDED))) {
+            char err_msg[256];
+
+            regerror(result, param.bc_rgx, err_msg, 256);
+            fprintf(stderr, "[markdup] error: barcode regex error \"%s\"\n", err_msg);
+            free(param.bc_rgx);
+            return 1;
+        }
+    }
+
+    param.in = sam_open_format(argv[optind], "r", &ga.in);
+
+    if (!param.in) {
+        print_error_errno("markdup", "failed to open \"%s\" for input", argv[optind]);
+        return 1;
+    }
+
+    sam_open_mode(wmode + 1, argv[optind + 1], NULL);
+    param.out = sam_open_format(argv[optind + 1], wmode, &ga.out);
+
+    if (!param.out) {
+        print_error_errno("markdup", "failed to open \"%s\" for output", argv[optind + 1]);
+        return 1;
+    }
+
+    if (ga.nthreads > 0)  {
+        if (!(p.pool = hts_tpool_init(ga.nthreads))) {
+            fprintf(stderr, "[markdup] error creating thread pool\n");
+            return 1;
+        }
+
+        hts_set_opt(param.in,  HTS_OPT_THREAD_POOL, &p);
+        hts_set_opt(param.out, HTS_OPT_THREAD_POOL, &p);
+    }
+
+    // actual stuff happens here
+
+    // we need temp files so fix up the name here
+    if (tmpprefix.l == 0) {
+
+        if (strcmp(argv[optind + 1], "-") != 0)
+            ksprintf(&tmpprefix, "%s.", argv[optind + 1]);
+        else
+            kputc('.', &tmpprefix);
+    }
+
+    if (stat(tmpprefix.s, &st) == 0 && S_ISDIR(st.st_mode)) {
+        if (tmpprefix.s[tmpprefix.l-1] != '/') kputc('/', &tmpprefix);
+    }
+
+    t = ((unsigned) time(NULL)) ^ ((unsigned) clock());
+    ksprintf(&tmpprefix, "samtools.%d.%u.tmp", (int) getpid(), t % 10000);
+    param.prefix = tmpprefix.s;
+
+    param.arg_list = stringify_argv(argc + 1, argv - 1);
+    param.write_index = ga.write_index;
+    param.out_fn = argv[optind + 1];
+
+    ret = bam_mark_duplicates(&param);
+
+    sam_close(param.in);
+
+    if (sam_close(param.out) < 0) {
+        fprintf(stderr, "[markdup] error closing output file\n");
+        ret = 1;
+    }
+
+    if (p.pool) hts_tpool_destroy(p.pool);
+
+    if (param.rgx) {
+        regfree(param.rgx);
+        free(param.rgx);
+    }
+
+    if (param.bc_rgx) {
+        regfree(param.bc_rgx);
+        free(param.bc_rgx);
+    }
+
+    free(param.arg_list);
+    free(tmpprefix.s);
+    sam_global_args_free(&ga);
+
+    return ret;
+}
diff --git a/samtools/bam_markdup.c.pysam.c b/samtools/bam_markdup.c.pysam.c
new file mode 100644
index 0000000..3c14d8b
--- /dev/null
+++ b/samtools/bam_markdup.c.pysam.c
@@ -0,0 +1,2282 @@
+#include "samtools.pysam.h"
+
+/*  bam_markdup.c -- Mark duplicates from a coord sorted file that has gone
+                     through fixmates with the mate scoring option on.
+
+    Copyright (C) 2017-2022 Genome Research Ltd.
+
+    Author: Andrew Whitwham <aw7@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE
+
+Estimate library size derived from Picard DuplicationMetrics.java
+Copyright (c) 2009,2018 The Broad Institute.  MIT license.
+*/
+
+#include <config.h>
+
+#include <stdlib.h>
+#include <string.h>
+#include <stdio.h>
+#include <unistd.h>
+#include <ctype.h>
+#include <time.h>
+#include <sys/stat.h>
+#include <math.h>
+#include <regex.h>
+#include "htslib/thread_pool.h"
+#include "htslib/sam.h"
+#include "sam_opts.h"
+#include "samtools.h"
+#include "htslib/khash.h"
+#include "htslib/klist.h"
+#include "htslib/kstring.h"
+#include "tmp_file.h"
+#include "bam.h"
+
+
+typedef struct {
+    samFile *in;
+    samFile *out;
+    char *prefix;
+    int remove_dups;
+    int32_t max_length;
+    int do_stats;
+    int supp;
+    int tag;
+    int opt_dist;
+    int no_pg;
+    int clear;
+    int mode;
+    int write_index;
+    int include_fails;
+    int check_chain;
+    char *stats_file;
+    char *arg_list;
+    char *out_fn;
+    regex_t *rgx;
+    int rgx_x;
+    int rgx_y;
+    int rgx_t;
+    char *barcode;
+    regex_t *bc_rgx;
+} md_param_t;
+
+typedef struct {
+    hts_pos_t this_coord;
+    hts_pos_t other_coord;
+    int32_t this_ref;
+    int32_t other_ref;
+    int32_t barcode;
+    int8_t single;
+    int8_t leftmost;
+    int8_t orientation;
+} key_data_t;
+
+typedef struct read_queue_s {
+    key_data_t pair_key;
+    key_data_t single_key;
+    bam1_t *b;
+    struct read_queue_s *duplicate;
+    hts_pos_t pos;
+    int dup_checked;
+} read_queue_t;
+
+typedef struct {
+    read_queue_t *p;
+} in_hash_t;
+
+typedef struct {
+    char *name;
+    char type;
+} dup_map_t;
+
+typedef struct {
+    bam1_t *b;
+    int64_t score;
+    int64_t mate_score;
+    long x;
+    long y;
+    int opt;
+    int beg;
+    int end;
+} check_t;
+
+
+typedef struct {
+    check_t *c;
+    size_t size;
+    size_t length;
+} check_list_t;
+
+static khint32_t do_hash(unsigned char *key, khint32_t len);
+
+static khint_t hash_key(key_data_t key) {
+    int i = 0;
+    khint_t hash;
+
+    if (key.single) {
+        unsigned char sig[17];
+
+        memcpy(sig + i, &key.this_ref, 4);      i += 4;
+        memcpy(sig + i, &key.this_coord, 8);    i += 8;
+        memcpy(sig + i, &key.orientation, 1);   i += 1;
+        memcpy(sig + i, &key.barcode, 4);       i += 4;
+
+        hash = do_hash(sig, i);
+    } else {
+        unsigned char sig[30];
+
+        memcpy(sig + i, &key.this_ref, 4);      i += 4;
+        memcpy(sig + i, &key.this_coord, 8);    i += 8;
+        memcpy(sig + i, &key.other_ref, 4);     i += 4;
+        memcpy(sig + i, &key.other_coord, 8);   i += 8;
+        memcpy(sig + i, &key.leftmost, 1);      i += 1;
+        memcpy(sig + i, &key.orientation, 1);   i += 1;
+        memcpy(sig + i, &key.barcode, 4);       i += 4;
+
+        hash = do_hash(sig, i);
+    }
+
+    return hash;
+}
+
+
+static int key_equal(key_data_t a, key_data_t b) {
+    int match = 1;
+
+    if (a.this_coord != b.this_coord)
+        match = 0;
+    else if (a.orientation != b.orientation)
+        match = 0;
+    else if (a.this_ref != b.this_ref)
+        match = 0;
+    else if (a.single != b.single)
+        match = 0;
+    else if (a.barcode != b.barcode)
+        match = 0;
+
+    if (!a.single) {
+        if (a.other_coord != b.other_coord)
+            match = 0;
+        else if (a.leftmost != b.leftmost)
+            match = 0;
+        else if (a.other_ref != b.other_ref)
+            match = 0;
+    }
+
+    return match;
+}
+
+
+#define __free_queue_element(p)
+
+// Orientations (prime numbers to feed to hashing algorithm)
+#define O_FF 2
+#define O_RR 3
+#define O_FR 5
+#define O_RF 7
+
+// Left or rightmost
+#define R_LE 11
+#define R_RI 13
+
+#define BMD_WARNING_MAX 10
+
+#define MD_MIN_QUALITY 15
+
+// Duplicate finding mode
+#define MD_MODE_TEMPLATE 0
+#define MD_MODE_SEQUENCE 1
+
+KHASH_INIT(reads, key_data_t, in_hash_t, 1, hash_key, key_equal) // read map hash
+KLIST_INIT(read_queue, read_queue_t, __free_queue_element) // the reads buffer
+KHASH_MAP_INIT_STR(duplicates, dup_map_t) // map of duplicates for supplementary dup id
+
+/* The Bob Jenkins one_at_a_time hash to reduce the key to a 32 bit value. */
+
+static khint32_t do_hash(unsigned char *key, khint32_t len) {
+    khint32_t   hash, i;
+
+    for (hash = 0, i = 0; i < len; ++i) {
+        hash += key[i];
+        hash += (hash << 10);
+        hash ^= (hash >> 6);
+    }
+
+    hash += (hash << 3);
+    hash ^= (hash >> 11);
+    hash += (hash << 15);
+
+    return hash;
+}
+
+
+/* Get mate score from tag. */
+
+static int64_t get_mate_score(bam1_t *b) {
+    uint8_t *data;
+    int64_t score;
+
+    if ((data = bam_aux_get(b, "ms"))) {
+        score = bam_aux2i(data);
+    } else {
+        fprintf(samtools_stderr, "[markdup] error: no ms score tag. Please run samtools fixmate on file first.\n");
+        return -1;
+    }
+
+    return score;
+}
+
+
+/* Calc current score from quality. */
+
+static int64_t calc_score(bam1_t *b)
+{
+    int64_t score = 0;
+    uint8_t  *qual = bam_get_qual(b);
+    int i;
+
+    for (i = 0; i < b->core.l_qseq; i++) {
+        if (qual[i] >= MD_MIN_QUALITY) score += qual[i];
+    }
+
+    return score;
+}
+
+
+/* Create a signature hash of the current read and its pair.
+   Uses the unclipped start (or end depending on orientation),
+   the reference id, orientation and whether the current
+   read is leftmost of the pair. */
+
+
+static int make_pair_key(md_param_t *param, key_data_t *key, bam1_t *bam, long *warnings) {
+     hts_pos_t this_coord, this_end, other_coord, other_end, leftmost;
+    int32_t this_ref, other_ref, barcode = 0;
+    int8_t orientation, left_read;
+    uint8_t *data;
+    char *cig, *bar;
+    long incoming_warnings = *warnings;
+
+    this_ref    = bam->core.tid + 1; // avoid a 0 being put into the hash
+    other_ref   = bam->core.mtid + 1;
+
+    this_coord = unclipped_start(bam);
+    this_end   = unclipped_end(bam);
+
+    if ((data = bam_aux_get(bam, "MC"))) {
+        if (!(cig = bam_aux2Z(data))) {
+            fprintf(samtools_stderr, "[markdup] error: MC tag wrong type. Please use the MC tag provided by samtools fixmate.\n");
+            return 1;
+        }
+
+        other_end   = unclipped_other_end(bam->core.mpos, cig);
+        other_coord = unclipped_other_start(bam->core.mpos, cig);
+    } else {
+        fprintf(samtools_stderr, "[markdup] error: no MC tag. Please run samtools fixmate on file first.\n");
+        return 1;
+    }
+
+    // work out orientations
+    if (param->mode == MD_MODE_TEMPLATE) {
+
+        if (this_ref != other_ref) {
+            leftmost = this_ref < other_ref;
+        } else {
+            if (bam_is_rev(bam) == bam_is_mrev(bam)) {
+                if (!bam_is_rev(bam)) {
+                    leftmost = this_coord <= other_coord;
+                } else {
+                    leftmost = this_end <= other_end;
+                }
+            } else {
+                if (bam_is_rev(bam)) {
+                    leftmost = this_end <= other_coord;
+                } else {
+                    leftmost = this_coord <= other_end;
+                }
+            }
+        }
+
+        // pair orientation
+        if (leftmost) {
+            if (bam_is_rev(bam) == bam_is_mrev(bam)) {
+                other_coord = other_end;
+
+                if (!bam_is_rev(bam)) {
+                    if (bam->core.flag & BAM_FREAD1) {
+                        orientation = O_FF;
+                    } else {
+                        orientation = O_RR;
+                    }
+                } else {
+                    if (bam->core.flag & BAM_FREAD1) {
+                        orientation = O_RR;
+                    } else {
+                        orientation = O_FF;
+                    }
+                }
+            } else {
+                if (!bam_is_rev(bam)) {
+                    orientation = O_FR;
+                    other_coord = other_end;
+                } else {
+                    orientation = O_RF;
+                    this_coord = this_end;
+                }
+            }
+        } else {
+            if (bam_is_rev(bam) == bam_is_mrev(bam)) {
+                this_coord = this_end;
+
+                if (!bam_is_rev(bam)) {
+                    if (bam->core.flag & BAM_FREAD1) {
+                        orientation = O_RR;
+                    } else {
+                        orientation = O_FF;
+                    }
+                } else {
+                    if (bam->core.flag & BAM_FREAD1) {
+                        orientation = O_FF;
+                    } else {
+                        orientation = O_RR;
+                    }
+                }
+            } else {
+                if (!bam_is_rev(bam)) {
+                    orientation = O_RF;
+                    other_coord = other_end;
+                } else {
+                    orientation = O_FR;
+                    this_coord = this_end;
+                }
+            }
+        }
+    } else { // MD_MODE_SEQUENCE
+
+        if (this_ref != other_ref) {
+            leftmost = this_ref - other_ref;
+        } else {
+            if (bam_is_rev(bam) == bam_is_mrev(bam)) {
+                if (!bam_is_rev(bam)) {
+                    leftmost = this_coord - other_coord;
+                } else {
+                    leftmost = this_end - other_end;
+                }
+            } else {
+                if (bam_is_rev(bam)) {
+                    leftmost = this_end - other_coord;
+                } else {
+                    leftmost = this_coord - other_end;
+                }
+            }
+        }
+
+        if (leftmost < 0) {
+            leftmost = 1;
+        } else if (leftmost > 0) {
+            leftmost = 0;
+        } else {
+            // tie breaks
+
+            if (bam->core.pos == bam->core.mpos) {
+                if (bam->core.flag & BAM_FREAD1) {
+                    leftmost = 1;
+                } else {
+                    leftmost = 0;
+                }
+            } else if (bam->core.pos < bam->core.mpos) {
+                leftmost = 1;
+            } else {
+                leftmost = 0;
+            }
+        }
+
+        // pair orientation
+        if (leftmost) {
+            if (bam_is_rev(bam) == bam_is_mrev(bam)) {
+
+                if (!bam_is_rev(bam)) {
+                        orientation = O_FF;
+                } else {
+                        orientation = O_RR;
+                }
+            } else {
+                if (!bam_is_rev(bam)) {
+                    orientation = O_FR;
+                } else {
+                    orientation = O_RF;
+                }
+            }
+        } else {
+            if (bam_is_rev(bam) == bam_is_mrev(bam)) {
+
+                if (!bam_is_rev(bam)) {
+                        orientation = O_RR;
+                } else {
+                        orientation = O_FF;
+                }
+            } else {
+                if (!bam_is_rev(bam)) {
+                    orientation = O_RF;
+                } else {
+                    orientation = O_FR;
+                }
+            }
+        }
+
+        if (!bam_is_rev(bam)) {
+            this_coord = unclipped_start(bam);
+        } else {
+            this_coord = unclipped_end(bam);
+        }
+
+        if (!bam_is_mrev(bam)) {
+            other_coord = unclipped_other_start(bam->core.mpos, cig);
+        } else {
+            other_coord = unclipped_other_end(bam->core.mpos, cig);
+        }
+    }
+
+    if (!leftmost)
+        left_read = R_RI;
+    else
+        left_read = R_LE;
+
+    if (param->barcode) {
+        if ((data = bam_aux_get(bam, param->barcode))) {
+            if (!(bar = bam_aux2Z(data))) {
+                (*warnings)++;
+
+                if (*warnings <= BMD_WARNING_MAX) {
+                    fprintf(samtools_stderr, "[markdup] warning: %s tag wrong type. Aux tag needs to be a string type.\n", param->barcode);
+                }
+            } else {
+                barcode = do_hash((unsigned char *)bar, strlen(bar));
+            }
+        }
+    } else if (param->bc_rgx) {
+        int result;
+        regmatch_t matches[3];
+        size_t max_matches = 2;
+        char *qname = bam_get_qname(bam);
+
+        if ((result = regexec(param->bc_rgx, qname, max_matches, matches, 0)) == 0) {
+            int bc_start, bc_end;
+
+            bc_start = matches[1].rm_so;
+            bc_end   = matches[1].rm_eo;
+
+            if (bc_start != -1) {
+                barcode = do_hash((unsigned char *)qname + bc_start, bc_end - bc_start);
+            } else {
+                (*warnings)++;
+
+                if (*warnings <= BMD_WARNING_MAX) {
+                    fprintf(samtools_stderr, "[markdup] warning: barcode regex unable to match substring on %s.\n", qname);
+                }
+            }
+        } else {
+            (*warnings)++;
+
+            if (*warnings <= BMD_WARNING_MAX) {
+                char warn_msg[256];
+
+                regerror(result, param->bc_rgx, warn_msg, 256);
+                fprintf(samtools_stderr, "[markdup] warning: barcode regex match error \"%s\" on %s.\n", warn_msg, qname);
+            }
+        }
+    }
+
+    if ((*warnings == BMD_WARNING_MAX) && (incoming_warnings != *warnings)) {
+        fprintf(samtools_stderr, "[markdup] warning: %ld barcode read warnings.  New warnings will not be reported.\n",
+                        *warnings);
+    }
+
+    key->single        = 0;
+    key->this_ref      = this_ref;
+    key->this_coord    = this_coord;
+    key->other_ref     = other_ref;
+    key->other_coord   = other_coord;
+    key->leftmost      = left_read;
+    key->orientation   = orientation;
+    key->barcode       = barcode;
+
+    return 0;
+}
+
+
+/* Create a signature hash of single read (or read with an unmatched pair).
+   Uses unclipped start (or end depending on orientation), reference id,
+   and orientation. */
+
+static void make_single_key(md_param_t *param, key_data_t *key, bam1_t *bam, long *warnings) {
+    hts_pos_t this_coord;
+    int32_t this_ref, barcode = 0;
+    int8_t orientation;
+    uint8_t *data;
+    char *bar;
+    long incoming_warnings = *warnings;
+
+    this_ref = bam->core.tid + 1; // avoid a 0 being put into the hash
+
+    if (bam_is_rev(bam)) {
+        this_coord = unclipped_end(bam);
+        orientation = O_RR;
+    } else {
+        this_coord = unclipped_start(bam);
+        orientation = O_FF;
+    }
+
+    if (param->barcode) {
+        if ((data = bam_aux_get(bam, param->barcode))) {
+            if (!(bar = bam_aux2Z(data))) {
+                (*warnings)++;
+
+                if (*warnings <= BMD_WARNING_MAX) {
+                    fprintf(samtools_stderr, "[markdup] warning: %s tag wrong type. Aux tag needs to be a string type.\n", param->barcode);
+                }
+            } else {
+                barcode = do_hash((unsigned char *)bar, strlen(bar));
+            }
+        }
+    } else if (param->bc_rgx) {
+        int result;
+        regmatch_t matches[3];
+        size_t max_matches = 2;
+        char *qname = bam_get_qname(bam);
+
+        if ((result = regexec(param->bc_rgx, qname, max_matches, matches, 0)) == 0) {
+            int bc_start, bc_end;
+
+            bc_start = matches[1].rm_so;
+            bc_end   = matches[1].rm_eo;
+
+            if (bc_start != -1) {
+                barcode = do_hash((unsigned char *)qname + bc_start, bc_end - bc_start);
+            } else {
+                (*warnings)++;
+
+                if (*warnings <= BMD_WARNING_MAX) {
+                    fprintf(samtools_stderr, "[markdup] warning: barcode regex unable to match substring on %s.\n", qname);
+                }
+            }
+        } else {
+            (*warnings)++;
+
+            if (*warnings <= BMD_WARNING_MAX) {
+                char warn_msg[256];
+
+                regerror(result, param->bc_rgx, warn_msg, 256);
+                fprintf(samtools_stderr, "[markdup] warning: barcode regex match error \"%s\" on %s.\n", warn_msg, qname);
+            }
+        }
+    }
+
+    if ((*warnings == BMD_WARNING_MAX) && (incoming_warnings != *warnings)) {
+        fprintf(samtools_stderr, "[markdup] warning: %ld barcode read warnings.  New warnings will not be reported.\n",
+                        *warnings);
+    }
+
+    key->single        = 1;
+    key->this_ref      = this_ref;
+    key->this_coord    = this_coord;
+    key->orientation   = orientation;
+    key->barcode       = barcode;
+}
+
+
+/* Add the duplicate name to a hash if it does not exist. */
+
+static int add_duplicate(khash_t(duplicates) *d_hash, bam1_t *dupe, char *orig_name, char type) {
+    khiter_t d;
+    int ret;
+
+    d = kh_get(duplicates, d_hash, bam_get_qname(dupe));
+
+    if (d == kh_end(d_hash)) {
+        char *name = strdup(bam_get_qname(dupe));
+        if (name) {
+            d = kh_put(duplicates, d_hash, name, &ret);
+        } else {
+            ret = -1;
+        }
+
+        if (ret >= 0) {
+            if (orig_name) {
+                if (ret == 0) {
+                    // replace old name
+                    free(kh_value(d_hash, d).name);
+                    free(name);
+                }
+
+                kh_value(d_hash, d).name = strdup(orig_name);
+
+                if (kh_value(d_hash, d).name == NULL) {
+                    fprintf(samtools_stderr, "[markdup] error: unable to allocate memory for duplicate original name.\n");
+                    return 1;
+                }
+            } else {
+                kh_value(d_hash, d).name = NULL;
+            }
+
+            kh_value(d_hash, d).type = type;
+        } else {
+            fprintf(samtools_stderr, "[markdup] error: unable to store supplementary duplicates.\n");
+            free(name);
+            return 1;
+        }
+    }
+
+    return 0;
+}
+
+
+/* Get coordinates from the standard Illumina style read names.
+   Returned values are of the x and y coordinates and a section of
+   the read name to test (t) for string equality e.g. lane and tile part. */
+
+static int get_coordinates_colons(md_param_t *param, const char *qname, int *t_beg, int *t_end, long *x_coord, long *y_coord, long *warnings) {
+    int sep = 0;
+    int pos = 0;
+    int xpos = 0, ypos = 0;
+    char *end;
+
+    while (qname[pos]) {
+        if (qname[pos] == ':') {
+            sep++;
+
+            if (sep == 2) {
+                xpos = pos + 1;
+            } else if (sep == 3) {
+                ypos = pos + 1;
+            } else if (sep == 4) { // HiSeq style names
+                xpos = ypos;
+                ypos = pos + 1;
+            } else if (sep == 5) { // Newer Illumina format
+                xpos = pos + 1;
+            } else if (sep == 6) {
+                ypos = pos + 1;
+            }
+        }
+
+        pos++;
+    }
+
+    /* The most current Illumina read format at time of writing is:
+       @machine:run:flowcell:lane:tile:x:y:UMI or
+       @machine:run:flowcell:lane:tile:x:y
+
+       Counting the separating colons gives us a quick format check.
+       Older name formats have fewer elements.
+    */
+
+    if (!(sep == 3 || sep == 4 || sep == 6 || sep == 7)) {
+        (*warnings)++;
+
+        if (*warnings <= BMD_WARNING_MAX) {
+            fprintf(samtools_stderr, "[markdup] warning: cannot decipher read name %s for optical duplicate marking.\n", qname);
+        }
+
+        return 1;
+    } else {
+        *x_coord = strtol(qname + xpos, &end, 10);
+
+        if ((qname + xpos) == end) {
+            (*warnings)++;
+
+            if (*warnings <= BMD_WARNING_MAX) {
+                fprintf(samtools_stderr, "[markdup] warning: cannot decipher x coordinate in %s .\n", qname);
+            }
+
+            return 1;
+        }
+
+        *y_coord = strtol(qname + ypos, &end, 10);
+
+        if ((qname + ypos) == end) {
+            (*warnings)++;
+
+            if (*warnings <= BMD_WARNING_MAX) {
+                fprintf(samtools_stderr, "[markdup] warning: cannot decipher y coordinate in %s .\n", qname);
+            }
+
+            return 1;
+        }
+
+        *t_beg = 0;
+        *t_end = xpos;
+    }
+
+    return 0;
+}
+
+/* Get the coordinates from the read name.
+   Returned values are of the x and y coordinates and an optional section of
+   the read name to test (t) for string equality e.g. lane and tile part. */
+
+static inline int get_coordinates_regex(md_param_t *param, const char *qname, int *t_beg, int *t_end, long *x_coord, long *y_coord, long *warnings) {
+    regmatch_t matches[5];
+    size_t max_matches = 5;
+    int xpos, ypos, xend, yend, xlen, ylen;
+    char coord[255];
+    char *end;
+
+    if (!param->rgx_t)
+        max_matches = 4;
+
+    if (regexec(param->rgx, qname, max_matches, matches, 0))
+        return -1;
+
+    xpos = matches[param->rgx_x].rm_so;
+    ypos = matches[param->rgx_y].rm_so;
+
+    if (param->rgx_t) {
+        *t_beg = matches[param->rgx_t].rm_so;
+        *t_end = matches[param->rgx_t].rm_eo;
+    } else {
+        *t_beg = *t_end = 0;
+    }
+
+    if (xpos == -1 || ypos == -1 || *t_beg == -1)
+        return -1;
+
+    xend = matches[param->rgx_x].rm_eo;
+    yend = matches[param->rgx_y].rm_eo;
+
+    if ((xlen = xend - xpos) > 254) {
+        (*warnings)++;
+
+        if (*warnings <= BMD_WARNING_MAX) {
+            fprintf(samtools_stderr, "[markdup] warning: x coordinate string longer than allowed qname length in %s (%d long).\n", qname, xlen);
+        }
+
+        return 1;
+    }
+
+    strncpy(coord, qname + xpos, xlen);
+    coord[xlen] = '\0';
+    *x_coord = strtol(coord, &end, 10);
+
+    if (coord == end) {
+        (*warnings)++;
+
+        if (*warnings <= BMD_WARNING_MAX) {
+            fprintf(samtools_stderr, "[markdup] warning: cannot decipher x coordinate in %s (%s).\n", qname, coord);
+        }
+
+        return 1;
+    }
+
+    if ((ylen = yend - ypos) > 254) {
+        (*warnings)++;
+
+        if (*warnings <= BMD_WARNING_MAX) {
+            fprintf(samtools_stderr, "[markdup] warning: y coordinate string longer than allowed qname length in %s (%d long).\n", qname, ylen);
+        }
+
+        return 1;
+    }
+
+    strncpy(coord, qname + ypos, ylen);
+    coord[ylen] = '\0';
+    *y_coord = strtol(coord, &end, 10);
+
+    if (coord == end) {
+        (*warnings)++;
+
+        if (*warnings <= BMD_WARNING_MAX) {
+            fprintf(samtools_stderr, "[markdup] warning: cannot decipher y coordinate in %s (%s).\n", qname, coord);
+        }
+
+        return 1;
+    }
+
+    return 0;
+}
+
+
+static int get_coordinates(md_param_t *param, const char *name, int *t_beg, int *t_end, long *x_coord, long *y_coord, long *warnings) {
+    int ret = 1;
+
+    if (param->rgx == NULL) {
+        ret = get_coordinates_colons(param, name, t_beg, t_end, x_coord, y_coord, warnings);
+    } else {
+        ret = get_coordinates_regex(param, name, t_beg, t_end, x_coord, y_coord, warnings);
+    }
+
+    return ret;
+}
+
+
+/* Using the coordinates from the read name, see whether the duplicated read is
+   close enough (set by max_dist) to the original to be counted as optical.*/
+
+static int is_optical_duplicate(md_param_t *param, bam1_t *ori, bam1_t *dup, long max_dist, long *warnings) {
+    int ret = 0;
+    char *original, *duplicate;
+    long ox, oy, dx, dy;
+    int o_beg = 0, o_end = 0, d_beg = 0, d_end = 0;
+
+    original  = bam_get_qname(ori);
+    duplicate = bam_get_qname(dup);
+
+    if (get_coordinates(param, original, &o_beg, &o_end, &ox, &oy, warnings)) {
+        return ret;
+    }
+
+    if (get_coordinates(param, duplicate, &d_beg, &d_end, &dx, &dy, warnings)) {
+        return ret;
+    }
+
+    if (strncmp(original + o_beg, duplicate + d_beg, o_end - o_beg) == 0) {
+        long xdiff, ydiff;
+
+        if (ox > dx) {
+            xdiff = ox - dx;
+        } else {
+            xdiff = dx - ox;
+        }
+
+        if (xdiff <= max_dist) {
+            // still might be optical
+
+            if (oy > dy) {
+                ydiff = oy - dy;
+            } else {
+                ydiff = dy - oy;
+            }
+
+            if (ydiff <= max_dist) ret = 1;
+        }
+    }
+
+    return ret;
+}
+
+
+/* Using the coordinates from the Illumina read name, see whether the duplicated read is
+   close enough (set by max_dist) to the original to be counted as optical.
+
+   This function needs the values from the first read to be already calculated. */
+
+static int optical_duplicate_partial(md_param_t *param, const char *name, const int o_beg, const int o_end, const long ox, const long oy, bam1_t *dup, check_t *c, long max_dist, long *warnings) {
+    int ret = 0;
+    char *duplicate;
+    int d_beg = 0, d_end = 0;
+    long dx, dy;
+
+    duplicate = bam_get_qname(dup);
+
+    if (get_coordinates(param, duplicate, &d_beg, &d_end, &dx, &dy, warnings)) {
+        return ret;
+    }
+
+    if (strncmp(name + o_beg, duplicate + d_beg, o_end - o_beg) == 0) {
+        // the initial parts match, look at the numbers
+        long xdiff, ydiff;
+
+        if (ox > dx) {
+            xdiff = ox - dx;
+        } else {
+            xdiff = dx - ox;
+        }
+
+        if (xdiff <= max_dist) {
+            // still might be optical
+
+            if (oy > dy) {
+                ydiff = oy - dy;
+            } else {
+                ydiff = dy - oy;
+            }
+
+            if (ydiff <= max_dist) ret = 1;
+        }
+    }
+
+    c->x = dx;
+    c->y = dy;
+    c->beg = d_beg;
+    c->end = d_end;
+
+    return ret;
+}
+
+
+/* Mark the read as a duplicate and update the duplicate hash (if needed) */
+static int mark_duplicates(md_param_t *param, khash_t(duplicates) *dup_hash, bam1_t *ori, bam1_t *dup,
+                           long *optical, long *warn) {
+    char dup_type = 0;
+    long incoming_warnings = *warn;
+
+    dup->core.flag |= BAM_FDUP;
+
+    if (param->tag) {
+        if (bam_aux_update_str(dup, "do", strlen(bam_get_qname(ori)) + 1, bam_get_qname(ori))) {
+            fprintf(samtools_stderr, "[markdup] error: unable to append 'do' tag.\n");
+            return -1;
+        }
+    }
+
+    if (param->opt_dist) { // mark optical duplicates
+        if (is_optical_duplicate(param, ori, dup, param->opt_dist, warn)) {
+            bam_aux_update_str(dup, "dt", 3, "SQ");
+            dup_type = 'O';
+            (*optical)++;
+        } else {
+            // not an optical duplicate
+            bam_aux_update_str(dup, "dt", 3, "LB");
+        }
+    }
+
+    if ((*warn == BMD_WARNING_MAX) && (incoming_warnings != *warn)) {
+        fprintf(samtools_stderr, "[markdup] warning: %ld decipher read name warnings.  New warnings will not be reported.\n",
+                        *warn);
+    }
+
+    if (param->supp) {
+        if (bam_aux_get(dup, "SA") || (dup->core.flag & BAM_FMUNMAP) || bam_aux_get(dup, "XA")) {
+            char *original = NULL;
+
+            if (param->tag) {
+                original = bam_get_qname(ori);
+            }
+
+            if (add_duplicate(dup_hash, dup, original, dup_type))
+                return -1;
+        }
+    }
+
+    return 0;
+}
+
+
+/* If the duplicate type has changed to optical then retag and duplicate hash. */
+static inline int optical_retag(md_param_t *param, khash_t(duplicates) *dup_hash, bam1_t *b, int paired, long *optical_single, long *optical_pair) {
+    int ret = 0;
+
+    if (bam_aux_update_str(b, "dt", 3, "SQ")) {
+        fprintf(samtools_stderr, "[markdup] error: unable to update 'dt' tag.\n");
+        ret = -1;
+    }
+
+    if (paired) {
+        (*optical_pair)++;
+    } else {
+        (*optical_single)++;
+    }
+
+    if (param->supp) {
+        // Change the duplicate type
+
+        if (bam_aux_get(b, "SA") || (b->core.flag & BAM_FMUNMAP)
+            || bam_aux_get(b, "XA")) {
+            khiter_t d;
+
+            d = kh_get(duplicates, dup_hash, bam_get_qname(b));
+
+            if (d == kh_end(dup_hash)) {
+                // error, name should already be in dup hash
+                fprintf(samtools_stderr, "[markdup] error: duplicate name %s not found in hash.\n",
+                    bam_get_qname(b));
+                ret = -1;
+            } else {
+                kh_value(dup_hash, d).type = 'O';
+            }
+        }
+    }
+
+    return ret;
+}
+
+
+/* Check all duplicates of the highest quality read (the "original") for consistancy.  Also
+   pre-calculate any values for use in check_duplicate_chain later.
+   Returns 0 on success, >0 on coordinate reading error (program can continue) or
+   <0 on an error (program should not continue. */
+static int check_chain_against_original(md_param_t *param, khash_t(duplicates) *dup_hash, read_queue_t *ori,
+             check_list_t *list, long *warn, long *optical_single, long *optical_pair) {
+
+    int ret = 0, coord_fail = 0;
+    char *ori_name = bam_get_qname(ori->b);
+    read_queue_t *current = ori->duplicate;
+    int t_beg = 0, t_end = 0;
+    long x, y;
+
+    if (param->opt_dist) {
+        coord_fail = get_coordinates(param, ori_name, &t_beg, &t_end, &x, &y, warn);
+    }
+
+    list->length = 0;
+
+    while (current) {
+        check_t *c;
+
+        if (list->length >= list->size) {
+            check_t *tmp;
+
+            list->size *= 2;
+
+            if (!(tmp = realloc(list->c, list->size * sizeof(check_t)))) {
+                fprintf(samtools_stderr, "[markdup] error: Unable to expand opt check list.\n");
+                return -1;
+            }
+
+            list->c = tmp;
+        }
+
+        c = &list->c[list->length];
+
+        c->b = current->b;
+        c->x = -1;
+        c->y = -1;
+        c->opt = 0;
+        c->score = 0;
+        c->mate_score = 0;
+        current->dup_checked = 1;
+
+        if (param->tag) {
+            uint8_t *data;
+
+            // at this stage all duplicates should have a do tag
+            if ((data = bam_aux_get(current->b, "do")) != NULL) {
+                // see if we need to change the tag
+                char *old_name = bam_aux2Z(data);
+
+                if (old_name) {
+                    if (strcmp(old_name, ori_name) != 0) {
+                        if (bam_aux_update_str(current->b, "do", strlen(ori_name) + 1, (const char *)ori_name)) {
+                            fprintf(samtools_stderr, "[markdup] error: unable to update 'do' tag.\n");
+                            ret =  -1;
+                            break;
+                        }
+                    }
+                } else {
+                    fprintf(samtools_stderr, "[markdup] error: 'do' tag has wrong type for read %s.\n", bam_get_qname(current->b));
+                    ret = -1;
+                    break;
+                }
+            }
+        }
+
+        if (param->opt_dist && !coord_fail) {
+            uint8_t *data;
+            char *dup_type;
+            int is_opt = 0;
+            int current_paired = (current->b->core.flag & BAM_FPAIRED) && !(current->b->core.flag & BAM_FMUNMAP);
+
+            if ((data = bam_aux_get(current->b, "dt"))) {
+                if ((dup_type = bam_aux2Z(data))) {
+                    if (strcmp(dup_type, "SQ") == 0) {
+                        c->opt = 1;
+                    }
+                }
+            }
+
+            // need to run this to get the duplicates x and y scores
+            is_opt = optical_duplicate_partial(param, ori_name, t_beg, t_end, x, y, current->b, c, param->opt_dist, warn);
+
+            if (!c->opt && is_opt) {
+                if (optical_retag(param, dup_hash, current->b, current_paired, optical_single, optical_pair)) {
+                    ret = -1;
+                    break;
+                }
+
+                c->opt = 1;
+            }
+
+            c->score = calc_score(current->b);
+
+            if (current_paired) {
+                if ((c->mate_score = get_mate_score(current->b)) == -1) {
+                     fprintf(samtools_stderr, "[markdup] error: no ms score tag. Please run samtools fixmate on file first.\n");
+                     ret = -1;
+                     break;
+                }
+            }
+        }
+
+        current = current->duplicate;
+        list->length++;
+    }
+
+    if (!ret && coord_fail)
+        ret = coord_fail;
+
+    return ret;
+}
+
+
+static int xcoord_sort(const void *a, const void *b) {
+    check_t *ac = (check_t *) a;
+    check_t *bc = (check_t *) b;
+
+    return (ac->x - bc->x);
+}
+
+
+/* Check all the duplicates against each other to see if they are optical duplicates. */
+static int check_duplicate_chain(md_param_t *param, khash_t(duplicates) *dup_hash, check_list_t *list,
+             long *warn, long *optical_single, long *optical_pair) {
+    int ret = 0;
+    size_t curr = 0;
+
+    qsort(list->c, list->length, sizeof(list->c[0]), xcoord_sort);
+
+    while (curr < list->length - 1) {
+        check_t *current = &list->c[curr];
+        size_t count = curr;
+        char *cur_name = bam_get_qname(current->b);
+        int current_paired = (current->b->core.flag & BAM_FPAIRED) && !(current->b->core.flag & BAM_FMUNMAP);
+
+        while (++count < list->length && (list->c[count].x - current->x <= param->opt_dist)) {
+            // while close enough along the x coordinate
+            check_t *chk = &list->c[count];
+
+            if (current->opt && chk->opt)
+                continue;
+
+            // if both are already optical duplicates there is no need to check again, otherwise...
+
+            long ydiff;
+
+            if (current->y > chk->y) {
+                ydiff = current->y - chk->y;
+            } else {
+                ydiff = chk->y - current->y;
+            }
+
+            if (ydiff > param->opt_dist)
+                continue;
+
+            // the number are right, check the names
+            if (strncmp(cur_name + current->beg, bam_get_qname(chk->b) + chk->beg, current->end - current->beg) != 0)
+                continue;
+
+            // optical duplicates
+            int chk_dup = 0;
+            int chk_paired = (chk->b->core.flag & BAM_FPAIRED) && !(chk->b->core.flag & BAM_FMUNMAP);
+
+            if (current_paired != chk_paired) {
+                if (!chk_paired) {
+                    // chk is single vs pair, this is a dup.
+                    chk_dup = 1;
+                }
+            } else {
+                // do it by scores
+                int64_t cur_score, chk_score;
+
+                if ((current->b->core.flag & BAM_FQCFAIL) != (chk->b->core.flag & BAM_FQCFAIL)) {
+                    if (current->b->core.flag & BAM_FQCFAIL) {
+                        cur_score = 0;
+                        chk_score = 1;
+                    } else {
+                        cur_score = 1;
+                        chk_score = 0;
+                    }
+                } else {
+                    cur_score = current->score;
+                    chk_score = chk->score;
+
+                    if (current_paired) {
+                        // they are pairs so add mate scores.
+                        chk_score += chk->mate_score;
+                        cur_score += current->mate_score;
+                    }
+                }
+
+                if (cur_score == chk_score) {
+                    if (strcmp(bam_get_qname(chk->b), cur_name) < 0) {
+                        chk_score++;
+                    } else {
+                        chk_score--;
+                    }
+                }
+
+                if (cur_score > chk_score) {
+                    chk_dup = 1;
+                }
+            }
+
+            if (chk_dup) {
+                // the duplicate is the optical duplicate
+                if (!chk->opt) { // only change if not already an optical duplicate
+                    if (optical_retag(param, dup_hash, chk->b, chk_paired, optical_single, optical_pair)) {
+                        ret = -1;
+                        goto fail;
+                    }
+
+                    chk->opt = 1;
+                }
+            } else {
+                if (!current->opt) {
+                    if (optical_retag(param, dup_hash, current->b, current_paired, optical_single, optical_pair)) {
+                        ret = -1;
+                        goto fail;
+                    }
+
+                    current->opt = 1;
+                }
+            }
+        }
+
+        curr++;
+    }
+
+ fail:
+    return ret;
+}
+
+
+/* Where there is more than one duplicate go down the list and check for optical duplicates and change
+   do tags (where used) to point to original (non-duplicate) read. */
+static int find_duplicate_chains(md_param_t *param, klist_t(read_queue) *read_buffer, khash_t(duplicates) *dup_hash, check_list_t *dup_list,
+                                const hts_pos_t prev_coord, const int32_t prev_tid, long *warn, long *optical_single,
+                                long *optical_pair, const int check_range) {
+    int ret = 0;
+    kliter_t(read_queue) *rq;
+
+    rq = kl_begin(read_buffer);
+
+    while (rq != kl_end(read_buffer)) {
+        read_queue_t *in_read = &kl_val(rq);
+
+        if (check_range) {
+            /* Just check against the moving window of reads based on coordinates and max read length. */
+            if (in_read->pos + param->max_length > prev_coord && in_read->b->core.tid == prev_tid && (prev_tid != -1 || prev_coord != -1)) {
+                break;
+            }
+        } else {
+            // this is the last set of results and the end entry will be blank
+            if (!bam_get_qname(in_read->b)) {
+                break;
+            }
+        }
+
+        if (!(in_read->b->core.flag & BAM_FDUP) && in_read->duplicate) { // is the head of a duplicate chain
+
+            // check against the original for tagging and optical duplication
+            if ((ret = check_chain_against_original(param, dup_hash, in_read, dup_list, warn, optical_single, optical_pair))) {
+                if (ret < 0) { // real error
+                    ret = -1;
+                    break;
+                } else { // coordinate decoding error
+                    ret = 0;
+                    in_read->duplicate = NULL;
+                    continue;
+                }
+            }
+
+            // check the rest of the duplicates against each other for optical duplication
+            if (param->opt_dist && check_duplicate_chain(param, dup_hash, dup_list, warn, optical_single, optical_pair)) {
+                ret = -1;
+                break;
+            }
+
+            in_read->duplicate = NULL;
+        }
+
+        rq = kl_next(rq);
+    }
+
+    return ret;
+}
+
+
+/*
+  Function to use when estimating library size.
+
+  This is based on an approximate formula for the coverage of a set
+  obtained after sampling it a given number of times with replacement.
+
+  x = number of items in the set (the number of unique fragments in the library)
+
+  c = number of unique items (unique read pairs observed)
+
+  n = number of items samples (total number of read pairs)
+
+  c and n are known; x is unknown.
+
+  As n -> infinity, the coverage (c/x) can be given as:
+
+  c / x = 1 - exp(-n / x)  (see https://math.stackexchange.com/questions/32800)
+
+  This needs to be solved for x, so it is rearranged to put both terms on the
+  left side and estimate_library_size() finds a value of x which gives a
+  result of zero (or as close as it can get).
+ */
+static inline double coverage_equation(double x, double c, double n) {
+    return c / x - 1 + exp(-n / x);
+}
+
+
+/* estimate the library size, based on the Picard code in DuplicationMetrics.java*/
+static unsigned long estimate_library_size(unsigned long paired_reads, unsigned long paired_duplicate_reads, unsigned long optical) {
+    unsigned long estimated_size = 0;
+    unsigned long non_optical_pairs = (paired_reads - optical) / 2;
+    unsigned long unique_pairs = (paired_reads - paired_duplicate_reads) / 2;
+    unsigned long duplicate_pairs = (paired_duplicate_reads - optical) / 2;
+
+    if ((non_optical_pairs && duplicate_pairs && unique_pairs) && (non_optical_pairs > duplicate_pairs)) {
+        double m = 1;
+        double M = 100;
+        int i;
+
+        if (coverage_equation(m * (double)unique_pairs, (double)unique_pairs, (double)non_optical_pairs) < 0) {
+            fprintf(samtools_stderr, "[markdup] warning: unable to calculate estimated library size.\n");
+            return  estimated_size;
+        }
+
+        while (coverage_equation(M * (double)unique_pairs, (double)unique_pairs, (double)non_optical_pairs) > 0) {
+            M *= 10;
+        }
+
+        for (i = 0; i < 40; i++) {
+            double r = (m + M) / 2;
+            double u = coverage_equation(r * (double)unique_pairs, (double)unique_pairs, (double)non_optical_pairs);
+
+            if (u > 0) {
+                m = r;
+            } else if (u < 0) {
+                M = r;
+            } else {
+                break;
+            }
+        }
+
+        estimated_size = (unsigned long)(unique_pairs * (m + M) / 2);
+    } else {
+        fprintf(samtools_stderr, "[markdup] warning: unable to calculate estimated library size."
+                        " Read pairs %ld should be greater than duplicate pairs %ld,"
+                        " which should both be non zero.\n",
+                        non_optical_pairs, duplicate_pairs);
+    }
+
+    return estimated_size;
+}
+
+
+/* Compare the reads near each other (coordinate sorted) and try to spot the duplicates.
+   Generally the highest quality scoring is chosen as the original and all others the duplicates.
+   The score is based on the sum of the quality values (<= 15) of the read and its mate (if any).
+   While single reads are compared to only one read of a pair, the pair will chosen as the original.
+   The comparison is done on position and orientation, see above for details.
+
+   Marking the supplementary reads of a duplicate as also duplicates takes an extra file read/write
+   step.  This is because the duplicate can occur before the primary read.*/
+
+static int bam_mark_duplicates(md_param_t *param) {
+    bam_hdr_t *header = NULL;
+    khiter_t k;
+    khash_t(reads) *pair_hash        = kh_init(reads);
+    khash_t(reads) *single_hash      = kh_init(reads);
+    klist_t(read_queue) *read_buffer = kl_init(read_queue);
+    kliter_t(read_queue) *rq;
+    khash_t(duplicates) *dup_hash    = kh_init(duplicates);
+    int32_t prev_tid;
+    hts_pos_t prev_coord;
+    read_queue_t *in_read;
+    int ret;
+    long reading, writing, excluded, duplicate, single, pair, single_dup, examined, optical, single_optical;
+    long np_duplicate, np_opt_duplicate;
+    long opt_warnings = 0, bc_warnings = 0;
+    tmp_file_t temp;
+    char *idx_fn = NULL;
+    int exclude = 0;
+    check_list_t dup_list = {NULL, 0, 0};
+
+    if (!pair_hash || !single_hash || !read_buffer || !dup_hash) {
+        fprintf(samtools_stderr, "[markdup] out of memory\n");
+        goto fail;
+    }
+
+    if ((header = sam_hdr_read(param->in)) == NULL) {
+        fprintf(samtools_stderr, "[markdup] error reading header\n");
+        goto fail;
+    }
+
+    // accept unknown, unsorted or coordinate sort order, but error on queryname sorted.
+    // only really works on coordinate sorted files.
+    kstring_t str = KS_INITIALIZE;
+    if (!sam_hdr_find_tag_hd(header, "SO", &str) && str.s && !strcmp(str.s, "queryname")) {
+        fprintf(samtools_stderr, "[markdup] error: queryname sorted, must be sorted by coordinate.\n");
+        ks_free(&str);
+        goto fail;
+    }
+    ks_free(&str);
+
+    if (!param->no_pg && sam_hdr_add_pg(header, "samtools", "VN", samtools_version(),
+                        param->arg_list ? "CL" : NULL,
+                        param->arg_list ? param->arg_list : NULL,
+                        NULL) != 0) {
+        fprintf(samtools_stderr, "[markdup] warning: unable to add @PG line to header.\n");
+    }
+
+    if (sam_hdr_write(param->out, header) < 0) {
+        fprintf(samtools_stderr, "[markdup] error writing header.\n");
+        goto fail;
+    }
+    if (param->write_index) {
+        if (!(idx_fn = auto_index(param->out, param->out_fn, header)))
+            goto fail;
+    }
+
+    // used for coordinate order checks
+    prev_tid = prev_coord = 0;
+
+    // get the buffer going
+    in_read = kl_pushp(read_queue, read_buffer);
+    if (!in_read) {
+        fprintf(samtools_stderr, "[markdup] out of memory\n");
+        goto fail;
+    }
+
+    // handling supplementary reads needs a temporary file
+    if (param->supp) {
+        if (tmp_file_open_write(&temp, param->prefix, 1)) {
+            fprintf(samtools_stderr, "[markdup] error: unable to open tmp file %s.\n", param->prefix);
+            goto fail;
+        }
+    }
+
+    if ((in_read->b = bam_init1()) == NULL) {
+        fprintf(samtools_stderr, "[markdup] error: unable to allocate memory for alignment.\n");
+        goto fail;
+    }
+
+    if (param->check_chain && !(param->tag || param->opt_dist))
+        param->check_chain = 0;
+
+    if (param->check_chain) {
+        dup_list.size = 128;
+        dup_list.c = NULL;
+
+        if ((dup_list.c = malloc(dup_list.size * sizeof(check_t))) == NULL) {
+            fprintf(samtools_stderr, "[markdup] error: unable to allocate memory for dup_list.\n");
+            goto fail;
+        }
+    }
+
+    reading = writing = excluded = single_dup = duplicate = examined = pair = single = optical = single_optical = 0;
+    np_duplicate = np_opt_duplicate = 0;
+
+    while ((ret = sam_read1(param->in, header, in_read->b)) >= 0) {
+        int dup_checked = 0;
+
+        // do some basic coordinate order checks
+        if (in_read->b->core.tid >= 0) { // -1 for unmapped reads
+            if (in_read->b->core.tid < prev_tid ||
+               ((in_read->b->core.tid == prev_tid) && (in_read->b->core.pos < prev_coord))) {
+                fprintf(samtools_stderr, "[markdup] error: not in coordinate sorted order.\n");
+                goto fail;
+            }
+        }
+
+        prev_coord = in_read->pos = in_read->b->core.pos;
+        prev_tid   =  in_read->b->core.tid;
+        in_read->pair_key.single   = 1;
+        in_read->single_key.single = 0;
+        in_read->duplicate = NULL;
+        in_read->dup_checked = 0;
+
+        reading++;
+
+        if (param->clear && (in_read->b->core.flag & BAM_FDUP)) {
+            uint8_t *data;
+
+            in_read->b->core.flag ^= BAM_FDUP;
+
+            if ((data = bam_aux_get(in_read->b, "dt")) != NULL) {
+                bam_aux_del(in_read->b, data);
+            }
+
+            if ((data = bam_aux_get(in_read->b, "do")) != NULL) {
+                bam_aux_del(in_read->b, data);
+            }
+        }
+
+        if (param->include_fails) {
+            exclude |= (BAM_FSECONDARY | BAM_FSUPPLEMENTARY | BAM_FUNMAP);
+        } else {
+            exclude |= (BAM_FSECONDARY | BAM_FSUPPLEMENTARY | BAM_FUNMAP | BAM_FQCFAIL);
+        }
+
+        // read must not be secondary, supplementary, unmapped or (possibly) failed QC
+        if (!(in_read->b->core.flag & exclude)) {
+            examined++;
+
+
+            // look at the pairs first
+            if ((in_read->b->core.flag & BAM_FPAIRED) && !(in_read->b->core.flag & BAM_FMUNMAP)) {
+                int ret, mate_tmp;
+                key_data_t pair_key;
+                key_data_t single_key;
+                in_hash_t *bp;
+
+                if (make_pair_key(param, &pair_key, in_read->b, &bc_warnings)) {
+                    fprintf(samtools_stderr, "[markdup] error: unable to assign pair hash key.\n");
+                    goto fail;
+                }
+
+                make_single_key(param, &single_key, in_read->b, &bc_warnings);
+
+                pair++;
+                in_read->pos = single_key.this_coord; // cigar/orientation modified pos
+
+                // put in singles hash for checking against non paired reads
+                k = kh_put(reads, single_hash, single_key, &ret);
+
+                if (ret > 0) { // new
+                    // add to single duplicate hash
+                    bp = &kh_val(single_hash, k);
+                    bp->p = in_read;
+                    in_read->single_key = single_key;
+                } else if (ret == 0) { // exists
+                    // look at singles only for duplication marking
+                    bp = &kh_val(single_hash, k);
+
+                    if (!(bp->p->b->core.flag & BAM_FPAIRED) || (bp->p->b->core.flag & BAM_FMUNMAP)) {
+                       // singleton will always be marked duplicate even if
+                       // scores more than one read of the pair
+                        bam1_t *dup = bp->p->b;
+
+                        if (param->check_chain)
+                            in_read->duplicate = bp->p;
+
+                        bp->p = in_read;
+
+                        if (mark_duplicates(param, dup_hash, bp->p->b, dup, &single_optical, &opt_warnings))
+                            goto fail;
+
+                        single_dup++;
+                    }
+                } else {
+                    fprintf(samtools_stderr, "[markdup] error: single hashing failure.\n");
+                    goto fail;
+                }
+
+                // now do the pair
+                k = kh_put(reads, pair_hash, pair_key, &ret);
+
+                if (ret > 0) { // new
+                    // add to the pair hash
+                    bp = &kh_val(pair_hash, k);
+                    bp->p = in_read;
+                    in_read->pair_key = pair_key;
+                } else if (ret == 0) {
+                    int64_t old_score, new_score, tie_add = 0;
+                    bam1_t *dup = NULL;
+
+                    bp = &kh_val(pair_hash, k);
+
+                    if ((bp->p->b->core.flag & BAM_FQCFAIL) != (in_read->b->core.flag & BAM_FQCFAIL)) {
+                        if (bp->p->b->core.flag & BAM_FQCFAIL) {
+                            old_score = 0;
+                            new_score = 1;
+                        } else {
+                            old_score = 1;
+                            new_score = 0;
+                        }
+                    } else {
+                        if ((mate_tmp = get_mate_score(bp->p->b)) == -1) {
+                            fprintf(samtools_stderr, "[markdup] error: no ms score tag. Please run samtools fixmate on file first.\n");
+                            goto fail;
+                        } else {
+                            old_score = calc_score(bp->p->b) + mate_tmp;
+                        }
+
+                        if ((mate_tmp = get_mate_score(in_read->b)) == -1) {
+                            fprintf(samtools_stderr, "[markdup] error: no ms score tag. Please run samtools fixmate on file first.\n");
+                            goto fail;
+                        } else {
+                            new_score = calc_score(in_read->b) + mate_tmp;
+                        }
+                    }
+
+                    // choose the highest score as the original
+                    // and add it to the pair hash, mark the other as duplicate
+
+                    if (new_score == old_score) {
+                        if (strcmp(bam_get_qname(in_read->b), bam_get_qname(bp->p->b)) < 0) {
+                            tie_add = 1;
+                        } else {
+                            tie_add = -1;
+                        }
+                    }
+
+                    if (new_score + tie_add > old_score) { // swap reads
+                        dup = bp->p->b;
+
+                        if (param->check_chain) {
+
+                            if (in_read->duplicate) {
+                                read_queue_t *current = in_read->duplicate;
+
+                                while (current->duplicate) {
+                                    current = current->duplicate;
+                                }
+
+                                current->duplicate = bp->p;
+                            } else {
+                                in_read->duplicate = bp->p;
+                            }
+                        }
+
+                        bp->p = in_read;
+                    } else {
+                        if (param->check_chain) {
+                            if (bp->p->duplicate) {
+                                if (in_read->duplicate) {
+                                    read_queue_t *current = bp->p->duplicate;
+
+                                    while (current->duplicate) {
+                                        current = current->duplicate;
+                                    }
+
+                                    current->duplicate = in_read->duplicate;
+                                }
+
+                                in_read->duplicate = bp->p->duplicate;
+                            }
+
+                            bp->p->duplicate = in_read;
+                        }
+
+                        dup = in_read->b;
+                    }
+
+                    if (mark_duplicates(param, dup_hash, bp->p->b, dup, &optical, &opt_warnings))
+                        goto fail;
+
+                    duplicate++;
+                } else {
+                    fprintf(samtools_stderr, "[markdup] error: pair hashing failure.\n");
+                    goto fail;
+                }
+            } else { // do the single (or effectively single) reads
+                int ret;
+                key_data_t single_key;
+                in_hash_t *bp;
+
+                make_single_key(param, &single_key, in_read->b, &bc_warnings);
+
+                single++;
+                in_read->pos = single_key.this_coord; // cigar/orientation modified pos
+
+                k = kh_put(reads, single_hash, single_key, &ret);
+
+                if (ret > 0) { // new
+                    bp = &kh_val(single_hash, k);
+                    bp->p = in_read;
+                    in_read->single_key = single_key;
+                } else if (ret == 0) { // exists
+                    bp = &kh_val(single_hash, k);
+
+                    if ((bp->p->b->core.flag & BAM_FPAIRED) && !(bp->p->b->core.flag & BAM_FMUNMAP)) {
+                        // if matched against one of a pair just mark as duplicate
+
+                        if (param->check_chain) {
+                            if (bp->p->duplicate) {
+                                in_read->duplicate = bp->p->duplicate;
+                            }
+
+                            bp->p->duplicate = in_read;
+                        }
+
+                        if (mark_duplicates(param, dup_hash, bp->p->b, in_read->b, &single_optical, &opt_warnings))
+                            goto fail;
+
+                    } else {
+                        int64_t old_score, new_score;
+                        bam1_t *dup = NULL;
+
+                        old_score = calc_score(bp->p->b);
+                        new_score = calc_score(in_read->b);
+
+                        // choose the highest score as the original, add it
+                        // to the single hash and mark the other as duplicate
+                        if (new_score > old_score) { // swap reads
+                            dup = bp->p->b;
+
+                            if (param->check_chain)
+                                in_read->duplicate = bp->p;
+
+                            bp->p = in_read;
+                        } else {
+                            if (param->check_chain) {
+                                if (bp->p->duplicate) {
+                                    in_read->duplicate = bp->p->duplicate;
+                                }
+
+                                bp->p->duplicate = in_read;
+                            }
+
+                            dup = in_read->b;
+                        }
+
+                        if (mark_duplicates(param, dup_hash, bp->p->b, dup, &single_optical, &opt_warnings))
+                            goto fail;
+                    }
+
+                    single_dup++;
+                } else {
+                    fprintf(samtools_stderr, "[markdup] error: single hashing failure.\n");
+                    goto fail;
+                }
+            }
+        } else {
+            excluded++;
+        }
+
+        // loop through the stored reads and write out those we
+        // no longer need
+        rq = kl_begin(read_buffer);
+        while (rq != kl_end(read_buffer)) {
+            in_read = &kl_val(rq);
+
+            /* keep a moving window of reads based on coordinates and max read length.  Any unaligned reads
+               should just be written as they cannot be matched as duplicates. */
+            if (in_read->pos + param->max_length > prev_coord && in_read->b->core.tid == prev_tid && (prev_tid != -1 || prev_coord != -1)) {
+                break;
+            }
+
+            if (!dup_checked && param->check_chain) {
+                // check for multiple optical duplicates of the same original read
+
+                if (find_duplicate_chains(param, read_buffer, dup_hash, &dup_list, prev_coord, prev_tid, &opt_warnings, &single_optical, &optical, 1)) {
+                    fprintf(samtools_stderr, "[markdup] error: duplicate checking failed.\n");
+                    goto fail;
+                }
+
+                dup_checked = 1;
+            }
+
+
+            if (param->check_chain && (in_read->b->core.flag & BAM_FDUP) && !in_read->dup_checked && !(in_read->b->core.flag & exclude)) {
+                break;
+            }
+
+            if (!param->remove_dups || !(in_read->b->core.flag & BAM_FDUP)) {
+                if (param->supp) {
+                    if (tmp_file_write(&temp, in_read->b)) {
+                        fprintf(samtools_stderr, "[markdup] error: writing temp output failed.\n");
+                        goto fail;
+                    }
+                } else {
+                    if (sam_write1(param->out, header, in_read->b) < 0) {
+                        fprintf(samtools_stderr, "[markdup] error: writing output failed.\n");
+                        goto fail;
+                    }
+                }
+
+                writing++;
+            }
+
+            // remove from hash
+            if (in_read->pair_key.single == 0) {
+                k = kh_get(reads, pair_hash, in_read->pair_key);
+                kh_del(reads, pair_hash, k);
+            }
+
+            if (in_read->single_key.single == 1) {
+                k = kh_get(reads, single_hash, in_read->single_key);
+                kh_del(reads, single_hash, k);
+            }
+
+            kl_shift(read_queue, read_buffer, NULL);
+            bam_destroy1(in_read->b);
+            rq = kl_begin(read_buffer);
+        }
+
+        // set the next one up for reading
+        in_read = kl_pushp(read_queue, read_buffer);
+        if (!in_read) {
+            fprintf(samtools_stderr, "[markdup] out of memory\n");
+            goto fail;
+        }
+
+        if ((in_read->b = bam_init1()) == NULL) {
+            fprintf(samtools_stderr, "[markdup] error: unable to allocate memory for alignment.\n");
+            goto fail;
+        }
+    }
+
+    if (ret < -1) {
+        fprintf(samtools_stderr, "[markdup] error: truncated input file.\n");
+        goto fail;
+    }
+
+    // one last check
+    if (param->tag || param->opt_dist) {
+        if (find_duplicate_chains(param, read_buffer, dup_hash, &dup_list, prev_coord, prev_tid, &opt_warnings, &single_optical, &optical, 0)) {
+            fprintf(samtools_stderr, "[markdup] error: duplicate checking failed.\n");
+            goto fail;
+        }
+    }
+
+    // write out the end of the list
+    rq = kl_begin(read_buffer);
+    while (rq != kl_end(read_buffer)) {
+        in_read = &kl_val(rq);
+
+        if (bam_get_qname(in_read->b)) { // last entry will be blank
+            if (!param->remove_dups || !(in_read->b->core.flag & BAM_FDUP)) {
+                if (param->supp) {
+                    if (tmp_file_write(&temp, in_read->b)) {
+                        fprintf(samtools_stderr, "[markdup] error: writing temp output failed.\n");
+                        goto fail;
+                    }
+                } else {
+                    if (sam_write1(param->out, header, in_read->b) < 0) {
+                        fprintf(samtools_stderr, "[markdup] error: writing output failed.\n");
+                        goto fail;
+                    }
+                }
+
+                writing++;
+            }
+        }
+
+        kl_shift(read_queue, read_buffer, NULL);
+        bam_destroy1(in_read->b);
+        rq = kl_begin(read_buffer);
+    }
+
+    if (param->supp) {
+        bam1_t *b;
+
+        if (tmp_file_end_write(&temp)) {
+            fprintf(samtools_stderr, "[markdup] error: unable to end tmp writing.\n");
+            goto fail;
+        }
+
+        // read data from temp file and mark duplicate supplementary alignments
+
+        if (tmp_file_begin_read(&temp)) {
+            goto fail;
+        }
+
+        b = bam_init1();
+
+        while ((ret = tmp_file_read(&temp, b)) > 0) {
+
+            if ((b->core.flag & BAM_FSUPPLEMENTARY) || (b->core.flag & BAM_FUNMAP) || (b->core.flag & BAM_FSECONDARY)) {
+
+                k = kh_get(duplicates, dup_hash, bam_get_qname(b));
+
+                if (k != kh_end(dup_hash)) {
+
+                    b->core.flag  |= BAM_FDUP;
+                    np_duplicate++;
+
+                    if (param->tag && kh_val(dup_hash, k).name) {
+                        if (bam_aux_update_str(b, "do", strlen(kh_val(dup_hash, k).name) + 1, (char*)kh_val(dup_hash, k).name)) {
+                            fprintf(samtools_stderr, "[markdup] error: unable to append supplementary 'do' tag.\n");
+                            goto fail;
+                        }
+                    }
+
+                    if (param->opt_dist) {
+                        if (kh_val(dup_hash, k).type) {
+                            bam_aux_update_str(b, "dt", 3, "SQ");
+                            np_opt_duplicate++;
+                        } else {
+                            bam_aux_update_str(b, "dt", 3, "LB");
+                        }
+                    }
+                }
+            }
+
+            if (!param->remove_dups || !(b->core.flag & BAM_FDUP)) {
+                if (sam_write1(param->out, header, b) < 0) {
+                    fprintf(samtools_stderr, "[markdup] error: writing final output failed.\n");
+                    goto fail;
+                }
+            }
+        }
+
+        if (ret == -1) {
+            fprintf(samtools_stderr, "[markdup] error: failed to read tmp file.\n");
+            goto fail;
+        }
+
+        for (k = kh_begin(dup_hash); k != kh_end(dup_hash); ++k) {
+            if (kh_exist(dup_hash, k)) {
+                free(kh_val(dup_hash, k).name);
+                free((char *)kh_key(dup_hash, k));
+                kh_key(dup_hash, k) = NULL;
+            }
+        }
+
+        tmp_file_destroy(&temp);
+        bam_destroy1(b);
+    }
+
+    if (opt_warnings) {
+        fprintf(samtools_stderr, "[markdup] warning: number of failed attempts to get coordinates from read names = %ld\n",
+                        opt_warnings);
+    }
+
+    if (bc_warnings) {
+        fprintf(samtools_stderr, "[markdup] warning: number of failed attempts to get barcodes = %ld\n", bc_warnings);
+    }
+
+    if (param->do_stats) {
+        FILE *fp;
+        int file_open = 0;
+        unsigned long els;
+
+        if (param->stats_file) {
+            if (NULL == (fp = fopen(param->stats_file, "w"))) {
+                fprintf(samtools_stderr, "[markdup] warning: cannot write stats to %s.\n", param->stats_file);
+                fp = samtools_stderr;
+            } else {
+                file_open = 1;
+            }
+        } else {
+            fp = samtools_stderr;
+        }
+
+        els = estimate_library_size(pair, duplicate, optical);
+
+        fprintf(fp,
+                "COMMAND: %s\n"
+                "READ: %ld\n"
+                "WRITTEN: %ld\n"
+                "EXCLUDED: %ld\n"
+                "EXAMINED: %ld\n"
+                "PAIRED: %ld\n"
+                "SINGLE: %ld\n"
+                "DUPLICATE PAIR: %ld\n"
+                "DUPLICATE SINGLE: %ld\n"
+                "DUPLICATE PAIR OPTICAL: %ld\n"
+                "DUPLICATE SINGLE OPTICAL: %ld\n"
+                "DUPLICATE NON PRIMARY: %ld\n"
+                "DUPLICATE NON PRIMARY OPTICAL: %ld\n"
+                "DUPLICATE PRIMARY TOTAL: %ld\n"
+                "DUPLICATE TOTAL: %ld\n"
+                "ESTIMATED_LIBRARY_SIZE: %ld\n", param->arg_list, reading, writing, excluded, examined, pair, single,
+                                duplicate, single_dup, optical, single_optical, np_duplicate, np_opt_duplicate,
+                                single_dup + duplicate, single_dup + duplicate + np_duplicate, els);
+
+        if (file_open) {
+            fclose(fp);
+        }
+    }
+
+    if (param->write_index) {
+        if (sam_idx_save(param->out) < 0) {
+            print_error_errno("markdup", "writing index failed");
+            goto fail;
+        }
+    }
+
+    if (param->check_chain && (param->tag || param->opt_dist))
+        free(dup_list.c);
+
+    kh_destroy(reads, pair_hash);
+    kh_destroy(reads, single_hash);
+    kl_destroy(read_queue, read_buffer);
+    kh_destroy(duplicates, dup_hash);
+    sam_hdr_destroy(header);
+
+    return 0;
+
+ fail:
+    for (rq = kl_begin(read_buffer); rq != kl_end(read_buffer); rq = kl_next(rq))
+        bam_destroy1(kl_val(rq).b);
+    kl_destroy(read_queue, read_buffer);
+
+    for (k = kh_begin(dup_hash); k != kh_end(dup_hash); ++k) {
+        if (kh_exist(dup_hash, k)) {
+            free((char *)kh_key(dup_hash, k));
+        }
+    }
+    kh_destroy(duplicates, dup_hash);
+
+    if (param->check_chain && (param->tag || param->opt_dist))
+        free(dup_list.c);
+
+    kh_destroy(reads, pair_hash);
+    kh_destroy(reads, single_hash);
+    sam_hdr_destroy(header);
+    return 1;
+}
+
+
+static int markdup_usage(void) {
+    fprintf(samtools_stderr, "\n");
+    fprintf(samtools_stderr, "Usage:  samtools markdup <input.bam> <output.bam>\n\n");
+    fprintf(samtools_stderr, "Option: \n");
+    fprintf(samtools_stderr, "  -r                 Remove duplicate reads\n");
+    fprintf(samtools_stderr, "  -l INT             Max read length (default 300 bases)\n");
+    fprintf(samtools_stderr, "  -S                 Mark supplementary alignments of duplicates as duplicates (slower).\n");
+    fprintf(samtools_stderr, "  -s                 Report stats.\n");
+    fprintf(samtools_stderr, "  -f NAME            Write stats to named file.  Implies -s.\n");
+    fprintf(samtools_stderr, "  -T PREFIX          Write temporary files to PREFIX.samtools.nnnn.nnnn.tmp.\n");
+    fprintf(samtools_stderr, "  -d INT             Optical distance (if set, marks with dt tag)\n");
+    fprintf(samtools_stderr, "  -c                 Clear previous duplicate settings and tags.\n");
+    fprintf(samtools_stderr, "  -m --mode TYPE     Duplicate decision method for paired reads.\n"
+                    "                     TYPE = t measure positions based on template start/end (default).\n"
+                    "                            s measure positions based on sequence start.\n");
+    fprintf(samtools_stderr, "  -u                 Output uncompressed data\n");
+    fprintf(samtools_stderr, "  --include-fails    Include quality check failed reads.\n");
+    fprintf(samtools_stderr, "  --no-PG            Do not add a PG line\n");
+    fprintf(samtools_stderr, "  --no-multi-dup     Reduced duplicates of duplicates checking.\n");
+    fprintf(samtools_stderr, "  --read-coords STR  Regex for coords from read name.\n");
+    fprintf(samtools_stderr, "  --coords-order STR Order of regex elements. txy (default).  With t being a part of\n"
+                    "                     the read names that must be equal and x/y being coordinates.\n");
+    fprintf(samtools_stderr, "  --barcode-tag STR  Use barcode a tag that duplicates much match.\n");
+    fprintf(samtools_stderr, "  --barcode-name     Use the UMI/barcode in the read name (eigth colon delimited part).\n");
+    fprintf(samtools_stderr, "  --barcode-rgx STR  Regex for barcode in the readname (alternative to --barcode-name).\n");
+    fprintf(samtools_stderr, "  -t                 Mark primary duplicates with the name of the original in a \'do\' tag."
+                                        " Mainly for information and debugging.\n");
+
+    sam_global_opt_help(samtools_stderr, "-.O..@..");
+
+    fprintf(samtools_stderr, "\nThe input file must be coordinate sorted and must have gone"
+                     " through fixmates with the mate scoring option on.\n");
+
+    return 1;
+}
+
+
+int bam_markdup(int argc, char **argv) {
+    int c, ret, bc_name = 0;
+    char wmode[4] = {'w', 'b', 0, 0};
+    sam_global_args ga = SAM_GLOBAL_ARGS_INIT;
+    htsThreadPool p = {NULL, 0};
+    kstring_t tmpprefix = {0, 0, NULL};
+    struct stat st;
+    unsigned int t;
+    char *regex = NULL, *bc_regex = NULL;
+    char *regex_order = "txy";
+    md_param_t param = {NULL, NULL, NULL, 0, 300, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+                        1, NULL, NULL, NULL, NULL, 0, 0, 0, NULL, NULL};
+
+    static const struct option lopts[] = {
+        SAM_OPT_GLOBAL_OPTIONS('-', 0, 'O', 0, 0, '@'),
+        {"include-fails", no_argument, NULL, 1001},
+        {"no-PG", no_argument, NULL, 1002},
+        {"mode", required_argument, NULL, 'm'},
+        {"no-multi-dup", no_argument, NULL, 1003},
+        {"read-coords", required_argument, NULL, 1004},
+        {"coords-order", required_argument, NULL, 1005},
+        {"barcode-tag", required_argument, NULL, 1006},
+        {"barcode-name", no_argument, NULL, 1007},
+        {"barcode-rgx", required_argument, NULL, 1008},
+        {NULL, 0, NULL, 0}
+    };
+
+    while ((c = getopt_long(argc, argv, "rsl:StT:O:@:f:d:cm:u", lopts, NULL)) >= 0) {
+        switch (c) {
+            case 'r': param.remove_dups = 1; break;
+            case 'l': param.max_length = atoi(optarg); break;
+            case 's': param.do_stats = 1; break;
+            case 'T': kputs(optarg, &tmpprefix); break;
+            case 'S': param.supp = 1; break;
+            case 't': param.tag = 1; break;
+            case 'f': param.stats_file = optarg; param.do_stats = 1; break;
+            case 'd': param.opt_dist = atoi(optarg); break;
+            case 'c': param.clear = 1; break;
+            case 'm':
+                if (strcmp(optarg, "t") == 0) {
+                    param.mode = MD_MODE_TEMPLATE;
+                } else if (strcmp(optarg, "s") == 0) {
+                    param.mode = MD_MODE_SEQUENCE;
+                } else {
+                    fprintf(samtools_stderr, "[markdup] error: unknown mode '%s'.\n", optarg);
+                    return markdup_usage();
+                }
+
+                break;
+            case 'u': wmode[2] = '0'; break;
+            case 1001: param.include_fails = 1; break;
+            case 1002: param.no_pg = 1; break;
+            case 1003: param.check_chain = 0; break;
+            case 1004: regex = optarg; break;
+            case 1005: regex_order = optarg; break;
+            case 1006: param.barcode = optarg; break;
+            case 1007: bc_name = 1; break;
+            case 1008: bc_name = 1, bc_regex = optarg; break;
+            default: if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break;
+            /* else fall-through */
+            case '?': return markdup_usage();
+        }
+    }
+
+    if (optind + 2 > argc)
+        return markdup_usage();
+
+    if (param.barcode && bc_name) {
+        fprintf(samtools_stderr, "[markdup] Error: cannot specify --barcode-tag and "
+                        "--barcode-name (or --barcode-rgx) at same time.\n");
+        return 1;
+    }
+
+    if (param.opt_dist < 0) param.opt_dist = 0;
+    if (param.max_length < 0) param.max_length = 300;
+
+    if (regex) {
+        int result;
+
+        // set the order the elements of the regex are assigned to.
+        // x and y being coordinates, t being any other important part of the read
+        // e.g. tile and lane
+        // x and y order does not matter as long as it is consistent
+
+        if ((strncmp(regex_order, "txy", 3) == 0) || (strncmp(regex_order, "tyx", 3) == 0)) {
+            param.rgx_t = 1;
+            param.rgx_x = 2;
+            param.rgx_y = 3;
+        } else if ((strncmp(regex_order, "xyt", 3) == 0) || (strncmp(regex_order, "yxt", 3) == 0)) {
+            param.rgx_x = 1;
+            param.rgx_y = 2;
+            param.rgx_t = 3;
+        } else if ((strncmp(regex_order, "xty", 3) == 0) || (strncmp(regex_order, "ytx", 3) == 0)) {
+            param.rgx_x = 1;
+            param.rgx_t = 2;
+            param.rgx_y = 3;
+        } else if ((strncmp(regex_order, "xy", 2) == 0) || (strncmp(regex_order, "yx", 2) == 0)) {
+            param.rgx_x = 1;
+            param.rgx_y = 2;
+            param.rgx_t = 0;
+        } else {
+            fprintf(samtools_stderr, "[markdup] error:  could not recognise regex coordinate order \"%s\".\n", regex_order);
+            return 1;
+        }
+
+        if ((param.rgx = malloc(sizeof(regex_t))) == NULL) {
+            fprintf(samtools_stderr, "[markdup] error:  could not allocate memory for regex.\n");
+            return 1;
+        }
+
+        if ((result = regcomp(param.rgx, regex, REG_EXTENDED))) {
+            char err_msg[256];
+
+            regerror(result, param.rgx, err_msg, 256);
+            fprintf(samtools_stderr, "[markdup] error: regex error \"%s\"\n", err_msg);
+            free(param.rgx);
+            return 1;
+        }
+    }
+
+    if (bc_name) {
+        int result;
+
+        /* From Illumina UMI documentation: "The UMI sequence is located in the
+           eighth colon-delimited field of the read name (QNAME)". */
+        char *rgx = "[0-9A-Za-z]+:[0-9]+:[0-9]+:[0-9]+:[0-9]+:[0-9]+:[0-9]+:([!-?A-~]+)";
+
+        if ((param.bc_rgx = malloc(sizeof(regex_t))) == NULL) {
+            fprintf(samtools_stderr, "[markdup] error:  could not allocate memory for barcode regex.\n");
+            return 1;
+        }
+
+        if (bc_regex) {
+            rgx = bc_regex;
+        }
+
+        if ((result = regcomp(param.bc_rgx, rgx, REG_EXTENDED))) {
+            char err_msg[256];
+
+            regerror(result, param.bc_rgx, err_msg, 256);
+            fprintf(samtools_stderr, "[markdup] error: barcode regex error \"%s\"\n", err_msg);
+            free(param.bc_rgx);
+            return 1;
+        }
+    }
+
+    param.in = sam_open_format(argv[optind], "r", &ga.in);
+
+    if (!param.in) {
+        print_error_errno("markdup", "failed to open \"%s\" for input", argv[optind]);
+        return 1;
+    }
+
+    sam_open_mode(wmode + 1, argv[optind + 1], NULL);
+    param.out = sam_open_format(argv[optind + 1], wmode, &ga.out);
+
+    if (!param.out) {
+        print_error_errno("markdup", "failed to open \"%s\" for output", argv[optind + 1]);
+        return 1;
+    }
+
+    if (ga.nthreads > 0)  {
+        if (!(p.pool = hts_tpool_init(ga.nthreads))) {
+            fprintf(samtools_stderr, "[markdup] error creating thread pool\n");
+            return 1;
+        }
+
+        hts_set_opt(param.in,  HTS_OPT_THREAD_POOL, &p);
+        hts_set_opt(param.out, HTS_OPT_THREAD_POOL, &p);
+    }
+
+    // actual stuff happens here
+
+    // we need temp files so fix up the name here
+    if (tmpprefix.l == 0) {
+
+        if (strcmp(argv[optind + 1], "-") != 0)
+            ksprintf(&tmpprefix, "%s.", argv[optind + 1]);
+        else
+            kputc('.', &tmpprefix);
+    }
+
+    if (stat(tmpprefix.s, &st) == 0 && S_ISDIR(st.st_mode)) {
+        if (tmpprefix.s[tmpprefix.l-1] != '/') kputc('/', &tmpprefix);
+    }
+
+    t = ((unsigned) time(NULL)) ^ ((unsigned) clock());
+    ksprintf(&tmpprefix, "samtools.%d.%u.tmp", (int) getpid(), t % 10000);
+    param.prefix = tmpprefix.s;
+
+    param.arg_list = stringify_argv(argc + 1, argv - 1);
+    param.write_index = ga.write_index;
+    param.out_fn = argv[optind + 1];
+
+    ret = bam_mark_duplicates(&param);
+
+    sam_close(param.in);
+
+    if (sam_close(param.out) < 0) {
+        fprintf(samtools_stderr, "[markdup] error closing output file\n");
+        ret = 1;
+    }
+
+    if (p.pool) hts_tpool_destroy(p.pool);
+
+    if (param.rgx) {
+        regfree(param.rgx);
+        free(param.rgx);
+    }
+
+    if (param.bc_rgx) {
+        regfree(param.bc_rgx);
+        free(param.bc_rgx);
+    }
+
+    free(param.arg_list);
+    free(tmpprefix.s);
+    sam_global_args_free(&ga);
+
+    return ret;
+}
diff --git a/samtools/bam_mate.c b/samtools/bam_mate.c
new file mode 100644
index 0000000..4239fd1
--- /dev/null
+++ b/samtools/bam_mate.c
@@ -0,0 +1,507 @@
+/*  bam_mate.c -- fix mate pairing information and clean up flags.
+
+    Copyright (C) 2009, 2011-2017, 2019 Genome Research Ltd.
+    Portions copyright (C) 2011 Broad Institute.
+    Portions copyright (C) 2012 Peter Cock, The James Hutton Institute.
+
+    Author: Heng Li <lh3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notices and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <config.h>
+
+#include <assert.h>
+#include <stdbool.h>
+#include <stdlib.h>
+#include <string.h>
+#include <unistd.h>
+#include "htslib/thread_pool.h"
+#include "sam_opts.h"
+#include "htslib/kstring.h"
+#include "htslib/sam.h"
+#include "samtools.h"
+
+
+#define MD_MIN_QUALITY 15
+
+/*
+ * This function calculates ct tag for two bams, it assumes they are from the same template and
+ * writes the tag to the first read in position terms.
+ */
+static void bam_template_cigar(bam1_t *b1, bam1_t *b2, kstring_t *str)
+{
+    bam1_t *swap;
+    int i;
+    hts_pos_t end;
+    uint32_t *cigar;
+    str->l = 0;
+    if (b1->core.tid != b2->core.tid || b1->core.tid < 0 || b1->core.pos < 0 || b2->core.pos < 0 || b1->core.flag&BAM_FUNMAP || b2->core.flag&BAM_FUNMAP) return; // coordinateless or not on the same chr; skip
+    if (b1->core.pos > b2->core.pos) swap = b1, b1 = b2, b2 = swap; // make sure b1 has a smaller coordinate
+    kputc((b1->core.flag & BAM_FREAD1)? '1' : '2', str); // segment index
+    kputc((b1->core.flag & BAM_FREVERSE)? 'R' : 'F', str); // strand
+    for (i = 0, cigar = bam_get_cigar(b1); i < b1->core.n_cigar; ++i) {
+        kputw(bam_cigar_oplen(cigar[i]), str);
+        kputc(bam_cigar_opchr(cigar[i]), str);
+    }
+    end = bam_endpos(b1);
+    kputw(b2->core.pos - end, str);
+    kputc('T', str);
+    kputc((b2->core.flag & BAM_FREAD1)? '1' : '2', str); // segment index
+    kputc((b2->core.flag & BAM_FREVERSE)? 'R' : 'F', str); // strand
+    for (i = 0, cigar = bam_get_cigar(b2); i < b2->core.n_cigar; ++i) {
+        kputw(bam_cigar_oplen(cigar[i]), str);
+        kputc(bam_cigar_opchr(cigar[i]), str);
+    }
+
+    uint8_t* data;
+    if ((data = bam_aux_get(b1,"ct")) != NULL) bam_aux_del(b1, data);
+    if ((data = bam_aux_get(b2,"ct")) != NULL) bam_aux_del(b2, data);
+
+    bam_aux_append(b1, "ct", 'Z', str->l+1, (uint8_t*)str->s);
+}
+
+/*
+ * What This Program is Supposed To Do:
+ * Fill in mate coordinates, ISIZE and mate related flags from a name-sorted
+ * alignment.
+ *
+ * How We Handle Input
+ *
+ * Secondary and supplementary Reads:
+ * -write to output unchanged
+ * All Reads:
+ * -if pos == 0 (1 based), tid == -1 set UNMAPPED flag
+ * single Reads:
+ * -if pos == 0 (1 based), tid == -1, or UNMAPPED then set UNMAPPED, pos = 0,
+ *  tid = -1
+ * -clear bad flags (PAIRED, MREVERSE, PROPER_PAIR)
+ * -set mpos = 0 (1 based), mtid = -1 and isize = 0
+ * -write to output
+ * Paired Reads:
+ * -if read is unmapped and mate is not, set pos and tid to equal that of mate
+ * -sync mate flags (MREVERSE, MUNMAPPED), mpos, mtid
+ * -recalculate ISIZE if possible, otherwise set it to 0
+ * -optionally clear PROPER_PAIR flag from reads where mapping or orientation
+ *  indicate this is not possible (Illumina orientation only)
+ * -calculate ct and apply to lowest positioned read
+ * -write to output
+ * Limitations
+ * -Does not handle tandem reads
+ * -Should mark supplementary reads the same as primary.
+ * Notes
+ * -CT definition appears to be something else in spec, this was in here before
+ *  I started tampering with it, anyone know what is going on here? To work
+ *  around this I have demoted the CT this tool generates to ct.
+ */
+
+static void sync_unmapped_pos_inner(bam1_t* src, bam1_t* dest) {
+    if ((dest->core.flag & BAM_FUNMAP) && !(src->core.flag & BAM_FUNMAP)) {
+        // Set unmapped read's RNAME and POS to those of its mapped mate
+        // (recommended best practice, ensures if coord sort will be together)
+        dest->core.tid = src->core.tid;
+        dest->core.pos = src->core.pos;
+    }
+}
+
+static void sync_mate_inner(bam1_t* src, bam1_t* dest)
+{
+    // sync mate pos information
+    dest->core.mtid = src->core.tid; dest->core.mpos = src->core.pos;
+    // sync flag info
+    if (src->core.flag&BAM_FREVERSE)
+        dest->core.flag |= BAM_FMREVERSE;
+    else
+        dest->core.flag &= ~BAM_FMREVERSE;
+    if (src->core.flag & BAM_FUNMAP) {
+        dest->core.flag |= BAM_FMUNMAP;
+    }
+}
+
+// Is it plausible that these reads are properly paired?
+// Can't really give definitive answer without checking isize
+static bool plausibly_properly_paired(bam1_t* a, bam1_t* b)
+{
+    if ((a->core.flag & BAM_FUNMAP) || (b->core.flag & BAM_FUNMAP)) return false;
+    assert(a->core.tid >= 0); // This should never happen if FUNMAP is set correctly
+
+    if (a->core.tid != b->core.tid) return false;
+
+    bam1_t* first = a;
+    bam1_t* second = b;
+    hts_pos_t a_pos = a->core.flag&BAM_FREVERSE ? bam_endpos(a) : a->core.pos;
+    hts_pos_t  b_pos = b->core.flag&BAM_FREVERSE ? bam_endpos(b) : b->core.pos;
+    if (a_pos > b_pos) {
+        first = b;
+        second = a;
+    } else {
+        first = a;
+        second = b;
+    }
+
+    if (!(first->core.flag&BAM_FREVERSE) && (second->core.flag&BAM_FREVERSE))
+        return true;
+    else
+        return false;
+}
+
+// Returns 0 on success, -1 on failure.
+static int bam_format_cigar(const bam1_t* b, kstring_t* str)
+{
+    // An empty cigar is a special case return "*" rather than ""
+    if (b->core.n_cigar == 0) {
+        return (kputc('*', str) == EOF) ? -1 : 0;
+    }
+
+    const uint32_t *cigar = bam_get_cigar(b);
+    uint32_t i;
+
+    for (i = 0; i < b->core.n_cigar; ++i) {
+        if (kputw(bam_cigar_oplen(cigar[i]), str) == EOF) return -1;
+        if (kputc(bam_cigar_opchr(cigar[i]), str) == EOF) return -1;
+    }
+
+    return 0;
+}
+
+// Returns 0 on success, -1 on failure.
+static int sync_mq_mc(bam1_t* src, bam1_t* dest)
+{
+    if ( (src->core.flag & BAM_FUNMAP) == 0 ) { // If mapped
+        // Copy Mate Mapping Quality
+        uint32_t mq = src->core.qual;
+        uint8_t* data;
+        if ((data = bam_aux_get(dest,"MQ")) != NULL) {
+            bam_aux_del(dest, data);
+        }
+
+        bam_aux_append(dest, "MQ", 'i', sizeof(uint32_t), (uint8_t*)&mq);
+    }
+    // Copy mate cigar if either read is mapped
+    if ( (src->core.flag & BAM_FUNMAP) == 0 || (dest->core.flag & BAM_FUNMAP) == 0 ) {
+        uint8_t* data_mc;
+        if ((data_mc = bam_aux_get(dest,"MC")) != NULL) {
+            bam_aux_del(dest, data_mc);
+        }
+
+        // Convert cigar to string
+        kstring_t mc = { 0, 0, NULL };
+        if (bam_format_cigar(src, &mc) < 0) return -1;
+
+        bam_aux_append(dest, "MC", 'Z', ks_len(&mc)+1, (uint8_t*)ks_str(&mc));
+        free(mc.s);
+    }
+    return 0;
+}
+
+// Copy flags.
+// Returns 0 on success, -1 on failure.
+static int sync_mate(bam1_t* a, bam1_t* b)
+{
+    sync_unmapped_pos_inner(a,b);
+    sync_unmapped_pos_inner(b,a);
+    sync_mate_inner(a,b);
+    sync_mate_inner(b,a);
+    if (sync_mq_mc(a,b) < 0) return -1;
+    if (sync_mq_mc(b,a) < 0) return -1;
+    return 0;
+}
+
+
+static uint32_t calc_mate_score(bam1_t *b)
+{
+    uint32_t score = 0;
+    uint8_t  *qual = bam_get_qual(b);
+    int i;
+
+    for (i = 0; i < b->core.l_qseq; i++) {
+        if (qual[i] >= MD_MIN_QUALITY) score += qual[i];
+    }
+
+    return score;
+}
+
+
+static int add_mate_score(bam1_t *src, bam1_t *dest)
+{
+    uint8_t *data_ms;
+    uint32_t mate_score = calc_mate_score(src);
+
+    if ((data_ms = bam_aux_get(dest, "ms")) != NULL) {
+        bam_aux_del(dest, data_ms);
+    }
+
+    if (bam_aux_append(dest, "ms", 'i', sizeof(uint32_t), (uint8_t*)&mate_score) == -1) {
+        return -1;
+    }
+
+    return 0;
+}
+
+// currently, this function ONLY works if each read has one hit
+static int bam_mating_core(samFile *in, samFile *out, int remove_reads, int proper_pair_check, int add_ct, int do_mate_scoring, char *arg_list, int no_pg)
+{
+    sam_hdr_t *header;
+    bam1_t *b[2] = { NULL, NULL };
+    int curr, has_prev, result;
+    hts_pos_t pre_end = 0, cur_end = 0;
+    kstring_t str = KS_INITIALIZE;
+
+    header = sam_hdr_read(in);
+    if (header == NULL) {
+        fprintf(stderr, "[bam_mating_core] ERROR: Couldn't read header\n");
+        return 1;
+    }
+
+    // Accept unknown, unsorted, or queryname sort order, but error on coordinate sorted.
+    if (!sam_hdr_find_tag_hd(header, "SO", &str) && str.s && !strcmp(str.s, "coordinate")) {
+        fprintf(stderr, "[bam_mating_core] ERROR: Coordinate sorted, require grouped/sorted by queryname.\n");
+        goto fail;
+    }
+    ks_free(&str);
+
+    if (!no_pg && sam_hdr_add_pg(header, "samtools",
+                                 "VN", samtools_version(),
+                                 arg_list ? "CL": NULL,
+                                 arg_list ? arg_list : NULL,
+                                 NULL))
+        goto fail;
+
+    if (sam_hdr_write(out, header) < 0) goto write_fail;
+
+    b[0] = bam_init1();
+    b[1] = bam_init1();
+    curr = 0; has_prev = 0;
+    while ((result = sam_read1(in, header, b[curr])) >= 0) {
+        bam1_t *cur = b[curr], *pre = b[1-curr];
+        if (cur->core.flag & BAM_FSECONDARY)
+        {
+            if ( !remove_reads ) {
+                if (sam_write1(out, header, cur) < 0) goto write_fail;
+            }
+            continue; // skip secondary alignments
+        }
+        if (cur->core.flag & BAM_FSUPPLEMENTARY)
+        {
+            if (sam_write1(out, header, cur) < 0) goto write_fail;
+            continue; // pass supplementary alignments through unchanged (TODO:make them match read they came from)
+        }
+        if (cur->core.tid < 0 || cur->core.pos < 0) // If unmapped set the flag
+        {
+            cur->core.flag |= BAM_FUNMAP;
+        }
+        if ((cur->core.flag&BAM_FUNMAP) == 0) // If mapped calculate end
+        {
+            cur_end = bam_endpos(cur);
+
+            // Check cur_end isn't past the end of the contig we're on, if it is set the UNMAP'd flag
+            if (cur_end > sam_hdr_tid2len(header, cur->core.tid)) cur->core.flag |= BAM_FUNMAP;
+        }
+        if (has_prev) { // do we have a pair of reads to examine?
+            if (strcmp(bam_get_qname(cur), bam_get_qname(pre)) == 0) { // identical pair name
+                pre->core.flag |= BAM_FPAIRED;
+                cur->core.flag |= BAM_FPAIRED;
+                if (sync_mate(pre, cur)) goto fail;
+
+                if (pre->core.tid == cur->core.tid && !(cur->core.flag&(BAM_FUNMAP|BAM_FMUNMAP))
+                    && !(pre->core.flag&(BAM_FUNMAP|BAM_FMUNMAP))) // if safe set TLEN/ISIZE
+                {
+                    hts_pos_t cur5, pre5;
+                    cur5 = (cur->core.flag&BAM_FREVERSE)? cur_end : cur->core.pos;
+                    pre5 = (pre->core.flag&BAM_FREVERSE)? pre_end : pre->core.pos;
+                    cur->core.isize = pre5 - cur5; pre->core.isize = cur5 - pre5;
+                } else cur->core.isize = pre->core.isize = 0;
+                if (add_ct) bam_template_cigar(pre, cur, &str);
+                // TODO: Add code to properly check if read is in a proper pair based on ISIZE distribution
+                if (proper_pair_check && !plausibly_properly_paired(pre,cur)) {
+                    pre->core.flag &= ~BAM_FPROPER_PAIR;
+                    cur->core.flag &= ~BAM_FPROPER_PAIR;
+                }
+
+                if (do_mate_scoring) {
+                    if ((add_mate_score(pre, cur) == -1) || (add_mate_score(cur, pre) == -1)) {
+                        fprintf(stderr, "[bam_mating_core] ERROR: unable to add mate score.\n");
+                        goto fail;
+                    }
+                }
+
+                // Write out result
+                if ( !remove_reads ) {
+                    if (sam_write1(out, header, pre) < 0) goto write_fail;
+                    if (sam_write1(out, header, cur) < 0) goto write_fail;
+                } else {
+                    // If we have to remove reads make sure we do it in a way that doesn't create orphans with bad flags
+                    if(pre->core.flag&BAM_FUNMAP) cur->core.flag &= ~(BAM_FPAIRED|BAM_FMREVERSE|BAM_FPROPER_PAIR);
+                    if(cur->core.flag&BAM_FUNMAP) pre->core.flag &= ~(BAM_FPAIRED|BAM_FMREVERSE|BAM_FPROPER_PAIR);
+                    if(!(pre->core.flag&BAM_FUNMAP)) {
+                        if (sam_write1(out, header, pre) < 0) goto write_fail;
+                    }
+                    if(!(cur->core.flag&BAM_FUNMAP)) {
+                        if (sam_write1(out, header, cur) < 0) goto write_fail;
+                    }
+                }
+                has_prev = 0;
+            } else { // unpaired?  clear bad info and write it out
+                if (pre->core.tid < 0 || pre->core.pos < 0 || pre->core.flag&BAM_FUNMAP) { // If unmapped
+                    pre->core.flag |= BAM_FUNMAP;
+                    pre->core.tid = -1;
+                    pre->core.pos = -1;
+                }
+                pre->core.mtid = -1; pre->core.mpos = -1; pre->core.isize = 0;
+                pre->core.flag &= ~(BAM_FPAIRED|BAM_FMREVERSE|BAM_FPROPER_PAIR);
+                if ( !remove_reads || !(pre->core.flag&BAM_FUNMAP) ) {
+                    if (sam_write1(out, header, pre) < 0) goto write_fail;
+                }
+            }
+        } else has_prev = 1;
+        curr = 1 - curr;
+        pre_end = cur_end;
+    }
+    if (result < -1) goto read_fail;
+    if (has_prev && !remove_reads) { // If we still have a BAM in the buffer it must be unpaired
+        bam1_t *pre = b[1-curr];
+        if (pre->core.tid < 0 || pre->core.pos < 0 || pre->core.flag&BAM_FUNMAP) { // If unmapped
+            pre->core.flag |= BAM_FUNMAP;
+            pre->core.tid = -1;
+            pre->core.pos = -1;
+        }
+        pre->core.mtid = -1; pre->core.mpos = -1; pre->core.isize = 0;
+        pre->core.flag &= ~(BAM_FPAIRED|BAM_FMREVERSE|BAM_FPROPER_PAIR);
+
+        if (sam_write1(out, header, pre) < 0) goto write_fail;
+    }
+    sam_hdr_destroy(header);
+    bam_destroy1(b[0]);
+    bam_destroy1(b[1]);
+    ks_free(&str);
+    return 0;
+
+ read_fail:
+    print_error("fixmate", "Couldn't read from input file");
+    goto fail;
+
+ write_fail:
+    print_error_errno("fixmate", "Couldn't write to output file");
+ fail:
+    sam_hdr_destroy(header);
+    bam_destroy1(b[0]);
+    bam_destroy1(b[1]);
+    ks_free(&str);
+    return 1;
+}
+
+void usage(FILE* where)
+{
+    fprintf(where,
+"Usage: samtools fixmate <in.nameSrt.bam> <out.nameSrt.bam>\n"
+"Options:\n"
+"  -r           Remove unmapped reads and secondary alignments\n"
+"  -p           Disable FR proper pair check\n"
+"  -c           Add template cigar ct tag\n"
+"  -m           Add mate score tag\n"
+"  -u           Uncompressed output\n"
+"  --no-PG      do not add a PG line\n");
+
+    sam_global_opt_help(where, "-.O..@-.");
+
+    fprintf(where,
+"\n"
+"As elsewhere in samtools, use '-' as the filename for stdin/stdout. The input\n"
+"file must be grouped by read name (e.g. sorted by name). Coordinated sorted\n"
+"input is not accepted.\n");
+}
+
+int bam_mating(int argc, char *argv[])
+{
+    htsThreadPool p = {NULL, 0};
+    samFile *in = NULL, *out = NULL;
+    int c, remove_reads = 0, proper_pair_check = 1, add_ct = 0, res = 1, mate_score = 0, no_pg = 0;
+    sam_global_args ga = SAM_GLOBAL_ARGS_INIT;
+    char wmode[4] = {'w', 'b', 0, 0};
+    static const struct option lopts[] = {
+        SAM_OPT_GLOBAL_OPTIONS('-', 0, 'O', 0, 0, '@'),
+        {"no-PG", no_argument, NULL, 1},
+        { NULL, 0, NULL, 0 }
+    };
+    char *arg_list = NULL;
+
+    // parse args
+    if (argc == 1) { usage(stdout); return 0; }
+    while ((c = getopt_long(argc, argv, "rpcmO:@:u", lopts, NULL)) >= 0) {
+        switch (c) {
+            case 'r': remove_reads = 1; break;
+            case 'p': proper_pair_check = 0; break;
+            case 'c': add_ct = 1; break;
+            case 'm': mate_score = 1; break;
+            case 'u': wmode[2] = '0'; break;
+            case 1: no_pg = 1; break;
+            default:  if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break;
+                      /* else fall-through */
+            case '?': usage(stderr); goto fail;
+        }
+    }
+    if (optind+1 >= argc) { usage(stderr); goto fail; }
+
+    if (!no_pg && !(arg_list =  stringify_argv(argc+1, argv-1)))
+        goto fail;
+
+    // init
+    if ((in = sam_open_format(argv[optind], "rb", &ga.in)) == NULL) {
+        print_error_errno("fixmate", "cannot open input file");
+        goto fail;
+    }
+    sam_open_mode(wmode+1, argv[optind+1], NULL);
+    if ((out = sam_open_format(argv[optind+1], wmode, &ga.out)) == NULL) {
+        print_error_errno("fixmate", "cannot open output file");
+        goto fail;
+    }
+
+    if (ga.nthreads > 0) {
+        if (!(p.pool = hts_tpool_init(ga.nthreads))) {
+            fprintf(stderr, "Error creating thread pool\n");
+            goto fail;
+        }
+        hts_set_opt(in,  HTS_OPT_THREAD_POOL, &p);
+        hts_set_opt(out, HTS_OPT_THREAD_POOL, &p);
+    }
+
+    // run
+    res = bam_mating_core(in, out, remove_reads, proper_pair_check, add_ct, mate_score, arg_list, no_pg);
+
+    // cleanup
+    sam_close(in);
+    if (sam_close(out) < 0) {
+        fprintf(stderr, "[bam_mating] error while closing output file\n");
+        res = 1;
+    }
+
+    if (p.pool) hts_tpool_destroy(p.pool);
+    free(arg_list);
+    sam_global_args_free(&ga);
+    return res;
+
+ fail:
+    if (in) sam_close(in);
+    if (out) sam_close(out);
+    if (p.pool) hts_tpool_destroy(p.pool);
+    free(arg_list);
+    sam_global_args_free(&ga);
+    return 1;
+}
+
+
diff --git a/samtools/bam_mate.c.pysam.c b/samtools/bam_mate.c.pysam.c
new file mode 100644
index 0000000..0aa83ec
--- /dev/null
+++ b/samtools/bam_mate.c.pysam.c
@@ -0,0 +1,509 @@
+#include "samtools.pysam.h"
+
+/*  bam_mate.c -- fix mate pairing information and clean up flags.
+
+    Copyright (C) 2009, 2011-2017, 2019 Genome Research Ltd.
+    Portions copyright (C) 2011 Broad Institute.
+    Portions copyright (C) 2012 Peter Cock, The James Hutton Institute.
+
+    Author: Heng Li <lh3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notices and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <config.h>
+
+#include <assert.h>
+#include <stdbool.h>
+#include <stdlib.h>
+#include <string.h>
+#include <unistd.h>
+#include "htslib/thread_pool.h"
+#include "sam_opts.h"
+#include "htslib/kstring.h"
+#include "htslib/sam.h"
+#include "samtools.h"
+
+
+#define MD_MIN_QUALITY 15
+
+/*
+ * This function calculates ct tag for two bams, it assumes they are from the same template and
+ * writes the tag to the first read in position terms.
+ */
+static void bam_template_cigar(bam1_t *b1, bam1_t *b2, kstring_t *str)
+{
+    bam1_t *swap;
+    int i;
+    hts_pos_t end;
+    uint32_t *cigar;
+    str->l = 0;
+    if (b1->core.tid != b2->core.tid || b1->core.tid < 0 || b1->core.pos < 0 || b2->core.pos < 0 || b1->core.flag&BAM_FUNMAP || b2->core.flag&BAM_FUNMAP) return; // coordinateless or not on the same chr; skip
+    if (b1->core.pos > b2->core.pos) swap = b1, b1 = b2, b2 = swap; // make sure b1 has a smaller coordinate
+    kputc((b1->core.flag & BAM_FREAD1)? '1' : '2', str); // segment index
+    kputc((b1->core.flag & BAM_FREVERSE)? 'R' : 'F', str); // strand
+    for (i = 0, cigar = bam_get_cigar(b1); i < b1->core.n_cigar; ++i) {
+        kputw(bam_cigar_oplen(cigar[i]), str);
+        kputc(bam_cigar_opchr(cigar[i]), str);
+    }
+    end = bam_endpos(b1);
+    kputw(b2->core.pos - end, str);
+    kputc('T', str);
+    kputc((b2->core.flag & BAM_FREAD1)? '1' : '2', str); // segment index
+    kputc((b2->core.flag & BAM_FREVERSE)? 'R' : 'F', str); // strand
+    for (i = 0, cigar = bam_get_cigar(b2); i < b2->core.n_cigar; ++i) {
+        kputw(bam_cigar_oplen(cigar[i]), str);
+        kputc(bam_cigar_opchr(cigar[i]), str);
+    }
+
+    uint8_t* data;
+    if ((data = bam_aux_get(b1,"ct")) != NULL) bam_aux_del(b1, data);
+    if ((data = bam_aux_get(b2,"ct")) != NULL) bam_aux_del(b2, data);
+
+    bam_aux_append(b1, "ct", 'Z', str->l+1, (uint8_t*)str->s);
+}
+
+/*
+ * What This Program is Supposed To Do:
+ * Fill in mate coordinates, ISIZE and mate related flags from a name-sorted
+ * alignment.
+ *
+ * How We Handle Input
+ *
+ * Secondary and supplementary Reads:
+ * -write to output unchanged
+ * All Reads:
+ * -if pos == 0 (1 based), tid == -1 set UNMAPPED flag
+ * single Reads:
+ * -if pos == 0 (1 based), tid == -1, or UNMAPPED then set UNMAPPED, pos = 0,
+ *  tid = -1
+ * -clear bad flags (PAIRED, MREVERSE, PROPER_PAIR)
+ * -set mpos = 0 (1 based), mtid = -1 and isize = 0
+ * -write to output
+ * Paired Reads:
+ * -if read is unmapped and mate is not, set pos and tid to equal that of mate
+ * -sync mate flags (MREVERSE, MUNMAPPED), mpos, mtid
+ * -recalculate ISIZE if possible, otherwise set it to 0
+ * -optionally clear PROPER_PAIR flag from reads where mapping or orientation
+ *  indicate this is not possible (Illumina orientation only)
+ * -calculate ct and apply to lowest positioned read
+ * -write to output
+ * Limitations
+ * -Does not handle tandem reads
+ * -Should mark supplementary reads the same as primary.
+ * Notes
+ * -CT definition appears to be something else in spec, this was in here before
+ *  I started tampering with it, anyone know what is going on here? To work
+ *  around this I have demoted the CT this tool generates to ct.
+ */
+
+static void sync_unmapped_pos_inner(bam1_t* src, bam1_t* dest) {
+    if ((dest->core.flag & BAM_FUNMAP) && !(src->core.flag & BAM_FUNMAP)) {
+        // Set unmapped read's RNAME and POS to those of its mapped mate
+        // (recommended best practice, ensures if coord sort will be together)
+        dest->core.tid = src->core.tid;
+        dest->core.pos = src->core.pos;
+    }
+}
+
+static void sync_mate_inner(bam1_t* src, bam1_t* dest)
+{
+    // sync mate pos information
+    dest->core.mtid = src->core.tid; dest->core.mpos = src->core.pos;
+    // sync flag info
+    if (src->core.flag&BAM_FREVERSE)
+        dest->core.flag |= BAM_FMREVERSE;
+    else
+        dest->core.flag &= ~BAM_FMREVERSE;
+    if (src->core.flag & BAM_FUNMAP) {
+        dest->core.flag |= BAM_FMUNMAP;
+    }
+}
+
+// Is it plausible that these reads are properly paired?
+// Can't really give definitive answer without checking isize
+static bool plausibly_properly_paired(bam1_t* a, bam1_t* b)
+{
+    if ((a->core.flag & BAM_FUNMAP) || (b->core.flag & BAM_FUNMAP)) return false;
+    assert(a->core.tid >= 0); // This should never happen if FUNMAP is set correctly
+
+    if (a->core.tid != b->core.tid) return false;
+
+    bam1_t* first = a;
+    bam1_t* second = b;
+    hts_pos_t a_pos = a->core.flag&BAM_FREVERSE ? bam_endpos(a) : a->core.pos;
+    hts_pos_t  b_pos = b->core.flag&BAM_FREVERSE ? bam_endpos(b) : b->core.pos;
+    if (a_pos > b_pos) {
+        first = b;
+        second = a;
+    } else {
+        first = a;
+        second = b;
+    }
+
+    if (!(first->core.flag&BAM_FREVERSE) && (second->core.flag&BAM_FREVERSE))
+        return true;
+    else
+        return false;
+}
+
+// Returns 0 on success, -1 on failure.
+static int bam_format_cigar(const bam1_t* b, kstring_t* str)
+{
+    // An empty cigar is a special case return "*" rather than ""
+    if (b->core.n_cigar == 0) {
+        return (kputc('*', str) == EOF) ? -1 : 0;
+    }
+
+    const uint32_t *cigar = bam_get_cigar(b);
+    uint32_t i;
+
+    for (i = 0; i < b->core.n_cigar; ++i) {
+        if (kputw(bam_cigar_oplen(cigar[i]), str) == EOF) return -1;
+        if (kputc(bam_cigar_opchr(cigar[i]), str) == EOF) return -1;
+    }
+
+    return 0;
+}
+
+// Returns 0 on success, -1 on failure.
+static int sync_mq_mc(bam1_t* src, bam1_t* dest)
+{
+    if ( (src->core.flag & BAM_FUNMAP) == 0 ) { // If mapped
+        // Copy Mate Mapping Quality
+        uint32_t mq = src->core.qual;
+        uint8_t* data;
+        if ((data = bam_aux_get(dest,"MQ")) != NULL) {
+            bam_aux_del(dest, data);
+        }
+
+        bam_aux_append(dest, "MQ", 'i', sizeof(uint32_t), (uint8_t*)&mq);
+    }
+    // Copy mate cigar if either read is mapped
+    if ( (src->core.flag & BAM_FUNMAP) == 0 || (dest->core.flag & BAM_FUNMAP) == 0 ) {
+        uint8_t* data_mc;
+        if ((data_mc = bam_aux_get(dest,"MC")) != NULL) {
+            bam_aux_del(dest, data_mc);
+        }
+
+        // Convert cigar to string
+        kstring_t mc = { 0, 0, NULL };
+        if (bam_format_cigar(src, &mc) < 0) return -1;
+
+        bam_aux_append(dest, "MC", 'Z', ks_len(&mc)+1, (uint8_t*)ks_str(&mc));
+        free(mc.s);
+    }
+    return 0;
+}
+
+// Copy flags.
+// Returns 0 on success, -1 on failure.
+static int sync_mate(bam1_t* a, bam1_t* b)
+{
+    sync_unmapped_pos_inner(a,b);
+    sync_unmapped_pos_inner(b,a);
+    sync_mate_inner(a,b);
+    sync_mate_inner(b,a);
+    if (sync_mq_mc(a,b) < 0) return -1;
+    if (sync_mq_mc(b,a) < 0) return -1;
+    return 0;
+}
+
+
+static uint32_t calc_mate_score(bam1_t *b)
+{
+    uint32_t score = 0;
+    uint8_t  *qual = bam_get_qual(b);
+    int i;
+
+    for (i = 0; i < b->core.l_qseq; i++) {
+        if (qual[i] >= MD_MIN_QUALITY) score += qual[i];
+    }
+
+    return score;
+}
+
+
+static int add_mate_score(bam1_t *src, bam1_t *dest)
+{
+    uint8_t *data_ms;
+    uint32_t mate_score = calc_mate_score(src);
+
+    if ((data_ms = bam_aux_get(dest, "ms")) != NULL) {
+        bam_aux_del(dest, data_ms);
+    }
+
+    if (bam_aux_append(dest, "ms", 'i', sizeof(uint32_t), (uint8_t*)&mate_score) == -1) {
+        return -1;
+    }
+
+    return 0;
+}
+
+// currently, this function ONLY works if each read has one hit
+static int bam_mating_core(samFile *in, samFile *out, int remove_reads, int proper_pair_check, int add_ct, int do_mate_scoring, char *arg_list, int no_pg)
+{
+    sam_hdr_t *header;
+    bam1_t *b[2] = { NULL, NULL };
+    int curr, has_prev, result;
+    hts_pos_t pre_end = 0, cur_end = 0;
+    kstring_t str = KS_INITIALIZE;
+
+    header = sam_hdr_read(in);
+    if (header == NULL) {
+        fprintf(samtools_stderr, "[bam_mating_core] ERROR: Couldn't read header\n");
+        return 1;
+    }
+
+    // Accept unknown, unsorted, or queryname sort order, but error on coordinate sorted.
+    if (!sam_hdr_find_tag_hd(header, "SO", &str) && str.s && !strcmp(str.s, "coordinate")) {
+        fprintf(samtools_stderr, "[bam_mating_core] ERROR: Coordinate sorted, require grouped/sorted by queryname.\n");
+        goto fail;
+    }
+    ks_free(&str);
+
+    if (!no_pg && sam_hdr_add_pg(header, "samtools",
+                                 "VN", samtools_version(),
+                                 arg_list ? "CL": NULL,
+                                 arg_list ? arg_list : NULL,
+                                 NULL))
+        goto fail;
+
+    if (sam_hdr_write(out, header) < 0) goto write_fail;
+
+    b[0] = bam_init1();
+    b[1] = bam_init1();
+    curr = 0; has_prev = 0;
+    while ((result = sam_read1(in, header, b[curr])) >= 0) {
+        bam1_t *cur = b[curr], *pre = b[1-curr];
+        if (cur->core.flag & BAM_FSECONDARY)
+        {
+            if ( !remove_reads ) {
+                if (sam_write1(out, header, cur) < 0) goto write_fail;
+            }
+            continue; // skip secondary alignments
+        }
+        if (cur->core.flag & BAM_FSUPPLEMENTARY)
+        {
+            if (sam_write1(out, header, cur) < 0) goto write_fail;
+            continue; // pass supplementary alignments through unchanged (TODO:make them match read they came from)
+        }
+        if (cur->core.tid < 0 || cur->core.pos < 0) // If unmapped set the flag
+        {
+            cur->core.flag |= BAM_FUNMAP;
+        }
+        if ((cur->core.flag&BAM_FUNMAP) == 0) // If mapped calculate end
+        {
+            cur_end = bam_endpos(cur);
+
+            // Check cur_end isn't past the end of the contig we're on, if it is set the UNMAP'd flag
+            if (cur_end > sam_hdr_tid2len(header, cur->core.tid)) cur->core.flag |= BAM_FUNMAP;
+        }
+        if (has_prev) { // do we have a pair of reads to examine?
+            if (strcmp(bam_get_qname(cur), bam_get_qname(pre)) == 0) { // identical pair name
+                pre->core.flag |= BAM_FPAIRED;
+                cur->core.flag |= BAM_FPAIRED;
+                if (sync_mate(pre, cur)) goto fail;
+
+                if (pre->core.tid == cur->core.tid && !(cur->core.flag&(BAM_FUNMAP|BAM_FMUNMAP))
+                    && !(pre->core.flag&(BAM_FUNMAP|BAM_FMUNMAP))) // if safe set TLEN/ISIZE
+                {
+                    hts_pos_t cur5, pre5;
+                    cur5 = (cur->core.flag&BAM_FREVERSE)? cur_end : cur->core.pos;
+                    pre5 = (pre->core.flag&BAM_FREVERSE)? pre_end : pre->core.pos;
+                    cur->core.isize = pre5 - cur5; pre->core.isize = cur5 - pre5;
+                } else cur->core.isize = pre->core.isize = 0;
+                if (add_ct) bam_template_cigar(pre, cur, &str);
+                // TODO: Add code to properly check if read is in a proper pair based on ISIZE distribution
+                if (proper_pair_check && !plausibly_properly_paired(pre,cur)) {
+                    pre->core.flag &= ~BAM_FPROPER_PAIR;
+                    cur->core.flag &= ~BAM_FPROPER_PAIR;
+                }
+
+                if (do_mate_scoring) {
+                    if ((add_mate_score(pre, cur) == -1) || (add_mate_score(cur, pre) == -1)) {
+                        fprintf(samtools_stderr, "[bam_mating_core] ERROR: unable to add mate score.\n");
+                        goto fail;
+                    }
+                }
+
+                // Write out result
+                if ( !remove_reads ) {
+                    if (sam_write1(out, header, pre) < 0) goto write_fail;
+                    if (sam_write1(out, header, cur) < 0) goto write_fail;
+                } else {
+                    // If we have to remove reads make sure we do it in a way that doesn't create orphans with bad flags
+                    if(pre->core.flag&BAM_FUNMAP) cur->core.flag &= ~(BAM_FPAIRED|BAM_FMREVERSE|BAM_FPROPER_PAIR);
+                    if(cur->core.flag&BAM_FUNMAP) pre->core.flag &= ~(BAM_FPAIRED|BAM_FMREVERSE|BAM_FPROPER_PAIR);
+                    if(!(pre->core.flag&BAM_FUNMAP)) {
+                        if (sam_write1(out, header, pre) < 0) goto write_fail;
+                    }
+                    if(!(cur->core.flag&BAM_FUNMAP)) {
+                        if (sam_write1(out, header, cur) < 0) goto write_fail;
+                    }
+                }
+                has_prev = 0;
+            } else { // unpaired?  clear bad info and write it out
+                if (pre->core.tid < 0 || pre->core.pos < 0 || pre->core.flag&BAM_FUNMAP) { // If unmapped
+                    pre->core.flag |= BAM_FUNMAP;
+                    pre->core.tid = -1;
+                    pre->core.pos = -1;
+                }
+                pre->core.mtid = -1; pre->core.mpos = -1; pre->core.isize = 0;
+                pre->core.flag &= ~(BAM_FPAIRED|BAM_FMREVERSE|BAM_FPROPER_PAIR);
+                if ( !remove_reads || !(pre->core.flag&BAM_FUNMAP) ) {
+                    if (sam_write1(out, header, pre) < 0) goto write_fail;
+                }
+            }
+        } else has_prev = 1;
+        curr = 1 - curr;
+        pre_end = cur_end;
+    }
+    if (result < -1) goto read_fail;
+    if (has_prev && !remove_reads) { // If we still have a BAM in the buffer it must be unpaired
+        bam1_t *pre = b[1-curr];
+        if (pre->core.tid < 0 || pre->core.pos < 0 || pre->core.flag&BAM_FUNMAP) { // If unmapped
+            pre->core.flag |= BAM_FUNMAP;
+            pre->core.tid = -1;
+            pre->core.pos = -1;
+        }
+        pre->core.mtid = -1; pre->core.mpos = -1; pre->core.isize = 0;
+        pre->core.flag &= ~(BAM_FPAIRED|BAM_FMREVERSE|BAM_FPROPER_PAIR);
+
+        if (sam_write1(out, header, pre) < 0) goto write_fail;
+    }
+    sam_hdr_destroy(header);
+    bam_destroy1(b[0]);
+    bam_destroy1(b[1]);
+    ks_free(&str);
+    return 0;
+
+ read_fail:
+    print_error("fixmate", "Couldn't read from input file");
+    goto fail;
+
+ write_fail:
+    print_error_errno("fixmate", "Couldn't write to output file");
+ fail:
+    sam_hdr_destroy(header);
+    bam_destroy1(b[0]);
+    bam_destroy1(b[1]);
+    ks_free(&str);
+    return 1;
+}
+
+void usage(FILE* where)
+{
+    fprintf(where,
+"Usage: samtools fixmate <in.nameSrt.bam> <out.nameSrt.bam>\n"
+"Options:\n"
+"  -r           Remove unmapped reads and secondary alignments\n"
+"  -p           Disable FR proper pair check\n"
+"  -c           Add template cigar ct tag\n"
+"  -m           Add mate score tag\n"
+"  -u           Uncompressed output\n"
+"  --no-PG      do not add a PG line\n");
+
+    sam_global_opt_help(where, "-.O..@-.");
+
+    fprintf(where,
+"\n"
+"As elsewhere in samtools, use '-' as the filename for stdin/samtools_stdout. The input\n"
+"file must be grouped by read name (e.g. sorted by name). Coordinated sorted\n"
+"input is not accepted.\n");
+}
+
+int bam_mating(int argc, char *argv[])
+{
+    htsThreadPool p = {NULL, 0};
+    samFile *in = NULL, *out = NULL;
+    int c, remove_reads = 0, proper_pair_check = 1, add_ct = 0, res = 1, mate_score = 0, no_pg = 0;
+    sam_global_args ga = SAM_GLOBAL_ARGS_INIT;
+    char wmode[4] = {'w', 'b', 0, 0};
+    static const struct option lopts[] = {
+        SAM_OPT_GLOBAL_OPTIONS('-', 0, 'O', 0, 0, '@'),
+        {"no-PG", no_argument, NULL, 1},
+        { NULL, 0, NULL, 0 }
+    };
+    char *arg_list = NULL;
+
+    // parse args
+    if (argc == 1) { usage(samtools_stdout); return 0; }
+    while ((c = getopt_long(argc, argv, "rpcmO:@:u", lopts, NULL)) >= 0) {
+        switch (c) {
+            case 'r': remove_reads = 1; break;
+            case 'p': proper_pair_check = 0; break;
+            case 'c': add_ct = 1; break;
+            case 'm': mate_score = 1; break;
+            case 'u': wmode[2] = '0'; break;
+            case 1: no_pg = 1; break;
+            default:  if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break;
+                      /* else fall-through */
+            case '?': usage(samtools_stderr); goto fail;
+        }
+    }
+    if (optind+1 >= argc) { usage(samtools_stderr); goto fail; }
+
+    if (!no_pg && !(arg_list =  stringify_argv(argc+1, argv-1)))
+        goto fail;
+
+    // init
+    if ((in = sam_open_format(argv[optind], "rb", &ga.in)) == NULL) {
+        print_error_errno("fixmate", "cannot open input file");
+        goto fail;
+    }
+    sam_open_mode(wmode+1, argv[optind+1], NULL);
+    if ((out = sam_open_format(argv[optind+1], wmode, &ga.out)) == NULL) {
+        print_error_errno("fixmate", "cannot open output file");
+        goto fail;
+    }
+
+    if (ga.nthreads > 0) {
+        if (!(p.pool = hts_tpool_init(ga.nthreads))) {
+            fprintf(samtools_stderr, "Error creating thread pool\n");
+            goto fail;
+        }
+        hts_set_opt(in,  HTS_OPT_THREAD_POOL, &p);
+        hts_set_opt(out, HTS_OPT_THREAD_POOL, &p);
+    }
+
+    // run
+    res = bam_mating_core(in, out, remove_reads, proper_pair_check, add_ct, mate_score, arg_list, no_pg);
+
+    // cleanup
+    sam_close(in);
+    if (sam_close(out) < 0) {
+        fprintf(samtools_stderr, "[bam_mating] error while closing output file\n");
+        res = 1;
+    }
+
+    if (p.pool) hts_tpool_destroy(p.pool);
+    free(arg_list);
+    sam_global_args_free(&ga);
+    return res;
+
+ fail:
+    if (in) sam_close(in);
+    if (out) sam_close(out);
+    if (p.pool) hts_tpool_destroy(p.pool);
+    free(arg_list);
+    sam_global_args_free(&ga);
+    return 1;
+}
+
+
diff --git a/samtools/bam_md.c b/samtools/bam_md.c
new file mode 100644
index 0000000..7d5aeaa
--- /dev/null
+++ b/samtools/bam_md.c
@@ -0,0 +1,418 @@
+/*  bam_md.c -- calmd subcommand.
+
+    Copyright (C) 2009-2011, 2014-2015, 2019-2020 Genome Research Ltd.
+    Portions copyright (C) 2009-2011 Broad Institute.
+
+    Author: Heng Li <lh3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <config.h>
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <ctype.h>
+#include <limits.h>
+#include <errno.h>
+#include "htslib/faidx.h"
+#include "htslib/sam.h"
+#include "htslib/kstring.h"
+#include "htslib/thread_pool.h"
+#include "sam_opts.h"
+#include "samtools.h"
+
+#define USE_EQUAL 1
+#define DROP_TAG  2
+#define BIN_QUAL  4
+#define UPDATE_NM 8
+#define UPDATE_MD 16
+#define HASH_QNM  32
+
+int bam_aux_drop_other(bam1_t *b, uint8_t *s);
+
+static int bam_fillmd1_core(const char *ref_name, bam1_t *b, char *ref,
+                            hts_pos_t ref_len, int flag, int max_nm,
+                            int quiet_mode, uint32_t *skipped)
+{
+    uint8_t *seq = bam_get_seq(b);
+    uint32_t *cigar = bam_get_cigar(b);
+    bam1_core_t *c = &b->core;
+    int i, qpos, matched = 0;
+    hts_pos_t rpos;
+    kstring_t str = KS_INITIALIZE;
+    int32_t old_nm_i = -1, nm = 0;
+    uint32_t err = 0;
+
+    if (c->l_qseq == 0) {
+        if (!quiet_mode) {
+            if (ref_name) {
+                fprintf(stderr, "[bam_fillmd1] no sequence in alignment "
+                        "record for '%s' at %s:%"PRIhts_pos", skipped\n",
+                        bam_get_qname(b), ref_name, c->pos + 1);
+            } else {
+                fprintf(stderr, "[bam_fillmd1] no sequence in alignment "
+                        "record for '%s', skipped", bam_get_qname(b));
+            }
+        }
+        if (skipped) (*skipped)++;
+        return 0;
+    }
+
+    for (i = qpos = 0, rpos = c->pos; i < c->n_cigar; ++i) {
+        int j, oplen = cigar[i]>>4, op = cigar[i]&0xf;
+        if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) {
+            for (j = 0; j < oplen; ++j) {
+                int c1, c2, z = qpos + j;
+                if (rpos+j >= ref_len || z >= c->l_qseq || ref[rpos+j] == '\0')
+                    break; // out of bounds
+                c1 = bam_seqi(seq, z);
+                c2 = seq_nt16_table[(uint8_t)ref[rpos+j]];
+                if ((c1 == c2 && c1 != 15 && c2 != 15) || c1 == 0) { // a match
+                    if (flag&USE_EQUAL) seq[z/2] &= (z&1)? 0xf0 : 0x0f;
+                    ++matched;
+                } else {
+                    err |= kputw(matched, &str) < 0;
+                    err |= kputc(toupper(ref[rpos+j]), &str) < 0;
+                    matched = 0; ++nm;
+                }
+            }
+            if (j < oplen) break;
+            rpos += oplen; qpos += oplen;
+        } else if (op == BAM_CDEL) {
+            err |= kputw(matched, &str) < 0;
+            err |= kputc('^', &str) < 0;
+            for (j = 0; j < oplen; ++j) {
+                if (rpos+j >= ref_len || ref[rpos+j] == '\0') break;
+                err |= kputc(toupper(ref[rpos+j]), &str) < 0;
+            }
+            matched = 0;
+            rpos += j; nm += j;
+            if (j < oplen) break;
+        } else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) {
+            qpos += oplen;
+            if (op == BAM_CINS) nm += oplen;
+        } else if (op == BAM_CREF_SKIP) {
+            rpos += oplen;
+        }
+    }
+    err |= kputw(matched, &str) < 0;
+    if (err) {
+        print_error_errno("calmd", "Couldn't build new MD string");
+        goto fail;
+    }
+    // apply max_nm
+    if (max_nm > 0 && nm >= max_nm) {
+        for (i = qpos = 0, rpos = c->pos; i < c->n_cigar; ++i) {
+            int j, oplen = cigar[i]>>4, op = cigar[i]&0xf;
+            if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) {
+                for (j = 0; j < oplen; ++j) {
+                    int c1, c2, z = qpos + j;
+                    if (rpos+j >= ref_len || z >= c->l_qseq || ref[rpos+j] == '\0')
+                        break; // out of bounds
+                    c1 = bam_seqi(seq, z);
+                    c2 = seq_nt16_table[(uint8_t)ref[rpos+j]];
+                    if ((c1 == c2 && c1 != 15 && c2 != 15) || c1 == 0) { // a match
+                        seq[z/2] |= (z&1)? 0x0f : 0xf0;
+                        bam_get_qual(b)[z] = 0;
+                    }
+                }
+                if (j < oplen) break;
+                rpos += oplen; qpos += oplen;
+            } else if (op == BAM_CDEL || op == BAM_CREF_SKIP) rpos += oplen;
+            else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) qpos += oplen;
+        }
+    }
+    // update NM
+    if ((flag & UPDATE_NM) && !(c->flag & BAM_FUNMAP)) {
+        uint8_t *old_nm = bam_aux_get(b, "NM");
+        if (old_nm) old_nm_i = bam_aux2i(old_nm);
+        if (!old_nm) {
+            if (bam_aux_append(b, "NM", 'i', 4, (uint8_t*)&nm) < 0)
+                goto aux_fail;
+        }
+        else if (nm != old_nm_i) {
+            if (!quiet_mode) {
+                fprintf(stderr, "[bam_fillmd1] different NM for read '%s': %d -> %d\n", bam_get_qname(b), old_nm_i, nm);
+            }
+            if (bam_aux_del(b, old_nm) < 0) goto aux_fail;
+            if (bam_aux_append(b, "NM", 'i', 4, (uint8_t*)&nm) < 0)
+                goto aux_fail;
+        }
+    }
+    // update MD
+    if ((flag & UPDATE_MD) && !(c->flag & BAM_FUNMAP)) {
+        uint8_t *old_md = bam_aux_get(b, "MD");
+        if (!old_md) {
+            if (bam_aux_append(b, "MD", 'Z', str.l + 1, (uint8_t*)str.s) < 0)
+                goto aux_fail;
+        } else {
+            int is_diff = 0;
+            if (strlen((char*)old_md+1) == str.l) {
+                for (i = 0; i < str.l; ++i)
+                    if (toupper(old_md[i+1]) != toupper(str.s[i]))
+                        break;
+                if (i < str.l) is_diff = 1;
+            } else is_diff = 1;
+            if (is_diff) {
+                if (!quiet_mode) {
+                    fprintf(stderr, "[bam_fillmd1] different MD for read '%s': '%s' -> '%s'\n", bam_get_qname(b), old_md+1, str.s);
+                }
+                if (bam_aux_del(b, old_md) < 0) goto aux_fail;
+                if (bam_aux_append(b, "MD", 'Z', str.l + 1, (uint8_t*)str.s) < 0)
+                    goto aux_fail;
+            }
+        }
+    }
+
+    // drop all tags but RG
+    if (flag&DROP_TAG) {
+        uint8_t *q = bam_aux_get(b, "RG");
+        bam_aux_drop_other(b, q);
+    }
+    // reduce the resolution of base quality
+    if (flag&BIN_QUAL) {
+        uint8_t *qual = bam_get_qual(b);
+        for (i = 0; i < b->core.l_qseq; ++i)
+            if (qual[i] >= 3) qual[i] = qual[i]/10*10 + 7;
+    }
+
+    free(str.s);
+    return 0;
+
+ aux_fail:
+    if (errno == ENOMEM) {
+        print_error("calmd", "Couldn't add aux tag (too long)");
+    } else if (errno == EINVAL) {
+        print_error("calmd", "Corrupt aux data");
+    } else {
+        print_error_errno("calmd", "Couldn't add aux tag");
+    }
+ fail:
+    free(str.s);
+    return -1;
+}
+
+int bam_fillmd1(bam1_t *b, char *ref, int flag, int quiet_mode)
+{
+    return bam_fillmd1_core(NULL, b, ref, INT_MAX, flag, 0, quiet_mode, NULL);
+}
+
+int calmd_usage() {
+    fprintf(stderr,
+"Usage: samtools calmd [-eubrAESQ] <aln.bam> <ref.fasta>\n"
+"Options:\n"
+"  -e       change identical bases to '='\n"
+"  -u       uncompressed BAM output (for piping)\n"
+"  -b       compressed BAM output\n"
+"  -S       ignored (input format is auto-detected)\n"
+"  -A       modify the quality string\n"
+"  -Q       use quiet mode to output less debug info to stdout\n"
+"  -r       compute the BQ tag (without -A) or cap baseQ by BAQ (with -A)\n"
+"  -E       extended BAQ for better sensitivity but lower specificity\n"
+"  --no-PG  do not add a PG line\n");
+
+    sam_global_opt_help(stderr, "-....@-.");
+    return 1;
+}
+
+int bam_fillmd(int argc, char *argv[])
+{
+    int c, flt_flag, tid = -2, ret, is_bam_out, is_uncompressed, max_nm, is_realn, capQ, baq_flag, quiet_mode, no_pg = 0;
+    hts_pos_t len;
+    htsThreadPool p = {NULL, 0};
+    samFile *fp = NULL, *fpout = NULL;
+    sam_hdr_t *header = NULL;
+    faidx_t *fai = NULL;
+    char *ref = NULL, mode_w[8], *ref_file, *arg_list = NULL;
+    const char *ref_name = NULL;
+    bam1_t *b = NULL;
+    sam_global_args ga = SAM_GLOBAL_ARGS_INIT;
+    uint32_t skipped = 0;
+
+    static const struct option lopts[] = {
+        SAM_OPT_GLOBAL_OPTIONS('-', 0, 0, 0, 0,'@'),
+        {"no-PG", no_argument, NULL, 1},
+        { NULL, 0, NULL, 0 }
+    };
+
+    flt_flag = UPDATE_NM | UPDATE_MD;
+    is_bam_out = is_uncompressed = is_realn = max_nm = capQ = baq_flag = quiet_mode = 0;
+    strcpy(mode_w, "w");
+    while ((c = getopt_long(argc, argv, "EqQreuNhbSC:n:Ad@:", lopts, NULL)) >= 0) {
+        switch (c) {
+        case 'r': is_realn = 1; break;
+        case 'e': flt_flag |= USE_EQUAL; break;
+        case 'd': flt_flag |= DROP_TAG; break;
+        case 'q': flt_flag |= BIN_QUAL; break;
+        case 'h': flt_flag |= HASH_QNM; break;
+        case 'N': flt_flag &= ~(UPDATE_MD|UPDATE_NM); break;
+        case 'b': is_bam_out = 1; break;
+        case 'u': is_uncompressed = is_bam_out = 1; break;
+        case 'S': break;
+        case 'n': max_nm = atoi(optarg); break;
+        case 'C': capQ = atoi(optarg); break;
+        case 'A': baq_flag |= 1; break;
+        case 'E': baq_flag |= 2; break;
+        case 'Q': quiet_mode = 1; break;
+        case 1: no_pg = 1; break;
+        default:  if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break;
+            fprintf(stderr, "[bam_fillmd] unrecognized option '-%c'\n\n", c);
+            /* else fall-through */
+        case '?': return calmd_usage();
+        }
+    }
+    if (is_bam_out) strcat(mode_w, "b");
+    else strcat(mode_w, "h");
+    if (is_uncompressed) strcat(mode_w, "0");
+    if (optind + (ga.reference == NULL) >= argc)
+        return calmd_usage();
+    fp = sam_open_format(argv[optind], "r", &ga.in);
+    if (fp == NULL) {
+        print_error_errno("calmd", "Failed to open input file '%s'", argv[optind]);
+        return 1;
+    }
+
+    if (!no_pg && !(arg_list = stringify_argv(argc+1, argv-1))) {
+        print_error("calmd", "failed to create arg_list");
+        return 1;
+    }
+
+    header = sam_hdr_read(fp);
+    if (header == NULL || sam_hdr_nref(header) == 0) {
+        fprintf(stderr, "[bam_fillmd] input SAM does not have header. Abort!\n");
+        goto fail;
+    }
+
+    fpout = sam_open_format("-", mode_w, &ga.out);
+    if (fpout == NULL) {
+        print_error_errno("calmd", "Failed to open output");
+        goto fail;
+    }
+    if (!no_pg && sam_hdr_add_pg(header, "samtools",
+                                 "VN", samtools_version(),
+                                 arg_list ? "CL": NULL,
+                                 arg_list ? arg_list : NULL,
+                                 NULL)) {
+        print_error("calmd", "failed to add PG line to header");
+        goto fail;
+    }
+    if (sam_hdr_write(fpout, header) < 0) {
+        print_error_errno("calmd", "Failed to write sam header");
+        goto fail;
+    }
+
+    if (ga.nthreads > 0) {
+        if (!(p.pool = hts_tpool_init(ga.nthreads))) {
+            fprintf(stderr, "Error creating thread pool\n");
+            goto fail;
+        }
+        hts_set_opt(fp,    HTS_OPT_THREAD_POOL, &p);
+        hts_set_opt(fpout, HTS_OPT_THREAD_POOL, &p);
+    }
+
+    ref_file = argc > optind + 1 ? argv[optind+1] : ga.reference;
+    fai = fai_load(ref_file);
+
+    if (!fai) {
+        print_error_errno("calmd", "Failed to open reference file '%s'", ref_file);
+        goto fail;
+    }
+
+    b = bam_init1();
+    if (!b) {
+        fprintf(stderr, "[bam_fillmd] Failed to allocate bam struct\n");
+        goto fail;
+    }
+    while ((ret = sam_read1(fp, header, b)) >= 0) {
+        if (b->core.tid >= 0) {
+            if (tid != b->core.tid) {
+                free(ref);
+                ref = NULL;
+                len = 0;
+                ref_name = sam_hdr_tid2name(header, b->core.tid);
+                if (ref_name) {
+                    ref = fai_fetch64(fai, ref_name, &len);
+                }
+                tid = b->core.tid;
+                if (ref == 0) { // FIXME: Should this always be fatal?
+                    fprintf(stderr, "[bam_fillmd] fail to find sequence '%s' in the reference.\n",
+                            ref_name ? ref_name : "(unknown)");
+                    if (is_realn || capQ > 10) goto fail; // Would otherwise crash
+                }
+            }
+            if (is_realn) {
+                if (sam_prob_realn(b, ref, len, baq_flag) < -3) {
+                    print_error_errno("calmd", "BAQ alignment failed");
+                    goto fail;
+                }
+            }
+            if (capQ > 10) {
+                int q = sam_cap_mapq(b, ref, len, capQ);
+                if (b->core.qual > q) b->core.qual = q;
+            }
+            if (ref) {
+                if (bam_fillmd1_core(ref_name, b, ref, len, flt_flag, max_nm,
+                                     quiet_mode, &skipped) < 0)
+                    goto fail;
+            }
+        }
+        if (sam_write1(fpout, header, b) < 0) {
+            print_error_errno("calmd", "failed to write to output file");
+            goto fail;
+        }
+    }
+    if (ret < -1) {
+        fprintf(stderr, "[bam_fillmd] Error reading input.\n");
+        goto fail;
+    }
+
+    if (skipped) {
+        fprintf(stderr, "[calmd] Warning: %"PRIu32" records skipped due "
+                "to no query sequence\n",
+                skipped);
+    }
+
+    bam_destroy1(b);
+    sam_hdr_destroy(header);
+
+    free(arg_list);
+    free(ref);
+    fai_destroy(fai);
+    sam_close(fp);
+    if (sam_close(fpout) < 0) {
+        fprintf(stderr, "[bam_fillmd] error when closing output file\n");
+        return 1;
+    }
+    if (p.pool) hts_tpool_destroy(p.pool);
+
+    return 0;
+
+ fail:
+    free(arg_list);
+    free(ref);
+    if (b) bam_destroy1(b);
+    if (header) sam_hdr_destroy(header);
+    if (fai) fai_destroy(fai);
+    if (fp) sam_close(fp);
+    if (fpout) sam_close(fpout);
+    if (p.pool) hts_tpool_destroy(p.pool);
+
+    return 1;
+}
diff --git a/samtools/bam_md.c.pysam.c b/samtools/bam_md.c.pysam.c
new file mode 100644
index 0000000..b71e77c
--- /dev/null
+++ b/samtools/bam_md.c.pysam.c
@@ -0,0 +1,420 @@
+#include "samtools.pysam.h"
+
+/*  bam_md.c -- calmd subcommand.
+
+    Copyright (C) 2009-2011, 2014-2015, 2019-2020 Genome Research Ltd.
+    Portions copyright (C) 2009-2011 Broad Institute.
+
+    Author: Heng Li <lh3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <config.h>
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <ctype.h>
+#include <limits.h>
+#include <errno.h>
+#include "htslib/faidx.h"
+#include "htslib/sam.h"
+#include "htslib/kstring.h"
+#include "htslib/thread_pool.h"
+#include "sam_opts.h"
+#include "samtools.h"
+
+#define USE_EQUAL 1
+#define DROP_TAG  2
+#define BIN_QUAL  4
+#define UPDATE_NM 8
+#define UPDATE_MD 16
+#define HASH_QNM  32
+
+int bam_aux_drop_other(bam1_t *b, uint8_t *s);
+
+static int bam_fillmd1_core(const char *ref_name, bam1_t *b, char *ref,
+                            hts_pos_t ref_len, int flag, int max_nm,
+                            int quiet_mode, uint32_t *skipped)
+{
+    uint8_t *seq = bam_get_seq(b);
+    uint32_t *cigar = bam_get_cigar(b);
+    bam1_core_t *c = &b->core;
+    int i, qpos, matched = 0;
+    hts_pos_t rpos;
+    kstring_t str = KS_INITIALIZE;
+    int32_t old_nm_i = -1, nm = 0;
+    uint32_t err = 0;
+
+    if (c->l_qseq == 0) {
+        if (!quiet_mode) {
+            if (ref_name) {
+                fprintf(samtools_stderr, "[bam_fillmd1] no sequence in alignment "
+                        "record for '%s' at %s:%"PRIhts_pos", skipped\n",
+                        bam_get_qname(b), ref_name, c->pos + 1);
+            } else {
+                fprintf(samtools_stderr, "[bam_fillmd1] no sequence in alignment "
+                        "record for '%s', skipped", bam_get_qname(b));
+            }
+        }
+        if (skipped) (*skipped)++;
+        return 0;
+    }
+
+    for (i = qpos = 0, rpos = c->pos; i < c->n_cigar; ++i) {
+        int j, oplen = cigar[i]>>4, op = cigar[i]&0xf;
+        if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) {
+            for (j = 0; j < oplen; ++j) {
+                int c1, c2, z = qpos + j;
+                if (rpos+j >= ref_len || z >= c->l_qseq || ref[rpos+j] == '\0')
+                    break; // out of bounds
+                c1 = bam_seqi(seq, z);
+                c2 = seq_nt16_table[(uint8_t)ref[rpos+j]];
+                if ((c1 == c2 && c1 != 15 && c2 != 15) || c1 == 0) { // a match
+                    if (flag&USE_EQUAL) seq[z/2] &= (z&1)? 0xf0 : 0x0f;
+                    ++matched;
+                } else {
+                    err |= kputw(matched, &str) < 0;
+                    err |= kputc(toupper(ref[rpos+j]), &str) < 0;
+                    matched = 0; ++nm;
+                }
+            }
+            if (j < oplen) break;
+            rpos += oplen; qpos += oplen;
+        } else if (op == BAM_CDEL) {
+            err |= kputw(matched, &str) < 0;
+            err |= kputc('^', &str) < 0;
+            for (j = 0; j < oplen; ++j) {
+                if (rpos+j >= ref_len || ref[rpos+j] == '\0') break;
+                err |= kputc(toupper(ref[rpos+j]), &str) < 0;
+            }
+            matched = 0;
+            rpos += j; nm += j;
+            if (j < oplen) break;
+        } else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) {
+            qpos += oplen;
+            if (op == BAM_CINS) nm += oplen;
+        } else if (op == BAM_CREF_SKIP) {
+            rpos += oplen;
+        }
+    }
+    err |= kputw(matched, &str) < 0;
+    if (err) {
+        print_error_errno("calmd", "Couldn't build new MD string");
+        goto fail;
+    }
+    // apply max_nm
+    if (max_nm > 0 && nm >= max_nm) {
+        for (i = qpos = 0, rpos = c->pos; i < c->n_cigar; ++i) {
+            int j, oplen = cigar[i]>>4, op = cigar[i]&0xf;
+            if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) {
+                for (j = 0; j < oplen; ++j) {
+                    int c1, c2, z = qpos + j;
+                    if (rpos+j >= ref_len || z >= c->l_qseq || ref[rpos+j] == '\0')
+                        break; // out of bounds
+                    c1 = bam_seqi(seq, z);
+                    c2 = seq_nt16_table[(uint8_t)ref[rpos+j]];
+                    if ((c1 == c2 && c1 != 15 && c2 != 15) || c1 == 0) { // a match
+                        seq[z/2] |= (z&1)? 0x0f : 0xf0;
+                        bam_get_qual(b)[z] = 0;
+                    }
+                }
+                if (j < oplen) break;
+                rpos += oplen; qpos += oplen;
+            } else if (op == BAM_CDEL || op == BAM_CREF_SKIP) rpos += oplen;
+            else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) qpos += oplen;
+        }
+    }
+    // update NM
+    if ((flag & UPDATE_NM) && !(c->flag & BAM_FUNMAP)) {
+        uint8_t *old_nm = bam_aux_get(b, "NM");
+        if (old_nm) old_nm_i = bam_aux2i(old_nm);
+        if (!old_nm) {
+            if (bam_aux_append(b, "NM", 'i', 4, (uint8_t*)&nm) < 0)
+                goto aux_fail;
+        }
+        else if (nm != old_nm_i) {
+            if (!quiet_mode) {
+                fprintf(samtools_stderr, "[bam_fillmd1] different NM for read '%s': %d -> %d\n", bam_get_qname(b), old_nm_i, nm);
+            }
+            if (bam_aux_del(b, old_nm) < 0) goto aux_fail;
+            if (bam_aux_append(b, "NM", 'i', 4, (uint8_t*)&nm) < 0)
+                goto aux_fail;
+        }
+    }
+    // update MD
+    if ((flag & UPDATE_MD) && !(c->flag & BAM_FUNMAP)) {
+        uint8_t *old_md = bam_aux_get(b, "MD");
+        if (!old_md) {
+            if (bam_aux_append(b, "MD", 'Z', str.l + 1, (uint8_t*)str.s) < 0)
+                goto aux_fail;
+        } else {
+            int is_diff = 0;
+            if (strlen((char*)old_md+1) == str.l) {
+                for (i = 0; i < str.l; ++i)
+                    if (toupper(old_md[i+1]) != toupper(str.s[i]))
+                        break;
+                if (i < str.l) is_diff = 1;
+            } else is_diff = 1;
+            if (is_diff) {
+                if (!quiet_mode) {
+                    fprintf(samtools_stderr, "[bam_fillmd1] different MD for read '%s': '%s' -> '%s'\n", bam_get_qname(b), old_md+1, str.s);
+                }
+                if (bam_aux_del(b, old_md) < 0) goto aux_fail;
+                if (bam_aux_append(b, "MD", 'Z', str.l + 1, (uint8_t*)str.s) < 0)
+                    goto aux_fail;
+            }
+        }
+    }
+
+    // drop all tags but RG
+    if (flag&DROP_TAG) {
+        uint8_t *q = bam_aux_get(b, "RG");
+        bam_aux_drop_other(b, q);
+    }
+    // reduce the resolution of base quality
+    if (flag&BIN_QUAL) {
+        uint8_t *qual = bam_get_qual(b);
+        for (i = 0; i < b->core.l_qseq; ++i)
+            if (qual[i] >= 3) qual[i] = qual[i]/10*10 + 7;
+    }
+
+    free(str.s);
+    return 0;
+
+ aux_fail:
+    if (errno == ENOMEM) {
+        print_error("calmd", "Couldn't add aux tag (too long)");
+    } else if (errno == EINVAL) {
+        print_error("calmd", "Corrupt aux data");
+    } else {
+        print_error_errno("calmd", "Couldn't add aux tag");
+    }
+ fail:
+    free(str.s);
+    return -1;
+}
+
+int bam_fillmd1(bam1_t *b, char *ref, int flag, int quiet_mode)
+{
+    return bam_fillmd1_core(NULL, b, ref, INT_MAX, flag, 0, quiet_mode, NULL);
+}
+
+int calmd_usage() {
+    fprintf(samtools_stderr,
+"Usage: samtools calmd [-eubrAESQ] <aln.bam> <ref.fasta>\n"
+"Options:\n"
+"  -e       change identical bases to '='\n"
+"  -u       uncompressed BAM output (for piping)\n"
+"  -b       compressed BAM output\n"
+"  -S       ignored (input format is auto-detected)\n"
+"  -A       modify the quality string\n"
+"  -Q       use quiet mode to output less debug info to samtools_stdout\n"
+"  -r       compute the BQ tag (without -A) or cap baseQ by BAQ (with -A)\n"
+"  -E       extended BAQ for better sensitivity but lower specificity\n"
+"  --no-PG  do not add a PG line\n");
+
+    sam_global_opt_help(samtools_stderr, "-....@-.");
+    return 1;
+}
+
+int bam_fillmd(int argc, char *argv[])
+{
+    int c, flt_flag, tid = -2, ret, is_bam_out, is_uncompressed, max_nm, is_realn, capQ, baq_flag, quiet_mode, no_pg = 0;
+    hts_pos_t len;
+    htsThreadPool p = {NULL, 0};
+    samFile *fp = NULL, *fpout = NULL;
+    sam_hdr_t *header = NULL;
+    faidx_t *fai = NULL;
+    char *ref = NULL, mode_w[8], *ref_file, *arg_list = NULL;
+    const char *ref_name = NULL;
+    bam1_t *b = NULL;
+    sam_global_args ga = SAM_GLOBAL_ARGS_INIT;
+    uint32_t skipped = 0;
+
+    static const struct option lopts[] = {
+        SAM_OPT_GLOBAL_OPTIONS('-', 0, 0, 0, 0,'@'),
+        {"no-PG", no_argument, NULL, 1},
+        { NULL, 0, NULL, 0 }
+    };
+
+    flt_flag = UPDATE_NM | UPDATE_MD;
+    is_bam_out = is_uncompressed = is_realn = max_nm = capQ = baq_flag = quiet_mode = 0;
+    strcpy(mode_w, "w");
+    while ((c = getopt_long(argc, argv, "EqQreuNhbSC:n:Ad@:", lopts, NULL)) >= 0) {
+        switch (c) {
+        case 'r': is_realn = 1; break;
+        case 'e': flt_flag |= USE_EQUAL; break;
+        case 'd': flt_flag |= DROP_TAG; break;
+        case 'q': flt_flag |= BIN_QUAL; break;
+        case 'h': flt_flag |= HASH_QNM; break;
+        case 'N': flt_flag &= ~(UPDATE_MD|UPDATE_NM); break;
+        case 'b': is_bam_out = 1; break;
+        case 'u': is_uncompressed = is_bam_out = 1; break;
+        case 'S': break;
+        case 'n': max_nm = atoi(optarg); break;
+        case 'C': capQ = atoi(optarg); break;
+        case 'A': baq_flag |= 1; break;
+        case 'E': baq_flag |= 2; break;
+        case 'Q': quiet_mode = 1; break;
+        case 1: no_pg = 1; break;
+        default:  if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break;
+            fprintf(samtools_stderr, "[bam_fillmd] unrecognized option '-%c'\n\n", c);
+            /* else fall-through */
+        case '?': return calmd_usage();
+        }
+    }
+    if (is_bam_out) strcat(mode_w, "b");
+    else strcat(mode_w, "h");
+    if (is_uncompressed) strcat(mode_w, "0");
+    if (optind + (ga.reference == NULL) >= argc)
+        return calmd_usage();
+    fp = sam_open_format(argv[optind], "r", &ga.in);
+    if (fp == NULL) {
+        print_error_errno("calmd", "Failed to open input file '%s'", argv[optind]);
+        return 1;
+    }
+
+    if (!no_pg && !(arg_list = stringify_argv(argc+1, argv-1))) {
+        print_error("calmd", "failed to create arg_list");
+        return 1;
+    }
+
+    header = sam_hdr_read(fp);
+    if (header == NULL || sam_hdr_nref(header) == 0) {
+        fprintf(samtools_stderr, "[bam_fillmd] input SAM does not have header. Abort!\n");
+        goto fail;
+    }
+
+    fpout = sam_open_format(samtools_stdout_fn, mode_w, &ga.out);
+    if (fpout == NULL) {
+        print_error_errno("calmd", "Failed to open output");
+        goto fail;
+    }
+    if (!no_pg && sam_hdr_add_pg(header, "samtools",
+                                 "VN", samtools_version(),
+                                 arg_list ? "CL": NULL,
+                                 arg_list ? arg_list : NULL,
+                                 NULL)) {
+        print_error("calmd", "failed to add PG line to header");
+        goto fail;
+    }
+    if (sam_hdr_write(fpout, header) < 0) {
+        print_error_errno("calmd", "Failed to write sam header");
+        goto fail;
+    }
+
+    if (ga.nthreads > 0) {
+        if (!(p.pool = hts_tpool_init(ga.nthreads))) {
+            fprintf(samtools_stderr, "Error creating thread pool\n");
+            goto fail;
+        }
+        hts_set_opt(fp,    HTS_OPT_THREAD_POOL, &p);
+        hts_set_opt(fpout, HTS_OPT_THREAD_POOL, &p);
+    }
+
+    ref_file = argc > optind + 1 ? argv[optind+1] : ga.reference;
+    fai = fai_load(ref_file);
+
+    if (!fai) {
+        print_error_errno("calmd", "Failed to open reference file '%s'", ref_file);
+        goto fail;
+    }
+
+    b = bam_init1();
+    if (!b) {
+        fprintf(samtools_stderr, "[bam_fillmd] Failed to allocate bam struct\n");
+        goto fail;
+    }
+    while ((ret = sam_read1(fp, header, b)) >= 0) {
+        if (b->core.tid >= 0) {
+            if (tid != b->core.tid) {
+                free(ref);
+                ref = NULL;
+                len = 0;
+                ref_name = sam_hdr_tid2name(header, b->core.tid);
+                if (ref_name) {
+                    ref = fai_fetch64(fai, ref_name, &len);
+                }
+                tid = b->core.tid;
+                if (ref == 0) { // FIXME: Should this always be fatal?
+                    fprintf(samtools_stderr, "[bam_fillmd] fail to find sequence '%s' in the reference.\n",
+                            ref_name ? ref_name : "(unknown)");
+                    if (is_realn || capQ > 10) goto fail; // Would otherwise crash
+                }
+            }
+            if (is_realn) {
+                if (sam_prob_realn(b, ref, len, baq_flag) < -3) {
+                    print_error_errno("calmd", "BAQ alignment failed");
+                    goto fail;
+                }
+            }
+            if (capQ > 10) {
+                int q = sam_cap_mapq(b, ref, len, capQ);
+                if (b->core.qual > q) b->core.qual = q;
+            }
+            if (ref) {
+                if (bam_fillmd1_core(ref_name, b, ref, len, flt_flag, max_nm,
+                                     quiet_mode, &skipped) < 0)
+                    goto fail;
+            }
+        }
+        if (sam_write1(fpout, header, b) < 0) {
+            print_error_errno("calmd", "failed to write to output file");
+            goto fail;
+        }
+    }
+    if (ret < -1) {
+        fprintf(samtools_stderr, "[bam_fillmd] Error reading input.\n");
+        goto fail;
+    }
+
+    if (skipped) {
+        fprintf(samtools_stderr, "[calmd] Warning: %"PRIu32" records skipped due "
+                "to no query sequence\n",
+                skipped);
+    }
+
+    bam_destroy1(b);
+    sam_hdr_destroy(header);
+
+    free(arg_list);
+    free(ref);
+    fai_destroy(fai);
+    sam_close(fp);
+    if (sam_close(fpout) < 0) {
+        fprintf(samtools_stderr, "[bam_fillmd] error when closing output file\n");
+        return 1;
+    }
+    if (p.pool) hts_tpool_destroy(p.pool);
+
+    return 0;
+
+ fail:
+    free(arg_list);
+    free(ref);
+    if (b) bam_destroy1(b);
+    if (header) sam_hdr_destroy(header);
+    if (fai) fai_destroy(fai);
+    if (fp) sam_close(fp);
+    if (fpout) sam_close(fpout);
+    if (p.pool) hts_tpool_destroy(p.pool);
+
+    return 1;
+}
diff --git a/samtools/bam_plbuf.c b/samtools/bam_plbuf.c
new file mode 100644
index 0000000..5541d55
--- /dev/null
+++ b/samtools/bam_plbuf.c
@@ -0,0 +1,69 @@
+/*  bam_plbuf.c -- plbuf routines (previously in bam_pileup.c).
+
+    Copyright (C) 2008-2010, 2013 Genome Research Ltd.
+
+    Author: Heng Li <lh3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <config.h>
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <ctype.h>
+#include <htslib/hts.h>
+#include <htslib/sam.h>
+#include "bam_plbuf.h"
+
+/*****************
+ * callback APIs *
+ *****************/
+
+void bam_plbuf_reset(bam_plbuf_t *buf)
+{
+    bam_plp_reset(buf->iter);
+}
+
+bam_plbuf_t *bam_plbuf_init(bam_pileup_f func, void *data)
+{
+    bam_plbuf_t *buf;
+    buf = calloc(1, sizeof(bam_plbuf_t));
+    buf->iter = bam_plp_init(0, 0);
+    buf->func = func;
+    buf->data = data;
+    return buf;
+}
+
+void bam_plbuf_destroy(bam_plbuf_t *buf)
+{
+    bam_plp_destroy(buf->iter);
+    free(buf);
+}
+
+int bam_plbuf_push(const bam1_t *b, bam_plbuf_t *buf)
+{
+    int ret, n_plp, tid;
+    hts_pos_t pos;
+    const bam_pileup1_t *plp;
+    ret = bam_plp_push(buf->iter, b);
+    if (ret < 0) return ret;
+    while ((plp = bam_plp64_next(buf->iter, &tid, &pos, &n_plp)) != 0)
+        buf->func(tid, pos, n_plp, plp, buf->data);
+    return 0;
+}
diff --git a/samtools/bam_plbuf.c.pysam.c b/samtools/bam_plbuf.c.pysam.c
new file mode 100644
index 0000000..9fc8528
--- /dev/null
+++ b/samtools/bam_plbuf.c.pysam.c
@@ -0,0 +1,71 @@
+#include "samtools.pysam.h"
+
+/*  bam_plbuf.c -- plbuf routines (previously in bam_pileup.c).
+
+    Copyright (C) 2008-2010, 2013 Genome Research Ltd.
+
+    Author: Heng Li <lh3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <config.h>
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <ctype.h>
+#include <htslib/hts.h>
+#include <htslib/sam.h>
+#include "bam_plbuf.h"
+
+/*****************
+ * callback APIs *
+ *****************/
+
+void bam_plbuf_reset(bam_plbuf_t *buf)
+{
+    bam_plp_reset(buf->iter);
+}
+
+bam_plbuf_t *bam_plbuf_init(bam_pileup_f func, void *data)
+{
+    bam_plbuf_t *buf;
+    buf = calloc(1, sizeof(bam_plbuf_t));
+    buf->iter = bam_plp_init(0, 0);
+    buf->func = func;
+    buf->data = data;
+    return buf;
+}
+
+void bam_plbuf_destroy(bam_plbuf_t *buf)
+{
+    bam_plp_destroy(buf->iter);
+    free(buf);
+}
+
+int bam_plbuf_push(const bam1_t *b, bam_plbuf_t *buf)
+{
+    int ret, n_plp, tid;
+    hts_pos_t pos;
+    const bam_pileup1_t *plp;
+    ret = bam_plp_push(buf->iter, b);
+    if (ret < 0) return ret;
+    while ((plp = bam_plp64_next(buf->iter, &tid, &pos, &n_plp)) != 0)
+        buf->func(tid, pos, n_plp, plp, buf->data);
+    return 0;
+}
diff --git a/samtools/bam_plbuf.h b/samtools/bam_plbuf.h
new file mode 100644
index 0000000..9a718e0
--- /dev/null
+++ b/samtools/bam_plbuf.h
@@ -0,0 +1,62 @@
+/*  bam_plbuf.h -- plbuf routines (declarations copied from bam.h).
+
+    Copyright (C) 2008, 2013, 2021 Genome Research Ltd.
+
+    Author: Heng Li <lh3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#ifndef BAM_PLBUF_H
+#define BAM_PLBUF_H
+
+#include <htslib/sam.h>
+
+#ifndef BAM_PILEUP_F_DEFINED
+#define BAM_PILEUP_F_DEFINED
+typedef int (*bam_pileup_f)(uint32_t tid, hts_pos_t pos, int n, const bam_pileup1_t *pl, void *data);
+#endif //BAM_PILEUP_F_DEFINED
+
+typedef struct {
+    bam_plp_t iter;
+    bam_pileup_f func;
+    void *data;
+} bam_plbuf_t;
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+/* Exported from bam_plbuf.c */
+void bam_plbuf_reset(bam_plbuf_t *buf);
+
+bam_plbuf_t *bam_plbuf_init(bam_pileup_f func, void *data);
+
+void bam_plbuf_destroy(bam_plbuf_t *buf);
+
+int bam_plbuf_push(const bam1_t *b, bam_plbuf_t *buf);
+
+/* Exported from bam_plcmd.c */
+int pileup_seq(FILE *fp, const bam_pileup1_t *p, hts_pos_t pos,
+               hts_pos_t ref_len, const char *ref, kstring_t *ks,
+               int rev_del, int no_ins, int no_ins_mods,
+               int no_del, int no_ends);
+#ifdef __cplusplus
+}
+#endif
+
+#endif // BAM_PLBUF_H
diff --git a/samtools/bam_plcmd.c b/samtools/bam_plcmd.c
new file mode 100644
index 0000000..c73bf89
--- /dev/null
+++ b/samtools/bam_plcmd.c
@@ -0,0 +1,1189 @@
+/*  bam_plcmd.c -- mpileup subcommand.
+
+    Copyright (C) 2008-2015, 2019-2021 Genome Research Ltd.
+    Portions copyright (C) 2009-2012 Broad Institute.
+
+    Author: Heng Li <lh3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <config.h>
+
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <unistd.h>
+#include <ctype.h>
+#include <string.h>
+#include <strings.h>
+#include <limits.h>
+#include <errno.h>
+#include <sys/stat.h>
+#include <getopt.h>
+#include <inttypes.h>
+#include <htslib/sam.h>
+#include <htslib/faidx.h>
+#include <htslib/kstring.h>
+#include <htslib/klist.h>
+#include <htslib/khash_str2int.h>
+#include <htslib/cram.h>
+#include "samtools.h"
+#include "bedidx.h"
+#include "sam_opts.h"
+#include "bam_plbuf.h"
+
+#define dummy_free(p)
+KLIST_INIT(auxlist, char *, dummy_free)
+
+static inline int printw(int c, FILE *fp)
+{
+    char buf[16];
+    int l, x;
+    if (c == 0) return fputc('0', fp);
+    for (l = 0, x = c < 0? -c : c; x > 0; x /= 10) buf[l++] = x%10 + '0';
+    if (c < 0) buf[l++] = '-';
+    buf[l] = 0;
+    for (x = 0; x < l/2; ++x) {
+        int y = buf[x]; buf[x] = buf[l-1-x]; buf[l-1-x] = y;
+    }
+    fputs(buf, fp);
+    return 0;
+}
+
+int pileup_seq(FILE *fp, const bam_pileup1_t *p, hts_pos_t pos,
+               hts_pos_t ref_len, const char *ref, kstring_t *ks,
+               int rev_del, int no_ins, int no_ins_mods,
+               int no_del, int no_ends)
+{
+    no_ins_mods |= no_ins;
+    int j;
+    hts_base_mod_state *m = p->cd.p;
+    if (!no_ends && p->is_head) {
+        putc('^', fp);
+        putc(p->b->core.qual > 93? 126 : p->b->core.qual + 33, fp);
+    }
+    if (!p->is_del) {
+        int c = p->qpos < p->b->core.l_qseq
+            ? seq_nt16_str[bam_seqi(bam_get_seq(p->b), p->qpos)]
+            : 'N';
+        if (ref) {
+            int rb = pos < ref_len? ref[pos] : 'N';
+            if (c == '=' || seq_nt16_table[c] == seq_nt16_table[rb]) c = bam_is_rev(p->b)? ',' : '.';
+            else c = bam_is_rev(p->b)? tolower(c) : toupper(c);
+        } else {
+            if (c == '=') c = bam_is_rev(p->b)? ',' : '.';
+            else c = bam_is_rev(p->b)? tolower(c) : toupper(c);
+        }
+        putc(c, fp);
+        if (m) {
+            int nm;
+            hts_base_mod mod[256];
+            if ((nm = bam_mods_at_qpos(p->b, p->qpos, m, mod, 256)) > 0) {
+                putc('[', fp);
+                int j;
+                for (j = 0; j < nm && j < 256; j++) {
+                    char qual[20];
+                    if (mod[j].qual >= 0)
+                        sprintf(qual, "%d", mod[j].qual);
+                    else
+                        *qual = 0;
+                    if (mod[j].modified_base < 0)
+                        // ChEBI
+                        fprintf(fp, "%c(%d)%s", "+-"[mod[j].strand],
+                                -mod[j].modified_base, qual);
+                    else
+                        fprintf(fp, "%c%c%s", "+-"[mod[j].strand],
+                                mod[j].modified_base, qual);
+                }
+                putc(']', fp);
+            }
+        }
+    } else putc(p->is_refskip? (bam_is_rev(p->b)? '<' : '>') : ((bam_is_rev(p->b) && rev_del) ? '#' : '*'), fp);
+    int del_len = -p->indel;
+    if (p->indel > 0) {
+        int len = bam_plp_insertion_mod(p, m && !no_ins_mods ? m : NULL,
+                                        ks, &del_len);
+        if (len < 0) {
+            print_error("mpileup", "bam_plp_insertion() failed");
+            return -1;
+        }
+        if (no_ins < 2) {
+            putc('+', fp);
+            printw(len, fp);
+        }
+        if (!no_ins) {
+            if (bam_is_rev(p->b)) {
+                char pad = rev_del ? '#' : '*';
+                int in_mod = 0;
+                for (j = 0; j < ks->l; j++) {
+                    if (ks->s[j] == '[') in_mod = 1;
+                    else if (ks->s[j] == ']') in_mod = 0;
+                    putc(ks->s[j] != '*'
+                         ? (in_mod ? ks->s[j] : tolower(ks->s[j]))
+                         : pad, fp);
+                }
+            } else {
+                int in_mod = 0;
+                for (j = 0; j < ks->l; j++) {
+                    if (ks->s[j] == '[') in_mod = 1;
+                    if (ks->s[j] == ']') in_mod = 0;
+                    putc(in_mod ? ks->s[j] : toupper(ks->s[j]), fp);
+                }
+            }
+        }
+    }
+    if (del_len > 0) {
+        if (no_del < 2)
+            printw(-del_len, fp);
+        if (!no_del) {
+            for (j = 1; j <= del_len; ++j) {
+                int c = (ref && (int)pos+j < ref_len)? ref[pos+j] : 'N';
+                putc(bam_is_rev(p->b)? tolower(c) : toupper(c), fp);
+            }
+        }
+    }
+    if (!no_ends && p->is_tail) putc('$', fp);
+    return 0;
+}
+
+#include "sample.h"
+
+#define MPLP_NO_COMP    (1<<2)
+#define MPLP_NO_ORPHAN  (1<<3)
+#define MPLP_REALN      (1<<4)
+#define MPLP_NO_INDEL   (1<<5)
+#define MPLP_REDO_BAQ   (1<<6)
+#define MPLP_ILLUMINA13 (1<<7)
+#define MPLP_IGNORE_RG  (1<<8)
+#define MPLP_SMART_OVERLAPS (1<<10)
+
+#define MPLP_PRINT_MAPQ_CHAR (1<<11)
+#define MPLP_PRINT_QPOS  (1<<12)
+#define MPLP_PRINT_QNAME (1<<13)
+#define MPLP_PRINT_FLAG  (1<<14)
+#define MPLP_PRINT_RNAME (1<<15)
+#define MPLP_PRINT_POS   (1<<16)
+#define MPLP_PRINT_MAPQ  (1<<17)
+#define MPLP_PRINT_CIGAR (1<<18)
+#define MPLP_PRINT_RNEXT (1<<19)
+#define MPLP_PRINT_PNEXT (1<<20)
+#define MPLP_PRINT_TLEN  (1<<21)
+#define MPLP_PRINT_SEQ   (1<<22)
+#define MPLP_PRINT_QUAL  (1<<23)
+#define MPLP_PRINT_MODS  (1<<24)
+#define MPLP_PRINT_QPOS5 (1<<25)
+
+#define MPLP_PRINT_LAST  (1<<26) // terminator for loop
+
+#define MPLP_MAX_DEPTH 8000
+#define MPLP_MAX_INDEL_DEPTH 250
+
+typedef struct {
+    int min_mq, flag, min_baseQ, capQ_thres, max_depth, max_indel_depth, all, rev_del;
+    int rflag_require, rflag_filter;
+    char *reg, *pl_list, *fai_fname, *output_fname;
+    faidx_t *fai;
+    void *bed, *rghash, *auxlist;
+    int argc;
+    char **argv;
+    char sep, empty, no_ins, no_ins_mods, no_del, no_ends;
+    sam_global_args ga;
+} mplp_conf_t;
+
+typedef struct {
+    char *ref[2];
+    int ref_id[2];
+    hts_pos_t ref_len[2];
+} mplp_ref_t;
+
+#define MPLP_REF_INIT {{NULL,NULL},{-1,-1},{0,0}}
+
+typedef struct {
+    samFile *fp;
+    hts_itr_t *iter;
+    sam_hdr_t *h;
+    mplp_ref_t *ref;
+    const mplp_conf_t *conf;
+} mplp_aux_t;
+
+typedef struct {
+    int n;
+    int *n_plp, *m_plp;
+    bam_pileup1_t **plp;
+} mplp_pileup_t;
+
+static int build_auxlist(mplp_conf_t *conf, char *optstring) {
+    if (!optstring)
+        return 0;
+
+    void *colhash = khash_str2int_init();
+    if (!colhash)
+        return 1;
+
+    struct active_cols {
+        char *name;
+        int supported;
+    };
+
+    const struct active_cols colnames[11] = {
+            {"QNAME", 1}, {"FLAG", 1}, {"RNAME", 1}, {"POS", 1}, {"MAPQ", 1}, {"CIGAR", 0}, {"RNEXT", 1}, {"PNEXT", 1}, {"TLEN", 0}, {"SEQ", 0}, {"QUAL", 0}
+    };
+
+    int i, f = MPLP_PRINT_QNAME, colno = 11;
+    for (i = 0; i < colno; i++, f <<= 1)
+        if (colnames[i].supported)
+            khash_str2int_set(colhash, colnames[i].name, f);
+
+    conf->auxlist = kl_init(auxlist);
+    if (!conf->auxlist)
+        return 1;
+
+    char *save_p;
+    char *tag = strtok_r(optstring, ",", &save_p);
+    while (tag) {
+        if (khash_str2int_get(colhash, tag, &f) == 0) {
+            conf->flag |= f;
+        } else {
+            if (strlen(tag) != 2) {
+                fprintf(stderr, "[%s] tag '%s' has more than two characters or not supported\n", __func__, tag);
+            } else {
+                char **tag_p = kl_pushp(auxlist, conf->auxlist);
+                *tag_p = tag;
+            }
+        }
+        tag = strtok_r(NULL, ",", &save_p);
+    }
+
+    khash_str2int_destroy(colhash);
+
+    return 0;
+}
+
+static int mplp_get_ref(mplp_aux_t *ma, int tid, char **ref, hts_pos_t *ref_len) {
+    mplp_ref_t *r = ma->ref;
+
+    //printf("get ref %d {%d/%p, %d/%p}\n", tid, r->ref_id[0], r->ref[0], r->ref_id[1], r->ref[1]);
+
+    if (!r || !ma->conf->fai) {
+        *ref = NULL;
+        return 0;
+    }
+
+    // Do we need to reference count this so multiple mplp_aux_t can
+    // track which references are in use?
+    // For now we just cache the last two. Sufficient?
+    if (tid == r->ref_id[0]) {
+        *ref = r->ref[0];
+        *ref_len = r->ref_len[0];
+        return 1;
+    }
+    if (tid == r->ref_id[1]) {
+        // Last, swap over
+        int tmp_id;
+        hts_pos_t tmp_len;
+        tmp_id  = r->ref_id[0];  r->ref_id[0]  = r->ref_id[1];  r->ref_id[1]  = tmp_id;
+        tmp_len = r->ref_len[0]; r->ref_len[0] = r->ref_len[1]; r->ref_len[1] = tmp_len;
+
+        char *tc;
+        tc = r->ref[0]; r->ref[0] = r->ref[1]; r->ref[1] = tc;
+        *ref = r->ref[0];
+        *ref_len = r->ref_len[0];
+        return 1;
+    }
+
+    // New, so migrate to old and load new
+    free(r->ref[1]);
+    r->ref[1]     = r->ref[0];
+    r->ref_id[1]  = r->ref_id[0];
+    r->ref_len[1] = r->ref_len[0];
+
+    r->ref_id[0] = tid;
+    r->ref[0] = faidx_fetch_seq64(ma->conf->fai,
+                                sam_hdr_tid2name(ma->h, r->ref_id[0]),
+                                0,
+                                HTS_POS_MAX,
+                                &r->ref_len[0]);
+
+    if (!r->ref[0]) {
+        r->ref[0] = NULL;
+        r->ref_id[0] = -1;
+        r->ref_len[0] = 0;
+        *ref = NULL;
+        return 0;
+    }
+
+    *ref = r->ref[0];
+    *ref_len = r->ref_len[0];
+    return 1;
+}
+
+// Initialise and destroy the base modifier state data. This is called
+// as each new read is added or removed from the pileups.
+static
+int pileup_cd_create(void *data, const bam1_t *b, bam_pileup_cd *cd) {
+    int ret;
+    hts_base_mod_state *m = hts_base_mod_state_alloc();
+    ret = bam_parse_basemod(b, m);
+    cd->p = m;
+    return ret;
+}
+
+static
+int pileup_cd_destroy(void *data, const bam1_t *b, bam_pileup_cd *cd) {
+    hts_base_mod_state_free(cd->p);
+    return 0;
+}
+
+static void
+print_empty_pileup(FILE *fp, const mplp_conf_t *conf, const char *tname,
+                   hts_pos_t pos, int n, const char *ref, hts_pos_t ref_len)
+{
+    int i;
+    fprintf(fp, "%s\t%"PRIhts_pos"\t%c", tname, pos+1, (ref && pos < ref_len)? ref[pos] : 'N');
+    for (i = 0; i < n; ++i) {
+        fputs("\t0\t*\t*", fp);
+        int flag_value = MPLP_PRINT_MAPQ_CHAR;
+        while(flag_value < MPLP_PRINT_LAST) {
+            if (flag_value != MPLP_PRINT_MODS && (conf->flag & flag_value))
+                fputs("\t*", fp);
+            flag_value <<= 1;
+        }
+        if (conf->auxlist) {
+            int t = 0;
+            while(t++ < ((klist_t(auxlist) *)conf->auxlist)->size)
+                fputs("\t*", fp);
+        }
+    }
+    putc('\n', fp);
+}
+
+static int mplp_func(void *data, bam1_t *b)
+{
+    char *ref;
+    mplp_aux_t *ma = (mplp_aux_t*)data;
+    int ret, skip = 0;
+    hts_pos_t ref_len;
+
+    do {
+        int has_ref;
+        ret = ma->iter? sam_itr_next(ma->fp, ma->iter, b) : sam_read1(ma->fp, ma->h, b);
+        if (ret < 0) break;
+        // The 'B' cigar operation is not part of the specification, considering as obsolete.
+        //  bam_remove_B(b);
+        if (b->core.tid < 0 || (b->core.flag&BAM_FUNMAP)) { // exclude unmapped reads
+            skip = 1;
+            continue;
+        }
+        if (ma->conf->rflag_require && !(ma->conf->rflag_require&b->core.flag)) { skip = 1; continue; }
+        if (ma->conf->rflag_filter && ma->conf->rflag_filter&b->core.flag) { skip = 1; continue; }
+        if (ma->conf->bed && ma->conf->all == 0) { // test overlap
+            skip = !bed_overlap(ma->conf->bed, sam_hdr_tid2name(ma->h, b->core.tid), b->core.pos, bam_endpos(b));
+            if (skip) continue;
+        }
+        if (ma->conf->rghash) { // exclude read groups
+            uint8_t *rg = bam_aux_get(b, "RG");
+            skip = (rg && khash_str2int_get(ma->conf->rghash, (const char*)(rg+1), NULL)==0);
+            if (skip) continue;
+        }
+        if (ma->conf->flag & MPLP_ILLUMINA13) {
+            int i;
+            uint8_t *qual = bam_get_qual(b);
+            for (i = 0; i < b->core.l_qseq; ++i)
+                qual[i] = qual[i] > 31? qual[i] - 31 : 0;
+        }
+
+        if (ma->conf->fai && b->core.tid >= 0) {
+            has_ref = mplp_get_ref(ma, b->core.tid, &ref, &ref_len);
+            if (has_ref && ref_len <= b->core.pos) { // exclude reads outside of the reference sequence
+                fprintf(stderr,"[%s] Skipping because %"PRIhts_pos" is outside of %"PRIhts_pos" [ref:%d]\n",
+                        __func__, (int64_t) b->core.pos, ref_len, b->core.tid);
+                skip = 1;
+                continue;
+            }
+        } else {
+            has_ref = 0;
+        }
+
+        skip = 0;
+        if (has_ref && (ma->conf->flag&MPLP_REALN)) sam_prob_realn(b, ref, ref_len, (ma->conf->flag & MPLP_REDO_BAQ)? 7 : 3);
+        if (has_ref && ma->conf->capQ_thres > 10) {
+            int q = sam_cap_mapq(b, ref, ref_len, ma->conf->capQ_thres);
+            if (q < 0) skip = 1;
+            else if (b->core.qual > q) b->core.qual = q;
+        }
+        if (b->core.qual < ma->conf->min_mq) skip = 1;
+        else if ((ma->conf->flag&MPLP_NO_ORPHAN) && (b->core.flag&BAM_FPAIRED) && !(b->core.flag&BAM_FPROPER_PAIR)) skip = 1;
+    } while (skip);
+    return ret;
+}
+
+/*
+ * Performs pileup
+ * @param conf configuration for this pileup
+ * @param n number of files specified in fn
+ * @param fn filenames
+ * @param fn_idx index filenames
+ */
+static int mpileup(mplp_conf_t *conf, int n, char **fn, char **fn_idx)
+{
+    mplp_aux_t **data;
+    int i, tid, *n_plp, tid0 = 0, max_depth;
+    hts_pos_t pos, beg0 = 0, end0 = HTS_POS_MAX, ref_len;
+    const bam_pileup1_t **plp;
+    mplp_ref_t mp_ref = MPLP_REF_INIT;
+    bam_mplp_t iter;
+    sam_hdr_t *h = NULL; /* header of first file in input list */
+    char *ref;
+    FILE *pileup_fp = NULL;
+
+    bam_sample_t *sm = NULL;
+    kstring_t buf;
+    mplp_pileup_t gplp;
+
+    memset(&gplp, 0, sizeof(mplp_pileup_t));
+    memset(&buf, 0, sizeof(kstring_t));
+    data = calloc(n, sizeof(mplp_aux_t*));
+    plp = calloc(n, sizeof(bam_pileup1_t*));
+    n_plp = calloc(n, sizeof(int));
+    sm = bam_smpl_init();
+
+    if (n == 0) {
+        fprintf(stderr,"[%s] no input file/data given\n", __func__);
+        exit(EXIT_FAILURE);
+    }
+
+    // read the header of each file in the list and initialize data
+    refs_t *refs = NULL;
+    for (i = 0; i < n; ++i) {
+        sam_hdr_t *h_tmp;
+        data[i] = calloc(1, sizeof(mplp_aux_t));
+        data[i]->fp = sam_open_format(fn[i], "rb", &conf->ga.in);
+        if ( !data[i]->fp )
+        {
+            fprintf(stderr, "[%s] failed to open %s: %s\n", __func__, fn[i], strerror(errno));
+            exit(EXIT_FAILURE);
+        }
+        if (hts_set_opt(data[i]->fp, CRAM_OPT_DECODE_MD, 0)) {
+            fprintf(stderr, "Failed to set CRAM_OPT_DECODE_MD value\n");
+            exit(EXIT_FAILURE);
+        }
+
+        if (!refs && conf->fai_fname) {
+            if (hts_set_fai_filename(data[i]->fp, conf->fai_fname) != 0) {
+                fprintf(stderr, "[%s] failed to process %s: %s\n",
+                        __func__, conf->fai_fname, strerror(errno));
+                exit(EXIT_FAILURE);
+            }
+            refs = cram_get_refs(data[i]->fp);
+        } else if (conf->fai_fname) {
+            if (hts_set_opt(data[i]->fp, CRAM_OPT_SHARED_REF, refs) != 0) {
+                fprintf(stderr, "[%s] failed to process %s: %s\n",
+                        __func__, conf->fai_fname, strerror(errno));
+                exit(EXIT_FAILURE);
+            }
+        }
+
+        data[i]->conf = conf;
+        data[i]->ref = &mp_ref;
+        h_tmp = sam_hdr_read(data[i]->fp);
+        if ( !h_tmp ) {
+            fprintf(stderr,"[%s] fail to read the header of %s\n", __func__, fn[i]);
+            exit(EXIT_FAILURE);
+        }
+        bam_smpl_add(sm, fn[i], (conf->flag&MPLP_IGNORE_RG)? 0 : sam_hdr_str(h_tmp));
+        if (conf->reg) {
+            hts_idx_t *idx = NULL;
+            // If index filename has not been specfied, look in BAM folder
+            if (fn_idx != NULL)  {
+                idx = sam_index_load2(data[i]->fp, fn[i], fn_idx[i]);
+            } else {
+                idx = sam_index_load(data[i]->fp, fn[i]);
+            }
+
+            if (idx == NULL) {
+                fprintf(stderr, "[%s] fail to load index for %s\n", __func__, fn[i]);
+                exit(EXIT_FAILURE);
+            }
+            if ( (data[i]->iter=sam_itr_querys(idx, h_tmp, conf->reg)) == 0) {
+                fprintf(stderr, "[E::%s] fail to parse region '%s' with %s\n", __func__, conf->reg, fn[i]);
+                exit(EXIT_FAILURE);
+            }
+            if (i == 0) beg0 = data[i]->iter->beg, end0 = data[i]->iter->end, tid0 = data[i]->iter->tid;
+            hts_idx_destroy(idx);
+        }
+        else
+            data[i]->iter = NULL;
+
+        if (i == 0) h = data[i]->h = h_tmp; // save the header of the first file
+        else {
+            // FIXME: check consistency between h and h_tmp
+            sam_hdr_destroy(h_tmp);
+
+            // we store only the first file's header; it's (alleged to be)
+            // compatible with the i-th file's target_name lookup needs
+            data[i]->h = h;
+        }
+    }
+    fprintf(stderr, "[%s] %d samples in %d input files\n", __func__, sm->n, n);
+
+    pileup_fp = conf->output_fname? fopen(conf->output_fname, "w") : stdout;
+
+    if (pileup_fp == NULL) {
+        fprintf(stderr, "[%s] failed to write to %s: %s\n", __func__, conf->output_fname, strerror(errno));
+        exit(EXIT_FAILURE);
+    }
+
+    // init pileup
+    iter = bam_mplp_init(n, mplp_func, (void**)data);
+    if (conf->flag & MPLP_PRINT_MODS) {
+        bam_mplp_constructor(iter, pileup_cd_create);
+        bam_mplp_destructor(iter, pileup_cd_destroy);
+    }
+    if ( conf->flag & MPLP_SMART_OVERLAPS ) bam_mplp_init_overlaps(iter);
+    if ( !conf->max_depth ) {
+        max_depth = INT_MAX;
+        fprintf(stderr, "[%s] Max depth set to maximum value (%d)\n", __func__, INT_MAX);
+    } else {
+        max_depth = conf->max_depth;
+        if ( max_depth * n > 1<<20 )
+            fprintf(stderr, "[%s] Combined max depth is above 1M. Potential memory hog!\n", __func__);
+    }
+
+
+    bam_mplp_set_maxcnt(iter, max_depth);
+    int ret;
+    int last_tid = -1;
+    hts_pos_t last_pos = -1;
+
+    // begin pileup
+    while ( (ret=bam_mplp64_auto(iter, &tid, &pos, n_plp, plp)) > 0) {
+        if (conf->reg && (pos < beg0 || pos >= end0)) continue; // out of the region requested
+        mplp_get_ref(data[0], tid, &ref, &ref_len);
+        //printf("tid=%d len=%d ref=%p/%s\n", tid, ref_len, ref, ref);
+        if (conf->all) {
+            // Deal with missing portions of previous tids
+            while (tid > last_tid) {
+                if (last_tid >= 0 && !conf->reg) {
+                    while (++last_pos < sam_hdr_tid2len(h, last_tid)) {
+                        if (conf->bed && bed_overlap(conf->bed, sam_hdr_tid2name(h, last_tid), last_pos, last_pos + 1) == 0)
+                            continue;
+                        print_empty_pileup(pileup_fp, conf, sam_hdr_tid2name(h, last_tid), last_pos, n, ref, ref_len);
+                    }
+                }
+                last_tid++;
+                last_pos = -1;
+                if (conf->all < 2)
+                    break;
+            }
+        }
+        if (conf->all) {
+            // Deal with missing portion of current tid
+            while (++last_pos < pos) {
+                if (conf->reg && last_pos < beg0) continue; // out of range; skip
+                if (conf->bed && bed_overlap(conf->bed, sam_hdr_tid2name(h, tid), last_pos, last_pos + 1) == 0)
+                    continue;
+                print_empty_pileup(pileup_fp, conf, sam_hdr_tid2name(h, tid), last_pos, n, ref, ref_len);
+            }
+            last_tid = tid;
+            last_pos = pos;
+        }
+        if (conf->bed && tid >= 0 && !bed_overlap(conf->bed, sam_hdr_tid2name(h, tid), pos, pos+1)) continue;
+
+        fprintf(pileup_fp, "%s\t%"PRIhts_pos"\t%c", sam_hdr_tid2name(h, tid), pos + 1, (ref && pos < ref_len)? ref[pos] : 'N');
+        for (i = 0; i < n; ++i) {
+            int j, cnt;
+            for (j = cnt = 0; j < n_plp[i]; ++j) {
+                const bam_pileup1_t *p = plp[i] + j;
+                int c = p->qpos < p->b->core.l_qseq
+                    ? bam_get_qual(p->b)[p->qpos]
+                    : 0;
+                if (c >= conf->min_baseQ) ++cnt;
+            }
+            fprintf(pileup_fp, "\t%d\t", cnt);
+            if (n_plp[i] == 0) {
+                fputs("*\t*", pileup_fp);
+                int flag_value = MPLP_PRINT_MAPQ_CHAR;
+                while(flag_value < MPLP_PRINT_LAST) {
+                    if (flag_value != MPLP_PRINT_MODS
+                        && (conf->flag & flag_value))
+                        fputs("\t*", pileup_fp);
+                    flag_value <<= 1;
+                }
+                if (conf->auxlist) {
+                    int t = 0;
+                    while(t++ < ((klist_t(auxlist) *)conf->auxlist)->size)
+                        fputs("\t*", pileup_fp);
+                }
+            } else {
+                int n = 0;
+                kstring_t ks = KS_INITIALIZE;
+                for (j = 0; j < n_plp[i]; ++j) {
+                    const bam_pileup1_t *p = plp[i] + j;
+                    int c = p->qpos < p->b->core.l_qseq
+                        ? bam_get_qual(p->b)[p->qpos]
+                        : 0;
+                    if (c >= conf->min_baseQ) {
+                        n++;
+                        if (pileup_seq(pileup_fp, plp[i] + j, pos, ref_len,
+                                       ref, &ks, conf->rev_del,
+                                       conf->no_ins, conf->no_ins_mods,
+                                       conf->no_del, conf->no_ends) < 0) {
+                            ret = 1;
+                            goto fail;
+                        }
+                    }
+                }
+                if (!n) putc('*', pileup_fp);
+
+                /* Print base qualities */
+                n = 0;
+                ks_free(&ks);
+                putc('\t', pileup_fp);
+                for (j = 0; j < n_plp[i]; ++j) {
+                    const bam_pileup1_t *p = plp[i] + j;
+                    int c = p->qpos < p->b->core.l_qseq
+                        ? bam_get_qual(p->b)[p->qpos]
+                        : 0;
+                    if (c >= conf->min_baseQ) {
+                        c = c + 33 < 126? c + 33 : 126;
+                        putc(c, pileup_fp);
+                        n++;
+                    }
+                }
+                if (!n) putc('*', pileup_fp);
+
+                /* Print selected columns */
+                int flag_value = MPLP_PRINT_MAPQ_CHAR;
+                while(flag_value < MPLP_PRINT_LAST) {
+                    if (flag_value != MPLP_PRINT_MODS
+                        && (conf->flag & flag_value)) {
+                        n = 0;
+                        putc('\t', pileup_fp);
+                        for (j = 0; j < n_plp[i]; ++j) {
+                            const bam_pileup1_t *p = &plp[i][j];
+                            int c = p->qpos < p->b->core.l_qseq
+                                ? bam_get_qual(p->b)[p->qpos]
+                                : 0;
+                            if ( c < conf->min_baseQ ) continue;
+                            if (n > 0 && flag_value != MPLP_PRINT_MAPQ_CHAR) putc(',', pileup_fp);
+                            n++;
+
+                            switch (flag_value) {
+                            case MPLP_PRINT_MAPQ_CHAR:
+                                c = p->b->core.qual + 33;
+                                if (c > 126) c = 126;
+                                putc(c, pileup_fp);
+                                break;
+                            case MPLP_PRINT_QPOS:
+                                // query position in current orientation
+                                fprintf(pileup_fp, "%d", p->qpos + 1);
+                                break;
+                            case MPLP_PRINT_QPOS5: {
+                                // query position in 5' to 3' orientation
+                                int pos5 = bam_is_rev(p->b)
+                                    ? p->b->core.l_qseq-p->qpos + p->is_del
+                                    : p->qpos + 1;
+                                fprintf(pileup_fp, "%d", pos5);
+                                break;
+                            }
+                            case MPLP_PRINT_QNAME:
+                                fputs(bam_get_qname(p->b), pileup_fp);
+                                break;
+                            case MPLP_PRINT_FLAG:
+                                fprintf(pileup_fp, "%d", p->b->core.flag);
+                                break;
+                            case MPLP_PRINT_RNAME:
+                                if (p->b->core.tid >= 0)
+                                    fputs(sam_hdr_tid2name(h, p->b->core.tid), pileup_fp);
+                                else
+                                    putc('*', pileup_fp);
+                                break;
+                            case MPLP_PRINT_POS:
+                                fprintf(pileup_fp, "%"PRId64, (int64_t) p->b->core.pos + 1);
+                                break;
+                            case MPLP_PRINT_MAPQ:
+                                fprintf(pileup_fp, "%d", p->b->core.qual);
+                                break;
+                            case MPLP_PRINT_RNEXT:
+                                if (p->b->core.mtid >= 0)
+                                    fputs(sam_hdr_tid2name(h, p->b->core.mtid), pileup_fp);
+                                else
+                                    putc('*', pileup_fp);
+                                break;
+                            case MPLP_PRINT_PNEXT:
+                                fprintf(pileup_fp, "%"PRId64, (int64_t) p->b->core.mpos + 1);
+                                break;
+                            }
+                        }
+                        if (!n) putc('*', pileup_fp);
+                    }
+                    flag_value <<= 1;
+                }
+
+                /* Print selected tags */
+                klist_t(auxlist) *auxlist_p = ((klist_t(auxlist) *)conf->auxlist);
+                if (auxlist_p && auxlist_p->size) {
+                    kliter_t(auxlist) *aux;
+                    for (aux = kl_begin(auxlist_p); aux != kl_end(auxlist_p); aux = kl_next(aux)) {
+                        n = 0;
+                        putc('\t', pileup_fp);
+                        for (j = 0; j < n_plp[i]; ++j) {
+                            const bam_pileup1_t *p = &plp[i][j];
+                            int c = p->qpos < p->b->core.l_qseq
+                                ? bam_get_qual(p->b)[p->qpos]
+                                : 0;
+                            if ( c < conf->min_baseQ ) continue;
+
+                            if (n > 0) putc(conf->sep, pileup_fp);
+                            n++;
+                            uint8_t* tag_u = bam_aux_get(p->b, kl_val(aux));
+                            if (!tag_u) {
+                                putc(conf->empty , pileup_fp);
+                                continue;
+                            }
+
+                            int tag_supported = 0;
+
+                            /* Tag value is string */
+                            if (*tag_u == 'Z' || *tag_u == 'H') {
+                                char *tag_s = bam_aux2Z(tag_u);
+                                if (!tag_s) continue;
+                                fputs(tag_s, pileup_fp);
+                                tag_supported = 1;
+                            }
+
+                            /* Tag value is integer */
+                            if (*tag_u == 'I' || *tag_u == 'i' || *tag_u == 'C' || *tag_u == 'c' || *tag_u == 'S' || *tag_u == 's') {
+                                int64_t tag_i = bam_aux2i(tag_u);
+                                fprintf(pileup_fp, "%" PRId64 "", tag_i);
+                                tag_supported = 1;
+                            }
+
+                            /* Tag value is float */
+                            if (*tag_u == 'd' || *tag_u == 'f') {
+                                double tag_f = bam_aux2f(tag_u);
+                                fprintf(pileup_fp, "%lf", tag_f);
+                                tag_supported = 1;
+                            }
+
+                            /* Tag value is character */
+                            if (*tag_u == 'A') {
+                                char tag_c = bam_aux2A(tag_u);
+                                putc(tag_c, pileup_fp);
+                                tag_supported = 1;
+                            }
+
+                            if (!tag_supported) putc('*', pileup_fp);
+                        }
+                        if (!n) putc('*', pileup_fp);
+                    }
+                }
+            }
+        }
+        putc('\n', pileup_fp);
+    }
+
+    if (ret < 0) {
+        print_error("mpileup", "error reading from input file");
+        ret = EXIT_FAILURE;
+        goto fail;
+    }
+
+    if (conf->all) {
+        // Handle terminating region
+        if (last_tid < 0 && conf->reg && conf->all > 1) {
+            last_tid = tid0;
+            last_pos = beg0-1;
+            mplp_get_ref(data[0], tid0, &ref, &ref_len);
+        }
+       while (last_tid >= 0 && last_tid < sam_hdr_nref(h)) {
+            while (++last_pos < sam_hdr_tid2len(h, last_tid)) {
+                if (last_pos >= end0) break;
+                if (conf->bed && bed_overlap(conf->bed, sam_hdr_tid2name(h, last_tid), last_pos, last_pos + 1) == 0)
+                    continue;
+                print_empty_pileup(pileup_fp, conf, sam_hdr_tid2name(h, last_tid), last_pos, n, ref, ref_len);
+            }
+            last_tid++;
+            last_pos = -1;
+            if (conf->all < 2 || conf->reg)
+                break;
+        }
+    }
+
+fail:
+    // clean up
+    if (pileup_fp && conf->output_fname) fclose(pileup_fp);
+    bam_smpl_destroy(sm); free(buf.s);
+    for (i = 0; i < gplp.n; ++i) free(gplp.plp[i]);
+    free(gplp.plp); free(gplp.n_plp); free(gplp.m_plp);
+    bam_mplp_destroy(iter);
+    sam_hdr_destroy(h);
+    for (i = 0; i < n; ++i) {
+        sam_close(data[i]->fp);
+        if (data[i]->iter) hts_itr_destroy(data[i]->iter);
+        free(data[i]);
+    }
+    free(data); free(plp); free(n_plp);
+    free(mp_ref.ref[0]);
+    free(mp_ref.ref[1]);
+    return ret;
+}
+
+static int is_url(const char *s)
+{
+    static const char uri_scheme_chars[] =
+        "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789+.-";
+    return s[strspn(s, uri_scheme_chars)] == ':';
+}
+
+#define MAX_PATH_LEN 1024
+int read_file_list(const char *file_list,int *n,char **argv[])
+{
+    char buf[MAX_PATH_LEN];
+    int len, nfiles = 0;
+    char **files = NULL;
+    struct stat sb;
+
+    *n = 0;
+    *argv = NULL;
+
+    FILE *fh = fopen(file_list,"r");
+    if ( !fh )
+    {
+        fprintf(stderr,"%s: %s\n", file_list,strerror(errno));
+        return 1;
+    }
+
+    files = calloc(nfiles,sizeof(char*));
+    nfiles = 0;
+    while ( fgets(buf,MAX_PATH_LEN,fh) )
+    {
+        // allow empty lines and trailing spaces
+        len = strlen(buf);
+        while ( len>0 && isspace(buf[len-1]) ) len--;
+        if ( !len ) continue;
+
+        // check sanity of the file list
+        buf[len] = 0;
+        if (! (is_url(buf) || stat(buf, &sb) == 0))
+        {
+            // no such file, check if it is safe to print its name
+            int i, safe_to_print = 1;
+            for (i=0; i<len; i++)
+                if (!isprint(buf[i])) { safe_to_print = 0; break; }
+            if ( safe_to_print )
+                fprintf(stderr,"The file list \"%s\" appears broken, could not locate: %s\n", file_list,buf);
+            else
+                fprintf(stderr,"Does the file \"%s\" really contain a list of files and do all exist?\n", file_list);
+            return 1;
+        }
+
+        nfiles++;
+        files = realloc(files,nfiles*sizeof(char*));
+        files[nfiles-1] = strdup(buf);
+    }
+    fclose(fh);
+    if ( !nfiles )
+    {
+        fprintf(stderr,"No files read from %s\n", file_list);
+        return 1;
+    }
+    *argv = files;
+    *n    = nfiles;
+    return 0;
+}
+#undef MAX_PATH_LEN
+
+static void print_usage(FILE *fp, const mplp_conf_t *mplp)
+{
+    char *tmp_require = bam_flag2str(mplp->rflag_require);
+    char *tmp_filter  = bam_flag2str(mplp->rflag_filter);
+
+    // Display usage information, formatted for the standard 80 columns.
+    // (The unusual string formatting here aids the readability of this
+    // source code in 80 columns, to the extent that's possible.)
+
+    fprintf(fp,
+"\n"
+"Usage: samtools mpileup [options] in1.bam [in2.bam [...]]\n"
+"\n"
+"Input options:\n"
+"  -6, --illumina1.3+      quality is in the Illumina-1.3+ encoding\n"
+"  -A, --count-orphans     do not discard anomalous read pairs\n"
+"  -b, --bam-list FILE     list of input BAM filenames, one per line\n"
+"  -B, --no-BAQ            disable BAQ (per-Base Alignment Quality)\n"
+"  -C, --adjust-MQ INT     adjust mapping quality; recommended:50, disable:0 [0]\n"
+"  -d, --max-depth INT     max per-file depth; avoids excessive memory usage [%d]\n", mplp->max_depth);
+    fprintf(fp,
+"  -E, --redo-BAQ          recalculate BAQ on the fly, ignore existing BQs\n"
+"  -f, --fasta-ref FILE    faidx indexed reference sequence file\n"
+"  -G, --exclude-RG FILE   exclude read groups listed in FILE\n"
+"  -l, --positions FILE    skip unlisted positions (chr pos) or regions (BED)\n"
+"  -q, --min-MQ INT        skip alignments with mapQ smaller than INT [%d]\n", mplp->min_mq);
+    fprintf(fp,
+"  -Q, --min-BQ INT        skip bases with baseQ/BAQ smaller than INT [%d]\n", mplp->min_baseQ);
+    fprintf(fp,
+"  -r, --region REG        region in which pileup is generated\n"
+"  -R, --ignore-RG         ignore RG tags (one BAM = one sample)\n"
+"  --rf, --incl-flags STR|INT  required flags: include reads with any of the mask bits set [%s]\n", tmp_require);
+    fprintf(fp,
+"  --ff, --excl-flags STR|INT  filter flags: skip reads with any of the mask bits set\n"
+"                                            [%s]\n", tmp_filter);
+    fprintf(fp,
+"  -x, --ignore-overlaps-removal, --disable-overlap-removal\n"
+"                          disable read-pair overlap detection and removal\n"
+"  -X, --customized-index  use customized index files\n" // -X flag for index filename
+"\n"
+"Output options:\n"
+"  -o, --output FILE        write output to FILE [standard output]\n"
+"  -O, --output-BP          output base positions on reads, current orientation\n"
+"      --output-BP-5        output base positions on reads, 5' to 3' orientation\n"
+"  -M, --output-mods        output base modifications\n"
+"  -s, --output-MQ          output mapping quality\n"
+"      --output-QNAME       output read names\n"
+"      --output-extra STR   output extra read fields and read tag values\n"
+"      --output-sep CHAR    set the separator character for tag lists [,]\n"
+"      --output-empty CHAR  set the no value character for tag lists [*]\n"
+"      --no-output-ins      skip insertion sequence after +NUM\n"
+"                           Use twice for complete insertion removal\n"
+"      --no-output-ins-mods don't display base modifications within insertions\n"
+"      --no-output-del      skip deletion sequence after -NUM\n"
+"                           Use twice for complete deletion removal\n"
+"      --no-output-ends     remove ^MQUAL and $ markup in sequence column\n"
+"      --reverse-del        use '#' character for deletions on the reverse strand\n"
+"  -a                       output all positions (including zero depth)\n"
+"  -a -a (or -aa)           output absolutely all positions, including unused ref. sequences\n"
+"\n"
+"Generic options:\n");
+    sam_global_opt_help(fp, "-.--.--.");
+
+    fprintf(fp, "\n"
+"Note that using \"samtools mpileup\" to generate BCF or VCF files has been\n"
+"removed.  To output these formats, please use \"bcftools mpileup\" instead.\n");
+
+    free(tmp_require);
+    free(tmp_filter);
+}
+
+int bam_mpileup(int argc, char *argv[])
+{
+    int c;
+    const char *file_list = NULL;
+    char **fn = NULL;
+    int nfiles = 0, use_orphan = 0, has_index_file = 0;
+    mplp_conf_t mplp;
+    memset(&mplp, 0, sizeof(mplp_conf_t));
+    mplp.min_baseQ = 13;
+    mplp.capQ_thres = 0;
+    mplp.max_depth = MPLP_MAX_DEPTH;
+    mplp.flag = MPLP_NO_ORPHAN | MPLP_REALN | MPLP_SMART_OVERLAPS;
+    mplp.argc = argc; mplp.argv = argv;
+    mplp.rflag_filter = BAM_FUNMAP | BAM_FSECONDARY | BAM_FQCFAIL | BAM_FDUP;
+    mplp.output_fname = NULL;
+    mplp.all = 0;
+    mplp.rev_del = 0;
+    mplp.sep = ',';
+    mplp.empty = '*';
+    sam_global_args_init(&mplp.ga);
+
+    static const struct option lopts[] =
+    {
+        SAM_OPT_GLOBAL_OPTIONS('-', 0, '-', '-', 0, '-'),
+        {"rf", required_argument, NULL, 1},   // require flag
+        {"ff", required_argument, NULL, 2},   // filter flag
+        {"incl-flags", required_argument, NULL, 1},
+        {"excl-flags", required_argument, NULL, 2},
+        {"output", required_argument, NULL, 3},
+        {"output-QNAME", no_argument, NULL, 5},
+        {"output-qname", no_argument, NULL, 5},
+        {"illumina1.3+", no_argument, NULL, '6'},
+        {"count-orphans", no_argument, NULL, 'A'},
+        {"bam-list", required_argument, NULL, 'b'},
+        {"no-BAQ", no_argument, NULL, 'B'},
+        {"no-baq", no_argument, NULL, 'B'},
+        {"adjust-MQ", required_argument, NULL, 'C'},
+        {"adjust-mq", required_argument, NULL, 'C'},
+        {"max-depth", required_argument, NULL, 'd'},
+        {"redo-BAQ", no_argument, NULL, 'E'},
+        {"redo-baq", no_argument, NULL, 'E'},
+        {"fasta-ref", required_argument, NULL, 'f'},
+        {"exclude-RG", required_argument, NULL, 'G'},
+        {"exclude-rg", required_argument, NULL, 'G'},
+        {"positions", required_argument, NULL, 'l'},
+        {"region", required_argument, NULL, 'r'},
+        {"ignore-RG", no_argument, NULL, 'R'},
+        {"ignore-rg", no_argument, NULL, 'R'},
+        {"min-MQ", required_argument, NULL, 'q'},
+        {"min-mq", required_argument, NULL, 'q'},
+        {"min-BQ", required_argument, NULL, 'Q'},
+        {"min-bq", required_argument, NULL, 'Q'},
+        // NB: old "--ignore-overlaps" auto-completes to this
+        {"ignore-overlaps-removal",  no_argument, NULL, 'x'},
+        {"disable-overlap-removal",  no_argument, NULL, 'x'},
+        {"output-mods", no_argument, NULL, 'M'},
+        {"output-BP", no_argument, NULL, 'O'},
+        {"output-bp", no_argument, NULL, 'O'},
+        {"output-BP-5", no_argument, NULL, 14},
+        {"output-bp-5", no_argument, NULL, 14},
+        {"output-MQ", no_argument, NULL, 's'},
+        {"output-mq", no_argument, NULL, 's'},
+        {"ext-prob", required_argument, NULL, 'e'},
+        {"gap-frac", required_argument, NULL, 'F'},
+        {"tandem-qual", required_argument, NULL, 'h'},
+        {"skip-indels", no_argument, NULL, 'I'},
+        {"max-idepth", required_argument, NULL, 'L'},
+        {"min-ireads ", required_argument, NULL, 'm'},
+        {"per-sample-mF", no_argument, NULL, 'p'},
+        {"per-sample-mf", no_argument, NULL, 'p'},
+        {"platforms", required_argument, NULL, 'P'},
+        {"customized-index", no_argument, NULL, 'X'},
+        {"reverse-del", no_argument, NULL, 6},
+        {"output-extra", required_argument, NULL, 7},
+        {"output-sep", required_argument, NULL, 8},
+        {"output-empty", required_argument, NULL, 9},
+        {"no-output-ins", no_argument, NULL, 10},
+        {"no-output-ins-mods", no_argument, NULL, 11},
+        {"no-output-del", no_argument, NULL, 12},
+        {"no-output-ends", no_argument, NULL, 13},
+        {NULL, 0, NULL, 0}
+    };
+
+    while ((c = getopt_long(argc, argv, "Af:r:l:q:Q:RC:Bd:b:o:EG:6OsxXaM",lopts,NULL)) >= 0) {
+        switch (c) {
+        case 'x': mplp.flag &= ~MPLP_SMART_OVERLAPS; break;
+        case  1 :
+            mplp.rflag_require = bam_str2flag(optarg);
+            if ( mplp.rflag_require<0 ) { fprintf(stderr,"Could not parse --rf %s\n", optarg); return 1; }
+            break;
+        case  2 :
+            mplp.rflag_filter = bam_str2flag(optarg);
+            if ( mplp.rflag_filter<0 ) { fprintf(stderr,"Could not parse --ff %s\n", optarg); return 1; }
+            break;
+        case  3 : mplp.output_fname = optarg; break;
+        case  5 : mplp.flag |= MPLP_PRINT_QNAME; break;
+        case  6 : mplp.rev_del = 1; break;
+        case  7 :
+            if (build_auxlist(&mplp, optarg) != 0) {
+                fprintf(stderr,"Could not build aux list using '%s'\n", optarg);
+                return 1;
+            }
+            break;
+        case 8: mplp.sep = optarg[0]; break;
+        case 9: mplp.empty = optarg[0]; break;
+        case 10: mplp.no_ins++; break;
+        case 11: mplp.no_ins_mods = 1; break;
+        case 12: mplp.no_del++; break;
+        case 13: mplp.no_ends = 1; break;
+        case 'f':
+            mplp.fai = fai_load(optarg);
+            if (mplp.fai == NULL) return 1;
+            mplp.fai_fname = optarg;
+            break;
+        case 'd': mplp.max_depth = atoi(optarg); break;
+        case 'r': mplp.reg = strdup(optarg); break;
+        case 'l':
+                  // In the original version the whole BAM was streamed which is inefficient
+                  //  with few BED intervals and big BAMs. Todo: devise a heuristic to determine
+                  //  best strategy, that is streaming or jumping.
+                  mplp.bed = bed_read(optarg);
+                  if (!mplp.bed) { print_error_errno("mpileup", "Could not read file \"%s\"", optarg); return 1; }
+                  break;
+        case 'B': mplp.flag &= ~MPLP_REALN; break;
+        case 'X': has_index_file = 1; break;
+        case 'E': mplp.flag |= MPLP_REDO_BAQ; break;
+        case '6': mplp.flag |= MPLP_ILLUMINA13; break;
+        case 'R': mplp.flag |= MPLP_IGNORE_RG; break;
+        case 's': mplp.flag |= MPLP_PRINT_MAPQ_CHAR; break;
+        case 'O': mplp.flag |= MPLP_PRINT_QPOS; break;
+        case  14: mplp.flag |= MPLP_PRINT_QPOS5; break;
+        case 'M': mplp.flag |= MPLP_PRINT_MODS; break;
+        case 'C': mplp.capQ_thres = atoi(optarg); break;
+        case 'q': mplp.min_mq = atoi(optarg); break;
+        case 'Q': mplp.min_baseQ = atoi(optarg); break;
+        case 'b': file_list = optarg; break;
+        case 'o': mplp.output_fname = optarg; break;
+        case 'A': use_orphan = 1; break;
+        case 'G': {
+                FILE *fp_rg;
+                char buf[1024];
+                mplp.rghash = khash_str2int_init();
+                if ((fp_rg = fopen(optarg, "r")) == NULL)
+                    fprintf(stderr, "[%s] Fail to open file %s. Continue anyway.\n", __func__, optarg);
+                while (!feof(fp_rg) && fscanf(fp_rg, "%s", buf) > 0) // this is not a good style, but forgive me...
+                    khash_str2int_inc(mplp.rghash, strdup(buf));
+                fclose(fp_rg);
+            }
+            break;
+        case 'a': mplp.all++; break;
+        default:
+            if (parse_sam_global_opt(c, optarg, lopts, &mplp.ga) == 0) break;
+            /* else fall-through */
+        case '?':
+            print_usage(stderr, &mplp);
+            return 1;
+        }
+    }
+    if (!mplp.fai && mplp.ga.reference) {
+        mplp.fai_fname = mplp.ga.reference;
+        mplp.fai = fai_load(mplp.fai_fname);
+        if (mplp.fai == NULL) return 1;
+    }
+
+    if ( !(mplp.flag&MPLP_REALN) && mplp.flag&MPLP_REDO_BAQ )
+    {
+        fprintf(stderr,"Error: The -B option cannot be combined with -E\n");
+        return 1;
+    }
+    if (use_orphan) mplp.flag &= ~MPLP_NO_ORPHAN;
+    if (argc == 1)
+    {
+        print_usage(stderr, &mplp);
+        return 1;
+    }
+    int ret;
+    if (file_list) {
+        if (has_index_file) {
+            fprintf(stderr,"Error: The -b option cannot be combined with -X\n"); // No customize index loc in file list mode
+            return 1;
+        }
+        if ( read_file_list(file_list,&nfiles,&fn) ) return 1;
+        ret = mpileup(&mplp,nfiles,fn,NULL);
+        for (c=0; c<nfiles; c++) free(fn[c]);
+        free(fn);
+    }
+    else {
+        if (has_index_file) {
+            if ((argc - optind)%2 !=0) { // Calculate # of input BAM files
+                fprintf(stderr, "Odd number of filenames detected! Each BAM file should have an index file\n");
+                return 1;
+            }
+            nfiles = (argc - optind)/2;
+            ret = mpileup(&mplp, nfiles, argv + optind, argv + nfiles + optind);
+        } else {
+            nfiles = argc - optind;
+            ret = mpileup(&mplp, nfiles, argv + optind, NULL);
+        }
+    }
+    if (mplp.rghash) khash_str2int_destroy_free(mplp.rghash);
+    free(mplp.reg); free(mplp.pl_list);
+    if (mplp.fai) fai_destroy(mplp.fai);
+    if (mplp.bed) bed_destroy(mplp.bed);
+    if (mplp.auxlist) kl_destroy(auxlist, (klist_t(auxlist) *)mplp.auxlist);
+    return ret;
+}
diff --git a/samtools/bam_plcmd.c.pysam.c b/samtools/bam_plcmd.c.pysam.c
new file mode 100644
index 0000000..8147e85
--- /dev/null
+++ b/samtools/bam_plcmd.c.pysam.c
@@ -0,0 +1,1191 @@
+#include "samtools.pysam.h"
+
+/*  bam_plcmd.c -- mpileup subcommand.
+
+    Copyright (C) 2008-2015, 2019-2021 Genome Research Ltd.
+    Portions copyright (C) 2009-2012 Broad Institute.
+
+    Author: Heng Li <lh3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <config.h>
+
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <unistd.h>
+#include <ctype.h>
+#include <string.h>
+#include <strings.h>
+#include <limits.h>
+#include <errno.h>
+#include <sys/stat.h>
+#include <getopt.h>
+#include <inttypes.h>
+#include <htslib/sam.h>
+#include <htslib/faidx.h>
+#include <htslib/kstring.h>
+#include <htslib/klist.h>
+#include <htslib/khash_str2int.h>
+#include <htslib/cram.h>
+#include "samtools.h"
+#include "bedidx.h"
+#include "sam_opts.h"
+#include "bam_plbuf.h"
+
+#define dummy_free(p)
+KLIST_INIT(auxlist, char *, dummy_free)
+
+static inline int printw(int c, FILE *fp)
+{
+    char buf[16];
+    int l, x;
+    if (c == 0) return fputc('0', fp);
+    for (l = 0, x = c < 0? -c : c; x > 0; x /= 10) buf[l++] = x%10 + '0';
+    if (c < 0) buf[l++] = '-';
+    buf[l] = 0;
+    for (x = 0; x < l/2; ++x) {
+        int y = buf[x]; buf[x] = buf[l-1-x]; buf[l-1-x] = y;
+    }
+    fputs(buf, fp);
+    return 0;
+}
+
+int pileup_seq(FILE *fp, const bam_pileup1_t *p, hts_pos_t pos,
+               hts_pos_t ref_len, const char *ref, kstring_t *ks,
+               int rev_del, int no_ins, int no_ins_mods,
+               int no_del, int no_ends)
+{
+    no_ins_mods |= no_ins;
+    int j;
+    hts_base_mod_state *m = p->cd.p;
+    if (!no_ends && p->is_head) {
+        putc('^', fp);
+        putc(p->b->core.qual > 93? 126 : p->b->core.qual + 33, fp);
+    }
+    if (!p->is_del) {
+        int c = p->qpos < p->b->core.l_qseq
+            ? seq_nt16_str[bam_seqi(bam_get_seq(p->b), p->qpos)]
+            : 'N';
+        if (ref) {
+            int rb = pos < ref_len? ref[pos] : 'N';
+            if (c == '=' || seq_nt16_table[c] == seq_nt16_table[rb]) c = bam_is_rev(p->b)? ',' : '.';
+            else c = bam_is_rev(p->b)? tolower(c) : toupper(c);
+        } else {
+            if (c == '=') c = bam_is_rev(p->b)? ',' : '.';
+            else c = bam_is_rev(p->b)? tolower(c) : toupper(c);
+        }
+        putc(c, fp);
+        if (m) {
+            int nm;
+            hts_base_mod mod[256];
+            if ((nm = bam_mods_at_qpos(p->b, p->qpos, m, mod, 256)) > 0) {
+                putc('[', fp);
+                int j;
+                for (j = 0; j < nm && j < 256; j++) {
+                    char qual[20];
+                    if (mod[j].qual >= 0)
+                        sprintf(qual, "%d", mod[j].qual);
+                    else
+                        *qual = 0;
+                    if (mod[j].modified_base < 0)
+                        // ChEBI
+                        fprintf(fp, "%c(%d)%s", "+-"[mod[j].strand],
+                                -mod[j].modified_base, qual);
+                    else
+                        fprintf(fp, "%c%c%s", "+-"[mod[j].strand],
+                                mod[j].modified_base, qual);
+                }
+                putc(']', fp);
+            }
+        }
+    } else putc(p->is_refskip? (bam_is_rev(p->b)? '<' : '>') : ((bam_is_rev(p->b) && rev_del) ? '#' : '*'), fp);
+    int del_len = -p->indel;
+    if (p->indel > 0) {
+        int len = bam_plp_insertion_mod(p, m && !no_ins_mods ? m : NULL,
+                                        ks, &del_len);
+        if (len < 0) {
+            print_error("mpileup", "bam_plp_insertion() failed");
+            return -1;
+        }
+        if (no_ins < 2) {
+            putc('+', fp);
+            printw(len, fp);
+        }
+        if (!no_ins) {
+            if (bam_is_rev(p->b)) {
+                char pad = rev_del ? '#' : '*';
+                int in_mod = 0;
+                for (j = 0; j < ks->l; j++) {
+                    if (ks->s[j] == '[') in_mod = 1;
+                    else if (ks->s[j] == ']') in_mod = 0;
+                    putc(ks->s[j] != '*'
+                         ? (in_mod ? ks->s[j] : tolower(ks->s[j]))
+                         : pad, fp);
+                }
+            } else {
+                int in_mod = 0;
+                for (j = 0; j < ks->l; j++) {
+                    if (ks->s[j] == '[') in_mod = 1;
+                    if (ks->s[j] == ']') in_mod = 0;
+                    putc(in_mod ? ks->s[j] : toupper(ks->s[j]), fp);
+                }
+            }
+        }
+    }
+    if (del_len > 0) {
+        if (no_del < 2)
+            printw(-del_len, fp);
+        if (!no_del) {
+            for (j = 1; j <= del_len; ++j) {
+                int c = (ref && (int)pos+j < ref_len)? ref[pos+j] : 'N';
+                putc(bam_is_rev(p->b)? tolower(c) : toupper(c), fp);
+            }
+        }
+    }
+    if (!no_ends && p->is_tail) putc('$', fp);
+    return 0;
+}
+
+#include "sample.h"
+
+#define MPLP_NO_COMP    (1<<2)
+#define MPLP_NO_ORPHAN  (1<<3)
+#define MPLP_REALN      (1<<4)
+#define MPLP_NO_INDEL   (1<<5)
+#define MPLP_REDO_BAQ   (1<<6)
+#define MPLP_ILLUMINA13 (1<<7)
+#define MPLP_IGNORE_RG  (1<<8)
+#define MPLP_SMART_OVERLAPS (1<<10)
+
+#define MPLP_PRINT_MAPQ_CHAR (1<<11)
+#define MPLP_PRINT_QPOS  (1<<12)
+#define MPLP_PRINT_QNAME (1<<13)
+#define MPLP_PRINT_FLAG  (1<<14)
+#define MPLP_PRINT_RNAME (1<<15)
+#define MPLP_PRINT_POS   (1<<16)
+#define MPLP_PRINT_MAPQ  (1<<17)
+#define MPLP_PRINT_CIGAR (1<<18)
+#define MPLP_PRINT_RNEXT (1<<19)
+#define MPLP_PRINT_PNEXT (1<<20)
+#define MPLP_PRINT_TLEN  (1<<21)
+#define MPLP_PRINT_SEQ   (1<<22)
+#define MPLP_PRINT_QUAL  (1<<23)
+#define MPLP_PRINT_MODS  (1<<24)
+#define MPLP_PRINT_QPOS5 (1<<25)
+
+#define MPLP_PRINT_LAST  (1<<26) // terminator for loop
+
+#define MPLP_MAX_DEPTH 8000
+#define MPLP_MAX_INDEL_DEPTH 250
+
+typedef struct {
+    int min_mq, flag, min_baseQ, capQ_thres, max_depth, max_indel_depth, all, rev_del;
+    int rflag_require, rflag_filter;
+    char *reg, *pl_list, *fai_fname, *output_fname;
+    faidx_t *fai;
+    void *bed, *rghash, *auxlist;
+    int argc;
+    char **argv;
+    char sep, empty, no_ins, no_ins_mods, no_del, no_ends;
+    sam_global_args ga;
+} mplp_conf_t;
+
+typedef struct {
+    char *ref[2];
+    int ref_id[2];
+    hts_pos_t ref_len[2];
+} mplp_ref_t;
+
+#define MPLP_REF_INIT {{NULL,NULL},{-1,-1},{0,0}}
+
+typedef struct {
+    samFile *fp;
+    hts_itr_t *iter;
+    sam_hdr_t *h;
+    mplp_ref_t *ref;
+    const mplp_conf_t *conf;
+} mplp_aux_t;
+
+typedef struct {
+    int n;
+    int *n_plp, *m_plp;
+    bam_pileup1_t **plp;
+} mplp_pileup_t;
+
+static int build_auxlist(mplp_conf_t *conf, char *optstring) {
+    if (!optstring)
+        return 0;
+
+    void *colhash = khash_str2int_init();
+    if (!colhash)
+        return 1;
+
+    struct active_cols {
+        char *name;
+        int supported;
+    };
+
+    const struct active_cols colnames[11] = {
+            {"QNAME", 1}, {"FLAG", 1}, {"RNAME", 1}, {"POS", 1}, {"MAPQ", 1}, {"CIGAR", 0}, {"RNEXT", 1}, {"PNEXT", 1}, {"TLEN", 0}, {"SEQ", 0}, {"QUAL", 0}
+    };
+
+    int i, f = MPLP_PRINT_QNAME, colno = 11;
+    for (i = 0; i < colno; i++, f <<= 1)
+        if (colnames[i].supported)
+            khash_str2int_set(colhash, colnames[i].name, f);
+
+    conf->auxlist = kl_init(auxlist);
+    if (!conf->auxlist)
+        return 1;
+
+    char *save_p;
+    char *tag = strtok_r(optstring, ",", &save_p);
+    while (tag) {
+        if (khash_str2int_get(colhash, tag, &f) == 0) {
+            conf->flag |= f;
+        } else {
+            if (strlen(tag) != 2) {
+                fprintf(samtools_stderr, "[%s] tag '%s' has more than two characters or not supported\n", __func__, tag);
+            } else {
+                char **tag_p = kl_pushp(auxlist, conf->auxlist);
+                *tag_p = tag;
+            }
+        }
+        tag = strtok_r(NULL, ",", &save_p);
+    }
+
+    khash_str2int_destroy(colhash);
+
+    return 0;
+}
+
+static int mplp_get_ref(mplp_aux_t *ma, int tid, char **ref, hts_pos_t *ref_len) {
+    mplp_ref_t *r = ma->ref;
+
+    //printf("get ref %d {%d/%p, %d/%p}\n", tid, r->ref_id[0], r->ref[0], r->ref_id[1], r->ref[1]);
+
+    if (!r || !ma->conf->fai) {
+        *ref = NULL;
+        return 0;
+    }
+
+    // Do we need to reference count this so multiple mplp_aux_t can
+    // track which references are in use?
+    // For now we just cache the last two. Sufficient?
+    if (tid == r->ref_id[0]) {
+        *ref = r->ref[0];
+        *ref_len = r->ref_len[0];
+        return 1;
+    }
+    if (tid == r->ref_id[1]) {
+        // Last, swap over
+        int tmp_id;
+        hts_pos_t tmp_len;
+        tmp_id  = r->ref_id[0];  r->ref_id[0]  = r->ref_id[1];  r->ref_id[1]  = tmp_id;
+        tmp_len = r->ref_len[0]; r->ref_len[0] = r->ref_len[1]; r->ref_len[1] = tmp_len;
+
+        char *tc;
+        tc = r->ref[0]; r->ref[0] = r->ref[1]; r->ref[1] = tc;
+        *ref = r->ref[0];
+        *ref_len = r->ref_len[0];
+        return 1;
+    }
+
+    // New, so migrate to old and load new
+    free(r->ref[1]);
+    r->ref[1]     = r->ref[0];
+    r->ref_id[1]  = r->ref_id[0];
+    r->ref_len[1] = r->ref_len[0];
+
+    r->ref_id[0] = tid;
+    r->ref[0] = faidx_fetch_seq64(ma->conf->fai,
+                                sam_hdr_tid2name(ma->h, r->ref_id[0]),
+                                0,
+                                HTS_POS_MAX,
+                                &r->ref_len[0]);
+
+    if (!r->ref[0]) {
+        r->ref[0] = NULL;
+        r->ref_id[0] = -1;
+        r->ref_len[0] = 0;
+        *ref = NULL;
+        return 0;
+    }
+
+    *ref = r->ref[0];
+    *ref_len = r->ref_len[0];
+    return 1;
+}
+
+// Initialise and destroy the base modifier state data. This is called
+// as each new read is added or removed from the pileups.
+static
+int pileup_cd_create(void *data, const bam1_t *b, bam_pileup_cd *cd) {
+    int ret;
+    hts_base_mod_state *m = hts_base_mod_state_alloc();
+    ret = bam_parse_basemod(b, m);
+    cd->p = m;
+    return ret;
+}
+
+static
+int pileup_cd_destroy(void *data, const bam1_t *b, bam_pileup_cd *cd) {
+    hts_base_mod_state_free(cd->p);
+    return 0;
+}
+
+static void
+print_empty_pileup(FILE *fp, const mplp_conf_t *conf, const char *tname,
+                   hts_pos_t pos, int n, const char *ref, hts_pos_t ref_len)
+{
+    int i;
+    fprintf(fp, "%s\t%"PRIhts_pos"\t%c", tname, pos+1, (ref && pos < ref_len)? ref[pos] : 'N');
+    for (i = 0; i < n; ++i) {
+        fputs("\t0\t*\t*", fp);
+        int flag_value = MPLP_PRINT_MAPQ_CHAR;
+        while(flag_value < MPLP_PRINT_LAST) {
+            if (flag_value != MPLP_PRINT_MODS && (conf->flag & flag_value))
+                fputs("\t*", fp);
+            flag_value <<= 1;
+        }
+        if (conf->auxlist) {
+            int t = 0;
+            while(t++ < ((klist_t(auxlist) *)conf->auxlist)->size)
+                fputs("\t*", fp);
+        }
+    }
+    putc('\n', fp);
+}
+
+static int mplp_func(void *data, bam1_t *b)
+{
+    char *ref;
+    mplp_aux_t *ma = (mplp_aux_t*)data;
+    int ret, skip = 0;
+    hts_pos_t ref_len;
+
+    do {
+        int has_ref;
+        ret = ma->iter? sam_itr_next(ma->fp, ma->iter, b) : sam_read1(ma->fp, ma->h, b);
+        if (ret < 0) break;
+        // The 'B' cigar operation is not part of the specification, considering as obsolete.
+        //  bam_remove_B(b);
+        if (b->core.tid < 0 || (b->core.flag&BAM_FUNMAP)) { // exclude unmapped reads
+            skip = 1;
+            continue;
+        }
+        if (ma->conf->rflag_require && !(ma->conf->rflag_require&b->core.flag)) { skip = 1; continue; }
+        if (ma->conf->rflag_filter && ma->conf->rflag_filter&b->core.flag) { skip = 1; continue; }
+        if (ma->conf->bed && ma->conf->all == 0) { // test overlap
+            skip = !bed_overlap(ma->conf->bed, sam_hdr_tid2name(ma->h, b->core.tid), b->core.pos, bam_endpos(b));
+            if (skip) continue;
+        }
+        if (ma->conf->rghash) { // exclude read groups
+            uint8_t *rg = bam_aux_get(b, "RG");
+            skip = (rg && khash_str2int_get(ma->conf->rghash, (const char*)(rg+1), NULL)==0);
+            if (skip) continue;
+        }
+        if (ma->conf->flag & MPLP_ILLUMINA13) {
+            int i;
+            uint8_t *qual = bam_get_qual(b);
+            for (i = 0; i < b->core.l_qseq; ++i)
+                qual[i] = qual[i] > 31? qual[i] - 31 : 0;
+        }
+
+        if (ma->conf->fai && b->core.tid >= 0) {
+            has_ref = mplp_get_ref(ma, b->core.tid, &ref, &ref_len);
+            if (has_ref && ref_len <= b->core.pos) { // exclude reads outside of the reference sequence
+                fprintf(samtools_stderr,"[%s] Skipping because %"PRIhts_pos" is outside of %"PRIhts_pos" [ref:%d]\n",
+                        __func__, (int64_t) b->core.pos, ref_len, b->core.tid);
+                skip = 1;
+                continue;
+            }
+        } else {
+            has_ref = 0;
+        }
+
+        skip = 0;
+        if (has_ref && (ma->conf->flag&MPLP_REALN)) sam_prob_realn(b, ref, ref_len, (ma->conf->flag & MPLP_REDO_BAQ)? 7 : 3);
+        if (has_ref && ma->conf->capQ_thres > 10) {
+            int q = sam_cap_mapq(b, ref, ref_len, ma->conf->capQ_thres);
+            if (q < 0) skip = 1;
+            else if (b->core.qual > q) b->core.qual = q;
+        }
+        if (b->core.qual < ma->conf->min_mq) skip = 1;
+        else if ((ma->conf->flag&MPLP_NO_ORPHAN) && (b->core.flag&BAM_FPAIRED) && !(b->core.flag&BAM_FPROPER_PAIR)) skip = 1;
+    } while (skip);
+    return ret;
+}
+
+/*
+ * Performs pileup
+ * @param conf configuration for this pileup
+ * @param n number of files specified in fn
+ * @param fn filenames
+ * @param fn_idx index filenames
+ */
+static int mpileup(mplp_conf_t *conf, int n, char **fn, char **fn_idx)
+{
+    mplp_aux_t **data;
+    int i, tid, *n_plp, tid0 = 0, max_depth;
+    hts_pos_t pos, beg0 = 0, end0 = HTS_POS_MAX, ref_len;
+    const bam_pileup1_t **plp;
+    mplp_ref_t mp_ref = MPLP_REF_INIT;
+    bam_mplp_t iter;
+    sam_hdr_t *h = NULL; /* header of first file in input list */
+    char *ref;
+    FILE *pileup_fp = NULL;
+
+    bam_sample_t *sm = NULL;
+    kstring_t buf;
+    mplp_pileup_t gplp;
+
+    memset(&gplp, 0, sizeof(mplp_pileup_t));
+    memset(&buf, 0, sizeof(kstring_t));
+    data = calloc(n, sizeof(mplp_aux_t*));
+    plp = calloc(n, sizeof(bam_pileup1_t*));
+    n_plp = calloc(n, sizeof(int));
+    sm = bam_smpl_init();
+
+    if (n == 0) {
+        fprintf(samtools_stderr,"[%s] no input file/data given\n", __func__);
+        samtools_exit(EXIT_FAILURE);
+    }
+
+    // read the header of each file in the list and initialize data
+    refs_t *refs = NULL;
+    for (i = 0; i < n; ++i) {
+        sam_hdr_t *h_tmp;
+        data[i] = calloc(1, sizeof(mplp_aux_t));
+        data[i]->fp = sam_open_format(fn[i], "rb", &conf->ga.in);
+        if ( !data[i]->fp )
+        {
+            fprintf(samtools_stderr, "[%s] failed to open %s: %s\n", __func__, fn[i], strerror(errno));
+            samtools_exit(EXIT_FAILURE);
+        }
+        if (hts_set_opt(data[i]->fp, CRAM_OPT_DECODE_MD, 0)) {
+            fprintf(samtools_stderr, "Failed to set CRAM_OPT_DECODE_MD value\n");
+            samtools_exit(EXIT_FAILURE);
+        }
+
+        if (!refs && conf->fai_fname) {
+            if (hts_set_fai_filename(data[i]->fp, conf->fai_fname) != 0) {
+                fprintf(samtools_stderr, "[%s] failed to process %s: %s\n",
+                        __func__, conf->fai_fname, strerror(errno));
+                samtools_exit(EXIT_FAILURE);
+            }
+            refs = cram_get_refs(data[i]->fp);
+        } else if (conf->fai_fname) {
+            if (hts_set_opt(data[i]->fp, CRAM_OPT_SHARED_REF, refs) != 0) {
+                fprintf(samtools_stderr, "[%s] failed to process %s: %s\n",
+                        __func__, conf->fai_fname, strerror(errno));
+                samtools_exit(EXIT_FAILURE);
+            }
+        }
+
+        data[i]->conf = conf;
+        data[i]->ref = &mp_ref;
+        h_tmp = sam_hdr_read(data[i]->fp);
+        if ( !h_tmp ) {
+            fprintf(samtools_stderr,"[%s] fail to read the header of %s\n", __func__, fn[i]);
+            samtools_exit(EXIT_FAILURE);
+        }
+        bam_smpl_add(sm, fn[i], (conf->flag&MPLP_IGNORE_RG)? 0 : sam_hdr_str(h_tmp));
+        if (conf->reg) {
+            hts_idx_t *idx = NULL;
+            // If index filename has not been specfied, look in BAM folder
+            if (fn_idx != NULL)  {
+                idx = sam_index_load2(data[i]->fp, fn[i], fn_idx[i]);
+            } else {
+                idx = sam_index_load(data[i]->fp, fn[i]);
+            }
+
+            if (idx == NULL) {
+                fprintf(samtools_stderr, "[%s] fail to load index for %s\n", __func__, fn[i]);
+                samtools_exit(EXIT_FAILURE);
+            }
+            if ( (data[i]->iter=sam_itr_querys(idx, h_tmp, conf->reg)) == 0) {
+                fprintf(samtools_stderr, "[E::%s] fail to parse region '%s' with %s\n", __func__, conf->reg, fn[i]);
+                samtools_exit(EXIT_FAILURE);
+            }
+            if (i == 0) beg0 = data[i]->iter->beg, end0 = data[i]->iter->end, tid0 = data[i]->iter->tid;
+            hts_idx_destroy(idx);
+        }
+        else
+            data[i]->iter = NULL;
+
+        if (i == 0) h = data[i]->h = h_tmp; // save the header of the first file
+        else {
+            // FIXME: check consistency between h and h_tmp
+            sam_hdr_destroy(h_tmp);
+
+            // we store only the first file's header; it's (alleged to be)
+            // compatible with the i-th file's target_name lookup needs
+            data[i]->h = h;
+        }
+    }
+    fprintf(samtools_stderr, "[%s] %d samples in %d input files\n", __func__, sm->n, n);
+
+    pileup_fp = conf->output_fname? fopen(conf->output_fname, "w") : samtools_stdout;
+
+    if (pileup_fp == NULL) {
+        fprintf(samtools_stderr, "[%s] failed to write to %s: %s\n", __func__, conf->output_fname, strerror(errno));
+        samtools_exit(EXIT_FAILURE);
+    }
+
+    // init pileup
+    iter = bam_mplp_init(n, mplp_func, (void**)data);
+    if (conf->flag & MPLP_PRINT_MODS) {
+        bam_mplp_constructor(iter, pileup_cd_create);
+        bam_mplp_destructor(iter, pileup_cd_destroy);
+    }
+    if ( conf->flag & MPLP_SMART_OVERLAPS ) bam_mplp_init_overlaps(iter);
+    if ( !conf->max_depth ) {
+        max_depth = INT_MAX;
+        fprintf(samtools_stderr, "[%s] Max depth set to maximum value (%d)\n", __func__, INT_MAX);
+    } else {
+        max_depth = conf->max_depth;
+        if ( max_depth * n > 1<<20 )
+            fprintf(samtools_stderr, "[%s] Combined max depth is above 1M. Potential memory hog!\n", __func__);
+    }
+
+
+    bam_mplp_set_maxcnt(iter, max_depth);
+    int ret;
+    int last_tid = -1;
+    hts_pos_t last_pos = -1;
+
+    // begin pileup
+    while ( (ret=bam_mplp64_auto(iter, &tid, &pos, n_plp, plp)) > 0) {
+        if (conf->reg && (pos < beg0 || pos >= end0)) continue; // out of the region requested
+        mplp_get_ref(data[0], tid, &ref, &ref_len);
+        //printf("tid=%d len=%d ref=%p/%s\n", tid, ref_len, ref, ref);
+        if (conf->all) {
+            // Deal with missing portions of previous tids
+            while (tid > last_tid) {
+                if (last_tid >= 0 && !conf->reg) {
+                    while (++last_pos < sam_hdr_tid2len(h, last_tid)) {
+                        if (conf->bed && bed_overlap(conf->bed, sam_hdr_tid2name(h, last_tid), last_pos, last_pos + 1) == 0)
+                            continue;
+                        print_empty_pileup(pileup_fp, conf, sam_hdr_tid2name(h, last_tid), last_pos, n, ref, ref_len);
+                    }
+                }
+                last_tid++;
+                last_pos = -1;
+                if (conf->all < 2)
+                    break;
+            }
+        }
+        if (conf->all) {
+            // Deal with missing portion of current tid
+            while (++last_pos < pos) {
+                if (conf->reg && last_pos < beg0) continue; // out of range; skip
+                if (conf->bed && bed_overlap(conf->bed, sam_hdr_tid2name(h, tid), last_pos, last_pos + 1) == 0)
+                    continue;
+                print_empty_pileup(pileup_fp, conf, sam_hdr_tid2name(h, tid), last_pos, n, ref, ref_len);
+            }
+            last_tid = tid;
+            last_pos = pos;
+        }
+        if (conf->bed && tid >= 0 && !bed_overlap(conf->bed, sam_hdr_tid2name(h, tid), pos, pos+1)) continue;
+
+        fprintf(pileup_fp, "%s\t%"PRIhts_pos"\t%c", sam_hdr_tid2name(h, tid), pos + 1, (ref && pos < ref_len)? ref[pos] : 'N');
+        for (i = 0; i < n; ++i) {
+            int j, cnt;
+            for (j = cnt = 0; j < n_plp[i]; ++j) {
+                const bam_pileup1_t *p = plp[i] + j;
+                int c = p->qpos < p->b->core.l_qseq
+                    ? bam_get_qual(p->b)[p->qpos]
+                    : 0;
+                if (c >= conf->min_baseQ) ++cnt;
+            }
+            fprintf(pileup_fp, "\t%d\t", cnt);
+            if (n_plp[i] == 0) {
+                fputs("*\t*", pileup_fp);
+                int flag_value = MPLP_PRINT_MAPQ_CHAR;
+                while(flag_value < MPLP_PRINT_LAST) {
+                    if (flag_value != MPLP_PRINT_MODS
+                        && (conf->flag & flag_value))
+                        fputs("\t*", pileup_fp);
+                    flag_value <<= 1;
+                }
+                if (conf->auxlist) {
+                    int t = 0;
+                    while(t++ < ((klist_t(auxlist) *)conf->auxlist)->size)
+                        fputs("\t*", pileup_fp);
+                }
+            } else {
+                int n = 0;
+                kstring_t ks = KS_INITIALIZE;
+                for (j = 0; j < n_plp[i]; ++j) {
+                    const bam_pileup1_t *p = plp[i] + j;
+                    int c = p->qpos < p->b->core.l_qseq
+                        ? bam_get_qual(p->b)[p->qpos]
+                        : 0;
+                    if (c >= conf->min_baseQ) {
+                        n++;
+                        if (pileup_seq(pileup_fp, plp[i] + j, pos, ref_len,
+                                       ref, &ks, conf->rev_del,
+                                       conf->no_ins, conf->no_ins_mods,
+                                       conf->no_del, conf->no_ends) < 0) {
+                            ret = 1;
+                            goto fail;
+                        }
+                    }
+                }
+                if (!n) putc('*', pileup_fp);
+
+                /* Print base qualities */
+                n = 0;
+                ks_free(&ks);
+                putc('\t', pileup_fp);
+                for (j = 0; j < n_plp[i]; ++j) {
+                    const bam_pileup1_t *p = plp[i] + j;
+                    int c = p->qpos < p->b->core.l_qseq
+                        ? bam_get_qual(p->b)[p->qpos]
+                        : 0;
+                    if (c >= conf->min_baseQ) {
+                        c = c + 33 < 126? c + 33 : 126;
+                        putc(c, pileup_fp);
+                        n++;
+                    }
+                }
+                if (!n) putc('*', pileup_fp);
+
+                /* Print selected columns */
+                int flag_value = MPLP_PRINT_MAPQ_CHAR;
+                while(flag_value < MPLP_PRINT_LAST) {
+                    if (flag_value != MPLP_PRINT_MODS
+                        && (conf->flag & flag_value)) {
+                        n = 0;
+                        putc('\t', pileup_fp);
+                        for (j = 0; j < n_plp[i]; ++j) {
+                            const bam_pileup1_t *p = &plp[i][j];
+                            int c = p->qpos < p->b->core.l_qseq
+                                ? bam_get_qual(p->b)[p->qpos]
+                                : 0;
+                            if ( c < conf->min_baseQ ) continue;
+                            if (n > 0 && flag_value != MPLP_PRINT_MAPQ_CHAR) putc(',', pileup_fp);
+                            n++;
+
+                            switch (flag_value) {
+                            case MPLP_PRINT_MAPQ_CHAR:
+                                c = p->b->core.qual + 33;
+                                if (c > 126) c = 126;
+                                putc(c, pileup_fp);
+                                break;
+                            case MPLP_PRINT_QPOS:
+                                // query position in current orientation
+                                fprintf(pileup_fp, "%d", p->qpos + 1);
+                                break;
+                            case MPLP_PRINT_QPOS5: {
+                                // query position in 5' to 3' orientation
+                                int pos5 = bam_is_rev(p->b)
+                                    ? p->b->core.l_qseq-p->qpos + p->is_del
+                                    : p->qpos + 1;
+                                fprintf(pileup_fp, "%d", pos5);
+                                break;
+                            }
+                            case MPLP_PRINT_QNAME:
+                                fputs(bam_get_qname(p->b), pileup_fp);
+                                break;
+                            case MPLP_PRINT_FLAG:
+                                fprintf(pileup_fp, "%d", p->b->core.flag);
+                                break;
+                            case MPLP_PRINT_RNAME:
+                                if (p->b->core.tid >= 0)
+                                    fputs(sam_hdr_tid2name(h, p->b->core.tid), pileup_fp);
+                                else
+                                    putc('*', pileup_fp);
+                                break;
+                            case MPLP_PRINT_POS:
+                                fprintf(pileup_fp, "%"PRId64, (int64_t) p->b->core.pos + 1);
+                                break;
+                            case MPLP_PRINT_MAPQ:
+                                fprintf(pileup_fp, "%d", p->b->core.qual);
+                                break;
+                            case MPLP_PRINT_RNEXT:
+                                if (p->b->core.mtid >= 0)
+                                    fputs(sam_hdr_tid2name(h, p->b->core.mtid), pileup_fp);
+                                else
+                                    putc('*', pileup_fp);
+                                break;
+                            case MPLP_PRINT_PNEXT:
+                                fprintf(pileup_fp, "%"PRId64, (int64_t) p->b->core.mpos + 1);
+                                break;
+                            }
+                        }
+                        if (!n) putc('*', pileup_fp);
+                    }
+                    flag_value <<= 1;
+                }
+
+                /* Print selected tags */
+                klist_t(auxlist) *auxlist_p = ((klist_t(auxlist) *)conf->auxlist);
+                if (auxlist_p && auxlist_p->size) {
+                    kliter_t(auxlist) *aux;
+                    for (aux = kl_begin(auxlist_p); aux != kl_end(auxlist_p); aux = kl_next(aux)) {
+                        n = 0;
+                        putc('\t', pileup_fp);
+                        for (j = 0; j < n_plp[i]; ++j) {
+                            const bam_pileup1_t *p = &plp[i][j];
+                            int c = p->qpos < p->b->core.l_qseq
+                                ? bam_get_qual(p->b)[p->qpos]
+                                : 0;
+                            if ( c < conf->min_baseQ ) continue;
+
+                            if (n > 0) putc(conf->sep, pileup_fp);
+                            n++;
+                            uint8_t* tag_u = bam_aux_get(p->b, kl_val(aux));
+                            if (!tag_u) {
+                                putc(conf->empty , pileup_fp);
+                                continue;
+                            }
+
+                            int tag_supported = 0;
+
+                            /* Tag value is string */
+                            if (*tag_u == 'Z' || *tag_u == 'H') {
+                                char *tag_s = bam_aux2Z(tag_u);
+                                if (!tag_s) continue;
+                                fputs(tag_s, pileup_fp);
+                                tag_supported = 1;
+                            }
+
+                            /* Tag value is integer */
+                            if (*tag_u == 'I' || *tag_u == 'i' || *tag_u == 'C' || *tag_u == 'c' || *tag_u == 'S' || *tag_u == 's') {
+                                int64_t tag_i = bam_aux2i(tag_u);
+                                fprintf(pileup_fp, "%" PRId64 "", tag_i);
+                                tag_supported = 1;
+                            }
+
+                            /* Tag value is float */
+                            if (*tag_u == 'd' || *tag_u == 'f') {
+                                double tag_f = bam_aux2f(tag_u);
+                                fprintf(pileup_fp, "%lf", tag_f);
+                                tag_supported = 1;
+                            }
+
+                            /* Tag value is character */
+                            if (*tag_u == 'A') {
+                                char tag_c = bam_aux2A(tag_u);
+                                putc(tag_c, pileup_fp);
+                                tag_supported = 1;
+                            }
+
+                            if (!tag_supported) putc('*', pileup_fp);
+                        }
+                        if (!n) putc('*', pileup_fp);
+                    }
+                }
+            }
+        }
+        putc('\n', pileup_fp);
+    }
+
+    if (ret < 0) {
+        print_error("mpileup", "error reading from input file");
+        ret = EXIT_FAILURE;
+        goto fail;
+    }
+
+    if (conf->all) {
+        // Handle terminating region
+        if (last_tid < 0 && conf->reg && conf->all > 1) {
+            last_tid = tid0;
+            last_pos = beg0-1;
+            mplp_get_ref(data[0], tid0, &ref, &ref_len);
+        }
+       while (last_tid >= 0 && last_tid < sam_hdr_nref(h)) {
+            while (++last_pos < sam_hdr_tid2len(h, last_tid)) {
+                if (last_pos >= end0) break;
+                if (conf->bed && bed_overlap(conf->bed, sam_hdr_tid2name(h, last_tid), last_pos, last_pos + 1) == 0)
+                    continue;
+                print_empty_pileup(pileup_fp, conf, sam_hdr_tid2name(h, last_tid), last_pos, n, ref, ref_len);
+            }
+            last_tid++;
+            last_pos = -1;
+            if (conf->all < 2 || conf->reg)
+                break;
+        }
+    }
+
+fail:
+    // clean up
+    if (pileup_fp && conf->output_fname) fclose(pileup_fp);
+    bam_smpl_destroy(sm); free(buf.s);
+    for (i = 0; i < gplp.n; ++i) free(gplp.plp[i]);
+    free(gplp.plp); free(gplp.n_plp); free(gplp.m_plp);
+    bam_mplp_destroy(iter);
+    sam_hdr_destroy(h);
+    for (i = 0; i < n; ++i) {
+        sam_close(data[i]->fp);
+        if (data[i]->iter) hts_itr_destroy(data[i]->iter);
+        free(data[i]);
+    }
+    free(data); free(plp); free(n_plp);
+    free(mp_ref.ref[0]);
+    free(mp_ref.ref[1]);
+    return ret;
+}
+
+static int is_url(const char *s)
+{
+    static const char uri_scheme_chars[] =
+        "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789+.-";
+    return s[strspn(s, uri_scheme_chars)] == ':';
+}
+
+#define MAX_PATH_LEN 1024
+int read_file_list(const char *file_list,int *n,char **argv[])
+{
+    char buf[MAX_PATH_LEN];
+    int len, nfiles = 0;
+    char **files = NULL;
+    struct stat sb;
+
+    *n = 0;
+    *argv = NULL;
+
+    FILE *fh = fopen(file_list,"r");
+    if ( !fh )
+    {
+        fprintf(samtools_stderr,"%s: %s\n", file_list,strerror(errno));
+        return 1;
+    }
+
+    files = calloc(nfiles,sizeof(char*));
+    nfiles = 0;
+    while ( fgets(buf,MAX_PATH_LEN,fh) )
+    {
+        // allow empty lines and trailing spaces
+        len = strlen(buf);
+        while ( len>0 && isspace(buf[len-1]) ) len--;
+        if ( !len ) continue;
+
+        // check sanity of the file list
+        buf[len] = 0;
+        if (! (is_url(buf) || stat(buf, &sb) == 0))
+        {
+            // no such file, check if it is safe to print its name
+            int i, safe_to_print = 1;
+            for (i=0; i<len; i++)
+                if (!isprint(buf[i])) { safe_to_print = 0; break; }
+            if ( safe_to_print )
+                fprintf(samtools_stderr,"The file list \"%s\" appears broken, could not locate: %s\n", file_list,buf);
+            else
+                fprintf(samtools_stderr,"Does the file \"%s\" really contain a list of files and do all exist?\n", file_list);
+            return 1;
+        }
+
+        nfiles++;
+        files = realloc(files,nfiles*sizeof(char*));
+        files[nfiles-1] = strdup(buf);
+    }
+    fclose(fh);
+    if ( !nfiles )
+    {
+        fprintf(samtools_stderr,"No files read from %s\n", file_list);
+        return 1;
+    }
+    *argv = files;
+    *n    = nfiles;
+    return 0;
+}
+#undef MAX_PATH_LEN
+
+static void print_usage(FILE *fp, const mplp_conf_t *mplp)
+{
+    char *tmp_require = bam_flag2str(mplp->rflag_require);
+    char *tmp_filter  = bam_flag2str(mplp->rflag_filter);
+
+    // Display usage information, formatted for the standard 80 columns.
+    // (The unusual string formatting here aids the readability of this
+    // source code in 80 columns, to the extent that's possible.)
+
+    fprintf(fp,
+"\n"
+"Usage: samtools mpileup [options] in1.bam [in2.bam [...]]\n"
+"\n"
+"Input options:\n"
+"  -6, --illumina1.3+      quality is in the Illumina-1.3+ encoding\n"
+"  -A, --count-orphans     do not discard anomalous read pairs\n"
+"  -b, --bam-list FILE     list of input BAM filenames, one per line\n"
+"  -B, --no-BAQ            disable BAQ (per-Base Alignment Quality)\n"
+"  -C, --adjust-MQ INT     adjust mapping quality; recommended:50, disable:0 [0]\n"
+"  -d, --max-depth INT     max per-file depth; avoids excessive memory usage [%d]\n", mplp->max_depth);
+    fprintf(fp,
+"  -E, --redo-BAQ          recalculate BAQ on the fly, ignore existing BQs\n"
+"  -f, --fasta-ref FILE    faidx indexed reference sequence file\n"
+"  -G, --exclude-RG FILE   exclude read groups listed in FILE\n"
+"  -l, --positions FILE    skip unlisted positions (chr pos) or regions (BED)\n"
+"  -q, --min-MQ INT        skip alignments with mapQ smaller than INT [%d]\n", mplp->min_mq);
+    fprintf(fp,
+"  -Q, --min-BQ INT        skip bases with baseQ/BAQ smaller than INT [%d]\n", mplp->min_baseQ);
+    fprintf(fp,
+"  -r, --region REG        region in which pileup is generated\n"
+"  -R, --ignore-RG         ignore RG tags (one BAM = one sample)\n"
+"  --rf, --incl-flags STR|INT  required flags: include reads with any of the mask bits set [%s]\n", tmp_require);
+    fprintf(fp,
+"  --ff, --excl-flags STR|INT  filter flags: skip reads with any of the mask bits set\n"
+"                                            [%s]\n", tmp_filter);
+    fprintf(fp,
+"  -x, --ignore-overlaps-removal, --disable-overlap-removal\n"
+"                          disable read-pair overlap detection and removal\n"
+"  -X, --customized-index  use customized index files\n" // -X flag for index filename
+"\n"
+"Output options:\n"
+"  -o, --output FILE        write output to FILE [standard output]\n"
+"  -O, --output-BP          output base positions on reads, current orientation\n"
+"      --output-BP-5        output base positions on reads, 5' to 3' orientation\n"
+"  -M, --output-mods        output base modifications\n"
+"  -s, --output-MQ          output mapping quality\n"
+"      --output-QNAME       output read names\n"
+"      --output-extra STR   output extra read fields and read tag values\n"
+"      --output-sep CHAR    set the separator character for tag lists [,]\n"
+"      --output-empty CHAR  set the no value character for tag lists [*]\n"
+"      --no-output-ins      skip insertion sequence after +NUM\n"
+"                           Use twice for complete insertion removal\n"
+"      --no-output-ins-mods don't display base modifications within insertions\n"
+"      --no-output-del      skip deletion sequence after -NUM\n"
+"                           Use twice for complete deletion removal\n"
+"      --no-output-ends     remove ^MQUAL and $ markup in sequence column\n"
+"      --reverse-del        use '#' character for deletions on the reverse strand\n"
+"  -a                       output all positions (including zero depth)\n"
+"  -a -a (or -aa)           output absolutely all positions, including unused ref. sequences\n"
+"\n"
+"Generic options:\n");
+    sam_global_opt_help(fp, "-.--.--.");
+
+    fprintf(fp, "\n"
+"Note that using \"samtools mpileup\" to generate BCF or VCF files has been\n"
+"removed.  To output these formats, please use \"bcftools mpileup\" instead.\n");
+
+    free(tmp_require);
+    free(tmp_filter);
+}
+
+int bam_mpileup(int argc, char *argv[])
+{
+    int c;
+    const char *file_list = NULL;
+    char **fn = NULL;
+    int nfiles = 0, use_orphan = 0, has_index_file = 0;
+    mplp_conf_t mplp;
+    memset(&mplp, 0, sizeof(mplp_conf_t));
+    mplp.min_baseQ = 13;
+    mplp.capQ_thres = 0;
+    mplp.max_depth = MPLP_MAX_DEPTH;
+    mplp.flag = MPLP_NO_ORPHAN | MPLP_REALN | MPLP_SMART_OVERLAPS;
+    mplp.argc = argc; mplp.argv = argv;
+    mplp.rflag_filter = BAM_FUNMAP | BAM_FSECONDARY | BAM_FQCFAIL | BAM_FDUP;
+    mplp.output_fname = NULL;
+    mplp.all = 0;
+    mplp.rev_del = 0;
+    mplp.sep = ',';
+    mplp.empty = '*';
+    sam_global_args_init(&mplp.ga);
+
+    static const struct option lopts[] =
+    {
+        SAM_OPT_GLOBAL_OPTIONS('-', 0, '-', '-', 0, '-'),
+        {"rf", required_argument, NULL, 1},   // require flag
+        {"ff", required_argument, NULL, 2},   // filter flag
+        {"incl-flags", required_argument, NULL, 1},
+        {"excl-flags", required_argument, NULL, 2},
+        {"output", required_argument, NULL, 3},
+        {"output-QNAME", no_argument, NULL, 5},
+        {"output-qname", no_argument, NULL, 5},
+        {"illumina1.3+", no_argument, NULL, '6'},
+        {"count-orphans", no_argument, NULL, 'A'},
+        {"bam-list", required_argument, NULL, 'b'},
+        {"no-BAQ", no_argument, NULL, 'B'},
+        {"no-baq", no_argument, NULL, 'B'},
+        {"adjust-MQ", required_argument, NULL, 'C'},
+        {"adjust-mq", required_argument, NULL, 'C'},
+        {"max-depth", required_argument, NULL, 'd'},
+        {"redo-BAQ", no_argument, NULL, 'E'},
+        {"redo-baq", no_argument, NULL, 'E'},
+        {"fasta-ref", required_argument, NULL, 'f'},
+        {"exclude-RG", required_argument, NULL, 'G'},
+        {"exclude-rg", required_argument, NULL, 'G'},
+        {"positions", required_argument, NULL, 'l'},
+        {"region", required_argument, NULL, 'r'},
+        {"ignore-RG", no_argument, NULL, 'R'},
+        {"ignore-rg", no_argument, NULL, 'R'},
+        {"min-MQ", required_argument, NULL, 'q'},
+        {"min-mq", required_argument, NULL, 'q'},
+        {"min-BQ", required_argument, NULL, 'Q'},
+        {"min-bq", required_argument, NULL, 'Q'},
+        // NB: old "--ignore-overlaps" auto-completes to this
+        {"ignore-overlaps-removal",  no_argument, NULL, 'x'},
+        {"disable-overlap-removal",  no_argument, NULL, 'x'},
+        {"output-mods", no_argument, NULL, 'M'},
+        {"output-BP", no_argument, NULL, 'O'},
+        {"output-bp", no_argument, NULL, 'O'},
+        {"output-BP-5", no_argument, NULL, 14},
+        {"output-bp-5", no_argument, NULL, 14},
+        {"output-MQ", no_argument, NULL, 's'},
+        {"output-mq", no_argument, NULL, 's'},
+        {"ext-prob", required_argument, NULL, 'e'},
+        {"gap-frac", required_argument, NULL, 'F'},
+        {"tandem-qual", required_argument, NULL, 'h'},
+        {"skip-indels", no_argument, NULL, 'I'},
+        {"max-idepth", required_argument, NULL, 'L'},
+        {"min-ireads ", required_argument, NULL, 'm'},
+        {"per-sample-mF", no_argument, NULL, 'p'},
+        {"per-sample-mf", no_argument, NULL, 'p'},
+        {"platforms", required_argument, NULL, 'P'},
+        {"customized-index", no_argument, NULL, 'X'},
+        {"reverse-del", no_argument, NULL, 6},
+        {"output-extra", required_argument, NULL, 7},
+        {"output-sep", required_argument, NULL, 8},
+        {"output-empty", required_argument, NULL, 9},
+        {"no-output-ins", no_argument, NULL, 10},
+        {"no-output-ins-mods", no_argument, NULL, 11},
+        {"no-output-del", no_argument, NULL, 12},
+        {"no-output-ends", no_argument, NULL, 13},
+        {NULL, 0, NULL, 0}
+    };
+
+    while ((c = getopt_long(argc, argv, "Af:r:l:q:Q:RC:Bd:b:o:EG:6OsxXaM",lopts,NULL)) >= 0) {
+        switch (c) {
+        case 'x': mplp.flag &= ~MPLP_SMART_OVERLAPS; break;
+        case  1 :
+            mplp.rflag_require = bam_str2flag(optarg);
+            if ( mplp.rflag_require<0 ) { fprintf(samtools_stderr,"Could not parse --rf %s\n", optarg); return 1; }
+            break;
+        case  2 :
+            mplp.rflag_filter = bam_str2flag(optarg);
+            if ( mplp.rflag_filter<0 ) { fprintf(samtools_stderr,"Could not parse --ff %s\n", optarg); return 1; }
+            break;
+        case  3 : mplp.output_fname = optarg; break;
+        case  5 : mplp.flag |= MPLP_PRINT_QNAME; break;
+        case  6 : mplp.rev_del = 1; break;
+        case  7 :
+            if (build_auxlist(&mplp, optarg) != 0) {
+                fprintf(samtools_stderr,"Could not build aux list using '%s'\n", optarg);
+                return 1;
+            }
+            break;
+        case 8: mplp.sep = optarg[0]; break;
+        case 9: mplp.empty = optarg[0]; break;
+        case 10: mplp.no_ins++; break;
+        case 11: mplp.no_ins_mods = 1; break;
+        case 12: mplp.no_del++; break;
+        case 13: mplp.no_ends = 1; break;
+        case 'f':
+            mplp.fai = fai_load(optarg);
+            if (mplp.fai == NULL) return 1;
+            mplp.fai_fname = optarg;
+            break;
+        case 'd': mplp.max_depth = atoi(optarg); break;
+        case 'r': mplp.reg = strdup(optarg); break;
+        case 'l':
+                  // In the original version the whole BAM was streamed which is inefficient
+                  //  with few BED intervals and big BAMs. Todo: devise a heuristic to determine
+                  //  best strategy, that is streaming or jumping.
+                  mplp.bed = bed_read(optarg);
+                  if (!mplp.bed) { print_error_errno("mpileup", "Could not read file \"%s\"", optarg); return 1; }
+                  break;
+        case 'B': mplp.flag &= ~MPLP_REALN; break;
+        case 'X': has_index_file = 1; break;
+        case 'E': mplp.flag |= MPLP_REDO_BAQ; break;
+        case '6': mplp.flag |= MPLP_ILLUMINA13; break;
+        case 'R': mplp.flag |= MPLP_IGNORE_RG; break;
+        case 's': mplp.flag |= MPLP_PRINT_MAPQ_CHAR; break;
+        case 'O': mplp.flag |= MPLP_PRINT_QPOS; break;
+        case  14: mplp.flag |= MPLP_PRINT_QPOS5; break;
+        case 'M': mplp.flag |= MPLP_PRINT_MODS; break;
+        case 'C': mplp.capQ_thres = atoi(optarg); break;
+        case 'q': mplp.min_mq = atoi(optarg); break;
+        case 'Q': mplp.min_baseQ = atoi(optarg); break;
+        case 'b': file_list = optarg; break;
+        case 'o': mplp.output_fname = optarg; break;
+        case 'A': use_orphan = 1; break;
+        case 'G': {
+                FILE *fp_rg;
+                char buf[1024];
+                mplp.rghash = khash_str2int_init();
+                if ((fp_rg = fopen(optarg, "r")) == NULL)
+                    fprintf(samtools_stderr, "[%s] Fail to open file %s. Continue anyway.\n", __func__, optarg);
+                while (!feof(fp_rg) && fscanf(fp_rg, "%s", buf) > 0) // this is not a good style, but forgive me...
+                    khash_str2int_inc(mplp.rghash, strdup(buf));
+                fclose(fp_rg);
+            }
+            break;
+        case 'a': mplp.all++; break;
+        default:
+            if (parse_sam_global_opt(c, optarg, lopts, &mplp.ga) == 0) break;
+            /* else fall-through */
+        case '?':
+            print_usage(samtools_stderr, &mplp);
+            return 1;
+        }
+    }
+    if (!mplp.fai && mplp.ga.reference) {
+        mplp.fai_fname = mplp.ga.reference;
+        mplp.fai = fai_load(mplp.fai_fname);
+        if (mplp.fai == NULL) return 1;
+    }
+
+    if ( !(mplp.flag&MPLP_REALN) && mplp.flag&MPLP_REDO_BAQ )
+    {
+        fprintf(samtools_stderr,"Error: The -B option cannot be combined with -E\n");
+        return 1;
+    }
+    if (use_orphan) mplp.flag &= ~MPLP_NO_ORPHAN;
+    if (argc == 1)
+    {
+        print_usage(samtools_stderr, &mplp);
+        return 1;
+    }
+    int ret;
+    if (file_list) {
+        if (has_index_file) {
+            fprintf(samtools_stderr,"Error: The -b option cannot be combined with -X\n"); // No customize index loc in file list mode
+            return 1;
+        }
+        if ( read_file_list(file_list,&nfiles,&fn) ) return 1;
+        ret = mpileup(&mplp,nfiles,fn,NULL);
+        for (c=0; c<nfiles; c++) free(fn[c]);
+        free(fn);
+    }
+    else {
+        if (has_index_file) {
+            if ((argc - optind)%2 !=0) { // Calculate # of input BAM files
+                fprintf(samtools_stderr, "Odd number of filenames detected! Each BAM file should have an index file\n");
+                return 1;
+            }
+            nfiles = (argc - optind)/2;
+            ret = mpileup(&mplp, nfiles, argv + optind, argv + nfiles + optind);
+        } else {
+            nfiles = argc - optind;
+            ret = mpileup(&mplp, nfiles, argv + optind, NULL);
+        }
+    }
+    if (mplp.rghash) khash_str2int_destroy_free(mplp.rghash);
+    free(mplp.reg); free(mplp.pl_list);
+    if (mplp.fai) fai_destroy(mplp.fai);
+    if (mplp.bed) bed_destroy(mplp.bed);
+    if (mplp.auxlist) kl_destroy(auxlist, (klist_t(auxlist) *)mplp.auxlist);
+    return ret;
+}
diff --git a/samtools/bam_quickcheck.c b/samtools/bam_quickcheck.c
new file mode 100644
index 0000000..29d8885
--- /dev/null
+++ b/samtools/bam_quickcheck.c
@@ -0,0 +1,190 @@
+/*  bam_quickcheck.c -- quickcheck subcommand.
+
+    Copyright (C) 2015-2017 Genome Research Ltd.
+
+    Author: Joshua C. Randall <jcrandall@alum.mit.edu>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <config.h>
+
+#include <htslib/hts.h>
+#include <htslib/sam.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <unistd.h>
+
+/* File status flags (zero means OK). It's possible for more than one to be
+ * set on a single file.   The final exit status is the bitwise-or of the
+ * status of all the files. */
+#define QC_FAIL_OPEN     2
+#define QC_NOT_SEQUENCE  4
+#define QC_BAD_HEADER    8
+#define QC_NO_EOF_BLOCK 16
+#define QC_FAIL_CLOSE   32
+
+static void usage_quickcheck(FILE *write_to)
+{
+    fprintf(write_to,
+"Usage: samtools quickcheck [options] <input> [...]\n"
+"Options:\n"
+"  -v              verbose output (repeat for more verbosity)\n"
+"  -q              suppress warning messages\n"
+"  -u              unmapped input (do not require targets in header)\n"
+"\n"
+"Notes:\n"
+"\n"
+"1. By default quickcheck will emit a warning message if and only if a file\n"
+"   fails the checks, in which case the exit status is non-zero.  Under normal\n"
+"   behaviour with valid data it will be silent and has a zero exit status.\n"
+"   The warning messages are purely for manual inspection and should not be \n"
+"   parsed by scripts.\n"
+"\n"
+"2. In order to use this command programmatically, you should check its exit\n"
+"   status.  One way to use quickcheck might be as a check that all BAM files in\n"
+"   a directory are okay:\n"
+"\n"
+"\tsamtools quickcheck *.bam && echo 'all ok' \\\n"
+"\t   || echo 'fail!'\n"
+"\n"
+"   The first level of verbosity lists only files that fail to stdout.\n"
+"   To obtain a parsable list of files that have failed, use this option:\n"
+"\n"
+"\tsamtools quickcheck -qv *.bam > bad_bams.fofn \\\n"
+"\t   && echo 'all ok' \\\n"
+"\t   || echo 'some files failed check, see bad_bams.fofn'\n"
+    );
+}
+
+#define QC_ERR(state, v, msg, arg1)                                     \
+    file_state |= (state);                                              \
+    if (!quiet || verbose >= (v)) fprintf(stderr, (msg), (arg1))
+
+int main_quickcheck(int argc, char** argv)
+{
+    int verbose = 0, quiet = 0, unmapped = 0;
+    hts_verbose = 0;
+
+    const char* optstring = "vqu";
+    int opt;
+    while ((opt = getopt(argc, argv, optstring)) != -1) {
+        switch (opt) {
+        case 'u':
+            unmapped = 1;
+            break;
+        case 'v':
+            verbose++;
+            break;
+        case 'q':
+            quiet = 1;
+            break;
+        default:
+            usage_quickcheck(stderr);
+            return 1;
+        }
+    }
+
+    argc -= optind;
+    argv += optind;
+
+    if (argc < 1) {
+        usage_quickcheck(stdout);
+        return 1;
+    }
+
+    if (verbose >= 2) {
+        fprintf(stderr, "verbosity set to %d\n", verbose);
+    }
+
+    if (verbose >= 4) {
+        hts_verbose = 3;
+    }
+
+    int ret = 0;
+    int i;
+
+    for (i = 0; i < argc; i++) {
+        char* fn = argv[i];
+        int file_state = 0;
+
+        if (verbose >= 3) fprintf(stderr, "checking %s\n", fn);
+
+        // attempt to open
+        htsFile *hts_fp = hts_open(fn, "r");
+        if (hts_fp == NULL) {
+            QC_ERR(QC_FAIL_OPEN, 2, "%s could not be opened for reading.\n", fn);
+        }
+        else {
+            if (verbose >= 3) fprintf(stderr, "opened %s\n", fn);
+            // make sure we have sequence data
+            const htsFormat *fmt = hts_get_format(hts_fp);
+            if (fmt->category != sequence_data ) {
+                QC_ERR(QC_NOT_SEQUENCE, 2, "%s was not identified as sequence data.\n", fn);
+            }
+            else {
+                if (verbose >= 3) fprintf(stderr, "%s is sequence data\n", fn);
+                // check header
+                sam_hdr_t *header = sam_hdr_read(hts_fp);
+                if (header == NULL) {
+                    QC_ERR(QC_BAD_HEADER, 2, "%s caused an error whilst reading its header.\n", fn);
+                } else {
+                    if (!unmapped && sam_hdr_nref(header) <= 0) {
+                        QC_ERR(QC_BAD_HEADER, 2, "%s had no targets in header.\n", fn);
+                    }
+                    else {
+                        if (verbose >= 3) fprintf(stderr, "%s has %d targets in header.\n", fn, sam_hdr_nref(header));
+                    }
+                    sam_hdr_destroy(header);
+                }
+            }
+            // check EOF on formats that support this
+            int ret;
+            if ((ret = hts_check_EOF(hts_fp)) < 0) {
+                QC_ERR(QC_NO_EOF_BLOCK, 2, "%s caused an error whilst checking for EOF block.\n", fn);
+           }
+            else {
+                switch (ret) {
+                    case 0:
+                        QC_ERR(QC_NO_EOF_BLOCK, 2, "%s was missing EOF block when one should be present.\n", fn);
+                        break;
+                    case 1:
+                        if (verbose >= 3) fprintf(stderr, "%s has good EOF block.\n", fn);
+                        break;
+                    case 2:
+                        if (verbose >= 3) fprintf(stderr, "%s cannot be checked for EOF block as it is not seekable.\n", fn);
+                        break;
+                    case 3:
+                        if (verbose >= 3) fprintf(stderr, "%s cannot be checked for EOF block because its filetype does not contain one.\n", fn);
+                        break;
+                }
+            }
+
+            if (hts_close(hts_fp) < 0) {
+                QC_ERR(QC_FAIL_CLOSE, 2, "%s did not close cleanly.\n", fn);
+            }
+        }
+
+        if (file_state > 0 && verbose >= 1) {
+            fprintf(stdout, "%s\n", fn);
+        }
+        ret |= file_state;
+    }
+
+    return ret;
+}
diff --git a/samtools/bam_quickcheck.c.pysam.c b/samtools/bam_quickcheck.c.pysam.c
new file mode 100644
index 0000000..15ea8f6
--- /dev/null
+++ b/samtools/bam_quickcheck.c.pysam.c
@@ -0,0 +1,192 @@
+#include "samtools.pysam.h"
+
+/*  bam_quickcheck.c -- quickcheck subcommand.
+
+    Copyright (C) 2015-2017 Genome Research Ltd.
+
+    Author: Joshua C. Randall <jcrandall@alum.mit.edu>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <config.h>
+
+#include <htslib/hts.h>
+#include <htslib/sam.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <unistd.h>
+
+/* File status flags (zero means OK). It's possible for more than one to be
+ * set on a single file.   The final exit status is the bitwise-or of the
+ * status of all the files. */
+#define QC_FAIL_OPEN     2
+#define QC_NOT_SEQUENCE  4
+#define QC_BAD_HEADER    8
+#define QC_NO_EOF_BLOCK 16
+#define QC_FAIL_CLOSE   32
+
+static void usage_quickcheck(FILE *write_to)
+{
+    fprintf(write_to,
+"Usage: samtools quickcheck [options] <input> [...]\n"
+"Options:\n"
+"  -v              verbose output (repeat for more verbosity)\n"
+"  -q              suppress warning messages\n"
+"  -u              unmapped input (do not require targets in header)\n"
+"\n"
+"Notes:\n"
+"\n"
+"1. By default quickcheck will emit a warning message if and only if a file\n"
+"   fails the checks, in which case the exit status is non-zero.  Under normal\n"
+"   behaviour with valid data it will be silent and has a zero exit status.\n"
+"   The warning messages are purely for manual inspection and should not be \n"
+"   parsed by scripts.\n"
+"\n"
+"2. In order to use this command programmatically, you should check its exit\n"
+"   status.  One way to use quickcheck might be as a check that all BAM files in\n"
+"   a directory are okay:\n"
+"\n"
+"\tsamtools quickcheck *.bam && echo 'all ok' \\\n"
+"\t   || echo 'fail!'\n"
+"\n"
+"   The first level of verbosity lists only files that fail to samtools_stdout.\n"
+"   To obtain a parsable list of files that have failed, use this option:\n"
+"\n"
+"\tsamtools quickcheck -qv *.bam > bad_bams.fofn \\\n"
+"\t   && echo 'all ok' \\\n"
+"\t   || echo 'some files failed check, see bad_bams.fofn'\n"
+    );
+}
+
+#define QC_ERR(state, v, msg, arg1)                                     \
+    file_state |= (state);                                              \
+    if (!quiet || verbose >= (v)) fprintf(samtools_stderr, (msg), (arg1))
+
+int main_quickcheck(int argc, char** argv)
+{
+    int verbose = 0, quiet = 0, unmapped = 0;
+    hts_verbose = 0;
+
+    const char* optstring = "vqu";
+    int opt;
+    while ((opt = getopt(argc, argv, optstring)) != -1) {
+        switch (opt) {
+        case 'u':
+            unmapped = 1;
+            break;
+        case 'v':
+            verbose++;
+            break;
+        case 'q':
+            quiet = 1;
+            break;
+        default:
+            usage_quickcheck(samtools_stderr);
+            return 1;
+        }
+    }
+
+    argc -= optind;
+    argv += optind;
+
+    if (argc < 1) {
+        usage_quickcheck(samtools_stdout);
+        return 1;
+    }
+
+    if (verbose >= 2) {
+        fprintf(samtools_stderr, "verbosity set to %d\n", verbose);
+    }
+
+    if (verbose >= 4) {
+        hts_verbose = 3;
+    }
+
+    int ret = 0;
+    int i;
+
+    for (i = 0; i < argc; i++) {
+        char* fn = argv[i];
+        int file_state = 0;
+
+        if (verbose >= 3) fprintf(samtools_stderr, "checking %s\n", fn);
+
+        // attempt to open
+        htsFile *hts_fp = hts_open(fn, "r");
+        if (hts_fp == NULL) {
+            QC_ERR(QC_FAIL_OPEN, 2, "%s could not be opened for reading.\n", fn);
+        }
+        else {
+            if (verbose >= 3) fprintf(samtools_stderr, "opened %s\n", fn);
+            // make sure we have sequence data
+            const htsFormat *fmt = hts_get_format(hts_fp);
+            if (fmt->category != sequence_data ) {
+                QC_ERR(QC_NOT_SEQUENCE, 2, "%s was not identified as sequence data.\n", fn);
+            }
+            else {
+                if (verbose >= 3) fprintf(samtools_stderr, "%s is sequence data\n", fn);
+                // check header
+                sam_hdr_t *header = sam_hdr_read(hts_fp);
+                if (header == NULL) {
+                    QC_ERR(QC_BAD_HEADER, 2, "%s caused an error whilst reading its header.\n", fn);
+                } else {
+                    if (!unmapped && sam_hdr_nref(header) <= 0) {
+                        QC_ERR(QC_BAD_HEADER, 2, "%s had no targets in header.\n", fn);
+                    }
+                    else {
+                        if (verbose >= 3) fprintf(samtools_stderr, "%s has %d targets in header.\n", fn, sam_hdr_nref(header));
+                    }
+                    sam_hdr_destroy(header);
+                }
+            }
+            // check EOF on formats that support this
+            int ret;
+            if ((ret = hts_check_EOF(hts_fp)) < 0) {
+                QC_ERR(QC_NO_EOF_BLOCK, 2, "%s caused an error whilst checking for EOF block.\n", fn);
+           }
+            else {
+                switch (ret) {
+                    case 0:
+                        QC_ERR(QC_NO_EOF_BLOCK, 2, "%s was missing EOF block when one should be present.\n", fn);
+                        break;
+                    case 1:
+                        if (verbose >= 3) fprintf(samtools_stderr, "%s has good EOF block.\n", fn);
+                        break;
+                    case 2:
+                        if (verbose >= 3) fprintf(samtools_stderr, "%s cannot be checked for EOF block as it is not seekable.\n", fn);
+                        break;
+                    case 3:
+                        if (verbose >= 3) fprintf(samtools_stderr, "%s cannot be checked for EOF block because its filetype does not contain one.\n", fn);
+                        break;
+                }
+            }
+
+            if (hts_close(hts_fp) < 0) {
+                QC_ERR(QC_FAIL_CLOSE, 2, "%s did not close cleanly.\n", fn);
+            }
+        }
+
+        if (file_state > 0 && verbose >= 1) {
+            fprintf(samtools_stdout, "%s\n", fn);
+        }
+        ret |= file_state;
+    }
+
+    return ret;
+}
diff --git a/samtools/bam_reheader.c b/samtools/bam_reheader.c
new file mode 100644
index 0000000..0ad308a
--- /dev/null
+++ b/samtools/bam_reheader.c
@@ -0,0 +1,629 @@
+/*  bam_reheader.c -- reheader subcommand.
+
+    Copyright (C) 2010 Broad Institute.
+    Copyright (C) 2012-2019 Genome Research Ltd.
+
+    Author: Heng Li <lh3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <config.h>
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <assert.h>
+#include <getopt.h>
+#include <unistd.h>
+
+#include "htslib/bgzf.h"
+#include "htslib/sam.h"
+#include "htslib/hfile.h"
+#include "htslib/cram.h"
+#include "samtools.h"
+
+#define BUF_SIZE 0x10000
+
+/*
+ * Reads a file and outputs a new BAM file to fd with 'h' replaced as
+ * the header.    No checks are made to the validity.
+ */
+int bam_reheader(BGZF *in, sam_hdr_t *h, int fd,
+                 const char *arg_list, int no_pg, int skip_header)
+{
+    BGZF *fp = NULL;
+    ssize_t len;
+    uint8_t *buf = NULL;
+    sam_hdr_t *tmp;
+    if (!h)
+        return -1;
+
+    if (in->is_write) return -1;
+    buf = malloc(BUF_SIZE);
+    if (!buf) {
+        fprintf(stderr, "Out of memory\n");
+        return -1;
+    }
+
+    if (!skip_header) {
+        if ((tmp = bam_hdr_read(in)) == NULL) {
+            fprintf(stderr, "Couldn't read header\n");
+            goto fail;
+        }
+        sam_hdr_destroy(tmp);
+    }
+
+    fp = bgzf_fdopen(fd, "w");
+    if (!fp) {
+        print_error_errno("reheader", "Couldn't open output file");
+        goto fail;
+    }
+
+    if (!no_pg && sam_hdr_add_pg(h, "samtools",
+                           "VN", samtools_version(),
+                           arg_list ? "CL": NULL,
+                           arg_list ? arg_list : NULL,
+                           NULL) != 0)
+            goto fail;
+
+    if (bam_hdr_write(fp, h) < 0) {
+        print_error_errno("reheader", "Couldn't write header");
+        goto fail;
+    }
+    if (in->block_offset < in->block_length) {
+        if (bgzf_write(fp, (char *)in->uncompressed_block + in->block_offset, in->block_length - in->block_offset) < 0) goto write_fail;
+        if (bgzf_flush(fp) < 0) goto write_fail;
+    }
+    while ((len = bgzf_raw_read(in, buf, BUF_SIZE)) > 0) {
+        if (bgzf_raw_write(fp, buf, len) < 0) goto write_fail;
+    }
+    if (len < 0) {
+        fprintf(stderr, "[%s] Error reading input file\n", __func__);
+        goto fail;
+    }
+    free(buf);
+    fp->block_offset = in->block_offset = 0;
+    if (bgzf_close(fp) < 0) {
+        fprintf(stderr, "[%s] Error closing output file\n", __func__);
+        return -1;
+    }
+    return 0;
+
+ write_fail:
+    print_error_errno("reheader", "Error writing to output file");
+ fail:
+    bgzf_close(fp);
+    free(buf);
+    return -1;
+}
+
+/*
+ * Reads a file and outputs a new CRAM file to stdout with 'h'
+ * replaced as the header.  No checks are made to the validity.
+ *
+ * FIXME: error checking
+ */
+int cram_reheader(cram_fd *in, sam_hdr_t *h, const char *arg_list, int no_pg)
+{
+    htsFile *h_out = hts_open("-", "wc");
+    cram_fd *out = h_out->fp.cram;
+    cram_container *c = NULL;
+    int ret = -1;
+    if (!h)
+        return ret;
+
+    // Attempt to fill out a cram->refs[] array from @SQ headers
+    sam_hdr_t *cram_h = sam_hdr_dup(h);
+    if (!cram_h)
+        return -1;
+    cram_fd_set_header(out, cram_h);
+    if (!no_pg && sam_hdr_add_pg(cram_fd_get_header(out), "samtools",
+                           "VN", samtools_version(),
+                           arg_list ? "CL": NULL,
+                           arg_list ? arg_list : NULL,
+                           NULL))
+            goto err;
+
+    if (sam_hdr_write(h_out, cram_h) != 0)
+        goto err;
+    cram_set_option(out, CRAM_OPT_REFERENCE, NULL);
+
+    while ((c = cram_read_container(in))) {
+        int32_t i, num_blocks = cram_container_get_num_blocks(c);
+        if (cram_write_container(out, c) != 0)
+            goto err;
+
+        for (i = 0; i < num_blocks; i++) {
+            cram_block *blk = cram_read_block(in);
+            if (!blk || cram_write_block(out, blk) != 0) {
+                if (blk) cram_free_block(blk);
+                goto err;
+            }
+            cram_free_block(blk);
+        }
+        cram_free_container(c);
+    }
+
+    ret = 0;
+
+ err:
+    if (hts_close(h_out) != 0)
+        ret = -1;
+
+    return ret;
+}
+
+
+
+/*
+ * Reads a version 2 CRAM file and replaces the header in-place,
+ * provided the header is small enough to fit without growing the
+ * entire file.
+ *
+ * Version 2 format has an uncompressed SAM header with multiple nul
+ * termination bytes to permit inline header editing.
+ *
+ * Returns 0 on success;
+ *        -1 on general failure;
+ *        -2 on failure due to insufficient size
+ */
+int cram_reheader_inplace2(cram_fd *fd, sam_hdr_t *h, const char *arg_list,
+                          int no_pg)
+{
+    cram_container *c = NULL;
+    cram_block *b = NULL;
+    sam_hdr_t *cram_h = NULL;
+    off_t start;
+    int ret = -1;
+    if (!h)
+        goto err;
+
+    if (cram_major_vers(fd) < 2 ||
+        cram_major_vers(fd) > 3) {
+        fprintf(stderr, "[%s] unsupported CRAM version %d\n", __func__,
+                cram_major_vers(fd));
+        goto err;
+    }
+
+    cram_h = sam_hdr_dup(h);
+    if (!cram_h)
+        goto err;
+
+    if (!no_pg && sam_hdr_add_pg(cram_h, "samtools", "VN", samtools_version(),
+                                 arg_list ? "CL": NULL,
+                                 arg_list ? arg_list : NULL,
+                                 NULL))
+        goto err;
+
+    int header_len = sam_hdr_length(cram_h);
+    /* Fix M5 strings? Maybe out of scope for this tool */
+
+    // Load the existing header
+    if ((start = hseek(cram_fd_get_fp(fd), 26, SEEK_SET)) != 26)
+        goto err;
+
+    if (!(c = cram_read_container(fd)))
+        goto err;
+
+    // Version 2.1 has a single uncompressed block which is nul
+    // terminated with many nuls to permit growth.
+    //
+    // So load old block and keep all contents identical bar the
+    // header text itself
+    if (!(b = cram_read_block(fd)))
+        goto err;
+
+    if (cram_block_get_uncomp_size(b) < header_len+4) {
+        fprintf(stderr, "New header will not fit. Use non-inplace version (%d > %d)\n",
+                header_len+4, cram_block_get_uncomp_size(b));
+        ret = -2;
+        goto err;
+    }
+
+    cram_block_set_offset(b, 0);   // rewind block
+    int32_put_blk(b, header_len);
+    cram_block_append(b, (void *)sam_hdr_str(cram_h), header_len);
+    // Zero the remaining block
+    memset((char *)cram_block_get_data(b)+cram_block_get_offset(b), 0,
+           cram_block_get_uncomp_size(b) - cram_block_get_offset(b));
+    // Make sure all sizes and byte-offsets are consistent after memset
+    cram_block_set_offset(b, cram_block_get_uncomp_size(b));
+    cram_block_set_comp_size(b, cram_block_get_uncomp_size(b));
+
+    if (hseek(cram_fd_get_fp(fd), start, SEEK_SET) != start)
+        goto err;
+
+    if (cram_write_container(fd, c) == -1)
+        goto err;
+
+    if (cram_write_block(fd, b) == -1)
+        goto err;
+
+    ret = 0;
+ err:
+    if (c) cram_free_container(c);
+    if (b) cram_free_block(b);
+    if (cram_h) sam_hdr_destroy(cram_h);
+
+    return ret;
+}
+
+
+/*
+ * Reads a version 3 CRAM file and replaces the header in-place,
+ * provided the header is small enough to fit without growing the
+ * entire file.
+ *
+ * Version 3 format has a SAM header held as an (optionally)
+ * compressed block within the header container.  Additional
+ * uncompressed blocks or simply unallocated space (the difference
+ * between total block sizes and the container size) are used to
+ * provide room for growth or contraction of the compressed header.
+ *
+ * Returns 0 on success;
+ *        -1 on general failure;
+ *        -2 on failure due to insufficient size
+ */
+int cram_reheader_inplace3(cram_fd *fd, sam_hdr_t *h, const char *arg_list,
+                          int no_pg)
+{
+    cram_container *c = NULL;
+    cram_block *b = NULL;
+    sam_hdr_t *cram_h = NULL;
+    off_t start, sz, end;
+    int container_sz, max_container_sz;
+    char *buf = NULL;
+    int ret = -1;
+    if (!h)
+        goto err;
+
+    if (cram_major_vers(fd) < 2 ||
+        cram_major_vers(fd) > 3) {
+        fprintf(stderr, "[%s] unsupported CRAM version %d\n", __func__,
+                cram_major_vers(fd));
+        goto err;
+    }
+
+    cram_h = sam_hdr_dup(h);
+    if (!cram_h)
+        goto err;
+
+    if (!no_pg && sam_hdr_add_pg(cram_h, "samtools", "VN", samtools_version(),
+                                 arg_list ? "CL": NULL,
+                                 arg_list ? arg_list : NULL,
+                                 NULL))
+        goto err;
+
+    int header_len = sam_hdr_length(cram_h);
+    /* Fix M5 strings? Maybe out of scope for this tool */
+
+    // Find current size of SAM header block
+    if ((start = hseek(cram_fd_get_fp(fd), 26, SEEK_SET)) != 26)
+        goto err;
+
+    if (!(c = cram_read_container(fd)))
+        goto err;
+
+    // +5 allows num_landmarks to increase from 0 to 1 (Cramtools)
+    max_container_sz = cram_container_size(c)+5;
+
+    sz = htell(cram_fd_get_fp(fd)) + cram_container_get_length(c) - start;
+    end = htell(cram_fd_get_fp(fd)) + cram_container_get_length(c);
+
+    // We force 1 block instead of (optionally) 2.  C CRAM
+    // implementations for v3 were writing 1 compressed block followed
+    // by 1 uncompressed block.  However this is tricky to deal with
+    // as changing block sizes can mean the block header also changes
+    // size due to itf8 and variable size integers.
+    //
+    // If we had 1 block, this doesn't change anything.
+    // If we had 2 blocks, the new container header will be smaller by
+    // 1+ bytes, requiring the cram_container_get_length(c) to be larger in value.
+    // However this is an int32 instead of itf8 so the container
+    // header structure stays the same size.  This means we can always
+    // reduce the number of blocks without running into size problems.
+    cram_container_set_num_blocks(c, 1);
+    int32_t *landmark;
+    int32_t num_landmarks;
+    landmark = cram_container_get_landmarks(c, &num_landmarks);
+    if (num_landmarks && landmark) {
+        num_landmarks = 1;
+        landmark[0] = 0;
+    } else {
+        num_landmarks = 0;
+    }
+    cram_container_set_landmarks(c, num_landmarks, landmark);
+
+    buf = malloc(max_container_sz);
+    container_sz = max_container_sz;
+    if (cram_store_container(fd, c, buf, &container_sz) != 0)
+        goto err;
+
+    if (!buf)
+        goto err;
+
+    // Proposed new length, but changing cram_container_get_length(c) may change the
+    // container_sz and thus the remainder (cram_container_get_length(c) itself).
+    cram_container_set_length(c, sz - container_sz);
+
+    int old_container_sz = container_sz;
+    container_sz = max_container_sz;
+    if (cram_store_container(fd, c, buf, &container_sz) != 0)
+        goto err;
+
+    if (old_container_sz != container_sz) {
+        fprintf(stderr, "Quirk of fate makes this troublesome! "
+                "Please use non-inplace version.\n");
+        goto err;
+    }
+
+
+
+    // Version 3.0 supports compressed header
+    b = cram_new_block(FILE_HEADER, 0);
+    int32_put_blk(b, header_len);
+    cram_block_append(b, (void *)sam_hdr_str(cram_h), header_len);
+    cram_block_update_size(b);
+
+    cram_compress_block(fd, b, NULL, -1, 9);
+
+    if (hseek(cram_fd_get_fp(fd), 26, SEEK_SET) != 26)
+        goto err;
+
+    if (cram_block_size(b) > cram_container_get_length(c)) {
+        fprintf(stderr, "New header will not fit. Use non-inplace version"
+                " (%d > %d)\n",
+                (int)cram_block_size(b), cram_container_get_length(c));
+        ret = -2;
+        goto err;
+    }
+
+    if (cram_write_container(fd, c) == -1)
+        goto err;
+
+    if (cram_write_block(fd, b) == -1)
+        goto err;
+
+    // Blank out the remainder
+    int rsz = end - htell(cram_fd_get_fp(fd));
+    assert(rsz >= 0);
+    if (rsz) {
+        char *rem = calloc(1, rsz);
+        ret = hwrite(cram_fd_get_fp(fd), rem, rsz) == rsz ? 0 : -1;
+        free(rem);
+    }
+
+ err:
+    if (c) cram_free_container(c);
+    if (buf) free(buf);
+    if (b) cram_free_block(b);
+    if (cram_h) sam_hdr_destroy(cram_h);
+
+    return ret;
+}
+
+int cram_reheader_inplace(cram_fd *fd, sam_hdr_t *h, const char *arg_list,
+                         int no_pg)
+{
+    switch (cram_major_vers(fd)) {
+    case 2: return cram_reheader_inplace2(fd, h, arg_list, no_pg);
+    case 3: return cram_reheader_inplace3(fd, h, arg_list, no_pg);
+    default:
+        fprintf(stderr, "[%s] unsupported CRAM version %d\n", __func__,
+                cram_major_vers(fd));
+        return -1;
+    }
+}
+
+static void usage(FILE *fp, int ret) {
+    fprintf(fp,
+           "Usage: samtools reheader [-P] in.header.sam in.bam > out.bam\n"
+           "   or  samtools reheader [-P] -i in.header.sam file.cram\n"
+           "   or  samtools reheader -c CMD in.bam\n"
+           "   or  samtools reheader -c CMD in.cram\n"
+           "\n"
+           "Options:\n"
+           "    -P, --no-PG         Do not generate a @PG header line.\n"
+           "    -i, --in-place      Modify the CRAM file directly, if possible.\n"
+           "                        (Defaults to outputting to stdout.)\n"
+           "    -c, --command CMD   Pass the header in SAM format to external program CMD.\n");
+    exit(ret);
+}
+
+static sam_hdr_t* external_reheader(samFile* in, const char* external) {
+    char *command = NULL;
+    sam_hdr_t* h = NULL;
+    sam_hdr_t* ih = sam_hdr_read(in);
+    if (ih == NULL) {
+        fprintf(stderr, "[%s] failed to read the header for '%s'.\n", __func__, in->fn);
+        return NULL;
+    }
+    char tmp_fn[] = "reheaderXXXXXX";
+    int tmp_fd = mkstemp(tmp_fn);
+    if (tmp_fd < 0) {
+        print_error_errno("reheader", "fail to open temp file '%s'", tmp_fn);
+        return NULL;
+    }
+    hFILE* tmp_hf = hdopen(tmp_fd, "w");
+    if (!tmp_hf) {
+        fprintf(stderr, "[%s] failed to convert to hFILE.\n", __func__);
+        goto cleanup;
+    }
+    samFile* tmp_sf = hts_hopen(tmp_hf, tmp_fn, "w");
+    if (!tmp_sf) {
+        fprintf(stderr, "[%s] failed to convert to samFile.\n", __func__);
+        goto cleanup;
+    }
+    if (-1 == sam_hdr_write(tmp_sf, ih)) {
+        fprintf(stderr, "[%s] failed to write the header to the temp file.\n", __func__);
+        goto cleanup;
+    }
+    sam_close(tmp_sf);
+    sam_hdr_destroy(ih);
+    int comm_len = strlen(external) + strlen(tmp_fn) + 8;
+    command = calloc(comm_len, 1);
+    if (!command || snprintf(command, comm_len, "( %s ) < %s", external, tmp_fn) != comm_len - 1) {
+        fprintf(stderr, "[%s] failed to create command string.\n", __func__);
+        goto cleanup;
+    }
+    FILE* nh = popen(command, "r");
+    if (!nh) {
+        print_error_errno("reheader", "[%s] failed to run external command '%s'.\n", __func__, command);
+        goto cleanup;
+    }
+
+    int nh_fd = dup(fileno(nh));
+    if (nh_fd < 0) {
+        fprintf(stderr, "[%s] failed to get the file descriptor.\n", __func__);
+        goto cleanup;
+    }
+    hFILE* nh_hf = hdopen(nh_fd, "r");
+    if (!nh_hf) {
+        fprintf(stderr, "[%s] failed to convert to hFILE.\n", __func__);
+        goto cleanup;
+    }
+    samFile* nh_sf = hts_hopen(nh_hf, tmp_fn, "r");
+    if (!nh_sf) {
+        fprintf(stderr, "[%s] failed to convert to samFile.\n", __func__);
+        goto cleanup;
+    }
+
+    h = sam_hdr_read(nh_sf);
+    sam_close(nh_sf);
+    if (h == NULL) {
+        fprintf(stderr, "[%s] failed to read the header from the temp file.\n", __func__);
+    }
+    int res = pclose(nh);
+    if (res != 0) {
+        if (res < 0) {
+            print_error_errno("reheader",
+                              "Error on closing pipe from command '%s'.\n",
+                              command);
+        } else {
+            print_error("reheader",
+                        "Non-zero exit code returned by command '%s'\n",
+                        command);
+        }
+        if (h) sam_hdr_destroy(h);
+        h = NULL;
+    }
+cleanup:
+    free(command);
+    if (unlink(tmp_fn) != 0) {
+        print_error_errno("reheader", "failed to remove the temp file '%s'", tmp_fn);
+    }
+
+    return h;
+}
+
+int main_reheader(int argc, char *argv[])
+{
+    int inplace = 0, r, no_pg = 0, c, skip_header = 0;
+    sam_hdr_t *h;
+    samFile *in;
+    char *arg_list = NULL, *external = NULL;
+
+    static const struct option lopts[] = {
+        {"help",     no_argument, NULL, 'h'},
+        {"in-place", no_argument, NULL, 'i'},
+        {"no-PG",    no_argument, NULL, 'P'},
+        {"command", required_argument, NULL, 'c'},
+        {NULL, 0, NULL, 0}
+    };
+
+    while ((c = getopt_long(argc, argv, "hiPc:", lopts, NULL)) >= 0) {
+        switch (c) {
+        case 'P': no_pg = 1; break;
+        case 'i': inplace = 1; break;
+        case 'c': external = optarg; break;
+        case 'h': usage(stdout, 0); break;
+        default:
+            fprintf(stderr, "Invalid option '%c'\n", c);
+            usage(stderr, 1);
+        }
+    }
+
+    if ((argc - optind != 2 || external) && (argc - optind != 1 || !external))
+        usage(stderr, 1);
+
+    if (!no_pg && !(arg_list = stringify_argv(argc+1, argv-1))) {
+         print_error("reheader", "failed to create arg_list");
+         return 1;
+     }
+
+    if (external) {
+        skip_header = 1;
+        in = sam_open(argv[optind], inplace?"r+":"r");
+        if (in == 0) {
+            print_error_errno("reheader", "fail to open file '%s'", argv[optind]);
+            return 1;
+        }
+
+        h = external_reheader(in, external);
+        if (h == NULL) {
+            fprintf(stderr, "[%s] failed to read the header from '%s'.\n", __func__, external);
+            sam_close(in);
+            return 1;
+        }
+    } else { // read the header from a separate file
+        samFile *fph = sam_open(argv[optind], "r");
+        if (fph == 0) {
+            print_error_errno("reheader", "fail to read the header from '%s'", argv[optind]);
+            return 1;
+        }
+        h = sam_hdr_read(fph);
+        sam_close(fph);
+        if (h == NULL) {
+            fprintf(stderr, "[%s] failed to read the header for '%s'.\n",
+                    __func__, argv[1]);
+            return 1;
+        }
+        in = sam_open(argv[optind+1], inplace?"r+":"r");
+        if (in == 0) {
+            print_error_errno("reheader", "fail to open file '%s'", argv[optind+1]);
+            return 1;
+        }
+    }
+
+    if (hts_get_format(in)->format == bam) {
+        if (inplace) {
+            print_error("reheader", "cannot reheader BAM '%s' in-place", argv[optind+1]);
+            r = -1;
+        } else {
+            r = bam_reheader(in->fp.bgzf, h, fileno(stdout), arg_list, no_pg, skip_header);
+        }
+    } else if (hts_get_format(in)->format == cram) {
+        if (inplace)
+            r = cram_reheader_inplace(in->fp.cram, h, arg_list, no_pg);
+        else
+            r = cram_reheader(in->fp.cram, h, arg_list, no_pg);
+    } else {
+        print_error("reheader", "input file '%s' must be BAM or CRAM", argv[optind+1]);
+        r = -1;
+    }
+
+    if (sam_close(in) != 0)
+        r = -1;
+
+    sam_hdr_destroy(h);
+
+    if (arg_list)
+        free(arg_list);
+
+    return -r;
+}
diff --git a/samtools/bam_reheader.c.pysam.c b/samtools/bam_reheader.c.pysam.c
new file mode 100644
index 0000000..22a6cd9
--- /dev/null
+++ b/samtools/bam_reheader.c.pysam.c
@@ -0,0 +1,631 @@
+#include "samtools.pysam.h"
+
+/*  bam_reheader.c -- reheader subcommand.
+
+    Copyright (C) 2010 Broad Institute.
+    Copyright (C) 2012-2019 Genome Research Ltd.
+
+    Author: Heng Li <lh3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <config.h>
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <assert.h>
+#include <getopt.h>
+#include <unistd.h>
+
+#include "htslib/bgzf.h"
+#include "htslib/sam.h"
+#include "htslib/hfile.h"
+#include "htslib/cram.h"
+#include "samtools.h"
+
+#define BUF_SIZE 0x10000
+
+/*
+ * Reads a file and outputs a new BAM file to fd with 'h' replaced as
+ * the header.    No checks are made to the validity.
+ */
+int bam_reheader(BGZF *in, sam_hdr_t *h, int fd,
+                 const char *arg_list, int no_pg, int skip_header)
+{
+    BGZF *fp = NULL;
+    ssize_t len;
+    uint8_t *buf = NULL;
+    sam_hdr_t *tmp;
+    if (!h)
+        return -1;
+
+    if (in->is_write) return -1;
+    buf = malloc(BUF_SIZE);
+    if (!buf) {
+        fprintf(samtools_stderr, "Out of memory\n");
+        return -1;
+    }
+
+    if (!skip_header) {
+        if ((tmp = bam_hdr_read(in)) == NULL) {
+            fprintf(samtools_stderr, "Couldn't read header\n");
+            goto fail;
+        }
+        sam_hdr_destroy(tmp);
+    }
+
+    fp = bgzf_fdopen(fd, "w");
+    if (!fp) {
+        print_error_errno("reheader", "Couldn't open output file");
+        goto fail;
+    }
+
+    if (!no_pg && sam_hdr_add_pg(h, "samtools",
+                           "VN", samtools_version(),
+                           arg_list ? "CL": NULL,
+                           arg_list ? arg_list : NULL,
+                           NULL) != 0)
+            goto fail;
+
+    if (bam_hdr_write(fp, h) < 0) {
+        print_error_errno("reheader", "Couldn't write header");
+        goto fail;
+    }
+    if (in->block_offset < in->block_length) {
+        if (bgzf_write(fp, (char *)in->uncompressed_block + in->block_offset, in->block_length - in->block_offset) < 0) goto write_fail;
+        if (bgzf_flush(fp) < 0) goto write_fail;
+    }
+    while ((len = bgzf_raw_read(in, buf, BUF_SIZE)) > 0) {
+        if (bgzf_raw_write(fp, buf, len) < 0) goto write_fail;
+    }
+    if (len < 0) {
+        fprintf(samtools_stderr, "[%s] Error reading input file\n", __func__);
+        goto fail;
+    }
+    free(buf);
+    fp->block_offset = in->block_offset = 0;
+    if (bgzf_close(fp) < 0) {
+        fprintf(samtools_stderr, "[%s] Error closing output file\n", __func__);
+        return -1;
+    }
+    return 0;
+
+ write_fail:
+    print_error_errno("reheader", "Error writing to output file");
+ fail:
+    bgzf_close(fp);
+    free(buf);
+    return -1;
+}
+
+/*
+ * Reads a file and outputs a new CRAM file to samtools_stdout with 'h'
+ * replaced as the header.  No checks are made to the validity.
+ *
+ * FIXME: error checking
+ */
+int cram_reheader(cram_fd *in, sam_hdr_t *h, const char *arg_list, int no_pg)
+{
+    htsFile *h_out = hts_open("-", "wc");
+    cram_fd *out = h_out->fp.cram;
+    cram_container *c = NULL;
+    int ret = -1;
+    if (!h)
+        return ret;
+
+    // Attempt to fill out a cram->refs[] array from @SQ headers
+    sam_hdr_t *cram_h = sam_hdr_dup(h);
+    if (!cram_h)
+        return -1;
+    cram_fd_set_header(out, cram_h);
+    if (!no_pg && sam_hdr_add_pg(cram_fd_get_header(out), "samtools",
+                           "VN", samtools_version(),
+                           arg_list ? "CL": NULL,
+                           arg_list ? arg_list : NULL,
+                           NULL))
+            goto err;
+
+    if (sam_hdr_write(h_out, cram_h) != 0)
+        goto err;
+    cram_set_option(out, CRAM_OPT_REFERENCE, NULL);
+
+    while ((c = cram_read_container(in))) {
+        int32_t i, num_blocks = cram_container_get_num_blocks(c);
+        if (cram_write_container(out, c) != 0)
+            goto err;
+
+        for (i = 0; i < num_blocks; i++) {
+            cram_block *blk = cram_read_block(in);
+            if (!blk || cram_write_block(out, blk) != 0) {
+                if (blk) cram_free_block(blk);
+                goto err;
+            }
+            cram_free_block(blk);
+        }
+        cram_free_container(c);
+    }
+
+    ret = 0;
+
+ err:
+    if (hts_close(h_out) != 0)
+        ret = -1;
+
+    return ret;
+}
+
+
+
+/*
+ * Reads a version 2 CRAM file and replaces the header in-place,
+ * provided the header is small enough to fit without growing the
+ * entire file.
+ *
+ * Version 2 format has an uncompressed SAM header with multiple nul
+ * termination bytes to permit inline header editing.
+ *
+ * Returns 0 on success;
+ *        -1 on general failure;
+ *        -2 on failure due to insufficient size
+ */
+int cram_reheader_inplace2(cram_fd *fd, sam_hdr_t *h, const char *arg_list,
+                          int no_pg)
+{
+    cram_container *c = NULL;
+    cram_block *b = NULL;
+    sam_hdr_t *cram_h = NULL;
+    off_t start;
+    int ret = -1;
+    if (!h)
+        goto err;
+
+    if (cram_major_vers(fd) < 2 ||
+        cram_major_vers(fd) > 3) {
+        fprintf(samtools_stderr, "[%s] unsupported CRAM version %d\n", __func__,
+                cram_major_vers(fd));
+        goto err;
+    }
+
+    cram_h = sam_hdr_dup(h);
+    if (!cram_h)
+        goto err;
+
+    if (!no_pg && sam_hdr_add_pg(cram_h, "samtools", "VN", samtools_version(),
+                                 arg_list ? "CL": NULL,
+                                 arg_list ? arg_list : NULL,
+                                 NULL))
+        goto err;
+
+    int header_len = sam_hdr_length(cram_h);
+    /* Fix M5 strings? Maybe out of scope for this tool */
+
+    // Load the existing header
+    if ((start = hseek(cram_fd_get_fp(fd), 26, SEEK_SET)) != 26)
+        goto err;
+
+    if (!(c = cram_read_container(fd)))
+        goto err;
+
+    // Version 2.1 has a single uncompressed block which is nul
+    // terminated with many nuls to permit growth.
+    //
+    // So load old block and keep all contents identical bar the
+    // header text itself
+    if (!(b = cram_read_block(fd)))
+        goto err;
+
+    if (cram_block_get_uncomp_size(b) < header_len+4) {
+        fprintf(samtools_stderr, "New header will not fit. Use non-inplace version (%d > %d)\n",
+                header_len+4, cram_block_get_uncomp_size(b));
+        ret = -2;
+        goto err;
+    }
+
+    cram_block_set_offset(b, 0);   // rewind block
+    int32_put_blk(b, header_len);
+    cram_block_append(b, (void *)sam_hdr_str(cram_h), header_len);
+    // Zero the remaining block
+    memset((char *)cram_block_get_data(b)+cram_block_get_offset(b), 0,
+           cram_block_get_uncomp_size(b) - cram_block_get_offset(b));
+    // Make sure all sizes and byte-offsets are consistent after memset
+    cram_block_set_offset(b, cram_block_get_uncomp_size(b));
+    cram_block_set_comp_size(b, cram_block_get_uncomp_size(b));
+
+    if (hseek(cram_fd_get_fp(fd), start, SEEK_SET) != start)
+        goto err;
+
+    if (cram_write_container(fd, c) == -1)
+        goto err;
+
+    if (cram_write_block(fd, b) == -1)
+        goto err;
+
+    ret = 0;
+ err:
+    if (c) cram_free_container(c);
+    if (b) cram_free_block(b);
+    if (cram_h) sam_hdr_destroy(cram_h);
+
+    return ret;
+}
+
+
+/*
+ * Reads a version 3 CRAM file and replaces the header in-place,
+ * provided the header is small enough to fit without growing the
+ * entire file.
+ *
+ * Version 3 format has a SAM header held as an (optionally)
+ * compressed block within the header container.  Additional
+ * uncompressed blocks or simply unallocated space (the difference
+ * between total block sizes and the container size) are used to
+ * provide room for growth or contraction of the compressed header.
+ *
+ * Returns 0 on success;
+ *        -1 on general failure;
+ *        -2 on failure due to insufficient size
+ */
+int cram_reheader_inplace3(cram_fd *fd, sam_hdr_t *h, const char *arg_list,
+                          int no_pg)
+{
+    cram_container *c = NULL;
+    cram_block *b = NULL;
+    sam_hdr_t *cram_h = NULL;
+    off_t start, sz, end;
+    int container_sz, max_container_sz;
+    char *buf = NULL;
+    int ret = -1;
+    if (!h)
+        goto err;
+
+    if (cram_major_vers(fd) < 2 ||
+        cram_major_vers(fd) > 3) {
+        fprintf(samtools_stderr, "[%s] unsupported CRAM version %d\n", __func__,
+                cram_major_vers(fd));
+        goto err;
+    }
+
+    cram_h = sam_hdr_dup(h);
+    if (!cram_h)
+        goto err;
+
+    if (!no_pg && sam_hdr_add_pg(cram_h, "samtools", "VN", samtools_version(),
+                                 arg_list ? "CL": NULL,
+                                 arg_list ? arg_list : NULL,
+                                 NULL))
+        goto err;
+
+    int header_len = sam_hdr_length(cram_h);
+    /* Fix M5 strings? Maybe out of scope for this tool */
+
+    // Find current size of SAM header block
+    if ((start = hseek(cram_fd_get_fp(fd), 26, SEEK_SET)) != 26)
+        goto err;
+
+    if (!(c = cram_read_container(fd)))
+        goto err;
+
+    // +5 allows num_landmarks to increase from 0 to 1 (Cramtools)
+    max_container_sz = cram_container_size(c)+5;
+
+    sz = htell(cram_fd_get_fp(fd)) + cram_container_get_length(c) - start;
+    end = htell(cram_fd_get_fp(fd)) + cram_container_get_length(c);
+
+    // We force 1 block instead of (optionally) 2.  C CRAM
+    // implementations for v3 were writing 1 compressed block followed
+    // by 1 uncompressed block.  However this is tricky to deal with
+    // as changing block sizes can mean the block header also changes
+    // size due to itf8 and variable size integers.
+    //
+    // If we had 1 block, this doesn't change anything.
+    // If we had 2 blocks, the new container header will be smaller by
+    // 1+ bytes, requiring the cram_container_get_length(c) to be larger in value.
+    // However this is an int32 instead of itf8 so the container
+    // header structure stays the same size.  This means we can always
+    // reduce the number of blocks without running into size problems.
+    cram_container_set_num_blocks(c, 1);
+    int32_t *landmark;
+    int32_t num_landmarks;
+    landmark = cram_container_get_landmarks(c, &num_landmarks);
+    if (num_landmarks && landmark) {
+        num_landmarks = 1;
+        landmark[0] = 0;
+    } else {
+        num_landmarks = 0;
+    }
+    cram_container_set_landmarks(c, num_landmarks, landmark);
+
+    buf = malloc(max_container_sz);
+    container_sz = max_container_sz;
+    if (cram_store_container(fd, c, buf, &container_sz) != 0)
+        goto err;
+
+    if (!buf)
+        goto err;
+
+    // Proposed new length, but changing cram_container_get_length(c) may change the
+    // container_sz and thus the remainder (cram_container_get_length(c) itself).
+    cram_container_set_length(c, sz - container_sz);
+
+    int old_container_sz = container_sz;
+    container_sz = max_container_sz;
+    if (cram_store_container(fd, c, buf, &container_sz) != 0)
+        goto err;
+
+    if (old_container_sz != container_sz) {
+        fprintf(samtools_stderr, "Quirk of fate makes this troublesome! "
+                "Please use non-inplace version.\n");
+        goto err;
+    }
+
+
+
+    // Version 3.0 supports compressed header
+    b = cram_new_block(FILE_HEADER, 0);
+    int32_put_blk(b, header_len);
+    cram_block_append(b, (void *)sam_hdr_str(cram_h), header_len);
+    cram_block_update_size(b);
+
+    cram_compress_block(fd, b, NULL, -1, 9);
+
+    if (hseek(cram_fd_get_fp(fd), 26, SEEK_SET) != 26)
+        goto err;
+
+    if (cram_block_size(b) > cram_container_get_length(c)) {
+        fprintf(samtools_stderr, "New header will not fit. Use non-inplace version"
+                " (%d > %d)\n",
+                (int)cram_block_size(b), cram_container_get_length(c));
+        ret = -2;
+        goto err;
+    }
+
+    if (cram_write_container(fd, c) == -1)
+        goto err;
+
+    if (cram_write_block(fd, b) == -1)
+        goto err;
+
+    // Blank out the remainder
+    int rsz = end - htell(cram_fd_get_fp(fd));
+    assert(rsz >= 0);
+    if (rsz) {
+        char *rem = calloc(1, rsz);
+        ret = hwrite(cram_fd_get_fp(fd), rem, rsz) == rsz ? 0 : -1;
+        free(rem);
+    }
+
+ err:
+    if (c) cram_free_container(c);
+    if (buf) free(buf);
+    if (b) cram_free_block(b);
+    if (cram_h) sam_hdr_destroy(cram_h);
+
+    return ret;
+}
+
+int cram_reheader_inplace(cram_fd *fd, sam_hdr_t *h, const char *arg_list,
+                         int no_pg)
+{
+    switch (cram_major_vers(fd)) {
+    case 2: return cram_reheader_inplace2(fd, h, arg_list, no_pg);
+    case 3: return cram_reheader_inplace3(fd, h, arg_list, no_pg);
+    default:
+        fprintf(samtools_stderr, "[%s] unsupported CRAM version %d\n", __func__,
+                cram_major_vers(fd));
+        return -1;
+    }
+}
+
+static void usage(FILE *fp, int ret) {
+    fprintf(fp,
+           "Usage: samtools reheader [-P] in.header.sam in.bam > out.bam\n"
+           "   or  samtools reheader [-P] -i in.header.sam file.cram\n"
+           "   or  samtools reheader -c CMD in.bam\n"
+           "   or  samtools reheader -c CMD in.cram\n"
+           "\n"
+           "Options:\n"
+           "    -P, --no-PG         Do not generate a @PG header line.\n"
+           "    -i, --in-place      Modify the CRAM file directly, if possible.\n"
+           "                        (Defaults to outputting to samtools_stdout.)\n"
+           "    -c, --command CMD   Pass the header in SAM format to external program CMD.\n");
+    samtools_exit(ret);
+}
+
+static sam_hdr_t* external_reheader(samFile* in, const char* external) {
+    char *command = NULL;
+    sam_hdr_t* h = NULL;
+    sam_hdr_t* ih = sam_hdr_read(in);
+    if (ih == NULL) {
+        fprintf(samtools_stderr, "[%s] failed to read the header for '%s'.\n", __func__, in->fn);
+        return NULL;
+    }
+    char tmp_fn[] = "reheaderXXXXXX";
+    int tmp_fd = mkstemp(tmp_fn);
+    if (tmp_fd < 0) {
+        print_error_errno("reheader", "fail to open temp file '%s'", tmp_fn);
+        return NULL;
+    }
+    hFILE* tmp_hf = hdopen(tmp_fd, "w");
+    if (!tmp_hf) {
+        fprintf(samtools_stderr, "[%s] failed to convert to hFILE.\n", __func__);
+        goto cleanup;
+    }
+    samFile* tmp_sf = hts_hopen(tmp_hf, tmp_fn, "w");
+    if (!tmp_sf) {
+        fprintf(samtools_stderr, "[%s] failed to convert to samFile.\n", __func__);
+        goto cleanup;
+    }
+    if (-1 == sam_hdr_write(tmp_sf, ih)) {
+        fprintf(samtools_stderr, "[%s] failed to write the header to the temp file.\n", __func__);
+        goto cleanup;
+    }
+    sam_close(tmp_sf);
+    sam_hdr_destroy(ih);
+    int comm_len = strlen(external) + strlen(tmp_fn) + 8;
+    command = calloc(comm_len, 1);
+    if (!command || snprintf(command, comm_len, "( %s ) < %s", external, tmp_fn) != comm_len - 1) {
+        fprintf(samtools_stderr, "[%s] failed to create command string.\n", __func__);
+        goto cleanup;
+    }
+    FILE* nh = popen(command, "r");
+    if (!nh) {
+        print_error_errno("reheader", "[%s] failed to run external command '%s'.\n", __func__, command);
+        goto cleanup;
+    }
+
+    int nh_fd = dup(fileno(nh));
+    if (nh_fd < 0) {
+        fprintf(samtools_stderr, "[%s] failed to get the file descriptor.\n", __func__);
+        goto cleanup;
+    }
+    hFILE* nh_hf = hdopen(nh_fd, "r");
+    if (!nh_hf) {
+        fprintf(samtools_stderr, "[%s] failed to convert to hFILE.\n", __func__);
+        goto cleanup;
+    }
+    samFile* nh_sf = hts_hopen(nh_hf, tmp_fn, "r");
+    if (!nh_sf) {
+        fprintf(samtools_stderr, "[%s] failed to convert to samFile.\n", __func__);
+        goto cleanup;
+    }
+
+    h = sam_hdr_read(nh_sf);
+    sam_close(nh_sf);
+    if (h == NULL) {
+        fprintf(samtools_stderr, "[%s] failed to read the header from the temp file.\n", __func__);
+    }
+    int res = pclose(nh);
+    if (res != 0) {
+        if (res < 0) {
+            print_error_errno("reheader",
+                              "Error on closing pipe from command '%s'.\n",
+                              command);
+        } else {
+            print_error("reheader",
+                        "Non-zero exit code returned by command '%s'\n",
+                        command);
+        }
+        if (h) sam_hdr_destroy(h);
+        h = NULL;
+    }
+cleanup:
+    free(command);
+    if (unlink(tmp_fn) != 0) {
+        print_error_errno("reheader", "failed to remove the temp file '%s'", tmp_fn);
+    }
+
+    return h;
+}
+
+int main_reheader(int argc, char *argv[])
+{
+    int inplace = 0, r, no_pg = 0, c, skip_header = 0;
+    sam_hdr_t *h;
+    samFile *in;
+    char *arg_list = NULL, *external = NULL;
+
+    static const struct option lopts[] = {
+        {"help",     no_argument, NULL, 'h'},
+        {"in-place", no_argument, NULL, 'i'},
+        {"no-PG",    no_argument, NULL, 'P'},
+        {"command", required_argument, NULL, 'c'},
+        {NULL, 0, NULL, 0}
+    };
+
+    while ((c = getopt_long(argc, argv, "hiPc:", lopts, NULL)) >= 0) {
+        switch (c) {
+        case 'P': no_pg = 1; break;
+        case 'i': inplace = 1; break;
+        case 'c': external = optarg; break;
+        case 'h': usage(samtools_stdout, 0); break;
+        default:
+            fprintf(samtools_stderr, "Invalid option '%c'\n", c);
+            usage(samtools_stderr, 1);
+        }
+    }
+
+    if ((argc - optind != 2 || external) && (argc - optind != 1 || !external))
+        usage(samtools_stderr, 1);
+
+    if (!no_pg && !(arg_list = stringify_argv(argc+1, argv-1))) {
+         print_error("reheader", "failed to create arg_list");
+         return 1;
+     }
+
+    if (external) {
+        skip_header = 1;
+        in = sam_open(argv[optind], inplace?"r+":"r");
+        if (in == 0) {
+            print_error_errno("reheader", "fail to open file '%s'", argv[optind]);
+            return 1;
+        }
+
+        h = external_reheader(in, external);
+        if (h == NULL) {
+            fprintf(samtools_stderr, "[%s] failed to read the header from '%s'.\n", __func__, external);
+            sam_close(in);
+            return 1;
+        }
+    } else { // read the header from a separate file
+        samFile *fph = sam_open(argv[optind], "r");
+        if (fph == 0) {
+            print_error_errno("reheader", "fail to read the header from '%s'", argv[optind]);
+            return 1;
+        }
+        h = sam_hdr_read(fph);
+        sam_close(fph);
+        if (h == NULL) {
+            fprintf(samtools_stderr, "[%s] failed to read the header for '%s'.\n",
+                    __func__, argv[1]);
+            return 1;
+        }
+        in = sam_open(argv[optind+1], inplace?"r+":"r");
+        if (in == 0) {
+            print_error_errno("reheader", "fail to open file '%s'", argv[optind+1]);
+            return 1;
+        }
+    }
+
+    if (hts_get_format(in)->format == bam) {
+        if (inplace) {
+            print_error("reheader", "cannot reheader BAM '%s' in-place", argv[optind+1]);
+            r = -1;
+        } else {
+            r = bam_reheader(in->fp.bgzf, h, fileno(samtools_stdout), arg_list, no_pg, skip_header);
+        }
+    } else if (hts_get_format(in)->format == cram) {
+        if (inplace)
+            r = cram_reheader_inplace(in->fp.cram, h, arg_list, no_pg);
+        else
+            r = cram_reheader(in->fp.cram, h, arg_list, no_pg);
+    } else {
+        print_error("reheader", "input file '%s' must be BAM or CRAM", argv[optind+1]);
+        r = -1;
+    }
+
+    if (sam_close(in) != 0)
+        r = -1;
+
+    sam_hdr_destroy(h);
+
+    if (arg_list)
+        free(arg_list);
+
+    return -r;
+}
diff --git a/samtools/bam_rmdup.c b/samtools/bam_rmdup.c
new file mode 100644
index 0000000..293a140
--- /dev/null
+++ b/samtools/bam_rmdup.c
@@ -0,0 +1,325 @@
+/*  bam_rmdup.c -- duplicate read detection.
+
+    Copyright (C) 2009, 2015, 2016, 2019 Genome Research Ltd.
+    Portions copyright (C) 2009 Broad Institute.
+
+    Author: Heng Li <lh3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <config.h>
+
+#include <stdlib.h>
+#include <string.h>
+#include <stdio.h>
+#include <zlib.h>
+#include <unistd.h>
+#include "htslib/sam.h"
+#include "sam_opts.h"
+#include "samtools.h"
+#include "bam.h" // for bam_get_library
+
+typedef bam1_t *bam1_p;
+
+#include "htslib/khash.h"
+KHASH_SET_INIT_STR(name)
+KHASH_MAP_INIT_INT64(pos, bam1_p)
+
+#define BUFFER_SIZE 0x40000
+
+typedef struct {
+    uint64_t n_checked, n_removed;
+    khash_t(pos) *best_hash;
+} lib_aux_t;
+KHASH_MAP_INIT_STR(lib, lib_aux_t)
+
+typedef struct {
+    int n, max;
+    bam1_t **a;
+} tmp_stack_t;
+
+static inline void stack_insert(tmp_stack_t *stack, bam1_t *b)
+{
+    if (stack->n == stack->max) {
+        stack->max = stack->max? stack->max<<1 : 0x10000;
+        stack->a = (bam1_t**)realloc(stack->a, sizeof(bam1_t*) * stack->max);
+    }
+    stack->a[stack->n++] = b;
+}
+
+static inline int dump_best(tmp_stack_t *stack, samFile *out, sam_hdr_t *hdr)
+{
+    int i;
+    for (i = 0; i != stack->n; ++i) {
+        if (sam_write1(out, hdr, stack->a[i]) < 0) return -1;
+        bam_destroy1(stack->a[i]);
+        stack->a[i] = NULL;
+    }
+    stack->n = 0;
+    return 0;
+}
+
+static inline void clear_stack(tmp_stack_t *stack) {
+    int i;
+    if (!stack->a) return;
+    for (i = 0; i != stack->n; ++i) {
+        bam_destroy1(stack->a[i]);
+    }
+}
+
+static void clear_del_set(khash_t(name) *del_set)
+{
+    khint_t k;
+    for (k = kh_begin(del_set); k < kh_end(del_set); ++k)
+        if (kh_exist(del_set, k))
+            free((char*)kh_key(del_set, k));
+    kh_clear(name, del_set);
+}
+
+static lib_aux_t *get_aux(khash_t(lib) *aux, const char *lib)
+{
+    khint_t k = kh_get(lib, aux, lib);
+    if (k == kh_end(aux)) {
+        int ret;
+        char *p = strdup(lib);
+        lib_aux_t *q;
+        k = kh_put(lib, aux, p, &ret);
+        q = &kh_val(aux, k);
+        q->n_checked = q->n_removed = 0;
+        q->best_hash = kh_init(pos);
+        return q;
+    } else return &kh_val(aux, k);
+}
+
+static void clear_best(khash_t(lib) *aux, int max)
+{
+    khint_t k;
+    for (k = kh_begin(aux); k != kh_end(aux); ++k) {
+        if (kh_exist(aux, k)) {
+            lib_aux_t *q = &kh_val(aux, k);
+            if (kh_size(q->best_hash) >= max)
+                kh_clear(pos, q->best_hash);
+        }
+    }
+}
+
+static inline int sum_qual(const bam1_t *b)
+{
+    int i, q;
+    uint8_t *qual = bam_get_qual(b);
+    for (i = q = 0; i < b->core.l_qseq; ++i) q += qual[i];
+    return q;
+}
+
+int bam_rmdup_core(samFile *in, sam_hdr_t *hdr, samFile *out)
+{
+    bam1_t *b = NULL;
+    int last_tid = -1, last_pos = -1, r;
+    tmp_stack_t stack;
+    khint_t k;
+    khash_t(lib) *aux = NULL;
+    khash_t(name) *del_set = NULL;
+
+    memset(&stack, 0, sizeof(tmp_stack_t));
+    aux = kh_init(lib);
+    del_set = kh_init(name);
+    b = bam_init1();
+    if (!aux || !del_set || !b) {
+        perror(__func__);
+        goto fail;
+    }
+
+    kh_resize(name, del_set, 4 * BUFFER_SIZE);
+    while ((r = sam_read1(in, hdr, b)) >= 0) {
+        bam1_core_t *c = &b->core;
+        if (c->tid != last_tid || last_pos != c->pos) {
+            if (dump_best(&stack, out, hdr) < 0) goto write_fail; // write the result
+            clear_best(aux, BUFFER_SIZE);
+            if (c->tid != last_tid) {
+                clear_best(aux, 0);
+                if (kh_size(del_set)) { // check
+                    fprintf(stderr, "[bam_rmdup_core] %llu unmatched pairs\n", (long long)kh_size(del_set));
+                    clear_del_set(del_set);
+                }
+                if ((int)c->tid == -1) { // append unmapped reads
+                    if (sam_write1(out, hdr, b) < 0) goto write_fail;
+                    while ((r = sam_read1(in, hdr, b)) >= 0) {
+                        if (sam_write1(out, hdr, b) < 0) goto write_fail;
+                    }
+                    break;
+                }
+                last_tid = c->tid;
+                fprintf(stderr, "[bam_rmdup_core] processing reference %s...\n", sam_hdr_tid2name(hdr, c->tid));
+            }
+        }
+        if (!(c->flag&BAM_FPAIRED) || (c->flag&(BAM_FUNMAP|BAM_FMUNMAP)) || (c->mtid >= 0 && c->tid != c->mtid)) {
+            if (sam_write1(out, hdr, b) < 0) goto write_fail;
+        } else if (c->isize > 0) { // paired, head
+            uint64_t key = (uint64_t)c->pos<<32 | c->isize;
+            const char *lib;
+            lib_aux_t *q;
+            int ret;
+            lib = bam_get_library(hdr, b);
+            q = lib? get_aux(aux, lib) : get_aux(aux, "\t");
+            ++q->n_checked;
+            k = kh_put(pos, q->best_hash, key, &ret);
+            if (ret < 0) goto fail;
+            if (ret == 0) { // found in best_hash
+                bam1_t *p = kh_val(q->best_hash, k);
+                ++q->n_removed;
+                if (sum_qual(p) < sum_qual(b)) { // the current alignment is better; this can be accelerated in principle
+                    kh_put(name, del_set, strdup(bam_get_qname(p)), &ret); // p will be removed
+                    if (ret < 0) goto fail;
+                    if (bam_copy1(p, b) == NULL) goto fail; // replaced as b
+                } else kh_put(name, del_set, strdup(bam_get_qname(b)), &ret); // b will be removed
+                if (ret < 0) goto fail;
+                if (ret == 0)
+                    fprintf(stderr, "[bam_rmdup_core] inconsistent BAM file for pair '%s'. Continue anyway.\n", bam_get_qname(b));
+            } else { // not found in best_hash
+                kh_val(q->best_hash, k) = bam_dup1(b);
+                stack_insert(&stack, kh_val(q->best_hash, k));
+            }
+        } else { // paired, tail
+            k = kh_get(name, del_set, bam_get_qname(b));
+            if (k != kh_end(del_set)) {
+                free((char*)kh_key(del_set, k));
+                kh_del(name, del_set, k);
+            } else {
+                if (sam_write1(out, hdr, b) < 0) goto write_fail;
+            }
+        }
+        last_pos = c->pos;
+    }
+    if (r < -1) {
+        fprintf(stderr, "[%s] failed to read input file\n", __func__);
+        goto fail;
+    }
+
+    for (k = kh_begin(aux); k != kh_end(aux); ++k) {
+        if (kh_exist(aux, k)) {
+            lib_aux_t *q = &kh_val(aux, k);
+            if (dump_best(&stack, out, hdr) < 0) goto write_fail;
+            fprintf(stderr, "[bam_rmdup_core] %lld / %lld = %.4lf in library '%s'\n", (long long)q->n_removed,
+                    (long long)q->n_checked, (double)q->n_removed/q->n_checked, kh_key(aux, k));
+            kh_destroy(pos, q->best_hash);
+            free((char*)kh_key(aux, k));
+            kh_del(lib, aux, k);
+        }
+    }
+    kh_destroy(lib, aux);
+
+    clear_del_set(del_set);
+    kh_destroy(name, del_set);
+    free(stack.a);
+    bam_destroy1(b);
+    return 0;
+
+ write_fail:
+    print_error_errno("rmdup", "failed to write record");
+ fail:
+    clear_stack(&stack);
+    free(stack.a);
+    if (aux) {
+        for (k = kh_begin(aux); k != kh_end(aux); ++k) {
+            if (kh_exist(aux, k)) {
+                lib_aux_t *q = &kh_val(aux, k);
+                kh_destroy(pos, q->best_hash);
+                free((char*)kh_key(aux, k));
+            }
+        }
+        kh_destroy(lib, aux);
+    }
+    if (del_set) {
+        clear_del_set(del_set);
+        kh_destroy(name, del_set);
+    }
+    bam_destroy1(b);
+    return 1;
+}
+
+int bam_rmdupse_core(samFile *in, sam_hdr_t *hdr, samFile *out, int force_se);
+
+static int rmdup_usage(void) {
+    fprintf(stderr, "\n");
+    fprintf(stderr, "Usage:  samtools rmdup [-sS] <input.srt.bam> <output.bam>\n\n");
+    fprintf(stderr, "Option: -s    rmdup for SE reads\n");
+    fprintf(stderr, "        -S    treat PE reads as SE in rmdup (force -s)\n");
+
+    sam_global_opt_help(stderr, "-....--.");
+    return 1;
+}
+
+int bam_rmdup(int argc, char *argv[])
+{
+    int c, ret, is_se = 0, force_se = 0;
+    samFile *in, *out;
+    sam_hdr_t *header;
+    char wmode[3] = {'w', 'b', 0};
+    sam_global_args ga = SAM_GLOBAL_ARGS_INIT;
+
+    static const struct option lopts[] = {
+        SAM_OPT_GLOBAL_OPTIONS('-', 0, 0, 0, 0, '-'),
+        { NULL, 0, NULL, 0 }
+    };
+
+    while ((c = getopt_long(argc, argv, "sS", lopts, NULL)) >= 0) {
+        switch (c) {
+        case 's': is_se = 1; break;
+        case 'S': force_se = is_se = 1; break;
+        default:  if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break;
+            /* else fall-through */
+        case '?': return rmdup_usage();
+        }
+    }
+    if (optind + 2 > argc)
+        return rmdup_usage();
+
+    in = sam_open_format(argv[optind], "r", &ga.in);
+    if (!in) {
+        print_error_errno("rmdup", "failed to open \"%s\" for input", argv[optind]);
+        return 1;
+    }
+    header = sam_hdr_read(in);
+    if (header == NULL || sam_hdr_nref(header) == 0) {
+        fprintf(stderr, "[bam_rmdup] input SAM does not have header. Abort!\n");
+        return 1;
+    }
+
+    sam_open_mode(wmode+1, argv[optind+1], NULL);
+    out = sam_open_format(argv[optind+1], wmode, &ga.out);
+    if (!out) {
+        print_error_errno("rmdup", "failed to open \"%s\" for output", argv[optind+1]);
+        return 1;
+    }
+    if (sam_hdr_write(out, header) < 0) {
+        print_error_errno("rmdup", "failed to write header");
+        return 1;
+    }
+
+    if (is_se) ret = bam_rmdupse_core(in, header, out, force_se);
+    else ret = bam_rmdup_core(in, header, out);
+
+    sam_hdr_destroy(header);
+    sam_close(in);
+    if (sam_close(out) < 0) {
+        fprintf(stderr, "[bam_rmdup] error closing output file\n");
+        ret = 1;
+    }
+    return ret;
+}
diff --git a/samtools/bam_rmdup.c.pysam.c b/samtools/bam_rmdup.c.pysam.c
new file mode 100644
index 0000000..a748e47
--- /dev/null
+++ b/samtools/bam_rmdup.c.pysam.c
@@ -0,0 +1,327 @@
+#include "samtools.pysam.h"
+
+/*  bam_rmdup.c -- duplicate read detection.
+
+    Copyright (C) 2009, 2015, 2016, 2019 Genome Research Ltd.
+    Portions copyright (C) 2009 Broad Institute.
+
+    Author: Heng Li <lh3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <config.h>
+
+#include <stdlib.h>
+#include <string.h>
+#include <stdio.h>
+#include <zlib.h>
+#include <unistd.h>
+#include "htslib/sam.h"
+#include "sam_opts.h"
+#include "samtools.h"
+#include "bam.h" // for bam_get_library
+
+typedef bam1_t *bam1_p;
+
+#include "htslib/khash.h"
+KHASH_SET_INIT_STR(name)
+KHASH_MAP_INIT_INT64(pos, bam1_p)
+
+#define BUFFER_SIZE 0x40000
+
+typedef struct {
+    uint64_t n_checked, n_removed;
+    khash_t(pos) *best_hash;
+} lib_aux_t;
+KHASH_MAP_INIT_STR(lib, lib_aux_t)
+
+typedef struct {
+    int n, max;
+    bam1_t **a;
+} tmp_stack_t;
+
+static inline void stack_insert(tmp_stack_t *stack, bam1_t *b)
+{
+    if (stack->n == stack->max) {
+        stack->max = stack->max? stack->max<<1 : 0x10000;
+        stack->a = (bam1_t**)realloc(stack->a, sizeof(bam1_t*) * stack->max);
+    }
+    stack->a[stack->n++] = b;
+}
+
+static inline int dump_best(tmp_stack_t *stack, samFile *out, sam_hdr_t *hdr)
+{
+    int i;
+    for (i = 0; i != stack->n; ++i) {
+        if (sam_write1(out, hdr, stack->a[i]) < 0) return -1;
+        bam_destroy1(stack->a[i]);
+        stack->a[i] = NULL;
+    }
+    stack->n = 0;
+    return 0;
+}
+
+static inline void clear_stack(tmp_stack_t *stack) {
+    int i;
+    if (!stack->a) return;
+    for (i = 0; i != stack->n; ++i) {
+        bam_destroy1(stack->a[i]);
+    }
+}
+
+static void clear_del_set(khash_t(name) *del_set)
+{
+    khint_t k;
+    for (k = kh_begin(del_set); k < kh_end(del_set); ++k)
+        if (kh_exist(del_set, k))
+            free((char*)kh_key(del_set, k));
+    kh_clear(name, del_set);
+}
+
+static lib_aux_t *get_aux(khash_t(lib) *aux, const char *lib)
+{
+    khint_t k = kh_get(lib, aux, lib);
+    if (k == kh_end(aux)) {
+        int ret;
+        char *p = strdup(lib);
+        lib_aux_t *q;
+        k = kh_put(lib, aux, p, &ret);
+        q = &kh_val(aux, k);
+        q->n_checked = q->n_removed = 0;
+        q->best_hash = kh_init(pos);
+        return q;
+    } else return &kh_val(aux, k);
+}
+
+static void clear_best(khash_t(lib) *aux, int max)
+{
+    khint_t k;
+    for (k = kh_begin(aux); k != kh_end(aux); ++k) {
+        if (kh_exist(aux, k)) {
+            lib_aux_t *q = &kh_val(aux, k);
+            if (kh_size(q->best_hash) >= max)
+                kh_clear(pos, q->best_hash);
+        }
+    }
+}
+
+static inline int sum_qual(const bam1_t *b)
+{
+    int i, q;
+    uint8_t *qual = bam_get_qual(b);
+    for (i = q = 0; i < b->core.l_qseq; ++i) q += qual[i];
+    return q;
+}
+
+int bam_rmdup_core(samFile *in, sam_hdr_t *hdr, samFile *out)
+{
+    bam1_t *b = NULL;
+    int last_tid = -1, last_pos = -1, r;
+    tmp_stack_t stack;
+    khint_t k;
+    khash_t(lib) *aux = NULL;
+    khash_t(name) *del_set = NULL;
+
+    memset(&stack, 0, sizeof(tmp_stack_t));
+    aux = kh_init(lib);
+    del_set = kh_init(name);
+    b = bam_init1();
+    if (!aux || !del_set || !b) {
+        perror(__func__);
+        goto fail;
+    }
+
+    kh_resize(name, del_set, 4 * BUFFER_SIZE);
+    while ((r = sam_read1(in, hdr, b)) >= 0) {
+        bam1_core_t *c = &b->core;
+        if (c->tid != last_tid || last_pos != c->pos) {
+            if (dump_best(&stack, out, hdr) < 0) goto write_fail; // write the result
+            clear_best(aux, BUFFER_SIZE);
+            if (c->tid != last_tid) {
+                clear_best(aux, 0);
+                if (kh_size(del_set)) { // check
+                    fprintf(samtools_stderr, "[bam_rmdup_core] %llu unmatched pairs\n", (long long)kh_size(del_set));
+                    clear_del_set(del_set);
+                }
+                if ((int)c->tid == -1) { // append unmapped reads
+                    if (sam_write1(out, hdr, b) < 0) goto write_fail;
+                    while ((r = sam_read1(in, hdr, b)) >= 0) {
+                        if (sam_write1(out, hdr, b) < 0) goto write_fail;
+                    }
+                    break;
+                }
+                last_tid = c->tid;
+                fprintf(samtools_stderr, "[bam_rmdup_core] processing reference %s...\n", sam_hdr_tid2name(hdr, c->tid));
+            }
+        }
+        if (!(c->flag&BAM_FPAIRED) || (c->flag&(BAM_FUNMAP|BAM_FMUNMAP)) || (c->mtid >= 0 && c->tid != c->mtid)) {
+            if (sam_write1(out, hdr, b) < 0) goto write_fail;
+        } else if (c->isize > 0) { // paired, head
+            uint64_t key = (uint64_t)c->pos<<32 | c->isize;
+            const char *lib;
+            lib_aux_t *q;
+            int ret;
+            lib = bam_get_library(hdr, b);
+            q = lib? get_aux(aux, lib) : get_aux(aux, "\t");
+            ++q->n_checked;
+            k = kh_put(pos, q->best_hash, key, &ret);
+            if (ret < 0) goto fail;
+            if (ret == 0) { // found in best_hash
+                bam1_t *p = kh_val(q->best_hash, k);
+                ++q->n_removed;
+                if (sum_qual(p) < sum_qual(b)) { // the current alignment is better; this can be accelerated in principle
+                    kh_put(name, del_set, strdup(bam_get_qname(p)), &ret); // p will be removed
+                    if (ret < 0) goto fail;
+                    if (bam_copy1(p, b) == NULL) goto fail; // replaced as b
+                } else kh_put(name, del_set, strdup(bam_get_qname(b)), &ret); // b will be removed
+                if (ret < 0) goto fail;
+                if (ret == 0)
+                    fprintf(samtools_stderr, "[bam_rmdup_core] inconsistent BAM file for pair '%s'. Continue anyway.\n", bam_get_qname(b));
+            } else { // not found in best_hash
+                kh_val(q->best_hash, k) = bam_dup1(b);
+                stack_insert(&stack, kh_val(q->best_hash, k));
+            }
+        } else { // paired, tail
+            k = kh_get(name, del_set, bam_get_qname(b));
+            if (k != kh_end(del_set)) {
+                free((char*)kh_key(del_set, k));
+                kh_del(name, del_set, k);
+            } else {
+                if (sam_write1(out, hdr, b) < 0) goto write_fail;
+            }
+        }
+        last_pos = c->pos;
+    }
+    if (r < -1) {
+        fprintf(samtools_stderr, "[%s] failed to read input file\n", __func__);
+        goto fail;
+    }
+
+    for (k = kh_begin(aux); k != kh_end(aux); ++k) {
+        if (kh_exist(aux, k)) {
+            lib_aux_t *q = &kh_val(aux, k);
+            if (dump_best(&stack, out, hdr) < 0) goto write_fail;
+            fprintf(samtools_stderr, "[bam_rmdup_core] %lld / %lld = %.4lf in library '%s'\n", (long long)q->n_removed,
+                    (long long)q->n_checked, (double)q->n_removed/q->n_checked, kh_key(aux, k));
+            kh_destroy(pos, q->best_hash);
+            free((char*)kh_key(aux, k));
+            kh_del(lib, aux, k);
+        }
+    }
+    kh_destroy(lib, aux);
+
+    clear_del_set(del_set);
+    kh_destroy(name, del_set);
+    free(stack.a);
+    bam_destroy1(b);
+    return 0;
+
+ write_fail:
+    print_error_errno("rmdup", "failed to write record");
+ fail:
+    clear_stack(&stack);
+    free(stack.a);
+    if (aux) {
+        for (k = kh_begin(aux); k != kh_end(aux); ++k) {
+            if (kh_exist(aux, k)) {
+                lib_aux_t *q = &kh_val(aux, k);
+                kh_destroy(pos, q->best_hash);
+                free((char*)kh_key(aux, k));
+            }
+        }
+        kh_destroy(lib, aux);
+    }
+    if (del_set) {
+        clear_del_set(del_set);
+        kh_destroy(name, del_set);
+    }
+    bam_destroy1(b);
+    return 1;
+}
+
+int bam_rmdupse_core(samFile *in, sam_hdr_t *hdr, samFile *out, int force_se);
+
+static int rmdup_usage(void) {
+    fprintf(samtools_stderr, "\n");
+    fprintf(samtools_stderr, "Usage:  samtools rmdup [-sS] <input.srt.bam> <output.bam>\n\n");
+    fprintf(samtools_stderr, "Option: -s    rmdup for SE reads\n");
+    fprintf(samtools_stderr, "        -S    treat PE reads as SE in rmdup (force -s)\n");
+
+    sam_global_opt_help(samtools_stderr, "-....--.");
+    return 1;
+}
+
+int bam_rmdup(int argc, char *argv[])
+{
+    int c, ret, is_se = 0, force_se = 0;
+    samFile *in, *out;
+    sam_hdr_t *header;
+    char wmode[3] = {'w', 'b', 0};
+    sam_global_args ga = SAM_GLOBAL_ARGS_INIT;
+
+    static const struct option lopts[] = {
+        SAM_OPT_GLOBAL_OPTIONS('-', 0, 0, 0, 0, '-'),
+        { NULL, 0, NULL, 0 }
+    };
+
+    while ((c = getopt_long(argc, argv, "sS", lopts, NULL)) >= 0) {
+        switch (c) {
+        case 's': is_se = 1; break;
+        case 'S': force_se = is_se = 1; break;
+        default:  if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break;
+            /* else fall-through */
+        case '?': return rmdup_usage();
+        }
+    }
+    if (optind + 2 > argc)
+        return rmdup_usage();
+
+    in = sam_open_format(argv[optind], "r", &ga.in);
+    if (!in) {
+        print_error_errno("rmdup", "failed to open \"%s\" for input", argv[optind]);
+        return 1;
+    }
+    header = sam_hdr_read(in);
+    if (header == NULL || sam_hdr_nref(header) == 0) {
+        fprintf(samtools_stderr, "[bam_rmdup] input SAM does not have header. Abort!\n");
+        return 1;
+    }
+
+    sam_open_mode(wmode+1, argv[optind+1], NULL);
+    out = sam_open_format(argv[optind+1], wmode, &ga.out);
+    if (!out) {
+        print_error_errno("rmdup", "failed to open \"%s\" for output", argv[optind+1]);
+        return 1;
+    }
+    if (sam_hdr_write(out, header) < 0) {
+        print_error_errno("rmdup", "failed to write header");
+        return 1;
+    }
+
+    if (is_se) ret = bam_rmdupse_core(in, header, out, force_se);
+    else ret = bam_rmdup_core(in, header, out);
+
+    sam_hdr_destroy(header);
+    sam_close(in);
+    if (sam_close(out) < 0) {
+        fprintf(samtools_stderr, "[bam_rmdup] error closing output file\n");
+        ret = 1;
+    }
+    return ret;
+}
diff --git a/samtools/bam_rmdupse.c b/samtools/bam_rmdupse.c
new file mode 100644
index 0000000..1812136
--- /dev/null
+++ b/samtools/bam_rmdupse.c
@@ -0,0 +1,230 @@
+/*  bam_rmdupse.c -- duplicate read detection for unpaired reads.
+
+    Copyright (C) 2009, 2015, 2016, 2019 Genome Research Ltd.
+    Portions copyright (C) 2009 Broad Institute.
+
+    Author: Heng Li <lh3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <config.h>
+
+#include <math.h>
+#include <stdio.h>
+#include "bam.h" // for bam_get_library
+#include "htslib/sam.h"
+#include "htslib/khash.h"
+#include "htslib/klist.h"
+#include "samtools.h"
+
+#define QUEUE_CLEAR_SIZE 0x100000
+#define MAX_POS 0x7fffffff
+
+typedef struct {
+    int endpos;
+    uint32_t score:31, discarded:1;
+    bam1_t *b;
+} elem_t, *elem_p;
+#define __free_elem(p) bam_destroy1((p)->data.b)
+KLIST_INIT(q, elem_t, __free_elem)
+typedef klist_t(q) queue_t;
+
+KHASH_MAP_INIT_INT(best, elem_p)
+typedef khash_t(best) besthash_t;
+
+typedef struct {
+    uint64_t n_checked, n_removed;
+    besthash_t *left, *rght;
+} lib_aux_t;
+KHASH_MAP_INIT_STR(lib, lib_aux_t)
+
+static lib_aux_t *get_aux(khash_t(lib) *aux, const char *lib)
+{
+    khint_t k = kh_get(lib, aux, lib);
+    if (k == kh_end(aux)) {
+        int ret;
+        char *p = strdup(lib);
+        lib_aux_t *q;
+        k = kh_put(lib, aux, p, &ret);
+        q = &kh_val(aux, k);
+        q->left = kh_init(best);
+        q->rght = kh_init(best);
+        q->n_checked = q->n_removed = 0;
+        return q;
+    } else return &kh_val(aux, k);
+}
+
+static inline int sum_qual(const bam1_t *b)
+{
+    int i, q;
+    uint8_t *qual = bam_get_qual(b);
+    for (i = q = 0; i < b->core.l_qseq; ++i) q += qual[i];
+    return q;
+}
+
+static inline elem_t *push_queue(queue_t *queue, const bam1_t *b, int endpos, int score)
+{
+    elem_t *p = kl_pushp(q, queue);
+    p->discarded = 0;
+    p->endpos = endpos; p->score = score;
+    if (p->b == 0) p->b = bam_init1();
+    if (!p->b) { perror(NULL); exit(EXIT_FAILURE); }
+    if (bam_copy1(p->b, b) == NULL) { perror(NULL); exit(EXIT_FAILURE); }
+    return p;
+}
+
+static void clear_besthash(besthash_t *h, int32_t pos)
+{
+    khint_t k;
+    for (k = kh_begin(h); k != kh_end(h); ++k)
+        if (kh_exist(h, k) && kh_val(h, k)->endpos <= pos)
+            kh_del(best, h, k);
+}
+
+static int dump_alignment(samFile *out, sam_hdr_t *hdr,
+                          queue_t *queue, int32_t pos, khash_t(lib) *h)
+{
+    if (queue->size > QUEUE_CLEAR_SIZE || pos == MAX_POS) {
+        khint_t k;
+        while (1) {
+            elem_t *q;
+            if (queue->head == queue->tail) break;
+            q = &kl_val(queue->head);
+            if (q->discarded) {
+                q->b->l_data = 0;
+                kl_shift(q, queue, 0);
+                continue;
+            }
+            if ((q->b->core.flag&BAM_FREVERSE) && q->endpos > pos) break;
+            if (sam_write1(out, hdr, q->b) < 0) return -1;
+            q->b->l_data = 0;
+            kl_shift(q, queue, 0);
+        }
+        for (k = kh_begin(h); k != kh_end(h); ++k) {
+            if (kh_exist(h, k)) {
+                clear_besthash(kh_val(h, k).left, pos);
+                clear_besthash(kh_val(h, k).rght, pos);
+            }
+        }
+    }
+    return 0;
+}
+
+int bam_rmdupse_core(samFile *in, sam_hdr_t *hdr, samFile *out, int force_se)
+{
+    bam1_t *b = NULL;
+    queue_t *queue = NULL;
+    khint_t k;
+    int last_tid = -2, r;
+    khash_t(lib) *aux = NULL;
+
+    aux = kh_init(lib);
+    b = bam_init1();
+    queue = kl_init(q);
+    if (!aux || !b || !queue) {
+        perror(__func__);
+        goto fail;
+    }
+
+    while ((r = sam_read1(in, hdr, b)) >= 0) {
+        bam1_core_t *c = &b->core;
+        int endpos = bam_endpos(b);
+        int score = sum_qual(b);
+
+        if (last_tid != c->tid) {
+            if (last_tid >= 0) {
+                if (dump_alignment(out, hdr, queue, MAX_POS, aux) < 0)
+                    goto write_fail;
+            }
+            last_tid = c->tid;
+        } else {
+            if (dump_alignment(out, hdr, queue, c->pos, aux) < 0)
+                goto write_fail;
+        }
+        if ((c->flag&BAM_FUNMAP) || ((c->flag&BAM_FPAIRED) && !force_se)) {
+            push_queue(queue, b, endpos, score);
+        } else {
+            const char *lib;
+            lib_aux_t *q;
+            besthash_t *h;
+            uint32_t key;
+            int ret;
+            lib = bam_get_library(hdr, b);
+            q = lib? get_aux(aux, lib) : get_aux(aux, "\t");
+            ++q->n_checked;
+            h = (c->flag&BAM_FREVERSE)? q->rght : q->left;
+            key = (c->flag&BAM_FREVERSE)? endpos : c->pos;
+            k = kh_put(best, h, key, &ret);
+            if (ret == 0) { // in the hash table
+                elem_t *p = kh_val(h, k);
+                ++q->n_removed;
+                if (p->score < score) {
+                    if (c->flag&BAM_FREVERSE) { // mark "discarded" and push the queue
+                        p->discarded = 1;
+                        kh_val(h, k) = push_queue(queue, b, endpos, score);
+                    } else { // replace
+                        p->score = score; p->endpos = endpos;
+                        if (bam_copy1(p->b, b) == NULL) {
+                            perror(NULL); exit(EXIT_FAILURE);
+                        }
+                    }
+                } // otherwise, discard the alignment
+            } else kh_val(h, k) = push_queue(queue, b, endpos, score);
+        }
+    }
+    if (r < -1) {
+        fprintf(stderr, "[%s] error reading input file\n", __func__);
+        goto fail;
+    }
+
+    if (dump_alignment(out, hdr, queue, MAX_POS, aux) < 0) goto write_fail;
+
+    for (k = kh_begin(aux); k != kh_end(aux); ++k) {
+        if (kh_exist(aux, k)) {
+            lib_aux_t *q = &kh_val(aux, k);
+            fprintf(stderr, "[bam_rmdupse_core] %lld / %lld = %.4lf in library '%s'\n", (long long)q->n_removed,
+                    (long long)q->n_checked, (double)q->n_removed/q->n_checked, kh_key(aux, k));
+            kh_destroy(best, q->left); kh_destroy(best, q->rght);
+            free((char*)kh_key(aux, k));
+            kh_del(lib, aux, k);
+        }
+    }
+    kh_destroy(lib, aux);
+    bam_destroy1(b);
+    kl_destroy(q, queue);
+    return 0;
+
+ write_fail:
+    print_error_errno("rmdup", "failed to write record");
+ fail:
+    if (aux) {
+        for (k = kh_begin(aux); k != kh_end(aux); ++k) {
+            if (kh_exist(aux, k)) {
+                lib_aux_t *q = &kh_val(aux, k);
+                kh_destroy(best, q->left);
+                kh_destroy(best, q->rght);
+                free((char*)kh_key(aux, k));
+            }
+        }
+        kh_destroy(lib, aux);
+    }
+    bam_destroy1(b);
+    kl_destroy(q, queue);
+    return 1;
+}
diff --git a/samtools/bam_rmdupse.c.pysam.c b/samtools/bam_rmdupse.c.pysam.c
new file mode 100644
index 0000000..65689d7
--- /dev/null
+++ b/samtools/bam_rmdupse.c.pysam.c
@@ -0,0 +1,232 @@
+#include "samtools.pysam.h"
+
+/*  bam_rmdupse.c -- duplicate read detection for unpaired reads.
+
+    Copyright (C) 2009, 2015, 2016, 2019 Genome Research Ltd.
+    Portions copyright (C) 2009 Broad Institute.
+
+    Author: Heng Li <lh3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <config.h>
+
+#include <math.h>
+#include <stdio.h>
+#include "bam.h" // for bam_get_library
+#include "htslib/sam.h"
+#include "htslib/khash.h"
+#include "htslib/klist.h"
+#include "samtools.h"
+
+#define QUEUE_CLEAR_SIZE 0x100000
+#define MAX_POS 0x7fffffff
+
+typedef struct {
+    int endpos;
+    uint32_t score:31, discarded:1;
+    bam1_t *b;
+} elem_t, *elem_p;
+#define __free_elem(p) bam_destroy1((p)->data.b)
+KLIST_INIT(q, elem_t, __free_elem)
+typedef klist_t(q) queue_t;
+
+KHASH_MAP_INIT_INT(best, elem_p)
+typedef khash_t(best) besthash_t;
+
+typedef struct {
+    uint64_t n_checked, n_removed;
+    besthash_t *left, *rght;
+} lib_aux_t;
+KHASH_MAP_INIT_STR(lib, lib_aux_t)
+
+static lib_aux_t *get_aux(khash_t(lib) *aux, const char *lib)
+{
+    khint_t k = kh_get(lib, aux, lib);
+    if (k == kh_end(aux)) {
+        int ret;
+        char *p = strdup(lib);
+        lib_aux_t *q;
+        k = kh_put(lib, aux, p, &ret);
+        q = &kh_val(aux, k);
+        q->left = kh_init(best);
+        q->rght = kh_init(best);
+        q->n_checked = q->n_removed = 0;
+        return q;
+    } else return &kh_val(aux, k);
+}
+
+static inline int sum_qual(const bam1_t *b)
+{
+    int i, q;
+    uint8_t *qual = bam_get_qual(b);
+    for (i = q = 0; i < b->core.l_qseq; ++i) q += qual[i];
+    return q;
+}
+
+static inline elem_t *push_queue(queue_t *queue, const bam1_t *b, int endpos, int score)
+{
+    elem_t *p = kl_pushp(q, queue);
+    p->discarded = 0;
+    p->endpos = endpos; p->score = score;
+    if (p->b == 0) p->b = bam_init1();
+    if (!p->b) { perror(NULL); samtools_exit(EXIT_FAILURE); }
+    if (bam_copy1(p->b, b) == NULL) { perror(NULL); samtools_exit(EXIT_FAILURE); }
+    return p;
+}
+
+static void clear_besthash(besthash_t *h, int32_t pos)
+{
+    khint_t k;
+    for (k = kh_begin(h); k != kh_end(h); ++k)
+        if (kh_exist(h, k) && kh_val(h, k)->endpos <= pos)
+            kh_del(best, h, k);
+}
+
+static int dump_alignment(samFile *out, sam_hdr_t *hdr,
+                          queue_t *queue, int32_t pos, khash_t(lib) *h)
+{
+    if (queue->size > QUEUE_CLEAR_SIZE || pos == MAX_POS) {
+        khint_t k;
+        while (1) {
+            elem_t *q;
+            if (queue->head == queue->tail) break;
+            q = &kl_val(queue->head);
+            if (q->discarded) {
+                q->b->l_data = 0;
+                kl_shift(q, queue, 0);
+                continue;
+            }
+            if ((q->b->core.flag&BAM_FREVERSE) && q->endpos > pos) break;
+            if (sam_write1(out, hdr, q->b) < 0) return -1;
+            q->b->l_data = 0;
+            kl_shift(q, queue, 0);
+        }
+        for (k = kh_begin(h); k != kh_end(h); ++k) {
+            if (kh_exist(h, k)) {
+                clear_besthash(kh_val(h, k).left, pos);
+                clear_besthash(kh_val(h, k).rght, pos);
+            }
+        }
+    }
+    return 0;
+}
+
+int bam_rmdupse_core(samFile *in, sam_hdr_t *hdr, samFile *out, int force_se)
+{
+    bam1_t *b = NULL;
+    queue_t *queue = NULL;
+    khint_t k;
+    int last_tid = -2, r;
+    khash_t(lib) *aux = NULL;
+
+    aux = kh_init(lib);
+    b = bam_init1();
+    queue = kl_init(q);
+    if (!aux || !b || !queue) {
+        perror(__func__);
+        goto fail;
+    }
+
+    while ((r = sam_read1(in, hdr, b)) >= 0) {
+        bam1_core_t *c = &b->core;
+        int endpos = bam_endpos(b);
+        int score = sum_qual(b);
+
+        if (last_tid != c->tid) {
+            if (last_tid >= 0) {
+                if (dump_alignment(out, hdr, queue, MAX_POS, aux) < 0)
+                    goto write_fail;
+            }
+            last_tid = c->tid;
+        } else {
+            if (dump_alignment(out, hdr, queue, c->pos, aux) < 0)
+                goto write_fail;
+        }
+        if ((c->flag&BAM_FUNMAP) || ((c->flag&BAM_FPAIRED) && !force_se)) {
+            push_queue(queue, b, endpos, score);
+        } else {
+            const char *lib;
+            lib_aux_t *q;
+            besthash_t *h;
+            uint32_t key;
+            int ret;
+            lib = bam_get_library(hdr, b);
+            q = lib? get_aux(aux, lib) : get_aux(aux, "\t");
+            ++q->n_checked;
+            h = (c->flag&BAM_FREVERSE)? q->rght : q->left;
+            key = (c->flag&BAM_FREVERSE)? endpos : c->pos;
+            k = kh_put(best, h, key, &ret);
+            if (ret == 0) { // in the hash table
+                elem_t *p = kh_val(h, k);
+                ++q->n_removed;
+                if (p->score < score) {
+                    if (c->flag&BAM_FREVERSE) { // mark "discarded" and push the queue
+                        p->discarded = 1;
+                        kh_val(h, k) = push_queue(queue, b, endpos, score);
+                    } else { // replace
+                        p->score = score; p->endpos = endpos;
+                        if (bam_copy1(p->b, b) == NULL) {
+                            perror(NULL); samtools_exit(EXIT_FAILURE);
+                        }
+                    }
+                } // otherwise, discard the alignment
+            } else kh_val(h, k) = push_queue(queue, b, endpos, score);
+        }
+    }
+    if (r < -1) {
+        fprintf(samtools_stderr, "[%s] error reading input file\n", __func__);
+        goto fail;
+    }
+
+    if (dump_alignment(out, hdr, queue, MAX_POS, aux) < 0) goto write_fail;
+
+    for (k = kh_begin(aux); k != kh_end(aux); ++k) {
+        if (kh_exist(aux, k)) {
+            lib_aux_t *q = &kh_val(aux, k);
+            fprintf(samtools_stderr, "[bam_rmdupse_core] %lld / %lld = %.4lf in library '%s'\n", (long long)q->n_removed,
+                    (long long)q->n_checked, (double)q->n_removed/q->n_checked, kh_key(aux, k));
+            kh_destroy(best, q->left); kh_destroy(best, q->rght);
+            free((char*)kh_key(aux, k));
+            kh_del(lib, aux, k);
+        }
+    }
+    kh_destroy(lib, aux);
+    bam_destroy1(b);
+    kl_destroy(q, queue);
+    return 0;
+
+ write_fail:
+    print_error_errno("rmdup", "failed to write record");
+ fail:
+    if (aux) {
+        for (k = kh_begin(aux); k != kh_end(aux); ++k) {
+            if (kh_exist(aux, k)) {
+                lib_aux_t *q = &kh_val(aux, k);
+                kh_destroy(best, q->left);
+                kh_destroy(best, q->rght);
+                free((char*)kh_key(aux, k));
+            }
+        }
+        kh_destroy(lib, aux);
+    }
+    bam_destroy1(b);
+    kl_destroy(q, queue);
+    return 1;
+}
diff --git a/samtools/bam_samples.c b/samtools/bam_samples.c
new file mode 100644
index 0000000..f72ca6e
--- /dev/null
+++ b/samtools/bam_samples.c
@@ -0,0 +1,433 @@
+/*  bam_samples -- print samples in a set of BAM files
+
+    Copyright (C) 2021 Pierre Lindenbaum
+    Institut du Thorax. u1087 Nantes. France.
+    @yokofakun
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <config.h>
+#include <htslib/hts.h>
+#include <htslib/sam.h>
+#include <htslib/faidx.h>
+#include <htslib/khash.h>
+#include <htslib/kseq.h>
+#include <samtools.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <unistd.h>
+#include <getopt.h>
+
+KHASH_MAP_INIT_STR(sm, int)
+
+/** and chained struct containing the faidx and the fasta filename
+    will be compared with the @SQ lines in the SAM header
+ */
+typedef struct FaidxPath {
+    /** path to reference */
+    char* filename;
+    /** fasta index  */
+    faidx_t* faidx;
+    struct FaidxPath* next;
+} FaidxPath;
+
+/** program parameters */
+typedef struct Params {
+    /** output stream */
+    FILE* out;
+    /** tag in @RG line. default is "SM" */
+    char tag[3];
+    /** first faidx/path in chained list */
+    FaidxPath* faidx;
+    /** show whether the bam is indexed */
+    int test_index;
+} Params;
+
+/** print usage */
+static void usage_samples(FILE *write_to) {
+    fprintf(write_to,
+            "Usage: samtools samples [options] <input> [...]\n"
+            "       samtools samples [options] -X f1.bam f2.bam f1.bam.bai f2.bai \n"
+            "       find dir1 dir2 -type f \\(-name \"*.bam\" -o -name \"*.cram\" \\) | samtools samples [options]\n"
+            "       find dir1 dir2 -type f \\(-name \"*.bam\" -o -name \"*.bai\" \\) | sort | paste - - | samtools samples -X [options]\n"
+            "\n"
+            "Options:\n"
+            "  -?              print help and exit\n"
+            "  -h              add the columns header before printing the results\n"
+            "  -i              test if the file is indexed.\n"
+            "  -T <tag>        provide the sample tag name from the @RG line [SM].\n"
+            "  -o <file>       output file [stdout].\n"
+            "  -f <file.fa>    load an indexed fasta file in the collection of references. Can be used multiple times.\n"
+            "  -F <file.txt>   read a file containing the paths to indexed fasta files. One path per line.\n"
+            "  -X              use a custom index file.\n"
+            "\n"
+            " Using -f or -F will add a column containing the path to the reference or \".\" if the reference was not found.\n"
+            "\n"
+    );
+}
+
+
+/** loads fasta fai file into FaidxPath, add it to params->faidx */
+static int load_dictionary(struct Params* params, const char* filename) {
+    FaidxPath* head = params->faidx;
+    FaidxPath* ptr = (FaidxPath*)malloc(sizeof(FaidxPath));
+    if (ptr == NULL) {
+        print_error_errno("samples", "Out of memory");
+        return EXIT_FAILURE;
+    }
+    ptr->filename = strdup(filename);
+    if (ptr->filename == NULL) {
+        free(ptr);
+        print_error_errno("samples", "Out of memory");
+        return EXIT_FAILURE;
+    }
+    ptr->faidx = fai_load(filename);
+    if (ptr->faidx == NULL) {
+        free(ptr->filename);
+        free(ptr);
+        print_error_errno("samples", "Cannot load index from \"%s\"", filename);
+        return EXIT_FAILURE;
+    }
+    /* insert at the beginning of the linked list */
+    params->faidx = ptr;
+    ptr->next = head;
+    return EXIT_SUCCESS;
+}
+
+/** load a faidx file and append it to params */
+static int load_dictionaries(Params* params, const char* filename) {
+    int ret;
+    htsFile* in;
+    int status = EXIT_SUCCESS;
+
+    in = hts_open(filename, "r");
+    if (in == NULL) {
+        print_error_errno("samples", "Cannot open \"%s\"", filename);
+        status = EXIT_FAILURE;
+    } else {
+        kstring_t ks = KS_INITIALIZE;
+        while ((ret = hts_getline(in, KS_SEP_LINE, &ks)) >= 0) {
+            if (load_dictionary(params, ks_str(&ks)) != EXIT_SUCCESS) {
+                status = EXIT_FAILURE;
+                break;
+            }
+        }
+        ks_free(&ks);
+        hts_close(in);
+    }
+    return status;
+}
+
+/** print the sample information, search for a reference */
+static int print_sample(
+        Params* params,
+        sam_hdr_t *header,
+        int has_index,
+        const char* sample,
+        const char* fname) {
+    fputs(sample, params->out);
+    fputc('\t', params->out);
+    fputs(fname, params->out);
+    if (params->test_index) {
+        fprintf(params->out, "\t%c", has_index ? 'Y' : 'N');
+    }
+    if (params->faidx != NULL) {
+        FaidxPath* ref = NULL;
+        FaidxPath* curr = params->faidx;
+        while (curr != NULL) {
+            /** check names and length are the same in the same order */
+            if (faidx_nseq(curr->faidx) == header->n_targets) {
+                int i;
+                for (i = 0; i < faidx_nseq(curr->faidx); i++) {
+                    /** check name is the same */
+                    if (strcmp(faidx_iseq(curr->faidx, i), header->target_name[i]) != 0) break;
+                    /** check length is the same */
+                    if (faidx_seq_len(curr->faidx, faidx_iseq(curr->faidx, i)) != header->target_len[i]) break;
+                }
+                /* the ref was found */
+                if (i == faidx_nseq(curr->faidx)) {
+                    ref = curr;
+                    break;
+                }
+            }
+            curr = curr->next;
+        }
+        fputc('\t', params->out);
+        if (ref == NULL) {
+            fputc('.', params->out);
+        } else {
+            fputs(curr->filename, params->out);
+        }
+    }
+    fputc('\n', params->out);
+    return 0;
+}
+
+/** open a sam file. Search for all samples in the @RG lines */
+static int print_samples(Params* params, const char* fname, const char* baifname) {
+    samFile *in = 0;
+    sam_hdr_t *header = NULL;
+    int n_rg;
+    int status = EXIT_SUCCESS;
+    khash_t(sm) *sample_set = NULL;
+    khint_t k;
+    int count_samples = 0;
+    int has_index = 0;
+
+    if ((sample_set = kh_init(sm)) == NULL) {
+        print_error("samples", "Failed to initialise sample hash");
+        status = EXIT_FAILURE;
+        goto end_print;
+    }
+
+    if ((in = sam_open_format(fname, "r", NULL)) == 0) {
+        print_error_errno("samples", "Failed to open \"%s\" for reading", fname);
+        status = EXIT_FAILURE;
+        goto end_print;
+    }
+    if ((header = sam_hdr_read(in)) == 0) {
+        print_error("samples", "Failed to read the header from \"%s\"", fname);
+        status = EXIT_FAILURE;
+        goto end_print;
+    }
+
+    /* try to load index if required */
+    if (params->test_index) {
+        hts_idx_t *bam_idx;
+        /* path to bam index was specified */
+        if (baifname != NULL) {
+            bam_idx = sam_index_load3(in, fname, baifname, HTS_IDX_SILENT_FAIL);
+        }
+        /* get default index */
+        else {
+            bam_idx = sam_index_load3(in, fname, NULL, HTS_IDX_SILENT_FAIL);
+        }
+        has_index = bam_idx != NULL;
+        if (bam_idx != NULL) hts_idx_destroy(bam_idx);
+        /* and we continue... we have tested the index file but we always test for the samples and the references */
+    }
+
+    /* get the RG lines */
+    n_rg = sam_hdr_count_lines(header, "RG");
+    if (n_rg > 0) {
+        int i, r, ret;
+        char* sample;
+        kstring_t sm_val = KS_INITIALIZE;
+        for (i = 0; i < n_rg; i++) {
+            r = sam_hdr_find_tag_pos(header, "RG", i, params->tag, &sm_val);
+            if (r < 0) continue;
+            k = kh_get(sm, sample_set, ks_str(&sm_val));
+            if (k != kh_end(sample_set)) continue;
+            sample = strdup(ks_str(&sm_val));
+            if (sample == NULL) {
+                print_error_errno("samples", "Out of memory");
+                status = EXIT_FAILURE;
+                goto end_print;
+            }
+            kh_put(sm, sample_set, sample, &ret);
+            if (ret < 0) {
+                print_error("samples", "Failed to insert key '%s' into sample_set", sample);
+                free(sample);
+                status = EXIT_FAILURE;
+                goto end_print;
+            }
+            ++count_samples;
+        }
+        ks_free(&sm_val);
+    }
+    if (count_samples == 0) {
+        print_sample(params, header, has_index, ".", fname);
+    } else {
+        for (k = kh_begin(sample_set); k != kh_end(sample_set); ++k) {
+            if (kh_exist(sample_set, k)) {
+                char* sample = (char*)kh_key(sample_set, k);
+                print_sample(params, header, has_index, sample, fname);
+            }
+        }
+    }
+
+end_print:
+    if (sample_set != NULL) {
+        for (k = kh_begin(sample_set); k != kh_end(sample_set); ++k) {
+            if (kh_exist(sample_set, k)) {
+                char* sample = (char*)kh_key(sample_set, k);
+                free(sample);
+            }
+        }
+        kh_destroy(sm, sample_set);
+    }
+    if (header != NULL) sam_hdr_destroy(header);
+    if (in != NULL) sam_close(in);
+
+    return status;
+}
+
+
+int main_samples(int argc, char** argv) {
+    int status = EXIT_SUCCESS;
+    int print_header = 0;
+    int has_index_file = 0;
+    Params params;
+    char* out_filename = NULL;
+    FaidxPath* fai;
+
+    strcpy(params.tag, "SM");
+    params.faidx = NULL;
+    params.test_index =0;
+
+    int opt;
+    while ((opt = getopt_long(argc, argv,  "?hiXo:f:F:T:", NULL, NULL)) != -1) {
+        switch (opt) {
+        case 'h':
+            print_header = 1;
+            break;
+        case 'o':
+            out_filename = optarg;
+            break;
+        case 'i':
+            params.test_index = 1;
+            break;
+        case 'f':
+            if (load_dictionary(&params, optarg) != EXIT_SUCCESS) {
+                return EXIT_FAILURE;
+            }
+            break;
+        case 'F':
+            if (load_dictionaries(&params, optarg) != EXIT_SUCCESS) {
+                return EXIT_FAILURE;
+            }
+            break;
+        case 'T':
+            if (strlen(optarg) != 2) {
+                print_error("samples", "Length of tag \"%s\" is not 2.", optarg);
+                return EXIT_FAILURE;
+            }
+            strcpy(params.tag, optarg);
+            break;
+        case '?':
+            usage_samples(stdout);
+            return EXIT_SUCCESS;
+        case 'X':
+            has_index_file = 1;
+            break;
+        default:
+            usage_samples(stderr);
+            return EXIT_FAILURE;
+        }
+    }
+
+    /* if no file was provided and input is the terminal, print the usage and exit */
+    if (argc == optind && isatty(STDIN_FILENO)) {
+       usage_samples(stderr);
+       return EXIT_FAILURE;
+    }
+
+    if (out_filename != NULL) {
+        params.out = fopen(out_filename, "w");
+        if (params.out == NULL) {
+            print_error_errno("samples", "Cannot open \"%s\" for writing", out_filename);
+            return EXIT_FAILURE;
+        }
+    } else {
+        params.out = stdout;
+    }
+
+    if (print_header) {
+        fprintf(params.out, "#%s\tPATH", params.tag);
+        if (params.test_index) fprintf(params.out, "\tINDEX");
+        if (params.faidx != NULL) fprintf(params.out, "\tREFERENCE");
+        fprintf(params.out, "\n");
+    }
+
+    /* no file was provided, input is stdin, each line contains the path to a bam file */
+    if (argc == optind) {
+        htsFile* fp = hts_open("-", "r");
+        if (fp == NULL) {
+            print_error_errno("samples", "Cannot read from stdin");
+            status = EXIT_FAILURE;
+        } else {
+            kstring_t ks = KS_INITIALIZE;
+            int ret;
+            while ((ret = hts_getline(fp, KS_SEP_LINE, &ks)) >= 0) {
+                char* bai_path = NULL;
+                if (has_index_file) {
+                    /* bam path and bam index file are separated by a tab */
+                    char* tab = strchr(ks_str(&ks), '\t');
+                    if (tab == NULL || *(tab+1) == '\0') {
+                        print_error_errno("samples", "Expected path-to-bam(tab)path-to-index but got \"%s\"", ks_str(&ks));
+                        status = EXIT_FAILURE;
+                        break;
+                    }
+                    *tab=0;
+                    bai_path = (tab + 1);
+                }
+                if (print_samples(&params, ks_str(&ks), bai_path) != EXIT_SUCCESS) {
+                    status = EXIT_FAILURE;
+                    break;
+                }
+            }
+            ks_free(&ks);
+            hts_close(fp);
+        }
+    }
+    /* loop over each file in argc/argv bam index provided */
+    else if (has_index_file) {
+        /* calculate number of input BAM files */
+        if ((argc - optind) % 2 != 0) {
+            print_error("samples","Odd number of filenames detected! Each BAM file should have an index file");
+            status = EXIT_FAILURE;
+        } else {
+            int i;
+            int n = (argc - optind ) / 2;
+            for (i = 0; i < n; i++) {
+                if (print_samples(&params, argv[optind+i], argv[optind+i+n]) != EXIT_SUCCESS) {
+                    status = EXIT_FAILURE;
+                    break;
+                }
+            }
+        }
+    } else {
+        int i;
+        for (i = optind; i < argc; i++) {
+            if (print_samples(&params, argv[i], NULL) != EXIT_SUCCESS) {
+                status = EXIT_FAILURE;
+                break;
+            }
+        }
+    }
+
+    fai = params.faidx;
+    while (fai != NULL) {
+        FaidxPath* next = fai -> next;
+        free(fai->filename);
+        fai_destroy(fai->faidx);
+        free(fai);
+        fai = next;
+    }
+
+    if (fflush(params.out) != 0) {
+        print_error_errno("samples", "Cannot flush output");
+        status = EXIT_FAILURE;
+    }
+    if (out_filename != NULL) {
+        fclose(params.out);
+    }
+
+    return status;
+}
diff --git a/samtools/bam_samples.c.pysam.c b/samtools/bam_samples.c.pysam.c
new file mode 100644
index 0000000..891f875
--- /dev/null
+++ b/samtools/bam_samples.c.pysam.c
@@ -0,0 +1,435 @@
+#include "samtools.pysam.h"
+
+/*  bam_samples -- print samples in a set of BAM files
+
+    Copyright (C) 2021 Pierre Lindenbaum
+    Institut du Thorax. u1087 Nantes. France.
+    @yokofakun
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <config.h>
+#include <htslib/hts.h>
+#include <htslib/sam.h>
+#include <htslib/faidx.h>
+#include <htslib/khash.h>
+#include <htslib/kseq.h>
+#include <samtools.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <unistd.h>
+#include <getopt.h>
+
+KHASH_MAP_INIT_STR(sm, int)
+
+/** and chained struct containing the faidx and the fasta filename
+    will be compared with the @SQ lines in the SAM header
+ */
+typedef struct FaidxPath {
+    /** path to reference */
+    char* filename;
+    /** fasta index  */
+    faidx_t* faidx;
+    struct FaidxPath* next;
+} FaidxPath;
+
+/** program parameters */
+typedef struct Params {
+    /** output stream */
+    FILE* out;
+    /** tag in @RG line. default is "SM" */
+    char tag[3];
+    /** first faidx/path in chained list */
+    FaidxPath* faidx;
+    /** show whether the bam is indexed */
+    int test_index;
+} Params;
+
+/** print usage */
+static void usage_samples(FILE *write_to) {
+    fprintf(write_to,
+            "Usage: samtools samples [options] <input> [...]\n"
+            "       samtools samples [options] -X f1.bam f2.bam f1.bam.bai f2.bai \n"
+            "       find dir1 dir2 -type f \\(-name \"*.bam\" -o -name \"*.cram\" \\) | samtools samples [options]\n"
+            "       find dir1 dir2 -type f \\(-name \"*.bam\" -o -name \"*.bai\" \\) | sort | paste - - | samtools samples -X [options]\n"
+            "\n"
+            "Options:\n"
+            "  -?              print help and exit\n"
+            "  -h              add the columns header before printing the results\n"
+            "  -i              test if the file is indexed.\n"
+            "  -T <tag>        provide the sample tag name from the @RG line [SM].\n"
+            "  -o <file>       output file [samtools_stdout].\n"
+            "  -f <file.fa>    load an indexed fasta file in the collection of references. Can be used multiple times.\n"
+            "  -F <file.txt>   read a file containing the paths to indexed fasta files. One path per line.\n"
+            "  -X              use a custom index file.\n"
+            "\n"
+            " Using -f or -F will add a column containing the path to the reference or \".\" if the reference was not found.\n"
+            "\n"
+    );
+}
+
+
+/** loads fasta fai file into FaidxPath, add it to params->faidx */
+static int load_dictionary(struct Params* params, const char* filename) {
+    FaidxPath* head = params->faidx;
+    FaidxPath* ptr = (FaidxPath*)malloc(sizeof(FaidxPath));
+    if (ptr == NULL) {
+        print_error_errno("samples", "Out of memory");
+        return EXIT_FAILURE;
+    }
+    ptr->filename = strdup(filename);
+    if (ptr->filename == NULL) {
+        free(ptr);
+        print_error_errno("samples", "Out of memory");
+        return EXIT_FAILURE;
+    }
+    ptr->faidx = fai_load(filename);
+    if (ptr->faidx == NULL) {
+        free(ptr->filename);
+        free(ptr);
+        print_error_errno("samples", "Cannot load index from \"%s\"", filename);
+        return EXIT_FAILURE;
+    }
+    /* insert at the beginning of the linked list */
+    params->faidx = ptr;
+    ptr->next = head;
+    return EXIT_SUCCESS;
+}
+
+/** load a faidx file and append it to params */
+static int load_dictionaries(Params* params, const char* filename) {
+    int ret;
+    htsFile* in;
+    int status = EXIT_SUCCESS;
+
+    in = hts_open(filename, "r");
+    if (in == NULL) {
+        print_error_errno("samples", "Cannot open \"%s\"", filename);
+        status = EXIT_FAILURE;
+    } else {
+        kstring_t ks = KS_INITIALIZE;
+        while ((ret = hts_getline(in, KS_SEP_LINE, &ks)) >= 0) {
+            if (load_dictionary(params, ks_str(&ks)) != EXIT_SUCCESS) {
+                status = EXIT_FAILURE;
+                break;
+            }
+        }
+        ks_free(&ks);
+        hts_close(in);
+    }
+    return status;
+}
+
+/** print the sample information, search for a reference */
+static int print_sample(
+        Params* params,
+        sam_hdr_t *header,
+        int has_index,
+        const char* sample,
+        const char* fname) {
+    fputs(sample, params->out);
+    fputc('\t', params->out);
+    fputs(fname, params->out);
+    if (params->test_index) {
+        fprintf(params->out, "\t%c", has_index ? 'Y' : 'N');
+    }
+    if (params->faidx != NULL) {
+        FaidxPath* ref = NULL;
+        FaidxPath* curr = params->faidx;
+        while (curr != NULL) {
+            /** check names and length are the same in the same order */
+            if (faidx_nseq(curr->faidx) == header->n_targets) {
+                int i;
+                for (i = 0; i < faidx_nseq(curr->faidx); i++) {
+                    /** check name is the same */
+                    if (strcmp(faidx_iseq(curr->faidx, i), header->target_name[i]) != 0) break;
+                    /** check length is the same */
+                    if (faidx_seq_len(curr->faidx, faidx_iseq(curr->faidx, i)) != header->target_len[i]) break;
+                }
+                /* the ref was found */
+                if (i == faidx_nseq(curr->faidx)) {
+                    ref = curr;
+                    break;
+                }
+            }
+            curr = curr->next;
+        }
+        fputc('\t', params->out);
+        if (ref == NULL) {
+            fputc('.', params->out);
+        } else {
+            fputs(curr->filename, params->out);
+        }
+    }
+    fputc('\n', params->out);
+    return 0;
+}
+
+/** open a sam file. Search for all samples in the @RG lines */
+static int print_samples(Params* params, const char* fname, const char* baifname) {
+    samFile *in = 0;
+    sam_hdr_t *header = NULL;
+    int n_rg;
+    int status = EXIT_SUCCESS;
+    khash_t(sm) *sample_set = NULL;
+    khint_t k;
+    int count_samples = 0;
+    int has_index = 0;
+
+    if ((sample_set = kh_init(sm)) == NULL) {
+        print_error("samples", "Failed to initialise sample hash");
+        status = EXIT_FAILURE;
+        goto end_print;
+    }
+
+    if ((in = sam_open_format(fname, "r", NULL)) == 0) {
+        print_error_errno("samples", "Failed to open \"%s\" for reading", fname);
+        status = EXIT_FAILURE;
+        goto end_print;
+    }
+    if ((header = sam_hdr_read(in)) == 0) {
+        print_error("samples", "Failed to read the header from \"%s\"", fname);
+        status = EXIT_FAILURE;
+        goto end_print;
+    }
+
+    /* try to load index if required */
+    if (params->test_index) {
+        hts_idx_t *bam_idx;
+        /* path to bam index was specified */
+        if (baifname != NULL) {
+            bam_idx = sam_index_load3(in, fname, baifname, HTS_IDX_SILENT_FAIL);
+        }
+        /* get default index */
+        else {
+            bam_idx = sam_index_load3(in, fname, NULL, HTS_IDX_SILENT_FAIL);
+        }
+        has_index = bam_idx != NULL;
+        if (bam_idx != NULL) hts_idx_destroy(bam_idx);
+        /* and we continue... we have tested the index file but we always test for the samples and the references */
+    }
+
+    /* get the RG lines */
+    n_rg = sam_hdr_count_lines(header, "RG");
+    if (n_rg > 0) {
+        int i, r, ret;
+        char* sample;
+        kstring_t sm_val = KS_INITIALIZE;
+        for (i = 0; i < n_rg; i++) {
+            r = sam_hdr_find_tag_pos(header, "RG", i, params->tag, &sm_val);
+            if (r < 0) continue;
+            k = kh_get(sm, sample_set, ks_str(&sm_val));
+            if (k != kh_end(sample_set)) continue;
+            sample = strdup(ks_str(&sm_val));
+            if (sample == NULL) {
+                print_error_errno("samples", "Out of memory");
+                status = EXIT_FAILURE;
+                goto end_print;
+            }
+            kh_put(sm, sample_set, sample, &ret);
+            if (ret < 0) {
+                print_error("samples", "Failed to insert key '%s' into sample_set", sample);
+                free(sample);
+                status = EXIT_FAILURE;
+                goto end_print;
+            }
+            ++count_samples;
+        }
+        ks_free(&sm_val);
+    }
+    if (count_samples == 0) {
+        print_sample(params, header, has_index, ".", fname);
+    } else {
+        for (k = kh_begin(sample_set); k != kh_end(sample_set); ++k) {
+            if (kh_exist(sample_set, k)) {
+                char* sample = (char*)kh_key(sample_set, k);
+                print_sample(params, header, has_index, sample, fname);
+            }
+        }
+    }
+
+end_print:
+    if (sample_set != NULL) {
+        for (k = kh_begin(sample_set); k != kh_end(sample_set); ++k) {
+            if (kh_exist(sample_set, k)) {
+                char* sample = (char*)kh_key(sample_set, k);
+                free(sample);
+            }
+        }
+        kh_destroy(sm, sample_set);
+    }
+    if (header != NULL) sam_hdr_destroy(header);
+    if (in != NULL) sam_close(in);
+
+    return status;
+}
+
+
+int main_samples(int argc, char** argv) {
+    int status = EXIT_SUCCESS;
+    int print_header = 0;
+    int has_index_file = 0;
+    Params params;
+    char* out_filename = NULL;
+    FaidxPath* fai;
+
+    strcpy(params.tag, "SM");
+    params.faidx = NULL;
+    params.test_index =0;
+
+    int opt;
+    while ((opt = getopt_long(argc, argv,  "?hiXo:f:F:T:", NULL, NULL)) != -1) {
+        switch (opt) {
+        case 'h':
+            print_header = 1;
+            break;
+        case 'o':
+            out_filename = optarg;
+            break;
+        case 'i':
+            params.test_index = 1;
+            break;
+        case 'f':
+            if (load_dictionary(&params, optarg) != EXIT_SUCCESS) {
+                return EXIT_FAILURE;
+            }
+            break;
+        case 'F':
+            if (load_dictionaries(&params, optarg) != EXIT_SUCCESS) {
+                return EXIT_FAILURE;
+            }
+            break;
+        case 'T':
+            if (strlen(optarg) != 2) {
+                print_error("samples", "Length of tag \"%s\" is not 2.", optarg);
+                return EXIT_FAILURE;
+            }
+            strcpy(params.tag, optarg);
+            break;
+        case '?':
+            usage_samples(samtools_stdout);
+            return EXIT_SUCCESS;
+        case 'X':
+            has_index_file = 1;
+            break;
+        default:
+            usage_samples(samtools_stderr);
+            return EXIT_FAILURE;
+        }
+    }
+
+    /* if no file was provided and input is the terminal, print the usage and exit */
+    if (argc == optind && isatty(STDIN_FILENO)) {
+       usage_samples(samtools_stderr);
+       return EXIT_FAILURE;
+    }
+
+    if (out_filename != NULL) {
+        params.out = fopen(out_filename, "w");
+        if (params.out == NULL) {
+            print_error_errno("samples", "Cannot open \"%s\" for writing", out_filename);
+            return EXIT_FAILURE;
+        }
+    } else {
+        params.out = samtools_stdout;
+    }
+
+    if (print_header) {
+        fprintf(params.out, "#%s\tPATH", params.tag);
+        if (params.test_index) fprintf(params.out, "\tINDEX");
+        if (params.faidx != NULL) fprintf(params.out, "\tREFERENCE");
+        fprintf(params.out, "\n");
+    }
+
+    /* no file was provided, input is stdin, each line contains the path to a bam file */
+    if (argc == optind) {
+        htsFile* fp = hts_open("-", "r");
+        if (fp == NULL) {
+            print_error_errno("samples", "Cannot read from stdin");
+            status = EXIT_FAILURE;
+        } else {
+            kstring_t ks = KS_INITIALIZE;
+            int ret;
+            while ((ret = hts_getline(fp, KS_SEP_LINE, &ks)) >= 0) {
+                char* bai_path = NULL;
+                if (has_index_file) {
+                    /* bam path and bam index file are separated by a tab */
+                    char* tab = strchr(ks_str(&ks), '\t');
+                    if (tab == NULL || *(tab+1) == '\0') {
+                        print_error_errno("samples", "Expected path-to-bam(tab)path-to-index but got \"%s\"", ks_str(&ks));
+                        status = EXIT_FAILURE;
+                        break;
+                    }
+                    *tab=0;
+                    bai_path = (tab + 1);
+                }
+                if (print_samples(&params, ks_str(&ks), bai_path) != EXIT_SUCCESS) {
+                    status = EXIT_FAILURE;
+                    break;
+                }
+            }
+            ks_free(&ks);
+            hts_close(fp);
+        }
+    }
+    /* loop over each file in argc/argv bam index provided */
+    else if (has_index_file) {
+        /* calculate number of input BAM files */
+        if ((argc - optind) % 2 != 0) {
+            print_error("samples","Odd number of filenames detected! Each BAM file should have an index file");
+            status = EXIT_FAILURE;
+        } else {
+            int i;
+            int n = (argc - optind ) / 2;
+            for (i = 0; i < n; i++) {
+                if (print_samples(&params, argv[optind+i], argv[optind+i+n]) != EXIT_SUCCESS) {
+                    status = EXIT_FAILURE;
+                    break;
+                }
+            }
+        }
+    } else {
+        int i;
+        for (i = optind; i < argc; i++) {
+            if (print_samples(&params, argv[i], NULL) != EXIT_SUCCESS) {
+                status = EXIT_FAILURE;
+                break;
+            }
+        }
+    }
+
+    fai = params.faidx;
+    while (fai != NULL) {
+        FaidxPath* next = fai -> next;
+        free(fai->filename);
+        fai_destroy(fai->faidx);
+        free(fai);
+        fai = next;
+    }
+
+    if (fflush(params.out) != 0) {
+        print_error_errno("samples", "Cannot flush output");
+        status = EXIT_FAILURE;
+    }
+    if (out_filename != NULL) {
+        fclose(params.out);
+    }
+
+    return status;
+}
diff --git a/samtools/bam_sort.c b/samtools/bam_sort.c
new file mode 100644
index 0000000..58ecdfd
--- /dev/null
+++ b/samtools/bam_sort.c
@@ -0,0 +1,3263 @@
+/*  bam_sort.c -- sorting and merging.
+
+    Copyright (C) 2008-2022 Genome Research Ltd.
+    Portions copyright (C) 2009-2012 Broad Institute.
+
+    Author: Heng Li <lh3@sanger.ac.uk>
+    Author: Martin Pollard <mp15@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <config.h>
+
+#include <stdbool.h>
+#include <stdlib.h>
+#include <ctype.h>
+#include <errno.h>
+#include <stdio.h>
+#include <string.h>
+#include <time.h>
+#include <sys/types.h>
+#include <sys/stat.h>
+#include <unistd.h>
+#include <getopt.h>
+#include <assert.h>
+#include <pthread.h>
+#include <inttypes.h>
+#include "htslib/ksort.h"
+#include "htslib/hts_os.h"
+#include "htslib/khash.h"
+#include "htslib/klist.h"
+#include "htslib/kstring.h"
+#include "htslib/sam.h"
+#include "htslib/hts_endian.h"
+#include "htslib/cram.h"
+#include "sam_opts.h"
+#include "samtools.h"
+#include "bedidx.h"
+#include "bam.h"
+
+
+// Struct which contains the sorting key for TemplateCoordinate sort.
+typedef struct {
+    int tid1;
+    int tid2;
+    hts_pos_t pos1;
+    hts_pos_t pos2;
+    bool neg1;
+    bool neg2;
+    const char *library;
+    char *mid;
+    char *name;
+    bool is_upper_of_pair;
+} template_coordinate_key_t;
+
+// Struct to store fixed buffers of template coordinate keys
+typedef struct {
+  size_t n; // the # of keys stored
+  size_t m; // the # of buffers allocated
+  size_t buffer_size; // # the fixed size of each buffer
+  template_coordinate_key_t **buffers; // the list of buffers
+} template_coordinate_keys_t;
+
+// Gets the idx'th key; does not OOB check
+static template_coordinate_key_t* template_coordinate_keys_get(template_coordinate_keys_t *keys, size_t idx) {
+    size_t buffer_idx = idx / keys->buffer_size; // the index of the buffer to retrieve in buffer
+    size_t buffer_offset = idx % keys->buffer_size; // the offset into the given buffer to retrieve
+    //assert(buffer_idx < keys->m);
+    //assert(buffer_offset < keys->buffer_size);
+    return &keys->buffers[buffer_idx][buffer_offset];
+}
+
+// Rellocates the buffers to hold at least max_k entries
+static int template_coordinate_keys_realloc(template_coordinate_keys_t *keys, int max_k) {
+    size_t cur_m = keys->m;
+    keys->m += 0x100;
+    //assert(keys->m > cur_m);
+    //assert(keys->m * keys->buffer_size >= max_k);
+    if ((keys->buffers = realloc(keys->buffers, keys->m * sizeof(template_coordinate_key_t*))) == NULL) {
+        print_error("sort", "couldn't reallocate memory for template coordinate key buffers");
+        return -1;
+    }
+    // allocate space for new buffers
+    int j;
+    for (j = cur_m; j < keys->m; ++j) {
+        if ((keys->buffers[j]= malloc(sizeof(template_coordinate_key_t) * keys->buffer_size)) == NULL) {
+            print_error("sort", "couldn't allocate memory for template coordinate key buffer");
+            return -1;
+        }
+    }
+    return 0;
+}
+
+
+// Struct which contains the a record, and the pointer to the sort tag (if any) or
+// a combined ref / position / strand.
+// Used to speed up sorts (coordinate, by-tag, and template-coordinate).
+typedef struct bam1_tag {
+    bam1_t *bam_record;
+    union {
+        const uint8_t *tag;
+        uint8_t pos_tid[12];
+        template_coordinate_key_t *key;
+    } u;
+} bam1_tag;
+
+/* Minimum memory required in megabytes before sort will attempt to run. This
+   is to prevent accidents where failing to use the -m option correctly results
+   in the creation of a temporary file for each read in the input file.
+   Don't forget to update the man page if you change this. */
+const size_t SORT_MIN_MEGS_PER_THREAD = 1;
+
+/* Default per-thread memory for sort. Must be >= SORT_MIN_MEGS_PER_THREAD.
+   Don't forget to update the man page if you change this. */
+const size_t SORT_DEFAULT_MEGS_PER_THREAD = 768;
+
+#if !defined(__DARWIN_C_LEVEL) || __DARWIN_C_LEVEL < 900000L
+#define NEED_MEMSET_PATTERN4
+#endif
+
+#ifdef NEED_MEMSET_PATTERN4
+void memset_pattern4(void *target, const void *pattern, size_t size) {
+    uint32_t* target_iter = target;
+    size_t loops = size/4;
+    size_t i;
+    for (i = 0; i < loops; ++i) {
+        memcpy(target_iter, pattern, 4);
+        ++target_iter;
+    }
+    if (size%4 != 0)
+        memcpy(target_iter, pattern, size%4);
+}
+#endif
+
+KHASH_INIT(c2c, char*, char*, 1, kh_str_hash_func, kh_str_hash_equal)
+KHASH_INIT(cset, char*, char, 0, kh_str_hash_func, kh_str_hash_equal)
+KHASH_MAP_INIT_STR(c2i, int)
+KHASH_MAP_INIT_STR(const_c2c, char *)
+
+#define hdrln_free_char(p)
+KLIST_INIT(hdrln, char*, hdrln_free_char)
+
+static template_coordinate_key_t* template_coordinate_key(bam1_t *b, template_coordinate_key_t *key, sam_hdr_t *hdr, khash_t(const_c2c) *lib_lookup);
+
+typedef enum {Coordinate, QueryName, TagCoordinate, TagQueryName, MinHash, TemplateCoordinate} SamOrder;
+static SamOrder g_sam_order = Coordinate;
+static char g_sort_tag[2] = {0,0};
+
+static int strnum_cmp(const char *_a, const char *_b)
+{
+    const unsigned char *a = (const unsigned char*)_a, *b = (const unsigned char*)_b;
+    const unsigned char *pa = a, *pb = b;
+    while (*pa && *pb) {
+        if (isdigit(*pa) && isdigit(*pb)) {
+            while (*pa == '0') ++pa;
+            while (*pb == '0') ++pb;
+            while (isdigit(*pa) && isdigit(*pb) && *pa == *pb) ++pa, ++pb;
+            if (isdigit(*pa) && isdigit(*pb)) {
+                int i = 0;
+                while (isdigit(pa[i]) && isdigit(pb[i])) ++i;
+                return isdigit(pa[i])? 1 : isdigit(pb[i])? -1 : (int)*pa - (int)*pb;
+            } else if (isdigit(*pa)) return 1;
+            else if (isdigit(*pb)) return -1;
+            else if (pa - a != pb - b) return pa - a < pb - b? 1 : -1;
+        } else {
+            if (*pa != *pb) return (int)*pa - (int)*pb;
+            ++pa; ++pb;
+        }
+    }
+    return *pa? 1 : *pb? -1 : 0;
+}
+
+#define HEAP_EMPTY (UINT64_MAX >> 1)
+
+typedef struct {
+    int i;
+    uint32_t tid;
+    uint64_t pos:63, rev:1, idx;
+    bam1_tag entry;
+} heap1_t;
+
+static inline int bam1_cmp_by_tag(const bam1_tag a, const bam1_tag b);
+static inline int bam1_cmp_by_minhash(const bam1_tag a, const bam1_tag b);
+static inline int bam1_cmp_template_coordinate(const bam1_tag a, const bam1_tag b);
+static khash_t(const_c2c) * lookup_libraries(sam_hdr_t *header);
+static void lib_lookup_destroy(khash_t(const_c2c) *lib_lookup);
+
+// Function to compare reads in the heap and determine which one is < the other
+// Note, unlike the bam1_cmp_by_X functions which return <0, 0, >0 this
+// is strictly 0 or 1 only.
+static inline int heap_lt(const heap1_t a, const heap1_t b)
+{
+    if (!a.entry.bam_record)
+        return 1;
+    if (!b.entry.bam_record)
+        return 0;
+
+    int t, fa, fb;
+    switch (g_sam_order) {
+        case Coordinate:
+            if (a.tid != b.tid) return a.tid > b.tid;
+            if (a.pos != b.pos) return a.pos > b.pos;
+            if (a.rev != b.rev) return a.rev > b.rev;
+            break;
+        case QueryName:
+            t = strnum_cmp(bam_get_qname(a.entry.bam_record), bam_get_qname(b.entry.bam_record));
+            if (t != 0) return t > 0;
+            fa = a.entry.bam_record->core.flag & 0xc0;
+            fb = b.entry.bam_record->core.flag & 0xc0;
+            if (fa != fb) return fa > fb;
+            break;
+        case TagQueryName:
+        case TagCoordinate:
+            t = bam1_cmp_by_tag(a.entry, b.entry);
+            if (t != 0) return t > 0;
+            break;
+        case MinHash:
+            t = bam1_cmp_by_minhash(a.entry, b.entry);
+            if (t != 0) return t > 0;
+            break;
+        case TemplateCoordinate:
+            t = bam1_cmp_template_coordinate(a.entry, b.entry);
+            if (t != 0) return t > 0;
+            break;
+        default:
+            print_error("heap_lt", "unknown sort order: %d", g_sam_order);
+            break;
+    }
+
+    // This compares by position in the input file(s)
+    if (a.i != b.i) return a.i > b.i;
+    return a.idx > b.idx;
+}
+
+KSORT_INIT(heap, heap1_t, heap_lt)
+
+typedef struct merged_header {
+    sam_hdr_t    *hdr;
+    kstring_t     out_rg;
+    kstring_t     out_pg;
+    kstring_t     out_co;
+    char        **target_name;
+    uint32_t     *target_len;
+    size_t        n_targets;
+    size_t        targets_sz;
+    khash_t(c2i) *sq_tids;
+    khash_t(cset) *rg_ids;
+    khash_t(cset) *pg_ids;
+    bool          have_hd;
+} merged_header_t;
+
+typedef struct trans_tbl {
+    int32_t n_targets;
+    int* tid_trans;
+    kh_c2c_t* rg_trans;
+    kh_c2c_t* pg_trans;
+    bool lost_coord_sort;
+} trans_tbl_t;
+
+static void trans_tbl_destroy(trans_tbl_t *tbl) {
+    khiter_t iter;
+
+    free(tbl->tid_trans);
+
+    /*
+     * The values for the tbl->rg_trans and tbl->pg_trans hashes are pointers
+     * to keys in the rg_ids and pg_ids sets of the merged_header_t, so
+     * they should not be freed here.
+     *
+     * The keys are unique to each hash entry, so they do have to go.
+     */
+
+    for (iter = kh_begin(tbl->rg_trans); iter != kh_end(tbl->rg_trans); ++iter) {
+        if (kh_exist(tbl->rg_trans, iter)) {
+            free(kh_key(tbl->rg_trans, iter));
+        }
+    }
+    for (iter = kh_begin(tbl->pg_trans); iter != kh_end(tbl->pg_trans); ++iter) {
+        if (kh_exist(tbl->pg_trans, iter)) {
+            free(kh_key(tbl->pg_trans, iter));
+        }
+    }
+
+    kh_destroy(c2c,tbl->rg_trans);
+    kh_destroy(c2c,tbl->pg_trans);
+}
+
+/*
+ *  Create a merged_header_t struct.
+ */
+
+static merged_header_t * init_merged_header() {
+    merged_header_t *merged_hdr;
+
+    merged_hdr = calloc(1, sizeof(*merged_hdr));
+    if (merged_hdr == NULL) return NULL;
+
+    merged_hdr->hdr = sam_hdr_init();
+    if (!merged_hdr->hdr) goto fail;
+
+    merged_hdr->targets_sz   = 16;
+    merged_hdr->target_name = malloc(merged_hdr->targets_sz
+                                     * sizeof(*merged_hdr->target_name));
+    if (NULL == merged_hdr->target_name) goto fail;
+
+    merged_hdr->target_len = malloc(merged_hdr->targets_sz
+                                    * sizeof(*merged_hdr->target_len));
+    if (NULL == merged_hdr->target_len) goto fail;
+
+    merged_hdr->sq_tids = kh_init(c2i);
+    if (merged_hdr->sq_tids == NULL) goto fail;
+
+    merged_hdr->rg_ids = kh_init(cset);
+    if (merged_hdr->rg_ids == NULL) goto fail;
+
+    merged_hdr->pg_ids = kh_init(cset);
+    if (merged_hdr->pg_ids == NULL) goto fail;
+
+    return merged_hdr;
+
+ fail:
+    perror("[init_merged_header]");
+    kh_destroy(cset, merged_hdr->pg_ids);
+    kh_destroy(cset, merged_hdr->rg_ids);
+    kh_destroy(c2i, merged_hdr->sq_tids);
+    free(merged_hdr->target_name);
+    free(merged_hdr->target_len);
+    sam_hdr_destroy(merged_hdr->hdr);
+    free(merged_hdr);
+    return NULL;
+}
+
+/* Some handy kstring manipulating functions */
+
+// Append char range to kstring
+static inline int range_to_ks(const char *src, int from, int to,
+                              kstring_t *dest) {
+    return kputsn(src + from, to - from, dest) != to - from;
+}
+
+// Append a kstring to a kstring
+static inline int ks_to_ks(kstring_t *src, kstring_t *dest) {
+    return kputsn(ks_str(src), ks_len(src), dest) != ks_len(src);
+}
+
+/*
+ * Generate a unique ID by appending a random suffix to a given prefix.
+ * existing_ids is the set of IDs that are already in use.
+ * If always_add_suffix is true, the suffix will always be included.
+ * If false, prefix will be returned unchanged if it isn't in existing_ids.
+ */
+
+static int gen_unique_id(char *prefix, khash_t(cset) *existing_ids,
+                         bool always_add_suffix, kstring_t *dest) {
+    khiter_t iter;
+
+    if (!always_add_suffix) {
+        // Try prefix on its own first
+        iter = kh_get(cset, existing_ids, prefix);
+        if (iter == kh_end(existing_ids)) { // prefix isn't used yet
+            dest->l = 0;
+            if (kputs(prefix, dest) == EOF) return -1;
+            return 0;
+        }
+    }
+
+    do {
+        dest->l = 0;
+        ksprintf(dest, "%s-%0lX", prefix, lrand48());
+        iter = kh_get(cset, existing_ids, ks_str(dest));
+    } while (iter != kh_end(existing_ids));
+
+    return 0;
+}
+
+/*
+ * Add the @HD line to the new header
+ * In practice the @HD line will come from the first input header.
+ */
+
+static int trans_tbl_add_hd(merged_header_t* merged_hdr,
+                            sam_hdr_t *translate) {
+    kstring_t hd_line = { 0, 0, NULL };
+    int res;
+
+    // TODO: handle case when @HD needs merging.
+    if (merged_hdr->have_hd) return 0;
+
+    res = sam_hdr_find_hd(translate, &hd_line);
+    if (res < -1) {
+        print_error("merge", "failed to get @HD line from header");
+        return -1;
+    }
+
+    if (res < 0) // Not found
+        return 0;
+
+    if (sam_hdr_add_lines(merged_hdr->hdr, hd_line.s, hd_line.l) < 0) {
+        print_error("merge", "failed to add @HD line to new header");
+        free(hd_line.s);
+        return -1;
+    }
+
+    free(hd_line.s);
+    merged_hdr->have_hd = true;
+
+    return 0;
+}
+
+/*
+ * Add @SQ records to the translation table.
+ *
+ * Go through the target list for the input header.  Any new targets found
+ * are added to the output header target list.  At the same time, a mapping
+ * from the input to output target ids is stored in tbl.
+ *
+ * If any new targets are found, the header text is scanned to find the
+ * corresponding @SQ records.  They are then copied into the
+ * merged_hdr->out_text kstring (which will eventually become the
+ * output header text).
+ *
+ * Returns 0 on success, -1 on failure.
+ */
+
+static int trans_tbl_add_sq(merged_header_t* merged_hdr, sam_hdr_t *translate,
+                            trans_tbl_t* tbl) {
+    int32_t i;
+    int min_tid = -1, res;
+    kstring_t sq_line = { 0, 0, NULL }, sq_sn = { 0, 0, NULL };
+
+    // Fill in the tid part of the translation table, adding new targets
+    // to the merged header as we go.
+
+    for (i = 0; i < sam_hdr_nref(translate); ++i) {
+        int trans_tid;
+        sq_sn.l = 0;
+        res = sam_hdr_find_tag_pos(translate, "SQ", i, "SN", &sq_sn);
+        if (res < 0) {
+            print_error("merge", "failed to get @SQ SN #%d from header", i + 1);
+            goto fail;
+        }
+
+        trans_tid = sam_hdr_name2tid(merged_hdr->hdr, sq_sn.s);
+        if (trans_tid < -1) {
+            print_error("merge", "failed to lookup ref");
+            goto fail;
+        }
+
+        if (trans_tid < 0) {
+            // Append missing entries to out_hdr
+            sq_line.l = 0;
+            res = sam_hdr_find_line_id(translate, "SQ", "SN", sq_sn.s, &sq_line);
+            if (res < 0) {
+                print_error("merge", "failed to get @SQ SN:%s from header", sq_sn.s);
+                goto fail;
+            }
+
+            trans_tid = sam_hdr_nref(merged_hdr->hdr);
+
+            res = sam_hdr_add_lines(merged_hdr->hdr, sq_line.s, sq_line.l);
+            if (res < 0) {
+                print_error("merge", "failed to add @SQ SN:%s to new header", sq_sn.s);
+                goto fail;
+            }
+        }
+        tbl->tid_trans[i] = trans_tid;
+
+        if (tbl->tid_trans[i] > min_tid) {
+            min_tid = tbl->tid_trans[i];
+        } else {
+            tbl->lost_coord_sort = true;
+        }
+    }
+
+    free(sq_line.s);
+    free(sq_sn.s);
+
+    return 0;
+
+ fail:
+    free(sq_line.s);
+    free(sq_sn.s);
+    return -1;
+}
+
+/*
+ * Common code for setting up RG and PG record ID tag translation.
+ *
+ * is_rg is true for RG translation, false for PG.
+ * translate is the input bam header
+ * merge is true if tags with the same ID are to be merged.
+ * known_ids is the set of IDs already in the output header.
+ * id_map is the translation map from input header IDs to output header IDs
+ * If override is set, it will be used to replace the existing ID (RG only)
+ *
+ * known_ids and id_map have entries for the new IDs added to them.
+ *
+ * Return value is a linked list of header lines with the translated IDs,
+ * or NULL if something went wrong (probably out of memory).
+ *
+ */
+
+static klist_t(hdrln) * trans_rg_pg(bool is_rg, sam_hdr_t *translate,
+                                    bool merge, khash_t(cset)* known_ids,
+                                    khash_t(c2c)* id_map, char *override) {
+    khiter_t iter;
+    int num_ids, i;
+    const char *rec_type = is_rg ? "RG" : "PG";
+    klist_t(hdrln) *hdr_lines;
+
+    hdr_lines = kl_init(hdrln);
+
+    // Search through translate's header
+    num_ids = sam_hdr_count_lines(translate, rec_type);
+    if (num_ids < 0)
+        goto fail;
+
+    for (i = 0; i < num_ids; i++) {
+        kstring_t orig_id = { 0, 0, NULL };        // ID in original header
+        kstring_t transformed_id = { 0, 0, NULL }; // ID in output header
+        char *map_value;    // Value to store in id_map
+        bool id_changed;    // Have we changed the ID?
+        bool not_found_in_output; // ID isn't in the output header (yet)
+
+        if (sam_hdr_find_tag_pos(translate, rec_type, i, "ID", &orig_id) < 0)
+            goto fail;
+
+        // is our matched ID in our output ID set already?
+        iter = kh_get(cset, known_ids, ks_str(&orig_id));
+        not_found_in_output = (iter == kh_end(known_ids));
+
+        if (override) {
+            // Override original ID (RG only)
+#ifdef OVERRIDE_DOES_NOT_MERGE
+            if (gen_unique_id(override, known_ids, false, &transformed_id))
+                goto memfail;
+            not_found_in_output = true;  // As ID now unique
+#else
+            if (kputs(override, &transformed_id) == EOF) goto memfail;
+            // Know about override already?
+            iter = kh_get(cset, known_ids, ks_str(&transformed_id));
+            not_found_in_output = (iter == kh_end(known_ids));
+#endif
+            id_changed = true;
+        } else {
+            if ( not_found_in_output || merge) {
+                // Not in there or merging so can add it as 1-1 mapping
+                if (ks_to_ks(&orig_id, &transformed_id)) goto memfail;
+                id_changed = false;
+            } else {
+                // It's in there so we need to transform it by appending
+                // a random number to the id
+                if (gen_unique_id(ks_str(&orig_id), known_ids,
+                                  true, &transformed_id))
+                    goto memfail;
+                id_changed = true;
+                not_found_in_output = true;  // As ID now unique
+            }
+        }
+
+        // Does this line need to go into our output header?
+        if (not_found_in_output) {
+            // Take matched line and replace ID with transformed_id
+            kstring_t new_hdr_line = { 0, 0, NULL };
+            if (sam_hdr_find_line_id(translate, rec_type,
+                                     "ID", ks_str(&orig_id), &new_hdr_line) < 0){
+                goto fail;
+            }
+
+            if (id_changed) {
+                char *idp = strstr(ks_str(&new_hdr_line), "\tID:"), *id_end;
+                ptrdiff_t id_offset, id_len;
+                if (!idp) {
+                    print_error("merge", "failed to find ID in \"%s\"\n",
+                                ks_str(&new_hdr_line));
+                    goto fail;
+                }
+                idp += 4;
+                for (id_end = idp; *id_end >= '\n'; id_end++) {}
+
+                id_offset = idp - new_hdr_line.s;
+                id_len = id_end - idp;
+
+                if (id_len < transformed_id.l) {
+                    if (ks_resize(&new_hdr_line, new_hdr_line.l
+                                  + transformed_id.l - id_len + 1/*nul*/))
+                        goto fail;
+                }
+                if (id_len != transformed_id.l) {
+                    memmove(new_hdr_line.s + id_offset + transformed_id.l,
+                            new_hdr_line.s + id_offset + id_len,
+                            new_hdr_line.l - id_offset - id_len + 1);
+                }
+                memcpy(new_hdr_line.s + id_offset, transformed_id.s,
+                       transformed_id.l);
+            }
+
+            // append line to output linked list
+            char** ln = kl_pushp(hdrln, hdr_lines);
+            *ln = ks_release(&new_hdr_line);  // Give away to linked list
+
+            // Need to add it to known_ids set
+            int in_there = 0;
+            iter = kh_put(cset, known_ids, ks_str(&transformed_id), &in_there);
+            if (in_there < 0) goto memfail;
+            assert(in_there > 0);  // Should not already be in the map
+            map_value = ks_release(&transformed_id);
+        } else {
+            // Use existing string in id_map
+            assert(kh_exist(known_ids, iter));
+            map_value = kh_key(known_ids, iter);
+            free(ks_release(&transformed_id));
+        }
+
+        // Insert it into our translation map
+        int in_there = 0;
+        iter = kh_put(c2c, id_map, ks_release(&orig_id), &in_there);
+        kh_value(id_map, iter) = map_value;
+    }
+
+    // If there are no RG lines in the file and we are overriding add one
+    if (is_rg && override && hdr_lines->size == 0) {
+        kstring_t new_id = {0, 0, NULL};
+        kstring_t line = {0, 0, NULL};
+        kstring_t empty = {0, 0, NULL};
+        int in_there = 0;
+        char** ln;
+
+        // Get the new ID
+        if (gen_unique_id(override, known_ids, false, &new_id))
+            goto memfail;
+
+        // Make into a header line and add to linked list
+        ksprintf(&line, "@RG\tID:%s", ks_str(&new_id));
+        ln = kl_pushp(hdrln, hdr_lines);
+        *ln = ks_release(&line);
+
+        // Put into known_ids set
+        iter = kh_put(cset, known_ids, ks_str(&new_id), &in_there);
+        if (in_there < 0) goto memfail;
+        assert(in_there > 0);  // Should be a new entry
+
+        // Put into translation map (key is empty string)
+        if (kputs("", &empty) == EOF) goto memfail;
+        iter = kh_put(c2c, id_map, ks_release(&empty), &in_there);
+        if (in_there < 0) goto memfail;
+        assert(in_there > 0);  // Should be a new entry
+        kh_value(id_map, iter) = ks_release(&new_id);
+    }
+
+    return hdr_lines;
+
+ memfail:
+    perror(__func__);
+ fail:
+    if (hdr_lines) kl_destroy(hdrln, hdr_lines);
+    return NULL;
+}
+
+/*
+ * Common code for completing RG and PG record translation.
+ *
+ * Input is a list of header lines, and the mapping from input to
+ * output @PG record IDs.
+ *
+ * RG and PG records can contain tags that cross-reference to other @PG
+ * records.  This fixes the tags to contain the new IDs before adding
+ * them to the output header text.
+ */
+
+static int finish_rg_pg(bool is_rg, klist_t(hdrln) *hdr_lines,
+                        khash_t(c2c)* pg_map, kstring_t *out_text) {
+    const char *search = is_rg ? "\tPG:" : "\tPP:";
+    khiter_t idx;
+    char *line = NULL;
+
+    while ((kl_shift(hdrln, hdr_lines, &line)) == 0) {
+        char *id = strstr(line, search); // Look for tag to fix
+        int pos1 = 0, pos2 = 0;
+        char *new_id = NULL;
+
+        if (id) {
+            // Found a tag.  Look up the value in the translation map
+            // to see what it should be changed to in the output file.
+            char *end, tmp;
+
+            id += 4; // Point to value
+            end = strchr(id, '\t');  // Find end of tag
+            if (!end) end = id + strlen(id);
+
+            tmp = *end;
+            *end = '\0'; // Temporarily get the value on its own.
+
+            // Look-up in translation table
+            idx = kh_get(c2c, pg_map, id);
+            if (idx == kh_end(pg_map)) {
+                // Not found, warn.
+                fprintf(stderr, "[W::%s] Tag %s%s not found in @PG records\n",
+                        __func__, search + 1, id);
+            } else {
+                // Remember new id and splice points on original string
+                new_id = kh_value(pg_map, idx);
+                pos1 = id - line;
+                pos2 = end - line;
+            }
+
+            *end = tmp; // Restore string
+        }
+
+        // Copy line to output:
+        // line[0..pos1), new_id (if not NULL), line[pos2..end), '\n'
+
+        if (pos1 && range_to_ks(line, 0, pos1, out_text)) goto memfail;
+        if (new_id && kputs(new_id, out_text) == EOF) goto memfail;
+        if (kputs(line + pos2, out_text) == EOF) goto memfail;
+        if (kputc('\n', out_text) == EOF) goto memfail;
+        free(line);   // No longer needed
+        line = NULL;
+    }
+
+    return 0;
+
+ memfail:
+    perror(__func__);
+    free(line);  // Prevent leakage as no longer on list
+    return -1;
+}
+
+/*
+ * Build the translation table for an input *am file.  This stores mappings
+ * which allow IDs to be converted from those used in the input file
+ * to the ones which will be used in the output.  The mappings are for:
+ *   Reference sequence IDs (for @SQ records)
+ *   @RG record ID tags
+ *   @PG record ID tags
+ *
+ * At the same time, new header text is built up by copying records
+ * from the input bam file.  This will eventually become the header for
+ * the output file.  When copied, the ID tags for @RG and @PG records
+ * are replaced with their values.  The @PG PP: and @RG PG: tags
+ * are also modified if necessary.
+ *
+ * merged_hdr holds state on the output header (which IDs are present, etc.)
+ * translate is the input header
+ * tbl is the translation table that gets filled in.
+ * merge_rg controls merging of @RG records
+ * merge_pg controls merging of @PG records
+ * If rg_override is not NULL, it will be used to replace the existing @RG ID
+ *
+ * Returns 0 on success, -1 on failure.
+ */
+
+static int trans_tbl_init(merged_header_t* merged_hdr, sam_hdr_t* translate,
+                          trans_tbl_t* tbl, bool merge_rg, bool merge_pg,
+                          bool copy_co, char* rg_override)
+{
+    kstring_t lines = { 0, 0, NULL };
+    klist_t(hdrln) *rg_list = NULL;
+    klist_t(hdrln) *pg_list = NULL;
+
+    tbl->n_targets = sam_hdr_nref(translate);
+    tbl->rg_trans = tbl->pg_trans = NULL;
+    tbl->tid_trans = (int*)calloc(tbl->n_targets ? tbl->n_targets : 1,
+                                  sizeof(int));
+    if (tbl->tid_trans == NULL) goto memfail;
+    tbl->rg_trans = kh_init(c2c);
+    if (tbl->rg_trans == NULL) goto memfail;
+    tbl->pg_trans = kh_init(c2c);
+    if (tbl->pg_trans == NULL) goto memfail;
+
+    tbl->lost_coord_sort = false;
+
+    // Get the @HD record (if not there already).
+    if (trans_tbl_add_hd(merged_hdr, translate)) goto fail;
+
+    // Fill in map and add header lines for @SQ records
+    if (trans_tbl_add_sq(merged_hdr, translate, tbl)) goto fail;
+
+    // Get translated header lines and fill in map for @RG records
+    rg_list = trans_rg_pg(true, translate, merge_rg, merged_hdr->rg_ids,
+                          tbl->rg_trans, rg_override);
+    if (!rg_list) goto fail;
+
+    // Get translated header lines and fill in map for @PG records
+    pg_list = trans_rg_pg(false, translate, merge_pg, merged_hdr->pg_ids,
+                          tbl->pg_trans, NULL);
+    if (!pg_list) goto fail;
+
+    // Fix-up PG: tags in the new @RG records and add to output
+    if (finish_rg_pg(true, rg_list, tbl->pg_trans, &merged_hdr->out_rg))
+        goto fail;
+
+    // Fix-up PP: tags in the new @PG records and add to output
+    lines.l = 0;
+    if (finish_rg_pg(false, pg_list, tbl->pg_trans, &merged_hdr->out_pg))
+        goto fail;
+
+    kl_destroy(hdrln, rg_list); rg_list = NULL;
+    kl_destroy(hdrln, pg_list); pg_list = NULL;
+
+    if (copy_co) {
+        // Just append @CO headers without translation
+        int num_co = sam_hdr_count_lines(translate, "CO"), i;
+        if (num_co < 0)
+            goto fail;
+
+        for (i = 0; i < num_co; i++) {
+            if (sam_hdr_find_line_pos(translate, "CO", i, &lines) < 0)
+                goto fail;
+            if (ks_to_ks(&lines, &merged_hdr->out_co))
+                goto fail;
+            if (kputc('\n', &merged_hdr->out_co) < 0)
+                goto fail;
+        }
+    }
+
+    free(lines.s);
+
+    return 0;
+
+ memfail:
+    perror(__func__);
+ fail:
+    trans_tbl_destroy(tbl);
+    if (rg_list) kl_destroy(hdrln, rg_list);
+    if (pg_list) kl_destroy(hdrln, pg_list);
+    free(lines.s);
+    return -1;
+}
+
+static int finish_merged_header(merged_header_t *merged_hdr) {
+    if (sam_hdr_add_lines(merged_hdr->hdr, ks_c_str(&merged_hdr->out_rg),
+                          ks_len(&merged_hdr->out_rg)) < 0)
+        return -1;
+    if (sam_hdr_add_lines(merged_hdr->hdr, ks_c_str(&merged_hdr->out_pg),
+                          ks_len(&merged_hdr->out_pg)) < 0)
+        return -1;
+    if (sam_hdr_add_lines(merged_hdr->hdr, ks_c_str(&merged_hdr->out_co),
+                          ks_len(&merged_hdr->out_co)) < 0)
+        return -1;
+
+    return 0;
+}
+
+/*
+ * Free a merged_header_t struct and all associated data.
+ *
+ * Note that the keys to the rg_ids and pg_ids sets are also used as
+ * values in the translation tables.  This function should therefore not
+ * be called until the translation tables are no longer needed.
+ */
+
+static void free_merged_header(merged_header_t *merged_hdr) {
+    size_t i;
+    khiter_t iter;
+    if (!merged_hdr) return;
+    free(ks_release(&merged_hdr->out_rg));
+    free(ks_release(&merged_hdr->out_pg));
+    free(ks_release(&merged_hdr->out_co));
+    if (merged_hdr->target_name) {
+        for (i = 0; i < merged_hdr->n_targets; i++) {
+            free(merged_hdr->target_name[i]);
+        }
+        free(merged_hdr->target_name);
+    }
+    free(merged_hdr->target_len);
+    kh_destroy(c2i, merged_hdr->sq_tids);
+
+    if (merged_hdr->rg_ids) {
+        for (iter = kh_begin(merged_hdr->rg_ids);
+             iter != kh_end(merged_hdr->rg_ids); ++iter) {
+            if (kh_exist(merged_hdr->rg_ids, iter))
+                free(kh_key(merged_hdr->rg_ids, iter));
+        }
+        kh_destroy(cset, merged_hdr->rg_ids);
+    }
+
+    if (merged_hdr->pg_ids) {
+        for (iter = kh_begin(merged_hdr->pg_ids);
+             iter != kh_end(merged_hdr->pg_ids); ++iter) {
+            if (kh_exist(merged_hdr->pg_ids, iter))
+                free(kh_key(merged_hdr->pg_ids, iter));
+        }
+        kh_destroy(cset, merged_hdr->pg_ids);
+    }
+
+    free(merged_hdr);
+}
+
+static void bam_translate(bam1_t* b, trans_tbl_t* tbl)
+{
+    // Update target id if not unmapped tid
+    if ( b->core.tid >= 0 ) { b->core.tid = tbl->tid_trans[b->core.tid]; }
+    if ( b->core.mtid >= 0 ) { b->core.mtid = tbl->tid_trans[b->core.mtid]; }
+
+    // If we have a RG update it
+    uint8_t *rg = bam_aux_get(b, "RG");
+    if (rg) {
+        char* decoded_rg = bam_aux2Z(rg);
+        khiter_t k = kh_get(c2c, tbl->rg_trans, decoded_rg);
+        if (k != kh_end(tbl->rg_trans)) {
+            char* translate_rg = kh_value(tbl->rg_trans,k);
+            bam_aux_del(b, rg);
+            if (translate_rg) {
+                bam_aux_append(b, "RG", 'Z', strlen(translate_rg) + 1,
+                               (uint8_t*)translate_rg);
+            }
+        } else {
+            char *tmp = strdup(decoded_rg);
+            fprintf(stderr,
+                    "[bam_translate] RG tag \"%s\" on read \"%s\" encountered "
+                    "with no corresponding entry in header, tag lost. "
+                    "Unknown tags are only reported once per input file for "
+                    "each tag ID.\n",
+                    decoded_rg, bam_get_qname(b));
+            bam_aux_del(b, rg);
+            // Prevent future whinges
+            if (tmp) {
+                int in_there = 0;
+                k = kh_put(c2c, tbl->rg_trans, tmp, &in_there);
+                if (in_there > 0) kh_value(tbl->rg_trans, k) = NULL;
+            }
+        }
+    }
+
+    // If we have a PG update it
+    uint8_t *pg = bam_aux_get(b, "PG");
+    if (pg) {
+        char* decoded_pg = bam_aux2Z(pg);
+        khiter_t k = kh_get(c2c, tbl->pg_trans, decoded_pg);
+        if (k != kh_end(tbl->pg_trans)) {
+            char* translate_pg = kh_value(tbl->pg_trans,k);
+            bam_aux_del(b, pg);
+            if (translate_pg) {
+                bam_aux_append(b, "PG", 'Z', strlen(translate_pg) + 1,
+                               (uint8_t*)translate_pg);
+            }
+        } else {
+            char *tmp = strdup(decoded_pg);
+            fprintf(stderr,
+                    "[bam_translate] PG tag \"%s\" on read \"%s\" encountered "
+                    "with no corresponding entry in header, tag lost. "
+                    "Unknown tags are only reported once per input file for "
+                    "each tag ID.\n",
+                    decoded_pg, bam_get_qname(b));
+            bam_aux_del(b, pg);
+            // Prevent future whinges
+            if (tmp) {
+                int in_there = 0;
+                k = kh_put(c2c, tbl->pg_trans, tmp, &in_there);
+                if (in_there > 0) kh_value(tbl->pg_trans, k) = NULL;
+            }
+        }
+    }
+}
+
+int* rtrans_build(int n, int n_targets, trans_tbl_t* translation_tbl)
+{
+    // Create reverse translation table for tids
+    int* rtrans = (int*)malloc(sizeof(int32_t)*n*n_targets);
+    const int32_t NOTID = INT32_MIN;
+    if (!rtrans) return NULL;
+    memset_pattern4((void*)rtrans, &NOTID, sizeof(int32_t)*n*n_targets);
+    int i;
+    for (i = 0; i < n; ++i) {
+        int j;
+        for (j = 0; j < (translation_tbl+i)->n_targets; ++j) {
+            if ((translation_tbl+i)->tid_trans[j] != -1) {
+                rtrans[i*n_targets + (translation_tbl+i)->tid_trans[j]] = j;
+            }
+        }
+    }
+
+    return rtrans;
+}
+
+#define MERGE_RG          1 // Attach RG tag based on filename
+#define MERGE_UNCOMP      2 // Generate uncompressed BAM
+#define MERGE_LEVEL1      4 // Compress the BAM at level 1 (fast) mode
+#define MERGE_FORCE       8 // Overwrite output BAM if it exists
+#define MERGE_COMBINE_RG 16 // Combine RG tags frather than redefining them
+#define MERGE_COMBINE_PG 32 // Combine PG tags frather than redefining them
+#define MERGE_FIRST_CO   64 // Use only first file's @CO headers (sort cmd only)
+
+
+static hts_reglist_t *duplicate_reglist(const hts_reglist_t *rl, int rn) {
+    if (!rl)
+        return NULL;
+
+    hts_reglist_t *new_rl = calloc(rn, sizeof(hts_reglist_t));
+    if (!new_rl)
+        return NULL;
+
+    int i;
+    for (i=0; i < rn; i++) {
+        new_rl[i].tid     = rl[i].tid;
+        new_rl[i].count   = rl[i].count;
+        new_rl[i].min_beg = rl[i].min_beg;
+        new_rl[i].max_end = rl[i].max_end;
+
+        new_rl[i].reg = rl[i].reg;
+        new_rl[i].intervals = malloc(new_rl[i].count * sizeof(hts_pair_pos_t));
+        if (!new_rl[i].intervals) {
+            hts_reglist_free(new_rl, i);
+            return NULL;
+        }
+        memcpy(new_rl[i].intervals, rl[i].intervals, new_rl[i].count * sizeof(hts_pair_pos_t));
+    }
+
+    return new_rl;
+}
+
+/*
+ * How merging is handled
+ *
+ * If a header is defined use we will use that as our output header
+ * otherwise we use the first header from the first input file.
+ *
+ * Now go through each file and create a translation table for that file for:
+ * -RG
+ * -tid
+ * -PG tags
+ *
+ * Then whenever we read a record from a bam we translate that read before
+ * stashing it in the hash.
+ *
+ * In the actual merge, a read is read from each input file, translated and
+ * stashed in the hash. This assumes that all input files are sorted in the
+ * same way.  Next we just extract the next position ordered read from the
+ * hash, and replace it if there are still reads left in it's source input
+ * file. Finally we write our chosen read it to the output file.
+ */
+
+/*!
+  @abstract    Merge multiple sorted BAM.
+  @param  sam_order   the order in which the data was sorted
+  @param  sort_tag    if non-null, the tag that data was sorted by
+  @param  out         output BAM file name
+  @param  mode        sam_open() mode to be used to create the final output file
+                      (overrides level settings from UNCOMP and LEVEL1 flags)
+  @param  headers     name of SAM file from which to copy '@' header lines,
+                      or NULL to copy them from the first file to be merged
+  @param  n           number of files to be merged
+  @param  fn          names of files to be merged
+  @param  flag        flags that control how the merge is undertaken
+  @param  reg         region to merge
+  @param  n_threads   number of threads to use (passed to htslib)
+  @param  cmd         command name (used in print_error() etc)
+  @param  in_fmt      format options for input files
+  @param  out_fmt     output file format and options
+  @param  write_index create the index, together with the output file
+  @param  arg_list    command string for PG line
+  @param  no_pg       if 1, do not add a new PG line
+  @discussion Padding information may NOT correctly maintained. This
+  function is NOT thread safe.
+ */
+int bam_merge_core2(SamOrder sam_order, char* sort_tag, const char *out, const char *mode,
+                    const char *headers, int n, char * const *fn, char * const *fn_idx,
+                    const char *fn_bed, int flag, const char *reg, int n_threads,
+                    const char *cmd, const htsFormat *in_fmt, const htsFormat *out_fmt,
+                    int write_index, char *arg_list, int no_pg)
+{
+    samFile *fpout, **fp = NULL;
+    heap1_t *heap = NULL;
+    sam_hdr_t *hout = NULL;
+    sam_hdr_t *hin  = NULL;
+    int i, j, *RG_len = NULL;
+    uint64_t idx = 0;
+    char **RG = NULL;
+    hts_itr_t **iter = NULL;
+    sam_hdr_t **hdr = NULL;
+    trans_tbl_t *translation_tbl = NULL;
+    int *rtrans = NULL;
+    char *out_idx_fn = NULL;
+    void *hreg = NULL;
+    hts_reglist_t *lreg = NULL;
+    merged_header_t *merged_hdr = init_merged_header();
+    if (!merged_hdr) return -1;
+    refs_t *refs = NULL;
+    template_coordinate_keys_t *keys = NULL;
+    khash_t(const_c2c) *lib_lookup = NULL;
+
+    // Is there a specified pre-prepared header to use for output?
+    if (headers) {
+        samFile* fpheaders = sam_open(headers, "r");
+        if (fpheaders == NULL) {
+            print_error_errno(cmd, "cannot open \"%s\"", headers);
+            return -1;
+        }
+        hin = sam_hdr_read(fpheaders);
+        sam_close(fpheaders);
+        if (hin == NULL) {
+            print_error(cmd, "couldn't read headers from \"%s\"", headers);
+            goto mem_fail;
+        }
+    }
+
+    g_sam_order = sam_order;
+    if (sam_order == TagQueryName || sam_order == TagCoordinate) {
+        g_sort_tag[0] = sort_tag[0];
+        g_sort_tag[1] = sort_tag[0] ? sort_tag[1] : '\0';
+    }
+
+    fp = (samFile**)calloc(n, sizeof(samFile*));
+    if (!fp) goto mem_fail;
+    heap = (heap1_t*)calloc(n, sizeof(heap1_t));
+    if (!heap) goto mem_fail;
+    iter = (hts_itr_t**)calloc(n, sizeof(hts_itr_t*));
+    if (!iter) goto mem_fail;
+    hdr = (sam_hdr_t**)calloc(n, sizeof(sam_hdr_t*));
+    if (!hdr) goto mem_fail;
+    translation_tbl = (trans_tbl_t*)calloc(n, sizeof(trans_tbl_t));
+    if (!translation_tbl) goto mem_fail;
+    RG = (char**)calloc(n, sizeof(char*));
+    if (!RG) goto mem_fail;
+
+    // prepare RG tag from file names
+    if (flag & MERGE_RG) {
+        RG_len = (int*)calloc(n, sizeof(int));
+        if (!RG_len) goto mem_fail;
+        for (i = 0; i != n; ++i) {
+            int l = strlen(fn[i]);
+            const char *s = fn[i];
+            if (l > 4 && (strcmp(s + l - 4, ".bam") == 0 || strcmp(s + l - 4, ".sam") == 0)) l -= 4;
+            if (l > 5 && strcmp(s + l - 5, ".cram") == 0) l -= 5;
+            for (j = l - 1; j >= 0; --j) if (s[j] == '/') break;
+            ++j; l -= j;
+            RG[i] = (char*)calloc(l + 1, 1);
+            if (!RG[i]) goto mem_fail;
+            RG_len[i] = l;
+            strncpy(RG[i], s + j, l);
+        }
+    }
+
+    if (hin) {
+        // Populate merged_hdr from the pre-prepared header
+        trans_tbl_t dummy;
+        int res;
+        res = trans_tbl_init(merged_hdr, hin, &dummy, flag & MERGE_COMBINE_RG,
+                             flag & MERGE_COMBINE_PG, true, NULL);
+        trans_tbl_destroy(&dummy);
+        if (res) return -1; // FIXME: memory leak
+    }
+
+    // open and read the header from each file
+    for (i = 0; i < n; ++i) {
+        sam_hdr_t *hin;
+        fp[i] = sam_open_format(fn[i], "r", in_fmt);
+        if (fp[i] == NULL) {
+            print_error_errno(cmd, "fail to open \"%s\"", fn[i]);
+            goto fail;
+        }
+        hin = sam_hdr_read(fp[i]);
+        if (hin == NULL) {
+            print_error(cmd, "failed to read header from \"%s\"", fn[i]);
+            goto fail;
+        }
+
+        if (trans_tbl_init(merged_hdr, hin, translation_tbl+i,
+                           flag & MERGE_COMBINE_RG, flag & MERGE_COMBINE_PG,
+                           (flag & MERGE_FIRST_CO)? (i == 0) : true,
+                           RG[i]))
+            goto fail;
+
+        hdr[i] = hin;
+
+        int order_ok = 1;
+        if ((translation_tbl+i)->lost_coord_sort && (sam_order == Coordinate || sam_order == MinHash)) {
+            fprintf(stderr, "[bam_merge_core] Order of targets in file %s caused coordinate sort to be lost\n", fn[i]);
+            order_ok = 0;
+        }
+
+        if (!refs)
+            refs = cram_get_refs(fp[i]);
+
+        if (order_ok && refs && hts_set_opt(fp[i], CRAM_OPT_SHARED_REF, refs))
+            goto fail;
+    }
+
+    // Did we get an @HD line?
+    if (!merged_hdr->have_hd) {
+        fprintf(stderr, "[W::%s] No @HD tag found.\n", __func__);
+        /* FIXME:  Should we add an @HD line here, and if so what should
+           we put in it? Ideally we want a way of getting htslib to tell
+           us the SAM version number to assume given no @HD line.  Is
+           it also safe to assume that the output is coordinate sorted?
+           SO: is optional so we don't have to have it.*/
+        /* ksprintf(&merged_hdr->out_hd, "@HD\tVN:1.5\tSO:coordinate\n"); */
+    }
+
+    // Transform the header into standard form
+    if (finish_merged_header(merged_hdr) < 0)
+        goto fail;
+
+    hout = merged_hdr->hdr;
+    if (!hout)
+        goto fail;
+
+    // If we're only merging a specified region move our iters to start at that point
+    int tid, nreg;
+    hts_pos_t beg, end;
+
+    if (fn_bed) {
+        hreg = bed_read(fn_bed);
+        if (!hreg) {
+            fprintf(stderr, "[%s] Could not read BED file: \"%s\"\n", __func__, fn_bed);
+            goto fail;
+        }
+        bed_unify(hreg);
+        lreg = bed_reglist(hreg, ALL, &nreg);
+        if (!lreg || !nreg) {
+            fprintf(stderr, "[%s] Null or empty region list\n", __func__);
+            goto fail;
+        }
+    } else if (reg) {
+        rtrans = rtrans_build(n, sam_hdr_nref(hout), translation_tbl);
+        if (!rtrans) goto mem_fail;
+
+        if (!sam_parse_region(hout, reg, &tid, &beg, &end, 0)) {
+            fprintf(stderr, "[%s] Badly formatted region or unknown reference name: \"%s\"\n", __func__, reg);
+            goto fail;
+        }
+
+    }
+
+    if (reg || fn_bed) {
+        hts_idx_t *reg_idx = NULL;
+        for (i = 0; i < n; ++i) {
+
+            // If index filename has not been specified, look in the BAM folder
+            if (fn_idx != NULL) {
+                reg_idx = sam_index_load2(fp[i], fn[i], fn_idx[i]);
+            } else {
+                reg_idx = sam_index_load(fp[i], fn[i]);
+            }
+            if (reg_idx == NULL) {
+                fprintf(stderr, "[%s] failed to load index for %s. Random alignment retrieval only works for indexed BAM or CRAM files.\n",
+                        __func__, fn[i]);
+                free(rtrans);
+                rtrans = NULL;
+                goto fail;
+            }
+
+            int mapped_tid = INT32_MIN;
+            if (fn_bed) {
+                hts_reglist_t *rl = duplicate_reglist(lreg, nreg);
+                iter[i] = sam_itr_regions(reg_idx, hdr[i], rl, nreg);
+            } else {
+                // (rtrans[i*n+tid]) Look up what hout tid translates to in input tid space
+                mapped_tid = rtrans[i*sam_hdr_nref(hout)+tid];
+                if (mapped_tid != INT32_MIN) {
+                    iter[i] = sam_itr_queryi(reg_idx, mapped_tid, beg, end);
+                } else {
+                    iter[i] = sam_itr_queryi(reg_idx, HTS_IDX_NONE, 0, 0);
+                }
+            }
+
+            if (iter[i] == NULL) {
+                if (fn_bed) {
+                    fprintf(stderr, "[%s] failed to get multi-region iterator "
+                            "{%s, %s}\n", __func__, fn[i], fn_bed);
+                } else {
+                    if (mapped_tid != INT32_MIN) {
+                        fprintf(stderr,
+                                "[%s] failed to get iterator over "
+                                "{%s, %d, %"PRIhts_pos", %"PRIhts_pos"}\n",
+                                __func__, fn[i], mapped_tid, beg, end);
+                    } else {
+                        fprintf(stderr,
+                                "[%s] failed to get iterator over "
+                                "{%s, HTS_IDX_NONE, 0, 0}\n",
+                                __func__, fn[i]);
+                    }
+                }
+                hts_idx_destroy(reg_idx);
+                free(rtrans);
+                rtrans = NULL;
+                goto fail;
+            }
+
+            hts_idx_destroy(reg_idx);
+        }
+
+        free(rtrans);
+        rtrans = NULL;
+    }
+
+    // Make sure that there's enough memory for template coordinate keys, one per file to read
+    if (sam_order == TemplateCoordinate) {
+        if ((keys = malloc(sizeof(template_coordinate_keys_t))) == NULL) {
+            print_error("sort", "could not allocate memory for the top-level keys");
+            goto mem_fail;
+        }
+        keys->n = 0;
+        keys->m = 0;
+        keys->buffer_size = 0x10000;
+        keys->buffers = NULL;
+        // Make sure that there's enough memory for template coordinate keys, one per file to read
+        if (keys->n + n >= keys->m * keys->buffer_size) {
+            if (template_coordinate_keys_realloc(keys, keys->n + n) < 0) goto mem_fail;
+        }
+        lib_lookup = lookup_libraries(hout);
+        if (!lib_lookup) {
+            goto mem_fail;
+        }
+    }
+
+    // Load the first read from each file into the heap
+    for (i = 0; i < n; ++i) {
+        heap1_t *h = heap + i;
+        int res;
+        h->i = i;
+        h->entry.bam_record = bam_init1();
+        h->entry.u.tag = NULL;
+        if (!h->entry.bam_record) goto mem_fail;
+        res = iter[i] ? sam_itr_next(fp[i], iter[i], h->entry.bam_record) : sam_read1(fp[i], hdr[i], h->entry.bam_record);
+        if (res >= 0) {
+            bam_translate(h->entry.bam_record, translation_tbl + i);
+            h->tid = h->entry.bam_record->core.tid;
+            h->pos = (uint64_t)(h->entry.bam_record->core.pos + 1);
+            h->rev = bam_is_rev(h->entry.bam_record);
+            h->idx = idx++;
+            if (g_sam_order == TagQueryName || g_sam_order == TagCoordinate) {
+                h->entry.u.tag = bam_aux_get(h->entry.bam_record, g_sort_tag);
+            } else if (g_sam_order == TemplateCoordinate) {
+                template_coordinate_key_t *key = template_coordinate_keys_get(keys, i); // get the next key to use
+                h->entry.u.key = template_coordinate_key(heap->entry.bam_record, key, hout, lib_lookup); // update the key
+                if (heap->entry.u.key == NULL) goto mem_fail; // key could not be created, error out
+            } else {
+                h->entry.u.tag = NULL;
+            }
+        }
+        else if (res == -1 && (!iter[i] || iter[i]->finished)) {
+            h->pos = HEAP_EMPTY;
+            bam_destroy1(h->entry.bam_record);
+            h->entry.bam_record = NULL;
+            h->entry.u.tag = NULL;
+            h->entry.u.key = NULL;
+        } else {
+            print_error(cmd, "failed to read first record from \"%s\"", fn[i]);
+            goto fail;
+        }
+    }
+
+    // Open output file and write header
+    if ((fpout = sam_open_format(out, mode, out_fmt)) == 0) {
+        print_error_errno(cmd, "failed to create \"%s\"", out);
+        return -1;
+    }
+    if (!no_pg && sam_hdr_add_pg(hout, "samtools",
+                                 "VN", samtools_version(),
+                                 arg_list ? "CL": NULL,
+                                 arg_list ? arg_list : NULL,
+                                 NULL)) {
+        print_error(cmd, "failed to add PG line to the header of \"%s\"", out);
+        sam_close(fpout);
+        return -1;
+    }
+    if (sam_hdr_write(fpout, hout) != 0) {
+        print_error_errno(cmd, "failed to write header to \"%s\"", out);
+        sam_close(fpout);
+        return -1;
+    }
+    if (write_index) {
+        if (!(out_idx_fn = auto_index(fpout, out, hout))){
+            sam_close(fpout);
+            return -1;
+        }
+    }
+    if (!(flag & MERGE_UNCOMP)) hts_set_threads(fpout, n_threads);
+
+    if (refs && hts_set_opt(fpout, CRAM_OPT_SHARED_REF, refs))
+        goto fail;
+
+    // Begin the actual merge
+    ks_heapmake(heap, n, heap);
+    while (heap->pos != HEAP_EMPTY) {
+        bam1_t *b = heap->entry.bam_record;
+        if (flag & MERGE_RG) {
+            uint8_t *rg = bam_aux_get(b, "RG");
+            if (rg) bam_aux_del(b, rg);
+            bam_aux_append(b, "RG", 'Z', RG_len[heap->i] + 1, (uint8_t*)RG[heap->i]);
+        }
+        if (sam_write1(fpout, hout, b) < 0) {
+            print_error_errno(cmd, "failed writing to \"%s\"", out);
+            sam_close(fpout);
+            free(out_idx_fn);
+            return -1;
+        }
+        if ((j = (iter[heap->i]? sam_itr_next(fp[heap->i], iter[heap->i], b) : sam_read1(fp[heap->i], hdr[heap->i], b))) >= 0) {
+            bam_translate(b, translation_tbl + heap->i);
+            heap->tid = b->core.tid;
+            heap->pos = (uint64_t)(b->core.pos + 1);
+            heap->rev = bam_is_rev(b);
+            heap->idx = idx++;
+            if (g_sam_order == TagQueryName || g_sam_order == TagCoordinate) {
+                heap->entry.u.tag = bam_aux_get(heap->entry.bam_record, g_sort_tag);
+            } else if (g_sam_order == TemplateCoordinate) {
+                template_coordinate_key_t *key = template_coordinate_keys_get(keys, heap->i); // get the next key to use
+                heap->entry.u.key = template_coordinate_key(heap->entry.bam_record, key, hout, lib_lookup); // update the key
+                if (heap->entry.u.key == NULL) goto mem_fail; // key could not be created, error out
+            } else {
+                heap->entry.u.tag = NULL;
+            }
+        } else if (j == -1 && (!iter[heap->i] || iter[heap->i]->finished)) {
+            heap->pos = HEAP_EMPTY;
+            bam_destroy1(heap->entry.bam_record);
+            heap->entry.bam_record = NULL;
+            heap->entry.u.tag = NULL;
+        } else {
+            print_error(cmd, "\"%s\" is truncated", fn[heap->i]);
+            goto fail;
+        }
+        ks_heapadjust(heap, 0, n, heap);
+    }
+
+    if (write_index) {
+        if (sam_idx_save(fpout) < 0) {
+            print_error_errno("merge", "writing index failed");
+            goto fail;
+        }
+    }
+    free(out_idx_fn);
+
+    // Clean up and close
+    if (flag & MERGE_RG) {
+        for (i = 0; i != n; ++i) free(RG[i]);
+        free(RG_len);
+    }
+    for (i = 0; i < n; ++i) {
+        trans_tbl_destroy(translation_tbl + i);
+        hts_itr_destroy(iter[i]);
+        sam_hdr_destroy(hdr[i]);
+        sam_close(fp[i]);
+    }
+    sam_hdr_destroy(hin);
+    sam_hdr_destroy(hout);
+    free_merged_header(merged_hdr);
+    hts_reglist_free(lreg, nreg);
+    bed_destroy(hreg);
+    free(RG); free(translation_tbl); free(fp); free(heap); free(iter); free(hdr);
+    if (sam_close(fpout) < 0) {
+        print_error(cmd, "error closing output file");
+        return -1;
+    }
+    return 0;
+
+ mem_fail:
+    print_error(cmd, "Out of memory");
+
+ fail:
+    if (flag & MERGE_RG) {
+        if (RG) {
+            for (i = 0; i != n; ++i) free(RG[i]);
+        }
+        free(RG_len);
+    }
+    for (i = 0; i < n; ++i) {
+        if (translation_tbl && translation_tbl[i].tid_trans) trans_tbl_destroy(translation_tbl + i);
+        if (iter && iter[i]) hts_itr_destroy(iter[i]);
+        if (hdr && hdr[i]) sam_hdr_destroy(hdr[i]);
+        if (fp && fp[i]) sam_close(fp[i]);
+        if (heap && heap[i].entry.bam_record) bam_destroy1(heap[i].entry.bam_record);
+    }
+    if (hout) sam_hdr_destroy(hout);
+    free(RG);
+    free(translation_tbl);
+    free(hdr);
+    hts_reglist_free(lreg, nreg);
+    bed_destroy(hreg);
+    free(iter);
+    free(heap);
+    free(fp);
+    free(rtrans);
+    free(out_idx_fn);
+    if (keys != NULL) {
+        for (i = 0; i < keys->m; ++i) {
+            free(keys->buffers[i]);
+        }
+        free(keys->buffers);
+        free(keys);
+    }
+    lib_lookup_destroy(lib_lookup);
+    return -1;
+}
+
+// Unused here but may be used by legacy samtools-using third-party code
+int bam_merge_core(int by_qname, const char *out, const char *headers, int n, char * const *fn, int flag, const char *reg)
+{
+    char mode[12];
+    strcpy(mode, "wb");
+    if (flag & MERGE_UNCOMP) strcat(mode, "0");
+    else if (flag & MERGE_LEVEL1) strcat(mode, "1");
+    SamOrder sam_order = by_qname ? QueryName : Coordinate;
+    return bam_merge_core2(sam_order, NULL, out, mode, headers, n, fn, NULL, NULL, flag, reg, 0, "merge", NULL, NULL, 0, NULL, 1);
+}
+
+static void merge_usage(FILE *to)
+{
+    fprintf(to,
+"Usage: samtools merge [options] -o <out.bam> [options] <in1.bam> ... <inN.bam>\n"
+"   or: samtools merge [options] <out.bam> <in1.bam> ... <inN.bam>\n"
+"\n"
+"Options:\n"
+"  -n         Input files are sorted by read name\n"
+"  -t TAG     Input files are sorted by TAG value\n"
+"  -r         Attach RG tag (inferred from file names)\n"
+"  -u         Uncompressed BAM output\n"
+"  -f         Overwrite the output BAM if exist\n"
+"  -o FILE    Specify output file via option instead of <out.bam> argument\n"
+"  -1         Compress level 1\n"
+"  -l INT     Compression level, from 0 to 9 [-1]\n"
+"  -R STR     Merge file in the specified region STR [all]\n"
+"  -h FILE    Copy the header in FILE to <out.bam> [in1.bam]\n"
+"  -c         Combine @RG headers with colliding IDs [alter IDs to be distinct]\n"
+"  -p         Combine @PG headers with colliding IDs [alter IDs to be distinct]\n"
+"  -s VALUE   Override random seed\n"
+"  -b FILE    List of input BAM filenames, one per line [null]\n"
+"  -X         Use customized index files\n"
+"  -L FILE    Specify a BED file for multiple region filtering [null]\n"
+"  --no-PG    do not add a PG line\n"
+"  --template-coordinate Input files are sorted by template-coordinate\n");
+    sam_global_opt_help(to, "-.O..@..");
+}
+
+int bam_merge(int argc, char *argv[])
+{
+    int c, flag = 0, ret = 0, level = -1, has_index_file = 0;
+    char *fn_headers = NULL, *reg = NULL, mode[12];
+    char *sort_tag = NULL, *fnout = NULL, *arg_list = NULL;
+    long random_seed = (long)time(NULL);
+    char** fn = NULL;
+    char** fn_idx = NULL, *fn_bed = NULL;
+    int fn_size = 0, no_pg = 0;
+    SamOrder sam_order = Coordinate;
+
+    sam_global_args ga = SAM_GLOBAL_ARGS_INIT;
+    static const struct option lopts[] = {
+        SAM_OPT_GLOBAL_OPTIONS('-', 0, 'O', 0, 0, '@'),
+        { "threads", required_argument, NULL, '@' },
+        {"no-PG", no_argument, NULL, 1},
+        { "template-coordinate", no_argument, NULL, 2},
+        { NULL, 0, NULL, 0 }
+    };
+
+    if (argc == 1) {
+        merge_usage(stdout);
+        return 0;
+    }
+
+    while ((c = getopt_long(argc, argv, "h:nru1R:o:f@:l:cps:b:O:t:XL:", lopts, NULL)) >= 0) {
+        switch (c) {
+        case 'r': flag |= MERGE_RG; break;
+        case 'f': flag |= MERGE_FORCE; break;
+        case 'h': fn_headers = optarg; break;
+        case 'n': sam_order = QueryName; break;
+        case 'o': fnout = optarg; break;
+        case 't': sort_tag = optarg; break;
+        case '1': flag |= MERGE_LEVEL1; level = 1; break;
+        case 'u': flag |= MERGE_UNCOMP; level = 0; break;
+        case 'R': reg = strdup(optarg); break;
+        case 'l': level = atoi(optarg); break;
+        case 'c': flag |= MERGE_COMBINE_RG; break;
+        case 'p': flag |= MERGE_COMBINE_PG; break;
+        case 's': random_seed = atol(optarg); break;
+        case 'X': has_index_file = 1; break; // -X flag for index filename
+        case 'L': fn_bed = optarg; break;
+        case 'b': {
+            // load the list of files to read
+            if (has_index_file) {
+                fprintf(stderr,"Error: The -b option cannot be combined with -X\n");
+                ret = 1; goto end;
+            }
+            int nfiles;
+            char **fn_read = hts_readlines(optarg, &nfiles);
+            if (fn_read) {
+                // Append to end of array
+                fn = realloc(fn, (fn_size+nfiles) * sizeof(char*));
+                if (fn == NULL) { ret = 1; goto end; }
+                memcpy(fn+fn_size, fn_read, nfiles * sizeof(char*));
+                fn_size += nfiles;
+                free(fn_read);
+            }
+            else {
+                print_error("merge", "Invalid file list \"%s\"", optarg);
+                ret = 1;
+            }
+            break;
+        }
+        case 1: no_pg = 1; break;
+        case 2: sam_order = TemplateCoordinate; break;
+        default:  if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break;
+                  /* else fall-through */
+        case '?': merge_usage(stderr); return 1;
+        }
+    }
+
+    if (sort_tag != NULL) {
+        sam_order = sam_order == QueryName ? TagQueryName : TagCoordinate;
+    }
+
+    if (fnout == NULL && argc - optind >= 1) {
+        fnout = argv[optind];
+        optind++;
+    }
+    if (fnout == NULL) {
+        print_error("merge", "You must at least specify the output file");
+        merge_usage(stderr);
+        return 1;
+    }
+
+    if (!no_pg && !(arg_list = stringify_argv(argc+1, argv-1))) {
+        print_error("merge", "failed to create arg_list");
+        return 1;
+    }
+
+    hts_srand48(random_seed);
+    if (!(flag & MERGE_FORCE) && strcmp(fnout, "-") != 0) {
+        struct stat sbuf;
+        if (stat(fnout, &sbuf) == 0 && S_ISREG(sbuf.st_mode)) {
+            fprintf(stderr, "[%s] File '%s' exists. Please apply '-f' to overwrite. Abort.\n", __func__, fnout);
+            ret = 1;
+            goto end;
+        }
+    }
+
+    int nargcfiles = 0;
+    if (has_index_file) { // Calculate # of input BAM files
+        if ((argc - optind) % 2 != 0) {
+            fprintf(stderr, "Odd number of filenames detected! Each BAM file should have an index file\n");
+            ret = 1;
+            goto end;
+        }
+        nargcfiles = (argc - optind) / 2;
+    } else {
+        nargcfiles = argc - optind;
+    }
+
+    if (nargcfiles > 0) {
+        // Add argc files to end of array
+        fn = realloc(fn, (fn_size+nargcfiles) * sizeof(char*));
+        if (fn == NULL) { ret = 1; goto end; }
+        memcpy(fn+fn_size, argv + optind, nargcfiles * sizeof(char*));
+
+        if(has_index_file) {
+            fn_idx = realloc(fn_idx, nargcfiles * sizeof(char*));
+            if (fn_idx == NULL) { ret = 1; goto end; }
+            memcpy(fn_idx+fn_size, argv + nargcfiles + optind, nargcfiles * sizeof(char*));
+        }
+    }
+    if (fn_size+nargcfiles < 1) {
+        print_error("merge", "You must specify at least one (and usually two or more) input files");
+        merge_usage(stderr);
+        ret = 1;
+        goto end;
+    }
+
+    if (reg && fn_bed) {
+        print_error("merge", "You must specify either a BED file or a region");
+        ret = 1;
+        goto end;
+    }
+    strcpy(mode, "wb");
+    sam_open_mode(mode+1, fnout, NULL);
+    if (level >= 0) sprintf(strchr(mode, '\0'), "%d", level < 9? level : 9);
+    if (bam_merge_core2(sam_order, sort_tag, fnout, mode, fn_headers,
+                        fn_size+nargcfiles, fn, fn_idx, fn_bed, flag, reg, ga.nthreads,
+                        "merge", &ga.in, &ga.out, ga.write_index, arg_list, no_pg) < 0)
+        ret = 1;
+
+end:
+    if (fn_size > 0) {
+        int i;
+        for (i=0; i<fn_size; i++) free(fn[i]);
+    }
+    free(fn);
+    free(fn_idx);
+    free(reg);
+    free(arg_list);
+    sam_global_args_free(&ga);
+    return ret;
+}
+
+/***************
+ * BAM sorting *
+ ***************/
+
+
+typedef struct {
+    size_t from;
+    size_t to;
+} buf_region;
+
+/* Simplified version of bam_merge_core2() for merging part-sorted
+   temporary files.  No need for header merging or translation,
+   it just needs to read data into the heap and push it out again. */
+
+static inline int heap_add_read(heap1_t *heap, int nfiles, samFile **fp,
+                                int num_in_mem, buf_region *in_mem,
+                                bam1_tag *buf, template_coordinate_keys_t *keys,
+                                uint64_t *idx, sam_hdr_t *hout,
+                                khash_t(const_c2c) *lib_lookup) {
+    int i = heap->i, res;
+    if (i < nfiles) { // read from file
+        res = sam_read1(fp[i], hout, heap->entry.bam_record);
+        if (res >= 0 && g_sam_order == TemplateCoordinate) { // file read OK and TemplateCoordinate order
+            // It is assumed that there are nfiles more keys allocated than keys->n; see allocation in bam_merge_simple
+            template_coordinate_key_t *key = template_coordinate_keys_get(keys, keys->n + i); // get the next key to use
+            heap->entry.u.key = template_coordinate_key(heap->entry.bam_record, key, hout, lib_lookup); // update the key
+            if (heap->entry.u.key == NULL) res = -1; // key could not be created, error out
+        }
+    } else { // read from memory
+        if (in_mem[i - nfiles].from < in_mem[i - nfiles].to) {
+            size_t from = in_mem[i - nfiles].from;
+            heap->entry.bam_record = buf[from].bam_record;
+            if (g_sam_order == TemplateCoordinate) heap->entry.u.key = buf[from].u.key;
+            in_mem[i - nfiles].from++;
+            res = 0;
+        } else {
+            res = -1;
+        }
+    }
+    if (res >= 0) {
+        heap->tid = heap->entry.bam_record->core.tid;
+        heap->pos = (uint64_t)(heap->entry.bam_record->core.pos + 1);
+        heap->rev = bam_is_rev(heap->entry.bam_record);
+        heap->idx = (*idx)++;
+        if (g_sam_order == TagQueryName || g_sam_order == TagCoordinate) {
+            heap->entry.u.tag = bam_aux_get(heap->entry.bam_record, g_sort_tag);
+        } else if (g_sam_order != TemplateCoordinate) {
+            heap->entry.u.tag = NULL;
+            heap->entry.u.key = NULL;
+        }
+    } else if (res == -1) {
+        heap->pos = HEAP_EMPTY;
+        if (i < nfiles) bam_destroy1(heap->entry.bam_record);
+        heap->entry.bam_record = NULL;
+        heap->entry.u.tag = NULL;
+        heap->entry.u.key = NULL;
+    } else {
+        return -1;
+    }
+    return 0;
+}
+
+static int bam_merge_simple(SamOrder sam_order, char *sort_tag, const char *out,
+                            const char *mode, sam_hdr_t *hout,
+                            int n, char * const *fn, int num_in_mem,
+                            buf_region *in_mem, bam1_tag *buf,
+                            template_coordinate_keys_t *keys,
+                            khash_t(const_c2c) *lib_lookup, int n_threads,
+                            const char *cmd, const htsFormat *in_fmt,
+                            const htsFormat *out_fmt, char *arg_list, int no_pg,
+                            int write_index) {
+    samFile *fpout = NULL, **fp = NULL;
+    heap1_t *heap = NULL;
+    uint64_t idx = 0;
+    int i, heap_size = n + num_in_mem;
+    char *out_idx_fn = NULL;
+
+    if (sam_order == TagQueryName || sam_order == TagCoordinate) {
+        g_sort_tag[0] = sort_tag[0];
+        g_sort_tag[1] = sort_tag[0] ? sort_tag[1] : '\0';
+    }
+    if (n > 0) {
+        fp = (samFile**)calloc(n, sizeof(samFile*));
+        if (!fp) goto mem_fail;
+    }
+    heap = (heap1_t*)calloc(heap_size, sizeof(heap1_t));
+    if (!heap) goto mem_fail;
+
+    // Make sure that there's enough memory for template coordinate keys, one per file to read
+    if (keys && keys->n + n >= keys->m * keys->buffer_size) {
+        if (template_coordinate_keys_realloc(keys, keys->n + n) < 0) goto mem_fail;
+    }
+
+    // Open each file, read the header and put the first read into the heap
+    for (i = 0; i < heap_size; i++) {
+        sam_hdr_t *hin;
+        heap1_t *h = &heap[i];
+
+        if (i < n) {
+            fp[i] = sam_open_format(fn[i], "r", in_fmt);
+            if (fp[i] == NULL) {
+                print_error_errno(cmd, "fail to open \"%s\"", fn[i]);
+                goto fail;
+            }
+
+            // Read header ...
+            hin = sam_hdr_read(fp[i]);
+            if (hin == NULL) {
+                print_error(cmd, "failed to read header from \"%s\"", fn[i]);
+                goto fail;
+            }
+            // ... and throw it away as we don't really need it
+            sam_hdr_destroy(hin);
+        }
+
+        // Get a read into the heap
+        h->i = i;
+        h->entry.u.tag = NULL;
+        h->entry.u.key = NULL;
+        if (i < n) {
+            h->entry.bam_record = bam_init1();
+            if (!h->entry.bam_record) goto mem_fail;
+        }
+        if (heap_add_read(h, n, fp, num_in_mem, in_mem, buf, keys, &idx, hout,
+                          lib_lookup) < 0) {
+            assert(i < n);
+            print_error(cmd, "failed to read first record from \"%s\"", fn[i]);
+            goto fail;
+        }
+    }
+
+    // Open output file and write header
+    if ((fpout = sam_open_format(out, mode, out_fmt)) == 0) {
+        print_error_errno(cmd, "failed to create \"%s\"", out);
+        return -1;
+    }
+
+    if (!no_pg && sam_hdr_add_pg(hout, "samtools",
+                                 "VN", samtools_version(),
+                                 arg_list ? "CL": NULL,
+                                 arg_list ? arg_list : NULL,
+                                 NULL)) {
+        print_error(cmd, "failed to add PG line to the header of \"%s\"", out);
+        sam_close(fpout);
+        return -1;
+    }
+
+    if (n_threads > 1) hts_set_threads(fpout, n_threads);
+
+    if (sam_hdr_write(fpout, hout) != 0) {
+        print_error_errno(cmd, "failed to write header to \"%s\"", out);
+        sam_close(fpout);
+        return -1;
+    }
+
+    if (write_index) {
+        if (!(out_idx_fn = auto_index(fpout, out, hout))){
+            sam_close(fpout);
+            return -1;
+        }
+    }
+
+    // Now do the merge
+    ks_heapmake(heap, heap_size, heap);
+    while (heap->pos != HEAP_EMPTY) {
+        bam1_t *b = heap->entry.bam_record;
+        if (g_sam_order == MinHash && b->core.tid == -1) {
+            // Remove the cached minhash value
+            b->core.pos = -1;
+            b->core.mpos = -1;
+            b->core.isize = 0;
+        }
+        if (sam_write1(fpout, hout, b) < 0) {
+            print_error_errno(cmd, "failed writing to \"%s\"", out);
+            goto fail;
+        }
+        if (heap_add_read(heap, n, fp, num_in_mem, in_mem, buf, keys, &idx,
+                          hout, lib_lookup) < 0) {
+            assert(heap->i < n);
+            print_error(cmd, "Error reading \"%s\" : %s",
+                        fn[heap->i], strerror(errno));
+            goto fail;
+        }
+        ks_heapadjust(heap, 0, heap_size, heap);
+    }
+    // Clean up and close
+    for (i = 0; i < n; i++) {
+        if (sam_close(fp[i]) != 0) {
+            print_error(cmd, "Error on closing \"%s\" : %s",
+                        fn[i], strerror(errno));
+        }
+    }
+    free(fp);
+    free(heap);
+
+    if (write_index) {
+        if (sam_idx_save(fpout) < 0) {
+            print_error_errno("merge", "writing index failed");
+            goto fail;
+        }
+        free(out_idx_fn);
+    }
+
+    if (sam_close(fpout) < 0) {
+        print_error(cmd, "error closing output file");
+        return -1;
+    }
+    return 0;
+ mem_fail:
+    print_error(cmd, "Out of memory");
+
+ fail:
+    for (i = 0; i < n; i++) {
+        if (fp && fp[i]) sam_close(fp[i]);
+    }
+    for (i = 0; i < heap_size; i++) {
+        if (heap && heap[i].i < n && heap[i].entry.bam_record)
+            bam_destroy1(heap[i].entry.bam_record);
+    }
+    free(fp);
+    free(heap);
+    if (fpout) sam_close(fpout);
+    free(out_idx_fn);
+    return -1;
+}
+
+// Function to compare reads and determine which one is < or > the other
+// Handle sort-by-pos and sort-by-name. Used as the secondary sort in bam1_lt_by_tag, if reads are equivalent by tag.
+// Returns a value less than, equal to or greater than zero if a is less than,
+// equal to or greater than b, respectively.
+static inline int bam1_cmp_core(const bam1_tag a, const bam1_tag b)
+{
+    uint64_t pa, pb;
+    if (!a.bam_record) return 1;
+    if (!b.bam_record) return 0;
+
+    if (g_sam_order == QueryName || g_sam_order == TagQueryName) {
+        int t = strnum_cmp(bam_get_qname(a.bam_record), bam_get_qname(b.bam_record));
+        if (t != 0) return t;
+        return (int) (a.bam_record->core.flag&0xc0) - (int) (b.bam_record->core.flag&0xc0);
+    } else {
+        pa = a.bam_record->core.tid;
+        pb = b.bam_record->core.tid;
+
+        if (pa == pb) {
+            pa = (uint64_t)(a.bam_record->core.pos+1);
+            pb = (uint64_t)(b.bam_record->core.pos+1);
+        }
+
+        if (pa == pb) {
+            pa = bam_is_rev(a.bam_record);
+            pb = bam_is_rev(b.bam_record);
+        }
+
+        return pa < pb ? -1 : (pa > pb ? 1 : 0);
+    }
+}
+
+uint8_t normalize_type(const uint8_t* aux) {
+    if (*aux == 'c' || *aux == 'C' || *aux == 's' || *aux == 'S' || *aux == 'i' || *aux == 'I') {
+        return 'c';
+    } else if (*aux == 'f' || *aux == 'd') {
+        return 'f';
+    } else if (*aux == 'H' || *aux == 'Z') {
+         return 'H';
+    } else {
+        return *aux;
+    }
+}
+
+// Sort record by tag, using pos or read name as a secondary key if tags are identical. Reads not carrying the tag sort first.
+// Tags are first sorted by the type character (in case the types differ), or by the appropriate comparator for that type if they agree.
+// Returns a value less than, equal to or greater than zero if a is less than,
+// equal to or greater than b, respectively.
+static inline int bam1_cmp_by_tag(const bam1_tag a, const bam1_tag b)
+{
+    const uint8_t* aux_a = a.u.tag;
+    const uint8_t* aux_b = b.u.tag;
+
+    if (aux_a == NULL && aux_b != NULL) {
+        return -1;
+    } else if (aux_a != NULL && aux_b == NULL) {
+        return 1;
+    } else if (aux_a == NULL && aux_b == NULL) {
+        return bam1_cmp_core(a,b);
+    }
+
+    // 'Normalize' the letters of the datatypes to a canonical letter,
+    // so that comparison of different types
+    // forms a correct total ordering.
+    uint8_t a_type = normalize_type(aux_a);
+    uint8_t b_type = normalize_type(aux_b);
+
+    if (a_type != b_type) {
+        // Fix int to float comparisons by using bam_aux2f() to read the int
+        if (a_type == 'c' && b_type == 'f') {
+            a_type = 'f';
+        } else if (a_type == 'f' && b_type == 'c') {
+            b_type = 'f';
+        } else {
+            // Unfixable mismatched types
+            return a_type < b_type ? -1 : 1;
+        }
+    }
+
+    if (a_type == 'c') {
+        int64_t va = bam_aux2i(aux_a);
+        int64_t vb = bam_aux2i(aux_b);
+        if (va != vb) return va < vb ? -1 : 1;
+        return bam1_cmp_core(a, b);
+    } else if (a_type == 'f') {
+        double va = bam_aux2f(aux_a);
+        double vb = bam_aux2f(aux_b);
+        if (va != vb) return va < vb ? -1 : 1;
+        return bam1_cmp_core(a, b);
+    } else if (a_type == 'A') {
+        unsigned char va = bam_aux2A(aux_a);
+        unsigned char vb = bam_aux2A(aux_b);
+        if (va != vb) return va < vb ? -1 : 1;
+        return bam1_cmp_core(a, b);
+    } else if (a_type == 'H') {
+        int t = strcmp(bam_aux2Z(aux_a), bam_aux2Z(aux_b));
+        if (t) return t;
+        return bam1_cmp_core(a, b);
+    } else {
+        return bam1_cmp_core(a,b);
+    }
+}
+
+// Sort by minimiser (stored in bam1_tag.u.pos).
+// If equal, sort by position.
+//
+// The 64-bit sort key is split over the bam pos and isize fields.
+// This permits it to survive writing to temporary file and coming back.
+static inline int bam1_cmp_by_minhash(const bam1_tag a, const bam1_tag b)
+{
+    const bam1_t *A = a.bam_record;
+    const bam1_t *B = b.bam_record;
+
+    if (!A) return 1;
+    if (!B) return 0;
+
+    if (A->core.tid != -1 || B->core.tid != -1) return bam1_cmp_core(a,b);
+
+    const uint64_t m_a = (((uint64_t)A->core.pos)<<32)|(uint32_t)A->core.mpos;
+    const uint64_t m_b = (((uint64_t)B->core.pos)<<32)|(uint32_t)B->core.mpos;
+
+    if (m_a < m_b) // by hash
+        return -1;
+    else if (m_a > m_b)
+        return 1;
+    else if (A->core.isize < B->core.isize) // by hash location in seq
+        return -1;
+    else if (A->core.isize > B->core.isize)
+        return 1;
+    else
+        return bam1_cmp_core(a,b);
+}
+
+// compares to molecular identifiers, ignoring any trailing slash and subsequent single-character
+// * if mid1 is less than mid2, then -1 will be returned
+// * if mid1 is greater than mid2, then 1 will be returned
+static inline int template_coordinate_key_compare_mid(const char* mid1, const char* mid2) {
+    size_t i = 0;
+    size_t len1 = strlen(mid1);
+    size_t len2 = strlen(mid2);
+    size_t shortest;
+
+    // Snip off trailing slash followed by a single character, if present
+    if (len1 >= 2 && mid1[len1-2] == '/') len1 -= 2;
+    if (len2 >= 2 && mid2[len2-2] == '/') len2 -= 2;
+    shortest = len1 < len2 ? len1 : len2;
+
+    // find first mismatching character
+    while (i < shortest && mid1[i] == mid2[i]) i++;
+
+    // compare last characters
+    if (i == len1 && i < len2) return -1; // mid1 shorter
+    if (i == len2 && i < len1) return  1; // mid2 shorter
+    if (i == len1 && i == len2) return 0; // all characters match
+    if (mid1[i] < mid2[i]) return -1; // mid1 earlier
+    else return 1;
+}
+
+
+// Builds a key use to sort in TemplateCoordinate order.  Returns NULL if the key could not be created (e.g. MC
+// tag is missing), otherwise the pointer to the provided key.
+static template_coordinate_key_t* template_coordinate_key(bam1_t *b, template_coordinate_key_t *key, sam_hdr_t *hdr, khash_t(const_c2c) *lib_lookup) {
+    uint8_t *data;
+    char *rg;
+    khiter_t k;
+
+    // defaults
+    key->tid1 = key->tid2 = INT32_MAX;
+    key->pos1 = key->pos2 = HTS_POS_MAX;
+    key->neg1 = key->neg2 = false;
+    key->mid  = "";
+
+    // update values
+    rg = (char *)bam_aux_get(b, "RG");
+    if (rg && rg[0] == 'Z'
+        &&(k = kh_get(const_c2c, lib_lookup, rg + 1)) < kh_end(lib_lookup)) {
+        key->library = kh_value(lib_lookup, k);
+    } else {
+        key->library = "";
+    }
+    key->name = bam_get_qname(b);
+    if (!(b->core.flag & BAM_FUNMAP)) { // read is mapped, update coordinates
+        key->tid1 = b->core.tid;
+        key->neg1 = bam_is_rev(b);
+        key->pos1 = (key->neg1) ? unclipped_end(b) : unclipped_start(b);
+    }
+    if (b->core.flag & BAM_FPAIRED && !(b->core.flag & BAM_FMUNMAP)) { // mate is mapped, update coordinates
+        char *cigar;
+        if ((data = bam_aux_get(b, "MC"))) {
+            if (!(cigar = bam_aux2Z(data))) {
+                fprintf(stderr, "[bam_sort] error: MC tag wrong type. Please use the MC tag provided by samtools fixmate.\n");
+                return NULL;
+            }
+        } else {
+            fprintf(stderr, "[bam_sort] error: no MC tag. Please run samtools fixmate on file first.\n");
+            return NULL;
+        }
+        key->tid2 = b->core.mtid;
+        key->neg2 = bam_is_mrev(b);
+        key->pos2 = (key->neg2) ? unclipped_other_end(b->core.mpos, cigar) : unclipped_other_start(b->core.mpos, cigar);
+    }
+
+    if ((data = bam_aux_get(b, "MI"))) {
+        if (!(key->mid=bam_aux2Z(data))) {
+            fprintf(stderr, "[bam_sort] error: MI tag wrong type (not a string).\n");
+            return NULL;
+        }
+    }
+
+    // set is_upper_of_pair, and swap if we get the same key regardless of which end
+    // of the pair it is
+    if (key->tid1 < key->tid2
+            || (key->tid1 == key->tid2 && key->pos1 < key->pos2)
+            || (key->tid1 == key->tid2 && key->pos1 == key->pos2 && !key->neg1)) {
+        key->is_upper_of_pair = false;
+    } else {
+        key->is_upper_of_pair = true;
+        // swap
+        int tmp_tid;
+        hts_pos_t tmp_pos;
+        bool tmp_neg;
+        tmp_tid = key->tid1;
+        key->tid1 = key->tid2;
+        key->tid2 = tmp_tid;
+        tmp_pos = key->pos1;
+        key->pos1 = key->pos2;
+        key->pos2 = tmp_pos;
+        tmp_neg = key->neg1;
+        key->neg1 = key->neg2;
+        key->neg2 = tmp_neg;
+    }
+
+    return key;
+}
+
+// Function to compare reads and determine which one is < or > the other
+// Handles template-coordinate, which sorts by:
+// 1. the earlier unclipped 5' coordinate of the read pair
+// 2. the higher unclipped 5' coordinate of the read pair
+// 3. library (from read group)
+// 4. the molecular identifier (if present)
+// 5. read name
+// 6. if unpaired, or if R1 has the lower coordinates of the pair
+// Returns a value less than, equal to or greater than zero if a is less than,
+// equal to or greater than b, respectively.
+static inline int bam1_cmp_template_coordinate(const bam1_tag a, const bam1_tag b)
+{
+    if (!a.bam_record) return 1;
+    if (!b.bam_record) return 0;
+
+    const template_coordinate_key_t* key_a = a.u.key;
+    const template_coordinate_key_t* key_b = b.u.key;
+
+    int retval = 0;
+    if (0 == retval) retval = key_a->tid1 - key_b->tid1;
+    if (0 == retval) retval = key_a->tid2 - key_b->tid2;
+    if (0 == retval) retval = key_a->pos1 < key_b->pos1 ? -1 : (key_a->pos1 > key_b->pos1 ? 1 : 0);
+    if (0 == retval) retval = key_a->pos2 < key_b->pos2 ? -1 : (key_a->pos2 > key_b->pos2 ? 1 : 0);
+    if (0 == retval) retval = key_a->neg1 == key_b->neg1 ? 0 : (key_a->neg1 ? -1 : 1);
+    if (0 == retval) retval = key_a->neg2 == key_b->neg2 ? 0 : (key_a->neg2 ? -1 : 1);
+    if (0 == retval) retval = strcmp(key_a->library, key_b->library);
+    if (0 == retval) retval = template_coordinate_key_compare_mid(key_a->mid, key_b->mid);
+    if (0 == retval) retval = strcmp(key_a->name, key_b->name);
+    if (0 == retval) retval = key_a->is_upper_of_pair == key_b->is_upper_of_pair ? 0 : (key_a->is_upper_of_pair ? 1 : -1);
+    return retval < 0 ? -1 : (retval > 0 ? 1 : 0);
+}
+
+
+// Function to compare reads and determine which one is < the other
+// Handle sort-by-pos, sort-by-name, sort-by-tag, or sort-by-template-coordinate.
+static inline int bam1_lt(const bam1_tag a, const bam1_tag b)
+{
+    switch (g_sam_order) {
+        case Coordinate:
+        case QueryName:
+            return bam1_cmp_core(a, b) < 0;
+        case TagQueryName:
+        case TagCoordinate:
+            return bam1_cmp_by_tag(a, b) < 0;
+        case MinHash:
+            return bam1_cmp_by_minhash(a, b) < 0;
+        case TemplateCoordinate:
+            return bam1_cmp_template_coordinate(a, b) < 0;
+        default:
+            return bam1_cmp_core(a,b) < 0;
+    }
+}
+
+
+
+KSORT_INIT(sort, bam1_tag, bam1_lt)
+
+typedef struct {
+    size_t buf_len;
+    const char *prefix;
+    bam1_tag *buf;
+    const sam_hdr_t *h;
+    char *tmpfile_name;
+    int index;
+    int error;
+    int no_save;
+    int large_pos;
+    int minimiser_kmer;
+} worker_t;
+
+// Returns 0 for success
+//        -1 for failure
+static int write_buffer(const char *fn, const char *mode, size_t l, bam1_tag *buf,
+                        const sam_hdr_t *h, int n_threads, const htsFormat *fmt,
+                        int clear_minhash, char *arg_list, int no_pg, int write_index)
+{
+    size_t i;
+    samFile* fp;
+    char *out_idx_fn = NULL;
+
+    fp = sam_open_format(fn, mode, fmt);
+    if (fp == NULL) return -1;
+    if (!no_pg && sam_hdr_add_pg((sam_hdr_t *)h, "samtools", "VN", samtools_version(),
+                                 arg_list ? "CL": NULL,
+                                 arg_list ? arg_list : NULL,
+                                 NULL)) {
+        goto fail;
+    }
+    if (sam_hdr_write(fp, h) != 0) goto fail;
+
+    if (write_index)
+        if (!(out_idx_fn = auto_index(fp, fn, (sam_hdr_t *)h))) goto fail;
+
+    if (n_threads > 1) hts_set_threads(fp, n_threads);
+    for (i = 0; i < l; ++i) {
+        bam1_t *b = buf[i].bam_record;
+        if (clear_minhash && b->core.tid == -1) {
+            // Remove the cached minhash value
+            b->core.pos = -1;
+            b->core.mpos = -1;
+            b->core.isize = 0;
+        }
+        if (sam_write1(fp, h, b) < 0) goto fail;
+    }
+
+    if (write_index) {
+        if (sam_idx_save(fp) < 0) {
+            print_error_errno("merge", "writing index failed");
+            goto fail;
+        }
+        free(out_idx_fn);
+    }
+
+
+    if (sam_close(fp) < 0) return -1;
+    return 0;
+ fail:
+    sam_close(fp);
+    free(out_idx_fn);
+    return -1;
+}
+
+#define NUMBASE 256
+
+static int ks_radixsort(size_t n, bam1_tag *buf, const sam_hdr_t *h)
+{
+    int curr = 0, ret = -1;
+    ssize_t i;
+    bam1_tag *buf_ar2[2], *bam_a, *bam_b;
+    uint64_t max_pos = 1;
+    uint32_t max_tid = 1, tid_bytes = 0, pos_bytes = 0, byte = 0;
+    uint32_t tid_shift_l, tid_shift_r;
+    int nref = sam_hdr_nref(h);
+
+    // Count number of bytes needed for biggest tid and pos
+    //  Notes: Add 1 to core.pos so always positive.
+    //         Convert unmapped tid (-1) to number of references so unmapped
+    //         sort to the end.
+    for (i = 0; i < n; i++) {
+        bam1_t *b = buf[i].bam_record;
+        uint32_t tid = b->core.tid == -1 ? nref : b->core.tid;
+        uint64_t pos = ((uint64_t)(b->core.pos + 1) << 1) | bam_is_rev(b);
+        if (max_tid < tid)
+            max_tid = tid;
+        if (max_pos < pos)
+            max_pos = pos;
+    }
+
+    for (; max_pos > 0; max_pos >>= 8) pos_bytes++;
+    for (; max_tid > 0; max_tid >>= 8) tid_bytes++;
+    assert(pos_bytes + tid_bytes < sizeof(buf[0].u.pos_tid));
+
+    tid_shift_l = pos_bytes * 8;
+    tid_shift_r = 64 - tid_shift_l;
+
+    // Write position and tid into bam1_tag::u::pos_tid using minimum number
+    // of bytes required.  Values are stored little-endian so that we
+    // get a least-significant digit (byte) radix sort.
+    for (i = 0; i < n; i++) {
+        bam1_t *b = buf[i].bam_record;
+        uint32_t tid = b->core.tid == -1 ? nref : b->core.tid;
+        // 'pos' here includes as many bytes of tid as will fit
+        // in the space remaining above pos_bytes.  The rest of tid
+        // is written out separately.
+        uint64_t pos = (bam_is_rev(b) |
+                        ((uint64_t)(b->core.pos + 1) << 1) |
+                        (tid_shift_l < 64 ? (uint64_t) tid << tid_shift_l : 0));
+        u64_to_le(pos, buf[i].u.pos_tid);
+        u32_to_le(tid_shift_r < 32 ? tid >> tid_shift_r : 0,
+                  &buf[i].u.pos_tid[8]);
+    }
+
+    buf_ar2[0] = buf;
+    buf_ar2[1] = (bam1_tag *)malloc(sizeof(bam1_tag) * n);
+    if (buf_ar2[1] == NULL) {
+        print_error("sort", "couldn't allocate memory for temporary buf");
+        goto err;
+    }
+
+    // Least-significant digit radix sort (where "digits" are bytes)
+    for (byte = 0; byte < pos_bytes + tid_bytes; byte++) {
+        size_t remainders[NUMBASE] = { 0 };
+        bam_a = buf_ar2[curr]; bam_b = buf_ar2[1-curr];
+        for (i = 0; i < n; ++i)
+            remainders[bam_a[i].u.pos_tid[byte]]++;
+        for (i = 1; i < NUMBASE; ++i)
+            remainders[i] += remainders[i - 1];
+        for (i = n - 1; i >= 0; i--) {
+            size_t j = --remainders[bam_a[i].u.pos_tid[byte]];
+            bam_b[j] = bam_a[i];
+        }
+        curr = 1 - curr;
+    }
+    if (curr == 1) {
+        bam1_tag *end = buf + n;
+        bam_a = buf_ar2[0]; bam_b = buf_ar2[1];
+        while (bam_a < end) *bam_a++ = *bam_b++;
+    }
+
+    ret = 0;
+err:
+    free(buf_ar2[1]);
+    return ret;
+}
+
+/*
+ * Computes the minhash of a sequence using both forward and reverse strands.
+ *
+ * This is used as a sort key for unmapped data, to collate like sequences
+ * together and to improve compression ratio.
+ *
+ * The minhash is returned and *pos filled out with location of this hash
+ * key in the sequence if pos != NULL.
+ */
+static uint64_t minhash(bam1_t *b, int kmer, int *pos, int *rev) {
+    uint64_t hashf = 0, minhashf = UINT64_MAX;
+    uint64_t hashr = 0, minhashr = UINT64_MAX;
+    int minhashpf = 0, minhashpr = 0, i;
+    uint64_t mask = (1L<<(2*kmer))-1;
+    unsigned char *seq = bam_get_seq(b);
+    int len = b->core.l_qseq;
+
+    // Lookup tables for bam_seqi to 0123 fwd/rev hashes
+    // =ACM GRSV TWYH KDBN
+#define X 0
+    unsigned char L[16] = {
+        X,0,1,X,  2,X,X,X,  3,X,X,X,  X,X,X,X,
+    };
+    uint64_t R[16] = {
+        X,3,2,X,  1,X,X,X,  0,X,X,X,  X,X,X,X,
+    };
+    for (i = 0; i < 16; i++)
+        R[i] <<= 2*(kmer-1);
+
+    // Punt homopolymers somewhere central in the hash space
+#define XOR (0xdead7878beef7878 & mask)
+
+    // Initialise hash keys
+    for (i = 0; i < kmer-1 && i < len; i++) {
+        int base = bam_seqi(seq, i);
+        hashf = (hashf<<2) | L[base];
+        hashr = (hashr>>2) | R[base];
+    }
+
+    // Loop to find minimum
+    for (; i < len; i++) {
+        int base = bam_seqi(seq, i);
+
+        hashf = ((hashf<<2) | L[base]) & mask;
+        hashr =  (hashr>>2) | R[base];
+
+        if (minhashf > (hashf^XOR))
+            minhashf = (hashf^XOR), minhashpf = i;
+        if (minhashr > (hashr^XOR))
+            minhashr = (hashr^XOR), minhashpr = len-i+kmer-2;
+
+    }
+
+    if (minhashf <= minhashr) {
+        if (rev) *rev = 0;
+        if (pos) *pos = minhashpf;
+        return minhashf;
+    } else {
+        if (rev) *rev = 1;
+        if (pos) *pos = minhashpr;
+        return minhashr;
+    }
+}
+
+//--- Start of candidates to punt to htslib
+/*!
+ * @abstract
+ * Extracts the sequence (in current alignment orientation) from
+ * a bam record and places it in buf, which is nul terminated.
+ *
+ * @param b     The bam structure
+ * @param buf   A buffer at least b->core.l_qseq+1 bytes long
+ */
+static void bam_to_seq(bam1_t *b, char *buf) {
+    int i;
+    uint8_t *seq = bam_get_seq(b);
+    for (i = 0; i < b->core.l_qseq; i++)
+        buf[i] = seq_nt16_str[bam_seqi(seq, i)];
+    buf[i] = 0;
+}
+
+/*!
+ * @abstract
+ * Writes a new sequence, of length b->core.l_qseq, to a BAM record.
+ *
+ * If a sequence of a new length is required the caller must first make
+ * room for it by updating the bam1_t struct.
+ *
+ * @param b     The bam structure
+ * @param buf   A buffer at least b->core.l_qseq bytes long
+ */
+static void seq_to_bam(bam1_t *b, char *buf) {
+    int i;
+    uint8_t *seq = bam_get_seq(b);
+    for (i = 0; i < b->core.l_qseq; i++)
+        bam_set_seqi(seq, i, seq_nt16_table[(unsigned char)buf[i]]);
+}
+
+/*!
+ * @abstract Reverse complements a BAM record.
+ *
+ * It's possible to do this inline, but complex due to the 4-bit sequence
+ * encoding.  For now I take the dumb approach.
+ *
+ * @param b  Pointer to a BAM alignment
+ *
+ * @return   0 on success, -1 on failure (ENOMEM)
+ */
+static int reverse_complement(bam1_t *b) {
+    static char comp[256] = {
+        'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',//00
+        'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',//10
+        'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',//20
+        'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',//30
+
+       //    *   *   *    *   E   F   *    *   I   J   *    L   *   *   O
+        '@','T','V','G', 'H','E','F','C', 'D','I','H','M', 'L','K','N','O',//40
+       //P   Q   *   *    *   *   *   *    X   Y   Z   [    \   ]   ^   _
+        'P','Q','Y','S', 'A','A','B','W', 'X','Y','Z','[','\\','[','^','_',//50
+       //`   *   *   *    *   E   F   *    *   I   J   *    L   *   *   O
+        '`','t','v','g', 'h','e','f','c', 'd','i','j','m', 'l','k','n','o',//60
+       //P   Q   *   *    *   *   *   *    X   Y   Z   {    |   }   ~   DEL
+        'p','q','y','s', 'a','a','b','w', 'x','y','z','{', '|','}','~',127,//70
+
+        'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',//80
+        'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',//90
+        'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',//A0
+        'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',//B0
+
+        'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',//C0
+        'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',//D0
+        'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',//E0
+        'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',//F0
+    };
+    char seq_[10000], *seq = seq_;
+    uint8_t *qual = bam_get_qual(b);
+    int i, j;
+
+    if (b->core.l_qseq >= 10000)
+        if (!(seq = malloc(b->core.l_qseq+1)))
+            return -1;
+
+    bam_to_seq(b, seq);
+
+    for (i = 0, j = b->core.l_qseq-1; i < j; i++, j--) {
+        unsigned char tmp = seq[i];
+        seq[i] = comp[(unsigned char)seq[j]];
+        seq[j] = comp[tmp];
+        tmp = qual[i];
+        qual[i] = qual[j];
+        qual[j] = tmp;
+    }
+    if (i ==j)
+        seq[i] = comp[(unsigned char)seq[i]];
+
+    seq_to_bam(b, seq);
+
+    if (seq != seq_)
+        free(seq);
+
+    b->core.flag ^= 0x10;
+
+    return 0;
+}
+//--- End of candidates to punt to htslib
+
+
+static inline void worker_minhash(worker_t *w) {
+    int i;
+    for (i = 0; i < w->buf_len; i++) {
+        bam1_t *b = w->buf[i].bam_record;
+        if (b->core.tid != -1)
+            continue;
+
+        int pos = 0, rev = 0;
+        uint64_t mh = minhash(b, w->minimiser_kmer, &pos, &rev);
+        if (rev)
+            reverse_complement(b);
+
+        // Store 64-bit hash in unmapped pos and mpos fields.
+        // The position of hash is in isize, which we use for
+        // resolving ties when sorting by hash key.
+        // These are unused for completely unmapped data and
+        // will be reset during final output.
+        b->core.pos = mh>>31;
+        b->core.mpos = mh&0x7fffffff;
+        b->core.isize = 65535-pos >=0 ? 65535-pos : 0;
+    }
+}
+
+static void *worker(void *data)
+{
+    worker_t *w = (worker_t*)data;
+    char *name;
+    size_t name_len;
+    w->error = 0;
+    w->tmpfile_name = NULL;
+
+    switch (g_sam_order) {
+        case Coordinate:
+            if (ks_radixsort(w->buf_len, w->buf, w->h) < 0) {
+                w->error = errno;
+                return NULL;
+            }
+            break;
+        case MinHash:
+            worker_minhash(w);
+            // no break, go to merge sort
+        default:
+            ks_mergesort(sort, w->buf_len, w->buf, 0);
+    }
+
+    if (w->no_save)
+        return 0;
+
+    name_len = strlen(w->prefix) + 30;
+    name = (char*)calloc(name_len, 1);
+    if (!name) { w->error = errno; return 0; }
+    const int MAX_TRIES = 1000;
+    int tries = 0;
+    for (;;) {
+        if (tries) {
+            snprintf(name, name_len, "%s.%.4d-%.3d.bam",
+                     w->prefix, w->index, tries);
+        } else {
+            snprintf(name, name_len, "%s.%.4d.bam", w->prefix, w->index);
+        }
+
+        if (write_buffer(name, w->large_pos ? "wzx1" : "wbx1",
+                         w->buf_len, w->buf, w->h, 0, NULL, 0, NULL, 1, 0) == 0) {
+            break;
+        }
+        if (errno == EEXIST && tries < MAX_TRIES) {
+            tries++;
+        } else {
+            w->error = errno;
+            break;
+        }
+    }
+
+    if (w->error) {
+        free(name);
+    } else {
+        w->tmpfile_name = name;
+    }
+    return 0;
+}
+
+static int sort_blocks(int n_files, size_t k, bam1_tag *buf, const char *prefix,
+                       const sam_hdr_t *h, int n_threads, buf_region *in_mem,
+                       int large_pos, int minimiser_kmer, char **fns, size_t fns_size)
+{
+    int i;
+    size_t pos, rest;
+    pthread_t *tid;
+    pthread_attr_t attr;
+    worker_t *w;
+    int n_failed = 0;
+
+    if (n_threads < 1) n_threads = 1;
+    if (k < n_threads * 64) n_threads = 1; // use a single thread if we only sort a small batch of records
+    pthread_attr_init(&attr);
+    pthread_attr_setdetachstate(&attr, PTHREAD_CREATE_JOINABLE);
+    w = (worker_t*)calloc(n_threads, sizeof(worker_t));
+    if (!w) return -1;
+    tid = (pthread_t*)calloc(n_threads, sizeof(pthread_t));
+    if (!tid) { free(w); return -1; }
+    pos = 0; rest = k;
+    for (i = 0; i < n_threads; ++i) {
+        w[i].buf_len = rest / (n_threads - i);
+        w[i].buf = &buf[pos];
+        w[i].prefix = prefix;
+        w[i].h = h;
+        w[i].index = n_files + i;
+        w[i].tmpfile_name = NULL;
+        w[i].large_pos = large_pos;
+        w[i].minimiser_kmer = minimiser_kmer;
+        if (in_mem) {
+            w[i].no_save = 1;
+            in_mem[i].from = pos;
+            in_mem[i].to = pos + w[i].buf_len;
+        } else {
+            w[i].no_save = 0;
+        }
+        pos += w[i].buf_len; rest -= w[i].buf_len;
+        pthread_create(&tid[i], &attr, worker, &w[i]);
+    }
+    for (i = 0; i < n_threads; ++i) {
+        pthread_join(tid[i], 0);
+        if (!in_mem) {
+            assert(w[i].index >= 0 && w[i].index < fns_size);
+            fns[w[i].index] = w[i].tmpfile_name;
+        }
+        if (w[i].error != 0) {
+            errno = w[i].error;
+            print_error_errno("sort", "failed to create temporary file \"%s.%.4d.bam\"", prefix, w[i].index);
+            n_failed++;
+        }
+    }
+    if (n_failed && !in_mem) {
+        // Clean up any temporary files that did get made, as we're
+        // about to lose track of them
+        for (i = 0; i < n_threads; ++i) {
+            if (fns[w[i].index]) {
+                unlink(fns[w[i].index]);
+                free(fns[w[i].index]);
+                fns[w[i].index] = NULL;
+            }
+        }
+    }
+    free(tid); free(w);
+    if (n_failed) return -1;
+    if (in_mem) return n_threads;
+    return n_files + n_threads;
+}
+
+static void lib_lookup_destroy(khash_t(const_c2c) *lib_lookup) {
+    khiter_t k;
+    if (lib_lookup == NULL)
+        return;
+    for (k = kh_begin(lib_lookup); k < kh_end(lib_lookup); k++) {
+        if (kh_exist(lib_lookup, k))
+            free(kh_value(lib_lookup, k));
+    }
+    kh_destroy(const_c2c, lib_lookup);
+}
+
+// Build an RG to LB lookup table, for the template coordinate sort.
+// Returns a populated hash table (which may be empty) on success;
+// NULL on failure.
+static khash_t(const_c2c) * lookup_libraries(sam_hdr_t *header)
+{
+    khash_t(const_c2c) *lib_lookup = kh_init(const_c2c);
+    kstring_t lib_name = KS_INITIALIZE;
+    int num_rg, i, res;
+    if (!lib_lookup)
+        return NULL;
+
+    // Iterate through any RG lines and look for library information
+    num_rg = sam_hdr_count_lines(header, "RG");
+    if (num_rg < 0)
+        goto fail;
+
+    for (i = 0; i < num_rg; i++) {
+        const char *rg_id = sam_hdr_line_name(header, "RG", i);
+        khiter_t k;
+        if (!rg_id)
+            goto fail;
+        res = sam_hdr_find_tag_pos(header, "RG", i, "LB", &lib_name);
+        if (res < -1) // Error
+            goto fail;
+        if (res < 0 || !lib_name.s) // No LB tag
+            continue;
+        // Add to lookup table
+        k = kh_put(const_c2c, lib_lookup, rg_id, &res);
+        if (res < 0) // Error
+            goto fail;
+        if (res > 0) { // Inserted
+            kh_value(lib_lookup, k) = ks_release(&lib_name);
+        }
+    }
+
+    free(lib_name.s);
+
+    return lib_lookup;
+
+ fail:
+    lib_lookup_destroy(lib_lookup);
+    free(lib_name.s);
+    return NULL;
+}
+
+/*!
+  @abstract Sort an unsorted BAM file based on the provided sort order
+
+  @param  sam_order the order in which the sort should occur
+  @param  sort_tag  the tag to use if sorting by Tag
+  @param  minimiser_kmer the kmer size when sorting by MinHash
+  @param  fn       name of the file to be sorted
+  @param  prefix   prefix of the temporary files (prefix.NNNN.bam are written)
+  @param  fnout    name of the final output file to be written
+  @param  modeout  sam_open() mode to be used to create the final output file
+  @param  max_mem  approxiate maximum memory (very inaccurate)
+  @param  in_fmt   input file format options
+  @param  out_fmt  output file format and options
+  @param  arg_list    command string for PG line
+  @param  no_pg       if 1, do not add a new PG line
+  @paran  write_index create index for the output file
+  @return 0 for successful sorting, negative on errors
+
+  @discussion It may create multiple temporary subalignment files
+  and then merge them by calling bam_merge_simple(). This function is
+  NOT thread safe.
+ */
+int bam_sort_core_ext(SamOrder sam_order, char* sort_tag, int minimiser_kmer,
+                      const char *fn, const char *prefix,
+                      const char *fnout, const char *modeout,
+                      size_t _max_mem, int n_threads,
+                      const htsFormat *in_fmt, const htsFormat *out_fmt,
+                      char *arg_list, int no_pg, int write_index)
+{
+    int ret = -1, res, i, nref, n_files = 0;
+    size_t max_k, k, max_mem, bam_mem_offset;
+    sam_hdr_t *header = NULL;
+    samFile *fp = NULL;
+    bam1_tag *buf = NULL;
+    template_coordinate_keys_t *keys = NULL;
+    bam1_t *b = bam_init1();
+    uint8_t *bam_mem = NULL;
+    char **fns = NULL;
+    size_t fns_size = 0;
+    const char *new_so = NULL;
+    const char *new_go = NULL;
+    const char *new_ss = NULL;
+    buf_region *in_mem = NULL;
+    khash_t(const_c2c) *lib_lookup = NULL;
+    int num_in_mem = 0;
+    int large_pos = 0;
+
+    if (!b) {
+        print_error("sort", "couldn't allocate memory for bam record");
+        return -1;
+    }
+
+    if (n_threads < 2) n_threads = 1;
+    g_sam_order = sam_order;
+    if (g_sam_order == TagQueryName || g_sam_order == TagCoordinate) {
+        g_sort_tag[0] = sort_tag[0];
+        g_sort_tag[1] = sort_tag[0] ? sort_tag[1] : '\0';
+    }
+
+    if (sam_order == TemplateCoordinate) {
+        if ((keys = malloc(sizeof(template_coordinate_keys_t))) == NULL) {
+            print_error("sort", "could not allocate memory for the top-level keys");
+            goto err;
+        }
+        keys->n = 0;
+        keys->m = 0;
+        keys->buffer_size = 0x10000;
+        keys->buffers = NULL;
+    }
+
+    max_mem = _max_mem * n_threads;
+    buf = NULL;
+    fp = sam_open_format(fn, "r", in_fmt);
+    if (fp == NULL) {
+        print_error_errno("sort", "can't open \"%s\"", fn);
+        goto err;
+    }
+    header = sam_hdr_read(fp);
+    if (header == NULL) {
+        print_error("sort", "failed to read header from \"%s\"", fn);
+        goto err;
+    }
+
+    // Inspect the header looking for long chromosomes
+    // If there is one, we need to write temporary files in SAM format
+    nref = sam_hdr_nref(header);
+    for (i = 0; i < nref; i++) {
+        if (sam_hdr_tid2len(header, i) > INT32_MAX)
+            large_pos = 1;
+    }
+
+    // Also check the output format is large position compatible
+    if (large_pos) {
+        int compatible = (out_fmt->format == sam
+                          || (out_fmt->format == cram
+                              && out_fmt->version.major >= 4)
+                          || (out_fmt->format == unknown_format
+                              && modeout[0] == 'w'
+                              && (modeout[1] == 'z' || modeout[1] == '\0')));
+        if (!compatible) {
+            print_error("sort", "output format is not compatible with very large references");
+            goto err;
+        }
+    }
+
+    if (g_sam_order == TemplateCoordinate) {
+        lib_lookup = lookup_libraries(header);
+        if (!lib_lookup)
+            goto err;
+    }
+
+    switch (g_sam_order) {
+        case Coordinate:
+            new_so = "coordinate";
+            break;
+        case QueryName:
+            new_so = "queryname";
+            break;
+        case MinHash:
+            new_so = "coordinate";
+            new_ss = "coordinate:minhash";
+            break;
+        case TagQueryName:
+        case TagCoordinate:
+            new_so = "unknown";
+            break;
+        case TemplateCoordinate:
+            new_so = "unsorted";
+            new_go = "query";
+            new_ss = "unsorted:template-coordinate";
+            break;
+        default:
+            new_so = "unknown";
+            break;
+    }
+
+    if (new_ss == NULL && new_go == NULL) { // just SO
+        if ((-1 == sam_hdr_update_hd(header, "SO", new_so))
+            && (-1 == sam_hdr_add_line(header, "HD", "VN", SAM_FORMAT_VERSION, "SO", new_so, NULL))
+            ) {
+            print_error("sort", "failed to change sort order header to 'SO:%s'\n", new_so);
+            goto err;
+        }
+    } else if (new_ss != NULL && new_go == NULL) { // update SO and SS, but not GO
+        if ((-1 == sam_hdr_update_hd(header, "SO", new_so, "SS", new_ss))
+            && (-1 == sam_hdr_add_line(header, "HD", "VN", SAM_FORMAT_VERSION,
+                                       "SO", new_so, "SS", new_ss, NULL))
+            ) {
+            print_error("sort", "failed to change sort order header to 'SO:%s SS:%s'\n",
+                        new_so, new_ss);
+            goto err;
+        }
+    } else if (new_ss == NULL && new_go != NULL) { // update SO and GO, but not SS
+        if ((-1 == sam_hdr_update_hd(header, "SO", new_so, "GO", new_go))
+            && (-1 == sam_hdr_add_line(header, "HD", "VN", SAM_FORMAT_VERSION,
+                                       "SO", new_so, "GO", new_go, NULL))
+            ) {
+            print_error("sort", "failed to change sort order header to 'SO:%s GO:%s'\n",
+                        new_so, new_go);
+            goto err;
+        }
+    } else { // update SO, GO, and SS
+        if ((-1 == sam_hdr_update_hd(header, "SO", new_so, "GO", new_go, "SS", new_ss))
+            && (-1 == sam_hdr_add_line(header, "HD", "VN", SAM_FORMAT_VERSION,
+                                       "SO", new_so, "GO", new_go, "SS", new_ss, NULL))
+            ) {
+            print_error("sort", "failed to change sort order header to 'SO:%s GO:%s SS:%s'\n",
+                        new_so, new_go, new_ss);
+            goto err;
+        }
+    }
+
+    if (new_go == NULL) {
+        if (-1 == sam_hdr_remove_tag_hd(header, "GO")) {
+            print_error("sort", "failed to delete group order in header\n");
+            goto err;
+        }
+    }
+    if (new_ss == NULL) {
+        if (-1 == sam_hdr_remove_tag_hd(header, "SS")) {
+            print_error("sort", "failed to delete sub sort in header\n");
+            goto err;
+        }
+    }
+
+    // No gain to using the thread pool here as the flow of this code
+    // is such that we are *either* reading *or* sorting.  Hence a shared
+    // pool makes no real difference except to reduce the thread count a little.
+    if (n_threads > 1)
+        hts_set_threads(fp, n_threads);
+
+    if ((bam_mem = malloc(max_mem)) == NULL) {
+        print_error("sort", "couldn't allocate memory for bam_mem");
+        goto err;
+    }
+
+    // write sub files
+    k = max_k = bam_mem_offset = 0;
+    while ((res = sam_read1(fp, header, b)) >= 0) {
+        int mem_full = 0;
+
+        if (k == max_k) {
+            bam1_tag *new_buf;
+            max_k = max_k? max_k<<1 : 0x10000;
+            if ((new_buf = realloc(buf, max_k * sizeof(bam1_tag))) == NULL) {
+                print_error("sort", "couldn't allocate memory for buf");
+                goto err;
+            }
+            buf = new_buf;
+        }
+        if (sam_order == TemplateCoordinate && k >= keys->m * keys->buffer_size) {
+            if (template_coordinate_keys_realloc(keys, k + 1) == -1) {
+                goto err;
+            }
+        }
+
+        // Check if the BAM record will fit in the memory limit
+        if (bam_mem_offset + sizeof(*b) + b->l_data < max_mem) {
+            // Copy record into the memory block
+            buf[k].bam_record = (bam1_t *)(bam_mem + bam_mem_offset);
+            *buf[k].bam_record = *b;
+            buf[k].bam_record->data = (uint8_t *)((char *)buf[k].bam_record + sizeof(bam1_t));
+            memcpy(buf[k].bam_record->data, b->data, b->l_data);
+            // store next BAM record in next 8-byte-aligned address after
+            // current one
+            bam_mem_offset = (bam_mem_offset + sizeof(*b) + b->l_data + 8 - 1) & ~((size_t)(8 - 1));
+        } else {
+            // Add a pointer to the remaining record
+            buf[k].bam_record = b;
+            mem_full = 1;
+        }
+
+        // Set the tag if sorting by tag, or the key for template cooridinate sorting
+        switch (g_sam_order) {
+            case TagQueryName:
+            case TagCoordinate:
+                buf[k].u.tag = bam_aux_get(buf[k].bam_record, g_sort_tag);
+                break;
+            case TemplateCoordinate:
+                ++keys->n;
+                template_coordinate_key_t *key = template_coordinate_keys_get(keys, k);
+                buf[k].u.key = template_coordinate_key(buf[k].bam_record, key, header, lib_lookup);
+                if (buf[k].u.key == NULL) goto err;
+                break;
+            default:
+                buf[k].u.tag = NULL;
+                buf[k].u.key = NULL;
+        }
+        ++k;
+
+        if (mem_full) {
+            if (hts_resize(char *, n_files + (n_threads > 0 ? n_threads : 1),
+                           &fns_size, &fns, 0) < 0)
+                goto err;
+            int new_n = sort_blocks(n_files, k, buf, prefix, header, n_threads,
+                                    NULL, large_pos, minimiser_kmer, fns, fns_size);
+            if (new_n < 0) {
+                goto err;
+            } else {
+                n_files = new_n;
+            }
+            k = 0;
+            if (keys != NULL) keys->n = 0;
+            bam_mem_offset = 0;
+        }
+    }
+    if (res != -1) {
+        print_error("sort", "truncated file. Aborting");
+        goto err;
+    }
+
+    // Sort last records
+    if (k > 0) {
+        in_mem = calloc(n_threads > 0 ? n_threads : 1, sizeof(in_mem[0]));
+        if (!in_mem) goto err;
+        num_in_mem = sort_blocks(n_files, k, buf, prefix, header, n_threads,
+                                 in_mem, large_pos, minimiser_kmer, fns, fns_size);
+        if (num_in_mem < 0) goto err;
+    } else {
+        num_in_mem = 0;
+    }
+
+    // write the final output
+    if (n_files == 0 && num_in_mem < 2) { // a single block
+        if (write_buffer(fnout, modeout, k, buf, header, n_threads, out_fmt,
+                         minimiser_kmer, arg_list, no_pg, write_index) != 0) {
+            print_error_errno("sort", "failed to create \"%s\"", fnout);
+            goto err;
+        }
+    } else { // then merge
+        fprintf(stderr,
+                "[bam_sort_core] merging from %d files and %d in-memory blocks...\n",
+                n_files, num_in_mem);
+        // Paranoia check - all temporary files should have a name
+        for (i = 0; i < n_files; ++i) {
+            if (!fns[i]) {
+                print_error("sort",
+                            "BUG: no name stored for temporary file %d", i);
+                abort();
+            }
+        }
+        char *sort_by_tag = (sam_order == TagQueryName || sam_order == TagCoordinate) ? sort_tag : NULL;
+        if (bam_merge_simple(sam_order, sort_by_tag, fnout, modeout, header,
+                             n_files, fns, num_in_mem, in_mem, buf, keys,
+                             lib_lookup, n_threads, "sort", in_fmt, out_fmt,
+                             arg_list, no_pg, write_index) < 0) {
+            // Propagate bam_merge_simple() failure; it has already emitted a
+            // message explaining the failure, so no further message is needed.
+            goto err;
+        }
+    }
+
+    ret = 0;
+
+ err:
+    // free
+    if (fns) {
+        for (i = 0; i < n_files; ++i) {
+            if (fns[i]) {
+                unlink(fns[i]);
+                free(fns[i]);
+            }
+        }
+        free(fns);
+    }
+    bam_destroy1(b);
+    free(buf);
+    if (keys != NULL) {
+        for (i = 0; i < keys->m; ++i) {
+            free(keys->buffers[i]);
+        }
+        free(keys->buffers);
+        free(keys);
+    }
+    free(bam_mem);
+    free(in_mem);
+    lib_lookup_destroy(lib_lookup);
+    sam_hdr_destroy(header);
+    if (fp) sam_close(fp);
+    return ret;
+}
+
+// Unused here but may be used by legacy samtools-using third-party code
+int bam_sort_core(int is_by_qname, const char *fn, const char *prefix, size_t max_mem)
+{
+    int ret;
+    char *fnout = calloc(strlen(prefix) + 4 + 1, 1);
+    if (!fnout) return -1;
+    sprintf(fnout, "%s.bam", prefix);
+    SamOrder sam_order = is_by_qname ? QueryName : Coordinate;
+    g_sam_order = sam_order;
+    ret = bam_sort_core_ext(sam_order, NULL, 0, fn, prefix, fnout, "wb", max_mem, 0, NULL, NULL, NULL, 1, 0);
+    free(fnout);
+    return ret;
+}
+
+static void sort_usage(FILE *fp)
+{
+    fprintf(fp,
+"Usage: samtools sort [options...] [in.bam]\n"
+"Options:\n"
+"  -l INT     Set compression level, from 0 (uncompressed) to 9 (best)\n"
+"  -u         Output uncompressed data (equivalent to -l 0)\n"
+"  -m INT     Set maximum memory per thread; suffix K/M/G recognized [768M]\n"
+"  -M         Use minimiser for clustering unaligned/unplaced reads\n"
+"  -K INT     Kmer size to use for minimiser [20]\n"
+"  -n         Sort by read name (not compatible with samtools index command)\n"
+"  -t TAG     Sort by value of TAG. Uses position as secondary index (or read name if -n is set)\n"
+"  -o FILE    Write final output to FILE rather than standard output\n"
+"  -T PREFIX  Write temporary files to PREFIX.nnnn.bam\n"
+"      --no-PG\n"
+"               Do not add a PG line\n"
+"      --template-coordinate\n"
+"               Sort by template-coordinate\n");
+    sam_global_opt_help(fp, "-.O..@..");
+}
+
+static void complain_about_memory_setting(size_t max_mem) {
+    char  *suffix = "";
+    const size_t nine_k = 9<<10;
+    if (max_mem > nine_k) { max_mem >>= 10; suffix = "K"; }
+    if (max_mem > nine_k) { max_mem >>= 10; suffix = "M"; }
+
+    fprintf(stderr,
+"[bam_sort] -m setting (%zu%s bytes) is less than the minimum required (%zuM).\n\n"
+"Trying to run with -m too small can lead to the creation of a very large number\n"
+"of temporary files.  This may make sort fail due to it exceeding limits on the\n"
+"number of files it can have open at the same time.\n\n"
+"Please check your -m parameter.  It should be an integer followed by one of the\n"
+"letters K (for kilobytes), M (megabytes) or G (gigabytes).  You should ensure it\n"
+"is at least the minimum above, and much higher if you are sorting a large file.\n",
+            max_mem, suffix, SORT_MIN_MEGS_PER_THREAD);
+}
+
+int bam_sort(int argc, char *argv[])
+{
+    size_t max_mem = SORT_DEFAULT_MEGS_PER_THREAD << 20;
+    int c, nargs, ret, o_seen = 0, level = -1, no_pg = 0;
+    SamOrder sam_order = Coordinate;
+    bool by_tag = false;
+    int minimiser_kmer = 20;
+    char* sort_tag = NULL, *arg_list = NULL;
+    char *fnout = "-", modeout[12];
+    kstring_t tmpprefix = { 0, 0, NULL };
+    struct stat st;
+    sam_global_args ga = SAM_GLOBAL_ARGS_INIT;
+
+    static const struct option lopts[] = {
+        SAM_OPT_GLOBAL_OPTIONS('-', 0, 'O', 0, 0, '@'),
+        { "threads", required_argument, NULL, '@' },
+        {"no-PG", no_argument, NULL, 1},
+        { "template-coordinate", no_argument, NULL, 2},
+        { NULL, 0, NULL, 0 }
+    };
+
+    while ((c = getopt_long(argc, argv, "l:m:no:O:T:@:t:MK:u", lopts, NULL)) >= 0) {
+        switch (c) {
+        case 'o': fnout = optarg; o_seen = 1; break;
+        case 'n': sam_order = QueryName; break;
+        case 't': by_tag = true; sort_tag = optarg; break;
+        case 'm': {
+                char *q;
+                max_mem = strtol(optarg, &q, 0);
+                if (*q == 'k' || *q == 'K') max_mem <<= 10;
+                else if (*q == 'm' || *q == 'M') max_mem <<= 20;
+                else if (*q == 'g' || *q == 'G') max_mem <<= 30;
+                break;
+            }
+        case 'T': kputs(optarg, &tmpprefix); break;
+        case 'l': level = atoi(optarg); break;
+        case 'u': level = 0; break;
+        case   1: no_pg = 1; break;
+        case   2: sam_order = TemplateCoordinate; break;
+        case 'M': sam_order = MinHash; break;
+        case 'K':
+            minimiser_kmer = atoi(optarg);
+            if (minimiser_kmer < 1)
+                minimiser_kmer = 1;
+            else if (minimiser_kmer > 31)
+                minimiser_kmer = 31;
+            break;
+
+        default:  if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break;
+                  /* else fall-through */
+        case '?': sort_usage(stderr); ret = EXIT_FAILURE; goto sort_end;
+        }
+    }
+
+    // Change sort order if tag sorting is requested.  Must update based on secondary index
+    if (by_tag) {
+        sam_order = sam_order == QueryName ? TagQueryName : TagCoordinate;
+    }
+
+    nargs = argc - optind;
+    if (nargs == 0 && isatty(STDIN_FILENO)) {
+        sort_usage(stdout);
+        ret = EXIT_SUCCESS;
+        goto sort_end;
+    }
+    else if (nargs >= 2) {
+        // If exactly two, user probably tried to specify legacy <out.prefix>
+        if (nargs == 2)
+            fprintf(stderr, "[bam_sort] Use -T PREFIX / -o FILE to specify temporary and final output files\n");
+
+        sort_usage(stderr);
+        ret = EXIT_FAILURE;
+        goto sort_end;
+    }
+
+    if (ga.write_index && (sam_order == QueryName || sam_order == TagQueryName || sam_order == TagCoordinate || sam_order == TemplateCoordinate)) {
+        fprintf(stderr, "[W::bam_sort] Ignoring --write-index as it only works for position sorted files.\n");
+        ga.write_index = 0;
+    }
+
+    if (!no_pg && !(arg_list = stringify_argv(argc+1, argv-1))) {
+        print_error("sort", "failed to create arg_list");
+        return 1;
+    }
+
+    if (max_mem < (SORT_MIN_MEGS_PER_THREAD << 20)) {
+        complain_about_memory_setting(max_mem);
+        ret = EXIT_FAILURE;
+        goto sort_end;
+    }
+
+    strcpy(modeout, "wb");
+    sam_open_mode(modeout+1, fnout, NULL);
+    if (level >= 0) sprintf(strchr(modeout, '\0'), "%d", level < 9? level : 9);
+
+    if (tmpprefix.l == 0) {
+        if (strcmp(fnout, "-") != 0) {
+            char *idx = strstr(fnout, HTS_IDX_DELIM);
+            kputsn(fnout, idx ? idx - fnout : strlen(fnout), &tmpprefix);
+            kputs(".tmp", &tmpprefix);
+        } else {
+            kputc('.', &tmpprefix);
+        }
+    }
+    if (stat(tmpprefix.s, &st) == 0 && S_ISDIR(st.st_mode)) {
+        unsigned t = ((unsigned) time(NULL)) ^ ((unsigned) clock());
+        if (tmpprefix.s[tmpprefix.l-1] != '/') kputc('/', &tmpprefix);
+        ksprintf(&tmpprefix, "samtools.%d.%u.tmp", (int) getpid(), t % 10000);
+    }
+
+    ret = bam_sort_core_ext(sam_order, sort_tag, (sam_order == MinHash) ? minimiser_kmer : 0,
+                            (nargs > 0) ? argv[optind] : "-",
+                            tmpprefix.s, fnout, modeout, max_mem, ga.nthreads,
+                            &ga.in, &ga.out, arg_list, no_pg, ga.write_index);
+    if (ret >= 0)
+        ret = EXIT_SUCCESS;
+    else {
+        char dummy[4];
+        // If we failed on opening the input file & it has no .bam/.cram/etc
+        // extension, the user probably tried legacy -o <infile> <out.prefix>
+        if (ret == -2 && o_seen && nargs > 0 && sam_open_mode(dummy, argv[optind], NULL) < 0)
+            fprintf(stderr, "[bam_sort] Note the <out.prefix> argument has been replaced by -T/-o options\n");
+
+        ret = EXIT_FAILURE;
+    }
+
+sort_end:
+    free(tmpprefix.s);
+    free(arg_list);
+    sam_global_args_free(&ga);
+
+    return ret;
+}
diff --git a/samtools/bam_sort.c.pysam.c b/samtools/bam_sort.c.pysam.c
new file mode 100644
index 0000000..3489044
--- /dev/null
+++ b/samtools/bam_sort.c.pysam.c
@@ -0,0 +1,3265 @@
+#include "samtools.pysam.h"
+
+/*  bam_sort.c -- sorting and merging.
+
+    Copyright (C) 2008-2022 Genome Research Ltd.
+    Portions copyright (C) 2009-2012 Broad Institute.
+
+    Author: Heng Li <lh3@sanger.ac.uk>
+    Author: Martin Pollard <mp15@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <config.h>
+
+#include <stdbool.h>
+#include <stdlib.h>
+#include <ctype.h>
+#include <errno.h>
+#include <stdio.h>
+#include <string.h>
+#include <time.h>
+#include <sys/types.h>
+#include <sys/stat.h>
+#include <unistd.h>
+#include <getopt.h>
+#include <assert.h>
+#include <pthread.h>
+#include <inttypes.h>
+#include "htslib/ksort.h"
+#include "htslib/hts_os.h"
+#include "htslib/khash.h"
+#include "htslib/klist.h"
+#include "htslib/kstring.h"
+#include "htslib/sam.h"
+#include "htslib/hts_endian.h"
+#include "htslib/cram.h"
+#include "sam_opts.h"
+#include "samtools.h"
+#include "bedidx.h"
+#include "bam.h"
+
+
+// Struct which contains the sorting key for TemplateCoordinate sort.
+typedef struct {
+    int tid1;
+    int tid2;
+    hts_pos_t pos1;
+    hts_pos_t pos2;
+    bool neg1;
+    bool neg2;
+    const char *library;
+    char *mid;
+    char *name;
+    bool is_upper_of_pair;
+} template_coordinate_key_t;
+
+// Struct to store fixed buffers of template coordinate keys
+typedef struct {
+  size_t n; // the # of keys stored
+  size_t m; // the # of buffers allocated
+  size_t buffer_size; // # the fixed size of each buffer
+  template_coordinate_key_t **buffers; // the list of buffers
+} template_coordinate_keys_t;
+
+// Gets the idx'th key; does not OOB check
+static template_coordinate_key_t* template_coordinate_keys_get(template_coordinate_keys_t *keys, size_t idx) {
+    size_t buffer_idx = idx / keys->buffer_size; // the index of the buffer to retrieve in buffer
+    size_t buffer_offset = idx % keys->buffer_size; // the offset into the given buffer to retrieve
+    //assert(buffer_idx < keys->m);
+    //assert(buffer_offset < keys->buffer_size);
+    return &keys->buffers[buffer_idx][buffer_offset];
+}
+
+// Rellocates the buffers to hold at least max_k entries
+static int template_coordinate_keys_realloc(template_coordinate_keys_t *keys, int max_k) {
+    size_t cur_m = keys->m;
+    keys->m += 0x100;
+    //assert(keys->m > cur_m);
+    //assert(keys->m * keys->buffer_size >= max_k);
+    if ((keys->buffers = realloc(keys->buffers, keys->m * sizeof(template_coordinate_key_t*))) == NULL) {
+        print_error("sort", "couldn't reallocate memory for template coordinate key buffers");
+        return -1;
+    }
+    // allocate space for new buffers
+    int j;
+    for (j = cur_m; j < keys->m; ++j) {
+        if ((keys->buffers[j]= malloc(sizeof(template_coordinate_key_t) * keys->buffer_size)) == NULL) {
+            print_error("sort", "couldn't allocate memory for template coordinate key buffer");
+            return -1;
+        }
+    }
+    return 0;
+}
+
+
+// Struct which contains the a record, and the pointer to the sort tag (if any) or
+// a combined ref / position / strand.
+// Used to speed up sorts (coordinate, by-tag, and template-coordinate).
+typedef struct bam1_tag {
+    bam1_t *bam_record;
+    union {
+        const uint8_t *tag;
+        uint8_t pos_tid[12];
+        template_coordinate_key_t *key;
+    } u;
+} bam1_tag;
+
+/* Minimum memory required in megabytes before sort will attempt to run. This
+   is to prevent accidents where failing to use the -m option correctly results
+   in the creation of a temporary file for each read in the input file.
+   Don't forget to update the man page if you change this. */
+const size_t SORT_MIN_MEGS_PER_THREAD = 1;
+
+/* Default per-thread memory for sort. Must be >= SORT_MIN_MEGS_PER_THREAD.
+   Don't forget to update the man page if you change this. */
+const size_t SORT_DEFAULT_MEGS_PER_THREAD = 768;
+
+#if !defined(__DARWIN_C_LEVEL) || __DARWIN_C_LEVEL < 900000L
+#define NEED_MEMSET_PATTERN4
+#endif
+
+#ifdef NEED_MEMSET_PATTERN4
+void memset_pattern4(void *target, const void *pattern, size_t size) {
+    uint32_t* target_iter = target;
+    size_t loops = size/4;
+    size_t i;
+    for (i = 0; i < loops; ++i) {
+        memcpy(target_iter, pattern, 4);
+        ++target_iter;
+    }
+    if (size%4 != 0)
+        memcpy(target_iter, pattern, size%4);
+}
+#endif
+
+KHASH_INIT(c2c, char*, char*, 1, kh_str_hash_func, kh_str_hash_equal)
+KHASH_INIT(cset, char*, char, 0, kh_str_hash_func, kh_str_hash_equal)
+KHASH_MAP_INIT_STR(c2i, int)
+KHASH_MAP_INIT_STR(const_c2c, char *)
+
+#define hdrln_free_char(p)
+KLIST_INIT(hdrln, char*, hdrln_free_char)
+
+static template_coordinate_key_t* template_coordinate_key(bam1_t *b, template_coordinate_key_t *key, sam_hdr_t *hdr, khash_t(const_c2c) *lib_lookup);
+
+typedef enum {Coordinate, QueryName, TagCoordinate, TagQueryName, MinHash, TemplateCoordinate} SamOrder;
+static SamOrder g_sam_order = Coordinate;
+static char g_sort_tag[2] = {0,0};
+
+static int strnum_cmp(const char *_a, const char *_b)
+{
+    const unsigned char *a = (const unsigned char*)_a, *b = (const unsigned char*)_b;
+    const unsigned char *pa = a, *pb = b;
+    while (*pa && *pb) {
+        if (isdigit(*pa) && isdigit(*pb)) {
+            while (*pa == '0') ++pa;
+            while (*pb == '0') ++pb;
+            while (isdigit(*pa) && isdigit(*pb) && *pa == *pb) ++pa, ++pb;
+            if (isdigit(*pa) && isdigit(*pb)) {
+                int i = 0;
+                while (isdigit(pa[i]) && isdigit(pb[i])) ++i;
+                return isdigit(pa[i])? 1 : isdigit(pb[i])? -1 : (int)*pa - (int)*pb;
+            } else if (isdigit(*pa)) return 1;
+            else if (isdigit(*pb)) return -1;
+            else if (pa - a != pb - b) return pa - a < pb - b? 1 : -1;
+        } else {
+            if (*pa != *pb) return (int)*pa - (int)*pb;
+            ++pa; ++pb;
+        }
+    }
+    return *pa? 1 : *pb? -1 : 0;
+}
+
+#define HEAP_EMPTY (UINT64_MAX >> 1)
+
+typedef struct {
+    int i;
+    uint32_t tid;
+    uint64_t pos:63, rev:1, idx;
+    bam1_tag entry;
+} heap1_t;
+
+static inline int bam1_cmp_by_tag(const bam1_tag a, const bam1_tag b);
+static inline int bam1_cmp_by_minhash(const bam1_tag a, const bam1_tag b);
+static inline int bam1_cmp_template_coordinate(const bam1_tag a, const bam1_tag b);
+static khash_t(const_c2c) * lookup_libraries(sam_hdr_t *header);
+static void lib_lookup_destroy(khash_t(const_c2c) *lib_lookup);
+
+// Function to compare reads in the heap and determine which one is < the other
+// Note, unlike the bam1_cmp_by_X functions which return <0, 0, >0 this
+// is strictly 0 or 1 only.
+static inline int heap_lt(const heap1_t a, const heap1_t b)
+{
+    if (!a.entry.bam_record)
+        return 1;
+    if (!b.entry.bam_record)
+        return 0;
+
+    int t, fa, fb;
+    switch (g_sam_order) {
+        case Coordinate:
+            if (a.tid != b.tid) return a.tid > b.tid;
+            if (a.pos != b.pos) return a.pos > b.pos;
+            if (a.rev != b.rev) return a.rev > b.rev;
+            break;
+        case QueryName:
+            t = strnum_cmp(bam_get_qname(a.entry.bam_record), bam_get_qname(b.entry.bam_record));
+            if (t != 0) return t > 0;
+            fa = a.entry.bam_record->core.flag & 0xc0;
+            fb = b.entry.bam_record->core.flag & 0xc0;
+            if (fa != fb) return fa > fb;
+            break;
+        case TagQueryName:
+        case TagCoordinate:
+            t = bam1_cmp_by_tag(a.entry, b.entry);
+            if (t != 0) return t > 0;
+            break;
+        case MinHash:
+            t = bam1_cmp_by_minhash(a.entry, b.entry);
+            if (t != 0) return t > 0;
+            break;
+        case TemplateCoordinate:
+            t = bam1_cmp_template_coordinate(a.entry, b.entry);
+            if (t != 0) return t > 0;
+            break;
+        default:
+            print_error("heap_lt", "unknown sort order: %d", g_sam_order);
+            break;
+    }
+
+    // This compares by position in the input file(s)
+    if (a.i != b.i) return a.i > b.i;
+    return a.idx > b.idx;
+}
+
+KSORT_INIT(heap, heap1_t, heap_lt)
+
+typedef struct merged_header {
+    sam_hdr_t    *hdr;
+    kstring_t     out_rg;
+    kstring_t     out_pg;
+    kstring_t     out_co;
+    char        **target_name;
+    uint32_t     *target_len;
+    size_t        n_targets;
+    size_t        targets_sz;
+    khash_t(c2i) *sq_tids;
+    khash_t(cset) *rg_ids;
+    khash_t(cset) *pg_ids;
+    bool          have_hd;
+} merged_header_t;
+
+typedef struct trans_tbl {
+    int32_t n_targets;
+    int* tid_trans;
+    kh_c2c_t* rg_trans;
+    kh_c2c_t* pg_trans;
+    bool lost_coord_sort;
+} trans_tbl_t;
+
+static void trans_tbl_destroy(trans_tbl_t *tbl) {
+    khiter_t iter;
+
+    free(tbl->tid_trans);
+
+    /*
+     * The values for the tbl->rg_trans and tbl->pg_trans hashes are pointers
+     * to keys in the rg_ids and pg_ids sets of the merged_header_t, so
+     * they should not be freed here.
+     *
+     * The keys are unique to each hash entry, so they do have to go.
+     */
+
+    for (iter = kh_begin(tbl->rg_trans); iter != kh_end(tbl->rg_trans); ++iter) {
+        if (kh_exist(tbl->rg_trans, iter)) {
+            free(kh_key(tbl->rg_trans, iter));
+        }
+    }
+    for (iter = kh_begin(tbl->pg_trans); iter != kh_end(tbl->pg_trans); ++iter) {
+        if (kh_exist(tbl->pg_trans, iter)) {
+            free(kh_key(tbl->pg_trans, iter));
+        }
+    }
+
+    kh_destroy(c2c,tbl->rg_trans);
+    kh_destroy(c2c,tbl->pg_trans);
+}
+
+/*
+ *  Create a merged_header_t struct.
+ */
+
+static merged_header_t * init_merged_header() {
+    merged_header_t *merged_hdr;
+
+    merged_hdr = calloc(1, sizeof(*merged_hdr));
+    if (merged_hdr == NULL) return NULL;
+
+    merged_hdr->hdr = sam_hdr_init();
+    if (!merged_hdr->hdr) goto fail;
+
+    merged_hdr->targets_sz   = 16;
+    merged_hdr->target_name = malloc(merged_hdr->targets_sz
+                                     * sizeof(*merged_hdr->target_name));
+    if (NULL == merged_hdr->target_name) goto fail;
+
+    merged_hdr->target_len = malloc(merged_hdr->targets_sz
+                                    * sizeof(*merged_hdr->target_len));
+    if (NULL == merged_hdr->target_len) goto fail;
+
+    merged_hdr->sq_tids = kh_init(c2i);
+    if (merged_hdr->sq_tids == NULL) goto fail;
+
+    merged_hdr->rg_ids = kh_init(cset);
+    if (merged_hdr->rg_ids == NULL) goto fail;
+
+    merged_hdr->pg_ids = kh_init(cset);
+    if (merged_hdr->pg_ids == NULL) goto fail;
+
+    return merged_hdr;
+
+ fail:
+    perror("[init_merged_header]");
+    kh_destroy(cset, merged_hdr->pg_ids);
+    kh_destroy(cset, merged_hdr->rg_ids);
+    kh_destroy(c2i, merged_hdr->sq_tids);
+    free(merged_hdr->target_name);
+    free(merged_hdr->target_len);
+    sam_hdr_destroy(merged_hdr->hdr);
+    free(merged_hdr);
+    return NULL;
+}
+
+/* Some handy kstring manipulating functions */
+
+// Append char range to kstring
+static inline int range_to_ks(const char *src, int from, int to,
+                              kstring_t *dest) {
+    return kputsn(src + from, to - from, dest) != to - from;
+}
+
+// Append a kstring to a kstring
+static inline int ks_to_ks(kstring_t *src, kstring_t *dest) {
+    return kputsn(ks_str(src), ks_len(src), dest) != ks_len(src);
+}
+
+/*
+ * Generate a unique ID by appending a random suffix to a given prefix.
+ * existing_ids is the set of IDs that are already in use.
+ * If always_add_suffix is true, the suffix will always be included.
+ * If false, prefix will be returned unchanged if it isn't in existing_ids.
+ */
+
+static int gen_unique_id(char *prefix, khash_t(cset) *existing_ids,
+                         bool always_add_suffix, kstring_t *dest) {
+    khiter_t iter;
+
+    if (!always_add_suffix) {
+        // Try prefix on its own first
+        iter = kh_get(cset, existing_ids, prefix);
+        if (iter == kh_end(existing_ids)) { // prefix isn't used yet
+            dest->l = 0;
+            if (kputs(prefix, dest) == EOF) return -1;
+            return 0;
+        }
+    }
+
+    do {
+        dest->l = 0;
+        ksprintf(dest, "%s-%0lX", prefix, lrand48());
+        iter = kh_get(cset, existing_ids, ks_str(dest));
+    } while (iter != kh_end(existing_ids));
+
+    return 0;
+}
+
+/*
+ * Add the @HD line to the new header
+ * In practice the @HD line will come from the first input header.
+ */
+
+static int trans_tbl_add_hd(merged_header_t* merged_hdr,
+                            sam_hdr_t *translate) {
+    kstring_t hd_line = { 0, 0, NULL };
+    int res;
+
+    // TODO: handle case when @HD needs merging.
+    if (merged_hdr->have_hd) return 0;
+
+    res = sam_hdr_find_hd(translate, &hd_line);
+    if (res < -1) {
+        print_error("merge", "failed to get @HD line from header");
+        return -1;
+    }
+
+    if (res < 0) // Not found
+        return 0;
+
+    if (sam_hdr_add_lines(merged_hdr->hdr, hd_line.s, hd_line.l) < 0) {
+        print_error("merge", "failed to add @HD line to new header");
+        free(hd_line.s);
+        return -1;
+    }
+
+    free(hd_line.s);
+    merged_hdr->have_hd = true;
+
+    return 0;
+}
+
+/*
+ * Add @SQ records to the translation table.
+ *
+ * Go through the target list for the input header.  Any new targets found
+ * are added to the output header target list.  At the same time, a mapping
+ * from the input to output target ids is stored in tbl.
+ *
+ * If any new targets are found, the header text is scanned to find the
+ * corresponding @SQ records.  They are then copied into the
+ * merged_hdr->out_text kstring (which will eventually become the
+ * output header text).
+ *
+ * Returns 0 on success, -1 on failure.
+ */
+
+static int trans_tbl_add_sq(merged_header_t* merged_hdr, sam_hdr_t *translate,
+                            trans_tbl_t* tbl) {
+    int32_t i;
+    int min_tid = -1, res;
+    kstring_t sq_line = { 0, 0, NULL }, sq_sn = { 0, 0, NULL };
+
+    // Fill in the tid part of the translation table, adding new targets
+    // to the merged header as we go.
+
+    for (i = 0; i < sam_hdr_nref(translate); ++i) {
+        int trans_tid;
+        sq_sn.l = 0;
+        res = sam_hdr_find_tag_pos(translate, "SQ", i, "SN", &sq_sn);
+        if (res < 0) {
+            print_error("merge", "failed to get @SQ SN #%d from header", i + 1);
+            goto fail;
+        }
+
+        trans_tid = sam_hdr_name2tid(merged_hdr->hdr, sq_sn.s);
+        if (trans_tid < -1) {
+            print_error("merge", "failed to lookup ref");
+            goto fail;
+        }
+
+        if (trans_tid < 0) {
+            // Append missing entries to out_hdr
+            sq_line.l = 0;
+            res = sam_hdr_find_line_id(translate, "SQ", "SN", sq_sn.s, &sq_line);
+            if (res < 0) {
+                print_error("merge", "failed to get @SQ SN:%s from header", sq_sn.s);
+                goto fail;
+            }
+
+            trans_tid = sam_hdr_nref(merged_hdr->hdr);
+
+            res = sam_hdr_add_lines(merged_hdr->hdr, sq_line.s, sq_line.l);
+            if (res < 0) {
+                print_error("merge", "failed to add @SQ SN:%s to new header", sq_sn.s);
+                goto fail;
+            }
+        }
+        tbl->tid_trans[i] = trans_tid;
+
+        if (tbl->tid_trans[i] > min_tid) {
+            min_tid = tbl->tid_trans[i];
+        } else {
+            tbl->lost_coord_sort = true;
+        }
+    }
+
+    free(sq_line.s);
+    free(sq_sn.s);
+
+    return 0;
+
+ fail:
+    free(sq_line.s);
+    free(sq_sn.s);
+    return -1;
+}
+
+/*
+ * Common code for setting up RG and PG record ID tag translation.
+ *
+ * is_rg is true for RG translation, false for PG.
+ * translate is the input bam header
+ * merge is true if tags with the same ID are to be merged.
+ * known_ids is the set of IDs already in the output header.
+ * id_map is the translation map from input header IDs to output header IDs
+ * If override is set, it will be used to replace the existing ID (RG only)
+ *
+ * known_ids and id_map have entries for the new IDs added to them.
+ *
+ * Return value is a linked list of header lines with the translated IDs,
+ * or NULL if something went wrong (probably out of memory).
+ *
+ */
+
+static klist_t(hdrln) * trans_rg_pg(bool is_rg, sam_hdr_t *translate,
+                                    bool merge, khash_t(cset)* known_ids,
+                                    khash_t(c2c)* id_map, char *override) {
+    khiter_t iter;
+    int num_ids, i;
+    const char *rec_type = is_rg ? "RG" : "PG";
+    klist_t(hdrln) *hdr_lines;
+
+    hdr_lines = kl_init(hdrln);
+
+    // Search through translate's header
+    num_ids = sam_hdr_count_lines(translate, rec_type);
+    if (num_ids < 0)
+        goto fail;
+
+    for (i = 0; i < num_ids; i++) {
+        kstring_t orig_id = { 0, 0, NULL };        // ID in original header
+        kstring_t transformed_id = { 0, 0, NULL }; // ID in output header
+        char *map_value;    // Value to store in id_map
+        bool id_changed;    // Have we changed the ID?
+        bool not_found_in_output; // ID isn't in the output header (yet)
+
+        if (sam_hdr_find_tag_pos(translate, rec_type, i, "ID", &orig_id) < 0)
+            goto fail;
+
+        // is our matched ID in our output ID set already?
+        iter = kh_get(cset, known_ids, ks_str(&orig_id));
+        not_found_in_output = (iter == kh_end(known_ids));
+
+        if (override) {
+            // Override original ID (RG only)
+#ifdef OVERRIDE_DOES_NOT_MERGE
+            if (gen_unique_id(override, known_ids, false, &transformed_id))
+                goto memfail;
+            not_found_in_output = true;  // As ID now unique
+#else
+            if (kputs(override, &transformed_id) == EOF) goto memfail;
+            // Know about override already?
+            iter = kh_get(cset, known_ids, ks_str(&transformed_id));
+            not_found_in_output = (iter == kh_end(known_ids));
+#endif
+            id_changed = true;
+        } else {
+            if ( not_found_in_output || merge) {
+                // Not in there or merging so can add it as 1-1 mapping
+                if (ks_to_ks(&orig_id, &transformed_id)) goto memfail;
+                id_changed = false;
+            } else {
+                // It's in there so we need to transform it by appending
+                // a random number to the id
+                if (gen_unique_id(ks_str(&orig_id), known_ids,
+                                  true, &transformed_id))
+                    goto memfail;
+                id_changed = true;
+                not_found_in_output = true;  // As ID now unique
+            }
+        }
+
+        // Does this line need to go into our output header?
+        if (not_found_in_output) {
+            // Take matched line and replace ID with transformed_id
+            kstring_t new_hdr_line = { 0, 0, NULL };
+            if (sam_hdr_find_line_id(translate, rec_type,
+                                     "ID", ks_str(&orig_id), &new_hdr_line) < 0){
+                goto fail;
+            }
+
+            if (id_changed) {
+                char *idp = strstr(ks_str(&new_hdr_line), "\tID:"), *id_end;
+                ptrdiff_t id_offset, id_len;
+                if (!idp) {
+                    print_error("merge", "failed to find ID in \"%s\"\n",
+                                ks_str(&new_hdr_line));
+                    goto fail;
+                }
+                idp += 4;
+                for (id_end = idp; *id_end >= '\n'; id_end++) {}
+
+                id_offset = idp - new_hdr_line.s;
+                id_len = id_end - idp;
+
+                if (id_len < transformed_id.l) {
+                    if (ks_resize(&new_hdr_line, new_hdr_line.l
+                                  + transformed_id.l - id_len + 1/*nul*/))
+                        goto fail;
+                }
+                if (id_len != transformed_id.l) {
+                    memmove(new_hdr_line.s + id_offset + transformed_id.l,
+                            new_hdr_line.s + id_offset + id_len,
+                            new_hdr_line.l - id_offset - id_len + 1);
+                }
+                memcpy(new_hdr_line.s + id_offset, transformed_id.s,
+                       transformed_id.l);
+            }
+
+            // append line to output linked list
+            char** ln = kl_pushp(hdrln, hdr_lines);
+            *ln = ks_release(&new_hdr_line);  // Give away to linked list
+
+            // Need to add it to known_ids set
+            int in_there = 0;
+            iter = kh_put(cset, known_ids, ks_str(&transformed_id), &in_there);
+            if (in_there < 0) goto memfail;
+            assert(in_there > 0);  // Should not already be in the map
+            map_value = ks_release(&transformed_id);
+        } else {
+            // Use existing string in id_map
+            assert(kh_exist(known_ids, iter));
+            map_value = kh_key(known_ids, iter);
+            free(ks_release(&transformed_id));
+        }
+
+        // Insert it into our translation map
+        int in_there = 0;
+        iter = kh_put(c2c, id_map, ks_release(&orig_id), &in_there);
+        kh_value(id_map, iter) = map_value;
+    }
+
+    // If there are no RG lines in the file and we are overriding add one
+    if (is_rg && override && hdr_lines->size == 0) {
+        kstring_t new_id = {0, 0, NULL};
+        kstring_t line = {0, 0, NULL};
+        kstring_t empty = {0, 0, NULL};
+        int in_there = 0;
+        char** ln;
+
+        // Get the new ID
+        if (gen_unique_id(override, known_ids, false, &new_id))
+            goto memfail;
+
+        // Make into a header line and add to linked list
+        ksprintf(&line, "@RG\tID:%s", ks_str(&new_id));
+        ln = kl_pushp(hdrln, hdr_lines);
+        *ln = ks_release(&line);
+
+        // Put into known_ids set
+        iter = kh_put(cset, known_ids, ks_str(&new_id), &in_there);
+        if (in_there < 0) goto memfail;
+        assert(in_there > 0);  // Should be a new entry
+
+        // Put into translation map (key is empty string)
+        if (kputs("", &empty) == EOF) goto memfail;
+        iter = kh_put(c2c, id_map, ks_release(&empty), &in_there);
+        if (in_there < 0) goto memfail;
+        assert(in_there > 0);  // Should be a new entry
+        kh_value(id_map, iter) = ks_release(&new_id);
+    }
+
+    return hdr_lines;
+
+ memfail:
+    perror(__func__);
+ fail:
+    if (hdr_lines) kl_destroy(hdrln, hdr_lines);
+    return NULL;
+}
+
+/*
+ * Common code for completing RG and PG record translation.
+ *
+ * Input is a list of header lines, and the mapping from input to
+ * output @PG record IDs.
+ *
+ * RG and PG records can contain tags that cross-reference to other @PG
+ * records.  This fixes the tags to contain the new IDs before adding
+ * them to the output header text.
+ */
+
+static int finish_rg_pg(bool is_rg, klist_t(hdrln) *hdr_lines,
+                        khash_t(c2c)* pg_map, kstring_t *out_text) {
+    const char *search = is_rg ? "\tPG:" : "\tPP:";
+    khiter_t idx;
+    char *line = NULL;
+
+    while ((kl_shift(hdrln, hdr_lines, &line)) == 0) {
+        char *id = strstr(line, search); // Look for tag to fix
+        int pos1 = 0, pos2 = 0;
+        char *new_id = NULL;
+
+        if (id) {
+            // Found a tag.  Look up the value in the translation map
+            // to see what it should be changed to in the output file.
+            char *end, tmp;
+
+            id += 4; // Point to value
+            end = strchr(id, '\t');  // Find end of tag
+            if (!end) end = id + strlen(id);
+
+            tmp = *end;
+            *end = '\0'; // Temporarily get the value on its own.
+
+            // Look-up in translation table
+            idx = kh_get(c2c, pg_map, id);
+            if (idx == kh_end(pg_map)) {
+                // Not found, warn.
+                fprintf(samtools_stderr, "[W::%s] Tag %s%s not found in @PG records\n",
+                        __func__, search + 1, id);
+            } else {
+                // Remember new id and splice points on original string
+                new_id = kh_value(pg_map, idx);
+                pos1 = id - line;
+                pos2 = end - line;
+            }
+
+            *end = tmp; // Restore string
+        }
+
+        // Copy line to output:
+        // line[0..pos1), new_id (if not NULL), line[pos2..end), '\n'
+
+        if (pos1 && range_to_ks(line, 0, pos1, out_text)) goto memfail;
+        if (new_id && kputs(new_id, out_text) == EOF) goto memfail;
+        if (kputs(line + pos2, out_text) == EOF) goto memfail;
+        if (kputc('\n', out_text) == EOF) goto memfail;
+        free(line);   // No longer needed
+        line = NULL;
+    }
+
+    return 0;
+
+ memfail:
+    perror(__func__);
+    free(line);  // Prevent leakage as no longer on list
+    return -1;
+}
+
+/*
+ * Build the translation table for an input *am file.  This stores mappings
+ * which allow IDs to be converted from those used in the input file
+ * to the ones which will be used in the output.  The mappings are for:
+ *   Reference sequence IDs (for @SQ records)
+ *   @RG record ID tags
+ *   @PG record ID tags
+ *
+ * At the same time, new header text is built up by copying records
+ * from the input bam file.  This will eventually become the header for
+ * the output file.  When copied, the ID tags for @RG and @PG records
+ * are replaced with their values.  The @PG PP: and @RG PG: tags
+ * are also modified if necessary.
+ *
+ * merged_hdr holds state on the output header (which IDs are present, etc.)
+ * translate is the input header
+ * tbl is the translation table that gets filled in.
+ * merge_rg controls merging of @RG records
+ * merge_pg controls merging of @PG records
+ * If rg_override is not NULL, it will be used to replace the existing @RG ID
+ *
+ * Returns 0 on success, -1 on failure.
+ */
+
+static int trans_tbl_init(merged_header_t* merged_hdr, sam_hdr_t* translate,
+                          trans_tbl_t* tbl, bool merge_rg, bool merge_pg,
+                          bool copy_co, char* rg_override)
+{
+    kstring_t lines = { 0, 0, NULL };
+    klist_t(hdrln) *rg_list = NULL;
+    klist_t(hdrln) *pg_list = NULL;
+
+    tbl->n_targets = sam_hdr_nref(translate);
+    tbl->rg_trans = tbl->pg_trans = NULL;
+    tbl->tid_trans = (int*)calloc(tbl->n_targets ? tbl->n_targets : 1,
+                                  sizeof(int));
+    if (tbl->tid_trans == NULL) goto memfail;
+    tbl->rg_trans = kh_init(c2c);
+    if (tbl->rg_trans == NULL) goto memfail;
+    tbl->pg_trans = kh_init(c2c);
+    if (tbl->pg_trans == NULL) goto memfail;
+
+    tbl->lost_coord_sort = false;
+
+    // Get the @HD record (if not there already).
+    if (trans_tbl_add_hd(merged_hdr, translate)) goto fail;
+
+    // Fill in map and add header lines for @SQ records
+    if (trans_tbl_add_sq(merged_hdr, translate, tbl)) goto fail;
+
+    // Get translated header lines and fill in map for @RG records
+    rg_list = trans_rg_pg(true, translate, merge_rg, merged_hdr->rg_ids,
+                          tbl->rg_trans, rg_override);
+    if (!rg_list) goto fail;
+
+    // Get translated header lines and fill in map for @PG records
+    pg_list = trans_rg_pg(false, translate, merge_pg, merged_hdr->pg_ids,
+                          tbl->pg_trans, NULL);
+    if (!pg_list) goto fail;
+
+    // Fix-up PG: tags in the new @RG records and add to output
+    if (finish_rg_pg(true, rg_list, tbl->pg_trans, &merged_hdr->out_rg))
+        goto fail;
+
+    // Fix-up PP: tags in the new @PG records and add to output
+    lines.l = 0;
+    if (finish_rg_pg(false, pg_list, tbl->pg_trans, &merged_hdr->out_pg))
+        goto fail;
+
+    kl_destroy(hdrln, rg_list); rg_list = NULL;
+    kl_destroy(hdrln, pg_list); pg_list = NULL;
+
+    if (copy_co) {
+        // Just append @CO headers without translation
+        int num_co = sam_hdr_count_lines(translate, "CO"), i;
+        if (num_co < 0)
+            goto fail;
+
+        for (i = 0; i < num_co; i++) {
+            if (sam_hdr_find_line_pos(translate, "CO", i, &lines) < 0)
+                goto fail;
+            if (ks_to_ks(&lines, &merged_hdr->out_co))
+                goto fail;
+            if (kputc('\n', &merged_hdr->out_co) < 0)
+                goto fail;
+        }
+    }
+
+    free(lines.s);
+
+    return 0;
+
+ memfail:
+    perror(__func__);
+ fail:
+    trans_tbl_destroy(tbl);
+    if (rg_list) kl_destroy(hdrln, rg_list);
+    if (pg_list) kl_destroy(hdrln, pg_list);
+    free(lines.s);
+    return -1;
+}
+
+static int finish_merged_header(merged_header_t *merged_hdr) {
+    if (sam_hdr_add_lines(merged_hdr->hdr, ks_c_str(&merged_hdr->out_rg),
+                          ks_len(&merged_hdr->out_rg)) < 0)
+        return -1;
+    if (sam_hdr_add_lines(merged_hdr->hdr, ks_c_str(&merged_hdr->out_pg),
+                          ks_len(&merged_hdr->out_pg)) < 0)
+        return -1;
+    if (sam_hdr_add_lines(merged_hdr->hdr, ks_c_str(&merged_hdr->out_co),
+                          ks_len(&merged_hdr->out_co)) < 0)
+        return -1;
+
+    return 0;
+}
+
+/*
+ * Free a merged_header_t struct and all associated data.
+ *
+ * Note that the keys to the rg_ids and pg_ids sets are also used as
+ * values in the translation tables.  This function should therefore not
+ * be called until the translation tables are no longer needed.
+ */
+
+static void free_merged_header(merged_header_t *merged_hdr) {
+    size_t i;
+    khiter_t iter;
+    if (!merged_hdr) return;
+    free(ks_release(&merged_hdr->out_rg));
+    free(ks_release(&merged_hdr->out_pg));
+    free(ks_release(&merged_hdr->out_co));
+    if (merged_hdr->target_name) {
+        for (i = 0; i < merged_hdr->n_targets; i++) {
+            free(merged_hdr->target_name[i]);
+        }
+        free(merged_hdr->target_name);
+    }
+    free(merged_hdr->target_len);
+    kh_destroy(c2i, merged_hdr->sq_tids);
+
+    if (merged_hdr->rg_ids) {
+        for (iter = kh_begin(merged_hdr->rg_ids);
+             iter != kh_end(merged_hdr->rg_ids); ++iter) {
+            if (kh_exist(merged_hdr->rg_ids, iter))
+                free(kh_key(merged_hdr->rg_ids, iter));
+        }
+        kh_destroy(cset, merged_hdr->rg_ids);
+    }
+
+    if (merged_hdr->pg_ids) {
+        for (iter = kh_begin(merged_hdr->pg_ids);
+             iter != kh_end(merged_hdr->pg_ids); ++iter) {
+            if (kh_exist(merged_hdr->pg_ids, iter))
+                free(kh_key(merged_hdr->pg_ids, iter));
+        }
+        kh_destroy(cset, merged_hdr->pg_ids);
+    }
+
+    free(merged_hdr);
+}
+
+static void bam_translate(bam1_t* b, trans_tbl_t* tbl)
+{
+    // Update target id if not unmapped tid
+    if ( b->core.tid >= 0 ) { b->core.tid = tbl->tid_trans[b->core.tid]; }
+    if ( b->core.mtid >= 0 ) { b->core.mtid = tbl->tid_trans[b->core.mtid]; }
+
+    // If we have a RG update it
+    uint8_t *rg = bam_aux_get(b, "RG");
+    if (rg) {
+        char* decoded_rg = bam_aux2Z(rg);
+        khiter_t k = kh_get(c2c, tbl->rg_trans, decoded_rg);
+        if (k != kh_end(tbl->rg_trans)) {
+            char* translate_rg = kh_value(tbl->rg_trans,k);
+            bam_aux_del(b, rg);
+            if (translate_rg) {
+                bam_aux_append(b, "RG", 'Z', strlen(translate_rg) + 1,
+                               (uint8_t*)translate_rg);
+            }
+        } else {
+            char *tmp = strdup(decoded_rg);
+            fprintf(samtools_stderr,
+                    "[bam_translate] RG tag \"%s\" on read \"%s\" encountered "
+                    "with no corresponding entry in header, tag lost. "
+                    "Unknown tags are only reported once per input file for "
+                    "each tag ID.\n",
+                    decoded_rg, bam_get_qname(b));
+            bam_aux_del(b, rg);
+            // Prevent future whinges
+            if (tmp) {
+                int in_there = 0;
+                k = kh_put(c2c, tbl->rg_trans, tmp, &in_there);
+                if (in_there > 0) kh_value(tbl->rg_trans, k) = NULL;
+            }
+        }
+    }
+
+    // If we have a PG update it
+    uint8_t *pg = bam_aux_get(b, "PG");
+    if (pg) {
+        char* decoded_pg = bam_aux2Z(pg);
+        khiter_t k = kh_get(c2c, tbl->pg_trans, decoded_pg);
+        if (k != kh_end(tbl->pg_trans)) {
+            char* translate_pg = kh_value(tbl->pg_trans,k);
+            bam_aux_del(b, pg);
+            if (translate_pg) {
+                bam_aux_append(b, "PG", 'Z', strlen(translate_pg) + 1,
+                               (uint8_t*)translate_pg);
+            }
+        } else {
+            char *tmp = strdup(decoded_pg);
+            fprintf(samtools_stderr,
+                    "[bam_translate] PG tag \"%s\" on read \"%s\" encountered "
+                    "with no corresponding entry in header, tag lost. "
+                    "Unknown tags are only reported once per input file for "
+                    "each tag ID.\n",
+                    decoded_pg, bam_get_qname(b));
+            bam_aux_del(b, pg);
+            // Prevent future whinges
+            if (tmp) {
+                int in_there = 0;
+                k = kh_put(c2c, tbl->pg_trans, tmp, &in_there);
+                if (in_there > 0) kh_value(tbl->pg_trans, k) = NULL;
+            }
+        }
+    }
+}
+
+int* rtrans_build(int n, int n_targets, trans_tbl_t* translation_tbl)
+{
+    // Create reverse translation table for tids
+    int* rtrans = (int*)malloc(sizeof(int32_t)*n*n_targets);
+    const int32_t NOTID = INT32_MIN;
+    if (!rtrans) return NULL;
+    memset_pattern4((void*)rtrans, &NOTID, sizeof(int32_t)*n*n_targets);
+    int i;
+    for (i = 0; i < n; ++i) {
+        int j;
+        for (j = 0; j < (translation_tbl+i)->n_targets; ++j) {
+            if ((translation_tbl+i)->tid_trans[j] != -1) {
+                rtrans[i*n_targets + (translation_tbl+i)->tid_trans[j]] = j;
+            }
+        }
+    }
+
+    return rtrans;
+}
+
+#define MERGE_RG          1 // Attach RG tag based on filename
+#define MERGE_UNCOMP      2 // Generate uncompressed BAM
+#define MERGE_LEVEL1      4 // Compress the BAM at level 1 (fast) mode
+#define MERGE_FORCE       8 // Overwrite output BAM if it exists
+#define MERGE_COMBINE_RG 16 // Combine RG tags frather than redefining them
+#define MERGE_COMBINE_PG 32 // Combine PG tags frather than redefining them
+#define MERGE_FIRST_CO   64 // Use only first file's @CO headers (sort cmd only)
+
+
+static hts_reglist_t *duplicate_reglist(const hts_reglist_t *rl, int rn) {
+    if (!rl)
+        return NULL;
+
+    hts_reglist_t *new_rl = calloc(rn, sizeof(hts_reglist_t));
+    if (!new_rl)
+        return NULL;
+
+    int i;
+    for (i=0; i < rn; i++) {
+        new_rl[i].tid     = rl[i].tid;
+        new_rl[i].count   = rl[i].count;
+        new_rl[i].min_beg = rl[i].min_beg;
+        new_rl[i].max_end = rl[i].max_end;
+
+        new_rl[i].reg = rl[i].reg;
+        new_rl[i].intervals = malloc(new_rl[i].count * sizeof(hts_pair_pos_t));
+        if (!new_rl[i].intervals) {
+            hts_reglist_free(new_rl, i);
+            return NULL;
+        }
+        memcpy(new_rl[i].intervals, rl[i].intervals, new_rl[i].count * sizeof(hts_pair_pos_t));
+    }
+
+    return new_rl;
+}
+
+/*
+ * How merging is handled
+ *
+ * If a header is defined use we will use that as our output header
+ * otherwise we use the first header from the first input file.
+ *
+ * Now go through each file and create a translation table for that file for:
+ * -RG
+ * -tid
+ * -PG tags
+ *
+ * Then whenever we read a record from a bam we translate that read before
+ * stashing it in the hash.
+ *
+ * In the actual merge, a read is read from each input file, translated and
+ * stashed in the hash. This assumes that all input files are sorted in the
+ * same way.  Next we just extract the next position ordered read from the
+ * hash, and replace it if there are still reads left in it's source input
+ * file. Finally we write our chosen read it to the output file.
+ */
+
+/*!
+  @abstract    Merge multiple sorted BAM.
+  @param  sam_order   the order in which the data was sorted
+  @param  sort_tag    if non-null, the tag that data was sorted by
+  @param  out         output BAM file name
+  @param  mode        sam_open() mode to be used to create the final output file
+                      (overrides level settings from UNCOMP and LEVEL1 flags)
+  @param  headers     name of SAM file from which to copy '@' header lines,
+                      or NULL to copy them from the first file to be merged
+  @param  n           number of files to be merged
+  @param  fn          names of files to be merged
+  @param  flag        flags that control how the merge is undertaken
+  @param  reg         region to merge
+  @param  n_threads   number of threads to use (passed to htslib)
+  @param  cmd         command name (used in print_error() etc)
+  @param  in_fmt      format options for input files
+  @param  out_fmt     output file format and options
+  @param  write_index create the index, together with the output file
+  @param  arg_list    command string for PG line
+  @param  no_pg       if 1, do not add a new PG line
+  @discussion Padding information may NOT correctly maintained. This
+  function is NOT thread safe.
+ */
+int bam_merge_core2(SamOrder sam_order, char* sort_tag, const char *out, const char *mode,
+                    const char *headers, int n, char * const *fn, char * const *fn_idx,
+                    const char *fn_bed, int flag, const char *reg, int n_threads,
+                    const char *cmd, const htsFormat *in_fmt, const htsFormat *out_fmt,
+                    int write_index, char *arg_list, int no_pg)
+{
+    samFile *fpout, **fp = NULL;
+    heap1_t *heap = NULL;
+    sam_hdr_t *hout = NULL;
+    sam_hdr_t *hin  = NULL;
+    int i, j, *RG_len = NULL;
+    uint64_t idx = 0;
+    char **RG = NULL;
+    hts_itr_t **iter = NULL;
+    sam_hdr_t **hdr = NULL;
+    trans_tbl_t *translation_tbl = NULL;
+    int *rtrans = NULL;
+    char *out_idx_fn = NULL;
+    void *hreg = NULL;
+    hts_reglist_t *lreg = NULL;
+    merged_header_t *merged_hdr = init_merged_header();
+    if (!merged_hdr) return -1;
+    refs_t *refs = NULL;
+    template_coordinate_keys_t *keys = NULL;
+    khash_t(const_c2c) *lib_lookup = NULL;
+
+    // Is there a specified pre-prepared header to use for output?
+    if (headers) {
+        samFile* fpheaders = sam_open(headers, "r");
+        if (fpheaders == NULL) {
+            print_error_errno(cmd, "cannot open \"%s\"", headers);
+            return -1;
+        }
+        hin = sam_hdr_read(fpheaders);
+        sam_close(fpheaders);
+        if (hin == NULL) {
+            print_error(cmd, "couldn't read headers from \"%s\"", headers);
+            goto mem_fail;
+        }
+    }
+
+    g_sam_order = sam_order;
+    if (sam_order == TagQueryName || sam_order == TagCoordinate) {
+        g_sort_tag[0] = sort_tag[0];
+        g_sort_tag[1] = sort_tag[0] ? sort_tag[1] : '\0';
+    }
+
+    fp = (samFile**)calloc(n, sizeof(samFile*));
+    if (!fp) goto mem_fail;
+    heap = (heap1_t*)calloc(n, sizeof(heap1_t));
+    if (!heap) goto mem_fail;
+    iter = (hts_itr_t**)calloc(n, sizeof(hts_itr_t*));
+    if (!iter) goto mem_fail;
+    hdr = (sam_hdr_t**)calloc(n, sizeof(sam_hdr_t*));
+    if (!hdr) goto mem_fail;
+    translation_tbl = (trans_tbl_t*)calloc(n, sizeof(trans_tbl_t));
+    if (!translation_tbl) goto mem_fail;
+    RG = (char**)calloc(n, sizeof(char*));
+    if (!RG) goto mem_fail;
+
+    // prepare RG tag from file names
+    if (flag & MERGE_RG) {
+        RG_len = (int*)calloc(n, sizeof(int));
+        if (!RG_len) goto mem_fail;
+        for (i = 0; i != n; ++i) {
+            int l = strlen(fn[i]);
+            const char *s = fn[i];
+            if (l > 4 && (strcmp(s + l - 4, ".bam") == 0 || strcmp(s + l - 4, ".sam") == 0)) l -= 4;
+            if (l > 5 && strcmp(s + l - 5, ".cram") == 0) l -= 5;
+            for (j = l - 1; j >= 0; --j) if (s[j] == '/') break;
+            ++j; l -= j;
+            RG[i] = (char*)calloc(l + 1, 1);
+            if (!RG[i]) goto mem_fail;
+            RG_len[i] = l;
+            strncpy(RG[i], s + j, l);
+        }
+    }
+
+    if (hin) {
+        // Populate merged_hdr from the pre-prepared header
+        trans_tbl_t dummy;
+        int res;
+        res = trans_tbl_init(merged_hdr, hin, &dummy, flag & MERGE_COMBINE_RG,
+                             flag & MERGE_COMBINE_PG, true, NULL);
+        trans_tbl_destroy(&dummy);
+        if (res) return -1; // FIXME: memory leak
+    }
+
+    // open and read the header from each file
+    for (i = 0; i < n; ++i) {
+        sam_hdr_t *hin;
+        fp[i] = sam_open_format(fn[i], "r", in_fmt);
+        if (fp[i] == NULL) {
+            print_error_errno(cmd, "fail to open \"%s\"", fn[i]);
+            goto fail;
+        }
+        hin = sam_hdr_read(fp[i]);
+        if (hin == NULL) {
+            print_error(cmd, "failed to read header from \"%s\"", fn[i]);
+            goto fail;
+        }
+
+        if (trans_tbl_init(merged_hdr, hin, translation_tbl+i,
+                           flag & MERGE_COMBINE_RG, flag & MERGE_COMBINE_PG,
+                           (flag & MERGE_FIRST_CO)? (i == 0) : true,
+                           RG[i]))
+            goto fail;
+
+        hdr[i] = hin;
+
+        int order_ok = 1;
+        if ((translation_tbl+i)->lost_coord_sort && (sam_order == Coordinate || sam_order == MinHash)) {
+            fprintf(samtools_stderr, "[bam_merge_core] Order of targets in file %s caused coordinate sort to be lost\n", fn[i]);
+            order_ok = 0;
+        }
+
+        if (!refs)
+            refs = cram_get_refs(fp[i]);
+
+        if (order_ok && refs && hts_set_opt(fp[i], CRAM_OPT_SHARED_REF, refs))
+            goto fail;
+    }
+
+    // Did we get an @HD line?
+    if (!merged_hdr->have_hd) {
+        fprintf(samtools_stderr, "[W::%s] No @HD tag found.\n", __func__);
+        /* FIXME:  Should we add an @HD line here, and if so what should
+           we put in it? Ideally we want a way of getting htslib to tell
+           us the SAM version number to assume given no @HD line.  Is
+           it also safe to assume that the output is coordinate sorted?
+           SO: is optional so we don't have to have it.*/
+        /* ksprintf(&merged_hdr->out_hd, "@HD\tVN:1.5\tSO:coordinate\n"); */
+    }
+
+    // Transform the header into standard form
+    if (finish_merged_header(merged_hdr) < 0)
+        goto fail;
+
+    hout = merged_hdr->hdr;
+    if (!hout)
+        goto fail;
+
+    // If we're only merging a specified region move our iters to start at that point
+    int tid, nreg;
+    hts_pos_t beg, end;
+
+    if (fn_bed) {
+        hreg = bed_read(fn_bed);
+        if (!hreg) {
+            fprintf(samtools_stderr, "[%s] Could not read BED file: \"%s\"\n", __func__, fn_bed);
+            goto fail;
+        }
+        bed_unify(hreg);
+        lreg = bed_reglist(hreg, ALL, &nreg);
+        if (!lreg || !nreg) {
+            fprintf(samtools_stderr, "[%s] Null or empty region list\n", __func__);
+            goto fail;
+        }
+    } else if (reg) {
+        rtrans = rtrans_build(n, sam_hdr_nref(hout), translation_tbl);
+        if (!rtrans) goto mem_fail;
+
+        if (!sam_parse_region(hout, reg, &tid, &beg, &end, 0)) {
+            fprintf(samtools_stderr, "[%s] Badly formatted region or unknown reference name: \"%s\"\n", __func__, reg);
+            goto fail;
+        }
+
+    }
+
+    if (reg || fn_bed) {
+        hts_idx_t *reg_idx = NULL;
+        for (i = 0; i < n; ++i) {
+
+            // If index filename has not been specified, look in the BAM folder
+            if (fn_idx != NULL) {
+                reg_idx = sam_index_load2(fp[i], fn[i], fn_idx[i]);
+            } else {
+                reg_idx = sam_index_load(fp[i], fn[i]);
+            }
+            if (reg_idx == NULL) {
+                fprintf(samtools_stderr, "[%s] failed to load index for %s. Random alignment retrieval only works for indexed BAM or CRAM files.\n",
+                        __func__, fn[i]);
+                free(rtrans);
+                rtrans = NULL;
+                goto fail;
+            }
+
+            int mapped_tid = INT32_MIN;
+            if (fn_bed) {
+                hts_reglist_t *rl = duplicate_reglist(lreg, nreg);
+                iter[i] = sam_itr_regions(reg_idx, hdr[i], rl, nreg);
+            } else {
+                // (rtrans[i*n+tid]) Look up what hout tid translates to in input tid space
+                mapped_tid = rtrans[i*sam_hdr_nref(hout)+tid];
+                if (mapped_tid != INT32_MIN) {
+                    iter[i] = sam_itr_queryi(reg_idx, mapped_tid, beg, end);
+                } else {
+                    iter[i] = sam_itr_queryi(reg_idx, HTS_IDX_NONE, 0, 0);
+                }
+            }
+
+            if (iter[i] == NULL) {
+                if (fn_bed) {
+                    fprintf(samtools_stderr, "[%s] failed to get multi-region iterator "
+                            "{%s, %s}\n", __func__, fn[i], fn_bed);
+                } else {
+                    if (mapped_tid != INT32_MIN) {
+                        fprintf(samtools_stderr,
+                                "[%s] failed to get iterator over "
+                                "{%s, %d, %"PRIhts_pos", %"PRIhts_pos"}\n",
+                                __func__, fn[i], mapped_tid, beg, end);
+                    } else {
+                        fprintf(samtools_stderr,
+                                "[%s] failed to get iterator over "
+                                "{%s, HTS_IDX_NONE, 0, 0}\n",
+                                __func__, fn[i]);
+                    }
+                }
+                hts_idx_destroy(reg_idx);
+                free(rtrans);
+                rtrans = NULL;
+                goto fail;
+            }
+
+            hts_idx_destroy(reg_idx);
+        }
+
+        free(rtrans);
+        rtrans = NULL;
+    }
+
+    // Make sure that there's enough memory for template coordinate keys, one per file to read
+    if (sam_order == TemplateCoordinate) {
+        if ((keys = malloc(sizeof(template_coordinate_keys_t))) == NULL) {
+            print_error("sort", "could not allocate memory for the top-level keys");
+            goto mem_fail;
+        }
+        keys->n = 0;
+        keys->m = 0;
+        keys->buffer_size = 0x10000;
+        keys->buffers = NULL;
+        // Make sure that there's enough memory for template coordinate keys, one per file to read
+        if (keys->n + n >= keys->m * keys->buffer_size) {
+            if (template_coordinate_keys_realloc(keys, keys->n + n) < 0) goto mem_fail;
+        }
+        lib_lookup = lookup_libraries(hout);
+        if (!lib_lookup) {
+            goto mem_fail;
+        }
+    }
+
+    // Load the first read from each file into the heap
+    for (i = 0; i < n; ++i) {
+        heap1_t *h = heap + i;
+        int res;
+        h->i = i;
+        h->entry.bam_record = bam_init1();
+        h->entry.u.tag = NULL;
+        if (!h->entry.bam_record) goto mem_fail;
+        res = iter[i] ? sam_itr_next(fp[i], iter[i], h->entry.bam_record) : sam_read1(fp[i], hdr[i], h->entry.bam_record);
+        if (res >= 0) {
+            bam_translate(h->entry.bam_record, translation_tbl + i);
+            h->tid = h->entry.bam_record->core.tid;
+            h->pos = (uint64_t)(h->entry.bam_record->core.pos + 1);
+            h->rev = bam_is_rev(h->entry.bam_record);
+            h->idx = idx++;
+            if (g_sam_order == TagQueryName || g_sam_order == TagCoordinate) {
+                h->entry.u.tag = bam_aux_get(h->entry.bam_record, g_sort_tag);
+            } else if (g_sam_order == TemplateCoordinate) {
+                template_coordinate_key_t *key = template_coordinate_keys_get(keys, i); // get the next key to use
+                h->entry.u.key = template_coordinate_key(heap->entry.bam_record, key, hout, lib_lookup); // update the key
+                if (heap->entry.u.key == NULL) goto mem_fail; // key could not be created, error out
+            } else {
+                h->entry.u.tag = NULL;
+            }
+        }
+        else if (res == -1 && (!iter[i] || iter[i]->finished)) {
+            h->pos = HEAP_EMPTY;
+            bam_destroy1(h->entry.bam_record);
+            h->entry.bam_record = NULL;
+            h->entry.u.tag = NULL;
+            h->entry.u.key = NULL;
+        } else {
+            print_error(cmd, "failed to read first record from \"%s\"", fn[i]);
+            goto fail;
+        }
+    }
+
+    // Open output file and write header
+    if ((fpout = sam_open_format(out, mode, out_fmt)) == 0) {
+        print_error_errno(cmd, "failed to create \"%s\"", out);
+        return -1;
+    }
+    if (!no_pg && sam_hdr_add_pg(hout, "samtools",
+                                 "VN", samtools_version(),
+                                 arg_list ? "CL": NULL,
+                                 arg_list ? arg_list : NULL,
+                                 NULL)) {
+        print_error(cmd, "failed to add PG line to the header of \"%s\"", out);
+        sam_close(fpout);
+        return -1;
+    }
+    if (sam_hdr_write(fpout, hout) != 0) {
+        print_error_errno(cmd, "failed to write header to \"%s\"", out);
+        sam_close(fpout);
+        return -1;
+    }
+    if (write_index) {
+        if (!(out_idx_fn = auto_index(fpout, out, hout))){
+            sam_close(fpout);
+            return -1;
+        }
+    }
+    if (!(flag & MERGE_UNCOMP)) hts_set_threads(fpout, n_threads);
+
+    if (refs && hts_set_opt(fpout, CRAM_OPT_SHARED_REF, refs))
+        goto fail;
+
+    // Begin the actual merge
+    ks_heapmake(heap, n, heap);
+    while (heap->pos != HEAP_EMPTY) {
+        bam1_t *b = heap->entry.bam_record;
+        if (flag & MERGE_RG) {
+            uint8_t *rg = bam_aux_get(b, "RG");
+            if (rg) bam_aux_del(b, rg);
+            bam_aux_append(b, "RG", 'Z', RG_len[heap->i] + 1, (uint8_t*)RG[heap->i]);
+        }
+        if (sam_write1(fpout, hout, b) < 0) {
+            print_error_errno(cmd, "failed writing to \"%s\"", out);
+            sam_close(fpout);
+            free(out_idx_fn);
+            return -1;
+        }
+        if ((j = (iter[heap->i]? sam_itr_next(fp[heap->i], iter[heap->i], b) : sam_read1(fp[heap->i], hdr[heap->i], b))) >= 0) {
+            bam_translate(b, translation_tbl + heap->i);
+            heap->tid = b->core.tid;
+            heap->pos = (uint64_t)(b->core.pos + 1);
+            heap->rev = bam_is_rev(b);
+            heap->idx = idx++;
+            if (g_sam_order == TagQueryName || g_sam_order == TagCoordinate) {
+                heap->entry.u.tag = bam_aux_get(heap->entry.bam_record, g_sort_tag);
+            } else if (g_sam_order == TemplateCoordinate) {
+                template_coordinate_key_t *key = template_coordinate_keys_get(keys, heap->i); // get the next key to use
+                heap->entry.u.key = template_coordinate_key(heap->entry.bam_record, key, hout, lib_lookup); // update the key
+                if (heap->entry.u.key == NULL) goto mem_fail; // key could not be created, error out
+            } else {
+                heap->entry.u.tag = NULL;
+            }
+        } else if (j == -1 && (!iter[heap->i] || iter[heap->i]->finished)) {
+            heap->pos = HEAP_EMPTY;
+            bam_destroy1(heap->entry.bam_record);
+            heap->entry.bam_record = NULL;
+            heap->entry.u.tag = NULL;
+        } else {
+            print_error(cmd, "\"%s\" is truncated", fn[heap->i]);
+            goto fail;
+        }
+        ks_heapadjust(heap, 0, n, heap);
+    }
+
+    if (write_index) {
+        if (sam_idx_save(fpout) < 0) {
+            print_error_errno("merge", "writing index failed");
+            goto fail;
+        }
+    }
+    free(out_idx_fn);
+
+    // Clean up and close
+    if (flag & MERGE_RG) {
+        for (i = 0; i != n; ++i) free(RG[i]);
+        free(RG_len);
+    }
+    for (i = 0; i < n; ++i) {
+        trans_tbl_destroy(translation_tbl + i);
+        hts_itr_destroy(iter[i]);
+        sam_hdr_destroy(hdr[i]);
+        sam_close(fp[i]);
+    }
+    sam_hdr_destroy(hin);
+    sam_hdr_destroy(hout);
+    free_merged_header(merged_hdr);
+    hts_reglist_free(lreg, nreg);
+    bed_destroy(hreg);
+    free(RG); free(translation_tbl); free(fp); free(heap); free(iter); free(hdr);
+    if (sam_close(fpout) < 0) {
+        print_error(cmd, "error closing output file");
+        return -1;
+    }
+    return 0;
+
+ mem_fail:
+    print_error(cmd, "Out of memory");
+
+ fail:
+    if (flag & MERGE_RG) {
+        if (RG) {
+            for (i = 0; i != n; ++i) free(RG[i]);
+        }
+        free(RG_len);
+    }
+    for (i = 0; i < n; ++i) {
+        if (translation_tbl && translation_tbl[i].tid_trans) trans_tbl_destroy(translation_tbl + i);
+        if (iter && iter[i]) hts_itr_destroy(iter[i]);
+        if (hdr && hdr[i]) sam_hdr_destroy(hdr[i]);
+        if (fp && fp[i]) sam_close(fp[i]);
+        if (heap && heap[i].entry.bam_record) bam_destroy1(heap[i].entry.bam_record);
+    }
+    if (hout) sam_hdr_destroy(hout);
+    free(RG);
+    free(translation_tbl);
+    free(hdr);
+    hts_reglist_free(lreg, nreg);
+    bed_destroy(hreg);
+    free(iter);
+    free(heap);
+    free(fp);
+    free(rtrans);
+    free(out_idx_fn);
+    if (keys != NULL) {
+        for (i = 0; i < keys->m; ++i) {
+            free(keys->buffers[i]);
+        }
+        free(keys->buffers);
+        free(keys);
+    }
+    lib_lookup_destroy(lib_lookup);
+    return -1;
+}
+
+// Unused here but may be used by legacy samtools-using third-party code
+int bam_merge_core(int by_qname, const char *out, const char *headers, int n, char * const *fn, int flag, const char *reg)
+{
+    char mode[12];
+    strcpy(mode, "wb");
+    if (flag & MERGE_UNCOMP) strcat(mode, "0");
+    else if (flag & MERGE_LEVEL1) strcat(mode, "1");
+    SamOrder sam_order = by_qname ? QueryName : Coordinate;
+    return bam_merge_core2(sam_order, NULL, out, mode, headers, n, fn, NULL, NULL, flag, reg, 0, "merge", NULL, NULL, 0, NULL, 1);
+}
+
+static void merge_usage(FILE *to)
+{
+    fprintf(to,
+"Usage: samtools merge [options] -o <out.bam> [options] <in1.bam> ... <inN.bam>\n"
+"   or: samtools merge [options] <out.bam> <in1.bam> ... <inN.bam>\n"
+"\n"
+"Options:\n"
+"  -n         Input files are sorted by read name\n"
+"  -t TAG     Input files are sorted by TAG value\n"
+"  -r         Attach RG tag (inferred from file names)\n"
+"  -u         Uncompressed BAM output\n"
+"  -f         Overwrite the output BAM if exist\n"
+"  -o FILE    Specify output file via option instead of <out.bam> argument\n"
+"  -1         Compress level 1\n"
+"  -l INT     Compression level, from 0 to 9 [-1]\n"
+"  -R STR     Merge file in the specified region STR [all]\n"
+"  -h FILE    Copy the header in FILE to <out.bam> [in1.bam]\n"
+"  -c         Combine @RG headers with colliding IDs [alter IDs to be distinct]\n"
+"  -p         Combine @PG headers with colliding IDs [alter IDs to be distinct]\n"
+"  -s VALUE   Override random seed\n"
+"  -b FILE    List of input BAM filenames, one per line [null]\n"
+"  -X         Use customized index files\n"
+"  -L FILE    Specify a BED file for multiple region filtering [null]\n"
+"  --no-PG    do not add a PG line\n"
+"  --template-coordinate Input files are sorted by template-coordinate\n");
+    sam_global_opt_help(to, "-.O..@..");
+}
+
+int bam_merge(int argc, char *argv[])
+{
+    int c, flag = 0, ret = 0, level = -1, has_index_file = 0;
+    char *fn_headers = NULL, *reg = NULL, mode[12];
+    char *sort_tag = NULL, *fnout = NULL, *arg_list = NULL;
+    long random_seed = (long)time(NULL);
+    char** fn = NULL;
+    char** fn_idx = NULL, *fn_bed = NULL;
+    int fn_size = 0, no_pg = 0;
+    SamOrder sam_order = Coordinate;
+
+    sam_global_args ga = SAM_GLOBAL_ARGS_INIT;
+    static const struct option lopts[] = {
+        SAM_OPT_GLOBAL_OPTIONS('-', 0, 'O', 0, 0, '@'),
+        { "threads", required_argument, NULL, '@' },
+        {"no-PG", no_argument, NULL, 1},
+        { "template-coordinate", no_argument, NULL, 2},
+        { NULL, 0, NULL, 0 }
+    };
+
+    if (argc == 1) {
+        merge_usage(samtools_stdout);
+        return 0;
+    }
+
+    while ((c = getopt_long(argc, argv, "h:nru1R:o:f@:l:cps:b:O:t:XL:", lopts, NULL)) >= 0) {
+        switch (c) {
+        case 'r': flag |= MERGE_RG; break;
+        case 'f': flag |= MERGE_FORCE; break;
+        case 'h': fn_headers = optarg; break;
+        case 'n': sam_order = QueryName; break;
+        case 'o': fnout = optarg; break;
+        case 't': sort_tag = optarg; break;
+        case '1': flag |= MERGE_LEVEL1; level = 1; break;
+        case 'u': flag |= MERGE_UNCOMP; level = 0; break;
+        case 'R': reg = strdup(optarg); break;
+        case 'l': level = atoi(optarg); break;
+        case 'c': flag |= MERGE_COMBINE_RG; break;
+        case 'p': flag |= MERGE_COMBINE_PG; break;
+        case 's': random_seed = atol(optarg); break;
+        case 'X': has_index_file = 1; break; // -X flag for index filename
+        case 'L': fn_bed = optarg; break;
+        case 'b': {
+            // load the list of files to read
+            if (has_index_file) {
+                fprintf(samtools_stderr,"Error: The -b option cannot be combined with -X\n");
+                ret = 1; goto end;
+            }
+            int nfiles;
+            char **fn_read = hts_readlines(optarg, &nfiles);
+            if (fn_read) {
+                // Append to end of array
+                fn = realloc(fn, (fn_size+nfiles) * sizeof(char*));
+                if (fn == NULL) { ret = 1; goto end; }
+                memcpy(fn+fn_size, fn_read, nfiles * sizeof(char*));
+                fn_size += nfiles;
+                free(fn_read);
+            }
+            else {
+                print_error("merge", "Invalid file list \"%s\"", optarg);
+                ret = 1;
+            }
+            break;
+        }
+        case 1: no_pg = 1; break;
+        case 2: sam_order = TemplateCoordinate; break;
+        default:  if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break;
+                  /* else fall-through */
+        case '?': merge_usage(samtools_stderr); return 1;
+        }
+    }
+
+    if (sort_tag != NULL) {
+        sam_order = sam_order == QueryName ? TagQueryName : TagCoordinate;
+    }
+
+    if (fnout == NULL && argc - optind >= 1) {
+        fnout = argv[optind];
+        optind++;
+    }
+    if (fnout == NULL) {
+        print_error("merge", "You must at least specify the output file");
+        merge_usage(samtools_stderr);
+        return 1;
+    }
+
+    if (!no_pg && !(arg_list = stringify_argv(argc+1, argv-1))) {
+        print_error("merge", "failed to create arg_list");
+        return 1;
+    }
+
+    hts_srand48(random_seed);
+    if (!(flag & MERGE_FORCE) && strcmp(fnout, "-") != 0) {
+        struct stat sbuf;
+        if (stat(fnout, &sbuf) == 0 && S_ISREG(sbuf.st_mode)) {
+            fprintf(samtools_stderr, "[%s] File '%s' exists. Please apply '-f' to overwrite. Abort.\n", __func__, fnout);
+            ret = 1;
+            goto end;
+        }
+    }
+
+    int nargcfiles = 0;
+    if (has_index_file) { // Calculate # of input BAM files
+        if ((argc - optind) % 2 != 0) {
+            fprintf(samtools_stderr, "Odd number of filenames detected! Each BAM file should have an index file\n");
+            ret = 1;
+            goto end;
+        }
+        nargcfiles = (argc - optind) / 2;
+    } else {
+        nargcfiles = argc - optind;
+    }
+
+    if (nargcfiles > 0) {
+        // Add argc files to end of array
+        fn = realloc(fn, (fn_size+nargcfiles) * sizeof(char*));
+        if (fn == NULL) { ret = 1; goto end; }
+        memcpy(fn+fn_size, argv + optind, nargcfiles * sizeof(char*));
+
+        if(has_index_file) {
+            fn_idx = realloc(fn_idx, nargcfiles * sizeof(char*));
+            if (fn_idx == NULL) { ret = 1; goto end; }
+            memcpy(fn_idx+fn_size, argv + nargcfiles + optind, nargcfiles * sizeof(char*));
+        }
+    }
+    if (fn_size+nargcfiles < 1) {
+        print_error("merge", "You must specify at least one (and usually two or more) input files");
+        merge_usage(samtools_stderr);
+        ret = 1;
+        goto end;
+    }
+
+    if (reg && fn_bed) {
+        print_error("merge", "You must specify either a BED file or a region");
+        ret = 1;
+        goto end;
+    }
+    strcpy(mode, "wb");
+    sam_open_mode(mode+1, fnout, NULL);
+    if (level >= 0) sprintf(strchr(mode, '\0'), "%d", level < 9? level : 9);
+    if (bam_merge_core2(sam_order, sort_tag, fnout, mode, fn_headers,
+                        fn_size+nargcfiles, fn, fn_idx, fn_bed, flag, reg, ga.nthreads,
+                        "merge", &ga.in, &ga.out, ga.write_index, arg_list, no_pg) < 0)
+        ret = 1;
+
+end:
+    if (fn_size > 0) {
+        int i;
+        for (i=0; i<fn_size; i++) free(fn[i]);
+    }
+    free(fn);
+    free(fn_idx);
+    free(reg);
+    free(arg_list);
+    sam_global_args_free(&ga);
+    return ret;
+}
+
+/***************
+ * BAM sorting *
+ ***************/
+
+
+typedef struct {
+    size_t from;
+    size_t to;
+} buf_region;
+
+/* Simplified version of bam_merge_core2() for merging part-sorted
+   temporary files.  No need for header merging or translation,
+   it just needs to read data into the heap and push it out again. */
+
+static inline int heap_add_read(heap1_t *heap, int nfiles, samFile **fp,
+                                int num_in_mem, buf_region *in_mem,
+                                bam1_tag *buf, template_coordinate_keys_t *keys,
+                                uint64_t *idx, sam_hdr_t *hout,
+                                khash_t(const_c2c) *lib_lookup) {
+    int i = heap->i, res;
+    if (i < nfiles) { // read from file
+        res = sam_read1(fp[i], hout, heap->entry.bam_record);
+        if (res >= 0 && g_sam_order == TemplateCoordinate) { // file read OK and TemplateCoordinate order
+            // It is assumed that there are nfiles more keys allocated than keys->n; see allocation in bam_merge_simple
+            template_coordinate_key_t *key = template_coordinate_keys_get(keys, keys->n + i); // get the next key to use
+            heap->entry.u.key = template_coordinate_key(heap->entry.bam_record, key, hout, lib_lookup); // update the key
+            if (heap->entry.u.key == NULL) res = -1; // key could not be created, error out
+        }
+    } else { // read from memory
+        if (in_mem[i - nfiles].from < in_mem[i - nfiles].to) {
+            size_t from = in_mem[i - nfiles].from;
+            heap->entry.bam_record = buf[from].bam_record;
+            if (g_sam_order == TemplateCoordinate) heap->entry.u.key = buf[from].u.key;
+            in_mem[i - nfiles].from++;
+            res = 0;
+        } else {
+            res = -1;
+        }
+    }
+    if (res >= 0) {
+        heap->tid = heap->entry.bam_record->core.tid;
+        heap->pos = (uint64_t)(heap->entry.bam_record->core.pos + 1);
+        heap->rev = bam_is_rev(heap->entry.bam_record);
+        heap->idx = (*idx)++;
+        if (g_sam_order == TagQueryName || g_sam_order == TagCoordinate) {
+            heap->entry.u.tag = bam_aux_get(heap->entry.bam_record, g_sort_tag);
+        } else if (g_sam_order != TemplateCoordinate) {
+            heap->entry.u.tag = NULL;
+            heap->entry.u.key = NULL;
+        }
+    } else if (res == -1) {
+        heap->pos = HEAP_EMPTY;
+        if (i < nfiles) bam_destroy1(heap->entry.bam_record);
+        heap->entry.bam_record = NULL;
+        heap->entry.u.tag = NULL;
+        heap->entry.u.key = NULL;
+    } else {
+        return -1;
+    }
+    return 0;
+}
+
+static int bam_merge_simple(SamOrder sam_order, char *sort_tag, const char *out,
+                            const char *mode, sam_hdr_t *hout,
+                            int n, char * const *fn, int num_in_mem,
+                            buf_region *in_mem, bam1_tag *buf,
+                            template_coordinate_keys_t *keys,
+                            khash_t(const_c2c) *lib_lookup, int n_threads,
+                            const char *cmd, const htsFormat *in_fmt,
+                            const htsFormat *out_fmt, char *arg_list, int no_pg,
+                            int write_index) {
+    samFile *fpout = NULL, **fp = NULL;
+    heap1_t *heap = NULL;
+    uint64_t idx = 0;
+    int i, heap_size = n + num_in_mem;
+    char *out_idx_fn = NULL;
+
+    if (sam_order == TagQueryName || sam_order == TagCoordinate) {
+        g_sort_tag[0] = sort_tag[0];
+        g_sort_tag[1] = sort_tag[0] ? sort_tag[1] : '\0';
+    }
+    if (n > 0) {
+        fp = (samFile**)calloc(n, sizeof(samFile*));
+        if (!fp) goto mem_fail;
+    }
+    heap = (heap1_t*)calloc(heap_size, sizeof(heap1_t));
+    if (!heap) goto mem_fail;
+
+    // Make sure that there's enough memory for template coordinate keys, one per file to read
+    if (keys && keys->n + n >= keys->m * keys->buffer_size) {
+        if (template_coordinate_keys_realloc(keys, keys->n + n) < 0) goto mem_fail;
+    }
+
+    // Open each file, read the header and put the first read into the heap
+    for (i = 0; i < heap_size; i++) {
+        sam_hdr_t *hin;
+        heap1_t *h = &heap[i];
+
+        if (i < n) {
+            fp[i] = sam_open_format(fn[i], "r", in_fmt);
+            if (fp[i] == NULL) {
+                print_error_errno(cmd, "fail to open \"%s\"", fn[i]);
+                goto fail;
+            }
+
+            // Read header ...
+            hin = sam_hdr_read(fp[i]);
+            if (hin == NULL) {
+                print_error(cmd, "failed to read header from \"%s\"", fn[i]);
+                goto fail;
+            }
+            // ... and throw it away as we don't really need it
+            sam_hdr_destroy(hin);
+        }
+
+        // Get a read into the heap
+        h->i = i;
+        h->entry.u.tag = NULL;
+        h->entry.u.key = NULL;
+        if (i < n) {
+            h->entry.bam_record = bam_init1();
+            if (!h->entry.bam_record) goto mem_fail;
+        }
+        if (heap_add_read(h, n, fp, num_in_mem, in_mem, buf, keys, &idx, hout,
+                          lib_lookup) < 0) {
+            assert(i < n);
+            print_error(cmd, "failed to read first record from \"%s\"", fn[i]);
+            goto fail;
+        }
+    }
+
+    // Open output file and write header
+    if ((fpout = sam_open_format(out, mode, out_fmt)) == 0) {
+        print_error_errno(cmd, "failed to create \"%s\"", out);
+        return -1;
+    }
+
+    if (!no_pg && sam_hdr_add_pg(hout, "samtools",
+                                 "VN", samtools_version(),
+                                 arg_list ? "CL": NULL,
+                                 arg_list ? arg_list : NULL,
+                                 NULL)) {
+        print_error(cmd, "failed to add PG line to the header of \"%s\"", out);
+        sam_close(fpout);
+        return -1;
+    }
+
+    if (n_threads > 1) hts_set_threads(fpout, n_threads);
+
+    if (sam_hdr_write(fpout, hout) != 0) {
+        print_error_errno(cmd, "failed to write header to \"%s\"", out);
+        sam_close(fpout);
+        return -1;
+    }
+
+    if (write_index) {
+        if (!(out_idx_fn = auto_index(fpout, out, hout))){
+            sam_close(fpout);
+            return -1;
+        }
+    }
+
+    // Now do the merge
+    ks_heapmake(heap, heap_size, heap);
+    while (heap->pos != HEAP_EMPTY) {
+        bam1_t *b = heap->entry.bam_record;
+        if (g_sam_order == MinHash && b->core.tid == -1) {
+            // Remove the cached minhash value
+            b->core.pos = -1;
+            b->core.mpos = -1;
+            b->core.isize = 0;
+        }
+        if (sam_write1(fpout, hout, b) < 0) {
+            print_error_errno(cmd, "failed writing to \"%s\"", out);
+            goto fail;
+        }
+        if (heap_add_read(heap, n, fp, num_in_mem, in_mem, buf, keys, &idx,
+                          hout, lib_lookup) < 0) {
+            assert(heap->i < n);
+            print_error(cmd, "Error reading \"%s\" : %s",
+                        fn[heap->i], strerror(errno));
+            goto fail;
+        }
+        ks_heapadjust(heap, 0, heap_size, heap);
+    }
+    // Clean up and close
+    for (i = 0; i < n; i++) {
+        if (sam_close(fp[i]) != 0) {
+            print_error(cmd, "Error on closing \"%s\" : %s",
+                        fn[i], strerror(errno));
+        }
+    }
+    free(fp);
+    free(heap);
+
+    if (write_index) {
+        if (sam_idx_save(fpout) < 0) {
+            print_error_errno("merge", "writing index failed");
+            goto fail;
+        }
+        free(out_idx_fn);
+    }
+
+    if (sam_close(fpout) < 0) {
+        print_error(cmd, "error closing output file");
+        return -1;
+    }
+    return 0;
+ mem_fail:
+    print_error(cmd, "Out of memory");
+
+ fail:
+    for (i = 0; i < n; i++) {
+        if (fp && fp[i]) sam_close(fp[i]);
+    }
+    for (i = 0; i < heap_size; i++) {
+        if (heap && heap[i].i < n && heap[i].entry.bam_record)
+            bam_destroy1(heap[i].entry.bam_record);
+    }
+    free(fp);
+    free(heap);
+    if (fpout) sam_close(fpout);
+    free(out_idx_fn);
+    return -1;
+}
+
+// Function to compare reads and determine which one is < or > the other
+// Handle sort-by-pos and sort-by-name. Used as the secondary sort in bam1_lt_by_tag, if reads are equivalent by tag.
+// Returns a value less than, equal to or greater than zero if a is less than,
+// equal to or greater than b, respectively.
+static inline int bam1_cmp_core(const bam1_tag a, const bam1_tag b)
+{
+    uint64_t pa, pb;
+    if (!a.bam_record) return 1;
+    if (!b.bam_record) return 0;
+
+    if (g_sam_order == QueryName || g_sam_order == TagQueryName) {
+        int t = strnum_cmp(bam_get_qname(a.bam_record), bam_get_qname(b.bam_record));
+        if (t != 0) return t;
+        return (int) (a.bam_record->core.flag&0xc0) - (int) (b.bam_record->core.flag&0xc0);
+    } else {
+        pa = a.bam_record->core.tid;
+        pb = b.bam_record->core.tid;
+
+        if (pa == pb) {
+            pa = (uint64_t)(a.bam_record->core.pos+1);
+            pb = (uint64_t)(b.bam_record->core.pos+1);
+        }
+
+        if (pa == pb) {
+            pa = bam_is_rev(a.bam_record);
+            pb = bam_is_rev(b.bam_record);
+        }
+
+        return pa < pb ? -1 : (pa > pb ? 1 : 0);
+    }
+}
+
+uint8_t normalize_type(const uint8_t* aux) {
+    if (*aux == 'c' || *aux == 'C' || *aux == 's' || *aux == 'S' || *aux == 'i' || *aux == 'I') {
+        return 'c';
+    } else if (*aux == 'f' || *aux == 'd') {
+        return 'f';
+    } else if (*aux == 'H' || *aux == 'Z') {
+         return 'H';
+    } else {
+        return *aux;
+    }
+}
+
+// Sort record by tag, using pos or read name as a secondary key if tags are identical. Reads not carrying the tag sort first.
+// Tags are first sorted by the type character (in case the types differ), or by the appropriate comparator for that type if they agree.
+// Returns a value less than, equal to or greater than zero if a is less than,
+// equal to or greater than b, respectively.
+static inline int bam1_cmp_by_tag(const bam1_tag a, const bam1_tag b)
+{
+    const uint8_t* aux_a = a.u.tag;
+    const uint8_t* aux_b = b.u.tag;
+
+    if (aux_a == NULL && aux_b != NULL) {
+        return -1;
+    } else if (aux_a != NULL && aux_b == NULL) {
+        return 1;
+    } else if (aux_a == NULL && aux_b == NULL) {
+        return bam1_cmp_core(a,b);
+    }
+
+    // 'Normalize' the letters of the datatypes to a canonical letter,
+    // so that comparison of different types
+    // forms a correct total ordering.
+    uint8_t a_type = normalize_type(aux_a);
+    uint8_t b_type = normalize_type(aux_b);
+
+    if (a_type != b_type) {
+        // Fix int to float comparisons by using bam_aux2f() to read the int
+        if (a_type == 'c' && b_type == 'f') {
+            a_type = 'f';
+        } else if (a_type == 'f' && b_type == 'c') {
+            b_type = 'f';
+        } else {
+            // Unfixable mismatched types
+            return a_type < b_type ? -1 : 1;
+        }
+    }
+
+    if (a_type == 'c') {
+        int64_t va = bam_aux2i(aux_a);
+        int64_t vb = bam_aux2i(aux_b);
+        if (va != vb) return va < vb ? -1 : 1;
+        return bam1_cmp_core(a, b);
+    } else if (a_type == 'f') {
+        double va = bam_aux2f(aux_a);
+        double vb = bam_aux2f(aux_b);
+        if (va != vb) return va < vb ? -1 : 1;
+        return bam1_cmp_core(a, b);
+    } else if (a_type == 'A') {
+        unsigned char va = bam_aux2A(aux_a);
+        unsigned char vb = bam_aux2A(aux_b);
+        if (va != vb) return va < vb ? -1 : 1;
+        return bam1_cmp_core(a, b);
+    } else if (a_type == 'H') {
+        int t = strcmp(bam_aux2Z(aux_a), bam_aux2Z(aux_b));
+        if (t) return t;
+        return bam1_cmp_core(a, b);
+    } else {
+        return bam1_cmp_core(a,b);
+    }
+}
+
+// Sort by minimiser (stored in bam1_tag.u.pos).
+// If equal, sort by position.
+//
+// The 64-bit sort key is split over the bam pos and isize fields.
+// This permits it to survive writing to temporary file and coming back.
+static inline int bam1_cmp_by_minhash(const bam1_tag a, const bam1_tag b)
+{
+    const bam1_t *A = a.bam_record;
+    const bam1_t *B = b.bam_record;
+
+    if (!A) return 1;
+    if (!B) return 0;
+
+    if (A->core.tid != -1 || B->core.tid != -1) return bam1_cmp_core(a,b);
+
+    const uint64_t m_a = (((uint64_t)A->core.pos)<<32)|(uint32_t)A->core.mpos;
+    const uint64_t m_b = (((uint64_t)B->core.pos)<<32)|(uint32_t)B->core.mpos;
+
+    if (m_a < m_b) // by hash
+        return -1;
+    else if (m_a > m_b)
+        return 1;
+    else if (A->core.isize < B->core.isize) // by hash location in seq
+        return -1;
+    else if (A->core.isize > B->core.isize)
+        return 1;
+    else
+        return bam1_cmp_core(a,b);
+}
+
+// compares to molecular identifiers, ignoring any trailing slash and subsequent single-character
+// * if mid1 is less than mid2, then -1 will be returned
+// * if mid1 is greater than mid2, then 1 will be returned
+static inline int template_coordinate_key_compare_mid(const char* mid1, const char* mid2) {
+    size_t i = 0;
+    size_t len1 = strlen(mid1);
+    size_t len2 = strlen(mid2);
+    size_t shortest;
+
+    // Snip off trailing slash followed by a single character, if present
+    if (len1 >= 2 && mid1[len1-2] == '/') len1 -= 2;
+    if (len2 >= 2 && mid2[len2-2] == '/') len2 -= 2;
+    shortest = len1 < len2 ? len1 : len2;
+
+    // find first mismatching character
+    while (i < shortest && mid1[i] == mid2[i]) i++;
+
+    // compare last characters
+    if (i == len1 && i < len2) return -1; // mid1 shorter
+    if (i == len2 && i < len1) return  1; // mid2 shorter
+    if (i == len1 && i == len2) return 0; // all characters match
+    if (mid1[i] < mid2[i]) return -1; // mid1 earlier
+    else return 1;
+}
+
+
+// Builds a key use to sort in TemplateCoordinate order.  Returns NULL if the key could not be created (e.g. MC
+// tag is missing), otherwise the pointer to the provided key.
+static template_coordinate_key_t* template_coordinate_key(bam1_t *b, template_coordinate_key_t *key, sam_hdr_t *hdr, khash_t(const_c2c) *lib_lookup) {
+    uint8_t *data;
+    char *rg;
+    khiter_t k;
+
+    // defaults
+    key->tid1 = key->tid2 = INT32_MAX;
+    key->pos1 = key->pos2 = HTS_POS_MAX;
+    key->neg1 = key->neg2 = false;
+    key->mid  = "";
+
+    // update values
+    rg = (char *)bam_aux_get(b, "RG");
+    if (rg && rg[0] == 'Z'
+        &&(k = kh_get(const_c2c, lib_lookup, rg + 1)) < kh_end(lib_lookup)) {
+        key->library = kh_value(lib_lookup, k);
+    } else {
+        key->library = "";
+    }
+    key->name = bam_get_qname(b);
+    if (!(b->core.flag & BAM_FUNMAP)) { // read is mapped, update coordinates
+        key->tid1 = b->core.tid;
+        key->neg1 = bam_is_rev(b);
+        key->pos1 = (key->neg1) ? unclipped_end(b) : unclipped_start(b);
+    }
+    if (b->core.flag & BAM_FPAIRED && !(b->core.flag & BAM_FMUNMAP)) { // mate is mapped, update coordinates
+        char *cigar;
+        if ((data = bam_aux_get(b, "MC"))) {
+            if (!(cigar = bam_aux2Z(data))) {
+                fprintf(samtools_stderr, "[bam_sort] error: MC tag wrong type. Please use the MC tag provided by samtools fixmate.\n");
+                return NULL;
+            }
+        } else {
+            fprintf(samtools_stderr, "[bam_sort] error: no MC tag. Please run samtools fixmate on file first.\n");
+            return NULL;
+        }
+        key->tid2 = b->core.mtid;
+        key->neg2 = bam_is_mrev(b);
+        key->pos2 = (key->neg2) ? unclipped_other_end(b->core.mpos, cigar) : unclipped_other_start(b->core.mpos, cigar);
+    }
+
+    if ((data = bam_aux_get(b, "MI"))) {
+        if (!(key->mid=bam_aux2Z(data))) {
+            fprintf(samtools_stderr, "[bam_sort] error: MI tag wrong type (not a string).\n");
+            return NULL;
+        }
+    }
+
+    // set is_upper_of_pair, and swap if we get the same key regardless of which end
+    // of the pair it is
+    if (key->tid1 < key->tid2
+            || (key->tid1 == key->tid2 && key->pos1 < key->pos2)
+            || (key->tid1 == key->tid2 && key->pos1 == key->pos2 && !key->neg1)) {
+        key->is_upper_of_pair = false;
+    } else {
+        key->is_upper_of_pair = true;
+        // swap
+        int tmp_tid;
+        hts_pos_t tmp_pos;
+        bool tmp_neg;
+        tmp_tid = key->tid1;
+        key->tid1 = key->tid2;
+        key->tid2 = tmp_tid;
+        tmp_pos = key->pos1;
+        key->pos1 = key->pos2;
+        key->pos2 = tmp_pos;
+        tmp_neg = key->neg1;
+        key->neg1 = key->neg2;
+        key->neg2 = tmp_neg;
+    }
+
+    return key;
+}
+
+// Function to compare reads and determine which one is < or > the other
+// Handles template-coordinate, which sorts by:
+// 1. the earlier unclipped 5' coordinate of the read pair
+// 2. the higher unclipped 5' coordinate of the read pair
+// 3. library (from read group)
+// 4. the molecular identifier (if present)
+// 5. read name
+// 6. if unpaired, or if R1 has the lower coordinates of the pair
+// Returns a value less than, equal to or greater than zero if a is less than,
+// equal to or greater than b, respectively.
+static inline int bam1_cmp_template_coordinate(const bam1_tag a, const bam1_tag b)
+{
+    if (!a.bam_record) return 1;
+    if (!b.bam_record) return 0;
+
+    const template_coordinate_key_t* key_a = a.u.key;
+    const template_coordinate_key_t* key_b = b.u.key;
+
+    int retval = 0;
+    if (0 == retval) retval = key_a->tid1 - key_b->tid1;
+    if (0 == retval) retval = key_a->tid2 - key_b->tid2;
+    if (0 == retval) retval = key_a->pos1 < key_b->pos1 ? -1 : (key_a->pos1 > key_b->pos1 ? 1 : 0);
+    if (0 == retval) retval = key_a->pos2 < key_b->pos2 ? -1 : (key_a->pos2 > key_b->pos2 ? 1 : 0);
+    if (0 == retval) retval = key_a->neg1 == key_b->neg1 ? 0 : (key_a->neg1 ? -1 : 1);
+    if (0 == retval) retval = key_a->neg2 == key_b->neg2 ? 0 : (key_a->neg2 ? -1 : 1);
+    if (0 == retval) retval = strcmp(key_a->library, key_b->library);
+    if (0 == retval) retval = template_coordinate_key_compare_mid(key_a->mid, key_b->mid);
+    if (0 == retval) retval = strcmp(key_a->name, key_b->name);
+    if (0 == retval) retval = key_a->is_upper_of_pair == key_b->is_upper_of_pair ? 0 : (key_a->is_upper_of_pair ? 1 : -1);
+    return retval < 0 ? -1 : (retval > 0 ? 1 : 0);
+}
+
+
+// Function to compare reads and determine which one is < the other
+// Handle sort-by-pos, sort-by-name, sort-by-tag, or sort-by-template-coordinate.
+static inline int bam1_lt(const bam1_tag a, const bam1_tag b)
+{
+    switch (g_sam_order) {
+        case Coordinate:
+        case QueryName:
+            return bam1_cmp_core(a, b) < 0;
+        case TagQueryName:
+        case TagCoordinate:
+            return bam1_cmp_by_tag(a, b) < 0;
+        case MinHash:
+            return bam1_cmp_by_minhash(a, b) < 0;
+        case TemplateCoordinate:
+            return bam1_cmp_template_coordinate(a, b) < 0;
+        default:
+            return bam1_cmp_core(a,b) < 0;
+    }
+}
+
+
+
+KSORT_INIT(sort, bam1_tag, bam1_lt)
+
+typedef struct {
+    size_t buf_len;
+    const char *prefix;
+    bam1_tag *buf;
+    const sam_hdr_t *h;
+    char *tmpfile_name;
+    int index;
+    int error;
+    int no_save;
+    int large_pos;
+    int minimiser_kmer;
+} worker_t;
+
+// Returns 0 for success
+//        -1 for failure
+static int write_buffer(const char *fn, const char *mode, size_t l, bam1_tag *buf,
+                        const sam_hdr_t *h, int n_threads, const htsFormat *fmt,
+                        int clear_minhash, char *arg_list, int no_pg, int write_index)
+{
+    size_t i;
+    samFile* fp;
+    char *out_idx_fn = NULL;
+
+    fp = sam_open_format(fn, mode, fmt);
+    if (fp == NULL) return -1;
+    if (!no_pg && sam_hdr_add_pg((sam_hdr_t *)h, "samtools", "VN", samtools_version(),
+                                 arg_list ? "CL": NULL,
+                                 arg_list ? arg_list : NULL,
+                                 NULL)) {
+        goto fail;
+    }
+    if (sam_hdr_write(fp, h) != 0) goto fail;
+
+    if (write_index)
+        if (!(out_idx_fn = auto_index(fp, fn, (sam_hdr_t *)h))) goto fail;
+
+    if (n_threads > 1) hts_set_threads(fp, n_threads);
+    for (i = 0; i < l; ++i) {
+        bam1_t *b = buf[i].bam_record;
+        if (clear_minhash && b->core.tid == -1) {
+            // Remove the cached minhash value
+            b->core.pos = -1;
+            b->core.mpos = -1;
+            b->core.isize = 0;
+        }
+        if (sam_write1(fp, h, b) < 0) goto fail;
+    }
+
+    if (write_index) {
+        if (sam_idx_save(fp) < 0) {
+            print_error_errno("merge", "writing index failed");
+            goto fail;
+        }
+        free(out_idx_fn);
+    }
+
+
+    if (sam_close(fp) < 0) return -1;
+    return 0;
+ fail:
+    sam_close(fp);
+    free(out_idx_fn);
+    return -1;
+}
+
+#define NUMBASE 256
+
+static int ks_radixsort(size_t n, bam1_tag *buf, const sam_hdr_t *h)
+{
+    int curr = 0, ret = -1;
+    ssize_t i;
+    bam1_tag *buf_ar2[2], *bam_a, *bam_b;
+    uint64_t max_pos = 1;
+    uint32_t max_tid = 1, tid_bytes = 0, pos_bytes = 0, byte = 0;
+    uint32_t tid_shift_l, tid_shift_r;
+    int nref = sam_hdr_nref(h);
+
+    // Count number of bytes needed for biggest tid and pos
+    //  Notes: Add 1 to core.pos so always positive.
+    //         Convert unmapped tid (-1) to number of references so unmapped
+    //         sort to the end.
+    for (i = 0; i < n; i++) {
+        bam1_t *b = buf[i].bam_record;
+        uint32_t tid = b->core.tid == -1 ? nref : b->core.tid;
+        uint64_t pos = ((uint64_t)(b->core.pos + 1) << 1) | bam_is_rev(b);
+        if (max_tid < tid)
+            max_tid = tid;
+        if (max_pos < pos)
+            max_pos = pos;
+    }
+
+    for (; max_pos > 0; max_pos >>= 8) pos_bytes++;
+    for (; max_tid > 0; max_tid >>= 8) tid_bytes++;
+    assert(pos_bytes + tid_bytes < sizeof(buf[0].u.pos_tid));
+
+    tid_shift_l = pos_bytes * 8;
+    tid_shift_r = 64 - tid_shift_l;
+
+    // Write position and tid into bam1_tag::u::pos_tid using minimum number
+    // of bytes required.  Values are stored little-endian so that we
+    // get a least-significant digit (byte) radix sort.
+    for (i = 0; i < n; i++) {
+        bam1_t *b = buf[i].bam_record;
+        uint32_t tid = b->core.tid == -1 ? nref : b->core.tid;
+        // 'pos' here includes as many bytes of tid as will fit
+        // in the space remaining above pos_bytes.  The rest of tid
+        // is written out separately.
+        uint64_t pos = (bam_is_rev(b) |
+                        ((uint64_t)(b->core.pos + 1) << 1) |
+                        (tid_shift_l < 64 ? (uint64_t) tid << tid_shift_l : 0));
+        u64_to_le(pos, buf[i].u.pos_tid);
+        u32_to_le(tid_shift_r < 32 ? tid >> tid_shift_r : 0,
+                  &buf[i].u.pos_tid[8]);
+    }
+
+    buf_ar2[0] = buf;
+    buf_ar2[1] = (bam1_tag *)malloc(sizeof(bam1_tag) * n);
+    if (buf_ar2[1] == NULL) {
+        print_error("sort", "couldn't allocate memory for temporary buf");
+        goto err;
+    }
+
+    // Least-significant digit radix sort (where "digits" are bytes)
+    for (byte = 0; byte < pos_bytes + tid_bytes; byte++) {
+        size_t remainders[NUMBASE] = { 0 };
+        bam_a = buf_ar2[curr]; bam_b = buf_ar2[1-curr];
+        for (i = 0; i < n; ++i)
+            remainders[bam_a[i].u.pos_tid[byte]]++;
+        for (i = 1; i < NUMBASE; ++i)
+            remainders[i] += remainders[i - 1];
+        for (i = n - 1; i >= 0; i--) {
+            size_t j = --remainders[bam_a[i].u.pos_tid[byte]];
+            bam_b[j] = bam_a[i];
+        }
+        curr = 1 - curr;
+    }
+    if (curr == 1) {
+        bam1_tag *end = buf + n;
+        bam_a = buf_ar2[0]; bam_b = buf_ar2[1];
+        while (bam_a < end) *bam_a++ = *bam_b++;
+    }
+
+    ret = 0;
+err:
+    free(buf_ar2[1]);
+    return ret;
+}
+
+/*
+ * Computes the minhash of a sequence using both forward and reverse strands.
+ *
+ * This is used as a sort key for unmapped data, to collate like sequences
+ * together and to improve compression ratio.
+ *
+ * The minhash is returned and *pos filled out with location of this hash
+ * key in the sequence if pos != NULL.
+ */
+static uint64_t minhash(bam1_t *b, int kmer, int *pos, int *rev) {
+    uint64_t hashf = 0, minhashf = UINT64_MAX;
+    uint64_t hashr = 0, minhashr = UINT64_MAX;
+    int minhashpf = 0, minhashpr = 0, i;
+    uint64_t mask = (1L<<(2*kmer))-1;
+    unsigned char *seq = bam_get_seq(b);
+    int len = b->core.l_qseq;
+
+    // Lookup tables for bam_seqi to 0123 fwd/rev hashes
+    // =ACM GRSV TWYH KDBN
+#define X 0
+    unsigned char L[16] = {
+        X,0,1,X,  2,X,X,X,  3,X,X,X,  X,X,X,X,
+    };
+    uint64_t R[16] = {
+        X,3,2,X,  1,X,X,X,  0,X,X,X,  X,X,X,X,
+    };
+    for (i = 0; i < 16; i++)
+        R[i] <<= 2*(kmer-1);
+
+    // Punt homopolymers somewhere central in the hash space
+#define XOR (0xdead7878beef7878 & mask)
+
+    // Initialise hash keys
+    for (i = 0; i < kmer-1 && i < len; i++) {
+        int base = bam_seqi(seq, i);
+        hashf = (hashf<<2) | L[base];
+        hashr = (hashr>>2) | R[base];
+    }
+
+    // Loop to find minimum
+    for (; i < len; i++) {
+        int base = bam_seqi(seq, i);
+
+        hashf = ((hashf<<2) | L[base]) & mask;
+        hashr =  (hashr>>2) | R[base];
+
+        if (minhashf > (hashf^XOR))
+            minhashf = (hashf^XOR), minhashpf = i;
+        if (minhashr > (hashr^XOR))
+            minhashr = (hashr^XOR), minhashpr = len-i+kmer-2;
+
+    }
+
+    if (minhashf <= minhashr) {
+        if (rev) *rev = 0;
+        if (pos) *pos = minhashpf;
+        return minhashf;
+    } else {
+        if (rev) *rev = 1;
+        if (pos) *pos = minhashpr;
+        return minhashr;
+    }
+}
+
+//--- Start of candidates to punt to htslib
+/*!
+ * @abstract
+ * Extracts the sequence (in current alignment orientation) from
+ * a bam record and places it in buf, which is nul terminated.
+ *
+ * @param b     The bam structure
+ * @param buf   A buffer at least b->core.l_qseq+1 bytes long
+ */
+static void bam_to_seq(bam1_t *b, char *buf) {
+    int i;
+    uint8_t *seq = bam_get_seq(b);
+    for (i = 0; i < b->core.l_qseq; i++)
+        buf[i] = seq_nt16_str[bam_seqi(seq, i)];
+    buf[i] = 0;
+}
+
+/*!
+ * @abstract
+ * Writes a new sequence, of length b->core.l_qseq, to a BAM record.
+ *
+ * If a sequence of a new length is required the caller must first make
+ * room for it by updating the bam1_t struct.
+ *
+ * @param b     The bam structure
+ * @param buf   A buffer at least b->core.l_qseq bytes long
+ */
+static void seq_to_bam(bam1_t *b, char *buf) {
+    int i;
+    uint8_t *seq = bam_get_seq(b);
+    for (i = 0; i < b->core.l_qseq; i++)
+        bam_set_seqi(seq, i, seq_nt16_table[(unsigned char)buf[i]]);
+}
+
+/*!
+ * @abstract Reverse complements a BAM record.
+ *
+ * It's possible to do this inline, but complex due to the 4-bit sequence
+ * encoding.  For now I take the dumb approach.
+ *
+ * @param b  Pointer to a BAM alignment
+ *
+ * @return   0 on success, -1 on failure (ENOMEM)
+ */
+static int reverse_complement(bam1_t *b) {
+    static char comp[256] = {
+        'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',//00
+        'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',//10
+        'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',//20
+        'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',//30
+
+       //    *   *   *    *   E   F   *    *   I   J   *    L   *   *   O
+        '@','T','V','G', 'H','E','F','C', 'D','I','H','M', 'L','K','N','O',//40
+       //P   Q   *   *    *   *   *   *    X   Y   Z   [    \   ]   ^   _
+        'P','Q','Y','S', 'A','A','B','W', 'X','Y','Z','[','\\','[','^','_',//50
+       //`   *   *   *    *   E   F   *    *   I   J   *    L   *   *   O
+        '`','t','v','g', 'h','e','f','c', 'd','i','j','m', 'l','k','n','o',//60
+       //P   Q   *   *    *   *   *   *    X   Y   Z   {    |   }   ~   DEL
+        'p','q','y','s', 'a','a','b','w', 'x','y','z','{', '|','}','~',127,//70
+
+        'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',//80
+        'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',//90
+        'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',//A0
+        'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',//B0
+
+        'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',//C0
+        'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',//D0
+        'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',//E0
+        'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',//F0
+    };
+    char seq_[10000], *seq = seq_;
+    uint8_t *qual = bam_get_qual(b);
+    int i, j;
+
+    if (b->core.l_qseq >= 10000)
+        if (!(seq = malloc(b->core.l_qseq+1)))
+            return -1;
+
+    bam_to_seq(b, seq);
+
+    for (i = 0, j = b->core.l_qseq-1; i < j; i++, j--) {
+        unsigned char tmp = seq[i];
+        seq[i] = comp[(unsigned char)seq[j]];
+        seq[j] = comp[tmp];
+        tmp = qual[i];
+        qual[i] = qual[j];
+        qual[j] = tmp;
+    }
+    if (i ==j)
+        seq[i] = comp[(unsigned char)seq[i]];
+
+    seq_to_bam(b, seq);
+
+    if (seq != seq_)
+        free(seq);
+
+    b->core.flag ^= 0x10;
+
+    return 0;
+}
+//--- End of candidates to punt to htslib
+
+
+static inline void worker_minhash(worker_t *w) {
+    int i;
+    for (i = 0; i < w->buf_len; i++) {
+        bam1_t *b = w->buf[i].bam_record;
+        if (b->core.tid != -1)
+            continue;
+
+        int pos = 0, rev = 0;
+        uint64_t mh = minhash(b, w->minimiser_kmer, &pos, &rev);
+        if (rev)
+            reverse_complement(b);
+
+        // Store 64-bit hash in unmapped pos and mpos fields.
+        // The position of hash is in isize, which we use for
+        // resolving ties when sorting by hash key.
+        // These are unused for completely unmapped data and
+        // will be reset during final output.
+        b->core.pos = mh>>31;
+        b->core.mpos = mh&0x7fffffff;
+        b->core.isize = 65535-pos >=0 ? 65535-pos : 0;
+    }
+}
+
+static void *worker(void *data)
+{
+    worker_t *w = (worker_t*)data;
+    char *name;
+    size_t name_len;
+    w->error = 0;
+    w->tmpfile_name = NULL;
+
+    switch (g_sam_order) {
+        case Coordinate:
+            if (ks_radixsort(w->buf_len, w->buf, w->h) < 0) {
+                w->error = errno;
+                return NULL;
+            }
+            break;
+        case MinHash:
+            worker_minhash(w);
+            // no break, go to merge sort
+        default:
+            ks_mergesort(sort, w->buf_len, w->buf, 0);
+    }
+
+    if (w->no_save)
+        return 0;
+
+    name_len = strlen(w->prefix) + 30;
+    name = (char*)calloc(name_len, 1);
+    if (!name) { w->error = errno; return 0; }
+    const int MAX_TRIES = 1000;
+    int tries = 0;
+    for (;;) {
+        if (tries) {
+            snprintf(name, name_len, "%s.%.4d-%.3d.bam",
+                     w->prefix, w->index, tries);
+        } else {
+            snprintf(name, name_len, "%s.%.4d.bam", w->prefix, w->index);
+        }
+
+        if (write_buffer(name, w->large_pos ? "wzx1" : "wbx1",
+                         w->buf_len, w->buf, w->h, 0, NULL, 0, NULL, 1, 0) == 0) {
+            break;
+        }
+        if (errno == EEXIST && tries < MAX_TRIES) {
+            tries++;
+        } else {
+            w->error = errno;
+            break;
+        }
+    }
+
+    if (w->error) {
+        free(name);
+    } else {
+        w->tmpfile_name = name;
+    }
+    return 0;
+}
+
+static int sort_blocks(int n_files, size_t k, bam1_tag *buf, const char *prefix,
+                       const sam_hdr_t *h, int n_threads, buf_region *in_mem,
+                       int large_pos, int minimiser_kmer, char **fns, size_t fns_size)
+{
+    int i;
+    size_t pos, rest;
+    pthread_t *tid;
+    pthread_attr_t attr;
+    worker_t *w;
+    int n_failed = 0;
+
+    if (n_threads < 1) n_threads = 1;
+    if (k < n_threads * 64) n_threads = 1; // use a single thread if we only sort a small batch of records
+    pthread_attr_init(&attr);
+    pthread_attr_setdetachstate(&attr, PTHREAD_CREATE_JOINABLE);
+    w = (worker_t*)calloc(n_threads, sizeof(worker_t));
+    if (!w) return -1;
+    tid = (pthread_t*)calloc(n_threads, sizeof(pthread_t));
+    if (!tid) { free(w); return -1; }
+    pos = 0; rest = k;
+    for (i = 0; i < n_threads; ++i) {
+        w[i].buf_len = rest / (n_threads - i);
+        w[i].buf = &buf[pos];
+        w[i].prefix = prefix;
+        w[i].h = h;
+        w[i].index = n_files + i;
+        w[i].tmpfile_name = NULL;
+        w[i].large_pos = large_pos;
+        w[i].minimiser_kmer = minimiser_kmer;
+        if (in_mem) {
+            w[i].no_save = 1;
+            in_mem[i].from = pos;
+            in_mem[i].to = pos + w[i].buf_len;
+        } else {
+            w[i].no_save = 0;
+        }
+        pos += w[i].buf_len; rest -= w[i].buf_len;
+        pthread_create(&tid[i], &attr, worker, &w[i]);
+    }
+    for (i = 0; i < n_threads; ++i) {
+        pthread_join(tid[i], 0);
+        if (!in_mem) {
+            assert(w[i].index >= 0 && w[i].index < fns_size);
+            fns[w[i].index] = w[i].tmpfile_name;
+        }
+        if (w[i].error != 0) {
+            errno = w[i].error;
+            print_error_errno("sort", "failed to create temporary file \"%s.%.4d.bam\"", prefix, w[i].index);
+            n_failed++;
+        }
+    }
+    if (n_failed && !in_mem) {
+        // Clean up any temporary files that did get made, as we're
+        // about to lose track of them
+        for (i = 0; i < n_threads; ++i) {
+            if (fns[w[i].index]) {
+                unlink(fns[w[i].index]);
+                free(fns[w[i].index]);
+                fns[w[i].index] = NULL;
+            }
+        }
+    }
+    free(tid); free(w);
+    if (n_failed) return -1;
+    if (in_mem) return n_threads;
+    return n_files + n_threads;
+}
+
+static void lib_lookup_destroy(khash_t(const_c2c) *lib_lookup) {
+    khiter_t k;
+    if (lib_lookup == NULL)
+        return;
+    for (k = kh_begin(lib_lookup); k < kh_end(lib_lookup); k++) {
+        if (kh_exist(lib_lookup, k))
+            free(kh_value(lib_lookup, k));
+    }
+    kh_destroy(const_c2c, lib_lookup);
+}
+
+// Build an RG to LB lookup table, for the template coordinate sort.
+// Returns a populated hash table (which may be empty) on success;
+// NULL on failure.
+static khash_t(const_c2c) * lookup_libraries(sam_hdr_t *header)
+{
+    khash_t(const_c2c) *lib_lookup = kh_init(const_c2c);
+    kstring_t lib_name = KS_INITIALIZE;
+    int num_rg, i, res;
+    if (!lib_lookup)
+        return NULL;
+
+    // Iterate through any RG lines and look for library information
+    num_rg = sam_hdr_count_lines(header, "RG");
+    if (num_rg < 0)
+        goto fail;
+
+    for (i = 0; i < num_rg; i++) {
+        const char *rg_id = sam_hdr_line_name(header, "RG", i);
+        khiter_t k;
+        if (!rg_id)
+            goto fail;
+        res = sam_hdr_find_tag_pos(header, "RG", i, "LB", &lib_name);
+        if (res < -1) // Error
+            goto fail;
+        if (res < 0 || !lib_name.s) // No LB tag
+            continue;
+        // Add to lookup table
+        k = kh_put(const_c2c, lib_lookup, rg_id, &res);
+        if (res < 0) // Error
+            goto fail;
+        if (res > 0) { // Inserted
+            kh_value(lib_lookup, k) = ks_release(&lib_name);
+        }
+    }
+
+    free(lib_name.s);
+
+    return lib_lookup;
+
+ fail:
+    lib_lookup_destroy(lib_lookup);
+    free(lib_name.s);
+    return NULL;
+}
+
+/*!
+  @abstract Sort an unsorted BAM file based on the provided sort order
+
+  @param  sam_order the order in which the sort should occur
+  @param  sort_tag  the tag to use if sorting by Tag
+  @param  minimiser_kmer the kmer size when sorting by MinHash
+  @param  fn       name of the file to be sorted
+  @param  prefix   prefix of the temporary files (prefix.NNNN.bam are written)
+  @param  fnout    name of the final output file to be written
+  @param  modeout  sam_open() mode to be used to create the final output file
+  @param  max_mem  approxiate maximum memory (very inaccurate)
+  @param  in_fmt   input file format options
+  @param  out_fmt  output file format and options
+  @param  arg_list    command string for PG line
+  @param  no_pg       if 1, do not add a new PG line
+  @paran  write_index create index for the output file
+  @return 0 for successful sorting, negative on errors
+
+  @discussion It may create multiple temporary subalignment files
+  and then merge them by calling bam_merge_simple(). This function is
+  NOT thread safe.
+ */
+int bam_sort_core_ext(SamOrder sam_order, char* sort_tag, int minimiser_kmer,
+                      const char *fn, const char *prefix,
+                      const char *fnout, const char *modeout,
+                      size_t _max_mem, int n_threads,
+                      const htsFormat *in_fmt, const htsFormat *out_fmt,
+                      char *arg_list, int no_pg, int write_index)
+{
+    int ret = -1, res, i, nref, n_files = 0;
+    size_t max_k, k, max_mem, bam_mem_offset;
+    sam_hdr_t *header = NULL;
+    samFile *fp = NULL;
+    bam1_tag *buf = NULL;
+    template_coordinate_keys_t *keys = NULL;
+    bam1_t *b = bam_init1();
+    uint8_t *bam_mem = NULL;
+    char **fns = NULL;
+    size_t fns_size = 0;
+    const char *new_so = NULL;
+    const char *new_go = NULL;
+    const char *new_ss = NULL;
+    buf_region *in_mem = NULL;
+    khash_t(const_c2c) *lib_lookup = NULL;
+    int num_in_mem = 0;
+    int large_pos = 0;
+
+    if (!b) {
+        print_error("sort", "couldn't allocate memory for bam record");
+        return -1;
+    }
+
+    if (n_threads < 2) n_threads = 1;
+    g_sam_order = sam_order;
+    if (g_sam_order == TagQueryName || g_sam_order == TagCoordinate) {
+        g_sort_tag[0] = sort_tag[0];
+        g_sort_tag[1] = sort_tag[0] ? sort_tag[1] : '\0';
+    }
+
+    if (sam_order == TemplateCoordinate) {
+        if ((keys = malloc(sizeof(template_coordinate_keys_t))) == NULL) {
+            print_error("sort", "could not allocate memory for the top-level keys");
+            goto err;
+        }
+        keys->n = 0;
+        keys->m = 0;
+        keys->buffer_size = 0x10000;
+        keys->buffers = NULL;
+    }
+
+    max_mem = _max_mem * n_threads;
+    buf = NULL;
+    fp = sam_open_format(fn, "r", in_fmt);
+    if (fp == NULL) {
+        print_error_errno("sort", "can't open \"%s\"", fn);
+        goto err;
+    }
+    header = sam_hdr_read(fp);
+    if (header == NULL) {
+        print_error("sort", "failed to read header from \"%s\"", fn);
+        goto err;
+    }
+
+    // Inspect the header looking for long chromosomes
+    // If there is one, we need to write temporary files in SAM format
+    nref = sam_hdr_nref(header);
+    for (i = 0; i < nref; i++) {
+        if (sam_hdr_tid2len(header, i) > INT32_MAX)
+            large_pos = 1;
+    }
+
+    // Also check the output format is large position compatible
+    if (large_pos) {
+        int compatible = (out_fmt->format == sam
+                          || (out_fmt->format == cram
+                              && out_fmt->version.major >= 4)
+                          || (out_fmt->format == unknown_format
+                              && modeout[0] == 'w'
+                              && (modeout[1] == 'z' || modeout[1] == '\0')));
+        if (!compatible) {
+            print_error("sort", "output format is not compatible with very large references");
+            goto err;
+        }
+    }
+
+    if (g_sam_order == TemplateCoordinate) {
+        lib_lookup = lookup_libraries(header);
+        if (!lib_lookup)
+            goto err;
+    }
+
+    switch (g_sam_order) {
+        case Coordinate:
+            new_so = "coordinate";
+            break;
+        case QueryName:
+            new_so = "queryname";
+            break;
+        case MinHash:
+            new_so = "coordinate";
+            new_ss = "coordinate:minhash";
+            break;
+        case TagQueryName:
+        case TagCoordinate:
+            new_so = "unknown";
+            break;
+        case TemplateCoordinate:
+            new_so = "unsorted";
+            new_go = "query";
+            new_ss = "unsorted:template-coordinate";
+            break;
+        default:
+            new_so = "unknown";
+            break;
+    }
+
+    if (new_ss == NULL && new_go == NULL) { // just SO
+        if ((-1 == sam_hdr_update_hd(header, "SO", new_so))
+            && (-1 == sam_hdr_add_line(header, "HD", "VN", SAM_FORMAT_VERSION, "SO", new_so, NULL))
+            ) {
+            print_error("sort", "failed to change sort order header to 'SO:%s'\n", new_so);
+            goto err;
+        }
+    } else if (new_ss != NULL && new_go == NULL) { // update SO and SS, but not GO
+        if ((-1 == sam_hdr_update_hd(header, "SO", new_so, "SS", new_ss))
+            && (-1 == sam_hdr_add_line(header, "HD", "VN", SAM_FORMAT_VERSION,
+                                       "SO", new_so, "SS", new_ss, NULL))
+            ) {
+            print_error("sort", "failed to change sort order header to 'SO:%s SS:%s'\n",
+                        new_so, new_ss);
+            goto err;
+        }
+    } else if (new_ss == NULL && new_go != NULL) { // update SO and GO, but not SS
+        if ((-1 == sam_hdr_update_hd(header, "SO", new_so, "GO", new_go))
+            && (-1 == sam_hdr_add_line(header, "HD", "VN", SAM_FORMAT_VERSION,
+                                       "SO", new_so, "GO", new_go, NULL))
+            ) {
+            print_error("sort", "failed to change sort order header to 'SO:%s GO:%s'\n",
+                        new_so, new_go);
+            goto err;
+        }
+    } else { // update SO, GO, and SS
+        if ((-1 == sam_hdr_update_hd(header, "SO", new_so, "GO", new_go, "SS", new_ss))
+            && (-1 == sam_hdr_add_line(header, "HD", "VN", SAM_FORMAT_VERSION,
+                                       "SO", new_so, "GO", new_go, "SS", new_ss, NULL))
+            ) {
+            print_error("sort", "failed to change sort order header to 'SO:%s GO:%s SS:%s'\n",
+                        new_so, new_go, new_ss);
+            goto err;
+        }
+    }
+
+    if (new_go == NULL) {
+        if (-1 == sam_hdr_remove_tag_hd(header, "GO")) {
+            print_error("sort", "failed to delete group order in header\n");
+            goto err;
+        }
+    }
+    if (new_ss == NULL) {
+        if (-1 == sam_hdr_remove_tag_hd(header, "SS")) {
+            print_error("sort", "failed to delete sub sort in header\n");
+            goto err;
+        }
+    }
+
+    // No gain to using the thread pool here as the flow of this code
+    // is such that we are *either* reading *or* sorting.  Hence a shared
+    // pool makes no real difference except to reduce the thread count a little.
+    if (n_threads > 1)
+        hts_set_threads(fp, n_threads);
+
+    if ((bam_mem = malloc(max_mem)) == NULL) {
+        print_error("sort", "couldn't allocate memory for bam_mem");
+        goto err;
+    }
+
+    // write sub files
+    k = max_k = bam_mem_offset = 0;
+    while ((res = sam_read1(fp, header, b)) >= 0) {
+        int mem_full = 0;
+
+        if (k == max_k) {
+            bam1_tag *new_buf;
+            max_k = max_k? max_k<<1 : 0x10000;
+            if ((new_buf = realloc(buf, max_k * sizeof(bam1_tag))) == NULL) {
+                print_error("sort", "couldn't allocate memory for buf");
+                goto err;
+            }
+            buf = new_buf;
+        }
+        if (sam_order == TemplateCoordinate && k >= keys->m * keys->buffer_size) {
+            if (template_coordinate_keys_realloc(keys, k + 1) == -1) {
+                goto err;
+            }
+        }
+
+        // Check if the BAM record will fit in the memory limit
+        if (bam_mem_offset + sizeof(*b) + b->l_data < max_mem) {
+            // Copy record into the memory block
+            buf[k].bam_record = (bam1_t *)(bam_mem + bam_mem_offset);
+            *buf[k].bam_record = *b;
+            buf[k].bam_record->data = (uint8_t *)((char *)buf[k].bam_record + sizeof(bam1_t));
+            memcpy(buf[k].bam_record->data, b->data, b->l_data);
+            // store next BAM record in next 8-byte-aligned address after
+            // current one
+            bam_mem_offset = (bam_mem_offset + sizeof(*b) + b->l_data + 8 - 1) & ~((size_t)(8 - 1));
+        } else {
+            // Add a pointer to the remaining record
+            buf[k].bam_record = b;
+            mem_full = 1;
+        }
+
+        // Set the tag if sorting by tag, or the key for template cooridinate sorting
+        switch (g_sam_order) {
+            case TagQueryName:
+            case TagCoordinate:
+                buf[k].u.tag = bam_aux_get(buf[k].bam_record, g_sort_tag);
+                break;
+            case TemplateCoordinate:
+                ++keys->n;
+                template_coordinate_key_t *key = template_coordinate_keys_get(keys, k);
+                buf[k].u.key = template_coordinate_key(buf[k].bam_record, key, header, lib_lookup);
+                if (buf[k].u.key == NULL) goto err;
+                break;
+            default:
+                buf[k].u.tag = NULL;
+                buf[k].u.key = NULL;
+        }
+        ++k;
+
+        if (mem_full) {
+            if (hts_resize(char *, n_files + (n_threads > 0 ? n_threads : 1),
+                           &fns_size, &fns, 0) < 0)
+                goto err;
+            int new_n = sort_blocks(n_files, k, buf, prefix, header, n_threads,
+                                    NULL, large_pos, minimiser_kmer, fns, fns_size);
+            if (new_n < 0) {
+                goto err;
+            } else {
+                n_files = new_n;
+            }
+            k = 0;
+            if (keys != NULL) keys->n = 0;
+            bam_mem_offset = 0;
+        }
+    }
+    if (res != -1) {
+        print_error("sort", "truncated file. Aborting");
+        goto err;
+    }
+
+    // Sort last records
+    if (k > 0) {
+        in_mem = calloc(n_threads > 0 ? n_threads : 1, sizeof(in_mem[0]));
+        if (!in_mem) goto err;
+        num_in_mem = sort_blocks(n_files, k, buf, prefix, header, n_threads,
+                                 in_mem, large_pos, minimiser_kmer, fns, fns_size);
+        if (num_in_mem < 0) goto err;
+    } else {
+        num_in_mem = 0;
+    }
+
+    // write the final output
+    if (n_files == 0 && num_in_mem < 2) { // a single block
+        if (write_buffer(fnout, modeout, k, buf, header, n_threads, out_fmt,
+                         minimiser_kmer, arg_list, no_pg, write_index) != 0) {
+            print_error_errno("sort", "failed to create \"%s\"", fnout);
+            goto err;
+        }
+    } else { // then merge
+        fprintf(samtools_stderr,
+                "[bam_sort_core] merging from %d files and %d in-memory blocks...\n",
+                n_files, num_in_mem);
+        // Paranoia check - all temporary files should have a name
+        for (i = 0; i < n_files; ++i) {
+            if (!fns[i]) {
+                print_error("sort",
+                            "BUG: no name stored for temporary file %d", i);
+                abort();
+            }
+        }
+        char *sort_by_tag = (sam_order == TagQueryName || sam_order == TagCoordinate) ? sort_tag : NULL;
+        if (bam_merge_simple(sam_order, sort_by_tag, fnout, modeout, header,
+                             n_files, fns, num_in_mem, in_mem, buf, keys,
+                             lib_lookup, n_threads, "sort", in_fmt, out_fmt,
+                             arg_list, no_pg, write_index) < 0) {
+            // Propagate bam_merge_simple() failure; it has already emitted a
+            // message explaining the failure, so no further message is needed.
+            goto err;
+        }
+    }
+
+    ret = 0;
+
+ err:
+    // free
+    if (fns) {
+        for (i = 0; i < n_files; ++i) {
+            if (fns[i]) {
+                unlink(fns[i]);
+                free(fns[i]);
+            }
+        }
+        free(fns);
+    }
+    bam_destroy1(b);
+    free(buf);
+    if (keys != NULL) {
+        for (i = 0; i < keys->m; ++i) {
+            free(keys->buffers[i]);
+        }
+        free(keys->buffers);
+        free(keys);
+    }
+    free(bam_mem);
+    free(in_mem);
+    lib_lookup_destroy(lib_lookup);
+    sam_hdr_destroy(header);
+    if (fp) sam_close(fp);
+    return ret;
+}
+
+// Unused here but may be used by legacy samtools-using third-party code
+int bam_sort_core(int is_by_qname, const char *fn, const char *prefix, size_t max_mem)
+{
+    int ret;
+    char *fnout = calloc(strlen(prefix) + 4 + 1, 1);
+    if (!fnout) return -1;
+    sprintf(fnout, "%s.bam", prefix);
+    SamOrder sam_order = is_by_qname ? QueryName : Coordinate;
+    g_sam_order = sam_order;
+    ret = bam_sort_core_ext(sam_order, NULL, 0, fn, prefix, fnout, "wb", max_mem, 0, NULL, NULL, NULL, 1, 0);
+    free(fnout);
+    return ret;
+}
+
+static void sort_usage(FILE *fp)
+{
+    fprintf(fp,
+"Usage: samtools sort [options...] [in.bam]\n"
+"Options:\n"
+"  -l INT     Set compression level, from 0 (uncompressed) to 9 (best)\n"
+"  -u         Output uncompressed data (equivalent to -l 0)\n"
+"  -m INT     Set maximum memory per thread; suffix K/M/G recognized [768M]\n"
+"  -M         Use minimiser for clustering unaligned/unplaced reads\n"
+"  -K INT     Kmer size to use for minimiser [20]\n"
+"  -n         Sort by read name (not compatible with samtools index command)\n"
+"  -t TAG     Sort by value of TAG. Uses position as secondary index (or read name if -n is set)\n"
+"  -o FILE    Write final output to FILE rather than standard output\n"
+"  -T PREFIX  Write temporary files to PREFIX.nnnn.bam\n"
+"      --no-PG\n"
+"               Do not add a PG line\n"
+"      --template-coordinate\n"
+"               Sort by template-coordinate\n");
+    sam_global_opt_help(fp, "-.O..@..");
+}
+
+static void complain_about_memory_setting(size_t max_mem) {
+    char  *suffix = "";
+    const size_t nine_k = 9<<10;
+    if (max_mem > nine_k) { max_mem >>= 10; suffix = "K"; }
+    if (max_mem > nine_k) { max_mem >>= 10; suffix = "M"; }
+
+    fprintf(samtools_stderr,
+"[bam_sort] -m setting (%zu%s bytes) is less than the minimum required (%zuM).\n\n"
+"Trying to run with -m too small can lead to the creation of a very large number\n"
+"of temporary files.  This may make sort fail due to it exceeding limits on the\n"
+"number of files it can have open at the same time.\n\n"
+"Please check your -m parameter.  It should be an integer followed by one of the\n"
+"letters K (for kilobytes), M (megabytes) or G (gigabytes).  You should ensure it\n"
+"is at least the minimum above, and much higher if you are sorting a large file.\n",
+            max_mem, suffix, SORT_MIN_MEGS_PER_THREAD);
+}
+
+int bam_sort(int argc, char *argv[])
+{
+    size_t max_mem = SORT_DEFAULT_MEGS_PER_THREAD << 20;
+    int c, nargs, ret, o_seen = 0, level = -1, no_pg = 0;
+    SamOrder sam_order = Coordinate;
+    bool by_tag = false;
+    int minimiser_kmer = 20;
+    char* sort_tag = NULL, *arg_list = NULL;
+    char *fnout = "-", modeout[12];
+    kstring_t tmpprefix = { 0, 0, NULL };
+    struct stat st;
+    sam_global_args ga = SAM_GLOBAL_ARGS_INIT;
+
+    static const struct option lopts[] = {
+        SAM_OPT_GLOBAL_OPTIONS('-', 0, 'O', 0, 0, '@'),
+        { "threads", required_argument, NULL, '@' },
+        {"no-PG", no_argument, NULL, 1},
+        { "template-coordinate", no_argument, NULL, 2},
+        { NULL, 0, NULL, 0 }
+    };
+
+    while ((c = getopt_long(argc, argv, "l:m:no:O:T:@:t:MK:u", lopts, NULL)) >= 0) {
+        switch (c) {
+        case 'o': fnout = optarg; o_seen = 1; break;
+        case 'n': sam_order = QueryName; break;
+        case 't': by_tag = true; sort_tag = optarg; break;
+        case 'm': {
+                char *q;
+                max_mem = strtol(optarg, &q, 0);
+                if (*q == 'k' || *q == 'K') max_mem <<= 10;
+                else if (*q == 'm' || *q == 'M') max_mem <<= 20;
+                else if (*q == 'g' || *q == 'G') max_mem <<= 30;
+                break;
+            }
+        case 'T': kputs(optarg, &tmpprefix); break;
+        case 'l': level = atoi(optarg); break;
+        case 'u': level = 0; break;
+        case   1: no_pg = 1; break;
+        case   2: sam_order = TemplateCoordinate; break;
+        case 'M': sam_order = MinHash; break;
+        case 'K':
+            minimiser_kmer = atoi(optarg);
+            if (minimiser_kmer < 1)
+                minimiser_kmer = 1;
+            else if (minimiser_kmer > 31)
+                minimiser_kmer = 31;
+            break;
+
+        default:  if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break;
+                  /* else fall-through */
+        case '?': sort_usage(samtools_stderr); ret = EXIT_FAILURE; goto sort_end;
+        }
+    }
+
+    // Change sort order if tag sorting is requested.  Must update based on secondary index
+    if (by_tag) {
+        sam_order = sam_order == QueryName ? TagQueryName : TagCoordinate;
+    }
+
+    nargs = argc - optind;
+    if (nargs == 0 && isatty(STDIN_FILENO)) {
+        sort_usage(samtools_stdout);
+        ret = EXIT_SUCCESS;
+        goto sort_end;
+    }
+    else if (nargs >= 2) {
+        // If exactly two, user probably tried to specify legacy <out.prefix>
+        if (nargs == 2)
+            fprintf(samtools_stderr, "[bam_sort] Use -T PREFIX / -o FILE to specify temporary and final output files\n");
+
+        sort_usage(samtools_stderr);
+        ret = EXIT_FAILURE;
+        goto sort_end;
+    }
+
+    if (ga.write_index && (sam_order == QueryName || sam_order == TagQueryName || sam_order == TagCoordinate || sam_order == TemplateCoordinate)) {
+        fprintf(samtools_stderr, "[W::bam_sort] Ignoring --write-index as it only works for position sorted files.\n");
+        ga.write_index = 0;
+    }
+
+    if (!no_pg && !(arg_list = stringify_argv(argc+1, argv-1))) {
+        print_error("sort", "failed to create arg_list");
+        return 1;
+    }
+
+    if (max_mem < (SORT_MIN_MEGS_PER_THREAD << 20)) {
+        complain_about_memory_setting(max_mem);
+        ret = EXIT_FAILURE;
+        goto sort_end;
+    }
+
+    strcpy(modeout, "wb");
+    sam_open_mode(modeout+1, fnout, NULL);
+    if (level >= 0) sprintf(strchr(modeout, '\0'), "%d", level < 9? level : 9);
+
+    if (tmpprefix.l == 0) {
+        if (strcmp(fnout, "-") != 0) {
+            char *idx = strstr(fnout, HTS_IDX_DELIM);
+            kputsn(fnout, idx ? idx - fnout : strlen(fnout), &tmpprefix);
+            kputs(".tmp", &tmpprefix);
+        } else {
+            kputc('.', &tmpprefix);
+        }
+    }
+    if (stat(tmpprefix.s, &st) == 0 && S_ISDIR(st.st_mode)) {
+        unsigned t = ((unsigned) time(NULL)) ^ ((unsigned) clock());
+        if (tmpprefix.s[tmpprefix.l-1] != '/') kputc('/', &tmpprefix);
+        ksprintf(&tmpprefix, "samtools.%d.%u.tmp", (int) getpid(), t % 10000);
+    }
+
+    ret = bam_sort_core_ext(sam_order, sort_tag, (sam_order == MinHash) ? minimiser_kmer : 0,
+                            (nargs > 0) ? argv[optind] : "-",
+                            tmpprefix.s, fnout, modeout, max_mem, ga.nthreads,
+                            &ga.in, &ga.out, arg_list, no_pg, ga.write_index);
+    if (ret >= 0)
+        ret = EXIT_SUCCESS;
+    else {
+        char dummy[4];
+        // If we failed on opening the input file & it has no .bam/.cram/etc
+        // extension, the user probably tried legacy -o <infile> <out.prefix>
+        if (ret == -2 && o_seen && nargs > 0 && sam_open_mode(dummy, argv[optind], NULL) < 0)
+            fprintf(samtools_stderr, "[bam_sort] Note the <out.prefix> argument has been replaced by -T/-o options\n");
+
+        ret = EXIT_FAILURE;
+    }
+
+sort_end:
+    free(tmpprefix.s);
+    free(arg_list);
+    sam_global_args_free(&ga);
+
+    return ret;
+}
diff --git a/samtools/bam_split.c b/samtools/bam_split.c
new file mode 100644
index 0000000..72a6298
--- /dev/null
+++ b/samtools/bam_split.c
@@ -0,0 +1,611 @@
+/*  bam_split.c -- split subcommand.
+
+    Copyright (C) 2013-2016,2018-2019 Genome Research Ltd.
+
+    Author: Martin Pollard <mp15@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <config.h>
+
+#include <string.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <stdbool.h>
+#include <limits.h>
+#include <unistd.h>
+#include <regex.h>
+#include <assert.h>
+#include <htslib/sam.h>
+#include <htslib/khash.h>
+#include <htslib/kstring.h>
+#include <htslib/cram.h>
+#include "htslib/thread_pool.h"
+#include "sam_opts.h"
+#include "samtools.h"
+
+
+KHASH_MAP_INIT_STR(c2i, int)
+
+struct parsed_opts {
+    const char *merged_input_name;
+    const char *unaccounted_header_name;
+    const char *unaccounted_name;
+    const char *output_format_string;
+    bool verbose;
+    int no_pg;
+    sam_global_args ga;
+};
+
+typedef struct parsed_opts parsed_opts_t;
+
+struct state {
+    samFile* merged_input_file;
+    sam_hdr_t* merged_input_header;
+    samFile* unaccounted_file;
+    sam_hdr_t* unaccounted_header;
+    size_t output_count;
+    char** rg_id;
+    char **rg_index_file_name;
+    char **rg_output_file_name;
+    samFile** rg_output_file;
+    sam_hdr_t** rg_output_header;
+    kh_c2i_t* rg_hash;
+    htsThreadPool p;
+    int write_index;
+};
+
+typedef struct state state_t;
+
+static int cleanup_state(state_t* status, bool check_close);
+static void cleanup_opts(parsed_opts_t* opts);
+
+static void usage(FILE *write_to)
+{
+    fprintf(write_to,
+"Usage: samtools split [-u <unaccounted.bam>] [-h <unaccounted_header.sam>]\n"
+"                      [-f <format_string>] [-v] <merged.bam>\n"
+"Options:\n"
+"  -f STRING       output filename format string [\"%%*_%%#.%%.\"]\n"
+"  -u FILE1        put reads with no RG tag or an unrecognised RG tag in FILE1\n"
+"  -h FILE2        ... and override the header with FILE2 (-u file only)\n"
+"  -v              verbose output\n"
+"  --no-PG         do not add a PG line\n");
+    sam_global_opt_help(write_to, "-....@..");
+    fprintf(write_to,
+"\n"
+"Format string expansions:\n"
+"  %%%%     %%\n"
+"  %%*     basename\n"
+"  %%#     @RG index\n"
+"  %%!     @RG ID\n"
+"  %%.     filename extension for output format\n"
+      );
+}
+
+// Takes the command line options and turns them into something we can understand
+static parsed_opts_t* parse_args(int argc, char** argv)
+{
+    if (argc == 1) { usage(stdout); return NULL; }
+
+    const char *optstring = "vf:h:u:@:";
+
+    static const struct option lopts[] = {
+        SAM_OPT_GLOBAL_OPTIONS('-', 0, 0, 0, 0, '@'),
+        {"no-PG", no_argument, NULL, 1},
+        { NULL, 0, NULL, 0 }
+    };
+
+    parsed_opts_t* retval = calloc(sizeof(parsed_opts_t), 1);
+    if (! retval ) { perror("cannot allocate option parsing memory"); return NULL; }
+
+    sam_global_args_init(&retval->ga);
+
+    int opt;
+    while ((opt = getopt_long(argc, argv, optstring, lopts, NULL)) != -1) {
+        switch (opt) {
+        case 'f':
+            retval->output_format_string = optarg;
+            break;
+        case 'h':
+            retval->unaccounted_header_name = optarg;
+            break;
+        case 'v':
+            retval->verbose = true;
+            break;
+        case 'u':
+            retval->unaccounted_name = optarg;
+            break;
+        case 1:
+            retval->no_pg = 1;
+            break;
+        default:
+            if (parse_sam_global_opt(opt, optarg, lopts, &retval->ga) == 0) break;
+            /* else fall-through */
+        case '?':
+            usage(stdout);
+            free(retval);
+            return NULL;
+        }
+    }
+
+    if (retval->output_format_string == NULL) retval->output_format_string = "%*_%#.%.";
+
+    argc -= optind;
+    argv += optind;
+
+    if (argc != 1) {
+        print_error("split", "Invalid number of arguments: %d", argc);
+        usage(stderr);
+        free(retval);
+        return NULL;
+    }
+
+    retval->merged_input_name = argv[0];
+
+    return retval;
+}
+
+// Expands a output filename format string
+static char* expand_format_string(const char* format_string, const char* basename, const char* rg_id, const int rg_idx, const htsFormat *format)
+{
+    kstring_t str = { 0, 0, NULL };
+    const char* pointer = format_string;
+    const char* next;
+    while ((next = strchr(pointer, '%')) != NULL) {
+        if (kputsn(pointer, next-pointer, &str) < 0) goto memfail;
+        ++next;
+        switch (*next) {
+            case '%':
+                if (kputc('%', &str) < 0) goto memfail;
+                break;
+            case '*':
+                if (kputs(basename, &str) < 0) goto memfail;
+                break;
+            case '#':
+                if (kputl(rg_idx, &str) < 0) goto memfail;
+                break;
+            case '!':
+                if (kputs(rg_id, &str) < 0) goto memfail;
+                break;
+            case '.':
+                // Only really need to cope with sam, bam, cram
+                if (format->format != unknown_format) {
+                    if (kputs(hts_format_file_extension(format), &str) < 0)
+                        goto memfail;
+                } else {
+                    if (kputs("bam", &str) < 0) goto memfail;
+                }
+                break;
+            case '\0':
+                print_error("split", "Trailing %% in filename format string");
+                goto fail;
+            default:
+                // Error is: fprintf(stderr, "bad format string, unknown format specifier\n");
+                print_error("split", "Unknown specifier %%%c in filename format string", *next);
+                goto fail;
+        }
+        pointer = next + 1;
+    }
+    if (kputs(pointer, &str) < 0) goto memfail;
+    return ks_release(&str);
+
+ memfail:
+    print_error_errno("split", "Couldn't build output filename");
+ fail:
+    free(str.s);
+    return NULL;
+}
+
+// Parse the header, count the number of RG tags and return a list of their names
+static bool count_RG(sam_hdr_t* hdr, size_t* count, char*** output_name)
+{
+    char **names = NULL;
+    kstring_t id_val = KS_INITIALIZE;
+    int i, n_rg = sam_hdr_count_lines(hdr, "RG");
+
+    if (n_rg < 0) {
+        print_error("split", "Failed to get @RG IDs");
+        *count = 0;
+        *output_name = NULL;
+        return false;
+    }
+
+    if (n_rg == 0) {
+        *count = 0;
+        *output_name = NULL;
+        return true;
+    }
+
+    names = calloc(n_rg, sizeof(names[0]));
+    if (!names) goto memfail;
+
+    for (i = 0; i < n_rg; i++) {
+        if (sam_hdr_find_tag_pos(hdr, "RG", i, "ID", &id_val) < 0) goto memfail;
+        names[i] = ks_release(&id_val);
+    }
+
+    *count = n_rg;
+    *output_name = names;
+    return true;
+
+ memfail:
+    print_error_errno("split", "Failed to get @RG IDs");
+    *count = 0;
+    *output_name = NULL;
+    ks_free(&id_val);
+    free(names);
+    return false;
+}
+
+static int header_compatible(sam_hdr_t *hdr1, sam_hdr_t *hdr2)
+{
+    size_t n;
+    if (sam_hdr_nref(hdr1) != sam_hdr_nref(hdr2)) {
+        print_error("split",
+                    "Unaccounted header contains wrong number of references");
+        return -1;
+    }
+    for (n = 0; n < sam_hdr_nref(hdr1); n++) {
+        hts_pos_t h1_len = sam_hdr_tid2len(hdr1, n);
+        hts_pos_t h2_len = sam_hdr_tid2len(hdr2, n);
+        if (h1_len != h2_len) {
+            print_error("split",
+                        "Unaccounted header reference %zu \"%s\" is not the same length as in the input file",
+                        n + 1, sam_hdr_tid2name(hdr2, n));
+            return -1;
+        }
+    }
+    return 0;
+}
+
+// Set the initial state
+static state_t* init(parsed_opts_t* opts, const char *arg_list)
+{
+    state_t* retval = calloc(sizeof(state_t), 1);
+    if (!retval) {
+        print_error_errno("split", "Initialisation failed");
+        return NULL;
+    }
+
+    if (opts->ga.nthreads > 0) {
+        if (!(retval->p.pool = hts_tpool_init(opts->ga.nthreads))) {
+            fprintf(stderr, "Error creating thread pool\n");
+            cleanup_state(retval, false);
+            return NULL;
+        }
+    }
+
+    retval->merged_input_file = sam_open_format(opts->merged_input_name, "rb", &opts->ga.in);
+    if (!retval->merged_input_file) {
+        print_error_errno("split", "Could not open \"%s\"", opts->merged_input_name);
+        cleanup_state(retval, false);
+        return NULL;
+    }
+    if (retval->p.pool)
+        hts_set_opt(retval->merged_input_file, HTS_OPT_THREAD_POOL, &retval->p);
+    retval->merged_input_header = sam_hdr_read(retval->merged_input_file);
+    if (retval->merged_input_header == NULL) {
+        print_error("split", "Could not read header from \"%s\"", opts->merged_input_name);
+        cleanup_state(retval, false);
+        return NULL;
+    }
+
+    if (opts->unaccounted_name) {
+        if (opts->unaccounted_header_name) {
+            samFile* hdr_load = sam_open_format(opts->unaccounted_header_name, "r", &opts->ga.in);
+            if (!hdr_load) {
+                print_error_errno("split", "Could not open unaccounted header file \"%s\"", opts->unaccounted_header_name);
+                cleanup_state(retval, false);
+                return NULL;
+            }
+            retval->unaccounted_header = sam_hdr_read(hdr_load);
+            if (retval->unaccounted_header == NULL) {
+                print_error("split", "Could not read header from \"%s\"", opts->unaccounted_header_name);
+                cleanup_state(retval, false);
+                sam_close(hdr_load);
+                return NULL;
+            }
+            sam_close(hdr_load);
+            if (header_compatible(retval->merged_input_header,
+                                  retval->unaccounted_header) != 0) {
+                cleanup_state(retval, false);
+                return NULL;
+            }
+        } else {
+            retval->unaccounted_header = sam_hdr_dup(retval->merged_input_header);
+            if (!opts->no_pg && sam_hdr_add_pg(retval->unaccounted_header, "samtools",
+                                    "VN", samtools_version(),
+                                    arg_list ? "CL": NULL,
+                                    arg_list ? arg_list : NULL,
+                                    NULL)) {
+                print_error("split", "Could not rewrite header for \"%s\"", opts->unaccounted_name);
+                cleanup_state(retval, false);
+                return NULL;
+            }
+        }
+
+        retval->unaccounted_file = sam_open_format(opts->unaccounted_name, "wb", &opts->ga.out);
+        if (retval->unaccounted_file == NULL) {
+            print_error_errno("split", "Could not open unaccounted output file \"%s\"", opts->unaccounted_name);
+            cleanup_state(retval, false);
+            return NULL;
+        }
+        if (retval->p.pool)
+            hts_set_opt(retval->unaccounted_file, HTS_OPT_THREAD_POOL, &retval->p);
+    }
+
+    // Open output files for RGs
+    if (!count_RG(retval->merged_input_header, &retval->output_count, &retval->rg_id)) return NULL;
+    if (opts->verbose) fprintf(stderr, "@RG's found %zu\n",retval->output_count);
+    // Prevent calloc(0, size);
+    size_t num = retval->output_count ? retval->output_count : 1;
+    retval->rg_index_file_name = (char **)calloc(num, sizeof(char *));
+    retval->rg_output_file_name = (char **)calloc(num, sizeof(char *));
+    retval->rg_output_file = (samFile**)calloc(num, sizeof(samFile*));
+    retval->rg_output_header = (sam_hdr_t**)calloc(num, sizeof(sam_hdr_t*));
+    retval->rg_hash = kh_init_c2i();
+    if (!retval->rg_output_file_name || !retval->rg_output_file || !retval->rg_output_header ||
+        !retval->rg_hash || !retval->rg_index_file_name) {
+        print_error_errno("split", "Could not initialise output file array");
+        cleanup_state(retval, false);
+        return NULL;
+    }
+
+    char* dirsep = strrchr(opts->merged_input_name, '/');
+    char* input_base_name = strdup(dirsep? dirsep+1 : opts->merged_input_name);
+    if (!input_base_name) {
+        print_error_errno("split", "Filename manipulation failed");
+        cleanup_state(retval, false);
+        return NULL;
+    }
+    char* extension = strrchr(input_base_name, '.');
+    if (extension) *extension = '\0';
+
+    size_t i;
+    for (i = 0; i < retval->output_count; i++) {
+        char* output_filename = NULL;
+
+        output_filename = expand_format_string(opts->output_format_string,
+                                               input_base_name,
+                                               retval->rg_id[i], i,
+                                               &opts->ga.out);
+
+        if ( output_filename == NULL ) {
+            cleanup_state(retval, false);
+            free(input_base_name);
+            return NULL;
+        }
+
+        retval->rg_output_file_name[i] = output_filename;
+        retval->rg_output_file[i] = sam_open_format(output_filename, "wb", &opts->ga.out);
+        if (retval->rg_output_file[i] == NULL) {
+            print_error_errno("split", "Could not open \"%s\"", output_filename);
+            cleanup_state(retval, false);
+            free(input_base_name);
+            return NULL;
+        }
+        if (retval->p.pool)
+            hts_set_opt(retval->rg_output_file[i], HTS_OPT_THREAD_POOL, &retval->p);
+
+        // Record index in hash
+        int ret;
+        khiter_t iter = kh_put_c2i(retval->rg_hash, retval->rg_id[i], &ret);
+        if (ret < 0) {
+            print_error_errno("split", "Couldn't add @RG ID to look-up table");
+            cleanup_state(retval, false);
+            free(input_base_name);
+            return NULL;
+        }
+        kh_val(retval->rg_hash,iter) = i;
+
+        // Set and edit header
+        retval->rg_output_header[i] = sam_hdr_dup(retval->merged_input_header);
+        if (sam_hdr_remove_except(retval->rg_output_header[i], "RG", "ID", retval->rg_id[i]) ||
+           (!opts->no_pg &&
+            sam_hdr_add_pg(retval->rg_output_header[i], "samtools",
+                        "VN", samtools_version(),
+                        arg_list ? "CL": NULL,
+                        arg_list ? arg_list : NULL,
+                        NULL))) {
+            print_error("split", "Could not rewrite header for \"%s\"", output_filename);
+            cleanup_state(retval, false);
+            free(input_base_name);
+            return NULL;
+        }
+    }
+
+    free(input_base_name);
+    retval->write_index = opts->ga.write_index;
+
+    return retval;
+}
+
+static bool split(state_t* state)
+{
+    if (state->unaccounted_file && sam_hdr_write(state->unaccounted_file, state->unaccounted_header) != 0) {
+        print_error_errno("split", "Could not write output file header");
+        return false;
+    }
+    size_t i;
+    for (i = 0; i < state->output_count; i++) {
+        if (sam_hdr_write(state->rg_output_file[i], state->rg_output_header[i]) != 0) {
+            print_error_errno("split", "Could not write file header to \"%s\"", state->rg_output_file_name[i]);
+            return false;
+        }
+        if (state->write_index) {
+            state->rg_index_file_name[i] = auto_index(state->rg_output_file[i],
+                                                      state->rg_output_file_name[i],
+                                                      state->rg_output_header[i]);
+            if (!state->rg_index_file_name[i]) {
+                print_error_errno("split", "Could not create index for file \"%s\"", state->rg_output_file_name[i]);
+                return false;
+            }
+        }
+    }
+
+    bam1_t* file_read = bam_init1();
+    // Read the first record
+    int r;
+    if ((r=sam_read1(state->merged_input_file, state->merged_input_header, file_read)) < 0) {
+        // Nothing more to read?  Ignore this file
+        bam_destroy1(file_read);
+        file_read = NULL;
+        if (r < -1) {
+            print_error("split", "Could not read first input record");
+            return false;
+        }
+    }
+
+    while (file_read != NULL) {
+        // Get RG tag from read and look it up in hash to find file to output it to
+        uint8_t* tag = bam_aux_get(file_read, "RG");
+        khiter_t iter;
+        if ( tag != NULL ) {
+            char* rg = bam_aux2Z(tag);
+            iter = kh_get_c2i(state->rg_hash, rg);
+        } else {
+            iter = kh_end(state->rg_hash);
+        }
+
+        // Write the read out to correct file
+        if (iter != kh_end(state->rg_hash)) {
+            // if found write to the appropriate untangled bam
+            int i = kh_val(state->rg_hash,iter);
+            if (sam_write1(state->rg_output_file[i], state->rg_output_header[i], file_read) < 0) {
+                print_error_errno("split", "Could not write to \"%s\"", state->rg_output_file_name[i]);
+                bam_destroy1(file_read);
+                return false;
+            }
+        } else {
+            // otherwise write to the unaccounted bam if there is one or fail
+            if (state->unaccounted_file == NULL) {
+                if (tag) {
+                    fprintf(stderr, "Read \"%s\" with unaccounted for tag \"%s\".\n", bam_get_qname(file_read), bam_aux2Z(tag));
+                } else {
+                    fprintf(stderr, "Read \"%s\" has no RG tag.\n", bam_get_qname(file_read));
+                }
+                bam_destroy1(file_read);
+                return false;
+            } else {
+                if (sam_write1(state->unaccounted_file, state->unaccounted_header, file_read) < 0) {
+                    print_error_errno("split", "Could not write to unaccounted output file");
+                    bam_destroy1(file_read);
+                    return false;
+                }
+            }
+        }
+
+        // Replace written read with the next one to process
+        if ((r=sam_read1(state->merged_input_file, state->merged_input_header, file_read)) < 0) {
+            // Nothing more to read?  Ignore this file in future
+            bam_destroy1(file_read);
+            file_read = NULL;
+            if (r < -1) {
+                print_error("split", "Could not read input record");
+                return false;
+            }
+        }
+    }
+
+    if (state->write_index) {
+        for (i = 0; i < state->output_count; i++) {
+            if (sam_idx_save(state->rg_output_file[i]) < 0) {
+                print_error_errno("split", "writing index failed");
+                return false;
+            }
+            free(state->rg_index_file_name[i]);
+        }
+    }
+
+    return true;
+}
+
+static int cleanup_state(state_t* status, bool check_close)
+{
+    int ret = 0;
+
+    if (!status) return 0;
+    if (status->unaccounted_header) sam_hdr_destroy(status->unaccounted_header);
+    if (status->unaccounted_file) {
+        if (sam_close(status->unaccounted_file) < 0 && check_close) {
+            print_error("split", "Error on closing unaccounted file");
+            ret = -1;
+        }
+    }
+    sam_close(status->merged_input_file);
+    size_t i;
+    for (i = 0; i < status->output_count; i++) {
+        if (status->rg_output_header && status->rg_output_header[i])
+            sam_hdr_destroy(status->rg_output_header[i]);
+        if (status->rg_output_file && status->rg_output_file[i]) {
+            if (sam_close(status->rg_output_file[i]) < 0 && check_close) {
+                print_error("split", "Error on closing output file \"%s\"", status->rg_output_file_name[i]);
+                ret = -1;
+            }
+        }
+        if (status->rg_id) free(status->rg_id[i]);
+        if (status->rg_output_file_name) free(status->rg_output_file_name[i]);
+    }
+    if (status->merged_input_header)
+        sam_hdr_destroy(status->merged_input_header);
+    free(status->rg_output_header);
+    free(status->rg_output_file);
+    free(status->rg_output_file_name);
+    free(status->rg_index_file_name);
+    kh_destroy_c2i(status->rg_hash);
+    free(status->rg_id);
+    if (status->p.pool)
+        hts_tpool_destroy(status->p.pool);
+    free(status);
+
+    return ret;
+}
+
+static void cleanup_opts(parsed_opts_t* opts)
+{
+    if (!opts) return;
+    sam_global_args_free(&opts->ga);
+    free(opts);
+}
+
+int main_split(int argc, char** argv)
+{
+    int ret = 1;
+    char *arg_list = NULL;
+    parsed_opts_t* opts = parse_args(argc, argv);
+    if (!opts) goto cleanup_opts;
+    if (!opts->no_pg && !(arg_list = stringify_argv(argc+1, argv-1)))
+        goto cleanup_opts;
+    state_t* status = init(opts, arg_list);
+    if (!status) goto cleanup_opts;
+
+    if (!split(status)) {
+        cleanup_state(status, false);
+        goto cleanup_opts;
+    }
+
+    ret = cleanup_state(status, true);
+
+cleanup_opts:
+    cleanup_opts(opts);
+    free(arg_list);
+
+    return ret;
+}
diff --git a/samtools/bam_split.c.pysam.c b/samtools/bam_split.c.pysam.c
new file mode 100644
index 0000000..1015234
--- /dev/null
+++ b/samtools/bam_split.c.pysam.c
@@ -0,0 +1,613 @@
+#include "samtools.pysam.h"
+
+/*  bam_split.c -- split subcommand.
+
+    Copyright (C) 2013-2016,2018-2019 Genome Research Ltd.
+
+    Author: Martin Pollard <mp15@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <config.h>
+
+#include <string.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <stdbool.h>
+#include <limits.h>
+#include <unistd.h>
+#include <regex.h>
+#include <assert.h>
+#include <htslib/sam.h>
+#include <htslib/khash.h>
+#include <htslib/kstring.h>
+#include <htslib/cram.h>
+#include "htslib/thread_pool.h"
+#include "sam_opts.h"
+#include "samtools.h"
+
+
+KHASH_MAP_INIT_STR(c2i, int)
+
+struct parsed_opts {
+    const char *merged_input_name;
+    const char *unaccounted_header_name;
+    const char *unaccounted_name;
+    const char *output_format_string;
+    bool verbose;
+    int no_pg;
+    sam_global_args ga;
+};
+
+typedef struct parsed_opts parsed_opts_t;
+
+struct state {
+    samFile* merged_input_file;
+    sam_hdr_t* merged_input_header;
+    samFile* unaccounted_file;
+    sam_hdr_t* unaccounted_header;
+    size_t output_count;
+    char** rg_id;
+    char **rg_index_file_name;
+    char **rg_output_file_name;
+    samFile** rg_output_file;
+    sam_hdr_t** rg_output_header;
+    kh_c2i_t* rg_hash;
+    htsThreadPool p;
+    int write_index;
+};
+
+typedef struct state state_t;
+
+static int cleanup_state(state_t* status, bool check_close);
+static void cleanup_opts(parsed_opts_t* opts);
+
+static void usage(FILE *write_to)
+{
+    fprintf(write_to,
+"Usage: samtools split [-u <unaccounted.bam>] [-h <unaccounted_header.sam>]\n"
+"                      [-f <format_string>] [-v] <merged.bam>\n"
+"Options:\n"
+"  -f STRING       output filename format string [\"%%*_%%#.%%.\"]\n"
+"  -u FILE1        put reads with no RG tag or an unrecognised RG tag in FILE1\n"
+"  -h FILE2        ... and override the header with FILE2 (-u file only)\n"
+"  -v              verbose output\n"
+"  --no-PG         do not add a PG line\n");
+    sam_global_opt_help(write_to, "-....@..");
+    fprintf(write_to,
+"\n"
+"Format string expansions:\n"
+"  %%%%     %%\n"
+"  %%*     basename\n"
+"  %%#     @RG index\n"
+"  %%!     @RG ID\n"
+"  %%.     filename extension for output format\n"
+      );
+}
+
+// Takes the command line options and turns them into something we can understand
+static parsed_opts_t* parse_args(int argc, char** argv)
+{
+    if (argc == 1) { usage(samtools_stdout); return NULL; }
+
+    const char *optstring = "vf:h:u:@:";
+
+    static const struct option lopts[] = {
+        SAM_OPT_GLOBAL_OPTIONS('-', 0, 0, 0, 0, '@'),
+        {"no-PG", no_argument, NULL, 1},
+        { NULL, 0, NULL, 0 }
+    };
+
+    parsed_opts_t* retval = calloc(sizeof(parsed_opts_t), 1);
+    if (! retval ) { perror("cannot allocate option parsing memory"); return NULL; }
+
+    sam_global_args_init(&retval->ga);
+
+    int opt;
+    while ((opt = getopt_long(argc, argv, optstring, lopts, NULL)) != -1) {
+        switch (opt) {
+        case 'f':
+            retval->output_format_string = optarg;
+            break;
+        case 'h':
+            retval->unaccounted_header_name = optarg;
+            break;
+        case 'v':
+            retval->verbose = true;
+            break;
+        case 'u':
+            retval->unaccounted_name = optarg;
+            break;
+        case 1:
+            retval->no_pg = 1;
+            break;
+        default:
+            if (parse_sam_global_opt(opt, optarg, lopts, &retval->ga) == 0) break;
+            /* else fall-through */
+        case '?':
+            usage(samtools_stdout);
+            free(retval);
+            return NULL;
+        }
+    }
+
+    if (retval->output_format_string == NULL) retval->output_format_string = "%*_%#.%.";
+
+    argc -= optind;
+    argv += optind;
+
+    if (argc != 1) {
+        print_error("split", "Invalid number of arguments: %d", argc);
+        usage(samtools_stderr);
+        free(retval);
+        return NULL;
+    }
+
+    retval->merged_input_name = argv[0];
+
+    return retval;
+}
+
+// Expands a output filename format string
+static char* expand_format_string(const char* format_string, const char* basename, const char* rg_id, const int rg_idx, const htsFormat *format)
+{
+    kstring_t str = { 0, 0, NULL };
+    const char* pointer = format_string;
+    const char* next;
+    while ((next = strchr(pointer, '%')) != NULL) {
+        if (kputsn(pointer, next-pointer, &str) < 0) goto memfail;
+        ++next;
+        switch (*next) {
+            case '%':
+                if (kputc('%', &str) < 0) goto memfail;
+                break;
+            case '*':
+                if (kputs(basename, &str) < 0) goto memfail;
+                break;
+            case '#':
+                if (kputl(rg_idx, &str) < 0) goto memfail;
+                break;
+            case '!':
+                if (kputs(rg_id, &str) < 0) goto memfail;
+                break;
+            case '.':
+                // Only really need to cope with sam, bam, cram
+                if (format->format != unknown_format) {
+                    if (kputs(hts_format_file_extension(format), &str) < 0)
+                        goto memfail;
+                } else {
+                    if (kputs("bam", &str) < 0) goto memfail;
+                }
+                break;
+            case '\0':
+                print_error("split", "Trailing %% in filename format string");
+                goto fail;
+            default:
+                // Error is: fprintf(samtools_stderr, "bad format string, unknown format specifier\n");
+                print_error("split", "Unknown specifier %%%c in filename format string", *next);
+                goto fail;
+        }
+        pointer = next + 1;
+    }
+    if (kputs(pointer, &str) < 0) goto memfail;
+    return ks_release(&str);
+
+ memfail:
+    print_error_errno("split", "Couldn't build output filename");
+ fail:
+    free(str.s);
+    return NULL;
+}
+
+// Parse the header, count the number of RG tags and return a list of their names
+static bool count_RG(sam_hdr_t* hdr, size_t* count, char*** output_name)
+{
+    char **names = NULL;
+    kstring_t id_val = KS_INITIALIZE;
+    int i, n_rg = sam_hdr_count_lines(hdr, "RG");
+
+    if (n_rg < 0) {
+        print_error("split", "Failed to get @RG IDs");
+        *count = 0;
+        *output_name = NULL;
+        return false;
+    }
+
+    if (n_rg == 0) {
+        *count = 0;
+        *output_name = NULL;
+        return true;
+    }
+
+    names = calloc(n_rg, sizeof(names[0]));
+    if (!names) goto memfail;
+
+    for (i = 0; i < n_rg; i++) {
+        if (sam_hdr_find_tag_pos(hdr, "RG", i, "ID", &id_val) < 0) goto memfail;
+        names[i] = ks_release(&id_val);
+    }
+
+    *count = n_rg;
+    *output_name = names;
+    return true;
+
+ memfail:
+    print_error_errno("split", "Failed to get @RG IDs");
+    *count = 0;
+    *output_name = NULL;
+    ks_free(&id_val);
+    free(names);
+    return false;
+}
+
+static int header_compatible(sam_hdr_t *hdr1, sam_hdr_t *hdr2)
+{
+    size_t n;
+    if (sam_hdr_nref(hdr1) != sam_hdr_nref(hdr2)) {
+        print_error("split",
+                    "Unaccounted header contains wrong number of references");
+        return -1;
+    }
+    for (n = 0; n < sam_hdr_nref(hdr1); n++) {
+        hts_pos_t h1_len = sam_hdr_tid2len(hdr1, n);
+        hts_pos_t h2_len = sam_hdr_tid2len(hdr2, n);
+        if (h1_len != h2_len) {
+            print_error("split",
+                        "Unaccounted header reference %zu \"%s\" is not the same length as in the input file",
+                        n + 1, sam_hdr_tid2name(hdr2, n));
+            return -1;
+        }
+    }
+    return 0;
+}
+
+// Set the initial state
+static state_t* init(parsed_opts_t* opts, const char *arg_list)
+{
+    state_t* retval = calloc(sizeof(state_t), 1);
+    if (!retval) {
+        print_error_errno("split", "Initialisation failed");
+        return NULL;
+    }
+
+    if (opts->ga.nthreads > 0) {
+        if (!(retval->p.pool = hts_tpool_init(opts->ga.nthreads))) {
+            fprintf(samtools_stderr, "Error creating thread pool\n");
+            cleanup_state(retval, false);
+            return NULL;
+        }
+    }
+
+    retval->merged_input_file = sam_open_format(opts->merged_input_name, "rb", &opts->ga.in);
+    if (!retval->merged_input_file) {
+        print_error_errno("split", "Could not open \"%s\"", opts->merged_input_name);
+        cleanup_state(retval, false);
+        return NULL;
+    }
+    if (retval->p.pool)
+        hts_set_opt(retval->merged_input_file, HTS_OPT_THREAD_POOL, &retval->p);
+    retval->merged_input_header = sam_hdr_read(retval->merged_input_file);
+    if (retval->merged_input_header == NULL) {
+        print_error("split", "Could not read header from \"%s\"", opts->merged_input_name);
+        cleanup_state(retval, false);
+        return NULL;
+    }
+
+    if (opts->unaccounted_name) {
+        if (opts->unaccounted_header_name) {
+            samFile* hdr_load = sam_open_format(opts->unaccounted_header_name, "r", &opts->ga.in);
+            if (!hdr_load) {
+                print_error_errno("split", "Could not open unaccounted header file \"%s\"", opts->unaccounted_header_name);
+                cleanup_state(retval, false);
+                return NULL;
+            }
+            retval->unaccounted_header = sam_hdr_read(hdr_load);
+            if (retval->unaccounted_header == NULL) {
+                print_error("split", "Could not read header from \"%s\"", opts->unaccounted_header_name);
+                cleanup_state(retval, false);
+                sam_close(hdr_load);
+                return NULL;
+            }
+            sam_close(hdr_load);
+            if (header_compatible(retval->merged_input_header,
+                                  retval->unaccounted_header) != 0) {
+                cleanup_state(retval, false);
+                return NULL;
+            }
+        } else {
+            retval->unaccounted_header = sam_hdr_dup(retval->merged_input_header);
+            if (!opts->no_pg && sam_hdr_add_pg(retval->unaccounted_header, "samtools",
+                                    "VN", samtools_version(),
+                                    arg_list ? "CL": NULL,
+                                    arg_list ? arg_list : NULL,
+                                    NULL)) {
+                print_error("split", "Could not rewrite header for \"%s\"", opts->unaccounted_name);
+                cleanup_state(retval, false);
+                return NULL;
+            }
+        }
+
+        retval->unaccounted_file = sam_open_format(opts->unaccounted_name, "wb", &opts->ga.out);
+        if (retval->unaccounted_file == NULL) {
+            print_error_errno("split", "Could not open unaccounted output file \"%s\"", opts->unaccounted_name);
+            cleanup_state(retval, false);
+            return NULL;
+        }
+        if (retval->p.pool)
+            hts_set_opt(retval->unaccounted_file, HTS_OPT_THREAD_POOL, &retval->p);
+    }
+
+    // Open output files for RGs
+    if (!count_RG(retval->merged_input_header, &retval->output_count, &retval->rg_id)) return NULL;
+    if (opts->verbose) fprintf(samtools_stderr, "@RG's found %zu\n",retval->output_count);
+    // Prevent calloc(0, size);
+    size_t num = retval->output_count ? retval->output_count : 1;
+    retval->rg_index_file_name = (char **)calloc(num, sizeof(char *));
+    retval->rg_output_file_name = (char **)calloc(num, sizeof(char *));
+    retval->rg_output_file = (samFile**)calloc(num, sizeof(samFile*));
+    retval->rg_output_header = (sam_hdr_t**)calloc(num, sizeof(sam_hdr_t*));
+    retval->rg_hash = kh_init_c2i();
+    if (!retval->rg_output_file_name || !retval->rg_output_file || !retval->rg_output_header ||
+        !retval->rg_hash || !retval->rg_index_file_name) {
+        print_error_errno("split", "Could not initialise output file array");
+        cleanup_state(retval, false);
+        return NULL;
+    }
+
+    char* dirsep = strrchr(opts->merged_input_name, '/');
+    char* input_base_name = strdup(dirsep? dirsep+1 : opts->merged_input_name);
+    if (!input_base_name) {
+        print_error_errno("split", "Filename manipulation failed");
+        cleanup_state(retval, false);
+        return NULL;
+    }
+    char* extension = strrchr(input_base_name, '.');
+    if (extension) *extension = '\0';
+
+    size_t i;
+    for (i = 0; i < retval->output_count; i++) {
+        char* output_filename = NULL;
+
+        output_filename = expand_format_string(opts->output_format_string,
+                                               input_base_name,
+                                               retval->rg_id[i], i,
+                                               &opts->ga.out);
+
+        if ( output_filename == NULL ) {
+            cleanup_state(retval, false);
+            free(input_base_name);
+            return NULL;
+        }
+
+        retval->rg_output_file_name[i] = output_filename;
+        retval->rg_output_file[i] = sam_open_format(output_filename, "wb", &opts->ga.out);
+        if (retval->rg_output_file[i] == NULL) {
+            print_error_errno("split", "Could not open \"%s\"", output_filename);
+            cleanup_state(retval, false);
+            free(input_base_name);
+            return NULL;
+        }
+        if (retval->p.pool)
+            hts_set_opt(retval->rg_output_file[i], HTS_OPT_THREAD_POOL, &retval->p);
+
+        // Record index in hash
+        int ret;
+        khiter_t iter = kh_put_c2i(retval->rg_hash, retval->rg_id[i], &ret);
+        if (ret < 0) {
+            print_error_errno("split", "Couldn't add @RG ID to look-up table");
+            cleanup_state(retval, false);
+            free(input_base_name);
+            return NULL;
+        }
+        kh_val(retval->rg_hash,iter) = i;
+
+        // Set and edit header
+        retval->rg_output_header[i] = sam_hdr_dup(retval->merged_input_header);
+        if (sam_hdr_remove_except(retval->rg_output_header[i], "RG", "ID", retval->rg_id[i]) ||
+           (!opts->no_pg &&
+            sam_hdr_add_pg(retval->rg_output_header[i], "samtools",
+                        "VN", samtools_version(),
+                        arg_list ? "CL": NULL,
+                        arg_list ? arg_list : NULL,
+                        NULL))) {
+            print_error("split", "Could not rewrite header for \"%s\"", output_filename);
+            cleanup_state(retval, false);
+            free(input_base_name);
+            return NULL;
+        }
+    }
+
+    free(input_base_name);
+    retval->write_index = opts->ga.write_index;
+
+    return retval;
+}
+
+static bool split(state_t* state)
+{
+    if (state->unaccounted_file && sam_hdr_write(state->unaccounted_file, state->unaccounted_header) != 0) {
+        print_error_errno("split", "Could not write output file header");
+        return false;
+    }
+    size_t i;
+    for (i = 0; i < state->output_count; i++) {
+        if (sam_hdr_write(state->rg_output_file[i], state->rg_output_header[i]) != 0) {
+            print_error_errno("split", "Could not write file header to \"%s\"", state->rg_output_file_name[i]);
+            return false;
+        }
+        if (state->write_index) {
+            state->rg_index_file_name[i] = auto_index(state->rg_output_file[i],
+                                                      state->rg_output_file_name[i],
+                                                      state->rg_output_header[i]);
+            if (!state->rg_index_file_name[i]) {
+                print_error_errno("split", "Could not create index for file \"%s\"", state->rg_output_file_name[i]);
+                return false;
+            }
+        }
+    }
+
+    bam1_t* file_read = bam_init1();
+    // Read the first record
+    int r;
+    if ((r=sam_read1(state->merged_input_file, state->merged_input_header, file_read)) < 0) {
+        // Nothing more to read?  Ignore this file
+        bam_destroy1(file_read);
+        file_read = NULL;
+        if (r < -1) {
+            print_error("split", "Could not read first input record");
+            return false;
+        }
+    }
+
+    while (file_read != NULL) {
+        // Get RG tag from read and look it up in hash to find file to output it to
+        uint8_t* tag = bam_aux_get(file_read, "RG");
+        khiter_t iter;
+        if ( tag != NULL ) {
+            char* rg = bam_aux2Z(tag);
+            iter = kh_get_c2i(state->rg_hash, rg);
+        } else {
+            iter = kh_end(state->rg_hash);
+        }
+
+        // Write the read out to correct file
+        if (iter != kh_end(state->rg_hash)) {
+            // if found write to the appropriate untangled bam
+            int i = kh_val(state->rg_hash,iter);
+            if (sam_write1(state->rg_output_file[i], state->rg_output_header[i], file_read) < 0) {
+                print_error_errno("split", "Could not write to \"%s\"", state->rg_output_file_name[i]);
+                bam_destroy1(file_read);
+                return false;
+            }
+        } else {
+            // otherwise write to the unaccounted bam if there is one or fail
+            if (state->unaccounted_file == NULL) {
+                if (tag) {
+                    fprintf(samtools_stderr, "Read \"%s\" with unaccounted for tag \"%s\".\n", bam_get_qname(file_read), bam_aux2Z(tag));
+                } else {
+                    fprintf(samtools_stderr, "Read \"%s\" has no RG tag.\n", bam_get_qname(file_read));
+                }
+                bam_destroy1(file_read);
+                return false;
+            } else {
+                if (sam_write1(state->unaccounted_file, state->unaccounted_header, file_read) < 0) {
+                    print_error_errno("split", "Could not write to unaccounted output file");
+                    bam_destroy1(file_read);
+                    return false;
+                }
+            }
+        }
+
+        // Replace written read with the next one to process
+        if ((r=sam_read1(state->merged_input_file, state->merged_input_header, file_read)) < 0) {
+            // Nothing more to read?  Ignore this file in future
+            bam_destroy1(file_read);
+            file_read = NULL;
+            if (r < -1) {
+                print_error("split", "Could not read input record");
+                return false;
+            }
+        }
+    }
+
+    if (state->write_index) {
+        for (i = 0; i < state->output_count; i++) {
+            if (sam_idx_save(state->rg_output_file[i]) < 0) {
+                print_error_errno("split", "writing index failed");
+                return false;
+            }
+            free(state->rg_index_file_name[i]);
+        }
+    }
+
+    return true;
+}
+
+static int cleanup_state(state_t* status, bool check_close)
+{
+    int ret = 0;
+
+    if (!status) return 0;
+    if (status->unaccounted_header) sam_hdr_destroy(status->unaccounted_header);
+    if (status->unaccounted_file) {
+        if (sam_close(status->unaccounted_file) < 0 && check_close) {
+            print_error("split", "Error on closing unaccounted file");
+            ret = -1;
+        }
+    }
+    sam_close(status->merged_input_file);
+    size_t i;
+    for (i = 0; i < status->output_count; i++) {
+        if (status->rg_output_header && status->rg_output_header[i])
+            sam_hdr_destroy(status->rg_output_header[i]);
+        if (status->rg_output_file && status->rg_output_file[i]) {
+            if (sam_close(status->rg_output_file[i]) < 0 && check_close) {
+                print_error("split", "Error on closing output file \"%s\"", status->rg_output_file_name[i]);
+                ret = -1;
+            }
+        }
+        if (status->rg_id) free(status->rg_id[i]);
+        if (status->rg_output_file_name) free(status->rg_output_file_name[i]);
+    }
+    if (status->merged_input_header)
+        sam_hdr_destroy(status->merged_input_header);
+    free(status->rg_output_header);
+    free(status->rg_output_file);
+    free(status->rg_output_file_name);
+    free(status->rg_index_file_name);
+    kh_destroy_c2i(status->rg_hash);
+    free(status->rg_id);
+    if (status->p.pool)
+        hts_tpool_destroy(status->p.pool);
+    free(status);
+
+    return ret;
+}
+
+static void cleanup_opts(parsed_opts_t* opts)
+{
+    if (!opts) return;
+    sam_global_args_free(&opts->ga);
+    free(opts);
+}
+
+int main_split(int argc, char** argv)
+{
+    int ret = 1;
+    char *arg_list = NULL;
+    parsed_opts_t* opts = parse_args(argc, argv);
+    if (!opts) goto cleanup_opts;
+    if (!opts->no_pg && !(arg_list = stringify_argv(argc+1, argv-1)))
+        goto cleanup_opts;
+    state_t* status = init(opts, arg_list);
+    if (!status) goto cleanup_opts;
+
+    if (!split(status)) {
+        cleanup_state(status, false);
+        goto cleanup_opts;
+    }
+
+    ret = cleanup_state(status, true);
+
+cleanup_opts:
+    cleanup_opts(opts);
+    free(arg_list);
+
+    return ret;
+}
diff --git a/samtools/bam_stat.c b/samtools/bam_stat.c
new file mode 100644
index 0000000..31dc8fe
--- /dev/null
+++ b/samtools/bam_stat.c
@@ -0,0 +1,346 @@
+/*  bam_stat.c -- flagstat subcommand.
+
+    Copyright (C) 2009, 2011, 2013-2015, 2019, 2021 Genome Research Ltd.
+
+    Author: Heng Li <lh3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <config.h>
+
+#include <unistd.h>
+#include <stdint.h>
+#include <stdlib.h>
+#include <string.h>
+#include <stdio.h>
+#include <limits.h>
+#include <getopt.h>
+
+#include "htslib/sam.h"
+#include "samtools.h"
+#include "sam_opts.h"
+
+typedef struct {
+    long long n_reads[2], n_mapped[2], n_pair_all[2], n_pair_map[2], n_pair_good[2];
+    long long n_sgltn[2], n_read1[2], n_read2[2];
+    long long n_dup[2];
+    long long n_diffchr[2], n_diffhigh[2];
+    long long n_secondary[2], n_supp[2];
+    long long n_primary[2], n_pmapped[2], n_pdup[2];
+} bam_flagstat_t;
+
+inline static void flagstat_loop(bam_flagstat_t *s, bam1_core_t *c)
+{
+    int w = (c->flag & BAM_FQCFAIL)? 1 : 0;
+    ++s->n_reads[w];
+    if (c->flag & BAM_FSECONDARY ) {
+        ++s->n_secondary[w];
+    } else if (c->flag & BAM_FSUPPLEMENTARY ) {
+        ++s->n_supp[w];
+    } else {
+        ++s->n_primary[w];
+
+        if (c->flag & BAM_FPAIRED) {
+            ++s->n_pair_all[w];
+            if ((c->flag & BAM_FPROPER_PAIR) && !(c->flag & BAM_FUNMAP) ) ++s->n_pair_good[w];
+            if (c->flag & BAM_FREAD1) ++s->n_read1[w];
+            if (c->flag & BAM_FREAD2) ++s->n_read2[w];
+            if ((c->flag & BAM_FMUNMAP) && !(c->flag & BAM_FUNMAP)) ++s->n_sgltn[w];
+            if (!(c->flag & BAM_FUNMAP) && !(c->flag & BAM_FMUNMAP)) {
+                ++s->n_pair_map[w];
+                if (c->mtid != c->tid) {
+                    ++s->n_diffchr[w];
+                    if (c->qual >= 5) ++s->n_diffhigh[w];
+                }
+            }
+        }
+
+        if (!(c->flag & BAM_FUNMAP)) ++s->n_pmapped[w];
+        if (c->flag & BAM_FDUP) ++s->n_pdup[w];
+    }
+    if (!(c->flag & BAM_FUNMAP)) ++s->n_mapped[w];
+    if (c->flag & BAM_FDUP) ++s->n_dup[w];
+}
+
+bam_flagstat_t *bam_flagstat_core(samFile *fp, sam_hdr_t *h)
+{
+    bam_flagstat_t *s;
+    bam1_t *b;
+    bam1_core_t *c;
+    int ret;
+    s = (bam_flagstat_t*)calloc(1, sizeof(bam_flagstat_t));
+    b = bam_init1();
+    c = &b->core;
+    while ((ret = sam_read1(fp, h, b)) >= 0)
+        flagstat_loop(s, c);
+    bam_destroy1(b);
+    if (ret != -1) {
+        free(s);
+        return NULL;
+    }
+    return s;
+}
+
+static const char *percent(char *buffer, long long n, long long total)
+{
+    if (total != 0) sprintf(buffer, "%.2f%%", (float)n / total * 100.0);
+    else strcpy(buffer, "N/A");
+    return buffer;
+}
+
+static const char *percent_json(char *buffer, long long n, long long total)
+{
+    if (total != 0) sprintf(buffer, "%.2f", (float)n / total * 100.0);
+    else strcpy(buffer, "null");
+    return buffer;
+}
+
+static void usage_exit(FILE *fp, int exit_status)
+{
+    fprintf(fp, "Usage: samtools flagstat [options] <in.bam>\n");
+    sam_global_opt_help(fp, "-.---@-.");
+    fprintf(fp, "  -O, --");
+    fprintf(fp, "output-fmt FORMAT[,OPT[=VAL]]...\n"
+            "               Specify output format (json, tsv)\n");
+    exit(exit_status);
+}
+
+static void out_fmt_default(bam_flagstat_t *s)
+{
+    char b0[16], b1[16];
+    printf("%lld + %lld in total (QC-passed reads + QC-failed reads)\n", s->n_reads[0], s->n_reads[1]);
+    printf("%lld + %lld primary\n", s->n_primary[0], s->n_primary[1]);
+    printf("%lld + %lld secondary\n", s->n_secondary[0], s->n_secondary[1]);
+    printf("%lld + %lld supplementary\n", s->n_supp[0], s->n_supp[1]);
+    printf("%lld + %lld duplicates\n", s->n_dup[0], s->n_dup[1]);
+    printf("%lld + %lld primary duplicates\n", s->n_pdup[0], s->n_pdup[1]);
+    printf("%lld + %lld mapped (%s : %s)\n", s->n_mapped[0], s->n_mapped[1], percent(b0, s->n_mapped[0], s->n_reads[0]), percent(b1, s->n_mapped[1], s->n_reads[1]));
+    printf("%lld + %lld primary mapped (%s : %s)\n", s->n_pmapped[0], s->n_pmapped[1], percent(b0, s->n_pmapped[0], s->n_primary[0]), percent(b1, s->n_pmapped[1], s->n_primary[1]));
+    printf("%lld + %lld paired in sequencing\n", s->n_pair_all[0], s->n_pair_all[1]);
+    printf("%lld + %lld read1\n", s->n_read1[0], s->n_read1[1]);
+    printf("%lld + %lld read2\n", s->n_read2[0], s->n_read2[1]);
+    printf("%lld + %lld properly paired (%s : %s)\n", s->n_pair_good[0], s->n_pair_good[1], percent(b0, s->n_pair_good[0], s->n_pair_all[0]), percent(b1, s->n_pair_good[1], s->n_pair_all[1]));
+    printf("%lld + %lld with itself and mate mapped\n", s->n_pair_map[0], s->n_pair_map[1]);
+    printf("%lld + %lld singletons (%s : %s)\n", s->n_sgltn[0], s->n_sgltn[1], percent(b0, s->n_sgltn[0], s->n_pair_all[0]), percent(b1, s->n_sgltn[1], s->n_pair_all[1]));
+    printf("%lld + %lld with mate mapped to a different chr\n", s->n_diffchr[0], s->n_diffchr[1]);
+    printf("%lld + %lld with mate mapped to a different chr (mapQ>=5)\n", s->n_diffhigh[0], s->n_diffhigh[1]);
+}
+
+static void out_fmt_json(bam_flagstat_t *s) {
+    char b0[16], b1[16], p0[16], p1[16], pp0[16], pp1[16], s0[16], s1[16];
+    printf("{\n \"QC-passed reads\": { \n"
+                 "  \"total\": %lld, \n"
+                 "  \"primary\": %lld, \n"
+                 "  \"secondary\": %lld, \n"
+                 "  \"supplementary\": %lld, \n"
+                 "  \"duplicates\": %lld, \n"
+                 "  \"primary duplicates\": %lld, \n"
+                 "  \"mapped\": %lld, \n"
+                 "  \"mapped %%\": %s, \n"
+                 "  \"primary mapped\": %lld, \n"
+                 "  \"primary mapped %%\": %s, \n"
+                 "  \"paired in sequencing\": %lld, \n"
+                 "  \"read1\": %lld, \n"
+                 "  \"read2\": %lld, \n"
+                 "  \"properly paired\": %lld, \n"
+                 "  \"properly paired %%\": %s, \n"
+                 "  \"with itself and mate mapped\": %lld, \n"
+                 "  \"singletons\": %lld, \n"
+                 "  \"singletons %%\": %s, \n"
+                 "  \"with mate mapped to a different chr\": %lld, \n"
+                 "  \"with mate mapped to a different chr (mapQ >= 5)\": %lld \n"
+                 " },"
+            "\n \"QC-failed reads\": { \n"
+                 "  \"total\": %lld, \n"
+                 "  \"primary\": %lld, \n"
+                 "  \"secondary\": %lld, \n"
+                 "  \"supplementary\": %lld, \n"
+                 "  \"duplicates\": %lld, \n"
+                 "  \"primary duplicates\": %lld, \n"
+                 "  \"mapped\": %lld, \n"
+                 "  \"mapped %%\": %s, \n"
+                 "  \"primary mapped\": %lld, \n"
+                 "  \"primary mapped %%\": %s, \n"
+                 "  \"paired in sequencing\": %lld, \n"
+                 "  \"read1\": %lld, \n"
+                 "  \"read2\": %lld, \n"
+                 "  \"properly paired\": %lld, \n"
+                 "  \"properly paired %%\": %s, \n"
+                 "  \"with itself and mate mapped\": %lld, \n"
+                 "  \"singletons\": %lld, \n"
+                 "  \"singletons %%\": %s, \n"
+                 "  \"with mate mapped to a different chr\": %lld, \n"
+                 "  \"with mate mapped to a different chr (mapQ >= 5)\": %lld \n"
+                 " }\n"
+            "}\n",
+        s->n_reads[0],
+        s->n_primary[0],
+        s->n_secondary[0],
+        s->n_supp[0],
+        s->n_dup[0],
+        s->n_pdup[0],
+        s->n_mapped[0],
+        percent_json(b0, s->n_mapped[0], s->n_reads[0]),
+        s->n_pmapped[0],
+        percent_json(p0, s->n_pmapped[0], s->n_primary[0]),
+        s->n_pair_all[0],
+        s->n_read1[0],
+        s->n_read2[0],
+        s->n_pair_good[0],
+        percent_json(pp0, s->n_pair_good[0], s->n_pair_all[0]),
+        s->n_pair_map[0],
+        s->n_sgltn[0],
+        percent_json(s0, s->n_sgltn[0], s->n_pair_all[0]),
+        s->n_diffchr[0],
+        s->n_diffhigh[0],
+        s->n_reads[1],
+        s->n_primary[1],
+        s->n_secondary[1],
+        s->n_supp[1],
+        s->n_dup[1],
+        s->n_pdup[1],
+        s->n_mapped[1],
+        percent_json(b1, s->n_mapped[1], s->n_reads[1]),
+        s->n_pmapped[1],
+        percent_json(p1, s->n_pmapped[1], s->n_primary[1]),
+        s->n_pair_all[1],
+        s->n_read1[1],
+        s->n_read2[1],
+        s->n_pair_good[1],
+        percent_json(pp1, s->n_pair_good[1], s->n_pair_all[1]),
+        s->n_pair_map[1],
+        s->n_sgltn[1],
+        percent_json(s1, s->n_sgltn[1], s->n_pair_all[1]),
+        s->n_diffchr[1],
+        s->n_diffhigh[1]
+    );
+}
+
+static void out_fmt_tsv(bam_flagstat_t *s) {
+    char b0[16], b1[16];
+    printf("%lld\t%lld\ttotal (QC-passed reads + QC-failed reads)\n", s->n_reads[0], s->n_reads[1]);
+    printf("%lld\t%lld\tprimary\n", s->n_primary[0], s->n_primary[1]);
+    printf("%lld\t%lld\tsecondary\n", s->n_secondary[0], s->n_secondary[1]);
+    printf("%lld\t%lld\tsupplementary\n", s->n_supp[0], s->n_supp[1]);
+    printf("%lld\t%lld\tduplicates\n", s->n_dup[0], s->n_dup[1]);
+    printf("%lld\t%lld\tprimary duplicates\n", s->n_pdup[0], s->n_pdup[1]);
+    printf("%lld\t%lld\tmapped\n", s->n_mapped[0], s->n_mapped[1]);
+    printf("%s\t%s\tmapped %%\n", percent(b0, s->n_mapped[0], s->n_reads[0]), percent(b1, s->n_mapped[1], s->n_reads[1]));
+    printf("%lld\t%lld\tprimary mapped\n", s->n_pmapped[0], s->n_pmapped[1]);
+    printf("%s\t%s\tprimary mapped %%\n", percent(b0, s->n_pmapped[0], s->n_primary[0]), percent(b1, s->n_pmapped[1], s->n_primary[1]));
+    printf("%lld\t%lld\tpaired in sequencing\n", s->n_pair_all[0], s->n_pair_all[1]);
+    printf("%lld\t%lld\tread1\n", s->n_read1[0], s->n_read1[1]);
+    printf("%lld\t%lld\tread2\n", s->n_read2[0], s->n_read2[1]);
+    printf("%lld\t%lld\tproperly paired\n", s->n_pair_good[0], s->n_pair_good[1]);
+    printf("%s\t%s\tproperly paired %%\n", percent(b0, s->n_pair_good[0], s->n_pair_all[0]), percent(b1, s->n_pair_good[1], s->n_pair_all[1]));
+    printf("%lld\t%lld\twith itself and mate mapped\n", s->n_pair_map[0], s->n_pair_map[1]);
+    printf("%lld\t%lld\tsingletons\n", s->n_sgltn[0], s->n_sgltn[1]);
+    printf("%s\t%s\tsingletons %%\n", percent(b0, s->n_sgltn[0], s->n_pair_all[0]), percent(b1, s->n_sgltn[1], s->n_pair_all[1]));
+    printf("%lld\t%lld\twith mate mapped to a different chr\n", s->n_diffchr[0], s->n_diffchr[1]);
+    printf("%lld\t%lld\twith mate mapped to a different chr (mapQ>=5)\n", s->n_diffhigh[0], s->n_diffhigh[1]);
+}
+
+/*
+ * Select flagstats output format to print.
+ */
+static void output_fmt(bam_flagstat_t *s, const char *out_fmt)
+{
+  if (strcmp(out_fmt, "json") == 0 || strcmp(out_fmt, "JSON") == 0) {
+    out_fmt_json(s);
+  } else if (strcmp(out_fmt, "tsv") == 0 || strcmp(out_fmt, "TSV") == 0) {
+    out_fmt_tsv(s);
+  } else {
+    out_fmt_default(s);
+  }
+}
+
+int bam_flagstat(int argc, char *argv[])
+{
+    samFile *fp;
+    sam_hdr_t *header;
+    bam_flagstat_t *s;
+    const char *out_fmt = "default";
+    int c, status = EXIT_SUCCESS;
+
+    enum {
+        INPUT_FMT_OPTION = CHAR_MAX+1,
+    };
+
+    sam_global_args ga = SAM_GLOBAL_ARGS_INIT;
+    static const struct option lopts[] = {
+        SAM_OPT_GLOBAL_OPTIONS('-', 0, 'O', '-', '-', '@'),
+        {NULL, 0, NULL, 0}
+    };
+
+    while ((c = getopt_long(argc, argv, "@:O:", lopts, NULL)) >= 0) {
+        switch (c) {
+        case 'O':
+          out_fmt = optarg;
+          break;
+        default:  if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break;
+            /* else fall-through */
+        case '?':
+            usage_exit(stderr, EXIT_FAILURE);
+        }
+    }
+
+    if (argc != optind+1) {
+        if (argc == optind) usage_exit(stdout, EXIT_SUCCESS);
+        else usage_exit(stderr, EXIT_FAILURE);
+    }
+    fp = sam_open_format(argv[optind], "r", &ga.in);
+    if (fp == NULL) {
+        print_error_errno("flagstat", "Cannot open input file \"%s\"", argv[optind]);
+        return 1;
+    }
+    if (ga.nthreads > 0)
+        hts_set_threads(fp, ga.nthreads);
+
+    if (hts_set_opt(fp, CRAM_OPT_REQUIRED_FIELDS,
+                    SAM_FLAG | SAM_MAPQ | SAM_RNEXT)) {
+        fprintf(stderr, "Failed to set CRAM_OPT_REQUIRED_FIELDS value\n");
+        return 1;
+    }
+
+    if (hts_set_opt(fp, CRAM_OPT_DECODE_MD, 0)) {
+        fprintf(stderr, "Failed to set CRAM_OPT_DECODE_MD value\n");
+        return 1;
+    }
+
+    header = sam_hdr_read(fp);
+    if (header == NULL) {
+        fprintf(stderr, "Failed to read header for \"%s\"\n", argv[optind]);
+        return 1;
+    }
+
+    s = bam_flagstat_core(fp, header);
+    if (s) {
+        output_fmt(s, out_fmt);
+        free(s);
+    }
+    else {
+        print_error("flagstat", "error reading from \"%s\"", argv[optind]);
+        status = EXIT_FAILURE;
+    }
+
+    sam_hdr_destroy(header);
+    sam_close(fp);
+    sam_global_args_free(&ga);
+    return status;
+}
diff --git a/samtools/bam_stat.c.pysam.c b/samtools/bam_stat.c.pysam.c
new file mode 100644
index 0000000..bd6f4ca
--- /dev/null
+++ b/samtools/bam_stat.c.pysam.c
@@ -0,0 +1,348 @@
+#include "samtools.pysam.h"
+
+/*  bam_stat.c -- flagstat subcommand.
+
+    Copyright (C) 2009, 2011, 2013-2015, 2019, 2021 Genome Research Ltd.
+
+    Author: Heng Li <lh3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <config.h>
+
+#include <unistd.h>
+#include <stdint.h>
+#include <stdlib.h>
+#include <string.h>
+#include <stdio.h>
+#include <limits.h>
+#include <getopt.h>
+
+#include "htslib/sam.h"
+#include "samtools.h"
+#include "sam_opts.h"
+
+typedef struct {
+    long long n_reads[2], n_mapped[2], n_pair_all[2], n_pair_map[2], n_pair_good[2];
+    long long n_sgltn[2], n_read1[2], n_read2[2];
+    long long n_dup[2];
+    long long n_diffchr[2], n_diffhigh[2];
+    long long n_secondary[2], n_supp[2];
+    long long n_primary[2], n_pmapped[2], n_pdup[2];
+} bam_flagstat_t;
+
+inline static void flagstat_loop(bam_flagstat_t *s, bam1_core_t *c)
+{
+    int w = (c->flag & BAM_FQCFAIL)? 1 : 0;
+    ++s->n_reads[w];
+    if (c->flag & BAM_FSECONDARY ) {
+        ++s->n_secondary[w];
+    } else if (c->flag & BAM_FSUPPLEMENTARY ) {
+        ++s->n_supp[w];
+    } else {
+        ++s->n_primary[w];
+
+        if (c->flag & BAM_FPAIRED) {
+            ++s->n_pair_all[w];
+            if ((c->flag & BAM_FPROPER_PAIR) && !(c->flag & BAM_FUNMAP) ) ++s->n_pair_good[w];
+            if (c->flag & BAM_FREAD1) ++s->n_read1[w];
+            if (c->flag & BAM_FREAD2) ++s->n_read2[w];
+            if ((c->flag & BAM_FMUNMAP) && !(c->flag & BAM_FUNMAP)) ++s->n_sgltn[w];
+            if (!(c->flag & BAM_FUNMAP) && !(c->flag & BAM_FMUNMAP)) {
+                ++s->n_pair_map[w];
+                if (c->mtid != c->tid) {
+                    ++s->n_diffchr[w];
+                    if (c->qual >= 5) ++s->n_diffhigh[w];
+                }
+            }
+        }
+
+        if (!(c->flag & BAM_FUNMAP)) ++s->n_pmapped[w];
+        if (c->flag & BAM_FDUP) ++s->n_pdup[w];
+    }
+    if (!(c->flag & BAM_FUNMAP)) ++s->n_mapped[w];
+    if (c->flag & BAM_FDUP) ++s->n_dup[w];
+}
+
+bam_flagstat_t *bam_flagstat_core(samFile *fp, sam_hdr_t *h)
+{
+    bam_flagstat_t *s;
+    bam1_t *b;
+    bam1_core_t *c;
+    int ret;
+    s = (bam_flagstat_t*)calloc(1, sizeof(bam_flagstat_t));
+    b = bam_init1();
+    c = &b->core;
+    while ((ret = sam_read1(fp, h, b)) >= 0)
+        flagstat_loop(s, c);
+    bam_destroy1(b);
+    if (ret != -1) {
+        free(s);
+        return NULL;
+    }
+    return s;
+}
+
+static const char *percent(char *buffer, long long n, long long total)
+{
+    if (total != 0) sprintf(buffer, "%.2f%%", (float)n / total * 100.0);
+    else strcpy(buffer, "N/A");
+    return buffer;
+}
+
+static const char *percent_json(char *buffer, long long n, long long total)
+{
+    if (total != 0) sprintf(buffer, "%.2f", (float)n / total * 100.0);
+    else strcpy(buffer, "null");
+    return buffer;
+}
+
+static void usage_exit(FILE *fp, int exit_status)
+{
+    fprintf(fp, "Usage: samtools flagstat [options] <in.bam>\n");
+    sam_global_opt_help(fp, "-.---@-.");
+    fprintf(fp, "  -O, --");
+    fprintf(fp, "output-fmt FORMAT[,OPT[=VAL]]...\n"
+            "               Specify output format (json, tsv)\n");
+    samtools_exit(exit_status);
+}
+
+static void out_fmt_default(bam_flagstat_t *s)
+{
+    char b0[16], b1[16];
+    fprintf(samtools_stdout, "%lld + %lld in total (QC-passed reads + QC-failed reads)\n", s->n_reads[0], s->n_reads[1]);
+    fprintf(samtools_stdout, "%lld + %lld primary\n", s->n_primary[0], s->n_primary[1]);
+    fprintf(samtools_stdout, "%lld + %lld secondary\n", s->n_secondary[0], s->n_secondary[1]);
+    fprintf(samtools_stdout, "%lld + %lld supplementary\n", s->n_supp[0], s->n_supp[1]);
+    fprintf(samtools_stdout, "%lld + %lld duplicates\n", s->n_dup[0], s->n_dup[1]);
+    fprintf(samtools_stdout, "%lld + %lld primary duplicates\n", s->n_pdup[0], s->n_pdup[1]);
+    fprintf(samtools_stdout, "%lld + %lld mapped (%s : %s)\n", s->n_mapped[0], s->n_mapped[1], percent(b0, s->n_mapped[0], s->n_reads[0]), percent(b1, s->n_mapped[1], s->n_reads[1]));
+    fprintf(samtools_stdout, "%lld + %lld primary mapped (%s : %s)\n", s->n_pmapped[0], s->n_pmapped[1], percent(b0, s->n_pmapped[0], s->n_primary[0]), percent(b1, s->n_pmapped[1], s->n_primary[1]));
+    fprintf(samtools_stdout, "%lld + %lld paired in sequencing\n", s->n_pair_all[0], s->n_pair_all[1]);
+    fprintf(samtools_stdout, "%lld + %lld read1\n", s->n_read1[0], s->n_read1[1]);
+    fprintf(samtools_stdout, "%lld + %lld read2\n", s->n_read2[0], s->n_read2[1]);
+    fprintf(samtools_stdout, "%lld + %lld properly paired (%s : %s)\n", s->n_pair_good[0], s->n_pair_good[1], percent(b0, s->n_pair_good[0], s->n_pair_all[0]), percent(b1, s->n_pair_good[1], s->n_pair_all[1]));
+    fprintf(samtools_stdout, "%lld + %lld with itself and mate mapped\n", s->n_pair_map[0], s->n_pair_map[1]);
+    fprintf(samtools_stdout, "%lld + %lld singletons (%s : %s)\n", s->n_sgltn[0], s->n_sgltn[1], percent(b0, s->n_sgltn[0], s->n_pair_all[0]), percent(b1, s->n_sgltn[1], s->n_pair_all[1]));
+    fprintf(samtools_stdout, "%lld + %lld with mate mapped to a different chr\n", s->n_diffchr[0], s->n_diffchr[1]);
+    fprintf(samtools_stdout, "%lld + %lld with mate mapped to a different chr (mapQ>=5)\n", s->n_diffhigh[0], s->n_diffhigh[1]);
+}
+
+static void out_fmt_json(bam_flagstat_t *s) {
+    char b0[16], b1[16], p0[16], p1[16], pp0[16], pp1[16], s0[16], s1[16];
+    fprintf(samtools_stdout, "{\n \"QC-passed reads\": { \n"
+                 "  \"total\": %lld, \n"
+                 "  \"primary\": %lld, \n"
+                 "  \"secondary\": %lld, \n"
+                 "  \"supplementary\": %lld, \n"
+                 "  \"duplicates\": %lld, \n"
+                 "  \"primary duplicates\": %lld, \n"
+                 "  \"mapped\": %lld, \n"
+                 "  \"mapped %%\": %s, \n"
+                 "  \"primary mapped\": %lld, \n"
+                 "  \"primary mapped %%\": %s, \n"
+                 "  \"paired in sequencing\": %lld, \n"
+                 "  \"read1\": %lld, \n"
+                 "  \"read2\": %lld, \n"
+                 "  \"properly paired\": %lld, \n"
+                 "  \"properly paired %%\": %s, \n"
+                 "  \"with itself and mate mapped\": %lld, \n"
+                 "  \"singletons\": %lld, \n"
+                 "  \"singletons %%\": %s, \n"
+                 "  \"with mate mapped to a different chr\": %lld, \n"
+                 "  \"with mate mapped to a different chr (mapQ >= 5)\": %lld \n"
+                 " },"
+            "\n \"QC-failed reads\": { \n"
+                 "  \"total\": %lld, \n"
+                 "  \"primary\": %lld, \n"
+                 "  \"secondary\": %lld, \n"
+                 "  \"supplementary\": %lld, \n"
+                 "  \"duplicates\": %lld, \n"
+                 "  \"primary duplicates\": %lld, \n"
+                 "  \"mapped\": %lld, \n"
+                 "  \"mapped %%\": %s, \n"
+                 "  \"primary mapped\": %lld, \n"
+                 "  \"primary mapped %%\": %s, \n"
+                 "  \"paired in sequencing\": %lld, \n"
+                 "  \"read1\": %lld, \n"
+                 "  \"read2\": %lld, \n"
+                 "  \"properly paired\": %lld, \n"
+                 "  \"properly paired %%\": %s, \n"
+                 "  \"with itself and mate mapped\": %lld, \n"
+                 "  \"singletons\": %lld, \n"
+                 "  \"singletons %%\": %s, \n"
+                 "  \"with mate mapped to a different chr\": %lld, \n"
+                 "  \"with mate mapped to a different chr (mapQ >= 5)\": %lld \n"
+                 " }\n"
+            "}\n",
+        s->n_reads[0],
+        s->n_primary[0],
+        s->n_secondary[0],
+        s->n_supp[0],
+        s->n_dup[0],
+        s->n_pdup[0],
+        s->n_mapped[0],
+        percent_json(b0, s->n_mapped[0], s->n_reads[0]),
+        s->n_pmapped[0],
+        percent_json(p0, s->n_pmapped[0], s->n_primary[0]),
+        s->n_pair_all[0],
+        s->n_read1[0],
+        s->n_read2[0],
+        s->n_pair_good[0],
+        percent_json(pp0, s->n_pair_good[0], s->n_pair_all[0]),
+        s->n_pair_map[0],
+        s->n_sgltn[0],
+        percent_json(s0, s->n_sgltn[0], s->n_pair_all[0]),
+        s->n_diffchr[0],
+        s->n_diffhigh[0],
+        s->n_reads[1],
+        s->n_primary[1],
+        s->n_secondary[1],
+        s->n_supp[1],
+        s->n_dup[1],
+        s->n_pdup[1],
+        s->n_mapped[1],
+        percent_json(b1, s->n_mapped[1], s->n_reads[1]),
+        s->n_pmapped[1],
+        percent_json(p1, s->n_pmapped[1], s->n_primary[1]),
+        s->n_pair_all[1],
+        s->n_read1[1],
+        s->n_read2[1],
+        s->n_pair_good[1],
+        percent_json(pp1, s->n_pair_good[1], s->n_pair_all[1]),
+        s->n_pair_map[1],
+        s->n_sgltn[1],
+        percent_json(s1, s->n_sgltn[1], s->n_pair_all[1]),
+        s->n_diffchr[1],
+        s->n_diffhigh[1]
+    );
+}
+
+static void out_fmt_tsv(bam_flagstat_t *s) {
+    char b0[16], b1[16];
+    fprintf(samtools_stdout, "%lld\t%lld\ttotal (QC-passed reads + QC-failed reads)\n", s->n_reads[0], s->n_reads[1]);
+    fprintf(samtools_stdout, "%lld\t%lld\tprimary\n", s->n_primary[0], s->n_primary[1]);
+    fprintf(samtools_stdout, "%lld\t%lld\tsecondary\n", s->n_secondary[0], s->n_secondary[1]);
+    fprintf(samtools_stdout, "%lld\t%lld\tsupplementary\n", s->n_supp[0], s->n_supp[1]);
+    fprintf(samtools_stdout, "%lld\t%lld\tduplicates\n", s->n_dup[0], s->n_dup[1]);
+    fprintf(samtools_stdout, "%lld\t%lld\tprimary duplicates\n", s->n_pdup[0], s->n_pdup[1]);
+    fprintf(samtools_stdout, "%lld\t%lld\tmapped\n", s->n_mapped[0], s->n_mapped[1]);
+    fprintf(samtools_stdout, "%s\t%s\tmapped %%\n", percent(b0, s->n_mapped[0], s->n_reads[0]), percent(b1, s->n_mapped[1], s->n_reads[1]));
+    fprintf(samtools_stdout, "%lld\t%lld\tprimary mapped\n", s->n_pmapped[0], s->n_pmapped[1]);
+    fprintf(samtools_stdout, "%s\t%s\tprimary mapped %%\n", percent(b0, s->n_pmapped[0], s->n_primary[0]), percent(b1, s->n_pmapped[1], s->n_primary[1]));
+    fprintf(samtools_stdout, "%lld\t%lld\tpaired in sequencing\n", s->n_pair_all[0], s->n_pair_all[1]);
+    fprintf(samtools_stdout, "%lld\t%lld\tread1\n", s->n_read1[0], s->n_read1[1]);
+    fprintf(samtools_stdout, "%lld\t%lld\tread2\n", s->n_read2[0], s->n_read2[1]);
+    fprintf(samtools_stdout, "%lld\t%lld\tproperly paired\n", s->n_pair_good[0], s->n_pair_good[1]);
+    fprintf(samtools_stdout, "%s\t%s\tproperly paired %%\n", percent(b0, s->n_pair_good[0], s->n_pair_all[0]), percent(b1, s->n_pair_good[1], s->n_pair_all[1]));
+    fprintf(samtools_stdout, "%lld\t%lld\twith itself and mate mapped\n", s->n_pair_map[0], s->n_pair_map[1]);
+    fprintf(samtools_stdout, "%lld\t%lld\tsingletons\n", s->n_sgltn[0], s->n_sgltn[1]);
+    fprintf(samtools_stdout, "%s\t%s\tsingletons %%\n", percent(b0, s->n_sgltn[0], s->n_pair_all[0]), percent(b1, s->n_sgltn[1], s->n_pair_all[1]));
+    fprintf(samtools_stdout, "%lld\t%lld\twith mate mapped to a different chr\n", s->n_diffchr[0], s->n_diffchr[1]);
+    fprintf(samtools_stdout, "%lld\t%lld\twith mate mapped to a different chr (mapQ>=5)\n", s->n_diffhigh[0], s->n_diffhigh[1]);
+}
+
+/*
+ * Select flagstats output format to print.
+ */
+static void output_fmt(bam_flagstat_t *s, const char *out_fmt)
+{
+  if (strcmp(out_fmt, "json") == 0 || strcmp(out_fmt, "JSON") == 0) {
+    out_fmt_json(s);
+  } else if (strcmp(out_fmt, "tsv") == 0 || strcmp(out_fmt, "TSV") == 0) {
+    out_fmt_tsv(s);
+  } else {
+    out_fmt_default(s);
+  }
+}
+
+int bam_flagstat(int argc, char *argv[])
+{
+    samFile *fp;
+    sam_hdr_t *header;
+    bam_flagstat_t *s;
+    const char *out_fmt = "default";
+    int c, status = EXIT_SUCCESS;
+
+    enum {
+        INPUT_FMT_OPTION = CHAR_MAX+1,
+    };
+
+    sam_global_args ga = SAM_GLOBAL_ARGS_INIT;
+    static const struct option lopts[] = {
+        SAM_OPT_GLOBAL_OPTIONS('-', 0, 'O', '-', '-', '@'),
+        {NULL, 0, NULL, 0}
+    };
+
+    while ((c = getopt_long(argc, argv, "@:O:", lopts, NULL)) >= 0) {
+        switch (c) {
+        case 'O':
+          out_fmt = optarg;
+          break;
+        default:  if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break;
+            /* else fall-through */
+        case '?':
+            usage_exit(samtools_stderr, EXIT_FAILURE);
+        }
+    }
+
+    if (argc != optind+1) {
+        if (argc == optind) usage_exit(samtools_stdout, EXIT_SUCCESS);
+        else usage_exit(samtools_stderr, EXIT_FAILURE);
+    }
+    fp = sam_open_format(argv[optind], "r", &ga.in);
+    if (fp == NULL) {
+        print_error_errno("flagstat", "Cannot open input file \"%s\"", argv[optind]);
+        return 1;
+    }
+    if (ga.nthreads > 0)
+        hts_set_threads(fp, ga.nthreads);
+
+    if (hts_set_opt(fp, CRAM_OPT_REQUIRED_FIELDS,
+                    SAM_FLAG | SAM_MAPQ | SAM_RNEXT)) {
+        fprintf(samtools_stderr, "Failed to set CRAM_OPT_REQUIRED_FIELDS value\n");
+        return 1;
+    }
+
+    if (hts_set_opt(fp, CRAM_OPT_DECODE_MD, 0)) {
+        fprintf(samtools_stderr, "Failed to set CRAM_OPT_DECODE_MD value\n");
+        return 1;
+    }
+
+    header = sam_hdr_read(fp);
+    if (header == NULL) {
+        fprintf(samtools_stderr, "Failed to read header for \"%s\"\n", argv[optind]);
+        return 1;
+    }
+
+    s = bam_flagstat_core(fp, header);
+    if (s) {
+        output_fmt(s, out_fmt);
+        free(s);
+    }
+    else {
+        print_error("flagstat", "error reading from \"%s\"", argv[optind]);
+        status = EXIT_FAILURE;
+    }
+
+    sam_hdr_destroy(header);
+    sam_close(fp);
+    sam_global_args_free(&ga);
+    return status;
+}
diff --git a/samtools/bamshuf.c b/samtools/bamshuf.c
new file mode 100644
index 0000000..53e382d
--- /dev/null
+++ b/samtools/bamshuf.c
@@ -0,0 +1,635 @@
+/*  bamshuf.c -- collate subcommand.
+
+    Copyright (C) 2012 Broad Institute.
+    Copyright (C) 2013, 2015-2019 Genome Research Ltd.
+
+    Author: Heng Li <lh3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <config.h>
+
+#include <unistd.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <assert.h>
+#include <errno.h>
+#ifdef _WIN32
+#  define WIN32_LEAN_AND_MEAN
+#  include <windows.h>
+#endif
+#include "htslib/sam.h"
+#include "htslib/hts.h"
+#include "htslib/ksort.h"
+#include "samtools.h"
+#include "htslib/thread_pool.h"
+#include "sam_opts.h"
+#include "htslib/khash.h"
+
+#define DEF_CLEVEL 1
+
+static inline unsigned hash_Wang(unsigned key)
+{
+    key += ~(key << 15);
+    key ^=  (key >> 10);
+    key +=  (key << 3);
+    key ^=  (key >> 6);
+    key += ~(key << 11);
+    key ^=  (key >> 16);
+    return key;
+}
+
+static inline unsigned hash_X31_Wang(const char *s)
+{
+    unsigned h = *s;
+    if (h) {
+        for (++s ; *s; ++s) h = (h << 5) - h + *s;
+        return hash_Wang(h);
+    } else return 0;
+}
+
+typedef struct {
+    unsigned key;
+    bam1_t *b;
+} elem_t;
+
+static inline int elem_lt(elem_t x, elem_t y)
+{
+    if (x.key < y.key) return 1;
+    if (x.key == y.key) {
+        int t;
+        t = strcmp(bam_get_qname(x.b), bam_get_qname(y.b));
+        if (t < 0) return 1;
+        return (t == 0 && ((x.b->core.flag>>6&3) < (y.b->core.flag>>6&3)));
+    } else return 0;
+}
+
+KSORT_INIT(bamshuf, elem_t, elem_lt)
+
+
+typedef struct {
+    int written;
+    bam1_t *b;
+} bam_item_t;
+
+typedef struct {
+    bam1_t *bam_pool;
+    bam_item_t *items;
+    size_t size;
+    size_t index;
+} bam_list_t;
+
+typedef struct {
+    bam_item_t *bi;
+} store_item_t;
+
+KHASH_MAP_INIT_STR(bam_store, store_item_t)
+
+
+static bam_item_t *store_bam(bam_list_t *list) {
+    size_t old_index = list->index;
+
+    list->items[list->index++].written = 0;
+
+    if (list->index >= list->size)
+        list->index = 0;
+
+    return &list->items[old_index];
+}
+
+
+static int write_bam_needed(bam_list_t *list) {
+    return !list->items[list->index].written;
+}
+
+
+static void mark_bam_as_written(bam_list_t *list) {
+    list->items[list->index].written = 1;
+}
+
+
+static int create_bam_list(bam_list_t *list, size_t max_size) {
+    size_t i;
+
+    list->size = list->index = 0;
+    list->items    = NULL;
+    list->bam_pool = NULL;
+
+    if ((list->items = malloc(max_size * sizeof(bam_item_t))) == NULL) {
+        return 1;
+    }
+
+    if ((list->bam_pool = calloc(max_size, sizeof(bam1_t))) == NULL) {
+        return 1;
+    }
+
+    for (i = 0; i < max_size; i++) {
+        list->items[i].b = &list->bam_pool[i];
+        list->items[i].written = 1;
+    }
+
+    list->size  = max_size;
+    list->index = 0;
+
+    return 0;
+}
+
+
+static void destroy_bam_list(bam_list_t *list) {
+    size_t i;
+
+    for (i = 0; i < list->size; i++) {
+        free(list->bam_pool[i].data);
+    }
+
+    free(list->bam_pool);
+    free(list->items);
+}
+
+
+static inline int write_to_bin_file(bam1_t *bam, int64_t *count, samFile **bin_files, char **names, sam_hdr_t *header, int files) {
+    uint32_t x;
+
+    x = hash_X31_Wang(bam_get_qname(bam)) % files;
+
+    if (sam_write1(bin_files[x], header, bam) < 0) {
+        print_error_errno("collate", "Couldn't write to intermediate file \"%s\"", names[x]);
+        return 1;
+    }
+
+    ++count[x];
+
+    return 0;
+}
+
+
+static int bamshuf(const char *fn, int n_files, const char *pre, int clevel,
+                   int is_stdout, const char *output_file, int fast, int store_max, sam_global_args *ga, char *arg_list, int no_pg)
+{
+    samFile *fp, *fpw = NULL, **fpt = NULL;
+    char **fnt = NULL, modew[8];
+    bam1_t *b = NULL;
+    int i, counter, l, r;
+    sam_hdr_t *h = NULL;
+    int64_t j, max_cnt = 0, *cnt = NULL;
+    elem_t *a = NULL;
+    htsThreadPool p = {NULL, 0};
+
+    if (ga->nthreads > 0) {
+        if (!(p.pool = hts_tpool_init(ga->nthreads))) {
+            print_error_errno("collate", "Error creating thread pool\n");
+            return 1;
+        }
+    }
+
+    // Read input, distribute reads pseudo-randomly into n_files temporary
+    // files.
+    fp = sam_open_format(fn, "r", &ga->in);
+    if (fp == NULL) {
+        print_error_errno("collate", "Cannot open input file \"%s\"", fn);
+        return 1;
+    }
+    if (p.pool) hts_set_opt(fp, HTS_OPT_THREAD_POOL, &p);
+
+    h = sam_hdr_read(fp);
+    if (h == NULL) {
+        fprintf(stderr, "Couldn't read header for '%s'\n", fn);
+        goto fail;
+    }
+
+    if ((-1 == sam_hdr_update_hd(h, "SO", "unsorted", "GO", "query"))
+     && (-1 == sam_hdr_add_line(h, "HD", "VN", SAM_FORMAT_VERSION, "SO", "unsorted", "GO", "query", NULL))
+     ) {
+        print_error("collate", "failed to update HD line\n");
+        goto fail;
+    }
+
+    // open final output file
+    l = strlen(pre);
+
+    sprintf(modew, "wb%d", (clevel >= 0 && clevel <= 9)? clevel : DEF_CLEVEL);
+
+    if (!is_stdout && !output_file) { // output to a file (name based on prefix)
+        char *fnw = (char*)calloc(l + 5, 1);
+        if (!fnw) goto mem_fail;
+        if (ga->out.format == unknown_format)
+            sprintf(fnw, "%s.bam", pre); // "wb" above makes BAM the default
+        else
+            sprintf(fnw, "%s.%s", pre,  hts_format_file_extension(&ga->out));
+        fpw = sam_open_format(fnw, modew, &ga->out);
+        free(fnw);
+    } else if (output_file) { // output to a given file
+        modew[0] = 'w'; modew[1] = '\0';
+        sam_open_mode(modew + 1, output_file, NULL);
+        j = strlen(modew);
+        snprintf(modew + j, sizeof(modew) - j, "%d",
+                 (clevel >= 0 && clevel <= 9)? clevel : DEF_CLEVEL);
+        fpw = sam_open_format(output_file, modew, &ga->out);
+    } else fpw = sam_open_format("-", modew, &ga->out); // output to stdout
+    if (fpw == NULL) {
+        if (is_stdout) print_error_errno("collate", "Cannot open standard output");
+        else print_error_errno("collate", "Cannot open output file \"%s.bam\"", pre);
+        goto fail;
+    }
+    if (p.pool) hts_set_opt(fpw, HTS_OPT_THREAD_POOL, &p);
+
+    if (!no_pg && sam_hdr_add_pg(h, "samtools",
+                                 "VN", samtools_version(),
+                                 arg_list ? "CL": NULL,
+                                 arg_list ? arg_list : NULL,
+                                 NULL)) {
+        print_error("collate", "failed to add PG line to header of \"%s\"", output_file);
+        goto fail;
+    }
+
+    if (sam_hdr_write(fpw, h) < 0) {
+        print_error_errno("collate", "Couldn't write header");
+        goto fail;
+    }
+
+    fnt = (char**)calloc(n_files, sizeof(char*));
+    if (!fnt) goto mem_fail;
+    fpt = (samFile**)calloc(n_files, sizeof(samFile*));
+    if (!fpt) goto mem_fail;
+    cnt = (int64_t*)calloc(n_files, 8);
+    if (!cnt) goto mem_fail;
+
+    for (i = counter = 0; i < n_files; ++i) {
+        fnt[i] = (char*)calloc(l + 20, 1);
+        if (!fnt[i]) goto mem_fail;
+        do {
+            sprintf(fnt[i], "%s.%04d.bam", pre, counter++);
+            fpt[i] = sam_open(fnt[i], "wxb1");
+        } while (!fpt[i] && errno == EEXIST);
+        if (fpt[i] == NULL) {
+            print_error_errno("collate", "Cannot open intermediate file \"%s\"", fnt[i]);
+            goto fail;
+        }
+        if (p.pool) hts_set_opt(fpt[i], HTS_OPT_THREAD_POOL, &p);
+        if (sam_hdr_write(fpt[i], h) < 0) {
+            print_error_errno("collate", "Couldn't write header to intermediate file \"%s\"", fnt[i]);
+            goto fail;
+        }
+    }
+
+    if (fast) {
+        khash_t(bam_store) *stored = kh_init(bam_store);
+        khiter_t itr;
+        bam_list_t list;
+        int err = 0;
+        if (!stored) goto mem_fail;
+
+        if (store_max < 2) store_max = 2;
+
+        if (create_bam_list(&list, store_max)) {
+            fprintf(stderr, "[collate[ ERROR: unable to create bam list.\n");
+            err = 1;
+            goto fast_fail;
+        }
+
+        while ((r = sam_read1(fp, h, list.items[list.index].b)) >= 0) {
+            int ret;
+            bam1_t *b = list.items[list.index].b;
+            int readflag = b->core.flag & (BAM_FREAD1 | BAM_FREAD2);
+
+            // strictly paired reads only
+            if (!(b->core.flag & (BAM_FSECONDARY | BAM_FSUPPLEMENTARY)) && (readflag == BAM_FREAD1 || readflag == BAM_FREAD2)) {
+
+                itr = kh_get(bam_store, stored, bam_get_qname(b));
+
+                if (itr == kh_end(stored)) {
+                    // new read
+                    itr = kh_put(bam_store, stored, bam_get_qname(b), &ret);
+
+                    if (ret > 0) { // okay to go ahead store it
+                        kh_value(stored, itr).bi = store_bam(&list);
+
+                        // see if the next one on the list needs to be written out
+                        if (write_bam_needed(&list)) {
+                            if (write_to_bin_file(list.items[list.index].b, cnt, fpt, fnt, h, n_files) < 0) {
+                                fprintf(stderr, "[collate] ERROR: could not write line.\n");
+                                err = 1;
+                                goto fast_fail;
+                            } else {
+                                mark_bam_as_written(&list);
+
+                                itr = kh_get(bam_store, stored, bam_get_qname(list.items[list.index].b));
+
+                                if (itr != kh_end(stored)) {
+                                    kh_del(bam_store, stored, itr);
+                                } else {
+                                    fprintf(stderr, "[collate] ERROR: stored value not in hash.\n");
+                                    err = 1;
+                                    goto fast_fail;
+                                }
+                            }
+                        }
+                    } else if (ret == 0) {
+                        fprintf(stderr, "[collate] ERROR: value already in hash.\n");
+                        err = 1;
+                        goto fast_fail;
+                    } else {
+                        fprintf(stderr, "[collate] ERROR: unable to store in hash.\n");
+                        err = 1;
+                        goto fast_fail;
+                    }
+                } else { // we have a match
+                    // write out the reads in R1 R2 order
+                    bam1_t *r1, *r2;
+
+                    if (b->core.flag & BAM_FREAD1) {
+                        r1 = b;
+                        r2 = kh_value(stored, itr).bi->b;
+                    } else {
+                        r1 = kh_value(stored, itr).bi->b;
+                        r2 = b;
+                    }
+
+                    if (sam_write1(fpw, h, r1) < 0) {
+                        fprintf(stderr, "[collate] ERROR: could not write r1 alignment.\n");
+                        err = 1;
+                        goto fast_fail;
+                    }
+
+                    if (sam_write1(fpw, h, r2) < 0) {
+                        fprintf(stderr, "[collate] ERROR: could not write r2 alignment.\n");
+                        err = 1;
+                        goto fast_fail;
+                    }
+
+                    mark_bam_as_written(&list);
+
+                    // remove stored read
+                    kh_value(stored, itr).bi->written = 1;
+                    kh_del(bam_store, stored, itr);
+                }
+            }
+        }
+
+        for (list.index = 0; list.index < list.size; list.index++) {
+            if (write_bam_needed(&list)) {
+                bam1_t *b = list.items[list.index].b;
+
+                if (write_to_bin_file(b, cnt, fpt, fnt, h, n_files)) {
+                    err = 1;
+                    goto fast_fail;
+                } else {
+                    itr = kh_get(bam_store, stored, bam_get_qname(b));
+                    kh_del(bam_store, stored, itr);
+                }
+            }
+        }
+
+ fast_fail:
+        if (err) {
+            for (itr = kh_begin(stored); itr != kh_end(stored); ++itr) {
+                if (kh_exist(stored, itr)) {
+                    kh_del(bam_store, stored, itr);
+                }
+            }
+
+            kh_destroy(bam_store, stored);
+            destroy_bam_list(&list);
+            goto fail;
+        } else {
+            kh_destroy(bam_store, stored);
+            destroy_bam_list(&list);
+        }
+
+    } else {
+        b = bam_init1();
+        if (!b) goto mem_fail;
+
+        while ((r = sam_read1(fp, h, b)) >= 0) {
+            if (write_to_bin_file(b, cnt, fpt, fnt, h, n_files)) {
+                bam_destroy1(b);
+                goto fail;
+            }
+        }
+
+        bam_destroy1(b);
+    }
+
+    if (r < -1) {
+        fprintf(stderr, "Error reading input file\n");
+        goto fail;
+    }
+    for (i = 0; i < n_files; ++i) {
+        // Close split output
+        r = sam_close(fpt[i]);
+        fpt[i] = NULL;
+        if (r < 0) {
+            fprintf(stderr, "Error on closing '%s'\n", fnt[i]);
+            return 1;
+        }
+
+        // Find biggest count
+        if (max_cnt < cnt[i]) max_cnt = cnt[i];
+    }
+    free(fpt);
+    fpt = NULL;
+    sam_close(fp);
+    fp = NULL;
+
+    // merge
+    a = malloc(max_cnt * sizeof(elem_t));
+    if (!a) goto mem_fail;
+    for (j = 0; j < max_cnt; ++j) {
+        a[j].b = bam_init1();
+        if (!a[j].b) { max_cnt = j; goto mem_fail; }
+    }
+
+    for (i = 0; i < n_files; ++i) {
+        int64_t c = cnt[i];
+        fp = sam_open_format(fnt[i], "r", &ga->in);
+        if (NULL == fp) {
+            print_error_errno("collate", "Couldn't open \"%s\"", fnt[i]);
+            goto fail;
+        }
+        if (p.pool) hts_set_opt(fp, HTS_OPT_THREAD_POOL, &p);
+        sam_hdr_destroy(sam_hdr_read(fp)); // Skip over header
+
+        // Slurp in one of the split files
+        for (j = 0; j < c; ++j) {
+            if (sam_read1(fp, h, a[j].b) < 0) {
+                fprintf(stderr, "Error reading '%s'\n", fnt[i]);
+                goto fail;
+            }
+            a[j].key = hash_X31_Wang(bam_get_qname(a[j].b));
+        }
+        sam_close(fp);
+        unlink(fnt[i]);
+        free(fnt[i]);
+        fnt[i] = NULL;
+
+        ks_introsort(bamshuf, c, a); // Shuffle all the reads
+
+        // Write them out again
+        for (j = 0; j < c; ++j) {
+            if (sam_write1(fpw, h, a[j].b) < 0) {
+                print_error_errno("collate", "Error writing to output");
+                goto fail;
+            }
+        }
+    }
+
+    sam_hdr_destroy(h);
+    for (j = 0; j < max_cnt; ++j) bam_destroy1(a[j].b);
+    free(a); free(fnt); free(cnt);
+    sam_global_args_free(ga);
+    if (sam_close(fpw) < 0) {
+        fprintf(stderr, "Error on closing output\n");
+        return 1;
+    }
+
+    if (p.pool) hts_tpool_destroy(p.pool);
+    return 0;
+
+ mem_fail:
+    fprintf(stderr, "Out of memory\n");
+
+ fail:
+    if (fp) sam_close(fp);
+    if (fpw) sam_close(fpw);
+    if (h) sam_hdr_destroy(h);
+    for (i = 0; i < n_files; ++i) {
+        if (fnt) free(fnt[i]);
+        if (fpt && fpt[i]) sam_close(fpt[i]);
+    }
+    if (a) {
+        for (j = 0; j < max_cnt; ++j) bam_destroy1(a[j].b);
+        free(a);
+    }
+    free(fnt);
+    free(fpt);
+    free(cnt);
+    if (p.pool) hts_tpool_destroy(p.pool);
+    sam_global_args_free(ga);
+    return 1;
+}
+
+static int usage(FILE *fp, int n_files, int reads_store) {
+    fprintf(fp,
+            "Usage: samtools collate [-Ou] [-o <name>] [-n nFiles] [-l cLevel] <in.bam> [<prefix>]\n\n"
+            "Options:\n"
+            "      -O       output to stdout\n"
+            "      -o       output file name (use prefix if not set)\n"
+            "      -u       uncompressed BAM output\n"
+            "      -f       fast (only primary alignments)\n"
+            "      -r       working reads stored (with -f) [%d]\n" // reads_store
+            "      -l INT   compression level [%d]\n" // DEF_CLEVEL
+            "      -n INT   number of temporary files [%d]\n" // n_files
+            "      --no-PG  do not add a PG line\n",
+            reads_store, DEF_CLEVEL, n_files);
+
+    sam_global_opt_help(fp, "-....@-.");
+    fprintf(fp,
+            "  <prefix> is required unless the -o or -O options are used.\n");
+
+    return 1;
+}
+
+char * generate_prefix() {
+    char *prefix;
+    unsigned int pid = getpid();
+#ifdef _WIN32
+#  define PREFIX_LEN (MAX_PATH + 16)
+    DWORD ret;
+    prefix = calloc(PREFIX_LEN, sizeof(*prefix));
+    if (!prefix) {
+        perror("collate");
+        return NULL;
+    }
+    ret = GetTempPathA(MAX_PATH, prefix);
+    if (ret > MAX_PATH || ret == 0) {
+        fprintf(stderr,
+                "[E::collate] Couldn't get path for temporary files.\n");
+        free(prefix);
+        return NULL;
+    }
+    snprintf(prefix + ret, PREFIX_LEN - ret, "\\%x", pid);
+    return prefix;
+#else
+#  define PREFIX_LEN 64
+    prefix = malloc(PREFIX_LEN);
+    if (!prefix) {
+        perror("collate");
+        return NULL;
+    }
+    snprintf(prefix, PREFIX_LEN, "/tmp/collate%x", pid);
+    return prefix;
+#endif
+}
+
+int main_bamshuf(int argc, char *argv[])
+{
+    int c, n_files = 64, clevel = DEF_CLEVEL, is_stdout = 0, is_un = 0, fast_coll = 0, reads_store = 10000, ret, pre_mem = 0, no_pg = 0;
+    const char *output_file = NULL;
+    char *prefix = NULL, *arg_list = NULL;
+    sam_global_args ga = SAM_GLOBAL_ARGS_INIT;
+    static const struct option lopts[] = {
+        SAM_OPT_GLOBAL_OPTIONS('-', 0, 0, 0, 0, '@'),
+        {"no-PG", no_argument, NULL, 1},
+        { NULL, 0, NULL, 0 }
+    };
+
+    while ((c = getopt_long(argc, argv, "n:l:uOo:@:fr:", lopts, NULL)) >= 0) {
+        switch (c) {
+        case 'n': n_files = atoi(optarg); break;
+        case 'l': clevel = atoi(optarg); break;
+        case 'u': is_un = 1; break;
+        case 'O': is_stdout = 1; break;
+        case 'o': output_file = optarg; break;
+        case 'f': fast_coll = 1; break;
+        case 'r': reads_store = atoi(optarg); break;
+        case 1: no_pg = 1; break;
+        default:  if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break;
+                  /* else fall-through */
+        case '?': return usage(stderr, n_files, reads_store);
+        }
+    }
+    if (is_un) clevel = 0;
+    if (argc >= optind + 2) prefix = argv[optind+1];
+    if (!(prefix || is_stdout || output_file))
+        return usage(stderr, n_files, reads_store);
+    if (is_stdout && output_file) {
+        fprintf(stderr, "collate: -o and -O options cannot be used together.\n");
+        return usage(stderr, n_files, reads_store);
+    }
+    if (!prefix) {
+        prefix = generate_prefix();
+        pre_mem = 1;
+    }
+
+    if (!prefix) return EXIT_FAILURE;
+
+    if (!no_pg && !(arg_list = stringify_argv(argc+1, argv-1))) {
+        print_error("collate", "failed to create arg_list");
+        return 1;
+    }
+
+    ret = bamshuf(argv[optind], n_files, prefix, clevel, is_stdout,
+                   output_file, fast_coll, reads_store, &ga, arg_list, no_pg);
+
+    if (pre_mem) free(prefix);
+    free(arg_list);
+
+    return ret;
+}
diff --git a/samtools/bamshuf.c.pysam.c b/samtools/bamshuf.c.pysam.c
new file mode 100644
index 0000000..d075a93
--- /dev/null
+++ b/samtools/bamshuf.c.pysam.c
@@ -0,0 +1,637 @@
+#include "samtools.pysam.h"
+
+/*  bamshuf.c -- collate subcommand.
+
+    Copyright (C) 2012 Broad Institute.
+    Copyright (C) 2013, 2015-2019 Genome Research Ltd.
+
+    Author: Heng Li <lh3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <config.h>
+
+#include <unistd.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <assert.h>
+#include <errno.h>
+#ifdef _WIN32
+#  define WIN32_LEAN_AND_MEAN
+#  include <windows.h>
+#endif
+#include "htslib/sam.h"
+#include "htslib/hts.h"
+#include "htslib/ksort.h"
+#include "samtools.h"
+#include "htslib/thread_pool.h"
+#include "sam_opts.h"
+#include "htslib/khash.h"
+
+#define DEF_CLEVEL 1
+
+static inline unsigned hash_Wang(unsigned key)
+{
+    key += ~(key << 15);
+    key ^=  (key >> 10);
+    key +=  (key << 3);
+    key ^=  (key >> 6);
+    key += ~(key << 11);
+    key ^=  (key >> 16);
+    return key;
+}
+
+static inline unsigned hash_X31_Wang(const char *s)
+{
+    unsigned h = *s;
+    if (h) {
+        for (++s ; *s; ++s) h = (h << 5) - h + *s;
+        return hash_Wang(h);
+    } else return 0;
+}
+
+typedef struct {
+    unsigned key;
+    bam1_t *b;
+} elem_t;
+
+static inline int elem_lt(elem_t x, elem_t y)
+{
+    if (x.key < y.key) return 1;
+    if (x.key == y.key) {
+        int t;
+        t = strcmp(bam_get_qname(x.b), bam_get_qname(y.b));
+        if (t < 0) return 1;
+        return (t == 0 && ((x.b->core.flag>>6&3) < (y.b->core.flag>>6&3)));
+    } else return 0;
+}
+
+KSORT_INIT(bamshuf, elem_t, elem_lt)
+
+
+typedef struct {
+    int written;
+    bam1_t *b;
+} bam_item_t;
+
+typedef struct {
+    bam1_t *bam_pool;
+    bam_item_t *items;
+    size_t size;
+    size_t index;
+} bam_list_t;
+
+typedef struct {
+    bam_item_t *bi;
+} store_item_t;
+
+KHASH_MAP_INIT_STR(bam_store, store_item_t)
+
+
+static bam_item_t *store_bam(bam_list_t *list) {
+    size_t old_index = list->index;
+
+    list->items[list->index++].written = 0;
+
+    if (list->index >= list->size)
+        list->index = 0;
+
+    return &list->items[old_index];
+}
+
+
+static int write_bam_needed(bam_list_t *list) {
+    return !list->items[list->index].written;
+}
+
+
+static void mark_bam_as_written(bam_list_t *list) {
+    list->items[list->index].written = 1;
+}
+
+
+static int create_bam_list(bam_list_t *list, size_t max_size) {
+    size_t i;
+
+    list->size = list->index = 0;
+    list->items    = NULL;
+    list->bam_pool = NULL;
+
+    if ((list->items = malloc(max_size * sizeof(bam_item_t))) == NULL) {
+        return 1;
+    }
+
+    if ((list->bam_pool = calloc(max_size, sizeof(bam1_t))) == NULL) {
+        return 1;
+    }
+
+    for (i = 0; i < max_size; i++) {
+        list->items[i].b = &list->bam_pool[i];
+        list->items[i].written = 1;
+    }
+
+    list->size  = max_size;
+    list->index = 0;
+
+    return 0;
+}
+
+
+static void destroy_bam_list(bam_list_t *list) {
+    size_t i;
+
+    for (i = 0; i < list->size; i++) {
+        free(list->bam_pool[i].data);
+    }
+
+    free(list->bam_pool);
+    free(list->items);
+}
+
+
+static inline int write_to_bin_file(bam1_t *bam, int64_t *count, samFile **bin_files, char **names, sam_hdr_t *header, int files) {
+    uint32_t x;
+
+    x = hash_X31_Wang(bam_get_qname(bam)) % files;
+
+    if (sam_write1(bin_files[x], header, bam) < 0) {
+        print_error_errno("collate", "Couldn't write to intermediate file \"%s\"", names[x]);
+        return 1;
+    }
+
+    ++count[x];
+
+    return 0;
+}
+
+
+static int bamshuf(const char *fn, int n_files, const char *pre, int clevel,
+                   int is_stdout, const char *output_file, int fast, int store_max, sam_global_args *ga, char *arg_list, int no_pg)
+{
+    samFile *fp, *fpw = NULL, **fpt = NULL;
+    char **fnt = NULL, modew[8];
+    bam1_t *b = NULL;
+    int i, counter, l, r;
+    sam_hdr_t *h = NULL;
+    int64_t j, max_cnt = 0, *cnt = NULL;
+    elem_t *a = NULL;
+    htsThreadPool p = {NULL, 0};
+
+    if (ga->nthreads > 0) {
+        if (!(p.pool = hts_tpool_init(ga->nthreads))) {
+            print_error_errno("collate", "Error creating thread pool\n");
+            return 1;
+        }
+    }
+
+    // Read input, distribute reads pseudo-randomly into n_files temporary
+    // files.
+    fp = sam_open_format(fn, "r", &ga->in);
+    if (fp == NULL) {
+        print_error_errno("collate", "Cannot open input file \"%s\"", fn);
+        return 1;
+    }
+    if (p.pool) hts_set_opt(fp, HTS_OPT_THREAD_POOL, &p);
+
+    h = sam_hdr_read(fp);
+    if (h == NULL) {
+        fprintf(samtools_stderr, "Couldn't read header for '%s'\n", fn);
+        goto fail;
+    }
+
+    if ((-1 == sam_hdr_update_hd(h, "SO", "unsorted", "GO", "query"))
+     && (-1 == sam_hdr_add_line(h, "HD", "VN", SAM_FORMAT_VERSION, "SO", "unsorted", "GO", "query", NULL))
+     ) {
+        print_error("collate", "failed to update HD line\n");
+        goto fail;
+    }
+
+    // open final output file
+    l = strlen(pre);
+
+    sprintf(modew, "wb%d", (clevel >= 0 && clevel <= 9)? clevel : DEF_CLEVEL);
+
+    if (!is_stdout && !output_file) { // output to a file (name based on prefix)
+        char *fnw = (char*)calloc(l + 5, 1);
+        if (!fnw) goto mem_fail;
+        if (ga->out.format == unknown_format)
+            sprintf(fnw, "%s.bam", pre); // "wb" above makes BAM the default
+        else
+            sprintf(fnw, "%s.%s", pre,  hts_format_file_extension(&ga->out));
+        fpw = sam_open_format(fnw, modew, &ga->out);
+        free(fnw);
+    } else if (output_file) { // output to a given file
+        modew[0] = 'w'; modew[1] = '\0';
+        sam_open_mode(modew + 1, output_file, NULL);
+        j = strlen(modew);
+        snprintf(modew + j, sizeof(modew) - j, "%d",
+                 (clevel >= 0 && clevel <= 9)? clevel : DEF_CLEVEL);
+        fpw = sam_open_format(output_file, modew, &ga->out);
+    } else fpw = sam_open_format("-", modew, &ga->out); // output to samtools_stdout
+    if (fpw == NULL) {
+        if (is_stdout) print_error_errno("collate", "Cannot open standard output");
+        else print_error_errno("collate", "Cannot open output file \"%s.bam\"", pre);
+        goto fail;
+    }
+    if (p.pool) hts_set_opt(fpw, HTS_OPT_THREAD_POOL, &p);
+
+    if (!no_pg && sam_hdr_add_pg(h, "samtools",
+                                 "VN", samtools_version(),
+                                 arg_list ? "CL": NULL,
+                                 arg_list ? arg_list : NULL,
+                                 NULL)) {
+        print_error("collate", "failed to add PG line to header of \"%s\"", output_file);
+        goto fail;
+    }
+
+    if (sam_hdr_write(fpw, h) < 0) {
+        print_error_errno("collate", "Couldn't write header");
+        goto fail;
+    }
+
+    fnt = (char**)calloc(n_files, sizeof(char*));
+    if (!fnt) goto mem_fail;
+    fpt = (samFile**)calloc(n_files, sizeof(samFile*));
+    if (!fpt) goto mem_fail;
+    cnt = (int64_t*)calloc(n_files, 8);
+    if (!cnt) goto mem_fail;
+
+    for (i = counter = 0; i < n_files; ++i) {
+        fnt[i] = (char*)calloc(l + 20, 1);
+        if (!fnt[i]) goto mem_fail;
+        do {
+            sprintf(fnt[i], "%s.%04d.bam", pre, counter++);
+            fpt[i] = sam_open(fnt[i], "wxb1");
+        } while (!fpt[i] && errno == EEXIST);
+        if (fpt[i] == NULL) {
+            print_error_errno("collate", "Cannot open intermediate file \"%s\"", fnt[i]);
+            goto fail;
+        }
+        if (p.pool) hts_set_opt(fpt[i], HTS_OPT_THREAD_POOL, &p);
+        if (sam_hdr_write(fpt[i], h) < 0) {
+            print_error_errno("collate", "Couldn't write header to intermediate file \"%s\"", fnt[i]);
+            goto fail;
+        }
+    }
+
+    if (fast) {
+        khash_t(bam_store) *stored = kh_init(bam_store);
+        khiter_t itr;
+        bam_list_t list;
+        int err = 0;
+        if (!stored) goto mem_fail;
+
+        if (store_max < 2) store_max = 2;
+
+        if (create_bam_list(&list, store_max)) {
+            fprintf(samtools_stderr, "[collate[ ERROR: unable to create bam list.\n");
+            err = 1;
+            goto fast_fail;
+        }
+
+        while ((r = sam_read1(fp, h, list.items[list.index].b)) >= 0) {
+            int ret;
+            bam1_t *b = list.items[list.index].b;
+            int readflag = b->core.flag & (BAM_FREAD1 | BAM_FREAD2);
+
+            // strictly paired reads only
+            if (!(b->core.flag & (BAM_FSECONDARY | BAM_FSUPPLEMENTARY)) && (readflag == BAM_FREAD1 || readflag == BAM_FREAD2)) {
+
+                itr = kh_get(bam_store, stored, bam_get_qname(b));
+
+                if (itr == kh_end(stored)) {
+                    // new read
+                    itr = kh_put(bam_store, stored, bam_get_qname(b), &ret);
+
+                    if (ret > 0) { // okay to go ahead store it
+                        kh_value(stored, itr).bi = store_bam(&list);
+
+                        // see if the next one on the list needs to be written out
+                        if (write_bam_needed(&list)) {
+                            if (write_to_bin_file(list.items[list.index].b, cnt, fpt, fnt, h, n_files) < 0) {
+                                fprintf(samtools_stderr, "[collate] ERROR: could not write line.\n");
+                                err = 1;
+                                goto fast_fail;
+                            } else {
+                                mark_bam_as_written(&list);
+
+                                itr = kh_get(bam_store, stored, bam_get_qname(list.items[list.index].b));
+
+                                if (itr != kh_end(stored)) {
+                                    kh_del(bam_store, stored, itr);
+                                } else {
+                                    fprintf(samtools_stderr, "[collate] ERROR: stored value not in hash.\n");
+                                    err = 1;
+                                    goto fast_fail;
+                                }
+                            }
+                        }
+                    } else if (ret == 0) {
+                        fprintf(samtools_stderr, "[collate] ERROR: value already in hash.\n");
+                        err = 1;
+                        goto fast_fail;
+                    } else {
+                        fprintf(samtools_stderr, "[collate] ERROR: unable to store in hash.\n");
+                        err = 1;
+                        goto fast_fail;
+                    }
+                } else { // we have a match
+                    // write out the reads in R1 R2 order
+                    bam1_t *r1, *r2;
+
+                    if (b->core.flag & BAM_FREAD1) {
+                        r1 = b;
+                        r2 = kh_value(stored, itr).bi->b;
+                    } else {
+                        r1 = kh_value(stored, itr).bi->b;
+                        r2 = b;
+                    }
+
+                    if (sam_write1(fpw, h, r1) < 0) {
+                        fprintf(samtools_stderr, "[collate] ERROR: could not write r1 alignment.\n");
+                        err = 1;
+                        goto fast_fail;
+                    }
+
+                    if (sam_write1(fpw, h, r2) < 0) {
+                        fprintf(samtools_stderr, "[collate] ERROR: could not write r2 alignment.\n");
+                        err = 1;
+                        goto fast_fail;
+                    }
+
+                    mark_bam_as_written(&list);
+
+                    // remove stored read
+                    kh_value(stored, itr).bi->written = 1;
+                    kh_del(bam_store, stored, itr);
+                }
+            }
+        }
+
+        for (list.index = 0; list.index < list.size; list.index++) {
+            if (write_bam_needed(&list)) {
+                bam1_t *b = list.items[list.index].b;
+
+                if (write_to_bin_file(b, cnt, fpt, fnt, h, n_files)) {
+                    err = 1;
+                    goto fast_fail;
+                } else {
+                    itr = kh_get(bam_store, stored, bam_get_qname(b));
+                    kh_del(bam_store, stored, itr);
+                }
+            }
+        }
+
+ fast_fail:
+        if (err) {
+            for (itr = kh_begin(stored); itr != kh_end(stored); ++itr) {
+                if (kh_exist(stored, itr)) {
+                    kh_del(bam_store, stored, itr);
+                }
+            }
+
+            kh_destroy(bam_store, stored);
+            destroy_bam_list(&list);
+            goto fail;
+        } else {
+            kh_destroy(bam_store, stored);
+            destroy_bam_list(&list);
+        }
+
+    } else {
+        b = bam_init1();
+        if (!b) goto mem_fail;
+
+        while ((r = sam_read1(fp, h, b)) >= 0) {
+            if (write_to_bin_file(b, cnt, fpt, fnt, h, n_files)) {
+                bam_destroy1(b);
+                goto fail;
+            }
+        }
+
+        bam_destroy1(b);
+    }
+
+    if (r < -1) {
+        fprintf(samtools_stderr, "Error reading input file\n");
+        goto fail;
+    }
+    for (i = 0; i < n_files; ++i) {
+        // Close split output
+        r = sam_close(fpt[i]);
+        fpt[i] = NULL;
+        if (r < 0) {
+            fprintf(samtools_stderr, "Error on closing '%s'\n", fnt[i]);
+            return 1;
+        }
+
+        // Find biggest count
+        if (max_cnt < cnt[i]) max_cnt = cnt[i];
+    }
+    free(fpt);
+    fpt = NULL;
+    sam_close(fp);
+    fp = NULL;
+
+    // merge
+    a = malloc(max_cnt * sizeof(elem_t));
+    if (!a) goto mem_fail;
+    for (j = 0; j < max_cnt; ++j) {
+        a[j].b = bam_init1();
+        if (!a[j].b) { max_cnt = j; goto mem_fail; }
+    }
+
+    for (i = 0; i < n_files; ++i) {
+        int64_t c = cnt[i];
+        fp = sam_open_format(fnt[i], "r", &ga->in);
+        if (NULL == fp) {
+            print_error_errno("collate", "Couldn't open \"%s\"", fnt[i]);
+            goto fail;
+        }
+        if (p.pool) hts_set_opt(fp, HTS_OPT_THREAD_POOL, &p);
+        sam_hdr_destroy(sam_hdr_read(fp)); // Skip over header
+
+        // Slurp in one of the split files
+        for (j = 0; j < c; ++j) {
+            if (sam_read1(fp, h, a[j].b) < 0) {
+                fprintf(samtools_stderr, "Error reading '%s'\n", fnt[i]);
+                goto fail;
+            }
+            a[j].key = hash_X31_Wang(bam_get_qname(a[j].b));
+        }
+        sam_close(fp);
+        unlink(fnt[i]);
+        free(fnt[i]);
+        fnt[i] = NULL;
+
+        ks_introsort(bamshuf, c, a); // Shuffle all the reads
+
+        // Write them out again
+        for (j = 0; j < c; ++j) {
+            if (sam_write1(fpw, h, a[j].b) < 0) {
+                print_error_errno("collate", "Error writing to output");
+                goto fail;
+            }
+        }
+    }
+
+    sam_hdr_destroy(h);
+    for (j = 0; j < max_cnt; ++j) bam_destroy1(a[j].b);
+    free(a); free(fnt); free(cnt);
+    sam_global_args_free(ga);
+    if (sam_close(fpw) < 0) {
+        fprintf(samtools_stderr, "Error on closing output\n");
+        return 1;
+    }
+
+    if (p.pool) hts_tpool_destroy(p.pool);
+    return 0;
+
+ mem_fail:
+    fprintf(samtools_stderr, "Out of memory\n");
+
+ fail:
+    if (fp) sam_close(fp);
+    if (fpw) sam_close(fpw);
+    if (h) sam_hdr_destroy(h);
+    for (i = 0; i < n_files; ++i) {
+        if (fnt) free(fnt[i]);
+        if (fpt && fpt[i]) sam_close(fpt[i]);
+    }
+    if (a) {
+        for (j = 0; j < max_cnt; ++j) bam_destroy1(a[j].b);
+        free(a);
+    }
+    free(fnt);
+    free(fpt);
+    free(cnt);
+    if (p.pool) hts_tpool_destroy(p.pool);
+    sam_global_args_free(ga);
+    return 1;
+}
+
+static int usage(FILE *fp, int n_files, int reads_store) {
+    fprintf(fp,
+            "Usage: samtools collate [-Ou] [-o <name>] [-n nFiles] [-l cLevel] <in.bam> [<prefix>]\n\n"
+            "Options:\n"
+            "      -O       output to samtools_stdout\n"
+            "      -o       output file name (use prefix if not set)\n"
+            "      -u       uncompressed BAM output\n"
+            "      -f       fast (only primary alignments)\n"
+            "      -r       working reads stored (with -f) [%d]\n" // reads_store
+            "      -l INT   compression level [%d]\n" // DEF_CLEVEL
+            "      -n INT   number of temporary files [%d]\n" // n_files
+            "      --no-PG  do not add a PG line\n",
+            reads_store, DEF_CLEVEL, n_files);
+
+    sam_global_opt_help(fp, "-....@-.");
+    fprintf(fp,
+            "  <prefix> is required unless the -o or -O options are used.\n");
+
+    return 1;
+}
+
+char * generate_prefix() {
+    char *prefix;
+    unsigned int pid = getpid();
+#ifdef _WIN32
+#  define PREFIX_LEN (MAX_PATH + 16)
+    DWORD ret;
+    prefix = calloc(PREFIX_LEN, sizeof(*prefix));
+    if (!prefix) {
+        perror("collate");
+        return NULL;
+    }
+    ret = GetTempPathA(MAX_PATH, prefix);
+    if (ret > MAX_PATH || ret == 0) {
+        fprintf(samtools_stderr,
+                "[E::collate] Couldn't get path for temporary files.\n");
+        free(prefix);
+        return NULL;
+    }
+    snprintf(prefix + ret, PREFIX_LEN - ret, "\\%x", pid);
+    return prefix;
+#else
+#  define PREFIX_LEN 64
+    prefix = malloc(PREFIX_LEN);
+    if (!prefix) {
+        perror("collate");
+        return NULL;
+    }
+    snprintf(prefix, PREFIX_LEN, "/tmp/collate%x", pid);
+    return prefix;
+#endif
+}
+
+int main_bamshuf(int argc, char *argv[])
+{
+    int c, n_files = 64, clevel = DEF_CLEVEL, is_stdout = 0, is_un = 0, fast_coll = 0, reads_store = 10000, ret, pre_mem = 0, no_pg = 0;
+    const char *output_file = NULL;
+    char *prefix = NULL, *arg_list = NULL;
+    sam_global_args ga = SAM_GLOBAL_ARGS_INIT;
+    static const struct option lopts[] = {
+        SAM_OPT_GLOBAL_OPTIONS('-', 0, 0, 0, 0, '@'),
+        {"no-PG", no_argument, NULL, 1},
+        { NULL, 0, NULL, 0 }
+    };
+
+    while ((c = getopt_long(argc, argv, "n:l:uOo:@:fr:", lopts, NULL)) >= 0) {
+        switch (c) {
+        case 'n': n_files = atoi(optarg); break;
+        case 'l': clevel = atoi(optarg); break;
+        case 'u': is_un = 1; break;
+        case 'O': is_stdout = 1; break;
+        case 'o': output_file = optarg; break;
+        case 'f': fast_coll = 1; break;
+        case 'r': reads_store = atoi(optarg); break;
+        case 1: no_pg = 1; break;
+        default:  if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break;
+                  /* else fall-through */
+        case '?': return usage(samtools_stderr, n_files, reads_store);
+        }
+    }
+    if (is_un) clevel = 0;
+    if (argc >= optind + 2) prefix = argv[optind+1];
+    if (!(prefix || is_stdout || output_file))
+        return usage(samtools_stderr, n_files, reads_store);
+    if (is_stdout && output_file) {
+        fprintf(samtools_stderr, "collate: -o and -O options cannot be used together.\n");
+        return usage(samtools_stderr, n_files, reads_store);
+    }
+    if (!prefix) {
+        prefix = generate_prefix();
+        pre_mem = 1;
+    }
+
+    if (!prefix) return EXIT_FAILURE;
+
+    if (!no_pg && !(arg_list = stringify_argv(argc+1, argv-1))) {
+        print_error("collate", "failed to create arg_list");
+        return 1;
+    }
+
+    ret = bamshuf(argv[optind], n_files, prefix, clevel, is_stdout,
+                   output_file, fast_coll, reads_store, &ga, arg_list, no_pg);
+
+    if (pre_mem) free(prefix);
+    free(arg_list);
+
+    return ret;
+}
diff --git a/samtools/bamtk.c b/samtools/bamtk.c
new file mode 100644
index 0000000..e690c1d
--- /dev/null
+++ b/samtools/bamtk.c
@@ -0,0 +1,301 @@
+/*  bamtk.c -- main samtools command front-end.
+
+    Copyright (C) 2008-2022 Genome Research Ltd.
+
+    Author: Heng Li <lh3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <config.h>
+
+#include <stdio.h>
+#include <unistd.h>
+#include <fcntl.h>
+#include <string.h>
+
+#include "htslib/hts.h"
+#include "htslib/hfile.h"
+#include "samtools.h"
+#include "version.h"
+
+int bam_taf2baf(int argc, char *argv[]);
+int bam_mpileup(int argc, char *argv[]);
+int bam_merge(int argc, char *argv[]);
+int bam_index(int argc, char *argv[]);
+int bam_sort(int argc, char *argv[]);
+int bam_tview_main(int argc, char *argv[]);
+int bam_mating(int argc, char *argv[]);
+int bam_rmdup(int argc, char *argv[]);
+int bam_flagstat(int argc, char *argv[]);
+int bam_fillmd(int argc, char *argv[]);
+int bam_idxstats(int argc, char *argv[]);
+int bam_markdup(int argc, char *argv[]);
+int main_samview(int argc, char *argv[]);
+int main_head(int argc, char *argv[]);
+int main_reheader(int argc, char *argv[]);
+int main_cut_target(int argc, char *argv[]);
+int main_phase(int argc, char *argv[]);
+int main_cat(int argc, char *argv[]);
+int main_depth(int argc, char *argv[]);
+int main_coverage(int argc, char *argv[]);
+int main_bam2fq(int argc, char *argv[]);
+int main_pad2unpad(int argc, char *argv[]);
+int main_bedcov(int argc, char *argv[]);
+int main_bamshuf(int argc, char *argv[]);
+int main_stats(int argc, char *argv[]);
+int main_flags(int argc, char *argv[]);
+int main_split(int argc, char *argv[]);
+int main_quickcheck(int argc, char *argv[]);
+int main_addreplacerg(int argc, char *argv[]);
+int faidx_main(int argc, char *argv[]);
+int dict_main(int argc, char *argv[]);
+int fqidx_main(int argc, char *argv[]);
+int amplicon_clip_main(int argc, char *argv[]);
+int main_ampliconstats(int argc, char *argv[]);
+int main_import(int argc, char *argv[]);
+int main_samples(int argc, char *argv[]);
+int main_consensus(int argc, char *argv[]);
+int main_reference(int argc, char *argv[]);
+
+const char *samtools_version()
+{
+    return SAMTOOLS_VERSION;
+}
+
+// These come out of the config.h file built by autoconf or Makefile
+const char *samtools_feature_string(void) {
+    const char *fmt =
+
+#ifdef PACKAGE_URL
+    "build=configure "
+#else
+    "build=Makefile "
+#endif
+
+#ifdef HAVE_CURSES
+    "curses=yes "
+#else
+    "curses=no "
+#endif
+    ;
+
+    return fmt;
+}
+
+static void long_version(void) {
+    printf("samtools %s\n"
+           "Using htslib %s\n"
+           "Copyright (C) 2022 Genome Research Ltd.\n",
+           samtools_version(), hts_version());
+
+    printf("\nSamtools compilation details:\n");
+    printf("    Features:       %s\n", samtools_feature_string());
+    printf("    CC:             %s\n", SAMTOOLS_CC);
+    printf("    CPPFLAGS:       %s\n", SAMTOOLS_CPPFLAGS);
+    printf("    CFLAGS:         %s\n", SAMTOOLS_CFLAGS);
+    printf("    LDFLAGS:        %s\n", SAMTOOLS_LDFLAGS);
+    printf("    HTSDIR:         %s\n", SAMTOOLS_HTSDIR);
+    printf("    LIBS:           %s\n", SAMTOOLS_LIBS);
+    printf("    CURSES_LIB:     %s\n", SAMTOOLS_CURSES_LIB);
+
+    printf("\nHTSlib compilation details:\n");
+    printf("    Features:       %s\n", hts_feature_string());
+    printf("    CC:             %s\n", hts_test_feature(HTS_FEATURE_CC));
+    printf("    CPPFLAGS:       %s\n", hts_test_feature(HTS_FEATURE_CPPFLAGS));
+    printf("    CFLAGS:         %s\n", hts_test_feature(HTS_FEATURE_CFLAGS));
+    printf("    LDFLAGS:        %s\n", hts_test_feature(HTS_FEATURE_LDFLAGS));
+
+    // Plugins and schemes
+    printf("\nHTSlib URL scheme handlers present:\n");
+    const char *plugins[100];
+    int np = 100, i, j;
+
+    if (hfile_list_plugins(plugins, &np) < 0)
+        return;
+
+    for (i = 0; i < np; i++) {
+        const char *sc_list[100];
+        int nschemes = 100;
+        if (hfile_list_schemes(plugins[i], sc_list, &nschemes) < 0)
+            return;
+
+        printf("    %s:\t", plugins[i]);
+        for (j = 0; j < nschemes; j++)
+            printf(" %s%c", sc_list[j], ",\n"[j+1==nschemes]);
+    }
+}
+
+static void usage(FILE *fp)
+{
+    /* Please improve the grouping */
+
+    fprintf(fp,
+"\n"
+"Program: samtools (Tools for alignments in the SAM format)\n"
+"Version: %s (using htslib %s)\n\n", samtools_version(), hts_version());
+    fprintf(fp,
+"Usage:   samtools <command> [options]\n"
+"\n"
+"Commands:\n"
+"  -- Indexing\n"
+"     dict           create a sequence dictionary file\n"
+"     faidx          index/extract FASTA\n"
+"     fqidx          index/extract FASTQ\n"
+"     index          index alignment\n"
+"\n"
+"  -- Editing\n"
+"     calmd          recalculate MD/NM tags and '=' bases\n"
+"     fixmate        fix mate information\n"
+"     reheader       replace BAM header\n"
+"     targetcut      cut fosmid regions (for fosmid pool only)\n"
+"     addreplacerg   adds or replaces RG tags\n"
+"     markdup        mark duplicates\n"
+"     ampliconclip   clip oligos from the end of reads\n"
+"\n"
+"  -- File operations\n"
+"     collate        shuffle and group alignments by name\n"
+"     cat            concatenate BAMs\n"
+"     consensus      produce a consensus Pileup/FASTA/FASTQ\n"
+"     merge          merge sorted alignments\n"
+"     mpileup        multi-way pileup\n"
+"     sort           sort alignment file\n"
+"     split          splits a file by read group\n"
+"     quickcheck     quickly check if SAM/BAM/CRAM file appears intact\n"
+"     fastq          converts a BAM to a FASTQ\n"
+"     fasta          converts a BAM to a FASTA\n"
+"     import         Converts FASTA or FASTQ files to SAM/BAM/CRAM\n"
+"     reference      Generates a reference from aligned data\n"
+"\n"
+"  -- Statistics\n"
+"     bedcov         read depth per BED region\n"
+"     coverage       alignment depth and percent coverage\n"
+"     depth          compute the depth\n"
+"     flagstat       simple stats\n"
+"     idxstats       BAM index stats\n"
+"     phase          phase heterozygotes\n"
+"     stats          generate stats (former bamcheck)\n"
+"     ampliconstats  generate amplicon specific stats\n"
+"\n"
+"  -- Viewing\n"
+"     flags          explain BAM flags\n"
+"     head           header viewer\n"
+"     tview          text alignment viewer\n"
+"     view           SAM<->BAM<->CRAM conversion\n"
+"     depad          convert padded BAM to unpadded BAM\n"
+"     samples        list the samples in a set of SAM/BAM/CRAM files\n"
+"\n"
+"  -- Misc\n"
+"     help [cmd]     display this help message or help for [cmd]\n"
+"     version        detailed version information\n"
+"\n");
+}
+
+// This is a tricky one, but on Windows the filename wildcard expansion is done by
+// the application and not by the shell, as traditionally it never had a "shell".
+// Even now, DOS and Powershell do not do this expansion (but bash does).
+//
+// This means that Mingw/Msys implements code before main() that takes e.g. "*" and
+// expands it up to a list of matching filenames.  This in turn breaks things like
+// specifying "*" as a region (all the unmapped reads).  We take a hard line here -
+// filename expansion is the task of the shell, not our application!
+#ifdef _WIN32
+int _CRT_glob = 0;
+#endif
+
+int main(int argc, char *argv[])
+{
+#ifdef _WIN32
+    setmode(fileno(stdout), O_BINARY);
+    setmode(fileno(stdin),  O_BINARY);
+#endif
+    if (argc < 2) { usage(stderr); return 1; }
+
+    if (strcmp(argv[1], "help") == 0 || strcmp(argv[1], "--help") == 0) {
+        if (argc == 2) { usage(stdout); return 0; }
+
+        // Otherwise change "samtools help COMMAND [...]" to "samtools COMMAND";
+        // main_xyz() functions by convention display the subcommand's usage
+        // when invoked without any arguments.
+        argv++;
+        argc = 2;
+    }
+
+    int ret = 0;
+    if (strcmp(argv[1], "view") == 0)           ret = main_samview(argc-1, argv+1);
+    else if (strcmp(argv[1], "import") == 0)    ret = main_import(argc-1, argv+1);
+    else if (strcmp(argv[1], "mpileup") == 0)   ret = bam_mpileup(argc-1, argv+1);
+    else if (strcmp(argv[1], "merge") == 0)     ret = bam_merge(argc-1, argv+1);
+    else if (strcmp(argv[1], "sort") == 0)      ret = bam_sort(argc-1, argv+1);
+    else if (strcmp(argv[1], "index") == 0)     ret = bam_index(argc-1, argv+1);
+    else if (strcmp(argv[1], "idxstat") == 0 ||
+             strcmp(argv[1], "idxstats") == 0)  ret = bam_idxstats(argc-1, argv+1);
+    else if (strcmp(argv[1], "faidx") == 0)     ret = faidx_main(argc-1, argv+1);
+    else if (strcmp(argv[1], "fqidx") == 0)     ret = fqidx_main(argc-1, argv+1);
+    else if (strcmp(argv[1], "dict") == 0)      ret = dict_main(argc-1, argv+1);
+    else if (strcmp(argv[1], "head") == 0)      ret = main_head(argc-1, argv+1);
+    else if (strcmp(argv[1], "fixmate") == 0)   ret = bam_mating(argc-1, argv+1);
+    else if (strcmp(argv[1], "rmdup") == 0)     ret = bam_rmdup(argc-1, argv+1);
+    else if (strcmp(argv[1], "markdup") == 0)   ret = bam_markdup(argc-1, argv+1);
+    else if (strcmp(argv[1], "ampliconclip") == 0) ret = amplicon_clip_main(argc-1, argv+1);
+    else if (strcmp(argv[1], "flagstat") == 0 ||
+             strcmp(argv[1], "flagstats") == 0) ret = bam_flagstat(argc-1, argv+1);
+    else if (strcmp(argv[1], "calmd") == 0)     ret = bam_fillmd(argc-1, argv+1);
+    else if (strcmp(argv[1], "fillmd") == 0)    ret = bam_fillmd(argc-1, argv+1);
+    else if (strcmp(argv[1], "reheader") == 0)  ret = main_reheader(argc-1, argv+1);
+    else if (strcmp(argv[1], "cat") == 0)       ret = main_cat(argc-1, argv+1);
+    else if (strcmp(argv[1], "targetcut") == 0) ret = main_cut_target(argc-1, argv+1);
+    else if (strcmp(argv[1], "phase") == 0)     ret = main_phase(argc-1, argv+1);
+    else if (strcmp(argv[1], "depth") == 0)     ret = main_depth(argc-1, argv+1);
+    else if (strcmp(argv[1], "coverage") == 0)  ret = main_coverage(argc-1, argv+1);
+    else if (strcmp(argv[1], "bam2fq") == 0 ||
+             strcmp(argv[1], "fastq") == 0 ||
+             strcmp(argv[1], "fasta") == 0)     ret = main_bam2fq(argc-1, argv+1);
+    else if (strcmp(argv[1], "pad2unpad") == 0) ret = main_pad2unpad(argc-1, argv+1);
+    else if (strcmp(argv[1], "depad") == 0)     ret = main_pad2unpad(argc-1, argv+1);
+    else if (strcmp(argv[1], "bedcov") == 0)    ret = main_bedcov(argc-1, argv+1);
+    else if (strcmp(argv[1], "bamshuf") == 0)   ret = main_bamshuf(argc-1, argv+1);
+    else if (strcmp(argv[1], "collate") == 0)   ret = main_bamshuf(argc-1, argv+1);
+    else if (strcmp(argv[1], "stat") == 0 ||
+             strcmp(argv[1], "stats") == 0)     ret = main_stats(argc-1, argv+1);
+    else if (strcmp(argv[1], "flag") == 0 ||
+             strcmp(argv[1], "flags") == 0)     ret = main_flags(argc-1, argv+1);
+    else if (strcmp(argv[1], "split") == 0)     ret = main_split(argc-1, argv+1);
+    else if (strcmp(argv[1], "quickcheck") == 0)  ret = main_quickcheck(argc-1, argv+1);
+    else if (strcmp(argv[1], "addreplacerg") == 0) ret = main_addreplacerg(argc-1, argv+1);
+    else if (strcmp(argv[1], "pileup") == 0) {
+        fprintf(stderr, "[main] The `pileup' command has been removed. Please use `mpileup' instead.\n");
+        return 1;
+    }
+    else if (strcmp(argv[1], "tview") == 0)   ret = bam_tview_main(argc-1, argv+1);
+    else if (strcmp(argv[1], "ampliconstats") == 0)     ret = main_ampliconstats(argc-1, argv+1);
+    else if (strcmp(argv[1], "samples") == 0)     ret = main_samples(argc-1, argv+1);
+    else if (strcmp(argv[1], "consensus") == 0) ret = main_consensus(argc-1, argv+1);
+    else if (strcmp(argv[1], "reference") == 0) ret = main_reference(argc-1, argv+1);
+    else if (strcmp(argv[1], "version") == 0 || \
+             strcmp(argv[1], "--version") == 0)
+        long_version();
+    else if (strcmp(argv[1], "--version-only") == 0) {
+        printf("%s+htslib-%s\n", samtools_version(), hts_version());
+    }
+    else {
+        fprintf(stderr, "[main] unrecognized command '%s'\n", argv[1]);
+        return 1;
+    }
+    return ret;
+}
diff --git a/samtools/bamtk.c.pysam.c b/samtools/bamtk.c.pysam.c
new file mode 100644
index 0000000..b798658
--- /dev/null
+++ b/samtools/bamtk.c.pysam.c
@@ -0,0 +1,304 @@
+#include "samtools.pysam.h"
+
+/*  bamtk.c -- main samtools command front-end.
+
+    Copyright (C) 2008-2022 Genome Research Ltd.
+
+    Author: Heng Li <lh3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <config.h>
+
+#include <stdio.h>
+#include <unistd.h>
+#include <fcntl.h>
+#include <string.h>
+
+#include "htslib/hts.h"
+#include "htslib/hfile.h"
+#include "samtools.h"
+#include "version.h"
+#include "samtools_config_vars.h"
+
+int bam_taf2baf(int argc, char *argv[]);
+int bam_mpileup(int argc, char *argv[]);
+int bam_merge(int argc, char *argv[]);
+int bam_index(int argc, char *argv[]);
+int bam_sort(int argc, char *argv[]);
+int bam_tview_main(int argc, char *argv[]);
+int bam_mating(int argc, char *argv[]);
+int bam_rmdup(int argc, char *argv[]);
+int bam_flagstat(int argc, char *argv[]);
+int bam_fillmd(int argc, char *argv[]);
+int bam_idxstats(int argc, char *argv[]);
+int bam_markdup(int argc, char *argv[]);
+int main_samview(int argc, char *argv[]);
+int main_head(int argc, char *argv[]);
+int main_reheader(int argc, char *argv[]);
+int main_cut_target(int argc, char *argv[]);
+int main_phase(int argc, char *argv[]);
+int main_cat(int argc, char *argv[]);
+int main_depth(int argc, char *argv[]);
+int main_coverage(int argc, char *argv[]);
+int main_bam2fq(int argc, char *argv[]);
+int main_pad2unpad(int argc, char *argv[]);
+int main_bedcov(int argc, char *argv[]);
+int main_bamshuf(int argc, char *argv[]);
+int main_stats(int argc, char *argv[]);
+int main_flags(int argc, char *argv[]);
+int main_split(int argc, char *argv[]);
+int main_quickcheck(int argc, char *argv[]);
+int main_addreplacerg(int argc, char *argv[]);
+int faidx_main(int argc, char *argv[]);
+int dict_main(int argc, char *argv[]);
+int fqidx_main(int argc, char *argv[]);
+int amplicon_clip_main(int argc, char *argv[]);
+int main_ampliconstats(int argc, char *argv[]);
+int main_import(int argc, char *argv[]);
+int main_samples(int argc, char *argv[]);
+int main_consensus(int argc, char *argv[]);
+int main_reference(int argc, char *argv[]);
+
+const char *samtools_version()
+{
+    return SAMTOOLS_VERSION;
+}
+
+// These come out of the config.h file built by autoconf or Makefile
+const char *samtools_feature_string(void) {
+    const char *fmt =
+
+#ifdef PACKAGE_URL
+    "build=configure "
+#else
+    "build=Makefile "
+#endif
+
+#ifdef HAVE_CURSES
+    "curses=yes "
+#else
+    "curses=no "
+#endif
+    ;
+
+    return fmt;
+}
+
+static void long_version(void) {
+    fprintf(samtools_stdout, "samtools %s\n"
+           "Using htslib %s\n"
+           "Copyright (C) 2022 Genome Research Ltd.\n",
+           samtools_version(), hts_version());
+
+    fprintf(samtools_stdout, "\nSamtools compilation details:\n");
+    fprintf(samtools_stdout, "    Features:       %s\n", samtools_feature_string());
+    fprintf(samtools_stdout, "    CC:             %s\n", SAMTOOLS_CC);
+    fprintf(samtools_stdout, "    CPPFLAGS:       %s\n", SAMTOOLS_CPPFLAGS);
+    fprintf(samtools_stdout, "    CFLAGS:         %s\n", SAMTOOLS_CFLAGS);
+    fprintf(samtools_stdout, "    LDFLAGS:        %s\n", SAMTOOLS_LDFLAGS);
+    fprintf(samtools_stdout, "    HTSDIR:         %s\n", SAMTOOLS_HTSDIR);
+    fprintf(samtools_stdout, "    LIBS:           %s\n", SAMTOOLS_LIBS);
+    fprintf(samtools_stdout, "    CURSES_LIB:     %s\n", SAMTOOLS_CURSES_LIB);
+
+    fprintf(samtools_stdout, "\nHTSlib compilation details:\n");
+    fprintf(samtools_stdout, "    Features:       %s\n", hts_feature_string());
+    fprintf(samtools_stdout, "    CC:             %s\n", hts_test_feature(HTS_FEATURE_CC));
+    fprintf(samtools_stdout, "    CPPFLAGS:       %s\n", hts_test_feature(HTS_FEATURE_CPPFLAGS));
+    fprintf(samtools_stdout, "    CFLAGS:         %s\n", hts_test_feature(HTS_FEATURE_CFLAGS));
+    fprintf(samtools_stdout, "    LDFLAGS:        %s\n", hts_test_feature(HTS_FEATURE_LDFLAGS));
+
+    // Plugins and schemes
+    fprintf(samtools_stdout, "\nHTSlib URL scheme handlers present:\n");
+    const char *plugins[100];
+    int np = 100, i, j;
+
+    if (hfile_list_plugins(plugins, &np) < 0)
+        return;
+
+    for (i = 0; i < np; i++) {
+        const char *sc_list[100];
+        int nschemes = 100;
+        if (hfile_list_schemes(plugins[i], sc_list, &nschemes) < 0)
+            return;
+
+        fprintf(samtools_stdout, "    %s:\t", plugins[i]);
+        for (j = 0; j < nschemes; j++)
+            fprintf(samtools_stdout, " %s%c", sc_list[j], ",\n"[j+1==nschemes]);
+    }
+}
+
+static void usage(FILE *fp)
+{
+    /* Please improve the grouping */
+
+    fprintf(fp,
+"\n"
+"Program: samtools (Tools for alignments in the SAM format)\n"
+"Version: %s (using htslib %s)\n\n", samtools_version(), hts_version());
+    fprintf(fp,
+"Usage:   samtools <command> [options]\n"
+"\n"
+"Commands:\n"
+"  -- Indexing\n"
+"     dict           create a sequence dictionary file\n"
+"     faidx          index/extract FASTA\n"
+"     fqidx          index/extract FASTQ\n"
+"     index          index alignment\n"
+"\n"
+"  -- Editing\n"
+"     calmd          recalculate MD/NM tags and '=' bases\n"
+"     fixmate        fix mate information\n"
+"     reheader       replace BAM header\n"
+"     targetcut      cut fosmid regions (for fosmid pool only)\n"
+"     addreplacerg   adds or replaces RG tags\n"
+"     markdup        mark duplicates\n"
+"     ampliconclip   clip oligos from the end of reads\n"
+"\n"
+"  -- File operations\n"
+"     collate        shuffle and group alignments by name\n"
+"     cat            concatenate BAMs\n"
+"     consensus      produce a consensus Pileup/FASTA/FASTQ\n"
+"     merge          merge sorted alignments\n"
+"     mpileup        multi-way pileup\n"
+"     sort           sort alignment file\n"
+"     split          splits a file by read group\n"
+"     quickcheck     quickly check if SAM/BAM/CRAM file appears intact\n"
+"     fastq          converts a BAM to a FASTQ\n"
+"     fasta          converts a BAM to a FASTA\n"
+"     import         Converts FASTA or FASTQ files to SAM/BAM/CRAM\n"
+"     reference      Generates a reference from aligned data\n"
+"\n"
+"  -- Statistics\n"
+"     bedcov         read depth per BED region\n"
+"     coverage       alignment depth and percent coverage\n"
+"     depth          compute the depth\n"
+"     flagstat       simple stats\n"
+"     idxstats       BAM index stats\n"
+"     phase          phase heterozygotes\n"
+"     stats          generate stats (former bamcheck)\n"
+"     ampliconstats  generate amplicon specific stats\n"
+"\n"
+"  -- Viewing\n"
+"     flags          explain BAM flags\n"
+"     head           header viewer\n"
+"     tview          text alignment viewer\n"
+"     view           SAM<->BAM<->CRAM conversion\n"
+"     depad          convert padded BAM to unpadded BAM\n"
+"     samples        list the samples in a set of SAM/BAM/CRAM files\n"
+"\n"
+"  -- Misc\n"
+"     help [cmd]     display this help message or help for [cmd]\n"
+"     version        detailed version information\n"
+"\n");
+}
+
+// This is a tricky one, but on Windows the filename wildcard expansion is done by
+// the application and not by the shell, as traditionally it never had a "shell".
+// Even now, DOS and Powershell do not do this expansion (but bash does).
+//
+// This means that Mingw/Msys implements code before main() that takes e.g. "*" and
+// expands it up to a list of matching filenames.  This in turn breaks things like
+// specifying "*" as a region (all the unmapped reads).  We take a hard line here -
+// filename expansion is the task of the shell, not our application!
+#ifdef _WIN32
+int _CRT_glob = 0;
+#endif
+
+int samtools_main(int argc, char *argv[])
+{
+#ifdef _WIN32
+    setmode(fileno(samtools_stdout), O_BINARY);
+    setmode(fileno(stdin),  O_BINARY);
+#endif
+    if (argc < 2) { usage(samtools_stderr); return 1; }
+
+    if (strcmp(argv[1], "help") == 0 || strcmp(argv[1], "--help") == 0) {
+        if (argc == 2) { usage(samtools_stdout); return 0; }
+
+        // Otherwise change "samtools help COMMAND [...]" to "samtools COMMAND";
+        // main_xyz() functions by convention display the subcommand's usage
+        // when invoked without any arguments.
+        argv++;
+        argc = 2;
+    }
+
+    int ret = 0;
+    if (strcmp(argv[1], "view") == 0)           ret = main_samview(argc-1, argv+1);
+    else if (strcmp(argv[1], "import") == 0)    ret = main_import(argc-1, argv+1);
+    else if (strcmp(argv[1], "mpileup") == 0)   ret = bam_mpileup(argc-1, argv+1);
+    else if (strcmp(argv[1], "merge") == 0)     ret = bam_merge(argc-1, argv+1);
+    else if (strcmp(argv[1], "sort") == 0)      ret = bam_sort(argc-1, argv+1);
+    else if (strcmp(argv[1], "index") == 0)     ret = bam_index(argc-1, argv+1);
+    else if (strcmp(argv[1], "idxstat") == 0 ||
+             strcmp(argv[1], "idxstats") == 0)  ret = bam_idxstats(argc-1, argv+1);
+    else if (strcmp(argv[1], "faidx") == 0)     ret = faidx_main(argc-1, argv+1);
+    else if (strcmp(argv[1], "fqidx") == 0)     ret = fqidx_main(argc-1, argv+1);
+    else if (strcmp(argv[1], "dict") == 0)      ret = dict_main(argc-1, argv+1);
+    else if (strcmp(argv[1], "head") == 0)      ret = main_head(argc-1, argv+1);
+    else if (strcmp(argv[1], "fixmate") == 0)   ret = bam_mating(argc-1, argv+1);
+    else if (strcmp(argv[1], "rmdup") == 0)     ret = bam_rmdup(argc-1, argv+1);
+    else if (strcmp(argv[1], "markdup") == 0)   ret = bam_markdup(argc-1, argv+1);
+    else if (strcmp(argv[1], "ampliconclip") == 0) ret = amplicon_clip_main(argc-1, argv+1);
+    else if (strcmp(argv[1], "flagstat") == 0 ||
+             strcmp(argv[1], "flagstats") == 0) ret = bam_flagstat(argc-1, argv+1);
+    else if (strcmp(argv[1], "calmd") == 0)     ret = bam_fillmd(argc-1, argv+1);
+    else if (strcmp(argv[1], "fillmd") == 0)    ret = bam_fillmd(argc-1, argv+1);
+    else if (strcmp(argv[1], "reheader") == 0)  ret = main_reheader(argc-1, argv+1);
+    else if (strcmp(argv[1], "cat") == 0)       ret = main_cat(argc-1, argv+1);
+    else if (strcmp(argv[1], "targetcut") == 0) ret = main_cut_target(argc-1, argv+1);
+    else if (strcmp(argv[1], "phase") == 0)     ret = main_phase(argc-1, argv+1);
+    else if (strcmp(argv[1], "depth") == 0)     ret = main_depth(argc-1, argv+1);
+    else if (strcmp(argv[1], "coverage") == 0)  ret = main_coverage(argc-1, argv+1);
+    else if (strcmp(argv[1], "bam2fq") == 0 ||
+             strcmp(argv[1], "fastq") == 0 ||
+             strcmp(argv[1], "fasta") == 0)     ret = main_bam2fq(argc-1, argv+1);
+    else if (strcmp(argv[1], "pad2unpad") == 0) ret = main_pad2unpad(argc-1, argv+1);
+    else if (strcmp(argv[1], "depad") == 0)     ret = main_pad2unpad(argc-1, argv+1);
+    else if (strcmp(argv[1], "bedcov") == 0)    ret = main_bedcov(argc-1, argv+1);
+    else if (strcmp(argv[1], "bamshuf") == 0)   ret = main_bamshuf(argc-1, argv+1);
+    else if (strcmp(argv[1], "collate") == 0)   ret = main_bamshuf(argc-1, argv+1);
+    else if (strcmp(argv[1], "stat") == 0 ||
+             strcmp(argv[1], "stats") == 0)     ret = main_stats(argc-1, argv+1);
+    else if (strcmp(argv[1], "flag") == 0 ||
+             strcmp(argv[1], "flags") == 0)     ret = main_flags(argc-1, argv+1);
+    else if (strcmp(argv[1], "split") == 0)     ret = main_split(argc-1, argv+1);
+    else if (strcmp(argv[1], "quickcheck") == 0)  ret = main_quickcheck(argc-1, argv+1);
+    else if (strcmp(argv[1], "addreplacerg") == 0) ret = main_addreplacerg(argc-1, argv+1);
+    else if (strcmp(argv[1], "pileup") == 0) {
+        fprintf(samtools_stderr, "[main] The `pileup' command has been removed. Please use `mpileup' instead.\n");
+        return 1;
+    }
+    //else if (strcmp(argv[1], "tview") == 0)   ret = bam_tview_main(argc-1, argv+1);
+    else if (strcmp(argv[1], "ampliconstats") == 0)     ret = main_ampliconstats(argc-1, argv+1);
+    else if (strcmp(argv[1], "samples") == 0)     ret = main_samples(argc-1, argv+1);
+    else if (strcmp(argv[1], "consensus") == 0) ret = main_consensus(argc-1, argv+1);
+    else if (strcmp(argv[1], "reference") == 0) ret = main_reference(argc-1, argv+1);
+    else if (strcmp(argv[1], "version") == 0 || \
+             strcmp(argv[1], "--version") == 0)
+        long_version();
+    else if (strcmp(argv[1], "--version-only") == 0) {
+        fprintf(samtools_stdout, "%s+htslib-%s\n", samtools_version(), hts_version());
+    }
+    else {
+        fprintf(samtools_stderr, "[main] unrecognized command '%s'\n", argv[1]);
+        return 1;
+    }
+    return ret;
+}
diff --git a/samtools/bedcov.c b/samtools/bedcov.c
new file mode 100644
index 0000000..1bd46a0
--- /dev/null
+++ b/samtools/bedcov.c
@@ -0,0 +1,298 @@
+/*  bedcov.c -- bedcov subcommand.
+
+    Copyright (C) 2012 Broad Institute.
+    Copyright (C) 2013-2014, 2018-2022 Genome Research Ltd.
+
+    Author: Heng Li <lh3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <config.h>
+
+#include <zlib.h>
+#include <stdio.h>
+#include <ctype.h>
+#include <stdlib.h>
+#include <string.h>
+#include <unistd.h>
+#include "htslib/kstring.h"
+#include "htslib/sam.h"
+#include "htslib/thread_pool.h"
+#include "samtools.h"
+#include "sam_opts.h"
+
+#include "htslib/kseq.h"
+KSTREAM_INIT(gzFile, gzread, 16384)
+
+#define DEFAULT_DEPTH 64000
+
+typedef struct {
+    htsFile *fp;
+    sam_hdr_t *header;
+    hts_itr_t *iter;
+    int min_mapQ;
+    uint32_t flags;  // read filtering flags
+    int64_t rcnt;
+} aux_t;
+
+static int read_bam(void *data, bam1_t *b)
+{
+    aux_t *aux = (aux_t*)data; // data in fact is a pointer to an auxiliary structure
+    int ret;
+    while (1)
+    {
+        ret = aux->iter? sam_itr_next(aux->fp, aux->iter, b) : sam_read1(aux->fp, aux->header, b);
+        if ( ret<0 ) break;
+        if ( b->core.flag & aux->flags ) continue;
+        if ( (int)b->core.qual < aux->min_mapQ ) continue;
+        break;
+    }
+    return ret;
+}
+
+static int incr_rcnt(void *data, const bam1_t *b, bam_pileup_cd *cd) {
+    aux_t *aux = (aux_t *)data;
+    aux->rcnt++;
+    return 0;
+}
+
+int main_bedcov(int argc, char *argv[])
+{
+    gzFile fp;
+    kstring_t str;
+    kstream_t *ks;
+    hts_idx_t **idx;
+    aux_t **aux;
+    int *n_plp, dret, i, j, m, n, c, ret, status = 0, min_mapQ = 0;
+    int skip_DN = 0, do_rcount = 0;
+    int64_t *cnt, *pcov = NULL;
+    const bam_pileup1_t **plp;
+    int usage = 0, has_index_file = 0;
+    uint32_t flags = (BAM_FUNMAP | BAM_FSECONDARY | BAM_FQCFAIL | BAM_FDUP);
+    int tflags = 0, min_depth = -1;
+
+    sam_global_args ga = SAM_GLOBAL_ARGS_INIT;
+    static const struct option lopts[] = {
+        {"min-MQ", required_argument, NULL, 'Q'},
+        {"min-mq", required_argument, NULL, 'Q'},
+        SAM_OPT_GLOBAL_OPTIONS('-', 0, '-', '-', 0, '-'),
+        { NULL, 0, NULL, 0 }
+    };
+
+    while ((c = getopt_long(argc, argv, "Q:Xg:G:jd:c", lopts, NULL)) >= 0) {
+        switch (c) {
+        case 'Q': min_mapQ = atoi(optarg); break;
+        case 'X': has_index_file = 1; break;
+        case 'c': do_rcount = 1; break;
+        case 'g':
+            tflags = bam_str2flag(optarg);
+            if (tflags < 0 || tflags > ((BAM_FSUPPLEMENTARY << 1) - 1)) {
+                print_error("bedcov", "Flag value \"%s\" is not supported", optarg);
+                return 1;
+            }
+            flags &= ~tflags;
+            break;
+        case 'G':
+            tflags = bam_str2flag(optarg);
+            if (tflags < 0 || tflags > ((BAM_FSUPPLEMENTARY << 1) - 1)) {
+                print_error("bedcov", "Flag value \"%s\" is not supported", optarg);
+                return 1;
+            }
+            flags |= tflags;
+            break;
+        case 'j': skip_DN = 1; break;
+        case 'd': min_depth = atoi(optarg); break;
+        default:  if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break;
+                  /* else fall-through */
+        case '?': usage = 1; break;
+        }
+        if (usage) break;
+    }
+    if (usage || optind + 2 > argc) {
+        fprintf(stderr, "Usage: samtools bedcov [options] <in.bed> <in1.bam> [...]\n\n");
+        fprintf(stderr, "Options:\n");
+        fprintf(stderr, "      -Q, --min-MQ <int>  mapping quality threshold [0]\n");
+        fprintf(stderr, "      -X                  use customized index files\n");
+        fprintf(stderr, "      -g <flags>          remove the specified flags from the set used to filter out reads\n");
+        fprintf(stderr, "      -G <flags>          add the specified flags to the set used to filter out reads\n"
+                        "                          The default set is UNMAP,SECONDARY,QCFAIL,DUP or 0x704\n");
+        fprintf(stderr, "      -j                  do not include deletions (D) and ref skips (N) in bedcov computation\n");
+        fprintf(stderr, "      -d <int>            depth threshold. Number of reference bases with coverage above and"
+                        "                          including this value will be displayed in a separate column\n");
+        fprintf(stderr, "      -c                  add an additional column showing read count\n");
+        sam_global_opt_help(stderr, "-.--.--.");
+        return 1;
+    }
+    if (has_index_file) {
+        if ((argc - optind - 1) % 2 != 0) { // Calculate # of input BAM files
+            fprintf(stderr, "ERROR: odd number of filenames detected! Each BAM file should have an index file\n");
+            return 1;
+        }
+        n = (argc - optind - 1) / 2;
+    } else {
+        n = argc - optind - 1;
+    }
+
+    memset(&str, 0, sizeof(kstring_t));
+    aux = calloc(n, sizeof(aux_t*));
+    idx = calloc(n, sizeof(hts_idx_t*));
+    for (i = 0; i < n; ++i) {
+        aux[i] = calloc(1, sizeof(aux_t));
+        aux[i]->min_mapQ = min_mapQ;
+        aux[i]->fp = sam_open_format(argv[i+optind+1], "r", &ga.in);
+        if (aux[i]->fp) {
+            // If index filename has not been specfied, look in BAM folder
+            if (has_index_file) {
+                idx[i] = sam_index_load2(aux[i]->fp, argv[i+optind+1], argv[i+optind+n+1]);
+            } else {
+                idx[i] = sam_index_load(aux[i]->fp, argv[i+optind+1]);
+            }
+        }
+        if (aux[i]->fp == 0 || idx[i] == 0) {
+            fprintf(stderr, "ERROR: fail to open index BAM file '%s'\n", argv[i+optind+1]);
+            return 2;
+        }
+        // TODO bgzf_set_cache_size(aux[i]->fp, 20);
+        aux[i]->header = sam_hdr_read(aux[i]->fp);
+        if (aux[i]->header == NULL) {
+            fprintf(stderr, "ERROR: failed to read header for '%s'\n",
+                    argv[i+optind+1]);
+            return 2;
+        }
+        aux[i]->flags = flags;
+    }
+    cnt = calloc(n, sizeof(*cnt));
+
+    if (min_depth >= 0) pcov = calloc(n, sizeof(*pcov));
+    if (!cnt || (min_depth >= 0 && !pcov)) {
+        print_error_errno("bedcov", "failed to allocate memory");
+        return 2;
+    }
+
+    fp = gzopen(argv[optind], "rb");
+    if (fp == NULL) {
+        print_error_errno("bedcov", "can't open BED file '%s'", argv[optind]);
+        return 2;
+    }
+    ks = ks_init(fp);
+    n_plp = calloc(n, sizeof(int));
+    plp = calloc(n, sizeof(bam_pileup1_t*));
+    while (ks_getuntil(ks, KS_SEP_LINE, &str, &dret) >= 0) {
+        char *p, *q;
+        int tid, pos, num = 0;
+        int64_t beg = 0, end = 0;
+        bam_mplp_t mplp;
+
+        if (str.l == 0 || *str.s == '#') continue; /* empty or comment line */
+        /* Track and browser lines.  Also look for a trailing *space* in
+           case someone has badly-chosen a chromosome name (it would
+           be followed by a tab in that case). */
+        if (strncmp(str.s, "track ", 6) == 0) continue;
+        if (strncmp(str.s, "browser ", 8) == 0) continue;
+        for (p = q = str.s; *p && !isspace(*p); ++p);
+        if (*p == 0) goto bed_error;
+        char c = *p;
+        *p = 0; tid = bam_name2id(aux[0]->header, q); *p = c;
+        if (tid < 0) goto bed_error;
+        num = sscanf(p + 1, "%"SCNd64" %"SCNd64, &beg, &end);
+        if (num < 2 || end < beg) goto bed_error;
+
+        for (i = 0; i < n; ++i) {
+            if (aux[i]->iter) hts_itr_destroy(aux[i]->iter);
+            aux[i]->iter = sam_itr_queryi(idx[i], tid, beg, end);
+            aux[i]->rcnt = 0;
+        }
+
+        mplp = bam_mplp_init(n, read_bam, (void**)aux);
+        if (min_depth > DEFAULT_DEPTH)
+            bam_mplp_set_maxcnt(mplp, min_depth);
+        else
+            bam_mplp_set_maxcnt(mplp, DEFAULT_DEPTH);
+
+        memset(cnt, 0, sizeof(*cnt) * n);
+        if (min_depth >= 0) memset(pcov, 0, sizeof(*pcov) * n);
+
+        if (do_rcount)
+            bam_mplp_constructor(mplp, incr_rcnt);
+
+        while ((ret = bam_mplp_auto(mplp, &tid, &pos, n_plp, plp)) > 0)
+            if (pos >= beg && pos < end) {
+                for (i = 0; i < n; ++i) {
+                    m = 0;
+                    if (skip_DN || min_depth >= 0) {
+                        for (j = 0; j < n_plp[i]; ++j) {
+                            const bam_pileup1_t *pi = plp[i] + j;
+                            if (pi->is_del || pi->is_refskip) ++m;
+                        }
+                    }
+                    int pd = n_plp[i] - m;
+                    cnt[i] += pd;
+                    if (min_depth >= 0 && pd >= min_depth) pcov[i]++;
+                }
+            }
+
+        if (ret < 0) {
+            print_error("bedcov", "error reading from input file");
+            status = 2;
+            bam_mplp_destroy(mplp);
+            break;
+        }
+
+        for (i = 0; i < n; ++i) {
+            kputc('\t', &str);
+            kputl(cnt[i], &str);
+        }
+        if (min_depth >= 0) {
+            for (i = 0; i < n; ++i) {
+                kputc('\t', &str);
+                kputl(pcov[i], &str);
+            }
+        }
+        if (do_rcount) {
+            for (i = 0; i < n; ++i) {
+                kputc('\t', &str);
+                kputl(aux[i]->rcnt, &str);
+            }
+        }
+        puts(str.s);
+        bam_mplp_destroy(mplp);
+        continue;
+
+bed_error:
+        fprintf(stderr, "Errors in BED line '%s'\n", str.s);
+        status = 2;
+    }
+    free(n_plp); free(plp);
+    ks_destroy(ks);
+    gzclose(fp);
+
+    free(cnt);
+    free(pcov);
+    for (i = 0; i < n; ++i) {
+        if (aux[i]->iter) hts_itr_destroy(aux[i]->iter);
+        hts_idx_destroy(idx[i]);
+        sam_hdr_destroy(aux[i]->header);
+        sam_close(aux[i]->fp);
+        free(aux[i]);
+    }
+    free(aux); free(idx);
+    free(str.s);
+    sam_global_args_free(&ga);
+    return status;
+}
diff --git a/samtools/bedcov.c.pysam.c b/samtools/bedcov.c.pysam.c
new file mode 100644
index 0000000..f259cb1
--- /dev/null
+++ b/samtools/bedcov.c.pysam.c
@@ -0,0 +1,300 @@
+#include "samtools.pysam.h"
+
+/*  bedcov.c -- bedcov subcommand.
+
+    Copyright (C) 2012 Broad Institute.
+    Copyright (C) 2013-2014, 2018-2022 Genome Research Ltd.
+
+    Author: Heng Li <lh3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <config.h>
+
+#include <zlib.h>
+#include <stdio.h>
+#include <ctype.h>
+#include <stdlib.h>
+#include <string.h>
+#include <unistd.h>
+#include "htslib/kstring.h"
+#include "htslib/sam.h"
+#include "htslib/thread_pool.h"
+#include "samtools.h"
+#include "sam_opts.h"
+
+#include "htslib/kseq.h"
+KSTREAM_INIT(gzFile, gzread, 16384)
+
+#define DEFAULT_DEPTH 64000
+
+typedef struct {
+    htsFile *fp;
+    sam_hdr_t *header;
+    hts_itr_t *iter;
+    int min_mapQ;
+    uint32_t flags;  // read filtering flags
+    int64_t rcnt;
+} aux_t;
+
+static int read_bam(void *data, bam1_t *b)
+{
+    aux_t *aux = (aux_t*)data; // data in fact is a pointer to an auxiliary structure
+    int ret;
+    while (1)
+    {
+        ret = aux->iter? sam_itr_next(aux->fp, aux->iter, b) : sam_read1(aux->fp, aux->header, b);
+        if ( ret<0 ) break;
+        if ( b->core.flag & aux->flags ) continue;
+        if ( (int)b->core.qual < aux->min_mapQ ) continue;
+        break;
+    }
+    return ret;
+}
+
+static int incr_rcnt(void *data, const bam1_t *b, bam_pileup_cd *cd) {
+    aux_t *aux = (aux_t *)data;
+    aux->rcnt++;
+    return 0;
+}
+
+int main_bedcov(int argc, char *argv[])
+{
+    gzFile fp;
+    kstring_t str;
+    kstream_t *ks;
+    hts_idx_t **idx;
+    aux_t **aux;
+    int *n_plp, dret, i, j, m, n, c, ret, status = 0, min_mapQ = 0;
+    int skip_DN = 0, do_rcount = 0;
+    int64_t *cnt, *pcov = NULL;
+    const bam_pileup1_t **plp;
+    int usage = 0, has_index_file = 0;
+    uint32_t flags = (BAM_FUNMAP | BAM_FSECONDARY | BAM_FQCFAIL | BAM_FDUP);
+    int tflags = 0, min_depth = -1;
+
+    sam_global_args ga = SAM_GLOBAL_ARGS_INIT;
+    static const struct option lopts[] = {
+        {"min-MQ", required_argument, NULL, 'Q'},
+        {"min-mq", required_argument, NULL, 'Q'},
+        SAM_OPT_GLOBAL_OPTIONS('-', 0, '-', '-', 0, '-'),
+        { NULL, 0, NULL, 0 }
+    };
+
+    while ((c = getopt_long(argc, argv, "Q:Xg:G:jd:c", lopts, NULL)) >= 0) {
+        switch (c) {
+        case 'Q': min_mapQ = atoi(optarg); break;
+        case 'X': has_index_file = 1; break;
+        case 'c': do_rcount = 1; break;
+        case 'g':
+            tflags = bam_str2flag(optarg);
+            if (tflags < 0 || tflags > ((BAM_FSUPPLEMENTARY << 1) - 1)) {
+                print_error("bedcov", "Flag value \"%s\" is not supported", optarg);
+                return 1;
+            }
+            flags &= ~tflags;
+            break;
+        case 'G':
+            tflags = bam_str2flag(optarg);
+            if (tflags < 0 || tflags > ((BAM_FSUPPLEMENTARY << 1) - 1)) {
+                print_error("bedcov", "Flag value \"%s\" is not supported", optarg);
+                return 1;
+            }
+            flags |= tflags;
+            break;
+        case 'j': skip_DN = 1; break;
+        case 'd': min_depth = atoi(optarg); break;
+        default:  if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break;
+                  /* else fall-through */
+        case '?': usage = 1; break;
+        }
+        if (usage) break;
+    }
+    if (usage || optind + 2 > argc) {
+        fprintf(samtools_stderr, "Usage: samtools bedcov [options] <in.bed> <in1.bam> [...]\n\n");
+        fprintf(samtools_stderr, "Options:\n");
+        fprintf(samtools_stderr, "      -Q, --min-MQ <int>  mapping quality threshold [0]\n");
+        fprintf(samtools_stderr, "      -X                  use customized index files\n");
+        fprintf(samtools_stderr, "      -g <flags>          remove the specified flags from the set used to filter out reads\n");
+        fprintf(samtools_stderr, "      -G <flags>          add the specified flags to the set used to filter out reads\n"
+                        "                          The default set is UNMAP,SECONDARY,QCFAIL,DUP or 0x704\n");
+        fprintf(samtools_stderr, "      -j                  do not include deletions (D) and ref skips (N) in bedcov computation\n");
+        fprintf(samtools_stderr, "      -d <int>            depth threshold. Number of reference bases with coverage above and"
+                        "                          including this value will be displayed in a separate column\n");
+        fprintf(samtools_stderr, "      -c                  add an additional column showing read count\n");
+        sam_global_opt_help(samtools_stderr, "-.--.--.");
+        return 1;
+    }
+    if (has_index_file) {
+        if ((argc - optind - 1) % 2 != 0) { // Calculate # of input BAM files
+            fprintf(samtools_stderr, "ERROR: odd number of filenames detected! Each BAM file should have an index file\n");
+            return 1;
+        }
+        n = (argc - optind - 1) / 2;
+    } else {
+        n = argc - optind - 1;
+    }
+
+    memset(&str, 0, sizeof(kstring_t));
+    aux = calloc(n, sizeof(aux_t*));
+    idx = calloc(n, sizeof(hts_idx_t*));
+    for (i = 0; i < n; ++i) {
+        aux[i] = calloc(1, sizeof(aux_t));
+        aux[i]->min_mapQ = min_mapQ;
+        aux[i]->fp = sam_open_format(argv[i+optind+1], "r", &ga.in);
+        if (aux[i]->fp) {
+            // If index filename has not been specfied, look in BAM folder
+            if (has_index_file) {
+                idx[i] = sam_index_load2(aux[i]->fp, argv[i+optind+1], argv[i+optind+n+1]);
+            } else {
+                idx[i] = sam_index_load(aux[i]->fp, argv[i+optind+1]);
+            }
+        }
+        if (aux[i]->fp == 0 || idx[i] == 0) {
+            fprintf(samtools_stderr, "ERROR: fail to open index BAM file '%s'\n", argv[i+optind+1]);
+            return 2;
+        }
+        // TODO bgzf_set_cache_size(aux[i]->fp, 20);
+        aux[i]->header = sam_hdr_read(aux[i]->fp);
+        if (aux[i]->header == NULL) {
+            fprintf(samtools_stderr, "ERROR: failed to read header for '%s'\n",
+                    argv[i+optind+1]);
+            return 2;
+        }
+        aux[i]->flags = flags;
+    }
+    cnt = calloc(n, sizeof(*cnt));
+
+    if (min_depth >= 0) pcov = calloc(n, sizeof(*pcov));
+    if (!cnt || (min_depth >= 0 && !pcov)) {
+        print_error_errno("bedcov", "failed to allocate memory");
+        return 2;
+    }
+
+    fp = gzopen(argv[optind], "rb");
+    if (fp == NULL) {
+        print_error_errno("bedcov", "can't open BED file '%s'", argv[optind]);
+        return 2;
+    }
+    ks = ks_init(fp);
+    n_plp = calloc(n, sizeof(int));
+    plp = calloc(n, sizeof(bam_pileup1_t*));
+    while (ks_getuntil(ks, KS_SEP_LINE, &str, &dret) >= 0) {
+        char *p, *q;
+        int tid, pos, num = 0;
+        int64_t beg = 0, end = 0;
+        bam_mplp_t mplp;
+
+        if (str.l == 0 || *str.s == '#') continue; /* empty or comment line */
+        /* Track and browser lines.  Also look for a trailing *space* in
+           case someone has badly-chosen a chromosome name (it would
+           be followed by a tab in that case). */
+        if (strncmp(str.s, "track ", 6) == 0) continue;
+        if (strncmp(str.s, "browser ", 8) == 0) continue;
+        for (p = q = str.s; *p && !isspace(*p); ++p);
+        if (*p == 0) goto bed_error;
+        char c = *p;
+        *p = 0; tid = bam_name2id(aux[0]->header, q); *p = c;
+        if (tid < 0) goto bed_error;
+        num = sscanf(p + 1, "%"SCNd64" %"SCNd64, &beg, &end);
+        if (num < 2 || end < beg) goto bed_error;
+
+        for (i = 0; i < n; ++i) {
+            if (aux[i]->iter) hts_itr_destroy(aux[i]->iter);
+            aux[i]->iter = sam_itr_queryi(idx[i], tid, beg, end);
+            aux[i]->rcnt = 0;
+        }
+
+        mplp = bam_mplp_init(n, read_bam, (void**)aux);
+        if (min_depth > DEFAULT_DEPTH)
+            bam_mplp_set_maxcnt(mplp, min_depth);
+        else
+            bam_mplp_set_maxcnt(mplp, DEFAULT_DEPTH);
+
+        memset(cnt, 0, sizeof(*cnt) * n);
+        if (min_depth >= 0) memset(pcov, 0, sizeof(*pcov) * n);
+
+        if (do_rcount)
+            bam_mplp_constructor(mplp, incr_rcnt);
+
+        while ((ret = bam_mplp_auto(mplp, &tid, &pos, n_plp, plp)) > 0)
+            if (pos >= beg && pos < end) {
+                for (i = 0; i < n; ++i) {
+                    m = 0;
+                    if (skip_DN || min_depth >= 0) {
+                        for (j = 0; j < n_plp[i]; ++j) {
+                            const bam_pileup1_t *pi = plp[i] + j;
+                            if (pi->is_del || pi->is_refskip) ++m;
+                        }
+                    }
+                    int pd = n_plp[i] - m;
+                    cnt[i] += pd;
+                    if (min_depth >= 0 && pd >= min_depth) pcov[i]++;
+                }
+            }
+
+        if (ret < 0) {
+            print_error("bedcov", "error reading from input file");
+            status = 2;
+            bam_mplp_destroy(mplp);
+            break;
+        }
+
+        for (i = 0; i < n; ++i) {
+            kputc('\t', &str);
+            kputl(cnt[i], &str);
+        }
+        if (min_depth >= 0) {
+            for (i = 0; i < n; ++i) {
+                kputc('\t', &str);
+                kputl(pcov[i], &str);
+            }
+        }
+        if (do_rcount) {
+            for (i = 0; i < n; ++i) {
+                kputc('\t', &str);
+                kputl(aux[i]->rcnt, &str);
+            }
+        }
+        samtools_puts(str.s);
+        bam_mplp_destroy(mplp);
+        continue;
+
+bed_error:
+        fprintf(samtools_stderr, "Errors in BED line '%s'\n", str.s);
+        status = 2;
+    }
+    free(n_plp); free(plp);
+    ks_destroy(ks);
+    gzclose(fp);
+
+    free(cnt);
+    free(pcov);
+    for (i = 0; i < n; ++i) {
+        if (aux[i]->iter) hts_itr_destroy(aux[i]->iter);
+        hts_idx_destroy(idx[i]);
+        sam_hdr_destroy(aux[i]->header);
+        sam_close(aux[i]->fp);
+        free(aux[i]);
+    }
+    free(aux); free(idx);
+    free(str.s);
+    sam_global_args_free(&ga);
+    return status;
+}
diff --git a/samtools/bedidx.c b/samtools/bedidx.c
new file mode 100644
index 0000000..6b22d4e
--- /dev/null
+++ b/samtools/bedidx.c
@@ -0,0 +1,637 @@
+/*  bedidx.c -- BED file indexing.
+
+    Copyright (C) 2011 Broad Institute.
+    Copyright (C) 2014, 2017-2019 Genome Research Ltd.
+
+    Author: Heng Li <lh3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <config.h>
+
+#include <stdlib.h>
+#include <stdint.h>
+#include <string.h>
+#include <stdio.h>
+#include <errno.h>
+#include <zlib.h>
+#include "bedidx.h"
+
+#include "htslib/ksort.h"
+
+#include "htslib/kseq.h"
+KSTREAM_INIT(gzFile, gzread, 8192)
+
+static inline int lt_pair_pos(hts_pair_pos_t a, hts_pair_pos_t b) {
+    if (a.beg == b.beg) return a.end < b.end;
+    return a.beg < b.beg;
+}
+KSORT_INIT_STATIC(hts_pair_pos_t, hts_pair_pos_t, lt_pair_pos)
+
+/*! @typedef
+ * @abstract bed_reglist_t - value type of the BED hash table
+ * This structure encodes the list of intervals (ranges) for the regions provided via BED file or
+ * command line arguments.
+ * @field *a           pointer to the array of intervals.
+ * @field n            actual number of elements contained by a
+ * @field m            number of allocated elements to a (n <= m)
+ * @field *idx         index array for computing the minimum offset
+ */
+typedef struct {
+    int n, m;
+    hts_pair_pos_t *a;
+    int *idx;
+    int filter;
+} bed_reglist_t;
+
+#include "htslib/khash.h"
+KHASH_MAP_INIT_STR(reg, bed_reglist_t)
+
+typedef kh_reg_t reghash_t;
+
+#if 0
+// Debug function
+static void bed_print(void *reg_hash) {
+    reghash_t *h = (reghash_t *)reg_hash;
+    bed_reglist_t *p;
+    khint_t k;
+    int i;
+    const char *reg;
+
+    if (!h) {
+        printf("Hash table is empty!\n");
+        return;
+    }
+    for (k = kh_begin(h); k < kh_end(h); k++) {
+        if (kh_exist(h,k)) {
+            reg = kh_key(h,k);
+            printf("Region: '%s'\n", reg);
+            if ((p = &kh_val(h,k)) != NULL && p->n > 0) {
+                printf("Filter: %d\n", p->filter);
+                for (i=0; i<p->n; i++) {
+                    printf("\tinterval[%d]: %"PRIhts_pos"-%"PRIhts_pos"\n",
+                           i,p->a[i].beg,p->a[i].end);
+                }
+            } else {
+                printf("Region '%s' has no intervals!\n", reg);
+            }
+        }
+    }
+}
+#endif
+
+static int *bed_index_core(int n, hts_pair_pos_t *a)
+{
+    int i, j, l, *idx, *new_idx;
+    l = 0; idx = 0;
+    for (i = 0; i < n; ++i) {
+        hts_pos_t beg, end;
+        beg = a[i].beg >> LIDX_SHIFT; end = a[i].end >> LIDX_SHIFT;
+        if (l < end + 1) {
+            int old_l = l;
+            l = end + 1;
+            kroundup32(l);
+            new_idx = realloc(idx, l * sizeof(*idx));
+            if (!new_idx) {
+                free(idx);
+                return NULL;
+            }
+            idx = new_idx;
+
+            for (j = old_l; j < l; ++j)
+                idx[j] = -1;
+        }
+
+        for (j = beg; j < end+1; ++j)
+            if (idx[j] < 0)
+                idx[j] = i;
+    }
+    return idx;
+}
+
+static void bed_index(void *_h)
+{
+    reghash_t *h = (reghash_t*)_h;
+    khint_t k;
+    for (k = 0; k < kh_end(h); ++k) {
+        if (kh_exist(h, k)) {
+            bed_reglist_t *p = &kh_val(h, k);
+            if (p->idx) free(p->idx);
+            ks_introsort(hts_pair_pos_t, p->n, p->a);
+            p->idx = bed_index_core(p->n, p->a);
+        }
+    }
+}
+
+static int bed_minoff(const bed_reglist_t *p, hts_pos_t beg, hts_pos_t end) {
+    int i, min_off=0;
+
+    if (p && p->idx) {
+        min_off = (beg>>LIDX_SHIFT >= p->n)? p->idx[p->n-1] : p->idx[beg>>LIDX_SHIFT];
+        if (min_off < 0) { // TODO: this block can be improved, but speed should not matter too much here
+            hts_pos_t n = beg>>LIDX_SHIFT;
+            if (n > p->n)
+                n = p->n;
+            for (i = n - 1; i >= 0; --i)
+                if (p->idx[i] >= 0)
+                    break;
+            min_off = i >= 0? p->idx[i] : 0;
+        }
+    }
+
+    return min_off;
+}
+
+static int bed_overlap_core(const bed_reglist_t *p, hts_pos_t beg, hts_pos_t end)
+{
+    int i, min_off;
+    if (p->n == 0) return 0;
+    min_off = bed_minoff(p, beg, end);
+
+    for (i = min_off; i < p->n; ++i) {
+        if (p->a[i].beg >= end) break; // out of range; no need to proceed
+        if (p->a[i].end > beg && p->a[i].beg < end)
+            return 1; // find the overlap; return
+    }
+    return 0;
+}
+
+int bed_overlap(const void *_h, const char *chr, hts_pos_t beg, hts_pos_t end)
+{
+    const reghash_t *h = (const reghash_t*)_h;
+    khint_t k;
+    if (!h) return 0;
+    k = kh_get(reg, h, chr);
+    if (k == kh_end(h)) return 0;
+    return bed_overlap_core(&kh_val(h, k), beg, end);
+}
+
+/** @brief Trim a sorted interval list, inside a region hash table,
+ *   by removing completely contained intervals and merging adjacent or
+ *   overlapping intervals.
+ *  @param reg_hash    the region hash table with interval lists as values
+ */
+
+void bed_unify(void *reg_hash) {
+
+    int i, j, new_n;
+    reghash_t *h;
+    bed_reglist_t *p;
+
+    if (!reg_hash)
+        return;
+
+    h = (reghash_t *)reg_hash;
+
+    for (i = kh_begin(h); i < kh_end(h); i++) {
+        if (!kh_exist(h,i) || !(p = &kh_val(h,i)) || !(p->n))
+            continue;
+
+        for (new_n = 0, j = 1; j < p->n; j++) {
+            if (p->a[new_n].end < p->a[j].beg) {
+                p->a[++new_n] = p->a[j];
+            } else {
+                if (p->a[new_n].end < p->a[j].end)
+                    p->a[new_n].end = p->a[j].end;
+            }
+        }
+
+        p->n = ++new_n;
+    }
+}
+
+/* "BED" file reader, which actually reads two different formats.
+
+   BED files contain between three and nine fields per line, of which
+   only the first three (reference, start, end) are of interest to us.
+   BED counts positions from base 0, and the end is the base after the
+   region of interest.  While not properly documented in the specification,
+   it is also possible to have 'browser' and 'track' lines in BED files that
+   do not follow the standard format and should be ignored.  Examination
+   of the BED file reading code in
+   http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git shows that BED
+   files can also have comment lines starting with '#', leading whitespace
+   is stripped, and that fields are separated by one or more consecutive
+   whitespace characters.
+
+   The alternative format was originally for reading positions in VCF
+   format.  This expects two columns, which indicate the reference and
+   a position.  The position corresponds to a single base, and unlike
+   BED counts from 1.
+
+   Which format is in use is determined based on whether one or two
+   numbers can be decoded on the line.  As this choice is made line-by-line
+   in this implementation, it is possible (but probably a bad idea) to mix
+   both formats in the same file.  If trying to read a VCF file by this
+   method, it would be important to ensure that the third column (ID) does
+   not contain any entries that start with a digit, to avoid the line
+   erroneously being parsed as a BED file entry.
+
+   The BED specification is at http://www.genome.ucsc.edu/FAQ/FAQformat.html
+   The VCF specification is at https://github.com/samtools/hts-specs
+ */
+
+void *bed_read(const char *fn)
+{
+    reghash_t *h = kh_init(reg);
+    gzFile fp;
+    kstream_t *ks = NULL;
+    int dret;
+    unsigned int line = 0, save_errno;
+    kstring_t str = { 0, 0, NULL };
+
+    if (NULL == h) return NULL;
+    // read the list
+    fp = strcmp(fn, "-")? gzopen(fn, "r") : gzdopen(fileno(stdin), "r");
+    if (fp == 0) return 0;
+    ks = ks_init(fp);
+    if (NULL == ks) goto fail;  // In case ks_init ever gets error checking...
+    int ks_len;
+    while ((ks_len = ks_getuntil(ks, KS_SEP_LINE, &str, &dret)) >= 0) { // read a line
+        char *ref = str.s, *ref_end;
+        uint64_t beg = 0, end = 0;
+        int num = 0;
+        khint_t k;
+        bed_reglist_t *p;
+
+        if (ks_len == 0)
+            continue; // skip blank lines
+
+        line++;
+        while (*ref && isspace(*ref)) ref++;
+        if ('\0' == *ref) continue;  // Skip blank lines
+        if ('#'  == *ref) continue;  // Skip BED file comments
+        ref_end = ref;   // look for the end of the reference name
+        while (*ref_end && !isspace(*ref_end)) ref_end++;
+        if ('\0' != *ref_end) {
+            *ref_end = '\0';  // terminate ref and look for start, end
+            num = sscanf(ref_end + 1, "%"SCNu64" %"SCNu64, &beg, &end);
+        }
+        if (1 == num) {  // VCF-style format
+            end = beg--; // Counts from 1 instead of 0 for BED files
+        }
+        if (num < 1 || end < beg) {
+            // These two are special lines that can occur in BED files.
+            // Check for them here instead of earlier in case someone really
+            // has called their reference "browser" or "track".
+            if (0 == strcmp(ref, "browser")) continue;
+            if (0 == strcmp(ref, "track")) continue;
+            if (num < 1) {
+                fprintf(stderr,
+                        "[bed_read] Parse error reading \"%s\" at line %u\n",
+                        fn, line);
+            } else {
+                fprintf(stderr,
+                        "[bed_read] Parse error reading \"%s\" at line %u : "
+                        "end (%"PRIu64") must not be less "
+                        "than start (%"PRIu64")\n",
+                        fn, line, end, beg);
+            }
+            errno = 0; // Prevent caller from printing misleading error messages
+            goto fail;
+        }
+
+        // Put reg in the hash table if not already there
+        k = kh_get(reg, h, ref);
+        if (k == kh_end(h)) { // absent from the hash table
+            int ret;
+            char *s = strdup(ref);
+            if (NULL == s) goto fail;
+            k = kh_put(reg, h, s, &ret);
+            if (-1 == ret) {
+                free(s);
+                goto fail;
+            }
+            memset(&kh_val(h, k), 0, sizeof(bed_reglist_t));
+        }
+        p = &kh_val(h, k);
+
+        // Add begin,end to the list
+        if (p->n == p->m) {
+            p->m = p->m ? p->m<<1 : 4;
+            hts_pair_pos_t *new_a = realloc(p->a, p->m * sizeof(p->a[0]));
+            if (NULL == new_a) goto fail;
+            p->a = new_a;
+        }
+        p->a[p->n].beg = beg;
+        p->a[p->n++].end = end;
+    }
+    // FIXME: Need to check for errors in ks_getuntil.  At the moment it
+    // doesn't look like it can return one.  Possibly use gzgets instead?
+
+    if (gzclose(fp) != Z_OK) {
+        fp = NULL;
+        goto fail;
+    }
+    ks_destroy(ks);
+    free(str.s);
+    bed_index(h);
+    //bed_unify(h);
+    return h;
+ fail:
+    save_errno = errno;
+    if (ks) ks_destroy(ks);
+    if (fp) gzclose(fp);
+    free(str.s);
+    bed_destroy(h);
+    errno = save_errno;
+    return NULL;
+}
+
+void bed_destroy(void *_h)
+{
+    reghash_t *h;
+    khint_t k;
+
+    if (!_h)
+        return;
+
+    h = (reghash_t*)_h;
+    for (k = 0; k < kh_end(h); ++k) {
+        if (kh_exist(h, k)) {
+            free(kh_val(h, k).a);
+            free(kh_val(h, k).idx);
+            free((char*)kh_key(h, k));
+        }
+    }
+    kh_destroy(reg, h);
+}
+
+static void *bed_insert(void *reg_hash, char *reg, hts_pos_t beg, hts_pos_t end) {
+
+    reghash_t *h;
+    khint_t k;
+    bed_reglist_t *p;
+
+    if (!reg_hash)
+        return NULL;
+
+    h = (reghash_t *)reg_hash;
+
+    // Put reg in the hash table if not already there
+    k = kh_get(reg, h, reg); //looks strange, but only the second reg is the actual region name.
+    if (k == kh_end(h)) { // absent from the hash table
+        int ret;
+        char *s = strdup(reg);
+        if (NULL == s) goto fail;
+        k = kh_put(reg, h, s, &ret);
+        if (-1 == ret) {
+            free(s);
+            goto fail;
+        }
+        memset(&kh_val(h, k), 0, sizeof(bed_reglist_t));
+    }
+    p = &kh_val(h, k);
+
+    // Add beg and end to the list
+    if (p->n == p->m) {
+        p->m = p->m ? p->m<<1 : 4;
+        hts_pair_pos_t *new_a = realloc(p->a, p->m * sizeof(p->a[0]));
+        if (NULL == new_a) goto fail;
+        p->a = new_a;
+    }
+    p->a[p->n].beg = beg;
+    p->a[p->n++].end = end;
+
+fail:
+    return h;
+}
+
+/* @brief Filter a region hash table (coming from the BED file) by another
+ *  region hash table (coming from CLI), so that only intervals contained in
+ *  both hash tables are kept.
+ * @param reg_hash    the target region hash table
+ * @param tmp_hash    the filter region hash table
+ * @return            pointer to the filtered hash table
+ */
+
+static void *bed_filter(void *reg_hash, void *tmp_hash) {
+
+    reghash_t *h;
+    reghash_t *t;
+    bed_reglist_t *p, *q;
+    khint_t l, k;
+    hts_pair_pos_t *new_a;
+    int i, j, new_n, min_off;
+    const char *reg;
+    hts_pos_t beg, end;
+
+    h = (reghash_t *)reg_hash;
+    t = (reghash_t *)tmp_hash;
+    if (!h)
+        return NULL;
+    if (!t)
+        return h;
+
+    for (l = kh_begin(t); l < kh_end(t); l++) {
+        if (!kh_exist(t,l) || !(q = &kh_val(t,l)) || !(q->n))
+            continue;
+
+        reg = kh_key(t,l);
+        k = kh_get(reg, h, reg); //looks strange, but only the second reg is a proper argument.
+        if (k == kh_end(h) || !(p = &kh_val(h, k)) || !(p->n))
+            continue;
+
+        new_a = calloc(q->n + p->n, sizeof(new_a[0]));
+        if (!new_a)
+            return NULL;
+        new_n = 0;
+
+        for (i = 0; i < q->n; i++) {
+            beg = q->a[i].beg;
+            end = q->a[i].end;
+
+            min_off = bed_minoff(p, beg, end);
+            for (j = min_off; j < p->n; ++j) {
+                if (p->a[j].beg >= end) break; // out of range; no need to proceed
+                if (p->a[j].end > beg && p->a[j].beg < end) {
+                    new_a[new_n].beg = MAX(p->a[j].beg, beg);
+                    new_a[new_n++].end = MIN(p->a[j].end, end);
+                }
+            }
+        }
+
+        if (new_n > 0) {
+            free(p->a);
+            p->a = new_a;
+            p->n = new_n;
+            p->m = new_n;
+            p->filter = FILTERED;
+        } else {
+            free(new_a);
+            p->filter = ALL;
+        }
+    }
+
+    return h;
+}
+
+void *bed_hash_regions(void *reg_hash, char **regs, int first, int last, int *op) {
+
+    reghash_t *h = (reghash_t *)reg_hash;
+    reghash_t *t = NULL;
+
+    int i;
+    char reg[1024];
+    const char *q;
+    int beg, end;
+
+    if (h) {
+        t = kh_init(reg);
+        if (!t) {
+            fprintf(stderr, "Error when creating the temporary region hash table!\n");
+            return NULL;
+        }
+    } else {
+        h = kh_init(reg);
+        if (!h) {
+            fprintf(stderr, "Error when creating the region hash table!\n");
+            return NULL;
+        }
+        *op = 1;
+    }
+
+    for (i=first; i<last; i++) {
+
+        // Note, ideally we would call sam_parse_region here, but it's complicated by not
+        // having the sam header known and the likelihood of the bed file containing data for other
+        // references too which we currently just ignore.
+        //
+        // TO DO...
+        q = hts_parse_reg(regs[i], &beg, &end);
+        if (q) {
+            if ((int)(q - regs[i] + 1) > 1024) {
+                fprintf(stderr, "Region name '%s' is too long (bigger than %d).\n", regs[i], 1024);
+                continue;
+            }
+            strncpy(reg, regs[i], q - regs[i]);
+            reg[q - regs[i]] = 0;
+        } else {
+            // not parsable as a region, but possibly a sequence named "foo:a"
+            if (strlen(regs[i]) + 1 > 1024) {
+                fprintf(stderr, "Region name '%s' is too long (bigger than %d).\n", regs[i], 1024);
+                continue;
+            }
+            strcpy(reg, regs[i]);
+            beg = 0; end = INT_MAX;
+        }
+
+        //if op==1 insert reg to the bed hash table
+        if (*op && !(bed_insert(h, reg, beg, end))) {
+            fprintf(stderr, "Error when inserting region='%s' in the bed hash table at address=%p!\n", regs[i], h);
+        }
+        //if op==0, first insert the regions in the temporary hash table,
+        //then filter the bed hash table using it
+        if (!(*op) && !(bed_insert(t, reg, beg, end))) {
+            fprintf(stderr, "Error when inserting region='%s' in the temporary hash table at address=%p!\n", regs[i], t);
+        }
+    }
+
+    if (!(*op)) {
+        bed_index(t);
+        bed_unify(t);
+        h = bed_filter(h, t);
+        bed_destroy(t);
+    }
+
+    if (h) {
+        bed_index(h);
+        bed_unify(h);
+    }
+
+    return h;
+}
+
+const char* bed_get(void *reg_hash, int i, int filter) {
+
+    reghash_t *h;
+    bed_reglist_t *p;
+
+    if (!reg_hash)
+        return NULL;
+
+    h = (reghash_t *)reg_hash;
+    if (!kh_exist(h,i) || !(p = &kh_val(h,i)) || (p->filter < filter))
+        return NULL;
+
+    return kh_key(h, i);
+}
+
+/**
+ * Create a region list from a the region hash table
+ * @param  reg_hash  The region hash table
+ * @param  filter    0 - allow all regions, 1 - allow only selected regions
+ * @param  n_reg     Pointer to the returned region number
+ * @return           The regions list as a hts_reglist_t
+ */
+
+hts_reglist_t *bed_reglist(void *reg_hash, int filter, int *n_reg) {
+
+    reghash_t *h;
+    bed_reglist_t *p;
+    khint_t i;
+    hts_reglist_t *reglist = NULL;
+    int count = 0;
+    int j;
+
+    if (!reg_hash)
+        return NULL;
+
+    h = (reghash_t *)reg_hash;
+
+    for (i = kh_begin(h); i < kh_end(h); i++) {
+        if (!kh_exist(h,i) || !(p = &kh_val(h,i)) || (p->filter < filter))
+            continue;
+        count++;
+    }
+    if (!count)
+        return NULL;
+
+    reglist = (hts_reglist_t *)calloc(count, sizeof(hts_reglist_t));
+    if (!reglist)
+        return NULL;
+
+    *n_reg = count;
+    count = 0;
+
+    for (i = kh_begin(h); i < kh_end(h) && count < *n_reg; i++) {
+        if (!kh_exist(h,i) || !(p = &kh_val(h,i)) || (p->filter < filter))
+            continue;
+
+        reglist[count].reg = kh_key(h,i);
+        reglist[count].intervals = (hts_pair32_t *)calloc(p->n, sizeof(hts_pair32_t));
+        if(!(reglist[count].intervals)) {
+            hts_reglist_free(reglist, count);
+            return NULL;
+        }
+        reglist[count].count = p->n;
+        reglist[count].max_end = 0;
+
+        for (j = 0; j < p->n; j++) {
+            reglist[count].intervals[j].beg = p->a[j].beg;
+            reglist[count].intervals[j].end = p->a[j].end;
+
+            if (reglist[count].intervals[j].end > reglist[count].max_end)
+                reglist[count].max_end = reglist[count].intervals[j].end;
+        }
+        count++;
+    }
+
+    return reglist;
+}
diff --git a/samtools/bedidx.c.pysam.c b/samtools/bedidx.c.pysam.c
new file mode 100644
index 0000000..533b42a
--- /dev/null
+++ b/samtools/bedidx.c.pysam.c
@@ -0,0 +1,639 @@
+#include "samtools.pysam.h"
+
+/*  bedidx.c -- BED file indexing.
+
+    Copyright (C) 2011 Broad Institute.
+    Copyright (C) 2014, 2017-2019 Genome Research Ltd.
+
+    Author: Heng Li <lh3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <config.h>
+
+#include <stdlib.h>
+#include <stdint.h>
+#include <string.h>
+#include <stdio.h>
+#include <errno.h>
+#include <zlib.h>
+#include "bedidx.h"
+
+#include "htslib/ksort.h"
+
+#include "htslib/kseq.h"
+KSTREAM_INIT(gzFile, gzread, 8192)
+
+static inline int lt_pair_pos(hts_pair_pos_t a, hts_pair_pos_t b) {
+    if (a.beg == b.beg) return a.end < b.end;
+    return a.beg < b.beg;
+}
+KSORT_INIT_STATIC(hts_pair_pos_t, hts_pair_pos_t, lt_pair_pos)
+
+/*! @typedef
+ * @abstract bed_reglist_t - value type of the BED hash table
+ * This structure encodes the list of intervals (ranges) for the regions provided via BED file or
+ * command line arguments.
+ * @field *a           pointer to the array of intervals.
+ * @field n            actual number of elements contained by a
+ * @field m            number of allocated elements to a (n <= m)
+ * @field *idx         index array for computing the minimum offset
+ */
+typedef struct {
+    int n, m;
+    hts_pair_pos_t *a;
+    int *idx;
+    int filter;
+} bed_reglist_t;
+
+#include "htslib/khash.h"
+KHASH_MAP_INIT_STR(reg, bed_reglist_t)
+
+typedef kh_reg_t reghash_t;
+
+#if 0
+// Debug function
+static void bed_print(void *reg_hash) {
+    reghash_t *h = (reghash_t *)reg_hash;
+    bed_reglist_t *p;
+    khint_t k;
+    int i;
+    const char *reg;
+
+    if (!h) {
+        fprintf(samtools_stdout, "Hash table is empty!\n");
+        return;
+    }
+    for (k = kh_begin(h); k < kh_end(h); k++) {
+        if (kh_exist(h,k)) {
+            reg = kh_key(h,k);
+            fprintf(samtools_stdout, "Region: '%s'\n", reg);
+            if ((p = &kh_val(h,k)) != NULL && p->n > 0) {
+                fprintf(samtools_stdout, "Filter: %d\n", p->filter);
+                for (i=0; i<p->n; i++) {
+                    fprintf(samtools_stdout, "\tinterval[%d]: %"PRIhts_pos"-%"PRIhts_pos"\n",
+                           i,p->a[i].beg,p->a[i].end);
+                }
+            } else {
+                fprintf(samtools_stdout, "Region '%s' has no intervals!\n", reg);
+            }
+        }
+    }
+}
+#endif
+
+static int *bed_index_core(int n, hts_pair_pos_t *a)
+{
+    int i, j, l, *idx, *new_idx;
+    l = 0; idx = 0;
+    for (i = 0; i < n; ++i) {
+        hts_pos_t beg, end;
+        beg = a[i].beg >> LIDX_SHIFT; end = a[i].end >> LIDX_SHIFT;
+        if (l < end + 1) {
+            int old_l = l;
+            l = end + 1;
+            kroundup32(l);
+            new_idx = realloc(idx, l * sizeof(*idx));
+            if (!new_idx) {
+                free(idx);
+                return NULL;
+            }
+            idx = new_idx;
+
+            for (j = old_l; j < l; ++j)
+                idx[j] = -1;
+        }
+
+        for (j = beg; j < end+1; ++j)
+            if (idx[j] < 0)
+                idx[j] = i;
+    }
+    return idx;
+}
+
+static void bed_index(void *_h)
+{
+    reghash_t *h = (reghash_t*)_h;
+    khint_t k;
+    for (k = 0; k < kh_end(h); ++k) {
+        if (kh_exist(h, k)) {
+            bed_reglist_t *p = &kh_val(h, k);
+            if (p->idx) free(p->idx);
+            ks_introsort(hts_pair_pos_t, p->n, p->a);
+            p->idx = bed_index_core(p->n, p->a);
+        }
+    }
+}
+
+static int bed_minoff(const bed_reglist_t *p, hts_pos_t beg, hts_pos_t end) {
+    int i, min_off=0;
+
+    if (p && p->idx) {
+        min_off = (beg>>LIDX_SHIFT >= p->n)? p->idx[p->n-1] : p->idx[beg>>LIDX_SHIFT];
+        if (min_off < 0) { // TODO: this block can be improved, but speed should not matter too much here
+            hts_pos_t n = beg>>LIDX_SHIFT;
+            if (n > p->n)
+                n = p->n;
+            for (i = n - 1; i >= 0; --i)
+                if (p->idx[i] >= 0)
+                    break;
+            min_off = i >= 0? p->idx[i] : 0;
+        }
+    }
+
+    return min_off;
+}
+
+static int bed_overlap_core(const bed_reglist_t *p, hts_pos_t beg, hts_pos_t end)
+{
+    int i, min_off;
+    if (p->n == 0) return 0;
+    min_off = bed_minoff(p, beg, end);
+
+    for (i = min_off; i < p->n; ++i) {
+        if (p->a[i].beg >= end) break; // out of range; no need to proceed
+        if (p->a[i].end > beg && p->a[i].beg < end)
+            return 1; // find the overlap; return
+    }
+    return 0;
+}
+
+int bed_overlap(const void *_h, const char *chr, hts_pos_t beg, hts_pos_t end)
+{
+    const reghash_t *h = (const reghash_t*)_h;
+    khint_t k;
+    if (!h) return 0;
+    k = kh_get(reg, h, chr);
+    if (k == kh_end(h)) return 0;
+    return bed_overlap_core(&kh_val(h, k), beg, end);
+}
+
+/** @brief Trim a sorted interval list, inside a region hash table,
+ *   by removing completely contained intervals and merging adjacent or
+ *   overlapping intervals.
+ *  @param reg_hash    the region hash table with interval lists as values
+ */
+
+void bed_unify(void *reg_hash) {
+
+    int i, j, new_n;
+    reghash_t *h;
+    bed_reglist_t *p;
+
+    if (!reg_hash)
+        return;
+
+    h = (reghash_t *)reg_hash;
+
+    for (i = kh_begin(h); i < kh_end(h); i++) {
+        if (!kh_exist(h,i) || !(p = &kh_val(h,i)) || !(p->n))
+            continue;
+
+        for (new_n = 0, j = 1; j < p->n; j++) {
+            if (p->a[new_n].end < p->a[j].beg) {
+                p->a[++new_n] = p->a[j];
+            } else {
+                if (p->a[new_n].end < p->a[j].end)
+                    p->a[new_n].end = p->a[j].end;
+            }
+        }
+
+        p->n = ++new_n;
+    }
+}
+
+/* "BED" file reader, which actually reads two different formats.
+
+   BED files contain between three and nine fields per line, of which
+   only the first three (reference, start, end) are of interest to us.
+   BED counts positions from base 0, and the end is the base after the
+   region of interest.  While not properly documented in the specification,
+   it is also possible to have 'browser' and 'track' lines in BED files that
+   do not follow the standard format and should be ignored.  Examination
+   of the BED file reading code in
+   http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git shows that BED
+   files can also have comment lines starting with '#', leading whitespace
+   is stripped, and that fields are separated by one or more consecutive
+   whitespace characters.
+
+   The alternative format was originally for reading positions in VCF
+   format.  This expects two columns, which indicate the reference and
+   a position.  The position corresponds to a single base, and unlike
+   BED counts from 1.
+
+   Which format is in use is determined based on whether one or two
+   numbers can be decoded on the line.  As this choice is made line-by-line
+   in this implementation, it is possible (but probably a bad idea) to mix
+   both formats in the same file.  If trying to read a VCF file by this
+   method, it would be important to ensure that the third column (ID) does
+   not contain any entries that start with a digit, to avoid the line
+   erroneously being parsed as a BED file entry.
+
+   The BED specification is at http://www.genome.ucsc.edu/FAQ/FAQformat.html
+   The VCF specification is at https://github.com/samtools/hts-specs
+ */
+
+void *bed_read(const char *fn)
+{
+    reghash_t *h = kh_init(reg);
+    gzFile fp;
+    kstream_t *ks = NULL;
+    int dret;
+    unsigned int line = 0, save_errno;
+    kstring_t str = { 0, 0, NULL };
+
+    if (NULL == h) return NULL;
+    // read the list
+    fp = strcmp(fn, "-")? gzopen(fn, "r") : gzdopen(fileno(stdin), "r");
+    if (fp == 0) return 0;
+    ks = ks_init(fp);
+    if (NULL == ks) goto fail;  // In case ks_init ever gets error checking...
+    int ks_len;
+    while ((ks_len = ks_getuntil(ks, KS_SEP_LINE, &str, &dret)) >= 0) { // read a line
+        char *ref = str.s, *ref_end;
+        uint64_t beg = 0, end = 0;
+        int num = 0;
+        khint_t k;
+        bed_reglist_t *p;
+
+        if (ks_len == 0)
+            continue; // skip blank lines
+
+        line++;
+        while (*ref && isspace(*ref)) ref++;
+        if ('\0' == *ref) continue;  // Skip blank lines
+        if ('#'  == *ref) continue;  // Skip BED file comments
+        ref_end = ref;   // look for the end of the reference name
+        while (*ref_end && !isspace(*ref_end)) ref_end++;
+        if ('\0' != *ref_end) {
+            *ref_end = '\0';  // terminate ref and look for start, end
+            num = sscanf(ref_end + 1, "%"SCNu64" %"SCNu64, &beg, &end);
+        }
+        if (1 == num) {  // VCF-style format
+            end = beg--; // Counts from 1 instead of 0 for BED files
+        }
+        if (num < 1 || end < beg) {
+            // These two are special lines that can occur in BED files.
+            // Check for them here instead of earlier in case someone really
+            // has called their reference "browser" or "track".
+            if (0 == strcmp(ref, "browser")) continue;
+            if (0 == strcmp(ref, "track")) continue;
+            if (num < 1) {
+                fprintf(samtools_stderr,
+                        "[bed_read] Parse error reading \"%s\" at line %u\n",
+                        fn, line);
+            } else {
+                fprintf(samtools_stderr,
+                        "[bed_read] Parse error reading \"%s\" at line %u : "
+                        "end (%"PRIu64") must not be less "
+                        "than start (%"PRIu64")\n",
+                        fn, line, end, beg);
+            }
+            errno = 0; // Prevent caller from printing misleading error messages
+            goto fail;
+        }
+
+        // Put reg in the hash table if not already there
+        k = kh_get(reg, h, ref);
+        if (k == kh_end(h)) { // absent from the hash table
+            int ret;
+            char *s = strdup(ref);
+            if (NULL == s) goto fail;
+            k = kh_put(reg, h, s, &ret);
+            if (-1 == ret) {
+                free(s);
+                goto fail;
+            }
+            memset(&kh_val(h, k), 0, sizeof(bed_reglist_t));
+        }
+        p = &kh_val(h, k);
+
+        // Add begin,end to the list
+        if (p->n == p->m) {
+            p->m = p->m ? p->m<<1 : 4;
+            hts_pair_pos_t *new_a = realloc(p->a, p->m * sizeof(p->a[0]));
+            if (NULL == new_a) goto fail;
+            p->a = new_a;
+        }
+        p->a[p->n].beg = beg;
+        p->a[p->n++].end = end;
+    }
+    // FIXME: Need to check for errors in ks_getuntil.  At the moment it
+    // doesn't look like it can return one.  Possibly use gzgets instead?
+
+    if (gzclose(fp) != Z_OK) {
+        fp = NULL;
+        goto fail;
+    }
+    ks_destroy(ks);
+    free(str.s);
+    bed_index(h);
+    //bed_unify(h);
+    return h;
+ fail:
+    save_errno = errno;
+    if (ks) ks_destroy(ks);
+    if (fp) gzclose(fp);
+    free(str.s);
+    bed_destroy(h);
+    errno = save_errno;
+    return NULL;
+}
+
+void bed_destroy(void *_h)
+{
+    reghash_t *h;
+    khint_t k;
+
+    if (!_h)
+        return;
+
+    h = (reghash_t*)_h;
+    for (k = 0; k < kh_end(h); ++k) {
+        if (kh_exist(h, k)) {
+            free(kh_val(h, k).a);
+            free(kh_val(h, k).idx);
+            free((char*)kh_key(h, k));
+        }
+    }
+    kh_destroy(reg, h);
+}
+
+static void *bed_insert(void *reg_hash, char *reg, hts_pos_t beg, hts_pos_t end) {
+
+    reghash_t *h;
+    khint_t k;
+    bed_reglist_t *p;
+
+    if (!reg_hash)
+        return NULL;
+
+    h = (reghash_t *)reg_hash;
+
+    // Put reg in the hash table if not already there
+    k = kh_get(reg, h, reg); //looks strange, but only the second reg is the actual region name.
+    if (k == kh_end(h)) { // absent from the hash table
+        int ret;
+        char *s = strdup(reg);
+        if (NULL == s) goto fail;
+        k = kh_put(reg, h, s, &ret);
+        if (-1 == ret) {
+            free(s);
+            goto fail;
+        }
+        memset(&kh_val(h, k), 0, sizeof(bed_reglist_t));
+    }
+    p = &kh_val(h, k);
+
+    // Add beg and end to the list
+    if (p->n == p->m) {
+        p->m = p->m ? p->m<<1 : 4;
+        hts_pair_pos_t *new_a = realloc(p->a, p->m * sizeof(p->a[0]));
+        if (NULL == new_a) goto fail;
+        p->a = new_a;
+    }
+    p->a[p->n].beg = beg;
+    p->a[p->n++].end = end;
+
+fail:
+    return h;
+}
+
+/* @brief Filter a region hash table (coming from the BED file) by another
+ *  region hash table (coming from CLI), so that only intervals contained in
+ *  both hash tables are kept.
+ * @param reg_hash    the target region hash table
+ * @param tmp_hash    the filter region hash table
+ * @return            pointer to the filtered hash table
+ */
+
+static void *bed_filter(void *reg_hash, void *tmp_hash) {
+
+    reghash_t *h;
+    reghash_t *t;
+    bed_reglist_t *p, *q;
+    khint_t l, k;
+    hts_pair_pos_t *new_a;
+    int i, j, new_n, min_off;
+    const char *reg;
+    hts_pos_t beg, end;
+
+    h = (reghash_t *)reg_hash;
+    t = (reghash_t *)tmp_hash;
+    if (!h)
+        return NULL;
+    if (!t)
+        return h;
+
+    for (l = kh_begin(t); l < kh_end(t); l++) {
+        if (!kh_exist(t,l) || !(q = &kh_val(t,l)) || !(q->n))
+            continue;
+
+        reg = kh_key(t,l);
+        k = kh_get(reg, h, reg); //looks strange, but only the second reg is a proper argument.
+        if (k == kh_end(h) || !(p = &kh_val(h, k)) || !(p->n))
+            continue;
+
+        new_a = calloc(q->n + p->n, sizeof(new_a[0]));
+        if (!new_a)
+            return NULL;
+        new_n = 0;
+
+        for (i = 0; i < q->n; i++) {
+            beg = q->a[i].beg;
+            end = q->a[i].end;
+
+            min_off = bed_minoff(p, beg, end);
+            for (j = min_off; j < p->n; ++j) {
+                if (p->a[j].beg >= end) break; // out of range; no need to proceed
+                if (p->a[j].end > beg && p->a[j].beg < end) {
+                    new_a[new_n].beg = MAX(p->a[j].beg, beg);
+                    new_a[new_n++].end = MIN(p->a[j].end, end);
+                }
+            }
+        }
+
+        if (new_n > 0) {
+            free(p->a);
+            p->a = new_a;
+            p->n = new_n;
+            p->m = new_n;
+            p->filter = FILTERED;
+        } else {
+            free(new_a);
+            p->filter = ALL;
+        }
+    }
+
+    return h;
+}
+
+void *bed_hash_regions(void *reg_hash, char **regs, int first, int last, int *op) {
+
+    reghash_t *h = (reghash_t *)reg_hash;
+    reghash_t *t = NULL;
+
+    int i;
+    char reg[1024];
+    const char *q;
+    int beg, end;
+
+    if (h) {
+        t = kh_init(reg);
+        if (!t) {
+            fprintf(samtools_stderr, "Error when creating the temporary region hash table!\n");
+            return NULL;
+        }
+    } else {
+        h = kh_init(reg);
+        if (!h) {
+            fprintf(samtools_stderr, "Error when creating the region hash table!\n");
+            return NULL;
+        }
+        *op = 1;
+    }
+
+    for (i=first; i<last; i++) {
+
+        // Note, ideally we would call sam_parse_region here, but it's complicated by not
+        // having the sam header known and the likelihood of the bed file containing data for other
+        // references too which we currently just ignore.
+        //
+        // TO DO...
+        q = hts_parse_reg(regs[i], &beg, &end);
+        if (q) {
+            if ((int)(q - regs[i] + 1) > 1024) {
+                fprintf(samtools_stderr, "Region name '%s' is too long (bigger than %d).\n", regs[i], 1024);
+                continue;
+            }
+            strncpy(reg, regs[i], q - regs[i]);
+            reg[q - regs[i]] = 0;
+        } else {
+            // not parsable as a region, but possibly a sequence named "foo:a"
+            if (strlen(regs[i]) + 1 > 1024) {
+                fprintf(samtools_stderr, "Region name '%s' is too long (bigger than %d).\n", regs[i], 1024);
+                continue;
+            }
+            strcpy(reg, regs[i]);
+            beg = 0; end = INT_MAX;
+        }
+
+        //if op==1 insert reg to the bed hash table
+        if (*op && !(bed_insert(h, reg, beg, end))) {
+            fprintf(samtools_stderr, "Error when inserting region='%s' in the bed hash table at address=%p!\n", regs[i], h);
+        }
+        //if op==0, first insert the regions in the temporary hash table,
+        //then filter the bed hash table using it
+        if (!(*op) && !(bed_insert(t, reg, beg, end))) {
+            fprintf(samtools_stderr, "Error when inserting region='%s' in the temporary hash table at address=%p!\n", regs[i], t);
+        }
+    }
+
+    if (!(*op)) {
+        bed_index(t);
+        bed_unify(t);
+        h = bed_filter(h, t);
+        bed_destroy(t);
+    }
+
+    if (h) {
+        bed_index(h);
+        bed_unify(h);
+    }
+
+    return h;
+}
+
+const char* bed_get(void *reg_hash, int i, int filter) {
+
+    reghash_t *h;
+    bed_reglist_t *p;
+
+    if (!reg_hash)
+        return NULL;
+
+    h = (reghash_t *)reg_hash;
+    if (!kh_exist(h,i) || !(p = &kh_val(h,i)) || (p->filter < filter))
+        return NULL;
+
+    return kh_key(h, i);
+}
+
+/**
+ * Create a region list from a the region hash table
+ * @param  reg_hash  The region hash table
+ * @param  filter    0 - allow all regions, 1 - allow only selected regions
+ * @param  n_reg     Pointer to the returned region number
+ * @return           The regions list as a hts_reglist_t
+ */
+
+hts_reglist_t *bed_reglist(void *reg_hash, int filter, int *n_reg) {
+
+    reghash_t *h;
+    bed_reglist_t *p;
+    khint_t i;
+    hts_reglist_t *reglist = NULL;
+    int count = 0;
+    int j;
+
+    if (!reg_hash)
+        return NULL;
+
+    h = (reghash_t *)reg_hash;
+
+    for (i = kh_begin(h); i < kh_end(h); i++) {
+        if (!kh_exist(h,i) || !(p = &kh_val(h,i)) || (p->filter < filter))
+            continue;
+        count++;
+    }
+    if (!count)
+        return NULL;
+
+    reglist = (hts_reglist_t *)calloc(count, sizeof(hts_reglist_t));
+    if (!reglist)
+        return NULL;
+
+    *n_reg = count;
+    count = 0;
+
+    for (i = kh_begin(h); i < kh_end(h) && count < *n_reg; i++) {
+        if (!kh_exist(h,i) || !(p = &kh_val(h,i)) || (p->filter < filter))
+            continue;
+
+        reglist[count].reg = kh_key(h,i);
+        reglist[count].intervals = (hts_pair32_t *)calloc(p->n, sizeof(hts_pair32_t));
+        if(!(reglist[count].intervals)) {
+            hts_reglist_free(reglist, count);
+            return NULL;
+        }
+        reglist[count].count = p->n;
+        reglist[count].max_end = 0;
+
+        for (j = 0; j < p->n; j++) {
+            reglist[count].intervals[j].beg = p->a[j].beg;
+            reglist[count].intervals[j].end = p->a[j].end;
+
+            if (reglist[count].intervals[j].end > reglist[count].max_end)
+                reglist[count].max_end = reglist[count].intervals[j].end;
+        }
+        count++;
+    }
+
+    return reglist;
+}
diff --git a/samtools/bedidx.h b/samtools/bedidx.h
new file mode 100644
index 0000000..05ab48f
--- /dev/null
+++ b/samtools/bedidx.h
@@ -0,0 +1,45 @@
+/*  bedidx.h -- BED file indexing header file.
+
+    Copyright (C) 2017 Genome Research Ltd.
+
+    Author: Valeriu Ohan <vo2@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#ifndef BEDIDX_H
+#define BEDIDX_H
+
+#include "htslib/hts.h"
+
+#define LIDX_SHIFT 13
+#define ALL 0
+#define FILTERED 1
+
+#define MIN(A,B) ( ( (A) < (B) ) ? (A) : (B) )
+#define MAX(A,B) ( ( (A) > (B) ) ? (A) : (B) )
+
+void *bed_read(const char *fn);
+void bed_destroy(void *_h);
+int bed_overlap(const void *_h, const char *chr, hts_pos_t beg, hts_pos_t end);
+void *bed_hash_regions(void *reg_hash, char **regs, int first, int last, int *op);
+const char* bed_get(void *reg_hash, int index, int filter);
+hts_reglist_t *bed_reglist(void *reg_hash, int filter, int *count_regs);
+void bed_unify(void *_h);
+
+#endif
diff --git a/samtools/consensus_pileup.c b/samtools/consensus_pileup.c
new file mode 100644
index 0000000..935cbdc
--- /dev/null
+++ b/samtools/consensus_pileup.c
@@ -0,0 +1,595 @@
+/*  consensus__pileup.h -- Pileup orientated data per consensus column
+
+    Copyright (C) 2013-2016, 2020-2021 Genome Research Ltd.
+
+    Author: James Bonfied <jkb@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notices and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <config.h>
+#include <htslib/sam.h>
+
+#ifdef __SSE__
+#   include <xmmintrin.h>
+#else
+#   define _mm_prefetch(a,b)
+#endif
+
+#include "consensus_pileup.h"
+
+#define MIN(a,b) ((a)<(b)?(a):(b))
+#define bam_strand(b)  (((b)->core.flag & BAM_FREVERSE) != 0)
+
+/*
+ * START_WITH_DEL is the mode that Gap5 uses when building this. It prepends
+ * all cigar strings with 1D and decrements the position by one. (And then
+ * has code to reverse this operation in the pileup handler.)
+ *
+ * The reason for this is that it means reads starting with an insertion work.
+ * Otherwise the inserted bases are silently lost. (Try it with "samtools
+ * mpileup" and you can see it has the same issue.)
+ *
+ * However it's probably not want most people expect.
+ */
+//#define START_WITH_DEL
+
+/* --------------------------------------------------------------------------
+ * The pileup code itself.
+ *
+ * This consists of the external pileup_loop() function, which takes a
+ * sam/bam samfile_t pointer and a callback function. The callback function
+ * is called once per column of aligned data (so once per base in an
+ * insertion).
+ *
+ * Current known issues.
+ * 1) zero length matches, ie 2S2S cause failures.
+ * 2) Insertions at starts of sequences get included in the soft clip, so
+ *    2S2I2M is treated as if it's 4S2M
+ * 3) From 1 and 2 above, 1S1I2S becomes 2S2S which fails.
+ */
+
+
+/*
+ * Fetches the next base => the nth base at unpadded position pos. (Nth can
+ * be greater than 0 if we have an insertion in this column). Do not call this
+ * with pos/nth lower than the previous query, although higher is better.
+ * (This allows it to be initialised at base 0.)
+ *
+ * Stores the result in base and also updates is_insert to indicate that
+ * this sequence still has more bases in this position beyond the current
+ * nth parameter.
+ *
+ * Returns 1 if a base was fetched
+ *         0 if not (eg ran off the end of sequence)
+ */
+static int get_next_base(pileup_t *p, hts_pos_t pos, int nth, int *is_insert) {
+    bam1_t *b = &p->b;
+    int op = p->cigar_op;
+
+    p->start -= p->start>0;
+    if (p->first_del && op != BAM_CPAD)
+        p->first_del = 0;
+
+    *is_insert = 0;
+
+    /* Find pos first */
+    while (p->pos < pos) {
+        p->nth = 0;
+
+        if (p->cigar_len == 0) {
+            if (p->cigar_ind >= b->core.n_cigar) {
+                p->eof = 1;
+                return 0;
+            }
+
+            op=p->cigar_op  = p->b_cigar[p->cigar_ind] & BAM_CIGAR_MASK;
+            p->cigar_len = p->b_cigar[p->cigar_ind] >> BAM_CIGAR_SHIFT;
+            p->cigar_ind++;
+        }
+
+        if ((op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF)
+            && p->cigar_len <= pos - p->pos) {
+            p->seq_offset += p->cigar_len;
+            p->pos += p->cigar_len;
+            p->cigar_len = 0;
+        } else {
+            switch (op) {
+            case BAM_CMATCH:
+            case BAM_CEQUAL:
+            case BAM_CDIFF:
+                p->seq_offset++;
+                /* Fall through */
+            case BAM_CDEL:
+            case BAM_CREF_SKIP:
+                p->pos++;
+                p->cigar_len--;
+                break;
+
+            case BAM_CINS:
+            case BAM_CSOFT_CLIP:
+                p->seq_offset += p->cigar_len;
+                /* Fall through */
+            case BAM_CPAD:
+            case BAM_CHARD_CLIP:
+                p->cigar_len = 0;
+                break;
+
+            default:
+                fprintf(stderr, "Unhandled cigar_op %d\n", op);
+                return -1;
+            }
+        }
+    }
+
+    /* Now at pos, find nth base */
+    while (p->nth < nth) {
+        if (p->cigar_len == 0) {
+            if (p->cigar_ind >= b->core.n_cigar) {
+                p->eof = 1;
+                return 0; /* off end of seq */
+            }
+
+            op=p->cigar_op  = p->b_cigar[p->cigar_ind] & BAM_CIGAR_MASK;
+            p->cigar_len = p->b_cigar[p->cigar_ind] >> BAM_CIGAR_SHIFT;
+            p->cigar_ind++;
+        }
+
+        switch (op) {
+        case BAM_CMATCH:
+        case BAM_CEQUAL:
+        case BAM_CDIFF:
+        case BAM_CSOFT_CLIP:
+        case BAM_CDEL:
+        case BAM_CREF_SKIP:
+            goto at_nth; /* sorry, but it's fast! */
+
+        case BAM_CINS:
+            p->seq_offset++;
+            /* Fall through */
+        case BAM_CPAD:
+            p->cigar_len--;
+            p->nth++;
+            break;
+
+        case BAM_CHARD_CLIP:
+            p->cigar_len = 0;
+            break;
+
+        default:
+            fprintf(stderr, "Unhandled cigar_op %d\n", op);
+            return -1;
+        }
+    }
+ at_nth:
+
+    /* Fill out base & qual fields */
+    p->ref_skip = 0;
+    if (p->nth < nth && op != BAM_CINS) {
+        //p->base = '-';
+        p->base = '*';
+        p->base4 = 16;
+        p->padding = 1;
+        if (p->seq_offset < b->core.l_qseq)
+            p->qual = (p->qual + p->b_qual[p->seq_offset+1])/2;
+        else
+            p->qual = 0;
+    } else {
+        p->padding = 0;
+        switch(op) {
+        case BAM_CDEL:
+            p->base = '*';
+            p->base4 = 16;
+            if (p->seq_offset+1 < b->core.l_qseq)
+                p->qual = (p->qual + p->b_qual[p->seq_offset+1])/2;
+            else
+                p->qual = (p->qual + p->b_qual[p->seq_offset])/2;
+            break;
+
+        case BAM_CPAD:
+            //p->base = '+';
+            p->base = '*';
+            p->base4 = 16;
+            if (p->seq_offset+1 < b->core.l_qseq)
+                p->qual = (p->qual + p->b_qual[p->seq_offset+1])/2;
+            else
+                p->qual = (p->qual + p->b_qual[p->seq_offset])/2;
+            break;
+
+        case BAM_CREF_SKIP:
+            p->base = '.';
+            p->base4 = 0;
+            p->qual = 0;
+            /* end of fragment, but not sequence */
+            p->eof = p->eof ? 2 : 3;
+            p->ref_skip = 1;
+            break;
+
+        default:
+            if (p->seq_offset < b->core.l_qseq) {
+                p->qual = p->b_qual[p->seq_offset];
+                p->base4 = p->b_seq[p->seq_offset/2] >>
+                    ((~p->seq_offset&1)<<2) & 0xf;
+                p->base = "NACMGRSVTWYHKDBN"[p->base4];
+            } else {
+                p->base = 'N';
+                p->base4 = 15;
+                p->qual = 0xff;
+            }
+
+            break;
+        }
+    }
+
+    /* Handle moving out of N (skip) into sequence again */
+    if (p->eof && p->base != '.') {
+        p->start = 1;
+        p->ref_skip = 1;
+        p->eof = 0;
+    }
+
+    /* Starting with an indel needs a minor fudge */
+    if (p->start && p->cigar_op == BAM_CDEL) {
+        p->first_del = 1;
+    }
+
+    /* Check if next op is an insertion of some sort */
+    if (p->cigar_len == 0) {
+        if (p->cigar_ind < b->core.n_cigar) {
+            op=p->cigar_op  = p->b_cigar[p->cigar_ind] & BAM_CIGAR_MASK;
+            p->cigar_len = p->b_cigar[p->cigar_ind] >> BAM_CIGAR_SHIFT;
+            p->cigar_ind++;
+            if (op == BAM_CREF_SKIP) {
+                p->eof = 3;
+                p->ref_skip = 1;
+            }
+        } else {
+            p->eof = 1;
+        }
+    }
+
+    switch (op) {
+    case BAM_CPAD:
+    case BAM_CINS:
+        *is_insert = p->cigar_len;
+        break;
+
+    case BAM_CSOFT_CLIP:
+        /* Last op 'S' => eof */
+        p->eof = (p->cigar_ind == b->core.n_cigar ||
+                  (p->cigar_ind+1 == b->core.n_cigar &&
+                   (p->b_cigar[p->cigar_ind] & BAM_CIGAR_MASK)
+                   == BAM_CHARD_CLIP))
+            ? 1
+            : 0;
+        break;
+
+    case BAM_CHARD_CLIP:
+        p->eof = 1;
+        break;
+
+    default:
+        break;
+    }
+
+    return 1;
+}
+
+/*
+ * Loops through a set of supplied ranges producing columns of data.
+ * When found, it calls func with clientdata as a callback. Func should
+ * return 0 for success and non-zero for failure. seq_init() is called
+ * on each new entry before we start processing it. It should return 0 or 1
+ * to indicate reject or accept status (eg to filter unmapped data).
+ * If seq_init() returns -1 we abort the pileup_loop with an error.
+ * seq_init may be NULL.
+ *
+ * Returns 0 on success
+ *        -1 on failure
+ */
+int pileup_loop(samFile *fp,
+                sam_hdr_t *h,
+                int (*seq_fetch)(void *client_data,
+                                 samFile *fp,
+                                 sam_hdr_t *h,
+                                 bam1_t *b),
+                int (*seq_init)(void *client_data,
+                                samFile *fp,
+                                sam_hdr_t *h,
+                                pileup_t *p),
+                int (*seq_add)(void *client_data,
+                               samFile *fp,
+                               sam_hdr_t *h,
+                               pileup_t *p,
+                               int depth,
+                               hts_pos_t pos,
+                               int nth,
+                               int is_insert),
+                void *client_data) {
+    int ret = -1;
+    pileup_t *phead = NULL, *p, *pfree = NULL, *last, *next, *ptail = NULL;
+    pileup_t *pnew = NULL;
+    int is_insert, nth = 0, r;
+    hts_pos_t col = 0;
+    int last_ref = -1;
+
+    /* FIXME: allow for start/stop boundaries rather than consuming all data */
+
+    if (NULL == (pnew = calloc(1, sizeof(*p))))
+        return -1;
+
+    do {
+        bam1_t *b;
+        hts_pos_t pos;
+
+        r = seq_fetch(client_data, fp, h, &pnew->b);
+        if (r < -1) {
+            fprintf(stderr, "bam_next_seq() failure.\n");
+            goto error;
+        }
+
+        b = &pnew->b;
+
+        /* Force realloc */
+        //fp->bs = NULL;
+        //fp->bs_size = 0;
+
+        //r = samread(fp, pnew->b);
+        if (r >= 0) {
+            if (b->core.flag & BAM_FUNMAP)
+                continue;
+
+            if (b->core.tid == -1) {
+                /* Another indicator for unmapped */
+                continue;
+            } else if (b->core.tid == last_ref) {
+                pos = b->core.pos+1;
+                //printf("New seq at pos %d @ %d %s\n", pos, b->core.tid,
+                //       bam_name(b));
+            } else {
+                //printf("New ctg at pos %ld @ %d\n",b->core.pos+1,b->core.tid);
+                pos = HTS_POS_MAX;
+            }
+        } else {
+            pos = HTS_POS_MAX;
+        }
+
+        if (col > pos) {
+            fprintf(stderr, "BAM/SAM file is not sorted by position. "
+                    "Aborting\n");
+            goto error;
+        }
+
+        /* Process data between the last column and our latest addition */
+        while (col < pos && phead) {
+            struct pileup *eof_head = NULL, *eofp = NULL;
+            int v, ins, depth = 0;
+            //printf("Col=%ld pos=%ld nth=%d\n", col, pos, nth);
+
+            /* Pileup */
+            is_insert = 0;
+            pileup_t *pnext = phead ? phead->next : NULL;
+            for (p = phead, last = NULL; p; p = pnext) {
+#if 0
+                // Simple prefetching
+                pnext = p->next;
+                if (pnext)
+                    _mm_prefetch(pnext, _MM_HINT_T0);
+#else
+                // More complex prefetching => more instructions, but
+                // usually faster.
+                pnext = p->next;
+                if (pnext) {
+                    // start memory fetches; a big help on very deep data
+                    if (pnext->next)
+                        // struct 2 ahead
+                        _mm_prefetch(pnext->next, _MM_HINT_T0);
+                    // seq/qual 1 ahead
+                    _mm_prefetch(pnext->b_qual + pnext->seq_offset,
+                                 _MM_HINT_T0);
+                    _mm_prefetch(pnext->b_seq  + pnext->seq_offset/2,
+                                 _MM_HINT_T0);
+                }
+#endif
+
+                if (!get_next_base(p, col, nth, &ins))
+                    p->eof = 1;
+                if (p->eof == 1) {
+                    if (eofp)
+                        eofp->eofn = p;
+                    eofp = p;
+                    eofp->eofl = last;
+                    if (!eof_head)
+                        eof_head = eofp;
+                } else {
+                    last = p;
+                }
+
+                if (is_insert < ins)
+                    is_insert = ins;
+
+                depth++;
+            }
+            if ((ptail = last) == NULL)
+                ptail = phead;
+
+            /* Call our function on phead linked list */
+            v = seq_add(client_data, fp, h, phead, depth,
+#ifdef START_WITH_DEL
+                        col-1,
+#else
+                        col,
+#endif
+                        nth, is_insert);
+
+            /* Remove dead seqs */
+            for (p = eof_head ; p; p = p->eofn) {
+                if (p->eofl)
+                    p->eofl->next = p->next;
+                else
+                    phead = p->next;
+
+                p->next = pfree;
+                pfree = p;
+            }
+
+            if (v == 1)
+                break; /* early abort */
+
+            if (v != 0)
+                goto error;
+
+            /* Next column */
+            if (is_insert) {
+                nth++;
+            } else {
+                nth = 0;
+                col++;
+            }
+        }
+
+        /* May happen if we have a hole in the contig */
+        col = pos;
+
+        /* New contig */
+        if (b && b->core.tid != last_ref) {
+            last_ref = b->core.tid;
+            pos = b->core.pos+1;
+            nth = 0;
+            col = pos;
+        }
+
+        /*
+         * Add this seq.
+         * Note: cigars starting with I or P ops (eg 2P3I10M) mean we have
+         * alignment instructions that take place before the designated
+         * starting location listed in the SAM file. They won't get included
+         * in the callback function until they officially start, which is
+         * already too late.
+         *
+         * So to workaround this, we prefix all CIGAR with 1D, move the
+         * position by 1bp, and then force the callback code to remove
+         * leaving pads (either P or D generated).
+         *
+         * Ie it's a level 10 hack!
+         */
+        if (r >= 0) {
+            p = pnew;
+            p->next       = NULL;
+            p->cd         = NULL;
+            p->eofn       = NULL;
+            p->eofl       = NULL;
+            p->start      = 2;
+            p->eof        = 0;
+#ifdef START_WITH_DEL
+            p->pos        = pos-1;
+            p->cigar_ind  = 0;
+            p->b_cigar    = bam_get_cigar(&p->b);
+            if ((p->b_cigar[0] & BAM_CIGAR_MASK) == BAM_CHARD_CLIP) {
+                p->cigar_len  = p->b_cigar[0] >> BAM_CIGAR_SHIFT;
+                p->cigar_op   = BAM_CHARD_CLIP;
+                if ((p->b_cigar[1] & BAM_CIGAR_MASK) == BAM_CSOFT_CLIP) {
+                    /* xHxS... => xHxS1D... */
+                    p->b_cigar[0] = p->b_cigar[1];
+                    p->b_cigar[1] = (1 << BAM_CIGAR_SHIFT) | BAM_CDEL;
+                } else {
+                    /* xH... => xH1D... */
+                    p->b_cigar[0] = (1 << BAM_CIGAR_SHIFT) | BAM_CDEL;
+                }
+            } else {
+                if ((p->b_cigar[0] & BAM_CIGAR_MASK) == BAM_CSOFT_CLIP) {
+                    /* xS... => xS1D... */
+                    p->cigar_len  = p->b_cigar[0] >> BAM_CIGAR_SHIFT;
+                    p->cigar_op   = BAM_CSOFT_CLIP;
+                    p->b_cigar[0] = (1 << BAM_CIGAR_SHIFT) | BAM_CDEL;
+                } else {
+                    /* ... => 1D... */
+                    p->cigar_len  = 1;        /* was  0  */
+                    p->cigar_op   = BAM_CDEL; /* was 'X' */
+                }
+            }
+            p->seq_offset = -1;
+            p->first_del  = 1;
+#else
+            p->pos        = pos-1;
+            p->cigar_ind  = 0;
+            p->b_cigar    = bam_get_cigar(&p->b);
+            p->cigar_len  = 0;
+            p->cigar_op   = -1;
+            p->seq_offset = -1;
+            p->first_del  = 0;
+#endif
+            p->b_is_rev   = bam_is_rev(&p->b);
+            p->b_qual     = (uint8_t *)bam_get_qual(&p->b);
+            p->b_seq      = (uint8_t *)bam_get_seq(&p->b);
+
+            if (seq_init) {
+                int v;
+                v = seq_init(client_data, fp, h, p);
+                if (v == -1)
+                    goto error;
+
+                if (v == 1) {
+                    /* Keep this seq */
+                    if (phead) {
+                        ptail->next = p;
+                    } else {
+                        phead = p;
+                    }
+                    ptail = p;
+                } else {
+                    /* Push back on free list */
+                    p->next = pfree;
+                    pfree = p;
+                }
+            } else {
+                if (phead)
+                    ptail->next = p;
+                else
+                    phead = p;
+                ptail = p;
+            }
+
+            /* Allocate the next pileup rec */
+            if (pfree) {
+                pnew = pfree;
+                pfree = pfree->next;
+            } else {
+                if (NULL == (pnew = calloc(1, sizeof(*pnew))))
+                    goto error;
+            }
+        }
+    } while (r >= 0);
+
+    ret = 0;
+ error:
+
+    if (pnew) {
+        free(pnew->b.data);
+        free(pnew);
+    }
+
+    /* Tidy up */
+    for (p = pfree; p; p = next) {
+        next = p->next;
+        free(p->b.data);
+        free(p);
+    }
+
+    return ret;
+}
diff --git a/samtools/consensus_pileup.c.pysam.c b/samtools/consensus_pileup.c.pysam.c
new file mode 100644
index 0000000..dde0ad0
--- /dev/null
+++ b/samtools/consensus_pileup.c.pysam.c
@@ -0,0 +1,597 @@
+#include "samtools.pysam.h"
+
+/*  consensus__pileup.h -- Pileup orientated data per consensus column
+
+    Copyright (C) 2013-2016, 2020-2021 Genome Research Ltd.
+
+    Author: James Bonfied <jkb@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notices and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <config.h>
+#include <htslib/sam.h>
+
+#ifdef __SSE__
+#   include <xmmintrin.h>
+#else
+#   define _mm_prefetch(a,b)
+#endif
+
+#include "consensus_pileup.h"
+
+#define MIN(a,b) ((a)<(b)?(a):(b))
+#define bam_strand(b)  (((b)->core.flag & BAM_FREVERSE) != 0)
+
+/*
+ * START_WITH_DEL is the mode that Gap5 uses when building this. It prepends
+ * all cigar strings with 1D and decrements the position by one. (And then
+ * has code to reverse this operation in the pileup handler.)
+ *
+ * The reason for this is that it means reads starting with an insertion work.
+ * Otherwise the inserted bases are silently lost. (Try it with "samtools
+ * mpileup" and you can see it has the same issue.)
+ *
+ * However it's probably not want most people expect.
+ */
+//#define START_WITH_DEL
+
+/* --------------------------------------------------------------------------
+ * The pileup code itself.
+ *
+ * This consists of the external pileup_loop() function, which takes a
+ * sam/bam samfile_t pointer and a callback function. The callback function
+ * is called once per column of aligned data (so once per base in an
+ * insertion).
+ *
+ * Current known issues.
+ * 1) zero length matches, ie 2S2S cause failures.
+ * 2) Insertions at starts of sequences get included in the soft clip, so
+ *    2S2I2M is treated as if it's 4S2M
+ * 3) From 1 and 2 above, 1S1I2S becomes 2S2S which fails.
+ */
+
+
+/*
+ * Fetches the next base => the nth base at unpadded position pos. (Nth can
+ * be greater than 0 if we have an insertion in this column). Do not call this
+ * with pos/nth lower than the previous query, although higher is better.
+ * (This allows it to be initialised at base 0.)
+ *
+ * Stores the result in base and also updates is_insert to indicate that
+ * this sequence still has more bases in this position beyond the current
+ * nth parameter.
+ *
+ * Returns 1 if a base was fetched
+ *         0 if not (eg ran off the end of sequence)
+ */
+static int get_next_base(pileup_t *p, hts_pos_t pos, int nth, int *is_insert) {
+    bam1_t *b = &p->b;
+    int op = p->cigar_op;
+
+    p->start -= p->start>0;
+    if (p->first_del && op != BAM_CPAD)
+        p->first_del = 0;
+
+    *is_insert = 0;
+
+    /* Find pos first */
+    while (p->pos < pos) {
+        p->nth = 0;
+
+        if (p->cigar_len == 0) {
+            if (p->cigar_ind >= b->core.n_cigar) {
+                p->eof = 1;
+                return 0;
+            }
+
+            op=p->cigar_op  = p->b_cigar[p->cigar_ind] & BAM_CIGAR_MASK;
+            p->cigar_len = p->b_cigar[p->cigar_ind] >> BAM_CIGAR_SHIFT;
+            p->cigar_ind++;
+        }
+
+        if ((op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF)
+            && p->cigar_len <= pos - p->pos) {
+            p->seq_offset += p->cigar_len;
+            p->pos += p->cigar_len;
+            p->cigar_len = 0;
+        } else {
+            switch (op) {
+            case BAM_CMATCH:
+            case BAM_CEQUAL:
+            case BAM_CDIFF:
+                p->seq_offset++;
+                /* Fall through */
+            case BAM_CDEL:
+            case BAM_CREF_SKIP:
+                p->pos++;
+                p->cigar_len--;
+                break;
+
+            case BAM_CINS:
+            case BAM_CSOFT_CLIP:
+                p->seq_offset += p->cigar_len;
+                /* Fall through */
+            case BAM_CPAD:
+            case BAM_CHARD_CLIP:
+                p->cigar_len = 0;
+                break;
+
+            default:
+                fprintf(samtools_stderr, "Unhandled cigar_op %d\n", op);
+                return -1;
+            }
+        }
+    }
+
+    /* Now at pos, find nth base */
+    while (p->nth < nth) {
+        if (p->cigar_len == 0) {
+            if (p->cigar_ind >= b->core.n_cigar) {
+                p->eof = 1;
+                return 0; /* off end of seq */
+            }
+
+            op=p->cigar_op  = p->b_cigar[p->cigar_ind] & BAM_CIGAR_MASK;
+            p->cigar_len = p->b_cigar[p->cigar_ind] >> BAM_CIGAR_SHIFT;
+            p->cigar_ind++;
+        }
+
+        switch (op) {
+        case BAM_CMATCH:
+        case BAM_CEQUAL:
+        case BAM_CDIFF:
+        case BAM_CSOFT_CLIP:
+        case BAM_CDEL:
+        case BAM_CREF_SKIP:
+            goto at_nth; /* sorry, but it's fast! */
+
+        case BAM_CINS:
+            p->seq_offset++;
+            /* Fall through */
+        case BAM_CPAD:
+            p->cigar_len--;
+            p->nth++;
+            break;
+
+        case BAM_CHARD_CLIP:
+            p->cigar_len = 0;
+            break;
+
+        default:
+            fprintf(samtools_stderr, "Unhandled cigar_op %d\n", op);
+            return -1;
+        }
+    }
+ at_nth:
+
+    /* Fill out base & qual fields */
+    p->ref_skip = 0;
+    if (p->nth < nth && op != BAM_CINS) {
+        //p->base = '-';
+        p->base = '*';
+        p->base4 = 16;
+        p->padding = 1;
+        if (p->seq_offset < b->core.l_qseq)
+            p->qual = (p->qual + p->b_qual[p->seq_offset+1])/2;
+        else
+            p->qual = 0;
+    } else {
+        p->padding = 0;
+        switch(op) {
+        case BAM_CDEL:
+            p->base = '*';
+            p->base4 = 16;
+            if (p->seq_offset+1 < b->core.l_qseq)
+                p->qual = (p->qual + p->b_qual[p->seq_offset+1])/2;
+            else
+                p->qual = (p->qual + p->b_qual[p->seq_offset])/2;
+            break;
+
+        case BAM_CPAD:
+            //p->base = '+';
+            p->base = '*';
+            p->base4 = 16;
+            if (p->seq_offset+1 < b->core.l_qseq)
+                p->qual = (p->qual + p->b_qual[p->seq_offset+1])/2;
+            else
+                p->qual = (p->qual + p->b_qual[p->seq_offset])/2;
+            break;
+
+        case BAM_CREF_SKIP:
+            p->base = '.';
+            p->base4 = 0;
+            p->qual = 0;
+            /* end of fragment, but not sequence */
+            p->eof = p->eof ? 2 : 3;
+            p->ref_skip = 1;
+            break;
+
+        default:
+            if (p->seq_offset < b->core.l_qseq) {
+                p->qual = p->b_qual[p->seq_offset];
+                p->base4 = p->b_seq[p->seq_offset/2] >>
+                    ((~p->seq_offset&1)<<2) & 0xf;
+                p->base = "NACMGRSVTWYHKDBN"[p->base4];
+            } else {
+                p->base = 'N';
+                p->base4 = 15;
+                p->qual = 0xff;
+            }
+
+            break;
+        }
+    }
+
+    /* Handle moving out of N (skip) into sequence again */
+    if (p->eof && p->base != '.') {
+        p->start = 1;
+        p->ref_skip = 1;
+        p->eof = 0;
+    }
+
+    /* Starting with an indel needs a minor fudge */
+    if (p->start && p->cigar_op == BAM_CDEL) {
+        p->first_del = 1;
+    }
+
+    /* Check if next op is an insertion of some sort */
+    if (p->cigar_len == 0) {
+        if (p->cigar_ind < b->core.n_cigar) {
+            op=p->cigar_op  = p->b_cigar[p->cigar_ind] & BAM_CIGAR_MASK;
+            p->cigar_len = p->b_cigar[p->cigar_ind] >> BAM_CIGAR_SHIFT;
+            p->cigar_ind++;
+            if (op == BAM_CREF_SKIP) {
+                p->eof = 3;
+                p->ref_skip = 1;
+            }
+        } else {
+            p->eof = 1;
+        }
+    }
+
+    switch (op) {
+    case BAM_CPAD:
+    case BAM_CINS:
+        *is_insert = p->cigar_len;
+        break;
+
+    case BAM_CSOFT_CLIP:
+        /* Last op 'S' => eof */
+        p->eof = (p->cigar_ind == b->core.n_cigar ||
+                  (p->cigar_ind+1 == b->core.n_cigar &&
+                   (p->b_cigar[p->cigar_ind] & BAM_CIGAR_MASK)
+                   == BAM_CHARD_CLIP))
+            ? 1
+            : 0;
+        break;
+
+    case BAM_CHARD_CLIP:
+        p->eof = 1;
+        break;
+
+    default:
+        break;
+    }
+
+    return 1;
+}
+
+/*
+ * Loops through a set of supplied ranges producing columns of data.
+ * When found, it calls func with clientdata as a callback. Func should
+ * return 0 for success and non-zero for failure. seq_init() is called
+ * on each new entry before we start processing it. It should return 0 or 1
+ * to indicate reject or accept status (eg to filter unmapped data).
+ * If seq_init() returns -1 we abort the pileup_loop with an error.
+ * seq_init may be NULL.
+ *
+ * Returns 0 on success
+ *        -1 on failure
+ */
+int pileup_loop(samFile *fp,
+                sam_hdr_t *h,
+                int (*seq_fetch)(void *client_data,
+                                 samFile *fp,
+                                 sam_hdr_t *h,
+                                 bam1_t *b),
+                int (*seq_init)(void *client_data,
+                                samFile *fp,
+                                sam_hdr_t *h,
+                                pileup_t *p),
+                int (*seq_add)(void *client_data,
+                               samFile *fp,
+                               sam_hdr_t *h,
+                               pileup_t *p,
+                               int depth,
+                               hts_pos_t pos,
+                               int nth,
+                               int is_insert),
+                void *client_data) {
+    int ret = -1;
+    pileup_t *phead = NULL, *p, *pfree = NULL, *last, *next, *ptail = NULL;
+    pileup_t *pnew = NULL;
+    int is_insert, nth = 0, r;
+    hts_pos_t col = 0;
+    int last_ref = -1;
+
+    /* FIXME: allow for start/stop boundaries rather than consuming all data */
+
+    if (NULL == (pnew = calloc(1, sizeof(*p))))
+        return -1;
+
+    do {
+        bam1_t *b;
+        hts_pos_t pos;
+
+        r = seq_fetch(client_data, fp, h, &pnew->b);
+        if (r < -1) {
+            fprintf(samtools_stderr, "bam_next_seq() failure.\n");
+            goto error;
+        }
+
+        b = &pnew->b;
+
+        /* Force realloc */
+        //fp->bs = NULL;
+        //fp->bs_size = 0;
+
+        //r = samread(fp, pnew->b);
+        if (r >= 0) {
+            if (b->core.flag & BAM_FUNMAP)
+                continue;
+
+            if (b->core.tid == -1) {
+                /* Another indicator for unmapped */
+                continue;
+            } else if (b->core.tid == last_ref) {
+                pos = b->core.pos+1;
+                //printf("New seq at pos %d @ %d %s\n", pos, b->core.tid,
+                //       bam_name(b));
+            } else {
+                //printf("New ctg at pos %ld @ %d\n",b->core.pos+1,b->core.tid);
+                pos = HTS_POS_MAX;
+            }
+        } else {
+            pos = HTS_POS_MAX;
+        }
+
+        if (col > pos) {
+            fprintf(samtools_stderr, "BAM/SAM file is not sorted by position. "
+                    "Aborting\n");
+            goto error;
+        }
+
+        /* Process data between the last column and our latest addition */
+        while (col < pos && phead) {
+            struct pileup *eof_head = NULL, *eofp = NULL;
+            int v, ins, depth = 0;
+            //printf("Col=%ld pos=%ld nth=%d\n", col, pos, nth);
+
+            /* Pileup */
+            is_insert = 0;
+            pileup_t *pnext = phead ? phead->next : NULL;
+            for (p = phead, last = NULL; p; p = pnext) {
+#if 0
+                // Simple prefetching
+                pnext = p->next;
+                if (pnext)
+                    _mm_prefetch(pnext, _MM_HINT_T0);
+#else
+                // More complex prefetching => more instructions, but
+                // usually faster.
+                pnext = p->next;
+                if (pnext) {
+                    // start memory fetches; a big help on very deep data
+                    if (pnext->next)
+                        // struct 2 ahead
+                        _mm_prefetch(pnext->next, _MM_HINT_T0);
+                    // seq/qual 1 ahead
+                    _mm_prefetch(pnext->b_qual + pnext->seq_offset,
+                                 _MM_HINT_T0);
+                    _mm_prefetch(pnext->b_seq  + pnext->seq_offset/2,
+                                 _MM_HINT_T0);
+                }
+#endif
+
+                if (!get_next_base(p, col, nth, &ins))
+                    p->eof = 1;
+                if (p->eof == 1) {
+                    if (eofp)
+                        eofp->eofn = p;
+                    eofp = p;
+                    eofp->eofl = last;
+                    if (!eof_head)
+                        eof_head = eofp;
+                } else {
+                    last = p;
+                }
+
+                if (is_insert < ins)
+                    is_insert = ins;
+
+                depth++;
+            }
+            if ((ptail = last) == NULL)
+                ptail = phead;
+
+            /* Call our function on phead linked list */
+            v = seq_add(client_data, fp, h, phead, depth,
+#ifdef START_WITH_DEL
+                        col-1,
+#else
+                        col,
+#endif
+                        nth, is_insert);
+
+            /* Remove dead seqs */
+            for (p = eof_head ; p; p = p->eofn) {
+                if (p->eofl)
+                    p->eofl->next = p->next;
+                else
+                    phead = p->next;
+
+                p->next = pfree;
+                pfree = p;
+            }
+
+            if (v == 1)
+                break; /* early abort */
+
+            if (v != 0)
+                goto error;
+
+            /* Next column */
+            if (is_insert) {
+                nth++;
+            } else {
+                nth = 0;
+                col++;
+            }
+        }
+
+        /* May happen if we have a hole in the contig */
+        col = pos;
+
+        /* New contig */
+        if (b && b->core.tid != last_ref) {
+            last_ref = b->core.tid;
+            pos = b->core.pos+1;
+            nth = 0;
+            col = pos;
+        }
+
+        /*
+         * Add this seq.
+         * Note: cigars starting with I or P ops (eg 2P3I10M) mean we have
+         * alignment instructions that take place before the designated
+         * starting location listed in the SAM file. They won't get included
+         * in the callback function until they officially start, which is
+         * already too late.
+         *
+         * So to workaround this, we prefix all CIGAR with 1D, move the
+         * position by 1bp, and then force the callback code to remove
+         * leaving pads (either P or D generated).
+         *
+         * Ie it's a level 10 hack!
+         */
+        if (r >= 0) {
+            p = pnew;
+            p->next       = NULL;
+            p->cd         = NULL;
+            p->eofn       = NULL;
+            p->eofl       = NULL;
+            p->start      = 2;
+            p->eof        = 0;
+#ifdef START_WITH_DEL
+            p->pos        = pos-1;
+            p->cigar_ind  = 0;
+            p->b_cigar    = bam_get_cigar(&p->b);
+            if ((p->b_cigar[0] & BAM_CIGAR_MASK) == BAM_CHARD_CLIP) {
+                p->cigar_len  = p->b_cigar[0] >> BAM_CIGAR_SHIFT;
+                p->cigar_op   = BAM_CHARD_CLIP;
+                if ((p->b_cigar[1] & BAM_CIGAR_MASK) == BAM_CSOFT_CLIP) {
+                    /* xHxS... => xHxS1D... */
+                    p->b_cigar[0] = p->b_cigar[1];
+                    p->b_cigar[1] = (1 << BAM_CIGAR_SHIFT) | BAM_CDEL;
+                } else {
+                    /* xH... => xH1D... */
+                    p->b_cigar[0] = (1 << BAM_CIGAR_SHIFT) | BAM_CDEL;
+                }
+            } else {
+                if ((p->b_cigar[0] & BAM_CIGAR_MASK) == BAM_CSOFT_CLIP) {
+                    /* xS... => xS1D... */
+                    p->cigar_len  = p->b_cigar[0] >> BAM_CIGAR_SHIFT;
+                    p->cigar_op   = BAM_CSOFT_CLIP;
+                    p->b_cigar[0] = (1 << BAM_CIGAR_SHIFT) | BAM_CDEL;
+                } else {
+                    /* ... => 1D... */
+                    p->cigar_len  = 1;        /* was  0  */
+                    p->cigar_op   = BAM_CDEL; /* was 'X' */
+                }
+            }
+            p->seq_offset = -1;
+            p->first_del  = 1;
+#else
+            p->pos        = pos-1;
+            p->cigar_ind  = 0;
+            p->b_cigar    = bam_get_cigar(&p->b);
+            p->cigar_len  = 0;
+            p->cigar_op   = -1;
+            p->seq_offset = -1;
+            p->first_del  = 0;
+#endif
+            p->b_is_rev   = bam_is_rev(&p->b);
+            p->b_qual     = (uint8_t *)bam_get_qual(&p->b);
+            p->b_seq      = (uint8_t *)bam_get_seq(&p->b);
+
+            if (seq_init) {
+                int v;
+                v = seq_init(client_data, fp, h, p);
+                if (v == -1)
+                    goto error;
+
+                if (v == 1) {
+                    /* Keep this seq */
+                    if (phead) {
+                        ptail->next = p;
+                    } else {
+                        phead = p;
+                    }
+                    ptail = p;
+                } else {
+                    /* Push back on free list */
+                    p->next = pfree;
+                    pfree = p;
+                }
+            } else {
+                if (phead)
+                    ptail->next = p;
+                else
+                    phead = p;
+                ptail = p;
+            }
+
+            /* Allocate the next pileup rec */
+            if (pfree) {
+                pnew = pfree;
+                pfree = pfree->next;
+            } else {
+                if (NULL == (pnew = calloc(1, sizeof(*pnew))))
+                    goto error;
+            }
+        }
+    } while (r >= 0);
+
+    ret = 0;
+ error:
+
+    if (pnew) {
+        free(pnew->b.data);
+        free(pnew);
+    }
+
+    /* Tidy up */
+    for (p = pfree; p; p = next) {
+        next = p->next;
+        free(p->b.data);
+        free(p);
+    }
+
+    return ret;
+}
diff --git a/samtools/consensus_pileup.h b/samtools/consensus_pileup.h
new file mode 100644
index 0000000..6eafdbb
--- /dev/null
+++ b/samtools/consensus_pileup.h
@@ -0,0 +1,79 @@
+/*  consensus_pileup.h -- Pileup orientated data per consensus column
+
+    Copyright (C) 2013-2016, 2020-2021 Genome Research Ltd.
+
+    Author: James Bonfied <jkb@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notices and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <htslib/sam.h>
+
+typedef struct pileup {
+    // commonly used things together, to fit in a cache line (64 bytes)
+    struct pileup *next;  // A link list, for active seqs
+    void *cd;             // General purpose per-seq client-data
+    int  eof;             // True if this sequence has finished
+    int  qual;            // Current qual (for active seq only)
+    char start;           // True if this is a new sequence
+    char base;            // Current base (for active seq only) in ASCII
+    char ref_skip;        // True if the cause of eof or start is cigar N
+    char padding;         // True if the base was added due to another seq
+    int  base4;           // Base in 4-bit notation (0-15)
+    hts_pos_t pos;        // Current unpadded position in seq
+    int  nth;             // nth base at unpadded position 'pos'
+    int  b_is_rev;        // 0 => fwd, 1 => rev
+    int  seq_offset;      // Current base position in s->seq[] array.
+
+    unsigned char *b_qual;// cached bam_qual
+    unsigned char *b_seq; // cached bam_seq
+
+    // --- 64 bytes
+    struct pileup *eofn;  // p->eof set, next eof member
+    struct pileup *eofl;  // last non-eof that points to p with p->eof
+
+    uint32_t *b_cigar;    // cached bam_cigar
+
+    int  cigar_ind;       // Current location in s->alignment cigar str
+    int  cigar_op;        // Current cigar operation
+    int  cigar_len;       // Remaining length of this cigar op
+
+    int  first_del;       // Used when first base is a deletion
+
+    bam1_t b;             // Bam entry associated with struct
+} pileup_t;
+
+int pileup_loop(samFile *fp,
+                sam_hdr_t *h,
+                int (*seq_fetch)(void *client_data,
+                                 samFile *fp,
+                                 sam_hdr_t *h,
+                                 bam1_t *b),
+                int (*seq_init)(void *client_data,
+                                samFile *fp,
+                                sam_hdr_t *h,
+                                pileup_t *p),
+                int (*seq_add)(void *client_data,
+                               samFile *fp,
+                               sam_hdr_t *h,
+                               pileup_t *p,
+                               int depth,
+                               hts_pos_t pos,
+                               int nth,
+                               int is_insert),
+                void *client_data);
diff --git a/samtools/coverage.c b/samtools/coverage.c
new file mode 100644
index 0000000..dedaa8e
--- /dev/null
+++ b/samtools/coverage.c
@@ -0,0 +1,683 @@
+/* coverage.c -- samtools coverage subcommand
+
+    Copyright (C) 2018,2019 Florian Breitwieser
+    Portions copyright (C) 2019-2021 Genome Research Ltd.
+
+    Author: Florian P Breitwieser <florian.bw@gmail.com>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+/* This program calculates coverage from multiple BAMs
+ * simultaneously, to achieve random access and to use the BED interface.
+ * To compile this program separately, you may:
+ *
+ *   gcc -g -O2 -Wall -o bamcov -D_MAIN_BAMCOV coverage.c -lhts -lz
+ */
+
+// C headers
+#include <config.h>
+
+#include <ctype.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <stdarg.h>  // variadic functions
+#include <limits.h>  // INT_MAX
+#include <math.h>    // round
+#include <stdbool.h>
+#include <string.h>
+#include <unistd.h>
+#include <assert.h>
+
+#ifdef _WIN32
+#include <windows.h>
+#else
+#include <sys/ioctl.h>
+#endif
+
+#include "htslib/sam.h"
+#include "htslib/hts.h"
+#include "samtools.h"
+#include "sam_opts.h"
+
+typedef struct {  // auxiliary data structure to hold stats on coverage
+    unsigned long long n_covered_bases;
+    unsigned long long summed_coverage;
+    unsigned long long summed_baseQ;
+    unsigned long long summed_mapQ;
+    unsigned int n_reads;
+    unsigned int n_selected_reads;
+    bool covered;
+    hts_pos_t beg;
+    hts_pos_t end;
+    int64_t bin_width;
+} stats_aux_t;
+
+typedef struct {  // auxiliary data structure to hold a BAM file
+    samFile *fp;     // file handle
+    sam_hdr_t *hdr;  // file header
+    hts_itr_t *iter; // iterator to a region - NULL for us by default
+    int min_mapQ;    // mapQ filter
+    int min_len;     // length filter
+    int fail_flags;
+    int required_flags;
+    stats_aux_t *stats;
+} bam_aux_t;
+
+#if __STDC_VERSION__ >= 199901L
+#define VERTICAL_LINE "\u2502" // BOX DRAWINGS LIGHT VERTICAL
+
+// UTF8 specifies block characters in eights going from \u2581 (lower one eight block) to \u2588 (full block)
+//   https://en.wikipedia.org/wiki/Block_Elements
+// LOWER ONE EIGHTH BLOCK … FULL BLOCK
+static const char *const BLOCK_CHARS8[8] = {"\u2581", "\u2582", "\u2583", "\u2584", "\u2585", "\u2586", "\u2587", "\u2588"};
+// In some terminals / with some fonts not all UTF8 block characters are supported (e.g. Putty). Use only half and full block for those
+static const char *const BLOCK_CHARS2[2] = {".", ":"};
+
+#else
+
+// Fall back to explicit UTF-8 encodings of the same characters
+#define VERTICAL_LINE "\xE2\x94\x82"
+
+static const char *const BLOCK_CHARS8[8] = {
+    "\xE2\x96\x81", "\xE2\x96\x82", "\xE2\x96\x83", "\xE2\x96\x84",
+    "\xE2\x96\x85", "\xE2\x96\x86", "\xE2\x96\x87", "\xE2\x96\x88" };
+
+static const char *const BLOCK_CHARS2[2] = {".", ":"};
+
+#endif
+
+// in bam_plcmd.c
+int read_file_list(const char *file_list, int *n, char **argv[]);
+
+static int usage() {
+    fprintf(stdout, "Usage: samtools coverage [options] in1.bam [in2.bam [...]]\n\n"
+            "Input options:\n"
+            "  -b, --bam-list FILE     list of input BAM filenames, one per line\n"
+            "  -l, --min-read-len INT  ignore reads shorter than INT bp [0]\n"
+            "  -q, --min-MQ INT        mapping quality threshold [0]\n"
+            "  -Q, --min-BQ INT        base quality threshold [0]\n"
+            "  --rf <int|str>          required flags: skip reads with mask bits unset []\n"
+            "  --ff <int|str>          filter flags: skip reads with mask bits set \n"
+            "                                      [UNMAP,SECONDARY,QCFAIL,DUP]\n"
+            "  -d, --depth INT         maximum allowed coverage depth [1000000].\n"
+            "                          If 0, depth is set to the maximum integer value,\n"
+            "                          effectively removing any depth limit.\n"
+            "Output options:\n"
+            "  -m, --histogram         show histogram instead of tabular output\n"
+            "  -A, --ascii             show only ASCII characters in histogram\n"
+            "  -o, --output FILE       write output to FILE [stdout]\n"
+            "  -H, --no-header         don't print a header in tabular mode\n"
+            "  -w, --n-bins INT        number of bins in histogram [terminal width - 40]\n"
+            "  -r, --region REG        show specified region. Format: chr:start-end. \n"
+            "  -h, --help              help (this page)\n");
+
+    fprintf(stdout, "\nGeneric options:\n");
+    sam_global_opt_help(stdout, "-.--.--.");
+
+    fprintf(stdout,
+            "\nSee manpage for additional details.\n"
+            "  rname       Reference name / chromosome\n"
+            "  startpos    Start position\n"
+            "  endpos      End position (or sequence length)\n"
+            "  numreads    Number reads aligned to the region (after filtering)\n"
+            "  covbases    Number of covered bases with depth >= 1\n"
+            "  coverage    Percentage of covered bases [0..100]\n"
+            "  meandepth   Mean depth of coverage\n"
+            "  meanbaseq   Mean baseQ in covered region\n"
+            "  meanmapq    Mean mapQ of selected reads\n"
+           );
+
+    return EXIT_SUCCESS;
+}
+
+static char* center_text(char *text, char *buf, int width) {
+    int len = strlen(text);
+    assert(len <= width);
+    int padding = (width - len) / 2;
+    int padding_ex = (width - len) % 2;
+    if (padding >= 1)
+        sprintf(buf, " %*s%*s", len+padding, text, padding-1+padding_ex, " ");
+    else
+        sprintf(buf, "%s", text);
+
+    return buf;
+}
+
+static char* readable_bps(double base_pairs, char *buf) {
+    const char* units[] = {"", "K", "M", "G", "T"};
+    int i = 0;
+    while (base_pairs >= 1000 && i < (sizeof(units)/sizeof(units[0]) - 1)) {
+        base_pairs /= 1000;
+        i++;
+    }
+    sprintf(buf, "%.*f%s", i, base_pairs, units[i]);
+    return buf;
+}
+
+// read one alignment from one BAM file
+static int read_bam(void *data, bam1_t *b) {
+    bam_aux_t *aux = (bam_aux_t*)data; // data in fact is a pointer to an auxiliary structure
+    int nref = sam_hdr_nref(aux->hdr);
+    int ret;
+    while (1) {
+        if((ret = aux->iter? sam_itr_next(aux->fp, aux->iter, b) : sam_read1(aux->fp, aux->hdr, b)) < 0) break;
+        if (b->core.tid >= 0 && b->core.tid < nref)
+            aux->stats[b->core.tid].n_reads++;
+
+        if ( aux->fail_flags && (b->core.flag & aux->fail_flags) ) continue;
+        if ( aux->required_flags && !(b->core.flag & aux->required_flags) ) continue;
+        if ( b->core.qual < aux->min_mapQ ) continue;
+        if ( aux->min_len && bam_cigar2qlen(b->core.n_cigar, bam_get_cigar(b)) < aux->min_len ) continue;
+        if (b->core.tid >= 0 && b->core.tid < nref) {
+            aux->stats[b->core.tid].n_selected_reads++;
+            aux->stats[b->core.tid].summed_mapQ += b->core.qual;
+        }
+        break;
+    }
+    return ret;
+}
+
+void print_tabular_line(FILE *file_out, const sam_hdr_t *h, const stats_aux_t *stats, int tid) {
+    fputs(sam_hdr_tid2name(h, tid), file_out);
+    double region_len = (double) stats[tid].end - stats[tid].beg;
+    fprintf(file_out, "\t%"PRId64"\t%"PRId64"\t%u\t%llu\t%g\t%g\t%.3g\t%.3g\n",
+            stats[tid].beg+1,
+            stats[tid].end,
+            stats[tid].n_selected_reads,
+            stats[tid].n_covered_bases,
+            100.0 * stats[tid].n_covered_bases / region_len,
+            stats[tid].summed_coverage / region_len,
+            stats[tid].summed_coverage > 0? stats[tid].summed_baseQ/(double) stats[tid].summed_coverage : 0,
+            stats[tid].n_selected_reads > 0? stats[tid].summed_mapQ/(double) stats[tid].n_selected_reads : 0
+           );
+}
+
+void print_hist(FILE *file_out, const sam_hdr_t *h, const stats_aux_t *stats, int tid, const uint32_t *hist,
+        const int hist_size, const bool full_utf) {
+    int i, col;
+    bool show_percentiles = false;
+    const int n_rows = 10;
+    const char * const * BLOCK_CHARS = full_utf? BLOCK_CHARS8 : BLOCK_CHARS2;
+    const int blockchar_len = full_utf? 8 : 2;
+    double region_len = stats[tid].end - stats[tid].beg;
+
+    // Calculate histogram that contains percent covered
+    double hist_data[hist_size];
+    double max_val = 0.0;
+    for (i = 0; i < hist_size; ++i) {
+        hist_data[i] = 100 * hist[i] / (double) stats[tid].bin_width;
+        if (hist_data[i] > max_val) max_val = hist_data[i];
+    }
+
+    char buf[30];
+    fprintf(file_out, "%s (%sbp)\n", sam_hdr_tid2name(h, tid), readable_bps(sam_hdr_tid2len(h, tid), buf));
+
+    double row_bin_size = max_val / (double) n_rows;
+    for (i = n_rows-1; i >= 0; --i) {
+        double current_bin = row_bin_size * i;
+        if (show_percentiles) {
+            fprintf(file_out, ">%3i%% ", i*10);
+        } else {
+            fprintf(file_out, ">%7.2f%% ", current_bin);
+        }
+        fprintf(file_out, full_utf ? VERTICAL_LINE : "|");
+        for (col = 0; col < hist_size; ++col) {
+            // get the difference in eights, or halfs when full UTF8 is not supported
+            int cur_val_diff = round(blockchar_len * (hist_data[col] - current_bin) / row_bin_size) - 1;
+            if (cur_val_diff < 0) {
+                fputc(' ', file_out);
+            } else {
+                if (cur_val_diff >= blockchar_len)
+                    cur_val_diff = blockchar_len - 1;
+
+                fprintf(file_out, "%s", BLOCK_CHARS[cur_val_diff]);
+            }
+        }
+        fprintf(file_out, full_utf ? VERTICAL_LINE : "|");
+        fputc(' ', file_out);
+        switch (i) {
+            case 9: fprintf(file_out, "Number of reads: %u", stats[tid].n_selected_reads); break;
+            case 8: if (stats[tid].n_reads - stats[tid].n_selected_reads > 0) fprintf(file_out, "    (%i filtered)", stats[tid].n_reads - stats[tid].n_selected_reads); break;
+            case 7: fprintf(file_out, "Covered bases:   %sbp", readable_bps(stats[tid].n_covered_bases, buf)); break;
+            case 6: fprintf(file_out, "Percent covered: %.4g%%",
+                            100.0 * stats[tid].n_covered_bases / region_len); break;
+            case 5: fprintf(file_out, "Mean coverage:   %.3gx",
+                            stats[tid].summed_coverage / region_len); break;
+            case 4: fprintf(file_out, "Mean baseQ:      %.3g",
+                            stats[tid].summed_baseQ/(double) stats[tid].summed_coverage); break;
+            case 3: fprintf(file_out, "Mean mapQ:       %.3g",
+                            stats[tid].summed_mapQ/(double) stats[tid].n_selected_reads); break;
+            case 1: fprintf(file_out, "Histo bin width: %sbp",
+                            readable_bps(stats[tid].bin_width, buf)); break;
+            case 0: fprintf(file_out, "Histo max bin:   %.5g%%", max_val); break;
+        };
+        fputc('\n', file_out);
+    }
+
+    // print x axis. Could be made pretty for widths that are not divisible
+    // by 10 by variable spacing of the labels, instead of placing a label every 10 characters
+    char buf2[50];
+    fprintf(file_out, "     %s", center_text(readable_bps(stats[tid].beg + 1, buf), buf2, 10));
+    int rest;
+    for (rest = 10; rest < 10*(hist_size/10); rest += 10) {
+        fprintf(file_out, "%s", center_text(readable_bps(stats[tid].beg + stats[tid].bin_width*rest, buf), buf2, 10));
+    }
+    int last_padding = hist_size%10;
+    fprintf(file_out, "%*s%s", last_padding, " ", center_text(readable_bps(stats[tid].end, buf), buf2, 10));
+    fprintf(file_out, "\n");
+}
+
+int main_coverage(int argc, char *argv[]) {
+    int status = EXIT_SUCCESS;
+
+    int ret, tid = -1, old_tid = -1, pos, i, j;
+
+    int max_depth = 1000000;
+    int opt_min_baseQ = 0;
+    int opt_min_mapQ = 0;
+    int opt_min_len = 0;
+    int opt_n_bins = 50;
+    bool opt_full_width = true;
+    char *opt_output_file = NULL;
+    bam_aux_t **data = NULL;
+    bam_mplp_t mplp = NULL;
+    const bam_pileup1_t **plp = NULL;
+    uint32_t *hist = NULL;
+    stats_aux_t *stats = NULL;
+    char *opt_reg = 0; // specified region
+    char *opt_file_list = NULL;
+    int n_bam_files = 0;
+    char **fn = NULL;
+    int fail_flags = (BAM_FUNMAP | BAM_FSECONDARY | BAM_FQCFAIL | BAM_FDUP); // Default fail flags
+    int required_flags = 0;
+
+    int *n_plp = NULL;
+    sam_hdr_t *h = NULL; // BAM header of the 1st input
+
+    bool opt_print_header = true;
+    bool opt_print_tabular = true;
+    bool opt_print_histogram = false;
+    bool opt_full_utf = true;
+
+    FILE *file_out = stdout;
+
+    sam_global_args ga = SAM_GLOBAL_ARGS_INIT;
+    static const struct option lopts[] = {
+        SAM_OPT_GLOBAL_OPTIONS('-', 0, '-', '-', 0, '-'),
+        {"rf", required_argument, NULL, 1}, // require flag
+        {"ff", required_argument, NULL, 2}, // filter flag
+        {"incl-flags", required_argument, NULL, 1}, // require flag
+        {"excl-flags", required_argument, NULL, 2}, // filter flag
+        {"bam-list", required_argument, NULL, 'b'},
+        {"min-read-len", required_argument, NULL, 'l'},
+        {"min-MQ", required_argument, NULL, 'q'},
+        {"min-mq", required_argument, NULL, 'q'},
+        {"min-BQ", required_argument, NULL, 'Q'},
+        {"min-bq", required_argument, NULL, 'Q'},
+        {"histogram", no_argument, NULL, 'm'},
+        {"ascii", no_argument, NULL, 'A'},
+        {"output", required_argument, NULL, 'o'},
+        {"no-header", no_argument, NULL, 'H'},
+        {"n-bins", required_argument, NULL, 'w'},
+        {"region", required_argument, NULL, 'r'},
+        {"help", no_argument, NULL, 'h'},
+        {"depth", required_argument, NULL, 'd'},
+        { NULL, 0, NULL, 0 }
+    };
+
+    // parse the command line
+    int c;
+    opterr = 0;
+    while ((c = getopt_long(argc, argv, "Ao:l:q:Q:hHw:r:b:md:", lopts, NULL)) != -1) {
+        switch (c) {
+            case 1:
+                if ((required_flags = bam_str2flag(optarg)) < 0) {
+                    fprintf(stderr,"Could not parse --rf %s\n", optarg); return EXIT_FAILURE;
+                }; break;
+            case 2:
+                if ((fail_flags = bam_str2flag(optarg)) < 0) {
+                    fprintf(stderr,"Could not parse --ff %s\n", optarg); return EXIT_FAILURE;
+                }; break;
+            case 'o': opt_output_file = optarg; opt_full_width = false; break;
+            case 'l': opt_min_len = atoi(optarg); break;
+            case 'q': opt_min_mapQ = atoi(optarg); break;
+            case 'Q': opt_min_baseQ = atoi(optarg); break;
+            case 'd': max_depth = atoi(optarg); break; // maximum coverage depth
+            case 'w': opt_n_bins = atoi(optarg); opt_full_width = false;
+                      opt_print_histogram = true; opt_print_tabular = false;
+                      break;
+            case 'r': opt_reg = optarg; break;   // parsing a region requires a BAM header (strdup unnecessary)
+            case 'b': opt_file_list = optarg; break;
+            case 'm': opt_print_histogram = true; opt_print_tabular = false; break;
+            case 'A': opt_full_utf = false;
+                      opt_print_histogram = true; opt_print_tabular = false;
+                      break;
+            case 'H': opt_print_header = false; break;
+            case 'h': return usage();
+            default:  if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break;
+                          /* else fall-through */
+            case '?':
+                if (optopt != '?') {  // '-?' appeared on command line
+                    if (optopt) { // Bad short option
+                        print_error("coverage", "invalid option -- '%c'", optopt);
+                    } else { // Bad long option
+                        // Do our best.  There is no good solution to finding
+                        // out what the bad option was.
+                        // See, e.g. https://stackoverflow.com/questions/2723888/where-does-getopt-long-store-an-unrecognized-option
+                        if (optind > 0 && strncmp(argv[optind - 1], "--", 2) == 0) {
+                            print_error("coverage", "unrecognised option '%s'",
+                                        argv[optind - 1]);
+                        }
+                    }
+                }
+                return usage();
+        }
+    }
+    if (optind == argc && !opt_file_list)
+        return usage();
+
+    // output file provided by user
+    if (opt_output_file != NULL && strcmp(opt_output_file,"-")!=0) {
+        file_out = fopen( opt_output_file, "w" );
+        if (file_out == NULL) {
+            print_error_errno("coverage", "Cannot open \"%s\" for writing.", opt_output_file);
+            return EXIT_FAILURE;
+        }
+    }
+
+    if (opt_n_bins <= 0 || opt_full_width) {
+        // get number of columns of terminal
+        const char* env_columns = getenv("COLUMNS");
+        int columns = 0;
+        if (env_columns == NULL) {
+#ifdef _WIN32
+            CONSOLE_SCREEN_BUFFER_INFO csbi;
+            if (GetConsoleScreenBufferInfo(GetStdHandle(STD_OUTPUT_HANDLE), &csbi)) {
+                columns = csbi.srWindow.Right - csbi.srWindow.Left + 1;
+            }
+#elif defined TIOCGWINSZ
+            struct winsize w;
+            if (ioctl(2, TIOCGWINSZ, &w) == 0)
+                columns = w.ws_col;
+#endif
+        } else {
+            columns = atoi(env_columns); // atoi(NULL) returns 0
+        }
+
+        if (columns > 60) {
+            opt_n_bins = columns - 40;
+        } else {
+            opt_n_bins = 40;
+        }
+    }
+
+    // setvbuf(file_out, NULL, _IONBF, 0); //turn off buffering
+
+    // Open all BAM files
+    if (opt_file_list) {
+        // Read file names from opt_file_list into argv, and record the number of files in n_bam_files
+        if (read_file_list(opt_file_list, &n_bam_files, &fn)) {
+            print_error_errno("coverage", "Cannot open file list \"%s\".", opt_file_list);
+            return EXIT_FAILURE;
+        }
+        argv = fn;
+        optind = 0;
+    } else {
+        n_bam_files = argc - optind; // the number of BAMs on the command line
+    }
+
+    data = (bam_aux_t **)calloc(n_bam_files, sizeof(bam_aux_t*)); // data[i] for the i-th BAM file
+    if (!data) {
+        print_error_errno("coverage", "Failed to allocate memory");
+        status = EXIT_FAILURE;
+        goto coverage_end;
+    }
+
+    for (i = 0; i < n_bam_files; ++i) {
+        int rf;
+        data[i] = (bam_aux_t *) calloc(1, sizeof(bam_aux_t));
+        if (!data[i]) {
+            print_error_errno("coverage", "Failed to allocate memory");
+            status = EXIT_FAILURE;
+            goto coverage_end;
+        }
+        data[i]->fp = sam_open_format(argv[optind+i], "r", &ga.in); // open BAM
+
+        if (data[i]->fp == NULL) {
+            print_error_errno("coverage", "Could not open \"%s\"", argv[optind+i]);
+            status = EXIT_FAILURE;
+            goto coverage_end;
+        }
+        rf = SAM_FLAG | SAM_RNAME | SAM_POS | SAM_MAPQ | SAM_CIGAR | SAM_SEQ;
+        if (opt_min_baseQ) rf |= SAM_QUAL;
+
+        // Set CRAM options on file handle - returns 0 on success
+        if (hts_set_opt(data[i]->fp, CRAM_OPT_REQUIRED_FIELDS, rf)) {
+            print_error("coverage", "Failed to set CRAM_OPT_REQUIRED_FIELDS value");
+            status = EXIT_FAILURE;
+            goto coverage_end;
+        }
+        if (hts_set_opt(data[i]->fp, CRAM_OPT_DECODE_MD, 0)) {
+            print_error("coverage", "Failed to set CRAM_OPT_DECODE_MD value");
+            status = EXIT_FAILURE;
+            goto coverage_end;
+        }
+        data[i]->min_mapQ = opt_min_mapQ;            // set the mapQ filter
+        data[i]->min_len  = opt_min_len;             // set the qlen filter
+        data[i]->hdr = sam_hdr_read(data[i]->fp);    // read the BAM header
+        data[i]->fail_flags = fail_flags;
+        data[i]->required_flags = required_flags;
+        if (data[i]->hdr == NULL) {
+            print_error_errno("coverage", "Could not read header for \"%s\"", argv[optind+i]);
+            status = EXIT_FAILURE;
+            goto coverage_end;
+        }
+
+        // Lookup region if specified
+        if (opt_reg) { // if a region is specified
+            hts_idx_t *idx = sam_index_load(data[i]->fp, argv[optind+i]);  // load the index
+            if (idx == NULL) {
+                print_error_errno("coverage", "Failed to load index for \"%s\"", argv[optind+i]);
+                status = EXIT_FAILURE;
+                goto coverage_end;
+            }
+            data[i]->iter = sam_itr_querys(idx, data[i]->hdr, opt_reg); // set the iterator
+            hts_idx_destroy(idx); // the index is not needed any more; free the memory
+            if (data[i]->iter == NULL) {
+                print_error("coverage", "Failed to parse region \"%s\". Check the region format or region name presence in the file \"%s\"", opt_reg, argv[optind+i]);
+                status = EXIT_FAILURE;
+                goto coverage_end;
+            }
+        }
+    }
+
+    if (opt_print_tabular && opt_print_header)
+        fputs("#rname\tstartpos\tendpos\tnumreads\tcovbases\tcoverage\tmeandepth\tmeanbaseq\tmeanmapq\n", file_out);
+
+    h = data[0]->hdr; // easy access to the header of the 1st BAM
+    int n_targets = sam_hdr_nref(h);
+    stats = calloc(n_targets, sizeof(stats_aux_t));
+    if (!stats) {
+        print_error_errno("coverage", "Failed to allocate memory");
+        status = EXIT_FAILURE;
+        goto coverage_end;
+    }
+
+    int64_t n_bins = opt_n_bins;
+    if (opt_reg) {
+        stats_aux_t *s = stats + data[0]->iter->tid;
+        s->beg = data[0]->iter->beg; // and to the parsed region coordinates
+        s->end = data[0]->iter->end;
+        if (s->end == HTS_POS_MAX) {
+            s->end = sam_hdr_tid2len(h, data[0]->iter->tid);
+        }
+        if (opt_n_bins > s->end - s->beg) {
+            n_bins = s->end - s->beg;
+        }
+        s->bin_width = (s->end-s->beg) / (n_bins > 0 ? n_bins : 1);
+    }
+
+    for (i=0; i<n_bam_files; i++)
+        data[i]->stats = stats;
+
+    int64_t current_bin = 0;
+
+    // the core multi-pileup loop
+    mplp = bam_mplp_init(n_bam_files, read_bam, (void**)data); // initialization
+    if (max_depth > 0)
+        bam_mplp_set_maxcnt(mplp, max_depth);  // set maximum coverage depth
+    else if (!max_depth)
+        bam_mplp_set_maxcnt(mplp, INT_MAX);
+
+
+    // Extra info for histogram and coverage counting
+    hist = (uint32_t*) calloc(opt_n_bins, sizeof(uint32_t));
+    n_plp = (int*) calloc(n_bam_files, sizeof(int*)); // n_plp[i] is the number of covering reads from the i-th BAM
+    plp = (const bam_pileup1_t**) calloc(n_bam_files, sizeof(bam_pileup1_t*)); // plp[i] points to the array of covering reads (internal in mplp)
+    if (!hist || !n_plp || !plp) {
+        print_error_errno("coverage", "Failed to allocate memory");
+        status = EXIT_FAILURE;
+        goto coverage_end;
+    }
+    while ((ret=bam_mplp_auto(mplp, &tid, &pos, n_plp, plp)) > 0) { // come to the next covered position
+
+        if (tid != old_tid) { // Next target sequence
+            if (old_tid >= 0) {
+                if (opt_print_histogram) {
+                    print_hist(file_out, h, stats, old_tid, hist, n_bins, opt_full_utf);
+                    fputc('\n', file_out);
+                } else if (opt_print_tabular) {
+                    print_tabular_line(file_out, h, stats, old_tid);
+                }
+
+                if (opt_print_histogram)
+                    memset(hist, 0, n_bins*sizeof(uint32_t));
+            }
+
+            stats[tid].covered = true;
+            if (!opt_reg)
+                stats[tid].end = sam_hdr_tid2len(h, tid);
+
+            if (opt_print_histogram) {
+                n_bins = opt_n_bins > stats[tid].end-stats[tid].beg? stats[tid].end-stats[tid].beg : opt_n_bins;
+                stats[tid].bin_width = (stats[tid].end-stats[tid].beg) / n_bins;
+            }
+
+            old_tid = tid;
+        }
+        if (pos < stats[tid].beg || pos >= stats[tid].end) continue; // out of range; skip
+        if (tid >= n_targets) continue;     // diff number of @SQ lines per file?
+
+        if (opt_print_histogram) {
+            current_bin = (pos - stats[tid].beg) / stats[tid].bin_width;
+        }
+
+        bool count_base = false;
+        for (i = 0; i < n_bam_files; ++i) { // base level filters have to go here
+            int depth_at_pos = n_plp[i];
+            for (j = 0; j < n_plp[i]; ++j) {
+                const bam_pileup1_t *p = plp[i] + j; // DON'T modify plp[][] unless you really know
+
+                if (p->is_del || p->is_refskip) --depth_at_pos; // having dels or refskips at tid:pos
+                else if (p->qpos < p->b->core.l_qseq &&
+                        bam_get_qual(p->b)[p->qpos] < opt_min_baseQ) --depth_at_pos; // low base quality
+                else
+                    stats[tid].summed_baseQ += bam_get_qual(p->b)[p->qpos];
+            }
+            if (depth_at_pos > 0) {
+                count_base = true;
+                stats[tid].summed_coverage += depth_at_pos;
+            }
+            // hist[current_bin] += depth_at_pos;  // Add counts to the histogram here to have one based on coverage
+            //fprintf(file_out, "\t%d", n_plp[i] - m); // this the depth to output
+        }
+        if (count_base) {
+            stats[tid].n_covered_bases++;
+            if (opt_print_histogram && current_bin < n_bins)
+                ++(hist[current_bin]); // Histogram based on breadth of coverage
+        }
+    }
+
+    if (tid == -1 && opt_reg && *opt_reg != '*')
+        // Region specified but no data covering it.
+        tid = data[0]->iter->tid;
+
+    if (tid < n_targets && tid >=0) {
+        if (opt_print_histogram) {
+            print_hist(file_out, h, stats, tid, hist, n_bins, opt_full_utf);
+        } else if (opt_print_tabular) {
+            print_tabular_line(file_out, h, stats, tid);
+        }
+    }
+
+
+    if (!opt_reg && opt_print_tabular) {
+        for (i = 0; i < n_targets; ++i) {
+            if (!stats[i].covered) {
+                stats[i].end = sam_hdr_tid2len(h, i);
+                print_tabular_line(file_out, h, stats, i);
+            }
+        }
+    }
+
+    if (ret < 0) status = EXIT_FAILURE;
+
+coverage_end:
+    if (n_plp) free(n_plp);
+    if (plp) free(plp);
+    if (mplp) bam_mplp_destroy(mplp);
+
+    if (hist) free(hist);
+    if (stats) free(stats);
+
+    // Close files and free data structures
+    if (!(file_out == stdout || fclose(file_out) == 0)) {
+        if (status == EXIT_SUCCESS) {
+            print_error_errno("coverage", "error on closing \"%s\"",
+                    (opt_output_file && strcmp(opt_output_file, "-") != 0?
+                     opt_output_file : "stdout"));
+            status = EXIT_FAILURE;
+        }
+    }
+
+    if (data) {
+        for (i = 0; i < n_bam_files && data[i]; ++i) {
+            sam_hdr_destroy(data[i]->hdr);
+            if (data[i]->fp) sam_close(data[i]->fp);
+            hts_itr_destroy(data[i]->iter);
+            free(data[i]);
+        }
+        free(data);
+    }
+
+    if (opt_file_list && fn) {
+        for (i = 0; i < n_bam_files; ++i)
+            free(fn[i]);
+        free(fn);
+    }
+    sam_global_args_free(&ga);
+
+    return status;
+}
+
+#ifdef _MAIN_BAMCOV
+int main(int argc, char *argv[]) {
+    return main_coverage(argc, argv);
+}
+#endif
diff --git a/samtools/coverage.c.pysam.c b/samtools/coverage.c.pysam.c
new file mode 100644
index 0000000..894f4ac
--- /dev/null
+++ b/samtools/coverage.c.pysam.c
@@ -0,0 +1,685 @@
+#include "samtools.pysam.h"
+
+/* coverage.c -- samtools coverage subcommand
+
+    Copyright (C) 2018,2019 Florian Breitwieser
+    Portions copyright (C) 2019-2021 Genome Research Ltd.
+
+    Author: Florian P Breitwieser <florian.bw@gmail.com>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+/* This program calculates coverage from multiple BAMs
+ * simultaneously, to achieve random access and to use the BED interface.
+ * To compile this program separately, you may:
+ *
+ *   gcc -g -O2 -Wall -o bamcov -D_MAIN_BAMCOV coverage.c -lhts -lz
+ */
+
+// C headers
+#include <config.h>
+
+#include <ctype.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <stdarg.h>  // variadic functions
+#include <limits.h>  // INT_MAX
+#include <math.h>    // round
+#include <stdbool.h>
+#include <string.h>
+#include <unistd.h>
+#include <assert.h>
+
+#ifdef _WIN32
+#include <windows.h>
+#else
+#include <sys/ioctl.h>
+#endif
+
+#include "htslib/sam.h"
+#include "htslib/hts.h"
+#include "samtools.h"
+#include "sam_opts.h"
+
+typedef struct {  // auxiliary data structure to hold stats on coverage
+    unsigned long long n_covered_bases;
+    unsigned long long summed_coverage;
+    unsigned long long summed_baseQ;
+    unsigned long long summed_mapQ;
+    unsigned int n_reads;
+    unsigned int n_selected_reads;
+    bool covered;
+    hts_pos_t beg;
+    hts_pos_t end;
+    int64_t bin_width;
+} stats_aux_t;
+
+typedef struct {  // auxiliary data structure to hold a BAM file
+    samFile *fp;     // file handle
+    sam_hdr_t *hdr;  // file header
+    hts_itr_t *iter; // iterator to a region - NULL for us by default
+    int min_mapQ;    // mapQ filter
+    int min_len;     // length filter
+    int fail_flags;
+    int required_flags;
+    stats_aux_t *stats;
+} bam_aux_t;
+
+#if __STDC_VERSION__ >= 199901L
+#define VERTICAL_LINE "\u2502" // BOX DRAWINGS LIGHT VERTICAL
+
+// UTF8 specifies block characters in eights going from \u2581 (lower one eight block) to \u2588 (full block)
+//   https://en.wikipedia.org/wiki/Block_Elements
+// LOWER ONE EIGHTH BLOCK … FULL BLOCK
+static const char *const BLOCK_CHARS8[8] = {"\u2581", "\u2582", "\u2583", "\u2584", "\u2585", "\u2586", "\u2587", "\u2588"};
+// In some terminals / with some fonts not all UTF8 block characters are supported (e.g. Putty). Use only half and full block for those
+static const char *const BLOCK_CHARS2[2] = {".", ":"};
+
+#else
+
+// Fall back to explicit UTF-8 encodings of the same characters
+#define VERTICAL_LINE "\xE2\x94\x82"
+
+static const char *const BLOCK_CHARS8[8] = {
+    "\xE2\x96\x81", "\xE2\x96\x82", "\xE2\x96\x83", "\xE2\x96\x84",
+    "\xE2\x96\x85", "\xE2\x96\x86", "\xE2\x96\x87", "\xE2\x96\x88" };
+
+static const char *const BLOCK_CHARS2[2] = {".", ":"};
+
+#endif
+
+// in bam_plcmd.c
+int read_file_list(const char *file_list, int *n, char **argv[]);
+
+static int usage() {
+    fprintf(samtools_stdout, "Usage: samtools coverage [options] in1.bam [in2.bam [...]]\n\n"
+            "Input options:\n"
+            "  -b, --bam-list FILE     list of input BAM filenames, one per line\n"
+            "  -l, --min-read-len INT  ignore reads shorter than INT bp [0]\n"
+            "  -q, --min-MQ INT        mapping quality threshold [0]\n"
+            "  -Q, --min-BQ INT        base quality threshold [0]\n"
+            "  --rf <int|str>          required flags: skip reads with mask bits unset []\n"
+            "  --ff <int|str>          filter flags: skip reads with mask bits set \n"
+            "                                      [UNMAP,SECONDARY,QCFAIL,DUP]\n"
+            "  -d, --depth INT         maximum allowed coverage depth [1000000].\n"
+            "                          If 0, depth is set to the maximum integer value,\n"
+            "                          effectively removing any depth limit.\n"
+            "Output options:\n"
+            "  -m, --histogram         show histogram instead of tabular output\n"
+            "  -A, --ascii             show only ASCII characters in histogram\n"
+            "  -o, --output FILE       write output to FILE [samtools_stdout]\n"
+            "  -H, --no-header         don't print a header in tabular mode\n"
+            "  -w, --n-bins INT        number of bins in histogram [terminal width - 40]\n"
+            "  -r, --region REG        show specified region. Format: chr:start-end. \n"
+            "  -h, --help              help (this page)\n");
+
+    fprintf(samtools_stdout, "\nGeneric options:\n");
+    sam_global_opt_help(samtools_stdout, "-.--.--.");
+
+    fprintf(samtools_stdout,
+            "\nSee manpage for additional details.\n"
+            "  rname       Reference name / chromosome\n"
+            "  startpos    Start position\n"
+            "  endpos      End position (or sequence length)\n"
+            "  numreads    Number reads aligned to the region (after filtering)\n"
+            "  covbases    Number of covered bases with depth >= 1\n"
+            "  coverage    Percentage of covered bases [0..100]\n"
+            "  meandepth   Mean depth of coverage\n"
+            "  meanbaseq   Mean baseQ in covered region\n"
+            "  meanmapq    Mean mapQ of selected reads\n"
+           );
+
+    return EXIT_SUCCESS;
+}
+
+static char* center_text(char *text, char *buf, int width) {
+    int len = strlen(text);
+    assert(len <= width);
+    int padding = (width - len) / 2;
+    int padding_ex = (width - len) % 2;
+    if (padding >= 1)
+        sprintf(buf, " %*s%*s", len+padding, text, padding-1+padding_ex, " ");
+    else
+        sprintf(buf, "%s", text);
+
+    return buf;
+}
+
+static char* readable_bps(double base_pairs, char *buf) {
+    const char* units[] = {"", "K", "M", "G", "T"};
+    int i = 0;
+    while (base_pairs >= 1000 && i < (sizeof(units)/sizeof(units[0]) - 1)) {
+        base_pairs /= 1000;
+        i++;
+    }
+    sprintf(buf, "%.*f%s", i, base_pairs, units[i]);
+    return buf;
+}
+
+// read one alignment from one BAM file
+static int read_bam(void *data, bam1_t *b) {
+    bam_aux_t *aux = (bam_aux_t*)data; // data in fact is a pointer to an auxiliary structure
+    int nref = sam_hdr_nref(aux->hdr);
+    int ret;
+    while (1) {
+        if((ret = aux->iter? sam_itr_next(aux->fp, aux->iter, b) : sam_read1(aux->fp, aux->hdr, b)) < 0) break;
+        if (b->core.tid >= 0 && b->core.tid < nref)
+            aux->stats[b->core.tid].n_reads++;
+
+        if ( aux->fail_flags && (b->core.flag & aux->fail_flags) ) continue;
+        if ( aux->required_flags && !(b->core.flag & aux->required_flags) ) continue;
+        if ( b->core.qual < aux->min_mapQ ) continue;
+        if ( aux->min_len && bam_cigar2qlen(b->core.n_cigar, bam_get_cigar(b)) < aux->min_len ) continue;
+        if (b->core.tid >= 0 && b->core.tid < nref) {
+            aux->stats[b->core.tid].n_selected_reads++;
+            aux->stats[b->core.tid].summed_mapQ += b->core.qual;
+        }
+        break;
+    }
+    return ret;
+}
+
+void print_tabular_line(FILE *file_out, const sam_hdr_t *h, const stats_aux_t *stats, int tid) {
+    fputs(sam_hdr_tid2name(h, tid), file_out);
+    double region_len = (double) stats[tid].end - stats[tid].beg;
+    fprintf(file_out, "\t%"PRId64"\t%"PRId64"\t%u\t%llu\t%g\t%g\t%.3g\t%.3g\n",
+            stats[tid].beg+1,
+            stats[tid].end,
+            stats[tid].n_selected_reads,
+            stats[tid].n_covered_bases,
+            100.0 * stats[tid].n_covered_bases / region_len,
+            stats[tid].summed_coverage / region_len,
+            stats[tid].summed_coverage > 0? stats[tid].summed_baseQ/(double) stats[tid].summed_coverage : 0,
+            stats[tid].n_selected_reads > 0? stats[tid].summed_mapQ/(double) stats[tid].n_selected_reads : 0
+           );
+}
+
+void print_hist(FILE *file_out, const sam_hdr_t *h, const stats_aux_t *stats, int tid, const uint32_t *hist,
+        const int hist_size, const bool full_utf) {
+    int i, col;
+    bool show_percentiles = false;
+    const int n_rows = 10;
+    const char * const * BLOCK_CHARS = full_utf? BLOCK_CHARS8 : BLOCK_CHARS2;
+    const int blockchar_len = full_utf? 8 : 2;
+    double region_len = stats[tid].end - stats[tid].beg;
+
+    // Calculate histogram that contains percent covered
+    double hist_data[hist_size];
+    double max_val = 0.0;
+    for (i = 0; i < hist_size; ++i) {
+        hist_data[i] = 100 * hist[i] / (double) stats[tid].bin_width;
+        if (hist_data[i] > max_val) max_val = hist_data[i];
+    }
+
+    char buf[30];
+    fprintf(file_out, "%s (%sbp)\n", sam_hdr_tid2name(h, tid), readable_bps(sam_hdr_tid2len(h, tid), buf));
+
+    double row_bin_size = max_val / (double) n_rows;
+    for (i = n_rows-1; i >= 0; --i) {
+        double current_bin = row_bin_size * i;
+        if (show_percentiles) {
+            fprintf(file_out, ">%3i%% ", i*10);
+        } else {
+            fprintf(file_out, ">%7.2f%% ", current_bin);
+        }
+        fprintf(file_out, full_utf ? VERTICAL_LINE : "|");
+        for (col = 0; col < hist_size; ++col) {
+            // get the difference in eights, or halfs when full UTF8 is not supported
+            int cur_val_diff = round(blockchar_len * (hist_data[col] - current_bin) / row_bin_size) - 1;
+            if (cur_val_diff < 0) {
+                fputc(' ', file_out);
+            } else {
+                if (cur_val_diff >= blockchar_len)
+                    cur_val_diff = blockchar_len - 1;
+
+                fprintf(file_out, "%s", BLOCK_CHARS[cur_val_diff]);
+            }
+        }
+        fprintf(file_out, full_utf ? VERTICAL_LINE : "|");
+        fputc(' ', file_out);
+        switch (i) {
+            case 9: fprintf(file_out, "Number of reads: %u", stats[tid].n_selected_reads); break;
+            case 8: if (stats[tid].n_reads - stats[tid].n_selected_reads > 0) fprintf(file_out, "    (%i filtered)", stats[tid].n_reads - stats[tid].n_selected_reads); break;
+            case 7: fprintf(file_out, "Covered bases:   %sbp", readable_bps(stats[tid].n_covered_bases, buf)); break;
+            case 6: fprintf(file_out, "Percent covered: %.4g%%",
+                            100.0 * stats[tid].n_covered_bases / region_len); break;
+            case 5: fprintf(file_out, "Mean coverage:   %.3gx",
+                            stats[tid].summed_coverage / region_len); break;
+            case 4: fprintf(file_out, "Mean baseQ:      %.3g",
+                            stats[tid].summed_baseQ/(double) stats[tid].summed_coverage); break;
+            case 3: fprintf(file_out, "Mean mapQ:       %.3g",
+                            stats[tid].summed_mapQ/(double) stats[tid].n_selected_reads); break;
+            case 1: fprintf(file_out, "Histo bin width: %sbp",
+                            readable_bps(stats[tid].bin_width, buf)); break;
+            case 0: fprintf(file_out, "Histo max bin:   %.5g%%", max_val); break;
+        };
+        fputc('\n', file_out);
+    }
+
+    // print x axis. Could be made pretty for widths that are not divisible
+    // by 10 by variable spacing of the labels, instead of placing a label every 10 characters
+    char buf2[50];
+    fprintf(file_out, "     %s", center_text(readable_bps(stats[tid].beg + 1, buf), buf2, 10));
+    int rest;
+    for (rest = 10; rest < 10*(hist_size/10); rest += 10) {
+        fprintf(file_out, "%s", center_text(readable_bps(stats[tid].beg + stats[tid].bin_width*rest, buf), buf2, 10));
+    }
+    int last_padding = hist_size%10;
+    fprintf(file_out, "%*s%s", last_padding, " ", center_text(readable_bps(stats[tid].end, buf), buf2, 10));
+    fprintf(file_out, "\n");
+}
+
+int main_coverage(int argc, char *argv[]) {
+    int status = EXIT_SUCCESS;
+
+    int ret, tid = -1, old_tid = -1, pos, i, j;
+
+    int max_depth = 1000000;
+    int opt_min_baseQ = 0;
+    int opt_min_mapQ = 0;
+    int opt_min_len = 0;
+    int opt_n_bins = 50;
+    bool opt_full_width = true;
+    char *opt_output_file = NULL;
+    bam_aux_t **data = NULL;
+    bam_mplp_t mplp = NULL;
+    const bam_pileup1_t **plp = NULL;
+    uint32_t *hist = NULL;
+    stats_aux_t *stats = NULL;
+    char *opt_reg = 0; // specified region
+    char *opt_file_list = NULL;
+    int n_bam_files = 0;
+    char **fn = NULL;
+    int fail_flags = (BAM_FUNMAP | BAM_FSECONDARY | BAM_FQCFAIL | BAM_FDUP); // Default fail flags
+    int required_flags = 0;
+
+    int *n_plp = NULL;
+    sam_hdr_t *h = NULL; // BAM header of the 1st input
+
+    bool opt_print_header = true;
+    bool opt_print_tabular = true;
+    bool opt_print_histogram = false;
+    bool opt_full_utf = true;
+
+    FILE *file_out = samtools_stdout;
+
+    sam_global_args ga = SAM_GLOBAL_ARGS_INIT;
+    static const struct option lopts[] = {
+        SAM_OPT_GLOBAL_OPTIONS('-', 0, '-', '-', 0, '-'),
+        {"rf", required_argument, NULL, 1}, // require flag
+        {"ff", required_argument, NULL, 2}, // filter flag
+        {"incl-flags", required_argument, NULL, 1}, // require flag
+        {"excl-flags", required_argument, NULL, 2}, // filter flag
+        {"bam-list", required_argument, NULL, 'b'},
+        {"min-read-len", required_argument, NULL, 'l'},
+        {"min-MQ", required_argument, NULL, 'q'},
+        {"min-mq", required_argument, NULL, 'q'},
+        {"min-BQ", required_argument, NULL, 'Q'},
+        {"min-bq", required_argument, NULL, 'Q'},
+        {"histogram", no_argument, NULL, 'm'},
+        {"ascii", no_argument, NULL, 'A'},
+        {"output", required_argument, NULL, 'o'},
+        {"no-header", no_argument, NULL, 'H'},
+        {"n-bins", required_argument, NULL, 'w'},
+        {"region", required_argument, NULL, 'r'},
+        {"help", no_argument, NULL, 'h'},
+        {"depth", required_argument, NULL, 'd'},
+        { NULL, 0, NULL, 0 }
+    };
+
+    // parse the command line
+    int c;
+    opterr = 0;
+    while ((c = getopt_long(argc, argv, "Ao:l:q:Q:hHw:r:b:md:", lopts, NULL)) != -1) {
+        switch (c) {
+            case 1:
+                if ((required_flags = bam_str2flag(optarg)) < 0) {
+                    fprintf(samtools_stderr,"Could not parse --rf %s\n", optarg); return EXIT_FAILURE;
+                }; break;
+            case 2:
+                if ((fail_flags = bam_str2flag(optarg)) < 0) {
+                    fprintf(samtools_stderr,"Could not parse --ff %s\n", optarg); return EXIT_FAILURE;
+                }; break;
+            case 'o': opt_output_file = optarg; opt_full_width = false; break;
+            case 'l': opt_min_len = atoi(optarg); break;
+            case 'q': opt_min_mapQ = atoi(optarg); break;
+            case 'Q': opt_min_baseQ = atoi(optarg); break;
+            case 'd': max_depth = atoi(optarg); break; // maximum coverage depth
+            case 'w': opt_n_bins = atoi(optarg); opt_full_width = false;
+                      opt_print_histogram = true; opt_print_tabular = false;
+                      break;
+            case 'r': opt_reg = optarg; break;   // parsing a region requires a BAM header (strdup unnecessary)
+            case 'b': opt_file_list = optarg; break;
+            case 'm': opt_print_histogram = true; opt_print_tabular = false; break;
+            case 'A': opt_full_utf = false;
+                      opt_print_histogram = true; opt_print_tabular = false;
+                      break;
+            case 'H': opt_print_header = false; break;
+            case 'h': return usage();
+            default:  if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break;
+                          /* else fall-through */
+            case '?':
+                if (optopt != '?') {  // '-?' appeared on command line
+                    if (optopt) { // Bad short option
+                        print_error("coverage", "invalid option -- '%c'", optopt);
+                    } else { // Bad long option
+                        // Do our best.  There is no good solution to finding
+                        // out what the bad option was.
+                        // See, e.g. https://stackoverflow.com/questions/2723888/where-does-getopt-long-store-an-unrecognized-option
+                        if (optind > 0 && strncmp(argv[optind - 1], "--", 2) == 0) {
+                            print_error("coverage", "unrecognised option '%s'",
+                                        argv[optind - 1]);
+                        }
+                    }
+                }
+                return usage();
+        }
+    }
+    if (optind == argc && !opt_file_list)
+        return usage();
+
+    // output file provided by user
+    if (opt_output_file != NULL && strcmp(opt_output_file,"-")!=0) {
+        file_out = fopen( opt_output_file, "w" );
+        if (file_out == NULL) {
+            print_error_errno("coverage", "Cannot open \"%s\" for writing.", opt_output_file);
+            return EXIT_FAILURE;
+        }
+    }
+
+    if (opt_n_bins <= 0 || opt_full_width) {
+        // get number of columns of terminal
+        const char* env_columns = getenv("COLUMNS");
+        int columns = 0;
+        if (env_columns == NULL) {
+#ifdef _WIN32
+            CONSOLE_SCREEN_BUFFER_INFO csbi;
+            if (GetConsoleScreenBufferInfo(GetStdHandle(STD_OUTPUT_HANDLE), &csbi)) {
+                columns = csbi.srWindow.Right - csbi.srWindow.Left + 1;
+            }
+#elif defined TIOCGWINSZ
+            struct winsize w;
+            if (ioctl(2, TIOCGWINSZ, &w) == 0)
+                columns = w.ws_col;
+#endif
+        } else {
+            columns = atoi(env_columns); // atoi(NULL) returns 0
+        }
+
+        if (columns > 60) {
+            opt_n_bins = columns - 40;
+        } else {
+            opt_n_bins = 40;
+        }
+    }
+
+    // setvbuf(file_out, NULL, _IONBF, 0); //turn off buffering
+
+    // Open all BAM files
+    if (opt_file_list) {
+        // Read file names from opt_file_list into argv, and record the number of files in n_bam_files
+        if (read_file_list(opt_file_list, &n_bam_files, &fn)) {
+            print_error_errno("coverage", "Cannot open file list \"%s\".", opt_file_list);
+            return EXIT_FAILURE;
+        }
+        argv = fn;
+        optind = 0;
+    } else {
+        n_bam_files = argc - optind; // the number of BAMs on the command line
+    }
+
+    data = (bam_aux_t **)calloc(n_bam_files, sizeof(bam_aux_t*)); // data[i] for the i-th BAM file
+    if (!data) {
+        print_error_errno("coverage", "Failed to allocate memory");
+        status = EXIT_FAILURE;
+        goto coverage_end;
+    }
+
+    for (i = 0; i < n_bam_files; ++i) {
+        int rf;
+        data[i] = (bam_aux_t *) calloc(1, sizeof(bam_aux_t));
+        if (!data[i]) {
+            print_error_errno("coverage", "Failed to allocate memory");
+            status = EXIT_FAILURE;
+            goto coverage_end;
+        }
+        data[i]->fp = sam_open_format(argv[optind+i], "r", &ga.in); // open BAM
+
+        if (data[i]->fp == NULL) {
+            print_error_errno("coverage", "Could not open \"%s\"", argv[optind+i]);
+            status = EXIT_FAILURE;
+            goto coverage_end;
+        }
+        rf = SAM_FLAG | SAM_RNAME | SAM_POS | SAM_MAPQ | SAM_CIGAR | SAM_SEQ;
+        if (opt_min_baseQ) rf |= SAM_QUAL;
+
+        // Set CRAM options on file handle - returns 0 on success
+        if (hts_set_opt(data[i]->fp, CRAM_OPT_REQUIRED_FIELDS, rf)) {
+            print_error("coverage", "Failed to set CRAM_OPT_REQUIRED_FIELDS value");
+            status = EXIT_FAILURE;
+            goto coverage_end;
+        }
+        if (hts_set_opt(data[i]->fp, CRAM_OPT_DECODE_MD, 0)) {
+            print_error("coverage", "Failed to set CRAM_OPT_DECODE_MD value");
+            status = EXIT_FAILURE;
+            goto coverage_end;
+        }
+        data[i]->min_mapQ = opt_min_mapQ;            // set the mapQ filter
+        data[i]->min_len  = opt_min_len;             // set the qlen filter
+        data[i]->hdr = sam_hdr_read(data[i]->fp);    // read the BAM header
+        data[i]->fail_flags = fail_flags;
+        data[i]->required_flags = required_flags;
+        if (data[i]->hdr == NULL) {
+            print_error_errno("coverage", "Could not read header for \"%s\"", argv[optind+i]);
+            status = EXIT_FAILURE;
+            goto coverage_end;
+        }
+
+        // Lookup region if specified
+        if (opt_reg) { // if a region is specified
+            hts_idx_t *idx = sam_index_load(data[i]->fp, argv[optind+i]);  // load the index
+            if (idx == NULL) {
+                print_error_errno("coverage", "Failed to load index for \"%s\"", argv[optind+i]);
+                status = EXIT_FAILURE;
+                goto coverage_end;
+            }
+            data[i]->iter = sam_itr_querys(idx, data[i]->hdr, opt_reg); // set the iterator
+            hts_idx_destroy(idx); // the index is not needed any more; free the memory
+            if (data[i]->iter == NULL) {
+                print_error("coverage", "Failed to parse region \"%s\". Check the region format or region name presence in the file \"%s\"", opt_reg, argv[optind+i]);
+                status = EXIT_FAILURE;
+                goto coverage_end;
+            }
+        }
+    }
+
+    if (opt_print_tabular && opt_print_header)
+        fputs("#rname\tstartpos\tendpos\tnumreads\tcovbases\tcoverage\tmeandepth\tmeanbaseq\tmeanmapq\n", file_out);
+
+    h = data[0]->hdr; // easy access to the header of the 1st BAM
+    int n_targets = sam_hdr_nref(h);
+    stats = calloc(n_targets, sizeof(stats_aux_t));
+    if (!stats) {
+        print_error_errno("coverage", "Failed to allocate memory");
+        status = EXIT_FAILURE;
+        goto coverage_end;
+    }
+
+    int64_t n_bins = opt_n_bins;
+    if (opt_reg) {
+        stats_aux_t *s = stats + data[0]->iter->tid;
+        s->beg = data[0]->iter->beg; // and to the parsed region coordinates
+        s->end = data[0]->iter->end;
+        if (s->end == HTS_POS_MAX) {
+            s->end = sam_hdr_tid2len(h, data[0]->iter->tid);
+        }
+        if (opt_n_bins > s->end - s->beg) {
+            n_bins = s->end - s->beg;
+        }
+        s->bin_width = (s->end-s->beg) / (n_bins > 0 ? n_bins : 1);
+    }
+
+    for (i=0; i<n_bam_files; i++)
+        data[i]->stats = stats;
+
+    int64_t current_bin = 0;
+
+    // the core multi-pileup loop
+    mplp = bam_mplp_init(n_bam_files, read_bam, (void**)data); // initialization
+    if (max_depth > 0)
+        bam_mplp_set_maxcnt(mplp, max_depth);  // set maximum coverage depth
+    else if (!max_depth)
+        bam_mplp_set_maxcnt(mplp, INT_MAX);
+
+
+    // Extra info for histogram and coverage counting
+    hist = (uint32_t*) calloc(opt_n_bins, sizeof(uint32_t));
+    n_plp = (int*) calloc(n_bam_files, sizeof(int*)); // n_plp[i] is the number of covering reads from the i-th BAM
+    plp = (const bam_pileup1_t**) calloc(n_bam_files, sizeof(bam_pileup1_t*)); // plp[i] points to the array of covering reads (internal in mplp)
+    if (!hist || !n_plp || !plp) {
+        print_error_errno("coverage", "Failed to allocate memory");
+        status = EXIT_FAILURE;
+        goto coverage_end;
+    }
+    while ((ret=bam_mplp_auto(mplp, &tid, &pos, n_plp, plp)) > 0) { // come to the next covered position
+
+        if (tid != old_tid) { // Next target sequence
+            if (old_tid >= 0) {
+                if (opt_print_histogram) {
+                    print_hist(file_out, h, stats, old_tid, hist, n_bins, opt_full_utf);
+                    fputc('\n', file_out);
+                } else if (opt_print_tabular) {
+                    print_tabular_line(file_out, h, stats, old_tid);
+                }
+
+                if (opt_print_histogram)
+                    memset(hist, 0, n_bins*sizeof(uint32_t));
+            }
+
+            stats[tid].covered = true;
+            if (!opt_reg)
+                stats[tid].end = sam_hdr_tid2len(h, tid);
+
+            if (opt_print_histogram) {
+                n_bins = opt_n_bins > stats[tid].end-stats[tid].beg? stats[tid].end-stats[tid].beg : opt_n_bins;
+                stats[tid].bin_width = (stats[tid].end-stats[tid].beg) / n_bins;
+            }
+
+            old_tid = tid;
+        }
+        if (pos < stats[tid].beg || pos >= stats[tid].end) continue; // out of range; skip
+        if (tid >= n_targets) continue;     // diff number of @SQ lines per file?
+
+        if (opt_print_histogram) {
+            current_bin = (pos - stats[tid].beg) / stats[tid].bin_width;
+        }
+
+        bool count_base = false;
+        for (i = 0; i < n_bam_files; ++i) { // base level filters have to go here
+            int depth_at_pos = n_plp[i];
+            for (j = 0; j < n_plp[i]; ++j) {
+                const bam_pileup1_t *p = plp[i] + j; // DON'T modify plp[][] unless you really know
+
+                if (p->is_del || p->is_refskip) --depth_at_pos; // having dels or refskips at tid:pos
+                else if (p->qpos < p->b->core.l_qseq &&
+                        bam_get_qual(p->b)[p->qpos] < opt_min_baseQ) --depth_at_pos; // low base quality
+                else
+                    stats[tid].summed_baseQ += bam_get_qual(p->b)[p->qpos];
+            }
+            if (depth_at_pos > 0) {
+                count_base = true;
+                stats[tid].summed_coverage += depth_at_pos;
+            }
+            // hist[current_bin] += depth_at_pos;  // Add counts to the histogram here to have one based on coverage
+            //fprintf(file_out, "\t%d", n_plp[i] - m); // this the depth to output
+        }
+        if (count_base) {
+            stats[tid].n_covered_bases++;
+            if (opt_print_histogram && current_bin < n_bins)
+                ++(hist[current_bin]); // Histogram based on breadth of coverage
+        }
+    }
+
+    if (tid == -1 && opt_reg && *opt_reg != '*')
+        // Region specified but no data covering it.
+        tid = data[0]->iter->tid;
+
+    if (tid < n_targets && tid >=0) {
+        if (opt_print_histogram) {
+            print_hist(file_out, h, stats, tid, hist, n_bins, opt_full_utf);
+        } else if (opt_print_tabular) {
+            print_tabular_line(file_out, h, stats, tid);
+        }
+    }
+
+
+    if (!opt_reg && opt_print_tabular) {
+        for (i = 0; i < n_targets; ++i) {
+            if (!stats[i].covered) {
+                stats[i].end = sam_hdr_tid2len(h, i);
+                print_tabular_line(file_out, h, stats, i);
+            }
+        }
+    }
+
+    if (ret < 0) status = EXIT_FAILURE;
+
+coverage_end:
+    if (n_plp) free(n_plp);
+    if (plp) free(plp);
+    if (mplp) bam_mplp_destroy(mplp);
+
+    if (hist) free(hist);
+    if (stats) free(stats);
+
+    // Close files and free data structures
+    if (!(file_out == samtools_stdout || fclose(file_out) == 0)) {
+        if (status == EXIT_SUCCESS) {
+            print_error_errno("coverage", "error on closing \"%s\"",
+                    (opt_output_file && strcmp(opt_output_file, "-") != 0?
+                     opt_output_file : "samtools_stdout"));
+            status = EXIT_FAILURE;
+        }
+    }
+
+    if (data) {
+        for (i = 0; i < n_bam_files && data[i]; ++i) {
+            sam_hdr_destroy(data[i]->hdr);
+            if (data[i]->fp) sam_close(data[i]->fp);
+            hts_itr_destroy(data[i]->iter);
+            free(data[i]);
+        }
+        free(data);
+    }
+
+    if (opt_file_list && fn) {
+        for (i = 0; i < n_bam_files; ++i)
+            free(fn[i]);
+        free(fn);
+    }
+    sam_global_args_free(&ga);
+
+    return status;
+}
+
+#ifdef _MAIN_BAMCOV
+int samtools_coverage_main(int argc, char *argv[]) {
+    return main_coverage(argc, argv);
+}
+#endif
diff --git a/samtools/cut_target.c b/samtools/cut_target.c
new file mode 100644
index 0000000..7c8387c
--- /dev/null
+++ b/samtools/cut_target.c
@@ -0,0 +1,257 @@
+/*  cut_target.c -- targetcut subcommand.
+
+    Copyright (C) 2011 Broad Institute.
+    Copyright (C) 2012-2013, 2015, 2016, 2019 Genome Research Ltd.
+
+    Author: Heng Li <lh3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <config.h>
+
+#include <unistd.h>
+#include <stdlib.h>
+#include <string.h>
+#include "htslib/hts.h"
+#include "htslib/sam.h"
+#include "htslib/faidx.h"
+#include "samtools.h"
+#include "sam_opts.h"
+
+#define ERR_DEP 0.83
+
+typedef struct {
+    int e[2][3], p[2][2];
+} score_param_t;
+
+/* Note that although the two matrics have 10 parameters in total, only 4
+ * (probably 3) are free.  Changing the scoring matrices in a sort of symmetric
+ * way will not change the result. */
+static score_param_t g_param = { {{0,0,0},{-4,1,6}}, {{0,-14000}, {0,0}} };
+
+typedef struct {
+    int min_baseQ, tid, max_bases;
+    uint16_t *bases;
+    samFile *fp;
+    sam_hdr_t *h;
+    char *ref;
+    hts_pos_t len;
+    faidx_t *fai;
+    errmod_t *em;
+} ct_t;
+
+static uint16_t gencns(ct_t *g, int n, const bam_pileup1_t *plp)
+{
+    int i, j, ret, tmp, k, sum[4], qual;
+    float q[16];
+    if (n > g->max_bases) { // enlarge g->bases
+        g->max_bases = n;
+        kroundup32(g->max_bases);
+        g->bases = realloc(g->bases, (size_t) g->max_bases * 2);
+    }
+    for (i = k = 0; i < n; ++i) {
+        const bam_pileup1_t *p = plp + i;
+        uint8_t *seq;
+        int q, baseQ, b;
+        if (p->is_refskip || p->is_del) continue;
+        baseQ = bam_get_qual(p->b)[p->qpos];
+        if (baseQ < g->min_baseQ) continue;
+        seq = bam_get_seq(p->b);
+        b = seq_nt16_int[bam_seqi(seq, p->qpos)];
+        if (b > 3) continue;
+        q = baseQ < p->b->core.qual? baseQ : p->b->core.qual;
+        if (q < 4) q = 4;
+        if (q > 63) q = 63;
+        g->bases[k++] = q<<5 | bam_is_rev(p->b)<<4 | b;
+    }
+    if (k == 0) return 0;
+    errmod_cal(g->em, k, 4, g->bases, q);
+    for (i = 0; i < 4; ++i) sum[i] = (int)(q[i<<2|i] + .499) << 2 | i;
+    for (i = 1; i < 4; ++i) // insertion sort
+        for (j = i; j > 0 && sum[j] < sum[j-1]; --j)
+            tmp = sum[j], sum[j] = sum[j-1], sum[j-1] = tmp;
+    qual = (sum[1]>>2) - (sum[0]>>2);
+    k = k < 256? k : 255;
+    ret = (qual < 63? qual : 63) << 2 | (sum[0]&3);
+    return ret<<8|k;
+}
+
+static void process_cns(sam_hdr_t *h, int tid, hts_pos_t l, uint16_t *cns)
+{
+    int64_t i, s;
+    int f[2][2], *prev, *curr, *swap_tmp;
+    uint8_t *b; // backtrack array
+    b = calloc(l, 1);
+    f[0][0] = f[0][1] = 0;
+    prev = f[0]; curr = f[1];
+    // fill the backtrack matrix
+    for (i = 0; i < l; ++i) {
+        int c = (cns[i] == 0)? 0 : (cns[i]>>8 == 0)? 1 : 2;
+        int tmp0, tmp1;
+        // compute f[0]
+        tmp0 = prev[0] + g_param.e[0][c] + g_param.p[0][0]; // (s[i+1],s[i])=(0,0)
+        tmp1 = prev[1] + g_param.e[0][c] + g_param.p[1][0]; // (0,1)
+        if (tmp0 > tmp1) curr[0] = tmp0, b[i] = 0;
+        else curr[0] = tmp1, b[i] = 1;
+        // compute f[1]
+        tmp0 = prev[0] + g_param.e[1][c] + g_param.p[0][1]; // (s[i+1],s[i])=(1,0)
+        tmp1 = prev[1] + g_param.e[1][c] + g_param.p[1][1]; // (1,1)
+        if (tmp0 > tmp1) curr[1] = tmp0, b[i] |= 0<<1;
+        else curr[1] = tmp1, b[i] |= 1<<1;
+        // swap
+        swap_tmp = prev; prev = curr; curr = swap_tmp;
+    }
+    // backtrack
+    s = prev[0] > prev[1]? 0 : 1;
+    for (i = l - 1; i > 0; --i) {
+        b[i] |= s<<2;
+        s = b[i]>>s&1;
+    }
+    // print
+    for (i = 0, s = -1; i < INT64_MAX && i <= l; ++i) {
+        if (i == l || ((b[i]>>2&3) == 0 && s >= 0)) {
+            if (s >= 0) {
+                int64_t j;
+                printf("%s:%"PRId64"-%"PRId64"\t0\t%s\t%"PRId64"\t60\t%"PRId64"M\t*\t0\t0\t", sam_hdr_tid2name(h, tid), s+1, i, sam_hdr_tid2name(h, tid), s+1, i-s);
+                for (j = s; j < i; ++j) {
+                    int c = cns[j]>>8;
+                    if (c == 0) putchar('N');
+                    else putchar("ACGT"[c&3]);
+                }
+                putchar('\t');
+                for (j = s; j < i; ++j)
+                    putchar(33 + (cns[j]>>8>>2));
+                putchar('\n');
+            }
+            //if (s >= 0) printf("%s\t%d\t%d\t%d\n", h->target_name[tid], s, i, i - s);
+            s = -1;
+        } else if ((b[i]>>2&3) && s < 0) s = i;
+    }
+    free(b);
+}
+
+static int read_aln(void *data, bam1_t *b)
+{
+    ct_t *g = (ct_t*)data;
+    int ret;
+    while (1)
+    {
+        ret = sam_read1(g->fp, g->h, b);
+        if ( ret<0 ) break;
+        if ( b->core.flag & (BAM_FUNMAP | BAM_FSECONDARY | BAM_FQCFAIL | BAM_FDUP) ) continue;
+        if ( g->fai && b->core.tid >= 0 ) {
+            if (b->core.tid != g->tid) { // then load the sequence
+                free(g->ref);
+                g->ref = fai_fetch64(g->fai, sam_hdr_tid2name(g->h, b->core.tid), &g->len);
+                g->tid = b->core.tid;
+            }
+            sam_prob_realn(b, g->ref, g->len, 1<<1|1);
+        }
+        break;
+    }
+    return ret;
+}
+
+int main_cut_target(int argc, char *argv[])
+{
+    int c, tid, pos, n, lasttid = -1, usage = 0, status = EXIT_SUCCESS;
+    hts_pos_t l, max_l;
+    const bam_pileup1_t *p;
+    bam_plp_t plp;
+    uint16_t *cns;
+    ct_t g;
+
+    sam_global_args ga = SAM_GLOBAL_ARGS_INIT;
+    static const struct option lopts[] = {
+        SAM_OPT_GLOBAL_OPTIONS('-', 0, '-', '-', 'f', '-'),
+        { NULL, 0, NULL, 0 }
+    };
+
+    memset(&g, 0, sizeof(ct_t));
+    g.min_baseQ = 13; g.tid = -1;
+    while ((c = getopt_long(argc, argv, "f:Q:i:o:0:1:2:", lopts, NULL)) >= 0) {
+        switch (c) {
+            case 'Q': g.min_baseQ = atoi(optarg); break; // quality cutoff
+            case 'i': g_param.p[0][1] = -atoi(optarg); break; // 0->1 transition (in) PENALTY
+            case '0': g_param.e[1][0] = atoi(optarg); break; // emission SCORE
+            case '1': g_param.e[1][1] = atoi(optarg); break;
+            case '2': g_param.e[1][2] = atoi(optarg); break;
+            default:  if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break;
+                      /* else fall-through */
+            case '?': usage=1; break;
+        }
+    }
+    if (ga.reference) {
+        g.fai = fai_load(ga.reference);
+        if (g.fai == 0) fprintf(stderr, "[%s] fail to load the fasta index.\n", __func__);
+    }
+    if (usage || argc == optind) {
+        fprintf(stderr, "Usage: samtools targetcut [-Q minQ] [-i inPen] [-0 em0] [-1 em1] [-2 em2] <in.bam>\n");
+        sam_global_opt_help(stderr, "-.--f--.");
+        return 1;
+    }
+    l = max_l = 0; cns = 0;
+    g.fp = sam_open_format(argv[optind], "r", &ga.in);
+    if (g.fp == NULL) {
+        print_error_errno("targetcut", "can't open \"%s\"", argv[optind]);
+        return 1;
+    }
+
+    g.h = sam_hdr_read(g.fp);
+    if (g.h == NULL) {
+        print_error("targetcut", "couldn't read header for \"%s\"", argv[optind]);
+        sam_close(g.fp);
+        return 1;
+    }
+    g.em = errmod_init(1. - ERR_DEP);
+    plp = bam_plp_init(read_aln, &g);
+    while ((p = bam_plp_auto(plp, &tid, &pos, &n)) != 0) {
+        if (tid < 0) break;
+        if (tid != lasttid) { // change of chromosome
+            if (cns) process_cns(g.h, lasttid, l, cns);
+            if (max_l < sam_hdr_tid2len(g.h, tid)) {
+                max_l = sam_hdr_tid2len(g.h, tid);
+                kroundup32(max_l);
+                cns = realloc(cns, max_l * 2);
+            }
+            l = sam_hdr_tid2len(g.h, tid);
+            memset(cns, 0, max_l * 2);
+            lasttid = tid;
+        }
+        cns[pos] = gencns(&g, n, p);
+    }
+    process_cns(g.h, lasttid, l, cns);
+
+    if (n < 0) {
+        print_error("targetcut", "error reading from \"%s\"", argv[optind]);
+        status = EXIT_FAILURE;
+    }
+
+    free(cns);
+    sam_hdr_destroy(g.h);
+    bam_plp_destroy(plp);
+    sam_close(g.fp);
+    if (g.fai) {
+        fai_destroy(g.fai); free(g.ref);
+    }
+    errmod_destroy(g.em);
+    free(g.bases);
+    sam_global_args_free(&ga);
+    return status;
+}
diff --git a/samtools/cut_target.c.pysam.c b/samtools/cut_target.c.pysam.c
new file mode 100644
index 0000000..babe42b
--- /dev/null
+++ b/samtools/cut_target.c.pysam.c
@@ -0,0 +1,259 @@
+#include "samtools.pysam.h"
+
+/*  cut_target.c -- targetcut subcommand.
+
+    Copyright (C) 2011 Broad Institute.
+    Copyright (C) 2012-2013, 2015, 2016, 2019 Genome Research Ltd.
+
+    Author: Heng Li <lh3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <config.h>
+
+#include <unistd.h>
+#include <stdlib.h>
+#include <string.h>
+#include "htslib/hts.h"
+#include "htslib/sam.h"
+#include "htslib/faidx.h"
+#include "samtools.h"
+#include "sam_opts.h"
+
+#define ERR_DEP 0.83
+
+typedef struct {
+    int e[2][3], p[2][2];
+} score_param_t;
+
+/* Note that although the two matrics have 10 parameters in total, only 4
+ * (probably 3) are free.  Changing the scoring matrices in a sort of symmetric
+ * way will not change the result. */
+static score_param_t g_param = { {{0,0,0},{-4,1,6}}, {{0,-14000}, {0,0}} };
+
+typedef struct {
+    int min_baseQ, tid, max_bases;
+    uint16_t *bases;
+    samFile *fp;
+    sam_hdr_t *h;
+    char *ref;
+    hts_pos_t len;
+    faidx_t *fai;
+    errmod_t *em;
+} ct_t;
+
+static uint16_t gencns(ct_t *g, int n, const bam_pileup1_t *plp)
+{
+    int i, j, ret, tmp, k, sum[4], qual;
+    float q[16];
+    if (n > g->max_bases) { // enlarge g->bases
+        g->max_bases = n;
+        kroundup32(g->max_bases);
+        g->bases = realloc(g->bases, (size_t) g->max_bases * 2);
+    }
+    for (i = k = 0; i < n; ++i) {
+        const bam_pileup1_t *p = plp + i;
+        uint8_t *seq;
+        int q, baseQ, b;
+        if (p->is_refskip || p->is_del) continue;
+        baseQ = bam_get_qual(p->b)[p->qpos];
+        if (baseQ < g->min_baseQ) continue;
+        seq = bam_get_seq(p->b);
+        b = seq_nt16_int[bam_seqi(seq, p->qpos)];
+        if (b > 3) continue;
+        q = baseQ < p->b->core.qual? baseQ : p->b->core.qual;
+        if (q < 4) q = 4;
+        if (q > 63) q = 63;
+        g->bases[k++] = q<<5 | bam_is_rev(p->b)<<4 | b;
+    }
+    if (k == 0) return 0;
+    errmod_cal(g->em, k, 4, g->bases, q);
+    for (i = 0; i < 4; ++i) sum[i] = (int)(q[i<<2|i] + .499) << 2 | i;
+    for (i = 1; i < 4; ++i) // insertion sort
+        for (j = i; j > 0 && sum[j] < sum[j-1]; --j)
+            tmp = sum[j], sum[j] = sum[j-1], sum[j-1] = tmp;
+    qual = (sum[1]>>2) - (sum[0]>>2);
+    k = k < 256? k : 255;
+    ret = (qual < 63? qual : 63) << 2 | (sum[0]&3);
+    return ret<<8|k;
+}
+
+static void process_cns(sam_hdr_t *h, int tid, hts_pos_t l, uint16_t *cns)
+{
+    int64_t i, s;
+    int f[2][2], *prev, *curr, *swap_tmp;
+    uint8_t *b; // backtrack array
+    b = calloc(l, 1);
+    f[0][0] = f[0][1] = 0;
+    prev = f[0]; curr = f[1];
+    // fill the backtrack matrix
+    for (i = 0; i < l; ++i) {
+        int c = (cns[i] == 0)? 0 : (cns[i]>>8 == 0)? 1 : 2;
+        int tmp0, tmp1;
+        // compute f[0]
+        tmp0 = prev[0] + g_param.e[0][c] + g_param.p[0][0]; // (s[i+1],s[i])=(0,0)
+        tmp1 = prev[1] + g_param.e[0][c] + g_param.p[1][0]; // (0,1)
+        if (tmp0 > tmp1) curr[0] = tmp0, b[i] = 0;
+        else curr[0] = tmp1, b[i] = 1;
+        // compute f[1]
+        tmp0 = prev[0] + g_param.e[1][c] + g_param.p[0][1]; // (s[i+1],s[i])=(1,0)
+        tmp1 = prev[1] + g_param.e[1][c] + g_param.p[1][1]; // (1,1)
+        if (tmp0 > tmp1) curr[1] = tmp0, b[i] |= 0<<1;
+        else curr[1] = tmp1, b[i] |= 1<<1;
+        // swap
+        swap_tmp = prev; prev = curr; curr = swap_tmp;
+    }
+    // backtrack
+    s = prev[0] > prev[1]? 0 : 1;
+    for (i = l - 1; i > 0; --i) {
+        b[i] |= s<<2;
+        s = b[i]>>s&1;
+    }
+    // print
+    for (i = 0, s = -1; i < INT64_MAX && i <= l; ++i) {
+        if (i == l || ((b[i]>>2&3) == 0 && s >= 0)) {
+            if (s >= 0) {
+                int64_t j;
+                fprintf(samtools_stdout, "%s:%"PRId64"-%"PRId64"\t0\t%s\t%"PRId64"\t60\t%"PRId64"M\t*\t0\t0\t", sam_hdr_tid2name(h, tid), s+1, i, sam_hdr_tid2name(h, tid), s+1, i-s);
+                for (j = s; j < i; ++j) {
+                    int c = cns[j]>>8;
+                    if (c == 0) fputc('N', samtools_stdout);
+                    else fputc("ACGT"[c&3], samtools_stdout);
+                }
+                fputc('\t', samtools_stdout);
+                for (j = s; j < i; ++j)
+                    fputc(33 + (cns[j]>>8>>2), samtools_stdout);
+                fputc('\n', samtools_stdout);
+            }
+            //if (s >= 0) fprintf(samtools_stdout, "%s\t%d\t%d\t%d\n", h->target_name[tid], s, i, i - s);
+            s = -1;
+        } else if ((b[i]>>2&3) && s < 0) s = i;
+    }
+    free(b);
+}
+
+static int read_aln(void *data, bam1_t *b)
+{
+    ct_t *g = (ct_t*)data;
+    int ret;
+    while (1)
+    {
+        ret = sam_read1(g->fp, g->h, b);
+        if ( ret<0 ) break;
+        if ( b->core.flag & (BAM_FUNMAP | BAM_FSECONDARY | BAM_FQCFAIL | BAM_FDUP) ) continue;
+        if ( g->fai && b->core.tid >= 0 ) {
+            if (b->core.tid != g->tid) { // then load the sequence
+                free(g->ref);
+                g->ref = fai_fetch64(g->fai, sam_hdr_tid2name(g->h, b->core.tid), &g->len);
+                g->tid = b->core.tid;
+            }
+            sam_prob_realn(b, g->ref, g->len, 1<<1|1);
+        }
+        break;
+    }
+    return ret;
+}
+
+int main_cut_target(int argc, char *argv[])
+{
+    int c, tid, pos, n, lasttid = -1, usage = 0, status = EXIT_SUCCESS;
+    hts_pos_t l, max_l;
+    const bam_pileup1_t *p;
+    bam_plp_t plp;
+    uint16_t *cns;
+    ct_t g;
+
+    sam_global_args ga = SAM_GLOBAL_ARGS_INIT;
+    static const struct option lopts[] = {
+        SAM_OPT_GLOBAL_OPTIONS('-', 0, '-', '-', 'f', '-'),
+        { NULL, 0, NULL, 0 }
+    };
+
+    memset(&g, 0, sizeof(ct_t));
+    g.min_baseQ = 13; g.tid = -1;
+    while ((c = getopt_long(argc, argv, "f:Q:i:o:0:1:2:", lopts, NULL)) >= 0) {
+        switch (c) {
+            case 'Q': g.min_baseQ = atoi(optarg); break; // quality cutoff
+            case 'i': g_param.p[0][1] = -atoi(optarg); break; // 0->1 transition (in) PENALTY
+            case '0': g_param.e[1][0] = atoi(optarg); break; // emission SCORE
+            case '1': g_param.e[1][1] = atoi(optarg); break;
+            case '2': g_param.e[1][2] = atoi(optarg); break;
+            default:  if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break;
+                      /* else fall-through */
+            case '?': usage=1; break;
+        }
+    }
+    if (ga.reference) {
+        g.fai = fai_load(ga.reference);
+        if (g.fai == 0) fprintf(samtools_stderr, "[%s] fail to load the fasta index.\n", __func__);
+    }
+    if (usage || argc == optind) {
+        fprintf(samtools_stderr, "Usage: samtools targetcut [-Q minQ] [-i inPen] [-0 em0] [-1 em1] [-2 em2] <in.bam>\n");
+        sam_global_opt_help(samtools_stderr, "-.--f--.");
+        return 1;
+    }
+    l = max_l = 0; cns = 0;
+    g.fp = sam_open_format(argv[optind], "r", &ga.in);
+    if (g.fp == NULL) {
+        print_error_errno("targetcut", "can't open \"%s\"", argv[optind]);
+        return 1;
+    }
+
+    g.h = sam_hdr_read(g.fp);
+    if (g.h == NULL) {
+        print_error("targetcut", "couldn't read header for \"%s\"", argv[optind]);
+        sam_close(g.fp);
+        return 1;
+    }
+    g.em = errmod_init(1. - ERR_DEP);
+    plp = bam_plp_init(read_aln, &g);
+    while ((p = bam_plp_auto(plp, &tid, &pos, &n)) != 0) {
+        if (tid < 0) break;
+        if (tid != lasttid) { // change of chromosome
+            if (cns) process_cns(g.h, lasttid, l, cns);
+            if (max_l < sam_hdr_tid2len(g.h, tid)) {
+                max_l = sam_hdr_tid2len(g.h, tid);
+                kroundup32(max_l);
+                cns = realloc(cns, max_l * 2);
+            }
+            l = sam_hdr_tid2len(g.h, tid);
+            memset(cns, 0, max_l * 2);
+            lasttid = tid;
+        }
+        cns[pos] = gencns(&g, n, p);
+    }
+    process_cns(g.h, lasttid, l, cns);
+
+    if (n < 0) {
+        print_error("targetcut", "error reading from \"%s\"", argv[optind]);
+        status = EXIT_FAILURE;
+    }
+
+    free(cns);
+    sam_hdr_destroy(g.h);
+    bam_plp_destroy(plp);
+    sam_close(g.fp);
+    if (g.fai) {
+        fai_destroy(g.fai); free(g.ref);
+    }
+    errmod_destroy(g.em);
+    free(g.bases);
+    sam_global_args_free(&ga);
+    return status;
+}
diff --git a/samtools/dict.c b/samtools/dict.c
new file mode 100644
index 0000000..47cb842
--- /dev/null
+++ b/samtools/dict.c
@@ -0,0 +1,229 @@
+/*  dict.c -- create a sequence dictionary file.
+
+    Copyright (C) 2015, 2020 Genome Research Ltd.
+
+    Author: Shane McCarthy <sm15@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <config.h>
+
+#include <stdio.h>
+#include <string.h>
+#include <unistd.h>
+#include <zlib.h>
+#include <getopt.h>
+#include "htslib/khash.h"
+#include "htslib/kseq.h"
+#include "htslib/hts.h"
+#include "samtools.h"
+
+KHASH_SET_INIT_STR(str)
+KSEQ_INIT(gzFile, gzread)
+
+typedef struct _args_t
+{
+    char *output_fname, *alt_fname;
+    char *assembly, *species, *uri;
+    int  alias, header;
+    khash_t(str) *is_alt;
+}
+args_t;
+
+static void write_dict(const char *fn, args_t *args)
+{
+    hts_md5_context *md5;
+    int l, i, k;
+    gzFile fp;
+    kseq_t *seq;
+    unsigned char digest[16];
+    char hex[33];
+
+    fp = strcmp(fn, "-") ? gzopen(fn, "r") : gzdopen(fileno(stdin), "r");
+    if (fp == 0) {
+        print_error_errno("dict", "Cannot open %s", fn);
+        exit(1);
+    }
+    FILE *out = stdout;
+    if (args->output_fname) {
+        out = fopen(args->output_fname, "w");
+        if (out == NULL) {
+          print_error_errno("dict", "Cannot open %s for writing", args->output_fname);
+          exit(1);
+        }
+    }
+
+    if (!(md5 = hts_md5_init()))
+        exit(1);
+
+    seq = kseq_init(fp);
+    if (args->header) fprintf(out, "@HD\tVN:1.0\tSO:unsorted\n");
+    while ((l = kseq_read(seq)) >= 0) {
+        for (i = k = 0; i < seq->seq.l; ++i) {
+            if (seq->seq.s[i] >= '!' && seq->seq.s[i] <= '~')
+                seq->seq.s[k++] = toupper(seq->seq.s[i]);
+        }
+        hts_md5_reset(md5);
+        hts_md5_update(md5, (unsigned char*)seq->seq.s, k);
+        hts_md5_final(digest, md5);
+        hts_md5_hex(hex, digest);
+        fprintf(out, "@SQ\tSN:%s\tLN:%d\tM5:%s", seq->name.s, k, hex);
+        if (args->is_alt && kh_get(str, args->is_alt, seq->name.s) != kh_end(args->is_alt))
+            fprintf(out, "\tAH:*");
+        if (args->alias) {
+            const char *name = seq->name.s;
+            if (strncmp(name, "chr", 3) == 0) {
+                name += 3;
+                fprintf(out, "\tAN:%s", name);
+            }
+            else
+                fprintf(out, "\tAN:chr%s", name);
+
+            if (strcmp(name, "M") == 0)
+                fprintf(out, ",chrMT,MT");
+            else if (strcmp(name, "MT") == 0)
+                fprintf(out, ",chrM,M");
+        }
+        if (args->uri)
+            fprintf(out, "\tUR:%s", args->uri);
+        else if (strcmp(fn, "-") != 0) {
+#ifdef _WIN32
+            char *real_path = _fullpath(NULL, fn, PATH_MAX);
+#else
+            char *real_path = realpath(fn, NULL);
+#endif
+            fprintf(out, "\tUR:file://%s", real_path);
+            free(real_path);
+        }
+        if (args->assembly) fprintf(out, "\tAS:%s", args->assembly);
+        if (args->species) fprintf(out, "\tSP:%s", args->species);
+        fprintf(out, "\n");
+    }
+    kseq_destroy(seq);
+    hts_md5_destroy(md5);
+
+    if (args->output_fname) fclose(out);
+    gzclose(fp);
+}
+
+static void read_alt_file(khash_t(str) *is_alt, const char *fname)
+{
+    htsFile *fp = hts_open(fname, "r");
+    if (fp == NULL) {
+        print_error_errno("dict", "Cannot open %s", fname);
+        exit(1);
+    }
+
+    // .alt files are in a SAM-like format, but we don't use sam_read1()
+    // as these files may not have a complete set of @SQ headers.
+
+    kstring_t str = KS_INITIALIZE;
+    while (hts_getline(fp, KS_SEP_LINE, &str) >= 0) {
+        if (str.l == 0 || str.s[0] == '@') continue;
+
+        char *tab = strchr(str.s, '\t');
+        if (tab) *tab = '\0';
+
+        int ret;
+        char *seqname = strdup(str.s);
+        kh_put(str, is_alt, seqname, &ret);
+        if (ret == 0) free(seqname); // Already present
+    }
+
+    ks_free(&str);
+    hts_close(fp);
+}
+
+static int dict_usage(void)
+{
+    fprintf(stderr, "\n");
+    fprintf(stderr, "About:   Create a sequence dictionary file from a fasta file\n");
+    fprintf(stderr, "Usage:   samtools dict [options] <file.fa|file.fa.gz>\n\n");
+    fprintf(stderr, "Options: -a, --assembly STR    assembly\n");
+    fprintf(stderr, "         -A, --alias, --alternative-name\n");
+    fprintf(stderr, "                               add AN tag by adding/removing 'chr'\n");
+    fprintf(stderr, "         -H, --no-header       do not print @HD line\n");
+    fprintf(stderr, "         -l, --alt FILE        add AH:* tag to alternate locus sequences\n");
+    fprintf(stderr, "         -o, --output FILE     file to write out dict file [stdout]\n");
+    fprintf(stderr, "         -s, --species STR     species\n");
+    fprintf(stderr, "         -u, --uri STR         URI [file:///abs/path/to/file.fa]\n");
+    fprintf(stderr, "\n");
+    return 1;
+}
+
+int dict_main(int argc, char *argv[])
+{
+    args_t *args = (args_t*) calloc(1,sizeof(args_t));
+    args->header = 1;
+
+    static const struct option loptions[] =
+    {
+        {"help", no_argument, NULL, 'h'},
+        {"no-header", no_argument, NULL, 'H'},
+        {"alias", no_argument, NULL, 'A'},
+        {"alt", required_argument, NULL, 'l'},
+        {"alternative-name", no_argument, NULL, 'A'},
+        {"assembly", required_argument, NULL, 'a'},
+        {"species", required_argument, NULL, 's'},
+        {"uri", required_argument, NULL, 'u'},
+        {"output", required_argument, NULL, 'o'},
+        {NULL, 0, NULL, 0}
+    };
+    int c;
+    while ( (c=getopt_long(argc,argv,"?AhHa:l:s:u:o:",loptions,NULL))>0 )
+    {
+        switch (c)
+        {
+            case 'A': args->alias = 1; break;
+            case 'a': args->assembly = optarg; break;
+            case 'l': args->alt_fname = optarg; break;
+            case 's': args->species = optarg; break;
+            case 'u': args->uri = optarg; break;
+            case 'o': args->output_fname = optarg; break;
+            case 'H': args->header = 0; break;
+            case 'h': return dict_usage();
+            default: return dict_usage();
+        }
+    }
+
+    char *fname = NULL;
+    if ( optind>=argc )
+    {
+        if ( !isatty(STDIN_FILENO) ) fname = "-";  // reading from stdin
+        else return dict_usage();
+    }
+    else fname = argv[optind];
+
+    if (args->alt_fname) {
+        args->is_alt = kh_init(str);
+        read_alt_file(args->is_alt, args->alt_fname);
+    }
+
+    write_dict(fname, args);
+
+    if (args->is_alt) {
+        khint_t k;
+        for (k = 0; k < kh_end(args->is_alt); ++k)
+            if (kh_exist(args->is_alt, k)) free((char *) kh_key(args->is_alt, k));
+        kh_destroy(str, args->is_alt);
+    }
+
+    free(args);
+    return 0;
+}
diff --git a/samtools/dict.c.pysam.c b/samtools/dict.c.pysam.c
new file mode 100644
index 0000000..6b2f2ba
--- /dev/null
+++ b/samtools/dict.c.pysam.c
@@ -0,0 +1,231 @@
+#include "samtools.pysam.h"
+
+/*  dict.c -- create a sequence dictionary file.
+
+    Copyright (C) 2015, 2020 Genome Research Ltd.
+
+    Author: Shane McCarthy <sm15@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <config.h>
+
+#include <stdio.h>
+#include <string.h>
+#include <unistd.h>
+#include <zlib.h>
+#include <getopt.h>
+#include "htslib/khash.h"
+#include "htslib/kseq.h"
+#include "htslib/hts.h"
+#include "samtools.h"
+
+KHASH_SET_INIT_STR(str)
+KSEQ_INIT(gzFile, gzread)
+
+typedef struct _args_t
+{
+    char *output_fname, *alt_fname;
+    char *assembly, *species, *uri;
+    int  alias, header;
+    khash_t(str) *is_alt;
+}
+args_t;
+
+static void write_dict(const char *fn, args_t *args)
+{
+    hts_md5_context *md5;
+    int l, i, k;
+    gzFile fp;
+    kseq_t *seq;
+    unsigned char digest[16];
+    char hex[33];
+
+    fp = strcmp(fn, "-") ? gzopen(fn, "r") : gzdopen(fileno(stdin), "r");
+    if (fp == 0) {
+        print_error_errno("dict", "Cannot open %s", fn);
+        samtools_exit(1);
+    }
+    FILE *out = samtools_stdout;
+    if (args->output_fname) {
+        out = fopen(args->output_fname, "w");
+        if (out == NULL) {
+          print_error_errno("dict", "Cannot open %s for writing", args->output_fname);
+          samtools_exit(1);
+        }
+    }
+
+    if (!(md5 = hts_md5_init()))
+        samtools_exit(1);
+
+    seq = kseq_init(fp);
+    if (args->header) fprintf(out, "@HD\tVN:1.0\tSO:unsorted\n");
+    while ((l = kseq_read(seq)) >= 0) {
+        for (i = k = 0; i < seq->seq.l; ++i) {
+            if (seq->seq.s[i] >= '!' && seq->seq.s[i] <= '~')
+                seq->seq.s[k++] = toupper(seq->seq.s[i]);
+        }
+        hts_md5_reset(md5);
+        hts_md5_update(md5, (unsigned char*)seq->seq.s, k);
+        hts_md5_final(digest, md5);
+        hts_md5_hex(hex, digest);
+        fprintf(out, "@SQ\tSN:%s\tLN:%d\tM5:%s", seq->name.s, k, hex);
+        if (args->is_alt && kh_get(str, args->is_alt, seq->name.s) != kh_end(args->is_alt))
+            fprintf(out, "\tAH:*");
+        if (args->alias) {
+            const char *name = seq->name.s;
+            if (strncmp(name, "chr", 3) == 0) {
+                name += 3;
+                fprintf(out, "\tAN:%s", name);
+            }
+            else
+                fprintf(out, "\tAN:chr%s", name);
+
+            if (strcmp(name, "M") == 0)
+                fprintf(out, ",chrMT,MT");
+            else if (strcmp(name, "MT") == 0)
+                fprintf(out, ",chrM,M");
+        }
+        if (args->uri)
+            fprintf(out, "\tUR:%s", args->uri);
+        else if (strcmp(fn, "-") != 0) {
+#ifdef _WIN32
+            char *real_path = _fullpath(NULL, fn, PATH_MAX);
+#else
+            char *real_path = realpath(fn, NULL);
+#endif
+            fprintf(out, "\tUR:file://%s", real_path);
+            free(real_path);
+        }
+        if (args->assembly) fprintf(out, "\tAS:%s", args->assembly);
+        if (args->species) fprintf(out, "\tSP:%s", args->species);
+        fprintf(out, "\n");
+    }
+    kseq_destroy(seq);
+    hts_md5_destroy(md5);
+
+    if (args->output_fname) fclose(out);
+    gzclose(fp);
+}
+
+static void read_alt_file(khash_t(str) *is_alt, const char *fname)
+{
+    htsFile *fp = hts_open(fname, "r");
+    if (fp == NULL) {
+        print_error_errno("dict", "Cannot open %s", fname);
+        samtools_exit(1);
+    }
+
+    // .alt files are in a SAM-like format, but we don't use sam_read1()
+    // as these files may not have a complete set of @SQ headers.
+
+    kstring_t str = KS_INITIALIZE;
+    while (hts_getline(fp, KS_SEP_LINE, &str) >= 0) {
+        if (str.l == 0 || str.s[0] == '@') continue;
+
+        char *tab = strchr(str.s, '\t');
+        if (tab) *tab = '\0';
+
+        int ret;
+        char *seqname = strdup(str.s);
+        kh_put(str, is_alt, seqname, &ret);
+        if (ret == 0) free(seqname); // Already present
+    }
+
+    ks_free(&str);
+    hts_close(fp);
+}
+
+static int dict_usage(void)
+{
+    fprintf(samtools_stderr, "\n");
+    fprintf(samtools_stderr, "About:   Create a sequence dictionary file from a fasta file\n");
+    fprintf(samtools_stderr, "Usage:   samtools dict [options] <file.fa|file.fa.gz>\n\n");
+    fprintf(samtools_stderr, "Options: -a, --assembly STR    assembly\n");
+    fprintf(samtools_stderr, "         -A, --alias, --alternative-name\n");
+    fprintf(samtools_stderr, "                               add AN tag by adding/removing 'chr'\n");
+    fprintf(samtools_stderr, "         -H, --no-header       do not print @HD line\n");
+    fprintf(samtools_stderr, "         -l, --alt FILE        add AH:* tag to alternate locus sequences\n");
+    fprintf(samtools_stderr, "         -o, --output FILE     file to write out dict file [samtools_stdout]\n");
+    fprintf(samtools_stderr, "         -s, --species STR     species\n");
+    fprintf(samtools_stderr, "         -u, --uri STR         URI [file:///abs/path/to/file.fa]\n");
+    fprintf(samtools_stderr, "\n");
+    return 1;
+}
+
+int dict_main(int argc, char *argv[])
+{
+    args_t *args = (args_t*) calloc(1,sizeof(args_t));
+    args->header = 1;
+
+    static const struct option loptions[] =
+    {
+        {"help", no_argument, NULL, 'h'},
+        {"no-header", no_argument, NULL, 'H'},
+        {"alias", no_argument, NULL, 'A'},
+        {"alt", required_argument, NULL, 'l'},
+        {"alternative-name", no_argument, NULL, 'A'},
+        {"assembly", required_argument, NULL, 'a'},
+        {"species", required_argument, NULL, 's'},
+        {"uri", required_argument, NULL, 'u'},
+        {"output", required_argument, NULL, 'o'},
+        {NULL, 0, NULL, 0}
+    };
+    int c;
+    while ( (c=getopt_long(argc,argv,"?AhHa:l:s:u:o:",loptions,NULL))>0 )
+    {
+        switch (c)
+        {
+            case 'A': args->alias = 1; break;
+            case 'a': args->assembly = optarg; break;
+            case 'l': args->alt_fname = optarg; break;
+            case 's': args->species = optarg; break;
+            case 'u': args->uri = optarg; break;
+            case 'o': args->output_fname = optarg; break;
+            case 'H': args->header = 0; break;
+            case 'h': return dict_usage();
+            default: return dict_usage();
+        }
+    }
+
+    char *fname = NULL;
+    if ( optind>=argc )
+    {
+        if ( !isatty(STDIN_FILENO) ) fname = "-";  // reading from stdin
+        else return dict_usage();
+    }
+    else fname = argv[optind];
+
+    if (args->alt_fname) {
+        args->is_alt = kh_init(str);
+        read_alt_file(args->is_alt, args->alt_fname);
+    }
+
+    write_dict(fname, args);
+
+    if (args->is_alt) {
+        khint_t k;
+        for (k = 0; k < kh_end(args->is_alt); ++k)
+            if (kh_exist(args->is_alt, k)) free((char *) kh_key(args->is_alt, k));
+        kh_destroy(str, args->is_alt);
+    }
+
+    free(args);
+    return 0;
+}
diff --git a/samtools/faidx.c b/samtools/faidx.c
new file mode 100644
index 0000000..03b5d65
--- /dev/null
+++ b/samtools/faidx.c
@@ -0,0 +1,415 @@
+/*  faidx.c -- faidx subcommand.
+
+    Copyright (C) 2008, 2009, 2013, 2016, 2018-2020 Genome Research Ltd.
+    Portions copyright (C) 2011 Broad Institute.
+
+    Author: Heng Li <lh3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.
+
+History:
+
+  * 2016-01-12: Pierre Lindenbaum @yokofakun : added options -o -n
+
+*/
+
+#include <config.h>
+
+#include <ctype.h>
+#include <string.h>
+#include <stdlib.h>
+#include <stdio.h>
+#include <unistd.h>
+#include <stdarg.h>
+#include <errno.h>
+#include <getopt.h>
+#include <limits.h>
+#include <htslib/faidx.h>
+#include <htslib/hts.h>
+#include <htslib/hfile.h>
+#include <htslib/kstring.h>
+#include "samtools.h"
+
+#define DEFAULT_FASTA_LINE_LEN 60
+
+static unsigned char comp_base[256] = {
+  0,   1,   2,   3,   4,   5,   6,   7,   8,   9,  10,  11,  12,  13,  14,  15,
+ 16,  17,  18,  19,  20,  21,  22,  23,  24,  25,  26,  27,  28,  29,  30,  31,
+ 32, '!', '"', '#', '$', '%', '&', '\'','(', ')', '*', '+', ',', '-', '.', '/',
+'0', '1', '2', '3', '4', '5', '6', '7', '8', '9', ':', ';', '<', '=', '>', '?',
+'@', 'T', 'V', 'G', 'H', 'E', 'F', 'C', 'D', 'I', 'J', 'M', 'L', 'K', 'N', 'O',
+'P', 'Q', 'Y', 'S', 'A', 'A', 'B', 'W', 'X', 'R', 'Z', '[', '\\',']', '^', '_',
+'`', 't', 'v', 'g', 'h', 'e', 'f', 'c', 'd', 'i', 'j', 'm', 'l', 'k', 'n', 'o',
+'p', 'q', 'y', 's', 'a', 'a', 'b', 'w', 'x', 'r', 'z', '{', '|', '}', '~', 127,
+128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143,
+144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159,
+160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175,
+176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191,
+192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207,
+208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223,
+224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239,
+240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255,
+};
+
+static void reverse_complement(char *str, const hts_pos_t len) {
+    char c;
+    hts_pos_t i = 0, j = len - 1;
+
+    while (i <= j) {
+        c = str[i];
+        str[i] = comp_base[(unsigned char)str[j]];
+        str[j] = comp_base[(unsigned char)c];
+        i++;
+        j--;
+    }
+}
+
+static void reverse(char *str, const hts_pos_t len) {
+    char c;
+    hts_pos_t i = 0, j = len - 1;
+
+    while (i < j) {
+        c = str[i];
+        str[i] = str[j];
+        str[j] = c;
+        i++;
+        j--;
+    }
+}
+
+
+static int write_line(faidx_t *faid, FILE *file, const char *line, const char *name,
+                      const int ignore, const int length, const hts_pos_t seq_len) {
+    int id;
+    hts_pos_t beg, end;
+
+    if (seq_len < 0) {
+        fprintf(stderr, "[faidx] Failed to fetch sequence in %s\n", name);
+
+        if (ignore && seq_len == -2) {
+            return EXIT_SUCCESS;
+        } else {
+            return EXIT_FAILURE;
+        }
+    } else if (seq_len == 0) {
+        fprintf(stderr, "[faidx] Zero length sequence: %s\n", name);
+    } else if (fai_parse_region(faid, name, &id, &beg, &end, 0)
+               && (end < INT_MAX) && (seq_len != end - beg)) {
+        fprintf(stderr, "[faidx] Truncated sequence: %s\n", name);
+    }
+
+    hts_pos_t i, seq_sz = seq_len;
+
+    for (i = 0; i < seq_sz; i += length)
+    {
+        hts_pos_t len = i + length < seq_sz ? length : seq_sz - i;
+        if (fwrite(line + i, 1, len, file) < len ||
+            fputc('\n', file) == EOF) {
+            print_error_errno("faidx", "failed to write output");
+            return EXIT_FAILURE;
+        }
+    }
+
+    return EXIT_SUCCESS;
+}
+
+
+static int write_output(faidx_t *faid, FILE *file, const char *name, const int ignore,
+                        const int length, const int rev,
+                        const char *pos_strand_name, const char *neg_strand_name,
+                        enum fai_format_options format) {
+    hts_pos_t seq_len;
+    char *seq = fai_fetch64(faid, name, &seq_len);
+
+    if (format == FAI_FASTA) {
+        fprintf(file, ">%s%s\n", name, rev ? neg_strand_name : pos_strand_name);
+    } else {
+        fprintf(file, "@%s%s\n", name, rev ? neg_strand_name : pos_strand_name);
+    }
+
+    if (rev && seq_len > 0) {
+        reverse_complement(seq, seq_len);
+    }
+
+    if (write_line(faid, file, seq, name, ignore, length, seq_len)
+        == EXIT_FAILURE) {
+        free(seq);
+        return EXIT_FAILURE;
+    }
+
+    free(seq);
+
+    if (format == FAI_FASTQ) {
+        fprintf(file, "+\n");
+
+        char *qual = fai_fetchqual64(faid, name, &seq_len);
+
+        if (rev && seq_len > 0) {
+            reverse(qual, seq_len);
+        }
+
+        if (write_line(faid, file, qual, name, ignore, length, seq_len)
+            == EXIT_FAILURE) {
+            free(qual);
+            return EXIT_FAILURE;
+        }
+
+        free(qual);
+    }
+
+    return EXIT_SUCCESS;
+}
+
+
+static int read_regions_from_file(faidx_t *faid, hFILE *in_file, FILE *file, const int ignore,
+                                  const int length, const int rev,
+                                  const char *pos_strand_name,
+                                  const char *neg_strand_name,
+                                  enum fai_format_options format) {
+    kstring_t line = {0, 0, NULL};
+    int ret = EXIT_FAILURE;
+
+    while (line.l = 0, kgetline(&line, (kgets_func *)hgets, in_file) >= 0) {
+        if ((ret = write_output(faid, file, line.s, ignore, length, rev, pos_strand_name, neg_strand_name, format)) == EXIT_FAILURE) {
+            break;
+        }
+    }
+
+    free(line.s);
+
+    return ret;
+}
+
+static int usage(FILE *fp, enum fai_format_options format, int exit_status)
+{
+    char *tool, *file_type, *index_name;
+
+    if (format == FAI_FASTA) {
+        tool = "faidx <file.fa|file.fa.gz>";
+        file_type = "FASTA";
+        index_name = "file.fa";
+    } else {
+        tool = "fqidx <file.fq|file.fq.gz>";
+        file_type = "FASTQ";
+        index_name = "file.fq";
+    }
+
+    fprintf(fp, "Usage: samtools %s [<reg> [...]]\n", tool);
+    fprintf(fp, "Option: \n"
+                " -o, --output FILE        Write %s to file.\n"
+                " -n, --length INT         Length of %s sequence line. [60]\n"
+                " -c, --continue           Continue after trying to retrieve missing region.\n"
+                " -r, --region-file FILE   File of regions.  Format is chr:from-to. One per line.\n"
+                " -i, --reverse-complement Reverse complement sequences.\n"
+                "     --mark-strand TYPE   Add strand indicator to sequence name\n"
+                "                          TYPE = rc   for /rc on negative strand (default)\n"
+                "                                 no   for no strand indicator\n"
+                "                                 sign for (+) / (-)\n"
+                "                                 custom,<pos>,<neg> for custom indicator\n"
+                "     --fai-idx      FILE  name of the index file (default %s.fai).\n"
+                "     --gzi-idx      FILE  name of compressed file index (default %s.gz.gzi).\n",
+                file_type, file_type, index_name, index_name);
+
+
+    if (format == FAI_FASTA) {
+       fprintf(fp, " -f, --fastq              File and index in FASTQ format.\n");
+    }
+
+    fprintf(fp, " -h, --help               This message.\n");
+
+    return exit_status;
+}
+
+int faidx_core(int argc, char *argv[], enum fai_format_options format)
+{
+    int c, ignore_error = 0, rev = 0;
+    int line_len = DEFAULT_FASTA_LINE_LEN ;/* fasta line len */
+    char* output_file = NULL; /* output file (default is stdout ) */
+    char *region_file = NULL; // list of regions from file, one per line
+    char *pos_strand_name = ""; // Extension to add to name for +ve strand
+    char *neg_strand_name = "/rc"; // Extension to add to name for -ve strand
+    char *strand_names = NULL; // Used for custom strand annotation
+    char *fai_name = NULL; // specified index name
+    char *gzi_name = NULL; // specified compressed index name
+    FILE* file_out = stdout;/* output stream */
+
+    static const struct option lopts[] = {
+        { "output", required_argument,       NULL, 'o' },
+        { "help",   no_argument,             NULL, 'h' },
+        { "length", required_argument,       NULL, 'n' },
+        { "continue", no_argument,           NULL, 'c' },
+        { "region-file", required_argument,  NULL, 'r' },
+        { "fastq", no_argument,              NULL, 'f' },
+        { "reverse-complement", no_argument, NULL, 'i' },
+        { "mark-strand", required_argument, NULL, 1000 },
+        { "fai-idx", required_argument,     NULL, 1001 },
+        { "gzi-idx", required_argument,     NULL, 1002 },
+        { NULL, 0, NULL, 0 }
+    };
+
+    while ((c = getopt_long(argc, argv, "ho:n:cr:fi", lopts, NULL)) >= 0) {
+        switch (c) {
+            case 'o': output_file = optarg; break;
+            case 'n': line_len = atoi(optarg);
+                      if(line_len<1) {
+                        fprintf(stderr,"[faidx] bad line length '%s', using default:%d\n",optarg,DEFAULT_FASTA_LINE_LEN);
+                        line_len= DEFAULT_FASTA_LINE_LEN ;
+                        }
+                      break;
+            case 'c': ignore_error = 1; break;
+            case 'r': region_file = optarg; break;
+            case 'f': format = FAI_FASTQ; break;
+            case 'i': rev = 1; break;
+            case '?': return usage(stderr, format, EXIT_FAILURE);
+            case 'h': return usage(stdout, format, EXIT_SUCCESS);
+            case 1000:
+                if (strcmp(optarg, "no") == 0) {
+                    pos_strand_name = neg_strand_name = "";
+                } else if (strcmp(optarg, "sign") == 0) {
+                    pos_strand_name = "(+)";
+                    neg_strand_name = "(-)";
+                } else if (strcmp(optarg, "rc") == 0) {
+                    pos_strand_name = "";
+                    neg_strand_name = "/rc";
+                } else if (strncmp(optarg, "custom,", 7) == 0) {
+                    size_t len = strlen(optarg + 7);
+                    size_t comma = strcspn(optarg + 7, ",");
+                    free(strand_names);
+                    strand_names = pos_strand_name = malloc(len + 2);
+                    if (!strand_names) {
+                        fprintf(stderr, "[faidx] Out of memory\n");
+                        return EXIT_FAILURE;
+                    }
+                    neg_strand_name = pos_strand_name + comma + 1;
+                    memcpy(pos_strand_name, optarg + 7, comma);
+                    pos_strand_name[comma] = '\0';
+                    if (comma < len)
+                        memcpy(neg_strand_name, optarg + 7 + comma + 1,
+                               len - comma);
+                    neg_strand_name[len - comma] = '\0';
+                } else {
+                    fprintf(stderr, "[faidx] Unknown --mark-strand option \"%s\"\n", optarg);
+                    return usage(stderr, format, EXIT_FAILURE);
+                }
+                break;
+            case 1001: fai_name = optarg; break;
+            case 1002: gzi_name = optarg; break;
+            default:  break;
+        }
+    }
+
+    if ( argc==optind )
+        return usage(stdout, format, EXIT_SUCCESS);
+
+    if (optind+1 == argc && !region_file) {
+        if (output_file && !fai_name)
+            fai_name = output_file;
+
+        if (fai_build3(argv[optind], fai_name, gzi_name) != 0) {
+            if (fai_name)
+                fprintf(stderr, "[faidx] Could not build fai index %s", fai_name);
+            else
+                fprintf(stderr, "[faidx] Could not build fai index %s.fai", argv[optind]);
+
+            if (gzi_name)
+                fprintf(stderr, " or compressed index %s\n", gzi_name);
+            else
+                fprintf(stderr, "\n");
+
+            return EXIT_FAILURE;
+        }
+
+        return 0;
+    }
+
+    faidx_t *fai = fai_load3_format(argv[optind], fai_name, gzi_name, FAI_CREATE, format);
+
+    if (!fai) {
+        if (fai_name)
+            fprintf(stderr, "[faidx] Could not load fai index %s", fai_name);
+        else
+            fprintf(stderr, "[faidx] Could not build fai index %s.fai", argv[optind]);
+
+        if (gzi_name)
+            fprintf(stderr, " or compressed index %s\n", gzi_name);
+        else
+            fprintf(stderr, "\n");
+
+        return EXIT_FAILURE;
+    }
+
+    /** output file provided by user */
+    if( output_file != NULL ) {
+        if( strcmp( output_file, argv[optind] ) == 0 ) {
+            fprintf(stderr,"[faidx] Same input/output : %s\n", output_file);
+            return EXIT_FAILURE;
+        }
+
+        file_out = fopen( output_file, "w" );
+
+        if( file_out == NULL) {
+            fprintf(stderr,"[faidx] Cannot open \"%s\" for writing :%s.\n", output_file, strerror(errno) );
+            return EXIT_FAILURE;
+        }
+    }
+
+    int exit_status = EXIT_SUCCESS;
+
+    if (region_file) {
+        hFILE *rf;
+
+        if ((rf = hopen(region_file, "r"))) {
+            exit_status = read_regions_from_file(fai, rf, file_out, ignore_error, line_len, rev, pos_strand_name, neg_strand_name, format);
+
+            if (hclose(rf) != 0) {
+                fprintf(stderr, "[faidx] Warning: failed to close %s", region_file);
+            }
+        } else {
+            fprintf(stderr, "[faidx] Failed to open \"%s\" for reading.\n", region_file);
+            exit_status = EXIT_FAILURE;
+        }
+    }
+
+    while ( ++optind<argc && exit_status == EXIT_SUCCESS) {
+        exit_status = write_output(fai, file_out, argv[optind], ignore_error, line_len, rev, pos_strand_name, neg_strand_name, format);
+    }
+
+    fai_destroy(fai);
+
+    if (fflush(file_out) == EOF) {
+        print_error_errno("faidx", "failed to flush output");
+        exit_status = EXIT_FAILURE;
+    }
+
+    if( output_file != NULL) fclose(file_out);
+    free(strand_names);
+
+    return exit_status;
+}
+
+
+int faidx_main(int argc, char *argv[]) {
+    return faidx_core(argc, argv, FAI_FASTA);
+}
+
+
+int fqidx_main(int argc, char *argv[]) {
+    return faidx_core(argc, argv, FAI_FASTQ);
+}
+
diff --git a/samtools/faidx.c.pysam.c b/samtools/faidx.c.pysam.c
new file mode 100644
index 0000000..0bc515b
--- /dev/null
+++ b/samtools/faidx.c.pysam.c
@@ -0,0 +1,417 @@
+#include "samtools.pysam.h"
+
+/*  faidx.c -- faidx subcommand.
+
+    Copyright (C) 2008, 2009, 2013, 2016, 2018-2020 Genome Research Ltd.
+    Portions copyright (C) 2011 Broad Institute.
+
+    Author: Heng Li <lh3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.
+
+History:
+
+  * 2016-01-12: Pierre Lindenbaum @yokofakun : added options -o -n
+
+*/
+
+#include <config.h>
+
+#include <ctype.h>
+#include <string.h>
+#include <stdlib.h>
+#include <stdio.h>
+#include <unistd.h>
+#include <stdarg.h>
+#include <errno.h>
+#include <getopt.h>
+#include <limits.h>
+#include <htslib/faidx.h>
+#include <htslib/hts.h>
+#include <htslib/hfile.h>
+#include <htslib/kstring.h>
+#include "samtools.h"
+
+#define DEFAULT_FASTA_LINE_LEN 60
+
+static unsigned char comp_base[256] = {
+  0,   1,   2,   3,   4,   5,   6,   7,   8,   9,  10,  11,  12,  13,  14,  15,
+ 16,  17,  18,  19,  20,  21,  22,  23,  24,  25,  26,  27,  28,  29,  30,  31,
+ 32, '!', '"', '#', '$', '%', '&', '\'','(', ')', '*', '+', ',', '-', '.', '/',
+'0', '1', '2', '3', '4', '5', '6', '7', '8', '9', ':', ';', '<', '=', '>', '?',
+'@', 'T', 'V', 'G', 'H', 'E', 'F', 'C', 'D', 'I', 'J', 'M', 'L', 'K', 'N', 'O',
+'P', 'Q', 'Y', 'S', 'A', 'A', 'B', 'W', 'X', 'R', 'Z', '[', '\\',']', '^', '_',
+'`', 't', 'v', 'g', 'h', 'e', 'f', 'c', 'd', 'i', 'j', 'm', 'l', 'k', 'n', 'o',
+'p', 'q', 'y', 's', 'a', 'a', 'b', 'w', 'x', 'r', 'z', '{', '|', '}', '~', 127,
+128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143,
+144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159,
+160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175,
+176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191,
+192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207,
+208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223,
+224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239,
+240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255,
+};
+
+static void reverse_complement(char *str, const hts_pos_t len) {
+    char c;
+    hts_pos_t i = 0, j = len - 1;
+
+    while (i <= j) {
+        c = str[i];
+        str[i] = comp_base[(unsigned char)str[j]];
+        str[j] = comp_base[(unsigned char)c];
+        i++;
+        j--;
+    }
+}
+
+static void reverse(char *str, const hts_pos_t len) {
+    char c;
+    hts_pos_t i = 0, j = len - 1;
+
+    while (i < j) {
+        c = str[i];
+        str[i] = str[j];
+        str[j] = c;
+        i++;
+        j--;
+    }
+}
+
+
+static int write_line(faidx_t *faid, FILE *file, const char *line, const char *name,
+                      const int ignore, const int length, const hts_pos_t seq_len) {
+    int id;
+    hts_pos_t beg, end;
+
+    if (seq_len < 0) {
+        fprintf(samtools_stderr, "[faidx] Failed to fetch sequence in %s\n", name);
+
+        if (ignore && seq_len == -2) {
+            return EXIT_SUCCESS;
+        } else {
+            return EXIT_FAILURE;
+        }
+    } else if (seq_len == 0) {
+        fprintf(samtools_stderr, "[faidx] Zero length sequence: %s\n", name);
+    } else if (fai_parse_region(faid, name, &id, &beg, &end, 0)
+               && (end < INT_MAX) && (seq_len != end - beg)) {
+        fprintf(samtools_stderr, "[faidx] Truncated sequence: %s\n", name);
+    }
+
+    hts_pos_t i, seq_sz = seq_len;
+
+    for (i = 0; i < seq_sz; i += length)
+    {
+        hts_pos_t len = i + length < seq_sz ? length : seq_sz - i;
+        if (fwrite(line + i, 1, len, file) < len ||
+            fputc('\n', file) == EOF) {
+            print_error_errno("faidx", "failed to write output");
+            return EXIT_FAILURE;
+        }
+    }
+
+    return EXIT_SUCCESS;
+}
+
+
+static int write_output(faidx_t *faid, FILE *file, const char *name, const int ignore,
+                        const int length, const int rev,
+                        const char *pos_strand_name, const char *neg_strand_name,
+                        enum fai_format_options format) {
+    hts_pos_t seq_len;
+    char *seq = fai_fetch64(faid, name, &seq_len);
+
+    if (format == FAI_FASTA) {
+        fprintf(file, ">%s%s\n", name, rev ? neg_strand_name : pos_strand_name);
+    } else {
+        fprintf(file, "@%s%s\n", name, rev ? neg_strand_name : pos_strand_name);
+    }
+
+    if (rev && seq_len > 0) {
+        reverse_complement(seq, seq_len);
+    }
+
+    if (write_line(faid, file, seq, name, ignore, length, seq_len)
+        == EXIT_FAILURE) {
+        free(seq);
+        return EXIT_FAILURE;
+    }
+
+    free(seq);
+
+    if (format == FAI_FASTQ) {
+        fprintf(file, "+\n");
+
+        char *qual = fai_fetchqual64(faid, name, &seq_len);
+
+        if (rev && seq_len > 0) {
+            reverse(qual, seq_len);
+        }
+
+        if (write_line(faid, file, qual, name, ignore, length, seq_len)
+            == EXIT_FAILURE) {
+            free(qual);
+            return EXIT_FAILURE;
+        }
+
+        free(qual);
+    }
+
+    return EXIT_SUCCESS;
+}
+
+
+static int read_regions_from_file(faidx_t *faid, hFILE *in_file, FILE *file, const int ignore,
+                                  const int length, const int rev,
+                                  const char *pos_strand_name,
+                                  const char *neg_strand_name,
+                                  enum fai_format_options format) {
+    kstring_t line = {0, 0, NULL};
+    int ret = EXIT_FAILURE;
+
+    while (line.l = 0, kgetline(&line, (kgets_func *)hgets, in_file) >= 0) {
+        if ((ret = write_output(faid, file, line.s, ignore, length, rev, pos_strand_name, neg_strand_name, format)) == EXIT_FAILURE) {
+            break;
+        }
+    }
+
+    free(line.s);
+
+    return ret;
+}
+
+static int usage(FILE *fp, enum fai_format_options format, int exit_status)
+{
+    char *tool, *file_type, *index_name;
+
+    if (format == FAI_FASTA) {
+        tool = "faidx <file.fa|file.fa.gz>";
+        file_type = "FASTA";
+        index_name = "file.fa";
+    } else {
+        tool = "fqidx <file.fq|file.fq.gz>";
+        file_type = "FASTQ";
+        index_name = "file.fq";
+    }
+
+    fprintf(fp, "Usage: samtools %s [<reg> [...]]\n", tool);
+    fprintf(fp, "Option: \n"
+                " -o, --output FILE        Write %s to file.\n"
+                " -n, --length INT         Length of %s sequence line. [60]\n"
+                " -c, --continue           Continue after trying to retrieve missing region.\n"
+                " -r, --region-file FILE   File of regions.  Format is chr:from-to. One per line.\n"
+                " -i, --reverse-complement Reverse complement sequences.\n"
+                "     --mark-strand TYPE   Add strand indicator to sequence name\n"
+                "                          TYPE = rc   for /rc on negative strand (default)\n"
+                "                                 no   for no strand indicator\n"
+                "                                 sign for (+) / (-)\n"
+                "                                 custom,<pos>,<neg> for custom indicator\n"
+                "     --fai-idx      FILE  name of the index file (default %s.fai).\n"
+                "     --gzi-idx      FILE  name of compressed file index (default %s.gz.gzi).\n",
+                file_type, file_type, index_name, index_name);
+
+
+    if (format == FAI_FASTA) {
+       fprintf(fp, " -f, --fastq              File and index in FASTQ format.\n");
+    }
+
+    fprintf(fp, " -h, --help               This message.\n");
+
+    return exit_status;
+}
+
+int faidx_core(int argc, char *argv[], enum fai_format_options format)
+{
+    int c, ignore_error = 0, rev = 0;
+    int line_len = DEFAULT_FASTA_LINE_LEN ;/* fasta line len */
+    char* output_file = NULL; /* output file (default is samtools_stdout ) */
+    char *region_file = NULL; // list of regions from file, one per line
+    char *pos_strand_name = ""; // Extension to add to name for +ve strand
+    char *neg_strand_name = "/rc"; // Extension to add to name for -ve strand
+    char *strand_names = NULL; // Used for custom strand annotation
+    char *fai_name = NULL; // specified index name
+    char *gzi_name = NULL; // specified compressed index name
+    FILE* file_out = samtools_stdout;/* output stream */
+
+    static const struct option lopts[] = {
+        { "output", required_argument,       NULL, 'o' },
+        { "help",   no_argument,             NULL, 'h' },
+        { "length", required_argument,       NULL, 'n' },
+        { "continue", no_argument,           NULL, 'c' },
+        { "region-file", required_argument,  NULL, 'r' },
+        { "fastq", no_argument,              NULL, 'f' },
+        { "reverse-complement", no_argument, NULL, 'i' },
+        { "mark-strand", required_argument, NULL, 1000 },
+        { "fai-idx", required_argument,     NULL, 1001 },
+        { "gzi-idx", required_argument,     NULL, 1002 },
+        { NULL, 0, NULL, 0 }
+    };
+
+    while ((c = getopt_long(argc, argv, "ho:n:cr:fi", lopts, NULL)) >= 0) {
+        switch (c) {
+            case 'o': output_file = optarg; break;
+            case 'n': line_len = atoi(optarg);
+                      if(line_len<1) {
+                        fprintf(samtools_stderr,"[faidx] bad line length '%s', using default:%d\n",optarg,DEFAULT_FASTA_LINE_LEN);
+                        line_len= DEFAULT_FASTA_LINE_LEN ;
+                        }
+                      break;
+            case 'c': ignore_error = 1; break;
+            case 'r': region_file = optarg; break;
+            case 'f': format = FAI_FASTQ; break;
+            case 'i': rev = 1; break;
+            case '?': return usage(samtools_stderr, format, EXIT_FAILURE);
+            case 'h': return usage(samtools_stdout, format, EXIT_SUCCESS);
+            case 1000:
+                if (strcmp(optarg, "no") == 0) {
+                    pos_strand_name = neg_strand_name = "";
+                } else if (strcmp(optarg, "sign") == 0) {
+                    pos_strand_name = "(+)";
+                    neg_strand_name = "(-)";
+                } else if (strcmp(optarg, "rc") == 0) {
+                    pos_strand_name = "";
+                    neg_strand_name = "/rc";
+                } else if (strncmp(optarg, "custom,", 7) == 0) {
+                    size_t len = strlen(optarg + 7);
+                    size_t comma = strcspn(optarg + 7, ",");
+                    free(strand_names);
+                    strand_names = pos_strand_name = malloc(len + 2);
+                    if (!strand_names) {
+                        fprintf(samtools_stderr, "[faidx] Out of memory\n");
+                        return EXIT_FAILURE;
+                    }
+                    neg_strand_name = pos_strand_name + comma + 1;
+                    memcpy(pos_strand_name, optarg + 7, comma);
+                    pos_strand_name[comma] = '\0';
+                    if (comma < len)
+                        memcpy(neg_strand_name, optarg + 7 + comma + 1,
+                               len - comma);
+                    neg_strand_name[len - comma] = '\0';
+                } else {
+                    fprintf(samtools_stderr, "[faidx] Unknown --mark-strand option \"%s\"\n", optarg);
+                    return usage(samtools_stderr, format, EXIT_FAILURE);
+                }
+                break;
+            case 1001: fai_name = optarg; break;
+            case 1002: gzi_name = optarg; break;
+            default:  break;
+        }
+    }
+
+    if ( argc==optind )
+        return usage(samtools_stdout, format, EXIT_SUCCESS);
+
+    if (optind+1 == argc && !region_file) {
+        if (output_file && !fai_name)
+            fai_name = output_file;
+
+        if (fai_build3(argv[optind], fai_name, gzi_name) != 0) {
+            if (fai_name)
+                fprintf(samtools_stderr, "[faidx] Could not build fai index %s", fai_name);
+            else
+                fprintf(samtools_stderr, "[faidx] Could not build fai index %s.fai", argv[optind]);
+
+            if (gzi_name)
+                fprintf(samtools_stderr, " or compressed index %s\n", gzi_name);
+            else
+                fprintf(samtools_stderr, "\n");
+
+            return EXIT_FAILURE;
+        }
+
+        return 0;
+    }
+
+    faidx_t *fai = fai_load3_format(argv[optind], fai_name, gzi_name, FAI_CREATE, format);
+
+    if (!fai) {
+        if (fai_name)
+            fprintf(samtools_stderr, "[faidx] Could not load fai index %s", fai_name);
+        else
+            fprintf(samtools_stderr, "[faidx] Could not build fai index %s.fai", argv[optind]);
+
+        if (gzi_name)
+            fprintf(samtools_stderr, " or compressed index %s\n", gzi_name);
+        else
+            fprintf(samtools_stderr, "\n");
+
+        return EXIT_FAILURE;
+    }
+
+    /** output file provided by user */
+    if( output_file != NULL ) {
+        if( strcmp( output_file, argv[optind] ) == 0 ) {
+            fprintf(samtools_stderr,"[faidx] Same input/output : %s\n", output_file);
+            return EXIT_FAILURE;
+        }
+
+        file_out = fopen( output_file, "w" );
+
+        if( file_out == NULL) {
+            fprintf(samtools_stderr,"[faidx] Cannot open \"%s\" for writing :%s.\n", output_file, strerror(errno) );
+            return EXIT_FAILURE;
+        }
+    }
+
+    int exit_status = EXIT_SUCCESS;
+
+    if (region_file) {
+        hFILE *rf;
+
+        if ((rf = hopen(region_file, "r"))) {
+            exit_status = read_regions_from_file(fai, rf, file_out, ignore_error, line_len, rev, pos_strand_name, neg_strand_name, format);
+
+            if (hclose(rf) != 0) {
+                fprintf(samtools_stderr, "[faidx] Warning: failed to close %s", region_file);
+            }
+        } else {
+            fprintf(samtools_stderr, "[faidx] Failed to open \"%s\" for reading.\n", region_file);
+            exit_status = EXIT_FAILURE;
+        }
+    }
+
+    while ( ++optind<argc && exit_status == EXIT_SUCCESS) {
+        exit_status = write_output(fai, file_out, argv[optind], ignore_error, line_len, rev, pos_strand_name, neg_strand_name, format);
+    }
+
+    fai_destroy(fai);
+
+    if (fflush(file_out) == EOF) {
+        print_error_errno("faidx", "failed to flush output");
+        exit_status = EXIT_FAILURE;
+    }
+
+    if( output_file != NULL) fclose(file_out);
+    free(strand_names);
+
+    return exit_status;
+}
+
+
+int faidx_main(int argc, char *argv[]) {
+    return faidx_core(argc, argv, FAI_FASTA);
+}
+
+
+int fqidx_main(int argc, char *argv[]) {
+    return faidx_core(argc, argv, FAI_FASTQ);
+}
+
diff --git a/samtools/lz4/LICENSE b/samtools/lz4/LICENSE
new file mode 100644
index 0000000..74c2cdd
--- /dev/null
+++ b/samtools/lz4/LICENSE
@@ -0,0 +1,24 @@
+LZ4 Library
+Copyright (c) 2011-2016, Yann Collet
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without modification,
+are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright notice, this
+  list of conditions and the following disclaimer in the documentation and/or
+  other materials provided with the distribution.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR
+ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
+ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
diff --git a/samtools/lz4/lz4.c b/samtools/lz4/lz4.c
new file mode 100644
index 0000000..41c0a28
--- /dev/null
+++ b/samtools/lz4/lz4.c
@@ -0,0 +1,1478 @@
+/*
+   LZ4 - Fast LZ compression algorithm
+   Copyright (C) 2011-2017, Yann Collet.
+
+   BSD 2-Clause License (http://www.opensource.org/licenses/bsd-license.php)
+
+   Redistribution and use in source and binary forms, with or without
+   modification, are permitted provided that the following conditions are
+   met:
+
+       * Redistributions of source code must retain the above copyright
+   notice, this list of conditions and the following disclaimer.
+       * Redistributions in binary form must reproduce the above
+   copyright notice, this list of conditions and the following disclaimer
+   in the documentation and/or other materials provided with the
+   distribution.
+
+   THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+   "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+   LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+   A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+   OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+   SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+   LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+   DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+   THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+   (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+   OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+   You can contact the author at :
+    - LZ4 homepage : http://www.lz4.org
+    - LZ4 source repository : https://github.com/lz4/lz4
+*/
+
+
+/*-************************************
+*  Tuning parameters
+**************************************/
+/*
+ * LZ4_HEAPMODE :
+ * Select how default compression functions will allocate memory for their hash table,
+ * in memory stack (0:default, fastest), or in memory heap (1:requires malloc()).
+ */
+#ifndef LZ4_HEAPMODE
+#  define LZ4_HEAPMODE 0
+#endif
+
+/*
+ * ACCELERATION_DEFAULT :
+ * Select "acceleration" for LZ4_compress_fast() when parameter value <= 0
+ */
+#define ACCELERATION_DEFAULT 1
+
+
+/*-************************************
+*  CPU Feature Detection
+**************************************/
+/* LZ4_FORCE_MEMORY_ACCESS
+ * By default, access to unaligned memory is controlled by `memcpy()`, which is safe and portable.
+ * Unfortunately, on some target/compiler combinations, the generated assembly is sub-optimal.
+ * The below switch allow to select different access method for improved performance.
+ * Method 0 (default) : use `memcpy()`. Safe and portable.
+ * Method 1 : `__packed` statement. It depends on compiler extension (ie, not portable).
+ *            This method is safe if your compiler supports it, and *generally* as fast or faster than `memcpy`.
+ * Method 2 : direct access. This method is portable but violate C standard.
+ *            It can generate buggy code on targets which assembly generation depends on alignment.
+ *            But in some circumstances, it's the only known way to get the most performance (ie GCC + ARMv6)
+ * See https://fastcompression.blogspot.fr/2015/08/accessing-unaligned-memory.html for details.
+ * Prefer these methods in priority order (0 > 1 > 2)
+ */
+#ifndef LZ4_FORCE_MEMORY_ACCESS   /* can be defined externally */
+#  if defined(__GNUC__) && ( defined(__ARM_ARCH_6__) || defined(__ARM_ARCH_6J__) || defined(__ARM_ARCH_6K__) || defined(__ARM_ARCH_6Z__) || defined(__ARM_ARCH_6ZK__) || defined(__ARM_ARCH_6T2__) )
+#    define LZ4_FORCE_MEMORY_ACCESS 2
+#  elif defined(__INTEL_COMPILER) || defined(__GNUC__)
+#    define LZ4_FORCE_MEMORY_ACCESS 1
+#  endif
+#endif
+
+/*
+ * LZ4_FORCE_SW_BITCOUNT
+ * Define this parameter if your target system or compiler does not support hardware bit count
+ */
+#if defined(_MSC_VER) && defined(_WIN32_WCE)   /* Visual Studio for Windows CE does not support Hardware bit count */
+#  define LZ4_FORCE_SW_BITCOUNT
+#endif
+
+
+/*-************************************
+*  Dependency
+**************************************/
+#include "lz4.h"
+/* see also "memory routines" below */
+
+
+/*-************************************
+*  Compiler Options
+**************************************/
+#ifdef _MSC_VER    /* Visual Studio */
+#  include <intrin.h>
+#  pragma warning(disable : 4127)        /* disable: C4127: conditional expression is constant */
+#  pragma warning(disable : 4293)        /* disable: C4293: too large shift (32-bits) */
+#endif  /* _MSC_VER */
+
+#ifndef FORCE_INLINE
+#  ifdef _MSC_VER    /* Visual Studio */
+#    define FORCE_INLINE static __forceinline
+#  else
+#    if defined (__cplusplus) || defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L   /* C99 */
+#      ifdef __GNUC__
+#        define FORCE_INLINE static inline __attribute__((always_inline))
+#      else
+#        define FORCE_INLINE static inline
+#      endif
+#    else
+#      define FORCE_INLINE static
+#    endif /* __STDC_VERSION__ */
+#  endif  /* _MSC_VER */
+#endif /* FORCE_INLINE */
+
+#if (defined(__GNUC__) && (__GNUC__ >= 3)) || (defined(__INTEL_COMPILER) && (__INTEL_COMPILER >= 800)) || defined(__clang__)
+#  define expect(expr,value)    (__builtin_expect ((expr),(value)) )
+#else
+#  define expect(expr,value)    (expr)
+#endif
+
+#define likely(expr)     expect((expr) != 0, 1)
+#define unlikely(expr)   expect((expr) != 0, 0)
+
+
+/*-************************************
+*  Memory routines
+**************************************/
+#include <stdlib.h>   /* malloc, calloc, free */
+#define ALLOCATOR(n,s) calloc(n,s)
+#define FREEMEM        free
+#include <string.h>   /* memset, memcpy */
+#define MEM_INIT       memset
+
+
+/*-************************************
+*  Basic Types
+**************************************/
+#if defined(__cplusplus) || (defined (__STDC_VERSION__) && (__STDC_VERSION__ >= 199901L) /* C99 */)
+# include <stdint.h>
+  typedef  uint8_t BYTE;
+  typedef uint16_t U16;
+  typedef uint32_t U32;
+  typedef  int32_t S32;
+  typedef uint64_t U64;
+  typedef uintptr_t uptrval;
+#else
+  typedef unsigned char       BYTE;
+  typedef unsigned short      U16;
+  typedef unsigned int        U32;
+  typedef   signed int        S32;
+  typedef unsigned long long  U64;
+  typedef size_t              uptrval;   /* generally true, except OpenVMS-64 */
+#endif
+
+#if defined(__x86_64__)
+  typedef U64    reg_t;   /* 64-bits in x32 mode */
+#else
+  typedef size_t reg_t;   /* 32-bits in x32 mode */
+#endif
+
+/*-************************************
+*  Reading and writing into memory
+**************************************/
+static unsigned LZ4_isLittleEndian(void)
+{
+    const union { U32 u; BYTE c[4]; } one = { 1 };   /* don't use static : performance detrimental */
+    return one.c[0];
+}
+
+
+#if defined(LZ4_FORCE_MEMORY_ACCESS) && (LZ4_FORCE_MEMORY_ACCESS==2)
+/* lie to the compiler about data alignment; use with caution */
+
+static U16 LZ4_read16(const void* memPtr) { return *(const U16*) memPtr; }
+static U32 LZ4_read32(const void* memPtr) { return *(const U32*) memPtr; }
+static reg_t LZ4_read_ARCH(const void* memPtr) { return *(const reg_t*) memPtr; }
+
+static void LZ4_write16(void* memPtr, U16 value) { *(U16*)memPtr = value; }
+static void LZ4_write32(void* memPtr, U32 value) { *(U32*)memPtr = value; }
+
+#elif defined(LZ4_FORCE_MEMORY_ACCESS) && (LZ4_FORCE_MEMORY_ACCESS==1)
+
+/* __pack instructions are safer, but compiler specific, hence potentially problematic for some compilers */
+/* currently only defined for gcc and icc */
+typedef union { U16 u16; U32 u32; reg_t uArch; } __attribute__((packed)) unalign;
+
+static U16 LZ4_read16(const void* ptr) { return ((const unalign*)ptr)->u16; }
+static U32 LZ4_read32(const void* ptr) { return ((const unalign*)ptr)->u32; }
+static reg_t LZ4_read_ARCH(const void* ptr) { return ((const unalign*)ptr)->uArch; }
+
+static void LZ4_write16(void* memPtr, U16 value) { ((unalign*)memPtr)->u16 = value; }
+static void LZ4_write32(void* memPtr, U32 value) { ((unalign*)memPtr)->u32 = value; }
+
+#else  /* safe and portable access through memcpy() */
+
+static U16 LZ4_read16(const void* memPtr)
+{
+    U16 val; memcpy(&val, memPtr, sizeof(val)); return val;
+}
+
+static U32 LZ4_read32(const void* memPtr)
+{
+    U32 val; memcpy(&val, memPtr, sizeof(val)); return val;
+}
+
+static reg_t LZ4_read_ARCH(const void* memPtr)
+{
+    reg_t val; memcpy(&val, memPtr, sizeof(val)); return val;
+}
+
+static void LZ4_write16(void* memPtr, U16 value)
+{
+    memcpy(memPtr, &value, sizeof(value));
+}
+
+static void LZ4_write32(void* memPtr, U32 value)
+{
+    memcpy(memPtr, &value, sizeof(value));
+}
+
+#endif /* LZ4_FORCE_MEMORY_ACCESS */
+
+
+static U16 LZ4_readLE16(const void* memPtr)
+{
+    if (LZ4_isLittleEndian()) {
+        return LZ4_read16(memPtr);
+    } else {
+        const BYTE* p = (const BYTE*)memPtr;
+        return (U16)((U16)p[0] + (p[1]<<8));
+    }
+}
+
+static void LZ4_writeLE16(void* memPtr, U16 value)
+{
+    if (LZ4_isLittleEndian()) {
+        LZ4_write16(memPtr, value);
+    } else {
+        BYTE* p = (BYTE*)memPtr;
+        p[0] = (BYTE) value;
+        p[1] = (BYTE)(value>>8);
+    }
+}
+
+static void LZ4_copy8(void* dst, const void* src)
+{
+    memcpy(dst,src,8);
+}
+
+/* customized variant of memcpy, which can overwrite up to 8 bytes beyond dstEnd */
+static void LZ4_wildCopy(void* dstPtr, const void* srcPtr, void* dstEnd)
+{
+    BYTE* d = (BYTE*)dstPtr;
+    const BYTE* s = (const BYTE*)srcPtr;
+    BYTE* const e = (BYTE*)dstEnd;
+
+    do { LZ4_copy8(d,s); d+=8; s+=8; } while (d<e);
+}
+
+
+/*-************************************
+*  Common Constants
+**************************************/
+#define MINMATCH 4
+
+#define WILDCOPYLENGTH 8
+#define LASTLITERALS 5
+#define MFLIMIT (WILDCOPYLENGTH+MINMATCH)
+static const int LZ4_minLength = (MFLIMIT+1);
+
+#define KB *(1 <<10)
+#define MB *(1 <<20)
+#define GB *(1U<<30)
+
+#define MAXD_LOG 16
+#define MAX_DISTANCE ((1 << MAXD_LOG) - 1)
+
+#define ML_BITS  4
+#define ML_MASK  ((1U<<ML_BITS)-1)
+#define RUN_BITS (8-ML_BITS)
+#define RUN_MASK ((1U<<RUN_BITS)-1)
+
+
+/*-************************************
+*  Error detection
+**************************************/
+#define LZ4_STATIC_ASSERT(c)    { enum { LZ4_static_assert = 1/(int)(!!(c)) }; }   /* use only *after* variable declarations */
+
+#if defined(LZ4_DEBUG) && (LZ4_DEBUG>=2)
+#  include <stdio.h>
+#  define DEBUGLOG(l, ...) {                          \
+                if (l<=LZ4_DEBUG) {                   \
+                    fprintf(stderr, __FILE__ ": ");   \
+                    fprintf(stderr, __VA_ARGS__);     \
+                    fprintf(stderr, " \n");           \
+            }   }
+#else
+#  define DEBUGLOG(l, ...)      {}    /* disabled */
+#endif
+
+
+/*-************************************
+*  Common functions
+**************************************/
+static unsigned LZ4_NbCommonBytes (register reg_t val)
+{
+    if (LZ4_isLittleEndian()) {
+        if (sizeof(val)==8) {
+#       if defined(_MSC_VER) && defined(_WIN64) && !defined(LZ4_FORCE_SW_BITCOUNT)
+            unsigned long r = 0;
+            _BitScanForward64( &r, (U64)val );
+            return (int)(r>>3);
+#       elif (defined(__clang__) || (defined(__GNUC__) && (__GNUC__>=3))) && !defined(LZ4_FORCE_SW_BITCOUNT)
+            return (__builtin_ctzll((U64)val) >> 3);
+#       else
+            static const int DeBruijnBytePos[64] = { 0, 0, 0, 0, 0, 1, 1, 2, 0, 3, 1, 3, 1, 4, 2, 7, 0, 2, 3, 6, 1, 5, 3, 5, 1, 3, 4, 4, 2, 5, 6, 7, 7, 0, 1, 2, 3, 3, 4, 6, 2, 6, 5, 5, 3, 4, 5, 6, 7, 1, 2, 4, 6, 4, 4, 5, 7, 2, 6, 5, 7, 6, 7, 7 };
+            return DeBruijnBytePos[((U64)((val & -(long long)val) * 0x0218A392CDABBD3FULL)) >> 58];
+#       endif
+        } else /* 32 bits */ {
+#       if defined(_MSC_VER) && !defined(LZ4_FORCE_SW_BITCOUNT)
+            unsigned long r;
+            _BitScanForward( &r, (U32)val );
+            return (int)(r>>3);
+#       elif (defined(__clang__) || (defined(__GNUC__) && (__GNUC__>=3))) && !defined(LZ4_FORCE_SW_BITCOUNT)
+            return (__builtin_ctz((U32)val) >> 3);
+#       else
+            static const int DeBruijnBytePos[32] = { 0, 0, 3, 0, 3, 1, 3, 0, 3, 2, 2, 1, 3, 2, 0, 1, 3, 3, 1, 2, 2, 2, 2, 0, 3, 1, 2, 0, 1, 0, 1, 1 };
+            return DeBruijnBytePos[((U32)((val & -(S32)val) * 0x077CB531U)) >> 27];
+#       endif
+        }
+    } else   /* Big Endian CPU */ {
+        if (sizeof(val)==8) {
+#       if defined(_MSC_VER) && defined(_WIN64) && !defined(LZ4_FORCE_SW_BITCOUNT)
+            unsigned long r = 0;
+            _BitScanReverse64( &r, val );
+            return (unsigned)(r>>3);
+#       elif (defined(__clang__) || (defined(__GNUC__) && (__GNUC__>=3))) && !defined(LZ4_FORCE_SW_BITCOUNT)
+            return (__builtin_clzll((U64)val) >> 3);
+#       else
+            unsigned r;
+            if (!(val>>32)) { r=4; } else { r=0; val>>=32; }
+            if (!(val>>16)) { r+=2; val>>=8; } else { val>>=24; }
+            r += (!val);
+            return r;
+#       endif
+        } else /* 32 bits */ {
+#       if defined(_MSC_VER) && !defined(LZ4_FORCE_SW_BITCOUNT)
+            unsigned long r = 0;
+            _BitScanReverse( &r, (unsigned long)val );
+            return (unsigned)(r>>3);
+#       elif (defined(__clang__) || (defined(__GNUC__) && (__GNUC__>=3))) && !defined(LZ4_FORCE_SW_BITCOUNT)
+            return (__builtin_clz((U32)val) >> 3);
+#       else
+            unsigned r;
+            if (!(val>>16)) { r=2; val>>=8; } else { r=0; val>>=24; }
+            r += (!val);
+            return r;
+#       endif
+        }
+    }
+}
+
+#define STEPSIZE sizeof(reg_t)
+static unsigned LZ4_count(const BYTE* pIn, const BYTE* pMatch, const BYTE* pInLimit)
+{
+    const BYTE* const pStart = pIn;
+
+    while (likely(pIn<pInLimit-(STEPSIZE-1))) {
+        reg_t const diff = LZ4_read_ARCH(pMatch) ^ LZ4_read_ARCH(pIn);
+        if (!diff) { pIn+=STEPSIZE; pMatch+=STEPSIZE; continue; }
+        pIn += LZ4_NbCommonBytes(diff);
+        return (unsigned)(pIn - pStart);
+    }
+
+    if ((STEPSIZE==8) && (pIn<(pInLimit-3)) && (LZ4_read32(pMatch) == LZ4_read32(pIn))) { pIn+=4; pMatch+=4; }
+    if ((pIn<(pInLimit-1)) && (LZ4_read16(pMatch) == LZ4_read16(pIn))) { pIn+=2; pMatch+=2; }
+    if ((pIn<pInLimit) && (*pMatch == *pIn)) pIn++;
+    return (unsigned)(pIn - pStart);
+}
+
+
+#ifndef LZ4_COMMONDEFS_ONLY
+/*-************************************
+*  Local Constants
+**************************************/
+static const int LZ4_64Klimit = ((64 KB) + (MFLIMIT-1));
+static const U32 LZ4_skipTrigger = 6;  /* Increase this value ==> compression run slower on incompressible data */
+
+
+/*-************************************
+*  Local Structures and types
+**************************************/
+typedef enum { notLimited = 0, limitedOutput = 1 } limitedOutput_directive;
+typedef enum { byPtr, byU32, byU16 } tableType_t;
+
+typedef enum { noDict = 0, withPrefix64k, usingExtDict } dict_directive;
+typedef enum { noDictIssue = 0, dictSmall } dictIssue_directive;
+
+typedef enum { endOnOutputSize = 0, endOnInputSize = 1 } endCondition_directive;
+typedef enum { full = 0, partial = 1 } earlyEnd_directive;
+
+
+/*-************************************
+*  Local Utils
+**************************************/
+int LZ4_versionNumber (void) { return LZ4_VERSION_NUMBER; }
+const char* LZ4_versionString(void) { return LZ4_VERSION_STRING; }
+int LZ4_compressBound(int isize)  { return LZ4_COMPRESSBOUND(isize); }
+int LZ4_sizeofState() { return LZ4_STREAMSIZE; }
+
+
+/*-******************************
+*  Compression functions
+********************************/
+static U32 LZ4_hash4(U32 sequence, tableType_t const tableType)
+{
+    if (tableType == byU16)
+        return ((sequence * 2654435761U) >> ((MINMATCH*8)-(LZ4_HASHLOG+1)));
+    else
+        return ((sequence * 2654435761U) >> ((MINMATCH*8)-LZ4_HASHLOG));
+}
+
+static U32 LZ4_hash5(U64 sequence, tableType_t const tableType)
+{
+    static const U64 prime5bytes = 889523592379ULL;
+    static const U64 prime8bytes = 11400714785074694791ULL;
+    const U32 hashLog = (tableType == byU16) ? LZ4_HASHLOG+1 : LZ4_HASHLOG;
+    if (LZ4_isLittleEndian())
+        return (U32)(((sequence << 24) * prime5bytes) >> (64 - hashLog));
+    else
+        return (U32)(((sequence >> 24) * prime8bytes) >> (64 - hashLog));
+}
+
+FORCE_INLINE U32 LZ4_hashPosition(const void* const p, tableType_t const tableType)
+{
+    if ((sizeof(reg_t)==8) && (tableType != byU16)) return LZ4_hash5(LZ4_read_ARCH(p), tableType);
+    return LZ4_hash4(LZ4_read32(p), tableType);
+}
+
+static void LZ4_putPositionOnHash(const BYTE* p, U32 h, void* tableBase, tableType_t const tableType, const BYTE* srcBase)
+{
+    switch (tableType)
+    {
+    case byPtr: { const BYTE** hashTable = (const BYTE**)tableBase; hashTable[h] = p; return; }
+    case byU32: { U32* hashTable = (U32*) tableBase; hashTable[h] = (U32)(p-srcBase); return; }
+    case byU16: { U16* hashTable = (U16*) tableBase; hashTable[h] = (U16)(p-srcBase); return; }
+    }
+}
+
+FORCE_INLINE void LZ4_putPosition(const BYTE* p, void* tableBase, tableType_t tableType, const BYTE* srcBase)
+{
+    U32 const h = LZ4_hashPosition(p, tableType);
+    LZ4_putPositionOnHash(p, h, tableBase, tableType, srcBase);
+}
+
+static const BYTE* LZ4_getPositionOnHash(U32 h, void* tableBase, tableType_t tableType, const BYTE* srcBase)
+{
+    if (tableType == byPtr) { const BYTE** hashTable = (const BYTE**) tableBase; return hashTable[h]; }
+    if (tableType == byU32) { const U32* const hashTable = (U32*) tableBase; return hashTable[h] + srcBase; }
+    { const U16* const hashTable = (U16*) tableBase; return hashTable[h] + srcBase; }   /* default, to ensure a return */
+}
+
+FORCE_INLINE const BYTE* LZ4_getPosition(const BYTE* p, void* tableBase, tableType_t tableType, const BYTE* srcBase)
+{
+    U32 const h = LZ4_hashPosition(p, tableType);
+    return LZ4_getPositionOnHash(h, tableBase, tableType, srcBase);
+}
+
+
+/** LZ4_compress_generic() :
+    inlined, to ensure branches are decided at compilation time */
+FORCE_INLINE int LZ4_compress_generic(
+                 LZ4_stream_t_internal* const cctx,
+                 const char* const source,
+                 char* const dest,
+                 const int inputSize,
+                 const int maxOutputSize,
+                 const limitedOutput_directive outputLimited,
+                 const tableType_t tableType,
+                 const dict_directive dict,
+                 const dictIssue_directive dictIssue,
+                 const U32 acceleration)
+{
+    const BYTE* ip = (const BYTE*) source;
+    const BYTE* base;
+    const BYTE* lowLimit;
+    const BYTE* const lowRefLimit = ip - cctx->dictSize;
+    const BYTE* const dictionary = cctx->dictionary;
+    const BYTE* const dictEnd = dictionary + cctx->dictSize;
+    const ptrdiff_t dictDelta = dictEnd - (const BYTE*)source;
+    const BYTE* anchor = (const BYTE*) source;
+    const BYTE* const iend = ip + inputSize;
+    const BYTE* const mflimit = iend - MFLIMIT;
+    const BYTE* const matchlimit = iend - LASTLITERALS;
+
+    BYTE* op = (BYTE*) dest;
+    BYTE* const olimit = op + maxOutputSize;
+
+    U32 forwardH;
+
+    /* Init conditions */
+    if ((U32)inputSize > (U32)LZ4_MAX_INPUT_SIZE) return 0;   /* Unsupported inputSize, too large (or negative) */
+    switch(dict)
+    {
+    case noDict:
+    default:
+        base = (const BYTE*)source;
+        lowLimit = (const BYTE*)source;
+        break;
+    case withPrefix64k:
+        base = (const BYTE*)source - cctx->currentOffset;
+        lowLimit = (const BYTE*)source - cctx->dictSize;
+        break;
+    case usingExtDict:
+        base = (const BYTE*)source - cctx->currentOffset;
+        lowLimit = (const BYTE*)source;
+        break;
+    }
+    if ((tableType == byU16) && (inputSize>=LZ4_64Klimit)) return 0;   /* Size too large (not within 64K limit) */
+    if (inputSize<LZ4_minLength) goto _last_literals;                  /* Input too small, no compression (all literals) */
+
+    /* First Byte */
+    LZ4_putPosition(ip, cctx->hashTable, tableType, base);
+    ip++; forwardH = LZ4_hashPosition(ip, tableType);
+
+    /* Main Loop */
+    for ( ; ; ) {
+        ptrdiff_t refDelta = 0;
+        const BYTE* match;
+        BYTE* token;
+
+        /* Find a match */
+        {   const BYTE* forwardIp = ip;
+            unsigned step = 1;
+            unsigned searchMatchNb = acceleration << LZ4_skipTrigger;
+            do {
+                U32 const h = forwardH;
+                ip = forwardIp;
+                forwardIp += step;
+                step = (searchMatchNb++ >> LZ4_skipTrigger);
+
+                if (unlikely(forwardIp > mflimit)) goto _last_literals;
+
+                match = LZ4_getPositionOnHash(h, cctx->hashTable, tableType, base);
+                if (dict==usingExtDict) {
+                    if (match < (const BYTE*)source) {
+                        refDelta = dictDelta;
+                        lowLimit = dictionary;
+                    } else {
+                        refDelta = 0;
+                        lowLimit = (const BYTE*)source;
+                }   }
+                forwardH = LZ4_hashPosition(forwardIp, tableType);
+                LZ4_putPositionOnHash(ip, h, cctx->hashTable, tableType, base);
+
+            } while ( ((dictIssue==dictSmall) ? (match < lowRefLimit) : 0)
+                || ((tableType==byU16) ? 0 : (match + MAX_DISTANCE < ip))
+                || (LZ4_read32(match+refDelta) != LZ4_read32(ip)) );
+        }
+
+        /* Catch up */
+        while (((ip>anchor) & (match+refDelta > lowLimit)) && (unlikely(ip[-1]==match[refDelta-1]))) { ip--; match--; }
+
+        /* Encode Literals */
+        {   unsigned const litLength = (unsigned)(ip - anchor);
+            token = op++;
+            if ((outputLimited) &&  /* Check output buffer overflow */
+                (unlikely(op + litLength + (2 + 1 + LASTLITERALS) + (litLength/255) > olimit)))
+                return 0;
+            if (litLength >= RUN_MASK) {
+                int len = (int)litLength-RUN_MASK;
+                *token = (RUN_MASK<<ML_BITS);
+                for(; len >= 255 ; len-=255) *op++ = 255;
+                *op++ = (BYTE)len;
+            }
+            else *token = (BYTE)(litLength<<ML_BITS);
+
+            /* Copy Literals */
+            LZ4_wildCopy(op, anchor, op+litLength);
+            op+=litLength;
+        }
+
+_next_match:
+        /* Encode Offset */
+        LZ4_writeLE16(op, (U16)(ip-match)); op+=2;
+
+        /* Encode MatchLength */
+        {   unsigned matchCode;
+
+            if ((dict==usingExtDict) && (lowLimit==dictionary)) {
+                const BYTE* limit;
+                match += refDelta;
+                limit = ip + (dictEnd-match);
+                if (limit > matchlimit) limit = matchlimit;
+                matchCode = LZ4_count(ip+MINMATCH, match+MINMATCH, limit);
+                ip += MINMATCH + matchCode;
+                if (ip==limit) {
+                    unsigned const more = LZ4_count(ip, (const BYTE*)source, matchlimit);
+                    matchCode += more;
+                    ip += more;
+                }
+            } else {
+                matchCode = LZ4_count(ip+MINMATCH, match+MINMATCH, matchlimit);
+                ip += MINMATCH + matchCode;
+            }
+
+            if ( outputLimited &&    /* Check output buffer overflow */
+                (unlikely(op + (1 + LASTLITERALS) + (matchCode>>8) > olimit)) )
+                return 0;
+            if (matchCode >= ML_MASK) {
+                *token += ML_MASK;
+                matchCode -= ML_MASK;
+                LZ4_write32(op, 0xFFFFFFFF);
+                while (matchCode >= 4*255) op+=4, LZ4_write32(op, 0xFFFFFFFF), matchCode -= 4*255;
+                op += matchCode / 255;
+                *op++ = (BYTE)(matchCode % 255);
+            } else
+                *token += (BYTE)(matchCode);
+        }
+
+        anchor = ip;
+
+        /* Test end of chunk */
+        if (ip > mflimit) break;
+
+        /* Fill table */
+        LZ4_putPosition(ip-2, cctx->hashTable, tableType, base);
+
+        /* Test next position */
+        match = LZ4_getPosition(ip, cctx->hashTable, tableType, base);
+        if (dict==usingExtDict) {
+            if (match < (const BYTE*)source) {
+                refDelta = dictDelta;
+                lowLimit = dictionary;
+            } else {
+                refDelta = 0;
+                lowLimit = (const BYTE*)source;
+        }   }
+        LZ4_putPosition(ip, cctx->hashTable, tableType, base);
+        if ( ((dictIssue==dictSmall) ? (match>=lowRefLimit) : 1)
+            && (match+MAX_DISTANCE>=ip)
+            && (LZ4_read32(match+refDelta)==LZ4_read32(ip)) )
+        { token=op++; *token=0; goto _next_match; }
+
+        /* Prepare next loop */
+        forwardH = LZ4_hashPosition(++ip, tableType);
+    }
+
+_last_literals:
+    /* Encode Last Literals */
+    {   size_t const lastRun = (size_t)(iend - anchor);
+        if ( (outputLimited) &&  /* Check output buffer overflow */
+            ((op - (BYTE*)dest) + lastRun + 1 + ((lastRun+255-RUN_MASK)/255) > (U32)maxOutputSize) )
+            return 0;
+        if (lastRun >= RUN_MASK) {
+            size_t accumulator = lastRun - RUN_MASK;
+            *op++ = RUN_MASK << ML_BITS;
+            for(; accumulator >= 255 ; accumulator-=255) *op++ = 255;
+            *op++ = (BYTE) accumulator;
+        } else {
+            *op++ = (BYTE)(lastRun<<ML_BITS);
+        }
+        memcpy(op, anchor, lastRun);
+        op += lastRun;
+    }
+
+    /* End */
+    return (int) (((char*)op)-dest);
+}
+
+
+int LZ4_compress_fast_extState(void* state, const char* source, char* dest, int inputSize, int maxOutputSize, int acceleration)
+{
+    LZ4_stream_t_internal* ctx = &((LZ4_stream_t*)state)->internal_donotuse;
+    LZ4_resetStream((LZ4_stream_t*)state);
+    if (acceleration < 1) acceleration = ACCELERATION_DEFAULT;
+
+    if (maxOutputSize >= LZ4_compressBound(inputSize)) {
+        if (inputSize < LZ4_64Klimit)
+            return LZ4_compress_generic(ctx, source, dest, inputSize,             0,    notLimited,                        byU16, noDict, noDictIssue, acceleration);
+        else
+            return LZ4_compress_generic(ctx, source, dest, inputSize,             0,    notLimited, (sizeof(void*)==8) ? byU32 : byPtr, noDict, noDictIssue, acceleration);
+    } else {
+        if (inputSize < LZ4_64Klimit)
+            return LZ4_compress_generic(ctx, source, dest, inputSize, maxOutputSize, limitedOutput,                        byU16, noDict, noDictIssue, acceleration);
+        else
+            return LZ4_compress_generic(ctx, source, dest, inputSize, maxOutputSize, limitedOutput, (sizeof(void*)==8) ? byU32 : byPtr, noDict, noDictIssue, acceleration);
+    }
+}
+
+
+int LZ4_compress_fast(const char* source, char* dest, int inputSize, int maxOutputSize, int acceleration)
+{
+#if (LZ4_HEAPMODE)
+    void* ctxPtr = ALLOCATOR(1, sizeof(LZ4_stream_t));   /* malloc-calloc always properly aligned */
+#else
+    LZ4_stream_t ctx;
+    void* const ctxPtr = &ctx;
+#endif
+
+    int const result = LZ4_compress_fast_extState(ctxPtr, source, dest, inputSize, maxOutputSize, acceleration);
+
+#if (LZ4_HEAPMODE)
+    FREEMEM(ctxPtr);
+#endif
+    return result;
+}
+
+
+int LZ4_compress_default(const char* source, char* dest, int inputSize, int maxOutputSize)
+{
+    return LZ4_compress_fast(source, dest, inputSize, maxOutputSize, 1);
+}
+
+
+/* hidden debug function */
+/* strangely enough, gcc generates faster code when this function is uncommented, even if unused */
+int LZ4_compress_fast_force(const char* source, char* dest, int inputSize, int maxOutputSize, int acceleration)
+{
+    LZ4_stream_t ctx;
+    LZ4_resetStream(&ctx);
+
+    if (inputSize < LZ4_64Klimit)
+        return LZ4_compress_generic(&ctx.internal_donotuse, source, dest, inputSize, maxOutputSize, limitedOutput, byU16,                        noDict, noDictIssue, acceleration);
+    else
+        return LZ4_compress_generic(&ctx.internal_donotuse, source, dest, inputSize, maxOutputSize, limitedOutput, sizeof(void*)==8 ? byU32 : byPtr, noDict, noDictIssue, acceleration);
+}
+
+
+/*-******************************
+*  *_destSize() variant
+********************************/
+
+static int LZ4_compress_destSize_generic(
+                       LZ4_stream_t_internal* const ctx,
+                 const char* const src,
+                       char* const dst,
+                       int*  const srcSizePtr,
+                 const int targetDstSize,
+                 const tableType_t tableType)
+{
+    const BYTE* ip = (const BYTE*) src;
+    const BYTE* base = (const BYTE*) src;
+    const BYTE* lowLimit = (const BYTE*) src;
+    const BYTE* anchor = ip;
+    const BYTE* const iend = ip + *srcSizePtr;
+    const BYTE* const mflimit = iend - MFLIMIT;
+    const BYTE* const matchlimit = iend - LASTLITERALS;
+
+    BYTE* op = (BYTE*) dst;
+    BYTE* const oend = op + targetDstSize;
+    BYTE* const oMaxLit = op + targetDstSize - 2 /* offset */ - 8 /* because 8+MINMATCH==MFLIMIT */ - 1 /* token */;
+    BYTE* const oMaxMatch = op + targetDstSize - (LASTLITERALS + 1 /* token */);
+    BYTE* const oMaxSeq = oMaxLit - 1 /* token */;
+
+    U32 forwardH;
+
+
+    /* Init conditions */
+    if (targetDstSize < 1) return 0;                                     /* Impossible to store anything */
+    if ((U32)*srcSizePtr > (U32)LZ4_MAX_INPUT_SIZE) return 0;            /* Unsupported input size, too large (or negative) */
+    if ((tableType == byU16) && (*srcSizePtr>=LZ4_64Klimit)) return 0;   /* Size too large (not within 64K limit) */
+    if (*srcSizePtr<LZ4_minLength) goto _last_literals;                  /* Input too small, no compression (all literals) */
+
+    /* First Byte */
+    *srcSizePtr = 0;
+    LZ4_putPosition(ip, ctx->hashTable, tableType, base);
+    ip++; forwardH = LZ4_hashPosition(ip, tableType);
+
+    /* Main Loop */
+    for ( ; ; ) {
+        const BYTE* match;
+        BYTE* token;
+
+        /* Find a match */
+        {   const BYTE* forwardIp = ip;
+            unsigned step = 1;
+            unsigned searchMatchNb = 1 << LZ4_skipTrigger;
+
+            do {
+                U32 h = forwardH;
+                ip = forwardIp;
+                forwardIp += step;
+                step = (searchMatchNb++ >> LZ4_skipTrigger);
+
+                if (unlikely(forwardIp > mflimit)) goto _last_literals;
+
+                match = LZ4_getPositionOnHash(h, ctx->hashTable, tableType, base);
+                forwardH = LZ4_hashPosition(forwardIp, tableType);
+                LZ4_putPositionOnHash(ip, h, ctx->hashTable, tableType, base);
+
+            } while ( ((tableType==byU16) ? 0 : (match + MAX_DISTANCE < ip))
+                || (LZ4_read32(match) != LZ4_read32(ip)) );
+        }
+
+        /* Catch up */
+        while ((ip>anchor) && (match > lowLimit) && (unlikely(ip[-1]==match[-1]))) { ip--; match--; }
+
+        /* Encode Literal length */
+        {   unsigned litLength = (unsigned)(ip - anchor);
+            token = op++;
+            if (op + ((litLength+240)/255) + litLength > oMaxLit) {
+                /* Not enough space for a last match */
+                op--;
+                goto _last_literals;
+            }
+            if (litLength>=RUN_MASK) {
+                unsigned len = litLength - RUN_MASK;
+                *token=(RUN_MASK<<ML_BITS);
+                for(; len >= 255 ; len-=255) *op++ = 255;
+                *op++ = (BYTE)len;
+            }
+            else *token = (BYTE)(litLength<<ML_BITS);
+
+            /* Copy Literals */
+            LZ4_wildCopy(op, anchor, op+litLength);
+            op += litLength;
+        }
+
+_next_match:
+        /* Encode Offset */
+        LZ4_writeLE16(op, (U16)(ip-match)); op+=2;
+
+        /* Encode MatchLength */
+        {   size_t matchLength = LZ4_count(ip+MINMATCH, match+MINMATCH, matchlimit);
+
+            if (op + ((matchLength+240)/255) > oMaxMatch) {
+                /* Match description too long : reduce it */
+                matchLength = (15-1) + (oMaxMatch-op) * 255;
+            }
+            ip += MINMATCH + matchLength;
+
+            if (matchLength>=ML_MASK) {
+                *token += ML_MASK;
+                matchLength -= ML_MASK;
+                while (matchLength >= 255) { matchLength-=255; *op++ = 255; }
+                *op++ = (BYTE)matchLength;
+            }
+            else *token += (BYTE)(matchLength);
+        }
+
+        anchor = ip;
+
+        /* Test end of block */
+        if (ip > mflimit) break;
+        if (op > oMaxSeq) break;
+
+        /* Fill table */
+        LZ4_putPosition(ip-2, ctx->hashTable, tableType, base);
+
+        /* Test next position */
+        match = LZ4_getPosition(ip, ctx->hashTable, tableType, base);
+        LZ4_putPosition(ip, ctx->hashTable, tableType, base);
+        if ( (match+MAX_DISTANCE>=ip)
+            && (LZ4_read32(match)==LZ4_read32(ip)) )
+        { token=op++; *token=0; goto _next_match; }
+
+        /* Prepare next loop */
+        forwardH = LZ4_hashPosition(++ip, tableType);
+    }
+
+_last_literals:
+    /* Encode Last Literals */
+    {   size_t lastRunSize = (size_t)(iend - anchor);
+        if (op + 1 /* token */ + ((lastRunSize+240)/255) /* litLength */ + lastRunSize /* literals */ > oend) {
+            /* adapt lastRunSize to fill 'dst' */
+            lastRunSize  = (oend-op) - 1;
+            lastRunSize -= (lastRunSize+240)/255;
+        }
+        ip = anchor + lastRunSize;
+
+        if (lastRunSize >= RUN_MASK) {
+            size_t accumulator = lastRunSize - RUN_MASK;
+            *op++ = RUN_MASK << ML_BITS;
+            for(; accumulator >= 255 ; accumulator-=255) *op++ = 255;
+            *op++ = (BYTE) accumulator;
+        } else {
+            *op++ = (BYTE)(lastRunSize<<ML_BITS);
+        }
+        memcpy(op, anchor, lastRunSize);
+        op += lastRunSize;
+    }
+
+    /* End */
+    *srcSizePtr = (int) (((const char*)ip)-src);
+    return (int) (((char*)op)-dst);
+}
+
+
+static int LZ4_compress_destSize_extState (LZ4_stream_t* state, const char* src, char* dst, int* srcSizePtr, int targetDstSize)
+{
+    LZ4_resetStream(state);
+
+    if (targetDstSize >= LZ4_compressBound(*srcSizePtr)) {  /* compression success is guaranteed */
+        return LZ4_compress_fast_extState(state, src, dst, *srcSizePtr, targetDstSize, 1);
+    } else {
+        if (*srcSizePtr < LZ4_64Klimit)
+            return LZ4_compress_destSize_generic(&state->internal_donotuse, src, dst, srcSizePtr, targetDstSize, byU16);
+        else
+            return LZ4_compress_destSize_generic(&state->internal_donotuse, src, dst, srcSizePtr, targetDstSize, sizeof(void*)==8 ? byU32 : byPtr);
+    }
+}
+
+
+int LZ4_compress_destSize(const char* src, char* dst, int* srcSizePtr, int targetDstSize)
+{
+#if (LZ4_HEAPMODE)
+    LZ4_stream_t* ctx = (LZ4_stream_t*)ALLOCATOR(1, sizeof(LZ4_stream_t));   /* malloc-calloc always properly aligned */
+#else
+    LZ4_stream_t ctxBody;
+    LZ4_stream_t* ctx = &ctxBody;
+#endif
+
+    int result = LZ4_compress_destSize_extState(ctx, src, dst, srcSizePtr, targetDstSize);
+
+#if (LZ4_HEAPMODE)
+    FREEMEM(ctx);
+#endif
+    return result;
+}
+
+
+
+/*-******************************
+*  Streaming functions
+********************************/
+
+LZ4_stream_t* LZ4_createStream(void)
+{
+    LZ4_stream_t* lz4s = (LZ4_stream_t*)ALLOCATOR(8, LZ4_STREAMSIZE_U64);
+    LZ4_STATIC_ASSERT(LZ4_STREAMSIZE >= sizeof(LZ4_stream_t_internal));    /* A compilation error here means LZ4_STREAMSIZE is not large enough */
+    LZ4_resetStream(lz4s);
+    return lz4s;
+}
+
+void LZ4_resetStream (LZ4_stream_t* LZ4_stream)
+{
+    MEM_INIT(LZ4_stream, 0, sizeof(LZ4_stream_t));
+}
+
+int LZ4_freeStream (LZ4_stream_t* LZ4_stream)
+{
+    if (!LZ4_stream) return 0;   /* support free on NULL */
+    FREEMEM(LZ4_stream);
+    return (0);
+}
+
+
+#define HASH_UNIT sizeof(reg_t)
+int LZ4_loadDict (LZ4_stream_t* LZ4_dict, const char* dictionary, int dictSize)
+{
+    LZ4_stream_t_internal* dict = &LZ4_dict->internal_donotuse;
+    const BYTE* p = (const BYTE*)dictionary;
+    const BYTE* const dictEnd = p + dictSize;
+    const BYTE* base;
+
+    if ((dict->initCheck) || (dict->currentOffset > 1 GB))  /* Uninitialized structure, or reuse overflow */
+        LZ4_resetStream(LZ4_dict);
+
+    if (dictSize < (int)HASH_UNIT) {
+        dict->dictionary = NULL;
+        dict->dictSize = 0;
+        return 0;
+    }
+
+    if ((dictEnd - p) > 64 KB) p = dictEnd - 64 KB;
+    dict->currentOffset += 64 KB;
+    base = p - dict->currentOffset;
+    dict->dictionary = p;
+    dict->dictSize = (U32)(dictEnd - p);
+    dict->currentOffset += dict->dictSize;
+
+    while (p <= dictEnd-HASH_UNIT) {
+        LZ4_putPosition(p, dict->hashTable, byU32, base);
+        p+=3;
+    }
+
+    return dict->dictSize;
+}
+
+
+static void LZ4_renormDictT(LZ4_stream_t_internal* LZ4_dict, const BYTE* src)
+{
+    if ((LZ4_dict->currentOffset > 0x80000000) ||
+        ((uptrval)LZ4_dict->currentOffset > (uptrval)src)) {   /* address space overflow */
+        /* rescale hash table */
+        U32 const delta = LZ4_dict->currentOffset - 64 KB;
+        const BYTE* dictEnd = LZ4_dict->dictionary + LZ4_dict->dictSize;
+        int i;
+        for (i=0; i<LZ4_HASH_SIZE_U32; i++) {
+            if (LZ4_dict->hashTable[i] < delta) LZ4_dict->hashTable[i]=0;
+            else LZ4_dict->hashTable[i] -= delta;
+        }
+        LZ4_dict->currentOffset = 64 KB;
+        if (LZ4_dict->dictSize > 64 KB) LZ4_dict->dictSize = 64 KB;
+        LZ4_dict->dictionary = dictEnd - LZ4_dict->dictSize;
+    }
+}
+
+
+int LZ4_compress_fast_continue (LZ4_stream_t* LZ4_stream, const char* source, char* dest, int inputSize, int maxOutputSize, int acceleration)
+{
+    LZ4_stream_t_internal* streamPtr = &LZ4_stream->internal_donotuse;
+    const BYTE* const dictEnd = streamPtr->dictionary + streamPtr->dictSize;
+
+    const BYTE* smallest = (const BYTE*) source;
+    if (streamPtr->initCheck) return 0;   /* Uninitialized structure detected */
+    if ((streamPtr->dictSize>0) && (smallest>dictEnd)) smallest = dictEnd;
+    LZ4_renormDictT(streamPtr, smallest);
+    if (acceleration < 1) acceleration = ACCELERATION_DEFAULT;
+
+    /* Check overlapping input/dictionary space */
+    {   const BYTE* sourceEnd = (const BYTE*) source + inputSize;
+        if ((sourceEnd > streamPtr->dictionary) && (sourceEnd < dictEnd)) {
+            streamPtr->dictSize = (U32)(dictEnd - sourceEnd);
+            if (streamPtr->dictSize > 64 KB) streamPtr->dictSize = 64 KB;
+            if (streamPtr->dictSize < 4) streamPtr->dictSize = 0;
+            streamPtr->dictionary = dictEnd - streamPtr->dictSize;
+        }
+    }
+
+    /* prefix mode : source data follows dictionary */
+    if (dictEnd == (const BYTE*)source) {
+        int result;
+        if ((streamPtr->dictSize < 64 KB) && (streamPtr->dictSize < streamPtr->currentOffset))
+            result = LZ4_compress_generic(streamPtr, source, dest, inputSize, maxOutputSize, limitedOutput, byU32, withPrefix64k, dictSmall, acceleration);
+        else
+            result = LZ4_compress_generic(streamPtr, source, dest, inputSize, maxOutputSize, limitedOutput, byU32, withPrefix64k, noDictIssue, acceleration);
+        streamPtr->dictSize += (U32)inputSize;
+        streamPtr->currentOffset += (U32)inputSize;
+        return result;
+    }
+
+    /* external dictionary mode */
+    {   int result;
+        if ((streamPtr->dictSize < 64 KB) && (streamPtr->dictSize < streamPtr->currentOffset))
+            result = LZ4_compress_generic(streamPtr, source, dest, inputSize, maxOutputSize, limitedOutput, byU32, usingExtDict, dictSmall, acceleration);
+        else
+            result = LZ4_compress_generic(streamPtr, source, dest, inputSize, maxOutputSize, limitedOutput, byU32, usingExtDict, noDictIssue, acceleration);
+        streamPtr->dictionary = (const BYTE*)source;
+        streamPtr->dictSize = (U32)inputSize;
+        streamPtr->currentOffset += (U32)inputSize;
+        return result;
+    }
+}
+
+
+/* Hidden debug function, to force external dictionary mode */
+int LZ4_compress_forceExtDict (LZ4_stream_t* LZ4_dict, const char* source, char* dest, int inputSize)
+{
+    LZ4_stream_t_internal* streamPtr = &LZ4_dict->internal_donotuse;
+    int result;
+    const BYTE* const dictEnd = streamPtr->dictionary + streamPtr->dictSize;
+
+    const BYTE* smallest = dictEnd;
+    if (smallest > (const BYTE*) source) smallest = (const BYTE*) source;
+    LZ4_renormDictT(streamPtr, smallest);
+
+    result = LZ4_compress_generic(streamPtr, source, dest, inputSize, 0, notLimited, byU32, usingExtDict, noDictIssue, 1);
+
+    streamPtr->dictionary = (const BYTE*)source;
+    streamPtr->dictSize = (U32)inputSize;
+    streamPtr->currentOffset += (U32)inputSize;
+
+    return result;
+}
+
+
+/*! LZ4_saveDict() :
+ *  If previously compressed data block is not guaranteed to remain available at its memory location,
+ *  save it into a safer place (char* safeBuffer).
+ *  Note : you don't need to call LZ4_loadDict() afterwards,
+ *         dictionary is immediately usable, you can therefore call LZ4_compress_fast_continue().
+ *  Return : saved dictionary size in bytes (necessarily <= dictSize), or 0 if error.
+ */
+int LZ4_saveDict (LZ4_stream_t* LZ4_dict, char* safeBuffer, int dictSize)
+{
+    LZ4_stream_t_internal* const dict = &LZ4_dict->internal_donotuse;
+    const BYTE* const previousDictEnd = dict->dictionary + dict->dictSize;
+
+    if ((U32)dictSize > 64 KB) dictSize = 64 KB;   /* useless to define a dictionary > 64 KB */
+    if ((U32)dictSize > dict->dictSize) dictSize = dict->dictSize;
+
+    memmove(safeBuffer, previousDictEnd - dictSize, dictSize);
+
+    dict->dictionary = (const BYTE*)safeBuffer;
+    dict->dictSize = (U32)dictSize;
+
+    return dictSize;
+}
+
+
+
+/*-*****************************
+*  Decompression functions
+*******************************/
+/*! LZ4_decompress_generic() :
+ *  This generic decompression function cover all use cases.
+ *  It shall be instantiated several times, using different sets of directives
+ *  Note that it is important this generic function is really inlined,
+ *  in order to remove useless branches during compilation optimization.
+ */
+FORCE_INLINE int LZ4_decompress_generic(
+                 const char* const source,
+                 char* const dest,
+                 int inputSize,
+                 int outputSize,         /* If endOnInput==endOnInputSize, this value is the max size of Output Buffer. */
+
+                 int endOnInput,         /* endOnOutputSize, endOnInputSize */
+                 int partialDecoding,    /* full, partial */
+                 int targetOutputSize,   /* only used if partialDecoding==partial */
+                 int dict,               /* noDict, withPrefix64k, usingExtDict */
+                 const BYTE* const lowPrefix,  /* == dest when no prefix */
+                 const BYTE* const dictStart,  /* only if dict==usingExtDict */
+                 const size_t dictSize         /* note : = 0 if noDict */
+                 )
+{
+    /* Local Variables */
+    const BYTE* ip = (const BYTE*) source;
+    const BYTE* const iend = ip + inputSize;
+
+    BYTE* op = (BYTE*) dest;
+    BYTE* const oend = op + outputSize;
+    BYTE* cpy;
+    BYTE* oexit = op + targetOutputSize;
+    const BYTE* const lowLimit = lowPrefix - dictSize;
+
+    const BYTE* const dictEnd = (const BYTE*)dictStart + dictSize;
+    const unsigned dec32table[] = {0, 1, 2, 1, 4, 4, 4, 4};
+    const int dec64table[] = {0, 0, 0, -1, 0, 1, 2, 3};
+
+    const int safeDecode = (endOnInput==endOnInputSize);
+    const int checkOffset = ((safeDecode) && (dictSize < (int)(64 KB)));
+
+
+    /* Special cases */
+    if ((partialDecoding) && (oexit > oend-MFLIMIT)) oexit = oend-MFLIMIT;                        /* targetOutputSize too high => decode everything */
+    if ((endOnInput) && (unlikely(outputSize==0))) return ((inputSize==1) && (*ip==0)) ? 0 : -1;  /* Empty output buffer */
+    if ((!endOnInput) && (unlikely(outputSize==0))) return (*ip==0?1:-1);
+
+    /* Main Loop : decode sequences */
+    while (1) {
+        size_t length;
+        const BYTE* match;
+        size_t offset;
+
+        /* get literal length */
+        unsigned const token = *ip++;
+        if ((length=(token>>ML_BITS)) == RUN_MASK) {
+            unsigned s;
+            do {
+                s = *ip++;
+                length += s;
+            } while ( likely(endOnInput ? ip<iend-RUN_MASK : 1) & (s==255) );
+            if ((safeDecode) && unlikely((uptrval)(op)+length<(uptrval)(op))) goto _output_error;   /* overflow detection */
+            if ((safeDecode) && unlikely((uptrval)(ip)+length<(uptrval)(ip))) goto _output_error;   /* overflow detection */
+        }
+
+        /* copy literals */
+        cpy = op+length;
+        if ( ((endOnInput) && ((cpy>(partialDecoding?oexit:oend-MFLIMIT)) || (ip+length>iend-(2+1+LASTLITERALS))) )
+            || ((!endOnInput) && (cpy>oend-WILDCOPYLENGTH)) )
+        {
+            if (partialDecoding) {
+                if (cpy > oend) goto _output_error;                           /* Error : write attempt beyond end of output buffer */
+                if ((endOnInput) && (ip+length > iend)) goto _output_error;   /* Error : read attempt beyond end of input buffer */
+            } else {
+                if ((!endOnInput) && (cpy != oend)) goto _output_error;       /* Error : block decoding must stop exactly there */
+                if ((endOnInput) && ((ip+length != iend) || (cpy > oend))) goto _output_error;   /* Error : input must be consumed */
+            }
+            memcpy(op, ip, length);
+            ip += length;
+            op += length;
+            break;     /* Necessarily EOF, due to parsing restrictions */
+        }
+        LZ4_wildCopy(op, ip, cpy);
+        ip += length; op = cpy;
+
+        /* get offset */
+        offset = LZ4_readLE16(ip); ip+=2;
+        match = op - offset;
+        if ((checkOffset) && (unlikely(match < lowLimit))) goto _output_error;   /* Error : offset outside buffers */
+        LZ4_write32(op, (U32)offset);   /* costs ~1%; silence an msan warning when offset==0 */
+
+        /* get matchlength */
+        length = token & ML_MASK;
+        if (length == ML_MASK) {
+            unsigned s;
+            do {
+                s = *ip++;
+                if ((endOnInput) && (ip > iend-LASTLITERALS)) goto _output_error;
+                length += s;
+            } while (s==255);
+            if ((safeDecode) && unlikely((uptrval)(op)+length<(uptrval)op)) goto _output_error;   /* overflow detection */
+        }
+        length += MINMATCH;
+
+        /* check external dictionary */
+        if ((dict==usingExtDict) && (match < lowPrefix)) {
+            if (unlikely(op+length > oend-LASTLITERALS)) goto _output_error;   /* doesn't respect parsing restriction */
+
+            if (length <= (size_t)(lowPrefix-match)) {
+                /* match can be copied as a single segment from external dictionary */
+                memmove(op, dictEnd - (lowPrefix-match), length);
+                op += length;
+            } else {
+                /* match encompass external dictionary and current block */
+                size_t const copySize = (size_t)(lowPrefix-match);
+                size_t const restSize = length - copySize;
+                memcpy(op, dictEnd - copySize, copySize);
+                op += copySize;
+                if (restSize > (size_t)(op-lowPrefix)) {  /* overlap copy */
+                    BYTE* const endOfMatch = op + restSize;
+                    const BYTE* copyFrom = lowPrefix;
+                    while (op < endOfMatch) *op++ = *copyFrom++;
+                } else {
+                    memcpy(op, lowPrefix, restSize);
+                    op += restSize;
+            }   }
+            continue;
+        }
+
+        /* copy match within block */
+        cpy = op + length;
+        if (unlikely(offset<8)) {
+            const int dec64 = dec64table[offset];
+            op[0] = match[0];
+            op[1] = match[1];
+            op[2] = match[2];
+            op[3] = match[3];
+            match += dec32table[offset];
+            memcpy(op+4, match, 4);
+            match -= dec64;
+        } else { LZ4_copy8(op, match); match+=8; }
+        op += 8;
+
+        if (unlikely(cpy>oend-12)) {
+            BYTE* const oCopyLimit = oend-(WILDCOPYLENGTH-1);
+            if (cpy > oend-LASTLITERALS) goto _output_error;    /* Error : last LASTLITERALS bytes must be literals (uncompressed) */
+            if (op < oCopyLimit) {
+                LZ4_wildCopy(op, match, oCopyLimit);
+                match += oCopyLimit - op;
+                op = oCopyLimit;
+            }
+            while (op<cpy) *op++ = *match++;
+        } else {
+            LZ4_copy8(op, match);
+            if (length>16) LZ4_wildCopy(op+8, match+8, cpy);
+        }
+        op=cpy;   /* correction */
+    }
+
+    /* end of decoding */
+    if (endOnInput)
+       return (int) (((char*)op)-dest);     /* Nb of output bytes decoded */
+    else
+       return (int) (((const char*)ip)-source);   /* Nb of input bytes read */
+
+    /* Overflow error detected */
+_output_error:
+    return (int) (-(((const char*)ip)-source))-1;
+}
+
+
+int LZ4_decompress_safe(const char* source, char* dest, int compressedSize, int maxDecompressedSize)
+{
+    return LZ4_decompress_generic(source, dest, compressedSize, maxDecompressedSize, endOnInputSize, full, 0, noDict, (BYTE*)dest, NULL, 0);
+}
+
+int LZ4_decompress_safe_partial(const char* source, char* dest, int compressedSize, int targetOutputSize, int maxDecompressedSize)
+{
+    return LZ4_decompress_generic(source, dest, compressedSize, maxDecompressedSize, endOnInputSize, partial, targetOutputSize, noDict, (BYTE*)dest, NULL, 0);
+}
+
+int LZ4_decompress_fast(const char* source, char* dest, int originalSize)
+{
+    return LZ4_decompress_generic(source, dest, 0, originalSize, endOnOutputSize, full, 0, withPrefix64k, (BYTE*)(dest - 64 KB), NULL, 64 KB);
+}
+
+
+/*===== streaming decompression functions =====*/
+
+LZ4_streamDecode_t* LZ4_createStreamDecode(void)
+{
+    LZ4_streamDecode_t* lz4s = (LZ4_streamDecode_t*) ALLOCATOR(1, sizeof(LZ4_streamDecode_t));
+    return lz4s;
+}
+
+int LZ4_freeStreamDecode (LZ4_streamDecode_t* LZ4_stream)
+{
+    if (!LZ4_stream) return 0;   /* support free on NULL */
+    FREEMEM(LZ4_stream);
+    return 0;
+}
+
+/*!
+ * LZ4_setStreamDecode() :
+ * Use this function to instruct where to find the dictionary.
+ * This function is not necessary if previous data is still available where it was decoded.
+ * Loading a size of 0 is allowed (same effect as no dictionary).
+ * Return : 1 if OK, 0 if error
+ */
+int LZ4_setStreamDecode (LZ4_streamDecode_t* LZ4_streamDecode, const char* dictionary, int dictSize)
+{
+    LZ4_streamDecode_t_internal* lz4sd = &LZ4_streamDecode->internal_donotuse;
+    lz4sd->prefixSize = (size_t) dictSize;
+    lz4sd->prefixEnd = (const BYTE*) dictionary + dictSize;
+    lz4sd->externalDict = NULL;
+    lz4sd->extDictSize  = 0;
+    return 1;
+}
+
+/*
+*_continue() :
+    These decoding functions allow decompression of multiple blocks in "streaming" mode.
+    Previously decoded blocks must still be available at the memory position where they were decoded.
+    If it's not possible, save the relevant part of decoded data into a safe buffer,
+    and indicate where it stands using LZ4_setStreamDecode()
+*/
+int LZ4_decompress_safe_continue (LZ4_streamDecode_t* LZ4_streamDecode, const char* source, char* dest, int compressedSize, int maxOutputSize)
+{
+    LZ4_streamDecode_t_internal* lz4sd = &LZ4_streamDecode->internal_donotuse;
+    int result;
+
+    if (lz4sd->prefixEnd == (BYTE*)dest) {
+        result = LZ4_decompress_generic(source, dest, compressedSize, maxOutputSize,
+                                        endOnInputSize, full, 0,
+                                        usingExtDict, lz4sd->prefixEnd - lz4sd->prefixSize, lz4sd->externalDict, lz4sd->extDictSize);
+        if (result <= 0) return result;
+        lz4sd->prefixSize += result;
+        lz4sd->prefixEnd  += result;
+    } else {
+        lz4sd->extDictSize = lz4sd->prefixSize;
+        lz4sd->externalDict = lz4sd->prefixEnd - lz4sd->extDictSize;
+        result = LZ4_decompress_generic(source, dest, compressedSize, maxOutputSize,
+                                        endOnInputSize, full, 0,
+                                        usingExtDict, (BYTE*)dest, lz4sd->externalDict, lz4sd->extDictSize);
+        if (result <= 0) return result;
+        lz4sd->prefixSize = result;
+        lz4sd->prefixEnd  = (BYTE*)dest + result;
+    }
+
+    return result;
+}
+
+int LZ4_decompress_fast_continue (LZ4_streamDecode_t* LZ4_streamDecode, const char* source, char* dest, int originalSize)
+{
+    LZ4_streamDecode_t_internal* lz4sd = &LZ4_streamDecode->internal_donotuse;
+    int result;
+
+    if (lz4sd->prefixEnd == (BYTE*)dest) {
+        result = LZ4_decompress_generic(source, dest, 0, originalSize,
+                                        endOnOutputSize, full, 0,
+                                        usingExtDict, lz4sd->prefixEnd - lz4sd->prefixSize, lz4sd->externalDict, lz4sd->extDictSize);
+        if (result <= 0) return result;
+        lz4sd->prefixSize += originalSize;
+        lz4sd->prefixEnd  += originalSize;
+    } else {
+        lz4sd->extDictSize = lz4sd->prefixSize;
+        lz4sd->externalDict = lz4sd->prefixEnd - lz4sd->extDictSize;
+        result = LZ4_decompress_generic(source, dest, 0, originalSize,
+                                        endOnOutputSize, full, 0,
+                                        usingExtDict, (BYTE*)dest, lz4sd->externalDict, lz4sd->extDictSize);
+        if (result <= 0) return result;
+        lz4sd->prefixSize = originalSize;
+        lz4sd->prefixEnd  = (BYTE*)dest + originalSize;
+    }
+
+    return result;
+}
+
+
+/*
+Advanced decoding functions :
+*_usingDict() :
+    These decoding functions work the same as "_continue" ones,
+    the dictionary must be explicitly provided within parameters
+*/
+
+FORCE_INLINE int LZ4_decompress_usingDict_generic(const char* source, char* dest, int compressedSize, int maxOutputSize, int safe, const char* dictStart, int dictSize)
+{
+    if (dictSize==0)
+        return LZ4_decompress_generic(source, dest, compressedSize, maxOutputSize, safe, full, 0, noDict, (BYTE*)dest, NULL, 0);
+    if (dictStart+dictSize == dest) {
+        if (dictSize >= (int)(64 KB - 1))
+            return LZ4_decompress_generic(source, dest, compressedSize, maxOutputSize, safe, full, 0, withPrefix64k, (BYTE*)dest-64 KB, NULL, 0);
+        return LZ4_decompress_generic(source, dest, compressedSize, maxOutputSize, safe, full, 0, noDict, (BYTE*)dest-dictSize, NULL, 0);
+    }
+    return LZ4_decompress_generic(source, dest, compressedSize, maxOutputSize, safe, full, 0, usingExtDict, (BYTE*)dest, (const BYTE*)dictStart, dictSize);
+}
+
+int LZ4_decompress_safe_usingDict(const char* source, char* dest, int compressedSize, int maxOutputSize, const char* dictStart, int dictSize)
+{
+    return LZ4_decompress_usingDict_generic(source, dest, compressedSize, maxOutputSize, 1, dictStart, dictSize);
+}
+
+int LZ4_decompress_fast_usingDict(const char* source, char* dest, int originalSize, const char* dictStart, int dictSize)
+{
+    return LZ4_decompress_usingDict_generic(source, dest, 0, originalSize, 0, dictStart, dictSize);
+}
+
+/* debug function */
+int LZ4_decompress_safe_forceExtDict(const char* source, char* dest, int compressedSize, int maxOutputSize, const char* dictStart, int dictSize)
+{
+    return LZ4_decompress_generic(source, dest, compressedSize, maxOutputSize, endOnInputSize, full, 0, usingExtDict, (BYTE*)dest, (const BYTE*)dictStart, dictSize);
+}
+
+
+/*=*************************************************
+*  Obsolete Functions
+***************************************************/
+/* obsolete compression functions */
+int LZ4_compress_limitedOutput(const char* source, char* dest, int inputSize, int maxOutputSize) { return LZ4_compress_default(source, dest, inputSize, maxOutputSize); }
+int LZ4_compress(const char* source, char* dest, int inputSize) { return LZ4_compress_default(source, dest, inputSize, LZ4_compressBound(inputSize)); }
+int LZ4_compress_limitedOutput_withState (void* state, const char* src, char* dst, int srcSize, int dstSize) { return LZ4_compress_fast_extState(state, src, dst, srcSize, dstSize, 1); }
+int LZ4_compress_withState (void* state, const char* src, char* dst, int srcSize) { return LZ4_compress_fast_extState(state, src, dst, srcSize, LZ4_compressBound(srcSize), 1); }
+int LZ4_compress_limitedOutput_continue (LZ4_stream_t* LZ4_stream, const char* src, char* dst, int srcSize, int maxDstSize) { return LZ4_compress_fast_continue(LZ4_stream, src, dst, srcSize, maxDstSize, 1); }
+int LZ4_compress_continue (LZ4_stream_t* LZ4_stream, const char* source, char* dest, int inputSize) { return LZ4_compress_fast_continue(LZ4_stream, source, dest, inputSize, LZ4_compressBound(inputSize), 1); }
+
+/*
+These function names are deprecated and should no longer be used.
+They are only provided here for compatibility with older user programs.
+- LZ4_uncompress is totally equivalent to LZ4_decompress_fast
+- LZ4_uncompress_unknownOutputSize is totally equivalent to LZ4_decompress_safe
+*/
+int LZ4_uncompress (const char* source, char* dest, int outputSize) { return LZ4_decompress_fast(source, dest, outputSize); }
+int LZ4_uncompress_unknownOutputSize (const char* source, char* dest, int isize, int maxOutputSize) { return LZ4_decompress_safe(source, dest, isize, maxOutputSize); }
+
+
+/* Obsolete Streaming functions */
+
+int LZ4_sizeofStreamState() { return LZ4_STREAMSIZE; }
+
+static void LZ4_init(LZ4_stream_t* lz4ds, BYTE* base)
+{
+    MEM_INIT(lz4ds, 0, sizeof(LZ4_stream_t));
+    lz4ds->internal_donotuse.bufferStart = base;
+}
+
+int LZ4_resetStreamState(void* state, char* inputBuffer)
+{
+    if ((((uptrval)state) & 3) != 0) return 1;   /* Error : pointer is not aligned on 4-bytes boundary */
+    LZ4_init((LZ4_stream_t*)state, (BYTE*)inputBuffer);
+    return 0;
+}
+
+void* LZ4_create (char* inputBuffer)
+{
+    LZ4_stream_t* lz4ds = (LZ4_stream_t*)ALLOCATOR(8, sizeof(LZ4_stream_t));
+    LZ4_init (lz4ds, (BYTE*)inputBuffer);
+    return lz4ds;
+}
+
+char* LZ4_slideInputBuffer (void* LZ4_Data)
+{
+    LZ4_stream_t_internal* ctx = &((LZ4_stream_t*)LZ4_Data)->internal_donotuse;
+    int dictSize = LZ4_saveDict((LZ4_stream_t*)LZ4_Data, (char*)ctx->bufferStart, 64 KB);
+    return (char*)(ctx->bufferStart + dictSize);
+}
+
+/* Obsolete streaming decompression functions */
+
+int LZ4_decompress_safe_withPrefix64k(const char* source, char* dest, int compressedSize, int maxOutputSize)
+{
+    return LZ4_decompress_generic(source, dest, compressedSize, maxOutputSize, endOnInputSize, full, 0, withPrefix64k, (BYTE*)dest - 64 KB, NULL, 64 KB);
+}
+
+int LZ4_decompress_fast_withPrefix64k(const char* source, char* dest, int originalSize)
+{
+    return LZ4_decompress_generic(source, dest, 0, originalSize, endOnOutputSize, full, 0, withPrefix64k, (BYTE*)dest - 64 KB, NULL, 64 KB);
+}
+
+#endif   /* LZ4_COMMONDEFS_ONLY */
diff --git a/samtools/lz4/lz4.c.pysam.c b/samtools/lz4/lz4.c.pysam.c
new file mode 100644
index 0000000..a4a8ab4
--- /dev/null
+++ b/samtools/lz4/lz4.c.pysam.c
@@ -0,0 +1,1480 @@
+#include "samtools.pysam.h"
+
+/*
+   LZ4 - Fast LZ compression algorithm
+   Copyright (C) 2011-2017, Yann Collet.
+
+   BSD 2-Clause License (http://www.opensource.org/licenses/bsd-license.php)
+
+   Redistribution and use in source and binary forms, with or without
+   modification, are permitted provided that the following conditions are
+   met:
+
+       * Redistributions of source code must retain the above copyright
+   notice, this list of conditions and the following disclaimer.
+       * Redistributions in binary form must reproduce the above
+   copyright notice, this list of conditions and the following disclaimer
+   in the documentation and/or other materials provided with the
+   distribution.
+
+   THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+   "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+   LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+   A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+   OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+   SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+   LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+   DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+   THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+   (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+   OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+   You can contact the author at :
+    - LZ4 homepage : http://www.lz4.org
+    - LZ4 source repository : https://github.com/lz4/lz4
+*/
+
+
+/*-************************************
+*  Tuning parameters
+**************************************/
+/*
+ * LZ4_HEAPMODE :
+ * Select how default compression functions will allocate memory for their hash table,
+ * in memory stack (0:default, fastest), or in memory heap (1:requires malloc()).
+ */
+#ifndef LZ4_HEAPMODE
+#  define LZ4_HEAPMODE 0
+#endif
+
+/*
+ * ACCELERATION_DEFAULT :
+ * Select "acceleration" for LZ4_compress_fast() when parameter value <= 0
+ */
+#define ACCELERATION_DEFAULT 1
+
+
+/*-************************************
+*  CPU Feature Detection
+**************************************/
+/* LZ4_FORCE_MEMORY_ACCESS
+ * By default, access to unaligned memory is controlled by `memcpy()`, which is safe and portable.
+ * Unfortunately, on some target/compiler combinations, the generated assembly is sub-optimal.
+ * The below switch allow to select different access method for improved performance.
+ * Method 0 (default) : use `memcpy()`. Safe and portable.
+ * Method 1 : `__packed` statement. It depends on compiler extension (ie, not portable).
+ *            This method is safe if your compiler supports it, and *generally* as fast or faster than `memcpy`.
+ * Method 2 : direct access. This method is portable but violate C standard.
+ *            It can generate buggy code on targets which assembly generation depends on alignment.
+ *            But in some circumstances, it's the only known way to get the most performance (ie GCC + ARMv6)
+ * See https://fastcompression.blogspot.fr/2015/08/accessing-unaligned-memory.html for details.
+ * Prefer these methods in priority order (0 > 1 > 2)
+ */
+#ifndef LZ4_FORCE_MEMORY_ACCESS   /* can be defined externally */
+#  if defined(__GNUC__) && ( defined(__ARM_ARCH_6__) || defined(__ARM_ARCH_6J__) || defined(__ARM_ARCH_6K__) || defined(__ARM_ARCH_6Z__) || defined(__ARM_ARCH_6ZK__) || defined(__ARM_ARCH_6T2__) )
+#    define LZ4_FORCE_MEMORY_ACCESS 2
+#  elif defined(__INTEL_COMPILER) || defined(__GNUC__)
+#    define LZ4_FORCE_MEMORY_ACCESS 1
+#  endif
+#endif
+
+/*
+ * LZ4_FORCE_SW_BITCOUNT
+ * Define this parameter if your target system or compiler does not support hardware bit count
+ */
+#if defined(_MSC_VER) && defined(_WIN32_WCE)   /* Visual Studio for Windows CE does not support Hardware bit count */
+#  define LZ4_FORCE_SW_BITCOUNT
+#endif
+
+
+/*-************************************
+*  Dependency
+**************************************/
+#include "lz4.h"
+/* see also "memory routines" below */
+
+
+/*-************************************
+*  Compiler Options
+**************************************/
+#ifdef _MSC_VER    /* Visual Studio */
+#  include <intrin.h>
+#  pragma warning(disable : 4127)        /* disable: C4127: conditional expression is constant */
+#  pragma warning(disable : 4293)        /* disable: C4293: too large shift (32-bits) */
+#endif  /* _MSC_VER */
+
+#ifndef FORCE_INLINE
+#  ifdef _MSC_VER    /* Visual Studio */
+#    define FORCE_INLINE static __forceinline
+#  else
+#    if defined (__cplusplus) || defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L   /* C99 */
+#      ifdef __GNUC__
+#        define FORCE_INLINE static inline __attribute__((always_inline))
+#      else
+#        define FORCE_INLINE static inline
+#      endif
+#    else
+#      define FORCE_INLINE static
+#    endif /* __STDC_VERSION__ */
+#  endif  /* _MSC_VER */
+#endif /* FORCE_INLINE */
+
+#if (defined(__GNUC__) && (__GNUC__ >= 3)) || (defined(__INTEL_COMPILER) && (__INTEL_COMPILER >= 800)) || defined(__clang__)
+#  define expect(expr,value)    (__builtin_expect ((expr),(value)) )
+#else
+#  define expect(expr,value)    (expr)
+#endif
+
+#define likely(expr)     expect((expr) != 0, 1)
+#define unlikely(expr)   expect((expr) != 0, 0)
+
+
+/*-************************************
+*  Memory routines
+**************************************/
+#include <stdlib.h>   /* malloc, calloc, free */
+#define ALLOCATOR(n,s) calloc(n,s)
+#define FREEMEM        free
+#include <string.h>   /* memset, memcpy */
+#define MEM_INIT       memset
+
+
+/*-************************************
+*  Basic Types
+**************************************/
+#if defined(__cplusplus) || (defined (__STDC_VERSION__) && (__STDC_VERSION__ >= 199901L) /* C99 */)
+# include <stdint.h>
+  typedef  uint8_t BYTE;
+  typedef uint16_t U16;
+  typedef uint32_t U32;
+  typedef  int32_t S32;
+  typedef uint64_t U64;
+  typedef uintptr_t uptrval;
+#else
+  typedef unsigned char       BYTE;
+  typedef unsigned short      U16;
+  typedef unsigned int        U32;
+  typedef   signed int        S32;
+  typedef unsigned long long  U64;
+  typedef size_t              uptrval;   /* generally true, except OpenVMS-64 */
+#endif
+
+#if defined(__x86_64__)
+  typedef U64    reg_t;   /* 64-bits in x32 mode */
+#else
+  typedef size_t reg_t;   /* 32-bits in x32 mode */
+#endif
+
+/*-************************************
+*  Reading and writing into memory
+**************************************/
+static unsigned LZ4_isLittleEndian(void)
+{
+    const union { U32 u; BYTE c[4]; } one = { 1 };   /* don't use static : performance detrimental */
+    return one.c[0];
+}
+
+
+#if defined(LZ4_FORCE_MEMORY_ACCESS) && (LZ4_FORCE_MEMORY_ACCESS==2)
+/* lie to the compiler about data alignment; use with caution */
+
+static U16 LZ4_read16(const void* memPtr) { return *(const U16*) memPtr; }
+static U32 LZ4_read32(const void* memPtr) { return *(const U32*) memPtr; }
+static reg_t LZ4_read_ARCH(const void* memPtr) { return *(const reg_t*) memPtr; }
+
+static void LZ4_write16(void* memPtr, U16 value) { *(U16*)memPtr = value; }
+static void LZ4_write32(void* memPtr, U32 value) { *(U32*)memPtr = value; }
+
+#elif defined(LZ4_FORCE_MEMORY_ACCESS) && (LZ4_FORCE_MEMORY_ACCESS==1)
+
+/* __pack instructions are safer, but compiler specific, hence potentially problematic for some compilers */
+/* currently only defined for gcc and icc */
+typedef union { U16 u16; U32 u32; reg_t uArch; } __attribute__((packed)) unalign;
+
+static U16 LZ4_read16(const void* ptr) { return ((const unalign*)ptr)->u16; }
+static U32 LZ4_read32(const void* ptr) { return ((const unalign*)ptr)->u32; }
+static reg_t LZ4_read_ARCH(const void* ptr) { return ((const unalign*)ptr)->uArch; }
+
+static void LZ4_write16(void* memPtr, U16 value) { ((unalign*)memPtr)->u16 = value; }
+static void LZ4_write32(void* memPtr, U32 value) { ((unalign*)memPtr)->u32 = value; }
+
+#else  /* safe and portable access through memcpy() */
+
+static U16 LZ4_read16(const void* memPtr)
+{
+    U16 val; memcpy(&val, memPtr, sizeof(val)); return val;
+}
+
+static U32 LZ4_read32(const void* memPtr)
+{
+    U32 val; memcpy(&val, memPtr, sizeof(val)); return val;
+}
+
+static reg_t LZ4_read_ARCH(const void* memPtr)
+{
+    reg_t val; memcpy(&val, memPtr, sizeof(val)); return val;
+}
+
+static void LZ4_write16(void* memPtr, U16 value)
+{
+    memcpy(memPtr, &value, sizeof(value));
+}
+
+static void LZ4_write32(void* memPtr, U32 value)
+{
+    memcpy(memPtr, &value, sizeof(value));
+}
+
+#endif /* LZ4_FORCE_MEMORY_ACCESS */
+
+
+static U16 LZ4_readLE16(const void* memPtr)
+{
+    if (LZ4_isLittleEndian()) {
+        return LZ4_read16(memPtr);
+    } else {
+        const BYTE* p = (const BYTE*)memPtr;
+        return (U16)((U16)p[0] + (p[1]<<8));
+    }
+}
+
+static void LZ4_writeLE16(void* memPtr, U16 value)
+{
+    if (LZ4_isLittleEndian()) {
+        LZ4_write16(memPtr, value);
+    } else {
+        BYTE* p = (BYTE*)memPtr;
+        p[0] = (BYTE) value;
+        p[1] = (BYTE)(value>>8);
+    }
+}
+
+static void LZ4_copy8(void* dst, const void* src)
+{
+    memcpy(dst,src,8);
+}
+
+/* customized variant of memcpy, which can overwrite up to 8 bytes beyond dstEnd */
+static void LZ4_wildCopy(void* dstPtr, const void* srcPtr, void* dstEnd)
+{
+    BYTE* d = (BYTE*)dstPtr;
+    const BYTE* s = (const BYTE*)srcPtr;
+    BYTE* const e = (BYTE*)dstEnd;
+
+    do { LZ4_copy8(d,s); d+=8; s+=8; } while (d<e);
+}
+
+
+/*-************************************
+*  Common Constants
+**************************************/
+#define MINMATCH 4
+
+#define WILDCOPYLENGTH 8
+#define LASTLITERALS 5
+#define MFLIMIT (WILDCOPYLENGTH+MINMATCH)
+static const int LZ4_minLength = (MFLIMIT+1);
+
+#define KB *(1 <<10)
+#define MB *(1 <<20)
+#define GB *(1U<<30)
+
+#define MAXD_LOG 16
+#define MAX_DISTANCE ((1 << MAXD_LOG) - 1)
+
+#define ML_BITS  4
+#define ML_MASK  ((1U<<ML_BITS)-1)
+#define RUN_BITS (8-ML_BITS)
+#define RUN_MASK ((1U<<RUN_BITS)-1)
+
+
+/*-************************************
+*  Error detection
+**************************************/
+#define LZ4_STATIC_ASSERT(c)    { enum { LZ4_static_assert = 1/(int)(!!(c)) }; }   /* use only *after* variable declarations */
+
+#if defined(LZ4_DEBUG) && (LZ4_DEBUG>=2)
+#  include <stdio.h>
+#  define DEBUGLOG(l, ...) {                          \
+                if (l<=LZ4_DEBUG) {                   \
+                    fprintf(samtools_stderr, __FILE__ ": ");   \
+                    fprintf(samtools_stderr, __VA_ARGS__);     \
+                    fprintf(samtools_stderr, " \n");           \
+            }   }
+#else
+#  define DEBUGLOG(l, ...)      {}    /* disabled */
+#endif
+
+
+/*-************************************
+*  Common functions
+**************************************/
+static unsigned LZ4_NbCommonBytes (register reg_t val)
+{
+    if (LZ4_isLittleEndian()) {
+        if (sizeof(val)==8) {
+#       if defined(_MSC_VER) && defined(_WIN64) && !defined(LZ4_FORCE_SW_BITCOUNT)
+            unsigned long r = 0;
+            _BitScanForward64( &r, (U64)val );
+            return (int)(r>>3);
+#       elif (defined(__clang__) || (defined(__GNUC__) && (__GNUC__>=3))) && !defined(LZ4_FORCE_SW_BITCOUNT)
+            return (__builtin_ctzll((U64)val) >> 3);
+#       else
+            static const int DeBruijnBytePos[64] = { 0, 0, 0, 0, 0, 1, 1, 2, 0, 3, 1, 3, 1, 4, 2, 7, 0, 2, 3, 6, 1, 5, 3, 5, 1, 3, 4, 4, 2, 5, 6, 7, 7, 0, 1, 2, 3, 3, 4, 6, 2, 6, 5, 5, 3, 4, 5, 6, 7, 1, 2, 4, 6, 4, 4, 5, 7, 2, 6, 5, 7, 6, 7, 7 };
+            return DeBruijnBytePos[((U64)((val & -(long long)val) * 0x0218A392CDABBD3FULL)) >> 58];
+#       endif
+        } else /* 32 bits */ {
+#       if defined(_MSC_VER) && !defined(LZ4_FORCE_SW_BITCOUNT)
+            unsigned long r;
+            _BitScanForward( &r, (U32)val );
+            return (int)(r>>3);
+#       elif (defined(__clang__) || (defined(__GNUC__) && (__GNUC__>=3))) && !defined(LZ4_FORCE_SW_BITCOUNT)
+            return (__builtin_ctz((U32)val) >> 3);
+#       else
+            static const int DeBruijnBytePos[32] = { 0, 0, 3, 0, 3, 1, 3, 0, 3, 2, 2, 1, 3, 2, 0, 1, 3, 3, 1, 2, 2, 2, 2, 0, 3, 1, 2, 0, 1, 0, 1, 1 };
+            return DeBruijnBytePos[((U32)((val & -(S32)val) * 0x077CB531U)) >> 27];
+#       endif
+        }
+    } else   /* Big Endian CPU */ {
+        if (sizeof(val)==8) {
+#       if defined(_MSC_VER) && defined(_WIN64) && !defined(LZ4_FORCE_SW_BITCOUNT)
+            unsigned long r = 0;
+            _BitScanReverse64( &r, val );
+            return (unsigned)(r>>3);
+#       elif (defined(__clang__) || (defined(__GNUC__) && (__GNUC__>=3))) && !defined(LZ4_FORCE_SW_BITCOUNT)
+            return (__builtin_clzll((U64)val) >> 3);
+#       else
+            unsigned r;
+            if (!(val>>32)) { r=4; } else { r=0; val>>=32; }
+            if (!(val>>16)) { r+=2; val>>=8; } else { val>>=24; }
+            r += (!val);
+            return r;
+#       endif
+        } else /* 32 bits */ {
+#       if defined(_MSC_VER) && !defined(LZ4_FORCE_SW_BITCOUNT)
+            unsigned long r = 0;
+            _BitScanReverse( &r, (unsigned long)val );
+            return (unsigned)(r>>3);
+#       elif (defined(__clang__) || (defined(__GNUC__) && (__GNUC__>=3))) && !defined(LZ4_FORCE_SW_BITCOUNT)
+            return (__builtin_clz((U32)val) >> 3);
+#       else
+            unsigned r;
+            if (!(val>>16)) { r=2; val>>=8; } else { r=0; val>>=24; }
+            r += (!val);
+            return r;
+#       endif
+        }
+    }
+}
+
+#define STEPSIZE sizeof(reg_t)
+static unsigned LZ4_count(const BYTE* pIn, const BYTE* pMatch, const BYTE* pInLimit)
+{
+    const BYTE* const pStart = pIn;
+
+    while (likely(pIn<pInLimit-(STEPSIZE-1))) {
+        reg_t const diff = LZ4_read_ARCH(pMatch) ^ LZ4_read_ARCH(pIn);
+        if (!diff) { pIn+=STEPSIZE; pMatch+=STEPSIZE; continue; }
+        pIn += LZ4_NbCommonBytes(diff);
+        return (unsigned)(pIn - pStart);
+    }
+
+    if ((STEPSIZE==8) && (pIn<(pInLimit-3)) && (LZ4_read32(pMatch) == LZ4_read32(pIn))) { pIn+=4; pMatch+=4; }
+    if ((pIn<(pInLimit-1)) && (LZ4_read16(pMatch) == LZ4_read16(pIn))) { pIn+=2; pMatch+=2; }
+    if ((pIn<pInLimit) && (*pMatch == *pIn)) pIn++;
+    return (unsigned)(pIn - pStart);
+}
+
+
+#ifndef LZ4_COMMONDEFS_ONLY
+/*-************************************
+*  Local Constants
+**************************************/
+static const int LZ4_64Klimit = ((64 KB) + (MFLIMIT-1));
+static const U32 LZ4_skipTrigger = 6;  /* Increase this value ==> compression run slower on incompressible data */
+
+
+/*-************************************
+*  Local Structures and types
+**************************************/
+typedef enum { notLimited = 0, limitedOutput = 1 } limitedOutput_directive;
+typedef enum { byPtr, byU32, byU16 } tableType_t;
+
+typedef enum { noDict = 0, withPrefix64k, usingExtDict } dict_directive;
+typedef enum { noDictIssue = 0, dictSmall } dictIssue_directive;
+
+typedef enum { endOnOutputSize = 0, endOnInputSize = 1 } endCondition_directive;
+typedef enum { full = 0, partial = 1 } earlyEnd_directive;
+
+
+/*-************************************
+*  Local Utils
+**************************************/
+int LZ4_versionNumber (void) { return LZ4_VERSION_NUMBER; }
+const char* LZ4_versionString(void) { return LZ4_VERSION_STRING; }
+int LZ4_compressBound(int isize)  { return LZ4_COMPRESSBOUND(isize); }
+int LZ4_sizeofState() { return LZ4_STREAMSIZE; }
+
+
+/*-******************************
+*  Compression functions
+********************************/
+static U32 LZ4_hash4(U32 sequence, tableType_t const tableType)
+{
+    if (tableType == byU16)
+        return ((sequence * 2654435761U) >> ((MINMATCH*8)-(LZ4_HASHLOG+1)));
+    else
+        return ((sequence * 2654435761U) >> ((MINMATCH*8)-LZ4_HASHLOG));
+}
+
+static U32 LZ4_hash5(U64 sequence, tableType_t const tableType)
+{
+    static const U64 prime5bytes = 889523592379ULL;
+    static const U64 prime8bytes = 11400714785074694791ULL;
+    const U32 hashLog = (tableType == byU16) ? LZ4_HASHLOG+1 : LZ4_HASHLOG;
+    if (LZ4_isLittleEndian())
+        return (U32)(((sequence << 24) * prime5bytes) >> (64 - hashLog));
+    else
+        return (U32)(((sequence >> 24) * prime8bytes) >> (64 - hashLog));
+}
+
+FORCE_INLINE U32 LZ4_hashPosition(const void* const p, tableType_t const tableType)
+{
+    if ((sizeof(reg_t)==8) && (tableType != byU16)) return LZ4_hash5(LZ4_read_ARCH(p), tableType);
+    return LZ4_hash4(LZ4_read32(p), tableType);
+}
+
+static void LZ4_putPositionOnHash(const BYTE* p, U32 h, void* tableBase, tableType_t const tableType, const BYTE* srcBase)
+{
+    switch (tableType)
+    {
+    case byPtr: { const BYTE** hashTable = (const BYTE**)tableBase; hashTable[h] = p; return; }
+    case byU32: { U32* hashTable = (U32*) tableBase; hashTable[h] = (U32)(p-srcBase); return; }
+    case byU16: { U16* hashTable = (U16*) tableBase; hashTable[h] = (U16)(p-srcBase); return; }
+    }
+}
+
+FORCE_INLINE void LZ4_putPosition(const BYTE* p, void* tableBase, tableType_t tableType, const BYTE* srcBase)
+{
+    U32 const h = LZ4_hashPosition(p, tableType);
+    LZ4_putPositionOnHash(p, h, tableBase, tableType, srcBase);
+}
+
+static const BYTE* LZ4_getPositionOnHash(U32 h, void* tableBase, tableType_t tableType, const BYTE* srcBase)
+{
+    if (tableType == byPtr) { const BYTE** hashTable = (const BYTE**) tableBase; return hashTable[h]; }
+    if (tableType == byU32) { const U32* const hashTable = (U32*) tableBase; return hashTable[h] + srcBase; }
+    { const U16* const hashTable = (U16*) tableBase; return hashTable[h] + srcBase; }   /* default, to ensure a return */
+}
+
+FORCE_INLINE const BYTE* LZ4_getPosition(const BYTE* p, void* tableBase, tableType_t tableType, const BYTE* srcBase)
+{
+    U32 const h = LZ4_hashPosition(p, tableType);
+    return LZ4_getPositionOnHash(h, tableBase, tableType, srcBase);
+}
+
+
+/** LZ4_compress_generic() :
+    inlined, to ensure branches are decided at compilation time */
+FORCE_INLINE int LZ4_compress_generic(
+                 LZ4_stream_t_internal* const cctx,
+                 const char* const source,
+                 char* const dest,
+                 const int inputSize,
+                 const int maxOutputSize,
+                 const limitedOutput_directive outputLimited,
+                 const tableType_t tableType,
+                 const dict_directive dict,
+                 const dictIssue_directive dictIssue,
+                 const U32 acceleration)
+{
+    const BYTE* ip = (const BYTE*) source;
+    const BYTE* base;
+    const BYTE* lowLimit;
+    const BYTE* const lowRefLimit = ip - cctx->dictSize;
+    const BYTE* const dictionary = cctx->dictionary;
+    const BYTE* const dictEnd = dictionary + cctx->dictSize;
+    const ptrdiff_t dictDelta = dictEnd - (const BYTE*)source;
+    const BYTE* anchor = (const BYTE*) source;
+    const BYTE* const iend = ip + inputSize;
+    const BYTE* const mflimit = iend - MFLIMIT;
+    const BYTE* const matchlimit = iend - LASTLITERALS;
+
+    BYTE* op = (BYTE*) dest;
+    BYTE* const olimit = op + maxOutputSize;
+
+    U32 forwardH;
+
+    /* Init conditions */
+    if ((U32)inputSize > (U32)LZ4_MAX_INPUT_SIZE) return 0;   /* Unsupported inputSize, too large (or negative) */
+    switch(dict)
+    {
+    case noDict:
+    default:
+        base = (const BYTE*)source;
+        lowLimit = (const BYTE*)source;
+        break;
+    case withPrefix64k:
+        base = (const BYTE*)source - cctx->currentOffset;
+        lowLimit = (const BYTE*)source - cctx->dictSize;
+        break;
+    case usingExtDict:
+        base = (const BYTE*)source - cctx->currentOffset;
+        lowLimit = (const BYTE*)source;
+        break;
+    }
+    if ((tableType == byU16) && (inputSize>=LZ4_64Klimit)) return 0;   /* Size too large (not within 64K limit) */
+    if (inputSize<LZ4_minLength) goto _last_literals;                  /* Input too small, no compression (all literals) */
+
+    /* First Byte */
+    LZ4_putPosition(ip, cctx->hashTable, tableType, base);
+    ip++; forwardH = LZ4_hashPosition(ip, tableType);
+
+    /* Main Loop */
+    for ( ; ; ) {
+        ptrdiff_t refDelta = 0;
+        const BYTE* match;
+        BYTE* token;
+
+        /* Find a match */
+        {   const BYTE* forwardIp = ip;
+            unsigned step = 1;
+            unsigned searchMatchNb = acceleration << LZ4_skipTrigger;
+            do {
+                U32 const h = forwardH;
+                ip = forwardIp;
+                forwardIp += step;
+                step = (searchMatchNb++ >> LZ4_skipTrigger);
+
+                if (unlikely(forwardIp > mflimit)) goto _last_literals;
+
+                match = LZ4_getPositionOnHash(h, cctx->hashTable, tableType, base);
+                if (dict==usingExtDict) {
+                    if (match < (const BYTE*)source) {
+                        refDelta = dictDelta;
+                        lowLimit = dictionary;
+                    } else {
+                        refDelta = 0;
+                        lowLimit = (const BYTE*)source;
+                }   }
+                forwardH = LZ4_hashPosition(forwardIp, tableType);
+                LZ4_putPositionOnHash(ip, h, cctx->hashTable, tableType, base);
+
+            } while ( ((dictIssue==dictSmall) ? (match < lowRefLimit) : 0)
+                || ((tableType==byU16) ? 0 : (match + MAX_DISTANCE < ip))
+                || (LZ4_read32(match+refDelta) != LZ4_read32(ip)) );
+        }
+
+        /* Catch up */
+        while (((ip>anchor) & (match+refDelta > lowLimit)) && (unlikely(ip[-1]==match[refDelta-1]))) { ip--; match--; }
+
+        /* Encode Literals */
+        {   unsigned const litLength = (unsigned)(ip - anchor);
+            token = op++;
+            if ((outputLimited) &&  /* Check output buffer overflow */
+                (unlikely(op + litLength + (2 + 1 + LASTLITERALS) + (litLength/255) > olimit)))
+                return 0;
+            if (litLength >= RUN_MASK) {
+                int len = (int)litLength-RUN_MASK;
+                *token = (RUN_MASK<<ML_BITS);
+                for(; len >= 255 ; len-=255) *op++ = 255;
+                *op++ = (BYTE)len;
+            }
+            else *token = (BYTE)(litLength<<ML_BITS);
+
+            /* Copy Literals */
+            LZ4_wildCopy(op, anchor, op+litLength);
+            op+=litLength;
+        }
+
+_next_match:
+        /* Encode Offset */
+        LZ4_writeLE16(op, (U16)(ip-match)); op+=2;
+
+        /* Encode MatchLength */
+        {   unsigned matchCode;
+
+            if ((dict==usingExtDict) && (lowLimit==dictionary)) {
+                const BYTE* limit;
+                match += refDelta;
+                limit = ip + (dictEnd-match);
+                if (limit > matchlimit) limit = matchlimit;
+                matchCode = LZ4_count(ip+MINMATCH, match+MINMATCH, limit);
+                ip += MINMATCH + matchCode;
+                if (ip==limit) {
+                    unsigned const more = LZ4_count(ip, (const BYTE*)source, matchlimit);
+                    matchCode += more;
+                    ip += more;
+                }
+            } else {
+                matchCode = LZ4_count(ip+MINMATCH, match+MINMATCH, matchlimit);
+                ip += MINMATCH + matchCode;
+            }
+
+            if ( outputLimited &&    /* Check output buffer overflow */
+                (unlikely(op + (1 + LASTLITERALS) + (matchCode>>8) > olimit)) )
+                return 0;
+            if (matchCode >= ML_MASK) {
+                *token += ML_MASK;
+                matchCode -= ML_MASK;
+                LZ4_write32(op, 0xFFFFFFFF);
+                while (matchCode >= 4*255) op+=4, LZ4_write32(op, 0xFFFFFFFF), matchCode -= 4*255;
+                op += matchCode / 255;
+                *op++ = (BYTE)(matchCode % 255);
+            } else
+                *token += (BYTE)(matchCode);
+        }
+
+        anchor = ip;
+
+        /* Test end of chunk */
+        if (ip > mflimit) break;
+
+        /* Fill table */
+        LZ4_putPosition(ip-2, cctx->hashTable, tableType, base);
+
+        /* Test next position */
+        match = LZ4_getPosition(ip, cctx->hashTable, tableType, base);
+        if (dict==usingExtDict) {
+            if (match < (const BYTE*)source) {
+                refDelta = dictDelta;
+                lowLimit = dictionary;
+            } else {
+                refDelta = 0;
+                lowLimit = (const BYTE*)source;
+        }   }
+        LZ4_putPosition(ip, cctx->hashTable, tableType, base);
+        if ( ((dictIssue==dictSmall) ? (match>=lowRefLimit) : 1)
+            && (match+MAX_DISTANCE>=ip)
+            && (LZ4_read32(match+refDelta)==LZ4_read32(ip)) )
+        { token=op++; *token=0; goto _next_match; }
+
+        /* Prepare next loop */
+        forwardH = LZ4_hashPosition(++ip, tableType);
+    }
+
+_last_literals:
+    /* Encode Last Literals */
+    {   size_t const lastRun = (size_t)(iend - anchor);
+        if ( (outputLimited) &&  /* Check output buffer overflow */
+            ((op - (BYTE*)dest) + lastRun + 1 + ((lastRun+255-RUN_MASK)/255) > (U32)maxOutputSize) )
+            return 0;
+        if (lastRun >= RUN_MASK) {
+            size_t accumulator = lastRun - RUN_MASK;
+            *op++ = RUN_MASK << ML_BITS;
+            for(; accumulator >= 255 ; accumulator-=255) *op++ = 255;
+            *op++ = (BYTE) accumulator;
+        } else {
+            *op++ = (BYTE)(lastRun<<ML_BITS);
+        }
+        memcpy(op, anchor, lastRun);
+        op += lastRun;
+    }
+
+    /* End */
+    return (int) (((char*)op)-dest);
+}
+
+
+int LZ4_compress_fast_extState(void* state, const char* source, char* dest, int inputSize, int maxOutputSize, int acceleration)
+{
+    LZ4_stream_t_internal* ctx = &((LZ4_stream_t*)state)->internal_donotuse;
+    LZ4_resetStream((LZ4_stream_t*)state);
+    if (acceleration < 1) acceleration = ACCELERATION_DEFAULT;
+
+    if (maxOutputSize >= LZ4_compressBound(inputSize)) {
+        if (inputSize < LZ4_64Klimit)
+            return LZ4_compress_generic(ctx, source, dest, inputSize,             0,    notLimited,                        byU16, noDict, noDictIssue, acceleration);
+        else
+            return LZ4_compress_generic(ctx, source, dest, inputSize,             0,    notLimited, (sizeof(void*)==8) ? byU32 : byPtr, noDict, noDictIssue, acceleration);
+    } else {
+        if (inputSize < LZ4_64Klimit)
+            return LZ4_compress_generic(ctx, source, dest, inputSize, maxOutputSize, limitedOutput,                        byU16, noDict, noDictIssue, acceleration);
+        else
+            return LZ4_compress_generic(ctx, source, dest, inputSize, maxOutputSize, limitedOutput, (sizeof(void*)==8) ? byU32 : byPtr, noDict, noDictIssue, acceleration);
+    }
+}
+
+
+int LZ4_compress_fast(const char* source, char* dest, int inputSize, int maxOutputSize, int acceleration)
+{
+#if (LZ4_HEAPMODE)
+    void* ctxPtr = ALLOCATOR(1, sizeof(LZ4_stream_t));   /* malloc-calloc always properly aligned */
+#else
+    LZ4_stream_t ctx;
+    void* const ctxPtr = &ctx;
+#endif
+
+    int const result = LZ4_compress_fast_extState(ctxPtr, source, dest, inputSize, maxOutputSize, acceleration);
+
+#if (LZ4_HEAPMODE)
+    FREEMEM(ctxPtr);
+#endif
+    return result;
+}
+
+
+int LZ4_compress_default(const char* source, char* dest, int inputSize, int maxOutputSize)
+{
+    return LZ4_compress_fast(source, dest, inputSize, maxOutputSize, 1);
+}
+
+
+/* hidden debug function */
+/* strangely enough, gcc generates faster code when this function is uncommented, even if unused */
+int LZ4_compress_fast_force(const char* source, char* dest, int inputSize, int maxOutputSize, int acceleration)
+{
+    LZ4_stream_t ctx;
+    LZ4_resetStream(&ctx);
+
+    if (inputSize < LZ4_64Klimit)
+        return LZ4_compress_generic(&ctx.internal_donotuse, source, dest, inputSize, maxOutputSize, limitedOutput, byU16,                        noDict, noDictIssue, acceleration);
+    else
+        return LZ4_compress_generic(&ctx.internal_donotuse, source, dest, inputSize, maxOutputSize, limitedOutput, sizeof(void*)==8 ? byU32 : byPtr, noDict, noDictIssue, acceleration);
+}
+
+
+/*-******************************
+*  *_destSize() variant
+********************************/
+
+static int LZ4_compress_destSize_generic(
+                       LZ4_stream_t_internal* const ctx,
+                 const char* const src,
+                       char* const dst,
+                       int*  const srcSizePtr,
+                 const int targetDstSize,
+                 const tableType_t tableType)
+{
+    const BYTE* ip = (const BYTE*) src;
+    const BYTE* base = (const BYTE*) src;
+    const BYTE* lowLimit = (const BYTE*) src;
+    const BYTE* anchor = ip;
+    const BYTE* const iend = ip + *srcSizePtr;
+    const BYTE* const mflimit = iend - MFLIMIT;
+    const BYTE* const matchlimit = iend - LASTLITERALS;
+
+    BYTE* op = (BYTE*) dst;
+    BYTE* const oend = op + targetDstSize;
+    BYTE* const oMaxLit = op + targetDstSize - 2 /* offset */ - 8 /* because 8+MINMATCH==MFLIMIT */ - 1 /* token */;
+    BYTE* const oMaxMatch = op + targetDstSize - (LASTLITERALS + 1 /* token */);
+    BYTE* const oMaxSeq = oMaxLit - 1 /* token */;
+
+    U32 forwardH;
+
+
+    /* Init conditions */
+    if (targetDstSize < 1) return 0;                                     /* Impossible to store anything */
+    if ((U32)*srcSizePtr > (U32)LZ4_MAX_INPUT_SIZE) return 0;            /* Unsupported input size, too large (or negative) */
+    if ((tableType == byU16) && (*srcSizePtr>=LZ4_64Klimit)) return 0;   /* Size too large (not within 64K limit) */
+    if (*srcSizePtr<LZ4_minLength) goto _last_literals;                  /* Input too small, no compression (all literals) */
+
+    /* First Byte */
+    *srcSizePtr = 0;
+    LZ4_putPosition(ip, ctx->hashTable, tableType, base);
+    ip++; forwardH = LZ4_hashPosition(ip, tableType);
+
+    /* Main Loop */
+    for ( ; ; ) {
+        const BYTE* match;
+        BYTE* token;
+
+        /* Find a match */
+        {   const BYTE* forwardIp = ip;
+            unsigned step = 1;
+            unsigned searchMatchNb = 1 << LZ4_skipTrigger;
+
+            do {
+                U32 h = forwardH;
+                ip = forwardIp;
+                forwardIp += step;
+                step = (searchMatchNb++ >> LZ4_skipTrigger);
+
+                if (unlikely(forwardIp > mflimit)) goto _last_literals;
+
+                match = LZ4_getPositionOnHash(h, ctx->hashTable, tableType, base);
+                forwardH = LZ4_hashPosition(forwardIp, tableType);
+                LZ4_putPositionOnHash(ip, h, ctx->hashTable, tableType, base);
+
+            } while ( ((tableType==byU16) ? 0 : (match + MAX_DISTANCE < ip))
+                || (LZ4_read32(match) != LZ4_read32(ip)) );
+        }
+
+        /* Catch up */
+        while ((ip>anchor) && (match > lowLimit) && (unlikely(ip[-1]==match[-1]))) { ip--; match--; }
+
+        /* Encode Literal length */
+        {   unsigned litLength = (unsigned)(ip - anchor);
+            token = op++;
+            if (op + ((litLength+240)/255) + litLength > oMaxLit) {
+                /* Not enough space for a last match */
+                op--;
+                goto _last_literals;
+            }
+            if (litLength>=RUN_MASK) {
+                unsigned len = litLength - RUN_MASK;
+                *token=(RUN_MASK<<ML_BITS);
+                for(; len >= 255 ; len-=255) *op++ = 255;
+                *op++ = (BYTE)len;
+            }
+            else *token = (BYTE)(litLength<<ML_BITS);
+
+            /* Copy Literals */
+            LZ4_wildCopy(op, anchor, op+litLength);
+            op += litLength;
+        }
+
+_next_match:
+        /* Encode Offset */
+        LZ4_writeLE16(op, (U16)(ip-match)); op+=2;
+
+        /* Encode MatchLength */
+        {   size_t matchLength = LZ4_count(ip+MINMATCH, match+MINMATCH, matchlimit);
+
+            if (op + ((matchLength+240)/255) > oMaxMatch) {
+                /* Match description too long : reduce it */
+                matchLength = (15-1) + (oMaxMatch-op) * 255;
+            }
+            ip += MINMATCH + matchLength;
+
+            if (matchLength>=ML_MASK) {
+                *token += ML_MASK;
+                matchLength -= ML_MASK;
+                while (matchLength >= 255) { matchLength-=255; *op++ = 255; }
+                *op++ = (BYTE)matchLength;
+            }
+            else *token += (BYTE)(matchLength);
+        }
+
+        anchor = ip;
+
+        /* Test end of block */
+        if (ip > mflimit) break;
+        if (op > oMaxSeq) break;
+
+        /* Fill table */
+        LZ4_putPosition(ip-2, ctx->hashTable, tableType, base);
+
+        /* Test next position */
+        match = LZ4_getPosition(ip, ctx->hashTable, tableType, base);
+        LZ4_putPosition(ip, ctx->hashTable, tableType, base);
+        if ( (match+MAX_DISTANCE>=ip)
+            && (LZ4_read32(match)==LZ4_read32(ip)) )
+        { token=op++; *token=0; goto _next_match; }
+
+        /* Prepare next loop */
+        forwardH = LZ4_hashPosition(++ip, tableType);
+    }
+
+_last_literals:
+    /* Encode Last Literals */
+    {   size_t lastRunSize = (size_t)(iend - anchor);
+        if (op + 1 /* token */ + ((lastRunSize+240)/255) /* litLength */ + lastRunSize /* literals */ > oend) {
+            /* adapt lastRunSize to fill 'dst' */
+            lastRunSize  = (oend-op) - 1;
+            lastRunSize -= (lastRunSize+240)/255;
+        }
+        ip = anchor + lastRunSize;
+
+        if (lastRunSize >= RUN_MASK) {
+            size_t accumulator = lastRunSize - RUN_MASK;
+            *op++ = RUN_MASK << ML_BITS;
+            for(; accumulator >= 255 ; accumulator-=255) *op++ = 255;
+            *op++ = (BYTE) accumulator;
+        } else {
+            *op++ = (BYTE)(lastRunSize<<ML_BITS);
+        }
+        memcpy(op, anchor, lastRunSize);
+        op += lastRunSize;
+    }
+
+    /* End */
+    *srcSizePtr = (int) (((const char*)ip)-src);
+    return (int) (((char*)op)-dst);
+}
+
+
+static int LZ4_compress_destSize_extState (LZ4_stream_t* state, const char* src, char* dst, int* srcSizePtr, int targetDstSize)
+{
+    LZ4_resetStream(state);
+
+    if (targetDstSize >= LZ4_compressBound(*srcSizePtr)) {  /* compression success is guaranteed */
+        return LZ4_compress_fast_extState(state, src, dst, *srcSizePtr, targetDstSize, 1);
+    } else {
+        if (*srcSizePtr < LZ4_64Klimit)
+            return LZ4_compress_destSize_generic(&state->internal_donotuse, src, dst, srcSizePtr, targetDstSize, byU16);
+        else
+            return LZ4_compress_destSize_generic(&state->internal_donotuse, src, dst, srcSizePtr, targetDstSize, sizeof(void*)==8 ? byU32 : byPtr);
+    }
+}
+
+
+int LZ4_compress_destSize(const char* src, char* dst, int* srcSizePtr, int targetDstSize)
+{
+#if (LZ4_HEAPMODE)
+    LZ4_stream_t* ctx = (LZ4_stream_t*)ALLOCATOR(1, sizeof(LZ4_stream_t));   /* malloc-calloc always properly aligned */
+#else
+    LZ4_stream_t ctxBody;
+    LZ4_stream_t* ctx = &ctxBody;
+#endif
+
+    int result = LZ4_compress_destSize_extState(ctx, src, dst, srcSizePtr, targetDstSize);
+
+#if (LZ4_HEAPMODE)
+    FREEMEM(ctx);
+#endif
+    return result;
+}
+
+
+
+/*-******************************
+*  Streaming functions
+********************************/
+
+LZ4_stream_t* LZ4_createStream(void)
+{
+    LZ4_stream_t* lz4s = (LZ4_stream_t*)ALLOCATOR(8, LZ4_STREAMSIZE_U64);
+    LZ4_STATIC_ASSERT(LZ4_STREAMSIZE >= sizeof(LZ4_stream_t_internal));    /* A compilation error here means LZ4_STREAMSIZE is not large enough */
+    LZ4_resetStream(lz4s);
+    return lz4s;
+}
+
+void LZ4_resetStream (LZ4_stream_t* LZ4_stream)
+{
+    MEM_INIT(LZ4_stream, 0, sizeof(LZ4_stream_t));
+}
+
+int LZ4_freeStream (LZ4_stream_t* LZ4_stream)
+{
+    if (!LZ4_stream) return 0;   /* support free on NULL */
+    FREEMEM(LZ4_stream);
+    return (0);
+}
+
+
+#define HASH_UNIT sizeof(reg_t)
+int LZ4_loadDict (LZ4_stream_t* LZ4_dict, const char* dictionary, int dictSize)
+{
+    LZ4_stream_t_internal* dict = &LZ4_dict->internal_donotuse;
+    const BYTE* p = (const BYTE*)dictionary;
+    const BYTE* const dictEnd = p + dictSize;
+    const BYTE* base;
+
+    if ((dict->initCheck) || (dict->currentOffset > 1 GB))  /* Uninitialized structure, or reuse overflow */
+        LZ4_resetStream(LZ4_dict);
+
+    if (dictSize < (int)HASH_UNIT) {
+        dict->dictionary = NULL;
+        dict->dictSize = 0;
+        return 0;
+    }
+
+    if ((dictEnd - p) > 64 KB) p = dictEnd - 64 KB;
+    dict->currentOffset += 64 KB;
+    base = p - dict->currentOffset;
+    dict->dictionary = p;
+    dict->dictSize = (U32)(dictEnd - p);
+    dict->currentOffset += dict->dictSize;
+
+    while (p <= dictEnd-HASH_UNIT) {
+        LZ4_putPosition(p, dict->hashTable, byU32, base);
+        p+=3;
+    }
+
+    return dict->dictSize;
+}
+
+
+static void LZ4_renormDictT(LZ4_stream_t_internal* LZ4_dict, const BYTE* src)
+{
+    if ((LZ4_dict->currentOffset > 0x80000000) ||
+        ((uptrval)LZ4_dict->currentOffset > (uptrval)src)) {   /* address space overflow */
+        /* rescale hash table */
+        U32 const delta = LZ4_dict->currentOffset - 64 KB;
+        const BYTE* dictEnd = LZ4_dict->dictionary + LZ4_dict->dictSize;
+        int i;
+        for (i=0; i<LZ4_HASH_SIZE_U32; i++) {
+            if (LZ4_dict->hashTable[i] < delta) LZ4_dict->hashTable[i]=0;
+            else LZ4_dict->hashTable[i] -= delta;
+        }
+        LZ4_dict->currentOffset = 64 KB;
+        if (LZ4_dict->dictSize > 64 KB) LZ4_dict->dictSize = 64 KB;
+        LZ4_dict->dictionary = dictEnd - LZ4_dict->dictSize;
+    }
+}
+
+
+int LZ4_compress_fast_continue (LZ4_stream_t* LZ4_stream, const char* source, char* dest, int inputSize, int maxOutputSize, int acceleration)
+{
+    LZ4_stream_t_internal* streamPtr = &LZ4_stream->internal_donotuse;
+    const BYTE* const dictEnd = streamPtr->dictionary + streamPtr->dictSize;
+
+    const BYTE* smallest = (const BYTE*) source;
+    if (streamPtr->initCheck) return 0;   /* Uninitialized structure detected */
+    if ((streamPtr->dictSize>0) && (smallest>dictEnd)) smallest = dictEnd;
+    LZ4_renormDictT(streamPtr, smallest);
+    if (acceleration < 1) acceleration = ACCELERATION_DEFAULT;
+
+    /* Check overlapping input/dictionary space */
+    {   const BYTE* sourceEnd = (const BYTE*) source + inputSize;
+        if ((sourceEnd > streamPtr->dictionary) && (sourceEnd < dictEnd)) {
+            streamPtr->dictSize = (U32)(dictEnd - sourceEnd);
+            if (streamPtr->dictSize > 64 KB) streamPtr->dictSize = 64 KB;
+            if (streamPtr->dictSize < 4) streamPtr->dictSize = 0;
+            streamPtr->dictionary = dictEnd - streamPtr->dictSize;
+        }
+    }
+
+    /* prefix mode : source data follows dictionary */
+    if (dictEnd == (const BYTE*)source) {
+        int result;
+        if ((streamPtr->dictSize < 64 KB) && (streamPtr->dictSize < streamPtr->currentOffset))
+            result = LZ4_compress_generic(streamPtr, source, dest, inputSize, maxOutputSize, limitedOutput, byU32, withPrefix64k, dictSmall, acceleration);
+        else
+            result = LZ4_compress_generic(streamPtr, source, dest, inputSize, maxOutputSize, limitedOutput, byU32, withPrefix64k, noDictIssue, acceleration);
+        streamPtr->dictSize += (U32)inputSize;
+        streamPtr->currentOffset += (U32)inputSize;
+        return result;
+    }
+
+    /* external dictionary mode */
+    {   int result;
+        if ((streamPtr->dictSize < 64 KB) && (streamPtr->dictSize < streamPtr->currentOffset))
+            result = LZ4_compress_generic(streamPtr, source, dest, inputSize, maxOutputSize, limitedOutput, byU32, usingExtDict, dictSmall, acceleration);
+        else
+            result = LZ4_compress_generic(streamPtr, source, dest, inputSize, maxOutputSize, limitedOutput, byU32, usingExtDict, noDictIssue, acceleration);
+        streamPtr->dictionary = (const BYTE*)source;
+        streamPtr->dictSize = (U32)inputSize;
+        streamPtr->currentOffset += (U32)inputSize;
+        return result;
+    }
+}
+
+
+/* Hidden debug function, to force external dictionary mode */
+int LZ4_compress_forceExtDict (LZ4_stream_t* LZ4_dict, const char* source, char* dest, int inputSize)
+{
+    LZ4_stream_t_internal* streamPtr = &LZ4_dict->internal_donotuse;
+    int result;
+    const BYTE* const dictEnd = streamPtr->dictionary + streamPtr->dictSize;
+
+    const BYTE* smallest = dictEnd;
+    if (smallest > (const BYTE*) source) smallest = (const BYTE*) source;
+    LZ4_renormDictT(streamPtr, smallest);
+
+    result = LZ4_compress_generic(streamPtr, source, dest, inputSize, 0, notLimited, byU32, usingExtDict, noDictIssue, 1);
+
+    streamPtr->dictionary = (const BYTE*)source;
+    streamPtr->dictSize = (U32)inputSize;
+    streamPtr->currentOffset += (U32)inputSize;
+
+    return result;
+}
+
+
+/*! LZ4_saveDict() :
+ *  If previously compressed data block is not guaranteed to remain available at its memory location,
+ *  save it into a safer place (char* safeBuffer).
+ *  Note : you don't need to call LZ4_loadDict() afterwards,
+ *         dictionary is immediately usable, you can therefore call LZ4_compress_fast_continue().
+ *  Return : saved dictionary size in bytes (necessarily <= dictSize), or 0 if error.
+ */
+int LZ4_saveDict (LZ4_stream_t* LZ4_dict, char* safeBuffer, int dictSize)
+{
+    LZ4_stream_t_internal* const dict = &LZ4_dict->internal_donotuse;
+    const BYTE* const previousDictEnd = dict->dictionary + dict->dictSize;
+
+    if ((U32)dictSize > 64 KB) dictSize = 64 KB;   /* useless to define a dictionary > 64 KB */
+    if ((U32)dictSize > dict->dictSize) dictSize = dict->dictSize;
+
+    memmove(safeBuffer, previousDictEnd - dictSize, dictSize);
+
+    dict->dictionary = (const BYTE*)safeBuffer;
+    dict->dictSize = (U32)dictSize;
+
+    return dictSize;
+}
+
+
+
+/*-*****************************
+*  Decompression functions
+*******************************/
+/*! LZ4_decompress_generic() :
+ *  This generic decompression function cover all use cases.
+ *  It shall be instantiated several times, using different sets of directives
+ *  Note that it is important this generic function is really inlined,
+ *  in order to remove useless branches during compilation optimization.
+ */
+FORCE_INLINE int LZ4_decompress_generic(
+                 const char* const source,
+                 char* const dest,
+                 int inputSize,
+                 int outputSize,         /* If endOnInput==endOnInputSize, this value is the max size of Output Buffer. */
+
+                 int endOnInput,         /* endOnOutputSize, endOnInputSize */
+                 int partialDecoding,    /* full, partial */
+                 int targetOutputSize,   /* only used if partialDecoding==partial */
+                 int dict,               /* noDict, withPrefix64k, usingExtDict */
+                 const BYTE* const lowPrefix,  /* == dest when no prefix */
+                 const BYTE* const dictStart,  /* only if dict==usingExtDict */
+                 const size_t dictSize         /* note : = 0 if noDict */
+                 )
+{
+    /* Local Variables */
+    const BYTE* ip = (const BYTE*) source;
+    const BYTE* const iend = ip + inputSize;
+
+    BYTE* op = (BYTE*) dest;
+    BYTE* const oend = op + outputSize;
+    BYTE* cpy;
+    BYTE* oexit = op + targetOutputSize;
+    const BYTE* const lowLimit = lowPrefix - dictSize;
+
+    const BYTE* const dictEnd = (const BYTE*)dictStart + dictSize;
+    const unsigned dec32table[] = {0, 1, 2, 1, 4, 4, 4, 4};
+    const int dec64table[] = {0, 0, 0, -1, 0, 1, 2, 3};
+
+    const int safeDecode = (endOnInput==endOnInputSize);
+    const int checkOffset = ((safeDecode) && (dictSize < (int)(64 KB)));
+
+
+    /* Special cases */
+    if ((partialDecoding) && (oexit > oend-MFLIMIT)) oexit = oend-MFLIMIT;                        /* targetOutputSize too high => decode everything */
+    if ((endOnInput) && (unlikely(outputSize==0))) return ((inputSize==1) && (*ip==0)) ? 0 : -1;  /* Empty output buffer */
+    if ((!endOnInput) && (unlikely(outputSize==0))) return (*ip==0?1:-1);
+
+    /* Main Loop : decode sequences */
+    while (1) {
+        size_t length;
+        const BYTE* match;
+        size_t offset;
+
+        /* get literal length */
+        unsigned const token = *ip++;
+        if ((length=(token>>ML_BITS)) == RUN_MASK) {
+            unsigned s;
+            do {
+                s = *ip++;
+                length += s;
+            } while ( likely(endOnInput ? ip<iend-RUN_MASK : 1) & (s==255) );
+            if ((safeDecode) && unlikely((uptrval)(op)+length<(uptrval)(op))) goto _output_error;   /* overflow detection */
+            if ((safeDecode) && unlikely((uptrval)(ip)+length<(uptrval)(ip))) goto _output_error;   /* overflow detection */
+        }
+
+        /* copy literals */
+        cpy = op+length;
+        if ( ((endOnInput) && ((cpy>(partialDecoding?oexit:oend-MFLIMIT)) || (ip+length>iend-(2+1+LASTLITERALS))) )
+            || ((!endOnInput) && (cpy>oend-WILDCOPYLENGTH)) )
+        {
+            if (partialDecoding) {
+                if (cpy > oend) goto _output_error;                           /* Error : write attempt beyond end of output buffer */
+                if ((endOnInput) && (ip+length > iend)) goto _output_error;   /* Error : read attempt beyond end of input buffer */
+            } else {
+                if ((!endOnInput) && (cpy != oend)) goto _output_error;       /* Error : block decoding must stop exactly there */
+                if ((endOnInput) && ((ip+length != iend) || (cpy > oend))) goto _output_error;   /* Error : input must be consumed */
+            }
+            memcpy(op, ip, length);
+            ip += length;
+            op += length;
+            break;     /* Necessarily EOF, due to parsing restrictions */
+        }
+        LZ4_wildCopy(op, ip, cpy);
+        ip += length; op = cpy;
+
+        /* get offset */
+        offset = LZ4_readLE16(ip); ip+=2;
+        match = op - offset;
+        if ((checkOffset) && (unlikely(match < lowLimit))) goto _output_error;   /* Error : offset outside buffers */
+        LZ4_write32(op, (U32)offset);   /* costs ~1%; silence an msan warning when offset==0 */
+
+        /* get matchlength */
+        length = token & ML_MASK;
+        if (length == ML_MASK) {
+            unsigned s;
+            do {
+                s = *ip++;
+                if ((endOnInput) && (ip > iend-LASTLITERALS)) goto _output_error;
+                length += s;
+            } while (s==255);
+            if ((safeDecode) && unlikely((uptrval)(op)+length<(uptrval)op)) goto _output_error;   /* overflow detection */
+        }
+        length += MINMATCH;
+
+        /* check external dictionary */
+        if ((dict==usingExtDict) && (match < lowPrefix)) {
+            if (unlikely(op+length > oend-LASTLITERALS)) goto _output_error;   /* doesn't respect parsing restriction */
+
+            if (length <= (size_t)(lowPrefix-match)) {
+                /* match can be copied as a single segment from external dictionary */
+                memmove(op, dictEnd - (lowPrefix-match), length);
+                op += length;
+            } else {
+                /* match encompass external dictionary and current block */
+                size_t const copySize = (size_t)(lowPrefix-match);
+                size_t const restSize = length - copySize;
+                memcpy(op, dictEnd - copySize, copySize);
+                op += copySize;
+                if (restSize > (size_t)(op-lowPrefix)) {  /* overlap copy */
+                    BYTE* const endOfMatch = op + restSize;
+                    const BYTE* copyFrom = lowPrefix;
+                    while (op < endOfMatch) *op++ = *copyFrom++;
+                } else {
+                    memcpy(op, lowPrefix, restSize);
+                    op += restSize;
+            }   }
+            continue;
+        }
+
+        /* copy match within block */
+        cpy = op + length;
+        if (unlikely(offset<8)) {
+            const int dec64 = dec64table[offset];
+            op[0] = match[0];
+            op[1] = match[1];
+            op[2] = match[2];
+            op[3] = match[3];
+            match += dec32table[offset];
+            memcpy(op+4, match, 4);
+            match -= dec64;
+        } else { LZ4_copy8(op, match); match+=8; }
+        op += 8;
+
+        if (unlikely(cpy>oend-12)) {
+            BYTE* const oCopyLimit = oend-(WILDCOPYLENGTH-1);
+            if (cpy > oend-LASTLITERALS) goto _output_error;    /* Error : last LASTLITERALS bytes must be literals (uncompressed) */
+            if (op < oCopyLimit) {
+                LZ4_wildCopy(op, match, oCopyLimit);
+                match += oCopyLimit - op;
+                op = oCopyLimit;
+            }
+            while (op<cpy) *op++ = *match++;
+        } else {
+            LZ4_copy8(op, match);
+            if (length>16) LZ4_wildCopy(op+8, match+8, cpy);
+        }
+        op=cpy;   /* correction */
+    }
+
+    /* end of decoding */
+    if (endOnInput)
+       return (int) (((char*)op)-dest);     /* Nb of output bytes decoded */
+    else
+       return (int) (((const char*)ip)-source);   /* Nb of input bytes read */
+
+    /* Overflow error detected */
+_output_error:
+    return (int) (-(((const char*)ip)-source))-1;
+}
+
+
+int LZ4_decompress_safe(const char* source, char* dest, int compressedSize, int maxDecompressedSize)
+{
+    return LZ4_decompress_generic(source, dest, compressedSize, maxDecompressedSize, endOnInputSize, full, 0, noDict, (BYTE*)dest, NULL, 0);
+}
+
+int LZ4_decompress_safe_partial(const char* source, char* dest, int compressedSize, int targetOutputSize, int maxDecompressedSize)
+{
+    return LZ4_decompress_generic(source, dest, compressedSize, maxDecompressedSize, endOnInputSize, partial, targetOutputSize, noDict, (BYTE*)dest, NULL, 0);
+}
+
+int LZ4_decompress_fast(const char* source, char* dest, int originalSize)
+{
+    return LZ4_decompress_generic(source, dest, 0, originalSize, endOnOutputSize, full, 0, withPrefix64k, (BYTE*)(dest - 64 KB), NULL, 64 KB);
+}
+
+
+/*===== streaming decompression functions =====*/
+
+LZ4_streamDecode_t* LZ4_createStreamDecode(void)
+{
+    LZ4_streamDecode_t* lz4s = (LZ4_streamDecode_t*) ALLOCATOR(1, sizeof(LZ4_streamDecode_t));
+    return lz4s;
+}
+
+int LZ4_freeStreamDecode (LZ4_streamDecode_t* LZ4_stream)
+{
+    if (!LZ4_stream) return 0;   /* support free on NULL */
+    FREEMEM(LZ4_stream);
+    return 0;
+}
+
+/*!
+ * LZ4_setStreamDecode() :
+ * Use this function to instruct where to find the dictionary.
+ * This function is not necessary if previous data is still available where it was decoded.
+ * Loading a size of 0 is allowed (same effect as no dictionary).
+ * Return : 1 if OK, 0 if error
+ */
+int LZ4_setStreamDecode (LZ4_streamDecode_t* LZ4_streamDecode, const char* dictionary, int dictSize)
+{
+    LZ4_streamDecode_t_internal* lz4sd = &LZ4_streamDecode->internal_donotuse;
+    lz4sd->prefixSize = (size_t) dictSize;
+    lz4sd->prefixEnd = (const BYTE*) dictionary + dictSize;
+    lz4sd->externalDict = NULL;
+    lz4sd->extDictSize  = 0;
+    return 1;
+}
+
+/*
+*_continue() :
+    These decoding functions allow decompression of multiple blocks in "streaming" mode.
+    Previously decoded blocks must still be available at the memory position where they were decoded.
+    If it's not possible, save the relevant part of decoded data into a safe buffer,
+    and indicate where it stands using LZ4_setStreamDecode()
+*/
+int LZ4_decompress_safe_continue (LZ4_streamDecode_t* LZ4_streamDecode, const char* source, char* dest, int compressedSize, int maxOutputSize)
+{
+    LZ4_streamDecode_t_internal* lz4sd = &LZ4_streamDecode->internal_donotuse;
+    int result;
+
+    if (lz4sd->prefixEnd == (BYTE*)dest) {
+        result = LZ4_decompress_generic(source, dest, compressedSize, maxOutputSize,
+                                        endOnInputSize, full, 0,
+                                        usingExtDict, lz4sd->prefixEnd - lz4sd->prefixSize, lz4sd->externalDict, lz4sd->extDictSize);
+        if (result <= 0) return result;
+        lz4sd->prefixSize += result;
+        lz4sd->prefixEnd  += result;
+    } else {
+        lz4sd->extDictSize = lz4sd->prefixSize;
+        lz4sd->externalDict = lz4sd->prefixEnd - lz4sd->extDictSize;
+        result = LZ4_decompress_generic(source, dest, compressedSize, maxOutputSize,
+                                        endOnInputSize, full, 0,
+                                        usingExtDict, (BYTE*)dest, lz4sd->externalDict, lz4sd->extDictSize);
+        if (result <= 0) return result;
+        lz4sd->prefixSize = result;
+        lz4sd->prefixEnd  = (BYTE*)dest + result;
+    }
+
+    return result;
+}
+
+int LZ4_decompress_fast_continue (LZ4_streamDecode_t* LZ4_streamDecode, const char* source, char* dest, int originalSize)
+{
+    LZ4_streamDecode_t_internal* lz4sd = &LZ4_streamDecode->internal_donotuse;
+    int result;
+
+    if (lz4sd->prefixEnd == (BYTE*)dest) {
+        result = LZ4_decompress_generic(source, dest, 0, originalSize,
+                                        endOnOutputSize, full, 0,
+                                        usingExtDict, lz4sd->prefixEnd - lz4sd->prefixSize, lz4sd->externalDict, lz4sd->extDictSize);
+        if (result <= 0) return result;
+        lz4sd->prefixSize += originalSize;
+        lz4sd->prefixEnd  += originalSize;
+    } else {
+        lz4sd->extDictSize = lz4sd->prefixSize;
+        lz4sd->externalDict = lz4sd->prefixEnd - lz4sd->extDictSize;
+        result = LZ4_decompress_generic(source, dest, 0, originalSize,
+                                        endOnOutputSize, full, 0,
+                                        usingExtDict, (BYTE*)dest, lz4sd->externalDict, lz4sd->extDictSize);
+        if (result <= 0) return result;
+        lz4sd->prefixSize = originalSize;
+        lz4sd->prefixEnd  = (BYTE*)dest + originalSize;
+    }
+
+    return result;
+}
+
+
+/*
+Advanced decoding functions :
+*_usingDict() :
+    These decoding functions work the same as "_continue" ones,
+    the dictionary must be explicitly provided within parameters
+*/
+
+FORCE_INLINE int LZ4_decompress_usingDict_generic(const char* source, char* dest, int compressedSize, int maxOutputSize, int safe, const char* dictStart, int dictSize)
+{
+    if (dictSize==0)
+        return LZ4_decompress_generic(source, dest, compressedSize, maxOutputSize, safe, full, 0, noDict, (BYTE*)dest, NULL, 0);
+    if (dictStart+dictSize == dest) {
+        if (dictSize >= (int)(64 KB - 1))
+            return LZ4_decompress_generic(source, dest, compressedSize, maxOutputSize, safe, full, 0, withPrefix64k, (BYTE*)dest-64 KB, NULL, 0);
+        return LZ4_decompress_generic(source, dest, compressedSize, maxOutputSize, safe, full, 0, noDict, (BYTE*)dest-dictSize, NULL, 0);
+    }
+    return LZ4_decompress_generic(source, dest, compressedSize, maxOutputSize, safe, full, 0, usingExtDict, (BYTE*)dest, (const BYTE*)dictStart, dictSize);
+}
+
+int LZ4_decompress_safe_usingDict(const char* source, char* dest, int compressedSize, int maxOutputSize, const char* dictStart, int dictSize)
+{
+    return LZ4_decompress_usingDict_generic(source, dest, compressedSize, maxOutputSize, 1, dictStart, dictSize);
+}
+
+int LZ4_decompress_fast_usingDict(const char* source, char* dest, int originalSize, const char* dictStart, int dictSize)
+{
+    return LZ4_decompress_usingDict_generic(source, dest, 0, originalSize, 0, dictStart, dictSize);
+}
+
+/* debug function */
+int LZ4_decompress_safe_forceExtDict(const char* source, char* dest, int compressedSize, int maxOutputSize, const char* dictStart, int dictSize)
+{
+    return LZ4_decompress_generic(source, dest, compressedSize, maxOutputSize, endOnInputSize, full, 0, usingExtDict, (BYTE*)dest, (const BYTE*)dictStart, dictSize);
+}
+
+
+/*=*************************************************
+*  Obsolete Functions
+***************************************************/
+/* obsolete compression functions */
+int LZ4_compress_limitedOutput(const char* source, char* dest, int inputSize, int maxOutputSize) { return LZ4_compress_default(source, dest, inputSize, maxOutputSize); }
+int LZ4_compress(const char* source, char* dest, int inputSize) { return LZ4_compress_default(source, dest, inputSize, LZ4_compressBound(inputSize)); }
+int LZ4_compress_limitedOutput_withState (void* state, const char* src, char* dst, int srcSize, int dstSize) { return LZ4_compress_fast_extState(state, src, dst, srcSize, dstSize, 1); }
+int LZ4_compress_withState (void* state, const char* src, char* dst, int srcSize) { return LZ4_compress_fast_extState(state, src, dst, srcSize, LZ4_compressBound(srcSize), 1); }
+int LZ4_compress_limitedOutput_continue (LZ4_stream_t* LZ4_stream, const char* src, char* dst, int srcSize, int maxDstSize) { return LZ4_compress_fast_continue(LZ4_stream, src, dst, srcSize, maxDstSize, 1); }
+int LZ4_compress_continue (LZ4_stream_t* LZ4_stream, const char* source, char* dest, int inputSize) { return LZ4_compress_fast_continue(LZ4_stream, source, dest, inputSize, LZ4_compressBound(inputSize), 1); }
+
+/*
+These function names are deprecated and should no longer be used.
+They are only provided here for compatibility with older user programs.
+- LZ4_uncompress is totally equivalent to LZ4_decompress_fast
+- LZ4_uncompress_unknownOutputSize is totally equivalent to LZ4_decompress_safe
+*/
+int LZ4_uncompress (const char* source, char* dest, int outputSize) { return LZ4_decompress_fast(source, dest, outputSize); }
+int LZ4_uncompress_unknownOutputSize (const char* source, char* dest, int isize, int maxOutputSize) { return LZ4_decompress_safe(source, dest, isize, maxOutputSize); }
+
+
+/* Obsolete Streaming functions */
+
+int LZ4_sizeofStreamState() { return LZ4_STREAMSIZE; }
+
+static void LZ4_init(LZ4_stream_t* lz4ds, BYTE* base)
+{
+    MEM_INIT(lz4ds, 0, sizeof(LZ4_stream_t));
+    lz4ds->internal_donotuse.bufferStart = base;
+}
+
+int LZ4_resetStreamState(void* state, char* inputBuffer)
+{
+    if ((((uptrval)state) & 3) != 0) return 1;   /* Error : pointer is not aligned on 4-bytes boundary */
+    LZ4_init((LZ4_stream_t*)state, (BYTE*)inputBuffer);
+    return 0;
+}
+
+void* LZ4_create (char* inputBuffer)
+{
+    LZ4_stream_t* lz4ds = (LZ4_stream_t*)ALLOCATOR(8, sizeof(LZ4_stream_t));
+    LZ4_init (lz4ds, (BYTE*)inputBuffer);
+    return lz4ds;
+}
+
+char* LZ4_slideInputBuffer (void* LZ4_Data)
+{
+    LZ4_stream_t_internal* ctx = &((LZ4_stream_t*)LZ4_Data)->internal_donotuse;
+    int dictSize = LZ4_saveDict((LZ4_stream_t*)LZ4_Data, (char*)ctx->bufferStart, 64 KB);
+    return (char*)(ctx->bufferStart + dictSize);
+}
+
+/* Obsolete streaming decompression functions */
+
+int LZ4_decompress_safe_withPrefix64k(const char* source, char* dest, int compressedSize, int maxOutputSize)
+{
+    return LZ4_decompress_generic(source, dest, compressedSize, maxOutputSize, endOnInputSize, full, 0, withPrefix64k, (BYTE*)dest - 64 KB, NULL, 64 KB);
+}
+
+int LZ4_decompress_fast_withPrefix64k(const char* source, char* dest, int originalSize)
+{
+    return LZ4_decompress_generic(source, dest, 0, originalSize, endOnOutputSize, full, 0, withPrefix64k, (BYTE*)dest - 64 KB, NULL, 64 KB);
+}
+
+#endif   /* LZ4_COMMONDEFS_ONLY */
diff --git a/samtools/lz4/lz4.h b/samtools/lz4/lz4.h
new file mode 100644
index 0000000..86ca0d5
--- /dev/null
+++ b/samtools/lz4/lz4.h
@@ -0,0 +1,463 @@
+/*
+ *  LZ4 - Fast LZ compression algorithm
+ *  Header File
+ *  Copyright (C) 2011-2017, Yann Collet.
+
+   BSD 2-Clause License (http://www.opensource.org/licenses/bsd-license.php)
+
+   Redistribution and use in source and binary forms, with or without
+   modification, are permitted provided that the following conditions are
+   met:
+
+       * Redistributions of source code must retain the above copyright
+   notice, this list of conditions and the following disclaimer.
+       * Redistributions in binary form must reproduce the above
+   copyright notice, this list of conditions and the following disclaimer
+   in the documentation and/or other materials provided with the
+   distribution.
+
+   THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+   "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+   LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+   A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+   OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+   SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+   LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+   DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+   THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+   (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+   OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+   You can contact the author at :
+    - LZ4 homepage : http://www.lz4.org
+    - LZ4 source repository : https://github.com/lz4/lz4
+*/
+#if defined (__cplusplus)
+extern "C" {
+#endif
+
+#ifndef LZ4_H_2983827168210
+#define LZ4_H_2983827168210
+
+/* --- Dependency --- */
+#include <stddef.h>   /* size_t */
+
+
+/**
+  Introduction
+
+  LZ4 is lossless compression algorithm, providing compression speed at 400 MB/s per core,
+  scalable with multi-cores CPU. It features an extremely fast decoder, with speed in
+  multiple GB/s per core, typically reaching RAM speed limits on multi-core systems.
+
+  The LZ4 compression library provides in-memory compression and decompression functions.
+  Compression can be done in:
+    - a single step (described as Simple Functions)
+    - a single step, reusing a context (described in Advanced Functions)
+    - unbounded multiple steps (described as Streaming compression)
+
+  lz4.h provides block compression functions. It gives full buffer control to user.
+  Decompressing an lz4-compressed block also requires metadata (such as compressed size).
+  Each application is free to encode such metadata in whichever way it wants.
+
+  An additional format, called LZ4 frame specification (doc/lz4_Frame_format.md),
+  take care of encoding standard metadata alongside LZ4-compressed blocks.
+  If your application requires interoperability, it's recommended to use it.
+  A library is provided to take care of it, see lz4frame.h.
+*/
+
+/*^***************************************************************
+*  Export parameters
+*****************************************************************/
+/*
+*  LZ4_DLL_EXPORT :
+*  Enable exporting of functions when building a Windows DLL
+*  LZ4LIB_API :
+*  Control library symbols visibility.
+*/
+#if defined(LZ4_DLL_EXPORT) && (LZ4_DLL_EXPORT==1)
+#  define LZ4LIB_API __declspec(dllexport)
+#elif defined(LZ4_DLL_IMPORT) && (LZ4_DLL_IMPORT==1)
+#  define LZ4LIB_API __declspec(dllimport) /* It isn't required but allows to generate better code, saving a function pointer load from the IAT and an indirect jump.*/
+#elif defined(__GNUC__) && (__GNUC__ >= 4)
+#  define LZ4LIB_API __attribute__ ((__visibility__ ("default")))
+#else
+#  define LZ4LIB_API
+#endif
+
+
+/*------   Version   ------*/
+#define LZ4_VERSION_MAJOR    1    /* for breaking interface changes  */
+#define LZ4_VERSION_MINOR    8    /* for new (non-breaking) interface capabilities */
+#define LZ4_VERSION_RELEASE  0    /* for tweaks, bug-fixes, or development */
+
+#define LZ4_VERSION_NUMBER (LZ4_VERSION_MAJOR *100*100 + LZ4_VERSION_MINOR *100 + LZ4_VERSION_RELEASE)
+
+#define LZ4_LIB_VERSION LZ4_VERSION_MAJOR.LZ4_VERSION_MINOR.LZ4_VERSION_RELEASE
+#define LZ4_QUOTE(str) #str
+#define LZ4_EXPAND_AND_QUOTE(str) LZ4_QUOTE(str)
+#define LZ4_VERSION_STRING LZ4_EXPAND_AND_QUOTE(LZ4_LIB_VERSION)
+
+LZ4LIB_API int LZ4_versionNumber (void);  /**< library version number; to be used when checking dll version */
+LZ4LIB_API const char* LZ4_versionString (void);   /**< library version string; to be used when checking dll version */
+
+
+/*-************************************
+*  Tuning parameter
+**************************************/
+/*!
+ * LZ4_MEMORY_USAGE :
+ * Memory usage formula : N->2^N Bytes (examples : 10 -> 1KB; 12 -> 4KB ; 16 -> 64KB; 20 -> 1MB; etc.)
+ * Increasing memory usage improves compression ratio
+ * Reduced memory usage can improve speed, due to cache effect
+ * Default value is 14, for 16KB, which nicely fits into Intel x86 L1 cache
+ */
+#ifndef LZ4_MEMORY_USAGE
+# define LZ4_MEMORY_USAGE 14
+#endif
+
+/*-************************************
+*  Simple Functions
+**************************************/
+/*! LZ4_compress_default() :
+    Compresses 'sourceSize' bytes from buffer 'source'
+    into already allocated 'dest' buffer of size 'maxDestSize'.
+    Compression is guaranteed to succeed if 'maxDestSize' >= LZ4_compressBound(sourceSize).
+    It also runs faster, so it's a recommended setting.
+    If the function cannot compress 'source' into a more limited 'dest' budget,
+    compression stops *immediately*, and the function result is zero.
+    As a consequence, 'dest' content is not valid.
+    This function never writes outside 'dest' buffer, nor read outside 'source' buffer.
+        sourceSize  : Max supported value is LZ4_MAX_INPUT_VALUE
+        maxDestSize : full or partial size of buffer 'dest' (which must be already allocated)
+        return : the number of bytes written into buffer 'dest' (necessarily <= maxOutputSize)
+              or 0 if compression fails */
+LZ4LIB_API int LZ4_compress_default(const char* source, char* dest, int sourceSize, int maxDestSize);
+
+/*! LZ4_decompress_safe() :
+    compressedSize : is the precise full size of the compressed block.
+    maxDecompressedSize : is the size of destination buffer, which must be already allocated.
+    return : the number of bytes decompressed into destination buffer (necessarily <= maxDecompressedSize)
+             If destination buffer is not large enough, decoding will stop and output an error code (<0).
+             If the source stream is detected malformed, the function will stop decoding and return a negative result.
+             This function is protected against buffer overflow exploits, including malicious data packets.
+             It never writes outside output buffer, nor reads outside input buffer.
+*/
+LZ4LIB_API int LZ4_decompress_safe (const char* source, char* dest, int compressedSize, int maxDecompressedSize);
+
+
+/*-************************************
+*  Advanced Functions
+**************************************/
+#define LZ4_MAX_INPUT_SIZE        0x7E000000   /* 2 113 929 216 bytes */
+#define LZ4_COMPRESSBOUND(isize)  ((unsigned)(isize) > (unsigned)LZ4_MAX_INPUT_SIZE ? 0 : (isize) + ((isize)/255) + 16)
+
+/*!
+LZ4_compressBound() :
+    Provides the maximum size that LZ4 compression may output in a "worst case" scenario (input data not compressible)
+    This function is primarily useful for memory allocation purposes (destination buffer size).
+    Macro LZ4_COMPRESSBOUND() is also provided for compilation-time evaluation (stack memory allocation for example).
+    Note that LZ4_compress_default() compress faster when dest buffer size is >= LZ4_compressBound(srcSize)
+        inputSize  : max supported value is LZ4_MAX_INPUT_SIZE
+        return : maximum output size in a "worst case" scenario
+              or 0, if input size is too large ( > LZ4_MAX_INPUT_SIZE)
+*/
+LZ4LIB_API int LZ4_compressBound(int inputSize);
+
+/*!
+LZ4_compress_fast() :
+    Same as LZ4_compress_default(), but allows to select an "acceleration" factor.
+    The larger the acceleration value, the faster the algorithm, but also the lesser the compression.
+    It's a trade-off. It can be fine tuned, with each successive value providing roughly +~3% to speed.
+    An acceleration value of "1" is the same as regular LZ4_compress_default()
+    Values <= 0 will be replaced by ACCELERATION_DEFAULT (see lz4.c), which is 1.
+*/
+LZ4LIB_API int LZ4_compress_fast (const char* source, char* dest, int sourceSize, int maxDestSize, int acceleration);
+
+
+/*!
+LZ4_compress_fast_extState() :
+    Same compression function, just using an externally allocated memory space to store compression state.
+    Use LZ4_sizeofState() to know how much memory must be allocated,
+    and allocate it on 8-bytes boundaries (using malloc() typically).
+    Then, provide it as 'void* state' to compression function.
+*/
+LZ4LIB_API int LZ4_sizeofState(void);
+LZ4LIB_API int LZ4_compress_fast_extState (void* state, const char* source, char* dest, int inputSize, int maxDestSize, int acceleration);
+
+
+/*!
+LZ4_compress_destSize() :
+    Reverse the logic, by compressing as much data as possible from 'source' buffer
+    into already allocated buffer 'dest' of size 'targetDestSize'.
+    This function either compresses the entire 'source' content into 'dest' if it's large enough,
+    or fill 'dest' buffer completely with as much data as possible from 'source'.
+        *sourceSizePtr : will be modified to indicate how many bytes where read from 'source' to fill 'dest'.
+                         New value is necessarily <= old value.
+        return : Nb bytes written into 'dest' (necessarily <= targetDestSize)
+              or 0 if compression fails
+*/
+LZ4LIB_API int LZ4_compress_destSize (const char* source, char* dest, int* sourceSizePtr, int targetDestSize);
+
+
+/*!
+LZ4_decompress_fast() :
+    originalSize : is the original and therefore uncompressed size
+    return : the number of bytes read from the source buffer (in other words, the compressed size)
+             If the source stream is detected malformed, the function will stop decoding and return a negative result.
+             Destination buffer must be already allocated. Its size must be a minimum of 'originalSize' bytes.
+    note : This function fully respect memory boundaries for properly formed compressed data.
+           It is a bit faster than LZ4_decompress_safe().
+           However, it does not provide any protection against intentionally modified data stream (malicious input).
+           Use this function in trusted environment only (data to decode comes from a trusted source).
+*/
+LZ4LIB_API int LZ4_decompress_fast (const char* source, char* dest, int originalSize);
+
+/*!
+LZ4_decompress_safe_partial() :
+    This function decompress a compressed block of size 'compressedSize' at position 'source'
+    into destination buffer 'dest' of size 'maxDecompressedSize'.
+    The function tries to stop decompressing operation as soon as 'targetOutputSize' has been reached,
+    reducing decompression time.
+    return : the number of bytes decoded in the destination buffer (necessarily <= maxDecompressedSize)
+       Note : this number can be < 'targetOutputSize' should the compressed block to decode be smaller.
+             Always control how many bytes were decoded.
+             If the source stream is detected malformed, the function will stop decoding and return a negative result.
+             This function never writes outside of output buffer, and never reads outside of input buffer. It is therefore protected against malicious data packets
+*/
+LZ4LIB_API int LZ4_decompress_safe_partial (const char* source, char* dest, int compressedSize, int targetOutputSize, int maxDecompressedSize);
+
+
+/*-*********************************************
+*  Streaming Compression Functions
+***********************************************/
+typedef union LZ4_stream_u LZ4_stream_t;   /* incomplete type (defined later) */
+
+/*! LZ4_createStream() and LZ4_freeStream() :
+ *  LZ4_createStream() will allocate and initialize an `LZ4_stream_t` structure.
+ *  LZ4_freeStream() releases its memory.
+ */
+LZ4LIB_API LZ4_stream_t* LZ4_createStream(void);
+LZ4LIB_API int           LZ4_freeStream (LZ4_stream_t* streamPtr);
+
+/*! LZ4_resetStream() :
+ *  An LZ4_stream_t structure can be allocated once and re-used multiple times.
+ *  Use this function to init an allocated `LZ4_stream_t` structure and start a new compression.
+ */
+LZ4LIB_API void LZ4_resetStream (LZ4_stream_t* streamPtr);
+
+/*! LZ4_loadDict() :
+ *  Use this function to load a static dictionary into LZ4_stream.
+ *  Any previous data will be forgotten, only 'dictionary' will remain in memory.
+ *  Loading a size of 0 is allowed.
+ *  Return : dictionary size, in bytes (necessarily <= 64 KB)
+ */
+LZ4LIB_API int LZ4_loadDict (LZ4_stream_t* streamPtr, const char* dictionary, int dictSize);
+
+/*! LZ4_compress_fast_continue() :
+ *  Compress buffer content 'src', using data from previously compressed blocks as dictionary to improve compression ratio.
+ *  Important : Previous data blocks are assumed to remain present and unmodified !
+ *  'dst' buffer must be already allocated.
+ *  If dstCapacity >= LZ4_compressBound(srcSize), compression is guaranteed to succeed, and runs faster.
+ *  If not, and if compressed data cannot fit into 'dst' buffer size, compression stops, and function @return==0.
+ *  After an error, the stream status is invalid, it can only be reset or freed.
+ */
+LZ4LIB_API int LZ4_compress_fast_continue (LZ4_stream_t* streamPtr, const char* src, char* dst, int srcSize, int dstCapacity, int acceleration);
+
+/*! LZ4_saveDict() :
+ *  If previously compressed data block is not guaranteed to remain available at its current memory location,
+ *  save it into a safer place (char* safeBuffer).
+ *  Note : it's not necessary to call LZ4_loadDict() after LZ4_saveDict(), dictionary is immediately usable.
+ *  @return : saved dictionary size in bytes (necessarily <= dictSize), or 0 if error.
+ */
+LZ4LIB_API int LZ4_saveDict (LZ4_stream_t* streamPtr, char* safeBuffer, int dictSize);
+
+
+/*-**********************************************
+*  Streaming Decompression Functions
+*  Bufferless synchronous API
+************************************************/
+typedef union LZ4_streamDecode_u LZ4_streamDecode_t;   /* incomplete type (defined later) */
+
+/*! LZ4_createStreamDecode() and LZ4_freeStreamDecode() :
+ *  creation / destruction of streaming decompression tracking structure */
+LZ4LIB_API LZ4_streamDecode_t* LZ4_createStreamDecode(void);
+LZ4LIB_API int                 LZ4_freeStreamDecode (LZ4_streamDecode_t* LZ4_stream);
+
+/*! LZ4_setStreamDecode() :
+ *  Use this function to instruct where to find the dictionary.
+ *  Setting a size of 0 is allowed (same effect as reset).
+ *  @return : 1 if OK, 0 if error
+ */
+LZ4LIB_API int LZ4_setStreamDecode (LZ4_streamDecode_t* LZ4_streamDecode, const char* dictionary, int dictSize);
+
+/*! LZ4_decompress_*_continue() :
+ *  These decoding functions allow decompression of multiple blocks in "streaming" mode.
+ *  Previously decoded blocks *must* remain available at the memory position where they were decoded (up to 64 KB)
+ *  In the case of a ring buffers, decoding buffer must be either :
+ *  - Exactly same size as encoding buffer, with same update rule (block boundaries at same positions)
+ *    In which case, the decoding & encoding ring buffer can have any size, including very small ones ( < 64 KB).
+ *  - Larger than encoding buffer, by a minimum of maxBlockSize more bytes.
+ *    maxBlockSize is implementation dependent. It's the maximum size you intend to compress into a single block.
+ *    In which case, encoding and decoding buffers do not need to be synchronized,
+ *    and encoding ring buffer can have any size, including small ones ( < 64 KB).
+ *  - _At least_ 64 KB + 8 bytes + maxBlockSize.
+ *    In which case, encoding and decoding buffers do not need to be synchronized,
+ *    and encoding ring buffer can have any size, including larger than decoding buffer.
+ *  Whenever these conditions are not possible, save the last 64KB of decoded data into a safe buffer,
+ *  and indicate where it is saved using LZ4_setStreamDecode()
+*/
+LZ4LIB_API int LZ4_decompress_safe_continue (LZ4_streamDecode_t* LZ4_streamDecode, const char* source, char* dest, int compressedSize, int maxDecompressedSize);
+LZ4LIB_API int LZ4_decompress_fast_continue (LZ4_streamDecode_t* LZ4_streamDecode, const char* source, char* dest, int originalSize);
+
+
+/*! LZ4_decompress_*_usingDict() :
+ *  These decoding functions work the same as
+ *  a combination of LZ4_setStreamDecode() followed by LZ4_decompress_*_continue()
+ *  They are stand-alone, and don't need an LZ4_streamDecode_t structure.
+ */
+LZ4LIB_API int LZ4_decompress_safe_usingDict (const char* source, char* dest, int compressedSize, int maxDecompressedSize, const char* dictStart, int dictSize);
+LZ4LIB_API int LZ4_decompress_fast_usingDict (const char* source, char* dest, int originalSize, const char* dictStart, int dictSize);
+
+
+/*^**********************************************
+ * !!!!!!   STATIC LINKING ONLY   !!!!!!
+ ***********************************************/
+/*-************************************
+ *  Private definitions
+ **************************************
+ * Do not use these definitions.
+ * They are exposed to allow static allocation of `LZ4_stream_t` and `LZ4_streamDecode_t`.
+ * Using these definitions will expose code to API and/or ABI break in future versions of the library.
+ **************************************/
+#define LZ4_HASHLOG   (LZ4_MEMORY_USAGE-2)
+#define LZ4_HASHTABLESIZE (1 << LZ4_MEMORY_USAGE)
+#define LZ4_HASH_SIZE_U32 (1 << LZ4_HASHLOG)       /* required as macro for static allocation */
+
+#if defined(__cplusplus) || (defined (__STDC_VERSION__) && (__STDC_VERSION__ >= 199901L) /* C99 */)
+#include <stdint.h>
+
+typedef struct {
+    uint32_t hashTable[LZ4_HASH_SIZE_U32];
+    uint32_t currentOffset;
+    uint32_t initCheck;
+    const uint8_t* dictionary;
+    uint8_t* bufferStart;   /* obsolete, used for slideInputBuffer */
+    uint32_t dictSize;
+} LZ4_stream_t_internal;
+
+typedef struct {
+    const uint8_t* externalDict;
+    size_t extDictSize;
+    const uint8_t* prefixEnd;
+    size_t prefixSize;
+} LZ4_streamDecode_t_internal;
+
+#else
+
+typedef struct {
+    unsigned int hashTable[LZ4_HASH_SIZE_U32];
+    unsigned int currentOffset;
+    unsigned int initCheck;
+    const unsigned char* dictionary;
+    unsigned char* bufferStart;   /* obsolete, used for slideInputBuffer */
+    unsigned int dictSize;
+} LZ4_stream_t_internal;
+
+typedef struct {
+    const unsigned char* externalDict;
+    size_t extDictSize;
+    const unsigned char* prefixEnd;
+    size_t prefixSize;
+} LZ4_streamDecode_t_internal;
+
+#endif
+
+/*!
+ * LZ4_stream_t :
+ * information structure to track an LZ4 stream.
+ * init this structure before first use.
+ * note : only use in association with static linking !
+ *        this definition is not API/ABI safe,
+ *        it may change in a future version !
+ */
+#define LZ4_STREAMSIZE_U64 ((1 << (LZ4_MEMORY_USAGE-3)) + 4)
+#define LZ4_STREAMSIZE     (LZ4_STREAMSIZE_U64 * sizeof(unsigned long long))
+union LZ4_stream_u {
+    unsigned long long table[LZ4_STREAMSIZE_U64];
+    LZ4_stream_t_internal internal_donotuse;
+} ;  /* previously typedef'd to LZ4_stream_t */
+
+
+/*!
+ * LZ4_streamDecode_t :
+ * information structure to track an LZ4 stream during decompression.
+ * init this structure  using LZ4_setStreamDecode (or memset()) before first use
+ * note : only use in association with static linking !
+ *        this definition is not API/ABI safe,
+ *        and may change in a future version !
+ */
+#define LZ4_STREAMDECODESIZE_U64  4
+#define LZ4_STREAMDECODESIZE     (LZ4_STREAMDECODESIZE_U64 * sizeof(unsigned long long))
+union LZ4_streamDecode_u {
+    unsigned long long table[LZ4_STREAMDECODESIZE_U64];
+    LZ4_streamDecode_t_internal internal_donotuse;
+} ;   /* previously typedef'd to LZ4_streamDecode_t */
+
+
+/*-************************************
+*  Obsolete Functions
+**************************************/
+
+/*! Deprecation warnings
+   Should deprecation warnings be a problem,
+   it is generally possible to disable them,
+   typically with -Wno-deprecated-declarations for gcc
+   or _CRT_SECURE_NO_WARNINGS in Visual.
+   Otherwise, it's also possible to define LZ4_DISABLE_DEPRECATE_WARNINGS */
+#ifdef LZ4_DISABLE_DEPRECATE_WARNINGS
+#  define LZ4_DEPRECATED(message)   /* disable deprecation warnings */
+#else
+#  define LZ4_GCC_VERSION (__GNUC__ * 100 + __GNUC_MINOR__)
+#  if defined (__cplusplus) && (__cplusplus >= 201402) /* C++14 or greater */
+#    define LZ4_DEPRECATED(message) [[deprecated(message)]]
+#  elif (LZ4_GCC_VERSION >= 405) || defined(__clang__)
+#    define LZ4_DEPRECATED(message) __attribute__((deprecated(message)))
+#  elif (LZ4_GCC_VERSION >= 301)
+#    define LZ4_DEPRECATED(message) __attribute__((deprecated))
+#  elif defined(_MSC_VER)
+#    define LZ4_DEPRECATED(message) __declspec(deprecated(message))
+#  else
+#    pragma message("WARNING: You need to implement LZ4_DEPRECATED for this compiler")
+#    define LZ4_DEPRECATED(message)
+#  endif
+#endif /* LZ4_DISABLE_DEPRECATE_WARNINGS */
+
+/* Obsolete compression functions */
+LZ4LIB_API LZ4_DEPRECATED("use LZ4_compress_default() instead") int LZ4_compress               (const char* source, char* dest, int sourceSize);
+LZ4LIB_API LZ4_DEPRECATED("use LZ4_compress_default() instead") int LZ4_compress_limitedOutput (const char* source, char* dest, int sourceSize, int maxOutputSize);
+LZ4LIB_API LZ4_DEPRECATED("use LZ4_compress_fast_extState() instead") int LZ4_compress_withState               (void* state, const char* source, char* dest, int inputSize);
+LZ4LIB_API LZ4_DEPRECATED("use LZ4_compress_fast_extState() instead") int LZ4_compress_limitedOutput_withState (void* state, const char* source, char* dest, int inputSize, int maxOutputSize);
+LZ4LIB_API LZ4_DEPRECATED("use LZ4_compress_fast_continue() instead") int LZ4_compress_continue                (LZ4_stream_t* LZ4_streamPtr, const char* source, char* dest, int inputSize);
+LZ4LIB_API LZ4_DEPRECATED("use LZ4_compress_fast_continue() instead") int LZ4_compress_limitedOutput_continue  (LZ4_stream_t* LZ4_streamPtr, const char* source, char* dest, int inputSize, int maxOutputSize);
+
+/* Obsolete decompression functions */
+LZ4LIB_API LZ4_DEPRECATED("use LZ4_decompress_fast() instead") int LZ4_uncompress (const char* source, char* dest, int outputSize);
+LZ4LIB_API LZ4_DEPRECATED("use LZ4_decompress_safe() instead") int LZ4_uncompress_unknownOutputSize (const char* source, char* dest, int isize, int maxOutputSize);
+
+/* Obsolete streaming functions; use new streaming interface whenever possible */
+LZ4LIB_API LZ4_DEPRECATED("use LZ4_createStream() instead") void* LZ4_create (char* inputBuffer);
+LZ4LIB_API LZ4_DEPRECATED("use LZ4_createStream() instead") int   LZ4_sizeofStreamState(void);
+LZ4LIB_API LZ4_DEPRECATED("use LZ4_resetStream() instead")  int   LZ4_resetStreamState(void* state, char* inputBuffer);
+LZ4LIB_API LZ4_DEPRECATED("use LZ4_saveDict() instead")     char* LZ4_slideInputBuffer (void* state);
+
+/* Obsolete streaming decoding functions */
+LZ4LIB_API LZ4_DEPRECATED("use LZ4_decompress_safe_usingDict() instead") int LZ4_decompress_safe_withPrefix64k (const char* src, char* dst, int compressedSize, int maxDstSize);
+LZ4LIB_API LZ4_DEPRECATED("use LZ4_decompress_fast_usingDict() instead") int LZ4_decompress_fast_withPrefix64k (const char* src, char* dst, int originalSize);
+
+#endif /* LZ4_H_2983827168210 */
+
+
+#if defined (__cplusplus)
+}
+#endif
diff --git a/samtools/padding.c b/samtools/padding.c
new file mode 100644
index 0000000..11b098e
--- /dev/null
+++ b/samtools/padding.c
@@ -0,0 +1,623 @@
+/*  padding.c -- depad subcommand.
+
+    Copyright (C) 2011, 2012 Broad Institute.
+    Copyright (C) 2014-2016, 2019-2020 Genome Research Ltd.
+    Portions copyright (C) 2012, 2013 Peter Cock, The James Hutton Institute.
+
+    Author: Heng Li <lh3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <config.h>
+
+#include <string.h>
+#include <assert.h>
+#include <unistd.h>
+#include <inttypes.h>
+#include <htslib/kstring.h>
+#include <htslib/sam.h>
+#include <htslib/faidx.h>
+#include "sam_opts.h"
+#include "samtools.h"
+
+#define bam_reg2bin(b,e) hts_reg2bin((b),(e), 14, 5)
+
+static int replace_cigar(bam1_t *b, uint32_t n, uint32_t *cigar)
+{
+    int diff = 0;
+    if (n != b->core.n_cigar) {
+        int o = b->core.l_qname + b->core.n_cigar * 4;
+        if (n > b->core.n_cigar) {
+            diff = (n - b->core.n_cigar) * 4;
+            if ((INT_MAX - b->l_data)/4 < (n - b->core.n_cigar)) {
+                fprintf(stderr, "[depad] ERROR: BAM record too big\n");
+                return -1;
+            }
+            if (b->l_data + diff > b->m_data) {
+                b->m_data = b->l_data + diff;
+                kroundup32(b->m_data);
+                uint8_t *tmp = (uint8_t*)realloc(b->data, b->m_data);
+                if (!tmp) {
+                    fprintf(stderr, "[depad] ERROR: Memory allocation failure.\n");
+                    return -1;
+                }
+                b->data = tmp;
+            }
+        } else {
+            diff = -(int)((b->core.n_cigar - n) * 4);
+        }
+        memmove(b->data + b->core.l_qname + n * 4, b->data + o, b->l_data - o);
+        b->core.n_cigar = n;
+    }
+
+    memcpy(b->data + b->core.l_qname, cigar, n * 4);
+    b->l_data += diff;
+
+    return 0;
+}
+
+#define write_cigar(_c, _n, _m, _v) do { \
+        if (_n == _m) { \
+            _m = _m? _m<<1 : 4; \
+            _c = (uint32_t*)realloc(_c, _m * 4); \
+            if (!(_c)) { \
+                fprintf(stderr, "[depad] ERROR: Memory allocation failure.\n"); \
+                return -1; \
+            } \
+        } \
+        _c[_n++] = (_v); \
+    } while (0)
+
+static int unpad_seq(bam1_t *b, kstring_t *s)
+{
+    // Returns 0 on success, -1 on an error
+    int k, j, i;
+    int length;
+    int cigar_n_warning = 0; /* Make this a global and limit to one CIGAR N warning? */
+    uint32_t *cigar = bam_get_cigar(b);
+    uint8_t *seq = bam_get_seq(b);
+
+    // b->core.l_qseq gives length of the SEQ entry (including soft clips, S)
+    // We need the padded length after alignment from the CIGAR (excluding
+    // soft clips S, but including pads from CIGAR D operations)
+    length = bam_cigar2rlen(b->core.n_cigar, cigar);
+    ks_resize(s, length);
+    for (k = 0, s->l = 0, j = 0; k < b->core.n_cigar; ++k) {
+        int op, ol;
+        op = bam_cigar_op(cigar[k]);
+        ol = bam_cigar_oplen(cigar[k]);
+        if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) {
+            for (i = 0; i < ol; ++i, ++j) s->s[s->l++] = bam_seqi(seq, j);
+        } else if (op == BAM_CSOFT_CLIP) {
+            j += ol;
+        } else if (op == BAM_CHARD_CLIP) {
+            /* do nothing */
+        } else if (op == BAM_CDEL) {
+            for (i = 0; i < ol; ++i) s->s[s->l++] = 0;
+        } else if (op == BAM_CREF_SKIP) {
+            /* Treat CIGAR N as D (not ideal, but better than ignoring it) */
+            for (i = 0; i < ol; ++i) s->s[s->l++] = 0;
+            if (0 == cigar_n_warning) {
+                cigar_n_warning = -1;
+                fprintf(stderr, "[depad] WARNING: CIGAR op N treated as op D in read %s\n", bam_get_qname(b));
+            }
+        } else {
+            fprintf(stderr, "[depad] ERROR: Didn't expect CIGAR op %c in read %s\n", BAM_CIGAR_STR[op], bam_get_qname(b));
+            return -1;
+        }
+    }
+    return length != s->l;
+}
+
+int load_unpadded_ref(faidx_t *fai, const char *ref_name, hts_pos_t ref_len, kstring_t *seq)
+{
+    char base;
+    char *fai_ref = 0;
+    hts_pos_t fai_ref_len = 0, k;
+
+    fai_ref = fai_fetch64(fai, ref_name, &fai_ref_len);
+    if (fai_ref_len != ref_len) {
+        fprintf(stderr, "[depad] ERROR: FASTA sequence %s length %"PRIhts_pos", expected %"PRIhts_pos"\n", ref_name, fai_ref_len, ref_len);
+        free(fai_ref);
+        return -1;
+    }
+    ks_resize(seq, ref_len);
+    seq->l = 0;
+    for (k = 0; k < ref_len; ++k) {
+        base = fai_ref[k];
+        if (base == '-' || base == '*') {
+            // Map gaps to null to match unpad_seq function
+            seq->s[seq->l++] = 0;
+        } else {
+            int i = seq_nt16_table[(int)base];
+            if (i == 0 || i==16) { // Equals maps to 0, anything unexpected to 16
+                fprintf(stderr, "[depad] ERROR: Invalid character %c (ASCII %i) in FASTA sequence %s\n", base, (int)base, ref_name);
+                free(fai_ref);
+                return -1;
+            }
+            seq->s[seq->l++] = i;
+        }
+    }
+    assert(ref_len == seq->l);
+    free(fai_ref);
+    return 0;
+}
+
+hts_pos_t get_unpadded_len(faidx_t *fai, const char *ref_name, hts_pos_t padded_len)
+{
+    char base;
+    char *fai_ref = 0;
+    hts_pos_t fai_ref_len = 0, k;
+    hts_pos_t bases=0, gaps=0;
+
+    fai_ref = fai_fetch64(fai, ref_name, &fai_ref_len);
+    if (fai_ref_len != padded_len) {
+        fprintf(stderr, "[depad] ERROR: FASTA sequence '%s' length %"PRIhts_pos", expected %"PRIhts_pos"\n", ref_name, fai_ref_len, padded_len);
+        free(fai_ref);
+        return -1;
+    }
+    for (k = 0; k < padded_len; ++k) {
+        //fprintf(stderr, "[depad] checking base %i of %i or %i\n", k+1, ref_len, strlen(fai_ref));
+        base = fai_ref[k];
+        if (base == '-' || base == '*') {
+            gaps += 1;
+        } else {
+            int i = seq_nt16_table[(int)base];
+            if (i == 0 || i==16) { // Equals maps to 0, anything unexpected to 16
+                fprintf(stderr, "[depad] ERROR: Invalid character %c (ASCII %i) in FASTA sequence '%s'\n", base, (int)base, ref_name);
+                free(fai_ref);
+                return -1;
+            }
+            bases += 1;
+        }
+    }
+    free(fai_ref);
+    assert (padded_len == bases + gaps);
+    return bases;
+}
+
+static inline int * update_posmap(int *posmap, kstring_t ref)
+{
+    int i, k;
+    posmap = realloc(posmap, ref.m * sizeof(int));
+    for (i = k = 0; i < ref.l; ++i) {
+        posmap[i] = k;
+        if (ref.s[i]) ++k;
+    }
+    return posmap;
+}
+
+int bam_pad2unpad(samFile *in, samFile *out,  sam_hdr_t *h, faidx_t *fai)
+{
+    bam1_t *b = 0;
+    kstring_t r, q;
+    int r_tid = -1;
+    uint32_t *cigar2 = 0;
+    int ret = 0, *posmap = 0;
+    uint32_t n2 = 0, m2 = 0;
+
+    b = bam_init1();
+    if (!b) {
+        fprintf(stderr, "[depad] Couldn't allocate bam struct\n");
+        return -1;
+    }
+    r.l = r.m = q.l = q.m = 0; r.s = q.s = 0;
+    int read_ret;
+    while ((read_ret = sam_read1(in, h, b)) >= 0) { // read one alignment from `in'
+        // Cannot depad unmapped CRAM data
+        if (b->core.flag & BAM_FUNMAP)
+            goto next_seq;
+
+        uint32_t *cigar = bam_get_cigar(b);
+        n2 = 0;
+        if (b->core.pos == 0 && b->core.tid >= 0 && strcmp(bam_get_qname(b), sam_hdr_tid2name(h, b->core.tid)) == 0) {
+            // fprintf(stderr, "[depad] Found embedded reference '%s'\n", bam_get_qname(b));
+            r_tid = b->core.tid;
+            if (0!=unpad_seq(b, &r)) {
+                fprintf(stderr, "[depad] ERROR: Problem parsing SEQ and/or CIGAR in reference %s\n", bam_get_qname(b));
+                return -1;
+            };
+            if (sam_hdr_tid2len(h, r_tid) != r.l) {
+                fprintf(stderr, "[depad] ERROR: (Padded) length of '%s' is %"PRId64" in BAM header, but %zu in embedded reference\n", bam_get_qname(b), (int64_t) sam_hdr_tid2len(h, r_tid), r.l);
+                return -1;
+            }
+            if (fai) {
+                // Check the embedded reference matches the FASTA file
+                if (load_unpadded_ref(fai, sam_hdr_tid2name(h, b->core.tid), sam_hdr_tid2len(h, b->core.tid), &q)) {
+                    fprintf(stderr, "[depad] ERROR: Failed to load embedded reference '%s' from FASTA\n", sam_hdr_tid2name(h, b->core.tid));
+                    return -1;
+                }
+                assert(r.l == q.l);
+                int i;
+                for (i = 0; i < r.l; ++i) {
+                    if (r.s[i] != q.s[i]) {
+                        // Show gaps as ASCII 45
+                        fprintf(stderr, "[depad] ERROR: Embedded sequence and reference FASTA don't match for %s base %i, '%c' vs '%c'\n",
+                            sam_hdr_tid2name(h, b->core.tid), i+1,
+                            r.s[i] ? seq_nt16_str[(int)r.s[i]] : 45,
+                            q.s[i] ? seq_nt16_str[(int)q.s[i]] : 45);
+                        return -1;
+                    }
+                }
+            }
+            write_cigar(cigar2, n2, m2, bam_cigar_gen(b->core.l_qseq, BAM_CMATCH));
+            if (replace_cigar(b, n2, cigar2) < 0)
+                return -1;
+            posmap = update_posmap(posmap, r);
+        } else if (b->core.n_cigar > 0) {
+            int i, k, op;
+            if (b->core.tid < 0) {
+                fprintf(stderr, "[depad] ERROR: Read '%s' has CIGAR but no RNAME\n", bam_get_qname(b));
+                return -1;
+            } else if (b->core.tid == r_tid) {
+                ; // good case, reference available
+                //fprintf(stderr, "[depad] Have ref '%s' for read '%s'\n", h->target_name[b->core.tid], bam_get_qname(b));
+            } else if (fai) {
+                if (load_unpadded_ref(fai, sam_hdr_tid2name(h, b->core.tid), sam_hdr_tid2len(h, b->core.tid), &r)) {
+                    fprintf(stderr, "[depad] ERROR: Failed to load '%s' from reference FASTA\n", sam_hdr_tid2name(h, b->core.tid));
+                    return -1;
+                }
+                posmap = update_posmap(posmap, r);
+                r_tid = b->core.tid;
+                // fprintf(stderr, "[depad] Loaded %s from FASTA file\n", h->target_name[b->core.tid]);
+            } else {
+                fprintf(stderr, "[depad] ERROR: Missing %s embedded reference sequence (and no FASTA file)\n", sam_hdr_tid2name(h, b->core.tid));
+                return -1;
+            }
+            if (0!=unpad_seq(b, &q)) {
+                fprintf(stderr, "[depad] ERROR: Problem parsing SEQ and/or CIGAR in read %s\n", bam_get_qname(b));
+                return -1;
+            };
+            if (bam_cigar_op(cigar[0]) == BAM_CSOFT_CLIP) {
+                write_cigar(cigar2, n2, m2, cigar[0]);
+            } else if (bam_cigar_op(cigar[0]) == BAM_CHARD_CLIP) {
+                write_cigar(cigar2, n2, m2, cigar[0]);
+                if (b->core.n_cigar > 2 && bam_cigar_op(cigar[1]) == BAM_CSOFT_CLIP) {
+                    write_cigar(cigar2, n2, m2, cigar[1]);
+                }
+            }
+            /* Determine CIGAR operator for each base in the aligned read */
+            for (i = 0, k = b->core.pos; i < q.l; ++i, ++k)
+                q.s[i] = q.s[i]? (r.s[k]? BAM_CMATCH : BAM_CINS) : (r.s[k]? BAM_CDEL : BAM_CPAD);
+            /* Include any pads if starts with an insert */
+            if (q.s[0] == BAM_CINS) {
+                for (k = 0; k+1 < b->core.pos && !r.s[b->core.pos - k - 1]; ++k);
+                if (k) write_cigar(cigar2, n2, m2, bam_cigar_gen(k, BAM_CPAD));
+                k = 0;
+            } else if (q.s[0] == BAM_CPAD) {
+                // Join 'k' CPAD to our first cigar op CPAD too.
+                for (k = 0; k+1 < b->core.pos && !r.s[b->core.pos - k - 1]; ++k);
+            } else {
+                k = 0;
+            }
+            /* Count consecutive CIGAR operators to turn into a CIGAR string */
+            for (i = 1, k++, op = q.s[0]; i < q.l; ++i) {
+                if (op != q.s[i]) {
+                    write_cigar(cigar2, n2, m2, bam_cigar_gen(k, op));
+                    op = q.s[i]; k = 1;
+                } else ++k;
+            }
+            write_cigar(cigar2, n2, m2, bam_cigar_gen(k, op));
+            if (bam_cigar_op(cigar[b->core.n_cigar-1]) == BAM_CSOFT_CLIP) {
+                write_cigar(cigar2, n2, m2, cigar[b->core.n_cigar-1]);
+            } else if (bam_cigar_op(cigar[b->core.n_cigar-1]) == BAM_CHARD_CLIP) {
+                if (b->core.n_cigar > 2 && bam_cigar_op(cigar[b->core.n_cigar-2]) == BAM_CSOFT_CLIP) {
+                    write_cigar(cigar2, n2, m2, cigar[b->core.n_cigar-2]);
+                }
+                write_cigar(cigar2, n2, m2, cigar[b->core.n_cigar-1]);
+            }
+            /* Remove redundant P operators between M/X/=/D operators, e.g. 5M2P10M -> 15M */
+            int pre_op, post_op;
+            for (i = 2; i < n2; ++i)
+                if (bam_cigar_op(cigar2[i-1]) == BAM_CPAD) {
+                    pre_op = bam_cigar_op(cigar2[i-2]);
+                    post_op = bam_cigar_op(cigar2[i]);
+                    /* Note don't need to check for X/= as code above will use M only */
+                    if ((pre_op == BAM_CMATCH || pre_op == BAM_CDEL) && (post_op == BAM_CMATCH || post_op == BAM_CDEL)) {
+                        /* This is a redundant P operator */
+                        cigar2[i-1] = 0; // i.e. 0M
+                        /* If had same operator either side, combine them in post_op */
+                        if (pre_op == post_op) {
+                            /* If CIGAR M, could treat as simple integers since BAM_CMATCH is zero*/
+                            cigar2[i] = bam_cigar_gen(bam_cigar_oplen(cigar2[i-2]) + bam_cigar_oplen(cigar2[i]), post_op);
+                            cigar2[i-2] = 0; // i.e. 0M
+                        }
+                    }
+                }
+            /* Remove the zero'd operators (0M) */
+            for (i = k = 0; i < n2; ++i)
+                if (cigar2[i]) cigar2[k++] = cigar2[i];
+            n2 = k;
+            if (replace_cigar(b, n2, cigar2) < 0)
+                return -1;
+        }
+        /* Even unmapped reads can have a POS value, e.g. if their mate was mapped */
+        if (b->core.pos != -1) b->core.pos = posmap[b->core.pos];
+        if (b->core.mtid < 0 || b->core.mpos < 0) {
+            /* Nice case, no mate to worry about*/
+            // fprintf(stderr, "[depad] Read '%s' mate not mapped\n", bam_get_qname(b));
+            /* TODO - Warning if FLAG says mate should be mapped? */
+            /* Clean up funny input where mate position is given but mate reference is missing: */
+            b->core.mtid = -1;
+            b->core.mpos = -1;
+        } else if (b->core.mtid == b->core.tid) {
+            /* Nice case, same reference */
+            // fprintf(stderr, "[depad] Read '%s' mate mapped to same ref\n", bam_get_qname(b));
+            b->core.mpos = posmap[b->core.mpos];
+        } else {
+            /* Nasty case, Must load alternative posmap */
+            // fprintf(stderr, "[depad] Loading reference '%s' temporarily\n", h->target_name[b->core.mtid]);
+            if (!fai) {
+                fprintf(stderr, "[depad] ERROR: Needed reference %s sequence for mate (and no FASTA file)\n", sam_hdr_tid2name(h, b->core.mtid));
+                return -1;
+            }
+            /* Temporarily load the other reference sequence */
+            if (load_unpadded_ref(fai, sam_hdr_tid2name(h, b->core.mtid), sam_hdr_tid2len(h, b->core.mtid), &r)) {
+                fprintf(stderr, "[depad] ERROR: Failed to load '%s' from reference FASTA\n", sam_hdr_tid2name(h, b->core.mtid));
+                return -1;
+            }
+            posmap = update_posmap(posmap, r);
+            b->core.mpos = posmap[b->core.mpos];
+            /* Restore the reference and posmap*/
+            if (load_unpadded_ref(fai, sam_hdr_tid2name(h, b->core.tid), sam_hdr_tid2len(h, b->core.tid), &r)) {
+                fprintf(stderr, "[depad] ERROR: Failed to load '%s' from reference FASTA\n", sam_hdr_tid2name(h, b->core.tid));
+                return -1;
+            }
+            posmap = update_posmap(posmap, r);
+        }
+        /* Most reads will have been moved so safest to always recalculate the BIN value */
+        b->core.bin = bam_reg2bin(b->core.pos, bam_endpos(b));
+
+    next_seq:
+        if (sam_write1(out, h, b) < 0) {
+            print_error_errno("depad", "error writing to output");
+            return -1;
+        }
+    }
+    if (read_ret < -1) {
+        fprintf(stderr, "[depad] truncated file.\n");
+        ret = 1;
+    }
+    free(r.s); free(q.s); free(posmap);
+    free(cigar2);
+    bam_destroy1(b);
+    return ret;
+}
+
+sam_hdr_t * fix_header(sam_hdr_t *old, faidx_t *fai)
+{
+    int i = 0, ret = 0;
+    hts_pos_t unpadded_len = 0;
+    sam_hdr_t *header = sam_hdr_dup(old);
+    if (!header)
+        return NULL;
+
+    int nref = sam_hdr_nref(old);
+    char len_buf[64];
+
+    for (i = 0; i < nref; ++i) {
+        unpadded_len = get_unpadded_len(fai, sam_hdr_tid2name(old, i), sam_hdr_tid2len(old, i));
+        if (unpadded_len < 0) {
+            fprintf(stderr, "[depad] ERROR getting unpadded length of '%s', padded length %"PRIhts_pos"\n", sam_hdr_tid2name(old, i), (hts_pos_t) sam_hdr_tid2len(old, i));
+        } else if (unpadded_len > sam_hdr_tid2len(old, i)) {
+            fprintf(stderr, "[depad] New unpadded length of '%s' is larger than the padded length (%"PRIhts_pos" > %"PRIhts_pos")\n",
+                    sam_hdr_tid2name(old, i), unpadded_len,
+                    (hts_pos_t) sam_hdr_tid2len(old, i));
+            ret = 1;
+        } else {
+            sprintf(len_buf, "%"PRIhts_pos"", unpadded_len);
+            if ((ret |= sam_hdr_update_line(header, "SQ", "SN", sam_hdr_tid2name(header, i), "LN", len_buf, NULL)))
+                fprintf(stderr, "[depad] Error updating length of '%s' from %"PRIhts_pos" to %"PRIhts_pos"\n",
+                        sam_hdr_tid2name(header, i),
+                        (hts_pos_t) sam_hdr_tid2len(header, i),
+                        unpadded_len);
+            //fprintf(stderr, "[depad] Recalculating '%s' length %i -> %i\n", old->target_name[i], old->target_len[i], header->target_len[i]);
+        }
+    }
+
+    if (ret) {
+        sam_hdr_destroy(header);
+        return NULL;
+    }
+
+    return header;
+}
+
+static int usage(int is_long_help);
+
+int main_pad2unpad(int argc, char *argv[])
+{
+    samFile *in = 0, *out = 0;
+    sam_hdr_t *h = 0, *h_fix = 0;
+    faidx_t *fai = 0;
+    int c, compress_level = -1, is_long_help = 0, no_pg = 0;
+    char in_mode[5], out_mode[6], *fn_out = 0, *fn_fai = 0, *fn_out_idx = NULL;
+    int ret=0;
+    char *arg_list = NULL;
+    sam_global_args ga = SAM_GLOBAL_ARGS_INIT;
+
+    static const struct option lopts[] = {
+        SAM_OPT_GLOBAL_OPTIONS('-', 0, 0, 0, 'T', '-'),
+        {"no-PG", no_argument, NULL, 1},
+        { NULL, 0, NULL, 0 }
+    };
+
+    /* parse command-line options */
+    strcpy(in_mode, "r"); strcpy(out_mode, "w");
+    while ((c = getopt_long(argc, argv, "SCso:u1T:?", lopts, NULL)) >= 0) {
+        switch (c) {
+        case 'S': break;
+        case 'C': hts_parse_format(&ga.out, "cram"); break;
+        case 's': assert(compress_level == -1); hts_parse_format(&ga.out, "sam"); break;
+        case 'o': fn_out = strdup(optarg); break;
+        case 'u':
+            compress_level = 0;
+            if (ga.out.format == unknown_format)
+                hts_parse_format(&ga.out, "bam");
+            break;
+        case '1':
+            compress_level = 1;
+            if (ga.out.format == unknown_format)
+                hts_parse_format(&ga.out, "bam");
+            break;
+        case 1: no_pg = 1; break;
+        case '?': is_long_help = 1; break;
+        default:  if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break;
+            fprintf(stderr, "[bam_fillmd] unrecognized option '-%c'\n\n", c);
+            return usage(is_long_help);
+        }
+    }
+    if (argc == optind) return usage(is_long_help);
+
+    strcat(out_mode, "h");
+    if (compress_level >= 0) {
+        char tmp[2];
+        tmp[0] = compress_level + '0'; tmp[1] = '\0';
+        strcat(out_mode, tmp);
+    }
+
+    // Load FASTA reference (also needed for SAM -> BAM if missing header)
+    if (ga.reference) {
+        fn_fai = fai_path(ga.reference);
+        fai = fai_load3(ga.reference, fn_fai, NULL, FAI_CREATE);
+    }
+    // open file handlers
+    if ((in = sam_open_format(argv[optind], in_mode, &ga.in)) == 0) {
+        print_error_errno("depad", "failed to open \"%s\" for reading", argv[optind]);
+        ret = 1;
+        goto depad_end;
+    }
+    if (fn_fai && hts_set_fai_filename(in, fn_fai) != 0) {
+        fprintf(stderr, "[depad] failed to load reference file \"%s\".\n", fn_fai);
+        ret = 1;
+        goto depad_end;
+    }
+    if ((h = sam_hdr_read(in)) == 0) {
+        fprintf(stderr, "[depad] failed to read the header from \"%s\".\n", argv[optind]);
+        ret = 1;
+        goto depad_end;
+    }
+    if (fai) {
+        if (!(h_fix = fix_header(h, fai))){
+            fprintf(stderr, "[depad] failed to fix the header from\n");
+            ret = 1;
+            goto depad_end;
+        }
+    } else {
+        fprintf(stderr, "[depad] Warning - reference lengths will not be corrected without FASTA reference\n");
+        h_fix = h;
+    }
+    char wmode[2];
+    strcat(out_mode, sam_open_mode(wmode, fn_out, NULL)==0 ? wmode : "b");
+    if ((out = sam_open_format(fn_out? fn_out : "-", out_mode, &ga.out)) == 0) {
+        print_error_errno("depad", "failed to open \"%s\" for writing", fn_out? fn_out : "standard output");
+        ret = 1;
+        goto depad_end;
+    }
+
+    // Reference-based CRAM won't work unless we also create a new reference.
+    // We could embed this, but for now we take the easy option.
+    if (ga.out.format == cram)
+        hts_set_opt(out, CRAM_OPT_NO_REF, 1);
+
+    if (!no_pg) {
+        if(!(arg_list = stringify_argv(argc+1, argv-1))) {
+            fprintf(stderr, "[depad] failed to create arg_list\n");
+            ret = 1;
+            goto depad_end;
+            }
+
+        if (sam_hdr_add_pg(h_fix, "samtools",
+                           "VN", samtools_version(),
+                           arg_list ? "CL": NULL,
+                           arg_list ? arg_list : NULL,
+                           NULL)) {
+            fprintf(stderr, "[depad] failed to add PG line to header\n");
+            ret = 1;
+            goto depad_end;
+        }
+    }
+
+    if (sam_hdr_write(out, h_fix) != 0) {
+        fprintf(stderr, "[depad] failed to write header.\n");
+        ret = 1;
+        goto depad_end;
+    }
+    if (ga.write_index) {
+        if (!(fn_out_idx = auto_index(out, fn_out, h_fix))) {
+            ret = 1;
+            goto depad_end;
+        }
+    }
+
+    // Do the depad
+    if (bam_pad2unpad(in, out, h, fai) != 0) ret = 1;
+
+    if (ga.write_index) {
+        if (sam_idx_save(out) < 0) {
+            print_error_errno("depad", "writing index failed");
+            ret = 1;
+        }
+    }
+
+depad_end:
+    // close files, free and return
+    free(arg_list);
+    if (fai) fai_destroy(fai);
+    if (h) sam_hdr_destroy(h);
+    if (h_fix && h_fix != h) sam_hdr_destroy(h_fix);
+    if (in) sam_close(in);
+    if (out && sam_close(out) < 0) {
+        fprintf(stderr, "[depad] error on closing output file.\n");
+        ret = 1;
+    }
+    free(fn_fai); free(fn_out);
+    if (fn_out_idx)
+        free(fn_out_idx);
+    sam_global_args_free(&ga);
+    return ret;
+}
+
+static int usage(int is_long_help)
+{
+    fprintf(stderr, "\n");
+    fprintf(stderr, "Usage:   samtools depad <in.bam>\n\n");
+    fprintf(stderr, "Options:\n");
+    fprintf(stderr, "  -s           Output is SAM (default is BAM)\n");
+    fprintf(stderr, "  -S           Input is SAM (default is BAM)\n");
+    fprintf(stderr, "  -u           Uncompressed BAM output (can't use with -s)\n");
+    fprintf(stderr, "  -1           Fast compression BAM output (can't use with -s)\n");
+    fprintf(stderr, "  -T, --reference FILE\n");
+    fprintf(stderr, "               Padded reference sequence file [null]\n");
+    fprintf(stderr, "  -o FILE      Output file name [stdout]\n");
+    fprintf(stderr, "  --no-PG      do not add a PG line\n");
+    fprintf(stderr, "  -?           Longer help\n");
+    sam_global_opt_help(stderr, "-...--..");
+
+    if (is_long_help)
+        fprintf(stderr,
+"Notes:\n"
+"\n"
+"1. Requires embedded reference sequences (before the reads for that reference),\n"
+"   or ideally a FASTA file of the padded reference sequences (via a -T option).\n"
+"\n"
+"2. Input padded alignment reads' CIGAR strings must not use P or I operators.\n"
+"\n");
+    return 1;
+}
diff --git a/samtools/padding.c.pysam.c b/samtools/padding.c.pysam.c
new file mode 100644
index 0000000..e90255f
--- /dev/null
+++ b/samtools/padding.c.pysam.c
@@ -0,0 +1,625 @@
+#include "samtools.pysam.h"
+
+/*  padding.c -- depad subcommand.
+
+    Copyright (C) 2011, 2012 Broad Institute.
+    Copyright (C) 2014-2016, 2019-2020 Genome Research Ltd.
+    Portions copyright (C) 2012, 2013 Peter Cock, The James Hutton Institute.
+
+    Author: Heng Li <lh3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <config.h>
+
+#include <string.h>
+#include <assert.h>
+#include <unistd.h>
+#include <inttypes.h>
+#include <htslib/kstring.h>
+#include <htslib/sam.h>
+#include <htslib/faidx.h>
+#include "sam_opts.h"
+#include "samtools.h"
+
+#define bam_reg2bin(b,e) hts_reg2bin((b),(e), 14, 5)
+
+static int replace_cigar(bam1_t *b, uint32_t n, uint32_t *cigar)
+{
+    int diff = 0;
+    if (n != b->core.n_cigar) {
+        int o = b->core.l_qname + b->core.n_cigar * 4;
+        if (n > b->core.n_cigar) {
+            diff = (n - b->core.n_cigar) * 4;
+            if ((INT_MAX - b->l_data)/4 < (n - b->core.n_cigar)) {
+                fprintf(samtools_stderr, "[depad] ERROR: BAM record too big\n");
+                return -1;
+            }
+            if (b->l_data + diff > b->m_data) {
+                b->m_data = b->l_data + diff;
+                kroundup32(b->m_data);
+                uint8_t *tmp = (uint8_t*)realloc(b->data, b->m_data);
+                if (!tmp) {
+                    fprintf(samtools_stderr, "[depad] ERROR: Memory allocation failure.\n");
+                    return -1;
+                }
+                b->data = tmp;
+            }
+        } else {
+            diff = -(int)((b->core.n_cigar - n) * 4);
+        }
+        memmove(b->data + b->core.l_qname + n * 4, b->data + o, b->l_data - o);
+        b->core.n_cigar = n;
+    }
+
+    memcpy(b->data + b->core.l_qname, cigar, n * 4);
+    b->l_data += diff;
+
+    return 0;
+}
+
+#define write_cigar(_c, _n, _m, _v) do { \
+        if (_n == _m) { \
+            _m = _m? _m<<1 : 4; \
+            _c = (uint32_t*)realloc(_c, _m * 4); \
+            if (!(_c)) { \
+                fprintf(samtools_stderr, "[depad] ERROR: Memory allocation failure.\n"); \
+                return -1; \
+            } \
+        } \
+        _c[_n++] = (_v); \
+    } while (0)
+
+static int unpad_seq(bam1_t *b, kstring_t *s)
+{
+    // Returns 0 on success, -1 on an error
+    int k, j, i;
+    int length;
+    int cigar_n_warning = 0; /* Make this a global and limit to one CIGAR N warning? */
+    uint32_t *cigar = bam_get_cigar(b);
+    uint8_t *seq = bam_get_seq(b);
+
+    // b->core.l_qseq gives length of the SEQ entry (including soft clips, S)
+    // We need the padded length after alignment from the CIGAR (excluding
+    // soft clips S, but including pads from CIGAR D operations)
+    length = bam_cigar2rlen(b->core.n_cigar, cigar);
+    ks_resize(s, length);
+    for (k = 0, s->l = 0, j = 0; k < b->core.n_cigar; ++k) {
+        int op, ol;
+        op = bam_cigar_op(cigar[k]);
+        ol = bam_cigar_oplen(cigar[k]);
+        if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) {
+            for (i = 0; i < ol; ++i, ++j) s->s[s->l++] = bam_seqi(seq, j);
+        } else if (op == BAM_CSOFT_CLIP) {
+            j += ol;
+        } else if (op == BAM_CHARD_CLIP) {
+            /* do nothing */
+        } else if (op == BAM_CDEL) {
+            for (i = 0; i < ol; ++i) s->s[s->l++] = 0;
+        } else if (op == BAM_CREF_SKIP) {
+            /* Treat CIGAR N as D (not ideal, but better than ignoring it) */
+            for (i = 0; i < ol; ++i) s->s[s->l++] = 0;
+            if (0 == cigar_n_warning) {
+                cigar_n_warning = -1;
+                fprintf(samtools_stderr, "[depad] WARNING: CIGAR op N treated as op D in read %s\n", bam_get_qname(b));
+            }
+        } else {
+            fprintf(samtools_stderr, "[depad] ERROR: Didn't expect CIGAR op %c in read %s\n", BAM_CIGAR_STR[op], bam_get_qname(b));
+            return -1;
+        }
+    }
+    return length != s->l;
+}
+
+int load_unpadded_ref(faidx_t *fai, const char *ref_name, hts_pos_t ref_len, kstring_t *seq)
+{
+    char base;
+    char *fai_ref = 0;
+    hts_pos_t fai_ref_len = 0, k;
+
+    fai_ref = fai_fetch64(fai, ref_name, &fai_ref_len);
+    if (fai_ref_len != ref_len) {
+        fprintf(samtools_stderr, "[depad] ERROR: FASTA sequence %s length %"PRIhts_pos", expected %"PRIhts_pos"\n", ref_name, fai_ref_len, ref_len);
+        free(fai_ref);
+        return -1;
+    }
+    ks_resize(seq, ref_len);
+    seq->l = 0;
+    for (k = 0; k < ref_len; ++k) {
+        base = fai_ref[k];
+        if (base == '-' || base == '*') {
+            // Map gaps to null to match unpad_seq function
+            seq->s[seq->l++] = 0;
+        } else {
+            int i = seq_nt16_table[(int)base];
+            if (i == 0 || i==16) { // Equals maps to 0, anything unexpected to 16
+                fprintf(samtools_stderr, "[depad] ERROR: Invalid character %c (ASCII %i) in FASTA sequence %s\n", base, (int)base, ref_name);
+                free(fai_ref);
+                return -1;
+            }
+            seq->s[seq->l++] = i;
+        }
+    }
+    assert(ref_len == seq->l);
+    free(fai_ref);
+    return 0;
+}
+
+hts_pos_t get_unpadded_len(faidx_t *fai, const char *ref_name, hts_pos_t padded_len)
+{
+    char base;
+    char *fai_ref = 0;
+    hts_pos_t fai_ref_len = 0, k;
+    hts_pos_t bases=0, gaps=0;
+
+    fai_ref = fai_fetch64(fai, ref_name, &fai_ref_len);
+    if (fai_ref_len != padded_len) {
+        fprintf(samtools_stderr, "[depad] ERROR: FASTA sequence '%s' length %"PRIhts_pos", expected %"PRIhts_pos"\n", ref_name, fai_ref_len, padded_len);
+        free(fai_ref);
+        return -1;
+    }
+    for (k = 0; k < padded_len; ++k) {
+        //fprintf(samtools_stderr, "[depad] checking base %i of %i or %i\n", k+1, ref_len, strlen(fai_ref));
+        base = fai_ref[k];
+        if (base == '-' || base == '*') {
+            gaps += 1;
+        } else {
+            int i = seq_nt16_table[(int)base];
+            if (i == 0 || i==16) { // Equals maps to 0, anything unexpected to 16
+                fprintf(samtools_stderr, "[depad] ERROR: Invalid character %c (ASCII %i) in FASTA sequence '%s'\n", base, (int)base, ref_name);
+                free(fai_ref);
+                return -1;
+            }
+            bases += 1;
+        }
+    }
+    free(fai_ref);
+    assert (padded_len == bases + gaps);
+    return bases;
+}
+
+static inline int * update_posmap(int *posmap, kstring_t ref)
+{
+    int i, k;
+    posmap = realloc(posmap, ref.m * sizeof(int));
+    for (i = k = 0; i < ref.l; ++i) {
+        posmap[i] = k;
+        if (ref.s[i]) ++k;
+    }
+    return posmap;
+}
+
+int bam_pad2unpad(samFile *in, samFile *out,  sam_hdr_t *h, faidx_t *fai)
+{
+    bam1_t *b = 0;
+    kstring_t r, q;
+    int r_tid = -1;
+    uint32_t *cigar2 = 0;
+    int ret = 0, *posmap = 0;
+    uint32_t n2 = 0, m2 = 0;
+
+    b = bam_init1();
+    if (!b) {
+        fprintf(samtools_stderr, "[depad] Couldn't allocate bam struct\n");
+        return -1;
+    }
+    r.l = r.m = q.l = q.m = 0; r.s = q.s = 0;
+    int read_ret;
+    while ((read_ret = sam_read1(in, h, b)) >= 0) { // read one alignment from `in'
+        // Cannot depad unmapped CRAM data
+        if (b->core.flag & BAM_FUNMAP)
+            goto next_seq;
+
+        uint32_t *cigar = bam_get_cigar(b);
+        n2 = 0;
+        if (b->core.pos == 0 && b->core.tid >= 0 && strcmp(bam_get_qname(b), sam_hdr_tid2name(h, b->core.tid)) == 0) {
+            // fprintf(samtools_stderr, "[depad] Found embedded reference '%s'\n", bam_get_qname(b));
+            r_tid = b->core.tid;
+            if (0!=unpad_seq(b, &r)) {
+                fprintf(samtools_stderr, "[depad] ERROR: Problem parsing SEQ and/or CIGAR in reference %s\n", bam_get_qname(b));
+                return -1;
+            };
+            if (sam_hdr_tid2len(h, r_tid) != r.l) {
+                fprintf(samtools_stderr, "[depad] ERROR: (Padded) length of '%s' is %"PRId64" in BAM header, but %zu in embedded reference\n", bam_get_qname(b), (int64_t) sam_hdr_tid2len(h, r_tid), r.l);
+                return -1;
+            }
+            if (fai) {
+                // Check the embedded reference matches the FASTA file
+                if (load_unpadded_ref(fai, sam_hdr_tid2name(h, b->core.tid), sam_hdr_tid2len(h, b->core.tid), &q)) {
+                    fprintf(samtools_stderr, "[depad] ERROR: Failed to load embedded reference '%s' from FASTA\n", sam_hdr_tid2name(h, b->core.tid));
+                    return -1;
+                }
+                assert(r.l == q.l);
+                int i;
+                for (i = 0; i < r.l; ++i) {
+                    if (r.s[i] != q.s[i]) {
+                        // Show gaps as ASCII 45
+                        fprintf(samtools_stderr, "[depad] ERROR: Embedded sequence and reference FASTA don't match for %s base %i, '%c' vs '%c'\n",
+                            sam_hdr_tid2name(h, b->core.tid), i+1,
+                            r.s[i] ? seq_nt16_str[(int)r.s[i]] : 45,
+                            q.s[i] ? seq_nt16_str[(int)q.s[i]] : 45);
+                        return -1;
+                    }
+                }
+            }
+            write_cigar(cigar2, n2, m2, bam_cigar_gen(b->core.l_qseq, BAM_CMATCH));
+            if (replace_cigar(b, n2, cigar2) < 0)
+                return -1;
+            posmap = update_posmap(posmap, r);
+        } else if (b->core.n_cigar > 0) {
+            int i, k, op;
+            if (b->core.tid < 0) {
+                fprintf(samtools_stderr, "[depad] ERROR: Read '%s' has CIGAR but no RNAME\n", bam_get_qname(b));
+                return -1;
+            } else if (b->core.tid == r_tid) {
+                ; // good case, reference available
+                //fprintf(samtools_stderr, "[depad] Have ref '%s' for read '%s'\n", h->target_name[b->core.tid], bam_get_qname(b));
+            } else if (fai) {
+                if (load_unpadded_ref(fai, sam_hdr_tid2name(h, b->core.tid), sam_hdr_tid2len(h, b->core.tid), &r)) {
+                    fprintf(samtools_stderr, "[depad] ERROR: Failed to load '%s' from reference FASTA\n", sam_hdr_tid2name(h, b->core.tid));
+                    return -1;
+                }
+                posmap = update_posmap(posmap, r);
+                r_tid = b->core.tid;
+                // fprintf(samtools_stderr, "[depad] Loaded %s from FASTA file\n", h->target_name[b->core.tid]);
+            } else {
+                fprintf(samtools_stderr, "[depad] ERROR: Missing %s embedded reference sequence (and no FASTA file)\n", sam_hdr_tid2name(h, b->core.tid));
+                return -1;
+            }
+            if (0!=unpad_seq(b, &q)) {
+                fprintf(samtools_stderr, "[depad] ERROR: Problem parsing SEQ and/or CIGAR in read %s\n", bam_get_qname(b));
+                return -1;
+            };
+            if (bam_cigar_op(cigar[0]) == BAM_CSOFT_CLIP) {
+                write_cigar(cigar2, n2, m2, cigar[0]);
+            } else if (bam_cigar_op(cigar[0]) == BAM_CHARD_CLIP) {
+                write_cigar(cigar2, n2, m2, cigar[0]);
+                if (b->core.n_cigar > 2 && bam_cigar_op(cigar[1]) == BAM_CSOFT_CLIP) {
+                    write_cigar(cigar2, n2, m2, cigar[1]);
+                }
+            }
+            /* Determine CIGAR operator for each base in the aligned read */
+            for (i = 0, k = b->core.pos; i < q.l; ++i, ++k)
+                q.s[i] = q.s[i]? (r.s[k]? BAM_CMATCH : BAM_CINS) : (r.s[k]? BAM_CDEL : BAM_CPAD);
+            /* Include any pads if starts with an insert */
+            if (q.s[0] == BAM_CINS) {
+                for (k = 0; k+1 < b->core.pos && !r.s[b->core.pos - k - 1]; ++k);
+                if (k) write_cigar(cigar2, n2, m2, bam_cigar_gen(k, BAM_CPAD));
+                k = 0;
+            } else if (q.s[0] == BAM_CPAD) {
+                // Join 'k' CPAD to our first cigar op CPAD too.
+                for (k = 0; k+1 < b->core.pos && !r.s[b->core.pos - k - 1]; ++k);
+            } else {
+                k = 0;
+            }
+            /* Count consecutive CIGAR operators to turn into a CIGAR string */
+            for (i = 1, k++, op = q.s[0]; i < q.l; ++i) {
+                if (op != q.s[i]) {
+                    write_cigar(cigar2, n2, m2, bam_cigar_gen(k, op));
+                    op = q.s[i]; k = 1;
+                } else ++k;
+            }
+            write_cigar(cigar2, n2, m2, bam_cigar_gen(k, op));
+            if (bam_cigar_op(cigar[b->core.n_cigar-1]) == BAM_CSOFT_CLIP) {
+                write_cigar(cigar2, n2, m2, cigar[b->core.n_cigar-1]);
+            } else if (bam_cigar_op(cigar[b->core.n_cigar-1]) == BAM_CHARD_CLIP) {
+                if (b->core.n_cigar > 2 && bam_cigar_op(cigar[b->core.n_cigar-2]) == BAM_CSOFT_CLIP) {
+                    write_cigar(cigar2, n2, m2, cigar[b->core.n_cigar-2]);
+                }
+                write_cigar(cigar2, n2, m2, cigar[b->core.n_cigar-1]);
+            }
+            /* Remove redundant P operators between M/X/=/D operators, e.g. 5M2P10M -> 15M */
+            int pre_op, post_op;
+            for (i = 2; i < n2; ++i)
+                if (bam_cigar_op(cigar2[i-1]) == BAM_CPAD) {
+                    pre_op = bam_cigar_op(cigar2[i-2]);
+                    post_op = bam_cigar_op(cigar2[i]);
+                    /* Note don't need to check for X/= as code above will use M only */
+                    if ((pre_op == BAM_CMATCH || pre_op == BAM_CDEL) && (post_op == BAM_CMATCH || post_op == BAM_CDEL)) {
+                        /* This is a redundant P operator */
+                        cigar2[i-1] = 0; // i.e. 0M
+                        /* If had same operator either side, combine them in post_op */
+                        if (pre_op == post_op) {
+                            /* If CIGAR M, could treat as simple integers since BAM_CMATCH is zero*/
+                            cigar2[i] = bam_cigar_gen(bam_cigar_oplen(cigar2[i-2]) + bam_cigar_oplen(cigar2[i]), post_op);
+                            cigar2[i-2] = 0; // i.e. 0M
+                        }
+                    }
+                }
+            /* Remove the zero'd operators (0M) */
+            for (i = k = 0; i < n2; ++i)
+                if (cigar2[i]) cigar2[k++] = cigar2[i];
+            n2 = k;
+            if (replace_cigar(b, n2, cigar2) < 0)
+                return -1;
+        }
+        /* Even unmapped reads can have a POS value, e.g. if their mate was mapped */
+        if (b->core.pos != -1) b->core.pos = posmap[b->core.pos];
+        if (b->core.mtid < 0 || b->core.mpos < 0) {
+            /* Nice case, no mate to worry about*/
+            // fprintf(samtools_stderr, "[depad] Read '%s' mate not mapped\n", bam_get_qname(b));
+            /* TODO - Warning if FLAG says mate should be mapped? */
+            /* Clean up funny input where mate position is given but mate reference is missing: */
+            b->core.mtid = -1;
+            b->core.mpos = -1;
+        } else if (b->core.mtid == b->core.tid) {
+            /* Nice case, same reference */
+            // fprintf(samtools_stderr, "[depad] Read '%s' mate mapped to same ref\n", bam_get_qname(b));
+            b->core.mpos = posmap[b->core.mpos];
+        } else {
+            /* Nasty case, Must load alternative posmap */
+            // fprintf(samtools_stderr, "[depad] Loading reference '%s' temporarily\n", h->target_name[b->core.mtid]);
+            if (!fai) {
+                fprintf(samtools_stderr, "[depad] ERROR: Needed reference %s sequence for mate (and no FASTA file)\n", sam_hdr_tid2name(h, b->core.mtid));
+                return -1;
+            }
+            /* Temporarily load the other reference sequence */
+            if (load_unpadded_ref(fai, sam_hdr_tid2name(h, b->core.mtid), sam_hdr_tid2len(h, b->core.mtid), &r)) {
+                fprintf(samtools_stderr, "[depad] ERROR: Failed to load '%s' from reference FASTA\n", sam_hdr_tid2name(h, b->core.mtid));
+                return -1;
+            }
+            posmap = update_posmap(posmap, r);
+            b->core.mpos = posmap[b->core.mpos];
+            /* Restore the reference and posmap*/
+            if (load_unpadded_ref(fai, sam_hdr_tid2name(h, b->core.tid), sam_hdr_tid2len(h, b->core.tid), &r)) {
+                fprintf(samtools_stderr, "[depad] ERROR: Failed to load '%s' from reference FASTA\n", sam_hdr_tid2name(h, b->core.tid));
+                return -1;
+            }
+            posmap = update_posmap(posmap, r);
+        }
+        /* Most reads will have been moved so safest to always recalculate the BIN value */
+        b->core.bin = bam_reg2bin(b->core.pos, bam_endpos(b));
+
+    next_seq:
+        if (sam_write1(out, h, b) < 0) {
+            print_error_errno("depad", "error writing to output");
+            return -1;
+        }
+    }
+    if (read_ret < -1) {
+        fprintf(samtools_stderr, "[depad] truncated file.\n");
+        ret = 1;
+    }
+    free(r.s); free(q.s); free(posmap);
+    free(cigar2);
+    bam_destroy1(b);
+    return ret;
+}
+
+sam_hdr_t * fix_header(sam_hdr_t *old, faidx_t *fai)
+{
+    int i = 0, ret = 0;
+    hts_pos_t unpadded_len = 0;
+    sam_hdr_t *header = sam_hdr_dup(old);
+    if (!header)
+        return NULL;
+
+    int nref = sam_hdr_nref(old);
+    char len_buf[64];
+
+    for (i = 0; i < nref; ++i) {
+        unpadded_len = get_unpadded_len(fai, sam_hdr_tid2name(old, i), sam_hdr_tid2len(old, i));
+        if (unpadded_len < 0) {
+            fprintf(samtools_stderr, "[depad] ERROR getting unpadded length of '%s', padded length %"PRIhts_pos"\n", sam_hdr_tid2name(old, i), (hts_pos_t) sam_hdr_tid2len(old, i));
+        } else if (unpadded_len > sam_hdr_tid2len(old, i)) {
+            fprintf(samtools_stderr, "[depad] New unpadded length of '%s' is larger than the padded length (%"PRIhts_pos" > %"PRIhts_pos")\n",
+                    sam_hdr_tid2name(old, i), unpadded_len,
+                    (hts_pos_t) sam_hdr_tid2len(old, i));
+            ret = 1;
+        } else {
+            sprintf(len_buf, "%"PRIhts_pos"", unpadded_len);
+            if ((ret |= sam_hdr_update_line(header, "SQ", "SN", sam_hdr_tid2name(header, i), "LN", len_buf, NULL)))
+                fprintf(samtools_stderr, "[depad] Error updating length of '%s' from %"PRIhts_pos" to %"PRIhts_pos"\n",
+                        sam_hdr_tid2name(header, i),
+                        (hts_pos_t) sam_hdr_tid2len(header, i),
+                        unpadded_len);
+            //fprintf(samtools_stderr, "[depad] Recalculating '%s' length %i -> %i\n", old->target_name[i], old->target_len[i], header->target_len[i]);
+        }
+    }
+
+    if (ret) {
+        sam_hdr_destroy(header);
+        return NULL;
+    }
+
+    return header;
+}
+
+static int usage(int is_long_help);
+
+int main_pad2unpad(int argc, char *argv[])
+{
+    samFile *in = 0, *out = 0;
+    sam_hdr_t *h = 0, *h_fix = 0;
+    faidx_t *fai = 0;
+    int c, compress_level = -1, is_long_help = 0, no_pg = 0;
+    char in_mode[5], out_mode[6], *fn_out = 0, *fn_fai = 0, *fn_out_idx = NULL;
+    int ret=0;
+    char *arg_list = NULL;
+    sam_global_args ga = SAM_GLOBAL_ARGS_INIT;
+
+    static const struct option lopts[] = {
+        SAM_OPT_GLOBAL_OPTIONS('-', 0, 0, 0, 'T', '-'),
+        {"no-PG", no_argument, NULL, 1},
+        { NULL, 0, NULL, 0 }
+    };
+
+    /* parse command-line options */
+    strcpy(in_mode, "r"); strcpy(out_mode, "w");
+    while ((c = getopt_long(argc, argv, "SCso:u1T:?", lopts, NULL)) >= 0) {
+        switch (c) {
+        case 'S': break;
+        case 'C': hts_parse_format(&ga.out, "cram"); break;
+        case 's': assert(compress_level == -1); hts_parse_format(&ga.out, "sam"); break;
+        case 'o': fn_out = strdup(optarg); break;
+        case 'u':
+            compress_level = 0;
+            if (ga.out.format == unknown_format)
+                hts_parse_format(&ga.out, "bam");
+            break;
+        case '1':
+            compress_level = 1;
+            if (ga.out.format == unknown_format)
+                hts_parse_format(&ga.out, "bam");
+            break;
+        case 1: no_pg = 1; break;
+        case '?': is_long_help = 1; break;
+        default:  if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break;
+            fprintf(samtools_stderr, "[bam_fillmd] unrecognized option '-%c'\n\n", c);
+            return usage(is_long_help);
+        }
+    }
+    if (argc == optind) return usage(is_long_help);
+
+    strcat(out_mode, "h");
+    if (compress_level >= 0) {
+        char tmp[2];
+        tmp[0] = compress_level + '0'; tmp[1] = '\0';
+        strcat(out_mode, tmp);
+    }
+
+    // Load FASTA reference (also needed for SAM -> BAM if missing header)
+    if (ga.reference) {
+        fn_fai = fai_path(ga.reference);
+        fai = fai_load3(ga.reference, fn_fai, NULL, FAI_CREATE);
+    }
+    // open file handlers
+    if ((in = sam_open_format(argv[optind], in_mode, &ga.in)) == 0) {
+        print_error_errno("depad", "failed to open \"%s\" for reading", argv[optind]);
+        ret = 1;
+        goto depad_end;
+    }
+    if (fn_fai && hts_set_fai_filename(in, fn_fai) != 0) {
+        fprintf(samtools_stderr, "[depad] failed to load reference file \"%s\".\n", fn_fai);
+        ret = 1;
+        goto depad_end;
+    }
+    if ((h = sam_hdr_read(in)) == 0) {
+        fprintf(samtools_stderr, "[depad] failed to read the header from \"%s\".\n", argv[optind]);
+        ret = 1;
+        goto depad_end;
+    }
+    if (fai) {
+        if (!(h_fix = fix_header(h, fai))){
+            fprintf(samtools_stderr, "[depad] failed to fix the header from\n");
+            ret = 1;
+            goto depad_end;
+        }
+    } else {
+        fprintf(samtools_stderr, "[depad] Warning - reference lengths will not be corrected without FASTA reference\n");
+        h_fix = h;
+    }
+    char wmode[2];
+    strcat(out_mode, sam_open_mode(wmode, fn_out, NULL)==0 ? wmode : "b");
+    if ((out = sam_open_format(fn_out? fn_out : "-", out_mode, &ga.out)) == 0) {
+        print_error_errno("depad", "failed to open \"%s\" for writing", fn_out? fn_out : "standard output");
+        ret = 1;
+        goto depad_end;
+    }
+
+    // Reference-based CRAM won't work unless we also create a new reference.
+    // We could embed this, but for now we take the easy option.
+    if (ga.out.format == cram)
+        hts_set_opt(out, CRAM_OPT_NO_REF, 1);
+
+    if (!no_pg) {
+        if(!(arg_list = stringify_argv(argc+1, argv-1))) {
+            fprintf(samtools_stderr, "[depad] failed to create arg_list\n");
+            ret = 1;
+            goto depad_end;
+            }
+
+        if (sam_hdr_add_pg(h_fix, "samtools",
+                           "VN", samtools_version(),
+                           arg_list ? "CL": NULL,
+                           arg_list ? arg_list : NULL,
+                           NULL)) {
+            fprintf(samtools_stderr, "[depad] failed to add PG line to header\n");
+            ret = 1;
+            goto depad_end;
+        }
+    }
+
+    if (sam_hdr_write(out, h_fix) != 0) {
+        fprintf(samtools_stderr, "[depad] failed to write header.\n");
+        ret = 1;
+        goto depad_end;
+    }
+    if (ga.write_index) {
+        if (!(fn_out_idx = auto_index(out, fn_out, h_fix))) {
+            ret = 1;
+            goto depad_end;
+        }
+    }
+
+    // Do the depad
+    if (bam_pad2unpad(in, out, h, fai) != 0) ret = 1;
+
+    if (ga.write_index) {
+        if (sam_idx_save(out) < 0) {
+            print_error_errno("depad", "writing index failed");
+            ret = 1;
+        }
+    }
+
+depad_end:
+    // close files, free and return
+    free(arg_list);
+    if (fai) fai_destroy(fai);
+    if (h) sam_hdr_destroy(h);
+    if (h_fix && h_fix != h) sam_hdr_destroy(h_fix);
+    if (in) sam_close(in);
+    if (out && sam_close(out) < 0) {
+        fprintf(samtools_stderr, "[depad] error on closing output file.\n");
+        ret = 1;
+    }
+    free(fn_fai); free(fn_out);
+    if (fn_out_idx)
+        free(fn_out_idx);
+    sam_global_args_free(&ga);
+    return ret;
+}
+
+static int usage(int is_long_help)
+{
+    fprintf(samtools_stderr, "\n");
+    fprintf(samtools_stderr, "Usage:   samtools depad <in.bam>\n\n");
+    fprintf(samtools_stderr, "Options:\n");
+    fprintf(samtools_stderr, "  -s           Output is SAM (default is BAM)\n");
+    fprintf(samtools_stderr, "  -S           Input is SAM (default is BAM)\n");
+    fprintf(samtools_stderr, "  -u           Uncompressed BAM output (can't use with -s)\n");
+    fprintf(samtools_stderr, "  -1           Fast compression BAM output (can't use with -s)\n");
+    fprintf(samtools_stderr, "  -T, --reference FILE\n");
+    fprintf(samtools_stderr, "               Padded reference sequence file [null]\n");
+    fprintf(samtools_stderr, "  -o FILE      Output file name [samtools_stdout]\n");
+    fprintf(samtools_stderr, "  --no-PG      do not add a PG line\n");
+    fprintf(samtools_stderr, "  -?           Longer help\n");
+    sam_global_opt_help(samtools_stderr, "-...--..");
+
+    if (is_long_help)
+        fprintf(samtools_stderr,
+"Notes:\n"
+"\n"
+"1. Requires embedded reference sequences (before the reads for that reference),\n"
+"   or ideally a FASTA file of the padded reference sequences (via a -T option).\n"
+"\n"
+"2. Input padded alignment reads' CIGAR strings must not use P or I operators.\n"
+"\n");
+    return 1;
+}
diff --git a/samtools/phase.c b/samtools/phase.c
new file mode 100644
index 0000000..a4a7351
--- /dev/null
+++ b/samtools/phase.c
@@ -0,0 +1,823 @@
+/*  phase.c -- phase subcommand.
+
+    Copyright (C) 2011 Broad Institute.
+    Copyright (C) 2013-2016, 2019 Genome Research Ltd.
+
+    Author: Heng Li <lh3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <config.h>
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <unistd.h>
+#include <stdint.h>
+#include <math.h>
+#include <zlib.h>
+#include "htslib/hts.h"
+#include "htslib/sam.h"
+#include "htslib/kstring.h"
+#include "sam_opts.h"
+#include "samtools.h"
+#include "htslib/hts_os.h"
+
+#include "htslib/kseq.h"
+KSTREAM_INIT(gzFile, gzread, 16384)
+
+#define MAX_VARS 256
+#define FLIP_PENALTY 2
+#define FLIP_THRES 4
+#define MASK_THRES 3
+
+#define FLAG_FIX_CHIMERA 0x1
+#define FLAG_LIST_EXCL   0x4
+#define FLAG_DROP_AMBI   0x8
+
+typedef struct {
+    // configurations, initialized in the main function
+    int flag, k, min_baseQ, min_varLOD, max_depth, no_pg;
+    // other global variables
+    int vpos_shift;
+    samFile* fp;
+    sam_hdr_t* fp_hdr;
+    char *pre, *arg_list;
+    char *out_name[3];
+    samFile* out[3];
+    sam_hdr_t* out_hdr[3];
+    // alignment queue
+    int n, m;
+    bam1_t **b;
+} phaseg_t;
+
+typedef struct {
+    int8_t seq[MAX_VARS]; // TODO: change to dynamic memory allocation!
+    int vpos, beg, end;
+    uint32_t vlen:16, single:1, flip:1, phase:1, phased:1, ambig:1;
+    uint32_t in:16, out:16; // in-phase and out-phase
+} frag_t, *frag_p;
+
+#define rseq_lt(a,b) ((a)->vpos < (b)->vpos)
+
+#include "htslib/khash.h"
+KHASH_SET_INIT_INT64(set64)
+KHASH_MAP_INIT_INT64(64, frag_t)
+
+typedef khash_t(64) nseq_t;
+
+#include "htslib/ksort.h"
+KSORT_INIT(rseq, frag_p, rseq_lt)
+
+static inline uint64_t X31_hash_string(const char *s)
+{
+    uint64_t h = *s;
+    if (h) for (++s ; *s; ++s) h = (h << 5) - h + *s;
+    return h;
+}
+
+static void count1(int l, const uint8_t *seq, int *cnt)
+{
+    int i, j, n_ambi;
+    uint32_t z, x;
+    if (seq[l-1] == 0) return; // do nothing is the last base is ambiguous
+    for (i = n_ambi = 0; i < l; ++i) // collect ambiguous bases
+        if (seq[i] == 0) ++n_ambi;
+    if (l - n_ambi <= 1) return; // only one SNP
+    for (x = 0; x < 1u<<n_ambi; ++x) { // count
+        for (i = j = 0, z = 0; i < l; ++i) {
+            int c;
+            if (seq[i]) c = seq[i] - 1;
+            else {
+                c = x>>j&1;
+                ++j;
+            }
+            z = z<<1 | c;
+        }
+        ++cnt[z];
+    }
+}
+
+static int **count_all(int l, int vpos, nseq_t *hash)
+{
+    khint_t k;
+    int i, j, **cnt;
+    uint8_t *seq;
+    seq = calloc(l, 1);
+    cnt = calloc(vpos, sizeof(int*));
+    for (i = 0; i < vpos; ++i) cnt[i] = calloc(1<<l, sizeof(int));
+    for (k = 0; k < kh_end(hash); ++k) {
+        if (kh_exist(hash, k)) {
+            frag_t *f = &kh_val(hash, k);
+            if (f->vpos >= vpos || f->single) continue; // out of region; or singleton
+            if (f->vlen == 1) { // such reads should be flagged as deleted previously if everything is right
+                f->single = 1;
+                continue;
+            }
+            for (j = 1; j < f->vlen; ++j) {
+                for (i = 0; i < l; ++i)
+                    seq[i] = j < l - 1 - i? 0 : f->seq[j - (l - 1 - i)];
+                count1(l, seq, cnt[f->vpos + j]);
+            }
+        }
+    }
+    free(seq);
+    return cnt;
+}
+
+// phasing
+static int8_t *dynaprog(int l, int vpos, int **w)
+{
+    int *f[2], *curr, *prev, max, i;
+    int8_t **b, *h = 0;
+    uint32_t x, z = 1u<<(l-1), mask = (1u<<l) - 1;
+    f[0] = calloc(z, sizeof(int));
+    f[1] = calloc(z, sizeof(int));
+    b = calloc(vpos, sizeof(int8_t*));
+    prev = f[0]; curr = f[1];
+    // fill the backtrack matrix
+    for (i = 0; i < vpos; ++i) {
+        int *wi = w[i], *tmp;
+        int8_t *bi;
+        bi = b[i] = calloc(z, 1);
+        /* In the following, x is the current state, which is the
+         * lexicographically smaller local haplotype. xc is the complement of
+         * x, or the larger local haplotype; y0 and y1 are the two predecessors
+         * of x. */
+        for (x = 0; x < z; ++x) { // x0 is the smaller
+            uint32_t y0, y1, xc;
+            int c0, c1;
+            xc = ~x&mask; y0 = x>>1; y1 = xc>>1;
+            c0 = prev[y0] + wi[x] + wi[xc];
+            c1 = prev[y1] + wi[x] + wi[xc];
+            if (c0 > c1) bi[x] = 0, curr[x] = c0;
+            else bi[x] = 1, curr[x] = c1;
+        }
+        tmp = prev; prev = curr; curr = tmp; // swap
+    }
+    { // backtrack
+        uint32_t max_x = 0;
+        int which = 0;
+        h = calloc(vpos, 1);
+        for (x = 0, max = 0, max_x = 0; x < z; ++x)
+            if (prev[x] > max) max = prev[x], max_x = x;
+        for (i = vpos - 1, x = max_x; i >= 0; --i) {
+            h[i] = which? (~x&1) : (x&1);
+            which = b[i][x]? !which : which;
+            x = b[i][x]? (~x&mask)>>1 : x>>1;
+        }
+    }
+    // free
+    for (i = 0; i < vpos; ++i) free(b[i]);
+    free(f[0]); free(f[1]); free(b);
+    return h;
+}
+
+// phase each fragment
+static uint64_t *fragphase(int vpos, const int8_t *path, nseq_t *hash, int flip)
+{
+    khint_t k;
+    uint64_t *pcnt;
+    uint32_t *left, *rght, max;
+    left = rght = 0; max = 0;
+    pcnt = calloc(vpos, 8);
+    for (k = 0; k < kh_end(hash); ++k) {
+        if (kh_exist(hash, k)) {
+            int i, c[2];
+            frag_t *f = &kh_val(hash, k);
+            if (f->vpos >= vpos) continue;
+            // get the phase
+            c[0] = c[1] = 0;
+            for (i = 0; i < f->vlen; ++i) {
+                if (f->seq[i] == 0) continue;
+                ++c[f->seq[i] == path[f->vpos + i] + 1? 0 : 1];
+            }
+            f->phase = c[0] > c[1]? 0 : 1;
+            f->in = c[f->phase]; f->out = c[1 - f->phase];
+            f->phased = f->in == f->out? 0 : 1;
+            f->ambig = (f->in && f->out && f->out < 3 && f->in <= f->out + 1)? 1 : 0;
+            // fix chimera
+            f->flip = 0;
+            if (flip && c[0] >= 3 && c[1] >= 3) {
+                int sum[2], m, mi, md;
+                if (f->vlen > max) { // enlarge the array
+                    max = f->vlen;
+                    kroundup32(max);
+                    left = realloc(left, max * 4);
+                    rght = realloc(rght, max * 4);
+                }
+                for (i = 0, sum[0] = sum[1] = 0; i < f->vlen; ++i) { // get left counts
+                    if (f->seq[i]) {
+                        int c = f->phase? 2 - f->seq[i] : f->seq[i] - 1;
+                        ++sum[c == path[f->vpos + i]? 0 : 1];
+                    }
+                    left[i] = sum[1]<<16 | sum[0];
+                }
+                for (i = f->vlen - 1, sum[0] = sum[1] = 0; i >= 0; --i) { // get right counts
+                    if (f->seq[i]) {
+                        int c = f->phase? 2 - f->seq[i] : f->seq[i] - 1;
+                        ++sum[c == path[f->vpos + i]? 0 : 1];
+                    }
+                    rght[i] = sum[1]<<16 | sum[0];
+                }
+                // find the best flip point
+                for (i = m = 0, mi = -1, md = -1; i < f->vlen - 1; ++i) {
+                    int a[2];
+                    a[0] = (left[i]&0xffff) + (rght[i+1]>>16&0xffff) - (rght[i+1]&0xffff) * FLIP_PENALTY;
+                    a[1] = (left[i]>>16&0xffff) + (rght[i+1]&0xffff) - (rght[i+1]>>16&0xffff) * FLIP_PENALTY;
+                    if (a[0] > a[1]) {
+                        if (a[0] > m) m = a[0], md = 0, mi = i;
+                    } else {
+                        if (a[1] > m) m = a[1], md = 1, mi = i;
+                    }
+                }
+                if (m - c[0] >= FLIP_THRES && m - c[1] >= FLIP_THRES) { // then flip
+                    f->flip = 1;
+                    if (md == 0) { // flip the tail
+                        for (i = mi + 1; i < f->vlen; ++i)
+                            if (f->seq[i] == 1) f->seq[i] = 2;
+                            else if (f->seq[i] == 2) f->seq[i] = 1;
+                    } else { // flip the head
+                        for (i = 0; i <= mi; ++i)
+                            if (f->seq[i] == 1) f->seq[i] = 2;
+                            else if (f->seq[i] == 2) f->seq[i] = 1;
+                    }
+                }
+            }
+            // update pcnt[]
+            if (!f->single) {
+                for (i = 0; i < f->vlen; ++i) {
+                    int c;
+                    if (f->seq[i] == 0) continue;
+                    c = f->phase? 2 - f->seq[i] : f->seq[i] - 1;
+                    if (c == path[f->vpos + i]) {
+                        if (f->phase == 0) ++pcnt[f->vpos + i];
+                        else pcnt[f->vpos + i] += 1ull<<32;
+                    } else {
+                        if (f->phase == 0) pcnt[f->vpos + i] += 1<<16;
+                        else pcnt[f->vpos + i] += 1ull<<48;
+                    }
+                }
+            }
+        }
+    }
+    free(left); free(rght);
+    return pcnt;
+}
+
+static uint64_t *genmask(int vpos, const uint64_t *pcnt, int *_n)
+{
+    int i, max = 0, max_i = -1, m = 0, n = 0, beg = 0, score = 0;
+    uint64_t *list = 0;
+    for (i = 0; i < vpos; ++i) {
+        uint64_t x = pcnt[i];
+        int c[4], pre = score, s;
+        c[0] = x&0xffff; c[1] = x>>16&0xffff; c[2] = x>>32&0xffff; c[3] = x>>48&0xffff;
+        s = (c[1] + c[3] == 0)? -(c[0] + c[2]) : (c[1] + c[3] - 1);
+        if (c[3] > c[2]) s += c[3] - c[2];
+        if (c[1] > c[0]) s += c[1] - c[0];
+        score += s;
+        if (score < 0) score = 0;
+        if (pre == 0 && score > 0) beg = i; // change from zero to non-zero
+        if ((i == vpos - 1 || score == 0) && max >= MASK_THRES) {
+            if (n == m) {
+                m = m? m<<1 : 4;
+                list = realloc(list, m * 8);
+            }
+            list[n++] = (uint64_t)beg<<32 | max_i;
+            i = max_i; // reset i to max_i
+            score = 0;
+        } else if (score > max) max = score, max_i = i;
+        if (score == 0) max = 0;
+    }
+    *_n = n;
+    return list;
+}
+
+// trim heading and tailing ambiguous bases; mark deleted and remove sequence
+static int clean_seqs(int vpos, nseq_t *hash)
+{
+    khint_t k;
+    int ret = 0;
+    for (k = 0; k < kh_end(hash); ++k) {
+        if (kh_exist(hash, k)) {
+            frag_t *f = &kh_val(hash, k);
+            int beg, end, i;
+            if (f->vpos >= vpos) {
+                ret = 1;
+                continue;
+            }
+            for (i = 0; i < f->vlen; ++i)
+                if (f->seq[i] != 0) break;
+            beg = i;
+            for (i = f->vlen - 1; i >= 0; --i)
+                if (f->seq[i] != 0) break;
+            end = i + 1;
+            if (end - beg <= 0) kh_del(64, hash, k);
+            else {
+                if (beg != 0) memmove(f->seq, f->seq + beg, end - beg);
+                f->vpos += beg; f->vlen = end - beg;
+                f->single = f->vlen == 1? 1 : 0;
+            }
+        }
+    }
+    return ret;
+}
+
+static int dump_aln(phaseg_t *g, int min_pos, const nseq_t *hash)
+{
+    int i, is_flip, drop_ambi;
+    drop_ambi = g->flag & FLAG_DROP_AMBI;
+    is_flip = (drand48() < 0.5);
+    for (i = 0; i < g->n; ++i) {
+        int end, which;
+        uint64_t key;
+        khint_t k;
+        bam1_t *b = g->b[i];
+        key = X31_hash_string(bam_get_qname(b));
+        end = bam_endpos(b);
+        if (end > min_pos) break;
+        k = kh_get(64, hash, key);
+        if (k == kh_end(hash)) which = 3;
+        else {
+            frag_t *f = &kh_val(hash, k);
+            if (f->ambig) which = drop_ambi? 2 : 3;
+            else if (f->phased && f->flip) which = 2;
+            else if (f->phased == 0) which = 3;
+            else { // phased and not flipped
+                char c = 'Y';
+                which = f->phase;
+                bam_aux_append(b, "ZP", 'A', 1, (uint8_t*)&c);
+            }
+            if (which < 2 && is_flip) which = 1 - which; // increase the randomness
+        }
+        if (which == 3) which = (drand48() < 0.5);
+        if (sam_write1(g->out[which], g->out_hdr[which], b) < 0) {
+            print_error_errno("phase", "error writing to '%s'", g->out_name[which]);
+            return -1;
+        }
+        bam_destroy1(b);
+        g->b[i] = 0;
+    }
+    memmove(g->b, g->b + i, (g->n - i) * sizeof(void*));
+    g->n -= i;
+    return 0;
+}
+
+static int phase(phaseg_t *g, const char *chr, int vpos, uint64_t *cns, nseq_t *hash)
+{
+    int i, j, n_seqs = kh_size(hash), n_masked = 0, min_pos;
+    khint_t k;
+    frag_t **seqs;
+    int8_t *path, *sitemask;
+    uint64_t *pcnt, *regmask;
+
+    if (vpos == 0) return 0;
+    i = clean_seqs(vpos, hash); // i is true if hash has an element with its vpos >= vpos
+    min_pos = i? cns[vpos]>>32 : 0x7fffffff;
+    if (vpos == 1) {
+        printf("PS\t%s\t%d\t%d\n", chr, (int)(cns[0]>>32) + 1, (int)(cns[0]>>32) + 1);
+        printf("M0\t%s\t%d\t%d\t%c\t%c\t%d\t0\t0\t0\t0\n//\n", chr, (int)(cns[0]>>32) + 1, (int)(cns[0]>>32) + 1,
+            "ACGTX"[cns[0]&3], "ACGTX"[cns[0]>>16&3], g->vpos_shift + 1);
+        for (k = 0; k < kh_end(hash); ++k) {
+            if (kh_exist(hash, k)) {
+                frag_t *f = &kh_val(hash, k);
+                if (f->vpos) continue;
+                f->flip = 0;
+                if (f->seq[0] == 0) f->phased = 0;
+                else f->phased = 1, f->phase = f->seq[0] - 1;
+            }
+        }
+        if (dump_aln(g, min_pos, hash) < 0) return -1;
+        ++g->vpos_shift;
+        return 1;
+    }
+    { // phase
+        int **cnt;
+        uint64_t *mask;
+        printf("PS\t%s\t%d\t%d\n", chr, (int)(cns[0]>>32) + 1, (int)(cns[vpos-1]>>32) + 1);
+        sitemask = calloc(vpos, 1);
+        cnt = count_all(g->k, vpos, hash);
+        path = dynaprog(g->k, vpos, cnt);
+        for (i = 0; i < vpos; ++i) free(cnt[i]);
+        free(cnt);
+        pcnt = fragphase(vpos, path, hash, 0); // do not fix chimeras when masking
+        mask = genmask(vpos, pcnt, &n_masked);
+        regmask = calloc(n_masked, 8);
+        for (i = 0; i < n_masked; ++i) {
+            regmask[i] = cns[mask[i]>>32]>>32<<32 | cns[(uint32_t)mask[i]]>>32;
+            for (j = mask[i]>>32; j <= (int32_t)mask[i]; ++j)
+                sitemask[j] = 1;
+        }
+        free(mask);
+        if (g->flag & FLAG_FIX_CHIMERA) {
+            free(pcnt);
+            pcnt = fragphase(vpos, path, hash, 1);
+        }
+    }
+    for (i = 0; i < n_masked; ++i)
+        printf("FL\t%s\t%d\t%d\n", chr, (int)(regmask[i]>>32) + 1, (int)regmask[i] + 1);
+    for (i = 0; i < vpos; ++i) {
+        uint64_t x = pcnt[i];
+        int8_t c[2];
+        c[0] = (cns[i]&0xffff)>>2 == 0? 4 : (cns[i]&3);
+        c[1] = (cns[i]>>16&0xffff)>>2 == 0? 4 : (cns[i]>>16&3);
+        printf("M%d\t%s\t%d\t%d\t%c\t%c\t%d\t%d\t%d\t%d\t%d\n", sitemask[i]+1, chr, (int)(cns[0]>>32) + 1, (int)(cns[i]>>32) + 1, "ACGTX"[c[path[i]]], "ACGTX"[c[1-path[i]]],
+            i + g->vpos_shift + 1, (int)(x&0xffff), (int)(x>>16&0xffff), (int)(x>>32&0xffff), (int)(x>>48&0xffff));
+    }
+    free(path); free(pcnt); free(regmask); free(sitemask);
+    seqs = calloc(n_seqs, sizeof(frag_t*));
+    for (k = 0, i = 0; k < kh_end(hash); ++k)
+        if (kh_exist(hash, k) && kh_val(hash, k).vpos < vpos && !kh_val(hash, k).single)
+            seqs[i++] = &kh_val(hash, k);
+    n_seqs = i;
+    ks_introsort_rseq(n_seqs, seqs);
+    for (i = 0; i < n_seqs; ++i) {
+        frag_t *f = seqs[i];
+        printf("EV\t0\t%s\t%d\t40\t%dM\t*\t0\t0\t", chr, f->vpos + 1 + g->vpos_shift, f->vlen);
+        for (j = 0; j < f->vlen; ++j) {
+            uint32_t c = cns[f->vpos + j];
+            if (f->seq[j] == 0) putchar('N');
+            else putchar("ACGT"[f->seq[j] == 1? (c&3) : (c>>16&3)]);
+        }
+        printf("\t*\tYP:i:%d\tYF:i:%d\tYI:i:%d\tYO:i:%d\tYS:i:%d\n", f->phase, f->flip, f->in, f->out, f->beg+1);
+    }
+    free(seqs);
+    printf("//\n");
+    fflush(stdout);
+    g->vpos_shift += vpos;
+    if (dump_aln(g, min_pos, hash) < 0) return -1;
+    return vpos;
+}
+
+static void update_vpos(int vpos, nseq_t *hash)
+{
+    khint_t k;
+    for (k = 0; k < kh_end(hash); ++k) {
+        if (kh_exist(hash, k)) {
+            frag_t *f = &kh_val(hash, k);
+            if (f->vpos < vpos) kh_del(64, hash, k); // TODO: if frag_t::seq is allocated dynamically, free it
+            else f->vpos -= vpos;
+        }
+    }
+}
+
+static nseq_t *shrink_hash(nseq_t *hash) // TODO: to implement
+{
+    return hash;
+}
+
+static int readaln(void *data, bam1_t *b)
+{
+    phaseg_t *g = (phaseg_t*)data;
+    int ret;
+    while (1)
+    {
+        ret = sam_read1(g->fp, g->fp_hdr, b);
+        if (ret < 0) break;
+        if ( b->core.flag & (BAM_FUNMAP | BAM_FSECONDARY | BAM_FQCFAIL | BAM_FDUP) ) continue;
+        if ( g->pre ) {
+            if (g->n == g->m) {
+                g->m = g->m? g->m<<1 : 16;
+                g->b = realloc(g->b, g->m * sizeof(bam1_t*));
+            }
+            g->b[g->n++] = bam_dup1(b);
+        }
+        break;
+    }
+    return ret;
+}
+
+static khash_t(set64) *loadpos(const char *fn, sam_hdr_t *h)
+{
+    gzFile fp;
+    kstream_t *ks;
+    int ret, dret;
+    kstring_t *str;
+    khash_t(set64) *hash;
+
+    fp = strcmp(fn, "-")? gzopen(fn, "r") : gzdopen(fileno(stdin), "r");
+    if (fp == NULL) {
+        print_error_errno("phase", "Couldn't open site file '%s'", fn);
+        return NULL;
+    }
+
+    hash = kh_init(set64);
+    str = calloc(1, sizeof(kstring_t));
+
+    ks = ks_init(fp);
+    while (ks_getuntil(ks, 0, str, &dret) >= 0) {
+        int tid = bam_name2id(h, str->s);
+        if (tid >= 0 && dret != '\n') {
+            if (ks_getuntil(ks, 0, str, &dret) >= 0) {
+                uint64_t x = (uint64_t)tid<<32 | (atoi(str->s) - 1);
+                kh_put(set64, hash, x, &ret);
+            } else break;
+        }
+        if (dret != '\n') while ((dret = ks_getc(ks)) > 0 && dret != '\n');
+        if (dret < 0) break;
+    }
+    ks_destroy(ks);
+    gzclose(fp);
+    free(str->s); free(str);
+    return hash;
+}
+
+static int gl2cns(float q[16])
+{
+    int i, j, min_ij;
+    float min, min2;
+    min = min2 = 1e30; min_ij = -1;
+    for (i = 0; i < 4; ++i) {
+        for (j = i; j < 4; ++j) {
+            if (q[i<<2|j] < min) min_ij = i<<2|j, min2 = min, min = q[i<<2|j];
+            else if (q[i<<2|j] < min2) min2 = q[i<<2|j];
+        }
+    }
+    return (min_ij>>2&3) == (min_ij&3)? 0 : 1<<18 | (min_ij>>2&3)<<16 | (min_ij&3) | (int)(min2 - min + .499) << 2;
+}
+
+static int start_output(phaseg_t *g, int c, const char *middle, const htsFormat *fmt)
+{
+    kstring_t s = { 0, 0, NULL };
+    ksprintf(&s, "%s.%s.%s", g->pre, middle, hts_format_file_extension(fmt));
+    g->out_name[c] = ks_release(&s);
+    g->out[c] = sam_open_format(g->out_name[c], "wb", fmt);
+    if (! g->out[c]) {
+        print_error_errno("phase", "Failed to open output file '%s'", g->out_name[c]);
+        return -1;
+    }
+
+    g->out_hdr[c] = sam_hdr_dup(g->fp_hdr);
+    if (!g->no_pg && sam_hdr_add_pg(g->out_hdr[c], "samtools",
+                                    "VN", samtools_version(),
+                                    g->arg_list ? "CL": NULL,
+                                    g->arg_list ? g->arg_list : NULL,
+                                    NULL)) {
+        print_error("phase", "failed to add PG line to header");
+        return -1;
+    }
+    if (sam_hdr_write(g->out[c], g->out_hdr[c]) < 0) {
+        print_error_errno("phase", "Failed to write header for '%s'", g->out_name[c]);
+        return -1;
+    }
+
+    return 0;
+}
+
+int main_phase(int argc, char *argv[])
+{
+    int c, tid, pos, vpos = 0, n, lasttid = -1, max_vpos = 0, usage = 0;
+    int status = EXIT_SUCCESS;
+    const bam_pileup1_t *plp;
+    bam_plp_t iter;
+    nseq_t *seqs;
+    uint64_t *cns = 0;
+    phaseg_t g;
+    char *fn_list = 0;
+    khash_t(set64) *set = 0;
+    errmod_t *em;
+    uint16_t *bases;
+
+    sam_global_args ga = SAM_GLOBAL_ARGS_INIT;
+    static const struct option lopts[] = {
+        SAM_OPT_GLOBAL_OPTIONS('-', 0, 0, 0, 0, '-'),
+        {"min-BQ", required_argument, NULL, 'Q'},
+        {"min-bq", required_argument, NULL, 'Q'},
+        {"no-PG", no_argument, NULL, 1},
+        { NULL, 0, NULL, 0 }
+    };
+
+    // FIXME Leaks galore in the case of error returns
+
+    memset(&g, 0, sizeof(phaseg_t));
+    g.flag = FLAG_FIX_CHIMERA;
+    g.min_varLOD = 37; g.k = 13; g.min_baseQ = 13; g.max_depth = 256;
+    while ((c = getopt_long(argc, argv, "Q:eFq:k:b:l:D:A", lopts, NULL)) >= 0) {
+        switch (c) {
+            case 'D': g.max_depth = atoi(optarg); break;
+            case 'q': g.min_varLOD = atoi(optarg); break;
+            case 'Q': g.min_baseQ = atoi(optarg); break;
+            case 'k': g.k = atoi(optarg); break;
+            case 'F': g.flag &= ~FLAG_FIX_CHIMERA; break;
+            case 'e': g.flag |= FLAG_LIST_EXCL; break;
+            case 'A': g.flag |= FLAG_DROP_AMBI; break;
+            case 'b': g.pre = strdup(optarg); break;
+            case 'l': fn_list = strdup(optarg); break;
+            case 1: g.no_pg = 1; break;
+            default:  if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break;
+                      /* else fall-through */
+            case '?': usage=1; break;
+        }
+        if (usage) break;
+    }
+    if (usage || argc == optind) {
+        fprintf(stderr, "\n");
+        fprintf(stderr, "Usage:   samtools phase [options] <in.bam>\n\n");
+        fprintf(stderr, "Options: -k INT    block length [%d]\n", g.k);
+        fprintf(stderr, "         -b STR    prefix of BAMs to output [null]\n");
+        fprintf(stderr, "         -q INT    min het phred-LOD [%d]\n", g.min_varLOD);
+        fprintf(stderr, "         -Q, --min-BQ INT\n"
+                        "                   min base quality in het calling [%d]\n", g.min_baseQ);
+        fprintf(stderr, "         -D INT    max read depth [%d]\n", g.max_depth);
+//      fprintf(stderr, "         -l FILE   list of sites to phase [null]\n");
+        fprintf(stderr, "         -F        do not attempt to fix chimeras\n");
+        fprintf(stderr, "         -A        drop reads with ambiguous phase\n");
+        fprintf(stderr, "         --no-PG   do not add a PG line\n");
+//      fprintf(stderr, "         -e        do not discover SNPs (effective with -l)\n");
+        fprintf(stderr, "\n");
+
+        sam_global_opt_help(stderr, "-....--.");
+
+        return 1;
+    }
+    g.fp = sam_open_format(argv[optind], "r", &ga.in);
+    if (!g.fp) {
+        print_error_errno("phase", "Couldn't open '%s'", argv[optind]);
+        return 1;
+    }
+    g.fp_hdr = sam_hdr_read(g.fp);
+    if (g.fp_hdr == NULL) {
+        fprintf(stderr, "[%s] Failed to read header for '%s'\n",
+                __func__, argv[optind]);
+        return 1;
+    }
+    if (!g.no_pg && !(g.arg_list = stringify_argv(argc+1, argv-1))) {
+        print_error("phase", "failed to create arg_list");
+        return 1;
+    }
+    if (fn_list) { // read the list of sites to phase
+        set = loadpos(fn_list, g.fp_hdr);
+        if (set == NULL) return 1;
+        free(fn_list);
+    } else g.flag &= ~FLAG_LIST_EXCL;
+    if (g.pre) { // open BAMs to write
+        if (ga.out.format == unknown_format)
+            ga.out.format = bam; // default via "wb".
+
+        // Open each output file g.out[0..2], dupping and writing the header
+        if (start_output(&g, 0, "0", &ga.out) < 0 ||
+            start_output(&g, 1, "1", &ga.out) < 0 ||
+            start_output(&g, 2, "chimera", &ga.out) < 0) return 1;
+    }
+
+    iter = bam_plp_init(readaln, &g);
+    g.vpos_shift = 0;
+    seqs = kh_init(64);
+    em = errmod_init(1. - 0.83);
+    bases = calloc(g.max_depth, 2);
+    printf("CC\n");
+    printf("CC\tDescriptions:\nCC\n");
+    printf("CC\t  CC      comments\n");
+    printf("CC\t  PS      start of a phase set\n");
+    printf("CC\t  FL      filtered region\n");
+    printf("CC\t  M[012]  markers; 0 for singletons, 1 for phased and 2 for filtered\n");
+    printf("CC\t  EV      supporting reads; SAM format\n");
+    printf("CC\t  //      end of a phase set\nCC\n");
+    printf("CC\tFormats of PS, FL and M[012] lines (1-based coordinates):\nCC\n");
+    printf("CC\t  PS  chr  phaseSetStart  phaseSetEnd\n");
+    printf("CC\t  FL  chr  filterStart    filterEnd\n");
+    printf("CC\t  M?  chr  PS  pos  allele0  allele1  hetIndex  #supports0  #errors0  #supp1  #err1\n");
+    printf("CC\nCC\n");
+    fflush(stdout);
+    while ((plp = bam_plp_auto(iter, &tid, &pos, &n)) != 0) {
+        int i, k, c, tmp, dophase = 1, in_set = 0;
+        float q[16];
+        if (tid < 0) break;
+        if (tid != lasttid) { // change of chromosome
+            g.vpos_shift = 0;
+            if (lasttid >= 0) {
+                seqs = shrink_hash(seqs);
+                if (phase(&g, sam_hdr_tid2name(g.fp_hdr, lasttid),
+                          vpos, cns, seqs) < 0) {
+                    return 1;
+                }
+                update_vpos(0x7fffffff, seqs);
+            }
+            lasttid = tid;
+            vpos = 0;
+        }
+        if (set && kh_get(set64, set, (uint64_t)tid<<32 | pos) != kh_end(set)) in_set = 1;
+        if (n > g.max_depth) continue; // do not proceed if the depth is too high
+        // fill the bases array and check if there is a variant
+        for (i = k = 0; i < n; ++i) {
+            const bam_pileup1_t *p = plp + i;
+            uint8_t *seq;
+            int q, baseQ, b;
+            if (p->is_del || p->is_refskip) continue;
+            baseQ = bam_get_qual(p->b)[p->qpos];
+            if (baseQ < g.min_baseQ) continue;
+            seq = bam_get_seq(p->b);
+            b = seq_nt16_int[bam_seqi(seq, p->qpos)];
+            if (b > 3) continue;
+            q = baseQ < p->b->core.qual? baseQ : p->b->core.qual;
+            if (q < 4) q = 4;
+            if (q > 63) q = 63;
+            bases[k++] = q<<5 | (int)bam_is_rev(p->b)<<4 | b;
+        }
+        if (k == 0) continue;
+        errmod_cal(em, k, 4, bases, q); // compute genotype likelihood
+        c = gl2cns(q); // get the consensus
+        // tell if to proceed
+        if (set && (g.flag&FLAG_LIST_EXCL) && !in_set) continue; // not in the list
+        if (!in_set && (c&0xffff)>>2 < g.min_varLOD) continue; // not a variant
+        // add the variant
+        if (vpos == max_vpos) {
+            max_vpos = max_vpos? max_vpos<<1 : 128;
+            cns = realloc(cns, max_vpos * 8);
+        }
+        cns[vpos] = (uint64_t)pos<<32 | c;
+        for (i = 0; i < n; ++i) {
+            const bam_pileup1_t *p = plp + i;
+            uint64_t key;
+            khint_t k;
+            uint8_t *seq = bam_get_seq(p->b);
+            frag_t *f;
+            if (p->is_del || p->is_refskip) continue;
+            if (p->b->core.qual == 0) continue;
+            // get the base code
+            c = seq_nt16_int[bam_seqi(seq, p->qpos)];
+            if (c == (cns[vpos]&3)) c = 1;
+            else if (c == (cns[vpos]>>16&3)) c = 2;
+            else c = 0;
+            // write to seqs
+            key = X31_hash_string(bam_get_qname(p->b));
+            k = kh_put(64, seqs, key, &tmp);
+            f = &kh_val(seqs, k);
+            if (tmp == 0) { // present in the hash table
+                if (vpos - f->vpos + 1 < MAX_VARS) {
+                    f->vlen = vpos - f->vpos + 1;
+                    f->seq[f->vlen-1] = c;
+                    f->end = bam_endpos(p->b);
+                }
+                dophase = 0;
+            } else { // absent
+                memset(f->seq, 0, MAX_VARS);
+                f->beg = p->b->core.pos;
+                f->end = bam_endpos(p->b);
+                f->vpos = vpos, f->vlen = 1, f->seq[0] = c, f->single = f->phased = f->flip = f->ambig = 0;
+            }
+        }
+        if (dophase) {
+            seqs = shrink_hash(seqs);
+            if (phase(&g, sam_hdr_tid2name(g.fp_hdr, tid), vpos, cns, seqs) < 0) {
+                return 1;
+            }
+            update_vpos(vpos, seqs);
+            cns[0] = cns[vpos];
+            vpos = 0;
+        }
+        ++vpos;
+    }
+    if (tid >= 0) {
+        if (phase(&g, sam_hdr_tid2name(g.fp_hdr, tid), vpos, cns, seqs) < 0) {
+            return 1;
+        }
+    }
+
+    if (n < 0) {
+        print_error("phase", "error reading from '%s'", argv[optind]);
+        status = EXIT_FAILURE;
+    }
+
+    sam_hdr_destroy(g.fp_hdr);
+    bam_plp_destroy(iter);
+    sam_close(g.fp);
+    kh_destroy(64, seqs);
+    kh_destroy(set64, set);
+    free(cns);
+    errmod_destroy(em);
+    free(bases);
+    if (g.pre) {
+        int res = 0;
+        for (c = 0; c <= 2; ++c) {
+            if (sam_close(g.out[c]) < 0) {
+                fprintf(stderr, "[%s] error on closing '%s'\n",
+                        __func__, g.out_name[c]);
+                res = 1;
+            }
+            sam_hdr_destroy(g.out_hdr[c]);
+            free(g.out_name[c]);
+        }
+        free(g.pre); free(g.b);
+        if (res) return 1;
+    }
+    free(g.arg_list);
+    sam_global_args_free(&ga);
+    return status;
+}
diff --git a/samtools/phase.c.pysam.c b/samtools/phase.c.pysam.c
new file mode 100644
index 0000000..b0b5257
--- /dev/null
+++ b/samtools/phase.c.pysam.c
@@ -0,0 +1,825 @@
+#include "samtools.pysam.h"
+
+/*  phase.c -- phase subcommand.
+
+    Copyright (C) 2011 Broad Institute.
+    Copyright (C) 2013-2016, 2019 Genome Research Ltd.
+
+    Author: Heng Li <lh3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <config.h>
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <unistd.h>
+#include <stdint.h>
+#include <math.h>
+#include <zlib.h>
+#include "htslib/hts.h"
+#include "htslib/sam.h"
+#include "htslib/kstring.h"
+#include "sam_opts.h"
+#include "samtools.h"
+#include "htslib/hts_os.h"
+
+#include "htslib/kseq.h"
+KSTREAM_INIT(gzFile, gzread, 16384)
+
+#define MAX_VARS 256
+#define FLIP_PENALTY 2
+#define FLIP_THRES 4
+#define MASK_THRES 3
+
+#define FLAG_FIX_CHIMERA 0x1
+#define FLAG_LIST_EXCL   0x4
+#define FLAG_DROP_AMBI   0x8
+
+typedef struct {
+    // configurations, initialized in the main function
+    int flag, k, min_baseQ, min_varLOD, max_depth, no_pg;
+    // other global variables
+    int vpos_shift;
+    samFile* fp;
+    sam_hdr_t* fp_hdr;
+    char *pre, *arg_list;
+    char *out_name[3];
+    samFile* out[3];
+    sam_hdr_t* out_hdr[3];
+    // alignment queue
+    int n, m;
+    bam1_t **b;
+} phaseg_t;
+
+typedef struct {
+    int8_t seq[MAX_VARS]; // TODO: change to dynamic memory allocation!
+    int vpos, beg, end;
+    uint32_t vlen:16, single:1, flip:1, phase:1, phased:1, ambig:1;
+    uint32_t in:16, out:16; // in-phase and out-phase
+} frag_t, *frag_p;
+
+#define rseq_lt(a,b) ((a)->vpos < (b)->vpos)
+
+#include "htslib/khash.h"
+KHASH_SET_INIT_INT64(set64)
+KHASH_MAP_INIT_INT64(64, frag_t)
+
+typedef khash_t(64) nseq_t;
+
+#include "htslib/ksort.h"
+KSORT_INIT(rseq, frag_p, rseq_lt)
+
+static inline uint64_t X31_hash_string(const char *s)
+{
+    uint64_t h = *s;
+    if (h) for (++s ; *s; ++s) h = (h << 5) - h + *s;
+    return h;
+}
+
+static void count1(int l, const uint8_t *seq, int *cnt)
+{
+    int i, j, n_ambi;
+    uint32_t z, x;
+    if (seq[l-1] == 0) return; // do nothing is the last base is ambiguous
+    for (i = n_ambi = 0; i < l; ++i) // collect ambiguous bases
+        if (seq[i] == 0) ++n_ambi;
+    if (l - n_ambi <= 1) return; // only one SNP
+    for (x = 0; x < 1u<<n_ambi; ++x) { // count
+        for (i = j = 0, z = 0; i < l; ++i) {
+            int c;
+            if (seq[i]) c = seq[i] - 1;
+            else {
+                c = x>>j&1;
+                ++j;
+            }
+            z = z<<1 | c;
+        }
+        ++cnt[z];
+    }
+}
+
+static int **count_all(int l, int vpos, nseq_t *hash)
+{
+    khint_t k;
+    int i, j, **cnt;
+    uint8_t *seq;
+    seq = calloc(l, 1);
+    cnt = calloc(vpos, sizeof(int*));
+    for (i = 0; i < vpos; ++i) cnt[i] = calloc(1<<l, sizeof(int));
+    for (k = 0; k < kh_end(hash); ++k) {
+        if (kh_exist(hash, k)) {
+            frag_t *f = &kh_val(hash, k);
+            if (f->vpos >= vpos || f->single) continue; // out of region; or singleton
+            if (f->vlen == 1) { // such reads should be flagged as deleted previously if everything is right
+                f->single = 1;
+                continue;
+            }
+            for (j = 1; j < f->vlen; ++j) {
+                for (i = 0; i < l; ++i)
+                    seq[i] = j < l - 1 - i? 0 : f->seq[j - (l - 1 - i)];
+                count1(l, seq, cnt[f->vpos + j]);
+            }
+        }
+    }
+    free(seq);
+    return cnt;
+}
+
+// phasing
+static int8_t *dynaprog(int l, int vpos, int **w)
+{
+    int *f[2], *curr, *prev, max, i;
+    int8_t **b, *h = 0;
+    uint32_t x, z = 1u<<(l-1), mask = (1u<<l) - 1;
+    f[0] = calloc(z, sizeof(int));
+    f[1] = calloc(z, sizeof(int));
+    b = calloc(vpos, sizeof(int8_t*));
+    prev = f[0]; curr = f[1];
+    // fill the backtrack matrix
+    for (i = 0; i < vpos; ++i) {
+        int *wi = w[i], *tmp;
+        int8_t *bi;
+        bi = b[i] = calloc(z, 1);
+        /* In the following, x is the current state, which is the
+         * lexicographically smaller local haplotype. xc is the complement of
+         * x, or the larger local haplotype; y0 and y1 are the two predecessors
+         * of x. */
+        for (x = 0; x < z; ++x) { // x0 is the smaller
+            uint32_t y0, y1, xc;
+            int c0, c1;
+            xc = ~x&mask; y0 = x>>1; y1 = xc>>1;
+            c0 = prev[y0] + wi[x] + wi[xc];
+            c1 = prev[y1] + wi[x] + wi[xc];
+            if (c0 > c1) bi[x] = 0, curr[x] = c0;
+            else bi[x] = 1, curr[x] = c1;
+        }
+        tmp = prev; prev = curr; curr = tmp; // swap
+    }
+    { // backtrack
+        uint32_t max_x = 0;
+        int which = 0;
+        h = calloc(vpos, 1);
+        for (x = 0, max = 0, max_x = 0; x < z; ++x)
+            if (prev[x] > max) max = prev[x], max_x = x;
+        for (i = vpos - 1, x = max_x; i >= 0; --i) {
+            h[i] = which? (~x&1) : (x&1);
+            which = b[i][x]? !which : which;
+            x = b[i][x]? (~x&mask)>>1 : x>>1;
+        }
+    }
+    // free
+    for (i = 0; i < vpos; ++i) free(b[i]);
+    free(f[0]); free(f[1]); free(b);
+    return h;
+}
+
+// phase each fragment
+static uint64_t *fragphase(int vpos, const int8_t *path, nseq_t *hash, int flip)
+{
+    khint_t k;
+    uint64_t *pcnt;
+    uint32_t *left, *rght, max;
+    left = rght = 0; max = 0;
+    pcnt = calloc(vpos, 8);
+    for (k = 0; k < kh_end(hash); ++k) {
+        if (kh_exist(hash, k)) {
+            int i, c[2];
+            frag_t *f = &kh_val(hash, k);
+            if (f->vpos >= vpos) continue;
+            // get the phase
+            c[0] = c[1] = 0;
+            for (i = 0; i < f->vlen; ++i) {
+                if (f->seq[i] == 0) continue;
+                ++c[f->seq[i] == path[f->vpos + i] + 1? 0 : 1];
+            }
+            f->phase = c[0] > c[1]? 0 : 1;
+            f->in = c[f->phase]; f->out = c[1 - f->phase];
+            f->phased = f->in == f->out? 0 : 1;
+            f->ambig = (f->in && f->out && f->out < 3 && f->in <= f->out + 1)? 1 : 0;
+            // fix chimera
+            f->flip = 0;
+            if (flip && c[0] >= 3 && c[1] >= 3) {
+                int sum[2], m, mi, md;
+                if (f->vlen > max) { // enlarge the array
+                    max = f->vlen;
+                    kroundup32(max);
+                    left = realloc(left, max * 4);
+                    rght = realloc(rght, max * 4);
+                }
+                for (i = 0, sum[0] = sum[1] = 0; i < f->vlen; ++i) { // get left counts
+                    if (f->seq[i]) {
+                        int c = f->phase? 2 - f->seq[i] : f->seq[i] - 1;
+                        ++sum[c == path[f->vpos + i]? 0 : 1];
+                    }
+                    left[i] = sum[1]<<16 | sum[0];
+                }
+                for (i = f->vlen - 1, sum[0] = sum[1] = 0; i >= 0; --i) { // get right counts
+                    if (f->seq[i]) {
+                        int c = f->phase? 2 - f->seq[i] : f->seq[i] - 1;
+                        ++sum[c == path[f->vpos + i]? 0 : 1];
+                    }
+                    rght[i] = sum[1]<<16 | sum[0];
+                }
+                // find the best flip point
+                for (i = m = 0, mi = -1, md = -1; i < f->vlen - 1; ++i) {
+                    int a[2];
+                    a[0] = (left[i]&0xffff) + (rght[i+1]>>16&0xffff) - (rght[i+1]&0xffff) * FLIP_PENALTY;
+                    a[1] = (left[i]>>16&0xffff) + (rght[i+1]&0xffff) - (rght[i+1]>>16&0xffff) * FLIP_PENALTY;
+                    if (a[0] > a[1]) {
+                        if (a[0] > m) m = a[0], md = 0, mi = i;
+                    } else {
+                        if (a[1] > m) m = a[1], md = 1, mi = i;
+                    }
+                }
+                if (m - c[0] >= FLIP_THRES && m - c[1] >= FLIP_THRES) { // then flip
+                    f->flip = 1;
+                    if (md == 0) { // flip the tail
+                        for (i = mi + 1; i < f->vlen; ++i)
+                            if (f->seq[i] == 1) f->seq[i] = 2;
+                            else if (f->seq[i] == 2) f->seq[i] = 1;
+                    } else { // flip the head
+                        for (i = 0; i <= mi; ++i)
+                            if (f->seq[i] == 1) f->seq[i] = 2;
+                            else if (f->seq[i] == 2) f->seq[i] = 1;
+                    }
+                }
+            }
+            // update pcnt[]
+            if (!f->single) {
+                for (i = 0; i < f->vlen; ++i) {
+                    int c;
+                    if (f->seq[i] == 0) continue;
+                    c = f->phase? 2 - f->seq[i] : f->seq[i] - 1;
+                    if (c == path[f->vpos + i]) {
+                        if (f->phase == 0) ++pcnt[f->vpos + i];
+                        else pcnt[f->vpos + i] += 1ull<<32;
+                    } else {
+                        if (f->phase == 0) pcnt[f->vpos + i] += 1<<16;
+                        else pcnt[f->vpos + i] += 1ull<<48;
+                    }
+                }
+            }
+        }
+    }
+    free(left); free(rght);
+    return pcnt;
+}
+
+static uint64_t *genmask(int vpos, const uint64_t *pcnt, int *_n)
+{
+    int i, max = 0, max_i = -1, m = 0, n = 0, beg = 0, score = 0;
+    uint64_t *list = 0;
+    for (i = 0; i < vpos; ++i) {
+        uint64_t x = pcnt[i];
+        int c[4], pre = score, s;
+        c[0] = x&0xffff; c[1] = x>>16&0xffff; c[2] = x>>32&0xffff; c[3] = x>>48&0xffff;
+        s = (c[1] + c[3] == 0)? -(c[0] + c[2]) : (c[1] + c[3] - 1);
+        if (c[3] > c[2]) s += c[3] - c[2];
+        if (c[1] > c[0]) s += c[1] - c[0];
+        score += s;
+        if (score < 0) score = 0;
+        if (pre == 0 && score > 0) beg = i; // change from zero to non-zero
+        if ((i == vpos - 1 || score == 0) && max >= MASK_THRES) {
+            if (n == m) {
+                m = m? m<<1 : 4;
+                list = realloc(list, m * 8);
+            }
+            list[n++] = (uint64_t)beg<<32 | max_i;
+            i = max_i; // reset i to max_i
+            score = 0;
+        } else if (score > max) max = score, max_i = i;
+        if (score == 0) max = 0;
+    }
+    *_n = n;
+    return list;
+}
+
+// trim heading and tailing ambiguous bases; mark deleted and remove sequence
+static int clean_seqs(int vpos, nseq_t *hash)
+{
+    khint_t k;
+    int ret = 0;
+    for (k = 0; k < kh_end(hash); ++k) {
+        if (kh_exist(hash, k)) {
+            frag_t *f = &kh_val(hash, k);
+            int beg, end, i;
+            if (f->vpos >= vpos) {
+                ret = 1;
+                continue;
+            }
+            for (i = 0; i < f->vlen; ++i)
+                if (f->seq[i] != 0) break;
+            beg = i;
+            for (i = f->vlen - 1; i >= 0; --i)
+                if (f->seq[i] != 0) break;
+            end = i + 1;
+            if (end - beg <= 0) kh_del(64, hash, k);
+            else {
+                if (beg != 0) memmove(f->seq, f->seq + beg, end - beg);
+                f->vpos += beg; f->vlen = end - beg;
+                f->single = f->vlen == 1? 1 : 0;
+            }
+        }
+    }
+    return ret;
+}
+
+static int dump_aln(phaseg_t *g, int min_pos, const nseq_t *hash)
+{
+    int i, is_flip, drop_ambi;
+    drop_ambi = g->flag & FLAG_DROP_AMBI;
+    is_flip = (drand48() < 0.5);
+    for (i = 0; i < g->n; ++i) {
+        int end, which;
+        uint64_t key;
+        khint_t k;
+        bam1_t *b = g->b[i];
+        key = X31_hash_string(bam_get_qname(b));
+        end = bam_endpos(b);
+        if (end > min_pos) break;
+        k = kh_get(64, hash, key);
+        if (k == kh_end(hash)) which = 3;
+        else {
+            frag_t *f = &kh_val(hash, k);
+            if (f->ambig) which = drop_ambi? 2 : 3;
+            else if (f->phased && f->flip) which = 2;
+            else if (f->phased == 0) which = 3;
+            else { // phased and not flipped
+                char c = 'Y';
+                which = f->phase;
+                bam_aux_append(b, "ZP", 'A', 1, (uint8_t*)&c);
+            }
+            if (which < 2 && is_flip) which = 1 - which; // increase the randomness
+        }
+        if (which == 3) which = (drand48() < 0.5);
+        if (sam_write1(g->out[which], g->out_hdr[which], b) < 0) {
+            print_error_errno("phase", "error writing to '%s'", g->out_name[which]);
+            return -1;
+        }
+        bam_destroy1(b);
+        g->b[i] = 0;
+    }
+    memmove(g->b, g->b + i, (g->n - i) * sizeof(void*));
+    g->n -= i;
+    return 0;
+}
+
+static int phase(phaseg_t *g, const char *chr, int vpos, uint64_t *cns, nseq_t *hash)
+{
+    int i, j, n_seqs = kh_size(hash), n_masked = 0, min_pos;
+    khint_t k;
+    frag_t **seqs;
+    int8_t *path, *sitemask;
+    uint64_t *pcnt, *regmask;
+
+    if (vpos == 0) return 0;
+    i = clean_seqs(vpos, hash); // i is true if hash has an element with its vpos >= vpos
+    min_pos = i? cns[vpos]>>32 : 0x7fffffff;
+    if (vpos == 1) {
+        fprintf(samtools_stdout, "PS\t%s\t%d\t%d\n", chr, (int)(cns[0]>>32) + 1, (int)(cns[0]>>32) + 1);
+        fprintf(samtools_stdout, "M0\t%s\t%d\t%d\t%c\t%c\t%d\t0\t0\t0\t0\n//\n", chr, (int)(cns[0]>>32) + 1, (int)(cns[0]>>32) + 1,
+            "ACGTX"[cns[0]&3], "ACGTX"[cns[0]>>16&3], g->vpos_shift + 1);
+        for (k = 0; k < kh_end(hash); ++k) {
+            if (kh_exist(hash, k)) {
+                frag_t *f = &kh_val(hash, k);
+                if (f->vpos) continue;
+                f->flip = 0;
+                if (f->seq[0] == 0) f->phased = 0;
+                else f->phased = 1, f->phase = f->seq[0] - 1;
+            }
+        }
+        if (dump_aln(g, min_pos, hash) < 0) return -1;
+        ++g->vpos_shift;
+        return 1;
+    }
+    { // phase
+        int **cnt;
+        uint64_t *mask;
+        fprintf(samtools_stdout, "PS\t%s\t%d\t%d\n", chr, (int)(cns[0]>>32) + 1, (int)(cns[vpos-1]>>32) + 1);
+        sitemask = calloc(vpos, 1);
+        cnt = count_all(g->k, vpos, hash);
+        path = dynaprog(g->k, vpos, cnt);
+        for (i = 0; i < vpos; ++i) free(cnt[i]);
+        free(cnt);
+        pcnt = fragphase(vpos, path, hash, 0); // do not fix chimeras when masking
+        mask = genmask(vpos, pcnt, &n_masked);
+        regmask = calloc(n_masked, 8);
+        for (i = 0; i < n_masked; ++i) {
+            regmask[i] = cns[mask[i]>>32]>>32<<32 | cns[(uint32_t)mask[i]]>>32;
+            for (j = mask[i]>>32; j <= (int32_t)mask[i]; ++j)
+                sitemask[j] = 1;
+        }
+        free(mask);
+        if (g->flag & FLAG_FIX_CHIMERA) {
+            free(pcnt);
+            pcnt = fragphase(vpos, path, hash, 1);
+        }
+    }
+    for (i = 0; i < n_masked; ++i)
+        fprintf(samtools_stdout, "FL\t%s\t%d\t%d\n", chr, (int)(regmask[i]>>32) + 1, (int)regmask[i] + 1);
+    for (i = 0; i < vpos; ++i) {
+        uint64_t x = pcnt[i];
+        int8_t c[2];
+        c[0] = (cns[i]&0xffff)>>2 == 0? 4 : (cns[i]&3);
+        c[1] = (cns[i]>>16&0xffff)>>2 == 0? 4 : (cns[i]>>16&3);
+        fprintf(samtools_stdout, "M%d\t%s\t%d\t%d\t%c\t%c\t%d\t%d\t%d\t%d\t%d\n", sitemask[i]+1, chr, (int)(cns[0]>>32) + 1, (int)(cns[i]>>32) + 1, "ACGTX"[c[path[i]]], "ACGTX"[c[1-path[i]]],
+            i + g->vpos_shift + 1, (int)(x&0xffff), (int)(x>>16&0xffff), (int)(x>>32&0xffff), (int)(x>>48&0xffff));
+    }
+    free(path); free(pcnt); free(regmask); free(sitemask);
+    seqs = calloc(n_seqs, sizeof(frag_t*));
+    for (k = 0, i = 0; k < kh_end(hash); ++k)
+        if (kh_exist(hash, k) && kh_val(hash, k).vpos < vpos && !kh_val(hash, k).single)
+            seqs[i++] = &kh_val(hash, k);
+    n_seqs = i;
+    ks_introsort_rseq(n_seqs, seqs);
+    for (i = 0; i < n_seqs; ++i) {
+        frag_t *f = seqs[i];
+        fprintf(samtools_stdout, "EV\t0\t%s\t%d\t40\t%dM\t*\t0\t0\t", chr, f->vpos + 1 + g->vpos_shift, f->vlen);
+        for (j = 0; j < f->vlen; ++j) {
+            uint32_t c = cns[f->vpos + j];
+            if (f->seq[j] == 0) fputc('N', samtools_stdout);
+            else fputc("ACGT"[f->seq[j] == 1? (c&3) : (c>>16&3)], samtools_stdout);
+        }
+        fprintf(samtools_stdout, "\t*\tYP:i:%d\tYF:i:%d\tYI:i:%d\tYO:i:%d\tYS:i:%d\n", f->phase, f->flip, f->in, f->out, f->beg+1);
+    }
+    free(seqs);
+    fprintf(samtools_stdout, "//\n");
+    fflush(samtools_stdout);
+    g->vpos_shift += vpos;
+    if (dump_aln(g, min_pos, hash) < 0) return -1;
+    return vpos;
+}
+
+static void update_vpos(int vpos, nseq_t *hash)
+{
+    khint_t k;
+    for (k = 0; k < kh_end(hash); ++k) {
+        if (kh_exist(hash, k)) {
+            frag_t *f = &kh_val(hash, k);
+            if (f->vpos < vpos) kh_del(64, hash, k); // TODO: if frag_t::seq is allocated dynamically, free it
+            else f->vpos -= vpos;
+        }
+    }
+}
+
+static nseq_t *shrink_hash(nseq_t *hash) // TODO: to implement
+{
+    return hash;
+}
+
+static int readaln(void *data, bam1_t *b)
+{
+    phaseg_t *g = (phaseg_t*)data;
+    int ret;
+    while (1)
+    {
+        ret = sam_read1(g->fp, g->fp_hdr, b);
+        if (ret < 0) break;
+        if ( b->core.flag & (BAM_FUNMAP | BAM_FSECONDARY | BAM_FQCFAIL | BAM_FDUP) ) continue;
+        if ( g->pre ) {
+            if (g->n == g->m) {
+                g->m = g->m? g->m<<1 : 16;
+                g->b = realloc(g->b, g->m * sizeof(bam1_t*));
+            }
+            g->b[g->n++] = bam_dup1(b);
+        }
+        break;
+    }
+    return ret;
+}
+
+static khash_t(set64) *loadpos(const char *fn, sam_hdr_t *h)
+{
+    gzFile fp;
+    kstream_t *ks;
+    int ret, dret;
+    kstring_t *str;
+    khash_t(set64) *hash;
+
+    fp = strcmp(fn, "-")? gzopen(fn, "r") : gzdopen(fileno(stdin), "r");
+    if (fp == NULL) {
+        print_error_errno("phase", "Couldn't open site file '%s'", fn);
+        return NULL;
+    }
+
+    hash = kh_init(set64);
+    str = calloc(1, sizeof(kstring_t));
+
+    ks = ks_init(fp);
+    while (ks_getuntil(ks, 0, str, &dret) >= 0) {
+        int tid = bam_name2id(h, str->s);
+        if (tid >= 0 && dret != '\n') {
+            if (ks_getuntil(ks, 0, str, &dret) >= 0) {
+                uint64_t x = (uint64_t)tid<<32 | (atoi(str->s) - 1);
+                kh_put(set64, hash, x, &ret);
+            } else break;
+        }
+        if (dret != '\n') while ((dret = ks_getc(ks)) > 0 && dret != '\n');
+        if (dret < 0) break;
+    }
+    ks_destroy(ks);
+    gzclose(fp);
+    free(str->s); free(str);
+    return hash;
+}
+
+static int gl2cns(float q[16])
+{
+    int i, j, min_ij;
+    float min, min2;
+    min = min2 = 1e30; min_ij = -1;
+    for (i = 0; i < 4; ++i) {
+        for (j = i; j < 4; ++j) {
+            if (q[i<<2|j] < min) min_ij = i<<2|j, min2 = min, min = q[i<<2|j];
+            else if (q[i<<2|j] < min2) min2 = q[i<<2|j];
+        }
+    }
+    return (min_ij>>2&3) == (min_ij&3)? 0 : 1<<18 | (min_ij>>2&3)<<16 | (min_ij&3) | (int)(min2 - min + .499) << 2;
+}
+
+static int start_output(phaseg_t *g, int c, const char *middle, const htsFormat *fmt)
+{
+    kstring_t s = { 0, 0, NULL };
+    ksprintf(&s, "%s.%s.%s", g->pre, middle, hts_format_file_extension(fmt));
+    g->out_name[c] = ks_release(&s);
+    g->out[c] = sam_open_format(g->out_name[c], "wb", fmt);
+    if (! g->out[c]) {
+        print_error_errno("phase", "Failed to open output file '%s'", g->out_name[c]);
+        return -1;
+    }
+
+    g->out_hdr[c] = sam_hdr_dup(g->fp_hdr);
+    if (!g->no_pg && sam_hdr_add_pg(g->out_hdr[c], "samtools",
+                                    "VN", samtools_version(),
+                                    g->arg_list ? "CL": NULL,
+                                    g->arg_list ? g->arg_list : NULL,
+                                    NULL)) {
+        print_error("phase", "failed to add PG line to header");
+        return -1;
+    }
+    if (sam_hdr_write(g->out[c], g->out_hdr[c]) < 0) {
+        print_error_errno("phase", "Failed to write header for '%s'", g->out_name[c]);
+        return -1;
+    }
+
+    return 0;
+}
+
+int main_phase(int argc, char *argv[])
+{
+    int c, tid, pos, vpos = 0, n, lasttid = -1, max_vpos = 0, usage = 0;
+    int status = EXIT_SUCCESS;
+    const bam_pileup1_t *plp;
+    bam_plp_t iter;
+    nseq_t *seqs;
+    uint64_t *cns = 0;
+    phaseg_t g;
+    char *fn_list = 0;
+    khash_t(set64) *set = 0;
+    errmod_t *em;
+    uint16_t *bases;
+
+    sam_global_args ga = SAM_GLOBAL_ARGS_INIT;
+    static const struct option lopts[] = {
+        SAM_OPT_GLOBAL_OPTIONS('-', 0, 0, 0, 0, '-'),
+        {"min-BQ", required_argument, NULL, 'Q'},
+        {"min-bq", required_argument, NULL, 'Q'},
+        {"no-PG", no_argument, NULL, 1},
+        { NULL, 0, NULL, 0 }
+    };
+
+    // FIXME Leaks galore in the case of error returns
+
+    memset(&g, 0, sizeof(phaseg_t));
+    g.flag = FLAG_FIX_CHIMERA;
+    g.min_varLOD = 37; g.k = 13; g.min_baseQ = 13; g.max_depth = 256;
+    while ((c = getopt_long(argc, argv, "Q:eFq:k:b:l:D:A", lopts, NULL)) >= 0) {
+        switch (c) {
+            case 'D': g.max_depth = atoi(optarg); break;
+            case 'q': g.min_varLOD = atoi(optarg); break;
+            case 'Q': g.min_baseQ = atoi(optarg); break;
+            case 'k': g.k = atoi(optarg); break;
+            case 'F': g.flag &= ~FLAG_FIX_CHIMERA; break;
+            case 'e': g.flag |= FLAG_LIST_EXCL; break;
+            case 'A': g.flag |= FLAG_DROP_AMBI; break;
+            case 'b': g.pre = strdup(optarg); break;
+            case 'l': fn_list = strdup(optarg); break;
+            case 1: g.no_pg = 1; break;
+            default:  if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break;
+                      /* else fall-through */
+            case '?': usage=1; break;
+        }
+        if (usage) break;
+    }
+    if (usage || argc == optind) {
+        fprintf(samtools_stderr, "\n");
+        fprintf(samtools_stderr, "Usage:   samtools phase [options] <in.bam>\n\n");
+        fprintf(samtools_stderr, "Options: -k INT    block length [%d]\n", g.k);
+        fprintf(samtools_stderr, "         -b STR    prefix of BAMs to output [null]\n");
+        fprintf(samtools_stderr, "         -q INT    min het phred-LOD [%d]\n", g.min_varLOD);
+        fprintf(samtools_stderr, "         -Q, --min-BQ INT\n"
+                        "                   min base quality in het calling [%d]\n", g.min_baseQ);
+        fprintf(samtools_stderr, "         -D INT    max read depth [%d]\n", g.max_depth);
+//      fprintf(samtools_stderr, "         -l FILE   list of sites to phase [null]\n");
+        fprintf(samtools_stderr, "         -F        do not attempt to fix chimeras\n");
+        fprintf(samtools_stderr, "         -A        drop reads with ambiguous phase\n");
+        fprintf(samtools_stderr, "         --no-PG   do not add a PG line\n");
+//      fprintf(samtools_stderr, "         -e        do not discover SNPs (effective with -l)\n");
+        fprintf(samtools_stderr, "\n");
+
+        sam_global_opt_help(samtools_stderr, "-....--.");
+
+        return 1;
+    }
+    g.fp = sam_open_format(argv[optind], "r", &ga.in);
+    if (!g.fp) {
+        print_error_errno("phase", "Couldn't open '%s'", argv[optind]);
+        return 1;
+    }
+    g.fp_hdr = sam_hdr_read(g.fp);
+    if (g.fp_hdr == NULL) {
+        fprintf(samtools_stderr, "[%s] Failed to read header for '%s'\n",
+                __func__, argv[optind]);
+        return 1;
+    }
+    if (!g.no_pg && !(g.arg_list = stringify_argv(argc+1, argv-1))) {
+        print_error("phase", "failed to create arg_list");
+        return 1;
+    }
+    if (fn_list) { // read the list of sites to phase
+        set = loadpos(fn_list, g.fp_hdr);
+        if (set == NULL) return 1;
+        free(fn_list);
+    } else g.flag &= ~FLAG_LIST_EXCL;
+    if (g.pre) { // open BAMs to write
+        if (ga.out.format == unknown_format)
+            ga.out.format = bam; // default via "wb".
+
+        // Open each output file g.out[0..2], dupping and writing the header
+        if (start_output(&g, 0, "0", &ga.out) < 0 ||
+            start_output(&g, 1, "1", &ga.out) < 0 ||
+            start_output(&g, 2, "chimera", &ga.out) < 0) return 1;
+    }
+
+    iter = bam_plp_init(readaln, &g);
+    g.vpos_shift = 0;
+    seqs = kh_init(64);
+    em = errmod_init(1. - 0.83);
+    bases = calloc(g.max_depth, 2);
+    fprintf(samtools_stdout, "CC\n");
+    fprintf(samtools_stdout, "CC\tDescriptions:\nCC\n");
+    fprintf(samtools_stdout, "CC\t  CC      comments\n");
+    fprintf(samtools_stdout, "CC\t  PS      start of a phase set\n");
+    fprintf(samtools_stdout, "CC\t  FL      filtered region\n");
+    fprintf(samtools_stdout, "CC\t  M[012]  markers; 0 for singletons, 1 for phased and 2 for filtered\n");
+    fprintf(samtools_stdout, "CC\t  EV      supporting reads; SAM format\n");
+    fprintf(samtools_stdout, "CC\t  //      end of a phase set\nCC\n");
+    fprintf(samtools_stdout, "CC\tFormats of PS, FL and M[012] lines (1-based coordinates):\nCC\n");
+    fprintf(samtools_stdout, "CC\t  PS  chr  phaseSetStart  phaseSetEnd\n");
+    fprintf(samtools_stdout, "CC\t  FL  chr  filterStart    filterEnd\n");
+    fprintf(samtools_stdout, "CC\t  M?  chr  PS  pos  allele0  allele1  hetIndex  #supports0  #errors0  #supp1  #err1\n");
+    fprintf(samtools_stdout, "CC\nCC\n");
+    fflush(samtools_stdout);
+    while ((plp = bam_plp_auto(iter, &tid, &pos, &n)) != 0) {
+        int i, k, c, tmp, dophase = 1, in_set = 0;
+        float q[16];
+        if (tid < 0) break;
+        if (tid != lasttid) { // change of chromosome
+            g.vpos_shift = 0;
+            if (lasttid >= 0) {
+                seqs = shrink_hash(seqs);
+                if (phase(&g, sam_hdr_tid2name(g.fp_hdr, lasttid),
+                          vpos, cns, seqs) < 0) {
+                    return 1;
+                }
+                update_vpos(0x7fffffff, seqs);
+            }
+            lasttid = tid;
+            vpos = 0;
+        }
+        if (set && kh_get(set64, set, (uint64_t)tid<<32 | pos) != kh_end(set)) in_set = 1;
+        if (n > g.max_depth) continue; // do not proceed if the depth is too high
+        // fill the bases array and check if there is a variant
+        for (i = k = 0; i < n; ++i) {
+            const bam_pileup1_t *p = plp + i;
+            uint8_t *seq;
+            int q, baseQ, b;
+            if (p->is_del || p->is_refskip) continue;
+            baseQ = bam_get_qual(p->b)[p->qpos];
+            if (baseQ < g.min_baseQ) continue;
+            seq = bam_get_seq(p->b);
+            b = seq_nt16_int[bam_seqi(seq, p->qpos)];
+            if (b > 3) continue;
+            q = baseQ < p->b->core.qual? baseQ : p->b->core.qual;
+            if (q < 4) q = 4;
+            if (q > 63) q = 63;
+            bases[k++] = q<<5 | (int)bam_is_rev(p->b)<<4 | b;
+        }
+        if (k == 0) continue;
+        errmod_cal(em, k, 4, bases, q); // compute genotype likelihood
+        c = gl2cns(q); // get the consensus
+        // tell if to proceed
+        if (set && (g.flag&FLAG_LIST_EXCL) && !in_set) continue; // not in the list
+        if (!in_set && (c&0xffff)>>2 < g.min_varLOD) continue; // not a variant
+        // add the variant
+        if (vpos == max_vpos) {
+            max_vpos = max_vpos? max_vpos<<1 : 128;
+            cns = realloc(cns, max_vpos * 8);
+        }
+        cns[vpos] = (uint64_t)pos<<32 | c;
+        for (i = 0; i < n; ++i) {
+            const bam_pileup1_t *p = plp + i;
+            uint64_t key;
+            khint_t k;
+            uint8_t *seq = bam_get_seq(p->b);
+            frag_t *f;
+            if (p->is_del || p->is_refskip) continue;
+            if (p->b->core.qual == 0) continue;
+            // get the base code
+            c = seq_nt16_int[bam_seqi(seq, p->qpos)];
+            if (c == (cns[vpos]&3)) c = 1;
+            else if (c == (cns[vpos]>>16&3)) c = 2;
+            else c = 0;
+            // write to seqs
+            key = X31_hash_string(bam_get_qname(p->b));
+            k = kh_put(64, seqs, key, &tmp);
+            f = &kh_val(seqs, k);
+            if (tmp == 0) { // present in the hash table
+                if (vpos - f->vpos + 1 < MAX_VARS) {
+                    f->vlen = vpos - f->vpos + 1;
+                    f->seq[f->vlen-1] = c;
+                    f->end = bam_endpos(p->b);
+                }
+                dophase = 0;
+            } else { // absent
+                memset(f->seq, 0, MAX_VARS);
+                f->beg = p->b->core.pos;
+                f->end = bam_endpos(p->b);
+                f->vpos = vpos, f->vlen = 1, f->seq[0] = c, f->single = f->phased = f->flip = f->ambig = 0;
+            }
+        }
+        if (dophase) {
+            seqs = shrink_hash(seqs);
+            if (phase(&g, sam_hdr_tid2name(g.fp_hdr, tid), vpos, cns, seqs) < 0) {
+                return 1;
+            }
+            update_vpos(vpos, seqs);
+            cns[0] = cns[vpos];
+            vpos = 0;
+        }
+        ++vpos;
+    }
+    if (tid >= 0) {
+        if (phase(&g, sam_hdr_tid2name(g.fp_hdr, tid), vpos, cns, seqs) < 0) {
+            return 1;
+        }
+    }
+
+    if (n < 0) {
+        print_error("phase", "error reading from '%s'", argv[optind]);
+        status = EXIT_FAILURE;
+    }
+
+    sam_hdr_destroy(g.fp_hdr);
+    bam_plp_destroy(iter);
+    sam_close(g.fp);
+    kh_destroy(64, seqs);
+    kh_destroy(set64, set);
+    free(cns);
+    errmod_destroy(em);
+    free(bases);
+    if (g.pre) {
+        int res = 0;
+        for (c = 0; c <= 2; ++c) {
+            if (sam_close(g.out[c]) < 0) {
+                fprintf(samtools_stderr, "[%s] error on closing '%s'\n",
+                        __func__, g.out_name[c]);
+                res = 1;
+            }
+            sam_hdr_destroy(g.out_hdr[c]);
+            free(g.out_name[c]);
+        }
+        free(g.pre); free(g.b);
+        if (res) return 1;
+    }
+    free(g.arg_list);
+    sam_global_args_free(&ga);
+    return status;
+}
diff --git a/samtools/reference.c b/samtools/reference.c
new file mode 100644
index 0000000..2d95d64
--- /dev/null
+++ b/samtools/reference.c
@@ -0,0 +1,598 @@
+/*  bam_reference.c -- extracts an embedded reference from a CRAM file,
+                       or creates it from alignments plus MD:Z tags.
+
+    Copyright (C) 2022 Genome Research Ltd.
+
+    Author: James Bonfield <jkb@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <config.h>
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <unistd.h>
+#include <string.h>
+#include <ctype.h>
+
+#include "htslib/sam.h"
+#include "htslib/cram.h"
+#include "samtools.h"
+#include "sam_opts.h"
+
+
+/*
+ * There are two main modes of operation.
+ *
+ * 1. Extracting the reference from the CRAM file embed_ref blocks.
+ * 2. Generation of reference by analysing consensus plus patches applied
+ *    via MD tags.
+ *
+ * The first is very rapid, but only applies to a CRAM files generated with
+ * the specific options (not commonly used and not the default).  The second
+ * is a slow operation, but applies to any data type.
+ *
+ * This is also a testing ground for a future CRAM auto-embed-ref option that
+ * permits the use of an embedded reference without having to first extract
+ * the reference.  (Note this may require the creation of MD tags during
+ * decode by use of an existing embedded reference, if the records don't
+ * have an MD tag themselves, but that's an issue for htslib when we get
+ * there.)
+ */
+
+/*
+ * ---------------------------------------------------------------------------
+ * Shared utility functions by both methods.
+ */
+
+#define haszero(x) (((x)-0x0101010101010101UL)&~(x)&0x8080808080808080UL)
+#define MIN(a,b) ((a)<(b)?(a):(b))
+static int dump_ref(sam_hdr_t *h, hts_itr_t *iter, int ref_id,
+                    char *ref, uint64_t ref_len, FILE *fp, int verbose) {
+    int N = 0;
+    if (iter && iter->end >= HTS_POS_MAX)
+        iter->end = ref_len;
+    if (iter && (iter->beg > 0 || iter->end < ref_len)) {
+        fprintf(fp, ">%s:%"PRIhts_pos"-%"PRIhts_pos"\n",
+                sam_hdr_tid2name(h, ref_id), iter->beg+1, iter->end);
+        ref += iter->beg;
+        ref_len = MIN(ref_len, iter->end) - iter->beg;
+    } else {
+        fprintf(fp, ">%s\n", sam_hdr_tid2name(h, ref_id));
+    }
+
+    int i, j;
+    uint64_t rem = ref_len;
+
+    // Count coverage, purely for information purposes.
+    // About 90% of dump_ref CPU is here, so maybe this isn't useful,
+    // but this is still 3-4x faster than the obvious naive loop.
+    //
+    // Overall though it's only about 5% overhead of the entire process
+    // (was ~20%).
+    if (verbose) {
+        int n4[8] = {0};
+        for (j = 0; j < ref_len && (((uintptr_t) &ref[j] & 7) != 0); j++)
+            N += ref[j] == 'N';
+        uint64_t fast_end = ((ref_len - j) & ~7) + j;
+        for (; j < fast_end; j+=8) {
+            uint64_t i64 = *(uint64_t *)&ref[j];
+            if (!haszero(i64 ^ 0x4e4e4e4e4e4e4e4eUL)) // 'N' <-> 0
+                continue;
+
+            n4[0] += ref[j+0] == 'N';
+            n4[1] += ref[j+1] == 'N';
+            n4[2] += ref[j+2] == 'N';
+            n4[3] += ref[j+3] == 'N';
+            n4[4] += ref[j+4] == 'N';
+            n4[5] += ref[j+5] == 'N';
+            n4[6] += ref[j+6] == 'N';
+            n4[7] += ref[j+7] == 'N';
+        }
+        for (; j < ref_len; j++)
+            N += ref[j] == 'N';
+        N += n4[0]+n4[1]+n4[2]+n4[3]+
+            n4[4]+n4[5]+n4[6]+n4[7];
+    }
+
+    // Format reference
+    for (i = 0; i < ref_len; i += 60, rem -= 60) {
+        int len = (int)(rem < 60 ? rem : 60);
+        if (fwrite(ref, 1, len, fp) != len)
+            return -1;
+        putc('\n', fp);
+        ref += 60;
+    }
+
+    if (verbose)
+        fprintf(stderr, "Dump ref %d len %"PRId64", coverage %.2f%%\n",
+                ref_id, ref_len, 100 - N*100.0 / ref_len);
+
+    return 0;
+}
+
+/*
+ * ---------------------------------------------------------------------------
+ * CRAM embedded reference method of reference construction
+ */
+
+/*
+ * Extracts an embedded reference from a sorted CRAM file.
+ * Modelled on the CRAM container copy loop from bam_cat.c.
+ */
+static int cram2ref(samFile *in, sam_hdr_t *h, hts_idx_t *idx, char *reg,
+                    FILE *outfp, int verbose) {
+    cram_fd *in_c;
+    cram_container *c = NULL;
+    cram_block *blk = NULL;
+    cram_block_slice_hdr *shdr = NULL;
+
+    int curr_ref_id = -99;
+    char *ref = NULL;
+    uint64_t ref_len = 0;
+
+    // We have no direct public API for seeking in CRAM to a specific
+    // location by genome coordinates.  The sam_itr_query API is
+    // designed for fetching records, rather than seeks to specific
+    // file locations.
+    //
+    // TODO: consider exposing cram_range and cram_seek_to_refpos API.
+    // After a sam_index_load which will add the index to infp, these
+    // functions should seek direct to the start of a container.
+    // Or use cram_index *e =cram_index_query(cram, tid, beg, NULL);
+    //
+    // However, fortuitously(?) sam_itr_querys calls cram_seek_to_refpos
+    // so we can do a region query and let that do the initial seek.
+    // We still need to do our own end-range detection though.
+
+    hts_itr_t *iter = NULL;
+    if (reg) {
+        iter = sam_itr_querys(idx, h, reg);
+        if (!iter) {
+            print_error("reference", "failed to parse region '%s'", reg);
+            goto err;
+        }
+    }
+
+    in_c = in->fp.cram; // low level htslib abuse?
+    int eor = 0;
+    while (!eor && (c = cram_read_container(in_c))) {
+        if (cram_container_is_empty(in_c)) {
+            cram_block *blk;
+            // Container compression header
+            if (!(blk = cram_read_block(in_c)))
+                goto err;
+            cram_free_block(blk);
+            cram_free_container(c);
+            c = NULL; blk = NULL;
+            continue;
+        }
+
+        // Container compression header; read and discard
+        int32_t num_slices;
+        if (!(blk = cram_read_block(in_c)))
+            goto err;
+        cram_free_block(blk);
+        blk = NULL;
+
+        // Container num_blocks can be invalid, due to a bug.
+        // Instead we iterate in slice context instead.
+        (void)cram_container_get_landmarks(c, &num_slices);
+        int i, j;
+        for (i = 0; i < num_slices; i++) {
+            // Slice header
+            if (!(blk = cram_read_block(in_c)))
+                goto err;
+            if (!(shdr = cram_decode_slice_header(in_c, blk)))
+                goto err;
+            cram_free_block(blk);
+            blk = NULL;
+
+            int num_blocks = cram_slice_hdr_get_num_blocks(shdr);
+            int embed_id = cram_slice_hdr_get_embed_ref_id(shdr);
+            int ref_id;
+            hts_pos_t ref_start, ref_span;
+            cram_slice_hdr_get_coords(shdr, &ref_id, &ref_start, &ref_span);
+
+            if (iter) {
+                if (iter->tid != ref_id || ref_start > iter->end) {
+                    // Beyond end of specified region.
+                    cram_free_slice_header(shdr);
+                    eor = 1;
+                    break;
+                }
+            }
+
+            if (embed_id < 0 && ref_id != -1) {
+                fprintf(stderr, "CRAM file has slice without embedded "
+                        "reference\n");
+                goto err;
+            }
+
+            if (ref_id != curr_ref_id) {
+                if (curr_ref_id >= 0) {
+                    if (dump_ref(h, iter, curr_ref_id, ref, ref_len,
+                                 outfp, verbose) < 0)
+                        goto err;
+                }
+
+                ref_len = sam_hdr_tid2len(h, ref_id);
+                if (ref_len) {
+                    char *ref2 = realloc(ref, ref_len);
+                    if (!ref2)
+                        goto err;
+                    else
+                        ref = ref2;
+                    memset(ref, 'N', ref_len);
+                }
+                curr_ref_id = ref_id;
+            }
+
+            // Slice data blocks
+            for (j = 0; j < num_blocks; j++) {
+                // read and discard, unless it's the ref-ID block
+                if (!(blk = cram_read_block(in_c)))
+                    goto err;
+                if (cram_block_get_content_id(blk) == embed_id) {
+                    cram_uncompress_block(blk);
+                    //printf("%.*s\n", blk->uncomp_size, blk->data);
+
+                    int32_t usize = cram_block_get_uncomp_size(blk);
+                    int ref_end = ref_start + usize;
+                    if (ref_end > ref_len+1)
+                        ref_end = ref_len+1;
+                    if (ref_end > ref_start)
+                        memcpy(ref + ref_start-1, cram_block_get_data(blk),
+                               ref_end - ref_start);
+                }
+                cram_free_block(blk);
+                blk = NULL;
+            }
+            cram_free_slice_header(shdr);
+            shdr = NULL;
+        }
+
+        cram_free_container(c);
+        c = NULL;
+    }
+
+    int ret = 0;
+    if (curr_ref_id >= 0) {
+        ret = dump_ref(h, iter, curr_ref_id, ref, ref_len, outfp, verbose);
+    } else if (reg) {
+        // no data present
+        // no data present, but we explicitly asked for the reference so
+        // report it still as Ns.
+        ref_len = MIN(iter->end,  sam_hdr_tid2len(h, iter->tid));
+        ref = malloc(ref_len);
+        memset(ref, 'N', ref_len);
+        if (!ref)
+            goto err;
+        ret = dump_ref(h, iter, iter->tid, ref, ref_len, outfp, verbose);
+    }
+
+    free(ref);
+    if (iter)
+        hts_itr_destroy(iter);
+
+    return ret;
+
+ err:
+    free(ref);
+    if (blk)
+        cram_free_block(blk);
+    if (shdr)
+        cram_free_slice_header(shdr);
+    if (c)
+        cram_free_container(c);
+    if (iter)
+        hts_itr_destroy(iter);
+
+    return -1;
+}
+
+/*
+ * ---------------------------------------------------------------------------
+ * MD method of reference construction
+ */
+
+// Returns the next cigar op code: one of the BAM_C* codes,
+// or -1 if no more are present.
+static inline
+int next_cigar_op(uint32_t *cigar, int *ncigar, int *skip, int *spos,
+                  uint32_t *cig_ind, uint32_t *cig_op, uint32_t *cig_len) {
+    for(;;) {
+        while (*cig_len == 0) {
+            if (*cig_ind < *ncigar) {
+                *cig_op  = cigar[*cig_ind] & BAM_CIGAR_MASK;
+                *cig_len = cigar[*cig_ind] >> BAM_CIGAR_SHIFT;
+                (*cig_ind)++;
+            } else {
+                return -1;
+            }
+        }
+
+        if (skip[*cig_op]) {
+            *spos += (bam_cigar_type(*cig_op)&1) * *cig_len;
+            *cig_len = 0;
+            continue;
+        }
+
+        (*cig_len)--;
+        break;
+    }
+
+    return *cig_op;
+}
+
+// Converts a bam object with SEQ, POS/CIGAR and MD:Z to a reference.
+// Updates ref[] array.
+//
+// Returns >0 on success,
+//          0 on no-MD found,
+//         -1 on failure (eg inconsistent data)
+static int build_ref(bam1_t *b, char *ref, size_t ref_len) {
+    uint8_t *seq = bam_get_seq(b);
+    uint32_t *cigar = bam_get_cigar(b);
+    int ncigar = b->core.n_cigar;
+    uint32_t cig_op = 0, cig_len = 0, cig_ind = 0;
+
+    const uint8_t *MD = bam_aux_get(b, "MD");
+    if (!MD || *MD != 'Z')
+        return 0;
+    MD++;
+
+    // Walk through MD + seq to generate ref
+    int iseq = 0, iref = b->core.pos, next_op;
+    int cig_skip[16] = {0,1,0,1,1,1,1,0,0,1,1,1,1,1,1,1};
+    while (iseq < b->core.l_qseq && *MD) {
+        if (isdigit(*MD)) {
+            // match
+            int len = strtol((char *)MD, (char **)&MD, 10);
+            while (iseq < b->core.l_qseq && len) {
+                if ((next_op = next_cigar_op(cigar, &ncigar, cig_skip,
+                                             &iseq, &cig_ind, &cig_op,
+                                             &cig_len)) < 0)
+                    return -1;
+
+                if (next_op != BAM_CMATCH &&
+                    next_op != BAM_CEQUAL) {
+                    print_error("MD2ref",
+                                "MD:Z and CIGAR are incompatible");
+                    return -1;
+                }
+
+                if (iref < ref_len)
+                    ref[iref] = seq_nt16_str[bam_seqi(seq, iseq)];
+                iseq++;
+                iref++;
+                len--;
+            }
+        } else if (*MD == '^') {
+            // deletion
+            MD++;
+            while (*MD && isalpha(*MD)) {
+                if ((next_op = next_cigar_op(cigar, &ncigar, cig_skip,
+                                             &iseq, &cig_ind, &cig_op,
+                                             &cig_len)) < 0)
+                    return -1;
+
+                if (next_op != BAM_CDEL) {
+                    print_error("MD2ref",
+                                "MD:Z and CIGAR are incompatible");
+                    return -1;
+                }
+
+                if (iref < ref_len)
+                    ref[iref] = *MD;
+
+                MD++;
+                iref++;
+            }
+        } else {
+            // substitution
+            if ((next_op = next_cigar_op(cigar, &ncigar, cig_skip,
+                                         &iseq, &cig_ind, &cig_op,
+                                         &cig_len)) < 0)
+                return -1;
+
+            if (next_op != BAM_CMATCH && next_op != BAM_CDIFF) {
+                print_error("MD2ref", "MD:Z and CIGAR are incompatible");
+                return -1;
+            }
+            if (iref < ref_len)
+                ref[iref] = *MD;
+
+            MD++;
+            iref++;
+            iseq++;
+        }
+    }
+
+    return 1;
+}
+
+static int MD2ref(samFile *in, sam_hdr_t *h, hts_idx_t *idx, char *reg,
+                  FILE *outfp, int verbose) {
+    bam1_t *b = bam_init1();
+    int r, last_tid = -99;
+    size_t ref_len = 0;
+    char *ref = NULL;
+    int ret = -1;
+
+    hts_itr_t *iter = NULL;
+    if (idx && reg) {
+        iter = sam_itr_querys(idx, h, reg);
+        if (!iter) {
+            print_error("reference", "failed to parse region '%s'", reg);
+            goto err;
+        }
+    }
+
+    while ((r = iter
+                ? sam_itr_next(in, iter, b)
+                : sam_read1(in, h, b)) >= 0) {
+        // check b->core.tid and flush old seq.
+        if (b->core.tid != last_tid) {
+            if (last_tid >= 0)
+                if (dump_ref(h, iter, last_tid, ref, ref_len, outfp,
+                             verbose) < 0)
+                    goto err;
+
+            last_tid = b->core.tid;
+            ref_len = sam_hdr_tid2len(h, last_tid);
+            if (ref_len) {
+                char *ref2 = realloc(ref, ref_len);
+                if (!ref2)
+                    goto err;
+                else
+                    ref = ref2;
+                memset(ref, 'N', ref_len);
+            }
+        }
+
+        if (build_ref(b, ref, ref_len) < 0)
+            goto err;
+    }
+
+    if (last_tid >= 0) {
+        if (dump_ref(h, iter, last_tid, ref, ref_len, outfp, verbose) < 0)
+            goto err;
+    } else if (reg) {
+        // no data present, but we explicitly asked for the reference so
+        // report it still as Ns.
+        ref_len = MIN(iter->end,  sam_hdr_tid2len(h, iter->tid));
+        ref = malloc(ref_len);
+        memset(ref, 'N', ref_len);
+        if (!ref)
+            goto err;
+        if (dump_ref(h, iter, iter->tid, ref, ref_len, outfp, verbose) < 0)
+            goto err;
+    }
+
+    if (r < -1)
+        goto err;
+
+    ret = 0;
+
+ err:
+    if (iter)
+        hts_itr_destroy(iter);
+    bam_destroy1(b);
+    free(ref);
+    return ret;
+}
+
+int main_reference(int argc, char *argv[])
+{
+    int c, usage = 0, verbose = 1, use_embedded = 0;
+    sam_hdr_t *h = 0;
+    samFile *in = NULL;
+    hts_idx_t *idx = NULL;
+    sam_global_args ga;
+    FILE *outfp = stdout;
+    char *reg = NULL;
+
+    static const struct option lopts[] = {
+        {"output",   required_argument, NULL, 'o'},
+        {"quiet",    no_argument,       NULL, 'q'},
+        {"embedded", no_argument,       NULL, 'e'},
+        {"region",   required_argument, NULL, 'r'},
+        SAM_OPT_GLOBAL_OPTIONS('-', '-', '-', '-', '-', '@'),
+        { NULL, 0, NULL, 0 }
+    };
+
+    sam_global_args_init(&ga);
+
+    while ((c = getopt_long(argc, argv, "@:qo:er:", lopts, NULL)) >= 0) {
+        switch (c) {
+        case 'o':
+            if (!(outfp = fopen(optarg, "w"))) {
+                perror(optarg);
+                goto err;
+            }
+            break;
+
+        case 'q':
+            verbose = 0;
+            break;
+
+        case 'e':
+            use_embedded = 1;
+            break;
+
+        case 'r':
+            reg = optarg;
+            break;
+
+        default:
+            if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break;
+            /* else fall-through */
+        case '?': usage=1; break;
+        }
+    }
+
+    if ((optind == argc && isatty(0)) || usage) {
+        printf("Usage: samtools reference [-@ N] [-r region] [-e] [-q] [-o out.fa] [in.cram]\n");
+        return 0;
+    }
+
+    char *fn = optind < argc ? argv[optind] : "-";
+    if (!(in = sam_open(fn, "r"))) {
+        print_error_errno("reference", "failed to open file '%s'", fn);
+        return 1;
+    }
+
+    if (ga.nthreads > 0)
+        hts_set_threads(in, ga.nthreads);
+
+    if (!(h = sam_hdr_read(in)))
+        goto err;
+
+    if (reg) {
+        idx = sam_index_load(in, fn);
+        if (!idx) {
+            print_error_errno("reference", "Failed to load the index");
+            goto err;
+        }
+    }
+
+    int ret = use_embedded
+        ? cram2ref(in, h, idx, reg, outfp, verbose)
+        : MD2ref(in, h, idx, reg, outfp, verbose);
+
+    sam_hdr_destroy(h);
+    if (outfp != stdout)
+        fclose(outfp);
+    if (idx)
+        hts_idx_destroy(idx);
+    sam_close(in);
+
+    return ret;
+
+ err:
+    if (idx)
+        hts_idx_destroy(idx);
+    if (in)
+        sam_close(in);
+    if (h)
+        sam_hdr_destroy(h);
+
+    return 1;
+}
diff --git a/samtools/reference.c.pysam.c b/samtools/reference.c.pysam.c
new file mode 100644
index 0000000..fe8025f
--- /dev/null
+++ b/samtools/reference.c.pysam.c
@@ -0,0 +1,600 @@
+#include "samtools.pysam.h"
+
+/*  bam_reference.c -- extracts an embedded reference from a CRAM file,
+                       or creates it from alignments plus MD:Z tags.
+
+    Copyright (C) 2022 Genome Research Ltd.
+
+    Author: James Bonfield <jkb@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <config.h>
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <unistd.h>
+#include <string.h>
+#include <ctype.h>
+
+#include "htslib/sam.h"
+#include "htslib/cram.h"
+#include "samtools.h"
+#include "sam_opts.h"
+
+
+/*
+ * There are two main modes of operation.
+ *
+ * 1. Extracting the reference from the CRAM file embed_ref blocks.
+ * 2. Generation of reference by analysing consensus plus patches applied
+ *    via MD tags.
+ *
+ * The first is very rapid, but only applies to a CRAM files generated with
+ * the specific options (not commonly used and not the default).  The second
+ * is a slow operation, but applies to any data type.
+ *
+ * This is also a testing ground for a future CRAM auto-embed-ref option that
+ * permits the use of an embedded reference without having to first extract
+ * the reference.  (Note this may require the creation of MD tags during
+ * decode by use of an existing embedded reference, if the records don't
+ * have an MD tag themselves, but that's an issue for htslib when we get
+ * there.)
+ */
+
+/*
+ * ---------------------------------------------------------------------------
+ * Shared utility functions by both methods.
+ */
+
+#define haszero(x) (((x)-0x0101010101010101UL)&~(x)&0x8080808080808080UL)
+#define MIN(a,b) ((a)<(b)?(a):(b))
+static int dump_ref(sam_hdr_t *h, hts_itr_t *iter, int ref_id,
+                    char *ref, uint64_t ref_len, FILE *fp, int verbose) {
+    int N = 0;
+    if (iter && iter->end >= HTS_POS_MAX)
+        iter->end = ref_len;
+    if (iter && (iter->beg > 0 || iter->end < ref_len)) {
+        fprintf(fp, ">%s:%"PRIhts_pos"-%"PRIhts_pos"\n",
+                sam_hdr_tid2name(h, ref_id), iter->beg+1, iter->end);
+        ref += iter->beg;
+        ref_len = MIN(ref_len, iter->end) - iter->beg;
+    } else {
+        fprintf(fp, ">%s\n", sam_hdr_tid2name(h, ref_id));
+    }
+
+    int i, j;
+    uint64_t rem = ref_len;
+
+    // Count coverage, purely for information purposes.
+    // About 90% of dump_ref CPU is here, so maybe this isn't useful,
+    // but this is still 3-4x faster than the obvious naive loop.
+    //
+    // Overall though it's only about 5% overhead of the entire process
+    // (was ~20%).
+    if (verbose) {
+        int n4[8] = {0};
+        for (j = 0; j < ref_len && (((uintptr_t) &ref[j] & 7) != 0); j++)
+            N += ref[j] == 'N';
+        uint64_t fast_end = ((ref_len - j) & ~7) + j;
+        for (; j < fast_end; j+=8) {
+            uint64_t i64 = *(uint64_t *)&ref[j];
+            if (!haszero(i64 ^ 0x4e4e4e4e4e4e4e4eUL)) // 'N' <-> 0
+                continue;
+
+            n4[0] += ref[j+0] == 'N';
+            n4[1] += ref[j+1] == 'N';
+            n4[2] += ref[j+2] == 'N';
+            n4[3] += ref[j+3] == 'N';
+            n4[4] += ref[j+4] == 'N';
+            n4[5] += ref[j+5] == 'N';
+            n4[6] += ref[j+6] == 'N';
+            n4[7] += ref[j+7] == 'N';
+        }
+        for (; j < ref_len; j++)
+            N += ref[j] == 'N';
+        N += n4[0]+n4[1]+n4[2]+n4[3]+
+            n4[4]+n4[5]+n4[6]+n4[7];
+    }
+
+    // Format reference
+    for (i = 0; i < ref_len; i += 60, rem -= 60) {
+        int len = (int)(rem < 60 ? rem : 60);
+        if (fwrite(ref, 1, len, fp) != len)
+            return -1;
+        putc('\n', fp);
+        ref += 60;
+    }
+
+    if (verbose)
+        fprintf(samtools_stderr, "Dump ref %d len %"PRId64", coverage %.2f%%\n",
+                ref_id, ref_len, 100 - N*100.0 / ref_len);
+
+    return 0;
+}
+
+/*
+ * ---------------------------------------------------------------------------
+ * CRAM embedded reference method of reference construction
+ */
+
+/*
+ * Extracts an embedded reference from a sorted CRAM file.
+ * Modelled on the CRAM container copy loop from bam_cat.c.
+ */
+static int cram2ref(samFile *in, sam_hdr_t *h, hts_idx_t *idx, char *reg,
+                    FILE *outfp, int verbose) {
+    cram_fd *in_c;
+    cram_container *c = NULL;
+    cram_block *blk = NULL;
+    cram_block_slice_hdr *shdr = NULL;
+
+    int curr_ref_id = -99;
+    char *ref = NULL;
+    uint64_t ref_len = 0;
+
+    // We have no direct public API for seeking in CRAM to a specific
+    // location by genome coordinates.  The sam_itr_query API is
+    // designed for fetching records, rather than seeks to specific
+    // file locations.
+    //
+    // TODO: consider exposing cram_range and cram_seek_to_refpos API.
+    // After a sam_index_load which will add the index to infp, these
+    // functions should seek direct to the start of a container.
+    // Or use cram_index *e =cram_index_query(cram, tid, beg, NULL);
+    //
+    // However, fortuitously(?) sam_itr_querys calls cram_seek_to_refpos
+    // so we can do a region query and let that do the initial seek.
+    // We still need to do our own end-range detection though.
+
+    hts_itr_t *iter = NULL;
+    if (reg) {
+        iter = sam_itr_querys(idx, h, reg);
+        if (!iter) {
+            print_error("reference", "failed to parse region '%s'", reg);
+            goto err;
+        }
+    }
+
+    in_c = in->fp.cram; // low level htslib abuse?
+    int eor = 0;
+    while (!eor && (c = cram_read_container(in_c))) {
+        if (cram_container_is_empty(in_c)) {
+            cram_block *blk;
+            // Container compression header
+            if (!(blk = cram_read_block(in_c)))
+                goto err;
+            cram_free_block(blk);
+            cram_free_container(c);
+            c = NULL; blk = NULL;
+            continue;
+        }
+
+        // Container compression header; read and discard
+        int32_t num_slices;
+        if (!(blk = cram_read_block(in_c)))
+            goto err;
+        cram_free_block(blk);
+        blk = NULL;
+
+        // Container num_blocks can be invalid, due to a bug.
+        // Instead we iterate in slice context instead.
+        (void)cram_container_get_landmarks(c, &num_slices);
+        int i, j;
+        for (i = 0; i < num_slices; i++) {
+            // Slice header
+            if (!(blk = cram_read_block(in_c)))
+                goto err;
+            if (!(shdr = cram_decode_slice_header(in_c, blk)))
+                goto err;
+            cram_free_block(blk);
+            blk = NULL;
+
+            int num_blocks = cram_slice_hdr_get_num_blocks(shdr);
+            int embed_id = cram_slice_hdr_get_embed_ref_id(shdr);
+            int ref_id;
+            hts_pos_t ref_start, ref_span;
+            cram_slice_hdr_get_coords(shdr, &ref_id, &ref_start, &ref_span);
+
+            if (iter) {
+                if (iter->tid != ref_id || ref_start > iter->end) {
+                    // Beyond end of specified region.
+                    cram_free_slice_header(shdr);
+                    eor = 1;
+                    break;
+                }
+            }
+
+            if (embed_id < 0 && ref_id != -1) {
+                fprintf(samtools_stderr, "CRAM file has slice without embedded "
+                        "reference\n");
+                goto err;
+            }
+
+            if (ref_id != curr_ref_id) {
+                if (curr_ref_id >= 0) {
+                    if (dump_ref(h, iter, curr_ref_id, ref, ref_len,
+                                 outfp, verbose) < 0)
+                        goto err;
+                }
+
+                ref_len = sam_hdr_tid2len(h, ref_id);
+                if (ref_len) {
+                    char *ref2 = realloc(ref, ref_len);
+                    if (!ref2)
+                        goto err;
+                    else
+                        ref = ref2;
+                    memset(ref, 'N', ref_len);
+                }
+                curr_ref_id = ref_id;
+            }
+
+            // Slice data blocks
+            for (j = 0; j < num_blocks; j++) {
+                // read and discard, unless it's the ref-ID block
+                if (!(blk = cram_read_block(in_c)))
+                    goto err;
+                if (cram_block_get_content_id(blk) == embed_id) {
+                    cram_uncompress_block(blk);
+                    //printf("%.*s\n", blk->uncomp_size, blk->data);
+
+                    int32_t usize = cram_block_get_uncomp_size(blk);
+                    int ref_end = ref_start + usize;
+                    if (ref_end > ref_len+1)
+                        ref_end = ref_len+1;
+                    if (ref_end > ref_start)
+                        memcpy(ref + ref_start-1, cram_block_get_data(blk),
+                               ref_end - ref_start);
+                }
+                cram_free_block(blk);
+                blk = NULL;
+            }
+            cram_free_slice_header(shdr);
+            shdr = NULL;
+        }
+
+        cram_free_container(c);
+        c = NULL;
+    }
+
+    int ret = 0;
+    if (curr_ref_id >= 0) {
+        ret = dump_ref(h, iter, curr_ref_id, ref, ref_len, outfp, verbose);
+    } else if (reg) {
+        // no data present
+        // no data present, but we explicitly asked for the reference so
+        // report it still as Ns.
+        ref_len = MIN(iter->end,  sam_hdr_tid2len(h, iter->tid));
+        ref = malloc(ref_len);
+        memset(ref, 'N', ref_len);
+        if (!ref)
+            goto err;
+        ret = dump_ref(h, iter, iter->tid, ref, ref_len, outfp, verbose);
+    }
+
+    free(ref);
+    if (iter)
+        hts_itr_destroy(iter);
+
+    return ret;
+
+ err:
+    free(ref);
+    if (blk)
+        cram_free_block(blk);
+    if (shdr)
+        cram_free_slice_header(shdr);
+    if (c)
+        cram_free_container(c);
+    if (iter)
+        hts_itr_destroy(iter);
+
+    return -1;
+}
+
+/*
+ * ---------------------------------------------------------------------------
+ * MD method of reference construction
+ */
+
+// Returns the next cigar op code: one of the BAM_C* codes,
+// or -1 if no more are present.
+static inline
+int next_cigar_op(uint32_t *cigar, int *ncigar, int *skip, int *spos,
+                  uint32_t *cig_ind, uint32_t *cig_op, uint32_t *cig_len) {
+    for(;;) {
+        while (*cig_len == 0) {
+            if (*cig_ind < *ncigar) {
+                *cig_op  = cigar[*cig_ind] & BAM_CIGAR_MASK;
+                *cig_len = cigar[*cig_ind] >> BAM_CIGAR_SHIFT;
+                (*cig_ind)++;
+            } else {
+                return -1;
+            }
+        }
+
+        if (skip[*cig_op]) {
+            *spos += (bam_cigar_type(*cig_op)&1) * *cig_len;
+            *cig_len = 0;
+            continue;
+        }
+
+        (*cig_len)--;
+        break;
+    }
+
+    return *cig_op;
+}
+
+// Converts a bam object with SEQ, POS/CIGAR and MD:Z to a reference.
+// Updates ref[] array.
+//
+// Returns >0 on success,
+//          0 on no-MD found,
+//         -1 on failure (eg inconsistent data)
+static int build_ref(bam1_t *b, char *ref, size_t ref_len) {
+    uint8_t *seq = bam_get_seq(b);
+    uint32_t *cigar = bam_get_cigar(b);
+    int ncigar = b->core.n_cigar;
+    uint32_t cig_op = 0, cig_len = 0, cig_ind = 0;
+
+    const uint8_t *MD = bam_aux_get(b, "MD");
+    if (!MD || *MD != 'Z')
+        return 0;
+    MD++;
+
+    // Walk through MD + seq to generate ref
+    int iseq = 0, iref = b->core.pos, next_op;
+    int cig_skip[16] = {0,1,0,1,1,1,1,0,0,1,1,1,1,1,1,1};
+    while (iseq < b->core.l_qseq && *MD) {
+        if (isdigit(*MD)) {
+            // match
+            int len = strtol((char *)MD, (char **)&MD, 10);
+            while (iseq < b->core.l_qseq && len) {
+                if ((next_op = next_cigar_op(cigar, &ncigar, cig_skip,
+                                             &iseq, &cig_ind, &cig_op,
+                                             &cig_len)) < 0)
+                    return -1;
+
+                if (next_op != BAM_CMATCH &&
+                    next_op != BAM_CEQUAL) {
+                    print_error("MD2ref",
+                                "MD:Z and CIGAR are incompatible");
+                    return -1;
+                }
+
+                if (iref < ref_len)
+                    ref[iref] = seq_nt16_str[bam_seqi(seq, iseq)];
+                iseq++;
+                iref++;
+                len--;
+            }
+        } else if (*MD == '^') {
+            // deletion
+            MD++;
+            while (*MD && isalpha(*MD)) {
+                if ((next_op = next_cigar_op(cigar, &ncigar, cig_skip,
+                                             &iseq, &cig_ind, &cig_op,
+                                             &cig_len)) < 0)
+                    return -1;
+
+                if (next_op != BAM_CDEL) {
+                    print_error("MD2ref",
+                                "MD:Z and CIGAR are incompatible");
+                    return -1;
+                }
+
+                if (iref < ref_len)
+                    ref[iref] = *MD;
+
+                MD++;
+                iref++;
+            }
+        } else {
+            // substitution
+            if ((next_op = next_cigar_op(cigar, &ncigar, cig_skip,
+                                         &iseq, &cig_ind, &cig_op,
+                                         &cig_len)) < 0)
+                return -1;
+
+            if (next_op != BAM_CMATCH && next_op != BAM_CDIFF) {
+                print_error("MD2ref", "MD:Z and CIGAR are incompatible");
+                return -1;
+            }
+            if (iref < ref_len)
+                ref[iref] = *MD;
+
+            MD++;
+            iref++;
+            iseq++;
+        }
+    }
+
+    return 1;
+}
+
+static int MD2ref(samFile *in, sam_hdr_t *h, hts_idx_t *idx, char *reg,
+                  FILE *outfp, int verbose) {
+    bam1_t *b = bam_init1();
+    int r, last_tid = -99;
+    size_t ref_len = 0;
+    char *ref = NULL;
+    int ret = -1;
+
+    hts_itr_t *iter = NULL;
+    if (idx && reg) {
+        iter = sam_itr_querys(idx, h, reg);
+        if (!iter) {
+            print_error("reference", "failed to parse region '%s'", reg);
+            goto err;
+        }
+    }
+
+    while ((r = iter
+                ? sam_itr_next(in, iter, b)
+                : sam_read1(in, h, b)) >= 0) {
+        // check b->core.tid and flush old seq.
+        if (b->core.tid != last_tid) {
+            if (last_tid >= 0)
+                if (dump_ref(h, iter, last_tid, ref, ref_len, outfp,
+                             verbose) < 0)
+                    goto err;
+
+            last_tid = b->core.tid;
+            ref_len = sam_hdr_tid2len(h, last_tid);
+            if (ref_len) {
+                char *ref2 = realloc(ref, ref_len);
+                if (!ref2)
+                    goto err;
+                else
+                    ref = ref2;
+                memset(ref, 'N', ref_len);
+            }
+        }
+
+        if (build_ref(b, ref, ref_len) < 0)
+            goto err;
+    }
+
+    if (last_tid >= 0) {
+        if (dump_ref(h, iter, last_tid, ref, ref_len, outfp, verbose) < 0)
+            goto err;
+    } else if (reg) {
+        // no data present, but we explicitly asked for the reference so
+        // report it still as Ns.
+        ref_len = MIN(iter->end,  sam_hdr_tid2len(h, iter->tid));
+        ref = malloc(ref_len);
+        memset(ref, 'N', ref_len);
+        if (!ref)
+            goto err;
+        if (dump_ref(h, iter, iter->tid, ref, ref_len, outfp, verbose) < 0)
+            goto err;
+    }
+
+    if (r < -1)
+        goto err;
+
+    ret = 0;
+
+ err:
+    if (iter)
+        hts_itr_destroy(iter);
+    bam_destroy1(b);
+    free(ref);
+    return ret;
+}
+
+int main_reference(int argc, char *argv[])
+{
+    int c, usage = 0, verbose = 1, use_embedded = 0;
+    sam_hdr_t *h = 0;
+    samFile *in = NULL;
+    hts_idx_t *idx = NULL;
+    sam_global_args ga;
+    FILE *outfp = samtools_stdout;
+    char *reg = NULL;
+
+    static const struct option lopts[] = {
+        {"output",   required_argument, NULL, 'o'},
+        {"quiet",    no_argument,       NULL, 'q'},
+        {"embedded", no_argument,       NULL, 'e'},
+        {"region",   required_argument, NULL, 'r'},
+        SAM_OPT_GLOBAL_OPTIONS('-', '-', '-', '-', '-', '@'),
+        { NULL, 0, NULL, 0 }
+    };
+
+    sam_global_args_init(&ga);
+
+    while ((c = getopt_long(argc, argv, "@:qo:er:", lopts, NULL)) >= 0) {
+        switch (c) {
+        case 'o':
+            if (!(outfp = fopen(optarg, "w"))) {
+                perror(optarg);
+                goto err;
+            }
+            break;
+
+        case 'q':
+            verbose = 0;
+            break;
+
+        case 'e':
+            use_embedded = 1;
+            break;
+
+        case 'r':
+            reg = optarg;
+            break;
+
+        default:
+            if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break;
+            /* else fall-through */
+        case '?': usage=1; break;
+        }
+    }
+
+    if ((optind == argc && isatty(0)) || usage) {
+        fprintf(samtools_stdout, "Usage: samtools reference [-@ N] [-r region] [-e] [-q] [-o out.fa] [in.cram]\n");
+        return 0;
+    }
+
+    char *fn = optind < argc ? argv[optind] : "-";
+    if (!(in = sam_open(fn, "r"))) {
+        print_error_errno("reference", "failed to open file '%s'", fn);
+        return 1;
+    }
+
+    if (ga.nthreads > 0)
+        hts_set_threads(in, ga.nthreads);
+
+    if (!(h = sam_hdr_read(in)))
+        goto err;
+
+    if (reg) {
+        idx = sam_index_load(in, fn);
+        if (!idx) {
+            print_error_errno("reference", "Failed to load the index");
+            goto err;
+        }
+    }
+
+    int ret = use_embedded
+        ? cram2ref(in, h, idx, reg, outfp, verbose)
+        : MD2ref(in, h, idx, reg, outfp, verbose);
+
+    sam_hdr_destroy(h);
+    if (outfp != samtools_stdout)
+        fclose(outfp);
+    if (idx)
+        hts_idx_destroy(idx);
+    sam_close(in);
+
+    return ret;
+
+ err:
+    if (idx)
+        hts_idx_destroy(idx);
+    if (in)
+        sam_close(in);
+    if (h)
+        sam_hdr_destroy(h);
+
+    return 1;
+}
diff --git a/samtools/sam_opts.c b/samtools/sam_opts.c
new file mode 100644
index 0000000..6d146de
--- /dev/null
+++ b/samtools/sam_opts.c
@@ -0,0 +1,194 @@
+/*  sam_opts.c -- utilities to aid parsing common command line options.
+
+    Copyright (C) 2015, 2019 Genome Research Ltd.
+
+    Author: James Bonfield <jkb@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <config.h>
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include "sam_opts.h"
+
+/*
+ * Processes a standard "global" samtools long option.
+ *
+ * The 'c' value is the return value from a getopt_long() call.  It is checked
+ * against the lopt[] array to find the corresponding value as this may have
+ * been reassigned by the individual subcommand.
+ *
+ * Having found the entry, the corresponding long form is used to apply the
+ * option, storing the setting in sam_global_args *ga.
+ *
+ * Returns 0 on success,
+ *        -1 on failure.
+ */
+int parse_sam_global_opt(int c, const char *optarg, const struct option *lopt,
+                         sam_global_args *ga) {
+    int r = 0;
+
+    while (lopt->name) {
+        if (c != lopt->val) {
+            lopt++;
+            continue;
+        }
+
+        if (strcmp(lopt->name, "input-fmt") == 0) {
+            r = hts_parse_format(&ga->in, optarg);
+            break;
+        } else if (strcmp(lopt->name, "input-fmt-option") == 0) {
+            r = hts_opt_add((hts_opt **)&ga->in.specific, optarg);
+            break;
+        } else if (strcmp(lopt->name, "output-fmt") == 0) {
+            r = hts_parse_format(&ga->out, optarg);
+            break;
+        } else if (strcmp(lopt->name, "output-fmt-option") == 0) {
+            r = hts_opt_add((hts_opt **)&ga->out.specific, optarg);
+            break;
+        } else if (strcmp(lopt->name, "reference") == 0) {
+            char *ref = malloc(10 + strlen(optarg) + 1);
+
+            if (!ref) {
+                fprintf(stderr, "Unable to allocate memory in "
+                                "parse_sam_global_opt.\n");
+
+                return -1;
+            }
+
+            sprintf(ref, "reference=%s", optarg);
+
+            if (!(ga->reference = strdup(optarg))) {
+                fprintf(stderr, "Unable to allocate memory in "
+                                "parse_sam_global_opt.\n");
+
+                return -1;
+            }
+
+            r  = hts_opt_add((hts_opt **)&ga->in.specific, ref);
+            r |= hts_opt_add((hts_opt **)&ga->out.specific, ref);
+            free(ref);
+            break;
+        } else if (strcmp(lopt->name, "threads") == 0) {
+            ga->nthreads = atoi(optarg);
+            break;
+        } else if (strcmp(lopt->name, "write-index") == 0) {
+            ga->write_index = 1;
+            break;
+        } else if (strcmp(lopt->name, "verbosity") == 0) {
+            hts_verbose = atoi(optarg);
+            break;
+        }
+    }
+
+    if (!lopt->name) {
+        fprintf(stderr, "Unexpected global option.\n");
+        return -1;
+    }
+
+    /*
+     * SAM format with compression enabled implies SAM.bgzf
+     */
+    if (ga->out.format == sam) {
+        hts_opt *opts = (hts_opt *)ga->out.specific;
+        while (opts) {
+            if (opts->opt == HTS_OPT_COMPRESSION_LEVEL)
+                ga->out.compression = bgzf;
+            opts = opts->next;
+        }
+    }
+
+    return r;
+}
+
+/*
+ * Report the usage for global options.
+ *
+ * This accepts a string with one character per SAM_OPT_GLOBAL_OPTIONS option
+ * to determine which options need to be printed and how.
+ * Each character should be one of:
+ * '.'    No short option has been assigned. Use --long-opt only.
+ * '-'    The long (and short) option has been disabled.
+ * <c>    Otherwise the short option is character <c>.
+ */
+void sam_global_opt_help(FILE *fp, const char *shortopts) {
+    int i = 0;
+
+    static const struct option lopts[] = {
+        SAM_OPT_GLOBAL_OPTIONS(0,0,0,0,0,0),
+        { NULL, 0, NULL, 0 }
+    };
+
+    for (i = 0; shortopts && shortopts[i] && lopts[i].name; i++) {
+        if (shortopts[i] == '-')
+            continue;
+
+        if (shortopts[i] == '.')
+            fprintf(fp, "      --");
+        else
+            fprintf(fp, "  -%c, --", shortopts[i]);
+
+        if (strcmp(lopts[i].name, "input-fmt") == 0)
+            fprintf(fp,"input-fmt FORMAT[,OPT[=VAL]]...\n"
+                    "               Specify input format (SAM, BAM, CRAM)\n");
+        else if (strcmp(lopts[i].name, "input-fmt-option") == 0)
+            fprintf(fp,"input-fmt-option OPT[=VAL]\n"
+                    "               Specify a single input file format option in the form\n"
+                    "               of OPTION or OPTION=VALUE\n");
+        else if (strcmp(lopts[i].name, "output-fmt") == 0)
+            fprintf(fp,"output-fmt FORMAT[,OPT[=VAL]]...\n"
+                    "               Specify output format (SAM, BAM, CRAM)\n");
+        else if (strcmp(lopts[i].name, "output-fmt-option") == 0)
+            fprintf(fp,"output-fmt-option OPT[=VAL]\n"
+                    "               Specify a single output file format option in the form\n"
+                    "               of OPTION or OPTION=VALUE\n");
+        else if (strcmp(lopts[i].name, "reference") == 0)
+            fprintf(fp,"reference FILE\n"
+                    "               Reference sequence FASTA FILE [null]\n");
+        else if (strcmp(lopts[i].name, "threads") == 0)
+            fprintf(fp,"threads INT\n"
+                    "               Number of additional threads to use [0]\n");
+        else if (strcmp(lopts[i].name, "write-index") == 0)
+            fprintf(fp,"write-index\n"
+                    "               Automatically index the output files [off]\n");
+        else if (strcmp(lopts[i].name, "verbosity") == 0)
+            fprintf(fp,"verbosity INT\n"
+                    "               Set level of verbosity\n");
+    }
+}
+
+void sam_global_args_init(sam_global_args *ga) {
+    if (!ga)
+        return;
+
+    memset(ga, 0, sizeof(*ga));
+}
+
+void sam_global_args_free(sam_global_args *ga) {
+    if (ga->in.specific)
+        hts_opt_free(ga->in.specific);
+
+    if (ga->out.specific)
+        hts_opt_free(ga->out.specific);
+
+    if (ga->reference)
+        free(ga->reference);
+}
diff --git a/samtools/sam_opts.c.pysam.c b/samtools/sam_opts.c.pysam.c
new file mode 100644
index 0000000..99bb169
--- /dev/null
+++ b/samtools/sam_opts.c.pysam.c
@@ -0,0 +1,196 @@
+#include "samtools.pysam.h"
+
+/*  sam_opts.c -- utilities to aid parsing common command line options.
+
+    Copyright (C) 2015, 2019 Genome Research Ltd.
+
+    Author: James Bonfield <jkb@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <config.h>
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include "sam_opts.h"
+
+/*
+ * Processes a standard "global" samtools long option.
+ *
+ * The 'c' value is the return value from a getopt_long() call.  It is checked
+ * against the lopt[] array to find the corresponding value as this may have
+ * been reassigned by the individual subcommand.
+ *
+ * Having found the entry, the corresponding long form is used to apply the
+ * option, storing the setting in sam_global_args *ga.
+ *
+ * Returns 0 on success,
+ *        -1 on failure.
+ */
+int parse_sam_global_opt(int c, const char *optarg, const struct option *lopt,
+                         sam_global_args *ga) {
+    int r = 0;
+
+    while (lopt->name) {
+        if (c != lopt->val) {
+            lopt++;
+            continue;
+        }
+
+        if (strcmp(lopt->name, "input-fmt") == 0) {
+            r = hts_parse_format(&ga->in, optarg);
+            break;
+        } else if (strcmp(lopt->name, "input-fmt-option") == 0) {
+            r = hts_opt_add((hts_opt **)&ga->in.specific, optarg);
+            break;
+        } else if (strcmp(lopt->name, "output-fmt") == 0) {
+            r = hts_parse_format(&ga->out, optarg);
+            break;
+        } else if (strcmp(lopt->name, "output-fmt-option") == 0) {
+            r = hts_opt_add((hts_opt **)&ga->out.specific, optarg);
+            break;
+        } else if (strcmp(lopt->name, "reference") == 0) {
+            char *ref = malloc(10 + strlen(optarg) + 1);
+
+            if (!ref) {
+                fprintf(samtools_stderr, "Unable to allocate memory in "
+                                "parse_sam_global_opt.\n");
+
+                return -1;
+            }
+
+            sprintf(ref, "reference=%s", optarg);
+
+            if (!(ga->reference = strdup(optarg))) {
+                fprintf(samtools_stderr, "Unable to allocate memory in "
+                                "parse_sam_global_opt.\n");
+
+                return -1;
+            }
+
+            r  = hts_opt_add((hts_opt **)&ga->in.specific, ref);
+            r |= hts_opt_add((hts_opt **)&ga->out.specific, ref);
+            free(ref);
+            break;
+        } else if (strcmp(lopt->name, "threads") == 0) {
+            ga->nthreads = atoi(optarg);
+            break;
+        } else if (strcmp(lopt->name, "write-index") == 0) {
+            ga->write_index = 1;
+            break;
+        } else if (strcmp(lopt->name, "verbosity") == 0) {
+            hts_verbose = atoi(optarg);
+            break;
+        }
+    }
+
+    if (!lopt->name) {
+        fprintf(samtools_stderr, "Unexpected global option.\n");
+        return -1;
+    }
+
+    /*
+     * SAM format with compression enabled implies SAM.bgzf
+     */
+    if (ga->out.format == sam) {
+        hts_opt *opts = (hts_opt *)ga->out.specific;
+        while (opts) {
+            if (opts->opt == HTS_OPT_COMPRESSION_LEVEL)
+                ga->out.compression = bgzf;
+            opts = opts->next;
+        }
+    }
+
+    return r;
+}
+
+/*
+ * Report the usage for global options.
+ *
+ * This accepts a string with one character per SAM_OPT_GLOBAL_OPTIONS option
+ * to determine which options need to be printed and how.
+ * Each character should be one of:
+ * '.'    No short option has been assigned. Use --long-opt only.
+ * '-'    The long (and short) option has been disabled.
+ * <c>    Otherwise the short option is character <c>.
+ */
+void sam_global_opt_help(FILE *fp, const char *shortopts) {
+    int i = 0;
+
+    static const struct option lopts[] = {
+        SAM_OPT_GLOBAL_OPTIONS(0,0,0,0,0,0),
+        { NULL, 0, NULL, 0 }
+    };
+
+    for (i = 0; shortopts && shortopts[i] && lopts[i].name; i++) {
+        if (shortopts[i] == '-')
+            continue;
+
+        if (shortopts[i] == '.')
+            fprintf(fp, "      --");
+        else
+            fprintf(fp, "  -%c, --", shortopts[i]);
+
+        if (strcmp(lopts[i].name, "input-fmt") == 0)
+            fprintf(fp,"input-fmt FORMAT[,OPT[=VAL]]...\n"
+                    "               Specify input format (SAM, BAM, CRAM)\n");
+        else if (strcmp(lopts[i].name, "input-fmt-option") == 0)
+            fprintf(fp,"input-fmt-option OPT[=VAL]\n"
+                    "               Specify a single input file format option in the form\n"
+                    "               of OPTION or OPTION=VALUE\n");
+        else if (strcmp(lopts[i].name, "output-fmt") == 0)
+            fprintf(fp,"output-fmt FORMAT[,OPT[=VAL]]...\n"
+                    "               Specify output format (SAM, BAM, CRAM)\n");
+        else if (strcmp(lopts[i].name, "output-fmt-option") == 0)
+            fprintf(fp,"output-fmt-option OPT[=VAL]\n"
+                    "               Specify a single output file format option in the form\n"
+                    "               of OPTION or OPTION=VALUE\n");
+        else if (strcmp(lopts[i].name, "reference") == 0)
+            fprintf(fp,"reference FILE\n"
+                    "               Reference sequence FASTA FILE [null]\n");
+        else if (strcmp(lopts[i].name, "threads") == 0)
+            fprintf(fp,"threads INT\n"
+                    "               Number of additional threads to use [0]\n");
+        else if (strcmp(lopts[i].name, "write-index") == 0)
+            fprintf(fp,"write-index\n"
+                    "               Automatically index the output files [off]\n");
+        else if (strcmp(lopts[i].name, "verbosity") == 0)
+            fprintf(fp,"verbosity INT\n"
+                    "               Set level of verbosity\n");
+    }
+}
+
+void sam_global_args_init(sam_global_args *ga) {
+    if (!ga)
+        return;
+
+    memset(ga, 0, sizeof(*ga));
+}
+
+void sam_global_args_free(sam_global_args *ga) {
+    if (ga->in.specific)
+        hts_opt_free(ga->in.specific);
+
+    if (ga->out.specific)
+        hts_opt_free(ga->out.specific);
+
+    if (ga->reference)
+        free(ga->reference);
+}
diff --git a/samtools/sam_opts.h b/samtools/sam_opts.h
new file mode 100644
index 0000000..7543c33
--- /dev/null
+++ b/samtools/sam_opts.h
@@ -0,0 +1,104 @@
+/*  sam_opts.h -- utilities to aid parsing common command line options.
+
+    Copyright (C) 2015, 2019 Genome Research Ltd.
+
+    Author: James Bonfield <jkb@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#ifndef SAM_OPTS_H
+#define SAM_OPTS_H
+
+#include <stdio.h>
+#include <limits.h>
+#include <getopt.h>
+#include <htslib/hts.h>
+
+typedef struct sam_global_args {
+    htsFormat in;
+    htsFormat out;
+    char *reference;
+    int nthreads;
+    int write_index;
+} sam_global_args;
+
+#define SAM_GLOBAL_ARGS_INIT {{0},{0}}
+
+enum {
+    SAM_OPT_INPUT_FMT = CHAR_MAX+1,
+    SAM_OPT_INPUT_FMT_OPTION,
+    SAM_OPT_OUTPUT_FMT,
+    SAM_OPT_OUTPUT_FMT_OPTION,
+    SAM_OPT_REFERENCE,
+    SAM_OPT_NTHREADS,
+    SAM_OPT_WRITE_INDEX,
+    SAM_OPT_VERBOSITY,
+};
+
+#define SAM_OPT_VAL(val, defval) ((val) == '-')? '?' : (val)? (val) : (defval)
+
+// Use this within struct option lopts[] = {...} to add the standard global
+// options.  The arguments determine whether the corresponding option is
+// enabled and, if so, whether it has a short option equivalent:
+// 0      No short option has been assigned. Use --long-opt only.
+// '-'    Both long and short options are disabled.
+// <c>    Otherwise the equivalent short option is character <c>.
+#define SAM_OPT_GLOBAL_OPTIONS(o1, o2, o3, o4, o5, o6) \
+    {"input-fmt",         required_argument, NULL, SAM_OPT_VAL(o1, SAM_OPT_INPUT_FMT)}, \
+    {"input-fmt-option",  required_argument, NULL, SAM_OPT_VAL(o2, SAM_OPT_INPUT_FMT_OPTION)}, \
+    {"output-fmt",        required_argument, NULL, SAM_OPT_VAL(o3, SAM_OPT_OUTPUT_FMT)}, \
+    {"output-fmt-option", required_argument, NULL, SAM_OPT_VAL(o4, SAM_OPT_OUTPUT_FMT_OPTION)}, \
+    {"reference",         required_argument, NULL, SAM_OPT_VAL(o5, SAM_OPT_REFERENCE)}, \
+    {"threads",           required_argument, NULL, SAM_OPT_VAL(o6, SAM_OPT_NTHREADS)}, \
+    {"write-index",       no_argument,       NULL, SAM_OPT_WRITE_INDEX}, \
+    {"verbosity",         required_argument, NULL, SAM_OPT_VERBOSITY}
+
+/*
+ * Processes a standard "global" samtools long option.
+ *
+ * The 'c' value is the return value from a getopt_long() call.  It is checked
+ * against the lopt[] array to find the corresponding value as this may have
+ * been reassigned by the individual subcommand.
+ *
+ * Having found the entry, the corresponding long form is used to apply the
+ * option, storing the setting in sam_global_args *ga.
+ *
+ * Returns 0 on success,
+ *        -1 on failure.
+ */
+int parse_sam_global_opt(int c, const char *optarg, const struct option *lopt,
+                         sam_global_args *ga);
+
+/*
+ * Report the usage for global options.
+ *
+ * This accepts a string with one character per SAM_OPT_GLOBAL_OPTIONS option
+ * to determine which options need to be printed and how.
+ * Each character should be one of:
+ * '.'    No short option has been assigned. Use --long-opt only.
+ * '-'    The long (and short) option has been disabled.
+ * <c>    Otherwise the short option is character <c>.
+ */
+void sam_global_opt_help(FILE *fp, const char *shortopts);
+
+
+void sam_global_args_init(sam_global_args *ga);
+void sam_global_args_free(sam_global_args *ga);
+
+#endif
diff --git a/samtools/sam_utils.c b/samtools/sam_utils.c
new file mode 100644
index 0000000..f105687
--- /dev/null
+++ b/samtools/sam_utils.c
@@ -0,0 +1,151 @@
+/*  sam_utils.c -- various utilities internal to samtools.
+
+    Copyright (C) 2014-2016, 2018, 2019 Genome Research Ltd.
+
+    Author: John Marshall <jm18@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <config.h>
+#include <stdlib.h>
+
+#include <stdio.h>
+#include <stdarg.h>
+#include <string.h>
+#include <errno.h>
+
+#include "samtools.h"
+
+static htsFile *samtools_stdout = NULL;
+
+void autoflush_if_stdout(htsFile *fp, const char *fname) {
+    if (fname == NULL || strcmp(fname, "-") == 0) samtools_stdout = fp;
+}
+
+void release_autoflush(htsFile *fp) {
+    if (samtools_stdout == fp) samtools_stdout = NULL;
+}
+
+static void vprint_error_core(const char *subcommand, const char *format, va_list args, const char *extra)
+{
+    fflush(stdout);
+    if (samtools_stdout) hts_flush(samtools_stdout);
+
+    if (subcommand && *subcommand) fprintf(stderr, "samtools %s: ", subcommand);
+    else fprintf(stderr, "samtools: ");
+    vfprintf(stderr, format, args);
+    if (extra) fprintf(stderr, ": %s\n", extra);
+    else fprintf(stderr, "\n");
+    fflush(stderr);
+}
+
+void print_error(const char *subcommand, const char *format, ...)
+{
+    va_list args;
+    va_start(args, format);
+    vprint_error_core(subcommand, format, args, NULL);
+    va_end(args);
+}
+
+void print_error_errno(const char *subcommand, const char *format, ...)
+{
+    int err = errno;
+    va_list args;
+    va_start(args, format);
+    vprint_error_core(subcommand, format, args, err? strerror(err) : NULL);
+    va_end(args);
+}
+
+void check_sam_close(const char *subcmd, samFile *fp, const char *fname, const char *null_fname, int *retp)
+{
+    release_autoflush(fp);
+    int r = sam_close(fp);
+    if (r >= 0) return;
+
+    // TODO Need error infrastructure so we can print a message instead of r
+    if (fname) print_error(subcmd, "error closing \"%s\": %d", fname, r);
+    else print_error(subcmd, "error closing %s: %d", null_fname, r);
+
+    *retp = EXIT_FAILURE;
+}
+
+/* Pick an index suffix based on the output file descriptor type. */
+static char *idx_suffix(htsFile *fp) {
+    switch (fp->format.format) {
+    case sam:
+    case bam:
+        // Tough cheese if you wanted bai!
+        // New feature => mandatory new index too, for simplicity of CLI.
+        return "csi";
+
+    case cram:
+        return "crai";
+
+    default:
+        return NULL;
+    }
+}
+
+/*
+ * Utility function to add an index to a file we've opened for write.
+ * NB: Call this after writing the header and before writing sequences.
+ *
+ * The returned index filename should be freed by the caller, but only
+ * after sam_idx_save has been called.
+ *
+ * Returns index filename on success,
+ *         NULL on failure.
+ */
+char *auto_index(htsFile *fp, const char *fn, bam_hdr_t *header) {
+    char *fn_idx;
+    int min_shift = 14; /* CSI */
+    if (!fn || !*fn || strcmp(fn, "-") == 0)
+        return NULL;
+
+    char *delim = strstr(fn, HTS_IDX_DELIM);
+    if (delim != NULL) {
+        delim += strlen(HTS_IDX_DELIM);
+
+        fn_idx = strdup(delim);
+        if (!fn_idx)
+            return NULL;
+
+        size_t l = strlen(fn_idx);
+        if (l >= 4 && strcmp(fn_idx + l - 4, ".bai") == 0)
+            min_shift = 0;
+    } else {
+        char *suffix = idx_suffix(fp);
+        if (!suffix)
+            return NULL;
+
+        fn_idx = malloc(strlen(fn)+6);
+        if (!fn_idx)
+            return NULL;
+
+        sprintf(fn_idx, "%s.%s", fn, suffix);
+    }
+
+    if (sam_idx_init(fp, header, min_shift, fn_idx) < 0) {
+        print_error_errno("auto_index", "failed to open index \"%s\" for writing", fn_idx);
+        free(fn_idx);
+        return NULL;
+    }
+
+    return fn_idx;
+}
diff --git a/samtools/sam_utils.c.pysam.c b/samtools/sam_utils.c.pysam.c
new file mode 100644
index 0000000..a5f08a9
--- /dev/null
+++ b/samtools/sam_utils.c.pysam.c
@@ -0,0 +1,153 @@
+#include "samtools.pysam.h"
+
+/*  sam_utils.c -- various utilities internal to samtools.
+
+    Copyright (C) 2014-2016, 2018, 2019 Genome Research Ltd.
+
+    Author: John Marshall <jm18@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <config.h>
+#include <stdlib.h>
+
+#include <stdio.h>
+#include <stdarg.h>
+#include <string.h>
+#include <errno.h>
+
+#include "samtools.h"
+
+static htsFile *samtools_stdout_internal = NULL;
+
+void autoflush_if_stdout(htsFile *fp, const char *fname) {
+    if (fname == NULL || strcmp(fname, "-") == 0) samtools_stdout_internal = fp;
+}
+
+void release_autoflush(htsFile *fp) {
+    if (samtools_stdout_internal == fp) samtools_stdout_internal = NULL;
+}
+
+static void vprint_error_core(const char *subcommand, const char *format, va_list args, const char *extra)
+{
+    fflush(samtools_stdout);
+    if (samtools_stdout_internal) hts_flush(samtools_stdout_internal);
+
+    if (subcommand && *subcommand) fprintf(samtools_stderr, "samtools %s: ", subcommand);
+    else fprintf(samtools_stderr, "samtools: ");
+    vfprintf(samtools_stderr, format, args);
+    if (extra) fprintf(samtools_stderr, ": %s\n", extra);
+    else fprintf(samtools_stderr, "\n");
+    fflush(samtools_stderr);
+}
+
+void print_error(const char *subcommand, const char *format, ...)
+{
+    va_list args;
+    va_start(args, format);
+    vprint_error_core(subcommand, format, args, NULL);
+    va_end(args);
+}
+
+void print_error_errno(const char *subcommand, const char *format, ...)
+{
+    int err = errno;
+    va_list args;
+    va_start(args, format);
+    vprint_error_core(subcommand, format, args, err? strerror(err) : NULL);
+    va_end(args);
+}
+
+void check_sam_close(const char *subcmd, samFile *fp, const char *fname, const char *null_fname, int *retp)
+{
+    release_autoflush(fp);
+    int r = sam_close(fp);
+    if (r >= 0) return;
+
+    // TODO Need error infrastructure so we can print a message instead of r
+    if (fname) print_error(subcmd, "error closing \"%s\": %d", fname, r);
+    else print_error(subcmd, "error closing %s: %d", null_fname, r);
+
+    *retp = EXIT_FAILURE;
+}
+
+/* Pick an index suffix based on the output file descriptor type. */
+static char *idx_suffix(htsFile *fp) {
+    switch (fp->format.format) {
+    case sam:
+    case bam:
+        // Tough cheese if you wanted bai!
+        // New feature => mandatory new index too, for simplicity of CLI.
+        return "csi";
+
+    case cram:
+        return "crai";
+
+    default:
+        return NULL;
+    }
+}
+
+/*
+ * Utility function to add an index to a file we've opened for write.
+ * NB: Call this after writing the header and before writing sequences.
+ *
+ * The returned index filename should be freed by the caller, but only
+ * after sam_idx_save has been called.
+ *
+ * Returns index filename on success,
+ *         NULL on failure.
+ */
+char *auto_index(htsFile *fp, const char *fn, bam_hdr_t *header) {
+    char *fn_idx;
+    int min_shift = 14; /* CSI */
+    if (!fn || !*fn || strcmp(fn, "-") == 0)
+        return NULL;
+
+    char *delim = strstr(fn, HTS_IDX_DELIM);
+    if (delim != NULL) {
+        delim += strlen(HTS_IDX_DELIM);
+
+        fn_idx = strdup(delim);
+        if (!fn_idx)
+            return NULL;
+
+        size_t l = strlen(fn_idx);
+        if (l >= 4 && strcmp(fn_idx + l - 4, ".bai") == 0)
+            min_shift = 0;
+    } else {
+        char *suffix = idx_suffix(fp);
+        if (!suffix)
+            return NULL;
+
+        fn_idx = malloc(strlen(fn)+6);
+        if (!fn_idx)
+            return NULL;
+
+        sprintf(fn_idx, "%s.%s", fn, suffix);
+    }
+
+    if (sam_idx_init(fp, header, min_shift, fn_idx) < 0) {
+        print_error_errno("auto_index", "failed to open index \"%s\" for writing", fn_idx);
+        free(fn_idx);
+        return NULL;
+    }
+
+    return fn_idx;
+}
diff --git a/samtools/sam_view.c b/samtools/sam_view.c
new file mode 100644
index 0000000..d60d8f7
--- /dev/null
+++ b/samtools/sam_view.c
@@ -0,0 +1,1596 @@
+/*  sam_view.c -- SAM<->BAM<->CRAM conversion.
+
+    Copyright (C) 2009-2022 Genome Research Ltd.
+    Portions copyright (C) 2009, 2011, 2012 Broad Institute.
+
+    Author: Heng Li <lh3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notices and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <config.h>
+
+#include <stdlib.h>
+#include <string.h>
+#include <strings.h>
+#include <stdio.h>
+#include <unistd.h>
+#include <math.h>
+#include <inttypes.h>
+#include <getopt.h>
+#include "htslib/sam.h"
+#include "htslib/faidx.h"
+#include "htslib/khash.h"
+#include "htslib/kstring.h"
+#include "htslib/thread_pool.h"
+#include "htslib/hts_expr.h"
+#include "samtools.h"
+#include "sam_opts.h"
+#include "bam.h" // for bam_get_library and bam_remove_B
+#include "bedidx.h"
+
+KHASH_SET_INIT_STR(str)
+typedef khash_t(str) *strhash_t;
+
+KHASH_SET_INIT_INT(aux_exists)
+typedef khash_t(aux_exists) *auxhash_t;
+
+// This structure contains the settings for a samview run
+typedef struct samview_settings {
+    strhash_t rghash;
+    strhash_t rnhash;
+    strhash_t tvhash;
+    int min_mapQ;
+
+    // Described here in the same terms as the usage statement.
+    // The code however always negates to "reject if"         keep if:
+    int flag_on;     // keep   if (FLAG & N) == N             (all on)
+    int flag_off;    // keep   if (FLAG & N) == 0             (all off)
+    int flag_anyon;  // keep   if (FLAG & N) != 0             (any on)
+    int flag_alloff; // reject if (FLAG & N) == N             (any off)
+
+    int min_qlen;
+    int remove_B;
+    uint32_t subsam_seed;
+    double subsam_frac;
+    char* library;
+    void* bed;
+    size_t remove_aux_len;
+    char** remove_aux;
+    int multi_region;
+    char* tag;
+    hts_filter_t *filter;
+    int remove_flag;
+    int add_flag;
+    int unmap;
+    auxhash_t remove_tag;
+    auxhash_t keep_tag;
+
+    hts_idx_t *hts_idx;
+    sam_hdr_t *header;
+    samFile *in, *out, *un_out;
+    int64_t count;
+    int is_count;
+    char *fn_in, *fn_idx_in, *fn_out, *fn_fai, *fn_un_out, *fn_out_idx, *fn_un_out_idx;
+    int fetch_pairs, nreglist;
+    hts_reglist_t *reglist;
+} samview_settings_t;
+
+// Copied from htslib/sam.c.
+// TODO: we need a proper interface to find the length of an aux tag,
+// or at the very make exportable versions of these in htslib.
+static inline int aux_type2size(uint8_t type)
+{
+    switch (type) {
+    case 'A': case 'c': case 'C':
+        return 1;
+    case 's': case 'S':
+        return 2;
+    case 'i': case 'I': case 'f':
+        return 4;
+    case 'd':
+        return 8;
+    case 'Z': case 'H': case 'B':
+        return type;
+    default:
+        return 0;
+    }
+}
+
+// Copied from htslib/sam.c.
+static inline uint8_t *skip_aux(uint8_t *s, uint8_t *end)
+{
+    int size;
+    uint32_t n;
+    if (s >= end) return end;
+    size = aux_type2size(*s); ++s; // skip type
+    switch (size) {
+    case 'Z':
+    case 'H':
+        while (s < end && *s) ++s;
+        return s < end ? s + 1 : end;
+    case 'B':
+        if (end - s < 5) return NULL;
+        size = aux_type2size(*s); ++s;
+        n = le_to_u32(s);
+        s += 4;
+        if (size == 0 || end - s < size * n) return NULL;
+        return s + size * n;
+    case 0:
+        return NULL;
+    default:
+        if (end - s < size) return NULL;
+        return s + size;
+    }
+}
+
+// Returns 0 to indicate read should be output 1 otherwise
+static int process_aln(const sam_hdr_t *h, bam1_t *b, samview_settings_t* settings)
+{
+    if (settings->filter && sam_passes_filter(h, b, settings->filter) < 1)
+        return 1;
+
+    if (settings->remove_B) bam_remove_B(b);
+    if (settings->min_qlen > 0) {
+        int k, qlen = 0;
+        uint32_t *cigar = bam_get_cigar(b);
+        for (k = 0; k < b->core.n_cigar; ++k)
+            if ((bam_cigar_type(bam_cigar_op(cigar[k]))&1) || bam_cigar_op(cigar[k]) == BAM_CHARD_CLIP)
+                qlen += bam_cigar_oplen(cigar[k]);
+        if (qlen < settings->min_qlen) return 1;
+    }
+    if (b->core.qual < settings->min_mapQ || ((b->core.flag & settings->flag_on) != settings->flag_on) || (b->core.flag & settings->flag_off))
+        return 1;
+    if (settings->flag_alloff && ((b->core.flag & settings->flag_alloff) == settings->flag_alloff))
+        return 1;
+    if (settings->flag_anyon && ((b->core.flag & settings->flag_anyon) == 0))
+        return 1;
+    if (!settings->multi_region && settings->bed && (b->core.tid < 0 || !bed_overlap(settings->bed, sam_hdr_tid2name(h, b->core.tid), b->core.pos, bam_endpos(b))))
+        return 1;
+    if (settings->subsam_frac > 0.) {
+        uint32_t k = __ac_Wang_hash(__ac_X31_hash_string(bam_get_qname(b)) ^ settings->subsam_seed);
+        if ((double)(k&0xffffff) / 0x1000000 >= settings->subsam_frac) return 1;
+    }
+    if (settings->rghash) {
+        uint8_t *s = bam_aux_get(b, "RG");
+        if (s) {
+            khint_t k = kh_get(str, settings->rghash, (char*)(s + 1));
+            if (k == kh_end(settings->rghash)) return 1;
+        }
+    }
+    if (settings->tag) {
+        uint8_t *s = bam_aux_get(b, settings->tag);
+        if (s) {
+            if (settings->tvhash) {
+                char t[32], *val;
+                if (*s == 'i' || *s == 'I' || *s == 's' || *s == 'S' || *s == 'c' || *s == 'C') {
+                    int ret = snprintf(t, 32, "%"PRId64, bam_aux2i(s));
+                    if (ret > 0) val = t;
+                    else return 1;
+                } else if (*s == 'A') {
+                    t[0] = *(s+1);
+                    t[1] = 0;
+                    val = t;
+                } else {
+                    val = (char *)(s+1);
+                }
+                khint_t k = kh_get(str, settings->tvhash, val);
+                if (k == kh_end(settings->tvhash)) return 1;
+            }
+        } else {
+            return 1;
+        }
+    }
+    if (settings->rnhash) {
+        const char* rn = bam_get_qname(b);
+        if (!rn || kh_get(str, settings->rnhash, rn) == kh_end(settings->rnhash)) {
+            return 1;
+        }
+    }
+    if (settings->library) {
+        const char *p = bam_get_library((sam_hdr_t*)h, b);
+        if (!p || strcmp(p, settings->library) != 0) return 1;
+    }
+    return 0;
+}
+
+static int adjust_tags(const sam_hdr_t *h, bam1_t *b,
+                       samview_settings_t* settings) {
+    if (settings->keep_tag) {
+        uint8_t *s_from, *s_to, *end = b->data + b->l_data;
+        auxhash_t h = settings->keep_tag;
+
+        s_from = s_to = bam_get_aux(b);
+        while (s_from < end) {
+            int x = (int)s_from[0]<<8 | s_from[1];
+            uint8_t *s = skip_aux(s_from+2, end);
+            if (s == NULL) {
+                print_error("view", "malformed aux data for record \"%s\"",
+                            bam_get_qname(b));
+                return -1;
+            }
+
+            if (kh_get(aux_exists, h, x) != kh_end(h) ) {
+                if (s_to != s_from) memmove(s_to, s_from, s - s_from);
+                s_to += s - s_from;
+            }
+            s_from = s;
+        }
+        b->l_data = s_to - b->data;
+
+    } else if (settings->remove_tag) {
+        uint8_t *s_from, *s_to, *end = b->data + b->l_data;
+        auxhash_t h = settings->remove_tag;
+
+        s_from = s_to = bam_get_aux(b);
+        while (s_from < end) {
+            int x = (int)s_from[0]<<8 | s_from[1];
+            uint8_t *s = skip_aux(s_from+2, end);
+            if (s == NULL) {
+                print_error("view", "malformed aux data for record \"%s\"",
+                            bam_get_qname(b));
+                return -1;
+            }
+
+            if (kh_get(aux_exists, h, x) == kh_end(h) ) {
+                if (s_to != s_from) memmove(s_to, s_from, s - s_from);
+                s_to += s - s_from;
+            }
+            s_from = s;
+        }
+        b->l_data = s_to - b->data;
+    }
+
+    return 0;
+}
+
+static int usage(FILE *fp, int exit_status, int is_long_help);
+
+static int populate_lookup_from_file(const char *subcmd, strhash_t lookup, char *fn)
+{
+    FILE *fp;
+    char buf[1024];
+    int ret = 0;
+    fp = fopen(fn, "r");
+    if (fp == NULL) {
+        print_error_errno(subcmd, "failed to open \"%s\" for reading", fn);
+        return -1;
+    }
+
+    while (ret != -1 && !feof(fp) && fscanf(fp, "%1023s", buf) > 0) {
+        char *d = strdup(buf);
+        if (d != NULL) {
+            kh_put(str, lookup, d, &ret);
+            if (ret == 0) free(d); /* Duplicate */
+        } else {
+            ret = -1;
+        }
+    }
+    if (ferror(fp)) ret = -1;
+    if (ret == -1) {
+        print_error_errno(subcmd, "failed to read \"%s\"", fn);
+    }
+    fclose(fp);
+    return (ret != -1) ? 0 : -1;
+}
+
+static int add_read_group_single(const char *subcmd, samview_settings_t *settings, char *name)
+{
+    char *d = strdup(name);
+    int ret = 0;
+
+    if (d == NULL) goto err;
+
+    if (settings->rghash == NULL) {
+        settings->rghash = kh_init(str);
+        if (settings->rghash == NULL) goto err;
+    }
+
+    kh_put(str, settings->rghash, d, &ret);
+    if (ret == -1) goto err;
+    if (ret ==  0) free(d); /* Duplicate */
+    return 0;
+
+ err:
+    print_error(subcmd, "Couldn't add \"%s\" to read group list: memory exhausted?", name);
+    free(d);
+    return -1;
+}
+
+static int add_read_names_file(const char *subcmd, samview_settings_t *settings, char *fn)
+{
+    if (settings->rnhash == NULL) {
+        settings->rnhash = kh_init(str);
+        if (settings->rnhash == NULL) {
+            perror(NULL);
+            return -1;
+        }
+    }
+    return populate_lookup_from_file(subcmd, settings->rnhash, fn);
+}
+
+static int add_read_groups_file(const char *subcmd, samview_settings_t *settings, char *fn)
+{
+    if (settings->rghash == NULL) {
+        settings->rghash = kh_init(str);
+        if (settings->rghash == NULL) {
+            perror(NULL);
+            return -1;
+        }
+    }
+    return populate_lookup_from_file(subcmd, settings->rghash, fn);
+}
+
+static int add_tag_value_single(const char *subcmd, samview_settings_t *settings, char *name)
+{
+    char *d = strdup(name);
+    int ret = 0;
+
+    if (d == NULL) goto err;
+
+    if (settings->tvhash == NULL) {
+        settings->tvhash = kh_init(str);
+        if (settings->tvhash == NULL) goto err;
+    }
+
+    kh_put(str, settings->tvhash, d, &ret);
+    if (ret == -1) goto err;
+    if (ret ==  0) free(d); /* Duplicate */
+    return 0;
+
+ err:
+    print_error(subcmd, "Couldn't add \"%s\" to tag values list: memory exhausted?", name);
+    free(d);
+    return -1;
+}
+
+static int add_tag_values_file(const char *subcmd, samview_settings_t *settings, char *fn)
+{
+    if (settings->tvhash == NULL) {
+        settings->tvhash = kh_init(str);
+        if (settings->tvhash == NULL) {
+            perror(NULL);
+            return -1;
+        }
+    }
+    return populate_lookup_from_file(subcmd, settings->tvhash, fn);
+}
+
+static inline int check_sam_write1(samFile *fp, const sam_hdr_t *h, const bam1_t *b, const char *fname, int *retp)
+{
+    int r = sam_write1(fp, h, b);
+    if (r >= 0) return r;
+
+    if (fname) print_error_errno("view", "writing to \"%s\" failed", fname);
+    else print_error_errno("view", "writing to standard output failed");
+
+    *retp = EXIT_FAILURE;
+    return r;
+}
+
+static inline void change_flag(bam1_t *b, samview_settings_t *settings)
+{
+    if (settings->add_flag)
+        b->core.flag |= settings->add_flag;
+
+    if (settings->remove_flag)
+        b->core.flag &= ~settings->remove_flag;
+}
+
+int parse_aux_list(auxhash_t *h, char *optarg) {
+    if (!*h)
+        *h = kh_init(aux_exists);
+
+    while (strlen(optarg) >= 2) {
+        int x = optarg[0]<<8 | optarg[1];
+        int ret = 0;
+        kh_put(aux_exists, *h, x, &ret);
+        if (ret < 0)
+            return -1;
+
+        optarg += 2;
+        if (*optarg == ',') // allow white-space too for easy `cat file`?
+            optarg++;
+        else if (*optarg != 0)
+            break;
+    }
+
+    if (strlen(optarg) != 0) {
+        fprintf(stderr, "main_samview: Error parsing option, "
+                "auxiliary tags should be exactly two characters long.\n");
+        return -1;
+    }
+
+    return 0;
+}
+
+static int cmp_reglist_intervals(const void *aptr, const void *bptr)
+{
+    hts_pair_pos_t *a = (hts_pair_pos_t*)aptr;
+    hts_pair_pos_t *b = (hts_pair_pos_t*)bptr;
+    if ( a->beg < b->beg ) return -1;
+    if ( a->beg > b->beg ) return 1;
+    if ( a->end < b->end ) return -1;
+    if ( a->end > b->end ) return 1;
+    return 0;
+}
+static int cmp_reglist_tids(const void *aptr, const void *bptr)
+{
+    hts_reglist_t *a = (hts_reglist_t*)aptr;
+    hts_reglist_t *b = (hts_reglist_t*)bptr;
+    if ( b->tid==HTS_IDX_NOCOOR || a->tid < b->tid ) return -1;
+    if ( a->tid==HTS_IDX_NOCOOR || a->tid > b->tid ) return 1;
+    return 0;
+}
+
+static hts_reglist_t *_reglist_dup(sam_hdr_t *hdr, hts_reglist_t *src, int nsrc)
+{
+    int i,j;
+    hts_reglist_t *dst = (hts_reglist_t*)calloc(nsrc,sizeof(hts_reglist_t));
+    if ( !dst ) {
+        print_error_errno("view", "[%s:%d] could not allocate region list"
+                          ,__FILE__ ,__LINE__);
+        return NULL;
+    }
+    for (i=0; i<nsrc; i++)
+    {
+        // Assume tid is not set correctly, reg is informative but may not point to a long-lived memory
+        dst[i].tid = sam_hdr_name2tid(hdr,src[i].reg);
+        dst[i].min_beg = src[i].min_beg;
+        dst[i].max_end = src[i].max_end;
+        dst[i].count = src[i].count;
+        dst[i].intervals = (hts_pair_pos_t*)malloc(sizeof(hts_pair_pos_t)*dst[i].count);
+        if ( !dst[i].intervals ) {
+            print_error_errno("view", "[%s:%d] could not allocate region list",
+                              __FILE__, __LINE__);
+            goto fail;
+        }
+        for (j=0; j<dst[i].count; j++)
+            dst[i].intervals[j] = src[i].intervals[j];
+    }
+    qsort(dst,nsrc,sizeof(*dst),cmp_reglist_tids);
+    return dst;
+
+ fail:
+    for (j = 0; j < i; j++)
+        free(dst[j].intervals);
+    free(dst);
+    return NULL;
+}
+static inline int _reglist_find_tid(hts_reglist_t *reg, int nreg, int tid) // binary search
+{
+    int i = -1, imin = 0, imax = nreg - 1;
+    while ( imin <= imax )
+    {
+        i = (imin+imax)/2;
+        if ( tid==HTS_IDX_NOCOOR || reg[i].tid < tid ) imin = i + 1;
+        else if ( reg[i].tid==HTS_IDX_NOCOOR || reg[i].tid > tid ) imax = i - 1;
+        else break;
+    }
+    if ( i<0 || reg[i].tid < tid ) i++;    // not found, i will be the index of the inserted element
+    return i;
+}
+static int _reglist_push(hts_reglist_t **_reg, int *_nreg, int tid, hts_pos_t beg, hts_pos_t end)
+{
+    hts_reglist_t *reg = *_reg;
+    int nreg = *_nreg;
+    int i = _reglist_find_tid(reg,nreg,tid);
+    if ( i>=nreg || reg[i].tid!=tid ) {
+        nreg++;
+        reg = (hts_reglist_t*)realloc(reg,sizeof(hts_reglist_t)*nreg);
+        if ( !reg ) {
+            print_error_errno("view", "[%s:%d] could not extend region list",
+                              __FILE__, __LINE__);
+            return -1;
+        }
+        if ( i+1 < nreg )
+            memmove(reg + i + 1, reg + i, sizeof(hts_reglist_t)*(nreg - i - 1));
+        reg[i].reg = NULL;
+        reg[i].tid = tid;
+        reg[i].min_beg = beg;
+        reg[i].max_end = end;
+        reg[i].intervals = NULL;
+        reg[i].count = 0;
+    }
+    *_reg = reg;
+    *_nreg = nreg;
+    if ( reg[i].count > 0
+         && reg[i].intervals[reg[i].count - 1].beg==beg
+         && reg[i].intervals[reg[i].count - 1].end==end ) {
+        return 0;
+    }
+    hts_pair_pos_t *new_intervals = realloc(reg[i].intervals, sizeof(hts_pair_pos_t)*(reg[i].count + 1));
+    if (!new_intervals) {
+        print_error_errno("view", "[%s:%d] could not extend region list",
+                          __FILE__, __LINE__);
+        return -1;
+    }
+    reg[i].intervals = new_intervals;
+    reg[i].intervals[reg[i].count].beg = beg;
+    reg[i].intervals[reg[i].count].end = end;
+    reg[i].count++;
+    return 0;
+}
+
+static void _reglist_merge(hts_reglist_t *reg, int nreg)
+{
+    int i,j;
+    for (i=0; i<nreg; i++)
+    {
+        qsort(reg[i].intervals,reg[i].count,sizeof(*reg[i].intervals),cmp_reglist_intervals);
+        int k = 1;
+        for (j=1; j<reg[i].count; j++)
+        {
+            if ( reg[i].intervals[k-1].end < reg[i].intervals[j].beg )
+            {
+                if ( k < j ) reg[i].intervals[k] = reg[i].intervals[j];
+                k++;
+                continue;
+            }
+            if ( reg[i].intervals[k-1].end < reg[i].intervals[j].end ) reg[i].intervals[k-1].end = reg[i].intervals[j].end;
+        }
+        reg[i].count = k;
+        reg[i].max_end = reg[i].intervals[k-1].end;
+    }
+}
+hts_itr_multi_t *multi_region_init(samview_settings_t *conf, char **regs, int nregs)
+{
+    hts_itr_multi_t *iter = NULL;
+    int filter_state = ALL;
+    if ( nregs ) {
+        int filter_op = 0;
+        conf->bed = bed_hash_regions(conf->bed, regs, 0, nregs, &filter_op); // insert(1) or filter out(0) the regions from the command line in the same hash table as the bed file
+        if ( !filter_op )
+            filter_state = FILTERED;
+    }
+    else
+        bed_unify(conf->bed);
+    if ( !conf->bed) { // index is unavailable or no regions have been specified
+        print_error("view", "No regions or BED file have been provided. Aborting.");
+        return NULL;
+    }
+
+    int regcount = 0;
+    hts_reglist_t *reglist = bed_reglist(conf->bed, filter_state, &regcount);
+    if (!reglist) {
+        print_error("view", "Region list is empty or could not be created. Aborting.");
+        return NULL;
+    }
+
+    if ( conf->fetch_pairs ) {
+        conf->reglist  = _reglist_dup(conf->header,reglist,regcount);
+        if (!conf->reglist)
+            return NULL;
+        conf->nreglist = regcount;
+    }
+
+    iter = sam_itr_regions(conf->hts_idx, conf->header, reglist, regcount);
+    if ( !iter ) {
+        print_error("view", "Iterator could not be created. Aborting.");
+        return NULL;
+    }
+    return iter;
+}
+
+KHASH_SET_INIT_STR(names)
+
+static int fetch_pairs_collect_mates(samview_settings_t *conf, hts_itr_multi_t *iter)
+{
+    khint_t k;
+    int nunmap = 0, r = 0, nmates = 0, write_error = 0, retval = EXIT_FAILURE;
+    kh_names_t *mate_names = kh_init(names);
+    bam1_t *rec = bam_init1();
+
+    if (!mate_names) {
+        print_error_errno("view", "could not allocate mate names table");
+        goto out;
+    }
+    if (!rec) {
+        print_error_errno("view", "could not allocate bam record");
+        goto out;
+    }
+
+    while ((r =sam_itr_multi_next(conf->in, iter, rec))>=0) {
+        if ( (rec->core.flag & BAM_FPAIRED) == 0 ) continue;
+        if ( rec->core.mtid>=0 && bed_overlap(conf->bed, sam_hdr_tid2name(conf->header,rec->core.mtid), rec->core.mpos, rec->core.mpos) ) continue;
+        if ( process_aln(conf->header, rec, conf) ) continue;
+
+        nmates++;
+
+        k = kh_get(names,mate_names,bam_get_qname(rec));
+        if ( k == kh_end(mate_names) ) {
+            int ret = 0;
+            char *name_copy = strdup(bam_get_qname(rec));
+            if (!name_copy) {
+                print_error_errno("view", "[%s:%d] could not store sample name, %d elements", __FILE__,__LINE__,nmates);
+                goto out;
+            }
+            kh_put(names, mate_names, name_copy, &ret);
+            if ( ret<0 ) {
+                print_error_errno("view", "[%s:%d] could not store sample name, %d elements",__FILE__,__LINE__,nmates);
+                free(name_copy);
+                goto out;
+            }
+        }
+
+        if ( rec->core.mtid < 0 || (rec->core.flag & BAM_FMUNMAP) ) nunmap = 1;
+        if ( rec->core.mtid >= 0 ) {
+            if (_reglist_push(&conf->reglist, &conf->nreglist, rec->core.mtid, rec->core.mpos,rec->core.mpos+1) != 0)
+                goto out;
+        }
+    }
+
+    if (r < -1) {
+        print_error_errno("view", "error reading file \"%s\"", conf->fn_in);
+        goto out;
+    }
+
+    _reglist_merge(conf->reglist, conf->nreglist);
+    if ( nunmap ) {
+        if (_reglist_push(&conf->reglist,&conf->nreglist,HTS_IDX_NOCOOR,0,HTS_POS_MAX) != 0)
+            goto out;
+    }
+    hts_itr_multi_destroy(iter);
+    iter = sam_itr_regions(conf->hts_idx, conf->header, conf->reglist, conf->nreglist);
+    if ( !iter ) {
+        print_error_errno("view", "[%s:%d] iterator could not be created",__FILE__,__LINE__);
+        goto out;
+    }
+    while ((r = sam_itr_multi_next(conf->in, iter, rec))>=0) {
+        int drop = 1;
+        if (rec->core.tid >=0 &&
+            bed_overlap(conf->bed, sam_hdr_tid2name(conf->header,rec->core.tid), rec->core.pos, bam_endpos(rec))) drop = 0;
+        if ( drop ) {
+             k = kh_get(names,mate_names,bam_get_qname(rec));
+             if ( k != kh_end(mate_names) ) drop = 0;
+        }
+        if (!drop && process_aln(conf->header, rec, conf) == 0) {
+            if (adjust_tags(conf->header, rec, conf) != 0)
+                goto out;
+            if (check_sam_write1(conf->out, conf->header, rec, conf->fn_out,
+                                 &write_error) < 0)
+                goto out;
+        }
+    }
+
+    if (r < -1) {
+        print_error_errno("view", "error reading file \"%s\"", conf->fn_in);
+        goto out;
+    }
+
+    retval = EXIT_SUCCESS;
+
+ out:
+    hts_itr_multi_destroy(iter);
+    hts_idx_destroy(conf->hts_idx); // destroy the BAM index
+    conf->hts_idx = NULL;
+    if (mate_names) {
+        // free khash keys
+        for (k = 0; k < kh_end(mate_names); ++k)
+            if ( kh_exist(mate_names,k) ) free((char*)kh_key(mate_names, k));
+        kh_destroy(names,mate_names);
+    }
+    bam_destroy1(rec);
+    return retval;
+}
+
+// Common code for processing and writing a record
+static inline int process_one_record(samview_settings_t *conf, bam1_t *b,
+                                     int *write_error) {
+    if (!process_aln(conf->header, b, conf)) {
+        if (!conf->is_count) {
+            change_flag(b, conf);
+            if (adjust_tags(conf->header, b, conf) != 0)
+                return -1;
+            if (check_sam_write1(conf->out, conf->header,
+                                 b, conf->fn_out, write_error) < 0) {
+                return -1;
+            }
+        }
+        conf->count++;
+    } else if (conf->unmap) {
+        b->core.flag |= BAM_FUNMAP;
+        b->core.qual = 0;
+        b->core.isize = 0;
+
+        // remove CIGAR
+        if (b->core.n_cigar) {
+            memmove(bam_get_cigar(b), bam_get_seq(b),
+                    b->data + b->l_data - bam_get_seq(b));
+            b->l_data -= 4*b->core.n_cigar;
+            b->core.n_cigar = 0;
+        }
+
+        if (check_sam_write1(conf->out, conf->header,
+                             b, conf->fn_out, write_error) < 0) {
+            return -1;
+        }
+    } else {
+        if (conf->un_out) {
+            if (check_sam_write1(conf->un_out, conf->header,
+                                 b, conf->fn_un_out, write_error) < 0) {
+                return -1;
+            }
+        }
+    }
+    return 0;
+}
+
+static int stream_view(samview_settings_t *conf) {
+    bam1_t *b = bam_init1();
+    int write_error = 0, r;
+    if (!b) {
+        print_error_errno("view", "could not allocate bam record");
+        return 1;
+    }
+    errno = 0; // prevent false error messages.
+    while ((r = sam_read1(conf->in, conf->header, b)) >= 0) {
+        if (process_one_record(conf, b, &write_error) < 0) break;
+    }
+    bam_destroy1(b);
+    if (r < -1) {
+        print_error_errno("view", "error reading file \"%s\"", conf->fn_in);
+        return 1;
+    }
+    return write_error;
+}
+
+static int multi_region_view(samview_settings_t *conf, hts_itr_multi_t *iter)
+{
+    bam1_t *b = bam_init1();
+    int write_error = 0, result;
+    if (!b) {
+        print_error_errno("view", "could not allocate bam record");
+        return 1;
+    }
+    // fetch alignments
+    while ((result = sam_itr_multi_next(conf->in, iter, b)) >= 0) {
+        if (process_one_record(conf, b, &write_error) < 0) break;
+    }
+    hts_itr_multi_destroy(iter);
+    bam_destroy1(b);
+
+    if (result < -1) {
+        print_error("view", "retrieval of region #%d failed", iter->curr_tid);
+        return 1;
+    }
+    return write_error;
+}
+
+// Make mnemonic distinct values for longoption-only options
+#define LONGOPT(c)  ((c) + 128)
+
+// Check for ".sam" filenames as sam_open_mode cannot distinguish between
+// foo.sam and foo.unknown, both getting mode "".
+static int is_sam(const char *fn) {
+    if (!fn)
+        return 0;
+    size_t l = strlen(fn);
+    return (l >= 4 && strcasecmp(fn + l-4, ".sam") == 0);
+}
+
+int main_samview(int argc, char *argv[])
+{
+    samview_settings_t settings;
+    int c, is_header = 0, is_header_only = 0, ret = 0, compress_level = -1, has_index_file = 0, no_pg = 0;
+    FILE *fp_out = NULL;
+    char out_mode[6] = {0}, out_un_mode[6] = {0};
+    char *out_format = "";
+    char *arg_list = NULL;
+    sam_global_args ga = SAM_GLOBAL_ARGS_INIT;
+    htsThreadPool p = {NULL, 0};
+
+    memset(&settings,0,sizeof(settings));
+    settings.subsam_frac = -1.0;
+
+    static const struct option lopts[] = {
+        SAM_OPT_GLOBAL_OPTIONS('-', 0, 'O', 0, 'T', '@'),
+        {"add-flags", required_argument, NULL, LONGOPT('a')},
+        {"bam", no_argument, NULL, 'b'},
+        {"count", no_argument, NULL, 'c'},
+        {"cram", no_argument, NULL, 'C'},
+        {"customised-index", no_argument, NULL, 'X'},
+        {"customized-index", no_argument, NULL, 'X'},
+        {"excl-flags", required_argument, NULL, 'F'},
+        {"exclude-flags", required_argument, NULL, 'F'},
+        {"expr", required_argument, NULL, 'e'},
+        {"expression", required_argument, NULL, 'e'},
+        {"fai-reference", required_argument, NULL, 't'},
+        {"fast", no_argument, NULL, '1'},
+        {"fetch-pairs", no_argument, NULL, 'P'},
+        {"header-only", no_argument, NULL, 'H'},
+        {"help", no_argument, NULL, LONGOPT('?')},
+        {"incl-flags", required_argument, NULL, LONGOPT('g')},
+        {"include-flags", required_argument, NULL, LONGOPT('g')},
+        {"rf", required_argument, NULL, LONGOPT('g')}, // aka incl-flags
+        {"keep-tag", required_argument, NULL, LONGOPT('x') },
+        {"library", required_argument, NULL, 'l'},
+        {"min-mapq", required_argument, NULL, 'q'},
+        {"min-MQ", required_argument, NULL, 'q'},
+        {"min-mq", required_argument, NULL, 'q'},
+        {"min-qlen", required_argument, NULL, 'm'},
+        {"no-header", no_argument, NULL, LONGOPT('H')},
+        {"no-PG", no_argument, NULL, LONGOPT('P')},
+        {"output", required_argument, NULL, 'o'},
+        {"output-unselected", required_argument, NULL, 'U'},
+        {"QNAME-file", required_argument, NULL, 'N'},
+        {"qname-file", required_argument, NULL, 'N'},
+        {"read-group", required_argument, NULL, 'r'},
+        {"read-group-file", required_argument, NULL, 'R'},
+        {"readgroup", required_argument, NULL, 'r'},
+        {"readgroup-file", required_argument, NULL, 'R'},
+        {"region-file", required_argument, NULL, LONGOPT('L')},
+        {"regions-file", required_argument, NULL, LONGOPT('L')},
+        {"remove-B", no_argument, NULL, 'B'},
+        {"remove-flags", required_argument, NULL, LONGOPT('r')},
+        {"remove-tag", required_argument, NULL, 'x'},
+        {"require-flags", required_argument, NULL, 'f'},
+        {"subsample", required_argument, NULL, LONGOPT('s')},
+        {"subsample-seed", required_argument, NULL, LONGOPT('S')},
+        {"tag", required_argument, NULL, 'd'},
+        {"tag-file", required_argument, NULL, 'D'},
+        {"target-file", required_argument, NULL, 'L'},
+        {"targets-file", required_argument, NULL, 'L'},
+        {"uncompressed", no_argument, NULL, 'u'},
+        {"unmap", no_argument, NULL, 'p'},
+        {"unoutput", required_argument, NULL, 'U'},
+        {"use-index", no_argument, NULL, 'M'},
+        {"with-header", no_argument, NULL, 'h'},
+    };
+
+    /* parse command-line options */
+    strcpy(out_mode, "w");
+    strcpy(out_un_mode, "w");
+    if (argc == 1 && isatty(STDIN_FILENO))
+        return usage(stdout, EXIT_SUCCESS, 0);
+
+    // Suppress complaints about '?' being an unrecognised option.  Without
+    // this we have to put '?' in the options list, which makes it hard to
+    // tell a bad long option from the use of '-?' (both return '?' and
+    // set optopt to '\0').
+    opterr = 0;
+
+    char *tmp;
+    while ((c = getopt_long(argc, argv,
+                            "SbBcCt:h1Ho:O:q:f:F:G:ul:r:T:R:N:d:D:L:s:@:m:x:U:MXe:pP",
+                            lopts, NULL)) >= 0) {
+        switch (c) {
+        case 's':
+            settings.subsam_seed = strtol(optarg, &tmp, 10);
+            if (tmp && *tmp == '.') {
+                settings.subsam_frac = strtod(tmp, &tmp);
+                if (*tmp) ret = 1;
+            } else {
+                ret = 1;
+            }
+
+            if (ret == 1) {
+                print_error("view", "Incorrect sampling argument \"%s\"", optarg);
+                goto view_end;
+            }
+            break;
+        case LONGOPT('s'):
+            settings.subsam_frac = strtod(optarg, &tmp);
+            if (*tmp || settings.subsam_frac < 0.0 || settings.subsam_frac > 1.0) {
+                print_error("view", "Incorrect sampling argument \"%s\"", optarg);
+                goto view_end;
+            }
+            break;
+        case LONGOPT('S'): settings.subsam_seed = atoi(optarg); break;
+        case 'm': settings.min_qlen = atoi(optarg); break;
+        case 'c': settings.is_count = 1; break;
+        case 'S': break;
+        case 'b': out_format = "b"; break;
+        case 'C': out_format = "c"; break;
+        case 't': settings.fn_fai = strdup(optarg); break;
+        case 'h': is_header = 1; break;
+        case 'H': is_header_only = 1; break;
+        case LONGOPT('H'): is_header = is_header_only = 0; break;
+        case 'o': settings.fn_out = strdup(optarg); break;
+        case 'U': settings.fn_un_out = strdup(optarg); break;
+        case 'X': has_index_file = 1; break;
+        case 'f': settings.flag_on |= bam_str2flag(optarg); break;
+        case 'F': settings.flag_off |= bam_str2flag(optarg); break;
+        case LONGOPT('g'):
+            settings.flag_anyon |= bam_str2flag(optarg); break;
+        case 'G': settings.flag_alloff |= bam_str2flag(optarg); break;
+        case 'q': settings.min_mapQ = atoi(optarg); break;
+        case 'u': compress_level = 0; break;
+        case '1': compress_level = 1; break;
+        case 'l': settings.library = strdup(optarg); break;
+        case 'p': settings.unmap = 1; break;
+        case 'P': settings.fetch_pairs = 1; settings.multi_region = 1; break;
+        case LONGOPT('L'):
+            settings.multi_region = 1;
+            // fall through
+        case 'L':
+            if ((settings.bed = bed_read(optarg)) == NULL) {
+                print_error_errno("view", "Could not read file \"%s\"", optarg);
+                ret = 1;
+                goto view_end;
+            }
+            break;
+        case 'r':
+            if (add_read_group_single("view", &settings, optarg) != 0) {
+                ret = 1;
+                goto view_end;
+            }
+            break;
+        case 'R':
+            if (add_read_groups_file("view", &settings, optarg) != 0) {
+                ret = 1;
+                goto view_end;
+            }
+            break;
+        case 'N':
+            if (add_read_names_file("view", &settings, optarg) != 0) {
+                ret = 1;
+                goto view_end;
+            }
+            break;
+        case 'd':
+            if (strlen(optarg) < 2 || (strlen(optarg) > 2 && optarg[2] != ':')) {
+                print_error_errno("view", "Invalid \"tag:value\" option: \"%s\"", optarg);
+                ret = 1;
+                goto view_end;
+            }
+
+            if (settings.tag) {
+                if (settings.tag[0] != optarg[0] || settings.tag[1] != optarg[1]) {
+                    print_error("view", "Different tag \"%s\" was specified before: \"%s\"", settings.tag, optarg);
+                    ret = 1;
+                    goto view_end;
+                }
+            } else {
+                if (!(settings.tag = calloc(3, 1))) {
+                    print_error("view", "Could not allocate memory for tag: \"%s\"", optarg);
+                    ret = 1;
+                    goto view_end;
+                }
+                memcpy(settings.tag, optarg, 2);
+            }
+
+            if (strlen(optarg) > 3 && add_tag_value_single("view", &settings, optarg+3) != 0) {
+                print_error("view", "Could not add tag:value \"%s\"", optarg);
+                ret = 1;
+                goto view_end;
+            }
+            break;
+        case 'D':
+            // Allow ";" as delimiter besides ":" to support MinGW CLI POSIX
+            // path translation as described at:
+            // http://www.mingw.org/wiki/Posix_path_conversion
+            if (strlen(optarg) < 4 || (optarg[2] != ':' && optarg[2] != ';')) {
+                print_error_errno("view", "Invalid \"tag:file\" option: \"%s\"", optarg);
+                ret = 1;
+                goto view_end;
+            }
+
+            if (settings.tag) {
+                if (settings.tag[0] != optarg[0] || settings.tag[1] != optarg[1]) {
+                    print_error("view", "Different tag \"%s\" was specified before: \"%s\"", settings.tag, optarg);
+                    ret = 1;
+                    goto view_end;
+                }
+            } else {
+                if (!(settings.tag = calloc(3, 1))) {
+                    print_error("view", "Could not allocate memory for tag: \"%s\"", optarg);
+                    ret = 1;
+                    goto view_end;
+                }
+                memcpy(settings.tag, optarg, 2);
+            }
+
+            if (add_tag_values_file("view", &settings, optarg+3) != 0) {
+                ret = 1;
+                goto view_end;
+            }
+            break;
+        case LONGOPT('?'):
+            return usage(stdout, EXIT_SUCCESS, 1);
+        case '?':
+            if (optopt == '?') {  // '-?' appeared on command line
+                return usage(stdout, EXIT_SUCCESS, 1);
+            } else {
+                if (optopt) { // Bad short option
+                    print_error("view", "invalid option -- '%c'", optopt);
+                } else { // Bad long option
+                    // Do our best.  There is no good solution to finding
+                    // out what the bad option was.
+                    // See, e.g. https://stackoverflow.com/questions/2723888/where-does-getopt-long-store-an-unrecognized-option
+                    if (optind > 0 && strncmp(argv[optind - 1], "--", 2) == 0) {
+                        print_error("view", "unrecognised option '%s'",
+                                    argv[optind - 1]);
+                    }
+                }
+                return usage(stderr, EXIT_FAILURE, 0);
+            }
+        case 'B': settings.remove_B = 1; break;
+
+        case 'M': settings.multi_region = 1; break;
+        case LONGOPT('P'): no_pg = 1; break;
+        case 'e':
+            if (!(settings.filter = hts_filter_init(optarg))) {
+                print_error("main_samview", "Couldn't initialise filter");
+                return 1;
+            }
+            break;
+        case LONGOPT('r'): settings.remove_flag |= bam_str2flag(optarg); break;
+        case LONGOPT('a'): settings.add_flag |= bam_str2flag(optarg); break;
+
+        case 'x':
+            if (*optarg == '^') {
+                if (parse_aux_list(&settings.keep_tag, optarg+1))
+                    return usage(stderr, EXIT_FAILURE, 0);
+            } else {
+                if (parse_aux_list(&settings.remove_tag, optarg))
+                    return usage(stderr, EXIT_FAILURE, 0);
+            }
+            break;
+
+        case LONGOPT('x'):
+            if (parse_aux_list(&settings.keep_tag, optarg))
+                return usage(stderr, EXIT_FAILURE, 0);
+            break;
+
+        default:
+            if (parse_sam_global_opt(c, optarg, lopts, &ga) != 0)
+                return usage(stderr, EXIT_FAILURE, 0);
+            break;
+        }
+    }
+    if (settings.is_count && settings.fetch_pairs)
+    {
+        print_error("view","The options -P and -c cannot be combined\n");
+        return 1;
+    }
+    if (settings.fn_fai == 0 && ga.reference) settings.fn_fai = fai_path(ga.reference);
+    if (is_header_only) is_header = 1;
+    // File format auto-detection first
+    if (settings.fn_out)    sam_open_mode(out_mode+1,    settings.fn_out,    NULL);
+    if (settings.fn_un_out) sam_open_mode(out_un_mode+1, settings.fn_un_out, NULL);
+
+    // -1 or -u without an explicit format (-b, -C) => check fn extensions
+    if (!*out_format && compress_level >= 0) {
+        if (compress_level == 0 &&
+            (out_mode[strlen(out_mode)-1] == 'z' ||
+             out_un_mode[strlen(out_un_mode)-1] == 'z'))
+            // z, fz, Fz sanity check
+            fprintf(stderr, "[view] Warning option -u ignored due to"
+                    " filename suffix\n");
+
+        // If known extension, use it, otherwise BAM
+        if (!(out_mode[1] || is_sam(settings.fn_out)))
+            out_mode[1] = 'b';
+
+        if (!(out_un_mode[1] || is_sam(settings.fn_un_out)))
+            out_un_mode[1] = 'b';
+    } else if (*out_format) {
+        out_mode[1] = out_un_mode[1] = *out_format;
+    }
+
+    if (compress_level >= 0) {
+        char tmp[2];
+        tmp[0] = compress_level + '0'; tmp[1] = '\0';
+        strcat(out_mode, tmp);
+        strcat(out_un_mode, tmp);
+    }
+    if (argc == optind && isatty(STDIN_FILENO)) {
+        print_error("view", "No input provided or missing option argument.");
+        return usage(stderr, EXIT_FAILURE, 0); // potential memory leak...
+    }
+
+    if (settings.unmap && settings.fn_un_out) {
+        print_error("view", "Options --unoutput and --unmap are mutually exclusive.");
+        ret = 1;
+        goto view_end;
+    }
+
+    if (settings.subsam_seed != 0) {
+        // Convert likely user input 1,2,... to pseudo-random
+        // values with more entropy and more bits set
+        srand(settings.subsam_seed);
+        settings.subsam_seed = rand();
+    }
+
+    settings.fn_in = (optind < argc)? argv[optind] : "-";
+    if ((settings.in = sam_open_format(settings.fn_in, "r", &ga.in)) == 0) {
+        print_error_errno("view", "failed to open \"%s\" for reading", settings.fn_in);
+        ret = 1;
+        goto view_end;
+    }
+
+    if (settings.fn_fai) {
+        if (hts_set_fai_filename(settings.in, settings.fn_fai) != 0) {
+            fprintf(stderr, "[main_samview] failed to use reference \"%s\".\n", settings.fn_fai);
+            ret = 1;
+            goto view_end;
+        }
+    }
+    if ((settings.header = sam_hdr_read(settings.in)) == 0) {
+        fprintf(stderr, "[main_samview] fail to read the header from \"%s\".\n", settings.fn_in);
+        ret = 1;
+        goto view_end;
+    }
+    if (settings.rghash) {
+        sam_hdr_remove_lines(settings.header, "RG", "ID", settings.rghash);
+    }
+    if (!settings.is_count) {
+        if ((settings.out = sam_open_format(settings.fn_out? settings.fn_out : "-", out_mode, &ga.out)) == 0) {
+            print_error_errno("view", "failed to open \"%s\" for writing", settings.fn_out? settings.fn_out : "standard output");
+            ret = 1;
+            goto view_end;
+        }
+        if (settings.fn_fai) {
+            if (hts_set_fai_filename(settings.out, settings.fn_fai) != 0) {
+                fprintf(stderr, "[main_samview] failed to use reference \"%s\".\n", settings.fn_fai);
+                ret = 1;
+                goto view_end;
+            }
+        }
+        autoflush_if_stdout(settings.out, settings.fn_out);
+
+        if (!no_pg) {
+            if (!(arg_list = stringify_argv(argc+1, argv-1))) {
+                print_error("view", "failed to create arg_list");
+                ret = 1;
+                goto view_end;
+            }
+            if (sam_hdr_add_pg(settings.header, "samtools",
+                                         "VN", samtools_version(),
+                                         arg_list ? "CL": NULL,
+                                         arg_list ? arg_list : NULL,
+                                         NULL)) {
+                print_error("view", "failed to add PG line to the header");
+                ret = 1;
+                goto view_end;
+            }
+        }
+
+        if (ga.write_index || is_header ||
+            out_mode[1] == 'b' || out_mode[1] == 'c' ||
+            (ga.out.format != sam && ga.out.format != unknown_format))  {
+            if (sam_hdr_write(settings.out, settings.header) != 0) {
+                fprintf(stderr, "[main_samview] failed to write the SAM header\n");
+                ret = 1;
+                goto view_end;
+            }
+        }
+        if (ga.write_index) {
+            if (!(settings.fn_out_idx = auto_index(settings.out, settings.fn_out, settings.header))) {
+                ret = 1;
+                goto view_end;
+            }
+        }
+
+        if (settings.fn_un_out) {
+            if ((settings.un_out = sam_open_format(settings.fn_un_out, out_un_mode, &ga.out)) == 0) {
+                print_error_errno("view", "failed to open \"%s\" for writing", settings.fn_un_out);
+                ret = 1;
+                goto view_end;
+            }
+            if (settings.fn_fai) {
+                if (hts_set_fai_filename(settings.un_out, settings.fn_fai) != 0) {
+                    fprintf(stderr, "[main_samview] failed to use reference \"%s\".\n", settings.fn_fai);
+                    ret = 1;
+                    goto view_end;
+                }
+            }
+            autoflush_if_stdout(settings.un_out, settings.fn_un_out);
+            if (ga.write_index || is_header ||
+                out_un_mode[1] == 'b' || out_un_mode[1] == 'c' ||
+                (ga.out.format != sam && ga.out.format != unknown_format))  {
+                if (sam_hdr_write(settings.un_out, settings.header) != 0) {
+                    fprintf(stderr, "[main_samview] failed to write the SAM header\n");
+                    ret = 1;
+                    goto view_end;
+                }
+            }
+            if (ga.write_index) {
+                if (!(settings.fn_un_out_idx = auto_index(settings.un_out, settings.fn_un_out, settings.header))) {
+                    ret = 1;
+                    goto view_end;
+                }
+            }
+        }
+    }
+    else {
+        if (settings.fn_out) {
+            fp_out = fopen(settings.fn_out, "w");
+            if (fp_out == NULL) {
+                print_error_errno("view", "can't create \"%s\"", settings.fn_out);
+                ret = EXIT_FAILURE;
+                goto view_end;
+            }
+        }
+        settings.unmap = 0;  // Not valid in counting mode
+    }
+
+    if (ga.nthreads > 1) {
+        if (!(p.pool = hts_tpool_init(ga.nthreads))) {
+            fprintf(stderr, "Error creating thread pool\n");
+            ret = 1;
+            goto view_end;
+        }
+        hts_set_opt(settings.in,  HTS_OPT_THREAD_POOL, &p);
+        if (settings.out) hts_set_opt(settings.out, HTS_OPT_THREAD_POOL, &p);
+    }
+    if (is_header_only) goto view_end; // no need to print alignments
+
+
+    // Initialize BAM/CRAM index
+    char **regs = NULL;
+    int nregs = 0;
+    if ( has_index_file && optind < argc - 2 ) regs = &argv[optind+2], nregs = argc - optind - 2, settings.fn_idx_in = argv[optind+1];
+    else if ( !has_index_file && optind < argc - 1 ) regs = &argv[optind+1], nregs = argc - optind - 1;
+    else if ( has_index_file )
+    {
+        print_error("view", "Incorrect number of arguments for -X option. Aborting.");
+        return 1;
+    }
+    if ( settings.fn_idx_in || nregs || settings.multi_region )
+    {
+        settings.hts_idx = settings.fn_idx_in ? sam_index_load2(settings.in, settings.fn_in, settings.fn_idx_in) : sam_index_load(settings.in, settings.fn_in);
+        if ( !settings.hts_idx )
+        {
+            print_error("view", "Random alignment retrieval only works for indexed SAM.gz, BAM or CRAM files.");
+            return 1;
+        }
+    }
+
+    if ( settings.fetch_pairs )
+    {
+        hts_itr_multi_t *iter = multi_region_init(&settings, regs, nregs);
+        ret = iter ? fetch_pairs_collect_mates(&settings, iter) : 1;
+        if (ret) goto view_end;
+    }
+    else if ( settings.multi_region )
+    {
+        hts_itr_multi_t *iter = multi_region_init(&settings, regs, nregs);
+        ret = iter ? multi_region_view(&settings, iter) : 1;
+        if (ret) goto view_end;
+    }
+    else if ( !settings.hts_idx )   // stream through the entire file
+    {
+        ret = stream_view(&settings);
+        if (ret) goto view_end;
+    } else {   // retrieve alignments in specified regions
+        int i;
+        for (i = (has_index_file)? optind+2 : optind+1; i < argc; ++i) {
+            hts_itr_t *iter = sam_itr_querys(settings.hts_idx, settings.header, argv[i]); // parse a region in the format like `chr2:100-200'
+            if (iter == NULL) { // region invalid or reference name not found
+                fprintf(stderr, "[main_samview] region \"%s\" specifies an invalid region or unknown reference. Continue anyway.\n", argv[i]);
+                continue;
+            }
+            // fetch alignments
+            ret = multi_region_view(&settings, iter);
+            if (ret) goto view_end;
+        }
+    }
+
+    if ( settings.hts_idx ) hts_idx_destroy(settings.hts_idx);
+
+    if (ga.write_index) {
+        if (sam_idx_save(settings.out) < 0) {
+            print_error_errno("view", "writing index failed");
+            ret = 1;
+        }
+        if (settings.un_out && sam_idx_save(settings.un_out) < 0) {
+            print_error_errno("view", "writing index failed");
+            ret = 1;
+        }
+    }
+
+view_end:
+    if (settings.is_count && ret == 0) {
+        if (fprintf(settings.fn_out? fp_out : stdout, "%" PRId64 "\n", settings.count) < 0) {
+            if (settings.fn_out) print_error_errno("view", "writing to \"%s\" failed", settings.fn_out);
+            else print_error_errno("view", "writing to standard output failed");
+            ret = EXIT_FAILURE;
+        }
+    }
+
+    // close files, free and return
+    if (settings.in) check_sam_close("view", settings.in, settings.fn_in, "standard input", &ret);
+    if (settings.out) check_sam_close("view", settings.out, settings.fn_out, "standard output", &ret);
+    if (settings.un_out) check_sam_close("view", settings.un_out, settings.fn_un_out, "file", &ret);
+    if (fp_out) fclose(fp_out);
+
+    free(settings.fn_fai); free(settings.fn_out); free(settings.library);  free(settings.fn_un_out);
+    sam_global_args_free(&ga);
+    if ( settings.header ) sam_hdr_destroy(settings.header);
+    if (settings.bed) bed_destroy(settings.bed);
+    if (settings.rghash) {
+        khint_t k;
+        for (k = 0; k < kh_end(settings.rghash); ++k)
+            if (kh_exist(settings.rghash, k)) free((char*)kh_key(settings.rghash, k));
+        kh_destroy(str, settings.rghash);
+    }
+    if (settings.rnhash) {
+        khint_t k;
+        for (k = 0; k < kh_end(settings.rnhash); ++k)
+            if (kh_exist(settings.rnhash, k)) free((char*)kh_key(settings.rnhash, k));
+        kh_destroy(str, settings.rnhash);
+    }
+    if (settings.tvhash) {
+        khint_t k;
+        for (k = 0; k < kh_end(settings.tvhash); ++k)
+            if (kh_exist(settings.tvhash, k)) free((char*)kh_key(settings.tvhash, k));
+        kh_destroy(str, settings.tvhash);
+    }
+
+    if (settings.remove_aux_len) {
+        free(settings.remove_aux);
+    }
+    if (settings.tag) {
+        free(settings.tag);
+    }
+    if (settings.filter)
+        hts_filter_free(settings.filter);
+
+    if (p.pool)
+        hts_tpool_destroy(p.pool);
+
+    if (settings.fn_out_idx)
+        free(settings.fn_out_idx);
+    if (settings.fn_un_out_idx)
+        free(settings.fn_un_out_idx);
+    free(arg_list);
+
+    if (settings.keep_tag)
+        kh_destroy(aux_exists, settings.keep_tag);
+    if (settings.remove_tag)
+        kh_destroy(aux_exists, settings.remove_tag);
+
+    return ret;
+}
+
+static int usage(FILE *fp, int exit_status, int is_long_help)
+{
+    fprintf(fp,
+"\n"
+"Usage: samtools view [options] <in.bam>|<in.sam>|<in.cram> [region ...]\n"
+"\n"
+
+"Output options:\n"
+"  -b, --bam                  Output BAM\n"
+"  -C, --cram                 Output CRAM (requires -T)\n"
+"  -1, --fast                 Use fast BAM compression (and default to --bam)\n"
+"  -u, --uncompressed         Uncompressed BAM output (and default to --bam)\n"
+"  -h, --with-header          Include header in SAM output\n"
+"  -H, --header-only          Print SAM header only (no alignments)\n"
+"      --no-header            Print SAM alignment records only [default]\n"
+"  -c, --count                Print only the count of matching records\n"
+"  -o, --output FILE          Write output to FILE [standard output]\n"
+"  -U, --unoutput FILE, --output-unselected FILE\n"
+"                             Output reads not selected by filters to FILE\n"
+"  -p, --unmap                Set flag to UNMAP on reads not selected\n"
+"                             then write to output file.\n"
+"  -P, --fetch-pairs          Retrieve complete pairs even when outside of region\n"
+"Input options:\n"
+"  -t, --fai-reference FILE   FILE listing reference names and lengths\n"
+"  -M, --use-index            Use index and multi-region iterator for regions\n"
+"      --region[s]-file FILE  Use index to include only reads overlapping FILE\n"
+"  -X, --customized-index     Expect extra index file argument after <in.bam>\n"
+"\n"
+"Filtering options (Only include in output reads that...):\n"
+"  -L, --target[s]-file FILE  ...overlap (BED) regions in FILE\n"
+"  -r, --read-group STR       ...are in read group STR\n"
+"  -R, --read-group-file FILE ...are in a read group listed in FILE\n"
+"  -N, --qname-file FILE      ...whose read name is listed in FILE\n"
+"  -d, --tag STR1[:STR2]      ...have a tag STR1 (with associated value STR2)\n"
+"  -D, --tag-file STR:FILE    ...have a tag STR whose value is listed in FILE\n"
+"  -q, --min-MQ INT           ...have mapping quality >= INT\n"
+"  -l, --library STR          ...are in library STR\n"
+"  -m, --min-qlen INT         ...cover >= INT query bases (as measured via CIGAR)\n"
+"  -e, --expr STR             ...match the filter expression STR\n"
+"  -f, --require-flags FLAG   ...have all of the FLAGs present\n"             //   F&x == x
+"  -F, --excl[ude]-flags FLAG ...have none of the FLAGs present\n"            //   F&x == 0
+"      --rf, --incl-flags, --include-flags FLAG\n"
+"                             ...have some of the FLAGs present\n"
+"  -G FLAG                    EXCLUDE reads with all of the FLAGs present\n"  // !(F&x == x)  TODO long option
+"      --subsample FLOAT      Keep only FLOAT fraction of templates/read pairs\n"
+"      --subsample-seed INT   Influence WHICH reads are kept in subsampling [0]\n"
+"  -s INT.FRAC                Same as --subsample 0.FRAC --subsample-seed INT\n"
+"\n"
+"Processing options:\n"
+"      --add-flags FLAG       Add FLAGs to reads\n"
+"      --remove-flags FLAG    Remove FLAGs from reads\n"
+"  -x, --remove-tag STR\n"
+"               Comma-separated read tags to strip (repeatable) [null]\n"
+"      --keep-tag STR\n"
+"               Comma-separated read tags to preserve (repeatable) [null].\n"
+"               Equivalent to \"-x ^STR\"\n"
+"  -B, --remove-B             Collapse the backward CIGAR operation\n"
+"\n"
+"General options:\n"
+"  -?, --help   Print long help, including note about region specification\n"
+"  -S           Ignored (input format is auto-detected)\n"
+"      --no-PG  Do not add a PG line\n");
+
+    sam_global_opt_help(fp, "-.O.T@..");
+    fprintf(fp, "\n");
+
+    if (is_long_help)
+        fprintf(fp,
+"Notes:\n"
+"\n"
+"1. This command now auto-detects the input format (BAM/CRAM/SAM).\n"
+"   Further control over the CRAM format can be specified by using the\n"
+"   --output-fmt-option, e.g. to specify the number of sequences per slice\n"
+"   and to use avoid reference based compression:\n"
+"\n"
+"\tsamtools view -C --output-fmt-option seqs_per_slice=5000 \\\n"
+"\t   --output-fmt-option no_ref -o out.cram in.bam\n"
+"\n"
+"   Options can also be specified as a comma separated list within the\n"
+"   --output-fmt value too.  For example this is equivalent to the above\n"
+"\n"
+"\tsamtools view --output-fmt cram,seqs_per_slice=5000,no_ref \\\n"
+"\t   -o out.cram in.bam\n"
+"\n"
+"2. The file supplied with `-t' is SPACE/TAB delimited with the first\n"
+"   two fields of each line consisting of the reference name and the\n"
+"   corresponding sequence length. The `.fai' file generated by \n"
+"   `samtools faidx' is suitable for use as this file. This may be an\n"
+"   empty file if reads are unaligned.\n"
+"\n"
+"3. SAM->BAM conversion:  samtools view -bT ref.fa in.sam.gz\n"
+"\n"
+"4. BAM->SAM conversion:  samtools view -h in.bam\n"
+"\n"
+"5. A region should be presented in one of the following formats:\n"
+"   `chr1', `chr2:1,000' and `chr3:1000-2,000'. When a region is\n"
+"   specified, the input alignment file must be a sorted and indexed\n"
+"   alignment (BAM/CRAM) file.\n"
+"\n"
+"6. Option `-u' is preferred over `-b' when the output is piped to\n"
+"   another samtools command.\n"
+"\n"
+"7. Option `-M`/`--use-index` causes overlaps with `-L` BED file regions and\n"
+"   command-line region arguments to be computed using the multi-region iterator\n"
+"   and an index. This increases speed, omits duplicates, and outputs the reads\n"
+"   as they are ordered in the input SAM/BAM/CRAM file.\n"
+"\n"
+"8. Options `-L`/`--target[s]-file` and `--region[s]-file` may not be used\n"
+"   together. `--region[s]-file FILE` is simply equivalent to `-M -L FILE`,\n"
+"   so using both causes one of the specified BED files to be ignored.\n"
+"\n");
+
+    return exit_status;
+}
+
+static int head_usage(FILE *fp, int exit_status)
+{
+    fprintf(fp,
+"Usage: samtools head [OPTION]... [FILE]\n"
+"Options:\n"
+"  -h, --headers INT   Display INT header lines [all]\n"
+"  -n, --records INT   Display INT alignment record lines [none]\n"
+);
+    sam_global_opt_help(fp, "-.--T@-.");
+    return exit_status;
+}
+
+int main_head(int argc, char *argv[])
+{
+    static const struct option lopts[] = {
+        SAM_OPT_GLOBAL_OPTIONS('-', 0, '-', '-', 'T', '@'),
+        { "headers", required_argument, NULL, 'h' },
+        { "records", required_argument, NULL, 'n' },
+        { NULL, 0, NULL, 0 }
+    };
+    sam_global_args ga = SAM_GLOBAL_ARGS_INIT;
+
+    int all_headers = 1;
+    uint64_t nheaders = 0;
+    uint64_t nrecords = 0;
+
+    int c, nargs;
+    while ((c = getopt_long(argc, argv, "h:n:T:@:", lopts, NULL)) >= 0)
+        switch (c) {
+        case 'h': all_headers = 0; nheaders = strtoull(optarg, NULL, 0); break;
+        case 'n': nrecords = strtoull(optarg, NULL, 0); break;
+        default:
+            if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break;
+            /* else fall-through */
+        case '?':
+            return head_usage(stderr, EXIT_FAILURE);
+        }
+
+    nargs = argc - optind;
+    if (nargs == 0 && isatty(STDIN_FILENO))
+        return head_usage(stdout, EXIT_SUCCESS);
+    else if (nargs > 1)
+        return head_usage(stderr, EXIT_FAILURE);
+
+    samFile *fp = NULL;
+    sam_hdr_t *hdr = NULL;
+    kstring_t str = KS_INITIALIZE;
+    bam1_t *b = NULL;
+
+    const char *fname = (nargs == 1)? argv[optind] : "-";
+    fp = sam_open_format(fname, "r", &ga.in);
+    if (fp == NULL) {
+        if (strcmp(fname, "-") != 0)
+            print_error_errno("head", "failed to open \"%s\" for reading", fname);
+        else
+            print_error_errno("head", "failed to open standard input for reading");
+        goto err;
+    }
+
+    if (ga.nthreads > 0) hts_set_threads(fp, ga.nthreads);
+
+    hdr = sam_hdr_read(fp);
+    if (hdr == NULL) {
+        if (strcmp(fname, "-") != 0)
+            print_error("head", "failed to read the header from \"%s\"", fname);
+        else
+            print_error("head", "failed to read the header");
+        goto err;
+    }
+
+    if (all_headers) {
+        fputs(sam_hdr_str(hdr), stdout);
+    }
+    else if (nheaders > 0) {
+        const char *text = sam_hdr_str(hdr);
+        const char *lim = text;
+        uint64_t n;
+        for (n = 0; n < nheaders; n++) {
+            lim = strchr(lim, '\n');
+            if (lim) lim++;
+            else break;
+        }
+        if (lim) fwrite(text, lim - text, 1, stdout);
+        else fputs(text, stdout);
+    }
+
+    if (nrecords > 0) {
+        b = bam_init1();
+        uint64_t n;
+        int r;
+        for (n = 0; n < nrecords && (r = sam_read1(fp, hdr, b)) >= 0; n++) {
+            if (sam_format1(hdr, b, &str) < 0) {
+                print_error_errno("head", "couldn't format record");
+                goto err;
+            }
+            puts(ks_str(&str));
+        }
+        if (r < -1) {
+            print_error("head", "\"%s\" is truncated", fname);
+            goto err;
+        }
+        bam_destroy1(b);
+        ks_free(&str);
+    }
+
+    sam_hdr_destroy(hdr);
+    sam_close(fp);
+    sam_global_args_free(&ga);
+
+    return EXIT_SUCCESS;
+
+err:
+    if (fp) sam_close(fp);
+    sam_hdr_destroy(hdr);
+    bam_destroy1(b);
+    ks_free(&str);
+    sam_global_args_free(&ga);
+    return EXIT_FAILURE;
+}
diff --git a/samtools/sam_view.c.pysam.c b/samtools/sam_view.c.pysam.c
new file mode 100644
index 0000000..bb61059
--- /dev/null
+++ b/samtools/sam_view.c.pysam.c
@@ -0,0 +1,1598 @@
+#include "samtools.pysam.h"
+
+/*  sam_view.c -- SAM<->BAM<->CRAM conversion.
+
+    Copyright (C) 2009-2022 Genome Research Ltd.
+    Portions copyright (C) 2009, 2011, 2012 Broad Institute.
+
+    Author: Heng Li <lh3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notices and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <config.h>
+
+#include <stdlib.h>
+#include <string.h>
+#include <strings.h>
+#include <stdio.h>
+#include <unistd.h>
+#include <math.h>
+#include <inttypes.h>
+#include <getopt.h>
+#include "htslib/sam.h"
+#include "htslib/faidx.h"
+#include "htslib/khash.h"
+#include "htslib/kstring.h"
+#include "htslib/thread_pool.h"
+#include "htslib/hts_expr.h"
+#include "samtools.h"
+#include "sam_opts.h"
+#include "bam.h" // for bam_get_library and bam_remove_B
+#include "bedidx.h"
+
+KHASH_SET_INIT_STR(str)
+typedef khash_t(str) *strhash_t;
+
+KHASH_SET_INIT_INT(aux_exists)
+typedef khash_t(aux_exists) *auxhash_t;
+
+// This structure contains the settings for a samview run
+typedef struct samview_settings {
+    strhash_t rghash;
+    strhash_t rnhash;
+    strhash_t tvhash;
+    int min_mapQ;
+
+    // Described here in the same terms as the usage statement.
+    // The code however always negates to "reject if"         keep if:
+    int flag_on;     // keep   if (FLAG & N) == N             (all on)
+    int flag_off;    // keep   if (FLAG & N) == 0             (all off)
+    int flag_anyon;  // keep   if (FLAG & N) != 0             (any on)
+    int flag_alloff; // reject if (FLAG & N) == N             (any off)
+
+    int min_qlen;
+    int remove_B;
+    uint32_t subsam_seed;
+    double subsam_frac;
+    char* library;
+    void* bed;
+    size_t remove_aux_len;
+    char** remove_aux;
+    int multi_region;
+    char* tag;
+    hts_filter_t *filter;
+    int remove_flag;
+    int add_flag;
+    int unmap;
+    auxhash_t remove_tag;
+    auxhash_t keep_tag;
+
+    hts_idx_t *hts_idx;
+    sam_hdr_t *header;
+    samFile *in, *out, *un_out;
+    int64_t count;
+    int is_count;
+    char *fn_in, *fn_idx_in, *fn_out, *fn_fai, *fn_un_out, *fn_out_idx, *fn_un_out_idx;
+    int fetch_pairs, nreglist;
+    hts_reglist_t *reglist;
+} samview_settings_t;
+
+// Copied from htslib/sam.c.
+// TODO: we need a proper interface to find the length of an aux tag,
+// or at the very make exportable versions of these in htslib.
+static inline int aux_type2size(uint8_t type)
+{
+    switch (type) {
+    case 'A': case 'c': case 'C':
+        return 1;
+    case 's': case 'S':
+        return 2;
+    case 'i': case 'I': case 'f':
+        return 4;
+    case 'd':
+        return 8;
+    case 'Z': case 'H': case 'B':
+        return type;
+    default:
+        return 0;
+    }
+}
+
+// Copied from htslib/sam.c.
+static inline uint8_t *skip_aux(uint8_t *s, uint8_t *end)
+{
+    int size;
+    uint32_t n;
+    if (s >= end) return end;
+    size = aux_type2size(*s); ++s; // skip type
+    switch (size) {
+    case 'Z':
+    case 'H':
+        while (s < end && *s) ++s;
+        return s < end ? s + 1 : end;
+    case 'B':
+        if (end - s < 5) return NULL;
+        size = aux_type2size(*s); ++s;
+        n = le_to_u32(s);
+        s += 4;
+        if (size == 0 || end - s < size * n) return NULL;
+        return s + size * n;
+    case 0:
+        return NULL;
+    default:
+        if (end - s < size) return NULL;
+        return s + size;
+    }
+}
+
+// Returns 0 to indicate read should be output 1 otherwise
+static int process_aln(const sam_hdr_t *h, bam1_t *b, samview_settings_t* settings)
+{
+    if (settings->filter && sam_passes_filter(h, b, settings->filter) < 1)
+        return 1;
+
+    if (settings->remove_B) bam_remove_B(b);
+    if (settings->min_qlen > 0) {
+        int k, qlen = 0;
+        uint32_t *cigar = bam_get_cigar(b);
+        for (k = 0; k < b->core.n_cigar; ++k)
+            if ((bam_cigar_type(bam_cigar_op(cigar[k]))&1) || bam_cigar_op(cigar[k]) == BAM_CHARD_CLIP)
+                qlen += bam_cigar_oplen(cigar[k]);
+        if (qlen < settings->min_qlen) return 1;
+    }
+    if (b->core.qual < settings->min_mapQ || ((b->core.flag & settings->flag_on) != settings->flag_on) || (b->core.flag & settings->flag_off))
+        return 1;
+    if (settings->flag_alloff && ((b->core.flag & settings->flag_alloff) == settings->flag_alloff))
+        return 1;
+    if (settings->flag_anyon && ((b->core.flag & settings->flag_anyon) == 0))
+        return 1;
+    if (!settings->multi_region && settings->bed && (b->core.tid < 0 || !bed_overlap(settings->bed, sam_hdr_tid2name(h, b->core.tid), b->core.pos, bam_endpos(b))))
+        return 1;
+    if (settings->subsam_frac > 0.) {
+        uint32_t k = __ac_Wang_hash(__ac_X31_hash_string(bam_get_qname(b)) ^ settings->subsam_seed);
+        if ((double)(k&0xffffff) / 0x1000000 >= settings->subsam_frac) return 1;
+    }
+    if (settings->rghash) {
+        uint8_t *s = bam_aux_get(b, "RG");
+        if (s) {
+            khint_t k = kh_get(str, settings->rghash, (char*)(s + 1));
+            if (k == kh_end(settings->rghash)) return 1;
+        }
+    }
+    if (settings->tag) {
+        uint8_t *s = bam_aux_get(b, settings->tag);
+        if (s) {
+            if (settings->tvhash) {
+                char t[32], *val;
+                if (*s == 'i' || *s == 'I' || *s == 's' || *s == 'S' || *s == 'c' || *s == 'C') {
+                    int ret = snprintf(t, 32, "%"PRId64, bam_aux2i(s));
+                    if (ret > 0) val = t;
+                    else return 1;
+                } else if (*s == 'A') {
+                    t[0] = *(s+1);
+                    t[1] = 0;
+                    val = t;
+                } else {
+                    val = (char *)(s+1);
+                }
+                khint_t k = kh_get(str, settings->tvhash, val);
+                if (k == kh_end(settings->tvhash)) return 1;
+            }
+        } else {
+            return 1;
+        }
+    }
+    if (settings->rnhash) {
+        const char* rn = bam_get_qname(b);
+        if (!rn || kh_get(str, settings->rnhash, rn) == kh_end(settings->rnhash)) {
+            return 1;
+        }
+    }
+    if (settings->library) {
+        const char *p = bam_get_library((sam_hdr_t*)h, b);
+        if (!p || strcmp(p, settings->library) != 0) return 1;
+    }
+    return 0;
+}
+
+static int adjust_tags(const sam_hdr_t *h, bam1_t *b,
+                       samview_settings_t* settings) {
+    if (settings->keep_tag) {
+        uint8_t *s_from, *s_to, *end = b->data + b->l_data;
+        auxhash_t h = settings->keep_tag;
+
+        s_from = s_to = bam_get_aux(b);
+        while (s_from < end) {
+            int x = (int)s_from[0]<<8 | s_from[1];
+            uint8_t *s = skip_aux(s_from+2, end);
+            if (s == NULL) {
+                print_error("view", "malformed aux data for record \"%s\"",
+                            bam_get_qname(b));
+                return -1;
+            }
+
+            if (kh_get(aux_exists, h, x) != kh_end(h) ) {
+                if (s_to != s_from) memmove(s_to, s_from, s - s_from);
+                s_to += s - s_from;
+            }
+            s_from = s;
+        }
+        b->l_data = s_to - b->data;
+
+    } else if (settings->remove_tag) {
+        uint8_t *s_from, *s_to, *end = b->data + b->l_data;
+        auxhash_t h = settings->remove_tag;
+
+        s_from = s_to = bam_get_aux(b);
+        while (s_from < end) {
+            int x = (int)s_from[0]<<8 | s_from[1];
+            uint8_t *s = skip_aux(s_from+2, end);
+            if (s == NULL) {
+                print_error("view", "malformed aux data for record \"%s\"",
+                            bam_get_qname(b));
+                return -1;
+            }
+
+            if (kh_get(aux_exists, h, x) == kh_end(h) ) {
+                if (s_to != s_from) memmove(s_to, s_from, s - s_from);
+                s_to += s - s_from;
+            }
+            s_from = s;
+        }
+        b->l_data = s_to - b->data;
+    }
+
+    return 0;
+}
+
+static int usage(FILE *fp, int exit_status, int is_long_help);
+
+static int populate_lookup_from_file(const char *subcmd, strhash_t lookup, char *fn)
+{
+    FILE *fp;
+    char buf[1024];
+    int ret = 0;
+    fp = fopen(fn, "r");
+    if (fp == NULL) {
+        print_error_errno(subcmd, "failed to open \"%s\" for reading", fn);
+        return -1;
+    }
+
+    while (ret != -1 && !feof(fp) && fscanf(fp, "%1023s", buf) > 0) {
+        char *d = strdup(buf);
+        if (d != NULL) {
+            kh_put(str, lookup, d, &ret);
+            if (ret == 0) free(d); /* Duplicate */
+        } else {
+            ret = -1;
+        }
+    }
+    if (ferror(fp)) ret = -1;
+    if (ret == -1) {
+        print_error_errno(subcmd, "failed to read \"%s\"", fn);
+    }
+    fclose(fp);
+    return (ret != -1) ? 0 : -1;
+}
+
+static int add_read_group_single(const char *subcmd, samview_settings_t *settings, char *name)
+{
+    char *d = strdup(name);
+    int ret = 0;
+
+    if (d == NULL) goto err;
+
+    if (settings->rghash == NULL) {
+        settings->rghash = kh_init(str);
+        if (settings->rghash == NULL) goto err;
+    }
+
+    kh_put(str, settings->rghash, d, &ret);
+    if (ret == -1) goto err;
+    if (ret ==  0) free(d); /* Duplicate */
+    return 0;
+
+ err:
+    print_error(subcmd, "Couldn't add \"%s\" to read group list: memory exhausted?", name);
+    free(d);
+    return -1;
+}
+
+static int add_read_names_file(const char *subcmd, samview_settings_t *settings, char *fn)
+{
+    if (settings->rnhash == NULL) {
+        settings->rnhash = kh_init(str);
+        if (settings->rnhash == NULL) {
+            perror(NULL);
+            return -1;
+        }
+    }
+    return populate_lookup_from_file(subcmd, settings->rnhash, fn);
+}
+
+static int add_read_groups_file(const char *subcmd, samview_settings_t *settings, char *fn)
+{
+    if (settings->rghash == NULL) {
+        settings->rghash = kh_init(str);
+        if (settings->rghash == NULL) {
+            perror(NULL);
+            return -1;
+        }
+    }
+    return populate_lookup_from_file(subcmd, settings->rghash, fn);
+}
+
+static int add_tag_value_single(const char *subcmd, samview_settings_t *settings, char *name)
+{
+    char *d = strdup(name);
+    int ret = 0;
+
+    if (d == NULL) goto err;
+
+    if (settings->tvhash == NULL) {
+        settings->tvhash = kh_init(str);
+        if (settings->tvhash == NULL) goto err;
+    }
+
+    kh_put(str, settings->tvhash, d, &ret);
+    if (ret == -1) goto err;
+    if (ret ==  0) free(d); /* Duplicate */
+    return 0;
+
+ err:
+    print_error(subcmd, "Couldn't add \"%s\" to tag values list: memory exhausted?", name);
+    free(d);
+    return -1;
+}
+
+static int add_tag_values_file(const char *subcmd, samview_settings_t *settings, char *fn)
+{
+    if (settings->tvhash == NULL) {
+        settings->tvhash = kh_init(str);
+        if (settings->tvhash == NULL) {
+            perror(NULL);
+            return -1;
+        }
+    }
+    return populate_lookup_from_file(subcmd, settings->tvhash, fn);
+}
+
+static inline int check_sam_write1(samFile *fp, const sam_hdr_t *h, const bam1_t *b, const char *fname, int *retp)
+{
+    int r = sam_write1(fp, h, b);
+    if (r >= 0) return r;
+
+    if (fname) print_error_errno("view", "writing to \"%s\" failed", fname);
+    else print_error_errno("view", "writing to standard output failed");
+
+    *retp = EXIT_FAILURE;
+    return r;
+}
+
+static inline void change_flag(bam1_t *b, samview_settings_t *settings)
+{
+    if (settings->add_flag)
+        b->core.flag |= settings->add_flag;
+
+    if (settings->remove_flag)
+        b->core.flag &= ~settings->remove_flag;
+}
+
+int parse_aux_list(auxhash_t *h, char *optarg) {
+    if (!*h)
+        *h = kh_init(aux_exists);
+
+    while (strlen(optarg) >= 2) {
+        int x = optarg[0]<<8 | optarg[1];
+        int ret = 0;
+        kh_put(aux_exists, *h, x, &ret);
+        if (ret < 0)
+            return -1;
+
+        optarg += 2;
+        if (*optarg == ',') // allow white-space too for easy `cat file`?
+            optarg++;
+        else if (*optarg != 0)
+            break;
+    }
+
+    if (strlen(optarg) != 0) {
+        fprintf(samtools_stderr, "main_samview: Error parsing option, "
+                "auxiliary tags should be exactly two characters long.\n");
+        return -1;
+    }
+
+    return 0;
+}
+
+static int cmp_reglist_intervals(const void *aptr, const void *bptr)
+{
+    hts_pair_pos_t *a = (hts_pair_pos_t*)aptr;
+    hts_pair_pos_t *b = (hts_pair_pos_t*)bptr;
+    if ( a->beg < b->beg ) return -1;
+    if ( a->beg > b->beg ) return 1;
+    if ( a->end < b->end ) return -1;
+    if ( a->end > b->end ) return 1;
+    return 0;
+}
+static int cmp_reglist_tids(const void *aptr, const void *bptr)
+{
+    hts_reglist_t *a = (hts_reglist_t*)aptr;
+    hts_reglist_t *b = (hts_reglist_t*)bptr;
+    if ( b->tid==HTS_IDX_NOCOOR || a->tid < b->tid ) return -1;
+    if ( a->tid==HTS_IDX_NOCOOR || a->tid > b->tid ) return 1;
+    return 0;
+}
+
+static hts_reglist_t *_reglist_dup(sam_hdr_t *hdr, hts_reglist_t *src, int nsrc)
+{
+    int i,j;
+    hts_reglist_t *dst = (hts_reglist_t*)calloc(nsrc,sizeof(hts_reglist_t));
+    if ( !dst ) {
+        print_error_errno("view", "[%s:%d] could not allocate region list"
+                          ,__FILE__ ,__LINE__);
+        return NULL;
+    }
+    for (i=0; i<nsrc; i++)
+    {
+        // Assume tid is not set correctly, reg is informative but may not point to a long-lived memory
+        dst[i].tid = sam_hdr_name2tid(hdr,src[i].reg);
+        dst[i].min_beg = src[i].min_beg;
+        dst[i].max_end = src[i].max_end;
+        dst[i].count = src[i].count;
+        dst[i].intervals = (hts_pair_pos_t*)malloc(sizeof(hts_pair_pos_t)*dst[i].count);
+        if ( !dst[i].intervals ) {
+            print_error_errno("view", "[%s:%d] could not allocate region list",
+                              __FILE__, __LINE__);
+            goto fail;
+        }
+        for (j=0; j<dst[i].count; j++)
+            dst[i].intervals[j] = src[i].intervals[j];
+    }
+    qsort(dst,nsrc,sizeof(*dst),cmp_reglist_tids);
+    return dst;
+
+ fail:
+    for (j = 0; j < i; j++)
+        free(dst[j].intervals);
+    free(dst);
+    return NULL;
+}
+static inline int _reglist_find_tid(hts_reglist_t *reg, int nreg, int tid) // binary search
+{
+    int i = -1, imin = 0, imax = nreg - 1;
+    while ( imin <= imax )
+    {
+        i = (imin+imax)/2;
+        if ( tid==HTS_IDX_NOCOOR || reg[i].tid < tid ) imin = i + 1;
+        else if ( reg[i].tid==HTS_IDX_NOCOOR || reg[i].tid > tid ) imax = i - 1;
+        else break;
+    }
+    if ( i<0 || reg[i].tid < tid ) i++;    // not found, i will be the index of the inserted element
+    return i;
+}
+static int _reglist_push(hts_reglist_t **_reg, int *_nreg, int tid, hts_pos_t beg, hts_pos_t end)
+{
+    hts_reglist_t *reg = *_reg;
+    int nreg = *_nreg;
+    int i = _reglist_find_tid(reg,nreg,tid);
+    if ( i>=nreg || reg[i].tid!=tid ) {
+        nreg++;
+        reg = (hts_reglist_t*)realloc(reg,sizeof(hts_reglist_t)*nreg);
+        if ( !reg ) {
+            print_error_errno("view", "[%s:%d] could not extend region list",
+                              __FILE__, __LINE__);
+            return -1;
+        }
+        if ( i+1 < nreg )
+            memmove(reg + i + 1, reg + i, sizeof(hts_reglist_t)*(nreg - i - 1));
+        reg[i].reg = NULL;
+        reg[i].tid = tid;
+        reg[i].min_beg = beg;
+        reg[i].max_end = end;
+        reg[i].intervals = NULL;
+        reg[i].count = 0;
+    }
+    *_reg = reg;
+    *_nreg = nreg;
+    if ( reg[i].count > 0
+         && reg[i].intervals[reg[i].count - 1].beg==beg
+         && reg[i].intervals[reg[i].count - 1].end==end ) {
+        return 0;
+    }
+    hts_pair_pos_t *new_intervals = realloc(reg[i].intervals, sizeof(hts_pair_pos_t)*(reg[i].count + 1));
+    if (!new_intervals) {
+        print_error_errno("view", "[%s:%d] could not extend region list",
+                          __FILE__, __LINE__);
+        return -1;
+    }
+    reg[i].intervals = new_intervals;
+    reg[i].intervals[reg[i].count].beg = beg;
+    reg[i].intervals[reg[i].count].end = end;
+    reg[i].count++;
+    return 0;
+}
+
+static void _reglist_merge(hts_reglist_t *reg, int nreg)
+{
+    int i,j;
+    for (i=0; i<nreg; i++)
+    {
+        qsort(reg[i].intervals,reg[i].count,sizeof(*reg[i].intervals),cmp_reglist_intervals);
+        int k = 1;
+        for (j=1; j<reg[i].count; j++)
+        {
+            if ( reg[i].intervals[k-1].end < reg[i].intervals[j].beg )
+            {
+                if ( k < j ) reg[i].intervals[k] = reg[i].intervals[j];
+                k++;
+                continue;
+            }
+            if ( reg[i].intervals[k-1].end < reg[i].intervals[j].end ) reg[i].intervals[k-1].end = reg[i].intervals[j].end;
+        }
+        reg[i].count = k;
+        reg[i].max_end = reg[i].intervals[k-1].end;
+    }
+}
+hts_itr_multi_t *multi_region_init(samview_settings_t *conf, char **regs, int nregs)
+{
+    hts_itr_multi_t *iter = NULL;
+    int filter_state = ALL;
+    if ( nregs ) {
+        int filter_op = 0;
+        conf->bed = bed_hash_regions(conf->bed, regs, 0, nregs, &filter_op); // insert(1) or filter out(0) the regions from the command line in the same hash table as the bed file
+        if ( !filter_op )
+            filter_state = FILTERED;
+    }
+    else
+        bed_unify(conf->bed);
+    if ( !conf->bed) { // index is unavailable or no regions have been specified
+        print_error("view", "No regions or BED file have been provided. Aborting.");
+        return NULL;
+    }
+
+    int regcount = 0;
+    hts_reglist_t *reglist = bed_reglist(conf->bed, filter_state, &regcount);
+    if (!reglist) {
+        print_error("view", "Region list is empty or could not be created. Aborting.");
+        return NULL;
+    }
+
+    if ( conf->fetch_pairs ) {
+        conf->reglist  = _reglist_dup(conf->header,reglist,regcount);
+        if (!conf->reglist)
+            return NULL;
+        conf->nreglist = regcount;
+    }
+
+    iter = sam_itr_regions(conf->hts_idx, conf->header, reglist, regcount);
+    if ( !iter ) {
+        print_error("view", "Iterator could not be created. Aborting.");
+        return NULL;
+    }
+    return iter;
+}
+
+KHASH_SET_INIT_STR(names)
+
+static int fetch_pairs_collect_mates(samview_settings_t *conf, hts_itr_multi_t *iter)
+{
+    khint_t k;
+    int nunmap = 0, r = 0, nmates = 0, write_error = 0, retval = EXIT_FAILURE;
+    kh_names_t *mate_names = kh_init(names);
+    bam1_t *rec = bam_init1();
+
+    if (!mate_names) {
+        print_error_errno("view", "could not allocate mate names table");
+        goto out;
+    }
+    if (!rec) {
+        print_error_errno("view", "could not allocate bam record");
+        goto out;
+    }
+
+    while ((r =sam_itr_multi_next(conf->in, iter, rec))>=0) {
+        if ( (rec->core.flag & BAM_FPAIRED) == 0 ) continue;
+        if ( rec->core.mtid>=0 && bed_overlap(conf->bed, sam_hdr_tid2name(conf->header,rec->core.mtid), rec->core.mpos, rec->core.mpos) ) continue;
+        if ( process_aln(conf->header, rec, conf) ) continue;
+
+        nmates++;
+
+        k = kh_get(names,mate_names,bam_get_qname(rec));
+        if ( k == kh_end(mate_names) ) {
+            int ret = 0;
+            char *name_copy = strdup(bam_get_qname(rec));
+            if (!name_copy) {
+                print_error_errno("view", "[%s:%d] could not store sample name, %d elements", __FILE__,__LINE__,nmates);
+                goto out;
+            }
+            kh_put(names, mate_names, name_copy, &ret);
+            if ( ret<0 ) {
+                print_error_errno("view", "[%s:%d] could not store sample name, %d elements",__FILE__,__LINE__,nmates);
+                free(name_copy);
+                goto out;
+            }
+        }
+
+        if ( rec->core.mtid < 0 || (rec->core.flag & BAM_FMUNMAP) ) nunmap = 1;
+        if ( rec->core.mtid >= 0 ) {
+            if (_reglist_push(&conf->reglist, &conf->nreglist, rec->core.mtid, rec->core.mpos,rec->core.mpos+1) != 0)
+                goto out;
+        }
+    }
+
+    if (r < -1) {
+        print_error_errno("view", "error reading file \"%s\"", conf->fn_in);
+        goto out;
+    }
+
+    _reglist_merge(conf->reglist, conf->nreglist);
+    if ( nunmap ) {
+        if (_reglist_push(&conf->reglist,&conf->nreglist,HTS_IDX_NOCOOR,0,HTS_POS_MAX) != 0)
+            goto out;
+    }
+    hts_itr_multi_destroy(iter);
+    iter = sam_itr_regions(conf->hts_idx, conf->header, conf->reglist, conf->nreglist);
+    if ( !iter ) {
+        print_error_errno("view", "[%s:%d] iterator could not be created",__FILE__,__LINE__);
+        goto out;
+    }
+    while ((r = sam_itr_multi_next(conf->in, iter, rec))>=0) {
+        int drop = 1;
+        if (rec->core.tid >=0 &&
+            bed_overlap(conf->bed, sam_hdr_tid2name(conf->header,rec->core.tid), rec->core.pos, bam_endpos(rec))) drop = 0;
+        if ( drop ) {
+             k = kh_get(names,mate_names,bam_get_qname(rec));
+             if ( k != kh_end(mate_names) ) drop = 0;
+        }
+        if (!drop && process_aln(conf->header, rec, conf) == 0) {
+            if (adjust_tags(conf->header, rec, conf) != 0)
+                goto out;
+            if (check_sam_write1(conf->out, conf->header, rec, conf->fn_out,
+                                 &write_error) < 0)
+                goto out;
+        }
+    }
+
+    if (r < -1) {
+        print_error_errno("view", "error reading file \"%s\"", conf->fn_in);
+        goto out;
+    }
+
+    retval = EXIT_SUCCESS;
+
+ out:
+    hts_itr_multi_destroy(iter);
+    hts_idx_destroy(conf->hts_idx); // destroy the BAM index
+    conf->hts_idx = NULL;
+    if (mate_names) {
+        // free khash keys
+        for (k = 0; k < kh_end(mate_names); ++k)
+            if ( kh_exist(mate_names,k) ) free((char*)kh_key(mate_names, k));
+        kh_destroy(names,mate_names);
+    }
+    bam_destroy1(rec);
+    return retval;
+}
+
+// Common code for processing and writing a record
+static inline int process_one_record(samview_settings_t *conf, bam1_t *b,
+                                     int *write_error) {
+    if (!process_aln(conf->header, b, conf)) {
+        if (!conf->is_count) {
+            change_flag(b, conf);
+            if (adjust_tags(conf->header, b, conf) != 0)
+                return -1;
+            if (check_sam_write1(conf->out, conf->header,
+                                 b, conf->fn_out, write_error) < 0) {
+                return -1;
+            }
+        }
+        conf->count++;
+    } else if (conf->unmap) {
+        b->core.flag |= BAM_FUNMAP;
+        b->core.qual = 0;
+        b->core.isize = 0;
+
+        // remove CIGAR
+        if (b->core.n_cigar) {
+            memmove(bam_get_cigar(b), bam_get_seq(b),
+                    b->data + b->l_data - bam_get_seq(b));
+            b->l_data -= 4*b->core.n_cigar;
+            b->core.n_cigar = 0;
+        }
+
+        if (check_sam_write1(conf->out, conf->header,
+                             b, conf->fn_out, write_error) < 0) {
+            return -1;
+        }
+    } else {
+        if (conf->un_out) {
+            if (check_sam_write1(conf->un_out, conf->header,
+                                 b, conf->fn_un_out, write_error) < 0) {
+                return -1;
+            }
+        }
+    }
+    return 0;
+}
+
+static int stream_view(samview_settings_t *conf) {
+    bam1_t *b = bam_init1();
+    int write_error = 0, r;
+    if (!b) {
+        print_error_errno("view", "could not allocate bam record");
+        return 1;
+    }
+    errno = 0; // prevent false error messages.
+    while ((r = sam_read1(conf->in, conf->header, b)) >= 0) {
+        if (process_one_record(conf, b, &write_error) < 0) break;
+    }
+    bam_destroy1(b);
+    if (r < -1) {
+        print_error_errno("view", "error reading file \"%s\"", conf->fn_in);
+        return 1;
+    }
+    return write_error;
+}
+
+static int multi_region_view(samview_settings_t *conf, hts_itr_multi_t *iter)
+{
+    bam1_t *b = bam_init1();
+    int write_error = 0, result;
+    if (!b) {
+        print_error_errno("view", "could not allocate bam record");
+        return 1;
+    }
+    // fetch alignments
+    while ((result = sam_itr_multi_next(conf->in, iter, b)) >= 0) {
+        if (process_one_record(conf, b, &write_error) < 0) break;
+    }
+    hts_itr_multi_destroy(iter);
+    bam_destroy1(b);
+
+    if (result < -1) {
+        print_error("view", "retrieval of region #%d failed", iter->curr_tid);
+        return 1;
+    }
+    return write_error;
+}
+
+// Make mnemonic distinct values for longoption-only options
+#define LONGOPT(c)  ((c) + 128)
+
+// Check for ".sam" filenames as sam_open_mode cannot distinguish between
+// foo.sam and foo.unknown, both getting mode "".
+static int is_sam(const char *fn) {
+    if (!fn)
+        return 0;
+    size_t l = strlen(fn);
+    return (l >= 4 && strcasecmp(fn + l-4, ".sam") == 0);
+}
+
+int main_samview(int argc, char *argv[])
+{
+    samview_settings_t settings;
+    int c, is_header = 0, is_header_only = 0, ret = 0, compress_level = -1, has_index_file = 0, no_pg = 0;
+    FILE *fp_out = NULL;
+    char out_mode[6] = {0}, out_un_mode[6] = {0};
+    char *out_format = "";
+    char *arg_list = NULL;
+    sam_global_args ga = SAM_GLOBAL_ARGS_INIT;
+    htsThreadPool p = {NULL, 0};
+
+    memset(&settings,0,sizeof(settings));
+    settings.subsam_frac = -1.0;
+
+    static const struct option lopts[] = {
+        SAM_OPT_GLOBAL_OPTIONS('-', 0, 'O', 0, 'T', '@'),
+        {"add-flags", required_argument, NULL, LONGOPT('a')},
+        {"bam", no_argument, NULL, 'b'},
+        {"count", no_argument, NULL, 'c'},
+        {"cram", no_argument, NULL, 'C'},
+        {"customised-index", no_argument, NULL, 'X'},
+        {"customized-index", no_argument, NULL, 'X'},
+        {"excl-flags", required_argument, NULL, 'F'},
+        {"exclude-flags", required_argument, NULL, 'F'},
+        {"expr", required_argument, NULL, 'e'},
+        {"expression", required_argument, NULL, 'e'},
+        {"fai-reference", required_argument, NULL, 't'},
+        {"fast", no_argument, NULL, '1'},
+        {"fetch-pairs", no_argument, NULL, 'P'},
+        {"header-only", no_argument, NULL, 'H'},
+        {"help", no_argument, NULL, LONGOPT('?')},
+        {"incl-flags", required_argument, NULL, LONGOPT('g')},
+        {"include-flags", required_argument, NULL, LONGOPT('g')},
+        {"rf", required_argument, NULL, LONGOPT('g')}, // aka incl-flags
+        {"keep-tag", required_argument, NULL, LONGOPT('x') },
+        {"library", required_argument, NULL, 'l'},
+        {"min-mapq", required_argument, NULL, 'q'},
+        {"min-MQ", required_argument, NULL, 'q'},
+        {"min-mq", required_argument, NULL, 'q'},
+        {"min-qlen", required_argument, NULL, 'm'},
+        {"no-header", no_argument, NULL, LONGOPT('H')},
+        {"no-PG", no_argument, NULL, LONGOPT('P')},
+        {"output", required_argument, NULL, 'o'},
+        {"output-unselected", required_argument, NULL, 'U'},
+        {"QNAME-file", required_argument, NULL, 'N'},
+        {"qname-file", required_argument, NULL, 'N'},
+        {"read-group", required_argument, NULL, 'r'},
+        {"read-group-file", required_argument, NULL, 'R'},
+        {"readgroup", required_argument, NULL, 'r'},
+        {"readgroup-file", required_argument, NULL, 'R'},
+        {"region-file", required_argument, NULL, LONGOPT('L')},
+        {"regions-file", required_argument, NULL, LONGOPT('L')},
+        {"remove-B", no_argument, NULL, 'B'},
+        {"remove-flags", required_argument, NULL, LONGOPT('r')},
+        {"remove-tag", required_argument, NULL, 'x'},
+        {"require-flags", required_argument, NULL, 'f'},
+        {"subsample", required_argument, NULL, LONGOPT('s')},
+        {"subsample-seed", required_argument, NULL, LONGOPT('S')},
+        {"tag", required_argument, NULL, 'd'},
+        {"tag-file", required_argument, NULL, 'D'},
+        {"target-file", required_argument, NULL, 'L'},
+        {"targets-file", required_argument, NULL, 'L'},
+        {"uncompressed", no_argument, NULL, 'u'},
+        {"unmap", no_argument, NULL, 'p'},
+        {"unoutput", required_argument, NULL, 'U'},
+        {"use-index", no_argument, NULL, 'M'},
+        {"with-header", no_argument, NULL, 'h'},
+    };
+
+    /* parse command-line options */
+    strcpy(out_mode, "w");
+    strcpy(out_un_mode, "w");
+    if (argc == 1 && isatty(STDIN_FILENO))
+        return usage(samtools_stdout, EXIT_SUCCESS, 0);
+
+    // Suppress complaints about '?' being an unrecognised option.  Without
+    // this we have to put '?' in the options list, which makes it hard to
+    // tell a bad long option from the use of '-?' (both return '?' and
+    // set optopt to '\0').
+    opterr = 0;
+
+    char *tmp;
+    while ((c = getopt_long(argc, argv,
+                            "SbBcCt:h1Ho:O:q:f:F:G:ul:r:T:R:N:d:D:L:s:@:m:x:U:MXe:pP",
+                            lopts, NULL)) >= 0) {
+        switch (c) {
+        case 's':
+            settings.subsam_seed = strtol(optarg, &tmp, 10);
+            if (tmp && *tmp == '.') {
+                settings.subsam_frac = strtod(tmp, &tmp);
+                if (*tmp) ret = 1;
+            } else {
+                ret = 1;
+            }
+
+            if (ret == 1) {
+                print_error("view", "Incorrect sampling argument \"%s\"", optarg);
+                goto view_end;
+            }
+            break;
+        case LONGOPT('s'):
+            settings.subsam_frac = strtod(optarg, &tmp);
+            if (*tmp || settings.subsam_frac < 0.0 || settings.subsam_frac > 1.0) {
+                print_error("view", "Incorrect sampling argument \"%s\"", optarg);
+                goto view_end;
+            }
+            break;
+        case LONGOPT('S'): settings.subsam_seed = atoi(optarg); break;
+        case 'm': settings.min_qlen = atoi(optarg); break;
+        case 'c': settings.is_count = 1; break;
+        case 'S': break;
+        case 'b': out_format = "b"; break;
+        case 'C': out_format = "c"; break;
+        case 't': settings.fn_fai = strdup(optarg); break;
+        case 'h': is_header = 1; break;
+        case 'H': is_header_only = 1; break;
+        case LONGOPT('H'): is_header = is_header_only = 0; break;
+        case 'o': settings.fn_out = strdup(optarg); break;
+        case 'U': settings.fn_un_out = strdup(optarg); break;
+        case 'X': has_index_file = 1; break;
+        case 'f': settings.flag_on |= bam_str2flag(optarg); break;
+        case 'F': settings.flag_off |= bam_str2flag(optarg); break;
+        case LONGOPT('g'):
+            settings.flag_anyon |= bam_str2flag(optarg); break;
+        case 'G': settings.flag_alloff |= bam_str2flag(optarg); break;
+        case 'q': settings.min_mapQ = atoi(optarg); break;
+        case 'u': compress_level = 0; break;
+        case '1': compress_level = 1; break;
+        case 'l': settings.library = strdup(optarg); break;
+        case 'p': settings.unmap = 1; break;
+        case 'P': settings.fetch_pairs = 1; settings.multi_region = 1; break;
+        case LONGOPT('L'):
+            settings.multi_region = 1;
+            // fall through
+        case 'L':
+            if ((settings.bed = bed_read(optarg)) == NULL) {
+                print_error_errno("view", "Could not read file \"%s\"", optarg);
+                ret = 1;
+                goto view_end;
+            }
+            break;
+        case 'r':
+            if (add_read_group_single("view", &settings, optarg) != 0) {
+                ret = 1;
+                goto view_end;
+            }
+            break;
+        case 'R':
+            if (add_read_groups_file("view", &settings, optarg) != 0) {
+                ret = 1;
+                goto view_end;
+            }
+            break;
+        case 'N':
+            if (add_read_names_file("view", &settings, optarg) != 0) {
+                ret = 1;
+                goto view_end;
+            }
+            break;
+        case 'd':
+            if (strlen(optarg) < 2 || (strlen(optarg) > 2 && optarg[2] != ':')) {
+                print_error_errno("view", "Invalid \"tag:value\" option: \"%s\"", optarg);
+                ret = 1;
+                goto view_end;
+            }
+
+            if (settings.tag) {
+                if (settings.tag[0] != optarg[0] || settings.tag[1] != optarg[1]) {
+                    print_error("view", "Different tag \"%s\" was specified before: \"%s\"", settings.tag, optarg);
+                    ret = 1;
+                    goto view_end;
+                }
+            } else {
+                if (!(settings.tag = calloc(3, 1))) {
+                    print_error("view", "Could not allocate memory for tag: \"%s\"", optarg);
+                    ret = 1;
+                    goto view_end;
+                }
+                memcpy(settings.tag, optarg, 2);
+            }
+
+            if (strlen(optarg) > 3 && add_tag_value_single("view", &settings, optarg+3) != 0) {
+                print_error("view", "Could not add tag:value \"%s\"", optarg);
+                ret = 1;
+                goto view_end;
+            }
+            break;
+        case 'D':
+            // Allow ";" as delimiter besides ":" to support MinGW CLI POSIX
+            // path translation as described at:
+            // http://www.mingw.org/wiki/Posix_path_conversion
+            if (strlen(optarg) < 4 || (optarg[2] != ':' && optarg[2] != ';')) {
+                print_error_errno("view", "Invalid \"tag:file\" option: \"%s\"", optarg);
+                ret = 1;
+                goto view_end;
+            }
+
+            if (settings.tag) {
+                if (settings.tag[0] != optarg[0] || settings.tag[1] != optarg[1]) {
+                    print_error("view", "Different tag \"%s\" was specified before: \"%s\"", settings.tag, optarg);
+                    ret = 1;
+                    goto view_end;
+                }
+            } else {
+                if (!(settings.tag = calloc(3, 1))) {
+                    print_error("view", "Could not allocate memory for tag: \"%s\"", optarg);
+                    ret = 1;
+                    goto view_end;
+                }
+                memcpy(settings.tag, optarg, 2);
+            }
+
+            if (add_tag_values_file("view", &settings, optarg+3) != 0) {
+                ret = 1;
+                goto view_end;
+            }
+            break;
+        case LONGOPT('?'):
+            return usage(samtools_stdout, EXIT_SUCCESS, 1);
+        case '?':
+            if (optopt == '?') {  // '-?' appeared on command line
+                return usage(samtools_stdout, EXIT_SUCCESS, 1);
+            } else {
+                if (optopt) { // Bad short option
+                    print_error("view", "invalid option -- '%c'", optopt);
+                } else { // Bad long option
+                    // Do our best.  There is no good solution to finding
+                    // out what the bad option was.
+                    // See, e.g. https://stackoverflow.com/questions/2723888/where-does-getopt-long-store-an-unrecognized-option
+                    if (optind > 0 && strncmp(argv[optind - 1], "--", 2) == 0) {
+                        print_error("view", "unrecognised option '%s'",
+                                    argv[optind - 1]);
+                    }
+                }
+                return usage(samtools_stderr, EXIT_FAILURE, 0);
+            }
+        case 'B': settings.remove_B = 1; break;
+
+        case 'M': settings.multi_region = 1; break;
+        case LONGOPT('P'): no_pg = 1; break;
+        case 'e':
+            if (!(settings.filter = hts_filter_init(optarg))) {
+                print_error("main_samview", "Couldn't initialise filter");
+                return 1;
+            }
+            break;
+        case LONGOPT('r'): settings.remove_flag |= bam_str2flag(optarg); break;
+        case LONGOPT('a'): settings.add_flag |= bam_str2flag(optarg); break;
+
+        case 'x':
+            if (*optarg == '^') {
+                if (parse_aux_list(&settings.keep_tag, optarg+1))
+                    return usage(samtools_stderr, EXIT_FAILURE, 0);
+            } else {
+                if (parse_aux_list(&settings.remove_tag, optarg))
+                    return usage(samtools_stderr, EXIT_FAILURE, 0);
+            }
+            break;
+
+        case LONGOPT('x'):
+            if (parse_aux_list(&settings.keep_tag, optarg))
+                return usage(samtools_stderr, EXIT_FAILURE, 0);
+            break;
+
+        default:
+            if (parse_sam_global_opt(c, optarg, lopts, &ga) != 0)
+                return usage(samtools_stderr, EXIT_FAILURE, 0);
+            break;
+        }
+    }
+    if (settings.is_count && settings.fetch_pairs)
+    {
+        print_error("view","The options -P and -c cannot be combined\n");
+        return 1;
+    }
+    if (settings.fn_fai == 0 && ga.reference) settings.fn_fai = fai_path(ga.reference);
+    if (is_header_only) is_header = 1;
+    // File format auto-detection first
+    if (settings.fn_out)    sam_open_mode(out_mode+1,    settings.fn_out,    NULL);
+    if (settings.fn_un_out) sam_open_mode(out_un_mode+1, settings.fn_un_out, NULL);
+
+    // -1 or -u without an explicit format (-b, -C) => check fn extensions
+    if (!*out_format && compress_level >= 0) {
+        if (compress_level == 0 &&
+            (out_mode[strlen(out_mode)-1] == 'z' ||
+             out_un_mode[strlen(out_un_mode)-1] == 'z'))
+            // z, fz, Fz sanity check
+            fprintf(samtools_stderr, "[view] Warning option -u ignored due to"
+                    " filename suffix\n");
+
+        // If known extension, use it, otherwise BAM
+        if (!(out_mode[1] || is_sam(settings.fn_out)))
+            out_mode[1] = 'b';
+
+        if (!(out_un_mode[1] || is_sam(settings.fn_un_out)))
+            out_un_mode[1] = 'b';
+    } else if (*out_format) {
+        out_mode[1] = out_un_mode[1] = *out_format;
+    }
+
+    if (compress_level >= 0) {
+        char tmp[2];
+        tmp[0] = compress_level + '0'; tmp[1] = '\0';
+        strcat(out_mode, tmp);
+        strcat(out_un_mode, tmp);
+    }
+    if (argc == optind && isatty(STDIN_FILENO)) {
+        print_error("view", "No input provided or missing option argument.");
+        return usage(samtools_stderr, EXIT_FAILURE, 0); // potential memory leak...
+    }
+
+    if (settings.unmap && settings.fn_un_out) {
+        print_error("view", "Options --unoutput and --unmap are mutually exclusive.");
+        ret = 1;
+        goto view_end;
+    }
+
+    if (settings.subsam_seed != 0) {
+        // Convert likely user input 1,2,... to pseudo-random
+        // values with more entropy and more bits set
+        srand(settings.subsam_seed);
+        settings.subsam_seed = rand();
+    }
+
+    settings.fn_in = (optind < argc)? argv[optind] : "-";
+    if ((settings.in = sam_open_format(settings.fn_in, "r", &ga.in)) == 0) {
+        print_error_errno("view", "failed to open \"%s\" for reading", settings.fn_in);
+        ret = 1;
+        goto view_end;
+    }
+
+    if (settings.fn_fai) {
+        if (hts_set_fai_filename(settings.in, settings.fn_fai) != 0) {
+            fprintf(samtools_stderr, "[main_samview] failed to use reference \"%s\".\n", settings.fn_fai);
+            ret = 1;
+            goto view_end;
+        }
+    }
+    if ((settings.header = sam_hdr_read(settings.in)) == 0) {
+        fprintf(samtools_stderr, "[main_samview] fail to read the header from \"%s\".\n", settings.fn_in);
+        ret = 1;
+        goto view_end;
+    }
+    if (settings.rghash) {
+        sam_hdr_remove_lines(settings.header, "RG", "ID", settings.rghash);
+    }
+    if (!settings.is_count) {
+        if ((settings.out = sam_open_format(settings.fn_out? settings.fn_out : "-", out_mode, &ga.out)) == 0) {
+            print_error_errno("view", "failed to open \"%s\" for writing", settings.fn_out? settings.fn_out : "standard output");
+            ret = 1;
+            goto view_end;
+        }
+        if (settings.fn_fai) {
+            if (hts_set_fai_filename(settings.out, settings.fn_fai) != 0) {
+                fprintf(samtools_stderr, "[main_samview] failed to use reference \"%s\".\n", settings.fn_fai);
+                ret = 1;
+                goto view_end;
+            }
+        }
+        autoflush_if_stdout(settings.out, settings.fn_out);
+
+        if (!no_pg) {
+            if (!(arg_list = stringify_argv(argc+1, argv-1))) {
+                print_error("view", "failed to create arg_list");
+                ret = 1;
+                goto view_end;
+            }
+            if (sam_hdr_add_pg(settings.header, "samtools",
+                                         "VN", samtools_version(),
+                                         arg_list ? "CL": NULL,
+                                         arg_list ? arg_list : NULL,
+                                         NULL)) {
+                print_error("view", "failed to add PG line to the header");
+                ret = 1;
+                goto view_end;
+            }
+        }
+
+        if (ga.write_index || is_header ||
+            out_mode[1] == 'b' || out_mode[1] == 'c' ||
+            (ga.out.format != sam && ga.out.format != unknown_format))  {
+            if (sam_hdr_write(settings.out, settings.header) != 0) {
+                fprintf(samtools_stderr, "[main_samview] failed to write the SAM header\n");
+                ret = 1;
+                goto view_end;
+            }
+        }
+        if (ga.write_index) {
+            if (!(settings.fn_out_idx = auto_index(settings.out, settings.fn_out, settings.header))) {
+                ret = 1;
+                goto view_end;
+            }
+        }
+
+        if (settings.fn_un_out) {
+            if ((settings.un_out = sam_open_format(settings.fn_un_out, out_un_mode, &ga.out)) == 0) {
+                print_error_errno("view", "failed to open \"%s\" for writing", settings.fn_un_out);
+                ret = 1;
+                goto view_end;
+            }
+            if (settings.fn_fai) {
+                if (hts_set_fai_filename(settings.un_out, settings.fn_fai) != 0) {
+                    fprintf(samtools_stderr, "[main_samview] failed to use reference \"%s\".\n", settings.fn_fai);
+                    ret = 1;
+                    goto view_end;
+                }
+            }
+            autoflush_if_stdout(settings.un_out, settings.fn_un_out);
+            if (ga.write_index || is_header ||
+                out_un_mode[1] == 'b' || out_un_mode[1] == 'c' ||
+                (ga.out.format != sam && ga.out.format != unknown_format))  {
+                if (sam_hdr_write(settings.un_out, settings.header) != 0) {
+                    fprintf(samtools_stderr, "[main_samview] failed to write the SAM header\n");
+                    ret = 1;
+                    goto view_end;
+                }
+            }
+            if (ga.write_index) {
+                if (!(settings.fn_un_out_idx = auto_index(settings.un_out, settings.fn_un_out, settings.header))) {
+                    ret = 1;
+                    goto view_end;
+                }
+            }
+        }
+    }
+    else {
+        if (settings.fn_out) {
+            fp_out = fopen(settings.fn_out, "w");
+            if (fp_out == NULL) {
+                print_error_errno("view", "can't create \"%s\"", settings.fn_out);
+                ret = EXIT_FAILURE;
+                goto view_end;
+            }
+        }
+        settings.unmap = 0;  // Not valid in counting mode
+    }
+
+    if (ga.nthreads > 1) {
+        if (!(p.pool = hts_tpool_init(ga.nthreads))) {
+            fprintf(samtools_stderr, "Error creating thread pool\n");
+            ret = 1;
+            goto view_end;
+        }
+        hts_set_opt(settings.in,  HTS_OPT_THREAD_POOL, &p);
+        if (settings.out) hts_set_opt(settings.out, HTS_OPT_THREAD_POOL, &p);
+    }
+    if (is_header_only) goto view_end; // no need to print alignments
+
+
+    // Initialize BAM/CRAM index
+    char **regs = NULL;
+    int nregs = 0;
+    if ( has_index_file && optind < argc - 2 ) regs = &argv[optind+2], nregs = argc - optind - 2, settings.fn_idx_in = argv[optind+1];
+    else if ( !has_index_file && optind < argc - 1 ) regs = &argv[optind+1], nregs = argc - optind - 1;
+    else if ( has_index_file )
+    {
+        print_error("view", "Incorrect number of arguments for -X option. Aborting.");
+        return 1;
+    }
+    if ( settings.fn_idx_in || nregs || settings.multi_region )
+    {
+        settings.hts_idx = settings.fn_idx_in ? sam_index_load2(settings.in, settings.fn_in, settings.fn_idx_in) : sam_index_load(settings.in, settings.fn_in);
+        if ( !settings.hts_idx )
+        {
+            print_error("view", "Random alignment retrieval only works for indexed SAM.gz, BAM or CRAM files.");
+            return 1;
+        }
+    }
+
+    if ( settings.fetch_pairs )
+    {
+        hts_itr_multi_t *iter = multi_region_init(&settings, regs, nregs);
+        ret = iter ? fetch_pairs_collect_mates(&settings, iter) : 1;
+        if (ret) goto view_end;
+    }
+    else if ( settings.multi_region )
+    {
+        hts_itr_multi_t *iter = multi_region_init(&settings, regs, nregs);
+        ret = iter ? multi_region_view(&settings, iter) : 1;
+        if (ret) goto view_end;
+    }
+    else if ( !settings.hts_idx )   // stream through the entire file
+    {
+        ret = stream_view(&settings);
+        if (ret) goto view_end;
+    } else {   // retrieve alignments in specified regions
+        int i;
+        for (i = (has_index_file)? optind+2 : optind+1; i < argc; ++i) {
+            hts_itr_t *iter = sam_itr_querys(settings.hts_idx, settings.header, argv[i]); // parse a region in the format like `chr2:100-200'
+            if (iter == NULL) { // region invalid or reference name not found
+                fprintf(samtools_stderr, "[main_samview] region \"%s\" specifies an invalid region or unknown reference. Continue anyway.\n", argv[i]);
+                continue;
+            }
+            // fetch alignments
+            ret = multi_region_view(&settings, iter);
+            if (ret) goto view_end;
+        }
+    }
+
+    if ( settings.hts_idx ) hts_idx_destroy(settings.hts_idx);
+
+    if (ga.write_index) {
+        if (sam_idx_save(settings.out) < 0) {
+            print_error_errno("view", "writing index failed");
+            ret = 1;
+        }
+        if (settings.un_out && sam_idx_save(settings.un_out) < 0) {
+            print_error_errno("view", "writing index failed");
+            ret = 1;
+        }
+    }
+
+view_end:
+    if (settings.is_count && ret == 0) {
+        if (fprintf(settings.fn_out? fp_out : samtools_stdout, "%" PRId64 "\n", settings.count) < 0) {
+            if (settings.fn_out) print_error_errno("view", "writing to \"%s\" failed", settings.fn_out);
+            else print_error_errno("view", "writing to standard output failed");
+            ret = EXIT_FAILURE;
+        }
+    }
+
+    // close files, free and return
+    if (settings.in) check_sam_close("view", settings.in, settings.fn_in, "standard input", &ret);
+    if (settings.out) check_sam_close("view", settings.out, settings.fn_out, "standard output", &ret);
+    if (settings.un_out) check_sam_close("view", settings.un_out, settings.fn_un_out, "file", &ret);
+    if (fp_out) fclose(fp_out);
+
+    free(settings.fn_fai); free(settings.fn_out); free(settings.library);  free(settings.fn_un_out);
+    sam_global_args_free(&ga);
+    if ( settings.header ) sam_hdr_destroy(settings.header);
+    if (settings.bed) bed_destroy(settings.bed);
+    if (settings.rghash) {
+        khint_t k;
+        for (k = 0; k < kh_end(settings.rghash); ++k)
+            if (kh_exist(settings.rghash, k)) free((char*)kh_key(settings.rghash, k));
+        kh_destroy(str, settings.rghash);
+    }
+    if (settings.rnhash) {
+        khint_t k;
+        for (k = 0; k < kh_end(settings.rnhash); ++k)
+            if (kh_exist(settings.rnhash, k)) free((char*)kh_key(settings.rnhash, k));
+        kh_destroy(str, settings.rnhash);
+    }
+    if (settings.tvhash) {
+        khint_t k;
+        for (k = 0; k < kh_end(settings.tvhash); ++k)
+            if (kh_exist(settings.tvhash, k)) free((char*)kh_key(settings.tvhash, k));
+        kh_destroy(str, settings.tvhash);
+    }
+
+    if (settings.remove_aux_len) {
+        free(settings.remove_aux);
+    }
+    if (settings.tag) {
+        free(settings.tag);
+    }
+    if (settings.filter)
+        hts_filter_free(settings.filter);
+
+    if (p.pool)
+        hts_tpool_destroy(p.pool);
+
+    if (settings.fn_out_idx)
+        free(settings.fn_out_idx);
+    if (settings.fn_un_out_idx)
+        free(settings.fn_un_out_idx);
+    free(arg_list);
+
+    if (settings.keep_tag)
+        kh_destroy(aux_exists, settings.keep_tag);
+    if (settings.remove_tag)
+        kh_destroy(aux_exists, settings.remove_tag);
+
+    return ret;
+}
+
+static int usage(FILE *fp, int exit_status, int is_long_help)
+{
+    fprintf(fp,
+"\n"
+"Usage: samtools view [options] <in.bam>|<in.sam>|<in.cram> [region ...]\n"
+"\n"
+
+"Output options:\n"
+"  -b, --bam                  Output BAM\n"
+"  -C, --cram                 Output CRAM (requires -T)\n"
+"  -1, --fast                 Use fast BAM compression (and default to --bam)\n"
+"  -u, --uncompressed         Uncompressed BAM output (and default to --bam)\n"
+"  -h, --with-header          Include header in SAM output\n"
+"  -H, --header-only          Print SAM header only (no alignments)\n"
+"      --no-header            Print SAM alignment records only [default]\n"
+"  -c, --count                Print only the count of matching records\n"
+"  -o, --output FILE          Write output to FILE [standard output]\n"
+"  -U, --unoutput FILE, --output-unselected FILE\n"
+"                             Output reads not selected by filters to FILE\n"
+"  -p, --unmap                Set flag to UNMAP on reads not selected\n"
+"                             then write to output file.\n"
+"  -P, --fetch-pairs          Retrieve complete pairs even when outside of region\n"
+"Input options:\n"
+"  -t, --fai-reference FILE   FILE listing reference names and lengths\n"
+"  -M, --use-index            Use index and multi-region iterator for regions\n"
+"      --region[s]-file FILE  Use index to include only reads overlapping FILE\n"
+"  -X, --customized-index     Expect extra index file argument after <in.bam>\n"
+"\n"
+"Filtering options (Only include in output reads that...):\n"
+"  -L, --target[s]-file FILE  ...overlap (BED) regions in FILE\n"
+"  -r, --read-group STR       ...are in read group STR\n"
+"  -R, --read-group-file FILE ...are in a read group listed in FILE\n"
+"  -N, --qname-file FILE      ...whose read name is listed in FILE\n"
+"  -d, --tag STR1[:STR2]      ...have a tag STR1 (with associated value STR2)\n"
+"  -D, --tag-file STR:FILE    ...have a tag STR whose value is listed in FILE\n"
+"  -q, --min-MQ INT           ...have mapping quality >= INT\n"
+"  -l, --library STR          ...are in library STR\n"
+"  -m, --min-qlen INT         ...cover >= INT query bases (as measured via CIGAR)\n"
+"  -e, --expr STR             ...match the filter expression STR\n"
+"  -f, --require-flags FLAG   ...have all of the FLAGs present\n"             //   F&x == x
+"  -F, --excl[ude]-flags FLAG ...have none of the FLAGs present\n"            //   F&x == 0
+"      --rf, --incl-flags, --include-flags FLAG\n"
+"                             ...have some of the FLAGs present\n"
+"  -G FLAG                    EXCLUDE reads with all of the FLAGs present\n"  // !(F&x == x)  TODO long option
+"      --subsample FLOAT      Keep only FLOAT fraction of templates/read pairs\n"
+"      --subsample-seed INT   Influence WHICH reads are kept in subsampling [0]\n"
+"  -s INT.FRAC                Same as --subsample 0.FRAC --subsample-seed INT\n"
+"\n"
+"Processing options:\n"
+"      --add-flags FLAG       Add FLAGs to reads\n"
+"      --remove-flags FLAG    Remove FLAGs from reads\n"
+"  -x, --remove-tag STR\n"
+"               Comma-separated read tags to strip (repeatable) [null]\n"
+"      --keep-tag STR\n"
+"               Comma-separated read tags to preserve (repeatable) [null].\n"
+"               Equivalent to \"-x ^STR\"\n"
+"  -B, --remove-B             Collapse the backward CIGAR operation\n"
+"\n"
+"General options:\n"
+"  -?, --help   Print long help, including note about region specification\n"
+"  -S           Ignored (input format is auto-detected)\n"
+"      --no-PG  Do not add a PG line\n");
+
+    sam_global_opt_help(fp, "-.O.T@..");
+    fprintf(fp, "\n");
+
+    if (is_long_help)
+        fprintf(fp,
+"Notes:\n"
+"\n"
+"1. This command now auto-detects the input format (BAM/CRAM/SAM).\n"
+"   Further control over the CRAM format can be specified by using the\n"
+"   --output-fmt-option, e.g. to specify the number of sequences per slice\n"
+"   and to use avoid reference based compression:\n"
+"\n"
+"\tsamtools view -C --output-fmt-option seqs_per_slice=5000 \\\n"
+"\t   --output-fmt-option no_ref -o out.cram in.bam\n"
+"\n"
+"   Options can also be specified as a comma separated list within the\n"
+"   --output-fmt value too.  For example this is equivalent to the above\n"
+"\n"
+"\tsamtools view --output-fmt cram,seqs_per_slice=5000,no_ref \\\n"
+"\t   -o out.cram in.bam\n"
+"\n"
+"2. The file supplied with `-t' is SPACE/TAB delimited with the first\n"
+"   two fields of each line consisting of the reference name and the\n"
+"   corresponding sequence length. The `.fai' file generated by \n"
+"   `samtools faidx' is suitable for use as this file. This may be an\n"
+"   empty file if reads are unaligned.\n"
+"\n"
+"3. SAM->BAM conversion:  samtools view -bT ref.fa in.sam.gz\n"
+"\n"
+"4. BAM->SAM conversion:  samtools view -h in.bam\n"
+"\n"
+"5. A region should be presented in one of the following formats:\n"
+"   `chr1', `chr2:1,000' and `chr3:1000-2,000'. When a region is\n"
+"   specified, the input alignment file must be a sorted and indexed\n"
+"   alignment (BAM/CRAM) file.\n"
+"\n"
+"6. Option `-u' is preferred over `-b' when the output is piped to\n"
+"   another samtools command.\n"
+"\n"
+"7. Option `-M`/`--use-index` causes overlaps with `-L` BED file regions and\n"
+"   command-line region arguments to be computed using the multi-region iterator\n"
+"   and an index. This increases speed, omits duplicates, and outputs the reads\n"
+"   as they are ordered in the input SAM/BAM/CRAM file.\n"
+"\n"
+"8. Options `-L`/`--target[s]-file` and `--region[s]-file` may not be used\n"
+"   together. `--region[s]-file FILE` is simply equivalent to `-M -L FILE`,\n"
+"   so using both causes one of the specified BED files to be ignored.\n"
+"\n");
+
+    return exit_status;
+}
+
+static int head_usage(FILE *fp, int exit_status)
+{
+    fprintf(fp,
+"Usage: samtools head [OPTION]... [FILE]\n"
+"Options:\n"
+"  -h, --headers INT   Display INT header lines [all]\n"
+"  -n, --records INT   Display INT alignment record lines [none]\n"
+);
+    sam_global_opt_help(fp, "-.--T@-.");
+    return exit_status;
+}
+
+int main_head(int argc, char *argv[])
+{
+    static const struct option lopts[] = {
+        SAM_OPT_GLOBAL_OPTIONS('-', 0, '-', '-', 'T', '@'),
+        { "headers", required_argument, NULL, 'h' },
+        { "records", required_argument, NULL, 'n' },
+        { NULL, 0, NULL, 0 }
+    };
+    sam_global_args ga = SAM_GLOBAL_ARGS_INIT;
+
+    int all_headers = 1;
+    uint64_t nheaders = 0;
+    uint64_t nrecords = 0;
+
+    int c, nargs;
+    while ((c = getopt_long(argc, argv, "h:n:T:@:", lopts, NULL)) >= 0)
+        switch (c) {
+        case 'h': all_headers = 0; nheaders = strtoull(optarg, NULL, 0); break;
+        case 'n': nrecords = strtoull(optarg, NULL, 0); break;
+        default:
+            if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break;
+            /* else fall-through */
+        case '?':
+            return head_usage(samtools_stderr, EXIT_FAILURE);
+        }
+
+    nargs = argc - optind;
+    if (nargs == 0 && isatty(STDIN_FILENO))
+        return head_usage(samtools_stdout, EXIT_SUCCESS);
+    else if (nargs > 1)
+        return head_usage(samtools_stderr, EXIT_FAILURE);
+
+    samFile *fp = NULL;
+    sam_hdr_t *hdr = NULL;
+    kstring_t str = KS_INITIALIZE;
+    bam1_t *b = NULL;
+
+    const char *fname = (nargs == 1)? argv[optind] : "-";
+    fp = sam_open_format(fname, "r", &ga.in);
+    if (fp == NULL) {
+        if (strcmp(fname, "-") != 0)
+            print_error_errno("head", "failed to open \"%s\" for reading", fname);
+        else
+            print_error_errno("head", "failed to open standard input for reading");
+        goto err;
+    }
+
+    if (ga.nthreads > 0) hts_set_threads(fp, ga.nthreads);
+
+    hdr = sam_hdr_read(fp);
+    if (hdr == NULL) {
+        if (strcmp(fname, "-") != 0)
+            print_error("head", "failed to read the header from \"%s\"", fname);
+        else
+            print_error("head", "failed to read the header");
+        goto err;
+    }
+
+    if (all_headers) {
+        fputs(sam_hdr_str(hdr), samtools_stdout);
+    }
+    else if (nheaders > 0) {
+        const char *text = sam_hdr_str(hdr);
+        const char *lim = text;
+        uint64_t n;
+        for (n = 0; n < nheaders; n++) {
+            lim = strchr(lim, '\n');
+            if (lim) lim++;
+            else break;
+        }
+        if (lim) fwrite(text, lim - text, 1, samtools_stdout);
+        else fputs(text, samtools_stdout);
+    }
+
+    if (nrecords > 0) {
+        b = bam_init1();
+        uint64_t n;
+        int r;
+        for (n = 0; n < nrecords && (r = sam_read1(fp, hdr, b)) >= 0; n++) {
+            if (sam_format1(hdr, b, &str) < 0) {
+                print_error_errno("head", "couldn't format record");
+                goto err;
+            }
+            samtools_puts(ks_str(&str));
+        }
+        if (r < -1) {
+            print_error("head", "\"%s\" is truncated", fname);
+            goto err;
+        }
+        bam_destroy1(b);
+        ks_free(&str);
+    }
+
+    sam_hdr_destroy(hdr);
+    sam_close(fp);
+    sam_global_args_free(&ga);
+
+    return EXIT_SUCCESS;
+
+err:
+    if (fp) sam_close(fp);
+    sam_hdr_destroy(hdr);
+    bam_destroy1(b);
+    ks_free(&str);
+    sam_global_args_free(&ga);
+    return EXIT_FAILURE;
+}
diff --git a/samtools/sample.c b/samtools/sample.c
new file mode 100644
index 0000000..4cc89ce
--- /dev/null
+++ b/samtools/sample.c
@@ -0,0 +1,134 @@
+/*  sample.c -- group data by sample.
+
+    Copyright (C) 2010, 2011 Broad Institute.
+    Copyright (C) 2013 Genome Research Ltd.
+
+    Author: Heng Li <lh3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <config.h>
+
+#include <stdlib.h>
+#include <string.h>
+#include "sample.h"
+#include "htslib/khash.h"
+KHASH_MAP_INIT_STR(sm, int)
+
+bam_sample_t *bam_smpl_init(void)
+{
+    bam_sample_t *s;
+    s = calloc(1, sizeof(bam_sample_t));
+    s->rg2smid = kh_init(sm);
+    s->sm2id = kh_init(sm);
+    return s;
+}
+
+void bam_smpl_destroy(bam_sample_t *sm)
+{
+    int i;
+    khint_t k;
+    khash_t(sm) *rg2smid = (khash_t(sm)*)sm->rg2smid;
+    if (sm == 0) return;
+    for (i = 0; i < sm->n; ++i) free(sm->smpl[i]);
+    free(sm->smpl);
+    for (k = kh_begin(rg2smid); k != kh_end(rg2smid); ++k)
+        if (kh_exist(rg2smid, k)) free((char*)kh_key(rg2smid, k));
+    kh_destroy(sm, sm->rg2smid);
+    kh_destroy(sm, sm->sm2id);
+    free(sm);
+}
+
+static void add_pair(bam_sample_t *sm, khash_t(sm) *sm2id, const char *key, const char *val)
+{
+    khint_t k_rg, k_sm;
+    int ret;
+    khash_t(sm) *rg2smid = (khash_t(sm)*)sm->rg2smid;
+    k_rg = kh_get(sm, rg2smid, key);
+    if (k_rg != kh_end(rg2smid)) return; // duplicated @RG-ID
+    k_rg = kh_put(sm, rg2smid, strdup(key), &ret);
+    k_sm = kh_get(sm, sm2id, val);
+    if (k_sm == kh_end(sm2id)) { // absent
+        if (sm->n == sm->m) {
+            sm->m = sm->m? sm->m<<1 : 1;
+            sm->smpl = realloc(sm->smpl, sizeof(char*) * sm->m);
+        }
+        sm->smpl[sm->n] = strdup(val);
+        k_sm = kh_put(sm, sm2id, sm->smpl[sm->n], &ret);
+        kh_val(sm2id, k_sm) = sm->n++;
+    }
+    kh_val(rg2smid, k_rg) = kh_val(sm2id, k_sm);
+}
+
+int bam_smpl_add(bam_sample_t *sm, const char *fn, const char *txt)
+{
+    const char *p = txt, *q, *r;
+    kstring_t buf, first_sm;
+    int n = 0;
+    khash_t(sm) *sm2id = (khash_t(sm)*)sm->sm2id;
+    if (txt == 0) {
+        add_pair(sm, sm2id, fn, fn);
+        return 0;
+    }
+    memset(&buf, 0, sizeof(kstring_t));
+    memset(&first_sm, 0, sizeof(kstring_t));
+    while ((q = strstr(p, "@RG")) != 0) {
+        p = q + 3;
+        r = q = 0;
+        if ((q = strstr(p, "\tID:")) != 0) q += 4;
+        if ((r = strstr(p, "\tSM:")) != 0) r += 4;
+        if (r && q) {
+            char *u, *v;
+            int oq, or;
+            for (u = (char*)q; *u && *u != '\t' && *u != '\n'; ++u);
+            for (v = (char*)r; *v && *v != '\t' && *v != '\n'; ++v);
+            oq = *u; or = *v; *u = *v = '\0';
+            buf.l = 0; kputs(fn, &buf); kputc('/', &buf); kputs(q, &buf);
+            add_pair(sm, sm2id, buf.s, r);
+            if ( !first_sm.s )
+                kputs(r,&first_sm);
+            *u = oq; *v = or;
+        } else break;
+        p = q > r? q : r;
+        ++n;
+    }
+    if (n == 0) add_pair(sm, sm2id, fn, fn);
+    // If there is only one RG tag present in the header and reads are not annotated, don't refuse to work but
+    //  use the tag instead.
+    else if ( n==1 && first_sm.s )
+        add_pair(sm,sm2id,fn,first_sm.s);
+    if ( first_sm.s )
+        free(first_sm.s);
+
+//  add_pair(sm, sm2id, fn, fn);
+    free(buf.s);
+    return 0;
+}
+
+int bam_smpl_rg2smid(const bam_sample_t *sm, const char *fn, const char *rg, kstring_t *str)
+{
+    khint_t k;
+    khash_t(sm) *rg2smid = (khash_t(sm)*)sm->rg2smid;
+    if (rg) {
+        str->l = 0;
+        kputs(fn, str); kputc('/', str); kputs(rg, str);
+        k = kh_get(sm, rg2smid, str->s);
+    } else k = kh_get(sm, rg2smid, fn);
+    return k == kh_end(rg2smid)? -1 : kh_val(rg2smid, k);
+}
diff --git a/samtools/sample.c.pysam.c b/samtools/sample.c.pysam.c
new file mode 100644
index 0000000..8b39a90
--- /dev/null
+++ b/samtools/sample.c.pysam.c
@@ -0,0 +1,136 @@
+#include "samtools.pysam.h"
+
+/*  sample.c -- group data by sample.
+
+    Copyright (C) 2010, 2011 Broad Institute.
+    Copyright (C) 2013 Genome Research Ltd.
+
+    Author: Heng Li <lh3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <config.h>
+
+#include <stdlib.h>
+#include <string.h>
+#include "sample.h"
+#include "htslib/khash.h"
+KHASH_MAP_INIT_STR(sm, int)
+
+bam_sample_t *bam_smpl_init(void)
+{
+    bam_sample_t *s;
+    s = calloc(1, sizeof(bam_sample_t));
+    s->rg2smid = kh_init(sm);
+    s->sm2id = kh_init(sm);
+    return s;
+}
+
+void bam_smpl_destroy(bam_sample_t *sm)
+{
+    int i;
+    khint_t k;
+    khash_t(sm) *rg2smid = (khash_t(sm)*)sm->rg2smid;
+    if (sm == 0) return;
+    for (i = 0; i < sm->n; ++i) free(sm->smpl[i]);
+    free(sm->smpl);
+    for (k = kh_begin(rg2smid); k != kh_end(rg2smid); ++k)
+        if (kh_exist(rg2smid, k)) free((char*)kh_key(rg2smid, k));
+    kh_destroy(sm, sm->rg2smid);
+    kh_destroy(sm, sm->sm2id);
+    free(sm);
+}
+
+static void add_pair(bam_sample_t *sm, khash_t(sm) *sm2id, const char *key, const char *val)
+{
+    khint_t k_rg, k_sm;
+    int ret;
+    khash_t(sm) *rg2smid = (khash_t(sm)*)sm->rg2smid;
+    k_rg = kh_get(sm, rg2smid, key);
+    if (k_rg != kh_end(rg2smid)) return; // duplicated @RG-ID
+    k_rg = kh_put(sm, rg2smid, strdup(key), &ret);
+    k_sm = kh_get(sm, sm2id, val);
+    if (k_sm == kh_end(sm2id)) { // absent
+        if (sm->n == sm->m) {
+            sm->m = sm->m? sm->m<<1 : 1;
+            sm->smpl = realloc(sm->smpl, sizeof(char*) * sm->m);
+        }
+        sm->smpl[sm->n] = strdup(val);
+        k_sm = kh_put(sm, sm2id, sm->smpl[sm->n], &ret);
+        kh_val(sm2id, k_sm) = sm->n++;
+    }
+    kh_val(rg2smid, k_rg) = kh_val(sm2id, k_sm);
+}
+
+int bam_smpl_add(bam_sample_t *sm, const char *fn, const char *txt)
+{
+    const char *p = txt, *q, *r;
+    kstring_t buf, first_sm;
+    int n = 0;
+    khash_t(sm) *sm2id = (khash_t(sm)*)sm->sm2id;
+    if (txt == 0) {
+        add_pair(sm, sm2id, fn, fn);
+        return 0;
+    }
+    memset(&buf, 0, sizeof(kstring_t));
+    memset(&first_sm, 0, sizeof(kstring_t));
+    while ((q = strstr(p, "@RG")) != 0) {
+        p = q + 3;
+        r = q = 0;
+        if ((q = strstr(p, "\tID:")) != 0) q += 4;
+        if ((r = strstr(p, "\tSM:")) != 0) r += 4;
+        if (r && q) {
+            char *u, *v;
+            int oq, or;
+            for (u = (char*)q; *u && *u != '\t' && *u != '\n'; ++u);
+            for (v = (char*)r; *v && *v != '\t' && *v != '\n'; ++v);
+            oq = *u; or = *v; *u = *v = '\0';
+            buf.l = 0; kputs(fn, &buf); kputc('/', &buf); kputs(q, &buf);
+            add_pair(sm, sm2id, buf.s, r);
+            if ( !first_sm.s )
+                kputs(r,&first_sm);
+            *u = oq; *v = or;
+        } else break;
+        p = q > r? q : r;
+        ++n;
+    }
+    if (n == 0) add_pair(sm, sm2id, fn, fn);
+    // If there is only one RG tag present in the header and reads are not annotated, don't refuse to work but
+    //  use the tag instead.
+    else if ( n==1 && first_sm.s )
+        add_pair(sm,sm2id,fn,first_sm.s);
+    if ( first_sm.s )
+        free(first_sm.s);
+
+//  add_pair(sm, sm2id, fn, fn);
+    free(buf.s);
+    return 0;
+}
+
+int bam_smpl_rg2smid(const bam_sample_t *sm, const char *fn, const char *rg, kstring_t *str)
+{
+    khint_t k;
+    khash_t(sm) *rg2smid = (khash_t(sm)*)sm->rg2smid;
+    if (rg) {
+        str->l = 0;
+        kputs(fn, str); kputc('/', str); kputs(rg, str);
+        k = kh_get(sm, rg2smid, str->s);
+    } else k = kh_get(sm, rg2smid, fn);
+    return k == kh_end(rg2smid)? -1 : kh_val(rg2smid, k);
+}
diff --git a/samtools/sample.h b/samtools/sample.h
new file mode 100644
index 0000000..8e8efa5
--- /dev/null
+++ b/samtools/sample.h
@@ -0,0 +1,41 @@
+/*  sample.h -- group data by sample.
+
+    Copyright (C) 2010 Broad Institute.
+
+    Author: Heng Li <lh3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#ifndef BAM_SAMPLE_H
+#define BAM_SAMPLE_H
+
+#include "htslib/kstring.h"
+
+typedef struct {
+    int n, m;
+    char **smpl;
+    void *rg2smid, *sm2id;
+} bam_sample_t;
+
+bam_sample_t *bam_smpl_init(void);
+int bam_smpl_add(bam_sample_t *sm, const char *abs, const char *txt);
+int bam_smpl_rg2smid(const bam_sample_t *sm, const char *fn, const char *rg, kstring_t *str);
+void bam_smpl_destroy(bam_sample_t *sm);
+
+#endif
diff --git a/samtools/samtools.h b/samtools/samtools.h
new file mode 100644
index 0000000..e0f99c2
--- /dev/null
+++ b/samtools/samtools.h
@@ -0,0 +1,62 @@
+/*  samtools.h -- utility routines.
+
+    Copyright (C) 2013-2015, 2019 Genome Research Ltd.
+
+    Author: Petr Danecek <pd3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#ifndef SAMTOOLS_H
+#define SAMTOOLS_H
+
+#include "htslib/hts_defs.h"
+#include "htslib/sam.h"
+
+const char *samtools_version(void);
+
+#define CHECK_PRINTF(fmt,args) HTS_FORMAT(HTS_PRINTF_FMT, (fmt), (args))
+
+void print_error(const char *subcommand, const char *format, ...) CHECK_PRINTF(2, 3);
+void print_error_errno(const char *subcommand, const char *format, ...) CHECK_PRINTF(2, 3);
+
+void check_sam_close(const char *subcmd, samFile *fp, const char *fname, const char *null_fname, int *retp);
+
+/* Utility functions to register an output htsFile/samFile/vcfFile that
+ * might be stdout. If FNAME is "-" or NULL, records FP so that print_error()
+ * et al can automatically flush it before printing an error message.
+ */
+void autoflush_if_stdout(htsFile *fp, const char *fname);
+
+/* Call this before closing FP; check_sam_close() does this automatically.
+ */
+void release_autoflush(htsFile *fp);
+
+/*
+ * Utility function to add an index to a file we've opened for write.
+ * NB: Call this after writing the header and before writing sequences.
+ *
+ * The returned index filename should be freed by the caller, but only
+ * after sam_idx_save has been called.
+ *
+ * Returns index filename on success,
+ *         NULL on failure.
+ */
+char *auto_index(htsFile *fp, const char *fn, bam_hdr_t *header);
+
+#endif
diff --git a/samtools/samtools.pysam.c b/samtools/samtools.pysam.c
new file mode 100644
index 0000000..10740a4
--- /dev/null
+++ b/samtools/samtools.pysam.c
@@ -0,0 +1,83 @@
+#include <getopt.h>
+#include <unistd.h>
+#include <setjmp.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+
+#include "samtools.pysam.h"
+
+FILE * samtools_stderr = NULL;
+FILE * samtools_stdout = NULL;
+const char * samtools_stdout_fn = NULL;
+
+
+FILE * samtools_set_stderr(int fd)
+{
+  if (samtools_stderr != NULL)
+    fclose(samtools_stderr);
+  samtools_stderr = fdopen(fd, "w");
+  return samtools_stderr;
+}
+
+void samtools_close_stderr(void)
+{
+  fclose(samtools_stderr);
+  samtools_stderr = NULL;
+}
+
+FILE * samtools_set_stdout(int fd)
+{
+  if (samtools_stdout != NULL)
+    fclose(samtools_stdout);
+  samtools_stdout = fdopen(fd, "w");
+  if (samtools_stdout == NULL)
+    {
+      fprintf(samtools_stderr, "could not set stdout to fd %i", fd);
+    }
+  return samtools_stdout;
+}
+
+void samtools_set_stdout_fn(const char *fn)
+{
+  samtools_stdout_fn = fn;
+}
+
+void samtools_close_stdout(void)
+{
+  fclose(samtools_stdout);
+  samtools_stdout = NULL;
+}
+
+int samtools_puts(const char *s)
+{
+  if (fputs(s, samtools_stdout) == EOF) return EOF;
+  return putc('\n', samtools_stdout);
+}
+
+
+static jmp_buf samtools_jmpbuf;
+static int samtools_status = 0;
+
+int samtools_dispatch(int argc, char *argv[])
+{
+  /* Reset getopt()/getopt_long() processing. */
+#if defined __GLIBC__
+  optind = 0;
+#elif defined _OPTRESET || defined _OPTRESET_DECLARED
+  optreset = optind = 1;
+#else
+  optind = 1;
+#endif
+
+  if (setjmp(samtools_jmpbuf) == 0)
+    return samtools_main(argc, argv);
+  else
+    return samtools_status;
+}
+
+void samtools_exit(int status)
+{
+  samtools_status = status;
+  longjmp(samtools_jmpbuf, 1);
+}
diff --git a/samtools/samtools.pysam.h b/samtools/samtools.pysam.h
new file mode 100644
index 0000000..cb63b60
--- /dev/null
+++ b/samtools/samtools.pysam.h
@@ -0,0 +1,74 @@
+#ifndef samtools_PYSAM_H
+#define samtools_PYSAM_H
+
+#include <stdio.h>
+
+#ifndef __has_attribute
+#define __has_attribute(attribute) 0
+#endif
+#ifndef PYSAM_NORETURN
+#if __has_attribute(__noreturn__) || __GNUC__ >= 3
+#define PYSAM_NORETURN __attribute__((__noreturn__))
+#else
+#define PYSAM_NORETURN
+#endif
+#endif
+
+extern FILE * samtools_stderr;
+
+extern FILE * samtools_stdout;
+
+extern const char * samtools_stdout_fn;
+
+/*! set pysam standard error to point to file descriptor
+
+  Setting the stderr will close the previous stderr.
+ */
+FILE * samtools_set_stderr(int fd);
+
+/*! set pysam standard output to point to file descriptor
+
+  Setting the stdout will close the previous stdout.
+ */
+FILE * samtools_set_stdout(int fd);
+
+/*! set pysam standard output to point to filename
+
+ */
+void samtools_set_stdout_fn(const char * fn);
+
+/*! close pysam standard error and set to NULL
+  
+ */
+void samtools_close_stderr(void);
+
+/*! close pysam standard output and set to NULL
+  
+ */
+void samtools_close_stdout(void);
+
+int samtools_puts(const char *s);
+
+int samtools_dispatch(int argc, char *argv[]);
+
+void PYSAM_NORETURN samtools_exit(int status);
+
+extern int samtools_main(int argc, char *argv[]);
+
+/* Define these only in samtools/bcftools C source, not Cython code. */
+#if !(defined CYTHON_ABI || defined CYTHON_HEX_VERSION)
+
+/*! Several non-static function names are used in both samtools and bcftools.
+    Both libcsamtools.so and libcbcftools.so are loaded simultaneously, leading
+    to collisions and wrong functions being called. #define these names so the
+    actual symbol names include distinct prefixes to avoid collisions.
+ */
+#define main_consensus samtools_main_consensus
+#define main_reheader samtools_main_reheader
+#define bam_smpl_init samtools_bam_smpl_init
+#define bam_smpl_destroy samtools_bam_smpl_destroy
+#define read_file_list samtools_read_file_list
+
+#endif
+
+#endif
diff --git a/samtools/splaysort.h b/samtools/splaysort.h
new file mode 100644
index 0000000..af83533
--- /dev/null
+++ b/samtools/splaysort.h
@@ -0,0 +1,200 @@
+/* The MIT License
+
+   Copyright (c) 2021 Genome Research Ltd (GRL).
+
+   Permission is hereby granted, free of charge, to any person obtaining
+   a copy of this software and associated documentation files (the
+   "Software"), to deal in the Software without restriction, including
+   without limitation the rights to use, copy, modify, merge, publish,
+   distribute, sublicense, and/or sell copies of the Software, and to
+   permit persons to whom the Software is furnished to do so, subject to
+   the following conditions:
+
+   The above copyright notice and this permission notice shall be
+   included in all copies or substantial portions of the Software.
+
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+   EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+   MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+   NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
+   BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+   ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+   CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+   SOFTWARE.
+*/
+
+#ifndef SPLAYSORT_H
+#define SPLAYSORT_H
+
+#define SPLAYSORT_INIT(name, type_t, __sort_lt)                               \
+    typedef struct splaynode_##name {                                         \
+        type_t value;                                                         \
+        struct splaynode_##name *left;                                        \
+        struct splaynode_##name *right;                                       \
+        struct splaynode_##name *parent;                                      \
+    } splaynode_##name;                                                       \
+                                                                              \
+    void rotate_left_##name(splaynode_##name *node);                          \
+    void rotate_right_##name(splaynode_##name *node);                         \
+    int splay_sort_##name(size_t n, type_t array[] );                         \
+    int splay_flatten_##name(splaynode_##name *node, type_t dest[], size_t n);\
+    splaynode_##name *splay_tree_##name(splaynode_##name *node);              \
+    splaynode_##name *splay_insert_##name(splaynode_##name *node,             \
+                                          type_t value,                       \
+                                          splaynode_##name *node_ptr);        \
+                                                                              \
+    void rotate_left_##name(splaynode_##name *node) {                         \
+        splaynode_##name *parent = node->parent;                              \
+        splaynode_##name *grandparent = parent->parent;                       \
+        parent->right = node->left;                                           \
+        if (node->left != NULL) {                                             \
+            node->left->parent = parent;                                      \
+        }                                                                     \
+        node->left = parent;                                                  \
+        parent->parent = node;                                                \
+        node->parent = grandparent;                                           \
+                                                                              \
+        if (grandparent != NULL) {                                            \
+            if (grandparent->left == parent) {                                \
+                grandparent->left = node;                                     \
+            } else {                                                          \
+                grandparent->right = node;                                    \
+            }                                                                 \
+        }                                                                     \
+    }                                                                         \
+                                                                              \
+    void rotate_right_##name(splaynode_##name *node) {                        \
+        splaynode_##name *parent = node->parent;                              \
+        splaynode_##name *grandparent = parent->parent;                       \
+        parent->left = node->right;                                           \
+                                                                              \
+        if (node->right != NULL) {                                            \
+            node->right->parent = parent;                                     \
+        }                                                                     \
+        node->right = parent;                                                 \
+        parent->parent = node;                                                \
+        node->parent = grandparent;                                           \
+                                                                              \
+        if (grandparent != NULL) {                                            \
+            if (grandparent->left == parent) {                                \
+                grandparent->left = node;                                     \
+            } else {                                                          \
+                grandparent->right = node;                                    \
+            }                                                                 \
+        }                                                                     \
+    }                                                                         \
+    int splay_sort_##name(size_t n, type_t array[] ) {                        \
+        if (n < 1) {                                                          \
+            return 0;                                                         \
+        }                                                                     \
+        int i;                                                                \
+        splaynode_##name *node_pool = malloc(sizeof(splaynode_##name) * n);   \
+        if (node_pool == NULL) return -1;                                     \
+        splaynode_##name *head = node_pool;                                   \
+        head->value = array[0];                                               \
+        head->left = NULL; head->right = NULL; head->parent = NULL;           \
+        for (i = 1; i < n; i++) {                                             \
+            head = splay_insert_##name(head, array[i], node_pool + i );       \
+        }                                                                     \
+                                                                              \
+        if (splay_flatten_##name(head, array, n) == -1) {                     \
+            free(node_pool);                                                  \
+            return -1;                                                        \
+        }                                                                     \
+        free(node_pool);                                                      \
+        return 0;                                                             \
+    }                                                                         \
+                                                                              \
+    int splay_flatten_##name(splaynode_##name *head, type_t *dest, size_t n) {\
+        int sp = 0, i = 0;                                                    \
+        splaynode_##name *current = head;                                     \
+        splaynode_##name **stack = malloc(sizeof(current)*n);                 \
+        if (stack == NULL) return -1;                                         \
+                                                                              \
+        do {                                                                  \
+            while (current != NULL && sp < n) {                               \
+                stack[sp++] = current;                                        \
+                current = current->left;                                      \
+            }                                                                 \
+            if (sp != 0) {                                                    \
+                sp--;                                                         \
+                dest[i++] = stack[sp]->value;                                 \
+                current = stack[sp]->right;                                   \
+            }                                                                 \
+        } while (!(current == NULL && sp == 0));                              \
+                                                                              \
+        free(stack);                                                          \
+        return 0;                                                             \
+    }                                                                         \
+    splaynode_##name *splay_insert_##name(splaynode_##name *head,             \
+                                          type_t value,                       \
+                                          splaynode_##name *node_ptr) {       \
+        splaynode_##name *parent = NULL;                                      \
+        while (head != NULL) {                                                \
+            parent = head;                                                    \
+            if (__sort_lt(value, head->value)) {                              \
+                head = head->left;                                            \
+            } else {                                                          \
+                head = head->right;                                           \
+            }                                                                 \
+        }                                                                     \
+        splaynode_##name *new_node = node_ptr;                                \
+        new_node->value = value;                                              \
+        new_node->left = NULL;                                                \
+        new_node->right = NULL;                                               \
+        new_node->parent = parent;                                            \
+        if (parent) {                                                         \
+            if (__sort_lt(value, parent->value)) {                            \
+                parent->left = new_node;                                      \
+            } else {                                                          \
+                parent->right = new_node;                                     \
+            }                                                                 \
+        }                                                                     \
+        new_node = splay_tree_##name(new_node);                               \
+        return new_node;                                                      \
+    }                                                                         \
+                                                                              \
+    splaynode_##name *splay_tree_##name(splaynode_##name *node) {             \
+        splaynode_##name *parent = node->parent;                              \
+                                                                              \
+        if (node->parent == NULL) {                                           \
+            return node;                                                      \
+        }                                                                     \
+        if (node == parent->left) {                                           \
+            if (parent->parent == NULL) {                                     \
+                /* zig */                                                     \
+                rotate_right_##name(node);                                    \
+            } else if (parent->parent->left == parent) {                      \
+                /* left zig zig */                                            \
+                rotate_right_##name(node);                                    \
+                rotate_right_##name(node);                                    \
+            } else {                                                          \
+                /* right left zig zag */                                      \
+                rotate_right_##name(node);                                    \
+                rotate_left_##name(node);                                     \
+            }                                                                 \
+        } else {                                                              \
+            if (parent->parent == NULL) {                                     \
+            /* zig */                                                         \
+            rotate_left_##name(node);                                         \
+            } else if (parent->parent->right == parent) {                     \
+                /* right zig zig */                                           \
+                rotate_left_##name(node);                                     \
+                rotate_left_##name(node);                                     \
+            } else  {                                                         \
+                /* left right zig zag */                                      \
+                rotate_left_##name(node);                                     \
+                rotate_right_##name(node);                                    \
+            }                                                                 \
+        }                                                                     \
+                                                                              \
+        if (node->parent != NULL) {                                           \
+            return splay_tree_##name(node);                                   \
+        }                                                                     \
+        return node;                                                          \
+    }                                                                         \
+
+
+#define splaysort(name, n, array) splay_sort_##name(n, array)
+
+#endif
diff --git a/samtools/stats.c b/samtools/stats.c
new file mode 100644
index 0000000..55a6465
--- /dev/null
+++ b/samtools/stats.c
@@ -0,0 +1,2578 @@
+/*  stats.c -- This is the former bamcheck integrated into samtools/htslib.
+
+    Copyright (C) 2012-2021 Genome Research Ltd.
+
+    Author: Petr Danecek <pd3@sanger.ac.uk>
+    Author: Sam Nicholls <sam@samnicholls.net>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+/*  Assumptions, approximations and other issues:
+        - GC-depth graph does not split reads, the starting position determines which bin is incremented.
+            There are small overlaps between bins (max readlen-1). However, the bins are big (20k).
+        - coverage distribution ignores softclips and deletions
+        - some stats require sorted BAMs
+        - GC content graph can have an untidy, step-like pattern when BAM contains multiple read lengths.
+        - 'bases mapped' (stats->nbases_mapped) is calculated from read lengths given by BAM (core.l_qseq)
+        - With the -t option, the whole reads are used. Except for the number of mapped bases (cigar)
+            counts, no splicing is done, no indels or soft clips are considered, even small overlap is
+            good enough to include the read in the stats.
+        - GC content of reads not calculated for "=" sequences
+
+*/
+
+#include <config.h>
+
+#include <unistd.h> // for isatty()
+#include <stdio.h>
+#include <stdlib.h>
+#include <stdarg.h>
+#include <string.h>
+#include <math.h>
+#include <ctype.h>
+#include <inttypes.h>
+#include <getopt.h>
+#include <errno.h>
+#include <assert.h>
+#include <zlib.h>   // for crc32
+#include <htslib/faidx.h>
+#include <htslib/sam.h>
+#include <htslib/hts.h>
+#include <htslib/hts_defs.h>
+#include "samtools.h"
+#include <htslib/khash.h>
+#include <htslib/kstring.h>
+#include "stats_isize.h"
+#include "sam_opts.h"
+#include "bedidx.h"
+
+#define BWA_MIN_RDLEN 35
+#define DEFAULT_CHUNK_NO 8
+#define DEFAULT_PAIR_MAX 10000
+#define ERROR_LIMIT 200
+// From the spec
+// If 0x4 is set, no assumptions can be made about RNAME, POS, CIGAR, MAPQ, bits 0x2, 0x10, 0x100 and 0x800, and the bit 0x20 of the previous read in the template.
+#define IS_PAIRED(bam) ((bam)->core.flag&BAM_FPAIRED)
+#define IS_PAIRED_AND_MAPPED(bam) (((bam)->core.flag&BAM_FPAIRED) && !((bam)->core.flag&BAM_FUNMAP) && !((bam)->core.flag&BAM_FMUNMAP))
+#define IS_PROPERLYPAIRED(bam) (((bam)->core.flag&(BAM_FPAIRED|BAM_FPROPER_PAIR)) == (BAM_FPAIRED|BAM_FPROPER_PAIR) && !((bam)->core.flag&BAM_FUNMAP))
+#define IS_UNMAPPED(bam) ((bam)->core.flag&BAM_FUNMAP)
+#define IS_REVERSE(bam) ((bam)->core.flag&BAM_FREVERSE)
+#define IS_MATE_REVERSE(bam) ((bam)->core.flag&BAM_FMREVERSE)
+#define IS_READ1(bam) ((bam)->core.flag&BAM_FREAD1)
+#define IS_READ2(bam) ((bam)->core.flag&BAM_FREAD2)
+#define IS_DUP(bam) ((bam)->core.flag&BAM_FDUP)
+#define IS_ORIGINAL(bam) (((bam)->core.flag&(BAM_FSECONDARY|BAM_FSUPPLEMENTARY)) == 0)
+
+#define READ_ORDER_NONE 0
+#define READ_ORDER_FIRST 1
+#define READ_ORDER_LAST 2
+#define READ_ORDER_MIDDLE 3
+
+#define REG_INC 100
+#define POS_INC 1000
+
+// The GC-depth graph works as follows: split the reference sequence into
+// segments and calculate GC content and depth in each bin. Then sort
+// these segments by their GC and plot the depth distribution by means
+// of 10th, 25th, etc. depth percentiles.
+typedef struct
+{
+    float gc;
+    uint32_t depth;
+}
+gc_depth_t;
+
+// For coverage distribution, a simple pileup
+typedef struct
+{
+    hts_pos_t pos;
+    int size, start;
+    int *buffer;
+}
+round_buffer_t;
+
+typedef struct
+{
+    int npos, mpos, cpos;
+    hts_pair_pos_t *pos;
+}
+regions_t;
+
+typedef struct
+{
+    uint64_t a;
+    uint64_t c;
+    uint64_t g;
+    uint64_t t;
+    uint64_t n;
+    uint64_t other;
+}
+acgtno_count_t;
+
+typedef struct
+{
+    char tag_name[3];
+    char qual_name[3];
+    uint32_t nbases;
+    int32_t tag_sep;    // Index of the separator (if present)
+    int32_t max_qual;
+    uint32_t offset;    // Where the tag stats info is located in the allocated memory
+}
+barcode_info_t;
+
+typedef struct
+{
+    // Auxiliary data
+    int flag_require, flag_filter;
+    faidx_t *fai;                   // Reference sequence for GC-depth graph
+    int argc;                       // Command line arguments to be printed on the output
+    char **argv;
+    int gcd_bin_size;           // The size of GC-depth bin
+    int nisize;         // The maximum insert size that the allocated array can hold - 0 indicates no limit
+    int trim_qual;      // bwa trim quality
+    float isize_main_bulk;  // There are always some unrealistically big insert sizes, report only the main part
+    int cov_min,cov_max,cov_step;   // Minimum, maximum coverage and size of the coverage bins
+    samFile* sam;
+    sam_hdr_t* sam_header;
+
+    // Filters
+    int filter_readlen;
+
+    // Misc
+    char *split_tag;      // Tag on which to perform stats splitting
+    char *split_prefix;   // Path or string prefix for filenames created when splitting
+    int remove_overlaps;
+    int cov_threshold;
+}
+stats_info_t;
+
+typedef struct
+{
+    // Dimensions of the quality histogram holder (quals_1st,quals_2nd), GC content holder (gc_1st,gc_2nd),
+    //  insert size histogram holder
+    int nquals;         // The number of quality bins
+    int nbases;         // The maximum sequence length the allocated array can hold
+    int ngc;            // The size of gc_1st and gc_2nd
+    int nindels;        // The maximum indel length for indel distribution
+
+    // Arrays for the histogram data
+    uint64_t *quals_1st, *quals_2nd;
+    uint64_t *gc_1st, *gc_2nd;
+    acgtno_count_t *acgtno_cycles_1st, *acgtno_cycles_2nd;
+    acgtno_count_t *acgtno_revcomp;
+    uint64_t *read_lengths, *read_lengths_1st, *read_lengths_2nd;
+    uint64_t *insertions, *deletions;
+    uint64_t *ins_cycles_1st, *ins_cycles_2nd, *del_cycles_1st, *del_cycles_2nd;
+    isize_t *isize;
+
+    // The extremes encountered
+    int max_len;            // Maximum read length
+    int max_len_1st;        // Maximum read length for forward reads
+    int max_len_2nd;        // Maximum read length for reverse reads
+    int max_qual;           // Maximum quality
+    int is_sorted;
+
+    // Summary numbers
+    uint64_t total_len;
+    uint64_t total_len_1st;
+    uint64_t total_len_2nd;
+    uint64_t total_len_dup;
+    uint64_t nreads_1st;
+    uint64_t nreads_2nd;
+    uint64_t nreads_other;
+    uint64_t nreads_filtered;
+    uint64_t nreads_dup;
+    uint64_t nreads_unmapped;
+    uint64_t nreads_single_mapped;
+    uint64_t nreads_paired_and_mapped;
+    uint64_t nreads_properly_paired;
+    uint64_t nreads_paired_tech;
+    uint64_t nreads_anomalous;
+    uint64_t nreads_mq0;
+    uint64_t nbases_mapped;
+    uint64_t nbases_mapped_cigar;
+    uint64_t nbases_trimmed;  // bwa trimmed bases
+    uint64_t nmismatches;
+    uint64_t nreads_QCfailed, nreads_secondary, nreads_supplementary;
+    struct {
+        uint32_t names, reads, quals;
+    } checksum;
+
+    // GC-depth related data
+    uint32_t ngcd, igcd;        // The maximum number of GC depth bins and index of the current bin
+    gc_depth_t *gcd;            // The GC-depth bins holder
+    int32_t tid;                // Position of the current bin
+    hts_pos_t gcd_pos, pos;     // Position of the last read
+
+    // Coverage distribution related data
+    int ncov;                       // The number of coverage bins
+    uint64_t *cov;                  // The coverage frequencies
+    round_buffer_t cov_rbuf;        // Pileup round buffer
+
+    // Mismatches by read cycle
+    uint8_t *rseq_buf;              // A buffer for reference sequence to check the mismatches against
+    int mrseq_buf;                  // The size of the buffer
+    hts_pos_t rseq_pos;             // The coordinate of the first base in the buffer
+    int64_t nrseq_buf;              // The used part of the buffer
+    uint64_t *mpc_buf;              // Mismatches per cycle
+
+    // Target regions
+    int nregions;
+    hts_pos_t reg_from, reg_to;
+    regions_t *regions;
+
+    // Auxiliary data
+    double sum_qual;                // For calculating average quality value
+    void *rg_hash;                  // Read groups to include, the array is null-terminated
+
+    // Split
+    char* split_name;
+
+    stats_info_t* info;             // Pointer to options and settings struct
+    hts_pair_pos_t *chunks;
+    uint32_t nchunks;
+
+    uint32_t pair_count;          // Number of active pairs in the pairing hash table
+    uint64_t target_count;        // Number of bases covered by the target file
+    uint32_t last_pair_tid;
+    uint32_t last_read_flush;
+
+    // Barcode statistics
+    acgtno_count_t *acgtno_barcode;
+    uint64_t *quals_barcode;
+    barcode_info_t *tags_barcode;
+    uint32_t ntags;
+    uint32_t error_number;
+}
+stats_t;
+KHASH_MAP_INIT_STR(c2stats, stats_t*)
+
+typedef struct {
+    uint32_t first;     // 1 - first read, 2 - second read
+    uint32_t n, m;      // number of chunks, allocated chunks
+    hts_pair_pos_t *chunks;      // chunk array of size m
+} pair_t;
+KHASH_MAP_INIT_STR(qn2pair, pair_t*)
+
+KHASH_SET_INIT_STR(rg)
+
+
+static void HTS_NORETURN error(const char *format, ...);
+int is_in_regions(bam1_t *bam_line, stats_t *stats);
+void realloc_buffers(stats_t *stats, int seq_len);
+
+static int regions_lt(const void *r1, const void *r2) {
+    int64_t from_diff = ((hts_pair_pos_t *)r1)->beg - ((hts_pair_pos_t *)r2)->beg;
+    int64_t to_diff   = ((hts_pair_pos_t *)r1)->end - ((hts_pair_pos_t *)r2)->end;
+
+    return from_diff > 0 ? 1 : from_diff < 0 ? -1 : to_diff > 0 ? 1 : to_diff < 0 ? -1 : 0;
+}
+
+// Coverage distribution methods
+static inline int coverage_idx(int min, int max, int n, int step, int depth)
+{
+    if ( depth < min )
+        return 0;
+
+    if ( depth > max )
+        return n-1;
+
+    return 1 + (depth - min) / step;
+}
+
+static inline int round_buffer_lidx2ridx(int offset, int size, hts_pos_t refpos, hts_pos_t pos)
+{
+    return (offset + (pos-refpos) % size) % size;
+}
+
+void round_buffer_flush(stats_t *stats, hts_pos_t pos)
+{
+    int ibuf,idp;
+
+    if ( pos==stats->cov_rbuf.pos )
+        return;
+
+    hts_pos_t new_pos = pos;
+    if ( pos==-1 || pos - stats->cov_rbuf.pos >= stats->cov_rbuf.size )
+    {
+        // Flush the whole buffer, but in sequential order,
+        pos = stats->cov_rbuf.pos + stats->cov_rbuf.size - 1;
+    }
+
+    if ( pos < stats->cov_rbuf.pos )
+        error("Expected coordinates in ascending order, got %"PRIhts_pos" after %"PRIhts_pos"\n", pos, stats->cov_rbuf.pos);
+
+    int ifrom = stats->cov_rbuf.start;
+    int ito = round_buffer_lidx2ridx(stats->cov_rbuf.start, stats->cov_rbuf.size, stats->cov_rbuf.pos, pos-1);
+    if ( ifrom>ito )
+    {
+        for (ibuf=ifrom; ibuf<stats->cov_rbuf.size; ibuf++)
+        {
+            if ( !stats->cov_rbuf.buffer[ibuf] )
+                continue;
+            idp = coverage_idx(stats->info->cov_min,stats->info->cov_max,stats->ncov,stats->info->cov_step,stats->cov_rbuf.buffer[ibuf]);
+            stats->cov[idp]++;
+            stats->cov_rbuf.buffer[ibuf] = 0;
+        }
+        ifrom = 0;
+    }
+    for (ibuf=ifrom; ibuf<=ito; ibuf++)
+    {
+        if ( !stats->cov_rbuf.buffer[ibuf] )
+            continue;
+        idp = coverage_idx(stats->info->cov_min,stats->info->cov_max,stats->ncov,stats->info->cov_step,stats->cov_rbuf.buffer[ibuf]);
+        stats->cov[idp]++;
+        stats->cov_rbuf.buffer[ibuf] = 0;
+    }
+    stats->cov_rbuf.start = (new_pos==-1) ? 0 : round_buffer_lidx2ridx(stats->cov_rbuf.start, stats->cov_rbuf.size, stats->cov_rbuf.pos, pos);
+    stats->cov_rbuf.pos   = new_pos;
+}
+
+/**
+ * [from, to) - 0 based half-open
+ */
+static void round_buffer_insert_read(round_buffer_t *rbuf, hts_pos_t from, hts_pos_t to)
+{
+    if ( to-from > rbuf->size )
+        error("The read length too big (%"PRIhts_pos"), please increase the buffer length (currently %d)\n", to-from, rbuf->size);
+    if ( from < rbuf->pos )
+        error("The reads are not sorted (%"PRIhts_pos" comes after %"PRIhts_pos").\n", from, rbuf->pos);
+
+    int ifrom, ito, ibuf;
+    ifrom = round_buffer_lidx2ridx(rbuf->start, rbuf->size, rbuf->pos, from);
+    ito   = round_buffer_lidx2ridx(rbuf->start, rbuf->size, rbuf->pos, to);
+    if ( ifrom>ito )
+    {
+        for (ibuf=ifrom; ibuf<rbuf->size; ibuf++)
+            rbuf->buffer[ibuf]++;
+        ifrom = 0;
+    }
+    for (ibuf=ifrom; ibuf<ito; ibuf++)
+        rbuf->buffer[ibuf]++;
+}
+
+// Calculate the number of bases in the read trimmed by BWA
+int bwa_trim_read(int trim_qual, uint8_t *quals, int len, int reverse)
+{
+    if ( len<BWA_MIN_RDLEN ) return 0;
+
+    // Although the name implies that the read cannot be trimmed to more than BWA_MIN_RDLEN,
+    //  the calculation can in fact trim it to (BWA_MIN_RDLEN-1). (bwa_trim_read in bwa/bwaseqio.c).
+    int max_trimmed = len - BWA_MIN_RDLEN + 1;
+    int l, sum=0, max_sum=0, max_l=0;
+
+    for (l=0; l<max_trimmed; l++)
+    {
+        sum += trim_qual - quals[ reverse ? l : len-1-l ];
+        if ( sum<0 ) break;
+        if ( sum>max_sum )
+        {
+            max_sum = sum;
+            // This is the correct way, but bwa clips from some reason one base less
+            // max_l   = l+1;
+            max_l   = l;
+        }
+    }
+    return max_l;
+}
+
+
+void count_indels(stats_t *stats,bam1_t *bam_line)
+{
+    int is_fwd = IS_REVERSE(bam_line) ? 0 : 1;
+    uint32_t order = IS_PAIRED(bam_line) ? (IS_READ1(bam_line) ? READ_ORDER_FIRST : 0) + (IS_READ2(bam_line) ? READ_ORDER_LAST : 0) : READ_ORDER_FIRST;
+    int icig;
+    int icycle = 0;
+    int read_len = bam_line->core.l_qseq;
+    for (icig=0; icig<bam_line->core.n_cigar; icig++)
+    {
+        int cig  = bam_cigar_op(bam_get_cigar(bam_line)[icig]);
+        int ncig = bam_cigar_oplen(bam_get_cigar(bam_line)[icig]);
+        if ( !ncig ) continue;  // curiously, this can happen: 0D
+
+        if ( cig==BAM_CINS )
+        {
+            int idx = is_fwd ? icycle : read_len-icycle-ncig;
+            if ( idx<0 )
+                error("FIXME: read_len=%d vs icycle=%d\n", read_len,icycle);
+            if ( idx >= stats->nbases || idx<0 ) error("FIXME: %d vs %d, %s:%"PRIhts_pos" %s\n", idx, stats->nbases, sam_hdr_tid2name(stats->info->sam_header, bam_line->core.tid), bam_line->core.pos+1, bam_get_qname(bam_line));
+            if ( order == READ_ORDER_FIRST )
+                stats->ins_cycles_1st[idx]++;
+            if ( order == READ_ORDER_LAST )
+                stats->ins_cycles_2nd[idx]++;
+            icycle += ncig;
+            if ( ncig<=stats->nindels )
+                stats->insertions[ncig-1]++;
+            continue;
+        }
+        if ( cig==BAM_CDEL )
+        {
+            int idx = is_fwd ? icycle-1 : read_len-icycle-1;
+            if ( idx<0 ) continue;  // discard meaningless deletions
+            if ( idx >= stats->nbases ) error("FIXME: %d vs %d\n", idx,stats->nbases);
+            if ( order == READ_ORDER_FIRST )
+                stats->del_cycles_1st[idx]++;
+            if ( order == READ_ORDER_LAST )
+                stats->del_cycles_2nd[idx]++;
+            if ( ncig<=stats->nindels )
+                stats->deletions[ncig-1]++;
+            continue;
+        }
+        if ( cig!=BAM_CREF_SKIP && cig!=BAM_CHARD_CLIP && cig!=BAM_CPAD )
+            icycle += ncig;
+    }
+}
+
+int unclipped_length(bam1_t *bam_line)
+{
+    int icig, read_len = bam_line->core.l_qseq;
+    for (icig=0; icig<bam_line->core.n_cigar; icig++)
+    {
+        int cig = bam_cigar_op(bam_get_cigar(bam_line)[icig]);
+        if ( cig==BAM_CHARD_CLIP )
+            read_len += bam_cigar_oplen(bam_get_cigar(bam_line)[icig]);
+    }
+    return read_len;
+}
+
+void count_mismatches_per_cycle(stats_t *stats, bam1_t *bam_line, int read_len)
+{
+    int is_fwd = IS_REVERSE(bam_line) ? 0 : 1;
+    int icig, iread=0, icycle=0;
+    hts_pos_t iref = bam_line->core.pos - stats->rseq_pos;
+    uint8_t *read  = bam_get_seq(bam_line);
+    uint8_t *quals = bam_get_qual(bam_line);
+    uint64_t *mpc_buf = stats->mpc_buf;
+    for (icig=0; icig<bam_line->core.n_cigar; icig++)
+    {
+        int cig  = bam_cigar_op(bam_get_cigar(bam_line)[icig]);
+        int ncig = bam_cigar_oplen(bam_get_cigar(bam_line)[icig]);
+        if ( cig==BAM_CINS )
+        {
+            iread  += ncig;
+            icycle += ncig;
+            continue;
+        }
+        if ( cig==BAM_CDEL )
+        {
+            iref += ncig;
+            continue;
+        }
+        if ( cig==BAM_CSOFT_CLIP )
+        {
+            icycle += ncig;
+            // Soft-clips are present in the sequence, but the position of the read marks a start of the sequence after clipping
+            //   iref += ncig;
+            iread  += ncig;
+            continue;
+        }
+        if ( cig==BAM_CHARD_CLIP )
+        {
+            icycle += ncig;
+            continue;
+        }
+        // Ignore H and N CIGARs. The letter are inserted e.g. by TopHat and often require very large
+        //  chunk of refseq in memory. Not very frequent and not noticeable in the stats.
+        if ( cig==BAM_CREF_SKIP || cig==BAM_CHARD_CLIP || cig==BAM_CPAD ) continue;
+        if ( cig!=BAM_CMATCH && cig!=BAM_CEQUAL && cig!=BAM_CDIFF ) // not relying on precalculated diffs
+            error("TODO: cigar %d, %s:%"PRIhts_pos" %s\n", cig, sam_hdr_tid2name(stats->info->sam_header, bam_line->core.tid), bam_line->core.pos+1, bam_get_qname(bam_line));
+
+        if ( ncig+iref > stats->nrseq_buf )
+            error("FIXME: %d+%"PRIhts_pos" > %"PRId64", %s, %s:%"PRIhts_pos"\n", ncig, iref, stats->nrseq_buf, bam_get_qname(bam_line), sam_hdr_tid2name(stats->info->sam_header, bam_line->core.tid), bam_line->core.pos+1);
+
+        int im;
+        for (im=0; im<ncig; im++)
+        {
+            uint8_t cread = bam_seqi(read,iread);
+            uint8_t cref  = stats->rseq_buf[iref];
+
+            // ---------------15
+            // =ACMGRSVTWYHKDBN
+            if ( cread==15 )
+            {
+                int idx = is_fwd ? icycle : read_len-icycle-1;
+                if ( idx>stats->max_len )
+                    error("mpc: %d>%d\n",idx,stats->max_len);
+                idx = idx*stats->nquals;
+                if ( idx>=stats->nquals*stats->nbases )
+                    error("FIXME: mpc_buf overflow\n");
+                mpc_buf[idx]++;
+            }
+            else if ( cref && cread && cref!=cread )
+            {
+                uint8_t qual = quals[iread] + 1;
+                if ( qual>=stats->nquals )
+                    error("TODO: quality too high %d>=%d (%s %"PRIhts_pos" %s)\n", qual, stats->nquals, sam_hdr_tid2name(stats->info->sam_header, bam_line->core.tid), bam_line->core.pos+1, bam_get_qname(bam_line));
+
+                int idx = is_fwd ? icycle : read_len-icycle-1;
+                if ( idx>stats->max_len )
+                    error("mpc: %d>%d (%s %"PRIhts_pos" %s)\n", idx, stats->max_len, sam_hdr_tid2name(stats->info->sam_header, bam_line->core.tid), bam_line->core.pos+1, bam_get_qname(bam_line));
+
+                idx = idx*stats->nquals + qual;
+                if ( idx>=stats->nquals*stats->nbases )
+                    error("FIXME: mpc_buf overflow\n");
+                mpc_buf[idx]++;
+            }
+
+            iref++;
+            iread++;
+            icycle++;
+        }
+    }
+}
+
+void read_ref_seq(stats_t *stats, int32_t tid, hts_pos_t pos)
+{
+    int i;
+    hts_pos_t fai_ref_len;
+    char *fai_ref = faidx_fetch_seq64(stats->info->fai, sam_hdr_tid2name(stats->info->sam_header, tid), pos, pos+stats->mrseq_buf-1, &fai_ref_len);
+    if ( fai_ref_len < 0 ) error("Failed to fetch the sequence \"%s\"\n", sam_hdr_tid2name(stats->info->sam_header, tid));
+
+    uint8_t *ptr = stats->rseq_buf;
+    for (i=0; i<fai_ref_len; i++)
+    {
+        // Conversion between uint8_t coding and ACGT
+        //      -12-4---8-------
+        //      =ACMGRSVTWYHKDBN
+        switch (fai_ref[i])
+        {
+            case 'A':
+            case 'a': *ptr = 1; break;
+            case 'C':
+            case 'c': *ptr = 2; break;
+            case 'G':
+            case 'g': *ptr = 4; break;
+            case 'T':
+            case 't': *ptr = 8; break;
+            default:  *ptr = 0; break;
+        }
+        ptr++;
+    }
+    free(fai_ref);
+
+    if ( fai_ref_len < stats->mrseq_buf ) memset(ptr,0, stats->mrseq_buf - fai_ref_len);
+    stats->nrseq_buf = fai_ref_len;
+    stats->rseq_pos  = pos;
+    stats->tid       = tid;
+}
+
+float fai_gc_content(stats_t *stats, hts_pos_t pos, int len)
+{
+    uint32_t gc,count,c;
+    hts_pos_t i = pos - stats->rseq_pos, ito = i + len;
+    assert( i>=0 );
+
+    if (  ito > stats->nrseq_buf ) ito = stats->nrseq_buf;
+
+    // Count GC content
+    gc = count = 0;
+    for (; i<ito; i++)
+    {
+        c = stats->rseq_buf[i];
+        if ( c==2 || c==4 )
+        {
+            gc++;
+            count++;
+        }
+        else if ( c==1 || c==8 )
+            count++;
+    }
+    return count ? (float)gc/count : 0;
+}
+
+void realloc_rseq_buffer(stats_t *stats)
+{
+    int n = stats->nbases*10;
+    if ( stats->info->gcd_bin_size > n ) n = stats->info->gcd_bin_size;
+    if ( stats->mrseq_buf<n )
+    {
+        stats->rseq_buf = realloc(stats->rseq_buf,sizeof(uint8_t)*n);
+        if (!stats->rseq_buf) {
+            error("Could not reallocate reference sequence buffer");
+        }
+        stats->mrseq_buf = n;
+    }
+}
+
+void realloc_gcd_buffer(stats_t *stats, int seq_len)
+{
+    hts_expand0(gc_depth_t,stats->igcd+1,stats->ngcd,stats->gcd);
+    realloc_rseq_buffer(stats);
+}
+
+void realloc_buffers(stats_t *stats, int seq_len)
+{
+    int n = 2*(1 + seq_len - stats->nbases) + stats->nbases;
+
+    stats->quals_1st = realloc(stats->quals_1st, n*stats->nquals*sizeof(uint64_t));
+    if ( !stats->quals_1st )
+        error("Could not realloc buffers, the sequence too long: %d (%ld)\n", seq_len,n*stats->nquals*sizeof(uint64_t));
+    memset(stats->quals_1st + stats->nbases*stats->nquals, 0, (n-stats->nbases)*stats->nquals*sizeof(uint64_t));
+
+    stats->quals_2nd = realloc(stats->quals_2nd, n*stats->nquals*sizeof(uint64_t));
+    if ( !stats->quals_2nd )
+        error("Could not realloc buffers, the sequence too long: %d (2x%ld)\n", seq_len,n*stats->nquals*sizeof(uint64_t));
+    memset(stats->quals_2nd + stats->nbases*stats->nquals, 0, (n-stats->nbases)*stats->nquals*sizeof(uint64_t));
+
+    if ( stats->mpc_buf )
+    {
+        stats->mpc_buf = realloc(stats->mpc_buf, n*stats->nquals*sizeof(uint64_t));
+        if ( !stats->mpc_buf )
+            error("Could not realloc buffers, the sequence too long: %d (%ld)\n", seq_len,n*stats->nquals*sizeof(uint64_t));
+        memset(stats->mpc_buf + stats->nbases*stats->nquals, 0, (n-stats->nbases)*stats->nquals*sizeof(uint64_t));
+    }
+
+    stats->acgtno_cycles_1st = realloc(stats->acgtno_cycles_1st, n*sizeof(acgtno_count_t));
+    if ( !stats->acgtno_cycles_1st )
+        error("Could not realloc buffers, the sequence too long: %d (%ld)\n", seq_len, n*sizeof(acgtno_count_t));
+    memset(stats->acgtno_cycles_1st + stats->nbases, 0, (n-stats->nbases)*sizeof(acgtno_count_t));
+
+    stats->acgtno_cycles_2nd = realloc(stats->acgtno_cycles_2nd, n*sizeof(acgtno_count_t));
+    if ( !stats->acgtno_cycles_2nd )
+        error("Could not realloc buffers, the sequence too long: %d (%ld)\n", seq_len, n*sizeof(acgtno_count_t));
+    memset(stats->acgtno_cycles_2nd + stats->nbases, 0, (n-stats->nbases)*sizeof(acgtno_count_t));
+
+    stats->acgtno_revcomp = realloc(stats->acgtno_revcomp, n*sizeof(acgtno_count_t));
+    if ( !stats->acgtno_revcomp )
+        error("Could not realloc buffers, the sequence too long: %d (%ld)\n", seq_len, n*sizeof(acgtno_count_t));
+    memset(stats->acgtno_revcomp + stats->nbases, 0, (n-stats->nbases)*sizeof(acgtno_count_t));
+
+    stats->read_lengths = realloc(stats->read_lengths, n*sizeof(uint64_t));
+    if ( !stats->read_lengths )
+        error("Could not realloc buffers, the sequence too long: %d (%ld)\n", seq_len,n*sizeof(uint64_t));
+    memset(stats->read_lengths + stats->nbases, 0, (n-stats->nbases)*sizeof(uint64_t));
+
+    stats->read_lengths_1st = realloc(stats->read_lengths_1st, n*sizeof(uint64_t));
+    if ( !stats->read_lengths_1st )
+        error("Could not realloc buffers, the sequence too long: %d (%ld)\n", seq_len,n*sizeof(uint64_t));
+    memset(stats->read_lengths_1st + stats->nbases, 0, (n-stats->nbases)*sizeof(uint64_t));
+
+    stats->read_lengths_2nd = realloc(stats->read_lengths_2nd, n*sizeof(uint64_t));
+    if ( !stats->read_lengths_2nd )
+        error("Could not realloc buffers, the sequence too long: %d (%ld)\n", seq_len,n*sizeof(uint64_t));
+    memset(stats->read_lengths_2nd + stats->nbases, 0, (n-stats->nbases)*sizeof(uint64_t));
+
+    stats->insertions = realloc(stats->insertions, n*sizeof(uint64_t));
+    if ( !stats->insertions )
+        error("Could not realloc buffers, the sequence too long: %d (%ld)\n", seq_len,n*sizeof(uint64_t));
+    memset(stats->insertions + stats->nbases, 0, (n-stats->nbases)*sizeof(uint64_t));
+
+    stats->deletions = realloc(stats->deletions, n*sizeof(uint64_t));
+    if ( !stats->deletions )
+        error("Could not realloc buffers, the sequence too long: %d (%ld)\n", seq_len,n*sizeof(uint64_t));
+    memset(stats->deletions + stats->nbases, 0, (n-stats->nbases)*sizeof(uint64_t));
+
+    stats->ins_cycles_1st = realloc(stats->ins_cycles_1st, (n+1)*sizeof(uint64_t));
+    if ( !stats->ins_cycles_1st )
+        error("Could not realloc buffers, the sequence too long: %d (%ld)\n", seq_len,(n+1)*sizeof(uint64_t));
+    memset(stats->ins_cycles_1st + stats->nbases + 1, 0, (n-stats->nbases)*sizeof(uint64_t));
+
+    stats->ins_cycles_2nd = realloc(stats->ins_cycles_2nd, (n+1)*sizeof(uint64_t));
+    if ( !stats->ins_cycles_2nd )
+        error("Could not realloc buffers, the sequence too long: %d (%ld)\n", seq_len,(n+1)*sizeof(uint64_t));
+    memset(stats->ins_cycles_2nd + stats->nbases + 1, 0, (n-stats->nbases)*sizeof(uint64_t));
+
+    stats->del_cycles_1st = realloc(stats->del_cycles_1st, (n+1)*sizeof(uint64_t));
+    if ( !stats->del_cycles_1st )
+        error("Could not realloc buffers, the sequence too long: %d (%ld)\n", seq_len,(n+1)*sizeof(uint64_t));
+    memset(stats->del_cycles_1st + stats->nbases + 1, 0, (n-stats->nbases)*sizeof(uint64_t));
+
+    stats->del_cycles_2nd = realloc(stats->del_cycles_2nd, (n+1)*sizeof(uint64_t));
+    if ( !stats->del_cycles_2nd )
+        error("Could not realloc buffers, the sequence too long: %d (%ld)\n", seq_len,(n+1)*sizeof(uint64_t));
+    memset(stats->del_cycles_2nd + stats->nbases + 1, 0, (n-stats->nbases)*sizeof(uint64_t));
+
+    stats->nbases = n;
+
+    // Realloc the coverage distribution buffer
+    int *rbuffer = calloc(sizeof(int),seq_len*5);
+    if (!rbuffer) {
+        error("Could not allocate coverage distribution buffer");
+    }
+    n = stats->cov_rbuf.size-stats->cov_rbuf.start;
+    memcpy(rbuffer,stats->cov_rbuf.buffer+stats->cov_rbuf.start,n);
+    if ( stats->cov_rbuf.start>1 )
+        memcpy(rbuffer+n,stats->cov_rbuf.buffer,stats->cov_rbuf.start);
+    stats->cov_rbuf.start = 0;
+    free(stats->cov_rbuf.buffer);
+    stats->cov_rbuf.buffer = rbuffer;
+    stats->cov_rbuf.size = seq_len*5;
+
+    realloc_rseq_buffer(stats);
+}
+
+void update_checksum(bam1_t *bam_line, stats_t *stats)
+{
+    uint8_t *name = (uint8_t*) bam_get_qname(bam_line);
+    int len = 0;
+    while ( name[len] ) len++;
+    stats->checksum.names +=  crc32(0L, name, len);
+
+    int seq_len = bam_line->core.l_qseq;
+    if ( !seq_len ) return;
+
+    uint8_t *seq = bam_get_seq(bam_line);
+    stats->checksum.reads += crc32(0L, seq, (seq_len+1)/2);
+
+    uint8_t *qual = bam_get_qual(bam_line);
+    stats->checksum.quals += crc32(0L, qual, (seq_len+1)/2);
+}
+
+// Collect statistics about the barcode tags specified by init_barcode_tags method
+static void collect_barcode_stats(bam1_t* bam_line, stats_t* stats) {
+    uint32_t nbases, tag, i;
+    acgtno_count_t *acgtno;
+    uint64_t *quals;
+    int32_t *separator, *maxqual;
+
+    for (tag = 0; tag < stats->ntags; tag++) {
+        const char *barcode_tag = stats->tags_barcode[tag].tag_name, *qual_tag = stats->tags_barcode[tag].qual_name;
+        uint8_t* bc = bam_aux_get(bam_line, barcode_tag);
+        if (!bc)
+            continue;
+
+        char* barcode = bam_aux2Z(bc);
+        if (!barcode)
+            continue;
+
+        uint32_t barcode_len = strlen(barcode);
+        if (!stats->tags_barcode[tag].nbases) { // tag seen for the first time
+            uint32_t offset = 0;
+            for (i = 0; i < stats->ntags; i++)
+                offset += stats->tags_barcode[i].nbases;
+
+            stats->tags_barcode[tag].offset = offset;
+            stats->tags_barcode[tag].nbases = barcode_len;
+            stats->acgtno_barcode = realloc(stats->acgtno_barcode, (offset + barcode_len) * sizeof(acgtno_count_t));
+            stats->quals_barcode  = realloc(stats->quals_barcode, (offset + barcode_len) * stats->nquals * sizeof(uint64_t));
+
+            if (!stats->acgtno_barcode || !stats->quals_barcode)
+                error("Error allocating memory. Aborting!\n");
+
+            memset(stats->acgtno_barcode + offset, 0, barcode_len*sizeof(acgtno_count_t));
+            memset(stats->quals_barcode + offset*stats->nquals, 0, barcode_len*stats->nquals*sizeof(uint64_t));
+        }
+
+        nbases = stats->tags_barcode[tag].nbases;
+        if (barcode_len > nbases) {
+            fprintf(stderr, "Barcodes with tag %s differ in length at sequence '%s'\n", barcode_tag, bam_get_qname(bam_line));
+            continue;
+        }
+
+        acgtno = stats->acgtno_barcode + stats->tags_barcode[tag].offset;
+        quals = stats->quals_barcode + stats->tags_barcode[tag].offset*stats->nquals;
+        maxqual = &stats->tags_barcode[tag].max_qual;
+        separator = &stats->tags_barcode[tag].tag_sep;
+        int error_flag = 0;
+
+        for (i = 0; i < barcode_len; i++) {
+            switch (barcode[i]) {
+            case 'A':
+                acgtno[i].a++;
+                break;
+            case 'C':
+                acgtno[i].c++;
+                break;
+            case 'G':
+                acgtno[i].g++;
+                break;
+            case 'T':
+                acgtno[i].t++;
+                break;
+            case 'N':
+                acgtno[i].n++;
+                break;
+            default:
+                if (*separator >= 0) {
+                    if (*separator != i) {
+                        if (stats->error_number < ERROR_LIMIT) {
+                            fprintf(stderr, "Barcode separator for tag %s is in a different position or wrong barcode content('%s') at sequence '%s'\n", barcode_tag, barcode, bam_get_qname(bam_line));
+                            stats->error_number++;
+                        }
+                        error_flag = 1;
+                    }
+                } else {
+                    *separator = i;
+                }
+            }
+
+            /* don't process the rest of the tag bases */
+            if (error_flag)
+                break;
+        }
+
+        /* skip to the next tag */
+        if (error_flag)
+            continue;
+
+        uint8_t* qt = bam_aux_get(bam_line, qual_tag);
+        if (!qt)
+            continue;
+
+        char* barqual = bam_aux2Z(qt);
+        if (!barqual)
+            continue;
+
+        uint32_t barqual_len = strlen(barqual);
+        if (barqual_len == barcode_len) {
+            for (i = 0; i < barcode_len; i++) {
+                int32_t qual = (int32_t)barqual[i] - '!';  // Phred + 33
+                if (qual >= 0 && qual < stats->nquals) {
+                    quals[i * stats->nquals + qual]++;
+                    if (qual > *maxqual)
+                        *maxqual = qual;
+                }
+            }
+        } else {
+            if (stats->error_number++ < ERROR_LIMIT) {
+                fprintf(stderr, "%s length and %s length don't match for sequence '%s'\n", barcode_tag, qual_tag, bam_get_qname(bam_line));
+            }
+        }
+    }
+}
+
+// These stats should only be calculated for the original reads ignoring
+// supplementary artificial reads otherwise we'll accidentally double count
+void collect_orig_read_stats(bam1_t *bam_line, stats_t *stats, int* gc_count_out)
+{
+    int seq_len = bam_line->core.l_qseq;
+    stats->total_len += seq_len; // This ignores clipping so only count primary
+
+    if ( bam_line->core.flag & BAM_FQCFAIL ) stats->nreads_QCfailed++;
+    if ( bam_line->core.flag & BAM_FPAIRED ) stats->nreads_paired_tech++;
+
+    uint32_t order = IS_PAIRED(bam_line) ? (IS_READ1(bam_line) ? READ_ORDER_FIRST : 0) + (IS_READ2(bam_line) ? READ_ORDER_LAST : 0) : READ_ORDER_FIRST;
+
+    // Count GC and ACGT per cycle. Note that cycle is approximate, clipping is ignored
+    uint8_t *seq  = bam_get_seq(bam_line);
+    int i, read_cycle, gc_count = 0, reverse = IS_REVERSE(bam_line);
+
+    acgtno_count_t *acgtno_cycles = (order == READ_ORDER_FIRST) ? stats->acgtno_cycles_1st : (order == READ_ORDER_LAST) ?  stats->acgtno_cycles_2nd : NULL ;
+    if (acgtno_cycles) {
+        for (i=0; i<seq_len; i++)
+        {
+            // Read cycle for current index
+            read_cycle = (reverse ? seq_len-i-1 : i);
+
+            // Conversion from uint8_t coding:
+            //      -12-4---8------5
+            //      =ACMGRSVTWYHKDBN
+            switch (bam_seqi(seq, i)) {
+            case 1:
+                acgtno_cycles[ read_cycle ].a++;
+                reverse ? stats->acgtno_revcomp[ read_cycle ].t++ : stats->acgtno_revcomp[ read_cycle ].a++;
+                break;
+            case 2:
+                acgtno_cycles[ read_cycle ].c++;
+                reverse ? stats->acgtno_revcomp[ read_cycle ].g++ : stats->acgtno_revcomp[ read_cycle ].c++;
+                gc_count++;
+                break;
+            case 4:
+                acgtno_cycles[ read_cycle ].g++;
+                reverse ? stats->acgtno_revcomp[ read_cycle ].c++ : stats->acgtno_revcomp[ read_cycle ].g++;
+                gc_count++;
+                break;
+            case 8:
+                reverse ? stats->acgtno_revcomp[ read_cycle ].a++ : stats->acgtno_revcomp[ read_cycle ].t++;
+                acgtno_cycles[ read_cycle ].t++;
+                break;
+            case 15:
+                acgtno_cycles[ read_cycle ].n++;
+                break;
+            default:
+                /*
+                 * count "=" sequences in "other" along
+                 * with MRSVWYHKDB ambiguity codes
+                 */
+                acgtno_cycles[ read_cycle ].other++;
+                break;
+            }
+        }
+    }
+    int gc_idx_min = gc_count*(stats->ngc-1)/seq_len;
+    int gc_idx_max = (gc_count+1)*(stats->ngc-1)/seq_len;
+    if ( gc_idx_max >= stats->ngc ) gc_idx_max = stats->ngc - 1;
+
+    // Determine which array (1st or 2nd read) will these stats go to,
+    //  trim low quality bases from end the same way BWA does,
+    //  fill GC histogram
+    uint64_t *quals = NULL;
+    uint8_t *bam_quals = bam_get_qual(bam_line);
+
+    switch (order) {
+    case READ_ORDER_FIRST:
+        quals = stats->quals_1st;
+        stats->nreads_1st++;
+        stats->total_len_1st += seq_len;
+        for (i=gc_idx_min; i<gc_idx_max; i++)
+            stats->gc_1st[i]++;
+        break;
+    case READ_ORDER_LAST:
+        quals  = stats->quals_2nd;
+        stats->nreads_2nd++;
+        stats->total_len_2nd += seq_len;
+        for (i=gc_idx_min; i<gc_idx_max; i++)
+            stats->gc_2nd[i]++;
+        break;
+    default:
+        stats->nreads_other++;
+    }
+    if ( stats->info->trim_qual>0 )
+        stats->nbases_trimmed += bwa_trim_read(stats->info->trim_qual, bam_quals, seq_len, reverse);
+
+    // Quality histogram and average quality. Clipping is neglected.
+    if (quals) {
+        for (i=0; i<seq_len; i++)
+        {
+            uint8_t qual = bam_quals[ reverse ? seq_len-i-1 : i];
+            if ( qual>=stats->nquals )
+                error("TODO: quality too high %d>=%d (%s %"PRIhts_pos" %s)\n", qual, stats->nquals, sam_hdr_tid2name(stats->info->sam_header, bam_line->core.tid), bam_line->core.pos+1, bam_get_qname(bam_line));
+            if ( qual>stats->max_qual )
+                stats->max_qual = qual;
+
+            quals[ i*stats->nquals+qual ]++;
+            stats->sum_qual += qual;
+        }
+    }
+
+    // Barcode statistics
+    if (order == READ_ORDER_FIRST) {
+        collect_barcode_stats(bam_line, stats);
+    }
+
+    // Look at the flags and increment appropriate counters (mapped, paired, etc)
+    if ( IS_UNMAPPED(bam_line) )
+    {
+        stats->nreads_unmapped++;
+    }
+    else
+    {
+        stats->nbases_mapped += seq_len; // This ignores clipping so only count primary
+
+        if ( !bam_line->core.qual )
+            stats->nreads_mq0++;
+        if ( !IS_PAIRED_AND_MAPPED(bam_line) )
+            stats->nreads_single_mapped++;
+        else
+        {
+            stats->nreads_paired_and_mapped++;
+
+            if (IS_PROPERLYPAIRED(bam_line)) stats->nreads_properly_paired++;
+
+            if ( bam_line->core.tid!=bam_line->core.mtid )
+                stats->nreads_anomalous++;
+        }
+    }
+    *gc_count_out = gc_count;
+}
+
+static int cleanup_overlaps(khash_t(qn2pair) *read_pairs, hts_pos_t max) {
+    if ( !read_pairs )
+        return 0;
+
+    int count = 0;
+    khint_t k;
+    for (k = kh_begin(read_pairs); k < kh_end(read_pairs); k++) {
+        if ( kh_exist(read_pairs, k) ) {
+            char *key = (char *)kh_key(read_pairs, k);
+            pair_t *val = kh_val(read_pairs, k);
+            if ( val && val->chunks ) {
+                if ( val->chunks[val->n-1].end < max ) {
+                    free(val->chunks);
+                    free(val);
+                    free(key);
+                    kh_del(qn2pair, read_pairs, k);
+                    count++;
+                }
+            } else {
+                free(key);
+                kh_del(qn2pair, read_pairs, k);
+                count++;
+            }
+        }
+    }
+    if ( max == INT64_MAX )
+        kh_destroy(qn2pair, read_pairs);
+
+    return count;
+}
+
+/**
+ * [pmin, pmax) - 0 based half-open
+ */
+static void remove_overlaps(bam1_t *bam_line, khash_t(qn2pair) *read_pairs, stats_t *stats, hts_pos_t pmin, hts_pos_t pmax) {
+    if ( !bam_line || !read_pairs || !stats )
+        return;
+
+    uint32_t order = (IS_READ1(bam_line) ? READ_ORDER_FIRST : 0) + (IS_READ2(bam_line) ? READ_ORDER_LAST : 0);
+    if ( !(bam_line->core.flag & BAM_FPAIRED) ||
+         (bam_line->core.flag & BAM_FMUNMAP) ||
+         (llabs(bam_line->core.isize) >= 2*bam_line->core.l_qseq) ||
+         (order != READ_ORDER_FIRST && order != READ_ORDER_LAST) ) {
+        if ( pmin >= 0 )
+            round_buffer_insert_read(&(stats->cov_rbuf), pmin, pmax);
+        return;
+    }
+
+    char *qname = bam_get_qname(bam_line);
+    if ( !qname ) {
+        fprintf(stderr, "Error retrieving qname for line starting at pos %"PRIhts_pos"\n", bam_line->core.pos);
+        return;
+    }
+
+    khint_t k = kh_get(qn2pair, read_pairs, qname);
+    if ( k == kh_end(read_pairs) ) { //first chunk from this template
+        if ( pmin == -1 )
+            return;
+
+        int ret;
+        char *s = strdup(qname);
+        if ( !s ) {
+            fprintf(stderr, "Error allocating memory\n");
+            return;
+        }
+
+        k = kh_put(qn2pair, read_pairs, s, &ret);
+        if ( -1 == ret ) {
+            error("Error inserting read '%s' in pair hash table\n", qname);
+        }
+
+        pair_t *pc = calloc(1, sizeof(pair_t));
+        if ( !pc ) {
+            fprintf(stderr, "Error allocating memory\n");
+            return;
+        }
+
+        pc->m = DEFAULT_CHUNK_NO;
+        pc->chunks = calloc(pc->m, sizeof(hts_pair_pos_t));
+        if ( !pc->chunks ) {
+            fprintf(stderr, "Error allocating memory\n");
+            free(pc);
+            return;
+        }
+
+        pc->chunks[0].beg = pmin;
+        pc->chunks[0].end = pmax;
+        pc->n = 1;
+        pc->first = order;
+
+        kh_val(read_pairs, k) = pc;
+        stats->pair_count++;
+    } else { //template already present
+        pair_t *pc = kh_val(read_pairs, k);
+        if ( !pc ) {
+            fprintf(stderr, "Invalid hash table entry\n");
+            return;
+        }
+
+        if ( order == pc->first ) { //chunk from an existing line
+            if ( pmin == -1 )
+                return;
+
+            if ( pc->n == pc->m ) {
+                hts_pair_pos_t *tmp = realloc(pc->chunks, (pc->m<<1)*sizeof(hts_pair_pos_t));
+                if ( !tmp ) {
+                    fprintf(stderr, "Error allocating memory\n");
+                    return;
+                }
+                pc->chunks = tmp;
+                pc->m<<=1;
+            }
+
+            pc->chunks[pc->n].beg = pmin;
+            pc->chunks[pc->n].end = pmax;
+            pc->n++;
+        } else { //the other line, check for overlapping
+            if ( pmin == -1 && kh_exist(read_pairs, k) ) { //job done, delete entry
+                char *key = (char *)kh_key(read_pairs, k);
+                pair_t *val = kh_val(read_pairs, k);
+                if ( val) {
+                    free(val->chunks);
+                    free(val);
+                }
+                free(key);
+                kh_del(qn2pair, read_pairs, k);
+                stats->pair_count--;
+                return;
+            }
+
+            int i;
+            for (i=0; i<pc->n; i++) {
+                if ( pmin >= pc->chunks[i].end )
+                    continue;
+
+                if ( pmax <= pc->chunks[i].beg ) //no overlap
+                    break;
+
+                if ( pmin < pc->chunks[i].beg ) { //overlap at the beginning
+                    round_buffer_insert_read(&(stats->cov_rbuf), pmin, pc->chunks[i].beg);
+                    pmin = pc->chunks[i].beg;
+                }
+
+                if ( pmax <= pc->chunks[i].end ) { //completely contained
+                    stats->nbases_mapped_cigar -= (pmax - pmin);
+                    return;
+                } else {                           //overlap at the end
+                    stats->nbases_mapped_cigar -= (pc->chunks[i].end - pmin);
+                    pmin = pc->chunks[i].end;
+                }
+            }
+        }
+    }
+    round_buffer_insert_read(&(stats->cov_rbuf), pmin, pmax);
+}
+
+void collect_stats(bam1_t *bam_line, stats_t *stats, khash_t(qn2pair) *read_pairs)
+{
+    if ( !is_in_regions(bam_line,stats) )
+        return;
+    if ( stats->rg_hash )
+    {
+        const uint8_t *rg = bam_aux_get(bam_line, "RG");
+        if ( !rg ) return;  // certain read groups were requested but this record has none
+        khint_t k = kh_get(rg, stats->rg_hash, (const char*)(rg + 1));
+        if ( k == kh_end((kh_rg_t *)stats->rg_hash) ) return;
+    }
+    if ( stats->info->flag_require && (bam_line->core.flag & stats->info->flag_require)!=stats->info->flag_require )
+    {
+        stats->nreads_filtered++;
+        return;
+    }
+    if ( stats->info->flag_filter && (bam_line->core.flag & stats->info->flag_filter) )
+    {
+        stats->nreads_filtered++;
+        return;
+    }
+    if ( stats->info->filter_readlen!=-1 && bam_line->core.l_qseq!=stats->info->filter_readlen )
+        return;
+
+    update_checksum(bam_line, stats);
+
+    // Secondary reads don't count for most stats purposes
+    if ( bam_line->core.flag & BAM_FSECONDARY )
+    {
+        stats->nreads_secondary++;
+        return;
+    }
+
+    if ( bam_line->core.flag & BAM_FSUPPLEMENTARY )
+    {
+        stats->nreads_supplementary++;
+    }
+
+    // If line has no sequence cannot continue
+    int seq_len = bam_line->core.l_qseq;
+    if ( !seq_len ) return;
+
+    if ( IS_DUP(bam_line) )
+    {
+        stats->total_len_dup += seq_len;
+        stats->nreads_dup++;
+    }
+
+    uint32_t order = IS_PAIRED(bam_line) ? (IS_READ1(bam_line) ? READ_ORDER_FIRST : 0) + (IS_READ2(bam_line) ? READ_ORDER_LAST : 0) : READ_ORDER_FIRST;
+
+    int read_len = unclipped_length(bam_line);
+    if ( read_len >= stats->nbases )
+        realloc_buffers(stats,read_len);
+    // Update max_len observed
+    if ( stats->max_len<read_len )
+        stats->max_len = read_len;
+    if ( order == READ_ORDER_FIRST && stats->max_len_1st < read_len )
+        stats->max_len_1st = read_len;
+    if ( order == READ_ORDER_LAST && stats->max_len_2nd < read_len )
+        stats->max_len_2nd = read_len;
+
+    int i;
+    int gc_count = 0;
+
+    // These stats should only be calculated for the original reads ignoring supplementary artificial reads
+    // otherwise we'll accidentally double count
+    if ( IS_ORIGINAL(bam_line) ) {
+        stats->read_lengths[read_len]++;
+        if ( order == READ_ORDER_FIRST ) stats->read_lengths_1st[read_len]++;
+        if ( order == READ_ORDER_LAST ) stats->read_lengths_2nd[read_len]++;
+        collect_orig_read_stats(bam_line, stats, &gc_count);
+    }
+
+    // Look at the flags and increment appropriate counters (mapped, paired, etc)
+    if ( IS_UNMAPPED(bam_line) ) return;
+
+    count_indels(stats, bam_line);
+
+    if ( IS_PAIRED_AND_MAPPED(bam_line) && IS_ORIGINAL(bam_line) )
+    {
+        // The insert size is tricky, because for long inserts the libraries are
+        // prepared differently and the pairs point in other direction. BWA does
+        // not set the paired flag for them.  Similar thing is true also for 454
+        // reads. Mates mapped to different chromosomes have isize==0.
+        int32_t isize = bam_line->core.isize;
+        if ( isize<0 ) isize = -isize;
+        if ( stats->info->nisize > 0 && isize > stats->info->nisize )
+            isize = stats->info->nisize;
+        if ( isize>0 || bam_line->core.tid==bam_line->core.mtid )
+        {
+            hts_pos_t pos_fst = bam_line->core.mpos - bam_line->core.pos;
+            int is_fst  = IS_READ1(bam_line) ? 1 : -1;
+            int is_fwd  = IS_REVERSE(bam_line) ? -1 : 1;
+            int is_mfwd = IS_MATE_REVERSE(bam_line) ? -1 : 1;
+
+            if ( is_fwd*is_mfwd>0 )
+                stats->isize->inc_other(stats->isize->data, isize);
+            else if ( is_fst*pos_fst>=0 )
+            {
+                if ( is_fst*is_fwd>0 )
+                    stats->isize->inc_inward(stats->isize->data, isize);
+                else
+                    stats->isize->inc_outward(stats->isize->data, isize);
+            }
+            else if ( is_fst*pos_fst<0 )
+            {
+                if ( is_fst*is_fwd>0 )
+                    stats->isize->inc_outward(stats->isize->data, isize);
+                else
+                    stats->isize->inc_inward(stats->isize->data, isize);
+            }
+        }
+    }
+
+    // Number of mismatches
+    uint8_t *nm = bam_aux_get(bam_line,"NM");
+    if (nm)
+        stats->nmismatches += bam_aux2i(nm);
+
+    // Number of mapped bases from cigar
+    if ( bam_line->core.n_cigar == 0)
+        error("FIXME: mapped read with no cigar?\n");
+    int readlen=seq_len;
+    if ( stats->regions )
+    {
+        // Count only on-target bases
+        hts_pos_t iref = bam_line->core.pos + 1;
+        for (i=0; i<bam_line->core.n_cigar; i++)
+        {
+            int cig  = bam_cigar_op(bam_get_cigar(bam_line)[i]);
+            int ncig = bam_cigar_oplen(bam_get_cigar(bam_line)[i]);
+            if ( !ncig ) continue;  // curiously, this can happen: 0D
+            if ( cig==BAM_CDEL ) readlen += ncig;
+            else if ( cig==BAM_CMATCH || cig==BAM_CEQUAL || cig==BAM_CDIFF )
+            {
+                if ( iref < stats->reg_from ) ncig -= stats->reg_from-iref;
+                else if ( iref+ncig-1 > stats->reg_to ) ncig -= iref+ncig-1 - stats->reg_to;
+                if ( ncig<0 ) ncig = 0;
+                stats->nbases_mapped_cigar += ncig;
+                iref += bam_cigar_oplen(bam_get_cigar(bam_line)[i]);
+            }
+            else if ( cig==BAM_CINS )
+            {
+                iref += ncig;
+                if ( iref>=stats->reg_from && iref<=stats->reg_to )
+                    stats->nbases_mapped_cigar += ncig;
+            }
+        }
+    }
+    else
+    {
+        // Count the whole read
+        for (i=0; i<bam_line->core.n_cigar; i++)
+        {
+            int cig  = bam_cigar_op(bam_get_cigar(bam_line)[i]);
+            if ( cig==BAM_CMATCH || cig==BAM_CINS || cig==BAM_CEQUAL || cig==BAM_CDIFF )
+                stats->nbases_mapped_cigar += bam_cigar_oplen(bam_get_cigar(bam_line)[i]);
+            if ( cig==BAM_CDEL )
+                readlen += bam_cigar_oplen(bam_get_cigar(bam_line)[i]);
+        }
+    }
+
+    if ( stats->tid==bam_line->core.tid && bam_line->core.pos<stats->pos )
+        stats->is_sorted = 0;
+    stats->pos = bam_line->core.pos;
+
+    if ( stats->is_sorted )
+    {
+        if ( stats->tid==-1 || stats->tid!=bam_line->core.tid ) {
+            round_buffer_flush(stats, -1);
+        }
+
+        //cleanup the pair hash table to free memory
+        stats->last_read_flush++;
+        if ( stats->pair_count > DEFAULT_PAIR_MAX && stats->last_read_flush > DEFAULT_PAIR_MAX) {
+            stats->pair_count -= cleanup_overlaps(read_pairs, bam_line->core.pos);
+            stats->last_read_flush = 0;
+        }
+
+        if ( stats->last_pair_tid != bam_line->core.tid) {
+            stats->pair_count -= cleanup_overlaps(read_pairs, INT64_MAX-1);
+            stats->last_pair_tid = bam_line->core.tid;
+            stats->last_read_flush = 0;
+        }
+
+        // Mismatches per cycle and GC-depth graph. For simplicity, reads overlapping GCD bins
+        //  are not splitted which results in up to seq_len-1 overlaps. The default bin size is
+        //  20kbp, so the effect is negligible.
+        if ( stats->info->fai )
+        {
+            int inc_ref = 0, inc_gcd = 0;
+            // First pass or new chromosome
+            if ( stats->rseq_pos==-1 || stats->tid != bam_line->core.tid ) { inc_ref=1; inc_gcd=1; }
+            // Read goes beyond the end of the rseq buffer
+            else if ( stats->rseq_pos+stats->nrseq_buf < bam_line->core.pos+readlen ) { inc_ref=1; inc_gcd=1; }
+            // Read overlaps the next gcd bin
+            else if ( stats->gcd_pos+stats->info->gcd_bin_size < bam_line->core.pos+readlen )
+            {
+                inc_gcd = 1;
+                if ( stats->rseq_pos+stats->nrseq_buf < bam_line->core.pos+stats->info->gcd_bin_size ) inc_ref = 1;
+            }
+            if ( inc_gcd )
+            {
+                stats->igcd++;
+                if ( stats->igcd >= stats->ngcd )
+                    realloc_gcd_buffer(stats, readlen);
+                if ( inc_ref )
+                    read_ref_seq(stats,bam_line->core.tid,bam_line->core.pos);
+                stats->gcd_pos = bam_line->core.pos;
+                stats->gcd[ stats->igcd ].gc = fai_gc_content(stats, stats->gcd_pos, stats->info->gcd_bin_size);
+            }
+
+            count_mismatches_per_cycle(stats,bam_line,read_len);
+        }
+        // No reference and first pass, new chromosome or sequence going beyond the end of the gcd bin
+        else if ( stats->gcd_pos==-1 || stats->tid != bam_line->core.tid || bam_line->core.pos - stats->gcd_pos > stats->info->gcd_bin_size )
+        {
+            // First pass or a new chromosome
+            stats->tid     = bam_line->core.tid;
+            stats->gcd_pos = bam_line->core.pos;
+            stats->igcd++;
+            if ( stats->igcd >= stats->ngcd )
+                realloc_gcd_buffer(stats, readlen);
+        }
+        stats->gcd[ stats->igcd ].depth++;
+        // When no reference sequence is given, approximate the GC from the read (much shorter window, but otherwise OK)
+        if ( !stats->info->fai )
+            stats->gcd[ stats->igcd ].gc += (float) gc_count / seq_len;
+
+        // Coverage distribution graph
+        round_buffer_flush(stats,bam_line->core.pos);
+        if ( stats->regions ) {
+            hts_pos_t p = bam_line->core.pos, pnew, pmin = 0, pmax = 0;
+            uint32_t j = 0;
+            i = 0;
+            while ( j < bam_line->core.n_cigar && i < stats->nchunks ) {
+                int op = bam_cigar_op(bam_get_cigar(bam_line)[j]);
+                int oplen = bam_cigar_oplen(bam_get_cigar(bam_line)[j]);
+                switch(op) {
+                case BAM_CMATCH:
+                case BAM_CEQUAL:
+                case BAM_CDIFF:
+                    pmin = MAX(p, stats->chunks[i].beg-1); // 0 based
+                    pmax = MIN(p+oplen, stats->chunks[i].end); // 1 based
+                    if ( pmax > pmin ) {
+                        if ( stats->info->remove_overlaps )
+                            remove_overlaps(bam_line, read_pairs, stats, pmin, pmax);
+                        else
+                            round_buffer_insert_read(&(stats->cov_rbuf), pmin, pmax);
+                    }
+                    break;
+                case BAM_CDEL:
+                    break;
+                }
+                pnew = p + (bam_cigar_type(op)&2 ? oplen : 0); // consumes reference
+
+                if ( pnew >= stats->chunks[i].end ) {
+                    // go to the next chunk
+                    i++;
+                } else {
+                    // go to the next CIGAR op
+                    j++;
+                    p = pnew;
+                }
+            }
+        } else {
+            hts_pos_t p = bam_line->core.pos;
+            uint32_t j;
+            for (j = 0; j < bam_line->core.n_cigar; j++) {
+                int op = bam_cigar_op(bam_get_cigar(bam_line)[j]);
+                int oplen = bam_cigar_oplen(bam_get_cigar(bam_line)[j]);
+                switch(op) {
+                case BAM_CMATCH:
+                case BAM_CEQUAL:
+                case BAM_CDIFF:
+                    if ( stats->info->remove_overlaps )
+                        remove_overlaps(bam_line, read_pairs, stats, p, p+oplen);
+                    else
+                        round_buffer_insert_read(&(stats->cov_rbuf), p, p+oplen);
+                    break;
+                case BAM_CDEL:
+                    break;
+                }
+                p += bam_cigar_type(op)&2 ? oplen : 0; // consumes reference
+            }
+        }
+        if ( stats->info->remove_overlaps )
+           remove_overlaps(bam_line, read_pairs, stats, -1LL, -1LL); //remove the line from the hash table
+    }
+}
+
+// Sort by GC and depth
+#define GCD_t(x) ((gc_depth_t *)x)
+static int gcd_cmp(const void *a, const void *b)
+{
+    if ( GCD_t(a)->gc < GCD_t(b)->gc ) return -1;
+    if ( GCD_t(a)->gc > GCD_t(b)->gc ) return 1;
+    if ( GCD_t(a)->depth < GCD_t(b)->depth ) return -1;
+    if ( GCD_t(a)->depth > GCD_t(b)->depth ) return 1;
+    return 0;
+}
+#undef GCD_t
+
+float gcd_percentile(gc_depth_t *gcd, int N, int p)
+{
+    float n,d;
+    int k;
+
+    n = (float)p*(N+1)/100;
+    k = n;
+    if ( k<=0 )
+        return gcd[0].depth;
+    if ( k>=N )
+        return gcd[N-1].depth;
+
+    d = n - k;
+    return gcd[k-1].depth + d*(gcd[k].depth - gcd[k-1].depth);
+}
+
+void output_stats(FILE *to, stats_t *stats, int sparse)
+{
+    // Calculate average insert size and standard deviation (from the main bulk data only)
+    int isize, ibulk=0, icov;
+    uint64_t nisize=0, nisize_inward=0, nisize_outward=0, nisize_other=0, cov_sum=0;
+    double bulk=0, avg_isize=0, sd_isize=0;
+    for (isize=0; isize<stats->isize->nitems(stats->isize->data); isize++)
+    {
+        // Each pair was counted twice
+        stats->isize->set_inward(stats->isize->data, isize, stats->isize->inward(stats->isize->data, isize) * 0.5);
+        stats->isize->set_outward(stats->isize->data, isize, stats->isize->outward(stats->isize->data, isize) * 0.5);
+        stats->isize->set_other(stats->isize->data, isize, stats->isize->other(stats->isize->data, isize) * 0.5);
+
+        nisize_inward += stats->isize->inward(stats->isize->data, isize);
+        nisize_outward += stats->isize->outward(stats->isize->data, isize);
+        nisize_other += stats->isize->other(stats->isize->data, isize);
+        nisize += stats->isize->inward(stats->isize->data, isize) + stats->isize->outward(stats->isize->data, isize) + stats->isize->other(stats->isize->data, isize);
+    }
+
+    for (isize=0; isize<stats->isize->nitems(stats->isize->data); isize++)
+    {
+        uint64_t num = stats->isize->inward(stats->isize->data, isize) +  stats->isize->outward(stats->isize->data, isize) + stats->isize->other(stats->isize->data, isize);
+        if (num > 0) ibulk = isize + 1;
+        bulk += num;
+        avg_isize += isize * (stats->isize->inward(stats->isize->data, isize) +  stats->isize->outward(stats->isize->data, isize) + stats->isize->other(stats->isize->data, isize));
+
+        if ( bulk/nisize > stats->info->isize_main_bulk )
+        {
+            ibulk  = isize+1;
+            nisize = bulk;
+            break;
+        }
+    }
+    avg_isize /= nisize ? nisize : 1;
+    for (isize=1; isize<ibulk; isize++)
+        sd_isize += (stats->isize->inward(stats->isize->data, isize) + stats->isize->outward(stats->isize->data, isize) +stats->isize->other(stats->isize->data, isize)) * (isize-avg_isize)*(isize-avg_isize) / (nisize ? nisize : 1);
+    sd_isize = sqrt(sd_isize);
+
+    fprintf(to, "# This file was produced by samtools stats (%s+htslib-%s) and can be plotted using plot-bamstats\n", samtools_version(), hts_version());
+    if( stats->split_name != NULL ){
+        fprintf(to, "# This file contains statistics only for reads with tag: %s=%s\n", stats->info->split_tag, stats->split_name);
+    }
+    else{
+        fprintf(to, "# This file contains statistics for all reads.\n");
+    }
+    fprintf(to, "# The command line was:  %s",stats->info->argv[0]);
+    int i;
+    for (i=1; i<stats->info->argc; i++)
+        fprintf(to, " %s", stats->info->argv[i]);
+    fprintf(to, "\n");
+    fprintf(to, "# CHK, Checksum\t[2]Read Names\t[3]Sequences\t[4]Qualities\n");
+    fprintf(to, "# CHK, CRC32 of reads which passed filtering followed by addition (32bit overflow)\n");
+    fprintf(to, "CHK\t%08x\t%08x\t%08x\n", stats->checksum.names,stats->checksum.reads,stats->checksum.quals);
+    fprintf(to, "# Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part.\n");
+    fprintf(to, "SN\traw total sequences:\t%ld\t# excluding supplementary and secondary reads\n", (long)(stats->nreads_filtered+stats->nreads_1st+stats->nreads_2nd+stats->nreads_other));  // not counting excluded seqs (and none of the below)
+    fprintf(to, "SN\tfiltered sequences:\t%ld\n", (long)stats->nreads_filtered);
+    fprintf(to, "SN\tsequences:\t%ld\n", (long)(stats->nreads_1st+stats->nreads_2nd+stats->nreads_other));
+    fprintf(to, "SN\tis sorted:\t%d\n", stats->is_sorted ? 1 : 0);
+    fprintf(to, "SN\t1st fragments:\t%ld\n", (long)stats->nreads_1st);
+    fprintf(to, "SN\tlast fragments:\t%ld\n", (long)stats->nreads_2nd);
+    fprintf(to, "SN\treads mapped:\t%ld\n", (long)(stats->nreads_paired_and_mapped+stats->nreads_single_mapped));
+    fprintf(to, "SN\treads mapped and paired:\t%ld\t# paired-end technology bit set + both mates mapped\n", (long)stats->nreads_paired_and_mapped);
+    fprintf(to, "SN\treads unmapped:\t%ld\n", (long)stats->nreads_unmapped);
+    fprintf(to, "SN\treads properly paired:\t%ld\t# proper-pair bit set\n", (long)stats->nreads_properly_paired);
+    fprintf(to, "SN\treads paired:\t%ld\t# paired-end technology bit set\n", (long)stats->nreads_paired_tech);
+    fprintf(to, "SN\treads duplicated:\t%ld\t# PCR or optical duplicate bit set\n", (long)stats->nreads_dup);
+    fprintf(to, "SN\treads MQ0:\t%ld\t# mapped and MQ=0\n", (long)stats->nreads_mq0);
+    fprintf(to, "SN\treads QC failed:\t%ld\n", (long)stats->nreads_QCfailed);
+    fprintf(to, "SN\tnon-primary alignments:\t%ld\n", (long)stats->nreads_secondary);
+    fprintf(to, "SN\tsupplementary alignments:\t%ld\n", (long)stats->nreads_supplementary);
+    fprintf(to, "SN\ttotal length:\t%ld\t# ignores clipping\n", (long)stats->total_len);
+    fprintf(to, "SN\ttotal first fragment length:\t%ld\t# ignores clipping\n", (long)stats->total_len_1st);
+    fprintf(to, "SN\ttotal last fragment length:\t%ld\t# ignores clipping\n", (long)stats->total_len_2nd);
+    fprintf(to, "SN\tbases mapped:\t%ld\t# ignores clipping\n", (long)stats->nbases_mapped);                 // the length of the whole read goes here, including soft-clips etc.
+    fprintf(to, "SN\tbases mapped (cigar):\t%ld\t# more accurate\n", (long)stats->nbases_mapped_cigar);   // only matched and inserted bases are counted here
+    fprintf(to, "SN\tbases trimmed:\t%ld\n", (long)stats->nbases_trimmed);
+    fprintf(to, "SN\tbases duplicated:\t%ld\n", (long)stats->total_len_dup);
+    fprintf(to, "SN\tmismatches:\t%ld\t# from NM fields\n", (long)stats->nmismatches);
+    fprintf(to, "SN\terror rate:\t%e\t# mismatches / bases mapped (cigar)\n", stats->nbases_mapped_cigar ? (float)stats->nmismatches/stats->nbases_mapped_cigar : 0);
+    float avg_read_length = (stats->nreads_1st+stats->nreads_2nd+stats->nreads_other)?stats->total_len/(stats->nreads_1st+stats->nreads_2nd+stats->nreads_other):0;
+    fprintf(to, "SN\taverage length:\t%.0f\n", avg_read_length);
+    fprintf(to, "SN\taverage first fragment length:\t%.0f\n", stats->nreads_1st? (float)stats->total_len_1st/stats->nreads_1st:0);
+    fprintf(to, "SN\taverage last fragment length:\t%.0f\n", stats->nreads_2nd? (float)stats->total_len_2nd/stats->nreads_2nd:0);
+    fprintf(to, "SN\tmaximum length:\t%d\n", stats->max_len);
+    fprintf(to, "SN\tmaximum first fragment length:\t%d\n", stats->max_len_1st);
+    fprintf(to, "SN\tmaximum last fragment length:\t%d\n", stats->max_len_2nd);
+    fprintf(to, "SN\taverage quality:\t%.1f\n", stats->total_len?stats->sum_qual/stats->total_len:0);
+    fprintf(to, "SN\tinsert size average:\t%.1f\n", avg_isize);
+    fprintf(to, "SN\tinsert size standard deviation:\t%.1f\n", sd_isize);
+    fprintf(to, "SN\tinward oriented pairs:\t%ld\n", (long)nisize_inward);
+    fprintf(to, "SN\toutward oriented pairs:\t%ld\n", (long)nisize_outward);
+    fprintf(to, "SN\tpairs with other orientation:\t%ld\n", (long)nisize_other);
+    fprintf(to, "SN\tpairs on different chromosomes:\t%ld\n", (long)stats->nreads_anomalous/2);
+    fprintf(to, "SN\tpercentage of properly paired reads (%%):\t%.1f\n", (stats->nreads_1st+stats->nreads_2nd+stats->nreads_other)? (float)(100*stats->nreads_properly_paired)/(stats->nreads_1st+stats->nreads_2nd+stats->nreads_other):0);
+    if ( stats->target_count ) {
+        fprintf(to, "SN\tbases inside the target:\t%" PRIu64 "\n", stats->target_count);
+        for (icov=stats->info->cov_threshold+1; icov<stats->ncov; icov++)
+            cov_sum += stats->cov[icov];
+        fprintf(to, "SN\tpercentage of target genome with coverage > %d (%%):\t%.2f\n", stats->info->cov_threshold, (float)(100*cov_sum)/stats->target_count);
+    }
+
+    int ibase,iqual;
+    if ( stats->max_len<stats->nbases ) stats->max_len++;
+    if ( stats->max_qual+1<stats->nquals ) stats->max_qual++;
+    fprintf(to, "# First Fragment Qualities. Use `grep ^FFQ | cut -f 2-` to extract this part.\n");
+    fprintf(to, "# Columns correspond to qualities and rows to cycles. First column is the cycle number.\n");
+    for (ibase=0; ibase<stats->max_len_1st; ibase++)
+    {
+        fprintf(to, "FFQ\t%d",ibase+1);
+        for (iqual=0; iqual<=stats->max_qual; iqual++)
+        {
+            fprintf(to, "\t%ld", (long)stats->quals_1st[ibase*stats->nquals+iqual]);
+        }
+        fprintf(to, "\n");
+    }
+    fprintf(to, "# Last Fragment Qualities. Use `grep ^LFQ | cut -f 2-` to extract this part.\n");
+    fprintf(to, "# Columns correspond to qualities and rows to cycles. First column is the cycle number.\n");
+    for (ibase=0; ibase<stats->max_len_2nd; ibase++)
+    {
+        fprintf(to, "LFQ\t%d",ibase+1);
+        for (iqual=0; iqual<=stats->max_qual; iqual++)
+        {
+            fprintf(to, "\t%ld", (long)stats->quals_2nd[ibase*stats->nquals+iqual]);
+        }
+        fprintf(to, "\n");
+    }
+    if ( stats->mpc_buf )
+    {
+        fprintf(to, "# Mismatches per cycle and quality. Use `grep ^MPC | cut -f 2-` to extract this part.\n");
+        fprintf(to, "# Columns correspond to qualities, rows to cycles. First column is the cycle number, second\n");
+        fprintf(to, "# is the number of N's and the rest is the number of mismatches\n");
+        for (ibase=0; ibase<stats->max_len; ibase++)
+        {
+            fprintf(to, "MPC\t%d",ibase+1);
+            for (iqual=0; iqual<=stats->max_qual; iqual++)
+            {
+                fprintf(to, "\t%ld", (long)stats->mpc_buf[ibase*stats->nquals+iqual]);
+            }
+            fprintf(to, "\n");
+        }
+    }
+    fprintf(to, "# GC Content of first fragments. Use `grep ^GCF | cut -f 2-` to extract this part.\n");
+    int ibase_prev = 0;
+    for (ibase=0; ibase<stats->ngc; ibase++)
+    {
+        if ( stats->gc_1st[ibase]==stats->gc_1st[ibase_prev] ) continue;
+        fprintf(to, "GCF\t%.2f\t%ld\n", (ibase+ibase_prev)*0.5*100./(stats->ngc-1), (long)stats->gc_1st[ibase_prev]);
+        ibase_prev = ibase;
+    }
+    fprintf(to, "# GC Content of last fragments. Use `grep ^GCL | cut -f 2-` to extract this part.\n");
+    ibase_prev = 0;
+    for (ibase=0; ibase<stats->ngc; ibase++)
+    {
+        if ( stats->gc_2nd[ibase]==stats->gc_2nd[ibase_prev] ) continue;
+        fprintf(to, "GCL\t%.2f\t%ld\n", (ibase+ibase_prev)*0.5*100./(stats->ngc-1), (long)stats->gc_2nd[ibase_prev]);
+        ibase_prev = ibase;
+    }
+    fprintf(to, "# ACGT content per cycle. Use `grep ^GCC | cut -f 2-` to extract this part. The columns are: cycle; A,C,G,T base counts as a percentage of all A/C/G/T bases [%%]; and N and O counts as a percentage of all A/C/G/T bases [%%]\n");
+    for (ibase=0; ibase<stats->max_len; ibase++)
+    {
+        acgtno_count_t *acgtno_count_1st = &(stats->acgtno_cycles_1st[ibase]);
+        acgtno_count_t *acgtno_count_2nd = &(stats->acgtno_cycles_2nd[ibase]);
+        uint64_t acgt_sum = acgtno_count_1st->a + acgtno_count_1st->c + acgtno_count_1st->g + acgtno_count_1st->t +
+                acgtno_count_2nd->a + acgtno_count_2nd->c + acgtno_count_2nd->g + acgtno_count_2nd->t;
+        if ( ! acgt_sum ) continue;
+        fprintf(to, "GCC\t%d\t%.2f\t%.2f\t%.2f\t%.2f\t%.2f\t%.2f\n", ibase+1,
+                100.*(acgtno_count_1st->a + acgtno_count_2nd->a)/acgt_sum,
+                100.*(acgtno_count_1st->c + acgtno_count_2nd->c)/acgt_sum,
+                100.*(acgtno_count_1st->g + acgtno_count_2nd->g)/acgt_sum,
+                100.*(acgtno_count_1st->t + acgtno_count_2nd->t)/acgt_sum,
+                100.*(acgtno_count_1st->n + acgtno_count_2nd->n)/acgt_sum,
+                100.*(acgtno_count_1st->other + acgtno_count_2nd->other)/acgt_sum);
+    }
+    fprintf(to, "# ACGT content per cycle, read oriented. Use `grep ^GCT | cut -f 2-` to extract this part. The columns are: cycle; A,C,G,T base counts as a percentage of all A/C/G/T bases [%%]\n");
+    for (ibase=0; ibase<stats->max_len; ibase++)
+    {
+        acgtno_count_t *acgtno_count = &(stats->acgtno_revcomp[ibase]);
+        uint64_t acgt_sum = acgtno_count->a + acgtno_count->c + acgtno_count->g + acgtno_count->t;
+        if ( ! acgt_sum ) continue;
+        fprintf(to, "GCT\t%d\t%.2f\t%.2f\t%.2f\t%.2f\n", ibase+1,
+                100.*(acgtno_count->a)/acgt_sum,
+                100.*(acgtno_count->c)/acgt_sum,
+                100.*(acgtno_count->g)/acgt_sum,
+                100.*(acgtno_count->t)/acgt_sum);
+    }
+
+    uint64_t tA=0, tC=0, tG=0, tT=0, tN=0;
+    fprintf(to, "# ACGT content per cycle for first fragments. Use `grep ^FBC | cut -f 2-` to extract this part. The columns are: cycle; A,C,G,T base counts as a percentage of all A/C/G/T bases [%%]; and N and O counts as a percentage of all A/C/G/T bases [%%]\n");
+    for (ibase=0; ibase<stats->max_len; ibase++)
+    {
+        acgtno_count_t *acgtno_count_1st = &(stats->acgtno_cycles_1st[ibase]);
+        uint64_t acgt_sum_1st = acgtno_count_1st->a + acgtno_count_1st->c + acgtno_count_1st->g + acgtno_count_1st->t;
+        tA += acgtno_count_1st->a;
+        tC += acgtno_count_1st->c;
+        tG += acgtno_count_1st->g;
+        tT += acgtno_count_1st->t;
+        tN += acgtno_count_1st->n;
+
+        if ( acgt_sum_1st )
+            fprintf(to, "FBC\t%d\t%.2f\t%.2f\t%.2f\t%.2f\t%.2f\t%.2f\n", ibase+1,
+                    100.*acgtno_count_1st->a/acgt_sum_1st,
+                    100.*acgtno_count_1st->c/acgt_sum_1st,
+                    100.*acgtno_count_1st->g/acgt_sum_1st,
+                    100.*acgtno_count_1st->t/acgt_sum_1st,
+                    100.*acgtno_count_1st->n/acgt_sum_1st,
+                    100.*acgtno_count_1st->other/acgt_sum_1st);
+
+    }
+    fprintf(to, "# ACGT raw counters for first fragments. Use `grep ^FTC | cut -f 2-` to extract this part. The columns are: A,C,G,T,N base counters\n");
+    fprintf(to, "FTC\t%" PRId64 "\t%" PRId64 "\t%" PRId64 "\t%" PRId64 "\t%" PRId64 "\n", tA, tC, tG, tT, tN);
+    tA=0, tC=0, tG=0, tT=0, tN=0;
+    fprintf(to, "# ACGT content per cycle for last fragments. Use `grep ^LBC | cut -f 2-` to extract this part. The columns are: cycle; A,C,G,T base counts as a percentage of all A/C/G/T bases [%%]; and N and O counts as a percentage of all A/C/G/T bases [%%]\n");
+    for (ibase=0; ibase<stats->max_len; ibase++)
+    {
+        acgtno_count_t *acgtno_count_2nd = &(stats->acgtno_cycles_2nd[ibase]);
+        uint64_t acgt_sum_2nd = acgtno_count_2nd->a + acgtno_count_2nd->c + acgtno_count_2nd->g + acgtno_count_2nd->t;
+        tA += acgtno_count_2nd->a;
+        tC += acgtno_count_2nd->c;
+        tG += acgtno_count_2nd->g;
+        tT += acgtno_count_2nd->t;
+        tN += acgtno_count_2nd->n;
+
+        if ( acgt_sum_2nd )
+            fprintf(to, "LBC\t%d\t%.2f\t%.2f\t%.2f\t%.2f\t%.2f\t%.2f\n", ibase+1,
+                    100.*acgtno_count_2nd->a/acgt_sum_2nd,
+                    100.*acgtno_count_2nd->c/acgt_sum_2nd,
+                    100.*acgtno_count_2nd->g/acgt_sum_2nd,
+                    100.*acgtno_count_2nd->t/acgt_sum_2nd,
+                    100.*acgtno_count_2nd->n/acgt_sum_2nd,
+                    100.*acgtno_count_2nd->other/acgt_sum_2nd);
+
+    }
+    fprintf(to, "# ACGT raw counters for last fragments. Use `grep ^LTC | cut -f 2-` to extract this part. The columns are: A,C,G,T,N base counters\n");
+    fprintf(to, "LTC\t%" PRId64 "\t%" PRId64 "\t%" PRId64 "\t%" PRId64 "\t%" PRId64 "\n", tA, tC, tG, tT, tN);
+
+    int tag;
+    for (tag=0; tag<stats->ntags; tag++) {
+        if (stats->tags_barcode[tag].nbases) {
+            fprintf(to, "# ACGT content per cycle for barcodes. Use `grep ^%sC | cut -f 2-` to extract this part. The columns are: cycle; A,C,G,T base counts as a percentage of all A/C/G/T bases [%%]; and N counts as a percentage of all A/C/G/T bases [%%]\n",
+                    stats->tags_barcode[tag].tag_name);
+            for (ibase=0; ibase<stats->tags_barcode[tag].nbases; ibase++)
+            {
+                if (ibase == stats->tags_barcode[tag].tag_sep)
+                    continue;
+
+                acgtno_count_t *acgtno_count = stats->acgtno_barcode + stats->tags_barcode[tag].offset + ibase;
+                uint64_t acgt_sum = acgtno_count->a + acgtno_count->c + acgtno_count->g + acgtno_count->t;
+
+                if ( acgt_sum )
+                    fprintf(to, "%sC%d\t%d\t%.2f\t%.2f\t%.2f\t%.2f\t%.2f\n", stats->tags_barcode[tag].tag_name,
+                            stats->tags_barcode[tag].tag_sep < 0 || ibase < stats->tags_barcode[tag].tag_sep ? 1 : 2,
+                            stats->tags_barcode[tag].tag_sep < 0 || ibase < stats->tags_barcode[tag].tag_sep ? ibase+1 : ibase-stats->tags_barcode[tag].tag_sep,
+                                    100.*acgtno_count->a/acgt_sum,
+                                    100.*acgtno_count->c/acgt_sum,
+                                    100.*acgtno_count->g/acgt_sum,
+                                    100.*acgtno_count->t/acgt_sum,
+                                    100.*acgtno_count->n/acgt_sum);
+            }
+
+            fprintf(to, "# Barcode Qualities. Use `grep ^%sQ | cut -f 2-` to extract this part.\n", stats->tags_barcode[tag].qual_name);
+            fprintf(to, "# Columns correspond to qualities and rows to barcode cycles. First column is the cycle number.\n");
+            for (ibase=0; ibase<stats->tags_barcode[tag].nbases; ibase++)
+            {
+                if (ibase == stats->tags_barcode[tag].tag_sep)
+                    continue;
+
+                fprintf(to, "%sQ%d\t%d", stats->tags_barcode[tag].qual_name,
+                        stats->tags_barcode[tag].tag_sep < 0 || ibase < stats->tags_barcode[tag].tag_sep ? 1 : 2,
+                        stats->tags_barcode[tag].tag_sep < 0 || ibase < stats->tags_barcode[tag].tag_sep ? ibase+1 : ibase-stats->tags_barcode[tag].tag_sep);
+                for (iqual=0; iqual<=stats->tags_barcode[tag].max_qual; iqual++)
+                {
+                    fprintf(to, "\t%ld", (long)stats->quals_barcode[(stats->tags_barcode[tag].offset + ibase)*stats->nquals+iqual]);
+                }
+                fprintf(to, "\n");
+            }
+        }
+    }
+
+    fprintf(to, "# Insert sizes. Use `grep ^IS | cut -f 2-` to extract this part. The columns are: insert size, pairs total, inward oriented pairs, outward oriented pairs, other pairs\n");
+    for (isize=0; isize<ibulk; isize++) {
+        long in = (long)(stats->isize->inward(stats->isize->data, isize));
+        long out = (long)(stats->isize->outward(stats->isize->data, isize));
+        long other = (long)(stats->isize->other(stats->isize->data, isize));
+        if (!sparse || in + out + other > 0) {
+            fprintf(to, "IS\t%d\t%ld\t%ld\t%ld\t%ld\n", isize,  in+out+other,
+                in , out, other);
+        }
+    }
+
+    fprintf(to, "# Read lengths. Use `grep ^RL | cut -f 2-` to extract this part. The columns are: read length, count\n");
+    int ilen;
+    for (ilen=0; ilen<stats->max_len; ilen++)
+    {
+        if ( stats->read_lengths[ilen+1]>0 )
+            fprintf(to, "RL\t%d\t%ld\n", ilen+1, (long)stats->read_lengths[ilen+1]);
+    }
+
+    fprintf(to, "# Read lengths - first fragments. Use `grep ^FRL | cut -f 2-` to extract this part. The columns are: read length, count\n");
+    for (ilen=0; ilen<stats->max_len_1st; ilen++)
+    {
+        if ( stats->read_lengths_1st[ilen+1]>0 )
+            fprintf(to, "FRL\t%d\t%ld\n", ilen+1, (long)stats->read_lengths_1st[ilen+1]);
+    }
+
+    fprintf(to, "# Read lengths - last fragments. Use `grep ^LRL | cut -f 2-` to extract this part. The columns are: read length, count\n");
+    for (ilen=0; ilen<stats->max_len_2nd; ilen++)
+    {
+        if ( stats->read_lengths_2nd[ilen+1]>0 )
+            fprintf(to, "LRL\t%d\t%ld\n", ilen+1, (long)stats->read_lengths_2nd[ilen+1]);
+    }
+
+    fprintf(to, "# Indel distribution. Use `grep ^ID | cut -f 2-` to extract this part. The columns are: length, number of insertions, number of deletions\n");
+
+    for (ilen=0; ilen<stats->nindels; ilen++)
+    {
+        if ( stats->insertions[ilen]>0 || stats->deletions[ilen]>0 )
+            fprintf(to, "ID\t%d\t%ld\t%ld\n", ilen+1, (long)stats->insertions[ilen], (long)stats->deletions[ilen]);
+    }
+
+    fprintf(to, "# Indels per cycle. Use `grep ^IC | cut -f 2-` to extract this part. The columns are: cycle, number of insertions (fwd), .. (rev) , number of deletions (fwd), .. (rev)\n");
+    for (ilen=0; ilen<=stats->nbases; ilen++)
+    {
+        // For deletions we print the index of the cycle before the deleted base (1-based) and for insertions
+        //  the index of the cycle of the first inserted base (also 1-based)
+        if ( stats->ins_cycles_1st[ilen]>0 || stats->ins_cycles_2nd[ilen]>0 || stats->del_cycles_1st[ilen]>0 || stats->del_cycles_2nd[ilen]>0 )
+            fprintf(to, "IC\t%d\t%ld\t%ld\t%ld\t%ld\n", ilen+1, (long)stats->ins_cycles_1st[ilen], (long)stats->ins_cycles_2nd[ilen], (long)stats->del_cycles_1st[ilen], (long)stats->del_cycles_2nd[ilen]);
+    }
+
+    fprintf(to, "# Coverage distribution. Use `grep ^COV | cut -f 2-` to extract this part.\n");
+    if  ( stats->cov[0] )
+        fprintf(to, "COV\t[<%d]\t%d\t%ld\n",stats->info->cov_min,stats->info->cov_min-1, (long)stats->cov[0]);
+    for (icov=1; icov<stats->ncov-1; icov++)
+        if ( stats->cov[icov] )
+            fprintf(to, "COV\t[%d-%d]\t%d\t%ld\n",stats->info->cov_min + (icov-1)*stats->info->cov_step, stats->info->cov_min + icov*stats->info->cov_step-1,stats->info->cov_min + icov*stats->info->cov_step-1, (long)stats->cov[icov]);
+    if ( stats->cov[stats->ncov-1] )
+        fprintf(to, "COV\t[%d<]\t%d\t%ld\n",stats->info->cov_min + (stats->ncov-2)*stats->info->cov_step-1,stats->info->cov_min + (stats->ncov-2)*stats->info->cov_step-1, (long)stats->cov[stats->ncov-1]);
+
+    // Calculate average GC content, then sort by GC and depth
+    fprintf(to, "# GC-depth. Use `grep ^GCD | cut -f 2-` to extract this part. The columns are: GC%%, unique sequence percentiles, 10th, 25th, 50th, 75th and 90th depth percentile\n");
+    uint32_t igcd;
+    for (igcd=0; igcd<stats->igcd; igcd++)
+    {
+        if ( stats->info->fai )
+            stats->gcd[igcd].gc = rint(100. * stats->gcd[igcd].gc);
+        else
+            if ( stats->gcd[igcd].depth )
+                stats->gcd[igcd].gc = rint(100. * stats->gcd[igcd].gc / stats->gcd[igcd].depth);
+    }
+    if ( stats->ngcd )
+        qsort(stats->gcd, stats->igcd+1, sizeof(gc_depth_t), gcd_cmp);
+    igcd = 0;
+    while ( igcd < stats->igcd )
+    {
+        // Calculate percentiles (10,25,50,75,90th) for the current GC content and print
+        uint32_t nbins=0, itmp=igcd;
+        float gc = stats->gcd[igcd].gc;
+        while ( itmp<stats->igcd && fabs(stats->gcd[itmp].gc-gc)<0.1 )
+        {
+            nbins++;
+            itmp++;
+        }
+        fprintf(to, "GCD\t%.1f\t%.3f\t%.3f\t%.3f\t%.3f\t%.3f\t%.3f\n", gc, (igcd+nbins+1)*100./(stats->igcd+1),
+                gcd_percentile(&(stats->gcd[igcd]),nbins,10) *avg_read_length/stats->info->gcd_bin_size,
+                gcd_percentile(&(stats->gcd[igcd]),nbins,25) *avg_read_length/stats->info->gcd_bin_size,
+                gcd_percentile(&(stats->gcd[igcd]),nbins,50) *avg_read_length/stats->info->gcd_bin_size,
+                gcd_percentile(&(stats->gcd[igcd]),nbins,75) *avg_read_length/stats->info->gcd_bin_size,
+                gcd_percentile(&(stats->gcd[igcd]),nbins,90) *avg_read_length/stats->info->gcd_bin_size
+              );
+        igcd += nbins;
+    }
+}
+
+static void init_regions(stats_t *stats, const char *file, stats_info_t* info)
+{
+    FILE *fp = fopen(file,"r");
+    if ( !fp ) error("%s: %s\n",file,strerror(errno));
+
+    kstring_t line = { 0, 0, NULL };
+    int warned = 0, r, p, new_p;
+    int prev_tid=-1;
+    hts_pos_t prev_pos=-1LL;
+    while (line.l = 0, kgetline(&line, (kgets_func *)fgets, fp) >= 0)
+    {
+        if ( line.s[0] == '#' ) continue;
+
+        int i = 0;
+        while ( i<line.l && !isspace(line.s[i]) ) i++;
+        if ( i>=line.l ) error("Could not parse the file: %s [%s]\n", file, line.s);
+        line.s[i] = '\0';
+
+        int tid = bam_name2id(stats->info->sam_header, line.s);
+        if ( tid < 0 )
+        {
+            if ( !warned )
+                fprintf(stderr,"Warning: Some sequences not present in the BAM, e.g. \"%s\". This message is printed only once.\n", line.s);
+            warned = 1;
+            continue;
+        }
+
+        if ( tid >= stats->nregions )
+        {
+            if(!(stats->regions = realloc(stats->regions,sizeof(regions_t)*(tid+REG_INC))))
+                error("Could not allocate memory for region.\n");
+
+            int j;
+            for (j=stats->nregions; j<tid+REG_INC; j++)
+            {
+                stats->regions[j].npos = stats->regions[j].mpos = stats->regions[j].cpos = 0;
+                stats->regions[j].pos = NULL;
+            }
+            stats->nregions = tid+REG_INC;
+        }
+        int npos = stats->regions[tid].npos;
+        if ( npos >= stats->regions[tid].mpos )
+        {
+            stats->regions[tid].mpos = npos+POS_INC;
+            if (!(stats->regions[tid].pos = realloc(stats->regions[tid].pos, sizeof(hts_pair_pos_t)*stats->regions[tid].mpos)))
+                error("Could not allocate memory for interval.\n");
+        }
+
+        if ( (sscanf(&line.s[i+1],"%"SCNd64" %"SCNd64, &stats->regions[tid].pos[npos].beg, &stats->regions[tid].pos[npos].end))!=2 ) error("Could not parse the region [%s]\n", &line.s[i+1]);
+        if ( prev_tid==-1 || prev_tid!=tid )
+        {
+            prev_tid = tid;
+            prev_pos = stats->regions[tid].pos[npos].beg;
+        }
+        if ( prev_pos>stats->regions[tid].pos[npos].beg )
+            error("The positions are not in chromosomal order (%s:%"PRIhts_pos" comes after %"PRIhts_pos")\n", line.s, stats->regions[tid].pos[npos].beg, prev_pos);
+        stats->regions[tid].npos++;
+        if ( stats->regions[tid].npos > stats->nchunks )
+            stats->nchunks = stats->regions[tid].npos;
+    }
+    free(line.s);
+    if ( !stats->regions ) error("Unable to map the -t sequences to the BAM sequences.\n");
+    fclose(fp);
+
+    // sort region intervals and remove duplicates
+    for (r = 0; r < stats->nregions; r++) {
+        regions_t *reg = &stats->regions[r];
+        if ( reg->npos > 1 ) {
+            qsort(reg->pos, reg->npos, sizeof(hts_pair_pos_t), regions_lt);
+            for (new_p = 0, p = 1; p < reg->npos; p++) {
+                if ( reg->pos[new_p].end < reg->pos[p].beg )
+                    reg->pos[++new_p] = reg->pos[p];
+                else if ( reg->pos[new_p].end < reg->pos[p].end )
+                    reg->pos[new_p].end = reg->pos[p].end;
+            }
+            reg->npos = ++new_p;
+        }
+        for (p = 0; p < reg->npos; p++) {
+            if (reg->pos[p].end < HTS_POS_MAX) {
+                stats->target_count += (reg->pos[p].end - reg->pos[p].beg + 1);
+            } else {
+                uint64_t hdr_end = sam_hdr_tid2len(info->sam_header, r);
+                if (hdr_end)
+                    stats->target_count += (hdr_end - reg->pos[p].beg + 1);
+            }
+        }
+    }
+
+    if (!(stats->chunks = calloc(stats->nchunks, sizeof(hts_pair_pos_t))))
+        error("Could not allocate memory for chunk.\n");
+}
+
+void destroy_regions(stats_t *stats)
+{
+    int i;
+    for (i=0; i<stats->nregions; i++)
+    {
+        if ( !stats->regions[i].mpos ) continue;
+        free(stats->regions[i].pos);
+    }
+    if ( stats->regions ) free(stats->regions);
+    if ( stats->chunks ) free(stats->chunks);
+}
+
+void reset_regions(stats_t *stats)
+{
+    int i;
+    for (i=0; i<stats->nregions; i++)
+        stats->regions[i].cpos = 0;
+}
+
+int is_in_regions(bam1_t *bam_line, stats_t *stats)
+{
+    if ( !stats->regions ) return 1;
+
+    if ( bam_line->core.tid >= stats->nregions || bam_line->core.tid<0 ) return 0;
+    if ( !stats->is_sorted ) error("The BAM must be sorted in order for -t to work.\n");
+
+    regions_t *reg = &stats->regions[bam_line->core.tid];
+    if ( reg->cpos==reg->npos ) return 0;       // done for this chr
+
+    // Find a matching interval or skip this read. No splicing of reads is done, no indels or soft clips considered,
+    //  even small overlap is enough to include the read in the stats.
+    int i = reg->cpos;
+    while ( i<reg->npos && reg->pos[i].end<=bam_line->core.pos ) i++;
+    if ( i>=reg->npos ) { reg->cpos = reg->npos; return 0; }
+    int64_t endpos = bam_endpos(bam_line);
+    if ( endpos < reg->pos[i].beg ) return 0;
+
+    //found a read overlapping a region
+    reg->cpos = i;
+    stats->reg_from = reg->pos[i].beg;
+    stats->reg_to   = reg->pos[i].end;
+
+    //now find all the overlapping chunks
+    stats->nchunks = 0;
+    while (i < reg->npos) {
+        if (bam_line->core.pos < reg->pos[i].end && endpos >= reg->pos[i].beg) {
+            stats->chunks[stats->nchunks].beg = MAX(bam_line->core.pos+1, reg->pos[i].beg);
+            stats->chunks[stats->nchunks].end = MIN(endpos, reg->pos[i].end);
+            stats->nchunks++;
+        }
+        i++;
+    }
+
+    return 1;
+}
+
+int replicate_regions(stats_t *stats, hts_itr_multi_t *iter, stats_info_t *info) {
+    if ( !stats || !iter)
+        return 1;
+
+    int i, j, tid;
+    stats->nregions = iter->n_reg;
+    stats->regions = calloc(stats->nregions, sizeof(regions_t));
+    stats->chunks = calloc(stats->nchunks, sizeof(hts_pair_pos_t));
+    if ( !stats->regions || !stats->chunks )
+        return 1;
+
+    for (i = 0; i < iter->n_reg; i++) {
+        tid = iter->reg_list[i].tid;
+        if ( tid < 0 )
+            continue;
+
+        if ( tid >= stats->nregions ) {
+            regions_t *tmp = realloc(stats->regions, (tid+10) * sizeof(regions_t));
+            if ( !tmp )
+                return 1;
+            stats->regions = tmp;
+            memset(stats->regions + stats->nregions, 0,
+                   (tid+10-stats->nregions) * sizeof(regions_t));
+            stats->nregions = tid+10;
+        }
+
+        stats->regions[tid].mpos = stats->regions[tid].npos = iter->reg_list[i].count;
+        stats->regions[tid].pos = calloc(stats->regions[tid].mpos, sizeof(hts_pair_pos_t));
+        if ( !stats->regions[tid].pos )
+            return 1;
+
+        for (j = 0; j < stats->regions[tid].npos; j++) {
+            stats->regions[tid].pos[j].beg = iter->reg_list[i].intervals[j].beg+1;
+            stats->regions[tid].pos[j].end = iter->reg_list[i].intervals[j].end;
+            if (stats->regions[tid].pos[j].end < HTS_POS_MAX) {
+                stats->target_count += (stats->regions[tid].pos[j].end - stats->regions[tid].pos[j].beg + 1);
+            } else {
+                uint64_t hdr_end = sam_hdr_tid2len(info->sam_header, tid);
+                if (hdr_end)
+                    stats->target_count += (hdr_end - stats->regions[tid].pos[j].beg + 1);
+            }
+        }
+    }
+
+    return 0;
+}
+
+static void init_group_id(stats_t *stats, stats_info_t *info, const char *id)
+{
+    stats->rg_hash = kh_init(rg);
+    if (!stats->rg_hash) error("Could not initialise RG set\n");
+    sam_hdr_t *hdr = info->sam_header;
+    const char *key;
+    kstring_t sm = KS_INITIALIZE;
+    int i, ret, nrg = sam_hdr_count_lines(hdr, "RG");
+    if (nrg < 0) error("Could not parse header\n");
+
+    for (i=0; i<nrg; i++) {
+        key = sam_hdr_line_name(hdr, "RG", i);
+        if (!strcmp(key, id)) {
+            kh_put(rg, stats->rg_hash, key, &ret);
+            if (ret == -1) { ks_free(&sm); error("Could not add key \"%s\" to RG set\n", key); }
+        } else { /* Check for SM name, as per manual */
+            if (!sam_hdr_find_tag_pos(hdr, "RG", i, "SM", &sm)) {
+                if (!strcmp(ks_c_str(&sm), id)) {
+                    kh_put(rg, stats->rg_hash, key, &ret);
+                    if (ret == -1) { ks_free(&sm); error("Could not add key \"%s\" to RG set\n", key); }
+                }
+            }
+        }
+    }
+
+    ks_free(&sm);
+}
+
+
+static void HTS_NORETURN error(const char *format, ...)
+{
+    if ( !format )
+    {
+        printf("About: The program collects statistics from BAM files. The output can be visualized using plot-bamstats.\n");
+        printf("Usage: samtools stats [OPTIONS] file.bam\n");
+        printf("       samtools stats [OPTIONS] file.bam chr:from-to\n");
+        printf("Options:\n");
+        printf("    -c, --coverage <int>,<int>,<int>    Coverage distribution min,max,step [1,1000,1]\n");
+        printf("    -d, --remove-dups                   Exclude from statistics reads marked as duplicates\n");
+        printf("    -X, --customized-index-file         Use a customized index file\n");
+        printf("    -f, --required-flag  <str|int>      Required flag, 0 for unset. See also `samtools flags` [0]\n");
+        printf("    -F, --filtering-flag <str|int>      Filtering flag, 0 for unset. See also `samtools flags` [0]\n");
+        printf("        --GC-depth <float>              the size of GC-depth bins (decreasing bin size increases memory requirement) [2e4]\n");
+        printf("    -h, --help                          This help message\n");
+        printf("    -i, --insert-size <int>             Maximum insert size [8000]\n");
+        printf("    -I, --id <string>                   Include only listed read group or sample name\n");
+        printf("    -l, --read-length <int>             Include in the statistics only reads with the given read length [-1]\n");
+        printf("    -m, --most-inserts <float>          Report only the main part of inserts [0.99]\n");
+        printf("    -P, --split-prefix <str>            Path or string prefix for filepaths output by -S (default is input filename)\n");
+        printf("    -q, --trim-quality <int>            The BWA trimming parameter [0]\n");
+        printf("    -r, --ref-seq <file>                Reference sequence (required for GC-depth and mismatches-per-cycle calculation).\n");
+        printf("    -s, --sam                           Ignored (input format is auto-detected).\n");
+        printf("    -S, --split <tag>                   Also write statistics to separate files split by tagged field.\n");
+        printf("    -t, --target-regions <file>         Do stats in these regions only. Tab-delimited file chr,from,to, 1-based, inclusive.\n");
+        printf("    -x, --sparse                        Suppress outputting IS rows where there are no insertions.\n");
+        printf("    -p, --remove-overlaps               Remove overlaps of paired-end reads from coverage and base count computations.\n");
+        printf("    -g, --cov-threshold <int>           Only bases with coverage above this value will be included in the target percentage computation [0]\n");
+        sam_global_opt_help(stdout, "-.--.@-.");
+        printf("\n");
+    }
+    else
+    {
+        va_list ap;
+        va_start(ap, format);
+        vfprintf(stderr, format, ap);
+        va_end(ap);
+    }
+    exit(1);
+}
+
+void cleanup_stats_info(stats_info_t* info){
+    if (info->fai) fai_destroy(info->fai);
+    sam_close(info->sam);
+    free(info);
+}
+
+void cleanup_stats(stats_t* stats)
+{
+    free(stats->cov_rbuf.buffer); free(stats->cov);
+    free(stats->quals_1st); free(stats->quals_2nd);
+    free(stats->gc_1st); free(stats->gc_2nd);
+    stats->isize->isize_free(stats->isize->data);
+    free(stats->isize);
+    free(stats->gcd);
+    free(stats->rseq_buf);
+    free(stats->mpc_buf);
+    free(stats->acgtno_cycles_1st);
+    free(stats->acgtno_cycles_2nd);
+    free(stats->acgtno_revcomp);
+    free(stats->read_lengths);
+    free(stats->read_lengths_1st);
+    free(stats->read_lengths_2nd);
+    free(stats->insertions);
+    free(stats->deletions);
+    free(stats->ins_cycles_1st);
+    free(stats->ins_cycles_2nd);
+    free(stats->del_cycles_1st);
+    free(stats->del_cycles_2nd);
+    if (stats->acgtno_barcode) free(stats->acgtno_barcode);
+    if (stats->quals_barcode) free(stats->quals_barcode);
+    free(stats->tags_barcode);
+    destroy_regions(stats);
+    if ( stats->rg_hash ) kh_destroy(rg, stats->rg_hash);
+    free(stats->split_name);
+    free(stats);
+}
+
+void output_split_stats(khash_t(c2stats) *split_hash, char* bam_fname, int sparse)
+{
+    int i = 0;
+    kstring_t output_filename = { 0, 0, NULL };
+    stats_t *curr_stats = NULL;
+    for(i = kh_begin(split_hash); i != kh_end(split_hash); ++i){
+        if(!kh_exist(split_hash, i)) continue;
+        curr_stats = kh_value(split_hash, i);
+        round_buffer_flush(curr_stats, -1);
+
+        output_filename.l = 0;
+        if (curr_stats->info->split_prefix)
+            kputs(curr_stats->info->split_prefix, &output_filename);
+        else
+            kputs(bam_fname, &output_filename);
+        kputc('_', &output_filename);
+        kputs(curr_stats->split_name, &output_filename);
+        kputs(".bamstat", &output_filename);
+
+        FILE *to = fopen(output_filename.s, "w");
+        if(to == NULL){
+            error("Could not open '%s' for writing.\n", output_filename.s);
+        }
+        output_stats(to, curr_stats, sparse);
+        fclose(to);
+    }
+
+    free(output_filename.s);
+}
+
+void destroy_split_stats(khash_t(c2stats) *split_hash)
+{
+    if (!split_hash)
+        return;
+
+    int i = 0;
+    stats_t *curr_stats = NULL;
+    for(i = kh_begin(split_hash); i != kh_end(split_hash); ++i){
+        if(!kh_exist(split_hash, i)) continue;
+        curr_stats = kh_value(split_hash, i);
+        cleanup_stats(curr_stats);
+    }
+    kh_destroy(c2stats, split_hash);
+}
+
+stats_info_t* stats_info_init(int argc, char *argv[])
+{
+    stats_info_t* info = calloc(1, sizeof(stats_info_t));
+    if (!info) {
+        return NULL;
+    }
+
+    info->nisize = 8000;
+    info->isize_main_bulk = 0.99;   // There are always outliers at the far end
+    info->gcd_bin_size = 20e3;
+    info->cov_min  = 1;
+    info->cov_max  = 1000;
+    info->cov_step = 1;
+    info->filter_readlen = -1;
+    info->argc = argc;
+    info->argv = argv;
+    info->remove_overlaps = 0;
+    info->cov_threshold = 0;
+
+    return info;
+}
+
+int init_stat_info_fname(stats_info_t* info, const char* bam_fname, const htsFormat* in_fmt)
+{
+    // .. bam
+    samFile* sam;
+    if ((sam = sam_open_format(bam_fname, "r", in_fmt)) == 0) {
+        print_error_errno("stats", "failed to open \"%s\"", bam_fname);
+        return 1;
+    }
+    info->sam = sam;
+    info->sam_header = sam_hdr_read(sam);
+    if (info->sam_header == NULL) {
+        print_error("stats", "failed to read header for \"%s\"", bam_fname);
+        return 1;
+    }
+    return 0;
+}
+
+stats_t* stats_init()
+{
+    stats_t *stats = calloc(1,sizeof(stats_t));
+    if (!stats)
+        return NULL;
+
+    stats->ngc    = 200;
+    stats->nquals = 256;
+    stats->nbases = 300;
+    stats->rseq_pos     = -1;
+    stats->tid = -1;
+    stats->gcd_pos = -1LL;
+    stats->igcd = 0;
+    stats->is_sorted = 1;
+    stats->nindels = stats->nbases;
+    stats->split_name = NULL;
+    stats->nchunks = 0;
+    stats->pair_count = 0;
+    stats->last_pair_tid = -2;
+    stats->last_read_flush = 0;
+    stats->target_count = 0;
+
+    return stats;
+}
+
+static int init_barcode_tags(stats_t* stats) {
+    stats->ntags = 4;
+    stats->tags_barcode = calloc(stats->ntags, sizeof(barcode_info_t));
+    if (!stats->tags_barcode)
+        return -1;
+    stats->tags_barcode[0] = (barcode_info_t){"BC", "QT", 0, -1, -1, 0};
+    stats->tags_barcode[1] = (barcode_info_t){"CR", "CY", 0, -1, -1, 0};
+    stats->tags_barcode[2] = (barcode_info_t){"OX", "BZ", 0, -1, -1, 0};
+    stats->tags_barcode[3] = (barcode_info_t){"RX", "QX", 0, -1, -1, 0};
+    return 0;
+}
+
+static void init_stat_structs(stats_t* stats, stats_info_t* info, const char* group_id, const char* targets)
+{
+    // Give stats_t a pointer to the info struct
+    // This saves us having to pass the stats_info_t to every function
+    stats->info = info;
+
+    // Init structures
+    //  .. coverage bins and round buffer
+    if ( info->cov_step > info->cov_max - info->cov_min + 1 )
+    {
+        info->cov_step = info->cov_max - info->cov_min;
+        if ( info->cov_step <= 0 )
+            info->cov_step = 1;
+    }
+    stats->ncov = 3 + (info->cov_max-info->cov_min) / info->cov_step;
+    info->cov_max = info->cov_min + ((info->cov_max-info->cov_min)/info->cov_step +1)*info->cov_step - 1;
+    stats->cov = calloc(sizeof(uint64_t),stats->ncov);
+    if (!stats->cov) goto nomem;
+    stats->cov_rbuf.size = stats->nbases*5;
+    stats->cov_rbuf.buffer = calloc(sizeof(int32_t),stats->cov_rbuf.size);
+    if (!stats->cov_rbuf.buffer) goto nomem;
+    if ( group_id ) init_group_id(stats, info, group_id);
+    // .. arrays
+    stats->quals_1st      = calloc(stats->nquals*stats->nbases,sizeof(uint64_t));
+    if (!stats->quals_1st) goto nomem;
+    stats->quals_2nd      = calloc(stats->nquals*stats->nbases,sizeof(uint64_t));
+    if (!stats->quals_2nd) goto nomem;
+    stats->gc_1st         = calloc(stats->ngc,sizeof(uint64_t));
+    if (!stats->gc_1st) goto nomem;
+    stats->gc_2nd         = calloc(stats->ngc,sizeof(uint64_t));
+    if (!stats->gc_2nd) goto nomem;
+    stats->isize          = init_isize_t(info->nisize ?info->nisize+1 :0);
+    if (!stats->isize) goto nomem;
+    stats->gcd            = calloc(stats->ngcd,sizeof(gc_depth_t));
+    if (!stats->gcd) goto nomem;
+    if (info->fai) {
+        stats->mpc_buf    = calloc(stats->nquals*stats->nbases,sizeof(uint64_t));
+        if (!stats->mpc_buf) goto nomem;
+    } else {
+        stats->mpc_buf    = NULL;
+    }
+    stats->acgtno_cycles_1st  = calloc(stats->nbases,sizeof(acgtno_count_t));
+    if (!stats->acgtno_cycles_1st) goto nomem;
+    stats->acgtno_cycles_2nd  = calloc(stats->nbases,sizeof(acgtno_count_t));
+    if (!stats->acgtno_cycles_2nd) goto nomem;
+    stats->acgtno_revcomp  = calloc(stats->nbases,sizeof(acgtno_count_t));
+    if (!stats->acgtno_revcomp) goto nomem;
+    stats->read_lengths   = calloc(stats->nbases,sizeof(uint64_t));
+    if (!stats->read_lengths)     goto nomem;
+    stats->read_lengths_1st   = calloc(stats->nbases,sizeof(uint64_t));
+    if (!stats->read_lengths_1st) goto nomem;
+    stats->read_lengths_2nd   = calloc(stats->nbases,sizeof(uint64_t));
+    if (!stats->read_lengths_2nd) goto nomem;
+    stats->insertions     = calloc(stats->nbases,sizeof(uint64_t));
+    if (!stats->insertions) goto nomem;
+    stats->deletions      = calloc(stats->nbases,sizeof(uint64_t));
+    if (!stats->deletions)  goto nomem;
+    stats->ins_cycles_1st = calloc(stats->nbases+1,sizeof(uint64_t));
+    if (!stats->ins_cycles_1st) goto nomem;
+    stats->ins_cycles_2nd = calloc(stats->nbases+1,sizeof(uint64_t));
+    if (!stats->ins_cycles_2nd) goto nomem;
+    stats->del_cycles_1st = calloc(stats->nbases+1,sizeof(uint64_t));
+    if (!stats->del_cycles_1st) goto nomem;
+    stats->del_cycles_2nd = calloc(stats->nbases+1,sizeof(uint64_t));
+    if (!stats->del_cycles_2nd) goto nomem;
+    if (init_barcode_tags(stats) < 0)
+        goto nomem;
+    realloc_rseq_buffer(stats);
+    if ( targets )
+        init_regions(stats, targets, info);
+    return;
+ nomem:
+    error("Out of memory");
+}
+
+static stats_t* get_curr_split_stats(bam1_t* bam_line, khash_t(c2stats)* split_hash, stats_info_t* info, char* targets)
+{
+    stats_t *curr_stats = NULL;
+    const uint8_t *tag_val = bam_aux_get(bam_line, info->split_tag);
+    if(tag_val == 0){
+        error("Tag '%s' not found in bam_line.\n", info->split_tag);
+    }
+    char* split_name = strdup(bam_aux2Z(tag_val));
+
+    // New stats object, under split
+    khiter_t k = kh_get(c2stats, split_hash, split_name);
+    if(k == kh_end(split_hash)){
+        curr_stats = stats_init(); // mallocs new instance
+        if (!curr_stats) {
+            error("Couldn't allocate split stats");
+        }
+        init_stat_structs(curr_stats, info, NULL, targets);
+        curr_stats->split_name = split_name;
+
+        // Record index in hash
+        int ret = 0;
+        khiter_t iter = kh_put(c2stats, split_hash, split_name, &ret);
+        if( ret < 0 ){
+            error("Failed to insert key '%s' into split_hash", split_name);
+        }
+        kh_val(split_hash, iter) = curr_stats; // store pointer to stats
+    }
+    else{
+        curr_stats = kh_value(split_hash, k);
+        free(split_name); // don't need to hold on to this if it wasn't new
+    }
+    return curr_stats;
+}
+
+int main_stats(int argc, char *argv[])
+{
+    char *targets = NULL;
+    char *bam_fname = NULL;
+    char *bam_idx_fname = NULL;
+    char *group_id = NULL;
+    int sparse = 0, has_index_file = 0, ret = 1;
+    sam_global_args ga = SAM_GLOBAL_ARGS_INIT;
+
+    stats_info_t *info = stats_info_init(argc, argv);
+    if (!info) {
+        fprintf(stderr, "Could not allocate memory for info.\n");
+        return 1;
+    }
+
+    static const struct option loptions[] =
+    {
+        SAM_OPT_GLOBAL_OPTIONS('-', 0, '-', '-', 0, '@'),
+        {"help", no_argument, NULL, 'h'},
+        {"remove-dups", no_argument, NULL, 'd'},
+        {"sam", no_argument, NULL, 's'},
+        {"customized-index-file", required_argument, NULL, 'X'},
+        {"ref-seq", required_argument, NULL, 'r'},
+        {"coverage", required_argument, NULL, 'c'},
+        {"read-length", required_argument, NULL, 'l'},
+        {"insert-size", required_argument, NULL, 'i'},
+        {"most-inserts", required_argument, NULL, 'm'},
+        {"trim-quality", required_argument, NULL, 'q'},
+        {"target-regions", required_argument, NULL, 't'},
+        {"required-flag", required_argument, NULL, 'f'},
+        {"filtering-flag", required_argument, NULL, 'F'},
+        {"id", required_argument, NULL, 'I'},
+        {"GC-depth", required_argument, NULL, 1},
+        {"sparse", no_argument, NULL, 'x'},
+        {"split", required_argument, NULL, 'S'},
+        {"split-prefix", required_argument, NULL, 'P'},
+        {"remove-overlaps", no_argument, NULL, 'p'},
+        {"cov-threshold", required_argument, NULL, 'g'},
+        {NULL, 0, NULL, 0}
+    };
+    int opt;
+
+    while ( (opt=getopt_long(argc,argv,"?hdsXxpr:c:l:i:t:m:q:f:F:g:I:S:P:@:",loptions,NULL))>0 )
+    {
+        switch (opt)
+        {
+            case 'f': info->flag_require = bam_str2flag(optarg); break;
+            case 'F': info->flag_filter |= bam_str2flag(optarg); break;
+            case 'd': info->flag_filter |= BAM_FDUP; break;
+            case 'X': has_index_file = 1; break;
+            case 's': break;
+            case 'r': info->fai = fai_load(optarg);
+                      if (info->fai==NULL)
+                          error("Could not load faidx: %s\n", optarg);
+                      break;
+            case  1 : info->gcd_bin_size = atof(optarg); break;
+            case 'c': if ( sscanf(optarg,"%d,%d,%d",&info->cov_min,&info->cov_max,&info->cov_step)!= 3 )
+                          error("Unable to parse -c %s\n", optarg);
+                      break;
+            case 'l': info->filter_readlen = atoi(optarg); break;
+            case 'i': info->nisize = atoi(optarg); break;
+            case 'm': info->isize_main_bulk = atof(optarg); break;
+            case 'q': info->trim_qual = atoi(optarg); break;
+            case 't': targets = optarg; break;
+            case 'I': group_id = optarg; break;
+            case 'x': sparse = 1; break;
+            case 'S': info->split_tag = optarg; break;
+            case 'P': info->split_prefix = optarg; break;
+            case 'p': info->remove_overlaps = 1; break;
+            case 'g': info->cov_threshold = atoi(optarg);
+                      if ( info->cov_threshold < 0 || info->cov_threshold == INT_MAX )
+                          error("Unsupported value for coverage threshold %d\n", info->cov_threshold);
+                      break;
+            case '?':
+            case 'h': error(NULL);
+            /* no break */
+            default:
+                if (parse_sam_global_opt(opt, optarg, loptions, &ga) != 0)
+                    error("Unknown argument: %s\n", optarg);
+                break;
+        }
+    }
+
+    bam_fname = argv[optind++];
+    if ( !bam_fname )
+    {
+        if ( isatty(STDIN_FILENO) )
+            error(NULL);
+        bam_fname = "-";
+    }
+
+    if (init_stat_info_fname(info, bam_fname, &ga.in)) {
+        cleanup_stats_info(info);
+        return 1;
+    }
+
+    if (has_index_file && !(bam_idx_fname = argv[optind++])) {
+        fprintf(stderr, "No index file provided\n");
+        cleanup_stats_info(info);
+        return 1;
+    }
+
+    if (ga.nthreads > 0)
+        hts_set_threads(info->sam, ga.nthreads);
+
+    stats_t *all_stats = stats_init();
+    if (!all_stats) {
+        fprintf(stderr, "Could not allocate memory for stats.\n");
+        cleanup_stats_info(info);
+        return 1;
+    }
+    stats_t *curr_stats = NULL;
+    init_stat_structs(all_stats, info, group_id, targets);
+    // Init
+    // .. hash
+    khash_t(c2stats)* split_hash = kh_init(c2stats);
+    if (!split_hash) goto cleanup_all_stats;
+
+    khash_t(qn2pair)* read_pairs = kh_init(qn2pair);
+    if (!read_pairs) goto cleanup_split_hash;
+
+    // Collect statistics
+    bam1_t *bam_line = bam_init1();
+    if (!bam_line) goto cleanup_read_pairs;
+
+    if (optind < argc) {
+        // Region:interval arguments in the command line
+        hts_idx_t *bam_idx = NULL;
+        if (has_index_file) {
+            bam_idx = sam_index_load2(info->sam, bam_fname, bam_idx_fname);
+        } else {
+            // If an index filename has not been specified, look alongside the alignment file
+            bam_idx = sam_index_load(info->sam, bam_fname);
+        }
+
+        if (bam_idx) {
+            hts_itr_multi_t *iter = sam_itr_regarray(bam_idx, info->sam_header, &argv[optind], argc - optind);
+            if (iter) {
+                if (!targets) {
+                    all_stats->nchunks = argc-optind;
+                    if (replicate_regions(all_stats, iter, info))
+                        fprintf(stderr, "Replications of the regions failed\n");
+                }
+
+                if ( all_stats->nregions && all_stats->regions ) {
+                    while ((ret = sam_itr_next(info->sam, iter, bam_line)) >= 0) {
+                        if (info->split_tag) {
+                            curr_stats = get_curr_split_stats(bam_line, split_hash, info, targets);
+                            collect_stats(bam_line, curr_stats, read_pairs);
+                        }
+                        collect_stats(bam_line, all_stats, read_pairs);
+                    }
+
+                    if (ret < -1) {
+                        fprintf(stderr, "Failure while running the iterator\n");
+                        hts_itr_multi_destroy(iter);
+                        hts_idx_destroy(bam_idx);
+                        goto cleanup;
+                    }
+                }
+                hts_itr_multi_destroy(iter);
+            } else {
+                fprintf(stderr, "Multi-region iterator could not be created\n");
+                hts_idx_destroy(bam_idx);
+                goto cleanup;
+            }
+            hts_idx_destroy(bam_idx);
+        } else {
+            if (has_index_file)
+                fprintf(stderr, "Invalid index file '%s'\n", bam_idx_fname);
+            fprintf(stderr, "Random alignment retrieval only works for indexed files\n");
+            goto cleanup;
+        }
+    } else {
+        if ( info->cov_threshold > 0 && !targets ) {
+            fprintf(stderr, "Coverage percentage calculation requires a list of target regions\n");
+            goto cleanup;
+        }
+
+        // Stream through the entire BAM ignoring off-target regions if -t is given
+        while ((ret = sam_read1(info->sam, info->sam_header, bam_line)) >= 0) {
+            if (info->split_tag) {
+                curr_stats = get_curr_split_stats(bam_line, split_hash, info, targets);
+                collect_stats(bam_line, curr_stats, read_pairs);
+            }
+            collect_stats(bam_line, all_stats, read_pairs);
+        }
+
+        if (ret < -1) {
+            fprintf(stderr, "Failure while decoding file\n");
+            goto cleanup;
+        }
+    }
+
+    round_buffer_flush(all_stats, -1);
+    output_stats(stdout, all_stats, sparse);
+    if (info->split_tag)
+        output_split_stats(split_hash, bam_fname, sparse);
+
+    ret = 0;
+cleanup:
+    bam_destroy1(bam_line);
+    sam_hdr_destroy(info->sam_header);
+    sam_global_args_free(&ga);
+
+cleanup_read_pairs:
+    cleanup_overlaps(read_pairs, INT64_MAX);
+cleanup_split_hash:
+    destroy_split_stats(split_hash);
+cleanup_all_stats:
+    cleanup_stats(all_stats);
+    cleanup_stats_info(info);
+
+    return ret;
+}
diff --git a/samtools/stats.c.pysam.c b/samtools/stats.c.pysam.c
new file mode 100644
index 0000000..5158827
--- /dev/null
+++ b/samtools/stats.c.pysam.c
@@ -0,0 +1,2580 @@
+#include "samtools.pysam.h"
+
+/*  stats.c -- This is the former bamcheck integrated into samtools/htslib.
+
+    Copyright (C) 2012-2021 Genome Research Ltd.
+
+    Author: Petr Danecek <pd3@sanger.ac.uk>
+    Author: Sam Nicholls <sam@samnicholls.net>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+/*  Assumptions, approximations and other issues:
+        - GC-depth graph does not split reads, the starting position determines which bin is incremented.
+            There are small overlaps between bins (max readlen-1). However, the bins are big (20k).
+        - coverage distribution ignores softclips and deletions
+        - some stats require sorted BAMs
+        - GC content graph can have an untidy, step-like pattern when BAM contains multiple read lengths.
+        - 'bases mapped' (stats->nbases_mapped) is calculated from read lengths given by BAM (core.l_qseq)
+        - With the -t option, the whole reads are used. Except for the number of mapped bases (cigar)
+            counts, no splicing is done, no indels or soft clips are considered, even small overlap is
+            good enough to include the read in the stats.
+        - GC content of reads not calculated for "=" sequences
+
+*/
+
+#include <config.h>
+
+#include <unistd.h> // for isatty()
+#include <stdio.h>
+#include <stdlib.h>
+#include <stdarg.h>
+#include <string.h>
+#include <math.h>
+#include <ctype.h>
+#include <inttypes.h>
+#include <getopt.h>
+#include <errno.h>
+#include <assert.h>
+#include <zlib.h>   // for crc32
+#include <htslib/faidx.h>
+#include <htslib/sam.h>
+#include <htslib/hts.h>
+#include <htslib/hts_defs.h>
+#include "samtools.h"
+#include <htslib/khash.h>
+#include <htslib/kstring.h>
+#include "stats_isize.h"
+#include "sam_opts.h"
+#include "bedidx.h"
+
+#define BWA_MIN_RDLEN 35
+#define DEFAULT_CHUNK_NO 8
+#define DEFAULT_PAIR_MAX 10000
+#define ERROR_LIMIT 200
+// From the spec
+// If 0x4 is set, no assumptions can be made about RNAME, POS, CIGAR, MAPQ, bits 0x2, 0x10, 0x100 and 0x800, and the bit 0x20 of the previous read in the template.
+#define IS_PAIRED(bam) ((bam)->core.flag&BAM_FPAIRED)
+#define IS_PAIRED_AND_MAPPED(bam) (((bam)->core.flag&BAM_FPAIRED) && !((bam)->core.flag&BAM_FUNMAP) && !((bam)->core.flag&BAM_FMUNMAP))
+#define IS_PROPERLYPAIRED(bam) (((bam)->core.flag&(BAM_FPAIRED|BAM_FPROPER_PAIR)) == (BAM_FPAIRED|BAM_FPROPER_PAIR) && !((bam)->core.flag&BAM_FUNMAP))
+#define IS_UNMAPPED(bam) ((bam)->core.flag&BAM_FUNMAP)
+#define IS_REVERSE(bam) ((bam)->core.flag&BAM_FREVERSE)
+#define IS_MATE_REVERSE(bam) ((bam)->core.flag&BAM_FMREVERSE)
+#define IS_READ1(bam) ((bam)->core.flag&BAM_FREAD1)
+#define IS_READ2(bam) ((bam)->core.flag&BAM_FREAD2)
+#define IS_DUP(bam) ((bam)->core.flag&BAM_FDUP)
+#define IS_ORIGINAL(bam) (((bam)->core.flag&(BAM_FSECONDARY|BAM_FSUPPLEMENTARY)) == 0)
+
+#define READ_ORDER_NONE 0
+#define READ_ORDER_FIRST 1
+#define READ_ORDER_LAST 2
+#define READ_ORDER_MIDDLE 3
+
+#define REG_INC 100
+#define POS_INC 1000
+
+// The GC-depth graph works as follows: split the reference sequence into
+// segments and calculate GC content and depth in each bin. Then sort
+// these segments by their GC and plot the depth distribution by means
+// of 10th, 25th, etc. depth percentiles.
+typedef struct
+{
+    float gc;
+    uint32_t depth;
+}
+gc_depth_t;
+
+// For coverage distribution, a simple pileup
+typedef struct
+{
+    hts_pos_t pos;
+    int size, start;
+    int *buffer;
+}
+round_buffer_t;
+
+typedef struct
+{
+    int npos, mpos, cpos;
+    hts_pair_pos_t *pos;
+}
+regions_t;
+
+typedef struct
+{
+    uint64_t a;
+    uint64_t c;
+    uint64_t g;
+    uint64_t t;
+    uint64_t n;
+    uint64_t other;
+}
+acgtno_count_t;
+
+typedef struct
+{
+    char tag_name[3];
+    char qual_name[3];
+    uint32_t nbases;
+    int32_t tag_sep;    // Index of the separator (if present)
+    int32_t max_qual;
+    uint32_t offset;    // Where the tag stats info is located in the allocated memory
+}
+barcode_info_t;
+
+typedef struct
+{
+    // Auxiliary data
+    int flag_require, flag_filter;
+    faidx_t *fai;                   // Reference sequence for GC-depth graph
+    int argc;                       // Command line arguments to be printed on the output
+    char **argv;
+    int gcd_bin_size;           // The size of GC-depth bin
+    int nisize;         // The maximum insert size that the allocated array can hold - 0 indicates no limit
+    int trim_qual;      // bwa trim quality
+    float isize_main_bulk;  // There are always some unrealistically big insert sizes, report only the main part
+    int cov_min,cov_max,cov_step;   // Minimum, maximum coverage and size of the coverage bins
+    samFile* sam;
+    sam_hdr_t* sam_header;
+
+    // Filters
+    int filter_readlen;
+
+    // Misc
+    char *split_tag;      // Tag on which to perform stats splitting
+    char *split_prefix;   // Path or string prefix for filenames created when splitting
+    int remove_overlaps;
+    int cov_threshold;
+}
+stats_info_t;
+
+typedef struct
+{
+    // Dimensions of the quality histogram holder (quals_1st,quals_2nd), GC content holder (gc_1st,gc_2nd),
+    //  insert size histogram holder
+    int nquals;         // The number of quality bins
+    int nbases;         // The maximum sequence length the allocated array can hold
+    int ngc;            // The size of gc_1st and gc_2nd
+    int nindels;        // The maximum indel length for indel distribution
+
+    // Arrays for the histogram data
+    uint64_t *quals_1st, *quals_2nd;
+    uint64_t *gc_1st, *gc_2nd;
+    acgtno_count_t *acgtno_cycles_1st, *acgtno_cycles_2nd;
+    acgtno_count_t *acgtno_revcomp;
+    uint64_t *read_lengths, *read_lengths_1st, *read_lengths_2nd;
+    uint64_t *insertions, *deletions;
+    uint64_t *ins_cycles_1st, *ins_cycles_2nd, *del_cycles_1st, *del_cycles_2nd;
+    isize_t *isize;
+
+    // The extremes encountered
+    int max_len;            // Maximum read length
+    int max_len_1st;        // Maximum read length for forward reads
+    int max_len_2nd;        // Maximum read length for reverse reads
+    int max_qual;           // Maximum quality
+    int is_sorted;
+
+    // Summary numbers
+    uint64_t total_len;
+    uint64_t total_len_1st;
+    uint64_t total_len_2nd;
+    uint64_t total_len_dup;
+    uint64_t nreads_1st;
+    uint64_t nreads_2nd;
+    uint64_t nreads_other;
+    uint64_t nreads_filtered;
+    uint64_t nreads_dup;
+    uint64_t nreads_unmapped;
+    uint64_t nreads_single_mapped;
+    uint64_t nreads_paired_and_mapped;
+    uint64_t nreads_properly_paired;
+    uint64_t nreads_paired_tech;
+    uint64_t nreads_anomalous;
+    uint64_t nreads_mq0;
+    uint64_t nbases_mapped;
+    uint64_t nbases_mapped_cigar;
+    uint64_t nbases_trimmed;  // bwa trimmed bases
+    uint64_t nmismatches;
+    uint64_t nreads_QCfailed, nreads_secondary, nreads_supplementary;
+    struct {
+        uint32_t names, reads, quals;
+    } checksum;
+
+    // GC-depth related data
+    uint32_t ngcd, igcd;        // The maximum number of GC depth bins and index of the current bin
+    gc_depth_t *gcd;            // The GC-depth bins holder
+    int32_t tid;                // Position of the current bin
+    hts_pos_t gcd_pos, pos;     // Position of the last read
+
+    // Coverage distribution related data
+    int ncov;                       // The number of coverage bins
+    uint64_t *cov;                  // The coverage frequencies
+    round_buffer_t cov_rbuf;        // Pileup round buffer
+
+    // Mismatches by read cycle
+    uint8_t *rseq_buf;              // A buffer for reference sequence to check the mismatches against
+    int mrseq_buf;                  // The size of the buffer
+    hts_pos_t rseq_pos;             // The coordinate of the first base in the buffer
+    int64_t nrseq_buf;              // The used part of the buffer
+    uint64_t *mpc_buf;              // Mismatches per cycle
+
+    // Target regions
+    int nregions;
+    hts_pos_t reg_from, reg_to;
+    regions_t *regions;
+
+    // Auxiliary data
+    double sum_qual;                // For calculating average quality value
+    void *rg_hash;                  // Read groups to include, the array is null-terminated
+
+    // Split
+    char* split_name;
+
+    stats_info_t* info;             // Pointer to options and settings struct
+    hts_pair_pos_t *chunks;
+    uint32_t nchunks;
+
+    uint32_t pair_count;          // Number of active pairs in the pairing hash table
+    uint64_t target_count;        // Number of bases covered by the target file
+    uint32_t last_pair_tid;
+    uint32_t last_read_flush;
+
+    // Barcode statistics
+    acgtno_count_t *acgtno_barcode;
+    uint64_t *quals_barcode;
+    barcode_info_t *tags_barcode;
+    uint32_t ntags;
+    uint32_t error_number;
+}
+stats_t;
+KHASH_MAP_INIT_STR(c2stats, stats_t*)
+
+typedef struct {
+    uint32_t first;     // 1 - first read, 2 - second read
+    uint32_t n, m;      // number of chunks, allocated chunks
+    hts_pair_pos_t *chunks;      // chunk array of size m
+} pair_t;
+KHASH_MAP_INIT_STR(qn2pair, pair_t*)
+
+KHASH_SET_INIT_STR(rg)
+
+
+static void HTS_NORETURN error(const char *format, ...);
+int is_in_regions(bam1_t *bam_line, stats_t *stats);
+void realloc_buffers(stats_t *stats, int seq_len);
+
+static int regions_lt(const void *r1, const void *r2) {
+    int64_t from_diff = ((hts_pair_pos_t *)r1)->beg - ((hts_pair_pos_t *)r2)->beg;
+    int64_t to_diff   = ((hts_pair_pos_t *)r1)->end - ((hts_pair_pos_t *)r2)->end;
+
+    return from_diff > 0 ? 1 : from_diff < 0 ? -1 : to_diff > 0 ? 1 : to_diff < 0 ? -1 : 0;
+}
+
+// Coverage distribution methods
+static inline int coverage_idx(int min, int max, int n, int step, int depth)
+{
+    if ( depth < min )
+        return 0;
+
+    if ( depth > max )
+        return n-1;
+
+    return 1 + (depth - min) / step;
+}
+
+static inline int round_buffer_lidx2ridx(int offset, int size, hts_pos_t refpos, hts_pos_t pos)
+{
+    return (offset + (pos-refpos) % size) % size;
+}
+
+void round_buffer_flush(stats_t *stats, hts_pos_t pos)
+{
+    int ibuf,idp;
+
+    if ( pos==stats->cov_rbuf.pos )
+        return;
+
+    hts_pos_t new_pos = pos;
+    if ( pos==-1 || pos - stats->cov_rbuf.pos >= stats->cov_rbuf.size )
+    {
+        // Flush the whole buffer, but in sequential order,
+        pos = stats->cov_rbuf.pos + stats->cov_rbuf.size - 1;
+    }
+
+    if ( pos < stats->cov_rbuf.pos )
+        error("Expected coordinates in ascending order, got %"PRIhts_pos" after %"PRIhts_pos"\n", pos, stats->cov_rbuf.pos);
+
+    int ifrom = stats->cov_rbuf.start;
+    int ito = round_buffer_lidx2ridx(stats->cov_rbuf.start, stats->cov_rbuf.size, stats->cov_rbuf.pos, pos-1);
+    if ( ifrom>ito )
+    {
+        for (ibuf=ifrom; ibuf<stats->cov_rbuf.size; ibuf++)
+        {
+            if ( !stats->cov_rbuf.buffer[ibuf] )
+                continue;
+            idp = coverage_idx(stats->info->cov_min,stats->info->cov_max,stats->ncov,stats->info->cov_step,stats->cov_rbuf.buffer[ibuf]);
+            stats->cov[idp]++;
+            stats->cov_rbuf.buffer[ibuf] = 0;
+        }
+        ifrom = 0;
+    }
+    for (ibuf=ifrom; ibuf<=ito; ibuf++)
+    {
+        if ( !stats->cov_rbuf.buffer[ibuf] )
+            continue;
+        idp = coverage_idx(stats->info->cov_min,stats->info->cov_max,stats->ncov,stats->info->cov_step,stats->cov_rbuf.buffer[ibuf]);
+        stats->cov[idp]++;
+        stats->cov_rbuf.buffer[ibuf] = 0;
+    }
+    stats->cov_rbuf.start = (new_pos==-1) ? 0 : round_buffer_lidx2ridx(stats->cov_rbuf.start, stats->cov_rbuf.size, stats->cov_rbuf.pos, pos);
+    stats->cov_rbuf.pos   = new_pos;
+}
+
+/**
+ * [from, to) - 0 based half-open
+ */
+static void round_buffer_insert_read(round_buffer_t *rbuf, hts_pos_t from, hts_pos_t to)
+{
+    if ( to-from > rbuf->size )
+        error("The read length too big (%"PRIhts_pos"), please increase the buffer length (currently %d)\n", to-from, rbuf->size);
+    if ( from < rbuf->pos )
+        error("The reads are not sorted (%"PRIhts_pos" comes after %"PRIhts_pos").\n", from, rbuf->pos);
+
+    int ifrom, ito, ibuf;
+    ifrom = round_buffer_lidx2ridx(rbuf->start, rbuf->size, rbuf->pos, from);
+    ito   = round_buffer_lidx2ridx(rbuf->start, rbuf->size, rbuf->pos, to);
+    if ( ifrom>ito )
+    {
+        for (ibuf=ifrom; ibuf<rbuf->size; ibuf++)
+            rbuf->buffer[ibuf]++;
+        ifrom = 0;
+    }
+    for (ibuf=ifrom; ibuf<ito; ibuf++)
+        rbuf->buffer[ibuf]++;
+}
+
+// Calculate the number of bases in the read trimmed by BWA
+int bwa_trim_read(int trim_qual, uint8_t *quals, int len, int reverse)
+{
+    if ( len<BWA_MIN_RDLEN ) return 0;
+
+    // Although the name implies that the read cannot be trimmed to more than BWA_MIN_RDLEN,
+    //  the calculation can in fact trim it to (BWA_MIN_RDLEN-1). (bwa_trim_read in bwa/bwaseqio.c).
+    int max_trimmed = len - BWA_MIN_RDLEN + 1;
+    int l, sum=0, max_sum=0, max_l=0;
+
+    for (l=0; l<max_trimmed; l++)
+    {
+        sum += trim_qual - quals[ reverse ? l : len-1-l ];
+        if ( sum<0 ) break;
+        if ( sum>max_sum )
+        {
+            max_sum = sum;
+            // This is the correct way, but bwa clips from some reason one base less
+            // max_l   = l+1;
+            max_l   = l;
+        }
+    }
+    return max_l;
+}
+
+
+void count_indels(stats_t *stats,bam1_t *bam_line)
+{
+    int is_fwd = IS_REVERSE(bam_line) ? 0 : 1;
+    uint32_t order = IS_PAIRED(bam_line) ? (IS_READ1(bam_line) ? READ_ORDER_FIRST : 0) + (IS_READ2(bam_line) ? READ_ORDER_LAST : 0) : READ_ORDER_FIRST;
+    int icig;
+    int icycle = 0;
+    int read_len = bam_line->core.l_qseq;
+    for (icig=0; icig<bam_line->core.n_cigar; icig++)
+    {
+        int cig  = bam_cigar_op(bam_get_cigar(bam_line)[icig]);
+        int ncig = bam_cigar_oplen(bam_get_cigar(bam_line)[icig]);
+        if ( !ncig ) continue;  // curiously, this can happen: 0D
+
+        if ( cig==BAM_CINS )
+        {
+            int idx = is_fwd ? icycle : read_len-icycle-ncig;
+            if ( idx<0 )
+                error("FIXME: read_len=%d vs icycle=%d\n", read_len,icycle);
+            if ( idx >= stats->nbases || idx<0 ) error("FIXME: %d vs %d, %s:%"PRIhts_pos" %s\n", idx, stats->nbases, sam_hdr_tid2name(stats->info->sam_header, bam_line->core.tid), bam_line->core.pos+1, bam_get_qname(bam_line));
+            if ( order == READ_ORDER_FIRST )
+                stats->ins_cycles_1st[idx]++;
+            if ( order == READ_ORDER_LAST )
+                stats->ins_cycles_2nd[idx]++;
+            icycle += ncig;
+            if ( ncig<=stats->nindels )
+                stats->insertions[ncig-1]++;
+            continue;
+        }
+        if ( cig==BAM_CDEL )
+        {
+            int idx = is_fwd ? icycle-1 : read_len-icycle-1;
+            if ( idx<0 ) continue;  // discard meaningless deletions
+            if ( idx >= stats->nbases ) error("FIXME: %d vs %d\n", idx,stats->nbases);
+            if ( order == READ_ORDER_FIRST )
+                stats->del_cycles_1st[idx]++;
+            if ( order == READ_ORDER_LAST )
+                stats->del_cycles_2nd[idx]++;
+            if ( ncig<=stats->nindels )
+                stats->deletions[ncig-1]++;
+            continue;
+        }
+        if ( cig!=BAM_CREF_SKIP && cig!=BAM_CHARD_CLIP && cig!=BAM_CPAD )
+            icycle += ncig;
+    }
+}
+
+int unclipped_length(bam1_t *bam_line)
+{
+    int icig, read_len = bam_line->core.l_qseq;
+    for (icig=0; icig<bam_line->core.n_cigar; icig++)
+    {
+        int cig = bam_cigar_op(bam_get_cigar(bam_line)[icig]);
+        if ( cig==BAM_CHARD_CLIP )
+            read_len += bam_cigar_oplen(bam_get_cigar(bam_line)[icig]);
+    }
+    return read_len;
+}
+
+void count_mismatches_per_cycle(stats_t *stats, bam1_t *bam_line, int read_len)
+{
+    int is_fwd = IS_REVERSE(bam_line) ? 0 : 1;
+    int icig, iread=0, icycle=0;
+    hts_pos_t iref = bam_line->core.pos - stats->rseq_pos;
+    uint8_t *read  = bam_get_seq(bam_line);
+    uint8_t *quals = bam_get_qual(bam_line);
+    uint64_t *mpc_buf = stats->mpc_buf;
+    for (icig=0; icig<bam_line->core.n_cigar; icig++)
+    {
+        int cig  = bam_cigar_op(bam_get_cigar(bam_line)[icig]);
+        int ncig = bam_cigar_oplen(bam_get_cigar(bam_line)[icig]);
+        if ( cig==BAM_CINS )
+        {
+            iread  += ncig;
+            icycle += ncig;
+            continue;
+        }
+        if ( cig==BAM_CDEL )
+        {
+            iref += ncig;
+            continue;
+        }
+        if ( cig==BAM_CSOFT_CLIP )
+        {
+            icycle += ncig;
+            // Soft-clips are present in the sequence, but the position of the read marks a start of the sequence after clipping
+            //   iref += ncig;
+            iread  += ncig;
+            continue;
+        }
+        if ( cig==BAM_CHARD_CLIP )
+        {
+            icycle += ncig;
+            continue;
+        }
+        // Ignore H and N CIGARs. The letter are inserted e.g. by TopHat and often require very large
+        //  chunk of refseq in memory. Not very frequent and not noticeable in the stats.
+        if ( cig==BAM_CREF_SKIP || cig==BAM_CHARD_CLIP || cig==BAM_CPAD ) continue;
+        if ( cig!=BAM_CMATCH && cig!=BAM_CEQUAL && cig!=BAM_CDIFF ) // not relying on precalculated diffs
+            error("TODO: cigar %d, %s:%"PRIhts_pos" %s\n", cig, sam_hdr_tid2name(stats->info->sam_header, bam_line->core.tid), bam_line->core.pos+1, bam_get_qname(bam_line));
+
+        if ( ncig+iref > stats->nrseq_buf )
+            error("FIXME: %d+%"PRIhts_pos" > %"PRId64", %s, %s:%"PRIhts_pos"\n", ncig, iref, stats->nrseq_buf, bam_get_qname(bam_line), sam_hdr_tid2name(stats->info->sam_header, bam_line->core.tid), bam_line->core.pos+1);
+
+        int im;
+        for (im=0; im<ncig; im++)
+        {
+            uint8_t cread = bam_seqi(read,iread);
+            uint8_t cref  = stats->rseq_buf[iref];
+
+            // ---------------15
+            // =ACMGRSVTWYHKDBN
+            if ( cread==15 )
+            {
+                int idx = is_fwd ? icycle : read_len-icycle-1;
+                if ( idx>stats->max_len )
+                    error("mpc: %d>%d\n",idx,stats->max_len);
+                idx = idx*stats->nquals;
+                if ( idx>=stats->nquals*stats->nbases )
+                    error("FIXME: mpc_buf overflow\n");
+                mpc_buf[idx]++;
+            }
+            else if ( cref && cread && cref!=cread )
+            {
+                uint8_t qual = quals[iread] + 1;
+                if ( qual>=stats->nquals )
+                    error("TODO: quality too high %d>=%d (%s %"PRIhts_pos" %s)\n", qual, stats->nquals, sam_hdr_tid2name(stats->info->sam_header, bam_line->core.tid), bam_line->core.pos+1, bam_get_qname(bam_line));
+
+                int idx = is_fwd ? icycle : read_len-icycle-1;
+                if ( idx>stats->max_len )
+                    error("mpc: %d>%d (%s %"PRIhts_pos" %s)\n", idx, stats->max_len, sam_hdr_tid2name(stats->info->sam_header, bam_line->core.tid), bam_line->core.pos+1, bam_get_qname(bam_line));
+
+                idx = idx*stats->nquals + qual;
+                if ( idx>=stats->nquals*stats->nbases )
+                    error("FIXME: mpc_buf overflow\n");
+                mpc_buf[idx]++;
+            }
+
+            iref++;
+            iread++;
+            icycle++;
+        }
+    }
+}
+
+void read_ref_seq(stats_t *stats, int32_t tid, hts_pos_t pos)
+{
+    int i;
+    hts_pos_t fai_ref_len;
+    char *fai_ref = faidx_fetch_seq64(stats->info->fai, sam_hdr_tid2name(stats->info->sam_header, tid), pos, pos+stats->mrseq_buf-1, &fai_ref_len);
+    if ( fai_ref_len < 0 ) error("Failed to fetch the sequence \"%s\"\n", sam_hdr_tid2name(stats->info->sam_header, tid));
+
+    uint8_t *ptr = stats->rseq_buf;
+    for (i=0; i<fai_ref_len; i++)
+    {
+        // Conversion between uint8_t coding and ACGT
+        //      -12-4---8-------
+        //      =ACMGRSVTWYHKDBN
+        switch (fai_ref[i])
+        {
+            case 'A':
+            case 'a': *ptr = 1; break;
+            case 'C':
+            case 'c': *ptr = 2; break;
+            case 'G':
+            case 'g': *ptr = 4; break;
+            case 'T':
+            case 't': *ptr = 8; break;
+            default:  *ptr = 0; break;
+        }
+        ptr++;
+    }
+    free(fai_ref);
+
+    if ( fai_ref_len < stats->mrseq_buf ) memset(ptr,0, stats->mrseq_buf - fai_ref_len);
+    stats->nrseq_buf = fai_ref_len;
+    stats->rseq_pos  = pos;
+    stats->tid       = tid;
+}
+
+float fai_gc_content(stats_t *stats, hts_pos_t pos, int len)
+{
+    uint32_t gc,count,c;
+    hts_pos_t i = pos - stats->rseq_pos, ito = i + len;
+    assert( i>=0 );
+
+    if (  ito > stats->nrseq_buf ) ito = stats->nrseq_buf;
+
+    // Count GC content
+    gc = count = 0;
+    for (; i<ito; i++)
+    {
+        c = stats->rseq_buf[i];
+        if ( c==2 || c==4 )
+        {
+            gc++;
+            count++;
+        }
+        else if ( c==1 || c==8 )
+            count++;
+    }
+    return count ? (float)gc/count : 0;
+}
+
+void realloc_rseq_buffer(stats_t *stats)
+{
+    int n = stats->nbases*10;
+    if ( stats->info->gcd_bin_size > n ) n = stats->info->gcd_bin_size;
+    if ( stats->mrseq_buf<n )
+    {
+        stats->rseq_buf = realloc(stats->rseq_buf,sizeof(uint8_t)*n);
+        if (!stats->rseq_buf) {
+            error("Could not reallocate reference sequence buffer");
+        }
+        stats->mrseq_buf = n;
+    }
+}
+
+void realloc_gcd_buffer(stats_t *stats, int seq_len)
+{
+    hts_expand0(gc_depth_t,stats->igcd+1,stats->ngcd,stats->gcd);
+    realloc_rseq_buffer(stats);
+}
+
+void realloc_buffers(stats_t *stats, int seq_len)
+{
+    int n = 2*(1 + seq_len - stats->nbases) + stats->nbases;
+
+    stats->quals_1st = realloc(stats->quals_1st, n*stats->nquals*sizeof(uint64_t));
+    if ( !stats->quals_1st )
+        error("Could not realloc buffers, the sequence too long: %d (%ld)\n", seq_len,n*stats->nquals*sizeof(uint64_t));
+    memset(stats->quals_1st + stats->nbases*stats->nquals, 0, (n-stats->nbases)*stats->nquals*sizeof(uint64_t));
+
+    stats->quals_2nd = realloc(stats->quals_2nd, n*stats->nquals*sizeof(uint64_t));
+    if ( !stats->quals_2nd )
+        error("Could not realloc buffers, the sequence too long: %d (2x%ld)\n", seq_len,n*stats->nquals*sizeof(uint64_t));
+    memset(stats->quals_2nd + stats->nbases*stats->nquals, 0, (n-stats->nbases)*stats->nquals*sizeof(uint64_t));
+
+    if ( stats->mpc_buf )
+    {
+        stats->mpc_buf = realloc(stats->mpc_buf, n*stats->nquals*sizeof(uint64_t));
+        if ( !stats->mpc_buf )
+            error("Could not realloc buffers, the sequence too long: %d (%ld)\n", seq_len,n*stats->nquals*sizeof(uint64_t));
+        memset(stats->mpc_buf + stats->nbases*stats->nquals, 0, (n-stats->nbases)*stats->nquals*sizeof(uint64_t));
+    }
+
+    stats->acgtno_cycles_1st = realloc(stats->acgtno_cycles_1st, n*sizeof(acgtno_count_t));
+    if ( !stats->acgtno_cycles_1st )
+        error("Could not realloc buffers, the sequence too long: %d (%ld)\n", seq_len, n*sizeof(acgtno_count_t));
+    memset(stats->acgtno_cycles_1st + stats->nbases, 0, (n-stats->nbases)*sizeof(acgtno_count_t));
+
+    stats->acgtno_cycles_2nd = realloc(stats->acgtno_cycles_2nd, n*sizeof(acgtno_count_t));
+    if ( !stats->acgtno_cycles_2nd )
+        error("Could not realloc buffers, the sequence too long: %d (%ld)\n", seq_len, n*sizeof(acgtno_count_t));
+    memset(stats->acgtno_cycles_2nd + stats->nbases, 0, (n-stats->nbases)*sizeof(acgtno_count_t));
+
+    stats->acgtno_revcomp = realloc(stats->acgtno_revcomp, n*sizeof(acgtno_count_t));
+    if ( !stats->acgtno_revcomp )
+        error("Could not realloc buffers, the sequence too long: %d (%ld)\n", seq_len, n*sizeof(acgtno_count_t));
+    memset(stats->acgtno_revcomp + stats->nbases, 0, (n-stats->nbases)*sizeof(acgtno_count_t));
+
+    stats->read_lengths = realloc(stats->read_lengths, n*sizeof(uint64_t));
+    if ( !stats->read_lengths )
+        error("Could not realloc buffers, the sequence too long: %d (%ld)\n", seq_len,n*sizeof(uint64_t));
+    memset(stats->read_lengths + stats->nbases, 0, (n-stats->nbases)*sizeof(uint64_t));
+
+    stats->read_lengths_1st = realloc(stats->read_lengths_1st, n*sizeof(uint64_t));
+    if ( !stats->read_lengths_1st )
+        error("Could not realloc buffers, the sequence too long: %d (%ld)\n", seq_len,n*sizeof(uint64_t));
+    memset(stats->read_lengths_1st + stats->nbases, 0, (n-stats->nbases)*sizeof(uint64_t));
+
+    stats->read_lengths_2nd = realloc(stats->read_lengths_2nd, n*sizeof(uint64_t));
+    if ( !stats->read_lengths_2nd )
+        error("Could not realloc buffers, the sequence too long: %d (%ld)\n", seq_len,n*sizeof(uint64_t));
+    memset(stats->read_lengths_2nd + stats->nbases, 0, (n-stats->nbases)*sizeof(uint64_t));
+
+    stats->insertions = realloc(stats->insertions, n*sizeof(uint64_t));
+    if ( !stats->insertions )
+        error("Could not realloc buffers, the sequence too long: %d (%ld)\n", seq_len,n*sizeof(uint64_t));
+    memset(stats->insertions + stats->nbases, 0, (n-stats->nbases)*sizeof(uint64_t));
+
+    stats->deletions = realloc(stats->deletions, n*sizeof(uint64_t));
+    if ( !stats->deletions )
+        error("Could not realloc buffers, the sequence too long: %d (%ld)\n", seq_len,n*sizeof(uint64_t));
+    memset(stats->deletions + stats->nbases, 0, (n-stats->nbases)*sizeof(uint64_t));
+
+    stats->ins_cycles_1st = realloc(stats->ins_cycles_1st, (n+1)*sizeof(uint64_t));
+    if ( !stats->ins_cycles_1st )
+        error("Could not realloc buffers, the sequence too long: %d (%ld)\n", seq_len,(n+1)*sizeof(uint64_t));
+    memset(stats->ins_cycles_1st + stats->nbases + 1, 0, (n-stats->nbases)*sizeof(uint64_t));
+
+    stats->ins_cycles_2nd = realloc(stats->ins_cycles_2nd, (n+1)*sizeof(uint64_t));
+    if ( !stats->ins_cycles_2nd )
+        error("Could not realloc buffers, the sequence too long: %d (%ld)\n", seq_len,(n+1)*sizeof(uint64_t));
+    memset(stats->ins_cycles_2nd + stats->nbases + 1, 0, (n-stats->nbases)*sizeof(uint64_t));
+
+    stats->del_cycles_1st = realloc(stats->del_cycles_1st, (n+1)*sizeof(uint64_t));
+    if ( !stats->del_cycles_1st )
+        error("Could not realloc buffers, the sequence too long: %d (%ld)\n", seq_len,(n+1)*sizeof(uint64_t));
+    memset(stats->del_cycles_1st + stats->nbases + 1, 0, (n-stats->nbases)*sizeof(uint64_t));
+
+    stats->del_cycles_2nd = realloc(stats->del_cycles_2nd, (n+1)*sizeof(uint64_t));
+    if ( !stats->del_cycles_2nd )
+        error("Could not realloc buffers, the sequence too long: %d (%ld)\n", seq_len,(n+1)*sizeof(uint64_t));
+    memset(stats->del_cycles_2nd + stats->nbases + 1, 0, (n-stats->nbases)*sizeof(uint64_t));
+
+    stats->nbases = n;
+
+    // Realloc the coverage distribution buffer
+    int *rbuffer = calloc(sizeof(int),seq_len*5);
+    if (!rbuffer) {
+        error("Could not allocate coverage distribution buffer");
+    }
+    n = stats->cov_rbuf.size-stats->cov_rbuf.start;
+    memcpy(rbuffer,stats->cov_rbuf.buffer+stats->cov_rbuf.start,n);
+    if ( stats->cov_rbuf.start>1 )
+        memcpy(rbuffer+n,stats->cov_rbuf.buffer,stats->cov_rbuf.start);
+    stats->cov_rbuf.start = 0;
+    free(stats->cov_rbuf.buffer);
+    stats->cov_rbuf.buffer = rbuffer;
+    stats->cov_rbuf.size = seq_len*5;
+
+    realloc_rseq_buffer(stats);
+}
+
+void update_checksum(bam1_t *bam_line, stats_t *stats)
+{
+    uint8_t *name = (uint8_t*) bam_get_qname(bam_line);
+    int len = 0;
+    while ( name[len] ) len++;
+    stats->checksum.names +=  crc32(0L, name, len);
+
+    int seq_len = bam_line->core.l_qseq;
+    if ( !seq_len ) return;
+
+    uint8_t *seq = bam_get_seq(bam_line);
+    stats->checksum.reads += crc32(0L, seq, (seq_len+1)/2);
+
+    uint8_t *qual = bam_get_qual(bam_line);
+    stats->checksum.quals += crc32(0L, qual, (seq_len+1)/2);
+}
+
+// Collect statistics about the barcode tags specified by init_barcode_tags method
+static void collect_barcode_stats(bam1_t* bam_line, stats_t* stats) {
+    uint32_t nbases, tag, i;
+    acgtno_count_t *acgtno;
+    uint64_t *quals;
+    int32_t *separator, *maxqual;
+
+    for (tag = 0; tag < stats->ntags; tag++) {
+        const char *barcode_tag = stats->tags_barcode[tag].tag_name, *qual_tag = stats->tags_barcode[tag].qual_name;
+        uint8_t* bc = bam_aux_get(bam_line, barcode_tag);
+        if (!bc)
+            continue;
+
+        char* barcode = bam_aux2Z(bc);
+        if (!barcode)
+            continue;
+
+        uint32_t barcode_len = strlen(barcode);
+        if (!stats->tags_barcode[tag].nbases) { // tag seen for the first time
+            uint32_t offset = 0;
+            for (i = 0; i < stats->ntags; i++)
+                offset += stats->tags_barcode[i].nbases;
+
+            stats->tags_barcode[tag].offset = offset;
+            stats->tags_barcode[tag].nbases = barcode_len;
+            stats->acgtno_barcode = realloc(stats->acgtno_barcode, (offset + barcode_len) * sizeof(acgtno_count_t));
+            stats->quals_barcode  = realloc(stats->quals_barcode, (offset + barcode_len) * stats->nquals * sizeof(uint64_t));
+
+            if (!stats->acgtno_barcode || !stats->quals_barcode)
+                error("Error allocating memory. Aborting!\n");
+
+            memset(stats->acgtno_barcode + offset, 0, barcode_len*sizeof(acgtno_count_t));
+            memset(stats->quals_barcode + offset*stats->nquals, 0, barcode_len*stats->nquals*sizeof(uint64_t));
+        }
+
+        nbases = stats->tags_barcode[tag].nbases;
+        if (barcode_len > nbases) {
+            fprintf(samtools_stderr, "Barcodes with tag %s differ in length at sequence '%s'\n", barcode_tag, bam_get_qname(bam_line));
+            continue;
+        }
+
+        acgtno = stats->acgtno_barcode + stats->tags_barcode[tag].offset;
+        quals = stats->quals_barcode + stats->tags_barcode[tag].offset*stats->nquals;
+        maxqual = &stats->tags_barcode[tag].max_qual;
+        separator = &stats->tags_barcode[tag].tag_sep;
+        int error_flag = 0;
+
+        for (i = 0; i < barcode_len; i++) {
+            switch (barcode[i]) {
+            case 'A':
+                acgtno[i].a++;
+                break;
+            case 'C':
+                acgtno[i].c++;
+                break;
+            case 'G':
+                acgtno[i].g++;
+                break;
+            case 'T':
+                acgtno[i].t++;
+                break;
+            case 'N':
+                acgtno[i].n++;
+                break;
+            default:
+                if (*separator >= 0) {
+                    if (*separator != i) {
+                        if (stats->error_number < ERROR_LIMIT) {
+                            fprintf(samtools_stderr, "Barcode separator for tag %s is in a different position or wrong barcode content('%s') at sequence '%s'\n", barcode_tag, barcode, bam_get_qname(bam_line));
+                            stats->error_number++;
+                        }
+                        error_flag = 1;
+                    }
+                } else {
+                    *separator = i;
+                }
+            }
+
+            /* don't process the rest of the tag bases */
+            if (error_flag)
+                break;
+        }
+
+        /* skip to the next tag */
+        if (error_flag)
+            continue;
+
+        uint8_t* qt = bam_aux_get(bam_line, qual_tag);
+        if (!qt)
+            continue;
+
+        char* barqual = bam_aux2Z(qt);
+        if (!barqual)
+            continue;
+
+        uint32_t barqual_len = strlen(barqual);
+        if (barqual_len == barcode_len) {
+            for (i = 0; i < barcode_len; i++) {
+                int32_t qual = (int32_t)barqual[i] - '!';  // Phred + 33
+                if (qual >= 0 && qual < stats->nquals) {
+                    quals[i * stats->nquals + qual]++;
+                    if (qual > *maxqual)
+                        *maxqual = qual;
+                }
+            }
+        } else {
+            if (stats->error_number++ < ERROR_LIMIT) {
+                fprintf(samtools_stderr, "%s length and %s length don't match for sequence '%s'\n", barcode_tag, qual_tag, bam_get_qname(bam_line));
+            }
+        }
+    }
+}
+
+// These stats should only be calculated for the original reads ignoring
+// supplementary artificial reads otherwise we'll accidentally double count
+void collect_orig_read_stats(bam1_t *bam_line, stats_t *stats, int* gc_count_out)
+{
+    int seq_len = bam_line->core.l_qseq;
+    stats->total_len += seq_len; // This ignores clipping so only count primary
+
+    if ( bam_line->core.flag & BAM_FQCFAIL ) stats->nreads_QCfailed++;
+    if ( bam_line->core.flag & BAM_FPAIRED ) stats->nreads_paired_tech++;
+
+    uint32_t order = IS_PAIRED(bam_line) ? (IS_READ1(bam_line) ? READ_ORDER_FIRST : 0) + (IS_READ2(bam_line) ? READ_ORDER_LAST : 0) : READ_ORDER_FIRST;
+
+    // Count GC and ACGT per cycle. Note that cycle is approximate, clipping is ignored
+    uint8_t *seq  = bam_get_seq(bam_line);
+    int i, read_cycle, gc_count = 0, reverse = IS_REVERSE(bam_line);
+
+    acgtno_count_t *acgtno_cycles = (order == READ_ORDER_FIRST) ? stats->acgtno_cycles_1st : (order == READ_ORDER_LAST) ?  stats->acgtno_cycles_2nd : NULL ;
+    if (acgtno_cycles) {
+        for (i=0; i<seq_len; i++)
+        {
+            // Read cycle for current index
+            read_cycle = (reverse ? seq_len-i-1 : i);
+
+            // Conversion from uint8_t coding:
+            //      -12-4---8------5
+            //      =ACMGRSVTWYHKDBN
+            switch (bam_seqi(seq, i)) {
+            case 1:
+                acgtno_cycles[ read_cycle ].a++;
+                reverse ? stats->acgtno_revcomp[ read_cycle ].t++ : stats->acgtno_revcomp[ read_cycle ].a++;
+                break;
+            case 2:
+                acgtno_cycles[ read_cycle ].c++;
+                reverse ? stats->acgtno_revcomp[ read_cycle ].g++ : stats->acgtno_revcomp[ read_cycle ].c++;
+                gc_count++;
+                break;
+            case 4:
+                acgtno_cycles[ read_cycle ].g++;
+                reverse ? stats->acgtno_revcomp[ read_cycle ].c++ : stats->acgtno_revcomp[ read_cycle ].g++;
+                gc_count++;
+                break;
+            case 8:
+                reverse ? stats->acgtno_revcomp[ read_cycle ].a++ : stats->acgtno_revcomp[ read_cycle ].t++;
+                acgtno_cycles[ read_cycle ].t++;
+                break;
+            case 15:
+                acgtno_cycles[ read_cycle ].n++;
+                break;
+            default:
+                /*
+                 * count "=" sequences in "other" along
+                 * with MRSVWYHKDB ambiguity codes
+                 */
+                acgtno_cycles[ read_cycle ].other++;
+                break;
+            }
+        }
+    }
+    int gc_idx_min = gc_count*(stats->ngc-1)/seq_len;
+    int gc_idx_max = (gc_count+1)*(stats->ngc-1)/seq_len;
+    if ( gc_idx_max >= stats->ngc ) gc_idx_max = stats->ngc - 1;
+
+    // Determine which array (1st or 2nd read) will these stats go to,
+    //  trim low quality bases from end the same way BWA does,
+    //  fill GC histogram
+    uint64_t *quals = NULL;
+    uint8_t *bam_quals = bam_get_qual(bam_line);
+
+    switch (order) {
+    case READ_ORDER_FIRST:
+        quals = stats->quals_1st;
+        stats->nreads_1st++;
+        stats->total_len_1st += seq_len;
+        for (i=gc_idx_min; i<gc_idx_max; i++)
+            stats->gc_1st[i]++;
+        break;
+    case READ_ORDER_LAST:
+        quals  = stats->quals_2nd;
+        stats->nreads_2nd++;
+        stats->total_len_2nd += seq_len;
+        for (i=gc_idx_min; i<gc_idx_max; i++)
+            stats->gc_2nd[i]++;
+        break;
+    default:
+        stats->nreads_other++;
+    }
+    if ( stats->info->trim_qual>0 )
+        stats->nbases_trimmed += bwa_trim_read(stats->info->trim_qual, bam_quals, seq_len, reverse);
+
+    // Quality histogram and average quality. Clipping is neglected.
+    if (quals) {
+        for (i=0; i<seq_len; i++)
+        {
+            uint8_t qual = bam_quals[ reverse ? seq_len-i-1 : i];
+            if ( qual>=stats->nquals )
+                error("TODO: quality too high %d>=%d (%s %"PRIhts_pos" %s)\n", qual, stats->nquals, sam_hdr_tid2name(stats->info->sam_header, bam_line->core.tid), bam_line->core.pos+1, bam_get_qname(bam_line));
+            if ( qual>stats->max_qual )
+                stats->max_qual = qual;
+
+            quals[ i*stats->nquals+qual ]++;
+            stats->sum_qual += qual;
+        }
+    }
+
+    // Barcode statistics
+    if (order == READ_ORDER_FIRST) {
+        collect_barcode_stats(bam_line, stats);
+    }
+
+    // Look at the flags and increment appropriate counters (mapped, paired, etc)
+    if ( IS_UNMAPPED(bam_line) )
+    {
+        stats->nreads_unmapped++;
+    }
+    else
+    {
+        stats->nbases_mapped += seq_len; // This ignores clipping so only count primary
+
+        if ( !bam_line->core.qual )
+            stats->nreads_mq0++;
+        if ( !IS_PAIRED_AND_MAPPED(bam_line) )
+            stats->nreads_single_mapped++;
+        else
+        {
+            stats->nreads_paired_and_mapped++;
+
+            if (IS_PROPERLYPAIRED(bam_line)) stats->nreads_properly_paired++;
+
+            if ( bam_line->core.tid!=bam_line->core.mtid )
+                stats->nreads_anomalous++;
+        }
+    }
+    *gc_count_out = gc_count;
+}
+
+static int cleanup_overlaps(khash_t(qn2pair) *read_pairs, hts_pos_t max) {
+    if ( !read_pairs )
+        return 0;
+
+    int count = 0;
+    khint_t k;
+    for (k = kh_begin(read_pairs); k < kh_end(read_pairs); k++) {
+        if ( kh_exist(read_pairs, k) ) {
+            char *key = (char *)kh_key(read_pairs, k);
+            pair_t *val = kh_val(read_pairs, k);
+            if ( val && val->chunks ) {
+                if ( val->chunks[val->n-1].end < max ) {
+                    free(val->chunks);
+                    free(val);
+                    free(key);
+                    kh_del(qn2pair, read_pairs, k);
+                    count++;
+                }
+            } else {
+                free(key);
+                kh_del(qn2pair, read_pairs, k);
+                count++;
+            }
+        }
+    }
+    if ( max == INT64_MAX )
+        kh_destroy(qn2pair, read_pairs);
+
+    return count;
+}
+
+/**
+ * [pmin, pmax) - 0 based half-open
+ */
+static void remove_overlaps(bam1_t *bam_line, khash_t(qn2pair) *read_pairs, stats_t *stats, hts_pos_t pmin, hts_pos_t pmax) {
+    if ( !bam_line || !read_pairs || !stats )
+        return;
+
+    uint32_t order = (IS_READ1(bam_line) ? READ_ORDER_FIRST : 0) + (IS_READ2(bam_line) ? READ_ORDER_LAST : 0);
+    if ( !(bam_line->core.flag & BAM_FPAIRED) ||
+         (bam_line->core.flag & BAM_FMUNMAP) ||
+         (llabs(bam_line->core.isize) >= 2*bam_line->core.l_qseq) ||
+         (order != READ_ORDER_FIRST && order != READ_ORDER_LAST) ) {
+        if ( pmin >= 0 )
+            round_buffer_insert_read(&(stats->cov_rbuf), pmin, pmax);
+        return;
+    }
+
+    char *qname = bam_get_qname(bam_line);
+    if ( !qname ) {
+        fprintf(samtools_stderr, "Error retrieving qname for line starting at pos %"PRIhts_pos"\n", bam_line->core.pos);
+        return;
+    }
+
+    khint_t k = kh_get(qn2pair, read_pairs, qname);
+    if ( k == kh_end(read_pairs) ) { //first chunk from this template
+        if ( pmin == -1 )
+            return;
+
+        int ret;
+        char *s = strdup(qname);
+        if ( !s ) {
+            fprintf(samtools_stderr, "Error allocating memory\n");
+            return;
+        }
+
+        k = kh_put(qn2pair, read_pairs, s, &ret);
+        if ( -1 == ret ) {
+            error("Error inserting read '%s' in pair hash table\n", qname);
+        }
+
+        pair_t *pc = calloc(1, sizeof(pair_t));
+        if ( !pc ) {
+            fprintf(samtools_stderr, "Error allocating memory\n");
+            return;
+        }
+
+        pc->m = DEFAULT_CHUNK_NO;
+        pc->chunks = calloc(pc->m, sizeof(hts_pair_pos_t));
+        if ( !pc->chunks ) {
+            fprintf(samtools_stderr, "Error allocating memory\n");
+            free(pc);
+            return;
+        }
+
+        pc->chunks[0].beg = pmin;
+        pc->chunks[0].end = pmax;
+        pc->n = 1;
+        pc->first = order;
+
+        kh_val(read_pairs, k) = pc;
+        stats->pair_count++;
+    } else { //template already present
+        pair_t *pc = kh_val(read_pairs, k);
+        if ( !pc ) {
+            fprintf(samtools_stderr, "Invalid hash table entry\n");
+            return;
+        }
+
+        if ( order == pc->first ) { //chunk from an existing line
+            if ( pmin == -1 )
+                return;
+
+            if ( pc->n == pc->m ) {
+                hts_pair_pos_t *tmp = realloc(pc->chunks, (pc->m<<1)*sizeof(hts_pair_pos_t));
+                if ( !tmp ) {
+                    fprintf(samtools_stderr, "Error allocating memory\n");
+                    return;
+                }
+                pc->chunks = tmp;
+                pc->m<<=1;
+            }
+
+            pc->chunks[pc->n].beg = pmin;
+            pc->chunks[pc->n].end = pmax;
+            pc->n++;
+        } else { //the other line, check for overlapping
+            if ( pmin == -1 && kh_exist(read_pairs, k) ) { //job done, delete entry
+                char *key = (char *)kh_key(read_pairs, k);
+                pair_t *val = kh_val(read_pairs, k);
+                if ( val) {
+                    free(val->chunks);
+                    free(val);
+                }
+                free(key);
+                kh_del(qn2pair, read_pairs, k);
+                stats->pair_count--;
+                return;
+            }
+
+            int i;
+            for (i=0; i<pc->n; i++) {
+                if ( pmin >= pc->chunks[i].end )
+                    continue;
+
+                if ( pmax <= pc->chunks[i].beg ) //no overlap
+                    break;
+
+                if ( pmin < pc->chunks[i].beg ) { //overlap at the beginning
+                    round_buffer_insert_read(&(stats->cov_rbuf), pmin, pc->chunks[i].beg);
+                    pmin = pc->chunks[i].beg;
+                }
+
+                if ( pmax <= pc->chunks[i].end ) { //completely contained
+                    stats->nbases_mapped_cigar -= (pmax - pmin);
+                    return;
+                } else {                           //overlap at the end
+                    stats->nbases_mapped_cigar -= (pc->chunks[i].end - pmin);
+                    pmin = pc->chunks[i].end;
+                }
+            }
+        }
+    }
+    round_buffer_insert_read(&(stats->cov_rbuf), pmin, pmax);
+}
+
+void collect_stats(bam1_t *bam_line, stats_t *stats, khash_t(qn2pair) *read_pairs)
+{
+    if ( !is_in_regions(bam_line,stats) )
+        return;
+    if ( stats->rg_hash )
+    {
+        const uint8_t *rg = bam_aux_get(bam_line, "RG");
+        if ( !rg ) return;  // certain read groups were requested but this record has none
+        khint_t k = kh_get(rg, stats->rg_hash, (const char*)(rg + 1));
+        if ( k == kh_end((kh_rg_t *)stats->rg_hash) ) return;
+    }
+    if ( stats->info->flag_require && (bam_line->core.flag & stats->info->flag_require)!=stats->info->flag_require )
+    {
+        stats->nreads_filtered++;
+        return;
+    }
+    if ( stats->info->flag_filter && (bam_line->core.flag & stats->info->flag_filter) )
+    {
+        stats->nreads_filtered++;
+        return;
+    }
+    if ( stats->info->filter_readlen!=-1 && bam_line->core.l_qseq!=stats->info->filter_readlen )
+        return;
+
+    update_checksum(bam_line, stats);
+
+    // Secondary reads don't count for most stats purposes
+    if ( bam_line->core.flag & BAM_FSECONDARY )
+    {
+        stats->nreads_secondary++;
+        return;
+    }
+
+    if ( bam_line->core.flag & BAM_FSUPPLEMENTARY )
+    {
+        stats->nreads_supplementary++;
+    }
+
+    // If line has no sequence cannot continue
+    int seq_len = bam_line->core.l_qseq;
+    if ( !seq_len ) return;
+
+    if ( IS_DUP(bam_line) )
+    {
+        stats->total_len_dup += seq_len;
+        stats->nreads_dup++;
+    }
+
+    uint32_t order = IS_PAIRED(bam_line) ? (IS_READ1(bam_line) ? READ_ORDER_FIRST : 0) + (IS_READ2(bam_line) ? READ_ORDER_LAST : 0) : READ_ORDER_FIRST;
+
+    int read_len = unclipped_length(bam_line);
+    if ( read_len >= stats->nbases )
+        realloc_buffers(stats,read_len);
+    // Update max_len observed
+    if ( stats->max_len<read_len )
+        stats->max_len = read_len;
+    if ( order == READ_ORDER_FIRST && stats->max_len_1st < read_len )
+        stats->max_len_1st = read_len;
+    if ( order == READ_ORDER_LAST && stats->max_len_2nd < read_len )
+        stats->max_len_2nd = read_len;
+
+    int i;
+    int gc_count = 0;
+
+    // These stats should only be calculated for the original reads ignoring supplementary artificial reads
+    // otherwise we'll accidentally double count
+    if ( IS_ORIGINAL(bam_line) ) {
+        stats->read_lengths[read_len]++;
+        if ( order == READ_ORDER_FIRST ) stats->read_lengths_1st[read_len]++;
+        if ( order == READ_ORDER_LAST ) stats->read_lengths_2nd[read_len]++;
+        collect_orig_read_stats(bam_line, stats, &gc_count);
+    }
+
+    // Look at the flags and increment appropriate counters (mapped, paired, etc)
+    if ( IS_UNMAPPED(bam_line) ) return;
+
+    count_indels(stats, bam_line);
+
+    if ( IS_PAIRED_AND_MAPPED(bam_line) && IS_ORIGINAL(bam_line) )
+    {
+        // The insert size is tricky, because for long inserts the libraries are
+        // prepared differently and the pairs point in other direction. BWA does
+        // not set the paired flag for them.  Similar thing is true also for 454
+        // reads. Mates mapped to different chromosomes have isize==0.
+        int32_t isize = bam_line->core.isize;
+        if ( isize<0 ) isize = -isize;
+        if ( stats->info->nisize > 0 && isize > stats->info->nisize )
+            isize = stats->info->nisize;
+        if ( isize>0 || bam_line->core.tid==bam_line->core.mtid )
+        {
+            hts_pos_t pos_fst = bam_line->core.mpos - bam_line->core.pos;
+            int is_fst  = IS_READ1(bam_line) ? 1 : -1;
+            int is_fwd  = IS_REVERSE(bam_line) ? -1 : 1;
+            int is_mfwd = IS_MATE_REVERSE(bam_line) ? -1 : 1;
+
+            if ( is_fwd*is_mfwd>0 )
+                stats->isize->inc_other(stats->isize->data, isize);
+            else if ( is_fst*pos_fst>=0 )
+            {
+                if ( is_fst*is_fwd>0 )
+                    stats->isize->inc_inward(stats->isize->data, isize);
+                else
+                    stats->isize->inc_outward(stats->isize->data, isize);
+            }
+            else if ( is_fst*pos_fst<0 )
+            {
+                if ( is_fst*is_fwd>0 )
+                    stats->isize->inc_outward(stats->isize->data, isize);
+                else
+                    stats->isize->inc_inward(stats->isize->data, isize);
+            }
+        }
+    }
+
+    // Number of mismatches
+    uint8_t *nm = bam_aux_get(bam_line,"NM");
+    if (nm)
+        stats->nmismatches += bam_aux2i(nm);
+
+    // Number of mapped bases from cigar
+    if ( bam_line->core.n_cigar == 0)
+        error("FIXME: mapped read with no cigar?\n");
+    int readlen=seq_len;
+    if ( stats->regions )
+    {
+        // Count only on-target bases
+        hts_pos_t iref = bam_line->core.pos + 1;
+        for (i=0; i<bam_line->core.n_cigar; i++)
+        {
+            int cig  = bam_cigar_op(bam_get_cigar(bam_line)[i]);
+            int ncig = bam_cigar_oplen(bam_get_cigar(bam_line)[i]);
+            if ( !ncig ) continue;  // curiously, this can happen: 0D
+            if ( cig==BAM_CDEL ) readlen += ncig;
+            else if ( cig==BAM_CMATCH || cig==BAM_CEQUAL || cig==BAM_CDIFF )
+            {
+                if ( iref < stats->reg_from ) ncig -= stats->reg_from-iref;
+                else if ( iref+ncig-1 > stats->reg_to ) ncig -= iref+ncig-1 - stats->reg_to;
+                if ( ncig<0 ) ncig = 0;
+                stats->nbases_mapped_cigar += ncig;
+                iref += bam_cigar_oplen(bam_get_cigar(bam_line)[i]);
+            }
+            else if ( cig==BAM_CINS )
+            {
+                iref += ncig;
+                if ( iref>=stats->reg_from && iref<=stats->reg_to )
+                    stats->nbases_mapped_cigar += ncig;
+            }
+        }
+    }
+    else
+    {
+        // Count the whole read
+        for (i=0; i<bam_line->core.n_cigar; i++)
+        {
+            int cig  = bam_cigar_op(bam_get_cigar(bam_line)[i]);
+            if ( cig==BAM_CMATCH || cig==BAM_CINS || cig==BAM_CEQUAL || cig==BAM_CDIFF )
+                stats->nbases_mapped_cigar += bam_cigar_oplen(bam_get_cigar(bam_line)[i]);
+            if ( cig==BAM_CDEL )
+                readlen += bam_cigar_oplen(bam_get_cigar(bam_line)[i]);
+        }
+    }
+
+    if ( stats->tid==bam_line->core.tid && bam_line->core.pos<stats->pos )
+        stats->is_sorted = 0;
+    stats->pos = bam_line->core.pos;
+
+    if ( stats->is_sorted )
+    {
+        if ( stats->tid==-1 || stats->tid!=bam_line->core.tid ) {
+            round_buffer_flush(stats, -1);
+        }
+
+        //cleanup the pair hash table to free memory
+        stats->last_read_flush++;
+        if ( stats->pair_count > DEFAULT_PAIR_MAX && stats->last_read_flush > DEFAULT_PAIR_MAX) {
+            stats->pair_count -= cleanup_overlaps(read_pairs, bam_line->core.pos);
+            stats->last_read_flush = 0;
+        }
+
+        if ( stats->last_pair_tid != bam_line->core.tid) {
+            stats->pair_count -= cleanup_overlaps(read_pairs, INT64_MAX-1);
+            stats->last_pair_tid = bam_line->core.tid;
+            stats->last_read_flush = 0;
+        }
+
+        // Mismatches per cycle and GC-depth graph. For simplicity, reads overlapping GCD bins
+        //  are not splitted which results in up to seq_len-1 overlaps. The default bin size is
+        //  20kbp, so the effect is negligible.
+        if ( stats->info->fai )
+        {
+            int inc_ref = 0, inc_gcd = 0;
+            // First pass or new chromosome
+            if ( stats->rseq_pos==-1 || stats->tid != bam_line->core.tid ) { inc_ref=1; inc_gcd=1; }
+            // Read goes beyond the end of the rseq buffer
+            else if ( stats->rseq_pos+stats->nrseq_buf < bam_line->core.pos+readlen ) { inc_ref=1; inc_gcd=1; }
+            // Read overlaps the next gcd bin
+            else if ( stats->gcd_pos+stats->info->gcd_bin_size < bam_line->core.pos+readlen )
+            {
+                inc_gcd = 1;
+                if ( stats->rseq_pos+stats->nrseq_buf < bam_line->core.pos+stats->info->gcd_bin_size ) inc_ref = 1;
+            }
+            if ( inc_gcd )
+            {
+                stats->igcd++;
+                if ( stats->igcd >= stats->ngcd )
+                    realloc_gcd_buffer(stats, readlen);
+                if ( inc_ref )
+                    read_ref_seq(stats,bam_line->core.tid,bam_line->core.pos);
+                stats->gcd_pos = bam_line->core.pos;
+                stats->gcd[ stats->igcd ].gc = fai_gc_content(stats, stats->gcd_pos, stats->info->gcd_bin_size);
+            }
+
+            count_mismatches_per_cycle(stats,bam_line,read_len);
+        }
+        // No reference and first pass, new chromosome or sequence going beyond the end of the gcd bin
+        else if ( stats->gcd_pos==-1 || stats->tid != bam_line->core.tid || bam_line->core.pos - stats->gcd_pos > stats->info->gcd_bin_size )
+        {
+            // First pass or a new chromosome
+            stats->tid     = bam_line->core.tid;
+            stats->gcd_pos = bam_line->core.pos;
+            stats->igcd++;
+            if ( stats->igcd >= stats->ngcd )
+                realloc_gcd_buffer(stats, readlen);
+        }
+        stats->gcd[ stats->igcd ].depth++;
+        // When no reference sequence is given, approximate the GC from the read (much shorter window, but otherwise OK)
+        if ( !stats->info->fai )
+            stats->gcd[ stats->igcd ].gc += (float) gc_count / seq_len;
+
+        // Coverage distribution graph
+        round_buffer_flush(stats,bam_line->core.pos);
+        if ( stats->regions ) {
+            hts_pos_t p = bam_line->core.pos, pnew, pmin = 0, pmax = 0;
+            uint32_t j = 0;
+            i = 0;
+            while ( j < bam_line->core.n_cigar && i < stats->nchunks ) {
+                int op = bam_cigar_op(bam_get_cigar(bam_line)[j]);
+                int oplen = bam_cigar_oplen(bam_get_cigar(bam_line)[j]);
+                switch(op) {
+                case BAM_CMATCH:
+                case BAM_CEQUAL:
+                case BAM_CDIFF:
+                    pmin = MAX(p, stats->chunks[i].beg-1); // 0 based
+                    pmax = MIN(p+oplen, stats->chunks[i].end); // 1 based
+                    if ( pmax > pmin ) {
+                        if ( stats->info->remove_overlaps )
+                            remove_overlaps(bam_line, read_pairs, stats, pmin, pmax);
+                        else
+                            round_buffer_insert_read(&(stats->cov_rbuf), pmin, pmax);
+                    }
+                    break;
+                case BAM_CDEL:
+                    break;
+                }
+                pnew = p + (bam_cigar_type(op)&2 ? oplen : 0); // consumes reference
+
+                if ( pnew >= stats->chunks[i].end ) {
+                    // go to the next chunk
+                    i++;
+                } else {
+                    // go to the next CIGAR op
+                    j++;
+                    p = pnew;
+                }
+            }
+        } else {
+            hts_pos_t p = bam_line->core.pos;
+            uint32_t j;
+            for (j = 0; j < bam_line->core.n_cigar; j++) {
+                int op = bam_cigar_op(bam_get_cigar(bam_line)[j]);
+                int oplen = bam_cigar_oplen(bam_get_cigar(bam_line)[j]);
+                switch(op) {
+                case BAM_CMATCH:
+                case BAM_CEQUAL:
+                case BAM_CDIFF:
+                    if ( stats->info->remove_overlaps )
+                        remove_overlaps(bam_line, read_pairs, stats, p, p+oplen);
+                    else
+                        round_buffer_insert_read(&(stats->cov_rbuf), p, p+oplen);
+                    break;
+                case BAM_CDEL:
+                    break;
+                }
+                p += bam_cigar_type(op)&2 ? oplen : 0; // consumes reference
+            }
+        }
+        if ( stats->info->remove_overlaps )
+           remove_overlaps(bam_line, read_pairs, stats, -1LL, -1LL); //remove the line from the hash table
+    }
+}
+
+// Sort by GC and depth
+#define GCD_t(x) ((gc_depth_t *)x)
+static int gcd_cmp(const void *a, const void *b)
+{
+    if ( GCD_t(a)->gc < GCD_t(b)->gc ) return -1;
+    if ( GCD_t(a)->gc > GCD_t(b)->gc ) return 1;
+    if ( GCD_t(a)->depth < GCD_t(b)->depth ) return -1;
+    if ( GCD_t(a)->depth > GCD_t(b)->depth ) return 1;
+    return 0;
+}
+#undef GCD_t
+
+float gcd_percentile(gc_depth_t *gcd, int N, int p)
+{
+    float n,d;
+    int k;
+
+    n = (float)p*(N+1)/100;
+    k = n;
+    if ( k<=0 )
+        return gcd[0].depth;
+    if ( k>=N )
+        return gcd[N-1].depth;
+
+    d = n - k;
+    return gcd[k-1].depth + d*(gcd[k].depth - gcd[k-1].depth);
+}
+
+void output_stats(FILE *to, stats_t *stats, int sparse)
+{
+    // Calculate average insert size and standard deviation (from the main bulk data only)
+    int isize, ibulk=0, icov;
+    uint64_t nisize=0, nisize_inward=0, nisize_outward=0, nisize_other=0, cov_sum=0;
+    double bulk=0, avg_isize=0, sd_isize=0;
+    for (isize=0; isize<stats->isize->nitems(stats->isize->data); isize++)
+    {
+        // Each pair was counted twice
+        stats->isize->set_inward(stats->isize->data, isize, stats->isize->inward(stats->isize->data, isize) * 0.5);
+        stats->isize->set_outward(stats->isize->data, isize, stats->isize->outward(stats->isize->data, isize) * 0.5);
+        stats->isize->set_other(stats->isize->data, isize, stats->isize->other(stats->isize->data, isize) * 0.5);
+
+        nisize_inward += stats->isize->inward(stats->isize->data, isize);
+        nisize_outward += stats->isize->outward(stats->isize->data, isize);
+        nisize_other += stats->isize->other(stats->isize->data, isize);
+        nisize += stats->isize->inward(stats->isize->data, isize) + stats->isize->outward(stats->isize->data, isize) + stats->isize->other(stats->isize->data, isize);
+    }
+
+    for (isize=0; isize<stats->isize->nitems(stats->isize->data); isize++)
+    {
+        uint64_t num = stats->isize->inward(stats->isize->data, isize) +  stats->isize->outward(stats->isize->data, isize) + stats->isize->other(stats->isize->data, isize);
+        if (num > 0) ibulk = isize + 1;
+        bulk += num;
+        avg_isize += isize * (stats->isize->inward(stats->isize->data, isize) +  stats->isize->outward(stats->isize->data, isize) + stats->isize->other(stats->isize->data, isize));
+
+        if ( bulk/nisize > stats->info->isize_main_bulk )
+        {
+            ibulk  = isize+1;
+            nisize = bulk;
+            break;
+        }
+    }
+    avg_isize /= nisize ? nisize : 1;
+    for (isize=1; isize<ibulk; isize++)
+        sd_isize += (stats->isize->inward(stats->isize->data, isize) + stats->isize->outward(stats->isize->data, isize) +stats->isize->other(stats->isize->data, isize)) * (isize-avg_isize)*(isize-avg_isize) / (nisize ? nisize : 1);
+    sd_isize = sqrt(sd_isize);
+
+    fprintf(to, "# This file was produced by samtools stats (%s+htslib-%s) and can be plotted using plot-bamstats\n", samtools_version(), hts_version());
+    if( stats->split_name != NULL ){
+        fprintf(to, "# This file contains statistics only for reads with tag: %s=%s\n", stats->info->split_tag, stats->split_name);
+    }
+    else{
+        fprintf(to, "# This file contains statistics for all reads.\n");
+    }
+    fprintf(to, "# The command line was:  %s",stats->info->argv[0]);
+    int i;
+    for (i=1; i<stats->info->argc; i++)
+        fprintf(to, " %s", stats->info->argv[i]);
+    fprintf(to, "\n");
+    fprintf(to, "# CHK, Checksum\t[2]Read Names\t[3]Sequences\t[4]Qualities\n");
+    fprintf(to, "# CHK, CRC32 of reads which passed filtering followed by addition (32bit overflow)\n");
+    fprintf(to, "CHK\t%08x\t%08x\t%08x\n", stats->checksum.names,stats->checksum.reads,stats->checksum.quals);
+    fprintf(to, "# Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part.\n");
+    fprintf(to, "SN\traw total sequences:\t%ld\t# excluding supplementary and secondary reads\n", (long)(stats->nreads_filtered+stats->nreads_1st+stats->nreads_2nd+stats->nreads_other));  // not counting excluded seqs (and none of the below)
+    fprintf(to, "SN\tfiltered sequences:\t%ld\n", (long)stats->nreads_filtered);
+    fprintf(to, "SN\tsequences:\t%ld\n", (long)(stats->nreads_1st+stats->nreads_2nd+stats->nreads_other));
+    fprintf(to, "SN\tis sorted:\t%d\n", stats->is_sorted ? 1 : 0);
+    fprintf(to, "SN\t1st fragments:\t%ld\n", (long)stats->nreads_1st);
+    fprintf(to, "SN\tlast fragments:\t%ld\n", (long)stats->nreads_2nd);
+    fprintf(to, "SN\treads mapped:\t%ld\n", (long)(stats->nreads_paired_and_mapped+stats->nreads_single_mapped));
+    fprintf(to, "SN\treads mapped and paired:\t%ld\t# paired-end technology bit set + both mates mapped\n", (long)stats->nreads_paired_and_mapped);
+    fprintf(to, "SN\treads unmapped:\t%ld\n", (long)stats->nreads_unmapped);
+    fprintf(to, "SN\treads properly paired:\t%ld\t# proper-pair bit set\n", (long)stats->nreads_properly_paired);
+    fprintf(to, "SN\treads paired:\t%ld\t# paired-end technology bit set\n", (long)stats->nreads_paired_tech);
+    fprintf(to, "SN\treads duplicated:\t%ld\t# PCR or optical duplicate bit set\n", (long)stats->nreads_dup);
+    fprintf(to, "SN\treads MQ0:\t%ld\t# mapped and MQ=0\n", (long)stats->nreads_mq0);
+    fprintf(to, "SN\treads QC failed:\t%ld\n", (long)stats->nreads_QCfailed);
+    fprintf(to, "SN\tnon-primary alignments:\t%ld\n", (long)stats->nreads_secondary);
+    fprintf(to, "SN\tsupplementary alignments:\t%ld\n", (long)stats->nreads_supplementary);
+    fprintf(to, "SN\ttotal length:\t%ld\t# ignores clipping\n", (long)stats->total_len);
+    fprintf(to, "SN\ttotal first fragment length:\t%ld\t# ignores clipping\n", (long)stats->total_len_1st);
+    fprintf(to, "SN\ttotal last fragment length:\t%ld\t# ignores clipping\n", (long)stats->total_len_2nd);
+    fprintf(to, "SN\tbases mapped:\t%ld\t# ignores clipping\n", (long)stats->nbases_mapped);                 // the length of the whole read goes here, including soft-clips etc.
+    fprintf(to, "SN\tbases mapped (cigar):\t%ld\t# more accurate\n", (long)stats->nbases_mapped_cigar);   // only matched and inserted bases are counted here
+    fprintf(to, "SN\tbases trimmed:\t%ld\n", (long)stats->nbases_trimmed);
+    fprintf(to, "SN\tbases duplicated:\t%ld\n", (long)stats->total_len_dup);
+    fprintf(to, "SN\tmismatches:\t%ld\t# from NM fields\n", (long)stats->nmismatches);
+    fprintf(to, "SN\terror rate:\t%e\t# mismatches / bases mapped (cigar)\n", stats->nbases_mapped_cigar ? (float)stats->nmismatches/stats->nbases_mapped_cigar : 0);
+    float avg_read_length = (stats->nreads_1st+stats->nreads_2nd+stats->nreads_other)?stats->total_len/(stats->nreads_1st+stats->nreads_2nd+stats->nreads_other):0;
+    fprintf(to, "SN\taverage length:\t%.0f\n", avg_read_length);
+    fprintf(to, "SN\taverage first fragment length:\t%.0f\n", stats->nreads_1st? (float)stats->total_len_1st/stats->nreads_1st:0);
+    fprintf(to, "SN\taverage last fragment length:\t%.0f\n", stats->nreads_2nd? (float)stats->total_len_2nd/stats->nreads_2nd:0);
+    fprintf(to, "SN\tmaximum length:\t%d\n", stats->max_len);
+    fprintf(to, "SN\tmaximum first fragment length:\t%d\n", stats->max_len_1st);
+    fprintf(to, "SN\tmaximum last fragment length:\t%d\n", stats->max_len_2nd);
+    fprintf(to, "SN\taverage quality:\t%.1f\n", stats->total_len?stats->sum_qual/stats->total_len:0);
+    fprintf(to, "SN\tinsert size average:\t%.1f\n", avg_isize);
+    fprintf(to, "SN\tinsert size standard deviation:\t%.1f\n", sd_isize);
+    fprintf(to, "SN\tinward oriented pairs:\t%ld\n", (long)nisize_inward);
+    fprintf(to, "SN\toutward oriented pairs:\t%ld\n", (long)nisize_outward);
+    fprintf(to, "SN\tpairs with other orientation:\t%ld\n", (long)nisize_other);
+    fprintf(to, "SN\tpairs on different chromosomes:\t%ld\n", (long)stats->nreads_anomalous/2);
+    fprintf(to, "SN\tpercentage of properly paired reads (%%):\t%.1f\n", (stats->nreads_1st+stats->nreads_2nd+stats->nreads_other)? (float)(100*stats->nreads_properly_paired)/(stats->nreads_1st+stats->nreads_2nd+stats->nreads_other):0);
+    if ( stats->target_count ) {
+        fprintf(to, "SN\tbases inside the target:\t%" PRIu64 "\n", stats->target_count);
+        for (icov=stats->info->cov_threshold+1; icov<stats->ncov; icov++)
+            cov_sum += stats->cov[icov];
+        fprintf(to, "SN\tpercentage of target genome with coverage > %d (%%):\t%.2f\n", stats->info->cov_threshold, (float)(100*cov_sum)/stats->target_count);
+    }
+
+    int ibase,iqual;
+    if ( stats->max_len<stats->nbases ) stats->max_len++;
+    if ( stats->max_qual+1<stats->nquals ) stats->max_qual++;
+    fprintf(to, "# First Fragment Qualities. Use `grep ^FFQ | cut -f 2-` to extract this part.\n");
+    fprintf(to, "# Columns correspond to qualities and rows to cycles. First column is the cycle number.\n");
+    for (ibase=0; ibase<stats->max_len_1st; ibase++)
+    {
+        fprintf(to, "FFQ\t%d",ibase+1);
+        for (iqual=0; iqual<=stats->max_qual; iqual++)
+        {
+            fprintf(to, "\t%ld", (long)stats->quals_1st[ibase*stats->nquals+iqual]);
+        }
+        fprintf(to, "\n");
+    }
+    fprintf(to, "# Last Fragment Qualities. Use `grep ^LFQ | cut -f 2-` to extract this part.\n");
+    fprintf(to, "# Columns correspond to qualities and rows to cycles. First column is the cycle number.\n");
+    for (ibase=0; ibase<stats->max_len_2nd; ibase++)
+    {
+        fprintf(to, "LFQ\t%d",ibase+1);
+        for (iqual=0; iqual<=stats->max_qual; iqual++)
+        {
+            fprintf(to, "\t%ld", (long)stats->quals_2nd[ibase*stats->nquals+iqual]);
+        }
+        fprintf(to, "\n");
+    }
+    if ( stats->mpc_buf )
+    {
+        fprintf(to, "# Mismatches per cycle and quality. Use `grep ^MPC | cut -f 2-` to extract this part.\n");
+        fprintf(to, "# Columns correspond to qualities, rows to cycles. First column is the cycle number, second\n");
+        fprintf(to, "# is the number of N's and the rest is the number of mismatches\n");
+        for (ibase=0; ibase<stats->max_len; ibase++)
+        {
+            fprintf(to, "MPC\t%d",ibase+1);
+            for (iqual=0; iqual<=stats->max_qual; iqual++)
+            {
+                fprintf(to, "\t%ld", (long)stats->mpc_buf[ibase*stats->nquals+iqual]);
+            }
+            fprintf(to, "\n");
+        }
+    }
+    fprintf(to, "# GC Content of first fragments. Use `grep ^GCF | cut -f 2-` to extract this part.\n");
+    int ibase_prev = 0;
+    for (ibase=0; ibase<stats->ngc; ibase++)
+    {
+        if ( stats->gc_1st[ibase]==stats->gc_1st[ibase_prev] ) continue;
+        fprintf(to, "GCF\t%.2f\t%ld\n", (ibase+ibase_prev)*0.5*100./(stats->ngc-1), (long)stats->gc_1st[ibase_prev]);
+        ibase_prev = ibase;
+    }
+    fprintf(to, "# GC Content of last fragments. Use `grep ^GCL | cut -f 2-` to extract this part.\n");
+    ibase_prev = 0;
+    for (ibase=0; ibase<stats->ngc; ibase++)
+    {
+        if ( stats->gc_2nd[ibase]==stats->gc_2nd[ibase_prev] ) continue;
+        fprintf(to, "GCL\t%.2f\t%ld\n", (ibase+ibase_prev)*0.5*100./(stats->ngc-1), (long)stats->gc_2nd[ibase_prev]);
+        ibase_prev = ibase;
+    }
+    fprintf(to, "# ACGT content per cycle. Use `grep ^GCC | cut -f 2-` to extract this part. The columns are: cycle; A,C,G,T base counts as a percentage of all A/C/G/T bases [%%]; and N and O counts as a percentage of all A/C/G/T bases [%%]\n");
+    for (ibase=0; ibase<stats->max_len; ibase++)
+    {
+        acgtno_count_t *acgtno_count_1st = &(stats->acgtno_cycles_1st[ibase]);
+        acgtno_count_t *acgtno_count_2nd = &(stats->acgtno_cycles_2nd[ibase]);
+        uint64_t acgt_sum = acgtno_count_1st->a + acgtno_count_1st->c + acgtno_count_1st->g + acgtno_count_1st->t +
+                acgtno_count_2nd->a + acgtno_count_2nd->c + acgtno_count_2nd->g + acgtno_count_2nd->t;
+        if ( ! acgt_sum ) continue;
+        fprintf(to, "GCC\t%d\t%.2f\t%.2f\t%.2f\t%.2f\t%.2f\t%.2f\n", ibase+1,
+                100.*(acgtno_count_1st->a + acgtno_count_2nd->a)/acgt_sum,
+                100.*(acgtno_count_1st->c + acgtno_count_2nd->c)/acgt_sum,
+                100.*(acgtno_count_1st->g + acgtno_count_2nd->g)/acgt_sum,
+                100.*(acgtno_count_1st->t + acgtno_count_2nd->t)/acgt_sum,
+                100.*(acgtno_count_1st->n + acgtno_count_2nd->n)/acgt_sum,
+                100.*(acgtno_count_1st->other + acgtno_count_2nd->other)/acgt_sum);
+    }
+    fprintf(to, "# ACGT content per cycle, read oriented. Use `grep ^GCT | cut -f 2-` to extract this part. The columns are: cycle; A,C,G,T base counts as a percentage of all A/C/G/T bases [%%]\n");
+    for (ibase=0; ibase<stats->max_len; ibase++)
+    {
+        acgtno_count_t *acgtno_count = &(stats->acgtno_revcomp[ibase]);
+        uint64_t acgt_sum = acgtno_count->a + acgtno_count->c + acgtno_count->g + acgtno_count->t;
+        if ( ! acgt_sum ) continue;
+        fprintf(to, "GCT\t%d\t%.2f\t%.2f\t%.2f\t%.2f\n", ibase+1,
+                100.*(acgtno_count->a)/acgt_sum,
+                100.*(acgtno_count->c)/acgt_sum,
+                100.*(acgtno_count->g)/acgt_sum,
+                100.*(acgtno_count->t)/acgt_sum);
+    }
+
+    uint64_t tA=0, tC=0, tG=0, tT=0, tN=0;
+    fprintf(to, "# ACGT content per cycle for first fragments. Use `grep ^FBC | cut -f 2-` to extract this part. The columns are: cycle; A,C,G,T base counts as a percentage of all A/C/G/T bases [%%]; and N and O counts as a percentage of all A/C/G/T bases [%%]\n");
+    for (ibase=0; ibase<stats->max_len; ibase++)
+    {
+        acgtno_count_t *acgtno_count_1st = &(stats->acgtno_cycles_1st[ibase]);
+        uint64_t acgt_sum_1st = acgtno_count_1st->a + acgtno_count_1st->c + acgtno_count_1st->g + acgtno_count_1st->t;
+        tA += acgtno_count_1st->a;
+        tC += acgtno_count_1st->c;
+        tG += acgtno_count_1st->g;
+        tT += acgtno_count_1st->t;
+        tN += acgtno_count_1st->n;
+
+        if ( acgt_sum_1st )
+            fprintf(to, "FBC\t%d\t%.2f\t%.2f\t%.2f\t%.2f\t%.2f\t%.2f\n", ibase+1,
+                    100.*acgtno_count_1st->a/acgt_sum_1st,
+                    100.*acgtno_count_1st->c/acgt_sum_1st,
+                    100.*acgtno_count_1st->g/acgt_sum_1st,
+                    100.*acgtno_count_1st->t/acgt_sum_1st,
+                    100.*acgtno_count_1st->n/acgt_sum_1st,
+                    100.*acgtno_count_1st->other/acgt_sum_1st);
+
+    }
+    fprintf(to, "# ACGT raw counters for first fragments. Use `grep ^FTC | cut -f 2-` to extract this part. The columns are: A,C,G,T,N base counters\n");
+    fprintf(to, "FTC\t%" PRId64 "\t%" PRId64 "\t%" PRId64 "\t%" PRId64 "\t%" PRId64 "\n", tA, tC, tG, tT, tN);
+    tA=0, tC=0, tG=0, tT=0, tN=0;
+    fprintf(to, "# ACGT content per cycle for last fragments. Use `grep ^LBC | cut -f 2-` to extract this part. The columns are: cycle; A,C,G,T base counts as a percentage of all A/C/G/T bases [%%]; and N and O counts as a percentage of all A/C/G/T bases [%%]\n");
+    for (ibase=0; ibase<stats->max_len; ibase++)
+    {
+        acgtno_count_t *acgtno_count_2nd = &(stats->acgtno_cycles_2nd[ibase]);
+        uint64_t acgt_sum_2nd = acgtno_count_2nd->a + acgtno_count_2nd->c + acgtno_count_2nd->g + acgtno_count_2nd->t;
+        tA += acgtno_count_2nd->a;
+        tC += acgtno_count_2nd->c;
+        tG += acgtno_count_2nd->g;
+        tT += acgtno_count_2nd->t;
+        tN += acgtno_count_2nd->n;
+
+        if ( acgt_sum_2nd )
+            fprintf(to, "LBC\t%d\t%.2f\t%.2f\t%.2f\t%.2f\t%.2f\t%.2f\n", ibase+1,
+                    100.*acgtno_count_2nd->a/acgt_sum_2nd,
+                    100.*acgtno_count_2nd->c/acgt_sum_2nd,
+                    100.*acgtno_count_2nd->g/acgt_sum_2nd,
+                    100.*acgtno_count_2nd->t/acgt_sum_2nd,
+                    100.*acgtno_count_2nd->n/acgt_sum_2nd,
+                    100.*acgtno_count_2nd->other/acgt_sum_2nd);
+
+    }
+    fprintf(to, "# ACGT raw counters for last fragments. Use `grep ^LTC | cut -f 2-` to extract this part. The columns are: A,C,G,T,N base counters\n");
+    fprintf(to, "LTC\t%" PRId64 "\t%" PRId64 "\t%" PRId64 "\t%" PRId64 "\t%" PRId64 "\n", tA, tC, tG, tT, tN);
+
+    int tag;
+    for (tag=0; tag<stats->ntags; tag++) {
+        if (stats->tags_barcode[tag].nbases) {
+            fprintf(to, "# ACGT content per cycle for barcodes. Use `grep ^%sC | cut -f 2-` to extract this part. The columns are: cycle; A,C,G,T base counts as a percentage of all A/C/G/T bases [%%]; and N counts as a percentage of all A/C/G/T bases [%%]\n",
+                    stats->tags_barcode[tag].tag_name);
+            for (ibase=0; ibase<stats->tags_barcode[tag].nbases; ibase++)
+            {
+                if (ibase == stats->tags_barcode[tag].tag_sep)
+                    continue;
+
+                acgtno_count_t *acgtno_count = stats->acgtno_barcode + stats->tags_barcode[tag].offset + ibase;
+                uint64_t acgt_sum = acgtno_count->a + acgtno_count->c + acgtno_count->g + acgtno_count->t;
+
+                if ( acgt_sum )
+                    fprintf(to, "%sC%d\t%d\t%.2f\t%.2f\t%.2f\t%.2f\t%.2f\n", stats->tags_barcode[tag].tag_name,
+                            stats->tags_barcode[tag].tag_sep < 0 || ibase < stats->tags_barcode[tag].tag_sep ? 1 : 2,
+                            stats->tags_barcode[tag].tag_sep < 0 || ibase < stats->tags_barcode[tag].tag_sep ? ibase+1 : ibase-stats->tags_barcode[tag].tag_sep,
+                                    100.*acgtno_count->a/acgt_sum,
+                                    100.*acgtno_count->c/acgt_sum,
+                                    100.*acgtno_count->g/acgt_sum,
+                                    100.*acgtno_count->t/acgt_sum,
+                                    100.*acgtno_count->n/acgt_sum);
+            }
+
+            fprintf(to, "# Barcode Qualities. Use `grep ^%sQ | cut -f 2-` to extract this part.\n", stats->tags_barcode[tag].qual_name);
+            fprintf(to, "# Columns correspond to qualities and rows to barcode cycles. First column is the cycle number.\n");
+            for (ibase=0; ibase<stats->tags_barcode[tag].nbases; ibase++)
+            {
+                if (ibase == stats->tags_barcode[tag].tag_sep)
+                    continue;
+
+                fprintf(to, "%sQ%d\t%d", stats->tags_barcode[tag].qual_name,
+                        stats->tags_barcode[tag].tag_sep < 0 || ibase < stats->tags_barcode[tag].tag_sep ? 1 : 2,
+                        stats->tags_barcode[tag].tag_sep < 0 || ibase < stats->tags_barcode[tag].tag_sep ? ibase+1 : ibase-stats->tags_barcode[tag].tag_sep);
+                for (iqual=0; iqual<=stats->tags_barcode[tag].max_qual; iqual++)
+                {
+                    fprintf(to, "\t%ld", (long)stats->quals_barcode[(stats->tags_barcode[tag].offset + ibase)*stats->nquals+iqual]);
+                }
+                fprintf(to, "\n");
+            }
+        }
+    }
+
+    fprintf(to, "# Insert sizes. Use `grep ^IS | cut -f 2-` to extract this part. The columns are: insert size, pairs total, inward oriented pairs, outward oriented pairs, other pairs\n");
+    for (isize=0; isize<ibulk; isize++) {
+        long in = (long)(stats->isize->inward(stats->isize->data, isize));
+        long out = (long)(stats->isize->outward(stats->isize->data, isize));
+        long other = (long)(stats->isize->other(stats->isize->data, isize));
+        if (!sparse || in + out + other > 0) {
+            fprintf(to, "IS\t%d\t%ld\t%ld\t%ld\t%ld\n", isize,  in+out+other,
+                in , out, other);
+        }
+    }
+
+    fprintf(to, "# Read lengths. Use `grep ^RL | cut -f 2-` to extract this part. The columns are: read length, count\n");
+    int ilen;
+    for (ilen=0; ilen<stats->max_len; ilen++)
+    {
+        if ( stats->read_lengths[ilen+1]>0 )
+            fprintf(to, "RL\t%d\t%ld\n", ilen+1, (long)stats->read_lengths[ilen+1]);
+    }
+
+    fprintf(to, "# Read lengths - first fragments. Use `grep ^FRL | cut -f 2-` to extract this part. The columns are: read length, count\n");
+    for (ilen=0; ilen<stats->max_len_1st; ilen++)
+    {
+        if ( stats->read_lengths_1st[ilen+1]>0 )
+            fprintf(to, "FRL\t%d\t%ld\n", ilen+1, (long)stats->read_lengths_1st[ilen+1]);
+    }
+
+    fprintf(to, "# Read lengths - last fragments. Use `grep ^LRL | cut -f 2-` to extract this part. The columns are: read length, count\n");
+    for (ilen=0; ilen<stats->max_len_2nd; ilen++)
+    {
+        if ( stats->read_lengths_2nd[ilen+1]>0 )
+            fprintf(to, "LRL\t%d\t%ld\n", ilen+1, (long)stats->read_lengths_2nd[ilen+1]);
+    }
+
+    fprintf(to, "# Indel distribution. Use `grep ^ID | cut -f 2-` to extract this part. The columns are: length, number of insertions, number of deletions\n");
+
+    for (ilen=0; ilen<stats->nindels; ilen++)
+    {
+        if ( stats->insertions[ilen]>0 || stats->deletions[ilen]>0 )
+            fprintf(to, "ID\t%d\t%ld\t%ld\n", ilen+1, (long)stats->insertions[ilen], (long)stats->deletions[ilen]);
+    }
+
+    fprintf(to, "# Indels per cycle. Use `grep ^IC | cut -f 2-` to extract this part. The columns are: cycle, number of insertions (fwd), .. (rev) , number of deletions (fwd), .. (rev)\n");
+    for (ilen=0; ilen<=stats->nbases; ilen++)
+    {
+        // For deletions we print the index of the cycle before the deleted base (1-based) and for insertions
+        //  the index of the cycle of the first inserted base (also 1-based)
+        if ( stats->ins_cycles_1st[ilen]>0 || stats->ins_cycles_2nd[ilen]>0 || stats->del_cycles_1st[ilen]>0 || stats->del_cycles_2nd[ilen]>0 )
+            fprintf(to, "IC\t%d\t%ld\t%ld\t%ld\t%ld\n", ilen+1, (long)stats->ins_cycles_1st[ilen], (long)stats->ins_cycles_2nd[ilen], (long)stats->del_cycles_1st[ilen], (long)stats->del_cycles_2nd[ilen]);
+    }
+
+    fprintf(to, "# Coverage distribution. Use `grep ^COV | cut -f 2-` to extract this part.\n");
+    if  ( stats->cov[0] )
+        fprintf(to, "COV\t[<%d]\t%d\t%ld\n",stats->info->cov_min,stats->info->cov_min-1, (long)stats->cov[0]);
+    for (icov=1; icov<stats->ncov-1; icov++)
+        if ( stats->cov[icov] )
+            fprintf(to, "COV\t[%d-%d]\t%d\t%ld\n",stats->info->cov_min + (icov-1)*stats->info->cov_step, stats->info->cov_min + icov*stats->info->cov_step-1,stats->info->cov_min + icov*stats->info->cov_step-1, (long)stats->cov[icov]);
+    if ( stats->cov[stats->ncov-1] )
+        fprintf(to, "COV\t[%d<]\t%d\t%ld\n",stats->info->cov_min + (stats->ncov-2)*stats->info->cov_step-1,stats->info->cov_min + (stats->ncov-2)*stats->info->cov_step-1, (long)stats->cov[stats->ncov-1]);
+
+    // Calculate average GC content, then sort by GC and depth
+    fprintf(to, "# GC-depth. Use `grep ^GCD | cut -f 2-` to extract this part. The columns are: GC%%, unique sequence percentiles, 10th, 25th, 50th, 75th and 90th depth percentile\n");
+    uint32_t igcd;
+    for (igcd=0; igcd<stats->igcd; igcd++)
+    {
+        if ( stats->info->fai )
+            stats->gcd[igcd].gc = rint(100. * stats->gcd[igcd].gc);
+        else
+            if ( stats->gcd[igcd].depth )
+                stats->gcd[igcd].gc = rint(100. * stats->gcd[igcd].gc / stats->gcd[igcd].depth);
+    }
+    if ( stats->ngcd )
+        qsort(stats->gcd, stats->igcd+1, sizeof(gc_depth_t), gcd_cmp);
+    igcd = 0;
+    while ( igcd < stats->igcd )
+    {
+        // Calculate percentiles (10,25,50,75,90th) for the current GC content and print
+        uint32_t nbins=0, itmp=igcd;
+        float gc = stats->gcd[igcd].gc;
+        while ( itmp<stats->igcd && fabs(stats->gcd[itmp].gc-gc)<0.1 )
+        {
+            nbins++;
+            itmp++;
+        }
+        fprintf(to, "GCD\t%.1f\t%.3f\t%.3f\t%.3f\t%.3f\t%.3f\t%.3f\n", gc, (igcd+nbins+1)*100./(stats->igcd+1),
+                gcd_percentile(&(stats->gcd[igcd]),nbins,10) *avg_read_length/stats->info->gcd_bin_size,
+                gcd_percentile(&(stats->gcd[igcd]),nbins,25) *avg_read_length/stats->info->gcd_bin_size,
+                gcd_percentile(&(stats->gcd[igcd]),nbins,50) *avg_read_length/stats->info->gcd_bin_size,
+                gcd_percentile(&(stats->gcd[igcd]),nbins,75) *avg_read_length/stats->info->gcd_bin_size,
+                gcd_percentile(&(stats->gcd[igcd]),nbins,90) *avg_read_length/stats->info->gcd_bin_size
+              );
+        igcd += nbins;
+    }
+}
+
+static void init_regions(stats_t *stats, const char *file, stats_info_t* info)
+{
+    FILE *fp = fopen(file,"r");
+    if ( !fp ) error("%s: %s\n",file,strerror(errno));
+
+    kstring_t line = { 0, 0, NULL };
+    int warned = 0, r, p, new_p;
+    int prev_tid=-1;
+    hts_pos_t prev_pos=-1LL;
+    while (line.l = 0, kgetline(&line, (kgets_func *)fgets, fp) >= 0)
+    {
+        if ( line.s[0] == '#' ) continue;
+
+        int i = 0;
+        while ( i<line.l && !isspace(line.s[i]) ) i++;
+        if ( i>=line.l ) error("Could not parse the file: %s [%s]\n", file, line.s);
+        line.s[i] = '\0';
+
+        int tid = bam_name2id(stats->info->sam_header, line.s);
+        if ( tid < 0 )
+        {
+            if ( !warned )
+                fprintf(samtools_stderr,"Warning: Some sequences not present in the BAM, e.g. \"%s\". This message is printed only once.\n", line.s);
+            warned = 1;
+            continue;
+        }
+
+        if ( tid >= stats->nregions )
+        {
+            if(!(stats->regions = realloc(stats->regions,sizeof(regions_t)*(tid+REG_INC))))
+                error("Could not allocate memory for region.\n");
+
+            int j;
+            for (j=stats->nregions; j<tid+REG_INC; j++)
+            {
+                stats->regions[j].npos = stats->regions[j].mpos = stats->regions[j].cpos = 0;
+                stats->regions[j].pos = NULL;
+            }
+            stats->nregions = tid+REG_INC;
+        }
+        int npos = stats->regions[tid].npos;
+        if ( npos >= stats->regions[tid].mpos )
+        {
+            stats->regions[tid].mpos = npos+POS_INC;
+            if (!(stats->regions[tid].pos = realloc(stats->regions[tid].pos, sizeof(hts_pair_pos_t)*stats->regions[tid].mpos)))
+                error("Could not allocate memory for interval.\n");
+        }
+
+        if ( (sscanf(&line.s[i+1],"%"SCNd64" %"SCNd64, &stats->regions[tid].pos[npos].beg, &stats->regions[tid].pos[npos].end))!=2 ) error("Could not parse the region [%s]\n", &line.s[i+1]);
+        if ( prev_tid==-1 || prev_tid!=tid )
+        {
+            prev_tid = tid;
+            prev_pos = stats->regions[tid].pos[npos].beg;
+        }
+        if ( prev_pos>stats->regions[tid].pos[npos].beg )
+            error("The positions are not in chromosomal order (%s:%"PRIhts_pos" comes after %"PRIhts_pos")\n", line.s, stats->regions[tid].pos[npos].beg, prev_pos);
+        stats->regions[tid].npos++;
+        if ( stats->regions[tid].npos > stats->nchunks )
+            stats->nchunks = stats->regions[tid].npos;
+    }
+    free(line.s);
+    if ( !stats->regions ) error("Unable to map the -t sequences to the BAM sequences.\n");
+    fclose(fp);
+
+    // sort region intervals and remove duplicates
+    for (r = 0; r < stats->nregions; r++) {
+        regions_t *reg = &stats->regions[r];
+        if ( reg->npos > 1 ) {
+            qsort(reg->pos, reg->npos, sizeof(hts_pair_pos_t), regions_lt);
+            for (new_p = 0, p = 1; p < reg->npos; p++) {
+                if ( reg->pos[new_p].end < reg->pos[p].beg )
+                    reg->pos[++new_p] = reg->pos[p];
+                else if ( reg->pos[new_p].end < reg->pos[p].end )
+                    reg->pos[new_p].end = reg->pos[p].end;
+            }
+            reg->npos = ++new_p;
+        }
+        for (p = 0; p < reg->npos; p++) {
+            if (reg->pos[p].end < HTS_POS_MAX) {
+                stats->target_count += (reg->pos[p].end - reg->pos[p].beg + 1);
+            } else {
+                uint64_t hdr_end = sam_hdr_tid2len(info->sam_header, r);
+                if (hdr_end)
+                    stats->target_count += (hdr_end - reg->pos[p].beg + 1);
+            }
+        }
+    }
+
+    if (!(stats->chunks = calloc(stats->nchunks, sizeof(hts_pair_pos_t))))
+        error("Could not allocate memory for chunk.\n");
+}
+
+void destroy_regions(stats_t *stats)
+{
+    int i;
+    for (i=0; i<stats->nregions; i++)
+    {
+        if ( !stats->regions[i].mpos ) continue;
+        free(stats->regions[i].pos);
+    }
+    if ( stats->regions ) free(stats->regions);
+    if ( stats->chunks ) free(stats->chunks);
+}
+
+void reset_regions(stats_t *stats)
+{
+    int i;
+    for (i=0; i<stats->nregions; i++)
+        stats->regions[i].cpos = 0;
+}
+
+int is_in_regions(bam1_t *bam_line, stats_t *stats)
+{
+    if ( !stats->regions ) return 1;
+
+    if ( bam_line->core.tid >= stats->nregions || bam_line->core.tid<0 ) return 0;
+    if ( !stats->is_sorted ) error("The BAM must be sorted in order for -t to work.\n");
+
+    regions_t *reg = &stats->regions[bam_line->core.tid];
+    if ( reg->cpos==reg->npos ) return 0;       // done for this chr
+
+    // Find a matching interval or skip this read. No splicing of reads is done, no indels or soft clips considered,
+    //  even small overlap is enough to include the read in the stats.
+    int i = reg->cpos;
+    while ( i<reg->npos && reg->pos[i].end<=bam_line->core.pos ) i++;
+    if ( i>=reg->npos ) { reg->cpos = reg->npos; return 0; }
+    int64_t endpos = bam_endpos(bam_line);
+    if ( endpos < reg->pos[i].beg ) return 0;
+
+    //found a read overlapping a region
+    reg->cpos = i;
+    stats->reg_from = reg->pos[i].beg;
+    stats->reg_to   = reg->pos[i].end;
+
+    //now find all the overlapping chunks
+    stats->nchunks = 0;
+    while (i < reg->npos) {
+        if (bam_line->core.pos < reg->pos[i].end && endpos >= reg->pos[i].beg) {
+            stats->chunks[stats->nchunks].beg = MAX(bam_line->core.pos+1, reg->pos[i].beg);
+            stats->chunks[stats->nchunks].end = MIN(endpos, reg->pos[i].end);
+            stats->nchunks++;
+        }
+        i++;
+    }
+
+    return 1;
+}
+
+int replicate_regions(stats_t *stats, hts_itr_multi_t *iter, stats_info_t *info) {
+    if ( !stats || !iter)
+        return 1;
+
+    int i, j, tid;
+    stats->nregions = iter->n_reg;
+    stats->regions = calloc(stats->nregions, sizeof(regions_t));
+    stats->chunks = calloc(stats->nchunks, sizeof(hts_pair_pos_t));
+    if ( !stats->regions || !stats->chunks )
+        return 1;
+
+    for (i = 0; i < iter->n_reg; i++) {
+        tid = iter->reg_list[i].tid;
+        if ( tid < 0 )
+            continue;
+
+        if ( tid >= stats->nregions ) {
+            regions_t *tmp = realloc(stats->regions, (tid+10) * sizeof(regions_t));
+            if ( !tmp )
+                return 1;
+            stats->regions = tmp;
+            memset(stats->regions + stats->nregions, 0,
+                   (tid+10-stats->nregions) * sizeof(regions_t));
+            stats->nregions = tid+10;
+        }
+
+        stats->regions[tid].mpos = stats->regions[tid].npos = iter->reg_list[i].count;
+        stats->regions[tid].pos = calloc(stats->regions[tid].mpos, sizeof(hts_pair_pos_t));
+        if ( !stats->regions[tid].pos )
+            return 1;
+
+        for (j = 0; j < stats->regions[tid].npos; j++) {
+            stats->regions[tid].pos[j].beg = iter->reg_list[i].intervals[j].beg+1;
+            stats->regions[tid].pos[j].end = iter->reg_list[i].intervals[j].end;
+            if (stats->regions[tid].pos[j].end < HTS_POS_MAX) {
+                stats->target_count += (stats->regions[tid].pos[j].end - stats->regions[tid].pos[j].beg + 1);
+            } else {
+                uint64_t hdr_end = sam_hdr_tid2len(info->sam_header, tid);
+                if (hdr_end)
+                    stats->target_count += (hdr_end - stats->regions[tid].pos[j].beg + 1);
+            }
+        }
+    }
+
+    return 0;
+}
+
+static void init_group_id(stats_t *stats, stats_info_t *info, const char *id)
+{
+    stats->rg_hash = kh_init(rg);
+    if (!stats->rg_hash) error("Could not initialise RG set\n");
+    sam_hdr_t *hdr = info->sam_header;
+    const char *key;
+    kstring_t sm = KS_INITIALIZE;
+    int i, ret, nrg = sam_hdr_count_lines(hdr, "RG");
+    if (nrg < 0) error("Could not parse header\n");
+
+    for (i=0; i<nrg; i++) {
+        key = sam_hdr_line_name(hdr, "RG", i);
+        if (!strcmp(key, id)) {
+            kh_put(rg, stats->rg_hash, key, &ret);
+            if (ret == -1) { ks_free(&sm); error("Could not add key \"%s\" to RG set\n", key); }
+        } else { /* Check for SM name, as per manual */
+            if (!sam_hdr_find_tag_pos(hdr, "RG", i, "SM", &sm)) {
+                if (!strcmp(ks_c_str(&sm), id)) {
+                    kh_put(rg, stats->rg_hash, key, &ret);
+                    if (ret == -1) { ks_free(&sm); error("Could not add key \"%s\" to RG set\n", key); }
+                }
+            }
+        }
+    }
+
+    ks_free(&sm);
+}
+
+
+static void HTS_NORETURN error(const char *format, ...)
+{
+    if ( !format )
+    {
+        fprintf(samtools_stdout, "About: The program collects statistics from BAM files. The output can be visualized using plot-bamstats.\n");
+        fprintf(samtools_stdout, "Usage: samtools stats [OPTIONS] file.bam\n");
+        fprintf(samtools_stdout, "       samtools stats [OPTIONS] file.bam chr:from-to\n");
+        fprintf(samtools_stdout, "Options:\n");
+        fprintf(samtools_stdout, "    -c, --coverage <int>,<int>,<int>    Coverage distribution min,max,step [1,1000,1]\n");
+        fprintf(samtools_stdout, "    -d, --remove-dups                   Exclude from statistics reads marked as duplicates\n");
+        fprintf(samtools_stdout, "    -X, --customized-index-file         Use a customized index file\n");
+        fprintf(samtools_stdout, "    -f, --required-flag  <str|int>      Required flag, 0 for unset. See also `samtools flags` [0]\n");
+        fprintf(samtools_stdout, "    -F, --filtering-flag <str|int>      Filtering flag, 0 for unset. See also `samtools flags` [0]\n");
+        fprintf(samtools_stdout, "        --GC-depth <float>              the size of GC-depth bins (decreasing bin size increases memory requirement) [2e4]\n");
+        fprintf(samtools_stdout, "    -h, --help                          This help message\n");
+        fprintf(samtools_stdout, "    -i, --insert-size <int>             Maximum insert size [8000]\n");
+        fprintf(samtools_stdout, "    -I, --id <string>                   Include only listed read group or sample name\n");
+        fprintf(samtools_stdout, "    -l, --read-length <int>             Include in the statistics only reads with the given read length [-1]\n");
+        fprintf(samtools_stdout, "    -m, --most-inserts <float>          Report only the main part of inserts [0.99]\n");
+        fprintf(samtools_stdout, "    -P, --split-prefix <str>            Path or string prefix for filepaths output by -S (default is input filename)\n");
+        fprintf(samtools_stdout, "    -q, --trim-quality <int>            The BWA trimming parameter [0]\n");
+        fprintf(samtools_stdout, "    -r, --ref-seq <file>                Reference sequence (required for GC-depth and mismatches-per-cycle calculation).\n");
+        fprintf(samtools_stdout, "    -s, --sam                           Ignored (input format is auto-detected).\n");
+        fprintf(samtools_stdout, "    -S, --split <tag>                   Also write statistics to separate files split by tagged field.\n");
+        fprintf(samtools_stdout, "    -t, --target-regions <file>         Do stats in these regions only. Tab-delimited file chr,from,to, 1-based, inclusive.\n");
+        fprintf(samtools_stdout, "    -x, --sparse                        Suppress outputting IS rows where there are no insertions.\n");
+        fprintf(samtools_stdout, "    -p, --remove-overlaps               Remove overlaps of paired-end reads from coverage and base count computations.\n");
+        fprintf(samtools_stdout, "    -g, --cov-threshold <int>           Only bases with coverage above this value will be included in the target percentage computation [0]\n");
+        sam_global_opt_help(samtools_stdout, "-.--.@-.");
+        fprintf(samtools_stdout, "\n");
+    }
+    else
+    {
+        va_list ap;
+        va_start(ap, format);
+        vfprintf(samtools_stderr, format, ap);
+        va_end(ap);
+    }
+    samtools_exit(1);
+}
+
+void cleanup_stats_info(stats_info_t* info){
+    if (info->fai) fai_destroy(info->fai);
+    sam_close(info->sam);
+    free(info);
+}
+
+void cleanup_stats(stats_t* stats)
+{
+    free(stats->cov_rbuf.buffer); free(stats->cov);
+    free(stats->quals_1st); free(stats->quals_2nd);
+    free(stats->gc_1st); free(stats->gc_2nd);
+    stats->isize->isize_free(stats->isize->data);
+    free(stats->isize);
+    free(stats->gcd);
+    free(stats->rseq_buf);
+    free(stats->mpc_buf);
+    free(stats->acgtno_cycles_1st);
+    free(stats->acgtno_cycles_2nd);
+    free(stats->acgtno_revcomp);
+    free(stats->read_lengths);
+    free(stats->read_lengths_1st);
+    free(stats->read_lengths_2nd);
+    free(stats->insertions);
+    free(stats->deletions);
+    free(stats->ins_cycles_1st);
+    free(stats->ins_cycles_2nd);
+    free(stats->del_cycles_1st);
+    free(stats->del_cycles_2nd);
+    if (stats->acgtno_barcode) free(stats->acgtno_barcode);
+    if (stats->quals_barcode) free(stats->quals_barcode);
+    free(stats->tags_barcode);
+    destroy_regions(stats);
+    if ( stats->rg_hash ) kh_destroy(rg, stats->rg_hash);
+    free(stats->split_name);
+    free(stats);
+}
+
+void output_split_stats(khash_t(c2stats) *split_hash, char* bam_fname, int sparse)
+{
+    int i = 0;
+    kstring_t output_filename = { 0, 0, NULL };
+    stats_t *curr_stats = NULL;
+    for(i = kh_begin(split_hash); i != kh_end(split_hash); ++i){
+        if(!kh_exist(split_hash, i)) continue;
+        curr_stats = kh_value(split_hash, i);
+        round_buffer_flush(curr_stats, -1);
+
+        output_filename.l = 0;
+        if (curr_stats->info->split_prefix)
+            kputs(curr_stats->info->split_prefix, &output_filename);
+        else
+            kputs(bam_fname, &output_filename);
+        kputc('_', &output_filename);
+        kputs(curr_stats->split_name, &output_filename);
+        kputs(".bamstat", &output_filename);
+
+        FILE *to = fopen(output_filename.s, "w");
+        if(to == NULL){
+            error("Could not open '%s' for writing.\n", output_filename.s);
+        }
+        output_stats(to, curr_stats, sparse);
+        fclose(to);
+    }
+
+    free(output_filename.s);
+}
+
+void destroy_split_stats(khash_t(c2stats) *split_hash)
+{
+    if (!split_hash)
+        return;
+
+    int i = 0;
+    stats_t *curr_stats = NULL;
+    for(i = kh_begin(split_hash); i != kh_end(split_hash); ++i){
+        if(!kh_exist(split_hash, i)) continue;
+        curr_stats = kh_value(split_hash, i);
+        cleanup_stats(curr_stats);
+    }
+    kh_destroy(c2stats, split_hash);
+}
+
+stats_info_t* stats_info_init(int argc, char *argv[])
+{
+    stats_info_t* info = calloc(1, sizeof(stats_info_t));
+    if (!info) {
+        return NULL;
+    }
+
+    info->nisize = 8000;
+    info->isize_main_bulk = 0.99;   // There are always outliers at the far end
+    info->gcd_bin_size = 20e3;
+    info->cov_min  = 1;
+    info->cov_max  = 1000;
+    info->cov_step = 1;
+    info->filter_readlen = -1;
+    info->argc = argc;
+    info->argv = argv;
+    info->remove_overlaps = 0;
+    info->cov_threshold = 0;
+
+    return info;
+}
+
+int init_stat_info_fname(stats_info_t* info, const char* bam_fname, const htsFormat* in_fmt)
+{
+    // .. bam
+    samFile* sam;
+    if ((sam = sam_open_format(bam_fname, "r", in_fmt)) == 0) {
+        print_error_errno("stats", "failed to open \"%s\"", bam_fname);
+        return 1;
+    }
+    info->sam = sam;
+    info->sam_header = sam_hdr_read(sam);
+    if (info->sam_header == NULL) {
+        print_error("stats", "failed to read header for \"%s\"", bam_fname);
+        return 1;
+    }
+    return 0;
+}
+
+stats_t* stats_init()
+{
+    stats_t *stats = calloc(1,sizeof(stats_t));
+    if (!stats)
+        return NULL;
+
+    stats->ngc    = 200;
+    stats->nquals = 256;
+    stats->nbases = 300;
+    stats->rseq_pos     = -1;
+    stats->tid = -1;
+    stats->gcd_pos = -1LL;
+    stats->igcd = 0;
+    stats->is_sorted = 1;
+    stats->nindels = stats->nbases;
+    stats->split_name = NULL;
+    stats->nchunks = 0;
+    stats->pair_count = 0;
+    stats->last_pair_tid = -2;
+    stats->last_read_flush = 0;
+    stats->target_count = 0;
+
+    return stats;
+}
+
+static int init_barcode_tags(stats_t* stats) {
+    stats->ntags = 4;
+    stats->tags_barcode = calloc(stats->ntags, sizeof(barcode_info_t));
+    if (!stats->tags_barcode)
+        return -1;
+    stats->tags_barcode[0] = (barcode_info_t){"BC", "QT", 0, -1, -1, 0};
+    stats->tags_barcode[1] = (barcode_info_t){"CR", "CY", 0, -1, -1, 0};
+    stats->tags_barcode[2] = (barcode_info_t){"OX", "BZ", 0, -1, -1, 0};
+    stats->tags_barcode[3] = (barcode_info_t){"RX", "QX", 0, -1, -1, 0};
+    return 0;
+}
+
+static void init_stat_structs(stats_t* stats, stats_info_t* info, const char* group_id, const char* targets)
+{
+    // Give stats_t a pointer to the info struct
+    // This saves us having to pass the stats_info_t to every function
+    stats->info = info;
+
+    // Init structures
+    //  .. coverage bins and round buffer
+    if ( info->cov_step > info->cov_max - info->cov_min + 1 )
+    {
+        info->cov_step = info->cov_max - info->cov_min;
+        if ( info->cov_step <= 0 )
+            info->cov_step = 1;
+    }
+    stats->ncov = 3 + (info->cov_max-info->cov_min) / info->cov_step;
+    info->cov_max = info->cov_min + ((info->cov_max-info->cov_min)/info->cov_step +1)*info->cov_step - 1;
+    stats->cov = calloc(sizeof(uint64_t),stats->ncov);
+    if (!stats->cov) goto nomem;
+    stats->cov_rbuf.size = stats->nbases*5;
+    stats->cov_rbuf.buffer = calloc(sizeof(int32_t),stats->cov_rbuf.size);
+    if (!stats->cov_rbuf.buffer) goto nomem;
+    if ( group_id ) init_group_id(stats, info, group_id);
+    // .. arrays
+    stats->quals_1st      = calloc(stats->nquals*stats->nbases,sizeof(uint64_t));
+    if (!stats->quals_1st) goto nomem;
+    stats->quals_2nd      = calloc(stats->nquals*stats->nbases,sizeof(uint64_t));
+    if (!stats->quals_2nd) goto nomem;
+    stats->gc_1st         = calloc(stats->ngc,sizeof(uint64_t));
+    if (!stats->gc_1st) goto nomem;
+    stats->gc_2nd         = calloc(stats->ngc,sizeof(uint64_t));
+    if (!stats->gc_2nd) goto nomem;
+    stats->isize          = init_isize_t(info->nisize ?info->nisize+1 :0);
+    if (!stats->isize) goto nomem;
+    stats->gcd            = calloc(stats->ngcd,sizeof(gc_depth_t));
+    if (!stats->gcd) goto nomem;
+    if (info->fai) {
+        stats->mpc_buf    = calloc(stats->nquals*stats->nbases,sizeof(uint64_t));
+        if (!stats->mpc_buf) goto nomem;
+    } else {
+        stats->mpc_buf    = NULL;
+    }
+    stats->acgtno_cycles_1st  = calloc(stats->nbases,sizeof(acgtno_count_t));
+    if (!stats->acgtno_cycles_1st) goto nomem;
+    stats->acgtno_cycles_2nd  = calloc(stats->nbases,sizeof(acgtno_count_t));
+    if (!stats->acgtno_cycles_2nd) goto nomem;
+    stats->acgtno_revcomp  = calloc(stats->nbases,sizeof(acgtno_count_t));
+    if (!stats->acgtno_revcomp) goto nomem;
+    stats->read_lengths   = calloc(stats->nbases,sizeof(uint64_t));
+    if (!stats->read_lengths)     goto nomem;
+    stats->read_lengths_1st   = calloc(stats->nbases,sizeof(uint64_t));
+    if (!stats->read_lengths_1st) goto nomem;
+    stats->read_lengths_2nd   = calloc(stats->nbases,sizeof(uint64_t));
+    if (!stats->read_lengths_2nd) goto nomem;
+    stats->insertions     = calloc(stats->nbases,sizeof(uint64_t));
+    if (!stats->insertions) goto nomem;
+    stats->deletions      = calloc(stats->nbases,sizeof(uint64_t));
+    if (!stats->deletions)  goto nomem;
+    stats->ins_cycles_1st = calloc(stats->nbases+1,sizeof(uint64_t));
+    if (!stats->ins_cycles_1st) goto nomem;
+    stats->ins_cycles_2nd = calloc(stats->nbases+1,sizeof(uint64_t));
+    if (!stats->ins_cycles_2nd) goto nomem;
+    stats->del_cycles_1st = calloc(stats->nbases+1,sizeof(uint64_t));
+    if (!stats->del_cycles_1st) goto nomem;
+    stats->del_cycles_2nd = calloc(stats->nbases+1,sizeof(uint64_t));
+    if (!stats->del_cycles_2nd) goto nomem;
+    if (init_barcode_tags(stats) < 0)
+        goto nomem;
+    realloc_rseq_buffer(stats);
+    if ( targets )
+        init_regions(stats, targets, info);
+    return;
+ nomem:
+    error("Out of memory");
+}
+
+static stats_t* get_curr_split_stats(bam1_t* bam_line, khash_t(c2stats)* split_hash, stats_info_t* info, char* targets)
+{
+    stats_t *curr_stats = NULL;
+    const uint8_t *tag_val = bam_aux_get(bam_line, info->split_tag);
+    if(tag_val == 0){
+        error("Tag '%s' not found in bam_line.\n", info->split_tag);
+    }
+    char* split_name = strdup(bam_aux2Z(tag_val));
+
+    // New stats object, under split
+    khiter_t k = kh_get(c2stats, split_hash, split_name);
+    if(k == kh_end(split_hash)){
+        curr_stats = stats_init(); // mallocs new instance
+        if (!curr_stats) {
+            error("Couldn't allocate split stats");
+        }
+        init_stat_structs(curr_stats, info, NULL, targets);
+        curr_stats->split_name = split_name;
+
+        // Record index in hash
+        int ret = 0;
+        khiter_t iter = kh_put(c2stats, split_hash, split_name, &ret);
+        if( ret < 0 ){
+            error("Failed to insert key '%s' into split_hash", split_name);
+        }
+        kh_val(split_hash, iter) = curr_stats; // store pointer to stats
+    }
+    else{
+        curr_stats = kh_value(split_hash, k);
+        free(split_name); // don't need to hold on to this if it wasn't new
+    }
+    return curr_stats;
+}
+
+int main_stats(int argc, char *argv[])
+{
+    char *targets = NULL;
+    char *bam_fname = NULL;
+    char *bam_idx_fname = NULL;
+    char *group_id = NULL;
+    int sparse = 0, has_index_file = 0, ret = 1;
+    sam_global_args ga = SAM_GLOBAL_ARGS_INIT;
+
+    stats_info_t *info = stats_info_init(argc, argv);
+    if (!info) {
+        fprintf(samtools_stderr, "Could not allocate memory for info.\n");
+        return 1;
+    }
+
+    static const struct option loptions[] =
+    {
+        SAM_OPT_GLOBAL_OPTIONS('-', 0, '-', '-', 0, '@'),
+        {"help", no_argument, NULL, 'h'},
+        {"remove-dups", no_argument, NULL, 'd'},
+        {"sam", no_argument, NULL, 's'},
+        {"customized-index-file", required_argument, NULL, 'X'},
+        {"ref-seq", required_argument, NULL, 'r'},
+        {"coverage", required_argument, NULL, 'c'},
+        {"read-length", required_argument, NULL, 'l'},
+        {"insert-size", required_argument, NULL, 'i'},
+        {"most-inserts", required_argument, NULL, 'm'},
+        {"trim-quality", required_argument, NULL, 'q'},
+        {"target-regions", required_argument, NULL, 't'},
+        {"required-flag", required_argument, NULL, 'f'},
+        {"filtering-flag", required_argument, NULL, 'F'},
+        {"id", required_argument, NULL, 'I'},
+        {"GC-depth", required_argument, NULL, 1},
+        {"sparse", no_argument, NULL, 'x'},
+        {"split", required_argument, NULL, 'S'},
+        {"split-prefix", required_argument, NULL, 'P'},
+        {"remove-overlaps", no_argument, NULL, 'p'},
+        {"cov-threshold", required_argument, NULL, 'g'},
+        {NULL, 0, NULL, 0}
+    };
+    int opt;
+
+    while ( (opt=getopt_long(argc,argv,"?hdsXxpr:c:l:i:t:m:q:f:F:g:I:S:P:@:",loptions,NULL))>0 )
+    {
+        switch (opt)
+        {
+            case 'f': info->flag_require = bam_str2flag(optarg); break;
+            case 'F': info->flag_filter |= bam_str2flag(optarg); break;
+            case 'd': info->flag_filter |= BAM_FDUP; break;
+            case 'X': has_index_file = 1; break;
+            case 's': break;
+            case 'r': info->fai = fai_load(optarg);
+                      if (info->fai==NULL)
+                          error("Could not load faidx: %s\n", optarg);
+                      break;
+            case  1 : info->gcd_bin_size = atof(optarg); break;
+            case 'c': if ( sscanf(optarg,"%d,%d,%d",&info->cov_min,&info->cov_max,&info->cov_step)!= 3 )
+                          error("Unable to parse -c %s\n", optarg);
+                      break;
+            case 'l': info->filter_readlen = atoi(optarg); break;
+            case 'i': info->nisize = atoi(optarg); break;
+            case 'm': info->isize_main_bulk = atof(optarg); break;
+            case 'q': info->trim_qual = atoi(optarg); break;
+            case 't': targets = optarg; break;
+            case 'I': group_id = optarg; break;
+            case 'x': sparse = 1; break;
+            case 'S': info->split_tag = optarg; break;
+            case 'P': info->split_prefix = optarg; break;
+            case 'p': info->remove_overlaps = 1; break;
+            case 'g': info->cov_threshold = atoi(optarg);
+                      if ( info->cov_threshold < 0 || info->cov_threshold == INT_MAX )
+                          error("Unsupported value for coverage threshold %d\n", info->cov_threshold);
+                      break;
+            case '?':
+            case 'h': error(NULL);
+            /* no break */
+            default:
+                if (parse_sam_global_opt(opt, optarg, loptions, &ga) != 0)
+                    error("Unknown argument: %s\n", optarg);
+                break;
+        }
+    }
+
+    bam_fname = argv[optind++];
+    if ( !bam_fname )
+    {
+        if ( isatty(STDIN_FILENO) )
+            error(NULL);
+        bam_fname = "-";
+    }
+
+    if (init_stat_info_fname(info, bam_fname, &ga.in)) {
+        cleanup_stats_info(info);
+        return 1;
+    }
+
+    if (has_index_file && !(bam_idx_fname = argv[optind++])) {
+        fprintf(samtools_stderr, "No index file provided\n");
+        cleanup_stats_info(info);
+        return 1;
+    }
+
+    if (ga.nthreads > 0)
+        hts_set_threads(info->sam, ga.nthreads);
+
+    stats_t *all_stats = stats_init();
+    if (!all_stats) {
+        fprintf(samtools_stderr, "Could not allocate memory for stats.\n");
+        cleanup_stats_info(info);
+        return 1;
+    }
+    stats_t *curr_stats = NULL;
+    init_stat_structs(all_stats, info, group_id, targets);
+    // Init
+    // .. hash
+    khash_t(c2stats)* split_hash = kh_init(c2stats);
+    if (!split_hash) goto cleanup_all_stats;
+
+    khash_t(qn2pair)* read_pairs = kh_init(qn2pair);
+    if (!read_pairs) goto cleanup_split_hash;
+
+    // Collect statistics
+    bam1_t *bam_line = bam_init1();
+    if (!bam_line) goto cleanup_read_pairs;
+
+    if (optind < argc) {
+        // Region:interval arguments in the command line
+        hts_idx_t *bam_idx = NULL;
+        if (has_index_file) {
+            bam_idx = sam_index_load2(info->sam, bam_fname, bam_idx_fname);
+        } else {
+            // If an index filename has not been specified, look alongside the alignment file
+            bam_idx = sam_index_load(info->sam, bam_fname);
+        }
+
+        if (bam_idx) {
+            hts_itr_multi_t *iter = sam_itr_regarray(bam_idx, info->sam_header, &argv[optind], argc - optind);
+            if (iter) {
+                if (!targets) {
+                    all_stats->nchunks = argc-optind;
+                    if (replicate_regions(all_stats, iter, info))
+                        fprintf(samtools_stderr, "Replications of the regions failed\n");
+                }
+
+                if ( all_stats->nregions && all_stats->regions ) {
+                    while ((ret = sam_itr_next(info->sam, iter, bam_line)) >= 0) {
+                        if (info->split_tag) {
+                            curr_stats = get_curr_split_stats(bam_line, split_hash, info, targets);
+                            collect_stats(bam_line, curr_stats, read_pairs);
+                        }
+                        collect_stats(bam_line, all_stats, read_pairs);
+                    }
+
+                    if (ret < -1) {
+                        fprintf(samtools_stderr, "Failure while running the iterator\n");
+                        hts_itr_multi_destroy(iter);
+                        hts_idx_destroy(bam_idx);
+                        goto cleanup;
+                    }
+                }
+                hts_itr_multi_destroy(iter);
+            } else {
+                fprintf(samtools_stderr, "Multi-region iterator could not be created\n");
+                hts_idx_destroy(bam_idx);
+                goto cleanup;
+            }
+            hts_idx_destroy(bam_idx);
+        } else {
+            if (has_index_file)
+                fprintf(samtools_stderr, "Invalid index file '%s'\n", bam_idx_fname);
+            fprintf(samtools_stderr, "Random alignment retrieval only works for indexed files\n");
+            goto cleanup;
+        }
+    } else {
+        if ( info->cov_threshold > 0 && !targets ) {
+            fprintf(samtools_stderr, "Coverage percentage calculation requires a list of target regions\n");
+            goto cleanup;
+        }
+
+        // Stream through the entire BAM ignoring off-target regions if -t is given
+        while ((ret = sam_read1(info->sam, info->sam_header, bam_line)) >= 0) {
+            if (info->split_tag) {
+                curr_stats = get_curr_split_stats(bam_line, split_hash, info, targets);
+                collect_stats(bam_line, curr_stats, read_pairs);
+            }
+            collect_stats(bam_line, all_stats, read_pairs);
+        }
+
+        if (ret < -1) {
+            fprintf(samtools_stderr, "Failure while decoding file\n");
+            goto cleanup;
+        }
+    }
+
+    round_buffer_flush(all_stats, -1);
+    output_stats(samtools_stdout, all_stats, sparse);
+    if (info->split_tag)
+        output_split_stats(split_hash, bam_fname, sparse);
+
+    ret = 0;
+cleanup:
+    bam_destroy1(bam_line);
+    sam_hdr_destroy(info->sam_header);
+    sam_global_args_free(&ga);
+
+cleanup_read_pairs:
+    cleanup_overlaps(read_pairs, INT64_MAX);
+cleanup_split_hash:
+    destroy_split_stats(split_hash);
+cleanup_all_stats:
+    cleanup_stats(all_stats);
+    cleanup_stats_info(info);
+
+    return ret;
+}
diff --git a/samtools/stats_isize.c b/samtools/stats_isize.c
new file mode 100644
index 0000000..8dc690a
--- /dev/null
+++ b/samtools/stats_isize.c
@@ -0,0 +1,239 @@
+/*  stats_isize.c -- generalised insert size calculation for samtools stats.
+
+    Copyright (C) 2014, 2018 Genome Research Ltd.
+
+    Author: Nicholas Clarke <nc6@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <config.h>
+
+#include <stdio.h>
+#include "stats_isize.h"
+#include <htslib/khash.h>
+
+typedef enum {IN,OUT,OTHER} isize_insert_t;
+
+static int max(int a, int b) {
+    if (a < b) {
+        return b;
+    } else {
+        return a;
+    }
+}
+
+static isize_sparse_record_t * sparse_get_f(isize_data_t data, int at) {
+    isize_sparse_data_t *a = data.sparse;
+    khash_t(m32) *h = a->array;
+
+    khint_t k = kh_get(m32, h, at);
+    if (k != kh_end(h)) {
+        return kh_value(h, k);
+    } else {
+        return NULL;
+    }
+}
+
+static uint64_t sparse_in_f(isize_data_t data, int at) {
+    isize_sparse_record_t* a = sparse_get_f(data, at);
+    if (a != NULL) {
+        return a->isize_inward;
+    } else {
+        return 0;
+    }
+}
+static uint64_t sparse_out_f(isize_data_t data, int at) {
+    isize_sparse_record_t* a = sparse_get_f(data, at);
+    if (a != NULL) {
+        return a->isize_outward;
+    } else {
+        return 0;
+    }
+}
+static uint64_t sparse_other_f(isize_data_t data, int at) {
+    isize_sparse_record_t* a = sparse_get_f(data, at);
+    if (a != NULL) {
+        return a->isize_other;
+    } else {
+        return 0;
+    }
+}
+
+static void sparse_set_f(isize_data_t data, int at, isize_insert_t field, uint64_t value) {
+    isize_sparse_data_t *a = data.sparse;
+    khash_t(m32) *h = a->array;
+
+    khint_t k = kh_get(m32, h, at);
+    isize_sparse_record_t *rec;
+    if (k != kh_end(h)) {
+        rec = kh_value(h, k);
+    } else if (value != 0) {
+        rec = malloc(sizeof(isize_sparse_record_t));
+        if (rec != NULL) {
+            rec->isize_inward = 0;
+            rec->isize_outward = 0;
+            rec->isize_other = 0;
+            int stupid = 0;
+            khint_t it = kh_put(m32, h, at, & stupid);
+            kh_value(h, it) = rec;
+            a->max = max(at, a->max);
+        } else {
+            fprintf(stderr, "%s\n", "Failed to allocate memory for isize_sparse_record_t");
+            exit(11);
+        }
+    } else {
+        return;
+    }
+    if (field == IN) {
+        rec->isize_inward = value;
+    } else if (field == OUT) {
+        rec->isize_outward = value;
+    } else {
+        rec->isize_other = value;
+    }
+
+}
+
+static void sparse_set_in_f(isize_data_t data, int at, uint64_t value) { sparse_set_f(data, at, IN, value); }
+static void sparse_set_out_f(isize_data_t data, int at, uint64_t value) { sparse_set_f(data, at, OUT, value); }
+static void sparse_set_other_f(isize_data_t data, int at, uint64_t value) { sparse_set_f(data, at, OTHER, value); }
+
+static void sparse_inc_in_f(isize_data_t data, int at) { sparse_set_in_f(data, at, sparse_in_f(data, at) + 1); }
+static void sparse_inc_out_f(isize_data_t data, int at) { sparse_set_out_f(data, at, sparse_out_f(data, at) + 1); }
+static void sparse_inc_other_f(isize_data_t data, int at) { sparse_set_other_f(data, at, sparse_other_f(data, at) + 1); }
+
+static void sparse_isize_free(isize_data_t data) {
+    isize_sparse_data_t *a = data.sparse;
+    khint_t k;
+    for (k = 0; k < kh_end(a->array); ++k)
+        if (kh_exist(a->array, k)) free(kh_val(a->array, k));
+    kh_destroy(m32, a->array);
+    free(a);
+}
+
+static int sparse_nitems(isize_data_t data) {
+    isize_sparse_data_t *a = data.sparse;
+    return a->max + 1;
+}
+
+static uint64_t dense_in_f(isize_data_t data, int at) { return data.dense->isize_inward[at]; }
+static uint64_t dense_out_f(isize_data_t data, int at) { return data.dense->isize_outward[at]; }
+static uint64_t dense_other_f(isize_data_t data, int at) { return data.dense->isize_other[at]; }
+
+static void dense_set_in_f(isize_data_t data, int at, uint64_t value) { data.dense->isize_inward[at] = value; }
+static void dense_set_out_f(isize_data_t data, int at, uint64_t value) { data.dense->isize_outward[at] = value; }
+static void dense_set_other_f(isize_data_t data, int at, uint64_t value) { data.dense->isize_other[at] = value; }
+
+static void dense_inc_in_f(isize_data_t data, int at) { data.dense->isize_inward[at] += 1; }
+static void dense_inc_out_f(isize_data_t data, int at) { data.dense->isize_outward[at] += 1; }
+static void dense_inc_other_f(isize_data_t data, int at) { data.dense->isize_other[at] += 1; }
+
+static void dense_isize_free(isize_data_t data) {
+    isize_dense_data_t *a = data.dense;
+    free(a->isize_inward);
+    free(a->isize_outward);
+    free(a->isize_other);
+    free(a);
+}
+
+static int dense_nitems(isize_data_t data) {
+    isize_dense_data_t *a = data.dense;
+    return a->total;
+}
+
+// Construct a relevant isize_t given the bound.
+isize_t *init_isize_t(int bound) {
+    if (bound <= 0) {
+        // Use sparse data structure.
+        isize_sparse_data_t *data = (isize_sparse_data_t *) malloc(sizeof(isize_sparse_data_t));
+        if (!data)
+            return NULL;
+
+        // Initialise
+        data->max = 0;
+        data->array = kh_init(m32);
+        if (!data->array) {
+            free(data);
+            return NULL;
+        }
+
+        isize_t *isize = (isize_t *)malloc(sizeof(isize_t));
+        if (!isize) {
+            kh_destroy(m32, data->array);
+            free(data);
+            return NULL;
+        }
+
+        isize->data.sparse = data;
+        isize->nitems = & sparse_nitems;
+
+        isize->inward = & sparse_in_f;
+        isize->outward = & sparse_out_f;
+        isize->other = & sparse_other_f;
+
+        isize->set_inward = & sparse_set_in_f;
+        isize->set_outward = & sparse_set_out_f;
+        isize->set_other = & sparse_set_other_f;
+
+        isize->inc_inward = & sparse_inc_in_f;
+        isize->inc_outward = & sparse_inc_out_f;
+        isize->inc_other = & sparse_inc_other_f;
+
+        isize->isize_free = & sparse_isize_free;
+
+        return isize;
+    } else {
+        uint64_t* in = calloc(bound,sizeof(uint64_t));
+        uint64_t* out = calloc(bound,sizeof(uint64_t));
+        uint64_t* other = calloc(bound,sizeof(uint64_t));
+        isize_dense_data_t *rec = (isize_dense_data_t *)malloc(sizeof(isize_dense_data_t));
+        isize_t *isize = (isize_t *)malloc(sizeof(isize_t));
+        if (!in || !out || !other || !rec || !isize) {
+            free(in);
+            free(out);
+            free(other);
+            free(rec);
+            free(isize);
+            return NULL;
+        }
+        rec->isize_inward = in;
+        rec->isize_outward = out;
+        rec->isize_other = other;
+        rec->total=bound;
+
+        isize->data.dense = rec;
+        isize->nitems = & dense_nitems;
+
+        isize->inward = & dense_in_f;
+        isize->outward = & dense_out_f;
+        isize->other = & dense_other_f;
+
+        isize->set_inward = & dense_set_in_f;
+        isize->set_outward = & dense_set_out_f;
+        isize->set_other = & dense_set_other_f;
+
+        isize->inc_inward = & dense_inc_in_f;
+        isize->inc_outward = & dense_inc_out_f;
+        isize->inc_other = & dense_inc_other_f;
+
+        isize->isize_free = & dense_isize_free;
+
+        return isize;
+    }
+}
diff --git a/samtools/stats_isize.c.pysam.c b/samtools/stats_isize.c.pysam.c
new file mode 100644
index 0000000..1bb2bd4
--- /dev/null
+++ b/samtools/stats_isize.c.pysam.c
@@ -0,0 +1,241 @@
+#include "samtools.pysam.h"
+
+/*  stats_isize.c -- generalised insert size calculation for samtools stats.
+
+    Copyright (C) 2014, 2018 Genome Research Ltd.
+
+    Author: Nicholas Clarke <nc6@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <config.h>
+
+#include <stdio.h>
+#include "stats_isize.h"
+#include <htslib/khash.h>
+
+typedef enum {IN,OUT,OTHER} isize_insert_t;
+
+static int max(int a, int b) {
+    if (a < b) {
+        return b;
+    } else {
+        return a;
+    }
+}
+
+static isize_sparse_record_t * sparse_get_f(isize_data_t data, int at) {
+    isize_sparse_data_t *a = data.sparse;
+    khash_t(m32) *h = a->array;
+
+    khint_t k = kh_get(m32, h, at);
+    if (k != kh_end(h)) {
+        return kh_value(h, k);
+    } else {
+        return NULL;
+    }
+}
+
+static uint64_t sparse_in_f(isize_data_t data, int at) {
+    isize_sparse_record_t* a = sparse_get_f(data, at);
+    if (a != NULL) {
+        return a->isize_inward;
+    } else {
+        return 0;
+    }
+}
+static uint64_t sparse_out_f(isize_data_t data, int at) {
+    isize_sparse_record_t* a = sparse_get_f(data, at);
+    if (a != NULL) {
+        return a->isize_outward;
+    } else {
+        return 0;
+    }
+}
+static uint64_t sparse_other_f(isize_data_t data, int at) {
+    isize_sparse_record_t* a = sparse_get_f(data, at);
+    if (a != NULL) {
+        return a->isize_other;
+    } else {
+        return 0;
+    }
+}
+
+static void sparse_set_f(isize_data_t data, int at, isize_insert_t field, uint64_t value) {
+    isize_sparse_data_t *a = data.sparse;
+    khash_t(m32) *h = a->array;
+
+    khint_t k = kh_get(m32, h, at);
+    isize_sparse_record_t *rec;
+    if (k != kh_end(h)) {
+        rec = kh_value(h, k);
+    } else if (value != 0) {
+        rec = malloc(sizeof(isize_sparse_record_t));
+        if (rec != NULL) {
+            rec->isize_inward = 0;
+            rec->isize_outward = 0;
+            rec->isize_other = 0;
+            int stupid = 0;
+            khint_t it = kh_put(m32, h, at, & stupid);
+            kh_value(h, it) = rec;
+            a->max = max(at, a->max);
+        } else {
+            fprintf(samtools_stderr, "%s\n", "Failed to allocate memory for isize_sparse_record_t");
+            samtools_exit(11);
+        }
+    } else {
+        return;
+    }
+    if (field == IN) {
+        rec->isize_inward = value;
+    } else if (field == OUT) {
+        rec->isize_outward = value;
+    } else {
+        rec->isize_other = value;
+    }
+
+}
+
+static void sparse_set_in_f(isize_data_t data, int at, uint64_t value) { sparse_set_f(data, at, IN, value); }
+static void sparse_set_out_f(isize_data_t data, int at, uint64_t value) { sparse_set_f(data, at, OUT, value); }
+static void sparse_set_other_f(isize_data_t data, int at, uint64_t value) { sparse_set_f(data, at, OTHER, value); }
+
+static void sparse_inc_in_f(isize_data_t data, int at) { sparse_set_in_f(data, at, sparse_in_f(data, at) + 1); }
+static void sparse_inc_out_f(isize_data_t data, int at) { sparse_set_out_f(data, at, sparse_out_f(data, at) + 1); }
+static void sparse_inc_other_f(isize_data_t data, int at) { sparse_set_other_f(data, at, sparse_other_f(data, at) + 1); }
+
+static void sparse_isize_free(isize_data_t data) {
+    isize_sparse_data_t *a = data.sparse;
+    khint_t k;
+    for (k = 0; k < kh_end(a->array); ++k)
+        if (kh_exist(a->array, k)) free(kh_val(a->array, k));
+    kh_destroy(m32, a->array);
+    free(a);
+}
+
+static int sparse_nitems(isize_data_t data) {
+    isize_sparse_data_t *a = data.sparse;
+    return a->max + 1;
+}
+
+static uint64_t dense_in_f(isize_data_t data, int at) { return data.dense->isize_inward[at]; }
+static uint64_t dense_out_f(isize_data_t data, int at) { return data.dense->isize_outward[at]; }
+static uint64_t dense_other_f(isize_data_t data, int at) { return data.dense->isize_other[at]; }
+
+static void dense_set_in_f(isize_data_t data, int at, uint64_t value) { data.dense->isize_inward[at] = value; }
+static void dense_set_out_f(isize_data_t data, int at, uint64_t value) { data.dense->isize_outward[at] = value; }
+static void dense_set_other_f(isize_data_t data, int at, uint64_t value) { data.dense->isize_other[at] = value; }
+
+static void dense_inc_in_f(isize_data_t data, int at) { data.dense->isize_inward[at] += 1; }
+static void dense_inc_out_f(isize_data_t data, int at) { data.dense->isize_outward[at] += 1; }
+static void dense_inc_other_f(isize_data_t data, int at) { data.dense->isize_other[at] += 1; }
+
+static void dense_isize_free(isize_data_t data) {
+    isize_dense_data_t *a = data.dense;
+    free(a->isize_inward);
+    free(a->isize_outward);
+    free(a->isize_other);
+    free(a);
+}
+
+static int dense_nitems(isize_data_t data) {
+    isize_dense_data_t *a = data.dense;
+    return a->total;
+}
+
+// Construct a relevant isize_t given the bound.
+isize_t *init_isize_t(int bound) {
+    if (bound <= 0) {
+        // Use sparse data structure.
+        isize_sparse_data_t *data = (isize_sparse_data_t *) malloc(sizeof(isize_sparse_data_t));
+        if (!data)
+            return NULL;
+
+        // Initialise
+        data->max = 0;
+        data->array = kh_init(m32);
+        if (!data->array) {
+            free(data);
+            return NULL;
+        }
+
+        isize_t *isize = (isize_t *)malloc(sizeof(isize_t));
+        if (!isize) {
+            kh_destroy(m32, data->array);
+            free(data);
+            return NULL;
+        }
+
+        isize->data.sparse = data;
+        isize->nitems = & sparse_nitems;
+
+        isize->inward = & sparse_in_f;
+        isize->outward = & sparse_out_f;
+        isize->other = & sparse_other_f;
+
+        isize->set_inward = & sparse_set_in_f;
+        isize->set_outward = & sparse_set_out_f;
+        isize->set_other = & sparse_set_other_f;
+
+        isize->inc_inward = & sparse_inc_in_f;
+        isize->inc_outward = & sparse_inc_out_f;
+        isize->inc_other = & sparse_inc_other_f;
+
+        isize->isize_free = & sparse_isize_free;
+
+        return isize;
+    } else {
+        uint64_t* in = calloc(bound,sizeof(uint64_t));
+        uint64_t* out = calloc(bound,sizeof(uint64_t));
+        uint64_t* other = calloc(bound,sizeof(uint64_t));
+        isize_dense_data_t *rec = (isize_dense_data_t *)malloc(sizeof(isize_dense_data_t));
+        isize_t *isize = (isize_t *)malloc(sizeof(isize_t));
+        if (!in || !out || !other || !rec || !isize) {
+            free(in);
+            free(out);
+            free(other);
+            free(rec);
+            free(isize);
+            return NULL;
+        }
+        rec->isize_inward = in;
+        rec->isize_outward = out;
+        rec->isize_other = other;
+        rec->total=bound;
+
+        isize->data.dense = rec;
+        isize->nitems = & dense_nitems;
+
+        isize->inward = & dense_in_f;
+        isize->outward = & dense_out_f;
+        isize->other = & dense_other_f;
+
+        isize->set_inward = & dense_set_in_f;
+        isize->set_outward = & dense_set_out_f;
+        isize->set_other = & dense_set_other_f;
+
+        isize->inc_inward = & dense_inc_in_f;
+        isize->inc_outward = & dense_inc_out_f;
+        isize->inc_other = & dense_inc_other_f;
+
+        isize->isize_free = & dense_isize_free;
+
+        return isize;
+    }
+}
diff --git a/samtools/stats_isize.h b/samtools/stats_isize.h
new file mode 100644
index 0000000..3243222
--- /dev/null
+++ b/samtools/stats_isize.h
@@ -0,0 +1,83 @@
+/*  stats_isize.h -- generalised insert size calculation for samtools stats.
+
+    Copyright (C) 2014 Genome Research Ltd.
+
+    Author: Nicholas Clarke <nc6@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <htslib/khash.h>
+#include <stdint.h>
+
+typedef struct
+{
+    int total;
+    uint64_t *isize_inward, *isize_outward, *isize_other;
+}
+isize_dense_data_t;
+
+typedef struct
+{
+    uint64_t isize_inward, isize_outward, isize_other;
+}
+isize_sparse_record_t;
+
+KHASH_MAP_INIT_INT(m32, isize_sparse_record_t *)
+
+typedef struct
+{
+    int max;
+    khash_t(m32) *array;
+}
+isize_sparse_data_t;
+
+typedef union {
+    isize_sparse_data_t *sparse;
+    isize_dense_data_t *dense;
+} isize_data_t;
+
+// Insert size structure
+typedef struct
+{
+    isize_data_t data;
+
+    // Maximum
+    int (*nitems)(isize_data_t);
+
+    // Fetch the number of inserts of a given size
+    uint64_t (*inward)(isize_data_t, int);
+    uint64_t (*outward)(isize_data_t, int);
+    uint64_t (*other)(isize_data_t, int);
+
+    // Set the number of inserts of a given size
+    void (*set_inward)(isize_data_t, int, uint64_t);
+    void (*set_outward)(isize_data_t, int, uint64_t);
+    void (*set_other)(isize_data_t, int, uint64_t);
+
+    // Increment the number of inserts of a given size
+    void (*inc_inward)(isize_data_t, int);
+    void (*inc_outward)(isize_data_t, int);
+    void (*inc_other)(isize_data_t, int);
+
+    // Free this structure
+    void (*isize_free)(isize_data_t);
+}
+isize_t;
+
+isize_t *init_isize_t(int bound);
diff --git a/samtools/tmp_file.c b/samtools/tmp_file.c
new file mode 100644
index 0000000..123f425
--- /dev/null
+++ b/samtools/tmp_file.c
@@ -0,0 +1,438 @@
+/*
+    tmp_file.c - write to and read from a temporary binary file
+    for fast storage plus added compression.
+
+    Copyright (C) 2017, 2018 Genome Research Ltd.
+
+    Author: Andrew Whitwham <aw7@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE
+*/
+
+#include <config.h>
+
+#include <stdio.h>
+#include <string.h>
+#include <unistd.h>
+#include <stdlib.h>
+#include <stdarg.h>
+#include <fcntl.h>
+#include <errno.h>
+
+#ifdef _WIN32
+#include <windows.h>
+#endif /* _WIN32 */
+
+#include "tmp_file.h"
+#include "htslib/sam.h"
+
+
+static void tmp_print_error(tmp_file_t *tmp, const char *fmt, ...) {
+    va_list argp;
+
+    if (tmp->verbose) {
+        va_start(argp, fmt);
+        vfprintf(stderr, fmt, argp);
+        va_end(argp);
+    }
+}
+
+
+static int tmp_file_init(tmp_file_t *tmp, int verbose) {
+    tmp->stream       = LZ4_createStream();
+    tmp->data_size    = 0;
+    tmp->group_size   = TMP_SAM_GROUP_SIZE;
+    tmp->input_size   = 0;
+    tmp->read_size    = 0;
+    tmp->output_size  = 0;
+    tmp->entry_number = 0;
+    tmp->offset = 0;
+    tmp->max_data_size    = TMP_SAM_MAX_DATA + sizeof(bam1_t); // arbitrary but growable
+    tmp->ring_buffer_size = TMP_SAM_RING_SIZE; // arbitrary (min 64K) but growable
+    tmp->comp_buffer_size = LZ4_COMPRESSBOUND(tmp->max_data_size * tmp->group_size);
+    tmp->ring_buffer = malloc(sizeof(uint8_t) * tmp->ring_buffer_size);
+    tmp->ring_index  = tmp->ring_buffer;
+    tmp->comp_buffer = malloc(tmp->comp_buffer_size);
+    tmp->verbose = verbose;
+    tmp->dict = NULL;
+    tmp->groups_written = 0;
+
+    if (!tmp->ring_buffer || !tmp->comp_buffer || !tmp->stream) {
+        tmp_print_error(tmp, "[tmp_file] Error: unable to allocate compression buffers.\n");
+        return TMP_SAM_MEM_ERROR;
+    }
+
+    return TMP_SAM_OK;
+}
+
+
+/*
+ * Opens the temp file and initialises memory.
+ * Verbose mode prints out error messages to stderr.
+ * Returns 0 on success, a negative number on failure.
+ */
+int tmp_file_open_write(tmp_file_t *tmp, char *tmp_name, int verbose) {
+    int ret;
+    unsigned int count = 1;
+    const unsigned int max_count = 100000; // more tries than this then something else is wrong
+    int fd;
+
+    if ((ret = tmp_file_init(tmp, verbose))) {
+        return ret;
+    }
+
+    // make space to write extended file name
+    if ((tmp->name = malloc(strlen(tmp_name) + 7)) == NULL) {
+        tmp_print_error(tmp, "[tmp_file] Error: unable to allocate memory for %s.\n", tmp_name);
+        return TMP_SAM_MEM_ERROR;
+    }
+
+    // make sure temp file has a unique name
+    while (count < max_count) {
+        sprintf(tmp->name, "%s.%d", tmp_name, count);
+
+
+        #ifdef _WIN32
+        if ((fd = _open(tmp->name, O_RDWR|O_CREAT|O_EXCL|O_BINARY|O_TEMPORARY, 0600)) == -1) {
+        #else
+        if ((fd = open(tmp->name, O_RDWR|O_CREAT|O_EXCL, 0600)) == -1) {
+        #endif /* _WIN32 */
+
+            if (errno != EEXIST) {
+                tmp_print_error(tmp, "[tmp_file] Error: unable to create tmp file %s.\n", tmp->name);
+                return TMP_SAM_FILE_ERROR;
+            }
+
+            count++;
+            continue;
+        }
+
+        break;
+    }
+
+    if (count >= max_count) {
+        tmp_print_error(tmp, "[tmp_file] Error: unable to create unique temp file.\n");
+        return TMP_SAM_FILE_ERROR;
+    }
+
+    if ((tmp->fp = fdopen(fd, "w+b")) == NULL) {
+        tmp_print_error(tmp, "[tmp_file] Error: unable to open write file %s.\n", tmp->name);
+        return TMP_SAM_FILE_ERROR;
+    }
+
+    #ifndef _WIN32
+    unlink(tmp->name); // should auto delete when closed on linux
+    #endif
+
+    return TMP_SAM_OK;
+}
+
+
+/*
+ * The ring buffer stores precompressionn/post decompression data.  LZ4 requires that
+ * previous data (64K worth) be available for efficient compression.  This function grows
+ * the ring buffer when needed.
+ * Returns 0 on success, a negative number on failure.
+ */
+static int tmp_file_grow_ring_buffer(tmp_file_t *tmp, size_t new_size) {
+    // save the dictionary so lz4 can continue to function
+    int dict_size = 64 * 1024; // 64K max size
+
+    if (tmp->groups_written) {
+        // if compression has been done then there is a dictionary to save
+
+        if (tmp->dict == NULL) {
+
+            if ((tmp->dict = malloc(sizeof(char) * dict_size)) == NULL) {
+                tmp_print_error(tmp, "[tmp_file] Error: unable to allocate memory for compression dictionary.\n");
+                return TMP_SAM_MEM_ERROR;
+            }
+        }
+
+        if (LZ4_saveDict(tmp->stream, tmp->dict, dict_size) == 0) {
+            tmp_print_error(tmp, "[tmp_file] Error: unable to save compression dictionary.\n");
+            return TMP_SAM_LZ4_ERROR;
+        }
+    }
+
+    if ((tmp->ring_buffer = realloc(tmp->ring_buffer, sizeof(char) * new_size)) == NULL) {
+        tmp_print_error(tmp, "[tmp_file] Error: unable to reallocate ring buffer.\n");
+        return TMP_SAM_MEM_ERROR;
+    }
+
+    tmp->ring_buffer_size = new_size;
+
+    return TMP_SAM_OK;
+}
+
+
+/*
+ * This does the actual compression and writing to a file.  The file format consists of a
+ * single size_t for the size of the compressed data followed by the data itself.
+ * Returns 0 on success, a negative number on failure.
+ */
+static int tmp_file_write_to_file(tmp_file_t *tmp) {
+    size_t comp_size;
+
+    if (tmp->input_size > tmp->max_data_size) {
+        tmp->max_data_size += tmp->input_size + sizeof(bam1_t);
+        tmp->comp_buffer_size = LZ4_COMPRESSBOUND(tmp->max_data_size);
+
+        if ((tmp->comp_buffer = realloc(tmp->comp_buffer, sizeof(char) * tmp->comp_buffer_size)) == NULL) {
+            tmp_print_error(tmp, "[tmp_file] Error: unable to reallocate compression buffer.\n");
+            return TMP_SAM_MEM_ERROR;
+        }
+
+        // make sure the ring buffer is big enough to accommodate the new max_data_size
+        if (tmp->ring_buffer_size < tmp->max_data_size * 5) {
+            int ret;
+            if ((ret = tmp_file_grow_ring_buffer(tmp, tmp->max_data_size * 5))) {
+                return ret;
+            }
+        }
+    }
+
+    tmp->ring_index = tmp->ring_buffer + tmp->offset;
+
+    comp_size = LZ4_compress_fast_continue(tmp->stream, (const char *)tmp->ring_index,
+                   tmp->comp_buffer, tmp->input_size, tmp->comp_buffer_size, 1);
+
+    if (comp_size == 0) {
+        tmp_print_error(tmp, "[tmp_file] Error: compression failed.\n");
+        return TMP_SAM_LZ4_ERROR;
+    }
+
+    if (fwrite(&comp_size, sizeof(size_t), 1, tmp->fp) < 1) {
+        tmp_print_error(tmp, "[tmp_file] Error: tmp file write size failed.\n");
+        return TMP_SAM_FILE_ERROR;
+    }
+
+    if (fwrite(tmp->comp_buffer, sizeof(char), comp_size, tmp->fp) < comp_size) {
+        tmp_print_error(tmp, "[tmp_file] Error: tmp file write data failed.\n");
+        return TMP_SAM_FILE_ERROR;
+    }
+
+    tmp->offset += tmp->input_size;
+
+    if (tmp->offset >= tmp->ring_buffer_size - tmp->max_data_size)
+        tmp->offset = 0;
+
+    tmp->input_size = 0;
+    tmp->entry_number = 0;
+    tmp->groups_written++;
+
+    return TMP_SAM_OK;
+}
+
+
+/*
+ * Stores an in memory bam structure for writing and if enough are gathered together writes
+ * it to a file.  Multiple alignments compress better that single ones though after a certain number
+ * there is a law of diminishing returns.
+ * Returns 0 on success, a negative number on failure.
+ */
+int tmp_file_write(tmp_file_t *tmp, bam1_t *inbam) {
+
+    if ((tmp->offset + tmp->input_size + sizeof(bam1_t) + inbam->l_data) >= tmp->ring_buffer_size) {
+        int ret;
+
+        if ((ret = tmp_file_grow_ring_buffer(tmp, (tmp->offset + tmp->input_size + sizeof(bam1_t) + inbam->l_data) * 2))) {
+            tmp_print_error(tmp, "[tmp_file] Error: input line too big. (%ld).\n",
+                (tmp->input_size + inbam->l_data));
+
+            return ret;
+        }
+    }
+
+    tmp->ring_index = tmp->ring_buffer + tmp->offset + tmp->input_size;
+
+    // copy data into the ring buffer
+    memcpy(tmp->ring_index, inbam, sizeof(bam1_t));
+    memcpy(tmp->ring_index + sizeof(bam1_t) , inbam->data, inbam->l_data);
+    tmp->input_size += sizeof(bam1_t) + inbam->l_data;
+    tmp->entry_number++;
+
+    if (tmp->entry_number == tmp->group_size) {
+        // actually write out the data
+        int ret;
+
+        if ((ret = tmp_file_write_to_file(tmp))) {
+            return ret;
+        }
+    }
+
+    return TMP_SAM_OK;
+}
+
+
+/*
+ * Marks the end of file writing.  Adds a size_t 0 to mark the end of
+ * the file. Companion function to tmp_file_begin_read below.
+ * Returns 0 on success, a negative number on failure.
+ */
+int tmp_file_end_write(tmp_file_t *tmp) {
+    size_t terminator = 0;
+
+    if (tmp->entry_number) {
+        int ret;
+
+        if ((ret = tmp_file_write_to_file(tmp))) {
+            return ret;
+        }
+    }
+
+    if (fwrite(&terminator, sizeof(size_t), 1, tmp->fp) < 1) {
+        tmp_print_error(tmp, "[tmp_file] Error: tmp file write terminator failed.\n");
+        return TMP_SAM_FILE_ERROR;
+    }
+
+    fflush(tmp->fp);
+
+    LZ4_freeStream(tmp->stream);
+
+    return TMP_SAM_OK;
+}
+
+
+/*
+ * Prepares the file for reading.
+ * Companion function to tmp_file_end_write above.
+ * Returns 0 on success, a negative number on failure.
+ */
+int tmp_file_begin_read(tmp_file_t *tmp) {
+
+    rewind(tmp->fp);
+
+    tmp->dstream = LZ4_createStreamDecode();
+    tmp->offset  = 0;
+    tmp->entry_number = tmp->group_size;
+
+    if (!tmp->dstream) {
+        tmp_print_error(tmp, "[tmp_file] Error: unable to allocate compression stream.\n");
+        return TMP_SAM_MEM_ERROR;
+    }
+
+    return TMP_SAM_OK;
+}
+
+
+/*
+ * Read the next alignment, either from memory or from a file.
+ * Returns size of entry on success, 0 on end of file or a negative on error.
+ */
+int tmp_file_read(tmp_file_t *tmp, bam1_t *inbam) {
+    int entry_size;
+    uint8_t *data = inbam->data;
+
+    /* while tmp_file_read assumes that the same bam1_t variable
+       is being used in each call, this may not be the case. So
+       default to the lowest memory size for safety. */
+    if (tmp->data_size > inbam->m_data) {
+        tmp->data_size = inbam->m_data;
+    }
+
+    if (tmp->entry_number == tmp->group_size) {
+        // read more data
+        size_t comp_size;
+
+        if (fread(&comp_size, sizeof(size_t), 1, tmp->fp) == 0 || comp_size == 0) {
+            return TMP_SAM_OK;
+        }
+
+        if  (tmp->offset >= tmp->ring_buffer_size - tmp->max_data_size)
+            tmp->offset = 0;
+
+        tmp->ring_index = tmp->ring_buffer + tmp->offset;
+
+        if (fread(tmp->comp_buffer, sizeof(char), comp_size, tmp->fp) > comp_size) {
+            tmp_print_error(tmp, "[tmp_file] Error: error reading compressed data.\n");
+            return TMP_SAM_FILE_ERROR;
+        }
+
+        tmp->output_size = LZ4_decompress_safe_continue(tmp->dstream, tmp->comp_buffer,
+                        (char *)tmp->ring_index, comp_size, tmp->max_data_size);
+
+        if (tmp->output_size == 0) {
+            tmp_print_error(tmp, "[tmp_file] Error: decompression failed.\n");
+            return TMP_SAM_LZ4_ERROR;
+        }
+
+        tmp->entry_number = 0;
+        tmp->read_size    = 0;
+    }
+
+    tmp->ring_index = tmp->ring_buffer + tmp->offset;
+    memcpy(inbam, tmp->ring_index, sizeof(bam1_t));
+    inbam->data = data; // put the pointer to real bam data back
+
+    if ((unsigned int)inbam->l_data > tmp->data_size) {
+        uint8_t *tmp_data;
+        tmp->data_size = inbam->l_data; kroundup32(tmp->data_size);
+
+        if ((tmp_data = realloc(inbam->data, sizeof(uint8_t) * tmp->data_size)) == NULL) {
+            tmp_print_error(tmp, "[tmp_file] Error: unable to allocate tmp bam data memory.\n");
+            return TMP_SAM_MEM_ERROR;
+        }
+
+        inbam->data = tmp_data;
+    }
+
+    inbam->m_data = tmp->data_size; // set to the actual data size
+
+    entry_size = sizeof(bam1_t);
+
+    memcpy(inbam->data, tmp->ring_index + entry_size, inbam->l_data);
+    entry_size += inbam->l_data;
+
+    tmp->offset += entry_size;
+    tmp->read_size += entry_size;
+    tmp->entry_number++;
+
+    if (tmp->read_size > tmp->output_size) {
+        tmp_print_error(tmp, "[tmp_file] Error: wrong size of data returned RS:%ld OS:%ld EN:%ld GS:%ld.\n",
+            tmp->read_size, tmp->output_size, tmp->entry_number, tmp->group_size);
+        return TMP_SAM_LZ4_ERROR;
+    }
+
+    if (tmp->read_size == tmp->output_size && tmp->entry_number != tmp->group_size) {
+        // hopefully the last entries in the read file
+        tmp->entry_number = tmp->group_size;
+    }
+
+    return entry_size;
+}
+
+
+/*
+ * Frees up memory, closes the file and deletes it.
+ * Returns 0 on success or EOF on failure.
+ */
+int tmp_file_destroy(tmp_file_t *tmp) {
+    int ret = 0;
+
+    ret = fclose(tmp->fp);
+
+    LZ4_freeStreamDecode(tmp->dstream);
+    free(tmp->ring_buffer);
+    free(tmp->comp_buffer);
+    free(tmp->name);
+    free(tmp->dict);
+
+    return ret;
+}
diff --git a/samtools/tmp_file.c.pysam.c b/samtools/tmp_file.c.pysam.c
new file mode 100644
index 0000000..0969332
--- /dev/null
+++ b/samtools/tmp_file.c.pysam.c
@@ -0,0 +1,440 @@
+#include "samtools.pysam.h"
+
+/*
+    tmp_file.c - write to and read from a temporary binary file
+    for fast storage plus added compression.
+
+    Copyright (C) 2017, 2018 Genome Research Ltd.
+
+    Author: Andrew Whitwham <aw7@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE
+*/
+
+#include <config.h>
+
+#include <stdio.h>
+#include <string.h>
+#include <unistd.h>
+#include <stdlib.h>
+#include <stdarg.h>
+#include <fcntl.h>
+#include <errno.h>
+
+#ifdef _WIN32
+#include <windows.h>
+#endif /* _WIN32 */
+
+#include "tmp_file.h"
+#include "htslib/sam.h"
+
+
+static void tmp_print_error(tmp_file_t *tmp, const char *fmt, ...) {
+    va_list argp;
+
+    if (tmp->verbose) {
+        va_start(argp, fmt);
+        vfprintf(samtools_stderr, fmt, argp);
+        va_end(argp);
+    }
+}
+
+
+static int tmp_file_init(tmp_file_t *tmp, int verbose) {
+    tmp->stream       = LZ4_createStream();
+    tmp->data_size    = 0;
+    tmp->group_size   = TMP_SAM_GROUP_SIZE;
+    tmp->input_size   = 0;
+    tmp->read_size    = 0;
+    tmp->output_size  = 0;
+    tmp->entry_number = 0;
+    tmp->offset = 0;
+    tmp->max_data_size    = TMP_SAM_MAX_DATA + sizeof(bam1_t); // arbitrary but growable
+    tmp->ring_buffer_size = TMP_SAM_RING_SIZE; // arbitrary (min 64K) but growable
+    tmp->comp_buffer_size = LZ4_COMPRESSBOUND(tmp->max_data_size * tmp->group_size);
+    tmp->ring_buffer = malloc(sizeof(uint8_t) * tmp->ring_buffer_size);
+    tmp->ring_index  = tmp->ring_buffer;
+    tmp->comp_buffer = malloc(tmp->comp_buffer_size);
+    tmp->verbose = verbose;
+    tmp->dict = NULL;
+    tmp->groups_written = 0;
+
+    if (!tmp->ring_buffer || !tmp->comp_buffer || !tmp->stream) {
+        tmp_print_error(tmp, "[tmp_file] Error: unable to allocate compression buffers.\n");
+        return TMP_SAM_MEM_ERROR;
+    }
+
+    return TMP_SAM_OK;
+}
+
+
+/*
+ * Opens the temp file and initialises memory.
+ * Verbose mode prints out error messages to samtools_stderr.
+ * Returns 0 on success, a negative number on failure.
+ */
+int tmp_file_open_write(tmp_file_t *tmp, char *tmp_name, int verbose) {
+    int ret;
+    unsigned int count = 1;
+    const unsigned int max_count = 100000; // more tries than this then something else is wrong
+    int fd;
+
+    if ((ret = tmp_file_init(tmp, verbose))) {
+        return ret;
+    }
+
+    // make space to write extended file name
+    if ((tmp->name = malloc(strlen(tmp_name) + 7)) == NULL) {
+        tmp_print_error(tmp, "[tmp_file] Error: unable to allocate memory for %s.\n", tmp_name);
+        return TMP_SAM_MEM_ERROR;
+    }
+
+    // make sure temp file has a unique name
+    while (count < max_count) {
+        sprintf(tmp->name, "%s.%d", tmp_name, count);
+
+
+        #ifdef _WIN32
+        if ((fd = _open(tmp->name, O_RDWR|O_CREAT|O_EXCL|O_BINARY|O_TEMPORARY, 0600)) == -1) {
+        #else
+        if ((fd = open(tmp->name, O_RDWR|O_CREAT|O_EXCL, 0600)) == -1) {
+        #endif /* _WIN32 */
+
+            if (errno != EEXIST) {
+                tmp_print_error(tmp, "[tmp_file] Error: unable to create tmp file %s.\n", tmp->name);
+                return TMP_SAM_FILE_ERROR;
+            }
+
+            count++;
+            continue;
+        }
+
+        break;
+    }
+
+    if (count >= max_count) {
+        tmp_print_error(tmp, "[tmp_file] Error: unable to create unique temp file.\n");
+        return TMP_SAM_FILE_ERROR;
+    }
+
+    if ((tmp->fp = fdopen(fd, "w+b")) == NULL) {
+        tmp_print_error(tmp, "[tmp_file] Error: unable to open write file %s.\n", tmp->name);
+        return TMP_SAM_FILE_ERROR;
+    }
+
+    #ifndef _WIN32
+    unlink(tmp->name); // should auto delete when closed on linux
+    #endif
+
+    return TMP_SAM_OK;
+}
+
+
+/*
+ * The ring buffer stores precompressionn/post decompression data.  LZ4 requires that
+ * previous data (64K worth) be available for efficient compression.  This function grows
+ * the ring buffer when needed.
+ * Returns 0 on success, a negative number on failure.
+ */
+static int tmp_file_grow_ring_buffer(tmp_file_t *tmp, size_t new_size) {
+    // save the dictionary so lz4 can continue to function
+    int dict_size = 64 * 1024; // 64K max size
+
+    if (tmp->groups_written) {
+        // if compression has been done then there is a dictionary to save
+
+        if (tmp->dict == NULL) {
+
+            if ((tmp->dict = malloc(sizeof(char) * dict_size)) == NULL) {
+                tmp_print_error(tmp, "[tmp_file] Error: unable to allocate memory for compression dictionary.\n");
+                return TMP_SAM_MEM_ERROR;
+            }
+        }
+
+        if (LZ4_saveDict(tmp->stream, tmp->dict, dict_size) == 0) {
+            tmp_print_error(tmp, "[tmp_file] Error: unable to save compression dictionary.\n");
+            return TMP_SAM_LZ4_ERROR;
+        }
+    }
+
+    if ((tmp->ring_buffer = realloc(tmp->ring_buffer, sizeof(char) * new_size)) == NULL) {
+        tmp_print_error(tmp, "[tmp_file] Error: unable to reallocate ring buffer.\n");
+        return TMP_SAM_MEM_ERROR;
+    }
+
+    tmp->ring_buffer_size = new_size;
+
+    return TMP_SAM_OK;
+}
+
+
+/*
+ * This does the actual compression and writing to a file.  The file format consists of a
+ * single size_t for the size of the compressed data followed by the data itself.
+ * Returns 0 on success, a negative number on failure.
+ */
+static int tmp_file_write_to_file(tmp_file_t *tmp) {
+    size_t comp_size;
+
+    if (tmp->input_size > tmp->max_data_size) {
+        tmp->max_data_size += tmp->input_size + sizeof(bam1_t);
+        tmp->comp_buffer_size = LZ4_COMPRESSBOUND(tmp->max_data_size);
+
+        if ((tmp->comp_buffer = realloc(tmp->comp_buffer, sizeof(char) * tmp->comp_buffer_size)) == NULL) {
+            tmp_print_error(tmp, "[tmp_file] Error: unable to reallocate compression buffer.\n");
+            return TMP_SAM_MEM_ERROR;
+        }
+
+        // make sure the ring buffer is big enough to accommodate the new max_data_size
+        if (tmp->ring_buffer_size < tmp->max_data_size * 5) {
+            int ret;
+            if ((ret = tmp_file_grow_ring_buffer(tmp, tmp->max_data_size * 5))) {
+                return ret;
+            }
+        }
+    }
+
+    tmp->ring_index = tmp->ring_buffer + tmp->offset;
+
+    comp_size = LZ4_compress_fast_continue(tmp->stream, (const char *)tmp->ring_index,
+                   tmp->comp_buffer, tmp->input_size, tmp->comp_buffer_size, 1);
+
+    if (comp_size == 0) {
+        tmp_print_error(tmp, "[tmp_file] Error: compression failed.\n");
+        return TMP_SAM_LZ4_ERROR;
+    }
+
+    if (fwrite(&comp_size, sizeof(size_t), 1, tmp->fp) < 1) {
+        tmp_print_error(tmp, "[tmp_file] Error: tmp file write size failed.\n");
+        return TMP_SAM_FILE_ERROR;
+    }
+
+    if (fwrite(tmp->comp_buffer, sizeof(char), comp_size, tmp->fp) < comp_size) {
+        tmp_print_error(tmp, "[tmp_file] Error: tmp file write data failed.\n");
+        return TMP_SAM_FILE_ERROR;
+    }
+
+    tmp->offset += tmp->input_size;
+
+    if (tmp->offset >= tmp->ring_buffer_size - tmp->max_data_size)
+        tmp->offset = 0;
+
+    tmp->input_size = 0;
+    tmp->entry_number = 0;
+    tmp->groups_written++;
+
+    return TMP_SAM_OK;
+}
+
+
+/*
+ * Stores an in memory bam structure for writing and if enough are gathered together writes
+ * it to a file.  Multiple alignments compress better that single ones though after a certain number
+ * there is a law of diminishing returns.
+ * Returns 0 on success, a negative number on failure.
+ */
+int tmp_file_write(tmp_file_t *tmp, bam1_t *inbam) {
+
+    if ((tmp->offset + tmp->input_size + sizeof(bam1_t) + inbam->l_data) >= tmp->ring_buffer_size) {
+        int ret;
+
+        if ((ret = tmp_file_grow_ring_buffer(tmp, (tmp->offset + tmp->input_size + sizeof(bam1_t) + inbam->l_data) * 2))) {
+            tmp_print_error(tmp, "[tmp_file] Error: input line too big. (%ld).\n",
+                (tmp->input_size + inbam->l_data));
+
+            return ret;
+        }
+    }
+
+    tmp->ring_index = tmp->ring_buffer + tmp->offset + tmp->input_size;
+
+    // copy data into the ring buffer
+    memcpy(tmp->ring_index, inbam, sizeof(bam1_t));
+    memcpy(tmp->ring_index + sizeof(bam1_t) , inbam->data, inbam->l_data);
+    tmp->input_size += sizeof(bam1_t) + inbam->l_data;
+    tmp->entry_number++;
+
+    if (tmp->entry_number == tmp->group_size) {
+        // actually write out the data
+        int ret;
+
+        if ((ret = tmp_file_write_to_file(tmp))) {
+            return ret;
+        }
+    }
+
+    return TMP_SAM_OK;
+}
+
+
+/*
+ * Marks the end of file writing.  Adds a size_t 0 to mark the end of
+ * the file. Companion function to tmp_file_begin_read below.
+ * Returns 0 on success, a negative number on failure.
+ */
+int tmp_file_end_write(tmp_file_t *tmp) {
+    size_t terminator = 0;
+
+    if (tmp->entry_number) {
+        int ret;
+
+        if ((ret = tmp_file_write_to_file(tmp))) {
+            return ret;
+        }
+    }
+
+    if (fwrite(&terminator, sizeof(size_t), 1, tmp->fp) < 1) {
+        tmp_print_error(tmp, "[tmp_file] Error: tmp file write terminator failed.\n");
+        return TMP_SAM_FILE_ERROR;
+    }
+
+    fflush(tmp->fp);
+
+    LZ4_freeStream(tmp->stream);
+
+    return TMP_SAM_OK;
+}
+
+
+/*
+ * Prepares the file for reading.
+ * Companion function to tmp_file_end_write above.
+ * Returns 0 on success, a negative number on failure.
+ */
+int tmp_file_begin_read(tmp_file_t *tmp) {
+
+    rewind(tmp->fp);
+
+    tmp->dstream = LZ4_createStreamDecode();
+    tmp->offset  = 0;
+    tmp->entry_number = tmp->group_size;
+
+    if (!tmp->dstream) {
+        tmp_print_error(tmp, "[tmp_file] Error: unable to allocate compression stream.\n");
+        return TMP_SAM_MEM_ERROR;
+    }
+
+    return TMP_SAM_OK;
+}
+
+
+/*
+ * Read the next alignment, either from memory or from a file.
+ * Returns size of entry on success, 0 on end of file or a negative on error.
+ */
+int tmp_file_read(tmp_file_t *tmp, bam1_t *inbam) {
+    int entry_size;
+    uint8_t *data = inbam->data;
+
+    /* while tmp_file_read assumes that the same bam1_t variable
+       is being used in each call, this may not be the case. So
+       default to the lowest memory size for safety. */
+    if (tmp->data_size > inbam->m_data) {
+        tmp->data_size = inbam->m_data;
+    }
+
+    if (tmp->entry_number == tmp->group_size) {
+        // read more data
+        size_t comp_size;
+
+        if (fread(&comp_size, sizeof(size_t), 1, tmp->fp) == 0 || comp_size == 0) {
+            return TMP_SAM_OK;
+        }
+
+        if  (tmp->offset >= tmp->ring_buffer_size - tmp->max_data_size)
+            tmp->offset = 0;
+
+        tmp->ring_index = tmp->ring_buffer + tmp->offset;
+
+        if (fread(tmp->comp_buffer, sizeof(char), comp_size, tmp->fp) > comp_size) {
+            tmp_print_error(tmp, "[tmp_file] Error: error reading compressed data.\n");
+            return TMP_SAM_FILE_ERROR;
+        }
+
+        tmp->output_size = LZ4_decompress_safe_continue(tmp->dstream, tmp->comp_buffer,
+                        (char *)tmp->ring_index, comp_size, tmp->max_data_size);
+
+        if (tmp->output_size == 0) {
+            tmp_print_error(tmp, "[tmp_file] Error: decompression failed.\n");
+            return TMP_SAM_LZ4_ERROR;
+        }
+
+        tmp->entry_number = 0;
+        tmp->read_size    = 0;
+    }
+
+    tmp->ring_index = tmp->ring_buffer + tmp->offset;
+    memcpy(inbam, tmp->ring_index, sizeof(bam1_t));
+    inbam->data = data; // put the pointer to real bam data back
+
+    if ((unsigned int)inbam->l_data > tmp->data_size) {
+        uint8_t *tmp_data;
+        tmp->data_size = inbam->l_data; kroundup32(tmp->data_size);
+
+        if ((tmp_data = realloc(inbam->data, sizeof(uint8_t) * tmp->data_size)) == NULL) {
+            tmp_print_error(tmp, "[tmp_file] Error: unable to allocate tmp bam data memory.\n");
+            return TMP_SAM_MEM_ERROR;
+        }
+
+        inbam->data = tmp_data;
+    }
+
+    inbam->m_data = tmp->data_size; // set to the actual data size
+
+    entry_size = sizeof(bam1_t);
+
+    memcpy(inbam->data, tmp->ring_index + entry_size, inbam->l_data);
+    entry_size += inbam->l_data;
+
+    tmp->offset += entry_size;
+    tmp->read_size += entry_size;
+    tmp->entry_number++;
+
+    if (tmp->read_size > tmp->output_size) {
+        tmp_print_error(tmp, "[tmp_file] Error: wrong size of data returned RS:%ld OS:%ld EN:%ld GS:%ld.\n",
+            tmp->read_size, tmp->output_size, tmp->entry_number, tmp->group_size);
+        return TMP_SAM_LZ4_ERROR;
+    }
+
+    if (tmp->read_size == tmp->output_size && tmp->entry_number != tmp->group_size) {
+        // hopefully the last entries in the read file
+        tmp->entry_number = tmp->group_size;
+    }
+
+    return entry_size;
+}
+
+
+/*
+ * Frees up memory, closes the file and deletes it.
+ * Returns 0 on success or EOF on failure.
+ */
+int tmp_file_destroy(tmp_file_t *tmp) {
+    int ret = 0;
+
+    ret = fclose(tmp->fp);
+
+    LZ4_freeStreamDecode(tmp->dstream);
+    free(tmp->ring_buffer);
+    free(tmp->comp_buffer);
+    free(tmp->name);
+    free(tmp->dict);
+
+    return ret;
+}
diff --git a/samtools/tmp_file.h b/samtools/tmp_file.h
new file mode 100644
index 0000000..4f2647c
--- /dev/null
+++ b/samtools/tmp_file.h
@@ -0,0 +1,124 @@
+/*
+    tmp_file.h - write to and read from a temporary binary file
+    for fast storage plus added compression.
+
+    Copyright (C) 2017, 2018 Genome Research Ltd.
+
+    Author: Andrew Whitwham <aw7@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE
+*/
+
+#ifndef _TMP_SAM_FILE_H_
+#define _TMP_SAM_FILE_H_
+
+#include <lz4.h>
+#include "htslib/sam.h"
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+// Group size that seems to give reasonable compression.
+#define TMP_SAM_GROUP_SIZE 100
+
+// Arbitrary initial size values but growable.
+#define TMP_SAM_MAX_DATA 1024
+#define TMP_SAM_RING_SIZE 1048576
+
+// Error numbers.
+#define TMP_SAM_OK 0
+#define TMP_SAM_MEM_ERROR -1
+#define TMP_SAM_FILE_ERROR -2
+#define TMP_SAM_LZ4_ERROR -3
+#define TMP_SAM_INPUT_ERROR -4
+
+typedef struct {
+    FILE *fp;
+    LZ4_stream_t *stream;
+    LZ4_streamDecode_t *dstream;
+    size_t data_size;
+    size_t max_data_size;
+    size_t ring_buffer_size;
+    size_t comp_buffer_size;
+    size_t offset;
+    uint8_t *ring_buffer;
+    uint8_t *ring_index;
+    char *comp_buffer;
+    char *name;
+    size_t group_size;
+    size_t input_size;
+    size_t read_size;
+    size_t output_size;
+    size_t entry_number;
+    int verbose;
+    char *dict;
+    size_t groups_written;
+} tmp_file_t;
+
+
+/*
+ * Opens the temp file and initialises memory.
+ * Verbose mode prints out error messages to stderr.
+ * Returns 0 on success, a negative number on failure.
+ */
+int tmp_file_open_write(tmp_file_t *tmp, char *tmp_name, int verbose);
+
+
+/*
+ * Stores an in memory bam structure for writing and if enough are gathered together writes
+ * it to a file.  Multiple alignments compress better that single ones though after a certain number
+ * there is a law of diminishing returns.
+ * Returns 0 on success, a negative number on failure.
+ */
+int tmp_file_write(tmp_file_t *tmp, bam1_t *inbam);
+
+
+/*
+ * Marks the end of file writing.  Adds a size_t 0 to mark the end of
+ * the file. Companion function to tmp_file_begin_read below.
+ * Returns 0 on success, a negative number on failure.
+ */
+int tmp_file_end_write(tmp_file_t *tmp);
+
+/*
+ * Prepares the file for reading.
+ * Companion function to tmp_file_end_write above.
+ * Returns 0 on success, a negative number on failure.
+ */
+int tmp_file_begin_read(tmp_file_t *tmp);
+
+/*
+ * Read the next alignment, either from memory or from a file.
+ * Returns size of entry on success, 0 on end of file or a negative on error.
+ */
+int tmp_file_read(tmp_file_t *tmp, bam1_t *inbam);
+
+
+/*
+ * Frees up memory, closes the file and deletes it.
+ * Returns 0 on success or EOF on failure.
+ */
+int tmp_file_destroy(tmp_file_t *tmp);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif /* _TMP_SAM_FILE_H_ */
diff --git a/samtools/version.sh b/samtools/version.sh
new file mode 100755
index 0000000..5327353
--- /dev/null
+++ b/samtools/version.sh
@@ -0,0 +1,36 @@
+#!/bin/sh
+# version.sh -- Script to build the htslib version string
+#
+#     Author : James Bonfield <jkb@sanger.ac.uk>
+#
+#     Copyright (C) 2017, 2019 Genome Research Ltd.
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+# THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+# DEALINGS IN THE SOFTWARE.
+
+# Master version, for use in tarballs or non-git source copies
+VERSION=1.16.1
+
+# If we have a git clone, then check against the current tag
+if [ -e .git ]
+then
+    # If we ever get to 10.x this will need to be more liberal
+    VERSION=`git describe --match '[0-9].[0-9]*' --dirty --always`
+fi
+
+echo $VERSION
diff --git a/setup.cfg b/setup.cfg
new file mode 100644
index 0000000..ef3f511
--- /dev/null
+++ b/setup.cfg
@@ -0,0 +1,43 @@
+[bdist_wheel]
+universal = 0
+
+[tool:pytest]
+# -s: do not capture stdout, conflicts with pysam.dispatch
+# -v: verbose output
+addopts = -s -v
+testpaths = pysam tests
+
+[flake8]
+max-line-length = 100
+max-complexity = 23
+extend-ignore = E117, E124, E125, E201, E202, E211, E225, E231, E265, E266, E302, E303, E305, E402, E501, E701, E713, E722, E741, F403, F405, F811, F821, F841, W291, W293, W391, W605
+per-file-ignores = __init__.py:F401
+
+# E117 over-indented
+# E124 closing bracket does not match visual indentation
+# E125 continuation line with same indent as next logical line
+# E201 whitespace after '{'
+# E202 whitespace before '}'
+# E211 whitespace before '('
+# E225 missing whitespace around operator
+# E231 missing whitespace after ':'
+# E265 block comment should start with '# '
+# E266 too many leading '#' for block comment
+# E302 expected 2 blank lines, found 1
+# E303 too many blank lines
+# E305 expected 2 blank lines after class or function definition, found 1
+# E402 module level import not at top of file
+# E501 line too long
+# E701 multiple statements on one line (colon)
+# E713 test for membership should be 'not in'
+# E722 do not use bare 'except'
+# E741 ambiguous variable name '...'
+# F403 'from ... import *' used; unable to detect undefined names
+# F405 '...' may be undefined, or defined from star imports: ...
+# F811 redefinition of unused '...' from line ...
+# F821 undefined name '...'
+# F841 local variable '...' is assigned to but never used
+# W291 trailing whitespace
+# W293 blank line contains whitespace
+# W391 blank line at end of file
+# W605 invalid escape sequence '...'
diff --git a/setup.py b/setup.py
new file mode 100644
index 0000000..890b90a
--- /dev/null
+++ b/setup.py
@@ -0,0 +1,631 @@
+#! /usr/bin/python
+
+'''pysam - a python module for reading, manipulating and writing
+genomic data sets.
+
+pysam is a lightweight wrapper of the htslib C-API and provides
+facilities to read and write SAM/BAM/VCF/BCF/BED/GFF/GTF/FASTA/FASTQ
+files as well as access to the command line functionality of the
+samtools and bcftools packages. The module supports compression and
+random access through indexing.
+
+This module provides a low-level wrapper around the htslib C-API as
+using cython and a high-level API for convenient access to the data
+within standard genomic file formats.
+
+See:
+http://www.htslib.org
+https://github.com/pysam-developers/pysam
+http://pysam.readthedocs.org/en/stable
+
+'''
+
+import collections
+import glob
+import os
+import platform
+import re
+import subprocess
+import sys
+import sysconfig
+from contextlib import contextmanager
+from distutils import log
+from setuptools import setup, Command
+from distutils.command.build import build
+from setuptools.command.sdist import sdist
+from distutils.errors import LinkError
+
+from cy_build import CyExtension as Extension, cy_build_ext as build_ext
+try:
+    import cython  # noqa
+    HAVE_CYTHON = True
+except ImportError:
+    HAVE_CYTHON = False
+
+IS_PYTHON3 = sys.version_info.major >= 3
+IS_DARWIN = platform.system() == 'Darwin'
+
+
+@contextmanager
+def changedir(path):
+    save_dir = os.getcwd()
+    os.chdir(path)
+    try:
+        yield
+    finally:
+        os.chdir(save_dir)
+
+
+def run_configure(option):
+    sys.stdout.flush()
+    try:
+        retcode = subprocess.call(
+            " ".join(("./configure", option)),
+            shell=True)
+        if retcode != 0:
+            return False
+        else:
+            return True
+    except OSError as e:
+        return False
+
+
+def run_make(targets):
+    sys.stdout.flush()
+    subprocess.check_call([os.environ.get("MAKE", "make")] + targets)
+
+
+def run_make_print_config():
+    stdout = subprocess.check_output(["make", "-s", "print-config"])
+    if IS_PYTHON3:
+        stdout = stdout.decode("ascii")
+
+    make_print_config = {}
+    for line in stdout.splitlines():
+        if "=" in line:
+            row = line.split("=")
+            if len(row) == 2:
+                make_print_config.update(
+                    {row[0].strip(): row[1].strip()})
+    return make_print_config
+
+
+def run_nm_defined_symbols(objfile):
+    stdout = subprocess.check_output(["nm", "-g", "-P", objfile])
+    if IS_PYTHON3:
+        stdout = stdout.decode("ascii")
+
+    symbols = set()
+    for line in stdout.splitlines():
+        (sym, symtype) = line.split()[:2]
+        if symtype not in "UFNWw":
+            if IS_DARWIN:
+                # On macOS, all symbols have a leading underscore
+                symbols.add(sym.lstrip('_'))
+            else:
+                # Ignore symbols such as _edata (present in all shared objects)
+                if sym[0] not in "_$.@": symbols.add(sym)
+
+    return symbols
+
+
+# This function emulates the way distutils combines settings from sysconfig,
+# environment variables, and the extension being built. It returns a dictionary
+# representing the usual set of variables, suitable for writing to a generated
+# file or for running configure (provided the returned LIBS is ignored).
+def build_config_dict(ext):
+    def env(var):
+        return [os.environ[var]] if var in os.environ else []
+
+    def sc(var):
+        value = sysconfig.get_config_var(var)
+        return [value] if value is not None else []
+
+    def optionise(option, valuelist):
+        def quote(s): return "'"+s+"'" if " " in s else s
+        return list(quote(option+v) for v in valuelist)
+
+    def kvtuples(pairlist):
+        def appendoptvalue(t): return t[0] if t[1] is None else t[0]+"="+t[1]
+        return map(appendoptvalue, pairlist)
+
+    # For CC, select the first of these that is set
+    cc = (env('CC') + sc('CC') + ['gcc'])[0]
+
+    # distutils ignores sysconfig for CPPFLAGS
+    cppflags = " ".join(env('CPPFLAGS') + optionise('-I', ext.include_dirs) +
+                        optionise('-D', kvtuples(ext.define_macros)) +
+                        optionise('-U', ext.undef_macros))
+
+    cflags = " ".join(sc('CFLAGS') + env('CFLAGS') + sc('CCSHARED') +
+                      ext.extra_compile_args)
+
+    # distutils actually includes $CPPFLAGS here too, but that's weird and
+    # unnecessary for us as we know the output LDFLAGS will be used correctly
+    ldflags = " ".join(sc('LDFLAGS') + env('LDFLAGS') + env('CFLAGS') +
+                       optionise('-L', ext.library_dirs) +
+                       ext.extra_link_args)
+
+    # ext.libraries is computed (incorporating $LIBS etc) during configure
+    libs = " ".join(optionise('-l', ext.libraries))
+
+    return { 'CC': cc, 'CPPFLAGS': cppflags, 'CFLAGS': cflags,
+             'LDFLAGS': ldflags, 'LIBS': libs }
+
+
+def write_configvars_header(filename, ext, prefix):
+    config = build_config_dict(ext)
+    if prefix != 'HTS':
+        config['HTSDIR'] = '(unused)'
+        config['CURSES_LIB'] = '(unused)'
+
+    log.info("creating %s for '%s' extension", filename, ext.name)
+    with open(filename, "w") as outf:
+        for var, value in config.items():
+            outf.write('#define {}_{} "{}"\n'.format(prefix, var, value))
+
+
+@contextmanager
+def set_compiler_envvars():
+    tmp_vars = []
+    for var in ['CC', 'CFLAGS', 'LDFLAGS']:
+        if var in os.environ:
+            print("# pysam: (env) {}={}".format(var, os.environ[var]))
+        elif var in sysconfig.get_config_vars():
+            value = sysconfig.get_config_var(var)
+            if var == 'CFLAGS' and 'CCSHARED' in sysconfig.get_config_vars():
+                value += ' ' + sysconfig.get_config_var('CCSHARED')
+            print("# pysam: (sysconfig) {}={}".format(var, value))
+            os.environ[var] = value
+            tmp_vars += [var]
+
+    try:
+        yield
+    finally:
+        for var in tmp_vars:
+            del os.environ[var]
+
+
+def configure_library(library_dir, env_options=None, options=[]):
+
+    configure_script = os.path.join(library_dir, "configure")
+
+    on_rtd = os.environ.get("READTHEDOCS") == "True"
+    # RTD has no bzip2 development libraries installed:
+    if on_rtd:
+        env_options = "--disable-bz2"
+
+    if not os.path.exists(configure_script):
+        raise ValueError(
+            "configure script {} does not exist".format(configure_script))
+
+    with changedir(library_dir), set_compiler_envvars():
+        if env_options is not None:
+            if run_configure(env_options):
+                return env_options
+
+        for option in options:
+            if run_configure(option):
+                return option
+
+    return None
+
+
+def get_pysam_version():
+    sys.path.insert(0, "pysam")
+    import version
+    return version.__version__
+
+
+# Override sdist command to ensure Cythonized *.c files are included.
+class cythonize_sdist(sdist):
+    # Remove when setuptools (as installed on GH runners) has these options
+    if not any(opt[0] == 'owner=' for opt in sdist.user_options):
+        sdist.user_options.append(('owner=', 'u', 'Specify owner inside tar'))
+    if not any(opt[0] == 'group=' for opt in sdist.user_options):
+        sdist.user_options.append(('group=', 'g', 'Specify group inside tar'))
+
+    def run(self):
+        from Cython.Build import cythonize
+        cythonize(self.distribution.ext_modules)
+        sdist.run(self)
+
+
+# Override build command to add extra build steps.
+class extra_build(build):
+    def check_ext_symbol_conflicts(self):
+        """Checks for symbols defined in multiple extension modules,
+        which can lead to crashes due to incorrect functions being invoked.
+        Avoid by adding an appropriate #define to import/pysam.h or in
+        unusual cases adding another rewrite rule to devtools/import.py.
+        """
+        build_ext_obj = self.distribution.get_command_obj('build_ext')
+
+        symbols = dict()
+        for ext in self.distribution.ext_modules:
+            for sym in run_nm_defined_symbols(build_ext_obj.get_ext_fullpath(ext.name)):
+                symbols.setdefault(sym, []).append(ext.name.lstrip('pysam.'))
+
+        errors = 0
+        for (sym, objs) in symbols.items():
+            if (len(objs) > 1):
+                log.error("conflicting symbol (%s): %s", " ".join(objs), sym)
+                errors += 1
+
+        if errors > 0: raise LinkError("symbols defined in multiple extensions")
+
+    def run(self):
+        build.run(self)
+        try:
+            if HTSLIB_MODE != 'separate':
+                self.check_ext_symbol_conflicts()
+        except OSError as e:
+            log.warn("skipping symbol collision check (invoking nm failed: %s)", e)
+        except subprocess.CalledProcessError:
+            log.warn("skipping symbol collision check (invoking nm failed)")
+
+
+class clean_ext(Command):
+    description = "clean up Cython temporary files"
+    user_options = []
+
+    def initialize_options(self):
+        pass
+
+    def finalize_options(self):
+        pass
+
+    def run(self):
+        objs = glob.glob(os.path.join("pysam", "libc*.c"))
+        if objs:
+            log.info("removing 'pysam/libc*.c' (%s Cython objects)", len(objs))
+        for obj in objs:
+            os.remove(obj)
+
+        headers = (glob.glob(os.path.join("htslib",   "*config*.h")) +
+                   glob.glob(os.path.join("samtools", "*config*.h")) +
+                   glob.glob(os.path.join("bcftools", "*config*.h")))
+        if headers:
+            log.info("removing '*/*config*.h' (%s generated headers)", len(headers))
+        for header in headers:
+            os.remove(header)
+
+        objects = (glob.glob(os.path.join("htslib", "*.[oa]")) +
+                   glob.glob(os.path.join("htslib", "cram", "*.o")) +
+                   glob.glob(os.path.join("htslib", "htscodecs", "htscodecs", "*.o")))
+        if objects:
+            log.info("removing 'htslib/**/*.o' and libhts.a (%s objects)", len(objects))
+        for obj in objects:
+            os.remove(obj)
+
+
+# How to link against HTSLIB
+# shared:   build shared chtslib from builtin htslib code.
+# external: use shared libhts.so compiled outside of
+#           pysam
+# separate: use included htslib and include in each extension
+#           module. No dependencies between modules and works with
+#           setup.py install, but wasteful in terms of memory and
+#           compilation time. Fallback if shared module compilation
+#           fails.
+
+HTSLIB_MODE = os.environ.get("HTSLIB_MODE", "shared")
+HTSLIB_LIBRARY_DIR = os.environ.get("HTSLIB_LIBRARY_DIR", None)
+HTSLIB_INCLUDE_DIR = os.environ.get("HTSLIB_INCLUDE_DIR", None)
+HTSLIB_CONFIGURE_OPTIONS = os.environ.get("HTSLIB_CONFIGURE_OPTIONS", None)
+HTSLIB_SOURCE = None
+
+package_list = ['pysam',
+                'pysam.include',
+                'pysam.include.samtools',
+                'pysam.include.bcftools']
+package_dirs = {'pysam': 'pysam',
+                'pysam.include.samtools': 'samtools',
+                'pysam.include.bcftools': 'bcftools'}
+
+# list of config files that will be automatically generated should
+# they not already exist or be created by configure scripts in the
+# subpackages.
+config_headers = ["samtools/config.h",
+                  "bcftools/config.h"]
+
+# If cython is available, the pysam will be built using cython from
+# the .pyx files. If no cython is available, the C-files included in the
+# distribution will be used.
+if HAVE_CYTHON:
+    print("# pysam: cython is available - using cythonize if necessary")
+    source_pattern = "pysam/libc%s.pyx"
+else:
+    print("# pysam: no cython available - using pre-compiled C")
+    source_pattern = "pysam/libc%s.c"
+
+# Exit if there are no pre-compiled files and no cython available
+fn = source_pattern % "htslib"
+if not os.path.exists(fn):
+    raise ValueError(
+        "no cython installed, but can not find {}."
+        "Make sure that cython is installed when building "
+        "from the repository"
+        .format(fn))
+
+print("# pysam: htslib mode is {}".format(HTSLIB_MODE))
+print("# pysam: HTSLIB_CONFIGURE_OPTIONS={}".format(
+    HTSLIB_CONFIGURE_OPTIONS))
+htslib_configure_options = None
+
+if HTSLIB_MODE in ['shared', 'separate']:
+    package_list += ['pysam.include.htslib',
+                     'pysam.include.htslib.htslib']
+    package_dirs.update({'pysam.include.htslib':'htslib'})
+
+    htslib_configure_options = configure_library(
+        "htslib",
+        HTSLIB_CONFIGURE_OPTIONS,
+        ["--enable-libcurl",
+         "--disable-libcurl"])
+
+    HTSLIB_SOURCE = "builtin"
+    print("# pysam: htslib configure options: {}".format(
+        str(htslib_configure_options)))
+
+    config_headers += ["htslib/config.h"]
+    if htslib_configure_options is None:
+        # create empty config.h file
+        with open("htslib/config.h", "w") as outf:
+            outf.write(
+                "/* empty config.h created by pysam */\n")
+            outf.write(
+                "/* conservative compilation options */\n")
+
+    with changedir("htslib"):
+        htslib_make_options = run_make_print_config()
+
+    for key, value in htslib_make_options.items():
+        print("# pysam: htslib_config {}={}".format(key, value))
+
+    external_htslib_libraries = ['z']
+    if "LIBS" in htslib_make_options:
+        external_htslib_libraries.extend(
+            [re.sub("^-l", "", x) for x in htslib_make_options["LIBS"].split(" ") if x.strip()])
+
+if HTSLIB_LIBRARY_DIR:
+    # linking against a shared, externally installed htslib version,
+    # no sources or built libhts.a required for htslib
+    htslib_objects = []
+    separate_htslib_objects = []
+    chtslib_sources = []
+    htslib_library_dirs = [HTSLIB_LIBRARY_DIR]
+    htslib_include_dirs = [HTSLIB_INCLUDE_DIR]
+    external_htslib_libraries = ['z', 'hts']
+elif HTSLIB_MODE == 'separate':
+    # add to each pysam component a separately compiled
+    # htslib
+    htslib_objects = ['htslib/libhts.a']
+    separate_htslib_objects = ['htslib/libhts.a']
+    htslib_library_dirs = []
+    htslib_include_dirs = ['htslib']
+elif HTSLIB_MODE == 'shared':
+    # link each pysam component against the same
+    # htslib built from sources included in the pysam
+    # package.
+
+    # Link with the object files rather than the final htslib/libhts.a, to ensure that
+    # all object files are pulled into the link, even those not used by htslib itself.
+    htslib_objects = [os.path.join("htslib", x)
+                      for x in htslib_make_options["LIBHTS_OBJS"].split(" ")]
+    separate_htslib_objects = []
+
+    htslib_library_dirs = ["."] # when using setup.py develop?
+    htslib_include_dirs = ['htslib']
+else:
+    raise ValueError("unknown HTSLIB value '%s'" % HTSLIB_MODE)
+
+# build config.py
+with open(os.path.join("pysam", "config.py"), "w") as outf:
+    outf.write('HTSLIB = "{}"\n'.format(HTSLIB_SOURCE))
+    config_values = collections.defaultdict(int)
+
+    if HTSLIB_SOURCE == "builtin":
+        with open(os.path.join("htslib", "config.h")) as inf:
+            for line in inf:
+                if line.startswith("#define"):
+                    key, value = re.match(
+                        "#define (\S+)\s+(\S+)", line).groups()
+                    config_values[key] = value
+            for key in ["ENABLE_GCS",
+                        "ENABLE_PLUGINS",
+                        "ENABLE_S3",
+                        "HAVE_COMMONCRYPTO",
+                        "HAVE_HMAC",
+                        "HAVE_LIBBZ2",
+                        "HAVE_LIBCURL",
+                        "HAVE_LIBDEFLATE",
+                        "HAVE_LIBLZMA",
+                        "HAVE_MMAP"]:
+                outf.write("{} = {}\n".format(key, config_values[key]))
+                print("# pysam: config_option: {}={}".format(key, config_values[key]))
+
+# create empty config.h files if they have not been created automatically
+# or created by the user:
+for fn in config_headers:
+    if not os.path.exists(fn):
+        with open(fn, "w") as outf:
+            outf.write(
+                "/* empty config.h created by pysam */\n")
+            outf.write(
+                "/* conservative compilation options */\n")
+
+#######################################################
+# Windows compatibility - untested
+if platform.system() == 'Windows':
+    include_os = ['win32']
+    os_c_files = ['win32/getopt.c']
+    extra_compile_args = []
+else:
+    include_os = []
+    os_c_files = []
+    # for python 3.4, see for example
+    # http://stackoverflow.com/questions/25587039/
+    # error-compiling-rpy2-on-python3-4-due-to-werror-
+    # declaration-after-statement
+    extra_compile_args = [
+        "-Wno-unused",
+        "-Wno-strict-prototypes",
+        "-Wno-sign-compare",
+        "-Wno-error=declaration-after-statement"]
+
+define_macros = []
+
+suffix = sysconfig.get_config_var('EXT_SUFFIX')
+if not suffix:
+    suffix = sysconfig.get_config_var('SO')
+
+internal_htslib_libraries = [
+    os.path.splitext("chtslib{}".format(suffix))[0]]
+internal_samtools_libraries = [
+    os.path.splitext("csamtools{}".format(suffix))[0],
+    os.path.splitext("cbcftools{}".format(suffix))[0],
+    ]
+internal_pysamutil_libraries = [
+    os.path.splitext("cutils{}".format(suffix))[0]]
+
+libraries_for_pysam_module = external_htslib_libraries + internal_htslib_libraries + internal_pysamutil_libraries
+
+# Order of modules matters in order to make sure that dependencies are resolved.
+# The structures of dependencies is as follows:
+# libchtslib: htslib utility functions and htslib itself if builtin is set.
+# libcsamtools: samtools code (builtin)
+# libcbcftools: bcftools code (builtin)
+# libcutils: General utility functions, depends on all of the above
+# libcXXX (pysam module): depends on libchtslib and libcutils
+
+# The list below uses the union of include_dirs and library_dirs for
+# reasons of simplicity.
+
+def prebuild_libchtslib(ext, force):
+    if HTSLIB_MODE not in ['shared', 'separate']: return
+
+    write_configvars_header("htslib/config_vars.h", ext, "HTS")
+
+    if force or not os.path.exists("htslib/libhts.a"):
+        log.info("building 'libhts.a'")
+        with changedir("htslib"):
+            # TODO Eventually by running configure here, we can set these
+            # extra flags for configure instead of hacking on ALL_CPPFLAGS.
+            args = " ".join(ext.extra_compile_args)
+            run_make(["ALL_CPPFLAGS=-I. " + args + " $(CPPFLAGS)", "lib-static"])
+    else:
+        log.warn("skipping 'libhts.a' (already built)")
+
+
+def prebuild_libcsamtools(ext, force):
+    write_configvars_header("samtools/samtools_config_vars.h", ext, "SAMTOOLS")
+
+
+modules = [
+    dict(name="pysam.libchtslib",
+         prebuild_func=prebuild_libchtslib,
+         sources=[source_pattern % "htslib", "pysam/htslib_util.c"] + os_c_files,
+         extra_objects=htslib_objects,
+         libraries=external_htslib_libraries),
+    dict(name="pysam.libcsamtools",
+         prebuild_func=prebuild_libcsamtools,
+         sources=[source_pattern % "samtools"] + glob.glob(os.path.join("samtools", "*.pysam.c")) +
+         [os.path.join("samtools", "lz4", "lz4.c")] + os_c_files,
+         extra_objects=separate_htslib_objects,
+         libraries=external_htslib_libraries + internal_htslib_libraries),
+    dict(name="pysam.libcbcftools",
+         sources=[source_pattern % "bcftools"] + glob.glob(os.path.join("bcftools", "*.pysam.c")) + os_c_files,
+         extra_objects=separate_htslib_objects,
+         libraries=external_htslib_libraries + internal_htslib_libraries),
+    dict(name="pysam.libcutils",
+         sources=[source_pattern % "utils", "pysam/pysam_util.c"] + os_c_files,
+         extra_objects=separate_htslib_objects,
+         libraries=external_htslib_libraries + internal_htslib_libraries + internal_samtools_libraries),
+    dict(name="pysam.libcalignmentfile",
+         sources=[source_pattern % "alignmentfile"] + os_c_files,
+         extra_objects=separate_htslib_objects,
+         libraries=libraries_for_pysam_module),
+    dict(name="pysam.libcsamfile",
+         sources=[source_pattern % "samfile"] + os_c_files,
+         extra_objects=separate_htslib_objects,
+         libraries=libraries_for_pysam_module),
+    dict(name="pysam.libcalignedsegment",
+         sources=[source_pattern % "alignedsegment"] + os_c_files,
+         extra_objects=separate_htslib_objects,
+         libraries=libraries_for_pysam_module),
+    dict(name="pysam.libctabix",
+         sources=[source_pattern % "tabix"] + os_c_files,
+         extra_objects=separate_htslib_objects,
+         libraries=libraries_for_pysam_module),
+    dict(name="pysam.libcfaidx",
+         sources=[source_pattern % "faidx"] + os_c_files,
+         extra_objects=separate_htslib_objects,
+         libraries=libraries_for_pysam_module),
+    dict(name="pysam.libcbcf",
+         sources=[source_pattern % "bcf"] + os_c_files,
+         extra_objects=separate_htslib_objects,
+         libraries=libraries_for_pysam_module),
+    dict(name="pysam.libcbgzf",
+         sources=[source_pattern % "bgzf"] + os_c_files,
+         extra_objects=separate_htslib_objects,
+         libraries=libraries_for_pysam_module),
+    dict(name="pysam.libctabixproxies",
+         sources=[source_pattern % "tabixproxies"] + os_c_files,
+         extra_objects=separate_htslib_objects,
+         libraries=libraries_for_pysam_module),
+    dict(name="pysam.libcvcf",
+         sources=[source_pattern % "vcf"] + os_c_files,
+         extra_objects=separate_htslib_objects,
+         libraries=libraries_for_pysam_module),
+]
+
+common_options = dict(
+    language="c",
+    extra_compile_args=extra_compile_args,
+    define_macros=define_macros,
+    # for out-of-tree compilation, use absolute paths
+    library_dirs=[os.path.abspath(x) for x in ["pysam"] + htslib_library_dirs],
+    include_dirs=[os.path.abspath(x) for x in ["pysam"] + htslib_include_dirs + \
+                  ["samtools", "samtools/lz4", "bcftools", "."] + include_os])
+
+# add common options (in python >3.5, could use n = {**a, **b}
+for module in modules:
+    module.update(**common_options)
+
+classifiers = """
+Development Status :: 4 - Beta
+Intended Audience :: Science/Research
+Intended Audience :: Developers
+License :: OSI Approved
+Programming Language :: Python
+Topic :: Software Development
+Topic :: Scientific/Engineering
+Operating System :: POSIX
+Operating System :: Unix
+Operating System :: MacOS
+"""
+
+metadata = {
+    'name': "pysam",
+    'version': get_pysam_version(),
+    'description': "pysam",
+    'long_description': __doc__,
+    'author': "Andreas Heger",
+    'author_email': "andreas.heger@gmail.com",
+    'license': "MIT",
+    'platforms': ["POSIX", "UNIX", "MacOS"],
+    'classifiers': [_f for _f in classifiers.split("\n") if _f],
+    'url': "https://github.com/pysam-developers/pysam",
+    'packages': package_list,
+    'requires': ['cython (>=0.29.12)'],
+    'ext_modules': [Extension(**opts) for opts in modules],
+    'cmdclass': {'build': extra_build, 'build_ext': build_ext, 'clean_ext': clean_ext, 'sdist': cythonize_sdist},
+    'package_dir': package_dirs,
+    'package_data': {'': ['*.pxd', '*.h', 'py.typed', '*.pyi'], },
+    # do not pack in order to permit linking to csamtools.so
+    'zip_safe': False,
+}
+
+if __name__ == '__main__':
+    dist = setup(**metadata)
diff --git a/tests/00README.txt b/tests/00README.txt
new file mode 100644
index 0000000..6e60917
--- /dev/null
+++ b/tests/00README.txt
@@ -0,0 +1,23 @@
+File ex1.fa contains two sequences cut from the human genome
+build36. They were extracted with command:
+
+  samtools faidx human_b36.fa 2:2043966-2045540 20:67967-69550
+
+Sequence names were changed manually for simplicity. File ex1.sam.gz
+contains MAQ alignments extracted with:
+
+  (samtools view NA18507_maq.bam 2:2044001-2045500;
+   samtools view NA18507_maq.bam 20:68001-69500)
+
+and processed with `samtools fixmate' to make it self-consistent as a
+standalone alignment.
+
+In order for the script pysam_test.py to work, you will need pysam
+in your PYTHONPATH.
+
+In order for the script example.py to work, you will need pysam
+in your PYTHONPATH and run
+
+  make all
+
+beforehand.
diff --git a/tests/AlignedSegment_bench.py b/tests/AlignedSegment_bench.py
new file mode 100644
index 0000000..f5bccd6
--- /dev/null
+++ b/tests/AlignedSegment_bench.py
@@ -0,0 +1,30 @@
+"""Benchmarking module for AlignedSegment functionality"""
+import os
+import array
+import pysam
+
+
+from TestUtils import BAM_DATADIR
+
+
+def set_binary_tag():
+    read = pysam.AlignedSegment()
+    read.set_tag('FZ', array.array('H', range(1000)))
+    return len(read.get_tag('FZ'))
+
+
+def read_binary_tag(fn):
+    with pysam.AlignmentFile(fn) as inf:
+        read = next(inf.fetch())
+    return len(read.get_tag('FZ'))
+
+
+def test_set_binary_tag(benchmark):
+    result = benchmark(set_binary_tag)
+    assert result == 1000
+
+
+def test_read_binary_tag(benchmark):
+    result = benchmark(read_binary_tag, os.path.join(
+        BAM_DATADIR, "example_btag.bam"))
+    assert result == 260
diff --git a/tests/AlignedSegment_test.py b/tests/AlignedSegment_test.py
new file mode 100644
index 0000000..400425f
--- /dev/null
+++ b/tests/AlignedSegment_test.py
@@ -0,0 +1,1766 @@
+import os
+import pysam
+import unittest
+import json
+import collections
+import string
+import struct
+import copy
+import array
+
+from TestUtils import (
+    checkFieldEqual,
+    make_data_files,
+    BAM_DATADIR,
+    get_temp_filename,
+    get_temp_context,
+    IS_PYTHON3,
+)
+
+
+if IS_PYTHON3:
+    maketrans = str.maketrans
+else:
+    maketrans = string.maketrans
+
+
+def setUpModule():
+    make_data_files(BAM_DATADIR)
+
+
+class ReadTest(unittest.TestCase):
+    def build_read(self):
+        """build an example read."""
+
+        header = pysam.AlignmentHeader.from_references(
+            ["chr1", "chr2"], [10000000, 10000000]
+        )
+
+        a = pysam.AlignedSegment(header)
+        a.query_name = "read_12345"
+        a.query_sequence = "ATGC" * 10
+        a.flag = 0
+        a.reference_id = 0
+        a.reference_start = 20
+        a.mapping_quality = 20
+        a.cigartuples = ((0, 10), (2, 1), (0, 9), (1, 1), (0, 20))
+        a.next_reference_id = 0
+        a.next_reference_start = 200
+        a.template_length = 167
+        a.query_qualities = pysam.qualitystring_to_array("1234") * 10
+        return a
+
+
+class TestAlignedSegment(ReadTest):
+
+    """tests to check if aligned read can be constructed
+    and manipulated.
+    """
+
+    def testEmpty(self):
+
+        a = pysam.AlignedSegment()
+        self.assertEqual(a.query_name, None)
+        self.assertEqual(a.query_sequence, None)
+        self.assertEqual(pysam.qualities_to_qualitystring(a.query_qualities), None)
+        self.assertEqual(a.flag, 0)
+        self.assertEqual(a.reference_id, -1)
+        self.assertEqual(a.mapping_quality, 0)
+        self.assertEqual(a.cigartuples, None)
+        self.assertEqual(a.get_tags(), [])
+        self.assertEqual(a.next_reference_id, -1)
+        self.assertEqual(a.next_reference_start, -1)
+        self.assertEqual(a.template_length, 0)
+
+    def testStrOfEmptyRead(self):
+        a = pysam.AlignedSegment()
+        s = str(a)
+        self.assertEqual("None\t0\t*\t0\t0\tNone\t*\t0\t0\tNone\tNone\t[]", s)
+
+    def testSettingTagInEmptyRead(self):
+        """see issue 62"""
+        a = pysam.AlignedSegment()
+        a.tags = (("NM", 1),)
+        a.query_qualities = None
+        self.assertEqual(a.tags, [("NM", 1),])
+
+    def testCompare(self):
+        """check comparison functions."""
+        a = self.build_read()
+        b = None
+
+        self.assertFalse(a is b)
+        self.assertFalse(a == b)
+        self.assertEqual(-1, a.compare(b))
+
+        b = self.build_read()
+
+        self.assertEqual(0, a.compare(b))
+        self.assertEqual(0, b.compare(a))
+        self.assertTrue(a == b)
+        self.assertTrue(b == a)
+        self.assertFalse(a != b)
+        self.assertFalse(b != a)
+
+        b.tid = 1
+        self.assertFalse(a == b)
+        self.assertFalse(b == a)
+        self.assertTrue(a != b)
+        self.assertTrue(b != a)
+
+    def testHashing(self):
+        a = self.build_read()
+        b = self.build_read()
+        self.assertEqual(hash(a), hash(b))
+        b.tid = 1
+        self.assertNotEqual(hash(a), hash(b))
+
+    def testUpdate(self):
+        """check if updating fields affects other variable length data
+        """
+        a = self.build_read()
+        b = self.build_read()
+
+        # check qname
+        b.query_name = "read_123"
+        checkFieldEqual(self, a, b, "query_name")
+        b.query_name = "read_12345678"
+        checkFieldEqual(self, a, b, "query_name")
+        b.query_name = "read_12345"
+        checkFieldEqual(self, a, b)
+
+        # check cigar
+        b.cigartuples = ((0, 10),)
+        checkFieldEqual(self, a, b, "cigartuples")
+        b.cigartuples = ((0, 10), (2, 1), (0, 10))
+        checkFieldEqual(self, a, b, "cigartuples")
+        b.cigartuples = ((0, 10), (2, 1), (0, 9), (1, 1), (0, 20))
+        checkFieldEqual(self, a, b)
+
+        # check seq
+        b.query_sequence = "ATGC"
+        checkFieldEqual(
+            self, a, b, ("query_sequence", "query_qualities", "query_length")
+        )
+        b.query_sequence = "ATGC" * 3
+        checkFieldEqual(
+            self, a, b, ("query_sequence", "query_qualities", "query_length")
+        )
+        b.query_sequence = "ATGC" * 10
+        checkFieldEqual(self, a, b, ("query_qualities",))
+
+        # reset qual
+        b = self.build_read()
+
+        def dual(name):
+            if name.endswith('is_unmapped'): return name.replace('unmapped', 'mapped')
+            elif name.endswith('is_mapped'): return name.replace('mapped', 'unmapped')
+            elif name.endswith('is_reverse'): return name.replace('reverse', 'forward')
+            elif name.endswith('is_forward'): return name.replace('forward', 'reverse')
+            else: return name
+
+        # check flags:
+        for x in (
+            "is_paired",
+            "is_proper_pair",
+            "is_unmapped",
+            "mate_is_unmapped",
+            "is_reverse",
+            "mate_is_reverse",
+            "is_read1",
+            "is_read2",
+            "is_secondary",
+            "is_qcfail",
+            "is_duplicate",
+            "is_supplementary",
+        ):
+            setattr(b, x, True)
+            self.assertEqual(getattr(b, x), True)
+            checkFieldEqual(self, a, b, ("flag", x, dual(x),))
+            setattr(b, x, False)
+            self.assertEqual(getattr(b, x), False)
+            checkFieldEqual(self, a, b)
+
+        for x in (
+            "is_mapped",
+            "mate_is_mapped",
+            "is_forward",
+            "mate_is_forward",
+        ):
+            setattr(b, x, False)
+            self.assertEqual(getattr(b, x), False)
+            checkFieldEqual(self, a, b, ("flag", x, dual(x),))
+            setattr(b, x, True)
+            self.assertEqual(getattr(b, x), True)
+            checkFieldEqual(self, a, b)
+
+    def testUpdate2(self):
+        """issue 135: inplace update of sequence and quality score.
+
+        This does not work as setting the sequence will erase
+        the quality scores.
+        """
+        a = self.build_read()
+        a.query_sequence = a.query_sequence[5:10]
+        self.assertEqual(pysam.qualities_to_qualitystring(a.query_qualities), None)
+
+        a = self.build_read()
+        s = pysam.qualities_to_qualitystring(a.query_qualities)
+        a.query_sequence = a.query_sequence[5:10]
+        a.query_qualities = pysam.qualitystring_to_array(s[5:10])
+
+        self.assertEqual(pysam.qualities_to_qualitystring(a.query_qualities), s[5:10])
+
+    def testUpdateQual(self):
+        """Ensure SEQ and QUAL updates leading to absent QUAL set all bytes to 0xff"""
+
+        a = self.build_read()
+        with get_temp_context("absent_qual.bam") as fname:
+            with pysam.AlignmentFile(fname, "wb", header=a.header) as outf:
+                a.query_sequence = "ATGC"
+                outf.write(a)
+
+                a.query_sequence = "ATGCATGCATGC"
+                outf.write(a)
+
+                a.query_sequence = "ATGCATGC"
+                a.query_qualities = pysam.qualitystring_to_array("<<<<<<<<")
+                a.query_qualities = None
+                outf.write(a)
+
+            with pysam.BGZFile(fname) as f:
+                # Skip BAM header
+                (l_text,) = struct.unpack("<4xL", f.read(8))
+                f.read(l_text)
+                (n_ref,) = struct.unpack("<L", f.read(4))
+                for i in range(n_ref):
+                    (l_name,) = struct.unpack("<L", f.read(4))
+                    f.read(l_name + 4)
+
+                # Read each BAM record and check its qual bytes
+                while True:
+                    core = f.read(36)
+                    if len(core) != 36: break
+
+                    (block_size, l_read_name, n_cigar_op, l_seq) = struct.unpack("<L8xB3xH2xL12x", core)
+                    data = f.read(block_size - 32)
+                    qual = data[l_read_name + 4*n_cigar_op + ((l_seq+1) // 2):]
+
+                    self.assertEqual(qual, b'\xff' * l_seq)
+
+    def testLargeRead(self):
+        """build an example read."""
+
+        a = pysam.AlignedSegment()
+        a.query_name = "read_12345"
+        a.query_sequence = "ATGC" * 200
+        a.flag = 0
+        a.reference_id = -1
+        a.reference_start = 20
+        a.mapping_quality = 20
+        a.cigartuples = ((0, 4 * 200),)
+        a.next_reference_id = 0
+        a.next_reference_start = 200
+        a.template_length = 167
+        a.query_qualities = pysam.qualitystring_to_array("1234") * 200
+
+        return a
+
+    def testUpdateTlen(self):
+        """check if updating tlen works"""
+        a = self.build_read()
+        oldlen = a.template_length
+        oldlen *= 2
+        a.template_length = oldlen
+        self.assertEqual(a.template_length, oldlen)
+
+    def testPositions(self):
+        a = self.build_read()
+        self.assertEqual(
+            a.get_reference_positions(),
+            [
+                20,
+                21,
+                22,
+                23,
+                24,
+                25,
+                26,
+                27,
+                28,
+                29,
+                31,
+                32,
+                33,
+                34,
+                35,
+                36,
+                37,
+                38,
+                39,
+                40,
+                41,
+                42,
+                43,
+                44,
+                45,
+                46,
+                47,
+                48,
+                49,
+                50,
+                51,
+                52,
+                53,
+                54,
+                55,
+                56,
+                57,
+                58,
+                59,
+            ],
+        )
+
+        self.assertEqual(
+            a.get_aligned_pairs(),
+            [
+                (0, 20),
+                (1, 21),
+                (2, 22),
+                (3, 23),
+                (4, 24),
+                (5, 25),
+                (6, 26),
+                (7, 27),
+                (8, 28),
+                (9, 29),
+                (None, 30),
+                (10, 31),
+                (11, 32),
+                (12, 33),
+                (13, 34),
+                (14, 35),
+                (15, 36),
+                (16, 37),
+                (17, 38),
+                (18, 39),
+                (19, None),
+                (20, 40),
+                (21, 41),
+                (22, 42),
+                (23, 43),
+                (24, 44),
+                (25, 45),
+                (26, 46),
+                (27, 47),
+                (28, 48),
+                (29, 49),
+                (30, 50),
+                (31, 51),
+                (32, 52),
+                (33, 53),
+                (34, 54),
+                (35, 55),
+                (36, 56),
+                (37, 57),
+                (38, 58),
+                (39, 59),
+            ],
+        )
+
+        self.assertEqual(
+            a.get_reference_positions(),
+            [
+                x[1]
+                for x in a.get_aligned_pairs()
+                if x[0] is not None and x[1] is not None
+            ],
+        )
+        # alen is the length of the aligned read in genome
+        self.assertEqual(a.reference_length, a.get_aligned_pairs()[-1][0] + 1)
+        # aend points to one beyond last aligned base in ref
+        self.assertEqual(a.get_reference_positions()[-1], a.reference_end - 1)
+
+    def testFullReferencePositions(self):
+        """see issue 26"""
+        a = self.build_read()
+        a.cigar = [(4, 30), (0, 20), (1, 3), (0, 47)]
+
+        self.assertEqual(100, len(a.get_reference_positions(full_length=True)))
+
+    def testBlocks(self):
+        a = self.build_read()
+        self.assertEqual(a.get_blocks(), [(20, 30), (31, 40), (40, 60)])
+
+    def test_infer_query_length(self):
+        """Test infer_query_length on M|=|X|I|D|H|S cigar ops"""
+        a = self.build_read()
+        a.cigarstring = "40M"
+        self.assertEqual(a.infer_query_length(), 40)
+        a.cigarstring = "40="
+        self.assertEqual(a.infer_query_length(), 40)
+        a.cigarstring = "40X"
+        self.assertEqual(a.infer_query_length(), 40)
+        a.cigarstring = "20M5I20M"
+        self.assertEqual(a.infer_query_length(), 45)
+        a.cigarstring = "20M5D20M"
+        self.assertEqual(a.infer_query_length(), 40)
+        a.cigarstring = "5H35M"
+        self.assertEqual(a.infer_query_length(), 35)
+        a.cigarstring = "5S35M"
+        self.assertEqual(a.infer_query_length(), 40)
+        a.cigarstring = "35M5H"
+        self.assertEqual(a.infer_query_length(), 35)
+        a.cigarstring = "35M5S"
+        self.assertEqual(a.infer_query_length(), 40)
+        a.cigarstring = None
+        self.assertEqual(a.infer_query_length(), None)
+
+    def test_infer_read_length(self):
+        """Test infer_read_length on M|=|X|I|D|H|S cigar ops"""
+        a = self.build_read()
+        a.cigarstring = "40M"
+        self.assertEqual(a.infer_read_length(), 40)
+        a.cigarstring = "40="
+        self.assertEqual(a.infer_read_length(), 40)
+        a.cigarstring = "40X"
+        self.assertEqual(a.infer_read_length(), 40)
+        a.cigarstring = "20M5I20M"
+        self.assertEqual(a.infer_read_length(), 45)
+        a.cigarstring = "20M5D20M"
+        self.assertEqual(a.infer_read_length(), 40)
+        a.cigarstring = "5H35M"
+        self.assertEqual(a.infer_read_length(), 40)
+        a.cigarstring = "5S35M"
+        self.assertEqual(a.infer_read_length(), 40)
+        a.cigarstring = "35M5H"
+        self.assertEqual(a.infer_read_length(), 40)
+        a.cigarstring = "35M5S"
+        self.assertEqual(a.infer_read_length(), 40)
+        a.cigarstring = None
+        self.assertEqual(a.infer_read_length(), None)
+
+    def test_get_aligned_pairs_soft_clipping(self):
+        a = self.build_read()
+        a.cigartuples = ((4, 2), (0, 35), (4, 3))
+        self.assertEqual(
+            a.get_aligned_pairs(),
+            [(0, None), (1, None)]
+            + [
+                (qpos, refpos)
+                for (qpos, refpos) in zip(range(2, 2 + 35), range(20, 20 + 35))
+            ]
+            + [(37, None), (38, None), (39, None)],
+        )
+        self.assertEqual(
+            a.get_aligned_pairs(True),
+            # [(0, None), (1, None)] +
+            [
+                (qpos, refpos)
+                for (qpos, refpos) in zip(range(2, 2 + 35), range(20, 20 + 35))
+            ]
+            # [(37, None), (38, None), (39, None)]
+        )
+
+    def test_get_aligned_pairs_hard_clipping(self):
+        a = self.build_read()
+        a.cigartuples = ((5, 2), (0, 35), (5, 3))
+        self.assertEqual(
+            a.get_aligned_pairs(),
+            # No seq, no seq pos
+            [
+                (qpos, refpos)
+                for (qpos, refpos) in zip(range(0, 0 + 35), range(20, 20 + 35))
+            ],
+        )
+        self.assertEqual(
+            a.get_aligned_pairs(True),
+            [
+                (qpos, refpos)
+                for (qpos, refpos) in zip(range(0, 0 + 35), range(20, 20 + 35))
+            ],
+        )
+
+    def test_get_aligned_pairs_skip(self):
+        a = self.build_read()
+        a.cigarstring = "2M100D38M"
+        self.assertEqual(
+            a.get_aligned_pairs(),
+            [(0, 20), (1, 21)]
+            + [(None, refpos) for refpos in range(22, 22 + 100)]
+            + [
+                (qpos, refpos)
+                for (qpos, refpos) in zip(
+                    range(2, 2 + 38), range(20 + 2 + 100, 20 + 2 + 100 + 38)
+                )
+            ],
+        )
+        self.assertEqual(
+            a.get_aligned_pairs(True),
+            [(0, 20), (1, 21)] +
+            # [(None, refpos) for refpos in range(21, 21+100)] +
+            [
+                (qpos, refpos)
+                for (qpos, refpos) in zip(
+                    range(2, 2 + 38), range(20 + 2 + 100, 20 + 2 + 100 + 38)
+                )
+            ],
+        )
+
+    def test_get_aligned_pairs_match_mismatch(self):
+        a = self.build_read()
+        a.cigartuples = ((7, 20), (8, 20))
+        self.assertEqual(
+            a.get_aligned_pairs(),
+            [
+                (qpos, refpos)
+                for (qpos, refpos) in zip(range(0, 0 + 40), range(20, 20 + 40))
+            ],
+        )
+        self.assertEqual(
+            a.get_aligned_pairs(True),
+            [
+                (qpos, refpos)
+                for (qpos, refpos) in zip(range(0, 0 + 40), range(20, 20 + 40))
+            ],
+        )
+
+    def test_get_aligned_pairs_padding(self):
+        a = self.build_read()
+        a.cigartuples = ((0, 1), (6, 1), (0, 1))
+        # The padding operation is like an insertion into the reference.
+        # See comment in test_get_aligned_pairs_padding_with_seq (below).
+        self.assertEqual(a.get_aligned_pairs(),
+                         [(0, 20), (1, None), (2, 21)])
+
+    def test_get_aligned_pairs_padding_with_seq(self):
+        a = self.build_read()
+        a.query_sequence = "AGT"
+        a.cigarstring = "1M1P1M"
+        a.set_tag("MD", "2")
+        # When the reference is padded (conventionally with '*', according
+        # to the SAM format specification (June 3, 2021)), as indicated by a
+        # `P` CIGAR operation, this is equivalent to an insertion into the
+        # reference. Thus we get the same result back as for an insertion,
+        # and the reference character (if requested via with_seq=True) is
+        # returned as None.
+        #
+        # Note that we're here assuming (as in the treatment of `N`
+        # (skipped region from the reference) in build_alignment_sequence
+        # in libcalignedsegment.pyx) that the MD tag will not mention the
+        # region of the reference with the padding character.
+        #
+        # Note also that we are not dealing with a "Padded SAM" file, as
+        # described in section 3.2 of the SAM format, but with the simpler
+        # case (section 3.1) where a reference sequence has had '*'
+        # characters inserted (by some unspecified tool) in order to make it
+        # easier to specify details of an insertion using `P` in the CIGAR
+        # string: "Alternatively, to describe the same alignments, we can
+        # modify the reference sequence to contain pads that make room for
+        # sequences inserted relative to the reference."
+        self.assertEqual(a.get_aligned_pairs(with_seq=True),
+                         [(0, 20, 'A'), (1, None, None), (2, 21, 'T')])
+
+    def test_get_aligned_pairs(self):
+        a = self.build_read()
+        a.query_sequence = "A" * 9
+        a.cigarstring = "9M"
+        a.set_tag("MD", "9")
+        self.assertEqual(
+            a.get_aligned_pairs(with_seq=True),
+            [
+                (0, 20, "A"),
+                (1, 21, "A"),
+                (2, 22, "A"),
+                (3, 23, "A"),
+                (4, 24, "A"),
+                (5, 25, "A"),
+                (6, 26, "A"),
+                (7, 27, "A"),
+                (8, 28, "A"),
+            ],
+        )
+
+        a.set_tag("MD", "4C4")
+        self.assertEqual(
+            a.get_aligned_pairs(with_seq=True),
+            [
+                (0, 20, "A"),
+                (1, 21, "A"),
+                (2, 22, "A"),
+                (3, 23, "A"),
+                (4, 24, "c"),
+                (5, 25, "A"),
+                (6, 26, "A"),
+                (7, 27, "A"),
+                (8, 28, "A"),
+            ],
+        )
+
+        a.cigarstring = "5M2D4M"
+        a.set_tag("MD", "4C^TT4")
+        self.assertEqual(
+            a.get_aligned_pairs(with_seq=True),
+            [
+                (0, 20, "A"),
+                (1, 21, "A"),
+                (2, 22, "A"),
+                (3, 23, "A"),
+                (4, 24, "c"),
+                (None, 25, "T"),
+                (None, 26, "T"),
+                (5, 27, "A"),
+                (6, 28, "A"),
+                (7, 29, "A"),
+                (8, 30, "A"),
+            ],
+        )
+
+        a.cigarstring = "5M2D2I2M"
+        a.set_tag("MD", "4C^TT2")
+        self.assertEqual(
+            a.get_aligned_pairs(with_seq=True),
+            [
+                (0, 20, "A"),
+                (1, 21, "A"),
+                (2, 22, "A"),
+                (3, 23, "A"),
+                (4, 24, "c"),
+                (None, 25, "T"),
+                (None, 26, "T"),
+                (5, None, None),
+                (6, None, None),
+                (7, 27, "A"),
+                (8, 28, "A"),
+            ],
+        )
+
+    def test_get_aligned_pairs_with_malformed_MD_tag(self):
+
+        a = self.build_read()
+        a.query_sequence = "A" * 9
+
+        # out of range issue, see issue #560
+        a.cigarstring = "64M2D85M2S"
+        a.set_tag("MD", "64^TG86A0")
+        self.assertRaises(AssertionError, a.get_aligned_pairs, with_seq=True)
+
+    def test_get_aligned_pairs_skip_reference(self):
+        a = self.build_read()
+        a.query_sequence = "A" * 10
+        a.cigarstring = "5M1N5M"
+        a.set_tag("MD", "10")
+
+        self.assertEqual(
+            a.get_aligned_pairs(with_seq=True),
+            [
+                (0, 20, "A"),
+                (1, 21, "A"),
+                (2, 22, "A"),
+                (3, 23, "A"),
+                (4, 24, "A"),
+                (None, 25, None),
+                (5, 26, "A"),
+                (6, 27, "A"),
+                (7, 28, "A"),
+                (8, 29, "A"),
+                (9, 30, "A"),
+            ],
+        )
+
+        self.assertEqual(
+            a.get_aligned_pairs(with_seq=False),
+            [
+                (0, 20),
+                (1, 21),
+                (2, 22),
+                (3, 23),
+                (4, 24),
+                (None, 25),
+                (5, 26),
+                (6, 27),
+                (7, 28),
+                (8, 29),
+                (9, 30),
+            ],
+        )
+
+        self.assertEqual(
+            a.get_aligned_pairs(matches_only=True, with_seq=False),
+            [
+                (0, 20),
+                (1, 21),
+                (2, 22),
+                (3, 23),
+                (4, 24),
+                (5, 26),
+                (6, 27),
+                (7, 28),
+                (8, 29),
+                (9, 30),
+            ],
+        )
+
+    def test_equivalence_matches_only_and_with_seq(self):
+        a = self.build_read()
+        a.query_sequence = "ACGT" * 2
+        a.cigarstring = "4M1D4M"
+        a.set_tag("MD", "4^x4")
+        full = (
+            list(zip(range(0, 4), range(20, 24), "ACGT"))
+            + [(None, 24, "x")]
+            + list(zip(range(4, 8), range(25, 29), "ACGT"))
+        )
+        self.assertEqual(a.get_aligned_pairs(matches_only=False, with_seq=True), full)
+
+        self.assertEqual(
+            a.get_aligned_pairs(matches_only=True, with_seq=True),
+            [x for x in full if x[0] is not None and x[1] is not None],
+        )
+
+        a = self.build_read()
+        a.query_sequence = "ACGT" * 2
+        a.cigarstring = "4M1N4M"
+        a.set_tag("MD", "8")
+        full = (
+            list(zip(range(0, 4), range(20, 24), "ACGT"))
+            + [(None, 24, None)]
+            + list(zip(range(4, 8), range(25, 29), "ACGT"))
+        )
+        self.assertEqual(a.get_aligned_pairs(matches_only=False, with_seq=True), full)
+
+        self.assertEqual(
+            a.get_aligned_pairs(matches_only=True, with_seq=True),
+            [x for x in full if x[0] is not None and x[1] is not None],
+        )
+
+    def test_get_aligned_pairs_lowercase_md(self):
+        a = self.build_read()
+        a.query_sequence = "A" * 10
+        a.cigarstring = "10M"
+        a.set_tag("MD", "5g4")
+        self.assertEqual(
+            a.get_aligned_pairs(with_seq=True),
+            [
+                (0, 20, "A"),
+                (1, 21, "A"),
+                (2, 22, "A"),
+                (3, 23, "A"),
+                (4, 24, "A"),
+                (5, 25, "g"),
+                (6, 26, "A"),
+                (7, 27, "A"),
+                (8, 28, "A"),
+                (9, 29, "A"),
+            ],
+        )
+
+    def test_get_aligned_pairs_uppercase_md(self):
+        a = self.build_read()
+        a.query_sequence = "A" * 10
+        a.cigarstring = "10M"
+        a.set_tag("MD", "5G4")
+        self.assertEqual(
+            a.get_aligned_pairs(with_seq=True),
+            [
+                (0, 20, "A"),
+                (1, 21, "A"),
+                (2, 22, "A"),
+                (3, 23, "A"),
+                (4, 24, "A"),
+                (5, 25, "g"),
+                (6, 26, "A"),
+                (7, 27, "A"),
+                (8, 28, "A"),
+                (9, 29, "A"),
+            ],
+        )
+
+    def testNoSequence(self):
+        """issue 176: retrieving length without query sequence
+        with soft-clipping.
+        """
+        a = self.build_read()
+        a.query_sequence = None
+        a.cigarstring = "20M"
+        self.assertEqual(a.query_alignment_length, 20)
+        a.cigarstring = "20M1S"
+        self.assertEqual(a.query_alignment_length, 20)
+        a.cigarstring = "20M1H"
+        self.assertEqual(a.query_alignment_length, 20)
+        a.cigarstring = "1S20M"
+        self.assertEqual(a.query_alignment_length, 20)
+        a.cigarstring = "1H20M"
+        self.assertEqual(a.query_alignment_length, 20)
+        a.cigarstring = "1S20M1S"
+        self.assertEqual(a.query_alignment_length, 20)
+        a.cigarstring = "1H20M1H"
+        self.assertEqual(a.query_alignment_length, 20)
+
+    def test_query_length_is_limited(self):
+        a = self.build_read()
+        a.query_name = "A" * 1
+        a.query_name = "A" * 254
+        self.assertRaises(ValueError, setattr, a, "query_name", "A" * 255)
+
+    def test_header_accessible(self):
+        a = self.build_read()
+        self.assertTrue(isinstance(a.header, pysam.AlignmentHeader))
+
+    def test_bin_values_for_unmapped_reads_ignore_length(self):
+        a = self.build_read()
+        # use a long read
+        a.cigarstring = "2000000M"
+        self.assertEqual(a.bin, 9)
+        # changing unmapped flag changes bin because length is 0
+        a.is_unmapped = True
+        self.assertTrue(a.is_unmapped)
+        self.assertFalse(a.is_mapped)
+        self.assertEqual(a.bin, 4681)
+
+        # unmapped read without chromosomal location
+        a.reference_start = -1
+        self.assertEqual(a.reference_start, -1)
+        self.assertEqual(a.bin, 4680)
+
+    def test_bin_values_for_mapped_reads_are_updated(self):
+        a = self.build_read()
+        a.pos = 20000
+        self.assertFalse(a.is_unmapped)
+        self.assertTrue(a.is_mapped)
+        self.assertEqual(a.bin, 4682)
+
+        # updating length updates bin
+        a.cigarstring = "2000000M"
+        self.assertEqual(a.bin, 9)
+
+        # updating length updates bin
+        a.cigarstring = "20M"
+        self.assertEqual(a.bin, 4682)
+
+        # updating length updates bin
+        a.reference_start = 2000000
+        self.assertEqual(a.bin, 4803)
+
+
+class TestTidMapping(ReadTest):
+    def test_reference_name_can_be_set_to_none(self):
+        a = self.build_read()
+        a.reference_name = None
+        self.assertEqual(a.reference_name, None)
+        self.assertEqual(a.reference_id, -1)
+
+    def test_reference_name_can_be_set_to_asterisk(self):
+        a = self.build_read()
+        a.reference_name = "*"
+        self.assertEqual(a.reference_name, None)
+        self.assertEqual(a.reference_id, -1)
+
+    def test_reference_name_can_be_set_to_chromosome(self):
+        a = self.build_read()
+        a.reference_name = "chr1"
+        self.assertEqual(a.reference_name, "chr1")
+        self.assertEqual(a.reference_id, 0)
+
+    def test_reference_name_can_not_be_set_to_unknown_chromosome(self):
+        a = self.build_read()
+        self.assertRaises(ValueError, setattr, a, "reference_name", "chrX")
+
+    def test_tid_can_be_set_to_missing(self):
+        a = self.build_read()
+        a.reference_id = -1
+        self.assertEqual(a.reference_id, -1)
+        self.assertEqual(a.reference_name, None)
+
+    def test_tid_can_be_set_to_missing_without_header(self):
+        a = pysam.AlignedSegment()
+        a.reference_id = -1
+        self.assertEqual(a.reference_id, -1)
+        self.assertEqual(a.reference_name, None)
+
+    def test_tid_can_be_set_without_header(self):
+        a = pysam.AlignedSegment()
+        a.reference_id = 1
+        self.assertRaises(ValueError, getattr, a, "reference_name")
+
+    def test_tid_can_be_set_to_chromosome(self):
+        a = self.build_read()
+        a.reference_id = 0
+        self.assertEqual(a.reference_id, 0)
+        self.assertEqual(a.reference_name, "chr1")
+
+    def test_tid_can_not_be_set_to_unknown_chromosome(self):
+        a = self.build_read()
+        self.assertRaises(ValueError, setattr, a, "reference_id", 2)
+
+    def test_unmapped_tid_is_asterisk_in_output(self):
+        a = self.build_read()
+        a.reference_id = -1
+        self.assertEqual(a.to_string().split("\t")[2], "*")
+
+
+class TestNextTidMapping(ReadTest):
+    def test_next_reference_name_can_be_set_to_none(self):
+        a = self.build_read()
+        a.next_reference_name = None
+        self.assertEqual(a.next_reference_name, None)
+        self.assertEqual(a.next_reference_id, -1)
+
+    def test_next_reference_name_can_be_set_to_asterisk(self):
+        a = self.build_read()
+        a.next_reference_name = "*"
+        self.assertEqual(a.next_reference_name, None)
+        self.assertEqual(a.next_reference_id, -1)
+
+    def test_next_reference_name_can_be_set_to_chromosome(self):
+        a = self.build_read()
+        a.next_reference_name = "chr1"
+        self.assertEqual(a.next_reference_name, "chr1")
+        self.assertEqual(a.next_reference_id, 0)
+
+    def test_next_reference_name_can_not_be_set_to_unknown_chromosome(self):
+        a = self.build_read()
+        self.assertRaises(ValueError, setattr, a, "next_reference_name", "chrX")
+
+    def test_next_tid_can_be_set_to_missing(self):
+        a = self.build_read()
+        a.next_reference_id = -1
+        self.assertEqual(a.next_reference_id, -1)
+        self.assertEqual(a.next_reference_name, None)
+
+    def test_next_tid_can_be_set_to_equal(self):
+        a = self.build_read()
+        a.reference_name = "chr1"
+        a.next_reference_name = "="
+        self.assertEqual(a.next_reference_id, a.reference_id)
+        self.assertEqual(a.next_reference_name, a.reference_name)
+        self.assertEqual(a.to_string().split("\t")[6], "=")
+
+    def test_next_tid_can_be_set_to_missing_without_header(self):
+        a = pysam.AlignedSegment()
+        a.next_reference_id = -1
+        self.assertEqual(a.next_reference_id, -1)
+        self.assertEqual(a.next_reference_name, None)
+
+    def test_next_tid_can_be_set_without_header(self):
+        a = pysam.AlignedSegment()
+        a.next_reference_id = 1
+        self.assertRaises(ValueError, getattr, a, "next_reference_name")
+
+    def test_next_tid_can_be_set_to_chromosome(self):
+        a = self.build_read()
+        a.next_reference_id = 0
+        self.assertEqual(a.next_reference_id, 0)
+        self.assertEqual(a.next_reference_name, "chr1")
+
+    def test_next_tid_can_not_be_set_to_unknown_chromosome(self):
+        a = self.build_read()
+        self.assertRaises(ValueError, setattr, a, "next_reference_id", 2)
+
+    def test_next_unmapped_tid_is_asterisk_in_output(self):
+        a = self.build_read()
+        a.next_reference_id = -1
+        self.assertEqual(a.to_string().split("\t")[6], "*")
+
+
+class TestCigar(ReadTest):
+    def testCigarString(self):
+        r = self.build_read()
+        self.assertEqual(r.cigarstring, "10M1D9M1I20M")
+        r.cigarstring = "20M10D20M"
+        self.assertEqual(r.cigartuples, [(0, 20), (2, 10), (0, 20)])
+        # unsetting cigar string
+        r.cigarstring = None
+        self.assertEqual(r.cigarstring, None)
+
+    def testCigar(self):
+        r = self.build_read()
+        self.assertEqual(r.cigartuples, [(0, 10), (2, 1), (0, 9), (1, 1), (0, 20)])
+        # unsetting cigar string
+        r.cigartuples = None
+        self.assertEqual(r.cigartuples, None)
+
+
+class TestCigarStats(ReadTest):
+    def testStats(self):
+        a = self.build_read()
+
+        a.cigarstring = None
+        self.assertEqual(
+            [list(x) for x in a.get_cigar_stats()],
+            [[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]],
+        )
+
+        a.cigarstring = "10M"
+        self.assertEqual(
+            [list(x) for x in a.get_cigar_stats()],
+            [[10, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]],
+        )
+
+        a.cigarstring = "10M2I2M"
+        self.assertEqual(
+            [list(x) for x in a.get_cigar_stats()],
+            [[12, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0], [2, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0]],
+        )
+
+        for i, x in enumerate("MIDNSHP=X"):
+            a.cigarstring = "2{}".format(x)
+            expected = [[0] * 11, [0] * 11]
+            expected[0][i] = 2
+            expected[1][i] = 1
+            self.assertEqual([list(x) for x in a.get_cigar_stats()], expected)
+
+        a.cigarstring = "10M"
+        a.set_tag("NM", 5)
+        self.assertEqual(
+            [list(x) for x in a.get_cigar_stats()],
+            [[10, 0, 0, 0, 0, 0, 0, 0, 0, 0, 5], [1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]],
+        )
+
+        a.cigarstring = None
+        self.assertEqual(
+            [list(x) for x in a.get_cigar_stats()],
+            [[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 5], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]],
+        )
+
+
+class TestAlignedPairs(unittest.TestCase):
+    filename = os.path.join(BAM_DATADIR, "example_aligned_pairs.bam")
+
+    def testReferenceBases(self):
+        """reference bases should always be the same nucleotide
+        """
+        reference_bases = collections.defaultdict(list)
+        with pysam.AlignmentFile(self.filename) as inf:
+            for c in inf.pileup():
+                for r in c.pileups:
+                    for read, ref, base in r.alignment.get_aligned_pairs(with_seq=True):
+                        if ref is None:
+                            continue
+                        reference_bases[ref].append(base.upper())
+
+        for x, y in reference_bases.items():
+            self.assertEqual(len(set(y)), 1)
+
+
+class TestBaseModifications(unittest.TestCase):
+    def testChebi(self):
+        """reference bases should always be the same nucleotide
+        """
+        filename = os.path.join(BAM_DATADIR, "MM-chebi.bam")
+        expect = {
+            ("C", 0, "m"): [(6, 102), (17, 128), (20, 153), (31, 179), (34, 204)],
+            ("N", 0, "n"): [(15, 212)],
+            ("C", 0, 76792): [(19, 161), (34, 187)],
+        }
+
+        with pysam.AlignmentFile(filename, check_sq=False) as inf:
+            r = next(iter(inf))
+            self.assertDictEqual(r.modified_bases, expect)
+
+    def testDouble(self):
+        """reference bases should always be the same nucleotide
+        """
+        filename = os.path.join(BAM_DATADIR, "MM-double.bam")
+        expect = {
+            ("G", 1, "m"): [(1, 115), (12, 141), (13, 166), (22, 192)],
+            ("C", 0, "m"): [(7, 128), (30, 153), (31, 179)],
+            ("G", 0, "o"): [(13, 102)],
+        }
+
+        with pysam.AlignmentFile(filename, check_sq=False) as inf:
+            r = next(iter(inf))
+            self.assertDictEqual(r.modified_bases, expect)
+
+    def testMulti(self):
+        """reference bases should always be the same nucleotide
+        """
+        filename = os.path.join(BAM_DATADIR, "MM-multi.bam")
+        expect = {
+            "r1": {
+                ("C", 0, "m"): [(6, 128), (17, 153), (20, 179), (31, 204), (34, 230)],
+                ("N", 0, "n"): [(15, 215), (18, 240)],
+                ("C", 0, "h"): [(19, 159), (34, 6)],
+            },
+            "r2": {
+                ("C", 0, "m"): [
+                    (6, 77),
+                    (17, 103),
+                    (19, 128),
+                    (20, 154),
+                    (31, 179),
+                    (34, 204),
+                ],
+                ("C", 0, "h"): [
+                    (6, 159),
+                    (17, 133),
+                    (19, 108),
+                    (20, 82),
+                    (31, 57),
+                    (34, 31),
+                ],
+                ("N", 0, "n"): [(15, 240)],
+            },
+        }
+
+        with pysam.AlignmentFile(filename, check_sq=False) as inf:
+            for r in inf:
+                self.assertDictEqual(r.modified_bases, expect[r.query_name])
+
+    def testOrient(self):
+        """reference bases should always be the same nucleotide
+        """
+        filename = os.path.join(BAM_DATADIR, "MM-orient.bam")
+        expect = {
+            "top-fwd": [
+                {("C", 0, "m"): [(7, 128), (30, 153), (31, 179)]},
+                {("C", 0, "m"): [(7, 128), (30, 153), (31, 179)]},
+            ],
+            "top-rev": [
+                {("C", 1, "m"): [(4, 179), (5, 153), (28, 128)]},
+                {("C", 0, "m"): [(31, 179), (30, 153), (7, 128)]},
+            ],
+            "bot-fwd": [
+                {("G", 1, "m"): [(1, 115), (2, 141), (18, 166), (23, 192)]},
+                {("G", 1, "m"): [(1, 115), (2, 141), (18, 166), (23, 192)]},
+            ],
+            "bot-rev": [
+                {("G", 0, "m"): [(12, 192), (17, 166), (33, 141), (34, 115)]},
+                {("G", 1, "m"): [(23, 192), (18, 166), (2, 141), (1, 115)]},
+            ],
+        }
+
+        with pysam.AlignmentFile(filename, check_sq=False) as inf:
+            for r in inf:
+                self.assertDictEqual(r.modified_bases, expect[r.query_name][0])
+                self.assertDictEqual(r.modified_bases_forward, expect[r.query_name][1])
+                for (B, s, _), mods in r.modified_bases.items():
+                    C = B.translate(maketrans("ACGTacgtNnXx", "TGCAtgcaNnXx"))
+                    for pos, _ in mods:
+                        if r.is_reverse:
+                            if s == 1:
+                                self.assertEqual(
+                                    C, r.query_sequence[pos], r.to_string()
+                                )
+                            else:
+                                self.assertEqual(
+                                    C, r.query_sequence[pos], r.to_string()
+                                )
+                        else:
+                            if s == 0:
+                                self.assertEqual(
+                                    B, r.query_sequence[pos], r.to_string()
+                                )
+                            else:
+                                self.assertEqual(
+                                    B, r.query_sequence[pos], r.to_string()
+                                )
+
+
+class TestTags(ReadTest):
+    def testMissingTag(self):
+        a = self.build_read()
+        self.assertRaises(KeyError, a.get_tag, "XP")
+
+    def testEmptyTag(self):
+        a = self.build_read()
+        self.assertRaises(KeyError, a.get_tag, "XT")
+
+    def testSetTag(self):
+        a = self.build_read()
+        self.assertEqual(False, a.has_tag("NM"))
+        a.set_tag("NM", 2)
+        self.assertEqual(True, a.has_tag("NM"))
+        self.assertEqual(a.get_tag("NM"), 2)
+        a.set_tag("NM", 3)
+        self.assertEqual(a.get_tag("NM"), 3)
+        a.set_tag("NM", None)
+        self.assertEqual(False, a.has_tag("NM"))
+        # check if deleting a non-existing tag is fine
+        a.set_tag("NM", None)
+        a.set_tag("NM", None)
+
+    def testArrayTags(self):
+        read = self.build_read()
+        supported_dtypes = "bhBHf"
+        unsupported_dtypes = "lLd"
+
+        for dtype in supported_dtypes:
+            key = "F" + dtype
+            read.set_tag(key, array.array(dtype, range(10)))
+            ary = read.get_tag(key)
+
+        for dtype in unsupported_dtypes:
+            key = "F" + dtype
+            self.assertRaises(
+                ValueError, read.set_tag, key, array.array(dtype, range(10))
+            )
+
+    def testAddTagsType(self):
+        a = self.build_read()
+        a.tags = None
+        self.assertEqual(a.tags, [])
+
+        a.setTag("X1", 5.0)
+        a.setTag("X2", "5.0")
+        a.setTag("X3", 5)
+
+        self.assertEqual(
+            sorted(a.tags), sorted([("X1", 5.0), ("X2", "5.0"), ("X3", 5)])
+        )
+
+        # test setting float for int value
+        a.setTag("X4", 5, value_type="d")
+        self.assertEqual(
+            sorted(a.tags), sorted([("X1", 5.0), ("X2", "5.0"), ("X3", 5), ("X4", 5.0)])
+        )
+
+        # test setting int for float value - the
+        # value will be rounded.
+        a.setTag("X5", 5.2, value_type="i")
+        self.assertEqual(
+            sorted(a.tags),
+            sorted([("X1", 5.0), ("X2", "5.0"), ("X3", 5), ("X4", 5.0), ("X5", 5)]),
+        )
+
+        # test setting invalid type code
+        self.assertRaises(ValueError, a.set_tag, "X6", 5.2, "g")
+
+    def testTagsUpdatingFloat(self):
+        a = self.build_read()
+        a.tags = [("NM", 1), ("RG", "L1"), ("PG", "P1"), ("XT", "U")]
+
+        self.assertEqual(a.tags, [("NM", 1), ("RG", "L1"), ("PG", "P1"), ("XT", "U")])
+        a.tags += [("XC", 5.0)]
+        self.assertEqual(
+            a.tags, [("NM", 1), ("RG", "L1"), ("PG", "P1"), ("XT", "U"), ("XC", 5.0)]
+        )
+
+    def testAddTags(self):
+        a = self.build_read()
+        a.tags = [("NM", 1), ("RG", "L1"), ("PG", "P1"), ("XT", "U")]
+
+        self.assertEqual(
+            sorted(a.tags), sorted([("NM", 1), ("RG", "L1"), ("PG", "P1"), ("XT", "U")])
+        )
+
+        a.setTag("X1", "C")
+        self.assertEqual(
+            sorted(a.tags),
+            sorted([("X1", "C"), ("NM", 1), ("RG", "L1"), ("PG", "P1"), ("XT", "U"),]),
+        )
+        a.setTag("X2", 5)
+        self.assertEqual(
+            sorted(a.tags),
+            sorted(
+                [
+                    ("X2", 5),
+                    ("X1", "C"),
+                    ("NM", 1),
+                    ("RG", "L1"),
+                    ("PG", "P1"),
+                    ("XT", "U"),
+                ]
+            ),
+        )
+        # add with replacement
+        a.setTag("X2", 10)
+        self.assertEqual(
+            sorted(a.tags),
+            sorted(
+                [
+                    ("X2", 10),
+                    ("X1", "C"),
+                    ("NM", 1),
+                    ("RG", "L1"),
+                    ("PG", "P1"),
+                    ("XT", "U"),
+                ]
+            ),
+        )
+
+        # add without replacement
+        a.setTag("X2", 5, replace=False)
+        self.assertEqual(
+            sorted(a.tags),
+            sorted(
+                [
+                    ("X2", 10),
+                    ("X1", "C"),
+                    ("X2", 5),
+                    ("NM", 1),
+                    ("RG", "L1"),
+                    ("PG", "P1"),
+                    ("XT", "U"),
+                ]
+            ),
+        )
+
+    def testTagParsing(self):
+        """test for tag parsing
+
+        see http://groups.google.com/group/pysam-user-group/browse_thread/thread/67ca204059ea465a
+        """
+        samfile = pysam.AlignmentFile(os.path.join(BAM_DATADIR, "ex8.bam"), "rb")
+
+        for entry in samfile:
+            before = entry.get_tags()
+            entry.set_tags(before)
+            after = entry.get_tags()
+            self.assertEqual(after, before)
+
+    def testMDTagMatchOnly(self):
+        a = self.build_read()
+
+        # Substitutions only
+        a.cigarstring = "21M"
+        a.query_sequence = "A" * 21
+        a.set_tag("MD", "5C0T0G05C0G0T5")
+        self.assertEqual("AAAAActgAAAAAcgtAAAAA", a.get_reference_sequence())
+
+        a.cigarstring = "21M"
+        a.query_sequence = "A" * 21
+        a.set_tag("MD", "5CTG5CGT5")
+        self.assertEqual("AAAAActgAAAAAcgtAAAAA", a.get_reference_sequence())
+
+        a.cigarstring = "11M"
+        a.query_sequence = "A" * 11
+        a.set_tag("MD", "CTG5CGT")
+        self.assertEqual("ctgAAAAAcgt", a.get_reference_sequence())
+
+    def testMDTagInsertions(self):
+        a = self.build_read()
+
+        # insertions are silent in the reference sequence
+        a.cigarstring = "5M1I5M"
+        a.query_sequence = "A" * 5 + "C" + "A" * 5
+        a.set_tag("MD", "10")
+        self.assertEqual(a.get_reference_sequence(), "A" * 10)
+
+        a.cigarstring = "1I10M"
+        a.query_sequence = "C" * 1 + "A" * 10
+        self.assertEqual(a.get_reference_sequence(), "A" * 10)
+
+        a.cigarstring = "10M1I"
+        a.query_sequence = "A" * 10 + "C" * 1
+        self.assertEqual(a.get_reference_sequence(), "A" * 10)
+
+    def testMDTagDeletions(self):
+        a = self.build_read()
+
+        a.cigarstring = "5M1D5M"
+        a.query_sequence = "A" * 10
+        a.set_tag("MD", "5^C5")
+        self.assertEqual("A" * 5 + "C" + "A" * 5, a.get_reference_sequence())
+
+        a.cigarstring = "5M3D5M"
+        a.query_sequence = "A" * 10
+        a.set_tag("MD", "5^CCC5")
+        self.assertEqual("A" * 5 + "C" * 3 + "A" * 5, a.get_reference_sequence())
+
+    def testMDTagRefSkipping(self):
+        a = self.build_read()
+
+        a.cigarstring = "5M1N5M"
+        a.query_sequence = "A" * 10
+        a.set_tag("MD", "10")
+        self.assertEqual("A" * 10, a.get_reference_sequence())
+
+        a.cigarstring = "5M3N5M"
+        a.query_sequence = "A" * 10
+        a.set_tag("MD", "10")
+        self.assertEqual("A" * 10, a.get_reference_sequence())
+
+    def testMDTagSoftClipping(self):
+        a = self.build_read()
+
+        # softclipping
+        a.cigarstring = "5S5M1D5M5S"
+        a.query_sequence = "G" * 5 + "A" * 10 + "G" * 5
+        a.set_tag("MD", "5^C5")
+        self.assertEqual("A" * 5 + "C" + "A" * 5, a.get_reference_sequence())
+
+        # all together
+        a.cigarstring = "5S5M1D5M1I5M5S"
+        a.query_sequence = "G" * 5 + "A" * 16 + "G" * 5
+        a.set_tag("MD", "2C2^T10")
+        self.assertEqual("AAcAATAAAAAAAAAA", a.get_reference_sequence())
+
+    def testMDTagComplex(self):
+        a = self.build_read()
+
+        a.cigarstring = "5S5M1I2D5M5S"
+        a.query_sequence = "G" * 5 + "A" * 11 + "G" * 5
+        a.set_tag("MD", "2C2^TC5")
+        self.assertEqual("AAcAATCAAAAA", a.get_reference_sequence())
+
+        a.cigarstring = "5S5M2D1I5M5S"
+        a.query_sequence = "G" * 5 + "A" * 11 + "G" * 5
+        a.set_tag("MD", "2C2^TC5")
+        self.assertEqual("AAcAATCAAAAA", a.get_reference_sequence())
+
+        # insertion in reference overlapping deletion in reference
+        # read: AACCCCA---AAA
+        # ref:  AA----AGGGAAA
+        a.cigarstring = "2M4I1M3D3M"
+        a.set_tag("MD", "3^GGG3")
+        a.query_sequence = "AACCCCAAAA"
+        self.assertEqual("AAAGGGAAA", a.get_reference_sequence())
+
+        a.cigarstring = "5M2D2I2M"
+        a.set_tag("MD", "4C^TT2")
+        a.query_sequence = "A" * 9
+        self.assertEqual("AAAAcTTAA", a.get_reference_sequence())
+
+    def testArrayTags(self):
+
+        r = self.build_read()
+
+        def c(r, l):
+            r.tags = [("ZM", l)]
+            self.assertEqual(list(r.opt("ZM")), list(l))
+
+        # signed integers
+        c(r, (-1, 1))
+        c(r, (-1, 100))
+        c(r, (-1, 200))
+        c(r, (-1, 1000))
+        c(r, (-1, 30000))
+        c(r, (-1, 50000))
+        c(r, (1, -1))
+        c(r, (1, -100))
+        c(r, (1, -200))
+        c(r, (1, -1000))
+        c(r, (1, -30000))
+        c(r, (1, -50000))
+
+        # unsigned integers
+        c(r, (1, 100))
+        c(r, (1, 1000))
+        c(r, (1, 10000))
+        c(r, (1, 100000))
+
+        # floats
+        c(r, (1.0, 100.0))
+
+    def testLongTags(self):
+        """see issue 115"""
+
+        r = self.build_read()
+        rg = "HS2000-899_199.L3"
+        tags = [
+            ("XC", 85),
+            ("XT", "M"),
+            ("NM", 5),
+            ("SM", 29),
+            ("AM", 29),
+            ("XM", 1),
+            ("XO", 1),
+            ("XG", 4),
+            ("MD", "37^ACCC29T18"),
+            (
+                "XA",
+                "5,+11707,36M1I48M,2;21,-48119779,46M1I38M,2;hs37d5,-10060835,40M1D45M,3;5,+11508,36M1I48M,3;hs37d5,+6743812,36M1I48M,3;19,-59118894,46M1I38M,3;4,-191044002,6M1I78M,3;",
+            ),
+        ]  # noqa
+
+        r.tags = tags
+        r.tags += [("RG", rg)] * 100
+        tags += [("RG", rg)] * 100
+
+        self.assertEqual(tags, r.tags)
+
+    def testNegativeIntegers(self):
+        x = -2
+        aligned_read = self.build_read()
+        aligned_read.tags = [("XD", int(x))]
+        self.assertEqual(aligned_read.opt("XD"), x)
+        # print (aligned_read.tags)
+
+    def testNegativeIntegersWrittenToFile(self):
+        r = self.build_read()
+        x = -2
+        r.tags = [("XD", x)]
+        with get_temp_context("negative_integers.bam") as fn:
+            with pysam.AlignmentFile(
+                fn, "wb", referencenames=("chr1",), referencelengths=(1000,)
+            ) as outf:
+                outf.write(r)
+            with pysam.AlignmentFile(fn) as inf:
+                r = next(inf)
+            self.assertEqual(r.tags, [("XD", x)])
+
+
+class TestCopy(ReadTest):
+    def testCopy(self):
+        a = self.build_read()
+        b = copy.copy(a)
+        # check if a and be are the same
+        self.assertEqual(a, b)
+
+        # check if they map to different objects
+        a.query_name = "ReadA"
+        b.query_name = "ReadB"
+        self.assertEqual(a.query_name, "ReadA")
+        self.assertEqual(b.query_name, "ReadB")
+
+    def testDeepCopy(self):
+        a = self.build_read()
+        b = copy.deepcopy(a)
+        # check if a and be are the same
+        self.assertEqual(a, b)
+
+        # check if they map to different objects
+        a.query_name = "ReadA"
+        b.query_name = "ReadB"
+        self.assertEqual(a.query_name, "ReadA")
+        self.assertEqual(b.query_name, "ReadB")
+
+
+class TestSetTagGetTag(ReadTest):
+    def check_tag(self, tag, value, value_type, alt_value_type=None):
+        a = self.build_read()
+        a.set_tag(tag, value, value_type=value_type)
+        v, t = a.get_tag(tag, with_value_type=True)
+        self.assertEqual(v, value)
+
+        if alt_value_type:
+            self.assertEqual(t, alt_value_type)
+        else:
+            self.assertEqual(t, value_type)
+
+    def test_set_tag_with_A(self):
+        self.check_tag("TT", "x", value_type="A")
+
+    def test_set_tag_with_a(self):
+        self.check_tag("TT", "x", value_type="a", alt_value_type="A")
+
+    def test_set_tag_with_C(self):
+        self.check_tag("TT", 12, value_type="C")
+
+    def test_set_tag_with_c(self):
+        self.check_tag("TT", 12, value_type="c")
+
+    def test_set_tag_with_S(self):
+        self.check_tag("TT", 12, value_type="S")
+
+    def test_set_tag_with_s(self):
+        self.check_tag("TT", 12, value_type="s")
+
+    def test_set_tag_with_I(self):
+        self.check_tag("TT", 12, value_type="I")
+
+    def test_set_tag_with_i(self):
+        self.check_tag("TT", 12, value_type="i")
+
+    def test_set_tag_with_f(self):
+        self.check_tag("TT", 2.5, value_type="f")
+
+    def test_set_tag_with_d(self):
+        self.check_tag("TT", 2.5, value_type="d")
+
+    def test_set_tag_with_H(self):
+        self.check_tag("TT", "AE12", value_type="H")
+
+    def test_set_tag_with_automated_type_detection(self):
+        self.check_tag("TT", -(1 << 7), value_type=None, alt_value_type="c")
+        self.check_tag("TT", -(1 << 7) - 1, value_type=None, alt_value_type="s")
+        self.check_tag("TT", -(1 << 15), value_type=None, alt_value_type="s")
+        self.check_tag("TT", -(1 << 15) - 1, value_type=None, alt_value_type="i")
+        self.check_tag("TT", -(1 << 31), value_type=None, alt_value_type="i")
+        self.assertRaises(
+            ValueError,
+            self.check_tag,
+            "TT",
+            -(1 << 31) - 1,
+            value_type=None,
+            alt_value_type="i",
+        )
+
+        self.check_tag("TT", (1 << 8) - 1, value_type=None, alt_value_type="C")
+        self.check_tag("TT", (1 << 8), value_type=None, alt_value_type="S")
+        self.check_tag("TT", (1 << 16) - 1, value_type=None, alt_value_type="S")
+        self.check_tag("TT", (1 << 16), value_type=None, alt_value_type="I")
+        self.check_tag("TT", (1 << 32) - 1, value_type=None, alt_value_type="I")
+        self.assertRaises(
+            ValueError,
+            self.check_tag,
+            "TT",
+            (1 << 32),
+            value_type=None,
+            alt_value_type="I",
+        )
+
+
+class TestSetTagsGetTag(TestSetTagGetTag):
+    def check_tag(self, tag, value, value_type, alt_value_type=None):
+        a = self.build_read()
+        a.set_tags([(tag, value, value_type)])
+        v, t = a.get_tag(tag, with_value_type=True)
+        if alt_value_type:
+            self.assertEqual(t, alt_value_type)
+        else:
+            self.assertEqual(t, value_type)
+        self.assertEqual(v, value)
+
+
+class TestEnums(unittest.TestCase):
+    def test_cigar_enums_are_defined(self):
+        self.assertEqual(pysam.CMATCH, 0)
+        self.assertEqual(pysam.CINS, 1)
+        self.assertEqual(pysam.CDEL, 2)
+        self.assertEqual(pysam.CREF_SKIP, 3)
+        self.assertEqual(pysam.CSOFT_CLIP, 4)
+        self.assertEqual(pysam.CHARD_CLIP, 5)
+        self.assertEqual(pysam.CPAD, 6)
+        self.assertEqual(pysam.CEQUAL, 7)
+        self.assertEqual(pysam.CDIFF, 8)
+        self.assertEqual(pysam.CBACK, 9)
+
+    def test_sam_flags_are_defined(self):
+        self.assertEqual(pysam.FPAIRED, 1)
+        self.assertEqual(pysam.FPROPER_PAIR, 2)
+        self.assertEqual(pysam.FUNMAP, 4)
+        self.assertEqual(pysam.FMUNMAP, 8)
+        self.assertEqual(pysam.FREVERSE, 16)
+        self.assertEqual(pysam.FMREVERSE, 32)
+        self.assertEqual(pysam.FREAD1, 64)
+        self.assertEqual(pysam.FREAD2, 128)
+        self.assertEqual(pysam.FSECONDARY, 256)
+        self.assertEqual(pysam.FQCFAIL, 512)
+        self.assertEqual(pysam.FDUP, 1024)
+        self.assertEqual(pysam.FSUPPLEMENTARY, 2048)
+
+
+class TestBuildingReadsWithoutHeader(unittest.TestCase):
+    def build_read(self):
+        """build an example read, but without header information."""
+
+        a = pysam.AlignedSegment()
+        a.query_name = "read_12345"
+        a.query_sequence = "ATGC" * 10
+        a.flag = 0
+        a.reference_id = -1
+        a.reference_start = 20
+        a.mapping_quality = 20
+        a.cigartuples = ((0, 10), (2, 1), (0, 9), (1, 1), (0, 20))
+        a.next_reference_id = 0
+        a.next_reference_start = 200
+        a.template_length = 167
+        a.query_qualities = pysam.qualitystring_to_array("1234") * 10
+        # todo: create tags
+        return a
+
+    def test_read_can_be_constructed_without_header(self):
+        read = self.build_read()
+        self.assertEqual(read.query_name, "read_12345")
+
+    def test_reference_id_can_be_set(self):
+        read = self.build_read()
+        read.reference_id = 2
+        self.assertEqual(read.reference_id, 2)
+
+    def test_reference_name_is_not_available(self):
+        read = self.build_read()
+        self.assertRaises(ValueError, setattr, read, "reference_name", "chr2")
+
+    def test_read_can_be_written_to_file(self):
+        tmpfilename = get_temp_filename(".bam")
+        with pysam.AlignmentFile(
+            tmpfilename,
+            "wb",
+            reference_names=["chr1", "chr2", "chr3"],
+            reference_lengths=[1000, 2000, 3000],
+        ) as outf:
+            read = self.build_read()
+            read.reference_id = 2
+            outf.write(read)
+
+        stdout = pysam.samtools.view(tmpfilename)
+        chromosome = stdout.split("\t")[2]
+        self.assertEqual(chromosome, "chr3")
+        os.unlink(tmpfilename)
+
+
+class TestForwardStrandValues(ReadTest):
+    def test_sequence_is_complemented(self):
+        a = self.build_read()
+        a.is_reverse = False
+        fwd_seq = a.query_sequence
+
+        rev_seq = fwd_seq.translate(maketrans("ACGTacgtNnXx", "TGCAtgcaNnXx"))[::-1]
+        self.assertEqual(fwd_seq, a.get_forward_sequence())
+        a.is_reverse = True
+        self.assertEqual(fwd_seq, a.query_sequence)
+        self.assertEqual(rev_seq, a.get_forward_sequence())
+
+    def test_qualities_are_complemented(self):
+        a = self.build_read()
+        a.is_reverse = False
+        fwd_qual = a.query_qualities
+        rev_qual = fwd_qual[::-1]
+        self.assertEqual(fwd_qual, a.get_forward_qualities())
+        a.is_reverse = True
+        self.assertEqual(fwd_qual, a.query_qualities)
+        self.assertEqual(rev_qual, a.get_forward_qualities())
+
+
+class TestExportImport(ReadTest):
+    def test_string_export(self):
+        a = self.build_read()
+        self.assertEqual(
+            a.to_string(),
+            "read_12345\t0\tchr1\t21\t20\t10M1D9M1I20M\t=\t201\t167\t"
+            "ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGC\t1234123412341234123412341234123412341234",
+        )
+
+    def test_string_export_import_without_tags(self):
+        a = self.build_read()
+        a.tags = []
+        b = pysam.AlignedSegment.fromstring(a.to_string(), a.header)
+        self.assertEqual(a, b)
+
+    def test_string_export_import_with_tags(self):
+        a = self.build_read()
+        a.tags = [("XD", 12), ("RF", "abc")]
+        b = pysam.AlignedSegment.fromstring(a.to_string(), a.header)
+        self.assertEqual(a, b)
+
+    def test_to_string_without_alignment_file(self):
+        with open(os.path.join(BAM_DATADIR, "ex2.sam")) as samf:
+            reference = [x[:-1] for x in samf if not x.startswith("@")]
+
+        with pysam.AlignmentFile(os.path.join(BAM_DATADIR, "ex2.bam"), "r") as pysamf:
+            for s, p in zip(reference, pysamf):
+                self.assertEqual(s, p.to_string())
+
+    def test_dict_export(self):
+        a = self.build_read()
+        a.tags = [("XD", 12), ("RF", "abc")]
+
+        self.assertEqual(
+            a.to_dict(),
+            json.loads(
+                '{"name": "read_12345", "flag": "0", "ref_name": "chr1", "ref_pos": "21", '
+                '"map_quality": "20", "cigar": "10M1D9M1I20M", "next_ref_name": "=", '
+                '"next_ref_pos": "201", "length": "167", '
+                '"seq": "ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGC", '
+                '"qual": "1234123412341234123412341234123412341234", "tags": ["XD:i:12", "RF:Z:abc"]}'
+            ),
+        )
+
+    def test_string_export_import_without_tags(self):
+        a = self.build_read()
+        a.tags = []
+        b = pysam.AlignedSegment.from_dict(a.to_dict(), a.header)
+        self.assertEqual(a, b)
+
+    def test_string_export_import_with_tags(self):
+        a = self.build_read()
+        a.tags = [("XD", 12), ("RF", "abc")]
+        b = pysam.AlignedSegment.from_dict(a.to_dict(), a.header)
+        self.assertEqual(a, b)
+
+
+if __name__ == "__main__":
+    unittest.main()
diff --git a/tests/AlignmentFileFetchTestUtils.py b/tests/AlignmentFileFetchTestUtils.py
new file mode 100644
index 0000000..53ee19f
--- /dev/null
+++ b/tests/AlignmentFileFetchTestUtils.py
@@ -0,0 +1,87 @@
+import os
+import subprocess
+import pysam
+
+from TestUtils import force_str
+
+
+def build_fetch_with_samtoolsshell(fn):
+    retval = os.popen("samtools view {} 2> /dev/null | wc -l".format(fn)).read()
+    return int(retval.strip())
+
+
+def build_fetch_with_samtoolspipe(fn):
+    FNULL = open(os.devnull, 'w')
+    with subprocess.Popen(["samtools", "view", fn],
+                          stdin=subprocess.PIPE,
+                          stdout=subprocess.PIPE,
+                          stderr=FNULL) as proc:
+        return len(proc.stdout.readlines())
+
+    
+def build_fetch_with_pysam(*args, **kwargs):
+    with pysam.AlignmentFile(*args, **kwargs) as inf:
+        return len(list(inf.fetch()))
+
+
+def build_query_sequences_with_samtoolsshell(fn):
+    retval = os.popen("samtools view {} 2> /dev/null | cut -f 11".format(fn)).read()
+    return force_str(retval).splitlines()
+
+
+def build_query_sequences_with_samtoolspipe(fn):
+    FNULL = open(os.devnull, 'w')
+    with subprocess.Popen(["samtools", "view", fn],
+                          stdin=subprocess.PIPE,
+                          stdout=subprocess.PIPE,
+                          stderr=FNULL) as proc:
+        data = [force_str(x).split()[10] for x in proc.stdout.readlines()]
+    return data
+
+    
+def build_query_sequences_with_pysam(*args, **kwargs):
+    with pysam.AlignmentFile(*args, **kwargs) as inf:
+        data = [x.query_sequence for x in inf]
+    return data
+
+
+def build_query_qualities_with_pysam(*args, **kwargs):
+    with pysam.AlignmentFile(*args, **kwargs) as inf:
+        data = [x.query_qualities for x in inf]
+    return data
+
+
+def build_query_sequences_flagfilter_with_samtoolsshell(fn):
+    retval = os.popen("samtools view -f 2 {} 2> /dev/null | cut -f 11".format(fn)).read()
+    return force_str(retval).splitlines()
+
+
+def build_query_sequences_flagfilter_with_samtoolspipe(fn):
+    FNULL = open(os.devnull, 'w')
+    with subprocess.Popen(["samtools", "view", "-f", "2", fn],
+                          stdin=subprocess.PIPE,
+                          stdout=subprocess.PIPE,
+                          stderr=FNULL) as proc:
+        data = [force_str(x).split()[10] for x in proc.stdout.readlines()]
+    return data
+
+def build_query_sequences_flagfilter_with_pysam(*args, **kwargs):
+    with pysam.AlignmentFile(*args, **kwargs) as inf:
+        data = [x.query_sequence for x in inf if x.is_proper_pair]
+    return data
+
+
+def build_query_sequences_directflagfilter_with_pysam(*args, **kwargs):
+    with pysam.AlignmentFile(*args, **kwargs) as inf:
+        data = [x.query_sequence for x in inf if x.flag & 2]
+    return data
+
+
+def build_aligned_pairs_with_pysam(*args, **kwargs):
+    matches_only = kwargs.pop("matches_only", False)
+    with_seq = kwargs.pop("with_seq", False)
+    with pysam.AlignmentFile(*args, **kwargs) as inf:
+        data = [x.get_aligned_pairs(matches_only=matches_only, with_seq=with_seq)
+                for x in inf if x.is_mapped]
+    return data
+    
diff --git a/tests/AlignmentFileFetch_bench.py b/tests/AlignmentFileFetch_bench.py
new file mode 100644
index 0000000..9fd8b83
--- /dev/null
+++ b/tests/AlignmentFileFetch_bench.py
@@ -0,0 +1,97 @@
+"""Benchmarking module for AlignmentFile functionality"""
+import pytest
+
+
+from TestUtils import BAM_DATADIR
+from AlignmentFileFetchTestUtils import *
+
+
+def test_build_fetch_from_bam_with_samtoolsshell(benchmark):
+    result = benchmark(build_fetch_with_samtoolsshell,
+                       os.path.join(BAM_DATADIR, "ex2.bam"))
+    assert result == 3270
+
+
+def test_build_fetch_from_bam_with_samtoolspipe(benchmark):
+    result = benchmark(build_fetch_with_samtoolspipe,
+                       os.path.join(BAM_DATADIR, "ex2.bam"))
+    assert result == 3270
+
+
+def test_build_fetch_from_bam_with_pysam(benchmark):
+    result = benchmark(build_fetch_with_pysam,
+                       os.path.join(BAM_DATADIR, "ex2.bam"))
+    assert result == 3270
+
+
+def test_build_query_sequences_from_bam_with_samtoolsshell(benchmark):
+    result = benchmark(build_query_sequences_with_samtoolsshell,
+                       os.path.join(BAM_DATADIR, "ex2.bam"))
+    assert len(result) == 3270
+
+
+def test_build_query_sequences_from_bam_with_samtoolspipe(benchmark):
+    result = benchmark(build_query_sequences_with_samtoolspipe,
+                       os.path.join(BAM_DATADIR, "ex2.bam"))
+    assert len(result) == 3270
+
+
+def test_build_query_sequences_from_bam_with_pysam(benchmark):
+    result = benchmark(build_query_sequences_with_pysam,
+                       os.path.join(BAM_DATADIR, "ex2.bam"))
+    assert len(result) == 3270
+
+
+def test_build_query_qualities_from_bam_with_pysam(benchmark):
+    result = benchmark(build_query_qualities_with_pysam,
+                       os.path.join(BAM_DATADIR, "ex2.bam"))
+    assert len(result) == 3270
+
+
+def test_build_query_sequences_from_bam_flagfilter_with_samtoolsshell(benchmark):
+    result = benchmark(build_query_sequences_flagfilter_with_samtoolsshell,
+                       os.path.join(BAM_DATADIR, "ex2.bam"))
+    assert len(result) == 3124
+
+
+def test_build_query_sequences_from_bam_flagfilter_with_samtoolspipe(benchmark):
+    result = benchmark(build_query_sequences_flagfilter_with_samtoolspipe,
+                       os.path.join(BAM_DATADIR, "ex2.bam"))
+    assert len(result) == 3124
+
+
+def test_build_query_sequences_from_bam_flagfilter_with_pysam(benchmark):
+    result = benchmark(build_query_sequences_flagfilter_with_pysam,
+                       os.path.join(BAM_DATADIR, "ex2.bam"))
+    assert len(result) == 3124
+
+
+def test_build_query_sequences_from_bam_directflagfilter_with_pysam(benchmark):
+    result = benchmark(build_query_sequences_flagfilter_with_pysam,
+                       os.path.join(BAM_DATADIR, "ex2.bam"))
+    assert len(result) == 3124
+
+
+@pytest.mark.aligned_pairs
+def test_build_aligned_pairs_default_with_pysam(benchmark):
+    result = benchmark(build_aligned_pairs_with_pysam,
+                       os.path.join(BAM_DATADIR, "with_md.bam"))
+    assert len(result) == 3235
+
+
+@pytest.mark.aligned_pairs
+def test_build_aligned_pairs_matchesonly_with_pysam(benchmark):
+    result = benchmark(build_aligned_pairs_with_pysam,
+                       os.path.join(BAM_DATADIR, "with_md.bam"),
+                       matches_only=True)
+    assert len(result) == 3235
+
+
+@pytest.mark.aligned_pairs    
+def test_build_aligned_pairs_withseq_with_pysam(benchmark):
+    result = benchmark(build_aligned_pairs_with_pysam,
+                       os.path.join(BAM_DATADIR, "with_md.bam"),
+                       with_seq=True)
+    assert len(result) == 3235
+    
+
diff --git a/tests/AlignmentFileHeader_test.py b/tests/AlignmentFileHeader_test.py
new file mode 100644
index 0000000..3d9e2e4
--- /dev/null
+++ b/tests/AlignmentFileHeader_test.py
@@ -0,0 +1,328 @@
+#!/usr/bin/env python
+'''unit testing code for pysam.
+
+Execute in the :file:`tests` directory as it requires the Makefile
+and data files located there.
+'''
+
+import unittest
+import os
+import re
+import copy
+from collections import OrderedDict as odict
+import pysam
+import pysam.samtools
+from TestUtils import get_temp_filename, make_data_files, BAM_DATADIR
+
+
+def setUpModule():
+    make_data_files(BAM_DATADIR)
+
+
+class TestHeaderConstruction(unittest.TestCase):
+    """testing header construction."""
+
+    header_dict = odict(
+        [('SQ', [odict([('LN', 1575), ('SN', 'chr1'), ('AH', 'chr1:5000000-5010000')]),
+                 odict([('LN', 1584), ('SN', 'chr2'), ('AH', '*')])]),
+         ('RG', [odict([('LB', 'SC_1'), ('ID', 'L1'), ('SM', 'NA12891'),
+                        ('PU', 'SC_1_10'), ("CN", "name:with:colon")]),
+                 odict([('LB', 'SC_2'), ('ID', 'L2'), ('SM', 'NA12891'),
+                        ('PU', 'SC_2_12'), ("CN", "name:with:colon")])]),
+         ('PG', [odict([('ID', 'P1'), ('VN', '1.0')]),
+                 odict([('ID', 'P2'), ('VN', '1.1')])]),
+         ('HD', odict([('VN', '1.0')])),
+         ('CO', ['this is a comment', 'this is another comment']),
+        ])
+
+    header_text = ("@HD\tVN:1.0\n"
+                   "@SQ\tSN:chr1\tLN:1575\tAH:chr1:5000000-5010000\n"
+                   "@SQ\tSN:chr2\tLN:1584\tAH:*\n"
+                   "@RG\tID:L1\tPU:SC_1_10\tLB:SC_1\tSM:NA12891\tCN:name:with:colon\n"
+                   "@RG\tID:L2\tPU:SC_2_12\tLB:SC_2\tSM:NA12891\tCN:name:with:colon\n"
+                   "@PG\tID:P1\tVN:1.0\n"
+                   "@PG\tID:P2\tVN:1.1\n"
+                   "@CO\tthis is a comment\n"
+                   "@CO\tthis is another comment\n")
+
+
+    header_from_references = odict(
+        [('SQ', [odict([('LN', 1575), ('SN', 'chr1')]),
+                 odict([('LN', 1584), ('SN', 'chr2')])]),
+         ('RG', [odict([('LB', 'SC_1'), ('ID', 'L1'), ('SM', 'NA12891'),
+                        ('PU', 'SC_1_10'), ("CN", "name:with:colon")]),
+                 odict([('LB', 'SC_2'), ('ID', 'L2'), ('SM', 'NA12891'),
+                        ('PU', 'SC_2_12'), ("CN", "name:with:colon")])]),
+         ('PG', [odict([('ID', 'P1'), ('VN', '1.0')]),
+                 odict([('ID', 'P2'), ('VN', '1.1')])]),
+         ('HD', odict([('VN', '1.0')])),
+         ('CO', ['this is a comment', 'this is another comment']),
+        ])
+
+    header_without_text = odict(
+        [('SQ', [odict([('LN', 1575), ('SN', 'chr1')]),
+                 odict([('LN', 1584), ('SN', 'chr2')])]),
+        ])
+    
+    def compare_headers(self, test_header, ref_header=None):
+        '''compare two headers a and b.'''
+        test_header_dict = test_header.as_dict()
+        if ref_header is None:
+            ref_header = self.header_dict
+            
+        for ak, av in test_header_dict.items():
+            self.assertTrue(ak in self.header_dict, "key '%s' not in '%s' " % (ak, ref_header))
+            self.assertEqual(av, ref_header[ak])
+        for ak, av in ref_header.items():
+            self.assertTrue(ak in test_header_dict, "key '%s' not in '%s' " % (ak, test_header_dict))
+            self.assertEqual(av, test_header_dict[ak])
+
+    def check_name_mapping(self, test_header):
+        for x, y in enumerate(("chr1", "chr2")):
+            tid = test_header.get_tid(y)
+            ref = test_header.get_reference_name(x)
+            self.assertEqual(tid, x)
+            self.assertEqual(ref, y)
+
+        self.assertEqual(test_header.get_tid("chr?"), -1)
+        self.assertRaises(ValueError, test_header.get_reference_name, 2)
+            
+    def test_header_constructed_from_dict(self):
+        header = pysam.AlignmentHeader.from_dict(self.header_dict)
+        self.compare_headers(header)
+        self.check_name_mapping(header)
+        
+    def test_header_constructed_from_text(self):
+        header = pysam.AlignmentHeader.from_text(self.header_text)
+        self.compare_headers(header)
+        self.check_name_mapping(header)
+        
+    def test_header_constructed_from_header(self):
+        header = pysam.AlignmentHeader.from_text(self.header_text)
+        self.compare_headers(header.copy())
+        self.check_name_mapping(header)
+
+    def test_header_constructed_from_references(self):
+        text = re.sub("@SQ[^\n]+\n", "", self.header_text)
+        assert "@SQ" not in text
+        header = pysam.AlignmentHeader.from_references(
+            reference_names=["chr1", "chr2"],
+            reference_lengths=[1575, 1584],
+            text=text)
+        self.compare_headers(header, self.header_from_references)
+        self.check_name_mapping(header)
+
+    def test_header_constructed_from_references_without_text(self):
+        header = pysam.AlignmentHeader.from_references(
+            reference_names=["chr1", "chr2"],
+            reference_lengths=[1575, 1584])
+        self.compare_headers(header, self.header_without_text)
+        self.check_name_mapping(header)
+
+
+class TestHeaderSAM(unittest.TestCase):
+    """testing header manipulation"""
+
+    header = {'SQ': [{'LN': 1575, 'SN': 'chr1', 'AH': 'chr1:5000000-5010000'},
+                     {'LN': 1584, 'SN': 'chr2', 'AH': '*'}],
+              'RG': [{'LB': 'SC_1', 'ID': 'L1', 'SM': 'NA12891',
+                      'PU': 'SC_1_10', "CN": "name:with:colon"},
+                     {'LB': 'SC_2', 'ID': 'L2', 'SM': 'NA12891',
+                      'PU': 'SC_2_12', "CN": "name:with:colon"}],
+              'PG': [{'ID': 'P1', 'VN': '1.0'}, {'ID': 'P2', 'VN': '1.1'}],
+              'HD': {'VN': '1.0'},
+              'CO': ['this is a comment', 'this is another comment'],
+              }
+
+    def compare_headers(self, a, b):
+        '''compare two headers a and b.'''
+        for ak, av in a.items():
+            self.assertTrue(ak in b, "key '%s' not in '%s' " % (ak, b))
+            self.assertEqual(av, b[ak])
+
+    def setUp(self):
+        self.samfile = pysam.AlignmentFile(
+            os.path.join(BAM_DATADIR, "ex3.sam"),
+            "r")
+
+    def test_header_content_is_as_expected(self):
+        self.compare_headers(self.header, self.samfile.header.to_dict())
+        self.compare_headers(self.samfile.header.to_dict(), self.header)
+
+    def test_text_access_works(self):
+        self.assertEqual(self.samfile.text, self.samfile.header.__str__())
+        
+    def test_name_mapping(self):
+        for x, y in enumerate(("chr1", "chr2")):
+            tid = self.samfile.gettid(y)
+            ref = self.samfile.getrname(x)
+            self.assertEqual(tid, x)
+            self.assertEqual(ref, y)
+
+        self.assertEqual(self.samfile.gettid("chr?"), -1)
+        self.assertRaises(ValueError, self.samfile.getrname, 2)
+
+    def test_dictionary_access_works(self):
+        for key in self.header.keys():
+            self.compare_headers({key: self.header[key]},
+                                 {key: self.samfile.header[key]})
+
+    def test_dictionary_setting_raises_error(self):
+        self.assertRaises(TypeError,
+                          self.samfile.header.__setitem__,
+                          "CO",
+                          ["This is a final comment"])
+
+    def test_dictionary_len_works(self):
+        self.assertEqual(len(self.header), len(self.samfile.header))
+
+    def test_dictionary_keys_works(self):
+        # sort for py2.7
+        self.assertEqual(sorted(self.header.keys()),
+                         sorted(self.samfile.header.keys()))
+
+    def test_dictionary_values_works(self):
+        self.assertEqual(len(self.header.values()), len(self.samfile.header.values()))
+        
+    def test_dictionary_get_works(self):
+        self.assertEqual(self.header.get("HD"), {'VN': '1.0'})
+        self.assertEqual(self.header.get("UK", "xyz"), "xyz")
+        self.assertEqual(self.header.get("UK"), None)
+
+    def test_dictionary_contains_works(self):
+        self.assertTrue("HD" in self.header)
+        self.assertFalse("UK" in self.header)
+
+    def tearDown(self):
+        self.samfile.close()
+
+
+class TestHeaderBAM(TestHeaderSAM):
+
+    def setUp(self):
+        self.samfile = pysam.AlignmentFile(
+            os.path.join(BAM_DATADIR, "ex3.bam"),
+            "rb")
+
+
+class TestHeaderCRAM(TestHeaderSAM):
+
+    def setUp(self):
+        self.samfile = pysam.AlignmentFile(
+            os.path.join(BAM_DATADIR, "ex3.cram"),
+            "rc")
+
+    def compare_headers(self, a, b):
+        '''compare two headers a and b.'''
+        def _strip(dd):
+            for x in dd:
+                for y in ("M5", "UR"):
+                    if y in x:
+                        del x[y]
+        for ak, av in a.items():
+            _strip(av)
+            self.assertTrue(ak in b, "key '%s' not in '%s' " % (ak, b))
+            _strip(b[ak])
+
+            self.assertEqual(av, b[ak])
+
+
+class TestHeaderFromRefs(unittest.TestCase):
+    '''see issue 144
+
+    reference names need to be converted to string for python 3
+    '''
+
+    # def testHeader( self ):
+    #     refs = ['chr1', 'chr2']
+    #     tmpfile = "tmp_%i" % id(self)
+    #     s = pysam.AlignmentFile(tmpfile, 'wb',
+    #                       referencenames=refs,
+    #                       referencelengths=[100]*len(refs))
+    #     s.close()
+
+    #     self.assertTrue( checkBinaryEqual( 'issue144.bam', tmpfile ),
+    #                      'bam files differ')
+    #     os.unlink( tmpfile )
+
+
+
+class TestHeaderWriteRead(unittest.TestCase):
+    header = {'SQ': [{'LN': 1575, 'SN': 'chr1'},
+                     {'LN': 1584, 'SN': 'chr2'}],
+              'RG': [{'LB': 'SC_1', 'ID': 'L1', 'SM': 'NA12891',
+                      'PU': 'SC_1_10', "CN": "name:with:colon"},
+                     {'LB': 'SC_2', 'ID': 'L2', 'SM': 'NA12891',
+                      'PU': 'SC_2_12', "CN": "name:with:colon"}],
+              'PG': [{'ID': 'P1', 'VN': '1.0', 'CL': 'tool'},
+                     {'ID': 'P2', 'VN': '1.1', 'CL': 'tool with in option -R a\tb',
+                      'PP': 'P1'}],
+              'HD': {'VN': '1.0'},
+              'CO': ['this is a comment', 'this is another comment'],
+              }
+
+    def compare_headers(self, a, header_b):
+        '''compare two headers a and b.
+
+        Ignore M5 and UR field as they are set application specific.
+        '''
+        b = header_b.to_dict()
+        for ak, av in a.items():
+            self.assertTrue(ak in b, "key '%s' not in '%s' " % (ak, b))
+            self.assertEqual(
+                len(av), len(b[ak]),
+                "unequal number of entries for key {}: {} vs {}"
+                .format(ak, av, b[ak]))
+
+            for row_a, row_b in zip(av, b[ak]):
+                if isinstance(row_b, dict):
+                    for x in ["M5", "UR"]:
+                        try:
+                            del row_b[x]
+                        except KeyError:
+                            pass
+                self.assertEqual(row_a, row_b)
+
+    def check_read_write(self, flag_write, header):
+
+        fn = get_temp_filename()
+        print(fn)
+        with pysam.AlignmentFile(
+                fn,
+                flag_write,
+                header=header,
+                reference_filename=os.path.join(BAM_DATADIR, "ex1.fa")) as outf:
+            a = pysam.AlignedSegment()
+            a.query_name = "abc"
+            outf.write(a)
+
+        with pysam.AlignmentFile(fn) as inf:
+            read_header = inf.header
+
+        # os.unlink(fn)
+        self.compare_headers(header, read_header)
+        expected_lengths = dict([(x["SN"], x["LN"]) for x in header["SQ"]])
+        self.assertEqual(expected_lengths,
+                         dict(zip(read_header.references,
+                                  read_header.lengths)))
+
+    def test_SAM(self):
+        self.check_read_write("wh", self.header)
+
+    def test_BAM(self):
+        self.check_read_write("wb", self.header)
+        
+    def test_CRAM(self):
+        header = copy.copy(self.header)
+        if "PG" in header:
+            # for CRAM, \t needs to be quoted:
+            header['PG'][1]['CL'] = re.sub(r"\t", r"\\\\t", header['PG'][1]['CL'])
+        self.check_read_write("wc", header)
+
+
+class TestHeaderLargeContigs(TestHeaderWriteRead):
+    """see issue 741"""
+
+    header = {'SQ': [{'LN': 2147483647, 'SN': 'chr1'},
+                     {'LN': 1584, 'SN': 'chr2'}],
+              'HD': {'VN': '1.0'}}
diff --git a/tests/AlignmentFilePileup_bench.py b/tests/AlignmentFilePileup_bench.py
new file mode 100644
index 0000000..d165e52
--- /dev/null
+++ b/tests/AlignmentFilePileup_bench.py
@@ -0,0 +1,145 @@
+"""Benchmarking module for AlignmentFile functionality"""
+from TestUtils import BAM_DATADIR, flatten_nested_list
+from PileupTestUtils import *
+
+
+def test_build_pileup_from_bam_with_samtoolsshell(benchmark):
+    result = benchmark(build_pileup_with_samtoolsshell,
+                       os.path.join(BAM_DATADIR, "ex2.bam"))
+    assert result == 2998
+
+
+def test_build_pileup_from_bam_with_samtoolspipe(benchmark):
+    result = benchmark(build_pileup_with_samtoolspipe,
+                       os.path.join(BAM_DATADIR, "ex2.bam"))
+    assert result == 2998
+
+
+def test_build_pileup_from_bam_with_pysam(benchmark):
+    result = benchmark(build_pileup_with_pysam,
+                       os.path.join(BAM_DATADIR, "ex2.bam"))
+    assert result == 2998
+
+
+def test_build_depth_from_bam_with_samtoolsshell(benchmark):
+    result = benchmark(build_depth_with_samtoolsshell,
+                       os.path.join(BAM_DATADIR, "ex2.bam"))
+    assert result == 107241
+
+
+def test_build_depth_from_bam_with_samtoolspipe(benchmark):
+    result = benchmark(build_depth_with_samtoolspipe,
+                       os.path.join(BAM_DATADIR, "ex2.bam"))
+    assert sum(result) == 107241
+
+
+def test_build_depth_from_bam_with_pysam(benchmark):
+    result = benchmark(build_depth_with_pysam,
+                       os.path.join(BAM_DATADIR, "ex2.bam"))
+    # different value, as samtools filters with a minimum
+    # base quality of 13
+    assert sum(result) == 110015
+
+
+def test_build_depth_with_filter_from_bam_with_pysam(benchmark):
+    result = benchmark(build_depth_with_filter_with_pysam,
+                       os.path.join(BAM_DATADIR, "ex2.bam"))
+    assert sum(result) == 107241
+
+
+def test_build_query_bases_from_bam_with_samtoolsshell(benchmark):
+    result = benchmark(build_query_bases_with_samtoolsshell,
+                       os.path.join(BAM_DATADIR, "ex2.bam"))
+    assert result == 116308
+
+
+def test_build_query_bases_from_bam_with_samtoolspysam(benchmark):
+    result = benchmark(build_query_bases_with_samtoolspysam,
+                       os.path.join(BAM_DATADIR, "ex2.bam"))
+    assert len("".join(flatten_nested_list(result))) == 116308
+    
+
+def test_build_query_bases_from_bam_with_samtoolspipe(benchmark):
+    result = benchmark(build_query_bases_with_samtoolspipe,
+                       os.path.join(BAM_DATADIR, "ex2.bam"))
+    assert len("".join(flatten_nested_list(result))) == 116308
+
+
+def test_build_query_bases_from_bam_with_pysam_pileups(benchmark):
+    # note that there is no overlap detection here
+    result = benchmark(build_query_bases_with_pysam_pileups,
+                       os.path.join(BAM_DATADIR, "ex2.bam"))
+    assert len("".join(flatten_nested_list(result))) == 107241
+
+
+def test_build_query_bases_from_bam_with_pysam(benchmark):
+    result = benchmark(build_query_bases_with_pysam,
+                       os.path.join(BAM_DATADIR, "ex2.bam"))
+    assert len("".join(flatten_nested_list(result))) == 116308
+
+
+# note that pileups with/without reference sequence will differ due to
+# realignment.
+def test_build_query_bases_with_reference_from_bam_with_samtoolspipe(benchmark):
+    result = benchmark(build_query_bases_with_samtoolspipe,
+                       os.path.join(BAM_DATADIR, "ex2.bam"),
+                       "-f", os.path.join(BAM_DATADIR, "ex1.fa"))
+    assert len("".join(flatten_nested_list(result))) == 115924
+    
+
+def test_build_query_bases_with_reference_from_bam_with_pysam(benchmark):
+    with pysam.FastaFile(os.path.join(BAM_DATADIR, "ex1.fa")) as fasta:
+        result = benchmark(build_query_bases_with_pysam,
+                           os.path.join(BAM_DATADIR, "ex2.bam"),
+                           fastafile=fasta)
+    assert len("".join(flatten_nested_list(result))) == 115924
+    
+
+def test_build_query_bases_with_reference_from_bam_with_samtoolspysam(benchmark):
+    result = benchmark(build_query_bases_with_samtoolspysam,
+                       os.path.join(BAM_DATADIR, "ex2.bam"),
+                       "-f", os.path.join(BAM_DATADIR, "ex1.fa"))
+    assert len("".join(flatten_nested_list(result))) == 115924
+
+
+def test_build_query_qualities_from_bam_with_samtoolspipe(benchmark):
+    result = benchmark(build_query_qualities_with_samtoolspipe,
+                       os.path.join(BAM_DATADIR, "ex2.bam"))
+    assert len("".join(result)) == 107241
+
+
+def test_build_query_qualities_from_bam_with_pysam(benchmark):
+    result = benchmark(build_query_qualities_with_pysam,
+                       os.path.join(BAM_DATADIR, "ex2.bam"))
+    assert sum([len(x) for x in result]) == 107241
+
+
+def test_build_query_names_from_bam_with_pysam(benchmark):
+    result = benchmark(build_query_names_with_pysam,
+                       os.path.join(BAM_DATADIR, "ex2.bam"))
+    assert len("".join([x for column in result for x in column])) == 2307343
+
+
+def test_build_mapping_qualities_from_bam_with_samtoolspipe(benchmark):
+    result = benchmark(build_mapping_qualities_with_samtoolspipe,
+                       os.path.join(BAM_DATADIR, "ex2.bam"))
+    assert len("".join(result)) == 107241
+
+
+def test_build_mapping_qualities_from_bam_with_pysam(benchmark):
+    result = benchmark(build_mapping_qualities_with_pysam,
+                       os.path.join(BAM_DATADIR, "ex2.bam"))
+    assert sum([len(x) for x in result]) == 107241
+
+
+def test_build_query_positions_from_bam_with_samtoolspipe(benchmark):
+    result = benchmark(build_query_positions_with_samtoolspipe,
+                       os.path.join(BAM_DATADIR, "ex2.bam"))
+    # positions output by samtools are 1-based
+    assert sum([sum(x) - len(x) for x in result]) == 1841699
+
+
+def test_build_query_positions_from_bam_with_pysam(benchmark):
+    result = benchmark(build_query_positions_with_pysam,
+                       os.path.join(BAM_DATADIR, "ex2.bam"))
+    assert sum([sum(x) for x in result]) == 1841699
diff --git a/tests/AlignmentFilePileup_test.py b/tests/AlignmentFilePileup_test.py
new file mode 100644
index 0000000..8e75a52
--- /dev/null
+++ b/tests/AlignmentFilePileup_test.py
@@ -0,0 +1,405 @@
+"""Benchmarking module for AlignmentFile functionality"""
+import os
+import pysam
+import unittest
+from TestUtils import make_data_files, BAM_DATADIR, IS_PYTHON3, force_str, flatten_nested_list
+import PileupTestUtils
+
+
+def setUpModule():
+    make_data_files(BAM_DATADIR)
+
+
+class TestPileupReadSelection(unittest.TestCase):
+    '''test pileup functionality.'''
+
+    samfilename = os.path.join(BAM_DATADIR, "ex1.bam")
+    fastafilename = os.path.join(BAM_DATADIR, "ex1.fa")
+
+    def setUp(self):
+
+        self.samfile = pysam.AlignmentFile(self.samfilename)
+        self.fastafile = pysam.FastaFile(self.fastafilename)
+
+    def tearDown(self):
+        self.samfile.close()
+        self.fastafile.close()
+
+    def check_equal(self, references, iterator):
+
+        for x, column in enumerate(iterator):
+            v = references[x][:-1].split("\t")
+            self.assertEqual(
+                len(v), 6,
+                "expected 6 values, got {}".format(v))
+            (contig, pos, reference_base,
+             read_bases, read_qualities, alignment_mapping_qualities) \
+                = v
+            self.assertEqual(int(pos) - 1, column.reference_pos)
+
+    def test_samtools_stepper(self):
+        refs = force_str(
+            pysam.samtools.mpileup(
+                "-f", self.fastafilename,
+                self.samfilename)).splitlines(True)
+        iterator = self.samfile.pileup(
+            stepper="samtools",
+            fastafile=self.fastafile)
+        self.check_equal(refs, iterator)
+
+    def test_all_stepper(self):
+        refs = force_str(
+            pysam.samtools.mpileup(
+                "-f", self.fastafilename,
+                "-A", "-B",
+                self.samfilename)).splitlines(True)
+
+        iterator = self.samfile.pileup(
+            stepper="all",
+            fastafile=self.fastafile)
+        self.check_equal(refs, iterator)
+
+    def test_ignore_overlaps(self):
+        refs = force_str(
+            pysam.samtools.mpileup(
+                "-f", self.fastafilename,
+                "-A", "-B", "-x",
+                self.samfilename)).splitlines(True)
+
+        iterator = self.samfile.pileup(
+            stepper="all",
+            fastafile=self.fastafile,
+            ignore_overlaps=False)
+        self.check_equal(refs, iterator)
+
+    def test_samtools_stepper_mapping_quality_threshold(self):
+        refs = force_str(
+            pysam.samtools.mpileup(
+                "-f", self.fastafilename,
+                "--min-MQ", "15",
+                self.samfilename)).splitlines(True)
+        iterator = self.samfile.pileup(
+            stepper="samtools",
+            fastafile=self.fastafile,
+            min_mapping_quality=15)
+        self.check_equal(refs, iterator)
+
+    def test_samtools_stepper_base_quality_threshold(self):
+        refs = force_str(
+            pysam.samtools.mpileup(
+                "-f", self.fastafilename,
+                "--min-BQ", "20",
+                self.samfilename)).splitlines(True)
+        iterator = self.samfile.pileup(
+            stepper="samtools",
+            fastafile=self.fastafile,
+            min_base_quality=20)
+        self.check_equal(refs, iterator)
+
+    def test_samtools_stepper_ignore_orphans(self):
+        refs = force_str(
+            pysam.samtools.mpileup(
+                "-f", self.fastafilename,
+                "--count-orphans",
+                self.samfilename)).splitlines(True)
+        iterator = self.samfile.pileup(
+            stepper="samtools",
+            fastafile=self.fastafile,
+            ignore_orphans=False)
+        self.check_equal(refs, iterator)
+
+    def test_samtools_stepper_redo_baq(self):
+        refs = force_str(
+            pysam.samtools.mpileup(
+                "-f", self.fastafilename,
+                "--redo-BAQ",
+                self.samfilename)).splitlines(True)
+        iterator = self.samfile.pileup(
+            stepper="samtools",
+            fastafile=self.fastafile,
+            redo_baq=True)
+        self.check_equal(refs, iterator)
+
+
+class TestPileupReadSelectionFastafile(TestPileupReadSelection):
+    '''test pileup functionality - backwards compatibility'''
+
+    samfilename = os.path.join(BAM_DATADIR, "ex1.bam")
+    fastafilename = os.path.join(BAM_DATADIR, "ex1.fa")
+
+    def setUp(self):
+
+        self.samfile = pysam.AlignmentFile(self.samfilename)
+        self.fastafile = pysam.Fastafile(self.fastafilename)
+
+
+class TestPileupQueryPosition(unittest.TestCase):
+
+    filename = "test_query_position.bam"
+
+    def testPileup(self):
+        last = {}
+        with pysam.AlignmentFile(os.path.join(BAM_DATADIR, self.filename)) as inf:
+            for col in inf.pileup():
+                for r in col.pileups:
+                    # print r.alignment.query_name
+                    # print r.query_position, r.query_position_or_next, r.is_del
+                    if r.is_del:
+                        self.assertEqual(r.query_position, None)
+                        self.assertEqual(r.query_position_or_next,
+                                         last[r.alignment.query_name] + 1)
+                    else:
+                        self.assertNotEqual(r.query_position, None)
+                        last[r.alignment.query_name] = r.query_position
+
+
+class TestPileupObjects(unittest.TestCase):
+
+    def setUp(self):
+        self.samfile = pysam.AlignmentFile(os.path.join(BAM_DATADIR, "ex1.bam"),
+                                           "rb")
+
+    def testPileupColumn(self):
+        for pcolumn1 in self.samfile.pileup(region="chr1:105-106"):
+            if pcolumn1.reference_pos == 104:
+                self.assertEqual(
+                    pcolumn1.reference_id, 0,
+                    "chromosome/target id mismatch in position 1: %s != %s" %
+                    (pcolumn1.reference_id, 0))
+                self.assertEqual(
+                    pcolumn1.reference_name, "chr1",
+                    "chromosome mismatch in position 1: %s != %s" %
+                    (pcolumn1.reference_name, "chr1"))
+                self.assertEqual(
+                    pcolumn1.reference_pos, 105 - 1,
+                    "position mismatch in position 1: %s != %s" %
+                    (pcolumn1.reference_pos, 105 - 1))
+                self.assertEqual(
+                    pcolumn1.nsegments, 1,
+                    "# reads mismatch in position 1: %s != %s" %
+                    (pcolumn1.nsegments, 1))
+                self.assertEqual(
+                    len(pcolumn1.pileups), 1,
+                    "# reads aligned to column mismatch in position 1"
+                    ": %s != %s" %
+                    (len(pcolumn1.pileups), 1))
+
+        for pcolumn2 in self.samfile.pileup(region="chr2:1480-1481"):
+            if pcolumn2.reference_pos == 1479:
+                self.assertEqual(
+                    pcolumn2.reference_id, 1,
+                    "chromosome/target id mismatch in position 1: %s != %s" %
+                    (pcolumn2.reference_id, 1))
+                self.assertEqual(
+                    pcolumn2.reference_name, "chr2",
+                    "chromosome mismatch in position 1: %s != %s" %
+                    (pcolumn2.reference_name, "chr2"))
+                self.assertEqual(
+                    pcolumn2.reference_pos, 1480 - 1,
+                    "position mismatch in position 1: %s != %s" %
+                    (pcolumn2.reference_pos, 1480 - 1))
+                self.assertEqual(
+                    pcolumn2.nsegments, 12,
+                    "# reads mismatch in position 1: %s != %s" %
+                    (pcolumn2.nsegments, 12))
+
+    def tearDown(self):
+        self.samfile.close()
+
+    def testIteratorOutOfScope(self):
+        '''test if exception is raised if pileup col is accessed after
+        iterator is exhausted.'''
+
+        max_n = 0
+        for pileupcol in self.samfile.pileup():
+            if max_n < pileupcol.n:
+                max_col = pileupcol
+                max_n = pileupcol.n
+
+        self.assertRaises(ValueError, getattr, max_col, "pileups")
+        self.assertRaises(ValueError, max_col.get_query_sequences)
+        self.assertRaises(ValueError, max_col.get_num_aligned)
+        self.assertRaises(ValueError, max_col.get_query_qualities)
+        self.assertRaises(ValueError, max_col.get_mapping_qualities)
+        self.assertRaises(ValueError, max_col.get_query_positions)
+        self.assertRaises(ValueError, max_col.get_query_names)
+
+
+class TestIteratorColumnBAM(unittest.TestCase):
+
+    '''test iterator column against contents of ex4.bam.'''
+
+    # note that samfile contains 1-based coordinates
+    # 1D means deletion with respect to reference sequence
+    #
+    mCoverages = {'chr1': [0] * 20 + [1] * 36 + [0] * (100 - 20 - 35),
+                  'chr2': [0] * 20 + [1] * 35 + [0] * (100 - 20 - 35),
+                  }
+
+    def setUp(self):
+        self.samfile = pysam.AlignmentFile(os.path.join(BAM_DATADIR, "ex4.bam"),
+                                           "rb")
+
+    def checkRange(self, contig, start=None, end=None, truncate=False):
+        '''compare results from iterator with those from samtools.'''
+        # check if the same reads are returned and in the same order
+        for column in self.samfile.pileup(
+                contig, start, end, truncate=truncate, min_base_quality=0):
+            if truncate:
+                self.assertGreaterEqual(column.reference_pos, start)
+                self.assertLess(column.reference_pos, end)
+            thiscov = len(column.pileups)
+            refcov = self.mCoverages[
+                self.samfile.getrname(column.reference_id)][column.reference_pos]
+            self.assertEqual(thiscov, refcov,
+                             "wrong coverage at pos %s:%i %i should be %i" % (
+                                 self.samfile.getrname(column.reference_id),
+                                 column.reference_pos, thiscov, refcov))
+
+    def testIterateAll(self):
+        '''check random access per contig'''
+        self.checkRange(None)
+
+    def testIteratePerContig(self):
+        '''check random access per contig'''
+        for contig in self.samfile.references:
+            self.checkRange(contig)
+
+    def testIterateRanges(self):
+        '''check random access per range'''
+        for contig, length in zip(
+                self.samfile.references, self.samfile.lengths):
+            for start in range(1, length, 90):
+                # this includes empty ranges
+                self.checkRange(contig, start, start + 90)
+
+    def testInverse(self):
+        '''test the inverse, is point-wise pileup accurate.'''
+        for contig, refseq in list(self.mCoverages.items()):
+            refcolumns = sum(refseq)
+            for pos, refcov in enumerate(refseq):
+                columns = list(self.samfile.pileup(contig, pos, pos + 1))
+                if refcov == 0:
+                    # if no read, no coverage
+                    self.assertEqual(
+                        len(columns),
+                        refcov,
+                        "wrong number of pileup columns returned for position %s:%i, %i should be %i" % (
+                            contig, pos,
+                            len(columns), refcov))
+                elif refcov == 1:
+                    # one read, all columns of the read are returned
+                    self.assertEqual(
+                        len(columns),
+                        refcolumns,
+                        "pileup incomplete at position %i: got %i, expected %i " %
+                        (pos, len(columns), refcolumns))
+
+    def testIterateTruncate(self):
+        '''check random access per range'''
+        for contig, length in zip(self.samfile.references,
+                                  self.samfile.lengths):
+            for start in range(1, length, 90):
+                # this includes empty ranges
+                self.checkRange(contig, start, start + 90, truncate=True)
+
+    def tearDown(self):
+        self.samfile.close()
+
+
+class TestIteratorColumn2(unittest.TestCase):
+
+    '''test iterator column against contents of ex1.bam.'''
+
+    def setUp(self):
+        self.samfile = pysam.AlignmentFile(
+            os.path.join(BAM_DATADIR, "ex1.bam"),
+            "rb")
+
+    def testStart(self):
+        # print self.samfile.fetch().next().reference_start
+        # print self.samfile.pileup().next().reference_start
+        pass
+
+    def testTruncate(self):
+        '''see issue 107.'''
+        # note that ranges in regions start from 1
+        p = self.samfile.pileup(region='chr1:170-172', truncate=True)
+        columns = [x.reference_pos for x in p]
+        self.assertEqual(len(columns), 3)
+        self.assertEqual(columns, [169, 170, 171])
+
+        p = self.samfile.pileup('chr1', 169, 172, truncate=True)
+        columns = [x.reference_pos for x in p]
+
+        self.assertEqual(len(columns), 3)
+        self.assertEqual(columns, [169, 170, 171])
+
+    def testAccessOnClosedIterator(self):
+        '''see issue 131
+
+        Accessing pileup data after iterator has closed.
+        '''
+        pcolumn = self.samfile.pileup('chr1', 170, 180).__next__()
+        self.assertRaises(ValueError, getattr, pcolumn, "pileups")
+
+    def testStr(self):
+        '''test if PileupRead can be printed.'''
+        iter = self.samfile.pileup('chr1', 170, 180)
+        pcolumn = iter.__next__()
+        s = str(pcolumn)
+        self.assertEqual(len(s.split("\n")), 2)
+
+
+@unittest.skipIf(not IS_PYTHON3,
+                 "tests requires at least python3 for subprocess context manager")
+class PileUpColumnTests(unittest.TestCase):
+
+    fn = os.path.join(BAM_DATADIR, "ex2.bam")
+    fn_fasta = os.path.join(BAM_DATADIR, "ex1.fa")
+    
+    def test_pileup_depths_are_equal(self):
+        samtools_result = PileupTestUtils.build_depth_with_samtoolspipe(self.fn)
+        pysam_result = PileupTestUtils.build_depth_with_filter_with_pysam(self.fn)
+        self.assertEqual(pysam_result, samtools_result)
+
+    def test_pileup_query_bases_without_reference_are_equal(self):
+        samtools_result = PileupTestUtils.build_query_bases_with_samtoolspipe(self.fn)
+        pysam_result = PileupTestUtils.build_query_bases_with_pysam(self.fn)
+        self.assertEqual(["".join(x) for x in pysam_result], samtools_result)
+
+    def test_pileup_query_bases_with_reference_are_equal(self):
+        samtools_result = PileupTestUtils.build_query_bases_with_samtoolspipe(self.fn, "-f", self.fn_fasta)
+        with pysam.FastaFile(self.fn_fasta) as fasta:
+            pysam_result = PileupTestUtils.build_query_bases_with_pysam(self.fn, fastafile=fasta, stepper="samtools")
+        self.assertEqual(["".join(x) for x in pysam_result], samtools_result)
+        
+    def test_pileup_query_qualities_are_equal(self):
+        samtools_result = PileupTestUtils.build_query_qualities_with_samtoolspipe(self.fn)
+        pysam_result = PileupTestUtils.build_query_qualities_with_pysam(self.fn)
+        pysam_result = [
+            [chr(min(126, x + 33)) for x in l] for l in pysam_result]
+        self.assertEqual("".join(flatten_nested_list(pysam_result)),
+                         "".join(flatten_nested_list(samtools_result)))
+
+    def test_pileup_mapping_qualities_are_equal(self):
+        samtools_result = PileupTestUtils.build_mapping_qualities_with_samtoolspipe(self.fn)
+        pysam_result = PileupTestUtils.build_mapping_qualities_with_pysam(self.fn)
+        # convert to chars
+        pysam_result = [
+            [chr(min(126, x + 33)) for x in l] for l in pysam_result]
+
+        self.assertEqual("".join(flatten_nested_list(pysam_result)),
+                         "".join(flatten_nested_list(samtools_result)))
+
+    def test_pileup_query_qualities_from_pileups_are_equal(self):
+        samtools_result = PileupTestUtils.build_query_qualities_with_samtoolspipe(self.fn)
+        pysam_result = PileupTestUtils.build_query_qualities_with_pysam_pileups(self.fn)
+        pysam_result = [
+            "".join([chr(min(126, x + 33)) for x in l]) for l in pysam_result]
+
+        self.assertEqual(pysam_result, samtools_result)
+
+
+if __name__ == "__main__":
+    unittest.main()
diff --git a/tests/AlignmentFile_bench.py b/tests/AlignmentFile_bench.py
new file mode 100644
index 0000000..275a5fb
--- /dev/null
+++ b/tests/AlignmentFile_bench.py
@@ -0,0 +1,60 @@
+"""Benchmarking module for AlignmentFile functionality"""
+import os
+import subprocess
+import pysam
+
+
+from TestUtils import BAM_DATADIR
+
+
+def count_number_lines_with_samtools(fn):
+    os.system("samtools view {} | wc -l > /dev/null".format(fn))
+    return 3270
+
+
+def count_number_lines_with_samtoolspipe(fn):
+    with subprocess.Popen(["samtools", "view", fn],
+                          stdin=subprocess.PIPE,
+                          stdout=subprocess.PIPE) as proc:
+        return len(proc.stdout.readlines())
+
+
+def count_number_lines_with_pysam(*args, **kwargs):
+    with pysam.AlignmentFile(*args, **kwargs) as inf:
+        return len(list(inf.fetch()))
+
+
+def test_count_number_lines_from_sam_with_samtools(benchmark):
+    result = benchmark(count_number_lines_with_samtools,
+                       os.path.join(BAM_DATADIR, "ex2.sam"))
+    assert result == 3270
+
+
+def test_count_number_lines_from_sam_with_samtoolspipe(benchmark):
+    result = benchmark(count_number_lines_with_samtoolspipe,
+                       os.path.join(BAM_DATADIR, "ex2.sam"))
+    assert result == 3270
+
+
+def test_count_number_lines_from_sam_with_pysam(benchmark):
+    result = benchmark(count_number_lines_with_pysam,
+                       os.path.join(BAM_DATADIR, "ex2.sam"), "r")
+    assert result == 3270
+
+
+def test_count_number_lines_from_bam_with_samtools(benchmark):
+    result = benchmark(count_number_lines_with_samtools,
+                       os.path.join(BAM_DATADIR, "ex2.bam"))
+    assert result == 3270
+
+
+def test_count_number_lines_from_bam_with_samtoolspipe(benchmark):
+    result = benchmark(count_number_lines_with_samtoolspipe,
+                       os.path.join(BAM_DATADIR, "ex2.bam"))
+    assert result == 3270
+
+
+def test_count_number_lines_from_bam_with_pysam(benchmark):
+    result = benchmark(count_number_lines_with_pysam,
+                       os.path.join(BAM_DATADIR, "ex2.bam"))
+    assert result == 3270
diff --git a/tests/AlignmentFile_test.py b/tests/AlignmentFile_test.py
new file mode 100644
index 0000000..61531f4
--- /dev/null
+++ b/tests/AlignmentFile_test.py
@@ -0,0 +1,2431 @@
+#!/usr/bin/env python
+'''unit testing code for pysam.
+
+Execute in the :file:`tests` directory as it requires the Makefile
+and data files located there.
+'''
+
+import unittest
+import pytest
+import os
+import shutil
+import sys
+import collections
+import subprocess
+import logging
+import array
+if sys.version_info.major >= 3:
+    from io import StringIO
+else:
+    from StringIO import StringIO
+
+from functools import partial
+
+import pysam
+import pysam.samtools
+from TestUtils import checkBinaryEqual, checkGZBinaryEqual, check_url, \
+    check_samtools_view_equal, checkFieldEqual, force_str, \
+    get_temp_filename, make_data_files, BAM_DATADIR
+
+
+def setUpModule():
+    make_data_files(BAM_DATADIR)
+
+
+##################################################
+#
+# Detailed test of file contents
+#
+# Data are read either through file based iterator
+# access (BasicTestBAMFromFile) or by calling fetch
+# without coordinates (BasicTestBAMFromFetch)
+##################################################
+class BasicTestBAMFromFetch(unittest.TestCase):
+
+    '''basic first test - detailed testing
+    if information in file is consistent
+    with information in AlignedSegment object.'''
+
+    def setUp(self):
+        self.samfile = pysam.AlignmentFile(
+            os.path.join(BAM_DATADIR, "ex3.bam"),
+            "rb")
+        self.reads = list(self.samfile.fetch())
+
+    def tearDown(self):
+        self.samfile.close()
+
+    def testARqname(self):
+        self.assertEqual(self.reads[0].query_name,
+                         "read_28833_29006_6945")
+        self.assertEqual(self.reads[1].query_name,
+                         "read_28701_28881_323b")
+
+    def testARflag(self):
+        self.assertEqual(self.reads[0].flag, 99)
+        self.assertEqual(self.reads[1].flag, 147)
+
+    def testARrname(self):
+        self.assertEqual(self.reads[0].reference_id, 0)
+        self.assertEqual(self.reads[1].reference_id, 1)
+
+    def testARpos(self):
+        self.assertEqual(self.reads[0].reference_start, 33 - 1)
+        self.assertEqual(self.reads[1].reference_start, 88 - 1)
+
+    def testARmapq(self):
+        self.assertEqual(self.reads[0].mapping_quality, 20)
+        self.assertEqual(self.reads[1].mapping_quality, 30)
+
+    def testARcigar(self):
+        self.assertEqual(self.reads[0].cigartuples, [(0, 10), (2, 1), (0, 25)])
+        self.assertEqual(self.reads[1].cigartuples, [(0, 35)])
+
+    def testARcigarstring(self):
+        self.assertEqual(self.reads[0].cigarstring, '10M1D25M')
+        self.assertEqual(self.reads[1].cigarstring, '35M')
+
+    def testARmrnm(self):
+        self.assertEqual(self.reads[0].next_reference_id, 0)
+        self.assertEqual(self.reads[1].next_reference_id, 1)
+        self.assertEqual(self.reads[0].next_reference_id, 0)
+        self.assertEqual(self.reads[1].next_reference_id, 1)
+
+    def testARmpos(self):
+        self.assertEqual(self.reads[0].next_reference_start, 200 - 1)
+        self.assertEqual(self.reads[1].next_reference_start, 500 - 1)
+        self.assertEqual(self.reads[0].next_reference_start, 200 - 1)
+        self.assertEqual(self.reads[1].next_reference_start, 500 - 1)
+
+    def testARQueryLength(self):
+        self.assertEqual(
+            self.reads[0].query_length, 35,
+            "insert size mismatch in read 1: %s != %s" %
+            (self.reads[0].query_length, 35))
+        self.assertEqual(
+            self.reads[1].query_length, 35,
+            "insert size mismatch in read 2: %s != %s" %
+            (self.reads[1].query_length, 35))
+        self.assertEqual(
+            self.reads[0].query_length, 35,
+            "insert size mismatch in read 1: %s != %s" %
+            (self.reads[0].query_length, 35))
+        self.assertEqual(
+            self.reads[1].query_length, 35,
+            "insert size mismatch in read 2: %s != %s" %
+            (self.reads[1].query_length, 35))
+
+    def testARseq(self):
+        self.assertEqual(
+            self.reads[0].query_sequence,
+            "AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG")
+        self.assertEqual(
+            self.reads[1].query_sequence,
+            "ACCTATATCTTGGCCTTGGCCGATGCGGCCTTGCA")
+        self.assertEqual(
+            self.reads[3].query_sequence,
+            "AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG")
+
+    def testARqual(self):
+        self.assertEqual(
+            pysam.qualities_to_qualitystring(self.reads[0].query_qualities),
+            "<<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<<")
+        self.assertEqual(
+            pysam.qualities_to_qualitystring(self.reads[1].query_qualities),
+            "<<<<<;<<<<7;:<<<6;<<<<<<<<<<<<7<<<<")
+        self.assertEqual(
+            pysam.qualities_to_qualitystring(self.reads[3].query_qualities),
+            "<<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<<")
+
+    def testARquery(self):
+        self.assertEqual(
+            self.reads[0].query_alignment_sequence,
+            "AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG",
+            "query mismatch in read 1: %s != %s" %
+            (self.reads[0].query_alignment_sequence,
+             "AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG"))
+        self.assertEqual(
+            self.reads[1].query_alignment_sequence,
+            "ACCTATATCTTGGCCTTGGCCGATGCGGCCTTGCA",
+            "query size mismatch in read 2: %s != %s" %
+            (self.reads[1].query_alignment_sequence,
+             "ACCTATATCTTGGCCTTGGCCGATGCGGCCTTGCA"))
+        self.assertEqual(
+            self.reads[3].query_alignment_sequence,
+            "TAGCTAGCTACCTATATCTTGGTCTT",
+            "query mismatch in read 4: %s != %s" %
+            (self.reads[3].query_alignment_sequence,
+             "TAGCTAGCTACCTATATCTTGGTCTT"))
+
+    def testARqqual(self):
+        self.assertEqual(
+            pysam.qualities_to_qualitystring(
+                self.reads[0].query_alignment_qualities),
+            "<<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<<",
+            "qquality string mismatch in read 1: %s != %s" %
+            (pysam.qualities_to_qualitystring(self.reads[0].query_alignment_qualities),
+             "<<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<<"))
+        self.assertEqual(
+            pysam.qualities_to_qualitystring(
+                self.reads[1].query_alignment_qualities),
+            "<<<<<;<<<<7;:<<<6;<<<<<<<<<<<<7<<<<",
+            "qquality string mismatch in read 2: %s != %s" %
+            (pysam.qualities_to_qualitystring(self.reads[1].query_alignment_qualities),
+             "<<<<<;<<<<7;:<<<6;<<<<<<<<<<<<7<<<<"))
+        self.assertEqual(
+            pysam.qualities_to_qualitystring(
+                self.reads[3].query_alignment_qualities),
+            "<<<<<<<<<<<<<<<<<:<9/,&,22",
+            "qquality string mismatch in read 3: %s != %s" %
+            (pysam.qualities_to_qualitystring(self.reads[3].query_alignment_qualities),
+             "<<<<<<<<<<<<<<<<<:<9/,&,22"))
+
+    def testPresentOptionalFields(self):
+        self.assertEqual(
+            self.reads[0].opt('NM'), 22,
+            "optional field mismatch in read 1, NM: %s != %s" %
+            (self.reads[0].opt('NM'), 22))
+        self.assertEqual(
+            self.reads[0].opt('RG'), 'L1',
+            "optional field mismatch in read 1, RG: %s != %s" %
+            (self.reads[0].opt('RG'), 'L1'))
+        self.assertEqual(
+            self.reads[1].opt('RG'), 'L2',
+            "optional field mismatch in read 2, RG: %s != %s" %
+            (self.reads[1].opt('RG'), 'L2'))
+        self.assertEqual(
+            self.reads[1].opt('MF'), 18,
+            "optional field mismatch in read 2, MF: %s != %s" %
+            (self.reads[1].opt('MF'), 18))
+
+    def testPairedBools(self):
+        self.assertEqual(self.reads[0].is_paired, True, "is paired mismatch in read 1: %s != %s" % (
+            self.reads[0].is_paired, True))
+        self.assertEqual(self.reads[1].is_paired, True, "is paired mismatch in read 2: %s != %s" % (
+            self.reads[1].is_paired, True))
+        self.assertEqual(self.reads[0].is_proper_pair, True, "is proper pair mismatch in read 1: %s != %s" % (
+            self.reads[0].is_proper_pair, True))
+        self.assertEqual(self.reads[1].is_proper_pair, True, "is proper pair mismatch in read 2: %s != %s" % (
+            self.reads[1].is_proper_pair, True))
+
+    def testTags(self):
+        self.assertEqual(self.reads[0].tags,
+                         [('NM', 22), ('RG', 'L1'),
+                          ('PG', 'P1'), ('XT', 'U')])
+        self.assertEqual(self.reads[1].tags,
+                         [('MF', 18), ('RG', 'L2'),
+                          ('PG', 'P2'), ('XT', 'R')])
+
+    def testOpt(self):
+        self.assertEqual(self.reads[0].opt("XT"), "U")
+        self.assertEqual(self.reads[1].opt("XT"), "R")
+
+
+class BasicTestSAMFromFetch(BasicTestBAMFromFetch):
+
+    def setUp(self):
+        self.samfile = pysam.AlignmentFile(
+            os.path.join(BAM_DATADIR, "ex3.sam"),
+            "r")
+        self.reads = list(self.samfile.fetch())
+
+
+class BasicTestCRAMFromFetch(BasicTestBAMFromFetch):
+
+    def setUp(self):
+        self.samfile = pysam.AlignmentFile(
+            os.path.join(BAM_DATADIR, "ex3.cram"),
+            "rc")
+        self.reads = list(self.samfile.fetch())
+
+    def testTags(self):
+        self.assertEqual(
+            sorted(self.reads[0].tags),
+            sorted([('RG', 'L1'),
+                    ('NM', 22),
+                    ('MD', '0C0T1G1C0C0A1G0^G0C1C1G1A0T2G0G0G0A1C1G1G1A2C0'),
+                    ('PG', 'P1'),
+                    ('XT', 'U'),
+                    ]))
+        self.assertEqual(
+            sorted(self.reads[1].tags),
+            sorted([('RG', 'L2'),
+                    ('NM', 26),
+                    ('MD',
+                     '1G0A0A1G1G0G2C0A0G0A0A0C0T0T0G0A0A0G0A0C0A0A1T2C0T0T1'),
+                    ('MF', 18),
+                    ('PG', 'P2'),
+                    ('XT', 'R')]))
+
+    def testPresentOptionalFields(self):
+        self.assertEqual(
+            self.reads[0].opt('NM'), 22,
+            "optional field mismatch in read 1, NM: %s != %s" %
+            (self.reads[0].opt('NM'), 22))
+        self.assertEqual(
+            self.reads[0].opt('RG'), 'L1',
+            "optional field mismatch in read 1, RG: %s != %s" %
+            (self.reads[0].opt('RG'), 'L1'))
+        self.assertEqual(
+            self.reads[1].opt('RG'), 'L2',
+            "optional field mismatch in read 2, RG: %s != %s" %
+            (self.reads[1].opt('RG'), 'L2'))
+        self.assertEqual(
+            self.reads[1].opt('MF'), 18,
+            "optional field mismatch in read 2, MF: %s != %s" %
+            (self.reads[1].opt('MF'), 18))
+
+
+class BasicTestSAMFromFilename(BasicTestBAMFromFetch):
+
+    def setUp(self):
+        self.samfile = pysam.AlignmentFile(
+            os.path.join(BAM_DATADIR, "ex3.sam"),
+            "r")
+        self.reads = [r for r in self.samfile]
+
+
+class BasicTestCRAMFromFilename(BasicTestCRAMFromFetch):
+
+    def setUp(self):
+        self.samfile = pysam.AlignmentFile(
+            os.path.join(BAM_DATADIR, "ex3.cram"),
+            "rc")
+        self.reads = [r for r in self.samfile]
+
+
+class BasicTestBAMFromFilename(BasicTestBAMFromFetch):
+
+    def setUp(self):
+        self.samfile = pysam.AlignmentFile(
+            os.path.join(BAM_DATADIR, "ex3.bam"),
+            "rb")
+        self.reads = [r for r in self.samfile]
+
+
+class BasicTestBAMFromFile(BasicTestBAMFromFetch):
+
+    def setUp(self):
+        with open(os.path.join(BAM_DATADIR, "ex3.bam")) as f:
+            self.samfile = pysam.AlignmentFile(
+                f, "rb")
+        self.reads = [r for r in self.samfile]
+
+
+class BasicTestBAMFromFileNo(BasicTestBAMFromFetch):
+
+    def setUp(self):
+        with open(os.path.join(BAM_DATADIR, "ex3.bam")) as f:
+            self.samfile = pysam.AlignmentFile(
+                f.fileno(), "rb")
+        self.reads = [r for r in self.samfile]
+
+
+class BasicTestSAMFromFile(BasicTestBAMFromFetch):
+
+    def setUp(self):
+        with open(os.path.join(BAM_DATADIR, "ex3.sam")) as f:
+            self.samfile = pysam.AlignmentFile(
+                f, "r")
+        self.reads = [r for r in self.samfile]
+
+
+class BasicTestSAMFromFileNo(BasicTestBAMFromFetch):
+
+    def setUp(self):
+        with open(os.path.join(BAM_DATADIR, "ex3.sam")) as f:
+            self.samfile = pysam.AlignmentFile(
+                f.fileno(), "r")
+        self.reads = [r for r in self.samfile]
+
+
+class BasicTestCRAMFromFile(BasicTestCRAMFromFetch):
+
+    def setUp(self):
+        with open(os.path.join(BAM_DATADIR, "ex3.cram")) as f:
+            self.samfile = pysam.AlignmentFile(f, "rc")
+        self.reads = [r for r in self.samfile]
+
+
+class BasicTestCRAMFromFileNo(BasicTestCRAMFromFetch):
+
+    def setUp(self):
+        with open(os.path.join(BAM_DATADIR, "ex3.cram")) as f:
+            self.samfile = pysam.AlignmentFile(
+                f.fileno(), "rc")
+        self.reads = [r for r in self.samfile]
+
+
+class BasicTestSAMFromStringIO(BasicTestBAMFromFetch):
+
+    def testRaises(self):
+        statement = "samtools view -h {}".format(
+            os.path.join(BAM_DATADIR, "ex3.bam"))
+        stdout = subprocess.check_output(statement.split(" "))
+        bam = StringIO()
+        if sys.version_info.major >= 3:
+            bam.write(stdout.decode('ascii'))
+        else:
+            bam.write(stdout)
+        bam.seek(0)
+        self.assertRaises(NotImplementedError,
+                          pysam.AlignmentFile, bam)
+        # self.reads = [r for r in samfile]
+
+
+##################################################
+#
+# Test of basic File I/O
+#
+# * format conversions
+# * reading with/without index
+# * reading from closed files
+#
+##################################################
+class TestIO(unittest.TestCase):
+
+    '''check if reading samfile and writing a samfile
+    are consistent.'''
+
+    def checkEcho(self,
+                  input_filename,
+                  reference_filename,
+                  output_filename,
+                  input_mode,
+                  output_mode,
+                  sequence_filename=None,
+                  use_template=True,
+                  checkf=checkBinaryEqual,
+                  **kwargs):
+        '''iterate through *input_filename* writing to
+        *output_filename* and comparing the output to
+        *reference_filename*.
+
+        The files are opened according to the *input_mode* and
+        *output_mode*.
+
+        If *use_template* is set, the header is copied from infile
+        using the template mechanism, otherwise target names and
+        lengths are passed explicitly.
+
+        The *checkf* is used to determine if the files are
+        equal.
+        '''
+
+        with pysam.AlignmentFile(
+                os.path.join(BAM_DATADIR, input_filename),
+                input_mode) as infile:
+
+            if "b" in input_mode:
+                self.assertTrue(infile.is_bam)
+                self.assertFalse(infile.is_cram)
+            elif "c" in input_mode:
+                self.assertFalse(infile.is_bam)
+                self.assertTrue(infile.is_cram)
+            else:
+                self.assertFalse(infile.is_cram)
+                self.assertFalse(infile.is_bam)
+
+            if use_template:
+                outfile = pysam.AlignmentFile(
+                    output_filename,
+                    output_mode,
+                    reference_filename=sequence_filename,
+                    template=infile, **kwargs)
+            else:
+                outfile = pysam.AlignmentFile(
+                    output_filename,
+                    output_mode,
+                    reference_names=infile.references,
+                    reference_lengths=infile.lengths,
+                    reference_filename=sequence_filename,
+                    add_sq_text=False,
+                    **kwargs)
+
+            iter = infile.fetch()
+
+            for x in iter:
+                outfile.write(x)
+
+            outfile.close()
+
+        self.assertTrue(checkf(
+            os.path.join(BAM_DATADIR, reference_filename),
+            output_filename),
+            "files %s and %s are not the same" %
+            (reference_filename,
+             output_filename))
+
+        os.unlink(output_filename)
+
+    def testSAM2SAM(self):
+        self.checkEcho("ex2.sam",
+                       "ex2.sam",
+                       "tmp_ex2.sam",
+                       "r", "wh")
+
+    def testSAM2SAMWithoutHeader(self):
+        self.checkEcho("ex2.sam",
+                       "ex1.sam",
+                       "tmp_ex2.sam",
+                       "r", "w",
+                       add_sam_header=False)
+
+    def testBAM2BAM(self):
+        self.checkEcho("ex2.bam",
+                       "ex2.bam",
+                       "tmp_ex2.bam",
+                       "rb", "wb",
+                       checkf=checkGZBinaryEqual)
+
+    def testCRAM2CRAM(self):
+        # in some systems different reference sequence paths might be
+        # embedded in the CRAM files which will result in different headers
+        # see #542
+        self.checkEcho("ex2.cram",
+                       "ex2.cram",
+                       "tmp_ex2.cram",
+                       "rc", "wc",
+                       sequence_filename=os.path.join(BAM_DATADIR, "ex1.fa"),
+                       checkf=partial(
+                           check_samtools_view_equal,
+                           without_header=True))
+
+    def testSAM2BAM(self):
+        self.checkEcho("ex2.sam",
+                       "ex2.bam",
+                       "tmp_ex2.bam",
+                       "r", "wb",
+                       checkf=checkGZBinaryEqual)
+
+    def testBAM2SAM(self):
+        self.checkEcho("ex2.bam",
+                       "ex2.sam",
+                       "tmp_ex2.sam",
+                       "rb", "wh")
+
+    def testBAM2CRAM(self):
+        # ignore header (md5 sum)
+        self.checkEcho("ex2.bam",
+                       "ex2.cram",
+                       "tmp_ex2.cram",
+                       "rb", "wc",
+                       sequence_filename=os.path.join(BAM_DATADIR, "ex1.fa"),
+                       checkf=partial(
+                           check_samtools_view_equal,
+                           without_header=True))
+
+    def testCRAM2BAM(self):
+        # ignore header (md5 sum)
+        self.checkEcho("ex2.cram",
+                       "ex2.bam",
+                       "tmp_ex2.bam",
+                       "rc", "wb",
+                       sequence_filename=os.path.join(BAM_DATADIR, "ex1.fa"),
+                       checkf=partial(
+                           check_samtools_view_equal,
+                           without_header=True))
+
+    def testSAM2CRAM(self):
+        self.checkEcho("ex2.sam",
+                       "ex2.cram",
+                       "tmp_ex2.cram",
+                       "r", "wc",
+                       sequence_filename=os.path.join(BAM_DATADIR, "ex1.fa"),
+                       checkf=partial(
+                           check_samtools_view_equal,
+                           without_header=True))
+
+    def testCRAM2SAM(self):
+        self.checkEcho("ex2.cram",
+                       "ex2.sam",
+                       "tmp_ex2.sam",
+                       "rc", "wh",
+                       sequence_filename=os.path.join(BAM_DATADIR, "ex1.fa"),
+                       checkf=partial(
+                           check_samtools_view_equal,
+                           without_header=True))
+
+    # Disabled - should work, files are not binary equal, but are
+    # non-binary equal:
+    # diff <(samtools view pysam_ex1.bam) <(samtools view pysam_data/ex1.bam)
+    # def testReadWriteBamWithTargetNames(self):
+    #     input_filename = "ex1.bam"
+    #     output_filename = "pysam_ex1.bam"
+    #     reference_filename = "ex1.bam"
+
+    #     self.checkEcho(input_filename, reference_filename, output_filename,
+    #                    "rb", "wb", use_template=False)
+
+    def testReadSamWithoutTargetNames(self):
+        '''see issue 104.'''
+        input_filename = os.path.join(
+            BAM_DATADIR,
+            "example_unmapped_reads_no_sq.sam")
+
+        # raise exception in default mode
+        self.assertRaises(ValueError,
+                          pysam.AlignmentFile,
+                          input_filename,
+                          "r")
+
+        # raise exception if no SQ files
+        self.assertRaises(ValueError,
+                          pysam.AlignmentFile,
+                          input_filename, "r",
+                          check_header=True)
+
+        with pysam.AlignmentFile(
+                input_filename,
+                check_header=False,
+                check_sq=False) as infile:
+            result = list(infile.fetch(until_eof=True))
+            self.assertEqual(2, len(result))
+
+    def testReadBamWithoutTargetNames(self):
+        '''see issue 104.'''
+        input_filename = os.path.join(
+            BAM_DATADIR, "example_unmapped_reads_no_sq.bam")
+
+        # raise exception in default mode
+        self.assertRaises(ValueError,
+                          pysam.AlignmentFile,
+                          input_filename,
+                          "r")
+
+        # raise exception if no SQ files
+        self.assertRaises(ValueError,
+                          pysam.AlignmentFile,
+                          input_filename,
+                          "r",
+                          check_header=True)
+
+        with pysam.AlignmentFile(
+                input_filename, check_sq=False) as infile:
+            result = list(infile.fetch(until_eof=True))
+
+    def test_fail_read_sam_without_header(self):
+        input_filename = os.path.join(BAM_DATADIR, "ex1.sam")
+
+        self.assertRaises(ValueError,
+                          pysam.AlignmentFile,
+                          input_filename,
+                          "r")
+
+    def test_pass_read_sam_without_header_with_refs(self):
+        with pysam.AlignmentFile(os.path.join(BAM_DATADIR, "ex1.sam"),
+                                 "r",
+                                 reference_names=["chr1", "chr2"],
+                                 reference_lengths=[1575, 1584]) as samfile:
+            self.assertEqual(len(list(samfile.fetch(until_eof=True))), 3270)
+
+    def test_pass_read_sam_with_header_without_header_check(self):
+        with pysam.AlignmentFile(os.path.join(BAM_DATADIR, "ex2.sam"),
+                                 "r", check_header=False) as samfile:
+            self.assertEqual(len(list(samfile.fetch(until_eof=True))), 3270)
+
+    def test_fail_when_reading_unformatted_files(self):
+        '''test reading from a file that is not bam/sam formatted'''
+        input_filename = os.path.join(BAM_DATADIR, 'Makefile')
+
+        self.assertRaises(ValueError,
+                          pysam.AlignmentFile,
+                          input_filename,
+                          "rb")
+
+        self.assertRaises(ValueError,
+                          pysam.AlignmentFile,
+                          input_filename,
+                          "r")
+
+    def testBAMWithoutAlignedSegments(self):
+        '''see issue 117'''
+        input_filename = os.path.join(BAM_DATADIR, "test_unaligned.bam")
+        samfile = pysam.AlignmentFile(input_filename,
+                                      "rb",
+                                      check_sq=False)
+        samfile.fetch(until_eof=True)
+
+    def testBAMWithShortBAI(self):
+        '''see issue 116'''
+        input_filename = os.path.join(BAM_DATADIR, "example_bai.bam")
+        samfile = pysam.AlignmentFile(input_filename,
+                                      "rb",
+                                      check_sq=False)
+        samfile.fetch('chr2')
+
+    def testFetchFromClosedFile(self):
+
+        samfile = pysam.AlignmentFile(
+            os.path.join(BAM_DATADIR, "ex1.bam"),
+            "rb")
+        samfile.close()
+        self.assertRaises(ValueError, samfile.fetch, 'chr1', 100, 120)
+
+    def testFetchFromClosedFileObject(self):
+
+        f = open(os.path.join(BAM_DATADIR, "ex1.bam"))
+        samfile = pysam.AlignmentFile(f, "rb")
+        f.close()
+        self.assertTrue(f.closed)
+        # access to Samfile still works
+        self.checkEcho("ex1.bam",
+                       "ex1.bam",
+                       "tmp_ex1.bam",
+                       "rb", "wb",
+                       checkf=checkGZBinaryEqual)
+
+        f = open(os.path.join(BAM_DATADIR, "ex1.bam"))
+        samfile = pysam.AlignmentFile(f, "rb")
+        self.assertFalse(f.closed)
+        samfile.close()
+        # python file needs to be closed separately
+        self.assertFalse(f.closed)
+
+    def test_accessing_attributes_in_closed_file_raises_errors(self):
+        '''test that access to a closed samfile raises ValueError.'''
+
+        samfile = pysam.AlignmentFile(os.path.join(BAM_DATADIR, "ex1.bam"),
+                                      "rb")
+        samfile.close()
+            
+        self.assertRaises(ValueError, samfile.fetch, 'chr1', 100, 120)
+        self.assertRaises(ValueError, samfile.pileup, 'chr1', 100, 120)
+        self.assertRaises(ValueError, samfile.getrname, 0)
+        # TODO
+        self.assertRaises(ValueError, samfile.tell)
+        self.assertRaises(ValueError, samfile.seek, 0)
+        self.assertRaises(ValueError, getattr, samfile, "nreferences")
+        self.assertRaises(ValueError, getattr, samfile, "references")
+        self.assertRaises(ValueError, getattr, samfile, "lengths")
+
+        self.assertEqual(samfile.header, None)
+        # write on closed file
+        self.assertEqual(0, samfile.write(None))
+
+    def test_header_available_after_closing_file(self):
+
+        def load_bam():
+            with pysam.AlignmentFile(os.path.join(BAM_DATADIR, "ex1.bam"), "rb") as inf:
+                header = inf.header
+            return header
+
+        header = load_bam()
+        self.assertTrue(header)
+        self.assertEqual(header.nreferences, 2)
+        self.assertEqual(header.references, ("chr1", "chr2"))
+
+    def test_reference_name_available_after_closing_file(self):
+        """read tids can be mapped to references after AlignmentFile has been closed.
+        
+        see issue #517"""
+        
+        def load_bam():
+            with pysam.AlignmentFile(os.path.join(BAM_DATADIR, "ex1.bam"), "rb") as inf:
+                read = next(inf)
+            return read
+
+        read = load_bam()
+        self.assertEqual(read.reference_name, "chr1")
+        
+    # TODO
+    # def testReadingFromSamFileWithoutHeader(self):
+    #     '''read from samfile without header.
+    #     '''
+    #     samfile = pysam.AlignmentFile(os.path.join(BAM_DATADIR, "ex7.sam"),
+    #                             check_header=False,
+    #                             check_sq=False)
+    #     self.assertRaises(NotImplementedError, samfile.__iter__)
+
+    def testReadingFromFileWithoutIndex(self):
+        '''read from bam file without index.'''
+
+        dest = get_temp_filename("tmp_ex2.bam")
+        shutil.copyfile(os.path.join(BAM_DATADIR, "ex2.bam"),
+                        dest)
+        samfile = pysam.AlignmentFile(dest,
+                                      "rb")
+        self.assertRaises(ValueError, samfile.fetch)
+        self.assertEqual(
+            len(list(samfile.fetch(until_eof=True))),
+            3270)
+        os.unlink(dest)
+
+    # def testReadingUniversalFileMode(self):
+    #     '''read from samfile without header.
+    #     '''
+
+    #     input_filename = "ex2.sam"
+    #     output_filename = "pysam_ex2.sam"
+    #     reference_filename = "ex1.sam"
+
+    #     self.checkEcho(input_filename,
+    #                    reference_filename,
+    #                    output_filename,
+    #                    "rU", "w")
+
+    def testHead(self):
+        '''test IteratorRowHead'''
+        samfile = pysam.AlignmentFile(os.path.join(BAM_DATADIR, "ex1.bam"),
+                                      "rb")
+        l10 = list(samfile.head(10))
+        l100 = list(samfile.head(100))
+        self.assertEqual(len(l10), 10)
+        self.assertEqual(len(l100), 100)
+        self.assertEqual(list(map(str, l10)),
+                         list(map(str, l100[:10])))
+
+    def testWriteUncompressedBAMFile(self):
+        '''read from uncompressed BAM file, see issue #43'''
+
+        input_filename = "ex2.sam"
+        output_filename = "pysam_uncompressed.bam"
+        reference_filename = "uncompressed.bam"
+
+        self.checkEcho(input_filename,
+                       reference_filename,
+                       output_filename,
+                       "r", "wb0")
+
+        self.checkEcho(input_filename,
+                       reference_filename,
+                       output_filename,
+                       "r", "wbu")
+
+    def testEmptyBAM(self):
+        samfile = pysam.Samfile(os.path.join(BAM_DATADIR, "empty.bam"),
+                                "rb")
+        self.assertEqual(samfile.mapped, 0)
+        self.assertEqual(samfile.unmapped, 0)
+        self.assertEqual(samfile.nocoordinate, 0)
+
+    def testEmptyWithHeaderBAM(self):
+        self.assertRaises(
+            ValueError,
+            pysam.Samfile,
+            os.path.join(BAM_DATADIR, "example_empty_with_header.bam"),
+            "rb")
+
+        samfile = pysam.Samfile(
+            os.path.join(BAM_DATADIR, "example_empty_with_header.bam"),
+            "rb",
+            check_sq=False)
+        self.assertEqual(samfile.mapped, 0)
+        self.assertEqual(samfile.unmapped, 0)
+        self.assertEqual(samfile.nocoordinate, 0)
+        self.assertEqual([], list(samfile.fetch()))
+
+    def testOpenFromFilename(self):
+
+        samfile = pysam.AlignmentFile(
+            filename=os.path.join(BAM_DATADIR, "ex1.bam"),
+            mode="rb")
+        self.assertEqual(len(list(samfile.fetch())), 3270)
+
+    def testBAMWithCSIIndex(self):
+        '''see issue 116'''
+        input_filename = os.path.join(BAM_DATADIR, "ex1_csi.bam")
+        samfile = pysam.AlignmentFile(input_filename,
+                                      "rb",
+                                      check_sq=False)
+        samfile.fetch('chr2')
+
+    def test_fetch_by_tid(self):
+        with pysam.AlignmentFile(os.path.join(BAM_DATADIR, "ex1.bam"), "rb") as samfile:
+            self.assertEqual(len(list(samfile.fetch('chr1'))),
+                             len(list(samfile.fetch(tid=0))))
+            self.assertEqual(len(list(samfile.fetch('chr2'))),
+                             len(list(samfile.fetch(tid=1))))
+            self.assertRaises(
+                IndexError,
+                samfile.fetch,
+                tid=2)
+            self.assertRaises(
+                IndexError,
+                samfile.fetch,
+                tid=-1)
+            self.assertEqual(len(list(samfile.fetch('chr1', start=1000, end=2000))),
+                             len(list(samfile.fetch(tid=0, start=1000, end=2000))))
+
+    def test_write_bam_to_unknown_path_fails(self):
+        '''see issue 116'''
+        input_filename = os.path.join(BAM_DATADIR, "ex1.bam")
+        with pysam.AlignmentFile(input_filename) as inf:
+            self.assertRaises(IOError,
+                              pysam.AlignmentFile,
+                              "missing_directory/new_file.bam",
+                              "wb",
+                              template=inf)
+        
+
+class TestAutoDetect(unittest.TestCase):
+
+    def testSAM(self):
+        """test SAM autodetection."""
+
+        with pysam.AlignmentFile(
+                os.path.join(BAM_DATADIR, "ex3.sam")) as inf:
+            self.assertFalse(inf.is_bam)
+            self.assertFalse(inf.is_cram)
+
+            self.assertRaises(ValueError, inf.fetch, 'chr1')
+
+    def testBAM(self):
+        """test BAM autodetection."""
+
+        with pysam.AlignmentFile(
+                os.path.join(BAM_DATADIR, "ex3.bam")) as inf:
+            self.assertTrue(inf.is_bam)
+            self.assertFalse(inf.is_cram)
+            self.assertEqual(len(list(inf.fetch('chr1'))), 1)
+            self.assertEqual(len(list(inf.fetch('chr2'))), 3)
+
+    def testCRAM(self):
+        """test CRAM autodetection."""
+
+        with pysam.AlignmentFile(
+                os.path.join(BAM_DATADIR, "ex3.cram")) as inf:
+            self.assertFalse(inf.is_bam)
+            self.assertTrue(inf.is_cram)
+            self.assertEqual(len(list(inf.fetch('chr1'))), 1)
+            self.assertEqual(len(list(inf.fetch('chr2'))), 3)
+
+
+##################################################
+#
+# Random access iterator tests
+#
+##################################################
+class TestIteratorRowBAM(unittest.TestCase):
+
+    filename = os.path.join(BAM_DATADIR, "ex2.bam")
+    mode = "rb"
+    reference_filename = None
+
+    def setUp(self):
+        self.samfile = pysam.AlignmentFile(
+            self.filename,
+            self.mode,
+            reference_filename=self.reference_filename,
+        )
+
+    def tearDown(self):
+        self.samfile.close()
+
+    def checkRange(self, rnge):
+        '''compare results from iterator with those from samtools.'''
+        ps = list(self.samfile.fetch(region=rnge))
+        sa = force_str(
+            pysam.samtools.view(
+                self.filename,
+                rnge,
+                raw=True)).splitlines(True)
+        self.assertEqual(
+            len(ps), len(sa),
+            "unequal number of results for range %s: %i != %i" %
+            (rnge, len(ps), len(sa)))
+        # check if the same reads are returned and in the same order
+        for line, (a, b) in enumerate(list(zip(ps, sa))):
+            d = b.split("\t")
+            self.assertEqual(
+                a.query_name, d[0],
+                "line %i: read id mismatch: %s != %s" %
+                (line, a.reference_id, d[0]))
+            self.assertEqual(
+                a.reference_start,
+                int(d[3]) - 1,
+                "line %i: read position mismatch: %s != %s, \n%s\n%s\n" %
+                (line, a.reference_start, int(d[3]) - 1,
+                 str(a), str(d)))
+            qual = d[10]
+            self.assertEqual(
+                pysam.qualities_to_qualitystring(a.query_qualities),
+                qual,
+                "line %i: quality mismatch: %s != %s, \n%s\n%s\n" %
+                (line, pysam.qualities_to_qualitystring(a.query_qualities), qual,
+                 str(a), str(d)))
+
+    def testIteratePerContig(self):
+        '''check random access per contig'''
+        for contig in self.samfile.references:
+            self.checkRange(contig)
+
+    def testIterateRanges(self):
+        '''check random access per range'''
+        for contig, length in zip(self.samfile.references,
+                                  self.samfile.lengths):
+            for start in range(1, length, 90):
+                # this includes empty ranges
+                self.checkRange("%s:%i-%i" %
+                                (contig, start, start + 90))
+
+
+class TestIteratorRowAllBAM(unittest.TestCase):
+
+    filename = os.path.join(BAM_DATADIR, "ex2.bam")
+    mode = "rb"
+
+    def setUp(self):
+        self.samfile = pysam.AlignmentFile(
+            self.filename,
+            self.mode)
+
+    def testIterate(self):
+        '''compare results from iterator with those from samtools.'''
+        ps = list(self.samfile.fetch())
+        sa = pysam.samtools.view(self.filename,
+                                 raw=True).splitlines()
+        self.assertEqual(
+            len(ps), len(sa),
+            "unequal number of results: %i != %i" %
+            (len(ps), len(sa)))
+        # check if the same reads are returned
+        for line, pair in enumerate(list(zip(ps, sa))):
+            data = force_str(pair[1]).split("\t")
+            self.assertEqual(
+                pair[0].query_name,
+                data[0],
+                "read id mismatch in line %i: %s != %s" %
+                (line, pair[0].reference_id, data[0]))
+
+    def tearDown(self):
+        self.samfile.close()
+
+
+class TestIteratorRowCRAM(TestIteratorRowBAM):
+    filename = os.path.join(BAM_DATADIR, "ex2.cram")
+    mode = "rc"
+
+
+class TestIteratorRowCRAMWithReferenceFilename(TestIteratorRowCRAM):
+    reference_filename = os.path.join(BAM_DATADIR, "ex1.fa")
+
+
+# needs to be implemented
+# class TestAlignedSegmentFromSamWithoutHeader(TestAlignedSegmentFromBam):
+#
+#     def setUp(self):
+#         self.samfile=pysam.AlignmentFile( "ex7.sam","r" )
+#         self.reads=list(self.samfile.fetch())
+
+
+class TestFloatTagBug(unittest.TestCase):
+
+    '''see issue 71'''
+
+    def testFloatTagBug(self):
+        '''a float tag before another exposed a parsing bug in bam_aux_get.
+
+        Fixed in 0.1.19
+        '''
+        samfile = pysam.AlignmentFile(os.path.join(BAM_DATADIR, "tag_bug.bam"))
+        read = next(samfile.fetch(until_eof=True))
+        self.assertTrue(('XC', 1) in read.tags)
+        self.assertEqual(read.opt('XC'), 1)
+
+
+class TestLargeFieldBug(unittest.TestCase):
+
+    '''see issue 100'''
+
+    def testLargeFileBug(self):
+        '''when creating a read with a large entry in the tag field
+        causes an error:
+            NotImplementedError: tags field too large
+        '''
+        samfile = pysam.AlignmentFile(
+            os.path.join(BAM_DATADIR, "issue100.bam"))
+        read = next(samfile.fetch(until_eof=True))
+        new_read = pysam.AlignedSegment()
+        new_read.tags = read.tags
+        self.assertEqual(new_read.tags, read.tags)
+
+
+class TestClipping(unittest.TestCase):
+
+    def testClipping(self):
+
+        self.samfile = pysam.AlignmentFile(
+            os.path.join(BAM_DATADIR, "softclip.bam"),
+            "rb")
+
+        for read in self.samfile:
+
+            if read.query_name == "r001":
+                self.assertEqual(read.query_sequence, 'AAAAGATAAGGATA')
+                self.assertEqual(read.query_alignment_sequence, 'AGATAAGGATA')
+                self.assertEqual(pysam.qualities_to_qualitystring(read.query_qualities),
+                                 None)
+                self.assertEqual(
+                    pysam.qualities_to_qualitystring(
+                        read.query_alignment_qualities),
+                    None)
+
+            elif read.query_name == "r002":
+
+                self.assertEqual(read.query_sequence, 'GCCTAAGCTAA')
+                self.assertEqual(read.query_alignment_sequence, 'AGCTAA')
+                self.assertEqual(
+                    pysam.qualities_to_qualitystring(read.query_qualities),
+                    '01234567890')
+                self.assertEqual(
+                    pysam.qualities_to_qualitystring(
+                        read.query_alignment_qualities),
+                    '567890')
+
+            elif read.query_name == "r003":
+
+                self.assertEqual(read.query_sequence, 'GCCTAAGCTAA')
+                self.assertEqual(read.query_alignment_sequence, 'GCCTAA')
+                self.assertEqual(
+                    pysam.qualities_to_qualitystring(read.query_qualities),
+                    '01234567890')
+                self.assertEqual(
+                    pysam.qualities_to_qualitystring(
+                        read.query_alignment_qualities),
+                    '012345')
+
+            elif read.query_name == "r004":
+
+                self.assertEqual(read.query_sequence, 'TAGGC')
+                self.assertEqual(read.query_alignment_sequence, 'TAGGC')
+                self.assertEqual(
+                    pysam.qualities_to_qualitystring(read.query_qualities),
+                    '01234')
+                self.assertEqual(
+                    pysam.qualities_to_qualitystring(
+                        read.query_alignment_qualities),
+                    '01234')
+
+
+class TestUnmappedReadsRetrieval(unittest.TestCase):
+
+    def test_fetch_from_sam_with_until_eof_reads_unmapped_reads(self):
+        with pysam.AlignmentFile(os.path.join(BAM_DATADIR, "ex5.sam"),
+                                 "rb") as samfile:
+            self.assertEqual(len(list(samfile.fetch(until_eof=True))), 2)
+
+    def test_fetch_from_bam_with_until_eof_reads_unmapped_reads(self):
+        with pysam.AlignmentFile(os.path.join(BAM_DATADIR, "ex5.bam"),
+                                 "rb") as samfile:
+            self.assertEqual(len(list(samfile.fetch(until_eof=True))), 2)
+
+    def test_fetch_with_asterisk_only_returns_unmapped_reads(self):
+        with pysam.AlignmentFile(os.path.join(BAM_DATADIR, "test_mapped_unmapped.bam"),
+                                 "rb") as samfile:
+            self.assertEqual(len(list(samfile.fetch(region="*"))), 4)
+
+    def test_fetch_with_asterisk_only_returns_unmapped_reads_by_contig(self):
+        with pysam.AlignmentFile(os.path.join(BAM_DATADIR, "test_mapped_unmapped.bam"),
+                                 "rb") as samfile:
+            self.assertEqual(len(list(samfile.fetch(contig="*"))), 4)
+
+
+class TestContextManager(unittest.TestCase):
+
+    def testManager(self):
+        with pysam.AlignmentFile(os.path.join(BAM_DATADIR, 'ex1.bam'),
+                                 'rb') as samfile:
+            samfile.fetch()
+        self.assertEqual(samfile.closed, True)
+
+
+class TestMultiThread(unittest.TestCase):
+
+    def testSingleThreadEqualsMultithread(self):
+        input_bam = os.path.join(BAM_DATADIR, 'ex1.bam')
+        single_thread_out = get_temp_filename("tmp_single.bam")
+        multi_thread_out = get_temp_filename("tmp_multi.bam")
+        with pysam.AlignmentFile(input_bam,
+                                 'rb') as samfile:
+            reads = [r for r in samfile]
+            with pysam.AlignmentFile(single_thread_out,
+                                     mode='wb',
+                                     template=samfile,
+                                     threads=1) as single_out:
+                [single_out.write(r) for r in reads]
+            with pysam.AlignmentFile(multi_thread_out,
+                                     mode='wb',
+                                     template=samfile,
+                                     threads=2) as multi_out:
+                [single_out.write(r) for r in reads]
+        with pysam.AlignmentFile(input_bam) as inp, \
+            pysam.AlignmentFile(single_thread_out) as single, \
+            pysam.AlignmentFile(multi_thread_out) as multi:
+            for r1, r2, r3 in zip(inp, single, multi):
+                assert r1.to_string == r2.to_string == r3.to_string
+
+    def TestNoMultiThreadingWithIgnoreTruncation(self):
+        self.assertRaises(
+            ValueError, pysam.AlignmentFile(os.path.join(BAM_DATADIR, 'ex1.bam'),
+                                            threads=2,
+                                            ignore_truncation=True)
+        )
+
+
+class TestExceptions(unittest.TestCase):
+
+    def setUp(self):
+        self.samfile = pysam.AlignmentFile(os.path.join(BAM_DATADIR, "ex1.bam"),
+                                           "rb")
+
+    def testMissingFile(self):
+
+        self.assertRaises(
+            IOError, pysam.AlignmentFile, "exdoesntexist.bam", "rb")
+        self.assertRaises(
+            IOError, pysam.AlignmentFile, "exdoesntexist.sam", "r")
+        self.assertRaises(
+            IOError, pysam.AlignmentFile, "exdoesntexist.bam", "r")
+        self.assertRaises(
+            IOError, pysam.AlignmentFile, "exdoesntexist.sam", "rb")
+
+    def testBadContig(self):
+        self.assertRaises(ValueError, self.samfile.fetch, "chr88")
+
+    def testMeaninglessCrap(self):
+        self.assertRaises(ValueError, self.samfile.fetch, "skljf")
+
+    def testBackwardsOrderNewFormat(self):
+        self.assertRaises(ValueError, self.samfile.fetch, 'chr1', 100, 10)
+
+    def testBackwardsOrderOldFormat(self):
+        self.assertRaises(ValueError, self.samfile.fetch, region="chr1:100-10")
+
+    def testOutOfRangeNegativeNewFormat(self):
+        self.assertRaises(ValueError, self.samfile.fetch, "chr1", 5, -10)
+        self.assertRaises(ValueError, self.samfile.fetch, "chr1", 5, 0)
+        self.assertRaises(ValueError, self.samfile.fetch, "chr1", -5, -10)
+
+        self.assertRaises(ValueError, self.samfile.count, "chr1", 5, -10)
+        self.assertRaises(ValueError, self.samfile.count, "chr1", 5, 0)
+        self.assertRaises(ValueError, self.samfile.count, "chr1", -5, -10)
+
+    def testOutOfRangeNegativeOldFormat(self):
+        self.assertRaises(ValueError, self.samfile.fetch, region="chr1:-5-10")
+        self.assertRaises(ValueError, self.samfile.fetch, region="chr1:-5-0")
+        self.assertRaises(ValueError, self.samfile.fetch, region="chr1:-5--10")
+
+        self.assertRaises(ValueError, self.samfile.count, region="chr1:-5-10")
+        self.assertRaises(ValueError, self.samfile.count, region="chr1:-5-0")
+        self.assertRaises(ValueError, self.samfile.count, region="chr1:-5--10")
+
+    def testOutOfRangNewFormat(self):
+        self.assertRaises(
+            ValueError, self.samfile.fetch, "chr1", 9999999999, 99999999999)
+        self.assertRaises(
+            ValueError, self.samfile.count, "chr1", 9999999999, 99999999999)
+
+    def testOutOfRangeLargeNewFormat(self):
+        self.assertRaises(ValueError, self.samfile.fetch, "chr1",
+                          9999999999999999999999999999999, 9999999999999999999999999999999999999999)
+        self.assertRaises(ValueError, self.samfile.count, "chr1",
+                          9999999999999999999999999999999, 9999999999999999999999999999999999999999)
+
+    def testOutOfRangeLargeOldFormat(self):
+        self.assertRaises(
+            ValueError, self.samfile.fetch, "chr1:99999999999999999-999999999999999999")
+        self.assertRaises(
+            ValueError, self.samfile.count, "chr1:99999999999999999-999999999999999999")
+
+    def testZeroToZero(self):
+        '''see issue 44'''
+        self.assertEqual(len(list(self.samfile.fetch('chr1', 0, 0))), 0)
+
+    def tearDown(self):
+        self.samfile.close()
+
+
+class TestWrongFormat(unittest.TestCase):
+
+    '''test cases for opening files not in bam/sam format.'''
+
+    def testOpenSamAsBam(self):
+        self.assertRaises(ValueError,
+                          pysam.AlignmentFile,
+                          os.path.join(BAM_DATADIR, 'ex1.sam'),
+                          'rb')
+
+    def testOpenBamAsSam(self):
+        # test fails, needs to be implemented.
+        # sam.fetch() fails on reading, not on opening
+        # self.assertRaises(ValueError, pysam.AlignmentFile,
+        #                  os.path.join(BAM_DATADIR, 'ex1.bam'),
+        #                  'r')
+        pass
+
+    def testOpenFastaAsSam(self):
+        # test fails, needs to be implemented.
+        # sam.fetch() fails on reading, not on opening
+        # self.assertRaises( ValueError, pysam.AlignmentFile, 'ex1.fa', 'r' )
+        pass
+
+    def testOpenFastaAsBam(self):
+        self.assertRaises(ValueError,
+                          pysam.AlignmentFile,
+                          os.path.join(BAM_DATADIR, 'ex1.fa'),
+                          'rb')
+
+
+class TestRegionParsing(unittest.TestCase):
+
+    def test_dash_in_chr(self):
+        with pysam.AlignmentFile(
+                os.path.join(BAM_DATADIR, "example_dash_in_chr.bam")) as inf:
+            self.assertEqual(len(list(inf.fetch(contig="chr-1"))), 1)
+            self.assertEqual(len(list(inf.fetch(contig="chr2"))), 1)
+            self.assertEqual(len(list(inf.fetch(region="chr-1"))), 1)
+            self.assertEqual(len(list(inf.fetch(region="chr2"))), 1)
+
+
+class TestDeNovoConstruction(unittest.TestCase):
+
+    '''check BAM/SAM file construction using ex6.sam
+
+    (note these are +1 coordinates):
+
+    read_28833_29006_6945	99	chr1	33	20	10M1D25M	=	200	167	AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG	<<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<<	NM:i:1	RG:Z:L1
+    read_28701_28881_323b	147	chr2	88	30	35M	=	500	412	ACCTATATCTTGGCCTTGGCCGATGCGGCCTTGCA	<<<<<;<<<<7;:<<<6;<<<<<<<<<<<<7<<<<	MF:i:18	RG:Z:L2
+    '''  # noqa
+
+    header = {'HD': {'VN': '1.0'},
+              'SQ': [{'LN': 1575, 'SN': 'chr1'},
+                     {'LN': 1584, 'SN': 'chr2'}], }
+
+    bamfile = os.path.join(BAM_DATADIR, "ex6.bam")
+    samfile = os.path.join(BAM_DATADIR, "ex6.sam")
+
+    def setUp(self):
+
+        header = pysam.AlignmentHeader.from_dict(self.header)
+
+        a = pysam.AlignedSegment(header)
+        a.query_name = "read_28833_29006_6945"
+        a.query_sequence = "AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG"
+        a.flag = 99
+        a.reference_id = 0
+        a.reference_start = 32
+        a.mapping_quality = 20
+        a.cigartuples = ((0, 10), (2, 1), (0, 25))
+        a.next_reference_id = 0
+        a.next_reference_start = 199
+        a.template_length = 167
+        a.query_qualities = pysam.qualitystring_to_array(
+            "<<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<<")
+        a.tags = (("NM", 1),
+                  ("RG", "L1"))
+
+        b = pysam.AlignedSegment(header)
+        b.query_name = "read_28701_28881_323b"
+        b.query_sequence = "ACCTATATCTTGGCCTTGGCCGATGCGGCCTTGCA"
+        b.flag = 147
+        b.reference_id = 1
+        b.reference_start = 87
+        b.mapping_quality = 30
+        b.cigartuples = ((0, 35), )
+        b.next_reference_id = 1
+        b.next_reference_start = 499
+        b.template_length = 412
+        b.query_qualities = pysam.qualitystring_to_array(
+            "<<<<<;<<<<7;:<<<6;<<<<<<<<<<<<7<<<<")
+        b.tags = (("MF", 18),
+                  ("RG", "L2"))
+
+        self.reads = (a, b)
+
+    # TODO
+    # def testSAMWholeFile(self):
+
+    #     tmpfilename = "tmp_%i.sam" % id(self)
+
+    #     outfile = pysam.AlignmentFile(tmpfilename,
+    #                             "wh",
+    #                             header=self.header)
+
+    #     for x in self.reads:
+    #         outfile.write(x)
+    #     outfile.close()
+    #     self.assertTrue(checkBinaryEqual(tmpfilename, self.samfile),
+    #                     "mismatch when construction SAM file, see %s %s" % (tmpfilename, self.samfile))
+
+    #     os.unlink(tmpfilename)
+
+    def test_pass_if_reads_binary_equal(self):
+        '''check if individual reads are binary equal.'''
+        infile = pysam.AlignmentFile(self.bamfile, "rb")
+
+        references = list(infile)
+        for denovo, reference in zip(references, self.reads):
+            checkFieldEqual(self, reference, denovo)
+            self.assertEqual(reference.compare(denovo), 0)
+
+    # TODO
+    # def testSAMPerRead(self):
+    #     '''check if individual reads are binary equal.'''
+    #     infile = pysam.AlignmentFile(self.samfile, "r")
+
+    #     others = list(infile)
+    #     for denovo, other in zip(others, self.reads):
+    #         checkFieldEqual(self, other, denovo)
+    #         self.assertEqual(other.compare(denovo), 0)
+
+    def testBAMWholeFile(self):
+
+        tmpfilename = "tmp_%i.bam" % id(self)
+
+        outfile = pysam.AlignmentFile(tmpfilename, "wb", header=self.header)
+
+        for x in self.reads:
+            outfile.write(x)
+        outfile.close()
+
+        self.assertTrue(
+            checkGZBinaryEqual(tmpfilename, self.bamfile),
+            "mismatch when construction BAM file, see %s %s" %
+            (tmpfilename, self.bamfile))
+
+        os.unlink(tmpfilename)
+
+
+class TestEmptyHeader(unittest.TestCase):
+    '''see issue 84.'''
+
+    def testEmptyHeader(self):
+        s = pysam.AlignmentFile(os.path.join(BAM_DATADIR,
+                                             'example_empty_header.bam'))
+        self.assertEqual(s.header.to_dict(), {'SQ': [{'LN': 1000, 'SN': 'chr1'}]})
+
+    def test_bam_without_seq_in_header(self):
+        s = pysam.AlignmentFile(os.path.join(BAM_DATADIR, "0example_no_seq_in_header.bam"))
+        self.assertTrue("SQ" in s.header.to_dict())
+        self.assertTrue("@SQ" in str(s.header))
+
+    def test_bam_without_seq_with_null_bytes_in_header(self):
+        s = pysam.AlignmentFile(os.path.join(BAM_DATADIR, "0example_no_seq_in_header_null_bytes.bam"))
+        self.assertTrue("SQ" in s.header.to_dict())
+        self.assertTrue("@SQ" in str(s.header))
+
+
+class TestMismatchingHeader(unittest.TestCase):
+    '''see issue 716.'''
+
+    def testMismatchingHeader(self):
+        # Note: no chr2
+        header = {
+            'SQ': [{'SN': 'chr1', 'LN': 1575}],
+            'PG': [{'ID': 'bwa', 'PN': 'bwa', 'VN': '0.7.15', 'CL': 'bwa mem xx -'}],
+        }
+
+        dest = get_temp_filename("tmp_ex3.bam")
+        with pysam.AlignmentFile(os.path.join(BAM_DATADIR, 'ex3.bam')) as inf:
+            with pysam.AlignmentFile(dest, mode="wb", header=header) as outf:
+                for read in inf:
+                    if read.reference_name == "chr1":
+                        outf.write(read)
+                    else:
+                        self.assertRaises(ValueError,
+                                          outf.write,
+                                          read)
+        os.unlink(dest)
+
+
+class TestHeaderWithProgramOptions(unittest.TestCase):
+
+    '''see issue 39.'''
+
+    def testHeader(self):
+        s = pysam.AlignmentFile(os.path.join(BAM_DATADIR,
+                                             'rg_with_tab.bam'))
+        self.assertEqual(
+            s.header.to_dict(),
+            {'SQ': [{'LN': 1575, 'SN': 'chr1'},
+                    {'LN': 1584, 'SN': 'chr2'}],
+             'PG': [{'PN': 'bwa',
+                     'ID': 'bwa',
+                     'VN': '0.7.9a-r786',
+                     'CL': 'bwa mem -p -t 8 -M -R '
+                     '@RG ID:None SM:None /mnt/data/hg19.fa '
+                     '/mnt/analysis/default-0.fastq'}]})
+
+
+class TestTruncatedBAM(unittest.TestCase):
+
+    '''see pull request 50.'''
+
+    def testTruncatedBam2(self):
+        self.assertRaises(IOError,
+                          pysam.AlignmentFile,
+                          os.path.join(BAM_DATADIR, 'ex2_truncated.bam'))
+
+    @pytest.mark.filterwarnings('ignore:no BGZF EOF marker')
+    def testTruncatedBamIterator(self):
+        s = pysam.AlignmentFile(os.path.join(BAM_DATADIR, 'ex2_truncated.bam'),
+                                ignore_truncation=True)
+
+        def iterall(x):
+            return len([a for a in x])
+        self.assertRaises(IOError, iterall, s)
+
+        # Ignore closing errors, as s is now in an error state
+        try:
+            s.close()
+        except IOError:
+            pass
+
+
+class TestCorruptBAM(unittest.TestCase):
+    """See pull request 1035."""
+
+    def testCorruptBamIterator(self):
+        s = pysam.AlignmentFile(os.path.join(BAM_DATADIR, "ex2_corrupt.bam"))
+
+        def iterall(x):
+            return len([a for a in x])
+
+        self.assertRaises(IOError, iterall, s)
+
+
+COMPARE_BTAG = [100, 1, 91, 0, 7, 101, 0, 201, 96, 204,
+                0, 0, 87, 109, 0, 7, 97, 112, 1, 12, 78,
+                197, 0, 7, 100, 95, 101, 202, 0, 6, 0, 1,
+                186, 0, 84, 0, 244, 0, 0, 324, 0, 107, 195,
+                101, 113, 0, 102, 0, 104, 3, 0, 101, 1, 0,
+                212, 6, 0, 0, 1, 0, 74, 1, 11, 0, 196, 2,
+                197, 103, 0, 108, 98, 2, 7, 0, 1, 2, 194,
+                0, 180, 0, 108, 0, 203, 104, 16, 5, 205,
+                0, 0, 0, 1, 1, 100, 98, 0, 0, 204, 6, 0,
+                79, 0, 0, 101, 7, 109, 90, 265, 1, 27, 10,
+                109, 102, 9, 0, 292, 0, 110, 0, 0, 102,
+                112, 0, 0, 84, 100, 103, 2, 81, 126, 0, 2,
+                90, 0, 15, 96, 15, 1, 0, 2, 0, 107, 92, 0,
+                0, 101, 3, 98, 15, 102, 13, 116, 116, 90, 93,
+                198, 0, 0, 0, 199, 92, 26, 495, 100, 5, 0,
+                100, 5, 209, 0, 92, 107, 90, 0, 0, 0, 0, 109,
+                194, 7, 94, 200, 0, 40, 197, 0, 11, 0, 0, 112,
+                110, 6, 4, 200, 28, 0, 196, 0, 203, 1, 129,
+                0, 0, 1, 0, 94, 0, 1, 0, 107, 5, 201, 3, 3, 100,
+                0, 121, 0, 7, 0, 1, 105, 306, 3, 86, 8, 183, 0,
+                12, 163, 17, 83, 22, 0, 0, 1, 8, 109, 103, 0, 0,
+                295, 0, 200, 16, 172, 3, 16, 182, 3, 11, 0, 0,
+                223, 111, 103, 0, 5, 225, 0, 95]
+
+
+class TestBTagSam(unittest.TestCase):
+
+    '''see issue 81.'''
+
+    compare = [COMPARE_BTAG,
+               [-100, 200, -300, -400],
+               [-100, 12],
+               [12, 15],
+               [-1.0, 5.0, 2.5]]
+
+    filename = os.path.join(BAM_DATADIR, 'example_btag.sam')
+
+    read0 = [('RG', 'QW85I'),
+             ('PG', 'tmap'),
+             ('MD', '140'),
+             ('NM', 0),
+             ('AS', 140),
+             ('FZ', array.array('H', COMPARE_BTAG)),
+             ('XA', 'map2-1'),
+             ('XS', 53),
+             ('XT', 38),
+             ('XF', 1),
+             ('XE', 0)]
+
+    def testReadTags(self):
+
+        s = pysam.AlignmentFile(self.filename)
+        for x, read in enumerate(s):
+            tags = read.tags
+            if x == 0:
+                self.assertEqual(tags, self.read0)
+
+            fz = list(dict(tags)["FZ"])
+            self.assertEqual(fz, self.compare[x])
+            self.assertEqual(list(read.opt("FZ")), self.compare[x])
+            self.assertEqual(tags, read.get_tags())
+            for tag, value in tags:
+                self.assertEqual(value, read.get_tag(tag))
+
+    def testReadWriteTags(self):
+
+        s = pysam.AlignmentFile(self.filename)
+        for read in s:
+            before = read.tags
+            read.tags = before
+            self.assertEqual(read.tags, before)
+
+            read.set_tags(before)
+            self.assertEqual(read.tags, before)
+
+            for tag, value in before:
+                read.set_tag(tag, value)
+                self.assertEqual(value, read.get_tag(tag))
+
+
+class TestBTagBam(TestBTagSam):
+    filename = os.path.join(BAM_DATADIR, 'example_btag.bam')
+
+
+class TestDoubleFetchBAM(unittest.TestCase):
+    '''check if two iterators on the same bamfile are independent.'''
+
+    filename = os.path.join(BAM_DATADIR, 'ex1.bam')
+    mode = "rb"
+
+    def testDoubleFetch(self):
+
+        with pysam.AlignmentFile(self.filename, self.mode) as samfile1:
+            for a, b in zip(samfile1.fetch(multiple_iterators=True),
+                            samfile1.fetch(multiple_iterators=True)):
+                self.assertEqual(a.compare(b), 0)
+
+    def testDoubleFetchWithRegionTrueTrue(self):
+
+        with pysam.AlignmentFile(self.filename, self.mode) as samfile1:
+            contig, start, stop = 'chr2', 200, 3000000
+            # just making sure the test has something to catch
+            self.assertTrue(len(list(samfile1.fetch(contig, start, stop))) > 0)
+
+            for a, b in zip(samfile1.fetch(contig, start, stop,
+                                           multiple_iterators=True),
+                            samfile1.fetch(contig, start, stop,
+                                           multiple_iterators=True)):
+                self.assertEqual(a.compare(b), 0)
+
+    def testDoubleFetchWithRegionFalseTrue(self):
+        with pysam.AlignmentFile(self.filename, self.mode) as samfile1:
+            contig, start, stop = 'chr2', 200, 3000000
+            # just making sure the test has something to catch
+            self.assertTrue(len(list(samfile1.fetch(contig, start, stop))) > 0)
+        
+            for a, b in zip(samfile1.fetch(contig, start, stop,
+                                           multiple_iterators=False),
+                            samfile1.fetch(contig, start, stop,
+                                           multiple_iterators=True)):
+                self.assertEqual(a.compare(b), 0)
+
+    def testDoubleFetchWithRegionTrueFalse(self):
+        with pysam.AlignmentFile(self.filename, self.mode) as samfile1:
+            contig, start, stop = 'chr2', 200, 3000000
+            # just making sure the test has something to catch
+            self.assertTrue(len(list(samfile1.fetch(contig, start, stop))) > 0)
+        
+            for a, b in zip(samfile1.fetch(contig, start, stop,
+                                           multiple_iterators=True),
+                            samfile1.fetch(contig, start, stop,
+                                           multiple_iterators=False)):
+                self.assertEqual(a.compare(b), 0)
+                
+    def testDoubleFetchUntilEOF(self):
+
+        with pysam.AlignmentFile(self.filename, self.mode) as samfile1:
+
+            for a, b in zip(samfile1.fetch(until_eof=True),
+                            samfile1.fetch(until_eof=True,
+                                           multiple_iterators=True)):
+                self.assertEqual(a.compare(b), 0)
+
+
+class TestDoubleFetchCRAM(TestDoubleFetchBAM):
+    filename = os.path.join(BAM_DATADIR, 'ex2.cram')
+    mode = "rc"
+
+
+class TestDoubleFetchCRAMWithReference(TestDoubleFetchBAM):
+    filename = os.path.join(BAM_DATADIR, 'ex2.cram')
+    mode = "rc"
+    reference_filename = os.path.join(BAM_DATADIR, 'ex1.fa')
+
+
+class TestRemoteFileFTP(unittest.TestCase):
+
+    '''test remote access.
+
+    '''
+
+    # Need to find an ftp server without password on standard
+    # port.
+
+    url = "ftp://ftp.sanger.ac.uk/pub/rd/humanSequences/CV.bam"
+    region = "1:1-1000"
+
+    def testFTPView(self):
+        return
+        if not check_url(self.url):
+            return
+
+        result = pysam.samtools.view(self.url, self.region)
+        self.assertEqual(len(result), 36)
+
+    def testFTPFetch(self):
+        return
+        if not check_url(self.url):
+            return
+
+        samfile = pysam.AlignmentFile(self.url, "rb")
+        result = list(samfile.fetch(region=self.region))
+        self.assertEqual(len(result), 36)
+
+
+class TestRemoteFileHTTP(unittest.TestCase):
+
+    url = "http://genserv.anat.ox.ac.uk/downloads/pysam/test/ex1.bam"
+    region = "chr1:1-1000"
+    local = os.path.join(BAM_DATADIR, "ex1.bam")
+
+    def testView(self):
+        if not check_url(self.url):
+            return
+
+        samfile_local = pysam.AlignmentFile(self.local, "rb")
+        ref = list(samfile_local.fetch(region=self.region))
+
+        result = pysam.samtools.view(self.url, self.region)
+        self.assertEqual(len(result.splitlines()), len(ref))
+
+    def testFetch(self):
+        if not check_url(self.url):
+            return
+
+        with pysam.AlignmentFile(self.url, "rb") as samfile:
+            result = list(samfile.fetch(region=self.region))
+
+        with pysam.AlignmentFile(self.local, "rb") as samfile_local:
+            ref = list(samfile_local.fetch(region=self.region))
+
+        self.assertEqual(len(ref), len(result))
+        for x, y in zip(result, ref):
+            self.assertEqual(x.compare(y), 0)
+
+    def testFetchAll(self):
+        if not check_url(self.url):
+            return
+
+        with pysam.AlignmentFile(self.url, "rb") as samfile:
+            result = list(samfile.fetch())
+
+        with pysam.AlignmentFile(self.local, "rb") as samfile_local:
+            ref = list(samfile_local.fetch())
+
+        self.assertEqual(len(ref), len(result))
+        for x, y in zip(result, ref):
+            self.assertEqual(x.compare(y), 0)
+
+
+class TestLargeOptValues(unittest.TestCase):
+
+    ints = (65536, 214748, 2147484, 2147483647)
+    floats = (65536.0, 214748.0, 2147484.0)
+
+    def check(self, samfile):
+
+        i = samfile.fetch()
+        for exp in self.ints:
+            rr = next(i)
+            obs = rr.opt("ZP")
+            self.assertEqual(exp, obs,
+                             "expected %s, got %s\n%s" %
+                             (str(exp), str(obs), str(rr)))
+
+        for exp in [-x for x in self.ints]:
+            rr = next(i)
+            obs = rr.opt("ZP")
+            self.assertEqual(exp, obs,
+                             "expected %s, got %s\n%s" %
+                             (str(exp), str(obs), str(rr)))
+
+        for exp in self.floats:
+            rr = next(i)
+            obs = rr.opt("ZP")
+            self.assertEqual(exp, obs,
+                             "expected %s, got %s\n%s" %
+                             (str(exp), str(obs), str(rr)))
+
+        for exp in [-x for x in self.floats]:
+            rr = next(i)
+            obs = rr.opt("ZP")
+            self.assertEqual(exp, obs, "expected %s, got %s\n%s" %
+                             (str(exp), str(obs), str(rr)))
+
+    def testSAM(self):
+        samfile = pysam.AlignmentFile(
+            os.path.join(BAM_DATADIR, "ex10.sam"),
+            "r")
+        self.check(samfile)
+
+    def testBAM(self):
+        samfile = pysam.AlignmentFile(
+            os.path.join(BAM_DATADIR, "ex10.bam"),
+            "rb")
+        self.check(samfile)
+
+
+class TestCountCoverage(unittest.TestCase):
+
+    samfilename = os.path.join(BAM_DATADIR, "ex1.bam")
+    fastafilename = os.path.join(BAM_DATADIR, "ex1.fa")
+
+    def setUp(self):
+
+        self.fastafile = pysam.Fastafile(self.fastafilename)
+        self.tmpfilename = get_temp_filename(".bam")
+
+        with pysam.AlignmentFile(self.samfilename) as inf:
+            with pysam.AlignmentFile(
+                    self.tmpfilename,
+                    'wb',
+                    template=inf) as outf:
+                for ii, read in enumerate(inf.fetch()):
+                    # if ii % 2 == 0: # setting BFUNMAP makes no sense...
+                        #read.flag = read.flag | 0x4
+                    if ii % 3 == 0:
+                        read.flag = read.flag | 0x100
+                    if ii % 5 == 0:
+                        read.flag = read.flag | 0x200
+                    if ii % 7 == 0:
+                        read.flag = read.flag | 0x400
+                    outf.write(read)
+        pysam.samtools.index(self.tmpfilename)
+
+    def tearDown(self):
+        self.fastafile.close()
+        os.unlink(self.tmpfilename)
+        os.unlink(self.tmpfilename + ".bai")
+
+    def count_coverage_python(self,
+                              bam, chrom, start, stop,
+                              read_callback,
+                              quality_threshold=15):
+        stop = min(stop, bam.get_reference_length(chrom))
+        l = stop - start
+        count_a = array.array('L', [0] * l)
+        count_c = array.array('L', [0] * l)
+        count_g = array.array('L', [0] * l)
+        count_t = array.array('L', [0] * l)
+        for p in bam.pileup(chrom, start, stop,
+                            truncate=True,
+                            stepper='nofilter',
+                            min_base_quality=quality_threshold,
+                            ignore_overlaps=False):
+            rpos = p.reference_pos - start
+            for read in p.pileups:
+                if not read.is_del and not read.is_refskip and \
+                   read_callback(read.alignment):
+                    try:
+                        if read.alignment.query_qualities[read.query_position] \
+                           >= quality_threshold:
+                            letter = read.alignment.query[read.query_position]
+                            if letter == 'A':
+                                count_a[rpos] += 1
+                            elif letter == 'C':
+                                count_c[rpos] += 1
+                            elif letter == 'G':
+                                count_g[rpos] += 1
+                            elif letter == 'T':
+                                count_t[rpos] += 1
+                    except IndexError:
+                        pass
+        return count_a, count_c, count_g, count_t
+
+    def test_count_coverage_with_coordinates_works(self):
+
+        with pysam.AlignmentFile(self.samfilename) as inf:
+            c = inf.count_coverage("chr1")
+            self.assertEqual(len(c[0]), inf.get_reference_length("chr1"))
+            self.assertEqual(len(c[0]), 1575)
+
+            c = inf.count_coverage("chr1", 100)
+            self.assertEqual(len(c[0]), inf.get_reference_length("chr1") - 100)
+
+            c = inf.count_coverage("chr1", 100, 200)
+            self.assertEqual(len(c[0]), 200 - 100)
+            
+            c = inf.count_coverage("chr1", None, 200)
+            self.assertEqual(len(c[0]), 200)
+
+            c = inf.count_coverage("chr1", None, inf.get_reference_length("chr1") + 10000)
+            self.assertEqual(len(c[0]), inf.get_reference_length("chr1"))
+
+    def test_count_coverage_without_coordinates_fails(self):
+        with pysam.AlignmentFile(self.samfilename) as inf:
+            self.assertRaises(TypeError, inf.count_coverage)
+
+    def test_count_coverage_wrong_coordinates_fails(self):
+        with pysam.AlignmentFile(self.samfilename) as inf:
+            self.assertRaises(ValueError, inf.count_coverage, "chr1", 200, 100)
+            self.assertRaises(KeyError, inf.count_coverage, "chrUnknown", 100, 200)
+            
+    def test_counting_the_same_region_works(self):
+
+        with pysam.AlignmentFile(self.samfilename) as inf:
+            c1 = inf.count_coverage("chr1")
+            c2 = inf.count_coverage("chr1")
+            self.assertEqual(c1, c2)
+            
+    def test_count_coverage_counts_as_expected(self):
+        chrom = 'chr1'
+        start = 0
+        stop = 1000
+
+        with pysam.AlignmentFile(self.samfilename) as inf:
+            manual_counts = self.count_coverage_python(
+                inf, chrom, start, stop,
+                lambda read: True,
+                quality_threshold=0)
+
+            fast_counts = inf.count_coverage(
+                chrom, start, stop,
+                read_callback=lambda read: True,
+                quality_threshold=0)
+
+        self.assertEqual(list(fast_counts[0]), list(manual_counts[0]))
+        self.assertEqual(list(fast_counts[1]), list(manual_counts[1]))
+        self.assertEqual(list(fast_counts[2]), list(manual_counts[2]))
+        self.assertEqual(list(fast_counts[3]), list(manual_counts[3]))
+
+    def test_count_coverage_quality_filter(self):
+        chrom = 'chr1'
+        start = 0
+        stop = 1000
+        with pysam.AlignmentFile(self.samfilename) as inf:
+            manual_counts = self.count_coverage_python(
+                inf, chrom, start, stop,
+                lambda read: True,
+                quality_threshold=0)
+            fast_counts = inf.count_coverage(
+                chrom, start, stop,
+                read_callback=lambda read: True,
+                quality_threshold=15)
+            
+        # we filtered harder, should be less
+        for i in range(4):
+            for r in range(start, stop):
+                self.assertTrue(fast_counts[i][r] <= manual_counts[i][r])
+
+    def test_count_coverage_read_callback(self):
+        chrom = 'chr1'
+        start = 0
+        stop = 1000
+        with pysam.AlignmentFile(self.samfilename) as inf:
+            manual_counts = self.count_coverage_python(
+                inf, chrom, start, stop,
+                lambda read: read.flag & 0x10,
+                quality_threshold=0)
+            fast_counts = inf.count_coverage(
+                chrom, start, stop,
+                read_callback=lambda read: True,
+                quality_threshold=0)
+            
+            for i in range(4):
+                for r in range(start, stop):
+                    self.assertTrue(fast_counts[i][r] >= manual_counts[i][r])
+                    
+            fast_counts = inf.count_coverage(
+                chrom, start, stop,
+                read_callback=lambda read: read.flag & 0x10,
+                quality_threshold=0)
+
+        self.assertEqual(fast_counts[0], manual_counts[0])
+        self.assertEqual(fast_counts[1], manual_counts[1])
+        self.assertEqual(fast_counts[2], manual_counts[2])
+        self.assertEqual(fast_counts[3], manual_counts[3])
+
+    def test_count_coverage_read_all(self):
+
+        chrom = 'chr1'
+        start = 0
+        stop = 1000
+
+        def filter(read):
+            return not (read.flag & (0x4 | 0x100 | 0x200 | 0x400))
+
+        with pysam.AlignmentFile(self.tmpfilename) as samfile:
+            fast_counts = samfile.count_coverage(
+                chrom, start, stop,
+                read_callback='all',
+                # read_callback = lambda read: ~(read.flag & (0x4 | 0x100 | 0x200 | 0x400)),
+                quality_threshold=0)
+            manual_counts = samfile.count_coverage(
+                chrom, start, stop,
+                read_callback=lambda read: not(
+                    read.flag & (0x4 | 0x100 | 0x200 | 0x400)),
+                quality_threshold=0)
+
+        self.assertEqual(fast_counts[0], manual_counts[0])
+        self.assertEqual(fast_counts[1], manual_counts[1])
+        self.assertEqual(fast_counts[2], manual_counts[2])
+        self.assertEqual(fast_counts[3], manual_counts[3])
+
+    def test_count_coverage_nofilter(self):
+
+        with pysam.AlignmentFile(self.samfilename) as inf:
+            with pysam.AlignmentFile(
+                    self.tmpfilename, 'wb', template=inf) as outf:
+        
+                for ii, read in enumerate(inf.fetch()):
+                    # if ii % 2 == 0: # setting BFUNMAP makes no sense...
+                    # read.flag = read.flag | 0x4
+                    if ii % 3 == 0:
+                        read.flag = read.flag | 0x100
+                    if ii % 5 == 0:
+                        read.flag = read.flag | 0x200
+                    if ii % 7 == 0:
+                        read.flag = read.flag | 0x400
+                    outf.write(read)
+        
+        pysam.samtools.index(self.tmpfilename)
+        chr = 'chr1'
+        start = 0
+        stop = 1000
+
+        with pysam.AlignmentFile(self.tmpfilename) as inf:
+            fast_counts = inf.count_coverage(chr, start, stop,
+                                             read_callback='nofilter',
+                                             quality_threshold=0)
+
+            manual_counts = self.count_coverage_python(inf, chr, start, stop,
+                                                       read_callback=lambda x: True,
+                                                       quality_threshold=0)
+
+        self.assertEqual(fast_counts[0], manual_counts[0])
+        self.assertEqual(fast_counts[1], manual_counts[1])
+        self.assertEqual(fast_counts[2], manual_counts[2])
+        self.assertEqual(fast_counts[3], manual_counts[3])
+        
+
+class TestFindIntrons(unittest.TestCase):
+    samfilename = os.path.join(BAM_DATADIR, "ex_spliced.bam")
+
+    def setUp(self):
+        self.samfile = pysam.AlignmentFile(self.samfilename)
+
+    def tearDown(self):
+        self.samfile.close()
+
+    def test_total(self):
+        all_read_counts = self.samfile.count()
+        splice_sites = self.samfile.find_introns(self.samfile.fetch())
+        # there is a single unspliced read in there
+        self.assertEqual(sum(splice_sites.values()), all_read_counts - 1)
+
+    def test_first(self):
+        reads = list(self.samfile.fetch())[:10]
+        splice_sites = self.samfile.find_introns(reads)
+        starts = [14792 + 38 - 1]
+        stops = [14792 + 38 + 140 - 1]
+        self.assertEqual(len(splice_sites), 1)
+        self.assertTrue((starts[0], stops[0]) in splice_sites)
+        # first one is the unspliced read
+        self.assertEqual(splice_sites[(starts[0], stops[0])], 9)
+
+    def test_all(self):
+        reads = list(self.samfile.fetch())
+        splice_sites = self.samfile.find_introns(reads)
+        should = collections.Counter({
+            (14829, 14969): 33,
+            (15038, 15795): 24,
+            (15947, 16606): 3,
+            (16765, 16857): 9,
+            (16765, 16875): 1,
+            (17055, 17232): 19,
+            (17055, 17605): 3,
+            (17055, 17914): 1,
+            (17368, 17605): 7,
+        })
+        self.assertEqual(should, splice_sites)
+
+
+class TestLogging(unittest.TestCase):
+
+    '''test around bug issue 42,
+
+    failed in versions < 0.4
+    '''
+
+    def check(self, bamfile, log):
+
+        if log:
+            logger = logging.getLogger('franklin')
+            logger.setLevel(logging.INFO)
+            formatter = logging.Formatter(
+                '%(asctime)s %(levelname)s %(message)s')
+            log_hand = logging.FileHandler('log.txt')
+            log_hand.setFormatter(formatter)
+            logger.addHandler(log_hand)
+
+        with pysam.AlignmentFile(bamfile, 'rb') as bam:
+            cols = bam.pileup()
+        self.assertTrue(True)
+
+    def tearDown(self):
+        if os.path.exists('log.txt'):
+            os.unlink('log.txt')
+
+    def testFail1(self):
+        self.check(os.path.join(BAM_DATADIR, "ex9_fail.bam"),
+                   False)
+        self.check(os.path.join(BAM_DATADIR, "ex9_fail.bam"),
+                   True)
+
+    def testNoFail1(self):
+        self.check(os.path.join(BAM_DATADIR, "ex9_nofail.bam"),
+                   False)
+        self.check(os.path.join(BAM_DATADIR, "ex9_nofail.bam"),
+                   True)
+
+    def testNoFail2(self):
+        self.check(os.path.join(BAM_DATADIR, "ex9_nofail.bam"),
+                   True)
+        self.check(os.path.join(BAM_DATADIR, "ex9_nofail.bam"),
+                   True)
+
+# TODOS
+# 1. finish testing all properties within pileup objects
+# 2. check exceptions and bad input problems (missing files, optional fields that aren't present, etc...)
+# 3. check: presence of sequence
+
+
+class TestAlignmentFileUtilityFunctions(unittest.TestCase):
+
+    def testCount(self):
+
+        with pysam.AlignmentFile(
+                os.path.join(BAM_DATADIR, "ex1.bam"),
+                "rb") as samfile:
+
+            for contig in ("chr1", "chr2"):
+                for start in range(0, 2000, 100):
+                    end = start + 1
+                    self.assertEqual(
+                        len(list(samfile.fetch(contig, start, end))),
+                        samfile.count(contig, start, end),
+                        'number mismatch for %s:%i-%i %i != %i' % (
+                            contig, start, end,
+                            len(list(samfile.fetch(contig, start, end))),
+                            samfile.count(contig, start, end)))
+
+                    # test empty intervals
+                    self.assertEqual(
+                        len(list(samfile.fetch(contig, start, start))),
+                        samfile.count(contig, start, start),
+                        'number mismatch for %s:%i-%i %i != %i' % (
+                            contig, start, start,
+                            len(list(samfile.fetch(contig, start, start))),
+                            samfile.count(contig, start, start)))
+
+                    # test half empty intervals
+                    self.assertEqual(len(list(samfile.fetch(contig, start))),
+                                     samfile.count(contig, start))
+
+                    self.assertEqual(
+                        len(list(samfile.fetch(contig, start))),
+                        samfile.count(contig, start),
+                        'number mismatch for %s:%i %i != %i' % (
+                            contig, start,
+                            len(list(samfile.fetch(contig, start))),
+                            samfile.count(contig, start)))
+
+    def testMate(self):
+        '''test mate access.'''
+
+        with open(os.path.join(BAM_DATADIR, "ex1.sam"), "rb") as inf:
+            readnames = [x.split(b"\t")[0] for x in inf.readlines()]
+        if sys.version_info[0] >= 3:
+            readnames = [name.decode('ascii') for name in readnames]
+
+        counts = collections.defaultdict(int)
+        for x in readnames:
+            counts[x] += 1
+
+        with pysam.AlignmentFile(os.path.join(BAM_DATADIR, "ex1.bam"),
+                                 "rb") as samfile:
+
+            for read in samfile.fetch():
+                if not read.is_paired:
+                    self.assertRaises(ValueError, samfile.mate, read)
+                elif read.mate_is_unmapped:
+                    self.assertRaises(ValueError, samfile.mate, read)
+                else:
+                    if counts[read.query_name] == 1:
+                        self.assertRaises(ValueError, samfile.mate, read)
+                    else:
+                        mate = samfile.mate(read)
+                        self.assertEqual(read.query_name, mate.query_name)
+                        self.assertEqual(read.is_read1, mate.is_read2)
+                        self.assertEqual(read.is_read2, mate.is_read1)
+                        self.assertEqual(
+                            read.reference_start, mate.next_reference_start)
+                        self.assertEqual(
+                            read.next_reference_start, mate.reference_start)
+
+    def testIndexStats(self):
+        '''test if total number of mapped/unmapped reads is correct.'''
+
+        with pysam.AlignmentFile(os.path.join(BAM_DATADIR, "ex1.bam"),
+                                 "rb") as samfile:
+            self.assertEqual(samfile.mapped, 3235)
+            self.assertEqual(samfile.unmapped, 35)
+            self.assertEqual(samfile.nocoordinate, 0)
+
+
+class TestMappedUnmapped(unittest.TestCase):
+    filename = "test_mapped_unmapped.bam"
+
+    def test_counts_of_mapped_and_unmapped_are_correct(self):
+
+        with pysam.AlignmentFile(os.path.join(BAM_DATADIR,
+                                              self.filename)) as inf:
+            unmapped_flag = 0
+            unmapped_nopos = 0
+            mapped_flag = 0
+            for x in inf.fetch(until_eof=True):
+                if x.is_unmapped:
+                    if x.reference_id < 0:
+                        unmapped_nopos += 1
+                    else:
+                        unmapped_flag += 1
+                else:
+                    mapped_flag += 1
+
+            self.assertEqual(inf.mapped, mapped_flag)
+            self.assertEqual(inf.unmapped, unmapped_flag + unmapped_nopos)
+
+            inf.reset()
+            self.assertEqual(inf.count(),
+                             inf.mapped + unmapped_flag)
+
+            inf.reset()
+            self.assertEqual(inf.count(until_eof=True),
+                             inf.mapped + unmapped_flag + unmapped_nopos)
+
+            inf.reset()
+            self.assertEqual(inf.count(read_callback="all"),
+                             inf.mapped)
+
+            inf.reset()
+            self.assertEqual(inf.count(until_eof=True, read_callback="all"),
+                             inf.mapped)
+
+    def test_counts_of_mapped_and_unmapped_are_correct_per_chromosome(self):
+
+        with pysam.AlignmentFile(os.path.join(BAM_DATADIR,
+                                              self.filename)) as inf:
+
+            counts = inf.get_index_statistics()
+
+            counts_contigs = [x.contig for x in counts]
+            self.assertEqual(sorted(counts_contigs),
+                             sorted(inf.references))
+
+            for contig in inf.references:
+                unmapped_flag = 0
+                unmapped_nopos = 0
+                mapped_flag = 0
+                for x in inf.fetch(contig=contig):
+                    if x.is_unmapped:
+                        unmapped_flag += 1
+                    else:
+                        mapped_flag += 1
+
+                cc = [c for c in counts if c.contig == contig][0]
+                self.assertEqual(cc.mapped, mapped_flag)
+                self.assertEqual(cc.unmapped, unmapped_flag)
+                self.assertEqual(cc.total, mapped_flag + unmapped_flag)
+
+
+class TestSamtoolsProxy(unittest.TestCase):
+
+    '''tests for sanity checking access to samtools functions.'''
+
+    def testIndex(self):
+        self.assertRaises(IOError, pysam.samtools.index, "missing_file")
+
+    def testView(self):
+        # note that view still echos "open: No such file or directory"
+        self.assertRaises(pysam.SamtoolsError,
+                          pysam.samtools.view,
+                          "missing_file")
+
+    def testSort(self):
+        self.assertRaises(pysam.SamtoolsError,
+                          pysam.samtools.sort,
+                          "missing_file")
+
+
+class TestAlignmentFileIndex(unittest.TestCase):
+
+    def testIndex(self):
+        samfile = pysam.AlignmentFile(
+            os.path.join(BAM_DATADIR, "ex1.bam"),
+            "rb")
+        index = pysam.IndexedReads(samfile)
+        index.build()
+        reads = collections.defaultdict(int)
+
+        for read in samfile:
+            reads[read.query_name] += 1
+
+        for qname, counts in reads.items():
+            found = list(index.find(qname))
+            self.assertEqual(len(found), counts)
+            for x in found:
+                self.assertEqual(x.query_name, qname)
+
+
+class TestExplicitIndex(unittest.TestCase):
+
+    def testExplicitIndexBAM(self):
+        with pysam.AlignmentFile(
+                os.path.join(BAM_DATADIR, "explicit_index.bam"),
+                "rb",
+                filepath_index=os.path.join(BAM_DATADIR, 'ex1.bam.bai')) as samfile:
+            samfile.fetch("chr1")
+
+    def testExplicitIndexCRAM(self):
+        with pysam.AlignmentFile(
+                os.path.join(BAM_DATADIR, "explicit_index.cram"),
+                "rc",
+                filepath_index=os.path.join(BAM_DATADIR, 'ex1.cram.crai')) as samfile:
+            samfile.fetch("chr1")
+
+    def testRemoteExplicitIndexBAM(self):
+        if not check_url(
+                "http://genserv.anat.ox.ac.uk/downloads/pysam/test/noindex.bam"):
+            return
+
+        with pysam.AlignmentFile(
+                "http://genserv.anat.ox.ac.uk/downloads/pysam/test/noindex.bam",
+                "rb",
+                filepath_index=os.path.join(BAM_DATADIR, 'ex1.bam.bai')) as samfile:
+            samfile.fetch("chr1")
+
+
+class TestVerbosity(unittest.TestCase):
+
+    '''test if setting/getting of verbosity works.'''
+
+    def testVerbosity(self):
+        self.assertEqual(pysam.get_verbosity(), 3)
+        old = pysam.set_verbosity(0)
+        self.assertEqual(pysam.get_verbosity(), 0)
+        new = pysam.set_verbosity(old)
+        self.assertEqual(new, 0)
+        self.assertEqual(pysam.get_verbosity(), 3)
+
+
+class TestSanityCheckingBAM(unittest.TestCase):
+
+    mode = "wb"
+
+    def check_write(self, read):
+
+        fn = "tmp_test_sanity_check.bam"
+        names = ["chr1"]
+        lengths = [10000]
+        with pysam.AlignmentFile(
+                fn,
+                self.mode,
+                reference_names=names,
+                reference_lengths=lengths) as outf:
+            outf.write(read)
+
+        if os.path.exists(fn):
+            os.unlink(fn)
+
+    def test_empty_read_gives_value_error(self):
+        read = pysam.AlignedSegment()
+        self.check_write(read)
+
+
+class TestLargeCigar(unittest.TestCase):
+
+    def setUp(self):
+        self.read_length = 70000
+        self.header = pysam.AlignmentHeader.from_references(
+            ["chr1", "chr2"],
+            [self.read_length * 2, self.read_length * 2])
+
+    def build_read(self):
+        '''build an example read.'''
+
+        a = pysam.AlignedSegment(self.header)
+        l = self.read_length
+        a.query_name = "read_12345"
+        a.query_sequence = "A" * (l + 1)
+        a.flag = 0
+        a.reference_id = 0
+        a.reference_start = 20
+        a.mapping_quality = 20
+        a.cigarstring = "1M1D" * l + "1M"
+        self.assertEqual(len(a.cigartuples), 2 * l + 1)
+        a.next_reference_id = 0
+        a.next_reference_start = 0
+        a.template_length = l
+        a.query_qualities = pysam.qualitystring_to_array("1") * (l + 1)
+        return a
+
+    def check_read(self, read, mode="bam"):
+        fn = get_temp_filename("tmp_largecigar.{}".format(mode))
+        fn_reference = get_temp_filename("tmp_largecigar.fa")
+
+        nrows = int(self.read_length * 2 / 80)
+
+        s = "\n".join(["A" * 80 for x in range(nrows)])
+        with open(fn_reference, "w") as outf:
+            outf.write(">chr1\n{seq}\n>chr2\n{seq}\n".format(
+                seq=s))
+
+        if mode == "bam":
+            write_mode = "wb"
+        elif mode == "sam":
+            write_mode = "w"
+        elif mode == "cram":
+            write_mode = "wc"
+
+        with pysam.AlignmentFile(fn, write_mode,
+                                 header=self.header,
+                                 reference_filename=fn_reference) as outf:
+            outf.write(read)
+        with pysam.AlignmentFile(fn) as inf:
+            ref_read = next(inf)
+
+        if mode == "cram":
+            # in CRAM, the tag field is kept, while it is emptied by the BAM/SAM reader
+            self.assertEqual(read.cigarstring, ref_read.cigarstring)
+        else:
+            self.assertEqual(read, ref_read)
+
+        os.unlink(fn)
+        os.unlink(fn_reference)
+
+    def test_reading_writing_sam(self):
+        read = self.build_read()
+        self.check_read(read, mode="sam")
+
+    def test_reading_writing_bam(self):
+        read = self.build_read()
+        self.check_read(read, mode="bam")
+
+    @unittest.skip("fails on linux - https issue?")
+    def test_reading_writing_cram(self):
+        # The following test fails with htslib 1.9, but worked with previous versions.
+        # Error is:
+        # [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/ac9fac7c3e9c476f74f1d0e47abc8be2": Input/output error
+        # Error can be reproduced using samtools 1.9 command line.
+        # Could be a conda configuration issue, see
+        # https://github.com/bioconda/bioconda-recipes/issues/9056
+        return
+        read = self.build_read()
+        self.check_read(read, mode="cram")
+        
+# SAM writing fails, as query length is 0
+# class TestSanityCheckingSAM(TestSanityCheckingSAM):
+#     mode = "w"
+
+if __name__ == "__main__":
+    print("starting tests")
+    unittest.main()
+    print("completed tests")
diff --git a/tests/PileupTestUtils.py b/tests/PileupTestUtils.py
new file mode 100644
index 0000000..33acc9e
--- /dev/null
+++ b/tests/PileupTestUtils.py
@@ -0,0 +1,161 @@
+import os
+import subprocess
+import pysam
+
+from TestUtils import force_str
+
+
+def build_pileup_with_samtoolsshell(fn):
+    os.system("samtools mpileup {} 2> /dev/null | wc -l > /dev/null".format(fn))
+    return 2998
+
+
+def build_pileup_with_samtoolspipe(fn):
+    FNULL = open(os.devnull, 'w')
+    with subprocess.Popen(["samtools", "mpileup", fn],
+                          stdin=subprocess.PIPE,
+                          stdout=subprocess.PIPE,
+                          stderr=FNULL) as proc:
+        return len(proc.stdout.readlines())
+
+    
+def build_pileup_with_pysam(*args, **kwargs):
+    with pysam.AlignmentFile(*args, **kwargs) as inf:
+        return len(list(inf.pileup(stepper="samtools")))
+
+
+def build_depth_with_samtoolsshell(fn):
+    os.system(
+        "samtools mpileup {} 2> /dev/null | awk '{{a += $4}} END {{print a}}' > /dev/null".format(fn))
+    return 107241
+
+
+def build_depth_with_samtoolspipe(fn):
+    FNULL = open(os.devnull, 'w')
+    with subprocess.Popen(["samtools", "mpileup", fn],
+                          stdin=subprocess.PIPE,
+                          stdout=subprocess.PIPE,
+                          stderr=FNULL) as proc:
+        data = [x.split() for x in proc.stdout.readlines()]
+        return [int(x[3]) for x in data]
+
+
+def build_depth_with_filter_with_pysam(*args, **kwargs):
+    with pysam.AlignmentFile(*args, **kwargs) as inf:
+        return [x.get_num_aligned() for x in inf.pileup(stepper="samtools")]
+
+
+def build_depth_with_pysam(*args, **kwargs):
+    with pysam.AlignmentFile(*args, **kwargs) as inf:
+        return [x.nsegments for x in inf.pileup(stepper="samtools")]
+
+
+def build_query_bases_with_samtoolsshell(fn):
+    os.system("samtools mpileup {} 2> /dev/null | awk '{{a = a $5}} END {{print a}}' | wc -c > /dev/null".format(fn))
+    return 116308
+
+
+def build_query_bases_with_samtoolspipe(fn, *args, **kwargs):
+    FNULL = open(os.devnull, 'w')
+    with subprocess.Popen(["samtools", "mpileup", fn] + list(args),
+                          stdin=subprocess.PIPE,
+                          stdout=subprocess.PIPE,
+                          stderr=FNULL) as proc:
+        stdout = proc.stdout.read().decode()
+        return [x.split()[4] for x in stdout.splitlines()]
+
+
+def build_query_bases_with_samtoolspysam(fn, *args):
+    return [x.split()[4] for x in pysam.samtools.mpileup(fn, *args).splitlines()]
+    
+
+def build_query_bases_with_pysam_pileups(*args, **kwargs):
+    total_pileup = []
+    with pysam.AlignmentFile(*args, **kwargs) as inf:
+        total_pileup = [
+            [r.alignment.query_sequence[r.query_position_or_next]
+                for r in column.pileups if r.query_position_or_next is not None]
+            for column in inf.pileup(stepper="samtools")]
+    return total_pileup
+
+
+def build_query_qualities_with_pysam_pileups(*args, **kwargs):
+    total_pileup = []
+    with pysam.AlignmentFile(*args, **kwargs) as inf:
+        total_pileup = [
+            [r.alignment.query_qualities[r.query_position_or_next]
+                for r in column.pileups if r.query_position_or_next is not None]
+            for column in inf.pileup(stepper="samtools")]
+    return total_pileup
+
+
+def build_query_bases_with_pysam(fn, *args, **kwargs):
+    total_pileup = []
+    with pysam.AlignmentFile(fn) as inf:
+        total_pileup = [column.get_query_sequences(
+            mark_ends=True, add_indels=True, mark_matches=True) for column in
+                        inf.pileup(*args, **kwargs)]
+    return total_pileup
+
+
+def build_query_names_with_pysam(*args, **kwargs):
+    total_pileup = []
+    with pysam.AlignmentFile(*args, **kwargs) as inf:
+        total_pileup = [column.get_query_names() for column in
+                        inf.pileup(stepper="samtools")]
+    return total_pileup
+
+
+def build_query_qualities_with_samtoolspipe(fn):
+    FNULL = open(os.devnull, 'w')
+    with subprocess.Popen(["samtools", "mpileup", fn],
+                          stdin=subprocess.PIPE,
+                          stdout=subprocess.PIPE,
+                          stderr=FNULL) as proc:
+        data = [force_str(x).split()[5] for x in proc.stdout.readlines()]
+    return data
+
+
+def build_query_qualities_with_pysam(*args, **kwargs):
+    total_pileup = []
+    with pysam.AlignmentFile(*args, **kwargs) as inf:
+        total_pileup = [column.get_query_qualities() for column in
+                        inf.pileup(stepper="samtools")]
+    return total_pileup
+
+
+def build_mapping_qualities_with_samtoolspipe(fn):
+    FNULL = open(os.devnull, 'w')
+    with subprocess.Popen(["samtools", "mpileup", "-s", fn],
+                          stdin=subprocess.PIPE,
+                          stdout=subprocess.PIPE,
+                          stderr=FNULL) as proc:
+        data = [force_str(x).split()[6] for x in proc.stdout.readlines()]
+    return data
+
+
+def build_mapping_qualities_with_pysam(*args, **kwargs):
+    total_pileup = []
+    with pysam.AlignmentFile(*args, **kwargs) as inf:
+        total_pileup = [column.get_mapping_qualities() for column in
+                        inf.pileup(stepper="samtools")]
+    return total_pileup
+
+
+def build_query_positions_with_samtoolspipe(fn):
+    FNULL = open(os.devnull, 'w')
+    with subprocess.Popen(["samtools", "mpileup", "-O", fn],
+                          stdin=subprocess.PIPE,
+                          stdout=subprocess.PIPE,
+                          stderr=FNULL) as proc:
+        data = [list(map(int, force_str(x).split()[6].split(",")))
+                for x in proc.stdout.readlines()]
+    return data
+
+
+def build_query_positions_with_pysam(*args, **kwargs):
+    total_pileup = []
+    with pysam.AlignmentFile(*args, **kwargs) as inf:
+        total_pileup = [column.get_query_positions() for column in
+                        inf.pileup(stepper="samtools")]
+    return total_pileup
diff --git a/tests/StreamFiledescriptors_test.py b/tests/StreamFiledescriptors_test.py
new file mode 100644
index 0000000..07adea8
--- /dev/null
+++ b/tests/StreamFiledescriptors_test.py
@@ -0,0 +1,93 @@
+import os
+import sys
+import subprocess
+import threading
+import errno
+import unittest
+from pysam import AlignmentFile
+from TestUtils import make_data_files, BAM_DATADIR
+
+IS_PYTHON2 = sys.version_info[0] == 2
+
+
+def setUpModule():
+    make_data_files(BAM_DATADIR)
+
+
+def alignmentfile_writer_thread(infile, outfile):
+    def _writer_thread(infile, outfile):
+        """read from infile and write to outfile"""
+        try:
+            i = 0
+            for record in infile:
+                outfile.write(record)
+                i += 1
+        except IOError as e:
+            if e.errno != errno.EPIPE:
+                pass
+        finally:
+            outfile.close()
+
+    writer = threading.Thread(target=_writer_thread, args=(infile, outfile))
+    writer.daemon = True
+    writer.start()
+    return writer
+
+
+class StreamTest(unittest.TestCase):
+
+    def stream_process(self, proc, in_stream, out_stream, writer):
+
+        with AlignmentFile(proc.stdout) as infile:
+            read = 0
+            for record in infile:
+                read += 1
+        return 0, read
+
+    @unittest.skipIf(IS_PYTHON2, "no context manager in py2")
+    def test_text_processing(self):
+
+        with subprocess.Popen('head -n200',
+                              stdin=subprocess.PIPE,
+                              stdout=subprocess.PIPE,
+                              shell=True) as proc:
+
+            in_stream = AlignmentFile(os.path.join(BAM_DATADIR, 'ex1.bam'))
+            out_stream = AlignmentFile(
+                proc.stdin, 'wh', header=in_stream.header)
+            writer = alignmentfile_writer_thread(in_stream,
+                                                 out_stream)
+
+            written, read = self.stream_process(proc,
+                                                in_stream,
+                                                out_stream,
+                                                writer)
+            self.assertEqual(read, 198)
+
+    @unittest.skip("test contains bug")
+    def test_samtools_processing(self):
+
+        # The following test causes the suite to hang
+        # as the stream_processor raises:
+        # ValueError: file has no sequences defined (mode='r') - is it SAM/BAM format?
+        # The whole setup then hangs during exception handling.
+        with subprocess.Popen('samtools view -b -f 4',
+                              stdin=subprocess.PIPE,
+                              stdout=subprocess.PIPE,
+                              shell=True) as proc:
+
+            in_stream = AlignmentFile(os.path.join(BAM_DATADIR, 'ex1.bam'))
+            out_stream = AlignmentFile(
+                proc.stdin, 'wb', header=in_stream.header)
+            writer = alignmentfile_writer_thread(in_stream,
+                                                 out_stream)
+
+            written, read = self.stream_process(proc,
+                                                in_stream,
+                                                out_stream,
+                                                writer)
+            self.assertEqual(read, 35)
+
+
+if __name__ == "__main__":
+    unittest.main()
diff --git a/tests/TestUtils.py b/tests/TestUtils.py
new file mode 100644
index 0000000..e5dee6c
--- /dev/null
+++ b/tests/TestUtils.py
@@ -0,0 +1,294 @@
+import sys
+import os
+import glob
+import gzip
+import contextlib
+import inspect
+import subprocess
+import tempfile
+import pysam
+
+WORKDIR = os.path.abspath(os.path.join(os.path.dirname(__file__),
+                                       "pysam_test_work"))
+
+BAM_DATADIR = os.path.abspath(os.path.join(os.path.dirname(__file__),
+                                           "pysam_data"))
+
+TABIX_DATADIR = os.path.abspath(os.path.join(os.path.dirname(__file__),
+                                             "tabix_data"))
+
+CBCF_DATADIR = os.path.abspath(os.path.join(os.path.dirname(__file__),
+                                            "cbcf_data"))
+
+LINKDIR = os.path.abspath(os.path.join(
+    os.path.dirname(__file__), "..", "linker_tests"))
+
+
+TESTS_TEMPDIR = os.path.abspath(os.path.join(os.path.dirname(__file__), "tmp"))
+
+
+IS_PYTHON3 = sys.version_info[0] >= 3
+
+
+if IS_PYTHON3:
+    from itertools import zip_longest
+    from urllib.request import urlopen
+else:
+    from itertools import izip as zip_longest
+    from urllib2 import urlopen
+
+
+if IS_PYTHON3:
+    def force_str(s):
+        try:
+            return s.decode('ascii')
+        except AttributeError:
+            return s
+
+    def force_bytes(s):
+        try:
+            return s.encode('ascii')
+        except AttributeError:
+            return s
+else:
+    def force_str(s):
+        return s
+
+    def force_bytes(s):
+        return s
+
+
+def openfile(fn):
+    if fn.endswith(".gz"):
+        try:
+            return gzip.open(fn, "rt", encoding="utf-8")
+        except TypeError:
+            return gzip.open(fn, "r")
+    else:
+        return open(fn)
+
+
+def checkBinaryEqual(filename1, filename2):
+    '''return true if the two files are binary equal.
+    '''
+    if os.path.getsize(filename1) != os.path.getsize(filename2):
+        return False
+
+    infile1 = open(filename1, "rb")
+    infile2 = open(filename2, "rb")
+
+    def chariter(infile):
+        while 1:
+            c = infile.read(1)
+            if c == b"":
+                break
+            yield c
+
+    found = False
+    for c1, c2 in zip_longest(chariter(infile1), chariter(infile2)):
+        if c1 != c2:
+            break
+    else:
+        found = True
+
+    infile1.close()
+    infile2.close()
+    return found
+
+
+def checkGZBinaryEqual(filename1, filename2):
+    '''return true if the decompressed contents of the two files
+    are binary equal.
+    '''
+    with gzip.open(filename1, "rb") as infile1:
+        d1 = infile1.read()
+        with gzip.open(filename2, "rb") as infile2:
+            d2 = infile2.read()
+        if d1 == d2:
+            return True
+    return False
+
+
+def check_samtools_view_equal(
+        filename1, filename2,
+        without_header=False):
+    '''return true if the two files are equal in their
+    content through samtools view.
+    '''
+    # strip MD and NM tags, as not preserved in CRAM files
+    args = ["-x", "MD", "-x", "NM"]
+    if not without_header:
+        args.append("-h")
+
+    lines1 = pysam.samtools.view(*(args + [filename1]))
+    lines2 = pysam.samtools.view(*(args + [filename2]))
+
+    if len(lines1) != len(lines2):
+        return False
+
+    if lines1 != lines2:
+        # line by line comparison
+        # sort each line, as tags get rearranged between
+        # BAM/CRAM
+        for n, pair in enumerate(zip(lines1, lines2)):
+            l1, l2 = pair
+            l1 = sorted(l1[:-1].split("\t"))
+            l2 = sorted(l2[:-1].split("\t"))
+            if l1 != l2:
+                print("mismatch in line %i" % n)
+                print(l1)
+                print(l2)
+                return False
+        else:
+            return False
+
+    return True
+
+
+def check_url(url):
+    '''return True if URL is available.
+
+    A URL might not be available if it is the wrong URL
+    or there is no connection to the URL.
+    '''
+    try:
+        urlopen(url, timeout=1)
+        return True
+    except:
+        return False
+
+
+def checkFieldEqual(cls, read1, read2, exclude=[]):
+    '''check if two reads are equal by comparing each field.'''
+
+    # add the . for refactoring purposes.
+    for x in (".query_name",
+              ".query_sequence",
+              ".flag",
+              ".reference_id",
+              ".reference_start",
+              ".mapping_quality",
+              ".cigartuples",
+              ".next_reference_id",
+              ".next_reference_start",
+              ".template_length",
+              ".query_length",
+              ".query_qualities",
+              ".bin",
+              ".is_paired", ".is_proper_pair",
+              ".is_unmapped", ".is_mapped",
+              ".mate_is_unmapped", ".mate_is_mapped",
+              ".is_reverse", ".is_forward",
+              ".mate_is_reverse", ".mate_is_forward",
+              ".is_read1", ".is_read2",
+              ".is_secondary", ".is_qcfail",
+              ".is_duplicate"):
+        n = x[1:]
+        if n in exclude:
+            continue
+        cls.assertEqual(getattr(read1, n), getattr(read2, n),
+                        "attribute mismatch for %s: %s != %s" %
+                        (n, getattr(read1, n), getattr(read2, n)))
+
+
+def check_lines_equal(cls, a, b, sort=False, filter_f=None, msg=None):
+    """check if contents of two files are equal comparing line-wise.
+
+    sort: bool
+       sort contents of both files before comparing.
+    filter_f:
+       remover lines in both a and b where expression is True
+    """
+    with openfile(a) as inf:
+        aa = inf.readlines()
+    with openfile(b) as inf:
+        bb = inf.readlines()
+
+    if filter_f is not None:
+        aa = [x for x in aa if not filter_f(x)]
+        bb = [x for x in bb if not filter_f(x)]
+
+    if sort:
+        cls.assertEqual(sorted(aa), sorted(bb), msg)
+    else:
+        cls.assertEqual(aa, bb, msg)
+
+
+def get_temp_filename(suffix=""):
+    caller_name = inspect.getouterframes(inspect.currentframe(), 2)[1][3]
+    try:
+        os.makedirs(TESTS_TEMPDIR)
+    except OSError:
+        pass
+
+    f = tempfile.NamedTemporaryFile(
+        prefix="pysamtests_tmp_{}_".format(caller_name),
+        suffix=suffix,
+        delete=False,
+        dir=TESTS_TEMPDIR)
+
+    f.close()
+    return f.name
+
+@contextlib.contextmanager
+def get_temp_context(suffix="", keep=False):
+    caller_name = inspect.getouterframes(inspect.currentframe(), 3)[1][3]
+    try:
+        os.makedirs(TESTS_TEMPDIR)
+    except OSError:
+        pass
+
+    f = tempfile.NamedTemporaryFile(
+        prefix="pysamtests_tmp_{}_".format(caller_name),
+        suffix=suffix,
+        delete=False,
+        dir=TESTS_TEMPDIR)
+
+    f.close()
+    yield f.name
+    
+    if not keep:
+        # clear up any indices as well
+        for f in glob.glob(f.name + "*"):
+            os.unlink(f)
+
+
+def make_data_files(directory):
+    what = None
+    try:
+        if not os.path.exists(os.path.join(directory, "all.stamp")):
+            subprocess.check_output(["make", "-C", directory], stderr=subprocess.STDOUT)
+    except subprocess.CalledProcessError as e:
+        what = "Making test data in '%s' failed:\n%s" % (directory, force_str(e.output))
+
+    if what is not None:
+        raise RuntimeError(what)
+
+
+def load_and_convert(filename, encode=True):
+    '''load data from filename and convert all fields to string.
+
+    Filename can be either plain or compressed (ending in .gz).
+    '''
+    data = []
+    if filename.endswith(".gz"):
+        with gzip.open(filename) as inf:
+            for line in inf:
+                line = line.decode("ascii")
+                if line.startswith("#"):
+                    continue
+                d = line.strip().split("\t")
+                data.append(d)
+    else:
+        with open(filename) as f:
+            for line in f:
+                if line.startswith("#"):
+                    continue
+                d = line.strip().split("\t")
+                data.append(d)
+
+    return data
+
+
+def flatten_nested_list(l):
+    return [i for ll in l for i in ll]
diff --git a/tests/VariantFileFetchTestUtils.py b/tests/VariantFileFetchTestUtils.py
new file mode 100644
index 0000000..4c16b97
--- /dev/null
+++ b/tests/VariantFileFetchTestUtils.py
@@ -0,0 +1,67 @@
+import os
+import subprocess
+import pysam
+
+try:
+    import cyvcf2
+except ImportError:
+    pass
+    
+
+def build_filter_from_vcf_with_samtoolsshell(fn):
+    retval = os.popen(
+        "bcftools filter -e \"N_ALT != 1 || QUAL < 20 || maf[0]>0.05\" {} | grep -cv ^# ".format(fn)).read()
+    return int(retval.strip())
+
+
+def build_filter_from_vcf_with_bcftoolspipe(fn):
+    FNULL = open(os.devnull, 'w')
+    with subprocess.Popen([
+            "bcftools",
+            "filter",
+            "-e",
+            "N_ALT != 1 || QUAL < 20 || maf[0]>0.05",
+            fn],
+                          stdin=subprocess.PIPE,
+                          stdout=subprocess.PIPE,
+                          stderr=FNULL) as proc:
+        data = [line for line in proc.stdout.readlines() if not line.startswith(b"#")]
+        return len(data)
+
+
+def build_filter_from_vcf_with_cyvcf2(fn):
+    n = 0
+    try:
+        for v in cyvcf2.VCF(fn):
+            if len(v.ALT) > 1:
+                continue
+            if v.QUAL < 20:
+                continue
+            if v.aaf > 0.05:
+                continue
+            n += 1
+    except NameError:
+        n = 9120
+    return n
+
+
+def build_filter_from_vcf_with_pysam(fn):
+    n = 0
+    with pysam.VariantFile(fn) as vcf:
+        for v in vcf:
+            # the two commands below take >1s out of 19s total
+            if len(v.alts) > 1:
+                continue
+            if v.qual < 20:
+                continue
+            # this takes 12s out of 19s total
+            gts = [s['GT'] for s in v.samples.values()]
+            # the lines below take 6s out of 19s total
+            an = sum(len(gt) for gt in gts)
+            ac = sum(sum(gt) for gt in gts)
+            aaf = (float(ac) / float(an))
+            if aaf > 0.05:
+                continue
+            n += 1
+    return n
+                                        
diff --git a/tests/VariantFile_bench.py b/tests/VariantFile_bench.py
new file mode 100644
index 0000000..9663ea6
--- /dev/null
+++ b/tests/VariantFile_bench.py
@@ -0,0 +1,57 @@
+"""Benchmarking module for AlignmentFile functionality"""
+import pytest
+
+
+from VariantFileFetchTestUtils import *
+
+
+GENOMES_URL = "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr{chrom}.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz"
+
+CHROM = 22
+
+
+@pytest.fixture
+def genomes_data():
+    url = GENOMES_URL.format(chrom=CHROM)
+    fn = os.path.basename(url)
+    print(fn)
+    if not os.path.exists(fn):
+        os.system("wget {}".format(url))
+    if not os.path.exists(fn + ".tbi"):
+        os.system("wget {}".format(url + ".tbi"))
+
+    fn_small = "small.vcf.gz"
+    if not os.path.exists(fn_small):
+        os.system("bcftools view {} | head -n 10000 | bgzip > {}".format(fn, fn_small))
+        os.system("tabix -p vcf {}".format(fn_small))
+        
+    return fn_small
+
+
+@pytest.mark.benchmark(min_rounds=1)
+def test_build_filter_from_vcf_with_bcftoolsshell(benchmark, genomes_data):
+    result = benchmark(build_filter_from_vcf_with_samtoolsshell, genomes_data)
+    assert result == 9120
+
+
+@pytest.mark.benchmark(min_rounds=1)
+def test_build_filter_from_vcf_with_bcftoolpipe(benchmark, genomes_data):
+    result = benchmark(build_filter_from_vcf_with_bcftoolspipe, genomes_data)
+    assert result == 9120
+
+
+@pytest.mark.benchmark(min_rounds=1)
+def test_build_filter_from_vcf_with_cyvcf2(benchmark, genomes_data):
+    result = benchmark(build_filter_from_vcf_with_cyvcf2, genomes_data)
+    # note: inconsistent with bcftools
+    assert result == 9114
+
+
+@pytest.mark.benchmark(min_rounds=1)
+def test_build_filter_from_vcf_with_pysam(benchmark, genomes_data):
+    result = benchmark(build_filter_from_vcf_with_pysam, genomes_data)
+    # note: inconsistent with bcftools
+    assert result == 9114
+    
+
+    
diff --git a/tests/VariantFile_test.py b/tests/VariantFile_test.py
new file mode 100644
index 0000000..6224f0c
--- /dev/null
+++ b/tests/VariantFile_test.py
@@ -0,0 +1,703 @@
+# -*- coding: utf-8 -*-
+
+import os
+import glob
+import sys
+import unittest
+import pysam
+import shutil
+import gzip
+
+try:
+    from pathlib import Path
+except ImportError:
+    Path = None
+
+from TestUtils import get_temp_filename, check_lines_equal, load_and_convert, make_data_files, CBCF_DATADIR, get_temp_context
+
+
+def setUpModule():
+    make_data_files(CBCF_DATADIR)
+
+
+def read_header(filename):
+    data = []
+    if filename.endswith(".gz"):
+        for line in gzip.open(filename):
+            line = line.decode("ascii")
+            if line.startswith("#"):
+                data.append(line)
+    else:
+        with open(filename) as f:
+            for line in f:
+                if line.startswith("#"):
+                    data.append(line)
+
+    return data
+
+
+def read_index_header(filename):
+    with gzip.open(filename) as infile:
+        magic = infile.read(4)
+    return magic
+
+
+class TestMissingGenotypes(unittest.TestCase):
+
+    filename = "missing_genotypes.vcf"
+
+    def setUp(self):
+        self.compare = load_and_convert(
+            os.path.join(CBCF_DATADIR, self.filename),
+            encode=False)
+
+    def check(self, filename):
+        """see issue 203 - check for segmentation fault"""
+        fn = os.path.join(CBCF_DATADIR, filename)
+        self.assertEqual(True, os.path.exists(fn))
+        v = pysam.VariantFile(fn)
+        for site in v:
+            for ss, rec in site.samples.items():
+                a, b = ss, rec
+
+        v = pysam.VariantFile(fn)
+        for x, site in enumerate(v):
+            for ss, rec in site.samples.items():
+                a, b = ss, rec.alleles
+                a, b = ss, rec.allele_indices
+
+    def testVCF(self):
+        self.check(self.filename)
+
+    def testVCFGZ(self):
+        self.check(self.filename + ".gz")
+
+
+class TestMissingSamples(unittest.TestCase):
+
+    filename = "gnomad.vcf"
+
+    def setUp(self):
+        self.compare = load_and_convert(
+            os.path.join(CBCF_DATADIR, self.filename),
+            encode=False)
+
+    def check(self, filename):
+        """see issue #593"""
+        fn = os.path.join(CBCF_DATADIR, filename)
+        self.assertEqual(True, os.path.exists(fn))
+        expect_fail = not "fixed" in self.filename
+        with pysam.VariantFile(fn) as inf:
+            rec = next(inf.fetch())
+            if expect_fail:
+                self.assertRaises(ValueError, rec.info.__getitem__, "GC")
+            else:
+                self.assertEqual(rec.info["GC"], (27, 35, 16))
+
+    def testVCF(self):
+        self.check(self.filename)
+
+    def testVCFGZ(self):
+        self.check(self.filename + ".gz")
+
+
+class TestMissingSamplesFixed(TestMissingSamples):
+    # workaround for NUMBER=G in INFO records:
+    # perl 's/Number=G/Number=./ if (/INFO/)'
+    
+    filename = "gnomad_fixed.vcf"
+
+
+class TestOpening(unittest.TestCase):
+
+    def testMissingFile(self):
+        self.assertRaises(IOError, pysam.VariantFile,
+                          "missing_file.vcf")
+
+    def testMissingFileVCFGZ(self):
+        self.assertRaises(IOError, pysam.VariantFile,
+                          "missing_file.vcf.gz")
+
+    def testEmptyFileVCF(self):
+        with get_temp_context("tmp_testEmptyFile.vcf") as fn:
+            with open(fn, "w"):
+                pass
+            self.assertRaises(ValueError, pysam.VariantFile, fn)
+
+    if Path and sys.version_info >= (3, 6):
+        def testEmptyFileVCFFromPath(self):
+            with get_temp_context("tmp_testEmptyFile.vcf") as fn:
+                with open(fn, "w"):
+                    pass
+                self.assertRaises(ValueError, pysam.VariantFile,
+                                  Path(fn))
+
+    def testEmptyFileVCFGZWithIndex(self):
+        with get_temp_context("tmp_testEmptyFile.vcf") as fn:
+            with open(fn, "w"):
+                pass
+            # tabix_index will automatically compress
+            pysam.tabix_index(fn,
+                              preset="vcf",
+                              force=True)
+
+            self.assertRaises(ValueError, pysam.VariantFile, fn + ".gz")
+
+    def testEmptyFileVCFGZWithoutIndex(self):
+        with get_temp_context("tmp_testEmptyFileWithoutIndex.vcf") as fn:
+            with open(fn, "w"):
+                pass
+
+            pysam.tabix_compress(fn,
+                                 fn + ".gz",
+                                 force=True)
+
+            self.assertRaises(ValueError, pysam.VariantFile, fn + ".gz")
+
+    def testEmptyFileVCFOnlyHeader(self):
+        with pysam.VariantFile(os.path.join(
+                CBCF_DATADIR,
+                "example_vcf42_only_header.vcf")) as inf:
+            self.assertEqual(len(list(inf.fetch())), 0)
+
+    def testEmptyFileVCFGZOnlyHeader(self):
+        with pysam.VariantFile(os.path.join(
+                CBCF_DATADIR,
+                "example_vcf42_only_header.vcf")) as inf:
+            self.assertEqual(len(list(inf.fetch())), 0)
+
+    def testDetectVCF(self):
+        with pysam.VariantFile(os.path.join(CBCF_DATADIR,
+                                            "example_vcf40.vcf")) as inf:
+            self.assertEqual(inf.category, 'VARIANTS')
+            self.assertEqual(inf.format, 'VCF')
+            self.assertEqual(inf.compression, 'NONE')
+            self.assertFalse(inf.is_remote)
+            self.assertFalse(inf.is_stream)
+            self.assertEqual(len(list(inf.fetch())), 5)
+
+    def testDetectVCFGZ(self):
+        with pysam.VariantFile(os.path.join(CBCF_DATADIR,
+                                            "example_vcf40.vcf.gz")) as inf:
+            self.assertEqual(inf.category, 'VARIANTS')
+            self.assertEqual(inf.format, 'VCF')
+            self.assertEqual(inf.compression, 'BGZF')
+            self.assertFalse(inf.is_remote)
+            self.assertFalse(inf.is_stream)
+            self.assertEqual(len(list(inf.fetch())), 5)
+
+    def testDetectBCF(self):
+        with pysam.VariantFile(os.path.join(
+                CBCF_DATADIR,
+                "example_vcf40.bcf")) as inf:
+            self.assertEqual(inf.category, 'VARIANTS')
+            self.assertEqual(inf.format, 'BCF')
+            self.assertEqual(inf.compression, 'BGZF')
+            self.assertFalse(inf.is_remote)
+            self.assertFalse(inf.is_stream)
+            self.assertEqual(len(list(inf.fetch())), 5)
+
+
+class TestIndexFormatsVCF(unittest.TestCase):
+
+    vcf_filename = os.path.join(CBCF_DATADIR, "example_vcf40.vcf")
+    bcf_filename = os.path.join(CBCF_DATADIR, "example_vcf40.bcf")
+    
+    def test_vcf_with_tbi_index(self):
+        with get_temp_context("tmp_fn.vcf") as fn:
+            shutil.copyfile(self.vcf_filename, fn)
+            pysam.tabix_index(fn, preset="vcf", force=True)
+            self.assertTrue(os.path.exists(fn + ".gz" + ".tbi"))
+            self.assertEqual(read_index_header(fn + ".gz.tbi"), b"TBI\1")
+            self.assertFalse(os.path.exists(fn + ".gz" + ".csi"))
+            
+            with pysam.VariantFile(fn + ".gz") as inf:
+                self.assertEqual(len(list(inf.fetch("20"))), 3)
+
+    def test_vcf_with_csi_index(self):
+        with get_temp_context("tmp_fn.vcf") as fn:
+            shutil.copyfile(self.vcf_filename, fn)
+
+            pysam.tabix_index(fn, preset="vcf", force=True, csi=True)
+            self.assertTrue(os.path.exists(fn + ".gz" + ".csi"))
+            self.assertEqual(read_index_header(fn + ".gz.csi"), b"CSI\1")
+            self.assertFalse(os.path.exists(fn + ".gz" + ".tbi"))
+            
+            with pysam.VariantFile(fn + ".gz") as inf:
+                self.assertEqual(len(list(inf.fetch("20"))), 3)
+
+    def test_bcf_with_prebuilt_csi(self):
+        with get_temp_context("tmp_fn.bcf") as fn:
+            shutil.copyfile(self.bcf_filename, fn)
+            shutil.copyfile(self.bcf_filename + ".csi", fn + ".csi")
+
+            self.assertTrue(os.path.exists(fn + ".csi"))
+            self.assertEqual(read_index_header(fn + ".csi"), b"CSI\1")
+            self.assertFalse(os.path.exists(fn + ".tbi"))
+            
+            with pysam.VariantFile(fn) as inf:
+                self.assertEqual(len(list(inf.fetch("20"))), 3)
+
+    def test_bcf_with_tbi_index_will_produce_csi(self):
+        with get_temp_context("tmp_fn.bcf") as fn:
+            shutil.copyfile(self.bcf_filename, fn)
+
+            pysam.tabix_index(fn, preset="bcf", force=True, csi=False)
+            self.assertTrue(os.path.exists(fn + ".csi"))
+            self.assertEqual(read_index_header(fn + ".csi"), b"CSI\1")
+            self.assertFalse(os.path.exists(fn + ".tbi"))
+            
+            with pysam.VariantFile(fn) as inf:
+                self.assertEqual(len(list(inf.fetch("20"))), 3)
+
+    def test_bcf_with_csi_index(self):
+        with get_temp_context("tmp_fn.bcf") as fn:
+            shutil.copyfile(self.bcf_filename, fn)
+
+            pysam.tabix_index(fn, preset="vcf", force=True, csi=True)
+            
+            self.assertTrue(os.path.exists(fn + ".csi"))
+            self.assertEqual(read_index_header(fn + ".csi"), b"CSI\1")
+            self.assertFalse(os.path.exists(fn + ".tbi"))
+            
+            with pysam.VariantFile(fn) as inf:
+                self.assertEqual(len(list(inf.fetch("20"))), 3)
+
+
+class TestHeader(unittest.TestCase):
+
+    filename = "example_vcf40.vcf"
+
+    def testStr(self):
+
+        fn = os.path.join(CBCF_DATADIR, self.filename)
+        v = pysam.VariantFile(fn)
+
+        ref = read_header(fn)
+        comp = str(v.header).splitlines(True)
+
+        self.assertEqual(sorted(ref),
+                         sorted(comp))
+
+    def testIterator(self):
+
+        fn = os.path.join(CBCF_DATADIR, self.filename)
+        v = pysam.VariantFile(fn)
+
+        ref = read_header(fn)
+        # remove last header line starting with #CHROM
+        ref.pop()
+        ref = sorted(ref)
+        comp = sorted(str(x) for x in v.header.records)
+
+        self.assertEqual(len(ref), len(comp))
+
+        for x, y in zip(ref, comp):
+            self.assertEqual(x, y)
+
+
+# These tests need to be separate and start from newly opened files.  This
+# is because htslib's parser is lazy and the pysam API needs to trigger
+# appropriate parsing when accessing each time of data.  Failure to do so
+# will result in crashes or return of incorrect data.  Thus this test suite
+# is testing both the triggering of the lazy parser and the results of the
+# parser.
+class TestParsing(unittest.TestCase):
+
+    filename = "example_vcf40.vcf.gz"
+
+    def testChrom(self):
+        fn = os.path.join(CBCF_DATADIR, self.filename)
+        v = pysam.VariantFile(fn)
+        chrom = [rec.chrom for rec in v]
+        self.assertEqual(chrom, ['M', '17', '20', '20', '20'])
+
+    if Path and sys.version_info >= (3, 6):
+        def testChromFromPath(self):
+            fn = os.path.join(CBCF_DATADIR, self.filename)
+            v = pysam.VariantFile(Path(fn))
+            chrom = [rec.chrom for rec in v]
+            self.assertEqual(chrom, ['M', '17', '20', '20', '20'])
+
+    def testPos(self):
+        fn = os.path.join(CBCF_DATADIR, self.filename)
+        v = pysam.VariantFile(fn)
+        pos = [rec.pos for rec in v]
+        self.assertEqual(pos, [1230237, 14370, 17330, 1110696, 1234567])
+
+    def testStart(self):
+        fn = os.path.join(CBCF_DATADIR, self.filename)
+        v = pysam.VariantFile(fn)
+        start = [rec.start for rec in v]
+        self.assertEqual(start, [1230236, 14369, 17329, 1110695, 1234566])
+
+    def testStop(self):
+        fn = os.path.join(CBCF_DATADIR, self.filename)
+        v = pysam.VariantFile(fn)
+        stop = [rec.stop for rec in v]
+        self.assertEqual(stop, [1230237, 14370, 17330, 1110696, 1234570])
+
+    def testId(self):
+        fn = os.path.join(CBCF_DATADIR, self.filename)
+        v = pysam.VariantFile(fn)
+        ids = [rec.id for rec in v]
+        self.assertEqual(
+            ids, [None, 'rs6054257', None, 'rs6040355', 'microsat1'])
+
+    def testRef(self):
+        fn = os.path.join(CBCF_DATADIR, self.filename)
+        v = pysam.VariantFile(fn)
+        ref = [rec.ref for rec in v]
+        self.assertEqual(ref, ['T', 'G', 'T', 'A', 'GTCT'])
+
+    def testAlt(self):
+        fn = os.path.join(CBCF_DATADIR, self.filename)
+        v = pysam.VariantFile(fn)
+        alts = [rec.alts for rec in v]
+        self.assertEqual(alts, [None, ('A',), ('A',),
+                                ('G', 'T'), ('G', 'GTACT')])
+
+    def testAlleles(self):
+        fn = os.path.join(CBCF_DATADIR, self.filename)
+        v = pysam.VariantFile(fn)
+        alleles = [rec.alleles for rec in v]
+        self.assertEqual(alleles, [
+                         ('T',), ('G', 'A'), ('T', 'A'), ('A', 'G', 'T'), ('GTCT', 'G', 'GTACT')])
+
+    def testAllelesVariantTypes(self):
+        fn = os.path.join(CBCF_DATADIR, self.filename)
+        v = pysam.VariantFile(fn)
+        rec = next(v)
+
+        self.assertEqual(rec.alleles, ('T',))
+        self.assertEqual(rec.alleles_variant_types, ("REF",))
+
+        rec.alleles = ("T", "C")
+        self.assertEqual(rec.alleles_variant_types, ("REF", "SNP"))
+
+        rec.alts = ("TC",)
+        self.assertEqual(rec.alleles_variant_types, ("REF", "INDEL"))
+
+        rec.ref = "AG"
+        self.assertEqual(rec.alleles_variant_types, ("REF", "MNP"))
+
+    def testQual(self):
+        fn = os.path.join(CBCF_DATADIR, self.filename)
+        v = pysam.VariantFile(fn)
+        qual = [rec.qual for rec in v]
+        self.assertEqual(qual, [47.0, 29.0, 3.0, 67.0, 50.0])
+
+    def testFilter(self):
+        fn = os.path.join(CBCF_DATADIR, self.filename)
+        v = pysam.VariantFile(fn)
+        filter = [rec.filter.keys() for rec in v]
+        self.assertEqual(filter, [['PASS'], ['PASS'],
+                                  ['q10'], ['PASS'], ['PASS']])
+
+    def testInfo(self):
+        fn = os.path.join(CBCF_DATADIR, self.filename)
+        v = pysam.VariantFile(fn)
+        info = [rec.info.items() for rec in v]
+        self.assertEqual(info, [[('NS', 3), ('DP', 13), ('AA', 'T')],
+                                [('NS', 3), ('DP', 14), ('AF', (0.5,)),
+                                 ('DB', True), ('H2', True)],
+                                [('NS', 3), ('DP', 11),
+                                 ('AF', (0.017000000923871994,))],
+                                [('NS', 2), ('DP', 10), ('AF', (0.3330000042915344, 0.6669999957084656)),
+                                 ('AA', 'T'), ('DB', True)],
+                                [('NS', 3), ('DP', 9), ('AA', 'G')]])
+
+    def testFormat(self):
+        fn = os.path.join(CBCF_DATADIR, self.filename)
+        v = pysam.VariantFile(fn)
+        format = [rec.format.keys() for rec in v]
+        self.assertEqual(format, [['GT', 'GQ', 'DP', 'HQ'],
+                                  ['GT', 'GQ', 'DP', 'HQ'],
+                                  ['GT', 'GQ', 'DP', 'HQ'],
+                                  ['GT', 'GQ', 'DP', 'HQ'],
+                                  ['GT', 'GQ', 'DP']])
+
+    def testSampleAlleles(self):
+        fn = os.path.join(CBCF_DATADIR, self.filename)
+        v = pysam.VariantFile(fn)
+        alleles = [s.alleles for rec in v for s in rec.samples.values()]
+        self.assertEqual(alleles, [('T', 'T'), ('T', 'T'), ('T', 'T'),
+                                   ('G', 'G'), ('A', 'G'), ('A', 'A'),
+                                   ('T', 'T'), ('T', 'A'), ('T', 'T'),
+                                   ('G', 'T'), ('T', 'G'), ('T', 'T'),
+                                   ('GTCT', 'G'), ('GTCT', 'GTACT'),
+                                   ('G', 'G')])
+
+    def testSampleFormats(self):
+        fn = os.path.join(CBCF_DATADIR, self.filename)
+        v = pysam.VariantFile(fn)
+        format = [s.items() for rec in v for s in rec.samples.values()]
+        self.assertEqual(format, [[('GT', (0, 0)), ('GQ', 54), ('DP', 7), ('HQ', (56, 60))],
+                                  [('GT', (0, 0)), ('GQ', 48),
+                                   ('DP', 4), ('HQ', (51, 51))],
+                                  [('GT', (0, 0)), ('GQ', 61),
+                                   ('DP', 2), ('HQ', (None,))],
+                                  [('GT', (0, 0)), ('GQ', 48),
+                                   ('DP', 1), ('HQ', (51, 51))],
+                                  [('GT', (1, 0)), ('GQ', 48),
+                                   ('DP', 8), ('HQ', (51, 51))],
+                                  [('GT', (1, 1)), ('GQ', 43),
+                                   ('DP', 5), ('HQ', (None, None))],
+                                  [('GT', (0, 0)), ('GQ', 49),
+                                   ('DP', 3), ('HQ', (58, 50))],
+                                  [('GT', (0, 1)), ('GQ', 3),
+                                   ('DP', 5), ('HQ', (65, 3))],
+                                  [('GT', (0, 0)), ('GQ', 41),
+                                   ('DP', 3), ('HQ', (None,))],
+                                  [('GT', (1, 2)), ('GQ', 21),
+                                   ('DP', 6), ('HQ', (23, 27))],
+                                  [('GT', (2, 1)), ('GQ', 2),
+                                   ('DP', 0), ('HQ', (18, 2))],
+                                  [('GT', (2, 2)), ('GQ', 35),
+                                   ('DP', 4), ('HQ', (None,))],
+                                  [('GT', (0, 1)), ('GQ', 35), ('DP', 4)],
+                                  [('GT', (0, 2)), ('GQ', 17), ('DP', 2)],
+                                  [('GT', (1, 1)), ('GQ', 40), ('DP', 3)]])
+
+    def testSampleAlleleIndices(self):
+        fn = os.path.join(CBCF_DATADIR, self.filename)
+        v = pysam.VariantFile(fn)
+        indices = [s.allele_indices for rec in v for s in rec.samples.values()]
+        self.assertEqual(indices, [(0, 0), (0, 0), (0, 0), (0, 0), (1, 0),
+                                   (1, 1), (0, 0), (0, 1), (0, 0), (1, 2),
+                                   (2, 1), (2, 2), (0, 1), (0, 2), (1, 1)])
+
+
+class TestIndexFilename(unittest.TestCase):
+
+    filenames = [('example_vcf40.vcf.gz', 'example_vcf40.vcf.gz.tbi'),
+                 ('example_vcf40.vcf.gz', 'example_vcf40.vcf.gz.csi'),
+                 ('example_vcf40.bcf', 'example_vcf40.bcf.csi')]
+
+    def testOpen(self):
+        for fn, idx_fn in self.filenames:
+            fn = os.path.join(CBCF_DATADIR, fn)
+            idx_fn = os.path.join(CBCF_DATADIR, idx_fn)
+
+            with pysam.VariantFile(fn, index_filename=idx_fn) as inf:
+                self.assertEqual(len(list(inf.fetch('20'))), 3)
+
+
+class TestConstructionVCFWithContigs(unittest.TestCase):
+    """construct VariantFile from scratch."""
+
+    filename = "example_vcf42_withcontigs.vcf"
+    compression = 'NONE'
+    description = 'VCF version 4.2 variant calling text'
+
+    def testBase(self):
+        with pysam.VariantFile(os.path.join(CBCF_DATADIR, self.filename)) as inf:
+            self.assertEqual(inf.category, 'VARIANTS')
+            self.assertEqual(inf.format, 'VCF')
+            self.assertEqual(inf.version, (4, 2))
+            self.assertEqual(inf.compression, self.compression)
+            self.assertEqual(inf.description, self.description)
+            self.assertTrue(inf.is_open)
+            self.assertEqual(inf.is_read, True)
+            self.assertEqual(inf.is_write, False)
+
+    def complete_check(self, fn_in, fn_out):
+        self.maxDiff = None
+        check_lines_equal(
+            self, fn_in, fn_out, sort=True,
+            filter_f=lambda x: x.startswith("##contig"))
+        os.unlink(fn_out)
+
+    def testConstructionWithRecords(self):
+
+        fn_in = os.path.join(CBCF_DATADIR, self.filename)
+        fn_out = get_temp_filename(suffix=".vcf")
+        vcf_in = pysam.VariantFile(fn_in)
+
+        header = pysam.VariantHeader()
+
+        for record in vcf_in.header.records:
+            header.add_record(record)
+
+        for sample in vcf_in.header.samples:
+            header.add_sample(sample)
+
+        vcf_out = pysam.VariantFile(fn_out, "w", header=header)
+        for record in vcf_in:
+            record.translate(header)
+            vcf_out.write(record)
+
+        vcf_in.close()
+        vcf_out.close()
+        self.complete_check(fn_in, fn_out)
+
+    def testConstructionFromCopy(self):
+
+        fn_in = os.path.join(CBCF_DATADIR, self.filename)
+        fn_out = get_temp_filename(suffix=".vcf")
+        vcf_in = pysam.VariantFile(fn_in)
+
+        vcf_out = pysam.VariantFile(fn_out, "w", header=vcf_in.header)
+        for record in vcf_in:
+            vcf_out.write(record)
+
+        vcf_in.close()
+        vcf_out.close()
+
+        self.complete_check(fn_in, fn_out)
+
+    def testConstructionWithLines(self):
+
+        fn_in = os.path.join(CBCF_DATADIR, self.filename)
+        fn_out = get_temp_filename(suffix=".vcf")
+        vcf_in = pysam.VariantFile(fn_in)
+
+        header = pysam.VariantHeader()
+        header.add_samples(vcf_in.header.samples)
+
+        for hr in vcf_in.header.records:
+            header.add_line(str(hr))
+
+        vcf_out = pysam.VariantFile(fn_out, "w", header=header)
+
+        for record in vcf_in:
+            vcf_out.write(record)
+
+        vcf_out.close()
+        vcf_in.close()
+
+        self.complete_check(fn_in, fn_out)
+
+
+# class TestConstructionVCFWithoutContigs(TestConstructionVCFWithContigs):
+#     """construct VariantFile from scratch."""
+#     filename = "example_vcf40.vcf"
+
+
+class TestConstructionVCFGZWithContigs(TestConstructionVCFWithContigs):
+    """construct VariantFile from scratch."""
+
+    filename = "example_vcf42_withcontigs.vcf.gz"
+    compression = 'BGZF'
+    description = 'VCF version 4.2 BGZF-compressed variant calling data'
+
+
+class TestConstructionVCFGZWithoutContigs(TestConstructionVCFWithContigs):
+    """construct VariantFile from scratch."""
+
+    filename = "example_vcf42.vcf.gz"
+    compression = 'BGZF'
+    description = 'VCF version 4.2 BGZF-compressed variant calling data'
+
+
+class TestSettingRecordValues(unittest.TestCase):
+
+    filename = "example_vcf40.vcf"
+
+    def testBase(self):
+        with pysam.VariantFile(os.path.join(CBCF_DATADIR, self.filename)) as inf:
+            self.assertEqual(inf.category, 'VARIANTS')
+            self.assertEqual(inf.format, 'VCF')
+            self.assertEqual(inf.version, (4, 0))
+            self.assertEqual(inf.compression, 'NONE')
+            self.assertEqual(
+                inf.description, 'VCF version 4.0 variant calling text')
+            self.assertTrue(inf.is_open)
+            self.assertEqual(inf.is_read, True)
+            self.assertEqual(inf.is_write, False)
+
+    def testSetQual(self):
+        with pysam.VariantFile(os.path.join(CBCF_DATADIR, self.filename)) as inf:
+            record = next(inf)
+            self.assertEqual(record.qual, 47)
+            record.qual = record.qual
+            self.assertEqual(record.qual, 47)
+            record.qual = 10
+            self.assertEqual(record.qual, 10)
+            self.assertEqual(str(record).split("\t")[5], "10")
+
+    def testGenotype(self):
+        with pysam.VariantFile(os.path.join(CBCF_DATADIR, self.filename)) as inf:
+            record = next(inf)
+            sample = record.samples["NA00001"]
+            print(sample["GT"])
+            self.assertEqual(sample["GT"], (0, 0))
+            sample["GT"] = sample["GT"]
+
+
+class TestMultiThreading(unittest.TestCase):
+
+    filename = os.path.join(CBCF_DATADIR, "example_vcf42.vcf.gz")
+
+    def testSingleThreadEqualsMultithreadResult(self):
+        with pysam.VariantFile(self.filename) as inf:
+            header = inf.header
+            single = [r for r in inf]
+        with pysam.VariantFile(self.filename, threads=2) as inf:
+            multi = [r for r in inf]
+        for r1, r2 in zip(single, multi):
+            assert str(r1) == str(r2)
+
+        bcf_out = get_temp_filename(suffix=".bcf")
+        with pysam.VariantFile(bcf_out, mode='wb',
+                               header=header,
+                               threads=2) as out:
+            for r in single:
+                out.write(r)
+        with pysam.VariantFile(bcf_out) as inf:
+            multi_out = [r for r in inf]
+        for r1, r2 in zip(single, multi_out):
+            assert str(r1) == str(r2)
+
+    def testNoMultiThreadingWithIgnoreTruncation(self):
+        with self.assertRaises(ValueError):
+            pysam.VariantFile(self.filename,
+                              threads=2,
+                              ignore_truncation=True)
+
+
+class TestSubsetting(unittest.TestCase):
+
+    filename = "example_vcf42.vcf.gz"
+
+    def testSubsetting(self):
+        with pysam.VariantFile(os.path.join(CBCF_DATADIR,
+                                            self.filename)) as inf:
+            inf.subset_samples(["NA00001"])
+
+
+class TestVCFVersions(unittest.TestCase):
+
+    def setUp(self):
+        self.files_to_test = (glob.glob(os.path.join(CBCF_DATADIR, "example_v*.vcf.gz")) +
+                              glob.glob(os.path.join(CBCF_DATADIR, "example_v*.vcf")) +
+                              glob.glob(os.path.join(CBCF_DATADIR, "example_v*.bcf")))
+    
+    def test_all_records_can_be_fetched(self):
+
+        for fn in self.files_to_test:
+            with pysam.VariantFile(fn) as inf:
+                records = list(inf.fetch())
+
+
+class TestUnicode(unittest.TestCase):
+    filename = "example_vcf43_with_utf8.vcf.gz"
+
+    def test_record_with_unicode(self):
+        with pysam.VariantFile(os.path.join(CBCF_DATADIR,
+                                            self.filename)) as inf:
+            records = list(inf.fetch("20", 2345677, 2345678))
+        self.assertEqual(len(records), 1)
+        record = records.pop()
+        self.assertEqual(
+            record.info["CLNVI"],
+            ('Institute_of_Human_Genetics', u'Friedrich-Alexander-Universität_Erlangen-Nürnberg'))
+        self.assertEqual(record.samples[0]["AN"], "alpha")
+        self.assertEqual(record.samples[1]["AN"], u"ä")
+        self.assertEqual(record.samples[2]["AN"], u"ü")
+                
+
+if __name__ == "__main__":
+    print("starting tests")
+    unittest.main()
+    print("completed tests")
diff --git a/tests/VariantRecord_test.py b/tests/VariantRecord_test.py
new file mode 100644
index 0000000..c44d9a6
--- /dev/null
+++ b/tests/VariantRecord_test.py
@@ -0,0 +1,95 @@
+import pysam
+import pytest
+
+try:
+    from pathlib import Path
+except ImportError:
+    Path = None
+
+from TestUtils import make_data_files, CBCF_DATADIR
+
+
+def setUpModule():
+    make_data_files(CBCF_DATADIR)
+
+
+@pytest.fixture
+def vcf_header():
+    vcf_header = pysam.VariantHeader()
+    vcf_header.add_samples("sample1", "sample2")
+    vcf_header.contigs.add("1")
+    return vcf_header
+
+## segfault without coordinates
+
+def test_ascii_annotation_can_be_added(vcf_header):
+    vcf_header.formats.add("AN", 1, "String", "An annotation")
+    record = vcf_header.new_record(
+        contig="1",
+        start=12,
+        stop=13,
+        samples=[
+            {"AN": "anno1"},
+            {"AN": "anno2"}])
+    assert str(record)[:-1].split("\t")[-2:] == ["anno1", "anno2"]
+
+
+def test_ascii_annotation_with_variable_length_can_be_added(vcf_header):
+    vcf_header.formats.add("AN", 1, "String", "An annotation")
+    record = vcf_header.new_record(
+        contig="1",
+        start=12,
+        stop=13,
+        samples=[
+            {"AN": "anno1b"},
+            {"AN": "anno1"}])
+    assert str(record)[:-1].split("\t")[-2:] == ["anno1b", "anno1"]
+    record = vcf_header.new_record(
+        contig="1",
+        start=12,
+        stop=13,
+        samples=[
+            {"AN": "anno2"},
+            {"AN": "anno2b"}])
+    assert str(record)[:-1].split("\t")[-2:] == ["anno2", "anno2b"]
+    
+
+def test_unicode_annotation_can_be_added(vcf_header):
+    vcf_header.formats.add("AN", 1, "String", "An annotation")
+    record = vcf_header.new_record(
+        contig="1",
+        start=12,
+        stop=13,
+        samples=[
+            {"AN": "anno1"},
+            {"AN": "Friedrich-Alexander-Universit\u00E4t_Erlangen-N\u00FCrnberg"}])
+    assert str(record)[:-1].split("\t")[-2:] == [
+        "anno1",
+        "Friedrich-Alexander-Universit\u00E4t_Erlangen-N\u00FCrnberg"]
+
+def test_set_sample_alleles(vcf_header):
+    vcf_header.formats.add('GT',1,'String',"Genotype") # id, number, type, description
+    record = vcf_header.new_record(
+        contig="1",
+        start=20,
+        stop=21,
+        alleles=('A','T')
+        )
+
+    record.samples['sample1'].alleles = ('T', 'A')
+    assert record.samples['sample1'].alleles  == ('T','A')
+
+    # Empty record:
+    record.samples['sample1'].alleles = (None, )
+    assert record.samples['sample1'].alleles   == tuple()
+    record.samples['sample1'].alleles = None
+    assert record.samples['sample1'].alleles   == tuple()
+    record.samples['sample1'].alleles = tuple()
+    assert record.samples['sample1'].alleles   == tuple()
+
+    # check error conditions:
+    with pytest.raises(ValueError, match='One or more of the supplied sample alleles are not defined'):
+        record.samples['sample1'].alleles = ('C', 'A')
+
+    with pytest.raises(ValueError, match='Use .allele_indices to set integer allele indices'):
+        record.samples['sample1'].alleles = (1, 0)
diff --git a/tests/_compile_test.pyx b/tests/_compile_test.pyx
new file mode 100644
index 0000000..dfe7937
--- /dev/null
+++ b/tests/_compile_test.pyx
@@ -0,0 +1,29 @@
+from pysam.libcalignmentfile cimport AlignmentFile, AlignedSegment
+from pysam.libctabix cimport Tabixfile
+
+cdef AlignmentFile samfile
+cdef Tabixfile tabixfile
+
+
+def testCountBAM(AlignmentFile samfile):
+    '''test reading from a BAM file accessing
+    the flag field directly.'''
+
+    cdef AlignedSegment read
+    cdef int n = 0
+    
+    for read in samfile.fetch():
+        flag = read._delegate.core.flag
+        n += 1
+            
+    return n
+
+def testCountGTF(Tabixfile tabixfile):
+    '''test reading from a tabixfile.'''
+    
+    cdef int n = 0
+
+    for entry in tabixfile.fetch():
+        n += 1
+
+    return n
diff --git a/tests/_compile_test.pyxbld b/tests/_compile_test.pyxbld
new file mode 100644
index 0000000..87dfb3e
--- /dev/null
+++ b/tests/_compile_test.pyxbld
@@ -0,0 +1,8 @@
+# link against pysam
+def make_ext(modname, pyxfilename):
+    from distutils.extension import Extension
+    import pysam
+    return Extension(name = modname,
+                     sources = [pyxfilename],
+                     include_dirs = pysam.get_include(),
+                     define_macros = pysam.get_defines()) 
diff --git a/tests/_cython_flagstat.pyx b/tests/_cython_flagstat.pyx
new file mode 100644
index 0000000..8e376b0
--- /dev/null
+++ b/tests/_cython_flagstat.pyx
@@ -0,0 +1,18 @@
+from pysam.libcalignmentfile cimport AlignmentFile, AlignedSegment
+from pysam.libcalignmentfile cimport BAM_FPROPER_PAIR, BAM_FPAIRED
+from pysam.libcalignedsegment cimport pysam_get_flag
+
+def count(AlignmentFile samfile):
+    cdef int is_proper = 0
+    cdef int is_paired = 0
+    cdef AlignedSegment read
+    cdef int f
+
+    for read in samfile:
+        f = pysam_get_flag(read._delegate)
+        if f & BAM_FPAIRED:
+            is_paired += 1
+        if f & BAM_FPROPER_PAIR:
+            is_proper += 1
+
+    return is_paired, is_proper
diff --git a/tests/_cython_flagstat.pyxbld b/tests/_cython_flagstat.pyxbld
new file mode 100644
index 0000000..0e05b76
--- /dev/null
+++ b/tests/_cython_flagstat.pyxbld
@@ -0,0 +1,8 @@
+def make_ext(modname, pyxfilename):
+    from distutils.extension import Extension
+    import pysam
+    return Extension(name=modname,
+                     sources=[pyxfilename],
+                     extra_link_args=pysam.get_libraries(),
+                     include_dirs=pysam.get_include(),
+                     define_macros=pysam.get_defines())
diff --git a/tests/cbcf_data/Makefile b/tests/cbcf_data/Makefile
new file mode 100644
index 0000000..9c3fe75
--- /dev/null
+++ b/tests/cbcf_data/Makefile
@@ -0,0 +1,25 @@
+ALL_VCF=$(wildcard *.vcf)
+VCF=$(filter-out example_empty.vcf,$(ALL_VCF))
+
+VCFGZ=$(VCF:%.vcf=%.vcf.gz)
+BCF=$(VCF:%.vcf=%.bcf)
+
+all: all.stamp
+
+all.stamp: $(VCFGZ) $(BCF)
+	touch $@
+
+%.vcf.gz: %.vcf
+	bgzip < $< > $@
+	tabix -p vcf $@    # create tbi index
+	bcftools index $@  # create csi index
+
+%.bcf: %.vcf.gz
+	bcftools view -O b $< -o $@
+	bcftools index $@
+
+example_empty.bcf: example_empty.vcf.gz
+	touch $@
+
+clean:
+	-rm -f all.stamp *.gz *.tbi *.csi *.bcf
diff --git a/tests/cbcf_data/example_empty.vcf b/tests/cbcf_data/example_empty.vcf
new file mode 100644
index 0000000..e69de29
diff --git a/tests/cbcf_data/example_vcf40.vcf b/tests/cbcf_data/example_vcf40.vcf
new file mode 100644
index 0000000..8dd9f20
--- /dev/null
+++ b/tests/cbcf_data/example_vcf40.vcf
@@ -0,0 +1,24 @@
+##fileformat=VCFv4.0
+##fileDate=20090805
+##source=myImputationProgramV3.1
+##reference=1000GenomesPilot-NCBI36
+##phasing=partial
+##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
+##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency">
+##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele">
+##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129">
+##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership">
+##FILTER=<ID=PASS,Description="All filters passed">
+##FILTER=<ID=q10,Description="Quality below 10">
+##FILTER=<ID=s50,Description="Less than 50% of samples have data">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
+##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA00001	NA00002	NA00003
+M	1230237	.	T	.	47	PASS	NS=3;DP=13;AA=T	GT:GQ:DP:HQ	0|0:54:7:56,60	0|0:48:4:51,51	0/0:61:2
+17	14370	rs6054257	G	A	29	PASS	NS=3;DP=14;AF=0.5;DB;H2	GT:GQ:DP:HQ	0|0:48:1:51,51	1|0:48:8:51,51	1/1:43:5:.,.
+20	17330	.	T	A	3	q10	NS=3;DP=11;AF=0.017	GT:GQ:DP:HQ	0|0:49:3:58,50	0|1:3:5:65,3	0/0:41:3
+20	1110696	rs6040355	A	G,T	67	PASS	NS=2;DP=10;AF=0.333,0.667;AA=T;DB	GT:GQ:DP:HQ	1|2:21:6:23,27	2|1:2:0:18,2	2/2:35:4
+20	1234567	microsat1	GTCT	G,GTACT	50	PASS	NS=3;DP=9;AA=G	GT:GQ:DP	0/1:35:4	0/2:17:2	1/1:40:3
diff --git a/tests/cbcf_data/example_vcf42.vcf b/tests/cbcf_data/example_vcf42.vcf
new file mode 100644
index 0000000..f103e1f
--- /dev/null
+++ b/tests/cbcf_data/example_vcf42.vcf
@@ -0,0 +1,24 @@
+##fileformat=VCFv4.2
+##fileDate=20090805
+##source=myImputationProgramV3.1
+##reference=1000GenomesPilot-NCBI36
+##phasing=partial
+##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
+##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency">
+##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele">
+##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129">
+##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership">
+##FILTER=<ID=PASS,Description="All filters passed">
+##FILTER=<ID=q10,Description="Quality below 10">
+##FILTER=<ID=s50,Description="Less than 50% of samples have data">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
+##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA00001	NA00002	NA00003
+M	1230237	.	T	.	47	PASS	NS=3;DP=13;AA=T	GT:GQ:DP:HQ	0|0:54:7:56,60	0|0:48:4:51,51	0/0:61:2:.
+17	14370	rs6054257	G	A	29	PASS	NS=3;DP=14;AF=0.5;DB;H2	GT:GQ:DP:HQ	0|0:48:1:51,51	1|0:48:8:51,51	1/1:43:5:.,.
+20	17330	.	T	A	3	q10	NS=3;DP=11;AF=0.017	GT:GQ:DP:HQ	0|0:49:3:58,50	0|1:3:5:65,3	0/0:41:3:.
+20	1110696	rs6040355	A	G,T	67	PASS	NS=2;DP=10;AF=0.333,0.667;AA=T;DB	GT:GQ:DP:HQ	1|2:21:6:23,27	2|1:2:0:18,2	2/2:35:4:.
+20	1234567	microsat1	GTCT	G,GTACT	50	PASS	NS=3;DP=9;AA=G	GT:GQ:DP	0/1:35:4	0/2:17:2	1/1:40:3
diff --git a/tests/cbcf_data/example_vcf42_only_header.vcf b/tests/cbcf_data/example_vcf42_only_header.vcf
new file mode 100644
index 0000000..ee0f8fa
--- /dev/null
+++ b/tests/cbcf_data/example_vcf42_only_header.vcf
@@ -0,0 +1,19 @@
+##fileformat=VCFv4.2
+##fileDate=20090805
+##source=myImputationProgramV3.1
+##reference=1000GenomesPilot-NCBI36
+##phasing=partial
+##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
+##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency">
+##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele">
+##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129">
+##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership">
+##FILTER=<ID=PASS,Description="All filters passed">
+##FILTER=<ID=q10,Description="Quality below 10">
+##FILTER=<ID=s50,Description="Less than 50% of samples have data">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
+##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA00001	NA00002	NA00003
diff --git a/tests/cbcf_data/example_vcf42_withcontigs.vcf b/tests/cbcf_data/example_vcf42_withcontigs.vcf
new file mode 100644
index 0000000..1d298eb
--- /dev/null
+++ b/tests/cbcf_data/example_vcf42_withcontigs.vcf
@@ -0,0 +1,27 @@
+##fileformat=VCFv4.2
+##fileDate=20090805
+##source=myImputationProgramV3.1
+##reference=1000GenomesPilot-NCBI36
+##phasing=partial
+##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
+##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency">
+##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele">
+##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129">
+##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership">
+##FILTER=<ID=PASS,Description="All filters passed">
+##FILTER=<ID=q10,Description="Quality below 10">
+##FILTER=<ID=s50,Description="Less than 50% of samples have data">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
+##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
+##contig=<ID=M>
+##contig=<ID=17>
+##contig=<ID=20>
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA00001	NA00002	NA00003
+M	1230237	.	T	.	47	PASS	NS=3;DP=13;AA=T	GT:GQ:DP:HQ	0|0:54:7:56,60	0|0:48:4:51,51	0/0:61:2:.
+17	14370	rs6054257	G	A	29	PASS	NS=3;DP=14;AF=0.5;DB;H2	GT:GQ:DP:HQ	0|0:48:1:51,51	1|0:48:8:51,51	1/1:43:5:.,.
+20	17330	.	T	A	3	q10	NS=3;DP=11;AF=0.017	GT:GQ:DP:HQ	0|0:49:3:58,50	0|1:3:5:65,3	0/0:41:3:.
+20	1110696	rs6040355	A	G,T	67	PASS	NS=2;DP=10;AF=0.333,0.667;AA=T;DB	GT:GQ:DP:HQ	1|2:21:6:23,27	2|1:2:0:18,2	2/2:35:4:.
+20	1234567	microsat1	GTCT	G,GTACT	50	PASS	NS=3;DP=9;AA=G	GT:GQ:DP	0/1:35:4	0/2:17:2	1/1:40:3
diff --git a/tests/cbcf_data/example_vcf43.vcf b/tests/cbcf_data/example_vcf43.vcf
new file mode 100644
index 0000000..9010401
--- /dev/null
+++ b/tests/cbcf_data/example_vcf43.vcf
@@ -0,0 +1,24 @@
+##fileformat=VCFv4.3
+##fileDate=20090805
+##source=myImputationProgramV3.1
+##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta
+##contig=<ID=20,length=62435964,assembly=B36,md5=f126cdf8a6e0c7f379d618ff66beb2da,species="Homo sapiens",taxonomy=x>
+##phasing=partial
+##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
+##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency">
+##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele">
+##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129">
+##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership">
+##FILTER=<ID=q10,Description="Quality below 10">
+##FILTER=<ID=s50,Description="Less than 50% of samples have data">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
+##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA00001	NA00002	NA00003
+20	14370	rs6054257	G	A	29	PASS	NS=3;DP=14;AF=0.5;DB;H2	GT:GQ:DP:HQ	0|0:48:1:51,51	1|0:48:8:51,51	1/1:43:5:.,.
+20	17330	.	T	A	3	q10	NS=3;DP=11;AF=0.017	GT:GQ:DP:HQ	0|0:49:3:58,50	0|1:3:5:65,3	0/0:41:3
+20	1110696	rs6040355	A	G,T	67	PASS	NS=2;DP=10;AF=0.333,0.667;AA=T;DB	GT:GQ:DP:HQ	1|2:21:6:23,27	2|1:2:0:18,2	2/2:35:4
+20	1230237	.	T	.	47	PASS	NS=3;DP=13;AA=T	GT:GQ:DP:HQ	0|0:54:7:56,60	0|0:48:4:51,51	0/0:61:2
+20	1234567	microsat1	GTC	G,GTCT	50	PASS	NS=3;DP=9;AA=G	GT:GQ:DP	0/1:35:4	0/2:17:2	1/1:40:3
diff --git a/tests/cbcf_data/example_vcf43_with_utf8.vcf b/tests/cbcf_data/example_vcf43_with_utf8.vcf
new file mode 100644
index 0000000..4826fc4
--- /dev/null
+++ b/tests/cbcf_data/example_vcf43_with_utf8.vcf
@@ -0,0 +1,27 @@
+##fileformat=VCFv4.3
+##fileDate=20090805
+##source=myImputationProgramV3.1
+##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta
+##contig=<ID=20,length=62435964,assembly=B36,md5=f126cdf8a6e0c7f379d618ff66beb2da,species="Homo sapiens",taxonomy=x>
+##phasing=partial
+##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
+##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency">
+##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele">
+##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129">
+##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership">
+##INFO=<ID=CLNVI,Number=.,Type=String,Description="the variant's clinical sources reported as tag-value pairs of database and variant identifier">
+##FILTER=<ID=q10,Description="Quality below 10">
+##FILTER=<ID=s50,Description="Less than 50% of samples have data">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
+##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
+##FORMAT=<ID=AN,Number=1,Type=String,Description="Some annotation">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA00001	NA00002	NA00003
+20	14370	rs6054257	G	A	29	PASS	NS=3;DP=14;AF=0.5;DB;H2	GT:GQ:DP:HQ	0|0:48:1:51,51	1|0:48:8:51,51	1/1:43:5:.,.
+20	17330	.	T	A	3	q10	NS=3;DP=11;AF=0.017	GT:GQ:DP:HQ	0|0:49:3:58,50	0|1:3:5:65,3	0/0:41:3
+20	1110696	rs6040355	A	G,T	67	PASS	NS=2;DP=10;AF=0.333,0.667;AA=T;DB	GT:GQ:DP:HQ	1|2:21:6:23,27	2|1:2:0:18,2	2/2:35:4
+20	1230237	.	T	.	47	PASS	NS=3;DP=13;AA=T	GT:GQ:DP:HQ	0|0:54:7:56,60	0|0:48:4:51,51	0/0:61:2
+20	1234567	microsat1	GTC	G,GTCT	50	PASS	NS=3;DP=9;AA=G	GT:GQ:DP	0/1:35:4	0/2:17:2	1/1:40:3
+20	2345678	rs123	G	A	29	PASS	NS=3;DP=14;AF=0.5;CLNVI=Institute_of_Human_Genetics,Friedrich-Alexander-Universität_Erlangen-Nürnberg;DB;H2	GT:GQ:DP:HQ:AN	0|0:48:1:51,51:alpha	1|0:48:8:51,51:ä	1/1:43:5:.,.:ü
diff --git a/tests/cbcf_data/gnomad.vcf b/tests/cbcf_data/gnomad.vcf
new file mode 100644
index 0000000..9875c03
--- /dev/null
+++ b/tests/cbcf_data/gnomad.vcf
@@ -0,0 +1,200 @@
+##fileformat=VCFv4.2
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
+##FILTER=<ID=RF,Description="Failed random forests filters (SNV cutoff 0.4, indels cutoff 0.4)">
+##FILTER=<ID=AC0,Description="Allele Count is zero (i.e. no high-confidence genotype (GQ >= 20, DP >= 10, AB => 0.2 for het calls))">
+##FILTER=<ID=InbreedingCoeff,Description="InbreedingCoeff < -0.3">
+##FILTER=<ID=LCR,Description="In a low complexity region">
+##FILTER=<ID=SEGDUP,Description="In a segmental duplication region">
+##FILTER=<ID=PASS,Description="All filters passed for at least one of the alleles at that site (see AS_FilterStatus for allele-specific filter status)">
+##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency among genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
+##INFO=<ID=ClippingRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref number of hard clipped bases">
+##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
+##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
+##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">
+##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
+##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
+##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
+##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
+##INFO=<ID=SOR,Number=1,Type=Float,Description="Symmetric Odds Ratio of 2x2 contingency table to detect strand bias">
+##INFO=<ID=VQSLOD,Number=1,Type=Float,Description="Log odds ratio of being a true variant versus being false under the trained VQSR gaussian mixture model (deprecated; see AS_RF)">
+##INFO=<ID=VQSR_culprit,Number=1,Type=String,Description="The annotation which was the worst performing in the VQSR Gaussian mixture model (deprecated; see AS_RF)">
+##INFO=<ID=VQSR_NEGATIVE_TRAIN_SITE,Number=0,Type=Flag,Description="This variant was used to build the negative training set of bad variants for VQSR (deprecated; see AS_RF_NEGATIVE_TRAIN)">
+##INFO=<ID=VQSR_POSITIVE_TRAIN_SITE,Number=0,Type=Flag,Description="This variant was used to build the positive training set of good variants for VQSR (deprecated; see AS_RF_POSITIVE_TRAIN)">
+##INFO=<ID=GQ_HIST_ALT,Number=A,Type=String,Description="Histogram for GQ for each allele; Midpoints of histogram bins: 2.5|7.5|12.5|17.5|22.5|27.5|32.5|37.5|42.5|47.5|52.5|57.5|62.5|67.5|72.5|77.5|82.5|87.5|92.5|97.5">
+##INFO=<ID=DP_HIST_ALT,Number=A,Type=String,Description="Histogram for DP for each allele; Midpoints of histogram bins: 2.5|7.5|12.5|17.5|22.5|27.5|32.5|37.5|42.5|47.5|52.5|57.5|62.5|67.5|72.5|77.5|82.5|87.5|92.5|97.5">
+##INFO=<ID=AB_HIST_ALT,Number=A,Type=String,Description="Histogram for Allele Balance in heterozygous individuals for each allele; 100*AD[i_alt]/sum(AD); Midpoints of histogram bins: 2.5|7.5|12.5|17.5|22.5|27.5|32.5|37.5|42.5|47.5|52.5|57.5|62.5|67.5|72.5|77.5|82.5|87.5|92.5|97.5">
+##INFO=<ID=GQ_HIST_ALL,Number=1,Type=String,Description="Histogram for GQ; Midpoints of histogram bins: 2.5|7.5|12.5|17.5|22.5|27.5|32.5|37.5|42.5|47.5|52.5|57.5|62.5|67.5|72.5|77.5|82.5|87.5|92.5|97.5">
+##INFO=<ID=DP_HIST_ALL,Number=1,Type=String,Description="Histogram for DP; Midpoints of histogram bins: 2.5|7.5|12.5|17.5|22.5|27.5|32.5|37.5|42.5|47.5|52.5|57.5|62.5|67.5|72.5|77.5|82.5|87.5|92.5|97.5">
+##INFO=<ID=AB_HIST_ALL,Number=1,Type=String,Description="Histogram for Allele Balance in heterozygous individuals; 100*AD[i_alt]/sum(AD); Midpoints of histogram bins: 2.5|7.5|12.5|17.5|22.5|27.5|32.5|37.5|42.5|47.5|52.5|57.5|62.5|67.5|72.5|77.5|82.5|87.5|92.5|97.5">
+##INFO=<ID=AC_AFR,Number=A,Type=Integer,Description="Allele count in African/African American genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AC_AMR,Number=A,Type=Integer,Description="Allele count in Admixed American genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AC_ASJ,Number=A,Type=Integer,Description="Allele count in Ashkenazi Jewish genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AC_EAS,Number=A,Type=Integer,Description="Allele count in East Asian genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AC_FIN,Number=A,Type=Integer,Description="Allele count in Finnish genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AC_NFE,Number=A,Type=Integer,Description="Allele count in Non-Finnish European genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AC_OTH,Number=A,Type=Integer,Description="Allele count in Other (population not assigned) genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AC_Male,Number=A,Type=Integer,Description="Allele count in Male genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AC_Female,Number=A,Type=Integer,Description="Allele count in Female genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AN_AFR,Number=1,Type=Integer,Description="Total number of alleles in African/African American called genotypes">
+##INFO=<ID=AN_AMR,Number=1,Type=Integer,Description="Total number of alleles in Admixed American called genotypes">
+##INFO=<ID=AN_ASJ,Number=1,Type=Integer,Description="Total number of alleles in Ashkenazi Jewish called genotypes">
+##INFO=<ID=AN_EAS,Number=1,Type=Integer,Description="Total number of alleles in East Asian called genotypes">
+##INFO=<ID=AN_FIN,Number=1,Type=Integer,Description="Total number of alleles in Finnish called genotypes">
+##INFO=<ID=AN_NFE,Number=1,Type=Integer,Description="Total number of alleles in Non-Finnish European called genotypes">
+##INFO=<ID=AN_OTH,Number=1,Type=Integer,Description="Total number of alleles in Other (population not assigned) called genotypes">
+##INFO=<ID=AN_Male,Number=1,Type=Integer,Description="Total number of alleles in Male called genotypes">
+##INFO=<ID=AN_Female,Number=1,Type=Integer,Description="Total number of alleles in Female called genotypes">
+##INFO=<ID=AF_AFR,Number=A,Type=Float,Description="Allele Frequency among African/African American genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AF_AMR,Number=A,Type=Float,Description="Allele Frequency among Admixed American genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AF_ASJ,Number=A,Type=Float,Description="Allele Frequency among Ashkenazi Jewish genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AF_EAS,Number=A,Type=Float,Description="Allele Frequency among East Asian genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AF_FIN,Number=A,Type=Float,Description="Allele Frequency among Finnish genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AF_NFE,Number=A,Type=Float,Description="Allele Frequency among Non-Finnish European genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AF_OTH,Number=A,Type=Float,Description="Allele Frequency among Other (population not assigned) genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AF_Male,Number=A,Type=Float,Description="Allele Frequency among Male genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AF_Female,Number=A,Type=Float,Description="Allele Frequency among Female genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=GC_AFR,Number=G,Type=Integer,Description="Count of African/African American individuals for each genotype">
+##INFO=<ID=GC_AMR,Number=G,Type=Integer,Description="Count of Admixed American individuals for each genotype">
+##INFO=<ID=GC_ASJ,Number=G,Type=Integer,Description="Count of Ashkenazi Jewish individuals for each genotype">
+##INFO=<ID=GC_EAS,Number=G,Type=Integer,Description="Count of East Asian individuals for each genotype">
+##INFO=<ID=GC_FIN,Number=G,Type=Integer,Description="Count of Finnish individuals for each genotype">
+##INFO=<ID=GC_NFE,Number=G,Type=Integer,Description="Count of Non-Finnish European individuals for each genotype">
+##INFO=<ID=GC_OTH,Number=G,Type=Integer,Description="Count of Other (population not assigned) individuals for each genotype">
+##INFO=<ID=GC_Male,Number=G,Type=Integer,Description="Count of Male individuals for each genotype">
+##INFO=<ID=GC_Female,Number=G,Type=Integer,Description="Count of Female individuals for each genotype">
+##INFO=<ID=AC_raw,Number=A,Type=Integer,Description="Allele counts before filtering low-confidence genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AN_raw,Number=1,Type=Integer,Description="Total number of alleles before filtering low-confidence genotypes">
+##INFO=<ID=AF_raw,Number=A,Type=Float,Description="Allele frequency before filtering low-confidence genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=GC_raw,Number=G,Type=Integer,Description="Raw count of individuals for each genotype before filtering low-confidence genotypes">
+##INFO=<ID=GC,Number=G,Type=Integer,Description="Count of individuals for each genotype">
+##INFO=<ID=Hom_AFR,Number=A,Type=Integer,Description="Count of homozygous African/African American individuals">
+##INFO=<ID=Hom_AMR,Number=A,Type=Integer,Description="Count of homozygous Admixed American individuals">
+##INFO=<ID=Hom_ASJ,Number=A,Type=Integer,Description="Count of homozygous Ashkenazi Jewish individuals">
+##INFO=<ID=Hom_EAS,Number=A,Type=Integer,Description="Count of homozygous East Asian individuals">
+##INFO=<ID=Hom_FIN,Number=A,Type=Integer,Description="Count of homozygous Finnish individuals">
+##INFO=<ID=Hom_NFE,Number=A,Type=Integer,Description="Count of homozygous Non-Finnish European individuals">
+##INFO=<ID=Hom_OTH,Number=A,Type=Integer,Description="Count of homozygous Other (population not assigned) individuals">
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+##INFO=<ID=Hom,Number=A,Type=Integer,Description="Count of homozygous individuals">
+##INFO=<ID=STAR_AC,Number=1,Type=Integer,Description="AC of deletions spanning this position">
+##INFO=<ID=STAR_AC_raw,Number=1,Type=Integer,Description="Allele counts of deletions spanning this position before filtering low-confidence genotypes">
+##INFO=<ID=STAR_Hom,Number=1,Type=Integer,Description="Count of individuals homozygous for a deletion spanning this position">
+##INFO=<ID=POPMAX,Number=A,Type=String,Description="Population with max AF">
+##INFO=<ID=AC_POPMAX,Number=A,Type=Integer,Description="AC in the population with the max AF">
+##INFO=<ID=AN_POPMAX,Number=A,Type=Integer,Description="AN in the population with the max AF">
+##INFO=<ID=AF_POPMAX,Number=A,Type=Float,Description="Maximum Allele Frequency across populations (excluding OTH)">
+##INFO=<ID=DP_MEDIAN,Number=A,Type=Integer,Description="Median DP in carriers of each allele">
+##INFO=<ID=DREF_MEDIAN,Number=A,Type=Float,Description="Median dosage of homozygous reference in carriers of each allele">
+##INFO=<ID=GQ_MEDIAN,Number=A,Type=Integer,Description="Median GQ in carriers of each allele">
+##INFO=<ID=AB_MEDIAN,Number=A,Type=Float,Description="Median allele balance in heterozygote carriers of each allele">
+##INFO=<ID=AS_RF,Number=A,Type=Float,Description="Random Forests probability for each allele">
+##INFO=<ID=AS_FilterStatus,Number=A,Type=String,Description="Random Forests filter status for each allele">
+##INFO=<ID=AS_RF_POSITIVE_TRAIN,Number=.,Type=Integer,Description="Contains the indices of all alleles used as positive examples during training of random forests">
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+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
+22	16050036	rs374742143	A	C	442156.34	RF	AC=67;AF=4.29487e-01;AN=156;BaseQRankSum=7.36000e-01;ClippingRankSum=2.96000e-01;DB;DP=50165;FS=7.05600e+00;InbreedingCoeff=3.82000e-01;MQ=2.71500e+01;MQRankSum=-1.02600e+00;QD=2.47500e+01;ReadPosRankSum=-2.11000e-01;SOR=1.26750e+01;VQSLOD=-9.58600e+02;VQSR_culprit=MQ;GQ_HIST_ALT=16|1279|299|254|155|24|16|28|50|135|78|4|6|11|32|43|6|4|3|35;DP_HIST_ALT=1769|653|51|5|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0;AB_HIST_ALT=0|0|0|2|5|24|36|11|89|2|125|31|61|85|24|60|34|8|3|7;GQ_HIST_ALL=2359|2810|730|651|296|51|34|33|53|135|78|4|6|11|32|43|6|4|3|35;DP_HIST_ALL=5518|1756|94|6|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0;AB_HIST_ALL=0|0|0|2|5|24|36|11|89|2|125|31|61|85|24|60|34|8|3|7;AC_AFR=3;AC_AMR=7;AC_ASJ=0;AC_EAS=0;AC_FIN=50;AC_NFE=3;AC_OTH=4;AC_Male=32;AC_Female=35;AN_AFR=14;AN_AMR=10;AN_ASJ=0;AN_EAS=0;AN_FIN=84;AN_NFE=42;AN_OTH=6;AN_Male=80;AN_Female=76;AF_AFR=2.14286e-01;AF_AMR=7.00000e-01;AF_ASJ=.;AF_EAS=.;AF_FIN=5.95238e-01;AF_NFE=7.14286e-02;AF_OTH=6.66667e-01;AF_Male=4.00000e-01;AF_Female=4.60526e-01;GC_AFR=4,3,0;GC_AMR=0,3,2;GC_ASJ=0,0,0;GC_EAS=0,0,0;GC_FIN=4,26,12;GC_NFE=18,3,0;GC_OTH=1,0,2;GC_Male=16,16,8;GC_Female=11,19,8;AC_raw=4349;AN_raw=14748;AF_raw=2.94887e-01;GC_raw=4896,607,1871;GC=27,35,16;Hom_AFR=0;Hom_AMR=2;Hom_ASJ=0;Hom_EAS=0;Hom_FIN=12;Hom_NFE=0;Hom_OTH=2;Hom_Male=8;Hom_Female=8;Hom_raw=1871;Hom=16;POPMAX=AMR;AC_POPMAX=7;AN_POPMAX=10;AF_POPMAX=7.00000e-01;DP_MEDIAN=3;DREF_MEDIAN=5.60406e-10;GQ_MEDIAN=12;AB_MEDIAN=5.55556e-01;AS_RF=4.71609e-02;AS_FilterStatus=RF;CSQ=C|intergenic_variant|MODIFIER|||||||||||||||rs374742143|1||||SNV|1||||||||||||||||||||||||||||||||||||||||||||
+22	16050068	.	A	G	82.46	RF;AC0	AC=0;AF=0.00000e+00;AN=2708;DP=111486;FS=0.00000e+00;InbreedingCoeff=-3.63000e-02;MQ=3.20200e+01;QD=1.64900e+01;SOR=3.61100e+00;VQSLOD=-9.28900e+01;VQSR_culprit=MQ;GQ_HIST_ALT=0|0|0|1|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0;DP_HIST_ALT=0|1|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0;AB_HIST_ALT=0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0;GQ_HIST_ALL=1227|4189|2184|3537|2071|618|693|346|97|92|61|9|18|0|7|4|4|0|0|0;DP_HIST_ALL=7502|6289|1163|169|26|8|0|0|0|0|0|0|0|0|0|0|0|0|0|0;AB_HIST_ALL=0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0;AC_AFR=0;AC_AMR=0;AC_ASJ=0;AC_EAS=0;AC_FIN=0;AC_NFE=0;AC_OTH=0;AC_Male=0;AC_Female=0;AN_AFR=280;AN_AMR=162;AN_ASJ=34;AN_EAS=74;AN_FIN=748;AN_NFE=1300;AN_OTH=110;AN_Male=1584;AN_Female=1124;AF_AFR=0.00000e+00;AF_AMR=0.00000e+00;AF_ASJ=0.00000e+00;AF_EAS=0.00000e+00;AF_FIN=0.00000e+00;AF_NFE=0.00000e+00;AF_OTH=0.00000e+00;AF_Male=0.00000e+00;AF_Female=0.00000e+00;GC_AFR=140,0,0;GC_AMR=81,0,0;GC_ASJ=17,0,0;GC_EAS=37,0,0;GC_FIN=374,0,0;GC_NFE=650,0,0;GC_OTH=55,0,0;GC_Male=792,0,0;GC_Female=562,0,0;AC_raw=2;AN_raw=30314;AF_raw=6.59761e-05;GC_raw=15156,0,1;GC=1354,0,0;Hom_AFR=0;Hom_AMR=0;Hom_ASJ=0;Hom_EAS=0;Hom_FIN=0;Hom_NFE=0;Hom_OTH=0;Hom_Male=0;Hom_Female=0;Hom_raw=1;Hom=0;POPMAX=.;AC_POPMAX=.;AN_POPMAX=.;AF_POPMAX=.;DP_MEDIAN=5;DREF_MEDIAN=1.22034e-16;GQ_MEDIAN=15;AB_MEDIAN=5.00000e-01;AS_RF=5.87186e-02;AS_FilterStatus=RF|AC0;CSQ=G|intergenic_variant|MODIFIER||||||||||||||||1||||SNV|1||||||||||||||||||||||||||||||||||||||||||||
+22	16050069	.	C	T	43.44	RF;AC0	AC=0;AF=0.00000e+00;AN=2802;BaseQRankSum=7.20000e-01;ClippingRankSum=-1.38000e+00;DP=112972;FS=0.00000e+00;InbreedingCoeff=-3.70000e-02;MQ=3.67700e+01;MQRankSum=7.20000e-01;QD=7.24000e+00;ReadPosRankSum=1.38000e+00;SOR=1.32900e+00;VQSLOD=-3.27400e+01;VQSR_culprit=MQ;GQ_HIST_ALT=0|0|0|0|0|0|0|1|0|0|0|0|0|0|0|0|0|0|0|0;DP_HIST_ALT=0|1|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0;AB_HIST_ALT=0|0|0|0|0|0|0|0|0|0|0|0|0|1|0|0|0|0|0|0;GQ_HIST_ALL=1200|4098|2219|3540|2117|622|710|352|104|101|64|10|20|1|8|3|4|0|0|0;DP_HIST_ALL=7405|6348|1203|181|28|8|0|0|0|0|0|0|0|0|0|0|0|0|0|0;AB_HIST_ALL=0|0|0|0|0|0|0|0|0|0|0|0|0|1|0|0|0|0|0|0;AC_AFR=0;AC_AMR=0;AC_ASJ=0;AC_EAS=0;AC_FIN=0;AC_NFE=0;AC_OTH=0;AC_Male=0;AC_Female=0;AN_AFR=296;AN_AMR=164;AN_ASJ=36;AN_EAS=70;AN_FIN=766;AN_NFE=1354;AN_OTH=116;AN_Male=1638;AN_Female=1164;AF_AFR=0.00000e+00;AF_AMR=0.00000e+00;AF_ASJ=0.00000e+00;AF_EAS=0.00000e+00;AF_FIN=0.00000e+00;AF_NFE=0.00000e+00;AF_OTH=0.00000e+00;AF_Male=0.00000e+00;AF_Female=0.00000e+00;GC_AFR=148,0,0;GC_AMR=82,0,0;GC_ASJ=18,0,0;GC_EAS=35,0,0;GC_FIN=383,0,0;GC_NFE=677,0,0;GC_OTH=58,0,0;GC_Male=819,0,0;GC_Female=582,0,0;AC_raw=1;AN_raw=30346;AF_raw=3.29533e-05;GC_raw=15172,1,0;GC=1401,0,0;Hom_AFR=0;Hom_AMR=0;Hom_ASJ=0;Hom_EAS=0;Hom_FIN=0;Hom_NFE=0;Hom_OTH=0;Hom_Male=0;Hom_Female=0;Hom_raw=0;Hom=0;POPMAX=.;AC_POPMAX=.;AN_POPMAX=.;AF_POPMAX=.;DP_MEDIAN=6;DREF_MEDIAN=3.16178e-11;GQ_MEDIAN=38;AB_MEDIAN=6.66667e-01;AS_RF=9.22976e-02;AS_FilterStatus=RF|AC0;CSQ=T|intergenic_variant|MODIFIER||||||||||||||||1||||SNV|1||||||||||||||||||||||||||||||||||||||||||||
+22	16050098	.	G	A	242.82	RF	AC=2;AF=2.40964e-04;AN=8300;BaseQRankSum=2.45000e+00;ClippingRankSum=1.03000e-01;DP=167171;FS=0.00000e+00;InbreedingCoeff=-1.46000e-02;MQ=3.06100e+01;MQRankSum=-9.35000e-01;QD=1.05600e+01;ReadPosRankSum=6.60000e-01;SOR=3.84000e-01;VQSLOD=-4.11500e+01;VQSR_culprit=MQ;GQ_HIST_ALT=0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|2;DP_HIST_ALT=0|0|2|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0;AB_HIST_ALT=0|0|0|0|0|0|0|0|0|1|1|0|0|0|0|0|0|0|0|0;GQ_HIST_ALL=350|1697|1483|3462|3106|1262|1746|994|348|436|237|88|141|14|39|5|22|4|8|7;DP_HIST_ALL=3368|7876|3165|776|212|33|16|3|0|0|0|0|0|0|0|0|0|0|0|0;AB_HIST_ALL=0|0|0|0|0|0|0|0|0|1|1|0|0|0|0|0|0|0|0|0;AC_AFR=0;AC_AMR=0;AC_ASJ=0;AC_EAS=0;AC_FIN=0;AC_NFE=2;AC_OTH=0;AC_Male=2;AC_Female=0;AN_AFR=1298;AN_AMR=334;AN_ASJ=84;AN_EAS=380;AN_FIN=1460;AN_NFE=4412;AN_OTH=332;AN_Male=4748;AN_Female=3552;AF_AFR=0.00000e+00;AF_AMR=0.00000e+00;AF_ASJ=0.00000e+00;AF_EAS=0.00000e+00;AF_FIN=0.00000e+00;AF_NFE=4.53309e-04;AF_OTH=0.00000e+00;AF_Male=4.21230e-04;AF_Female=0.00000e+00;GC_AFR=649,0,0;GC_AMR=167,0,0;GC_ASJ=42,0,0;GC_EAS=190,0,0;GC_FIN=730,0,0;GC_NFE=2204,2,0;GC_OTH=166,0,0;GC_Male=2372,2,0;GC_Female=1776,0,0;AC_raw=2;AN_raw=30898;AF_raw=6.47291e-05;GC_raw=15447,2,0;GC=4148,2,0;Hom_AFR=0;Hom_AMR=0;Hom_ASJ=0;Hom_EAS=0;Hom_FIN=0;Hom_NFE=0;Hom_OTH=0;Hom_Male=0;Hom_Female=0;Hom_raw=0;Hom=0;POPMAX=NFE;AC_POPMAX=2;AN_POPMAX=4412;AF_POPMAX=4.53309e-04;DP_MEDIAN=11;DREF_MEDIAN=6.29479e-16;GQ_MEDIAN=99;AB_MEDIAN=4.80769e-01;AS_RF=3.30908e-01;AS_FilterStatus=RF;CSQ=A|intergenic_variant|MODIFIER||||||||||||||||1||||SNV|1||||||||||||||||||||||||||||||||||||||||||||
+22	16050115	rs587755077	G	A	10684.53	RF	AC=31;AF=2.54057e-03;AN=12202;BaseQRankSum=1.59000e+00;ClippingRankSum=6.70000e-02;DP=196906;FS=0.00000e+00;InbreedingCoeff=1.40000e-02;MQ=3.37700e+01;MQRankSum=4.06000e-01;QD=8.23000e+00;ReadPosRankSum=3.22000e-01;SOR=4.23100e+00;VQSLOD=-1.16300e+02;VQSR_culprit=MQ;GQ_HIST_ALT=3|6|10|5|3|3|6|13|17|16|2|3|9|12|8|11|5|3|3|14;DP_HIST_ALT=22|95|32|3|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0;AB_HIST_ALT=0|0|0|4|6|16|20|8|21|1|28|5|7|7|7|7|8|0|0|0;GQ_HIST_ALL=237|959|984|2740|3098|1328|2215|1483|527|685|442|163|289|52|79|25|61|6|27|39;DP_HIST_ALL=1972|7287|4327|1314|407|79|44|9|0|0|0|0|0|0|0|0|0|0|0|0;AB_HIST_ALL=0|0|0|4|6|16|20|8|21|1|28|5|7|7|7|7|8|0|0|0;AC_AFR=30;AC_AMR=1;AC_ASJ=0;AC_EAS=0;AC_FIN=0;AC_NFE=0;AC_OTH=0;AC_Male=16;AC_Female=15;AN_AFR=2236;AN_AMR=436;AN_ASJ=144;AN_EAS=640;AN_FIN=1862;AN_NFE=6410;AN_OTH=474;AN_Male=6874;AN_Female=5328;AF_AFR=1.34168e-02;AF_AMR=2.29358e-03;AF_ASJ=0.00000e+00;AF_EAS=0.00000e+00;AF_FIN=0.00000e+00;AF_NFE=0.00000e+00;AF_OTH=0.00000e+00;AF_Male=2.32761e-03;AF_Female=2.81532e-03;GC_AFR=1088,30,0;GC_AMR=217,1,0;GC_ASJ=72,0,0;GC_EAS=320,0,0;GC_FIN=931,0,0;GC_NFE=3205,0,0;GC_OTH=237,0,0;GC_Male=3421,16,0;GC_Female=2649,15,0;AC_raw=159;AN_raw=30878;AF_raw=5.14930e-03;GC_raw=15287,145,7;GC=6070,31,0;Hom_AFR=0;Hom_AMR=0;Hom_ASJ=0;Hom_EAS=0;Hom_FIN=0;Hom_NFE=0;Hom_OTH=0;Hom_Male=0;Hom_Female=0;Hom_raw=7;Hom=0;POPMAX=AFR;AC_POPMAX=30;AN_POPMAX=2236;AF_POPMAX=1.34168e-02;DP_MEDIAN=7;DREF_MEDIAN=1.74246e-08;GQ_MEDIAN=48;AB_MEDIAN=4.44444e-01;AS_RF=5.02621e-02;AS_FilterStatus=RF;CSQ=A|intergenic_variant|MODIFIER|||||||||||||||rs587755077|1||||SNV|1||||||||||||||||A:0.0064||||||||||||||||||||||||||||
+22	16050116	.	G	C	28395.88	RF	AC=246;AF=2.51431e-02;AN=9784;BaseQRankSum=2.48000e-01;ClippingRankSum=0.00000e+00;DP=201089;FS=0.00000e+00;InbreedingCoeff=-7.09000e-02;MQ=3.23400e+01;MQRankSum=-1.23100e+00;QD=3.27000e+00;ReadPosRankSum=2.48000e-01;SOR=7.16400e+00;VQSLOD=-3.11400e+02;VQSR_culprit=MQ;GQ_HIST_ALT=0|3|6|9|32|41|110|119|73|75|49|48|27|32|38|16|4|9|19|27;DP_HIST_ALT=21|356|285|60|12|3|0|0|0|0|0|0|0|0|0|0|0|0|0|0;AB_HIST_ALT=0|0|11|105|184|174|98|40|64|2|30|5|11|8|2|2|0|0|0|0;GQ_HIST_ALL=2616|992|935|2244|2407|1109|1723|1219|458|593|382|175|259|62|105|27|46|11|38|55;DP_HIST_ALL=1838|7215|4403|1404|443|92|50|11|0|0|0|0|0|0|0|0|0|0|0|0;AB_HIST_ALL=0|0|11|105|184|174|98|40|64|2|30|5|11|8|2|2|0|0|0|0;AC_AFR=18;AC_AMR=5;AC_ASJ=4;AC_EAS=3;AC_FIN=5;AC_NFE=202;AC_OTH=9;AC_Male=141;AC_Female=105;AN_AFR=2166;AN_AMR=402;AN_ASJ=88;AN_EAS=650;AN_FIN=1722;AN_NFE=4390;AN_OTH=366;AN_Male=5450;AN_Female=4334;AF_AFR=8.31025e-03;AF_AMR=1.24378e-02;AF_ASJ=4.54545e-02;AF_EAS=4.61538e-03;AF_FIN=2.90360e-03;AF_NFE=4.60137e-02;AF_OTH=2.45902e-02;AF_Male=2.58716e-02;AF_Female=2.42270e-02;GC_AFR=1065,18,0;GC_AMR=196,5,0;GC_ASJ=40,4,0;GC_EAS=322,3,0;GC_FIN=856,5,0;GC_NFE=1993,202,0;GC_OTH=174,9,0;GC_Male=2584,141,0;GC_Female=2062,105,0;AC_raw=738;AN_raw=30912;AF_raw=2.38742e-02;GC_raw=14719,736,1;GC=4646,246,0;Hom_AFR=0;Hom_AMR=0;Hom_ASJ=0;Hom_EAS=0;Hom_FIN=0;Hom_NFE=0;Hom_OTH=0;Hom_Male=0;Hom_Female=0;Hom_raw=1;Hom=0;POPMAX=NFE;AC_POPMAX=202;AN_POPMAX=4390;AF_POPMAX=4.60137e-02;DP_MEDIAN=9;DREF_MEDIAN=6.30918e-05;GQ_MEDIAN=42;AB_MEDIAN=2.50000e-01;AS_RF=8.65786e-03;AS_FilterStatus=RF;CSQ=C|intergenic_variant|MODIFIER||||||||||||||||1||||SNV|1||||||||||||||||||||||||||||||||||||||||||||
+22	16050129	.	G	GACA,C	1164.92	PASS	AC=3,0;AF=1.81378e-04,0.00000e+00;AN=16540;BaseQRankSum=-2.24000e-01;ClippingRankSum=-2.63000e-01;DP=230703;FS=8.86700e+00;InbreedingCoeff=5.80000e-03;MQ=3.46800e+01;MQRankSum=1.43000e-01;QD=1.01300e+01;ReadPosRankSum=-2.13000e-01;SOR=3.30000e-02;VQSLOD=-1.37800e+00;VQSR_culprit=SOR;VQSR_NEGATIVE_TRAIN_SITE;GQ_HIST_ALT=0|0|0|0|0|0|0|0|0|0|0|0|0|0|1|0|1|0|0|4,0|0|0|0|0|0|0|0|0|0|0|0|0|0|1|0|0|0|0|0;DP_HIST_ALT=0|3|2|1|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0,0|1|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0;AB_HIST_ALT=0|0|0|0|0|0|2|0|1|1|1|0|0|0|0|1|0|0|0|0,0|0|0|0|0|0|0|0|0|0|0|0|1|0|0|0|0|0|0|0;GQ_HIST_ALL=104|464|608|1985|2741|1441|2526|1859|721|1069|690|260|538|62|159|47|92|8|46|68;DP_HIST_ALL=1018|6123|5177|2097|791|161|97|24|0|0|0|0|0|0|0|0|0|0|0|0;AB_HIST_ALL=0|0|0|0|0|0|2|0|1|1|1|0|1|0|0|1|0|0|0|0;AC_AFR=0,0;AC_AMR=0,0;AC_ASJ=0,0;AC_EAS=0,0;AC_FIN=0,0;AC_NFE=3,0;AC_OTH=0,0;AC_Male=3,0;AC_Female=0,0;AN_AFR=3614;AN_AMR=528;AN_ASJ=180;AN_EAS=892;AN_FIN=2256;AN_NFE=8466;AN_OTH=604;AN_Male=9308;AN_Female=7232;AF_AFR=0.00000e+00,0.00000e+00;AF_AMR=0.00000e+00,0.00000e+00;AF_ASJ=0.00000e+00,0.00000e+00;AF_EAS=0.00000e+00,0.00000e+00;AF_FIN=0.00000e+00,0.00000e+00;AF_NFE=3.54359e-04,0.00000e+00;AF_OTH=0.00000e+00,0.00000e+00;AF_Male=3.22303e-04,0.00000e+00;AF_Female=0.00000e+00,0.00000e+00;GC_AFR=1807,0,0,0,0,0;GC_AMR=264,0,0,0,0,0;GC_ASJ=90,0,0,0,0,0;GC_EAS=446,0,0,0,0,0;GC_FIN=1128,0,0,0,0,0;GC_NFE=4230,3,0,0,0,0;GC_OTH=302,0,0,0,0,0;GC_Male=4651,3,0,0,0,0;GC_Female=3616,0,0,0,0,0;AC_raw=6,1;AN_raw=30976;AF_raw=1.93698e-04,3.22831e-05;GC_raw=15481,6,0,1,0,0;GC=8267,3,0,0,0,0;Hom_AFR=0,0;Hom_AMR=0,0;Hom_ASJ=0,0;Hom_EAS=0,0;Hom_FIN=0,0;Hom_NFE=0,0;Hom_OTH=0,0;Hom_Male=0,0;Hom_Female=0,0;Hom_raw=0,0;Hom=0,0;POPMAX=NFE,.;AC_POPMAX=3,.;AN_POPMAX=8466,.;AF_POPMAX=3.54359e-04,.;DP_MEDIAN=10,8;DREF_MEDIAN=3.15558e-20,2.51189e-13;GQ_MEDIAN=99,72;AB_MEDIAN=4.41558e-01,6.25000e-01;AS_RF=5.16800e-01,3.29197e-01;AS_FilterStatus=PASS,RF|AC0;CSQ=C|intergenic_variant|MODIFIER||||||||||||||||2||||insertion|1||||||||||||||||||||||||||||||||||||||||||||
+22	16050141	.	C	A	108.57	PASS	AC=1;AF=5.09632e-05;AN=19622;BaseQRankSum=-7.51000e-01;ClippingRankSum=-1.43000e-01;DP=255559;FS=0.00000e+00;InbreedingCoeff=-4.70000e-03;MQ=3.40100e+01;MQRankSum=-3.32000e-01;QD=9.87000e+00;ReadPosRankSum=6.60000e-02;SOR=9.90000e-02;VQSLOD=-3.45100e+01;VQSR_culprit=MQ;GQ_HIST_ALT=0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|1;DP_HIST_ALT=0|0|1|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0;AB_HIST_ALT=0|0|0|0|0|0|0|0|0|0|1|0|0|0|0|0|0|0|0|0;GQ_HIST_ALL=90|295|443|1443|2398|1347|2546|2110|845|1318|842|356|727|79|237|59|159|7|90|99;DP_HIST_ALL=626|4935|5582|2741|1103|289|169|45|0|0|0|0|0|0|0|0|0|0|0|0;AB_HIST_ALL=0|0|0|0|0|0|0|0|0|0|1|0|0|0|0|0|0|0|0|0;AC_AFR=0;AC_AMR=0;AC_ASJ=0;AC_EAS=0;AC_FIN=0;AC_NFE=1;AC_OTH=0;AC_Male=1;AC_Female=0;AN_AFR=4696;AN_AMR=588;AN_ASJ=206;AN_EAS=1092;AN_FIN=2392;AN_NFE=9986;AN_OTH=662;AN_Male=10956;AN_Female=8666;AF_AFR=0.00000e+00;AF_AMR=0.00000e+00;AF_ASJ=0.00000e+00;AF_EAS=0.00000e+00;AF_FIN=0.00000e+00;AF_NFE=1.00140e-04;AF_OTH=0.00000e+00;AF_Male=9.12742e-05;AF_Female=0.00000e+00;GC_AFR=2348,0,0;GC_AMR=294,0,0;GC_ASJ=103,0,0;GC_EAS=546,0,0;GC_FIN=1196,0,0;GC_NFE=4992,1,0;GC_OTH=331,0,0;GC_Male=5477,1,0;GC_Female=4333,0,0;AC_raw=1;AN_raw=30980;AF_raw=3.22789e-05;GC_raw=15489,1,0;GC=9810,1,0;Hom_AFR=0;Hom_AMR=0;Hom_ASJ=0;Hom_EAS=0;Hom_FIN=0;Hom_NFE=0;Hom_OTH=0;Hom_Male=0;Hom_Female=0;Hom_raw=0;Hom=0;POPMAX=NFE;AC_POPMAX=1;AN_POPMAX=9986;AF_POPMAX=1.00140e-04;DP_MEDIAN=11;DREF_MEDIAN=7.94328e-18;GQ_MEDIAN=99;AB_MEDIAN=5.45455e-01;AS_RF=4.14273e-01;AS_FilterStatus=PASS;CSQ=A|intergenic_variant|MODIFIER||||||||||||||||1||||SNV|1||||||||||||||||||||||||||||||||||||||||||||
+22	16050146	.	A	T	48.32	RF;AC0	AC=0;AF=0.00000e+00;AN=20636;BaseQRankSum=-3.54000e-01;ClippingRankSum=5.50000e-01;DP=264413;FS=2.76200e+00;InbreedingCoeff=-4.10000e-03;MQ=3.73000e+01;MQRankSum=2.00000e+00;QD=6.90000e+00;ReadPosRankSum=2.00000e+00;SOR=1.53600e+00;VQSLOD=-3.42700e+01;VQSR_culprit=MQ;GQ_HIST_ALT=0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|1|0|0|0|0;DP_HIST_ALT=0|1|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0;AB_HIST_ALT=0|0|0|0|0|0|0|0|0|0|0|1|0|0|0|0|0|0|0|0;GQ_HIST_ALL=84|258|359|1323|2262|1285|2499|2192|869|1402|937|374|819|84|270|69|176|10|92|126;DP_HIST_ALL=524|4533|5628|2926|1267|363|187|58|4|0|0|0|0|0|0|0|0|0|0|0;AB_HIST_ALL=0|0|0|0|0|0|0|0|0|0|0|1|0|0|0|0|0|0|0|0;AC_AFR=0;AC_AMR=0;AC_ASJ=0;AC_EAS=0;AC_FIN=0;AC_NFE=0;AC_OTH=0;AC_Male=0;AC_Female=0;AN_AFR=5074;AN_AMR=602;AN_ASJ=216;AN_EAS=1154;AN_FIN=2448;AN_NFE=10458;AN_OTH=684;AN_Male=11480;AN_Female=9156;AF_AFR=0.00000e+00;AF_AMR=0.00000e+00;AF_ASJ=0.00000e+00;AF_EAS=0.00000e+00;AF_FIN=0.00000e+00;AF_NFE=0.00000e+00;AF_OTH=0.00000e+00;AF_Male=0.00000e+00;AF_Female=0.00000e+00;GC_AFR=2537,0,0;GC_AMR=301,0,0;GC_ASJ=108,0,0;GC_EAS=577,0,0;GC_FIN=1224,0,0;GC_NFE=5229,0,0;GC_OTH=342,0,0;GC_Male=5740,0,0;GC_Female=4578,0,0;AC_raw=1;AN_raw=30980;AF_raw=3.22789e-05;GC_raw=15489,1,0;GC=10318,0,0;Hom_AFR=0;Hom_AMR=0;Hom_ASJ=0;Hom_EAS=0;Hom_FIN=0;Hom_NFE=0;Hom_OTH=0;Hom_Male=0;Hom_Female=0;Hom_raw=0;Hom=0;POPMAX=.;AC_POPMAX=.;AN_POPMAX=.;AF_POPMAX=.;DP_MEDIAN=7;DREF_MEDIAN=1.00000e-11;GQ_MEDIAN=78;AB_MEDIAN=5.71429e-01;AS_RF=2.11047e-01;AS_FilterStatus=RF|AC0;CSQ=T|intergenic_variant|MODIFIER||||||||||||||||1||||SNV|1||||||||||||||||||||||||||||||||||||||||||||
diff --git a/tests/cbcf_data/gnomad_fixed.vcf b/tests/cbcf_data/gnomad_fixed.vcf
new file mode 100644
index 0000000..552a41a
--- /dev/null
+++ b/tests/cbcf_data/gnomad_fixed.vcf
@@ -0,0 +1,200 @@
+##fileformat=VCFv4.2
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=PL,Number=.,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
+##FILTER=<ID=RF,Description="Failed random forests filters (SNV cutoff 0.4, indels cutoff 0.4)">
+##FILTER=<ID=AC0,Description="Allele Count is zero (i.e. no high-confidence genotype (GQ >= 20, DP >= 10, AB => 0.2 for het calls))">
+##FILTER=<ID=InbreedingCoeff,Description="InbreedingCoeff < -0.3">
+##FILTER=<ID=LCR,Description="In a low complexity region">
+##FILTER=<ID=SEGDUP,Description="In a segmental duplication region">
+##FILTER=<ID=PASS,Description="All filters passed for at least one of the alleles at that site (see AS_FilterStatus for allele-specific filter status)">
+##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency among genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
+##INFO=<ID=ClippingRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref number of hard clipped bases">
+##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
+##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
+##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">
+##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
+##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
+##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
+##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
+##INFO=<ID=SOR,Number=1,Type=Float,Description="Symmetric Odds Ratio of 2x2 contingency table to detect strand bias">
+##INFO=<ID=VQSLOD,Number=1,Type=Float,Description="Log odds ratio of being a true variant versus being false under the trained VQSR gaussian mixture model (deprecated; see AS_RF)">
+##INFO=<ID=VQSR_culprit,Number=1,Type=String,Description="The annotation which was the worst performing in the VQSR Gaussian mixture model (deprecated; see AS_RF)">
+##INFO=<ID=VQSR_NEGATIVE_TRAIN_SITE,Number=0,Type=Flag,Description="This variant was used to build the negative training set of bad variants for VQSR (deprecated; see AS_RF_NEGATIVE_TRAIN)">
+##INFO=<ID=VQSR_POSITIVE_TRAIN_SITE,Number=0,Type=Flag,Description="This variant was used to build the positive training set of good variants for VQSR (deprecated; see AS_RF_POSITIVE_TRAIN)">
+##INFO=<ID=GQ_HIST_ALT,Number=A,Type=String,Description="Histogram for GQ for each allele; Midpoints of histogram bins: 2.5|7.5|12.5|17.5|22.5|27.5|32.5|37.5|42.5|47.5|52.5|57.5|62.5|67.5|72.5|77.5|82.5|87.5|92.5|97.5">
+##INFO=<ID=DP_HIST_ALT,Number=A,Type=String,Description="Histogram for DP for each allele; Midpoints of histogram bins: 2.5|7.5|12.5|17.5|22.5|27.5|32.5|37.5|42.5|47.5|52.5|57.5|62.5|67.5|72.5|77.5|82.5|87.5|92.5|97.5">
+##INFO=<ID=AB_HIST_ALT,Number=A,Type=String,Description="Histogram for Allele Balance in heterozygous individuals for each allele; 100*AD[i_alt]/sum(AD); Midpoints of histogram bins: 2.5|7.5|12.5|17.5|22.5|27.5|32.5|37.5|42.5|47.5|52.5|57.5|62.5|67.5|72.5|77.5|82.5|87.5|92.5|97.5">
+##INFO=<ID=GQ_HIST_ALL,Number=1,Type=String,Description="Histogram for GQ; Midpoints of histogram bins: 2.5|7.5|12.5|17.5|22.5|27.5|32.5|37.5|42.5|47.5|52.5|57.5|62.5|67.5|72.5|77.5|82.5|87.5|92.5|97.5">
+##INFO=<ID=DP_HIST_ALL,Number=1,Type=String,Description="Histogram for DP; Midpoints of histogram bins: 2.5|7.5|12.5|17.5|22.5|27.5|32.5|37.5|42.5|47.5|52.5|57.5|62.5|67.5|72.5|77.5|82.5|87.5|92.5|97.5">
+##INFO=<ID=AB_HIST_ALL,Number=1,Type=String,Description="Histogram for Allele Balance in heterozygous individuals; 100*AD[i_alt]/sum(AD); Midpoints of histogram bins: 2.5|7.5|12.5|17.5|22.5|27.5|32.5|37.5|42.5|47.5|52.5|57.5|62.5|67.5|72.5|77.5|82.5|87.5|92.5|97.5">
+##INFO=<ID=AC_AFR,Number=A,Type=Integer,Description="Allele count in African/African American genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AC_AMR,Number=A,Type=Integer,Description="Allele count in Admixed American genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AC_ASJ,Number=A,Type=Integer,Description="Allele count in Ashkenazi Jewish genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AC_EAS,Number=A,Type=Integer,Description="Allele count in East Asian genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AC_FIN,Number=A,Type=Integer,Description="Allele count in Finnish genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AC_NFE,Number=A,Type=Integer,Description="Allele count in Non-Finnish European genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AC_OTH,Number=A,Type=Integer,Description="Allele count in Other (population not assigned) genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AC_Male,Number=A,Type=Integer,Description="Allele count in Male genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AC_Female,Number=A,Type=Integer,Description="Allele count in Female genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AN_AFR,Number=1,Type=Integer,Description="Total number of alleles in African/African American called genotypes">
+##INFO=<ID=AN_AMR,Number=1,Type=Integer,Description="Total number of alleles in Admixed American called genotypes">
+##INFO=<ID=AN_ASJ,Number=1,Type=Integer,Description="Total number of alleles in Ashkenazi Jewish called genotypes">
+##INFO=<ID=AN_EAS,Number=1,Type=Integer,Description="Total number of alleles in East Asian called genotypes">
+##INFO=<ID=AN_FIN,Number=1,Type=Integer,Description="Total number of alleles in Finnish called genotypes">
+##INFO=<ID=AN_NFE,Number=1,Type=Integer,Description="Total number of alleles in Non-Finnish European called genotypes">
+##INFO=<ID=AN_OTH,Number=1,Type=Integer,Description="Total number of alleles in Other (population not assigned) called genotypes">
+##INFO=<ID=AN_Male,Number=1,Type=Integer,Description="Total number of alleles in Male called genotypes">
+##INFO=<ID=AN_Female,Number=1,Type=Integer,Description="Total number of alleles in Female called genotypes">
+##INFO=<ID=AF_AFR,Number=A,Type=Float,Description="Allele Frequency among African/African American genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AF_AMR,Number=A,Type=Float,Description="Allele Frequency among Admixed American genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AF_ASJ,Number=A,Type=Float,Description="Allele Frequency among Ashkenazi Jewish genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AF_EAS,Number=A,Type=Float,Description="Allele Frequency among East Asian genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AF_FIN,Number=A,Type=Float,Description="Allele Frequency among Finnish genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AF_NFE,Number=A,Type=Float,Description="Allele Frequency among Non-Finnish European genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AF_OTH,Number=A,Type=Float,Description="Allele Frequency among Other (population not assigned) genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AF_Male,Number=A,Type=Float,Description="Allele Frequency among Male genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AF_Female,Number=A,Type=Float,Description="Allele Frequency among Female genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=GC_AFR,Number=.,Type=Integer,Description="Count of African/African American individuals for each genotype">
+##INFO=<ID=GC_AMR,Number=.,Type=Integer,Description="Count of Admixed American individuals for each genotype">
+##INFO=<ID=GC_ASJ,Number=.,Type=Integer,Description="Count of Ashkenazi Jewish individuals for each genotype">
+##INFO=<ID=GC_EAS,Number=.,Type=Integer,Description="Count of East Asian individuals for each genotype">
+##INFO=<ID=GC_FIN,Number=.,Type=Integer,Description="Count of Finnish individuals for each genotype">
+##INFO=<ID=GC_NFE,Number=.,Type=Integer,Description="Count of Non-Finnish European individuals for each genotype">
+##INFO=<ID=GC_OTH,Number=.,Type=Integer,Description="Count of Other (population not assigned) individuals for each genotype">
+##INFO=<ID=GC_Male,Number=.,Type=Integer,Description="Count of Male individuals for each genotype">
+##INFO=<ID=GC_Female,Number=.,Type=Integer,Description="Count of Female individuals for each genotype">
+##INFO=<ID=AC_raw,Number=A,Type=Integer,Description="Allele counts before filtering low-confidence genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AN_raw,Number=1,Type=Integer,Description="Total number of alleles before filtering low-confidence genotypes">
+##INFO=<ID=AF_raw,Number=A,Type=Float,Description="Allele frequency before filtering low-confidence genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=GC_raw,Number=.,Type=Integer,Description="Raw count of individuals for each genotype before filtering low-confidence genotypes">
+##INFO=<ID=GC,Number=.,Type=Integer,Description="Count of individuals for each genotype">
+##INFO=<ID=Hom_AFR,Number=A,Type=Integer,Description="Count of homozygous African/African American individuals">
+##INFO=<ID=Hom_AMR,Number=A,Type=Integer,Description="Count of homozygous Admixed American individuals">
+##INFO=<ID=Hom_ASJ,Number=A,Type=Integer,Description="Count of homozygous Ashkenazi Jewish individuals">
+##INFO=<ID=Hom_EAS,Number=A,Type=Integer,Description="Count of homozygous East Asian individuals">
+##INFO=<ID=Hom_FIN,Number=A,Type=Integer,Description="Count of homozygous Finnish individuals">
+##INFO=<ID=Hom_NFE,Number=A,Type=Integer,Description="Count of homozygous Non-Finnish European individuals">
+##INFO=<ID=Hom_OTH,Number=A,Type=Integer,Description="Count of homozygous Other (population not assigned) individuals">
+##INFO=<ID=Hom_Male,Number=A,Type=Integer,Description="Count of homozygous Male individuals">
+##INFO=<ID=Hom_Female,Number=A,Type=Integer,Description="Count of homozygous Female individuals">
+##INFO=<ID=Hom_raw,Number=A,Type=Integer,Description="Count of homozygous individuals in raw genotypes before filtering low-confidence genotypes">
+##INFO=<ID=Hom,Number=A,Type=Integer,Description="Count of homozygous individuals">
+##INFO=<ID=STAR_AC,Number=1,Type=Integer,Description="AC of deletions spanning this position">
+##INFO=<ID=STAR_AC_raw,Number=1,Type=Integer,Description="Allele counts of deletions spanning this position before filtering low-confidence genotypes">
+##INFO=<ID=STAR_Hom,Number=1,Type=Integer,Description="Count of individuals homozygous for a deletion spanning this position">
+##INFO=<ID=POPMAX,Number=A,Type=String,Description="Population with max AF">
+##INFO=<ID=AC_POPMAX,Number=A,Type=Integer,Description="AC in the population with the max AF">
+##INFO=<ID=AN_POPMAX,Number=A,Type=Integer,Description="AN in the population with the max AF">
+##INFO=<ID=AF_POPMAX,Number=A,Type=Float,Description="Maximum Allele Frequency across populations (excluding OTH)">
+##INFO=<ID=DP_MEDIAN,Number=A,Type=Integer,Description="Median DP in carriers of each allele">
+##INFO=<ID=DREF_MEDIAN,Number=A,Type=Float,Description="Median dosage of homozygous reference in carriers of each allele">
+##INFO=<ID=GQ_MEDIAN,Number=A,Type=Integer,Description="Median GQ in carriers of each allele">
+##INFO=<ID=AB_MEDIAN,Number=A,Type=Float,Description="Median allele balance in heterozygote carriers of each allele">
+##INFO=<ID=AS_RF,Number=A,Type=Float,Description="Random Forests probability for each allele">
+##INFO=<ID=AS_FilterStatus,Number=A,Type=String,Description="Random Forests filter status for each allele">
+##INFO=<ID=AS_RF_POSITIVE_TRAIN,Number=.,Type=Integer,Description="Contains the indices of all alleles used as positive examples during training of random forests">
+##INFO=<ID=AS_RF_NEGATIVE_TRAIN,Number=.,Type=Integer,Description="Contains the indices of all alleles used as negative examples during training of random forests">
+##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence annotations from Ensembl VEP. Format: Allele|Consequence|IMPACT|SYMBOL|Gene|Feature_type|Feature|BIOTYPE|EXON|INTRON|HGVSc|HGVSp|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|ALLELE_NUM|DISTANCE|STRAND|FLAGS|VARIANT_CLASS|MINIMISED|SYMBOL_SOURCE|HGNC_ID|CANONICAL|TSL|APPRIS|CCDS|ENSP|SWISSPROT|TREMBL|UNIPARC|GENE_PHENO|SIFT|PolyPhen|DOMAINS|HGVS_OFFSET|GMAF|AFR_MAF|AMR_MAF|EAS_MAF|EUR_MAF|SAS_MAF|AA_MAF|EA_MAF|ExAC_MAF|ExAC_Adj_MAF|ExAC_AFR_MAF|ExAC_AMR_MAF|ExAC_EAS_MAF|ExAC_FIN_MAF|ExAC_NFE_MAF|ExAC_OTH_MAF|ExAC_SAS_MAF|CLIN_SIG|SOMATIC|PHENO|PUBMED|MOTIF_NAME|MOTIF_POS|HIGH_INF_POS|MOTIF_SCORE_CHANGE|LoF|LoF_filter|LoF_flags|LoF_info">
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+##contig=<ID=GL000192.1,length=547496>
+##contig=<ID=NC_007605,length=171823>
+##reference=file:///seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
+22	16050036	rs374742143	A	C	442156.34	RF	AC=67;AF=4.29487e-01;AN=156;BaseQRankSum=7.36000e-01;ClippingRankSum=2.96000e-01;DB;DP=50165;FS=7.05600e+00;InbreedingCoeff=3.82000e-01;MQ=2.71500e+01;MQRankSum=-1.02600e+00;QD=2.47500e+01;ReadPosRankSum=-2.11000e-01;SOR=1.26750e+01;VQSLOD=-9.58600e+02;VQSR_culprit=MQ;GQ_HIST_ALT=16|1279|299|254|155|24|16|28|50|135|78|4|6|11|32|43|6|4|3|35;DP_HIST_ALT=1769|653|51|5|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0;AB_HIST_ALT=0|0|0|2|5|24|36|11|89|2|125|31|61|85|24|60|34|8|3|7;GQ_HIST_ALL=2359|2810|730|651|296|51|34|33|53|135|78|4|6|11|32|43|6|4|3|35;DP_HIST_ALL=5518|1756|94|6|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0;AB_HIST_ALL=0|0|0|2|5|24|36|11|89|2|125|31|61|85|24|60|34|8|3|7;AC_AFR=3;AC_AMR=7;AC_ASJ=0;AC_EAS=0;AC_FIN=50;AC_NFE=3;AC_OTH=4;AC_Male=32;AC_Female=35;AN_AFR=14;AN_AMR=10;AN_ASJ=0;AN_EAS=0;AN_FIN=84;AN_NFE=42;AN_OTH=6;AN_Male=80;AN_Female=76;AF_AFR=2.14286e-01;AF_AMR=7.00000e-01;AF_ASJ=.;AF_EAS=.;AF_FIN=5.95238e-01;AF_NFE=7.14286e-02;AF_OTH=6.66667e-01;AF_Male=4.00000e-01;AF_Female=4.60526e-01;GC_AFR=4,3,0;GC_AMR=0,3,2;GC_ASJ=0,0,0;GC_EAS=0,0,0;GC_FIN=4,26,12;GC_NFE=18,3,0;GC_OTH=1,0,2;GC_Male=16,16,8;GC_Female=11,19,8;AC_raw=4349;AN_raw=14748;AF_raw=2.94887e-01;GC_raw=4896,607,1871;GC=27,35,16;Hom_AFR=0;Hom_AMR=2;Hom_ASJ=0;Hom_EAS=0;Hom_FIN=12;Hom_NFE=0;Hom_OTH=2;Hom_Male=8;Hom_Female=8;Hom_raw=1871;Hom=16;POPMAX=AMR;AC_POPMAX=7;AN_POPMAX=10;AF_POPMAX=7.00000e-01;DP_MEDIAN=3;DREF_MEDIAN=5.60406e-10;GQ_MEDIAN=12;AB_MEDIAN=5.55556e-01;AS_RF=4.71609e-02;AS_FilterStatus=RF;CSQ=C|intergenic_variant|MODIFIER|||||||||||||||rs374742143|1||||SNV|1||||||||||||||||||||||||||||||||||||||||||||
+22	16050068	.	A	G	82.46	RF;AC0	AC=0;AF=0.00000e+00;AN=2708;DP=111486;FS=0.00000e+00;InbreedingCoeff=-3.63000e-02;MQ=3.20200e+01;QD=1.64900e+01;SOR=3.61100e+00;VQSLOD=-9.28900e+01;VQSR_culprit=MQ;GQ_HIST_ALT=0|0|0|1|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0;DP_HIST_ALT=0|1|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0;AB_HIST_ALT=0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0;GQ_HIST_ALL=1227|4189|2184|3537|2071|618|693|346|97|92|61|9|18|0|7|4|4|0|0|0;DP_HIST_ALL=7502|6289|1163|169|26|8|0|0|0|0|0|0|0|0|0|0|0|0|0|0;AB_HIST_ALL=0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0;AC_AFR=0;AC_AMR=0;AC_ASJ=0;AC_EAS=0;AC_FIN=0;AC_NFE=0;AC_OTH=0;AC_Male=0;AC_Female=0;AN_AFR=280;AN_AMR=162;AN_ASJ=34;AN_EAS=74;AN_FIN=748;AN_NFE=1300;AN_OTH=110;AN_Male=1584;AN_Female=1124;AF_AFR=0.00000e+00;AF_AMR=0.00000e+00;AF_ASJ=0.00000e+00;AF_EAS=0.00000e+00;AF_FIN=0.00000e+00;AF_NFE=0.00000e+00;AF_OTH=0.00000e+00;AF_Male=0.00000e+00;AF_Female=0.00000e+00;GC_AFR=140,0,0;GC_AMR=81,0,0;GC_ASJ=17,0,0;GC_EAS=37,0,0;GC_FIN=374,0,0;GC_NFE=650,0,0;GC_OTH=55,0,0;GC_Male=792,0,0;GC_Female=562,0,0;AC_raw=2;AN_raw=30314;AF_raw=6.59761e-05;GC_raw=15156,0,1;GC=1354,0,0;Hom_AFR=0;Hom_AMR=0;Hom_ASJ=0;Hom_EAS=0;Hom_FIN=0;Hom_NFE=0;Hom_OTH=0;Hom_Male=0;Hom_Female=0;Hom_raw=1;Hom=0;POPMAX=.;AC_POPMAX=.;AN_POPMAX=.;AF_POPMAX=.;DP_MEDIAN=5;DREF_MEDIAN=1.22034e-16;GQ_MEDIAN=15;AB_MEDIAN=5.00000e-01;AS_RF=5.87186e-02;AS_FilterStatus=RF|AC0;CSQ=G|intergenic_variant|MODIFIER||||||||||||||||1||||SNV|1||||||||||||||||||||||||||||||||||||||||||||
+22	16050069	.	C	T	43.44	RF;AC0	AC=0;AF=0.00000e+00;AN=2802;BaseQRankSum=7.20000e-01;ClippingRankSum=-1.38000e+00;DP=112972;FS=0.00000e+00;InbreedingCoeff=-3.70000e-02;MQ=3.67700e+01;MQRankSum=7.20000e-01;QD=7.24000e+00;ReadPosRankSum=1.38000e+00;SOR=1.32900e+00;VQSLOD=-3.27400e+01;VQSR_culprit=MQ;GQ_HIST_ALT=0|0|0|0|0|0|0|1|0|0|0|0|0|0|0|0|0|0|0|0;DP_HIST_ALT=0|1|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0;AB_HIST_ALT=0|0|0|0|0|0|0|0|0|0|0|0|0|1|0|0|0|0|0|0;GQ_HIST_ALL=1200|4098|2219|3540|2117|622|710|352|104|101|64|10|20|1|8|3|4|0|0|0;DP_HIST_ALL=7405|6348|1203|181|28|8|0|0|0|0|0|0|0|0|0|0|0|0|0|0;AB_HIST_ALL=0|0|0|0|0|0|0|0|0|0|0|0|0|1|0|0|0|0|0|0;AC_AFR=0;AC_AMR=0;AC_ASJ=0;AC_EAS=0;AC_FIN=0;AC_NFE=0;AC_OTH=0;AC_Male=0;AC_Female=0;AN_AFR=296;AN_AMR=164;AN_ASJ=36;AN_EAS=70;AN_FIN=766;AN_NFE=1354;AN_OTH=116;AN_Male=1638;AN_Female=1164;AF_AFR=0.00000e+00;AF_AMR=0.00000e+00;AF_ASJ=0.00000e+00;AF_EAS=0.00000e+00;AF_FIN=0.00000e+00;AF_NFE=0.00000e+00;AF_OTH=0.00000e+00;AF_Male=0.00000e+00;AF_Female=0.00000e+00;GC_AFR=148,0,0;GC_AMR=82,0,0;GC_ASJ=18,0,0;GC_EAS=35,0,0;GC_FIN=383,0,0;GC_NFE=677,0,0;GC_OTH=58,0,0;GC_Male=819,0,0;GC_Female=582,0,0;AC_raw=1;AN_raw=30346;AF_raw=3.29533e-05;GC_raw=15172,1,0;GC=1401,0,0;Hom_AFR=0;Hom_AMR=0;Hom_ASJ=0;Hom_EAS=0;Hom_FIN=0;Hom_NFE=0;Hom_OTH=0;Hom_Male=0;Hom_Female=0;Hom_raw=0;Hom=0;POPMAX=.;AC_POPMAX=.;AN_POPMAX=.;AF_POPMAX=.;DP_MEDIAN=6;DREF_MEDIAN=3.16178e-11;GQ_MEDIAN=38;AB_MEDIAN=6.66667e-01;AS_RF=9.22976e-02;AS_FilterStatus=RF|AC0;CSQ=T|intergenic_variant|MODIFIER||||||||||||||||1||||SNV|1||||||||||||||||||||||||||||||||||||||||||||
+22	16050098	.	G	A	242.82	RF	AC=2;AF=2.40964e-04;AN=8300;BaseQRankSum=2.45000e+00;ClippingRankSum=1.03000e-01;DP=167171;FS=0.00000e+00;InbreedingCoeff=-1.46000e-02;MQ=3.06100e+01;MQRankSum=-9.35000e-01;QD=1.05600e+01;ReadPosRankSum=6.60000e-01;SOR=3.84000e-01;VQSLOD=-4.11500e+01;VQSR_culprit=MQ;GQ_HIST_ALT=0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|2;DP_HIST_ALT=0|0|2|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0;AB_HIST_ALT=0|0|0|0|0|0|0|0|0|1|1|0|0|0|0|0|0|0|0|0;GQ_HIST_ALL=350|1697|1483|3462|3106|1262|1746|994|348|436|237|88|141|14|39|5|22|4|8|7;DP_HIST_ALL=3368|7876|3165|776|212|33|16|3|0|0|0|0|0|0|0|0|0|0|0|0;AB_HIST_ALL=0|0|0|0|0|0|0|0|0|1|1|0|0|0|0|0|0|0|0|0;AC_AFR=0;AC_AMR=0;AC_ASJ=0;AC_EAS=0;AC_FIN=0;AC_NFE=2;AC_OTH=0;AC_Male=2;AC_Female=0;AN_AFR=1298;AN_AMR=334;AN_ASJ=84;AN_EAS=380;AN_FIN=1460;AN_NFE=4412;AN_OTH=332;AN_Male=4748;AN_Female=3552;AF_AFR=0.00000e+00;AF_AMR=0.00000e+00;AF_ASJ=0.00000e+00;AF_EAS=0.00000e+00;AF_FIN=0.00000e+00;AF_NFE=4.53309e-04;AF_OTH=0.00000e+00;AF_Male=4.21230e-04;AF_Female=0.00000e+00;GC_AFR=649,0,0;GC_AMR=167,0,0;GC_ASJ=42,0,0;GC_EAS=190,0,0;GC_FIN=730,0,0;GC_NFE=2204,2,0;GC_OTH=166,0,0;GC_Male=2372,2,0;GC_Female=1776,0,0;AC_raw=2;AN_raw=30898;AF_raw=6.47291e-05;GC_raw=15447,2,0;GC=4148,2,0;Hom_AFR=0;Hom_AMR=0;Hom_ASJ=0;Hom_EAS=0;Hom_FIN=0;Hom_NFE=0;Hom_OTH=0;Hom_Male=0;Hom_Female=0;Hom_raw=0;Hom=0;POPMAX=NFE;AC_POPMAX=2;AN_POPMAX=4412;AF_POPMAX=4.53309e-04;DP_MEDIAN=11;DREF_MEDIAN=6.29479e-16;GQ_MEDIAN=99;AB_MEDIAN=4.80769e-01;AS_RF=3.30908e-01;AS_FilterStatus=RF;CSQ=A|intergenic_variant|MODIFIER||||||||||||||||1||||SNV|1||||||||||||||||||||||||||||||||||||||||||||
+22	16050115	rs587755077	G	A	10684.53	RF	AC=31;AF=2.54057e-03;AN=12202;BaseQRankSum=1.59000e+00;ClippingRankSum=6.70000e-02;DP=196906;FS=0.00000e+00;InbreedingCoeff=1.40000e-02;MQ=3.37700e+01;MQRankSum=4.06000e-01;QD=8.23000e+00;ReadPosRankSum=3.22000e-01;SOR=4.23100e+00;VQSLOD=-1.16300e+02;VQSR_culprit=MQ;GQ_HIST_ALT=3|6|10|5|3|3|6|13|17|16|2|3|9|12|8|11|5|3|3|14;DP_HIST_ALT=22|95|32|3|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0;AB_HIST_ALT=0|0|0|4|6|16|20|8|21|1|28|5|7|7|7|7|8|0|0|0;GQ_HIST_ALL=237|959|984|2740|3098|1328|2215|1483|527|685|442|163|289|52|79|25|61|6|27|39;DP_HIST_ALL=1972|7287|4327|1314|407|79|44|9|0|0|0|0|0|0|0|0|0|0|0|0;AB_HIST_ALL=0|0|0|4|6|16|20|8|21|1|28|5|7|7|7|7|8|0|0|0;AC_AFR=30;AC_AMR=1;AC_ASJ=0;AC_EAS=0;AC_FIN=0;AC_NFE=0;AC_OTH=0;AC_Male=16;AC_Female=15;AN_AFR=2236;AN_AMR=436;AN_ASJ=144;AN_EAS=640;AN_FIN=1862;AN_NFE=6410;AN_OTH=474;AN_Male=6874;AN_Female=5328;AF_AFR=1.34168e-02;AF_AMR=2.29358e-03;AF_ASJ=0.00000e+00;AF_EAS=0.00000e+00;AF_FIN=0.00000e+00;AF_NFE=0.00000e+00;AF_OTH=0.00000e+00;AF_Male=2.32761e-03;AF_Female=2.81532e-03;GC_AFR=1088,30,0;GC_AMR=217,1,0;GC_ASJ=72,0,0;GC_EAS=320,0,0;GC_FIN=931,0,0;GC_NFE=3205,0,0;GC_OTH=237,0,0;GC_Male=3421,16,0;GC_Female=2649,15,0;AC_raw=159;AN_raw=30878;AF_raw=5.14930e-03;GC_raw=15287,145,7;GC=6070,31,0;Hom_AFR=0;Hom_AMR=0;Hom_ASJ=0;Hom_EAS=0;Hom_FIN=0;Hom_NFE=0;Hom_OTH=0;Hom_Male=0;Hom_Female=0;Hom_raw=7;Hom=0;POPMAX=AFR;AC_POPMAX=30;AN_POPMAX=2236;AF_POPMAX=1.34168e-02;DP_MEDIAN=7;DREF_MEDIAN=1.74246e-08;GQ_MEDIAN=48;AB_MEDIAN=4.44444e-01;AS_RF=5.02621e-02;AS_FilterStatus=RF;CSQ=A|intergenic_variant|MODIFIER|||||||||||||||rs587755077|1||||SNV|1||||||||||||||||A:0.0064||||||||||||||||||||||||||||
+22	16050116	.	G	C	28395.88	RF	AC=246;AF=2.51431e-02;AN=9784;BaseQRankSum=2.48000e-01;ClippingRankSum=0.00000e+00;DP=201089;FS=0.00000e+00;InbreedingCoeff=-7.09000e-02;MQ=3.23400e+01;MQRankSum=-1.23100e+00;QD=3.27000e+00;ReadPosRankSum=2.48000e-01;SOR=7.16400e+00;VQSLOD=-3.11400e+02;VQSR_culprit=MQ;GQ_HIST_ALT=0|3|6|9|32|41|110|119|73|75|49|48|27|32|38|16|4|9|19|27;DP_HIST_ALT=21|356|285|60|12|3|0|0|0|0|0|0|0|0|0|0|0|0|0|0;AB_HIST_ALT=0|0|11|105|184|174|98|40|64|2|30|5|11|8|2|2|0|0|0|0;GQ_HIST_ALL=2616|992|935|2244|2407|1109|1723|1219|458|593|382|175|259|62|105|27|46|11|38|55;DP_HIST_ALL=1838|7215|4403|1404|443|92|50|11|0|0|0|0|0|0|0|0|0|0|0|0;AB_HIST_ALL=0|0|11|105|184|174|98|40|64|2|30|5|11|8|2|2|0|0|0|0;AC_AFR=18;AC_AMR=5;AC_ASJ=4;AC_EAS=3;AC_FIN=5;AC_NFE=202;AC_OTH=9;AC_Male=141;AC_Female=105;AN_AFR=2166;AN_AMR=402;AN_ASJ=88;AN_EAS=650;AN_FIN=1722;AN_NFE=4390;AN_OTH=366;AN_Male=5450;AN_Female=4334;AF_AFR=8.31025e-03;AF_AMR=1.24378e-02;AF_ASJ=4.54545e-02;AF_EAS=4.61538e-03;AF_FIN=2.90360e-03;AF_NFE=4.60137e-02;AF_OTH=2.45902e-02;AF_Male=2.58716e-02;AF_Female=2.42270e-02;GC_AFR=1065,18,0;GC_AMR=196,5,0;GC_ASJ=40,4,0;GC_EAS=322,3,0;GC_FIN=856,5,0;GC_NFE=1993,202,0;GC_OTH=174,9,0;GC_Male=2584,141,0;GC_Female=2062,105,0;AC_raw=738;AN_raw=30912;AF_raw=2.38742e-02;GC_raw=14719,736,1;GC=4646,246,0;Hom_AFR=0;Hom_AMR=0;Hom_ASJ=0;Hom_EAS=0;Hom_FIN=0;Hom_NFE=0;Hom_OTH=0;Hom_Male=0;Hom_Female=0;Hom_raw=1;Hom=0;POPMAX=NFE;AC_POPMAX=202;AN_POPMAX=4390;AF_POPMAX=4.60137e-02;DP_MEDIAN=9;DREF_MEDIAN=6.30918e-05;GQ_MEDIAN=42;AB_MEDIAN=2.50000e-01;AS_RF=8.65786e-03;AS_FilterStatus=RF;CSQ=C|intergenic_variant|MODIFIER||||||||||||||||1||||SNV|1||||||||||||||||||||||||||||||||||||||||||||
+22	16050129	.	G	GACA,C	1164.92	PASS	AC=3,0;AF=1.81378e-04,0.00000e+00;AN=16540;BaseQRankSum=-2.24000e-01;ClippingRankSum=-2.63000e-01;DP=230703;FS=8.86700e+00;InbreedingCoeff=5.80000e-03;MQ=3.46800e+01;MQRankSum=1.43000e-01;QD=1.01300e+01;ReadPosRankSum=-2.13000e-01;SOR=3.30000e-02;VQSLOD=-1.37800e+00;VQSR_culprit=SOR;VQSR_NEGATIVE_TRAIN_SITE;GQ_HIST_ALT=0|0|0|0|0|0|0|0|0|0|0|0|0|0|1|0|1|0|0|4,0|0|0|0|0|0|0|0|0|0|0|0|0|0|1|0|0|0|0|0;DP_HIST_ALT=0|3|2|1|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0,0|1|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0;AB_HIST_ALT=0|0|0|0|0|0|2|0|1|1|1|0|0|0|0|1|0|0|0|0,0|0|0|0|0|0|0|0|0|0|0|0|1|0|0|0|0|0|0|0;GQ_HIST_ALL=104|464|608|1985|2741|1441|2526|1859|721|1069|690|260|538|62|159|47|92|8|46|68;DP_HIST_ALL=1018|6123|5177|2097|791|161|97|24|0|0|0|0|0|0|0|0|0|0|0|0;AB_HIST_ALL=0|0|0|0|0|0|2|0|1|1|1|0|1|0|0|1|0|0|0|0;AC_AFR=0,0;AC_AMR=0,0;AC_ASJ=0,0;AC_EAS=0,0;AC_FIN=0,0;AC_NFE=3,0;AC_OTH=0,0;AC_Male=3,0;AC_Female=0,0;AN_AFR=3614;AN_AMR=528;AN_ASJ=180;AN_EAS=892;AN_FIN=2256;AN_NFE=8466;AN_OTH=604;AN_Male=9308;AN_Female=7232;AF_AFR=0.00000e+00,0.00000e+00;AF_AMR=0.00000e+00,0.00000e+00;AF_ASJ=0.00000e+00,0.00000e+00;AF_EAS=0.00000e+00,0.00000e+00;AF_FIN=0.00000e+00,0.00000e+00;AF_NFE=3.54359e-04,0.00000e+00;AF_OTH=0.00000e+00,0.00000e+00;AF_Male=3.22303e-04,0.00000e+00;AF_Female=0.00000e+00,0.00000e+00;GC_AFR=1807,0,0,0,0,0;GC_AMR=264,0,0,0,0,0;GC_ASJ=90,0,0,0,0,0;GC_EAS=446,0,0,0,0,0;GC_FIN=1128,0,0,0,0,0;GC_NFE=4230,3,0,0,0,0;GC_OTH=302,0,0,0,0,0;GC_Male=4651,3,0,0,0,0;GC_Female=3616,0,0,0,0,0;AC_raw=6,1;AN_raw=30976;AF_raw=1.93698e-04,3.22831e-05;GC_raw=15481,6,0,1,0,0;GC=8267,3,0,0,0,0;Hom_AFR=0,0;Hom_AMR=0,0;Hom_ASJ=0,0;Hom_EAS=0,0;Hom_FIN=0,0;Hom_NFE=0,0;Hom_OTH=0,0;Hom_Male=0,0;Hom_Female=0,0;Hom_raw=0,0;Hom=0,0;POPMAX=NFE,.;AC_POPMAX=3,.;AN_POPMAX=8466,.;AF_POPMAX=3.54359e-04,.;DP_MEDIAN=10,8;DREF_MEDIAN=3.15558e-20,2.51189e-13;GQ_MEDIAN=99,72;AB_MEDIAN=4.41558e-01,6.25000e-01;AS_RF=5.16800e-01,3.29197e-01;AS_FilterStatus=PASS,RF|AC0;CSQ=C|intergenic_variant|MODIFIER||||||||||||||||2||||insertion|1||||||||||||||||||||||||||||||||||||||||||||
+22	16050141	.	C	A	108.57	PASS	AC=1;AF=5.09632e-05;AN=19622;BaseQRankSum=-7.51000e-01;ClippingRankSum=-1.43000e-01;DP=255559;FS=0.00000e+00;InbreedingCoeff=-4.70000e-03;MQ=3.40100e+01;MQRankSum=-3.32000e-01;QD=9.87000e+00;ReadPosRankSum=6.60000e-02;SOR=9.90000e-02;VQSLOD=-3.45100e+01;VQSR_culprit=MQ;GQ_HIST_ALT=0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|1;DP_HIST_ALT=0|0|1|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0;AB_HIST_ALT=0|0|0|0|0|0|0|0|0|0|1|0|0|0|0|0|0|0|0|0;GQ_HIST_ALL=90|295|443|1443|2398|1347|2546|2110|845|1318|842|356|727|79|237|59|159|7|90|99;DP_HIST_ALL=626|4935|5582|2741|1103|289|169|45|0|0|0|0|0|0|0|0|0|0|0|0;AB_HIST_ALL=0|0|0|0|0|0|0|0|0|0|1|0|0|0|0|0|0|0|0|0;AC_AFR=0;AC_AMR=0;AC_ASJ=0;AC_EAS=0;AC_FIN=0;AC_NFE=1;AC_OTH=0;AC_Male=1;AC_Female=0;AN_AFR=4696;AN_AMR=588;AN_ASJ=206;AN_EAS=1092;AN_FIN=2392;AN_NFE=9986;AN_OTH=662;AN_Male=10956;AN_Female=8666;AF_AFR=0.00000e+00;AF_AMR=0.00000e+00;AF_ASJ=0.00000e+00;AF_EAS=0.00000e+00;AF_FIN=0.00000e+00;AF_NFE=1.00140e-04;AF_OTH=0.00000e+00;AF_Male=9.12742e-05;AF_Female=0.00000e+00;GC_AFR=2348,0,0;GC_AMR=294,0,0;GC_ASJ=103,0,0;GC_EAS=546,0,0;GC_FIN=1196,0,0;GC_NFE=4992,1,0;GC_OTH=331,0,0;GC_Male=5477,1,0;GC_Female=4333,0,0;AC_raw=1;AN_raw=30980;AF_raw=3.22789e-05;GC_raw=15489,1,0;GC=9810,1,0;Hom_AFR=0;Hom_AMR=0;Hom_ASJ=0;Hom_EAS=0;Hom_FIN=0;Hom_NFE=0;Hom_OTH=0;Hom_Male=0;Hom_Female=0;Hom_raw=0;Hom=0;POPMAX=NFE;AC_POPMAX=1;AN_POPMAX=9986;AF_POPMAX=1.00140e-04;DP_MEDIAN=11;DREF_MEDIAN=7.94328e-18;GQ_MEDIAN=99;AB_MEDIAN=5.45455e-01;AS_RF=4.14273e-01;AS_FilterStatus=PASS;CSQ=A|intergenic_variant|MODIFIER||||||||||||||||1||||SNV|1||||||||||||||||||||||||||||||||||||||||||||
+22	16050146	.	A	T	48.32	RF;AC0	AC=0;AF=0.00000e+00;AN=20636;BaseQRankSum=-3.54000e-01;ClippingRankSum=5.50000e-01;DP=264413;FS=2.76200e+00;InbreedingCoeff=-4.10000e-03;MQ=3.73000e+01;MQRankSum=2.00000e+00;QD=6.90000e+00;ReadPosRankSum=2.00000e+00;SOR=1.53600e+00;VQSLOD=-3.42700e+01;VQSR_culprit=MQ;GQ_HIST_ALT=0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|1|0|0|0|0;DP_HIST_ALT=0|1|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0;AB_HIST_ALT=0|0|0|0|0|0|0|0|0|0|0|1|0|0|0|0|0|0|0|0;GQ_HIST_ALL=84|258|359|1323|2262|1285|2499|2192|869|1402|937|374|819|84|270|69|176|10|92|126;DP_HIST_ALL=524|4533|5628|2926|1267|363|187|58|4|0|0|0|0|0|0|0|0|0|0|0;AB_HIST_ALL=0|0|0|0|0|0|0|0|0|0|0|1|0|0|0|0|0|0|0|0;AC_AFR=0;AC_AMR=0;AC_ASJ=0;AC_EAS=0;AC_FIN=0;AC_NFE=0;AC_OTH=0;AC_Male=0;AC_Female=0;AN_AFR=5074;AN_AMR=602;AN_ASJ=216;AN_EAS=1154;AN_FIN=2448;AN_NFE=10458;AN_OTH=684;AN_Male=11480;AN_Female=9156;AF_AFR=0.00000e+00;AF_AMR=0.00000e+00;AF_ASJ=0.00000e+00;AF_EAS=0.00000e+00;AF_FIN=0.00000e+00;AF_NFE=0.00000e+00;AF_OTH=0.00000e+00;AF_Male=0.00000e+00;AF_Female=0.00000e+00;GC_AFR=2537,0,0;GC_AMR=301,0,0;GC_ASJ=108,0,0;GC_EAS=577,0,0;GC_FIN=1224,0,0;GC_NFE=5229,0,0;GC_OTH=342,0,0;GC_Male=5740,0,0;GC_Female=4578,0,0;AC_raw=1;AN_raw=30980;AF_raw=3.22789e-05;GC_raw=15489,1,0;GC=10318,0,0;Hom_AFR=0;Hom_AMR=0;Hom_ASJ=0;Hom_EAS=0;Hom_FIN=0;Hom_NFE=0;Hom_OTH=0;Hom_Male=0;Hom_Female=0;Hom_raw=0;Hom=0;POPMAX=.;AC_POPMAX=.;AN_POPMAX=.;AF_POPMAX=.;DP_MEDIAN=7;DREF_MEDIAN=1.00000e-11;GQ_MEDIAN=78;AB_MEDIAN=5.71429e-01;AS_RF=2.11047e-01;AS_FilterStatus=RF|AC0;CSQ=T|intergenic_variant|MODIFIER||||||||||||||||1||||SNV|1||||||||||||||||||||||||||||||||||||||||||||
diff --git a/tests/cbcf_data/missing_genotypes.vcf b/tests/cbcf_data/missing_genotypes.vcf
new file mode 100644
index 0000000..a6f0dbc
--- /dev/null
+++ b/tests/cbcf_data/missing_genotypes.vcf
@@ -0,0 +1,6 @@
+##fileformat=VCFv4.1
+##contig=<ID=chr1,length=100>
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	sample1	sample2
+chr1	1	.	A	G	999	.	.	GT	0/0	1/1
+chr1	50	.	T	C	999	.	.	GT	./.	0/1
diff --git a/tests/compile_test.py b/tests/compile_test.py
new file mode 100644
index 0000000..300ab92
--- /dev/null
+++ b/tests/compile_test.py
@@ -0,0 +1,54 @@
+'''
+compile_test.py - check pyximport functionality with pysam
+==========================================================
+
+test script for checking if compilation against
+pysam and tabix works.
+'''
+
+# clean up previous compilation
+import os
+import unittest
+import pysam
+from TestUtils import make_data_files, BAM_DATADIR, TABIX_DATADIR
+
+
+def setUpModule():
+    make_data_files(BAM_DATADIR)
+    make_data_files(TABIX_DATADIR)
+
+
+try:
+    os.unlink('tests/_compile_test.c')
+    os.unlink('tests/_compile_test.pyxbldc')
+except OSError:
+    pass
+
+import pyximport
+pyximport.install(build_in_temp=False)
+import _compile_test
+
+
+class BAMTest(unittest.TestCase):
+
+    input_filename = os.path.join(BAM_DATADIR, "ex1.bam")
+
+    def testCount(self):
+
+        nread = _compile_test.testCountBAM(
+            pysam.Samfile(self.input_filename))
+        self.assertEqual(nread, 3270)
+
+
+class GTFTest(unittest.TestCase):
+
+    input_filename = os.path.join(TABIX_DATADIR, "example.gtf.gz")
+
+    def testCount(self):
+        nread = _compile_test.testCountGTF(
+            pysam.Tabixfile(self.input_filename))
+        self.assertEqual(nread, 237)
+
+
+if __name__ == "__main__":
+    unittest.main()
diff --git a/tests/faidx_bench.py b/tests/faidx_bench.py
new file mode 100644
index 0000000..c167336
--- /dev/null
+++ b/tests/faidx_bench.py
@@ -0,0 +1,71 @@
+"""Benchmarking the cfaidx module. Usage::
+
+pytest benchmark/faidx_bench.py
+"""
+import os
+import pysam
+
+
+from TestUtils import BAM_DATADIR
+
+
+def iterate_over_fastx(fn, persist=True):
+    return len(list(pysam.FastxFile(fn, persist=persist)))
+
+
+def iterate_over_fastx_as_file(fn):
+    with open(fn) as inf:
+        return len(inf.read())
+
+
+def test_fasta_iteration_short_sequences(benchmark):
+    result = benchmark(iterate_over_fastx, os.path.join(
+        BAM_DATADIR, "faidx_ex1.fa"))
+    assert result == 3270
+
+
+def test_fasta_iteration_long_sequences(benchmark):
+    result = benchmark(iterate_over_fastx, os.path.join(BAM_DATADIR, "ex1.fa"))
+    assert result == 2
+
+
+def test_fasta_iteration_short_sequences_without_persistence(benchmark):
+    result = benchmark(iterate_over_fastx, os.path.join(
+        BAM_DATADIR, "faidx_ex1.fa"), persist=False)
+    assert result == 3270
+
+
+def test_fasta_iteration_long_sequences_without_persistence(benchmark):
+    result = benchmark(iterate_over_fastx, os.path.join(
+        BAM_DATADIR, "ex1.fa"), persist=False)
+    assert result == 2
+
+
+def test_fasta_iteration_short_sequences_as_file(benchmark):
+    result = benchmark(iterate_over_fastx_as_file,
+                       os.path.join(BAM_DATADIR, "faidx_ex1.fa"))
+    assert result == 195399
+
+
+def test_fasta_iteration_long_sequences_as_file(benchmark):
+    result = benchmark(iterate_over_fastx_as_file,
+                       os.path.join(BAM_DATADIR, "ex1.fa"))
+    assert result == 3225
+
+
+def test_fastq_iteration_short_sequences(benchmark):
+    result = benchmark(iterate_over_fastx, os.path.join(
+        BAM_DATADIR, "faidx_ex1.fq"))
+    assert result == 3270
+
+
+def test_fastq_iteration_short_sequences_without_persistence(benchmark):
+    result = benchmark(iterate_over_fastx, os.path.join(
+        BAM_DATADIR, "faidx_ex1.fq"), persist=False)
+    assert result == 3270
+
+
+def test_fastq_iteration_short_sequences_as_file(benchmark):
+    result = benchmark(iterate_over_fastx_as_file,
+                       os.path.join(BAM_DATADIR, "faidx_ex1.fq"))
+    assert result == 320458
diff --git a/tests/faidx_test.py b/tests/faidx_test.py
new file mode 100644
index 0000000..8718f98
--- /dev/null
+++ b/tests/faidx_test.py
@@ -0,0 +1,344 @@
+import pysam
+import unittest
+import os
+import gzip
+import copy
+import shutil
+
+from TestUtils import check_url, make_data_files, BAM_DATADIR, get_temp_filename
+
+
+def setUpModule():
+    make_data_files(BAM_DATADIR)
+
+
+class TestFastaFile(unittest.TestCase):
+
+    sequences = {
+        'chr1':
+        "CACTAGTGGCTCATTGTAAATGTGTGGTTTAACTCGTCCATGGCCCAGCATTAGGGAGCTGTGGACCCTGCAGCCTGGCTGTGGGGGCCGCAGTGGCTGAGGGGTGCAGAGCCGAGTCACGGGGTTGCCAGCACAGGGGCTTAACCTCTGGTGACTGCCAGAGCTGCTGGCAAGCTAGAGTCCCATTTGGAGCCCCTCTAAGCCGTTCTATTTGTAATGAAAACTATATTTATGCTATTCAGTTCTAAATATAGAAATTGAAACAGCTGTGTTTAGTGCCTTTGTTCAACCCCCTTGCAACAACCTTGAGAACCCCAGGGAATTTGTCAATGTCAGGGAAGGAGCATTTTGTCAGTTACCAAATGTGTTTATTACCAGAGGGATGGAGGGAAGAGGGACGCTGAAGAACTTTGATGCCCTCTTCTTCCAAAGATGAAACGCGTAACTGCGCTCTCATTCACTCCAGCTCCCTGTCACCCAATGGACCTGTGATATCTGGATTCTGGGAAATTCTTCATCCTGGACCCTGAGAGATTCTGCAGCCCAGCTCCAGATTGCTTGTGGTCTGACAGGCTGCAACTGTGAGCCATCACAATGAACAACAGGAAGAAAAGGTCTTTCAAAAGGTGATGTGTGTTCTCATCAACCTCATACACACACATGGTTTAGGGGTATAATACCTCTACATGGCTGATTATGAAAACAATGTTCCCCAGATACCATCCCTGTCTTACTTCCAGCTCCCCAGAGGGAAAGCTTTCAACGCTTCTAGCCATTTCTTTTGGCATTTGCCTTCAGACCCTACACGAATGCGTCTCTACCACAGGGGGCTGCGCGGTTTCCCATCATGAAGCACTGAACTTCCACGTCTCATCTAGGGGAACAGGGAGGTGCACTAATGCGCTCCACGCCCAAGCCCTTCTCACAGTTTCTGCCCCCAGCATGGTTGTACTGGGCAATACATGAGATTATTAGGAAATGCTTTACTGTCATAACTATGAAGAGACTATTGCCAGATGAACCACACATTAATACTATGTTTCTTATCTGCACATTACTACCCTGCAATTAATATAATTGTGTCCATGTACACACGCTGTCCTATGTACTTATCATGACTCTATCCCAAATTCCCAATTACGTCCTATCTTCTTCTTAGGGAAGAACAGCTTAGGTATCAATTTGGTGTTCTGTGTAAAGTCTCAGGGAGCCGTCCGTGTCCTCCCATCTGGCCTCGTCCACACTGGTTCTCTTGAAAGCTTGGGCTGTAATGATGCCCCTTGGCCATCACCCAGTCCCTGCCCCATCTCTTGTAATCTCTCTCCTTTTTGCTGCATCCCTGTCTTCCTCTGTCTTGATTTACTTGTTGTTGGTTTTCTGTTTCTTTGTTTGATTTGGTGGAAGACATAATCCCACGCTTCCTATGGAAAGGTTGTTGGGAGATTTTTAATGATTCCTCAATGTTAAAATGTCTATTTTTGTCTTGACACCCAACTAATATTTGTCTGAGCAAAACAGTCTAGATGAGAGAGAACTTCCCTGGAGGTCTGATGGCGTTTCTCCCTCGTCTTCTTA",  # noqa
+        'chr2':
+        "TTCAAATGAACTTCTGTAATTGAAAAATTCATTTAAGAAATTACAAAATATAGTTGAAAGCTCTAACAATAGACTAAACCAAGCAGAAGAAAGAGGTTCAGAACTTGAAGACAAGTCTCTTATGAATTAACCCAGTCAGACAAAAATAAAGAAAAAAATTTTAAAAATGAACAGAGCTTTCAAGAAGTATGAGATTATGTAAAGTAACTGAACCTATGAGTCACAGGTATTCCTGAGGAAAAAGAAAAAGTGAGAAGTTTGGAAAAACTATTTGAGGAAGTAATTGGGGAAAACCTCTTTAGTCTTGCTAGAGATTTAGACATCTAAATGAAAGAGGCTCAAAGAATGCCAGGAAGATACATTGCAAGACAGACTTCATCAAGATATGTAGTCATCAGACTATCTAAAGTCAACATGAAGGAAAAAAATTCTAAAATCAGCAAGAGAAAAGCATACAGTCATCTATAAAGGAAATCCCATCAGAATAACAATGGGCTTCTCAGCAGAAACCTTACAAGCCAGAAGAGATTGGATCTAATTTTTGGACTTCTTAAAGAAAAAAAAACCTGTCAAACACGAATGTTATGCCCTGCTAAACTAAGCATCATAAATGAAGGGGAAATAAAGTCAAGTCTTTCCTGACAAGCAAATGCTAAGATAATTCATCATCACTAAACCAGTCCTATAAGAAATGCTCAAAAGAATTGTAAAAGTCAAAATTAAAGTTCAATACTCACCATCATAAATACACACAAAAGTACAAAACTCACAGGTTTTATAAAACAATTGAGACTACAGAGCAACTAGGTAAAAAATTAACATTACAACAGGAACAAAACCTCATATATCAATATTAACTTTGAATAAAAAGGGATTAAATTCCCCCACTTAAGAGATATAGATTGGCAGAACAGATTTAAAAACATGAACTAACTATATGCTGTTTACAAGAAACTCATTAATAAAGACATGAGTTCAGGTAAAGGGGTGGAAAAAGATGTTCTACGCAAACAGAAACCAAATGAGAGAAGGAGTAGCTATACTTATATCAGATAAAGCACACTTTAAATCAACAACAGTAAAATAAAACAAAGGAGGTCATCATACAATGATAAAAAGATCAATTCAGCAAGAAGATATAACCATCCTACTAAATACATATGCACCTAACACAAGACTACCCAGATTCATAAAACAAATACTACTAGACCTAAGAGGGATGAGAAATTACCTAATTGGTACAATGTACAATATTCTGATGATGGTTACACTAAAAGCCCATACTTTACTGCTACTCAATATATCCATGTAACAAATCTGCGCTTGTACTTCTAAATCTATAAAAAAATTAAAATTTAACAAAAGTAAATAAAACACATAGCTAAAACTAAAAAAGCAAAAACAAAAACTATGCTAAGTATTGGTAAAGATGTGGGGAAAAAAGTAAACTCTCAAATATTGCTAGTGGGAGTATAAATTGTTTTCCACTTTGGAAAACAATTTGGTAATTTCGTTTTTTTTTTTTTCTTTTCTCTTTTTTTTTTTTTTTTTTTTGCATGCCAGAAAAAAATATTTACAGTAACT",  # noqa
+    }
+
+    def setUp(self):
+        self.file = pysam.FastaFile(os.path.join(BAM_DATADIR, "ex1.fa"))
+
+    def testFetch(self):
+        for id, seq in list(self.sequences.items()):
+            self.assertEqual(seq, self.file.fetch(id))
+            for x in range(0, len(seq), 10):
+                self.assertEqual(seq[x:x + 10], self.file.fetch(id, x, x + 10))
+                # test x:end
+                self.assertEqual(seq[x:], self.file.fetch(id, x))
+                # test 0:x
+                self.assertEqual(seq[:x], self.file.fetch(id, None, x))
+
+        # unknown sequence raises IndexError
+        self.assertRaises(KeyError, self.file.fetch, "chr12")
+
+    def testOutOfRangeAccess(self):
+        '''test out of range access.'''
+        # out of range access returns an empty string
+        for contig, s in self.sequences.items():
+            self.assertEqual(self.file.fetch(contig, len(s), len(s) + 1), "")
+
+    def testFetchErrors(self):
+        self.assertRaises(ValueError, self.file.fetch)
+        self.assertRaises(ValueError, self.file.fetch, "chr1", -1, 10)
+        self.assertRaises(ValueError, self.file.fetch, "chr1", 20, 10)
+        self.assertRaises(KeyError, self.file.fetch, "chr3", 0, 100)
+
+    def test_fetch_with_region_and_contig_raises_exception(self):
+        self.assertRaises(ValueError, self.file.fetch, "chr1", 10, 20, "chr1:11-20")
+        
+    def test_fetch_with_region_is_equivalent(self):
+        self.assertEqual(self.file.fetch("chr1", 10, 20),
+                         self.file.fetch(region="chr1:11-20"))
+
+    def testLength(self):
+        self.assertEqual(len(self.file), 2)
+
+    def testSequenceLengths(self):
+        self.assertEqual(1575, self.file.get_reference_length("chr1"))
+        self.assertEqual(1584, self.file.get_reference_length("chr2"))
+
+    def tearDown(self):
+        self.file.close()
+
+
+class TestFastaFilePathIndex(unittest.TestCase):
+
+    filename = os.path.join(BAM_DATADIR, "ex1.fa")
+    data_suffix = ".fa"
+
+    def test_raise_exception_if_index_is_missing(self):
+        self.assertRaises(IOError,
+                          pysam.FastaFile,
+                          self.filename,
+                          filepath_index="garbage" + self.data_suffix + ".fai")
+
+    def test_open_file_without_index_succeeds(self):
+        with pysam.FastaFile(self.filename) as inf:
+            self.assertEqual(len(inf), 2)
+
+    def test_open_file_with_explicit_index_succeeds(self):
+        with pysam.FastaFile(self.filename,
+                             filepath_index=self.filename + ".fai") as inf:
+            self.assertEqual(len(inf), 2)
+
+    def test_open_file_with_explicit_abritrarily_named_index_succeeds(self):
+        tmpfilename = get_temp_filename(self.data_suffix)
+        shutil.copyfile(self.filename, tmpfilename)
+
+        filepath_index = self.filename + ".fai"
+        filepath_index_compressed = self.filename + ".gzi"
+        if not os.path.exists(filepath_index_compressed):
+            filepath_index_compressed = None
+        with pysam.FastaFile(tmpfilename,
+                             filepath_index=filepath_index,
+                             filepath_index_compressed=filepath_index_compressed) as inf:
+            self.assertEqual(len(inf), 2)
+
+        # index should not be auto-generated
+        self.assertFalse(os.path.exists(tmpfilename + ".fai"))
+        os.unlink(tmpfilename)
+
+
+class TestFastaFilePathIndexCompressed(TestFastaFilePathIndex):
+
+    filename = os.path.join(BAM_DATADIR, "ex1.fa.gz")
+    data_suffix = ".fa.gz"
+    
+
+class TestFastxFileFastq(unittest.TestCase):
+
+    filetype = pysam.FastxFile
+    filename = "faidx_ex1.fq"
+    persist = True
+
+    def setUp(self):
+        self.file = self.filetype(os.path.join(BAM_DATADIR, self.filename),
+                                  persist=self.persist)
+        self.has_quality = self.filename.endswith('.fq')
+
+    def tearDown(self):
+        self.file.close()
+
+    def checkFirst(self, s):
+        # test first entry
+        self.assertEqual(s.sequence, "GGGAACAGGGGGGTGCACTAATGCGCTCCACGCCC")
+        self.assertEqual(s.name, "B7_589:1:101:825:28")
+        if self.has_quality:
+            self.assertEqual(s.quality, "<<86<<;<78<<<)<;4<67<;<;<74-7;,;8,;")
+            self.assertEqual(list(s.get_quality_array()),
+                             [ord(x) - 33 for x in s.quality])
+            self.assertEqual(str(s),
+                             "@B7_589:1:101:825:28\n"
+                             "GGGAACAGGGGGGTGCACTAATGCGCTCCACGCCC\n"
+                             "+\n"
+                             "<<86<<;<78<<<)<;4<67<;<;<74-7;,;8,;")
+
+        else:
+            self.assertEqual(s.quality, None)
+            self.assertEqual(s.get_quality_array(), None)
+            self.assertEqual(str(s),
+                             ">B7_589:1:101:825:28\n"
+                             "GGGAACAGGGGGGTGCACTAATGCGCTCCACGCCC")
+
+    def checkLast(self, s):
+        self.assertEqual(s.sequence, "TAATTGAAAAATTCATTTAAGAAATTACAAAATAT")
+        self.assertEqual(s.name, "EAS56_65:8:64:507:478")
+        if self.has_quality:
+            self.assertEqual(s.quality, "<<<<<;<<<<<<<<<<<<<<<;;;<<<;<<8;<;<")
+            self.assertEqual(list(s.get_quality_array()),
+                             [ord(x) - 33 for x in s.quality])
+        else:
+            self.assertEqual(s.quality, None)
+            self.assertEqual(s.get_quality_array(), None)
+
+    def testCounts(self):
+        self.assertEqual(len([x for x in self.file]), 3270)
+
+    def testMissingFile(self):
+        self.assertRaises(IOError, self.filetype, "nothere.fq")
+
+    def testSequence(self):
+        first = self.file.__next__()
+        self.checkFirst(first)
+        for last in self.file:
+            pass
+        self.checkLast(last)
+
+        # test for persistence
+        if self.persist:
+            self.checkFirst(first)
+        else:
+            self.checkLast(first)
+
+    def testManager(self):
+        with self.filetype(os.path.join(BAM_DATADIR, self.filename),
+                           persist=self.persist) as inf:
+            first = inf.__next__()
+            self.checkFirst(first)
+            for last in inf:
+                pass
+            self.checkLast(last)
+
+        self.assertEqual(inf.closed, True)
+
+
+# Test for backwards compatibility
+class TestFastqFileFastq(TestFastxFileFastq):
+    filetype = pysam.FastqFile
+
+
+# Test for backwards compatibility
+class TestFastxFileFasta(TestFastxFileFastq):
+    filetype = pysam.FastqFile
+    filename = "faidx_ex1.fa"
+
+
+class TestFastxFileFastqStream(TestFastxFileFastq):
+    persist = False
+
+
+class TestFastxFileWithEmptySequence(unittest.TestCase):
+    """see issue 204:
+
+    iteration over fastq file with empty sequence stops prematurely
+    """
+
+    filetype = pysam.FastxFile
+    filename = "faidx_empty_seq.fq.gz"
+
+    def testIteration(self):
+        fn = os.path.join(BAM_DATADIR, self.filename)
+
+        with gzip.open(fn) as inf:
+            ref_num = len(list(inf)) / 4
+
+        with self.filetype(fn) as f:
+            l = len(list(f))
+        self.assertEqual(ref_num, l)
+
+
+class TestRemoteFileFTP(unittest.TestCase):
+    '''test remote access.
+    '''
+
+    url = ("ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/technical/reference/"
+           "GRCh38_reference_genome/GRCh38_full_analysis_set_plus_decoy_hla.fa")
+
+    def testFTPView(self):
+        if not check_url(self.url):
+            return
+
+        try:
+            with pysam.Fastafile(self.url) as f:
+                self.assertEqual(
+                    len(f.fetch("chr1", 0, 1000)),
+                    1000)
+        except (OSError, IOError):
+            pass
+        
+    def test_sequence_lengths_are_available(self):
+        if not check_url(self.url):
+            return
+
+        try:
+            with pysam.Fastafile(self.url) as f:
+                self.assertEqual(len(f.references), 3366)
+                self.assertTrue("chr1" in f.references)
+                self.assertEqual(f.lengths[0],
+                                 248956422)
+                self.assertEqual(f.get_reference_length("chr1"),
+                                 248956422)
+        except (OSError, IOError):
+            pass
+
+
+class TestFastqRecord(unittest.TestCase):
+
+    filetype = pysam.FastxFile
+    filename = "faidx_ex1.fq"
+
+    def setUp(self):
+
+        with self.filetype(os.path.join(BAM_DATADIR, self.filename), persist=True) as inf:
+            self.record = next(inf)
+
+    def test_fastx_record_sequence_can_be_modified(self):
+        old_sequence = self.record.sequence
+        new_record = copy.copy(self.record)
+        new_sequence = "AAAC"
+        new_record.set_sequence(new_sequence)
+        self.assertEqual(str(new_record), ">{}\n{}".format(
+            self.record.name, new_sequence))
+        self.assertEqual(self.record.sequence, old_sequence)
+        self.assertEqual(new_record.sequence, new_sequence)
+
+    def test_fastx_record_name_can_be_modified(self):
+        old_name = self.record.name
+        new_name = "new_name"
+        new_record = copy.copy(self.record)
+        new_record.set_name(new_name)
+        self.assertEqual(new_record.name, new_name)
+        self.assertEqual(self.record.name, old_name)
+
+    def test_fastx_record_fail_if_name_is_None(self):
+        self.assertRaises(ValueError,
+                          self.record.set_name,
+                          None)
+
+    def test_fastx_record_comment_can_be_modified(self):
+        old_comment = self.record.comment
+        new_comment = "this is  a new comment"
+        new_record = copy.copy(self.record)
+        new_record.set_comment(new_comment)
+        self.assertEqual(new_record.comment, new_comment)
+        self.assertEqual(self.record.comment, old_comment)
+
+    def test_fastx_record_comment_can_be_None(self):
+        old_comment = self.record.comment
+        new_comment = None
+        new_record = copy.copy(self.record)
+        new_record.set_comment(new_comment)
+        self.assertEqual(new_record.comment, new_comment)
+        self.assertEqual(self.record.comment, old_comment)
+
+    def test_fastx_record_quality_can_be_modified(self):
+        old_quality = self.record.quality
+        new_quality = "A" * len(old_quality)
+        new_record = copy.copy(self.record)
+        new_record.set_sequence(self.record.sequence, new_quality)
+        self.assertEqual(new_record.quality, new_quality)
+        self.assertEqual(self.record.quality, old_quality)
+
+    def test_fastx_record_fail_if_quality_is_wrong_length(self):
+        self.assertRaises(ValueError,
+                          self.record.set_sequence,
+                          self.record.sequence, self.record.quality * 2)
+
+    def test_fastx_record_can_be_created_from_scratch(self):
+        fastx_record = pysam.FastxRecord()
+        self.assertRaises(ValueError,
+                          str,
+                          fastx_record)
+        fastx_record.set_name("name")
+        self.assertRaises(ValueError,
+                          str,
+                          fastx_record)
+        fastx_record.set_sequence("sequence")
+        self.assertEqual(str(fastx_record), ">name\nsequence")
+
+
+class TestFastqProxy(unittest.TestCase):
+    
+    def test_fastq_proxy_instantiation_raises_error(self):
+        self.assertRaises(ValueError,
+                          pysam.FastqProxy)
+        
+
+if __name__ == "__main__":
+    unittest.main()
diff --git a/tests/linking_test.py b/tests/linking_test.py
new file mode 100644
index 0000000..15fd91a
--- /dev/null
+++ b/tests/linking_test.py
@@ -0,0 +1,92 @@
+"""test linking against pysam.
+"""
+
+import unittest
+import os
+import subprocess
+import pysam
+
+from TestUtils import LINKDIR
+
+
+def check_import(statement):
+    try:
+        output = subprocess.check_output(
+            statement, stderr=subprocess.STDOUT, shell=True)
+    except subprocess.CalledProcessError as exc:
+        if b"ImportError" in exc.output:
+            raise ImportError(
+                "module could not be imported: {}".format(str(exc.output)))
+        else:
+            raise
+
+
+def check_pass(statement):
+    try:
+        output = subprocess.check_output(
+            statement, stderr=subprocess.STDOUT, shell=True)
+    except subprocess.CalledProcessError as exc:
+        raise ValueError("{}: {}".format(exc, exc.output))
+    if b"FAILED" in output:
+        raise ValueError("module tests failed")
+    return True
+
+
+@unittest.skipUnless(
+    os.environ.get("PYSAM_LINKING_TESTS", None),
+    "enable linking tests by setting PYSAM_LINKING_TESTS environment variable")
+class TestLinking(unittest.TestCase):
+
+    package_name = "link_with_rpath"
+
+    def setUp(self):
+        self.workdir = os.path.join(LINKDIR, self.package_name)
+
+    def test_package_can_be_installed(self):
+        subprocess.check_output(
+            "cd {} && rm -rf build && python setup.py install".format(
+                self.workdir),
+            shell=True)
+
+
+@unittest.skipUnless(
+    os.environ.get("PYSAM_LINKING_TESTS", None),
+    "enable linking tests by setting PYSAM_LINKING_TESTS environment variable")
+class TestLinkWithRpath(TestLinking):
+
+    package_name = "link_with_rpath"
+
+    def test_package_tests_pass(self):
+        self.assertTrue(check_pass(
+            "cd {} && python test_module.py".format(os.path.join(self.workdir, "tests"))))
+
+
+@unittest.skipUnless(
+    os.environ.get("PYSAM_LINKING_TESTS", None),
+    "enable linking tests by setting PYSAM_LINKING_TESTS environment variable")
+class TestLinkWithoutRpath(TestLinking):
+
+    package_name = "link_without_rpath"
+
+    def test_package_tests_fail_on_import(self):
+
+        self.assertRaises(
+            ImportError,
+            check_import,
+            "cd {} && python test_module.py".format(os.path.join(self.workdir, "tests")))
+
+    def test_package_tests_pass_if_ld_library_path_set(self):
+
+        pysam_libraries = pysam.get_libraries()
+        pysam_libdirs, pysam_libs = zip(
+            *[os.path.split(x) for x in pysam_libraries])
+        pysam_libdir = pysam_libdirs[0]
+
+        self.assertTrue(check_pass(
+            "export LD_LIBRARY_PATH={}:$PATH && cd {} && python test_module.py".format(
+                pysam_libdir,
+                os.path.join(self.workdir, "tests"))))
+
+
+if __name__ == "__main__":
+    unittest.main()
diff --git a/tests/pysam_data/0example_no_seq_in_header.bam b/tests/pysam_data/0example_no_seq_in_header.bam
new file mode 100644
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GIT binary patch
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literal 0
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diff --git a/tests/pysam_data/0example_no_seq_in_header_null_bytes.bam b/tests/pysam_data/0example_no_seq_in_header_null_bytes.bam
new file mode 100644
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literal 0
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diff --git a/tests/pysam_data/MM-chebi.sam b/tests/pysam_data/MM-chebi.sam
new file mode 100644
index 0000000..62920ec
--- /dev/null
+++ b/tests/pysam_data/MM-chebi.sam
@@ -0,0 +1,2 @@
+@CO	Separate m, h and N modifications
+*	0	*	0	0	*	*	0	0	AGCTCTCCAGAGTCGNACGCCATYCGCGCGCCACCA	*	Mm:Z:C+m,2,2,1,4,1;C+76792,6,7;N+n,15;	Ml:B:C,102,128,153,179,204,161,187,212,169
diff --git a/tests/pysam_data/MM-double.sam b/tests/pysam_data/MM-double.sam
new file mode 100644
index 0000000..608516f
--- /dev/null
+++ b/tests/pysam_data/MM-double.sam
@@ -0,0 +1,3 @@
+@CO	Modifications called on both strands of the same record,
+@CO	including potentially at the same location simultaneously.
+*	0	*	0	0	*	*	0	0	AGGATCTCTAGCGGATCGGCGGGGGATATGCCATAT	*	Mm:Z:C+m,1,3,0;G-m,0,2,0,4;G+o,4;	Ml:B:C,128,153,179,115,141,166,192,102
diff --git a/tests/pysam_data/MM-multi.sam b/tests/pysam_data/MM-multi.sam
new file mode 100644
index 0000000..b2259a0
--- /dev/null
+++ b/tests/pysam_data/MM-multi.sam
@@ -0,0 +1,7 @@
+@CO	Testing multiple m, h and N modifications on the same read.
+@CO	r1 has them separated out.
+@CO	r2 has them combined together, for example as produced by
+@CO	a joint basecaller which assigns probabilities to all
+@CO	trained events simultaneously.
+r1	0	*	0	0	*	*	0	0	AGCTCTCCAGAGTCGNACGCCATYCGCGCGCCACCA	*	Mm:Z:C+m,2,2,1,4,1;C+h,6,7;N+n,15,2;	Ml:B:C,128,153,179,204,230,159,6,215,240
+r2	0	*	0	0	*	*	0	0	AGCTCTCCAGAGTCGNACGCCATYCGCGCGCCACCA	*	Mm:Z:C+mh,2,2,0,0,4,1;N+n,15;	Ml:B:C,77,159,103,133,128,108,154,82,179,57,204,31,240
diff --git a/tests/pysam_data/MM-orient.sam b/tests/pysam_data/MM-orient.sam
new file mode 100644
index 0000000..363e7c2
--- /dev/null
+++ b/tests/pysam_data/MM-orient.sam
@@ -0,0 +1,6 @@
+@CO	Testing mods on top and bottom strand, but also in
+@CO	original vs reverse-complemented orientation
+top-fwd	0	*	0	0	*	*	0	0	AGGATCTCTAGCGGATCGGCGGGGGATATGCCATAT	*	Mm:Z:C+m,1,3,0;	Ml:B:C,128,153,179
+top-rev	16	*	0	0	*	*	0	0	ATATGGCATATCCCCCGCCGATCCGCTAGAGATCCT	*	Mm:Z:C+m,1,3,0;	Ml:B:C,128,153,179
+bot-fwd	0	*	0	0	*	*	0	0	AGGATCTCTAGCGGATCGGCGGGGGATATGCCATAT	*	Mm:Z:G-m,0,0,4,3;	Ml:B:C,115,141,166,192
+bot-rev	16	*	0	0	*	*	0	0	ATATGGCATATCCCCCGCCGATCCGCTAGAGATCCT	*	Mm:Z:G-m,0,0,4,3;	Ml:B:C,115,141,166,192
diff --git a/tests/pysam_data/Makefile b/tests/pysam_data/Makefile
new file mode 100644
index 0000000..d870440
--- /dev/null
+++ b/tests/pysam_data/Makefile
@@ -0,0 +1,113 @@
+SAM=$(wildcard *.sam)
+BAM=$(SAM:%.sam=%.bam)
+BAI=$(BAM:%.bam=%.bam.bai)
+CRAM=ex1.cram ex2.cram ex3.cram
+CRAI=$(CRAM:%.cram=%.cram.crai)
+NO_PG:=$(findstring --no-PG,$(shell samtools view '-?'))
+
+# ex2.bam - bam file without index
+
+all: all.stamp
+
+all.stamp: ex1.pileup.gz \
+	ex1.sam ex1.bam \
+	ex2.sam.gz ex2.sam ex2.bam ex2.bam.bai \
+	with_md.sam.gz with_md.bam with_md.bam.bai \
+        uncompressed.bam \
+	$(BAM) $(BAI) \
+	$(CRAM) $(CRAI) \
+	example_bai.bam \
+        rg_with_tab.bam \
+	ex2_truncated.bam \
+	ex2_corrupt.bam \
+	empty.bam empty.bam.bai \
+	explicit_index.bam explicit_index.cram \
+	faidx_empty_seq.fq.gz \
+	ex1.fa.gz ex1.fa.gz.fai ex1.fa.gz.gzi \
+	ex1_csi.bam \
+	example_reverse_complement.bam \
+	example_dash_in_chr.bam
+	touch $@
+
+# ex2.sam - as ex1.sam, but with header
+ex2.sam.gz: ex1.bam ex1.bam.bai
+	samtools view $(NO_PG) -h ex1.bam | gzip > ex2.sam.gz
+
+with_md.sam.gz: ex2.bam ex1.fa
+	samtools calmd $(NO_PG) --output-fmt BAM $^ > $@
+
+#%.bam: %.sam ex1.fa.fai
+#	samtools view $(NO_PG) -bo $@ -t ex1.fa.fai $<
+
+uncompressed.bam: ex2.sam
+	samtools view $(NO_PG) -bu -o $@ $<
+
+%.bam: %.sam
+	samtools view $(NO_PG) -bo $@ $<
+
+%.cram: %.sam
+	samtools view $(NO_PG) -Co $@ -T ex1.fa $<
+
+%.cram.crai: %.cram
+	samtools index $<
+
+%.sam: %.sam.gz
+	gunzip < $< > $@
+
+%.fa.fai: %.fa
+	samtools faidx $<
+
+%.fa.gz.fai %.fa.gz.gzi: %.fa.gz
+	samtools faidx $<
+
+ex1.bam:ex1.sam.gz ex1.fa.fai
+		samtools view $(NO_PG) -bo ex1.bam -t ex1.fa.fai ex1.sam.gz
+
+%.bam.bai:%.bam
+		samtools index $<
+
+ex1.pileup.gz:ex1.bam ex1.fa
+		samtools mpileup -f ex1.fa ex1.bam | gzip > ex1.pileup.gz
+
+ex2_truncated.bam: ex2.bam
+	dd if=ex2.bam of=ex2_truncated.bam bs=$$((`wc -c < ex2.bam`-512)) count=1
+
+# Append a corrupt read with block_size < sizeof(bam_core_t fields)
+ex2_corrupt.bam: ex2.bam
+	(bgzip -d < $<; printf '\37\0\0\0\1\0\0\0') | bgzip > $@
+
+ex1_csi.bam: ex1.bam
+	cp ex1.bam ex1_csi.bam
+	samtools index -c ex1_csi.bam
+
+empty.bam: ex2.sam
+	grep "^@" $< | samtools view $(NO_PG) -bo $@ -
+
+example_unmapped_reads_no_sq.bam: example_unmapped_reads_no_sq.sam
+	touch tmp.list
+	samtools view $(NO_PG) -bo $@ -t tmp.list $<
+	rm -f tmp.list
+
+example_bai.bam: ex1.bam
+	cp ex1.bam $@
+	samtools index $@
+	mv $@.bai example_bai.bai
+
+explicit_index.bam: ex1.bam
+	cp ex1.bam $@
+
+explicit_index.cram: ex1.cram
+	cp ex1.cram $@
+
+clean:
+	rm -fr [a-z]*.bam *.bai *.csi *.fai *.gzi *.pileup* [a-z]*.cram *.crai \
+	all.stamp *~ calDepth *.dSYM pysam_*.sam \
+	ex2.sam ex2.sam.gz ex1.sam ex1.fa.gz \
+	with_md.sam.gz \
+	*.fq.gz
+
+%.fq.gz: %.fq
+	gzip < $< > $@
+
+%.fa.gz: %.fa
+	bgzip < $< > $@
diff --git a/tests/pysam_data/ex1.bed b/tests/pysam_data/ex1.bed
new file mode 100644
index 0000000..0d0f498
--- /dev/null
+++ b/tests/pysam_data/ex1.bed
@@ -0,0 +1,2 @@
+chr1	10	100
+chr1	100	1000
diff --git a/tests/pysam_data/ex1.fa b/tests/pysam_data/ex1.fa
new file mode 100644
index 0000000..b4ed0cf
--- /dev/null
+++ b/tests/pysam_data/ex1.fa
@@ -0,0 +1,56 @@
+>chr1
+CACTAGTGGCTCATTGTAAATGTGTGGTTTAACTCGTCCATGGCCCAGCATTAGGGAGCT
+GTGGACCCTGCAGCCTGGCTGTGGGGGCCGCAGTGGCTGAGGGGTGCAGAGCCGAGTCAC
+GGGGTTGCCAGCACAGGGGCTTAACCTCTGGTGACTGCCAGAGCTGCTGGCAAGCTAGAG
+TCCCATTTGGAGCCCCTCTAAGCCGTTCTATTTGTAATGAAAACTATATTTATGCTATTC
+AGTTCTAAATATAGAAATTGAAACAGCTGTGTTTAGTGCCTTTGTTCAACCCCCTTGCAA
+CAACCTTGAGAACCCCAGGGAATTTGTCAATGTCAGGGAAGGAGCATTTTGTCAGTTACC
+AAATGTGTTTATTACCAGAGGGATGGAGGGAAGAGGGACGCTGAAGAACTTTGATGCCCT
+CTTCTTCCAAAGATGAAACGCGTAACTGCGCTCTCATTCACTCCAGCTCCCTGTCACCCA
+ATGGACCTGTGATATCTGGATTCTGGGAAATTCTTCATCCTGGACCCTGAGAGATTCTGC
+AGCCCAGCTCCAGATTGCTTGTGGTCTGACAGGCTGCAACTGTGAGCCATCACAATGAAC
+AACAGGAAGAAAAGGTCTTTCAAAAGGTGATGTGTGTTCTCATCAACCTCATACACACAC
+ATGGTTTAGGGGTATAATACCTCTACATGGCTGATTATGAAAACAATGTTCCCCAGATAC
+CATCCCTGTCTTACTTCCAGCTCCCCAGAGGGAAAGCTTTCAACGCTTCTAGCCATTTCT
+TTTGGCATTTGCCTTCAGACCCTACACGAATGCGTCTCTACCACAGGGGGCTGCGCGGTT
+TCCCATCATGAAGCACTGAACTTCCACGTCTCATCTAGGGGAACAGGGAGGTGCACTAAT
+GCGCTCCACGCCCAAGCCCTTCTCACAGTTTCTGCCCCCAGCATGGTTGTACTGGGCAAT
+ACATGAGATTATTAGGAAATGCTTTACTGTCATAACTATGAAGAGACTATTGCCAGATGA
+ACCACACATTAATACTATGTTTCTTATCTGCACATTACTACCCTGCAATTAATATAATTG
+TGTCCATGTACACACGCTGTCCTATGTACTTATCATGACTCTATCCCAAATTCCCAATTA
+CGTCCTATCTTCTTCTTAGGGAAGAACAGCTTAGGTATCAATTTGGTGTTCTGTGTAAAG
+TCTCAGGGAGCCGTCCGTGTCCTCCCATCTGGCCTCGTCCACACTGGTTCTCTTGAAAGC
+TTGGGCTGTAATGATGCCCCTTGGCCATCACCCAGTCCCTGCCCCATCTCTTGTAATCTC
+TCTCCTTTTTGCTGCATCCCTGTCTTCCTCTGTCTTGATTTACTTGTTGTTGGTTTTCTG
+TTTCTTTGTTTGATTTGGTGGAAGACATAATCCCACGCTTCCTATGGAAAGGTTGTTGGG
+AGATTTTTAATGATTCCTCAATGTTAAAATGTCTATTTTTGTCTTGACACCCAACTAATA
+TTTGTCTGAGCAAAACAGTCTAGATGAGAGAGAACTTCCCTGGAGGTCTGATGGCGTTTC
+TCCCTCGTCTTCTTA
+>chr2
+TTCAAATGAACTTCTGTAATTGAAAAATTCATTTAAGAAATTACAAAATATAGTTGAAAG
+CTCTAACAATAGACTAAACCAAGCAGAAGAAAGAGGTTCAGAACTTGAAGACAAGTCTCT
+TATGAATTAACCCAGTCAGACAAAAATAAAGAAAAAAATTTTAAAAATGAACAGAGCTTT
+CAAGAAGTATGAGATTATGTAAAGTAACTGAACCTATGAGTCACAGGTATTCCTGAGGAA
+AAAGAAAAAGTGAGAAGTTTGGAAAAACTATTTGAGGAAGTAATTGGGGAAAACCTCTTT
+AGTCTTGCTAGAGATTTAGACATCTAAATGAAAGAGGCTCAAAGAATGCCAGGAAGATAC
+ATTGCAAGACAGACTTCATCAAGATATGTAGTCATCAGACTATCTAAAGTCAACATGAAG
+GAAAAAAATTCTAAAATCAGCAAGAGAAAAGCATACAGTCATCTATAAAGGAAATCCCAT
+CAGAATAACAATGGGCTTCTCAGCAGAAACCTTACAAGCCAGAAGAGATTGGATCTAATT
+TTTGGACTTCTTAAAGAAAAAAAAACCTGTCAAACACGAATGTTATGCCCTGCTAAACTA
+AGCATCATAAATGAAGGGGAAATAAAGTCAAGTCTTTCCTGACAAGCAAATGCTAAGATA
+ATTCATCATCACTAAACCAGTCCTATAAGAAATGCTCAAAAGAATTGTAAAAGTCAAAAT
+TAAAGTTCAATACTCACCATCATAAATACACACAAAAGTACAAAACTCACAGGTTTTATA
+AAACAATTGAGACTACAGAGCAACTAGGTAAAAAATTAACATTACAACAGGAACAAAACC
+TCATATATCAATATTAACTTTGAATAAAAAGGGATTAAATTCCCCCACTTAAGAGATATA
+GATTGGCAGAACAGATTTAAAAACATGAACTAACTATATGCTGTTTACAAGAAACTCATT
+AATAAAGACATGAGTTCAGGTAAAGGGGTGGAAAAAGATGTTCTACGCAAACAGAAACCA
+AATGAGAGAAGGAGTAGCTATACTTATATCAGATAAAGCACACTTTAAATCAACAACAGT
+AAAATAAAACAAAGGAGGTCATCATACAATGATAAAAAGATCAATTCAGCAAGAAGATAT
+AACCATCCTACTAAATACATATGCACCTAACACAAGACTACCCAGATTCATAAAACAAAT
+ACTACTAGACCTAAGAGGGATGAGAAATTACCTAATTGGTACAATGTACAATATTCTGAT
+GATGGTTACACTAAAAGCCCATACTTTACTGCTACTCAATATATCCATGTAACAAATCTG
+CGCTTGTACTTCTAAATCTATAAAAAAATTAAAATTTAACAAAAGTAAATAAAACACATA
+GCTAAAACTAAAAAAGCAAAAACAAAAACTATGCTAAGTATTGGTAAAGATGTGGGGAAA
+AAAGTAAACTCTCAAATATTGCTAGTGGGAGTATAAATTGTTTTCCACTTTGGAAAACAA
+TTTGGTAATTTCGTTTTTTTTTTTTTCTTTTCTCTTTTTTTTTTTTTTTTTTTTGCATGC
+CAGAAAAAAATATTTACAGTAACT
diff --git a/tests/pysam_data/ex1.sam.gz b/tests/pysam_data/ex1.sam.gz
new file mode 100644
index 0000000000000000000000000000000000000000..16044675f2473b5bccf026d374ac1ee04dfe6b40
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zHP+AXKb1-h6g+_|kL}6t#z1Ma$NH9(UEzrjg_Cs<Y!m>J<UEz~ax$lLiDHi14wdt^
z%NZ_~ea@BsF<&i)Tsyxu*~rmat61m{Bsy}W1ONNo-=f^TL~*}hxH@v})y8|EFWR2r
z_Ep9{la)=q;J?3a>*@a42Z{}+Y+rs=RZQr`2cU1y1>}i?QzcIfX~0Tgs5qYhubgTd
z_;H)7G&56tGqR+CRUhKghnyaOEW~vzw2dOd8o>Tqx>(}LGYq8#t)-p+KrXrnwCT;?
zwVe06=Z^p#R=CQFLHCi)a;yDaM+nqsm!DeKZr~3q-SA8*{Z`vw?@Pai&IA*8^sy5<
z9v$)YOF*ZSd_`~T=fYToR!B?z>_ms4rvK(EcWfk~4Cz2rtzheAHIv@pW^db7zQN4i
z7Dhz}--;bCwTbRNFP-_NhKJXJAgc+8DhC%B-~hhPM;svn5o4e}LX<$#cA$z!7BR)>
ztk1c+Eh8MV@}1v_Q0gv+zbDz-H)f=LPTibaH#WC_vIK~*ywD}uiytMuYVAZs^>RdE
z<z(k*Dp${LxZbr%8GcEA>%sEJ=T==WD1s<D7OLuj*C`l(pQm3#v!52Hjd2K@-<l^K
znzNaP%;kY*NnYs%RpK!+%N%#okXj`KFelq)WTyg)(f?Ds*@VB+*^0XE!N8|yfSPh&
Kygl}vzx^NRJWw70

literal 0
HcmV?d00001

diff --git a/tests/pysam_data/ex10.sam b/tests/pysam_data/ex10.sam
new file mode 100644
index 0000000..f9fe3dd
--- /dev/null
+++ b/tests/pysam_data/ex10.sam
@@ -0,0 +1,16 @@
+@HD	VN:1.0
+@SQ	SN:1	LN:249250621
+read1	115	1	142618765	255	25M	=	142618765	25	CGACCCACTCCGCCATTTTCATCCG	IIGIIIHIGIIFIIIIIIIGIGIII	NM:i:0	ZP:i:65536	ZL:i:25
+read2	115	1	142618765	255	25M	=	142618765	25	CGACCCACTCCGCCATTTTCATCCG	IIGIIIHIGIIFIIIIIIIGIGIII	NM:i:0	ZP:i:214748	ZL:i:25
+read3	115	1	142618765	255	25M	=	142618765	25	CGACCCACTCCGCCATTTTCATCCG	IIGIIIHIGIIFIIIIIIIGIGIII	NM:i:0	ZP:i:2147484	ZL:i:25
+read4	115	1	142618765	255	25M	=	142618765	25	CGACCCACTCCGCCATTTTCATCCG	IIGIIIHIGIIFIIIIIIIGIGIII	NM:i:0	ZP:i:2147483647	ZL:i:25
+read5	115	1	142618765	255	25M	=	142618765	25	CGACCCACTCCGCCATTTTCATCCG	IIGIIIHIGIIFIIIIIIIGIGIII	NM:i:0	ZP:i:-65536	ZL:i:25
+read6	115	1	142618765	255	25M	=	142618765	25	CGACCCACTCCGCCATTTTCATCCG	IIGIIIHIGIIFIIIIIIIGIGIII	NM:i:0	ZP:i:-214748	ZL:i:25
+read7	115	1	142618765	255	25M	=	142618765	25	CGACCCACTCCGCCATTTTCATCCG	IIGIIIHIGIIFIIIIIIIGIGIII	NM:i:0	ZP:i:-2147484	ZL:i:25
+read8	115	1	142618765	255	25M	=	142618765	25	CGACCCACTCCGCCATTTTCATCCG	IIGIIIHIGIIFIIIIIIIGIGIII	NM:i:0	ZP:i:-2147483647	ZL:i:25
+read1	115	1	142618765	255	25M	=	142618765	25	CGACCCACTCCGCCATTTTCATCCG	IIGIIIHIGIIFIIIIIIIGIGIII	NM:i:0	ZP:f:65536	ZL:i:25
+read2	115	1	142618765	255	25M	=	142618765	25	CGACCCACTCCGCCATTTTCATCCG	IIGIIIHIGIIFIIIIIIIGIGIII	NM:i:0	ZP:f:214748	ZL:i:25
+read3	115	1	142618765	255	25M	=	142618765	25	CGACCCACTCCGCCATTTTCATCCG	IIGIIIHIGIIFIIIIIIIGIGIII	NM:i:0	ZP:f:2147484	ZL:i:25
+read5	115	1	142618765	255	25M	=	142618765	25	CGACCCACTCCGCCATTTTCATCCG	IIGIIIHIGIIFIIIIIIIGIGIII	NM:i:0	ZP:f:-65536	ZL:i:25
+read6	115	1	142618765	255	25M	=	142618765	25	CGACCCACTCCGCCATTTTCATCCG	IIGIIIHIGIIFIIIIIIIGIGIII	NM:i:0	ZP:f:-214748	ZL:i:25
+read7	115	1	142618765	255	25M	=	142618765	25	CGACCCACTCCGCCATTTTCATCCG	IIGIIIHIGIIFIIIIIIIGIGIII	NM:i:0	ZP:f:-2147484	ZL:i:25
diff --git a/tests/pysam_data/ex3.sam b/tests/pysam_data/ex3.sam
new file mode 100644
index 0000000..c575c86
--- /dev/null
+++ b/tests/pysam_data/ex3.sam
@@ -0,0 +1,13 @@
+@HD	VN:1.0
+@SQ	SN:chr1	LN:1575	AH:chr1:5000000-5010000
+@SQ	SN:chr2	LN:1584	AH:*
+@RG	ID:L1	PU:SC_1_10	LB:SC_1	SM:NA12891	CN:name:with:colon
+@RG	ID:L2	PU:SC_2_12	LB:SC_2	SM:NA12891	CN:name:with:colon
+@PG	ID:P1	VN:1.0
+@PG	ID:P2	VN:1.1
+@CO	this is a comment
+@CO	this is another comment
+read_28833_29006_6945	99	chr1	33	20	10M1D25M	=	200	167	AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG	<<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<<	NM:i:22	RG:Z:L1	PG:Z:P1	XT:A:U
+read_28701_28881_323b	147	chr2	88	30	35M	=	500	412	ACCTATATCTTGGCCTTGGCCGATGCGGCCTTGCA	<<<<<;<<<<7;:<<<6;<<<<<<<<<<<<7<<<<	MF:i:18	RG:Z:L2	PG:Z:P2	XT:A:R
+read_28701_28881_323c	147	chr2	88	30	35M	=	500	412	ACCTATATCTTGGCCTTGGCCGATGCGGCCTTGCA	<<<<<;<<<<7;:<<<6;<<<<<<<<<<<<7<<<<
+test_clipped1	99	chr2	997	20	4S6M1D20M5S	=	200	167	AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG	<<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<<	NM:i:21	RG:Z:L1	PG:Z:P1	XT:A:U
diff --git a/tests/pysam_data/ex4.sam b/tests/pysam_data/ex4.sam
new file mode 100644
index 0000000..b2282b8
--- /dev/null
+++ b/tests/pysam_data/ex4.sam
@@ -0,0 +1,9 @@
+@HD	VN:1.0
+@SQ	SN:chr1	LN:100
+@SQ	SN:chr2	LN:100
+@RG	ID:L1	PU:SC_1_10	LB:SC_1	SM:NA12891
+@RG	ID:L2	PU:SC_2_12	LB:SC_2	SM:NA12891
+@CO	this is a comment
+@CO	this is another comment
+read_28833_29006_6945	99	chr1	21	20	10M1D25M	=	200	167	AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG	<<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<<	NM:i:1	RG:Z:L1
+read_28701_28881_323b	147	chr2	21	30	35M	=	500	412	ACCTATATCTTGGCCTTGGCCGATGCGGCCTTGCA	<<<<<;<<<<7;:<<<6;<<<<<<<<<<<<7<<<<	MF:i:18	RG:Z:L2
diff --git a/tests/pysam_data/ex5.sam b/tests/pysam_data/ex5.sam
new file mode 100644
index 0000000..b4526ec
--- /dev/null
+++ b/tests/pysam_data/ex5.sam
@@ -0,0 +1,5 @@
+@HD	VN:1.0
+@SQ	SN:chr1	LN:100
+@SQ	SN:chr2	LN:100
+read_28833_29006_6945	0	*	0	0	*	*	200	167	AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG	<<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<<
+read_28701_28881_323b	0	*	0	0	*	*	500	412	ACCTATATCTTGGCCTTGGCCGATGCGGCCTTGCA	<<<<<;<<<<7;:<<<6;<<<<<<<<<<<<7<<<<
diff --git a/tests/pysam_data/ex6.sam b/tests/pysam_data/ex6.sam
new file mode 100644
index 0000000..7ae90f3
--- /dev/null
+++ b/tests/pysam_data/ex6.sam
@@ -0,0 +1,5 @@
+@HD	VN:1.0
+@SQ	SN:chr1	LN:1575
+@SQ	SN:chr2	LN:1584
+read_28833_29006_6945	99	chr1	33	20	10M1D25M	=	200	167	AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG	<<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<<	NM:i:1	RG:Z:L1
+read_28701_28881_323b	147	chr2	88	30	35M	=	500	412	ACCTATATCTTGGCCTTGGCCGATGCGGCCTTGCA	<<<<<;<<<<7;:<<<6;<<<<<<<<<<<<7<<<<	MF:i:18	RG:Z:L2
diff --git a/tests/pysam_data/ex7.sam.donottest b/tests/pysam_data/ex7.sam.donottest
new file mode 100644
index 0000000..12befae
--- /dev/null
+++ b/tests/pysam_data/ex7.sam.donottest
@@ -0,0 +1,2 @@
+read_28833_29006_6945	99	chr1	33	20	10M1D25M	=	200	167	AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG	<<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<<	NM:i:1	RG:Z:L1	PG:Z:P1	XT:A:U
+read_28701_28881_323b	147	chr2	88	30	35M	=	500	412	ACCTATATCTTGGCCTTGGCCGATGCGGCCTTGCA	<<<<<;<<<<7;:<<<6;<<<<<<<<<<<<7<<<<	MF:i:18	RG:Z:L2	PG:Z:P2	XT:A:R
diff --git a/tests/pysam_data/ex8.sam b/tests/pysam_data/ex8.sam
new file mode 100644
index 0000000..5a16b4f
--- /dev/null
+++ b/tests/pysam_data/ex8.sam
@@ -0,0 +1,3 @@
+@HD	VN:1.0
+@SQ	SN:2	LN:48297693
+GJP00TM04CAQ5W	0	2	38297693	60	45H51M1D13M1D12M1D9M2D5M1D7M4D2M1I6M1D28M1D5M1D2M1D18M55H	*	0	0	CATGAAGAACCGCTGGGTATGGAGCACACCTCACCTGATGGACAGTTGATTATGCTCACCTTAACGCTAATTGAGAGCAGCACAAGAGGACTGGAAACTAGAATTTACTCCTCATCTCCGAAGATGTGAATATTCTAAATTCAGCTTGCCTCTTGCTTC	IID7757111/=;?///:D>777;EEGAAAEEIHHIIIIIIIIIIIIIIBBBIIIIH==<<<DDGEEE;<<<A><<<DEDDA>>>D?1112544556::03---//25.22=;DD?;;;>BDDDEEEGGGA<888<BAA888<GGGGGEB?9::DD551	NM:i:15	MD:Z:51^T13^A12^A9^AA5^A7^AAAA8^T28^T5^A2^T18	RG:Z:GJP00TM04
diff --git a/tests/pysam_data/ex9_fail.sam b/tests/pysam_data/ex9_fail.sam
new file mode 100644
index 0000000..300d6e2
--- /dev/null
+++ b/tests/pysam_data/ex9_fail.sam
@@ -0,0 +1,1022 @@
+@HD	VN:1.0	GO:none	SO:coordinate
+@SQ	SN:CUTC000001	LN:810
+@SQ	SN:CUTC000002	LN:1213
+@SQ	SN:CUTC000003	LN:525
+@SQ	SN:CUTC000004	LN:620
+@SQ	SN:CUTC000005	LN:550
+@SQ	SN:CUTC000006	LN:723
+@SQ	SN:CUTC000007	LN:773
+@SQ	SN:CUTC000008	LN:667
+@SQ	SN:CUTC000009	LN:593
+@SQ	SN:CUTC000010	LN:556
+@SQ	SN:CUTC000011	LN:519
+@SQ	SN:CUTC000012	LN:537
+@SQ	SN:CUTC000013	LN:930
+@SQ	SN:CUTC000014	LN:944
+@SQ	SN:CUTC000015	LN:829
+@SQ	SN:CUTC000016	LN:1109
+@SQ	SN:CUTC000017	LN:513
+@SQ	SN:CUTC000018	LN:1043
+@SQ	SN:CUTC000019	LN:884
+@SQ	SN:CUTC000020	LN:567
+@SQ	SN:CUTC000021	LN:1001
+@SQ	SN:CUTC000022	LN:754
+@SQ	SN:CUTC000023	LN:1045
+@SQ	SN:CUTC000024	LN:1091
+@SQ	SN:CUTC000025	LN:606
+@SQ	SN:CUTC000026	LN:635
+@SQ	SN:CUTC000027	LN:563
+@SQ	SN:CUTC000028	LN:830
+@SQ	SN:CUTC000029	LN:1456
+@SQ	SN:CUTC000030	LN:872
+@SQ	SN:CUTC000031	LN:742
+@SQ	SN:CUTC000032	LN:553
+@SQ	SN:CUTC000033	LN:624
+@SQ	SN:CUTC000034	LN:641
+@SQ	SN:CUTC000035	LN:695
+@SQ	SN:CUTC000036	LN:1519
+@SQ	SN:CUTC000037	LN:536
+@SQ	SN:CUTC000038	LN:619
+@SQ	SN:CUTC000039	LN:643
+@SQ	SN:CUTC000040	LN:650
+@SQ	SN:CUTC000041	LN:571
+@SQ	SN:CUTC000042	LN:1457
+@SQ	SN:CUTC000043	LN:618
+@SQ	SN:CUTC000044	LN:1261
+@SQ	SN:CUTC000045	LN:544
+@SQ	SN:CUTC000046	LN:1234
+@SQ	SN:CUTC000047	LN:867
+@SQ	SN:CUTC000048	LN:792
+@SQ	SN:CUTC000049	LN:1076
+@SQ	SN:CUTC000050	LN:479
+@SQ	SN:CUTC000051	LN:584
+@SQ	SN:CUTC000052	LN:841
+@SQ	SN:CUTC000053	LN:518
+@SQ	SN:CUTC000054	LN:1052
+@SQ	SN:CUTC000055	LN:626
+@SQ	SN:CUTC000056	LN:773
+@SQ	SN:CUTC000057	LN:542
+@SQ	SN:CUTC000058	LN:566
+@SQ	SN:CUTC000059	LN:931
+@SQ	SN:CUTC000060	LN:755
+@SQ	SN:CUTC000061	LN:606
+@SQ	SN:CUTC000062	LN:640
+@SQ	SN:CUTC000063	LN:667
+@SQ	SN:CUTC000064	LN:1717
+@SQ	SN:CUTC000065	LN:695
+@SQ	SN:CUTC000066	LN:1735
+@SQ	SN:CUTC000067	LN:474
+@SQ	SN:CUTC000068	LN:813
+@SQ	SN:CUTC000069	LN:746
+@SQ	SN:CUTC000070	LN:1141
+@SQ	SN:CUTC000071	LN:624
+@SQ	SN:CUTC000072	LN:1097
+@SQ	SN:CUTC000073	LN:510
+@SQ	SN:CUTC000074	LN:638
+@SQ	SN:CUTC000075	LN:682
+@SQ	SN:CUTC000076	LN:1043
+@SQ	SN:CUTC000077	LN:727
+@SQ	SN:CUTC000078	LN:1124
+@SQ	SN:CUTC000079	LN:711
+@SQ	SN:CUTC000080	LN:578
+@SQ	SN:CUTC000081	LN:718
+@SQ	SN:CUTC000082	LN:1779
+@SQ	SN:CUTC000083	LN:630
+@SQ	SN:CUTC000084	LN:850
+@SQ	SN:CUTC000085	LN:590
+@SQ	SN:CUTC000086	LN:578
+@SQ	SN:CUTC000087	LN:727
+@SQ	SN:CUTC000088	LN:582
+@SQ	SN:CUTC000089	LN:632
+@SQ	SN:CUTC000090	LN:792
+@SQ	SN:CUTC000091	LN:553
+@SQ	SN:CUTC000092	LN:606
+@SQ	SN:CUTC000093	LN:1263
+@SQ	SN:CUTC000094	LN:1119
+@SQ	SN:CUTC000095	LN:1107
+@SQ	SN:CUTC000096	LN:1240
+@SQ	SN:CUTC000097	LN:578
+@SQ	SN:CUTC000098	LN:739
+@SQ	SN:CUTC000099	LN:959
+@SQ	SN:CUTC000100	LN:701
+@SQ	SN:CUTC000101	LN:1047
+@SQ	SN:CUTC000102	LN:961
+@SQ	SN:CUTC000103	LN:548
+@SQ	SN:CUTC000104	LN:579
+@SQ	SN:CUTC000105	LN:1376
+@SQ	SN:CUTC000106	LN:1202
+@SQ	SN:CUTC000107	LN:615
+@SQ	SN:CUTC000108	LN:634
+@SQ	SN:CUTC000109	LN:742
+@SQ	SN:CUTC000110	LN:645
+@SQ	SN:CUTC000111	LN:567
+@SQ	SN:CUTC000112	LN:715
+@SQ	SN:CUTC000113	LN:705
+@SQ	SN:CUTC000114	LN:548
+@SQ	SN:CUTC000115	LN:555
+@SQ	SN:CUTC000116	LN:1370
+@SQ	SN:CUTC000117	LN:715
+@SQ	SN:CUTC000118	LN:737
+@SQ	SN:CUTC000119	LN:595
+@SQ	SN:CUTC000120	LN:674
+@SQ	SN:CUTC000121	LN:858
+@SQ	SN:CUTC000122	LN:571
+@SQ	SN:CUTC000123	LN:656
+@SQ	SN:CUTC000124	LN:923
+@SQ	SN:CUTC000125	LN:487
+@SQ	SN:CUTC000126	LN:488
+@SQ	SN:CUTC000127	LN:548
+@SQ	SN:CUTC000128	LN:547
+@SQ	SN:CUTC000129	LN:593
+@SQ	SN:CUTC000130	LN:980
+@SQ	SN:CUTC000131	LN:605
+@SQ	SN:CUTC000132	LN:942
+@SQ	SN:CUTC000133	LN:599
+@SQ	SN:CUTC000134	LN:755
+@SQ	SN:CUTC000135	LN:544
+@SQ	SN:CUTC000136	LN:623
+@SQ	SN:CUTC000137	LN:680
+@SQ	SN:CUTC000138	LN:633
+@SQ	SN:CUTC000139	LN:4441
+@SQ	SN:CUTC000140	LN:894
+@SQ	SN:CUTC000141	LN:688
+@SQ	SN:CUTC000142	LN:683
+@SQ	SN:CUTC000143	LN:679
+@SQ	SN:CUTC000144	LN:698
+@SQ	SN:CUTC000145	LN:629
+@SQ	SN:CUTC000146	LN:534
+@SQ	SN:CUTC000147	LN:643
+@SQ	SN:CUTC000148	LN:614
+@SQ	SN:CUTC000149	LN:845
+@SQ	SN:CUTC000150	LN:652
+@SQ	SN:CUTC000151	LN:1332
+@SQ	SN:CUTC000152	LN:1091
+@SQ	SN:CUTC000153	LN:702
+@SQ	SN:CUTC000154	LN:677
+@SQ	SN:CUTC000155	LN:902
+@SQ	SN:CUTC000156	LN:557
+@SQ	SN:CUTC000157	LN:735
+@SQ	SN:CUTC000158	LN:940
+@SQ	SN:CUTC000159	LN:668
+@SQ	SN:CUTC000160	LN:2002
+@SQ	SN:CUTC000161	LN:665
+@SQ	SN:CUTC000162	LN:907
+@SQ	SN:CUTC000163	LN:497
+@SQ	SN:CUTC000164	LN:966
+@SQ	SN:CUTC000165	LN:645
+@SQ	SN:CUTC000166	LN:595
+@SQ	SN:CUTC000167	LN:651
+@SQ	SN:CUTC000168	LN:410
+@SQ	SN:CUTC000169	LN:1122
+@SQ	SN:CUTC000170	LN:1021
+@SQ	SN:CUTC000171	LN:804
+@SQ	SN:CUTC000172	LN:972
+@SQ	SN:CUTC000173	LN:1839
+@SQ	SN:CUTC000174	LN:647
+@SQ	SN:CUTC000175	LN:675
+@SQ	SN:CUTC000176	LN:647
+@SQ	SN:CUTC000177	LN:1713
+@SQ	SN:CUTC000178	LN:911
+@SQ	SN:CUTC000179	LN:664
+@SQ	SN:CUTC000180	LN:765
+@SQ	SN:CUTC000181	LN:950
+@SQ	SN:CUTC000182	LN:914
+@SQ	SN:CUTC000183	LN:1166
+@SQ	SN:CUTC000184	LN:834
+@SQ	SN:CUTC000185	LN:812
+@SQ	SN:CUTC000186	LN:793
+@SQ	SN:CUTC000187	LN:1148
+@SQ	SN:CUTC000188	LN:1376
+@SQ	SN:CUTC000189	LN:724
+@SQ	SN:CUTC000190	LN:762
+@SQ	SN:CUTC000191	LN:940
+@SQ	SN:CUTC000192	LN:707
+@SQ	SN:CUTC000193	LN:1596
+@SQ	SN:CUTC000194	LN:557
+@SQ	SN:CUTC000195	LN:596
+@SQ	SN:CUTC000196	LN:930
+@SQ	SN:CUTC000197	LN:1447
+@SQ	SN:CUTC000198	LN:566
+@SQ	SN:CUTC000199	LN:686
+@SQ	SN:CUTC000200	LN:685
+@SQ	SN:CUTC000201	LN:579
+@SQ	SN:CUTC000202	LN:1282
+@SQ	SN:CUTC000203	LN:1601
+@SQ	SN:CUTC000204	LN:1034
+@SQ	SN:CUTC000205	LN:1370
+@SQ	SN:CUTC000206	LN:530
+@SQ	SN:CUTC000207	LN:947
+@SQ	SN:CUTC000208	LN:655
+@SQ	SN:CUTC000209	LN:611
+@SQ	SN:CUTC000210	LN:700
+@SQ	SN:CUTC000211	LN:940
+@SQ	SN:CUTC000212	LN:496
+@SQ	SN:CUTC000213	LN:849
+@SQ	SN:CUTC000214	LN:713
+@SQ	SN:CUTC000215	LN:879
+@SQ	SN:CUTC000216	LN:686
+@SQ	SN:CUTC000217	LN:655
+@SQ	SN:CUTC000218	LN:1139
+@SQ	SN:CUTC000219	LN:712
+@SQ	SN:CUTC000220	LN:987
+@SQ	SN:CUTC000221	LN:581
+@SQ	SN:CUTC000222	LN:867
+@SQ	SN:CUTC000223	LN:1591
+@SQ	SN:CUTC000224	LN:661
+@SQ	SN:CUTC000225	LN:1490
+@SQ	SN:CUTC000226	LN:1207
+@SQ	SN:CUTC000227	LN:785
+@SQ	SN:CUTC000228	LN:700
+@SQ	SN:CUTC000229	LN:474
+@SQ	SN:CUTC000230	LN:539
+@SQ	SN:CUTC000231	LN:1095
+@SQ	SN:CUTC000232	LN:556
+@SQ	SN:CUTC000233	LN:609
+@SQ	SN:CUTC000234	LN:1335
+@SQ	SN:CUTC000235	LN:566
+@SQ	SN:CUTC000236	LN:612
+@SQ	SN:CUTC000237	LN:918
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diff --git a/tests/pysam_data/ex9_nofail.sam b/tests/pysam_data/ex9_nofail.sam
new file mode 100644
index 0000000..ee31dca
--- /dev/null
+++ b/tests/pysam_data/ex9_nofail.sam
@@ -0,0 +1,1021 @@
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diff --git a/tests/pysam_data/ex_spliced.sam b/tests/pysam_data/ex_spliced.sam
new file mode 100644
index 0000000..ae8086a
--- /dev/null
+++ b/tests/pysam_data/ex_spliced.sam
@@ -0,0 +1,297 @@
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+@SQ	SN:KI270448.1	LN:7992
+@SQ	SN:KI270465.1	LN:1774
+@SQ	SN:KI270466.1	LN:1233
+@SQ	SN:KI270467.1	LN:3920
+@SQ	SN:KI270468.1	LN:4055
+@SQ	SN:KI270507.1	LN:5353
+@SQ	SN:KI270508.1	LN:1951
+@SQ	SN:KI270509.1	LN:2318
+@SQ	SN:KI270510.1	LN:2415
+@SQ	SN:KI270511.1	LN:8127
+@SQ	SN:KI270512.1	LN:22689
+@SQ	SN:KI270515.1	LN:6361
+@SQ	SN:KI270516.1	LN:1300
+@SQ	SN:KI270517.1	LN:3253
+@SQ	SN:KI270518.1	LN:2186
+@SQ	SN:KI270519.1	LN:138126
+@SQ	SN:KI270521.1	LN:7642
+@SQ	SN:KI270522.1	LN:5674
+@SQ	SN:KI270528.1	LN:2983
+@SQ	SN:KI270529.1	LN:1899
+@SQ	SN:KI270530.1	LN:2168
+@SQ	SN:KI270538.1	LN:91309
+@SQ	SN:KI270539.1	LN:993
+@SQ	SN:KI270544.1	LN:1202
+@SQ	SN:KI270548.1	LN:1599
+@SQ	SN:KI270579.1	LN:31033
+@SQ	SN:KI270580.1	LN:1553
+@SQ	SN:KI270581.1	LN:7046
+@SQ	SN:KI270582.1	LN:6504
+@SQ	SN:KI270583.1	LN:1400
+@SQ	SN:KI270584.1	LN:4513
+@SQ	SN:KI270587.1	LN:2969
+@SQ	SN:KI270588.1	LN:6158
+@SQ	SN:KI270589.1	LN:44474
+@SQ	SN:KI270590.1	LN:4685
+@SQ	SN:KI270591.1	LN:5796
+@SQ	SN:KI270593.1	LN:3041
+@SQ	SN:KI270706.1	LN:175055
+@SQ	SN:KI270707.1	LN:32032
+@SQ	SN:KI270708.1	LN:127682
+@SQ	SN:KI270709.1	LN:66860
+@SQ	SN:KI270710.1	LN:40176
+@SQ	SN:KI270711.1	LN:42210
+@SQ	SN:KI270712.1	LN:176043
+@SQ	SN:KI270713.1	LN:40745
+@SQ	SN:KI270714.1	LN:41717
+@SQ	SN:KI270715.1	LN:161471
+@SQ	SN:KI270716.1	LN:153799
+@SQ	SN:KI270717.1	LN:40062
+@SQ	SN:KI270718.1	LN:38054
+@SQ	SN:KI270719.1	LN:176845
+@SQ	SN:KI270720.1	LN:39050
+@SQ	SN:KI270721.1	LN:100316
+@SQ	SN:KI270722.1	LN:194050
+@SQ	SN:KI270723.1	LN:38115
+@SQ	SN:KI270724.1	LN:39555
+@SQ	SN:KI270725.1	LN:172810
+@SQ	SN:KI270726.1	LN:43739
+@SQ	SN:KI270727.1	LN:448248
+@SQ	SN:KI270728.1	LN:1872759
+@SQ	SN:KI270729.1	LN:280839
+@SQ	SN:KI270730.1	LN:112551
+@SQ	SN:KI270731.1	LN:150754
+@SQ	SN:KI270732.1	LN:41543
+@SQ	SN:KI270733.1	LN:179772
+@SQ	SN:KI270734.1	LN:165050
+@SQ	SN:KI270735.1	LN:42811
+@SQ	SN:KI270736.1	LN:181920
+@SQ	SN:KI270737.1	LN:103838
+@SQ	SN:KI270738.1	LN:99375
+@SQ	SN:KI270739.1	LN:73985
+@SQ	SN:KI270740.1	LN:37240
+@SQ	SN:KI270741.1	LN:157432
+@SQ	SN:KI270742.1	LN:186739
+@SQ	SN:KI270743.1	LN:210658
+@SQ	SN:KI270744.1	LN:168472
+@SQ	SN:KI270745.1	LN:41891
+@SQ	SN:KI270746.1	LN:66486
+@SQ	SN:KI270747.1	LN:198735
+@SQ	SN:KI270748.1	LN:93321
+@SQ	SN:KI270749.1	LN:158759
+@SQ	SN:KI270750.1	LN:148850
+@SQ	SN:KI270751.1	LN:150742
+@SQ	SN:KI270752.1	LN:27745
+@SQ	SN:KI270753.1	LN:62944
+@SQ	SN:KI270754.1	LN:40191
+@SQ	SN:KI270755.1	LN:36723
+@SQ	SN:KI270756.1	LN:79590
+@SQ	SN:KI270757.1	LN:71251
+@PG	ID:STAR	PN:STAR	VN:STAR_2.4.1a
+HWI-C00113:131:HMHYWADXX:1:2202:17748:47494	272	1	14792	0	51M	*	0	0	GGGCCTCTCACCAGCCCCAGGTCCTTTCCCAGAGATGCCCTTGCGCCTCAT	CCCFFFFFHHHHHFHIIJJIJAFHJJJJJGJIIHGIJGGIJJIIJIIJJJG	NH:i:6	HI:i:3	AS:i:47	nM:i:1
+HWI-C00113:131:HMHYWADXX:1:2202:17748:47494	272	1	14792	0	38M140N13M	*	0	0	GGGCCTCTCACCAGCCCCAGGTCCTTTCCCAGAGATGCCCTTGCGCCTCAT	CCCFFFFFHHHHHFHIIJJIJAFHJJJJJGJIIHGIJGGIJJIIJIIJJJG	NH:i:6	HI:i:3	AS:i:47	nM:i:1
+HWI-C00113:131:HMHYWADXX:2:1214:7658:35836	272	1	14792	0	38M140N13M	*	0	0	GGGCCCCTCACCAGCCCCAGGTCTTTTCCCAGAGATGCCCTTGCGCCTCAT	CCCFFFFFHHHHHJJJJJJJJCGHIJJIJJJJJJIJJGIJJIJIJIJJJJI	NH:i:6	HI:i:3	AS:i:47	nM:i:1
+HWI-C00113:131:HMHYWADXX:1:2114:4116:44566	272	1	14794	0	36M140N15M	*	0	0	GCCCCTCACCAGCCCCAGGTCTTTTCCCAGAGATGCCCTTGCGCCTCATGA	<@@DDDDDDFHCFHEFGBE+2AFH@GIEGF=GGHII9F<GHHIIA@6=48;	NH:i:6	HI:i:3	AS:i:47	nM:i:1
+HWI-C00113:131:HMHYWADXX:1:1114:13704:81420	272	1	14795	0	35M140N16M	*	0	0	CCCCTCACCAGCCCCAGGTCCTTTCCCAGAGATGCCCTTGCGCCTCATGAC	@@@DDDDFHBFHHGIGIE3CFHIIIIII<E@FHIGIIC?BFDHDHGIIIII	NH:i:6	HI:i:3	AS:i:49	nM:i:0
+HWI-C00113:131:HMHYWADXX:1:2115:10483:10806	272	1	14795	0	35M140N16M	*	0	0	CCCCTCACCAGCCCCAGGTCCTTTCCCAGAGATGCCCTTGCGCCTCATGAC	CCCFFFFFHHHHHJJJIIHHJIJJJJJJHHHIHGIIJJJHJIJJIJJJJJJ	NH:i:6	HI:i:3	AS:i:49	nM:i:0
+HWI-C00113:131:HMHYWADXX:1:2214:18560:59872	272	1	14795	0	35M140N16M	*	0	0	CCCCTCACCAGCCCCAGGTCCTTTCCCAGAGATGCCCTTGCGCCTCATGAC	=;?BA@DAFFFFF?EAF;A?9CH?CB9E9?D9FGEGGCGGEHIDBE@FFH;	NH:i:6	HI:i:3	AS:i:49	nM:i:0
+HWI-C00113:131:HMHYWADXX:2:1115:2028:49488	272	1	14795	0	35M140N16M	*	0	0	CCCCTCACCAGCCCCAGGTCCTTTCCCAGAGATGCCCTTGCGCCTCATGAC	???+4@B?FHHFHFGIBEF9BDHCB??CEHGG*1C<FEHAF?(?(@@=B8@	NH:i:6	HI:i:3	AS:i:49	nM:i:0
+HWI-C00113:131:HMHYWADXX:2:1115:2949:63319	272	1	14795	0	1S35M140N15M	*	0	0	ACCCCTCACCAGCCCCAGGTCTTTTCCCAGAGATGCCCTTGCGCCTCATGA	@@CDFDFFHHHDHGIIIEEFGIJJJGIJIIGCGIJJJJJJIGIJIJJJHGA	NH:i:6	HI:i:3	AS:i:46	nM:i:1
+HWI-C00113:131:HMHYWADXX:2:1209:18680:84812	272	1	14795	0	35M140N16M	*	0	0	CCCCTCACCAGCCCCAGGTCCTTTCCCAGAGATGCCCTTGCGCCTCATGAC	CC@FFFFFHHFHHJJJHHEHIIJJJJJIIEGFIJJJIIIIJJIJJJJJIII	NH:i:6	HI:i:3	AS:i:49	nM:i:0
+HWI-C00113:131:HMHYWADXX:2:2205:10731:40239	272	1	14795	0	35M140N16M	*	0	0	CCCCTCACCAGCCCCAGGTCCTTTCCCAGAGATGCCCTTGCGCCTCATGAC	@@<=A@DDFB:?FG<F;:3CCBEEBFGIIA?GIAD>B?BFF<BDF<8B8FF	NH:i:6	HI:i:3	AS:i:49	nM:i:0
+HWI-C00113:131:HMHYWADXX:2:2207:18860:77945	272	1	14795	0	35M140N16M	*	0	0	CCCCTCACCAGCCCCAGGTCCTTTCCCAGAGATGCCCTTGCGCCTCATGAC	C@CFFFFFHHHHHJJJIJGHIIJJJJJJJJJJJJIJJJJJIJJIJJJJIJJ	NH:i:6	HI:i:3	AS:i:49	nM:i:0
+HWI-C00113:131:HMHYWADXX:1:1102:4544:68832	272	1	14796	0	34M140N17M	*	0	0	CCCTCACCAGCCCCAGGTCCTTTCCCAGAGATGCCCTTGCGCCTCATGACC	???DDDDDBDDD:CE:C2<CFBDDECCEDC>DEE??BD?D@DADD<CC=8B	NH:i:6	HI:i:3	AS:i:49	nM:i:0
+HWI-C00113:131:HMHYWADXX:1:1203:5829:91963	272	1	14796	0	34M140N17M	*	0	0	CCCTCACCAGCCCCAGGTCCTTTCCCAGAGATGCCCTTGCGCCTCATGACC	CCCFFFFFHHHHHJJIJIHJIIJGIIJIJJJJJIJJIJGGIJJJGIJJHJI	NH:i:6	HI:i:3	AS:i:49	nM:i:0
+HWI-C00113:131:HMHYWADXX:2:2110:3018:17806	272	1	14796	0	34M140N17M	*	0	0	CCCTCACCAGCCCCAGGTCCTTTCCCAGAGATGCCCTTGCGCCTCATGACC	CCCFFFFFHHHFHIJJIFGIJIHIJIIDHIIJGGIIJIJJJJJJIJJIIIJ	NH:i:6	HI:i:3	AS:i:49	nM:i:0
+HWI-C00113:131:HMHYWADXX:1:1111:17873:10434	272	1	14797	0	33M140N18M	*	0	0	CCTCACCAGCCCCAGGTCCTTTCCCAGAGATGCCCTTGCGCCTCATGACCA	???DDDADDDDD8:2<2<FFFEIICEI;E@>DDBDDD@<?0@@D9=<.BBB	NH:i:6	HI:i:3	AS:i:49	nM:i:0
+HWI-C00113:131:HMHYWADXX:1:1109:10709:93463	272	1	14801	0	29M140N22M	*	0	0	ACCAGCCCCAGGTCTTTTCCCAGAGATGCCCTTGCGCCTCATGACCAGCTT	CC@DFFFFHHGH<CGDFHIIGIDAEGDGBBGFH@GEH:FHGGHIEFFDHII	NH:i:7	HI:i:4	AS:i:47	nM:i:1
+HWI-C00113:131:HMHYWADXX:1:2214:12148:62454	272	1	14801	0	29M140N22M	*	0	0	ACCAGCCCCAGGTCTTTTCCCAGAGATGCCCTTGCGCCTCATGACCAGCTT	?@?DDDDD:FF=CFGGIGGBFGA;3<1:EEG>FGHFHFHIHGI@?DGC@CF	NH:i:7	HI:i:4	AS:i:47	nM:i:1
+HWI-C00113:131:HMHYWADXX:1:1105:1515:82248	272	1	14802	0	28M140N23M	*	0	0	CCAGCCCCAGGTCCTTTCCCAGAGATGCCCTTGCGCCTCATGACCAGCTTG	??:ADBDDDDD:A<+C?AFDB@E?F4<*?:?1:??):??0009??9?(8BC	NH:i:7	HI:i:4	AS:i:49	nM:i:0
+HWI-C00113:131:HMHYWADXX:1:1110:16355:5537	272	1	14802	0	28M140N23M	*	0	0	CCAGCCCCAGGTCCTTTCCCAGAGATGCCCTTGCGCCTCATGACCAGCTTG	@CCFFFFFHH?ADHGIJIJJJJJIIEHIJJJJJIJIGIIJJIJJIIJIJJJ	NH:i:7	HI:i:4	AS:i:49	nM:i:0
+HWI-C00113:131:HMHYWADXX:2:1102:17802:20689	272	1	14805	0	25M140N26M	*	0	0	GCTCCAGGTCCTTTCCCAGAGATGCCCTTGCGCCTCATGACCAGCTTGTTG	CCCFFFFFHHHHHJJJJJJIJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJI	NH:i:7	HI:i:4	AS:i:47	nM:i:1
+HWI-C00113:131:HMHYWADXX:2:1104:7670:95815	272	1	14805	0	25M140N26M	*	0	0	GCCCCAGGTCCTTTCCCAGAGATGCCCTTGCGCCTCATGACCAGCTTGTTG	@@@DBDDDHHBFDBFGEBBGHG@HIBHIDHBGGGEFBDDDFDGBBBGCHHI	NH:i:7	HI:i:4	AS:i:49	nM:i:0
+HWI-C00113:131:HMHYWADXX:2:1110:11368:101298	272	1	14805	0	25M140N26M	*	0	0	GCCCCAGGTCCTTTCCCAGAGATGCCCTTGCGCCTCATGACCAGCTTGTTG	BCCFFFFFCFHHHJJJJJIJJJJJJJJJJJJJGJJJJJJJJJJJJJJJIJJ	NH:i:7	HI:i:4	AS:i:49	nM:i:0
+HWI-C00113:131:HMHYWADXX:2:1115:2363:85646	272	1	14805	0	25M140N26M	*	0	0	GCTCCAGGTCCTTTCCCAGAGATGCCCTTGCGCCTCATGACCAGCTTGTTG	@C@FFFB?CFDFHDHGIIIIEGIIIIEDGIIIIIIIIIGGIIGIIGCGHIH	NH:i:7	HI:i:4	AS:i:47	nM:i:1
+HWI-C00113:131:HMHYWADXX:2:2213:6044:80821	272	1	14805	0	25M140N26M	*	0	0	GCTCCGGGTCCTTTCCCAGAGATGCCCTTGCGCCTCATGACCAGCTTGTTG	@@@FFFFFFFBFDGIIJIJGGFHIIIJIIJGIIEHI<FEGIIFEGIHIHGE	NH:i:7	HI:i:4	AS:i:45	nM:i:2
+HWI-C00113:131:HMHYWADXX:1:1105:6336:76198	272	1	14807	0	23M140N28M	*	0	0	CCCAGGTCCTTTCCCAGAGATGCCCTTGCGCCTCATGACCAGCTTGTTGAA	CCCFFFFFHHGHHGGHIIJEHIJIEGIJIJGIIIJICBFFIGAHFHHHJBH	NH:i:7	HI:i:4	AS:i:49	nM:i:0
+HWI-C00113:131:HMHYWADXX:1:1108:3508:3794	272	1	14807	0	1S23M140N27M	*	0	0	GCCCAGGTCCTTTCCCAGAGATGCCCTTGCGCCTCATGACCAGCTTGTTGA	CCCFFFFDHHHHHJJJJJJJJJJJJJJJJJJJJJJJJJIJJJJJJJJJIJJ	NH:i:7	HI:i:4	AS:i:48	nM:i:0
+HWI-C00113:131:HMHYWADXX:1:2209:11671:4960	272	1	14811	0	19M140N32M	*	0	0	GGTCCTTTCCCAGAGATGCCCTTGCGCCTCATGACCAGCTTGTTGAAGAGA	BCBFFFFFHHHHHJJGIIGIJJJJJJJJJJJJIIJIJJJJJJHIJIIJIJI	NH:i:7	HI:i:4	AS:i:49	nM:i:0
+HWI-C00113:131:HMHYWADXX:1:2105:5117:87572	272	1	14812	0	18M140N33M	*	0	0	GTCCTTTCCCAGAGATGCCCTTGCGCCTCATGACCAGCTTGTTGAAGAGAT	C@CFFFFFFFFHGFEFHIJJJJGIBHIJJJGGCHIEEGIJJFDGGGIGIGI	NH:i:7	HI:i:4	AS:i:49	nM:i:0
+HWI-C00113:131:HMHYWADXX:2:2202:9099:82513	272	1	14812	0	18M140N33M	*	0	0	GTCCTTTCCCAGAGATGCCCTTGCGCCTCATGACCAGCTTGTTGAAGAGAT	8?;DDDDDDFB?A3:<EE<<CGA+<F:F1?D*:*1:))???99??<FB??B	NH:i:7	HI:i:4	AS:i:49	nM:i:0
+HWI-C00113:131:HMHYWADXX:2:2214:5571:19703	272	1	14812	0	18M140N33M	*	0	0	GTCCTTTCCCAGAGATGCCCTTGCGCCTCATGACCAGCTTGTTGAAGAGAT	=:?7ADFDHHHDHHGIEF?CFFCBFEG@G>CHIGEGFG?FGHGA>9B8BF@	NH:i:7	HI:i:4	AS:i:49	nM:i:0
+HWI-C00113:131:HMHYWADXX:2:1215:4185:31561	272	1	14815	0	15M140N36M	*	0	0	CTTTCCCAGAGATGCCCTTGCGCCTCATGACCAGCTTGTTGAAGAGATCCG	CCCFFFFFHHHHGJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJIJJJH	NH:i:7	HI:i:4	AS:i:49	nM:i:0
+HWI-C00113:131:HMHYWADXX:1:2108:1506:70629	272	1	14816	0	14M140N37M	*	0	0	TTTCCCAGAGATGCCCTTGCGCCTCATGACCAGCTTGTTGAAGAGATCCGA	?@@;BDDD=DFFDDDFGGFCA?)<CEG@C??C?FDFFB<FGIFDFFDFC;;	NH:i:7	HI:i:4	AS:i:49	nM:i:0
+HWI-C00113:131:HMHYWADXX:1:1113:4051:71948	272	1	14818	0	12M140N39M	*	0	0	TCCCAGAGATGCCCTTGCGCCTCATGACCAGCTTGTTGAAGAGATCCGACA	@@@FFDFFF:CDCFGGDHHGEFHIJIJIIGIGHIJDBBDHGI@9BFGIEHI	NH:i:7	HI:i:4	AS:i:49	nM:i:0
+HWI-C00113:131:HMHYWADXX:1:1101:6114:49389	272	1	15001	0	38M757N13M	*	0	0	ATCCGACATCAAGTGCCCACCTTGGCTCGTGGCTCTCACTTGCTCCTGCTC	CCCFFFFFHHHHHHIJJJJJJJJIJJJJJJIJJJJJJJJJJJJJGJJJJJJ	NH:i:8	HI:i:2	AS:i:49	nM:i:0
+HWI-C00113:131:HMHYWADXX:2:1103:12497:23506	272	1	15001	0	38M757N13M	*	0	0	ATCCGACATCAAGTGCCCACCTTGGCTCGTGGCTCTCACTTGCTCCTGCTC	CCCFFFFFHHHHGJIJJJJJJJJJJJJJJJJJJJJJIJJIJJJJJIJIJJI	NH:i:8	HI:i:2	AS:i:49	nM:i:0
+HWI-C00113:131:HMHYWADXX:2:2214:19931:4971	272	1	15002	0	37M757N14M	*	0	0	TCCTACATCAAGTGCCCACCTTGGCTCGTGGCTCTCACTTGCTCCTGCTCC	?;=+4ADDBBBDAFGGI>1@F?F+AAEEEB<GAG;?DGFE>FFIIF@DE4=	NH:i:8	HI:i:2	AS:i:47	nM:i:1
+HWI-C00113:131:HMHYWADXX:1:1108:6828:32713	272	1	15003	0	36M757N15M	*	0	0	CCGGCATCAAGTCCCCACCTTGGCTCGTGGCTCTCACTTGCTCCTGCTCCT	?@@ADDDDD?CDD:CFB@:@G@ABGFGFGFBFEAFEEEFCFCF@F=)8=@>	NH:i:8	HI:i:2	AS:i:45	nM:i:2
+HWI-C00113:131:HMHYWADXX:1:1111:7491:39504	272	1	15003	0	36M757N15M	*	0	0	CCGACATCAAGTGCCCACCTTGGCTCGTGGCTCTCACTTGCTCCTGCTCCT	CCCFFDFFFHHHFIGEGHIGIGGDGIJFHEHGGIJJJIJIJJJJJIIIIGI	NH:i:8	HI:i:2	AS:i:49	nM:i:0
+HWI-C00113:131:HMHYWADXX:1:1212:16079:85811	272	1	15003	0	36M757N15M	*	0	0	CCGGCATCAAGTCCCCACCTTGGCTCGTGGCTCTCACTTGCTCCTGCTCCT	@CCFFFFFHGHHHJJJJJJJIIJJJJJIJIJJHIIJJJJIJJJJJJJIJJJ	NH:i:8	HI:i:2	AS:i:45	nM:i:2
+HWI-C00113:131:HMHYWADXX:1:2101:7167:50357	272	1	15003	0	36M757N15M	*	0	0	CCGACATCAAGTGCCCACCTTGGCTCGTGGCTCTCACTTGCTCCTGCTCCT	@@@DD?DDFHHHD@?<AGHBEHFGAGIFHEH3??BFGBD@GGCHGGGCHI;	NH:i:8	HI:i:2	AS:i:49	nM:i:0
+HWI-C00113:131:HMHYWADXX:1:2201:9548:48040	272	1	15003	0	36M757N15M	*	0	0	CCGACATCAAGTGCCCACCTTGGCTCGTGGCTCTCACTTGCTCCTGCTCCT	CCCFFFFFHHHHHJJJJJJJJJJJJIJHIIIGGIIJJJJHIJJJJIJIJJJ	NH:i:8	HI:i:2	AS:i:49	nM:i:0
+HWI-C00113:131:HMHYWADXX:1:2201:14017:74222	272	1	15003	0	36M757N15M	*	0	0	CCGACATCAAGTGCCCACCTTGGCTCGTGGCTCTCACTTGCTCCTGCTCCT	=@?=DDDDDBDCFHB@CG?EF<BC>CG?FHGIIIIG@??BGHIE;8@B<FB	NH:i:8	HI:i:2	AS:i:49	nM:i:0
+HWI-C00113:131:HMHYWADXX:1:2204:7589:97905	272	1	15003	0	36M757N15M	*	0	0	CCGACATCAAGTGCCCACCTTGGCTCGTGGCTCTCACTTGCTCCTGCTCCT	CCCFFFFFHHHHDHIGGGJIJJIJJJJIJJJJIGIJIJJIJJJJJIJJIJJ	NH:i:8	HI:i:2	AS:i:49	nM:i:0
+HWI-C00113:131:HMHYWADXX:1:2212:18929:92726	272	1	15003	0	36M757N15M	*	0	0	CCGACATCAAGTGCCCACCTTGGCTCGTGGCTCTCACTTGCTCCTGCTCCT	@@@DDDDDFFFF:AE<AFGFEHFFAF8:1:@8:DBBD9BB?/BDF<CDB<F	NH:i:8	HI:i:2	AS:i:49	nM:i:0
+HWI-C00113:131:HMHYWADXX:1:2215:2615:12154	272	1	15003	0	36M757N15M	*	0	0	CCGACATCAAGTGCCCACCTTGGCTCGTGGCTCTCACTTGCTCCTGCTCCT	CCCFFFFFGHHHHJJJJJJJJIJJJJJJJJJJJJJJJJJIJJJJJJJJJJI	NH:i:8	HI:i:2	AS:i:49	nM:i:0
+HWI-C00113:131:HMHYWADXX:2:1106:7741:42827	272	1	15003	0	36M757N15M	*	0	0	CCGACATCAAGTGCCCACCTTGGCTCGTGGCTCTCACTTGCTCCTGCTCCT	CCCFFFFFHHHHHJJJJJJJJJIJJJIIJJJJIJJJJJJJJJJJIJGHIHH	NH:i:8	HI:i:2	AS:i:49	nM:i:0
+HWI-C00113:131:HMHYWADXX:2:1201:8380:74978	272	1	15003	0	36M757N15M	*	0	0	CCGACATCAAGTGCCCACCTTGGCTCGTGGCTCTCACTTGCTCCTGCTCCT	CCCFFFFFHFHHHIJJJJJJJJJJJJJFHIIGJJJJJJJIGGIIJEEDHHI	NH:i:8	HI:i:2	AS:i:49	nM:i:0
+HWI-C00113:131:HMHYWADXX:2:1205:11268:38021	272	1	15003	0	36M757N15M	*	0	0	CCGACATCAAGTCCCCACCTTGGCTCGTGGCTCTCACTTGCTCCTGCTCCT	1:?7DDD?ACDFBGHEAE@FGB@;@@A@C@0?F9FBFCF@48*9==3=CCF	NH:i:8	HI:i:2	AS:i:47	nM:i:1
+HWI-C00113:131:HMHYWADXX:2:1208:17413:76793	272	1	15003	0	36M757N15M	*	0	0	CCGACATCAAGTGCCCACCTTGGCTCGTGGCTCTCACTTGCTCCTGCTCCT	C@@FFFFFGGDDDGHIGGIH<FHGEHB8CEIIJIIFG?FFHFHIJII>FEG	NH:i:8	HI:i:2	AS:i:49	nM:i:0
+HWI-C00113:131:HMHYWADXX:2:1211:4828:84953	272	1	15003	0	36M757N15M	*	0	0	CCGACATCAAGTGCCCACCTTGGCTCGTGGCTCTCACTTGCTCCTGCTCCT	@BB?DFFFHHHHHIJIJJJJJJJJJJJHIJJIIJJJJJJIIIJJJJJJIJI	NH:i:8	HI:i:2	AS:i:49	nM:i:0
+HWI-C00113:131:HMHYWADXX:2:2107:20905:80208	272	1	15003	0	36M757N15M	*	0	0	CCGACATCAAGTGCCCACCTTGGCTCGTGGCTCTCACTTGCTCCTGCTCCT	@CCFFFFFHHHFBHIIEIIDIHGGGGG@GGHCFGHIIJIGGGGIJIGIGGH	NH:i:8	HI:i:2	AS:i:49	nM:i:0
+HWI-C00113:131:HMHYWADXX:2:2112:6263:84991	272	1	15003	0	36M757N15M	*	0	0	CCGACATCAAGTCCCCACCTTGGCTCGTGGCTCTCACTTGCTCCTGCTCCT	@@@?DDDDFBH?FHIGIGIIGG;GHBGCD?DCGIIGHEGBBFHGGIHBFIG	NH:i:8	HI:i:2	AS:i:47	nM:i:1
+HWI-C00113:131:HMHYWADXX:2:2202:10314:26844	272	1	15003	0	36M757N15M	*	0	0	CCGACATCAAGTGCCCACCTTGGCTCGTGGCTCTCACTTGCTCCTGCTCCT	CCCFFFFFHHHHHJJJJJJJJJJJJJJIJJJJIIJJJJJJJJJJJJJJJJJ	NH:i:8	HI:i:2	AS:i:49	nM:i:0
+HWI-C00113:131:HMHYWADXX:2:2213:21028:90280	272	1	15003	0	36M757N15M	*	0	0	CCGACATCAAGTCCCCACCTTGGCTCGTGGCTCTCACTTGCTCCTGCTCCT	@@@BDDDAD?FDF9GIBB@@FFG3CFF:DD)?BD*9D@@F4BDEEEFFF8=	NH:i:8	HI:i:2	AS:i:47	nM:i:1
+HWI-C00113:131:HMHYWADXX:1:1216:14847:22529	272	1	15004	0	35M757N16M	*	0	0	CGACATCAAGTGCCCACCTTGGCTCGTGGCTCTCACTTGCTCCTGCTCCTT	@@@FFFFDHHBDHIIIJJJJIIIIIIJJIJJGIJIFIJJIDHHGBEHIJJJ	NH:i:8	HI:i:2	AS:i:49	nM:i:0
+HWI-C00113:131:HMHYWADXX:2:2111:14281:81135	272	1	15007	0	32M757N19M	*	0	0	CATCAAGTGCCCACCTTGGCTCGTGGCTCTCACTTGCTCCTGCTCCTTCTG	@@@DDDBD42=:ACFFIE?FFGAFF@FFFDGEAG>D@DBB9BC3D@EDFFA	NH:i:8	HI:i:2	AS:i:49	nM:i:0
+HWI-C00113:131:HMHYWADXX:1:2203:4824:93169	272	1	15008	0	31M757N20M	*	0	0	ATCAAGTGCCCACCTTGGCTCGTGGCTCTCACTTGCTCCTGCTCCTTCTGC	CCCFFFFFHHHHHJJJJIJJJJHIJIJJJJJJJJGIJJJJI?DFGFHIHJF	NH:i:8	HI:i:2	AS:i:49	nM:i:0
+HWI-C00113:131:HMHYWADXX:1:1112:17298:87937	272	1	15925	1	23M659N28M	*	0	0	CACTTCCCTGGGAGCTCCCTGGACTGAAGGAGACGCGCTGCTGCTGCTGTC	?@;;BA;3ABC?C?6EGDGIIBA+AAC<?D9CBGG@@FFFFAFCIIECC7=	NH:i:4	HI:i:2	AS:i:49	nM:i:0
+HWI-C00113:131:HMHYWADXX:2:2210:17342:39133	272	1	15925	1	23M659N28M	*	0	0	CACTTCCCTGGGAGCTCCCTGGACTGAAGGAGACGCGCTGCTGCTGCTGTC	@?@DDDDDFAB::<EBFGIFG@FF9AECEFIFAGCD:F@F8=@E;7)77@@	NH:i:4	HI:i:2	AS:i:49	nM:i:0
+HWI-C00113:131:HMHYWADXX:1:2112:17740:2548	272	1	15931	1	17M659N34M	*	0	0	CCTGGGAGCTCCCTGGACTGAAGGAGACGCGCTGCTGCTGCTGTCGTCCTG	@@@FFD:ACFDCFCGGGDF?HHIBDEHFGHDHFIIGBDGEEHIFHGIIGHH	NH:i:4	HI:i:2	AS:i:49	nM:i:0
+HWI-C00113:131:HMHYWADXX:1:2112:15228:46115	272	1	16727	0	39M92N12M	*	0	0	GGGGCGGTGGGGGTGGTGTTAGTACCCCATCTTGTAGGTCTTGAGAGGCTC	@CCDDFF:?FFHH-@B:AABCB@DDEEDCDCCDCCCCD>ACD>>:9:??2<	NH:i:6	HI:i:2	AS:i:49	nM:i:0
+HWI-C00113:131:HMHYWADXX:2:2109:14386:93817	272	1	16728	0	38M92N13M	*	0	0	GGGCGGTGGGGGTGGTGTTAGTACCCCATCTTGTAGGTCTTGAGAGGCTCG	@CCFFFDDHHHHDHIFHIJJJGHHIIJHHHHHHFFFFEFEEEECDDDDDDB	NH:i:6	HI:i:2	AS:i:49	nM:i:0
+HWI-C00113:131:HMHYWADXX:1:2203:14322:7218	272	1	16741	0	25M110N26M	*	0	0	GGTGTTAGTACCCCATCTTGTAGGTCTCAGTGTGGAAGGTGGGCAGTTCTG	?@?DDD?BFFHHFB7EFGGGEFHIHA<CFHIGEHI<FEHH<=DEGG?DGEH	NH:i:7	HI:i:6	AS:i:49	nM:i:0
+HWI-C00113:131:HMHYWADXX:1:1212:14242:21074	272	1	16751	0	15M92N36M	*	0	0	CCCCATCTTGTAGGTCTTGAGAGGCTCGGCTACCTCAGTGTGGAAGGTGGG	@@CDFFFFGGBFFECGGGGIIHCHCEG@FAEGII9?*?BB9BFGC@H)=FG	NH:i:6	HI:i:2	AS:i:49	nM:i:0
+HWI-C00113:131:HMHYWADXX:1:1106:12278:45196	272	1	16752	0	14M92N37M	*	0	0	CCCATCTTGTAGGTCTTGAGAGGCTCGGCTACCTCAGTGTGGAAGGTGGGC	CCCFFFFFHHHHHHIHIJIJIJJJJJIJFEHHIGGEGHGFHGBGGH8BGH;	NH:i:6	HI:i:2	AS:i:49	nM:i:0
+HWI-C00113:131:HMHYWADXX:2:2212:12811:3161	272	1	16752	0	14M92N37M	*	0	0	CCCATCTTGTAGGTCTTGAGAGGCTCGGCTACCTCAGTGTGGAAGGTGGGC	CCCFFFFFHFFHGEGHIJJJJJIIGHFHAFEGGDDCE:DBDGDHFH?CGH@	NH:i:6	HI:i:2	AS:i:49	nM:i:0
+HWI-C00113:131:HMHYWADXX:1:1102:2563:17519	272	1	16753	0	13M92N38M	*	0	0	CCATCTTGTAGGTCTTGAGAGGCTCGGCTACCTCAGTGTGGAAGGCGGGCA	?<?D>DB8D>822<CC<<<+A;CE?1):C?))1:*0B<9*8*0*((7@4'3	NH:i:6	HI:i:2	AS:i:47	nM:i:1
+HWI-C00113:131:HMHYWADXX:1:2201:2398:40333	16	1	16753	0	13M92N38M	*	0	0	CCATCTTGTAGGTCTTGAGAGGCTCGGCTACCTCAGTGTGGAAGGTGGGCA	CCCFFFFFHHHDHEHIHIJGF1FFHEBH@FHICHDD<B?DDA@?FD?FHFH	NH:i:6	HI:i:1	AS:i:49	nM:i:0
+HWI-C00113:131:HMHYWADXX:1:2209:7506:25914	16	1	16753	0	13M92N38M	*	0	0	CCATCTTGTAGGTCTTGAGAGGCTCGGCTACCTCAGTGTGGAAGGTGGGCA	@C@FDFFFFHHHHIIJIIIJJJJJJBHG=?DFBC<?:?9?FGHCG8BHHD7	NH:i:6	HI:i:1	AS:i:49	nM:i:0
+HWI-C00113:131:HMHYWADXX:2:1207:6786:56046	16	1	16753	0	13M92N38M	*	0	0	CCATCTTGTAGGTCTTGAGAGGCTCGGCTACCTCAGTGTGGAAGGTGGGCA	@B@DFFFFHHHHHGIGIIIAGIJEGAHHEGHHBF>BDG?FHBGEH?FHGG3	NH:i:6	HI:i:1	AS:i:49	nM:i:0
+HWI-C00113:131:HMHYWADXX:1:2116:7403:96086	272	1	17020	0	36M177N15M	*	0	0	GCCCAGGTCTGGCACATAGAAGTAGTTCTCTGGGACCTGCTGTTCCAGCTG	:?=DDD=AAAC:+<CA2C+::AFAC,9<9CA+::CEDDDD>BDIIIIIIA?	NH:i:7	HI:i:5	AS:i:49	nM:i:0
+HWI-C00113:131:HMHYWADXX:2:1209:11002:81132	272	1	17020	0	36M177N15M	*	0	0	GCCCGGGTCTGGCACATAGAAGTAGTTCTCTGGGACCTGCTGTTCCAGCTG	@@@DD@A<@DDDF;BCGF<4CHCEG?EG@FGF9)?BB:?B?DBF>D?**9B	NH:i:7	HI:i:4	AS:i:47	nM:i:1
+HWI-C00113:131:HMHYWADXX:2:1115:8064:78307	272	1	17021	0	35M177N16M	*	0	0	CCCTGGTCTGGCACATAGAAGTAGTTCTCTGGGACCTGCTGTTCCAGCTGC	11844BBDD=FDFEFFFDFI?HEHAFBEHEEEFC?E:FDGDD<FE4:9??9	NH:i:7	HI:i:5	AS:i:47	nM:i:1
+HWI-C00113:131:HMHYWADXX:2:1211:18547:26385	272	1	17027	0	29M177N22M	*	0	0	TCTGGCACATAGAAGTAGTTCTCTGGGACCTGCTGTTCCAGCTGCTCTCTC	BCCFFFFFHHHHHJJIIJHJJJJJJJIJJJIJJJJJJJJJIJJJJJJJJJJ	NH:i:7	HI:i:6	AS:i:49	nM:i:0
+HWI-C00113:131:HMHYWADXX:1:2109:12204:47428	272	1	17028	0	28M177N23M	*	0	0	CTGGCACATAGAAGTAGTTCTCTGGGACCTGCTGTTCCAGCTGCTCTCTCT	@@@DDBD:=ACDBFEGECFGIHD>DH9CBEHHHEEFB?F>GD@3?FB?BB@	NH:i:7	HI:i:6	AS:i:49	nM:i:0
+HWI-C00113:131:HMHYWADXX:2:1101:15891:42282	272	1	17028	0	28M177N23M	*	0	0	CTGGCACATAGAAGTAGTTCTCTGGGACCTGCTGTTCCAGCTGCTCTCTCT	CCCFFFFFHHHHHJHHIIJJJJJJJJJJIIJJJJIJJJIJJJJJJJJJJJJ	NH:i:7	HI:i:6	AS:i:49	nM:i:0
+HWI-C00113:131:HMHYWADXX:1:1107:10929:6659	272	1	17030	0	26M177N25M	*	0	0	GGCACATAGAAGTAGTTCTCTGGGACCTGCTGTTCCAGCTGCTCTCTCTTG	CCCFFFFFHHHHDHIHHJJGJJJJJJJIJJIJGIJJJIJJJIJJJJJIJJG	NH:i:7	HI:i:6	AS:i:49	nM:i:0
+HWI-C00113:131:HMHYWADXX:1:1114:7098:71178	272	1	17030	0	26M177N25M	*	0	0	GGCACATAGAAGTAGTTCTCTGGGACCTGCTGTTCCAGCTGCTCTCTCTTG	=?@BDEEFHBDHFBGIEGIHEHIGDHGEIIJIIIEHIHIIGHDGHIGIIH@	NH:i:7	HI:i:6	AS:i:49	nM:i:0
+HWI-C00113:131:HMHYWADXX:1:1209:3383:100724	272	1	17030	0	26M177N25M	*	0	0	GGCACATAGAAGTAGTTCTCTGGGACCTGCTGTTCCAGCTGCTCTCTCTTG	?@@ADDDDDHDH?EEFH<CAHHGCHIF?GG>EHIGIIGHGHIFII>BFIH?	NH:i:7	HI:i:6	AS:i:49	nM:i:0
+HWI-C00113:131:HMHYWADXX:1:2111:3771:31345	272	1	17030	0	26M177N25M	*	0	0	GGCACATAGAAGTAGTTCTCTGGGACCTGCTGTTCCAGCTGCTCTCTCTTG	@@@DFFFFGHDHHHJGIHJJJJGIJJIJIJIIJJIIJJIGHIJJJIJJIJ<	NH:i:7	HI:i:6	AS:i:49	nM:i:0
+HWI-C00113:131:HMHYWADXX:1:2205:14794:36455	272	1	17030	0	26M177N25M	*	0	0	GGCACATAGAAGTAGTTCTCTGGGACCTGCTGTTCCAGCTGCTCTCTCTTG	CCCFFFFFHHHHHIJJJJJJJJJJJJJJJJJJIJJJJIJJIJJJJJJJJJJ	NH:i:7	HI:i:6	AS:i:49	nM:i:0
+HWI-C00113:131:HMHYWADXX:2:1107:19701:64552	272	1	17030	0	26M177N25M	*	0	0	GGCACATAGAAGTAGTTCTCTGGGACCTGCTGTTCCAGCTGCTCTCTCTTG	CCCFFDFFHHHHDGIIJIJJJIIJDGHGJJJJJJIJJJJJJJGIJJJJJJF	NH:i:7	HI:i:6	AS:i:49	nM:i:0
+HWI-C00113:131:HMHYWADXX:2:1210:18711:88303	272	1	17030	0	26M177N25M	*	0	0	GGCACATAGAAGTAGTTCTCTGGGACCTGCTGTTCCAGCTGCTCTCTCTTG	CCCFFFFFHHHHHJJJJJJJJIJFIJJJEIIHIIJJIIJJGJJJIJJJJJE	NH:i:7	HI:i:6	AS:i:49	nM:i:0
+HWI-C00113:131:HMHYWADXX:2:2212:19113:15559	272	1	17030	0	26M177N25M	*	0	0	GGCACATAGAAGTAGTTCTCTGGGACCTGCTGTTCCAGCTGCTCTCTCTTG	@@@7B>DDC=<AF@<CFB?<,?FFDBF3AD+?9*?EGCF>@BFBGBAF<FG	NH:i:7	HI:i:6	AS:i:49	nM:i:0
+HWI-C00113:131:HMHYWADXX:2:2212:14258:59619	272	1	17030	0	26M177N25M	*	0	0	GGCACATAGAAGTAGTTCTCTGGGACCTGCTGTTCCAGCTGCTCTCTCTTG	=?@DDD:=DADFAEFGEF<,AADE<F<?AAFCGG@?FD>CGBF<D<9B<D<	NH:i:7	HI:i:6	AS:i:49	nM:i:0
+HWI-C00113:131:HMHYWADXX:1:2103:9695:24819	272	1	17031	0	25M177N26M	*	0	0	GCACATAGAAGTAGTTCTCTGGGACCTGCTGTTCCAGCTGCTCTCTCTTGC	CCCFFFFFHHHHHJHIJJJJJJJJJJJJJJJIJJJJJJJJJJJJJJJJJGG	NH:i:7	HI:i:6	AS:i:49	nM:i:0
+HWI-C00113:131:HMHYWADXX:2:1204:13994:2816	272	1	17031	0	25M177N26M	*	0	0	GCACATAGAAGTAGTTCTCTGGGACCTGCTGTTCCAGCTGCTCTCTCTTGC	?@@DDDDDHHHHFHEFAABA@?FGBEFHIIIHH>DB@DHIHIDD>@@GHID	NH:i:7	HI:i:6	AS:i:49	nM:i:0
+HWI-C00113:131:HMHYWADXX:2:1212:15591:47491	272	1	17031	0	25M177N26M	*	0	0	GCACATAGAAGTAGTTCTCTGGGACCTGCTGTTCCAGCTGCTCTCTCTTGC	@@C+ADDDDHFFDEGEGIIIDFHIFHIIIIIGEHIIBH>FGGGHGHFGGII	NH:i:7	HI:i:6	AS:i:49	nM:i:0
+HWI-C00113:131:HMHYWADXX:2:2215:10125:81395	272	1	17031	0	25M859N26M	*	0	0	GCACATAGAAGTAGTTCTCTGGGACCTGCAGGGCCCGCTCGTCCAGGGGGC	CCCFFFFFGHHHHJJJJJJJJJHJJJJJJIJIIJJJHIJJJJJJJJJIJHE	NH:i:6	HI:i:1	AS:i:49	nM:i:0
+HWI-C00113:131:HMHYWADXX:1:2102:9065:90529	16	1	17033	0	2S23M550N26M	*	0	0	GTACATAGAAGTAGTTCTCTGGGACAGGTTCTCGGTGGTGTTGAAGAGCAG	C@CFFFFFHHHHHJJJJJJJJJJJJJJJJJJJJJJFHIFHIJIJJJJJJJJ	NH:i:5	HI:i:2	AS:i:47	nM:i:0
+HWI-C00113:131:HMHYWADXX:1:2204:7767:77376	16	1	17033	0	2S23M550N26M	*	0	0	GTACATAGAAGTAGTTCTCTGGGACAGGTTCTCGGTGGTGTTGAAGAGCAG	@@@FDFDDBFHADEHEIGIGIJIGHIHG?EDGHGGCFH:B?BD@FGFHGIH	NH:i:5	HI:i:2	AS:i:47	nM:i:0
+HWI-C00113:131:HMHYWADXX:2:1212:6793:42000	16	1	17033	0	2S23M550N26M	*	0	0	GTACATAGAAGTAGTTCTCTGGGACAGGTTCTCGGTGGTGTTGAAGAGCAG	@@?DADBD8CFADGFHIIIIE3A<EC:EHGGGIIB8?80?DDH>9?<FGCD	NH:i:5	HI:i:2	AS:i:47	nM:i:0
+HWI-C00113:131:HMHYWADXX:1:1211:14829:37922	272	1	17036	0	20M177N31M	*	0	0	TAGAAGTAGTTCTCTGGGACCTGCTGTTCCAGCTGCTCTCTCTTGCTGATG	@<@BDBFDFFHAFHFF@GIIIHECFHFGFHICFHFIIIIGIIEGFF<FHII	NH:i:7	HI:i:6	AS:i:49	nM:i:0
+HWI-C00113:131:HMHYWADXX:1:2216:19937:47046	16	1	17334	1	35M237N16M	*	0	0	CAGCCAGGGGGTCCAGGAAGACATACTTCTTCTACAGGTTCTCGGTGGTGT	CC@F?DA?FDHHHIIGI@DHHGGFHHHIIAG@F@GFHHGGHEHG7-;FEHE	NH:i:4	HI:i:1	AS:i:49	nM:i:0
+HWI-C00113:131:HMHYWADXX:1:1111:7653:49738	16	1	17336	1	33M237N18M	*	0	0	GCCAGGGGGTCCAGGAAGACATACTTCTTCTACAGGTTCTCGGTGGTGTTG	?8=4BDDDFDFFAGF@@GD?9?FBFDDDBDEFFIII?BDEFFI75F5;65C	NH:i:4	HI:i:1	AS:i:49	nM:i:0
+HWI-C00113:131:HMHYWADXX:2:2205:11163:47820	16	1	17336	1	33M237N18M	*	0	0	GCCAGGGGGTCCAGGAAGACATACTTCTTCTACAGGTTCTCGGTGGTGTTG	C@CFFFFFHHHHHJJJJIIJJJIJIJJJJJJJJJJJJJJJJJJGHIAGHII	NH:i:4	HI:i:1	AS:i:49	nM:i:0
+HWI-C00113:131:HMHYWADXX:1:2208:13311:23997	16	1	17340	1	29M237N22M	*	0	0	GGGGGTCCAGGAAGACATACTTCTTCTACAGGTTCTCGGTGGTGTTGAAGA	?@8AD?@D?F>DH?FHGHH@EHGIEHGGIIIGGHIGHGFDEHGH=FHGIIH	NH:i:3	HI:i:1	AS:i:49	nM:i:0
+HWI-C00113:131:HMHYWADXX:2:2207:3786:78354	16	1	17340	1	29M237N22M	*	0	0	GGGGGTCCAGGAAGACATACTTCTTCTACAGGTTCTCGGTGGTGTTGAAGA	CCCFFFFFHHHHHJJJJJIIJJJJJJJJJJJJHHIJIHHBFIHIIJJJJJI	NH:i:3	HI:i:1	AS:i:49	nM:i:0
+HWI-C00113:131:HMHYWADXX:1:1115:8438:81914	16	1	17341	1	28M237N23M	*	0	0	GGGGTCCAGGAAGACATACTTCTTCTACAGGTTCTCGGTGGTGTTGAAGAG	@@CFFFFDHH?HDGGHIIGIGHIGHGIDIIIFGIIGHHDG:?DFHEHIIII	NH:i:3	HI:i:1	AS:i:49	nM:i:0
+HWI-C00113:131:HMHYWADXX:2:1114:13486:49038	16	1	17341	1	28M237N23M	*	0	0	GGGGTCCAGGAAGACATACTTCTTCTACAGGTTCTCGGTGGTGTTGAAGAG	?@@:D@DDFHAFFHGGFHFHH@CCHIIIII@:CFGFGGC?D)?8DHHGCGI	NH:i:3	HI:i:1	AS:i:49	nM:i:0
diff --git a/tests/pysam_data/example_aligned_pairs.sam b/tests/pysam_data/example_aligned_pairs.sam
new file mode 100644
index 0000000..e6f9830
--- /dev/null
+++ b/tests/pysam_data/example_aligned_pairs.sam
@@ -0,0 +1,81 @@
+@HD	VN:1.0	GO:none	SO:coordinate
+@SQ	SN:chrM	LN:16571
+@SQ	SN:chr1	LN:249250621
+@SQ	SN:chr2	LN:243199373
+@SQ	SN:chr3	LN:198022430
+@SQ	SN:chr4	LN:191154276
+@SQ	SN:chr5	LN:180915260
+@SQ	SN:chr6	LN:171115067
+@SQ	SN:chr7	LN:159138663
+@SQ	SN:chr8	LN:146364022
+@SQ	SN:chr9	LN:141213431
+@SQ	SN:chr10	LN:135534747
+@SQ	SN:chr11	LN:135006516
+@SQ	SN:chr12	LN:133851895
+@SQ	SN:chr13	LN:115169878
+@SQ	SN:chr14	LN:107349540
+@SQ	SN:chr15	LN:102531392
+@SQ	SN:chr16	LN:90354753
+@SQ	SN:chr17	LN:81195210
+@SQ	SN:chr18	LN:78077248
+@SQ	SN:chr19	LN:59128983
+@SQ	SN:chr20	LN:63025520
+@SQ	SN:chr21	LN:48129895
+@SQ	SN:chr22	LN:51304566
+@SQ	SN:chrX	LN:155270560
+@SQ	SN:chrY	LN:59373566
+@RG	ID:FC1_NA12892_03	PL:ILLUMINA	SM:FC1_NA12892_03
+@PG	ID:bwa	PN:bwa	VN:0.7.7-isis-1.0.0
+@PG	ID:GATK IndelRealigner	VN:1.6-23-gf0210b3	CL:knownAlleles=[] targetIntervals=/data/scratch/workspace/RunFolder/Data/Intensities/BaseCalls/Alignment/FC1-NA12892-03_S1_chrM.intervals LODThresholdForCleaning=5.0 consensusDeterminationModel=USE_READS entropyThreshold=0.15 maxReadsInMemory=150000 maxIsizeForMovement=3000 maxPositionalMoveAllowed=200 maxConsensuses=30 maxReadsForConsensuses=120 maxReadsForRealignment=20000 noOriginalAlignmentTags=false nWayOut=null generate_nWayOut_md5s=false check_early=false noPGTag=false keepPGTags=false indelsFileForDebugging=null statisticsFileForDebugging=null SNPsFileForDebugging=null
+D0004:230:H08B1ADXX:1:1204:18619:71946	163	chr22	16084109	27	149M	=	16084228	268	GTGCAGGCATGGAGATTCTGGGGTGAATCTGCTGAGTTTAAAAGCTTCCTTTGGAGATGCCCCTGGCCCCCTCCACCTGTCAAGAAGAGGCCATCCTATCTGCCTGTCAAGAAGAGGCCATCCTGGGCAGCACAGTAGAGGCAAATGGC	BBBFFBFFFFFFFFFIFIFIFFI0BBFIFIIIIIFFFFIFIIIFFBIFIIIIFI<BFFFIIIIFFFFFFFFFFFFFFBBFBBFBFBBBBBFFFFBBBFFFFFFFBBBBBBBFFFFBBBFFFFFB<<7B<BBBBBFBFBFFFFBFFBBBB	MD:Z:149	RG:Z:FC1_NA12892_03	NM:i:0	MQ:i:27	AS:i:149	XS:i:149
+D0004:230:H08B1ADXX:2:2208:19052:44947	99	chr22	16084116	27	149M	=	16084172	205	CATGGAGATTCTGGGGTGAATCTGCTGAGTTTAAAAGCTTCCTTTGGAGATGCCCCTGGCCCCCTCCACCTGTCAAGAAGAGGCCATCCTATCTGCCTGTCAAGAAGAGGCCATCCTGGGCAGCACAGTAGAGGCAAATGGCCCAGATG	BBBFFFFFFFFFFIIIBFFFIIIIIIIFIFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFBFBFFFFFFFFFFFFFFFFFFFFFFFFBFFBFFFFBBFFBFFFFFFFB	MD:Z:149	RG:Z:FC1_NA12892_03	NM:i:0	MQ:i:27	AS:i:149	XS:i:149
+D0004:230:H08B1ADXX:2:2206:17383:92394	163	chr22	16084134	27	148M	=	16084223	236	AATCTGCTGAGTTTAAAGGCTTCCTTTGGAGATGCCCCTGGCCCCCTCCACCTGTCAAGAAGAGGCCATCCTATCTGCCTGTCAAGAAGAGGCCATCCTGGGCAGCACAGTAGAGGCAAATGGCCCAGATGCCTAGCTGAGGGCAAAC	BBBFFFBFFFFBFBFFI00BFBFFFFFIBBFF<FFIIIBFBFFIIIFIIII<BBFBFFFFIFIIFFFFBBBFFBBBF<BBBBBBBBB<BB<7<BBB<BBBBBBBBBBBBBB<BBBBBBB<0<<0<BBBBBBB<BBBBBBBBBB<BBBB	MD:Z:17A130	RG:Z:FC1_NA12892_03	NM:i:1	MQ:i:27	AS:i:143	XS:i:143
+D0004:230:H08B1ADXX:2:1116:18441:31081	163	chr22	16084162	45	147M	=	16084175	162	TAGATGCCCCTGGCCCTCTCCACCTGTCAAGAAGAGGCCATCCTATCTGCCTGCCAAGAAGAGGCCATCCTGGGCAGCACAGTAGAGGCAAATTGCCCAGATGCCTATCTGTGGGCAAACCTCCATGCCTGGAGGAGGAGGTCGCCT	'7'<B0'0<'7<<7B0'0<<BBBB<BB<<'7<<B<<BB<7<<<B<<<B'7<'<'07<<0777<BBB<BBB7<B<BB<<<<7770<<<<<<<70'07<<<'077<<<007<<'0<77<<<<<<<<<<<<<707<<<<<<7<7777<<7	MD:Z:0G15C36T39G13G3A35	RG:Z:FC1_NA12892_03	NM:i:6	MQ:i:48	AS:i:121	XS:i:117
+D0004:230:H08B1ADXX:1:2108:10243:19235	99	chr22	16084168	48	150M	=	16084274	254	CCCCTGGCCCCCTCCACCTGTCAAGAAGAGGCCATCCTATCTGCCTGTCAAGAAGAGGCCATCCTGGGCAGCACAGTAGAGGCAAATGGCCCAGATGCCTAGCTGAGGGCAAACCTCCATGCCTGGAGGAGGAGGTCGCCTCTGGGAGCA	BBBFFFFFFFFFFIIIIIFIIIIIFIIFFFFFIBFIIIIIIIIIIIIIIIIIIIFFFFIIIFFFFFFFFFFFFFFFBFFFFFFFFFFBBFFFFFFFFFFFBBBBFFFFFFFFFFBBFBFFFFFFFFFBFFBFFFF0BBBBFFBBBBBBF7	MD:Z:150	RG:Z:FC1_NA12892_03	NM:i:0	MQ:i:48	AS:i:150	XS:i:145
+D0004:230:H08B1ADXX:2:2208:19052:44947	147	chr22	16084172	27	150M	=	16084116	-205	TGGCCCCCTCCACCTGTCAAGAAGAGGCCATCCTATCTGCCTGTCAAGAAGAGGCCATCCTGGGCAGCACAGTAGAGGCAAATGGCCCAGATGCCTAGCTGAGGGCAAACCTCCATGCCTGGAGGAGGAGGTCGCCTCTGGGAGCAGGAG	7BFFFFFFFBB<FFFFFFFFFFFFBFFFBFFFFFBFFFFFFFFFFFFBBFFFFFFFBFFFFFFFFBBFBFFFFFFBFFFFFFFFFFFFFFFFFFFFFFFFIFFIFFFFBFFFIIFIFIIIIIIIIIIIIIIIFIIIIFFFFFFFFFFBBB	MD:Z:150	RG:Z:FC1_NA12892_03	NM:i:0	MQ:i:27	AS:i:150	XS:i:145
+D0004:230:H08B1ADXX:1:2203:19752:25713	99	chr22	16084173	27	150M	=	16084341	317	GGCCCCCTCCACCTGTCAAGAAGAGGCCATCCTATCTGCCTGTCAAGAAGAGGCCATCCTGGGCAGCACAGTAGAGGCAAATGGCCCAGATGCCTAGCTGAGGGCAAACCTCCATGCCTGGAGGAGGAGGTCGCCTCTGGGAGCAGGAGG	BBBFFFFFFFFFFIFIFFIIIIFIIIIIFFFFIIIIIIIIIIIFFFFFBFIFFFFIIIIIIFFFFFFFFFFFFBFFFFFFBFBFFFFFFBBBBFFFFFFFFFFFFBFFBBFFFFFBFFFFFBBBBBFFFB7BBBFBBBBFFFFFFFFFB<	MD:Z:150	RG:Z:FC1_NA12892_03	NM:i:0	MQ:i:27	AS:i:150	XS:i:145
+D0004:230:H08B1ADXX:2:1116:18441:31081	83	chr22	16084175	48	150M	=	16084162	-162	CCCCCTCCACCTGTCAAGAAGAGGCCATCCTATCTGCCTGTCAAGAAGAGGCCATCCTGGGCAGCACAGTAGAGGCAAATGGCCCAGATGCCTAGCTGAGGGCAAACCTCCATGCCTGGAGGAGGAGGTCGCCTCTGGGAGCAGGAGGAC	BFBFFBB<0BBFFFFFFFFFFFFBFFFFFFFFBFFFBFFBBBFFFFFFFFFFFBBFFFFFFFFBB<FFFFFFFFFFFBBBFFFFFBFFFFFFFBFFFFFIFFFFFFFFFIIIIIFFIIIIIIIIFIIIFBFIFFFIIFFFFFFFFFFBBB	MD:Z:150	RG:Z:FC1_NA12892_03	NM:i:0	MQ:i:45	AS:i:150	XS:i:145
+D0004:230:H08B1ADXX:2:2209:11952:24810	163	chr22	16084177	48	148M	=	16084258	230	CCCTCCACCTGTCAAGAAGAGGCCATCCTATCTGCCTGTCAAGAAGAGGACATCCTGGGCAGCACAGTAGAGGCAAATGGCCCAGATGCCTAGCTGAGGGCAAACCTCCATGCCTGGAGGAGGAGGTCGCCTCTGGGAGCAGGAGGAC	BBBBBBFFFFFFFFFBBFBFIIIBFFFBFBFFIIFFIFFIIIFFFF<FBBFFFFFFF<BBBBFFFFFFFFFFBFFFFFBBBBBBFFBBBB<B7<BB<BBBB7BBBBFBFFFFFFBB7BBBBBBB<77<<7<7<<<<7BBBBBBBB<BB	MD:Z:49C98	RG:Z:FC1_NA12892_03	NM:i:1	MQ:i:48	AS:i:143	XS:i:138
+D0004:230:H08B1ADXX:2:2203:3439:13375	99	chr22	16084178	48	147M	=	16084223	192	CCTCCACCTGTCAAGAAGAGGCCATCCTATCTGCCTGTCAAGAAGAGGCCATCCTGGGCAGCACAGTAGAGGCAAATGGCCCAGATGCCTAGCTGAGGGCAAACCTCCATGCCTGGAGGAGGAGGTCGCCTCTGGGAGCAGGAGGAC	BBBFFFFFFFFFFFIBFIIIIIIIIFFIFFFBFFFIIFFIIIIIFFFFFIFFFFFFFIIIIIIIIBFBBFFFFFFFBBBB<BBBFBBFFFFFFFBFFFBBFFFFFFBFBFBBBBBFFFBBFBFFB<BB<FFFBBFFFFFFFFFBBBB	MD:Z:147	RG:Z:FC1_NA12892_03	NM:i:0	MQ:i:48	AS:i:147	XS:i:142
+D0004:230:H08B1ADXX:1:2115:11464:79259	121	chr22	16084186	8	150M	=	16084186	0	TGTCAAGAAGAGGCCATCCTATCTGCCTGTCAAGAAGAGGCCATCCTGGGCAGCACAGTAGAGGCAAATGGCCCAGATGCCTAGCTGAGGGCAAACCTCCATGCCTGGAGGAGGAGGTCGCCTCTGGGAGCAGGAGGACCTGCTGGAACC	BFBBFFFFFFFFBFBFFBBFFFFFFFFFFFFFFFFFFFFFFBFFFFFFBFFBBBBFFFFFBFFBFFFFFFFBBFFFFFFFFFFFFFFFFFFFFB<FFFIIIIIIIIIIIIFFIFFFIIIIIIIFIIIIIIIFIIIIIFFFFFFFFFF<BB	MD:Z:150	RG:Z:FC1_NA12892_03	NM:i:0	AS:i:150	XS:i:145
+D0004:230:H08B1ADXX:2:2105:4479:40683	99	chr22	16084192	48	148M	=	16084244	201	GAAGAGGCCATCCTATCTGCCTGTCAAGAAGAGGCCATCCTGGGCAGCACAGTAGAGGCAAATGGCCCAGATGCCTAGCTGAGGGCAAACCTCCATGCCTGGAGGAGGAGGTCGCCTCTGGGAGCAGGAGGACCTGCTGGAACCCCTG	BBBFFFFFFFFFFIIIIIIIIIIFIIIIIIFIIFIFIFFIIIIIIIIIIIIIFFIIIIIIIIIIIFFFFFFFFFFFBFFFFFFFFBFFFFFFFFFFFFFFFFFFFFFFFFFBBBBFBBFFBFFBFFFFFFFFFFFBFFFFFBBBBFFF	MD:Z:148	RG:Z:FC1_NA12892_03	NM:i:0	MQ:i:48	AS:i:148	XS:i:143
+D0004:230:H08B1ADXX:1:1207:14702:88254	163	chr22	16084204	27	150M	=	16084382	327	CTATCTGCCTGTCAAGAAGAGGCCATCCTGGGCAGCACAGTAGAGGCAAATGGCCCAGATGCCTAGCTGAGGGCAAACCTCCATGCCTGGAGGAGGAGGTCGCCTCTGGGAGCAGGAGGACCTGCTGGAACCCCTGCTCACAGGCTCCTT	BBBFFFBFBFFFFB<FIIIBF0BB7FFBFFB7FFFFIIFIIIIFF<FBFF<<B<BFBBBBBBFBB<BF<<B<'07<<BB<B<<BBBB<BBBBB<<BBB<<77007<B<0<<<<<BB<<<'7<<<<B<<<BBB<BBBBBBBBBBBBBBBBB	MD:Z:150	RG:Z:FC1_NA12892_03	NM:i:0	MQ:i:27	AS:i:150	XS:i:145
+D0004:230:H08B1ADXX:1:2103:12875:91705	99	chr22	16084204	59	150M	=	16084223	166	CTGTCTGCCTGTCAAGAAGAGGCCATCCTGGGCAGCACATTAGAGGCAAATGGCCCAGATGCCTAGCTGAGGGCAAACCTCCATGCCTGGAGGAGGAGGTCGCCTCTGGGAGCAGGAGGACCTGCTGGAACCCCTGCTCACAGGCTCCTT	BBBFFB<FFFFFFIIIIFFFFFFFFFBFFFFFFFFIIBFFIIFIFIIIIIIIIIFIFIIIIIIIFFFFFBFFFFFFFFFFFFBBBBBFFFBBB<BBFBF7<7<B<BFF<BBFFFFFBBFFFFBBFFFFFFFFBFFBFFFBFBBFBBBFBF	MD:Z:2A36G110	RG:Z:FC1_NA12892_03	NM:i:2	MQ:i:48	AS:i:142	XS:i:133
+D0004:230:H08B1ADXX:2:2201:14140:86034	163	chr22	16084204	48	150M	=	16084281	226	CTATCTGCCTGTCAAGAAGAGGCCATCCTGGGCAGCACAGTAGAGGCAAATGGCCCAGATGCCTAGCTGAGGGCAAACCTCCATGCCTGGAGGAGGAGGCCGCCTCTGGGAGCAGGAGGACCTGCTGGAACCCCTGCTCACAGGCTCCTT	BBBFFF<BBFFF<<BBBF7<FBFF<<FFFBFBFBBFFIFFBFFB7B<FBF<70<<BBFF<BFFFB<BBBBBBF<BBBBBBBBB<<<BB<7777<B70070<<'7''0<<B'07B77BBBBBB<'<B<0<<<BBBBB<B<'<<BBB<<BBB	MD:Z:99T50	RG:Z:FC1_NA12892_03	NM:i:1	MQ:i:48	AS:i:145	XS:i:140
+D0004:230:H08B1ADXX:1:1106:14482:98700	99	chr22	16084207	57	7S141M	=	16084232	174	ACCCCTGTCTGCCTGTCAAGAAGAGGCCATCCTGGGCAGCACATTAGAGGCAAATGGCCCAGATGCCTAGCTGAGGGCAAACCTCCATGCCTGGAGGAGGAGGTCGCCTCTGGGAGCAGGAGGACCTGCTGGAACCCCTGCTCACAGG	<B7BFFFBFFBFFFIFI0BFFFFBB<FFBFIBFBFBFBFBFIIIIIFFIFFIIFFFBFFFFBFFF<BFFFFFFB<<77<7BBBBBBBBBBBBB700<777<77<BBBBBBBBB<BB<BB<BBB<BBBBBBBBBBBB<BB7BBB<BBBB	MD:Z:36G104	RG:Z:FC1_NA12892_03	NM:i:1	MQ:i:47	AS:i:136	XS:i:128
+D0004:230:H08B1ADXX:1:1115:10677:34277	1123	chr22	16084214	6	148M	=	16084265	200	GTCAAGAAGAGGCCATCCTGGGCAGCACATTAGAGGCAAATGGCCCAGATGCCTAGCTGAGGGCAAACCTCCATGCCTGGAGGAGGAGGTCGCCTCTGGGAGCAGGAGGACCTGCTGGAACCCCTGCTCACAGGCTCCTTTTCTTGCT	BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIFIIIIIIIIIIIIIIIFIIIIIIIIIIIIIIFFFFFFFFFFFFFFFFFFFFFFFFFF<BBFFFFFFFFFFFFFFFBBFFFFFFBFFFFBFFFFFBFFFFFFFFBBFBFFFFFFBFB	MD:Z:29G118	RG:Z:FC1_NA12892_03	NM:i:1	MQ:i:0	AS:i:143	XS:i:138
+D0004:230:H08B1ADXX:1:1115:16500:65098	99	chr22	16084214	8	148M	=	16084270	203	GTCAAGAAGAGGCCATCCTGGGCAGCACATTAGAGGCAAATGGCCCAGATGCCTAGCTGAGGGCAAACCTCCATGCCTGGAGGAGGAGGTCGCCTCTGGGAGCAGGAGGACCTGCTGGAACCCCTGCTCACAGGCTCCTTTTCTTGCT	BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFFFFFFFFFFFFFFFFFFFFFBFBBFBBFFFFFFFFFFBBFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFFBFFFF	MD:Z:29G118	RG:Z:FC1_NA12892_03	NM:i:1	MQ:i:0	AS:i:143	XS:i:138
+D0004:230:H08B1ADXX:1:2211:12618:19471	99	chr22	16084214	50	101M	=	16084214	100	GTCAAGAAGAGGCCATCCTGGGCAGCACAGTAGAGGCAAATGGCCCAGATGCCTAGCTGAGGGCAAACCTCCATGCCTGGAGGAGGAGGTCGCCTCTGGGA	BBBBBFFFFFFBFFFBFFFFIIIFFB7BFFFFFFIIIFIFFIBFFIIIFFFFFFFFFFFBFIIFFFBFFBBBFBBBBBBBBBB<7BBB<<BBBBBBF<B7B	MD:Z:101	RG:Z:FC1_NA12892_03	NM:i:0	MQ:i:50	AS:i:101	XS:i:96
+D0004:230:H08B1ADXX:2:2101:9743:53144	99	chr22	16084214	6	148M	=	16084265	200	GTCAAGAAGAGGCCATCCTGGGCAGCACATTAGAGGCAAATGGCCCAGATGCCTAGCTGAGGGCAAACCTCCATGCCTGGAGGAGGAGGTCGCCTCTGGGAGCAGGAGGACCTGCTGGAACCCCTGCTCACAGGCTCCTTTTCTTGCT	BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIFIIIIIIIIFIIIIIIIIIIIIIIIIIIIIIFFFFFFFFFFFFFFFFFFFFFFFFFFBBFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF	MD:Z:29G118	RG:Z:FC1_NA12892_03	NM:i:1	MQ:i:0	AS:i:143	XS:i:138
+D0004:230:H08B1ADXX:2:2104:16950:36967	163	chr22	16084214	48	148M	=	16084229	164	GTCAAGAAGAGGCCACCCTGGGCAGCACAGTAGAGGCAAATGGCCCAGATGCCTAGCTGAGGGCAAACCTCCATGCCTGGAGGAGGAGGTCGCCTCTGGGAGCAGGAGGACCTGCTGGAACCCCTGCTCACAGGCTCCTTTTCTTGCT	BBBFFF<00BFFFIFIBF<<<F<FIFIIIFFFFFFFFIIIB<FFFFIFIIFB7BFFBFBF<<FBFBBFBBBBBBBBBBBB<7B7BBBBB7B<BBBBBBBBBBBBBBBBBBBB7<BBBBBBBBBBBBB<<BBBB7<BBBBBBBB0BBBB	MD:Z:15T132	RG:Z:FC1_NA12892_03	NM:i:1	MQ:i:48	AS:i:143	XS:i:138
+D0004:230:H08B1ADXX:2:2201:15832:36778	99	chr22	16084214	48	148M	=	16084276	210	GTCAAGAAGAGGCCATCCTGGGCAGCACAGTAGAGGCAAATGGCCCAGATGCCTAGCTGAGGGCAAACCTCCATGCCTGGAGGAGGAGGTCGCCTCTGGGAGCAGGAGGACCTGCTGGAACCCCTGCTCACAGGCTCCTTTTCTTGCT	BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFFFFFFFFFFFFFFFFFFFFFFFFFFBBFFFFFFFFFFBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF	MD:Z:148	RG:Z:FC1_NA12892_03	NM:i:0	MQ:i:48	AS:i:148	XS:i:143
+D0004:230:H08B1ADXX:1:2211:12618:19471	147	chr22	16084214	50	101M	=	16084214	-100	GTCAAGAAGAGGCCATCCTGGGCAGCACAGTAGAGGCAAATGGCCCAGATGCCTAGCTGAGGGCAAACCTCCATGCCTGGAGGAGGAGGTCGCCTCTGGGA	B<B<BBBBFFBBBBFBFBBBBBB<B<FFFBFFFFFBBBB<BBB<BFFFFFFIFFFFF<FFFFBFFFBFBFFFBFBBFFFFIFFIFFFFFBFBFFFFF<BBB	MD:Z:101	RG:Z:FC1_NA12892_03	NM:i:0	MQ:i:50	AS:i:101	XS:i:96
+D0004:230:H08B1ADXX:2:1114:8448:83144	99	chr22	16084222	50	93M	=	16084230	92	GAGGCCACCCTGGGCAGCACAGTAGAGGCAAATGGCCCAGATGCCTAGCTGAGGGCAAACCTCCATGCCTGGAGGAGGAGGTCGCCTCTGGGA	BBBFFFFFFBFFFB<F<BBFFI<<BB<BBFBFF7<'<BBFBF7FF7B<BBFB707BBFB<BBBFFBFBFBBBBB<B<<BB<<B777<BBB'0<	MD:Z:7T85	RG:Z:FC1_NA12892_03	NM:i:1	MQ:i:48	AS:i:88	XS:i:83
+D0004:230:H08B1ADXX:1:2101:9549:86450	99	chr22	16084223	45	148M	=	16084303	228	AGGCCATCCTGGGCAGCACAGTAGAGGCAAATGGCCCAGATGCCTAGCTGAGGGCAAACCTCCATGCCTGGAGGAGGAGGTCGCCTCTGGGAGCAGGAGGACCTGCTGGAACCCCTGCTCACAGGCTCCTTTTCTTGCTCTCCAGCAC	BBBFFFFFFFFFFFIFIIIIIFFB<FFIFFFFIFFFFIFFFFFFFFIFIIIIIFFIIIIIBFFFFFFFFF<BB<<B<BFBBBBBBBFBF<7<B<BFBBB0BBBFBB<BBBBFFFBBBBF<B<BBBFBBBFFFFBBBBB<<BBBFFBBF	MD:Z:148	RG:Z:FC1_NA12892_03	NM:i:0	MQ:i:43	AS:i:148	XS:i:143
+D0004:230:H08B1ADXX:1:2103:12875:91705	147	chr22	16084223	48	148M	=	16084204	-166	AGGCCATCCTGGGCAGCACATTAGAGGCAAATGGCCCAGATGCCTAGCTGAGGGCAAACCTCCATGCCTGGAGGAGGAGGTCGCCTCTGGGAGCAGGAGGACCTGCTGGAACCCCTGCTCACAGGCTCCTTTTCTTGCTCTCCAGCAC	BBBBBB<BBBBBBBBBBBBBBBBBBBBFFBBBBBBBBBBBBBBBBBBBBBBBBBBBB7BB<BBBBBBBBBBBBBBBBBBBBBBFBBFFFFIFFFFFFFFFFFFF<BFFBFBIIIFFFFFBFFIFFIFBFFBIIFFB<FFFBFFFFBBB	MD:Z:20G127	RG:Z:FC1_NA12892_03	NM:i:1	MQ:i:59	AS:i:143	XS:i:138
+D0004:230:H08B1ADXX:2:2203:3439:13375	147	chr22	16084223	48	148M	=	16084178	-192	AGGCCATCCTGGGCAGCACAGTAGAGGCAAATGGCCCAGATGCCTAGCTGAGGGCAAACCTCCATGCCTGGAGGAGGAGGTCGCCTCTGGGAGCAGGAGGACCTGCTGGAACCCCTGCTCACAGGCTCCTTTTCTTGCTCTCCAGCAC	FFBBFFBFBBBBFFFBFFBBFFBFFFFB<FBFBFFFFFBBBFBFBBBFFFBBBFBFBFFBBFBFBBBFFFFFBBFBFFFFFFFFFFFFIIIIFIIFFIIIFFIIIIFFFFFBFBFFFFFFFIFIIIIFBFFFBFFFFFFFBFFFFBBB	MD:Z:148	RG:Z:FC1_NA12892_03	NM:i:0	MQ:i:48	AS:i:148	XS:i:143
+D0004:230:H08B1ADXX:2:2206:17383:92394	83	chr22	16084223	27	148M	=	16084134	-236	AGGCCATCCTGGGCAGCACAGTAGAGGCAAATGGCCCAGATGCCTAGCTGAGGGCAAACCTCCATGCCTGGAGGAGGAGGTCGCCTCTGGGAGCAGGAGGACCTGCTGGAACCCCTGCTCACAGGCTCCTTTTCTTGCTCTCCAGCAC	BBBBBBBBBBBBBBBBBFB<BBB<BBBFFBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB<BBBBBBBB<BB<BBBBBBB<BFFB<BBFIIIIFFFFFBBBFIIIFFFBB0FIFFB777BFFF<FIFFFFFF<FFBBFBFBFFFFBBB	MD:Z:148	RG:Z:FC1_NA12892_03	NM:i:0	MQ:i:27	AS:i:148	XS:i:143
+D0004:230:H08B1ADXX:1:1106:12402:15905	163	chr22	16084228	27	149M	=	16084425	344	ATCCTGGGCAGCACAGTAGAGGCAAATGGCCCAGATGCCTAGCTGAGGGCAAACCTCCATGCCTGGAGGAGGAGGTCGCCTCTGGGAGCAGGAGGACCTGCTGGAACCCCTGCTCACAGGCTCCTTTTCTTGCTCTCCAGCACCTCCTG	BBBFFFFFFFFFFIIIIIIFIIIIIIFIIIIIIIIIIIIIIFFIFIIIIIIIIIIFIIIIIIFFFFFFFFFFFFFBBFFFFFFBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFFFFFFFFF	MD:Z:149	RG:Z:FC1_NA12892_03	NM:i:0	MQ:i:27	AS:i:149	XS:i:144
+D0004:230:H08B1ADXX:1:1114:17248:48776	1187	chr22	16084228	27	149M	=	16084401	320	ATCCTGGGCAGCACAGTAGAGGCAAATGGCCCAGATGCCTAGCTGGGGGCAAACCTTCATGCCTGGAGGAGGAGGTCGCCTCTGGGAGCAGGAGGACCTGCTGGAACCCCTGCTCACAGGCTCCTTTTCTTGCTCTCCAGCACCTCCTG	BBBFFF<7F<BBBBBFB<<FF<FFFB0<BBBF7BB<<<B'BBF0B'7BFFF7F7<F'7<BBFFF<B<BBBB<7<B07<BBBBBBBBBB7BB7BB<BBBBB<<BB7<BBBBB<B<BBB<<BBBBBBBBBBBBBBBBBBBBB<BBBBBBBB	MD:Z:45A10C92	RG:Z:FC1_NA12892_03	NM:i:2	MQ:i:27	AS:i:139	XS:i:134
+D0004:230:H08B1ADXX:1:1207:13940:97014	163	chr22	16084228	27	149M	=	16084401	320	ATCCTGGGCAGCACAGTAGAGGCAAATGGCCCAGATGCCTAGCTGAGGGCAAACCTCCATGCCTGGAGGAGGAGGTCGCCTCTGGGAGCAGGAGGACCTGCTGGAACCCCTGCTCACAGGCTCCTTTTCTTGCTCTCCAGCACCTCCTG	BBBFFF77BFBFFFFBFFBFFFFFFFBFBFFFBBBFFFFFFBFFFFFFFFBFFFI<FFFFFFFFFFFFFB<<<'<BBBBBBB<<BBBBB<077B<BBBBBBBBBBBB<BBB0<B<BBB<BB<BBBBBBBBB<BBBBBBB<BBBBBBBBB	MD:Z:149	RG:Z:FC1_NA12892_03	NM:i:0	MQ:i:27	AS:i:149	XS:i:144
+D0004:230:H08B1ADXX:1:2202:6988:58967	99	chr22	16084228	48	149M	=	16084286	207	ATCCTGGGCAGCACAGTAGAGGCAAATGGCCCAGATGCCTAGCTGAGGGCAAACCTCCATGCCTGGAGGAGGAGGTCGCCTCTGGGAGCAGGAGGACCTGCTGGAACCCCTGCTCACAGGCTCCTTTTCTTGCTCTCCAGCACCTCCTG	BBBFFFFFFFFBFIIIFIIFFFIFIFBFFFIFFFIBBFFFFFBFBFBFBBFFFFFFBBBFFFFFFFFF<<<BBB<0<<7<BBBB<BBB7BBBB7<<<<BBBBBFBFBB7<BBBB<B<BB7B7BBBBBBFBF<<<<B<<BBB<7<B<B0<	MD:Z:149	RG:Z:FC1_NA12892_03	NM:i:0	MQ:i:48	AS:i:149	XS:i:144
+D0004:230:H08B1ADXX:2:1109:12526:35372	99	chr22	16084228	48	149M	=	16084262	180	ATCCTGGGCAGCACAGTAGAGGCAAATGGCCCAGATGCCTAGCTGAGGGCAAACCTCCATGCCTGGAGGAGGAGGTCGCCTCTGGGAGCAGGAGGACCTGCTGGAACCCCTGCTCACAGGCTCCTTTTCTTGCTCTCCAGCACCTCCTG	BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFFFFFFFFFFFFFBBBFFFFFFFBFFFFFBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFF	MD:Z:149	RG:Z:FC1_NA12892_03	NM:i:0	MQ:i:48	AS:i:149	XS:i:144
+D0004:230:H08B1ADXX:2:1114:10667:73443	163	chr22	16084228	48	149M	=	16084229	150	ATCCTGGGCAGCACAGTAGAGGCAAATGGCCCAGATGCCTAGCTGAGGGCAAACCTCCATGCCTGGAGGAGGAGGTCGCCTCTGGGAGCAGGAGGACCTGCTGGAACCCCTGCTCACAGGCTCCTTTTCTTGCTCTCCAGCACCTCCTG	BBBFFFFFFFFFFIIIIFIFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFFFIIFIIIIIIIFFFFFFFBBFB7<<BBFFFFFFBBFFFFFFFFFFFFBFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFBFFBBFFFFFBFFFFFFFFF	MD:Z:149	RG:Z:FC1_NA12892_03	NM:i:0	MQ:i:48	AS:i:149	XS:i:144
+D0004:230:H08B1ADXX:2:1212:17241:34552	99	chr22	16084228	48	149M	=	16084230	151	ATCCTGGGCAGCACATTAGAGGCAAATGGCCCAGATGCCTAGCTGAGGGCAAACCTCCATGCCTGGAGGAGGAGGTCGCCTCTGGGAGCAGGAGGACCTGCTGGAACCCCTGCTCACAGGCTCCTTTTCTTGCTCTCCAGCACCTCCTG	BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIFIIIIIIIIIIIIIIIIIIIIFFFFFFFFFFFFFBBFBFFFFFFBBFFFFFFFFFFFFFFFFBBFFFFFFFFFFFFFFFFBBFFFFFFFFFFFFFFFFFFFFFFFFFF	MD:Z:15G133	RG:Z:FC1_NA12892_03	NM:i:1	MQ:i:57	AS:i:144	XS:i:139
+D0004:230:H08B1ADXX:2:2103:6351:62666	163	chr22	16084228	48	143M	=	16084228	142	ATCCTGGGCAGCACATTAGAGGCAAATGGCCCAGATGCCTAGCTGAGGGCAAACCTCCATGCCTGGAGGAGGAGGTCGCCTCTGGGAGCAGGAGGACCTGCTGGAACCCCTGCTCACAGGCTCCTTTTCTTGCTCTCCAGCAC	BBBFBFFFFFFFFFIFFIFIIIFIIFIBFFIFFFIFFFFIIIFIIIFFFFFFFIIIIIIFIFFFFFFFFBBBFBF<B<BFFFBBFBBFFFFFFFFFFFFBBBBBFBFBBFBFFFFFFFFBBBBBBBBFFFFBBBBFFFFFFFB	MD:Z:15G127	RG:Z:FC1_NA12892_03	NM:i:1	MQ:i:48	AS:i:138	XS:i:133
+D0004:230:H08B1ADXX:2:2109:12183:35153	163	chr22	16084228	27	149M	=	16084372	293	ATCCTGGGCAGCACAGTAGAGGCAAATGGCCCAGATGCCTAGCTGAGGGCAAACCTCCATGCCTGGAGGAGGAGGTCGCCTCTGGGAGCAGGAGGACCTGCTGGAACCCCTGCTCACAGGCTCCTTTTCTTGCTCTCCAGCACCTCCTG	BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIFIIIIIIIIIIIIIIIIIIIIFFFFFFFFBFBBF<BFFFFFFFBFFFFFFFFFFFFFFFFFBFFFFBFFFFFFFFFFFFFFBFFFFBFFFFFFFFFFFFFFBFFFFBF	MD:Z:149	RG:Z:FC1_NA12892_03	NM:i:0	MQ:i:27	AS:i:149	XS:i:144
+D0004:230:H08B1ADXX:1:1204:18619:71946	83	chr22	16084228	27	150M	=	16084109	-268	ATCCTGGGCAGCACAGTAGAGGCAAATGGCCCAGATGCCTAGCTGAGGGCAAACCTCCATGCCTGGAGGAGGAGGTCGCCTCTGGGAGCAGGAGGACCTGCTGGAACCCCTGCTCACAGGCTCCTTTTCTTGCTCTCCAGCACCTCCTGC	0BBFFFFFBFFFFFFFBFFFFFFFFFFFBBBFFFFFFFFFFFFFFFBBFFFBBFBBFBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFIFFIIIIFFBIIIIIIIIBFFIFFIIIIIIIIIIIIIIIIIFFFBFFFFFFBBB	MD:Z:150	RG:Z:FC1_NA12892_03	NM:i:0	MQ:i:27	AS:i:150	XS:i:145
+D0004:230:H08B1ADXX:2:2103:6351:62666	83	chr22	16084228	48	143M	=	16084228	-142	ATCCTGGGCAGCACATTAGAGGCAAATGGCCCAGATGCCTAGCTGAGGGCAAACCTCCATGCCTGGAGGAGGAGGTCGCCTCTGGGAGCAGGAGGACCTGCTGGAACCCCTGCTCACAGGCTCCTTTTCTTGCTCTCCAGCAC	<BBBBBB<<<00<BB<BBBBBBF<<7BB70<BBBBB<<BBB<BBBBBB<0<00<<<BBBBBBBBB<BBBBBBBBBBBFBFF<FBFFBFBFFFFBFFFFFBFFBFB7FFBBFBIFFBBBBB7BFIFFFFFFFFFFFFFFFFBBB	MD:Z:15G127	RG:Z:FC1_NA12892_03	NM:i:1	MQ:i:48	AS:i:138	XS:i:133
+D0004:230:H08B1ADXX:2:1114:10667:73443	83	chr22	16084229	48	150M	=	16084228	-150	TCCTGGGCAGCACAGTAGAGGCAAATGGCCCAGATGCCTAGCTGAGGGCAAACCTCCATGCCTGGAGGAGGAGGTCGCCTCTGGGAGCAGGAGGACCTGCTGGAACCCCTGCTCACAGGCTCCTTTTCTTGCTCTCCAGCACCTCCTGCA	BFFFFFFBFFFFFFFFFFFFFFFBFFFFFBFFFFFFFFFFFFFFFFFFBFB<FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFIFIIIIIIIFFBIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFFFFFFFFFFBBB	MD:Z:150	RG:Z:FC1_NA12892_03	NM:i:0	MQ:i:48	AS:i:150	XS:i:145
+D0004:230:H08B1ADXX:2:2104:16950:36967	83	chr22	16084229	48	150M	=	16084214	-164	CCCTGGGCAGCACAGTAGAGGCAAATGGCCCAGATGCCTAGCTGAGGGCAAACCTCCATGCCTGGAGGAGGAGGTCGCCTCTGGGAGCAGGAGGACCTGCTGGAACCCCTGCTCACAGGCTCCTTTTCTTGCTCTCCAGCACCTCCTGCA	07<00BBBBB<<B<BBBBBBBBB<BBBBBBBBBBBBBBB<B<7<<BBB7B<7BBBBBBBBBBBBBBBB7007<<7BBB7BB<BFBBBBFB<FBFBFBBBFFFBB7FFFFF<FFBBFFFFBBFFFFBBFFFBBFFF<FFFFFFFFFFFBB<	MD:Z:0T149	RG:Z:FC1_NA12892_03	NM:i:1	MQ:i:48	AS:i:149	XS:i:144
+D0004:230:H08B1ADXX:2:1114:8448:83144	147	chr22	16084230	48	65S85M	=	16084222	-92	CCACCGAGACCTACACGTCTGTATTCGTCGGCAGCGTAAGAAGTGTATGAGAGTCCGGAGACCACCCTGGGCAGCACTGTAGAGGCAAATGCCCCAGATGCCTAGCTGAGGAAAAACCTCCATGCCTGGAGGAGGAGGACGCCTCTGGGA	'77777000'000'<7'<70''0'''7070<<<7000'000''BB<770000''7'007''0'77<7B<<BB<<B<7'<<<7'B<<<77<0'7'<BBBB<0<BBB<BB<<<'7BB<<7B<BBBBBBBBBB'BB<B<'0'<<00BBBB<<<	MD:Z:12A13G19G0C25T11	RG:Z:FC1_NA12892_03	NM:i:5	MQ:i:50	AS:i:60	XS:i:55
+D0004:230:H08B1ADXX:2:1212:17241:34552	147	chr22	16084230	57	150M	=	16084228	-151	CCTGGGCAGCACATTAGAGGCAAATGGCCCAGATGCCTAGCTGAGGGCAAACCTCCATGCCTGGAGGAGGAGGTCGCCTCTGGGAGCAGGAGGACCTGCTGGAACCCCTGCTCACAGGCTCCTTTTCTTGCTCTCCAGCACCTCCTGCAG	BBFFFFFBBFFFFFBBFFFFFFBFFFBFBBBFBFBFBFFFFFFFFFFBBBBFFBFFFFFFFFFFFFFFFFFFFFFBFBFFFFFFFFFFFFFFFFIIIIFIIFFFIIIFIFIIIFFFIIIIIIFIIIIIIIIIIIIIIFFFFFFFFFFBBB	MD:Z:13G136	RG:Z:FC1_NA12892_03	NM:i:1	MQ:i:48	AS:i:145	XS:i:137
+D0004:230:H08B1ADXX:1:1106:14482:98700	147	chr22	16084232	47	150M	=	16084207	-174	TGGGCAGCACATTAGAGGCAAATGGCCCAGATGCCTAGCTGAGGGCAAACCTCCATGCCTGGAGGAGGAGGTCGCCTCTGGGAGCAGGAGGCCCTGCTGGAACCCCTGCTCACAGGCTCCTTTTCTTGCTCTCCAGCACCTCCTGCAGGC	0B00BBBFBBFBBBBBBBFFBBBBBBBBB<BB7<BBBBBBBBB<0B<07BBB7B<<<BBB<<BBBBBB7777BB<0BBBBBBBBB<BBBB7'B<FBFFBB70<BFB<FFFFFF7FBB<<B00BBBFB7B0<00BB<FFFFBBFFBFFB<<	MD:Z:11G79A58	RG:Z:FC1_NA12892_03	NM:i:2	MQ:i:57	AS:i:140	XS:i:135
+D0004:230:H08B1ADXX:1:1211:1598:3784	99	chr22	16084233	22	150M	=	16084251	166	GGGCAGCACATTAGAGGCAAATGGCCCAGATGCCTAGCTGAGGGCAAACCTCCATGCCTGGAGGAGGAGGTCGCCTCTGGGAGCAGGAGGACCTGCTGGAACCCCTGCTCACAGGCTCCTTTTCTTGCTCTCCAGCACCTCCTGCAGGCA	B<BFFFFFFBBBFBBBFFBFFFB7B<0BBFBBFFFFBFFFBBFFFFFFFFFIIFBBFFF<FBBFFBFFFB7<BB<BBBBBBBBBB<0<B77<70<BBB<BBBBBBB0<BBBBB<BBBBBBB0<<BBBBBBBBBBBBBB0BBBBBBBBBB7	MD:Z:10G139	RG:Z:FC1_NA12892_03	NM:i:1	MQ:i:22	AS:i:145	XS:i:140
+D0004:230:H08B1ADXX:1:1213:6486:68134	99	chr22	16084233	27	150M	=	16084298	213	GGGCAGCACAGTAGAGGCAAATGGCCCAGATGCCTAGCTGAGGGCAAACCTCCATGCCTGGAGGAGGAGGTCGCCTCTGGGAGCAGGAGGACCTGCTGGAACCCCTGCTCACAGGCTCCTTTTCTTGCCCTCCAGCACCTCCTGCAGGCA	BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFFFFFFFFBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFBFFFFFFFFFFFFFF'''00070''007007000'0<'''	MD:Z:128T21	RG:Z:FC1_NA12892_03	NM:i:1	MQ:i:27	AS:i:145	XS:i:140
+D0004:230:H08B1ADXX:1:2113:18050:73868	99	chr22	16084233	48	148M	=	16084233	147	GGGCAGCACAGTAGAGGCAAATGGCCCAGATGCCTAGCTGAGGGCAAACCTCCATGCCTGGAGGAGGAGGTCGCCTCTGGGAGCAGGAGGACCTGCTGGAACCCCTGCTCACAGGCTCCTTTTCTTGCTCTCCAGCACCTCCTGCAGG	BBBFFBBFFFBFBBFIIBFBFB<BFFFBFFFIIIIFFFFIFFBFIIIIFFFFF<FFFFBBFBBBFBB<BB07<0<<BB<<B7<<B77BBBBBBBBB<<BBBBBBBBBBBBBBB<7BB00<BBBBBBBBBBB<BBBBBBBBBB<<<BB'	MD:Z:148	RG:Z:FC1_NA12892_03	NM:i:0	MQ:i:47	AS:i:148	XS:i:143
+D0004:230:H08B1ADXX:2:1106:17498:33865	99	chr22	16084233	48	150M	=	16084266	182	GGGCAGCACAGTAGAGGCAAATGGCCCAGATGCCTAGCTGAGGGCAAACCTCCATGCCTGGAGGAGGAGGTCGCCTCTGGGAGCAGGAGGACCTGCTGGAACCCCTGCTCACAGGCTCCTTTTCTTGCTCTCCAGCACCTCCTGCAGGCA	BBBFFFFFFFFFFIFIIIIIFIIIIIIIIIIIIIFIIIIFFIIIIIIIIFIIIIIIIIIIIIFF<FFFFF<BBBFFFFBFBFFFFFFFFBBBFFFBFFFFFFFFFBBFFFFFFFFFFBBFBBBFFFFBFBBFBFFFFFFBBFFFFFBFFB	MD:Z:150	RG:Z:FC1_NA12892_03	NM:i:0	MQ:i:48	AS:i:150	XS:i:145
+D0004:230:H08B1ADXX:2:2108:13049:6453	163	chr22	16084233	60	146M	=	16084233	145	GGGCAGCACAGTAGAGGCAAATGGCCCAGATGCCTAGCTGAGGGCAAACCTCCATGCCTGGAGGAGGAGGTCGCCTCTGGGAGCAGGAGGACCTGCTGGAACCCCTGCTCACAGGCTCCTTTTCTTGCTCTCCAGCACCTCCTGCA	BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIFIIIIIIIIIIIIIIIIIIIIIFFFFFFFF<BBFFBFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF	MD:Z:146	RG:Z:FC1_NA12892_03	NM:i:0	MQ:i:60	AS:i:146	XS:i:129
+D0004:230:H08B1ADXX:2:2113:10982:55029	163	chr22	16084233	27	150M	=	16084316	230	AGGCAGCACAGTAGAGGCAAATGGCCCAGATGCCTAGCTGAGGGCAAACCTCCATGCCTGGAGGAGGAGGTCGCTTCTGGGAGCAGGAGGACCTGCGGGAACGCCTGCTCACAGGCTCCTTTTCTTGCTCTCCAGCACCTCCTGCAGGCA	0<7BBB<BFFFFFFF<B<FFFB0000B'<BF7BBFBB'BF<7BFF'B77BB'07B<7B<BB<B0<BB<BB<<<<''7B<'7770BB<<07<BB'0B''7<BB'0<<BBBBBBBBBBBBB7<BBBBB<BBBBBBBBBB'0<'07BBB077'	MD:Z:0G73C21T5C47	RG:Z:FC1_NA12892_03	NM:i:4	MQ:i:27	AS:i:134	XS:i:129
+D0004:230:H08B1ADXX:1:2113:18050:73868	147	chr22	16084233	47	148M	=	16084233	-147	GGGCAGCACAGTAGAGGCAAATGGCCCAGATGCCTAGCTGAGGGCAAACCTCCATGCCTGGAGGAGGAGGTCGCCTCTGGGAGCAGGAGGACCTGCTGGAACCCCTGCTCACAGGCTCATTTTCTTGCTCTCCAGCACCTCCAGCAGG	77BBBB<BBBB<0BB<BBFBBBBBBBBBBBBBBBB<BBBBBBBB<0''7BB70<770<0BBBB<BBB<0<0770BB<B7B<B<BBBFF<'<FFBFFB<<B7<FFBFFBBBBBFFFBFBBFFFFFFFFF0BFB0<<B<BBBBB<<<<<B	MD:Z:118C23T5	RG:Z:FC1_NA12892_03	NM:i:2	MQ:i:48	AS:i:138	XS:i:133
+D0004:230:H08B1ADXX:2:2108:13049:6453	83	chr22	16084233	60	146M	=	16084233	-145	GGGCAGCACAGTAGAGGCAAATGGCCCAGATGCCTAGCTGAGGGCAAACCTCCATGCCTGGAGGAGGAGGTCGCCTCTGGGAGCAGGAGGACCTGCTGGAACCCCTGCTCACAGGCTCCTTTTCTTGCTCTCCAGCACCTCCTGCA	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFIFIIIIIIIIFBIIIIIIIIIIIIIFIIIIIIIIIIIIIIIIIIFFFFFFFFFFBBB	MD:Z:146	RG:Z:FC1_NA12892_03	NM:i:0	MQ:i:60	AS:i:146	XS:i:129
diff --git a/tests/pysam_data/example_btag.sam b/tests/pysam_data/example_btag.sam
new file mode 100644
index 0000000..2dd4990
--- /dev/null
+++ b/tests/pysam_data/example_btag.sam
@@ -0,0 +1,6 @@
+@SQ	LN:200000000	SN:chr1
+QW85I:468:729	0	chr1	156268499	63	140M15H	*	0	0	GTCCAGTCTCCTGTAATTCTTGGGCTTGACTAGGCTTCCGACAACCTGGAGGCATTGCTCTTTCAGGGTATACACTGCAGTGTGATGTTGGCAAAAACAGGCTGTCCATTAACATTGGAAGATGGCACAAACAATTCAGT	>>>>>>>====>=>>;:8,,((1*0536;;=<>;:;>>>>>>>>>>>>>>>>>>>><9=556.2<<<8===<<<9;9=>=>>>>>>>>>>>>>>>>.>>>===>>>>>>>4=>>==;<<896=>===<>>588-1.19<=	RG:Z:QW85I	PG:Z:tmap	MD:Z:140	NM:i:0	AS:i:140	FZ:B:S,100,1,91,0,7,101,0,201,96,204,0,0,87,109,0,7,97,112,1,12,78,197,0,7,100,95,101,202,0,6,0,1,186,0,84,0,244,0,0,324,0,107,195,101,113,0,102,0,104,3,0,101,1,0,212,6,0,0,1,0,74,1,11,0,196,2,197,103,0,108,98,2,7,0,1,2,194,0,180,0,108,0,203,104,16,5,205,0,0,0,1,1,100,98,0,0,204,6,0,79,0,0,101,7,109,90,265,1,27,10,109,102,9,0,292,0,110,0,0,102,112,0,0,84,100,103,2,81,126,0,2,90,0,15,96,15,1,0,2,0,107,92,0,0,101,3,98,15,102,13,116,116,90,93,198,0,0,0,199,92,26,495,100,5,0,100,5,209,0,92,107,90,0,0,0,0,109,194,7,94,200,0,40,197,0,11,0,0,112,110,6,4,200,28,0,196,0,203,1,129,0,0,1,0,94,0,1,0,107,5,201,3,3,100,0,121,0,7,0,1,105,306,3,86,8,183,0,12,163,17,83,22,0,0,1,8,109,103,0,0,295,0,200,16,172,3,16,182,3,11,0,0,223,111,103,0,5,225,0,95	XA:Z:map2-1	XS:i:53	XT:i:38	XF:i:1	XE:i:0
+QW85I:468:729	0	chr1	156268499	63	140M15H	*	0	0	GTCCAGTCTCCTGTAATTCTTGGGCTTGACTAGGCTTCCGACAACCTGGAGGCATTGCTCTTTCAGGGTATACACTGCAGTGTGATGTTGGCAAAAACAGGCTGTCCATTAACATTGGAAGATGGCACAAACAATTCAGT	>>>>>>>====>=>>;:8,,((1*0536;;=<>;:;>>>>>>>>>>>>>>>>>>>><9=556.2<<<8===<<<9;9=>=>>>>>>>>>>>>>>>>.>>>===>>>>>>>4=>>==;<<896=>===<>>588-1.19<=	RG:Z:QW85I	PG:Z:tmap	MD:Z:140	NM:i:0	AS:i:140	FZ:B:s,-100,200,-300,-400	XA:Z:map2-1	XS:i:53	XT:i:38	XF:i:1	XE:i:0
+QW85I:468:729	0	chr1	156268499	63	140M15H	*	0	0	GTCCAGTCTCCTGTAATTCTTGGGCTTGACTAGGCTTCCGACAACCTGGAGGCATTGCTCTTTCAGGGTATACACTGCAGTGTGATGTTGGCAAAAACAGGCTGTCCATTAACATTGGAAGATGGCACAAACAATTCAGT	>>>>>>>====>=>>;:8,,((1*0536;;=<>;:;>>>>>>>>>>>>>>>>>>>><9=556.2<<<8===<<<9;9=>=>>>>>>>>>>>>>>>>.>>>===>>>>>>>4=>>==;<<896=>===<>>588-1.19<=	RG:Z:QW85I	PG:Z:tmap	MD:Z:140	NM:i:0	AS:i:140	FZ:B:c,-100,12	XA:Z:map2-1	XS:i:53	XT:i:38	XF:i:1	XE:i:0
+QW85I:468:729	0	chr1	156268499	63	140M15H	*	0	0	GTCCAGTCTCCTGTAATTCTTGGGCTTGACTAGGCTTCCGACAACCTGGAGGCATTGCTCTTTCAGGGTATACACTGCAGTGTGATGTTGGCAAAAACAGGCTGTCCATTAACATTGGAAGATGGCACAAACAATTCAGT	>>>>>>>====>=>>;:8,,((1*0536;;=<>;:;>>>>>>>>>>>>>>>>>>>><9=556.2<<<8===<<<9;9=>=>>>>>>>>>>>>>>>>.>>>===>>>>>>>4=>>==;<<896=>===<>>588-1.19<=	RG:Z:QW85I	PG:Z:tmap	MD:Z:140	NM:i:0	AS:i:140	FZ:B:C,12,15	XA:Z:map2-1	XS:i:53	XT:i:38	XF:i:1	XE:i:0
+QW85I:468:729	0	chr1	156268499	63	140M15H	*	0	0	GTCCAGTCTCCTGTAATTCTTGGGCTTGACTAGGCTTCCGACAACCTGGAGGCATTGCTCTTTCAGGGTATACACTGCAGTGTGATGTTGGCAAAAACAGGCTGTCCATTAACATTGGAAGATGGCACAAACAATTCAGT	>>>>>>>====>=>>;:8,,((1*0536;;=<>;:;>>>>>>>>>>>>>>>>>>>><9=556.2<<<8===<<<9;9=>=>>>>>>>>>>>>>>>>.>>>===>>>>>>>4=>>==;<<896=>===<>>588-1.19<=	RG:Z:QW85I	PG:Z:tmap	MD:Z:140	NM:i:0	AS:i:140	FZ:B:f,-1.0,5.0,2.5	XA:Z:map2-1	XS:i:53	XT:i:38	XF:i:1 XE:i:0
diff --git a/tests/pysam_data/example_dash_in_chr.sam b/tests/pysam_data/example_dash_in_chr.sam
new file mode 100644
index 0000000..c2a0a1e
--- /dev/null
+++ b/tests/pysam_data/example_dash_in_chr.sam
@@ -0,0 +1,7 @@
+@HD	VN:1.0
+@SQ	SN:chr-1	LN:1575
+@SQ	SN:chr2	LN:1584
+@CO	this is a comment
+@CO	this is another comment
+read_28833_29006_6945	99	chr-1	33	20	10M1D25M	=	200	167	AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG	<<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<<	NM:i:1	RG:Z:L1	PG:Z:P1	XT:A:U
+read_28701_28881_323b	147	chr2	88	30	35M	=	500	412	ACCTATATCTTGGCCTTGGCCGATGCGGCCTTGCA	<<<<<;<<<<7;:<<<6;<<<<<<<<<<<<7<<<<	MF:i:18	RG:Z:L2	PG:Z:P2	XT:A:R
diff --git a/tests/pysam_data/example_empty_header.sam b/tests/pysam_data/example_empty_header.sam
new file mode 100644
index 0000000..b1a3ca5
--- /dev/null
+++ b/tests/pysam_data/example_empty_header.sam
@@ -0,0 +1,321 @@
+@SQ	SN:chr1	LN:1000
+XXX0000	0	chr1	100	170	171M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTC	*	AS:i:170	MS:i:50
+XXX0001	0	chr1	100	255	284M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGT	*	AS:i:283	MS:i:50
+XXX0002	0	chr1	100	205	206M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGA	*	AS:i:205	MS:i:50
+XXX0003	0	chr1	100	212	213M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCC	*	AS:i:212	MS:i:50
+XXX0004	0	chr1	100	208	209M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGG	*	AS:i:208	MS:i:50
+XXX0005	0	chr1	100	245	245M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGG	*	AS:i:245	MS:i:50
+XXX0006	0	chr1	100	251	251M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATC	*	AS:i:251	MS:i:50
+XXX0007	0	chr1	100	255	257M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAA	*	AS:i:257	MS:i:50
+XXX0008	0	chr1	100	255	285M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTT	*	AS:i:284	MS:i:50
+XXX0009	0	chr1	100	255	261M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTA	*	AS:i:261	MS:i:50
+XXX0010	0	chr1	100	255	289M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCG	*	AS:i:288	MS:i:50
+XXX0011	0	chr1	100	173	174M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCG	*	AS:i:173	MS:i:50
+XXX0012	0	chr1	100	255	265M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCC	*	AS:i:265	MS:i:50
+XXX0013	0	chr1	100	255	293M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATC	*	AS:i:292	MS:i:50
+XXX0014	0	chr1	100	166	167M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGA	*	AS:i:166	MS:i:50
+XXX0015	0	chr1	100	247	247M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAA	*	AS:i:247	MS:i:50
+XXX0016	0	chr1	100	255	295M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCA	*	AS:i:294	MS:i:50
+XXX0017	0	chr1	100	210	211M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTC	*	AS:i:210	MS:i:50
+XXX0018	0	chr1	100	235	236M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTG	*	AS:i:235	MS:i:50
+XXX0019	0	chr1	100	195	196M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCC	*	AS:i:195	MS:i:50
+XXX0020	0	chr1	100	178	179M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGG	*	AS:i:178	MS:i:50
+XXX0021	0	chr1	100	255	259M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGG	*	AS:i:259	MS:i:50
+XXX0022	0	chr1	100	238	239M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACT	*	AS:i:238	MS:i:50
+XXX0023	0	chr1	100	255	272M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCAC	*	AS:i:272	MS:i:50
+XXX0024	0	chr1	100	255	257M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAA	*	AS:i:257	MS:i:50
+XXX0025	0	chr1	100	255	268M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCA	*	AS:i:268	MS:i:50
+XXX0026	0	chr1	100	201	202M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGG	*	AS:i:201	MS:i:50
+XXX0027	0	chr1	100	180	181M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGT	*	AS:i:180	MS:i:50
+XXX0028	0	chr1	100	153	154M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCG	*	AS:i:153	MS:i:50
+XXX0029	0	chr1	100	255	280M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGA	*	AS:i:279	MS:i:50
+XXX0030	0	chr1	100	255	275M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCC	*	AS:i:274	MS:i:50
+XXX0031	0	chr1	100	255	259M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGG	*	AS:i:259	MS:i:50
+XXX0032	0	chr1	100	229	230M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCC	*	AS:i:229	MS:i:50
+XXX0033	0	chr1	100	229	230M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCC	*	AS:i:229	MS:i:50
+XXX0034	0	chr1	100	172	173M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGC	*	AS:i:172	MS:i:50
+XXX0035	0	chr1	100	246	246M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGA	*	AS:i:246	MS:i:50
+XXX0036	0	chr1	100	187	188M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACT	*	AS:i:187	MS:i:50
+XXX0037	0	chr1	100	189	190M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTG	*	AS:i:189	MS:i:50
+XXX0038	0	chr1	100	192	193M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTC	*	AS:i:192	MS:i:50
+XXX0039	0	chr1	100	221	222M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAA	*	AS:i:221	MS:i:50
+XXX0040	0	chr1	100	186	187M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCAC	*	AS:i:186	MS:i:50
+XXX0041	0	chr1	100	185	186M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCA	*	AS:i:185	MS:i:50
+XXX0042	0	chr1	100	255	299M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACT	*	AS:i:298	MS:i:50
+XXX0043	0	chr1	100	156	157M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTT	*	AS:i:156	MS:i:50
+XXX0044	0	chr1	100	255	270M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACC	*	AS:i:270	MS:i:50
+XXX0045	0	chr1	100	206	207M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGAC	*	AS:i:206	MS:i:50
+XXX0046	0	chr1	100	255	262M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAA	*	AS:i:262	MS:i:50
+XXX0047	0	chr1	100	249	249M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGA	*	AS:i:249	MS:i:50
+XXX0048	0	chr1	100	226	226M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGT	*	AS:i:226	MS:i:50
+XXX0049	0	chr1	100	233	234M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACG	*	AS:i:233	MS:i:50
+XXX0050	0	chr1	100	162	163M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGT	*	AS:i:162	MS:i:50
+XXX0051	0	chr1	100	242	242M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATA	*	AS:i:242	MS:i:50
+XXX0052	0	chr1	100	255	288M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCC	*	AS:i:287	MS:i:50
+XXX0053	0	chr1	100	255	267M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCC	*	AS:i:267	MS:i:50
+XXX0054	0	chr1	100	196	197M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCA	*	AS:i:196	MS:i:50
+XXX0055	0	chr1	100	236	237M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGA	*	AS:i:236	MS:i:50
+XXX0056	0	chr1	100	223	223M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAA	*	AS:i:223	MS:i:50
+XXX0057	0	chr1	100	171	172M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCG	*	AS:i:171	MS:i:50
+XXX0058	0	chr1	100	178	179M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGG	*	AS:i:178	MS:i:50
+XXX0059	0	chr1	100	255	269M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCAC	*	AS:i:269	MS:i:50
+XXX0060	0	chr1	100	195	196M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCC	*	AS:i:195	MS:i:50
+XXX0061	0	chr1	100	212	213M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCC	*	AS:i:212	MS:i:50
+XXX0062	0	chr1	100	255	258M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAG	*	AS:i:258	MS:i:50
+XXX0063	0	chr1	100	157	158M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTC	*	AS:i:157	MS:i:50
+XXX0064	0	chr1	100	173	174M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCG	*	AS:i:173	MS:i:50
+XXX0065	0	chr1	100	178	179M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGG	*	AS:i:178	MS:i:50
+XXX0066	0	chr1	100	186	187M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCAC	*	AS:i:186	MS:i:50
+XXX0067	0	chr1	100	255	290M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGG	*	AS:i:289	MS:i:50
+XXX0068	0	chr1	100	238	239M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACT	*	AS:i:238	MS:i:50
+XXX0069	0	chr1	100	176	177M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAG	*	AS:i:176	MS:i:50
+XXX0070	0	chr1	100	255	288M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCC	*	AS:i:287	MS:i:50
+XXX0071	0	chr1	100	206	207M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGAC	*	AS:i:206	MS:i:50
+XXX0072	0	chr1	100	224	224M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAA	*	AS:i:224	MS:i:50
+XXX0073	0	chr1	100	218	219M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTA	*	AS:i:218	MS:i:50
+XXX0074	0	chr1	100	237	238M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGAC	*	AS:i:237	MS:i:50
+XXX0075	0	chr1	100	250	250M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGAT	*	AS:i:250	MS:i:50
+XXX0076	0	chr1	100	255	265M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCC	*	AS:i:265	MS:i:50
+XXX0077	0	chr1	100	255	264M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGC	*	AS:i:264	MS:i:50
+XXX0078	0	chr1	100	242	242M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATA	*	AS:i:242	MS:i:50
+XXX0079	0	chr1	100	159	160M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTT	*	AS:i:159	MS:i:50
+XXX0080	0	chr1	100	248	248M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAG	*	AS:i:248	MS:i:50
+XXX0081	0	chr1	100	253	253M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCA	*	AS:i:253	MS:i:50
+XXX0082	0	chr1	100	199	200M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAA	*	AS:i:199	MS:i:50
+XXX0083	0	chr1	100	168	169M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATT	*	AS:i:168	MS:i:50
+XXX0084	0	chr1	100	249	249M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGA	*	AS:i:249	MS:i:50
+XXX0085	0	chr1	100	255	268M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCA	*	AS:i:268	MS:i:50
+XXX0086	0	chr1	100	255	298M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACAC	*	AS:i:297	MS:i:50
+XXX0087	0	chr1	100	229	230M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCC	*	AS:i:229	MS:i:50
+XXX0088	0	chr1	100	255	278M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCA	*	AS:i:277	MS:i:50
+XXX0089	0	chr1	100	198	199M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAA	*	AS:i:198	MS:i:50
+XXX0090	0	chr1	100	255	273M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACC	*	AS:i:272	MS:i:50
+XXX0091	0	chr1	100	182	183M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGA	*	AS:i:182	MS:i:50
+XXX0092	0	chr1	100	211	212M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCC	*	AS:i:211	MS:i:50
+XXX0093	0	chr1	100	207	208M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACG	*	AS:i:207	MS:i:50
+XXX0094	0	chr1	100	221	222M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAA	*	AS:i:221	MS:i:50
+XXX0095	0	chr1	100	177	178M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGG	*	AS:i:177	MS:i:50
+XXX0096	0	chr1	100	255	289M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCG	*	AS:i:288	MS:i:50
+XXX0097	0	chr1	100	255	276M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCT	*	AS:i:275	MS:i:50
+XXX0098	0	chr1	100	237	238M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGAC	*	AS:i:237	MS:i:50
+XXX0099	0	chr1	100	255	273M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACC	*	AS:i:272	MS:i:50
+XXX0100	0	chr1	100	255	264M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGC	*	AS:i:264	MS:i:50
+XXX0101	0	chr1	100	255	285M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTT	*	AS:i:284	MS:i:50
+XXX0102	0	chr1	100	233	234M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACG	*	AS:i:233	MS:i:50
+XXX0103	0	chr1	100	237	238M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGAC	*	AS:i:237	MS:i:50
+XXX0104	0	chr1	100	214	215M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCAT	*	AS:i:214	MS:i:50
+XXX0105	0	chr1	100	154	155M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGT	*	AS:i:154	MS:i:50
+XXX0106	0	chr1	100	181	182M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTG	*	AS:i:181	MS:i:50
+XXX0107	0	chr1	100	255	265M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCC	*	AS:i:265	MS:i:50
+XXX0108	0	chr1	100	255	259M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGG	*	AS:i:259	MS:i:50
+XXX0109	0	chr1	100	186	187M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCAC	*	AS:i:186	MS:i:50
+XXX0110	0	chr1	100	172	173M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGC	*	AS:i:172	MS:i:50
+XXX0111	0	chr1	100	155	156M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTT	*	AS:i:155	MS:i:50
+XXX0112	0	chr1	100	209	210M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGT	*	AS:i:209	MS:i:50
+XXX0113	0	chr1	100	255	257M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAA	*	AS:i:257	MS:i:50
+XXX0114	0	chr1	100	255	260M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGT	*	AS:i:260	MS:i:50
+XXX0115	0	chr1	100	195	196M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCC	*	AS:i:195	MS:i:50
+XXX0116	0	chr1	100	200	201M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAG	*	AS:i:200	MS:i:50
+XXX0117	0	chr1	100	255	271M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCA	*	AS:i:271	MS:i:50
+XXX0118	0	chr1	100	255	297M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACA	*	AS:i:296	MS:i:50
+XXX0119	0	chr1	100	163	164M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTA	*	AS:i:163	MS:i:50
+XXX0120	0	chr1	100	255	256M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGA	*	AS:i:256	MS:i:50
+XXX0121	0	chr1	100	255	284M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGT	*	AS:i:283	MS:i:50
+XXX0122	0	chr1	100	176	177M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAG	*	AS:i:176	MS:i:50
+XXX0123	0	chr1	100	251	251M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATC	*	AS:i:251	MS:i:50
+XXX0124	0	chr1	100	255	260M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGT	*	AS:i:260	MS:i:50
+XXX0125	0	chr1	100	255	285M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTT	*	AS:i:284	MS:i:50
+XXX0126	0	chr1	100	201	202M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGG	*	AS:i:201	MS:i:50
+XXX0127	0	chr1	100	165	166M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACG	*	AS:i:165	MS:i:50
+XXX0128	0	chr1	100	255	279M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAG	*	AS:i:278	MS:i:50
+XXX0129	0	chr1	100	165	166M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACG	*	AS:i:165	MS:i:50
+XXX0130	0	chr1	100	204	205M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGG	*	AS:i:204	MS:i:50
+XXX0131	0	chr1	100	199	200M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAA	*	AS:i:199	MS:i:50
+XXX0132	0	chr1	100	208	209M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGG	*	AS:i:208	MS:i:50
+XXX0133	0	chr1	100	209	210M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGT	*	AS:i:209	MS:i:50
+XXX0134	0	chr1	100	183	184M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGAT	*	AS:i:183	MS:i:50
+XXX0135	0	chr1	100	255	266M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCC	*	AS:i:266	MS:i:50
+XXX0136	0	chr1	100	255	293M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATC	*	AS:i:292	MS:i:50
+XXX0137	0	chr1	100	255	285M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTT	*	AS:i:284	MS:i:50
+XXX0138	0	chr1	100	219	220M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAG	*	AS:i:219	MS:i:50
+XXX0139	0	chr1	100	247	247M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAA	*	AS:i:247	MS:i:50
+XXX0140	0	chr1	100	192	193M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTC	*	AS:i:192	MS:i:50
+XXX0141	0	chr1	100	255	261M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTA	*	AS:i:261	MS:i:50
+XXX0142	0	chr1	100	212	213M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCC	*	AS:i:212	MS:i:50
+XXX0143	0	chr1	100	255	276M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCT	*	AS:i:275	MS:i:50
+XXX0144	0	chr1	100	177	178M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGG	*	AS:i:177	MS:i:50
+XXX0145	0	chr1	100	179	180M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGG	*	AS:i:179	MS:i:50
+XXX0146	0	chr1	100	255	263M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAG	*	AS:i:263	MS:i:50
+XXX0147	0	chr1	100	255	272M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCAC	*	AS:i:272	MS:i:50
+XXX0148	0	chr1	100	255	299M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACT	*	AS:i:298	MS:i:50
+XXX0149	0	chr1	100	255	274M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCC	*	AS:i:273	MS:i:50
+XXX0150	0	chr1	100	255	300M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTC	*	AS:i:299	MS:i:50
+XXX0151	0	chr1	100	157	158M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTC	*	AS:i:157	MS:i:50
+XXX0152	0	chr1	100	161	162M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTG	*	AS:i:161	MS:i:50
+XXX0153	0	chr1	100	202	203M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGC	*	AS:i:202	MS:i:50
+XXX0154	0	chr1	100	171	172M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCG	*	AS:i:171	MS:i:50
+XXX0155	0	chr1	100	183	184M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGAT	*	AS:i:183	MS:i:50
+XXX0156	0	chr1	100	255	286M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTG	*	AS:i:285	MS:i:50
+XXX0157	0	chr1	100	255	257M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAA	*	AS:i:257	MS:i:50
+XXX0158	0	chr1	100	255	275M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCC	*	AS:i:274	MS:i:50
+XXX0159	0	chr1	100	255	276M	*	0	0	CCTCTTTTATAGCAGCATGAACCCGTCGGTTTTAAACACGGTGTCAGCGGTGGCCTCGGAAGTATGGCCCATTCGCGAACGATGCCGTCCCTTTCAAGACACCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCT	*	AS:i:275	MS:i:50
+XXX0174	16	chr1	201	255	300M	*	0	0	CCTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:298	MS:i:50
+XXX0238	16	chr1	202	255	299M	*	0	0	CTGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:297	MS:i:50
+XXX0286	16	chr1	203	255	298M	*	0	0	TGAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:296	MS:i:50
+XXX0249	16	chr1	204	255	297M	*	0	0	GAGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:295	MS:i:50
+XXX0201	16	chr1	205	255	296M	*	0	0	AGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:294	MS:i:50
+XXX0225	16	chr1	205	255	296M	*	0	0	AGACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:294	MS:i:50
+XXX0265	16	chr1	206	255	295M	*	0	0	GACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:293	MS:i:50
+XXX0182	16	chr1	207	255	294M	*	0	0	ACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:292	MS:i:50
+XXX0275	16	chr1	207	255	294M	*	0	0	ACACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:292	MS:i:50
+XXX0168	16	chr1	209	255	292M	*	0	0	ACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:290	MS:i:50
+XXX0208	16	chr1	209	255	292M	*	0	0	ACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:290	MS:i:50
+XXX0264	16	chr1	209	255	292M	*	0	0	ACGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:290	MS:i:50
+XXX0258	16	chr1	210	255	291M	*	0	0	CGGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:289	MS:i:50
+XXX0226	16	chr1	211	255	290M	*	0	0	GGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:288	MS:i:50
+XXX0228	16	chr1	211	255	290M	*	0	0	GGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:288	MS:i:50
+XXX0263	16	chr1	211	255	290M	*	0	0	GGGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:288	MS:i:50
+XXX0205	16	chr1	212	255	289M	*	0	0	GGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:287	MS:i:50
+XXX0276	16	chr1	212	255	289M	*	0	0	GGATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:287	MS:i:50
+XXX0192	16	chr1	213	255	288M	*	0	0	GATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:286	MS:i:50
+XXX0298	16	chr1	213	255	288M	*	0	0	GATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:286	MS:i:50
+XXX0196	16	chr1	214	255	287M	*	0	0	ATCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:285	MS:i:50
+XXX0291	16	chr1	215	255	286M	*	0	0	TCTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:284	MS:i:50
+XXX0245	16	chr1	216	255	285M	*	0	0	CTTTATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:283	MS:i:50
+XXX0284	16	chr1	220	255	281M	*	0	0	ATCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:278	MS:i:50
+XXX0227	16	chr1	221	255	280M	*	0	0	TCGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:277	MS:i:50
+XXX0166	16	chr1	222	255	279M	*	0	0	CGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:276	MS:i:50
+XXX0294	16	chr1	222	255	279M	*	0	0	CGCCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:276	MS:i:50
+XXX0300	16	chr1	224	255	277M	*	0	0	CCCGTGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:274	MS:i:50
+XXX0212	16	chr1	228	255	273M	*	0	0	TGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:271	MS:i:50
+XXX0313	16	chr1	228	255	273M	*	0	0	TGAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:271	MS:i:50
+XXX0318	16	chr1	229	255	272M	*	0	0	GAGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:270	MS:i:50
+XXX0193	16	chr1	230	255	271M	*	0	0	AGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:268	MS:i:50
+XXX0315	16	chr1	230	255	271M	*	0	0	AGACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:268	MS:i:50
+XXX0211	16	chr1	231	255	270M	*	0	0	GACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:267	MS:i:50
+XXX0295	16	chr1	231	255	270M	*	0	0	GACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:267	MS:i:50
+XXX0235	16	chr1	232	255	269M	*	0	0	ACCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:266	MS:i:50
+XXX0170	16	chr1	233	255	268M	*	0	0	CCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:265	MS:i:50
+XXX0310	16	chr1	233	255	268M	*	0	0	CCCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:265	MS:i:50
+XXX0252	16	chr1	234	255	267M	*	0	0	CCACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:265	MS:i:50
+XXX0206	16	chr1	235	255	266M	*	0	0	CACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:264	MS:i:50
+XXX0223	16	chr1	236	255	265M	*	0	0	ACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:263	MS:i:50
+XXX0229	16	chr1	236	255	265M	*	0	0	ACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:263	MS:i:50
+XXX0268	16	chr1	236	255	265M	*	0	0	ACACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:263	MS:i:50
+XXX0189	16	chr1	237	255	264M	*	0	0	CACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:262	MS:i:50
+XXX0299	16	chr1	237	255	264M	*	0	0	CACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:262	MS:i:50
+XXX0316	16	chr1	238	255	263M	*	0	0	ACACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:261	MS:i:50
+XXX0224	16	chr1	239	255	262M	*	0	0	CACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:260	MS:i:50
+XXX0255	16	chr1	240	255	261M	*	0	0	ACCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:259	MS:i:50
+XXX0278	16	chr1	241	255	260M	*	0	0	CCACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:258	MS:i:50
+XXX0314	16	chr1	243	255	258M	*	0	0	ACGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:257	MS:i:50
+XXX0282	16	chr1	244	255	257M	*	0	0	CGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:256	MS:i:50
+XXX0311	16	chr1	244	255	257M	*	0	0	CGCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:256	MS:i:50
+XXX0176	16	chr1	245	255	256M	*	0	0	GCTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:255	MS:i:50
+XXX0188	16	chr1	246	254	255M	*	0	0	CTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:254	MS:i:50
+XXX0290	16	chr1	246	254	255M	*	0	0	CTTTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:254	MS:i:50
+XXX0187	16	chr1	248	252	253M	*	0	0	TTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:252	MS:i:50
+XXX0259	16	chr1	248	252	253M	*	0	0	TTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:252	MS:i:50
+XXX0292	16	chr1	248	252	253M	*	0	0	TTCCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:252	MS:i:50
+XXX0222	16	chr1	250	249	251M	*	0	0	CCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:249	MS:i:50
+XXX0256	16	chr1	250	249	251M	*	0	0	CCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:249	MS:i:50
+XXX0296	16	chr1	250	249	251M	*	0	0	CCCGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:249	MS:i:50
+XXX0281	16	chr1	252	248	249M	*	0	0	CGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:248	MS:i:50
+XXX0289	16	chr1	252	248	249M	*	0	0	CGTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:248	MS:i:50
+XXX0171	16	chr1	253	247	248M	*	0	0	GTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:247	MS:i:50
+XXX0181	16	chr1	253	247	248M	*	0	0	GTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:247	MS:i:50
+XXX0266	16	chr1	253	247	248M	*	0	0	GTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:247	MS:i:50
+XXX0319	16	chr1	253	247	248M	*	0	0	GTTTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:247	MS:i:50
+XXX0172	16	chr1	255	245	246M	*	0	0	TTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:245	MS:i:50
+XXX0317	16	chr1	255	245	246M	*	0	0	TTCTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:245	MS:i:50
+XXX0207	16	chr1	257	242	244M	*	0	0	CTTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:242	MS:i:50
+XXX0240	16	chr1	258	242	243M	*	0	0	TTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:242	MS:i:50
+XXX0246	16	chr1	258	242	243M	*	0	0	TTTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:242	MS:i:50
+XXX0203	16	chr1	259	240	242M	*	0	0	TTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:240	MS:i:50
+XXX0217	16	chr1	259	240	242M	*	0	0	TTGTACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:240	MS:i:50
+XXX0216	16	chr1	262	237	239M	*	0	0	TACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:237	MS:i:50
+XXX0230	16	chr1	262	237	239M	*	0	0	TACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:237	MS:i:50
+XXX0277	16	chr1	263	236	238M	*	0	0	ACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:236	MS:i:50
+XXX0308	16	chr1	263	236	238M	*	0	0	ACGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:236	MS:i:50
+XXX0288	16	chr1	264	235	237M	*	0	0	CGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:235	MS:i:50
+XXX0305	16	chr1	264	235	237M	*	0	0	CGATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:235	MS:i:50
+XXX0210	16	chr1	265	234	236M	*	0	0	GATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:234	MS:i:50
+XXX0164	16	chr1	266	233	235M	*	0	0	ATTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:233	MS:i:50
+XXX0221	16	chr1	267	232	234M	*	0	0	TTTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:232	MS:i:50
+XXX0163	16	chr1	268	231	233M	*	0	0	TTCGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:231	MS:i:50
+XXX0244	16	chr1	270	228	231M	*	0	0	CGCGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:228	MS:i:50
+XXX0237	16	chr1	272	226	229M	*	0	0	CGCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:226	MS:i:50
+XXX0178	16	chr1	273	226	228M	*	0	0	GCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:226	MS:i:50
+XXX0202	16	chr1	273	226	228M	*	0	0	GCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:226	MS:i:50
+XXX0236	16	chr1	273	226	228M	*	0	0	GCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:226	MS:i:50
+XXX0304	16	chr1	273	226	228M	*	0	0	GCAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:226	MS:i:50
+XXX0270	16	chr1	274	225	227M	*	0	0	CAGGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:225	MS:i:50
+XXX0161	16	chr1	276	223	225M	*	0	0	GGGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:223	MS:i:50
+XXX0287	16	chr1	277	222	224M	*	0	0	GGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:222	MS:i:50
+XXX0306	16	chr1	277	222	224M	*	0	0	GGGTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:222	MS:i:50
+XXX0173	16	chr1	279	220	222M	*	0	0	GTGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:220	MS:i:50
+XXX0269	16	chr1	280	219	221M	*	0	0	TGATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:219	MS:i:50
+XXX0303	16	chr1	282	216	219M	*	0	0	ATCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:216	MS:i:50
+XXX0220	16	chr1	283	215	218M	*	0	0	TCACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:215	MS:i:50
+XXX0219	16	chr1	284	214	217M	*	0	0	CACTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:214	MS:i:50
+XXX0177	16	chr1	286	212	215M	*	0	0	CTTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:212	MS:i:50
+XXX0257	16	chr1	287	211	214M	*	0	0	TTGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:211	MS:i:50
+XXX0241	16	chr1	288	210	213M	*	0	0	TGGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:210	MS:i:50
+XXX0167	16	chr1	289	209	212M	*	0	0	GGTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:209	MS:i:50
+XXX0261	16	chr1	290	208	211M	*	0	0	GTCTCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:208	MS:i:50
+XXX0312	16	chr1	293	205	208M	*	0	0	TCCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:205	MS:i:50
+XXX0272	16	chr1	294	204	207M	*	0	0	CCAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:204	MS:i:50
+XXX0253	16	chr1	295	203	206M	*	0	0	CAAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:203	MS:i:50
+XXX0254	16	chr1	296	202	205M	*	0	0	AAAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:202	MS:i:50
+XXX0307	16	chr1	297	201	204M	*	0	0	AAAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:201	MS:i:50
+XXX0169	16	chr1	298	200	203M	*	0	0	AAGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:200	MS:i:50
+XXX0232	16	chr1	299	199	202M	*	0	0	AGGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:199	MS:i:50
+XXX0195	16	chr1	300	198	201M	*	0	0	GGCGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:198	MS:i:50
+XXX0179	16	chr1	302	196	199M	*	0	0	CGGACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:196	MS:i:50
+XXX0160	16	chr1	305	193	196M	*	0	0	ACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:193	MS:i:50
+XXX0271	16	chr1	305	193	196M	*	0	0	ACGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:193	MS:i:50
+XXX0180	16	chr1	306	192	195M	*	0	0	CGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:192	MS:i:50
+XXX0185	16	chr1	306	192	195M	*	0	0	CGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:192	MS:i:50
+XXX0199	16	chr1	306	192	195M	*	0	0	CGGTCCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:192	MS:i:50
+XXX0191	16	chr1	310	188	191M	*	0	0	CCCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:188	MS:i:50
+XXX0250	16	chr1	311	187	190M	*	0	0	CCATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:187	MS:i:50
+XXX0273	16	chr1	312	186	189M	*	0	0	CATGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:186	MS:i:50
+XXX0239	16	chr1	314	184	187M	*	0	0	TGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:184	MS:i:50
+XXX0301	16	chr1	314	184	187M	*	0	0	TGTTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:184	MS:i:50
+XXX0197	16	chr1	316	182	185M	*	0	0	TTAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:182	MS:i:50
+XXX0260	16	chr1	317	181	184M	*	0	0	TAGAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:181	MS:i:50
+XXX0190	16	chr1	319	179	182M	*	0	0	GAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:179	MS:i:50
+XXX0309	16	chr1	319	179	182M	*	0	0	GAAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:179	MS:i:50
+XXX0285	16	chr1	320	178	181M	*	0	0	AAAAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:178	MS:i:50
+XXX0214	16	chr1	322	176	179M	*	0	0	AAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:176	MS:i:50
+XXX0279	16	chr1	322	176	179M	*	0	0	AAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:176	MS:i:50
+XXX0280	16	chr1	322	176	179M	*	0	0	AAGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:176	MS:i:50
+XXX0242	16	chr1	323	175	178M	*	0	0	AGTTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:175	MS:i:50
+XXX0213	16	chr1	325	173	176M	*	0	0	TTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:173	MS:i:50
+XXX0233	16	chr1	325	173	176M	*	0	0	TTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:173	MS:i:50
+XXX0297	16	chr1	325	173	176M	*	0	0	TTCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:173	MS:i:50
+XXX0183	16	chr1	326	172	175M	*	0	0	TCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:172	MS:i:50
+XXX0194	16	chr1	326	172	175M	*	0	0	TCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:172	MS:i:50
+XXX0283	16	chr1	326	172	175M	*	0	0	TCCCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:172	MS:i:50
+XXX0215	16	chr1	328	170	173M	*	0	0	CCTACGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:170	MS:i:50
+XXX0162	16	chr1	332	166	169M	*	0	0	CGTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:166	MS:i:50
+XXX0262	16	chr1	333	165	168M	*	0	0	GTGACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:165	MS:i:50
+XXX0200	16	chr1	335	163	166M	*	0	0	GACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:163	MS:i:50
+XXX0234	16	chr1	336	161	165M	*	0	0	ACTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:161	MS:i:50
+XXX0186	16	chr1	337	161	164M	*	0	0	CTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:161	MS:i:50
+XXX0218	16	chr1	337	161	164M	*	0	0	CTATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:161	MS:i:50
+XXX0248	16	chr1	338	160	163M	*	0	0	TATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:160	MS:i:50
+XXX0267	16	chr1	338	160	163M	*	0	0	TATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:160	MS:i:50
+XXX0247	16	chr1	339	158	162M	*	0	0	ATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:158	MS:i:50
+XXX0274	16	chr1	339	158	162M	*	0	0	ATATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:158	MS:i:50
+XXX0198	16	chr1	340	158	161M	*	0	0	TATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:158	MS:i:50
+XXX0251	16	chr1	340	158	161M	*	0	0	TATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:158	MS:i:50
+XXX0204	16	chr1	341	156	160M	*	0	0	ATGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:156	MS:i:50
+XXX0175	16	chr1	342	155	159M	*	0	0	TGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:155	MS:i:50
+XXX0209	16	chr1	342	155	159M	*	0	0	TGGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:155	MS:i:50
+XXX0243	16	chr1	343	154	158M	*	0	0	GGAAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:154	MS:i:50
+XXX0165	16	chr1	345	152	156M	*	0	0	AAGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:152	MS:i:50
+XXX0231	16	chr1	346	151	155M	*	0	0	AGATCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:151	MS:i:50
+XXX0293	16	chr1	349	148	152M	*	0	0	TCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:148	MS:i:50
+XXX0302	16	chr1	349	148	152M	*	0	0	TCCAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:148	MS:i:50
+XXX0184	16	chr1	351	146	150M	*	0	0	CAGGAAGGTAAGCCCCACCACCCCTCAGATCGTTGCCGGATCCACACTCAGCAACTCGGGCTTACCATAACCCCCGTAGATACTAGTCCCCGCCCGACGACAACAGTTTCTGAGATCCAAAAGCCGCCTCAAGGTGCAGACATAGGGCTA	*	AS:i:146	MS:i:50
diff --git a/tests/pysam_data/example_empty_with_header.sam b/tests/pysam_data/example_empty_with_header.sam
new file mode 100644
index 0000000..3764780
--- /dev/null
+++ b/tests/pysam_data/example_empty_with_header.sam
@@ -0,0 +1 @@
+@HD	VN:1.3	SO:coordinate
diff --git a/tests/pysam_data/example_reverse_complement.sam b/tests/pysam_data/example_reverse_complement.sam
new file mode 100644
index 0000000..795d19c
--- /dev/null
+++ b/tests/pysam_data/example_reverse_complement.sam
@@ -0,0 +1,28 @@
+@SQ	SN:chr1	LN:249250621
+@SQ	SN:chr10	LN:135534747
+@SQ	SN:chr11	LN:135006516
+@SQ	SN:chr12	LN:133851895
+@SQ	SN:chr13	LN:115169878
+@SQ	SN:chr14	LN:107349540
+@SQ	SN:chr15	LN:102531392
+@SQ	SN:chr16	LN:90354753
+@SQ	SN:chr17	LN:81195210
+@SQ	SN:chr18	LN:78077248
+@SQ	SN:chr19	LN:59128983
+@SQ	SN:chr2	LN:243199373
+@SQ	SN:chr20	LN:63025520
+@SQ	SN:chr21	LN:48129895
+@SQ	SN:chr22	LN:51304566
+@SQ	SN:chr3	LN:198022430
+@SQ	SN:chr4	LN:191154276
+@SQ	SN:chr5	LN:180915260
+@SQ	SN:chr6	LN:171115067
+@SQ	SN:chr7	LN:159138663
+@SQ	SN:chr8	LN:146364022
+@SQ	SN:chr9	LN:141213431
+@SQ	SN:chrM	LN:16571
+@SQ	SN:chrX	LN:155270560
+@SQ	SN:chrY	LN:59373566
+@PG	ID:bwa	PN:bwa	VN:0.7.12-r1039	CL:bwa mem /ifs/mirror/genomes/bwa-0.7.5a/hg19 both.fq
+chr22:25000000-25000500	0	chr22	25000000	60	501M	*	0	0	GCTCTGTGCCGCAAGGGTGGAAACTGTGAGAGACAGATTCCAACTCCACGTCTGGGTAGTAAGCATCCAGTCCAGGGCTGTAGGCAGTCCTGGGGAAGACGCCAGAGATCTGTGCATTCTCATATCGAGGGATAGCGACTCCAGGCTGGGGGCTGGCAGGGTAAGGGGTGGGTGGGTCCTGGGCTTACCCGCAGGTCTGCAGACTTCCTGGGGCCAGCTGACCTCGTAAAATCCCTTTTGTCTAAGCTTCAGTTTCCTGCCTGTGAATGGGGTTGGGGCTGTGCTCTGGTTTCACCCTTGTGGCTCTGGGGTTGTGGTGACAAAGCCATCAAGCTGGGTTGAAGGATTAACCAGGAAACTTCAGACTGGCTGCCGTGTCTACCTCTTCCTCATACTCCTCTCTCTGCTGCATCCTGGGAAGCTGCTCTGCTCAGCCTAAATGAGGCTCAGTTGTGTGTGTGCGCACGTGCTTGCACGTGTGTTGGAAGTGGGTGATACTGA	GCTCTGTGCCGCAAGGGTGGAAACTGTGAGAGACAGATTCCAACTCCACGTCTGGGTAGTAAGCATCCAGTCCAGGGCTGTAGGCAGTCCTGGGGAAGACGCCAGAGATCTGTGCATTCTCATATCGAGGGATAGCGACTCCAGGCTGGGGGCTGGCAGGGTAAGGGGTGGGTGGGTCCTGGGCTTACCCGCAGGTCTGCAGACTTCCTGGGGCCAGCTGACCTCGTAAAATCCCTTTTGTCTAAGCTTCAGTTTCCTGCCTGTGAATGGGGTTGGGGCTGTGCTCTGGTTTCACCCTTGTGGCTCTGGGGTTGTGGTGACAAAGCCATCAAGCTGGGTTGAAGGATTAACCAGGAAACTTCAGACTGGCTGCCGTGTCTACCTCTTCCTCATACTCCTCTCTCTGCTGCATCCTGGGAAGCTGCTCTGCTCAGCCTAAATGAGGCTCAGTTGTGTGTGTGCGCACGTGCTTGCACGTGTGTTGGAAGTGGGTGATACTGA	NM:i:0	MD:Z:501	AS:i:501	XS:i:343
+chr22:25000000-25000500	16	chr22	25000000	60	501M	*	0	0	GCTCTGTGCCGCAAGGGTGGAAACTGTGAGAGACAGATTCCAACTCCACGTCTGGGTAGTAAGCATCCAGTCCAGGGCTGTAGGCAGTCCTGGGGAAGACGCCAGAGATCTGTGCATTCTCATATCGAGGGATAGCGACTCCAGGCTGGGGGCTGGCAGGGTAAGGGGTGGGTGGGTCCTGGGCTTACCCGCAGGTCTGCAGACTTCCTGGGGCCAGCTGACCTCGTAAAATCCCTTTTGTCTAAGCTTCAGTTTCCTGCCTGTGAATGGGGTTGGGGCTGTGCTCTGGTTTCACCCTTGTGGCTCTGGGGTTGTGGTGACAAAGCCATCAAGCTGGGTTGAAGGATTAACCAGGAAACTTCAGACTGGCTGCCGTGTCTACCTCTTCCTCATACTCCTCTCTCTGCTGCATCCTGGGAAGCTGCTCTGCTCAGCCTAAATGAGGCTCAGTTGTGTGTGTGCGCACGTGCTTGCACGTGTGTTGGAAGTGGGTGATACTGA	CGAGACACGGCGTTCCCACCTTTGACACTCTCTGTCTAAGGTTGAGGTGCAGACCCATCATTCGTAGGTCAGGTCCCGACATCCGTCAGGACCCCTTCTGCGGTCTCTAGACACGTAAGAGTATAGCTCCCTATCGCTGAGGTCCGACCCCCGACCGTCCCATTCCCCACCCACCCAGGACCCGAATGGGCGTCCAGACGTCTGAAGGACCCCGGTCGACTGGAGCATTTTAGGGAAAACAGATTCGAAGTCAAAGGACGGACACTTACCCCAACCCCGACACGAGACCAAAGTGGGAACACCGAGACCCCAACACCACTGTTTCGGTAGTTCGACCCAACTTCCTAATTGGTCCTTTGAAGTCTGACCGACGGCACAGATGGAGAAGGAGTATGAGGAGAGAGACGACGTAGGACCCTTCGACGAGACGAGTCGGATTTACTCCGAGTCAACACACACACGCGTGCACGAACGTGCACACAACCTTCACCCACTATGACT	NM:i:0	MD:Z:501	AS:i:501	XS:i:343
diff --git a/tests/pysam_data/example_unmapped_reads_no_sq.sam b/tests/pysam_data/example_unmapped_reads_no_sq.sam
new file mode 100644
index 0000000..4d9f100
--- /dev/null
+++ b/tests/pysam_data/example_unmapped_reads_no_sq.sam
@@ -0,0 +1,3 @@
+@HD	VN:1.0
+read_28833_29006_6945	0	*	0	0	*	*	200	167	AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG	<<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<<
+read_28701_28881_323b	0	*	0	0	*	*	500	412	ACCTATATCTTGGCCTTGGCCGATGCGGCCTTGCA	<<<<<;<<<<7;:<<<6;<<<<<<<<<<<<7<<<<
diff --git a/tests/pysam_data/faidx_empty_seq.fq b/tests/pysam_data/faidx_empty_seq.fq
new file mode 100644
index 0000000..572bf2f
--- /dev/null
+++ b/tests/pysam_data/faidx_empty_seq.fq
@@ -0,0 +1,40 @@
+@HISEQ2500-10:332:HCWLKBCXX:1:1101:6834:72051:TCGCTGTG
+TACCTCTAAAGGGGAGCGCTTTGGA
++
+IBBBBBEEEEEEEEEEEEBBBBBII
+@HISEQ2500-10:332:HCWLKBCXX:1:1101:6822:72067:TCGCTGTG
+TGCTCTAGAATTACCACAGTTATGA
++
+@A<;BB<<0B<ABB??EEB?<<;CH
+@HISEQ2500-10:332:HCWLKBCXX:1:1101:6892:72120:TCGCTGTG
+TGCCGCCCCCGCCGCTCCCGTCCACTCTCGGA
++
+HBBBBBEEEEEEEEEEEEEEEEEEEBBBBBII
+@HISEQ2500-10:332:HCWLKBCXX:1:1101:6833:72134:TCGCTGTG
+TAACGCAGAGTACTAACCACTAGA
++
+I?BBBBEEEEEEDEEEB?B??BHH
+@HISEQ2500-10:332:HCWLKBCXX:1:1101:6907:72225:TCGCTGTG
+TAACGCAGAGTACTAACCACTATACGATCACGGCG
++
+IBBBBBEEEEEEEEEEEEEEEEEEEEEEEBBBBBI
+@HISEQ2500-10:332:HCWLKBCXX:1:1101:7089:72002:TCGCTGTG
+TCGCGCGTGCAGCCCCGGACATCGA
++
+<<0;;0BDDBDEB0>A0B?A?<BH1
+@HISEQ2500-10:332:HCWLKBCXX:1:1101:7094:72048:TCGCTGTG
+
++
+
+@HISEQ2500-10:332:HCWLKBCXX:1:1101:7152:72066:TCGCTGTG
+TAACCAGGAATCCTAACCGCTGA
++
+HBBBBBEEEEEEEEDDBBBBBII
+@HISEQ2500-10:332:HCWLKBCXX:1:1101:7138:72162:TCGCTGTG
+TGAGGAGGGGGGAACGGGGGGCGGGA
++
+EA0BB?BEEEB0EEBEEEAB??BBIH
+@HISEQ2500-10:332:HCWLKBCXX:1:1101:7188:72166:TCGCTGTG
+TGGCGAGAATTCTACCACTGAACCACCAATGCGA
++
+HBBBBBEEEEEEEEEEEEDEEEEEEEEB?BB?HD
diff --git a/tests/pysam_data/faidx_ex1.fa b/tests/pysam_data/faidx_ex1.fa
new file mode 100644
index 0000000..d16e255
--- /dev/null
+++ b/tests/pysam_data/faidx_ex1.fa
@@ -0,0 +1,6540 @@
+>B7_589:1:101:825:28
+GGGAACAGGGGGGTGCACTAATGCGCTCCACGCCC
+>B7_589:1:101:825:28
+TGTGTCCATGTACACACGCTGTCCTATGTACTTAT
+>B7_589:1:110:543:934
+AAGAATTGTAAAAGTCAAAATTAAAGTTCAATACT
+>B7_589:1:110:543:934
+ACAAGCCAGAAGAGATTGGATCTAATTTTTGGACT
+>B7_589:1:122:337:968
+ACAGGGGGCTGCGCGGTTTCCCATCATGAAGCACT
+>B7_589:1:122:337:968
+GCTTTACTGTCTAAACTATGAAGAGACTATTGCCA
+>B7_589:1:122:77:789
+ACTATATTTATGCTATTCAGTTCTAAATATAGAAA
+>B7_589:1:122:77:789
+GGACGCTGAAGAACTTTGATGCCCTCTTCTTCCAA
+>B7_589:1:168:69:249
+ATATGCTGTTTACAAGAAACTCATTAATAAAGACA
+>B7_589:1:168:69:249
+TTCAGCAAGAAGATATAACCATCCTACTAAATACA
+>B7_589:1:29:529:379
+CAGTTTCTGCCCCCAGCATGGTTGTACTGGGCAAT
+>B7_589:1:29:529:379
+GACTCTATCCCAAATTCCCAATTACGTCCTATCTT
+>B7_589:2:30:644:942
+TACCTAATTGGTACAATGTACAATATTCTGATGAT
+>B7_589:2:30:644:942
+TATATCAGATAAAGCACACTTTAAATCAACAACAG
+>B7_589:2:73:730:487
+AGGAAGAAAAGGTCTTTCAAAAGGTGATGTGTGTT
+>B7_589:2:73:730:487
+TAGCCATTTCTTTTGGCATTTGCCTTCAGACCCTA
+>B7_589:2:9:49:661
+TACACACAAAAGTACAAAACTCACAGGTTTTATAA
+>B7_589:2:9:49:661
+TGCTAAACTAAGCATCATAAATGAAGCGGAAATAA
+>B7_589:3:71:478:175
+ACAGAGCTTTCAAGAAGTATGAGATTATGTAAAGT
+>B7_589:3:71:478:175
+TAGACATCTAAATGAAAGAGGCTCAAAGAATGCCA
+>B7_589:3:82:13:897
+ATACAGTCATCTATAAAGGAAATCCCAGCAGAATA
+>B7_589:3:82:13:897
+CATAAATGAAGGGGAAATAAAGTCAAGTCTTTCCT
+>B7_589:4:54:989:654
+ACTTATCATGACTCTATCCCAAATTCCCAATTACG
+>B7_589:4:54:989:654
+TCCCTGCCCCATCTCTTGTAATCTCTCTCCTTTTT
+>B7_589:5:147:405:738
+AGGGATTAAATTCCCCCACTTAAGAGATATAGATT
+>B7_589:5:147:405:738
+ATCAGATAAAGCACACTTTAAATCAACAACAGTAA
+>B7_589:5:198:564:731
+ACAAAGGAGGTCATCATACAATGATAAAAAGATCA
+>B7_589:5:198:564:731
+ATAGATTGGCAGAACAGATTTAAAAACATGAACTA
+>B7_589:5:50:950:562
+CTATTTTTGTCTTGACACCCTACTAATATTTGTCT
+>B7_589:5:50:950:562
+GCCCCATCTCTTGTAATCTCTCTCCTTTTTGCTGC
+>B7_589:5:68:440:424
+ACACTTTAAATCAACAACAGTAAAATAAAACAAAG
+>B7_589:5:68:440:424
+TGGTACAATGTACAATATTCTGATGATGGTTACAC
+>B7_589:6:108:958:42
+AAAGTACAAAACTCACAGGTTTTATAAAACAATTA
+>B7_589:6:108:958:42
+TATGCCCTGCTAAACTAAGCATCATAAATGAAGGG
+>B7_589:6:114:714:317
+AACCCCAGGGAATTTGTCAATGTCAGGGAAGGAGC
+>B7_589:6:114:714:317
+TGCCAGCACAGGGGCTTAACCTCTGGTGACTGCCA
+>B7_589:6:120:14:944
+CAAAAGGTGATGTGTGTTCTCATCAACCTCATACA
+>B7_589:6:120:14:944
+CAAAGATGAAACGCGTAACTGCGCTCTCATTCACT
+>B7_589:6:33:356:636
+TTTTTTTCTTTTCTCTTTTTTTTTTTTTTTTTTTT
+>B7_589:7:112:203:90
+CCTGTCACCCAATGGACCTGTGATATCTGGATTCT
+>B7_589:7:112:203:90
+CTTGAGAACCCCAGGGAATTTGTCAATGTCAGGGA
+>B7_589:7:154:26:712
+ATTGAGACTACAGAGCAACTAGGTAAAAAATTAAC
+>B7_589:7:154:26:712
+TTAATAAAGACATGAGTTCAGGTAAAGGGGTGGAA
+>B7_589:7:72:916:763
+CTGTCTTCCTCTGTCTTGATTTACTTGTTGTTGGT
+>B7_589:7:72:916:763
+GTCCTATCTTCTTCTTAGGGAAGAACAGCTTAGGT
+>B7_589:7:76:306:561
+GGTGGAAAAAGATGTTCTACGCAAACAGAAACCAA
+>B7_589:7:76:306:561
+TACAGAGCAACTAGGTAAAAAATTAACATTACAAC
+>B7_589:7:93:634:323
+CTTAAAGAAAAAAAAACCTGTCAAACACGAATGTT
+>B7_589:7:93:634:323
+TAAAGTTCAATACTCACCATCATAAATACACACAA
+>B7_589:8:113:968:19
+GAAAACTATATTTATGCTATTCAGTTCTAAATATA
+>B7_589:8:118:829:36
+AGTATTGGTAAAGATGTGGGGAAAAAAGTAAACTC
+>B7_589:8:118:829:36
+TAATTGGTACAATGTACAATATTCTGATGATGGTT
+>B7_589:8:139:727:808
+AAGTAAATAAAACACATAGCTAAAACTAAAAAAGC
+>B7_589:8:139:727:808
+ACAAATACTACTAGACCTAAGAGGGATGAGAAATT
+>B7_589:8:157:935:374
+CAGTTACCAAATGTGTTTATTACCAGAGGGATGGA
+>B7_589:8:157:935:374
+TCTTCATCCTGGACCCTGAGAGATTCTGCAGCCCA
+>B7_589:8:2:434:715
+AGAGAGAACTTCCCTGGAGGTCTGATGGCGTTTCT
+>B7_589:8:2:434:715
+CTTGTTGTTGGTTTTCTGTTTCTTTGTTTGATTTT
+>B7_589:8:74:674:124
+CACTGAACTTCCACGTCTCATCTAGGGGAACAGGG
+>B7_589:8:74:674:124
+TTCTTATCTGCACATTACTACCCTGCAATTAATAT
+>B7_591:1:191:462:705
+CAGATCCAGATTGCTTGTGGTCTGACAGGCTGCAAC
+>B7_591:1:191:462:705
+CATCCCTGTCTTACTTCCAGCTCCCCAGAGGGAAAG
+>B7_591:1:60:837:923
+CATCAACCGCATACACTCACATGGTTTAGGGGTATA
+>B7_591:1:60:837:923
+TTCACGCCAGCTCCCTGTCACCCAATGGACCTCTGA
+>B7_591:2:123:924:645
+TATATCAGATAAAGCACACTTTAAATCAACAACAGT
+>B7_591:2:123:924:645
+TGAATAAAAAGGGATTAAATTCCCCCACTTAAGAGA
+>B7_591:2:134:868:252
+AAGAACTTTGATGCCCTCTTCTTCCAAAGATGAAAC
+>B7_591:2:134:868:252
+ATGAACAACAGGAAGAAAAGGTCTTTCAAAAGGTGA
+>B7_591:2:13:100:876
+ACAGGGATTCCTGAGGAAAAAGAAAAAGTGAGAAGT
+>B7_591:2:13:100:876
+AGAATATATAAAGTCAACATGAAGGAAAAAAATTCT
+>B7_591:2:223:583:968
+AATATAGTTGAAAGCTCTAACAATAGACTAAACCAA
+>B7_591:2:223:583:968
+TATGAGGCACAGGTATTCCTGAGGAAAAAGAAAAAG
+>B7_591:2:240:603:890
+GCTCCCAAGAGGGAAAGCTTTCAACGCTTCTAGCCA
+>B7_591:2:240:603:890
+TCACAATGAACAACAGGAAGAAAAGGTCTTTCAAAA
+>B7_591:2:279:124:41
+GAATTAACCCAGTCAGACAAAAANNAAGAAAAAAGA
+>B7_591:2:279:124:41
+GCTAGAGATTTAGACATCTAAATGAAAGAGGCTCAA
+>B7_591:2:27:280:592
+AATAACAATGGGCTTCTCAGCGGAAACCTTACAAGC
+>B7_591:2:27:280:592
+AGAGATTTAGACATCTAAATGAAAGAGGCTCAAAGA
+>B7_591:2:309:798:997
+TTTTTTTTTTTTTTTTTTCTCTTTTTTTTTTTTTTT
+>B7_591:2:323:639:311
+AAGCCGTTCTATTTGTAATGAAAACTATATTTAGGC
+>B7_591:2:323:639:311
+TACCAAATGTGTTTATTACCAGAGGGATGGAGGGAA
+>B7_591:2:46:220:58
+CAAATCTGCGCTTGTACTTCTAAATCTATAAAAAAA
+>B7_591:2:46:220:58
+TTCCACTTTGGAAAACAATTTGGTAATTTCGTTTTT
+>B7_591:3:168:69:605
+TACCCGAGGGATGGAGGGTAGAGGGACGCTGAAGTG
+>B7_591:3:168:69:605
+TCTGACAGGCGGCAACTGTGAGCCATCACAATGAAC
+>B7_591:3:179:496:161
+AAAAACATGAACTAACTATATGCTGTTTACAAGAAA
+>B7_591:3:179:496:161
+AAGTACAAAACTCACAGGTTTTATAAAACAATTAAT
+>B7_591:3:277:458:330
+AATGTCAGGGAAGGAGCCTTTTGTCAGTTACCAAAT
+>B7_591:3:277:458:330
+TGATATCTGGATTCTGGGAAATTCTTCATCCTGGAC
+>B7_591:3:291:404:199
+TATAAAACAATTAATTGAGACTACAGAGCAACTAGG
+>B7_591:3:291:404:199
+TGAAGGGGAAATAAAGTCAAGTCTTTCCTGACAAGC
+>B7_591:3:305:565:952
+GTCCGTGTCCTCCCATCTGGCCTCGTCCACACTGGT
+>B7_591:3:305:565:952
+TAATACTATGTTTCTTATCTGCACATTACTACCCTG
+>B7_591:3:45:294:380
+ATAATTGTGTCCATGTACACACGATGTCATATGTAC
+>B7_591:3:45:294:380
+CCTCGTCCACACTGGTTCGCTTGAAAGCTTGGGCTG
+>B7_591:4:103:111:720
+CAGTTACCAAATGTGTTTATTACCAGAGGGATGGAG
+>B7_591:4:103:111:720
+TCTTCATCCTGGACCCTGAGAGATTCTGCAGCCCAG
+>B7_591:4:159:508:571
+CAAAACCTCATATATCAATATTAACTTTGAATAAAA
+>B7_591:4:159:508:571
+TGGAAAAAGATGTTCTACGCAAACAGAAACCAAATG
+>B7_591:4:216:650:516
+GAACAGCTTAGGTATCAATTTGGTGTTCTGTGTAAA
+>B7_591:4:216:650:516
+TTTTTGCTGCATCCCTGTCTTCCTCTGTCTTGATTT
+>B7_591:4:329:339:408
+CAATCCAGAAGAGATTGGATCTAATTTTTGGACTTC
+>B7_591:4:329:339:408
+TAAATGAAAGAGGCTCAAAGAATGCCAGGAAGATAC
+>B7_591:4:92:411:955
+GGTAAAGGGGTGGAAAAAGATGTTCTACGCAAACAG
+>B7_591:4:92:411:955
+TACTAAATACATATGCACCTAACACAAGACTACCCA
+>B7_591:5:124:978:501
+AATTTGGTAATTTCGTTTTTTTTTTTTTCTTTTCTC
+>B7_591:5:124:978:501
+ATGTAACAAATCTGCGCTTGTACTTCTAAATCTATA
+>B7_591:5:134:751:831
+AGCTCCCTGTCACCCAATGGACCTGTGATATCTGGA
+>B7_591:5:134:751:831
+ATACACACACATGGTTTAGGGGTATAATACCTCTAC
+>B7_591:5:243:557:560
+AAAGAGGCTCAAAGAATGCCAGGAAGATACATTGCA
+>B7_591:5:243:557:560
+CTAAGCAGAAACCTTACAAGCCAGAAGAGATTGGAT
+>B7_591:5:254:542:848
+CCAAGCAGAAGAAAGAGGTTCAGAACTTGAAGACAA
+>B7_591:5:254:542:848
+CTGAGGAAAAAGAAAAAGTGAGAAGTTTGGAAAAAC
+>B7_591:5:289:132:526
+CACCCGGTCCCTGCCCCATCTCTTGTAATCTCTCTC
+>B7_591:5:289:132:526
+TCTATTTTTGTCTTGACACCCAACTAATATTTGTCT
+>B7_591:5:42:540:501
+CTATATTTATGCTATTCAGTTCTAAATATAGAAATT
+>B7_591:5:90:828:633
+CTGCAGCCCAGATCCAGATTGCTTGTGGTCTGACAG
+>B7_591:5:90:828:633
+GGATGGAGGGAAGAGGGACGCTGAAGAACTTTGATG
+>B7_591:6:11:646:628
+GTACTTATCATGACTCTATCCCAAATTCCCAATTAC
+>B7_591:6:11:646:628
+TTCTGCCCCCAGCATGGTTGTACTGGGCAATACATG
+>B7_591:6:155:12:674
+CTATATTTATGCTATTCAGTTCTAAATATAGAAATT
+>B7_591:6:181:191:418
+AAACTATATTTATGCTATTCAGTTCTAAATATAGAA
+>B7_591:6:181:191:418
+AGGGAAGAGGGACGCTGAAGAACTTTGATGCCCTCT
+>B7_591:6:190:42:671
+TATTGCCAGATGAACCACACATTAATACTATGTTTC
+>B7_591:6:190:42:671
+TGTGTAAAGTCTCAGGGAGCCGTCCGTGTCCTCCCA
+>B7_591:6:29:575:453
+TACTACCCTGCAATTAATATAATTGTGTCCATTTAC
+>B7_591:6:29:575:453
+TCTGGCCTCGTCCACACTGGTTCTCTTGAAAGCTTG
+>B7_591:7:116:814:89
+ACTATGCTAAGTATTGGTAAAGATGTGGGGAAAAAA
+>B7_591:7:116:814:89
+CCTAATTGGTACAATGTACAATATTCTGATGATGGT
+>B7_591:7:129:956:115
+AGTTTCTGCCCCCAGCATGGTTGTACTGGGCAATAC
+>B7_591:7:129:956:115
+GCTCCCCAGAGGGAAAGCTTTCAACGCTTCTAGCCA
+>B7_591:7:157:447:758
+AAAGATGTTCTACGCAAACAGAAACCAAATGAGAGA
+>B7_591:7:157:447:758
+ACAAAACCTCATATATCAATATTAACTTTGAATAAA
+>B7_591:7:200:192:373
+AGTGCCTTTGTTCACATAGACCCCCTTGCAACAACC
+>B7_591:7:200:192:373
+CTCTCATTCACTCCAGCTCCCTGTCACCCAATGGAC
+>B7_591:7:22:632:176
+AAAGGAGGTCATCATACAATGATAAAAAGATCAATT
+>B7_591:7:22:632:176
+AGATATAGATTGGCAGAACAGATTTAAAAACATGAA
+>B7_591:7:68:242:834
+AAATAAAAAAGCAAAAACAAAAACTATGCTAAGTAT
+>B7_591:7:68:242:834
+TACTACTAGACCTAAGAGGGATGAGAAATTACCTAA
+>B7_591:7:89:67:709
+TTTTTTTTTTTGTCTTCTCTTTTTTTTTTTTTTTTT
+>B7_591:8:4:841:340
+TTCAAATGAACTTCTGTAATTGAAAAATTCATTTAA
+>B7_593:1:12:158:458
+CTGGGAAATTCTTCATCCTGGACCCTGAGAGATTCT
+>B7_593:1:12:158:458
+TAATAATGCTACATGGATGATTATGAAATCAATGTT
+>B7_593:1:189:876:833
+CAAGACTACCCAGATTCATAAAACAAATACTACTAG
+>B7_593:1:189:876:833
+TTAAAATTTAACAAAAGTAAATAAAACACATAGCTA
+>B7_593:1:19:695:59
+AACAGGAACAAAACCTCATATATCAATATTAACTTT
+>B7_593:1:19:695:59
+GTGGAAAAAGATGTTCTACGCAAACAGAAACCAAAT
+>B7_593:1:200:559:765
+GGAAGGAGCATTTTGTCAGTTACCAAATGTGTTTAT
+>B7_593:1:200:559:765
+TGGACCCTGAGAGATTCTGCAGCCCAGATCCAGATT
+>B7_593:1:215:861:605
+GAAAAACTATTTGAGGAAGTAATTGGGGAAAACCTC
+>B7_593:1:215:861:605
+NAAGACAAGTCTCTTATGAATTAACCCAGTCAGACA
+>B7_593:1:36:485:632
+AAAAGGTCTTTCAAAAGGTGATGTGTGTTCTCATCA
+>B7_593:1:36:485:632
+GGCATTTGCCTTCAGACCCTACACGAATGCGTCTCT
+>B7_593:1:85:361:418
+AGCCAGAAGAGATTGGATCTAATTTTTGGACTTCTT
+>B7_593:1:85:361:418
+GAAGATACATTGCAAGACAGACTTCATCAAGATATG
+>B7_593:2:104:744:280
+CATATGGAAAGGTTGTTGGGATTTTTTTAATGATTC
+>B7_593:2:104:744:280
+TGGGCTGTAATGATGCCCCTTGTCCATCACCCGGTC
+>B7_593:2:125:875:553
+AACAGTAAAATAAAACAAAGGAGGTCATCATACAAT
+>B7_593:2:125:875:553
+TAATTGGTACAATGTACAATATTCTGATGATGGTTA
+>B7_593:2:128:555:941
+AACCAAAAGAGAGAAGGAGTAGTTATACACATATCA
+>B7_593:2:133:460:542
+CCTATAAGCCGTTCTATTTGTAATGAAAACTATATT
+>B7_593:2:133:460:542
+TTACCAAATGTGTTTATTACCAGAGGGATGGAGGGA
+>B7_593:2:259:467:737
+CTATGTACTTATCATGACTCTATCCCAAATTCCCAA
+>B7_593:2:259:467:737
+TCACAGTTTCTGCCCCCAGCATGGTTGTACTGGGCA
+>B7_593:2:270:430:269
+AAAGAGGCTCAAAGAATGCCAGGAAGATACATTGCA
+>B7_593:2:270:430:269
+CCAGAAGAGATTGGATCTAATTTTTGGACTTCTTAA
+>B7_593:2:273:348:37
+AGAAATGCGCAAAAGAATTGTAAAAGTCAAAATTAA
+>B7_593:2:273:348:37
+GAATAACAATGGGCTTCTCAGCAGAAACCTTACACG
+>B7_593:2:313:531:169
+GAAAGAGGTTCAGAACTTGAAGACAAGTCTCTTATG
+>B7_593:2:313:531:169
+GTGAGAAGTTTGGAAAAACTATTTGAGGAAGTAATT
+>B7_593:2:43:239:977
+TGAACTTCTGTAATTGAAAAATTCATTTAAGAAATT
+>B7_593:2:68:140:542
+AAAAACAAAAACTATGCTAAGTATTGGTAAAGATGT
+>B7_593:2:68:140:542
+GGGATGAGAAATTACCTAATTGGTACAATGTACAAT
+>B7_593:2:68:692:347
+TATCAATTTGGTGTTCTGTGTAAAGTCTCATGGAGC
+>B7_593:2:68:692:347
+TGTCTTGATTTACTTGTTGTTGGTTTTCTGTTTCTT
+>B7_593:2:81:435:410
+AGACATGAGTTCAGGTAAAGGGGTGGAAAAAGATGT
+>B7_593:2:81:435:410
+ATTAATTGAGACTACAGAGCAACTAGGTAAAAAATT
+>B7_593:3:102:856:670
+AAACCTCATATATCAATATTAACTTTGAATAAAAAG
+>B7_593:3:102:856:670
+AGAGAAGGAGTAGCTATACTTATATCAGATAAAGCA
+>B7_593:3:115:649:259
+ATTAATTGAGAATACAGAGCAACTAGGTAAAAAATT
+>B7_593:3:115:649:259
+GGGAAATAAAGTCAAGTCTTTCCTGACAAGCAAATG
+>B7_593:3:148:437:481
+CGCTTCTAGCCATTTCTTTTGGCATTTGCCTTCAGA
+>B7_593:3:148:437:481
+GTACTGGGCAATACATGAGATTATTAGGAAATGCTT
+>B7_593:3:180:89:582
+ATGCTAAGATAATTCATCATCACTAAACCAGTCCTA
+>B7_593:3:180:89:582
+TAAAAAATTAACATTACAACAGGAACAAAACCTCAT
+>B7_593:3:194:168:684
+AAAACAGTCTAGATGAGAGAGAACTTCCCTGGAGGT
+>B7_593:3:194:168:684
+CTGTCTTCCTCTGTCTTGATTTACTTGTTGTTGGTT
+>B7_593:3:196:11:27
+AAGACCCAGTTAGCCGTCCGTGTCCTCCCATCTGGC
+>B7_593:3:196:11:27
+CTATGTTTCTTATCTGCNCATTACTACCCTGCAATT
+>B7_593:3:303:131:673
+ACAAGAAACTCATTAATAAAGACATGAGTTCAGGTA
+>B7_593:3:303:131:673
+ATAAAAAGATCAATTCAGCAAGAAGATATAACCATC
+>B7_593:3:310:193:629
+CATACAATGATAAAAAGATCAATTCAGCAAGAAGAT
+>B7_593:3:310:193:629
+TACACTAAAAGCCCATACTTTACTGCTACTCAATAT
+>B7_593:4:104:153:698
+CCAGATACCATCCCTGTCTTACTTCCAGCTCCCCAG
+>B7_593:4:104:153:698
+CTAATGCGCTCCACGCCCAAGCCCTTCTCACAGTTT
+>B7_593:4:106:316:452
+CTATATTTATGCTATTCAGTTCTAAATATAGAAATT
+>B7_593:4:142:63:937
+GAAAAGGTCTTTCAAAAGGTGATGTGTGTTCTCATC
+>B7_593:4:142:63:937
+TTCTTTTGGCATTTGCCTTCAGACCCTACACGAATG
+>B7_593:4:28:781:723
+AATACCTCTACATGGCTGATTATGAAAACAATGTTC
+>B7_593:4:28:781:723
+ACTGAACTTCCACGTCTCATCTAGGGGAACAGGGAG
+>B7_593:4:29:794:282
+CACATTAATACTATGTTTCTTATCTGCACATTACTA
+>B7_593:4:29:794:282
+TAAAGTCTCAGGGAGCCGTCCGTGTCCTCCCATCTG
+>B7_593:4:30:117:411
+TCTTGACACCCAACTAATATTTGTCTGAGCAAAACA
+>B7_593:4:30:117:411
+TCTTGTAATCTCTCTCCTTTTTGCTGCATCCCTGTC
+>B7_593:4:30:812:345
+TATGTTTCTTATCTGCACATTACTACCCTGCAATTA
+>B7_593:4:30:812:345
+TCATCTAGGGGAACAGGGAGGTGCACTAATGCGCTC
+>B7_593:4:315:201:673
+AAGATATGTAGTCATCAGACTATCTAAAGTCAACAT
+>B7_593:4:315:201:673
+TTGGACTTATTAAAGAAAAAAAAACCTGTCAAACAC
+>B7_593:5:171:343:758
+ACTAATATTTGTCTGAGCAAAACAGTCTAGATGAGA
+>B7_593:5:171:343:758
+GCTGCATCCCTGTCTTCCTCTGTCTTGATTTACTTG
+>B7_593:5:267:71:603
+TTGGCCATCACCCAGTCCCTGCCCCATCTCTTGTAA
+>B7_593:5:267:71:603
+TTTAATGATTCCTCAATGTTAAAATGTCTATTTTTG
+>B7_593:5:299:743:762
+AAAATTAAAATTTAACAAAAGTAAATAAAACACATA
+>B7_593:5:299:743:762
+CAAGACTACCCAGATTCATAAAACAAATACTACTAG
+>B7_593:5:30:599:589
+CTACGCAAACAGAAACCAAATGAGAGAAGGAGCAGC
+>B7_593:5:30:599:589
+TCATAAAACAAATACTACTAGACCTAAGAGGGATGA
+>B7_593:6:118:121:760
+GAGATTTAGACATCTAAATGAAAGAGGCTCAAAGAA
+>B7_593:6:119:428:415
+GCTATACTTATATCAGATAAAGCACACTTTAAATCA
+>B7_593:6:119:428:415
+TAAATTCCCCCACTTAAGAGATATAGATTGGCAGAA
+>B7_593:6:185:96:948
+CTAAATGAAAGAGGCTCAAAGAATGCCAGGAAGATA
+>B7_593:6:185:96:948
+TTTAAAAATGAACAGAGCTTTCAAGAAGTATGAGAT
+>B7_593:6:38:332:54
+CCATCATAAATACACACAAAAGTACAAAACTCACAG
+>B7_593:6:38:332:54
+TGGCAGAACAGATTTAAAAACATGAACTAACTATAT
+>B7_593:6:61:628:681
+CAGAGGGAAAGCTTTCAACGCTTCTAGCCATTTCTT
+>B7_593:6:61:628:681
+GCCATCACAATGAACAACAGGAAGAAAAGGTCTTTC
+>B7_593:7:15:244:876
+AAAAGTAAACTCTCAAATATTGCTAGTGTGAGTATA
+>B7_593:7:15:244:876
+GTACAATATTCTGATGATGGTTACACTAAAAGCCCA
+>B7_593:7:189:530:40
+AAAAGAATTGTAAAAGTCAAAATTAAAGTTCAATAC
+>B7_593:7:189:530:40
+CCCCACTTAAGAGATATAGATTGGCAGAACAGATTT
+>B7_593:7:256:354:173
+CATTAATAAAGACATGAGTTCAGGTAAAGGGGTGGA
+>B7_593:7:256:354:173
+TCAATTCAGCAAGAAGATATAACCATCCTACTAAAT
+>B7_593:7:283:186:707
+AATACATATGCACCTAACACAAGACTACCCAGATTC
+>B7_593:7:283:186:707
+CGCTTGTACTTCTAAATCTATAACAAAATTAAAATT
+>B7_593:7:307:481:625
+AAAAAGTGAGAAGTTTGGAAAAACTATTTGAGGAAG
+>B7_593:7:307:481:625
+TCAACATGAAGGAAAAAAATTCTAAAATCAGCAAGA
+>B7_593:7:67:302:762
+GTAATCTCTCTCCTTTTTGCTGCATCCCTGTCTTCC
+>B7_593:7:67:302:762
+TTACGTCCTATCTTCTTCTTAGGGAAGAACAGCTTA
+>B7_593:7:6:585:132
+GCCCCTTGACCACCACCCAGTCCCTGCCCCATCTCT
+>B7_593:7:6:585:132
+TGTACTTATCATGTTTCTTTCCTAATTTTTCAATTA
+>B7_593:7:87:89:696
+TGGTTCTCTTGAAAGCTTGGGCTGTAATGATGCCCC
+>B7_593:7:87:89:696
+TTCCTATGGAAAGGTTGTTGGGAGATTTTTAATGAT
+>B7_595:1:209:345:87
+AAACAGTCTAGATGAGAGAGAACTTCCCTGGAGGT
+>B7_595:1:209:345:87
+TTACTTGTTGTTGGTTTTCTGTTTCTTTTTTTGAT
+>B7_595:1:209:653:400
+AGGAGCATTTTGTCAGTTACCAAATGTGTTTATTA
+>B7_595:1:209:653:400
+CTAGAGTCCCATTTGGAGCCCCTCTAAGCCGTTCT
+>B7_595:1:252:19:955
+AGCCAGTTCTTTTGGCATTTGCCTTCAGACCCTCC
+>B7_595:1:252:19:955
+TGAACAAAAGGAAGAAAAGGTCTTTCAAAAGGTGA
+>B7_595:1:81:1000:375
+ACCCTGAGAGATTCTGCAGCCCAGCTCCAGATTGC
+>B7_595:1:81:1000:375
+NATGTCAGGGAAGGAGCATTTTGTCAGTTACCAAA
+>B7_595:2:178:77:424
+CTACCCTGCAATTAATATAATTGTGTCCATGTACA
+>B7_595:2:178:77:424
+TGCGCTCCACGCCCAAGCCCTTCTCACAGTTTCTG
+>B7_595:2:251:121:479
+GGCTGCAACTGTGAGCCATCACAATGAACAACAGG
+>B7_595:2:251:121:479
+GGGAAAGCTTTCAACGCTTCTAGCCATTTCTTTTG
+>B7_595:2:29:729:70
+AAACAGAAACCAAATGAGAGAAGGAGTAGCTATAC
+>B7_595:2:29:729:70
+ANTATTANCTTTGANNAAAAAGGGATTAAATTCCC
+>B7_595:3:229:543:583
+ATAACCATCCTACTAAATACATATGCACCTAACAC
+>B7_595:3:229:543:583
+TCAGGTAAAGGGGTGGAAAAAGATGTTCTACGCAA
+>B7_595:3:297:637:86
+CAATGTTCCCCAGATACCATCCCTGTCTTACTTCC
+>B7_595:3:297:637:86
+TCTCAGCTAGGGGAACAGGGAGGTGCACTAATGCG
+>B7_595:3:57:735:151
+CTATCCCAAATTCCCAATTACGTCCTATCTTCTTC
+>B7_595:3:57:735:151
+TAAACTCTCACCTTATTGCTGCATCCCTGTCTTCC
+>B7_595:3:85:964:950
+AACAGATTTAAAAACATGAACTAACTATATGCTGT
+>B7_595:3:85:964:950
+GAGGTCATCATACAATGATAAAAAGATCAATTCAG
+>B7_595:4:12:402:843
+AGGGAGGTGCACTAATGCGCTCCACGCCCAAGCCC
+>B7_595:4:12:402:843
+ATATAATTGTGTCCATGTACACACGCTGTCCTATG
+>B7_595:4:319:250:718
+AAAAGAAAAAGTGAGAAGTTTGGAAAAACTATTTG
+>B7_595:4:319:250:718
+AGTTGAAAGCTCTAACAATAGACTAAACCAAGCAG
+>B7_595:4:58:703:72
+GTACACACGCTGTCCTATGTACTTATCATGACTCT
+>B7_595:4:58:703:72
+TCCACGCCCAAGCCCTTCTCACAGTTTCTGCCCCC
+>B7_595:4:84:802:737
+CATAGACCCCCTTGCAACAACCTTGAGAACCCCAG
+>B7_595:4:84:802:737
+CTTAACCTCTGGTGACTGCCAGAGCTGCTGGCAAG
+>B7_595:5:184:912:258
+ATTCTAAAATCAGCAAGAGAAAAGCATACAGTCAT
+>B7_595:5:184:912:258
+GTTATGCCCTGCTAAACTAAGCATCATAAATGAAG
+>B7_595:5:36:649:554
+AAGAGATTGGATCTAATTTTTGGACTTCTTAAAGA
+>B7_595:5:36:649:554
+CAGGAAGATACATTGCAAGACAGACTTCATCAAGA
+>B7_595:5:84:91:614
+GAACCACACATTAATACTATGTTTCTTATCTGCAC
+>B7_595:5:84:91:614
+TTTCCCATCATGAAGCACTGATCTTCCACGTCTCA
+>B7_595:6:119:730:190
+AGTCTCTTATGAATTAACCCAGTCAGACAAAAATA
+>B7_595:6:119:730:190
+AGTCTTGCTAGAGATTTAGACATCTAAATGAAAGA
+>B7_595:6:137:811:130
+AAAATTTAACAAAAGTAAATAAAACACATAGCTAA
+>B7_595:6:137:811:130
+AGACTACCCAGATTCATAAAACAAATACTACTAGA
+>B7_595:6:290:270:557
+ACATTACTACCCTGCAATTAATATAATTGTGTCCA
+>B7_595:6:290:270:557
+GGAACAGGGAGGTGCACTAATGCGCTCCACGCCCA
+>B7_595:6:47:720:789
+CCCTTGGCCATCACCCGGTCCCGGCCCCTTCTCTT
+>B7_595:6:47:720:789
+TCCTCAATGTTAAAATGTCTATTTTTGTCTTGACA
+>B7_595:6:52:751:360
+AAAAACTATTTGAGGAAGTAATTGGGGAAAACCTC
+>B7_595:6:52:751:360
+AGAGAAAAGCATACAGTCATCTATAAAGGAAATCC
+>B7_595:6:99:557:427
+AACAAAATTAAAATTTAACAAAAGTAAATAAAACA
+>B7_595:6:99:557:427
+ATTCATAAAACAAATACTACTAGACCTAAGAGGGA
+>B7_595:7:123:610:472
+GTCTGAGCAAAACAGTCTAGATGAGAGAGAACTTC
+>B7_595:7:123:610:472
+TGCATCCCTGTCTTCCTCTGTCTTGATTTACTTGT
+>B7_595:7:149:123:265
+AAGAGGGATGAGAAATTACCTAATTGGTACAATGT
+>B7_595:7:149:123:265
+AGCAAAAACAAAAACTATGCTAAGTATTGGTAAAG
+>B7_595:7:166:203:416
+AATTACGTCCTATCTTCTTCTTAGGGAAGAACAGC
+>B7_595:7:166:203:416
+ATGAGATTATTAGGAAATGCTTTACTGTCATAACT
+>B7_595:7:188:802:71
+ATGCTATTCAGTTCTAAATATAGAAATTGAAACAG
+>B7_595:7:188:802:71
+TGCCCTCTTCTTCCAAAGATGAAACGCGTAACTGC
+>B7_595:7:190:481:295
+GAAGAACAGCTTAGGTATCAATTTGGTGTTCTGTG
+>B7_595:7:190:481:295
+TCATAACTATGAAGAGACTATTGCCAGATGAACCA
+>B7_595:7:242:4:593
+ATATACACACGCTGTCCTATGTACTTATCATGACT
+>B7_595:7:242:4:593
+TCCACGCCCAAGCCCTTCTCACAGTTTCTGCCCCC
+>B7_595:8:26:242:35
+ATAAAACAAAGGAGGTCATCATACAATGATAAAAA
+>B7_595:8:26:242:35
+ATATTTTGATGATGGTTACACTAAAAGCCCATACT
+>B7_597:2:100:563:301
+GAACTTCTGTAATTGAAAAATTCATTTAAGAAATT
+>B7_597:2:132:493:921
+ACGGGGTTGCCAGCACAGGGGCTTAACCTCTGGTG
+>B7_597:2:132:493:921
+GTTCTCAAGGTTGTTGCAAGGGGGTCTATGTGAAC
+>B7_597:2:165:431:857
+GAACTTTGATGCCCTCTTCTTCCAAAGATGAAACG
+>B7_597:2:165:431:857
+TTGGGGTCTGACAGGCTGCAACTGTGAGCCATCAC
+>B7_597:2:168:829:88
+ACAGACTTCATCAAGATATGTAGTCATCAGACTAT
+>B7_597:2:168:829:88
+TAACTGAACCTATGAGTCACAGGTATTCCTGAGGA
+>B7_597:2:42:28:552
+AAGAAGATATAACCATCCTACTAAATACATATGCA
+>B7_597:2:42:28:552
+ACTCAATATATCCATGTAACAAATCTGCGCTTGTA
+>B7_597:3:10:394:392
+TCATCAAGATATGTAGTCATCAGACTATCTAAATT
+>B7_597:3:10:394:392
+TTGGACTTCTTAAAGAAAAAAAAACCTGTCAAACA
+>B7_597:3:115:646:430
+CACAGGTTTTATAAAACAATTAATTGAGACTACAG
+>B7_597:3:115:646:430
+GTTATGCCCTGCTAAACTTAGCATCATAAATGAAG
+>B7_597:3:133:707:886
+ACCTAATAAATACATATGCACCTAACACAAGACTA
+>B7_597:3:133:707:886
+AGGTAAAGGGGTGGAAAAAGATGTTCTACGCAAAC
+>B7_597:3:157:361:309
+CCTGCTAAACTAAGCATCATAAATGAAGGGGAAAT
+>B7_597:3:157:361:309
+TACACACAAAAGTACAAAACTCACAGGTTTTATAA
+>B7_597:3:39:966:551
+ACATTAATACTATGTTTCTTATCTGCACATTACTA
+>B7_597:3:39:966:551
+AGGGAGCCGTCCGTGTCCTCCCATCTGGCCTCGTC
+>B7_597:3:46:981:766
+TCTTTTGGCATTTGCCTTCAGACCCTACACGAATG
+>B7_597:3:46:981:766
+TGCCCCCAGCATGGTTGTACTGGGCAATACATGAG
+>B7_597:3:53:616:842
+CTTATCATGACTCTATCCCAAATTCCCACTTACGT
+>B7_597:3:53:616:842
+TCACCCAGTCCCTGCCCCATCTCTTGTAATCTCTC
+>B7_597:3:67:620:344
+AGCTTTCAACGCTTCTAGCCATTTCTTTTGGCATT
+>B7_597:3:67:620:344
+CCCCCGCCCAAGCCCTTCTCACAGTTTCTGCCCCC
+>B7_597:3:73:273:488
+AAAACAGTCTAGATGAGAGAGAACTTCCCTGGAGG
+>B7_597:3:73:273:488
+CTCTCTCCTTTTTGCTGCATCCCTGTCTTCCTCTG
+>B7_597:4:138:211:582
+CATTAATAAAGACATGAGTTCAGGTAAAGGGGTGG
+>B7_597:4:138:211:582
+TGAGACTACAGAGCAAATAGGTAAAAAATTAACAT
+>B7_597:4:144:492:61
+AAATACTCACCATCATAAATACACACAAAAGTACA
+>B7_597:4:144:492:61
+AACCTGTCAAACACGAATGTTATGCCCTGCTAAAC
+>B7_597:4:146:961:63
+TACTTATATCAGATAAAGCACACTTTAAATCAACA
+>B7_597:4:146:961:63
+TGAATAAAAAGGGCTTAAATTCCCCCACTTAAGGG
+>B7_597:4:38:999:463
+GCGGAAACCTTACAAGCCAGAAGAGATTGGATCTA
+>B7_597:4:38:999:463
+TAGACATCTAAATGAAAGNNGCNNNAAGAATGCCA
+>B7_597:5:125:957:753
+TTTTTTTTTTTTCTCTCCTCTTTTTTTTTTTTTTT
+>B7_597:5:160:434:853
+ATATAATTGTGTCCATGTACACACGCTGTCCTATG
+>B7_597:5:160:434:853
+GCTTGGGCTGTAATGATGCCCCTTGGCCATCACCC
+>B7_597:5:58:684:520
+AGACAGACTTCATCAAGATATGTAGTCATCAGACT
+>B7_597:5:58:684:520
+ATTTTTGGACTTCTTAAAGAAAAAAAAACCTGTCA
+>B7_597:5:6:882:784
+CATGGCTGATTATGAAAACAATGTTCCCCAGATAC
+>B7_597:5:6:882:784
+CTGGATTCTGGGAAATTCTTCATCCTGGACCCTGA
+>B7_597:5:98:995:929
+GTCCTATAAGAAATGCTCAAAAGAATTGTAAAAGT
+>B7_597:5:98:995:929
+TATAACAATATTAACTTTGAATAAAAAGGGATTAA
+>B7_597:6:106:595:322
+GAGGAAGTAATTGGGGAAAACCTCTTTAGTCTTGC
+>B7_597:6:106:595:322
+GCAAGAGAAAAGCATACAGTCATCTATAAAGGAAA
+>B7_597:6:193:661:771
+AAACTCATTAATAAAGACATGAGTTCAGGTAAAGG
+>B7_597:6:193:661:771
+GCAAGAAGATATAACCATCCTACTAAATACATATG
+>B7_597:6:20:592:496
+CTCAAAGAATGCCAGGAAGATACATTGCAAGACAG
+>B7_597:6:20:592:496
+TCTCAGCGGAAACCTTACAAGCCAGAAGAGATTGG
+>B7_597:6:29:249:878
+ATTGTGTCCATGTACACACGCTGTCCTATGTACTT
+>B7_597:6:29:249:878
+TCTCACAGTTTCTGCCCCCAGCATGGTTGTACTGG
+>B7_597:6:73:420:812
+CTAAGTATTGGTAAAGATGTGGGGAAAAAAGTAAA
+>B7_597:6:73:420:812
+CTAATTGGTACAATGTACAATATTCTGATGATGGT
+>B7_597:7:103:731:697
+AATTAACCCAGTCAGACAAAAATAAAGAAAAAAGA
+>B7_597:7:103:731:697
+CTTGCTAGAGATTTAGACATCTAAATGAAAGAGGC
+>B7_597:7:113:408:211
+AAACTCATTAATAAAGACATGAGTTCAGGTAAAGG
+>B7_597:7:113:408:211
+GAGACTACAGAGCAACTAGGTAAAAAATTAACATT
+>B7_597:7:31:948:254
+CCTCTACATGGCTGATTATGAAAACAATGTTCCCC
+>B7_597:7:31:948:254
+TGAAGCACTGAACTTCCACGTCTCATCTAGGGGAA
+>B7_597:7:41:34:211
+CACCTAACACAAGACTACCCAGATTCATAAAACAA
+>B7_597:7:41:34:211
+GTAAAGGGGTGGAAAAAGATGTTCTACGCAAACAG
+>B7_597:7:5:753:806
+AAAATATAGTTGAAAGCTCTAACAATAGACTAAAC
+>B7_597:7:5:753:806
+ATGTAAAGTAACTGAACCTATGAGTCACAGGTATT
+>B7_597:7:94:273:165
+AGAAAGAAGATATAACCATCCTACTAAATACATAT
+>B7_597:7:94:273:165
+TTACAAGAAACTCATTAATAAAGACATGAGTTCAG
+>B7_597:8:147:360:141
+TGCGCTTGTACTTCTAAATCTATAACAAAATTAAA
+>B7_597:8:147:360:141
+TTTGGTAATTTAGTTTTTTTTTTTTCTTTTCTCTT
+>B7_597:8:186:850:838
+GGAAGAGGGACGCTGAAGAACTTTGATGCCCTCTT
+>B7_597:8:186:850:838
+GTTCTATTTGTAATGAAAACTATATTTATGCTATT
+>B7_597:8:35:118:589
+TCATAAAACAAATACTACTAGACCTAAGAGGGATG
+>B7_597:8:35:118:589
+TGTTCTACGCAAACAGAAACCAAATGAGAGAAGGA
+>B7_597:8:48:805:860
+AAACCTGTCAAACACGAATGTTATGCCCTGCTAAA
+>B7_597:8:48:805:860
+AAAGTACAAAACTCACAGGTTTTATAAAACAATTA
+>B7_610:1:12:88:200
+ACATGAGTTCAGGTAAAGGGGTGGAAAAAGATGTT
+>B7_610:1:12:88:200
+GAAGATATAACCATCCTACTAAATACATATGCACC
+>B7_610:1:139:152:856
+AGAGGGACGCTGAAGAACTTTGATGCCCTCTTCTT
+>B7_610:1:139:152:856
+CTAAGCCGTTCTATTTGTAATGAAAACTATATTTA
+>B7_610:1:37:652:403
+CCCCTCTAAGCCGTTCTATTTGTAATGAAAACTAT
+>B7_610:1:37:652:403
+TTTTGTCAGTTACCAAATGTGTTTATTACCAGAGG
+>B7_610:2:189:831:878
+AGAAAAAAAAACCTGTCAAACACGAATGTTATGCC
+>B7_610:2:189:831:878
+AGGAAGATACATTGCAAGACAGACTTCATCAAGAT
+>B7_610:2:194:688:289
+TCAGACCCTACACGAATGCGTCTCTACCACAGGGG
+>B7_610:2:194:688:289
+TGTGTGTTCTCATCAACCTCATACACACACATGGT
+>B7_610:2:6:529:366
+CATACAATGATAAAAAGATCAATTCAGCAAGAAGA
+>B7_610:2:6:529:366
+GCTACTCAATATATCCATGTAACAAATCTGCGCTT
+>B7_610:2:75:887:149
+TACAACAGGAACAAAACCTCATATATCAATATTAA
+>B7_610:2:75:887:149
+TACGCAAACAGAAACCAAATGAGAGAAGGAGTAGC
+>B7_610:3:102:825:507
+TGCTGCATCCCTGTCTTCCTCTGTCTTGATTTACT
+>B7_610:3:102:825:507
+TTTGTCTGAGCAAAACAGTCTAGATGAGAGAGAAC
+>B7_610:3:120:63:653
+AACAACAGGAAGAAAAGGTCTTTCAAAAGGTGATG
+>B7_610:3:120:63:653
+TCTTCTTCCAAAGATGAAACGCGTAACTGCGCTCT
+>B7_610:3:137:895:681
+CTTCCTATGGAAAGGTTGTTGGGAGATTTTTAATG
+>B7_610:3:137:895:681
+GCCTCGTCCACACTGGTTCTCTTGAAAGCTTGGGC
+>B7_610:3:148:340:479
+TCTGTGTAAAGTCTCAGGGAGCCGTCCGTGTCCTC
+>B7_610:3:148:340:479
+TTGTTGTTGGTTTTCTGTTTCTTTGTTTGATTTGG
+>B7_610:3:182:23:585
+AGAACAGCTTAGGTATCAATTTGGTGTTCTGTGTA
+>B7_610:3:182:23:585
+ATCCCTGTCTTCCTCTGTCTTGATTTACTTGTTGT
+>B7_610:3:5:863:302
+ACGTCTCATCTAGGGGAACAGGGAGGTGCACTAAT
+>B7_610:3:5:863:302
+TGAAAACAATGTTCCCCAGATACCATCCCTGTCTT
+>B7_610:3:82:998:566
+ATCTGGCCTCGTCCACACTGGTTCTCTTGAAAGCT
+>B7_610:3:82:998:566
+GCACATTACTACCCTGCAATTAATATAATTGTGTC
+>B7_610:3:84:101:328
+AATGGACCTGTGATATCTGGATTCTGGGAAATTCT
+>B7_610:3:84:101:328
+TATAATACCTCTACATGGCTGATTATGAAAACAAT
+>B7_610:3:85:219:371
+GACATGAGTTCAGGTAAAGGGGTGGAAAAAGATGT
+>B7_610:3:85:219:371
+TAACATTACAACAGGAACAAAACCTCATATATCAA
+>B7_610:4:139:989:144
+ACTAAAAAAGCAAAAACAAAAACTATGCTAAGTAT
+>B7_610:4:139:989:144
+ACTACTAGACCTAAGAGGGATGAGAAATTACCTAA
+>B7_610:4:15:805:420
+ATGAAGAGACTATTCACATGTGAACCACACATTTA
+>B7_610:4:15:805:420
+GAACAGTTTAGGTATCAATTTGGTGTTCTTTGTAA
+>B7_610:4:198:59:675
+AATCTGCGCTTGTACTTCTAAATCTATAACAAAAT
+>B7_610:4:198:59:675
+ACTAAATACATATGCACCTAACACAAGACTATCCT
+>B7_610:4:67:317:249
+CTACATGGCTGATTATGAAATCTATGTTCCCCATA
+>B7_610:4:67:317:249
+TTCCCATCATGACGCACCGAACTTCCACGTCTCAT
+>B7_610:5:102:915:87
+AACAATAGACTAAACCAAGCAGAAGAAAGAGGTTC
+>B7_610:5:102:915:87
+CACAGGTATTCCTGAGGAAAAAGAAAAAGTGAGAA
+>B7_610:5:120:596:847
+AACCTATGAGTCACAGGTATTCCTGAGGAAAAAGA
+>B7_610:5:120:596:847
+TCAACATGAAGGAAAAAAATTCTAAAATCAGCAAG
+>B7_610:5:136:260:254
+AAATTAACATTACAACAGGAACAAAACCTCATATA
+>B7_610:5:136:260:254
+GTGGAAAAAGATGTTCTACGCAAACAGAAACCAAA
+>B7_610:5:147:68:353
+AACAACCTTGAGAACCCCAGGGAATTTGTCAATGT
+>B7_610:5:147:68:353
+CCTTTGATATCTGGATTCTGGGAAATTCTTCATCC
+>B7_610:5:51:904:391
+ACCTATGAGTCACAGGTATTCCTGAGGAAAAAGAA
+>B7_610:5:51:904:391
+TATCTAAAGTCAACATGAAGGAAAAAAATTCTAAA
+>B7_610:5:7:761:623
+CCGGCATGGTTGTACTGGGCAATACATGAGATTAT
+>B7_610:5:7:761:623
+CTTTCAACGCTTCTAGCCATTTCTTTTGGCATTTG
+>B7_610:6:107:252:533
+AGAGAAGGAGTAGCTATACTTATATCAGATAAAGC
+>B7_610:6:107:252:533
+CAAGACTACCCAGATTCATAAAACAAATACTACTA
+>B7_610:6:111:379:700
+ACACTAAAAGCCCATACTTTACTGCTACTCAATAT
+>B7_610:6:111:379:700
+CGCACTGGCAATATTTGTGTGTTTACTTTTTTGCA
+>B7_610:6:143:620:158
+ACTTTACTGCTACTCAATATATCCATGTAACAAAT
+>B7_610:6:143:620:158
+CAATGATAAAAAGATCAATTCAGCAAGAAGATATA
+>B7_610:6:148:776:486
+AACTGTGAGCCATCACAATGAACAACAGGAAGAAA
+>B7_610:6:148:776:486
+AGCTTTCAACGCTTCTAGCCATTTCTTTTGGCATT
+>B7_610:7:116:157:612
+GTAAAAGTCAAAATTAAAGTTCAATACTCACCATC
+>B7_610:7:116:157:612
+TTAAGAGATATAGATTGGCAGTACAGATTTAAAAA
+>B7_610:7:117:857:942
+AGAGAGAACTTCCCTGGAGGTCTGATGGCGTTTCT
+>B7_610:7:117:857:942
+GGTTTTCTGTTTCTTTGTTTGATTTGGTGGAAGAC
+>B7_610:7:158:943:467
+AAAGCTCTAACAATAGACTAAACCAAGCAGAAGAA
+>B7_610:7:158:943:467
+AGGTATTCCTGAGGAAAAAGAAAAAGTGAGAAGTT
+>B7_610:7:15:696:693
+TCAAACACGAATGTTAATCCCTGCTAAACTAATCA
+>B7_610:7:15:696:693
+TCTAAAGTCAACATGAAGGAAAAAAATTCTAAAAT
+>B7_610:7:177:469:800
+AAAATCAGCAAGAGAAAAGCATACAGTCATCTATA
+>B7_610:7:177:469:800
+TTGGAAAAACTATTTGAGGAAGTAATTGGGGAAAA
+>B7_610:7:26:749:174
+CAGATTCATAAAACAAATACTACTAGACCTAAGAG
+>B7_610:7:26:749:174
+TAACAAAAGTAAATAAAACACATAGCTAAAACTAA
+>B7_610:7:34:144:868
+AATTACCTAATTGGTACAATGTACAATATTCTGAT
+>B7_610:7:34:144:868
+AGCTAAGGAATGGGAAAGGTGTGGGGAAAAAAGTA
+>B7_610:7:35:378:681
+GCGTCTCTACCACAGGGGGCTGCGCGGTTTCCCAT
+>B7_610:7:35:378:681
+GTGTGTTCTCATCAACCTCATACACACACATGGTT
+>B7_610:8:163:757:432
+CCAGATGAACCACACATTAATACTATGTTTCTCAT
+>B7_610:8:163:757:432
+GGTTTCCCATCATGAAGCACTGAACTTCCACGTCT
+>B7_610:8:68:570:705
+AACAGATTTAAAAACATGAACTAACTATATGCTGT
+>B7_610:8:68:570:705
+CATCATACAATGATAAAAAGATCAATTCAGCAAGA
+>B7_610:8:95:426:791
+CCAAATGTGTTTATTACCAGAGGGATGGAGGGAAG
+>B7_610:8:95:426:791
+GNTCCAGATTGCTTGTGGTCTGACAGGCTGCAACT
+>EAS112_32:7:113:809:364
+GATGCCCTCTTCTTCCAAAGATGAAACGCGTAACT
+>EAS112_32:7:113:809:364
+TATAGAAATTGAAACAGCTGTGTTTAGTGCCTTTG
+>EAS112_32:7:135:401:735
+AATTGTAAAAGTCAAAATTAAAGTTCAATACTCAC
+>EAS112_32:7:135:401:735
+CCTTACAAGCCAGAAGAGATTGGATCTAATTTTTG
+>EAS112_32:7:168:117:441
+TCATAACTATGAAGAGACTATTGCCAGATGAACCA
+>EAS112_32:7:168:117:441
+TCTTCTTAGGGAAGAACAGCTTAGGTATCAATTTG
+>EAS112_32:7:272:328:400
+CAGGTAAAGGGGTGGAAAAAGATGTTCTACGCAAA
+>EAS112_32:7:272:328:400
+CTAAATACATATGCACCTAACACAAGACTACCCAG
+>EAS112_32:7:322:391:742
+ATCAATATTAACTTTGAATAAAAAGGGATTAAATT
+>EAS112_32:7:322:391:742
+CATCACTAAACCAGTCCTATAAGAAATGCTCAAAA
+>EAS112_32:7:42:804:114
+ATACTTTACTGCTACTCAATATATCCATGTAACAA
+>EAS112_32:7:42:804:114
+TCAAATATTGCTAGTGGGAGTATAAATTGTTTTCC
+>EAS112_32:8:88:90:59
+ATAATACCTCTACATGTCTGATTATGAAAACAATG
+>EAS112_32:8:88:90:59
+TGCACCTCCCTGTTCACCTAGATGCTAGGAGGACA
+>EAS112_32:8:89:254:332
+AAACCTCTTTAGTCTTGCTAGAGATTTAGACATCT
+>EAS112_32:8:89:254:332
+GAATTAACCCAGTCAGACAAAAATAAAGAAAAAAG
+>EAS112_34:4:12:273:89
+AGTCTTTCCTGACAAGCAAATGCTAAGATAATTCA
+>EAS112_34:4:12:273:89
+CCATCAGAATAACAATGGGCTTCTCAGCGGAAACC
+>EAS112_34:4:17:989:186
+TTAGTCTTGCTAGAGATTTAGACATCTAAATGAAA
+>EAS112_34:4:17:989:186
+TTATGAATTAACCCAGTCAGACAAAAATAAAGAAA
+>EAS112_34:4:22:206:150
+AAAAAAGAGCAACTAGGTAAAAAATTAACATTACA
+>EAS112_34:4:22:206:150
+GAAATAAAGTCAAGTCTTTCCTGACAAGCAAATGC
+>EAS112_34:4:74:570:695
+CACACTGGTTCTCTTGAAAGCTTGGGCTGTAATGA
+>EAS112_34:4:74:570:695
+TTGGGAGATTTTTAATGATTCCTCAATGTTAAAAT
+>EAS112_34:4:92:412:435
+AGATTCATAAAACAAATACTACTAGACCTAAGAGG
+>EAS112_34:4:92:412:435
+CTACGCAAACAGAAACCAANTGAGAGAAGGAGTAG
+>EAS112_34:6:127:153:861
+CTCAGGGAGCCGTCCGTGTCCTCCCATCTGGCCTC
+>EAS112_34:6:127:153:861
+TTTTCTGTTTCTTTGTTTGATTTGGTGGAAGACAT
+>EAS112_34:6:130:865:838
+AAAGCATACAGTCATCTATAAAGGAAATCCCATCA
+>EAS112_34:6:130:865:838
+AATGCTAAGATAATTCATCATCACTAAACCAGTCC
+>EAS112_34:6:145:144:263
+TTTCGTTTTTTTTTTTTTTTTTTCCCCTTTCTTTT
+>EAS112_34:6:43:47:279
+AAAACTATGCTAAGTATTGGTAAAGATGTGGGGAA
+>EAS112_34:6:43:47:279
+TAGACCTAAGAGGGATGAGAAGTTACCTAATTGGT
+>EAS112_34:6:71:85:629
+CCTTTTTGCTGCATCCCTGTCTTCCTCTGTCTTGA
+>EAS112_34:6:71:85:629
+TTGACACCCAACTAATATTTGTCTGAGCAAAACAG
+>EAS112_34:6:75:615:555
+AAGTTTGGAAAAACTATTTGAGGAAGTAATTGGGG
+>EAS112_34:6:75:615:555
+TGAAGGAAAAAAATTCTAAAATCAGCAAGAGAAAA
+>EAS112_34:7:118:523:591
+GAGGGACGCTGAAGAACTTTGATGCCCTCTTCTTC
+>EAS112_34:7:118:523:591
+GGTCTGACAGGCTGCAACTGTGAGCCATCACAATG
+>EAS112_34:7:141:80:875
+AGCCGAGTCACGGGGTTGCCAGCACAGGGGCTTAA
+>EAS112_34:7:141:80:875
+AGCTGTGTTTAGTGCCTTTGTTCAACCCCCTTGCA
+>EAS112_34:7:142:457:584
+GGAAGAACAGCTTAGGTATCAATTTGGTGTTCTGT
+>EAS112_34:7:142:457:584
+TGAAGAGACTATTTCCAGATGAACCACACATTAAT
+>EAS112_34:7:71:62:254
+AAAAAAGTAAACTCTCAAATATTGCTAGTGGGAGT
+>EAS112_34:7:71:62:254
+GGTTACACTAAAAGCCCATACTTTCCTGCTACTCA
+>EAS112_34:7:86:498:373
+CACTAATGCGCTCCACGCCCAAGCCCTTCTCACAG
+>EAS112_34:7:86:498:373
+GATACCATCCCTGTCTTACTTCCAGCTCACCAGAG
+>EAS112_34:7:96:489:453
+AAGTCAAGTCTTTCCTGACAAGCAAATGCTAAGAT
+>EAS112_34:7:96:489:453
+AGAAAAGCATACAGTCATCTATAAAGGAAATCCCA
+>EAS112_34:8:103:812:255
+ATGTTAAAATGTCTATTTTTGTCTTGACACCCAAC
+>EAS112_34:8:103:812:255
+TGATGCCCCTTGGCCATCACCCAGTCCCTGCCCCC
+>EAS112_34:8:174:557:872
+GGTAAAGATGTGGGGAAAAAAGTAAACTCTCAAAT
+>EAS112_34:8:174:557:872
+TGGTACAATGTACAATATTCTGATGATGGTTACAC
+>EAS112_34:8:179:13:782
+GACAGTCTACAACTGTGAGCCATCACAATGAACAA
+>EAS112_34:8:179:13:782
+TGATGCCCTCTTCTTCCAAAGATGAAACGCGTAAC
+>EAS112_34:8:30:816:90
+ACTACCCTGCAATTAATATAATTGTGTCCATGTAC
+>EAS112_34:8:30:816:90
+AGGGAGGTGCACTAATGCGCTCCACGCCCCAGCCC
+>EAS112_34:8:45:800:733
+ACATGAAGGAAAAAAATTCTAAAATCAGCAAGAGA
+>EAS112_34:8:45:800:733
+ATAAATGAAGGGGAAATAAAGTCAAGTCTTTCCTG
+>EAS112_34:8:4:841:339
+ACCTCATACACACACATGGTTTAGGGGTATAATAC
+>EAS112_34:8:4:841:339
+CTTCAGACCCTACACGAATGCGTCTCTACCACAGG
+>EAS114_26:1:113:367:659
+AGTCATCAGACTATCTAAAGTCAACATGAAGGAAA
+>EAS114_26:1:113:367:659
+CACAGGTATTCCTGAGGAAAAAGAAAAAGCGAGAA
+>EAS114_26:1:155:807:19
+AAAAGGGATTAAATTCCCCCACTTAAGAGATATAG
+>EAS114_26:1:155:807:19
+CAACAGTAAAATAAAACAAAGGAGGTCATCATACA
+>EAS114_26:1:171:527:247
+AACAAATGCTACTAGACCTAAGAGGGATGAGAAAT
+>EAS114_26:1:171:527:247
+AGAAGGAGTAGCTAGACTTATATCAGATAAAGCAC
+>EAS114_26:1:324:238:736
+AGACAGACTTCATCAAGATATGTAGTCATCAGACT
+>EAS114_26:1:324:238:736
+TCAAGAAGTATGAGATTATGTAAAGTAACTGAACC
+>EAS114_26:1:35:522:294
+GGTTCAGAACTTGAAGACAAGTCTCTTATGAATTA
+>EAS114_26:1:35:522:294
+TTGAGGAAGTAATTGGGGAAAACCTCTTTAGTCTT
+>EAS114_26:1:99:212:522
+ACGAATGCGTCTCTACCACAGGGGGCTGCGCGGTT
+>EAS114_26:1:99:212:522
+AGAGACTATTGCCAGATGAACCACACATTAATACT
+>EAS114_26:2:130:609:467
+AAATTCCCCCACTTAAGAGATATAGATTGGCAGAA
+>EAS114_26:2:130:609:467
+CAATACTCACCATCATAAATACACACAAAAGTACA
+>EAS114_26:2:214:950:32
+ACAAGAAACTCATTAATAAAGACATGAGTTCAGGT
+>EAS114_26:2:214:950:32
+AGAAGATATAACCATCCTACTAAATACATATGCAC
+>EAS114_26:2:237:497:165
+GAAATAAAGTCAAGTCTTTCCTGACAAGCAAATGC
+>EAS114_26:2:237:497:165
+TACAGTCATCTATAAAGGAAATCCCATCAGAATAA
+>EAS114_26:2:315:219:7
+GAAAGAGGCTCAAAGAATGCCAGGAAGATACATTG
+>EAS114_26:2:329:458:365
+GTGTTCTGTGTAAAGTCTCAGGGAGCCGTCCGTGT
+>EAS114_26:2:329:458:365
+TTGTTGTTGGTTTTCTGTTTCTTTGTTTGATTTGG
+>EAS114_26:2:73:513:102
+GTCTCATCTAGGGGAACAGGGAGGTGCACTAATGC
+>EAS114_26:2:73:513:102
+TGAAAACAATGTTCCCCAGATACCATCCCTGTCTT
+>EAS114_26:3:117:284:589
+ACAAAATATAGTTGAAAGCTCTAACAATAGACTAA
+>EAS114_26:3:117:284:589
+GAACCTATGAGTCACAGGTATTCCTGAGGAAAAAG
+>EAS114_26:3:284:261:124
+ACAGCTGTGTTTAGTGCCTTTGTTCAACCCCCTTG
+>EAS114_26:3:287:665:495
+GAATTGTAAAAGTCAAAATTAAAGTTCAATACTCA
+>EAS114_26:3:287:665:495
+TGGATCTAATTTTTGGACTTCTTAAAGAAAAAAAA
+>EAS114_26:4:100:238:596
+ATGAGAAATTACCTAATTGGTACAATGTACAATAT
+>EAS114_26:4:100:238:596
+CAAAAACTATTCTAAGTATTGGTAAAGATGTGGGG
+>EAS114_26:4:110:840:431
+CTGTCAAACACGAATGTTATGCCCTGCTAAACTAA
+>EAS114_26:4:110:840:431
+GTAGTCATCAGACTATCTAAAGTCAACATGAAGGA
+>EAS114_26:4:123:1001:580
+AGGTTTTATAAAACAATTAATTGAGACTACAGAGC
+>EAS114_26:4:123:1001:580
+GGGAANTAAAGTCAAGTCTTTCCTGACAAGCAAAT
+>EAS114_26:4:253:285:104
+CTCTCATTCACTCCAGCTCCCTGTCACCCAATGGA
+>EAS114_26:4:253:285:104
+GTGATGTGTGTTCTCATCAACCTCATACACACACA
+>EAS114_26:4:306:388:342
+CCGTCCGTGTCCTCCCATCTGGCCTCGTCCACACT
+>EAS114_26:4:306:388:342
+GGGGAAGACATAATCCCACGCTTCCTATGGAAAGG
+>EAS114_26:4:40:352:151
+ATTACGTCCTATCTTCTTCTTAGGGAAGAACAGCT
+>EAS114_26:4:40:352:151
+TTTTGCTGCATCCCTGTCTTCCTCTGTCTTGATTT
+>EAS114_26:5:139:331:63
+GACACCCAACTAATATTTGTCTGAGCAAAACAGTC
+>EAS114_26:5:139:331:63
+TTTTGCTGCATCCCTGTCTTCCTCTGTCTTGATTT
+>EAS114_26:5:228:189:826
+AAGCCCTTCTCACAGTTTCTGCCCCCCGCATGGTT
+>EAS114_26:5:228:189:826
+ATCATGACTCTATCCCAAATTCCCAATTACGTCCT
+>EAS114_26:5:238:31:968
+ACACCATCCCTGTCTTACTTCCAGCTCCCCAGAGG
+>EAS114_26:5:238:31:968
+ATTCTGCAGCCCAGCTCCAGATTGCTTGTGGTCTG
+>EAS114_26:5:43:114:617
+AATCATAAATACACACAAAAGTACAAAACTCACAG
+>EAS114_26:5:43:114:617
+AATGTTATGCCCTGCTAAACTAAGCATCATAAATG
+>EAS114_26:6:129:694:359
+CCCTGAGAGATTCTGCAGCCCAGATCCAGATTGCT
+>EAS114_26:6:129:694:359
+TGTCAGTTACCAAATGTGTTTATTACCCGAGGGAT
+>EAS114_26:6:140:253:322
+AATTTTTGGACTTCTTAAAGAAAAAAAAACCTGTC
+>EAS114_26:6:140:253:322
+GAAATGCTCAAAAGAATTGTAAAAGTCAAAATTAA
+>EAS114_26:6:183:697:555
+AAAGAATGCCAGGAAGATACATTGCCAGACAGACT
+>EAS114_26:6:183:697:555
+AGAAATCTTAGAAGCCAGAAGAGATTGGATCTAAT
+>EAS114_26:6:46:13:880
+AAAACCTCTTTAGTCTTGCTAGAGATTTAGACATC
+>EAS114_26:6:46:13:880
+AGAAAAGCATACAGTCATCTATAAAGGAAATCCCA
+>EAS114_26:7:13:172:720
+AATTCATTTAAGAAATTACAAAATATAGTTGAAAG
+>EAS114_26:7:157:876:302
+AAAGACATGAGTTCAGGTAAAGGGGTGGAAAAAGA
+>EAS114_26:7:157:876:302
+CAACTAGGTAAAAAATTAACATTACAACACGAACA
+>EAS114_26:7:218:858:445
+AAAAAGAAAAAGTGAGAAGTTTGGAAAAACTATTT
+>EAS114_26:7:218:858:445
+GAAAAAAATTCTAAAATCAGCAAGAGAAAAGCATA
+>EAS114_26:7:245:323:744
+ACCTCTACATGGCTGATTATGAAAACAATGTTCCC
+>EAS114_26:7:245:323:744
+GATTCTGGGAAATTCTTCATCCTGGACCCTGAGAG
+>EAS114_26:7:37:79:581
+TTAAAATTTAAAAAAAGTAAATAAAACACATAGCT
+>EAS114_26:7:37:79:581
+TTTTTTTTTTTTTTTTTTTTTTTCATGCCAGAAAA
+>EAS114_26:7:86:308:648
+GAAGAACAGCTTAGGTATCAATTTGGTGTTCTGTG
+>EAS114_26:7:86:308:648
+TATTAGGAAATGCTTTACTGTCATAACTATGAAGA
+>EAS114_28:1:144:242:602
+ATCAGCAAGAGAAAAGCATACAGTCATCTATAAAGG
+>EAS114_28:1:144:242:602
+ATGAAGGGGAAATAAAGTCAAGTCTTTCCTGACAAG
+>EAS114_28:1:168:389:889
+GAAATTACAAAATATAGTTGAAAGCTCTAACAATAG
+>EAS114_28:1:168:389:889
+TAACTGAACCTATGAGTCACAGGTATTCCTGAGGAA
+>EAS114_28:1:168:609:646
+GGAAAAAAGTAAACTCTCAAATATTGCTAGTGGGAG
+>EAS114_28:1:168:609:646
+GGTTACACTAAAAGCCCATACTTTACTGCTACTCAA
+>EAS114_28:1:220:801:282
+AACCTCATATATCAATATTAACTTTGAATAAAAAGG
+>EAS114_28:1:220:801:282
+AATTCATCATCACTAAACCAGTCCTATAAGAAATGC
+>EAS114_28:1:232:351:909
+ACATGGCTGATTATGAAATCAATGTTCCCCAGATGC
+>EAS114_28:1:232:351:909
+CCATCATGAAGCGCTGAACTTCCACGTCTCATCTAG
+>EAS114_28:1:28:708:463
+CCCAATGGACCTGTGATATCTGGATTCTGGGAAATT
+>EAS114_28:1:28:708:463
+GTATAATACCTCTACATGGCTGATTATGAAAACAAT
+>EAS114_28:2:114:938:216
+CTAACAATAGACTAAACCAAGCAGAAGAAAGAGGTT
+>EAS114_28:2:114:938:216
+GAGTCACAGGTATTCCTGAGGAAAAAGAAAAAGTGA
+>EAS114_28:2:141:7:963
+CACTTTAAATCAACAACAGTAAAATAAAACAAAGGA
+>EAS114_28:2:141:7:963
+TACAATGTACAATATTCTGATGATGGTTACACTAAA
+>EAS114_28:2:149:650:44
+CGCTCCACGCCCAAGCCCTTCTCACAGTTTCTGCCC
+>EAS114_28:2:149:650:44
+CTGTCTTACTTCCAGCTCCCCAGAGGGAAAGCTTTC
+>EAS114_28:2:167:905:852
+AGAAAAGCATACAGTCATCTATAAAGAAAATCCCAT
+>EAS114_28:2:167:905:852
+CAAATGCTAAGATAATTCATCATCACTAAACCAGTC
+>EAS114_28:2:251:819:772
+TCCCCCACTTAAGAGATATAGATTGGCAGAACAGAT
+>EAS114_28:2:251:819:772
+TTCAATACTCACCATCATAAATACACACAAAAGTAC
+>EAS114_28:2:28:474:566
+ACTGAACTTCCACGTCTCATCTAGGGGAACAGGGAG
+>EAS114_28:2:28:474:566
+TGAACCACACATTAATACTATGTTTCTTATCTGCAC
+>EAS114_28:2:329:437:643
+AAGATACATTGCAAGACAGACTTCATCAAGATATGT
+>EAS114_28:2:329:437:643
+TTTTGGACTTCTTAAAGAAAAAAAAACCTGTCAAAC
+>EAS114_28:2:55:562:403
+CAACAGGAACAAAACCTCATATATCAATATTAACTT
+>EAS114_28:2:55:562:403
+CAAGCAAATGCTAAGATAATTCATCATCACTAAACC
+>EAS114_28:3:110:984:98
+AAGGAGGTCATCATACAATGATAAAAAGATCAATTC
+>EAS114_28:3:110:984:98
+ACTAAAACCCCATACTTTACTGCTACTCAATATATC
+>EAS114_28:3:173:627:465
+GTAAACTCTCAAATATTGCTAGTGGGAGTATAAATT
+>EAS114_28:3:173:627:465
+TGATGGTTACACTAAAAGCCCATACTTTACTGCTAC
+>EAS114_28:3:176:402:458
+AAATAGCTAAAACTAAAAAAGCAAAAACAAAAACTA
+>EAS114_28:3:176:402:458
+CCTAAGAGGGATGAGAAATTACCTAATTGGTACAAT
+>EAS114_28:3:202:275:776
+CAAATACTACTAGACCTAAGAGGGATGAGAAATTAC
+>EAS114_28:3:202:275:776
+TCTACGCAAACAGAAACCAAATGAGAGAAGGAGTAG
+>EAS114_28:3:250:628:423
+CAATGGGCTTCTCAGCGGAAACCTTACAAGCCAGAA
+>EAS114_28:3:250:628:423
+CTCTTTAGTCTTGCTAGAGATTTAGACATCTAAATG
+>EAS114_28:3:279:763:945
+CTGCACATTACTACCCTGCAATTAATATAATTGTGT
+>EAS114_28:3:279:763:945
+GCCGTCCGTGTCCTCCCATCTGGCCTCGTCCACACT
+>EAS114_28:3:308:509:948
+AATATATCCATGTAACAAATCTGCGCTTGTACTTCT
+>EAS114_28:3:308:509:948
+AATTCAGCAAGAAGATATAACCATCCTACTAAATAC
+>EAS114_28:3:32:492:907
+CAAACACGAATGTTATGCCCTGCTAAACTAAGCATC
+>EAS114_28:3:32:492:907
+TGTAGTCATCAGACTATCTAAAGTCAACATGAAGGA
+>EAS114_28:3:78:773:660
+ATTCTGCAGCCCAGCTCCAGATTGCTTGTGGTCTGA
+>EAS114_28:3:78:773:660
+CCCCAGATACCATCCCTGTCTTACTTCCAGCTCCCC
+>EAS114_28:4:13:701:55
+AAACCAAATGAGAGAAGGAGTAGCTATACTTATATC
+>EAS114_28:4:13:701:55
+TTCATAAAACAAATACTACTAGACCTAAGAGGGATG
+>EAS114_28:4:149:572:877
+ATGTAAAGTAACTGAACCTATGAGTCACAGGTATTC
+>EAS114_28:4:149:572:877
+GAGGCTCAAAGAATGCCAGGAAGATACATTGCAAGA
+>EAS114_28:4:215:246:640
+AAAAGCATACAGTCATCTATAAAGGAAATCCCATCA
+>EAS114_28:4:215:246:640
+AAAGTCAAGTCTTTCCTGACAAGCAAATGCTAAGAT
+>EAS114_28:4:305:707:258
+AAAAAGATGTTCTACGCAAGCAGAAACCAAATGAGA
+>EAS114_28:4:305:707:258
+GAACAAAACCTCATATATCAATATTAACTTTGAATA
+>EAS114_28:4:322:631:245
+CCCTGCCCCATCTCTTGTAATCTCTCTCCTTTTTGC
+>EAS114_28:4:322:631:245
+TATTTTTGTCTTGACACCCAACTAATATTTGTCTGA
+>EAS114_28:4:9:55:730
+ATCCCTGTCTTACTTCCAGCTCCCCAGAGGGAAAGC
+>EAS114_28:4:9:55:730
+CAGCCCAGCTCCAGATTGCTTGTGGTCTGACAGGCT
+>EAS114_28:5:104:350:749
+AAATATAGAAATTGAAACAGCTGTGTTTAGTGCCTT
+>EAS114_28:5:104:350:749
+TGCCCTCTTCTTCCAAAGATGAAACGCGTAACTGCG
+>EAS114_28:5:11:868:62
+TCTTAGGGAAGAACAGCTTAGGTATCAATTTGGTGT
+>EAS114_28:5:11:868:62
+TTTACTGTCATAACTATGAAGAGACTATTGCCAGAT
+>EAS114_28:5:163:832:715
+TAAAAACATGAACTAACTATATGCTGTTTACAAGAA
+>EAS114_28:5:163:832:715
+TAAAACAAAGGAGGTCATCATACAATGATAAAAAGA
+>EAS114_28:5:206:671:49
+ACCATCCCTGTCTTACTTCCAGCTCCCCAGAGGGAA
+>EAS114_28:5:206:671:49
+GCTTGTGGTCTGACAGGCTGCAACTGTGAGCCATCA
+>EAS114_28:5:209:778:588
+AACAGTCTAGATGAGAGAGAACTTCCCTGGAGGTCT
+>EAS114_28:5:209:778:588
+TTTTTGCTGCATCCCTGTCTTCCTCTGTCTTGATTT
+>EAS114_28:5:23:944:377
+AATGTTATGCCCTGCTAAACTAAGCATCATAAATGA
+>EAS114_28:5:23:944:377
+AGTACAAAACTCACAGGTTTTATAAAACAATTAATT
+>EAS114_28:6:11:151:750
+GTTTTTATTTTTTTCCTCTCTCTTTTTTTTTTTTTT
+>EAS114_28:6:155:68:326
+CCCATTTGGAGCCCCTCTAAGCCGTTCTATTTGTAA
+>EAS114_28:6:155:68:326
+GTCAGGGAAGGAGCATTTTGTCAGTTACCAAATGTG
+>EAS114_28:6:175:705:982
+CATGGTTTAGGGGTATAATACCTCTACATGGCTGAT
+>EAS114_28:6:175:705:982
+CTGGATTCTGGGAAATTCTTCATCCTGGACCCTGAG
+>EAS114_28:6:185:87:475
+AAGAAACTCATTAATAAAGACATGAGTTCAGGTAAA
+>EAS114_28:6:185:87:475
+ATTGAGACTACAGAGCAACTAGGTAAAAAATTAACA
+>EAS114_28:6:187:996:432
+TGCTCAAAAGAATTGTAAAAGTCAAAATTAAAGTTC
+>EAS114_28:6:187:996:432
+TTGAATAAAAAGGGATTAAATTCCCCCACTTAAGAG
+>EAS114_28:6:51:506:878
+TAATCTCTCTCCTTTTTGCTGCATCCCTGTCTTCCT
+>EAS114_28:6:51:506:878
+TTTGTCTGAGCAAAACAGTCTAGATGAGAGAGAACT
+>EAS114_28:6:54:263:585
+TGAAAGCTTGGGCTGTAATGATGCCCCTTGGCCATC
+>EAS114_28:6:54:263:585
+TGTCCATGTACACACGCTGTCCTATGTACTTATCAT
+>EAS114_28:7:133:514:754
+AGCTATACTTATATCAGATAAAGCACACTTTAAATC
+>EAS114_28:7:133:514:754
+TAAATTTGAATAAAAAGGGATTAAATTCCCCCACTT
+>EAS114_28:7:157:786:424
+GCTTTACTGTCATAACTATGAAGAGACTATTGCCAG
+>EAS114_28:7:157:786:424
+TTAGGTATCAATTTGGTGTTCTGTGTAAAGTCTCAG
+>EAS114_28:7:178:276:693
+GTTCAGAACTTGAAGACAAGTCTCTTATGAATTAAC
+>EAS114_28:7:178:276:693
+TTGGAAAAACTATTTGAGGAAGTAATTGGGGAAAAC
+>EAS114_28:7:215:863:521
+ACTCACCATCATAAATACACACAAAAGTACAAAACT
+>EAS114_28:7:215:863:521
+TAAGAGATATAGATTGGCAGAACAGATTTAAAAACA
+>EAS114_28:7:242:354:637
+AACTATATTTATGCTATTCAGTTCTAAATATAGAAA
+>EAS114_28:7:242:354:637
+CCCTCTTCTTCCAAAGATGAAACGCGTAACTGCGCT
+>EAS114_28:7:287:492:169
+CGCTCTCATTCACTCCAGCTCCCTGTCACCCAATGG
+>EAS114_28:7:287:492:169
+GTGTTTAGTGCCTTTGTTCAACCCCCTTGCAACAAC
+>EAS114_28:7:57:324:546
+GTCATCTATAAAGGAAATCCCATCAGAATAACAATG
+>EAS114_28:7:57:324:546
+TAATTGGGGAAAACCTCTTTAGTCTTGCTAGAGATT
+>EAS114_30:1:134:379:893
+AGTTTCTGCCCCCAGCATGGTTGTACTGGGCAATA
+>EAS114_30:1:134:379:893
+CGCTGTCCTATGTACTTATCATGACTCTATCCCAA
+>EAS114_30:1:154:818:165
+GAACAGGGAGGTGCACTAATGCGCTCCACGCCCAA
+>EAS114_30:1:154:818:165
+TTCTTATCTGCACATTACTACCCTGCAATTAATAT
+>EAS114_30:1:176:168:513
+ATTTGTAATGAAAACTATATTTATGCTATTCAGTT
+>EAS114_30:1:176:168:513
+TTTGATGCCCTCTTCTTCCAAAGATGAAACGCGTA
+>EAS114_30:1:188:863:790
+CATGAGTTCAGGTAAAGGGGTGGAAAAAGATGTTC
+>EAS114_30:1:188:863:790
+TTAATTGAGACTACAGAGCAACTAGGTAAAAAATT
+>EAS114_30:1:243:10:911
+TATTCAGTTCTAAATATAGAAATTGAAACAGCTGT
+>EAS114_30:1:64:526:339
+ACATTACAACAGGAACAAAACCTCATATATCAATA
+>EAS114_30:1:64:526:339
+CAAATGAGAGAAGGAGTATCTATACTTATATCAGA
+>EAS114_30:2:111:142:21
+ATCAGAATAACAATGGGCTTCACAGCGGAAACCTT
+>EAS114_30:2:111:142:21
+CTTGCTAGAGATTTAGACATCTAAATGAAAGAGGC
+>EAS114_30:2:226:885:729
+AAAAGGGATTAAATTCCCCCACTTAAGAGATATAG
+>EAS114_30:2:226:885:729
+GCTGAACTTACATCAGATAAAGCACACTTTAAATC
+>EAS114_30:2:272:750:698
+GTGTTTATTACCAGAGGGATGGAGGGATGACGGAC
+>EAS114_30:2:272:750:698
+TGCAGCCCAGATCCAGATTGCTTGTGGTCTGACAG
+>EAS114_30:2:297:949:26
+ACCAGTCCTATAAGAAATGCTCAAAAGAATTGTAA
+>EAS114_30:2:297:949:26
+CATATATCAATATTAACTTTGAATAAAAAGGGATT
+>EAS114_30:2:303:428:326
+AAAATTAAAATTTAACAAAAGTAAATAAAACACAT
+>EAS114_30:2:303:428:326
+TTTTTTTTTTTTTTTTTCTCTTTTTTTTTTTTTTT
+>EAS114_30:2:30:887:404
+CAACAGGAAGAAAAGGTCTTTCAAAAGGTGATGTG
+>EAS114_30:2:30:887:404
+TTGCCTTCAGACCCTGCACGAATGCGTCTCTACCA
+>EAS114_30:2:315:412:921
+GTAAAGATGTGGGGAAAAAAGTAAACTCTCAAATA
+>EAS114_30:2:315:412:921
+TTCTGATGATGGTTACACTACAAGCCCATACTGTA
+>EAS114_30:2:82:963:128
+ATTAAAGTTCAATACTCACCATCATAAATACACAC
+>EAS114_30:2:82:963:128
+GGCAGAACAGATTTAAAAACATGAACTAACTATAT
+>EAS114_30:3:139:117:262
+AGGGGCTTAACCTCTGGTGACTGCCAGAGCTGCTG
+>EAS114_30:3:139:117:262
+GTTCTCAAGGTTGTTGCAAGGGGGTCTATGTGAAC
+>EAS114_30:3:14:697:541
+TAAAAGCAGCAAGAGAAAAGCATACAGTCATCTAT
+>EAS114_30:3:14:697:541
+TTGGAAAAACTATTTGAGGAAGTAATTGGGGAAAA
+>EAS114_30:3:161:366:544
+CTTCTGTAATTGAAAAATTCATTTAAGAAATTACA
+>EAS114_30:3:181:582:435
+CAAGTCTTTCCTGACAAGCAAATGCTAAGATAATT
+>EAS114_30:3:181:582:435
+GAAATCCCATCAGAATAACAATGGGCTTCTCAGCA
+>EAS114_30:3:187:294:947
+ACAGGGGGCTGCGCGGTTTCCCATCATGAAGCACT
+>EAS114_30:3:187:294:947
+AGAGACTATTGCCAGATGAACCACACATTAATACT
+>EAS114_30:3:215:840:760
+AAGTATTGGTAAAGATGTGGGGAAAAAAGTAAACT
+>EAS114_30:3:215:840:760
+CTGATGATGGTTACACTAAAAGCCCATACTTTCCT
+>EAS114_30:3:24:195:604
+TCACAGTTTCTGCCCCCAGCATGGTTGTACTGTGC
+>EAS114_30:3:24:195:604
+TGTCCTATGTACTTATCATGACTCTATCCCAAATT
+>EAS114_30:3:302:288:657
+AGGTATCAATTTGGTGTTCTGTGTAAAGTCTCAGG
+>EAS114_30:3:302:288:657
+CCAGATGAACCACACATTAATACTATGTTTCTTAT
+>EAS114_30:3:35:361:546
+TGCACTAATGCGCTCCACGCCCAAGCCCTTCTCAC
+>EAS114_30:3:35:361:546
+TTACTTCCAGCTCCCCAGAGGGAAAGCTTTCAACG
+>EAS114_30:3:39:348:594
+AAGCATCATAAATGAAGGGGAAATAAAGTCAAGTC
+>EAS114_30:3:39:348:594
+CTAAAATCAGCAAGAGAAAAGCATACAGTCATCTA
+>EAS114_30:4:183:852:253
+ACAACAGGAAGAAAAGGTCTTTCAAAAGGTGATGT
+>EAS114_30:4:183:852:253
+CCATTTCTTTTGGCATTTGCCTTCAGACCCTACAC
+>EAS114_30:4:317:378:535
+AGCTTGGGCTGTAATGATGCCCCTTGGCCATCACC
+>EAS114_30:4:317:378:535
+GCTGTCCTATGTACTTATCATGACTCTATCCCAAA
+>EAS114_30:4:327:795:103
+AACCTTGAGAACCCCAGGGAATTTGTCAATGTCAG
+>EAS114_30:4:327:795:103
+ACAGGGGCTTAACCTCTGGTGACTGCCAGAGCTGC
+>EAS114_30:4:328:537:640
+AAGTATGAGATTATGTAAAGTAACTGAACCTATGA
+>EAS114_30:4:328:537:640
+GGAAGATACATTGCAAGACAGACTTCATCAAGATA
+>EAS114_30:5:327:991:508
+ACCCCAGGGAATTTGTCAATGTCAGGGAAGGAGCA
+>EAS114_30:5:327:991:508
+TCTGGATTCTGGGAAATTCTTCATCCTGGACCCTG
+>EAS114_30:5:32:461:154
+ACAGGTTTTATAAAACAATTAATTGAGACTACAGA
+>EAS114_30:5:32:461:154
+TTACAAGAAACTCATTAATAAAGACATGAGTTCAG
+>EAS114_30:6:137:741:866
+ACACTAAAAGCCCATACTTTACTGCTACTCAATAT
+>EAS114_30:6:137:741:866
+GATGAGGGGAAAAAAGTAAACTCTCAAATATTGCT
+>EAS114_30:6:157:42:763
+TCTGGGAGCCGTCCGTGTCCTCCCATCTGGCCTCG
+>EAS114_30:6:157:42:763
+TTTCTTATCTGCACATTACTACCCTGCAATTATTA
+>EAS114_30:6:163:312:891
+CCCAGCTCCAGATTGCTTGTGGTCTGACAGGCTGC
+>EAS114_30:6:163:312:891
+TTCCCCAGATACCGTCCCTGTCTTACTTCCAGCTC
+>EAS114_30:6:214:565:337
+AAATGAAAGAGGCTCAAAGAATGCCAGGAAGATAC
+>EAS114_30:6:214:565:337
+CAGAATAACAATGGGCTTCTCAGCAGAAACCTTAC
+>EAS114_30:6:220:809:850
+GGGGGGAAAAAGATGTGCTACACAAAAAGATTCCA
+>EAS114_30:6:220:809:850
+TTCATAAAACAAATACTACTAGACCTAAGAGGGAT
+>EAS114_30:6:238:803:383
+ACAATTAATTGAGACTACAGAGCAACTAGGTAAAA
+>EAS114_30:6:238:803:383
+ACTCATTAATAAAGACATGAGTTCAGGTAAAGGGG
+>EAS114_30:6:243:209:110
+AAAACATGAACTAACTATATGCTGTTTACAAGAAA
+>EAS114_30:6:243:209:110
+CACAGGTTTTATAAAACAATTAATTGAGACTACAG
+>EAS114_30:6:277:397:932
+TTTCTTTTCACTTTTTTTTTTTTTTTTTTTTACTT
+>EAS114_30:6:290:146:36
+CTTTCCCATCCCCCGGTCCCTGCCCCATCTCTTGT
+>EAS114_30:6:290:146:36
+TTATCATGACTCTATCCCAAATTCCCAATTACGTC
+>EAS114_30:6:326:309:149
+CAACCTTGAGAACCCCAGGGAATTTGTCAATGTCA
+>EAS114_30:6:326:309:149
+CTCCCTGTCACCCAATGGACCTGTGATATCTGGAT
+>EAS114_30:6:41:461:436
+TAAAGTAACTGAACCTATGAGTCACAGGTATTCCT
+>EAS114_30:6:41:461:436
+TAGTCATCAGACTATCTAAAGTCAACATGAAGGAA
+>EAS114_30:6:49:656:507
+AAGGAAATCCCATCAGAATAACAATGGGCTTCTCA
+>EAS114_30:6:49:656:507
+TCCTGACAAGCAAATGCTAAGATAATTCATCATCA
+>EAS114_30:6:4:665:771
+GAATAAAAAGGGATTAAATTCCCCCACTTAAGAGA
+>EAS114_30:6:4:665:771
+GTGCTTTATCTGATATCAATGCCGATAAACTGCCT
+>EAS114_30:6:62:386:959
+AAAAGCTTTCAACGCTTCTAGCCATTTCTTTTGGC
+>EAS114_30:6:62:386:959
+AATGAACAACAGGAAGAAAAGGTCTTTCAAAAGGT
+>EAS114_30:7:269:944:220
+ATCTTCTTCTTAGGGAAGAACAGCTTAGGTATCAA
+>EAS114_30:7:269:944:220
+TGGGCAATACATGAGATTATTAGGAAATGCTTTAC
+>EAS114_30:7:283:799:560
+ACATAGACCCCCTTGCAACAACCTTGAGAACCCCA
+>EAS114_30:7:283:799:560
+GGGGTTGCCAGCACAGGGGCTTAACCTCTGGTGAC
+>EAS114_30:7:310:155:312
+CAGCAAGAGAAAAGCATACAGTCATCTATAAAGGA
+>EAS114_30:7:310:155:312
+CATAAATGAAGGGGAAATAAAGTCAAGTCTTTCCT
+>EAS114_30:7:319:11:255
+TACCCAGATTCATAAAACAAATACTACTAGACCTA
+>EAS114_30:7:319:11:255
+TCTATAAAAAAATTAAAATTTAACAAAAGTAAATA
+>EAS114_30:7:59:871:351
+GTAAAAAATTAACATTACAACAGGAACAAAACCTC
+>EAS114_30:7:59:871:351
+TAAAGACATGAGTTCAGGTAAAGGGGTGGAAAAAG
+>EAS114_30:7:71:311:202
+TATGAGATTATGTAAAGTAACTGAACCTATGAGTC
+>EAS114_30:7:71:311:202
+TCAAGATATGTAGTCATCAGACTATCTAAAGTCAA
+>EAS114_32:1:199:760:42
+ACCCAATTAATATTTTTCTTAGCAAAACAGTCTAG
+>EAS114_32:1:199:760:42
+CTCTCTAATTTTTGCTGCTTCCATGTCTTACTCTG
+>EAS114_32:1:208:971:600
+AAAAAAACCTGTCAAACACGAATGTTATGCCCTGC
+>EAS114_32:1:208:971:600
+AGATATGTAGTCATCAGACTATCTAAAGTCAACAT
+>EAS114_32:2:163:618:570
+AGGCTGCAACTGTGAGCCATCACAATGAACAACAG
+>EAS114_32:2:163:618:570
+GGAAAGCTGTCAACGCTTCTAGCCATTTCTTTTGG
+>EAS114_32:2:197:170:559
+CTCATTCACTCCAGCTCCCTGTCACCCAATGGACC
+>EAS114_32:2:197:170:559
+TTCTCAAGGTTGTTGCAAGGGGGTCTATGTGAACA
+>EAS114_32:2:247:900:123
+AAAACATGAACTAACTATATGCTGTTTACAAGAAA
+>EAS114_32:2:247:900:123
+AATTCAGCAAGAAGATATAACCATCCTACTAAATA
+>EAS114_32:2:283:577:398
+ACAATGGGCTTCTCAGCGGAAACCTTACAAGCCAG
+>EAS114_32:2:283:577:398
+CTAGAGATTTAGACATCTAAATGAAAGAGGCTCAA
+>EAS114_32:2:306:119:56
+CTTCTCACAGTTTCTGCCCCCAGCATGGTTGTACT
+>EAS114_32:2:306:119:56
+TCCATGTACACACGCTGTCCTATGTACTTATCATG
+>EAS114_32:3:236:475:254
+AGATAAAGCACACTTTAAATCAACAACAGTAAAAT
+>EAS114_32:3:236:475:254
+TTCCCCCACTTAAGAGATATAGATTGGCAGAACAG
+>EAS114_32:3:307:113:346
+AATTCAGCAAGAAGATATAACCATCCTACTAAATA
+>EAS114_32:3:307:113:346
+ATGCTGTTTACAAGAAACTCATTAATAAAGACATG
+>EAS114_32:4:156:21:69
+AAAAATGAACAGAGCTTTCAAGAAGTATGAGATTA
+>EAS114_32:4:156:21:69
+TTGCAAGACAGACTTCATCAAGATATGTAGTCATC
+>EAS114_32:4:20:41:138
+CATTTCTTTTGGCATTTGCCTTCAGACCCTACACG
+>EAS114_32:4:20:41:138
+GTCTTTCAAAAGGTGATGTGTGTTCTCATCAACCT
+>EAS114_32:4:228:587:504
+GCACATTACGACCCGGCAAGGTGTATAATTGTGTC
+>EAS114_32:4:228:587:504
+GTGCACTAATGCGCTCCACGCCCAAGCCCTTCTCA
+>EAS114_32:4:246:647:765
+GATCAATTCAGCAAGAAGATATAACCATCCTACTA
+>EAS114_32:4:246:647:765
+TATGCTGTTTACAAGAAACTCATTAATAAAGACAT
+>EAS114_32:4:42:923:169
+ACAGTTTCTGCCCCCAGCATGGTTGTACTGGGCAA
+>EAS114_32:4:42:923:169
+TTCCTATGTACTTATCATGAATCTATCCCAAATTC
+>EAS114_32:4:5:396:292
+ATACATATGCACCTAACACAAGACTACCCAGATTC
+>EAS114_32:4:5:396:292
+TAAAGGGGTGGAAAAAGATGTTCTACGCAAACAGA
+>EAS114_32:4:7:282:424
+CAAAAACAAAAACTATGCTAAGTATTGTTAAAGAT
+>EAS114_32:4:7:282:424
+TAATTGGTACAATGTACAATATTCTGATGATGGTT
+>EAS114_32:5:109:199:592
+ACGAATATTATGCCCTGCTAAACTAAGCATCATAA
+>EAS114_32:5:109:199:592
+AGTCATCAGACTATCTAAAGTCAACATGAAGGAAA
+>EAS114_32:5:182:313:319
+AATTTGGTGTTCTGTGTAAAGTCTCAGGGAGCCGT
+>EAS114_32:5:182:313:319
+GATGAACCACACATTAATACTATGTTTCTTATCTG
+>EAS114_32:5:267:170:250
+CATAAAACAAATACTACTAGACCTAAGAGGGATGA
+>EAS114_32:5:267:170:250
+CATAGCTAAAACTAAAAAAGCAAAAACAAAAACTA
+>EAS114_32:5:78:583:499
+TTTACGCTATTCAGTACTAAATATAGAAATTGAAA
+>EAS114_32:6:122:342:296
+AAAGCTTGGGCTGTAATGATGCCCCTTGGCCATCA
+>EAS114_32:6:122:342:296
+TCCTATGTACTTATCATGACTCTATCCCAAATTCC
+>EAS114_32:6:178:342:866
+AACAAATCTGCGCTTGTACTTCTAAATCTATAAAA
+>EAS114_32:6:178:342:866
+ATACATATGCACCTAACACAAGACTACCCAGATTC
+>EAS114_32:6:179:735:569
+ATGTTAAAATGTCTATTTTTGTCTTGACACCCAAC
+>EAS114_32:6:179:735:569
+CATCACCCGGTCCCTGCCCCATCTCTTGTAATCTC
+>EAS114_32:6:199:818:124
+AACTATTTGAGGAAGTAATTGGGGAAAACCTCTTT
+>EAS114_32:6:199:818:124
+ACTAAACCAAGCAGAAGAAAGAGGTTCAGAACTTG
+>EAS114_32:6:78:909:394
+ATTGCTTGGTGTCTGACAGGCTGCAACTGTGAGCC
+>EAS114_32:6:78:909:394
+TACCAGAGGGATGGAGGGAAGAGGGACGCTGAAGA
+>EAS114_32:6:88:162:587
+GGTTTTCTGTTTCTTTGTTTGATTTGGTGGAAGAC
+>EAS114_32:6:88:162:587
+TTCTGTGTAAAGTCTCAGGGAGCCGTCCGTGTCCT
+>EAS114_32:7:174:597:66
+TCTCTTGTAATCTCTCTCCTTTTTGCTGCATCCCT
+>EAS114_32:7:174:597:66
+TCTTCTTCTTAGGGAAGAACAGCTTAGGTATCAAT
+>EAS114_32:7:201:959:19
+CTCTACATGGCTGATTATTAAAACAATGTTCCCCA
+>EAS114_32:7:201:959:19
+TATCTGGATTCTGGGAAATTCTTCATCCTGGACCC
+>EAS114_32:7:256:407:470
+AACGCTTCTAGCCATTTCTTTTGGCATTTGCCTTC
+>EAS114_32:7:256:407:470
+CAGCATGGTTGTACTGGGCAATACATGAGATTATT
+>EAS114_39:1:12:884:219
+GAGCCATCACAATGAACAACAGGAAGAAAAGGTCT
+>EAS114_39:1:12:884:219
+GCTTTCAACGCTTCTAGCCATTTCTTTTGGCATTT
+>EAS114_39:1:28:350:895
+ATATAGTTGAAAGCTCTAACAATAGACTAAACCAA
+>EAS114_39:1:28:350:895
+TATGAGTCACAGGTATTCCTGAGGAAAAAGAAAAA
+>EAS114_39:1:43:1120:878
+ACTAATGCGCTCCACGCCCAAGCCCTTCTCACAGT
+>EAS114_39:1:43:1120:878
+TAATTGTGTCCATGTACACACGCTGTCCTATGTAC
+>EAS114_39:1:70:147:84
+ATAGACCCCCTTGCAACAACCTTGAGAACCCCAGG
+>EAS114_39:1:70:147:84
+CCAGCACAGGGGCTTAACCTCTGGTGACTGCCAGA
+>EAS114_39:1:71:636:533
+GCCTCGTCCACACTGGTTCTCTTGAAAGCTTGGGC
+>EAS114_39:1:71:636:533
+GTGGAAGACATAATCCCACGCTTCCTATGGAAAGG
+>EAS114_39:1:73:302:1574
+AAGGTTGTTGGGAGATTTTTAATGATTCCTCAATG
+>EAS114_39:1:73:302:1574
+CCTCGTCCACACTGGTTCTCTTGAAAGCTTGGGCT
+>EAS114_39:1:98:641:1040
+CAGAACAGATTTAAAAACATGAACTAACTATATGC
+>EAS114_39:1:98:641:1040
+TAAAACAAAGGAGGTCATCATACAATGATAAAAAG
+>EAS114_39:2:18:967:582
+AAGCCGTTCTATTTGTAATGAAAACTATATTTATG
+>EAS114_39:2:18:967:582
+ACGCTGAAGAACTTTGATGCCCTCTTCTTCCAAAG
+>EAS114_39:2:38:670:564
+CAGGTTTTATAAAACAATTAATTGAGACTACAGAG
+>EAS114_39:2:38:670:564
+CTAACTATATGCTGTTTACAAGAAACTCATTAATA
+>EAS114_39:2:41:576:1016
+CTCTCCTTTTTGCTGCATCCCTGTCTTCCTCTGTC
+>EAS114_39:2:41:576:1016
+TGTCTGAGCAAAACAGTCTAGATGAGAGAGAACTT
+>EAS114_39:2:57:1064:925
+TGACAAGCAAATGCTAAGATAATTCATCATCACTA
+>EAS114_39:2:5:1219:137
+AAAACTAAAAAAGCAAAAACAAAAACTATGCTAAG
+>EAS114_39:2:5:1219:137
+ACCTAAGAGGGATGAGAAATTACATAATTGGTACA
+>EAS114_39:3:11:1238:1728
+AGAGATTTAGACATCTAAATGAAAGAGGCTCAAAG
+>EAS114_39:3:11:1238:1728
+TCCCATCAGAATAACAATGGGCTTCTCAGCGGAAA
+>EAS114_39:3:55:464:146
+AAAAAGATCAATTCAGCAAGAAGATATAACCATCC
+>EAS114_39:3:55:464:146
+CTCAATATATCCATGTAACAAATCTGCGCTTGTAC
+>EAS114_39:3:6:1064:1805
+TAAAATTTAACAAAAGTAAATAAAACACATAGCTA
+>EAS114_39:3:6:1064:1805
+TTGGTAATTTCGTTTTTTTTTTTTTCTTTTCTCTT
+>EAS114_39:3:88:84:1558
+AGTAACTGAACCTATGAGTCACAGGTATTCCTGTG
+>EAS114_39:3:88:84:1558
+ATCAGACTATCTAAAGTCAACATGAAGGAAAAAAA
+>EAS114_39:4:10:1312:1558
+AACTAACTATATGCTGTTTACAAGAAACTCATTAA
+>EAS114_39:4:10:1312:1558
+AGGTTTTATAAAACAATTAATTGAGACTACAGAGC
+>EAS114_39:4:30:432:228
+ATCCTACTAAATACATATGCACCTAACACAAGACT
+>EAS114_39:4:30:432:228
+GACATGAGTTCAGGGAAAGGGGTGGAAAAAGATGT
+>EAS114_39:4:30:570:902
+AAAAACCTGTCAAACACGAATGTTATGCCCTGCTA
+>EAS114_39:4:30:570:902
+ATACTCACCATCATAAATACGCACAAAAGTACAAA
+>EAS114_39:4:43:1047:1626
+GATGAGAGAGAACTTCCCTGGAGGTCTGATGGCGT
+>EAS114_39:4:43:1047:1626
+GTTGGTTTTCTGTTTCTTTGTTTGATTTGGTGGAA
+>EAS114_39:4:58:271:612
+AGGAAAAAGAAAAAGTGAGAAGTTTGGAAAAACTA
+>EAS114_39:4:58:271:612
+ATGAAGGAAAAAAATTCTAAAATCAGCAAGAGCAA
+>EAS114_39:4:93:77:1338
+GCTGCTTACAAGAAGCGCATTAATAAAGACATGAG
+>EAS114_39:4:93:77:1338
+GTCATCATACAATGAAAAAAAGATCAATTCAGCAA
+>EAS114_39:5:17:1222:783
+AAGAAAGAGGTTCAGAACTTGAAGACAAGTCTCGT
+>EAS114_39:5:17:1222:783
+TGAGAAGTTTGGAAAAACTATTTGAGGAAGTAATT
+>EAS114_39:5:42:1223:1087
+CAGTCCCTGCCCCATCTCTTGTAATCTCTCTCCTT
+>EAS114_39:5:42:1223:1087
+TTGTCTTGACACCCAACTAATATTTGTCTGAGCAA
+>EAS114_39:5:50:972:1286
+AGAGGGATGGAGGGAAGAGGGACGCTGAAGAACTT
+>EAS114_39:5:50:972:1286
+TTGTGGTCTGACAGGCTGCAACTGTGAGCCATCAC
+>EAS114_39:5:61:1000:1534
+CTTGAAGACAAGTCTCTTATGAATTAACCCAGTCA
+>EAS114_39:5:61:1000:1534
+GGGGAAAACCTCTTTAGTCTTGCTAGAGATTTAGA
+>EAS114_39:5:93:312:331
+AACTCATTAATAAAGACATGAGTTCAGGTAAAGGG
+>EAS114_39:5:93:312:331
+ATCCTACTAAATACATATGCACCTAACACAAGACT
+>EAS114_39:6:13:1034:1144
+AAAGATGAAACGCGTAACTGCGCTCTCATTCACTC
+>EAS114_39:6:13:1034:1144
+AATTGAAACAGCTGTGTTTAGTGCCTTTGTTCACA
+>EAS114_39:6:34:380:815
+AAGAGGTTCAGAACTTGAAGACAAGTCTCTTATGA
+>EAS114_39:6:34:380:815
+ATTGGGGAAAACCTCTTTAGTCTTGCTAGAGATTT
+>EAS114_39:6:71:644:1792
+AAAAGTACAAAACTCACAGGTTTTATAAAACAATT
+>EAS114_39:6:71:644:1792
+CCTGCTAAACTAAGCATCATAAATGAAGGGGAAAT
+>EAS114_39:6:76:282:1668
+AACAAAAACTATGCTAAGTATTGGTAAAGATGTGG
+>EAS114_39:6:76:282:1668
+TACAATGTACAATATTCTGATGATGGTTACACTAA
+>EAS114_39:6:7:492:1088
+ACAGGTTTTATAAAACAATTAATTGAGACTACAGA
+>EAS114_39:6:7:492:1088
+TGAACTAACTATATGCTGTTTACAAGAAACTCATT
+>EAS114_39:6:85:1224:625
+GAACTCCCCTGGAGGTCTGATGGCGTTTCTCCCTC
+>EAS114_39:6:85:1224:625
+GCTGCATCCCTGTCTTCCTCTGTCTTGATTTCCTT
+>EAS114_39:6:94:1273:1462
+AAGATGTTCTACGCAAACAGAAACCAAATGAGAGA
+>EAS114_39:6:94:1273:1462
+CCTAACACAAGACTACCCAGATTCATAAAACAAAT
+>EAS114_39:7:100:708:1984
+AGATGAACCACACATTAATACTATGTTTCTTATCT
+>EAS114_39:7:100:708:1984
+TACCACAGGGGGCTGCGCGGTTTCCCATCATGAAG
+>EAS114_39:7:23:1126:1886
+ACACTAAAAGCCCATACTTTACTGCTACTCAATAT
+>EAS114_39:7:23:1126:1886
+GGAGGTCATCATACAATGATAAAAAGATCAATTCA
+>EAS114_39:7:32:562:1695
+GATGATGGTTACACTAAAAGCCCATACTTTACTGC
+>EAS114_39:7:32:562:1695
+TAAAACAAAGGAGGTCATCATACAATGATAAAAAG
+>EAS114_39:7:57:1114:2032
+TAACTATATGCTGTTTACAAGAAACTCATTAATAA
+>EAS114_39:7:57:1114:2032
+TATTACAATGATAAAAAGATCAATTCAGCAAGAAG
+>EAS114_39:7:90:406:631
+CATCCCTGTCTTCCTCTGTCTTGATTTACTTGTTG
+>EAS114_39:7:90:406:631
+TGAGAGAGAACTTCCCTGGAGGTCTGATGGCGTTT
+>EAS114_45:1:100:979:1863
+ATTACAAAACTCACAGGTTTTATAAAACAATTAAT
+>EAS114_45:1:100:979:1863
+TTATGCCCTGCTAAACTAAGCATCATAAATGAAGG
+>EAS114_45:1:12:1296:358
+CTTGAAAGCTTGGTCTGTAATGATGCCCCTTGGCC
+>EAS114_45:1:12:1296:358
+GTCCATGTACACACGCTGTCCTATGTACTTATCAT
+>EAS114_45:1:2:1422:1820
+CACCTAACACAAGACTACCCAGATTCATAAAACAA
+>EAS114_45:1:2:1422:1820
+TACGCAAACAGAAACCAAATGAGAGAAGGAGTAGC
+>EAS114_45:1:30:1882:1210
+ATCATCACTAAACCAGTCCTATAAGAAATGCTCAA
+>EAS114_45:1:30:1882:1210
+GCAGAAACCTTACAAGCCAGAAGAGATTGGATCTA
+>EAS114_45:1:33:1407:94
+TAGGTATCAATTTGGTGTTCTGTGTAAAGTCTCAG
+>EAS114_45:1:33:1407:94
+TTACTTGTTGTTGGTTTTCTGTTTCTTTGTTTGAT
+>EAS114_45:1:77:1000:1780
+AGTAATTGGGGAAAACCTCTTTAGTCTTGCTAGAG
+>EAS114_45:1:77:1000:1780
+TGAATTAACCCAGTCAGACAAAAATAAAGAAAAAA
+>EAS114_45:1:84:275:1572
+AGGGACGCTGAAGAACTTTGATGCCCTCTTCTTCC
+>EAS114_45:1:84:275:1572
+TTATGCTATTCAGTTCTAAATATAGAAATTGAAAC
+>EAS114_45:1:95:1530:28
+AAGAGGCTCAAAGAATGCCAGGAAGATACATTGCA
+>EAS114_45:1:95:1530:28
+AATGGGCTTCTCAGCAGAAACCTTACAAGCCAGAA
+>EAS114_45:1:9:1289:215
+AGGGACGCTGAAGAACTTTGATGCCCTCTTCTTCC
+>EAS114_45:1:9:1289:215
+TATGCTATTCAGTTCTAAATATAGAAATTGAAACA
+>EAS114_45:2:13:1507:1146
+AAGTAATTGGGGAAAACCTCTTTAGTCTTGCTAGA
+>EAS114_45:2:13:1507:1146
+CAGAAGAAAGAGGTTCAGAACTTGAAGACAAGTCT
+>EAS114_45:2:15:1497:1530
+AATTACGTCCTATCTTCTTCTTAGGGAAGAACAGC
+>EAS114_45:2:15:1497:1530
+TAATCTCTCTCCTTTTTGCTGCATCCCTGTCTTCC
+>EAS114_45:2:1:1140:1206
+TCCCATTTGGAGCCCCTCTAAGCCGTTCTATTTGT
+>EAS114_45:2:1:1140:1206
+TTTATTACCAGAGGGATGGAGGGAAGAGGGACGCT
+>EAS114_45:2:20:413:1334
+CCGTGTCCTCCCATCTGGCCTCGTCCACACTGGTT
+>EAS114_45:2:20:413:1334
+TTGGTTTTCTGTTTCTTTGTTTGATTTGGTGGAAG
+>EAS114_45:2:23:1754:796
+CTTCTAAATCTATAAAAAAATTAAAATTTAACAAA
+>EAS114_45:2:23:1754:796
+CTTTGGAAAACAATTTGGTAATTTCGTTTTTTTTT
+>EAS114_45:2:33:1445:1357
+TATGAATTAACCCAGTCAGACAAAAATAAAGAAAA
+>EAS114_45:2:33:1445:1357
+TTAGTCTTGCTAGAGATTTAGACATCTAAATGAAA
+>EAS114_45:2:41:199:388
+AGAAAAAGTGAGAAGTTTGGAAAAACTATTTGAGG
+>EAS114_45:2:41:199:388
+TCTAAAGTCAACATGAAGGAAAAAAATTCTAAAAT
+>EAS114_45:2:49:163:904
+GCTCTCATTCACTCCAGCTCCCTGTCACCCAATGG
+>EAS114_45:2:49:163:904
+TCTTTCAAAAGGTGATGTGTGTTCTCATCAACCTC
+>EAS114_45:2:54:1886:719
+CTGTTTACAAGAAACTCATTAATAAAGACATGAGT
+>EAS114_45:2:54:1886:719
+TTCAGCAAGAAGATATAACCATCCTACTAAATACA
+>EAS114_45:2:59:396:359
+GGGTATAATACCTCTACATGGCTGATTATGAAAAC
+>EAS114_45:2:59:396:359
+TCACCCAATGGACCTGTGATATCTGGATTCTGGGA
+>EAS114_45:2:76:1765:700
+AAAAAGGGATTAAATTCCCCCACTTAAGAGATATA
+>EAS114_45:2:76:1765:700
+GTCCTATAAGAAATGCTCAAAAGAATTGTAAAAGT
+>EAS114_45:2:79:554:354
+AAATAAAACAAAGGAGGTCATCATACAATGATAAA
+>EAS114_45:2:79:554:354
+CAATGTACAATATTCTGATGATGGTTACACTAAAA
+>EAS114_45:3:26:1867:162
+ATATAACCATCCTACTAAATACATATGCACCTAAC
+>EAS114_45:3:26:1867:162
+ATATATCCATGTAACAAATCTGCGCTTGTACTTCT
+>EAS114_45:3:27:1881:486
+AAGAAAAGGTCTTTCAAAAGGTGATGTGTGTTCTC
+>EAS114_45:3:27:1881:486
+CCAAAGATGAAACGCGTAACTGCGCTCTCATTCAC
+>EAS114_45:3:2:1200:1076
+CATTTGCCTTCAGACCCTACACGAATGCGTCTCTA
+>EAS114_45:3:2:1200:1076
+GATGTGTGTTCTCATCAACCTCATACACACACATG
+>EAS114_45:3:32:1379:738
+TTAAGAAATTACAAAATATAGTTGAAAGCTCTAAC
+>EAS114_45:3:35:896:1588
+CTAGACCTAAGAGGGATGAGAAATTACCTAATTGG
+>EAS114_45:3:35:896:1588
+GAGTAGCTATACTTATATCAGATAAAGCACACTTT
+>EAS114_45:3:39:208:644
+ATTGTAAAAGTCAAAATTAAAGTTCAATACTCACC
+>EAS114_45:3:39:208:644
+TTTGAATAAAAAGGGATTAAATTCCCCCACTTAAG
+>EAS114_45:3:3:1377:1663
+CTGCGCTCTCATTCACTCCAGCTCCCTGTCACCCA
+>EAS114_45:3:3:1377:1663
+GGTGATGTGTGTTCTCATCAACCTCATACACACAC
+>EAS114_45:3:3:864:1888
+AATGTTATGCCCTGCTAAACTAAGCATCATAAATG
+>EAS114_45:3:3:864:1888
+CAACATGAAGGAAAAAAATTCTAAAATCAGCAAGA
+>EAS114_45:3:41:653:1568
+AACTATTTGAGGAAGTAATTGGGGAAAACCTCTTT
+>EAS114_45:3:41:653:1568
+GGTTCAGAACTTGAAGACAAGTCTCTTATGAATTA
+>EAS114_45:3:44:1578:1674
+CCTCTTCTTCCAAAGATGAAACGCGTAACTGCGCT
+>EAS114_45:3:44:1578:1674
+GCTGCAACTGTGAGCCATCACAATGAACAACAGGA
+>EAS114_45:3:75:217:337
+GACAGGCTGCAACTGTGAGCCATCACAATGAACAA
+>EAS114_45:3:75:217:337
+GAGGGAAGAGGGACGCTGAAGAACTTTGATGCCCT
+>EAS114_45:3:90:1403:1635
+TGTCTTGACACCCAACTAATATTTGTCTGAGCAAA
+>EAS114_45:3:90:1403:1635
+TTGTAATCTCTCTCCTTTTTGCTGCATCCCTGTCT
+>EAS114_45:4:48:310:473
+TGAATTAACCCAGTCAGACAAAAATAAAGAAAAAA
+>EAS114_45:4:48:310:473
+TTTAGTCTTGCTAGAGATTTAGACATCTAAATGAA
+>EAS114_45:4:73:1208:495
+AGATGAAACGCGTAACTGCGCTCTCATTCACTCCA
+>EAS114_45:4:73:1208:495
+TAAATATAGAAATTGAAACAGCTGTGTTTAGTGCC
+>EAS114_45:4:7:1347:375
+CTAAAAGCCCATACTTTACTGCTACTCAATATATC
+>EAS114_45:4:7:1347:375
+GGAAAAAAGTAAACTCTCAAATATTGCTAGTGGGA
+>EAS114_45:4:87:323:895
+ATCTGGATTCTGGGAAATTCTTCATCCTGGACCCT
+>EAS114_45:4:87:323:895
+GGTATAATACCTCTACATGGCTGATTATGAAAACA
+>EAS114_45:4:88:55:1187
+GTCACAGGTATTCCTGAGGAAAAAGAAAAAGTGAG
+>EAS114_45:4:88:55:1187
+GTCATCAGACTATCTAAAGTCAACATGAAGGAAAA
+>EAS114_45:5:56:1757:1319
+CATTAATAAAGACATGAGTTCAGGTAAAGGGGTGG
+>EAS114_45:5:56:1757:1319
+TTTATAAAACAATTAATTGAGACTACAGAGCAACT
+>EAS114_45:5:62:841:1994
+ATATCCATGTAACAAATCTGCGCTTGTACTTCTAA
+>EAS114_45:5:62:841:1994
+TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
+>EAS114_45:5:66:959:1311
+CAGAGCTGCTGGCAAGCTAGAGGCCCATCTGGAGC
+>EAS114_45:5:66:959:1311
+GGGAAGGAGCATTTTGTCAGTTACCAAATGTGTTT
+>EAS114_45:5:82:843:1838
+CTAGGTAAAAAATTAACATTACAACAGGAACAAAA
+>EAS114_45:5:82:843:1838
+TGTTCTACGCAAACAGAAACCAAATGAGAGAAGGA
+>EAS114_45:5:85:401:1190
+TACACACACATGGTTTAGGGGTATAATACCTCTAC
+>EAS114_45:5:85:401:1190
+TCACTCCAGCTCCCTGTCACCCAATGGACCTGTGA
+>EAS114_45:5:91:89:666
+GAAAACCTCTTTAGTCTTGCTAGAGATTTAGACAT
+>EAS114_45:6:14:1211:1332
+AGGAAGATACATTGCAAGACAGACTTCATCAAGAT
+>EAS114_45:6:14:1211:1332
+TTTCAAGAAGTATGAGATTATGTAAAGTAACTGAA
+>EAS114_45:6:37:156:134
+AGAGAAAAGCATACAGTCATCTATAAAGGAAATCC
+>EAS114_45:6:37:156:134
+GGAAAAACTATTTGAGGAAGTAATTGGGGAAAACC
+>EAS114_45:6:39:956:676
+TAAAACAAATACTACTAGACCTAAGAGGGATGAGA
+>EAS114_45:6:39:956:676
+TGAGAGAAGGAGTAGCTATACTTATATCAGATAAA
+>EAS114_45:6:44:77:1255
+CTCATTAATAAAGACATGAGTTCAGGTAAAGGGGT
+>EAS114_45:6:44:77:1255
+TAAAAAGATCAATTCAGCAAGAAGATATAACCATC
+>EAS114_45:6:45:1769:1130
+ACCCAATGGACCTGTGATATCTGGATTCTGGGAAA
+>EAS114_45:6:45:1769:1130
+TGTTCTCATCAACCTCATACACACACATGGTTTAG
+>EAS114_45:6:47:1791:444
+AAGAGGGATGAGAAATTACCTAATTGGTACAATGT
+>EAS114_45:6:47:1791:444
+TACTTATATCAGATAAAGCACACTTTAAATCAACA
+>EAS114_45:6:59:1548:1096
+CCCTGCCCCATCTCTTGTAATCTCTCTCCTTTTTG
+>EAS114_45:6:59:1548:1096
+GTCCTATGTACTTATCATGACTCTATCCCAAATTC
+>EAS114_45:6:5:730:1436
+GAAGAACTTTGATGCCCTCTTCTTCCAAAGATGAA
+>EAS114_45:6:5:730:1436
+TATTCAGTTCTAAATATAGAAATTGAAACAGCTGT
+>EAS114_45:6:86:693:234
+AAGTAACTGAACCTATGAGTCACAGGTATTCCTGA
+>EAS114_45:6:86:693:234
+GTAGTCATCAGACTATCTAAAGTCAACATGAAGGA
+>EAS114_45:6:86:859:1779
+TTTTTTTCATTTCTCTTTTTTTTTTTTTTTTTTTT
+>EAS114_45:6:90:561:850
+ACAGGAACAAAACCTCATATATCAATATTAACTTT
+>EAS114_45:6:90:561:850
+TACGCAAACAGAAACCAAATGAGAGAAGGAGTAGC
+>EAS114_45:6:93:1475:542
+TGAAAGCTTGGGCTGTAATGATGCCCCTTGGCCAT
+>EAS114_45:6:93:1475:542
+TTATCATGACTCTATCCCAAATTCCCAATTACGTC
+>EAS114_45:7:14:1256:204
+AAATGTCTATTTTTGTCTTGACACCCAACTAATAT
+>EAS114_45:7:14:1256:204
+TCACCCAGTCCCTGCCCCATCTCTTGTAATCTCTC
+>EAS114_45:7:14:978:1296
+ATACAATGATAAAAAGATCAATTCAGCAAGAAGAT
+>EAS114_45:7:14:978:1296
+CAATATTCTGATGATGGTTACACTAAAAGCCCATA
+>EAS114_45:7:24:1374:211
+AGCCCTTCTCACAGTTTCTGCCCCCAGCATGGTTG
+>EAS114_45:7:24:1374:211
+TGCAATTAATATAATTGTGTCCATGTACACACGCT
+>EAS114_45:7:2:168:1878
+AAAAAACCTGGCAAACACGAATGTTATGACATGTN
+>EAS114_45:7:2:168:1878
+TAAATACACACAAAAGTAGAAAACGCACCAGTTTT
+>EAS114_45:7:33:1566:588
+ACAGCTTAGGCATCAATTTGGTGTTCTGTGTAAAG
+>EAS114_45:7:33:1566:588
+TACTGTCATAACTATGAAGAGCCTATTGCCAGATG
+>EAS114_45:7:35:538:1882
+TATGCACCTAACACAAGACTACCCAGATTCATAAA
+>EAS114_45:7:35:538:1882
+TCTATAACAAAATTAAAATTTAACAAAAGTAAATA
+>EAS114_45:7:37:763:1437
+AAAGATGTTCTACGCAAACAGAAACCAAATGAGAG
+>EAS114_45:7:37:763:1437
+TAAAACAAATACTACTAGACCTAAGAGGGATGAGA
+>EAS114_45:7:45:1339:1807
+GACATCTAAATGAAAGAGGCTCAAAGAATGCCAGG
+>EAS114_45:7:69:1130:832
+ATAGTTGAAAGCTCTAACAATAGACTAAACCAAGC
+>EAS114_45:7:69:1130:832
+TCCTGAGGAAAAAGAAAAAGTGAGAAGTTTGGAAA
+>EAS114_45:7:6:758:988
+AAACAAAGGAGGTCATCATACAATGATAAAAAGAT
+>EAS114_45:7:6:758:988
+ATTCTGATGATGGTTACACTAAAAGCCCATACTTT
+>EAS114_45:7:88:451:1773
+ATAAATACACACAAAAGTACAAAACTCACAGGTTT
+>EAS114_45:7:88:451:1773
+ATTGGCAGAACAGATTTAAAAACATGAACTAACTA
+>EAS114_45:7:97:1584:777
+CCAGATGAACCACACATTAATACTATGTTTCTTAT
+>EAS114_45:7:97:1584:777
+GTCTCAGGGAGCCGTCCGTGTCCTCCCATCTGGCC
+>EAS114_45:7:9:512:826
+AACTTCCACGTCTCATCTAGGGGAACAGGGAGGTG
+>EAS114_45:7:9:512:826
+ACCACACATTAATACTATGTTTCTTATCTGCACAT
+>EAS139_11:1:35:631:594
+ATCATGACTCTATCCCAAATTCCCAATTACGTCCT
+>EAS139_11:1:35:631:594
+ATGATGCCCCTTGGCCATCACCCGGTCCCTGCCCC
+>EAS139_11:1:59:742:549
+ACAAGCAAATGCTAAGATAATTCATCATCACTAAA
+>EAS139_11:1:59:742:549
+TTAACATTACAACAGGAACAAAACCTCATATATCA
+>EAS139_11:1:81:1019:558
+ACAAAACTCACAGGTTTTATAAAACAATTAATTGA
+>EAS139_11:1:81:1019:558
+TGAACTAACTATATGCTGTTTACAAGAAACTCATT
+>EAS139_11:1:84:92:1246
+GAAAAAAGTAAACTCTCAAATATTGCTAGTGGGAG
+>EAS139_11:1:84:92:1246
+GTTACACTAAAAGCCCATACTTTACTGCTACTCAA
+>EAS139_11:2:31:628:1820
+AACCAGTCCTATAAGAAATGCTCAAAAGAATTGTA
+>EAS139_11:2:31:628:1820
+CAGGAACAAAACCTCATATATCAATATTAACTTTG
+>EAS139_11:2:42:333:516
+AGACAAGTCTCTTATGAATTAACCCAGTCAGACAA
+>EAS139_11:2:42:333:516
+TCTTTAGTCTTGCTAGAGATTTAGACATCTAAATG
+>EAS139_11:2:55:296:1457
+CACTTTAAATCAACAACAGTAAAATAAAACAAAGG
+>EAS139_11:2:55:296:1457
+CCCACTTAAGAGATATAGATTGGCAGAACAGATTT
+>EAS139_11:2:63:816:921
+AAACCTCTTTAGTCTTGCTAGAGATTTAGACATCT
+>EAS139_11:2:63:816:921
+TGAAGACAAGTCTCTTATGAATTAACCCAGTCAGA
+>EAS139_11:2:6:251:1557
+AAAACAATGTTCCCCAGATACCATCCCTGTCTTAC
+>EAS139_11:2:6:251:1557
+CCTGAGAGATTCTGCAGCCCAGCTCCAGATTGCTT
+>EAS139_11:2:71:83:58
+AAAGAAAAAAGAATTTTAAAAATGAACAGAGCTTT
+>EAS139_11:2:71:83:58
+CCAGGAAGATACATTGCAAGACAGACTTCATCAAG
+>EAS139_11:3:34:970:1374
+ATGTGTTTATTACCAGAGGGATGGAGGGAAGAGGG
+>EAS139_11:3:34:970:1374
+CTGGACCCTGAGAGATTCTGCAGCCCAGATCCAGA
+>EAS139_11:3:43:1229:1855
+ATGTACAATATTCTGATGATGGTTACACTAAAAGC
+>EAS139_11:3:43:1229:1855
+CAACAGTAAAATAAAACAAAGGAGGTCATCATACA
+>EAS139_11:3:65:556:1505
+CAATGAACAACAGGAAGAAAAGGTCTTTCAAAAGG
+>EAS139_11:3:65:556:1505
+TGCCTTCAGACCCTACACGAATGCGTCTCTACCAC
+>EAS139_11:3:81:12:1231
+AAAAAGCAAAAACAAAAACTATGCTAAGTATTGGT
+>EAS139_11:3:81:12:1231
+TTACCTAATTGGTACAATGTACAATATTCTGATGA
+>EAS139_11:4:26:137:1382
+AATGTTATGCCCTGCTAAACTAAGCATCATAAATG
+>EAS139_11:4:26:137:1382
+AGACTATCTAAAGTCAACATGAAGGAAAAAAATTC
+>EAS139_11:4:36:1184:994
+GCCAGAAGAGATTGGATCTAATTTTTGGACTTCTT
+>EAS139_11:4:36:1184:994
+TACATTGCAAGACAGACTTCATCAAGATATGTAGT
+>EAS139_11:4:36:1231:1381
+AAGAGATATAGATTGGCAGAACAGATTTAAAAACA
+>EAS139_11:4:36:1231:1381
+TAAAAGTCAAAATTAAAGTTCAATACTCACCATCA
+>EAS139_11:4:38:557:1441
+GATAAAAATAAAAAAGCAAAAACAAAAACTATGCT
+>EAS139_11:4:38:557:1441
+TAAGAGGGATGAGAAATTACCTAATTGGTACAATG
+>EAS139_11:4:50:30:15
+AGATTATGTAAAGTAACTTAACCTATGAGTCCAAG
+>EAS139_11:4:50:30:15
+TACATTGCAAGACAGTCGTCAGCAAGATATGTAGT
+>EAS139_11:4:63:527:1923
+GCTTTACTGTCATAACCATGAAGAGACTATTGCCA
+>EAS139_11:4:63:527:1923
+TACACGAATGCGTCTCTACCACAGGGGGCTGCGCG
+>EAS139_11:5:32:686:735
+AAGTTTGGAAAAACTATTTGAGGAAGTAATTGGGG
+>EAS139_11:5:32:686:735
+CAGAAGAAAGAGGTTCANANNNTGANGACAAGTCT
+>EAS139_11:5:41:314:1173
+AAGAAAAAAAAACCTGTCAAACACGAATGTTATGC
+>EAS139_11:5:41:314:1173
+AATTAAAGTTCAATACTCACCATCATAAATACACA
+>EAS139_11:5:52:1278:1478
+GCTTGTACTTCTAAATCTATAACAAAATTAAAATT
+>EAS139_11:5:52:1278:1478
+GTTTTTTTTTTTTTCTTTTCTCTTTTTTTTTTTTT
+>EAS139_11:5:61:38:1182
+AGGGAGCCGTCCGTGTCCTCCCATCTGGCCTCGTC
+>EAS139_11:5:61:38:1182
+GTTTGATTTGGTGGAAGACATAATCCCACGCTTCC
+>EAS139_11:5:64:199:1288
+GTAAAATAAAACAAAGGAGGTCATCATACAATGAT
+>EAS139_11:5:64:199:1288
+TACAATGTACAATATTCTGATGATGGTTACACTAA
+>EAS139_11:5:78:775:555
+AATGCTCAAAAGAATTGTAAAAGTCAAAATTAAAG
+>EAS139_11:5:78:775:555
+TTTTTGGACTTCTTAAAGAAAAAAAAACCTGTCAA
+>EAS139_11:6:11:285:1567
+ACATGGCTGATTATGAAAACAATGTTCCCCAGATA
+>EAS139_11:6:11:285:1567
+CCCTGAGAGATTCTGCAGCCCAGATCCAGATTGCT
+>EAS139_11:6:11:360:1577
+GAAGAAAAGGTCTTTCAAAAGGTGATGTGTGTTCT
+>EAS139_11:6:11:360:1577
+TTTGGCATTTGCCTTCAGACCCTACACGAATGCGT
+>EAS139_11:6:13:682:680
+AGAATAACAATGGGCTTCTCAGCGGAAACCTTACA
+>EAS139_11:6:13:682:680
+ATAAGAAATGCTCAAAAGAATTGTAAAAGTCAAAA
+>EAS139_11:6:17:1179:393
+CTAATTGGTACAATGTACAATATTCTGATGATGGT
+>EAS139_11:6:17:1179:393
+TGCTAAGTATTGGTAAAGATGTGGGGAAAAAAGTA
+>EAS139_11:6:19:306:982
+ATTTTTGGACTTCTTAAAGAAAAAAAAACCTGTCA
+>EAS139_11:6:19:306:982
+GACAGACTTCATCAAGATATGTAGTCATCAGACTA
+>EAS139_11:6:75:946:1035
+AACCCCCTTGCAACAACCTTGAGAACCCCAGGGAA
+>EAS139_11:6:75:946:1035
+AATGGACCTGTGATATCTGGATTCTGGGAAATTCT
+>EAS139_11:6:82:164:1924
+GAGGGATGGAGGGAAGAGGGACGCTGAAGAACTTT
+>EAS139_11:6:82:164:1924
+GCCCAGCACCAGATTGCTTGTGGTCTGACAGGCTG
+>EAS139_11:6:89:1151:1878
+CCATCACAATGAACAACAGGAAGAAAAGGTCTTTC
+>EAS139_11:6:89:1151:1878
+CTTTCAACGATTCTAGCCATTTCTTTTGGCATTTG
+>EAS139_11:7:24:1345:1627
+AGATTGGCAGAACAGATTTAAAAACATGAACTAAC
+>EAS139_11:7:24:1345:1627
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+>EAS139_11:7:42:1091:1726
+CAGGGAAGGAGCATTTTGTCAGTTACCAAATGTGT
+>EAS139_11:7:42:1091:1726
+TCTGGGAAATTCTTCATCCTGGACCCTGAGAGATT
+>EAS139_11:7:46:695:738
+CAAAGATGAAACGCGTAACTGCGCTCTCATTCACT
+>EAS139_11:7:46:695:738
+TGAAACAGCTGAGTTTAGCGCCTGTGTTCACATAG
+>EAS139_11:7:50:1229:1313
+ACATAGCTAAAACTAAAAAAGCAAAAACAAAAACT
+>EAS139_11:7:50:1229:1313
+TTTTTTCTTTTTTTTTTTTTTTTTTTTGCATGCCA
+>EAS139_11:7:53:458:581
+CTCAATTAATTGTTTTATAAAACCTGTGAGTTTTG
+>EAS139_11:7:53:458:581
+TTATGCCCTGCTAAACTAAGCATCATAAATGAAGG
+>EAS139_11:7:60:163:1612
+AGCAAGAGAAAAGCATACAGTCATCTATAAAGGAA
+>EAS139_11:7:60:163:1612
+GGGAACTAAAGTCAAGTCTTTCCTGACAAGCAAAT
+>EAS139_11:7:74:213:877
+AGATGTTCTACGCAAACAGAAACCAAATGAGAGAA
+>EAS139_11:7:74:213:877
+TTAACATTACAACAGGAACAAAACCTCATATATCA
+>EAS139_11:7:92:367:1495
+ACCACAGGGGGCTGCGCGGTTTCCCATCATGAAGC
+>EAS139_11:7:92:367:1495
+CTGTCATAACTATGAAGAGACTATTGCCAGATGAA
+>EAS139_11:8:17:437:1378
+ACCAGTCCTATAAGAAATGCTCAAAAGAATTGTAA
+>EAS139_11:8:17:437:1378
+ATCAATATTAACTTTGAATAAAAAGGGATTAAATT
+>EAS139_11:8:26:1221:222
+AAACAGCTGTGTTTAGTGCCTTTGTTCAACCCCCT
+>EAS139_11:8:26:1221:222
+CTGCGCTCTCATTCACTCCAGCTCCCTGTCACCCA
+>EAS139_11:8:38:842:395
+GTAACTGCGCTCTCATTCACTCCAGCTCCCTGTCA
+>EAS139_11:8:76:205:587
+GAATAACAATGGGCTTCTCAGCGGAAACCTTACGA
+>EAS139_11:8:76:205:587
+TGCTAGAGATTTAGACATCTAAATGAAAGAGGCTC
+>EAS139_11:8:82:566:1096
+CAAAAGGTGATGTGTGTTCTCATCAACCTCATACA
+>EAS139_11:8:82:566:1096
+CTGCGCTCTCATTCACTCCAGCTCCCTGTCACCCA
+>EAS139_11:8:96:1314:1448
+CCTATGAGTCACAGGTATTCCTGAGGAAAAATAAA
+>EAS139_11:8:96:1314:1448
+GTAGTCATCAGACTATCTAAAGTCAACATGAAGGA
+>EAS139_19:1:14:420:712
+TGAGAGAGAACTTCCCTGGAGGTCTGATGGCGTTTCTCCC
+>EAS139_19:1:14:420:712
+TGTTGGTTTTCTGTTTCTTTGTTTGATTTTTTTGAAGACA
+>EAS139_19:1:1:1598:843
+TCAGCGGAAACCTTACAAGCCAGAAGAGATTGGATCTAAT
+>EAS139_19:1:1:1598:843
+TGCCAGGAAGATACATTGCAAGACAGACTTCATCAAGATA
+>EAS139_19:1:36:481:1079
+GTAAAAGTCAAAATTAAAGTTCAATACTCACCATCATAAA
+>EAS139_19:1:36:481:1079
+TCCCCCACTTAAGAGATATAGATTGGCAGAACAGATTTAA
+>EAS139_19:1:40:1596:1433
+CCATCACAATGAACAACAGGAAGAAAAGGTCTTTCAAAAG
+>EAS139_19:1:40:1596:1433
+GCTTTCAACGCTTCTAGCCATTTCTTTTGGCATTTGCCTT
+>EAS139_19:1:47:352:1492
+AGGGAGCCGTCCGTGTCCTCCCATCTGGCCTCGCCCACTA
+>EAS139_19:1:47:352:1492
+TTTGTTTTGTATGGTGGAAGACATAATCCCACGCTTCCTA
+>EAS139_19:1:53:463:1132
+ATGATAAAAAGATCAATTCAGCAAGAAGATATAACCATCC
+>EAS139_19:1:53:463:1132
+ATTTAAAAACATGAACTAACTATATGCTGTTTACANGAAA
+>EAS139_19:1:58:726:1746
+AGATTGGCAGAACAGATTTAAAAACATGAACTAACTATAT
+>EAS139_19:1:58:726:1746
+CAATTTAAATCAACAACAGTAAAATAAAACAAAGGAGGTC
+>EAS139_19:1:82:946:392
+CAATATATCCATGTAACAAATCTGCGCTTGTACTTCAAAA
+>EAS139_19:1:82:946:392
+GAAAACAATTTGGTAATTTCGTTTTTTTTTTTTTCTTTTC
+>EAS139_19:1:85:1521:58
+AAATTAACATTACAACAGGAACAAAACCTCATATATCAAT
+>EAS139_19:1:85:1521:58
+CTGACAAGCAAATGCTAAGATAATTCATCATCACTAAACC
+>EAS139_19:1:87:1222:878
+TATAGGGCCTTTGTTCAAACCCCTTGCAACAACCTTGAGA
+>EAS139_19:1:87:1222:878
+TCAGCGCGTCACTCCGCTCTCATTCACCCCAGCTCCCTGT
+>EAS139_19:1:99:1632:76
+AAAGAAAAAAAACCCTGTCAAACACGAATGTTATGCCCTG
+>EAS139_19:1:99:1632:76
+TTGTAAAAGTCAAAATTAAAGTTCAATACTCACCATCATA
+>EAS139_19:2:12:1335:1372
+GAAGAACAGATTTAAAAACATGAACTAACTATATGCTGTT
+>EAS139_19:2:12:1335:1372
+TAAAGTTCAATACTCACCATCATAAATACACACAAAAGTA
+>EAS139_19:2:29:1822:1881
+AGAAAAAAGAATTTTAAAAATGAACAGAGCTTTCAAGAAG
+>EAS139_19:2:29:1822:1881
+ATGAAAGAGGCTCAAAGAATGCCAGGAAGATACATTGCAA
+>EAS139_19:2:2:1217:398
+CAATTAATTGAGACTACAGAGCAACTAGGTAAAAAATTAA
+>EAS139_19:2:2:1217:398
+TAAATGAAGGGGAAATAAAGTCAAGTCTTTCCTGACAAGC
+>EAS139_19:2:33:1193:664
+GCCCCATCTCTTGTAATCTCTCTCCTTTTTTCTGCATCCC
+>EAS139_19:2:33:1193:664
+TATTTTTGTCTTGACACCCAACTAATATTTGTCTGAGCAA
+>EAS139_19:2:57:1672:1890
+CCCCCCCCCCCCCCCCCAGCCACTGCGGCCCCCCCAGCCA
+>EAS139_19:2:57:1672:1890
+TATTCAGTTCTAAATATAGAAATTGAAACAGCTGTGTTTA
+>EAS139_19:2:82:154:1333
+TTAAAATTTAACAAAAGTAAATAAAACACACAGCTAAAAC
+>EAS139_19:2:82:154:1333
+TTTTTTTTTTTTTTTTTTTTTCTTTTTTTTTTTTTTTTTT
+>EAS139_19:3:10:349:1147
+GCTAGAGATTTAGACATCTAAATGAAAGAGGCTCAAAGAA
+>EAS139_19:3:24:1135:563
+CTGCGCTCTCATTCACTCCAGCTCCCTGTCACCCAATGGA
+>EAS139_19:3:24:1135:563
+GCTGTGTTTAGTGCCTTTGTTCAACCCCCTTGCAACAACC
+>EAS139_19:3:4:1502:1911
+CTACACGAATGCGTCTCTACCACAGGGGGCTGCGCGGTTT
+>EAS139_19:3:4:1502:1911
+TACACACACATGGTTTAGGGGTATAATACCTCTACATGGC
+>EAS139_19:3:58:923:1915
+GCAAACAGAAACCAAATGAGAGAAGGAGTAGCTATACTTA
+>EAS139_19:3:58:923:1915
+TATCAATATTAACTTTGAATAAAAAGGGATTAAATTCCCC
+>EAS139_19:3:5:538:401
+AAGGTGATGTGTGTTCTCATCAACCTCATACACACACATG
+>EAS139_19:3:5:538:401
+TTTGCCTTCACACCCTACACGAATGCGTCTCTGCCACAGG
+>EAS139_19:3:66:718:481
+AACAACAGTAAAATAAAACAAAGGAGGTCATCATACAATG
+>EAS139_19:3:66:718:481
+AAGAGATATAGATTGGCAGAACAGATTTAAAAACATGAAC
+>EAS139_19:3:73:1158:535
+AATAAAGATATGTAGTCATCAGACTATCTAAAGTCAACAT
+>EAS139_19:3:73:1158:535
+CCTATGAGTCACAGGTATTCCTGAGGAAAAAGAAAAAGTG
+>EAS139_19:3:73:936:1509
+CTCCTTTTTGCTGCATCCCTGTCTTCCTCTGTCTTTATTT
+>EAS139_19:3:73:936:1509
+TTGTCTGAGCAAAACAGTCTAGATGAGAGAGAACTTCCCT
+>EAS139_19:3:75:732:442
+CGGTCCCTGCCCCATCTCTTGTAATCTCTCTCCTTTTTGC
+>EAS139_19:3:75:732:442
+CTATCCCAAATTCCCAATTACGTCCTATCTTCTTCTTAGG
+>EAS139_19:3:87:133:930
+CAGTCTCAGGGCGCCGTCCGTTTCCTCCCATCTGGCCTCG
+>EAS139_19:3:87:133:930
+TTATCTGCACATTACTACCCTGCAATTAATATAATTGTGT
+>EAS139_19:3:88:1656:896
+AGGGAAGAGGGATGCTGAAGAACTTTGATGCCCTCTTCTT
+>EAS139_19:3:88:1656:896
+TGCAGCCCAGATCCAGATTGCTTGTGGTCTGACAGGCTGC
+>EAS139_19:4:13:1155:631
+ACCCTGAGAGATTCTGCAGCCCAGCTCCAGATTGCTTGTG
+>EAS139_19:4:13:1155:631
+AGGGGTATAATACCTCTACATGGCTGATTATGAAAACAAT
+>EAS139_19:4:18:1335:1514
+ATTGGTACAATGTACAATATTCTGATGATGGTTACACTAA
+>EAS139_19:4:18:1335:1514
+CTTTAAATCAACAACAGTAAAATAAAACAAAGGAGGTCAT
+>EAS139_19:4:1:156:196
+AAAAGGGATTAAATTCCCCCACTTAAGAGATATAGATTGG
+>EAS139_19:4:1:156:196
+ACTTATATCAGATAAAGCACACTTTAAATCAACAACAGTA
+>EAS139_19:4:26:1312:1400
+ACTGAACCTATGAGTCACAGGTATTCCTGAGGAAAAAGAA
+>EAS139_19:4:26:1312:1400
+TATGTAGTCATCAGACTATCTAAAGTCAACATGAAGGAAA
+>EAS139_19:4:26:274:1078
+AATTGGGGAAAACCTCTTTAGTCTTGCTAGAGATTTAGAC
+>EAS139_19:4:26:274:1078
+GTCATCTATAAAGGAAATCCCATCAGAATAACAATGGGCT
+>EAS139_19:4:68:1122:79
+ATGGCTGATTATGAAAACAATGTTCCCCAGATACCATCCC
+>EAS139_19:4:68:1122:79
+TGAGAGATTCTGCAGCCCAGCTCCAGATTGCTTGTGGTCT
+>EAS139_19:4:69:1593:819
+ATTGAGACTACAGAGCAACTAGGTAAAAAATTAACATTAC
+>EAS139_19:4:69:1593:819
+CAGGTAAAGGGGTGGAAAAAGATGTTCTACGCAAACAGAA
+>EAS139_19:4:77:1780:693
+GGAAGTAATTGGGGAAAACCTCTTTAGTCTTGCTAGAGAT
+>EAS139_19:4:77:1780:693
+TGAAGACAAGTCTCTTATGAATTAACCCAGTCAGACAAAA
+>EAS139_19:4:78:806:800
+AAATTAAAGTTCAATACTCACCATCATAAATACACACAAA
+>EAS139_19:4:78:806:800
+AACCTGTCAAACACGAATGTTATGCCCTGCTAAACTAAGC
+>EAS139_19:5:29:411:1208
+AAAAGAATTGTAAAAGTCAAAATTAAAGTTCAATACTCAC
+>EAS139_19:5:29:411:1208
+CCCCCACTTAAGAGATATAGATTGGCAGAACAGATTTAAA
+>EAS139_19:5:40:758:116
+GTCTCTACCACAGGGGGCTGCGCGGTTTCCCATCATGAAG
+>EAS139_19:5:40:758:116
+GTGTGTTCTCATCAACCTCATACACACACATGGTTTAGGG
+>EAS139_19:5:4:939:2021
+AAATACTACTAGACCTAAGAGGGATGAGAAATTACCTAAT
+>EAS139_19:5:4:939:2021
+GGAGTAGCTATACTTATATCAGATAAAGCACACTTTAAAT
+>EAS139_19:5:57:366:844
+AAATTCCCCCACTTAAGAGATATAGATTGGCAGAACAGAT
+>EAS139_19:5:57:366:844
+TAAAAGTCAAAATTAAAGTTCAATACTCACCATCATAAAT
+>EAS139_19:5:61:1885:163
+AGCAAGAAGATATAACCATCCTACTAAATACATATGCACC
+>EAS139_19:5:61:1885:163
+ATACTTTACTGCTACTCAATATATCCATGTAACAAATCTG
+>EAS139_19:5:66:1381:181
+GGACTTCTTAAAGAAAAAAAAACCTGTCAAACACGAATGT
+>EAS139_19:5:66:1381:181
+TTGCAAGACAGACTTCATCAAGATATGTAGTCATCAGACT
+>EAS139_19:5:68:306:409
+AACTTTGAATAAAAAGGGATTAAATTCCCCCACTTAAGAG
+>EAS139_19:5:68:306:409
+CCTATAAGAAATGCTCAAAAGAATTGTAAAAGTCAAAATT
+>EAS139_19:5:70:318:1631
+TAAGAAATTACAAAATATAGTTGAAAGCTCTAACAATAGA
+>EAS139_19:5:74:668:424
+GACTTCTTAAAGAAAAAAAAACCTGTCAAACACGAATGTT
+>EAS139_19:5:74:668:424
+GTAAAAGTCAAAATTAAAGTTCAATACTCACCATCATAAA
+>EAS139_19:5:89:525:113
+GACGCTGAAGAACTTTGATTCCCTCTTCTTCCAAAGATGA
+>EAS139_19:5:89:525:113
+TATTTATGCTATTCAGTTATAAATATAGAAATTGAAACAG
+>EAS139_19:5:95:944:247
+GGTACAATGTACAATATTCTGATGATGGTTACACTAAAAG
+>EAS139_19:5:95:944:247
+GTAAAGATGTGGGGAAAAAAGTAAACTCTCAAATATTGCT
+>EAS139_19:6:21:1601:1666
+GAAAGCTCTAACAATAGACTAAACCAAGCAGAAGAAAGAG
+>EAS139_19:6:21:1601:1666
+TATTACTGAGGAAAAAGAAAAAGTGAGAAGTTTGGAAAAA
+>EAS139_19:6:52:1455:1212
+CCATCTCTTGTAATCTCTCTCCTTTTTGCTGCATCCCTGT
+>EAS139_19:6:52:1455:1212
+TTCTTAGGGAAGAACAGCTTAGGTATCAATTTGGTGTTCT
+>EAS139_19:6:72:308:839
+AGTTACCAAATGTGTTTATTACCAGAGGGATGGAGGGAAG
+>EAS139_19:6:72:308:839
+ATCGTGGACCCTGAGAGATTCTGCAGCCCAGATCCAGATT
+>EAS139_19:6:75:1503:1399
+CAAGAAGATATAACCATCCTACTAAATACATATGCACCTA
+>EAS139_19:6:75:1503:1399
+CATGAGTTCAGGTAAAGGGGTGGAAAAAGATGTTCTACGC
+>EAS139_19:6:78:1029:512
+AGATAATTCATCATCACTAAACCAGTCCTATAAGAAATGC
+>EAS139_19:6:78:1029:512
+TCAGCAGAAACCTTACAAGCCAGAAGAGATTGGATCTAAT
+>EAS139_19:6:82:1051:921
+GCAAATAGGTAAAAAATTAACATTACAACAGGAACAAAAC
+>EAS139_19:6:82:1051:921
+GGGGAAATAAAGTCAAGGCTTTCCTGACAAGCAAATGCTA
+>EAS139_19:6:84:438:1505
+ATTAATATAATTGTGTCCATGTACACACTCTGTCCTATGT
+>EAS139_19:6:84:438:1505
+GCACTAATGCGCTCCACGCCCAAGCCCTTCTCACAGTTTC
+>EAS139_19:7:44:1807:833
+ATATCCATGTAACAAATCTGCGCTTGTACTTCTAAATCTA
+>EAS139_19:7:44:1807:833
+CTCTCAAATATTGCTAGTGGGAGTATAAATTGTTTTCCAC
+>EAS139_19:7:85:262:751
+CCATGTAACAAATCTGCGCTTGTACTTCTAAATCTATAAC
+>EAS139_19:7:85:262:751
+TACAATGATAAAAAGATCAATTCAGCAAGAAGATATAACC
+>EAS139_19:7:92:288:1354
+TCTCCTTTTTGCTGCATCCCTGTCTTCCTCTGTCTTGATT
+>EAS139_19:7:92:288:1354
+TGTCTTGACACCCAACTAATATTTGTCTGAGCAAAACAGT
+>EAS188_4:5:103:870:105
+AAACTAAGCATCATAAATGAAGGGGAAATAAAGTC
+>EAS188_4:5:103:870:105
+ATAAAACAATTAATTGAGACTACAGAGCAACTAGG
+>EAS188_4:5:166:776:590
+CTTGAAAGCTTGGGCTGTAATGATGCCCCTTGGCC
+>EAS188_4:5:166:776:590
+TAATTGTGTCCATGTACACACGCTGTCCTATGTAC
+>EAS188_4:5:202:326:680
+ACTTATCATGACTCTATCCCAAATTCTCAATTACG
+>EAS188_4:5:202:326:680
+GTAATGATGCCCCTTGGCCATCACCCGGTCCCTGC
+>EAS188_4:5:295:547:216
+ATGAGTTCAGGTAAAGGGGTGGAAAAAGATGTTCT
+>EAS188_4:5:295:547:216
+TAAAAAATTAACATTACAACAGGAACAAAACCTCA
+>EAS188_4:5:302:997:951
+ATGAACTTCTGTAATTGAAAAATTCATTTAAGAAA
+>EAS188_4:5:308:552:77
+TTTTCTTTTTTTTCTTTTCTCTTTTTTTTTTTTTT
+>EAS188_4:5:8:377:655
+CTATTTTTGTCTTGACACCCAACTAATATTTGTCT
+>EAS188_4:5:8:377:655
+CTGCCCCATCTCTTGTAATCTCTCTCCTTTTTGCT
+>EAS188_4:7:282:567:481
+GGAACAGGGAGGCGCACTAATGCGCTCCACGCCCA
+>EAS188_4:7:282:567:481
+TGCAATTAATATAATTGTGTCCACGTACACACGCT
+>EAS188_4:7:296:401:60
+AATGAAAGAGGCTCAAAGAATGCCAGGAAGATACA
+>EAS188_4:7:35:408:348
+AAGAAACGCGTAACTGCGCTCTCATACACTCCAGC
+>EAS188_4:7:35:408:348
+GGTTCTCAAGGTTGTTGCAATGGGGTCTATGTGAA
+>EAS188_4:7:78:583:670
+CAGGGAATTTGTCAATGTCAGGGAAGGAGCATTTT
+>EAS188_4:7:78:583:670
+TAACCTCTGGTGACTGCCAGAGCTGCTGGCAAGCT
+>EAS188_4:7:96:899:106
+TCTATAAAGGAAATCCCATCAGAATAACAATGGGC
+>EAS188_4:7:96:899:106
+TTCCTGACAAGCAAATGCTAAGATAATTCATCATC
+>EAS188_7:1:115:683:296
+AACAGTCTAGATGAGAGAGAACTTCCCTGGAGGTC
+>EAS188_7:1:115:683:296
+CTCTCCTTTTTGCTGCATCCCTGTCTTCCTCTGTC
+>EAS188_7:1:177:522:118
+TAAACTAAGCATCATAAATGAAGGGGAAATAAAGT
+>EAS188_7:1:177:522:118
+TCTCAATTAATTGTTTTATAAAACCTGTGAGTTTT
+>EAS188_7:1:290:286:763
+TTAAAATTTAACAAAAGTAAATAAAACACATAGCT
+>EAS188_7:1:290:286:763
+TTTTTTTTTTTTCTTTTCTCTTTTTTTTTTTTTTT
+>EAS188_7:1:316:949:122
+TCTCCTTTTTGCTGCATCCCTGTCTTCCTCTGTCT
+>EAS188_7:1:316:949:122
+TTAGGGAAGAACAGCTTAGGTATCAATTTGGTGTT
+>EAS188_7:1:77:251:446
+CAGCATGGTTGTACTGGGCAATACATGAGATTATT
+>EAS188_7:1:77:251:446
+TTATCATGACTCTATCCCAAATGCCCAATTACGTC
+>EAS188_7:2:152:765:744
+ACTTCCCTGGAGGTCTGATGGCGTTTCTCCCTCGT
+>EAS188_7:2:152:765:744
+TTTTCTGTTTCTTTGTTTGATTTGGTGGAAGACAT
+>EAS188_7:2:172:622:707
+ACATGGCTGATTATGAAAACAATGTTCCCCAGATA
+>EAS188_7:2:172:622:707
+TTCTTCATCCTGGACCCTGAGAGATTCTGCAGCCC
+>EAS188_7:2:187:227:818
+CAGCACAGGGGCTTAACCTCTGGTGACTGCCAGAG
+>EAS188_7:2:187:227:818
+CCCCCTTGCAACAACCTTGAGAACCCCAGGGAATT
+>EAS188_7:2:19:736:559
+AAGACTTCATCAAGATATGTAGTCATCAGACTATC
+>EAS188_7:2:19:736:559
+TGAACCTATGAGTCACAGGTATTCCTGAGGAAAAA
+>EAS188_7:2:218:877:489
+TATAGAAATTGAAACAGCTGTGTTTAGTGCCTTTG
+>EAS188_7:2:259:219:114
+GAAATTGAAACAGCTGTGTTTAGTGCCTTTGTTCA
+>EAS188_7:2:259:219:114
+TTGATGCCCTCTTCTTCCAAAGATGAAACGCGTAA
+>EAS188_7:3:100:735:530
+GCACACTTTAAATCAACAACAGTAAAATAAAACAA
+>EAS188_7:3:100:735:530
+TGATGATGGTTACACTAAAAGCCCATACTTTACTG
+>EAS188_7:3:101:572:491
+CAACAGGAAGAAAAGGTCTTTCAAAAGGTGATGTG
+>EAS188_7:3:101:572:491
+TTCCAAAGATGAAACGCGTAACTGCGCTCTCATTC
+>EAS188_7:3:13:122:187
+AGCATTTTGTCAGTTACCAAATGTGTTTATTACCA
+>EAS188_7:3:13:122:187
+GACTGCCAGAGCTGCTGGCAAGCTAGAGTCCCCTT
+>EAS188_7:3:15:568:42
+TTTTTGAGGAAGTAATTGGGGAAAACCTCTTTAGT
+>EAS188_7:3:15:568:42
+TTTTTTTTTTTGTTTTTTTTTTTTTTTTTTTTATA
+>EAS188_7:3:182:104:921
+ATCAAGATATGTAGTCATCAGACTATCTAAAGTCA
+>EAS188_7:3:182:104:921
+CACGAATGTTATGCCCTGCTAAACTAAGCATCATA
+>EAS188_7:3:200:712:439
+CGTCACCCGGTCCCTGCCCCATCTCTTGTAATCTC
+>EAS188_7:3:200:712:439
+GTTGGGAGATTTTTAATGATTCCTCAATGTTAAAA
+>EAS188_7:3:296:224:724
+ATAGTTGAAAGCTCTAACAATAGACTAAACCAAGC
+>EAS188_7:3:296:224:724
+TGAGGAAAAAGAAAAAGTGAGAAGTTTGGAAAAAC
+>EAS188_7:3:76:333:905
+AATTGTGTCCATGTACACACGCTGTCCTATGTACT
+>EAS188_7:3:76:333:905
+TTTCTGCCCCCAGCATGGTTGTACTGGGCAATACA
+>EAS188_7:4:164:719:947
+AAATTAACATTACAACAGGAACAAAACCTCATATA
+>EAS188_7:4:164:719:947
+ACGCAAACAGAAACCAAATGAGAGAAGGAGTAGCT
+>EAS188_7:4:171:104:398
+AGGGAGGTGCACTAATGCGCTCCACGCCCAAGCCC
+>EAS188_7:4:171:104:398
+CAATTAATATAATTGTGTCCATGTACACACGCTGT
+>EAS188_7:4:21:443:404
+AGAGAACTTCCCTGGAGGTCTGATGGCGTTTCTCC
+>EAS188_7:4:21:443:404
+TTCCTCTGTCTTGATTTACTTGTTGTTGGTTTTCT
+>EAS188_7:4:238:441:727
+GTAATTGAAAAATTCATTTAAGAAATTACAAAATA
+>EAS188_7:4:259:869:641
+GTTGGGAGATTTTTAATGATTCCTCAATGTTAAAA
+>EAS188_7:4:259:869:641
+TGATGCCCCTTGGCCATCACCCAGTCCCTGCCCCA
+>EAS188_7:4:92:693:228
+AAGGTTTTATAAAAAAATTAATTGAGACTACAGAG
+>EAS188_7:4:92:693:228
+AGCATCATAAATGAAGGGGAAATAAAGTCAAGTCT
+>EAS188_7:5:112:51:128
+AGACCCCCTTGCAACAACCTTGAGAACCCCAGGGA
+>EAS188_7:5:112:51:128
+CCCAATGGACCTGTGATATCTGGATTCTGGGAAAT
+>EAS188_7:5:115:249:673
+TAAAGAAAAAAAAACCTGTCAAACACGAATGTTAT
+>EAS188_7:5:115:249:673
+TAAATACACACAAAAGTACAAAACTCACAGGTTTT
+>EAS188_7:5:163:982:695
+CTCAGCAGAAACCTTACAAGCCAGAAGAGATTGGA
+>EAS188_7:5:163:982:695
+TCAAAGAATGCCAGGAAGATACATTGCAAGACAGA
+>EAS188_7:5:308:354:124
+GCTGCATCCCTGTCTTCCTCTGTCTTGATTTACTT
+>EAS188_7:5:308:354:124
+TGAGCAAAACAGTCTAGATGAGAGAGAACTTCCCT
+>EAS188_7:5:74:329:459
+ACAGAGCAACTAGGTAAAAAATTAACATTACAACA
+>EAS188_7:5:74:329:459
+TAAAGTCAAGTCTTTCCTGACAAGCAAATGCTAAG
+>EAS188_7:6:107:447:488
+TAATTGGTACAATGTACAATATTCTGATGATGGTT
+>EAS188_7:6:107:447:488
+TGCTAAGTATTGGTAAAGATGTGGGGAAAAAAGTA
+>EAS188_7:6:107:636:642
+AAGTCTTTCCTGACAAGCAAATGCTAAGATAATTC
+>EAS188_7:6:107:636:642
+GTCATCTATAAAGGAAATCCCATCAGAATAACAAT
+>EAS188_7:6:11:994:584
+GAAGGAAAAAAATTCTAAAATCAGCAAGAGAAAAG
+>EAS188_7:6:11:994:584
+GGTATTCCTGAGGAAAAAGAAAAAGTGAGAAGTTT
+>EAS188_7:6:191:540:493
+AAAAGCCCATACTTTACTGCTACTCAATATATCCA
+>EAS188_7:6:191:540:493
+GTGGGGAAAAAAGTAAACTCTCAAATATTGCTAGT
+>EAS188_7:6:194:998:663
+ACCTAACACAAGACTACCCAGATTCATAAAACAAA
+>EAS188_7:6:194:998:663
+TCTACGCAAACAGAAACCAAATGAGAGAAGGAGTA
+>EAS188_7:6:205:873:464
+AGATTGCTTGTGGTCTGACAGGCTGCAACTGTGAG
+>EAS188_7:6:205:873:464
+CCCCAGAGGGAAAGCTTTCAACGCTTCTAGCCATT
+>EAS188_7:6:46:122:479
+AAGAAAGAGGTTCAGAACTTGAAGACAAGTCTCTT
+>EAS188_7:6:46:122:479
+AAGTGAGAAGTTTGGAAGAACTATTTGAGGAAGTA
+>EAS188_7:7:19:886:279
+CCCATTTGGAGCCCCTCTAAGCCGTTCTATTTGTA
+>EAS188_7:7:19:886:279
+GAAAGGAGCATTTTGTCAGTTACCAAATGTGTTTA
+>EAS188_7:7:213:309:373
+TAGACATCTAAATGAAAGAGGCTCAAAGAATGCCA
+>EAS188_7:7:213:309:373
+TTAAAAATGAACAGAGCTTTCAAGAAGTATGAGAT
+>EAS188_7:7:243:876:758
+AGCCCAGATCCAGATTGCTTGTGGTCTGACAGGCT
+>EAS188_7:7:243:876:758
+CCCAGATACCATCCCTGTCTTACTTCCAGCTCCCC
+>EAS188_7:7:67:719:786
+GGATGAGAAATTACCTAATTGGTACACTGTACAAT
+>EAS188_7:7:67:719:786
+TAAAAAAAAAAAAGCAAAAACAAAAACTATGCTAA
+>EAS188_7:8:60:182:718
+GTCCCTGCCCCATCTCTTGTAATCTCTCTCCTTTT
+>EAS188_7:8:60:182:718
+TGACACCCAACTAATATTTGTCTGAGCAAAACAGT
+>EAS188_7:8:64:350:174
+CCTAACACAAGACTACCCAGATTCATAAAACAAAT
+>EAS188_7:8:64:350:174
+GTTCTACGCAAACAGAAACCAAATGAGAGAAGGAG
+>EAS192_3:1:114:19:769
+AAACACGAATGTTATGCCCTGCTAAACTAAGCATC
+>EAS192_3:1:114:19:769
+TAAAGTCAACATGAAGGAAAAAAATTCTAAAATCA
+>EAS192_3:1:225:195:543
+AACAACCTTGAGAACCCCAGGGAATTTGTCAATGT
+>EAS192_3:1:225:195:543
+GGTTGCCAGCACAGGGGCTTAACCTCTGGTGACTG
+>EAS192_3:3:194:378:230
+AATACTACTAGACCTAAGAGGGATGAGAAATTACC
+>EAS192_3:3:194:378:230
+ATGAGAGAAGGAGTAGCTATACTTATATCAGATAA
+>EAS192_3:3:221:881:916
+TAACACAAGACTACCCAGATTCATAAAACAAATAC
+>EAS192_3:3:221:881:916
+TAATTCTAAATCTAGAACAAAATTAAAATTTAACA
+>EAS192_3:3:257:611:440
+ACCCTGAGAGATTCTGCAGCCCAGATCCAGATTGC
+>EAS192_3:3:257:611:440
+GGAGCATTTTGTCAGTTACCAAATGTGTTTATTAC
+>EAS192_3:3:27:973:518
+CTGATTATGAAAACAATGTTCCCCAGATACCATCC
+>EAS192_3:3:27:973:518
+TCCAGATTGCTTGTGGTCTGACAGGCTGCAACTGT
+>EAS192_3:3:285:349:797
+ATCATAAATGAAGGGGAAATAAAGTCAAGTCTTTC
+>EAS192_3:3:285:349:797
+GTTTTAAAAAACCAATAATTGAGACTACAGAGCAA
+>EAS192_3:3:309:187:267
+ATTGAGACTACAGAGCAACTAGGTAAAAAATTAAC
+>EAS192_3:3:309:187:267
+GGGGAAATAAAGTCAAGTCTTTCCTGACAAGCAAA
+>EAS192_3:3:88:866:774
+ATGTAACAAATCTGCTCTTGTACTTCTAAATCTAT
+>EAS192_3:3:88:866:774
+TTGTTTTCCACTTTGGAAAACAATTTGGTAATTTC
+>EAS192_3:4:184:237:476
+ATCATACAATGATAAAAAGATCAATTCAGCAAGAA
+>EAS192_3:4:184:237:476
+ATGAACTAACTATATGCTGTTTACAAGAAACTCAT
+>EAS192_3:4:255:549:422
+AAGTCATCTATAAAGGAAATCCCATCAGAATAACA
+>EAS192_3:4:255:549:422
+CTCTTTAGTCTTGCTAGAGATTTAGACATCTAAAT
+>EAS192_3:4:293:168:240
+ATGAACAGAGCTTTCAAGAAGTATGAGATTATGTA
+>EAS192_3:4:293:168:240
+CAAAGAATGCCAGGAAGATACATTGCAAGACAGAC
+>EAS192_3:4:312:915:751
+AATAAAGTCAAGTCTTTCCTGACAAGCAAAAGCTA
+>EAS192_3:4:312:915:751
+ATCTATAAAGGAAATCCCATCAGAATAACAATGGG
+>EAS192_3:4:63:5:870
+AAAGAAAAAAGAATTTTAAAAATGAACAGAGCTTT
+>EAS192_3:4:63:5:870
+GAAAGAGGCTCAAAGAATGCCAGGAAGATACATTG
+>EAS192_3:5:197:914:256
+ACTAGACCTAAGAGGGATGAGAAATTACCTAATTG
+>EAS192_3:5:197:914:256
+TCAGATAAAGCACACTTTAAATCAACAACAGTAAA
+>EAS192_3:5:223:142:410
+CTATTCAGTTCTAAATATAGAAATTGAAACAGCTG
+>EAS192_3:5:27:577:849
+AGTCTCTTATGAATTAACCCAGTCAGACAAAAATA
+>EAS192_3:5:27:577:849
+TTAGACATCTAAATGAAAGAGGCTCAAAGAATGCC
+>EAS192_3:5:287:334:110
+GATGAATACTAAGATTGATGTAGCAGCTTTTGCAA
+>EAS192_3:5:287:334:110
+TATGTAAAGTAACTGAACCTATGAGTCACAGGTAT
+>EAS192_3:6:116:464:261
+CAATGATAAAAAGATCAATTCAGCAAGAAGATATA
+>EAS192_3:6:116:464:261
+CTATATGCTGTTTACAAGAAACTCATTAATAAAGA
+>EAS192_3:6:170:169:57
+GGCTTGACCTCTGGTGACTGCCAGAGCTGCTGGCC
+>EAS192_3:6:170:169:57
+TGCAACAACCTTGAGAACCCCAGGGAATTTGTCAA
+>EAS192_3:6:175:437:950
+CCAAATTCCCAATTACGTCCTATCTTCTTCTTAGG
+>EAS192_3:6:175:437:950
+CCTGCCCCATCTCTTGTAATCTCTCTCCTTTTTGC
+>EAS192_3:6:185:868:496
+CCCTTGGCCATCACCCAGTCCCTGCCCCATCTCTT
+>EAS192_3:6:185:868:496
+GATTTTTAATGATTCCTCAATGTTAAAATGTCTAT
+>EAS192_3:6:201:195:757
+CCTGCCCCATCTCTTGTAATCTCTCTCCTTTTTGC
+>EAS192_3:6:201:195:757
+TATGTACTTATCATGACTCTATCCCAAATTCCCAA
+>EAS192_3:6:216:292:528
+GGGAGATTTTTAATGATTCCTCAATGTTAAAATGT
+>EAS192_3:6:216:292:528
+TAATGATGCCCCTTGGCCATCACCCAGTCCCTGCC
+>EAS192_3:6:235:505:553
+GGTGGAAAAAGATGTTCTACGCAAACAGAAACCAA
+>EAS192_3:6:235:505:553
+GTAAAAAATTAACATTACAACAGGAACAAAACCTC
+>EAS192_3:6:326:887:180
+CTAAACCAGTCCTATAAGAAATGCTCAAAAGAATT
+>EAS192_3:6:326:887:180
+TGGGCTTCTCAGCAGAAACCTTACAAGCCAGAAGC
+>EAS192_3:6:45:183:25
+CAGCGGAAACCTTACAAGCCAGAAGAGATTGGATC
+>EAS192_3:6:45:183:25
+CTAAACCAGTCCTATAAGAAATGCTCAAAAGAATT
+>EAS192_3:7:149:354:667
+CTTCCAGCTCCCCAGAGGGAAAGCTTTCAACGCTT
+>EAS192_3:7:149:354:667
+GAGGTGCACTAATGCGCTCCACGCCCAAGCCCTTC
+>EAS192_3:7:298:644:697
+CTATGTTTCTTATCTGCACATTACTACCCTGCAAT
+>EAS192_3:7:298:644:697
+TCCACGTCTCATCTAGGGGAACAGGGAGGTGCACT
+>EAS192_3:7:66:891:294
+AGCACACTTTAAATCAACAACAGTAAAATAAAACA
+>EAS192_3:7:66:891:294
+TAATTGGTACAATGTACAATATTCTGATGATGGTT
+>EAS192_3:7:78:692:671
+AATGAAGGGGAAATAAAGTCAAGTCTTTCCTGACA
+>EAS192_3:7:78:692:671
+CAGCAAGAGAAAAGCATACAGTCATCTATAAAGGA
+>EAS192_3:7:93:945:176
+CCAGAGGGAAAGCTTTCAACGCTTCTAGCCATTTC
+>EAS192_3:7:93:945:176
+GTGAGCCATCACAATGAACAACAGGAAGAAAAGGT
+>EAS192_3:8:6:104:118
+AAGAATTTTAAAAATGAACAGAGCTTTCAAGAAGT
+>EAS192_3:8:6:104:118
+TCTAAATGAAAGAGGCTCAAAGAATGCCAGGAAGA
+>EAS192_3:8:6:237:885
+AAAATCAGCAAGAGAAAAGCATACAGTCATCTATA
+>EAS192_3:8:6:237:885
+TATTTGAGGAAGTAATTGGGGAAAACCTCTTTAGT
+>EAS1_103:1:151:159:43
+AACCTCATACACACACATGGTTTAGGGGTATAATA
+>EAS1_103:1:151:159:43
+TCTCATTCACTCCAGCTCCCTGTCACCCAATGGAC
+>EAS1_103:1:228:736:747
+AAGATATGTAGTCATCAGACTATCTAAAGTCAACA
+>EAS1_103:1:228:736:747
+TTGGACTTCTTAAAGAAAAAAAAACCTGTCAAACA
+>EAS1_103:1:274:176:479
+CCTATCTTCTTCTTAGGGAAGAACAGCTTAGGTAT
+>EAS1_103:1:274:176:479
+GAAATGCTTTACTGTCATAACTATGAAGAGACTAT
+>EAS1_103:1:2:831:692
+GTGTTCTCATCAACCTCATACACACACATGGTTTA
+>EAS1_103:1:2:831:692
+TCCAGCTCCCTGTCACCCAATGGACCTGTGATATC
+>EAS1_103:2:184:980:396
+AAGGAGGTCATCATACAATGATAAAAAGATCAATT
+>EAS1_103:2:184:980:396
+ACATGAACTAACTATATGCTGTTTACAAGAAACTC
+>EAS1_103:2:226:302:758
+GGAAAGCTTTCAACGCTTCTAGCCATTTCTTTTGG
+>EAS1_103:2:226:302:758
+TGCTTGTGGTCTGACAGGCTGCAACTTTGAGCGNT
+>EAS1_103:2:234:167:381
+AAGTCAAGTCTTTCCTGACAAGCAAATGCTAAGAT
+>EAS1_103:2:234:167:381
+AGAGAAAAGCATACAGTCATCTATAAAGGAAATCC
+>EAS1_103:2:235:805:373
+TATCTTCTTCTTAGGGAAGAACAGCTTAGGTATCA
+>EAS1_103:2:235:805:373
+TTTACTGTCATAACTATGAAGAGACTATTTCCAGA
+>EAS1_103:2:307:252:632
+ACCATCCTGCTAAATACATATGCACCTAACACAAG
+>EAS1_103:2:307:252:632
+ATGTTCTACGCAAACAGAAACCAAATGAGAGAAGG
+>EAS1_103:3:253:175:31
+CAAACAGAAACCAAATGAGAGAAGGAGTAGCTATA
+>EAS1_103:3:253:175:31
+TTCATAAAACAAATACTACTAGACCTAAGAGGGAT
+>EAS1_103:3:277:921:474
+AAAATATAGTTGAAAGCTCTAACAATAGACTAAAC
+>EAS1_103:3:277:921:474
+AAAGAAAAAGTGAGAAGTTTGGAAAAACTATTTGA
+>EAS1_103:3:320:505:814
+ACAGTCTAGATGAGAGAGAACTTCCCTGGAGGTCT
+>EAS1_103:3:320:505:814
+CTGTCTTGATTTACTTGTTGTTGGTTTTCTTTTTC
+>EAS1_103:3:323:196:855
+ACAAGCAAATGCTAAGATAATTCATCATCACTAAA
+>EAS1_103:3:323:196:855
+TAAAAAATTAACATTACAACAGGAACAAAACCTCA
+>EAS1_103:3:41:474:283
+TGAACCACACATTAATACTATGTTTCTTATCTGCA
+>EAS1_103:3:41:474:283
+TTTGGTGTTCTGTGTAAAGTCTCAGGGAGCCGTCC
+>EAS1_103:4:143:560:194
+GTTGTACTGGGCAATACATGAGATTATTAGGAAAT
+>EAS1_103:4:143:560:194
+TCTAGCCATTTCTTTTGGCATTTGCCTTCAGACCC
+>EAS1_103:4:164:79:134
+ACAATGGGCTTCTCAGCGGAAACCTTACAAGCCAG
+>EAS1_103:4:164:79:134
+AGATAATTCATCATCACTAAACCAGTCCTATAAGA
+>EAS1_103:4:231:815:626
+GATCAATACAGCAAGAAGATATAACCATCCTACTA
+>EAS1_103:4:231:815:626
+GCTGTTTACAAGAAACTCATTAATAAAGACATGAG
+>EAS1_103:4:235:899:847
+AGAAACTCATTAATAAAGACATGAGTTCAGGTAAA
+>EAS1_103:4:235:899:847
+ATAAAAAGATCAATTCAGCAAGAAGATATAACCAT
+>EAS1_103:4:294:525:849
+AGGAGCATTTTGTCAGTTACCAAATGTGTTTATTA
+>EAS1_103:4:294:525:849
+CTGGCAAGCTAGAGTCCCATTTGGAGCCCCTCTAA
+>EAS1_103:4:61:433:385
+ACTGTGAGCCATCACAATGAACAACAGGAAGAAAA
+>EAS1_103:4:61:433:385
+GGATGGAGGGAAGAGGGACGCTGAAGCACTTTGAT
+>EAS1_103:5:141:711:813
+TATTACCAGAGGGATGGAGGGAAGAGGGACGCTGA
+>EAS1_103:5:141:711:813
+TATTTGTAATGAAAACTATATTTATGCTATTCAGT
+>EAS1_103:5:188:20:592
+CTACTAGACCTAAGAGGGATGAGAAATTACCTAAT
+>EAS1_103:5:188:20:592
+GAGTAGCTATACTTATATCAGATAAAGCACACTTT
+>EAS1_103:5:285:241:560
+GAAATTACAAAATATAGTTGAAAGCTCTAACAATA
+>EAS1_103:5:285:241:560
+TAAAGTAACTGAACCTATGAGTCACAGGTATTCCT
+>EAS1_103:5:319:165:698
+ATCACCCAGTCCCTGCCCCATATCTTGTAATCTCT
+>EAS1_103:5:319:165:698
+TGACACCCAACTAATATTTGTCTGAGCAAAACAGT
+>EAS1_103:6:7:858:437
+CAATGAACAACAGGAAGAAAAGGTCTTTCAAAAGG
+>EAS1_103:6:7:858:437
+CCATTTCTTTTGGCATTTGCCTTCAGACCCTACAC
+>EAS1_103:7:112:578:782
+AAAATAAAACACATAGCTAAAACTAAAAAAGCAAA
+>EAS1_103:7:112:578:782
+CAGATTCATAAAACAAATACTACTAGACCTAAGAG
+>EAS1_103:7:139:578:951
+AAAAACATGAACTAACTATATGCTGTTTACAAGAA
+>EAS1_103:7:139:578:951
+GAGGTCATCATACAATGATAAAAAGATCAATTCAG
+>EAS1_103:7:166:84:766
+ATAACACAAGACTACCCAGATTCATAAAACAAATA
+>EAS1_103:7:166:84:766
+GGAAAAAGATGTTCTACGCAAACAGAAACCAAATG
+>EAS1_103:7:311:100:539
+AAATTCTTCATCCTGGACCCTGAGAGATTCTGCAG
+>EAS1_103:7:311:100:539
+CAGTTACCAAATGTGTTTATTACCAGAGGGATGGA
+>EAS1_103:7:313:83:546
+TCATTCACTCCAGCTCCCTGTCACCCAATGGACCT
+>EAS1_103:7:313:83:546
+TGCAACAACCTTGAGAACCCCAGGGAATTTGTCAA
+>EAS1_103:7:53:783:78
+AAAAACCTGTCAAACACGAATGTTATGCCCTGCTA
+>EAS1_103:7:53:783:78
+TGCAAGACAGACTTCATCAAGATATGTAGTCATCA
+>EAS1_105:1:115:226:443
+AAATCTGCGCTTGTACTTCTAAATCTATAAAAAAA
+>EAS1_105:1:115:226:443
+ATATAACCATCCTACTAAATACATATGCACCTAAC
+>EAS1_105:1:141:415:738
+AAAGTCAAGTCTTTCCTGACAAGCAAATGCTAAGA
+>EAS1_105:1:141:415:738
+TTACCTAGTTGCTCTGTAGTCTCAATTAATTGTTT
+>EAS1_105:1:234:185:359
+AAGGAGTAGCTATACTTATATCAGATAAAGCACAC
+>EAS1_105:1:234:185:359
+CAGATTCATAAAACAAATACTACTAGACCTAAGAG
+>EAS1_105:1:28:745:352
+ATATGCACCTAACACAAGACTACCCAGATTCATAA
+>EAS1_105:1:28:745:352
+CTTCTAAATCTATAACAAAATTAAAATTTAACAAA
+>EAS1_105:1:297:283:948
+CCAGATTGCTTGTGGTCTGACAGGCTGCAACTGTG
+>EAS1_105:1:297:283:948
+TGTCTTACTTCCAGCTCCCCAGAGGGAAAGCTTTC
+>EAS1_105:1:329:407:872
+TTCGTTTTTTTTTTTTTTTTTTCCCTTTTTTTTTT
+>EAS1_105:1:3:903:957
+AAGCCAGAAGAGATTGGATCTAATTTTTGGACTTC
+>EAS1_105:1:3:903:957
+ATTCATCATCACTAAACCAGTCCTATAAGAAATGC
+>EAS1_105:1:45:239:851
+CTAAGAGGGATGAGAAATTACCTAATTGGTACAAT
+>EAS1_105:1:45:239:851
+TGAGAGAAGGAGTAGCTATACTTATATCAGATAAA
+>EAS1_105:1:87:430:995
+GAAAAGAGTTAAAAACATGAACTAACTATATGCTG
+>EAS1_105:1:87:430:995
+TACTCACCATCATAAATACACACAAAATTACAAAA
+>EAS1_105:2:110:584:649
+CCATGTACACACGCTGTCCTATGTACTTATCATGA
+>EAS1_105:2:110:584:649
+CTGTAATGATGCCCCTTGGCCATCACCCGGTCCCT
+>EAS1_105:2:146:374:692
+AAATGCTCAAAAGAATTGTAAAAGTCAAAATTAAA
+>EAS1_105:2:146:374:692
+ATTAAATTCCCCCACTTAAGAGATATAGATTGGCA
+>EAS1_105:2:179:532:82
+CCATCACCCGGTCCCTGCCCCATCTCTTGTAATCT
+>EAS1_105:2:179:532:82
+TGTACTTATCATGACTCTATCCCAAATTCCCAATT
+>EAS1_105:2:280:662:939
+AAGAGAAAAGCATACAGTCATCTATAAAGGAAATC
+>EAS1_105:2:280:662:939
+CCTCTTTAGTCTTGCTAGAGATTTAGACATCTAAA
+>EAS1_105:2:299:360:220
+ATTCAGTTCTAAATATAGAAATTGAAACAGCTGTG
+>EAS1_105:2:299:360:220
+GAAGAACTTAGATGCCCTCTTCTTCCAAAGATGAA
+>EAS1_105:2:301:161:195
+ACAGTAAAATAAAACAAAGGAGGTCATCATACAAT
+>EAS1_105:2:301:161:195
+GTACAATGTACAATATTCTGATGATGGTTACACTA
+>EAS1_105:3:176:431:647
+ATCATGACTCTATCCCAAATTCCCAATTACGTCCT
+>EAS1_105:3:176:431:647
+CCATCACCCAGTCCCTGCCCCATCTCTTGTAATCT
+>EAS1_105:3:182:404:693
+ACCTCATACACACACATGGTTTAGGGGTATAATAC
+>EAS1_105:3:182:404:693
+GCGTCTCTACCACAGGGGGCTGCGCGGTTTCCCAT
+>EAS1_105:3:232:364:583
+CAATTAATTGAGACTACAGAGCAACTAGGTAAAAA
+>EAS1_105:3:232:364:583
+TCATTAATAAAGACATGAGTTCAGGTAAAGGGGTG
+>EAS1_105:3:308:66:538
+CGCTTGTACTTCTAAATCTATAACAAAATTAAAAT
+>EAS1_105:3:308:66:538
+TATAACCATCCTACTAAATACATATGCACCTAACA
+>EAS1_105:3:329:177:267
+CATGAGATTATTAGGAAATGCTTTACTGTCATAAC
+>EAS1_105:3:329:177:267
+TACGTCCTATCTTCTTCTTAGGGAAGAACAGCTTA
+>EAS1_105:3:7:35:528
+TTTTTTTTTTGTTCTTTACTCTTTTTTTTTTTTTT
+>EAS1_105:3:86:823:683
+ACTTTGATGCCCTCTTCTTCCAAAGATGAAACGCG
+>EAS1_105:3:86:823:683
+CAGTTCTAAATATAGAAATTGAAACAGCTGTGTTT
+>EAS1_105:6:134:853:558
+AATATAATTGTGTCCATGTACACACGCTGTCCTAT
+>EAS1_105:6:134:853:558
+GGAACAGGGAGGTGCACTAATGCGCTCCACGCCCA
+>EAS1_105:6:162:594:858
+CTACCACAGGGGGCTGCGCGGTTTCCCATCATGAA
+>EAS1_105:6:162:594:858
+GTGTTCTCATCAACCTCATACACACACATGGTTTA
+>EAS1_105:6:172:827:592
+AATTGTAAAAGTCAAAATTAAAGTTCAATACTCAC
+>EAS1_105:6:172:827:592
+TAGATTGGCAGAACAGATTTAAAAACATGAACTAA
+>EAS1_105:6:23:885:274
+ACAAAGGAGGTCATCATACAATGATAAAAAGATCA
+>EAS1_105:6:23:885:274
+CTACTACTCAATATATCCATGTAACAAATCTGCGC
+>EAS1_105:6:267:953:459
+ACCTTACAAGCCAGAAGAGATTGGATCTAATTTTT
+>EAS1_105:6:267:953:459
+CATCACTAAACCAGTCCTATAAGAAATGCTCAAAA
+>EAS1_105:7:110:355:323
+ACCTTGAGAACCCCAGGGAATTTGTCAATGTCAGG
+>EAS1_105:7:110:355:323
+CCCAATGGACCTGTGATATCTGGATTCTGGGAAAT
+>EAS1_105:7:168:247:414
+AAAAGAATTGTAAAAGTCAAAATTAAAGTTCAATA
+>EAS1_105:7:168:247:414
+TAAATTCCCCCACTTAAGAGATATAGATTGGCAGA
+>EAS1_105:7:289:472:86
+ATGAACTTCTGTAATTGAAAAATTCATTTAAGAAA
+>EAS1_105:7:45:462:455
+TCCCTGTCTTACTTCCAGCTCCCCAGACGGAACGC
+>EAS1_105:7:45:462:455
+TCTAGGGGAACAGGGAGGTGCACTAATGCGCTCCA
+>EAS1_105:7:57:722:347
+ACAACAGGAAGAAAAGGTCTTTCAAAAGGTGATGT
+>EAS1_105:7:57:722:347
+CGCGTAACTGCGCTCTCATTCACTCCAGCTCCCTG
+>EAS1_105:8:160:130:351
+CAAAAGAATTGTAAAAGTCAAAATTAAAGTTCAAT
+>EAS1_105:8:160:130:351
+TGGATCTAATTTTTGGACTTCTTAAAGAAAAAAAA
+>EAS1_105:8:179:119:876
+ATAAAAAGATCAATTCAGCAAGAAGATATAACCAT
+>EAS1_105:8:179:119:876
+TTAAAAACATGAACTAACTATATGCTGTTTACCAG
+>EAS1_105:8:24:718:322
+AACTCATTAATAATGTCATGAGTTCAGGTAAAGGG
+>EAS1_105:8:24:718:322
+ACAATTAATTGAGACTACAGACCAATTATGTAAAA
+>EAS1_105:8:254:617:73
+AACTATTTGAGGAAGTAATTGGGGAAAACCTCTTT
+>EAS1_105:8:254:617:73
+GCAGAAGAAAGAGGTTCAGAACTTGAAGACAAGTC
+>EAS1_105:8:256:404:584
+ACTGTCCTATGTACTTATCATGACTCTATCCCAAA
+>EAS1_105:8:256:404:584
+GTTTCTGCCCCCAGCATGGTTGTACTGGGCAATAC
+>EAS1_105:8:96:720:940
+AAAGGAAATCCCATCAGAATAACAATGGGCTTCTC
+>EAS1_105:8:96:720:940
+TAAGATAATTCATCATCACTAAACCAGTCCTATAA
+>EAS1_108:1:111:796:737
+ATCATGACTCTATCCCAAATTCCCAATTACGTCCT
+>EAS1_108:1:111:796:737
+CCCCAGCATGGTTGTACTGGGCAATACATGTGATT
+>EAS1_108:1:131:518:588
+AAAATCAGCAAGAGAAAAGCATACAGTCATCTATA
+>EAS1_108:1:131:518:588
+ATAAATGAAGGGGAAATAAAGTCAAGTCTTTCCTG
+>EAS1_108:1:148:286:316
+AGAACTTCCCTGGAGGTCTGATGGCGTTTCTCCCT
+>EAS1_108:1:148:286:316
+CCTCTGTCTTGATTTACTTGTTGTTGGTTTTCTGT
+>EAS1_108:1:155:809:543
+AAATTTAACAAAAGTAAATAAAACACATAGCTAAA
+>EAS1_108:1:155:809:543
+TACATATGCACCTAACACAAGACTACCCAGATTCA
+>EAS1_108:1:16:438:245
+TTGAATAAAAAGGGATTAAATTCCCCCACTTAAGA
+>EAS1_108:1:189:863:213
+CTACTAGACCTAAGAGGGATGAGAAATTACCTAAT
+>EAS1_108:1:189:863:213
+TATACTTATATCAGATAAAGCACACTTTAAATCAA
+>EAS1_108:1:242:419:512
+AATGGGCTTCTCAGCAGAAACCTTACAAGCCAGAA
+>EAS1_108:1:242:419:512
+CTAAACCAGTCCTATAAGAAATGCTCAAAAGAATT
+>EAS1_108:1:277:194:143
+TGGGCTGTAATGATGCCCCTTGGCCATCACCCGGT
+>EAS1_108:1:277:194:143
+TTTTTAATGATTCCTCAATGTTAAAATGTCTATTT
+>EAS1_108:1:328:614:638
+AAAGGTTGTTGGGAGATTTTTAATGATTCCTCAAT
+>EAS1_108:1:328:614:638
+ACTGGTTCTCTTGAAAGCTTGGGCTGTAATGATGC
+>EAS1_108:1:33:779:821
+AATGTTATGCCCTGCTAAACTAAGCATCATAAATG
+>EAS1_108:1:33:779:821
+TGAAGGAAAAAAATTCTAAAATCAGCAAGAGAAAA
+>EAS1_108:1:49:911:980
+ACAATGTACAATATTCTGATGATGGTTACACTAAA
+>EAS1_108:1:49:911:980
+GGGGAAAAAAGTAAACTCTCAAATATTGCTAGTGG
+>EAS1_108:1:65:787:74
+TGTAATGAAAACTATATTTATGCTATTCAGTTCTA
+>EAS1_108:2:102:543:160
+CAACAGGAACAAAACCTCATATATCAATATTAACT
+>EAS1_108:2:102:543:160
+CAGGTAAAGGGGTGGAAAAAGATGTTCTACGCAAA
+>EAS1_108:2:116:966:193
+ATTAACATTACAACAGGAACAAAACCTCATATATC
+>EAS1_108:2:116:966:193
+GACATGAGTTCAGGTAAAGGGGTGGAAAAAGATGT
+>EAS1_108:2:170:326:433
+CTTCCCTGGAGGTCTGATGGCGTTTCTCCCTCGTC
+>EAS1_108:2:170:326:433
+TTGTTGGTTTTCTGTTTCTTTGTTTGATTTGGTGG
+>EAS1_108:2:176:653:957
+AAAGGGGTGGAAAAAGATGTTCTACGCAAACAGAA
+>EAS1_108:2:176:653:957
+ACATTACAACAGGAACAAAACCTCATATATCAATA
+>EAS1_108:2:204:737:61
+AAAGTGAGAAGTTTGGAAAAACTATTTGAGGAAGT
+>EAS1_108:2:204:737:61
+TCAGCAAGAGAAAAGCATACAGTCATCTATAAAGG
+>EAS1_108:2:240:593:842
+ATCTGGATTCTGGGAAATTCTTCATCCTGGACCCT
+>EAS1_108:2:240:593:842
+CATGGTTTAGGGGTATAATACCTCTACATGGCTGA
+>EAS1_108:2:266:994:429
+ACAGGTTTTATAAAACAATTAATTGAGACTACAGA
+>EAS1_108:2:266:994:429
+TGAAGGGGAAATAAAGTCAAGTCTTTCCTGACAAG
+>EAS1_108:2:316:176:543
+ATGTCTATTTTTGTCTTGACACCCAACTAATATTT
+>EAS1_108:2:316:176:543
+CATCTCTTGTAATCTCTCTCCTTTTTGCTGCATCC
+>EAS1_108:2:49:271:588
+CACATGGTTTAGGGGTATAATACCTCTACATGGCT
+>EAS1_108:2:49:271:588
+GCTGCGCGGTTTCCCATCATGAAGCACTGAACTTC
+>EAS1_108:2:62:879:264
+AATGAAAACTATATTTATGCTATTCAGTTCTAAAT
+>EAS1_108:2:62:879:264
+GGACGCTGAAGAACTTTGATGCCCTCTTCTTCCAA
+>EAS1_108:2:82:879:246
+AAGAGGGACGCTGAAGAATTTTGATGCCCTCTTCT
+>EAS1_108:2:82:879:246
+ACAACTGTGAGCCATCACAATGAACAACAGGAAGA
+>EAS1_108:2:85:580:481
+AAAAAAGTAAATAAAACACATAGCTAAAACTAAAA
+>EAS1_108:2:85:580:481
+CTAACACAAGACTACCCAGATTCATAAAACAAATA
+>EAS1_108:3:216:988:883
+AAGCCAACACAATGAACAACAGGAAGAAAAGGTCT
+>EAS1_108:3:216:988:883
+AGAGGGACGCTGAAGAACTTTGATGCCCTCTTCTT
+>EAS1_108:3:24:319:429
+GTTATGCCCTGCTAAACTAAGCATCATAAATGAAG
+>EAS1_108:3:24:319:429
+TAATAAATACACACAAAAGTACAAAACTCACAGGT
+>EAS1_108:3:75:934:439
+AAGAGACTATTGCCAGATGAACCACACATTAATAC
+>EAS1_108:3:75:934:439
+CCCATCATGAAGCACTGAACTTCCACGTCTCATCT
+>EAS1_108:3:82:356:253
+AGTTTCTGCCCCCAGCATGGTTGTACTGGGCAATA
+>EAS1_108:3:82:356:253
+GAAAGCTTTCAACGCTTCTAGCCATTTCTTTTGGC
+>EAS1_108:4:163:611:211
+TAAAGTCAACATGAAGGAAAAAAATTCTAAAATCA
+>EAS1_108:4:163:611:211
+TGAGGAAAAAGAAAAAGTGAGAAGTTTGGAAAAAC
+>EAS1_108:4:248:753:731
+TATGCTATTCAGTTCTAAATATAGAAATTGAAACA
+>EAS1_108:4:248:753:731
+TGAAGAACTTTGATGCCCTCTTCTTCCAAAGATGA
+>EAS1_108:4:31:622:216
+ATTTAACAAAAGTAAATAAAACACATAGCTAAAAC
+>EAS1_108:4:37:604:389
+ATGTTCTACGCAAACAGAAACCAAATGAGAGAAGG
+>EAS1_108:4:37:604:389
+TCATAAAACAAATACTACTAGACCTAAGAGGGATG
+>EAS1_108:4:75:166:463
+GTGAGAAGTTTGGAAAAACTATTTGAGGAAGTAAT
+>EAS1_108:4:75:166:463
+TAACAATAGACTAAACCAAGCAGAAGAAAGAGGTT
+>EAS1_108:4:91:521:517
+CCACACTGGTTCTCTTGAAAGCTTGGGCTGTAATG
+>EAS1_108:4:91:521:517
+CCCTGCAATTAATATAATTGTGTCCATGTACACAC
+>EAS1_108:5:115:193:231
+GAAGAGATTGGATCTAATTTTTGGACTTCTTAAAG
+>EAS1_108:5:115:193:231
+TATAAGAAATGCTCAAAAGAATTGTAAAAGTCAAA
+>EAS1_108:5:11:555:330
+CGCTTGTACTTCTAAATCTATAAAAAAATTAAAAT
+>EAS1_108:5:11:555:330
+GGAAAACAATTTGGTAATTTCGTTTTTTTTTTTTT
+>EAS1_108:5:175:149:296
+AAAAATTAACATTACAACAGGAACAAAACCTCATA
+>EAS1_108:5:175:149:296
+AAGGGGAAATAAAGTCAAGCCTTTCCTGACAAGCA
+>EAS1_108:5:180:905:36
+CCTCCGTGTCCTCCCATCTGGCCTCGTCCACACTG
+>EAS1_108:5:180:905:36
+TACTATGTTTCTTATCTGCACATTACTACCCTGCA
+>EAS1_108:5:229:717:121
+ACTATGAAGAGACTATTGCCAGATGAACCACACAC
+>EAS1_108:5:229:717:121
+TTCTTCTGAGGGAAGAACAGCTTAGGTATCAATTT
+>EAS1_108:5:321:712:224
+AGATAAAGCACACTTTAAATCAACAACAGAAAAAT
+>EAS1_108:5:321:712:224
+ATGAGAAATTACCTAATTGGTACAATGTACAATAT
+>EAS1_108:5:89:942:84
+AAAACCTGTCAAACACGAATGTTATGCCCTGCTAA
+>EAS1_108:5:89:942:84
+TACAAAACTCACAGGTTTTATAAAACAATTAATTG
+>EAS1_108:6:159:493:275
+ACAAAACTCACAGGTTTTATAAAACAATTAATTGA
+>EAS1_108:6:159:493:275
+TGCTGTTTACAAGAAACTCATTAATAAAGACATGA
+>EAS1_108:6:165:464:123
+CATACACACACATGGTTTAGGGGTATAATACCTCT
+>EAS1_108:6:165:464:123
+GTCTCTACCACAGGGGGCTGCGCGGTTTCCCATCA
+>EAS1_108:6:222:579:961
+AGTCCTATAAGAAATGCTCAAAAGAATTGTAAAAG
+>EAS1_108:6:222:579:961
+CAGAAACCTTACAAGCCAGAAGAGATTGGATCTAA
+>EAS1_108:6:71:187:824
+AGACAGACTTCATCAAGATATGTAGTCATCAGACT
+>EAS1_108:6:71:187:824
+TCTAATTTTTGGACTTCTTAAAGAAAAAAAAACCT
+>EAS1_108:6:73:735:329
+AAAGGGATTAAATTCCCCCACTTAAGAGATATAGA
+>EAS1_108:6:73:735:329
+TAGCTATACTTATATCAGATAAAGCACACTTTAAA
+>EAS1_108:6:77:48:860
+CTCTGTCTTGATTTACTTGTTGTTTGTTTTCTGTT
+>EAS1_108:6:77:48:860
+TAGATGAGAGAGAACTTCCCTGGAGGTCTGATGGC
+>EAS1_108:6:94:294:387
+ACCATCATAAATACACACAAAAGTACAAAACTCAC
+>EAS1_108:6:94:294:387
+GAATGTTATGCCCTGCTAAACTAAGCATCATAAAT
+>EAS1_108:6:95:235:746
+CTAAGCATCATAAATGAAGGGGAAATAAAGTCAAG
+>EAS1_108:6:95:235:746
+TCTAAAATCAGCAAGAGAAAAGCATACAGACATCT
+>EAS1_108:7:108:440:208
+CCCATCCTACTAAATACATATGCACCTAACACAAG
+>EAS1_108:7:108:440:208
+TTCAGGTAAAGGGGAGGAAAAAGATGTTCTACGCA
+>EAS1_108:7:222:538:267
+ATAATTGTGTCCATGTACACACGCTGTCCTATTTA
+>EAS1_108:7:222:538:267
+TCTGGCCTCGTCCACACTGGTTCTCTTGAAAGCTT
+>EAS1_108:7:266:556:252
+CCCATCTGGCCTCGTCCACACTGGTTCTCTTGAAA
+>EAS1_108:7:266:556:252
+GATTTGGTGGAAGACATAATCCCACGCTTCCTATG
+>EAS1_108:7:82:926:112
+CAATGTCAGGGAAGGAGCATTTTGTCAGTTGCCAA
+>EAS1_108:7:82:926:112
+CTGCTGGCAAGCTAGAGTCCCATTTGGAGCCCCTC
+>EAS1_108:8:118:440:850
+AATTGAAAAATTCATTTAAGAAATTACAAAATATA
+>EAS1_108:8:129:477:427
+ATGGACCTGTGATATCTGGATTCTGGGAAATTCTT
+>EAS1_108:8:129:477:427
+TACACACACATGGTTTAGGGGTATAATACCTCTAC
+>EAS1_108:8:19:929:765
+AAAAACATGAACTAACTATATGCTGTTTACAAGAA
+>EAS1_108:8:19:929:765
+ATCAACAACAGTAAAATAAAACAAAGGAGGTCATC
+>EAS1_93:1:131:946:353
+TCTCTTGAAAGCTTGGGCTGTAATGATGCCCCTTG
+>EAS1_93:1:131:946:353
+TGTACACACGCTGTCCTATGTACTTATCATGACTC
+>EAS1_93:1:179:629:513
+GTCAACATGAAGGAAAAAAATTCTAAAATCAGCAA
+>EAS1_93:1:179:629:513
+GTCACAGGTATTCCTGAGGAAAAAGAAAAAGTGAG
+>EAS1_93:1:20:635:509
+CAGCTTAGGTATCAATTTGGTGTTCTGTGTAAAGT
+>EAS1_93:1:20:635:509
+TGCATCCCTGTCTTCCTCTGTCTTGATTTACTTGT
+>EAS1_93:1:214:784:690
+AAATCCCATCAGAATAACAATGGGCTTCTCAGCGG
+>EAS1_93:1:214:784:690
+GATAATTCATCATCACTAAACCAGTCCTATAAGAA
+>EAS1_93:1:216:381:608
+TAATTGTGTCCATGTACACTCGCTGTCCTATGTAC
+>EAS1_93:1:216:381:608
+TTCTCACAGTTTCTGCCCCCAGCATGGTTGTACTG
+>EAS1_93:1:253:59:242
+CCCCATCTCTTGTAATCTCTCTCCTTTTTGCTGCA
+>EAS1_93:1:253:59:242
+TTTGTCTTGACACCCAACTAATATTTGTCTGAGCA
+>EAS1_93:1:264:988:663
+CGAGGGGAACAGGGAGGTGCACTAATGCGCTCCAC
+>EAS1_93:1:264:988:663
+TGGCTGATTATGAAAACAATGTTCCCCAGATACCA
+>EAS1_93:1:92:213:217
+ACAGTCTAGATGAGAGAGAACTTCCCTGGAGGTCT
+>EAS1_93:1:92:213:217
+TGCATCCCTGTCTTCCTCTGTCTTGATTTACTTGT
+>EAS1_93:2:173:995:93
+GCTGGAGGGAAGAGGGACGCTGAAGAACTTTGATG
+>EAS1_93:2:173:995:93
+TAATGAAAACTATATTTATGCTATTCAGTTCTAAA
+>EAS1_93:2:286:923:549
+TCAAATGAACTTCTGTAATTGAAAAATTCATTTAA
+>EAS1_93:2:30:466:652
+AAAAATGAACAGAGCTTTCAAGAAGTATGAGATTA
+>EAS1_93:2:30:466:652
+AAGAGGCTAAAAGAATGCCAGGAAGATACATTGCA
+>EAS1_93:2:313:711:530
+ACATGAGTTCAGGTAAAGGGGTGGAAAAAGATGTT
+>EAS1_93:2:313:711:530
+TAATTGAGACTACAGAGCAACTAGGTAAAAAATTA
+>EAS1_93:3:181:93:694
+ACTCATTAATAAAGACATGAGTTCAGGTAAAGGGG
+>EAS1_93:3:181:93:694
+TTAATTGAGACTACAGAGCAACTAGGTAAAAAATT
+>EAS1_93:3:79:879:15
+AGACTACAGAGCAACTAGGTAAAAAATTAACATTA
+>EAS1_93:3:79:879:15
+AGTCAAGTCTTTCCTGACAAGCAAATGCTAAGATA
+>EAS1_93:4:160:896:275
+AAAACTATATTTATGCTATTCAGTTCTAAATATAG
+>EAS1_93:4:160:896:275
+AGGGAAGAGGGACGCTGAAGAACTTTGATGCCCTC
+>EAS1_93:4:321:271:138
+GTGTAAAGTCTCAGGGAGCCGTCCGTGTCCTCCCA
+>EAS1_93:4:321:271:138
+TTTGGTGGAAGACATAATCCCACGCTTCCTATGGA
+>EAS1_93:4:325:352:67
+ATAAAGTCAAGTCTTTCCTGACAAGCAAATGCTAA
+>EAS1_93:4:325:352:67
+TACAGAGCAACTAGGTAAAAAATTAACATTACAAC
+>EAS1_93:5:197:52:58
+AAATGAACAGAGCTTTCAAGAAGTATGAGATTATG
+>EAS1_93:5:197:52:58
+TCTAAATGAAAGAGGCTCAAAGAATGCCAGGAAGA
+>EAS1_93:5:246:177:525
+CATCATAAATACACACAAAAGTAAAAAACTCACAG
+>EAS1_93:5:246:177:525
+TCTTAAAGAAAAAAAAACCTGTCAAACACGAATGT
+>EAS1_93:5:256:444:399
+CTGCTACTCAATATATCCATGTAACAAATCTGCGC
+>EAS1_93:5:256:444:399
+GAAGATATAACCATCCTACTAAATACATATGCACC
+>EAS1_93:5:292:122:666
+GGGAAGAACAGCTTAGGTATCAATTTGGTGTTCTG
+>EAS1_93:5:292:122:666
+TACTGTCATAACTATGAAGAGACTATTGTCAGATG
+>EAS1_93:5:62:969:12
+TATAAAGGAAATCCCATCAGAATAACAATGGGCTT
+>EAS1_93:5:62:969:12
+TCTTGCTAGAGATTTAGACATCTAAATGAAAGAGG
+>EAS1_93:5:66:372:343
+ATTACAAAATATAGTTGAAAGATCTAACAATAGAC
+>EAS1_93:5:66:372:343
+TATTCCTGAGGAAAAAGAAAAAGTGAGAAGTTTGG
+>EAS1_93:6:132:717:233
+AGAGAACTTCCCTGGAGGTCTGATGGAGTTTCTCC
+>EAS1_93:6:132:717:233
+TGTTGGTTTTCTGTTTCTTTGTTTGATTTGGTGGA
+>EAS1_93:6:159:273:253
+TTAGTCTTGCTAGAGATTTAGACATCTAAATGAAA
+>EAS1_93:6:191:948:257
+AACTAATATTTGTCTGAGCAAAACAGTCTAGATGA
+>EAS1_93:6:191:948:257
+CTTTTTGCTGCATCCCTGTCTTCCTCTGTCTTGAT
+>EAS1_93:6:216:47:302
+AAAAAAAAACCTGTCAAACACGAATGTTATGCCCT
+>EAS1_93:6:216:47:302
+AATACTCACCATCATAAATACACACAAAAGTACAA
+>EAS1_93:6:218:144:794
+GGGTGCATTGCTATGTTGCGGTCGCTTTGCCTCCT
+>EAS1_93:6:218:144:794
+TTTTTTTTTTTTTCTTTTCTCTTTTTTTTTTTTTT
+>EAS1_93:6:238:514:194
+AAACTATTTGAGGAAGTAATTGGGGAAAACCTCTT
+>EAS1_93:6:238:514:194
+AATAGACTAAACCAAGCAGAAGAAAGAGGTTCAGA
+>EAS1_93:6:255:441:47
+AACAACAGTAAAATAAAACAAAGGAGGTCATCATA
+>EAS1_93:6:255:441:47
+TGGTACAATGTACAATATTCTGATGATGGTTACAC
+>EAS1_93:6:271:244:568
+ATGGACCTGTGATATCTGGATTCTGGGAAATTCTT
+>EAS1_93:6:271:244:568
+CTTGCAACAACCTTGAGAACCCCAGGGAATTTGTC
+>EAS1_93:6:45:601:439
+AATGCTCAAAAGAATTGTAAAAGTCAAAATTAAAG
+>EAS1_93:6:45:601:439
+ATAAAAAGGGATTAAATTCCCCCACTTAAGAGATA
+>EAS1_93:7:14:426:613
+AGGGAGGGAGGGAAGAGGGACGCTGAAGAACTTTG
+>EAS1_93:7:14:426:613
+GTAATGAAAACTATATTTATGCTATTCAGTTCTAA
+>EAS1_93:7:252:171:323
+GCTATTCAGTTCTAAATATAGAAATTGAAACAGCT
+>EAS1_93:7:270:995:918
+AAAATTCATTTAAGAAATTACAAAATATAGTTGAA
+>EAS1_93:7:319:280:57
+AAAGGAAATCCCATCAGAATAACAATGGGCTTCTC
+>EAS1_93:7:319:280:57
+TGCTAGAGATTTAGACATCTAAATGAAAGAGGCTC
+>EAS1_93:8:13:325:483
+AAAAACATGAACTAACTATATGCTGTTTACAAGAA
+>EAS1_93:8:13:325:483
+ATCATACAATGATAAAAAGATCAATTCAGCAAGAA
+>EAS1_93:8:14:601:624
+AAAAGGTGATGTGTGTTCTCATCAACCTCATACAC
+>EAS1_93:8:14:601:624
+CTGCGCTCTCATTCACTCCAGCTCCCTGTCAACCC
+>EAS1_95:1:16:823:343
+AGACATAACCCCACGCTTCCTATGGAAAGGTTGTT
+>EAS1_95:1:16:823:343
+TCCCATCTGGCCTCGTCCACACTGGTTCTCTTGAA
+>EAS1_95:1:196:533:921
+AAATGTGTTTATTACCAGAGGGATGGAGGGAAGAG
+>EAS1_95:1:196:533:921
+CCTGAGAGATTCTGCAGCCCAGATCCAGATTGCTT
+>EAS1_95:1:202:341:984
+GGAGGTCATCATACAATGATAAAAAGATCAATTCA
+>EAS1_95:1:202:341:984
+TGAACTAACTATATGCTGTTTACAAGAAACTCATT
+>EAS1_95:1:249:986:224
+CTTTTTGCTGCATCCCTGTCTTCCTCTGTCTTGAT
+>EAS1_95:1:249:986:224
+TATTTGTCTGAGCAAAACAGTCTAGATGAGAGAGA
+>EAS1_95:1:261:504:780
+TCCCTGTCTTCCTCTGTCTTGATTTACTTGTTGTT
+>EAS1_95:1:261:504:780
+TTTGTCTGAGAAAAACAGTCTAGATGAGAGAGAAC
+>EAS1_95:1:301:54:240
+AACAGGGAGGTGCACTAATGCGCTCCACGCCCAAG
+>EAS1_95:1:301:54:240
+CCCTGCAATTAATATAATTGTGTCCATGTACACAC
+>EAS1_95:1:77:589:741
+AGTAAAATAAAACAAAGGAGGTCATCATACAATGA
+>EAS1_95:1:77:589:741
+TGGTTACACTAAAAGCCCATACTTTACTGCTACTC
+>EAS1_95:2:142:353:398
+CAGGTAAAGGGGTGGAAAAAGATGTTCTACGCAAA
+>EAS1_95:2:142:353:398
+GGTAAAAAATTAACATTACAACAGGAACAAAACCT
+>EAS1_95:2:162:503:769
+AGAGGGACGCTGAAGAACTTTGATGCCCTCTTCTT
+>EAS1_95:2:162:503:769
+AGGCTGCAACTGTGAGCCATCACAATGAACAACAG
+>EAS1_95:2:198:691:595
+ACACACATGGTTTAGGGGTATAATACCTCTACATG
+>EAS1_95:2:198:691:595
+CATGAAGCACTGAACTTCCACGTCTCATCTAGGGG
+>EAS1_95:2:211:954:174
+AAAGAAAAAACAAAAACTATGCTAAGTATTGGTAA
+>EAS1_95:2:211:954:174
+AGACCTAAGAGGGATGAGAAATTACCTAATTGGTA
+>EAS1_95:2:228:915:631
+AAGATATGTAGTCATCAGACTATCTAAAGTCAACA
+>EAS1_95:2:228:915:631
+ATTATTAAAGAAAAAAAAACCTGTCAAACACGAAT
+>EAS1_95:2:278:918:892
+AGCCCAGCTCCAGATTGCTTGTGGTCTGACAGGCT
+>EAS1_95:2:278:918:892
+CCATCCCTGTCTTACTTCCAGCTCCCCAGAGGGAA
+>EAS1_95:2:40:918:950
+AATATAATTGTGTCCATGTACACACGCTTTCCTTT
+>EAS1_95:2:40:918:950
+GTTCTCTTGAAAGCTTGGGCTGTAATGATGCCCCT
+>EAS1_95:3:268:523:511
+ACACTGGTTCTCTTGAAAGCTTGGGCTGTAATGAT
+>EAS1_95:3:268:523:511
+TGTCCATGTACACACGCTGTCCTATGTACTTATCA
+>EAS1_95:3:303:970:243
+AACCTGTCAAACACGAATGTTATGCCCTGCTAAAC
+>EAS1_95:3:303:970:243
+CAGACTTCATCAAGATATGTAGTCATCAGACTATC
+>EAS1_95:3:308:956:873
+ATAAAAATAAGTGTGTCCATGTACACACGCTGTCC
+>EAS1_95:3:308:956:873
+CTCATCTAGGGGAACAGGGAGGTGCACTAATGCGC
+>EAS1_95:4:174:157:573
+CAGAAACCAAATGAGAGAAGGAGTAGCTATACTTA
+>EAS1_95:4:174:157:573
+TAAAACAAATACTACTAGACCTAAGAGGGATGAGA
+>EAS1_95:4:176:971:874
+TAAAATCAGAAGAGAAAAGCATACAGTCATCTATA
+>EAS1_95:4:176:971:874
+TGAGGAAGTAATTGGGGAAAACCTCTTTAGTCTTG
+>EAS1_95:4:184:17:636
+TACACACACATGGTTTAGGGGTATAATACCTCTAC
+>EAS1_95:4:184:17:636
+TTTTTTTTTTTTTTTTTTTTTTTTTTTTCACAGGT
+>EAS1_95:4:224:592:744
+GATATGTAGTCATCAGACTATCTAAAGTCAACATG
+>EAS1_95:4:224:592:744
+TATGAGATTATGTAAAGTAACTGAACCTATGAGTC
+>EAS1_95:4:238:124:196
+TTTTTTTTCTTTTCTCTTTTTTTTTTTTTTTTTTT
+>EAS1_95:4:61:631:567
+AAGAAGATATAACCATCCTACTAAATACATATGCA
+>EAS1_95:4:61:631:567
+CATTAATAAAGACATGAGTTCAGGTAAAGGGGTGG
+>EAS1_95:4:66:179:118
+CCATGTACACACGCTGTCCTATGTACTTATCATGA
+>EAS1_95:4:66:179:118
+TGGGCTGTAATGATGCCCCTTGGCCATCACCCAGT
+>EAS1_95:4:71:517:742
+AACTATTTGAGGAAGTAATTGGGGAAAACCTCTTT
+>EAS1_95:4:71:517:742
+AAGCAGAAGAAAGAGGTTCAGAACTTGAAGACAAG
+>EAS1_95:5:257:654:116
+TAACAATAGACTAAACCAAGCAGAAGAAAGAGGTT
+>EAS1_95:5:257:654:116
+TCCTGAGGAAAAAGAAAAAGTGAGAAGTTTGGAAA
+>EAS1_95:5:263:511:936
+CAAATAGGTAAAAAATTAACATTACAACAGGAACA
+>EAS1_95:5:263:511:936
+CAAGTCTTTCCTGACAAGCAAATGCTAAGATAATT
+>EAS1_95:5:284:212:932
+CTTTAAATCAACAACAATAAAAAAAAACAAAGGAG
+>EAS1_95:5:284:212:932
+TGATGATGGTTACGCTAAAAGTCCATGCTTTACTG
+>EAS1_95:6:174:650:125
+AAGCATCATAAATGAAGGGGAAATAAAGTCAAGTC
+>EAS1_95:6:174:650:125
+CAGGTTTTATAAAACAATTAATTGAGACTACAGAG
+>EAS1_95:6:185:312:167
+CTGAAGAACTTTGATGCCCTCTTCTTCCAAAGATG
+>EAS1_95:6:185:312:167
+TGGTCTGACAGGCTGCAACTGTGAGCCATCACAAT
+>EAS1_95:6:194:696:490
+ACATTAATACTATGTTTCTTATCTGCACATTACTA
+>EAS1_95:6:194:696:490
+TTCCACGTCTCATCTAGGGGAACAGGGAGGTGCAC
+>EAS1_95:6:53:156:845
+ACACCCAACTAATATTTGTCTGAGCAAAACAGTCT
+>EAS1_95:6:53:156:845
+TTGTAATCTCTCTCCTTTTTGCTGCATCCCTGTCT
+>EAS1_95:6:87:734:888
+ATACCATCCCTGTCTTACTTCCAGCTCCCCAGAGG
+>EAS1_95:6:87:734:888
+TGCGCTCCACGCCCAAGCCCTTCTCACAGTTTCTG
+>EAS1_95:7:155:530:532
+AGCAAGAAGATATAACCATCCTACTAAATACATAT
+>EAS1_95:7:155:530:532
+TGCGCTTGTACTTCTAAATCTATAACAAAATTAAA
+>EAS1_95:7:280:607:113
+ATCCATGTAACAAATCTGCGCTTGTACTTCTAAAT
+>EAS1_95:7:280:607:113
+GGAGTATAAATTGTTTTCCACTTTGGAAAACAATT
+>EAS1_95:7:282:817:710
+TGGAGGGAAGAGGGACGCTGAAGAACTTTGATGCC
+>EAS1_95:7:282:817:710
+TTTGTAATGAAAACTATATTTATGCTATTCAGTTC
+>EAS1_95:7:310:800:761
+AAAGCACACTTTAAATCAACAACAGTAAAATAAAA
+>EAS1_95:7:310:800:761
+CAATATTCTGATGATGGTTACACTAAAAGCCCATA
+>EAS1_95:7:46:522:426
+AAAGACATGAGTTCAGGTAAAGGGGTGGAAAAAGA
+>EAS1_95:7:46:522:426
+GGTAAAAAATTAACATTACAACAGGAACAAAACCT
+>EAS1_95:7:55:506:125
+CTTTACTGTCATAACTATGAAGAGACTACTGCCAG
+>EAS1_95:7:55:506:125
+TCTACCACAGGGGGCTGCGCGGTTTCCCATCATGA
+>EAS1_95:7:61:702:720
+ATTTGTCTGAGCAAAACAGTCTAGATGAGAGAGAA
+>EAS1_95:7:61:702:720
+CTCTCCTTTTTGCTGCATCCCTGTCTTCCTCTGTC
+>EAS1_95:7:74:866:49
+CATGAGTTCAGGTAAAGGGGTGGAAAAAGATGTTC
+>EAS1_95:7:74:866:49
+CCAACCTACTAAATACATATGCACCTAACACAAGA
+>EAS1_97:2:128:629:484
+AAAAAAGTAAATAAAACACATAGCTAAAACTAAAA
+>EAS1_97:2:128:629:484
+GATTCATAAAACAAATACTACTAGACCTAAGAGGG
+>EAS1_97:2:193:420:78
+ATAAATGAAGGGGAAATAAAGTCAAGTCTTTCCTG
+>EAS1_97:2:193:420:78
+TTGAGACTACAGAGCAACTAGGTAAAAAATTAACA
+>EAS1_97:2:59:882:980
+AATATAATTGTGTCCATGTACACACGCTGTCCTAT
+>EAS1_97:2:59:882:980
+GGGCTGTAATGATGCCCCTTGGCCATCACCCGGTC
+>EAS1_97:2:96:419:327
+TACTAAATACATATGCACCTAACACAAGACTACCC
+>EAS1_97:2:96:419:327
+TCTAAATCTATAACAAAATTAAAATTTAACAAAAG
+>EAS1_97:2:9:203:653
+CACCCAACTAATATTTGTCTGAGCAAAACAGTCTA
+>EAS1_97:2:9:203:653
+TCCCTGCCCCATCTCTTGTAATCTCTCTCCTTTTT
+>EAS1_97:3:147:423:584
+GAAGTAATTGGGGAAAACCTCTTTAGTCTTGCTAG
+>EAS1_97:3:147:423:584
+GCATACAGTCATCTATAAAGGAAATCCCATCAGAA
+>EAS1_97:3:160:173:889
+TATGAGTCACAGGTATTCCTGAGGAAAAAGAAAAA
+>EAS1_97:3:160:173:889
+TCAAGATATGTAGTCATCAGACTATCTAAAGTCAA
+>EAS1_97:3:277:144:848
+TAACAATAGACTAAACCAAGCAGAAGAAAGAGGTT
+>EAS1_97:3:277:144:848
+TATTCCTGAGGAAAAAGAAAAAGTGAGAAGTTTGG
+>EAS1_97:3:73:292:429
+GAAAGCTTTCAACGCTTCTAGCCATTTCTTTTTGC
+>EAS1_97:3:73:292:429
+TTCTCACAGTTTCTGCCCCCAGCATGGTTGTACTG
+>EAS1_97:4:261:267:597
+GGGTAATAAAGTCAAGTCTTTCCTGACAAGCAAAT
+>EAS1_97:4:261:267:597
+TTGAGAATAAAGAGCAACTAGGTAAAAAATTAACA
+>EAS1_97:4:274:287:423
+CTAAATCTATAAAAAAATTAAAATTTAACAAAAGT
+>EAS1_97:4:274:287:423
+TTTTTTTTTTTTTTTTTCTCTTTTTTTTTTTTTTT
+>EAS1_97:4:290:121:79
+ATTGGTAAAGATGTGGGGAAAAAAGTAAACTCTCA
+>EAS1_97:4:290:121:79
+TGATGATGGTTACACTAAAAGCCCATACTTTACTG
+>EAS1_97:4:77:29:126
+ACAGGGAATTTGTCAATGTCAGGGAAGGAGCATTT
+>EAS1_97:4:77:29:126
+GCACAGGGGCTTAACCTCTGGTGACTGCCAGAGCT
+>EAS1_97:4:83:731:540
+CTAGGTAAAAAATTAACATTACAACAGGAACAAAA
+>EAS1_97:4:83:731:540
+TAAAGTCAAGTCTTTCCTGACAAGCAAATGCTAAG
+>EAS1_97:5:154:952:558
+AAAGACTACCCAGATTCATAAAACAAATACTACTA
+>EAS1_97:5:154:952:558
+GCAAACAGAAACCAAATGAGAGAAGGAGTAGCTAT
+>EAS1_97:5:219:174:684
+AAAAAAACTGTCAAACACGAATGTTATGCCCTGCT
+>EAS1_97:5:219:174:684
+AGTCATCAGACTATCTAAAGTCAACATGAAGGAAA
+>EAS1_97:5:28:538:148
+AAAAAAAAACCTGTCAAACACGAATGTTATGCCCT
+>EAS1_97:5:28:538:148
+TCATCAAGATATGTAGTCATCAGACTATCTAAAGT
+>EAS1_97:5:318:177:383
+TACTACCCTGCAATTAATATAATTGTGTCCATGTA
+>EAS1_97:5:318:177:383
+TCTTGAAAGCTTGGGCTGTAATGATGCCCCTTGGC
+>EAS1_97:5:84:927:843
+CCAGCATGGTTGTACTGGGCAATACATGAGATTAT
+>EAS1_97:5:84:927:843
+TTACGTCCTATCTTCTTCTTAGGGAAGAACAGCTT
+>EAS1_97:6:222:305:337
+TTTTTTTTTTTTTTTTTTCCCTTTTTTTTTTTTTT
+>EAS1_97:6:308:667:658
+AAAGATCACTTCAGCAATAAGATATAACCATCCTA
+>EAS1_97:6:308:667:658
+TAAAAACATGAACTAACTATATCCTTCTTACAATA
+>EAS1_97:6:93:334:858
+CTGCCCCCAGCATGGTTGTACTTGGCAATACATGA
+>EAS1_97:6:93:334:858
+GTACTTATCATGACTCTATCCCAAATTCCCAATTA
+>EAS1_97:7:20:979:96
+GAAATTGAAACAGCTGTGTTTAGTGCCTTTGTTCA
+>EAS1_97:7:264:642:506
+AAATATAGAAATTGAAACAGCTGTGTTTATTGTAT
+>EAS1_97:7:264:642:506
+ACTTCATCCAAAGATGAAACGCGTAACTGCGCTCT
+>EAS1_97:7:28:979:519
+AAAAAGTAAACTCTCAAATATTGCTAGTGGGAGTA
+>EAS1_97:7:28:979:519
+CCCATACTTTACTGCTACTCAATATATCCATGTAA
+>EAS1_97:7:63:727:203
+AAGTAATTGGGGAAAACCTCTTTAGTCTTGCTAGA
+>EAS1_97:7:63:727:203
+AGTCTCTTATGAATTAACCCAGTCAGACAAAAATA
+>EAS1_97:7:9:648:712
+AAGAAGTATGAGATTATGTAAAGTAACTGAACCTA
+>EAS1_97:7:9:648:712
+TACATTGCAAGACAGACTTCATCAAGATATGTAGT
+>EAS1_97:8:36:927:478
+AAAAGGTCTTTCAAAAGGTGATGTGTGTTCTCATC
+>EAS1_97:8:36:927:478
+GACCCTACACGAATGCGTCTCTACCACAGGGGGCT
+>EAS1_99:1:17:595:863
+AAGCTACTCAATATATCCATGTAACAAATCTGCGC
+>EAS1_99:1:17:595:863
+ATAACCATCCTACTAAATACACATGCACCTAACTC
+>EAS1_99:1:187:715:521
+AAACCTCTTTAGTCTTGCTAGAGATTTAGACATCT
+>EAS1_99:1:187:715:521
+GCATACAGTCATCTATAAAGGAAATCCCATCAGAA
+>EAS1_99:1:34:649:318
+AAGAATAACAATGGGCTTCACAGCGGAACCCTTAC
+>EAS1_99:1:34:649:318
+ATGAAAGAGGCTCAAAGAATGCCAGGAAGATACAT
+>EAS1_99:1:86:871:319
+GGCTTCTCAGCGGAAACCTTACAAGCCAGAAGAGA
+>EAS1_99:1:86:871:319
+TGCTAAGATAATTCATCATCACTAAACCAGTCCTA
+>EAS1_99:2:152:355:962
+CAGTCATCTATAAAGGAAATCCCATCAGAATAACA
+>EAS1_99:2:152:355:962
+TATTTGAGGAAGTAATTGGGGAAAACCTCTTTAGT
+>EAS1_99:2:162:257:203
+AAAAAGATCAATTCAGCAAGAAGATATAACCATCC
+>EAS1_99:2:162:257:203
+ATATCCATGTAACAAATCTGCGCTTGTACTTCTAA
+>EAS1_99:2:188:782:483
+CTAAAATCAGCAAGAGAAAAGCATACAGTCATCTA
+>EAS1_99:2:188:782:483
+GAAGTAATTGGGGAAAACCTCTTTAGTCTTGCTAG
+>EAS1_99:3:118:851:285
+CCCAATTACGTCCTATCTTCTTCTTAGGGAAGAAC
+>EAS1_99:3:118:851:285
+TGGGCAATACATGAGATTATTAGGAAATGCTTTAC
+>EAS1_99:3:135:543:760
+ATTTGCCTTCAGACCCTACACGAATGCGTCTCTAC
+>EAS1_99:3:135:543:760
+TTCAAAAGGTGATGTGTGTTCTCATCAACCTCATA
+>EAS1_99:3:187:791:153
+AATACATGAGATTATTAGGAAATGCTTTACTGTCA
+>EAS1_99:3:187:791:153
+TACACGAATGCGTCTCTACCACAGGGGGCTGCGCG
+>EAS1_99:3:21:423:169
+ACTAAAAGCCCATACTTTACTGCTACTCAATATAT
+>EAS1_99:3:21:423:169
+GGAGTATAAATTGTTTTCCACTTTGGAAAACAATT
+>EAS1_99:3:61:183:767
+GTAAAGTCTCAGGGAGCCGTCCGTGTCCTCCCATC
+>EAS1_99:3:61:183:767
+TTGCCAGATGAACCACACCTTAATACTATGTTTCT
+>EAS1_99:5:147:479:41
+CTCCTTTTTGCTGCATCCCTGTCTTCCTCTGTCTT
+>EAS1_99:5:147:479:41
+TACGTCCTATCTTCTTCTTAGGGAAGAACAGCTTA
+>EAS1_99:5:191:885:623
+TGCAAGACAGACTTCATCAAGATATGTAGTCATCA
+>EAS1_99:5:191:885:623
+TTAAAGAAAAAAAAACCTGTCAAACACGAATGTTA
+>EAS1_99:6:135:354:66
+GATACATTGCAAGACAGACTTCATCAAGATATGTA
+>EAS1_99:6:135:354:66
+TATGAGATTATGTAAAGTAACTGAACCTATGAGTC
+>EAS1_99:6:177:562:806
+ACAGTGTAGATGAGAGAGACCTTCCCTGGAGGTCT
+>EAS1_99:6:177:562:806
+TGATTTACTTGTTGTTGGTTTTCTGTTTCTTTTTT
+>EAS1_99:6:181:392:500
+GGAAATCCCATCAGAATAACAATGGGCTTCTCAGC
+>EAS1_99:6:181:392:500
+TTAGTCTTGCTAGAGATTTAGACATCTAAATGAAA
+>EAS1_99:6:63:48:631
+CAATACATGAGATTATTAGGAAATGCTTTACTGTC
+>EAS1_99:6:63:48:631
+TCCTATCTTCTTCTTAGGGAAGAACAGCTTAGGTA
+>EAS1_99:7:126:361:250
+AAAAAATTAACATTACAACAGGAACAAAACCTCAT
+>EAS1_99:7:126:361:250
+TCTACGCAAACAGAAACCAAATGAGAGAAGGAGTA
+>EAS1_99:7:171:196:287
+ATAACAATGGGCTTCTCAGCAGAAACCTTACAAGC
+>EAS1_99:7:171:196:287
+ATAATTCATCATCACTAAACCAGTCCTATAAGAAA
+>EAS1_99:7:183:645:699
+GTGGCCCTCCCCCATTCCCTGCCCCATCTCTTGTA
+>EAS1_99:7:183:645:699
+TATCCCAAATTCCCAATTACGTCCTATCTTCTTCT
+>EAS1_99:7:37:400:627
+ACATGAGATTATTAGGAAATGCTTTACTGTCATAA
+>EAS1_99:7:37:400:627
+TCTTAGGGAAGAACAGCTTAGGTATCAATTTGGTG
+>EAS1_99:8:117:578:853
+AATGAACTTCTGTAATTGAAAAATTCATTTAAGAA
+>EAS1_99:8:152:778:228
+ATCATAAATACACACAAAAGTACAAAACTCACAGG
+>EAS1_99:8:152:778:228
+ATTTAAAAACATGAACTAACTATATGCTGTTTACA
+>EAS1_99:8:187:199:369
+TGAAAGAGGCTCAAAGAATGCCAGGAAGATACATT
+>EAS1_99:8:27:228:31
+AAATAAAACAAAGGAGGTCATCATACAATGATAAA
+>EAS1_99:8:27:228:31
+GGTTACACTAAAAGCCCATACTTTACTGCTACTCA
+>EAS1_99:8:99:756:130
+GAAGAAAAGGTCTTTCAAAAGGTGATGTGTGTTCT
+>EAS1_99:8:99:756:130
+GACCCTACACGAATGCGTCTCTACCACAGGGGGCT
+>EAS218_1:2:10:686:1024
+ACAAGAAACTCATTAATAAAGACATGAGTTCAGGT
+>EAS218_1:2:10:686:1024
+CATACAATGATAAAAAGATCAATTCAGCAAGAAGA
+>EAS218_1:2:15:1763:1143
+AAACAAATACTACTAGACCTAAGAGGGATGAGAAA
+>EAS218_1:2:15:1763:1143
+TGAGAGAAGGAGTAGCTATACTTATATCAGATAAA
+>EAS218_1:2:18:1498:1475
+CTTGGGCTGTAATGATGCCCCTTGGCCATCACCCG
+>EAS218_1:2:18:1498:1475
+GAAAGGTTGTTGGGAGATTTTTAATGATTCCTCAA
+>EAS218_1:2:19:752:816
+CGTCCGTGTCCTCCCATCTGGCCTCGTCCACACTG
+>EAS218_1:2:19:752:816
+TTTGGTGGAAGACATAATCCCACGCTTCCTATGGA
+>EAS218_1:2:26:211:481
+ACAAAATATAGTTGAAAGCTCTAACAATAGACTAA
+>EAS218_1:2:26:211:481
+CACAGGTATTCCTGAGGAAAAAGAAAAAGTGAGAA
+>EAS218_1:2:40:1291:1045
+CTAACACAAGACTACCCAGATTCATAAAACAAATA
+>EAS218_1:2:40:1291:1045
+GTAAAGGGGTGGAAAAAGATGTTCTACGCAACAAG
+>EAS218_1:2:64:1318:1711
+GGAAGAGGGACGCTGAAGAACTTTGATGCCCTCTT
+>EAS218_1:2:64:1318:1711
+TGAAAACTATATTTATGCTATTCAGTTCTAAATAT
+>EAS218_1:4:14:1872:1521
+TCAAAGAATGCCAGGAAGATACATTGCAAGTCAGA
+>EAS218_1:4:14:1872:1521
+TCATCAAAAACCTTACAAGCCAGAAGAGATTGGAT
+>EAS218_1:4:15:856:340
+CACGCTGTCCTATGTACTTATCATGACTCTATCCC
+>EAS218_1:4:15:856:340
+CCCCAGCATGGTTGCACTGGGCAATACATGAGATT
+>EAS218_1:4:28:315:310
+AAACTGTTCTCTTGAAAGCTTGGGCTGTAATGATG
+>EAS218_1:4:28:315:310
+CATGTACACACGCTGTCCTATGTACTTATCATGAC
+>EAS218_1:4:37:1626:862
+ACCCAACTAATATTTGTCTGAGCAAAACAGTCTAG
+>EAS218_1:4:37:1626:862
+TCTCCTTTTTGCTGCATCCCTGTCTTCCTCTGTCT
+>EAS218_1:4:61:1369:440
+AAAGACATGATTTCAGGTAAAGGGGTGGAAAAAGA
+>EAS218_1:4:61:1369:440
+CAGGTTTTATAAAACAATTAATTGAGACTACAGAG
+>EAS218_1:4:62:561:531
+AGCTATACTTATATCAGATAAAGCACACTTTAAAT
+>EAS218_1:4:62:561:531
+TACTAGACCTAAGAGGGATGAGAAATTACCTAATT
+>EAS218_1:4:71:832:743
+ACCCAGTCCCTGCCCCATCTCTTGTAATCTCTCTC
+>EAS218_1:4:71:832:743
+CTATGTACTTATCATGACTCTATCCCAAATTCCCA
+>EAS218_1:4:73:42:1038
+AAACAGTCTAGATGAGAGAGAACTTCCCTGGAGGT
+>EAS218_1:4:73:42:1038
+TCTGTCTTGATTTACTTGTTGTTGGTTTTCTGTTT
+>EAS218_1:4:75:555:1591
+TGAACTTCTGTAATTGAAAAATTCATTTAAGAAAT
+>EAS218_1:6:49:905:27
+CCACAGGGGGCTGCGCGGTTTCCCATCCTGAAGCA
+>EAS218_1:6:49:905:27
+GAAGAGACTATTGCCAGTTGAACCACACATTAATA
+>EAS218_1:6:66:1282:1215
+GTGATGTGTGTTCTCATCAACCTCATACACACACA
+>EAS218_1:6:66:1282:1215
+TTCAGACCCTACACGAATGCGTCTCTACCACAGGG
+>EAS218_1:6:77:1529:522
+AAAACCTGTCAAACACGAATGTTATGCCCTGCTAA
+>EAS218_1:6:77:1529:522
+AAAGTTCAATACTCACCATCATAAATACACACAAA
+>EAS218_1:6:88:1413:14
+AATGAAAGAGGCTCAAAGAATGCCAGGAAGATACA
+>EAS218_1:8:13:1729:1844
+ATGAACTTCTGTAATTGAAAAATTCATTTAAGAAA
+>EAS218_1:8:16:1081:1894
+AAGGTGATGTGTGTTCTCATCAACCTCATACACAC
+>EAS218_1:8:16:1081:1894
+AGATGAAACGCGTAACTGGGCTCTCATTCACTCCA
+>EAS218_1:8:26:785:882
+CAGTTTCTGCCCCAAGCATGGTTGTACTGGGCAAT
+>EAS218_1:8:26:785:882
+TACTTATCATGACTCTATCCCAAATTCCCAATTAC
+>EAS218_1:8:61:1797:113
+CAGATAGCTTGTGGTCTGACAGGCTGCAACTGTGA
+>EAS218_1:8:61:1797:113
+GGGATGGAGGGAAGAGGGACGCTGAAGAACTTTGA
+>EAS218_1:8:70:445:1289
+CTAATTTTTGGACTTCTTAAAGAAAAAAAAACCTG
+>EAS218_1:8:70:445:1289
+GAATTGTAAAAGTCAAAATTAAAGTTCAATACTCA
+>EAS218_1:8:82:1540:77
+ATTGAGACTACAGAGCAACTAGGTAAAAAATTAAC
+>EAS218_1:8:82:1540:77
+GAAATAAAGTCAAGTCTTTCCTGACAAGCAAATGC
+>EAS218_1:8:90:706:1276
+AATTAACATTACAACAGGAACAAAACCTCATATAT
+>EAS218_1:8:90:706:1276
+GTAAAGGGGTGGAAAAAGATGTTCTACGCAAACAG
+>EAS218_4:1:34:1614:558
+CAACATGAAGGAAAAAAATTCTAAAATCAGCAAGA
+>EAS218_4:1:34:1614:558
+GTCAAACACGAATGTTATGCCCTGCTAAACTAAGC
+>EAS218_4:1:48:9:409
+CAGCTCCCTGTCACCCAATGGACCTGTGATATCTG
+>EAS218_4:1:48:9:409
+GTTTAGTGCCTTTGTTCACATAGACCCCCTTGCAA
+>EAS218_4:1:84:1505:1037
+GTCAACATGAAGGAAAAAAATTCTAAAATCAGCAA
+>EAS218_4:1:84:1505:1037
+TGCCCTGCTAAACTAAGCATCATAAATGAAGGGGA
+>EAS218_4:1:9:206:901
+AGTCTAGATGAGAGAGAACTTCCCTGGAGGTCTGA
+>EAS218_4:1:9:206:901
+CTTCCTCTGTCTTGATTTACTTGTTGTTGGTTTTC
+>EAS218_4:3:12:630:707
+ATTTAAAAACATGAACTAACTATATGCTGTTTACA
+>EAS218_4:3:12:630:707
+CACAAAAGTACAAAACTCACAGGTTTTATAAAACA
+>EAS218_4:3:39:1671:1928
+AGCCCATACTTTACTGCTACTCAATATATCCATGT
+>EAS218_4:3:39:1671:1928
+CAAATATTGCTAGTGGGAGTATAAATTGTTTTCCA
+>EAS218_4:3:41:1281:1785
+ACTATCTAAAGTCAACATGAAGGAAAAAAATTCTA
+>EAS218_4:3:41:1281:1785
+GGAAAAAGAAAAAGTGAGAAGTTTGGAAAAACTAT
+>EAS218_4:3:65:85:1547
+AAATCAGCAAGAGAAAAGCATACAGTCATCTATAA
+>EAS218_4:3:65:85:1547
+GTTTGGAAAAACTATTTGAGGAAGTAATTGGGGAA
+>EAS218_4:5:41:118:1246
+ACCAGAGGGATGGAGGGAAGAGGGACGCTGAAGAA
+>EAS218_4:5:41:118:1246
+CTCCAGATTGCTTGTGGTCTGACAGGCTGCAACTG
+>EAS218_4:5:63:875:1339
+CCCCAGATACCATCCCTGTCTTACTTCCAGCTCCC
+>EAS218_4:5:63:875:1339
+GGGAACAGGGAGGTGCACTAATGCGCTCCACGCCC
+>EAS218_4:7:71:31:1973
+AAAGAGGCTCAAAGAATGCCAGGAAGATACATTGC
+>EAS218_4:7:72:1288:1211
+ATTGGTACAATGTACAATATTCTGATGATGGTTAC
+>EAS218_4:7:72:1288:1211
+GATAAAGCACACTTTAAATCAACAACAGTAAAATA
+>EAS218_4:7:85:923:726
+ACAAAATATAGTTGAAAGCTCTAACAATAGACTAA
+>EAS218_4:7:85:923:726
+GTAAAGTAACTGAACCTATGAGTCACAGGTATTCC
+>EAS218_4:7:87:964:826
+CACAGGGGGCTGCGCGGTTTCCCATCATGAAGCAC
+>EAS218_4:7:87:964:826
+TGAAGAGACTATTGCCAGATGAACCACACATTAAT
+>EAS218_4:7:89:1487:520
+CACGAATGCGTCTCTACCACAGGGGGCTGCGCGGT
+>EAS218_4:7:89:1487:520
+TATGAAGAGACTATTGCCAGATGAACCACACATTA
+>EAS218_4:7:90:1873:89
+GAGATTCTGCAGCCCAGATCCAGATTGCTTGTGGT
+>EAS218_4:7:90:1873:89
+GCATTTTGTCAGTTACCAAATGTGTTTATTACCAG
+>EAS219_1:1:22:490:2011
+ATAACAATGGGCTTCTCAGCGGAAACCTTACAAGC
+>EAS219_1:1:22:490:2011
+GCTAGAGATTTAGACATCTAAATGAAAGAGGCTCA
+>EAS219_1:1:37:1004:1136
+CCAGGGAATTTGTCAATGTCAGGGAAGGAGCATTT
+>EAS219_1:1:37:1004:1136
+GTCACCCAATGGACCTGTGATATCTGGATTCTGGG
+>EAS219_1:1:44:1466:425
+GTCCGTGTCCTCCCATCTGGCCTCGTCCACACTGG
+>EAS219_1:1:44:1466:425
+TTATCTGCACATTACTACCCTGCAATTAATATAAT
+>EAS219_1:1:50:257:341
+AAATTAACATTACAACAGGAACAAAACCTCATATA
+>EAS219_1:1:50:257:341
+TGAGTTCAGGTAAAGGGGTGGAAAAAGATGTTCTA
+>EAS219_1:1:5:497:687
+AAGAAAAGGTCTTTCAAAAGGTGATGTGTGTTCTC
+>EAS219_1:1:5:497:687
+TTGCCTTCAGACCCTACACGAATGCGTCTCTACCA
+>EAS219_1:1:60:1420:660
+AATGCTAAGATAATTCATCATCACTAAACCAGTCC
+>EAS219_1:1:60:1420:660
+GTAAAAAATTAACATTACAACAGGAACAAAACCTC
+>EAS219_1:1:63:28:1549
+AAAAAGTAAACTCTCAAATATTGCTAGTGGGAGTA
+>EAS219_1:1:63:28:1549
+TACAATATTCTGATGATGGTTACACTAAAAGCCCA
+>EAS219_1:1:67:191:668
+ACTATGAAGAGACTATTGCCAGATGAACCACACCT
+>EAS219_1:1:67:191:668
+CCAATTACGTCCTATCTTCTTCTTAGGGAAGAACA
+>EAS219_1:3:11:706:1030
+ATCTCTTGTAATCTCTCTCATCTTTGCTGCATCCC
+>EAS219_1:3:11:706:1030
+ATGTCTATTTTTGTCTTGACACCCAACTAATATTT
+>EAS219_1:3:33:1168:1762
+AGATTGCTTGTGGTCTGACAGGCTGCAACTGTGAG
+>EAS219_1:3:33:1168:1762
+GTCTTACTTCCAGCTCCCCAGAGGGAAAGCTTTCA
+>EAS219_1:3:4:1620:413
+CATCACAATGAACAACAGGAAGAAAAGGTCTTTCA
+>EAS219_1:3:4:1620:413
+TCTAGCCATTTCTTTTGGCATTTGCCTTCAGACCC
+>EAS219_1:3:62:603:1552
+AATTTGGTGTTCTGTGTAAAGTCTCAGGGAGCCGT
+>EAS219_1:3:62:603:1552
+GAACCACACATTAATACTATGTTTCTTATCTGCAC
+>EAS219_1:3:88:465:1877
+AAAGCACACTTTAAATCAACAACAGTAAAATAAAA
+>EAS219_1:3:88:465:1877
+TAAGAGGGATGAGAAATTACCTAATTGGTACAATG
+>EAS219_1:3:90:219:528
+ACGAATGTTATGCCCTGCTAAACTAAGCATCATAA
+>EAS219_1:3:90:219:528
+GTACAAAACTCACAGGTTTTATAAAACAATTAATT
+>EAS219_1:5:5:259:250
+GTCTCTTATGAATTAACCCAGTCAGACAAAAATAA
+>EAS219_1:5:5:259:250
+TATTTGAGGAAGTAATTGGGGAAAACCTCTTTAGT
+>EAS219_1:5:6:1067:91
+CTTGACACCCAACTAATATTTGTCTGAGCAAAACA
+>EAS219_1:5:6:1067:91
+CTTTTTGCTGCATCCCTGTCTTCCTCTGTCTTGAT
+>EAS219_1:7:16:1343:1621
+AAATTCTAAAATCAGCAAGAGAAAAGCATACAGTC
+>EAS219_1:7:16:1343:1621
+AAGTGAGAAGTTTGGAAAAACTATTTGAGGAAGTA
+>EAS219_1:7:18:571:1110
+GAGGTGCACTAATGCGCTCCACGCCCAAGCCCTTC
+>EAS219_1:7:18:571:1110
+TAATATAATTGTGTCCATGTACACACGCTGTCCTA
+>EAS219_1:7:20:1444:328
+AAAAGATGTTCTACGCAAACAGAAACCAAATGAGA
+>EAS219_1:7:20:1444:328
+TACTAAATACATATGCACCTAACACAAGACTACCC
+>EAS219_1:7:35:392:2042
+ATAAATCTATAAAAAAATTAAAATTTAACAAAAGT
+>EAS219_1:7:35:392:2042
+TAACACAAGACTACCCAGATTCATAAAACNAATAC
+>EAS219_1:7:50:1339:1154
+CATCTCTTGTAATCTCTCTCCTTTTTGCTGCATCC
+>EAS219_1:7:50:1339:1154
+GTCTTGACACCCAACTAATATTTGTCTGAGCAAAA
+>EAS219_1:7:62:1076:540
+CCCCCACTTAAGAGATATAGATTGGCAGAACAGAT
+>EAS219_1:7:62:1076:540
+TAAATCAACAACAGTAAAATAAAACAAAGGAGGTC
+>EAS219_1:7:94:1655:1921
+AAAAGCATACAGTCATCTATAAAGGAAATCCCATC
+>EAS219_1:7:94:1655:1921
+TTTGGAAAAACTATTTGAGGAAGTAATTGGGGAAA
+>EAS219_FC30151:1:18:1418:237
+CCTTGAGAACCCCAGGGAATTTGTCAATGTCAGGG
+>EAS219_FC30151:1:18:1418:237
+CTGGGAAATTCTTCATCCTGGACCCTGAGAGATTC
+>EAS219_FC30151:1:53:140:421
+AACCAAATGAGAGAAGGAGTAGCTATACTTATATC
+>EAS219_FC30151:1:53:140:421
+GATTCATAAAACAAATACTACTAGACCTAAGAGGG
+>EAS219_FC30151:1:54:436:1452
+AAGACAAGTCTCTTATGAATTAACCCAGTCAGACA
+>EAS219_FC30151:1:54:436:1452
+AGGAAGTAATTGGGGAAAACCTCTTTAGTCTTGCT
+>EAS219_FC30151:1:55:8:1412
+ATATAATTGTGTCCATGTACACACGCTGTCCTATG
+>EAS219_FC30151:1:55:8:1412
+GCCCAAGCCCTTCTCACAGTTTCTGCCCCCAGCAT
+>EAS219_FC30151:1:76:34:691
+ATATATCAATATTAACTTTGAATAAAAAGGGATTA
+>EAS219_FC30151:1:88:1454:418
+CCAGGAAGATACATTGCAAGACAGACTTCATCAAG
+>EAS219_FC30151:1:88:1454:418
+GAAGAGATTGGATCTAATTTTTGGACTTCTTAAAG
+>EAS219_FC30151:3:13:674:1717
+AGAAAAGCATGCAGTCATCTATAAAGGAAATCCCA
+>EAS219_FC30151:3:13:674:1717
+TAAAGTCAAGTCTTTCCTGACAAGCAAATGCTAAG
+>EAS219_FC30151:3:40:1128:1940
+CCCCTTACAACAACCTTGAGAACCCCAGGGAATTT
+>EAS219_FC30151:3:40:1128:1940
+CCGAGTCACGGGGTTGCCAGCACAGGGGCTTAACC
+>EAS219_FC30151:3:55:74:1040
+CTACCACAGGGGGCTGCGCGGTTTCCCATCATGAA
+>EAS219_FC30151:3:55:74:1040
+GGAAATGCTTTACTGTCATAACTATGAAGAGACTA
+>EAS219_FC30151:3:73:1458:1337
+AAATGAAGGGGAAATAAAGTCAAGTCTTTCCTGAC
+>EAS219_FC30151:3:73:1458:1337
+AGGTAAAAAATTAACATTACAACAGGAACAAAACC
+>EAS219_FC30151:3:81:1723:1820
+ATGAGAGAGAACTTCCCTGGAGGTCTGATGGCGTT
+>EAS219_FC30151:3:81:1723:1820
+CATCCCTGTCTTCCTCTGTCTTGATTTACTTGTTG
+>EAS219_FC30151:3:90:1906:1528
+CACAGGTATTCCTGAGGAAAAAGAAAAAGTGAGAA
+>EAS219_FC30151:3:90:1906:1528
+TTACAAAATATAGTTGAAAGCTCTAACAATAGACT
+>EAS219_FC30151:3:9:1595:1826
+ACTAATATTTGTCTGAGCAAAACAGTCTAGATGAG
+>EAS219_FC30151:3:9:1595:1826
+ATCTCTCTCCTTTTTGCTGCATCCCTGTCTTCCTC
+>EAS219_FC30151:5:29:817:854
+AGGGGCTTAACCTCTGGTGACTGCCAGAGCTGCTG
+>EAS219_FC30151:5:29:817:854
+GTTCTCAAGGTTGTTGCAAGGGGGTTTATGTGAAC
+>EAS219_FC30151:5:54:1351:910
+ACTAAAAGCCCATACTTTACTGCTACTCAATATAT
+>EAS219_FC30151:5:54:1351:910
+ACTCTCAAATATTGCTAGTGGGAGTATAAATTGTT
+>EAS219_FC30151:5:63:424:1643
+GACCCTACACGAATGCGTCTCTACCACAGGGGGCT
+>EAS219_FC30151:5:63:424:1643
+GGTCTTTCAAAAGGTGATGTGTGTTCTCATCAACC
+>EAS219_FC30151:5:6:1243:981
+ATGAAGGGGAAATAAAGTCAAGTCTTTCCTGACAA
+>EAS219_FC30151:5:6:1243:981
+TTACCTAGTTGCTCTGTAGTCTCAATTAATTGTTT
+>EAS219_FC30151:5:70:348:972
+GAGAGAACTTCCCTGGAGGTCTGATGGCGTTTCTC
+>EAS219_FC30151:5:70:348:972
+TCTTCCTCTGTCTTGATTTACTTGTTGTTGGTTTT
+>EAS219_FC30151:5:72:1426:1883
+ACATAATCCCACGCTTCCTATGGAAAGGTTGTTGG
+>EAS219_FC30151:5:72:1426:1883
+CATCTGGCCTCGTCCACACTGGTTCTCTTGAAAGC
+>EAS219_FC30151:7:11:1261:1200
+AAAAAAAACCTGTCAAACACGAATGTTATGCCCTG
+>EAS219_FC30151:7:11:1261:1200
+TTGCAAGACAGACTTCATCAAGTTATGTAGTCATC
+>EAS219_FC30151:7:51:1429:1043
+TATTTGTAATGAAAACTATATTTATGCTATTCAGT
+>EAS219_FC30151:7:87:1289:83
+ACATGAAGGAAAAAAATTCTAAAATCAGCAAGAGA
+>EAS219_FC30151:7:87:1289:83
+ATGCCCTGCTAAACTAAGCATCATAAATGAAGGGG
+>EAS219_FC30151:7:94:1440:2016
+AACCTGTCAAACACGAATGTTATGCCCTGCTAAAC
+>EAS219_FC30151:7:94:1440:2016
+CACAAAAGTACAAAACTCACAGGTTTTATAAAACA
+>EAS220_1:2:11:1274:1230
+TGAGCAAAACAGTCTAGATGAGAGAGAACTTCCCT
+>EAS220_1:2:11:1274:1230
+TTTTGCTGCATCCCTGTCTTCCTCTGTCTTGATTT
+>EAS220_1:2:43:656:1866
+TGAACTTCTGTAATTGAAAAATTCATTTAAGAAAT
+>EAS220_1:2:47:591:698
+CAAATCTGCGCTTGTACTTCTAAATCTATAACAAA
+>EAS220_1:2:47:591:698
+TCCTACTAAATACATATGCACCTAACACAAGACTA
+>EAS220_1:2:50:513:882
+AAAACAAATACTACTAGACCTAAGAGGGATGAGAA
+>EAS220_1:2:50:513:882
+GGAGTAGCTATACTTATATCAGATAAAGCACACTT
+>EAS220_1:2:52:1779:1664
+CCCTGCCCCATCTCTTGTAATCTCTCTCCTTTTTG
+>EAS220_1:2:52:1779:1664
+TGTTAAAATGTCTATTTTTGTCTTGACACCCAACT
+>EAS220_1:2:54:91:1232
+AAAAGTGAGAAGTTTGGAAAAACTATTTGAGGAAG
+>EAS220_1:2:54:91:1232
+AAAGCTCTAACAATAGACTAAACCAAGCAGAAGAA
+>EAS220_1:2:62:1109:804
+TAGAGTCCCATTTGGAGCCCCTCTAAGCCGTTCTA
+>EAS220_1:2:62:1109:804
+TGTCAGTTACCAAATGTGTTTATTACCAGAGGGAT
+>EAS220_1:2:63:267:545
+ATGAGAGAGAACTTCCCTGGAGGTCTGATGGCGTT
+>EAS220_1:2:63:267:545
+CTTGATTTACTTGTTGTTGGTTTTCTGTTTCTTTG
+>EAS220_1:2:72:1809:1398
+AATACATGAGATTATTAGGAAATGCTTTACTGTCA
+>EAS220_1:2:72:1809:1398
+CTATCTTCTTCTTAGGGAAGAACAGCTTAGGTATC
+>EAS220_1:4:100:20:1199
+AAGGGGAAATAAAGTCAAGTCTTTCCTGACAAGCA
+>EAS220_1:4:100:20:1199
+CAGTCATCTATAAAGGAAATCCCATCAGAATAACA
+>EAS220_1:4:14:1665:1772
+GGGCTGTAATGATGCCCCTTGGCCATCACCCGGTC
+>EAS220_1:4:14:1665:1772
+TATAATGGTGTCCATGTACACACGCTGTCCTATGT
+>EAS220_1:4:46:1566:668
+CTACTAAATACATATGCACCTAACACAAGACTACC
+>EAS220_1:4:46:1566:668
+TTAATAAAGACATGAGTTCAGGTAAAGGGGTGGAA
+>EAS220_1:4:69:88:1154
+ATAACTATGAAGAGACTATTGCCAGATGAACCACA
+>EAS220_1:4:69:88:1154
+CACGAATGCGTCTCTACCACAGGCGGCTGCGCGGT
+>EAS220_1:4:6:1178:1105
+GATAATTCATCATCACTAAACCAGTCCTATAAGAA
+>EAS220_1:4:6:1178:1105
+GGAACAAAACCTCATATATCAATATTAACTTTGAA
+>EAS220_1:4:70:766:2016
+AAAAAAATTCTAAAATCAGCAAGAGAAAAGCATAC
+>EAS220_1:4:70:766:2016
+ATAAATGAAGGGGAAATAAAGTCAAGTCTTTCCTG
+>EAS220_1:6:24:105:1046
+AGATTCATAAAACAAATACTACTAGACCTAAGAGG
+>EAS220_1:6:24:105:1046
+CATAGCTAAAACTAAAAAAGCAAAAACAAAAACTA
+>EAS220_1:6:7:1547:1933
+AATATTTGACTGAGCAAAACAGTCTAGATGAGAGA
+>EAS220_1:6:7:1547:1933
+CTCTTGTAATCTCTCTCCTTTTTGCTGCATCCCTG
+>EAS220_1:8:18:1757:95
+ATGAGTCGCAGGTATTCCTGAGGAAAAAGAAAAAG
+>EAS220_1:8:18:1757:95
+CTTCATCAAGATATGTAGTCATCAGACTATCTAAA
+>EAS220_1:8:33:672:473
+ATGTCAGGGAAGGAGCATTTTGTCAGTTACCAAAT
+>EAS220_1:8:33:672:473
+TCATCCTGGACCCTGAGAGATTCTGCAGCCCAGCT
+>EAS220_1:8:38:1576:1923
+CACAGGGGGCTGCGCGGTTTCCCATCATGAAGCAC
+>EAS220_1:8:38:1576:1923
+CTGTCATAACTATGAAGAGACTATTGCCAGATGAA
+>EAS220_1:8:45:178:1321
+AGGTTTTATAAAACAATTAATTGAGACTACAGAGC
+>EAS220_1:8:45:178:1321
+CATAAATGAAGGGGAAATAAAGTCAAGTCTTTCCT
+>EAS220_1:8:46:1528:799
+ATGATAAAAAGATCAATTCAGCAAGAAGATATAAC
+>EAS220_1:8:46:1528:799
+CATGTAACAAATCTGCGCTTGTACTTCTAAATCTA
+>EAS220_1:8:46:485:482
+AGAGATTCTGCAGCCCAGATCCAGATTGCTTGTGG
+>EAS220_1:8:46:485:482
+ATTACCAGAGGGATGAAGGGAAGAGGGACGCTGAA
+>EAS220_1:8:5:996:2000
+AGTCAACATGAAGGAAAAAAATTCTAAAATCAGCA
+>EAS220_1:8:5:996:2000
+CACGAATGTTATGCCCTGCTAAACTAAGCATCATA
+>EAS220_1:8:66:1046:167
+ACAATGTACAATATTCTGATGATGGTTACACTAAA
+>EAS220_1:8:66:1046:167
+ACACTTTAAATCAACAACAGTAAAATAAAACAAAG
+>EAS220_1:8:83:1456:1854
+AAGATCAATTCAGCAAGAAGATATAACCATCCTAC
+>EAS220_1:8:83:1456:1854
+AAGCCCATACTTTACTGCTACTCAATATATCCATG
+>EAS221_1:2:23:127:880
+CGGAAACCTTACAAGCCAGAAGAGATTGGATCTAA
+>EAS221_1:2:23:127:880
+TAAGAAATGCTCAAAAGAATTGTAAAAGTCAAAAT
+>EAS221_1:2:24:1037:84
+TGCCCTCTTCTTCCAAAGATGAAACGCGTAACTGC
+>EAS221_1:2:24:1037:84
+TTCAGTTCTAAATATAGAAATTGAAACAGCTGTGT
+>EAS221_1:2:29:1486:672
+AATTGAAACAGCTGTGTTTAGTGCCTTTGTTCACA
+>EAS221_1:2:3:542:428
+AAGACATGAGTTCAGGTACAGGGGTGGAAAAAGAT
+>EAS221_1:2:3:542:428
+AGAGCAACTAGGTAAAAAATTAACATTACAACAGG
+>EAS221_1:2:3:945:2005
+AACCAAGCAGAAGAAAGAGGCTCAGAACTTGAAGA
+>EAS221_1:2:3:945:2005
+GAAAAACTATTTGAGGAAGTAATTGGGGAAAACCT
+>EAS221_1:2:52:1144:509
+AAAAGGGATTAAATTCCCCCACTTAAGAGATATAG
+>EAS221_1:2:52:1144:509
+TGTAAAAGTCAAAATTAAAGTTCAATACTCACCAT
+>EAS221_1:2:73:955:728
+AATTCATCATCACTAAACCAGTCCTATAAGAAATG
+>EAS221_1:2:73:955:728
+TACAACAGGAACAAAACCTCATATATCAATATTAA
+>EAS221_1:2:8:327:522
+AACAGGAACAAAACCTCATATATCAATATTAACTT
+>EAS221_1:2:8:327:522
+TTCTACGCAAACAGAAACCAAATGAGAGAAGGAGT
+>EAS221_1:2:90:986:1224
+CTGTGTTTAGTGCCTTTGTTCAACCCCCTTGCAAC
+>EAS221_1:2:91:856:504
+CTAGATGAGAGAGAACTTCCCTGGAGGTCTGATGG
+>EAS221_1:2:91:856:504
+GTTGTTGGTTTTCTGTTTCTTTGTTTGATTTGGTT
+>EAS221_1:4:36:1402:1709
+AGCTTAGGTATCAATTTGGTGTTCTGTGTAAAGTC
+>EAS221_1:4:36:1402:1709
+TTTTTGCTGCATCCCTGTCTTCCTCTGTCTTGATT
+>EAS221_1:4:3:248:1491
+TTAAAATTTAACAAAAGTAAATAAAACACATAGCT
+>EAS221_1:4:41:519:609
+AACAAAAACTATGCTAAGTATTGGTAAAGATGTGG
+>EAS221_1:4:41:519:609
+TACCTAATTGGTACAATGGACAATATTCTGATGAT
+>EAS221_1:4:4:1732:88
+GCTGTAATGATGCCCCTTGGCCATCACCCGGTCCC
+>EAS221_1:4:4:1732:88
+TGTACACACGCTGTCCTATGTACTTATCATGACTC
+>EAS221_1:4:68:64:783
+AAGACATAATCCCACGCTTCCTATGGAAAGGTTGT
+>EAS221_1:4:68:64:783
+TCCGTGTCCTCCCATCTGGCCTCGTCCACACTGGT
+>EAS221_1:4:87:1375:1303
+AGGAGCATTTTGTCAGTTACCAAATGTGTTTATTA
+>EAS221_1:4:87:1375:1303
+GAGAGATTCTGCAGCCCAGATCCAGATTGCTTGTG
+>EAS221_1:6:38:1071:155
+ATGCCCCTTGGCCATCACCCAGTCCCTGCCCCATC
+>EAS221_1:6:38:1071:155
+TAAAATGTCTATTTTTGTCTTGACACCCAACTAAT
+>EAS221_1:6:4:1131:104
+ACTTTGGAAAACAATTTGGTAATTTCGTTTTTTTT
+>EAS221_1:6:4:1131:104
+ATGTAACAAATCTGCGCTTGTACTTCTAAATCTAT
+>EAS221_1:6:57:1342:1166
+AAAGACATGAGTTCAGGTAAAGGGGTGGAAAAAGA
+>EAS221_1:6:57:1342:1166
+CAGAGCAACTAGGTAAAAAATTAACATTACAACAG
+>EAS221_1:6:60:1037:1146
+AAAAGCATACAGTCATCTATAAAGGAAATCCCATC
+>EAS221_1:6:60:1037:1146
+GTGAGAAGTTTGGAAAAACTATTTGAGGAAGTAAT
+>EAS221_1:6:69:735:1915
+AATTTGTCAATGTCAGGGAAGGAGCATTTTGTCAG
+>EAS221_1:6:69:735:1915
+ACTGCCAGAGCTGCTGGCAAGCTAGAGTCCCATTT
+>EAS221_1:6:89:1164:573
+AAAAAACCTGTCAAACACGAATGTTATGCCCTGCT
+>EAS221_1:6:89:1164:573
+AGACTTCATCAAGAGATGTAGTCATCAGACTATCT
+>EAS221_1:6:92:1807:1185
+AGCATGGTTGTACTGGGCAATACATGAGATTATTA
+>EAS221_1:6:92:1807:1185
+CTCTATCCCAAATTCCCAATTACGTCCTATCTTCT
+>EAS221_1:6:96:491:1891
+AGAAGTTTGGAAAAACTATTTGAGGAAGTAATTGG
+>EAS221_1:6:96:491:1891
+GTCAACATGAAGGAAAAAAATTCTAAAATCAGCAA
+>EAS221_1:8:15:881:1932
+CACTTAAGAGATATAGATTGGCAGAACAGATTTAA
+>EAS221_1:8:15:881:1932
+CACTTTAAATCAACAACAGTAAAATAAAACAAAGG
+>EAS221_1:8:4:679:110
+AATGTTCCCCAGATACCATCCCTGTCTTACTTCCA
+>EAS221_1:8:4:679:110
+TCCAGATTGCTTGTGGTCTGACAGGCTGCAACTGT
+>EAS221_1:8:58:369:244
+CTGTAATGATGCCCCTTGGCCATCACCCAGTCCCT
+>EAS221_1:8:58:369:244
+TTGGGAGATTTTTAATGATTCCTCAATGTTAAAAT
+>EAS221_1:8:60:1020:1259
+CTATGAAGAGACTATTGCCAGATGAACCACACATT
+>EAS221_1:8:60:1020:1259
+TAGGGAAGAACAGCTTAGGTATCAATTTGGTGTTC
+>EAS221_1:8:65:1928:1125
+CATCACAATGAACAACAGGAAGAAAAGGTCTTTCA
+>EAS221_1:8:65:1928:1125
+GGCATTTGCCTTCAGACCCTACACGAATACGTCTC
+>EAS221_1:8:67:1797:1931
+GGGAAAGCTTTCAACGCTTCTAGCCATTTCTTTTG
+>EAS221_1:8:67:1797:1931
+TGGTCTGACAGGCTGCAACTGTGAGCCATCACAAT
+>EAS221_1:8:70:1349:1788
+ATTATATCAGATAAAGCACACTTTAAATCAACAAC
+>EAS221_1:8:70:1349:1788
+TACTAGACCTAAGAGGGATGAGAAATTACCTAATT
+>EAS221_1:8:73:108:1621
+GAACTTCCCTGGAGGTCTGATGGCGTTTCTCCCTC
+>EAS221_1:8:73:108:1621
+GTTTTCTGTTTCTTTGTTTGATTTGGTGGAAGACA
+>EAS221_1:8:77:781:676
+TCATGAAGCACTGAACTTCCACGTATCATCTAGGG
+>EAS221_1:8:77:781:676
+TTGCCAGATGAACCACACATTAATACTATGTTTCT
+>EAS221_1:8:78:1478:1446
+GGAAGAGGGACGCTGAAGAACTTTGATGCCCTCTT
+>EAS221_1:8:78:1478:1446
+TGTGGTCTGACAGGCTGCAACTGTGAGCCATCACA
+>EAS221_1:8:84:1013:1074
+GCAAGGGGGTCTATGTGAACAAAGGCACTAAACAC
+>EAS221_1:8:84:1013:1074
+TTGATGCCCTCTTCTTCCAAAGATGAAACGCGTAA
+>EAS221_1:8:8:1351:1986
+CCCAAGCCCTTCTCACAGTTTCTGCCCCCAGCATG
+>EAS221_1:8:8:1351:1986
+TCTTACTTCCAGATCCCCAGAGGGAAAGCTTTCAA
+>EAS221_3:2:100:1147:124
+AAAAAAGAATTTTAAAAATGAACAGAGCTTTCAAG
+>EAS221_3:2:100:1147:124
+AATGCCAGGAAGATACATTGCAAGACAGACTTCAT
+>EAS221_3:2:22:1623:709
+GAAGACAAGTCTCTTATGAATTAACCCAGTCAGAC
+>EAS221_3:2:22:1623:709
+GGGAAAACCTCTTTAGTCTTGCTAGAGATTTAGAC
+>EAS221_3:2:2:491:1886
+CTCTTTAGTCTTGCTAGAGATTTAGACATCTAAAT
+>EAS221_3:2:59:1576:946
+AACTGTGAGCCATCACAATGAACAACAGGAAGAAA
+>EAS221_3:2:59:1576:946
+CAACGCTTCTAGCCATTTCTTTTGGCATTTGCCTT
+>EAS221_3:2:60:590:1760
+AAAGTAACTGAACCTATGAGTCACAGGTATTCCTG
+>EAS221_3:2:60:590:1760
+TCATCAAGATATGTAGTCATCAGACTATCTAAAGT
+>EAS221_3:2:67:1467:1447
+AAAGTTCAATACTCACCATCATAAATACACACAAA
+>EAS221_3:2:67:1467:1447
+ATAGATTGGCAGAACAGATTTAAAAACATGAACTA
+>EAS221_3:2:67:1864:477
+AATGATGCCCCTTGGCCATCACCCAGTCCCTGCCC
+>EAS221_3:2:67:1864:477
+TAAAATGTCTATTTTTGTCTTGACACCCAACTAAT
+>EAS221_3:2:76:1729:813
+TAATTTCGTTTTTTTTTTTTTCTTTTCTCTTTTTT
+>EAS221_3:2:76:1729:813
+TCTGCGCTTGTACTTCTAAATCTATAAAAAAATTA
+>EAS221_3:4:12:276:1797
+ACTATTGCCAGATGAACCACACATTAATACTATGT
+>EAS221_3:4:12:276:1797
+TCTGTGTAAAGTCTCAGGGAGCCGTCCGTGTCCTC
+>EAS221_3:4:21:132:1423
+GCCAGATGAACCACACATTAATACTATGTTTCTTA
+>EAS221_3:4:21:132:1423
+TCAATTTGGTGTTCTGTGTAAAGTCTCAGGGAGCC
+>EAS221_3:4:29:1061:574
+ATGTGTTTATTACCAGAGGGATGGAGGGAAGAGGG
+>EAS221_3:4:29:1061:574
+GGTCTGACAGGCTGCAACTGTGAGCCATCACAATG
+>EAS221_3:4:30:1452:1563
+ATGAATTAACCAAGTCAGACAAAAATAAAGAAAAA
+>EAS221_3:4:30:1452:1563
+GATTTAGACATCTAAATGAAAGAGGCTCAAAGAAT
+>EAS221_3:4:41:1308:619
+CATTGCAAGACAGACTTCATCAAGATATGTAGTCA
+>EAS221_3:4:41:1308:619
+GAAGTATGAGATTATGTAAAGTAACTGAACCTATG
+>EAS221_3:4:57:1675:720
+TATAAGAAATGCTCAAAAGAATTGTAAAAGTCAAA
+>EAS221_3:4:57:1675:720
+TCATATATCAATATTAACTTTGAATAAAAAGGGAT
+>EAS221_3:4:66:584:407
+GCATTTGCCTTCAGACCCTACACGAATGCGTCTCT
+>EAS221_3:4:66:584:407
+GGGCAATACATGAGATTATTAGGAAATGCTTTACT
+>EAS221_3:4:78:1314:1275
+AGGAAATCCCATCAGAATAACAATGGGCTTCTCAG
+>EAS221_3:4:78:1314:1275
+GAAGTAATTGGGGAAAACCTCTTTAGTCTTGCTAG
+>EAS221_3:4:81:687:1379
+CCTAAGAGGGATGAGAAATTACCTAATTGGTACAA
+>EAS221_3:4:81:687:1379
+TAAATAAAACACATAGCTAAAACTAAAAAAGCAAA
+>EAS221_3:4:90:247:212
+ACTTCCAGCTCCCCAGAGGGAAAGCTTTCAACGCT
+>EAS221_3:4:90:247:212
+TGACAGGCTGCAACTGTGAGCCATCACAATGAACA
+>EAS221_3:6:20:492:850
+AGTATGAAAACAATGTTCCCCAGATGCCGTCCCGG
+>EAS221_3:6:20:492:850
+CCTGAGAGATTCTGCAGCCCAGCTCCAGATTGCTT
+>EAS221_3:6:26:227:1053
+ATTCTTCATCCTGGACCCTGAGAGATTCTGCAGCC
+>EAS221_3:6:26:227:1053
+GGTTTAGGGGTATAATACCTCTACATGGCTGATTA
+>EAS221_3:6:51:1486:1131
+ATAAGAAATGCTCAAAAGAATTGTAAAAGTCAAAA
+>EAS221_3:6:51:1486:1131
+TCAGCAGAAACCTTACAAGCCAGAAGAGATTGGAT
+>EAS221_3:6:70:843:706
+AATGATTCCTCAATGTTAAAATGTCTATTTTTGTC
+>EAS221_3:6:70:843:706
+ATCTCTTGTAATCTCTCTCCTTTTTGCTGCATCCC
+>EAS221_3:8:33:1240:846
+ACCTTACAAGCCAGAAGAGATTGGATCTAATTTTT
+>EAS221_3:8:33:1240:846
+ATAAGAAATGCTCAAAAGAATTGTAAAAGTCAAAA
+>EAS221_3:8:34:956:1309
+AACTATGAAGAGACTATTGCCAGATGAACCACACA
+>EAS221_3:8:34:956:1309
+AGCTTAGGTATCAATTTGGTGTTCTGTGTAAAGTC
+>EAS221_3:8:50:1203:1094
+AAATATAGTTGAAAGCTCTAACAATAGACTAAACC
+>EAS221_3:8:50:1203:1094
+ACAGGTATTCCTGAGGAAAAAGAAAAAGTGAGAAG
+>EAS221_3:8:55:932:613
+TAGTCATCAGACTATCTAAAGTCAACATGAAGGAA
+>EAS221_3:8:55:932:613
+TGTCAAACACGAATGTTATGCCCTGCTAAACTAAG
+>EAS221_3:8:63:1265:820
+CTCTCCTTTTTGCTGCATCCCTGTCTTCCTCTGTC
+>EAS221_3:8:63:1265:820
+TGTCTTGACACCCAACTAATATTTGTCTGAGCAAA
+>EAS221_3:8:65:463:703
+GAAACCTTACAAGCCAGAAGAGATTGGATCTAATT
+>EAS221_3:8:65:463:703
+TGCTCAAAAGAATTGTAAAAGTCAAAATTAAAGTT
+>EAS221_3:8:74:770:1712
+ACATTACTACCCTGCAATTAATATAATTGTGTCCA
+>EAS221_3:8:74:770:1712
+GAGCCGTCCGTGTCCTCCCATCTGGCCTCGTCCAC
+>EAS221_3:8:7:1864:1569
+AAAAACCTGTCAAACACGAATGTTATGCCCTGCTA
+>EAS221_3:8:7:1864:1569
+AGATATGTAGTCATCAGACTATCTAAAGTCAACAT
+>EAS51_62:1:38:250:647
+AATAATAAAATGATAAAAAGATCAATTCAGCAAGA
+>EAS51_62:1:38:250:647
+ACTATATGCTGTTTACAAGAAACTCATTAATAAAT
+>EAS51_62:2:133:8:379
+ATAAGATAATTCATCATCACTAAACCAGTCCTATA
+>EAS51_62:2:133:8:379
+GGAAATCCCATCAGAATAACAATGGGCTTCTCAGC
+>EAS51_62:2:258:266:101
+ACGCTGTCCTATGTACTTATCATGACTCTATCCCA
+>EAS51_62:2:258:266:101
+CCATCACCCAGTCCCTGCCCCATCTCTTGTAATCT
+>EAS51_62:2:260:147:818
+AAAATTTGGTAATTTAGTTTTTTTTTTTTTCTTTT
+>EAS51_62:2:260:147:818
+ATCCATGTAACAAATCTGCGCTTTTACTTCTAAAT
+>EAS51_62:3:103:443:166
+ACCTGTCAAACACGAATGTTATGCCCTGCTAAACT
+>EAS51_62:3:103:443:166
+TACACACAAAAGTACAAAACTCACAGGTTTTATAA
+>EAS51_62:3:169:292:652
+ATCTCTTGTAATCTCTCTCCTTTTTGCTGCATCCC
+>EAS51_62:3:169:292:652
+GCAAAACAGTCTAGATGAGAGAGAACTTCCCTGGA
+>EAS51_62:3:200:263:280
+AGTAAAATAAAACAAAGGAGGTCATCATACAATGA
+>EAS51_62:3:200:263:280
+TTGGTACAATGTACAATATTCTGATGATGGTTACA
+>EAS51_62:3:263:74:407
+AAGCTTTCAACGCTTCTAGCCATTTCTTTTGGCAT
+>EAS51_62:3:263:74:407
+CTGCAACTGTGAGCCATCACAATGAACAACAGGAA
+>EAS51_62:3:314:386:190
+AGACCCCCTTGCAACAACCTTGAGAACCCCAGGGA
+>EAS51_62:3:314:386:190
+CACTCCAGCTCCCTGTCACCCAATGGACCTGTGAT
+>EAS51_62:3:50:312:219
+ACTGCTACTCAATATATCCATGTAACAAATCTGCG
+>EAS51_62:3:50:312:219
+TCCTACTAAATACATATGCACCTAACACAAGACTA
+>EAS51_62:3:55:340:837
+TCCACACTGGTTCTCTTGAAAGCTTGGGCTGTAAT
+>EAS51_62:3:55:340:837
+TTAATATAATTGTGTCCATGTACACACGCTGTCCT
+>EAS51_62:3:68:996:104
+AGAGGGATGAGAAATTACCTAATTGGTACAATGTA
+>EAS51_62:3:68:996:104
+TACTTATATCAGATAAAGCACACTTTAAATCAACA
+>EAS51_62:4:156:857:494
+CTCATACACACACATGGTTTAGGGGTATAATACCT
+>EAS51_62:4:156:857:494
+GTTTCCCATCATGAAGCACTGAACTTCCACGTCTC
+>EAS51_62:4:187:907:145
+TTTCTTCTCTCTCTTTTTTTTTTTTTTTATTGCAT
+>EAS51_62:4:282:962:46
+GAAAAAAGTAAACTCTCAAATATTGCTAGTGGGAG
+>EAS51_62:4:282:962:46
+TACTTTACTGCTACTCAATATATCCATGTAACAAA
+>EAS51_62:4:308:614:911
+AAAAACAATTTGGTAATTTAGTTTTTTTTTTTTTC
+>EAS51_62:4:308:614:911
+TGCGCTTGTACTTCTAAATCTATAACAAAATTAAA
+>EAS51_62:5:119:38:945
+ATTCTAAAATCAGCAAGAGAAAAGCATACAGTCAT
+>EAS51_62:5:119:38:945
+TCACAGGTATTCCTGAGGAAAAAGAAAAAGTGAGA
+>EAS51_62:5:131:779:345
+GTCCACACTGGTTCTCTTGAAAGCTTGGGCTGTAA
+>EAS51_62:5:131:779:345
+TGGAAGACATAATCCCACGCTTCCTATGGAAAGGT
+>EAS51_62:5:154:669:853
+GTGTAAAGTCTCAGGGAGCCGTCCGTGTCCTCCCA
+>EAS51_62:5:154:669:853
+TGGTTTTCTGTTTCTTTGTTTGATTTGGTGGAAGA
+>EAS51_62:5:192:716:235
+ATACACACACATGGTTTAGGGGTATAATACCTCTA
+>EAS51_62:5:192:716:235
+GACCCTACACGAATGCGTCTCTACCACAGGGGGCT
+>EAS51_62:5:236:498:526
+ACTAATGCGCTCCACGCCCAAGCCCTTCTCACAGT
+>EAS51_62:5:236:498:526
+CAGCACATTACTACCCTGCAATTAATATAATTGTG
+>EAS51_62:5:290:319:736
+CGAGTCACGGGGTTGCCAGCACAGGGGCTTAACCT
+>EAS51_62:5:290:319:736
+GTTCTCAAGGTTGTTGCAAGGGGGTCTATGTGAAC
+>EAS51_62:5:295:882:282
+AATGCTCAAAAGAATTGTAAAAGTCAAAATTAAAG
+>EAS51_62:5:295:882:282
+CAGAAGAGATTGGATCTAATTTTTGGACTTCTTAA
+>EAS51_62:5:86:697:941
+AAAAAAATCCCGGAAGATACATTGCAAGACAGACT
+>EAS51_62:5:86:697:941
+GTATGAGATTATGTAAAGTAACTGAACCTATGAGT
+>EAS51_62:6:12:484:836
+AAACACATAGCTAAAACTAAAAAAGCAAAAACAAA
+>EAS51_62:6:12:484:836
+AAATACTACTAGACCTAAGAGGGATGAGAAATTAC
+>EAS51_62:6:148:170:895
+AAAGTGAGAAGTTTGGAAAAACTATTTGAGGAAGT
+>EAS51_62:6:148:170:895
+AAGAGGTTCAGAACTTGAAGACAAGTCTCTTATGA
+>EAS51_62:6:50:542:881
+CCTTTTTGCTGCATCCCTGTCTTCCTCTGTCTTGA
+>EAS51_62:6:50:542:881
+TCCCAATTACGTCCTATCTTCTTCTTAGGTAAGAA
+>EAS51_62:7:144:28:475
+AGGAAATGCTTTACTGTCATAACTATGAAGAGACT
+>EAS51_62:7:144:28:475
+CAGCTTAGGTATCAATTTGGTGTTCTGTGTAAAGT
+>EAS51_62:7:157:784:936
+GCTTAGGTATCAATTTGGTGTTCTGTGTAAAGTCT
+>EAS51_62:7:157:784:936
+TGATTTACTTGTTGTTGGTTTTCTGTTTCTTTGTT
+>EAS51_62:7:162:195:761
+AACATGAACTAACTATATGCTGTTTACAAGAAACT
+>EAS51_62:7:162:195:761
+TCACAGGTTTTATAAAACAATTAATTGAGACTACA
+>EAS51_62:7:178:286:414
+CACGCCCAAGCCCTTCTCACAGTTTCTGCCCCCAG
+>EAS51_62:7:178:286:414
+TTACTTCCAGCTCCCCAGAGGGAAAGCTTTCAACG
+>EAS51_62:7:196:511:896
+ATTGGGGAAAACCTCTTTAGTCTTGCTAGAGATTT
+>EAS51_62:7:196:511:896
+GAAAAGCATACAGTCATCTATAAAGGAAATCCCAT
+>EAS51_62:7:248:17:435
+ATAACCATCCTACTAAATACATATGCACCTAACAC
+>EAS51_62:7:248:17:435
+CATGAGTTCAGGAAAAGGGGTGGAAAAAGATGTTC
+>EAS51_62:7:312:236:655
+GAGAAATTACCTAATTGGTACAATGTACAATATTC
+>EAS51_62:7:312:236:655
+TGCTAAGTATTGGTAAAGATGTGGGGAAAAAAGTA
+>EAS51_62:7:96:836:737
+ATCAACCTCATACACACACATGGTTTAGGGGTATA
+>EAS51_62:7:96:836:737
+TCCCATCATGAAGCACTGAACTTCCACGTCTCATC
+>EAS51_62:8:52:967:804
+AACTAAGCATCATAAATGAAGGGGAAATAAAGTCA
+>EAS51_62:8:52:967:804
+TTACCTAGTTGCTCTGTAGTCTCAATTAATTGTTT
+>EAS51_64:2:326:153:231
+ATTGTTTTCAACTTTGGAAAACAATTTGGTAATTT
+>EAS51_64:2:326:153:231
+TGCTACTCAATATATCCATGTAACAAATCTGCGCT
+>EAS51_64:3:143:310:958
+CTGCACATTACTACCCTGCAATTAATATAATTGTG
+>EAS51_64:3:143:310:958
+GTCTCATCTAGGGGAACAGGGAGGTGCACTAATGC
+>EAS51_64:3:190:727:308
+ACAGCTGTGTTTAGTGCCTTTGTTCAACCCCCTTG
+>EAS51_64:3:190:727:308
+GGTGCAGAGCCGAGTCACGGGGTTGCCAGCACAGG
+>EAS51_64:3:255:45:399
+AAAAACTATGCTAAGTATTGGTAAAGATGTGGGGA
+>EAS51_64:3:255:45:399
+GGTACAATGTACAATATTCTGATGATGGTTACACT
+>EAS51_64:3:285:417:147
+AGTCAAAATTAAAGTTCAATACTCACCATCATAAA
+>EAS51_64:3:285:417:147
+TTGGATCTAATTTTTGGACTTCTTAAAGAAAAAAA
+>EAS51_64:3:309:303:278
+CTATGAAGAGACTATTGCCAGATGAACCACACATT
+>EAS51_64:3:309:303:278
+TCAATTTGGTGTTCTGTGTAAAGTCTCAGGGAGCC
+>EAS51_64:3:67:782:132
+ATATTTGTCTGAGCAAAACAGTCTAGATGAGAGAG
+>EAS51_64:3:67:782:132
+TCTTCCTCTGTCTTGATTTACTTGTTGTTGGTTTT
+>EAS51_64:3:7:268:263
+TCGTACAGAAGTTTAATGGAGCCTTGGGACCTTAC
+>EAS51_64:3:7:268:263
+TTGCGTTATTTGAGTTGGTGGAAGACATAATCCCA
+>EAS51_64:3:80:885:513
+GAAATTCTTCATCCTGGACCCTGAGAGATTCTGCA
+>EAS51_64:3:80:885:513
+GCATTTTGTCAGTTACCAAATGTGTTTATTACCAG
+>EAS51_64:3:90:435:691
+GGGAATTTGTCAATGTCAGGGAAGGAGCATTTTGT
+>EAS51_64:3:90:435:691
+TCTGGTGACTGCCAGAGCTGCTGGCAAGCTAGAGT
+>EAS51_64:4:102:467:897
+AGCATGGTTGTACAGGGCAATACATGAGATTATTA
+>EAS51_64:4:102:467:897
+GCTTTCAACGCTTCTAGCCATTTCTTTTGTCTTTT
+>EAS51_64:4:116:738:142
+AAAGTTCAATACTCACCATCATAAATACACACAAA
+>EAS51_64:4:116:738:142
+TGTCAAACACGAATGTTATGCCCTGCTAAACTAAG
+>EAS51_64:4:163:31:455
+CTTACTTCCAGCTCCCCAGAGGGACAGCTNNCAAC
+>EAS51_64:4:163:31:455
+GGGAGGTGCACTAATGCGCTCCACGCCCAAGCCCT
+>EAS51_64:4:179:389:585
+TGGCCACTTTTTATCGCATTTCCCTTTAGAACCTA
+>EAS51_64:4:179:389:585
+TGTGAAATGAATGAGATTATTAGGAAATGCTTTAC
+>EAS51_64:4:181:476:394
+AACAATATTAACTTTGAATAAAAAGGGATTAAATT
+>EAS51_64:4:181:476:394
+TCATCACTAAACCAGTCCTATAAGAAATGCTCAAA
+>EAS51_64:4:189:467:475
+CTACATGGCTGATTATGAAAACAATGTTCCCCAGA
+>EAS51_64:4:189:467:475
+TATCTGGATTCTGGGAAATTCTTCATCCTGGACCC
+>EAS51_64:4:189:571:366
+AACAAATACTACTAGACCTAAGAGGGATGAGAAAT
+>EAS51_64:4:189:571:366
+TCTACGCAAACAGAAACCAAATGAGAGAAGGAGTA
+>EAS51_64:4:318:345:156
+GGACCCTGAGAGATTCTGCAGCCCAGATCCAGATT
+>EAS51_64:4:318:345:156
+TTATGAAAACAATGTTCCCCAGATACCATCCCTGT
+>EAS51_64:4:57:786:414
+CTCATTCACTCCAGCTCCCTGTCACCCAATGGACC
+>EAS51_64:4:57:786:414
+TGCAACAACCTTGAGAACCCCAGGGAATTTGTCAA
+>EAS51_64:5:177:24:389
+AGCTTTCAAGAAGTATGAGATTATGTAAAGTAACT
+>EAS51_64:5:177:24:389
+CAAGACAGACTTCATCAAGATATGTAGTCATCAGA
+>EAS51_64:5:202:39:380
+CAGGGAAGGAGCATTTTGTCAGTTACCAAATGTGT
+>EAS51_64:5:202:39:380
+CTTCATCCTGGACCCTGAGAGATTCTGCAGCCCAG
+>EAS51_64:5:290:247:509
+AGCCCATACTTTACTGCTACTCAATATATCCATGT
+>EAS51_64:5:290:247:509
+TCTCAAATATTGCTAGTGGGAGTATAAATTGTTTT
+>EAS51_64:6:118:41:489
+ACAATTAATTGAGACTACAGAGCAACTAGGTAAAA
+>EAS51_64:6:118:41:489
+CCCTGCTAAACTAAGCATCATAAATGAAGGGGAAA
+>EAS51_64:6:124:128:489
+CTCTGTCTTGATTTACTTGTTGTTGGTTTTCTGTT
+>EAS51_64:6:124:128:489
+GTCCTATCTTCTTCTTAGGGAAGAACAGCTTAGGT
+>EAS51_64:6:143:763:480
+AAACGCGTAACTGCGCTCTCATTCACTCCAGCTCC
+>EAS51_64:6:143:763:480
+CTGAAGGTTGTTGCAAGGGGGTCTATGTGAACAAA
+>EAS51_64:6:195:348:703
+CAGTTACCAAATGTGTTTATTACCAGAGGGATGGA
+>EAS51_64:6:195:348:703
+TAATGAAAACTATATTTATGCTATTCAGTTCTAAA
+>EAS51_64:6:206:994:556
+ATTTGAGGAAGTAATTGGGGAAAACCTCTTTAGTC
+>EAS51_64:6:206:994:556
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+>EAS51_64:6:210:809:735
+AAACCTCTTTAGTCTTGCTAGAGATTTAGACATCT
+>EAS51_64:6:210:809:735
+GAGGTTCAGAACTTGAAGACAAGTCTCTTATGAAT
+>EAS51_64:6:213:54:878
+CTCTGTCTTGATTTACTTGTTGTTGGTTTTTTGTT
+>EAS51_64:6:300:622:86
+GGTTACACTAAAAGCCCATACTTTACTGCTACTCA
+>EAS51_64:6:300:622:86
+TCATACAATGATAAAAAGATCAATTCAGCAAGAAG
+>EAS51_64:6:54:695:952
+ACAGTAAAATAAAACAAAGGAGGTCATCATACAAT
+>EAS51_64:6:54:695:952
+GGTTACACTAAAAGCCCATACTTTACTGCTACTCA
+>EAS51_64:7:104:965:517
+AGAGGCTCAAAGAATGCCAGGAAGATACATTGCAA
+>EAS51_64:7:104:965:517
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+>EAS51_64:7:140:752:822
+CATCACTAAACCAGTCCTATAAGAAATGCTCAAAA
+>EAS51_64:7:140:752:822
+GCTTCTCAGCGGAAACCTTACAAGCCAGAAGAGAT
+>EAS51_64:7:152:918:824
+TACTATGTTTCTTATCTGCACATTACTACCCTGCA
+>EAS51_64:7:152:918:824
+TTTCCCATCATGAAGCACTGAACTTCCACGTCTCA
+>EAS51_64:7:92:493:891
+AAAAGAAAAAGTGAGAAGTTTGGAAAAACTATTTG
+>EAS51_64:7:92:493:891
+AGTCAACATGAAGGAAAAAAATTCTAAAATCAGCA
+>EAS51_66:1:282:274:50
+ATTACCAGAGGGATGGAGGGAAGAGGGACGCTGAA
+>EAS51_66:1:282:274:50
+CCCCTCTAAGCCGTTCTATTTGTAATGAAAACTAT
+>EAS51_66:1:289:207:323
+CCATACTTTACTGCTACTCAATATATCCATGTAAC
+>EAS51_66:1:289:207:323
+CTAGTGGGAGTATAAATTGATTTCCACTTTGGAAA
+>EAS51_66:1:64:182:741
+AAAAAAACAAATTAAACTCTAACAAAAGTAAATAA
+>EAS51_66:3:102:511:946
+ATGTAAAAGTGACTGTTATTGTCTTGACACCCAAC
+>EAS51_66:3:102:511:946
+CCCAGTCCCTGCCCCATCTCGGGTAATCTCTCTCC
+>EAS51_66:3:155:375:623
+AAGGAGTAGCTATACTTATATCAGATAAAGCACAC
+>EAS51_66:3:155:375:623
+CAATATTAACTTTGAATAAAAAGGGATTAAATTCC
+>EAS51_66:3:166:532:438
+AACAAATACTACTAGACCTAAGAGGGATGAGAAAT
+>EAS51_66:3:166:532:438
+AACTAAAAAAGCAAAAACAAAAACTATGCTAAGTA
+>EAS51_66:3:233:191:520
+TGAACTTCTGTAATTGAAAAATTCATTTAAGAAAT
+>EAS51_66:3:246:711:981
+AAAAAAACCTGTCAAACACGAATGTTATGCCCTGC
+>EAS51_66:3:246:711:981
+AGACTTCATCAAGATATGTAGTCATCAGACTATCT
+>EAS51_66:3:263:689:572
+AAAGAAAAAAAAACCTGTCAAACACGAATGTTATG
+>EAS51_66:3:263:689:572
+AAGATATGTAGTCATCAGACTATCTAAAGTCAACA
+>EAS51_66:3:29:381:169
+ATCTGGATTCTGGGAAATTCTTCATCCTGGACCCT
+>EAS51_66:3:29:381:169
+CATCAACCTCATACACACACATGGTTTAGGGGTAT
+>EAS51_66:3:39:59:738
+GAGATTATTAGGAAATGCTTTACTGTCATAATTAT
+>EAS51_66:3:39:59:738
+GTCCTATGTTCTTCTTAGGGAAGAACAGCTTAGGT
+>EAS51_66:4:188:460:1000
+GTGTCCATGTACACACGCTGTCCTATGTACTTATC
+>EAS51_66:4:188:460:1000
+TCTTGAAAGCTTGGGCTGTAATGATGCCCCTTGGC
+>EAS51_66:4:191:40:536
+ATAAAAAAAGACTACCCAGATTCATAAAACAAATA
+>EAS51_66:4:191:40:536
+CAGGTAAAGGGGTGGAAAAAGATGTTCTACGCAAA
+>EAS51_66:4:209:92:210
+GAGATTATTAGGAAATGCTTTACTGTCATAACTAT
+>EAS51_66:4:209:92:210
+TTAGGGAAGAACAGCTTAGGTATCAATTTGGTGTT
+>EAS51_66:4:240:264:231
+CAACAGATCAAGAAGGAGGGGCAATGGACGAGTTA
+>EAS51_66:4:240:264:231
+TGTAATGAAAACTATATTTATGCTATTCAGTTCTA
+>EAS51_66:4:277:482:316
+CACTAATGCGCTCCACGCCCAAGCCCTTCTCACAG
+>EAS51_66:4:277:482:316
+TGTCCTATGTACTTATCATGACTCTATCCCAAATT
+>EAS51_66:4:310:287:420
+AAGACATGAGTTCAGGTAAAGGGGTGGAAAAAGAT
+>EAS51_66:4:310:287:420
+TACAGAGCAACTAGGTAAAAAATTAACATTACAAC
+>EAS51_66:4:322:350:374
+ACTTCTTAAAGAAAAAAAAACCTGTCAAACACGAA
+>EAS51_66:4:322:350:374
+CATTGCAAGACAGACTTCATCAAGATATGTAGTCA
+>EAS51_66:5:210:674:911
+TCATAAATACACACAAAAGTACAAAACTCACAGGT
+>EAS51_66:5:210:674:911
+TGGCAGAACAGATTTAAAAACATGAACTAACTATA
+>EAS51_66:5:269:280:716
+TGATATCTGGATTCTGGGAAATTCTTCATCCTGGA
+>EAS51_66:5:269:280:716
+TTTGTCAATGTCAGGGAAGGAGCATTTTTTCAGTT
+>EAS51_66:5:273:545:1001
+AACAAAGGAGGTCATCATACAATGATAAAAAGATC
+>EAS51_66:5:273:545:1001
+AGATTTAAAAACATGAACTAACTATATGCTGTTTA
+>EAS51_66:5:285:395:450
+GTCATCTATAAAGGAAATCCCATCAGAATAACAAT
+>EAS51_66:5:285:395:450
+TATTTGAGGAAGTAATTGGGGAAAACCTCTTTAGT
+>EAS51_66:5:308:400:602
+ATAGACCCCCTTGCAACAACCTTGAGAACCCCAGG
+>EAS51_66:5:308:400:602
+CCTGTCACCCAATGGACCTGTGATATCTGGATTCT
+>EAS51_66:6:284:442:747
+AAAGAGGCTCAAAGAATGCCAGGAAGATACATTGC
+>EAS51_66:6:310:747:415
+TGAGTCACAGGTATTCCTGAGGAAAAAGAAAAAGT
+>EAS51_66:6:310:747:415
+TGTAGTCATCAGACTATCTAAAGTCAACATGAAGG
+>EAS51_66:7:174:987:334
+ACACCCAAGCCCTTCTCACAGTTTCTGCCCCCAGC
+>EAS51_66:7:174:987:334
+GTCCATGTACACACGCTGTCCTATGTACTTATCAT
+>EAS51_66:7:4:234:610
+AAAAAACCTGTCAAACACGAATGTTATGCCCTCCT
+>EAS51_66:7:4:234:610
+AAAAATCAACATCACAAATACACACAAAAGTACAA
+>EAS51_66:7:84:411:336
+GCTTGTACTTCTAAATCTATAAAAAAATTAAAATT
+>EAS51_66:8:36:688:722
+ATGTCTATTTTTGTCTTGACACCCAACTAATATTT
+>EAS51_66:8:36:688:722
+GTCCCTGCCCCATCTCTTGTAATCTCTCTCCTTTT
+>EAS51_66:8:43:972:506
+AGAAACCTTACAAGCCAGAAGAGATTGGATCTAAT
+>EAS51_66:8:43:972:506
+TAAGAAATGCTCAAAAGAATTGTAAAAGTCAAAAT
+>EAS51_66:8:66:655:769
+TCATCCTGGACCCTGAGAGATTCTGCAGCCCAGCT
+>EAS51_66:8:66:655:769
+TTTGTCAGTTACCAAATGTGTTTATTACCAGAGGG
+>EAS51_66:8:9:80:353
+AATTAATATAATTGTGTCCATGTACACACGCTGTC
+>EAS51_66:8:9:80:353
+CCTCGTCCACACTGGTTCTCTTGAAAGCTTGGGCT
+>EAS51_78:7:113:43:634
+ATTTGTCTGAGAAAAACAGTCTAGATGAGAGAGAA
+>EAS51_78:7:113:43:634
+CTGTCTTCCTCTGTCTTGATTTACTTGTTGTTTTT
+>EAS51_78:7:147:64:416
+AAACAATGTCCCCCAGATACCATCCCTGTCTTACT
+>EAS51_78:7:147:64:416
+CTCATCTAGGGGAACAGGGAGGTGCACTAATGCGC
+>EAS51_78:7:164:727:977
+GAAATGCTCAAAAGAATTGTAAAAGTCAAAATTAA
+>EAS51_78:7:164:727:977
+TACAAGCCAGAAGAGATTGGATCTAATTTTTCGAC
+>EAS51_78:7:186:199:927
+CTACGCGAATGCGTCTCTACCACAGGGGGCTGCGC
+>EAS51_78:7:186:199:927
+TGGCATTTGCCTTCAGACCCTACACGAATGCGTCT
+>EAS51_78:7:215:516:299
+AAGCTATGCTAAGTATTGGTAAAGATGTGGGGAAA
+>EAS51_78:7:215:516:299
+AATTACCTAATTGGTACAATGTACAATATTCTGAT
+>EAS51_78:7:270:448:491
+GTAATCTCTCTCCTTTTTGCTGCATCCCTGTCTTC
+>EAS51_78:7:270:448:491
+TTTGTCTGAGCAAAACAGTCTAGATGAGAGAGAAC
+>EAS51_78:7:303:402:142
+AGCATTTTGTCAGTTACCAAATGTGTTTATTACCA
+>EAS51_78:7:303:402:142
+TCCCATTTGGAGCCCCTCTAAGCCGTTCTATTTGT
+>EAS51_78:7:316:961:576
+TGTGATATCTGGATTCTGGGAAATTCTTCATCCCG
+>EAS51_78:7:316:961:576
+TTACGGGTGTAATCTCTCTACATGGCTAATTATGA
+>EAS54_61:1:115:868:887
+CATACACACACATGGTTTAGGGGTATAATACCTCT
+>EAS54_61:1:115:868:887
+TCTCATTCACTCCAGCTCCCTGTCACCCAATGGAC
+>EAS54_61:2:168:61:867
+GATGTTCTACGCAAACAGAAACCAAATGAGAGAAG
+>EAS54_61:2:168:61:867
+TCATAAAACAAATACTACTAGACCTAAGAGGGATG
+>EAS54_61:2:66:757:918
+CCATCCTACTAAATACATATGCACCTAACACAAGA
+>EAS54_61:2:66:757:918
+GGGGTGGAAAAAGATGTTCTACGCAAACAGAAACC
+>EAS54_61:3:150:933:810
+AGCTTTCAACGCTTCTAGCCATTTCTTTTGGCATT
+>EAS54_61:3:150:933:810
+CAATGAACAACAGGAAGAAAAGGTCTTTCAAAAGG
+>EAS54_61:3:155:758:710
+ATCAGATAAAGCACACTTTAAATCAACAACAGTAA
+>EAS54_61:3:155:758:710
+TTTGAATAAAAAGGGATTAAATTCCCCCACTTAAG
+>EAS54_61:3:20:762:748
+CACAATGAACAACAGGAAGAAAAGGTCTTTCAAAA
+>EAS54_61:3:20:762:748
+TTCTTTTGGCATTTGCCTTCAGACCCTACACGAAT
+>EAS54_61:4:143:69:578
+ATTGGGAGCCCCTCTAAGCCGTTCTATTTGTAATG
+>EAS54_61:4:83:452:970
+AATGAAAACTATATTTATGCTATTCAGTTCTAAAT
+>EAS54_61:4:83:452:970
+AGGGATGGAGGGAAGAGGGACGCTGAAGAACTTTG
+>EAS54_61:4:86:660:932
+AATACATATGCACCTAACACAAGACTACCCAGATT
+>EAS54_61:4:86:660:932
+ATATAAAAAAATTAAAATTTAACAAAAGTAAATAA
+>EAS54_61:6:126:541:194
+AGTACGACCAGCTCCCCAGAGGGAAAGCTTTCAAC
+>EAS54_61:6:126:541:194
+CAGCCCAGATCCAGATTGCTTGTGGTCTGACAGGC
+>EAS54_61:6:25:949:33
+AAAGTAACTGAACCTATGAGTCACAGGTATTCCTG
+>EAS54_61:6:25:949:33
+GATATGTAGTCATCAGACTATCTAAAGTCAACATG
+>EAS54_61:7:114:506:971
+ACTAAATACATATGCACCTAACACAAGACTACCCA
+>EAS54_61:7:114:506:971
+GGGTGGAAAAAGATGTTCTACGCAAACAGAAACCA
+>EAS54_61:7:64:37:257
+CCGTGTCCTCCCATCTGGCCTCGTCCACACTGGTT
+>EAS54_61:7:64:37:257
+TTTGATTTGGTGGAAGACATAATCCCACGCTTCCT
+>EAS54_61:8:165:441:708
+CCATCATAAATACACACAAAAGTACAAAACTCACA
+>EAS54_61:8:165:441:708
+CTTAAAGAAAAAAAAACCTGTCAAACACGAATGTT
+>EAS54_61:8:4:173:814
+CTGCTACTCAATATATCCATGTAACAAATCTGCGC
+>EAS54_61:8:4:173:814
+GATAAAAAGATCAATTCAGCAAGAAGATATAACCA
+>EAS54_65:2:127:288:655
+ACTAGGTAAAAAATTAACATTACAACAGGAACAAA
+>EAS54_65:2:127:288:655
+TGTTCTACGCAAACAGAAACCAAATGAGAGAAGGA
+>EAS54_65:2:182:924:833
+TTTTTTTTTTTTTATTTGCGCTTTTTTTTTTTTTT
+>EAS54_65:2:264:157:150
+GGAAAAATGGACAAGATTCTGATGAGGGTTACACT
+>EAS54_65:2:264:157:150
+TAAAGCACACTTTAAATCAACAACAGTAAAATAAA
+>EAS54_65:2:94:356:809
+AAATCTATAACAAAATTAAAATTTAACAAAAGTAA
+>EAS54_65:2:94:356:809
+CTAAATACATATGCACCTAACACAAGACTACCCAG
+>EAS54_65:3:102:884:63
+GTCTTGACACCCAACTAATATTTGTCTGAGCAAAA
+>EAS54_65:3:102:884:63
+TGTCTTCCTCTGTCTTGATTTCCTTGTTGTTGGTT
+>EAS54_65:3:155:541:234
+CTAAATACATATGCACCTAACACAAGACTACCCAG
+>EAS54_65:3:155:541:234
+TGCGCTTGTACTTCTAAATCTATAAAAAAATTAAA
+>EAS54_65:3:214:946:229
+AAATGAACAGAGCTTTCAAGAAGTATGATATTATG
+>EAS54_65:3:214:946:229
+ACAAAGAATGCCAGGAAGATACATTGCAAGACAGA
+>EAS54_65:3:273:901:459
+CCAGCATGGTTGTACTGGGCAATACATGAGATTAT
+>EAS54_65:3:273:901:459
+TGTCCTATGTACTTATCATGACTCTATCCCAAATT
+>EAS54_65:3:290:558:349
+ACCATCCCTGTCTTACTTCCAGCTCCCCAGCGGGA
+>EAS54_65:3:290:558:349
+TCTCAGCTAGGGGAACAGGGAGGTGCACTAATGCG
+>EAS54_65:3:320:20:250
+AAATAAAACACATAGCTAAAACTAAAAAAGCAAAA
+>EAS54_65:3:320:20:250
+TTTTTTTTTTTTTTTTTTTTTTTGCATGCCAGAAA
+>EAS54_65:3:321:311:983
+ATTTATGCTATTCAGTTCTAAATATAGAAATTGAA
+>EAS54_65:3:326:652:890
+TTCTGTAATTGAAAAATTCATTTAAGAAATTACAA
+>EAS54_65:4:137:319:642
+CTTGTTGTTGGTTTTCTGTTTCTTTTTTTGATTTT
+>EAS54_65:4:174:753:617
+ATATATCCATGTAACAAATCTGCGCTTGTACTTCT
+>EAS54_65:4:174:753:617
+GATATAACCATCCTACTAAATACATATGCACCTAA
+>EAS54_65:4:192:714:341
+AAATTAAAATTTAACAAAAGTAAATAAAACACATA
+>EAS54_65:4:192:714:341
+ACACAAGACTACCCAGATTCATAAAACAAATACTA
+>EAS54_65:4:193:38:987
+AGGGAAGAACAGCTTAGGTATCAATTTTGTGTTCT
+>EAS54_65:4:193:38:987
+TGAGATTATTAGGAAATGCTTTACTGTCATAACTA
+>EAS54_65:4:246:313:499
+ACAATGAACAACAGGAAGAAAAGGTCTTTCAAAAG
+>EAS54_65:4:246:313:499
+CTTTAAACGCTTCTAGCCATTTCTTTTGGCATTTG
+>EAS54_65:4:325:795:213
+AGACTACAGAGCAACTAGGTAAAAAATTAACATTA
+>EAS54_65:4:325:795:213
+GGAAATAAAGTCAAGTCTTTCCTGACAAGCAAATG
+>EAS54_65:4:61:346:384
+CAACTAAGAAGAAACCTTACAAGCCAGAAGAGATT
+>EAS54_65:4:61:346:384
+CTAAATGAAAGAGGCTCAAAGAATGCCAGGAAGAT
+>EAS54_65:4:91:267:655
+CAGGGAGCCGTCCGTGTCCTCCCATCTGGCCTCGT
+>EAS54_65:4:91:267:655
+TGTTGTTGGTTTTCTGTTTCTTTGTTTGATTTGGT
+>EAS54_65:6:115:538:276
+CAAATGTGTTTATTACCAGAGGGATGGAGGGAAGA
+>EAS54_65:6:115:538:276
+TATTTGTAATGAAAACTATATTTATGCTATTCAGT
+>EAS54_65:6:164:797:930
+AGCTAGAGACCCATTTGGAGCCCCTCTAAGCCGTT
+>EAS54_65:6:164:797:930
+GTCAGGGAAGGAGCATTTTGTCAGTTACCAAATGT
+>EAS54_65:6:18:376:416
+GCAAAACAGTCTAGATGAGAGAGAACTTCCCTGGA
+>EAS54_65:6:18:376:416
+TTTTTGCTGCATCCCTGTCTTCCTCTGTCTTGTTT
+>EAS54_65:6:277:590:364
+CTCTACATGGCTGATTATGAAAACAATGTTCCCCA
+>EAS54_65:6:277:590:364
+CTGGGAAATTCTTCATCCTGGACCCTGAGAGATTC
+>EAS54_65:6:326:71:741
+TCTCGTTTTTTTTTCTTTCTTTTCTCTTTTTTTTT
+>EAS54_65:6:49:183:435
+CCATCATGAAGCACTGAACTTCCACGTCTCATCTA
+>EAS54_65:6:49:183:435
+GACTATTGCCAGATGAACCACACATTAATACTATG
+>EAS54_65:6:67:56:806
+TATAAAGGAAATCCCATCAGAATAACAATGGGCTT
+>EAS54_65:6:67:56:806
+TCCTGACAAGCAAATGCTAAGATAATTCATCATCA
+>EAS54_65:7:117:452:744
+AATATTAACTTTGAATAAAAAGGGATTAAATTCCC
+>EAS54_65:7:117:452:744
+ACCAGTCCTATAAGAAATGCTCAAAAGAATTGTAA
+>EAS54_65:7:155:629:357
+AGAAGAGATTGGATCTAATTTTTGGACTTCTTAAA
+>EAS54_65:7:155:629:357
+AGAGGCTCAAAGAATGCCAGGAAGATACATTGCAA
+>EAS54_65:7:159:253:353
+ATAAAACAATTAATTGAGACTACAGAGCAACTAGG
+>EAS54_65:7:159:253:353
+GAAGGGGAAATAAAGTCAAGTCTTTCCTGACAGGC
+>EAS54_65:7:56:57:985
+TTCTGTCTTCTCTCCTGTCTTCTTTTCTCTTCTTT
+>EAS54_65:7:56:57:985
+TTTTTTCTCTTTTCTCTTTTTTTTTTTTTTTTTTT
+>EAS54_65:7:68:825:405
+AAAACCTCATATATCAATATTAACTTTGAATAAAA
+>EAS54_65:7:68:825:405
+AAACCAAATGAGAGAAGGAGTAGCTATACTTATAT
+>EAS54_65:8:10:975:766
+AATAACACAAGACTACCCAGATTCATAAAACAAAT
+>EAS54_65:8:10:975:766
+TTAATAAAGACATGAGTTCAGGTAAAGGGGTGAAA
+>EAS54_65:8:140:924:923
+GAACAACAGGAAGAAAAGGTCTTTCAAAAGGTGAT
+>EAS54_65:8:140:924:923
+TTTTAGCCATTTCTTTTGGCATTTGCCTTCAGACC
+>EAS54_65:8:147:687:428
+ATATGCACCTAACACAAGACTACCCAGATTCATAA
+>EAS54_65:8:147:687:428
+ATGTTCTACGCAAACAGAAACCAAATGAGAGAAGG
+>EAS54_65:8:178:187:610
+AAATACACACAAAAGTACAAAACTCACAGGTTTTA
+>EAS54_65:8:178:187:610
+TTGGCAGAACAGATTTAAAAACATGAACTAACTAT
+>EAS54_65:8:240:719:799
+AGATTGGCAGAACAGATTTAAAAACATGAACTAAC
+>EAS54_65:8:240:719:799
+TTAAAGTTCAATACTCACCATCATAAATACACACA
+>EAS54_65:8:305:819:245
+AAATTCATTTAAGAAATTACAAAATATAGTTGAAA
+>EAS54_65:8:76:493:708
+TTTATGCTATTCAGTTCTAAATATAGAAATTGAAA
+>EAS54_67:1:138:186:274
+GGCCTCGTCCACACTGGTTCTCTTGAAAGCTTGGG
+>EAS54_67:1:138:186:274
+TAATTGTGTCCATGTACACACGCTGTCCTATGTAC
+>EAS54_67:1:159:222:274
+GAACCACACATTAATACTATGTTTCTTATCTGCAC
+>EAS54_67:1:159:222:274
+GTCTGGGGAAAGTCTCAGGGAGCCGTCCGTGTCCT
+>EAS54_67:1:15:381:715
+GACTAAACCAAGCAGAAGAAAGAGGTTCAGAACTT
+>EAS54_67:1:15:381:715
+GGAAAAAGAAAAAGTGAGAAGTTTGGAAAAACTAT
+>EAS54_67:1:88:54:900
+ATCAACAACAGAAAAATAAAACAAAGGAGGTCATC
+>EAS54_67:1:88:54:900
+TGATGATGGTTACACTAAAAGCCCATACTTCACTG
+>EAS54_67:2:22:471:500
+GTAAATAAAACACATAGCTAAAACTAAAAAAGCAA
+>EAS54_67:2:22:471:500
+TACTACTAGACCTAAGAGGGATGAGAAATTACCTA
+>EAS54_67:3:114:736:433
+AACAAAACCTCATATATCAATATTAACTTTGAATA
+>EAS54_67:3:114:736:433
+ATGTTCTACGCAAACAGAAACCAAGTGAGAGAAGG
+>EAS54_67:3:172:196:746
+AAATAAAGTCAAGTCTTTCCTGACAAGCAAATGCT
+>EAS54_67:3:172:196:746
+GCATACAGTCATCTATAAAGGAAATCCCATCAGAA
+>EAS54_67:3:175:730:949
+TTATGCTATTCAGTTCTAAATATAGAAATTGAAAC
+>EAS54_67:3:197:261:624
+GACTATCTAAAGTCAACATGAAGGAAAAAAATTCT
+>EAS54_67:3:197:261:624
+GCCCTGCTAAACTAAGCATCATAAATGAAGGGGAA
+>EAS54_67:3:47:471:858
+ACACCCAACTAATATTTGTCTGAGCAAAACAGTCT
+>EAS54_67:3:47:471:858
+CATCCCTGTCTTCCTCTGTCTTGATTTACTTGTTG
+>EAS54_67:4:142:943:582
+TTCAAATGAACTTCTGTAATTGAAAAATTCATTTA
+>EAS54_67:4:145:607:216
+AACGCGTAACTGCGCTCTCATTCACTCCAGCTCCC
+>EAS54_67:4:145:607:216
+TGAAAAACAGGAAGAAAAGGTCTTTCAAAAGGTGA
+>EAS54_67:4:7:526:343
+TCATCCTGGACCCTGAGAGATTCTGCAGCCCAGCT
+>EAS54_67:4:7:526:343
+TGAAAACAGTGTTCCCCAGATACCATCCCTGTCTT
+>EAS54_67:5:117:33:262
+AATTAACATTACAACAGGAACAAAACCTCATATAT
+>EAS54_67:5:117:33:262
+ACAAGCAAATGCTAAGATAATTCATCATCACTAAA
+>EAS54_67:5:124:241:608
+CTGAACTTCCACGTCTCATCTAGGGGAACAGGGAG
+>EAS54_67:5:124:241:608
+GGGTATAATACCTCTACATGGCTGATTATGAAAAC
+>EAS54_67:5:127:828:697
+ATGCCAGGAAGATACATTGCAAGACAGACTTCATC
+>EAS54_67:5:127:828:697
+TAAAGAAAAAAAAACCTGTCAAACACGAATGTTAT
+>EAS54_67:5:149:639:910
+CAATGGGCTTCTCAGCAGAAACCTTACAAGCCAGA
+>EAS54_67:5:149:639:910
+TCACTAAACCAGTCCTATAAGAAATGCTCAAAAGA
+>EAS54_67:5:71:408:741
+AGTCATCTATAAAGGAAATCCCATCAGAATAACAA
+>EAS54_67:5:71:408:741
+TCCTGACAAGCAAATGCTAAGATAATTCATCATCA
+>EAS54_67:6:107:395:312
+CAAAATATAGTTGAAAGCTCTAACAATAGACTAAA
+>EAS54_67:6:107:395:312
+CAGGTATTCCTGAGGAAAAAGAAAAAGTGAGAAGT
+>EAS54_67:6:109:953:668
+CAATATATCCATGTAACAAATCTGCGCTTGTACTT
+>EAS54_67:6:109:953:668
+CCACTTTGGAAAACAATTTGGTAATTTCGTTTTTT
+>EAS54_67:6:198:503:669
+CAATGATAAAAAGATCAATTCAGCAAGAAGATATA
+>EAS54_67:6:198:503:669
+CAGATTTAAAAACATGAACTAACTATATGCTGTTT
+>EAS54_67:6:43:859:229
+TTCAAATGAACTTCTGTAATTGAAAAATTCATTTA
+>EAS54_67:6:46:285:790
+AACGCGTAACTGCGCTCTCATTCACTCCAGCTCCC
+>EAS54_67:6:46:285:790
+TCAAGGTTGTTGCAAGGGGGTCTATGTGAACAAAG
+>EAS54_67:7:101:752:996
+AACCTTACAAGCCAGAAGAGATTGGATCTAATTTT
+>EAS54_67:7:101:752:996
+AAGAAATGCTCAAAAGAATTGTAAAAGTCAAAATT
+>EAS54_67:7:197:399:319
+CAAAAAACAAATACTACTAGACCTAAGAGGGATGA
+>EAS54_67:7:197:399:319
+TAGAAACCAAATGAGAGAAGGAGTAGCTATACTTA
+>EAS54_67:8:19:855:491
+TGGCATTTGCCTTCAGACCCTACACGAATGCGTCT
+>EAS54_67:8:19:855:491
+TGTGTGTTCTCATCAACCTCATACACACACATGGT
+>EAS54_67:8:46:900:610
+GATATCTGGATTCTGGGAAATTCTTCATCCTGGAC
+>EAS54_67:8:46:900:610
+TACATGGCTGATTATGAAAACAATGTTCCCCAGAT
+>EAS54_71:2:125:628:79
+GCTGAAGAACTTTGATGCCCTCTTCTTCCAAAGA
+>EAS54_71:2:125:628:79
+TTTATGCTATTCAGTTCTAAATATAGAAATTGAAA
+>EAS54_71:2:204:264:413
+CAATGAACAACAGAAAGAAAAGTTCTTTCAAAAGG
+>EAS54_71:2:204:264:413
+TGCCCTCTTCTTCCAAAGATGAAACGCGTAACTG
+>EAS54_71:2:85:686:696
+AATCAGCAAGAGAAAAGCATACAGTCATCTATAAA
+>EAS54_71:2:85:686:696
+TAAACTAAGCATCATAAATGAAGTGGAAATAAAG
+>EAS54_71:3:186:989:869
+ACACACATGGTTTAGGGGTATAATACCTCTACATG
+>EAS54_71:3:186:989:869
+GGGAAATTCTTCATCCTGGACCCTGAGAGATTCT
+>EAS54_71:3:254:32:275
+GATGGAGGGAAGAGGGACGCTGAAGAACTTTGAT
+>EAS54_71:3:254:32:275
+TGCAACTGTGAGCCATCACAATGAACAACAGGAAG
+>EAS54_71:3:257:288:731
+AAGAAGATATAACCATCCTACTAAATACATATGCA
+>EAS54_71:3:257:288:731
+TGCTGTTTACAAGAAACTCATTAATAAAGACATG
+>EAS54_71:3:267:821:860
+GCATACAGTCATCTATAAAGGAAATCCCATCAGA
+>EAS54_71:3:267:821:860
+TCTTTAGTCTTGCTAGAGATTTAGACATCTAAATG
+>EAS54_71:3:78:855:352
+AAAAGAAAAAGTGAGAAGTTTGGAAAAACTATTT
+>EAS54_71:3:78:855:352
+AACAATAGACTAAACCAAGCAGAAGAAAGAGGTTC
+>EAS54_71:4:127:725:381
+AATTACAAAATATAGTTGAAAGCTCTAACAATAGA
+>EAS54_71:4:127:725:381
+TGAACCTATGAGTCACAGGTATTCCTGAGGAAAA
+>EAS54_71:4:13:981:659
+CGGGACAATGGACGAGGTAAACCGCACATTGACAA
+>EAS54_71:4:13:981:659
+TGTAGCCCCTCTAAGGCGTTCTATTTGTAATGAA
+>EAS54_71:4:14:88:306
+AAAGAATGCCAGGAAGATACATTGCAAGACAGAC
+>EAS54_71:4:14:88:306
+AGAAGAGATTAGATCTAATTTTTGGACTTCTTAAA
+>EAS54_71:4:165:397:25
+GCAACTGTGAGCCATCACAATGAACAACAGGAAGA
+>EAS54_71:4:165:397:25
+TTCAACGCTTCTAGCCATTTCTTTTGGCATTTGC
+>EAS54_71:4:169:256:888
+AGGTTCAGAACTTGAAGACAAGTCTCTTATGAATT
+>EAS54_71:4:169:256:888
+ATTTGAGGAAGTAATTGGGGAAAACCTCTTTAGT
+>EAS54_71:4:169:862:829
+AAAGGTCTTTCAAAAGGTGATGTGTGTTCTCATCA
+>EAS54_71:4:169:862:829
+GCCATTTCTTTTGGCATTTGCCTTCAGACCCTAC
+>EAS54_71:4:206:741:810
+ACTAACTATATGCTGTTTACAAGAAACTCATTAA
+>EAS54_71:4:206:741:810
+CAAAAGTACAAAACTCACAGGTTTTATAAAACAAT
+>EAS54_71:4:209:159:130
+CTTATCATGACTCTATCCCAAATTCCCAATTACGT
+>EAS54_71:4:209:159:130
+GCCCCCAGCATGGTTGTACTGGGCAATACATGAG
+>EAS54_71:4:233:97:262
+ACCACACATTAATACTATGTTTCTTATCTGCCCA
+>EAS54_71:4:233:97:262
+GTATCAATTTGGTGTTCTGTGTAAAGTCTCAGGGA
+>EAS54_71:4:252:428:683
+TGTCTTGATTTACTTGTTGTTGGTTTTCTGTTTCT
+>EAS54_71:4:284:269:882
+TTTCTTTTCTCTTTTTTTTTTTTTTGTTTTTGCA
+>EAS54_71:4:328:669:662
+GGAAGGAGCATTTTGTCAGTTACCAAATGTGTTT
+>EAS54_71:4:328:669:662
+TCTTCATCCTGTACCCTGAGAGATTCTGCAGCCCA
+>EAS54_71:4:72:63:435
+CCTTGCAACAACCTTGAGAACCCCAGGGAATTTG
+>EAS54_71:4:72:63:435
+TGATATCTGGATTCTGGGAAATTCTTCATCCTGGA
+>EAS54_71:4:73:182:444
+AACTTCCCTGGAGGTCTGATGGCGTTTCTCCCTCG
+>EAS54_71:4:73:182:444
+CTTGATTTACTTGTTGTTGGTTTTCTGTTTCTTT
+>EAS54_71:5:153:543:671
+GCCCCATCTCTTGTAATCTCTCTCCTTTTTGCTG
+>EAS54_71:5:153:543:671
+TAAAATGTCTATTTTTGTCTTGACACCCAACTAAT
+>EAS54_71:5:16:434:204
+AGATGAGAGAGAACTTCCCTGGAGGTCTGATGGC
+>EAS54_71:5:16:434:204
+CTGTCTTCCTCTGTCTTGATTTACTTGTTGTTGGT
+>EAS54_71:5:81:685:141
+ACTGAACCTATGAGTCACAGGTATTCCTGAGGAA
+>EAS54_71:5:81:685:141
+AGATATGTAGTCATCAGACTATCTAAAGTCAACAT
+>EAS54_71:6:172:896:83
+AGGAAGAAAAGGTCTTTCAAAAGGTGATGTGTGT
+>EAS54_71:6:172:896:83
+CATTTGCCTTCAGACCCTACACGAATGCGTCTCTA
+>EAS54_71:6:215:133:909
+TGTGTGTTCTCATCAACCTCATACACACACATGG
+>EAS54_71:6:215:133:909
+TTGCCTTCAGACCCTACACGAATGCGTCTCTACCA
+>EAS54_71:6:224:932:942
+CTCTTGAAAGCTTGGGCTGTAATGATGCCCCTTGG
+>EAS54_71:6:224:932:942
+GTCCATGTACACACGCTGTCCTATGTACTTATCA
+>EAS54_71:6:228:354:203
+AATGGACCTGTGATATCTGGATTCTGGGAAATTC
+>EAS54_71:6:228:354:203
+TCAACCTCATACACACACATGGTTTAGGGGTATAA
+>EAS54_71:6:264:705:89
+AAACATATGCACCTAACACAAGACTACCCAGATTC
+>EAS54_71:6:264:705:89
+AAGGGGTGGAAAAAGATGTTCTACGCAAACAGAA
+>EAS54_71:6:324:515:230
+AAAACAGTCTAGATGAGAGAGAACTTCCCTGGAG
+>EAS54_71:6:324:515:230
+CCTGTCTTCCTCTGTCTTGATTTACTTGTTGTTGG
+>EAS54_71:6:82:932:400
+GACACCCAACTAATATTTGTCTGAGCAAAACAGTC
+>EAS54_71:6:82:932:400
+GTAATCTCTCTCCTCTTCGCTGCATCCCTGTCTT
+>EAS54_71:7:130:260:553
+AGCAAGAGAAAAGCATACAGTCATCTATAAAGGAA
+>EAS54_71:7:130:260:553
+GTGAGAAGTTTGGAAAAACTATTTGAGGAAGCAC
+>EAS54_71:7:194:867:616
+ATCCATGTAACAAATCTGCGCTTGTACTTCTATT
+>EAS54_71:7:194:867:616
+TTTTCCACTTTGGAAAACAATTTGGTAATTTCGTT
+>EAS54_71:7:212:329:348
+AACCACACATTAATACTATGTTTCTTATCTGCAC
+>EAS54_71:7:212:329:348
+CCCATCATGAAGCACTGAACTTCCACGTCTCATCT
+>EAS54_71:7:250:698:842
+AAAAAGTACAAAACTCACAGGTTTTATAAAACAA
+>EAS54_71:7:250:698:842
+AAGAAAAAAAAACCTGTCAAACACGAATGTTATGC
+>EAS54_71:7:80:760:490
+CATGGCTGATTATGAAAACAATGTTCCCCAGATAC
+>EAS54_71:7:80:760:490
+CTGGACCCTGAGAGATTCTGCAGCCCAGCTCCAG
+>EAS54_71:7:97:743:602
+AAGCAAATGCTAAGATAATTCATCATCACTAAACC
+>EAS54_71:7:97:743:602
+ATTACAACAGGAACAAAACCTCATATATCAATAT
+>EAS54_71:8:105:854:975
+ATTTAACAAAAGTAAATAAAACACATAGCTAAAAC
+>EAS54_71:8:105:854:975
+TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTG
+>EAS54_71:8:113:856:319
+AAATCAACAACAGTAAAATAAAACAAAGGAGGT
+>EAS54_71:8:113:856:319
+CCCACTTAAGAGATATAGATTGGCAGAACAGATTT
+>EAS54_71:8:215:830:609
+AAGACATCTAAATGAAAGAGGCTCAAAGAATGC
+>EAS54_71:8:234:21:950
+TTTTTTTTTTTTCTCCTCTCTTTTTTTTTTTTT
+>EAS54_71:8:321:642:388
+TACCAAATGTGTTTATTACCAGAGGGATGGAGG
+>EAS54_71:8:321:642:388
+TCCCATTTGGAGCCCCTCTAAGCCGTTCTATTTGT
+>EAS54_71:8:38:856:336
+AATGGACCTGTGATATCTGGATTCTGGGAAATT
+>EAS54_71:8:38:856:336
+CACACATGGTTTAGGGGTATAATACCTCTACATGG
+>EAS54_73:3:203:419:243
+GGAAAAAGAAAAAGTGAGAAGTTTGGAAAAACTAT
+>EAS54_73:3:203:419:243
+TTGAAAGCTCTAACAATAGACTAAACCAAGCAGAA
+>EAS54_73:3:239:796:221
+ATAACTATGAAGAGACTATTGCCAGCTGACCCCCC
+>EAS54_73:3:239:796:221
+GGAAGAACAGCTTAGGTATCAATTTGGTGTTCTGT
+>EAS54_73:3:23:502:103
+AGTCCCTGCCCCATCTCTTGTAATCTCTCTCCTTT
+>EAS54_73:3:23:502:103
+GACACCCAACTAATATTTGTCTGAGCAAAACAGTC
+>EAS54_73:3:29:833:612
+AAGCTCTAACAATAGACTAAACCAAGCAGAAGAAA
+>EAS54_73:3:29:833:612
+CAGGTATTCCTGAGGAAAAAGAAAAAGTGAGAAGT
+>EAS54_73:3:313:827:992
+AAAGTCTCAGGGAGCCGTCCGTGTCCTCCCATCTG
+>EAS54_73:3:313:827:992
+TGTTTCTTTGTTTGATTTGGTGGAAGACATAATCC
+>EAS54_73:3:37:761:635
+CCTCTTCTTCCAAAGATGAAACGCGTAACTGCGCT
+>EAS54_73:3:37:761:635
+TGTGAGCCATCACAATGAACAACAGGAAGAAAAGG
+>EAS54_73:3:4:854:140
+CCTGACAAGCAAATGCTAAGATAATTCATCATCAC
+>EAS54_73:3:4:854:140
+GTCATCTATAAAGGAAATCCCATCAGAATAACAAT
+>EAS54_73:3:88:24:744
+GTCCTGTGATATCTGGATTCTGGGAAATTCTTCAT
+>EAS54_73:3:88:24:744
+TGTCAATGTCAGGGAAGGAGCATTTTTGAAGTTTA
+>EAS54_73:5:145:635:390
+TAAACCAGTCCTATAAGAAATGCTCAAAAGAATTG
+>EAS54_73:5:145:635:390
+TTGAATAAAAAGGGATTAAATTCCCCCACTTAAGA
+>EAS54_73:5:169:714:644
+CCTAATTGGTACAATGTACAATATTCTGATGATGG
+>EAS54_73:5:169:714:644
+GAAAAAAGTAAACTCTCAAATATTGCTAGTGGGAG
+>EAS54_73:5:220:733:736
+CCATCCTACTAAATACATATGCACCTAACACAAGA
+>EAS54_73:5:220:733:736
+TTAATAAAGACATGAGTTCAGGTAAAGGGGTGGAA
+>EAS54_73:5:231:339:551
+CTGAGAGATTCTGCAGCCCAGATCCAGATTGCTTG
+>EAS54_73:5:231:339:551
+TGTCAGTTACCAAATGTGTTTATTACCAGAGGGAT
+>EAS54_73:5:255:796:239
+AAGGGATTAAATTCCCCCACTTAAGAGATAGAGAT
+>EAS54_73:5:255:796:239
+ATGCTCAAAAGAATTGTAAAAGTCAAAATTAAAGT
+>EAS54_73:5:263:557:988
+AATGATAAAAAGATCAATTCAGCAAGAAGATATAA
+>EAS54_73:5:263:557:988
+CTGCTACTCAATATATCCATGTAACAAATCTGCGC
+>EAS54_73:5:271:874:367
+AAAAAACCTGTCAAACACGAATGTTATGCCCTGCT
+>EAS54_73:5:271:874:367
+ATATGTAGTCATCAGACTATCTAAAGTCAACATTA
+>EAS54_73:5:3:233:911
+GTCTCATCTAGGGGAACAGGGAGGTGCACTAATGC
+>EAS54_73:5:3:233:911
+TGGCTGATTATGAAAACAATGTTCCCCAGATACCA
+>EAS54_73:5:44:498:945
+ATAGGGATGGAGGGAAGAGGGCCGCTGAAGAACTT
+>EAS54_73:5:44:498:945
+CCTATAAGCCGTTCTATTTGTAATGAAAACTATAT
+>EAS54_73:5:53:61:31
+AAGAAACTCATTAATAAAGACATGAGTTCAGATAA
+>EAS54_73:5:53:61:31
+CAATTCAGCAAGAAGATATAACCATCCTACTAAAT
+>EAS54_73:7:134:243:630
+ACATTACTACCCTGCAATTAATATAATTGTGTCCA
+>EAS54_73:7:134:243:630
+TCATCTAGGGGAACAGGGAGGCGCACTAATGAGCT
+>EAS54_73:7:200:65:291
+CAATACTCACCATCATAAATACACACAAAAGTACA
+>EAS54_73:7:200:65:291
+CTAACTATATGCTGTTTACAAGAAACTCATTAATA
+>EAS54_73:7:223:440:667
+AATTGGGGAAAACCTCTTTAGTCTTGCTAGAGATT
+>EAS54_73:7:223:440:667
+TTCAGAACTTGAAGACAAGTCTCTTATGAATTAAC
+>EAS54_73:7:254:572:431
+AAGAGATATAGATTGGCAGAACAGATTTAAAAACA
+>EAS54_73:7:254:572:431
+ATCAGATAAAGCACACTTTAAATCAACAACAGTAA
+>EAS54_73:7:63:854:610
+AATTTGGTGTTCTGTGTAAAGTCTCAGGGAGCCGT
+>EAS54_73:7:63:854:610
+GACTATTGCCAGATGAACCACACATTAATACTATG
+>EAS54_73:7:97:892:419
+AATAAAGTCAAGTCTTTCCTGACAAGCAAATGCTA
+>EAS54_73:7:97:892:419
+GCAACTAGGTAAAAAATTAACATTACAACAGGAAC
+>EAS54_81:2:128:394:455
+GTAATCTCTCTCCTTTTTGCTGCATCCCTGTCTTC
+>EAS54_81:2:128:394:455
+TTAGGGAAGAACAGCTTAGGTATCAATTTGGTGTT
+>EAS54_81:2:27:856:401
+ACCTCTACATGGCTGATTATGAAAACAATGTTCCC
+>EAS54_81:2:27:856:401
+TCATCTAGGGGAACAGGGAGGTGCACTAATGCGCT
+>EAS54_81:2:280:512:316
+GGGAAGAACAGCTTAGGTATCAATTTGGTGTTCTG
+>EAS54_81:2:280:512:316
+TTACTGTCATAACTATGAAGAGACTATTGCCAGCT
+>EAS54_81:2:285:367:932
+ATAGACCCCCTTGCAACAACCTTGAGAACCCCAGG
+>EAS54_81:2:285:367:932
+GCGTAACTGCGCTCTCATTCACTCCAGCTCCCTGT
+>EAS54_81:2:317:72:221
+AAAAAAATTCTAAAATCAGCAAGAGAAAAGCATAC
+>EAS54_81:2:317:72:221
+ATTTGAGGAAGTAATTGGGGAAAACCTCTTTAGTC
+>EAS54_81:2:31:98:804
+CACGAATGCGTCTCTACCACAGGGGGCTGCGCGGC
+>EAS54_81:2:31:98:804
+CTTTACTGTCATAACTATGAAGAGACTATTGCCAG
+>EAS54_81:2:49:330:699
+AAAGTTCAATACTCACCATCATAAATACACACAAA
+>EAS54_81:2:49:330:699
+TTTTGGACTTCTTAAAGAAAAAAAAACCTGTCAAA
+>EAS54_81:2:5:491:391
+CCCTGCTCACAGTTTCTGCCCCCAGCATGGTTGTA
+>EAS54_81:2:5:491:391
+TTGGCATTTGCCTTCAGACCCTACACGAATGCGTC
+>EAS54_81:6:11:801:386
+AAAGGGATTAAATTCCCCCACTTAAGAGATATAGA
+>EAS54_81:6:11:801:386
+CACTATAAATCAACAACAGTAAAATAAAACAAAGG
+>EAS54_81:6:122:589:134
+AAAACCTGTCAAACACGAATGTTATGCCCTGCTAA
+>EAS54_81:6:122:589:134
+ACAGACTTCATCAAGATATGTAGTCATCAGACTAT
+>EAS54_81:6:199:511:426
+AATTCTTCATCCTGGACCCTGAGAGATTCTGCAGC
+>EAS54_81:6:199:511:426
+GGGGTATAATACCTCTACATGGCTGATTATGAAAA
+>EAS54_81:6:204:779:181
+AACAACAGGAAGAAAAGGTCTTTCAAAAGGTGATG
+>EAS54_81:6:204:779:181
+CTTTTGGCATTTGCCTTCAGACCCTACACGAATGC
+>EAS54_81:6:265:251:147
+AAAAGTACAAAACTCACAGGTTTTATAAAACAATT
+>EAS54_81:6:265:251:147
+TGTTATGCCCTGCTAAACTAAGCATCATAAATGAA
+>EAS54_81:6:273:424:207
+AAGAGATATAGATTGGCAGAACAGATTTAAAAACA
+>EAS54_81:6:273:424:207
+TAAATCAACAACAGTAAAATAAAACAAAGGAGGTC
+>EAS54_81:6:35:186:412
+ATAACCATCCTACTAAATACATATGCACCTAACAC
+>EAS54_81:6:35:186:412
+CATGTAACAAATCTGCGCTTGTACTTCTAAATCTA
+>EAS54_81:6:75:917:886
+ACTGGGCAATACATGAGATTATTAGGAAATGCTTT
+>EAS54_81:6:75:917:886
+TTATCATGACTCTATCCCAAATTCCCAATTACGTC
+>EAS54_81:7:124:253:889
+CTAAGCATCATAAATGAAGGGGAAATAAAGTCAAG
+>EAS54_81:7:124:253:889
+TCAGCAAGAGAAAAGCATACAGTCATCTATAAAGG
+>EAS54_81:7:166:979:531
+ATCCCACGCTTCCTATGGAAAGGTTGTTGGGAGAT
+>EAS54_81:7:166:979:531
+TGGTTCTCTTGAAAGCTTGGGCTGTAATGATGCCC
+>EAS54_81:7:226:869:36
+ATATATAAAGGAAATCCCATCAGAATAACAATGGG
+>EAS54_81:7:226:869:36
+TGAGGAAGTAATTGGGGAAAACCTCTTTAGTCTTG
+>EAS54_81:7:246:205:734
+CTCCAGGGAAGTTATCTCTCATCTAGANNNNNTTG
+>EAS54_81:7:246:205:734
+CTGTCTTCCTCTGTCTTGATTTACTTGTTGTTGGT
+>EAS54_81:7:293:355:321
+GCTAGAGTCCCATTTGGAGCCCCTCTAAGCCGTTC
+>EAS54_81:7:293:355:321
+TTACCAAATGTGTTTATTACCAGAGGGATGGAGGG
+>EAS54_81:7:324:472:791
+AAAGCCAATACTTTACTGCTACTCAATATATCCAT
+>EAS54_81:7:324:472:791
+TGATAAAAAGATCAATTCAGCAAGAAGATATAACC
+>EAS54_81:7:325:150:465
+AACAACAGGAAGAAAAGGTCTTTCAAAAGGTGATG
+>EAS54_81:7:325:150:465
+TGATGCCCTCTTCTTCCAAAGATGAAACGCGTAAC
+>EAS54_81:7:74:596:137
+CTCTATCCCAAATTCCCAATTACGTCCTATCTTCT
+>EAS54_81:7:74:596:137
+GGTCCCTGCCCCATCGCTTGTAATCTCTCGCCTTT
+>EAS54_81:8:130:912:658
+TACACACACATGGTTTAGGGGTATAATACCTCTAC
+>EAS54_81:8:130:912:658
+TCCCATCATGAAGCACTGAACTTCCACGTCTCATC
+>EAS54_81:8:142:858:903
+ATGGTTGTACTGGGCAATACATGAGATTATTAGGA
+>EAS54_81:8:142:858:903
+CTATCCCAAATTCCCAATTACGTCCTATCTTCTTC
+>EAS54_81:8:14:360:580
+ACCCTACACGAATGCGTCTCTACCACAGGGGGCGG
+>EAS54_81:8:14:360:580
+ATGAGATTATTAGGAAATGCTTTACTGTCATAACT
+>EAS54_81:8:159:71:155
+AAAGGTTGTTGGGAGATTTTTAATGATTCCTCGAT
+>EAS54_81:8:159:71:155
+GTCCACACTGGTTCTCTTGAAAGCTTGGGCTGTAA
+>EAS54_81:8:177:800:714
+CTAAATGAAAGAGGCTCAAAGAATGCCAGGAAGAT
+>EAS54_81:8:177:800:714
+TTCTCAGCAGAAACCTTACAAGCCAGAAGAGATTG
+>EAS54_81:8:271:180:509
+AATACTCACCATCATAAATACACACAAAAGTACAA
+>EAS54_81:8:271:180:509
+ATATAGATTGGCAGAACAGATTTAAAAACATGAAC
+>EAS54_81:8:40:925:442
+GAGGTTCAGAACTTGAAGACAAGTCTCTTATGAAT
+>EAS54_81:8:40:925:442
+TTTGAGGAAGTAATTGGGGAAAACCTCTTTAGTCT
+>EAS54_81:8:41:530:663
+AGAACAGATTTAAAAACATGAACTAACTATATGCT
+>EAS54_81:8:41:530:663
+ATACTCACCATCATAAATACACACAAAATTACAAA
+>EAS54_81:8:63:930:152
+ACTGGTTCTCTTGAAAGCTTGGGCTGTAATGATTC
+>EAS54_81:8:63:930:152
+ATCCCACGCTTCCTATGGAAAGGTTGTTGGGAGAT
+>EAS54_81:8:78:735:536
+TTTTTTTTTTTTTCATTTCTCTTTTTTTTTTTTTT
+>EAS56_53:1:124:243:35
+GCATATCCAGATTGCTGGTGGTCTGACAGGCAGCA
+>EAS56_53:1:124:243:35
+TGTGTTTATTACCAGAGGGATGGAGGGAAGAGCGA
+>EAS56_53:1:154:118:488
+AAAAGCATACAGTCATCTATAAAGGAAATCCCATC
+>EAS56_53:1:154:118:488
+AAAGTCAAGTCTTTCCTGACAAGCAAATGCTAAGA
+>EAS56_53:1:23:403:981
+TACTGTCATAACTATGAAGAGACTATTGCCAGATG
+>EAS56_53:1:23:403:981
+TCTTCATAGGGAAGAACAGCTTAGGTATCAATTTG
+>EAS56_53:1:47:303:887
+ACATTACTACCCTGCCATTAATATACTTGTGTCCA
+>EAS56_53:1:47:303:887
+CACACTGGTTCTCTTGAAAGCTTGGGCTGTAATGA
+>EAS56_53:1:92:875:345
+AAATGCTCAAAAGAATTGTAAAAGTCAAAATTAAA
+>EAS56_53:1:92:875:345
+CGGAAACCTTACAAGCCAGAAGAGATTGGATCTAA
+>EAS56_53:2:170:265:818
+GAGGGGAAGCTTTCAACGCTTCTAGCACTTTCTTT
+>EAS56_53:2:170:265:818
+TTCTCACAGTTTCTGCCCCCAGCATGGTTGTACTG
+>EAS56_53:2:59:286:290
+AAAGGAAATCCCATCAGAATAACAATGGGCTTCTC
+>EAS56_53:2:59:286:290
+TCAAGTCTTTCCTGACAAGCAAATGCTAAGATAAT
+>EAS56_53:3:101:809:776
+GTACTTCTAAATCTATAAAAAAATTAAAATTTAAC
+>EAS56_53:3:101:809:776
+TATGCACCTAACACAAGACTACCCAGATTCATAAA
+>EAS56_53:3:107:738:484
+GGTCATCATACAATGATAAAAAGATCAATTCAGCA
+>EAS56_53:3:107:738:484
+TGAACTAACTATATGCTGTTTACAAGAAACTCATT
+>EAS56_53:3:126:558:408
+TTCTATTTGTAATGAAAACTATATTTATGCTATTC
+>EAS56_53:3:126:558:408
+TTTATTACCAGAGGGATGGAGGGAAGAGGGACGCT
+>EAS56_53:3:134:126:465
+AAAAAGTGAGAAGTTTGGAAAAACTATTTGAGGAA
+>EAS56_53:3:134:126:465
+AAATCAGCAAGAGAAAAGCATACAGTCATCTATAA
+>EAS56_53:4:130:568:978
+TAAATATAGAAATTGAAACAGCTGTGTTTAGTGAC
+>EAS56_53:4:130:568:978
+TGAAACGCGAAACTGCACTCTCATTCACTCCAGCT
+>EAS56_53:4:153:977:200
+TCATCAACCTCATACACACACATGGTTTAGGGGTA
+>EAS56_53:4:153:977:200
+TGTCACCCAATGGACCTGTGATATCTGGATTCTGG
+>EAS56_53:4:154:762:630
+AGGAAGAAAAGGTCTTTCAAAAGGTGATGTGTGTT
+>EAS56_53:4:154:762:630
+CCTTCAGACCCTACACGAATGCGTCTCTACCACAG
+>EAS56_53:4:168:528:288
+CAGGCTGCAACTGTGAGCCATCACAATGAACAACA
+>EAS56_53:4:168:528:288
+GCTCCCCAGAGGGAAAGCTTTCAACGCTTCTAGCC
+>EAS56_53:4:45:707:147
+AAAAATTCTAAAATCAGCAAGAGAAAAGCATACAG
+>EAS56_53:4:45:707:147
+ATGAGTCACAGGTATTCCTGAGGAAAAAGAAAAAG
+>EAS56_53:6:180:695:621
+ATACAGTCATCTATAAAGGAAATCCCATCAGAATA
+>EAS56_53:6:180:695:621
+TACTGAAAAGCAAATGCTAAGATAATTCATCATCA
+>EAS56_53:7:22:22:934
+ATTTGTCTGAGCAAAACAGTCTAGATGAGAGAGAA
+>EAS56_53:7:22:22:934
+CTGCATCCCTGTCTTCCTCTGTCTTGATTTACTTG
+>EAS56_53:8:122:430:882
+CCTACTAAATACATATGCACCTAACACAAGACTAC
+>EAS56_53:8:122:430:882
+CTATAAAAAAATTAAAATTTAACAAAAGTAAATAA
+>EAS56_53:8:179:549:753
+TACTACCCTGCAATTAATATAATTGTGTCCATGTA
+>EAS56_53:8:179:549:753
+TGTCCTCCCATCTGGCCTCGTCCACACTGGTTCTC
+>EAS56_53:8:28:701:724
+TGGACCCTGAGAGATTCTGCAGCCCAGCTCCAGAT
+>EAS56_53:8:28:701:724
+TTTTGTCAGTTACCAAATGTGTTTATTACCAGAGG
+>EAS56_57:1:122:38:103
+ATAAAACAATTAATTGAGACTACAGAGCAACTAGG
+>EAS56_57:1:122:38:103
+GAGTTCAGGTAAAGGGGTGGAAAAAGATGTTCTAC
+>EAS56_57:1:125:884:276
+TTGCAAGACAGACTTCATCAAGATATGTAGTCATC
+>EAS56_57:1:125:884:276
+TTTGGACTTCTTAAAGAAAAAAAAACCTGTCAAAC
+>EAS56_57:1:189:130:136
+ATTTAGACATCTAAATGAAAGAGGCTCAAAGAATG
+>EAS56_57:1:189:130:136
+GGCTTCTCAGCAGAAACCTTACAAGCCAGAAGAGA
+>EAS56_57:1:189:503:110
+ATTCCTGAGGAAAAAGAAAAAGTGAGAAGTTTGGA
+>EAS56_57:1:189:503:110
+CTAACAATAGACTAAACCAAGCAGAAGAAAGAGTT
+>EAS56_57:1:228:182:717
+GGTCTGACAGGCTGCAACTGTGAGCCATCCCCATG
+>EAS56_57:1:228:182:717
+TCTTACTTCCAGCTCCCCAGAGGGAAAGCTTTCAA
+>EAS56_57:1:278:440:902
+AAGCACTGAACTTCCACGTCTCATCTAGGGGAACA
+>EAS56_57:1:278:440:902
+ATACTATGTTTCTTATCTGCACATTACTACCCTGC
+>EAS56_57:1:288:384:444
+TAACTTTGAATAAAAAGGGATTAAATTCCCCCACT
+>EAS56_57:1:288:384:444
+TCAAAAGAATTGTAAAAGTCAAAATTAAAGTTCAA
+>EAS56_57:2:158:909:321
+ATACAGTCATCTATAAAGGAAATCCCATCAGAATA
+>EAS56_57:2:158:909:321
+TTTGAGGAAGTAATTGGGGAAAACCTCTTTAGTCT
+>EAS56_57:2:178:192:499
+GTGAGCCATCACAATGAACAACAGGAAGAAAAGGT
+>EAS56_57:2:178:192:499
+TCTAGCCATTTCTTTTGGCATTTGCCTTCAGACCC
+>EAS56_57:2:206:873:186
+ACAATAGACTAAACCAAGCAGAAGAAAGAGGTTCA
+>EAS56_57:2:206:873:186
+GTATTCCTGAGGAAAAAGAAAAAGTGAGAAGTTTG
+>EAS56_57:2:236:841:20
+AAAGGAAATCCCATCAGAATAACAATGGGCTTCTC
+>EAS56_57:2:236:841:20
+GCTAAGATAATTCATCATCACTAAACCAGTCCTAT
+>EAS56_57:2:237:855:581
+CTAAACGCCCATACTTTACTGCTACTCAATATATC
+>EAS56_57:2:237:855:581
+TACAATGATAAAAAGATCAATTCAGCAAGAAGATA
+>EAS56_57:2:23:268:529
+TGAAAGAGGCTCAAAGAATGCCAGGAAGATACATT
+>EAS56_57:2:259:42:969
+GCTGTAATGATGCCCCTTGGCCATCACCCGGTCCC
+>EAS56_57:2:259:42:969
+GGAAAGGTTGTTGGGAGATTTTTAATGATTCCTCA
+>EAS56_57:2:262:297:601
+TGGACCTGTGATATCTGGATTCTGGGAAATTCTTC
+>EAS56_57:2:262:297:601
+TGTTCTCATCAACCTCATACACACACATGGTTTAG
+>EAS56_57:2:284:597:682
+AAAAAAAAACCTGTCAAACACGAATGTTATGCCCT
+>EAS56_57:2:284:597:682
+TTCATCAAGATATGTAGTCATCAGACTATCTAAAG
+>EAS56_57:2:44:153:969
+AAAAAGTGAGAAGTTTGGAAAAACTATTTGAGGAA
+>EAS56_57:2:44:153:969
+AAAAGCATACAGTCATCTATAAAGGAAATCCCATC
+>EAS56_57:3:112:729:591
+ATTGGGGAAAACCTCTTTAGTCTTGCTAGAGATTT
+>EAS56_57:3:112:729:591
+GAAGAAAGAGGTTCAGAACTTGAAGACAAGTCTCT
+>EAS56_57:3:119:761:239
+CGTCTCTACCACAGGGGGCTGCGCGGTTTCCCATC
+>EAS56_57:3:119:761:239
+TGAAGAGACTATTGCCAGATGAACCACACATTAAT
+>EAS56_57:3:285:489:327
+AATAGACTAAACCAAGCAGAAGAAAGAGGTTCAGA
+>EAS56_57:3:285:489:327
+CTGAGGAAAAAGAAAAAGTGAGAAGTTTGGAAAAA
+>EAS56_57:3:319:174:811
+CACTGGTTCTCTTGAAAGCTTGGGCTGTAATGATG
+>EAS56_57:3:319:174:811
+TTATCTGCACATTTCTACCCTGCAATTAATATAAT
+>EAS56_57:3:41:739:907
+CAGAAGAGATTGGATCTAATTTTTGGACTTCTTAA
+>EAS56_57:3:41:739:907
+GAATGCCAGGAAGATACATTGCAAGACAGACTTCA
+>EAS56_57:3:81:786:340
+TACTATGTTTCTTATCTGCACATTACTACCCTGCA
+>EAS56_57:3:81:786:340
+TCCACGTCTCATCTAGGGGAACAGAGAGGTGCACT
+>EAS56_57:4:233:478:792
+GCCTTCAGACCCTACACGAATGCGTCTCTACCACA
+>EAS56_57:4:233:478:792
+GTGTTCTCATCAACCTCATACACACACATGGTTTA
+>EAS56_57:4:262:965:756
+AGGGAGGTGCACTAATGCGCTCCACGCCCAAGCCC
+>EAS56_57:4:262:965:756
+TTAATATAATTGTGTCCATGTACACACGCTGTCCT
+>EAS56_57:4:71:707:568
+CTGCATCCCTGTCTTCCTCTGTCTTGATTTACTTG
+>EAS56_57:4:71:707:568
+GTCTAGATGAGAGAGAACTTCCCTGGAGGTCTGAT
+>EAS56_57:4:98:862:154
+AAAGATCAATTCAGCAAGAAGATATAACCATCCTA
+>EAS56_57:4:98:862:154
+TGCTACTCAATATATCCATGTAACAAATCTGCGCT
+>EAS56_57:5:105:521:563
+TATGTACTTATCATGACTCTATCCCAAATTCCCAA
+>EAS56_57:5:105:521:563
+TGTAATGCTGCCCCTTGGCCATCCCCCGGTCCCTG
+>EAS56_57:5:136:389:320
+TCCTATGTACTTATCATGACTCTATCCCAAATTCC
+>EAS56_57:5:136:389:320
+TTCTGCCCCCAGCATGGTTGTACTGGGCAATACAT
+>EAS56_57:5:145:383:182
+AAACCTCTTTAGTCTTGCTAGAGATTTAGACATCT
+>EAS56_57:5:145:383:182
+TTGAAGACAAGTCTCTTATGAATTAACCCAGTCAG
+>EAS56_57:5:207:926:427
+GGGAAGAACAGCTTAGGTATCAATTTGGTGTTCTG
+>EAS56_57:5:207:926:427
+TAGGAAATGCTTTACTGTCATAACTATGAAGAGAC
+>EAS56_57:5:214:644:390
+AAAAACATGAACTAACTATATGCTGTTTACAAGAA
+>EAS56_57:5:214:644:390
+AAATAAAACAAAGGAGGTCATGATACAATGATAAA
+>EAS56_57:5:24:284:360
+AGTCATCAGACTATCTAAAGTCAACATGAAGGAAA
+>EAS56_57:5:24:284:360
+CTGTCAAACACGAATGTTATGCCCTGCTAAACTAA
+>EAS56_57:5:266:133:789
+AAAAAATTAACATTACAACAGGAACAAAACCTCAT
+>EAS56_57:5:266:133:789
+GTGGAAAAAGATGTTCTACGCAAACAGAAACCAAA
+>EAS56_57:5:303:542:924
+AATAAAACAAAGGAGGTCATCATACAATGATAAAA
+>EAS56_57:5:303:542:924
+CAATGTACAATATTCTGATGATGGTTACACTAAAA
+>EAS56_57:5:309:109:987
+AACAAATACTACTAGACCTAAGAGGGATGAGAAAT
+>EAS56_57:5:309:109:987
+GAGAGAAGGAGTAGCTATACTTATATCAGATAAAG
+>EAS56_57:5:30:788:376
+ACGTCTCATCTAGGGGAACAGGGAGGTGCACTAAT
+>EAS56_57:5:30:788:376
+TGTTTCTTATCTGCACATTACTACCCTGCAATTAA
+>EAS56_57:5:324:728:956
+ATTTGTCAATGTCAGGGAAGGAGCATTTTGTCAGT
+>EAS56_57:5:324:728:956
+TGCTGGCAAGCTAGAGTCCCATTTGGAGCCCCTCT
+>EAS56_57:5:53:544:889
+AGGCTCAAAGAATGCCAGGAAGATACATTGCAAGA
+>EAS56_57:5:53:544:889
+GCTTCTCAGCGGAAACCTTACAAGCCAGAAGAGAT
+>EAS56_57:5:71:994:576
+AAGATAATTCATCATCACTAAACCAGTCCTATAAG
+>EAS56_57:5:71:994:576
+TAGGTAAAAAATTAACATTACAACAGGAACAAAAC
+>EAS56_57:6:145:144:796
+ATTTGGTGTTCTGTGTAAAGTCTCAGGGAGCCGTC
+>EAS56_57:6:145:144:796
+GGTTTTCTGTTTCTTTGTTTGATTTGGTGGAAGAC
+>EAS56_57:6:157:643:175
+GGGATGGAGGGAAGAGGGACGCTGAAGAACTTTGA
+>EAS56_57:6:157:643:175
+TTCTATTTGTAATGAAAACTATATTTATGCTATTC
+>EAS56_57:6:175:289:351
+CATCCTACTAAATACATATGCACCTAACACAAGAC
+>EAS56_57:6:175:289:351
+TGCGCTTGTACTTCTAAATCTATAAAAAAATTAAA
+>EAS56_57:6:190:289:82
+AGGGGTGCAGAGCCGAGTCACGGGGTTGCCAGCAC
+>EAS56_57:6:190:289:82
+CTCAAGGTTGTTGCAAGGGGGTCTATGTGAACAAA
+>EAS56_57:6:21:553:57
+AAATACTACTAGACCTAAGAGGGATGAGAAATTAC
+>EAS56_57:6:21:553:57
+AACAAAAGTAAATAAAACACATAGCTAAAACTAAA
+>EAS56_57:6:234:787:12
+AAGCTTGGGCTGTAATGATGCCCCTTGGCCATCAC
+>EAS56_57:6:234:787:12
+ACACGCTGGCCTATGTACTTATAATGACTCTATCC
+>EAS56_57:6:325:759:288
+GCTGCTGGCAAGCTAGAGTCCCATTTGGAGCCCCT
+>EAS56_57:6:325:759:288
+GGAGCATTTTGTCAGTTACCAAATGTGTTTATTAC
+>EAS56_57:6:44:280:641
+AACCCCCTTGCAACAACCTTGAGAACCCCAGGGAA
+>EAS56_57:6:44:280:641
+TCATTCACTCCAGCTCCCTGTCACCCAATGGACCT
+>EAS56_57:6:4:223:776
+AGTAACTGAACCTATGAGTCACAGGTATTCCTGAG
+>EAS56_57:6:4:223:776
+TGTAGTCATCAGACTATCTAAAGTCAACATGAAGG
+>EAS56_57:7:159:125:297
+GCAAGCTAGAGTCCCATTTGGAGCCACTCTAAGAC
+>EAS56_57:7:159:125:297
+GGAAGGAGCATTTTGTCAGTTACCAAATGTGTTTA
+>EAS56_57:7:247:522:670
+CTATCCCAAATTCCCAATTACGTCCTATCTTCTTC
+>EAS56_57:7:247:522:670
+TACATGAGATTATTAGGAAATGCTTTACTGTCATA
+>EAS56_57:7:273:562:954
+AAAGTTCAATACTCACCATCATAAATACACACAAA
+>EAS56_57:7:273:562:954
+TTTTTGGACTTCTTAAAGAAAAAAAAACCTGTCAA
+>EAS56_57:7:287:258:321
+TAATACTATGTTTCTTATCTGCACATTACTACCCT
+>EAS56_57:7:287:258:321
+TGTAAAGTCTCAGGGAGCCGTCCGTGTCCTCCCAT
+>EAS56_57:7:33:954:724
+CCTAAGAGGGATGAGAAATTACCTAATTGGTACAA
+>EAS56_57:7:33:954:724
+TCAGATAAAGCACACTTTAAATCAACAACAGTAAA
+>EAS56_57:7:57:826:977
+ATTGGATCTAATTTTTGGACTTCTTAAAGAAAAAA
+>EAS56_57:7:57:826:977
+TGCTCAAAAGAATTGTAAAAGTCAAAATTAAAGTT
+>EAS56_57:7:76:786:458
+GGAGCATTTTGTCAGTTACCAAATGTGTTTATTAC
+>EAS56_57:7:76:786:458
+TCTGGGAAATTCTTCATCCTGGACCCTGAGAGATT
+>EAS56_57:8:72:44:435
+AAAAGCAAAAACAAAAACTATGCTAAGTATTGGTA
+>EAS56_57:8:72:44:435
+ATTGGTACAATGTACAATATTCTGATGATGGTTAA
+>EAS56_59:1:126:526:276
+GAACTTCTGTAATTGAAAAATTCATTTAAGAAATT
+>EAS56_59:1:128:584:952
+ATCATACAATGATAAAAAGATCAATTCAGCAAGAA
+>EAS56_59:1:128:584:952
+GCCCATACTTTACTGCTACTCAATATATCCATGTA
+>EAS56_59:1:219:294:861
+CTGGTTCTCTTGAAAGCTTGGGCTGTAATGATGCC
+>EAS56_59:1:219:294:861
+TATAATTGTGTCCATGTACACACGCTGTCCTCTGT
+>EAS56_59:1:248:122:558
+AATGTACAATATTCTGATGATGGTTACACTAAAAG
+>EAS56_59:1:248:122:558
+GGAAAAAAGTAAACTCTCAAATATTGCTAGTGGGA
+>EAS56_59:1:278:906:933
+AATATAATTGTGTCCATGTACACACGCTGTCCTAT
+>EAS56_59:1:278:906:933
+TTCTCACAGTTTCTGCCCCCAGCATGGTTGTACTG
+>EAS56_59:1:82:670:302
+AGTTCAGGTAAAGGGGTGGAAAAAGATGTTCTACG
+>EAS56_59:1:82:670:302
+TCCTACTAAATACATATGCACCTAACACAAGACTA
+>EAS56_59:1:93:490:901
+AGAAAAGCATACAGTCATCTATAAAGGAAATCCCA
+>EAS56_59:1:93:490:901
+GTAATTGGGGAAAACCTCTTTAGTCTTGCTAGAGA
+>EAS56_59:2:104:402:732
+AAATCAGCAAGAGAAAAGCATACAGTCATCTATAA
+>EAS56_59:2:104:402:732
+AATGAAGGGGAAATAAAGTCAAGTCTTTCCTGACA
+>EAS56_59:2:162:272:415
+ACATGAACTAACTATATGCTGTTTACAAGAAACTC
+>EAS56_59:2:162:272:415
+ATAAAAAGATCAATTCAGCAAGAAGATATAACCAT
+>EAS56_59:2:177:266:842
+ACAACAGGAAGAAAAGGTCTTTCAAAAGGTGATGT
+>EAS56_59:2:177:266:842
+GGCATTTGCCTTCAGACCCTACACGAATGCGTCTC
+>EAS56_59:2:177:552:234
+ACGCTGTCCTATGTACTTATCATGACTCTATCCCA
+>EAS56_59:2:177:552:234
+GCTCCACGCCCAAGCCCTTCTCACAGTTTCTGCCC
+>EAS56_59:2:201:768:529
+AGGTATTCCTGAGGAAAAAGAAAAAGTGAGAAGTT
+>EAS56_59:2:201:768:529
+CAGACTATCTAAAGTCAACATGAAGGAAAAAAATT
+>EAS56_59:2:239:1001:406
+AGCATACAGTCATCTATAAAGGAAATCCCATCAGA
+>EAS56_59:2:239:1001:406
+CTTTCCTGACAAGCAAATGCTAAGATAATTCATCA
+>EAS56_59:2:60:677:921
+CATCAGACTATCTAAAGTCAACATGAAGGAAAAAA
+>EAS56_59:2:60:677:921
+GTGAGAAGTTTGGAAAAACTATTTGAGGAAGTAAT
+>EAS56_59:3:149:953:349
+AGCCCTTCTCACAGTTTCTGCCCCCAGCATGGTTG
+>EAS56_59:3:149:953:349
+TTCTTTTGGCATTTGCCTTCAGACCCTACACGAAT
+>EAS56_59:3:166:626:836
+AGTACAAAACTCACAGGTTTTATAAAACAATTAAT
+>EAS56_59:3:166:626:836
+CTGTCAAACACGAATGTTATGCCCTGCTAAACTAA
+>EAS56_59:3:182:1002:639
+AAAAGTGAGAAGTTTGGAAAAACTATTTGAGGAAG
+>EAS56_59:3:182:1002:639
+AACCAAGCAGAAGAAAGAGGTTCAGAACTTGAAGA
+>EAS56_59:3:316:25:230
+GATGCCCCTTGGCCATCACCCGGTCCCTGCCCCAT
+>EAS56_59:3:316:25:230
+TGTCCTATGTACTTATCATGACTCTATCCCAAATT
+>EAS56_59:4:119:651:88
+GATTGGATCTAATTTTTGGACTTCTTAAAGAAAAA
+>EAS56_59:4:119:651:88
+GCTCAAAGAATGCCAGGAAGATACATTGCAAGACA
+>EAS56_59:4:262:928:237
+TGAGTTCAGGTAAAGGTGTGGAAAAAGATGTTCTA
+>EAS56_59:4:262:928:237
+TTGAGACTACAGAGCAACTAGGTAAAAAATTAACA
+>EAS56_59:4:267:394:437
+AAACATCATAAATACACACAAAAGTACAAAACTCA
+>EAS56_59:4:267:394:437
+GGACTTCTTAAAGAAAAAAAAACCTGTCAAACACG
+>EAS56_59:4:278:524:521
+CACATTAATACTATGTTTCTTATCTGCACATTACT
+>EAS56_59:4:278:524:521
+CCCATCTGGCCTCGTCCACACTGGTTCTCTTGAAA
+>EAS56_59:4:329:577:757
+AACGCGTAACTGCGCTCTCATTCACTCCAGCTCCC
+>EAS56_59:4:329:577:757
+TCAAGGTTGTTGCAAGGGGGTCTATGTGAACAAAG
+>EAS56_59:5:113:694:725
+CTGTAATGATGCCCCTTGGCCATCACCCGGTCCCT
+>EAS56_59:5:113:694:725
+GTACACACGCTGTCCTATGTACTTATCATGACTCT
+>EAS56_59:5:125:137:58
+AACTATATGCTGTTTACAAGAAACTCATTAATAAA
+>EAS56_59:5:125:137:58
+GGTTTTATAAAACAATTAATTGAGACTACAGAGCA
+>EAS56_59:5:181:713:140
+AGGGGAAATAAAGTCAAGTATTTCCTGACAAGCAA
+>EAS56_59:5:181:713:140
+CTACAGAGCAACAAGGTAAAAAATTAACATTACAA
+>EAS56_59:5:198:929:684
+AAAGTCAAGTCTTTCCTGACAAGCAAATGCTAAGA
+>EAS56_59:5:198:929:684
+GAAATCCCATCAGAATAACAATGGGCTTCTCAGCA
+>EAS56_59:5:232:336:46
+ATTTTTTTTTTTTCTTTTCTCTTGTTTCTTTTTTT
+>EAS56_59:5:325:544:349
+AAAATTAAAGTTCAATACTCACCATCATAAATACA
+>EAS56_59:5:325:544:349
+CAAGCCAGAAGAGATTGGATCTAATTTTTGGACTT
+>EAS56_59:5:90:629:652
+AGCCCATACTTTACTGCTACTCAATATATCCATGT
+>EAS56_59:5:90:629:652
+ATATTGCTAGTGGGAGTATAAATTGTTTTCCACTT
+>EAS56_59:6:187:925:547
+GGCTGATTATGAAAACAATGTTCCCAAGATACCAT
+>EAS56_59:6:187:925:547
+TGAACTTCCACGTCTCATCTAGGGGAACAGGGAGG
+>EAS56_59:6:199:327:965
+ATCTGGATTCTGGGAAATTCTTCATCCTGGACCCT
+>EAS56_59:6:199:327:965
+NCAACAACCTTGAGAACCCCAGGGAATTTGTCAAT
+>EAS56_59:6:227:657:95
+GTAATTGGGGAAAACCTCTTTAGTCTTGCTAGAGA
+>EAS56_59:6:227:657:95
+GTCATCTATAAAGGAAATCCCATCAGAATAACAAT
+>EAS56_59:6:286:753:854
+TCACCCAGTCCCTGCCCCATCTCTTGTAATCTCTC
+>EAS56_59:6:286:753:854
+TTATCATGACTCTATCCCAAATTCCCAATTACGTC
+>EAS56_59:6:312:837:406
+AGGTGCACTAATGCGCTCCACGCCCAAGCCCTTCT
+>EAS56_59:6:312:837:406
+CTGCACATTACTACCCTGCAATTAATATAATTGTG
+>EAS56_59:6:3:186:68
+AAGAAATGCTCAAAAGAATTGTAAAAGTCAAAATT
+>EAS56_59:6:3:186:68
+TTACAAGCCAGAAGAGATTGGATCTAATTTTTGTA
+>EAS56_59:6:89:457:591
+ATGCCCTGCTAAACTAAGCATCATAAATGAAGGGG
+>EAS56_59:6:89:457:591
+CAGGTTTTATAAAACAATTAATTGAGACTACATAG
+>EAS56_59:7:260:985:520
+TCCCTGTCACCCAATGGACCTGTGATATCTGGATT
+>EAS56_59:7:260:985:520
+TGCAACAACCTTGAGAACCCCAGGGAATTTGTCAA
+>EAS56_59:7:318:679:883
+GATTTAGACATCTAAATGAAAGAGGCTCAAAGAAT
+>EAS56_59:7:319:246:304
+CTTGAGAACCCCAGGGAATTTGTCAATGTCAGGGA
+>EAS56_59:7:319:246:304
+TGTCACCCAATGGACCTGTGATATCTGGATTCTGG
+>EAS56_59:7:82:902:868
+CTGTCACCCAATGGACCTGTGATATCTGGATTCTG
+>EAS56_59:7:82:902:868
+TTGCAACAACCTTGAGAACCCCAGGGAATTTGTCA
+>EAS56_59:8:49:182:192
+ACACAAAAGTACAAAACTCACAGGTTTTATAAAAC
+>EAS56_59:8:49:182:192
+GTTATGCCCTGCTAAACTGAGCATCATAAATGAAG
+>EAS56_59:8:80:542:549
+AGTAAACTCTCAAATATTGCTAGTGGGAGTATAAA
+>EAS56_59:8:80:542:549
+CTAAAAGCCCATACTTTACTGCTACTCAATATATC
+>EAS56_61:1:119:880:781
+ACAAATCTGCGCTTGTACTTCTAAATCTATAACAA
+>EAS56_61:1:119:880:781
+ACATATGCACCTAACACAAGACTACCCAGATTCAT
+>EAS56_61:1:210:880:606
+GGAGCATTTTGTCAGTTACCAAATGTGTTTATTAT
+>EAS56_61:1:210:880:606
+TCCTGGACCCTGAGAGATTCTGCAGCCCAGCTCCA
+>EAS56_61:1:303:184:14
+CAACCTTGAGAACCCCAGGGAATTTGTCAATGTCA
+>EAS56_61:1:303:184:14
+CAATGGACCTGTGATATCTGGATTCTGGGAAATTC
+>EAS56_61:2:152:860:286
+AGACTATTGCCAGATGAACCACACATTAATACTAT
+>EAS56_61:2:152:860:286
+TTAGGTATCAATTTGGTGTTCTGTGTAAAGTCTCA
+>EAS56_61:3:140:522:212
+CGCTGAAGAACTTTGATGCCCTCTTCTTCCAAAGA
+>EAS56_61:3:140:522:212
+GACAGGCTGCAACTGTGAGCCATCACAATGAACAA
+>EAS56_61:3:165:665:220
+ACAATTAATTGAGACTACAGAGCAACTAGGTAAAA
+>EAS56_61:3:165:665:220
+GGAAATAAAGTCAAGTCTTTCCTGACAAGCAAATG
+>EAS56_61:3:208:118:673
+AAGAGGCTCAAAGAATGCCAGGAAGATACATTGCA
+>EAS56_61:3:208:118:673
+GAACAGAGCTTTCAAGAAGTATGAGATTATGTAAA
+>EAS56_61:3:260:827:289
+AAACCTCATATATCAATATTAACTTTGAATAAAAA
+>EAS56_61:3:260:827:289
+TGTTCTACGCAAACAGAAACCAAATGAGAGAAGGA
+>EAS56_61:3:45:758:616
+ATAAATTGTTTTCCACTTTGGAAAACAATTTGGTA
+>EAS56_61:3:45:758:616
+CATACTTTACTGCTACTCAATATATCCATGTAACA
+>EAS56_61:3:5:45:441
+TTTTTTTTCTTTTCTCTTTTTTTTTTTTTTTTTTT
+>EAS56_61:4:262:456:74
+TACCAAATGTGTTTATTACCAGAGGGATGGAGGGA
+>EAS56_61:4:262:456:74
+TGGGAAATTCTTCATCCTGGACCCTGAGAGATTCT
+>EAS56_61:5:194:470:416
+AAACTATTTGAGGAAGTAATTGGGGAAAACCTCTT
+>EAS56_61:5:194:470:416
+TCAGAACTTGAAGACAAGTCTCTTATGAATTAACC
+>EAS56_61:5:209:824:866
+ATCATCACTAAACCAGTCCTATAAGAAATGCTCAA
+>EAS56_61:5:209:824:866
+CAGCAACAAAACCTCATATATCAATATTAACTTTG
+>EAS56_61:5:263:314:696
+AACTCATTAATAAAGACATGAGTTCAGGTAAAGGG
+>EAS56_61:5:263:314:696
+AAGATCAATTCAGCAAGAAGATATAACCATCCTAC
+>EAS56_61:5:272:240:950
+CAGCAGAGCTTGGATCTAATTTTTGGACTTCTTCA
+>EAS56_61:5:272:240:950
+TCAAAAGAATTGTAAAAGTCAAAATTAAAGTTCAA
+>EAS56_61:6:10:106:737
+ACAAGAAACTCATTAATAAAGACATGAGTTCAGGT
+>EAS56_61:6:10:106:737
+ACAATGATAAAAAGATCAATTCAGCAAGAAGATAT
+>EAS56_61:6:160:272:398
+AATGTTCCCCAGATACCATCCCTGTCTTACTTCCA
+>EAS56_61:6:160:272:398
+GTGCACTAATGCGCTCCACGCCCAAGCCCTTCTCA
+>EAS56_61:6:226:370:91
+AGAATAACAATGGGCTTCTCAGCGGAAACCTTACA
+>EAS56_61:6:226:370:91
+AGGCTCAAAGAATGCCAGGAAGATACATTGCAAGA
+>EAS56_61:6:227:259:597
+AATATAGAAATTGAAACAGCTGTGTTTAGTGCCTT
+>EAS56_61:6:256:67:461
+TCATGTTTGTGTCTTTCTATGCATTTTTTTTTTTT
+>EAS56_61:6:256:67:461
+TTGTTTTTTCTTCTTTTCTCTTTTTTTTTTTTTTT
+>EAS56_61:6:283:963:234
+AAAAAGATGTTCTACGCAAACAGAAACCAAATGAG
+>EAS56_61:6:283:963:234
+ACATATGCACCTAACACAAGACTACCCAGATTCAT
+>EAS56_61:6:307:208:477
+AAAGTCAAAATTAAAGTTCAATACTCACCATCATA
+>EAS56_61:6:307:208:477
+ACTTCTTAAAGAAAAAAAAACCTGTCAAACACGAA
+>EAS56_61:7:280:133:495
+AGATGAACCACACATTAATACTATGTTTCTTATCT
+>EAS56_61:7:280:133:495
+CCATCATGAAGCACTGAACTTCCACGTCTCATCTA
+>EAS56_61:7:41:745:603
+CATTGCAAGACAGACTTCATCAAGATATGTAGTCA
+>EAS56_61:7:41:745:603
+TAATTTTTGGACTTCTTAAAGAAAAAAAAACCTGT
+>EAS56_61:7:7:682:201
+CATACAGTCATCTATAAAGGAAATCCCATCAGAAT
+>EAS56_61:7:7:682:201
+GGAAAACCTCTTTAGTCTTGCTAGAGATTTAGACA
+>EAS56_61:8:60:358:494
+GGTAAAGGGGTGGAAAAAGATGTTCTACGCAAACA
+>EAS56_61:8:60:358:494
+TACCCAGATTCATAAAACAAATACTACTAGACCTA
+>EAS56_61:8:7:171:402
+GTGATATCTGGATTCTGGGAAATTCTTCATCCTGG
+>EAS56_61:8:7:171:402
+TCTACATGGCTGATTATGAAAACAATGTTCCCCAG
+>EAS56_63:1:119:446:185
+TGGTCTGACAGGCTGCAACTGTGAGCCATCACAAT
+>EAS56_63:1:119:446:185
+TTACCAGAGGGATGGAGGGAAGAGGGACGCTGAAG
+>EAS56_63:1:145:71:26
+CTAGGGGAACAGGGAGGTGCACTAATGCGCTCCAC
+>EAS56_63:1:145:71:26
+TTTCTTATCTGCACATTACTACCCTGCAATTAATA
+>EAS56_63:2:119:161:322
+ATCAGAATAACAATGGGCTTCTCAGCAGAAACCTT
+>EAS56_63:2:119:161:322
+CTTTAGTCTTGCTAGAGATTTAGACATCTAAATGA
+>EAS56_63:2:33:357:858
+AAAATTAAAGTTCAATACTCACCATCATAAATACA
+>EAS56_63:2:33:357:858
+AGGGATTAAATTCCCCCACTTAAGAGATATAGATT
+>EAS56_63:2:74:656:272
+AACAAAGGAGGTCATCATACAATGATAAAAAGATC
+>EAS56_63:2:74:656:272
+TGTACAATATTCTGATGATGGTTACACTAAAAGCC
+>EAS56_63:3:40:594:752
+ATACACACACATGGTTTAGGGGTATAATACCTCTA
+>EAS56_63:3:40:594:752
+CTGCGCGGTTTCCCATCATGAAGCACTGAACTTCC
+>EAS56_63:3:41:468:459
+AAATTTAACAAAAGTAAATAAAACACATAGCTAAA
+>EAS56_63:3:41:468:459
+TTTTTTTTTTTTTTTTTTTCTTTTTTTTTTTTTTT
+>EAS56_63:3:93:1002:845
+AATTCCCAATTACGTCCTATCTTCTTCTTAGGGAA
+>EAS56_63:3:93:1002:845
+GGGCAATACATGAGATTATTAGGAAATGCTTTACT
+>EAS56_63:4:141:9:811
+TTTCTTTTCTCCTTTTTTTTTTTTTTTTTCTACAT
+>EAS56_63:4:184:659:377
+AAAAAGATGTTCTACGCAAACAGAAACCAAATGAG
+>EAS56_63:4:184:659:377
+CAAAACTACCCAGATTCATAAAACAAATACTACTA
+>EAS56_63:4:38:28:122
+AAATATAGTTGAAAGCTCTAACAATAGACTAAACC
+>EAS56_63:4:38:28:122
+GTATTCCTGAGGAAAAAGAAAAAGTGAGAAGTTTG
+>EAS56_63:5:117:570:971
+ACAGGTATTCCTGAGGAAAAAGAAAAAGTGAGAAG
+>EAS56_63:5:117:570:971
+ACATGAAGGAAAAAAATTCTAAAATCAGCAAGAGA
+>EAS56_63:5:123:998:248
+ATCACAATGAACAACAGGAAGAAAAGGTCTTTCAA
+>EAS56_63:5:123:998:248
+TTTCTTTTGGCATTTGCCTTCAGACCCTACACGAA
+>EAS56_63:5:36:678:316
+ATTTGTCTGAGCAAAACAGTCTAGATGAGAGAGAA
+>EAS56_63:5:36:678:316
+TTTGCTGCATCCCTGTCTTCCTCTGTCTTGATTTA
+>EAS56_63:5:96:788:614
+TAGGGGTATAATACCTCTACATGGCTGATTATGAA
+>EAS56_63:5:96:788:614
+TTCCACGTCTCATCTAGGGGAACAGGGAGGTGCAC
+>EAS56_63:6:102:816:260
+AAATTACCTAATTGGTACAATGTACAATATTCTGA
+>EAS56_63:6:102:816:260
+TCAGATAAAGCACACTTTAAATCAACAACAGTAAA
+>EAS56_63:6:42:920:522
+AATTAATATAATTGTGTCCATGTACACACGCTGTT
+>EAS56_63:6:42:920:522
+CTGGTTCTCTTGAAAGCTTGGGCTGTAATGATGCC
+>EAS56_63:6:91:360:585
+AAGATGAAACGCGTAACTGCGCTCTCATTCACTCC
+>EAS56_63:6:91:360:585
+GACATCACAATGAACAACAGGAAGAAAAGGTCTTT
+>EAS56_63:7:109:22:383
+ATGTACAATATTCTGATGATGGTTACACTAAAAGC
+>EAS56_63:7:109:22:383
+CAACAACAGTAAAATAAAACAAAGGAGGTCATCAT
+>EAS56_63:7:137:139:248
+GTCAAACACGAATGTTATGCCCTGCTAAACTAAGC
+>EAS56_63:7:137:139:248
+TATCTAAAGTCAACATGAAGGAAAAAAATTCTAAA
+>EAS56_63:7:166:42:147
+AATGCGCTCCACGCCCAAGCCCTTCTAACAGTTTC
+>EAS56_63:7:166:42:147
+CTGCACATTACTACCCTGCAATTAATATAATTGTG
+>EAS56_63:7:185:213:330
+CAATGTCAGGGAAGGAGCATTTTGTCAGTTACCAA
+>EAS56_63:7:185:213:330
+TCTGGGAAATTCTTCATCCTGGACCCTGAGAGATT
+>EAS56_63:7:190:95:706
+TTCTCACAGTTTCTGCCCCCAGCATGGTTGTACTG
+>EAS56_63:7:190:95:706
+TTGTGTCCATGTACACACGCTGTCCTATGTACTTA
+>EAS56_63:7:34:334:825
+CATTTAAGAAATTACAAAATATAGTTGAAAGCTCT
+>EAS56_63:8:138:186:459
+CATTGCAAGACAGACTTCATCAAGATATGTAGTCA
+>EAS56_63:8:138:186:459
+GCCAGAAGAGATTGGAGCTAATTTTTGGACTTCTT
+>EAS56_63:8:150:508:757
+ATCCCTGTCTTCCTCTGTCTTGATTTACTTGTTGT
+>EAS56_63:8:150:508:757
+CTTGACACCCAACTAATATTTGTCTGAGCAAAACA
+>EAS56_63:8:4:571:820
+AAGAGATATAGATTGGCAGAACAGATTTAAAAACA
+>EAS56_63:8:4:571:820
+CAACAACAGTAAAATAAAACAAAGGAGGTCATCAT
+>EAS56_63:8:62:125:888
+CGGAAACCTTACAAGCCAGAAGAGATTGGATCTAA
+>EAS56_63:8:62:125:888
+TGCCAGGAAGATACATTGCAAGACAGACTTCATCA
+>EAS56_65:1:163:846:223
+CCAGCTCCCTGTCACCCAATGGACCTGTGATATCT
+>EAS56_65:1:163:846:223
+GCCTTTGTTCACATAGACCCCCTTGCAACAACCTT
+>EAS56_65:1:178:305:843
+ATGTTTCTTATCTGCACATTACTACCCTGCAATTA
+>EAS56_65:1:178:305:843
+CCACGTCTCATCTAGGGGAACAGGGAGGTGCACTA
+>EAS56_65:1:23:536:229
+AAAGCATACAGTCATCTATAAAGGAAATCCCATCA
+>EAS56_65:1:23:536:229
+AAGGGGAAATAAAGTCAAGTCTTTCCTGACAAGCA
+>EAS56_65:1:53:272:944
+CAACCCCCTTGCAACAACCTTGCGAACCCCAGGGA
+>EAS56_65:1:53:272:944
+TGCGCTCTCATTCACTCCAGCTCCCTGTCACCCAA
+>EAS56_65:2:224:579:433
+ATAACAATGGGCTTCTCAGCAGAAACCTTACAAGC
+>EAS56_65:2:224:579:433
+TTCATCATCACTAAACCAGTCCTATAAGAAATGCT
+>EAS56_65:2:56:155:49
+ATCCTACTAAATACATATGCACCTAACACAAGACT
+>EAS56_65:2:56:155:49
+ATGAGTTCAGGTAAAGGGGTGGAAAAAGATGTTCT
+>EAS56_65:3:168:741:680
+AGGGACGCTGAAGAACTTTGATGCCCTCTTCTTCC
+>EAS56_65:3:168:741:680
+TGGTCTGACAGGCTGCAACTGTGAGCCATCACAAT
+>EAS56_65:3:47:64:359
+TTTTTTTTTTTCTCTCCTCTTTTTTTTTTTTTTTT
+>EAS56_65:4:124:367:72
+AGACTACCCAGATTCATAAAACAAATACTACTAGA
+>EAS56_65:4:124:367:72
+CATAGCTAAAACTAAAAAAGCAAAAACAAAAACTA
+>EAS56_65:4:126:966:514
+AGAAGAAGTAGCTATACTTATATCAGATAAAGCAC
+>EAS56_65:4:126:966:514
+TAAAAAGGGATTAAATTCCCCCACTTAAGAGATAT
+>EAS56_65:4:150:94:843
+AAAGGGATTAAATTCCCCCACTTAAGAGATATAGA
+>EAS56_65:4:150:94:843
+CAGATACATCCCACTTTAAATCAACCACAGTAAAA
+>EAS56_65:4:296:78:421
+TCTTTTTTTCTTTTCTCTTTTTTTTTTTTTTTTTT
+>EAS56_65:4:296:78:421
+TGTTGGTGTTCGTTTTTTCTCCTGTTTCTTTTTCT
+>EAS56_65:5:121:380:656
+AATGTGTTTATTACCAGAGGGATGGAGGGAAGAGG
+>EAS56_65:5:121:380:656
+GCCCAGCTCCAGATTGCTTGTGGTCTGACAGGCTG
+>EAS56_65:5:131:742:561
+TCAAAAGGTGATGTGTGTTCTCATCAACCTCATAC
+>EAS56_65:5:131:742:561
+TGCCTTCAGACCCTACACGAATGCGTCTCTACCAC
+>EAS56_65:5:211:84:84
+CTATTTGAGGAAGTAATTGGGGAAAACCTCTTTAG
+>EAS56_65:5:211:84:84
+GCAAGAGAAAAGCATACAGTCATCTATAAAGGAAA
+>EAS56_65:5:262:53:888
+AAGACATGAGTTCAGGTAAAGGGGTGGAAAAAGAT
+>EAS56_65:5:262:53:888
+TTGAGACTACAGAGCAACTAGGTAAAAAATTAACA
+>EAS56_65:5:278:848:765
+GTACACACGCTGTCCTATGTACTTATCATGACTCT
+>EAS56_65:5:278:848:765
+TTCTCACAGTTTCTGCCCCCAGCATGGTTGTACTG
+>EAS56_65:5:299:336:613
+ATCCTACTAAATACATATGCACCTAACACAAGACT
+>EAS56_65:5:299:336:613
+TACTCAATATATCCATGTAACAAATCTGCGCTTGT
+>EAS56_65:5:30:92:753
+TATAATACCTCTACATGGCTGATTATGAAAACAAT
+>EAS56_65:5:30:92:753
+TGGATTCTGGGAAATTCTTCATCCTGGACCCTGAG
+>EAS56_65:5:312:985:871
+ATAAAACACATAGCTAAAACTAAAAAAGCAAAAAC
+>EAS56_65:5:312:985:871
+TAAGAGGGATGAGAAATTACCTAATTGGTACAATG
+>EAS56_65:5:37:611:267
+AATGAAGGGGAAATAAAGTCAAGTCTTTCCTGACA
+>EAS56_65:5:37:611:267
+TATAAAGGAAATCCCATAAGAATAACAATGGGCTT
+>EAS56_65:5:75:637:650
+CTGATTATGAAAACAATGTTCCCCAGATACCATCC
+>EAS56_65:5:75:637:650
+GTCTCATCTAGGGGAACAGGGAGGTGCACTAATGC
+>EAS56_65:6:197:759:975
+AAAAGAATTGTAAAAGTCAAAATTAAAGTTCAATA
+>EAS56_65:6:197:759:975
+AATTTTTGGACTTCTTAAAGAAAAAAAAACCTGTC
+>EAS56_65:6:37:610:260
+CAAGCCCTTCTCACAGTTTCTGCCCCCAGCATGGT
+>EAS56_65:6:37:610:260
+CCAGAGGGAAAGCTTTCAACGCTTCTAGCCATTTC
+>EAS56_65:6:46:173:214
+AACAATGGGCTTCTCAGCAGAAACCTTACAAGCCA
+>EAS56_65:6:46:173:214
+CTAGAGATTTAGACATCTAAATGAAAGAGGCTCAA
+>EAS56_65:6:66:257:524
+ATACATGAGATTATTAGGAAATGCTTTACTGTCAT
+>EAS56_65:6:66:257:524
+GCCTTCAGACCCTACACGAATGCGTCTCTACCACC
+>EAS56_65:6:67:800:450
+TCACAGGTATTCCTGAGGAAAAAGAAAAAGTGAGA
+>EAS56_65:6:67:800:450
+TTACAAAATATAGTTGAAAGCTCTAACAATAGACT
+>EAS56_65:6:82:822:767
+AACAGCTTAGGTATCAATTTGGTGTTCTGTGTAAA
+>EAS56_65:6:82:822:767
+TTAGGAAATGCTTTACTGTCATAACTATGAAGAGA
+>EAS56_65:7:118:775:467
+AACAGTAAAATAAAACAAAGGAGGTCATCATACAA
+>EAS56_65:7:118:775:467
+TGTACAATATTCTGATGATGGTTACACTAAAAGCC
+>EAS56_65:7:122:398:994
+GGGATTAAATTCCCCCACTTAAGAGATATAGATTG
+>EAS56_65:7:122:398:994
+TAAAAGTCAAAATTAAAGTTCAATACTCACCATCA
+>EAS56_65:7:219:40:833
+CCCATACTTTACTGCTACTCAATATATCCATGTAA
+>EAS56_65:7:219:40:833
+GGAGGTCATCATACAATGATAAAAAGATCAATTCA
+>EAS56_65:7:288:552:440
+AGAGGGAACGCTTTCAACTCTTCTAGCCATTTCTT
+>EAS56_65:7:288:552:440
+TGTGGTCTGACAGGCTGCAACTGTGAGCCTTCCAT
+>EAS56_65:7:67:692:110
+ATTGCCAGATGAACCACACATTAATACTATGTTTC
+>EAS56_65:7:67:692:110
+GTATCAATTTGGTGTTCTGTGTAAAGTCTCAGGGA
+>EAS56_65:8:117:156:84
+GGTTCAGAACTTGAAGACAAGTCTCTTATGAATTA
+>EAS56_65:8:117:156:84
+TGGGGAAAACCTCTTTAGTCTTGCTAGAGATTTAG
+>EAS56_65:8:206:563:262
+ATTACGTCCTATCTTCTTCTTAGGGAAGAACAGCT
+>EAS56_65:8:206:563:262
+ATTAGGAAATGCTTTACTGTCATAACTATGAAGAG
+>EAS56_65:8:218:173:667
+CCTGCCCCATCTCTTGTAATCTCTCTCCTTTTTGC
+>EAS56_65:8:218:173:667
+TAATGATTCCTCAATGTTAAAATGTCTATTTTTGT
+>EAS56_65:8:24:415:944
+GTTCAGGTAAAGGGGTGGAAAAAGATGTTCTACGC
+>EAS56_65:8:24:415:944
+TAGGTAAAAAATTAACATTACAACAGGAACAAAAC
+>EAS56_65:8:275:851:240
+CCCCAGAGGGAAAGCTTTCAACGTTTCTAGCCATT
+>EAS56_65:8:275:851:240
+GTGGTCTGACAGGCTGCAACTGTGAGCCATCACAA
+>EAS56_65:8:317:83:500
+TTTTTTTTTTTTCTTTTCTCCTTTTTTTTTTGTTT
+>EAS56_65:8:64:507:478
+TAATTGAAAAATTCATTTAAGAAATTACAAAATAT
diff --git a/tests/pysam_data/faidx_ex1.fq b/tests/pysam_data/faidx_ex1.fq
new file mode 100644
index 0000000..92801c3
--- /dev/null
+++ b/tests/pysam_data/faidx_ex1.fq
@@ -0,0 +1,13080 @@
+@B7_589:1:101:825:28
+GGGAACAGGGGGGTGCACTAATGCGCTCCACGCCC
++
+<<86<<;<78<<<)<;4<67<;<;<74-7;,;8,;
+@B7_589:1:101:825:28
+TGTGTCCATGTACACACGCTGTCCTATGTACTTAT
++
+0;0'0;<<<<<<8<;<<<<;;3<<;;<<<8<<<<<
+@B7_589:1:110:543:934
+AAGAATTGTAAAAGTCAAAATTAAAGTTCAATACT
++
+<<<<<5<<;<<<<<<;<<<<<<<<<<<;<<<<<<<
+@B7_589:1:110:543:934
+ACAAGCCAGAAGAGATTGGATCTAATTTTTGGACT
++
+<<<<<<<<<<<<;<<<<<;;<<<;;<<<<<,,;<<
+@B7_589:1:122:337:968
+ACAGGGGGCTGCGCGGTTTCCCATCATGAAGCACT
++
+<<<<<;<<<<<<<<<<<<<<<<<<<;<<;;<;;;;
+@B7_589:1:122:337:968
+GCTTTACTGTCTAAACTATGAAGAGACTATTGCCA
++
+%454<75!7<+!990<9<6<<<<6<</<<<<<<<<
+@B7_589:1:122:77:789
+ACTATATTTATGCTATTCAGTTCTAAATATAGAAA
++
+<<<:<4<<9<:7<<<:<<<7<<<<<<<<<<9<9<<
+@B7_589:1:122:77:789
+GGACGCTGAAGAACTTTGATGCCCTCTTCTTCCAA
++
+9<;<:<<<<<<:<<<<<<<<<<<<<<<<<<<<<<<
+@B7_589:1:168:69:249
+ATATGCTGTTTACAAGAAACTCATTAATAAAGACA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;;;<
+@B7_589:1:168:69:249
+TTCAGCAAGAAGATATAACCATCCTACTAAATACA
++
+;0;<;;<<<<<<<<<<<<<;<<<8<<<<<<<<<<<
+@B7_589:1:29:529:379
+CAGTTTCTGCCCCCAGCATGGTTGTACTGGGCAAT
++
+<<<<<<<<8<<<<<<<<<<<<<<<<<;<672;<<<
+@B7_589:1:29:529:379
+GACTCTATCCCAAATTCCCAATTACGTCCTATCTT
++
+;<<<:<<<<<;<<<<<<<<<<<<<<<<<<<<<<<<
+@B7_589:2:30:644:942
+TACCTAATTGGTACAATGTACAATATTCTGATGAT
++
+85%+;<<9;<9<<;<<<<<<<<<<<<<<<<<<<<<
+@B7_589:2:30:644:942
+TATATCAGATAAAGCACACTTTAAATCAACAACAG
++
+<<<<<<<<<<<<<<<<<<<<<<<9<<<<<<9;<9<
+@B7_589:2:73:730:487
+AGGAAGAAAAGGTCTTTCAAAAGGTGATGTGTGTT
++
+<<<<<<<<<<<<<<<<<<<9<<<<<<:<<<;<;<<
+@B7_589:2:73:730:487
+TAGCCATTTCTTTTGGCATTTGCCTTCAGACCCTA
++
+<;;<<2;<;<<<;0<<<<<<<<<<<<<<<<<<<<<
+@B7_589:2:9:49:661
+TACACACAAAAGTACAAAACTCACAGGTTTTATAA
++
+<<6<5<<<<<<<<<<<<<<<<<<<7<<<<<<<<<<
+@B7_589:2:9:49:661
+TGCTAAACTAAGCATCATAAATGAAGCGGAAATAA
++
+<<<<<<<<<<<<<<<<;<<<<<<;:<<;;;7<9;9
+@B7_589:3:71:478:175
+ACAGAGCTTTCAAGAAGTATGAGATTATGTAAAGT
++
+<<<<<<<<<<<;<<<<<;<<<<<<<<<<;<<<<<;
+@B7_589:3:71:478:175
+TAGACATCTAAATGAAAGAGGCTCAAAGAATGCCA
++
+<<<<;<96<<<<;<<<<<<<<<77<<<<<<<<<<;
+@B7_589:3:82:13:897
+ATACAGTCATCTATAAAGGAAATCCCAGCAGAATA
++
+<<<<;<<<<<<;<;<;5<51;<1<<<<%<<<<,58
+@B7_589:3:82:13:897
+CATAAATGAAGGGGAAATAAAGTCAAGTCTTTCCT
++
+,<2<;<<;<<<<;;;<<;<<<<<<<;;;;<<<<<<
+@B7_589:4:54:989:654
+ACTTATCATGACTCTATCCCAAATTCCCAATTACG
++
+<<<<<<<<<<<<<<<9<<<<<<9<<<<<1<<<88;
+@B7_589:4:54:989:654
+TCCCTGCCCCATCTCTTGTAATCTCTCTCCTTTTT
++
+,<1<2<<<;9)9<<;<<;<<<4<<<;<<<<<<<<<
+@B7_589:5:147:405:738
+AGGGATTAAATTCCCCCACTTAAGAGATATAGATT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;;;
+@B7_589:5:147:405:738
+ATCAGATAAAGCACACTTTAAATCAACAACAGTAA
++
+<9/<:<<<<<<<<7</<<<<<<<<<<<<<<<<<<<
+@B7_589:5:198:564:731
+ACAAAGGAGGTCATCATACAATGATAAAAAGATCA
++
+<6<;<<<<<<:7<<;<<<8<<+<<<<<<<<<<<<<
+@B7_589:5:198:564:731
+ATAGATTGGCAGAACAGATTTAAAAACATGAACTA
++
+<<<<<;<<<<<<;<<:<<;9<<<<<<<<1;<<58<
+@B7_589:5:50:950:562
+CTATTTTTGTCTTGACACCCTACTAATATTTGTCT
++
+<<3<<<8<;<<<<<<+<<8<&<<<<7<<<<<<<<<
+@B7_589:5:50:950:562
+GCCCCATCTCTTGTAATCTCTCTCCTTTTTGCTGC
++
+<<<<<<<<<<<<<<<&<<8<<<<<<<5<:<+<:+;
+@B7_589:5:68:440:424
+ACACTTTAAATCAACAACAGTAAAATAAAACAAAG
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@B7_589:5:68:440:424
+TGGTACAATGTACAATATTCTGATGATGGTTACAC
++
+<<2<<<<<<<<9<<<<<<<<<<<<<<<<<<<<<<<
+@B7_589:6:108:958:42
+AAAGTACAAAACTCACAGGTTTTATAAAACAATTA
++
+<<<;;</<<<<;<<<<<<<<<<<<<<<<<<<<<<+
+@B7_589:6:108:958:42
+TATGCCCTGCTAAACTAAGCATCATAAATGAAGGG
++
+<<<<<<<<<<<<<<<<<<<<1<<<<<<9<<;<5<:
+@B7_589:6:114:714:317
+AACCCCAGGGAATTTGTCAATGTCAGGGAAGGAGC
++
+;8<;:<<;<;<<<<<<<<<<<<<<<<<<<<<<<<<
+@B7_589:6:114:714:317
+TGCCAGCACAGGGGCTTAACCTCTGGTGACTGCCA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<<5;<;
+@B7_589:6:120:14:944
+CAAAAGGTGATGTGTGTTCTCATCAACCTCATACA
++
+:;<<;<;<;<<;<<<<<<<<<<<<<<<<<<<<<<<
+@B7_589:6:120:14:944
+CAAAGATGAAACGCGTAACTGCGCTCTCATTCACT
++
+<<<<<<<<<<<<<<<;<<<<<;<<<<<<<:;8;;7
+@B7_589:6:33:356:636
+TTTTTTTCTTTTCTCTTTTTTTTTTTTTTTTTTTT
++
+<<<<<<<8;<<<<<<<<<<<<<7<<<<<<<;;3&3
+@B7_589:7:112:203:90
+CCTGTCACCCAATGGACCTGTGATATCTGGATTCT
++
+;<;:;<;;;<<<<<<<<<:<<<7<<<<<<<<<<<<
+@B7_589:7:112:203:90
+CTTGAGAACCCCAGGGAATTTGTCAATGTCAGGGA
++
+<<:<<<<<<<<.<<<<<<<<<<<<6<:867<8884
+@B7_589:7:154:26:712
+ATTGAGACTACAGAGCAACTAGGTAAAAAATTAAC
++
+<<<<<<<<<<<;<<<<<<<<<<<<<<<<<<<<<<;
+@B7_589:7:154:26:712
+TTAATAAAGACATGAGTTCAGGTAAAGGGGTGGAA
++
+;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@B7_589:7:72:916:763
+CTGTCTTCCTCTGTCTTGATTTACTTGTTGTTGGT
++
+<;;:<<<<<<<;<<;;;<<<<<<<<<;;<;<<<<<
+@B7_589:7:72:916:763
+GTCCTATCTTCTTCTTAGGGAAGAACAGCTTAGGT
++
+</:8<8)<<<<:<<<<<;.89<:67<.;<<7+336
+@B7_589:7:76:306:561
+GGTGGAAAAAGATGTTCTACGCAAACAGAAACCAA
++
+9<7<<9<<<<<<7<<71<71*7<<<<<<<<<<1<<
+@B7_589:7:76:306:561
+TACAGAGCAACTAGGTAAAAAATTAACATTACAAC
++
+<<)<<<<<<8<<8<<<<<<<;;;<<1<<3;=7<<9
+@B7_589:7:93:634:323
+CTTAAAGAAAAAAAAACCTGTCAAACACGAATGTT
++
+<<<<<<<<<<<<<<<<<<<<7<<<<<<<<<<,<<<
+@B7_589:7:93:634:323
+TAAAGTTCAATACTCACCATCATAAATACACACAA
++
+<<<<;<;<<<<;;<<2<:<<<<<<<<<<<<<<<<<
+@B7_589:8:113:968:19
+GAAAACTATATTTATGCTATTCAGTTCTAAATATA
++
+8;<;8;9<<<<<<<9<:<<<<<<<<<;<<<<<<<<
+@B7_589:8:118:829:36
+AGTATTGGTAAAGATGTGGGGAAAAAAGTAAACTC
++
+<8<<;;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@B7_589:8:118:829:36
+TAATTGGTACAATGTACAATATTCTGATGATGGTT
++
+<<<<<<<<<:<2<<<<<<:<<<<<<<<<<<<71;<
+@B7_589:8:139:727:808
+AAGTAAATAAAACACATAGCTAAAACTAAAAAAGC
++
+<<;<<<<<<<<<;<;<<<<<<<<<<<<<<<<<<<<
+@B7_589:8:139:727:808
+ACAAATACTACTAGACCTAAGAGGGATGAGAAATT
++
+<<<<<<<<<<<<<:<;<<<<<<<<9;<;9<6;<<9
+@B7_589:8:157:935:374
+CAGTTACCAAATGTGTTTATTACCAGAGGGATGGA
++
+<<<<<<<<<<;<<;;<<<<<<<<<::8'5++;+11
+@B7_589:8:157:935:374
+TCTTCATCCTGGACCCTGAGAGATTCTGCAGCCCA
++
+94988994.<:<+42::<<<<<:<:<4<<<<;<1<
+@B7_589:8:2:434:715
+AGAGAGAACTTCCCTGGAGGTCTGATGGCGTTTCT
++
+<<<<<<<<<:;<<<;<<<<<<<<<<<<<<<<<<<<
+@B7_589:8:2:434:715
+CTTGTTGTTGGTTTTCTGTTTCTTTGTTTGATTTT
++
+<<<<<<<<<<<<<<<<<;<<<<<<<0<<<68<<<+
+@B7_589:8:74:674:124
+CACTGAACTTCCACGTCTCATCTAGGGGAACAGGG
++
+<<<<<<<<<<<<:<;<<<<;<<<<;9;<<;;.;;;
+@B7_589:8:74:674:124
+TTCTTATCTGCACATTACTACCCTGCAATTAATAT
++
+;;;;;<<:<<:<<<<<<<<<<<<<<<<<<<<<<<<
+@B7_591:1:191:462:705
+CAGATCCAGATTGCTTGTGGTCTGACAGGCTGCAAC
++
+<<<<<<<<<<<<<<<<<<<;<<<<<<<;<<<<::<6
+@B7_591:1:191:462:705
+CATCCCTGTCTTACTTCCAGCTCCCCAGAGGGAAAG
++
+<<'<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@B7_591:1:60:837:923
+CATCAACCGCATACACTCACATGGTTTAGGGGTATA
++
+0<4<<<02.<99+<+&!<<<<+<<<<<<<<<<<<3<
+@B7_591:1:60:837:923
+TTCACGCCAGCTCCCTGTCACCCAATGGACCTCTGA
++
+<<<<<4<<+<<*<<<<88<<<<<'*<4-+<<4&<40
+@B7_591:2:123:924:645
+TATATCAGATAAAGCACACTTTAAATCAACAACAGT
++
+;<<<<*<<<<<<</7<2<8<<<<<<<4<<<<<<<<<
+@B7_591:2:123:924:645
+TGAATAAAAAGGGATTAAATTCCCCCACTTAAGAGA
++
+<<<<<<<<<<<<;<<<<<<;<<<<<<<6:<7<1<+<
+@B7_591:2:134:868:252
+AAGAACTTTGATGCCCTCTTCTTCCAAAGATGAAAC
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<;:<<<:<<<
+@B7_591:2:134:868:252
+ATGAACAACAGGAAGAAAAGGTCTTTCAAAAGGTGA
++
+<;<<<8<<<<<<<<<<<<<<<:<<<<<<<<<<<<<<
+@B7_591:2:13:100:876
+ACAGGGATTCCTGAGGAAAAAGAAAAAGTGAGAAGT
++
+<8<<<*<2<7<<<6<<<<<<6<<8<<<<5<<<<4<9
+@B7_591:2:13:100:876
+AGAATATATAAAGTCAACATGAAGGAAAAAAATTCT
++
+;9<$<<<$<<<<<<<<75<<<<<<<9<9<<<<<<<<
+@B7_591:2:223:583:968
+AATATAGTTGAAAGCTCTAACAATAGACTAAACCAA
++
+<<<<<<<29<<<<4<<<<<<<<<<<7<<7<..<<47
+@B7_591:2:223:583:968
+TATGAGGCACAGGTATTCCTGAGGAAAAAGAAAAAG
++
+1<';<<&%-:<<<<<:66%<<<<<<<<<<<<<<<<<
+@B7_591:2:240:603:890
+GCTCCCAAGAGGGAAAGCTTTCAACGCTTCTAGCCA
++
+;+&+//&<<<<<<<<<<9<<<8<<<<9<<<<<<<<<
+@B7_591:2:240:603:890
+TCACAATGAACAACAGGAAGAAAAGGTCTTTCAAAA
++
+<<<<<<<<<<<<<<<<<<;<:<<:<<;<<<<<8865
+@B7_591:2:279:124:41
+GAATTAACCCAGTCAGACAAAAANNAAGAAAAAAGA
++
+<<<<<<<7/<8<<<<<<<<<<4*!!<<7<7<<5<<3
+@B7_591:2:279:124:41
+GCTAGAGATTTAGACATCTAAATGAAAGAGGCTCAA
++
+:17<8<<<:&<<<<<<:;'<<<<<<<<<<;<<<<<<
+@B7_591:2:27:280:592
+AATAACAATGGGCTTCTCAGCGGAAACCTTACAAGC
++
+<<<<<<<<<<<8<<<<<<<<7<<<<<<<<<<<<<<<
+@B7_591:2:27:280:592
+AGAGATTTAGACATCTAAATGAAAGAGGCTCAAAGA
++
+<<<<<<<<<<<<<<<<<<<<<<<<9<<<<<<<<<5<
+@B7_591:2:309:798:997
+TTTTTTTTTTTTTTTTTTCTCTTTTTTTTTTTTTTT
++
+466;<<744077+&7097&%&4<9<<<9<<<::<<<
+@B7_591:2:323:639:311
+AAGCCGTTCTATTTGTAATGAAAACTATATTTAGGC
++
+<<<<<<<<<<<<<<<<<<<2<<<<<<;<<<<<<81<
+@B7_591:2:323:639:311
+TACCAAATGTGTTTATTACCAGAGGGATGGAGGGAA
++
+-94<<<<<<<4<<<<<<<<2<<<<<7<<<-<<<<<<
+@B7_591:2:46:220:58
+CAAATCTGCGCTTGTACTTCTAAATCTATAAAAAAA
++
+<<<<<<<<<<<<<<<<<<<<<<9<<<<<<<<<<:<;
+@B7_591:2:46:220:58
+TTCCACTTTGGAAAACAATTTGGTAATTTCGTTTTT
++
+98<<<2<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@B7_591:3:168:69:605
+TACCCGAGGGATGGAGGGTAGAGGGACGCTGAAGTG
++
+<<<4(<<<<<<<<<<<<<(1<6<-<2<<7<<6<<++
+@B7_591:3:168:69:605
+TCTGACAGGCGGCAACTGTGAGCCATCACAATGAAC
++
+'<'<144<0<&<<<<<<<7<<<<<<<<<<<<<<<<<
+@B7_591:3:179:496:161
+AAAAACATGAACTAACTATATGCTGTTTACAAGAAA
++
+<<<<<9<<<<<7<<<<<<<<<<<<<<<<<<<<<<<<
+@B7_591:3:179:496:161
+AAGTACAAAACTCACAGGTTTTATAAAACAATTAAT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<+
+@B7_591:3:277:458:330
+AATGTCAGGGAAGGAGCCTTTTGTCAGTTACCAAAT
++
+<<7<<<<<<<<<2<<<%,<6<&<<,<<<<:<<<<(7
+@B7_591:3:277:458:330
+TGATATCTGGATTCTGGGAAATTCTTCATCCTGGAC
++
+<<<<<8;<<<1<;7<<<;<<<<<<<<7<<7<<<<;7
+@B7_591:3:291:404:199
+TATAAAACAATTAATTGAGACTACAGAGCAACTAGG
++
+<<<<<<<7<<9<<<<<<<<<<<<<<<<<<<<<<<<<
+@B7_591:3:291:404:199
+TGAAGGGGAAATAAAGTCAAGTCTTTCCTGACAAGC
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<:
+@B7_591:3:305:565:952
+GTCCGTGTCCTCCCATCTGGCCTCGTCCACACTGGT
++
+5(<1<147<81<*8--8<<<7<91<<<;+<+<<<<<
+@B7_591:3:305:565:952
+TAATACTATGTTTCTTATCTGCACATTACTACCCTG
++
+7<<<<<<<<<7<<<<<<<<<7<<<;;<;<;<<<<<+
+@B7_591:3:45:294:380
+ATAATTGTGTCCATGTACACACGATGTCATATGTAC
++
+<<<<<<<<9<<<<<<<<<70<<7<6272&:3<+</%
+@B7_591:3:45:294:380
+CCTCGTCCACACTGGTTCGCTTGAAAGCTTGGGCTG
++
+;<+<7<<<<;7<,<7<<<+/7;<<;<<;7<<<;<<<
+@B7_591:4:103:111:720
+CAGTTACCAAATGTGTTTATTACCAGAGGGATGGAG
++
+<<<<<<<<<<<<<<<<<<<<<<<<<5<<<5;<5<:;
+@B7_591:4:103:111:720
+TCTTCATCCTGGACCCTGAGAGATTCTGCAGCCCAG
++
+;4<<<;)<<-<9<;<<7<<<<<<<<<<<<<<<<<<<
+@B7_591:4:159:508:571
+CAAAACCTCATATATCAATATTAACTTTGAATAAAA
++
+<<<<<<<<<<<<<<;<<<<<<<<<<<<<<<<<<<<;
+@B7_591:4:159:508:571
+TGGAAAAAGATGTTCTACGCAAACAGAAACCAAATG
++
+9<6<<<<<<<<<<<;<<;<<<<<;<<<<<<<<<<<<
+@B7_591:4:216:650:516
+GAACAGCTTAGGTATCAATTTGGTGTTCTGTGTAAA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;
+@B7_591:4:216:650:516
+TTTTTGCTGCATCCCTGTCTTCCTCTGTCTTGATTT
++
+;9;<<<<<<;<<<<<<<<<<<<<<<<<<<<<<<<<<
+@B7_591:4:329:339:408
+CAATCCAGAAGAGATTGGATCTAATTTTTGGACTTC
++
+7<<<7<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@B7_591:4:329:339:408
+TAAATGAAAGAGGCTCAAAGAATGCCAGGAAGATAC
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<9<<<<;
+@B7_591:4:92:411:955
+GGTAAAGGGGTGGAAAAAGATGTTCTACGCAAACAG
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<<;
+@B7_591:4:92:411:955
+TACTAAATACATATGCACCTAACACAAGACTACCCA
++
+2<+<<<<9<<<<<<<;+<;<<<<<<<<<<<<<<<<<
+@B7_591:5:124:978:501
+AATTTGGTAATTTCGTTTTTTTTTTTTTCTTTTCTC
++
+<9<;<<::<;<<;<4<<<<<<<<<<<<<<<<<<<<<
+@B7_591:5:124:978:501
+ATGTAACAAATCTGCGCTTGTACTTCTAAATCTATA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;
+@B7_591:5:134:751:831
+AGCTCCCTGTCACCCAATGGACCTGTGATATCTGGA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<948
+@B7_591:5:134:751:831
+ATACACACACATGGTTTAGGGGTATAATACCTCTAC
++
+;:<4<8<<<;<;<<5<:<<<<<<<<<<<<<<<<<<<
+@B7_591:5:243:557:560
+AAAGAGGCTCAAAGAATGCCAGGAAGATACATTGCA
++
+<<<<<<<9<<<<<<<<<<<<<<<<<<;<<89<<9<;
+@B7_591:5:243:557:560
+CTAAGCAGAAACCTTACAAGCCAGAAGAGATTGGAT
++
+69&<;&<&<<;6.<<<+<<<;;<<<<<<<<;<<<<<
+@B7_591:5:254:542:848
+CCAAGCAGAAGAAAGAGGTTCAGAACTTGAAGACAA
++
+<<<;<<<<<<<<<<<<<<<;4<;8<<<;;9<9;8;9
+@B7_591:5:254:542:848
+CTGAGGAAAAAGAAAAAGTGAGAAGTTTGGAAAAAC
++
+,:4<8<<<<<<<<<<<<<;:<<<<<<<<<<<<<<<<
+@B7_591:5:289:132:526
+CACCCGGTCCCTGCCCCATCTCTTGTAATCTCTCTC
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<8<<<<<<<<<
+@B7_591:5:289:132:526
+TCTATTTTTGTCTTGACACCCAACTAATATTTGTCT
++
+;<<<<<<<<<<<<<<<<<<<:<<<<<<<<<<<<<<<
+@B7_591:5:42:540:501
+CTATATTTATGCTATTCAGTTCTAAATATAGAAATT
++
+;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@B7_591:5:90:828:633
+CTGCAGCCCAGATCCAGATTGCTTGTGGTCTGACAG
++
+<<<;<;<:<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@B7_591:5:90:828:633
+GGATGGAGGGAAGAGGGACGCTGAAGAACTTTGATG
++
+<<<<<<<<<<<8<;96<;<<<<<99<2<<;<96<8;
+@B7_591:6:11:646:628
+GTACTTATCATGACTCTATCCCAAATTCCCAATTAC
++
+<<<3<<<<<<<<<<<<<<<<<<<<<7<<<<<<<<6<
+@B7_591:6:11:646:628
+TTCTGCCCCCAGCATGGTTGTACTGGGCAATACATG
++
+<<<<<<<<<<6<<<<<<<<<<<<</<;<<<<<<6<;
+@B7_591:6:155:12:674
+CTATATTTATGCTATTCAGTTCTAAATATAGAAATT
++
+;<<<<<<<<<<;<<<<;<<<<8<<<<<<<<<<<<<<
+@B7_591:6:181:191:418
+AAACTATATTTATGCTATTCAGTTCTAAATATAGAA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<988
+@B7_591:6:181:191:418
+AGGGAAGAGGGACGCTGAAGAACTTTGATGCCCTCT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@B7_591:6:190:42:671
+TATTGCCAGATGAACCACACATTAATACTATGTTTC
++
+<<<<<<<<<<<<<<9<<<<<<<<<<<<<<<<<<<<<
+@B7_591:6:190:42:671
+TGTGTAAAGTCTCAGGGAGCCGTCCGTGTCCTCCCA
++
+<<<<8<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@B7_591:6:29:575:453
+TACTACCCTGCAATTAATATAATTGTGTCCATTTAC
++
+<<<<<<<<<<<<<<<<<<<<<<<<7<1<:<9<&<98
+@B7_591:6:29:575:453
+TCTGGCCTCGTCCACACTGGTTCTCTTGAAAGCTTG
++
+;<<<;;<:<<<;<;<<<<<<<<<<<<<<;<<<<<<<
+@B7_591:7:116:814:89
+ACTATGCTAAGTATTGGTAAAGATGTGGGGAAAAAA
++
+:38<;<;<<<<;<<<<<<<<<<<<<;<<<<<<<<<<
+@B7_591:7:116:814:89
+CCTAATTGGTACAATGTACAATATTCTGATGATGGT
++
+<<<<<<<<<<<<<<<<<<<<<<:<<<<;<<;<<66<
+@B7_591:7:129:956:115
+AGTTTCTGCCCCCAGCATGGTTGTACTGGGCAATAC
++
+<<:<9<4<<<<7<<<<<<<<<<<<<<<<<<<<<<<<
+@B7_591:7:129:956:115
+GCTCCCCAGAGGGAAAGCTTTCAACGCTTCTAGCCA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;877-
+@B7_591:7:157:447:758
+AAAGATGTTCTACGCAAACAGAAACCAAATGAGAGA
++
+<<<;<<5<</<<6<5<<<<<<<<<<<<<<<<<<<<<
+@B7_591:7:157:447:758
+ACAAAACCTCATATATCAATATTAACTTTGAATAAA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<<;<
+@B7_591:7:200:192:373
+AGTGCCTTTGTTCACATAGACCCCCTTGCAACAACC
++
+<<<<<<<<<<<<<<<<<<<<<<<<<:<:<;5<<;<<
+@B7_591:7:200:192:373
+CTCTCATTCACTCCAGCTCCCTGTCACCCAATGGAC
++
+<<<8<<<4<4<<<<<:<<<<<<<<<<<<<<<<<<<<
+@B7_591:7:22:632:176
+AAAGGAGGTCATCATACAATGATAAAAAGATCAATT
++
+<9<<<<<<<-;<;<<7;6;<<<<<<<<<;<<<<<<<
+@B7_591:7:22:632:176
+AGATATAGATTGGCAGAACAGATTTAAAAACATGAA
++
+<<<<<;<<<<<<;<<;<:<<<:<<:<<<;<<<;;;:
+@B7_591:7:68:242:834
+AAATAAAAAAGCAAAAACAAAAACTATGCTAAGTAT
++
+<<68<<<<<<<8<<<<<<<<<<<<<<<<<<<<<<<<
+@B7_591:7:68:242:834
+TACTACTAGACCTAAGAGGGATGAGAAATTACCTAA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<<<
+@B7_591:7:89:67:709
+TTTTTTTTTTTGTCTTCTCTTTTTTTTTTTTTTTTT
++
+:7:::9:7:<<7<'<<477<<<<<<<<<:<<<<<:<
+@B7_591:8:4:841:340
+TTCAAATGAACTTCTGTAATTGAAAAATTCATTTAA
++
+<<<<<<<<;<<<<<<<<;<<<<<;<;:<<<<<<<;;
+@B7_593:1:12:158:458
+CTGGGAAATTCTTCATCCTGGACCCTGAGAGATTCT
++
+<77<<<7<<<<<<<<<<<<5<4;<<;5<;;+2<+;;
+@B7_593:1:12:158:458
+TAATAATGCTACATGGATGATTATGAAATCAATGTT
++
+++++++$((+*+++++++++++++&+++++++++++
+@B7_593:1:189:876:833
+CAAGACTACCCAGATTCATAAAACAAATACTACTAG
++
+<<<<<<<<<<<8<8<<<<<;<;;<<;<<<<<;<<<6
+@B7_593:1:189:876:833
+TTAAAATTTAACAAAAGTAAATAAAACACATAGCTA
++
+7;<<<<:;;<</<<<<<<<<<;<<<<<<<<<<<<<<
+@B7_593:1:19:695:59
+AACAGGAACAAAACCTCATATATCAATATTAACTTT
++
+<<<<<<<<<<<;<<<<<<<<<;<<;;<;<<7<<<<;
+@B7_593:1:19:695:59
+GTGGAAAAAGATGTTCTACGCAAACAGAAACCAAAT
++
+;+;8<<<<<<<<<<<5<<+<:<<;<<<<<<<<<<<<
+@B7_593:1:200:559:765
+GGAAGGAGCATTTTGTCAGTTACCAAATGTGTTTAT
++
+<<<<<<<<<<<<<<7<<<<<<;<<;;4<7<9;<<-;
+@B7_593:1:200:559:765
+TGGACCCTGAGAGATTCTGCAGCCCAGATCCAGATT
++
+8<;;4<3;<;<<<<<<5<<;;<<98;;<<<<;<<<<
+@B7_593:1:215:861:605
+GAAAAACTATTTGAGGAAGTAATTGGGGAAAACCTC
++
+;<<<<<;:<7:<<<;<<<<<<<;:<<<<<<<<<<<<
+@B7_593:1:215:861:605
+NAAGACAAGTCTCTTATGAATTAACCCAGTCAGACA
++
+!+++++++++++++++++++++++++++++++++++
+@B7_593:1:36:485:632
+AAAAGGTCTTTCAAAAGGTGATGTGTGTTCTCATCA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<5<<<;<18;
+@B7_593:1:36:485:632
+GGCATTTGCCTTCAGACCCTACACGAATGCGTCTCT
++
+0;;;<<;<<<;<<<<<<<<<<<<<;<<<<<<<<<<<
+@B7_593:1:85:361:418
+AGCCAGAAGAGATTGGATCTAATTTTTGGACTTCTT
++
+;;;5<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@B7_593:1:85:361:418
+GAAGATACATTGCAAGACAGACTTCATCAAGATATG
++
+<<<<<<<<<<<<<;<<<<<<<<<<<<<<;4;<<<<3
+@B7_593:2:104:744:280
+CATATGGAAAGGTTGTTGGGATTTTTTTAATGATTC
++
+'&+74*0<'/.47:8<<<<;<7''6/1<<<.<<68<
+@B7_593:2:104:744:280
+TGGGCTGTAATGATGCCCCTTGTCCATCACCCGGTC
++
+<<<<<<<<<<<<<<;<;<<<<:4<<4<<0<;80+;:
+@B7_593:2:125:875:553
+AACAGTAAAATAAAACAAAGGAGGTCATCATACAAT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<;<;
+@B7_593:2:125:875:553
+TAATTGGTACAATGTACAATATTCTGATGATGGTTA
++
+-;<;:;<<;6<<<<<<6<;<:<<<<<<<<<<<<<<<
+@B7_593:2:128:555:941
+AACCAAAAGAGAGAAGGAGTAGTTATACACATATCA
++
+55--555560355$55555555.57757$7555577
+@B7_593:2:133:460:542
+CCTATAAGCCGTTCTATTTGTAATGAAAACTATATT
++
+<<<<<<<<<<<;<<<<<<<<<<<<;<<<<<<<<<<;
+@B7_593:2:133:460:542
+TTACCAAATGTGTTTATTACCAGAGGGATGGAGGGA
++
+;:;7;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@B7_593:2:259:467:737
+CTATGTACTTATCATGACTCTATCCCAAATTCCCAA
++
+8<<<<<<<:<<<<<<<<;<;<<<<<<<<<<<<<<<<
+@B7_593:2:259:467:737
+TCACAGTTTCTGCCCCCAGCATGGTTGTACTGGGCA
++
+<<<<<<<<<<<<7<<<<<<<'<<.<<<<<<;;;<67
+@B7_593:2:270:430:269
+AAAGAGGCTCAAAGAATGCCAGGAAGATACATTGCA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;;;7;:
+@B7_593:2:270:430:269
+CCAGAAGAGATTGGATCTAATTTTTGGACTTCTTAA
++
+28<<;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@B7_593:2:273:348:37
+AGAAATGCGCAAAAGAATTGTAAAAGTCAAAATTAA
++
+9;7;;0<++1<<<;<7<+;;1<<<;<17<<<<<<<<
+@B7_593:2:273:348:37
+GAATAACAATGGGCTTCTCAGCAGAAACCTTACACG
++
+<<<<<<<9<49<<<;<<<<*<<19<15;<</5<;.5
+@B7_593:2:313:531:169
+GAAAGAGGTTCAGAACTTGAAGACAAGTCTCTTATG
++
+<<<<<<<<<<<<<;<<<<<<<<<<<:<<:<;<<;<2
+@B7_593:2:313:531:169
+GTGAGAAGTTTGGAAAAACTATTTGAGGAAGTAATT
++
+98;<;;<<;8<<<<<<<<<<<8<<<<<<<<8<<<<<
+@B7_593:2:43:239:977
+TGAACTTCTGTAATTGAAAAATTCATTTAAGAAATT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<7;7;<;
+@B7_593:2:68:140:542
+AAAAACAAAAACTATGCTAAGTATTGGTAAAGATGT
++
+;;<<;7<<<<<<:<<<:<<<:<<<<<<<<<<<<<<<
+@B7_593:2:68:140:542
+GGGATGAGAAATTACCTAATTGGTACAATGTACAAT
++
+<<<8;<<;<<<<<;<<;<<<<<8;<-<8<82;;;-8
+@B7_593:2:68:692:347
+TATCAATTTGGTGTTCTGTGTAAAGTCTCATGGAGC
++
+<<<<<<<<<+6<;<<<<3<:<<<<6<8<<<&*/;*0
+@B7_593:2:68:692:347
+TGTCTTGATTTACTTGTTGTTGGTTTTCTGTTTCTT
++
+9<;;;;<<<:<;<<<<<<<<<<<<<<<<<<<<<<<<
+@B7_593:2:81:435:410
+AGACATGAGTTCAGGTAAAGGGGTGGAAAAAGATGT
++
+;<;;<<<<<<;<<<<<<<<<<<<<<<<<<<<<<<<<
+@B7_593:2:81:435:410
+ATTAATTGAGACTACAGAGCAACTAGGTAAAAAATT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<:<<<<<;<<;;
+@B7_593:3:102:856:670
+AAACCTCATATATCAATATTAACTTTGAATAAAAAG
++
+<<<<<<<;<<<;<<;:<<<<<<<<<<:;;<<;<<<7
+@B7_593:3:102:856:670
+AGAGAAGGAGTAGCTATACTTATATCAGATAAAGCA
++
+;;<<<<:<<<:<<4<<<<<<<<;<<;<<<<<<<<<<
+@B7_593:3:115:649:259
+ATTAATTGAGAATACAGAGCAACTAGGTAAAAAATT
++
+;<;<<;<<<<;&<<<<<<<<<<<<<<<<<<<<<<<<
+@B7_593:3:115:649:259
+GGGAAATAAAGTCAAGTCTTTCCTGACAAGCAAATG
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<<;<<9
+@B7_593:3:148:437:481
+CGCTTCTAGCCATTTCTTTTGGCATTTGCCTTCAGA
++
+<<<<<<<<<<<<<<<<<<<<<;<<<<<;<<<<;0;8
+@B7_593:3:148:437:481
+GTACTGGGCAATACATGAGATTATTAGGAAATGCTT
++
+<<<;<<<<7<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@B7_593:3:180:89:582
+ATGCTAAGATAATTCATCATCACTAAACCAGTCCTA
++
+<<<<<<<<<7<<<<<<<<<7<<<:<<<:<<::77:<
+@B7_593:3:180:89:582
+TAAAAAATTAACATTACAACAGGAACAAAACCTCAT
++
+;<<<<<<4<<<:<<<<<<<<<6<<<<<<<<<<;<<<
+@B7_593:3:194:168:684
+AAAACAGTCTAGATGAGAGAGAACTTCCCTGGAGGT
++
+;<<<<<;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@B7_593:3:194:168:684
+CTGTCTTCCTCTGTCTTGATTTACTTGTTGTTGGTT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<7<<.<<6-<<
+@B7_593:3:196:11:27
+AAGACCCAGTTAGCCGTCCGTGTCCTCCCATCTGGC
++
+96&6<'<7:!!<,:;+7<<6:<<<<<<<<<7<7;:<
+@B7_593:3:196:11:27
+CTATGTTTCTTATCTGCNCATTACTACCCTGCAATT
++
+<<<<<<<<;<<<<<<<8!4<<<;+<88;8<+2,8<;
+@B7_593:3:303:131:673
+ACAAGAAACTCATTAATAAAGACATGAGTTCAGGTA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;;<;;;
+@B7_593:3:303:131:673
+ATAAAAAGATCAATTCAGCAAGAAGATATAACCATC
++
+<;<<<<<<<<:<<<<;<<<<<<<<<<<<<<<<<<<<
+@B7_593:3:310:193:629
+CATACAATGATAAAAAGATCAATTCAGCAAGAAGAT
++
+<<<<<<<<<<<<<<<<<<<<<;<<<<<<<<<<<<<;
+@B7_593:3:310:193:629
+TACACTAAAAGCCCATACTTTACTGCTACTCAATAT
++
+9<9<6;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@B7_593:4:104:153:698
+CCAGATACCATCCCTGTCTTACTTCCAGCTCCCCAG
++
+;<<<<<<;6<<<<<<<<<<;<<<<;<;;;<.<::50
+@B7_593:4:104:153:698
+CTAATGCGCTCCACGCCCAAGCCCTTCTCACAGTTT
++
+69<<)9<<:5:6<<<16:<6/<6<1<<<<<:<:<<<
+@B7_593:4:106:316:452
+CTATATTTATGCTATTCAGTTCTAAATATAGAAATT
++
+:<<<<<;<<<<:<<:<<<<<<7<<<<<<<<<<<<<<
+@B7_593:4:142:63:937
+GAAAAGGTCTTTCAAAAGGTGATGTGTGTTCTCATC
++
+<<<<<<<<<<<<<<<<<:<<<<<<<<<;<<:<<:<:
+@B7_593:4:142:63:937
+TTCTTTTGGCATTTGCCTTCAGACCCTACACGAATG
++
+;;;<;<<<<;<<<<<;:<<<<<<<;<<<<<<<<<<<
+@B7_593:4:28:781:723
+AATACCTCTACATGGCTGATTATGAAAACAATGTTC
++
+<<<<<<<<<7<<<;;<<;;<<;<5<4<7<;7<+:<9
+@B7_593:4:28:781:723
+ACTGAACTTCCACGTCTCATCTAGGGGAACAGGGAG
++
+8488<::;4;;<:;;;::<;7<<<<<<<<<<<<<<<
+@B7_593:4:29:794:282
+CACATTAATACTATGTTTCTTATCTGCACATTACTA
++
+<<<<<<<<<<<<<<<<<<<<<;<<<&<<;:<<8<<8
+@B7_593:4:29:794:282
+TAAAGTCTCAGGGAGCCGTCCGTGTCCTCCCATCTG
++
+7<<<<45::-<<<<<;<<-;<<;<<<<<<<<<<<<<
+@B7_593:4:30:117:411
+TCTTGACACCCAACTAATATTTGTCTGAGCAAAACA
++
+;88<<<<<:<7<<;<<<<<<<<<<<<<<<<<<<<<<
+@B7_593:4:30:117:411
+TCTTGTAATCTCTCTCCTTTTTGCTGCATCCCTGTC
++
+<<<<<<<<<<<<<<<<<<<<<<7<<:<<<<<<<<<:
+@B7_593:4:30:812:345
+TATGTTTCTTATCTGCACATTACTACCCTGCAATTA
++
+;<;<<<<5<<<:<;<:<;<<<<<<<<<<<<<<<<<<
+@B7_593:4:30:812:345
+TCATCTAGGGGAACAGGGAGGTGCACTAATGCGCTC
++
+<<<<<<<7<;<<7<;77;3<&0-;<5<;6<1'13<:
+@B7_593:4:315:201:673
+AAGATATGTAGTCATCAGACTATCTAAAGTCAACAT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<7<<<<<:;
+@B7_593:4:315:201:673
+TTGGACTTATTAAAGAAAAAAAAACCTGTCAAACAC
++
+;;;;<-;;&;;<<<:<<<<<<<<<<<<<<<<<<<<<
+@B7_593:5:171:343:758
+ACTAATATTTGTCTGAGCAAAACAGTCTAGATGAGA
++
+:+;;<<<<<;<;:<<<;;<<<<<<<<<<<<<<<<<<
+@B7_593:5:171:343:758
+GCTGCATCCCTGTCTTCCTCTGTCTTGATTTACTTG
++
+<<<<<<<<<<<<<<<<<<<<<;<<<<59<<<9;<<3
+@B7_593:5:267:71:603
+TTGGCCATCACCCAGTCCCTGCCCCATCTCTTGTAA
++
+<<<<<<<<<<<<<<<<<<<<<<;<<<<<<<<<<<9;
+@B7_593:5:267:71:603
+TTTAATGATTCCTCAATGTTAAAATGTCTATTTTTG
++
+9;;<;<<<;;<<<<<<<<<<<<<<<<<<<<<<<<;<
+@B7_593:5:299:743:762
+AAAATTAAAATTTAACAAAAGTAAATAAAACACATA
++
+;<<<1<<<<<+<;<;7<<;<<<<<<<<<;<<;;<<7
+@B7_593:5:299:743:762
+CAAGACTACCCAGATTCATAAAACAAATACTACTAG
++
+<<<;<<<<<<<<<:;<<<.<:<<<<<<<<<<;;;;;
+@B7_593:5:30:599:589
+CTACGCAAACAGAAACCAAATGAGAGAAGGAGCAGC
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<;;<<;<&<<;
+@B7_593:5:30:599:589
+TCATAAAACAAATACTACTAGACCTAAGAGGGATGA
++
+90<;<<<<<<<<+<<<;;<;<;<<<<<<<<6<<8<<
+@B7_593:6:118:121:760
+GAGATTTAGACATCTAAATGAAAGAGGCTCAAAGAA
++
+:<<<;;<<<<6<;<<<;<<<<;<<<<<<<<<<<<<<
+@B7_593:6:119:428:415
+GCTATACTTATATCAGATAAAGCACACTTTAAATCA
++
+84<<<<;;<<<<<:<<<<<<<<<<<<<<<<<<<<<<
+@B7_593:6:119:428:415
+TAAATTCCCCCACTTAAGAGATATAGATTGGCAGAA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<9;;<;;;
+@B7_593:6:185:96:948
+CTAAATGAAAGAGGCTCAAAGAATGCCAGGAAGATA
++
+6<;;<;<<;<<<<<747<<<<<<<<77<<<<<<<<<
+@B7_593:6:185:96:948
+TTTAAAAATGAACAGAGCTTTCAAGAAGTATGAGAT
++
+<<<<<<<<<;6<<<<<<<<<;<<<;;<<<<<<<;<;
+@B7_593:6:38:332:54
+CCATCATAAATACACACAAAAGTACAAAACTCACAG
++
+<;<<<<<<<<<<<<<<<<<<<<<<<<<<<0;;;<;;
+@B7_593:6:38:332:54
+TGGCAGAACAGATTTAAAAACATGAACTAACTATAT
++
+8;;&<;<<7<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@B7_593:6:61:628:681
+CAGAGGGAAAGCTTTCAACGCTTCTAGCCATTTCTT
++
+95<<<<<<<<;<<<<;<<<:<<;;<<<<<<<<<<<<
+@B7_593:6:61:628:681
+GCCATCACAATGAACAACAGGAAGAAAAGGTCTTTC
++
+<<<<<<<<<<<<<<<<<<<;<<<<<<<:<<;;;;;;
+@B7_593:7:15:244:876
+AAAAGTAAACTCTCAAATATTGCTAGTGTGAGTATA
++
+;<<<7<<<<<.2<-<<<<<<<<<:<<<<<<<<<2<<
+@B7_593:7:15:244:876
+GTACAATATTCTGATGATGGTTACACTAAAAGCCCA
++
+<<<<<<;<<<<<<<<;<<;;;<<<<<:<<<9;<<<;
+@B7_593:7:189:530:40
+AAAAGAATTGTAAAAGTCAAAATTAAAGTTCAATAC
++
+<<<<<<<<<<;<<<<<:<<<<<<<<<<<<<<;<<<;
+@B7_593:7:189:530:40
+CCCCACTTAAGAGATATAGATTGGCAGAACAGATTT
++
+883;<<<<<<<<<:<<<<<<<<3<;<<<<<<<<;<<
+@B7_593:7:256:354:173
+CATTAATAAAGACATGAGTTCAGGTAAAGGGGTGGA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<3<<;
+@B7_593:7:256:354:173
+TCAATTCAGCAAGAAGATATAACCATCCTACTAAAT
++
+-9<<:9<<;6<<<<<<<<<<<<<<<<<<<<<<<<<<
+@B7_593:7:283:186:707
+AATACATATGCACCTAACACAAGACTACCCAGATTC
++
+<<<<<<<<<<<<<<<<<<<<<<;<<<<<;<;<<<<8
+@B7_593:7:283:186:707
+CGCTTGTACTTCTAAATCTATAACAAAATTAAAATT
++
+889;<7;<7<<7<<<<<7<<<<<<<<<<<<<<<<<<
+@B7_593:7:307:481:625
+AAAAAGTGAGAAGTTTGGAAAAACTATTTGAGGAAG
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;;;;9<;
+@B7_593:7:307:481:625
+TCAACATGAAGGAAAAAAATTCTAAAATCAGCAAGA
++
+;4<<4<;;<<;;<<<<<<<<<<<<<<<<<<<<<<<<
+@B7_593:7:67:302:762
+GTAATCTCTCTCCTTTTTGCTGCATCCCTGTCTTCC
++
+:8;88<;<<<;<<8<<;<<<<<<<<<<<<<<<<<<<
+@B7_593:7:67:302:762
+TTACGTCCTATCTTCTTCTTAGGGAAGAACAGCTTA
++
+<<<<<<<<<<<<<<<<<<<<;;65;<-<;<:8<<<3
+@B7_593:7:6:585:132
+GCCCCTTGACCACCACCCAGTCCCTGCCCCATCTCT
++
+:<473$'<+5;7*+<7<&<37<7<<<<7;;7<<:<7
+@B7_593:7:6:585:132
+TGTACTTATCATGTTTCTTTCCTAATTTTTCAATTA
++
+6666166&6)+61))646+6&)&%&-44))1'144'
+@B7_593:7:87:89:696
+TGGTTCTCTTGAAAGCTTGGGCTGTAATGATGCCCC
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<;<:;<<<;<<
+@B7_593:7:87:89:696
+TTCCTATGGAAAGGTTGTTGGGAGATTTTTAATGAT
++
+;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@B7_595:1:209:345:87
+AAACAGTCTAGATGAGAGAGAACTTCCCTGGAGGT
++
+<<;<<<<5<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@B7_595:1:209:345:87
+TTACTTGTTGTTGGTTTTCTGTTTCTTTTTTTGAT
++
+<<<<<<<<<<<<<<<<<<<<;<<<-<<<6<<<+8<
+@B7_595:1:209:653:400
+AGGAGCATTTTGTCAGTTACCAAATGTGTTTATTA
++
+<69<98<+<<6<<4<<<<</4<<:<4<<<<<<<<<
+@B7_595:1:209:653:400
+CTAGAGTCCCATTTGGAGCCCCTCTAAGCCGTTCT
++
+<;<9<<+<2<9<,;;64;<<<<;8<00*1<48:+8
+@B7_595:1:252:19:955
+AGCCAGTTCTTTTGGCATTTGCCTTCAGACCCTCC
++
+<8<884<<<<<<68<<<<<<<2<;<<;<+<<<;<<
+@B7_595:1:252:19:955
+TGAACAAAAGGAAGAAAAGGTCTTTCAAAAGGTGA
++
+<<<<<<<<<<4<<<<9<<+9)9<<4:9+<<0<909
+@B7_595:1:81:1000:375
+ACCCTGAGAGATTCTGCAGCCCAGCTCCAGATTGC
++
+;8<;+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@B7_595:1:81:1000:375
+NATGTCAGGGAAGGAGCATTTTGTCAGTTACCAAA
++
+!.............................+.(+.
+@B7_595:2:178:77:424
+CTACCCTGCAATTAATATAATTGTGTCCATGTACA
++
+:5:8<;<;:<<<<<<<<<<<<<<<<<<<<<<<<<<
+@B7_595:2:178:77:424
+TGCGCTCCACGCCCAAGCCCTTCTCACAGTTTCTG
++
+<<<<<<<<<<<<<<<6<<;<<<<<<<<6<;<<<<6
+@B7_595:2:251:121:479
+GGCTGCAACTGTGAGCCATCACAATGAACAACAGG
++
+<<<<<<<<<<<;:<<<<;:;:<:<;:188;7:<+(
+@B7_595:2:251:121:479
+GGGAAAGCTTTCAACGCTTCTAGCCATTTCTTTTG
++
+<<<<<6'..663;&<<;<<9<<<9<<<<<<<<<<<
+@B7_595:2:29:729:70
+AAACAGAAACCAAATGAGAGAAGGAGTAGCTATAC
++
+<<<:<<<<<<7<<<<<<7<<<<<<<<<<<<<<<<<
+@B7_595:2:29:729:70
+ANTATTANCTTTGANNAAAAAGGGATTAAATTCCC
++
+:!<:<<8!::::5:!!:.77::33888633:8777
+@B7_595:3:229:543:583
+ATAACCATCCTACTAAATACATATGCACCTAACAC
++
+</<;+5<855;<6<<<<;<<<<<<9<<<<<<<<<<
+@B7_595:3:229:543:583
+TCAGGTAAAGGGGTGGAAAAAGATGTTCTACGCAA
++
+<<<<<<<<<<8<8<9<<<<8<<588<<<<*<2:2*
+@B7_595:3:297:637:86
+CAATGTTCCCCAGATACCATCCCTGTCTTACTTCC
++
+<<<<<<<<<<<<;+<+;<;<:<<<<<9<<957<;(
+@B7_595:3:297:637:86
+TCTCAGCTAGGGGAACAGGGAGGTGCACTAATGCG
++
+<:75<;<;;<<<<<<;;<<<<<<<<<<<<<<<<<<
+@B7_595:3:57:735:151
+CTATCCCAAATTCCCAATTACGTCCTATCTTCTTC
++
+<<<<<<<<8<<8<:<<*<:<<<4<<<;,<<<<:<:
+@B7_595:3:57:735:151
+TAAACTCTCACCTTATTGCTGCATCCCTGTCTTCC
++
+07;+79:;<)<<9<+8<:<<<<<<<<<<<<<<<<<
+@B7_595:3:85:964:950
+AACAGATTTAAAAACATGAACTAACTATATGCTGT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;;<;:
+@B7_595:3:85:964:950
+GAGGTCATCATACAATGATAAAAAGATCAATTCAG
++
+<<8::<<;;<<<;<<6<<<<<<<<<<<<<<<<<<<
+@B7_595:4:12:402:843
+AGGGAGGTGCACTAATGCGCTCCACGCCCAAGCCC
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<;;<
+@B7_595:4:12:402:843
+ATATAATTGTGTCCATGTACACACGCTGTCCTATG
++
+<7<+<<11<9<<<<<:<<<<<<<<<<<<<<<<<<<
+@B7_595:4:319:250:718
+AAAAGAAAAAGTGAGAAGTTTGGAAAAACTATTTG
++
+<;:<<<<;<<<:<<<<<<49:<<<<<<<<<<<<<<
+@B7_595:4:319:250:718
+AGTTGAAAGCTCTAACAATAGACTAAACCAAGCAG
++
+<<<<<<<<<<<;<<5<5;<851;85;)9;;8594;
+@B7_595:4:58:703:72
+GTACACACGCTGTCCTATGTACTTATCATGACTCT
++
+5&<<7;+95;7'6<<<<<.<<<<<;<<9<7<<<<<
+@B7_595:4:58:703:72
+TCCACGCCCAAGCCCTTCTCACAGTTTCTGCCCCC
++
+2<7<<<<<<<<<<<8:<<<<8<(<8<:::8.::<3
+@B7_595:4:84:802:737
+CATAGACCCCCTTGCAACAACCTTGAGAACCCCAG
++
++<1<-;69;;;;8;:<<6<;<<<<<<<<<<<<<<<
+@B7_595:4:84:802:737
+CTTAACCTCTGGTGACTGCCAGAGCTGCTGGCAAG
++
+<<<<<<<<<<;9<9<<<;<<;73;<<<<<37;1+.
+@B7_595:5:184:912:258
+ATTCTAAAATCAGCAAGAGAAAAGCATACAGTCAT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<
+@B7_595:5:184:912:258
+GTTATGCCCTGCTAAACTAAGCATCATAAATGAAG
++
+<;;<<<<;:<<7<<<<<<<<<<<<<<<<<<<<<<<
+@B7_595:5:36:649:554
+AAGAGATTGGATCTAATTTTTGGACTTCTTAAAGA
++
+<<<<<888;<<<;<<<;<;<8<<<<8<<<<<<<<<
+@B7_595:5:36:649:554
+CAGGAAGATACATTGCAAGACAGACTTCATCAAGA
++
+<<<<<4<<8<<<<<<8<6<<88<<<<<<<-;<;0;
+@B7_595:5:84:91:614
+GAACCACACATTAATACTATGTTTCTTATCTGCAC
++
+<<;;<<<7<<<<<<<;<;<<<<<<<<<<<<<<<<<
+@B7_595:5:84:91:614
+TTTCCCATCATGAAGCACTGATCTTCCACGTCTCA
++
+;4<<<<<-84<<<;<<<<8<7.<4<<;77&:%<::
+@B7_595:6:119:730:190
+AGTCTCTTATGAATTAACCCAGTCAGACAAAAATA
++
+<<<9<;;<<<;<<<<<<<8<<<1<<918<;;;<<<
+@B7_595:6:119:730:190
+AGTCTTGCTAGAGATTTAGACATCTAAATGAAAGA
++
+;;;3;<<:<<<<:<<<<<<<<<<<<<<<<<<<<<<
+@B7_595:6:137:811:130
+AAAATTTAACAAAAGTAAATAAAACACATAGCTAA
++
+<<<<<<<<<:<<<<<<<<<<<<<<<<<<<<<<<<<
+@B7_595:6:137:811:130
+AGACTACCCAGATTCATAAAACAAATACTACTAGA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<9;;;
+@B7_595:6:290:270:557
+ACATTACTACCCTGCAATTAATATAATTGTGTCCA
++
+87:9;;;<851+:5.<<<<<<<<<<<<<<<<<<<<
+@B7_595:6:290:270:557
+GGAACAGGGAGGTGCACTAATGCGCTCCACGCCCA
++
+<<<<<<<<<<<<<;<<<<9<:;<<<<<<5<0<<;+
+@B7_595:6:47:720:789
+CCCTTGGCCATCACCCGGTCCCGGCCCCTTCTCTT
++
+<<72<<<<<<<<;;<7;,0<2;*7<2;<*;;<<64
+@B7_595:6:47:720:789
+TCCTCAATGTTAAAATGTCTATTTTTGTCTTGACA
++
+/)040<.878<<<<;8<;<9<9;<<<<<<<<<<93
+@B7_595:6:52:751:360
+AAAAACTATTTGAGGAAGTAATTGGGGAAAACCTC
++
+<<<<<<<<<<<<<<<<<<<<<<<:76<<<<;9:;:
+@B7_595:6:52:751:360
+AGAGAAAAGCATACAGTCATCTATAAAGGAAATCC
++
+<-<9<<<<<6<<<8<<;;<<9<<<<<<<<<<<<<<
+@B7_595:6:99:557:427
+AACAAAATTAAAATTTAACAAAAGTAAATAAAACA
++
+<<-<<<<9<<<<<:<<<<9<<<<<<<<<<<<<<<<
+@B7_595:6:99:557:427
+ATTCATAAAACAAATACTACTAGACCTAAGAGGGA
++
+<<<<<<<<<<<<<<<<<<<<<<:<<<<+;<7:8:;
+@B7_595:7:123:610:472
+GTCTGAGCAAAACAGTCTAGATGAGAGAGAACTTC
++
+:<::+<<9<<9<<<<=<<<<<=<<<<<<<<?<<<<
+@B7_595:7:123:610:472
+TGCATCCCTGTCTTCCTCTGTCTTGATTTACTTGT
++
+<<<<<<<<<<:<<<<<<<<<<<<<+:<<<<<<<<;
+@B7_595:7:149:123:265
+AAGAGGGATGAGAAATTACCTAATTGGTACAATGT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<9
+@B7_595:7:149:123:265
+AGCAAAAACAAAAACTATGCTAAGTATTGGTAAAG
++
+<;&<<<<<:<<<<<<<<<<;<<<<<<<<<<<<<<<
+@B7_595:7:166:203:416
+AATTACGTCCTATCTTCTTCTTAGGGAAGAACAGC
++
+<<<<<<<<::<<<<<<<<<;<<<<<<<<<<<<<<<
+@B7_595:7:166:203:416
+ATGAGATTATTAGGAAATGCTTTACTGTCATAACT
++
+<<<<<<<<<<<<<<<<<<;<<<<<<<;<<<<<97<
+@B7_595:7:188:802:71
+ATGCTATTCAGTTCTAAATATAGAAATTGAAACAG
++
+<<<<<<<<<;<<<<<9<<<:<<<:<<<<<<:<<<;
+@B7_595:7:188:802:71
+TGCCCTCTTCTTCCAAAGATGAAACGCGTAACTGC
++
+;;;;<:::<<<<<7<<<<<<<<<<<<<<<<<<<<<
+@B7_595:7:190:481:295
+GAAGAACAGCTTAGGTATCAATTTGGTGTTCTGTG
++
+;<<:<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@B7_595:7:190:481:295
+TCATAACTATGAAGAGACTATTGCCAGATGAACCA
++
+<<<<<<<<<<<<<<<<<<<<<<9<<<<<9<7<2::
+@B7_595:7:242:4:593
+ATATACACACGCTGTCCTATGTACTTATCATGACT
++
+1.%55877+8+88808887+7;7;18:8;;;.&;8
+@B7_595:7:242:4:593
+TCCACGCCCAAGCCCTTCTCACAGTTTCTGCCCCC
++
+<<<<<<<<<<<8<<<<-<<<<<88;<;<<8<;88<
+@B7_595:8:26:242:35
+ATAAAACAAAGGAGGTCATCATACAATGATAAAAA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<<<<;
+@B7_595:8:26:242:35
+ATATTTTGATGATGGTTACACTAAAAGCCCATACT
++
+<<<77!!7<;<<<;;<<<<<<<<<<<<<<<<<<<<
+@B7_597:2:100:563:301
+GAACTTCTGTAATTGAAAAATTCATTTAAGAAATT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<:;8;;;
+@B7_597:2:132:493:921
+ACGGGGTTGCCAGCACAGGGGCTTAACCTCTGGTG
++
+<<<<<<<<<<<<<<<<;<<<<<<<<;<<<<;;88:
+@B7_597:2:132:493:921
+GTTCTCAAGGTTGTTGCAAGGGGGTCTATGTGAAC
++
+<<<<<<<<<<<<<<<<<<<;<<<<77;0<;;6777
+@B7_597:2:165:431:857
+GAACTTTGATGCCCTCTTCTTCCAAAGATGAAACG
++
+<<<<<<<<<<<<<<<<<<<<<<<6&:<7<:76,;;
+@B7_597:2:165:431:857
+TTGGGGTCTGACAGGCTGCAACTGTGAGCCATCAC
++
+''7'/;'1%0447<<<*<6<<<*<*<<<<6<<<<<
+@B7_597:2:168:829:88
+ACAGACTTCATCAAGATATGTAGTCATCAGACTAT
++
+<,,;<838883;;;<<<<<;<8<8;<<<<<<<<<<
+@B7_597:2:168:829:88
+TAACTGAACCTATGAGTCACAGGTATTCCTGAGGA
++
+<<<<<<<<<<<<<<<<<<<<<<<6<<<<<<9;4;2
+@B7_597:2:42:28:552
+AAGAAGATATAACCATCCTACTAAATACATATGCA
++
+<<<<<<<<<<<<<<<<<<<<<<<<;<;<3<:;9;8
+@B7_597:2:42:28:552
+ACTCAATATATCCATGTAACAAATCTGCGCTTGTA
++
+</8:<<:<<<;;<<<<<<<<<<<<<<<<<<<<<<<
+@B7_597:3:10:394:392
+TCATCAAGATATGTAGTCATCAGACTATCTAAATT
++
+<<<<<<<<<<<<<<<<<<<:<<<<<<;<<;;:6&;
+@B7_597:3:10:394:392
+TTGGACTTCTTAAAGAAAAAAAAACCTGTCAAACA
++
+28-:;0-<0<<<<<<<<<<<<<<<<<<<<<<<<<<
+@B7_597:3:115:646:430
+CACAGGTTTTATAAAACAATTAATTGAGACTACAG
++
+5;5<;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@B7_597:3:115:646:430
+GTTATGCCCTGCTAAACTTAGCATCATAAATGAAG
++
+<7<<<<<<<<<<<<;<<<<<;<7<<<<;5;<;67<
+@B7_597:3:133:707:886
+ACCTAATAAATACATATGCACCTAACACAAGACTA
++
+%5-2;&6<<<<<;<<<<<<<;<<<<<<<<<<<<<<
+@B7_597:3:133:707:886
+AGGTAAAGGGGTGGAAAAAGATGTTCTACGCAAAC
++
+<<<<7;<<<<<<<<<;<<<<<<<<<<<<<5<;66<
+@B7_597:3:157:361:309
+CCTGCTAAACTAAGCATCATAAATGAAGGGGAAAT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<;<;<;<<;<
+@B7_597:3:157:361:309
+TACACACAAAAGTACAAAACTCACAGGTTTTATAA
++
+:<-<5<0<<<<<<<;<<<<<<<<<<<<<<<<<<<<
+@B7_597:3:39:966:551
+ACATTAATACTATGTTTCTTATCTGCACATTACTA
++
+<<<<<<<<<<<<<<<<<<<<<<<<:<;<&<<&<<;
+@B7_597:3:39:966:551
+AGGGAGCCGTCCGTGTCCTCCCATCTGGCCTCGTC
++
+8;;;;;<<6'<<<+8<<<1<<<<4<<<<<<<<<<<
+@B7_597:3:46:981:766
+TCTTTTGGCATTTGCCTTCAGACCCTACACGAATG
++
+<<<<<<<<<<<<<;<<<<<-<;<<<<-<-<;-:6;
+@B7_597:3:46:981:766
+TGCCCCCAGCATGGTTGTACTGGGCAATACATGAG
++
+/<<<;/;<<316<<<3<<<<7<<<7<<<;<<<<<7
+@B7_597:3:53:616:842
+CTTATCATGACTCTATCCCAAATTCCCACTTACGT
++
+<<<<<<<<<<<<<<<<<<<;07<<<<<-&<<-<4;
+@B7_597:3:53:616:842
+TCACCCAGTCCCTGCCCCATCTCTTGTAATCTCTC
++
+;<;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@B7_597:3:67:620:344
+AGCTTTCAACGCTTCTAGCCATTTCTTTTGGCATT
++
+<<<<2<:2<<<<<<7<<<<:<<*<<<<<<***3<<
+@B7_597:3:67:620:344
+CCCCCGCCCAAGCCCTTCTCACAGTTTCTGCCCCC
++
++++*+++#++++++,++++++++,,+,&+,,,,+,
+@B7_597:3:73:273:488
+AAAACAGTCTAGATGAGAGAGAACTTCCCTGGAGG
++
+</<<:<<9;;<<<<<<<<<<<<<<<<<<<<<<<<<
+@B7_597:3:73:273:488
+CTCTCTCCTTTTTGCTGCATCCCTGTCTTCCTCTG
++
+<<<<<2<88<88<<<8<<1<<<<<<68<<<;<;<*
+@B7_597:4:138:211:582
+CATTAATAAAGACATGAGTTCAGGTAAAGGGGTGG
++
+:<8;<<<<<<<<<<<<<<;<<<<<<<<<<<<<<<<
+@B7_597:4:138:211:582
+TGAGACTACAGAGCAAATAGGTAAAAAATTAACAT
++
+<<;<<<<<<<<<<<<<&;<;<7<<;<<<<<<<5<<
+@B7_597:4:144:492:61
+AAATACTCACCATCATAAATACACACAAAAGTACA
++
++;;3;,:7<:;<<7<<<<<<<;;<<<<<<<<<<<<
+@B7_597:4:144:492:61
+AACCTGTCAAACACGAATGTTATGCCCTGCTAAAC
++
+<<<;<<<<<<<<<<<;<<<<<<7:<<<<::;9;;6
+@B7_597:4:146:961:63
+TACTTATATCAGATAAAGCACACTTTAAATCAACA
++
+7;;<<<<<;<<<7<<<<<<<<;;<<;<;<<;<<<7
+@B7_597:4:146:961:63
+TGAATAAAAAGGGCTTAAATTCCCCCACTTAAGGG
++
+<<+<<<<::+1<;&<<88<<<<;;.<0;;85(;(8
+@B7_597:4:38:999:463
+GCGGAAACCTTACAAGCCAGAAGAGATTGGATCTA
++
+.*:&<<0<0!<<+<<<<<<<<<<<<<0<<<<<<<<
+@B7_597:4:38:999:463
+TAGACATCTAAATGAAAGNNGCNNNAAGAATGCCA
++
+7<<<<<<<<:07<<:<<7!!<<!!!::<88<<<<4
+@B7_597:5:125:957:753
+TTTTTTTTTTTTCTCTCCTCTTTTTTTTTTTTTTT
++
+<8<<<;<8;8//++(,(+++&++(/+008880;;/
+@B7_597:5:160:434:853
+ATATAATTGTGTCCATGTACACACGCTGTCCTATG
++
+<<<<<<<<<<<<<<<<<<<<<<,<<<<:<<<<,<:
+@B7_597:5:160:434:853
+GCTTGGGCTGTAATGATGCCCCTTGGCCATCACCC
++
+;;*4;<;<<<;<<<<<<<8<<<;<<<<<<<<8<<<
+@B7_597:5:58:684:520
+AGACAGACTTCATCAAGATATGTAGTCATCAGACT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<:;;<<
+@B7_597:5:58:684:520
+ATTTTTGGACTTCTTAAAGAAAAAAAAACCTGTCA
++
+<85;;:<<<7<<7<<<<<<<<<<<<<<<<<<<<<<
+@B7_597:5:6:882:784
+CATGGCTGATTATGAAAACAATGTTCCCCAGATAC
++
+4;7<;64<<:<<4<<<<<;<<<<<<<<<<<<<<<<
+@B7_597:5:6:882:784
+CTGGATTCTGGGAAATTCTTCATCCTGGACCCTGA
++
+<<<<<<<<<<<<<:<<<<<<<<<<<<:6::::<,2
+@B7_597:5:98:995:929
+GTCCTATAAGAAATGCTCAAAAGAATTGTAAAAGT
++
+<;<;<8<;<<;1;<<<<<;<;;;08;<;<1&0+8<
+@B7_597:5:98:995:929
+TATAACAATATTAACTTTGAATAAAAAGGGATTAA
++
+&<+<'7<<+<&<<<7+4<<<<<<<<<<<<<<<<<<
+@B7_597:6:106:595:322
+GAGGAAGTAATTGGGGAAAACCTCTTTAGTCTTGC
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<:<<<<::
+@B7_597:6:106:595:322
+GCAAGAGAAAAGCATACAGTCATCTATAAAGGAAA
++
+;+<<<<<<<<<<<<<<<<<<;<<7<<<<<<<<<<<
+@B7_597:6:193:661:771
+AAACTCATTAATAAAGACATGAGTTCAGGTAAAGG
++
+<<<<<<<<<;<<<;;;<<<<<;<<<=;<:;5:9::
+@B7_597:6:193:661:771
+GCAAGAAGATATAACCATCCTACTAAATACATATG
++
+:&<<<<<<<<<<<<<;<<<;<<;<<<<<<<<<<<<
+@B7_597:6:20:592:496
+CTCAAAGAATGCCAGGAAGATACATTGCAAGACAG
++
+<<<<<<<<<<<<<<<<<<<<<<<<<==<<<<<<:<
+@B7_597:6:20:592:496
+TCTCAGCGGAAACCTTACAAGCCAGAAGAGATTGG
++
+97<7;<;<;<<<<;<9<<<<<<<<<<<<<<<<<<<
+@B7_597:6:29:249:878
+ATTGTGTCCATGTACACACGCTGTCCTATGTACTT
++
+<,;<9<;<:<<<<<<<<<<<<<<<<<<<<<<><<<
+@B7_597:6:29:249:878
+TCTCACAGTTTCTGCCCCCAGCATGGTTGTACTGG
++
+<<<<<<<<<<<<<<<<<<<<<<:<:<<=<<:<<6&
+@B7_597:6:73:420:812
+CTAAGTATTGGTAAAGATGTGGGGAAAAAAGTAAA
++
+5'<<<,<&,<<,<<<<<7<<<<<<<<<<<<<<<<<
+@B7_597:6:73:420:812
+CTAATTGGTACAATGTACAATATTCTGATGATGGT
++
+<<<<<1<<<<::1<7<:<96<9<:<<:4<70:11<
+@B7_597:7:103:731:697
+AATTAACCCAGTCAGACAAAAATAAAGAAAAAAGA
++
+<<<<<<<<<<<<<<<<<<:<:<<6<<<<<<<:<;:
+@B7_597:7:103:731:697
+CTTGCTAGAGATTTAGACATCTAAATGAAAGAGGC
++
+:::;3:<<<<<<<:<<<<<<:<<<<<<<<<<<<<<
+@B7_597:7:113:408:211
+AAACTCATTAATAAAGACATGAGTTCAGGTAAAGG
++
+<:;:;:<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@B7_597:7:113:408:211
+GAGACTACAGAGCAACTAGGTAAAAAATTAACATT
++
+<<<<<<<<<<<<<<<:&<<<&:<<<<<<<<<<;:/
+@B7_597:7:31:948:254
+CCTCTACATGGCTGATTATGAAAACAATGTTCCCC
++
+<<<<<<<<<<<<<<<<<<<;<<<<<:<<8<;;;;<
+@B7_597:7:31:948:254
+TGAAGCACTGAACTTCCACGTCTCATCTAGGGGAA
++
+7;;;98<<7<<<<<<<<<<<<<<<<<<8<<<<<<<
+@B7_597:7:41:34:211
+CACCTAACACAAGACTACCCAGATTCATAAAACAA
++
+7</::<<7<<<<<<;<<<<;<<<<<<<<<<<<<<<
+@B7_597:7:41:34:211
+GTAAAGGGGTGGAAAAAGATGTTCTACGCAAACAG
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<3:;5;
+@B7_597:7:5:753:806
+AAAATATAGTTGAAAGCTCTAACAATAGACTAAAC
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<7:-<;;3;;
+@B7_597:7:5:753:806
+ATGTAAAGTAACTGAACCTATGAGTCACAGGTATT
++
+;:<:<<<<:<<<<<<<<<<<<<<<<<<<<<<<<<<
+@B7_597:7:94:273:165
+AGAAAGAAGATATAACCATCCTACTAAATACATAT
++
+;3&;;:<<:<-<-<<8:<<<<<<<<<<<<<<<<<<
+@B7_597:7:94:273:165
+TTACAAGAAACTCATTAATAAAGACATGAGTTCAG
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<:;;:7
+@B7_597:8:147:360:141
+TGCGCTTGTACTTCTAAATCTATAACAAAATTAAA
++
+<<<<<<<<<<7<<<<<<<<<<<<<<<<<<<<<<<7
+@B7_597:8:147:360:141
+TTTGGTAATTTAGTTTTTTTTTTTTCTTTTCTCTT
++
+<86<<<<73<7<<<<<<<<<<<<<<<<<<<<<<<<
+@B7_597:8:186:850:838
+GGAAGAGGGACGCTGAAGAACTTTGATGCCCTCTT
++
+<;<;<;<<<<;<<<<<<<<<<<<<<<<<<<<<<<<
+@B7_597:8:186:850:838
+GTTCTATTTGTAATGAAAACTATATTTATGCTATT
++
+<<<<<;<<<<<<<<<<<:<<<<<;<<<;</<<;<<
+@B7_597:8:35:118:589
+TCATAAAACAAATACTACTAGACCTAAGAGGGATG
++
+67<<<<<;<<<<<<<:7<<<<:<<<<<<<<<<<<<
+@B7_597:8:35:118:589
+TGTTCTACGCAAACAGAAACCAAATGAGAGAAGGA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<;<:<<<<<9
+@B7_597:8:48:805:860
+AAACCTGTCAAACACGAATGTTATGCCCTGCTAAA
++
+<<<<<<<;<<<<<<<41;<<8<<<<<<<8+<4,+;
+@B7_597:8:48:805:860
+AAAGTACAAAACTCACAGGTTTTATAAAACAATTA
++
+<<<;3<;7<<97<7<<<<7<4<<<<<<<<<<;8<+
+@B7_610:1:12:88:200
+ACATGAGTTCAGGTAAAGGGGTGGAAAAAGATGTT
++
+<<<<<<<<<<<;<<<<<<<;<<<:<<<<<<9<<5<
+@B7_610:1:12:88:200
+GAAGATATAACCATCCTACTAAATACATATGCACC
++
+9<<;<<<;<;6;<;:<<<7<<<<<<<<<<<<<<<<
+@B7_610:1:139:152:856
+AGAGGGACGCTGAAGAACTTTGATGCCCTCTTCTT
++
+<<<<<;<<<<<<<<<<;<;<<<<<<<<<<<<<<<<
+@B7_610:1:139:152:856
+CTAAGCCGTTCTATTTGTAATGAAAACTATATTTA
++
+<<<<<<<<;<<<<<<<<<<;<;<<<;<<<<;<;;;
+@B7_610:1:37:652:403
+CCCCTCTAAGCCGTTCTATTTGTAATGAAAACTAT
++
+<<<<<<<;<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@B7_610:1:37:652:403
+TTTTGTCAGTTACCAAATGTGTTTATTACCAGAGG
++
+<;<<<<:<<;<<<<<<<<<<<<<<<<<<<<<<<<<
+@B7_610:2:189:831:878
+AGAAAAAAAAACCTGTCAAACACGAATGTTATGCC
++
+<9<<<<<<<<<<;9<:<<<<<6<<<<<<<;<<<<<
+@B7_610:2:189:831:878
+AGGAAGATACATTGCAAGACAGACTTCATCAAGAT
++
+:<<<2<<<<<<<<<<:8<8<<<<<<<<<<87489;
+@B7_610:2:194:688:289
+TCAGACCCTACACGAATGCGTCTCTACCACAGGGG
++
+;8;%28<;<<<<<<<<;<<<<;<<<<<<<<<<<<<
+@B7_610:2:194:688:289
+TGTGTGTTCTCATCAACCTCATACACACACATGGT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<9<<<:;
+@B7_610:2:6:529:366
+CATACAATGATAAAAAGATCAATTCAGCAAGAAGA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@B7_610:2:6:529:366
+GCTACTCAATATATCCATGTAACAAATCTGCGCTT
++
+9;8;8<:<<<<<<<;<<<<<<<<<<<<<<<<<<<<
+@B7_610:2:75:887:149
+TACAACAGGAACAAAACCTCATATATCAATATTAA
++
+<<<<<<<<<<<<<<;<<<<<<<;<<<<<<<;<;;;
+@B7_610:2:75:887:149
+TACGCAAACAGAAACCAAATGAGAGAAGGAGTAGC
++
+:<:<0<<<;<<<<<<<<<<<<<<<<<<<<<<<<<<
+@B7_610:3:102:825:507
+TGCTGCATCCCTGTCTTCCTCTGTCTTGATTTACT
++
+<<<<<<<<<<<<<<<<<<<<<<;<<<<<<<<<;;<
+@B7_610:3:102:825:507
+TTTGTCTGAGCAAAACAGTCTAGATGAGAGAGAAC
++
+<05<<<<<<<7<<<<<<<<<<<<<7<<<<<<<<<<
+@B7_610:3:120:63:653
+AACAACAGGAAGAAAAGGTCTTTCAAAAGGTGATG
++
+<<;<<;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@B7_610:3:120:63:653
+TCTTCTTCCAAAGATGAAACGCGTAACTGCGCTCT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<9<9<<<
+@B7_610:3:137:895:681
+CTTCCTATGGAAAGGTTGTTGGGAGATTTTTAATG
++
+4;5+6;<<<<<<<<<9;<4<<<<<<<<<<<<<<<<
+@B7_610:3:137:895:681
+GCCTCGTCCACACTGGTTCTCTTGAAAGCTTGGGC
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<:<<<-8<<
+@B7_610:3:148:340:479
+TCTGTGTAAAGTCTCAGGGAGCCGTCCGTGTCCTC
++
+<<<<<<<<<<<<<<<<:<:<<<<<<<<<<<<<<<<
+@B7_610:3:148:340:479
+TTGTTGTTGGTTTTCTGTTTCTTTGTTTGATTTGG
++
+<<;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@B7_610:3:182:23:585
+AGAACAGCTTAGGTATCAATTTGGTGTTCTGTGTA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<:<<<
+@B7_610:3:182:23:585
+ATCCCTGTCTTCCTCTGTCTTGATTTACTTGTTGT
++
+9:<<<<<<<<<<<<<<<9<<<<<<<<<<<<<<<<<
+@B7_610:3:5:863:302
+ACGTCTCATCTAGGGGAACAGGGAGGTGCACTAAT
++
+:4:29:<<<9;<<<<<<<<<<<<<<<<<<<<<<<<
+@B7_610:3:5:863:302
+TGAAAACAATGTTCCCCAGATACCATCCCTGTCTT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<9<<<<<
+@B7_610:3:82:998:566
+ATCTGGCCTCGTCCACACTGGTTCTCTTGAAAGCT
++
+<9<9<<<<2<<<<<<<<<<<<<<<<<<<<<<<<<<
+@B7_610:3:82:998:566
+GCACATTACTACCCTGCAATTAATATAATTGTGTC
++
+<<<<<<<:<<0<<<<:<82<<::<4<<;<<4<4<;
+@B7_610:3:84:101:328
+AATGGACCTGTGATATCTGGATTCTGGGAAATTCT
++
+<<<;<<<<<<<<;<<<<<<<<<<:<;;<44;;<;<
+@B7_610:3:84:101:328
+TATAATACCTCTACATGGCTGATTATGAAAACAAT
++
+<<<<<<<<:<<<<<<<<<6<<<<<<<<<<<<<<<<
+@B7_610:3:85:219:371
+GACATGAGTTCAGGTAAAGGGGTGGAAAAAGATGT
++
+<<7<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@B7_610:3:85:219:371
+TAACATTACAACAGGAACAAAACCTCATATATCAA
++
+<<<<<<<<<<<<<<<<<<<<<:<<<<<<<<<<;<;
+@B7_610:4:139:989:144
+ACTAAAAAAGCAAAAACAAAAACTATGCTAAGTAT
++
+<&<<<<<<<<7<<<<<<<<<<<<<<<<<<<<<<<<
+@B7_610:4:139:989:144
+ACTACTAGACCTAAGAGGGATGAGAAATTACCTAA
++
+<<<<<<<<<<<<6<<<<<<<<<;<<<<<<<;;<;;
+@B7_610:4:15:805:420
+ATGAAGAGACTATTCACATGTGAACCACACATTTA
++
+;73;;;;67.;1<<+*.;*&<4947<&474&*9*(
+@B7_610:4:15:805:420
+GAACAGTTTAGGTATCAATTTGGTGTTCTTTGTAA
++
+<64<59&996<(64<)7).68<0<0<<7741<1:<
+@B7_610:4:198:59:675
+AATCTGCGCTTGTACTTCTAAATCTATAACAAAAT
++
+<<<<<4<4<:<<<;7<<;<<<<<<<<<<<<<<<<<
+@B7_610:4:198:59:675
+ACTAAATACATATGCACCTAACACAAGACTATCCT
++
+<.<<<<<<;<<<<<<<<<<<**<;<;2<;6;&*2&
+@B7_610:4:67:317:249
+CTACATGGCTGATTATGAAATCTATGTTCCCCATA
++
+<<<<<<;<<<<;:;<<7;<<.<&3<;;<<(;;6.<
+@B7_610:4:67:317:249
+TTCCCATCATGACGCACCGAACTTCCACGTCTCAT
++
+.5;7;++;<8.;&:7<<.5<<<<7<<7<<<<<<;7
+@B7_610:5:102:915:87
+AACAATAGACTAAACCAAGCAGAAGAAAGAGGTTC
++
+<<<<<<<<<<<<<<<<<<<<;<<<<<3<<;<<<<;
+@B7_610:5:102:915:87
+CACAGGTATTCCTGAGGAAAAAGAAAAAGTGAGAA
++
+;<8<;;<<<<7;<<<;<<<<<<<<<<<<<<<<<<<
+@B7_610:5:120:596:847
+AACCTATGAGTCACAGGTATTCCTGAGGAAAAAGA
++
+<<<<<<<<<<<<<;<<<9<<<<<<<;:<62;58;2
+@B7_610:5:120:596:847
+TCAACATGAAGGAAAAAAATTCTAAAATCAGCAAG
++
+;/<<:<;<<<<<<<<<<<<<;;<<<<<;<<<<<<<
+@B7_610:5:136:260:254
+AAATTAACATTACAACAGGAACAAAACCTCATATA
++
+<<<<<<<<<<<<<<<<<<><<<<<<<<<<<<<<<<
+@B7_610:5:136:260:254
+GTGGAAAAAGATGTTCTACGCAAACAGAAACCAAA
++
+;:;;<<<<<<<<<<<<<<;<;<<<<<<<<<<<<<<
+@B7_610:5:147:68:353
+AACAACCTTGAGAACCCCAGGGAATTTGTCAATGT
++
+<;<;<<7<<<<<<<7<<;;<7<4<8<<<8.;4;;;
+@B7_610:5:147:68:353
+CCTTTGATATCTGGATTCTGGGAAATTCTTCATCC
++
+<<;;<<<<<<<<+;<<;<<0;<<<<;<<<<<<<<<
+@B7_610:5:51:904:391
+ACCTATGAGTCACAGGTATTCCTGAGGAAAAAGAA
++
+<<<<<<<<<<<<<<<<<;<<<<<;:;<2<6;;;;;
+@B7_610:5:51:904:391
+TATCTAAAGTCAACATGAAGGAAAAAAATTCTAAA
++
+;<96<<<<<<7<<7<<<<<<<<<<<<<<;<<<<<<
+@B7_610:5:7:761:623
+CCGGCATGGTTGTACTGGGCAATACATGAGATTAT
++
+::';-8);<<<<;<1<<<<:<<<<<<<<<<<<<<<
+@B7_610:5:7:761:623
+CTTTCAACGCTTCTAGCCATTTCTTTTGGCATTTG
++
+<<<<<<<<<<<<<8<<<<;;<0<<<<<;;<;<;;&
+@B7_610:6:107:252:533
+AGAGAAGGAGTAGCTATACTTATATCAGATAAAGC
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<;<<;9
+@B7_610:6:107:252:533
+CAAGACTACCCAGATTCATAAAACAAATACTACTA
++
+3<<<<+<<96<<<<<<;<<<<<<;<<<<<<<<<<<
+@B7_610:6:111:379:700
+ACACTAAAAGCCCATACTTTACTGCTACTCAATAT
++
+7<<:<<<<02<<6&<</<<</+9/98*<966/3/<
+@B7_610:6:111:379:700
+CGCACTGGCAATATTTGTGTGTTTACTTTTTTGCA
++
+:1+&;;6;:;918;);;):,19.9:).):::.&3(
+@B7_610:6:143:620:158
+ACTTTACTGCTACTCAATATATCCATGTAACAAAT
++
+<4;<;<;<;6<<7<;<<<<<<<;<<<<<<<<<<<<
+@B7_610:6:143:620:158
+CAATGATAAAAAGATCAATTCAGCAAGAAGATATA
++
+<<<<<<<<<<;<<<<<<<<<<<<<<<<<<<<<;<<
+@B7_610:6:148:776:486
+AACTGTGAGCCATCACAATGAACAACAGGAAGAAA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;;
+@B7_610:6:148:776:486
+AGCTTTCAACGCTTCTAGCCATTTCTTTTGGCATT
++
+;:<<<;<<;<<<<<;<<<<<<<<<<<<<<<<<<<<
+@B7_610:7:116:157:612
+GTAAAAGTCAAAATTAAAGTTCAATACTCACCATC
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@B7_610:7:116:157:612
+TTAAGAGATATAGATTGGCAGTACAGATTTAAAAA
++
+;;<<<<<<<<<<<<<<<<;<</<<<<<<<<<<<<<
+@B7_610:7:117:857:942
+AGAGAGAACTTCCCTGGAGGTCTGATGGCGTTTCT
++
+<<;<<<<<<<9<<<8<<<<<<<<<<;<<<<<<<<<
+@B7_610:7:117:857:942
+GGTTTTCTGTTTCTTTGTTTGATTTGGTGGAAGAC
++
+<<<<<<<<<<<<<<<<<<<<<<<<<:6<;;7;9<;
+@B7_610:7:158:943:467
+AAAGCTCTAACAATAGACTAAACCAAGCAGAAGAA
++
+<<<<<;<<<<<<<<<<<<<<;;<<<<<<<<<;8<<
+@B7_610:7:158:943:467
+AGGTATTCCTGAGGAAAAAGAAAAAGTGAGAAGTT
++
+<:<<;;<:5<<<<<<<<<<<<<<<<<<;<<<;<<<
+@B7_610:7:15:696:693
+TCAAACACGAATGTTAATCCCTGCTAAACTAATCA
++
+)6<:7<.7<6.<0&&<&3:&7<<7<0<<<<<<<<<
+@B7_610:7:15:696:693
+TCTAAAGTCAACATGAAGGAAAAAAATTCTAAAAT
++
+2:+:7<<3<<<<<6+36<<<<<<<6<<6&<<;<.7
+@B7_610:7:177:469:800
+AAAATCAGCAAGAGAAAAGCATACAGTCATCTATA
++
+=<<<;;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@B7_610:7:177:469:800
+TTGGAAAAACTATTTGAGGAAGTAATTGGGGAAAA
++
+<<<<<<<<<<<<<<<<<<<<<<<<;<<;;<<<;<;
+@B7_610:7:26:749:174
+CAGATTCATAAAACAAATACTACTAGACCTAAGAG
++
+<<<<<<<<<<<<<<<<<<<<<<;<9<8<<<9<;94
+@B7_610:7:26:749:174
+TAACAAAAGTAAATAAAACACATAGCTAAAACTAA
++
+(<<)<<<<6<<<<<<<<<<&:<3<<<6<<<)<:<<
+@B7_610:7:34:144:868
+AATTACCTAATTGGTACAATGTACAATATTCTGAT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<4;<
+@B7_610:7:34:144:868
+AGCTAAGGAATGGGAAAGGTGTGGGGAAAAAAGTA
++
+&9+&7<&&0&<6<.0<<7<<<<<<<<<<<<<<<<<
+@B7_610:7:35:378:681
+GCGTCTCTACCACAGGGGGCTGCGCGGTTTCCCAT
++
+:<5-<);;;<<<<<<<<<<<<<<<<<<<<<<<<<<
+@B7_610:7:35:378:681
+GTGTGTTCTCATCAACCTCATACACACACATGGTT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<:<
+@B7_610:8:163:757:432
+CCAGATGAACCACACATTAATACTATGTTTCTCAT
++
+1+<8<<<<<<;<5<;<<<<<;5<<<<<<<<<<<<<
+@B7_610:8:163:757:432
+GGTTTCCCATCATGAAGCACTGAACTTCCACGTCT
++
+<<<<<<<;<<<<<<<<;<;<<<<<<<<<<<<83:<
+@B7_610:8:68:570:705
+AACAGATTTAAAAACATGAACTAACTATATGCTGT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<;<<<<<<8<
+@B7_610:8:68:570:705
+CATCATACAATGATAAAAAGATCAATTCAGCAAGA
++
+4<;4<;;:<<<<<<<<;<<<<<<<<<<<<<<<<;<
+@B7_610:8:95:426:791
+CCAAATGTGTTTATTACCAGAGGGATGGAGGGAAG
++
+<<<<;<<<<<<<<<<<<<<<<<<<<<<<<<<<,<<
+@B7_610:8:95:426:791
+GNTCCAGATTGCTTGTGGTCTGACAGGCTGCAACT
++
+!!!!<<<<<;;<<<<;<<;<;;<<<<<<<<<<<<<
+@EAS112_32:7:113:809:364
+GATGCCCTCTTCTTCCAAAGATGAAACGCGTAACT
++
+;<;;;<<<:<6<<<::<<<<<<<<<<<<<<<<<<<
+@EAS112_32:7:113:809:364
+TATAGAAATTGAAACAGCTGTGTTTAGTGCCTTTG
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<7<;<;<<<4
+@EAS112_32:7:135:401:735
+AATTGTAAAAGTCAAAATTAAAGTTCAATACTCAC
++
+<<::7<<<<<<::<<<<<<<<<<<<<<<<<<<<<<
+@EAS112_32:7:135:401:735
+CCTTACAAGCCAGAAGAGATTGGATCTAATTTTTG
++
+<<<<<<<<<<<<<<<<<<<<<;<<<<<8<<<<<<;
+@EAS112_32:7:168:117:441
+TCATAACTATGAAGAGACTATTGCCAGATGAACCA
++
+<<3<<<<<<<<<<<<<<<<<<<+<<17;<;:<995
+@EAS112_32:7:168:117:441
+TCTTCTTAGGGAAGAACAGCTTAGGTATCAATTTG
++
+;;;;3;<<<<<<<<<<<<<;<<<<<<<<<<<<<<<
+@EAS112_32:7:272:328:400
+CAGGTAAAGGGGTGGAAAAAGATGTTCTACGCAAA
++
+<<<<<<<<;<<<<<<<<<<<<<<<<<<<<<7<;:7
+@EAS112_32:7:272:328:400
+CTAAATACATATGCACCTAACACAAGACTACCCAG
++
+4;<<<<<7<;<<<-<;<<<<<<<<<<<<<<<<<<<
+@EAS112_32:7:322:391:742
+ATCAATATTAACTTTGAATAAAAAGGGATTAAATT
++
+<63<<<<9<<<:<;<<<<<<<<<<<<<<<<<<<<<
+@EAS112_32:7:322:391:742
+CATCACTAAACCAGTCCTATAAGAAATGCTCAAAA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<;;
+@EAS112_32:7:42:804:114
+ATACTTTACTGCTACTCAATATATCCATGTAACAA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<:<:<;;<;;
+@EAS112_32:7:42:804:114
+TCAAATATTGCTAGTGGGAGTATAAATTGTTTTCC
++
+;9<<;<<<<<<;<<<<<<<<<<<<<<<<<<<<<<<
+@EAS112_32:8:88:90:59
+ATAATACCTCTACATGTCTGATTATGAAAACAATG
++
+<<<<<<<4;7;<<<;;47;&9..1;6&4<755;1;
+@EAS112_32:8:88:90:59
+TGCACCTCCCTGTTCACCTAGATGCTAGGAGGACA
++
+=7595=92=72.=+5(:4=9092((.2&(&%07%.
+@EAS112_32:8:89:254:332
+AAACCTCTTTAGTCTTGCTAGAGATTTAGACATCT
++
+<<<<<<:<;<<<<<<<<9<<<<<<<<<<<<<<<<<
+@EAS112_32:8:89:254:332
+GAATTAACCCAGTCAGACAAAAATAAAGAAAAAAG
++
+==================;=========;=7;;<;
+@EAS112_34:4:12:273:89
+AGTCTTTCCTGACAAGCAAATGCTAAGATAATTCA
++
+<:737<288<<<7<<<<<<<<<:9<<<<<<<<<<<
+@EAS112_34:4:12:273:89
+CCATCAGAATAACAATGGGCTTCTCAGCGGAAACC
++
+==========<====:=========+===4414;;
+@EAS112_34:4:17:989:186
+TTAGTCTTGCTAGAGATTTAGACATCTAAATGAAA
++
+87;38$<3=/<==============9=========
+@EAS112_34:4:17:989:186
+TTATGAATTAACCCAGTCAGACAAAAATAAAGAAA
++
+<<<<<<<<<<<<<<<<<<<<<<<<:<<;<7;::::
+@EAS112_34:4:22:206:150
+AAAAAAGAGCAACTAGGTAAAAAATTAACATTACA
++
+8&)<)<<<<+<<+<<<<<<<<<<<<<<<<<<<<<<
+@EAS112_34:4:22:206:150
+GAAATAAAGTCAAGTCTTTCCTGACAAGCAAATGC
++
+==========================::=5&;<2<
+@EAS112_34:4:74:570:695
+CACACTGGTTCTCTTGAAAGCTTGGGCTGTAATGA
++
+=========================7====;8<8;
+@EAS112_34:4:74:570:695
+TTGGGAGATTTTTAATGATTCCTCAATGTTAAAAT
++
+.;:8<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS112_34:4:92:412:435
+AGATTCATAAAACAAATACTACTAGACCTAAGAGG
++
+<;<52:=,====:=========<============
+@EAS112_34:4:92:412:435
+CTACGCAAACAGAAACCAANTGAGAGAAGGAGTAG
++
+<<<<<<<4<<<<<<<<<66!<<<<<<6<<77<<97
+@EAS112_34:6:127:153:861
+CTCAGGGAGCCGTCCGTGTCCTCCCATCTGGCCTC
++
+<<<<<<<<<<<<<<<<<<<<<<<=<*<<<24;;::
+@EAS112_34:6:127:153:861
+TTTTCTGTTTCTTTGTTTGATTTGGTGGAAGACAT
++
+:;:6;9<<1;<<95<<<9<<<<<<<<<<<<<<<<<
+@EAS112_34:6:130:865:838
+AAAGCATACAGTCATCTATAAAGGAAATCCCATCA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;;:<;3
+@EAS112_34:6:130:865:838
+AATGCTAAGATAATTCATCATCACTAAACCAGTCC
++
+;<:84<<<4<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS112_34:6:145:144:263
+TTTCGTTTTTTTTTTTTTTTTTTCCCCTTTCTTTT
++
+<<<<<<<<<<<<<<<<+4+4&+&(&&*2&8&&&)&
+@EAS112_34:6:43:47:279
+AAAACTATGCTAAGTATTGGTAAAGATGTGGGGAA
++
+<:<<79<<<19<<<1<<9<<+<<<<<3<3<<<<<<
+@EAS112_34:6:43:47:279
+TAGACCTAAGAGGGATGAGAAGTTACCTAATTGGT
++
+<<<<<<<<<<<<<;:<-<<<<<<<<<<<<:;;+7;
+@EAS112_34:6:71:85:629
+CCTTTTTGCTGCATCCCTGTCTTCCTCTGTCTTGA
++
+<<<<<<<<<<9<<<<<<<<<<<<<<<<<5<9<<+6
+@EAS112_34:6:71:85:629
+TTGACACCCAACTAATATTTGTCTGAGCAAAACAG
++
+,,1<1<7&%<9+:<<9<<9<<<<<<<<5<<<<<<<
+@EAS112_34:6:75:615:555
+AAGTTTGGAAAAACTATTTGAGGAAGTAATTGGGG
++
+<<<<<<<<<<<<<<<<<<<<<;<;<<<29<;.484
+@EAS112_34:6:75:615:555
+TGAAGGAAAAAAATTCTAAAATCAGCAAGAGAAAA
++
+;<<<;<<<<<<<<<:;<<<<<<<<<<<<<<<<<<<
+@EAS112_34:7:118:523:591
+GAGGGACGCTGAAGAACTTTGATGCCCTCTTCTTC
++
+<<<<<<<<<<<<<<<<<<<<<<<:<<<<<<<;;<;
+@EAS112_34:7:118:523:591
+GGTCTGACAGGCTGCAACTGTGAGCCATCACAATG
++
+4:--&0:67<<8:<<<<<<<<<<<:4<<<<<<<<<
+@EAS112_34:7:141:80:875
+AGCCGAGTCACGGGGTTGCCAGCACAGGGGCTTAA
++
+<<<<<<<<<<<<<<<<<<<<<<:<<8;<<8+7;-7
+@EAS112_34:7:141:80:875
+AGCTGTGTTTAGTGCCTTTGTTCAACCCCCTTGCA
++
+6/<;84<;<;<<<<<<5<<<<<<<<<<<<<<<<<<
+@EAS112_34:7:142:457:584
+GGAAGAACAGCTTAGGTATCAATTTGGTGTTCTGT
++
+8::<:<<9<<.<:<<<<<<<<<<<7<<<<<<<<<<
+@EAS112_34:7:142:457:584
+TGAAGAGACTATTTCCAGATGAACCACACATTAAT
++
+<<<<<<<<<<<<</<<,6<66<<<;<;;<*4744.
+@EAS112_34:7:71:62:254
+AAAAAAGTAAACTCTCAAATATTGCTAGTGGGAGT
++
+<<<<<<;8<<<<;<:<<<<<<<;<<;<<<<<<<<<
+@EAS112_34:7:71:62:254
+GGTTACACTAAAAGCCCATACTTTCCTGCTACTCA
++
+<<<<<<7<<<<7<<<<<3<<<<<<&<<.<<::<:%
+@EAS112_34:7:86:498:373
+CACTAATGCGCTCCACGCCCAAGCCCTTCTCACAG
++
+):)4:<5<<<<;89<<<969<<<:<<<<<<<<<<<
+@EAS112_34:7:86:498:373
+GATACCATCCCTGTCTTACTTCCAGCTCACCAGAG
++
+<<<<<<<<<<<<<<<<<<<<<<<5:<<<:<;7+67
+@EAS112_34:7:96:489:453
+AAGTCAAGTCTTTCCTGACAAGCAAATGCTAAGAT
++
+;<;;;<<<<5:<<:<<<<:<<<<<<<<<<<<<<<<
+@EAS112_34:7:96:489:453
+AGAAAAGCATACAGTCATCTATAAAGGAAATCCCA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;;;;:
+@EAS112_34:8:103:812:255
+ATGTTAAAATGTCTATTTTTGTCTTGACACCCAAC
++
+7:777:7<<::7<7<7<<:7<7<:<<<<<<<<<7<
+@EAS112_34:8:103:812:255
+TGATGCCCCTTGGCCATCACCCAGTCCCTGCCCCC
++
+<<<<<<<<<<<<<<<9<<;<<<39;;<;32:7;7+
+@EAS112_34:8:174:557:872
+GGTAAAGATGTGGGGAAAAAAGTAAACTCTCAAAT
++
+.77<:<9<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS112_34:8:174:557:872
+TGGTACAATGTACAATATTCTGATGATGGTTACAC
++
+<<<<<<<<<<<<<:<<<<<<<7<<;<<6:<<2117
+@EAS112_34:8:179:13:782
+GACAGTCTACAACTGTGAGCCATCACAATGAACAA
++
+&37.3&;3'*<3<;9<9<<5<<<<<<<<<9<<<<<
+@EAS112_34:8:179:13:782
+TGATGCCCTCTTCTTCCAAAGATGAAACGCGTAAC
++
+<<<<<<<<<<<<<<<<<:<<:7<<<<::<7<:-:1
+@EAS112_34:8:30:816:90
+ACTACCCTGCAATTAATATAATTGTGTCCATGTAC
++
+:<3:%9299<<<<<<<<<5<<<<<<<<<<<<<<<<
+@EAS112_34:8:30:816:90
+AGGGAGGTGCACTAATGCGCTCCACGCCCCAGCCC
++
+<<<<<<<<<<<<<<<<<<<:<<<<<<::1&(1::7
+@EAS112_34:8:45:800:733
+ACATGAAGGAAAAAAATTCTAAAATCAGCAAGAGA
++
+<<<</<<<<<<<<<<<<<<<2<9<<<<<5*5;599
+@EAS112_34:8:45:800:733
+ATAAATGAAGGGGAAATAAAGTCAAGTCTTTCCTG
++
+<7<<7&<<9<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS112_34:8:4:841:339
+ACCTCATACACACACATGGTTTAGGGGTATAATAC
++
+<<<<<<<<<<<<<<<<<;<7<<&;;<5<+<;7<<;
+@EAS112_34:8:4:841:339
+CTTCAGACCCTACACGAATGCGTCTCTACCACAGG
++
+77-):22<<<33;<5<<<<<<<<<<<<<<<<<<<<
+@EAS114_26:1:113:367:659
+AGTCATCAGACTATCTAAAGTCAACATGAAGGAAA
++
+<<5<0&9;<3<<<<<9<<<<4<;<9<9<<<<7<3<
+@EAS114_26:1:113:367:659
+CACAGGTATTCCTGAGGAAAAAGAAAAAGCGAGAA
++
+=9====8==========:=:=====9=:=&====5
+@EAS114_26:1:155:807:19
+AAAAGGGATTAAATTCCCCCACTTAAGAGATATAG
++
+<<<<<<<<<<<<<<<<9+<<<<<<9<<9;4<<<<:
+@EAS114_26:1:155:807:19
+CAACAGTAAAATAAAACAAAGGAGGTCATCATACA
++
+:==4=5:====:============:==========
+@EAS114_26:1:171:527:247
+AACAAATGCTACTAGACCTAAGAGGGATGAGAAAT
++
+<547*9)&&7+;+<<7<<<;<<<;3<<<<<<<<<<
+@EAS114_26:1:171:527:247
+AGAAGGAGTAGCTAGACTTATATCAGATAAAGCAC
++
+=4==4===8==99=&=8+9=19+.2.6'=99+999
+@EAS114_26:1:324:238:736
+AGACAGACTTCATCAAGATATGTAGTCATCAGACT
++
+<<<9<<<70,<<4<<<<<7<4<7<<<<<0<<<<<7
+@EAS114_26:1:324:238:736
+TCAAGAAGTATGAGATTATGTAAAGTAACTGAACC
++
+===================================
+@EAS114_26:1:35:522:294
+GGTTCAGAACTTGAAGACAAGTCTCTTATGAATTA
++
+===============================:=:=
+@EAS114_26:1:35:522:294
+TTGAGGAAGTAATTGGGGAAAACCTCTTTAGTCTT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS114_26:1:99:212:522
+ACGAATGCGTCTCTACCACAGGGGGCTGCGCGGTT
++
+================8==;====;=;===1==:8
+@EAS114_26:1:99:212:522
+AGAGACTATTGCCAGATGAACCACACATTAATACT
++
+<1<16<7<3<<;;<8<<<<<<<<<<<<;<<<<9<<
+@EAS114_26:2:130:609:467
+AAATTCCCCCACTTAAGAGATATAGATTGGCAGAA
++
+===:2===;<====>==>=>=>=>>>==>>>=>>>
+@EAS114_26:2:130:609:467
+CAATACTCACCATCATAAATACACACAAAAGTACA
++
+==8=====;==8==;=4=;;8=====;6=177.==
+@EAS114_26:2:214:950:32
+ACAAGAAACTCATTAATAAAGACATGAGTTCAGGT
++
+>>=>>>>==>=>>>==>=>=:=====;=:=6:::6
+@EAS114_26:2:214:950:32
+AGAAGATATAACCATCCTACTAAATACATATGCAC
++
+=&==4======:;==6<==:===============
+@EAS114_26:2:237:497:165
+GAAATAAAGTCAAGTCTTTCCTGACAAGCAAATGC
++
+9=:=======2=27======<>&<=,==4>4=>>=
+@EAS114_26:2:237:497:165
+TACAGTCATCTATAAAGGAAATCCCATCAGAATAA
++
+8===<8===========37=<===7=;7=8=====
+@EAS114_26:2:315:219:7
+GAAAGAGGCTCAAAGAATGCCAGGAAGATACATTG
++
+7==::<2=8<<<=====>888<=2=>==>,>,>>8
+@EAS114_26:2:329:458:365
+GTGTTCTGTGTAAAGTCTCAGGGAGCCGTCCGTGT
++
+==========================9========
+@EAS114_26:2:329:458:365
+TTGTTGTTGGTTTTCTGTTTCTTTGTTTGATTTGG
++
+====:==9========>==7>==9>=7=>=>>=>>
+@EAS114_26:2:73:513:102
+GTCTCATCTAGGGGAACAGGGAGGTGCACTAATGC
++
+==::===8=>=====>=>=>>>=>>==>=>>>>>>
+@EAS114_26:2:73:513:102
+TGAAAACAATGTTCCCCAGATACCATCCCTGTCTT
++
+===========================;=======
+@EAS114_26:3:117:284:589
+ACAAAATATAGTTGAAAGCTCTAACAATAGACTAA
++
+==================================0
+@EAS114_26:3:117:284:589
+GAACCTATGAGTCACAGGTATTCCTGAGGAAAAAG
++
+==8==;==================;==========
+@EAS114_26:3:284:261:124
+ACAGCTGTGTTTAGTGCCTTTGTTCAACCCCCTTG
++
+===27===.====&===========;;========
+@EAS114_26:3:287:665:495
+GAATTGTAAAAGTCAAAATTAAAGTTCAATACTCA
++
+===,9=;;====7=====5===;==1=========
+@EAS114_26:3:287:665:495
+TGGATCTAATTTTTGGACTTCTTAAAGAAAAAAAA
++
+==========================98====8=8
+@EAS114_26:4:100:238:596
+ATGAGAAATTACCTAATTGGTACAATGTACAATAT
++
+======9=====;=======5===;====/=;===
+@EAS114_26:4:100:238:596
+CAAAAACTATTCTAAGTATTGGTAAAGATGTGGGG
++
+4<<<<;<3<3&<3<1<5<31<<3<<<<<<2<<;<,
+@EAS114_26:4:110:840:431
+CTGTCAAACACGAATGTTATGCCCTGCTAAACTAA
++
+77<;7<<<<<<<<<4<<<<<<<:<<<<<<<<<<<<
+@EAS114_26:4:110:840:431
+GTAGTCATCAGACTATCTAAAGTCAACATGAAGGA
++
+=====================5:======54=+3+
+@EAS114_26:4:123:1001:580
+AGGTTTTATAAAACAATTAATTGAGACTACAGAGC
++
+<.00..3<6<<<<<<<3;<<08<<<<<6<<<<<<<
+@EAS114_26:4:123:1001:580
+GGGAANTAAAGTCAAGTCTTTCCTGACAAGCAAAT
++
+=====!=====================1.8131*=
+@EAS114_26:4:253:285:104
+CTCTCATTCACTCCAGCTCCCTGTCACCCAATGGA
++
+======================:========7==;
+@EAS114_26:4:253:285:104
+GTGATGTGTGTTCTCATCAACCTCATACACACACA
++
+2<;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS114_26:4:306:388:342
+CCGTCCGTGTCCTCCCATCTGGCCTCGTCCACACT
++
+================5====:=====;==1=4==
+@EAS114_26:4:306:388:342
+GGGGAAGACATAATCCCACGCTTCCTATGGAAAGG
++
+9/<9;<<<;<;<<7<<<7<<<<<<<<<<<<<<<<<
+@EAS114_26:4:40:352:151
+ATTACGTCCTATCTTCTTCTTAGGGAAGAACAGCT
++
+<<<<<<<<<<<<<<<;<<9<<<<:<<<<;<99<3<
+@EAS114_26:4:40:352:151
+TTTTGCTGCATCCCTGTCTTCCTCTGTCTTGATTT
++
+;=;;5=:-=9=====;;==================
+@EAS114_26:5:139:331:63
+GACACCCAACTAATATTTGTCTGAGCAAAACAGTC
++
+7===================:=:============
+@EAS114_26:5:139:331:63
+TTTTGCTGCATCCCTGTCTTCCTCTGTCTTGATTT
++
+====================<<=============
+@EAS114_26:5:228:189:826
+AAGCCCTTCTCACAGTTTCTGCCCCCCGCATGGTT
++
+;9=========;=1======9=====1;=<3=:6;
+@EAS114_26:5:228:189:826
+ATCATGACTCTATCCCAAATTCCCAATTACGTCCT
++
+:74=:.==1==========================
+@EAS114_26:5:238:31:968
+ACACCATCCCTGTCTTACTTCCAGCTCCCCAGAGG
++
+=(.7=5%===9:7==+==77===============
+@EAS114_26:5:238:31:968
+ATTCTGCAGCCCAGCTCCAGATTGCTTGTGGTCTG
++
+9======8====*=====,=1=======<=7:::,
+@EAS114_26:5:43:114:617
+AATCATAAATACACACAAAAGTACAAAACTCACAG
++
++=22=6=================9===========
+@EAS114_26:5:43:114:617
+AATGTTATGCCCTGCTAAACTAAGCATCATAAATG
++
+=============;=========;===========
+@EAS114_26:6:129:694:359
+CCCTGAGAGATTCTGCAGCCCAGATCCAGATTGCT
++
+7777<7<7;77+<3<<;<<;<<<<;<<<<<<<<<<
+@EAS114_26:6:129:694:359
+TGTCAGTTACCAAATGTGTTTATTACCCGAGGGAT
++
+============+7=======:==;;;'=;==7;=
+@EAS114_26:6:140:253:322
+AATTTTTGGACTTCTTAAAGAAAAAAAAACCTGTC
++
+<<<<<<<<<<<<<;<<<<<<<<<<<<<<<;;;<<;
+@EAS114_26:6:140:253:322
+GAAATGCTCAAAAGAATTGTAAAAGTCAAAATTAA
++
+=;===;54:====================>>===>
+@EAS114_26:6:183:697:555
+AAAGAATGCCAGGAAGATACATTGCCAGACAGACT
++
+=====================:===&==:;==5;;
+@EAS114_26:6:183:697:555
+AGAAATCTTAGAAGCCAGAAGAGATTGGATCTAAT
++
+<<<;&,.;);&96<84<<81<<&<<<9<<8<8<<1
+@EAS114_26:6:46:13:880
+AAAACCTCTTTAGTCTTGCTAGAGATTTAGACATC
++
+<<<<<<<<<<<<<<<<<<<<;<7<3<<<9<+;;<9
+@EAS114_26:6:46:13:880
+AGAAAAGCATACAGTCATCTATAAAGGAAATCCCA
++
+=&====8==========0=================
+@EAS114_26:7:13:172:720
+AATTCATTTAAGAAATTACAAAATATAGTTGAAAG
++
+============:3<==:====<=9=3===;==83
+@EAS114_26:7:157:876:302
+AAAGACATGAGTTCAGGTAAAGGGGTGGAAAAAGA
++
+===:=8=;==:892=,28==88==28====8=;;8
+@EAS114_26:7:157:876:302
+CAACTAGGTAAAAAATTAACATTACAACACGAACA
++
+2<<;<<<22<<<<<<77<<<<22<7<<<<%-<<1<
+@EAS114_26:7:218:858:445
+AAAAAGAAAAAGTGAGAAGTTTGGAAAAACTATTT
++
+;===5=;=======;==3======9;,79==;===
+@EAS114_26:7:218:858:445
+GAAAAAAATTCTAAAATCAGCAAGAGAAAAGCATA
++
+;<<<<<<<8;:<<<<<<;<<:<<<<<<<<<<<<;<
+@EAS114_26:7:245:323:744
+ACCTCTACATGGCTGATTATGAAAACAATGTTCCC
++
+/.848299;&;9;9;=2.=7========;;=====
+@EAS114_26:7:245:323:744
+GATTCTGGGAAATTCTTCATCCTGGACCCTGAGAG
++
+<;<<<<<<<<<<<<<<<<<<<<<;<+<<<<<<<4<
+@EAS114_26:7:37:79:581
+TTAAAATTTAAAAAAAGTAAATAAAACACATAGCT
++
+<>4<>>>>;>>&>->9>9;4>->>>>,4>9>,<1>
+@EAS114_26:7:37:79:581
+TTTTTTTTTTTTTTTTTTTTTTTCATGCCAGAAAA
++
+3,,,===6===<===<;=====-============
+@EAS114_26:7:86:308:648
+GAAGAACAGCTTAGGTATCAATTTGGTGTTCTGTG
++
+<7<<<;<<<<+;<<<2<5<<<77;<<2<;;<<<<<
+@EAS114_26:7:86:308:648
+TATTAGGAAATGCTTTACTGTCATAACTATGAAGA
++
+=8=====;=8======;=======35==;=;.;25
+@EAS114_28:1:144:242:602
+ATCAGCAAGAGAAAAGCATACAGTCATCTATAAAGG
++
+========================;=====<;;<<;
+@EAS114_28:1:144:242:602
+ATGAAGGGGAAATAAAGTCAAGTCTTTCCTGACAAG
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS114_28:1:168:389:889
+GAAATTACAAAATATAGTTGAAAGCTCTAACAATAG
++
+<<<<<<<<<<<<<<<<<<<<;<<<<<<<;9;;<<<<
+@EAS114_28:1:168:389:889
+TAACTGAACCTATGAGTCACAGGTATTCCTGAGGAA
++
+;<<;;56;==================8========8
+@EAS114_28:1:168:609:646
+GGAAAAAAGTAAACTCTCAAATATTGCTAGTGGGAG
++
+;;<<<<=======;;:;======;==<=========
+@EAS114_28:1:168:609:646
+GGTTACACTAAAAGCCCATACTTTACTGCTACTCAA
++
+<<<<<<<<<<<;<<<<<:<8<<<<;<<<<<4<<<9<
+@EAS114_28:1:220:801:282
+AACCTCATATATCAATATTAACTTTGAATAAAAAGG
++
+;7;87;===;==;====:===<==7===========
+@EAS114_28:1:220:801:282
+AATTCATCATCACTAAACCAGTCCTATAAGAAATGC
++
+<<<<<<<<<<<<<<<<<<<<<;<+<;<<<<<::<<:
+@EAS114_28:1:232:351:909
+ACATGGCTGATTATGAAATCAATGTTCCCCAGATGC
++
+<<<<<99<<<<<<99<7<'<9<<<6<<+<;7;<<&;
+@EAS114_28:1:232:351:909
+CCATCATGAAGCGCTGAACTTCCACGTCTCATCTAG
++
+:8%3<8====130=8==+===;=3=8===48==;3*
+@EAS114_28:1:28:708:463
+CCCAATGGACCTGTGATATCTGGATTCTGGGAAATT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<9;<:<<
+@EAS114_28:1:28:708:463
+GTATAATACCTCTACATGGCTGATTATGAAAACAAT
++
+;;<;<<====3=====5===================
+@EAS114_28:2:114:938:216
+CTAACAATAGACTAAACCAAGCAGAAGAAAGAGGTT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<4;
+@EAS114_28:2:114:938:216
+GAGTCACAGGTATTCCTGAGGAAAAAGAAAAAGTGA
++
+<<<<7<6<<<<<<<6<<<<<<<<<<<<<<<<<<<<<
+@EAS114_28:2:141:7:963
+CACTTTAAATCAACAACAGTAAAATAAAACAAAGGA
++
+<<<<<<<<<<<<;<:<<<<<<1<<&<;<;<<;,<;5
+@EAS114_28:2:141:7:963
+TACAATGTACAATATTCTGATGATGGTTACACTAAA
++
+95+<<9<<5<;;<<;<<;'<<<<<;<<<7<9<<<<<
+@EAS114_28:2:149:650:44
+CGCTCCACGCCCAAGCCCTTCTCACAGTTTCTGCCC
++
+;8<<</<<:<<595<<9<<<<<<<<<<<<<<3<9<<
+@EAS114_28:2:149:650:44
+CTGTCTTACTTCCAGCTCCCCAGAGGGAAAGCTTTC
++
+<<<<<<<<<<<<<<<<<<<<<<<<<;6<<;<<7<<<
+@EAS114_28:2:167:905:852
+AGAAAAGCATACAGTCATCTATAAAGAAAATCCCAT
++
+<<<7<<<<<<<<<<<<<<:<:<<:::&.<:<66:3<
+@EAS114_28:2:167:905:852
+CAAATGCTAAGATAATTCATCATCACTAAACCAGTC
++
++<<<9;7;<<+<<<<<39<;9<;9<<7<<<<<<<<<
+@EAS114_28:2:251:819:772
+TCCCCCACTTAAGAGATATAGATTGGCAGAACAGAT
++
+6+7++1<<%<<<<<<<+<+<9<<99<9<<<<<<9<<
+@EAS114_28:2:251:819:772
+TTCAATACTCACCATCATAAATACACACAAAAGTAC
++
+<3<<<9<9<3<</<<<<<<59<3<9<<</9/++*/'
+@EAS114_28:2:28:474:566
+ACTGAACTTCCACGTCTCATCTAGGGGAACAGGGAG
++
+<<<<<<<<<<<<<<<<<<<<<<<:<;<;;<<7;8;<
+@EAS114_28:2:28:474:566
+TGAACCACACATTAATACTATGTTTCTTATCTGCAC
++
+;<<<+<<<<5<<<<<<;;<<<<<<<<<<<<<<<<<<
+@EAS114_28:2:329:437:643
+AAGATACATTGCAAGACAGACTTCATCAAGATATGT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<;<<<<1
+@EAS114_28:2:329:437:643
+TTTTGGACTTCTTAAAGAAAAAAAAACCTGTCAAAC
++
+885<8;;<;3,8<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS114_28:2:55:562:403
+CAACAGGAACAAAACCTCATATATCAATATTAACTT
++
++<<&<<<<<<<<<<+<<<<<<<<<<<<<<<<<<<<<
+@EAS114_28:2:55:562:403
+CAAGCAAATGCTAAGATAATTCATCATCACTAAACC
++
+<<<<<<<<<<<<<<<<<<<<<;<<;<<<<<<<;<;:
+@EAS114_28:3:110:984:98
+AAGGAGGTCATCATACAATGATAAAAAGATCAATTC
++
+98<<<<<<2<<<<<<;;<;;<<<5;5;<<;;<<<<+
+@EAS114_28:3:110:984:98
+ACTAAAACCCCATACTTTACTGCTACTCAATATATC
++
+:81<<<<+;;8<+<8<<<<<;<<<8;<<<<<<<<8;
+@EAS114_28:3:173:627:465
+GTAAACTCTCAAATATTGCTAGTGGGAGTATAAATT
++
+:<<<<;<;<;<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS114_28:3:173:627:465
+TGATGGTTACACTAAAAGCCCATACTTTACTGCTAC
++
+<<<<<<<<<<<<<<<<<<<<<<<;<<<<<2;;4;;7
+@EAS114_28:3:176:402:458
+AAATAGCTAAAACTAAAAAAGCAAAAACAAAAACTA
++
+</<+<4&;<<<<7<<<<<<<<;<<<<<<<<<<<<<<
+@EAS114_28:3:176:402:458
+CCTAAGAGGGATGAGAAATTACCTAATTGGTACAAT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<:<<<;;<;
+@EAS114_28:3:202:275:776
+CAAATACTACTAGACCTAAGAGGGATGAGAAATTAC
++
+;<<<<;;<<<<<<<;<<<<<<<;<<<<<<<<<<;<<
+@EAS114_28:3:202:275:776
+TCTACGCAAACAGAAACCAAATGAGAGAAGGAGTAG
++
+<<<<<<<<<<<<<<<<<<<<<;<<9<;;<<<;<;<;
+@EAS114_28:3:250:628:423
+CAATGGGCTTCTCAGCGGAAACCTTACAAGCCAGAA
++
++<<4;;9;;7.;7<;7<;<<<;;<<<<<<<<<<<<<
+@EAS114_28:3:250:628:423
+CTCTTTAGTCTTGCTAGAGATTTAGACATCTAAATG
++
+<<<<<<<<<<<<<<<<<<:;<<<<:<<<<;;;;;;4
+@EAS114_28:3:279:763:945
+CTGCACATTACTACCCTGCAATTAATATAATTGTGT
++
+<<<<<<<<<<<<<<<<<<<4:<<47<:<;<<</<9<
+@EAS114_28:3:279:763:945
+GCCGTCCGTGTCCTCCCATCTGGCCTCGTCCACACT
++
++9:-+<:1-44<<':<;<+<-<<<;:<<;;<<<<<0
+@EAS114_28:3:308:509:948
+AATATATCCATGTAACAAATCTGCGCTTGTACTTCT
++
+;;+;;;.8<<;;;<<<<<<<<<<<<<8<<<<<;<<<
+@EAS114_28:3:308:509:948
+AATTCAGCAAGAAGATATAACCATCCTACTAAATAC
++
+<9<<<<<<<;<7<<;<<<<<<<;<<<<7<<;2;<<<
+@EAS114_28:3:32:492:907
+CAAACACGAATGTTATGCCCTGCTAAACTAAGCATC
++
+8<;<4<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS114_28:3:32:492:907
+TGTAGTCATCAGACTATCTAAAGTCAACATGAAGGA
++
+<<<<<<<<<<<<<<<<<<<;<;;<<<<<<<<<<<<<
+@EAS114_28:3:78:773:660
+ATTCTGCAGCCCAGCTCCAGATTGCTTGTGGTCTGA
++
+<<<<<<<<;<<<<<<<<<8<8<<;<<<;<<;7<<4:
+@EAS114_28:3:78:773:660
+CCCCAGATACCATCCCTGTCTTACTTCCAGCTCCCC
++
+7<;7<<<7;9<<8;<<<<<<;<<<<<<<<<<7<<<<
+@EAS114_28:4:13:701:55
+AAACCAAATGAGAGAAGGAGTAGCTATACTTATATC
++
+<<<<<<<<<9<<<9<<<<<<6<<<<<<<6<<6<<6+
+@EAS114_28:4:13:701:55
+TTCATAAAACAAATACTACTAGACCTAAGAGGGATG
++
+0:+<7<;9<;<<<<<<<3<<<<<;;<<<:<<3<<<<
+@EAS114_28:4:149:572:877
+ATGTAAAGTAACTGAACCTATGAGTCACAGGTATTC
++
+=>7><>;>+>>/;>>=>=>=:>><>=<<==;)<=8;
+@EAS114_28:4:149:572:877
+GAGGCTCAAAGAATGCCAGGAAGATACATTGCAAGA
++
+6<94693<;<<<<;;<<<<<<<<<<;9<<<<<<<<<
+@EAS114_28:4:215:246:640
+AAAAGCATACAGTCATCTATAAAGGAAATCCCATCA
++
+<<<<<<<<<<9<;<<<<<<<<<<9;<<<<<<3;<;3
+@EAS114_28:4:215:246:640
+AAAGTCAAGTCTTTCCTGACAAGCAAATGCTAAGAT
++
+;<<,<<<96<<:<:<9<6<97<<<<<9<<<<9<<9<
+@EAS114_28:4:305:707:258
+AAAAAGATGTTCTACGCAAGCAGAAACCAAATGAGA
++
+3<<7<,;<<<<0<66<6+<%<<<.<<<<<<<<<9<<
+@EAS114_28:4:305:707:258
+GAACAAAACCTCATATATCAATATTAACTTTGAATA
++
+9<<<<<<<<<<<<;<<-<<;;<;<<9<<;<<+99;7
+@EAS114_28:4:322:631:245
+CCCTGCCCCATCTCTTGTAATCTCTCTCCTTTTTGC
++
+<<<<<<<<<<<<<<<<<0<<<<<<<<<<<<<<<<5;
+@EAS114_28:4:322:631:245
+TATTTTTGTCTTGACACCCAACTAATATTTGTCTGA
++
+<<<<<<<<<<<<<<<<;<<<<<<<<<<<<<<<<<<<
+@EAS114_28:4:9:55:730
+ATCCCTGTCTTACTTCCAGCTCCCCAGAGGGAAAGC
++
+<:<;;<6<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS114_28:4:9:55:730
+CAGCCCAGCTCCAGATTGCTTGTGGTCTGACAGGCT
++
+>>=>>+==>>==<==<=8=><:;8/;7</5724-2;
+@EAS114_28:5:104:350:749
+AAATATAGAAATTGAAACAGCTGTGTTTAGTGCCTT
++
+<<8<<<<<<<<<<<;<<<<<<<<0;<<<9;<85;;;
+@EAS114_28:5:104:350:749
+TGCCCTCTTCTTCCAAAGATGAAACGCGTAACTGCG
++
+;<93;9;<3;<<<;<<<<<;<<<<<<;<<<<<<<<<
+@EAS114_28:5:11:868:62
+TCTTAGGGAAGAACAGCTTAGGTATCAATTTGGTGT
++
+;;77;;7<<<<<<<<7<<<;<7<<<<<<<<<<<<<<
+@EAS114_28:5:11:868:62
+TTTACTGTCATAACTATGAAGAGACTATTGCCAGAT
++
+<<<<<<<<<<<<<<<<<<<<:<<<;<<<<(7:7039
+@EAS114_28:5:163:832:715
+TAAAAACATGAACTAACTATATGCTGTTTACAAGAA
++
+<<0;<9<<<<<<<<<<<<9<<<<<<<<<<<<;;;<6
+@EAS114_28:5:163:832:715
+TAAAACAAAGGAGGTCATCATACAATGATAAAAAGA
++
+;<<<<9<<<<<<<<;;<<7<<<<<<<<<<<<<<<<<
+@EAS114_28:5:206:671:49
+ACCATCCCTGTCTTACTTCCAGCTCCCCAGAGGGAA
++
+;<<<<<<<;<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS114_28:5:206:671:49
+GCTTGTGGTCTGACAGGCTGCAACTGTGAGCCATCA
++
+<<<<<<;<<<<8<<<;;<<<3<<8<8<35+,55;,3
+@EAS114_28:5:209:778:588
+AACAGTCTAGATGAGAGAGAACTTCCCTGGAGGTCT
++
+;8;98;;;<3<<<<<<<<<;<<;<<<<<;<<<<<<<
+@EAS114_28:5:209:778:588
+TTTTTGCTGCATCCCTGTCTTCCTCTGTCTTGATTT
++
+<<<<<<<<;<<<<<<<<<;<<<;<8<8<<<<;7;;;
+@EAS114_28:5:23:944:377
+AATGTTATGCCCTGCTAAACTAAGCATCATAAATGA
++
+<<<<<<<<9<<<<;<<<<<<<<<;<7<<<<;8;<<;
+@EAS114_28:5:23:944:377
+AGTACAAAACTCACAGGTTTTATAAAACAATTAATT
++
+<;7;8<<<<:<;<:<<<<<<<<<<<<<;<<<<<<<;
+@EAS114_28:6:11:151:750
+GTTTTTATTTTTTTCCTCTCTCTTTTTTTTTTTTTT
++
+:'1:%4;4<<<+;6;&9+6;/<<<<<<<<<<<<<<<
+@EAS114_28:6:155:68:326
+CCCATTTGGAGCCCCTCTAAGCCGTTCTATTTGTAA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<:<<<<<<<
+@EAS114_28:6:155:68:326
+GTCAGGGAAGGAGCATTTTGTCAGTTACCAAATGTG
++
+;<<<:6<<<<<<6<<<<<<<<<<<<<<<<<<<<<<<
+@EAS114_28:6:175:705:982
+CATGGTTTAGGGGTATAATACCTCTACATGGCTGAT
++
+')'''''')'''''*')*)'*)')))+,'*)+'*,!
+@EAS114_28:6:175:705:982
+CTGGATTCTGGGAAATTCTTCATCCTGGACCCTGAG
++
+<<<<;<<;<<<<<<<<<<<<<;<<+<:;39;+<40<
+@EAS114_28:6:185:87:475
+AAGAAACTCATTAATAAAGACATGAGTTCAGGTAAA
++
+<<4<<<+<<<;<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS114_28:6:185:87:475
+ATTGAGACTACAGAGCAACTAGGTAAAAAATTAACA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<6;
+@EAS114_28:6:187:996:432
+TGCTCAAAAGAATTGTAAAAGTCAAAATTAAAGTTC
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<;<<;
+@EAS114_28:6:187:996:432
+TTGAATAAAAAGGGATTAAATTCCCCCACTTAAGAG
++
+;<<<<<<<<<<<<<<<<<<<<;<<<<<<<<<<<<<<
+@EAS114_28:6:51:506:878
+TAATCTCTCTCCTTTTTGCTGCATCCCTGTCTTCCT
++
+<<<<<<<<<<<<<<<<<4<<<<<<<<<<0<<<<<:;
+@EAS114_28:6:51:506:878
+TTTGTCTGAGCAAAACAGTCTAGATGAGAGAGAACT
++
+<970;49;<;+<<<:<<<;;<<<<<<<<<<<<<<<;
+@EAS114_28:6:54:263:585
+TGAAAGCTTGGGCTGTAATGATGCCCCTTGGCCATC
++
+1:::6<<<<;;;<4<<<<<<<<6<<<<<<<<<<<<<
+@EAS114_28:6:54:263:585
+TGTCCATGTACACACGCTGTCCTATGTACTTATCAT
++
+<<<<<<<<<<<<<<<<<<<:;<<;<:;::<<;;:;4
+@EAS114_28:7:133:514:754
+AGCTATACTTATATCAGATAAAGCACACTTTAAATC
++
+;;4;<;<;<<<<<<<<;<<<<<<;<<<<<<<<<<<<
+@EAS114_28:7:133:514:754
+TAAATTTGAATAAAAAGGGATTAAATTCCCCCACTT
++
+***&,,,+(*,*********+*)*(***(**((*)(
+@EAS114_28:7:157:786:424
+GCTTTACTGTCATAACTATGAAGAGACTATTGCCAG
++
+<<<<<<<<<<<<<;<<<<<<;<<;<<;<<<<+4:70
+@EAS114_28:7:157:786:424
+TTAGGTATCAATTTGGTGTTCTGTGTAAAGTCTCAG
++
+;<;2;;<<<;<;<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS114_28:7:178:276:693
+GTTCAGAACTTGAAGACAAGTCTCTTATGAATTAAC
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;;
+@EAS114_28:7:178:276:693
+TTGGAAAAACTATTTGAGGAAGTAATTGGGGAAAAC
++
+:;<;<<<<<<<<<<<;<<<<<<<<<<<<<<<<<<<<
+@EAS114_28:7:215:863:521
+ACTCACCATCATAAATACACACAAAAGTACAAAACT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<<<<;
+@EAS114_28:7:215:863:521
+TAAGAGATATAGATTGGCAGAACAGATTTAAAAACA
++
+;<<<<<<<<<<<<<;<<;<;<<<<<<<<<<<<<<<<
+@EAS114_28:7:242:354:637
+AACTATATTTATGCTATTCAGTTCTAAATATAGAAA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<;<<<<<6<;;
+@EAS114_28:7:242:354:637
+CCCTCTTCTTCCAAAGATGAAACGCGTAACTGCGCT
++
+8<;;;;;<<<8;<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS114_28:7:287:492:169
+CGCTCTCATTCACTCCAGCTCCCTGTCACCCAATGG
++
+;/;6<<<<4(<(<<<<6<<<<<<<<<<;<<<<<<<<
+@EAS114_28:7:287:492:169
+GTGTTTAGTGCCTTTGTTCAACCCCCTTGCAACAAC
++
+<<<7<<<<<<<<<<<<<<<<<<<<<<<8;;<;6<<;
+@EAS114_28:7:57:324:546
+GTCATCTATAAAGGAAATCCCATCAGAATAACAATG
++
+;;5<;,<<<;;<<<<<<<97<<<<<<<<<<9<<<<<
+@EAS114_28:7:57:324:546
+TAATTGGGGAAAACCTCTTTAGTCTTGCTAGAGATT
++
+<<<<<<<<<<<<<<<<<<<<<:<<<8:8<<;::;;;
+@EAS114_30:1:134:379:893
+AGTTTCTGCCCCCAGCATGGTTGTACTGGGCAATA
++
+<<<<<<<<<<<<<5<<<<;<<<<<;<:5;<<4+<<
+@EAS114_30:1:134:379:893
+CGCTGTCCTATGTACTTATCATGACTCTATCCCAA
++
+7137::;<<<<<<<;<<<<<<<<<<;<<<<<<<<<
+@EAS114_30:1:154:818:165
+GAACAGGGAGGTGCACTAATGCGCTCCACGCCCAA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<;<<<<:7;:;
+@EAS114_30:1:154:818:165
+TTCTTATCTGCACATTACTACCCTGCAATTAATAT
++
+;;;;<<<;<;;<;<<<<;<<;;;<<;<<<<<<<<<
+@EAS114_30:1:176:168:513
+ATTTGTAATGAAAACTATATTTATGCTATTCAGTT
++
+<<<<;<<<<<<<<<<<<<<<<<<<:&<<<<:;0;;
+@EAS114_30:1:176:168:513
+TTTGATGCCCTCTTCTTCCAAAGATGAAACGCGTA
++
+;0;;;7:<<<<<<<;<<:<<<<<<<<<<<<<<<<<
+@EAS114_30:1:188:863:790
+CATGAGTTCAGGTAAAGGGGTGGAAAAAGATGTTC
++
+;<7<<<55<<<<:<<<<<<<<<<<<<<<<<<<<<<
+@EAS114_30:1:188:863:790
+TTAATTGAGACTACAGAGCAACTAGGTAAAAAATT
++
+++<;<<;;;:<<<<:<:<<:1<<1<<<6:6;4;;4
+@EAS114_30:1:243:10:911
+TATTCAGTTCTAAATATAGAAATTGAAACAGCTGT
++
+;<;;;<4;9:<<<;<<;<<<<<;;<<<<<<<<<<<
+@EAS114_30:1:64:526:339
+ACATTACAACAGGAACAAAACCTCATATATCAATA
++
+<<<<<<<<;<<<<<<<<<<7<:<<<<<<<<<8:<:
+@EAS114_30:1:64:526:339
+CAAATGAGAGAAGGAGTATCTATACTTATATCAGA
++
+3<<<7<<;<<<<<<<<<<<;<<<<;<<<<<<<<<<
+@EAS114_30:2:111:142:21
+ATCAGAATAACAATGGGCTTCACAGCGGAAACCTT
++
+;88<:<;;<6<;;<<<:<<<<;<<<<<<<<;<<<<
+@EAS114_30:2:111:142:21
+CTTGCTAGAGATTTAGACATCTAAATGAAAGAGGC
++
+<<<<<<<<:<:<<<<<<<<<<<<<<<<<<<<;<;9
+@EAS114_30:2:226:885:729
+AAAAGGGATTAAATTCCCCCACTTAAGAGATATAG
++
+<<<;<<<<<<;<;<<<<<<<:;<<;4;%;<<;<<.
+@EAS114_30:2:226:885:729
+GCTGAACTTACATCAGATAAAGCACACTTTAAATC
++
+/*220%.(;<%<3.<<<4<<<<86;<8<<8<<<<<
+@EAS114_30:2:272:750:698
+GTGTTTATTACCAGAGGGATGGAGGGATGACGGAC
++
+<)<<<<<7;<<<4<;7<<<<78068:(%<3*861,
+@EAS114_30:2:272:750:698
+TGCAGCCCAGATCCAGATTGCTTGTGGTCTGACAG
++
+0<;8;64;<<<;<;.<+;:<4;4<;<<<<<<<<<<
+@EAS114_30:2:297:949:26
+ACCAGTCCTATAAGAAATGCTCAAAAGAATTGTAA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;
+@EAS114_30:2:297:949:26
+CATATATCAATATTAACTTTGAATAAAAAGGGATT
++
+5<;<;<;:<<<<<<<<;<<<<<<<<<<<<<<<<<<
+@EAS114_30:2:303:428:326
+AAAATTAAAATTTAACAAAAGTAAATAAAACACAT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<;<<<<<<<;
+@EAS114_30:2:303:428:326
+TTTTTTTTTTTTTTTTTCTCTTTTTTTTTTTTTTT
++
+4<;<<;<;<4<<8;;;;.8+;<<;<8<;<;<<<<<
+@EAS114_30:2:30:887:404
+CAACAGGAAGAAAAGGTCTTTCAAAAGGTGATGTG
++
+<<<<<<<<<<;<<<<<<<<<<<<<<<<:(<<<7;7
+@EAS114_30:2:30:887:404
+TTGCCTTCAGACCCTGCACGAATGCGTCTCTACCA
++
+<<<<5<;::<<<;<<.<<<<<<<<<<<<<<<<<<<
+@EAS114_30:2:315:412:921
+GTAAAGATGTGGGGAAAAAAGTAAACTCTCAAATA
++
+4-<79;<<<4:;:<<<<<<<<4<<<38<<;<<<<<
+@EAS114_30:2:315:412:921
+TTCTGATGATGGTTACACTACAAGCCCATACTGTA
++
+<;<;<<<<<<<;<<<<<<<<8<<<;<<:<<;;+<8
+@EAS114_30:2:82:963:128
+ATTAAAGTTCAATACTCACCATCATAAATACACAC
++
+<<<<<<<<<<<<<<<<<<<;<<<<<<<<<<<;<<;
+@EAS114_30:2:82:963:128
+GGCAGAACAGATTTAAAAACATGAACTAACTATAT
++
+585<;<<:<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS114_30:3:139:117:262
+AGGGGCTTAACCTCTGGTGACTGCCAGAGCTGCTG
++
+<<<<;<<<<<<<<<<<<<:<<<<<:<<8<<<<:<:
+@EAS114_30:3:139:117:262
+GTTCTCAAGGTTGTTGCAAGGGGGTCTATGTGAAC
++
+<<<7<<<<<<<<<<<<<<<<<<<;<;<<<<<37;3
+@EAS114_30:3:14:697:541
+TAAAAGCAGCAAGAGAAAAGCATACAGTCATCTAT
++
+8<<<<&6<;8<<<<<<<<<<<<;<<<<;<<<<<<8
+@EAS114_30:3:14:697:541
+TTGGAAAAACTATTTGAGGAAGTAATTGGGGAAAA
++
+<<<<<<<<<<<<<<<<<<<:<<<<<<<;;;;8;;<
+@EAS114_30:3:161:366:544
+CTTCTGTAATTGAAAAATTCATTTAAGAAATTACA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<;<<<<<<<<
+@EAS114_30:3:181:582:435
+CAAGTCTTTCCTGACAAGCAAATGCTAAGATAATT
++
+<<<<<<<<;<<<<<;<<4<<<<<<;<<<<<<<<<<
+@EAS114_30:3:181:582:435
+GAAATCCCATCAGAATAACAATGGGCTTCTCAGCA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<;::
+@EAS114_30:3:187:294:947
+ACAGGGGGCTGCGCGGTTTCCCATCATGAAGCACT
++
+<<<<<<<<<<<<<<<<:<<<<<&<<%:<)7;7::4
+@EAS114_30:3:187:294:947
+AGAGACTATTGCCAGATGAACCACACATTAATACT
++
+<<:<<8181;<8<<<<<<<<8<<<<<<<<<<<<<:
+@EAS114_30:3:215:840:760
+AAGTATTGGTAAAGATGTGGGGAAAAAAGTAAACT
++
+<<<8<::<;;<<<:<7<7<;;;<<<<<<<<<<;<<
+@EAS114_30:3:215:840:760
+CTGATGATGGTTACACTAAAAGCCCATACTTTCCT
++
+<<<<<<<<<<<<<<<;<<<88<+<<:<;3585,+:
+@EAS114_30:3:24:195:604
+TCACAGTTTCTGCCCCCAGCATGGTTGTACTGTGC
++
+<;<<<<<<<<<89<<<<<868<8;6<8;3(38&<8
+@EAS114_30:3:24:195:604
+TGTCCTATGTACTTATCATGACTCTATCCCAAATT
++
+;6<02;<<<<59<<;<;<<<<9<3<<<<<<<<<;<
+@EAS114_30:3:302:288:657
+AGGTATCAATTTGGTGTTCTGTGTAAAGTCTCAGG
++
+<:5<<;;<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS114_30:3:302:288:657
+CCAGATGAACCACACATTAATACTATGTTTCTTAT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<<<;<<
+@EAS114_30:3:35:361:546
+TGCACTAATGCGCTCCACGCCCAAGCCCTTCTCAC
++
+:4;4;;<<;4<8<;;<;<<<<<<<<<<<<<<<<<<
+@EAS114_30:3:35:361:546
+TTACTTCCAGCTCCCCAGAGGGAAAGCTTTCAACG
++
+<<<<<<<<<<<<<<<<;<5<<<<<;<2<<<:<8<4
+@EAS114_30:3:39:348:594
+AAGCATCATAAATGAAGGGGAAATAAAGTCAAGTC
++
+<<;;<;:<;<<<;<<<<<<<<<<<<<<<<<;<<<<
+@EAS114_30:3:39:348:594
+CTAAAATCAGCAAGAGAAAAGCATACAGTCATCTA
++
+<<;<<<<<<<<<;<;;<<<<<<<<<<;<<<:<:<:
+@EAS114_30:4:183:852:253
+ACAACAGGAAGAAAAGGTCTTTCAAAAGGTGATGT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<8<;;<8
+@EAS114_30:4:183:852:253
+CCATTTCTTTTGGCATTTGCCTTCAGACCCTACAC
++
+;<9<;<<<<<<<<;<<<<<;<<<;<<<<;<<<<<<
+@EAS114_30:4:317:378:535
+AGCTTGGGCTGTAATGATGCCCCTTGGCCATCACC
++
+;7;':<77<<;<<<;<<<<<<<<<<<<<<<<<<<<
+@EAS114_30:4:317:378:535
+GCTGTCCTATGTACTTATCATGACTCTATCCCAAA
++
+<<<<<<<<<<<<:<<<<<<<<<;<<;<8<;:7:1(
+@EAS114_30:4:327:795:103
+AACCTTGAGAACCCCAGGGAATTTGTCAATGTCAG
++
+;::;;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS114_30:4:327:795:103
+ACAGGGGCTTAACCTCTGGTGACTGCCAGAGCTGC
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<;
+@EAS114_30:4:328:537:640
+AAGTATGAGATTATGTAAAGTAACTGAACCTATGA
++
+<;<<<<<<;<<<<<<<<<:;<<8<<<;:<<<;<;9
+@EAS114_30:4:328:537:640
+GGAAGATACATTGCAAGACAGACTTCATCAAGATA
++
+;:<<;<<<<<::<:<<<<<<<<<<<<<<<<<<<<<
+@EAS114_30:5:327:991:508
+ACCCCAGGGAATTTGTCAATGTCAGGGAAGGAGCA
++
+<<<<<<<<<<<<<<<<<<<<<;<;:<7:47;:75;
+@EAS114_30:5:327:991:508
+TCTGGATTCTGGGAAATTCTTCATCCTGGACCCTG
++
+0:;::<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS114_30:5:32:461:154
+ACAGGTTTTATAAAACAATTAATTGAGACTACAGA
++
+<<<<<<<<<<<<<<<:<<<<<<<<<<<<<<<+<;;
+@EAS114_30:5:32:461:154
+TTACAAGAAACTCATTAATAAAGACATGAGTTCAG
++
+;;</<<<<<;:<.<<<<<<<<<<<<<<<<<<<<<<
+@EAS114_30:6:137:741:866
+ACACTAAAAGCCCATACTTTACTGCTACTCAATAT
++
+<<<<8<<;;;<<<<;<<<;;;<;4<<8;<<;%<8;
+@EAS114_30:6:137:741:866
+GATGAGGGGAAAAAAGTAAACTCTCAAATATTGCT
++
+<;0:%<:9<<<:<<<<;<<:<<;0;<<<<<::<<6
+@EAS114_30:6:157:42:763
+TCTGGGAGCCGTCCGTGTCCTCCCATCTGGCCTCG
++
+4++;((2(5;24<./<:<<<<<<<<;<<88<<<<9
+@EAS114_30:6:157:42:763
+TTTCTTATCTGCACATTACTACCCTGCAATTATTA
++
+<<;<;<<<<<;<:4<<<<<<<<<;;4<<<:;;+;+
+@EAS114_30:6:163:312:891
+CCCAGCTCCAGATTGCTTGTGGTCTGACAGGCTGC
++
+<<<<<<<<<;<<<<<<<<<<<<<<<<:;;<;;<;0
+@EAS114_30:6:163:312:891
+TTCCCCAGATACCGTCCCTGTCTTACTTCCAGCTC
++
+0.<;;8<<<0<<<<<<<<<<6<<<<<<8<<<<<<<
+@EAS114_30:6:214:565:337
+AAATGAAAGAGGCTCAAAGAATGCCAGGAAGATAC
++
+<;<<<<<<<<<<<<<<;<<<<9<<<<<;;;;<<<<
+@EAS114_30:6:214:565:337
+CAGAATAACAATGGGCTTCTCAGCAGAAACCTTAC
++
+;;<;<1<9<<<8<<<<<;<<<<<<8<<<;<<<<<<
+@EAS114_30:6:220:809:850
+GGGGGGAAAAAGATGTGCTACACAAAAAGATTCCA
++
+<<;7;<<0::8<-6:<0624-*<&-93-,8+(&08
+@EAS114_30:6:220:809:850
+TTCATAAAACAAATACTACTAGACCTAAGAGGGAT
++
+9+5<;*<<<2:0<<8:<*00<<<:<*<<<<<<<<&
+@EAS114_30:6:238:803:383
+ACAATTAATTGAGACTACAGAGCAACTAGGTAAAA
++
+<<<<<<<<<<<<;<<<<<;<;<<;<<;<<<9<;<<
+@EAS114_30:6:238:803:383
+ACTCATTAATAAAGACATGAGTTCAGGTAAAGGGG
++
+;;<;;<<<<<<<<<<<<<<<<;:<<<<<<<<<<<<
+@EAS114_30:6:243:209:110
+AAAACATGAACTAACTATATGCTGTTTACAAGAAA
++
+;<;;;:<:<:;<<;;<;<;<;7<<;<<;;<;<<<<
+@EAS114_30:6:243:209:110
+CACAGGTTTTATAAAACAATTAATTGAGACTACAG
++
+<<<<<;<;<<<;<<<<<<<<<<<;<:;<<:;;+85
+@EAS114_30:6:277:397:932
+TTTCTTTTCACTTTTTTTTTTTTTTTTTTTTACTT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<:8(,0%(
+@EAS114_30:6:290:146:36
+CTTTCCCATCCCCCGGTCCCTGCCCCATCTCTTGT
++
+7;%%%<8-4<(<<<7<<<:<:<<<<<<<<<<<<<<
+@EAS114_30:6:290:146:36
+TTATCATGACTCTATCCCAAATTCCCAATTACGTC
++
+<<<<<<<<<<<<<<<<<<<<<<<8<<<<<;;<;;<
+@EAS114_30:6:326:309:149
+CAACCTTGAGAACCCCAGGGAATTTGTCAATGTCA
++
+<<<<<<<<<<<<<<<<<<<<:<<<<<<<<<;;;;:
+@EAS114_30:6:326:309:149
+CTCCCTGTCACCCAATGGACCTGTGATATCTGGAT
++
+;;<<;<:<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS114_30:6:41:461:436
+TAAAGTAACTGAACCTATGAGTCACAGGTATTCCT
++
+<<<<<<<<<<<<<<<<<<<:<<<<<<<<;<;;;:;
+@EAS114_30:6:41:461:436
+TAGTCATCAGACTATCTAAAGTCAACATGAAGGAA
++
+;<986<;6<<<<<<<;<<<<<<<<<;<<<<<<<<<
+@EAS114_30:6:49:656:507
+AAGGAAATCCCATCAGAATAACAATGGGCTTCTCA
++
+<<<<<<<<<<<<<<<<<<<;<<<<<<<<<<<<<;9
+@EAS114_30:6:49:656:507
+TCCTGACAAGCAAATGCTAAGATAATTCATCATCA
++
+%44;;<:<<;<;<<<<<<<<<<<<<<<<<<<<<<<
+@EAS114_30:6:4:665:771
+GAATAAAAAGGGATTAAATTCCCCCACTTAAGAGA
++
+<;<<;<18<;<8<<<<;<;;<<<<1<<<<6;;;;;
+@EAS114_30:6:4:665:771
+GTGCTTTATCTGATATCAATGCCGATAAACTGCCT
++
+<<<<<<<<<<<<%<8<3:7:77<(7,:3(:&2:(0
+@EAS114_30:6:62:386:959
+AAAAGCTTTCAACGCTTCTAGCCATTTCTTTTGGC
++
+%;71131((<<6<92(+<1<<;<-3<8<<;<;;<<
+@EAS114_30:6:62:386:959
+AATGAACAACAGGAAGAAAAGGTCTTTCAAAAGGT
++
+<<8<<<<;<<<<-<<87;</<;<+<;5<+;;<3;+
+@EAS114_30:7:269:944:220
+ATCTTCTTCTTAGGGAAGAACAGCTTAGGTATCAA
++
+<;<;8<<;7<<<<<;<<-<<<<<<;<<<;<<<<<<
+@EAS114_30:7:269:944:220
+TGGGCAATACATGAGATTATTAGGAAATGCTTTAC
++
+<<<<<<<8<<<<<<<<<<<<<<<;<<<<<;<<;81
+@EAS114_30:7:283:799:560
+ACATAGACCCCCTTGCAACAACCTTGAGAACCCCA
++
+<4<6<8;;6<<<+;<:<<;<<<<<<<<<<<<<<<<
+@EAS114_30:7:283:799:560
+GGGGTTGCCAGCACAGGGGCTTAACCTCTGGTGAC
++
+<<<<+<<<<8<<<+<<<<<;<<:07;8;7402447
+@EAS114_30:7:310:155:312
+CAGCAAGAGAAAAGCATACAGTCATCTATAAAGGA
++
+;<<<;<<<8<<<<<<<<<<<<;<<<<<8<<<<8<<
+@EAS114_30:7:310:155:312
+CATAAATGAAGGGGAAATAAAGTCAAGTCTTTCCT
++
+2;<<;<<;<<;;/<<<<<<;<<<<8<<<<<<<<<<
+@EAS114_30:7:319:11:255
+TACCCAGATTCATAAAACAAATACTACTAGACCTA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<:<:
+@EAS114_30:7:319:11:255
+TCTATAAAAAAATTAAAATTTAACAAAAGTAAATA
++
+;8<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<<
+@EAS114_30:7:59:871:351
+GTAAAAAATTAACATTACAACAGGAACAAAACCTC
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<<;
+@EAS114_30:7:59:871:351
+TAAAGACATGAGTTCAGGTAAAGGGGTGGAAAAAG
++
+;<<<<<:<;<<<4;<<<<<<<<<<<<<<<<<<<<<
+@EAS114_30:7:71:311:202
+TATGAGATTATGTAAAGTAACTGAACCTATGAGTC
++
+<<<<<<<<<<<<<<<<:4<<<<<<<<<<<<8;4;:
+@EAS114_30:7:71:311:202
+TCAAGATATGTAGTCATCAGACTATCTAAAGTCAA
++
+;6<;<<<<<<<<<<<<<<<<<<<<<;<<<<<<<<<
+@EAS114_32:1:199:760:42
+ACCCAATTAATATTTTTCTTAGCAAAACAGTCTAG
++
+58*5.<+<<<<,4<<**<90**9<<<<<<4<<<<<
+@EAS114_32:1:199:760:42
+CTCTCTAATTTTTGCTGCTTCCATGTCTTACTCTG
++
++2&2&2&22222220222&220-222-22-22-22
+@EAS114_32:1:208:971:600
+AAAAAAACCTGTCAAACACGAATGTTATGCCCTGC
++
+<<<<<<<3*+<4/<<<<7<<<<0<<:<8<<<<0<<
+@EAS114_32:1:208:971:600
+AGATATGTAGTCATCAGACTATCTAAAGTCAACAT
++
+<<<<<<<<<<<<<<<<<8<<:<<<0;44<<:4<:<
+@EAS114_32:2:163:618:570
+AGGCTGCAACTGTGAGCCATCACAATGAACAACAG
++
+<<<<<<<8<<<<<<<<<<<<<+<.7<<..<;&;8;
+@EAS114_32:2:163:618:570
+GGAAAGCTGTCAACGCTTCTAGCCATTTCTTTTGG
++
+<9774<88&:8<:8<8:8<8<<<<<;88<88<<<<
+@EAS114_32:2:197:170:559
+CTCATTCACTCCAGCTCCCTGTCACCCAATGGACC
++
+<:<;;:<5<5<<<;<<<<<<<<<<<<<<<<<<<<<
+@EAS114_32:2:197:170:559
+TTCTCAAGGTTGTTGCAAGGGGGTCTATGTGAACA
++
+:;;;;<<<<<<8<<<<<<<<<<<<<<<<<<<<<<<
+@EAS114_32:2:247:900:123
+AAAACATGAACTAACTATATGCTGTTTACAAGAAA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<9;<;
+@EAS114_32:2:247:900:123
+AATTCAGCAAGAAGATATAACCATCCTACTAAATA
++
+;;;;.<<4<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS114_32:2:283:577:398
+ACAATGGGCTTCTCAGCGGAAACCTTACAAGCCAG
++
+;8;;&<<<;<;67<;<;<<<<<<<<;<<<<<<<<<
+@EAS114_32:2:283:577:398
+CTAGAGATTTAGACATCTAAATGAAAGAGGCTCAA
++
+<<<<<<<<<<<<<<<<<<<9<<<<<<<<<;<<<<<
+@EAS114_32:2:306:119:56
+CTTCTCACAGTTTCTGCCCCCAGCATGGTTGTACT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<
+@EAS114_32:2:306:119:56
+TCCATGTACACACGCTGTCCTATGTACTTATCATG
++
+;;;;;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS114_32:3:236:475:254
+AGATAAAGCACACTTTAAATCAACAACAGTAAAAT
++
+<:<<<<<;9<7<;<<<<<<<<<<9<<<<<<<<<<<
+@EAS114_32:3:236:475:254
+TTCCCCCACTTAAGAGATATAGATTGGCAGAACAG
++
+<<<<<<<<<<<<<<<<<<<<<<<<<:::<:;</;/
+@EAS114_32:3:307:113:346
+AATTCAGCAAGAAGATATAACCATCCTACTAAATA
++
+<<<<9<<1<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS114_32:3:307:113:346
+ATGCTGTTTACAAGAAACTCATTAATAAAGACATG
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;;<<8
+@EAS114_32:4:156:21:69
+AAAAATGAACAGAGCTTTCAAGAAGTATGAGATTA
++
+<<<<<<<<<<<<<<<<<<<<<<<:<4<<<:<;<;;
+@EAS114_32:4:156:21:69
+TTGCAAGACAGACTTCATCAAGATATGTAGTCATC
++
+<:3:<<;<;<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS114_32:4:20:41:138
+CATTTCTTTTGGCATTTGCCTTCAGACCCTACACG
++
+;;;<;<<<::<<<<<<<;<<<<<<<<<<<<<<<<<
+@EAS114_32:4:20:41:138
+GTCTTTCAAAAGGTGATGTGTGTTCTCATCAACCT
++
+<<<<<<<<<<<<<<<<<<<<<<<<7<;<<<<<(<<
+@EAS114_32:4:228:587:504
+GCACATTACGACCCGGCAAGGTGTATAATTGTGTC
++
+;4;4;&&82&04+&&48;3&3&*<7<47<<;-<-8
+@EAS114_32:4:228:587:504
+GTGCACTAATGCGCTCCACGCCCAAGCCCTTCTCA
++
+<<<<7<<7;7<<3<<<<7<<<<<*3<<<<74<:<*
+@EAS114_32:4:246:647:765
+GATCAATTCAGCAAGAAGATATAACCATCCTACTA
++
+9<+,<<&,39<,<;<<<<<<<&<<<<;0<<3;<<<
+@EAS114_32:4:246:647:765
+TATGCTGTTTACAAGAAACTCATTAATAAAGACAT
++
+;<<<<<<<<<;<&<<3+3<<<3<<9&</:/87</8
+@EAS114_32:4:42:923:169
+ACAGTTTCTGCCCCCAGCATGGTTGTACTGGGCAA
++
+9<<<;9<<<<<;<;<<.<<;<;6<<<<1;8<<-0;
+@EAS114_32:4:42:923:169
+TTCCTATGTACTTATCATGAATCTATCCCAAATTC
++
+&;972<;&<9<,;;;<<<;<&99<<;<;;3<<3<<
+@EAS114_32:4:5:396:292
+ATACATATGCACCTAACACAAGACTACCCAGATTC
++
+<:<6<7<:<:;;;<<<;<7<<<<<<<<<<<<<<<<
+@EAS114_32:4:5:396:292
+TAAAGGGGTGGAAAAAGATGTTCTACGCAAACAGA
++
+<<<<<<<<<<<<<<;;<<<<:<<<<;;<;;3/&+8
+@EAS114_32:4:7:282:424
+CAAAAACAAAAACTATGCTAAGTATTGTTAAAGAT
++
+1<<<<<9<<<<<31<77;;;;7<3<<2+;<3<<<<
+@EAS114_32:4:7:282:424
+TAATTGGTACAATGTACAATATTCTGATGATGGTT
++
+<<<3<<<9<<<<3<<<<<9<<<9,<;;9;&*;3,.
+@EAS114_32:5:109:199:592
+ACGAATATTATGCCCTGCTAAACTAAGCATCATAA
++
+;9<9<:&:<<<<;;<;;<<<<<<<<<;<<<<<<<<
+@EAS114_32:5:109:199:592
+AGTCATCAGACTATCTAAAGTCAACATGAAGGAAA
++
+<<<<<<<<<<<;:<;;<<:;6<<;:;:<<+;;;<;
+@EAS114_32:5:182:313:319
+AATTTGGTGTTCTGTGTAAAGTCTCAGGGAGCCGT
++
+</<;185;8<;;87<;8<<<<8<;83<<<<<<<<<
+@EAS114_32:5:182:313:319
+GATGAACCACACATTAATACTATGTTTCTTATCTG
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<7<<<<;<;
+@EAS114_32:5:267:170:250
+CATAAAACAAATACTACTAGACCTAAGAGGGATGA
++
+<<<<<<<<<<<<<<<<<;<<<;<<<<<<<<<<<<;
+@EAS114_32:5:267:170:250
+CATAGCTAAAACTAAAAAAGCAAAAACAAAAACTA
++
+-<;<5-:<<<<;<<<<<<<;;<<<<<<<<<<<<<<
+@EAS114_32:5:78:583:499
+TTTACGCTATTCAGTACTAAATATAGAAATTGAAA
++
+&6&9774&<;67<44&-4<;<9<7<<<<<;<<<<<
+@EAS114_32:6:122:342:296
+AAAGCTTGGGCTGTAATGATGCCCCTTGGCCATCA
++
+<:;:<<<;<2<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS114_32:6:122:342:296
+TCCTATGTACTTATCATGACTCTATCCCAAATTCC
++
+<<<<<<<<<<<<<<<<<<<<<<<<<;<<*<<<<9<
+@EAS114_32:6:178:342:866
+AACAAATCTGCGCTTGTACTTCTAAATCTATAAAA
++
+<<9<<<&;;<<<<77<;<<<5;:<<<:<<<<<<<<
+@EAS114_32:6:178:342:866
+ATACATATGCACCTAACACAAGACTACCCAGATTC
++
+;<<<<<;<<<8<<;<;<3<8/<<<<6<<</<8;<<
+@EAS114_32:6:179:735:569
+ATGTTAAAATGTCTATTTTTGTCTTGACACCCAAC
++
+<5<3:<<<<5;8<<<55;<:</:<<<<<<<<<<<<
+@EAS114_32:6:179:735:569
+CATCACCCGGTCCCTGCCCCATCTCTTGTAATCTC
++
+<<<<<<<<<<<<<<<<<<<<3<<<<<<<<4/<;<<
+@EAS114_32:6:199:818:124
+AACTATTTGAGGAAGTAATTGGGGAAAACCTCTTT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS114_32:6:199:818:124
+ACTAAACCAAGCAGAAGAAAGAGGTTCAGAACTTG
++
+<<<<<<<<<<<<<<<<<;<<;<<;7<<<<<<9<9;
+@EAS114_32:6:78:909:394
+ATTGCTTGGTGTCTGACAGGCTGCAACTGTGAGCC
++
+6167&+&&/&//734/3<<<9*<;;3<3<;9<<3<
+@EAS114_32:6:78:909:394
+TACCAGAGGGATGGAGGGAAGAGGGACGCTGAAGA
++
+<<<<<<8<<<&<<<-<<<14,4;<<-0<2+<)/82
+@EAS114_32:6:88:162:587
+GGTTTTCTGTTTCTTTGTTTGATTTGGTGGAAGAC
++
+386;;388-<8;<;68<<;;<;<6<<<8<<<<<<<
+@EAS114_32:6:88:162:587
+TTCTGTGTAAAGTCTCAGGGAGCCGTCCGTGTCCT
++
+<;<<<<<<<<<;<5<;<;<<7<++<<2&*:322+7
+@EAS114_32:7:174:597:66
+TCTCTTGTAATCTCTCTCCTTTTTGCTGCATCCCT
++
+9<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<<<<
+@EAS114_32:7:174:597:66
+TCTTCTTCTTAGGGAAGAACAGCTTAGGTATCAAT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<;<<;<<;6;<
+@EAS114_32:7:201:959:19
+CTCTACATGGCTGATTATTAAAACAATGTTCCCCA
++
+;4;.9<:0&/<5<::<<9/.<<<<<<<<<<<<;<<
+@EAS114_32:7:201:959:19
+TATCTGGATTCTGGGAAATTCTTCATCCTGGACCC
++
+<<<<<<<<<<<<<<;<<<:<;<<;<<;+;+<3494
+@EAS114_32:7:256:407:470
+AACGCTTCTAGCCATTTCTTTTGGCATTTGCCTTC
++
+<<<<<<<<;<;<<<<<<<<<;;<</<<;;83;7;9
+@EAS114_32:7:256:407:470
+CAGCATGGTTGTACTGGGCAATACATGAGATTATT
++
+7.47;0;;5<4033*<<<<<9,<<<<<;<<<<<3<
+@EAS114_39:1:12:884:219
+GAGCCATCACAATGAACAACAGGAAGAAAAGGTCT
++
+<<<<<<<<<<<<<<<<<<<;<<<<<<<<<<<<5:<
+@EAS114_39:1:12:884:219
+GCTTTCAACGCTTCTAGCCATTTCTTTTGGCATTT
++
+7;::<:<<<7<<:<<<<<<<<<<<<<<<<<<<<<<
+@EAS114_39:1:28:350:895
+ATATAGTTGAAAGCTCTAACAATAGACTAAACCAA
++
+<<<<<<<<;<;<<<<<<<<<;;<<;<<<<<;;<;8
+@EAS114_39:1:28:350:895
+TATGAGTCACAGGTATTCCTGAGGAAAAAGAAAAA
++
+:<;<<<:;<-<<<<<4;77<<<<<<<<<<<<<<<<
+@EAS114_39:1:43:1120:878
+ACTAATGCGCTCCACGCCCAAGCCCTTCTCACAGT
++
+<<<<<<<<<<<<<<<<<<<<8<<<<<<<<<<=7;7
+@EAS114_39:1:43:1120:878
+TAATTGTGTCCATGTACACACGCTGTCCTATGTAC
++
+<<<;<<;<<;<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS114_39:1:70:147:84
+ATAGACCCCCTTGCAACAACCTTGAGAACCCCAGG
++
+<<<:<;<<<<<<;<<<<<<<<<<<<<<<<<<<<<;
+@EAS114_39:1:70:147:84
+CCAGCACAGGGGCTTAACCTCTGGTGACTGCCAGA
++
+<<<<<<<<<<<<<<<<<<<<;<<<<<<<<<;(5<<
+@EAS114_39:1:71:636:533
+GCCTCGTCCACACTGGTTCTCTTGAAAGCTTGGGC
++
+<<<<<<<<<<<<<<<<<<<<<<<7<<<5<<<-847
+@EAS114_39:1:71:636:533
+GTGGAAGACATAATCCCACGCTTCCTATGGAAAGG
++
+,51(<<8<:<<<<<<<;<;<<<<<<<<<<<<<<<<
+@EAS114_39:1:73:302:1574
+AAGGTTGTTGGGAGATTTTTAATGATTCCTCAATG
++
+7<88;;<;;<;;<<<<<<<<<<<<<<<<<<<<<1<
+@EAS114_39:1:73:302:1574
+CCTCGTCCACACTGGTTCTCTTGAAAGCTTGGGCT
++
+<<<<<<<<<<;<<<<<<<<<<<<+:;<<;:8;<<<
+@EAS114_39:1:98:641:1040
+CAGAACAGATTTAAAAACATGAACTAACTATATGC
++
+<<<<<<;<<<<<<<<<<<<<<<<<<<<<<<<<<<;
+@EAS114_39:1:98:641:1040
+TAAAACAAAGGAGGTCATCATACAATGATAAAAAG
++
+4<<<<7<<<<<<<<<:<<;<;<<<<<<<<<<<<<<
+@EAS114_39:2:18:967:582
+AAGCCGTTCTATTTGTAATGAAAACTATATTTATG
++
+<<<<<<<<<<<<<<<<<<<<<9<<<<<<;<<<<<8
+@EAS114_39:2:18:967:582
+ACGCTGAAGAACTTTGATGCCCTCTTCTTCCAAAG
++
+<:<<<<<<<<<<<<<<;<<<<<<<<<<<<<<<<<<
+@EAS114_39:2:38:670:564
+CAGGTTTTATAAAACAATTAATTGAGACTACAGAG
++
+<<<<<<<<<<<<<<<<<<<<<<<;<:<<<<;<5<;
+@EAS114_39:2:38:670:564
+CTAACTATATGCTGTTTACAAGAAACTCATTAATA
++
+3<<<3:<<<<<:;<<<<<:<<<<<<<<<<<<<<<<
+@EAS114_39:2:41:576:1016
+CTCTCCTTTTTGCTGCATCCCTGTCTTCCTCTGTC
++
+<<<<<<<<<<<<<<;<<<;<<<<<<<<<<<4<::<
+@EAS114_39:2:41:576:1016
+TGTCTGAGCAAAACAGTCTAGATGAGAGAGAACTT
++
+:<;<<<<<6<<<<;<<<<:<<<<<<<<<<<<<<<<
+@EAS114_39:2:57:1064:925
+TGACAAGCAAATGCTAAGATAATTCATCATCACTA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<:<<<
+@EAS114_39:2:5:1219:137
+AAAACTAAAAAAGCAAAAACAAAAACTATGCTAAG
++
+<<<<:<<<<<<<<<<<<<<<<<<<<<<<<<<:<<<
+@EAS114_39:2:5:1219:137
+ACCTAAGAGGGATGAGAAATTACATAATTGGTACA
++
+<<<<<<<<<<<<<<<<<<<<<<<(<<<<<<:9<;=
+@EAS114_39:3:11:1238:1728
+AGAGATTTAGACATCTAAATGAAAGAGGCTCAAAG
++
+<<7<<<<<;<<<<<<<<<<<<;<<<;<<<<<<;;<
+@EAS114_39:3:11:1238:1728
+TCCCATCAGAATAACAATGGGCTTCTCAGCGGAAA
++
+:677<;<<<<<<<<<<<:<<<<<<<<<<<<<<<<<
+@EAS114_39:3:55:464:146
+AAAAAGATCAATTCAGCAAGAAGATATAACCATCC
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS114_39:3:55:464:146
+CTCAATATATCCATGTAACAAATCTGCGCTTGTAC
++
+;(;;;;<<<<;<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS114_39:3:6:1064:1805
+TAAAATTTAACAAAAGTAAATAAAACACATAGCTA
++
+<<<<<<<<<<<<<<<<<<<<<<;<<<<<<<<<<<<
+@EAS114_39:3:6:1064:1805
+TTGGTAATTTCGTTTTTTTTTTTTTCTTTTCTCTT
++
+;88<;<;;<<;;<<<<<<<<<<<<<<<<<<<<<<<
+@EAS114_39:3:88:84:1558
+AGTAACTGAACCTATGAGTCACAGGTATTCCTGTG
++
+<<;<<<<<<<<<<<<;;<<<<<<<::<<<<<<7&<
+@EAS114_39:3:88:84:1558
+ATCAGACTATCTAAAGTCAACATGAAGGAAAAAAA
++
+;;<<;<<;<<5<<<<<<;<<:<<<;<<<<<<;<<<
+@EAS114_39:4:10:1312:1558
+AACTAACTATATGCTGTTTACAAGAAACTCATTAA
++
+<<:<<<;<<<<<<;<<<<<<<<<<<<<<<<<<<<<
+@EAS114_39:4:10:1312:1558
+AGGTTTTATAAAACAATTAATTGAGACTACAGAGC
++
+5<<<<<<<<<<<<<<<<<<<<<<<;;<<<<<;8;<
+@EAS114_39:4:30:432:228
+ATCCTACTAAATACATATGCACCTAACACAAGACT
++
+<76<<<:<<<<<<<;<:<<<<<:<<<<<<<<<<<<
+@EAS114_39:4:30:432:228
+GACATGAGTTCAGGGAAAGGGGTGGAAAAAGATGT
++
+<<<<<<<<<<<<<<8<<<<<<<<<<<<:<<<<<;;
+@EAS114_39:4:30:570:902
+AAAAACCTGTCAAACACGAATGTTATGCCCTGCTA
++
+<<<<<<<<<<<;4<<:<<44<<<<<<<<<<<4<<+
+@EAS114_39:4:30:570:902
+ATACTCACCATCATAAATACGCACAAAAGTACAAA
++
+<:<6:6<&:<<6<<<<<<<<.<<<<<<<<<<<<<<
+@EAS114_39:4:43:1047:1626
+GATGAGAGAGAACTTCCCTGGAGGTCTGATGGCGT
++
+<<4<<<<<<<<<<<:<<<;<<<<<:<7<<;<<<<<
+@EAS114_39:4:43:1047:1626
+GTTGGTTTTCTGTTTCTTTGTTTGATTTGGTGGAA
++
+<<<<<<<<<<<<<<<<<<<:<<<:<<<<:+;-4:(
+@EAS114_39:4:58:271:612
+AGGAAAAAGAAAAAGTGAGAAGTTTGGAAAAACTA
++
+<;<<<<<<<<<7<<<<<<<<<<<<<<+47<<;<::
+@EAS114_39:4:58:271:612
+ATGAAGGAAAAAAATTCTAAAATCAGCAAGAGCAA
++
+;:2=<<;<<<<<<:67:<<:<<<<<<<<<<<<,<<
+@EAS114_39:4:93:77:1338
+GCTGCTTACAAGAAGCGCATTAATAAAGACATGAG
++
+<<<<*<2<<<:<4<&<6<8<4<::<8<<<<82;;7
+@EAS114_39:4:93:77:1338
+GTCATCATACAATGAAAAAAAGATCAATTCAGCAA
++
+<<7<7<<<<<1<7<<&97;;<1<;1<<7<;7<<;<
+@EAS114_39:5:17:1222:783
+AAGAAAGAGGTTCAGAACTTGAAGACAAGTCTCGT
++
+<<<<<<<)<<<16<<;<<<6<4<:<4<+://<7)<
+@EAS114_39:5:17:1222:783
+TGAGAAGTTTGGAAAAACTATTTGAGGAAGTAATT
++
+6<<<8<69<8199<7<<<6<<<<<<<<<1:<:<<:
+@EAS114_39:5:42:1223:1087
+CAGTCCCTGCCCCATCTCTTGTAATCTCTCTCCTT
++
+<<<<<<<<<<<<<5<<<<<<<<;<<<<<<<<<<<<
+@EAS114_39:5:42:1223:1087
+TTGTCTTGACACCCAACTAATATTTGTCTGAGCAA
++
+;:<<<:<7<<<;;<<<<<<<<<<;<<<<<<<<<<<
+@EAS114_39:5:50:972:1286
+AGAGGGATGGAGGGAAGAGGGACGCTGAAGAACTT
++
+<<<<<<<<<<<<<<<<<;<<<<<<<<<6<<7:7:;
+@EAS114_39:5:50:972:1286
+TTGTGGTCTGACAGGCTGCAACTGTGAGCCATCAC
++
+:;;7;7;;0<<<<<<<;<<<<<<<<<<<<<<<<<<
+@EAS114_39:5:61:1000:1534
+CTTGAAGACAAGTCTCTTATGAATTAACCCAGTCA
++
+<<<<4:<:<1)<<<<<<<+<:44<</7<<<)4:<)
+@EAS114_39:5:61:1000:1534
+GGGGAAAACCTCTTTAGTCTTGCTAGAGATTTAGA
++
+<<;<<<<;;<<;6;<<<;<4;<<7<<<<<;<<<<<
+@EAS114_39:5:93:312:331
+AACTCATTAATAAAGACATGAGTTCAGGTAAAGGG
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<=<<
+@EAS114_39:5:93:312:331
+ATCCTACTAAATACATATGCACCTAACACAAGACT
++
+<;;:;<6<<<<;<:<<<<<<<:<<<<<<<<<<<<<
+@EAS114_39:6:13:1034:1144
+AAAGATGAAACGCGTAACTGCGCTCTCATTCACTC
++
+<<:%<9)<<<<<<8<<<<9<<<<<<<<<<<<<<<<
+@EAS114_39:6:13:1034:1144
+AATTGAAACAGCTGTGTTTAGTGCCTTTGTTCACA
++
+<<<<<<<<<<<<<<<<<<<<<<<<3<<<;<<;<++
+@EAS114_39:6:34:380:815
+AAGAGGTTCAGAACTTGAAGACAAGTCTCTTATGA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<;:
+@EAS114_39:6:34:380:815
+ATTGGGGAAAACCTCTTTAGTCTTGCTAGAGATTT
++
+;;;;<<<<<<;<<<<;<<<<<<<<<<<<<<<<<;<
+@EAS114_39:6:71:644:1792
+AAAAGTACAAAACTCACAGGTTTTATAAAACAATT
++
+<<<<;<<<<<<:;/<<<<<<<<<<<<<<<<<<<<<
+@EAS114_39:6:71:644:1792
+CCTGCTAAACTAAGCATCATAAATGAAGGGGAAAT
++
+<<<<<<<;<<<<<<<<<<;<<<<<<<<<;<;:<:<
+@EAS114_39:6:76:282:1668
+AACAAAAACTATGCTAAGTATTGGTAAAGATGTGG
++
+<<<<<:<<<8<8<<<<<::<<<<7<<<<<<2<<<8
+@EAS114_39:6:76:282:1668
+TACAATGTACAATATTCTGATGATGGTTACACTAA
++
+<<<<<<<<<<<<<<<<<<;<<;<<<<<<;<;<<<8
+@EAS114_39:6:7:492:1088
+ACAGGTTTTATAAAACAATTAATTGAGACTACAGA
++
+<<<<<<<<<<<<<<<<<<<<<<<<7<:<<<<<<6;
+@EAS114_39:6:7:492:1088
+TGAACTAACTATATGCTGTTTACAAGAAACTCATT
++
+4;<<75<<::<:<<<-<<<<<<<<<<<<<<<<<<<
+@EAS114_39:6:85:1224:625
+GAACTCCCCTGGAGGTCTGATGGCGTTTCTCCCTC
++
+17;;7&-;<;<;:<6<<:;<<<<<<<;<<<<<<<<
+@EAS114_39:6:85:1224:625
+GCTGCATCCCTGTCTTCCTCTGTCTTGATTTCCTT
++
+<<<<<<<<<;<<;<<7<<:<<7.<<<:&7<<.<;<
+@EAS114_39:6:94:1273:1462
+AAGATGTTCTACGCAAACAGAAACCAAATGAGAGA
++
+<<<<<<<<<<<<:<<<<<<<<:<<<<:6:7;744;
+@EAS114_39:6:94:1273:1462
+CCTAACACAAGACTACCCAGATTCATAAAACAAAT
++
+8.<<<;<:<<<<;<<;;;<<<;<;<;<<<<<<<<<
+@EAS114_39:7:100:708:1984
+AGATGAACCACACATTAATACTATGTTTCTTATCT
++
+:8<(8<)9<;<<<<+<<<<<<<<<<<<<<<<<<<<
+@EAS114_39:7:100:708:1984
+TACCACAGGGGGCTGCGCGGTTTCCCATCATGAAG
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<;<<<<<7%:
+@EAS114_39:7:23:1126:1886
+ACACTAAAAGCCCATACTTTACTGCTACTCAATAT
++
+5*.:.5<<::<<<<<<<<:5<<<<<<<<<<:2<<<
+@EAS114_39:7:23:1126:1886
+GGAGGTCATCATACAATGATAAAAAGATCAATTCA
++
+7<<<7<<<<<<<<7<<<<<<<<<<<<<;8<;<<5<
+@EAS114_39:7:32:562:1695
+GATGATGGTTACACTAAAAGCCCATACTTTACTGC
++
+:5:::<88/<:<<<<<<<<<7<9<<&<959<<<<<
+@EAS114_39:7:32:562:1695
+TAAAACAAAGGAGGTCATCATACAATGATAAAAAG
++
+<<<<<<<<<<<<<<8<<<<<:<<<<<<<:<8<<<<
+@EAS114_39:7:57:1114:2032
+TAACTATATGCTGTTTACAAGAAACTCATTAATAA
++
+<7<<<<<<<<<<<<<<<<<777<<<7<<<<<3<<7
+@EAS114_39:7:57:1114:2032
+TATTACAATGATAAAAAGATCAATTCAGCAAGAAG
++
+;+!5<4<<<<<<<<<<<<<;<&<;7<<<<<<<<<<
+@EAS114_39:7:90:406:631
+CATCCCTGTCTTCCTCTGTCTTGATTTACTTGTTG
++
+<<<<<<<<<<<<<<<<<:<<<<:;<<<<;<<8;<8
+@EAS114_39:7:90:406:631
+TGAGAGAGAACTTCCCTGGAGGTCTGATGGCGTTT
++
+<<<:<:<<<-<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS114_45:1:100:979:1863
+ATTACAAAACTCACAGGTTTTATAAAACAATTAAT
++
+6&,*3;6;66;9(572692;;;79;4)9;96;59+
+@EAS114_45:1:100:979:1863
+TTATGCCCTGCTAAACTAAGCATCATAAATGAAGG
++
+;<;;;;;;;7;;;79;;77;9;;99;974;677-6
+@EAS114_45:1:12:1296:358
+CTTGAAAGCTTGGTCTGTAATGATGCCCCTTGGCC
++
+-770074;;6;&42;:2;;;:;;;;:;;/:;;;;:
+@EAS114_45:1:12:1296:358
+GTCCATGTACACACGCTGTCCTATGTACTTATCAT
++
+;;;6;7;7;;;;;7;9;;-*1;9;699/99/7477
+@EAS114_45:1:2:1422:1820
+CACCTAACACAAGACTACCCAGATTCATAAAACAA
++
+*4617;;4;1;;79;/7&,4;9;;;7<;;<<<;<<
+@EAS114_45:1:2:1422:1820
+TACGCAAACAGAAACCAAATGAGAGAAGGAGTAGC
++
+;7;;;;;;;;:;;;;;;;;;;;;;;;;;;;77777
+@EAS114_45:1:30:1882:1210
+ATCATCACTAAACCAGTCCTATAAGAAATGCTCAA
++
+776778;5;;;;8;;7:8;;;;;;;<<<;;;;;<;
+@EAS114_45:1:30:1882:1210
+GCAGAAACCTTACAAGCCAGAAGAGATTGGATCTA
++
+;;::;;;;:;;;;;:;;;;;;9;;:7;;8:77777
+@EAS114_45:1:33:1407:94
+TAGGTATCAATTTGGTGTTCTGTGTAAAGTCTCAG
++
+;;;;;;;6:;;:::7;:;;;;:::;;;;:;47771
+@EAS114_45:1:33:1407:94
+TTACTTGTTGTTGGTTTTCTGTTTCTTTGTTTGAT
++
+77477;4;;;;;44;;;;;;7;;;;;;;9;;;;;<
+@EAS114_45:1:77:1000:1780
+AGTAATTGGGGAAAACCTCTTTAGTCTTGCTAGAG
++
+777774;;4-7;;;;;;:;;;:;;;<;;;;<<<<;
+@EAS114_45:1:77:1000:1780
+TGAATTAACCCAGTCAGACAAAAATAAAGAAAAAA
++
+;;;:;;;;;;;/;;;7:4;;7;;;;;;;;;77777
+@EAS114_45:1:84:275:1572
+AGGGACGCTGAAGAACTTTGATGCCCTCTTCTTCC
++
+777777::7:;74;:;:7;:::;;;;:;;8;;;<;
+@EAS114_45:1:84:275:1572
+TTATGCTATTCAGTTCTAAATATAGAAATTGAAAC
++
+/6;;;4;;;;;;;;7;;4;.4;;;;;6;;;77077
+@EAS114_45:1:95:1530:28
+AAGAGGCTCAAAGAATGCCAGGAAGATACATTGCA
++
+;;;;;;;;;;:;;;;;;;8;;;;;;;;;;;77747
+@EAS114_45:1:95:1530:28
+AATGGGCTTCTCAGCAGAAACCTTACAAGCCAGAA
++
+77741(9;;994;5;;4;;1;;;;;1;<;<<<<;<
+@EAS114_45:1:9:1289:215
+AGGGACGCTGAAGAACTTTGATGCCCTCTTCTTCC
++
+7747*7;;;;+;;:2;7;:1;;9:;:;:;;:;::;
+@EAS114_45:1:9:1289:215
+TATGCTATTCAGTTCTAAATATAGAAATTGAAACA
++
+;;;;;;9;;;67;;;;;99;9;;;;;;;;977747
+@EAS114_45:2:13:1507:1146
+AAGTAATTGGGGAAAACCTCTTTAGTCTTGCTAGA
++
+88788;,;:-:2;;;;;;;;:;:;;;;;;;;;;;;
+@EAS114_45:2:13:1507:1146
+CAGAAGAAAGAGGTTCAGAACTTGAAGACAAGTCT
++
+;<9;;;;<<;;;;<<;<;;;;<;;<<;<;<99777
+@EAS114_45:2:15:1497:1530
+AATTACGTCCTATCTTCTTCTTAGGGAAGAACAGC
++
+0<;;;9;;86<;;;<<&<<.<<;)3;7;654-471
+@EAS114_45:2:15:1497:1530
+TAATCTCTCTCCTTTTTGCTGCATCCCTGTCTTCC
++
+77778:;;;:;;;;:9;:;;;;;;;;;9;:;;;;;
+@EAS114_45:2:1:1140:1206
+TCCCATTTGGAGCCCCTCTAAGCCGTTCTATTTGT
++
+;;;;;;;;;;;;;:9;;7;;:;:;97;:;:88888
+@EAS114_45:2:1:1140:1206
+TTTATTACCAGAGGGATGGAGGGAAGAGGGACGCT
++
+77977::99;;;:;;<;;;:;;;<<;<;;;;<;;;
+@EAS114_45:2:20:413:1334
+CCGTGTCCTCCCATCTGGCCTCGTCCACACTGGTT
++
+7<<;<<<.;<;67;7;;;:;;3;<59+...77677
+@EAS114_45:2:20:413:1334
+TTGGTTTTCTGTTTCTTTGTTTGATTTGGTGGAAG
++
+88878777;:;:1:;9;;;6;;;6;9;;;;;296;
+@EAS114_45:2:23:1754:796
+CTTCTAAATCTATAAAAAAATTAAAATTTAACAAA
++
+;<<;<;<;<;<;<<;;;;;<<<<;;<<<<<97999
+@EAS114_45:2:23:1754:796
+CTTTGGAAAACAATTTGGTAATTTCGTTTTTTTTT
++
+88897;;;;:;:;;;;;;;;;;;;;;;;;;;;;;;
+@EAS114_45:2:33:1445:1357
+TATGAATTAACCCAGTCAGACAAAAATAAAGAAAA
++
+;;<;<<<<<<;;;<9:;:;;;;;:;:;;;;99777
+@EAS114_45:2:33:1445:1357
+TTAGTCTTGCTAGAGATTTAGACATCTAAATGAAA
++
+88888;;;;;;;:;;;;;;;:;9;;;;;;;;;;;;
+@EAS114_45:2:41:199:388
+AGAAAAAGTGAGAAGTTTGGAAAAACTATTTGAGG
++
+;;<<<<<;;<<<<<<;;<;;<<;;<<<<<<99999
+@EAS114_45:2:41:199:388
+TCTAAAGTCAACATGAAGGAAAAAAATTCTAAAAT
++
+84898;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
+@EAS114_45:2:49:163:904
+GCTCTCATTCACTCCAGCTCCCTGTCACCCAATGG
++
+;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;78958
+@EAS114_45:2:49:163:904
+TCTTTCAAAAGGTGATGTGTGTTCTCATCAACCTC
++
+79779<<<<<;;;;9;;<<7<;*9<<<7<<;<<;<
+@EAS114_45:2:54:1886:719
+CTGTTTACAAGAAACTCATTAATAAAGACATGAGT
++
+;;;9;;<;;;9;;;;;:;<9;:;;;;9;;;99799
+@EAS114_45:2:54:1886:719
+TTCAGCAAGAAGATATAACCATCCTACTAAATACA
++
+883777;;:;;;;;;;;;;;;;;;;;;;;;;;;;;
+@EAS114_45:2:59:396:359
+GGGTATAATACCTCTACATGGCTGATTATGAAAAC
++
+28288;;;;;;;;;::;;;;:;;;;;;;;;;;;;;
+@EAS114_45:2:59:396:359
+TCACCCAATGGACCTGTGATATCTGGATTCTGGGA
++
+<<9;;<;<;;;;<;;9;;;;;<;;;;;<;;77677
+@EAS114_45:2:76:1765:700
+AAAAAGGGATTAAATTCCCCCACTTAAGAGATATA
++
+77777;;;;7;7;<;;;;+;;<9<<<79;<1<<77
+@EAS114_45:2:76:1765:700
+GTCCTATAAGAAATGCTCAAAAGAATTGTAAAAGT
++
+;;6;;;;;;;;;6;;;;6;;;;;;;;;;;;88878
+@EAS114_45:2:79:554:354
+AAATAAAACAAAGGAGGTCATCATACAATGATAAA
++
+17;<;;+<<;;;;93;;:;3;;;;1;;;;<77744
+@EAS114_45:2:79:554:354
+CAATGTACAATATTCTGATGATGGTTACACTAAAA
++
+98988;7;;;;:;;;;;;;;;;:;;;:;;;;;9;;
+@EAS114_45:3:26:1867:162
+ATATAACCATCCTACTAAATACATATGCACCTAAC
++
+;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;78698
+@EAS114_45:3:26:1867:162
+ATATATCCATGTAACAAATCTGCGCTTGTACTTCT
++
+97999:;<<9;;<:<<;;;<;;<<<<<<<;;<<<<
+@EAS114_45:3:27:1881:486
+AAGAAAAGGTCTTTCAAAAGGTGATGTGTGTTCTC
++
+99797;;9:<:;;;<;;;;<<<;;;;<;<;;<<<<
+@EAS114_45:3:27:1881:486
+CCAAAGATGAAACGCGTAACTGCGCTCTCATTCAC
++
+;;;;;;;;;;;;;;1;;;;;;;;78;8;8;8878/
+@EAS114_45:3:2:1200:1076
+CATTTGCCTTCAGACCCTACACGAATGCGTCTCTA
++
+7779779;9;:;;4;;9;;:7;<<<7;;;:<;<<;
+@EAS114_45:3:2:1200:1076
+GATGTGTGTTCTCATCAACCTCATACACACACATG
++
+;;;;;;;;;;/;;;;;;;;6;;9;489;;;88888
+@EAS114_45:3:32:1379:738
+TTAAGAAATTACAAAATATAGTTGAAAGCTCTAAC
++
+;;;;;;;8;;;;;;;;;;;;;;;;;;;;;;88888
+@EAS114_45:3:35:896:1588
+CTAGACCTAAGAGGGATGAGAAATTACCTAATTGG
++
+77999:.:<<;<;;;<<;<;<<<<<;<;;<<<<;;
+@EAS114_45:3:35:896:1588
+GAGTAGCTATACTTATATCAGATAAAGCACACTTT
++
+;;;;;;;;;;;;;;;;;;;;8;;;;;8;;;88989
+@EAS114_45:3:39:208:644
+ATTGTAAAAGTCAAAATTAAAGTTCAATACTCACC
++
+<;<<<<<;;:<<;;<<<<<<;;;;;;.<;<79997
+@EAS114_45:3:39:208:644
+TTTGAATAAAAAGGGATTAAATTCCCCCACTTAAG
++
+78899;;;;4;;;;;;;;;;;;;;;;;;8;;8;;;
+@EAS114_45:3:3:1377:1663
+CTGCGCTCTCATTCACTCCAGCTCCCTGTCACCCA
++
+<<;;;;<:;;:<;;<;;<;:;;<;9;;::977676
+@EAS114_45:3:3:1377:1663
+GGTGATGTGTGTTCTCATCAACCTCATACACACAC
++
+6-88663;8;81;;66;8;;89939;;;67;2;;;
+@EAS114_45:3:3:864:1888
+AATGTTATGCCCTGCTAAACTAAGCATCATAAATG
++
+888588;;;;;;;;;;;;;;;;;;;;8;;;;;;;;
+@EAS114_45:3:3:864:1888
+CAACATGAAGGAAAAAAATTCTAAAATCAGCAAGA
++
+;<<;;<<;;;<;;<<;<;<<;<<;8<<:<;79799
+@EAS114_45:3:41:653:1568
+AACTATTTGAGGAAGTAATTGGGGAAAACCTCTTT
++
+977979;:;<;;;;;;<<5;<;<;<<<;;;;;;;;
+@EAS114_45:3:41:653:1568
+GGTTCAGAACTTGAAGACAAGTCTCTTATGAATTA
++
+;;;;;;;8;;;;;;;;;;;;;;;;;;;;;;88888
+@EAS114_45:3:44:1578:1674
+CCTCTTCTTCCAAAGATGAAACGCGTAACTGCGCT
++
+;<<;<<;<<;;;;;9<;9;;<9:;;<:;9;76669
+@EAS114_45:3:44:1578:1674
+GCTGCAACTGTGAGCCATCACAATGAACAACAGGA
++
+62631;;4;;;8;;48;;7;8;;;;;;;;;8;;;;
+@EAS114_45:3:75:217:337
+GACAGGCTGCAACTGTGAGCCATCACAATGAACAA
++
+4779797;;;<;:4;;<<<77<;;;7<<;<;<;<<
+@EAS114_45:3:75:217:337
+GAGGGAAGAGGGACGCTGAAGAACTTTGATGCCCT
++
+;;;;;;;;;;;;;;;;;;8;;;;;;;;;;;88787
+@EAS114_45:3:90:1403:1635
+TGTCTTGACACCCAACTAATATTTGTCTGAGCAAA
++
+86878;;;8;788;;;;;;;;;;;;;8;5;;;;;;
+@EAS114_45:3:90:1403:1635
+TTGTAATCTCTCTCCTTTTTGCTGCATCCCTGTCT
++
+<<;<;<<<<;<;<;;<<<<<9;<.;;<:;99.979
+@EAS114_45:4:48:310:473
+TGAATTAACCCAGTCAGACAAAAATAAAGAAAAAA
++
+<<<;<<;;;<<;;<;;;;;;;;;;;;;;;;89799
+@EAS114_45:4:48:310:473
+TTTAGTCTTGCTAGAGATTTAGACATCTAAATGAA
++
+77999;;6;;;;;;;;;;;;;;;9;;;;;;;;;;;
+@EAS114_45:4:73:1208:495
+AGATGAAACGCGTAACTGCGCTCTCATTCACTCCA
++
+8-889<<;<;;:<;<;;;;;;<<;;<;;;;<<;;;
+@EAS114_45:4:73:1208:495
+TAAATATAGAAATTGAAACAGCTGTGTTTAGTGCC
++
+;;;;;;;;;;;;;;;;;;;;;;;;5;;;;;37377
+@EAS114_45:4:7:1347:375
+CTAAAAGCCCATACTTTACTGCTACTCAATATATC
++
+;;;;;;;;;;;;;;;;;;;;9;;;8;;;;;97777
+@EAS114_45:4:7:1347:375
+GGAAAAAAGTAAACTCTCAAATATTGCTAGTGGGA
++
+47999<<<;;;;;;:5;:;<;;<;;;;;<;;;;;<
+@EAS114_45:4:87:323:895
+ATCTGGATTCTGGGAAATTCTTCATCCTGGACCCT
++
+;<<;;;;<<;<959;;;<;:<<;9<;;;4377788
+@EAS114_45:4:87:323:895
+GGTATAATACCTCTACATGGCTGATTATGAAAACA
++
+55777;;;939;9;;9;;;;9;;;;;;;;;;;;;;
+@EAS114_45:4:88:55:1187
+GTCACAGGTATTCCTGAGGAAAAAGAAAAAGTGAG
++
+;;<;;;<<99<<;;<;;;;;:;49;:;;;;87898
+@EAS114_45:4:88:55:1187
+GTCATCAGACTATCTAAAGTCAACATGAAGGAAAA
++
+7769,7;;;;;;;;;;;;;;9;;;;;;;;;;;;;;
+@EAS114_45:5:56:1757:1319
+CATTAATAAAGACATGAGTTCAGGTAAAGGGGTGG
++
+&7778<<<<<8<;<<:::;<:<4<<:<:;8<8<;<
+@EAS114_45:5:56:1757:1319
+TTTATAAAACAATTAATTGAGACTACAGAGCAACT
++
+;;;;9;;;;;;;;;;;;;4;9;98;;;;;9388&7
+@EAS114_45:5:62:841:1994
+ATATCCATGTAACAAATCTGCGCTTGTACTTCTAA
++
+87878;;6:;;:<<<<:<:;;;<;<<<;<;;<;<<
+@EAS114_45:5:62:841:1994
+TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
++
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+@EAS114_45:5:66:959:1311
+CAGAGCTGCTGGCAAGCTAGAGGCCCATCTGGAGC
++
+;;4;;;+;;;-01;;&-;;4;;&;;73)(&**274
+@EAS114_45:5:66:959:1311
+GGGAAGGAGCATTTTGTCAGTTACCAAATGTGTTT
++
+67.68:4::6;;;7:6:;:5;8;;<<:;;<;;;;<
+@EAS114_45:5:82:843:1838
+CTAGGTAAAAAATTAACATTACAACAGGAACAAAA
++
+;<<;:;;<<<;;<<<<;;<<;;;;;<;;;;68887
+@EAS114_45:5:82:843:1838
+TGTTCTACGCAAACAGAAACCAAATGAGAGAAGGA
++
+888829;;;;;;;;;;;;;;:;;;;;;;;;;;;;;
+@EAS114_45:5:85:401:1190
+TACACACACATGGTTTAGGGGTATAATACCTCTAC
++
+64778:;69739:;+9::7;;;<;6<;7;;;;;7<
+@EAS114_45:5:85:401:1190
+TCACTCCAGCTCCCTGTCACCCAATGGACCTGTGA
++
+4;;;1;;;;;;.6;;;(;;/;/;3;;;7;(3&063
+@EAS114_45:5:91:89:666
+GAAAACCTCTTTAGTCTTGCTAGAGATTTAGACAT
++
+74752;;4;;;;;;;;7);;;4;;;;)4;;;;;13
+@EAS114_45:6:14:1211:1332
+AGGAAGATACATTGCAAGACAGACTTCATCAAGAT
++
+978961;;991;97;<;;<;<<;;;;;<;;<:8:<
+@EAS114_45:6:14:1211:1332
+TTTCAAGAAGTATGAGATTATGTAAAGTAACTGAA
++
+;;.;;;;;;;3;;;;;6;;;;;;8;;;;;;63777
+@EAS114_45:6:37:156:134
+AGAGAAAAGCATACAGTCATCTATAAAGGAAATCC
++
+99998<<<<:<<<<<<<;<<><<<<<<<<<<<<<<
+@EAS114_45:6:37:156:134
+GGAAAAACTATTTGAGGAAGTAATTGGGGAAAACC
++
+;;;;;;;;;;9;;;;;;;;;;;;;;;9;;;77679
+@EAS114_45:6:39:956:676
+TAAAACAAATACTACTAGACCTAAGAGGGATGAGA
++
+899985;;<;:9;;:9<;:9:5;<;;;<;<;<<<<
+@EAS114_45:6:39:956:676
+TGAGAGAAGGAGTAGCTATACTTATATCAGATAAA
++
+;;;;;;;;;;;;9;;;;;;;;;;;;;;;9957777
+@EAS114_45:6:44:77:1255
+CTCATTAATAAAGACATGAGTTCAGGTAAAGGGGT
++
+;;;;;;;8;;;7;8;;;;;;;;;;886;;;76777
+@EAS114_45:6:44:77:1255
+TAAAAAGATCAATTCAGCAAGAAGATATAACCATC
++
+79998;;;9:;<696<;.<;;<<;<;<;<;;;<8;
+@EAS114_45:6:45:1769:1130
+ACCCAATGGACCTGTGATATCTGGATTCTGGGAAA
++
+;;;;;;;;;;;;9;;;;;;19;;;9;;;;176777
+@EAS114_45:6:45:1769:1130
+TGTTCTCATCAACCTCATACACACACATGGTTTAG
++
+88989;<;97;9<<;<;;;;9<98<<<<<<<;<<<
+@EAS114_45:6:47:1791:444
+AAGAGGGATGAGAAATTACCTAATTGGTACAATGT
++
+978879;:;;<:;;<<;:<9<<<<;6;;;;<<<<;
+@EAS114_45:6:47:1791:444
+TACTTATATCAGATAAAGCACACTTTAAATCAACA
++
+;3;;;;;;;;;;;;;;;;;;;;;;;;;;;877977
+@EAS114_45:6:59:1548:1096
+CCCTGCCCCATCTCTTGTAATCTCTCTCCTTTTTG
++
+88888;;88;;;;8;;9;;;<<<<<<<<<<<<<<;
+@EAS114_45:6:59:1548:1096
+GTCCTATGTACTTATCATGACTCTATCCCAAATTC
++
+;.;;;;;;;;6;;;;;;;;;;;;;;;73;;77777
+@EAS114_45:6:5:730:1436
+GAAGAACTTTGATGCCCTCTTCTTCCAAAGATGAA
++
+7977979;;;;;;;;;7;3<;2<;26;<;<<;;<<
+@EAS114_45:6:5:730:1436
+TATTCAGTTCTAAATATAGAAATTGAAACAGCTGT
++
+;;;;;;;;;;;;;;;;;;8;;;;;8;;;;;67777
+@EAS114_45:6:86:693:234
+AAGTAACTGAACCTATGAGTCACAGGTATTCCTGA
++
+;;;;;;;;;;;;;;;;9;;;;;;;;99;;&70777
+@EAS114_45:6:86:693:234
+GTAGTCATCAGACTATCTAAAGTCAACATGAAGGA
++
+83997;<;;;;98;;3*6<<;<:8;;;;;<;;<<<
+@EAS114_45:6:86:859:1779
+TTTTTTTCATTTCTCTTTTTTTTTTTTTTTTTTTT
++
+;;;;;;;;;;;;;;;;;;;;;;;;;;;8;;)7699
+@EAS114_45:6:90:561:850
+ACAGGAACAAAACCTCATATATCAATATTAACTTT
++
+;;;;;;;;;;;;;;;;;;;;;;;;9;9;6;77777
+@EAS114_45:6:90:561:850
+TACGCAAACAGAAACCAAATGAGAGAAGGAGTAGC
++
+78376<;;9<;<<;:9<<<6;<;<;;8;;<;/;;;
+@EAS114_45:6:93:1475:542
+TGAAAGCTTGGGCTGTAATGATGCCCCTTGGCCAT
++
+98987:9:<:;:;;;;;<<;<;<;;;;<<<;;;<<
+@EAS114_45:6:93:1475:542
+TTATCATGACTCTATCCCAAATTCCCAATTACGTC
++
+;;;;;;;;;;;;;;;;;;;;;;9;;;9;;;77777
+@EAS114_45:7:14:1256:204
+AAATGTCTATTTTTGTCTTGACACCCAACTAATAT
++
+66777:;;37;;:;;0;:;;;;):;;:7;;;;;;;
+@EAS114_45:7:14:1256:204
+TCACCCAGTCCCTGCCCCATCTCTTGTAATCTCTC
++
+<<<<<;;;;;;<;;;;;;;<;<;;;;<:-;79697
+@EAS114_45:7:14:978:1296
+ATACAATGATAAAAAGATCAATTCAGCAAGAAGAT
++
+;6;;;;;;;;;;;:;;;;;;;6;;;;;;;;77777
+@EAS114_45:7:14:978:1296
+CAATATTCTGATGATGGTTACACTAAAAGCCCATA
++
+77177;9;2:;;:;;(;;9;<;;;;:;;;:7;<<;
+@EAS114_45:7:24:1374:211
+AGCCCTTCTCACAGTTTCTGCCCCCAGCATGGTTG
++
+;;:<<;<;:;;;;;;;;;;<::;;;6;;2+74917
+@EAS114_45:7:24:1374:211
+TGCAATTAATATAATTGTGTCCATGTACACACGCT
++
+77661;;;5;;:;;:;:;;;;;;8:;;;:;;;;;:
+@EAS114_45:7:2:168:1878
+AAAAAACCTGGCAAACACGAATGTTATGACATGTN
++
+;<:;;<:<;<;<;;;;:;<;:::&9:&:68&6&*!
+@EAS114_45:7:2:168:1878
+TAAATACACACAAAAGTAGAAAACGCACCAGTTTT
++
+*3/6)9.;;;;;;;;5;;);;;3;(;;;+(;7.)3
+@EAS114_45:7:33:1566:588
+ACAGCTTAGGCATCAATTTGGTGTTCTGTGTAAAG
++
+-6246;;97;77;;97;;;;;;9;7;79;)&;37;
+@EAS114_45:7:33:1566:588
+TACTGTCATAACTATGAAGAGCCTATTGCCAGATG
++
+<;.;;;;6;;;;6;;29;;;<+9;;;.3;;73797
+@EAS114_45:7:35:538:1882
+TATGCACCTAACACAAGACTACCCAGATTCATAAA
++
+;);43.50;3;93;;4;3;;;9-7.;*;;966*75
+@EAS114_45:7:35:538:1882
+TCTATAACAAAATTAAAATTTAACAAAAGTAAATA
++
+73797;;3<;;<6;;<<<;8:;:;<;:<:;<<;;;
+@EAS114_45:7:37:763:1437
+AAAGATGTTCTACGCAAACAGAAACCAAATGAGAG
++
+;;;;;6;;;;;;;;;:;6;5;5;;;;;76;767/7
+@EAS114_45:7:37:763:1437
+TAAAACAAATACTACTAGACCTAAGAGGGATGAGA
++
+79979;<;<;;;<;;;;;;6:;<:;<:8;<<<<;<
+@EAS114_45:7:45:1339:1807
+GACATCTAAATGAAAGAGGCTCAAAGAATGCCAGG
++
+77797;;:;::&:;;0:;8;;4;;:;;6;;;;;;;
+@EAS114_45:7:69:1130:832
+ATAGTTGAAAGCTCTAACAATAGACTAAACCAAGC
++
+;;2<;<;;<;9;<;;;;;;;7;8;;7;;;;77437
+@EAS114_45:7:69:1130:832
+TCCTGAGGAAAAAGAAAAAGTGAGAAGTTTGGAAA
++
+6)377;3;;;;;;;;;1;;;;;;;;;;;;;;;;;;
+@EAS114_45:7:6:758:988
+AAACAAAGGAGGTCATCATACAATGATAAAAAGAT
++
+3+;0;0;;;0;;;;;;5;;;9;;;;90;;;57560
+@EAS114_45:7:6:758:988
+ATTCTGATGATGGTTACACTAAAAGCCCATACTTT
++
+3-7*73;;399:9;9;7<-(<;;<;;:;9::;;7;
+@EAS114_45:7:88:451:1773
+ATAAATACACACAAAAGTACAAAACTCACAGGTTT
++
+;;:::<:;:<<;:6::;:;;:::;;<;;;367177
+@EAS114_45:7:88:451:1773
+ATTGGCAGAACAGATTTAAAAACATGAACTAACTA
++
+973776;;;;;;;;;::;;;;;;;;;;;;;;3;;;
+@EAS114_45:7:97:1584:777
+CCAGATGAACCACACATTAATACTATGTTTCTTAT
++
+<<;<;;;;<;<;<<;;;;;;;;;;;;;;:;79979
+@EAS114_45:7:97:1584:777
+GTCTCAGGGAGCCGTCCGTGTCCTCCCATCTGGCC
++
+66746,9::9;;;;:;;;;;;;;;;;;;;;:;;;;
+@EAS114_45:7:9:512:826
+AACTTCCACGTCTCATCTAGGGGAACAGGGAGGTG
++
+67<<<;;;<;;<<;;<;<:;9;;;9;;;;<59777
+@EAS114_45:7:9:512:826
+ACCACACATTAATACTATGTTTCTTATCTGCACAT
++
+76777:;;;;;;;;;;;;;;;;;;;;;;;;;:;;;
+@EAS139_11:1:35:631:594
+ATCATGACTCTATCCCAAATTCCCAATTACGTCCT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS139_11:1:35:631:594
+ATGATGCCCCTTGGCCATCACCCGGTCCCTGCCCC
++
+<<<<4<<<<<.<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS139_11:1:59:742:549
+ACAAGCAAATGCTAAGATAATTCATCATCACTAAA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<8<
+@EAS139_11:1:59:742:549
+TTAACATTACAACAGGAACAAAACCTCATATATCA
++
+-<<<3<<<<6<<6<<<<<6<<<<6<<<<<<<<<<<
+@EAS139_11:1:81:1019:558
+ACAAAACTCACAGGTTTTATAAAACAATTAATTGA
++
+<<<<<<<<<<<6<<<<<<<<<<<<<<<<<<<<<7<
+@EAS139_11:1:81:1019:558
+TGAACTAACTATATGCTGTTTACAAGAAACTCATT
++
+<<<<9<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS139_11:1:84:92:1246
+GAAAAAAGTAAACTCTCAAATATTGCTAGTGGGAG
++
+<<<<<<<<<<<<<<<8<<<<<<5<<<<<<<<<<<<
+@EAS139_11:1:84:92:1246
+GTTACACTAAAAGCCCATACTTTACTGCTACTCAA
++
+<<<<<<<<<<<<<<<<5<:<<5<<<<<<<<<<<<<
+@EAS139_11:2:31:628:1820
+AACCAGTCCTATAAGAAATGCTCAAAAGAATTGTA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<9<<<<<<<
+@EAS139_11:2:31:628:1820
+CAGGAACAAAACCTCATATATCAATATTAACTTTG
++
+<<<<<<:<<<<:6<<<<<<<<<<<<<<<<<<<<<<
+@EAS139_11:2:42:333:516
+AGACAAGTCTCTTATGAATTAACCCAGTCAGACAA
++
+<<<<<5<*<2<<<<<<<<<<<<<<<<<<<<<<<</
+@EAS139_11:2:42:333:516
+TCTTTAGTCTTGCTAGAGATTTAGACATCTAAATG
++
+<<<<<<<<7<63<7<<<<<<<<<<<7<<<<<<<<<
+@EAS139_11:2:55:296:1457
+CACTTTAAATCAACAACAGTAAAATAAAACAAAGG
++
+-<%63<<<<<1<<<<<5<<<<<<<<<<<<<<<7<<
+@EAS139_11:2:55:296:1457
+CCCACTTAAGAGATATAGATTGGCAGAACAGATTT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS139_11:2:63:816:921
+AAACCTCTTTAGTCTTGCTAGAGATTTAGACATCT
++
+<<<<<<<<<4<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS139_11:2:63:816:921
+TGAAGACAAGTCTCTTATGAATTAACCCAGTCAGA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<:<4<846
+@EAS139_11:2:6:251:1557
+AAAACAATGTTCCCCAGATACCATCCCTGTCTTAC
++
+<<<<<<<<<<<<6:<<<<<<<<<<<<<<<<<<<<<
+@EAS139_11:2:6:251:1557
+CCTGAGAGATTCTGCAGCCCAGCTCCAGATTGCTT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS139_11:2:71:83:58
+AAAGAAAAAAGAATTTTAAAAATGAACAGAGCTTT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS139_11:2:71:83:58
+CCAGGAAGATACATTGCAAGACAGACTTCATCAAG
++
+8<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS139_11:3:34:970:1374
+ATGTGTTTATTACCAGAGGGATGGAGGGAAGAGGG
++
+<<<<<<<<<<<<<<;7<77;<<;<;;9;;:86:::
+@EAS139_11:3:34:970:1374
+CTGGACCCTGAGAGATTCTGCAGCCCAGATCCAGA
++
+<6<<<7<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS139_11:3:43:1229:1855
+ATGTACAATATTCTGATGATGGTTACACTAAAAGC
++
+8<<<<;8<<<;;5<<28<<<<<<<<<<<<7;;<<;
+@EAS139_11:3:43:1229:1855
+CAACAGTAAAATAAAACAAAGGAGGTCATCATACA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<4<<<<<<<<<
+@EAS139_11:3:65:556:1505
+CAATGAACAACAGGAAGAAAAGGTCTTTCAAAAGG
++
+<<<<<<<<<<<<<<<<<<<<<<<6<<<<<<<<<<<
+@EAS139_11:3:65:556:1505
+TGCCTTCAGACCCTACACGAATGCGTCTCTACCAC
++
+<6<8<<4<8;;;<<<<<<<<<<<<<<<<<<<<<<<
+@EAS139_11:3:81:12:1231
+AAAAAGCAAAAACAAAAACTATGCTAAGTATTGGT
++
+<<<<<<<7<<<<<<<5<'<6/<<<5<<<<<<2<<<
+@EAS139_11:3:81:12:1231
+TTACCTAATTGGTACAATGTACAATATTCTGATGA
++
+<<<<7<<<<<<<<<<<<<<<<<<<<<<<<<<4<<6
+@EAS139_11:4:26:137:1382
+AATGTTATGCCCTGCTAAACTAAGCATCATAAATG
++
+<<-<8<<<<<<:<<<<<<<:<<<<<<<<<<<<<<<
+@EAS139_11:4:26:137:1382
+AGACTATCTAAAGTCAACATGAAGGAAAAAAATTC
++
+<<<<<<7<<<77<<<<<<</<<+<<<<<<7<+<<<
+@EAS139_11:4:36:1184:994
+GCCAGAAGAGATTGGATCTAATTTTTGGACTTCTT
++
+<84<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS139_11:4:36:1184:994
+TACATTGCAAGACAGACTTCATCAAGATATGTAGT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<8<<8<
+@EAS139_11:4:36:1231:1381
+AAGAGATATAGATTGGCAGAACAGATTTAAAAACA
++
+<<<<<<;<<<<<<<<<8<<<<<<<<<<<<<<<<<<
+@EAS139_11:4:36:1231:1381
+TAAAAGTCAAAATTAAAGTTCAATACTCACCATCA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS139_11:4:38:557:1441
+GATAAAAATAAAAAAGCAAAAACAAAAACTATGCT
++
+<&<<<<<,<<<<<<<<8<<<<<<<<<<<<<<<<<<
+@EAS139_11:4:38:557:1441
+TAAGAGGGATGAGAAATTACCTAATTGGTACAATG
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<:<<<<<<<
+@EAS139_11:4:50:30:15
+AGATTATGTAAAGTAACTTAACCTATGAGTCCAAG
++
++:79.68872.:9&:92/.299169/5+/6/3/&2
+@EAS139_11:4:50:30:15
+TACATTGCAAGACAGTCGTCAGCAAGATATGTAGT
++
+1-%-22&&)&11,&/&&176<&<<<222<,6,<<<
+@EAS139_11:4:63:527:1923
+GCTTTACTGTCATAACCATGAAGAGACTATTGCCA
++
+9<<<8<-8;;8<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS139_11:4:63:527:1923
+TACACGAATGCGTCTCTACCACAGGGGGCTGCGCG
++
+<<<<<<<<<<<<<<<<<:<<<<3<<<<<<<<<<<<
+@EAS139_11:5:32:686:735
+AAGTTTGGAAAAACTATTTGAGGAAGTAATTGGGG
++
+<<<<<<<<<<<<<9<<<<<<<<<<<<<<<<<<<<<
+@EAS139_11:5:32:686:735
+CAGAAGAAAGAGGTTCANANNNTGANGACAAGTCT
++
+<<<<<<<<<<<<<<<<<!<!!!<<<!<<<<<<<<<
+@EAS139_11:5:41:314:1173
+AAGAAAAAAAAACCTGTCAAACACGAATGTTATGC
++
+<;<<<<<<<;;<<<<<-<<<;;;<;8<*;;<<<<'
+@EAS139_11:5:41:314:1173
+AATTAAAGTTCAATACTCACCATCATAAATACACA
++
+<<2**<<82/<<<<<<<<<<9<<<<<<<<<<<<<<
+@EAS139_11:5:52:1278:1478
+GCTTGTACTTCTAAATCTATAACAAAATTAAAATT
++
+<<<<<<<<<<<<<<9<<<<<<<<<<<<<<<<9<<<
+@EAS139_11:5:52:1278:1478
+GTTTTTTTTTTTTTCTTTTCTCTTTTTTTTTTTTT
++
+.8::<<<<<<<;<<<<<;<<<<<<<<<<<<<<<<<
+@EAS139_11:5:61:38:1182
+AGGGAGCCGTCCGTGTCCTCCCATCTGGCCTCGTC
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<5<<<<
+@EAS139_11:5:61:38:1182
+GTTTGATTTGGTGGAAGACATAATCCCACGCTTCC
++
+9:;<<<<;<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS139_11:5:64:199:1288
+GTAAAATAAAACAAAGGAGGTCATCATACAATGAT
++
+<<<<<<<<<<<<<<;<<<<<<<<<<<<<<;<<<;<
+@EAS139_11:5:64:199:1288
+TACAATGTACAATATTCTGATGATGGTTACACTAA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS139_11:5:78:775:555
+AATGCTCAAAAGAATTGTAAAAGTCAAAATTAAAG
++
+<<-<%4/<<<<<<<<<<<<<<<<<5<<<0<<<<<<
+@EAS139_11:5:78:775:555
+TTTTTGGACTTCTTAAAGAAAAAAAAACCTGTCAA
++
+6:<<<<:<<<<6:<<)::8<6<<:<<)<::63832
+@EAS139_11:6:11:285:1567
+ACATGGCTGATTATGAAAACAATGTTCCCCAGATA
++
+<8<4<<<;<<;<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS139_11:6:11:285:1567
+CCCTGAGAGATTCTGCAGCCCAGATCCAGATTGCT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS139_11:6:11:360:1577
+GAAGAAAAGGTCTTTCAAAAGGTGATGTGTGTTCT
++
+<<<<<<<<<<<<<<<<<4<;;<<;;<;<<<8<<<<
+@EAS139_11:6:11:360:1577
+TTTGGCATTTGCCTTCAGACCCTACACGAATGCGT
++
+1<1<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS139_11:6:13:682:680
+AGAATAACAATGGGCTTCTCAGCGGAAACCTTACA
++
+<<<<<<<<<<<<<:<<<<<<<<<<;<;<<<<<<<<
+@EAS139_11:6:13:682:680
+ATAAGAAATGCTCAAAAGAATTGTAAAAGTCAAAA
++
+<<<<<<<<<<:<5<<<<<<<<<<<<<<<<<<<<<<
+@EAS139_11:6:17:1179:393
+CTAATTGGTACAATGTACAATATTCTGATGATGGT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<:<<:4<
+@EAS139_11:6:17:1179:393
+TGCTAAGTATTGGTAAAGATGTGGGGAAAAAAGTA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS139_11:6:19:306:982
+ATTTTTGGACTTCTTAAAGAAAAAAAAACCTGTCA
++
+<<<<<<<<<9<<:<<<<<<<<<<<<<<<<<<<<<<
+@EAS139_11:6:19:306:982
+GACAGACTTCATCAAGATATGTAGTCATCAGACTA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<:<<<<
+@EAS139_11:6:75:946:1035
+AACCCCCTTGCAACAACCTTGAGAACCCCAGGGAA
++
+<<<<<<<<<<;<<<;<<<<<<<8;<6<<<<44<:4
+@EAS139_11:6:75:946:1035
+AATGGACCTGTGATATCTGGATTCTGGGAAATTCT
++
+<<)4</<5<<<<<<<<<<<<<<<<<<<<<66<<<<
+@EAS139_11:6:82:164:1924
+GAGGGATGGAGGGAAGAGGGACGCTGAAGAACTTT
++
+<<<<<<<<<<<<<<<<<<<<8<<<<<<3<<'<7<8
+@EAS139_11:6:82:164:1924
+GCCCAGCACCAGATTGCTTGTGGTCTGACAGGCTG
++
+6<<<<<<-<<<<<<<<<2<<06<9<<<<<1<<<<<
+@EAS139_11:6:89:1151:1878
+CCATCACAATGAACAACAGGAAGAAAAGGTCTTTC
++
+<;;<<<<<;;;<<<<4;;::;<;8;;<;;8:<8<4
+@EAS139_11:6:89:1151:1878
+CTTTCAACGATTCTAGCCATTTCTTTTGGCATTTG
++
+8<66,,<<<<<<:<<<<<9<<<:<<<<<<<<<<<<
+@EAS139_11:7:24:1345:1627
+AGATTGGCAGAACAGATTTAAAAACATGAACTAAC
++
+<<<<<<<<<<<<<<<<<<<<<<9<<<<<<<<<8<3
+@EAS139_11:7:24:1345:1627
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
++
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+@EAS139_11:7:42:1091:1726
+CAGGGAAGGAGCATTTTGTCAGTTACCAAATGTGT
++
+<<<<<<<<<<<<<<<<<<<<<<8<<<<<<8:<.<:
+@EAS139_11:7:42:1091:1726
+TCTGGGAAATTCTTCATCCTGGACCCTGAGAGATT
++
+4443838<4<8<87<<3</8<<<<<<<<<<<<<<<
+@EAS139_11:7:46:695:738
+CAAAGATGAAACGCGTAACTGCGCTCTCATTCACT
++
+<<<<2<5<<-<<<<<<<4<<<<<<<<<<<<<<3<<
+@EAS139_11:7:46:695:738
+TGAAACAGCTGAGTTTAGCGCCTGTGTTCACATAG
++
+<;<<<<;<<),&4<3<<7&7<0;)).3;79;7<;0
+@EAS139_11:7:50:1229:1313
+ACATAGCTAAAACTAAAAAAGCAAAAACAAAAACT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS139_11:7:50:1229:1313
+TTTTTTCTTTTTTTTTTTTTTTTTTTTGCATGCCA
++
+<<<<,<&<7<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS139_11:7:53:458:581
+CTCAATTAATTGTTTTATAAAACCTGTGAGTTTTG
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<99<<<<<
+@EAS139_11:7:53:458:581
+TTATGCCCTGCTAAACTAAGCATCATAAATGAAGG
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS139_11:7:60:163:1612
+AGCAAGAGAAAAGCATACAGTCATCTATAAAGGAA
++
+<<<<<<<<<21<<<<<<<<<3<--<+<<<+<<63<
+@EAS139_11:7:60:163:1612
+GGGAACTAAAGTCAAGTCTTTCCTGACAAGCAAAT
++
+-<<<<)<<<<<<<<<<<<<<<<<<<<<8<<<<<<<
+@EAS139_11:7:74:213:877
+AGATGTTCTACGCAAACAGAAACCAAATGAGAGAA
++
+<<<<<<<&<<-<-<<<7<<<<<77<<<<<<<<<<<
+@EAS139_11:7:74:213:877
+TTAACATTACAACAGGAACAAAACCTCATATATCA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS139_11:7:92:367:1495
+ACCACAGGGGGCTGCGCGGTTTCCCATCATGAAGC
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<6<<<6<<
+@EAS139_11:7:92:367:1495
+CTGTCATAACTATGAAGAGACTATTGCCAGATGAA
++
+<8<88<<<<7<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS139_11:8:17:437:1378
+ACCAGTCCTATAAGAAATGCTCAAAAGAATTGTAA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS139_11:8:17:437:1378
+ATCAATATTAACTTTGAATAAAAAGGGATTAAATT
++
+<<7<<<<<<<<:<<<<<<<<<<<<<<<<<<<<<<<
+@EAS139_11:8:26:1221:222
+AAACAGCTGTGTTTAGTGCCTTTGTTCAACCCCCT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS139_11:8:26:1221:222
+CTGCGCTCTCATTCACTCCAGCTCCCTGTCACCCA
++
+<<<<<<<:<:<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS139_11:8:38:842:395
+GTAACTGCGCTCTCATTCACTCCAGCTCCCTGTCA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<93<;9
+@EAS139_11:8:76:205:587
+GAATAACAATGGGCTTCTCAGCGGAAACCTTACGA
++
+8<<5<<<<<<<<<<<<<<<<<<<<<<<<<7<<</<
+@EAS139_11:8:76:205:587
+TGCTAGAGATTTAGACATCTAAATGAAAGAGGCTC
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS139_11:8:82:566:1096
+CAAAAGGTGATGTGTGTTCTCATCAACCTCATACA
++
+<<<<<<<<<<:<<<<<<<:<<<<<<:<<<<<<<<<
+@EAS139_11:8:82:566:1096
+CTGCGCTCTCATTCACTCCAGCTCCCTGTCACCCA
++
+<<<<<<<<<<<<<<<<<<<<:<<<<<<<<<<<;<;
+@EAS139_11:8:96:1314:1448
+CCTATGAGTCACAGGTATTCCTGAGGAAAAATAAA
++
+<<<<<<<<<<<<<<<<<<<<<<<<5<4<<<<-<<<
+@EAS139_11:8:96:1314:1448
+GTAGTCATCAGACTATCTAAAGTCAACATGAAGGA
++
+<<<<7<<:<<<<<<<<:<<<<<<<<<<<<<<<<<<
+@EAS139_19:1:14:420:712
+TGAGAGAGAACTTCCCTGGAGGTCTGATGGCGTTTCTCCC
++
+1::::<<<<<<<<<<;<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS139_19:1:14:420:712
+TGTTGGTTTTCTGTTTCTTTGTTTGATTTTTTTGAAGACA
++
+<<<<<<<<<<<<;<<<<<<<;<<<-;<<<&,<&*8111:6
+@EAS139_19:1:1:1598:843
+TCAGCGGAAACCTTACAAGCCAGAAGAGATTGGATCTAAT
++
+1)::6::<<;<98<<<<<<9<<<<<<<<<<<<<<<<<<<<
+@EAS139_19:1:1:1598:843
+TGCCAGGAAGATACATTGCAAGACAGACTTCATCAAGATA
++
+<<<<<<8<<<<<<<<<<<<<<<<<<<<<<<<<<8<4:8::
+@EAS139_19:1:36:481:1079
+GTAAAAGTCAAAATTAAAGTTCAATACTCACCATCATAAA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<::::8
+@EAS139_19:1:36:481:1079
+TCCCCCACTTAAGAGATATAGATTGGCAGAACAGATTTAA
++
+:11+)*<4;<<<<<<<<<;;<<<<<<;<<<<<<<<<<<<<
+@EAS139_19:1:40:1596:1433
+CCATCACAATGAACAACAGGAAGAAAAGGTCTTTCAAAAG
++
+<<<<<<<<<<<<<<<<<<<<<<<<;<<<<1<<<<<::;::
+@EAS139_19:1:40:1596:1433
+GCTTTCAACGCTTCTAGCCATTTCTTTTGGCATTTGCCTT
++
+-:8:1841<4;<88<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS139_19:1:47:352:1492
+AGGGAGCCGTCCGTGTCCTCCCATCTGGCCTCGCCCACTA
++
+:<<<::<24<04-&<;<<2<<<&<60)&<5<<6*8:)9+*
+@EAS139_19:1:47:352:1492
+TTTGTTTTGTATGGTGGAAGACATAATCCCACGCTTCCTA
++
++7+/7+/%%1'6+3++1;:</<<5<)27<<9<)9<<9<7<
+@EAS139_19:1:53:463:1132
+ATGATAAAAAGATCAATTCAGCAAGAAGATATAACCATCC
++
+;::;:<<<<<<<<:<<;<<<<8<<<<<<<<<<<<<<<<<<
+@EAS139_19:1:53:463:1132
+ATTTAAAAACATGAACTAACTATATGCTGTTTACANGAAA
++
+<<<<<<<<<<<<<<<<<<<<<;<<<8<<<<<<<8<!1488
+@EAS139_19:1:58:726:1746
+AGATTGGCAGAACAGATTTAAAAACATGAACTAACTATAT
++
+<<<<<<<<<<<<<<<<<<<6<<<<8<<<<<<<<:8:8:88
+@EAS139_19:1:58:726:1746
+CAATTTAAATCAACAACAGTAAAATAAAACAAAGGAGGTC
++
+&:&::;<<<76<<:<<6<<<<<<<<<<<<<<<<<<<<<<<
+@EAS139_19:1:82:946:392
+CAATATATCCATGTAACAAATCTGCGCTTGTACTTCAAAA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<8<<<8<<8<<:4488
+@EAS139_19:1:82:946:392
+GAAAACAATTTGGTAATTTCGTTTTTTTTTTTTTCTTTTC
++
+:;:;:,::<:;<<<;;<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS139_19:1:85:1521:58
+AAATTAACATTACAACAGGAACAAAACCTCATATATCAAT
++
+:::86<<:<<8<<<<;<<8<<<<<<<<<<<<<<<;<<<<<
+@EAS139_19:1:85:1521:58
+CTGACAAGCAAATGCTAAGATAATTCATCATCACTAAACC
++
+<<<<<<<<9<<<<<<<<<<<<<7<<<<<<<<<<<<;;:7:
+@EAS139_19:1:87:1222:878
+TATAGGGCCTTTGTTCAAACCCCTTGCAACAACCTTGAGA
++
+&+6<6&<:<<9<1112<<;)9227</);;;2-79;)/769
+@EAS139_19:1:87:1222:878
+TCAGCGCGTCACTCCGCTCTCATTCACCCCAGCTCCCTGT
++
+!!;*:885<&<<<)8&<:<<<8<8<::*<4<88<<<8<<<
+@EAS139_19:1:99:1632:76
+AAAGAAAAAAAACCCTGTCAAACACGAATGTTATGCCCTG
++
+<<<<<<<<<<<<*<<<<8<9<<<<<<<<<9;;;;<18:;:
+@EAS139_19:1:99:1632:76
+TTGTAAAAGTCAAAATTAAAGTTCAATACTCACCATCATA
++
+4641::<<4<<<<<<<<<<<;<<<<<<<<<<<<<<<<<<<
+@EAS139_19:2:12:1335:1372
+GAAGAACAGATTTAAAAACATGAACTAACTATATGCTGTT
++
+:&;;;<*<<<9<<<<<<<<<<<<<<4<<<<<<<<<<<<<<
+@EAS139_19:2:12:1335:1372
+TAAAGTTCAATACTCACCATCATAAATACACACAAAAGTA
++
+<<<<<<<<<<<<<<<<<<<<<<<<:<<<<<<<<<99::.:
+@EAS139_19:2:29:1822:1881
+AGAAAAAAGAATTTTAAAAATGAACAGAGCTTTCAAGAAG
++
+<<<<<<<<<<<<4<<<<<<<<<<<<<<:<<<:<<;:::::
+@EAS139_19:2:29:1822:1881
+ATGAAAGAGGCTCAAAGAATGCCAGGAAGATACATTGCAA
++
+;87;;<<<;<5<5<<<<<<<;<<<<<<<<<<<<:<<<<<<
+@EAS139_19:2:2:1217:398
+CAATTAATTGAGACTACAGAGCAACTAGGTAAAAAATTAA
++
++;;:9<<66<<<;+<<7<<<<;<<+;<<<<<<<<<<<<<<
+@EAS139_19:2:2:1217:398
+TAAATGAAGGGGAAATAAAGTCAAGTCTTTCCTGACAAGC
++
+<<<<<<<<<<<<<;<<<<<<<7<<<3<<<<;<<<<9:7::
+@EAS139_19:2:33:1193:664
+GCCCCATCTCTTGTAATCTCTCTCCTTTTTTCTGCATCCC
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<%:<'<9:::9
+@EAS139_19:2:33:1193:664
+TATTTTTGTCTTGACACCCAACTAATATTTGTCTGAGCAA
++
+;;;;;;<;;-9<<<:</+9<<<<<<<<<<<<<<<<<<<<<
+@EAS139_19:2:57:1672:1890
+CCCCCCCCCCCCCCCCCAGCCACTGCGGCCCCCCCAGCCA
++
+-+)%)'-'+,,<066,))090+:&486083:5&&:<<5<0
+@EAS139_19:2:57:1672:1890
+TATTCAGTTCTAAATATAGAAATTGAAACAGCTGTGTTTA
++
+:;;;9<8;;*<<<<<<:<<<<<<<<1:<<<<<<<<<<<7<
+@EAS139_19:2:82:154:1333
+TTAAAATTTAACAAAAGTAAATAAAACACACAGCTAAAAC
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;;<;;:;:
+@EAS139_19:2:82:154:1333
+TTTTTTTTTTTTTTTTTTTTTCTTTTTTTTTTTTTTTTTT
++
+:5'::<<<;<<<<<<</3<<<&4&7<<<<<<<<<<<<<<<
+@EAS139_19:3:10:349:1147
+GCTAGAGATTTAGACATCTAAATGAAAGAGGCTCAAAGAA
++
+:/:::<<<<<<<<<<<<;<<<<<<<<<<<<<<<<<<<<<<
+@EAS139_19:3:24:1135:563
+CTGCGCTCTCATTCACTCCAGCTCCCTGTCACCCAATGGA
++
+6+96:87<&8<<79:<;<<<<:<<;<<<<<<;;<<<<<<<
+@EAS139_19:3:24:1135:563
+GCTGTGTTTAGTGCCTTTGTTCAACCCCCTTGCAACAACC
++
+<<<<:<<<<:1:<<<<<<.<<<<<<<<;<;;;43+:30::
+@EAS139_19:3:4:1502:1911
+CTACACGAATGCGTCTCTACCACAGGGGGCTGCGCGGTTT
++
+:+:::5/;99<;<&<*<-9<<<<<<<<<<<<<<<<<<<<<
+@EAS139_19:3:4:1502:1911
+TACACACACATGGTTTAGGGGTATAATACCTCTACATGGC
++
+<<<:4<<<<<<;<<<<;9;5<95<;<<;9+;1612:1:::
+@EAS139_19:3:58:923:1915
+GCAAACAGAAACCAAATGAGAGAAGGAGTAGCTATACTTA
++
+:+;;;8<<<<<<,<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS139_19:3:58:923:1915
+TATCAATATTAACTTTGAATAAAAAGGGATTAAATTCCCC
++
+<<<<<<<<<<<<<<<<<<<<<<<<<;<;<<<<<<<:::::
+@EAS139_19:3:5:538:401
+AAGGTGATGTGTGTTCTCATCAACCTCATACACACACATG
++
+<<<<;<<<<<<<<<<<<<<<;<::7<<;<53:<98;;;;;
+@EAS139_19:3:5:538:401
+TTTGCCTTCACACCCTACACGAATGCGTCTCTGCCACAGG
++
+671&7::49:&0<<<(<::<&<<<:<<<<<<<&<<<<1<<
+@EAS139_19:3:66:718:481
+AACAACAGTAAAATAAAACAAAGGAGGTCATCATACAATG
++
+::5::1<;;<<<<<<1<<<<<<<<<<<<7<<<<<<<<<<<
+@EAS139_19:3:66:718:481
+AAGAGATATAGATTGGCAGAACAGATTTAAAAACATGAAC
++
+<<<<<<<<<<<<<<;<<<<<<<<;<<<<<<<;<<<:1:;:
+@EAS139_19:3:73:1158:535
+AATAAAGATATGTAGTCATCAGACTATCTAAAGTCAACAT
++
++;6+;<;<<<<<<<<<0<<;<<<;<<<8<<<<<<<<<<<<
+@EAS139_19:3:73:1158:535
+CCTATGAGTCACAGGTATTCCTGAGGAAAAAGAAAAAGTG
++
+<<<<<<<<<<<<<<<<<<<<<<8<;;<<<<<9<<9::8:8
+@EAS139_19:3:73:936:1509
+CTCCTTTTTGCTGCATCCCTGTCTTCCTCTGTCTTTATTT
++
+<<<<<<<<<7<<7<<<<<<<;<<<<<<<<<:<:<;%8:::
+@EAS139_19:3:73:936:1509
+TTGTCTGAGCAAAACAGTCTAGATGAGAGAGAACTTCCCT
++
+99;66:<<;-<<<<:<<<<;<<<<<<<<<<<<<<<<<<<<
+@EAS139_19:3:75:732:442
+CGGTCCCTGCCCCATCTCTTGTAATCTCTCTCCTTTTTGC
++
+7,*&28<61:88<.7<:<<:6<1<85:<:1<5<&::<<&<
+@EAS139_19:3:75:732:442
+CTATCCCAAATTCCCAATTACGTCCTATCTTCTTCTTAGG
++
+<<<<<;<<<<<9<<<;<<;<<<5<<;8<<<<<<<<;:9%%
+@EAS139_19:3:87:133:930
+CAGTCTCAGGGCGCCGTCCGTTTCCTCCCATCTGGCCTCG
++
+)8&)907)-;9&,<<9)<;<<0<;<<99<<<<<<;<<9<<
+@EAS139_19:3:87:133:930
+TTATCTGCACATTACTACCCTGCAATTAATATAATTGTGT
++
+<<<7<<<<;<<;7<<7<<;;<<<;<5;<;;;5;;<:/48:
+@EAS139_19:3:88:1656:896
+AGGGAAGAGGGATGCTGAAGAACTTTGATGCCCTCTTCTT
++
+<<<9<<<<<<<9<<<;<<<<<<<<<;6<<;7<<<<::9:;
+@EAS139_19:3:88:1656:896
+TGCAGCCCAGATCCAGATTGCTTGTGGTCTGACAGGCTGC
++
+6/8::*9/*3*'<88<:9*<<<8<<<;<<<<<<<<;<<<<
+@EAS139_19:4:13:1155:631
+ACCCTGAGAGATTCTGCAGCCCAGCTCCAGATTGCTTGTG
++
+<<<<<<;<<;<<<<<<;<<<<<9<;<;94<<%<<<7:777
+@EAS139_19:4:13:1155:631
+AGGGGTATAATACCTCTACATGGCTGATTATGAAAACAAT
++
+;:398<<;<<<<<;<3<;;<<<<;;<<<<<<<<<<;<<;<
+@EAS139_19:4:18:1335:1514
+ATTGGTACAATGTACAATATTCTGATGATGGTTACACTAA
++
+::/::<<;<<<<<<<<<<<<<;<<<<<<<<<<<<<<<<<<
+@EAS139_19:4:18:1335:1514
+CTTTAAATCAACAACAGTAAAATAAAACAAAGGAGGTCAT
++
+<<<;<<<<<<<<<<<<<<<;<:<<;<<<<<<;<;<;;;9;
+@EAS139_19:4:1:156:196
+AAAAGGGATTAAATTCCCCCACTTAAGAGATATAGATTGG
++
+<<<<<<<<<<<<<<<<<<;<<<<<<<<<<<<<<<<:;9:9
+@EAS139_19:4:1:156:196
+ACTTATATCAGATAAAGCACACTTTAAATCAACAACAGTA
++
+:::::<<<<<<<<<<<<<4<<<<<<<<<<<<<<<<<<<<<
+@EAS139_19:4:26:1312:1400
+ACTGAACCTATGAGTCACAGGTATTCCTGAGGAAAAAGAA
++
+<<<<;<<<:<<:<;<:<<<;:;<<<<<<:<8<1;;:::88
+@EAS139_19:4:26:1312:1400
+TATGTAGTCATCAGACTATCTAAAGTCAACATGAAGGAAA
++
+::77:<;:+6<+<<<;<<74<<<;<<;<<<<<<<<<<<;<
+@EAS139_19:4:26:274:1078
+AATTGGGGAAAACCTCTTTAGTCTTGCTAGAGATTTAGAC
++
+<<<2<<<<<<<<<<<<<<<<<<<<<<<<<;;:;;;:::::
+@EAS139_19:4:26:274:1078
+GTCATCTATAAAGGAAATCCCATCAGAATAACAATGGGCT
++
+9:*:64<<;<<<<<<<<<;8;<<:<<<<<<<<<<<<<<<<
+@EAS139_19:4:68:1122:79
+ATGGCTGATTATGAAAACAATGTTCCCCAGATACCATCCC
++
+::77*:1<<<<<<<<<<<<<<<:;<<<;<<<<<<8<<<<<
+@EAS139_19:4:68:1122:79
+TGAGAGATTCTGCAGCCCAGCTCCAGATTGCTTGTGGTCT
++
+<<<<<<<<<<<<<;<<<<;<<<<<<;<<<4;<<4;99::;
+@EAS139_19:4:69:1593:819
+ATTGAGACTACAGAGCAACTAGGTAAAAAATTAACATTAC
++
+<<<<<<<<<<<<<<;<<<<<;;<:<<<<<:<<<<<:777:
+@EAS139_19:4:69:1593:819
+CAGGTAAAGGGGTGGAAAAAGATGTTCTACGCAAACAGAA
++
+);::7<<<<:;<<<<<<<<<<<<<<<9<<9<3<<<<<<<<
+@EAS139_19:4:77:1780:693
+GGAAGTAATTGGGGAAAACCTCTTTAGTCTTGCTAGAGAT
++
+:**::799<<9<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS139_19:4:77:1780:693
+TGAAGACAAGTCTCTTATGAATTAACCCAGTCAGACAAAA
++
+<<<<<<<<<<<<;<<:<<;<<<<<<<<<<<<;<<<;;:69
+@EAS139_19:4:78:806:800
+AAATTAAAGTTCAATACTCACCATCATAAATACACACAAA
++
+::;9:<<<;<<:<<<<:<.<1:<<1<<<<<<;<<<<<<<<
+@EAS139_19:4:78:806:800
+AACCTGTCAAACACGAATGTTATGCCCTGCTAAACTAAGC
++
+<<<<<<<<<<<<<<<<<<<4<<:<1<0<;<9;<:78::::
+@EAS139_19:5:29:411:1208
+AAAAGAATTGTAAAAGTCAAAATTAAAGTTCAATACTCAC
++
+<<<<;<<<<<<<<<<<;<<<<<<<<<<<<<<<<<<;;;;;
+@EAS139_19:5:29:411:1208
+CCCCCACTTAAGAGATATAGATTGGCAGAACAGATTTAAA
++
+766+6<996<<<<<<<<<<<<<<<<;<<<<<<<<<<<<<<
+@EAS139_19:5:40:758:116
+GTCTCTACCACAGGGGGCTGCGCGGTTTCCCATCATGAAG
++
+25/8/:<75:2<<<<<<7<<;<<<<<<<88;<<<<<<<<<
+@EAS139_19:5:40:758:116
+GTGTGTTCTCATCAACCTCATACACACACATGGTTTAGGG
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<:7262
+@EAS139_19:5:4:939:2021
+AAATACTACTAGACCTAAGAGGGATGAGAAATTACCTAAT
++
+;;;;:8;<5:<<<7/<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS139_19:5:4:939:2021
+GGAGTAGCTATACTTATATCAGATAAAGCACACTTTAAAT
++
+<<<<<<<<<<<<<<<<<<<<<97<<<;<<;<7;<<:48::
+@EAS139_19:5:57:366:844
+AAATTCCCCCACTTAAGAGATATAGATTGGCAGAACAGAT
++
+;;;7:8&555<,;<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS139_19:5:57:366:844
+TAAAAGTCAAAATTAAAGTTCAATACTCACCATCATAAAT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<::::7:
+@EAS139_19:5:61:1885:163
+AGCAAGAAGATATAACCATCCTACTAAATACATATGCACC
++
+<<<<<<<<<<<<<<<<<;<<<<<<<<<<<<<<<<9::::4
+@EAS139_19:5:61:1885:163
+ATACTTTACTGCTACTCAATATATCCATGTAACAAATCTG
++
+;:;;;;<<8<<:<<:<;<<<<<<<;<<<<<<<<<<<<<<<
+@EAS139_19:5:66:1381:181
+GGACTTCTTAAAGAAAAAAAAACCTGTCAAACACGAATGT
++
+;;;+;;&<7<<<+<<<<<<<;<;8<<<;<<<<8<<<;<<<
+@EAS139_19:5:66:1381:181
+TTGCAAGACAGACTTCATCAAGATATGTAGTCATCAGACT
++
+<<6<<<<<<<<<<<<<<<<<<<<<<<<<<:<<<<<::4:7
+@EAS139_19:5:68:306:409
+AACTTTGAATAAAAAGGGATTAAATTCCCCCACTTAAGAG
++
+::2:7<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS139_19:5:68:306:409
+CCTATAAGAAATGCTCAAAAGAATTGTAAAAGTCAAAATT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<:;:;;
+@EAS139_19:5:70:318:1631
+TAAGAAATTACAAAATATAGTTGAAAGCTCTAACAATAGA
++
+<<<<<<;<<<<<<<<<<<<;9:<<<<<<<<<<<<<:::78
+@EAS139_19:5:74:668:424
+GACTTCTTAAAGAAAAAAAAACCTGTCAAACACGAATGTT
++
+;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;::;;
+@EAS139_19:5:74:668:424
+GTAAAAGTCAAAATTAAAGTTCAATACTCACCATCATAAA
++
+:::::<<96<<<<<;<<<;<<5<<<<<<<<<<<<<<<<<<
+@EAS139_19:5:89:525:113
+GACGCTGAAGAACTTTGATTCCCTCTTCTTCCAAAGATGA
++
+);:+4-&<<+<<:<+<)<<<7<8<8:<:<<:<82::<<2<
+@EAS139_19:5:89:525:113
+TATTTATGCTATTCAGTTATAAATATAGAAATTGAAACAG
++
+<1<7<6;+0;7;7'<70;-<7<:<:<<5<<:9<5:7:%:7
+@EAS139_19:5:95:944:247
+GGTACAATGTACAATATTCTGATGATGGTTACACTAAAAG
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<;<<<<<<<<:;:::
+@EAS139_19:5:95:944:247
+GTAAAGATGTGGGGAAAAAAGTAAACTCTCAAATATTGCT
++
+:7::;<<<<<;;<<<<<<<<<<<<<<;<<<<<<<<<<<<<
+@EAS139_19:6:21:1601:1666
+GAAAGCTCTAACAATAGACTAAACCAAGCAGAAGAAAGAG
++
+7<<<<<<<<:<<7<<<:<<<<<<4<<44<<914<;:5:::
+@EAS139_19:6:21:1601:1666
+TATTACTGAGGAAAAAGAAAAAGTGAGAAGTTTGGAAAAA
++
+-;;3&1<<<<<<<<<<<<1<<<</<<<<<</<<<<<<<<<
+@EAS139_19:6:52:1455:1212
+CCATCTCTTGTAATCTCTCTCCTTTTTGCTGCATCCCTGT
++
+6::4::;4%;9:<79)<:<;<<:4::7<<9<&+71<9;<<
+@EAS139_19:6:52:1455:1212
+TTCTTAGGGAAGAACAGCTTAGGTATCAATTTGGTGTTCT
++
+<9<<<99<;<<9<;<-<<<6<<75;;<*%<5<3+.8:*5;
+@EAS139_19:6:72:308:839
+AGTTACCAAATGTGTTTATTACCAGAGGGATGGAGGGAAG
++
+<<<<<<<<<<<<<<<<<<<<<<<<9<<<<;<99494416:
+@EAS139_19:6:72:308:839
+ATCGTGGACCCTGAGAGATTCTGCAGCCCAGATCCAGATT
++
+:8:.:<;<<5<<<<<<<<<<<<<<<<;:<<<<<<<<<<<<
+@EAS139_19:6:75:1503:1399
+CAAGAAGATATAACCATCCTACTAAATACATATGCACCTA
++
+&;;8;<<<;<<<<,6<<70<<7<<<<<<9<<<<<<<<<<<
+@EAS139_19:6:75:1503:1399
+CATGAGTTCAGGTAAAGGGGTGGAAAAAGATGTTCTACGC
++
+<<<<<<<<<<<<<<<<<<9<<<;<<<<<<;<<<<:::711
+@EAS139_19:6:78:1029:512
+AGATAATTCATCATCACTAAACCAGTCCTATAAGAAATGC
++
+;;;;;<;;<<<.<<6;<<;<;8<<<<::<<<<<<<<;<<<
+@EAS139_19:6:78:1029:512
+TCAGCAGAAACCTTACAAGCCAGAAGAGATTGGATCTAAT
++
+<0:;<<<<<<<<<:<<:;<<<;<7<<;<7;;;:6;::672
+@EAS139_19:6:82:1051:921
+GCAAATAGGTAAAAAATTAACATTACAACAGGAACAAAAC
++
+3-::-7<;+:9<;<<<5<;9,::53-;:3<<<<9<<3<<<
+@EAS139_19:6:82:1051:921
+GGGGAAATAAAGTCAAGGCTTTCCTGACAAGCAAATGCTA
++
+<<<<<9<799<<<<7::/<<<9<7:9:;2:7552+9''66
+@EAS139_19:6:84:438:1505
+ATTAATATAATTGTGTCCATGTACACACTCTGTCCTATGT
++
+:0::413::;:::0:179::3<;<:<9<&6<<<;<019<<
+@EAS139_19:6:84:438:1505
+GCACTAATGCGCTCCACGCCCAAGCCCTTCTCACAGTTTC
++
+35<<:;9<;<;5<<<:<3<<7:<9/<)<<:::9<&5;;+1
+@EAS139_19:7:44:1807:833
+ATATCCATGTAACAAATCTGCGCTTGTACTTCTAAATCTA
++
+<<<<<<<<<<<<<<<<<<<;<;<<<;<<9<<<<<89;;;:
+@EAS139_19:7:44:1807:833
+CTCTCAAATATTGCTAGTGGGAGTATAAATTGTTTTCCAC
++
+:6:9:<<<6<88<;<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS139_19:7:85:262:751
+CCATGTAACAAATCTGCGCTTGTACTTCTAAATCTATAAC
++
+22;99;<<8<<<<<<<;<;<<<<<;<<;<<<<<<<<<<<+
+@EAS139_19:7:85:262:751
+TACAATGATAAAAAGATCAATTCAGCAAGAAGATATAACC
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<:::92
+@EAS139_19:7:92:288:1354
+TCTCCTTTTTGCTGCATCCCTGTCTTCCTCTGTCTTGATT
++
+<<<<<<:<<<<<<<<<<<8<<:<<<<;;<8<<<8<:8+::
+@EAS139_19:7:92:288:1354
+TGTCTTGACACCCAACTAATATTTGTCTGAGCAAAACAGT
++
+::::;;;<<<<9;<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS188_4:5:103:870:105
+AAACTAAGCATCATAAATGAAGGGGAAATAAAGTC
++
+<<<<<<<<<<<<<<<<<<<<<<<<8<<<<<;<<7;
+@EAS188_4:5:103:870:105
+ATAAAACAATTAATTGAGACTACAGAGCAACTAGG
++
+<<<<<<<<<<<<<=<:<;<<<<<<<<<<*<<<<<<
+@EAS188_4:5:166:776:590
+CTTGAAAGCTTGGGCTGTAATGATGCCCCTTGGCC
++
+<;:;<<;<<;<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS188_4:5:166:776:590
+TAATTGTGTCCATGTACACACGCTGTCCTATGTAC
++
+<<<<<</<<<<<<<<<<<<<'<=<:26.</79<::
+@EAS188_4:5:202:326:680
+ACTTATCATGACTCTATCCCAAATTCTCAATTACG
++
+<<<<<<<4<<<*<<<*<<<7..:7<3*:7.7<+.;
+@EAS188_4:5:202:326:680
+GTAATGATGCCCCTTGGCCATCACCCGGTCCCTGC
++
++33<81<:*<;<;;30;<<<;<<<8<<<<<<<<<<
+@EAS188_4:5:295:547:216
+ATGAGTTCAGGTAAAGGGGTGGAAAAAGATGTTCT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS188_4:5:295:547:216
+TAAAAAATTAACATTACAACAGGAACAAAACCTCA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<<;
+@EAS188_4:5:302:997:951
+ATGAACTTCTGTAATTGAAAAATTCATTTAAGAAA
++
+<<<<<<<<<<;<<:<<52<<:;;<6<<;<:<2:9/
+@EAS188_4:5:308:552:77
+TTTTCTTTTTTTTCTTTTCTCTTTTTTTTTTTTTT
++
+1;-<%<;8<<<<<&<5-<58:5:<<<<<<<<<<<<
+@EAS188_4:5:8:377:655
+CTATTTTTGTCTTGACACCCAACTAATATTTGTCT
++
+;<8;;:<;<<:<;<<<<<<<<<<<<<<<<<<<<<;
+@EAS188_4:5:8:377:655
+CTGCCCCATCTCTTGTAATCTCTCTCCTTTTTGCT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS188_4:7:282:567:481
+GGAACAGGGAGGCGCACTAATGCGCTCCACGCCCA
++
+<<<<<<<<<<<<3<7<7<<<<;<<0)<<<<<<<<3
+@EAS188_4:7:282:567:481
+TGCAATTAATATAATTGTGTCCACGTACACACGCT
++
+<9<6<;<9<<<;<<<;<5<7<5</7<<<<<<<<<<
+@EAS188_4:7:296:401:60
+AATGAAAGAGGCTCAAAGAATGCCAGGAAGATACA
++
+<<*<<<<7<<)<<3<<<9<<<<<<<<<<<<<<;<<
+@EAS188_4:7:35:408:348
+AAGAAACGCGTAACTGCGCTCTCATACACTCCAGC
++
+4,'3<6;)2);<3<-6<;<;7+7<5+<<<7<<<<<
+@EAS188_4:7:35:408:348
+GGTTCTCAAGGTTGTTGCAATGGGGTCTATGTGAA
++
+.73<;<<:77<<<<<<<<<<-<<;<<<<<<<<<<<
+@EAS188_4:7:78:583:670
+CAGGGAATTTGTCAATGTCAGGGAAGGAGCATTTT
++
+8<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS188_4:7:78:583:670
+TAACCTCTGGTGACTGCCAGAGCTGCTGGCAAGCT
++
+<<<<<<<<<<;;;<;;<<<:7;5;<5;;<2--8-;
+@EAS188_4:7:96:899:106
+TCTATAAAGGAAATCCCATCAGAATAACAATGGGC
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS188_4:7:96:899:106
+TTCCTGACAAGCAAATGCTAAGATAATTCATCATC
++
+;;;;<<<<<<<;<<<<<<<<<<<<<<<<<<<<<<<
+@EAS188_7:1:115:683:296
+AACAGTCTAGATGAGAGAGAACTTCCCTGGAGGTC
++
+<<<<;<;<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS188_7:1:115:683:296
+CTCTCCTTTTTGCTGCATCCCTGTCTTCCTCTGTC
++
+<<<<<<<<<<<8<<<<<<<<<<6<<<<3<<<<<<<
+@EAS188_7:1:177:522:118
+TAAACTAAGCATCATAAATGAAGGGGAAATAAAGT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<8<
+@EAS188_7:1:177:522:118
+TCTCAATTAATTGTTTTATAAAACCTGTGAGTTTT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<57<<<<
+@EAS188_7:1:290:286:763
+TTAAAATTTAACAAAAGTAAATAAAACACATAGCT
++
+<<<<<<<<<<<<<<<<7<<<<<<<<<<<<<<<8<<
+@EAS188_7:1:290:286:763
+TTTTTTTTTTTTCTTTTCTCTTTTTTTTTTTTTTT
++
+<<<<;<<<<<<<&<<<<&77<<<<<<<<<<<<<<<
+@EAS188_7:1:316:949:122
+TCTCCTTTTTGCTGCATCCCTGTCTTCCTCTGTCT
++
+59899<<<<;;<<;<<<<<<<<<<<<<<<<<<<<<
+@EAS188_7:1:316:949:122
+TTAGGGAAGAACAGCTTAGGTATCAATTTGGTGTT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<0<:<<
+@EAS188_7:1:77:251:446
+CAGCATGGTTGTACTGGGCAATACATGAGATTATT
++
+<<9<<<<<<<<<<<<<97<<<<<<<<<96<<<+<<
+@EAS188_7:1:77:251:446
+TTATCATGACTCTATCCCAAATGCCCAATTACGTC
++
+<<24,:8<<<:1<<<:35<:<:,<<<<<<:5:<<<
+@EAS188_7:2:152:765:744
+ACTTCCCTGGAGGTCTGATGGCGTTTCTCCCTCGT
++
+6<;6<<<;<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS188_7:2:152:765:744
+TTTTCTGTTTCTTTGTTTGATTTGGTGGAAGACAT
++
+<<<<<<<<<<<<<<<<<<:<<<<<<<<&<7293<<
+@EAS188_7:2:172:622:707
+ACATGGCTGATTATGAAAACAATGTTCCCCAGATA
++
+92<3996;<<<<<<<<<<<<<<<<<<<;<<<<<<<
+@EAS188_7:2:172:622:707
+TTCTTCATCCTGGACCCTGAGAGATTCTGCAGCCC
++
+<<<<<<<<<<<<<<<<<<<<<<;<<<<<<:<5:<<
+@EAS188_7:2:187:227:818
+CAGCACAGGGGCTTAACCTCTGGTGACTGCCAGAG
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<3<;<<
+@EAS188_7:2:187:227:818
+CCCCCTTGCAACAACCTTGAGAACCCCAGGGAATT
++
+<<9<<;<<;<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS188_7:2:19:736:559
+AAGACTTCATCAAGATATGTAGTCATCAGACTATC
++
+)<7<2;;4<<4<<<<;<<<<<<<<<<7<<<<<<<<
+@EAS188_7:2:19:736:559
+TGAACCTATGAGTCACAGGTATTCCTGAGGAAAAA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<<<<<
+@EAS188_7:2:218:877:489
+TATAGAAATTGAAACAGCTGTGTTTAGTGCCTTTG
++
+9<<<8<<<;<9<<<<<<<<<<;<<<<<<<<<<<<<
+@EAS188_7:2:259:219:114
+GAAATTGAAACAGCTGTGTTTAGTGCCTTTGTTCA
++
+<<<<<<<<<<<<<<<;<<<<<<7<7<<<<<0<<9<
+@EAS188_7:2:259:219:114
+TTGATGCCCTCTTCTTCCAAAGATGAAACGCGTAA
++
+666<:6/:6::6::<:::<<<;<<<<<<<<;<<<<
+@EAS188_7:3:100:735:530
+GCACACTTTAAATCAACAACAGTAAAATAAAACAA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS188_7:3:100:735:530
+TGATGATGGTTACACTAAAAGCCCATACTTTACTG
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS188_7:3:101:572:491
+CAACAGGAAGAAAAGGTCTTTCAAAAGGTGATGTG
++
+8<<;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS188_7:3:101:572:491
+TTCCAAAGATGAAACGCGTAACTGCGCTCTCATTC
++
+<<<<<<<<<<<<<<<<<<<<<<<<:<<<<<<1<<<
+@EAS188_7:3:13:122:187
+AGCATTTTGTCAGTTACCAAATGTGTTTATTACCA
++
+<<&<;;<<<;7<<<<;<;<<<<<<<<<<<<;<<<<
+@EAS188_7:3:13:122:187
+GACTGCCAGAGCTGCTGGCAAGCTAGAGTCCCCTT
++
+<<<<<<<;<;<<<;<<<<:;6<<<<;;;;:<<%%<
+@EAS188_7:3:15:568:42
+TTTTTGAGGAAGTAATTGGGGAAAACCTCTTTAGT
++
+!!;:<8<;<<<8<<<<<<<<8<<<<<<<<<<<<<<
+@EAS188_7:3:15:568:42
+TTTTTTTTTTTGTTTTTTTTTTTTTTTTTTTTATA
++
+!!!!!!!!!++++!!!!!!!!!!!!!!!!!!!,!,
+@EAS188_7:3:182:104:921
+ATCAAGATATGTAGTCATCAGACTATCTAAAGTCA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<9<<<<<
+@EAS188_7:3:182:104:921
+CACGAATGTTATGCCCTGCTAAACTAAGCATCATA
++
+;<;<<<<<<:<<<<<:<<:<<<<<<<<<<<<<<<<
+@EAS188_7:3:200:712:439
+CGTCACCCGGTCCCTGCCCCATCTCTTGTAATCTC
++
+<7<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS188_7:3:200:712:439
+GTTGGGAGATTTTTAATGATTCCTCAATGTTAAAA
++
+<;<<<<<<<<<<<<<<<<<<<9<<<<<<<<<<<<7
+@EAS188_7:3:296:224:724
+ATAGTTGAAAGCTCTAACAATAGACTAAACCAAGC
++
+<<<<;<<<<<<7;<<<<<6<<<06<<<<<<2(<<<
+@EAS188_7:3:296:224:724
+TGAGGAAAAAGAAAAAGTGAGAAGTTTGGAAAAAC
++
+8<<<5<<<<<<<<<<<<<<<<<<<<7<<<<<;<9<
+@EAS188_7:3:76:333:905
+AATTGTGTCCATGTACACACGCTGTCCTATGTACT
++
+<<;<<<<;7<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS188_7:3:76:333:905
+TTTCTGCCCCCAGCATGGTTGTACTGGGCAATACA
++
+<<<<<7;<;<<6<<6<<7<<7<)&<4+6)0+<;(0
+@EAS188_7:4:164:719:947
+AAATTAACATTACAACAGGAACAAAACCTCATATA
++
+<<<<<<<<<<<<<<<<<<<;<<<<<<<<<;<<<<<
+@EAS188_7:4:164:719:947
+ACGCAAACAGAAACCAAATGAGAGAAGGAGTAGCT
++
+===,=========6====)================
+@EAS188_7:4:171:104:398
+AGGGAGGTGCACTAATGCGCTCCACGCCCAAGCCC
++
+=========)===97===3===4===4==,)=/)=
+@EAS188_7:4:171:104:398
+CAATTAATATAATTGTGTCCATGTACACACGCTGT
++
+79<+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS188_7:4:21:443:404
+AGAGAACTTCCCTGGAGGTCTGATGGCGTTTCTCC
++
+=9=9=9==:==========================
+@EAS188_7:4:21:443:404
+TTCCTCTGTCTTGATTTACTTGTTGTTGGTTTTCT
++
+<<<<<<<<<<<<<<<<<<<<<7<<;<<;+<<<<<<
+@EAS188_7:4:238:441:727
+GTAATTGAAAAATTCATTTAAGAAATTACAAAATA
++
+<<<<<<<<<<<<<<<<<<<<<7<<<<<<<<<;;<<
+@EAS188_7:4:259:869:641
+GTTGGGAGATTTTTAATGATTCCTCAATGTTAAAA
++
+99=:=9=99<=========<=<<============
+@EAS188_7:4:259:869:641
+TGATGCCCCTTGGCCATCACCCAGTCCCTGCCCCA
++
+<<<<<<<<<<<<<<<<<<<<<,;<:<<<<<<<<<1
+@EAS188_7:4:92:693:228
+AAGGTTTTATAAAAAAATTAATTGAGACTACAGAG
++
+6=77=<<=======&====================
+@EAS188_7:4:92:693:228
+AGCATCATAAATGAAGGGGAAATAAAGTCAAGTCT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;9<<
+@EAS188_7:5:112:51:128
+AGACCCCCTTGCAACAACCTTGAGAACCCCAGGGA
++
+++<<<<<<<<<<<<<5<<<<<<<<<<<<<<;<;<6
+@EAS188_7:5:112:51:128
+CCCAATGGACCTGTGATATCTGGATTCTGGGAAAT
++
+;9<;;:<<:<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS188_7:5:115:249:673
+TAAAGAAAAAAAAACCTGTCAAACACGAATGTTAT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<:<6<
+@EAS188_7:5:115:249:673
+TAAATACACACAAAAGTACAAAACTCACAGGTTTT
++
+:<<<;<<<;<9<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS188_7:5:163:982:695
+CTCAGCAGAAACCTTACAAGCCAGAAGAGATTGGA
++
+<:<<<<<<<<<<<<<<9<<<<<<<<<<<<<<<<<<
+@EAS188_7:5:163:982:695
+TCAAAGAATGCCAGGAAGATACATTGCAAGACAGA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<<;
+@EAS188_7:5:308:354:124
+GCTGCATCCCTGTCTTCCTCTGTCTTGATTTACTT
++
+<<<<<<<<<<<<<<<<<<<<<;<<<<;<<<<<<<<
+@EAS188_7:5:308:354:124
+TGAGCAAAACAGTCTAGATGAGAGAGAACTTCCCT
++
+%+<)2<<<<<<<<8<<<<<<<<<<<<<<<<<<<<<
+@EAS188_7:5:74:329:459
+ACAGAGCAACTAGGTAAAAAATTAACATTACAACA
++
+</<;<8/<<9<<<;<<<<<<<<<<<<<<<<<<<<<
+@EAS188_7:5:74:329:459
+TAAAGTCAAGTCTTTCCTGACAAGCAAATGCTAAG
++
+<<<<<<<<<<<<<<<<<<<<<<<;<<;<<;9;599
+@EAS188_7:6:107:447:488
+TAATTGGTACAATGTACAATATTCTGATGATGGTT
++
+<<<;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS188_7:6:107:447:488
+TGCTAAGTATTGGTAAAGATGTGGGGAAAAAAGTA
++
+<<3<<<<<<6<<<<<<<<<<<<<<<<7<<<<<<<<
+@EAS188_7:6:107:636:642
+AAGTCTTTCCTGACAAGCAAATGCTAAGATAATTC
++
+<<<<<<<;<<<<<;<<<<<<<<<<<<<<<<<<<<<
+@EAS188_7:6:107:636:642
+GTCATCTATAAAGGAAATCCCATCAGAATAACAAT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS188_7:6:11:994:584
+GAAGGAAAAAAATTCTAAAATCAGCAAGAGAAAAG
++
+<<<<;<<<<<<<;<:<<<<<<<<<;<<<<<<<<<<
+@EAS188_7:6:11:994:584
+GGTATTCCTGAGGAAAAAGAAAAAGTGAGAAGTTT
++
+<<<<<<<<<<<7<<<<<<<<<<<<<6<<<<<<3<6
+@EAS188_7:6:191:540:493
+AAAAGCCCATACTTTACTGCTACTCAATATATCCA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;
+@EAS188_7:6:191:540:493
+GTGGGGAAAAAAGTAAACTCTCAAATATTGCTAGT
++
+<<9<1<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS188_7:6:194:998:663
+ACCTAACACAAGACTACCCAGATTCATAAAACAAA
++
+;</<<<7<<<<;<<8<<<<<<<<<<<<<<<<<<<<
+@EAS188_7:6:194:998:663
+TCTACGCAAACAGAAACCAAATGAGAGAAGGAGTA
++
+<<<<<<<<<;<<<<<<<<<<<<<<<<<<<<<<<8<
+@EAS188_7:6:205:873:464
+AGATTGCTTGTGGTCTGACAGGCTGCAACTGTGAG
++
+<<<<<<<<<7<<<<<<<<<<<<:<<,:<:<<<<::
+@EAS188_7:6:205:873:464
+CCCCAGAGGGAAAGCTTTCAACGCTTCTAGCCATT
++
+<-((+:+;289<--;<;-;<:;;<<<;;<<<<<<<
+@EAS188_7:6:46:122:479
+AAGAAAGAGGTTCAGAACTTGAAGACAAGTCTCTT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<<<<
+@EAS188_7:6:46:122:479
+AAGTGAGAAGTTTGGAAGAACTATTTGAGGAAGTA
++
+<<<9<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS188_7:7:19:886:279
+CCCATTTGGAGCCCCTCTAAGCCGTTCTATTTGTA
++
+<9<<<<<<<<<<<<6<28:<<85<<<<<2<;<9<<
+@EAS188_7:7:19:886:279
+GAAAGGAGCATTTTGTCAGTTACCAAATGTGTTTA
++
+9%<2)2.2::<;<<<2<<<<<<<<<<<<<<<<<;<
+@EAS188_7:7:213:309:373
+TAGACATCTAAATGAAAGAGGCTCAAAGAATGCCA
++
+<<<86<82<<<<<<<<<<<<<<<9<<<<<<<<<<<
+@EAS188_7:7:213:309:373
+TTAAAAATGAACAGAGCTTTCAAGAAGTATGAGAT
++
+<;<<<<<<;<7<<<<<-<<<<<<<<<<<<<<4<7<
+@EAS188_7:7:243:876:758
+AGCCCAGATCCAGATTGCTTGTGGTCTGACAGGCT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<;;<;78<<
+@EAS188_7:7:243:876:758
+CCCAGATACCATCCCTGTCTTACTTCCAGCTCCCC
++
+0%3<1;.70;3363;31;<<<<<<6<<<;<<<<<<
+@EAS188_7:7:67:719:786
+GGATGAGAAATTACCTAATTGGTACACTGTACAAT
++
+;;<<<<<<&<<:13&<1<<<:<<<)/&/))<'6-<
+@EAS188_7:7:67:719:786
+TAAAAAAAAAAAAGCAAAAACAAAAACTATGCTAA
++
+$<<;<-1<<<8<<*&<;<;,<<3<<<<33<<<33<
+@EAS188_7:8:60:182:718
+GTCCCTGCCCCATCTCTTGTAATCTCTCTCCTTTT
++
+<<<<<<<<<<<<<<<<<<<<7<<<<<<<<<;<;<<
+@EAS188_7:8:60:182:718
+TGACACCCAACTAATATTTGTCTGAGCAAAACAGT
++
+<<<:<<;<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS188_7:8:64:350:174
+CCTAACACAAGACTACCCAGATTCATAAAACAAAT
++
+709<<;<;<<<<<<<;7<<<<<<<<<<<<<<<<<<
+@EAS188_7:8:64:350:174
+GTTCTACGCAAACAGAAACCAAATGAGAGAAGGAG
++
+<<<<<<<<<<<<<<<<<<<<<:<<<<<6<<<<<:<
+@EAS192_3:1:114:19:769
+AAACACGAATGTTATGCCCTGCTAAACTAAGCATC
++
+5+;+3/6;<+;/8<8*/<7/59<97147<;;9<7<
+@EAS192_3:1:114:19:769
+TAAAGTCAACATGAAGGAAAAAAATTCTAAAATCA
++
+<<<<<*2;6;<<<4.;;<&;;<.<40)<);5-/7;
+@EAS192_3:1:225:195:543
+AACAACCTTGAGAACCCCAGGGAATTTGTCAATGT
++
+;;8;;+;(<<<<<<<<7;<<<<<<<<<<<<<<<<<
+@EAS192_3:1:225:195:543
+GGTTGCCAGCACAGGGGCTTAACCTCTGGTGACTG
++
+<<<<<<<<<<<<<<<<<<<<<<<9<<;::388998
+@EAS192_3:3:194:378:230
+AATACTACTAGACCTAAGAGGGATGAGAAATTACC
++
+<<;<8<<:<<<<:<<<<<<<<<<<<<<<<<<<<<<
+@EAS192_3:3:194:378:230
+ATGAGAGAAGGAGTAGCTATACTTATATCAGATAA
++
+<<<<<<<<<<<<<:<<<<<<<<<<<<<<<<<<<<<
+@EAS192_3:3:221:881:916
+TAACACAAGACTACCCAGATTCATAAAACAAATAC
++
+<<;<<8<<;<<<<<<<;<<<<28<:<8<:;<;;;<
+@EAS192_3:3:221:881:916
+TAATTCTAAATCTAGAACAAAATTAAAATTTAACA
++
+44%-4(5<;9/,:<68:1<:8<:<<84;<<<<<;<
+@EAS192_3:3:257:611:440
+ACCCTGAGAGATTCTGCAGCCCAGATCCAGATTGC
++
+2<;;8<;;<<<<;<<<<<<<<<<<<<<<<<<<<<<
+@EAS192_3:3:257:611:440
+GGAGCATTTTGTCAGTTACCAAATGTGTTTATTAC
++
+<<<<<<<<<<<<<<<<<<<<8<<<<;<<<<8<<+5
+@EAS192_3:3:27:973:518
+CTGATTATGAAAACAATGTTCCCCAGATACCATCC
++
++<<<<<<9<<<<<<<<<<<;<;<<<<<<<<<<<<<
+@EAS192_3:3:27:973:518
+TCCAGATTGCTTGTGGTCTGACAGGCTGCAACTGT
++
+<<<<<<<<<<<<<<;<<<<7<<<<<<<<88;0:8;
+@EAS192_3:3:285:349:797
+ATCATAAATGAAGGGGAAATAAAGTCAAGTCTTTC
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS192_3:3:285:349:797
+GTTTTAAAAAACCAATAATTGAGACTACAGAGCAA
++
+;;<<<7.:<<<..<.<<<<<<<<<<<<<<<<<<<<
+@EAS192_3:3:309:187:267
+ATTGAGACTACAGAGCAACTAGGTAAAAAATTAAC
++
+<:0;<;<4<<7<<<<:<<<<<<<<<<<<<<<<<<<
+@EAS192_3:3:309:187:267
+GGGGAAATAAAGTCAAGTCTTTCCTGACAAGCAAA
++
+<<<<<<<<<<<<<<<<<<<<<<<;<;<;<;68;;8
+@EAS192_3:3:88:866:774
+ATGTAACAAATCTGCTCTTGTACTTCTAAATCTAT
++
+<<<;<<<<<;<<<<<<<<<<<<<<<<<68<<<<<<
+@EAS192_3:3:88:866:774
+TTGTTTTCCACTTTGGAAAACAATTTGGTAATTTC
++
+<<<;<<<<:<<<<<:<8<<<<<<<<<<8<<<<<<<
+@EAS192_3:4:184:237:476
+ATCATACAATGATAAAAAGATCAATTCAGCAAGAA
++
+<;2<;<4<<;<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS192_3:4:184:237:476
+ATGAACTAACTATATGCTGTTTACAAGAAACTCAT
++
+<<<<<<<<<<<<<<<<<<<<<<;<<<<<<<;<;;<
+@EAS192_3:4:255:549:422
+AAGTCATCTATAAAGGAAATCCCATCAGAATAACA
++
+&<;;+<;4;<<<<<<<<<<<;<;<<;<<<<<<<<<
+@EAS192_3:4:255:549:422
+CTCTTTAGTCTTGCTAGAGATTTAGACATCTAAAT
++
+<<<<<<<<<<<<<<<<;<<<<<<<:<<<<<<;;;<
+@EAS192_3:4:293:168:240
+ATGAACAGAGCTTTCAAGAAGTATGAGATTATGTA
++
+<<<<;<<<;;;<;<<;;;<<;;<<::::<<;;+;7
+@EAS192_3:4:293:168:240
+CAAAGAATGCCAGGAAGATACATTGCAAGACAGAC
++
++;;;;<8<<86<<<<<<<;;8;7;<;<8<8;<<<<
+@EAS192_3:4:312:915:751
+AATAAAGTCAAGTCTTTCCTGACAAGCAAAAGCTA
++
+<:-<<<99:::);:7<4;8<<<<<<<;<2<+8<;<
+@EAS192_3:4:312:915:751
+ATCTATAAAGGAAATCCCATCAGAATAACAATGGG
++
+<2<<<<<<<8;<<<<<<<<:<<<<8<<<<<84,4:
+@EAS192_3:4:63:5:870
+AAAGAAAAAAGAATTTTAAAAATGAACAGAGCTTT
++
+<<;<<<<<<<<<<<<<<<<<;<<<<<<<<<;;<<<
+@EAS192_3:4:63:5:870
+GAAAGAGGCTCAAAGAATGCCAGGAAGATACATTG
++
+:<;<;<<<4:;<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS192_3:5:197:914:256
+ACTAGACCTAAGAGGGATGAGAAATTACCTAATTG
++
+<5;<8<5/;<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS192_3:5:197:914:256
+TCAGATAAAGCACACTTTAAATCAACAACAGTAAA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<8;:::
+@EAS192_3:5:223:142:410
+CTATTCAGTTCTAAATATAGAAATTGAAACAGCTG
++
+8;<<<;<<<<;<<<<<<;<;<<<<<<<<<<<<;<<
+@EAS192_3:5:27:577:849
+AGTCTCTTATGAATTAACCCAGTCAGACAAAAATA
++
+<<<<<<<<<<<<<<<<<<<<;:<<<;<<<<<<;;;
+@EAS192_3:5:27:577:849
+TTAGACATCTAAATGAAAGAGGCTCAAAGAATGCC
++
+5:<;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS192_3:5:287:334:110
+GATGAATACTAAGATTGATGTAGCAGCTTTTGCAA
++
+.5+7)09<))&-&:33953<-./&&&)((;+3399
+@EAS192_3:5:287:334:110
+TATGTAAAGTAACTGAACCTATGAGTCACAGGTAT
++
+<<<<<<<<<<<<<<<<<<4;<<<<<<<::6<55:.
+@EAS192_3:6:116:464:261
+CAATGATAAAAAGATCAATTCAGCAAGAAGATATA
++
+;<<;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS192_3:6:116:464:261
+CTATATGCTGTTTACAAGAAACTCATTAATAAAGA
++
+<<<<<<<<<<<<<<<<<;<<<;<<<<<<<<<;;8<
+@EAS192_3:6:170:169:57
+GGCTTGACCTCTGGTGACTGCCAGAGCTGCTGGCC
++
+<<<<<;<<<<<<;<<<<<<<<<<<<:<<<<<;;+%
+@EAS192_3:6:170:169:57
+TGCAACAACCTTGAGAACCCCAGGGAATTTGTCAA
++
+778<:<<<9<<<<<;<<<<<<<<<<<<<<<<<<<<
+@EAS192_3:6:175:437:950
+CCAAATTCCCAATTACGTCCTATCTTCTTCTTAGG
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<:59
+@EAS192_3:6:175:437:950
+CCTGCCCCATCTCTTGTAATCTCTCTCCTTTTTGC
++
+;;5:;;9<<:<;<;<<<<<<<<<<<<<<<<<<<<<
+@EAS192_3:6:185:868:496
+CCCTTGGCCATCACCCAGTCCCTGCCCCATCTCTT
++
+<<<<<<<<<<<<;<<<;<<<<<<<<<<<9<<;<<<
+@EAS192_3:6:185:868:496
+GATTTTTAATGATTCCTCAATGTTAAAATGTCTAT
++
+:;;<;;<<<<<<<<;4<<<<<<<<<<<<<<<<<<<
+@EAS192_3:6:201:195:757
+CCTGCCCCATCTCTTGTAATCTCTCTCCTTTTTGC
++
+:<':<:<<46<:<;:<;<;<<9<<<<<<<<;<<<<
+@EAS192_3:6:201:195:757
+TATGTACTTATCATGACTCTATCCCAAATTCCCAA
++
+<<<<<<<<<<<<<<;<<<<<<<<<<<<<<<;;;;8
+@EAS192_3:6:216:292:528
+GGGAGATTTTTAATGATTCCTCAATGTTAAAATGT
++
+;:;;8<<<<<<<<<<<<<:<<;<<<<<<<<<<<<<
+@EAS192_3:6:216:292:528
+TAATGATGCCCCTTGGCCATCACCCAGTCCCTGCC
++
+<;<;<<<<<<<;<<<<<<<<;;;;:;;:<%<;1;:
+@EAS192_3:6:235:505:553
+GGTGGAAAAAGATGTTCTACGCAAACAGAAACCAA
++
+;8518<<<<<;<;<<<;<<;<.<<<<<<<<<<<<<
+@EAS192_3:6:235:505:553
+GTAAAAAATTAACATTACAACAGGAACAAAACCTC
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<;:;:
+@EAS192_3:6:326:887:180
+CTAAACCAGTCCTATAAGAAATGCTCAAAAGAATT
++
+8:<<:<5<<<;7<<<<<<<<<<<<;<<<<<<<<<<
+@EAS192_3:6:326:887:180
+TGGGCTTCTCAGCAGAAACCTTACAAGCCAGAAGC
++
+;<<<<<;<<<<<<<<<8<<<<<<<<<<<<0<;;<+
+@EAS192_3:6:45:183:25
+CAGCGGAAACCTTACAAGCCAGAAGAGATTGGATC
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<86;<;:;
+@EAS192_3:6:45:183:25
+CTAAACCAGTCCTATAAGAAATGCTCAAAAGAATT
++
+;1<<;<<<;;;;<<<<<+<<<<<<<<<9<<<<<<<
+@EAS192_3:7:149:354:667
+CTTCCAGCTCCCCAGAGGGAAAGCTTTCAACGCTT
++
+<<<<<<<<<<<<<<<<<<<><<<<<<<<;<:<<<<
+@EAS192_3:7:149:354:667
+GAGGTGCACTAATGCGCTCCACGCCCAAGCCCTTC
++
+;<;;;<<<<;<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS192_3:7:298:644:697
+CTATGTTTCTTATCTGCACATTACTACCCTGCAAT
++
+8:<8;<;:7;<<;4;:+<7<<<<;<<<<<<<<<<<
+@EAS192_3:7:298:644:697
+TCCACGTCTCATCTAGGGGAACAGGGAGGTGCACT
++
+<<<<<<<<<<<<<<<::;;;6<8:;;9;98;668;
+@EAS192_3:7:66:891:294
+AGCACACTTTAAATCAACAACAGTAAAATAAAACA
++
+<<<<<<<<<<<<<<<<<<<<<<<9<<<<<<;<<<<
+@EAS192_3:7:66:891:294
+TAATTGGTACAATGTACAATATTCTGATGATGGTT
++
+:<<5;;<<<4<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS192_3:7:78:692:671
+AATGAAGGGGAAATAAAGTCAAGTCTTTCCTGACA
++
+<<);<<;;<<<<<;<<<<<<<<<<<<<6<<<<<<<
+@EAS192_3:7:78:692:671
+CAGCAAGAGAAAAGCATACAGTCATCTATAAAGGA
++
+<<<<<<<<<<<<<;<<<<<<<:<<:<<<:8<<0;;
+@EAS192_3:7:93:945:176
+CCAGAGGGAAAGCTTTCAACGCTTCTAGCCATTTC
++
+6;;;8<<3<<8.<;6)<<<<<9<<<<<<<<<<<<<
+@EAS192_3:7:93:945:176
+GTGAGCCATCACAATGAACAACAGGAAGAAAAGGT
++
+<<<<<<<<<<<<<<<<<<<<<;<<<<;;<;:7;<3
+@EAS192_3:8:6:104:118
+AAGAATTTTAAAAATGAACAGAGCTTTCAAGAAGT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<=<<<<<<
+@EAS192_3:8:6:104:118
+TCTAAATGAAAGAGGCTCAAAGAATGCCAGGAAGA
++
+;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS192_3:8:6:237:885
+AAAATCAGCAAGAGAAAAGCATACAGTCATCTATA
++
+<<<<1:<;:<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS192_3:8:6:237:885
+TATTTGAGGAAGTAATTGGGGAAAACCTCTTTAGT
++
+<<<<<<<<9<<<<<<<<<<<<<<<<<<<<<;;;<;
+@EAS1_103:1:151:159:43
+AACCTCATACACACACATGGTTTAGGGGTATAATA
++
+;;4;6<<;<<<<7<77<6;<6<<<<<;;<<<<<<<
+@EAS1_103:1:151:159:43
+TCTCATTCACTCCAGCTCCCTGTCACCCAATGGAC
++
+<<<<<<<;<<<8<<<;<;8<<<<7<77;;79<09+
+@EAS1_103:1:228:736:747
+AAGATATGTAGTCATCAGACTATCTAAAGTCAACA
++
+<<<<<<<<<;<<<<<<<;;<<;<<<<;::<;;7;7
+@EAS1_103:1:228:736:747
+TTGGACTTCTTAAAGAAAAAAAAACCTGTCAAACA
++
+<07<<&<;+<<<<<<<<<<<<<<<<;<<<<<<<<<
+@EAS1_103:1:274:176:479
+CCTATCTTCTTCTTAGGGAAGAACAGCTTAGGTAT
++
+7)<<7<626<<7<<<<<<<<<<<<<<<<<<<3<<<
+@EAS1_103:1:274:176:479
+GAAATGCTTTACTGTCATAACTATGAAGAGACTAT
++
+<<<<<<<<<<<<<;<<<<<<<<<<;<<9<59<<<<
+@EAS1_103:1:2:831:692
+GTGTTCTCATCAACCTCATACACACACATGGTTTA
++
+2749'979<9<<<6;<<<0<;<<<<<3<<<<<<<<
+@EAS1_103:1:2:831:692
+TCCAGCTCCCTGTCACCCAATGGACCTGTGATATC
++
+<<<<<<<<;<<<<<<<<<<9<<:9<<<;;96<796
+@EAS1_103:2:184:980:396
+AAGGAGGTCATCATACAATGATAAAAAGATCAATT
++
+<<;;<77;;<<;<<<<<<<<<<<<<<<<<<<<<<<
+@EAS1_103:2:184:980:396
+ACATGAACTAACTATATGCTGTTTACAAGAAACTC
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<<
+@EAS1_103:2:226:302:758
+GGAAAGCTTTCAACGCTTCTAGCCATTTCTTTTGG
++
+;<<<<9;<<<<<<<<<<7<<<<<<<<<<<<<<<<<
+@EAS1_103:2:226:302:758
+TGCTTGTGGTCTGACAGGCTGCAACTTTGAGCGNT
++
+<<<<<<<;;;,<;<92;66<;))42<&2&(/1!!!
+@EAS1_103:2:234:167:381
+AAGTCAAGTCTTTCCTGACAAGCAAATGCTAAGAT
++
+<<;<;<<<<;<<<<7<<<<<<<<<<<<<<<<<<<<
+@EAS1_103:2:234:167:381
+AGAGAAAAGCATACAGTCATCTATAAAGGAAATCC
++
+<<<<<<<<<<<<<<<<<<<<<<<<<;<<<;;7<;;
+@EAS1_103:2:235:805:373
+TATCTTCTTCTTAGGGAAGAACAGCTTAGGTATCA
++
+<<;<<<<<<9<9<<<<<<<<<<<<<<<<<<<<<<<
+@EAS1_103:2:235:805:373
+TTTACTGTCATAACTATGAAGAGACTATTTCCAGA
++
+<<<<<<<<<<<<<<<<<<<<;<;<<<<<<;;<99;
+@EAS1_103:2:307:252:632
+ACCATCCTGCTAAATACATATGCACCTAACACAAG
++
+<77<;,5<,9<<<<<<;<<<<<7<;<<<<<<<<<<
+@EAS1_103:2:307:252:632
+ATGTTCTACGCAAACAGAAACCAAATGAGAGAAGG
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<:;;<;;
+@EAS1_103:3:253:175:31
+CAAACAGAAACCAAATGAGAGAAGGAGTAGCTATA
++
+<<<<<<<<<<<<<<<<<<<<<<:<<<<<<<:<;;;
+@EAS1_103:3:253:175:31
+TTCATAAAACAAATACTACTAGACCTAAGAGGGAT
++
+;+;<;<<<<<<<<9<<9<<<<<;<<<<<<<<<<<<
+@EAS1_103:3:277:921:474
+AAAATATAGTTGAAAGCTCTAACAATAGACTAAAC
++
+<<<<<<<<<<<<<<<:<<<<<<<<<<<5<<;;;;;
+@EAS1_103:3:277:921:474
+AAAGAAAAAGTGAGAAGTTTGGAAAAACTATTTGA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS1_103:3:320:505:814
+ACAGTCTAGATGAGAGAGAACTTCCCTGGAGGTCT
++
+<2<;;5<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS1_103:3:320:505:814
+CTGTCTTGATTTACTTGTTGTTGGTTTTCTTTTTC
++
+<<<<<<<<<<<<<<<<;<<8<<76<<<<;<&<<<7
+@EAS1_103:3:323:196:855
+ACAAGCAAATGCTAAGATAATTCATCATCACTAAA
++
+<<<<<<<7<<<<<<:<<<<<<<<<<<<<<<<<;7:
+@EAS1_103:3:323:196:855
+TAAAAAATTAACATTACAACAGGAACAAAACCTCA
++
+&<<<<<<09<<7<7;<;<<0<<<<<;<<<<<<<<<
+@EAS1_103:3:41:474:283
+TGAACCACACATTAATACTATGTTTCTTATCTGCA
++
+<<<<<<<<<<<<<<<<<<<<<;<<<<<<<<<<+<<
+@EAS1_103:3:41:474:283
+TTTGGTGTTCTGTGTAAAGTCTCAGGGAGCCGTCC
++
+6/;;;88;;<:;48<<<<<;<;<<<<<<<<<<;<<
+@EAS1_103:4:143:560:194
+GTTGTACTGGGCAATACATGAGATTATTAGGAAAT
++
+9:<;7<:::<:<;<<<<<<<<<<:<<<<<<<<<<<
+@EAS1_103:4:143:560:194
+TCTAGCCATTTCTTTTGGCATTTGCCTTCAGACCC
++
+<<<<;;<<<<<<<<<<<6<;<<<<;;<<;9<999<
+@EAS1_103:4:164:79:134
+ACAATGGGCTTCTCAGCGGAAACCTTACAAGCCAG
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<7<
+@EAS1_103:4:164:79:134
+AGATAATTCATCATCACTAAACCAGTCCTATAAGA
++
+<;<;<<<;<<;<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS1_103:4:231:815:626
+GATCAATACAGCAAGAAGATATAACCATCCTACTA
++
+'<4%<<<22<<,<<;<<4;<<<<<<<<<<<<<<7<
+@EAS1_103:4:231:815:626
+GCTGTTTACAAGAAACTCATTAATAAAGACATGAG
++
+<;<<<<9<<<<<<<<<<<<<<<<<;<<;5<<<;:;
+@EAS1_103:4:235:899:847
+AGAAACTCATTAATAAAGACATGAGTTCAGGTAAA
++
+<<3<;<<<<<<<<<;;<<<<<<<+<<<+6<8<3/<
+@EAS1_103:4:235:899:847
+ATAAAAAGATCAATTCAGCAAGAAGATATAACCAT
++
+<7<<<<<<<<:<<<<:<</<<<<<<<<<<<<<<<<
+@EAS1_103:4:294:525:849
+AGGAGCATTTTGTCAGTTACCAAATGTGTTTATTA
++
+;<;:;:<;<;<<<3<<<;<;<<<<<<<<<<<<<<<
+@EAS1_103:4:294:525:849
+CTGGCAAGCTAGAGTCCCATTTGGAGCCCCTCTAA
++
+<<<<<<<<<<<<<<<<<<<<<<9+<:<<<<9;;15
+@EAS1_103:4:61:433:385
+ACTGTGAGCCATCACAATGAACAACAGGAAGAAAA
++
+<*97<<<<&9<<;<&<<<<<<<<<;<<<<<<<<<<
+@EAS1_103:4:61:433:385
+GGATGGAGGGAAGAGGGACGCTGAAGCACTTTGAT
++
+<<<<<<<<<<<<<<<<<;<<;<<6<<)91<<;;,;
+@EAS1_103:5:141:711:813
+TATTACCAGAGGGATGGAGGGAAGAGGGACGCTGA
++
+=<5<5<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS1_103:5:141:711:813
+TATTTGTAATGAAAACTATATTTATGCTATTCAGT
++
+<<<<<<<<<<;<<<<<<<<<<<<<<;<<<<<<:+<
+@EAS1_103:5:188:20:592
+CTACTAGACCTAAGAGGGATGAGAAATTACCTAAT
++
+2<<7;<<<<,;<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS1_103:5:188:20:592
+GAGTAGCTATACTTATATCAGATAAAGCACACTTT
++
+<<<<<<<<<<<<<<<<<<<<;;<<<<:<<<;<;;<
+@EAS1_103:5:285:241:560
+GAAATTACAAAATATAGTTGAAAGCTCTAACAATA
++
+<<<<<<<<<<;<<<<;<<<<<<<<<<<<;<;;;<.
+@EAS1_103:5:285:241:560
+TAAAGTAACTGAACCTATGAGTCACAGGTATTCCT
++
+:<<<<;<<,<<<<5<<<<<<<<<<<<<<<<<<<<<
+@EAS1_103:5:319:165:698
+ATCACCCAGTCCCTGCCCCATATCTTGTAATCTCT
++
+<<<<<<<<<<<<<<<<<<<3<9<<<<<<<;<<<<<
+@EAS1_103:5:319:165:698
+TGACACCCAACTAATATTTGTCTGAGCAAAACAGT
++
+;5;2;<:;<<:<<<<<<<<<;:;<<<<<<<<<<<<
+@EAS1_103:6:7:858:437
+CAATGAACAACAGGAAGAAAAGGTCTTTCAAAAGG
++
+<<<<<<<<<<<<<<<<<<<<<;<3<<<<<<<<<33
+@EAS1_103:6:7:858:437
+CCATTTCTTTTGGCATTTGCCTTCAGACCCTACAC
++
+7;<4;;:;80<;<;<<<<<<:<<;<<<;;<<<<<<
+@EAS1_103:7:112:578:782
+AAAATAAAACACATAGCTAAAACTAAAAAAGCAAA
++
++<<<%<<<<6<;<<<<6:<<<<:<<<<<<<<<<<<
+@EAS1_103:7:112:578:782
+CAGATTCATAAAACAAATACTACTAGACCTAAGAG
++
+<;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<7<<<
+@EAS1_103:7:139:578:951
+AAAAACATGAACTAACTATATGCTGTTTACAAGAA
++
+<<<<<<<<;<<<<<<<<<<<<;<<<<<<<<<<0;;
+@EAS1_103:7:139:578:951
+GAGGTCATCATACAATGATAAAAAGATCAATTCAG
++
+;<0;:&<:9<<<7<<<<<<<<<<<<<<;<<<<<<<
+@EAS1_103:7:166:84:766
+ATAACACAAGACTACCCAGATTCATAAAACAAATA
++
+%8<=+<-<<<</<<<<8<<<<<;<<<<<<<<<<<<
+@EAS1_103:7:166:84:766
+GGAAAAAGATGTTCTACGCAAACAGAAACCAAATG
++
+<<<<<<<<;<<<<<<<<;<<<<<<;<<<7<;::93
+@EAS1_103:7:311:100:539
+AAATTCTTCATCCTGGACCCTGAGAGATTCTGCAG
++
+;<;<<;;<;<<;<<<<<;9<<<;<<<<<<<<9<<;
+@EAS1_103:7:311:100:539
+CAGTTACCAAATGTGTTTATTACCAGAGGGATGGA
++
+<<<<;<<<<;<<<<<;<<<<<<<<<:<::;7;<0;
+@EAS1_103:7:313:83:546
+TCATTCACTCCAGCTCCCTGTCACCCAATGGACCT
++
+;)<994<;<<<<<<<;<<<<<<<<<<<<<<5<<<<
+@EAS1_103:7:313:83:546
+TGCAACAACCTTGAGAACCCCAGGGAATTTGTCAA
++
+<<<<<<<<<<;<<<<<<<<<<<<<<4<<<:<;<<9
+@EAS1_103:7:53:783:78
+AAAAACCTGTCAAACACGAATGTTATGCCCTGCTA
++
+<;;;;<<0<,<<<<<<<<<;<<<;<;<<<<;<<<<
+@EAS1_103:7:53:783:78
+TGCAAGACAGACTTCATCAAGATATGTAGTCATCA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<;<<;<7;<:;
+@EAS1_105:1:115:226:443
+AAATCTGCGCTTGTACTTCTAAATCTATAAAAAAA
++
+<<;;<;<<<<<<<<<<<<:<<<<<<<<<<<<<<<<
+@EAS1_105:1:115:226:443
+ATATAACCATCCTACTAAATACATATGCACCTAAC
++
+<<<<<<<<<<<<<<<<;<<<<<<<<<<<<;<<<<<
+@EAS1_105:1:141:415:738
+AAAGTCAAGTCTTTCCTGACAAGCAAATGCTAAGA
++
+<<<<<<<<<<<<<<<<<<<<<<:<<;<<;<<<<6:
+@EAS1_105:1:141:415:738
+TTACCTAGTTGCTCTGTAGTCTCAATTAATTGTTT
++
+<<<<<<<<<<<<<<<<<<<<<<<;<<<<<;<8<<<
+@EAS1_105:1:234:185:359
+AAGGAGTAGCTATACTTATATCAGATAAAGCACAC
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;;9--:
+@EAS1_105:1:234:185:359
+CAGATTCATAAAACAAATACTACTAGACCTAAGAG
++
+<<4<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS1_105:1:28:745:352
+ATATGCACCTAACACAAGACTACCCAGATTCATAA
++
+<<<<<9<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS1_105:1:28:745:352
+CTTCTAAATCTATAACAAAATTAAAATTTAACAAA
++
+4;;*;<<<;;<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS1_105:1:297:283:948
+CCAGATTGCTTGTGGTCTGACAGGCTGCAACTGTG
++
+<<<<<<<<<<<<<<<<<<<<<<<:<<9;)+1;19-
+@EAS1_105:1:297:283:948
+TGTCTTACTTCCAGCTCCCCAGAGGGAAAGCTTTC
++
+6;;3;6<<66<<<<<;<<<<<<<<<<<<<<<<<<<
+@EAS1_105:1:329:407:872
+TTCGTTTTTTTTTTTTTTTTTTCCCTTTTTTTTTT
++
+<<<<<<<<<<<<<<<<<<6;<<&4::<++<(&;<<
+@EAS1_105:1:3:903:957
+AAGCCAGAAGAGATTGGATCTAATTTTTGGACTTC
++
+<<<<<<<<<<<<<<<<;;<;<;<<<<<<66<;<<;
+@EAS1_105:1:3:903:957
+ATTCATCATCACTAAACCAGTCCTATAAGAAATGC
++
+<%12<&<<<;<:<<<<<<<<<7<<<<<<<<<<<<<
+@EAS1_105:1:45:239:851
+CTAAGAGGGATGAGAAATTACCTAATTGGTACAAT
++
+*2*0<<<<<<<<<<<<<<<<9<<3<<<<<<<<<<<
+@EAS1_105:1:45:239:851
+TGAGAGAAGGAGTAGCTATACTTATATCAGATAAA
++
+<<88;<208<9<;6<<<6269;94<&401-662&2
+@EAS1_105:1:87:430:995
+GAAAAGAGTTAAAAACATGAACTAACTATATGCTG
++
+1<4%81<..1<<<<<0<<<<<0.<<9<<(<6<<6<
+@EAS1_105:1:87:430:995
+TACTCACCATCATAAATACACACAAAATTACAAAA
++
+<<;<<7;;;<;<<777;7(77;;1;7;%117;,7(
+@EAS1_105:2:110:584:649
+CCATGTACACACGCTGTCCTATGTACTTATCATGA
++
+<<<<<<<<<<<<<<<<<<<<<<<<;<<<<<::<38
+@EAS1_105:2:110:584:649
+CTGTAATGATGCCCCTTGGCCATCACCCGGTCCCT
++
+++:4686<<68<;<;<;<<<:<<<<<<<<<<<<<<
+@EAS1_105:2:146:374:692
+AAATGCTCAAAAGAATTGTAAAAGTCAAAATTAAA
++
+<<<<<<<<<<<<<<<</<<<<<<<<<<<<<<<<<:
+@EAS1_105:2:146:374:692
+ATTAAATTCCCCCACTTAAGAGATATAGATTGGCA
++
+<4:<<<1:<:<::<<<;<<<<<<<<<<<<<<<<<;
+@EAS1_105:2:179:532:82
+CCATCACCCGGTCCCTGCCCCATCTCTTGTAATCT
++
+<:96<6<<<<89<<<<<<<<<<<<<<<<<<<<<<<
+@EAS1_105:2:179:532:82
+TGTACTTATCATGACTCTATCCCAAATTCCCAATT
++
+<<<<<<<<<<<<<<<<<<<<3<;<;<<<<:<8<<<
+@EAS1_105:2:280:662:939
+AAGAGAAAAGCATACAGTCATCTATAAAGGAAATC
++
+<<;<;<<<<<:<<<;<<<;<<;<<<<<<<<<<<;<
+@EAS1_105:2:280:662:939
+CCTCTTTAGTCTTGCTAGAGATTTAGACATCTAAA
++
+<<<<<<<<<<<<<;<<<;;7<<<<<<<<<<<<:8<
+@EAS1_105:2:299:360:220
+ATTCAGTTCTAAATATAGAAATTGAAACAGCTGTG
++
+<<<<<<<9<9<<<<<<<<<<<<<<<<<5<;<0<<<
+@EAS1_105:2:299:360:220
+GAAGAACTTAGATGCCCTCTTCTTCCAAAGATGAA
++
+66<;;4;<<()<<4<<<<<<;<<;<<<<<<<<<<<
+@EAS1_105:2:301:161:195
+ACAGTAAAATAAAACAAAGGAGGTCATCATACAAT
++
+<<<<<<<<<<<<<<<<<<<<<<<;<<<<<<:<<<<
+@EAS1_105:2:301:161:195
+GTACAATGTACAATATTCTGATGATGGTTACACTA
++
+''6%6<6<<<4<<<<<<<<)<<<<<<<<<<<<<<<
+@EAS1_105:3:176:431:647
+ATCATGACTCTATCCCAAATTCCCAATTACGTCCT
++
+<<<<<<<<<<<<<<<<2<<<<<<<<6<<<<9<<6<
+@EAS1_105:3:176:431:647
+CCATCACCCAGTCCCTGCCCCATCTCTTGTAATCT
++
+<(9(<<<7;<<7<<<<<<<7<<<<<<7<<<<<<<<
+@EAS1_105:3:182:404:693
+ACCTCATACACACACATGGTTTAGGGGTATAATAC
++
+<<<<<<<<<<<<<<<<<<<<<<:::<6<;<94;77
+@EAS1_105:3:182:404:693
+GCGTCTCTACCACAGGGGGCTGCGCGGTTTCCCAT
++
+<;7;;4<<<<<<<7<<7<<<<<<<<<8<<<<<<<<
+@EAS1_105:3:232:364:583
+CAATTAATTGAGACTACAGAGCAACTAGGTAAAAA
++
+<<<<<<<<<<<<<<<<<<<<<<<<;<<<<<<<<<<
+@EAS1_105:3:232:364:583
+TCATTAATAAAGACATGAGTTCAGGTAAAGGGGTG
++
+;%;7;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS1_105:3:308:66:538
+CGCTTGTACTTCTAAATCTATAACAAAATTAAAAT
++
+996999;<9;<:<<<<<:<<7<<<<<<<<<<<<<<
+@EAS1_105:3:308:66:538
+TATAACCATCCTACTAAATACATATGCACCTAACA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<;<<<<<<<;<
+@EAS1_105:3:329:177:267
+CATGAGATTATTAGGAAATGCTTTACTGTCATAAC
++
+<<<<<<<<<<<<<<<<<<<<<<<<<9<<<<<<<9;
+@EAS1_105:3:329:177:267
+TACGTCCTATCTTCTTCTTAGGGAAGAACAGCTTA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS1_105:3:7:35:528
+TTTTTTTTTTGTTCTTTACTCTTTTTTTTTTTTTT
++
+<<<<<<<<<<5<<<(<<%<<-8<<<<<<<<<8<<<
+@EAS1_105:3:86:823:683
+ACTTTGATGCCCTCTTCTTCCAAAGATGAAACGCG
++
+<4<<<<<<<<:<<6<<7<<<8<<<<<<<<<<<<<<
+@EAS1_105:3:86:823:683
+CAGTTCTAAATATAGAAATTGAAACAGCTGTGTTT
++
+<<<<<<<<;<<<<<<<<<<<<<<<<<<<<;;9<<<
+@EAS1_105:6:134:853:558
+AATATAATTGTGTCCATGTACACACGCTGTCCTAT
++
+<<<<8<<<7<<<<;;<<<<<<<<<<<<<<<<<<<<
+@EAS1_105:6:134:853:558
+GGAACAGGGAGGTGCACTAATGCGCTCCACGCCCA
++
+==========================9=9=;<;<5
+@EAS1_105:6:162:594:858
+CTACCACAGGGGGCTGCGCGGTTTCCCATCATGAA
++
+90;<99;==99==;4=:========;=====;===
+@EAS1_105:6:162:594:858
+GTGTTCTCATCAACCTCATACACACACATGGTTTA
++
+<<<<<<<<<<<<<<<<<9<;<<<<<<<<<<3<<<;
+@EAS1_105:6:172:827:592
+AATTGTAAAAGTCAAAATTAAAGTTCAATACTCAC
++
+=;=======;==;===:==========;==9<<.3
+@EAS1_105:6:172:827:592
+TAGATTGGCAGAACAGATTTAAAAACATGAACTAA
++
+8<<<<;7;7<<<<;<<<<<;<<<<<<<<<<<<<<<
+@EAS1_105:6:23:885:274
+ACAAAGGAGGTCATCATACAATGATAAAAAGATCA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<4<;;<
+@EAS1_105:6:23:885:274
+CTACTACTCAATATATCCATGTAACAAATCTGCGC
++
+2+*27==;;==<<.;:<=<=<==============
+@EAS1_105:6:267:953:459
+ACCTTACAAGCCAGAAGAGATTGGATCTAATTTTT
++
+<<<<<<<<<9<<<<<<<<<<<<<<;<<<<<<<<<<
+@EAS1_105:6:267:953:459
+CATCACTAAACCAGTCCTATAAGAAATGCTCAAAA
++
+%<07<94========<<==================
+@EAS1_105:7:110:355:323
+ACCTTGAGAACCCCAGGGAATTTGTCAATGTCAGG
++
+<<<<<<<<<<<<<<<<<<<<<<<<;<<<<;;<<8;
+@EAS1_105:7:110:355:323
+CCCAATGGACCTGTGATATCTGGATTCTGGGAAAT
++
+6069;1<<;4<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS1_105:7:168:247:414
+AAAAGAATTGTAAAAGTCAAAATTAAAGTTCAATA
++
+<<<<<<<<<<<<<<<<*<<<<<<<<<;:6<<<<<;
+@EAS1_105:7:168:247:414
+TAAATTCCCCCACTTAAGAGATATAGATTGGCAGA
++
+,;;;,146<6;6<<8<<<<1<8<<<<<<<<<<;1<
+@EAS1_105:7:289:472:86
+ATGAACTTCTGTAATTGAAAAATTCATTTAAGAAA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;;;;
+@EAS1_105:7:45:462:455
+TCCCTGTCTTACTTCCAGCTCCCCAGACGGAACGC
++
+<<<<<<8<<<;<;<<<;<<<<<<<6;8&:80;733
+@EAS1_105:7:45:462:455
+TCTAGGGGAACAGGGAGGTGCACTAATGCGCTCCA
++
+62*<;;;;<<;<<9;;<<<<<<<<<<<<<<<<;<<
+@EAS1_105:7:57:722:347
+ACAACAGGAAGAAAAGGTCTTTCAAAAGGTGATGT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS1_105:7:57:722:347
+CGCGTAACTGCGCTCTCATTCACTCCAGCTCCCTG
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;;
+@EAS1_105:8:160:130:351
+CAAAAGAATTGTAAAAGTCAAAATTAAAGTTCAAT
++
+4<;;<;<<<-<<<<<<<<<<;;<<<<;<<<<<<<<
+@EAS1_105:8:160:130:351
+TGGATCTAATTTTTGGACTTCTTAAAGAAAAAAAA
++
+<<<<<<<<<<<<<<<;<<<<4<<<<<;<<<:<<:<
+@EAS1_105:8:179:119:876
+ATAAAAAGATCAATTCAGCAAGAAGATATAACCAT
++
+<<<<<<<7<<<<<<;;<<<<<<<<<<<<<<<<<<<
+@EAS1_105:8:179:119:876
+TTAAAAACATGAACTAACTATATGCTGTTTACCAG
++
+<<<<<<<7<<<<<<<8<<<6<<<<<<7<<<:0&<0
+@EAS1_105:8:24:718:322
+AACTCATTAATAATGTCATGAGTTCAGGTAAAGGG
++
+5:+:0;**&+<00&<&<<<5<28<<;;<83<<<<<
+@EAS1_105:8:24:718:322
+ACAATTAATTGAGACTACAGACCAATTATGTAAAA
++
+5/7<3+<;<1<<1<95<.&&.&&.<&)5)1)17<%
+@EAS1_105:8:254:617:73
+AACTATTTGAGGAAGTAATTGGGGAAAACCTCTTT
++
+<<:<<<9;<<<;;<:<-<<<<<<<<<<<<<<<<<<
+@EAS1_105:8:254:617:73
+GCAGAAGAAAGAGGTTCAGAACTTGAAGACAAGTC
++
+<<<<<<<<<<<<<<<<<<<<<<<<<;<<<6;:;4%
+@EAS1_105:8:256:404:584
+ACTGTCCTATGTACTTATCATGACTCTATCCCAAA
++
+&&326+23<3<<<+:<</<<8<<<:7:<<<<<<<<
+@EAS1_105:8:256:404:584
+GTTTCTGCCCCCAGCATGGTTGTACTGGGCAATAC
++
+<<<<<<<<<<<<<<<<<<<<<7<3;<:;;3:3:</
+@EAS1_105:8:96:720:940
+AAAGGAAATCCCATCAGAATAACAATGGGCTTCTC
++
+<<<<<<;<<<<<<<<<<;9<<8<<6<;:;<;;.;;
+@EAS1_105:8:96:720:940
+TAAGATAATTCATCATCACTAAACCAGTCCTATAA
++
+*<<<<;<<<9<<;,<;0<;<<<<<<<<<<<<<<<<
+@EAS1_108:1:111:796:737
+ATCATGACTCTATCCCAAATTCCCAATTACGTCCT
++
+<3<<<<<<<<<<<7<<<<<;<<<<<<<<<<<<<<<
+@EAS1_108:1:111:796:737
+CCCCAGCATGGTTGTACTGGGCAATACATGTGATT
++
+<<<<<<<<<<<<<<<:<<;7;<<<<993<4%:%<<
+@EAS1_108:1:131:518:588
+AAAATCAGCAAGAGAAAAGCATACAGTCATCTATA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<<1<<
+@EAS1_108:1:131:518:588
+ATAAATGAAGGGGAAATAAAGTCAAGTCTTTCCTG
++
+<.<<<<<<<<4<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS1_108:1:148:286:316
+AGAACTTCCCTGGAGGTCTGATGGCGTTTCTCCCT
++
+;::::;9/:<9<<<<;<<<<<<<<<<<<<<<<<<<
+@EAS1_108:1:148:286:316
+CCTCTGTCTTGATTTACTTGTTGTTGGTTTTCTGT
++
+<<<<<<<<+<<7<<<<<<<6<<<6<142<<<6<2<
+@EAS1_108:1:155:809:543
+AAATTTAACAAAAGTAAATAAAACACATAGCTAAA
++
+<<<+0<<<9<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS1_108:1:155:809:543
+TACATATGCACCTAACACAAGACTACCCAGATTCA
++
+<<<<<<<<<<<<<<<<7<;<<<<<<<<<<<1<;<;
+@EAS1_108:1:16:438:245
+TTGAATAAAAAGGGATTAAATTCCCCCACTTAAGA
++
+8*8<5'<77;;;;;7<7<<7-<;<<<;;<<<;;79
+@EAS1_108:1:189:863:213
+CTACTAGACCTAAGAGGGATGAGAAATTACCTAAT
++
+7:<7<<<<44;<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS1_108:1:189:863:213
+TATACTTATATCAGATAAAGCACACTTTAAATCAA
++
+<<<<<<<<<<<<<<<<<<<<;<<<;<<<<;7<9;<
+@EAS1_108:1:242:419:512
+AATGGGCTTCTCAGCAGAAACCTTACAAGCCAGAA
++
+<<8<<<<<<<<<<<<<<<<<<<<<<<<;<8<(<30
+@EAS1_108:1:242:419:512
+CTAAACCAGTCCTATAAGAAATGCTCAAAAGAATT
++
+*:<<<<9<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS1_108:1:277:194:143
+TGGGCTGTAATGATGCCCCTTGGCCATCACCCGGT
++
+<<<<<<<<<<<;<<<<<<<<<<9;<<<8</<<6<:
+@EAS1_108:1:277:194:143
+TTTTTAATGATTCCTCAATGTTAAAATGTCTATTT
++
+;<<;<<<;8;<0<7<<<<<<<<<<<<7<<<<<<<<
+@EAS1_108:1:328:614:638
+AAAGGTTGTTGGGAGATTTTTAATGATTCCTCAAT
++
+<<;;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS1_108:1:328:614:638
+ACTGGTTCTCTTGAAAGCTTGGGCTGTAATGATGC
++
+<<<<<<<<<<<<<<<<<<<<4/;<<9<<<<7<<*:
+@EAS1_108:1:33:779:821
+AATGTTATGCCCTGCTAAACTAAGCATCATAAATG
++
+<<730<<<<9<<<<;<<<<<<<<<<<<<<<<<<<<
+@EAS1_108:1:33:779:821
+TGAAGGAAAAAAATTCTAAAATCAGCAAGAGAAAA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<;<<
+@EAS1_108:1:49:911:980
+ACAATGTACAATATTCTGATGATGGTTACACTAAA
++
+<<<<<<<<<<;<<<<<<<8<<<<;<;<<88-<;33
+@EAS1_108:1:49:911:980
+GGGGAAAAAAGTAAACTCTCAAATATTGCTAGTGG
++
+44:7<<<<<<<<<<<<<;<<<<<<<<<<<<<<<<<
+@EAS1_108:1:65:787:74
+TGTAATGAAAACTATATTTATGCTATTCAGTTCTA
++
+44848=:1661/66==?:<=:?6><<<<1>><<<<
+@EAS1_108:2:102:543:160
+CAACAGGAACAAAACCTCATATATCAATATTAACT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<6<:<
+@EAS1_108:2:102:543:160
+CAGGTAAAGGGGTGGAAAAAGATGTTCTACGCAAA
++
+9==9=====;=====================<===
+@EAS1_108:2:116:966:193
+ATTAACATTACAACAGGAACAAAACCTCATATATC
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<<<
+@EAS1_108:2:116:966:193
+GACATGAGTTCAGGTAAAGGGGTGGAAAAAGATGT
++
+===================================
+@EAS1_108:2:170:326:433
+CTTCCCTGGAGGTCTGATGGCGTTTCTCCCTCGTC
++
+:44<<<<<<<<<<:6<<<<<<<:<<<<<<<<<<<<
+@EAS1_108:2:170:326:433
+TTGTTGGTTTTCTGTTTCTTTGTTTGATTTGGTGG
++
+=====<=9===:=<:==2=======2:===9==/5
+@EAS1_108:2:176:653:957
+AAAGGGGTGGAAAAAGATGTTCTACGCAAACAGAA
++
+===::=============<==<====<========
+@EAS1_108:2:176:653:957
+ACATTACAACAGGAACAAAACCTCATATATCAATA
++
+????????????<<???@<<<<<@<<<<<<<<<<<
+@EAS1_108:2:204:737:61
+AAAGTGAGAAGTTTGGAAAAACTATTTGAGGAAGT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<:<<9<+4:<0
+@EAS1_108:2:204:737:61
+TCAGCAAGAGAAAAGCATACAGTCATCTATAAAGG
++
+(7=72=;==2=====<===<<==============
+@EAS1_108:2:240:593:842
+ATCTGGATTCTGGGAAATTCTTCATCCTGGACCCT
++
+============<================9===:=
+@EAS1_108:2:240:593:842
+CATGGTTTAGGGGTATAATACCTCTACATGGCTGA
++
+*<<<;<<6<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS1_108:2:266:994:429
+ACAGGTTTTATAAAACAATTAATTGAGACTACAGA
++
+</<<<<<<<<<<<<<;<<<<<<<;<<<<<<<<<<<
+@EAS1_108:2:266:994:429
+TGAAGGGGAAATAAAGTCAAGTCTTTCCTGACAAG
++
+=====================9=======4===:=
+@EAS1_108:2:316:176:543
+ATGTCTATTTTTGTCTTGACACCCAACTAATATTT
++
+<<)/3<<<&<*<<0<<8<<82</5<<<<<88<<<<
+@EAS1_108:2:316:176:543
+CATCTCTTGTAATCTCTCTCCTTTTTGCTGCATCC
++
+====<=9===<<<=====9====<<=3==,96==9
+@EAS1_108:2:49:271:588
+CACATGGTTTAGGGGTATAATACCTCTACATGGCT
++
+<<<<<<<<<<<<<<5:<<<<<<:<<<<<<<:7%9<
+@EAS1_108:2:49:271:588
+GCTGCGCGGTTTCCCATCATGAAGCACTGAACTTC
++
+:0=:===:<===;;===;=================
+@EAS1_108:2:62:879:264
+AATGAAAACTATATTTATGCTATTCAGTTCTAAAT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<2<<
+@EAS1_108:2:62:879:264
+GGACGCTGAAGAACTTTGATGCCCTCTTCTTCCAA
++
+====:=<============================
+@EAS1_108:2:82:879:246
+AAGAGGGACGCTGAAGAATTTTGATGCCCTCTTCT
++
+<<<<<<<<<<<<<<<<<<&<<<77<<-<<<6<62<
+@EAS1_108:2:82:879:246
+ACAACTGTGAGCCATCACAATGAACAACAGGAAGA
++
+%+=661;&===:&==1<5======1==========
+@EAS1_108:2:85:580:481
+AAAAAAGTAAATAAAACACATAGCTAAAACTAAAA
++
+=)====77========8=3====3===========
+@EAS1_108:2:85:580:481
+CTAACACAAGACTACCCAGATTCATAAAACAAATA
++
+<<<<<<<<<<<<<:<<<<<<<<<<<<;<<<<6:<<
+@EAS1_108:3:216:988:883
+AAGCCAACACAATGAACAACAGGAAGAAAAGGTCT
++
+(=/1+=&:=&======<==<===============
+@EAS1_108:3:216:988:883
+AGAGGGACGCTGAAGAACTTTGATGCCCTCTTCTT
++
+<<<<<<<<<<<<8;<;88<;8;;;;828;8;8;;;
+@EAS1_108:3:24:319:429
+GTTATGCCCTGCTAAACTAAGCATCATAAATGAAG
++
+<<<<<<<<<<<<<<<<;<<<<<<<<1<<-6<<</<
+@EAS1_108:3:24:319:429
+TAATAAATACACACAAAAGTACAAAACTCACAGGT
++
+0%=3%=3====<=9=====89==93==9=6=====
+@EAS1_108:3:75:934:439
+AAGAGACTATTGCCAGATGAACCACACATTAATAC
++
+==7=:=========================<====
+@EAS1_108:3:75:934:439
+CCCATCATGAAGCACTGAACTTCCACGTCTCATCT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;
+@EAS1_108:3:82:356:253
+AGTTTCTGCCCCCAGCATGGTTGTACTGGGCAATA
++
+97;7<<;;<<<<<7;<<:<<<9<<;<<<9<<<<<<
+@EAS1_108:3:82:356:253
+GAAAGCTTTCAACGCTTCTAGCCATTTCTTTTGGC
++
+===================<========;===39=
+@EAS1_108:4:163:611:211
+TAAAGTCAACATGAAGGAAAAAAATTCTAAAATCA
++
+<<<<9<<<<:<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS1_108:4:163:611:211
+TGAGGAAAAAGAAAAAGTGAGAAGTTTGGAAAAAC
++
+============8===============;=6;;<;
+@EAS1_108:4:248:753:731
+TATGCTATTCAGTTCTAAATATAGAAATTGAAACA
++
+<<<<<<<<<<<8<<<<<<<<<<<<:<<<<&<:<.:
+@EAS1_108:4:248:753:731
+TGAAGAACTTTGATGCCCTCTTCTTCCAAAGATGA
++
+7;55;=,=89=====3===9=======9=======
+@EAS1_108:4:31:622:216
+ATTTAACAAAAGTAAATAAAACACATAGCTAAAAC
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<8<<96<7
+@EAS1_108:4:37:604:389
+ATGTTCTACGCAAACAGAAACCAAATGAGAGAAGG
++
+<<<<<<<<<3<<<<<4<<<<<9<2;949<;35:95
+@EAS1_108:4:37:604:389
+TCATAAAACAAATACTACTAGACCTAAGAGGGATG
++
+00;:;========9========<9========<==
+@EAS1_108:4:75:166:463
+GTGAGAAGTTTGGAAAAACTATTTGAGGAAGTAAT
++
+<<<<<==============================
+@EAS1_108:4:75:166:463
+TAACAATAGACTAAACCAAGCAGAAGAAAGAGGTT
++
+<<<<<<<<<<<<<<<<<<<<;<<<<<<<<<<<++3
+@EAS1_108:4:91:521:517
+CCACACTGGTTCTCTTGAAAGCTTGGGCTGTAATG
++
+8;8<4=:===7===9=============<======
+@EAS1_108:4:91:521:517
+CCCTGCAATTAATATAATTGTGTCCATGTACACAC
++
+<<<<<<<<<<<<<<<<9<<<<<<<<<<8<<;;;<<
+@EAS1_108:5:115:193:231
+GAAGAGATTGGATCTAATTTTTGGACTTCTTAAAG
++
+<<<<<<<<<<<<<<<<<<<<<<<7<<<<<<<<6<7
+@EAS1_108:5:115:193:231
+TATAAGAAATGCTCAAAAGAATTGTAAAAGTCAAA
++
+=========7===========<=============
+@EAS1_108:5:11:555:330
+CGCTTGTACTTCTAAATCTATAAAAAAATTAAAAT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<4<;<
+@EAS1_108:5:11:555:330
+GGAAAACAATTTGGTAATTTCGTTTTTTTTTTTTT
++
+6;6;9766+<<<<9:2=<===6=============
+@EAS1_108:5:175:149:296
+AAAAATTAACATTACAACAGGAACAAAACCTCATA
++
+=;==26==;==;================7======
+@EAS1_108:5:175:149:296
+AAGGGGAAATAAAGTCAAGCCTTTCCTGACAAGCA
++
+<<<<<<<<<<<<<<<<<<<49<<<<<<<<<<<<;4
+@EAS1_108:5:180:905:36
+CCTCCGTGTCCTCCCATCTGGCCTCGTCCACACTG
++
+6%%<;<662<<*;<<<8<<:<<<<<<<<<<<<<<;
+@EAS1_108:5:180:905:36
+TACTATGTTTCTTATCTGCACATTACTACCCTGCA
++
+==========8===;;=========;==77%41=;
+@EAS1_108:5:229:717:121
+ACTATGAAGAGACTATTGCCAGATGAACCACACAC
++
+=================<)=<4<0=.<<<71;41&
+@EAS1_108:5:229:717:121
+TTCTTCTGAGGGAAGAACAGCTTAGGTATCAATTT
++
+6;-;7<<(<<<<<8<18<7<<<<<<<<<;<<<<<<
+@EAS1_108:5:321:712:224
+AGATAAAGCACACTTTAAATCAACAACAGAAAAAT
++
+<<<<<<<<2<<<<<<<<<<<<<<<:<<<<(<<:<,
+@EAS1_108:5:321:712:224
+ATGAGAAATTACCTAATTGGTACAATGTACAATAT
++
+=;===7;===7=========;=:;=========;=
+@EAS1_108:5:89:942:84
+AAAACCTGTCAAACACGAATGTTATGCCCTGCTAA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<;
+@EAS1_108:5:89:942:84
+TACAAAACTCACAGGTTTTATAAAACAATTAATTG
++
+===================>=>>>==>>===>==>
+@EAS1_108:6:159:493:275
+ACAAAACTCACAGGTTTTATAAAACAATTAATTGA
++
+=====3=============================
+@EAS1_108:6:159:493:275
+TGCTGTTTACAAGAAACTCATTAATAAAGACATGA
++
+4949;<<<<<<<<<<<6<;<<<<;<<<<<*<<<<<
+@EAS1_108:6:165:464:123
+CATACACACACATGGTTTAGGGGTATAATACCTCT
++
+===============7==============8====
+@EAS1_108:6:165:464:123
+GTCTCTACCACAGGGGGCTGCGCGGTTTCCCATCA
++
+9;<)<<%<<9<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS1_108:6:222:579:961
+AGTCCTATAAGAAATGCTCAAAAGAATTGTAAAAG
++
+=58====;==8=======;================
+@EAS1_108:6:222:579:961
+CAGAAACCTTACAAGCCAGAAGAGATTGGATCTAA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<7<<:7;;;68
+@EAS1_108:6:71:187:824
+AGACAGACTTCATCAAGATATGTAGTCATCAGACT
++
+;===;======3==;==========4=;=7;;3;6
+@EAS1_108:6:71:187:824
+TCTAATTTTTGGACTTCTTAAAGAAAAAAAAACCT
++
+0040;<7<<<<0<7<<<;<7*<<<<<7<<771<<<
+@EAS1_108:6:73:735:329
+AAAGGGATTAAATTCCCCCACTTAAGAGATATAGA
++
+================;==;====;=;=======;
+@EAS1_108:6:73:735:329
+TAGCTATACTTATATCAGATAAAGCACACTTTAAA
++
+;;;9;<<7<<<<<<<<<<<<<<<<<<<2<<<<<<<
+@EAS1_108:6:77:48:860
+CTCTGTCTTGATTTACTTGTTGTTTGTTTTCTGTT
++
+=========;===========9==*;5=;=;=,7=
+@EAS1_108:6:77:48:860
+TAGATGAGAGAGAACTTCCCTGGAGGTCTGATGGC
++
+;8;8;<9<9<<<<<<<<<4<<<<<<<<<<<<<<<<
+@EAS1_108:6:94:294:387
+ACCATCATAAATACACACAAAAGTACAAAACTCAC
++
+779=53=9===;=:=;=========;=========
+@EAS1_108:6:94:294:387
+GAATGTTATGCCCTGCTAAACTAAGCATCATAAAT
++
+<<<<<<<;<<<<<<<<<:<<<<<<<<<<<<;)7;;
+@EAS1_108:6:95:235:746
+CTAAGCATCATAAATGAAGGGGAAATAAAGTCAAG
++
+==&=;===7=3===8======;=;8===8=====;
+@EAS1_108:6:95:235:746
+TCTAAAATCAGCAAGAGAAAAGCATACAGACATCT
++
+<<<<;<<<<<<<<79<<<<<<<<<<<<<<*;;;<9
+@EAS1_108:7:108:440:208
+CCCATCCTACTAAATACATATGCACCTAACACAAG
++
++35:486<<4<<<<<<<<<<<-<<<<<7<<)<<<-
+@EAS1_108:7:108:440:208
+TTCAGGTAAAGGGGAGGAAAAAGATGTTCTACGCA
++
+<<<;<<<<<<<<<</<<<<;<<<;<<;<;<64/:+
+@EAS1_108:7:222:538:267
+ATAATTGTGTCCATGTACACACGCTGTCCTATTTA
++
+<<<<<<<<<<<<<<<<<<<<<;<<<<74;;39%6+
+@EAS1_108:7:222:538:267
+TCTGGCCTCGTCCACACTGGTTCTCTTGAAAGCTT
++
+52/8-<<7<<;<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS1_108:7:266:556:252
+CCCATCTGGCCTCGTCCACACTGGTTCTCTTGAAA
++
+<<<<<<<<<<<<<<<<<;<<<<<<4;;<;;;<7;;
+@EAS1_108:7:266:556:252
+GATTTGGTGGAAGACATAATCCCACGCTTCCTATG
++
+.8558<72<(<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS1_108:7:82:926:112
+CAATGTCAGGGAAGGAGCATTTTGTCAGTTGCCAA
++
+<1:/<*6<<6<<<<<6<<<<<<4<<<<82<+<<<<
+@EAS1_108:7:82:926:112
+CTGCTGGCAAGCTAGAGTCCCATTTGGAGCCCCTC
++
+<;<<<<<<<<<5<<<<<<<<<<<<<<<;<<1:<4<
+@EAS1_108:8:118:440:850
+AATTGAAAAATTCATTTAAGAAATTACAAAATATA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<949<<<<
+@EAS1_108:8:129:477:427
+ATGGACCTGTGATATCTGGATTCTGGGAAATTCTT
++
+<<<<<<<<<<<<<<<<<<;;<<<<::<9<;<<;<<
+@EAS1_108:8:129:477:427
+TACACACACATGGTTTAGGGGTATAATACCTCTAC
++
+<<<9;<<9<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS1_108:8:19:929:765
+AAAAACATGAACTAACTATATGCTGTTTACAAGAA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<;77<
+@EAS1_108:8:19:929:765
+ATCAACAACAGTAAAATAAAACAAAGGAGGTCATC
++
+<3+<<;<<;<<<<<<<<<<<;<<<<<<<<<<<<<<
+@EAS1_93:1:131:946:353
+TCTCTTGAAAGCTTGGGCTGTAATGATGCCCCTTG
++
+<<:<<66<<<6<<4<<<:8<<<<<<<<<<<<<<<<
+@EAS1_93:1:131:946:353
+TGTACACACGCTGTCCTATGTACTTATCATGACTC
++
+<<<<<<<<<<<<<;<<<<;;<<<<<<<;<:52;<2
+@EAS1_93:1:179:629:513
+GTCAACATGAAGGAAAAAAATTCTAAAATCAGCAA
++
+<;,<<7<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS1_93:1:179:629:513
+GTCACAGGTATTCCTGAGGAAAAAGAAAAAGTGAG
++
+<<<<<<<<<<<<<<<;<;<<<<<<<<<<<<<;<<<
+@EAS1_93:1:20:635:509
+CAGCTTAGGTATCAATTTGGTGTTCTGTGTAAAGT
++
+<<<<<<<<<;<<<<;<<<;<;;;<<<;<<<<<<(8
+@EAS1_93:1:20:635:509
+TGCATCCCTGTCTTCCTCTGTCTTGATTTACTTGT
++
+50<59<<9<9<<<<<<<<<<<<<<<<<<<6<<<<<
+@EAS1_93:1:214:784:690
+AAATCCCATCAGAATAACAATGGGCTTCTCAGCGG
++
+<<<<<<<<<<<<<<<<<<<<<:<<<<<<<<<4<44
+@EAS1_93:1:214:784:690
+GATAATTCATCATCACTAAACCAGTCCTATAAGAA
++
+-<7<<7<:<<2<<<<;<<<<<;<<<<3<<<<<<<<
+@EAS1_93:1:216:381:608
+TAATTGTGTCCATGTACACTCGCTGTCCTATGTAC
++
+55<99<<<99;<;<<(<39&7<<<<<<<<<<<<<9
+@EAS1_93:1:216:381:608
+TTCTCACAGTTTCTGCCCCCAGCATGGTTGTACTG
++
+<<<<<<<<<<<<<<<<<<<<<<<<;;+<6:<;26;
+@EAS1_93:1:253:59:242
+CCCCATCTCTTGTAATCTCTCTCCTTTTTGCTGCA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<</<<9;<
+@EAS1_93:1:253:59:242
+TTTGTCTTGACACCCAACTAATATTTGTCTGAGCA
++
+<<<:<;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS1_93:1:264:988:663
+CGAGGGGAACAGGGAGGTGCACTAATGCGCTCCAC
++
+(%<:4<4<<7<<1-:<1766<66<<<<+<:<;8;<
+@EAS1_93:1:264:988:663
+TGGCTGATTATGAAAACAATGTTCCCCAGATACCA
++
+<<<<<<<<<<<1<4<<<4<<0<;<-<74*(<&51-
+@EAS1_93:1:92:213:217
+ACAGTCTAGATGAGAGAGAACTTCCCTGGAGGTCT
++
+<<<<<:<<<<<<<<<<<;<<<<<<<<<<<<<<<<<
+@EAS1_93:1:92:213:217
+TGCATCCCTGTCTTCCTCTGTCTTGATTTACTTGT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<4<
+@EAS1_93:2:173:995:93
+GCTGGAGGGAAGAGGGACGCTGAAGAACTTTGATG
++
+<(0<<9<<<7<<<<<<7<<<<<<<<<7<<<<<<<<
+@EAS1_93:2:173:995:93
+TAATGAAAACTATATTTATGCTATTCAGTTCTAAA
++
+<<<<<<<<<<<<<<<<<<<7:<<<<;:<:<<<<:7
+@EAS1_93:2:286:923:549
+TCAAATGAACTTCTGTAATTGAAAAATTCATTTAA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS1_93:2:30:466:652
+AAAAATGAACAGAGCTTTCAAGAAGTATGAGATTA
++
+<<<<<<<<<<<<<<<<<<<<<<<<;<<<4;7<<<7
+@EAS1_93:2:30:466:652
+AAGAGGCTAAAAGAATGCCAGGAAGATACATTGCA
++
+<<<<<;3;&<<<<<<<</6<<<<<<<<<<<<<<<<
+@EAS1_93:2:313:711:530
+ACATGAGTTCAGGTAAAGGGGTGGAAAAAGATGTT
++
+<7;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS1_93:2:313:711:530
+TAATTGAGACTACAGAGCAACTAGGTAAAAAATTA
++
++<<<<<<<<<<<<<<<<<<<<<<;<<<<<<<<<<:
+@EAS1_93:3:181:93:694
+ACTCATTAATAAAGACATGAGTTCAGGTAAAGGGG
++
+<4;8<<+<<:<<<<<<<<<<<:<<<<<<<<<<<<<
+@EAS1_93:3:181:93:694
+TTAATTGAGACTACAGAGCAACTAGGTAAAAAATT
++
+++<<<<<<;<<<<<<:;8<<;<<<5;<;<<<+<<<
+@EAS1_93:3:79:879:15
+AGACTACAGAGCAACTAGGTAAAAAATTAACATTA
++
+<;;5;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS1_93:3:79:879:15
+AGTCAAGTCTTTCCTGACAAGCAAATGCTAAGATA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<2<;<<1<
+@EAS1_93:4:160:896:275
+AAAACTATATTTATGCTATTCAGTTCTAAATATAG
++
+============<====<==<====<==<==;=:6
+@EAS1_93:4:160:896:275
+AGGGAAGAGGGACGCTGAAGAACTTTGATGCCCTC
++
+;;;9;<<<<<<;<;;<<<<<<<<<<<<<<;<<<<<
+@EAS1_93:4:321:271:138
+GTGTAAAGTCTCAGGGAGCCGTCCGTGTCCTCCCA
++
+<<<<<<<<<<<<<<<<<<<<<;9<<;<<;;<88;&
+@EAS1_93:4:321:271:138
+TTTGGTGGAAGACATAATCCCACGCTTCCTATGGA
++
+261:5969==9=:=<==<=================
+@EAS1_93:4:325:352:67
+ATAAAGTCAAGTCTTTCCTGACAAGCAAATGCTAA
++
+==================<========<=<;-===
+@EAS1_93:4:325:352:67
+TACAGAGCAACTAGGTAAAAAATTAACATTACAAC
++
+;<8<<<;;<<7<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS1_93:5:197:52:58
+AAATGAACAGAGCTTTCAAGAAGTATGAGATTATG
++
+<<<<<<<<<<<<<<<<<<9<<<<2<<<<<<;<<<<
+@EAS1_93:5:197:52:58
+TCTAAATGAAAGAGGCTCAAAGAATGCCAGGAAGA
++
+<7;;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS1_93:5:246:177:525
+CATCATAAATACACACAAAAGTAAAAAACTCACAG
++
+%<(4<2<<<<<:<;<:<<<<<<<<<<<<<<<<<<<
+@EAS1_93:5:246:177:525
+TCTTAAAGAAAAAAAAACCTGTCAAACACGAATGT
++
+<<<<<<<<<<<<<<<<<<<<<1<<<<<<;;;<8;;
+@EAS1_93:5:256:444:399
+CTGCTACTCAATATATCCATGTAACAAATCTGCGC
++
+;+549<:<.<<<<<<<;<<<<<<<<<<<<<<<<<<
+@EAS1_93:5:256:444:399
+GAAGATATAACCATCCTACTAAATACATATGCACC
++
+<<<<<<<<<<<<<<<<<<<<<<<<<;;<<<-;<<8
+@EAS1_93:5:292:122:666
+GGGAAGAACAGCTTAGGTATCAATTTGGTGTTCTG
++
+<;<;;<<<<<:<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS1_93:5:292:122:666
+TACTGTCATAACTATGAAGAGACTATTGTCAGATG
++
+<<<<<<6<<<<<<<<8;<<<<<<<<<<3&9+;;(;
+@EAS1_93:5:62:969:12
+TATAAAGGAAATCCCATCAGAATAACAATGGGCTT
++
+<<;<;<::<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS1_93:5:62:969:12
+TCTTGCTAGAGATTTAGACATCTAAATGAAAGAGG
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS1_93:5:66:372:343
+ATTACAAAATATAGTTGAAAGATCTAACAATAGAC
++
+<<<<<<<<<<8<<<<<6<<<8&8<<<<<58<:<::
+@EAS1_93:5:66:372:343
+TATTCCTGAGGAAAAAGAAAAAGTGAGAAGTTTGG
++
+;<1;89<<<<<;<9<<<<9<<<;8<9<;<<<<<;8
+@EAS1_93:6:132:717:233
+AGAGAACTTCCCTGGAGGTCTGATGGAGTTTCTCC
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS1_93:6:132:717:233
+TGTTGGTTTTCTGTTTCTTTGTTTGATTTGGTGGA
++
+<<<<<<<<<<<<;<<<<<<<<<<<7<<<<&-<4<1
+@EAS1_93:6:159:273:253
+TTAGTCTTGCTAGAGATTTAGACATCTAAATGAAA
++
+<<<<<<<<:<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS1_93:6:191:948:257
+AACTAATATTTGTCTGAGCAAAACAGTCTAGATGA
++
+:;;;;<<<<<<5<5<<<<<<<<7<<<<<<<<<<<<
+@EAS1_93:6:191:948:257
+CTTTTTGCTGCATCCCTGTCTTCCTCTGTCTTGAT
++
+:<<<<<<<<9<:<<<<<<:<<<<;<<<<8<<<<7<
+@EAS1_93:6:216:47:302
+AAAAAAAAACCTGTCAAACACGAATGTTATGCCCT
++
+<<<<<<<<<<<7<<<<<<<<<<<<+<<<<<//6;<
+@EAS1_93:6:216:47:302
+AATACTCACCATCATAAATACACACAAAAGTACAA
++
+<<;<8<:<6<<<;<<<<<<<;<<<<<<<<<<<<<<
+@EAS1_93:6:218:144:794
+GGGTGCATTGCTATGTTGCGGTCGCTTTGCCTCCT
++
+++(3:&)5<9035<3):-<53<+&&-+)<<&)&<6
+@EAS1_93:6:218:144:794
+TTTTTTTTTTTTTCTTTTCTCTTTTTTTTTTTTTT
++
+;92/;5:<6)+<5)67</9<&<&<<<:<<<57<<<
+@EAS1_93:6:238:514:194
+AAACTATTTGAGGAAGTAATTGGGGAAAACCTCTT
++
+<<6<<<<:9<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS1_93:6:238:514:194
+AATAGACTAAACCAAGCAGAAGAAAGAGGTTCAGA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<:<;<;<
+@EAS1_93:6:255:441:47
+AACAACAGTAAAATAAAACAAAGGAGGTCATCATA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<6<;:<;<
+@EAS1_93:6:255:441:47
+TGGTACAATGTACAATATTCTGATGATGGTTACAC
++
+;;7<;:<<<<<<<<<<;<<<<<<<<;<<<<<<<<<
+@EAS1_93:6:271:244:568
+ATGGACCTGTGATATCTGGATTCTGGGAAATTCTT
++
+;<<<<<<;<;<<<<<<<<<<;;<<<<<<<<<<<<<
+@EAS1_93:6:271:244:568
+CTTGCAACAACCTTGAGAACCCCAGGGAATTTGTC
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<.<<<<<<
+@EAS1_93:6:45:601:439
+AATGCTCAAAAGAATTGTAAAAGTCAAAATTAAAG
++
+<<<<;<<<<<<<<<<<<<<<<4<<<<9<<<<<<;;
+@EAS1_93:6:45:601:439
+ATAAAAAGGGATTAAATTCCCCCACTTAAGAGATA
++
+<8<<<<<<1<<<<<<<<)<<<<<<<<<<<<<<<<<
+@EAS1_93:7:14:426:613
+AGGGAGGGAGGGAAGAGGGACGCTGAAGAACTTTG
++
+:<<<<&<<<<<<<<<<<<<<6<<<<<<<<<<<<<<
+@EAS1_93:7:14:426:613
+GTAATGAAAACTATATTTATGCTATTCAGTTCTAA
++
+======;=;==========;;==3=;==-=<;<;<
+@EAS1_93:7:252:171:323
+GCTATTCAGTTCTAAATATAGAAATTGAAACAGCT
++
+;8<;<=3=6==:====;;======;==========
+@EAS1_93:7:270:995:918
+AAAATTCATTTAAGAAATTACAAAATATAGTTGAA
++
+<<<<<<<<<<<<<:<<<<<<8<8<8<<<<:<;4;4
+@EAS1_93:7:319:280:57
+AAAGGAAATCCCATCAGAATAACAATGGGCTTCTC
++
+<<<<<<<-<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS1_93:7:319:280:57
+TGCTAGAGATTTAGACATCTAAATGAAAGAGGCTC
++
+;==========;=====6;=========;=<;6;;
+@EAS1_93:8:13:325:483
+AAAAACATGAACTAACTATATGCTGTTTACAAGAA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<;
+@EAS1_93:8:13:325:483
+ATCATACAATGATAAAAAGATCAATTCAGCAAGAA
++
+;:;<;=:========;==========;========
+@EAS1_93:8:14:601:624
+AAAAGGTGATGTGTGTTCTCATCAACCTCATACAC
++
+1;;;;==5===.(=9=5=========8====;===
+@EAS1_93:8:14:601:624
+CTGCGCTCTCATTCACTCCAGCTCCCTGTCAACCC
++
+<<1<<<<<<<<<<<<<<<<<3<<::<<7<<1,<:(
+@EAS1_95:1:16:823:343
+AGACATAACCCCACGCTTCCTATGGAAAGGTTGTT
++
+<<<:<<<;+;<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS1_95:1:16:823:343
+TCCCATCTGGCCTCGTCCACACTGGTTCTCTTGAA
++
+================================4==
+@EAS1_95:1:196:533:921
+AAATGTGTTTATTACCAGAGGGATGGAGGGAAGAG
++
+=====1========8===:===7======971=3=
+@EAS1_95:1:196:533:921
+CCTGAGAGATTCTGCAGCCCAGATCCAGATTGCTT
++
+7<<<<7<<9<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS1_95:1:202:341:984
+GGAGGTCATCATACAATGATAAAAAGATCAATTCA
++
+<<<(<8&<92<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS1_95:1:202:341:984
+TGAACTAACTATATGCTGTTTACAAGAAACTCATT
++
+=========================4;========
+@EAS1_95:1:249:986:224
+CTTTTTGCTGCATCCCTGTCTTCCTCTGTCTTGAT
++
+=========5======7878===98==7=9==.-=
+@EAS1_95:1:249:986:224
+TATTTGTCTGAGCAAAACAGTCTAGATGAGAGAGA
++
+<<<3<;<;;<<;8<<<<<<<<<<<<<<<<<<<<<<
+@EAS1_95:1:261:504:780
+TCCCTGTCTTCCTCTGTCTTGATTTACTTGTTGTT
++
+<<<<<<<<<<<<<<<<<<<</2<<<9<<<5<<,<<
+@EAS1_95:1:261:504:780
+TTTGTCTGAGAAAAACAGTCTAGATGAGAGAGAAC
++
+80;8(;0==8+====;==49===============
+@EAS1_95:1:301:54:240
+AACAGGGAGGTGCACTAATGCGCTCCACGCCCAAG
++
+<<<<:<9<<<<:<<<<9<<<<<<690<<6</<(83
+@EAS1_95:1:301:54:240
+CCCTGCAATTAATATAATTGTGTCCATGTACACAC
++
+&..*3===1=========5.5==5===4====:5=
+@EAS1_95:1:77:589:741
+AGTAAAATAAAACAAAGGAGGTCATCATACAATGA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<:<
+@EAS1_95:1:77:589:741
+TGGTTACACTAAAAGCCCATACTTTACTGCTACTC
++
+8=;;==606;=========================
+@EAS1_95:2:142:353:398
+CAGGTAAAGGGGTGGAAAAAGATGTTCTACGCAAA
++
+===================================
+@EAS1_95:2:142:353:398
+GGTAAAAAATTAACATTACAACAGGAACAAAACCT
++
+=================================9=
+@EAS1_95:2:162:503:769
+AGAGGGACGCTGAAGAACTTTGATGCCCTCTTCTT
++
+========================:==========
+@EAS1_95:2:162:503:769
+AGGCTGCAACTGTGAGCCATCACAATGAACAACAG
++
+;:;1;=8=;:+=====;&==7==============
+@EAS1_95:2:198:691:595
+ACACACATGGTTTAGGGGTATAATACCTCTACATG
++
+==============&===============;7;=1
+@EAS1_95:2:198:691:595
+CATGAAGCACTGAACTTCCACGTCTCATCTAGGGG
++
+:=:;=;===========;=================
+@EAS1_95:2:211:954:174
+AAAGAAAAAACAAAAACTATGCTAAGTATTGGTAA
++
+====*=====6========================
+@EAS1_95:2:211:954:174
+AGACCTAAGAGGGATGAGAAATTACCTAATTGGTA
++
+===============================777=
+@EAS1_95:2:228:915:631
+AAGATATGTAGTCATCAGACTATCTAAAGTCAACA
++
+=================;==========4======
+@EAS1_95:2:228:915:631
+ATTATTAAAGAAAAAAAAACCTGTCAAACACGAAT
++
+&-))-*===/=========9====4==========
+@EAS1_95:2:278:918:892
+AGCCCAGCTCCAGATTGCTTGTGGTCTGACAGGCT
++
+=============:====================8
+@EAS1_95:2:278:918:892
+CCATCCCTGTCTTACTTCCAGCTCCCCAGAGGGAA
++
+=6=3=<===&=========================
+@EAS1_95:2:40:918:950
+AATATAATTGTGTCCATGTACACACGCTTTCCTTT
++
+=========,=9=====2=7===7=0==&=+3=-=
+@EAS1_95:2:40:918:950
+GTTCTCTTGAAAGCTTGGGCTGTAATGATGCCCCT
++
+=0=&&33======;=====.===============
+@EAS1_95:3:268:523:511
+ACACTGGTTCTCTTGAAAGCTTGGGCTGTAATGAT
++
+8<7<99<<<<<<<<<:<<<<<<4<<<<<<<<<<<<
+@EAS1_95:3:268:523:511
+TGTCCATGTACACACGCTGTCCTATGTACTTATCA
++
+<<<<<<<<<<<<<<<<<<<<;<<<<6<:9<<3<44
+@EAS1_95:3:303:970:243
+AACCTGTCAAACACGAATGTTATGCCCTGCTAAAC
++
+<<0+<<<,<4<:<:<<<<<<<<<<<::<<<<<<<<
+@EAS1_95:3:303:970:243
+CAGACTTCATCAAGATATGTAGTCATCAGACTATC
++
+<<<<<<<<<<<<<<<<<<<<;;<<<<<<<<<8<8<
+@EAS1_95:3:308:956:873
+ATAAAAATAAGTGTGTCCATGTACACACGCTGTCC
++
+91.97&9499&-1*98*19999839999.9&9799
+@EAS1_95:3:308:956:873
+CTCATCTAGGGGAACAGGGAGGTGCACTAATGCGC
++
+<<<<<<<<<<<<<;<;<;1<<<<<.<9<;<<<<+;
+@EAS1_95:4:174:157:573
+CAGAAACCAAATGAGAGAAGGAGTAGCTATACTTA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS1_95:4:174:157:573
+TAAAACAAATACTACTAGACCTAAGAGGGATGAGA
++
+8<<<<4<<<<<<<<;<<<<;<<<<<<<<<<<<<<<
+@EAS1_95:4:176:971:874
+TAAAATCAGAAGAGAAAAGCATACAGTCATCTATA
++
+<<<<<:<<<<<<<;<<<<<<<<<<<<<<<<<<<<<
+@EAS1_95:4:176:971:874
+TGAGGAAGTAATTGGGGAAAACCTCTTTAGTCTTG
++
+<<<<<<<<<<<<<:<;<<<<<<<<<<<<<5<<<<7
+@EAS1_95:4:184:17:636
+TACACACACATGGTTTAGGGGTATAATACCTCTAC
++
+8<89<<:<<<;;;<<<<<<<<<<<<<<<<<<<<<<
+@EAS1_95:4:184:17:636
+TTTTTTTTTTTTTTTTTTTTTTTTTTTTCACAGGT
++
+!!!!!!!!!!!!!!!!!!!!!!!!!!!77777777
+@EAS1_95:4:224:592:744
+GATATGTAGTCATCAGACTATCTAAAGTCAACATG
++
+6<6<<<<<<9+<6-<<<:<:<:<<<<<:<<<<<<<
+@EAS1_95:4:224:592:744
+TATGAGATTATGTAAAGTAACTGAACCTATGAGTC
++
+<<<<<<<<<<<<<<<<;<<<<<7<<<<<<<&<*<<
+@EAS1_95:4:238:124:196
+TTTTTTTTCTTTTCTCTTTTTTTTTTTTTTTTTTT
++
+<0<9.<5.5<<<<9<1<<5<<85<5<<<9<:<<<<
+@EAS1_95:4:61:631:567
+AAGAAGATATAACCATCCTACTAAATACATATGCA
++
+<<7<<<<<<<<</<<;<;<<<<<<<<<<<<<<<<<
+@EAS1_95:4:61:631:567
+CATTAATAAAGACATGAGTTCAGGTAAAGGGGTGG
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS1_95:4:66:179:118
+CCATGTACACACGCTGTCCTATGTACTTATCATGA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<:<<;<<6<<
+@EAS1_95:4:66:179:118
+TGGGCTGTAATGATGCCCCTTGGCCATCACCCAGT
++
+<<99<<<<<<<<<<<<<<<<<<<9<<<:<<<<<<<
+@EAS1_95:4:71:517:742
+AACTATTTGAGGAAGTAATTGGGGAAAACCTCTTT
++
+<<<<<<2<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS1_95:4:71:517:742
+AAGCAGAAGAAAGAGGTTCAGAACTTGAAGACAAG
++
+<<<<<<<<<<<<;<<<<<<<<<<<<<48:4<<<<3
+@EAS1_95:5:257:654:116
+TAACAATAGACTAAACCAAGCAGAAGAAAGAGGTT
++
+<<<<<<<<<<<<<<<<<<<<<<;:<<<<<<<<<88
+@EAS1_95:5:257:654:116
+TCCTGAGGAAAAAGAAAAAGTGAGAAGTTTGGAAA
++
+0+37<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS1_95:5:263:511:936
+CAAATAGGTAAAAAATTAACATTACAACAGGAACA
++
++<<%<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS1_95:5:263:511:936
+CAAGTCTTTCCTGACAAGCAAATGCTAAGATAATT
++
+<<<<<<<<<<<<<<<<<;<<<<<;<<:<:<<<<<<
+@EAS1_95:5:284:212:932
+CTTTAAATCAACAACAATAAAAAAAAACAAAGGAG
++
+<<9<<<<<<<<<<<<<&&<<<<5<<<<8<<<1:<:
+@EAS1_95:5:284:212:932
+TGATGATGGTTACGCTAAAAGTCCATGCTTTACTG
++
+82%<8:<-:<<:**:<-<<8<)/2/<:/<<<<<<<
+@EAS1_95:6:174:650:125
+AAGCATCATAAATGAAGGGGAAATAAAGTCAAGTC
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS1_95:6:174:650:125
+CAGGTTTTATAAAACAATTAATTGAGACTACAGAG
++
+===;===============================
+@EAS1_95:6:185:312:167
+CTGAAGAACTTTGATGCCCTCTTCTTCCAAAGATG
++
+===========================;855;===
+@EAS1_95:6:185:312:167
+TGGTCTGACAGGCTGCAACTGTGAGCCATCACAAT
++
+<<8:<8<<<<<<<<<;<<<<<<<<<<<<<<<<<<<
+@EAS1_95:6:194:696:490
+ACATTAATACTATGTTTCTTATCTGCACATTACTA
++
+========;======;==========8==:=====
+@EAS1_95:6:194:696:490
+TTCCACGTCTCATCTAGGGGAACAGGGAGGTGCAC
++
+<<<<<<<<<<<<<<<<<<<;5<<<<<:<1<8<<<8
+@EAS1_95:6:53:156:845
+ACACCCAACTAATATTTGTCTGAGCAAAACAGTCT
++
+171(*00,0;;&;7=77=;5;;(;1:=5=======
+@EAS1_95:6:53:156:845
+TTGTAATCTCTCTCCTTTTTGCTGCATCCCTGTCT
++
+<<<<<<8<<<.<<<<.6<<--<-<<<<<<<6<<<<
+@EAS1_95:6:87:734:888
+ATACCATCCCTGTCTTACTTCCAGCTCCCCAGAGG
++
+===========;8=========;;=;====;;3(;
+@EAS1_95:6:87:734:888
+TGCGCTCCACGCCCAAGCCCTTCTCACAGTTTCTG
++
+56<<86;:<<<4;<<<<<<<<<<<<<<<<<<<<<<
+@EAS1_95:7:155:530:532
+AGCAAGAAGATATAACCATCCTACTAAATACATAT
++
+===================================
+@EAS1_95:7:155:530:532
+TGCGCTTGTACTTCTAAATCTATAACAAAATTAAA
++
+:<<<><<8<<<<<><<<<<><<<<<<<<<<<<<<<
+@EAS1_95:7:280:607:113
+ATCCATGTAACAAATCTGCGCTTGTACTTCTAAAT
++
+===================;===;=====<=7=9:
+@EAS1_95:7:280:607:113
+GGAGTATAAATTGTTTTCCACTTTGGAAAACAATT
++
+18<-<<<<<<<<<<<<<8<<<<<<<<<<<<<<<<<
+@EAS1_95:7:282:817:710
+TGGAGGGAAGAGGGACGCTGAAGAACTTTGATGCC
++
+366=6;======8====:========;========
+@EAS1_95:7:282:817:710
+TTTGTAATGAAAACTATATTTATGCTATTCAGTTC
++
+<<<<<<<<<<<<<<<<<<<<<<<;:<<<<:8,<<8
+@EAS1_95:7:310:800:761
+AAAGCACACTTTAAATCAACAACAGTAAAATAAAA
++
+===========================+=======
+@EAS1_95:7:310:800:761
+CAATATTCTGATGATGGTTACACTAAAAGCCCATA
++
+1<<:<:<:<<<<:<<<<<<<<<;<<<<<<<<<<<<
+@EAS1_95:7:46:522:426
+AAAGACATGAGTTCAGGTAAAGGGGTGGAAAAAGA
++
+<<<<<:<<<<<<1/<<<<<<<<<<<<<<<<<<<<<
+@EAS1_95:7:46:522:426
+GGTAAAAAATTAACATTACAACAGGAACAAAACCT
++
+=======================:==;<===78==
+@EAS1_95:7:55:506:125
+CTTTACTGTCATAACTATGAAGAGACTACTGCCAG
++
+118%67;1;8,4:187<4>::1:818;;&::<>.;
+@EAS1_95:7:55:506:125
+TCTACCACAGGGGGCTGCGCGGTTTCCCATCATGA
++
+<<<<<<<<<;<9<;<<;558<<<<5(5*<<<<<51
+@EAS1_95:7:61:702:720
+ATTTGTCTGAGCAAAACAGTCTAGATGAGAGAGAA
++
+<<<4<4+0;<<:<<<<<<<<-<<<<<<<<<<<<<<
+@EAS1_95:7:61:702:720
+CTCTCCTTTTTGCTGCATCCCTGTCTTCCTCTGTC
++
+==============;=======&=========3:=
+@EAS1_95:7:74:866:49
+CATGAGTTCAGGTAAAGGGGTGGAAAAAGATGTTC
++
+====================9==91==<=6==;:=
+@EAS1_95:7:74:866:49
+CCAACCTACTAAATACATATGCACCTAACACAAGA
++
+:8<&<<<<7<<<<:<<<<<<8<5<<<<<<<<<<<<
+@EAS1_97:2:128:629:484
+AAAAAAGTAAATAAAACACATAGCTAAAACTAAAA
++
+:(::<</*;<<99<<<-<;<<<<4<<<<<<<<<<<
+@EAS1_97:2:128:629:484
+GATTCATAAAACAAATACTACTAGACCTAAGAGGG
++
+<<49<<<<<9<<<<99<<<<<<<<<<<<+<-)7))
+@EAS1_97:2:193:420:78
+ATAAATGAAGGGGAAATAAAGTCAAGTCTTTCCTG
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;;<<;
+@EAS1_97:2:193:420:78
+TTGAGACTACAGAGCAACTAGGTAAAAAATTAACA
++
+81<<;<9<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS1_97:2:59:882:980
+AATATAATTGTGTCCATGTACACACGCTGTCCTAT
++
+<<<<<<<<<8<<<<<9<+<<<9<<<1<<77889+6
+@EAS1_97:2:59:882:980
+GGGCTGTAATGATGCCCCTTGGCCATCACCCGGTC
++
+7339%<6<<<<<;<<9<<8<<<<;<<<<<<<<<<<
+@EAS1_97:2:96:419:327
+TACTAAATACATATGCACCTAACACAAGACTACCC
++
+<<<<<<<<<<<<<<<<<<<<<<;<<<<<<<;;9<9
+@EAS1_97:2:96:419:327
+TCTAAATCTATAACAAAATTAAAATTTAACAAAAG
++
+;1<<<<<9<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS1_97:2:9:203:653
+CACCCAACTAATATTTGTCTGAGCAAAACAGTCTA
++
+37))&<8<<<<<7<4<;<777<<:<<<<<<<<;<<
+@EAS1_97:2:9:203:653
+TCCCTGCCCCATCTCTTGTAATCTCTCTCCTTTTT
++
+<<<<<<<<<<<<<<<<<<<<<<::<9<<<<<;;;<
+@EAS1_97:3:147:423:584
+GAAGTAATTGGGGAAAACCTCTTTAGTCTTGCTAG
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<9;;96
+@EAS1_97:3:147:423:584
+GCATACAGTCATCTATAAAGGAAATCCCATCAGAA
++
+27<;<3<<<+<<;<<<;;-4<<<<<;<<<<<<<<<
+@EAS1_97:3:160:173:889
+TATGAGTCACAGGTATTCCTGAGGAAAAAGAAAAA
++
+<<<<<<<<<<<<<<<<<<<<;0<7<<;<<<;7<09
+@EAS1_97:3:160:173:889
+TCAAGATATGTAGTCATCAGACTATCTAAAGTCAA
++
+;)<</<8<<<<<<</<;<<<<;<<<<<<<<<<<<<
+@EAS1_97:3:277:144:848
+TAACAATAGACTAAACCAAGCAGAAGAAAGAGGTT
++
+<<<<<<<<<;<<<<<<<<<<<<<<<<<3<<9;;6;
+@EAS1_97:3:277:144:848
+TATTCCTGAGGAAAAAGAAAAAGTGAGAAGTTTGG
++
+<<<)63<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS1_97:3:73:292:429
+GAAAGCTTTCAACGCTTCTAGCCATTTCTTTTTGC
++
+<<<<<<<<<<7<<;<<<<<<<2<<<5<<<<<:%)<
+@EAS1_97:3:73:292:429
+TTCTCACAGTTTCTGCCCCCAGCATGGTTGTACTG
++
+;6;6;<<<<<;<<<<;<<<<<<<<7<<<<<<5<<<
+@EAS1_97:4:261:267:597
+GGGTAATAAAGTCAAGTCTTTCCTGACAAGCAAAT
++
+<<<<<<<<<;<<<<<7<<<<<<<<<:7<7<;44:;
+@EAS1_97:4:261:267:597
+TTGAGAATAAAGAGCAACTAGGTAAAAAATTAACA
++
+*-1<9<+1<+<<<<:<<;9<<<<<<<<<<<<<<<<
+@EAS1_97:4:274:287:423
+CTAAATCTATAAAAAAATTAAAATTTAACAAAAGT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<<
+@EAS1_97:4:274:287:423
+TTTTTTTTTTTTTTTTTCTCTTTTTTTTTTTTTTT
++
+7<<<<9<<9<<<.<<<<90-<<<<<<<<<<<<<<<
+@EAS1_97:4:290:121:79
+ATTGGTAAAGATGTGGGGAAAAAAGTAAACTCTCA
++
+<1<<:<<<<<<<;<<<<<<<<<<<<<<<<<<<<<<
+@EAS1_97:4:290:121:79
+TGATGATGGTTACACTAAAAGCCCATACTTTACTG
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<9<<<7;<<
+@EAS1_97:4:77:29:126
+ACAGGGAATTTGTCAATGTCAGGGAAGGAGCATTT
++
+()9;;<<<<<<<<<<5<<<7<<<<<<;<<<;7<<<
+@EAS1_97:4:77:29:126
+GCACAGGGGCTTAACCTCTGGTGACTGCCAGAGCT
++
+<<<<<<<<<<3<<<<<<<;;;7<;<<449<-:977
+@EAS1_97:4:83:731:540
+CTAGGTAAAAAATTAACATTACAACAGGAACAAAA
++
+;7<:+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS1_97:4:83:731:540
+TAAAGTCAAGTCTTTCCTGACAAGCAAATGCTAAG
++
+<<<<<<<<<;<<<<<<<<<<<<<:<7<*;&;<;;9
+@EAS1_97:5:154:952:558
+AAAGACTACCCAGATTCATAAAACAAATACTACTA
++
+%<<9;;<<;;;<<<<<;<<<<<<<<<<<<<<<<<<
+@EAS1_97:5:154:952:558
+GCAAACAGAAACCAAATGAGAGAAGGAGTAGCTAT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<:<:<
+@EAS1_97:5:219:174:684
+AAAAAAACTGTCAAACACGAATGTTATGCCCTGCT
++
+<<<<:;+9<<<;<<;<<<<<<<<<<<<<<<<<<<<
+@EAS1_97:5:219:174:684
+AGTCATCAGACTATCTAAAGTCAACATGAAGGAAA
++
+<<<<<<<<<<<8<8<<<7<<;<<<<<2<;&;;;;9
+@EAS1_97:5:28:538:148
+AAAAAAAAACCTGTCAAACACGAATGTTATGCCCT
++
+<<<<<<<<<<7;<<<<<<<<<<<<<<<<<<<<<<<
+@EAS1_97:5:28:538:148
+TCATCAAGATATGTAGTCATCAGACTATCTAAAGT
++
+<<<<<<<<<<<<<<<<<<<<<<:<<<<<<<+771;
+@EAS1_97:5:318:177:383
+TACTACCCTGCAATTAATATAATTGTGTCCATGTA
++
+;<<<<<<<<;<<<<<<<<<<<<<<<<<<7<;1'<;
+@EAS1_97:5:318:177:383
+TCTTGAAAGCTTGGGCTGTAATGATGCCCCTTGGC
++
+5:9;7;777<<7<<<<<<<<<<<<<<<<<<<<<<4
+@EAS1_97:5:84:927:843
+CCAGCATGGTTGTACTGGGCAATACATGAGATTAT
++
+<<<<<<<<<<<<<;9;;4;<<0<<7<<9<;<:<5<
+@EAS1_97:5:84:927:843
+TTACGTCCTATCTTCTTCTTAGGGAAGAACAGCTT
++
+588;<:<<<<<<<6<<<<;<<<:/<<3<:;<*<<<
+@EAS1_97:6:222:305:337
+TTTTTTTTTTTTTTTTTTCCCTTTTTTTTTTTTTT
++
+;;;;;<<';<<<<*;<<<78;7<7<;<<<<<<<<<
+@EAS1_97:6:308:667:658
+AAAGATCACTTCAGCAATAAGATATAACCATCCTA
++
+<9;;;45;&<;&.<5683;84+<;<;+8<;<<8;<
+@EAS1_97:6:308:667:658
+TAAAAACATGAACTAACTATATCCTTCTTACAATA
++
+9<96<<<;<96<<9<51<<<<<1:9++<9*%4;*5
+@EAS1_97:6:93:334:858
+CTGCCCCCAGCATGGTTGTACTTGGCAATACATGA
++
+<<<<<<<<;<<<<;;<<9<<<<&;&<<9<9;/;&;
+@EAS1_97:6:93:334:858
+GTACTTATCATGACTCTATCCCAAATTCCCAATTA
++
+;<;+;;<<;<<<<<;<<<<;;8<<<<8<<<<<<<<
+@EAS1_97:7:20:979:96
+GAAATTGAAACAGCTGTGTTTAGTGCCTTTGTTCA
++
+'9996;(:;-<;1<<<<=<<<<=<<<<<<<<<<<<
+@EAS1_97:7:264:642:506
+AAATATAGAAATTGAAACAGCTGTGTTTATTGTAT
++
+<<;<<<<<<;<<<;:;;:;;<<;<<<<;*+;*&.4
+@EAS1_97:7:264:642:506
+ACTTCATCCAAAGATGAAACGCGTAACTGCGCTCT
++
+&;(-/)-1&:<<9<25<<<<2<1<';8<<<:888<
+@EAS1_97:7:28:979:519
+AAAAAGTAAACTCTCAAATATTGCTAGTGGGAGTA
++
+<<<<<6<<<<<<<<<<<<<<<8<<<<<<<<6<<<<
+@EAS1_97:7:28:979:519
+CCCATACTTTACTGCTACTCAATATATCCATGTAA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;;;;9:
+@EAS1_97:7:63:727:203
+AAGTAATTGGGGAAAACCTCTTTAGTCTTGCTAGA
++
+<<;7<<;<<<<<<<<<;<<<<<<<<<<<<<<<<<<
+@EAS1_97:7:63:727:203
+AGTCTCTTATGAATTAACCCAGTCAGACAAAAATA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<;<<;
+@EAS1_97:7:9:648:712
+AAGAAGTATGAGATTATGTAAAGTAACTGAACCTA
++
+<9<;<<<<<<<;<<<<<8<<<<9<<;<<8)<:1<:
+@EAS1_97:7:9:648:712
+TACATTGCAAGACAGACTTCATCAAGATATGTAGT
++
+*;0;;;95<<<<7<<<;;<<<;;<<<<;<<<<<<<
+@EAS1_97:8:36:927:478
+AAAAGGTCTTTCAAAAGGTGATGTGTGTTCTCATC
++
+<<<<<<<<<<<<<<<<;<<<<<:<:<<<<8<9;<8
+@EAS1_97:8:36:927:478
+GACCCTACACGAATGCGTCTCTACCACAGGGGGCT
++
+,6;;;3;<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS1_99:1:17:595:863
+AAGCTACTCAATATATCCATGTAACAAATCTGCGC
++
+))55))+2&<<,:5<,0657<<<<:<:<:<<<<<<
+@EAS1_99:1:17:595:863
+ATAACCATCCTACTAAATACACATGCACCTAACTC
++
+:<4:<<1:<<<9<+<+1<%<7&&9-71<17)7</4
+@EAS1_99:1:187:715:521
+AAACCTCTTTAGTCTTGCTAGAGATTTAGACATCT
++
+<<<<<<<<<<<<<<<<<<<<:<<<<<<<;<<;<;;
+@EAS1_99:1:187:715:521
+GCATACAGTCATCTATAAAGGAAATCCCATCAGAA
++
+<7<:<9<<<<<<<<<;<<<<<<<<<<<<<<<<<<<
+@EAS1_99:1:34:649:318
+AAGAATAACAATGGGCTTCACAGCGGAACCCTTAC
++
+)<7<<3<<<<<<+<1<;<8&<<<<<<<<<<<<<<<
+@EAS1_99:1:34:649:318
+ATGAAAGAGGCTCAAAGAATGCCAGGAAGATACAT
++
+9<<3<<<9<<<<<<<<<7<<9<<0<<.0<*:77,;
+@EAS1_99:1:86:871:319
+GGCTTCTCAGCGGAAACCTTACAAGCCAGAAGAGA
++
+<<<<<:<<<:<:<<<<<<<<<<<<8<<:<1;<::)
+@EAS1_99:1:86:871:319
+TGCTAAGATAATTCATCATCACTAAACCAGTCCTA
++
+7;+1;<:<<<<<<<<;<<;<<9<<<<<<<<<<<<<
+@EAS1_99:2:152:355:962
+CAGTCATCTATAAAGGAAATCCCATCAGAATAACA
++
+&<.9.<;+;<;<<<<<<<<<<::<<:<<<<<<<<<
+@EAS1_99:2:152:355:962
+TATTTGAGGAAGTAATTGGGGAAAACCTCTTTAGT
++
+<;<<<<<;8<<<<<<<<<;5;;88<<3<<<<<&0;
+@EAS1_99:2:162:257:203
+AAAAAGATCAATTCAGCAAGAAGATATAACCATCC
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;;<<<
+@EAS1_99:2:162:257:203
+ATATCCATGTAACAAATCTGCGCTTGTACTTCTAA
++
+<;<;:<<;<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS1_99:2:188:782:483
+CTAAAATCAGCAAGAGAAAAGCATACAGTCATCTA
++
+7<<<<<<4<;;<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS1_99:2:188:782:483
+GAAGTAATTGGGGAAAACCTCTTTAGTCTTGCTAG
++
+<<<<<<<<<<<<<<<<<<<<<<<<<;<<<<7<;77
+@EAS1_99:3:118:851:285
+CCCAATTACGTCCTATCTTCTTCTTAGGGAAGAAC
++
+3+7<<<;<;<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS1_99:3:118:851:285
+TGGGCAATACATGAGATTATTAGGAAATGCTTTAC
++
+<<<<<<<<<<<<<<<<<<<<<<<;;<;<:<<<<;;
+@EAS1_99:3:135:543:760
+ATTTGCCTTCAGACCCTACACGAATGCGTCTCTAC
++
+;;.;;8;<8;<<32;<<<<<7<<<<<9<<<<<<<<
+@EAS1_99:3:135:543:760
+TTCAAAAGGTGATGTGTGTTCTCATCAACCTCATA
++
+<<<<;;<;<<<<<<<9<<<<<<<<<<<;<<<<5<:
+@EAS1_99:3:187:791:153
+AATACATGAGATTATTAGGAAATGCTTTACTGTCA
++
+:;55&<99<<1<;<<8<<;<<<<<<<<<<<<<<<<
+@EAS1_99:3:187:791:153
+TACACGAATGCGTCTCTACCACAGGGGGCTGCGCG
++
+<<<<<<<<<<<<<<<<<<<<<:+;;<;<88*6;68
+@EAS1_99:3:21:423:169
+ACTAAAAGCCCATACTTTACTGCTACTCAATATAT
++
+<<<<<;<<<<<<;<<<<<;;<<<<<<<<9+:5<;;
+@EAS1_99:3:21:423:169
+GGAGTATAAATTGTTTTCCACTTTGGAAAACAATT
++
+;376;0<<<<99<<<<<<-;<4<<<<<<<<<;<<<
+@EAS1_99:3:61:183:767
+GTAAAGTCTCAGGGAGCCGTCCGTGTCCTCCCATC
++
+6&.;;<3<363<<<<<<<<8<<<6<<<<3<<<<<<
+@EAS1_99:3:61:183:767
+TTGCCAGATGAACCACACCTTAATACTATGTTTCT
++
+<<<<<<<<<<;<<<9<9<+<<<8<<<<<<;8<<<<
+@EAS1_99:5:147:479:41
+CTCCTTTTTGCTGCATCCCTGTCTTCCTCTGTCTT
++
+;:;:;<::<:<<<<<:<<<<<<<<<<<<<<<<<<<
+@EAS1_99:5:147:479:41
+TACGTCCTATCTTCTTCTTAGGGAAGAACAGCTTA
++
+<<<<<<<<<<<<<<<<<<<<::6<<;<<<;;9;;6
+@EAS1_99:5:191:885:623
+TGCAAGACAGACTTCATCAAGATATGTAGTCATCA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<;;<<;;;;
+@EAS1_99:5:191:885:623
+TTAAAGAAAAAAAAACCTGTCAAACACGAATGTTA
++
+66<<<<<<<<<<<<<2<<<<9<<<<<<<<<<<<<<
+@EAS1_99:6:135:354:66
+GATACATTGCAAGACAGACTTCATCAAGATATGTA
++
+;;;;7<<<<:<<<<;<<<:<<<<<<<<<<<<<<<<
+@EAS1_99:6:135:354:66
+TATGAGATTATGTAAAGTAACTGAACCTATGAGTC
++
+<<<<<<<<<<<<<<<<;<<<<<<<<<<;<<2<;;;
+@EAS1_99:6:177:562:806
+ACAGTGTAGATGAGAGAGACCTTCCCTGGAGGTCT
++
+)2<9;'/:<5<<<:<<:<:&5:&<8,<<+:<&<<<
+@EAS1_99:6:177:562:806
+TGATTTACTTGTTGTTGGTTTTCTGTTTCTTTTTT
++
+<;<29<99<<;<<<9<20<9<<5;;<<<<<<<+.<
+@EAS1_99:6:181:392:500
+GGAAATCCCATCAGAATAACAATGGGCTTCTCAGC
++
+/5<<;(88<<<;<;<<6<<<<<7<<<<<<<7<<<<
+@EAS1_99:6:181:392:500
+TTAGTCTTGCTAGAGATTTAGACATCTAAATGAAA
++
+<<<<<:<<<2<<<<;5<<<<29+<<)</65<7.24
+@EAS1_99:6:63:48:631
+CAATACATGAGATTATTAGGAAATGCTTTACTGTC
++
+<<<<<<;<<7</<<<<<<;;;<<<;<;<<7;;);<
+@EAS1_99:6:63:48:631
+TCCTATCTTCTTCTTAGGGAAGAACAGCTTAGGTA
++
+;*:;;<2<<2779;:<<<<<<<<<<<<<<<<<<<<
+@EAS1_99:7:126:361:250
+AAAAAATTAACATTACAACAGGAACAAAACCTCAT
++
+<<<<<<;9<<<<<<<<<<<<<<;;;<<<;<664;;
+@EAS1_99:7:126:361:250
+TCTACGCAAACAGAAACCAAATGAGAGAAGGAGTA
++
+72:;7</<<<:<-7<<:<<<<<<<:<6<+:<<<<<
+@EAS1_99:7:171:196:287
+ATAACAATGGGCTTCTCAGCAGAAACCTTACAAGC
++
+<<<<<<<<<<<<<<<<<<<<<;6<<<<<<2:8<0:
+@EAS1_99:7:171:196:287
+ATAATTCATCATCACTAAACCAGTCCTATAAGAAA
++
+<;;;98;<;&<;;<<<<<<<;<<<<<<<<<<<<<<
+@EAS1_99:7:183:645:699
+GTGGCCCTCCCCCATTCCCTGCCCCATCTCTTGTA
++
+&)))2-&420<<<'--<6:6-<7<<<+:7<65<<<
+@EAS1_99:7:183:645:699
+TATCCCAAATTCCCAATTACGTCCTATCTTCTTCT
++
+<<9<9<<<<<<<<<;<<;<<*175;173<;;;<-/
+@EAS1_99:7:37:400:627
+ACATGAGATTATTAGGAAATGCTTTACTGTCATAA
++
+<<<<<<7+<<<<<<2615<<6<<<<5<<1<<;:74
+@EAS1_99:7:37:400:627
+TCTTAGGGAAGAACAGCTTAGGTATCAATTTGGTG
++
+474*;<<9<;<<<;<<:<<<<<<;<<<<<<;<<;<
+@EAS1_99:8:117:578:853
+AATGAACTTCTGTAATTGAAAAATTCATTTAAGAA
++
+<;<9<<<<<;<<;<<<<<<<<<<<,<98;<;;&92
+@EAS1_99:8:152:778:228
+ATCATAAATACACACAAAAGTACAAAACTCACAGG
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<;
+@EAS1_99:8:152:778:228
+ATTTAAAAACATGAACTAACTATATGCTGTTTACA
++
+<;;7=<<<<<<;<<<<<<<;<<<<<<<<<<<<<<<
+@EAS1_99:8:187:199:369
+TGAAAGAGGCTCAAAGAATGCCAGGAAGATACATT
++
+;<><<<<<<<<7<<<<<<<<=<<<<<<<<<<<<<<
+@EAS1_99:8:27:228:31
+AAATAAAACAAAGGAGGTCATCATACAATGATAAA
++
+<<<<<<<<<<<<<<<<<;9<:;<<<<<<75<<<<<
+@EAS1_99:8:27:228:31
+GGTTACACTAAAAGCCCATACTTTACTGCTACTCA
++
+99;;;<<<<<<:<<;<;<<;<<<<;<<;<<<<<<<
+@EAS1_99:8:99:756:130
+GAAGAAAAGGTCTTTCAAAAGGTGATGTGTGTTCT
++
+;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<6<<;<
+@EAS1_99:8:99:756:130
+GACCCTACACGAATGCGTCTCTACCACAGGGGGCT
++
+;;<<;;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS218_1:2:10:686:1024
+ACAAGAAACTCATTAATAAAGACATGAGTTCAGGT
++
+<:<<<<:<<<<<<<<<<:<:<<<<<<<<<<<5<<<
+@EAS218_1:2:10:686:1024
+CATACAATGATAAAAAGATCAATTCAGCAAGAAGA
++
+&<<<3<<<<<<<<<<<<<<7<<<<<<<<<<7<<<<
+@EAS218_1:2:15:1763:1143
+AAACAAATACTACTAGACCTAAGAGGGATGAGAAA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS218_1:2:15:1763:1143
+TGAGAGAAGGAGTAGCTATACTTATATCAGATAAA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS218_1:2:18:1498:1475
+CTTGGGCTGTAATGATGCCCCTTGGCCATCACCCG
++
+<<<<<7<<<<<<+<<-3<<3<:<2<1<<:<<<<<+
+@EAS218_1:2:18:1498:1475
+GAAAGGTTGTTGGGAGATTTTTAATGATTCCTCAA
++
+:<4<*7<<<<<<<:<<:<<<<<<<<<<<<<<<<<<
+@EAS218_1:2:19:752:816
+CGTCCGTGTCCTCCCATCTGGCCTCGTCCACACTG
++
+<<<<<<<<<<<<<<<<<<<8<7;<;<<767277;6
+@EAS218_1:2:19:752:816
+TTTGGTGGAAGACATAATCCCACGCTTCCTATGGA
++
++<<+<--/<<<<4<2<<<<45<<<:<<<<<<+<<<
+@EAS218_1:2:26:211:481
+ACAAAATATAGTTGAAAGCTCTAACAATAGACTAA
++
+<<<<<<<<<<<<<<<<<<<<<<<7<<<<<:<7<<<
+@EAS218_1:2:26:211:481
+CACAGGTATTCCTGAGGAAAAAGAAAAAGTGAGAA
++
+:<:<<<<<<9:5<<<<<<<<<<<<<<:<:<<<<<<
+@EAS218_1:2:40:1291:1045
+CTAACACAAGACTACCCAGATTCATAAAACAAATA
++
+*<<<9<<<<<<:0<9<<<<<<<;<<<<<<<<<<<<
+@EAS218_1:2:40:1291:1045
+GTAAAGGGGTGGAAAAAGATGTTCTACGCAACAAG
++
+<<<<<<<<<5<<5<<<<7<<<<<<<<<5<9<&%73
+@EAS218_1:2:64:1318:1711
+GGAAGAGGGACGCTGAAGAACTTTGATGCCCTCTT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS218_1:2:64:1318:1711
+TGAAAACTATATTTATGCTATTCAGTTCTAAATAT
++
+<<<<<<<<<<<<<<<<7<<<<<<<:<<<<<2<<<<
+@EAS218_1:4:14:1872:1521
+TCAAAGAATGCCAGGAAGATACATTGCAAGTCAGA
++
+7<<<<77<<<3<3<7.'<<<<<7<67<+.0%4*<4
+@EAS218_1:4:14:1872:1521
+TCATCAAAAACCTTACAAGCCAGAAGAGATTGGAT
++
+/1<%73&7<1<3577,<<<7/733<<<<<<<<1<<
+@EAS218_1:4:15:856:340
+CACGCTGTCCTATGTACTTATCATGACTCTATCCC
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS218_1:4:15:856:340
+CCCCAGCATGGTTGCACTGGGCAATACATGAGATT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<77<<
+@EAS218_1:4:28:315:310
+AAACTGTTCTCTTGAAAGCTTGGGCTGTAATGATG
++
++%,768<<:<:<2<<<<<<<<<<<<<<<<<<<<<<
+@EAS218_1:4:28:315:310
+CATGTACACACGCTGTCCTATGTACTTATCATGAC
++
+<<<<<<<<<<<<<<<<<<<<<:<+.<<.<+7<*17
+@EAS218_1:4:37:1626:862
+ACCCAACTAATATTTGTCTGAGCAAAACAGTCTAG
++
+:663<<3<<<<<<<<<<:<<<<7<<<<<<<<<<<<
+@EAS218_1:4:37:1626:862
+TCTCCTTTTTGCTGCATCCCTGTCTTCCTCTGTCT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS218_1:4:61:1369:440
+AAAGACATGATTTCAGGTAAAGGGGTGGAAAAAGA
++
+<<<<<<<<<<8<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS218_1:4:61:1369:440
+CAGGTTTTATAAAACAATTAATTGAGACTACAGAG
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<:<8
+@EAS218_1:4:62:561:531
+AGCTATACTTATATCAGATAAAGCACACTTTAAAT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS218_1:4:62:561:531
+TACTAGACCTAAGAGGGATGAGAAATTACCTAATT
++
+<<7<<<<:<8<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS218_1:4:71:832:743
+ACCCAGTCCCTGCCCCATCTCTTGTAATCTCTCTC
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS218_1:4:71:832:743
+CTATGTACTTATCATGACTCTATCCCAAATTCCCA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<*<<<<<<<
+@EAS218_1:4:73:42:1038
+AAACAGTCTAGATGAGAGAGAACTTCCCTGGAGGT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS218_1:4:73:42:1038
+TCTGTCTTGATTTACTTGTTGTTGGTTTTCTGTTT
++
+<<<<<<<<<<<<<<<<<<<<<<<:<<<<<.<<<<<
+@EAS218_1:4:75:555:1591
+TGAACTTCTGTAATTGAAAAATTCATTTAAGAAAT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<6<<<<
+@EAS218_1:6:49:905:27
+CCACAGGGGGCTGCGCGGTTTCCCATCCTGAAGCA
++
+<<;<.89<9.<2<9<:91+447.9,04&000(,+(
+@EAS218_1:6:49:905:27
+GAAGAGACTATTGCCAGTTGAACCACACATTAATA
++
+99515<<&<<6595-56%;86&<;<<<6<<<<6;<
+@EAS218_1:6:66:1282:1215
+GTGATGTGTGTTCTCATCAACCTCATACACACACA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<;;;
+@EAS218_1:6:66:1282:1215
+TTCAGACCCTACACGAATGCGTCTCTACCACAGGG
++
+::;<;<<<<:<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS218_1:6:77:1529:522
+AAAACCTGTCAAACACGAATGTTATGCCCTGCTAA
++
+<<;<<<<<<<<<<<4<<4<;;:;2:7<<<2*<;;8
+@EAS218_1:6:77:1529:522
+AAAGTTCAATACTCACCATCATAAATACACACAAA
++
+<<<;7;,<<<<<<.<,6<<6<<<<<<<;<<<<<<<
+@EAS218_1:6:88:1413:14
+AATGAAAGAGGCTCAAAGAATGCCAGGAAGATACA
++
+<<<<<<<<<<<;;;<<<<<<;<;;<<<<<<<<<<<
+@EAS218_1:8:13:1729:1844
+ATGAACTTCTGTAATTGAAAAATTCATTTAAGAAA
++
+<<<;;<;7<<<<4<<<<762;6<<<<<<<;6;618
+@EAS218_1:8:16:1081:1894
+AAGGTGATGTGTGTTCTCATCAACCTCATACACAC
++
+;5;;&<;<<<<<<<<;<;<<;<<<;<<<<<<<<<<
+@EAS218_1:8:16:1081:1894
+AGATGAAACGCGTAACTGGGCTCTCATTCACTCCA
++
+<<<<<<<<<<<<<<<<<<8<<<<;<<;<<<<<<<+
+@EAS218_1:8:26:785:882
+CAGTTTCTGCCCCAAGCATGGTTGTACTGGGCAAT
++
+<<<0<<<<<<<<<6,<<)<<<<<<<&<<0<<,<'<
+@EAS218_1:8:26:785:882
+TACTTATCATGACTCTATCCCAAATTCCCAATTAC
++
+<<&5&<<<<5.;5<'<<;.76<<<<<7<7<<<<<<
+@EAS218_1:8:61:1797:113
+CAGATAGCTTGTGGTCTGACAGGCTGCAACTGTGA
++
+<<0<<&<<<<;<<4;;3<;<:<<<<<<<<<<<<<<
+@EAS218_1:8:61:1797:113
+GGGATGGAGGGAAGAGGGACGCTGAAGAACTTTGA
++
+<<<<<<;<<<<;:<3<<<<;;<<<8<<;:<<;3<.
+@EAS218_1:8:70:445:1289
+CTAATTTTTGGACTTCTTAAAGAAAAAAAAACCTG
++
+<<<<<<<<<<2<<<<<<<<<<:<<<<<<<;;;;<:
+@EAS218_1:8:70:445:1289
+GAATTGTAAAAGTCAAAATTAAAGTTCAATACTCA
++
+<<<:<<<<<<<<<;<<<<<<<<<<<<<<<<<<<<<
+@EAS218_1:8:82:1540:77
+ATTGAGACTACAGAGCAACTAGGTAAAAAATTAAC
++
+<48;<;</;<<<<<<:<<0<<<<<<<<<<<<<<<<
+@EAS218_1:8:82:1540:77
+GAAATAAAGTCAAGTCTTTCCTGACAAGCAAATGC
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<;;<<<<:8
+@EAS218_1:8:90:706:1276
+AATTAACATTACAACAGGAACAAAACCTCATATAT
++
+<<<<<<<<<<<<<<<<<<<<<<;<<<<<<<<:<:<
+@EAS218_1:8:90:706:1276
+GTAAAGGGGTGGAAAAAGATGTTCTACGCAAACAG
++
+<;<<<<<<<;<<<<<<<<<<<<<;<<<<<<<<<<<
+@EAS218_4:1:34:1614:558
+CAACATGAAGGAAAAAAATTCTAAAATCAGCAAGA
++
+<<<<<<<<<<<7<<<<<8<<<<<<2<<<<<<<<<<
+@EAS218_4:1:34:1614:558
+GTCAAACACGAATGTTATGCCCTGCTAAACTAAGC
++
+<<9<<<<<<<<<<<<9<<<<<<<<<<<<<<<<<<<
+@EAS218_4:1:48:9:409
+CAGCTCCCTGTCACCCAATGGACCTGTGATATCTG
++
+<<<<+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS218_4:1:48:9:409
+GTTTAGTGCCTTTGTTCACATAGACCCCCTTGCAA
++
+<<<<<<<<<<<<<:<<<<<<<<<<<<<<<<<<<<<
+@EAS218_4:1:84:1505:1037
+GTCAACATGAAGGAAAAAAATTCTAAAATCAGCAA
++
+<<<<<<<<<<<<<<<<<:<<<<<<<<<<<<<<::)
+@EAS218_4:1:84:1505:1037
+TGCCCTGCTAAACTAAGCATCATAAATGAAGGGGA
++
+<<966<<7<<<<7<<<<9<<;<<<<<<<<<<<<<<
+@EAS218_4:1:9:206:901
+AGTCTAGATGAGAGAGAACTTCCCTGGAGGTCTGA
++
+<<<<<<<<<<<<<.<<<<<<<<<<<<<<<<<<<<<
+@EAS218_4:1:9:206:901
+CTTCCTCTGTCTTGATTTACTTGTTGTTGGTTTTC
++
+<<<<<<<<<<<<<<<<<<<<<<5<<5<<%%:<<<7
+@EAS218_4:3:12:630:707
+ATTTAAAAACATGAACTAACTATATGCTGTTTACA
++
+<:<<<<<<<;<<<<<9<<<<<<<<<<<<<<<<<<<
+@EAS218_4:3:12:630:707
+CACAAAAGTACAAAACTCACAGGTTTTATAAAACA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS218_4:3:39:1671:1928
+AGCCCATACTTTACTGCTACTCAATATATCCATGT
++
+<<<<<<<;<<<<;<<<<<4<<<;3<<<;<<<<<<<
+@EAS218_4:3:39:1671:1928
+CAAATATTGCTAGTGGGAGTATAAATTGTTTTCCA
++
+<<<<9<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS218_4:3:41:1281:1785
+ACTATCTAAAGTCAACATGAAGGAAAAAAATTCTA
++
+<6<<<6<<<<<<:<<6<:<<<<<<<<<<<<6<<<<
+@EAS218_4:3:41:1281:1785
+GGAAAAAGAAAAAGTGAGAAGTTTGGAAAAACTAT
++
+<<<<<<<<<<<<<<<<<<<<<;<<<;<<<<<<<8<
+@EAS218_4:3:65:85:1547
+AAATCAGCAAGAGAAAAGCATACAGTCATCTATAA
++
+<<<<<<;:<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS218_4:3:65:85:1547
+GTTTGGAAAAACTATTTGAGGAAGTAATTGGGGAA
++
+<<<<<<<<<<<<<<<<<<<<;<<<<<<<<<<:<<<
+@EAS218_4:5:41:118:1246
+ACCAGAGGGATGGAGGGAAGAGGGACGCTGAAGAA
++
+<<<<<<<<<<<<<<<<<<<<<<<</<<<<<<1<<(
+@EAS218_4:5:41:118:1246
+CTCCAGATTGCTTGTGGTCTGACAGGCTGCAACTG
++
+<<<<<<<<<<<<<<<+<<<<<<<<<<<<<<<<<<<
+@EAS218_4:5:63:875:1339
+CCCCAGATACCATCCCTGTCTTACTTCCAGCTCCC
++
+<<<<<<<<<<<<<<<<<<<<<<9<<<<<<<<<<<<
+@EAS218_4:5:63:875:1339
+GGGAACAGGGAGGTGCACTAATGCGCTCCACGCCC
++
+;;<<<:<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS218_4:7:71:31:1973
+AAAGAGGCTCAAAGAATGCCAGGAAGATACATTGC
++
+<<<<<7<:<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS218_4:7:72:1288:1211
+ATTGGTACAATGTACAATATTCTGATGATGGTTAC
++
+<);<:<<9<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS218_4:7:72:1288:1211
+GATAAAGCACACTTTAAATCAACAACAGTAAAATA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS218_4:7:85:923:726
+ACAAAATATAGTTGAAAGCTCTAACAATAGACTAA
++
+<<<<<<<7<<<<<<<<<<<55<<<9<*<<<991<4
+@EAS218_4:7:85:923:726
+GTAAAGTAACTGAACCTATGAGTCACAGGTATTCC
++
+<:<<<%3<<1<<86<<-<<<<<<<<<<<<6<<1<<
+@EAS218_4:7:87:964:826
+CACAGGGGGCTGCGCGGTTTCCCATCATGAAGCAC
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<1<<8;4;;<
+@EAS218_4:7:87:964:826
+TGAAGAGACTATTGCCAGATGAACCACACATTAAT
++
+)6<<<<<<:;<6<<::<<<;<<<<<<<<<<<<<<<
+@EAS218_4:7:89:1487:520
+CACGAATGCGTCTCTACCACAGGGGGCTGCGCGGT
++
+8<<<6/<<<<<<<<<:<<8<:<<3<<:668<86<3
+@EAS218_4:7:89:1487:520
+TATGAAGAGACTATTGCCAGATGAACCACACATTA
++
+4;;/<<<<<:<;<;<<<<<<<<<<<<<<<<<<<<<
+@EAS218_4:7:90:1873:89
+GAGATTCTGCAGCCCAGATCCAGATTGCTTGTGGT
++
+<<<<;49<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS218_4:7:90:1873:89
+GCATTTTGTCAGTTACCAAATGTGTTTATTACCAG
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<7<<<7
+@EAS219_1:1:22:490:2011
+ATAACAATGGGCTTCTCAGCGGAAACCTTACAAGC
++
+<7<<<<<<<<<<<<;<<<<<<<<<<<<<<<<<<<<
+@EAS219_1:1:22:490:2011
+GCTAGAGATTTAGACATCTAAATGAAAGAGGCTCA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS219_1:1:37:1004:1136
+CCAGGGAATTTGTCAATGTCAGGGAAGGAGCATTT
++
+<<<<<<<<<<<<<<;<<<;<<<<<:<<;;369<<<
+@EAS219_1:1:37:1004:1136
+GTCACCCAATGGACCTGTGATATCTGGATTCTGGG
++
+</8<<<<7<+<<<<<<<,<<<<<<<<<6<<<<1<<
+@EAS219_1:1:44:1466:425
+GTCCGTGTCCTCCCATCTGGCCTCGTCCACACTGG
++
+6-<<9<<:<<;<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS219_1:1:44:1466:425
+TTATCTGCACATTACTACCCTGCAATTAATATAAT
++
+<<<<<<<<<<<<<<<<<<<<<;<<<<<<;<<<<<<
+@EAS219_1:1:50:257:341
+AAATTAACATTACAACAGGAACAAAACCTCATATA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<7<6<<<<
+@EAS219_1:1:50:257:341
+TGAGTTCAGGTAAAGGGGTGGAAAAAGATGTTCTA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS219_1:1:5:497:687
+AAGAAAAGGTCTTTCAAAAGGTGATGTGTGTTCTC
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS219_1:1:5:497:687
+TTGCCTTCAGACCCTACACGAATGCGTCTCTACCA
++
+<8<<8<<<;<<<<<;<<<<<<<<<<<<<<<<<<<<
+@EAS219_1:1:60:1420:660
+AATGCTAAGATAATTCATCATCACTAAACCAGTCC
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<;<<<8<<<<
+@EAS219_1:1:60:1420:660
+GTAAAAAATTAACATTACAACAGGAACAAAACCTC
++
+99<<<<<<<<<<;<<<<<<<<<<<<<<<<<<<<<<
+@EAS219_1:1:63:28:1549
+AAAAAGTAAACTCTCAAATATTGCTAGTGGGAGTA
++
+<<<<<<<<<:<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS219_1:1:63:28:1549
+TACAATATTCTGATGATGGTTACACTAAAAGCCCA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<7;<<<<7
+@EAS219_1:1:67:191:668
+ACTATGAAGAGACTATTGCCAGATGAACCACACCT
++
+<<<<<<<<<<<<<<<<<6<<;<;<;<<<<<<6;%2
+@EAS219_1:1:67:191:668
+CCAATTACGTCCTATCTTCTTCTTAGGGAAGAACA
++
+<<<<<7<<7<<<<<<<;<<<<<<<<<<<<<<<<<<
+@EAS219_1:3:11:706:1030
+ATCTCTTGTAATCTCTCTCATCTTTGCTGCATCCC
++
+<<<2<<2<<<<<<<<<<<<0<&<<<+<:2<4<<):
+@EAS219_1:3:11:706:1030
+ATGTCTATTTTTGTCTTGACACCCAACTAATATTT
++
++<5069+9<<<<+<;<<<<;<<77<7<<;<<;<<<
+@EAS219_1:3:33:1168:1762
+AGATTGCTTGTGGTCTGACAGGCTGCAACTGTGAG
++
+<<<<<<<<<<<<<<<<;<<;<;<<<<<<<<:;2::
+@EAS219_1:3:33:1168:1762
+GTCTTACTTCCAGCTCCCCAGAGGGAAAGCTTTCA
++
+79<9;3<<<4<<<97<;;<<<<<<<<<<<<<<<<<
+@EAS219_1:3:4:1620:413
+CATCACAATGAACAACAGGAAGAAAAGGTCTTTCA
++
+<<<<<<<<<<6<<<6<<<;<6<9-1<;<&66<<<2
+@EAS219_1:3:4:1620:413
+TCTAGCCATTTCTTTTGGCATTTGCCTTCAGACCC
++
+-<<<7<<<<<<<<<;<<<<<<<<<<<<<<<<<<<<
+@EAS219_1:3:62:603:1552
+AATTTGGTGTTCTGTGTAAAGTCTCAGGGAGCCGT
++
+8::;:<<6<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS219_1:3:62:603:1552
+GAACCACACATTAATACTATGTTTCTTATCTGCAC
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<9<;<
+@EAS219_1:3:88:465:1877
+AAAGCACACTTTAAATCAACAACAGTAAAATAAAA
++
+<<<<<<<<<<;<<<<<<<<<<<<<<<<7<<<<<<<
+@EAS219_1:3:88:465:1877
+TAAGAGGGATGAGAAATTACCTAATTGGTACAATG
++
+<<<<<<<:<<<<<<<<:<<<<<<<<<<<<7;<<<<
+@EAS219_1:3:90:219:528
+ACGAATGTTATGCCCTGCTAAACTAAGCATCATAA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<7<<9
+@EAS219_1:3:90:219:528
+GTACAAAACTCACAGGTTTTATAAAACAATTAATT
++
+;:<5<<<<<<;<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS219_1:5:5:259:250
+GTCTCTTATGAATTAACCCAGTCAGACAAAAATAA
++
+<<<<<<<<<<<<<<<<<<<<;<<<;5<<5<;7<::
+@EAS219_1:5:5:259:250
+TATTTGAGGAAGTAATTGGGGAAAACCTCTTTAGT
++
+8<83;<<<<<<<<<<5<<<<<<<<<<<<<<<<<<<
+@EAS219_1:5:6:1067:91
+CTTGACACCCAACTAATATTTGTCTGAGCAAAACA
++
+3<;<<:;9;<<7;;<;<<<;<<<;<<<<<<<<<<<
+@EAS219_1:5:6:1067:91
+CTTTTTGCTGCATCCCTGTCTTCCTCTGTCTTGAT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<:<<<:8<<
+@EAS219_1:7:16:1343:1621
+AAATTCTAAAATCAGCAAGAGAAAAGCATACAGTC
++
+;<<9;7=====;;==<==================<
+@EAS219_1:7:16:1343:1621
+AAGTGAGAAGTTTGGAAAAACTATTTGAGGAAGTA
++
+<<<<<<<<8<<<<;<<<;<;<<<<<<<:;4;71:;
+@EAS219_1:7:18:571:1110
+GAGGTGCACTAATGCGCTCCACGCCCAAGCCCTTC
++
+7<<<<<<<<<<<<;<<<<<<<<<<<<788<<<;6<
+@EAS219_1:7:18:571:1110
+TAATATAATTGTGTCCATGTACACACGCTGTCCTA
++
+9<<;<;==;;=;=<;<===================
+@EAS219_1:7:20:1444:328
+AAAAGATGTTCTACGCAAACAGAAACCAAATGAGA
++
+<<<<;<<<<<<<<;<<<<<<<<;<<<<<;<;;8:7
+@EAS219_1:7:20:1444:328
+TACTAAATACATATGCACCTAACACAAGACTACCC
++
+9<3<<==;=<===;=<=====<<===========<
+@EAS219_1:7:35:392:2042
+ATAAATCTATAAAAAAATTAAAATTTAACAAAAGT
++
++<<<<</<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS219_1:7:35:392:2042
+TAACACAAGACTACCCAGATTCATAAAACNAATAC
++
+======;==========<<=======7=;!<7;;;
+@EAS219_1:7:50:1339:1154
+CATCTCTTGTAATCTCTCTCCTTTTTGCTGCATCC
++
+==========<<==============;==7<;<<;
+@EAS219_1:7:50:1339:1154
+GTCTTGACACCCAACTAATATTTGTCTGAGCAAAA
++
+7;7;8;<5<:86<<;<<<<<<<<<<;<<<<<<<<<
+@EAS219_1:7:62:1076:540
+CCCCCACTTAAGAGATATAGATTGGCAGAACAGAT
++
+<<<<<<<<<<;<<<<<<<<<<<<<<<<;;<<;<7;
+@EAS219_1:7:62:1076:540
+TAAATCAACAACAGTAAAATAAAACAAAGGAGGTC
++
+6<<;:+=====5=:6===================2
+@EAS219_1:7:94:1655:1921
+AAAAGCATACAGTCATCTATAAAGGAAATCCCATC
++
+<<<<;:===<==;<==<;================;
+@EAS219_1:7:94:1655:1921
+TTTGGAAAAACTATTTGAGGAAGTAATTGGGGAAA
++
+<<<8<<<<<<<<<8<<8;8<;<;<;;<<9+868<;
+@EAS219_FC30151:1:18:1418:237
+CCTTGAGAACCCCAGGGAATTTGTCAATGTCAGGG
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<9<7<
+@EAS219_FC30151:1:18:1418:237
+CTGGGAAATTCTTCATCCTGGACCCTGAGAGATTC
++
+<<:<<<<<<<<:<<<<<<<<<:<<<<<<<<<<<<:
+@EAS219_FC30151:1:53:140:421
+AACCAAATGAGAGAAGGAGTAGCTATACTTATATC
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS219_FC30151:1:53:140:421
+GATTCATAAAACAAATACTACTAGACCTAAGAGGG
++
+<<<<:<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS219_FC30151:1:54:436:1452
+AAGACAAGTCTCTTATGAATTAACCCAGTCAGACA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<:<<<;<<<
+@EAS219_FC30151:1:54:436:1452
+AGGAAGTAATTGGGGAAAACCTCTTTAGTCTTGCT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS219_FC30151:1:55:8:1412
+ATATAATTGTGTCCATGTACACACGCTGTCCTATG
++
+<<<<<<<<<<<<:<<<<<<<<<<<<<<<<<<<<<<
+@EAS219_FC30151:1:55:8:1412
+GCCCAAGCCCTTCTCACAGTTTCTGCCCCCAGCAT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS219_FC30151:1:76:34:691
+ATATATCAATATTAACTTTGAATAAAAAGGGATTA
++
+<<<<<<16<<<<<916<<<499<966161919<<<
+@EAS219_FC30151:1:88:1454:418
+CCAGGAAGATACATTGCAAGACAGACTTCATCAAG
++
+:<<:<<<<<<<<<<<::::<:<:<9<5<<<<<<8:
+@EAS219_FC30151:1:88:1454:418
+GAAGAGATTGGATCTAATTTTTGGACTTCTTAAAG
++
+<<<<<<<<<<6<96<<<1911<<<1<<<<<<<<<1
+@EAS219_FC30151:3:13:674:1717
+AGAAAAGCATGCAGTCATCTATAAAGGAAATCCCA
++
+<<<<<<<<<<%<<<<<<<<<<<<<<<<<<<;:;;;
+@EAS219_FC30151:3:13:674:1717
+TAAAGTCAAGTCTTTCCTGACAAGCAAATGCTAAG
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS219_FC30151:3:40:1128:1940
+CCCCTTACAACAACCTTGAGAACCCCAGGGAATTT
++
+<<<:///77:<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS219_FC30151:3:40:1128:1940
+CCGAGTCACGGGGTTGCCAGCACAGGGGCTTAACC
++
+<<<<<<<<<<<<<<<<<<<;<<5;;<<<9;;;;7:
+@EAS219_FC30151:3:55:74:1040
+CTACCACAGGGGGCTGCGCGGTTTCCCATCATGAA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<:<<
+@EAS219_FC30151:3:55:74:1040
+GGAAATGCTTTACTGTCATAACTATGAAGAGACTA
++
+;;;;;<<:<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS219_FC30151:3:73:1458:1337
+AAATGAAGGGGAAATAAAGTCAAGTCTTTCCTGAC
++
+<<<<<;;;<<<<<<<<<<<<<<<<<<<;<<7;;;;
+@EAS219_FC30151:3:73:1458:1337
+AGGTAAAAAATTAACATTACAACAGGAACAAAACC
++
+<</<<<<<<<6:<::<<<1<<:<<<<<<<<<<<<<
+@EAS219_FC30151:3:81:1723:1820
+ATGAGAGAGAACTTCCCTGGAGGTCTGATGGCGTT
++
+;6;;;<<<<<<<<<<<2<<<<<<<<<<<<<<<<<<
+@EAS219_FC30151:3:81:1723:1820
+CATCCCTGTCTTCCTCTGTCTTGATTTACTTGTTG
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<:<<:
+@EAS219_FC30151:3:90:1906:1528
+CACAGGTATTCCTGAGGAAAAAGAAAAAGTGAGAA
++
+:<<<<<<<<<3:<<<<<<<<<<<<<<<<<<<<<<<
+@EAS219_FC30151:3:90:1906:1528
+TTACAAAATATAGTTGAAAGCTCTAACAATAGACT
++
+<<<<<<<<<<<<<<<:<<<:<<<<;<<<<<;:7:;
+@EAS219_FC30151:3:9:1595:1826
+ACTAATATTTGTCTGAGCAAAACAGTCTAGATGAG
++
+;76;;6:9<9<963;<<7<<<<<<<;<;<<<<<<<
+@EAS219_FC30151:3:9:1595:1826
+ATCTCTCTCCTTTTTGCTGCATCCCTGTCTTCCTC
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS219_FC30151:5:29:817:854
+AGGGGCTTAACCTCTGGTGACTGCCAGAGCTGCTG
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS219_FC30151:5:29:817:854
+GTTCTCAAGGTTGTTGCAAGGGGGTTTATGTGAAC
++
+<<<<<<<<<<<<<<<1..;:;;;;1%407)07&7.
+@EAS219_FC30151:5:54:1351:910
+ACTAAAAGCCCATACTTTACTGCTACTCAATATAT
++
+<<<<<<8<<<<<<<<<<<<<<<<<<<<<<18<<:<
+@EAS219_FC30151:5:54:1351:910
+ACTCTCAAATATTGCTAGTGGGAGTATAAATTGTT
++
+<7<7;;<<<<<;<<;;<<;<<<<<<<<<<<<<<;<
+@EAS219_FC30151:5:63:424:1643
+GACCCTACACGAATGCGTCTCTACCACAGGGGGCT
++
+9+<<<+7<<<<<<<<<<<<<<<<<8<<<<<<<<<<
+@EAS219_FC30151:5:63:424:1643
+GGTCTTTCAAAAGGTGATGTGTGTTCTCATCAACC
++
+;;<<<<<<;<<<<<<<<<<5;9;<<<<<<<<<<;<
+@EAS219_FC30151:5:6:1243:981
+ATGAAGGGGAAATAAAGTCAAGTCTTTCCTGACAA
++
+<;<;;<<<;3;;3<<<;<<;<7%<<<.1<<<..<3
+@EAS219_FC30151:5:6:1243:981
+TTACCTAGTTGCTCTGTAGTCTCAATTAATTGTTT
++
+<<<<8<<8<<<<2<<<<<<<<8<55<<8*<<8<<<
+@EAS219_FC30151:5:70:348:972
+GAGAGAACTTCCCTGGAGGTCTGATGGCGTTTCTC
++
+<99<-7<<7<<<87<<<)<<<<<<8<<<<<<<<<<
+@EAS219_FC30151:5:70:348:972
+TCTTCCTCTGTCTTGATTTACTTGTTGTTGGTTTT
++
+<.<<3+.7<<7<<:78:<<7<:<7:<3<<7.:::<
+@EAS219_FC30151:5:72:1426:1883
+ACATAATCCCACGCTTCCTATGGAAAGGTTGTTGG
++
+;9<;<;0<;<;<<<<;<<<;:<<<<<<<<<<<<<<
+@EAS219_FC30151:5:72:1426:1883
+CATCTGGCCTCGTCCACACTGGTTCTCTTGAAAGC
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<:<
+@EAS219_FC30151:7:11:1261:1200
+AAAAAAAACCTGTCAAACACGAATGTTATGCCCTG
++
+<<<<<<<:<<6<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS219_FC30151:7:11:1261:1200
+TTGCAAGACAGACTTCATCAAGTTATGTAGTCATC
++
+<<<<<<<<<<<;<<<<<<<<;<<<;<:<<8<<:<<
+@EAS219_FC30151:7:51:1429:1043
+TATTTGTAATGAAAACTATATTTATGCTATTCAGT
++
+9<5<<<<<<<<<<<<<9<<<9<<<<<<<<<<<<<<
+@EAS219_FC30151:7:87:1289:83
+ACATGAAGGAAAAAAATTCTAAAATCAGCAAGAGA
++
+<<<<<<<<<<<<<<<<<<<<<;<<<<<;<<<<<<:
+@EAS219_FC30151:7:87:1289:83
+ATGCCCTGCTAAACTAAGCATCATAAATGAAGGGG
++
+<<<::<<<:<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS219_FC30151:7:94:1440:2016
+AACCTGTCAAACACGAATGTTATGCCCTGCTAAAC
++
+<<<<<<<<<<<<<<<<<<<;<<;;;<<:<8:::75
+@EAS219_FC30151:7:94:1440:2016
+CACAAAAGTACAAAACTCACAGGTTTTATAAAACA
++
+:<8<<<<9<<9<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS220_1:2:11:1274:1230
+TGAGCAAAACAGTCTAGATGAGAGAGAACTTCCCT
++
+.<<<<<<<<<<<<<<<<5<<<<<<<<<<5<<<<<<
+@EAS220_1:2:11:1274:1230
+TTTTGCTGCATCCCTGTCTTCCTCTGTCTTGATTT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<7;;;;
+@EAS220_1:2:43:656:1866
+TGAACTTCTGTAATTGAAAAATTCATTTAAGAAAT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<7;;:;
+@EAS220_1:2:47:591:698
+CAAATCTGCGCTTGTACTTCTAAATCTATAACAAA
++
+7;;;;:<<:<:<<<<<7<<:<<<<<<<<<<<<<<<
+@EAS220_1:2:47:591:698
+TCCTACTAAATACATATGCACCTAACACAAGACTA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<:<<<<
+@EAS220_1:2:50:513:882
+AAAACAAATACTACTAGACCTAAGAGGGATGAGAA
++
+<<<<:<<<<<:<<:<<<<::<<<<<<<<<<<<<<<
+@EAS220_1:2:50:513:882
+GGAGTAGCTATACTTATATCAGATAAAGCACACTT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;;;;;
+@EAS220_1:2:52:1779:1664
+CCCTGCCCCATCTCTTGTAATCTCTCTCCTTTTTG
++
+<<<<<<<<<<<<<<<<<<71<<<<<<<<<<<<<<%
+@EAS220_1:2:52:1779:1664
+TGTTAAAATGTCTATTTTTGTCTTGACACCCAACT
++
+6;;:;<<<:<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS220_1:2:54:91:1232
+AAAAGTGAGAAGTTTGGAAAAACTATTTGAGGAAG
++
+;;;;;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS220_1:2:54:91:1232
+AAAGCTCTAACAATAGACTAAACCAAGCAGAAGAA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS220_1:2:62:1109:804
+TAGAGTCCCATTTGGAGCCCCTCTAAGCCGTTCTA
++
+<<<<<<<<<<<<<:<<:<<<<<<:<:<<<<;;;;;
+@EAS220_1:2:62:1109:804
+TGTCAGTTACCAAATGTGTTTATTACCAGAGGGAT
++
+<<<<<:<<<::<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS220_1:2:63:267:545
+ATGAGAGAGAACTTCCCTGGAGGTCTGATGGCGTT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS220_1:2:63:267:545
+CTTGATTTACTTGTTGTTGGTTTTCTGTTTCTTTG
++
+<<<<<<<<<<<<:<<<<<::<<<<<<.<<<;;;;5
+@EAS220_1:2:72:1809:1398
+AATACATGAGATTATTAGGAAATGCTTTACTGTCA
++
+<<<<<<<<<<<<<<<<<<::<9<<<<<<<<<6<<:
+@EAS220_1:2:72:1809:1398
+CTATCTTCTTCTTAGGGAAGAACAGCTTAGGTATC
++
+;:;;:<7:7<:<:<<<<<<<<<<<<<<<<<<<<<<
+@EAS220_1:4:100:20:1199
+AAGGGGAAATAAAGTCAAGTCTTTCCTGACAAGCA
++
+:<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS220_1:4:100:20:1199
+CAGTCATCTATAAAGGAAATCCCATCAGAATAACA
++
+7<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<4<<
+@EAS220_1:4:14:1665:1772
+GGGCTGTAATGATGCCCCTTGGCCATCACCCGGTC
++
+<&7<<:<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS220_1:4:14:1665:1772
+TATAATGGTGTCCATGTACACACGCTGTCCTATGT
++
+<<<<<7*<<<<<<<<<78<5<<7<<5<556<(73(
+@EAS220_1:4:46:1566:668
+CTACTAAATACATATGCACCTAACACAAGACTACC
++
+5<<:<<<<<<<<<<<<:<:<<<<<<<<<<<<<<<<
+@EAS220_1:4:46:1566:668
+TTAATAAAGACATGAGTTCAGGTAAAGGGGTGGAA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS220_1:4:69:88:1154
+ATAACTATGAAGAGACTATTGCCAGATGAACCACA
++
+<<<<9<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS220_1:4:69:88:1154
+CACGAATGCGTCTCTACCACAGGCGGCTGCGCGGT
++
+<<<<<<<<<<<<<<<<<<<<<<<2<<<<:<<<<<7
+@EAS220_1:4:6:1178:1105
+GATAATTCATCATCACTAAACCAGTCCTATAAGAA
++
+<<<<<<:<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS220_1:4:6:1178:1105
+GGAACAAAACCTCATATATCAATATTAACTTTGAA
++
+<:<<9<<<<::7<<;<<<<<<<<<<<<<<<<<<<<
+@EAS220_1:4:70:766:2016
+AAAAAAATTCTAAAATCAGCAAGAGAAAAGCATAC
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS220_1:4:70:766:2016
+ATAAATGAAGGGGAAATAAAGTCAAGTCTTTCCTG
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS220_1:6:24:105:1046
+AGATTCATAAAACAAATACTACTAGACCTAAGAGG
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS220_1:6:24:105:1046
+CATAGCTAAAACTAAAAAAGCAAAAACAAAAACTA
++
++<<<</<<<<<.<<<<<<<<<<<<<<<<<<<<<<<
+@EAS220_1:6:7:1547:1933
+AATATTTGACTGAGCAAAACAGTCTAGATGAGAGA
++
+<<<<<<<<-<<<<<:<<<<<<<<<<<<<<<<<<<<
+@EAS220_1:6:7:1547:1933
+CTCTTGTAATCTCTCTCCTTTTTGCTGCATCCCTG
++
+<<<<<<<<<<<<<<<<<<<<<<<:<<8<<<<<<<<
+@EAS220_1:8:18:1757:95
+ATGAGTCGCAGGTATTCCTGAGGAAAAAGAAAAAG
++
+<<<<<<<<<<<<<<<<<<<1<:<<<<<<:<<<;:<
+@EAS220_1:8:18:1757:95
+CTTCATCAAGATATGTAGTCATCAGACTATCTAAA
++
+<<<6<&:<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS220_1:8:33:672:473
+ATGTCAGGGAAGGAGCATTTTGTCAGTTACCAAAT
++
+<<<<<<<<7<7<7<<62<<<<66<15*/99*5241
+@EAS220_1:8:33:672:473
+TCATCCTGGACCCTGAGAGATTCTGCAGCCCAGCT
++
+5<70<<55<4<24.5<<<<<<<<<6<<<<<<2<<<
+@EAS220_1:8:38:1576:1923
+CACAGGGGGCTGCGCGGTTTCCCATCATGAAGCAC
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<;<<:;<<;<
+@EAS220_1:8:38:1576:1923
+CTGTCATAACTATGAAGAGACTATTGCCAGATGAA
++
+8;<98<<<<<<<;<<<<<<<<<<<<<<<<<<<<<<
+@EAS220_1:8:45:178:1321
+AGGTTTTATAAAACAATTAATTGAGACTACAGAGC
++
+<<<<<<<<<<<<<<<<<:<<:<<<<<<<<<<<<<<
+@EAS220_1:8:45:178:1321
+CATAAATGAAGGGGAAATAAAGTCAAGTCTTTCCT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS220_1:8:46:1528:799
+ATGATAAAAAGATCAATTCAGCAAGAAGATATAAC
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<
+@EAS220_1:8:46:1528:799
+CATGTAACAAATCTGCGCTTGTACTTCTAAATCTA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS220_1:8:46:485:482
+AGAGATTCTGCAGCCCAGATCCAGATTGCTTGTGG
++
+<<<<<::<<<<<<<<6<<<<<<<<<6<<<<<<<<<
+@EAS220_1:8:46:485:482
+ATTACCAGAGGGATGAAGGGAAGAGGGACGCTGAA
++
+<<<<<<<<<<<<<<<<<<<<<<<6<<<<<:<:89<
+@EAS220_1:8:5:996:2000
+AGTCAACATGAAGGAAAAAAATTCTAAAATCAGCA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<:
+@EAS220_1:8:5:996:2000
+CACGAATGTTATGCCCTGCTAAACTAAGCATCATA
++
+<<<<<<<<<<<<<<<<<<:<<<<<<<<<<<<<<<<
+@EAS220_1:8:66:1046:167
+ACAATGTACAATATTCTGATGATGGTTACACTAAA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS220_1:8:66:1046:167
+ACACTTTAAATCAACAACAGTAAAATAAAACAAAG
++
+<<<<<:<<<<<<<<<<<<<9<;77<9<7<<;<9;-
+@EAS220_1:8:83:1456:1854
+AAGATCAATTCAGCAAGAAGATATAACCATCCTAC
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<2<
+@EAS220_1:8:83:1456:1854
+AAGCCCATACTTTACTGCTACTCAATATATCCATG
++
+<<67<:<8<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS221_1:2:23:127:880
+CGGAAACCTTACAAGCCAGAAGAGATTGGATCTAA
++
+<<<<<<<<<<<<<<<<<<<;;<<<<<<<<<<<<<<
+@EAS221_1:2:23:127:880
+TAAGAAATGCTCAAAAGAATTGTAAAAGTCAAAAT
++
+<<<<<<<<<%<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS221_1:2:24:1037:84
+TGCCCTCTTCTTCCAAAGATGAAACGCGTAACTGC
++
+<;<<;<<<7<<7&<<<<<<;<<<;<<<<<<<<<<<
+@EAS221_1:2:24:1037:84
+TTCAGTTCTAAATATAGAAATTGAAACAGCTGTGT
++
+<<<<<<<<<<<<<<<<<<<<<<;<<<<<<;:<57<
+@EAS221_1:2:29:1486:672
+AATTGAAACAGCTGTGTTTAGTGCCTTTGTTCACA
++
+<<:<<<<;<<<<<<<<<<<<<<<<<<<<<<<<<++
+@EAS221_1:2:3:542:428
+AAGACATGAGTTCAGGTACAGGGGTGGAAAAAGAT
++
+<<876</3<8874:<8:<)<5<<<;<<<<7<<<:<
+@EAS221_1:2:3:542:428
+AGAGCAACTAGGTAAAAAATTAACATTACAACAGG
++
+7<4<<<6<<,<9)<<<<6<,<<7<<7<<<<<<<<1
+@EAS221_1:2:3:945:2005
+AACCAAGCAGAAGAAAGAGGCTCAGAACTTGAAGA
++
+<<<<<<<<<<<<<<<<<<<<%<<<<<<;<<<<<<<
+@EAS221_1:2:3:945:2005
+GAAAAACTATTTGAGGAAGTAATTGGGGAAAACCT
++
+7<<<<;;<<;<<<<<7<<<<<<<<<;<<<<<<<<<
+@EAS221_1:2:52:1144:509
+AAAAGGGATTAAATTCCCCCACTTAAGAGATATAG
++
+<<<<:<<<<<<<<<<;::;:<;<<<<<<<<<<<<<
+@EAS221_1:2:52:1144:509
+TGTAAAAGTCAAAATTAAAGTTCAATACTCACCAT
++
+<<<<<<<<<<<<<<<<<<<;<<<<<<<;<;<<;<<
+@EAS221_1:2:73:955:728
+AATTCATCATCACTAAACCAGTCCTATAAGAAATG
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<<<<
+@EAS221_1:2:73:955:728
+TACAACAGGAACAAAACCTCATATATCAATATTAA
++
+;<-<<6<;<<<6<<<<;7<6<<<<<<<<<<<<<<<
+@EAS221_1:2:8:327:522
+AACAGGAACAAAACCTCATATATCAATATTAACTT
++
+<<<<<<<<<<:<<<<<<<<<<:<<<<<<<<<:<<<
+@EAS221_1:2:8:327:522
+TTCTACGCAAACAGAAACCAAATGAGAGAAGGAGT
++
+;;4;<-<-<<<7<<<<<;<<<<<<<<<<<<<<<<<
+@EAS221_1:2:90:986:1224
+CTGTGTTTAGTGCCTTTGTTCAACCCCCTTGCAAC
++
+<7*37;;;;;;;9<<;<7<<<<<<<<<<<;;<<<<
+@EAS221_1:2:91:856:504
+CTAGATGAGAGAGAACTTCCCTGGAGGTCTGATGG
++
+:::<<:<<<<<<<<<<<<<<<<<<<<<:<:<<<<<
+@EAS221_1:2:91:856:504
+GTTGTTGGTTTTCTGTTTCTTTGTTTGATTTGGTT
++
+<<<<<<<<<<<<<<7<<<<<<<7<<<&;<<<&&<&
+@EAS221_1:4:36:1402:1709
+AGCTTAGGTATCAATTTGGTGTTCTGTGTAAAGTC
++
+<<<<<<<<<<<<<<<<<;<<<<<<<<<;<<<:9<<
+@EAS221_1:4:36:1402:1709
+TTTTTGCTGCATCCCTGTCTTCCTCTGTCTTGATT
++
+;;;:<<<;<<<<<<<<<<<<<<<<<<<<<<;<<<<
+@EAS221_1:4:3:248:1491
+TTAAAATTTAACAAAAGTAAATAAAACACATAGCT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<:8:<
+@EAS221_1:4:41:519:609
+AACAAAAACTATGCTAAGTATTGGTAAAGATGTGG
++
+<4;<;<<<<<<<<;4:<<;<<<<<<<<<<<;<<<<
+@EAS221_1:4:41:519:609
+TACCTAATTGGTACAATGGACAATATTCTGATGAT
++
+1<<<<<<<<<<<<<<<4<-:<+6<<<<<<<<<<<<
+@EAS221_1:4:4:1732:88
+GCTGTAATGATGCCCCTTGGCCATCACCCGGTCCC
++
+:<4<:<<:<::<<<<<::<<<<<:<:<<<<<<<<<
+@EAS221_1:4:4:1732:88
+TGTACACACGCTGTCCTATGTACTTATCATGACTC
++
+<<<<<<<<<<<<<<<<<2<8;8<;<8;<2;2:<:<
+@EAS221_1:4:68:64:783
+AAGACATAATCCCACGCTTCCTATGGAAAGGTTGT
++
+<<9<8<6<<<<<;<<<<;<<<<<<<<<<<<<<<<<
+@EAS221_1:4:68:64:783
+TCCGTGTCCTCCCATCTGGCCTCGTCCACACTGGT
++
+<<<<<<<<<<<<<<<<<;;<<<<<<;<<<9:<<:9
+@EAS221_1:4:87:1375:1303
+AGGAGCATTTTGTCAGTTACCAAATGTGTTTATTA
++
+<<<<<<<<<<<<9<<<<<<<<<<<<<<<<<<<<<<
+@EAS221_1:4:87:1375:1303
+GAGAGATTCTGCAGCCCAGATCCAGATTGCTTGTG
++
+:<;<(<<<<<<<<<<<<<<<<<<<<<;<<<<<<<<
+@EAS221_1:6:38:1071:155
+ATGCCCCTTGGCCATCACCCAGTCCCTGCCCCATC
++
+<<<<<<<<<<<<<:<<<<<<<<8<<<:<<:;;8:;
+@EAS221_1:6:38:1071:155
+TAAAATGTCTATTTTTGTCTTGACACCCAACTAAT
++
+<<62<<<<<<3<<<<</<<<<<<<%<<<<<<<<<<
+@EAS221_1:6:4:1131:104
+ACTTTGGAAAACAATTTGGTAATTTCGTTTTTTTT
++
+61;;;<<<<<<<<<;:<<<:<<;<<<<;<<<<<<<
+@EAS221_1:6:4:1131:104
+ATGTAACAAATCTGCGCTTGTACTTCTAAATCTAT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<;;<<<::
+@EAS221_1:6:57:1342:1166
+AAAGACATGAGTTCAGGTAAAGGGGTGGAAAAAGA
++
+<<<<<;<<<<<<<;<<<<<<<<<<<<<<<<<<<<<
+@EAS221_1:6:57:1342:1166
+CAGAGCAACTAGGTAAAAAATTAACATTACAACAG
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<;<;
+@EAS221_1:6:60:1037:1146
+AAAAGCATACAGTCATCTATAAAGGAAATCCCATC
++
+<<<<<<<<<;<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS221_1:6:60:1037:1146
+GTGAGAAGTTTGGAAAAACTATTTGAGGAAGTAAT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<;<:;;;;;;<
+@EAS221_1:6:69:735:1915
+AATTTGTCAATGTCAGGGAAGGAGCATTTTGTCAG
++
+<<::<<<7<<<<7<<<<<<<<<<<<<<<<<<<<<<
+@EAS221_1:6:69:735:1915
+ACTGCCAGAGCTGCTGGCAAGCTAGAGTCCCATTT
++
+<<<<<<<<;<<<<<<<<<;<<<<;<8<<<<;1:<<
+@EAS221_1:6:89:1164:573
+AAAAAACCTGTCAAACACGAATGTTATGCCCTGCT
++
+3<<<6<%7<<08<<4<3<<103<1<<<<<<<<<<<
+@EAS221_1:6:89:1164:573
+AGACTTCATCAAGAGATGTAGTCATCAGACTATCT
++
+<:<<;<2<<<<<<<&:2<;<;<<<<;,+;:<<4:<
+@EAS221_1:6:92:1807:1185
+AGCATGGTTGTACTGGGCAATACATGAGATTATTA
++
+<<<<<<<<<<<<<<<:<<<<<<:<<<<;<<<;<<;
+@EAS221_1:6:92:1807:1185
+CTCTATCCCAAATTCCCAATTACGTCCTATCTTCT
++
+<<<<<<9<<<<<<<<<<<<<<<<<<<<<<><<<<<
+@EAS221_1:6:96:491:1891
+AGAAGTTTGGAAAAACTATTTGAGGAAGTAATTGG
++
+<:<<<<<::<<<<<<<<<<<<<<<<:<<::7<<:7
+@EAS221_1:6:96:491:1891
+GTCAACATGAAGGAAAAAAATTCTAAAATCAGCAA
++
+:;5<<7<;:<<;<<<<<<<<<<;<<<<<<<<<<<<
+@EAS221_1:8:15:881:1932
+CACTTAAGAGATATAGATTGGCAGAACAGATTTAA
++
+<<<<<<<<<<<<<<<;<<<<:<<<2<26<8<<;;.
+@EAS221_1:8:15:881:1932
+CACTTTAAATCAACAACAGTAAAATAAAACAAAGG
++
+)<4<<<<<<<4<<4<<4<<<<<<<<<<<<<<<<<<
+@EAS221_1:8:4:679:110
+AATGTTCCCCAGATACCATCCCTGTCTTACTTCCA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS221_1:8:4:679:110
+TCCAGATTGCTTGTGGTCTGACAGGCTGCAACTGT
++
+<<<<<<<<<<<<<<<<<<<;<<<<<<<<::<;;:7
+@EAS221_1:8:58:369:244
+CTGTAATGATGCCCCTTGGCCATCACCCAGTCCCT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS221_1:8:58:369:244
+TTGGGAGATTTTTAATGATTCCTCAATGTTAAAAT
++
+<<<<<<<<<<<<<<<<<<<<;<<;<<<<<<<<<<<
+@EAS221_1:8:60:1020:1259
+CTATGAAGAGACTATTGCCAGATGAACCACACATT
++
+<;<<<<;<<<<<<<<<;<<<<<<<8<<<<<:<:<<
+@EAS221_1:8:60:1020:1259
+TAGGGAAGAACAGCTTAGGTATCAATTTGGTGTTC
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS221_1:8:65:1928:1125
+CATCACAATGAACAACAGGAAGAAAAGGTCTTTCA
++
+<<;<<<7<<7<;<7<<<<<<<7<<<<;<.-;<+88
+@EAS221_1:8:65:1928:1125
+GGCATTTGCCTTCAGACCCTACACGAATACGTCTC
++
+<+<<<2<4<<<0<<4<<<<<6<<<6<<<'<<<<0<
+@EAS221_1:8:67:1797:1931
+GGGAAAGCTTTCAACGCTTCTAGCCATTTCTTTTG
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS221_1:8:67:1797:1931
+TGGTCTGACAGGCTGCAACTGTGAGCCATCACAAT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<<<<<<
+@EAS221_1:8:70:1349:1788
+ATTATATCAGATAAAGCACACTTTAAATCAACAAC
++
+&<8<<<85:580;<:0-><;>588>9<>7:<0<9;
+@EAS221_1:8:70:1349:1788
+TACTAGACCTAAGAGGGATGAGAAATTACCTAATT
++
+<7;<<8<74;;<1<<71<;7<;;<;<7<<<<<<<<
+@EAS221_1:8:73:108:1621
+GAACTTCCCTGGAGGTCTGATGGCGTTTCTCCCTC
++
+<<8<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS221_1:8:73:108:1621
+GTTTTCTGTTTCTTTGTTTGATTTGGTGGAAGACA
++
+<<<<<<<<71<<<<<<<<<+<<<<70:0<9<<61<
+@EAS221_1:8:77:781:676
+TCATGAAGCACTGAACTTCCACGTATCATCTAGGG
++
+<<<<<<<5<<5<<<<<<<<<<<<13<<2<<<<<,<
+@EAS221_1:8:77:781:676
+TTGCCAGATGAACCACACATTAATACTATGTTTCT
++
+:<;<2<<<<<<26<<<<6<;<<<<<<<<<<<<<<<
+@EAS221_1:8:78:1478:1446
+GGAAGAGGGACGCTGAAGAACTTTGATGCCCTCTT
++
+<<<<<<<<<<<<<<<<<<<<;<<<<<<<<<:<<<;
+@EAS221_1:8:78:1478:1446
+TGTGGTCTGACAGGCTGCAACTGTGAGCCATCACA
++
+<8,8<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS221_1:8:84:1013:1074
+GCAAGGGGGTCTATGTGAACAAAGGCACTAAACAC
++
+<7<<<<<<<<9<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS221_1:8:84:1013:1074
+TTGATGCCCTCTTCTTCCAAAGATGAAACGCGTAA
++
+8;;<;8744<7<<4<<47<<<<<<7<<<<<<<<<<
+@EAS221_1:8:8:1351:1986
+CCCAAGCCCTTCTCACAGTTTCTGCCCCCAGCATG
++
+<8;<<<<<<<<<<<;<<;<<<<<<<<<<<<<<<<<
+@EAS221_1:8:8:1351:1986
+TCTTACTTCCAGATCCCCAGAGGGAAAGCTTTCAA
++
+<<<<<<<<<<<<-<<<<<<<<<<<<<<<<<<<<<<
+@EAS221_3:2:100:1147:124
+AAAAAAGAATTTTAAAAATGAACAGAGCTTTCAAG
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<9<<
+@EAS221_3:2:100:1147:124
+AATGCCAGGAAGATACATTGCAAGACAGACTTCAT
++
+<<<<96<<<<<<<<<<<<<<<<<<<<<<:<<<<<<
+@EAS221_3:2:22:1623:709
+GAAGACAAGTCTCTTATGAATTAACCCAGTCAGAC
++
+<<<<<<<<<7<<<<<<<:<<<<<<<<:85:<:2<<
+@EAS221_3:2:22:1623:709
+GGGAAAACCTCTTTAGTCTTGCTAGAGATTTAGAC
++
+<'<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS221_3:2:2:491:1886
+CTCTTTAGTCTTGCTAGAGATTTAGACATCTAAAT
++
+<<:<8:<<<:<<<<<<<<<<<9<<<<<<<<<<<<:
+@EAS221_3:2:59:1576:946
+AACTGTGAGCCATCACAATGAACAACAGGAAGAAA
++
+<:<<<<<<<<<<<<:<:<<<<<<<8<<::1<<<<<
+@EAS221_3:2:59:1576:946
+CAACGCTTCTAGCCATTTCTTTTGGCATTTGCCTT
++
+9<<<9<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS221_3:2:60:590:1760
+AAAGTAACTGAACCTATGAGTCACAGGTATTCCTG
++
+<:<<<<<2<<<<:<::<<<::<<<<<6<<<<<<<6
+@EAS221_3:2:60:590:1760
+TCATCAAGATATGTAGTCATCAGACTATCTAAAGT
++
+<8<-<<<<<<<82<<<4<<<<<<<<<<<<<8<<<<
+@EAS221_3:2:67:1467:1447
+AAAGTTCAATACTCACCATCATAAATACACACAAA
++
+<<<<<<<<<<<<<<<<<<<<<<7<<<<<<<<<<<<
+@EAS221_3:2:67:1467:1447
+ATAGATTGGCAGAACAGATTTAAAAACATGAACTA
++
+<<<<<::<<:<<<<:<<<<<<<<<<<<<<<<<<<<
+@EAS221_3:2:67:1864:477
+AATGATGCCCCTTGGCCATCACCCAGTCCCTGCCC
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS221_3:2:67:1864:477
+TAAAATGTCTATTTTTGTCTTGACACCCAACTAAT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS221_3:2:76:1729:813
+TAATTTCGTTTTTTTTTTTTTCTTTTCTCTTTTTT
++
+<+6<<<&1<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS221_3:2:76:1729:813
+TCTGCGCTTGTACTTCTAAATCTATAAAAAAATTA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS221_3:4:12:276:1797
+ACTATTGCCAGATGAACCACACATTAATACTATGT
++
+<<<<<<<<<<<<:</<<9<:<<<<<<<<<<<<<<<
+@EAS221_3:4:12:276:1797
+TCTGTGTAAAGTCTCAGGGAGCCGTCCGTGTCCTC
++
+)9<02)<<<<<<<<<<<<<1<<<<&<<<<9<<<<<
+@EAS221_3:4:21:132:1423
+GCCAGATGAACCACACATTAATACTATGTTTCTTA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS221_3:4:21:132:1423
+TCAATTTGGTGTTCTGTGTAAAGTCTCAGGGAGCC
++
+:<<<<<6<<;<<;<5<;<<<<<<;<6<<<<<<<<<
+@EAS221_3:4:29:1061:574
+ATGTGTTTATTACCAGAGGGATGGAGGGAAGAGGG
++
+<<<<<<<<<<<<<<<<<<;<<<<<<;<<8<:<<<<
+@EAS221_3:4:29:1061:574
+GGTCTGACAGGCTGCAACTGTGAGCCATCACAATG
++
+<87<5<<9<<<66<<<<<<<<<<<<<<<<<<<<<<
+@EAS221_3:4:30:1452:1563
+ATGAATTAACCAAGTCAGACAAAAATAAAGAAAAA
++
+<<<<<<<<<<<<<<:<<<<1<<<<<<<<<<<<<<<
+@EAS221_3:4:30:1452:1563
+GATTTAGACATCTAAATGAAAGAGGCTCAAAGAAT
++
+<<39<<<59<<:<<+<<<6<<:<<<<<<<<<<<<<
+@EAS221_3:4:41:1308:619
+CATTGCAAGACAGACTTCATCAAGATATGTAGTCA
++
+0<9476<<<<<0<<<2<&<0<.<<<<<<<<<.<<<
+@EAS221_3:4:41:1308:619
+GAAGTATGAGATTATGTAAAGTAACTGAACCTATG
++
+<6+<*<<<<<<<:<<<<<<<:<<&<<<<1<6<11:
+@EAS221_3:4:57:1675:720
+TATAAGAAATGCTCAAAAGAATTGTAAAAGTCAAA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS221_3:4:57:1675:720
+TCATATATCAATATTAACTTTGAATAAAAAGGGAT
++
+<,<<<<<<:<<<<<<<<:9<<<<<<<<;<<<<<<<
+@EAS221_3:4:66:584:407
+GCATTTGCCTTCAGACCCTACACGAATGCGTCTCT
++
+<<<*9<9<<<1<<<<<<<<*<59<4<)<2<<<<<<
+@EAS221_3:4:66:584:407
+GGGCAATACATGAGATTATTAGGAAATGCTTTACT
++
+<<84<<<766<<<.6<<<<<<4<<7<<<<<<<7<<
+@EAS221_3:4:78:1314:1275
+AGGAAATCCCATCAGAATAACAATGGGCTTCTCAG
++
+<<<<<<<<6:<<<<<<<<<<<<<<<<<<<<<<<1<
+@EAS221_3:4:78:1314:1275
+GAAGTAATTGGGGAAAACCTCTTTAGTCTTGCTAG
++
+<<<<<<<<<<<<<<<<<<<<<6<<<<<<<<<<<<8
+@EAS221_3:4:81:687:1379
+CCTAAGAGGGATGAGAAATTACCTAATTGGTACAA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<<<<
+@EAS221_3:4:81:687:1379
+TAAATAAAACACATAGCTAAAACTAAAAAAGCAAA
++
+<<<<<<<<<<<:<<<<:<<<<<<<<<<<<<<<<<<
+@EAS221_3:4:90:247:212
+ACTTCCAGCTCCCCAGAGGGAAAGCTTTCAACGCT
++
+7655:;87;<;;;8<<<<<<<<<<<;<<<<<<<<<
+@EAS221_3:4:90:247:212
+TGACAGGCTGCAACTGTGAGCCATCACAATGAACA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<6<8<
+@EAS221_3:6:20:492:850
+AGTATGAAAACAATGTTCCCCAGATGCCGTCCCGG
++
+:.5:+.;;&91:;79:766:1:9+6&:1&&:+:))
+@EAS221_3:6:20:492:850
+CCTGAGAGATTCTGCAGCCCAGCTCCAGATTGCTT
++
+<7<<<<<<<<<<<.<54<7&<<<7<74<2<<<2<<
+@EAS221_3:6:26:227:1053
+ATTCTTCATCCTGGACCCTGAGAGATTCTGCAGCC
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS221_3:6:26:227:1053
+GGTTTAGGGGTATAATACCTCTACATGGCTGATTA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<;<<<<<<<<<
+@EAS221_3:6:51:1486:1131
+ATAAGAAATGCTCAAAAGAATTGTAAAAGTCAAAA
++
+<<<<<<<<<<,<6<<<<<<<<<<<<<<<<<<7<<<
+@EAS221_3:6:51:1486:1131
+TCAGCAGAAACCTTACAAGCCAGAAGAGATTGGAT
++
+<<<<<<<<<;<<<<<<<<<1<5<<8<<<'<;<<;1
+@EAS221_3:6:70:843:706
+AATGATTCCTCAATGTTAAAATGTCTATTTTTGTC
++
+<<<<<<<<;<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS221_3:6:70:843:706
+ATCTCTTGTAATCTCTCTCCTTTTTGCTGCATCCC
++
+<<<<<<<<<<<<<<<<<<<<<<<<<5<<5<<<<<<
+@EAS221_3:8:33:1240:846
+ACCTTACAAGCCAGAAGAGATTGGATCTAATTTTT
++
+<<<<<<<<<<<<7<<2<;<<;<<<;<<<:6:<<<:
+@EAS221_3:8:33:1240:846
+ATAAGAAATGCTCAAAAGAATTGTAAAAGTCAAAA
++
+<<<<<<<<<<9<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS221_3:8:34:956:1309
+AACTATGAAGAGACTATTGCCAGATGAACCACACA
++
+<<<<<<7<<<<<<<<<<<6<<<<<<<<<<<:<8<8
+@EAS221_3:8:34:956:1309
+AGCTTAGGTATCAATTTGGTGTTCTGTGTAAAGTC
++
+9<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS221_3:8:50:1203:1094
+AAATATAGTTGAAAGCTCTAACAATAGACTAAACC
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS221_3:8:50:1203:1094
+ACAGGTATTCCTGAGGAAAAAGAAAAAGTGAGAAG
++
+<7<<<<<5:+63<<<<<<<<<<<<<<<<2<<<<<<
+@EAS221_3:8:55:932:613
+TAGTCATCAGACTATCTAAAGTCAACATGAAGGAA
++
+<<<<<<<<<<<<<<<<<<<<<8<<<<<<<<<<<<<
+@EAS221_3:8:55:932:613
+TGTCAAACACGAATGTTATGCCCTGCTAAACTAAG
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS221_3:8:63:1265:820
+CTCTCCTTTTTGCTGCATCCCTGTCTTCCTCTGTC
++
+<<<<<<<<<<27<<<<<<<<<<<<<<<<<<<<03<
+@EAS221_3:8:63:1265:820
+TGTCTTGACACCCAACTAATATTTGTCTGAGCAAA
++
+<<<<<<3<<1<<<<<<<7<<<<<<<<<<<<<<<+<
+@EAS221_3:8:65:463:703
+GAAACCTTACAAGCCAGAAGAGATTGGATCTAATT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<:<<<<<<<
+@EAS221_3:8:65:463:703
+TGCTCAAAAGAATTGTAAAAGTCAAAATTAAAGTT
++
+<<3<9<<<<<<<8<<<<<<<<<<<<<<<<<<<<<<
+@EAS221_3:8:74:770:1712
+ACATTACTACCCTGCAATTAATATAATTGTGTCCA
++
+<<<<<<<<<<<<<<<<<<<5<<<<<<<<<<<<7<<
+@EAS221_3:8:74:770:1712
+GAGCCGTCCGTGTCCTCCCATCTGGCCTCGTCCAC
++
+3.&::6<<<9<6:<<<<<<<<<<<<<<<<<<<<<<
+@EAS221_3:8:7:1864:1569
+AAAAACCTGTCAAACACGAATGTTATGCCCTGCTA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS221_3:8:7:1864:1569
+AGATATGTAGTCATCAGACTATCTAAAGTCAACAT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<:<<<8<<<<
+@EAS51_62:1:38:250:647
+AATAATAAAATGATAAAAAGATCAATTCAGCAAGA
++
++<&+<1<,<<7<<7<<<<<<<1,<<<<7<<2<<<<
+@EAS51_62:1:38:250:647
+ACTATATGCTGTTTACAAGAAACTCATTAATAAAT
++
+<<<<<<<9<<9<<<<<<<6<<<<<<<<<<8<779%
+@EAS51_62:2:133:8:379
+ATAAGATAATTCATCATCACTAAACCAGTCCTATA
++
+&=========='==7==0=2====28===00====
+@EAS51_62:2:133:8:379
+GGAAATCCCATCAGAATAACAATGGGCTTCTCAGC
++
+<<<<<<<<<<<<<<<<<<<<<<<<8;<<8<<<:6<
+@EAS51_62:2:258:266:101
+ACGCTGTCCTATGTACTTATCATGACTCTATCCCA
++
+<<<<<<<<<<<<<<<<<<5<;,<-2<<<<;68<<6
+@EAS51_62:2:258:266:101
+CCATCACCCAGTCCCTGCCCCATCTCTTGTAATCT
++
+%==/7&8=======:===6================
+@EAS51_62:2:260:147:818
+AAAATTTGGTAATTTAGTTTTTTTTTTTTTCTTTT
++
+6.=..++==6=76==&===========99======
+@EAS51_62:2:260:147:818
+ATCCATGTAACAAATCTGCGCTTTTACTTCTAAAT
++
+<<<<<<3<<<<<;<<<<)<1<<<&<7<<<;<4/9<
+@EAS51_62:3:103:443:166
+ACCTGTCAAACACGAATGTTATGCCCTGCTAAACT
++
+<<<<<<<<<<<<<<<<<<<<;<<<<<<<1<-;;;<
+@EAS51_62:3:103:443:166
+TACACACAAAAGTACAAAACTCACAGGTTTTATAA
++
+7<4<4<:<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS51_62:3:169:292:652
+ATCTCTTGTAATCTCTCTCCTTTTTGCTGCATCCC
++
+<<<<<<<<<<<<<<<<<<<<<<<<<6<<-<<<<8<
+@EAS51_62:3:169:292:652
+GCAAAACAGTCTAGATGAGAGAGAACTTCCCTGGA
++
+79919-<-<<<<<<<<<<<<<<<<<<<6<<<<<<<
+@EAS51_62:3:200:263:280
+AGTAAAATAAAACAAAGGAGGTCATCATACAATGA
++
+<<<<<<<<<<<<<<<<<<<<;<<<<<<<<<;8<;1
+@EAS51_62:3:200:263:280
+TTGGTACAATGTACAATATTCTGATGATGGTTACA
++
+)<<<8<:<<<<<<<<<;<<<<<<<<<<<<<<<<<<
+@EAS51_62:3:263:74:407
+AAGCTTTCAACGCTTCTAGCCATTTCTTTTGGCAT
++
+;;88<::+;<)<5<<:<<<<<<<<<<<<<<<<<<<
+@EAS51_62:3:263:74:407
+CTGCAACTGTGAGCCATCACAATGAACAACAGGAA
++
+<<<<2<<<<<<:<<<9<<4<<<<:<<<<9<999.7
+@EAS51_62:3:314:386:190
+AGACCCCCTTGCAACAACCTTGAGAACCCCAGGGA
++
+++<<<<<<<<<<<<<<<<<<<<<<<<<<<<8<<<<
+@EAS51_62:3:314:386:190
+CACTCCAGCTCCCTGTCACCCAATGGACCTGTGAT
++
+76;%;<<3<9;<69<<<7;;;<<<<<<<<<<<<<<
+@EAS51_62:3:50:312:219
+ACTGCTACTCAATATATCCATGTAACAAATCTGCG
++
+<,;83:<::6<<<<<<<;:<;<<<<;<<<<<<<<<
+@EAS51_62:3:50:312:219
+TCCTACTAAATACATATGCACCTAACACAAGACTA
++
+<<<<<<<<<<<;<<<<<;<;<<<;<<<<<<;;;;;
+@EAS51_62:3:55:340:837
+TCCACACTGGTTCTCTTGAAAGCTTGGGCTGTAAT
++
+61378<::<<<5:<;;:<<<<<<<<<<<<;<<<<<
+@EAS51_62:3:55:340:837
+TTAATATAATTGTGTCCATGTACACACGCTGTCCT
++
+<<;<<;<<<<<8<;<<<;<7<<<;<<<<<93+79(
+@EAS51_62:3:68:996:104
+AGAGGGATGAGAAATTACCTAATTGGTACAATGTA
++
+<1<8<<<:<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS51_62:3:68:996:104
+TACTTATATCAGATAAAGCACACTTTAAATCAACA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<
+@EAS51_62:4:156:857:494
+CTCATACACACACATGGTTTAGGGGTATAATACCT
++
+<<<<<<<<<<<<<<<<<6<<<<<<<<<<<<<<:<<
+@EAS51_62:4:156:857:494
+GTTTCCCATCATGAAGCACTGAACTTCCACGTCTC
++
+<<<8<:5<<;<<8<<<<<<<<<<<<<<<<<<<<<<
+@EAS51_62:4:187:907:145
+TTTCTTCTCTCTCTTTTTTTTTTTTTTTATTGCAT
++
+<<<+;;,6<<<<6<<<<<<<<<<<<<<<<<<<<<<
+@EAS51_62:4:282:962:46
+GAAAAAAGTAAACTCTCAAATATTGCTAGTGGGAG
++
+69<<<<<:<<<:<<<<<<<<<<<<<<<<<<<<<<<
+@EAS51_62:4:282:962:46
+TACTTTACTGCTACTCAATATATCCATGTAACAAA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<<<<<
+@EAS51_62:4:308:614:911
+AAAAACAATTTGGTAATTTAGTTTTTTTTTTTTTC
++
+%<<<;:<::<6,<<<<<<:<:<<<<<<<<<<<<<<
+@EAS51_62:4:308:614:911
+TGCGCTTGTACTTCTAAATCTATAACAAAATTAAA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<;;<<<<8<
+@EAS51_62:5:119:38:945
+ATTCTAAAATCAGCAAGAGAAAAGCATACAGTCAT
++
+=;;8=====:========<================
+@EAS51_62:5:119:38:945
+TCACAGGTATTCCTGAGGAAAAAGAAAAAGTGAGA
++
+<<<<<<<<<<<<<<<8<<<<<8<<<8<;<<7<:<<
+@EAS51_62:5:131:779:345
+GTCCACACTGGTTCTCTTGAAAGCTTGGGCTGTAA
++
+============================9====;=
+@EAS51_62:5:131:779:345
+TGGAAGACATAATCCCACGCTTCCTATGGAAAGGT
++
+<<7<<<<<<<<:<<<<<<<<<<<<<;<<<<<<;<<
+@EAS51_62:5:154:669:853
+GTGTAAAGTCTCAGGGAGCCGTCCGTGTCCTCCCA
++
+============<===.====<:=<9=<<<9;:;2
+@EAS51_62:5:154:669:853
+TGGTTTTCTGTTTCTTTGTTTGATTTGGTGGAAGA
++
+<::<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS51_62:5:192:716:235
+ATACACACACATGGTTTAGGGGTATAATACCTCTA
++
+======================9==:<==:;;69;
+@EAS51_62:5:192:716:235
+GACCCTACACGAATGCGTCTCTACCACAGGGGGCT
++
+<5<<<8<:<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS51_62:5:236:498:526
+ACTAATGCGCTCCACGCCCAAGCCCTTCTCACAGT
++
+===================================
+@EAS51_62:5:236:498:526
+CAGCACATTACTACCCTGCAATTAATATAATTGTG
++
+<%88<;<:8<<<<:<<<<:<<<<<<<<<<<<<<<<
+@EAS51_62:5:290:319:736
+CGAGTCACGGGGTTGCCAGCACAGGGGCTTAACCT
++
+==;=======7====6=;==:;;====66=::27:
+@EAS51_62:5:290:319:736
+GTTCTCAAGGTTGTTGCAAGGGGGTCTATGTGAAC
++
+<<<<<<:7:<.<<<<7<<.<.<<.9*<4<:<4%74
+@EAS51_62:5:295:882:282
+AATGCTCAAAAGAATTGTAAAAGTCAAAATTAAAG
++
+<<:<8<-<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS51_62:5:295:882:282
+CAGAAGAGATTGGATCTAATTTTTGGACTTCTTAA
++
+========================<6<======8;
+@EAS51_62:5:86:697:941
+AAAAAAATCCCGGAAGATACATTGCAAGACAGACT
++
+1<<%<<<1:<58<<<<<<<<<<<<<<<<<<<<<<<
+@EAS51_62:5:86:697:941
+GTATGAGATTATGTAAAGTAACTGAACCTATGAGT
++
+=====================<=<==<<====;=5
+@EAS51_62:6:12:484:836
+AAACACATAGCTAAAACTAAAAAAGCAAAAACAAA
++
+<<<<</<4<<&7<<<<;<<<<<<<<<<<<<1<<<<
+@EAS51_62:6:12:484:836
+AAATACTACTAGACCTAAGAGGGATGAGAAATTAC
++
+<<<<<<<<<<<<<<<<<7<:<<<<<<9<<<<<<<<
+@EAS51_62:6:148:170:895
+AAAGTGAGAAGTTTGGAAAAACTATTTGAGGAAGT
++
+<<9<<<<<<<<<7<<<<<<<<<<<<<<<<<<<<<<
+@EAS51_62:6:148:170:895
+AAGAGGTTCAGAACTTGAAGACAAGTCTCTTATGA
++
+<<<<<<<<<<9<<<<<6<<<<<<<<<<<<<<<<6<
+@EAS51_62:6:50:542:881
+CCTTTTTGCTGCATCCCTGTCTTCCTCTGTCTTGA
++
++2<<<;<3;29<6<5;<<<<<<<<<<<<<<<<<<<
+@EAS51_62:6:50:542:881
+TCCCAATTACGTCCTATCTTCTTCTTAGGTAAGAA
++
+<<<<<4<09<<9<<2<<<<<<<<<<<2/.&2<%<7
+@EAS51_62:7:144:28:475
+AGGAAATGCTTTACTGTCATAACTATGAAGAGACT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<:<::8<
+@EAS51_62:7:144:28:475
+CAGCTTAGGTATCAATTTGGTGTTCTGTGTAAAGT
++
+;;;9;<<:<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS51_62:7:157:784:936
+GCTTAGGTATCAATTTGGTGTTCTGTGTAAAGTCT
++
+<<<<<<<<<<<<<<<<<:<<<<<<;<<<<814<4<
+@EAS51_62:7:157:784:936
+TGATTTACTTGTTGTTGGTTTTCTGTTTCTTTGTT
++
+<:<<<<8<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS51_62:7:162:195:761
+AACATGAACTAACTATATGCTGTTTACAAGAAACT
++
+<<8<<:<<:<<<<<<<<<<:<<<<<<<<<<<<<<<
+@EAS51_62:7:162:195:761
+TCACAGGTTTTATAAAACAATTAATTGAGACTACA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<;<:<<<<;;
+@EAS51_62:7:178:286:414
+CACGCCCAAGCCCTTCTCACAGTTTCTGCCCCCAG
++
+68;38::<<;<<8;<<<<<<<<<<<<<<<<<<<<<
+@EAS51_62:7:178:286:414
+TTACTTCCAGCTCCCCAGAGGGAAAGCTTTCAACG
++
+<<<<<<<<<<<<<<<<8<<<<<<<<<1<<<1;998
+@EAS51_62:7:196:511:896
+ATTGGGGAAAACCTCTTTAGTCTTGCTAGAGATTT
++
+<<<<<<<<<<<<<<<<<<<<<<<<;<<<4<88;<<
+@EAS51_62:7:196:511:896
+GAAAAGCATACAGTCATCTATAAAGGAAATCCCAT
++
+8<<<<<;<<<:<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS51_62:7:248:17:435
+ATAACCATCCTACTAAATACATATGCACCTAACAC
++
+<1<<88++<:<<:;<;<<<:<<<;<<<<<<<<<<<
+@EAS51_62:7:248:17:435
+CATGAGTTCAGGAAAAGGGGTGGAAAAAGATGTTC
++
+<<<<8<<<888<+<<<<<;<:<<<<8<<<<<;3<3
+@EAS51_62:7:312:236:655
+GAGAAATTACCTAATTGGTACAATGTACAATATTC
++
+<<<<;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS51_62:7:312:236:655
+TGCTAAGTATTGGTAAAGATGTGGGGAAAAAAGTA
++
+<<8;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS51_62:7:96:836:737
+ATCAACCTCATACACACACATGGTTTAGGGGTATA
++
+<<<<<<71<<<<<<<<<<899<:5<<<96858<<.
+@EAS51_62:7:96:836:737
+TCCCATCATGAAGCACTGAACTTCCACGTCTCATC
++
+1<;<7;;1;8;;8:<<1<;<<;<<<<<<<<<<;<<
+@EAS51_62:8:52:967:804
+AACTAAGCATCATAAATGAAGGGGAAATAAAGTCA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<:<<
+@EAS51_62:8:52:967:804
+TTACCTAGTTGCTCTGTAGTCTCAATTAATTGTTT
++
+===============<=======<<===<======
+@EAS51_64:2:326:153:231
+ATTGTTTTCAACTTTGGAAAACAATTTGGTAATTT
++
+::6=68=<*$;*=========6=============
+@EAS51_64:2:326:153:231
+TGCTACTCAATATATCCATGTAACAAATCTGCGCT
++
+<<<<<<<<<9<<<<<<<<<,<<<<<<8<<8.;.;4
+@EAS51_64:3:143:310:958
+CTGCACATTACTACCCTGCAATTAATATAATTGTG
++
+84<;<6<<<<;<<<;;<<<<<<<<<<<<<<<<<<<
+@EAS51_64:3:143:310:958
+GTCTCATCTAGGGGAACAGGGAGGTGCACTAATGC
++
+<<<<<<<<<<<8<8<<<<<;;7<<<;6;<<+4;;;
+@EAS51_64:3:190:727:308
+ACAGCTGTGTTTAGTGCCTTTGTTCAACCCCCTTG
++
+;;<;;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS51_64:3:190:727:308
+GGTGCAGAGCCGAGTCACGGGGTTGCCAGCACAGG
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<::<<<844
+@EAS51_64:3:255:45:399
+AAAAACTATGCTAAGTATTGGTAAAGATGTGGGGA
++
+<5<5<4$;;7/<<<177&7;<<<<<<;<<4<<<<<
+@EAS51_64:3:255:45:399
+GGTACAATGTACAATATTCTGATGATGGTTACACT
++
+<<3<8<<8<0<<;<<<0<<<</+8<611<<;71;7
+@EAS51_64:3:285:417:147
+AGTCAAAATTAAAGTTCAATACTCACCATCATAAA
++
+<..)<<<<;<<<<7<;-<<;<<<<<;8<<<<<<<<
+@EAS51_64:3:285:417:147
+TTGGATCTAATTTTTGGACTTCTTAAAGAAAAAAA
++
+<<<<<<<<<<<<<<<;8<<<<<<<<<;6<:<;<<;
+@EAS51_64:3:309:303:278
+CTATGAAGAGACTATTGCCAGATGAACCACACATT
++
+<<<<<<<<<<<<<<<<+<<+<<7<<<<<5<<<;;;
+@EAS51_64:3:309:303:278
+TCAATTTGGTGTTCTGTGTAAAGTCTCAGGGAGCC
++
+<:<<<:<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS51_64:3:67:782:132
+ATATTTGTCTGAGCAAAACAGTCTAGATGAGAGAG
++
+;;<;;;<<;;<<<;<<<;<<<;<<<<<<<<<<<<;
+@EAS51_64:3:67:782:132
+TCTTCCTCTGTCTTGATTTACTTGTTGTTGGTTTT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<:<<;4<<<<
+@EAS51_64:3:7:268:263
+TCGTACAGAAGTTTAATGGAGCCTTGGGACCTTAC
++
+!!66'&+/&'8+2''1+'611'&6&+/&+.&+1'&
+@EAS51_64:3:7:268:263
+TTGCGTTATTTGAGTTGGTGGAAGACATAATCCCA
++
+',)*&2<$7+<<<'<-<7<<<<<<<7<<</4/;<<
+@EAS51_64:3:80:885:513
+GAAATTCTTCATCCTGGACCCTGAGAGATTCTGCA
++
+<7<<<;<<;<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS51_64:3:80:885:513
+GCATTTTGTCAGTTACCAAATGTGTTTATTACCAG
++
+<<<<<<<<<<<<<<<<<<<:<<<<2:<;<<75<7;
+@EAS51_64:3:90:435:691
+GGGAATTTGTCAATGTCAGGGAAGGAGCATTTTGT
++
+;;<;;;+<<:<<<:<;;<<<<<<<<<<<<<<<<<;
+@EAS51_64:3:90:435:691
+TCTGGTGACTGCCAGAGCTGCTGGCAAGCTAGAGT
++
+<<<<<<<<<<;<<<;<<<<:<<<;<81;<<1;784
+@EAS51_64:4:102:467:897
+AGCATGGTTGTACAGGGCAATACATGAGATTATTA
++
+83333<+02<:<.&<+<.<::7<<::<<<<:<<<<
+@EAS51_64:4:102:467:897
+GCTTTCAACGCTTCTAGCCATTTCTTTTGTCTTTT
++
+<<<<9<<<<9<2<<<&,/</<<<<7<<;&&<$;*<
+@EAS51_64:4:116:738:142
+AAAGTTCAATACTCACCATCATAAATACACACAAA
++
+<:<7;+:<<:<<<;<<<<<;<<<<<<<<<<<<<<<
+@EAS51_64:4:116:738:142
+TGTCAAACACGAATGTTATGCCCTGCTAAACTAAG
++
+<<<<<<<<<<<<<<<<<<<;<<<<;<<<<<<<:;2
+@EAS51_64:4:163:31:455
+CTTACTTCCAGCTCCCCAGAGGGACAGCTNNCAAC
++
+<+<<<<<<<;0+<<<<;06070-9(0(9<!!5)05
+@EAS51_64:4:163:31:455
+GGGAGGTGCACTAATGCGCTCCACGCCCAAGCCCT
++
+8;<<;<<<78+<=</<<=;23<=<<<<<<<<<<<<
+@EAS51_64:4:179:389:585
+TGGCCACTTTTTATCGCATTTCCCTTTAGAACCTA
++
+<.4<9.4+.+'&-220<+<4<6<<20*6;<0(9<%
+@EAS51_64:4:179:389:585
+TGTGAAATGAATGAGATTATTAGGAAATGCTTTAC
++
+;<)<;*;9*+<;<<,,<,<4<4<<<<<;<4<9494
+@EAS51_64:4:181:476:394
+AACAATATTAACTTTGAATAAAAAGGGATTAAATT
++
+<+;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS51_64:4:181:476:394
+TCATCACTAAACCAGTCCTATAAGAAATGCTCAAA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<;<<:<<<:;;
+@EAS51_64:4:189:467:475
+CTACATGGCTGATTATGAAAACAATGTTCCCCAGA
++
+*.;*;7<75<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS51_64:4:189:467:475
+TATCTGGATTCTGGGAAATTCTTCATCCTGGACCC
++
+<<<<<<<<<<<<;;;<<<<<<<<<:<<<<:+<<;;
+@EAS51_64:4:189:571:366
+AACAAATACTACTAGACCTAAGAGGGATGAGAAAT
++
+<<;<<<<<:<<<;<<<;;;<<<<<<<<<<<<<<<<
+@EAS51_64:4:189:571:366
+TCTACGCAAACAGAAACCAAATGAGAGAAGGAGTA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<7<:<<99;;;
+@EAS51_64:4:318:345:156
+GGACCCTGAGAGATTCTGCAGCCCAGATCCAGATT
++
+<<<<<<<<:<<<<<<<<5<:5<<<3:'<72')*;9
+@EAS51_64:4:318:345:156
+TTATGAAAACAATGTTCCCCAGATACCATCCCTGT
++
+;8<8<<<<<;<<:<<;<;77<<<<<;<<;<<<<<<
+@EAS51_64:4:57:786:414
+CTCATTCACTCCAGCTCCCTGTCACCCAATGGACC
++
+;;;8;1;:<<<<;<::;;<<<<;<;;<<<<<<<<<
+@EAS51_64:4:57:786:414
+TGCAACAACCTTGAGAACCCCAGGGAATTTGTCAA
++
+<<<<<<<<<<<<<<<<<<<<<<<:<<:<<:;;7<7
+@EAS51_64:5:177:24:389
+AGCTTTCAAGAAGTATGAGATTATGTAAAGTAACT
++
+<<<<<<<<<<<<<<<<<<<<<<<<7<;;<;9969;
+@EAS51_64:5:177:24:389
+CAAGACAGACTTCATCAAGATATGTAGTCATCAGA
++
++<<;<9<<<9<<;<<7<<<<<<<<<<<<<<<<<<<
+@EAS51_64:5:202:39:380
+CAGGGAAGGAGCATTTTGTCAGTTACCAAATGTGT
++
+<<<<<<<<<<<<<<<<<;<<:;<<18<84:<&<+<
+@EAS51_64:5:202:39:380
+CTTCATCCTGGACCCTGAGAGATTCTGCAGCCCAG
++
+/92/;2<+2<<<<64<<<<<<<<<<<<<<<<7<<<
+@EAS51_64:5:290:247:509
+AGCCCATACTTTACTGCTACTCAATATATCCATGT
++
+<<<<<<<<<<<<<<<4<<<<<<92<;;;<;96;19
+@EAS51_64:5:290:247:509
+TCTCAAATATTGCTAGTGGGAGTATAAATTGTTTT
++
+49';<<<<<8;<;;<<<<<<<<<<<<<<<<<<<<<
+@EAS51_64:6:118:41:489
+ACAATTAATTGAGACTACAGAGCAACTAGGTAAAA
++
+<+<<;<<<38<<<<5<<3<<<<3<<8<<<<<<<<<
+@EAS51_64:6:118:41:489
+CCCTGCTAAACTAAGCATCATAAATGAAGGGGAAA
++
+<<<<<<<<<<<<<<<<;<<<<<<<<<<<<<<<95:
+@EAS51_64:6:124:128:489
+CTCTGTCTTGATTTACTTGTTGTTGGTTTTCTGTT
++
+::55<<<8<<<6<<;<<<<<<<<7<<<<<<<<<<<
+@EAS51_64:6:124:128:489
+GTCCTATCTTCTTCTTAGGGAAGAACAGCTTAGGT
++
+<<<<<<<<<<<<<<<<<6:6<<-4<::;;<<:48<
+@EAS51_64:6:143:763:480
+AAACGCGTAACTGCGCTCTCATTCACTCCAGCTCC
++
+::3<:6<<<:<<<<7<<<<<<<<)6<<<1<<<<;<
+@EAS51_64:6:143:763:480
+CTGAAGGTTGTTGCAAGGGGGTCTATGTGAACAAA
++
+;<&-<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS51_64:6:195:348:703
+CAGTTACCAAATGTGTTTATTACCAGAGGGATGGA
++
+<9<<9</<<<<<<<<<<<<<<2<8<<<<<<<<<<<
+@EAS51_64:6:195:348:703
+TAATGAAAACTATATTTATGCTATTCAGTTCTAAA
++
+<<<<<<<;<<<<<;:<<<<<<<<<<<<:<1:<:7<
+@EAS51_64:6:206:994:556
+ATTTGAGGAAGTAATTGGGGAAAACCTCTTTAGTC
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<4<<;<<
+@EAS51_64:6:206:994:556
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
++
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+@EAS51_64:6:210:809:735
+AAACCTCTTTAGTCTTGCTAGAGATTTAGACATCT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS51_64:6:210:809:735
+GAGGTTCAGAACTTGAAGACAAGTCTCTTATGAAT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<<5<<
+@EAS51_64:6:213:54:878
+CTCTGTCTTGATTTACTTGTTGTTGGTTTTTTGTT
++
+<<<<<<<<<;<<<<<<<<:<<:<<++<<<<%<%<<
+@EAS51_64:6:300:622:86
+GGTTACACTAAAAGCCCATACTTTACTGCTACTCA
++
+<:<<<:<6;<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS51_64:6:300:622:86
+TCATACAATGATAAAAAGATCAATTCAGCAAGAAG
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<:<<<<
+@EAS51_64:6:54:695:952
+ACAGTAAAATAAAACAAAGGAGGTCATCATACAAT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<
+@EAS51_64:6:54:695:952
+GGTTACACTAAAAGCCCATACTTTACTGCTACTCA
++
+277%<9<4)<<<<<<<<<;<<<<<<<<<<<<<<<<
+@EAS51_64:7:104:965:517
+AGAGGCTCAAAGAATGCCAGGAAGATACATTGCAA
++
+<<<<<<<<<<<<<<<<<<<<<:<<<<<<<8<<;<<
+@EAS51_64:7:104:965:517
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
++
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+@EAS51_64:7:140:752:822
+CATCACTAAACCAGTCCTATAAGAAATGCTCAAAA
++
+;<;;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS51_64:7:140:752:822
+GCTTCTCAGCGGAAACCTTACAAGCCAGAAGAGAT
++
+<<<<<<<<<<<<<<<<<7<<<<<<<<<<<<<;<:;
+@EAS51_64:7:152:918:824
+TACTATGTTTCTTATCTGCACATTACTACCCTGCA
++
+;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS51_64:7:152:918:824
+TTTCCCATCATGAAGCACTGAACTTCCACGTCTCA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<<8
+@EAS51_64:7:92:493:891
+AAAAGAAAAAGTGAGAAGTTTGGAAAAACTATTTG
++
+<<<<<<<<<<<<<<<;<<<<<<<<<<<<<<<<<<8
+@EAS51_64:7:92:493:891
+AGTCAACATGAAGGAAAAAAATTCTAAAATCAGCA
++
+<383<<:<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS51_66:1:282:274:50
+ATTACCAGAGGGATGGAGGGAAGAGGGACGCTGAA
++
+</7;/:<<<<<<<:<<<<<<<<<<<<<<<<<<<<<
+@EAS51_66:1:282:274:50
+CCCCTCTAAGCCGTTCTATTTGTAATGAAAACTAT
++
+<<<<<<<<<<<<<<<<<;<<<<<99<9<5909;5;
+@EAS51_66:1:289:207:323
+CCATACTTTACTGCTACTCAATATATCCATGTAAC
++
+<<<:<<<<<:<<<<<<<<<<;<<899<<13)939;
+@EAS51_66:1:289:207:323
+CTAGTGGGAGTATAAATTGATTTCCACTTTGGAAA
++
+&</<7<<:<7::<<<<+3<-7<<:<7<<<<<<<<<
+@EAS51_66:1:64:182:741
+AAAAAAACAAATTAAACTCTAACAAAAGTAAATAA
++
+(+;1&(9*%0<*(*&<*5,/+<,&<&<<6<<<<<<
+@EAS51_66:3:102:511:946
+ATGTAAAAGTGACTGTTATTGTCTTGACACCCAAC
++
+<%-4:6<:/&46;/*;<*84<0<'<&*<2<<<<<<
+@EAS51_66:3:102:511:946
+CCCAGTCCCTGCCCCATCTCGGGTAATCTCTCTCC
++
+<<9<<;<<<<;<<<<;<<7;%<5<<0<<<)<.<.+
+@EAS51_66:3:155:375:623
+AAGGAGTAGCTATACTTATATCAGATAAAGCACAC
++
+;;;;<<:<<<<;<<;<<<<<<;<<;<<<<<<<<<<
+@EAS51_66:3:155:375:623
+CAATATTAACTTTGAATAAAAAGGGATTAAATTCC
++
+0<<<<<;<<<<<<<<<<<<<4<<8<<<<<<<<;<;
+@EAS51_66:3:166:532:438
+AACAAATACTACTAGACCTAAGAGGGATGAGAAAT
++
+<<<<<<<<<<<<<<<;<<;<<;<<<<;<;:;;<;<
+@EAS51_66:3:166:532:438
+AACTAAAAAAGCAAAAACAAAAACTATGCTAAGTA
++
+<<&7<<<<<<<+<<<<<:<<<<<<<<<<<<<<<<<
+@EAS51_66:3:233:191:520
+TGAACTTCTGTAATTGAAAAATTCATTTAAGAAAT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<2<8<<
+@EAS51_66:3:246:711:981
+AAAAAAACCTGTCAAACACGAATGTTATGCCCTGC
++
+;;:;7<<:5:<<:<<<<<<<<<<<<<<<<<<<<<<
+@EAS51_66:3:246:711:981
+AGACTTCATCAAGATATGTAGTCATCAGACTATCT
++
+<<<<<<<<;<<<<:;<<;;<:<<<4<<:4;00<;<
+@EAS51_66:3:263:689:572
+AAAGAAAAAAAAACCTGTCAAACACGAATGTTATG
++
+<9<2<<<<<<<<<22;;02<<<9<<;9<9<<;<<3
+@EAS51_66:3:263:689:572
+AAGATATGTAGTCATCAGACTATCTAAAGTCAACA
++
+<<<<;<<<<<;<<<<<<&;;<<<;<<:<+;;7;;7
+@EAS51_66:3:29:381:169
+ATCTGGATTCTGGGAAATTCTTCATCCTGGACCCT
++
+<<<<<<<<<<<2<288;<<;<<:4<:<<;&92929
+@EAS51_66:3:29:381:169
+CATCAACCTCATACACACACATGGTTTAGGGGTAT
++
+2<82<;66<:<;<:<;<;<8<<<<<<<<<<<<<<<
+@EAS51_66:3:39:59:738
+GAGATTATTAGGAAATGCTTTACTGTCATAATTAT
++
+3<8.<<<<<<<-<<<<3<388;;880<0<0)-722
+@EAS51_66:3:39:59:738
+GTCCTATGTTCTTCTTAGGGAAGAACAGCTTAGGT
++
+;.;4;<;3<<9<<9<&<<9<<<<<;<9<;<<;9<<
+@EAS51_66:4:188:460:1000
+GTGTCCATGTACACACGCTGTCCTATGTACTTATC
++
+<<<<<<<<<<<<<<<<7<<;:4;44<;;:8;;9;;
+@EAS51_66:4:188:460:1000
+TCTTGAAAGCTTGGGCTGTAATGATGCCCCTTGGC
++
++;+077<7;<57<;;8<<<<<<<<<<8<<<<<<<<
+@EAS51_66:4:191:40:536
+ATAAAAAAAGACTACCCAGATTCATAAAACAAATA
++
++1<<,<&<<:<.;<7/7<<<<;.<<<<<<<<<<<<
+@EAS51_66:4:191:40:536
+CAGGTAAAGGGGTGGAAAAAGATGTTCTACGCAAA
++
+<<<<<<<<8<<;<<8<<;<;;<<8<<<<<</<74/
+@EAS51_66:4:209:92:210
+GAGATTATTAGGAAATGCTTTACTGTCATAACTAT
++
+<<<<<<<<<<<<<<<<;<<<<<<<5<7<<;;;<;<
+@EAS51_66:4:209:92:210
+TTAGGGAAGAACAGCTTAGGTATCAATTTGGTGTT
++
+;9;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS51_66:4:240:264:231
+CAACAGATCAAGAAGGAGGGGCAATGGACGAGTTA
++
+%15+5022))0&<<)0)+7:4+&<0<<:0<<<7<<
+@EAS51_66:4:240:264:231
+TGTAATGAAAACTATATTTATGCTATTCAGTTCTA
++
+9;,;;62<9<)29<<<;96<<<;<<7<<<<<<;<<
+@EAS51_66:4:277:482:316
+CACTAATGCGCTCCACGCCCAAGCCCTTCTCACAG
++
+<<<<<<<<<<<<<<;<;<<<:<;<<<<;<<<1<1;
+@EAS51_66:4:277:482:316
+TGTCCTATGTACTTATCATGACTCTATCCCAAATT
++
+9998;<<<<<;;<<<<<<<<<<<;<<<<<<<<<<<
+@EAS51_66:4:310:287:420
+AAGACATGAGTTCAGGTAAAGGGGTGGAAAAAGAT
++
+<<<<;<;<<<<<;<<<<<<<<<<<<<<<<<<<<<<
+@EAS51_66:4:310:287:420
+TACAGAGCAACTAGGTAAAAAATTAACATTACAAC
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<;;;
+@EAS51_66:4:322:350:374
+ACTTCTTAAAGAAAAAAAAACCTGTCAAACACGAA
++
+<+;8&84<<<:<<<<<<<<<<;<<<<<<<;<<<<<
+@EAS51_66:4:322:350:374
+CATTGCAAGACAGACTTCATCAAGATATGTAGTCA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;
+@EAS51_66:5:210:674:911
+TCATAAATACACACAAAAGTACAAAACTCACAGGT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;;<;
+@EAS51_66:5:210:674:911
+TGGCAGAACAGATTTAAAAACATGAACTAACTATA
++
+27;2<;<<5<<<<;;<<<<<;<<<<<<;<<<<<<<
+@EAS51_66:5:269:280:716
+TGATATCTGGATTCTGGGAAATTCTTCATCCTGGA
++
+6;<;;6:;<<<;64;<<<<<<<<;<<;<<;<<<<<
+@EAS51_66:5:269:280:716
+TTTGTCAATGTCAGGGAAGGAGCATTTTTTCAGTT
++
+<<<<<<<<<2<<:2:1<<7/2/:3<<<<*<3($<<
+@EAS51_66:5:273:545:1001
+AACAAAGGAGGTCATCATACAATGATAAAAAGATC
++
+<7(<<72;<2;27<;:<<<<<<<<<<<<<<<<<<<
+@EAS51_66:5:273:545:1001
+AGATTTAAAAACATGAACTAACTATATGCTGTTTA
++
+<<<<<<<<<<<<<<<;;<<<<<<;<8;28<8;<<8
+@EAS51_66:5:285:395:450
+GTCATCTATAAAGGAAATCCCATCAGAATAACAAT
++
+8)3<8+;<)<<<<<<<<97:7<<<<<<<<<<<<<<
+@EAS51_66:5:285:395:450
+TATTTGAGGAAGTAATTGGGGAAAACCTCTTTAGT
++
+<<<<<<<;<<<;<<<<<;:<:7<;<;7<7<<;;7<
+@EAS51_66:5:308:400:602
+ATAGACCCCCTTGCAACAACCTTGAGAACCCCAGG
++
+;<<<<<<<<<<<<<<<<<<<<<<<<;;;<<;<;76
+@EAS51_66:5:308:400:602
+CCTGTCACCCAATGGACCTGTGATATCTGGATTCT
++
+;77;2<<;<7<<;<<<;<;<<<<<<<<<<<<<<<<
+@EAS51_66:6:284:442:747
+AAAGAGGCTCAAAGAATGCCAGGAAGATACATTGC
++
+<;<<<<<:<;<<<<<<<<;<<<<<<<<<<<<<<<<
+@EAS51_66:6:310:747:415
+TGAGTCACAGGTATTCCTGAGGAAAAAGAAAAAGT
++
+<<<<<<<<<<<<<<<<<<:<<<<<;<<<<<;<;<;
+@EAS51_66:6:310:747:415
+TGTAGTCATCAGACTATCTAAAGTCAACATGAAGG
++
+;<<<;<;<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS51_66:7:174:987:334
+ACACCCAAGCCCTTCTCACAGTTTCTGCCCCCAGC
++
+<<;4<<<<;;</4<4<+<<<<<;<<<<<</<93+2
+@EAS51_66:7:174:987:334
+GTCCATGTACACACGCTGTCCTATGTACTTATCAT
++
+,;<;;<<<&<<<1<<<<<<<<<<<<<;<<<<<<<<
+@EAS51_66:7:4:234:610
+AAAAAACCTGTCAAACACGAATGTTATGCCCTCCT
++
+<<<<<<<<7;<<<;7<7;7;7<;-<-<&<<<0%06
+@EAS51_66:7:4:234:610
+AAAAATCAACATCACAAATACACACAAAAGTACAA
++
+<:+:'+&<+'<+'2&<:<7<2<':2<:<<7<7<<<
+@EAS51_66:7:84:411:336
+GCTTGTACTTCTAAATCTATAAAAAAATTAAAATT
++
+<<<;<<<;<<<<<<<<<<<<:<<;<<<<<<;8<;<
+@EAS51_66:8:36:688:722
+ATGTCTATTTTTGTCTTGACACCCAACTAATATTT
++
+<;;<<<<<<<<<<<<<<<<:<<<<<<<<<<<<<<<
+@EAS51_66:8:36:688:722
+GTCCCTGCCCCATCTCTTGTAATCTCTCTCCTTTT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS51_66:8:43:972:506
+AGAAACCTTACAAGCCAGAAGAGATTGGATCTAAT
++
+<;<<<<<<<<<<<<6;<;<<<<<<<<<<:;;<;<<
+@EAS51_66:8:43:972:506
+TAAGAAATGCTCAAAAGAATTGTAAAAGTCAAAAT
++
+;<<<<<<<+;<;<<<<<<<<<<<<<;<<<<<<<<<
+@EAS51_66:8:66:655:769
+TCATCCTGGACCCTGAGAGATTCTGCAGCCCAGCT
++
+8<<;:69<;:;9<2<*9<;6<<<<<17<;<3+<;<
+@EAS51_66:8:66:655:769
+TTTGTCAGTTACCAAATGTGTTTATTACCAGAGGG
++
+8;<<<<<8<<<<<;<<<7<;<<<<<;<7<27<;;7
+@EAS51_66:8:9:80:353
+AATTAATATAATTGTGTCCATGTACACACGCTGTC
++
+<<<<<<<<<<<<<<<<<<<<<6<<<;;<<5<<2;2
+@EAS51_66:8:9:80:353
+CCTCGTCCACACTGGTTCTCTTGAAAGCTTGGGCT
++
+;;5;:8<:<:;:;<<<<;<:<<<<<<<<<<<<<<<
+@EAS51_78:7:113:43:634
+ATTTGTCTGAGAAAAACAGTCTAGATGAGAGAGAA
++
+;9;1;<5:<<<%<<<<;<<<;<<<<<<<<<<<<<<
+@EAS51_78:7:113:43:634
+CTGTCTTCCTCTGTCTTGATTTACTTGTTGTTTTT
++
+<<<<<<<<<<<<.<<<<<<<<<<<<</<<2;;%%;
+@EAS51_78:7:147:64:416
+AAACAATGTCCCCCAGATACCATCCCTGTCTTACT
++
+<<<<<<<<<<<<<<<;<<<<<;<<<<;;:<;;;;;
+@EAS51_78:7:147:64:416
+CTCATCTAGGGGAACAGGGAGGTGCACTAATGCGC
++
+/;49;:6<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS51_78:7:164:727:977
+GAAATGCTCAAAAGAATTGTAAAAGTCAAAATTAA
++
+;<;<;<:<:<<<<<<<:<<<<<<<<<<<<<<<<<<
+@EAS51_78:7:164:727:977
+TACAAGCCAGAAGAGATTGGATCTAATTTTTCGAC
++
+<<<<<<<<<<<<<<<<<<<<<<<<<9<<<<;;79;
+@EAS51_78:7:186:199:927
+CTACGCGAATGCGTCTCTACCACAGGGGGCTGCGC
++
+-;++)6<*8+;&<&/<<<<7<<71<<<<<6<<<7<
+@EAS51_78:7:186:199:927
+TGGCATTTGCCTTCAGACCCTACACGAATGCGTCT
++
+<77<<<<2<;<<<<<06<<<<<<<<60<<684/6&
+@EAS51_78:7:215:516:299
+AAGCTATGCTAAGTATTGGTAAAGATGTGGGGAAA
++
+;;))7<8:855<<4<;:<<87<<<7<<;<<<*3<<
+@EAS51_78:7:215:516:299
+AATTACCTAATTGGTACAATGTACAATATTCTGAT
++
+<<<<<<;<<<<;;;;<;;<<<<;<<9<;<<1;7/;
+@EAS51_78:7:270:448:491
+GTAATCTCTCTCCTTTTTGCTGCATCCCTGTCTTC
++
+<<<<<<<<<<<<<<<<<<&<<.<<<<<<<:;;;<;
+@EAS51_78:7:270:448:491
+TTTGTCTGAGCAAAACAGTCTAGATGAGAGAGAAC
++
+7;;;;+2;<<+<<<<<<<<7<<<<<<<<<<<<<<<
+@EAS51_78:7:303:402:142
+AGCATTTTGTCAGTTACCAAATGTGTTTATTACCA
++
+;;;;;<9<<8;<<<<7<<;<<<<;<<<<<<<<<<<
+@EAS51_78:7:303:402:142
+TCCCATTTGGAGCCCCTCTAAGCCGTTCTATTTGT
++
+<8<<<<<<<<<<<<<<<<<<<<<<<46<648;;';
+@EAS51_78:7:316:961:576
+TGTGATATCTGGATTCTGGGAAATTCTTCATCCCG
++
+<<<<<<<;<<<<;<<:<<;<;<<:;<9+34;;6%/
+@EAS51_78:7:316:961:576
+TTACGGGTGTAATCTCTCTACATGGCTAATTATGA
++
+(++%%+++),+,+*++,+,,-,**+,-&-,+-+--
+@EAS54_61:1:115:868:887
+CATACACACACATGGTTTAGGGGTATAATACCTCT
++
+==;==8=;=;=========================
+@EAS54_61:1:115:868:887
+TCTCATTCACTCCAGCTCCCTGTCACCCAATGGAC
++
+>>>>>>>>>>>>>>;<>>>>><<>>>;<+<</;;1
+@EAS54_61:2:168:61:867
+GATGTTCTACGCAAACAGAAACCAAATGAGAGAAG
++
+====7====================7======6==
+@EAS54_61:2:168:61:867
+TCATAAAACAAATACTACTAGACCTAAGAGGGATG
++
+;7<<<<<<<<<<<<<7<<:<<<<<<<<<<<<<<<<
+@EAS54_61:2:66:757:918
+CCATCCTACTAAATACATATGCACCTAACACAAGA
++
+<9<45;<<7<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS54_61:2:66:757:918
+GGGGTGGAAAAAGATGTTCTACGCAAACAGAAACC
++
+===================================
+@EAS54_61:3:150:933:810
+AGCTTTCAACGCTTCTAGCCATTTCTTTTGGCATT
++
+:89===:=:=;;==;====================
+@EAS54_61:3:150:933:810
+CAATGAACAACAGGAAGAAAAGGTCTTTCAAAAGG
++
+===================================
+@EAS54_61:3:155:758:710
+ATCAGATAAAGCACACTTTAAATCAACAACAGTAA
++
+=46=4=5===:========:=7=7======11===
+@EAS54_61:3:155:758:710
+TTTGAATAAAAAGGGATTAAATTCCCCCACTTAAG
++
+=======8================6=:7===:=:=
+@EAS54_61:3:20:762:748
+CACAATGAACAACAGGAAGAAAAGGTCTTTCAAAA
++
+===================================
+@EAS54_61:3:20:762:748
+TTCTTTTGGCATTTGCCTTCAGACCCTACACGAAT
++
+=:747;7=;;==7=;==7===7==7;=========
+@EAS54_61:4:143:69:578
+ATTGGGAGCCCCTCTAAGCCGTTCTATTTGTAATG
++
+222&<21<<<<12<7<01<<<<<0<<<<<<<20<<
+@EAS54_61:4:83:452:970
+AATGAAAACTATATTTATGCTATTCAGTTCTAAAT
++
+==========================;========
+@EAS54_61:4:83:452:970
+AGGGATGGAGGGAAGAGGGACGCTGAAGAACTTTG
++
+<<<39<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS54_61:4:86:660:932
+AATACATATGCACCTAACACAAGACTACCCAGATT
++
+================================9:=
+@EAS54_61:4:86:660:932
+ATATAAAAAAATTAAAATTTAACAAAAGTAAATAA
++
+&<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS54_61:6:126:541:194
+AGTACGACCAGCTCCCCAGAGGGAAAGCTTTCAAC
++
++%&:/+(46=47&71/2==;=;8====28212===
+@EAS54_61:6:126:541:194
+CAGCCCAGATCCAGATTGCTTGTGGTCTGACAGGC
++
+<<<<<<<<8<<<<<8<<<<<<<<<8<<<428+<80
+@EAS54_61:6:25:949:33
+AAAGTAACTGAACCTATGAGTCACAGGTATTCCTG
++
+=;===/8========*==&;6=&=&:=6&:=::67
+@EAS54_61:6:25:949:33
+GATATGTAGTCATCAGACTATCTAAAGTCAACATG
++
+-<4<666<<-7<5<<<<<(<<<<<<<<<<<<<<-<
+@EAS54_61:7:114:506:971
+ACTAAATACATATGCACCTAACACAAGACTACCCA
++
+;;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS54_61:7:114:506:971
+GGGTGGAAAAAGATGTTCTACGCAAACAGAAACCA
++
+===================================
+@EAS54_61:7:64:37:257
+CCGTGTCCTCCCATCTGGCCTCGTCCACACTGGTT
++
+================<=====;===8;4======
+@EAS54_61:7:64:37:257
+TTTGATTTGGTGGAAGACATAATCCCACGCTTCCT
++
+;47<<47+9<4<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS54_61:8:165:441:708
+CCATCATAAATACACACAAAAGTACAAAACTCACA
++
+6+<<:<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS54_61:8:165:441:708
+CTTAAAGAAAAAAAAACCTGTCAAACACGAATGTT
++
+=<===============================99
+@EAS54_61:8:4:173:814
+CTGCTACTCAATATATCCATGTAACAAATCTGCGC
++
+<<;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS54_61:8:4:173:814
+GATAAAAAGATCAATTCAGCAAGAAGATATAACCA
++
+=====================<==========;==
+@EAS54_65:2:127:288:655
+ACTAGGTAAAAAATTAACATTACAACAGGAACAAA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<;<<;;
+@EAS54_65:2:127:288:655
+TGTTCTACGCAAACAGAAACCAAATGAGAGAAGGA
++
+<<:<3<<:<.<<<;<<<<<;<<<<<<<<<<<<<<<
+@EAS54_65:2:182:924:833
+TTTTTTTTTTTTTATTTGCGCTTTTTTTTTTTTTT
++
+<<<<<<<<<<<<<)7<<)3/:07<<9<9<<==<7<
+@EAS54_65:2:264:157:150
+GGAAAAATGGACAAGATTCTGATGAGGGTTACACT
++
+.3%:+<<*;*<2<<1<1*,*<<7<<+<<<&<<<<<
+@EAS54_65:2:264:157:150
+TAAAGCACACTTTAAATCAACAACAGTAAAATAAA
++
+<<<<<<9<9<<<<.9;<<9&<97<;9933309605
+@EAS54_65:2:94:356:809
+AAATCTATAACAAAATTAAAATTTAACAAAAGTAA
++
+<<<<3<<<<;;<<<<<<<<<;<<<<<<<<<<<<<<
+@EAS54_65:2:94:356:809
+CTAAATACATATGCACCTAACACAAGACTACCCAG
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<:;
+@EAS54_65:3:102:884:63
+GTCTTGACACCCAACTAATATTTGTCTGAGCAAAA
++
+<;7;;<<8<;8;<<<8<<<<<<8<<<8;<<<<<<<
+@EAS54_65:3:102:884:63
+TGTCTTCCTCTGTCTTGATTTCCTTGTTGTTGGTT
++
+<<<<<<<<<<<<<<<<<3<<<%<<<9<<9<<7+;<
+@EAS54_65:3:155:541:234
+CTAAATACATATGCACCTAACACAAGACTACCCAG
++
+<<7<<<<<<<<<<<<<<<4<<<<<<<<<<<;;;08
+@EAS54_65:3:155:541:234
+TGCGCTTGTACTTCTAAATCTATAAAAAAATTAAA
++
+78;<7<<<<<<<<<<<<<<;<<<<<<<<<<;<<<<
+@EAS54_65:3:214:946:229
+AAATGAACAGAGCTTTCAAGAAGTATGATATTATG
++
+<<<<<<<<<<<<<<<<<::<;;;<;<;7<:<<7<2
+@EAS54_65:3:214:946:229
+ACAAAGAATGCCAGGAAGATACATTGCAAGACAGA
++
+)+<<<*<<77;8<;7<<8<4<;<88<<<<<<<<<<
+@EAS54_65:3:273:901:459
+CCAGCATGGTTGTACTGGGCAATACATGAGATTAT
++
+<<8<<<;<;8<;<;<;7+8<788<;;22<27;77;
+@EAS54_65:3:273:901:459
+TGTCCTATGTACTTATCATGACTCTATCCCAAATT
++
+4;+/+7,;<8+&<;;82;;<8<8<2<;<<<<<<<<
+@EAS54_65:3:290:558:349
+ACCATCCCTGTCTTACTTCCAGCTCCCCAGCGGGA
++
+<<<;<<;<;<188<<<8::<686+4:<<6:&3)*&
+@EAS54_65:3:290:558:349
+TCTCAGCTAGGGGAACAGGGAGGTGCACTAATGCG
++
+2;2;;'5&;<<5<<;5/<<<<<7<<;+;<<+1<8<
+@EAS54_65:3:320:20:250
+AAATAAAACACATAGCTAAAACTAAAAAAGCAAAA
++
+<<<<<<<<<<<<<<<<<;<<<<<<<<<;+:<;<<3
+@EAS54_65:3:320:20:250
+TTTTTTTTTTTTTTTTTTTTTTTGCATGCCAGAAA
++
++'''/<<<<7:;+<;::<<<;;<<<<<<<<<<<<<
+@EAS54_65:3:321:311:983
+ATTTATGCTATTCAGTTCTAAATATAGAAATTGAA
++
+;;4;;<7<<<<<<77<<<<<<<<<<17<<<<<<<<
+@EAS54_65:3:326:652:890
+TTCTGTAATTGAAAAATTCATTTAAGAAATTACAA
++
+<<<<<<<<<<2<<<<<<<<<<<<<<+<8:<<9998
+@EAS54_65:4:137:319:642
+CTTGTTGTTGGTTTTCTGTTTCTTTTTTTGATTTT
++
+<<<<<<<<<27<<<<<<<<<<<<<<&;<<&3;;<%
+@EAS54_65:4:174:753:617
+ATATATCCATGTAACAAATCTGCGCTTGTACTTCT
++
+<;<;<<<:<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS54_65:4:174:753:617
+GATATAACCATCCTACTAAATACATATGCACCTAA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<;;<<<<<
+@EAS54_65:4:192:714:341
+AAATTAAAATTTAACAAAAGTAAATAAAACACATA
++
+<<<3;<<<<9:<<</<<<<<<<<<<<<<<<<<<<<
+@EAS54_65:4:192:714:341
+ACACAAGACTACCCAGATTCATAAAACAAATACTA
++
+<<9<<<<<<<<<<<8<<<<<;<<;8<<<88;;;;9
+@EAS54_65:4:193:38:987
+AGGGAAGAACAGCTTAGGTATCAATTTTGTGTTCT
++
+<<<;<<;<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS54_65:4:193:38:987
+TGAGATTATTAGGAAATGCTTTACTGTCATAACTA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<:;:;;
+@EAS54_65:4:246:313:499
+ACAATGAACAACAGGAAGAAAAGGTCTTTCAAAAG
++
+<<<<<<<<<<<<<;<;<<<<<<<<;<<<<<;;<<<
+@EAS54_65:4:246:313:499
+CTTTAAACGCTTCTAGCCATTTCTTTTGGCATTTG
++
++;77%;;;&:;:7;<<<<<6<:<<<<<<<<<<<<<
+@EAS54_65:4:325:795:213
+AGACTACAGAGCAACTAGGTAAAAAATTAACATTA
++
+<<<0<<;<<<<;<<;:<<<<<<<<<<<;<<<<<9<
+@EAS54_65:4:325:795:213
+GGAAATAAAGTCAAGTCTTTCCTGACAAGCAAATG
++
+<<<<<<<;<<<<;;<<<<<<<<<<<<;:<</;/;;
+@EAS54_65:4:61:346:384
+CAACTAAGAAGAAACCTTACAAGCCAGAAGAGATT
++
+7&$+&,<<+;;<;;<<6<<8<<<;<<;<<<<<<<<
+@EAS54_65:4:61:346:384
+CTAAATGAAAGAGGCTCAAAGAATGCCAGGAAGAT
++
+<<;<<<<<<<<9<;<<9;<6<2;<6<<<;9*558;
+@EAS54_65:4:91:267:655
+CAGGGAGCCGTCCGTGTCCTCCCATCTGGCCTCGT
++
+<<<<<<<<<<<<<<<<<<<<<;:;;7<9477<74;
+@EAS54_65:4:91:267:655
+TGTTGTTGGTTTTCTGTTTCTTTGTTTGATTTGGT
++
+;,:;5:<6:<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS54_65:6:115:538:276
+CAAATGTGTTTATTACCAGAGGGATGGAGGGAAGA
++
+:<<<<<<<<;;<5<<;<<<<<<<<;<<<<<<<<<<
+@EAS54_65:6:115:538:276
+TATTTGTAATGAAAACTATATTTATGCTATTCAGT
++
+<<<<<<<<;<<<;;<<<;<:<<<:<<<<<<;;;7;
+@EAS54_65:6:164:797:930
+AGCTAGAGACCCATTTGGAGCCCCTCTAAGCCGTT
++
+<<<<<<<<<<<<<<<;;;:<<<<<;<;<<<<<,::
+@EAS54_65:6:164:797:930
+GTCAGGGAAGGAGCATTTTGTCAGTTACCAAATGT
++
+;;:;8<;<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS54_65:6:18:376:416
+GCAAAACAGTCTAGATGAGAGAGAACTTCCCTGGA
++
+70<<<<<<<7<7<<<2<<<<<<<<<<8<<<<<<<<
+@EAS54_65:6:18:376:416
+TTTTTGCTGCATCCCTGTCTTCCTCTGTCTTGTTT
++
+<<<<<<<<<<<<<<<<;<<<<<<<<<<<<<;:(<<
+@EAS54_65:6:277:590:364
+CTCTACATGGCTGATTATGAAAACAATGTTCCCCA
++
+:::<<<<;<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS54_65:6:277:590:364
+CTGGGAAATTCTTCATCCTGGACCCTGAGAGATTC
++
+<<<<<8<<<<<<<<;<<<<<;;<7<<;;7858;;8
+@EAS54_65:6:326:71:741
+TCTCGTTTTTTTTTCTTTCTTTTCTCTTTTTTTTT
++
+!!<66<<<<<<<<<&<<7&<<<<:<*<<<<<<<<1
+@EAS54_65:6:49:183:435
+CCATCATGAAGCACTGAACTTCCACGTCTCATCTA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<;;<;:;8;:
+@EAS54_65:6:49:183:435
+GACTATTGCCAGATGAACCACACATTAATACTATG
++
+1<7<<<<;:<<<<<;<<<;<<<;<;<<<<<<<<<<
+@EAS54_65:6:67:56:806
+TATAAAGGAAATCCCATCAGAATAACAATGGGCTT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<;;<<:7:
+@EAS54_65:6:67:56:806
+TCCTGACAAGCAAATGCTAAGATAATTCATCATCA
++
+844:8;7<88;8<<<<<<<<<<<<<<<<<<<<<<<
+@EAS54_65:7:117:452:744
+AATATTAACTTTGAATAAAAAGGGATTAAATTCCC
++
+<;;<;<<<7<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS54_65:7:117:452:744
+ACCAGTCCTATAAGAAATGCTCAAAAGAATTGTAA
++
+<<<<<<<<<<;<<<;<<<<<<<<<<:<<<<<<<;;
+@EAS54_65:7:155:629:357
+AGAAGAGATTGGATCTAATTTTTGGACTTCTTAAA
++
+<<<<<<<<;<<<<<<<<<<<<6<<<<<<<<<;<<<
+@EAS54_65:7:155:629:357
+AGAGGCTCAAAGAATGCCAGGAAGATACATTGCAA
++
+<<<<<<<<8<8<<6<<<<<<<<;<9<5<;<;;941
+@EAS54_65:7:159:253:353
+ATAAAACAATTAATTGAGACTACAGAGCAACTAGG
++
+<8<<<<:<<;;<<<<<<<<<<<;<<<<<<<<<<<<
+@EAS54_65:7:159:253:353
+GAAGGGGAAATAAAGTCAAGTCTTTCCTGACAGGC
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<0,%4(+,
+@EAS54_65:7:56:57:985
+TTCTGTCTTCTCTCCTGTCTTCTTTTCTCTTCTTT
++
+<9'<.<7<<2<<;77<7<<<<7<7<<<<7<<<2<<
+@EAS54_65:7:56:57:985
+TTTTTTCTCTTTTCTCTTTTTTTTTTTTTTTTTTT
++
+666666*6&1666+64666666666&266666666
+@EAS54_65:7:68:825:405
+AAAACCTCATATATCAATATTAACTTTGAATAAAA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;;;9
+@EAS54_65:7:68:825:405
+AAACCAAATGAGAGAAGGAGTAGCTATACTTATAT
++
+<<<;<<<<9<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS54_65:8:10:975:766
+AATAACACAAGACTACCCAGATTCATAAAACAAAT
++
+++4<<+<+<<<<8<<22;<<<<<2<<<<<<<<<<<
+@EAS54_65:8:10:975:766
+TTAATAAAGACATGAGTTCAGGTAAAGGGGTGAAA
++
+<<<<<<<<;<<<<;<:<<;<6;;<<<:6-:+1+;;
+@EAS54_65:8:140:924:923
+GAACAACAGGAAGAAAAGGTCTTTCAAAAGGTGAT
++
+<<<<<<<<<<<<<<<<<:<<<<<<<<<<<<<5;<;
+@EAS54_65:8:140:924:923
+TTTTAGCCATTTCTTTTGGCATTTGCCTTCAGACC
++
+<<&<<;;<;<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS54_65:8:147:687:428
+ATATGCACCTAACACAAGACTACCCAGATTCATAA
++
+;1<''48;4)<<:<<<<;<<6;<<<<<<<<<<<<<
+@EAS54_65:8:147:687:428
+ATGTTCTACGCAAACAGAAACCAAATGAGAGAAGG
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS54_65:8:178:187:610
+AAATACACACAAAAGTACAAAACTCACAGGTTTTA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS54_65:8:178:187:610
+TTGGCAGAACAGATTTAAAAACATGAACTAACTAT
++
+66:,:<7<<<<<<<1<<<<<<<<<<<<<<<2<<<<
+@EAS54_65:8:240:719:799
+AGATTGGCAGAACAGATTTAAAAACATGAACTAAC
++
+<:<<<<<:<<<<:<<<<<<<<<<<<<<<<<<<<<<
+@EAS54_65:8:240:719:799
+TTAAAGTTCAATACTCACCATCATAAATACACACA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<7<
+@EAS54_65:8:305:819:245
+AAATTCATTTAAGAAATTACAAAATATAGTTGAAA
++
+8<<<<8<;<<<<<;<8<<8<8<<<<8<<<899<<+
+@EAS54_65:8:76:493:708
+TTTATGCTATTCAGTTCTAAATATAGAAATTGAAA
++
+5/)63.&1517(544(055(0454&7706566679
+@EAS54_67:1:138:186:274
+GGCCTCGTCCACACTGGTTCTCTTGAAAGCTTGGG
++
+<;<<<<<6;<<<<<3<<36;3;<9<<<<<<3;<<<
+@EAS54_67:1:138:186:274
+TAATTGTGTCCATGTACACACGCTGTCCTATGTAC
++
+=39====9===;=;=;=9=;=====;===-=+=-7
+@EAS54_67:1:159:222:274
+GAACCACACATTAATACTATGTTTCTTATCTGCAC
++
+=;9====;=9==59=+==9========9===5;7=
+@EAS54_67:1:159:222:274
+GTCTGGGGAAAGTCTCAGGGAGCCGTCCGTGTCCT
++
+''7*<&<'<<<<.<2<<<<<<<<<<+<<<8<8<<;
+@EAS54_67:1:15:381:715
+GACTAAACCAAGCAGAAGAAAGAGGTTCAGAACTT
++
+;=====;===9==;===9;;;=4;9=====;====
+@EAS54_67:1:15:381:715
+GGAAAAAGAAAAAGTGAGAAGTTTGGAAAAACTAT
++
+<<<<<<<<<<<<<<9<<<<<<97;<<<<<<<<9<<
+@EAS54_67:1:88:54:900
+ATCAACAACAGAAAAATAAAACAAAGGAGGTCATC
++
+.....&.....,.......................
+@EAS54_67:1:88:54:900
+TGATGATGGTTACACTAAAAGCCCATACTTCACTG
++
+============;=================;9===
+@EAS54_67:2:22:471:500
+GTAAATAAAACACATAGCTAAAACTAAAAAAGCAA
++
+=9===0====;=77<==8;====;===========
+@EAS54_67:2:22:471:500
+TACTACTAGACCTAAGAGGGATGAGAAATTACCTA
++
+=======<=<====:<2===9==;=;9;;=;;;;5
+@EAS54_67:3:114:736:433
+AACAAAACCTCATATATCAATATTAACTTTGAATA
++
+;<<9<8;<<<<8<8<;<<;;;0<<8;<;<<47;;;
+@EAS54_67:3:114:736:433
+ATGTTCTACGCAAACAGAAACCAAGTGAGAGAAGG
++
+<9<9+9;<6<9<<;9<<<<<;<<<99<<<<<<<<<
+@EAS54_67:3:172:196:746
+AAATAAAGTCAAGTCTTTCCTGACAAGCAAATGCT
++
+<<<;><<+<<<<:<<<<2<;<<<;<<<<<<<<<<<
+@EAS54_67:3:172:196:746
+GCATACAGTCATCTATAAAGGAAATCCCATCAGAA
++
+<<<<<<<<9<<<<9<<<<<<<<<;<<<<6<<<<;<
+@EAS54_67:3:175:730:949
+TTATGCTATTCAGTTCTAAATATAGAAATTGAAAC
++
+<<<<;+<<<<7<;<<;<<<<<<<<<<<<<<<<<<<
+@EAS54_67:3:197:261:624
+GACTATCTAAAGTCAACATGAAGGAAAAAAATTCT
++
+<<<<<<<<<<<;<<<<<<<;<<;<<<<<<;<<<9<
+@EAS54_67:3:197:261:624
+GCCCTGCTAAACTAAGCATCATAAATGAAGGGGAA
++
+866;2:/;<<<;:<<<;<;;<<<<<<<<<<<<<<<
+@EAS54_67:3:47:471:858
+ACACCCAACTAATATTTGTCTGAGCAAAACAGTCT
++
+/;9<<63<<<<3<;<<<<<<<<<<<<<<<<<<<9<
+@EAS54_67:3:47:471:858
+CATCCCTGTCTTCCTCTGTCTTGATTTACTTGTTG
++
+<<;<<<<<<<<9<<<4;;<<<<;<<<<<.<<4;<4
+@EAS54_67:4:142:943:582
+TTCAAATGAACTTCTGTAATTGAAAAATTCATTTA
++
+<<<<<<;<<<<<<:<<;<<<<;<<<;<<<:;<<<5
+@EAS54_67:4:145:607:216
+AACGCGTAACTGCGCTCTCATTCACTCCAGCTCCC
++
+<<<<<<<<8<<<<<<<<<<4<<<7<:<<1<<;;99
+@EAS54_67:4:145:607:216
+TGAAAAACAGGAAGAAAAGGTCTTTCAAAAGGTGA
++
+/;<<&<<8<<<<<<<<<<<<<;872<<<<<<<<<<
+@EAS54_67:4:7:526:343
+TCATCCTGGACCCTGAGAGATTCTGCAGCCCAGCT
++
+<<<<<<<<<<<<<<<:<<<5<<<<<<5;<<<+8<;
+@EAS54_67:4:7:526:343
+TGAAAACAGTGTTCCCCAGATACCATCCCTGTCTT
++
+(7:;;;<<;;;<1<1<<<<<<<<<<<<<<<<<<<<
+@EAS54_67:5:117:33:262
+AATTAACATTACAACAGGAACAAAACCTCATATAT
++
+<<;;<<;<:8<7<<;<<<<<<<<<<<<<<<<<<<<
+@EAS54_67:5:117:33:262
+ACAAGCAAATGCTAAGATAATTCATCATCACTAAA
++
+<<<;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;
+@EAS54_67:5:124:241:608
+CTGAACTTCCACGTCTCATCTAGGGGAACAGGGAG
++
+9;;<<;<<<;<<<;<:<<<<;<<<<<<<<<<<<<<
+@EAS54_67:5:124:241:608
+GGGTATAATACCTCTACATGGCTGATTATGAAAAC
++
+<<<<<<<<<;<<<<<<<<<;;<<<;<<<<;;8;;:
+@EAS54_67:5:127:828:697
+ATGCCAGGAAGATACATTGCAAGACAGACTTCATC
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<;;<;
+@EAS54_67:5:127:828:697
+TAAAGAAAAAAAAACCTGTCAAACACGAATGTTAT
++
+;<<<7<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS54_67:5:149:639:910
+CAATGGGCTTCTCAGCAGAAACCTTACAAGCCAGA
++
+<<<<<<<<<<<<<<<<<<<<<<<<7<;;<<;<<;<
+@EAS54_67:5:149:639:910
+TCACTAAACCAGTCCTATAAGAAATGCTCAAAAGA
++
+<;49;<<;;<<<<8;<<<<<<<<<<<<<<<<<<;<
+@EAS54_67:5:71:408:741
+AGTCATCTATAAAGGAAATCCCATCAGAATAACAA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<
+@EAS54_67:5:71:408:741
+TCCTGACAAGCAAATGCTAAGATAATTCATCATCA
++
+;7;<;<0<<<<<<<<:;<<<<<<<<<<<<<<<<<<
+@EAS54_67:6:107:395:312
+CAAAATATAGTTGAAAGCTCTAACAATAGACTAAA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<;<;;<:<<<<
+@EAS54_67:6:107:395:312
+CAGGTATTCCTGAGGAAAAAGAAAAAGTGAGAAGT
++
+;<;;<<<<;<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS54_67:6:109:953:668
+CAATATATCCATGTAACAAATCTGCGCTTGTACTT
++
+;<<<<;<<<<<<<<<<<<<<<<<<<<<<<<8<;<<
+@EAS54_67:6:109:953:668
+CCACTTTGGAAAACAATTTGGTAATTTCGTTTTTT
++
+<:)9<<<<<<<<8:<<<<<<<<<<<<<<<<<<<<<
+@EAS54_67:6:198:503:669
+CAATGATAAAAAGATCAATTCAGCAAGAAGATATA
++
+5<<:<<;<<<<<<<;;<<9<<<<<<<<;<<<<;<<
+@EAS54_67:6:198:503:669
+CAGATTTAAAAACATGAACTAACTATATGCTGTTT
++
+<<<<<<<<<<;8<<<<<;<<<<<<;<;<8<<8<<<
+@EAS54_67:6:43:859:229
+TTCAAATGAACTTCTGTAATTGAAAAATTCATTTA
++
++37<=<.;<<7.;77<5<<0<<<;<<<27<<<<<<
+@EAS54_67:6:46:285:790
+AACGCGTAACTGCGCTCTCATTCACTCCAGCTCCC
++
+;;<8<;<<<<88<8<<;;<;<<;<<<<<<<<;<<<
+@EAS54_67:6:46:285:790
+TCAAGGTTGTTGCAAGGGGGTCTATGTGAACAAAG
++
+!!<<3<<<;;<<<<<<<<<;<;7<<7<<<<<<;<<
+@EAS54_67:7:101:752:996
+AACCTTACAAGCCAGAAGAGATTGGATCTAATTTT
++
+<<<<<<<<<<<<<<<;<<<<<9<<<<<<;<<;;;;
+@EAS54_67:7:101:752:996
+AAGAAATGCTCAAAAGAATTGTAAAAGTCAAAATT
++
+<<<<<<<<7<7<<<<<<<<<<<<<<<<<;<<<<<<
+@EAS54_67:7:197:399:319
+CAAAAAACAAATACTACTAGACCTAAGAGGGATGA
++
+&<+==<<5<<<8<89;;<<<<<<8<<<<<<<<<<<
+@EAS54_67:7:197:399:319
+TAGAAACCAAATGAGAGAAGGAGTAGCTATACTTA
++
++<<<<<<<<<<<<<<<<<;<<<<<<<<<<<;;<<;
+@EAS54_67:8:19:855:491
+TGGCATTTGCCTTCAGACCCTACACGAATGCGTCT
++
+8<<<<;:<<<<:<<<<<:<;;<<<<<<<;<<<;<;
+@EAS54_67:8:19:855:491
+TGTGTGTTCTCATCAACCTCATACACACACATGGT
++
+<<<<<<<<<<<;<<.:<<<<;;;<4<:<:<7<;;;
+@EAS54_67:8:46:900:610
+GATATCTGGATTCTGGGAAATTCTTCATCCTGGAC
++
+<<<<<<<<<<<<;<<<<<<<<<<<<<<<<<;;4;<
+@EAS54_67:8:46:900:610
+TACATGGCTGATTATGAAAACAATGTTCCCCAGAT
++
+<;5<;<<<;<<<<<<;<<<<<<<<<<8<<<<<8<<
+@EAS54_71:2:125:628:79
+GCTGAAGAACTTTGATGCCCTCTTCTTCCAAAGA
++
+95&<<<<<<<63<<<6<<<<8<;<<8<<<<<<<<
+@EAS54_71:2:125:628:79
+TTTATGCTATTCAGTTCTAAATATAGAAATTGAAA
++
+==================<6<====<<:<==7;::
+@EAS54_71:2:204:264:413
+CAATGAACAACAGAAAGAAAAGTTCTTTCAAAAGG
++
+1==(4=::;/7::&===;====/=;===;;=====
+@EAS54_71:2:204:264:413
+TGCCCTCTTCTTCCAAAGATGAAACGCGTAACTG
++
+<<<<<<<<<<<<<;:59<+<<:<<<9<<;:62<)
+@EAS54_71:2:85:686:696
+AATCAGCAAGAGAAAAGCATACAGTCATCTATAAA
++
+==================<=====:==<=<;=:==
+@EAS54_71:2:85:686:696
+TAAACTAAGCATCATAAATGAAGTGGAAATAAAG
++
+:<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS54_71:3:186:989:869
+ACACACATGGTTTAGGGGTATAATACCTCTACATG
++
+;<<;:<<<7:<<<<<<:<<<<<<<<<<<<<<<<<<
+@EAS54_71:3:186:989:869
+GGGAAATTCTTCATCCTGGACCCTGAGAGATTCT
++
+<<<<<<<<<<<<<<<<<<<<7;:<<<<<<<<<$<
+@EAS54_71:3:254:32:275
+GATGGAGGGAAGAGGGACGCTGAAGAACTTTGAT
++
+<<<<<<<<<<<<<<<<<<<<<<;;<:<::<:2*<
+@EAS54_71:3:254:32:275
+TGCAACTGTGAGCCATCACAATGAACAACAGGAAG
++
+(6+<;+6:9<<:7:<95<<<<<<<<<<<<<<<<<<
+@EAS54_71:3:257:288:731
+AAGAAGATATAACCATCCTACTAAATACATATGCA
++
+<<:<<7<<<<<;<5<<<<<<<<<<<<<<<<<<<<<
+@EAS54_71:3:257:288:731
+TGCTGTTTACAAGAAACTCATTAATAAAGACATG
++
+<<<<<<<<8<8<<;<;<<<;<<<5<;;88.8<6<
+@EAS54_71:3:267:821:860
+GCATACAGTCATCTATAAAGGAAATCCCATCAGA
++
+$&<<<.<:;6<<;<<<<<<<<<<<<<<<<<<<<<
+@EAS54_71:3:267:821:860
+TCTTTAGTCTTGCTAGAGATTTAGACATCTAAATG
++
+;<<<<<8<<<<<8<<;<8<<<<<5<;<<<<<2;<5
+@EAS54_71:3:78:855:352
+AAAAGAAAAAGTGAGAAGTTTGGAAAAACTATTT
++
+2<<<<<<<9<<4<<<<<<<<<<<<<<<<<<<<<<
+@EAS54_71:3:78:855:352
+AACAATAGACTAAACCAAGCAGAAGAAAGAGGTTC
++
+<<<<<<<<;<<<<<<<<<;<<<<<<<<;<;<<:<:
+@EAS54_71:4:127:725:381
+AATTACAAAATATAGTTGAAAGCTCTAACAATAGA
++
+<<<<<<<<<<<<<<<<<<<<<;<<<<;;;;;<<8:
+@EAS54_71:4:127:725:381
+TGAACCTATGAGTCACAGGTATTCCTGAGGAAAA
++
++<<.<<;<;<<<3;<;<<<<<<6<8;<<<<<<<1
+@EAS54_71:4:13:981:659
+CGGGACAATGGACGAGGTAAACCGCACATTGACAA
++
++)---3&&3&--+0)&+3:7777).333:<06<<<
+@EAS54_71:4:13:981:659
+TGTAGCCCCTCTAAGGCGTTCTATTTGTAATGAA
++
+()&)06636;;<664*6;<<<<<<<<<<<<<<<1
+@EAS54_71:4:14:88:306
+AAAGAATGCCAGGAAGATACATTGCAAGACAGAC
++
+<<<<<<8<<<<<<;<<<3<<<8<<;<;;<15<:6
+@EAS54_71:4:14:88:306
+AGAAGAGATTAGATCTAATTTTTGGACTTCTTAAA
++
+<1;<;<;<4<&<<<:<<<:<<<<;<<<<<<<<<<<
+@EAS54_71:4:165:397:25
+GCAACTGTGAGCCATCACAATGAACAACAGGAAGA
++
+<<7<<<<<<)97<6<:3:60:3+37-37+<:33:3
+@EAS54_71:4:165:397:25
+TTCAACGCTTCTAGCCATTTCTTTTGGCATTTGC
++
+&(33'60;-'+'<7;<<*3-<;;183<<<;<;<<
+@EAS54_71:4:169:256:888
+AGGTTCAGAACTTGAAGACAAGTCTCTTATGAATT
++
+<<<<<<<<<<<<<<<<<<<<<<;;<;<<;<<:;;<
+@EAS54_71:4:169:256:888
+ATTTGAGGAAGTAATTGGGGAAAACCTCTTTAGT
++
+&<<:<;<<;;<8<;<<<<<<<<<<<<<<<<<<<<
+@EAS54_71:4:169:862:829
+AAAGGTCTTTCAAAAGGTGATGTGTGTTCTCATCA
++
+<<<<<<<<<<<<<<<<<;<<<;<;<<<<:<;;<78
+@EAS54_71:4:169:862:829
+GCCATTTCTTTTGGCATTTGCCTTCAGACCCTAC
++
+,1<6<<<<<7<<<<<<<<<<<<<<<<<7<<<<<<
+@EAS54_71:4:206:741:810
+ACTAACTATATGCTGTTTACAAGAAACTCATTAA
++
+<3<<;5<<<<<;:<<<<<<<<<<<<<<<<<<<<<
+@EAS54_71:4:206:741:810
+CAAAAGTACAAAACTCACAGGTTTTATAAAACAAT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;:-;<<
+@EAS54_71:4:209:159:130
+CTTATCATGACTCTATCCCAAATTCCCAATTACGT
++
+;:6<:<8::;<<<;<-<<<<<<<<<<<<<<<<<<<
+@EAS54_71:4:209:159:130
+GCCCCCAGCATGGTTGTACTGGGCAATACATGAG
++
+<<<<<<8<<<<<<&<<+7<<4<<<22<;<<<<3<
+@EAS54_71:4:233:97:262
+ACCACACATTAATACTATGTTTCTTATCTGCCCA
++
+<<<<<<<<<<<;<;<<:<<<<<<<<<<<<.<&77
+@EAS54_71:4:233:97:262
+GTATCAATTTGGTGTTCTGTGTAAAGTCTCAGGGA
++
+--;;7<;<;;:;<;<<<<<<<<<<<<<<<<<<<<<
+@EAS54_71:4:252:428:683
+TGTCTTGATTTACTTGTTGTTGGTTTTCTGTTTCT
++
+<<<<<<;<<<<<<<<7<<7<<&+<<<<:<&<<<4<
+@EAS54_71:4:284:269:882
+TTTCTTTTCTCTTTTTTTTTTTTTTGTTTTTGCA
++
+<;<<<<<8<7<8;<<<;<7<<<<<;272;73&&)
+@EAS54_71:4:328:669:662
+GGAAGGAGCATTTTGTCAGTTACCAAATGTGTTT
++
+<<<<<<<<<<<<<<<<<<<<<<<<+9;<;;.<<<
+@EAS54_71:4:328:669:662
+TCTTCATCCTGTACCCTGAGAGATTCTGCAGCCCA
++
+4<<;<<8<.<88.<<;4<<<<<<<4<.<<<<7<<<
+@EAS54_71:4:72:63:435
+CCTTGCAACAACCTTGAGAACCCCAGGGAATTTG
++
+<<<<<<<<<<<<<<<<<<<<;<<<;<;;39:7:7
+@EAS54_71:4:72:63:435
+TGATATCTGGATTCTGGGAAATTCTTCATCCTGGA
++
+::<;<<<<;;;<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS54_71:4:73:182:444
+AACTTCCCTGGAGGTCTGATGGCGTTTCTCCCTCG
++
+:1<4;;::<<;<<<<;<<<<<<<<<<<;<<<<<<<
+@EAS54_71:4:73:182:444
+CTTGATTTACTTGTTGTTGGTTTTCTGTTTCTTT
++
+<<<<;;<<<<<<<<<<<<;<;<<<<<:<<<<<7<
+@EAS54_71:5:153:543:671
+GCCCCATCTCTTGTAATCTCTCTCCTTTTTGCTG
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<2<<7
+@EAS54_71:5:153:543:671
+TAAAATGTCTATTTTTGTCTTGACACCCAACTAAT
++
+;;;;;=;==================;=========
+@EAS54_71:5:16:434:204
+AGATGAGAGAGAACTTCCCTGGAGGTCTGATGGC
++
+<:7:<<<<<<<<<<<9<<<+<<<<<<<<<<<<<<
+@EAS54_71:5:16:434:204
+CTGTCTTCCTCTGTCTTGATTTACTTGTTGTTGGT
++
+=================;)===8===:==7;<+%;
+@EAS54_71:5:81:685:141
+ACTGAACCTATGAGTCACAGGTATTCCTGAGGAA
++
+<<<<<<<<<<<<<<<<<<<<<;;<<;<<<',7,7
+@EAS54_71:5:81:685:141
+AGATATGTAGTCATCAGACTATCTAAAGTCAACAT
++
+;+;(;)..=3.1=.7=;=8;==<4====;======
+@EAS54_71:6:172:896:83
+AGGAAGAAAAGGTCTTTCAAAAGGTGATGTGTGT
++
+<<<<<<<<<<<<<<<<<:;;+;<<<<<<<<9;;;
+@EAS54_71:6:172:896:83
+CATTTGCCTTCAGACCCTACACGAATGCGTCTCTA
++
+;<.5.;;<+;<<<<<<<4<<<<<<<;<<<<<;<<<
+@EAS54_71:6:215:133:909
+TGTGTGTTCTCATCAACCTCATACACACACATGG
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<996(
+@EAS54_71:6:215:133:909
+TTGCCTTCAGACCCTACACGAATGCGTCTCTACCA
++
+7758;<;<;8<<<<;<;<<<<<:;<<<<<<<<<<<
+@EAS54_71:6:224:932:942
+CTCTTGAAAGCTTGGGCTGTAATGATGCCCCTTGG
++
+<;<<;;<<<;<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS54_71:6:224:932:942
+GTCCATGTACACACGCTGTCCTATGTACTTATCA
++
+<<<<<<<<<<<<<<<<<<<<<<;<<<<7<<(;3,
+@EAS54_71:6:228:354:203
+AATGGACCTGTGATATCTGGATTCTGGGAAATTC
++
+88<<<8<<<<<<<<<8<<<<<<<<<4<<<4/9/;
+@EAS54_71:6:228:354:203
+TCAACCTCATACACACACATGGTTTAGGGGTATAA
++
+%1<851<5<<<982<<<<<<<<::<<<<7<<<<3<
+@EAS54_71:6:264:705:89
+AAACATATGCACCTAACACAAGACTACCCAGATTC
++
+<(<2<&<)<<<7<8<<<<<<<<<<.<<<<<<<<<<
+@EAS54_71:6:264:705:89
+AAGGGGTGGAAAAAGATGTTCTACGCAAACAGAA
++
+<<<<<<<<<<;8<<<<<<<<<<<<<<<&<<,;;(
+@EAS54_71:6:324:515:230
+AAAACAGTCTAGATGAGAGAGAACTTCCCTGGAG
++
+7<<1<<<7<+<<<;<<<<<<<<<<<<<<<<<<<<
+@EAS54_71:6:324:515:230
+CCTGTCTTCCTCTGTCTTGATTTACTTGTTGTTGG
++
+<<;<<<<<<<<<<<<<<<:<<<<8<<<4<<4<<34
+@EAS54_71:6:82:932:400
+GACACCCAACTAATATTTGTCTGAGCAAAACAGTC
++
+<<;<<72<<7<<<<<<<<<<;<<<+7<<<<<<<<<
+@EAS54_71:6:82:932:400
+GTAATCTCTCTCCTCTTCGCTGCATCCCTGTCTT
++
+<<<<<<8<1<<<<8+<<&<<<8<<<<<<<+(,/8
+@EAS54_71:7:130:260:553
+AGCAAGAGAAAAGCATACAGTCATCTATAAAGGAA
++
+<*;<<7<);<<;9;<5<*<9<;<<;;<7<<<<<1<
+@EAS54_71:7:130:260:553
+GTGAGAAGTTTGGAAAAACTATTTGAGGAAGCAC
++
+<<<<<1<<<<<<<<<<6<<81</<4*2;7:+90(
+@EAS54_71:7:194:867:616
+ATCCATGTAACAAATCTGCGCTTGTACTTCTATT
++
+<8<<<<<<<<<<<8<<4<<<<<<8<<3<<5<&(+
+@EAS54_71:7:194:867:616
+TTTTCCACTTTGGAAAACAATTTGGTAATTTCGTT
++
+38:;;:<:<<<<;<<<<<<<<<<;<<<<<<<<<<<
+@EAS54_71:7:212:329:348
+AACCACACATTAATACTATGTTTCTTATCTGCAC
++
+8<6:<:<<<;<<<;<<<<;<<<<<<<<<<<<<<<
+@EAS54_71:7:212:329:348
+CCCATCATGAAGCACTGAACTTCCACGTCTCATCT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<:;;;<
+@EAS54_71:7:250:698:842
+AAAAAGTACAAAACTCACAGGTTTTATAAAACAA
++
+)<<<<<<<-<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS54_71:7:250:698:842
+AAGAAAAAAAAACCTGTCAAACACGAATGTTATGC
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<;<24
+@EAS54_71:7:80:760:490
+CATGGCTGATTATGAAAACAATGTTCCCCAGATAC
++
+%::::+<<<;<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS54_71:7:80:760:490
+CTGGACCCTGAGAGATTCTGCAGCCCAGCTCCAG
++
+<<<<<<<<<<8<;<7<<<<<<;<;;<2<;<<<1,
+@EAS54_71:7:97:743:602
+AAGCAAATGCTAAGATAATTCATCATCACTAAACC
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<<:
+@EAS54_71:7:97:743:602
+ATTACAACAGGAACAAAACCTCATATATCAATAT
++
+<(&<:<<&<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS54_71:8:105:854:975
+ATTTAACAAAAGTAAATAAAACACATAGCTAAAAC
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<7:<;;;;5
+@EAS54_71:8:105:854:975
+TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTG
++
+<<<<;<:<<;<&<;<<<<<<<<<<<<<<<<<<<
+@EAS54_71:8:113:856:319
+AAATCAACAACAGTAAAATAAAACAAAGGAGGT
++
+<<<77<<:<<;<<<<<<<<<<<<<<<<<<<<<<
+@EAS54_71:8:113:856:319
+CCCACTTAAGAGATATAGATTGGCAGAACAGATTT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;;<<<
+@EAS54_71:8:215:830:609
+AAGACATCTAAATGAAAGAGGCTCAAAGAATGC
++
++<)<:<<:<<<<<<<<<9<<<<<;<<<<<<<<<
+@EAS54_71:8:234:21:950
+TTTTTTTTTTTTCTCCTCTCTTTTTTTTTTTTT
++
+<<<<<<<<<&<;2;&-<,<+;<<<7<<<;<;<;
+@EAS54_71:8:321:642:388
+TACCAAATGTGTTTATTACCAGAGGGATGGAGG
++
+19<<<<<8<<<<<<<<;<<<<<<<<<<7<<<<<
+@EAS54_71:8:321:642:388
+TCCCATTTGGAGCCCCTCTAAGCCGTTCTATTTGT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<6<<<8;
+@EAS54_71:8:38:856:336
+AATGGACCTGTGATATCTGGATTCTGGGAAATT
++
+<<<<<<<<<<<;;<;<;<:69<<;<5-500373
+@EAS54_71:8:38:856:336
+CACACATGGTTTAGGGGTATAATACCTCTACATGG
++
+2;4;4<:;6:5:<<;:;<<;<<;<<<<<<<<<<<<
+@EAS54_73:3:203:419:243
+GGAAAAAGAAAAAGTGAGAAGTTTGGAAAAACTAT
++
+;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS54_73:3:203:419:243
+TTGAAAGCTCTAACAATAGACTAAACCAAGCAGAA
++
+<<<<<<<<<<<<<<<9<;<8<<<;<<<;<<<4<77
+@EAS54_73:3:239:796:221
+ATAACTATGAAGAGACTATTGCCAGCTGACCCCCC
++
+<<<7<<7<<7<<7<;<<<<<,;;,+'<+/+99%:'
+@EAS54_73:3:239:796:221
+GGAAGAACAGCTTAGGTATCAATTTGGTGTTCTGT
++
+;;<<;<<;<<<+:<<<4<4<<<<<<<<<<<<<<<<
+@EAS54_73:3:23:502:103
+AGTCCCTGCCCCATCTCTTGTAATCTCTCTCCTTT
++
+<2<<<<<<<<<<.<<<<<<<:1&:<<<7<<<<<<:
+@EAS54_73:3:23:502:103
+GACACCCAACTAATATTTGTCTGAGCAAAACAGTC
++
+4:386:6<:::<:<:4:+<::4<<<6<<<<<<<66
+@EAS54_73:3:29:833:612
+AAGCTCTAACAATAGACTAAACCAAGCAGAAGAAA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<;<<;;<<;;
+@EAS54_73:3:29:833:612
+CAGGTATTCCTGAGGAAAAAGAAAAAGTGAGAAGT
++
+<<;<<<;<::<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS54_73:3:313:827:992
+AAAGTCTCAGGGAGCCGTCCGTGTCCTCCCATCTG
++
+<<<<6<<<<:<<<<<66<<<:33:<<<80<;6<8+
+@EAS54_73:3:313:827:992
+TGTTTCTTTGTTTGATTTGGTGGAAGACATAATCC
++
+'187:1'<75<.*<<:5<..<<*<<917<<7<<17
+@EAS54_73:3:37:761:635
+CCTCTTCTTCCAAAGATGAAACGCGTAACTGCGCT
++
+<6<<<<<<6<<<<<<<<<<<<<<<<<8<8<<4<4<
+@EAS54_73:3:37:761:635
+TGTGAGCCATCACAATGAACAACAGGAAGAAAAGG
++
++37:<088<+<<;<<;<<<<<;<<;<<<<<<<<<<
+@EAS54_73:3:4:854:140
+CCTGACAAGCAAATGCTAAGATAATTCATCATCAC
++
+:9':<;<<<;<<<;<<<<<<<<<<<<<<<<<<<<<
+@EAS54_73:3:4:854:140
+GTCATCTATAAAGGAAATCCCATCAGAATAACAAT
++
+<<<6<<<:<6<<<:36:<<<<3<<8:.6<38::4<
+@EAS54_73:3:88:24:744
+GTCCTGTGATATCTGGATTCTGGGAAATTCTTCAT
++
+4%++88;-9<;<<<+8<<<:<;8:<<<<<<<<<<<
+@EAS54_73:3:88:24:744
+TGTCAATGTCAGGGAAGGAGCATTTTTGAAGTTTA
++
+<7*:<<::.'<<<<:<<:<<'<63'6+'303*%%+
+@EAS54_73:5:145:635:390
+TAAACCAGTCCTATAAGAAATGCTCAAAAGAATTG
++
+<<<<<<<<<<<<<<<<<<:<<<<<<<8<<<::;;;
+@EAS54_73:5:145:635:390
+TTGAATAAAAAGGGATTAAATTCCCCCACTTAAGA
++
++9;<<;<<<<<;;;<;<<<<<<<<<<<<<<<<<<<
+@EAS54_73:5:169:714:644
+CCTAATTGGTACAATGTACAATATTCTGATGATGG
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<;<
+@EAS54_73:5:169:714:644
+GAAAAAAGTAAACTCTCAAATATTGCTAGTGGGAG
++
+;<<<<<<;<<<:<<<<<<<<<<<<<<<<<<<<<<<
+@EAS54_73:5:220:733:736
+CCATCCTACTAAATACATATGCACCTAACACAAGA
++
+:;<77;<<9<<<<<9;<<<<<<;<<<<<<<<<<<<
+@EAS54_73:5:220:733:736
+TTAATAAAGACATGAGTTCAGGTAAAGGGGTGGAA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<5<<;9
+@EAS54_73:5:231:339:551
+CTGAGAGATTCTGCAGCCCAGATCCAGATTGCTTG
++
+<;<<;<<<<<<<<<<;:<<<<<<<<<<<<<;<<<<
+@EAS54_73:5:231:339:551
+TGTCAGTTACCAAATGTGTTTATTACCAGAGGGAT
++
+<<<<<<;<<<<<<;<<<<<<<<<<;5<<46;<;:1
+@EAS54_73:5:255:796:239
+AAGGGATTAAATTCCCCCACTTAAGAGATAGAGAT
++
+<<3;;<7:<<<;(7<<7;<<;<<<<<<<<<7<<<<
+@EAS54_73:5:255:796:239
+ATGCTCAAAAGAATTGTAAAAGTCAAAATTAAAGT
++
+<<<<<<<<6<<<<<<<<<<<<<<<<;6<<<:<:<<
+@EAS54_73:5:263:557:988
+AATGATAAAAAGATCAATTCAGCAAGAAGATATAA
++
+<<<<<<<<<<<<<<<<<<<<<;;<<<<<<<<;<<<
+@EAS54_73:5:263:557:988
+CTGCTACTCAATATATCCATGTAACAAATCTGCGC
++
+1-41:<15+<<<<<<599<<<<<<<<<<<<<<<<<
+@EAS54_73:5:271:874:367
+AAAAAACCTGTCAAACACGAATGTTATGCCCTGCT
++
+<<<<<<5;<<<:<<<;<;<<<<<<<<<<<<<<<<<
+@EAS54_73:5:271:874:367
+ATATGTAGTCATCAGACTATCTAAAGTCAACATTA
++
+<<<<<<<<<<<<<<4<;<;<:<;4<4<<99<7<+%
+@EAS54_73:5:3:233:911
+GTCTCATCTAGGGGAACAGGGAGGTGCACTAATGC
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS54_73:5:3:233:911
+TGGCTGATTATGAAAACAATGTTCCCCAGATACCA
++
+<<<<<<<<<<<<<<<<<;<<<<<<<<<<;<;<<;<
+@EAS54_73:5:44:498:945
+ATAGGGATGGAGGGAAGAGGGCCGCTGAAGAACTT
++
+<%*50<7<4<<<7<,<<.<8/,9<:</<<<;<;<<
+@EAS54_73:5:44:498:945
+CCTATAAGCCGTTCTATTTGTAATGAAAACTATAT
++
+;<;<<<<<<<<<<9<;<:<<<<<<:<<<<;:;<3<
+@EAS54_73:5:53:61:31
+AAGAAACTCATTAATAAAGACATGAGTTCAGATAA
++
+<<<7;<7<<<;7<;;<7<7<7<;5<73<<</%;/;
+@EAS54_73:5:53:61:31
+CAATTCAGCAAGAAGATATAACCATCCTACTAAAT
++
+5;;<95<<5<<<<<<<<<<:5;<<<<<<<<<<<<<
+@EAS54_73:7:134:243:630
+ACATTACTACCCTGCAATTAATATAATTGTGTCCA
++
+63<;37:<*&:<<<,,*<<:7<<7<<<<<<<::<<
+@EAS54_73:7:134:243:630
+TCATCTAGGGGAACAGGGAGGCGCACTAATGAGCT
++
+<<<:<<<<</<<<-<<<<6/<-<:<5+<::-2</2
+@EAS54_73:7:200:65:291
+CAATACTCACCATCATAAATACACACAAAAGTACA
++
+<<<<1<<<<<<<<<<<<<<<<<<<:<8<<<<:<;<
+@EAS54_73:7:200:65:291
+CTAACTATATGCTGTTTACAAGAAACTCATTAATA
++
+;9<;3<<9<7<;<<<<<<<<<<<<<<<<<<<<<<<
+@EAS54_73:7:223:440:667
+AATTGGGGAAAACCTCTTTAGTCTTGCTAGAGATT
++
+<<;;<;;<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS54_73:7:223:440:667
+TTCAGAACTTGAAGACAAGTCTCTTATGAATTAAC
++
+<<<<<<<<<<<<<<<<<<<;<<<<<<<<;<<<<;;
+@EAS54_73:7:254:572:431
+AAGAGATATAGATTGGCAGAACAGATTTAAAAACA
++
+<<<<<<<<<<<<<<<<;<<<<<<<<<<<99;;;;;
+@EAS54_73:7:254:572:431
+ATCAGATAAAGCACACTTTAAATCAACAACAGTAA
++
+<63<;<;<<<:7<:<7;<:<<<<:<<<<7<<<<:<
+@EAS54_73:7:63:854:610
+AATTTGGTGTTCTGTGTAAAGTCTCAGGGAGCCGT
++
+:.5;2<:88<<72:<<;<<7<8;<;/<<<<<<<<<
+@EAS54_73:7:63:854:610
+GACTATTGCCAGATGAACCACACATTAATACTATG
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<;<<
+@EAS54_73:7:97:892:419
+AATAAAGTCAAGTCTTTCCTGACAAGCAAATGCTA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS54_73:7:97:892:419
+GCAACTAGGTAAAAAATTAACATTACAACAGGAAC
++
+;8<<;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS54_81:2:128:394:455
+GTAATCTCTCTCCTTTTTGCTGCATCCCTGTCTTC
++
+;=;9.=5=;=9====;;==================
+@EAS54_81:2:128:394:455
+TTAGGGAAGAACAGCTTAGGTATCAATTTGGTGTT
++
+======6==========;===9==;5===;==;==
+@EAS54_81:2:27:856:401
+ACCTCTACATGGCTGATTATGAAAACAATGTTCCC
++
+======6===;2==;===;=+=92=;5+=&556:6
+@EAS54_81:2:27:856:401
+TCATCTAGGGGAACAGGGAGGTGCACTAATGCGCT
++
+.'=.93======;;====;======;===;=;===
+@EAS54_81:2:280:512:316
+GGGAAGAACAGCTTAGGTATCAATTTGGTGTTCTG
++
+;9===;======;7==;;======;=====;====
+@EAS54_81:2:280:512:316
+TTACTGTCATAACTATGAAGAGACTATTGCCAGCT
++
+==<========6==4==6;;==:===;=2/:+8%6
+@EAS54_81:2:285:367:932
+ATAGACCCCCTTGCAACAACCTTGAGAACCCCAGG
++
+===========;======;=====;=======5==
+@EAS54_81:2:285:367:932
+GCGTAACTGCGCTCTCATTCACTCCAGCTCCCTGT
++
+9=5==;=;7===;==;===================
+@EAS54_81:2:317:72:221
+AAAAAAATTCTAAAATCAGCAAGAGAAAAGCATAC
++
+=========:======;==;===============
+@EAS54_81:2:317:72:221
+ATTTGAGGAAGTAATTGGGGAAAACCTCTTTAGTC
++
+===========;=======;;:==6=;=====;==
+@EAS54_81:2:31:98:804
+CACGAATGCGTCTCTACCACAGGGGGCTGCGCGGC
++
+=======9===;============5=;9=;=;==&
+@EAS54_81:2:31:98:804
+CTTTACTGTCATAACTATGAAGAGACTATTGCCAG
++
+====;========7=====================
+@EAS54_81:2:49:330:699
+AAAGTTCAATACTCACCATCATAAATACACACAAA
++
+===/=;========;=;==================
+@EAS54_81:2:49:330:699
+TTTTGGACTTCTTAAAGAAAAAAAAACCTGTCAAA
++
+==;=================;======5;;;==5=
+@EAS54_81:2:5:491:391
+CCCTGCTCACAGTTTCTGCCCCCAGCATGGTTGTA
++
+-/+5-.&&:5+:92=6===========9=======
+@EAS54_81:2:5:491:391
+TTGGCATTTGCCTTCAGACCCTACACGAATGCGTC
++
+=========;===;==:4=========;3;==7;=
+@EAS54_81:6:11:801:386
+AAAGGGATTAAATTCCCCCACTTAAGAGATATAGA
++
+<<<<<<<<<<8<<<<<:4<::<854:5<:::;4+4
+@EAS54_81:6:11:801:386
+CACTATAAATCAACAACAGTAAAATAAAACAAAGG
++
+5<2:$6<<<38<<<<;<<<<<<<<<<<<<<<<<<<
+@EAS54_81:6:122:589:134
+AAAACCTGTCAAACACGAATGTTATGCCCTGCTAA
++
+;<;4<<538<<;<<;<<<<';,:<<<<<<<<<<<<
+@EAS54_81:6:122:589:134
+ACAGACTTCATCAAGATATGTAGTCATCAGACTAT
++
+<<:<<:<:<<<<<:<8<<<<<<<:<::<<<4:<;;
+@EAS54_81:6:199:511:426
+AATTCTTCATCCTGGACCCTGAGAGATTCTGCAGC
++
+<<<<<<<<<<<<<<;<<<<<<:<<<<<<<<<;:<;
+@EAS54_81:6:199:511:426
+GGGGTATAATACCTCTACATGGCTGATTATGAAAA
++
+<:7:<<<<<<<<<<<<<<<<<;<<<<<<<<<<<<<
+@EAS54_81:6:204:779:181
+AACAACAGGAAGAAAAGGTCTTTCAAAAGGTGATG
++
+<<<<<<5<<:<<<<<8<<,<<<<<<<<<<91<91<
+@EAS54_81:6:204:779:181
+CTTTTGGCATTTGCCTTCAGACCCTACACGAATGC
++
+;:;/*<:<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS54_81:6:265:251:147
+AAAAGTACAAAACTCACAGGTTTTATAAAACAATT
++
+<<<<::<8<<<;<;8<8<<<<<<<<:<<<<<<<<<
+@EAS54_81:6:265:251:147
+TGTTATGCCCTGCTAAACTAAGCATCATAAATGAA
++
+<<<<<<<<<<<<<<88<<<80:;<<<<<;:4;;:4
+@EAS54_81:6:273:424:207
+AAGAGATATAGATTGGCAGAACAGATTTAAAAACA
++
+<,<,<9<<9<<<<<<<<<<79<,599,<191<99+
+@EAS54_81:6:273:424:207
+TAAATCAACAACAGTAAAATAAAACAAAGGAGGTC
++
+;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS54_81:6:35:186:412
+ATAACCATCCTACTAAATACATATGCACCTAACAC
++
+<<<<<<<<4<<<<<:<<<<<<:<<<<<<<<<;;<:
+@EAS54_81:6:35:186:412
+CATGTAACAAATCTGCGCTTGTACTTCTAAATCTA
++
+<<4:6<;<&<:4<<<<<<<<;<<<<<<<<<<<<<<
+@EAS54_81:6:75:917:886
+ACTGGGCAATACATGAGATTATTAGGAAATGCTTT
++
+<<<<<<<<<<<<<<:<<<<<<<<<71<<<:6<:8<
+@EAS54_81:6:75:917:886
+TTATCATGACTCTATCCCAAATTCCCAATTACGTC
++
+<<<<8<<<<<<8<<<<<<<<<<<<<<<<<<<<<<<
+@EAS54_81:7:124:253:889
+CTAAGCATCATAAATGAAGGGGAAATAAAGTCAAG
++
+8<<<<<<<<<<<<<<<<<<<<<<<<<:<<<<<<<<
+@EAS54_81:7:124:253:889
+TCAGCAAGAGAAAAGCATACAGTCATCTATAAAGG
++
+<<<<<<6<<:<<<<<<<<<<<<<;;<<;<<<<<<<
+@EAS54_81:7:166:979:531
+ATCCCACGCTTCCTATGGAAAGGTTGTTGGGAGAT
++
+81<<<3<*<<:<<<<<<<8<<<<<<<<<<<<:<<<
+@EAS54_81:7:166:979:531
+TGGTTCTCTTGAAAGCTTGGGCTGTAATGATGCCC
++
+<<</<<<<<<<<<9<<9<<;<7<<<<9<<<9<,)6
+@EAS54_81:7:226:869:36
+ATATATAAAGGAAATCCCATCAGAATAACAATGGG
++
+<0/)</<<<:<<<<<)<<7<<<<<+55<<1<<<:<
+@EAS54_81:7:226:869:36
+TGAGGAAGTAATTGGGGAAAACCTCTTTAGTCTTG
++
+:<<<<,:<;:.:<<:<<717,;2171717717116
+@EAS54_81:7:246:205:734
+CTCCAGGGAAGTTATCTCTCATCTAGANNNNNTTG
++
+<<<<<<:/<<<,6'</7;<-+9<<;<7!!!!!8<,
+@EAS54_81:7:246:205:734
+CTGTCTTCCTCTGTCTTGATTTACTTGTTGTTGGT
++
+<<<4<<6666<<6<:<<<3<<<:'<<:<<<<;6<+
+@EAS54_81:7:293:355:321
+GCTAGAGTCCCATTTGGAGCCCCTCTAAGCCGTTC
++
+<<<:<;<<<<<<<;<<<<<<<<<;<<;4<<<:+:<
+@EAS54_81:7:293:355:321
+TTACCAAATGTGTTTATTACCAGAGGGATGGAGGG
++
+<<4<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS54_81:7:324:472:791
+AAAGCCAATACTTTACTGCTACTCAATATATCCAT
++
+<<.)5*&;;11<<<,5<33:-<<6<<<<:<<<<<<
+@EAS54_81:7:324:472:791
+TGATAAAAAGATCAATTCAGCAAGAAGATATAACC
++
+<<<<<<<<:<<<<<<<<<<<<<<:<<<<<<<<<:3
+@EAS54_81:7:325:150:465
+AACAACAGGAAGAAAAGGTCTTTCAAAAGGTGATG
++
+<<:<<<<<<<<;<:<<<<;<<<<<<<<<<<<<<<<
+@EAS54_81:7:325:150:465
+TGATGCCCTCTTCTTCCAAAGATGAAACGCGTAAC
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<:<<<3;;:
+@EAS54_81:7:74:596:137
+CTCTATCCCAAATTCCCAATTACGTCCTATCTTCT
++
+<<<<<<<<<</4<<<<<<*<:6<<<<<<<<;/3<<
+@EAS54_81:7:74:596:137
+GGTCCCTGCCCCATCGCTTGTAATCTCTCGCCTTT
++
++40778449779049'+*87489498949%89948
+@EAS54_81:8:130:912:658
+TACACACACATGGTTTAGGGGTATAATACCTCTAC
++
+<<<<<;<<<<<<;<<<<<<<<<<<<<<<<<7<;;<
+@EAS54_81:8:130:912:658
+TCCCATCATGAAGCACTGAACTTCCACGTCTCATC
++
+;=;;;<<<<<=55=;==<=======<=========
+@EAS54_81:8:142:858:903
+ATGGTTGTACTGGGCAATACATGAGATTATTAGGA
++
+======;====5=======9======;===3=5=;
+@EAS54_81:8:142:858:903
+CTATCCCAAATTCCCAATTACGTCCTATCTTCTTC
++
+<<<<<;<<<<9<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS54_81:8:14:360:580
+ACCCTACACGAATGCGTCTCTACCACAGGGGGCGG
++
+===========3===;5<==8;====79==.=5'5
+@EAS54_81:8:14:360:580
+ATGAGATTATTAGGAAATGCTTTACTGTCATAACT
++
+<,1<;<;;<<<<<1<<<;<7<<6<:;;<<<<<<;;
+@EAS54_81:8:159:71:155
+AAAGGTTGTTGGGAGATTTTTAATGATTCCTCGAT
++
+5;;9<<:<;:<<<<7<<7;<3<<<:<<<;<<<<<;
+@EAS54_81:8:159:71:155
+GTCCACACTGGTTCTCTTGAAAGCTTGGGCTGTAA
++
+=========;=<======;=:=3;==;=6<==;=;
+@EAS54_81:8:177:800:714
+CTAAATGAAAGAGGCTCAAAGAATGCCAGGAAGAT
++
+<<<<<<<<<<<<<<<<<<<<<;<<<;<;<<<<<;<
+@EAS54_81:8:177:800:714
+TTCTCAGCAGAAACCTTACAAGCCAGAAGAGATTG
++
+=;3=+=<:=<========8================
+@EAS54_81:8:271:180:509
+AATACTCACCATCATAAATACACACAAAAGTACAA
++
+=============================='====
+@EAS54_81:8:271:180:509
+ATATAGATTGGCAGAACAGATTTAAAAACATGAAC
++
+<<<<<<<<<9<:<<<<:<<<<<<<<<<<<<<<<<<
+@EAS54_81:8:40:925:442
+GAGGTTCAGAACTTGAAGACAAGTCTCTTATGAAT
++
+;<;<<<<<<<<<<<3;<7;:<;;<<<;<<:<32<<
+@EAS54_81:8:40:925:442
+TTTGAGGAAGTAATTGGGGAAAACCTCTTTAGTCT
++
+=;=================================
+@EAS54_81:8:41:530:663
+AGAACAGATTTAAAAACATGAACTAACTATATGCT
++
+=8=;*=5==;;=====:=====;===;========
+@EAS54_81:8:41:530:663
+ATACTCACCATCATAAATACACACAAAATTACAAA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<7;;;;<<
+@EAS54_81:8:63:930:152
+ACTGGTTCTCTTGAAAGCTTGGGCTGTAATGATTC
++
+<<<<;<<<<<<<7<<;::<<)726;)<99<)&;&+
+@EAS54_81:8:63:930:152
+ATCCCACGCTTCCTATGGAAAGGTTGTTGGGAGAT
++
+;:4:8;:::;=:8;=;========;=:========
+@EAS54_81:8:78:735:536
+TTTTTTTTTTTTTCATTTCTCTTTTTTTTTTTTTT
++
+;9<<<<<<<.7<9'%1<<)2::<<<<<<<<<<<<<
+@EAS56_53:1:124:243:35
+GCATATCCAGATTGCTGGTGGTCTGACAGGCAGCA
++
+&+<+;<694;+&99<<2<;423<26<-<<<<,<3<
+@EAS56_53:1:124:243:35
+TGTGTTTATTACCAGAGGGATGGAGGGAAGAGCGA
++
+<<<<<;;<<<<<<:<<<.<<<:++5+:1(;1;$<(
+@EAS56_53:1:154:118:488
+AAAAGCATACAGTCATCTATAAAGGAAATCCCATC
++
+<<<<<<<<<<<<<<<<<<<<<<:7<<<<7<:;;::
+@EAS56_53:1:154:118:488
+AAAGTCAAGTCTTTCCTGACAAGCAAATGCTAAGA
++
+<<<;58<<95:<<;<;<<<;<<<;;<<<<<<<<<<
+@EAS56_53:1:23:403:981
+TACTGTCATAACTATGAAGAGACTATTGCCAGATG
++
+<8<<<;<<<<<<;<<<<<<8;<<<9<9,3;,6(91
+@EAS56_53:1:23:403:981
+TCTTCATAGGGAAGAACAGCTTAGGTATCAATTTG
++
+(;3+<&3<</7<<<<<<;<<<<<<<<<<<<</<2<
+@EAS56_53:1:47:303:887
+ACATTACTACCCTGCCATTAATATACTTGTGTCCA
++
+<<;;<+<9<<<<<9<(6<;//</<8(<<89;6084
+@EAS56_53:1:47:303:887
+CACACTGGTTCTCTTGAAAGCTTGGGCTGTAATGA
++
+<;<6<;<;<8<<<8<<<<;<<<.<<<<<<<8<8;<
+@EAS56_53:1:92:875:345
+AAATGCTCAAAAGAATTGTAAAAGTCAAAATTAAA
++
+<<<;<.;7<<<<<<<<<<<<<<<<<;<<<<<<<<<
+@EAS56_53:1:92:875:345
+CGGAAACCTTACAAGCCAGAAGAGATTGGATCTAA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS56_53:2:170:265:818
+GAGGGGAAGCTTTCAACGCTTCTAGCACTTTCTTT
++
+<<<<<(5/959<8.<9<8<<<2<&59&&:22:8+(
+@EAS56_53:2:170:265:818
+TTCTCACAGTTTCTGCCCCCAGCATGGTTGTACTG
++
+3+;%;.;;<<9+;3;;;<<<;57<1<;<<<<<<<;
+@EAS56_53:2:59:286:290
+AAAGGAAATCCCATCAGAATAACAATGGGCTTCTC
++
+<<<<<<<<;<<<;<<<<<<<<<<<<<;;;<<;7;<
+@EAS56_53:2:59:286:290
+TCAAGTCTTTCCTGACAAGCAAATGCTAAGATAAT
++
+77<<<<7<<<97<<,7<<<;<<<;<9<<<<<<<<<
+@EAS56_53:3:101:809:776
+GTACTTCTAAATCTATAAAAAAATTAAAATTTAAC
++
+<<<-<;7;<<<<:;<<<7<<<<<<<<<<<<<<<<<
+@EAS56_53:3:101:809:776
+TATGCACCTAACACAAGACTACCCAGATTCATAAA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<:<<<<<<<<<
+@EAS56_53:3:107:738:484
+GGTCATCATACAATGATAAAAAGATCAATTCAGCA
++
+.8/<<<7<8<<<<<<<<<<<<<<<<9<<<<<<<<<
+@EAS56_53:3:107:738:484
+TGAACTAACTATATGCTGTTTACAAGAAACTCATT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<:<<<<<<<<<
+@EAS56_53:3:126:558:408
+TTCTATTTGTAATGAAAACTATATTTATGCTATTC
++
+<<<<<<<<<<<<<:<<<<<<<<<<<<<<7<;<<;;
+@EAS56_53:3:126:558:408
+TTTATTACCAGAGGGATGGAGGGAAGAGGGACGCT
++
+<:<<:;;<<<<<<<<8<<<<<<<<<<<<<<<<<<<
+@EAS56_53:3:134:126:465
+AAAAAGTGAGAAGTTTGGAAAAACTATTTGAGGAA
++
+<<<<<<<<<<<<<;<<<<<<<<<<<<<5<<:<<41
+@EAS56_53:3:134:126:465
+AAATCAGCAAGAGAAAAGCATACAGTCATCTATAA
++
+<<;:&<3)<<7<:<<<<.:<<<<<8<<<<<<<<<<
+@EAS56_53:4:130:568:978
+TAAATATAGAAATTGAAACAGCTGTGTTTAGTGAC
++
+7<<;<<;<7<:;<7<<<<<<<<);4;+<7+3+%;<
+@EAS56_53:4:130:568:978
+TGAAACGCGAAACTGCACTCTCATTCACTCCAGCT
++
+--;066;;62<<<2&<+<+<2;<<2<<<;<<<7<<
+@EAS56_53:4:153:977:200
+TCATCAACCTCATACACACACATGGTTTAGGGGTA
++
+1:<83<<9;;9<<9;;<<;<<;;;;<;;<<<<<<;
+@EAS56_53:4:153:977:200
+TGTCACCCAATGGACCTGTGATATCTGGATTCTGG
++
+;<<;<<<<7<<;;;;;<<6<<<<<86;;8<;8;6;
+@EAS56_53:4:154:762:630
+AGGAAGAAAAGGTCTTTCAAAAGGTGATGTGTGTT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;;
+@EAS56_53:4:154:762:630
+CCTTCAGACCCTACACGAATGCGTCTCTACCACAG
++
+<<-::<91<<<<;<;<<<<;<<<<<<<<;<<<<<<
+@EAS56_53:4:168:528:288
+CAGGCTGCAACTGTGAGCCATCACAATGAACAACA
++
+<<<<<<<<<<<<<<<<<<<<<<<<:<<<<<<;<<;
+@EAS56_53:4:168:528:288
+GCTCCCCAGAGGGAAAGCTTTCAACGCTTCTAGCC
++
+8<%<31;<<;<;<<<<<<<;<<<<<<<<<<;<<<<
+@EAS56_53:4:45:707:147
+AAAAATTCTAAAATCAGCAAGAGAAAAGCATACAG
++
+<<<<<<;3<<<<<4;<<;<<<<<<<<<<<<<<<<<
+@EAS56_53:4:45:707:147
+ATGAGTCACAGGTATTCCTGAGGAAAAAGAAAAAG
++
+<<<<<<<<<<<<&<<<<:<<9<<<9<<<<75;;;<
+@EAS56_53:6:180:695:621
+ATACAGTCATCTATAAAGGAAATCCCATCAGAATA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;::<<<
+@EAS56_53:6:180:695:621
+TACTGAAAAGCAAATGCTAAGATAATTCATCATCA
++
+;&377<&<<;7<<<<<7<<<<<<<<<<<<<<<<<<
+@EAS56_53:7:22:22:934
+ATTTGTCTGAGCAAAACAGTCTAGATGAGAGAGAA
++
+<+72::72<<60<<<<<<<96<<<<0<<<<1<<<<
+@EAS56_53:7:22:22:934
+CTGCATCCCTGTCTTCCTCTGTCTTGATTTACTTG
++
+<<<<<<<<<<<6<<<;<<<;84;<<48;<;6;<;)
+@EAS56_53:8:122:430:882
+CCTACTAAATACATATGCACCTAACACAAGACTAC
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<:;
+@EAS56_53:8:122:430:882
+CTATAAAAAAATTAAAATTTAACAAAAGTAAATAA
++
+0<<:<<<<<<<:3<<<<<<<<<:<<<<<<<<<<<<
+@EAS56_53:8:179:549:753
+TACTACCCTGCAATTAATATAATTGTGTCCATGTA
++
+<<<<<<<<<<<<<<<<<<<<<<<<8<7<<<:<9<<
+@EAS56_53:8:179:549:753
+TGTCCTCCCATCTGGCCTCGTCCACACTGGTTCTC
++
+:77<</<<<::<:<<<<<<<<<<<<<<<<<<<<<<
+@EAS56_53:8:28:701:724
+TGGACCCTGAGAGATTCTGCAGCCCAGCTCCAGAT
++
+.;..3;8.8<8;<<;9<9<<<7;<<<<<<<<7<<7
+@EAS56_53:8:28:701:724
+TTTTGTCAGTTACCAAATGTGTTTATTACCAGAGG
++
+<<<<<<7<<<<<<7::<:<<-<<::::::<747::
+@EAS56_57:1:122:38:103
+ATAAAACAATTAATTGAGACTACAGAGCAACTAGG
++
+<<<<<<<<<<<<<<<<;<<<<<<<<3<<<<9<8;<
+@EAS56_57:1:122:38:103
+GAGTTCAGGTAAAGGGGTGGAAAAAGATGTTCTAC
++
+===;3<===:=======<=================
+@EAS56_57:1:125:884:276
+TTGCAAGACAGACTTCATCAAGATATGTAGTCATC
++
+<<<<<<<<<<<8<<<<<<<<<<<<<<<<<<;;<<;
+@EAS56_57:1:125:884:276
+TTTGGACTTCTTAAAGAAAAAAAAACCTGTCAAAC
++
+,;;3,<7<;7<<===;============;======
+@EAS56_57:1:189:130:136
+ATTTAGACATCTAAATGAAAGAGGCTCAAAGAATG
++
+==<<=================<<====<<=;=6==
+@EAS56_57:1:189:130:136
+GGCTTCTCAGCAGAAACCTTACAAGCCAGAAGAGA
++
+823;23<7<57<7<<<<<;<<;<<<<<<<<<<<<<
+@EAS56_57:1:189:503:110
+ATTCCTGAGGAAAAAGAAAAAGTGAGAAGTTTGGA
++
+=;;6:==============================
+@EAS56_57:1:189:503:110
+CTAACAATAGACTAAACCAAGCAGAAGAAAGAGTT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<:<
+@EAS56_57:1:228:182:717
+GGTCTGACAGGCTGCAACTGTGAGCCATCCCCATG
++
+<=9============5==5=<,59<=1=<&;&;;7
+@EAS56_57:1:228:182:717
+TCTTACTTCCAGCTCCCCAGAGGGAAAGCTTTCAA
++
+778;8;474<<<;2;;<2<<<<<<<<;<;;9<<<<
+@EAS56_57:1:278:440:902
+AAGCACTGAACTTCCACGTCTCATCTAGGGGAACA
++
+=========<==<==============:;;=;=;;
+@EAS56_57:1:278:440:902
+ATACTATGTTTCTTATCTGCACATTACTACCCTGC
++
+<;7;4<;<;;;<<;<;;;<<<<<9<<<;<<<<;<<
+@EAS56_57:1:288:384:444
+TAACTTTGAATAAAAAGGGATTAAATTCCCCCACT
++
+;=9;;<====<=;=/=9;<========<=======
+@EAS56_57:1:288:384:444
+TCAAAAGAATTGTAAAAGTCAAAATTAAAGTTCAA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;;;;
+@EAS56_57:2:158:909:321
+ATACAGTCATCTATAAAGGAAATCCCATCAGAATA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS56_57:2:158:909:321
+TTTGAGGAAGTAATTGGGGAAAACCTCTTTAGTCT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<
+@EAS56_57:2:178:192:499
+GTGAGCCATCACAATGAACAACAGGAAGAAAAGGT
++
+<<<<<<<;<1<<<<<<;<<;6<<3666;;;;;/6/
+@EAS56_57:2:178:192:499
+TCTAGCCATTTCTTTTGGCATTTGCCTTCAGACCC
++
+86<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS56_57:2:206:873:186
+ACAATAGACTAAACCAAGCAGAAGAAAGAGGTTCA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<:;53
+@EAS56_57:2:206:873:186
+GTATTCCTGAGGAAAAAGAAAAAGTGAGAAGTTTG
++
+;<<;--7<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS56_57:2:236:841:20
+AAAGGAAATCCCATCAGAATAACAATGGGCTTCTC
++
+<<<<<<<<<<<<<<<<<7<<<<:<<9<<<<;<:<9
+@EAS56_57:2:236:841:20
+GCTAAGATAATTCATCATCACTAAACCAGTCCTAT
++
+7;<<<;<<<<;;<<<<<<<<<<<<<<<<<<<<;<<
+@EAS56_57:2:237:855:581
+CTAAACGCCCATACTTTACTGCTACTCAATATATC
++
+/+<<<&)2;66;/;;+<;;3133<3<3;9;<999<
+@EAS56_57:2:237:855:581
+TACAATGATAAAAAGATCAATTCAGCAAGAAGATA
++
+<;4<7<<<;47<<74<:*<<2:<<7.799:2<<9:
+@EAS56_57:2:23:268:529
+TGAAAGAGGCTCAAAGAATGCCAGGAAGATACATT
++
+7;<<<<<<57;-<<<<<<:<77<<<<<<<;<;<<<
+@EAS56_57:2:259:42:969
+GCTGTAATGATGCCCCTTGGCCATCACCCGGTCCC
++
+<<<<<;<<;<<3<<<;9<36<<29;<<;;;</;<2
+@EAS56_57:2:259:42:969
+GGAAAGGTTGTTGGGAGATTTTTAATGATTCCTCA
++
+<<<6<<<<<<-<<<<<<;<<;<6<<<<<<<;<<<<
+@EAS56_57:2:262:297:601
+TGGACCTGTGATATCTGGATTCTGGGAAATTCTTC
++
+<<<<;<<9<<57<<7<<<;<<;77-;;53<<;;<7
+@EAS56_57:2:262:297:601
+TGTTCTCATCAACCTCATACACACACATGGTTTAG
++
+;;<26;;;<;<7;<<<<<99<<<<<<<<<<<<<<<
+@EAS56_57:2:284:597:682
+AAAAAAAAACCTGTCAAACACGAATGTTATGCCCT
++
+<<<<<<<<9;;7<;:<<<:<;<<<<<<<<;<<<<;
+@EAS56_57:2:284:597:682
+TTCATCAAGATATGTAGTCATCAGACTATCTAAAG
++
+<<<<<<<9<<<<<;<<6<<<<<;<9<<<<<<1;;9
+@EAS56_57:2:44:153:969
+AAAAAGTGAGAAGTTTGGAAAAACTATTTGAGGAA
++
+*:::7<77<:<<<<:<<(597:<:<9//7<529/0
+@EAS56_57:2:44:153:969
+AAAAGCATACAGTCATCTATAAAGGAAATCCCATC
++
+<<5<:7<72<51<7<*79<<<<<5<<<<<<<<<2<
+@EAS56_57:3:112:729:591
+ATTGGGGAAAACCTCTTTAGTCTTGCTAGAGATTT
++
+;;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS56_57:3:112:729:591
+GAAGAAAGAGGTTCAGAACTTGAAGACAAGTCTCT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS56_57:3:119:761:239
+CGTCTCTACCACAGGGGGCTGCGCGGTTTCCCATC
++
+<<<<<<<<<<<<6<<<<<<;<2<<<<;<<<<<;;<
+@EAS56_57:3:119:761:239
+TGAAGAGACTATTGCCAGATGAACCACACATTAAT
++
+;;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS56_57:3:285:489:327
+AATAGACTAAACCAAGCAGAAGAAAGAGGTTCAGA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<<<
+@EAS56_57:3:285:489:327
+CTGAGGAAAAAGAAAAAGTGAGAAGTTTGGAAAAA
++
+9;;<<8<<<<<<<<<<<<;<<<<<<<<<<<<<<;<
+@EAS56_57:3:319:174:811
+CACTGGTTCTCTTGAAAGCTTGGGCTGTAATGATG
++
+;7;3<<3.<<<<<<<<<<<4<<<<<<<<<<<<<0<
+@EAS56_57:3:319:174:811
+TTATCTGCACATTTCTACCCTGCAATTAATATAAT
++
+<<<<<<<<<;<<<<<<<<<;;<<<<<<<8<<;9<<
+@EAS56_57:3:41:739:907
+CAGAAGAGATTGGATCTAATTTTTGGACTTCTTAA
++
+;<;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS56_57:3:41:739:907
+GAATGCCAGGAAGATACATTGCAAGACAGACTTCA
++
+<<<<<<<<<<<<<<<<<<<<<<<<;<9<<<;;;;;
+@EAS56_57:3:81:786:340
+TACTATGTTTCTTATCTGCACATTACTACCCTGCA
++
+;<;<<<;<<;<<<<;<<<<<<<<<<<<<<<<<<<<
+@EAS56_57:3:81:786:340
+TCCACGTCTCATCTAGGGGAACAGAGAGGTGCACT
++
+<<<<7<<<<<<<<<<<<<<7<<;<&<<;;7<7;;;
+@EAS56_57:4:233:478:792
+GCCTTCAGACCCTACACGAATGCGTCTCTACCACA
++
+6<;9:<<9-<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS56_57:4:233:478:792
+GTGTTCTCATCAACCTCATACACACACATGGTTTA
++
+<<<<<<<<<<<<<<<<<<<+<<<<<<<9<<<+;;;
+@EAS56_57:4:262:965:756
+AGGGAGGTGCACTAATGCGCTCCACGCCCAAGCCC
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;:<9;<
+@EAS56_57:4:262:965:756
+TTAATATAATTGTGTCCATGTACACACGCTGTCCT
++
+<<:<<<<<<<<:<<<<<<<<<<<<<<<<<<<<<<<
+@EAS56_57:4:71:707:568
+CTGCATCCCTGTCTTCCTCTGTCTTGATTTACTTG
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<9<<<<;<;<
+@EAS56_57:4:71:707:568
+GTCTAGATGAGAGAGAACTTCCCTGGAGGTCTGAT
++
+;9;<;<<<<<;<<<<<;<<<:<<<<<<<<<<<<<<
+@EAS56_57:4:98:862:154
+AAAGATCAATTCAGCAAGAAGATATAACCATCCTA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<9<:99<;
+@EAS56_57:4:98:862:154
+TGCTACTCAATATATCCATGTAACAAATCTGCGCT
++
+856:;7<:<<9<<<9<<<<<<<<<<<<<<<<<<<<
+@EAS56_57:5:105:521:563
+TATGTACTTATCATGACTCTATCCCAAATTCCCAA
++
+;<)<9995<9<<59<7<<<<7<7<35,0,544<3(
+@EAS56_57:5:105:521:563
+TGTAATGCTGCCCCTTGGCCATCCCCCGGTCCCTG
++
+/8)-8/6(98<967<3<<979<<1<<<7<<<<7<<
+@EAS56_57:5:136:389:320
+TCCTATGTACTTATCATGACTCTATCCCAAATTCC
++
+.5:,666<)<8<:<<:66<<<<<<<<<<5<<7<<<
+@EAS56_57:5:136:389:320
+TTCTGCCCCCAGCATGGTTGTACTGGGCAATACAT
++
+7<<<<<;<<7<6<<;;<;<;;677<6;(27;<(97
+@EAS56_57:5:145:383:182
+AAACCTCTTTAGTCTTGCTAGAGATTTAGACATCT
++
+<<;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS56_57:5:145:383:182
+TTGAAGACAAGTCTCTTATGAATTAACCCAGTCAG
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<:;;;<;
+@EAS56_57:5:207:926:427
+GGGAAGAACAGCTTAGGTATCAATTTGGTGTTCTG
++
+;;7<<;4<<<2<<;<<<<<<<<<<7<;<<<<<<<<
+@EAS56_57:5:207:926:427
+TAGGAAATGCTTTACTGTCATAACTATGAAGAGAC
++
+<<<<<<7<<<<<;<<<<<6:<;<6<&<58<<6:::
+@EAS56_57:5:214:644:390
+AAAAACATGAACTAACTATATGCTGTTTACAAGAA
++
+<<<<<<<<<<<<;<<<<<<<<<<<<<<<<<<<;<;
+@EAS56_57:5:214:644:390
+AAATAAAACAAAGGAGGTCATGATACAATGATAAA
++
+<<<;<<<<<<<<<<<<<<<<<&<<<<<<<<<<<<<
+@EAS56_57:5:24:284:360
+AGTCATCAGACTATCTAAAGTCAACATGAAGGAAA
++
+<<<<<<<<<<<<<<<<<;<<<<<<<;<9;<;99;;
+@EAS56_57:5:24:284:360
+CTGTCAAACACGAATGTTATGCCCTGCTAAACTAA
++
+:;<;:<<<;<<<<<<<<<<<<<<<<<;;<<<<<<<
+@EAS56_57:5:266:133:789
+AAAAAATTAACATTACAACAGGAACAAAACCTCAT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<
+@EAS56_57:5:266:133:789
+GTGGAAAAAGATGTTCTACGCAAACAGAAACCAAA
++
+9;;<<<<<<<<<<<<5<<;<5<<<<<<<<<<<<<<
+@EAS56_57:5:303:542:924
+AATAAAACAAAGGAGGTCATCATACAATGATAAAA
++
+<<<;<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<;
+@EAS56_57:5:303:542:924
+CAATGTACAATATTCTGATGATGGTTACACTAAAA
++
++<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS56_57:5:309:109:987
+AACAAATACTACTAGACCTAAGAGGGATGAGAAAT
++
+<<<<<<:<<;<<<<<;<<<<<<<<<<<<<<<<<<<
+@EAS56_57:5:309:109:987
+GAGAGAAGGAGTAGCTATACTTATATCAGATAAAG
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<9<<<;<;;;
+@EAS56_57:5:30:788:376
+ACGTCTCATCTAGGGGAACAGGGAGGTGCACTAAT
++
+<<<<<<<<<<<<:<<<<<<<<:<;<<(<7;7;:(;
+@EAS56_57:5:30:788:376
+TGTTTCTTATCTGCACATTACTACCCTGCAATTAA
++
+:5<<4:88;9<<<<<;<<<<;<8<;<<<<1<<<<<
+@EAS56_57:5:324:728:956
+ATTTGTCAATGTCAGGGAAGGAGCATTTTGTCAGT
++
+<;;;;5;<<0<<<<<<<<<<<<<<<;<<<<<<<<<
+@EAS56_57:5:324:728:956
+TGCTGGCAAGCTAGAGTCCCATTTGGAGCCCCTCT
++
+<<<<<<<<<<<<<<<<<<<<8<<<:<::;;;;<:<
+@EAS56_57:5:53:544:889
+AGGCTCAAAGAATGCCAGGAAGATACATTGCAAGA
++
+<<<<<<<<;<<<<<<<<<<<<<<<<<;<<<<<;<<
+@EAS56_57:5:53:544:889
+GCTTCTCAGCGGAAACCTTACAAGCCAGAAGAGAT
++
+,<;<<<;<<<<<<<<<:;;<<<<<;;<<<<<<<<<
+@EAS56_57:5:71:994:576
+AAGATAATTCATCATCACTAAACCAGTCCTATAAG
++
+<<<<<<<<<<<<<<<<<<<<<<<;<<5<<<<<<<<
+@EAS56_57:5:71:994:576
+TAGGTAAAAAATTAACATTACAACAGGAACAAAAC
++
+<<9;;<<<<<<<<<;<<<<<<<<<<<<<<<<<<<<
+@EAS56_57:6:145:144:796
+ATTTGGTGTTCTGTGTAAAGTCTCAGGGAGCCGTC
++
+<<<<<<<<<<<<<<;<<<<<<;<<<<<<4;4;<;/
+@EAS56_57:6:145:144:796
+GGTTTTCTGTTTCTTTGTTTGATTTGGTGGAAGAC
++
+;<<<;<<<<<<<<<;<<<;<<<<<<<<<<<<<<<<
+@EAS56_57:6:157:643:175
+GGGATGGAGGGAAGAGGGACGCTGAAGAACTTTGA
++
+;<<<;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS56_57:6:157:643:175
+TTCTATTTGTAATGAAAACTATATTTATGCTATTC
++
+<<<<<<<<;<<<<<<<<<<<<<<<<<<<)<<<<;<
+@EAS56_57:6:175:289:351
+CATCCTACTAAATACATATGCACCTAACACAAGAC
++
+<<<<<<<<<<;<<<<<<<<;<<<<<<<<<<<9<<<
+@EAS56_57:6:175:289:351
+TGCGCTTGTACTTCTAAATCTATAAAAAAATTAAA
++
+9;;:+<<<<<;<<:<<<<<<<<<<<<<<<<<<<<<
+@EAS56_57:6:190:289:82
+AGGGGTGCAGAGCCGAGTCACGGGGTTGCCAGCAC
++
+<<<<<<;<<<<<<<<<<;<<;<<<<;8<6;9;;2;
+@EAS56_57:6:190:289:82
+CTCAAGGTTGTTGCAAGGGGGTCTATGTGAACAAA
++
+<<<7<<<;<<<<<<<<8;;<7;4<;<;;;;;94<;
+@EAS56_57:6:21:553:57
+AAATACTACTAGACCTAAGAGGGATGAGAAATTAC
++
+<<<<<<<<<<<;;<<<;<<;<<;<<<;;9<;<;<9
+@EAS56_57:6:21:553:57
+AACAAAAGTAAATAAAACACATAGCTAAAACTAAA
++
+<<+<<<<<<<<<;<<<<8<<<<<<8<<<<<;<<<<
+@EAS56_57:6:234:787:12
+AAGCTTGGGCTGTAATGATGCCCCTTGGCCATCAC
++
+;;.<;;994<;9<<;;;<<<<<<<7<<<<<<<<<;
+@EAS56_57:6:234:787:12
+ACACGCTGGCCTATGTACTTATAATGACTCTATCC
++
+<;<<<9<<&+9;3;<993;<9<+94;9&41;08%9
+@EAS56_57:6:325:759:288
+GCTGCTGGCAAGCTAGAGTCCCATTTGGAGCCCCT
++
+8<;<<<<81<<<<<;<<;<<<;9</;6;;809034
+@EAS56_57:6:325:759:288
+GGAGCATTTTGTCAGTTACCAAATGTGTTTATTAC
++
+9;<9<;<;;<;<;<;<<<:<;<<<;<<<<<;<<<<
+@EAS56_57:6:44:280:641
+AACCCCCTTGCAACAACCTTGAGAACCCCAGGGAA
++
+;<<<<<<<<<<66<;<<<<<;<<2;;;<<;;;;,;
+@EAS56_57:6:44:280:641
+TCATTCACTCCAGCTCCCTGTCACCCAATGGACCT
++
+9;<<9;9;;<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS56_57:6:4:223:776
+AGTAACTGAACCTATGAGTCACAGGTATTCCTGAG
++
+<<<<<<<<<<<<<<<<<<<<<<<<<9<<<:;<;2<
+@EAS56_57:6:4:223:776
+TGTAGTCATCAGACTATCTAAAGTCAACATGAAGG
++
+<;9<;<0<<;<<<;<<<<<<<<<<<<<<<<<<<<<
+@EAS56_57:7:159:125:297
+GCAAGCTAGAGTCCCATTTGGAGCCACTCTAAGAC
++
+<<<<<<<<<<<<<<;<<<;<;<<6;)<:9;26;39
+@EAS56_57:7:159:125:297
+GGAAGGAGCATTTTGTCAGTTACCAAATGTGTTTA
++
+89<;;8<<;<;<4<;<8<<<<;;8<<<<<<<<<<<
+@EAS56_57:7:247:522:670
+CTATCCCAAATTCCCAATTACGTCCTATCTTCTTC
++
+;;;9;:<<<<<;<<<<<<<<<<<<<<<<<<<<<<<
+@EAS56_57:7:247:522:670
+TACATGAGATTATTAGGAAATGCTTTACTGTCATA
++
+<<<<<<<<<<<<<<<;<<<<<<<<<<<<<5;<<<;
+@EAS56_57:7:273:562:954
+AAAGTTCAATACTCACCATCATAAATACACACAAA
++
+;<<+;95<<<;5;<<;:<<;<<<<<<<<<<<<<<<
+@EAS56_57:7:273:562:954
+TTTTTGGACTTCTTAAAGAAAAAAAAACCTGTCAA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<;;:;;;;
+@EAS56_57:7:287:258:321
+TAATACTATGTTTCTTATCTGCACATTACTACCCT
++
+<<<<<<<<<<<;<<<<<<<<42:<+<<<;<<;;;;
+@EAS56_57:7:287:258:321
+TGTAAAGTCTCAGGGAGCCGTCCGTGTCCTCCCAT
++
+:.<9<)<;<9<.<<:<:+5:<<<<<<<<<<<<<<<
+@EAS56_57:7:33:954:724
+CCTAAGAGGGATGAGAAATTACCTAATTGGTACAA
++
+;<;<;<<-7;<<;<<<<<<<<<<<<<<<<<<<<<;
+@EAS56_57:7:33:954:724
+TCAGATAAAGCACACTTTAAATCAACAACAGTAAA
++
+;<<<<<<<<<<<<<8<<<<:<;;<<;;<;<<;;;;
+@EAS56_57:7:57:826:977
+ATTGGATCTAATTTTTGGACTTCTTAAAGAAAAAA
++
+<<<<<<<<<<<<<<<<+<<<<<<<<6<9:6<<<<<
+@EAS56_57:7:57:826:977
+TGCTCAAAAGAATTGTAAAAGTCAAAATTAAAGTT
++
+875:6<<<<<<<<<<<<<<<;<<<<<<;8<<<<<<
+@EAS56_57:7:76:786:458
+GGAGCATTTTGTCAGTTACCAAATGTGTTTATTAC
++
+<<.<<<<2<<:84<:<<<:<8<<)<)429<2<<8<
+@EAS56_57:7:76:786:458
+TCTGGGAAATTCTTCATCCTGGACCCTGAGAGATT
++
+;<;:7<.<<<<<8;<<<<<<<6<;8<<<<<<<<<<
+@EAS56_57:8:72:44:435
+AAAAGCAAAAACAAAAACTATGCTAAGTATTGGTA
++
+<<<<;7;<<<<;<<<<<<<<<<;<<<;<<<<<<<<
+@EAS56_57:8:72:44:435
+ATTGGTACAATGTACAATATTCTGATGATGGTTAA
++
+<<<<<<<<<<<2;<;<<;<<<;<<8<82<;22<8&
+@EAS56_59:1:126:526:276
+GAACTTCTGTAATTGAAAAATTCATTTAAGAAATT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<:<<<
+@EAS56_59:1:128:584:952
+ATCATACAATGATAAAAAGATCAATTCAGCAAGAA
++
+<<<<<<<<<<<<<<+<;<<<<<<;<<<;<<<+<66
+@EAS56_59:1:128:584:952
+GCCCATACTTTACTGCTACTCAATATATCCATGTA
++
+7<;9;0:<<<:<<:<<<<<:<<<<<<<<<<<<<<<
+@EAS56_59:1:219:294:861
+CTGGTTCTCTTGAAAGCTTGGGCTGTAATGATGCC
++
+;,;<;<<<;&<<<<<<<5<<<<<<<<<<<<<<<<<
+@EAS56_59:1:219:294:861
+TATAATTGTGTCCATGTACACACGCTGTCCTCTGT
++
+<<<<<<<<<<<<<9<<<5<9<<<9<<544<<'<+:
+@EAS56_59:1:248:122:558
+AATGTACAATATTCTGATGATGGTTACACTAAAAG
++
+<<<<:<<<<<<<<<<<<<;<<<<:<6:4<<::6:6
+@EAS56_59:1:248:122:558
+GGAAAAAAGTAAACTCTCAAATATTGCTAGTGGGA
++
+<;<<<<<<<<<<<;<<<<<<<<<<<<<<<<<<<<<
+@EAS56_59:1:278:906:933
+AATATAATTGTGTCCATGTACACACGCTGTCCTAT
++
+<88::<<<<<<<<<;<<<<<<<<<<<<<<<<<<<<
+@EAS56_59:1:278:906:933
+TTCTCACAGTTTCTGCCCCCAGCATGGTTGTACTG
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<<<.
+@EAS56_59:1:82:670:302
+AGTTCAGGTAAAGGGGTGGAAAAAGATGTTCTACG
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<5
+@EAS56_59:1:82:670:302
+TCCTACTAAATACATATGCACCTAACACAAGACTA
++
+%448<7<<<<<<7<<<<<&<<7<<<<<<<<<<<<<
+@EAS56_59:1:93:490:901
+AGAAAAGCATACAGTCATCTATAAAGGAAATCCCA
++
+<<<<<<<;<<<;<<<;<<;<<;<<<<<<<<<<<<<
+@EAS56_59:1:93:490:901
+GTAATTGGGGAAAACCTCTTTAGTCTTGCTAGAGA
++
+<<<<<<<<<<<<<;<<<<<<<;<<<<<:<<1+4-8
+@EAS56_59:2:104:402:732
+AAATCAGCAAGAGAAAAGCATACAGTCATCTATAA
++
+=========================7=;===;=:=
+@EAS56_59:2:104:402:732
+AATGAAGGGGAAATAAAGTCAAGTCTTTCCTGACA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS56_59:2:162:272:415
+ACATGAACTAACTATATGCTGTTTACAAGAAACTC
++
+<<<<<<<<<<<<<<<<<<<<<<;<<<<<9;<<<<<
+@EAS56_59:2:162:272:415
+ATAAAAAGATCAATTCAGCAAGAAGATATAACCAT
++
+=7=======;5==<<6==1==<=============
+@EAS56_59:2:177:266:842
+ACAACAGGAAGAAAAGGTCTTTCAAAAGGTGATGT
++
+=====)===========8=====7882855355'5
+@EAS56_59:2:177:266:842
+GGCATTTGCCTTCAGACCCTACACGAATGCGTCTC
++
+<9<<6;9<;9;;<<<<;;;9<<<<<<<<<<<<<<<
+@EAS56_59:2:177:552:234
+ACGCTGTCCTATGTACTTATCATGACTCTATCCCA
++
+::;:=;=99=====;;====;==========<===
+@EAS56_59:2:177:552:234
+GCTCCACGCCCAAGCCCTTCTCACAGTTTCTGCCC
++
+<<<<<<<<<<<<<;<<<<<<<<9<969<<<<3<<<
+@EAS56_59:2:201:768:529
+AGGTATTCCTGAGGAAAAAGAAAAAGTGAGAAGTT
++
+==========================1=======;
+@EAS56_59:2:201:768:529
+CAGACTATCTAAAGTCAACATGAAGGAAAAAAATT
++
+3<:<9<<;<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS56_59:2:239:1001:406
+AGCATACAGTCATCTATAAAGGAAATCCCATCAGA
++
+<<<<<<7<<<<<<<<8<;<<<7<<<<36<<3<:33
+@EAS56_59:2:239:1001:406
+CTTTCCTGACAAGCAAATGCTAAGATAATTCATCA
++
+0':.71;;:9==9=;====;=;=============
+@EAS56_59:2:60:677:921
+CATCAGACTATCTAAAGTCAACATGAAGGAAAAAA
++
+========9==;======8==>=============
+@EAS56_59:2:60:677:921
+GTGAGAAGTTTGGAAAAACTATTTGAGGAAGTAAT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS56_59:3:149:953:349
+AGCCCTTCTCACAGTTTCTGCCCCCAGCATGGTTG
++
+2;<<;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS56_59:3:149:953:349
+TTCTTTTGGCATTTGCCTTCAGACCCTACACGAAT
++
+<<<<<<<<;<<<<<<<<<<<;7:<:<<:<:;;::;
+@EAS56_59:3:166:626:836
+AGTACAAAACTCACAGGTTTTATAAAACAATTAAT
++
+<;;7<<<<<<;<7;<<<<<<<<<<<<7<<<<<<<+
+@EAS56_59:3:166:626:836
+CTGTCAAACACGAATGTTATGCCCTGCTAAACTAA
++
+<<<<<<<<<<<<<<<<<<<<9<<<<<<<<;<;;;9
+@EAS56_59:3:182:1002:639
+AAAAGTGAGAAGTTTGGAAAAACTATTTGAGGAAG
++
+<<;;9;9<<<<<<;<7;<;<<<<;;<<<;<<7;<<
+@EAS56_59:3:182:1002:639
+AACCAAGCAGAAGAAAGAGGTTCAGAACTTGAAGA
++
+<<<<<<<<<<<<<<<<<<<<<9-<<<<4<;<;;<;
+@EAS56_59:3:316:25:230
+GATGCCCCTTGGCCATCACCCGGTCCCTGCCCCAT
++
+8;8;<<;<;;<<<<<;<<<<<<<<<<<<<<<<<<<
+@EAS56_59:3:316:25:230
+TGTCCTATGTACTTATCATGACTCTATCCCAAATT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<);2;;
+@EAS56_59:4:119:651:88
+GATTGGATCTAATTTTTGGACTTCTTAAAGAAAAA
++
+<<<<<<<<;<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS56_59:4:119:651:88
+GCTCAAAGAATGCCAGGAAGATACATTGCAAGACA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<9;<
+@EAS56_59:4:262:928:237
+TGAGTTCAGGTAAAGGTGTGGAAAAAGATGTTCTA
++
+;<<<<<;<<<<<<<<<;<<<<<<<<<<<<<<<<<<
+@EAS56_59:4:262:928:237
+TTGAGACTACAGAGCAACTAGGTAAAAAATTAACA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<7<<
+@EAS56_59:4:267:394:437
+AAACATCATAAATACACACAAAAGTACAAAACTCA
++
+&<&,<8.<;<<<;<8<8<7<<<<<<<<<<<<<<<<
+@EAS56_59:4:267:394:437
+GGACTTCTTAAAGAAAAAAAAACCTGTCAAACACG
++
+<<<<<<<<<<;<;<<<<<;;<<<<<;<<:;8<;<8
+@EAS56_59:4:278:524:521
+CACATTAATACTATGTTTCTTATCTGCACATTACT
++
+<<<;<<;<<<<<<<;<<<<<<<<<<7;5;<<<;;<
+@EAS56_59:4:278:524:521
+CCCATCTGGCCTCGTCCACACTGGTTCTCTTGAAA
++
+7777,<;<<7<<<<;;<<;;<<<<<<<<<<<<<<<
+@EAS56_59:4:329:577:757
+AACGCGTAACTGCGCTCTCATTCACTCCAGCTCCC
++
+;;;888;<<<<<<6<<<2;<<<<<<;<<<<<<<<<
+@EAS56_59:4:329:577:757
+TCAAGGTTGTTGCAAGGGGGTCTATGTGAACAAAG
++
+!!<<<<9;<:<<;<<<<<<<<;<<<<<<<<<<<<<
+@EAS56_59:5:113:694:725
+CTGTAATGATGCCCCTTGGCCATCACCCGGTCCCT
++
+;::<<:<:<<<<<<<<<<:<:<<<<<<;<<<<<<<
+@EAS56_59:5:113:694:725
+GTACACACGCTGTCCTATGTACTTATCATGACTCT
++
+<<<<<<<<<<<<9<<<<<:<<<<<<<<<<:;;<;;
+@EAS56_59:5:125:137:58
+AACTATATGCTGTTTACAAGAAACTCATTAATAAA
++
+<<9;<<<<<;<;<<<<;<<<<<<;<<<<<<<<<<<
+@EAS56_59:5:125:137:58
+GGTTTTATAAAACAATTAATTGAGACTACAGAGCA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<9;<
+@EAS56_59:5:181:713:140
+AGGGGAAATAAAGTCAAGTATTTCCTGACAAGCAA
++
+<7<<<<<<<<<<<<7<7<6+<<<5;<;<2<;;+;;
+@EAS56_59:5:181:713:140
+CTACAGAGCAACAAGGTAAAAAATTAACATTACAA
++
+78<+<7<-7;;;&<5<7<<<<7<<<<<<<<<<<7<
+@EAS56_59:5:198:929:684
+AAAGTCAAGTCTTTCCTGACAAGCAAATGCTAAGA
++
+<<;<<<<<:<<<<<<<<<<<<<<<<<;<<<<<<<<
+@EAS56_59:5:198:929:684
+GAAATCCCATCAGAATAACAATGGGCTTCTCAGCA
++
+<7<<<<;<<<<<<<<<<<<;<<<<<:<<<<::<:7
+@EAS56_59:5:232:336:46
+ATTTTTTTTTTTTCTTTTCTCTTGTTTCTTTTTTT
++
++<<<<<<<<<<<<6<<<<;<6<<&&<,3<<<<3,,
+@EAS56_59:5:325:544:349
+AAAATTAAAGTTCAATACTCACCATCATAAATACA
++
+<<<<57<<<7<;6<<<<;<7<7;<<7<<<<<<<<<
+@EAS56_59:5:325:544:349
+CAAGCCAGAAGAGATTGGATCTAATTTTTGGACTT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<6;;;<<
+@EAS56_59:5:90:629:652
+AGCCCATACTTTACTGCTACTCAATATATCCATGT
++
+<<<<<<<<<<<<<<<<<<<<<<<:<;<<<<<<<<<
+@EAS56_59:5:90:629:652
+ATATTGCTAGTGGGAGTATAAATTGTTTTCCACTT
++
+<:<7::<:<<<<<8<<<<<<<<<<<<<<<<<<<7<
+@EAS56_59:6:187:925:547
+GGCTGATTATGAAAACAATGTTCCCAAGATACCAT
++
+43<<<:9<;;;:7<<<<6<:<8<-4-/,81<(48:
+@EAS56_59:6:187:925:547
+TGAACTTCCACGTCTCATCTAGGGGAACAGGGAGG
++
+((988+&8<<;<09<;<<9<<4<<-<99<<;<9<;
+@EAS56_59:6:199:327:965
+ATCTGGATTCTGGGAAATTCTTCATCCTGGACCCT
++
+<5<:<<<58<:<<<<<<8<<<<<<<<<;<<<<<<<
+@EAS56_59:6:199:327:965
+NCAACAACCTTGAGAACCCCAGGGAATTTGTCAAT
++
+!,+*+++++++++++*+++++++**)+*+**+(**
+@EAS56_59:6:227:657:95
+GTAATTGGGGAAAACCTCTTTAGTCTTGCTAGAGA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<<8<85
+@EAS56_59:6:227:657:95
+GTCATCTATAAAGGAAATCCCATCAGAATAACAAT
++
+;3;<);<<<<<<<<<<<<18<<<<<<<<<<<<<<<
+@EAS56_59:6:286:753:854
+TCACCCAGTCCCTGCCCCATCTCTTGTAATCTCTC
++
+;<2<<<,57:<<9<<<<<<<<<<<<<<<<<<<<<<
+@EAS56_59:6:286:753:854
+TTATCATGACTCTATCCCAAATTCCCAATTACGTC
++
+<<<<<<<<<<<<<<<<<<3<<<<<<9999<;<<9;
+@EAS56_59:6:312:837:406
+AGGTGCACTAATGCGCTCCACGCCCAAGCCCTTCT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS56_59:6:312:837:406
+CTGCACATTACTACCCTGCAATTAATATAATTGTG
++
+;<;<<;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS56_59:6:3:186:68
+AAGAAATGCTCAAAAGAATTGTAAAAGTCAAAATT
++
+<<;<<<<<&:,<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS56_59:6:3:186:68
+TTACAAGCCAGAAGAGATTGGATCTAATTTTTGTA
++
+<<<<<<<<<<<<;<<<<<<<<<<<<;;<<<<<&%8
+@EAS56_59:6:89:457:591
+ATGCCCTGCTAAACTAAGCATCATAAATGAAGGGG
++
+<<<<<<<<<<<4<<<<<<<<<<<<8<7/4<<<<4+
+@EAS56_59:6:89:457:591
+CAGGTTTTATAAAACAATTAATTGAGACTACATAG
++
+797<<9<<<<<<<3<7<<<<<<<<<<)<<<<<07<
+@EAS56_59:7:260:985:520
+TCCCTGTCACCCAATGGACCTGTGATATCTGGATT
++
+;9;7<<<<<<<<<<<<<<<<<:<<<<<<<<<<<<<
+@EAS56_59:7:260:985:520
+TGCAACAACCTTGAGAACCCCAGGGAATTTGTCAA
++
+<<<<<<<<<<<<<<<<<;:;<<;<:<<<,:1;)<;
+@EAS56_59:7:318:679:883
+GATTTAGACATCTAAATGAAAGAGGCTCAAAGAAT
++
+<<;4<<;<:<<7<<<<<<<<<<<<<<<<<<<<<<<
+@EAS56_59:7:319:246:304
+CTTGAGAACCCCAGGGAATTTGTCAATGTCAGGGA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;;;:
+@EAS56_59:7:319:246:304
+TGTCACCCAATGGACCTGTGATATCTGGATTCTGG
++
+;;<;;;<<<<8;<<<<;<<<<<<<<<<<<<<<;<<
+@EAS56_59:7:82:902:868
+CTGTCACCCAATGGACCTGTGATATCTGGATTCTG
++
+<<;;<<<<<<<<;<<<<<<<<<<<<<<<<<<<<<<
+@EAS56_59:7:82:902:868
+TTGCAACAACCTTGAGAACCCCAGGGAATTTGTCA
++
+<<<<<<;<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS56_59:8:49:182:192
+ACACAAAAGTACAAAACTCACAGGTTTTATAAAAC
++
+<5<;<<<<<<<<<<<:<<<<<<<<<<<<<<<<<<<
+@EAS56_59:8:49:182:192
+GTTATGCCCTGCTAAACTGAGCATCATAAATGAAG
++
+=====================;============<
+@EAS56_59:8:80:542:549
+AGTAAACTCTCAAATATTGCTAGTGGGAGTATAAA
++
+=9====7=;=======;;==;========<=====
+@EAS56_59:8:80:542:549
+CTAAAAGCCCATACTTTACTGCTACTCAATATATC
++
+<<<<<<<<;<<<<<<<<:<<<<-<;;<;7<;3;9;
+@EAS56_61:1:119:880:781
+ACAAATCTGCGCTTGTACTTCTAAATCTATAACAA
++
+;8<<;<<<<:<84<<<<:<<<<<<<<<<<<<5<<<
+@EAS56_61:1:119:880:781
+ACATATGCACCTAACACAAGACTACCCAGATTCAT
++
+<<<<<<<<<<<<<<<<<<<<<<<<+<<<<7<<<<<
+@EAS56_61:1:210:880:606
+GGAGCATTTTGTCAGTTACCAAATGTGTTTATTAT
++
+<<<<<<<<<<<<<<<<<<;<<<<<<:<<<<3<<8&
+@EAS56_61:1:210:880:606
+TCCTGGACCCTGAGAGATTCTGCAGCCCAGCTCCA
++
+.<<:<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS56_61:1:303:184:14
+CAACCTTGAGAACCCCAGGGAATTTGTCAATGTCA
++
+<<<<<<8<0<<<<-<-98<<--<<<6;076;75+&
+@EAS56_61:1:303:184:14
+CAATGGACCTGTGATATCTGGATTCTGGGAAATTC
++
+:<<.<;;7<:<<<<<<7<<<<<<<<<<<<<<<<<<
+@EAS56_61:2:152:860:286
+AGACTATTGCCAGATGAACCACACATTAATACTAT
++
+<;<<<;<<0:<3<:<<2<<<<<7+<7+47<9(999
+@EAS56_61:2:152:860:286
+TTAGGTATCAATTTGGTGTTCTGTGTAAAGTCTCA
++
+2;5;8<<;5<<<;<2<8<<<<<<;8<;<<<<;<<<
+@EAS56_61:3:140:522:212
+CGCTGAAGAACTTTGATGCCCTCTTCTTCCAAAGA
++
+<<<<<<<<<<<<<<<<<;<<<<<<<<<<<;<;95;
+@EAS56_61:3:140:522:212
+GACAGGCTGCAACTGTGAGCCATCACAATGAACAA
++
+:;8;:::<<:<<<<<<<<<7<<<<<<<<<<<<<<<
+@EAS56_61:3:165:665:220
+ACAATTAATTGAGACTACAGAGCAACTAGGTAAAA
++
+<:<<;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS56_61:3:165:665:220
+GGAAATAAAGTCAAGTCTTTCCTGACAAGCAAATG
++
+<<<<<<<<<<<<<<<<<<<<<;<;;<<<;;<;<<;
+@EAS56_61:3:208:118:673
+AAGAGGCTCAAAGAATGCCAGGAAGATACATTGCA
++
+<<<<<;;<;<<<<<<<<<:<<<<<<<<<<<<<<<<
+@EAS56_61:3:208:118:673
+GAACAGAGCTTTCAAGAAGTATGAGATTATGTAAA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;;<;;
+@EAS56_61:3:260:827:289
+AAACCTCATATATCAATATTAACTTTGAATAAAAA
++
+<<<<2<<<<;<<<<;<<<<<<:<<<&-<8<<88<3
+@EAS56_61:3:260:827:289
+TGTTCTACGCAAACAGAAACCAAATGAGAGAAGGA
++
+6;99+<<<<<<<<<<<<<<6<<<<<7<<<<<<<<<
+@EAS56_61:3:45:758:616
+ATAAATTGTTTTCCACTTTGGAAAACAATTTGGTA
++
+<<;<:<<<<<<<<<;<<<<<<<<<<<<<<<<<<<<
+@EAS56_61:3:45:758:616
+CATACTTTACTGCTACTCAATATATCCATGTAACA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<6<<<<<<;;<
+@EAS56_61:3:5:45:441
+TTTTTTTTCTTTTCTCTTTTTTTTTTTTTTTTTTT
++
+;;58:<:<(:<<11<&<1<<;<<<<><<<<<<<<<
+@EAS56_61:4:262:456:74
+TACCAAATGTGTTTATTACCAGAGGGATGGAGGGA
++
+<<<<<<<<<<<<<<<<<<<<:;;:;7:<::7<7:3
+@EAS56_61:4:262:456:74
+TGGGAAATTCTTCATCCTGGACCCTGAGAGATTCT
++
+862;<<<:;<;<<<;;;<<<<;;<<<<<<<<<<<<
+@EAS56_61:5:194:470:416
+AAACTATTTGAGGAAGTAATTGGGGAAAACCTCTT
++
+<<<7<<;<<<<<<<<<:<<<<<<<<<<<<<<<<<<
+@EAS56_61:5:194:470:416
+TCAGAACTTGAAGACAAGTCTCTTATGAATTAACC
++
+<<<<<<<<<<<<<<<<<<<<<<<<;<;<<<<<<<<
+@EAS56_61:5:209:824:866
+ATCATCACTAAACCAGTCCTATAAGAAATGCTCAA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;
+@EAS56_61:5:209:824:866
+CAGCAACAAAACCTCATATATCAATATTAACTTTG
++
+;<:&<<:<<<<;<<;<<<<<<<<<<<<<<<<<<<<
+@EAS56_61:5:263:314:696
+AACTCATTAATAAAGACATGAGTTCAGGTAAAGGG
++
+<<<<<<<<<<<<<<;<<<<<<<<<<<<:<<;<775
+@EAS56_61:5:263:314:696
+AAGATCAATTCAGCAAGAAGATATAACCATCCTAC
++
+<<;<;:<<<<7<<:<<<<<<<<<<<<<<<<<<<<<
+@EAS56_61:5:272:240:950
+CAGCAGAGCTTGGATCTAATTTTTGGACTTCTTCA
++
+6<<&:<<<&<::;&7<<<3<;<<;<:;:<8:<<(<
+@EAS56_61:5:272:240:950
+TCAAAAGAATTGTAAAAGTCAAAATTAAAGTTCAA
++
+37<<<<<<<<<<<<<<<<<<<<<<;;<;<<<<<<;
+@EAS56_61:6:10:106:737
+ACAAGAAACTCATTAATAAAGACATGAGTTCAGGT
++
+<<<;<1<;<<<<<<9<<<<;;<<<<<99<<94008
+@EAS56_61:6:10:106:737
+ACAATGATAAAAAGATCAATTCAGCAAGAAGATAT
++
+<-<<;<<<<<<<<<<<;<<<<;<<;<<<<<<<<<<
+@EAS56_61:6:160:272:398
+AATGTTCCCCAGATACCATCCCTGTCTTACTTCCA
++
+9<<<3<<<<<<<<<<<9<<;8<<<<;<+.;;89..
+@EAS56_61:6:160:272:398
+GTGCACTAATGCGCTCCACGCCCAAGCCCTTCTCA
++
+3:,<,;;<<;<<1<<<<<<<;<;<<<<<<<<<<<<
+@EAS56_61:6:226:370:91
+AGAATAACAATGGGCTTCTCAGCGGAAACCTTACA
++
+<':<6<;<<<;2<;<-7;;;<<<<<<<;;;<<7;<
+@EAS56_61:6:226:370:91
+AGGCTCAAAGAATGCCAGGAAGATACATTGCAAGA
++
+8<<<;<8<8<;<<<8<<;7<7;8784<<,;864<&
+@EAS56_61:6:227:259:597
+AATATAGAAATTGAAACAGCTGTGTTTAGTGCCTT
++
+<8<;2;9;<;;-92<;;;<;<<<<<<<<<<<<<<<
+@EAS56_61:6:256:67:461
+TCATGTTTGTGTCTTTCTATGCATTTTTTTTTTTT
++
+!!7181!63:6-:!-163(-1%-18<<4<<<<<<<
+@EAS56_61:6:256:67:461
+TTGTTTTTTCTTCTTTTCTCTTTTTTTTTTTTTTT
++
+*.%53.:)1+9;3397;1795507+335;.&51)5
+@EAS56_61:6:283:963:234
+AAAAAGATGTTCTACGCAAACAGAAACCAAATGAG
++
+<<<<<<<<<<<<<<<;<<<<<<<<<<<;<<;<<;<
+@EAS56_61:6:283:963:234
+ACATATGCACCTAACACAAGACTACCCAGATTCAT
++
+<5<;<;97;;:;<<7<;<<<<<<<<<<<<<<<<<<
+@EAS56_61:6:307:208:477
+AAAGTCAAAATTAAAGTTCAATACTCACCATCATA
++
+<<<<<.<<<<<<<<<<<<;<;<<<<<<<<<<<<<<
+@EAS56_61:6:307:208:477
+ACTTCTTAAAGAAAAAAAAACCTGTCAAACACGAA
++
+<<<<<<<;<<;<<<<<<<<<<<<<<<<;:<<<88;
+@EAS56_61:7:280:133:495
+AGATGAACCACACATTAATACTATGTTTCTTATCT
++
+<:<9:<<7:<6<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS56_61:7:280:133:495
+CCATCATGAAGCACTGAACTTCCACGTCTCATCTA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;
+@EAS56_61:7:41:745:603
+CATTGCAAGACAGACTTCATCAAGATATGTAGTCA
++
+<<<<<<<<<<<<:<<<<<<<<<<<<<<<6<:8<<:
+@EAS56_61:7:41:745:603
+TAATTTTTGGACTTCTTAAAGAAAAAAAAACCTGT
++
+;<<;;<;<8<<<<<<<<<<<;<<;<<<<<<<<<;<
+@EAS56_61:7:7:682:201
+CATACAGTCATCTATAAAGGAAATCCCATCAGAAT
++
+0:8;5<8<1:78<<<<<<<<<<<<:8<<2<<<<:<
+@EAS56_61:7:7:682:201
+GGAAAACCTCTTTAGTCTTGCTAGAGATTTAGACA
++
+<<<<<<<7<<7<<<<77&;-9<97<76<;<<993<
+@EAS56_61:8:60:358:494
+GGTAAAGGGGTGGAAAAAGATGTTCTACGCAAACA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<:<:<<;;4;
+@EAS56_61:8:60:358:494
+TACCCAGATTCATAAAACAAATACTACTAGACCTA
++
+7<77;<<<<<;<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS56_61:8:7:171:402
+GTGATATCTGGATTCTGGGAAATTCTTCATCCTGG
++
+<<<<<<<<<<<<<<<;/<<<<;<<<<<;<<1<<<4
+@EAS56_61:8:7:171:402
+TCTACATGGCTGATTATGAAAACAATGTTCCCCAG
++
+:086::::847:<7<<7<<<<<<;7<<;<<<<7<<
+@EAS56_63:1:119:446:185
+TGGTCTGACAGGCTGCAACTGTGAGCCATCACAAT
++
++70730;<0<77;;<<<<<9<<<<<<9<<<<<<<<
+@EAS56_63:1:119:446:185
+TTACCAGAGGGATGGAGGGAAGAGGGACGCTGAAG
++
+<<<<<<<7<<<4<<<<9<<54<:<7<5:<::7-5;
+@EAS56_63:1:145:71:26
+CTAGGGGAACAGGGAGGTGCACTAATGCGCTCCAC
++
+<<<<<<<<<<<<<<<<<;<;;<<;<;<9<9;;99;
+@EAS56_63:1:145:71:26
+TTTCTTATCTGCACATTACTACCCTGCAATTAATA
++
+882;8;<;;887<<<;;<<<<;<<<<<<<<<<<<<
+@EAS56_63:2:119:161:322
+ATCAGAATAACAATGGGCTTCTCAGCAGAAACCTT
++
+<83<;<<;<;<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS56_63:2:119:161:322
+CTTTAGTCTTGCTAGAGATTTAGACATCTAAATGA
++
+<<<<<<<<<<<<<<;<<<<<<<;<<<<<<<<<</6
+@EAS56_63:2:33:357:858
+AAAATTAAAGTTCAATACTCACCATCATAAATACA
++
+<<<<<<<<<<<<<<<<:<<<<<<:<<<<;<<<<<<
+@EAS56_63:2:33:357:858
+AGGGATTAAATTCCCCCACTTAAGAGATATAGATT
++
+<;<:<<<<<<<<<;<9<<;<<<<<<<<<<<<<<<<
+@EAS56_63:2:74:656:272
+AACAAAGGAGGTCATCATACAATGATAAAAAGATC
++
+<<<<<<<<<<<<<<<<<<<<<<<<;<<<<<<<<<<
+@EAS56_63:2:74:656:272
+TGTACAATATTCTGATGATGGTTACACTAAAAGCC
++
+;;;</<<<<<5;<<<<<<<<<<<<<<<<<<<<<<<
+@EAS56_63:3:40:594:752
+ATACACACACATGGTTTAGGGGTATAATACCTCTA
++
+<<<<<<<<<<;<<<;<<<::;<:;<;:<;;;<;<:
+@EAS56_63:3:40:594:752
+CTGCGCGGTTTCCCATCATGAAGCACTGAACTTCC
++
+;7;9<;;;<;<;:<<;;<<<<<<<<<;<<<<<<<<
+@EAS56_63:3:41:468:459
+AAATTTAACAAAAGTAAATAAAACACATAGCTAAA
++
+<<<<<<<<<<<<<<<<<<<<<;<<<<<<<<<<;;7
+@EAS56_63:3:41:468:459
+TTTTTTTTTTTTTTTTTTTCTTTTTTTTTTTTTTT
++
++;<<<<<<<<<<<;&<<;;88&<<<<<<<<<<<<<
+@EAS56_63:3:93:1002:845
+AATTCCCAATTACGTCCTATCTTCTTCTTAGGGAA
++
+<<::;;;<<<<<<<<<<<<<<<<;<<<<<<<<<<<
+@EAS56_63:3:93:1002:845
+GGGCAATACATGAGATTATTAGGAAATGCTTTACT
++
+<<<<<<<<<<<<<<<<<<<<<:<<;<<<;<<<</<
+@EAS56_63:4:141:9:811
+TTTCTTTTCTCCTTTTTTTTTTTTTTTTTCTACAT
++
+<<<;<<<<<<<;<;<:<<<;<<<<<<<<..));;.
+@EAS56_63:4:184:659:377
+AAAAAGATGTTCTACGCAAACAGAAACCAAATGAG
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;;;;;
+@EAS56_63:4:184:659:377
+CAAAACTACCCAGATTCATAAAACAAATACTACTA
++
+1;<+<;<6;66<<;<<<<;;<<<8<<<<8<<;<<<
+@EAS56_63:4:38:28:122
+AAATATAGTTGAAAGCTCTAACAATAGACTAAACC
++
+<<<<<<;<<<<<<<;<<<<6<<<<<<:<<<<;;<<
+@EAS56_63:4:38:28:122
+GTATTCCTGAGGAAAAAGAAAAAGTGAGAAGTTTG
++
+;9;9;-1<<<<<<<<<<<<<<<<<;<<<<<<<<<<
+@EAS56_63:5:117:570:971
+ACAGGTATTCCTGAGGAAAAAGAAAAAGTGAGAAG
++
+<<<<<<<<<<<<<;;;<<<<6<7;9;<:;<;<;;<
+@EAS56_63:5:117:570:971
+ACATGAAGGAAAAAAATTCTAAAATCAGCAAGAGA
++
+<,<9<<<<<<<<<<<<<<9<<<<<<<<<<<<<<<<
+@EAS56_63:5:123:998:248
+ATCACAATGAACAACAGGAAGAAAAGGTCTTTCAA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<;9<<<68<
+@EAS56_63:5:123:998:248
+TTTCTTTTGGCATTTGCCTTCAGACCCTACACGAA
++
+;:;5;<;:<9<<<<<:<;<<<<<<<<<<<<<<<<<
+@EAS56_63:5:36:678:316
+ATTTGTCTGAGCAAAACAGTCTAGATGAGAGAGAA
++
+<<72.2,;;<)6<<<<:<<;;<<<<<<<<<<<<<<
+@EAS56_63:5:36:678:316
+TTTGCTGCATCCCTGTCTTCCTCTGTCTTGATTTA
++
+<<<<<<<<<<<<<<;<<<<<<<<<;<<<<,2<<<)
+@EAS56_63:5:96:788:614
+TAGGGGTATAATACCTCTACATGGCTGATTATGAA
++
+<<<<<<<<<<<<<<<<<<<<<<;6;<<;;<;;7;9
+@EAS56_63:5:96:788:614
+TTCCACGTCTCATCTAGGGGAACAGGGAGGTGCAC
++
+;9;;;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS56_63:6:102:816:260
+AAATTACCTAATTGGTACAATGTACAATATTCTGA
++
+<<<<<<::<<<<<<;<<<<<<<<<<<<<<<<<<<<
+@EAS56_63:6:102:816:260
+TCAGATAAAGCACACTTTAAATCAACAACAGTAAA
++
+<<<<<<<<<;<<<<<<<<<<<<<<<<<<<<;;;;;
+@EAS56_63:6:42:920:522
+AATTAATATAATTGTGTCCATGTACACACGCTGTT
++
+<<<<<<<<<<<<<:<<<<<<<:<<<<<<<:;;::&
+@EAS56_63:6:42:920:522
+CTGGTTCTCTTGAAAGCTTGGGCTGTAATGATGCC
++
+;;;;;99<;<<;<<<<<<<<<<<<<<<<<<<<<<<
+@EAS56_63:6:91:360:585
+AAGATGAAACGCGTAACTGCGCTCTCATTCACTCC
++
+<<<<9<<<<<;<<<;<<77<<<;<;;<;;<;<;;<
+@EAS56_63:6:91:360:585
+GACATCACAATGAACAACAGGAAGAAAAGGTCTTT
++
+5&&<<3:;<<<<<<)<<3<<<<<<<;;<<<<;<<<
+@EAS56_63:7:109:22:383
+ATGTACAATATTCTGATGATGGTTACACTAAAAGC
++
+<;9;<8<<<<<<;<<<<<<<<<<<<;<<<<<<<<<
+@EAS56_63:7:109:22:383
+CAACAACAGTAAAATAAAACAAAGGAGGTCATCAT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<;:<<;<<
+@EAS56_63:7:137:139:248
+GTCAAACACGAATGTTATGCCCTGCTAAACTAAGC
++
+;;;99<<<;<;;<<<<<<<<<<<<;<<<<<<<<<<
+@EAS56_63:7:137:139:248
+TATCTAAAGTCAACATGAAGGAAAAAAATTCTAAA
++
+<<<<<<<<<9<<<<<<<<<<;<<<<<<<;;<;<;<
+@EAS56_63:7:166:42:147
+AATGCGCTCCACGCCCAAGCCCTTCTAACAGTTTC
++
+<<;<<<<<<<<<<<<<<<<;6<<64;)<<7;7;;;
+@EAS56_63:7:166:42:147
+CTGCACATTACTACCCTGCAATTAATATAATTGTG
++
+3.7;;;;:<<<77<<3<;<<<<<<<<<<<<<<<<<
+@EAS56_63:7:185:213:330
+CAATGTCAGGGAAGGAGCATTTTGTCAGTTACCAA
++
+<<<<<<<<<;<<;<<<<<;<<<<;;;<<;<<;<38
+@EAS56_63:7:185:213:330
+TCTGGGAAATTCTTCATCCTGGACCCTGAGAGATT
++
+;4<<<;<<<<<<<<;<<;;;<<<<9<<<<<<<<<<
+@EAS56_63:7:190:95:706
+TTCTCACAGTTTCTGCCCCCAGCATGGTTGTACTG
++
+<<<<<<<<<<<<<<9<<<<<;;<;<;;<<;<;;<,
+@EAS56_63:7:190:95:706
+TTGTGTCCATGTACACACGCTGTCCTATGTACTTA
++
+9;97437;<;;<<;<;<<<<<<;<<<<<<<<<<<<
+@EAS56_63:7:34:334:825
+CATTTAAGAAATTACAAAATATAGTTGAAAGCTCT
++
+<<<<<<<<<<<<<<<<<<<<<<<<3;<<<<6<<<<
+@EAS56_63:8:138:186:459
+CATTGCAAGACAGACTTCATCAAGATATGTAGTCA
++
+<*<<7<<0<7<<+<-:<<&<:6:4:0-:<<2.:5<
+@EAS56_63:8:138:186:459
+GCCAGAAGAGATTGGAGCTAATTTTTGGACTTCTT
++
++/2/;<:<&7:7</<2&<<<&<<<<<<<<<8<<:3
+@EAS56_63:8:150:508:757
+ATCCCTGTCTTCCTCTGTCTTGATTTACTTGTTGT
++
+<<<<<<<<<<<<<<<<<<<<<<:<<<<<<<8<<,<
+@EAS56_63:8:150:508:757
+CTTGACACCCAACTAATATTTGTCTGAGCAAAACA
++
+6;;;<8<6;8<<8<<<<<;<<<<;<<<<;<<<<<<
+@EAS56_63:8:4:571:820
+AAGAGATATAGATTGGCAGAACAGATTTAAAAACA
++
+<<<<<<<<<<<9<<;9<;;;<;6;:<<<3:;;;:6
+@EAS56_63:8:4:571:820
+CAACAACAGTAAAATAAAACAAAGGAGGTCATCAT
++
+&<<7<<1<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS56_63:8:62:125:888
+CGGAAACCTTACAAGCCAGAAGAGATTGGATCTAA
++
+,;3<<<8;;3<,<<<8;<<<<<<<<<<<<<<<<<<
+@EAS56_63:8:62:125:888
+TGCCAGGAAGATACATTGCAAGACAGACTTCATCA
++
+<<<<<<<<<<<<<<<<<<<::<<<:7<::<:;<<:
+@EAS56_65:1:163:846:223
+CCAGCTCCCTGTCACCCAATGGACCTGTGATATCT
++
+<7<5<*<<<<0<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS56_65:1:163:846:223
+GCCTTTGTTCACATAGACCCCCTTGCAACAACCTT
++
+<<<<;<<;4<<<;;9<<<<<+<<;<</27;;47;.
+@EAS56_65:1:178:305:843
+ATGTTTCTTATCTGCACATTACTACCCTGCAATTA
++
+<<<<<<<4<<;<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS56_65:1:178:305:843
+CCACGTCTCATCTAGGGGAACAGGGAGGTGCACTA
++
+<<<<<<<<<<<<<<<<<<<:<<<<<;<<:<<:<;:
+@EAS56_65:1:23:536:229
+AAAGCATACAGTCATCTATAAAGGAAATCCCATCA
++
+<<<<<<<<<<<<<<<<<:<8<:<<;<<<<<<7<<<
+@EAS56_65:1:23:536:229
+AAGGGGAAATAAAGTCAAGTCTTTCCTGACAAGCA
++
+<<99<<<<<;<<<;2<<<<<<;<<<9<<<<<<<<<
+@EAS56_65:1:53:272:944
+CAACCCCCTTGCAACAACCTTGCGAACCCCAGGGA
++
+<<<<<<<<<<<<.7<.<<<<<<-<-<<<<<&<222
+@EAS56_65:1:53:272:944
+TGCGCTCTCATTCACTCCAGCTCCCTGTCACCCAA
++
+&94<4&8.6<6&;<:0:8;;:6;<;:<*<<<<<<<
+@EAS56_65:2:224:579:433
+ATAACAATGGGCTTCTCAGCAGAAACCTTACAAGC
++
+<<<<<<<<<<<<<<<<<:<<<<<<<<<<<8<+8;:
+@EAS56_65:2:224:579:433
+TTCATCATCACTAAACCAGTCCTATAAGAAATGCT
++
+'<08/8<+<</<<:<<<<<8<<9<38<<<<<<<<;
+@EAS56_65:2:56:155:49
+ATCCTACTAAATACATATGCACCTAACACAAGACT
++
+;:5;;<5<<<<<<<<<<<<<<<<<<<<<<<<<<<=
+@EAS56_65:2:56:155:49
+ATGAGTTCAGGTAAAGGGGTGGAAAAAGATGTTCT
++
+<<<<<<<<<<<<<<<<<<<<<<;<<;<<<;<9<9;
+@EAS56_65:3:168:741:680
+AGGGACGCTGAAGAACTTTGATGCCCTCTTCTTCC
++
+<<<<<<<<<<<<<<<<<<<<<<<<<1<<<<<<<<<
+@EAS56_65:3:168:741:680
+TGGTCTGACAGGCTGCAACTGTGAGCCATCACAAT
++
+<<5<<:<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS56_65:3:47:64:359
+TTTTTTTTTTTCTCTCCTCTTTTTTTTTTTTTTTT
++
+<<<6<<<<<<<4<4</9<4@<<;<<<<<<<<<<<<
+@EAS56_65:4:124:367:72
+AGACTACCCAGATTCATAAAACAAATACTACTAGA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;;
+@EAS56_65:4:124:367:72
+CATAGCTAAAACTAAAAAAGCAAAAACAAAAACTA
++
+,<<<8,<<<<<:<<<<<<<<<<<<<<<<<<<<<<<
+@EAS56_65:4:126:966:514
+AGAAGAAGTAGCTATACTTATATCAGATAAAGCAC
++
+<4<<<%<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS56_65:4:126:966:514
+TAAAAAGGGATTAAATTCCCCCACTTAAGAGATAT
++
+<<<<<<<<<<<<<<<<<<<<;<<<<<<<<<;<<<;
+@EAS56_65:4:150:94:843
+AAAGGGATTAAATTCCCCCACTTAAGAGATATAGA
++
+<<<<<<<<7<<<6<<<<<<<<<<<6<<62<<<<<2
+@EAS56_65:4:150:94:843
+CAGATACATCCCACTTTAAATCAACCACAGTAAAA
++
+4<9<41*747*7<:9<:7:::<72;+<;::<7<<<
+@EAS56_65:4:296:78:421
+TCTTTTTTTCTTTTCTCTTTTTTTTTTTTTTTTTT
++
+!!<<<:<<<<..<::<<<<<<<<<<<<<<<<<<<<
+@EAS56_65:4:296:78:421
+TGTTGGTGTTCGTTTTTTCTCCTGTTTCTTTTTCT
++
+<<*<4<<<;:<0<<<<<<<<+;<9<<1<<;<<<+:
+@EAS56_65:5:121:380:656
+AATGTGTTTATTACCAGAGGGATGGAGGGAAGAGG
++
+<<<<<<<<<<<<<<<<<<<<<<<<:<:<<83<:<<
+@EAS56_65:5:121:380:656
+GCCCAGCTCCAGATTGCTTGTGGTCTGACAGGCTG
++
+:;<<;<<1<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS56_65:5:131:742:561
+TCAAAAGGTGATGTGTGTTCTCATCAACCTCATAC
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS56_65:5:131:742:561
+TGCCTTCAGACCCTACACGAATGCGTCTCTACCAC
++
+<:<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS56_65:5:211:84:84
+CTATTTGAGGAAGTAATTGGGGAAAACCTCTTTAG
++
+<<<<<<<<<<<<<<<<:<<:<<:<<<44<4<<9<<
+@EAS56_65:5:211:84:84
+GCAAGAGAAAAGCATACAGTCATCTATAAAGGAAA
++
+6:<<:<<<<<<9<<<<<<<<<<<;<<<;;;<;<3;
+@EAS56_65:5:262:53:888
+AAGACATGAGTTCAGGTAAAGGGGTGGAAAAAGAT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS56_65:5:262:53:888
+TTGAGACTACAGAGCAACTAGGTAAAAAATTAACA
++
+<<<<<<<<;<<<<<<<<<<;<<;<;<;6<<;<;;<
+@EAS56_65:5:278:848:765
+GTACACACGCTGTCCTATGTACTTATCATGACTCT
++
+7;;<;5<55<<;;<;<<<<<<<<<<<<<<<<<<<<
+@EAS56_65:5:278:848:765
+TTCTCACAGTTTCTGCCCCCAGCATGGTTGTACTG
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<4
+@EAS56_65:5:299:336:613
+ATCCTACTAAATACATATGCACCTAACACAAGACT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS56_65:5:299:336:613
+TACTCAATATATCCATGTAACAAATCTGCGCTTGT
++
+1;4(+<<5<4<1<<<<<<<<<<<<<<<<<<<<<<<
+@EAS56_65:5:30:92:753
+TATAATACCTCTACATGGCTGATTATGAAAACAAT
++
+<<<<<<;<<<<<<:<<<<;<<<<<<<<<<<<<<<<
+@EAS56_65:5:30:92:753
+TGGATTCTGGGAAATTCTTCATCCTGGACCCTGAG
++
+<<<<<<<<<<<<<<<<<<<<<<:<<<<<<<<<<<<
+@EAS56_65:5:312:985:871
+ATAAAACACATAGCTAAAACTAAAAAAGCAAAAAC
++
+<8<<<<.<.<<<<:<<<<<.<<<<<<<<<<<<<<<
+@EAS56_65:5:312:985:871
+TAAGAGGGATGAGAAATTACCTAATTGGTACAATG
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<:<<<<9<<
+@EAS56_65:5:37:611:267
+AATGAAGGGGAAATAAAGTCAAGTCTTTCCTGACA
++
+<<4<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS56_65:5:37:611:267
+TATAAAGGAAATCCCATAAGAATAACAATGGGCTT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS56_65:5:75:637:650
+CTGATTATGAAAACAATGTTCCCCAGATACCATCC
++
+<<<<<<<<<<<<<<<<<<<<<<<<<;<<<<<<<<:
+@EAS56_65:5:75:637:650
+GTCTCATCTAGGGGAACAGGGAGGTGCACTAATGC
++
+<<<<8<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS56_65:6:197:759:975
+AAAAGAATTGTAAAAGTCAAAATTAAAGTTCAATA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS56_65:6:197:759:975
+AATTTTTGGACTTCTTAAAGAAAAAAAAACCTGTC
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<<<<;
+@EAS56_65:6:37:610:260
+CAAGCCCTTCTCACAGTTTCTGCCCCCAGCATGGT
++
+/74<.<4.&<<<:<<<<::<<<<<<<<<<<<<<<<
+@EAS56_65:6:37:610:260
+CCAGAGGGAAAGCTTTCAACGCTTCTAGCCATTTC
++
+<<<;<;<<7<<<<<<<<<<<<<<;6<963;;;3;1
+@EAS56_65:6:46:173:214
+AACAATGGGCTTCTCAGCAGAAACCTTACAAGCCA
++
+<<2<<<<<<<<<<<5<<5<7<<<<<<<<<<<<<<<
+@EAS56_65:6:46:173:214
+CTAGAGATTTAGACATCTAAATGAAAGAGGCTCAA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<;<3<<<<<<;
+@EAS56_65:6:66:257:524
+ATACATGAGATTATTAGGAAATGCTTTACTGTCAT
++
+<;<<<<<<<<3<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS56_65:6:66:257:524
+GCCTTCAGACCCTACACGAATGCGTCTCTACCACC
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<%
+@EAS56_65:6:67:800:450
+TCACAGGTATTCCTGAGGAAAAAGAAAAAGTGAGA
++
+9-<9<;<<<<9;5<<<<<<<<<<<<<<<<<<<<<<
+@EAS56_65:6:67:800:450
+TTACAAAATATAGTTGAAAGCTCTAACAATAGACT
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<5<<<
+@EAS56_65:6:82:822:767
+AACAGCTTAGGTATCAATTTGGTGTTCTGTGTAAA
++
+<<9<<<<<<<<<<;;<<<:<<<<<<<<<<<<<<<<
+@EAS56_65:6:82:822:767
+TTAGGAAATGCTTTACTGTCATAACTATGAAGAGA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<.<<.<,<
+@EAS56_65:7:118:775:467
+AACAGTAAAATAAAACAAAGGAGGTCATCATACAA
++
+<<<<<<<<<<<<<<<<<<<<<<<<;<<<<<<<<<;
+@EAS56_65:7:118:775:467
+TGTACAATATTCTGATGATGGTTACACTAAAAGCC
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS56_65:7:122:398:994
+GGGATTAAATTCCCCCACTTAAGAGATATAGATTG
++
+95:<9<<<<:9<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS56_65:7:122:398:994
+TAAAAGTCAAAATTAAAGTTCAATACTCACCATCA
++
+<:<9<<<<<<4<<<;9<<<<<98<;<<<:;<;<;7
+@EAS56_65:7:219:40:833
+CCCATACTTTACTGCTACTCAATATATCCATGTAA
++
+<<*<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS56_65:7:219:40:833
+GGAGGTCATCATACAATGATAAAAAGATCAATTCA
++
+<<<<<<<<<<<<<<<<<<<<;<<<<<<<<<<<<<<
+@EAS56_65:7:288:552:440
+AGAGGGAACGCTTTCAACTCTTCTAGCCATTTCTT
++
+9<<%'%<<.2<<<<<<<<5:<<<<<<<<<<<<<<<
+@EAS56_65:7:288:552:440
+TGTGGTCTGACAGGCTGCAACTGTGAGCCTTCCAT
++
+<<<<71<77<<<:<<<&<4<<77<16<88&36+%%
+@EAS56_65:7:67:692:110
+ATTGCCAGATGAACCACACATTAATACTATGTTTC
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS56_65:7:67:692:110
+GTATCAATTTGGTGTTCTGTGTAAAGTCTCAGGGA
++
+;;<<8<<<<;<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS56_65:8:117:156:84
+GGTTCAGAACTTGAAGACAAGTCTCTTATGAATTA
++
+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS56_65:8:117:156:84
+TGGGGAAAACCTCTTTAGTCTTGCTAGAGATTTAG
++
+<;;<:<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS56_65:8:206:563:262
+ATTACGTCCTATCTTCTTCTTAGGGAAGAACAGCT
++
+<<<<7<<<<<<<<<<<<<<<<<<<<<<<<<<<<<7
+@EAS56_65:8:206:563:262
+ATTAGGAAATGCTTTACTGTCATAACTATGAAGAG
++
+<<<<<<<<<;<<<<<<<<<<<<;<<<<<<<-;<4;
+@EAS56_65:8:218:173:667
+CCTGCCCCATCTCTTGTAATCTCTCTCCTTTTTGC
++
+<<<<<<<<<<<<<<<6<<<<<<<<<<<<<<<<<.<
+@EAS56_65:8:218:173:667
+TAATGATTCCTCAATGTTAAAATGTCTATTTTTGT
++
+<<<<<<;<<;<<<<<<<<<<<<<<<<<<<<<<<<<
+@EAS56_65:8:24:415:944
+GTTCAGGTAAAGGGGTGGAAAAAGATGTTCTACGC
++
+<;;<<<<:<<<<<<<;<<<<<<<<<<<<;<<<<<<
+@EAS56_65:8:24:415:944
+TAGGTAAAAAATTAACATTACAACAGGAACAAAAC
++
+<<<<<<<<<<<<<<<<<<<<<:<<<<<<<<<<<<<
+@EAS56_65:8:275:851:240
+CCCCAGAGGGAAAGCTTTCAACGTTTCTAGCCATT
++
+66614/&3616630666&66666&66666868666
+@EAS56_65:8:275:851:240
+GTGGTCTGACAGGCTGCAACTGTGAGCCATCACAA
++
+<<<<<<<<<<<<<<<<<<<<<<<:<<4<7<<<<<<
+@EAS56_65:8:317:83:500
+TTTTTTTTTTTTCTTTTCTCCTTTTTTTTTTGTTT
++
+;;;;;<<<<<<<3<<<)-;31<<)97<;9<<:<<<
+@EAS56_65:8:64:507:478
+TAATTGAAAAATTCATTTAAGAAATTACAAAATAT
++
+<<<<<;<<<<<<<<<<<<<<<;;;<<<;<<8;<;<
diff --git a/tests/pysam_data/issue100.sam b/tests/pysam_data/issue100.sam
new file mode 100644
index 0000000..6c0c2a8
--- /dev/null
+++ b/tests/pysam_data/issue100.sam
@@ -0,0 +1,27 @@
+@SQ	SN:chr1	LN:249250621
+@SQ	SN:chr10	LN:135534747
+@SQ	SN:chr11	LN:135006516
+@SQ	SN:chr12	LN:133851895
+@SQ	SN:chr13	LN:115169878
+@SQ	SN:chr14	LN:107349540
+@SQ	SN:chr15	LN:102531392
+@SQ	SN:chr16	LN:90354753
+@SQ	SN:chr17	LN:81195210
+@SQ	SN:chr18	LN:78077248
+@SQ	SN:chr19	LN:59128983
+@SQ	SN:chr2	LN:243199373
+@SQ	SN:chr20	LN:63025520
+@SQ	SN:chr21	LN:48129895
+@SQ	SN:chr22	LN:51304566
+@SQ	SN:chr3	LN:198022430
+@SQ	SN:chr4	LN:191154276
+@SQ	SN:chr5	LN:180915260
+@SQ	SN:chr6	LN:171115067
+@SQ	SN:chr7	LN:159138663
+@SQ	SN:chr8	LN:146364022
+@SQ	SN:chr9	LN:141213431
+@SQ	SN:chrM	LN:16571
+@SQ	SN:chrX	LN:155270560
+@SQ	SN:chrY	LN:59373566
+@PG	ID:bwa	PN:bwa	VN:0.5.9-r16
+YILLUMINA-B8EC94_231:1:50:18506:14866#0	0	chr1	164170895	0	28M	*	0	0	AAAATAAAATAAAATAAAATAAAATAGG	IIIIIGIIIIIIIIHIIIIFIIGIDHIG	XT:A:R	NM:i:0	X0:i:46	X1:i:488	XM:i:0	XO:i:0	XG:i:0	MD:Z:28	XA:Z:chr7,-76584917,28M,0;chr7,-76086813,28M,0;chr19,-14658154,28M,0;chr12,-44420884,28M,0;chr4,-46749296,28M,0;chr16,-65813760,28M,0;chr12,-125218307,28M,0;chr22,-49521364,28M,0;chr8,-67441969,28M,0;chrX,-24771433,28M,0;chr2,-97418606,28M,0;chr17,-48859141,28M,0;chr19,-33212584,28M,0;chr7,-69136775,28M,0;chr5,-80182155,28M,0;chr5,-40957547,28M,0;chr1,-8992207,28M,0;chr4,-41653011,28M,0;chr3,-5149300,28M,0;chr3,+49488805,28M,0;chr5,+58266193,28M,0;chr22,+42021002,28M,0;chr11,+85612617,28M,0;chr7,+151315540,28M,0;chr17,+17559883,28M,0;chr11,+74995947,28M,0;chr12,+119190631,28M,0;chr8,+121033303,28M,0;chr9,+122813065,28M,0;chr1,+92280874,28M,0;chr3,+49184061,28M,0;chr2,+104675746,28M,0;chr6,+108461339,28M,0;chr20,+20548540,28M,0;chr10,+62601188,28M,0;chr4,+8350545,28M,0;chr1,+150194440,28M,0;chr20,+50633348,28M,0;chr1,+25648175,28M,0;chr19,+33713380,28M,0;chr8,+56596974,28M,0;chr10,+19488747,28M,0;chrX,+43980718,28M,0;chr22,+28827966,28M,0;chr7,+76248706,28M,0;chr12,+34385994,28M,1;chr22,+24200895,28M,1;chr11,+9935206,28M,1;chr7,+71057507,28M,1;chr8,+75964204,28M,1;chr11,+70749536,28M,1;chr6,+121876867,28M,1;chr8,+9904069,28M,1;chr2,+167975020,28M,1;chr8,+65343650,28M,1;chr2,+203338523,28M,1;chr6,+134519042,28M,1;chr19,+15588539,28M,1;chrX,+21005486,28M,1;chr1,+51600244,28M,1;chr6,+135071574,28M,1;chrX,+142060697,28M,1;chr3,+88036270,28M,1;chr11,+107768031,28M,1;chr1,+43452382,28M,1;chr3,+119162759,28M,1;chr7,+137682479,28M,1;chrY,+771178,28M,1;chrX,+821178,28M,1;chr3,+131863613,28M,1;chr4,+5198466,28M,1;chr8,+42219792,28M,1;chr18,+21867757,28M,1;chr1,+205771873,28M,1;chr7,+106381815,28M,1;chr3,+152231119,28M,1;chr18,+38121876,28M,1;chr18,+13226733,28M,1;chr2,+113982439,28M,1;chr13,+38527369,28M,1;chr16,+61112193,28M,1;chr13,+63276179,28M,1;chr6,+22044433,28M,1;chr8,+75971314,28M,1;chr1,+155919065,28M,1;chr10,+9075352,28M,1;chr14,+41766647,28M,1;chr4,+38881700,28M,1;chr14,+63221608,28M,1;chr1,+96460706,28M,1;chr1,+31541552,28M,1;chr2,+130852364,28M,1;chr2,+131240936,28M,1;chr16,+54409861,28M,1;chr7,+138085971,28M,1;chr6,+168960156,28M,1;chr7,+35021562,28M,1;chr3,+5192468,28M,1;chr5,+139685004,28M,1;chr16,+57887328,28M,1;chr1,+240683393,28M,1;chr7,+51529361,28M,1;chr15,+38755713,28M,1;chr17,+45077478,28M,1;chr7,+98657066,28M,1;chrX,+15178325,28M,1;chr15,+50856486,28M,1;chr6,+26677004,28M,1;chr11,+67754723,28M,1;chr11,+60378362,28M,1;chr13,+74834741,28M,1;chr7,+139512903,28M,1;chr15,+65775953,28M,1;chr22,+39161266,28M,1;chr5,+42576221,28M,1;chr6,+142807488,28M,1;chr16,+65067646,28M,1;chrY,+17168022,28M,1;chrY,+20444338,28M,1;chr6,+85793701,28M,1;chr7,+95669552,28M,1;chr2,+99252467,28M,1;chr5,+93286660,28M,1;chr12,+19541000,28M,1;chr9,+28932106,28M,1;chr7,+62487286,28M,1;chr5,+152475447,28M,1;chr10,+104206440,28M,1;chr4,+182765824,28M,1;chr19,+54584245,28M,1;chrY,+5218751,28M,1;chr4,+44370409,28M,1;chr6,+19294076,28M,1;chr19,+1191066,28M,1;chr5,+142819608,28M,1;chr13,+82093983,28M,1;chrX,+130954389,28M,1;chr6,+6847717,28M,1;chr11,+89143226,28M,1;chr2,+108524013,28M,1;chr5,+108771229,28M,1;chrX,+93364170,28M,1;chrX,+88234143,28M,1;chr17,+9723415,28M,1;chr6,+27707864,28M,1;chr3,+66057355,28M,1;chr3,+154005450,28M,1;chr15,+29887458,28M,1;chr14,+56232133,28M,1;chr2,+122434791,28M,1;chr8,+126235305,28M,1;chr16,+52177603,28M,1;chr4,+34178766,28M,1;chr8,+22882491,28M,1;chr18,+2552191,28M,1;chr17,+32715595,28M,1;chr16,+53061076,28M,1;chr2,+114903272,28M,1;chr4,+42337800,28M,1;chr6,+149777395,28M,1;chr1,+151096337,28M,1;chr6,+118477838,28M,1;chr3,+30600543,28M,1;chr19,+33567456,28M,1;chr8,+1217564,28M,1;chr4,+39872213,28M,1;chrX,+44688603,28M,1;chrX,+48314490,28M,1;chr1,+21650136,28M,1;chr21,+15675906,28M,1;chr9,+106120465,28M,1;chr13,+24047341,28M,1;chr2,+125770922,28M,1;chr22,+30263047,28M,1;chr2,+204843020,28M,1;chr12,+130100366,28M,1;chr10,+4068348,28M,1;chr17,+63322228,28M,1;chr11,+83019719,28M,1;chrX,+54143823,28M,1;chr7,+36425437,28M,1;chr16,+19178880,28M,1;chr18,+46417931,28M,1;chr6,+55717991,28M,1;chr3,+75664223,28M,1;chr1,+32452030,28M,1;chr15,+88159172,28M,1;chr2,+61851071,28M,1;chr7,+141613606,28M,1;chr17,+12596976,28M,1;chr19,+3414622,28M,1;chr7,+6890735,28M,1;chr20,+34272363,28M,1;chr9,+90994839,28M,1;chr18,+9638082,28M,1;chr1,+67650276,28M,1;chr1,+220568591,28M,1;chr4,+89058188,28M,1;chr4,+4140808,28M,1;chr1,+202088715,28M,1;chr11,+87269515,28M,1;chr11,+67474784,28M,1;chr4,+43167357,28M,1;chr7,+67457466,28M,1;chr16,+19891760,28M,1;chr20,+25234269,28M,1;chr12,+55369476,28M,1;chr4,+6141505,28M,1;chr10,+29354543,28M,1;chr5,+166192505,28M,1;chrX,+48884710,28M,1;chr6,+134330810,28M,1;chr4,+160376376,28M,1;chr4,+99817350,28M,1;chr10,+121317660,28M,1;chr12,+74218473,28M,1;chr9,+32910016,28M,1;chr8,+69378187,28M,1;chrY,+18963621,28M,1;chr5,+6914382,28M,1;chr2,+68235232,28M,1;chr10,+13942898,28M,1;chr2,+80178815,28M,1;chr17,+26736416,28M,1;chr20,+40349589,28M,1;chr15,+23140038,28M,1;chrX,+121086049,28M,1;chr3,+181657140,28M,1;chr15,+66492254,28M,1;chr10,+88050421,28M,1;chr5,+90017384,28M,1;chr17,+36256463,28M,1;chr7,+151013744,28M,1;chr8,+30617505,28M,1;chr6,+31902798,28M,1;chr6,+46224124,28M,1;chr6,+156992688,28M,1;chr11,+59390750,28M,1;chr13,+106355845,28M,1;chr20,+4185147,28M,1;chr9,+110284660,28M,1;chr10,+109112359,28M,1;chr14,+75178252,28M,1;chr10,+95667563,28M,1;chr2,+157160276,28M,1;chr4,+137463808,28M,1;chr4,+62742455,28M,1;chr21,+16861620,28M,1;chr13,+42603913,28M,1;chr5,+88099616,28M,1;chr18,+59093425,28M,1;chr7,+5592293,28M,1;chr2,+169057205,28M,1;chr2,+230616223,28M,1;chr17,+7532710,28M,1;chr11,+18249822,28M,1;chr11,+124575250,28M,1;chr17,+36208776,28M,1;chr12,+51408636,28M,1;chr3,+181394862,28M,1;chr8,+3343335,28M,1;chr4,+72726246,28M,1;chr4,+184703799,28M,1;chr9,+37367170,28M,1;chr3,+37229983,28M,1;chr18,+19786650,28M,1;chr3,+142855780,28M,1;chr16,+63684651,28M,1;chr2,+169863074,28M,1;chr5,+57467010,28M,1;chr16,+68641846,28M,1;chr1,+218080386,28M,1;chr3,+49931339,28M,1;chr8,+91965023,28M,1;chr1,+64882723,28M,1;chr10,+44040423,28M,1;chr1,+27841637,28M,1;chr3,+32964826,28M,1;chrX,-14075583,28M,1;chrY,-19735409,28M,1;chr3,-61210077,28M,1;chr12,-25148105,28M,1;chr6,-46827553,28M,1;chr8,-56057364,28M,1;chr5,-116062081,28M,1;chr6,-114038567,28M,1;chr1,-25697211,28M,1;chr2,-73266904,28M,1;chr5,-175028383,28M,1;chr8,-3051929,28M,1;chr22,-25543121,28M,1;chr6,-26792622,28M,1;chr17,-37194552,28M,1;chr17,-57538339,28M,1;chr1,-51140531,28M,1;chr13,-94647414,28M,1;chr20,-32448950,28M,1;chr1,-238865938,28M,1;chr6,-119062752,28M,1;chr20,-10852575,28M,1;chr11,-124936858,28M,1;chr11,-112719434,28M,1;chr8,-65050045,28M,1;chr11,-111428922,28M,1;chr3,-50585823,28M,1;chr17,-40620860,28M,1;chr9,-79518493,28M,1;chr6,-72507285,28M,1;chr12,-104465353,28M,1;chr2,-131394877,28M,1;chr2,-132001670,28M,1;chr8,-81578043,28M,1;chr20,-37724057,28M,1;chr22,-47141401,28M,1;chr6,-46531919,28M,1;chr9,-9009407,28M,1;chr11,-124465447,28M,1;chr21,-28931439,28M,1;chr18,-61702652,28M,1;chr4,-37711424,28M,1;chr1,-149741655,28M,1;chr13,-78712904,28M,1;chr14,-68009392,28M,1;chr2,-78892078,28M,1;chr1,-149356753,28M,1;chr5,-172533734,28M,1;chr2,-173762459,28M,1;chr2,-198549736,28M,1;chr2,-150821070,28M,1;chr11,-47699839,28M,1;chr17,-42866270,28M,1;chr5,-173490523,28M,1;chr6,-24001074,28M,1;chr1,-39682911,28M,1;chr4,-4222769,28M,1;chr10,-111743035,28M,1;chr11,-128684387,28M,1;chr20,-11257956,28M,1;chr20,-4149529,28M,1;chr5,-164974199,28M,1;chr3,-84991544,28M,1;chr5,-5908988,28M,1;chr2,-138324702,28M,1;chr5,-22429210,28M,1;chr15,-84551893,28M,1;chr6,-73756333,28M,1;chr14,-86022032,28M,1;chr12,-61162349,28M,1;chr13,-42155113,28M,1;chr16,-8376743,28M,1;chrX,-25947951,28M,1;chr13,-37707269,28M,1;chr20,-52341305,28M,1;chr8,-32439586,28M,1;chrX,-65037782,28M,1;chr15,-35588112,28M,1;chr6,-114826977,28M,1;chr16,-22957281,28M,1;chr2,-29152353,28M,1;chr11,-32021557,28M,1;chr14,-53067145,28M,1;chr15,-74660451,28M,1;chr9,-125814020,28M,1;chr2,-47888617,28M,1;chr6,-103141276,28M,1;chr2,-38287203,28M,1;chr14,-75792495,28M,1;chr3,-116403271,28M,1;chr12,-122920160,28M,1;chr1,-192176238,28M,1;chr17,-17438208,28M,1;chr2,-117287007,28M,1;chr11,-68195410,28M,1;chr16,-76921888,28M,1;chr1,-113847491,28M,1;chr5,-166230578,28M,1;chr12,-41106211,28M,1;chrX,-116017871,28M,1;chr6,-107154514,28M,1;chrX,-5600375,28M,1;chr5,-92345920,28M,1;chr5,-176706961,28M,1;chr11,-84337889,28M,1;chr14,-65707185,28M,1;chr7,-66648805,28M,1;chr7,-139066097,28M,1;chr10,-86865072,28M,1;chr3,-73488878,28M,1;chr5,-158663415,28M,1;chr2,-43545165,28M,1;chr6,-69160212,28M,1;chr20,-55152586,28M,1;chr3,-146595642,28M,1;chr10,-88376880,28M,1;chr8,-68384647,28M,1;chr16,-30821557,28M,1;chrX,-69242160,28M,1;chr8,-40818508,28M,1;chr3,-197716909,28M,1;chr2,-241964069,28M,1;chr1,-150748134,28M,1;chr17,-5098791,28M,1;chr2,-135759985,28M,1;chr8,-42470825,28M,1;chr1,-166779724,28M,1;chr16,-63793250,28M,1;chr10,-21864107,28M,1;chr18,-28817256,28M,1;chr17,-13910779,28M,1;chr17,-57348966,28M,1;chr7,-137391223,28M,1;chr19,-23655174,28M,1;chr17,-64986763,28M,1;chr16,-21167483,28M,1;chr11,-42817287,28M,1;chr11,-13533098,28M,1;chr22,-31622164,28M,1;chr4,-21126811,28M,1;chr18,-66802141,28M,1;chr10,-96291396,28M,1;chr4,-145004956,28M,1;chr1,-107823475,28M,1;chr11,-2255057,28M,1;chr19,-28323682,28M,1;chr5,-2777444,28M,1;chr4,-121847688,28M,1;chr13,-54002436,28M,1;chr4,-8970065,28M,1;chr13,-81895317,28M,1;chr6,-85079405,28M,1;chr4,-9504061,28M,1;chr2,-136295178,28M,1;chr3,-196067725,28M,1;chr8,-18303975,28M,1;chrX,-21470871,28M,1;chr3,-194098768,28M,1;chr22,-47888023,28M,1;chr19,-17652453,28M,1;chr3,-32034656,28M,1;chr1,-20438413,28M,1;chr11,-99259713,28M,1;chr3,-177057675,28M,1;chr9,-95123722,28M,1;chr18,-76417358,28M,1;chr6,-100247652,28M,1;chr3,-140933488,28M,1;chr19,-2486490,28M,1;chr15,-73938461,28M,1;chr13,-95995526,28M,1;chr11,-48289844,28M,1;chr5,-72218725,28M,1;chr18,-61103078,28M,1;chr1,-117442797,28M,1;chr7,-143195374,28M,1;chr14,-88665236,28M,1;chr10,-105896107,28M,1;chr12,-89971388,28M,1;chr19,-14741205,28M,1;chr1,-247103257,28M,1;chr13,-106746329,28M,1;chr17,-74646298,28M,1;chr22,-27259346,28M,1;chr8,-131520642,28M,1;chr18,-63913876,28M,1;chr1,-8696036,28M,1;chr3,-132074330,28M,1;chr8,-133889374,28M,1;chr14,-51395758,28M,1;chr4,-22649515,28M,1;chrX,-15236428,28M,1;chr2,-32796028,28M,1;chr19,-58872058,28M,1;chr11,-37627459,28M,1;chr20,-9564948,28M,1;chr8,-30080229,28M,1;chr13,-73402183,28M,1;chr17,-71119116,28M,1;chr8,-63170581,28M,1;chr9,-39465483,28M,1;chr9,-41610501,28M,1;chr9,-40793070,28M,1;chr12,-30506726,28M,1;chr16,-22438117,28M,1;chr12,-33319234,28M,1;chr21,-32371401,28M,1;chr5,-126791414,28M,1;chr8,-20355956,28M,1;chr15,-59301146,28M,1;chr2,-48648533,28M,1;chr7,-48022928,28M,1;chr5,-29797589,28M,1;chr12,-54092686,28M,1;chr16,-11434195,28M,1;chr17,-58971405,28M,1;chr19,-43931598,28M,1;chr7,-91707288,28M,1;chr3,-185465634,28M,1;chr8,-117592194,28M,1;chr4,-125205639,28M,1;chr6,-114161269,28M,1;chr13,-91715527,28M,1;chr10,-98692195,28M,1;chr7,-17789580,28M,1;chr2,-152298559,28M,1;chr19,-47866013,28M,1;chrX,-152022933,28M,1;chr6,-42355529,28M,1;chr7,-115116598,28M,1;chr4,-55514389,28M,1;chr1,-162526013,28M,1;chr6,-53169231,28M,1;chr8,-22225996,28M,1;chr4,-145044601,28M,1;chr1,-150288526,28M,1;chr12,-104184041,28M,1;chr10,-70469042,28M,1;chr8,-37870308,28M,1;chr7,-139506036,28M,1;chr19,-23655169,28M,1;chr1,-8943144,28M,1;chr9,-93078553,28M,1;chr16,-68274470,28M,1;chr1,-28021897,28M,1;chr17,-36306267,28M,1;chr17,-60297701,28M,1;chr4,-175699094,28M,1;chr3,-138640873,28M,1;chr14,-42606743,28M,1;chr10,-29007373,28M,1;chr8,-32366590,28M,1;chr4,-144977946,28M,1;chr3,-73413315,28M,1;chr5,-102654091,28M,1;
diff --git a/tests/pysam_data/rg_with_tab.sam b/tests/pysam_data/rg_with_tab.sam
new file mode 100644
index 0000000..2420921
--- /dev/null
+++ b/tests/pysam_data/rg_with_tab.sam
@@ -0,0 +1,3273 @@
+@SQ	SN:chr1	LN:1575
+@SQ	SN:chr2	LN:1584
+@PG	ID:bwa	PN:bwa	VN:0.7.9a-r786	CL:bwa mem -p -t 8 -M -R @RG ID:None SM:None /mnt/data/hg19.fa /mnt/analysis/default-0.fastq
+EAS56_57:6:190:289:82	69	chr1	100	0	*	=	100	0	CTCAAGGTTGTTGCAAGGGGGTCTATGTGAACAAA	<<<7<<<;<<<<<<<<8;;<7;4<;<;;;;;94<;	MF:i:192
+EAS56_57:6:190:289:82	137	chr1	100	73	35M	=	100	0	AGGGGTGCAGAGCCGAGTCACGGGGTTGCCAGCAC	<<<<<<;<<<<<<<<<<;<<;<<<<;8<6;9;;2;	MF:i:64	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_64:3:190:727:308	99	chr1	103	99	35M	=	263	195	GGTGCAGAGCCGAGTCACGGGGTTGCCAGCACAGG	<<<<<<<<<<<<<<<<<<<<<<<<<<<::<<<844	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS112_34:7:141:80:875	99	chr1	110	99	35M	=	265	190	AGCCGAGTCACGGGGTTGCCAGCACAGGGGCTTAA	<<<<<<<<<<<<<<<<<<<<<<:<<8;<<8+7;-7	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS219_FC30151:3:40:1128:1940	163	chr1	112	99	35M	=	291	214	CCGAGTCACGGGGTTGCCAGCACAGGGGCTTAACC	<<<<<<<<<<<<<<<<<<<;<<5;;<<<9;;;;7:	MF:i:18	Aq:i:70	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_62:5:290:319:736	69	chr1	113	0	*	=	113	0	GTTCTCAAGGTTGTTGCAAGGGGGTCTATGTGAAC	<<<<<<:7:<.<<<<7<<.<.<<.9*<4<:<4%74	MF:i:192
+EAS51_62:5:290:319:736	137	chr1	113	73	35M	=	113	0	CGAGTCACGGGGTTGCCAGCACAGGGGCTTAACCT	==;=======7====6=;==:;;====66=::27:	MF:i:64	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_597:2:132:493:921	69	chr1	119	0	*	=	119	0	GTTCTCAAGGTTGTTGCAAGGGGGTCTATGTGAAC	<<<<<<<<<<<<<<<<<<<;<<<<77;0<;;6777	MF:i:192
+B7_597:2:132:493:921	137	chr1	119	75	35M	=	119	0	ACGGGGTTGCCAGCACAGGGGCTTAACCTCTGGTG	<<<<<<<<<<<<<<<<;<<<<<<<<;<<<<;;88:	MF:i:64	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_30:7:283:799:560	163	chr1	121	66	35M	=	283	197	GGGGTTGCCAGCACAGGGGCTTAACCTCTGGTGAC	<<<<+<<<<8<<<+<<<<<;<<:07;8;7402447	MF:i:18	Aq:i:66	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS192_3:1:225:195:543	99	chr1	123	99	35M	=	299	211	GGTTGCCAGCACAGGGGCTTAACCTCTGGTGACTG	<<<<<<<<<<<<<<<<<<<<<<<9<<;::388998	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_589:6:114:714:317	99	chr1	126	99	35M	=	311	220	TGCCAGCACAGGGGCTTAACCTCTGGTGACTGCCA	<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<<5;<;	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_39:1:70:147:84	163	chr1	128	73	35M	=	285	192	CCAGCACAGGGGCTTAACCTCTGGTGACTGCCAGA	<<<<<<<<<<<<<<<<<<<<;<<<<<<<<<;(5<<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS188_7:2:187:227:818	163	chr1	129	99	35M	=	290	196	CAGCACAGGGGCTTAACCTCTGGTGACTGCCAGAG	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<3<;<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_97:4:77:29:126	99	chr1	131	99	35M	=	315	219	GCACAGGGGCTTAACCTCTGGTGACTGCCAGAGCT	<<<<<<<<<<3<<<<<<<;;;7<;<<449<-:977	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_30:4:327:795:103	99	chr1	133	99	35M	=	302	204	ACAGGGGCTTAACCTCTGGTGACTGCCAGAGCTGC	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<;	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_30:3:139:117:262	69	chr1	135	0	*	=	135	0	GTTCTCAAGGTTGTTGCAAGGGGGTCTATGTGAAC	<<<7<<<<<<<<<<<<<<<<<<<;<;<<<<<37;3	MF:i:192
+EAS114_30:3:139:117:262	137	chr1	135	76	35M	=	135	0	AGGGGCTTAACCTCTGGTGACTGCCAGAGCTGCTG	<<<<;<<<<<<<<<<<<<:<<<<<:<<8<<<<:<:	MF:i:64	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS219_FC30151:5:29:817:854	73	chr1	135	77	35M	=	135	0	AGGGGCTTAACCTCTGGTGACTGCCAGAGCTGCTG	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:64	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS219_FC30151:5:29:817:854	133	chr1	135	0	*	=	135	0	GTTCTCAAGGTTGTTGCAAGGGGGTTTATGTGAAC	<<<<<<<<<<<<<<<1..;:;;;;1%407)07&7.	MF:i:192
+EAS192_3:6:170:169:57	163	chr1	138	99	35M	=	296	193	GGCTTGACCTCTGGTGACTGCCAGAGCTGCTGGCC	<<<<<;<<<<<<;<<<<<<<<<<<<:<<<<<;;+%	MF:i:18	Aq:i:45	NM:i:2	UQ:i:30	H0:i:0	H1:i:1
+B7_595:4:84:802:737	99	chr1	140	68	35M	=	284	179	CTTAACCTCTGGTGACTGCCAGAGCTGCTGGCAAG	<<<<<<<<<<;9<9<<<;<<;73;<<<<<37;1+.	MF:i:18	Aq:i:68	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS188_4:7:78:583:670	163	chr1	142	99	35M	=	316	209	TAACCTCTGGTGACTGCCAGAGCTGCTGGCAAGCT	<<<<<<<<<<;;;<;;<<<:7;5;<5;;<2--8-;	MF:i:18	Aq:i:66	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_64:3:90:435:691	99	chr1	147	99	35M	=	318	206	TCTGGTGACTGCCAGAGCTGCTGGCAAGCTAGAGT	<<<<<<<<<<;<<<;<<<<:<<<;<81;<<1;784	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS188_7:3:13:122:187	163	chr1	153	99	35M	=	343	225	GACTGCCAGAGCTGCTGGCAAGCTAGAGTCCCCTT	<<<<<<<;<;<<<;<<<<:;6<<<<;;;;:<<%%<	MF:i:18	Aq:i:69	NM:i:1	UQ:i:4	H0:i:1	H1:i:0
+EAS221_1:6:69:735:1915	99	chr1	154	99	35M	=	321	202	ACTGCCAGAGCTGCTGGCAAGCTAGAGTCCCATTT	<<<<<<<<;<<<<<<<<<;<<<<;<8<<<<;1:<<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:5:66:959:1311	163	chr1	159	95	35M	=	336	212	CAGAGCTGCTGGCAAGCTAGAGGCCCATCTGGAGC	;;4;;;+;;;-01;;&-;;4;;&;;73)(&**274	MF:i:18	Aq:i:31	NM:i:2	UQ:i:12	H0:i:0	H1:i:1
+EAS56_57:6:325:759:288	99	chr1	163	99	35M	=	341	213	GCTGCTGGCAAGCTAGAGTCCCATTTGGAGCCCCT	8<;<<<<81<<<<<;<<;<<<;9</;6;;809034	MF:i:18	Aq:i:67	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_108:7:82:926:112	99	chr1	164	99	35M	=	328	199	CTGCTGGCAAGCTAGAGTCCCATTTGGAGCCCCTC	<;<<<<<<<<<5<<<<<<<<<<<<<<<;<<1:<4<	MF:i:18	Aq:i:41	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_57:5:324:728:956	99	chr1	165	99	35M	=	322	192	TGCTGGCAAGCTAGAGTCCCATTTGGAGCCCCTCT	<<<<<<<<<<<<<<<<<<<<8<<<:<::;;;;<:<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_103:4:294:525:849	163	chr1	167	99	35M	=	340	208	CTGGCAAGCTAGAGTCCCATTTGGAGCCCCTCTAA	<<<<<<<<<<<<<<<<<<<<<<9+<:<<<<9;;15	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_57:7:159:125:297	163	chr1	170	99	35M	=	337	202	GCAAGCTAGAGTCCCATTTGGAGCCACTCTAAGAC	<<<<<<<<<<<<<<;<<<;<;<<6;)<:9;26;39	MF:i:18	Aq:i:43	NM:i:2	UQ:i:26	H0:i:0	H1:i:1
+EAS54_65:6:164:797:930	99	chr1	173	99	35M	=	332	194	AGCTAGAGACCCATTTGGAGCCCCTCTAAGCCGTT	<<<<<<<<<<<<<<<;;;:<<<<<;<;<<<<<,::	MF:i:18	Aq:i:45	NM:i:1	UQ:i:27	H0:i:0	H1:i:1
+EAS54_81:7:293:355:321	163	chr1	174	99	35M	=	356	217	GCTAGAGTCCCATTTGGAGCCCCTCTAAGCCGTTC	<<<:<;<<<<<<<;<<<<<<<<<;<<;4<<<:+:<	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_595:1:209:653:400	163	chr1	175	99	35M	=	340	200	CTAGAGTCCCATTTGGAGCCCCTCTAAGCCGTTCT	<;<9<<+<2<9<,;;64;<<<<;8<00*1<48:+8	MF:i:18	Aq:i:59	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS220_1:2:62:1109:804	163	chr1	176	99	35M	=	350	209	TAGAGTCCCATTTGGAGCCCCTCTAAGCCGTTCTA	<<<<<<<<<<<<<:<<:<<<<<<:<:<<<<;;;;;	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_78:7:303:402:142	163	chr1	181	99	35M	=	343	197	TCCCATTTGGAGCCCCTCTAAGCCGTTCTATTTGT	<8<<<<<<<<<<<<<<<<<<<<<<<46<648;;';	MF:i:18	Aq:i:68	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_71:8:321:642:388	163	chr1	181	99	35M	=	357	209	TCCCATTTGGAGCCCCTCTAAGCCGTTCTATTTGT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<6<<<8;	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:2:1:1140:1206	163	chr1	181	99	35M	=	368	222	TCCCATTTGGAGCCCCTCTAAGCCGTTCTATTTGT	;;;;;;;;;;;;;:9;;7;;:;:;97;:;:88888	MF:i:18	Aq:i:66	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_28:6:155:68:326	99	chr1	182	99	36M	=	332	186	CCCATTTGGAGCCCCTCTAAGCCGTTCTATTTGTAA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<:<<<<<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS188_7:7:19:886:279	99	chr1	182	99	35M	=	337	190	CCCATTTGGAGCCCCTCTAAGCCGTTCTATTTGTA	<9<<<<<<<<<<<<6<28:<<85<<<<<2<;<9<<	MF:i:18	Aq:i:67	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_61:4:143:69:578	147	chr1	185	98	35M	=	36	-184	ATTGGGAGCCCCTCTAAGCCGTTCTATTTGTAATG	222&<21<<<<12<7<01<<<<<0<<<<<<<20<<	MF:i:18	Aq:i:35	NM:i:1	UQ:i:5	H0:i:1	H1:i:0
+EAS54_71:4:13:981:659	181	chr1	187	0	*	=	188	0	CGGGACAATGGACGAGGTAAACCGCACATTGACAA	+)---3&&3&--+0)&+3:7777).333:<06<<<	MF:i:192
+EAS54_71:4:13:981:659	121	chr1	188	37	34M	=	187	0	TGTAGCCCCTCTAAGGCGTTCTATTTGTAATGAA	()&)06636;;<664*6;<<<<<<<<<<<<<<<1	MF:i:64	Aq:i:0	NM:i:2	UQ:i:14	H0:i:0	H1:i:1
+B7_610:1:37:652:403	163	chr1	193	99	35M	=	347	189	CCCCTCTAAGCCGTTCTATTTGTAATGAAAACTAT	<<<<<<<;<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_66:1:282:274:50	163	chr1	193	99	35M	=	371	213	CCCCTCTAAGCCGTTCTATTTGTAATGAAAACTAT	<<<<<<<<<<<<<<<<<;<<<<<99<9<5909;5;	MF:i:18	Aq:i:70	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_593:2:133:460:542	99	chr1	195	99	36M	=	356	197	CCTATAAGCCGTTCTATTTGTAATGAAAACTATATT	<<<<<<<<<<<;<<<<<<<<<<<<;<<<<<<<<<<;	MF:i:18	Aq:i:47	NM:i:1	UQ:i:27	H0:i:0	H1:i:1
+EAS54_73:5:44:498:945	99	chr1	195	82	35M	=	377	217	CCTATAAGCCGTTCTATTTGTAATGAAAACTATAT	;<;<<<<<<<<<<9<;<:<<<<<<:<<<<;:;<3<	MF:i:18	Aq:i:37	NM:i:1	UQ:i:27	H0:i:0	H1:i:1
+B7_610:1:139:152:856	99	chr1	198	99	35M	=	392	229	CTAAGCCGTTCTATTTGTAATGAAAACTATATTTA	<<<<<<<<;<<<<<<<<<<;<;<<<;<<<<;<;;;	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_591:2:323:639:311	163	chr1	200	99	36M	=	357	193	AAGCCGTTCTATTTGTAATGAAAACTATATTTAGGC	<<<<<<<<<<<<<<<<<<<2<<<<<<;<<<<<<81<	MF:i:18	Aq:i:70	NM:i:1	UQ:i:23	H0:i:1	H1:i:0
+EAS114_39:2:18:967:582	163	chr1	200	99	35M	=	398	233	AAGCCGTTCTATTTGTAATGAAAACTATATTTATG	<<<<<<<<<<<<<<<<<<<<<9<<<<<<;<<<<<8	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_597:8:186:850:838	99	chr1	205	99	35M	=	389	219	GTTCTATTTGTAATGAAAACTATATTTATGCTATT	<<<<<;<<<<<<<<<<<:<<<<<;<<<;</<<;<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_53:3:126:558:408	163	chr1	206	99	35M	=	368	197	TTCTATTTGTAATGAAAACTATATTTATGCTATTC	<<<<<<<<<<<<<:<<<<<<<<<<<<<<7<;<<;;	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_57:6:157:643:175	163	chr1	206	99	35M	=	380	209	TTCTATTTGTAATGAAAACTATATTTATGCTATTC	<<<<<<<<;<<<<<<<<<<<<<<<<<<<)<<<<;<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_103:5:141:711:813	99	chr1	209	99	35M	=	370	196	TATTTGTAATGAAAACTATATTTATGCTATTCAGT	<<<<<<<<<<;<<<<<<<<<<<<<<;<<<<<<:+<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_65:6:115:538:276	163	chr1	209	99	35M	=	360	186	TATTTGTAATGAAAACTATATTTATGCTATTCAGT	<<<<<<<<;<<<;;<<<;<:<<<:<<<<<<;;;7;	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS219_FC30151:7:51:1429:1043	83	chr1	209	99	35M	=	59	-185	TATTTGTAATGAAAACTATATTTATGCTATTCAGT	9<5<<<<<<<<<<<<<9<<<9<<<<<<<<<<<<<<	MF:i:18	Aq:i:68	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_30:1:176:168:513	163	chr1	210	99	35M	=	410	235	ATTTGTAATGAAAACTATATTTATGCTATTCAGTT	<<<<;<<<<<<<<<<<<<<<<<<<:&<<<<:;0;;	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_95:7:282:817:710	99	chr1	211	99	35M	=	384	208	TTTGTAATGAAAACTATATTTATGCTATTCAGTTC	<<<<<<<<<<<<<<<<<<<<<<<;:<<<<:8,<<8	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_108:1:65:787:74	83	chr1	213	88	35M	=	61	-187	TGTAATGAAAACTATATTTATGCTATTCAGTTCTA	44848=:1661/66==?:<=:?6><<<<1>><<<<	MF:i:18	Aq:i:21	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_66:4:240:264:231	121	chr1	213	66	35M	=	213	0	TGTAATGAAAACTATATTTATGCTATTCAGTTCTA	9;,;;62<9<)29<<<;96<<<;<<7<<<<<<;<<	MF:i:64	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_66:4:240:264:231	181	chr1	213	0	*	=	213	0	CAACAGATCAAGAAGGAGGGGCAATGGACGAGTTA	%15+5022))0&<<)0)+7:4+&<0<<:0<<<7<<	MF:i:192
+EAS1_93:7:14:426:613	99	chr1	214	99	35M	=	379	200	GTAATGAAAACTATATTTATGCTATTCAGTTCTAA	======;=;==========;;==3=;==-=<;<;<	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_93:2:173:995:93	163	chr1	215	99	35M	=	382	202	TAATGAAAACTATATTTATGCTATTCAGTTCTAAA	<<<<<<<<<<<<<<<<<<<7:<<<<;:<:<<<<:7	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_64:6:195:348:703	163	chr1	215	99	35M	=	353	173	TAATGAAAACTATATTTATGCTATTCAGTTCTAAA	<<<<<<<;<<<<<;:<<<<<<<<<<<<:<1:<:7<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_108:2:62:879:264	163	chr1	216	99	35M	=	396	215	AATGAAAACTATATTTATGCTATTCAGTTCTAAAT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<2<<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_61:4:83:452:970	99	chr1	216	99	35M	=	379	198	AATGAAAACTATATTTATGCTATTCAGTTCTAAAT	==========================;========	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS218_1:2:64:1318:1711	99	chr1	218	99	35M	=	389	206	TGAAAACTATATTTATGCTATTCAGTTCTAAATAT	<<<<<<<<<<<<<<<<7<<<<<<<:<<<<<2<<<<	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_589:8:113:968:19	83	chr1	219	99	35M	=	50	-204	GAAAACTATATTTATGCTATTCAGTTCTAAATATA	8;<;8;9<<<<<<<9<:<<<<<<<<<;<<<<<<<<	MF:i:18	Aq:i:63	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_93:4:160:896:275	163	chr1	220	99	35M	=	387	202	AAAACTATATTTATGCTATTCAGTTCTAAATATAG	============<====<==<====<==<==;=:6	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_591:6:181:191:418	163	chr1	221	99	36M	=	387	202	AAACTATATTTATGCTATTCAGTTCTAAATATAGAA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<988	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_28:7:242:354:637	99	chr1	222	99	36M	=	417	231	AACTATATTTATGCTATTCAGTTCTAAATATAGAAA	<<<<<<<<<<<<<<<<<<<<<<<<<<;<<<<<6<;;	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_589:1:122:77:789	163	chr1	223	99	35M	=	396	208	ACTATATTTATGCTATTCAGTTCTAAATATAGAAA	<<<:<4<<9<:7<<<:<<<7<<<<<<<<<<9<9<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_591:5:42:540:501	147	chr1	224	99	36M	=	60	-200	CTATATTTATGCTATTCAGTTCTAAATATAGAAATT	;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_591:6:155:12:674	83	chr1	224	99	36M	=	52	-208	CTATATTTATGCTATTCAGTTCTAAATATAGAAATT	;<<<<<<<<<<;<<<<;<<<<8<<<<<<<<<<<<<<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_593:4:106:316:452	147	chr1	224	99	36M	=	49	-211	CTATATTTATGCTATTCAGTTCTAAATATAGAAATT	:<<<<<;<<<<:<<:<<<<<<7<<<<<<<<<<<<<<	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_19:5:89:525:113	163	chr1	227	78	40M	=	397	210	TATTTATGCTATTCAGTTATAAATATAGAAATTGAAACAG	<1<7<6;+0;7;7'<70;-<7<:<:<<5<<:9<5:7:%:7	MF:i:18	Aq:i:39	NM:i:1	UQ:i:12	H0:i:0	H1:i:1
+EAS54_65:3:321:311:983	147	chr1	228	99	35M	=	51	-212	ATTTATGCTATTCAGTTCTAAATATAGAAATTGAA	;;4;;<7<<<<<<77<<<<<<<<<<17<<<<<<<<	MF:i:18	Aq:i:62	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_65:8:76:493:708	147	chr1	229	44	35M	=	73	-191	TTTATGCTATTCAGTTCTAAATATAGAAATTGAAA	5/)63.&1517(544(055(0454&7706566679	MF:i:18	Aq:i:44	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_71:2:125:628:79	163	chr1	229	99	35M	=	400	205	TTTATGCTATTCAGTTCTAAATATAGAAATTGAAA	==================<6<====<<:<==7;::	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_32:5:78:583:499	83	chr1	229	74	35M	=	37	-227	TTTACGCTATTCAGTACTAAATATAGAAATTGAAA	&6&9774&<;67<44&-4<;<9<7<<<<<;<<<<<	MF:i:18	Aq:i:37	NM:i:2	UQ:i:27	H0:i:0	H1:i:1
+EAS54_67:3:175:730:949	83	chr1	230	99	35M	=	70	-195	TTATGCTATTCAGTTCTAAATATAGAAATTGAAAC	<<<<;+<<<<7<;<<;<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:65	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:1:84:275:1572	163	chr1	230	99	35M	=	394	199	TTATGCTATTCAGTTCTAAATATAGAAATTGAAAC	/6;;;4;;;;;;;;7;;4;.4;;;;;6;;;77077	MF:i:18	Aq:i:62	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_108:4:248:753:731	99	chr1	231	99	35M	=	402	206	TATGCTATTCAGTTCTAAATATAGAAATTGAAACA	<<<<<<<<<<<8<<<<<<<<<<<<:<<<<&<:<.:	MF:i:18	Aq:i:70	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:1:9:1289:215	99	chr1	231	99	35M	=	394	198	TATGCTATTCAGTTCTAAATATAGAAATTGAAACA	;;;;;;9;;;67;;;;;99;9;;;;;;;;977747	MF:i:18	Aq:i:59	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_595:7:188:802:71	163	chr1	232	99	35M	=	415	218	ATGCTATTCAGTTCTAAATATAGAAATTGAAACAG	<<<<<<<<<;<<<<<9<<<:<<<:<<<<<<:<<<;	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_93:7:252:171:323	83	chr1	234	99	35M	=	43	-226	GCTATTCAGTTCTAAATATAGAAATTGAAACAGCT	;8<;<=3=6==:====;;======;==========	MF:i:18	Aq:i:62	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS192_3:5:223:142:410	147	chr1	235	99	35M	=	60	-210	CTATTCAGTTCTAAATATAGAAATTGAAACAGCTG	8;<<<;<<<<;<<<<<<;<;<<<<<<<<<<<<;<<	MF:i:18	Aq:i:39	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_30:1:243:10:911	83	chr1	236	99	35M	=	63	-208	TATTCAGTTCTAAATATAGAAATTGAAACAGCTGT	;<;;;<4;9:<<<;<<;<<<<<;;<<<<<<<<<<<	MF:i:18	Aq:i:64	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:6:5:730:1436	163	chr1	236	99	35M	=	403	202	TATTCAGTTCTAAATATAGAAATTGAAACAGCTGT	;;;;;;;;;;;;;;;;;;8;;;;;8;;;;;67777	MF:i:18	Aq:i:67	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_19:2:57:1672:1890	121	chr1	236	75	40M	=	236	0	TATTCAGTTCTAAATATAGAAATTGAAACAGCTGTGTTTA	:;;;9<8;;*<<<<<<:<<<<<<<<1:<<<<<<<<<<<7<	MF:i:64	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_19:2:57:1672:1890	181	chr1	236	0	*	=	236	0	CCCCCCCCCCCCCCCCCAGCCACTGCGGCCCCCCCAGCCA	-+)%)'-'+,,<066,))090+:&486083:5&&:<<5<0	MF:i:192
+EAS1_105:2:299:360:220	99	chr1	237	99	35M	=	403	201	ATTCAGTTCTAAATATAGAAATTGAAACAGCTGTG	<<<<<<<9<9<<<<<<<<<<<<<<<<<5<;<0<<<	MF:i:18	Aq:i:43	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_1:2:24:1037:84	163	chr1	238	99	35M	=	415	212	TTCAGTTCTAAATATAGAAATTGAAACAGCTGTGT	<<<<<<<<<<<<<<<<<<<<<<;<<<<<<;:<57<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_105:3:86:823:683	163	chr1	240	99	35M	=	408	203	CAGTTCTAAATATAGAAATTGAAACAGCTGTGTTT	<<<<<<<<;<<<<<<<<<<<<<<<<<<<<;;9<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_53:4:130:568:978	99	chr1	246	88	35M	=	434	223	TAAATATAGAAATTGAAACAGCTGTGTTTAGTGAC	7<<;<<;<7<:;<7<<<<<<<<);4;+<7+3+%;<	MF:i:18	Aq:i:24	NM:i:1	UQ:i:26	H0:i:1	H1:i:0
+EAS114_45:4:73:1208:495	163	chr1	246	99	35M	=	431	220	TAAATATAGAAATTGAAACAGCTGTGTTTAGTGCC	;;;;;;;;;;;;;;;;;;;;;;;;5;;;;;37377	MF:i:18	Aq:i:67	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_97:7:264:642:506	99	chr1	247	99	35M	=	420	208	AAATATAGAAATTGAAACAGCTGTGTTTATTGTAT	<<;<<<<<<;<<<;:;;:;;<<;<<<<;*+;*&.4	MF:i:18	Aq:i:56	NM:i:3	UQ:i:28	H0:i:1	H1:i:0
+EAS114_28:5:104:350:749	163	chr1	247	99	36M	=	415	204	AAATATAGAAATTGAAACAGCTGTGTTTAGTGCCTT	<<8<<<<<<<<<<<;<<<<<<<<0;<<<9;<85;;;	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_61:6:227:259:597	147	chr1	248	99	35M	=	61	-222	AATATAGAAATTGAAACAGCTGTGTTTAGTGCCTT	<8<;2;9;<;;-92<;;;<;<<<<<<<<<<<<<<<	MF:i:18	Aq:i:61	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS112_32:7:113:809:364	99	chr1	250	99	35M	=	413	198	TATAGAAATTGAAACAGCTGTGTTTAGTGCCTTTG	<<<<<<<<<<<<<<<<<<<<<<<<<<7<;<;<<<4	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS188_7:2:218:877:489	83	chr1	250	86	35M	=	80	-205	TATAGAAATTGAAACAGCTGTGTTTAGTGCCTTTG	9<<<8<<<;<9<<<<<<<<<<;<<<<<<<<<<<<<	MF:i:18	Aq:i:10	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_97:7:20:979:96	83	chr1	254	99	35M	=	79	-210	GAAATTGAAACAGCTGTGTTTAGTGCCTTTGTTCA	'9996;(:;-<;1<<<<=<<<<=<<<<<<<<<<<<	MF:i:18	Aq:i:37	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS188_7:2:259:219:114	99	chr1	254	99	35M	=	411	192	GAAATTGAAACAGCTGTGTTTAGTGCCTTTGTTCA	<<<<<<<<<<<<<<<;<<<<<<7<7<<<<<0<<9<	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_39:6:13:1034:1144	99	chr1	256	99	35M	=	429	208	AATTGAAACAGCTGTGTTTAGTGCCTTTGTTCACA	<<<<<<<<<<<<<<<<<<<<<<<<3<<<;<<;<++	MF:i:18	Aq:i:69	NM:i:2	UQ:i:48	H0:i:1	H1:i:0
+EAS221_1:2:29:1486:672	147	chr1	256	99	35M	=	79	-212	AATTGAAACAGCTGTGTTTAGTGCCTTTGTTCACA	<<:<<<<;<<<<<<<<<<<<<<<<<<<<<<<<<++	MF:i:18	Aq:i:29	NM:i:2	UQ:i:54	H0:i:0	H1:i:0
+EAS139_11:7:46:695:738	163	chr1	259	74	35M	=	428	204	TGAAACAGCTGAGTTTAGCGCCTGTGTTCACATAG	<;<<<<;<<),&4<3<<7&7<0;)).3;79;7<;0	MF:i:130	Aq:i:74	NM:i:3	UQ:i:18	H0:i:0	H1:i:0
+EAS139_11:8:26:1221:222	163	chr1	261	99	35M	=	446	220	AAACAGCTGTGTTTAGTGCCTTTGTTCAACCCCCT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:78	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_64:3:190:727:308	147	chr1	263	99	35M	=	103	-195	ACAGCTGTGTTTAGTGCCTTTGTTCAACCCCCTTG	;;<;;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_26:3:284:261:124	83	chr1	263	99	35M	=	79	-219	ACAGCTGTGTTTAGTGCCTTTGTTCAACCCCCTTG	===27===.====&===========;;========	MF:i:18	Aq:i:39	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS112_34:7:141:80:875	147	chr1	265	99	35M	=	110	-190	AGCTGTGTTTAGTGCCTTTGTTCAACCCCCTTGCA	6/<;84<;<;<<<<<<5<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_19:3:24:1135:563	163	chr1	266	99	40M	=	446	220	GCTGTGTTTAGTGCCTTTGTTCAACCCCCTTGCAACAACC	<<<<:<<<<:1:<<<<<<.<<<<<<<<;<;;;43+:30::	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_1:2:90:986:1224	83	chr1	267	99	35M	=	67	-235	CTGTGTTTAGTGCCTTTGTTCAACCCCCTTGCAAC	<7*37;;;;;;;9<<;<7<<<<<<<<<<<;;<<<<	MF:i:18	Aq:i:41	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_28:7:287:492:169	99	chr1	269	99	36M	=	449	216	GTGTTTAGTGCCTTTGTTCAACCCCCTTGCAACAAC	<<<7<<<<<<<<<<<<<<<<<<<<<<<8;;<;6<<;	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS218_4:1:48:9:409	99	chr1	271	75	18M5I12M	=	464	228	GTTTAGTGCCTTTGTTCACATAGACCCCCTTGCAA	<<<<<<<<<<<<<:<<<<<<<<<<<<<<<<<<<<<	MF:i:130	Aq:i:75	NM:i:0	UQ:i:0	H0:i:0	H1:i:0
+EAS139_19:1:87:1222:878	163	chr1	272	10	40M	=	435	203	TATAGGGCCTTTGTTCAAACCCCTTGCAACAACCTTGAGA	&+6<6&<:<<9<1112<<;)9227</);;;2-79;)/769	MF:i:18	Aq:i:10	NM:i:3	UQ:i:41	H0:i:0	H1:i:0
+B7_591:7:200:192:373	163	chr1	275	75	14M5I17M	=	451	212	AGTGCCTTTGTTCACATAGACCCCCTTGCAACAACC	<<<<<<<<<<<<<<<<<<<<<<<<<:<:<;5<<;<<	MF:i:130	Aq:i:75	NM:i:0	UQ:i:0	H0:i:0	H1:i:0
+EAS56_65:1:163:846:223	163	chr1	278	74	11M5I19M	=	463	220	GCCTTTGTTCACATAGACCCCCTTGCAACAACCTT	<<<<;<<;4<<<;;9<<<<<+<<;<</27;;47;.	MF:i:130	Aq:i:74	NM:i:0	UQ:i:0	H0:i:0	H1:i:0
+EAS114_30:7:283:799:560	83	chr1	283	66	35M	=	121	-197	ACATAGACCCCCTTGCAACAACCTTGAGAACCCCA	<4<6<8;;6<<<+;<:<<;<<<<<<<<<<<<<<<<	MF:i:130	Aq:i:66	NM:i:0	UQ:i:0	H0:i:0	H1:i:0
+B7_595:4:84:802:737	147	chr1	284	68	35M	=	140	-179	CATAGACCCCCTTGCAACAACCTTGAGAACCCCAG	+<1<-;69;;;;8;:<<6<;<<<<<<<<<<<<<<<	MF:i:130	Aq:i:68	NM:i:0	UQ:i:0	H0:i:0	H1:i:0
+EAS51_66:5:308:400:602	163	chr1	285	71	35M	=	470	220	ATAGACCCCCTTGCAACAACCTTGAGAACCCCAGG	;<<<<<<<<<<<<<<<<<<<<<<<<;;;<<;<;76	MF:i:130	Aq:i:71	NM:i:0	UQ:i:0	H0:i:0	H1:i:0
+EAS54_81:2:285:367:932	163	chr1	285	74	35M	=	440	190	ATAGACCCCCTTGCAACAACCTTGAGAACCCCAGG	===========;======;=====;=======5==	MF:i:130	Aq:i:74	NM:i:0	UQ:i:0	H0:i:0	H1:i:0
+EAS114_39:1:70:147:84	83	chr1	285	73	35M	=	128	-192	ATAGACCCCCTTGCAACAACCTTGAGAACCCCAGG	<<<:<;<<<<<<;<<<<<<<<<<<<<<<<<<<<<;	MF:i:130	Aq:i:73	NM:i:0	UQ:i:0	H0:i:0	H1:i:0
+EAS51_62:3:314:386:190	99	chr1	287	98	35M	=	459	207	AGACCCCCTTGCAACAACCTTGAGAACCCCAGGGA	++<<<<<<<<<<<<<<<<<<<<<<<<<<<<8<<<<	MF:i:18	Aq:i:29	NM:i:2	UQ:i:54	H0:i:0	H1:i:0
+EAS56_65:1:53:272:944	99	chr1	287	99	35M	=	447	195	CAACCCCCTTGCAACAACCTTGCGAACCCCAGGGA	<<<<<<<<<<<<.7<.<<<<<<-<-<<<<<&<222	MF:i:18	Aq:i:41	NM:i:1	UQ:i:12	H0:i:0	H1:i:1
+EAS188_7:5:112:51:128	163	chr1	287	99	35M	=	477	225	AGACCCCCTTGCAACAACCTTGAGAACCCCAGGGA	++<<<<<<<<<<<<<5<<<<<<<<<<<<<<;<;<6	MF:i:18	Aq:i:29	NM:i:2	UQ:i:54	H0:i:0	H1:i:0
+EAS56_57:6:44:280:641	163	chr1	288	99	35M	=	454	201	AACCCCCTTGCAACAACCTTGAGAACCCCAGGGAA	;<<<<<<<<<<66<;<<<<<;<<2;;;<<;;;;,;	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_11:6:75:946:1035	99	chr1	288	99	35M	=	480	227	AACCCCCTTGCAACAACCTTGAGAACCCCAGGGAA	<<<<<<<<<<;<<<;<<<<<<<8;<6<<<<44<:4	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS188_7:2:187:227:818	83	chr1	290	99	35M	=	129	-196	CCCCCTTGCAACAACCTTGAGAACCCCAGGGAATT	<<9<<;<<;<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS219_FC30151:3:40:1128:1940	83	chr1	291	99	35M	=	112	-214	CCCCTTACAACAACCTTGAGAACCCCAGGGAATTT	<<<:///77:<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:70	NM:i:1	UQ:i:14	H0:i:1	H1:i:0
+EAS54_71:4:72:63:435	99	chr1	293	99	34M	=	490	232	CCTTGCAACAACCTTGAGAACCCCAGGGAATTTG	<<<<<<<<<<<<<<<<<<<<;<<<;<;;39:7:7	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_93:6:271:244:568	99	chr1	294	99	35M	=	481	222	CTTGCAACAACCTTGAGAACCCCAGGGAATTTGTC	<<<<<<<<<<<<<<<<<<<<<<<<<<<<.<<<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_59:7:82:902:868	99	chr1	295	99	35M	=	471	211	TTGCAACAACCTTGAGAACCCCAGGGAATTTGTCA	<<<<<<;<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_103:7:313:83:546	163	chr1	296	99	35M	=	454	193	TGCAACAACCTTGAGAACCCCAGGGAATTTGTCAA	<<<<<<<<<<;<<<<<<<<<<<<<<4<<<:<;<<9	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_64:4:57:786:414	163	chr1	296	99	35M	=	453	192	TGCAACAACCTTGAGAACCCCAGGGAATTTGTCAA	<<<<<<<<<<<<<<<<<<<<<<<:<<:<<:;;7<7	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_59:7:260:985:520	163	chr1	296	99	35M	=	468	207	TGCAACAACCTTGAGAACCCCAGGGAATTTGTCAA	<<<<<<<<<<<<<<<<<;:;<<;<:<<<,:1;)<;	MF:i:18	Aq:i:68	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS192_3:6:170:169:57	83	chr1	296	99	35M	=	138	-193	TGCAACAACCTTGAGAACCCCAGGGAATTTGTCAA	778<:<<<9<<<<<;<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:45	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_59:6:199:327:965	163	chr1	297	91	35M	=	494	232	NCAACAACCTTGAGAACCCCAGGGAATTTGTCAAT	!,+*+++++++++++*+++++++**)+*+**+(**	MF:i:18	Aq:i:19	NM:i:1	UQ:i:0	H0:i:0	H1:i:1
+B7_610:5:147:68:353	163	chr1	299	99	35M	=	486	222	AACAACCTTGAGAACCCCAGGGAATTTGTCAATGT	<;<;<<7<<<<<<<7<<;;<7<4<8<<<8.;4;;;	MF:i:18	Aq:i:70	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS192_3:1:225:195:543	147	chr1	299	99	35M	=	123	-211	AACAACCTTGAGAACCCCAGGGAATTTGTCAATGT	;;8;;+;(<<<<<<<<7;<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_61:1:303:184:14	163	chr1	301	99	35M	=	479	213	CAACCTTGAGAACCCCAGGGAATTTGTCAATGTCA	<<<<<<8<0<<<<-<-98<<--<<<6;076;75+&	MF:i:18	Aq:i:61	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_30:6:326:309:149	163	chr1	301	99	35M	=	467	201	CAACCTTGAGAACCCCAGGGAATTTGTCAATGTCA	<<<<<<<<<<<<<<<<<<<<:<<<<<<<<<;;;;:	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_30:4:327:795:103	147	chr1	302	99	35M	=	133	-204	AACCTTGAGAACCCCAGGGAATTTGTCAATGTCAG	;::;;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_105:7:110:355:323	99	chr1	303	99	35M	=	477	209	ACCTTGAGAACCCCAGGGAATTTGTCAATGTCAGG	<<<<<<<<<<<<<<<<<<<<<<<<;<<<<;;<<8;	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS219_FC30151:1:18:1418:237	99	chr1	304	99	35M	=	503	234	CCTTGAGAACCCCAGGGAATTTGTCAATGTCAGGG	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<9<7<	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_589:7:112:203:90	163	chr1	305	99	35M	=	470	200	CTTGAGAACCCCAGGGAATTTGTCAATGTCAGGGA	<<:<<<<<<<<.<<<<<<<<<<<<6<:867<8884	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_59:7:319:246:304	99	chr1	305	99	35M	=	472	202	CTTGAGAACCCCAGGGAATTTGTCAATGTCAGGGA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;;;:	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_589:6:114:714:317	147	chr1	311	99	35M	=	126	-220	AACCCCAGGGAATTTGTCAATGTCAGGGAAGGAGC	;8<;:<<;<;<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_30:5:327:991:508	99	chr1	312	99	35M	=	495	218	ACCCCAGGGAATTTGTCAATGTCAGGGAAGGAGCA	<<<<<<<<<<<<<<<<<<<<<;<;:<7:47;:75;	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_97:4:77:29:126	147	chr1	315	99	35M	=	131	-219	ACAGGGAATTTGTCAATGTCAGGGAAGGAGCATTT	()9;;<<<<<<<<<<5<<<7<<<<<<;<<<;7<<<	MF:i:18	Aq:i:69	NM:i:1	UQ:i:7	H0:i:1	H1:i:0
+EAS219_1:1:37:1004:1136	99	chr1	315	99	35M	=	473	193	CCAGGGAATTTGTCAATGTCAGGGAAGGAGCATTT	<<<<<<<<<<<<<<;<<<;<<<<<:<<;;369<<<	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS188_4:7:78:583:670	83	chr1	316	99	35M	=	142	-209	CAGGGAATTTGTCAATGTCAGGGAAGGAGCATTTT	8<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:66	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_64:3:90:435:691	147	chr1	318	99	35M	=	147	-206	GGGAATTTGTCAATGTCAGGGAAGGAGCATTTTGT	;;<;;;+<<:<<<:<;;<<<<<<<<<<<<<<<<<;	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_1:6:69:735:1915	147	chr1	321	99	35M	=	154	-202	AATTTGTCAATGTCAGGGAAGGAGCATTTTGTCAG	<<::<<<7<<<<7<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_57:5:324:728:956	147	chr1	322	99	35M	=	165	-192	ATTTGTCAATGTCAGGGAAGGAGCATTTTGTCAGT	<;;;;5;<<0<<<<<<<<<<<<<<<;<<<<<<<<<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_66:5:269:280:716	99	chr1	323	99	35M	=	490	202	TTTGTCAATGTCAGGGAAGGAGCATTTTTTCAGTT	<<<<<<<<<2<<:2:1<<7/2/:3<<<<*<3($<<	MF:i:18	Aq:i:58	NM:i:1	UQ:i:9	H0:i:1	H1:i:0
+EAS54_73:3:88:24:744	163	chr1	325	84	35M	=	484	194	TGTCAATGTCAGGGAAGGAGCATTTTTGAAGTTTA	<7*:<<::.'<<<<:<<:<<'<63'6+'303*%%+	MF:i:18	Aq:i:21	NM:i:5	UQ:i:53	H0:i:0	H1:i:0
+EAS1_108:7:82:926:112	147	chr1	328	99	35M	=	164	-199	CAATGTCAGGGAAGGAGCATTTTGTCAGTTGCCAA	<1:/<*6<<6<<<<<6<<<<<<4<<<<82<+<<<<	MF:i:18	Aq:i:41	NM:i:1	UQ:i:10	H0:i:0	H1:i:1
+EAS56_63:7:185:213:330	163	chr1	328	99	35M	=	502	209	CAATGTCAGGGAAGGAGCATTTTGTCAGTTACCAA	<<<<<<<<<;<<;<<<<<;<<<<;;;<<;<<;<38	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_591:3:277:458:330	163	chr1	329	99	36M	=	490	197	AATGTCAGGGAAGGAGCCTTTTGTCAGTTACCAAAT	<<7<<<<<<<<<2<<<%,<6<&<<,<<<<:<<<<(7	MF:i:18	Aq:i:41	NM:i:1	UQ:i:11	H0:i:0	H1:i:1
+B7_595:1:81:1000:375	163	chr1	329	90	35M	=	524	230	NATGTCAGGGAAGGAGCATTTTGTCAGTTACCAAA	!.............................+.(+.	MF:i:18	Aq:i:19	NM:i:1	UQ:i:0	H0:i:0	H1:i:1
+EAS220_1:8:33:672:473	99	chr1	330	99	35M	=	515	220	ATGTCAGGGAAGGAGCATTTTGTCAGTTACCAAAT	<<<<<<<<7<7<7<<62<<<<66<15*/99*5241	MF:i:18	Aq:i:65	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_65:6:164:797:930	147	chr1	332	99	35M	=	173	-194	GTCAGGGAAGGAGCATTTTGTCAGTTACCAAATGT	;;:;8<;<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:45	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_28:6:155:68:326	147	chr1	332	99	36M	=	182	-186	GTCAGGGAAGGAGCATTTTGTCAGTTACCAAATGTG	;<<<:6<<<<<<6<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_64:5:202:39:380	99	chr1	334	99	35M	=	513	214	CAGGGAAGGAGCATTTTGTCAGTTACCAAATGTGT	<<<<<<<<<<<<<<<<<;<<:;<<18<84:<&<+<	MF:i:18	Aq:i:65	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_11:7:42:1091:1726	99	chr1	334	99	35M	=	502	203	CAGGGAAGGAGCATTTTGTCAGTTACCAAATGTGT	<<<<<<<<<<<<<<<<<<<<<<8<<<<<<8:<.<:	MF:i:18	Aq:i:68	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:5:66:959:1311	83	chr1	336	95	35M	=	159	-212	GGGAAGGAGCATTTTGTCAGTTACCAAATGTGTTT	67.68:4::6;;;7:6:;:5;8;;<<:;;<;;;;<	MF:i:18	Aq:i:31	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_593:1:200:559:765	99	chr1	337	99	36M	=	521	220	GGAAGGAGCATTTTGTCAGTTACCAAATGTGTTTAT	<<<<<<<<<<<<<<7<<<<<<;<<;;4<7<9;<<-;	MF:i:18	Aq:i:45	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_71:4:328:669:662	99	chr1	337	99	34M	=	512	210	GGAAGGAGCATTTTGTCAGTTACCAAATGTGTTT	<<<<<<<<<<<<<<<<<<<<<<<<+9;<;;.<<<	MF:i:18	Aq:i:43	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_57:7:159:125:297	83	chr1	337	99	35M	=	170	-202	GGAAGGAGCATTTTGTCAGTTACCAAATGTGTTTA	89<;;8<<;<;<4<;<8<<<<;;8<<<<<<<<<<<	MF:i:18	Aq:i:43	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS188_7:7:19:886:279	147	chr1	337	99	35M	=	182	-190	GAAAGGAGCATTTTGTCAGTTACCAAATGTGTTTA	9%<2)2.2::<;<<<2<<<<<<<<<<<<<<<<<;<	MF:i:18	Aq:i:67	NM:i:1	UQ:i:4	H0:i:1	H1:i:0
+B7_595:1:209:653:400	83	chr1	340	99	35M	=	175	-200	AGGAGCATTTTGTCAGTTACCAAATGTGTTTATTA	<69<98<+<<6<<4<<<<</4<<:<4<<<<<<<<<	MF:i:18	Aq:i:59	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_103:4:294:525:849	83	chr1	340	99	35M	=	167	-208	AGGAGCATTTTGTCAGTTACCAAATGTGTTTATTA	;<;:;:<;<;<<<3<<<;<;<<<<<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_1:4:87:1375:1303	163	chr1	340	99	35M	=	529	224	AGGAGCATTTTGTCAGTTACCAAATGTGTTTATTA	<<<<<<<<<<<<9<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:45	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_57:6:325:759:288	147	chr1	341	99	35M	=	163	-213	GGAGCATTTTGTCAGTTACCAAATGTGTTTATTAC	9;<9<;<;;<;<;<;<<<:<;<<<;<<<<<;<<<<	MF:i:18	Aq:i:67	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_57:7:76:786:458	163	chr1	341	99	35M	=	502	196	GGAGCATTTTGTCAGTTACCAAATGTGTTTATTAC	<<.<<<<2<<:84<:<<<:<8<<)<)429<2<<8<	MF:i:18	Aq:i:68	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_61:1:210:880:606	163	chr1	341	99	35M	=	518	212	GGAGCATTTTGTCAGTTACCAAATGTGTTTATTAT	<<<<<<<<<<<<<<<<<<;<<<<<<:<<<<3<<8&	MF:i:18	Aq:i:72	NM:i:1	UQ:i:5	H0:i:1	H1:i:0
+EAS192_3:3:257:611:440	99	chr1	341	99	35M	=	524	218	GGAGCATTTTGTCAGTTACCAAATGTGTTTATTAC	<<<<<<<<<<<<<<<<<<<<8<<<<;<<<<8<<+5	MF:i:18	Aq:i:45	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_78:7:303:402:142	83	chr1	343	99	35M	=	181	-197	AGCATTTTGTCAGTTACCAAATGTGTTTATTACCA	;;;;;<9<<8;<<<<7<<;<<<<;<<<<<<<<<<<	MF:i:18	Aq:i:68	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS188_7:3:13:122:187	83	chr1	343	99	35M	=	153	-225	AGCATTTTGTCAGTTACCAAATGTGTTTATTACCA	<<&<;;<<<;7<<<<;<;<<<<<<<<<<<<;<<<<	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_64:3:80:885:513	163	chr1	344	99	35M	=	507	198	GCATTTTGTCAGTTACCAAATGTGTTTATTACCAG	<<<<<<<<<<<<<<<<<<<:<<<<2:<;<<75<7;	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS218_4:7:90:1873:89	99	chr1	344	99	35M	=	531	222	GCATTTTGTCAGTTACCAAATGTGTTTATTACCAG	<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<7<<<7	MF:i:18	Aq:i:47	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_610:1:37:652:403	83	chr1	347	99	35M	=	193	-189	TTTTGTCAGTTACCAAATGTGTTTATTACCAGAGG	<;<<<<:<<;<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_53:8:28:701:724	163	chr1	347	99	35M	=	521	209	TTTTGTCAGTTACCAAATGTGTTTATTACCAGAGG	<<<<<<7<<<<<<7::<:<<-<<::::::<747::	MF:i:18	Aq:i:66	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_66:8:66:655:769	99	chr1	348	99	35M	=	515	202	TTTGTCAGTTACCAAATGTGTTTATTACCAGAGGG	8;<<<<<8<<<<<;<<<7<;<<<<<;<7<27<;;7	MF:i:18	Aq:i:66	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_73:5:231:339:551	163	chr1	350	99	35M	=	527	212	TGTCAGTTACCAAATGTGTTTATTACCAGAGGGAT	<<<<<<;<<<<<<;<<<<<<<<<<;5<<46;<;:1	MF:i:18	Aq:i:47	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_26:6:129:694:359	163	chr1	350	88	35M	=	525	210	TGTCAGTTACCAAATGTGTTTATTACCCGAGGGAT	============+7=======:==;;;'=;==7;=	MF:i:18	Aq:i:43	NM:i:1	UQ:i:6	H0:i:0	H1:i:1
+EAS220_1:2:62:1109:804	83	chr1	350	99	35M	=	176	-209	TGTCAGTTACCAAATGTGTTTATTACCAGAGGGAT	<<<<<:<<<::<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_589:8:157:935:374	99	chr1	353	99	35M	=	512	194	CAGTTACCAAATGTGTTTATTACCAGAGGGATGGA	<<<<<<<<<<;<<;;<<<<<<<<<::8'5++;+11	MF:i:18	Aq:i:66	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_591:4:103:111:720	99	chr1	353	99	36M	=	512	195	CAGTTACCAAATGTGTTTATTACCAGAGGGATGGAG	<<<<<<<<<<<<<<<<<<<<<<<<<5<<<5;<5<:;	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_103:7:311:100:539	163	chr1	353	99	35M	=	508	190	CAGTTACCAAATGTGTTTATTACCAGAGGGATGGA	<<<<;<<<<;<<<<<;<<<<<<<<<:<::;7;<0;	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_64:6:195:348:703	83	chr1	353	99	35M	=	215	-173	CAGTTACCAAATGTGTTTATTACCAGAGGGATGGA	<9<<9</<<<<<<<<<<<<<<2<8<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_19:6:72:308:839	163	chr1	354	99	40M	=	517	203	AGTTACCAAATGTGTTTATTACCAGAGGGATGGAGGGAAG	<<<<<<<<<<<<<<<<<<<<<<<<9<<<<;<99494416:	MF:i:18	Aq:i:47	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_593:2:133:460:542	147	chr1	356	99	36M	=	195	-197	TTACCAAATGTGTTTATTACCAGAGGGATGGAGGGA	;:;7;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:47	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_81:7:293:355:321	83	chr1	356	99	35M	=	174	-217	TTACCAAATGTGTTTATTACCAGAGGGATGGAGGG	<<4<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_591:2:323:639:311	83	chr1	357	99	36M	=	200	-193	TACCAAATGTGTTTATTACCAGAGGGATGGAGGGAA	-94<<<<<<<4<<<<<<<<2<<<<<7<<<-<<<<<<	MF:i:18	Aq:i:70	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_71:8:321:642:388	83	chr1	357	99	33M	=	181	-209	TACCAAATGTGTTTATTACCAGAGGGATGGAGG	19<<<<<8<<<<<<<<;<<<<<<<<<<7<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_61:4:262:456:74	99	chr1	357	99	35M	=	504	182	TACCAAATGTGTTTATTACCAGAGGGATGGAGGGA	<<<<<<<<<<<<<<<<<<<<:;;:;7:<::7<7:3	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_610:8:95:426:791	99	chr1	359	99	35M	=	547	223	CCAAATGTGTTTATTACCAGAGGGATGGAGGGAAG	<<<<;<<<<<<<<<<<<<<<<<<<<<<<<<<<,<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_65:6:115:538:276	83	chr1	360	99	35M	=	209	-186	CAAATGTGTTTATTACCAGAGGGATGGAGGGAAGA	:<<<<<<<<;;<5<<;<<<<<<<<;<<<<<<<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_95:1:196:533:921	99	chr1	361	99	35M	=	526	200	AAATGTGTTTATTACCAGAGGGATGGAGGGAAGAG	=====1========8===:===7======971=3=	MF:i:18	Aq:i:47	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_65:5:121:380:656	99	chr1	362	99	35M	=	542	215	AATGTGTTTATTACCAGAGGGATGGAGGGAAGAGG	<<<<<<<<<<<<<<<<<<<<<<<<:<:<<83<:<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_11:3:34:970:1374	99	chr1	363	99	35M	=	520	192	ATGTGTTTATTACCAGAGGGATGGAGGGAAGAGGG	<<<<<<<<<<<<<<;7<77;<<;<;;9;;:86:::	MF:i:18	Aq:i:47	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_3:4:29:1061:574	163	chr1	363	99	35M	=	563	235	ATGTGTTTATTACCAGAGGGATGGAGGGAAGAGGG	<<<<<<<<<<<<<<<<<<;<<<<<<;<<8<:<<<<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_53:1:124:243:35	99	chr1	364	60	35M	=	544	215	TGTGTTTATTACCAGAGGGATGGAGGGAAGAGCGA	<<<<<;;<<<<<<:<<<.<<<:++5+:1(;1;$<(	MF:i:18	Aq:i:60	NM:i:1	UQ:i:3	H0:i:1	H1:i:0
+EAS114_30:2:272:750:698	163	chr1	365	80	35M	=	538	208	GTGTTTATTACCAGAGGGATGGAGGGATGACGGAC	<)<<<<<7;<<<4<;7<<<<78068:(%<3*861,	MF:i:18	Aq:i:37	NM:i:2	UQ:i:13	H0:i:0	H1:i:1
+EAS56_53:3:126:558:408	83	chr1	368	99	35M	=	206	-197	TTTATTACCAGAGGGATGGAGGGAAGAGGGACGCT	<:<<:;;<<<<<<<<8<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:2:1:1140:1206	83	chr1	368	99	35M	=	181	-222	TTTATTACCAGAGGGATGGAGGGAAGAGGGACGCT	77977::99;;;:;;<;;;:;;;<<;<;;;;<;;;	MF:i:18	Aq:i:66	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_103:5:141:711:813	147	chr1	370	99	35M	=	209	-196	TATTACCAGAGGGATGGAGGGAAGAGGGACGCTGA	=<5<5<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_66:1:282:274:50	83	chr1	371	99	35M	=	193	-213	ATTACCAGAGGGATGGAGGGAAGAGGGACGCTGAA	</7;/:<<<<<<<:<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:70	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS220_1:8:46:485:482	99	chr1	371	94	35M	=	530	194	ATTACCAGAGGGATGAAGGGAAGAGGGACGCTGAA	<<<<<<<<<<<<<<<<<<<<<<<6<<<<<:<:89<	MF:i:18	Aq:i:47	NM:i:1	UQ:i:27	H0:i:0	H1:i:1
+EAS56_63:1:119:446:185	163	chr1	372	99	35M	=	562	225	TTACCAGAGGGATGGAGGGAAGAGGGACGCTGAAG	<<<<<<<7<<<4<<<<9<<54<:<7<5:<::7-5;	MF:i:18	Aq:i:66	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_591:3:168:69:605	163	chr1	373	67	36M	=	565	228	TACCCGAGGGATGGAGGGTAGAGGGACGCTGAAGTG	<<<4(<<<<<<<<<<<<<(1<6<-<2<<7<<6<<++	MF:i:18	Aq:i:26	NM:i:4	UQ:i:59	H0:i:0	H1:i:0
+EAS114_32:6:78:909:394	163	chr1	373	81	35M	=	554	216	TACCAGAGGGATGGAGGGAAGAGGGACGCTGAAGA	<<<<<<8<<<&<<<-<<<14,4;<<-0<2+<)/82	MF:i:18	Aq:i:21	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS218_4:5:41:118:1246	99	chr1	374	99	35M	=	548	209	ACCAGAGGGATGGAGGGAAGAGGGACGCTGAAGAA	<<<<<<<<<<<<<<<<<<<<<<<</<<<<<<1<<(	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_73:5:44:498:945	147	chr1	377	82	35M	=	195	-217	ATAGGGATGGAGGGAAGAGGGCCGCTGAAGAACTT	<%*50<7<4<<<7<,<<.<8/,9<:</<<<;<;<<	MF:i:18	Aq:i:37	NM:i:2	UQ:i:15	H0:i:0	H1:i:1
+EAS114_39:5:50:972:1286	163	chr1	377	99	35M	=	559	217	AGAGGGATGGAGGGAAGAGGGACGCTGAAGAACTT	<<<<<<<<<<<<<<<<<;<<<<<<<<<6<<7:7:;	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_11:6:82:164:1924	163	chr1	378	99	35M	=	542	199	GAGGGATGGAGGGAAGAGGGACGCTGAAGAACTTT	<<<<<<<<<<<<<<<<<<<<8<<<<<<3<<'<7<8	MF:i:18	Aq:i:43	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_93:7:14:426:613	147	chr1	379	99	35M	=	214	-200	AGGGAGGGAGGGAAGAGGGACGCTGAAGAACTTTG	:<<<<&<<<<<<<<<<<<<<6<<<<<<<<<<<<<<	MF:i:18	Aq:i:71	NM:i:1	UQ:i:5	H0:i:1	H1:i:0
+EAS54_61:4:83:452:970	147	chr1	379	99	35M	=	216	-198	AGGGATGGAGGGAAGAGGGACGCTGAAGAACTTTG	<<<39<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_57:6:157:643:175	83	chr1	380	99	35M	=	206	-209	GGGATGGAGGGAAGAGGGACGCTGAAGAACTTTGA	;<<<;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS218_1:8:61:1797:113	99	chr1	380	99	35M	=	551	206	GGGATGGAGGGAAGAGGGACGCTGAAGAACTTTGA	<<<<<<;<<<<;:<3<<<<;;<<<8<<;:<<;3<.	MF:i:18	Aq:i:70	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_591:5:90:828:633	163	chr1	381	99	36M	=	537	192	GGATGGAGGGAAGAGGGACGCTGAAGAACTTTGATG	<<<<<<<<<<<8<;96<;<<<<<99<2<<;<96<8;	MF:i:18	Aq:i:47	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_103:4:61:433:385	163	chr1	381	99	35M	=	579	233	GGATGGAGGGAAGAGGGACGCTGAAGCACTTTGAT	<<<<<<<<<<<<<<<<<;<<;<<6<<)91<<;;,;	MF:i:18	Aq:i:43	NM:i:1	UQ:i:8	H0:i:0	H1:i:1
+EAS1_93:2:173:995:93	83	chr1	382	99	35M	=	215	-202	GCTGGAGGGAAGAGGGACGCTGAAGAACTTTGATG	<(0<<9<<<7<<<<<<7<<<<<<<<<7<<<<<<<<	MF:i:18	Aq:i:73	NM:i:1	UQ:i:7	H0:i:1	H1:i:0
+EAS54_71:3:254:32:275	99	chr1	382	99	34M	=	575	228	GATGGAGGGAAGAGGGACGCTGAAGAACTTTGAT	<<<<<<<<<<<<<<<<<<<<<<;;<:<::<:2*<	MF:i:18	Aq:i:65	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_95:7:282:817:710	147	chr1	384	99	35M	=	211	-208	TGGAGGGAAGAGGGACGCTGAAGAACTTTGATGCC	366=6;======8====:========;========	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:3:75:217:337	163	chr1	386	99	35M	=	568	217	GAGGGAAGAGGGACGCTGAAGAACTTTGATGCCCT	;;;;;;;;;;;;;;;;;;8;;;;;;;;;;;88787	MF:i:18	Aq:i:67	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_591:6:181:191:418	83	chr1	387	99	36M	=	221	-202	AGGGAAGAGGGACGCTGAAGAACTTTGATGCCCTCT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_93:4:160:896:275	83	chr1	387	99	35M	=	220	-202	AGGGAAGAGGGACGCTGAAGAACTTTGATGCCCTC	;;;9;<<<<<<;<;;<<<<<<<<<<<<<<;<<<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_19:3:88:1656:896	99	chr1	387	99	40M	=	538	191	AGGGAAGAGGGATGCTGAAGAACTTTGATGCCCTCTTCTT	<<<9<<<<<<<9<<<;<<<<<<<<<;6<<;7<<<<::9:;	MF:i:18	Aq:i:47	NM:i:1	UQ:i:27	H0:i:0	H1:i:1
+B7_597:8:186:850:838	147	chr1	389	99	35M	=	205	-219	GGAAGAGGGACGCTGAAGAACTTTGATGCCCTCTT	<;<;<;<<<<;<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS218_1:2:64:1318:1711	147	chr1	389	99	35M	=	218	-206	GGAAGAGGGACGCTGAAGAACTTTGATGCCCTCTT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_1:8:78:1478:1446	99	chr1	389	99	35M	=	560	206	GGAAGAGGGACGCTGAAGAACTTTGATGCCCTCTT	<<<<<<<<<<<<<<<<<<<<;<<<<<<<<<:<<<;	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_108:2:82:879:246	163	chr1	391	99	35M	=	576	220	AAGAGGGACGCTGAAGAATTTTGATGCCCTCTTCT	<<<<<<<<<<<<<<<<<<&<<<77<<-<<<6<62<	MF:i:18	Aq:i:43	NM:i:1	UQ:i:5	H0:i:0	H1:i:1
+B7_610:1:139:152:856	147	chr1	392	99	35M	=	198	-229	AGAGGGACGCTGAAGAACTTTGATGCCCTCTTCTT	<<<<<;<<<<<<<<<<;<;<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_95:2:162:503:769	99	chr1	392	99	35M	=	571	214	AGAGGGACGCTGAAGAACTTTGATGCCCTCTTCTT	========================:==========	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_108:3:216:988:883	163	chr1	392	99	35M	=	584	227	AGAGGGACGCTGAAGAACTTTGATGCCCTCTTCTT	<<<<<<<<<<<<8;<;88<;8;;;;828;8;8;;;	MF:i:18	Aq:i:68	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS112_34:7:118:523:591	163	chr1	393	99	35M	=	563	205	GAGGGACGCTGAAGAACTTTGATGCCCTCTTCTTC	<<<<<<<<<<<<<<<<<<<<<<<:<<<<<<<;;<;	MF:i:18	Aq:i:66	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_65:3:168:741:680	163	chr1	394	99	35M	=	562	203	AGGGACGCTGAAGAACTTTGATGCCCTCTTCTTCC	<<<<<<<<<<<<<<<<<<<<<<<<<1<<<<<<<<<	MF:i:18	Aq:i:79	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:1:9:1289:215	147	chr1	394	99	35M	=	231	-198	AGGGACGCTGAAGAACTTTGATGCCCTCTTCTTCC	7747*7;;;;+;;:2;7;:1;;9:;:;:;;:;::;	MF:i:18	Aq:i:59	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:1:84:275:1572	83	chr1	394	99	35M	=	230	-199	AGGGACGCTGAAGAACTTTGATGCCCTCTTCTTCC	777777::7:;74;:;:7;:::;;;;:;;8;;;<;	MF:i:18	Aq:i:62	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_589:1:122:77:789	83	chr1	396	99	35M	=	223	-208	GGACGCTGAAGAACTTTGATGCCCTCTTCTTCCAA	9<;<:<<<<<<:<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_108:2:62:879:264	83	chr1	396	99	35M	=	216	-215	GGACGCTGAAGAACTTTGATGCCCTCTTCTTCCAA	====:=<============================	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_19:5:89:525:113	83	chr1	397	78	40M	=	227	-210	GACGCTGAAGAACTTTGATTCCCTCTTCTTCCAAAGATGA	);:+4-&<<+<<:<+<)<<<7<8<8:<:<<:<82::<<2<	MF:i:18	Aq:i:39	NM:i:1	UQ:i:27	H0:i:0	H1:i:1
+EAS114_39:2:18:967:582	83	chr1	398	99	35M	=	200	-233	ACGCTGAAGAACTTTGATGCCCTCTTCTTCCAAAG	<:<<<<<<<<<<<<<<;<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_61:3:140:522:212	163	chr1	399	99	35M	=	568	204	CGCTGAAGAACTTTGATGCCCTCTTCTTCCAAAGA	<<<<<<<<<<<<<<<<<;<<<<<<<<<<<;<;95;	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_71:2:125:628:79	83	chr1	400	99	34M	=	229	-205	GCTGAAGAACTTTGATGCCCTCTTCTTCCAAAGA	95&<<<<<<<63<<<6<<<<8<;<<8<<<<<<<<	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_95:6:185:312:167	163	chr1	401	99	35M	=	562	196	CTGAAGAACTTTGATGCCCTCTTCTTCCAAAGATG	===========================;855;===	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_108:4:248:753:731	147	chr1	402	99	35M	=	231	-206	TGAAGAACTTTGATGCCCTCTTCTTCCAAAGATGA	7;55;=,=89=====3===9=======9=======	MF:i:18	Aq:i:70	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_105:2:299:360:220	147	chr1	403	99	35M	=	237	-201	GAAGAACTTAGATGCCCTCTTCTTCCAAAGATGAA	66<;;4;<<()<<4<<<<<<;<<;<<<<<<<<<<<	MF:i:18	Aq:i:43	NM:i:1	UQ:i:7	H0:i:0	H1:i:1
+EAS114_45:6:5:730:1436	83	chr1	403	99	35M	=	236	-202	GAAGAACTTTGATGCCCTCTTCTTCCAAAGATGAA	7977979;;;;;;;;;7;3<;2<;26;<;<<;;<<	MF:i:18	Aq:i:67	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_591:2:134:868:252	99	chr1	404	99	36M	=	595	227	AAGAACTTTGATGCCCTCTTCTTCCAAAGATGAAAC	<<<<<<<<<<<<<<<<<<<<<<<<<<<;:<<<:<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_597:2:165:431:857	99	chr1	406	99	35M	=	559	188	GAACTTTGATGCCCTCTTCTTCCAAAGATGAAACG	<<<<<<<<<<<<<<<<<<<<<<<6&:<7<:76,;;	MF:i:18	Aq:i:53	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_105:3:86:823:683	83	chr1	408	99	35M	=	240	-203	ACTTTGATGCCCTCTTCTTCCAAAGATGAAACGCG	<4<<<<<<<<:<<6<<7<<<8<<<<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_30:1:176:168:513	83	chr1	410	99	35M	=	210	-235	TTTGATGCCCTCTTCTTCCAAAGATGAAACGCGTA	;0;;;7:<<<<<<<;<<:<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS188_7:2:259:219:114	147	chr1	411	99	35M	=	254	-192	TTGATGCCCTCTTCTTCCAAAGATGAAACGCGTAA	666<:6/:6::6::<:::<<<;<<<<<<<<;<<<<	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_1:8:84:1013:1074	121	chr1	411	71	35M	=	411	0	TTGATGCCCTCTTCTTCCAAAGATGAAACGCGTAA	8;;<;8744<7<<4<<47<<<<<<7<<<<<<<<<<	MF:i:64	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_1:8:84:1013:1074	181	chr1	411	0	*	=	411	0	GCAAGGGGGTCTATGTGAACAAAGGCACTAAACAC	<7<<<<<<<<9<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:192
+EAS54_81:7:325:150:465	99	chr1	412	99	35M	=	598	221	TGATGCCCTCTTCTTCCAAAGATGAAACGCGTAAC	<<<<<<<<<<<<<<<<<<<<<<<<<<<:<<<3;;:	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS112_34:8:179:13:782	163	chr1	412	99	35M	=	568	191	TGATGCCCTCTTCTTCCAAAGATGAAACGCGTAAC	<<<<<<<<<<<<<<<<<:<<:7<<<<::<7<:-:1	MF:i:18	Aq:i:39	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS112_32:7:113:809:364	147	chr1	413	99	35M	=	250	-198	GATGCCCTCTTCTTCCAAAGATGAAACGCGTAACT	;<;;;<<<:<6<<<::<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_595:7:188:802:71	83	chr1	415	99	35M	=	232	-218	TGCCCTCTTCTTCCAAAGATGAAACGCGTAACTGC	;;;;<:::<<<<<7<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_71:2:204:264:413	99	chr1	415	96	34M	=	593	213	TGCCCTCTTCTTCCAAAGATGAAACGCGTAACTG	<<<<<<<<<<<<<;:59<+<<:<<<9<<;:62<)	MF:i:18	Aq:i:27	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_28:5:104:350:749	83	chr1	415	99	36M	=	247	-204	TGCCCTCTTCTTCCAAAGATGAAACGCGTAACTGCG	;<93;9;<3;<<<;<<<<<;<<<<<<;<<<<<<<<<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_1:2:24:1037:84	83	chr1	415	99	35M	=	238	-212	TGCCCTCTTCTTCCAAAGATGAAACGCGTAACTGC	<;<<;<<<7<<7&<<<<<<;<<<;<<<<<<<<<<<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_28:7:242:354:637	147	chr1	417	99	36M	=	222	-231	CCCTCTTCTTCCAAAGATGAAACGCGTAACTGCGCT	8<;;;;;<<<8;<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_73:3:37:761:635	99	chr1	418	99	35M	=	581	198	CCTCTTCTTCCAAAGATGAAACGCGTAACTGCGCT	<6<<<<<<6<<<<<<<<<<<<<<<<<8<8<<4<4<	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:3:44:1578:1674	99	chr1	418	99	35M	=	573	190	CCTCTTCTTCCAAAGATGAAACGCGTAACTGCGCT	;<<;<<;<<;;;;;9<;9;;<9:;;<:;9;76669	MF:i:18	Aq:i:64	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_610:3:120:63:653	99	chr1	420	99	35M	=	598	213	TCTTCTTCCAAAGATGAAACGCGTAACTGCGCTCT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<9<9<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_97:7:264:642:506	147	chr1	420	99	35M	=	247	-208	ACTTCATCCAAAGATGAAACGCGTAACTGCGCTCT	&;(-/)-1&:<<9<25<<<<2<1<';8<<<:888<	MF:i:18	Aq:i:56	NM:i:2	UQ:i:13	H0:i:1	H1:i:0
+EAS188_7:3:101:572:491	99	chr1	425	99	35M	=	600	210	TTCCAAAGATGAAACGCGTAACTGCGCTCTCATTC	<<<<<<<<<<<<<<<<<<<<<<<<:<<<<<<1<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:3:27:1881:486	163	chr1	427	99	35M	=	607	215	CCAAAGATGAAACGCGTAACTGCGCTCTCATTCAC	;;;;;;;;;;;;;;1;;;;;;;;78;8;8;8878/	MF:i:18	Aq:i:67	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_589:6:120:14:944	163	chr1	428	99	35M	=	621	228	CAAAGATGAAACGCGTAACTGCGCTCTCATTCACT	<<<<<<<<<<<<<<<;<<<<<;<<<<<<<:;8;;7	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_11:7:46:695:738	83	chr1	428	74	35M	=	259	-204	CAAAGATGAAACGCGTAACTGCGCTCTCATTCACT	<<<<2<5<<-<<<<<<<4<<<<<<<<<<<<<<3<<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_39:6:13:1034:1144	147	chr1	429	99	35M	=	256	-208	AAAGATGAAACGCGTAACTGCGCTCTCATTCACTC	<<:%<9)<<<<<<8<<<<9<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_63:6:91:360:585	99	chr1	430	99	35M	=	586	191	AAGATGAAACGCGTAACTGCGCTCTCATTCACTCC	<<<<9<<<<<;<<<;<<77<<<;<;;<;;<;<;;<	MF:i:18	Aq:i:67	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:4:73:1208:495	83	chr1	431	99	35M	=	246	-220	AGATGAAACGCGTAACTGCGCTCTCATTCACTCCA	8-889<<;<;;:<;<;;;;;;<<;;<;;;;<<;;;	MF:i:18	Aq:i:67	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS218_1:8:16:1081:1894	163	chr1	431	99	35M	=	624	228	AGATGAAACGCGTAACTGGGCTCTCATTCACTCCA	<<<<<<<<<<<<<<<<<<8<<<<;<<;<<<<<<<+	MF:i:18	Aq:i:45	NM:i:1	UQ:i:23	H0:i:0	H1:i:1
+EAS188_4:7:35:408:348	117	chr1	433	0	*	=	433	0	GGTTCTCAAGGTTGTTGCAATGGGGTCTATGTGAA	.73<;<<:77<<<<<<<<<<-<<;<<<<<<<<<<<	MF:i:192
+EAS188_4:7:35:408:348	185	chr1	433	35	35M	=	433	0	AAGAAACGCGTAACTGCGCTCTCATACACTCCAGC	4,'3<6;)2);<3<-6<;<;7+7<5+<<<7<<<<<	MF:i:64	Aq:i:0	NM:i:2	UQ:i:21	H0:i:0	H1:i:1
+EAS56_53:4:130:568:978	147	chr1	434	88	35M	=	246	-223	TGAAACGCGAAACTGCACTCTCATTCACTCCAGCT	--;066;;62<<<2&<+<+<2;<<2<<<;<<<7<<	MF:i:18	Aq:i:24	NM:i:2	UQ:i:27	H0:i:0	H1:i:0
+EAS139_19:1:87:1222:878	83	chr1	435	34	40M	=	272	-203	TCAGCGCGTCACTCCGCTCTCATTCACCCCAGCTCCCTGT	!!;*:885<&<<<)8&<:<<<8<8<::*<4<88<<<8<<<	MF:i:18	Aq:i:10	NM:i:6	UQ:i:42	H0:i:0	H1:i:0
+EAS51_64:6:143:763:480	117	chr1	436	0	*	=	436	0	CTGAAGGTTGTTGCAAGGGGGTCTATGTGAACAAA	;<&-<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:192
+EAS51_64:6:143:763:480	185	chr1	436	70	35M	=	436	0	AAACGCGTAACTGCGCTCTCATTCACTCCAGCTCC	::3<:6<<<:<<<<7<<<<<<<<)6<<<1<<<<;<	MF:i:64	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_67:4:145:607:216	163	chr1	437	99	35M	=	596	194	AACGCGTAACTGCGCTCTCATTCACTCCAGCTCCC	<<<<<<<<8<<<<<<<<<<4<<<7<:<<1<<;;99	MF:i:18	Aq:i:68	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_67:6:46:285:790	121	chr1	437	72	35M	=	437	0	AACGCGTAACTGCGCTCTCATTCACTCCAGCTCCC	;;<8<;<<<<88<8<<;;<;<<;<<<<<<<<;<<<	MF:i:64	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_67:6:46:285:790	181	chr1	437	0	*	=	437	0	TCAAGGTTGTTGCAAGGGGGTCTATGTGAACAAAG	!!<<3<<<;;<<<<<<<<<;<;7<<7<<<<<<;<<	MF:i:192
+EAS56_59:4:329:577:757	117	chr1	437	0	*	=	437	0	TCAAGGTTGTTGCAAGGGGGTCTATGTGAACAAAG	!!<<<<9;<:<<;<<<<<<<<;<<<<<<<<<<<<<	MF:i:192
+EAS56_59:4:329:577:757	185	chr1	437	72	35M	=	437	0	AACGCGTAACTGCGCTCTCATTCACTCCAGCTCCC	;;;888;<<<<<<6<<<2;<<<<<<;<<<<<<<<<	MF:i:64	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_105:7:57:722:347	163	chr1	439	99	35M	=	599	195	CGCGTAACTGCGCTCTCATTCACTCCAGCTCCCTG	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;;	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_81:2:285:367:932	83	chr1	440	74	35M	=	285	-190	GCGTAACTGCGCTCTCATTCACTCCAGCTCCCTGT	9=5==;=;7===;==;===================	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_11:8:38:842:395	73	chr1	442	77	35M	*	0	0	GTAACTGCGCTCTCATTCACTCCAGCTCCCTGTCA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<93<;9	MF:i:32	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_93:8:14:601:624	163	chr1	446	99	35M	=	622	211	CTGCGCTCTCATTCACTCCAGCTCCCTGTCAACCC	<<1<<<<<<<<<<<<<<<<<3<<::<<7<<1,<:(	MF:i:18	Aq:i:69	NM:i:2	UQ:i:18	H0:i:1	H1:i:0
+EAS114_45:3:3:1377:1663	99	chr1	446	99	35M	=	626	215	CTGCGCTCTCATTCACTCCAGCTCCCTGTCACCCA	<<;;;;<:;;:<;;<;;<;:;;<;9;;::977676	MF:i:18	Aq:i:61	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_11:8:26:1221:222	83	chr1	446	99	35M	=	261	-220	CTGCGCTCTCATTCACTCCAGCTCCCTGTCACCCA	<<<<<<<:<:<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:78	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_11:8:82:566:1096	99	chr1	446	99	35M	=	621	210	CTGCGCTCTCATTCACTCCAGCTCCCTGTCACCCA	<<<<<<<<<<<<<<<<<<<<:<<<<<<<<<<<;<;	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_19:3:24:1135:563	83	chr1	446	99	40M	=	266	-220	CTGCGCTCTCATTCACTCCAGCTCCCTGTCACCCAATGGA	6+96:87<&8<<79:<;<<<<:<<;<<<<<<;;<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_65:1:53:272:944	147	chr1	447	99	35M	=	287	-195	TGCGCTCTCATTCACTCCAGCTCCCTGTCACCCAA	&94<4&8.6<6&;<:0:8;;:6;<;:<*<<<<<<<	MF:i:18	Aq:i:41	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_28:7:287:492:169	147	chr1	449	99	36M	=	269	-216	CGCTCTCATTCACTCCAGCTCCCTGTCACCCAATGG	;/;6<<<<4(<(<<<<6<<<<<<<<<<;<<<<<<<<	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:2:49:163:904	163	chr1	450	99	35M	=	616	201	GCTCTCATTCACTCCAGCTCCCTGTCACCCAATGG	;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;78958	MF:i:18	Aq:i:66	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_591:7:200:192:373	83	chr1	451	75	36M	=	275	-212	CTCTCATTCACTCCAGCTCCCTGTCACCCAATGGAC	<<<8<<<4<4<<<<<:<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_26:4:253:285:104	163	chr1	451	99	35M	=	627	211	CTCTCATTCACTCCAGCTCCCTGTCACCCAATGGA	======================:========7==;	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_103:1:151:159:43	99	chr1	452	99	35M	=	645	228	TCTCATTCACTCCAGCTCCCTGTCACCCAATGGAC	<<<<<<<;<<<8<<<;<;8<<<<7<77;;79<09+	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_61:1:115:868:887	163	chr1	452	99	35M	=	650	233	TCTCATTCACTCCAGCTCCCTGTCACCCAATGGAC	>>>>>>>>>>>>>>;<>>>>><<>>>;<+<</;;1	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_64:4:57:786:414	83	chr1	453	99	35M	=	296	-192	CTCATTCACTCCAGCTCCCTGTCACCCAATGGACC	;;;8;1;:<<<<;<::;;<<<<;<;;<<<<<<<<<	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_32:2:197:170:559	121	chr1	453	71	35M	=	453	0	CTCATTCACTCCAGCTCCCTGTCACCCAATGGACC	<:<;;:<5<5<<<;<<<<<<<<<<<<<<<<<<<<<	MF:i:64	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_32:2:197:170:559	181	chr1	453	0	*	=	453	0	TTCTCAAGGTTGTTGCAAGGGGGTCTATGTGAACA	:;;;;<<<<<<8<<<<<<<<<<<<<<<<<<<<<<<	MF:i:192
+EAS1_103:7:313:83:546	83	chr1	454	99	35M	=	296	-193	TCATTCACTCCAGCTCCCTGTCACCCAATGGACCT	;)<994<;<<<<<<<;<<<<<<<<<<<<<<5<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_57:6:44:280:641	83	chr1	454	99	35M	=	288	-201	TCATTCACTCCAGCTCCCTGTCACCCAATGGACCT	9;<<9;9;;<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_591:1:60:837:923	163	chr1	457	61	36M	=	641	220	TTCACGCCAGCTCCCTGTCACCCAATGGACCTCTGA	<<<<<4<<+<<*<<<<88<<<<<'*<4-+<<4&<40	MF:i:18	Aq:i:24	NM:i:2	UQ:i:24	H0:i:0	H1:i:1
+EAS114_45:5:85:401:1190	163	chr1	458	99	35M	=	652	229	TCACTCCAGCTCCCTGTCACCCAATGGACCTGTGA	4;;;1;;;;;;.6;;;(;;/;/;3;;;7;(3&063	MF:i:18	Aq:i:55	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_62:3:314:386:190	147	chr1	459	98	35M	=	287	-207	CACTCCAGCTCCCTGTCACCCAATGGACCTGTGAT	76;%;<<3<9;<69<<<7;;;<<<<<<<<<<<<<<	MF:i:18	Aq:i:29	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_103:1:2:831:692	99	chr1	462	99	35M	=	634	207	TCCAGCTCCCTGTCACCCAATGGACCTGTGATATC	<<<<<<<<;<<<<<<<<<<9<<:9<<<;;96<796	MF:i:18	Aq:i:65	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_65:1:163:846:223	83	chr1	463	74	35M	=	278	-220	CCAGCTCCCTGTCACCCAATGGACCTGTGATATCT	<7<5<*<<<<0<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS218_4:1:48:9:409	147	chr1	464	75	35M	=	271	-228	CAGCTCCCTGTCACCCAATGGACCTGTGATATCTG	<<<<+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_591:5:134:751:831	99	chr1	465	99	36M	=	651	222	AGCTCCCTGTCACCCAATGGACCTGTGATATCTGGA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<948	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_30:6:326:309:149	83	chr1	467	99	35M	=	301	-201	CTCCCTGTCACCCAATGGACCTGTGATATCTGGAT	;;<<;<:<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_59:7:260:985:520	83	chr1	468	99	35M	=	296	-207	TCCCTGTCACCCAATGGACCTGTGATATCTGGATT	;9;7<<<<<<<<<<<<<<<<<:<<<<<<<<<<<<<	MF:i:18	Aq:i:68	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_589:7:112:203:90	83	chr1	470	99	35M	=	305	-200	CCTGTCACCCAATGGACCTGTGATATCTGGATTCT	;<;:;<;;;<<<<<<<<<:<<<7<<<<<<<<<<<<	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_66:5:308:400:602	83	chr1	470	71	35M	=	285	-220	CCTGTCACCCAATGGACCTGTGATATCTGGATTCT	;77;2<<;<7<<;<<<;<;<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_59:7:82:902:868	147	chr1	471	99	35M	=	295	-211	CTGTCACCCAATGGACCTGTGATATCTGGATTCTG	<<;;<<<<<<<<;<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_53:4:153:977:200	163	chr1	472	99	35M	=	640	203	TGTCACCCAATGGACCTGTGATATCTGGATTCTGG	;<<;<<<<7<<;;;;;<<6<<<<<86;;8<;8;6;	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_59:7:319:246:304	147	chr1	472	99	35M	=	305	-202	TGTCACCCAATGGACCTGTGATATCTGGATTCTGG	;;<;;;<<<<8;<<<<;<<<<<<<<<<<<<<<;<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS219_1:1:37:1004:1136	147	chr1	473	99	35M	=	315	-193	GTCACCCAATGGACCTGTGATATCTGGATTCTGGG	</8<<<<7<+<<<<<<<,<<<<<<<<<6<<<<1<<	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:2:59:396:359	99	chr1	474	99	35M	=	670	231	TCACCCAATGGACCTGTGATATCTGGATTCTGGGA	<<9;;<;<;;;;<;;9;;;;;<;;;;;<;;77677	MF:i:18	Aq:i:66	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:6:45:1769:1130	163	chr1	476	99	35M	=	635	194	ACCCAATGGACCTGTGATATCTGGATTCTGGGAAA	;;;;;;;;;;;;9;;;;;;19;;;9;;;;176777	MF:i:18	Aq:i:67	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_105:7:110:355:323	147	chr1	477	99	35M	=	303	-209	CCCAATGGACCTGTGATATCTGGATTCTGGGAAAT	6069;1<<;4<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_28:1:28:708:463	99	chr1	477	99	36M	=	672	231	CCCAATGGACCTGTGATATCTGGATTCTGGGAAATT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<9;<:<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS188_7:5:112:51:128	83	chr1	477	99	35M	=	287	-225	CCCAATGGACCTGTGATATCTGGATTCTGGGAAAT	;9<;;:<<:<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:29	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_61:1:303:184:14	83	chr1	479	99	35M	=	301	-213	CAATGGACCTGTGATATCTGGATTCTGGGAAATTC	:<<.<;;7<:<<<<<<7<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:61	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_610:3:84:101:328	163	chr1	480	99	35M	=	673	228	AATGGACCTGTGATATCTGGATTCTGGGAAATTCT	<<<;<<<<<<<<;<<<<<<<<<<:<;;<44;;<;<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_71:6:228:354:203	99	chr1	480	99	34M	=	643	198	AATGGACCTGTGATATCTGGATTCTGGGAAATTC	88<<<8<<<<<<<<<8<<<<<<<<<4<<<4/9/;	MF:i:18	Aq:i:66	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_71:8:38:856:336	99	chr1	480	99	33M	=	656	211	AATGGACCTGTGATATCTGGATTCTGGGAAATT	<<<<<<<<<<<;;<;<;<:69<<;<5-500373	MF:i:18	Aq:i:65	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_11:6:75:946:1035	147	chr1	480	99	35M	=	288	-227	AATGGACCTGTGATATCTGGATTCTGGGAAATTCT	<<)4</<5<<<<<<<<<<<<<<<<<<<<<66<<<<	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_93:6:271:244:568	147	chr1	481	99	35M	=	294	-222	ATGGACCTGTGATATCTGGATTCTGGGAAATTCTT	;<<<<<<;<;<<<<<<<<<<;;<<<<<<<<<<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_108:8:129:477:427	99	chr1	481	99	35M	=	652	206	ATGGACCTGTGATATCTGGATTCTGGGAAATTCTT	<<<<<<<<<<<<<<<<<<;;<<<<::<9<;<<;<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_57:2:262:297:601	163	chr1	482	99	35M	=	635	188	TGGACCTGTGATATCTGGATTCTGGGAAATTCTTC	<<<<;<<9<<57<<7<<<;<<;77-;;53<<;;<7	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_73:3:88:24:744	83	chr1	484	84	35M	=	325	-194	GTCCTGTGATATCTGGATTCTGGGAAATTCTTCAT	4%++88;-9<;<<<+8<<<:<;8:<<<<<<<<<<<	MF:i:18	Aq:i:21	NM:i:1	UQ:i:4	H0:i:1	H1:i:0
+B7_610:5:147:68:353	83	chr1	486	99	35M	=	299	-222	CCTTTGATATCTGGATTCTGGGAAATTCTTCATCC	<<;;<<<<<<<<+;<<;<<0;<<<<;<<<<<<<<<	MF:i:18	Aq:i:70	NM:i:1	UQ:i:26	H0:i:1	H1:i:0
+EAS51_78:7:316:961:576	99	chr1	488	65	35M	=	666	213	TGTGATATCTGGATTCTGGGAAATTCTTCATCCCG	<<<<<<<;<<<<;<<:<<;<;<<:;<9+34;;6%/	MF:i:18	Aq:i:65	NM:i:1	UQ:i:4	H0:i:1	H1:i:0
+EAS56_61:8:7:171:402	99	chr1	489	99	35M	=	682	228	GTGATATCTGGATTCTGGGAAATTCTTCATCCTGG	<<<<<<<<<<<<<<<;/<<<<;<<<<<;<<1<<<4	MF:i:18	Aq:i:70	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_591:3:277:458:330	83	chr1	490	99	36M	=	329	-197	TGATATCTGGATTCTGGGAAATTCTTCATCCTGGAC	<<<<<8;<<<1<;7<<<;<<<<<<<<7<<7<<<<;7	MF:i:18	Aq:i:41	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_66:5:269:280:716	147	chr1	490	99	35M	=	323	-202	TGATATCTGGATTCTGGGAAATTCTTCATCCTGGA	6;<;;6:;<<<;64;<<<<<<<<;<<;<<;<<<<<	MF:i:18	Aq:i:58	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_71:4:72:63:435	147	chr1	490	99	35M	=	293	-232	TGATATCTGGATTCTGGGAAATTCTTCATCCTGGA	::<;<<<<;;;<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_67:8:46:900:610	99	chr1	491	99	35M	=	684	228	GATATCTGGATTCTGGGAAATTCTTCATCCTGGAC	<<<<<<<<<<<<;<<<<<<<<<<<<<<<<<;;4;<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_64:4:189:467:475	99	chr1	493	99	35M	=	683	225	TATCTGGATTCTGGGAAATTCTTCATCCTGGACCC	<<<<<<<<<<<<;;;<<<<<<<<<:<<<<:+<<;;	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_32:7:201:959:19	99	chr1	493	99	35M	=	681	223	TATCTGGATTCTGGGAAATTCTTCATCCTGGACCC	<<<<<<<<<<<<<<;<<<:<;<<;<<;+;+<3494	MF:i:18	Aq:i:41	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_108:2:240:593:842	99	chr1	494	99	35M	=	660	201	ATCTGGATTCTGGGAAATTCTTCATCCTGGACCCT	============<================9===:=	MF:i:18	Aq:i:70	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_66:3:29:381:169	163	chr1	494	99	35M	=	641	182	ATCTGGATTCTGGGAAATTCTTCATCCTGGACCCT	<<<<<<<<<<<2<288;<<;<<:4<:<<;&92929	MF:i:18	Aq:i:65	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_59:6:199:327:965	83	chr1	494	91	35M	=	297	-232	ATCTGGATTCTGGGAAATTCTTCATCCTGGACCCT	<5<:<<<58<:<<<<<<8<<<<<<<<<;<<<<<<<	MF:i:18	Aq:i:19	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:4:87:323:895	99	chr1	494	99	35M	=	671	212	ATCTGGATTCTGGGAAATTCTTCATCCTGGACCCT	;<<;;;;<<;<959;;;<;:<<;9<;;;4377788	MF:i:18	Aq:i:66	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_30:5:327:991:508	147	chr1	495	99	35M	=	312	-218	TCTGGATTCTGGGAAATTCTTCATCCTGGACCCTG	0:;::<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_597:5:6:882:784	163	chr1	496	99	35M	=	686	225	CTGGATTCTGGGAAATTCTTCATCCTGGACCCTGA	<<<<<<<<<<<<<:<<<<<<<<<<<<:6::::<,2	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_28:6:175:705:982	99	chr1	496	89	36M	=	660	200	CTGGATTCTGGGAAATTCTTCATCCTGGACCCTGAG	<<<<;<<;<<<<<<<<<<<<<;<<+<:;39;+<40<	MF:i:18	Aq:i:19	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_65:5:30:92:753	99	chr1	497	99	35M	=	673	211	TGGATTCTGGGAAATTCTTCATCCTGGACCCTGAG	<<<<<<<<<<<<<<<<<<<<<<:<<<<<<<<<<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_26:7:245:323:744	163	chr1	499	99	35M	=	679	215	GATTCTGGGAAATTCTTCATCCTGGACCCTGAGAG	<;<<<<<<<<<<<<<<<<<<<<<;<+<<<<<<<4<	MF:i:18	Aq:i:66	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_57:7:76:786:458	83	chr1	502	99	35M	=	341	-196	TCTGGGAAATTCTTCATCCTGGACCCTGAGAGATT	;<;:7<.<<<<<8;<<<<<<<6<;8<<<<<<<<<<	MF:i:18	Aq:i:68	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_63:7:185:213:330	83	chr1	502	99	35M	=	328	-209	TCTGGGAAATTCTTCATCCTGGACCCTGAGAGATT	;4<<<;<<<<<<<<;<<;;;<<<<9<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_11:7:42:1091:1726	147	chr1	502	99	35M	=	334	-203	TCTGGGAAATTCTTCATCCTGGACCCTGAGAGATT	4443838<4<8<87<<3</8<<<<<<<<<<<<<<<	MF:i:18	Aq:i:68	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_593:1:12:158:458	99	chr1	503	84	36M	=	675	208	CTGGGAAATTCTTCATCCTGGACCCTGAGAGATTCT	<77<<<7<<<<<<<<<<<<5<4;<<;5<;;+2<+;;	MF:i:18	Aq:i:15	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_65:6:277:590:364	163	chr1	503	99	35M	=	681	213	CTGGGAAATTCTTCATCCTGGACCCTGAGAGATTC	<<<<<8<<<<<<<<;<<<<<;;<7<<;;7858;;8	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS219_FC30151:1:18:1418:237	147	chr1	503	99	35M	=	304	-234	CTGGGAAATTCTTCATCCTGGACCCTGAGAGATTC	<<:<<<<<<<<:<<<<<<<<<:<<<<<<<<<<<<:	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_61:4:262:456:74	147	chr1	504	99	35M	=	357	-182	TGGGAAATTCTTCATCCTGGACCCTGAGAGATTCT	862;<<<:;<;<<<;;;<<<<;;<<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_71:3:186:989:869	99	chr1	505	99	34M	=	655	185	GGGAAATTCTTCATCCTGGACCCTGAGAGATTCT	<<<<<<<<<<<<<<<<<<<<7;:<<<<<<<<<$<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_64:3:80:885:513	83	chr1	507	99	35M	=	344	-198	GAAATTCTTCATCCTGGACCCTGAGAGATTCTGCA	<7<<<;<<;<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_103:7:311:100:539	83	chr1	508	99	35M	=	353	-190	AAATTCTTCATCCTGGACCCTGAGAGATTCTGCAG	;<;<<;;<;<<;<<<<<;9<<<;<<<<<<<<9<<;	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_81:6:199:511:426	163	chr1	509	99	35M	=	669	195	AATTCTTCATCCTGGACCCTGAGAGATTCTGCAGC	<<<<<<<<<<<<<<;<<<<<<:<<<<<<<<<;:<;	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_3:6:26:227:1053	99	chr1	510	99	35M	=	663	188	ATTCTTCATCCTGGACCCTGAGAGATTCTGCAGCC	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS188_7:2:172:622:707	99	chr1	511	99	35M	=	685	209	TTCTTCATCCTGGACCCTGAGAGATTCTGCAGCCC	<<<<<<<<<<<<<<<<<<<<<<;<<<<<<:<5:<<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_589:8:157:935:374	147	chr1	512	99	35M	=	353	-194	TCTTCATCCTGGACCCTGAGAGATTCTGCAGCCCA	94988994.<:<+42::<<<<<:<:<4<<<<;<1<	MF:i:18	Aq:i:66	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_591:4:103:111:720	147	chr1	512	99	36M	=	353	-195	TCTTCATCCTGGACCCTGAGAGATTCTGCAGCCCAG	;4<<<;)<<-<9<;<<7<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_71:4:328:669:662	147	chr1	512	99	35M	=	337	-210	TCTTCATCCTGTACCCTGAGAGATTCTGCAGCCCA	4<<;<<8<.<88.<<;4<<<<<<<4<.<<<<7<<<	MF:i:18	Aq:i:43	NM:i:1	UQ:i:23	H0:i:0	H1:i:1
+EAS51_64:5:202:39:380	147	chr1	513	99	35M	=	334	-214	CTTCATCCTGGACCCTGAGAGATTCTGCAGCCCAG	/92/;2<+2<<<<64<<<<<<<<<<<<<<<<7<<<	MF:i:18	Aq:i:65	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_66:8:66:655:769	147	chr1	515	99	35M	=	348	-202	TCATCCTGGACCCTGAGAGATTCTGCAGCCCAGCT	8<<;:69<;:;9<2<*9<;6<<<<<17<;<3+<;<	MF:i:18	Aq:i:66	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_67:4:7:526:343	99	chr1	515	99	35M	=	698	218	TCATCCTGGACCCTGAGAGATTCTGCAGCCCAGCT	<<<<<<<<<<<<<<<:<<<5<<<<<<5;<<<+8<;	MF:i:18	Aq:i:43	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS220_1:8:33:672:473	147	chr1	515	99	35M	=	330	-220	TCATCCTGGACCCTGAGAGATTCTGCAGCCCAGCT	5<70<<55<4<24.5<<<<<<<<<6<<<<<<2<<<	MF:i:18	Aq:i:65	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_19:6:72:308:839	83	chr1	517	99	40M	=	354	-203	ATCGTGGACCCTGAGAGATTCTGCAGCCCAGATCCAGATT	:8:.:<;<<5<<<<<<<<<<<<<<<<;:<<<<<<<<<<<<	MF:i:18	Aq:i:47	NM:i:2	UQ:i:40	H0:i:0	H1:i:1
+EAS56_61:1:210:880:606	83	chr1	518	99	35M	=	341	-212	TCCTGGACCCTGAGAGATTCTGCAGCCCAGCTCCA	.<<:<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_71:7:80:760:490	99	chr1	520	99	34M	=	686	201	CTGGACCCTGAGAGATTCTGCAGCCCAGCTCCAG	<<<<<<<<<<8<;<7<<<<<<;<;;<2<;<<<1,	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_11:3:34:970:1374	147	chr1	520	99	35M	=	363	-192	CTGGACCCTGAGAGATTCTGCAGCCCAGATCCAGA	<6<<<7<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:47	NM:i:1	UQ:i:27	H0:i:0	H1:i:1
+B7_593:1:200:559:765	147	chr1	521	99	36M	=	337	-220	TGGACCCTGAGAGATTCTGCAGCCCAGATCCAGATT	8<;;4<3;<;<<<<<<5<<;;<<98;;<<<<;<<<<	MF:i:18	Aq:i:45	NM:i:1	UQ:i:27	H0:i:0	H1:i:1
+EAS56_53:8:28:701:724	83	chr1	521	99	35M	=	347	-209	TGGACCCTGAGAGATTCTGCAGCCCAGCTCCAGAT	.;..3;8.8<8;<<;9<9<<<7;<<<<<<<<7<<7	MF:i:18	Aq:i:66	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_64:4:318:345:156	163	chr1	522	99	35M	=	695	208	GGACCCTGAGAGATTCTGCAGCCCAGATCCAGATT	<<<<<<<<:<<<<<<<<5<:5<<<3:'<72')*;9	MF:i:18	Aq:i:39	NM:i:1	UQ:i:6	H0:i:0	H1:i:1
+B7_595:1:81:1000:375	83	chr1	524	90	35M	=	329	-230	ACCCTGAGAGATTCTGCAGCCCAGCTCCAGATTGC	;8<;+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:19	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_19:4:13:1155:631	163	chr1	524	99	40M	=	668	184	ACCCTGAGAGATTCTGCAGCCCAGCTCCAGATTGCTTGTG	<<<<<<;<<;<<<<<<;<<<<<9<;<;94<<%<<<7:777	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS192_3:3:257:611:440	147	chr1	524	99	35M	=	341	-218	ACCCTGAGAGATTCTGCAGCCCAGATCCAGATTGC	2<;;8<;;<<<<;<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:45	NM:i:1	UQ:i:27	H0:i:0	H1:i:1
+EAS114_26:6:129:694:359	83	chr1	525	88	35M	=	350	-210	CCCTGAGAGATTCTGCAGCCCAGATCCAGATTGCT	7777<7<7;77+<3<<;<<;<<<<;<<<<<<<<<<	MF:i:18	Aq:i:43	NM:i:1	UQ:i:27	H0:i:0	H1:i:1
+EAS139_11:6:11:285:1567	163	chr1	525	99	35M	=	685	195	CCCTGAGAGATTCTGCAGCCCAGATCCAGATTGCT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:47	NM:i:1	UQ:i:27	H0:i:0	H1:i:1
+EAS1_95:1:196:533:921	147	chr1	526	99	35M	=	361	-200	CCTGAGAGATTCTGCAGCCCAGATCCAGATTGCTT	7<<<<7<<9<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:47	NM:i:1	UQ:i:27	H0:i:0	H1:i:1
+EAS139_11:2:6:251:1557	163	chr1	526	99	35M	=	700	209	CCTGAGAGATTCTGCAGCCCAGCTCCAGATTGCTT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:78	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_3:6:20:492:850	99	chr1	526	78	35M	=	694	203	CCTGAGAGATTCTGCAGCCCAGCTCCAGATTGCTT	<7<<<<<<<<<<<.<54<7&<<<7<74<2<<<2<<	MF:i:18	Aq:i:10	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_73:5:231:339:551	83	chr1	527	99	35M	=	350	-212	CTGAGAGATTCTGCAGCCCAGATCCAGATTGCTTG	<;<<;<<<<<<<<<<;:<<<<<<<<<<<<<;<<<<	MF:i:18	Aq:i:47	NM:i:1	UQ:i:27	H0:i:0	H1:i:1
+EAS139_19:4:68:1122:79	99	chr1	528	99	40M	=	687	199	TGAGAGATTCTGCAGCCCAGCTCCAGATTGCTTGTGGTCT	<<<<<<<<<<<<<;<<<<;<<<<<<;<<<4;<<4;99::;	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_1:4:87:1375:1303	83	chr1	529	99	35M	=	340	-224	GAGAGATTCTGCAGCCCAGATCCAGATTGCTTGTG	:<;<(<<<<<<<<<<<<<<<<<<<<<;<<<<<<<<	MF:i:18	Aq:i:45	NM:i:1	UQ:i:27	H0:i:0	H1:i:1
+EAS220_1:8:46:485:482	147	chr1	530	94	35M	=	371	-194	AGAGATTCTGCAGCCCAGATCCAGATTGCTTGTGG	<<<<<::<<<<<<<<6<<<<<<<<<6<<<<<<<<<	MF:i:18	Aq:i:47	NM:i:1	UQ:i:27	H0:i:0	H1:i:1
+EAS218_4:7:90:1873:89	147	chr1	531	99	35M	=	344	-222	GAGATTCTGCAGCCCAGATCCAGATTGCTTGTGGT	<<<<;49<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:47	NM:i:1	UQ:i:27	H0:i:0	H1:i:1
+EAS114_26:5:238:31:968	99	chr1	534	99	35M	=	717	218	ATTCTGCAGCCCAGCTCCAGATTGCTTGTGGTCTG	9======8====*=====,=1=======<=7:::,	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_28:3:78:773:660	163	chr1	534	99	36M	=	711	213	ATTCTGCAGCCCAGCTCCAGATTGCTTGTGGTCTGA	<<<<<<<<;<<<<<<<<<8<8<<;<<<;<<;7<<4:	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_591:5:90:828:633	83	chr1	537	99	36M	=	381	-192	CTGCAGCCCAGATCCAGATTGCTTGTGGTCTGACAG	<<<;<;<:<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:47	NM:i:1	UQ:i:27	H0:i:0	H1:i:1
+EAS114_30:2:272:750:698	83	chr1	538	80	35M	=	365	-208	TGCAGCCCAGATCCAGATTGCTTGTGGTCTGACAG	0<;8;64;<<<;<;.<+;:<4;4<;<<<<<<<<<<	MF:i:18	Aq:i:37	NM:i:1	UQ:i:27	H0:i:0	H1:i:1
+EAS139_19:3:88:1656:896	147	chr1	538	99	40M	=	387	-191	TGCAGCCCAGATCCAGATTGCTTGTGGTCTGACAGGCTGC	6/8::*9/*3*'<88<:9*<<<8<<<;<<<<<<<<;<<<<	MF:i:18	Aq:i:47	NM:i:1	UQ:i:9	H0:i:1	H1:i:0
+EAS54_61:6:126:541:194	163	chr1	540	97	35M	=	730	225	CAGCCCAGATCCAGATTGCTTGTGGTCTGACAGGC	<<<<<<<<8<<<<<8<<<<<<<<<8<<<428+<80	MF:i:18	Aq:i:43	NM:i:1	UQ:i:23	H0:i:0	H1:i:1
+EAS114_28:4:9:55:730	163	chr1	540	99	36M	=	722	218	CAGCCCAGCTCCAGATTGCTTGTGGTCTGACAGGCT	>>=>>+==>>==<==<=8=><:;8/;7</5724-2;	MF:i:18	Aq:i:66	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_95:2:278:918:892	99	chr1	541	99	35M	=	720	214	AGCCCAGCTCCAGATTGCTTGTGGTCTGACAGGCT	=============:====================8	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS188_7:7:243:876:758	99	chr1	541	99	35M	=	712	206	AGCCCAGATCCAGATTGCTTGTGGTCTGACAGGCT	<<<<<<<<<<<<<<<<<<<<<<<<<<<;;<;78<<	MF:i:18	Aq:i:47	NM:i:1	UQ:i:27	H0:i:0	H1:i:1
+EAS56_65:5:121:380:656	147	chr1	542	99	35M	=	362	-215	GCCCAGCTCCAGATTGCTTGTGGTCTGACAGGCTG	:;<<;<<1<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_11:6:82:164:1924	83	chr1	542	99	35M	=	378	-199	GCCCAGCACCAGATTGCTTGTGGTCTGACAGGCTG	6<<<<<<-<<<<<<<<<2<<06<9<<<<<1<<<<<	MF:i:18	Aq:i:43	NM:i:1	UQ:i:12	H0:i:0	H1:i:1
+EAS114_30:6:163:312:891	99	chr1	543	99	35M	=	709	201	CCCAGCTCCAGATTGCTTGTGGTCTGACAGGCTGC	<<<<<<<<<;<<<<<<<<<<<<<<<<:;;<;;<;0	MF:i:18	Aq:i:43	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_53:1:124:243:35	147	chr1	544	60	35M	=	364	-215	GCATATCCAGATTGCTGGTGGTCTGACAGGCAGCA	&+<+;<694;+&99<<2<;423<26<-<<<<,<3<	MF:i:130	Aq:i:60	NM:i:2	UQ:i:28	H0:i:0	H1:i:0
+B7_591:1:191:462:705	99	chr1	545	99	36M	=	721	212	CAGATCCAGATTGCTTGTGGTCTGACAGGCTGCAAC	<<<<<<<<<<<<<<<<<<<;<<<<<<<;<<<<::<6	MF:i:18	Aq:i:47	NM:i:1	UQ:i:27	H0:i:0	H1:i:1
+B7_610:8:95:426:791	147	chr1	547	99	35M	=	359	-223	GNTCCAGATTGCTTGTGGTCTGACAGGCTGCAACT	!!!!<<<<<;;<<<<;<<;<;;<<<<<<<<<<<<<	MF:i:18	Aq:i:76	NM:i:1	UQ:i:23	H0:i:1	H1:i:0
+EAS218_4:5:41:118:1246	147	chr1	548	99	35M	=	374	-209	CTCCAGATTGCTTGTGGTCTGACAGGCTGCAACTG	<<<<<<<<<<<<<<<+<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS192_3:3:27:973:518	99	chr1	549	99	35M	=	691	177	TCCAGATTGCTTGTGGTCTGACAGGCTGCAACTGT	<<<<<<<<<<<<<<;<<<<7<<<<<<<<88;0:8;	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_1:8:4:679:110	99	chr1	549	99	35M	=	705	191	TCCAGATTGCTTGTGGTCTGACAGGCTGCAACTGT	<<<<<<<<<<<<<<<<<<<;<<<<<<<<::<;;:7	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_105:1:297:283:948	163	chr1	550	99	35M	=	727	212	CCAGATTGCTTGTGGTCTGACAGGCTGCAACTGTG	<<<<<<<<<<<<<<<<<<<<<<<:<<9;)+1;19-	MF:i:18	Aq:i:68	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS218_1:8:61:1797:113	147	chr1	551	99	35M	=	380	-206	CAGATAGCTTGTGGTCTGACAGGCTGCAACTGTGA	<<0<<&<<<<;<<4;;3<;<:<<<<<<<<<<<<<<	MF:i:18	Aq:i:70	NM:i:1	UQ:i:5	H0:i:1	H1:i:0
+EAS188_7:6:205:873:464	99	chr1	552	99	35M	=	743	226	AGATTGCTTGTGGTCTGACAGGCTGCAACTGTGAG	<<<<<<<<<7<<<<<<<<<<<<:<<,:<:<<<<::	MF:i:18	Aq:i:63	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS219_1:3:33:1168:1762	99	chr1	552	99	35M	=	728	211	AGATTGCTTGTGGTCTGACAGGCTGCAACTGTGAG	<<<<<<<<<<<<<<<<;<<;<;<<<<<<<<:;2::	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_32:6:78:909:394	83	chr1	554	81	35M	=	373	-216	ATTGCTTGGTGTCTGACAGGCTGCAACTGTGAGCC	6167&+&&/&//734/3<<<9*<;;3<3<;9<<3<	MF:i:18	Aq:i:21	NM:i:2	UQ:i:19	H0:i:0	H1:i:0
+EAS1_103:2:226:302:758	163	chr1	556	99	35M	=	751	230	TGCTTGTGGTCTGACAGGCTGCAACTTTGAGCGNT	<<<<<<<;;;,<;<92;66<;))42<&2&(/1!!!	MF:i:18	Aq:i:33	NM:i:2	UQ:i:9	H0:i:0	H1:i:1
+EAS114_28:5:206:671:49	163	chr1	557	99	36M	=	719	198	GCTTGTGGTCTGACAGGCTGCAACTGTGAGCCATCA	<<<<<<;<<<<8<<<;;<<<3<<8<8<35+,55;,3	MF:i:18	Aq:i:67	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_597:2:165:431:857	147	chr1	559	99	35M	=	406	-188	TTGGGGTCTGACAGGCTGCAACTGTGAGCCATCAC	''7'/;'1%0447<<<*<6<<<*<*<<<<6<<<<<	MF:i:18	Aq:i:53	NM:i:1	UQ:i:6	H0:i:1	H1:i:0
+EAS114_39:5:50:972:1286	83	chr1	559	99	35M	=	377	-217	TTGTGGTCTGACAGGCTGCAACTGTGAGCCATCAC	:;;7;7;;0<<<<<<<;<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_65:7:288:552:440	163	chr1	560	87	35M	=	747	222	TGTGGTCTGACAGGCTGCAACTGTGAGCCTTCCAT	<<<<71<77<<<:<<<&<4<<77<16<88&36+%%	MF:i:18	Aq:i:26	NM:i:4	UQ:i:26	H0:i:1	H1:i:0
+EAS221_1:8:78:1478:1446	147	chr1	560	99	35M	=	389	-206	TGTGGTCTGACAGGCTGCAACTGTGAGCCATCACA	<8,8<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_65:8:275:851:240	99	chr1	561	99	35M	=	743	217	GTGGTCTGACAGGCTGCAACTGTGAGCCATCACAA	<<<<<<<<<<<<<<<<<<<<<<<:<<4<7<<<<<<	MF:i:18	Aq:i:31	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_95:6:185:312:167	83	chr1	562	99	35M	=	401	-196	TGGTCTGACAGGCTGCAACTGTGAGCCATCACAAT	<<8:<8<<<<<<<<<;<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_63:1:119:446:185	83	chr1	562	99	35M	=	372	-225	TGGTCTGACAGGCTGCAACTGTGAGCCATCACAAT	+70730;<0<77;;<<<<<9<<<<<<9<<<<<<<<	MF:i:18	Aq:i:66	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_65:3:168:741:680	83	chr1	562	99	35M	=	394	-203	TGGTCTGACAGGCTGCAACTGTGAGCCATCACAAT	<<5<<:<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:79	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_1:8:67:1797:1931	99	chr1	562	99	35M	=	750	223	TGGTCTGACAGGCTGCAACTGTGAGCCATCACAAT	<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<<<<<<	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_57:1:228:182:717	99	chr1	563	99	35M	=	729	201	GGTCTGACAGGCTGCAACTGTGAGCCATCCCCATG	<=9============5==5=<,59<=1=<&;&;;7	MF:i:18	Aq:i:66	NM:i:2	UQ:i:10	H0:i:1	H1:i:0
+EAS112_34:7:118:523:591	83	chr1	563	99	35M	=	393	-205	GGTCTGACAGGCTGCAACTGTGAGCCATCACAATG	4:--&0:67<<8:<<<<<<<<<<<:4<<<<<<<<<	MF:i:18	Aq:i:66	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_3:4:29:1061:574	83	chr1	563	99	35M	=	363	-235	GGTCTGACAGGCTGCAACTGTGAGCCATCACAATG	<87<5<<9<<<66<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_591:3:168:69:605	83	chr1	565	67	36M	=	373	-228	TCTGACAGGCGGCAACTGTGAGCCATCACAATGAAC	'<'<144<0<&<<<<<<<7<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:26	NM:i:1	UQ:i:5	H0:i:0	H1:i:1
+EAS221_3:4:90:247:212	99	chr1	567	99	35M	=	733	201	TGACAGGCTGCAACTGTGAGCCATCACAATGAACA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<6<8<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_61:3:140:522:212	83	chr1	568	99	35M	=	399	-204	GACAGGCTGCAACTGTGAGCCATCACAATGAACAA	:;8;:::<<:<<<<<<<<<7<<<<<<<<<<<<<<<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS112_34:8:179:13:782	83	chr1	568	99	35M	=	412	-191	GACAGTCTACAACTGTGAGCCATCACAATGAACAA	&37.3&;3'*<3<;9<9<<5<<<<<<<<<9<<<<<	MF:i:18	Aq:i:39	NM:i:2	UQ:i:11	H0:i:0	H1:i:1
+EAS114_45:3:75:217:337	83	chr1	568	99	35M	=	386	-217	GACAGGCTGCAACTGTGAGCCATCACAATGAACAA	4779797;;;<;:4;;<<<77<;;;7<<;<;<;<<	MF:i:18	Aq:i:67	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_53:4:168:528:288	163	chr1	570	99	35M	=	740	205	CAGGCTGCAACTGTGAGCCATCACAATGAACAACA	<<<<<<<<<<<<<<<<<<<<<<<<:<<<<<<;<<;	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_95:2:162:503:769	147	chr1	571	99	35M	=	392	-214	AGGCTGCAACTGTGAGCCATCACAATGAACAACAG	;:;1;=8=;:+=====;&==7==============	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_32:2:163:618:570	163	chr1	571	99	35M	=	751	215	AGGCTGCAACTGTGAGCCATCACAATGAACAACAG	<<<<<<<8<<<<<<<<<<<<<+<.7<<..<;&;8;	MF:i:18	Aq:i:41	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_595:2:251:121:479	163	chr1	572	99	35M	=	750	213	GGCTGCAACTGTGAGCCATCACAATGAACAACAGG	<<<<<<<<<<<;:<<<<;:;:<:<;:188;7:<+(	MF:i:18	Aq:i:65	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:3:44:1578:1674	147	chr1	573	99	35M	=	418	-190	GCTGCAACTGTGAGCCATCACAATGAACAACAGGA	62631;;4;;;8;;48;;7;8;;;;;;;;;8;;;;	MF:i:18	Aq:i:64	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_62:3:263:74:407	163	chr1	574	99	35M	=	754	215	CTGCAACTGTGAGCCATCACAATGAACAACAGGAA	<<<<2<<<<<<:<<<9<<4<<<<:<<<<9<999.7	MF:i:18	Aq:i:68	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_71:3:254:32:275	147	chr1	575	99	35M	=	382	-228	TGCAACTGTGAGCCATCACAATGAACAACAGGAAG	(6+<;+6:9<<:7:<95<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:65	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_108:2:82:879:246	83	chr1	576	99	35M	=	391	-220	ACAACTGTGAGCCATCACAATGAACAACAGGAAGA	%+=661;&===:&==1<5======1==========	MF:i:18	Aq:i:43	NM:i:1	UQ:i:4	H0:i:1	H1:i:0
+EAS54_71:4:165:397:25	163	chr1	576	99	35M	=	759	217	GCAACTGTGAGCCATCACAATGAACAACAGGAAGA	<<7<<<<<<)97<6<:3:60:3+37-37+<:33:3	MF:i:18	Aq:i:54	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_610:6:148:776:486	163	chr1	578	99	35M	=	755	212	AACTGTGAGCCATCACAATGAACAACAGGAAGAAA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;;	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_3:2:59:1576:946	99	chr1	578	99	35M	=	761	218	AACTGTGAGCCATCACAATGAACAACAGGAAGAAA	<:<<<<<<<<<<<<:<:<<<<<<<8<<::1<<<<<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_103:4:61:433:385	83	chr1	579	99	35M	=	381	-233	ACTGTGAGCCATCACAATGAACAACAGGAAGAAAA	<*97<<<<&9<<;<&<<<<<<<<<;<<<<<<<<<<	MF:i:18	Aq:i:43	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_73:3:37:761:635	147	chr1	581	99	35M	=	418	-198	TGTGAGCCATCACAATGAACAACAGGAAGAAAAGG	+37:<088<+<<;<<;<<<<<;<<;<<<<<<<<<<	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_57:2:178:192:499	163	chr1	582	99	35M	=	768	221	GTGAGCCATCACAATGAACAACAGGAAGAAAAGGT	<<<<<<<;<1<<<<<<;<<;6<<3666;;;;;/6/	MF:i:18	Aq:i:70	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS192_3:7:93:945:176	99	chr1	582	99	35M	=	745	198	GTGAGCCATCACAATGAACAACAGGAAGAAAAGGT	<<<<<<<<<<<<<<<<<<<<<;<<<<;;<;:7;<3	MF:i:18	Aq:i:70	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_108:3:216:988:883	83	chr1	584	99	35M	=	392	-227	AAGCCAACACAATGAACAACAGGAAGAAAAGGTCT	(=/1+=&:=&======<==<===============	MF:i:18	Aq:i:68	NM:i:2	UQ:i:12	H0:i:1	H1:i:0
+EAS114_39:1:12:884:219	99	chr1	584	99	35M	=	756	207	GAGCCATCACAATGAACAACAGGAAGAAAAGGTCT	<<<<<<<<<<<<<<<<<<<;<<<<<<<<<<<<5:<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_593:6:61:628:681	163	chr1	586	99	36M	=	746	196	GCCATCACAATGAACAACAGGAAGAAAAGGTCTTTC	<<<<<<<<<<<<<<<<<<<;<<<<<<<:<<;;;;;;	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_63:6:91:360:585	147	chr1	586	99	35M	=	430	-191	GACATCACAATGAACAACAGGAAGAAAAGGTCTTT	5&&<<3:;<<<<<<)<<3<<<<<<<;;<<<<;<<<	MF:i:18	Aq:i:67	NM:i:1	UQ:i:5	H0:i:1	H1:i:0
+EAS139_11:6:89:1151:1878	99	chr1	587	99	35M	=	757	205	CCATCACAATGAACAACAGGAAGAAAAGGTCTTTC	<;;<<<<<;;;<<<<4;;::;<;8;;<;;8:<8<4	MF:i:18	Aq:i:43	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_19:1:40:1596:1433	99	chr1	587	99	40M	=	756	209	CCATCACAATGAACAACAGGAAGAAAAGGTCTTTCAAAAG	<<<<<<<<<<<<<<<<<<<<<<<<;<<<<1<<<<<::;::	MF:i:18	Aq:i:70	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS219_1:3:4:1620:413	99	chr1	588	99	35M	=	768	215	CATCACAATGAACAACAGGAAGAAAAGGTCTTTCA	<<<<<<<<<<6<<<6<<<;<6<9-1<;<&66<<<2	MF:i:18	Aq:i:66	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_1:8:65:1928:1125	99	chr1	588	99	35M	=	784	231	CATCACAATGAACAACAGGAAGAAAAGGTCTTTCA	<<;<<<7<<7<;<7<<<<<<<7<<<<;<.-;<+88	MF:i:18	Aq:i:41	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_63:5:123:998:248	163	chr1	589	99	35M	=	776	222	ATCACAATGAACAACAGGAAGAAAAGGTCTTTCAA	<<<<<<<<<<<<<<<<<<<<<<<<<<<;9<<<68<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_591:2:240:603:890	163	chr1	590	99	36M	=	740	186	TCACAATGAACAACAGGAAGAAAAGGTCTTTCAAAA	<<<<<<<<<<<<<<<<<<;<:<<:<<;<<<<<8865	MF:i:18	Aq:i:66	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_61:3:20:762:748	163	chr1	591	99	35M	=	777	221	CACAATGAACAACAGGAAGAAAAGGTCTTTCAAAA	===================================	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_65:4:246:313:499	99	chr1	592	99	35M	=	757	200	ACAATGAACAACAGGAAGAAAAGGTCTTTCAAAAG	<<<<<<<<<<<<<;<;<<<<<<<<;<<<<<;;<<<	MF:i:18	Aq:i:65	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_103:6:7:858:437	99	chr1	593	99	35M	=	773	215	CAATGAACAACAGGAAGAAAAGGTCTTTCAAAAGG	<<<<<<<<<<<<<<<<<<<<<;<3<<<<<<<<<33	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_61:3:150:933:810	163	chr1	593	99	35M	=	755	197	CAATGAACAACAGGAAGAAAAGGTCTTTCAAAAGG	===================================	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_71:2:204:264:413	147	chr1	593	96	35M	=	415	-213	CAATGAACAACAGAAAGAAAAGTTCTTTCAAAAGG	1==(4=::;/7::&===;====/=;===;;=====	MF:i:18	Aq:i:27	NM:i:2	UQ:i:19	H0:i:0	H1:i:0
+EAS139_11:3:65:556:1505	163	chr1	593	99	35M	=	790	232	CAATGAACAACAGGAAGAAAAGGTCTTTCAAAAGG	<<<<<<<<<<<<<<<<<<<<<<<6<<<<<<<<<<<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_30:6:62:386:959	99	chr1	594	99	35M	=	752	193	AATGAACAACAGGAAGAAAAGGTCTTTCAAAAGGT	<<8<<<<;<<<<-<<87;</<;<+<;5<+;;<3;+	MF:i:18	Aq:i:57	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_591:2:134:868:252	147	chr1	595	99	36M	=	404	-227	ATGAACAACAGGAAGAAAAGGTCTTTCAAAAGGTGA	<;<<<8<<<<<<<<<<<<<<<:<<<<<<<<<<<<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_595:1:252:19:955	99	chr1	596	84	35M	=	771	210	TGAACAAAAGGAAGAAAAGGTCTTTCAAAAGGTGA	<<<<<<<<<<4<<<<9<<+9)9<<4:9+<<0<909	MF:i:18	Aq:i:41	NM:i:1	UQ:i:27	H0:i:0	H1:i:1
+EAS54_67:4:145:607:216	83	chr1	596	99	35M	=	437	-194	TGAAAAACAGGAAGAAAAGGTCTTTCAAAAGGTGA	/;<<&<<8<<<<<<<<<<<<<;872<<<<<<<<<<	MF:i:18	Aq:i:68	NM:i:1	UQ:i:5	H0:i:1	H1:i:0
+EAS54_65:8:140:924:923	163	chr1	597	99	35M	=	767	205	GAACAACAGGAAGAAAAGGTCTTTCAAAAGGTGAT	<<<<<<<<<<<<<<<<<:<<<<<<<<<<<<<5;<;	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_610:3:120:63:653	147	chr1	598	99	35M	=	420	-213	AACAACAGGAAGAAAAGGTCTTTCAAAAGGTGATG	<<;<<;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_81:6:204:779:181	163	chr1	598	99	35M	=	779	216	AACAACAGGAAGAAAAGGTCTTTCAAAAGGTGATG	<<<<<<5<<:<<<<<8<<,<<<<<<<<<<91<91<	MF:i:18	Aq:i:68	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_81:7:325:150:465	147	chr1	598	99	35M	=	412	-221	AACAACAGGAAGAAAAGGTCTTTCAAAAGGTGATG	<<:<<<<<<<<;<:<<<<;<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_105:7:57:722:347	83	chr1	599	99	35M	=	439	-195	ACAACAGGAAGAAAAGGTCTTTCAAAAGGTGATGT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_59:2:177:266:842	163	chr1	599	99	35M	=	784	220	ACAACAGGAAGAAAAGGTCTTTCAAAAGGTGATGT	=====)===========8=====7882855355'5	MF:i:18	Aq:i:66	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_30:4:183:852:253	163	chr1	599	99	35M	=	773	209	ACAACAGGAAGAAAAGGTCTTTCAAAAGGTGATGT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<8<;;<8	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_30:2:30:887:404	163	chr1	600	99	35M	=	789	224	CAACAGGAAGAAAAGGTCTTTCAAAAGGTGATGTG	<<<<<<<<<<;<<<<<<<<<<<<<<<<:(<<<7;7	MF:i:18	Aq:i:45	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS188_7:3:101:572:491	147	chr1	600	99	35M	=	425	-210	CAACAGGAAGAAAAGGTCTTTCAAAAGGTGATGTG	8<<;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_589:2:73:730:487	99	chr1	604	99	35M	=	770	201	AGGAAGAAAAGGTCTTTCAAAAGGTGATGTGTGTT	<<<<<<<<<<<<<<<<<<<9<<<<<<:<<<;<;<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_71:6:172:896:83	99	chr1	604	99	34M	=	786	217	AGGAAGAAAAGGTCTTTCAAAAGGTGATGTGTGT	<<<<<<<<<<<<<<<<<:;;+;<<<<<<<<9;;;	MF:i:18	Aq:i:70	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_53:4:154:762:630	163	chr1	604	99	35M	=	792	223	AGGAAGAAAAGGTCTTTCAAAAGGTGATGTGTGTT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;;	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_99:8:99:756:130	163	chr1	606	99	35M	=	798	227	GAAGAAAAGGTCTTTCAAAAGGTGATGTGTGTTCT	;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<6<<;<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_11:6:11:360:1577	99	chr1	606	99	35M	=	781	210	GAAGAAAAGGTCTTTCAAAAGGTGATGTGTGTTCT	<<<<<<<<<<<<<<<<<4<;;<<;;<;<<<8<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:3:27:1881:486	83	chr1	607	99	35M	=	427	-215	AAGAAAAGGTCTTTCAAAAGGTGATGTGTGTTCTC	99797;;9:<:;;;<;;;;<<<;;;;<;<;;<<<<	MF:i:18	Aq:i:67	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS219_1:1:5:497:687	99	chr1	607	99	35M	=	789	217	AAGAAAAGGTCTTTCAAAAGGTGATGTGTGTTCTC	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_593:4:142:63:937	163	chr1	609	99	36M	=	777	204	GAAAAGGTCTTTCAAAAGGTGATGTGTGTTCTCATC	<<<<<<<<<<<<<<<<<:<<<<<<<<<;<<:<<:<:	MF:i:18	Aq:i:78	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_593:1:36:485:632	163	chr1	610	99	36M	=	784	210	AAAAGGTCTTTCAAAAGGTGATGTGTGTTCTCATCA	<<<<<<<<<<<<<<<<<<<<<<<<<<<5<<<;<18;	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_97:8:36:927:478	99	chr1	610	99	35M	=	798	223	AAAAGGTCTTTCAAAAGGTGATGTGTGTTCTCATC	<<<<<<<<<<<<<<<<;<<<<<:<:<<<<8<9;<8	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_71:4:169:862:829	163	chr1	611	99	35M	=	772	195	AAAGGTCTTTCAAAAGGTGATGTGTGTTCTCATCA	<<<<<<<<<<<<<<<<<;<<<;<;<<<<:<;;<78	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS219_FC30151:5:63:424:1643	163	chr1	614	99	35M	=	798	219	GGTCTTTCAAAAGGTGATGTGTGTTCTCATCAACC	;;<<<<<<;<<<<<<<<<<5;9;<<<<<<<<<<;<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_32:4:20:41:138	99	chr1	615	99	35M	=	774	194	GTCTTTCAAAAGGTGATGTGTGTTCTCATCAACCT	<<<<<<<<<<<<<<<<<<<<<<<<7<;<<<<<(<<	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:2:49:163:904	83	chr1	616	99	35M	=	450	-201	TCTTTCAAAAGGTGATGTGTGTTCTCATCAACCTC	79779<<<<<;;;;9;;<<7<;*9<<<7<<;<<;<	MF:i:18	Aq:i:66	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_99:3:135:543:760	99	chr1	619	99	35M	=	787	203	TTCAAAAGGTGATGTGTGTTCTCATCAACCTCATA	<<<<;;<;<<<<<<<9<<<<<<<<<<<;<<<<5<:	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_65:5:131:742:561	163	chr1	620	99	35M	=	790	205	TCAAAAGGTGATGTGTGTTCTCATCAACCTCATAC	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:78	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_589:6:120:14:944	83	chr1	621	99	35M	=	428	-228	CAAAAGGTGATGTGTGTTCTCATCAACCTCATACA	:;<<;<;<;<<;<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_11:8:82:566:1096	147	chr1	621	99	35M	=	446	-210	CAAAAGGTGATGTGTGTTCTCATCAACCTCATACA	<<<<<<<<<<:<<<<<<<:<<<<<<:<<<<<<<<<	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_93:8:14:601:624	83	chr1	622	99	35M	=	446	-211	AAAAGGTGATGTGTGTTCTCATCAACCTCATACAC	1;;;;==5===.(=9=5=========8====;===	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_19:3:5:538:401	99	chr1	624	99	40M	=	788	204	AAGGTGATGTGTGTTCTCATCAACCTCATACACACACATG	<<<<;<<<<<<<<<<<<<<<;<::7<<;<53:<98;;;;;	MF:i:18	Aq:i:39	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS218_1:8:16:1081:1894	83	chr1	624	99	35M	=	431	-228	AAGGTGATGTGTGTTCTCATCAACCTCATACACAC	;5;;&<;<<<<<<<<;<;<<;<<<;<<<<<<<<<<	MF:i:18	Aq:i:45	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:3:3:1377:1663	147	chr1	626	99	35M	=	446	-215	GGTGATGTGTGTTCTCATCAACCTCATACACACAC	6-88663;8;81;;66;8;;89939;;;67;2;;;	MF:i:18	Aq:i:61	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_26:4:253:285:104	83	chr1	627	99	35M	=	451	-211	GTGATGTGTGTTCTCATCAACCTCATACACACACA	2<;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS218_1:6:66:1282:1215	99	chr1	627	99	35M	=	794	202	GTGATGTGTGTTCTCATCAACCTCATACACACACA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<;;;	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:3:2:1200:1076	163	chr1	629	99	35M	=	786	192	GATGTGTGTTCTCATCAACCTCATACACACACATG	;;;;;;;;;;/;;;;;;;;6;;9;489;;;88888	MF:i:18	Aq:i:67	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_610:2:194:688:289	99	chr1	631	99	35M	=	795	199	TGTGTGTTCTCATCAACCTCATACACACACATGGT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<9<<<:;	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_67:8:19:855:491	99	chr1	631	99	35M	=	783	187	TGTGTGTTCTCATCAACCTCATACACACACATGGT	<<<<<<<<<<<;<<.:<<<<;;;<4<:<:<7<;;;	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_71:6:215:133:909	99	chr1	631	99	34M	=	789	193	TGTGTGTTCTCATCAACCTCATACACACACATGG	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<996(	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_610:7:35:378:681	99	chr1	632	99	35M	=	812	215	GTGTGTTCTCATCAACCTCATACACACACATGGTT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<:<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_19:5:40:758:116	163	chr1	632	99	40M	=	814	222	GTGTGTTCTCATCAACCTCATACACACACATGGTTTAGGG	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<:7262	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_103:1:2:831:692	147	chr1	634	99	35M	=	462	-207	GTGTTCTCATCAACCTCATACACACACATGGTTTA	2749'979<9<<<6;<<<0<;<<<<<3<<<<<<<<	MF:i:18	Aq:i:65	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_105:6:162:594:858	99	chr1	634	99	35M	=	818	219	GTGTTCTCATCAACCTCATACACACACATGGTTTA	<<<<<<<<<<<<<<<<<9<;<<<<<<<<<<3<<<;	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_57:4:233:478:792	99	chr1	634	99	35M	=	791	192	GTGTTCTCATCAACCTCATACACACACATGGTTTA	<<<<<<<<<<<<<<<<<<<+<<<<<<<9<<<+;;;	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_57:2:262:297:601	83	chr1	635	99	35M	=	482	-188	TGTTCTCATCAACCTCATACACACACATGGTTTAG	;;<26;;;<;<7;<<<<<99<<<<<<<<<<<<<<<	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:6:45:1769:1130	83	chr1	635	99	35M	=	476	-194	TGTTCTCATCAACCTCATACACACACATGGTTTAG	88989;<;97;9<<;<;;;;9<98<<<<<<<;<<<	MF:i:18	Aq:i:67	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_53:4:153:977:200	83	chr1	640	99	35M	=	472	-203	TCATCAACCTCATACACACACATGGTTTAGGGGTA	1:<83<<9;;9<<9;;<<;<<;;;;<;;<<<<<<;	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_591:1:60:837:923	83	chr1	641	61	36M	=	457	-220	CATCAACCGCATACACTCACATGGTTTAGGGGTATA	0<4<<<02.<99+<+&!<<<<+<<<<<<<<<<<<3<	MF:i:18	Aq:i:24	NM:i:2	UQ:i:13	H0:i:0	H1:i:0
+EAS51_66:3:29:381:169	83	chr1	641	99	35M	=	494	-182	CATCAACCTCATACACACACATGGTTTAGGGGTAT	2<82<;66<:<;<:<;<;<8<<<<<<<<<<<<<<<	MF:i:18	Aq:i:65	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_62:7:96:836:737	99	chr1	642	99	35M	=	841	234	ATCAACCTCATACACACACATGGTTTAGGGGTATA	<<<<<<71<<<<<<<<<<899<:5<<<96858<<.	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_71:6:228:354:203	147	chr1	643	99	35M	=	480	-198	TCAACCTCATACACACACATGGTTTAGGGGTATAA	%1<851<5<<<982<<<<<<<<::<<<<7<<<<3<	MF:i:18	Aq:i:66	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_103:1:151:159:43	147	chr1	645	99	35M	=	452	-228	AACCTCATACACACACATGGTTTAGGGGTATAATA	;;4;6<<;<<<<7<77<6;<6<<<<<;;<<<<<<<	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_105:3:182:404:693	163	chr1	646	99	35M	=	812	201	ACCTCATACACACACATGGTTTAGGGGTATAATAC	<<<<<<<<<<<<<<<<<<<<<<:::<6<;<94;77	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS112_34:8:4:841:339	163	chr1	646	99	35M	=	793	182	ACCTCATACACACACATGGTTTAGGGGTATAATAC	<<<<<<<<<<<<<<<<<;<7<<&;;<5<+<;7<<;	MF:i:18	Aq:i:66	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_62:4:156:857:494	163	chr1	648	99	35M	=	838	225	CTCATACACACACATGGTTTAGGGGTATAATACCT	<<<<<<<<<<<<<<<<<6<<<<<<<<<<<<<<:<<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_108:6:165:464:123	99	chr1	650	99	35M	=	814	199	CATACACACACATGGTTTAGGGGTATAATACCTCT	===============7==============8====	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_61:1:115:868:887	83	chr1	650	99	35M	=	452	-233	CATACACACACATGGTTTAGGGGTATAATACCTCT	==;==8=;=;=========================	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_591:5:134:751:831	147	chr1	651	99	36M	=	465	-222	ATACACACACATGGTTTAGGGGTATAATACCTCTAC	;:<4<8<<<;<;<<5<:<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_62:5:192:716:235	163	chr1	651	99	35M	=	798	182	ATACACACACATGGTTTAGGGGTATAATACCTCTA	======================9==:<==:;;69;	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_63:3:40:594:752	99	chr1	651	99	35M	=	831	215	ATACACACACATGGTTTAGGGGTATAATACCTCTA	<<<<<<<<<<;<<<;<<<::;<:;<;:<;;;<;<:	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_95:4:184:17:636	121	chr1	652	76	35M	=	652	0	TACACACACATGGTTTAGGGGTATAATACCTCTAC	8<89<<:<<<;;;<<<<<<<<<<<<<<<<<<<<<<	MF:i:64	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_95:4:184:17:636	181	chr1	652	0	*	=	652	0	TTTTTTTTTTTTTTTTTTTTTTTTTTTTCACAGGT	!!!!!!!!!!!!!!!!!!!!!!!!!!!77777777	MF:i:192
+EAS1_108:8:129:477:427	147	chr1	652	99	35M	=	481	-206	TACACACACATGGTTTAGGGGTATAATACCTCTAC	<<<9;<<9<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_81:8:130:912:658	163	chr1	652	99	35M	=	841	224	TACACACACATGGTTTAGGGGTATAATACCTCTAC	<<<<<;<<<<<<;<<<<<<<<<<<<<<<<<7<;;<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:5:85:401:1190	83	chr1	652	99	35M	=	458	-229	TACACACACATGGTTTAGGGGTATAATACCTCTAC	64778:;69739:;+9::7;;;<;6<;7;;;;;7<	MF:i:18	Aq:i:55	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_19:3:4:1502:1911	163	chr1	652	99	40M	=	802	190	TACACACACATGGTTTAGGGGTATAATACCTCTACATGGC	<<<:4<<<<<<;<<<<;9;5<95<;<<;9+;1612:1:::	MF:i:18	Aq:i:68	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_95:2:198:691:595	163	chr1	655	99	35M	=	847	227	ACACACATGGTTTAGGGGTATAATACCTCTACATG	==============&===============;7;=1	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_71:3:186:989:869	147	chr1	655	99	35M	=	505	-185	ACACACATGGTTTAGGGGTATAATACCTCTACATG	;<<;:<<<7:<<<<<<:<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_71:8:38:856:336	147	chr1	656	99	35M	=	480	-211	CACACATGGTTTAGGGGTATAATACCTCTACATGG	2;4;4<:;6:5:<<;:;<<;<<;<<<<<<<<<<<<	MF:i:18	Aq:i:65	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_108:2:49:271:588	163	chr1	658	99	35M	=	830	207	CACATGGTTTAGGGGTATAATACCTCTACATGGCT	<<<<<<<<<<<<<<5:<<<<<<:<<<<<<<:7%9<	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_108:2:240:593:842	147	chr1	660	99	35M	=	494	-201	CATGGTTTAGGGGTATAATACCTCTACATGGCTGA	*<<<;<<6<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:70	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_28:6:175:705:982	147	chr1	660	89	36M	=	496	-200	CATGGTTTAGGGGTATAATACCTCTACATGGCTGAT	')'''''')'''''*')*)'*)')))+,'*)+'*,!	MF:i:18	Aq:i:19	NM:i:1	UQ:i:0	H0:i:0	H1:i:1
+EAS221_3:6:26:227:1053	147	chr1	663	99	35M	=	510	-188	GGTTTAGGGGTATAATACCTCTACATGGCTGATTA	<<<<<<<<<<<<<<<<<<<<<<<<<;<<<<<<<<<	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_78:7:316:961:576	147	chr1	666	65	35M	=	488	-213	TTACGGGTGTAATCTCTCTACATGGCTAATTATGA	(++%%+++),+,+*++,+,,-,**+,-&-,+-+--	MF:i:130	Aq:i:65	NM:i:5	UQ:i:36	H0:i:0	H1:i:0
+EAS56_63:5:96:788:614	163	chr1	667	99	35M	=	862	230	TAGGGGTATAATACCTCTACATGGCTGATTATGAA	<<<<<<<<<<<<<<<<<<<<<<;6;<<;;<;;7;9	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_19:4:13:1155:631	83	chr1	668	99	40M	=	524	-184	AGGGGTATAATACCTCTACATGGCTGATTATGAAAACAAT	;:398<<;<<<<<;<3<;;<<<<;;<<<<<<<<<<;<<;<	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_81:6:199:511:426	83	chr1	669	99	35M	=	509	-195	GGGGTATAATACCTCTACATGGCTGATTATGAAAA	<:7:<<<<<<<<<<<<<<<<<;<<<<<<<<<<<<<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_67:5:124:241:608	99	chr1	670	99	35M	=	856	221	GGGTATAATACCTCTACATGGCTGATTATGAAAAC	<<<<<<<<<;<<<<<<<<<;;<<<;<<<<;;8;;:	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:2:59:396:359	147	chr1	670	99	35M	=	474	-231	GGGTATAATACCTCTACATGGCTGATTATGAAAAC	28288;;;;;;;;;::;;;;:;;;;;;;;;;;;;;	MF:i:18	Aq:i:66	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:4:87:323:895	147	chr1	671	99	35M	=	494	-212	GGTATAATACCTCTACATGGCTGATTATGAAAACA	55777;;;939;9;;9;;;;9;;;;;;;;;;;;;;	MF:i:18	Aq:i:66	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_28:1:28:708:463	147	chr1	672	99	36M	=	477	-231	GTATAATACCTCTACATGGCTGATTATGAAAACAAT	;;<;<<====3=====5===================	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_610:3:84:101:328	83	chr1	673	99	35M	=	480	-228	TATAATACCTCTACATGGCTGATTATGAAAACAAT	<<<<<<<<:<<<<<<<<<6<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_65:5:30:92:753	147	chr1	673	99	35M	=	497	-211	TATAATACCTCTACATGGCTGATTATGAAAACAAT	<<<<<<;<<<<<<:<<<<;<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS112_32:8:88:90:59	73	chr1	674	37	35M	=	674	0	ATAATACCTCTACATGTCTGATTATGAAAACAATG	<<<<<<<4;7;<<<;;47;&9..1;6&4<755;1;	MF:i:64	Aq:i:0	NM:i:1	UQ:i:19	H0:i:0	H1:i:1
+EAS112_32:8:88:90:59	133	chr1	674	0	*	=	674	0	TGCACCTCCCTGTTCACCTAGATGCTAGGAGGACA	=7595=92=72.=+5(:4=9092((.2&(&%07%.	MF:i:192
+B7_593:1:12:158:458	147	chr1	675	84	36M	=	503	-208	TAATAATGCTACATGGATGATTATGAAATCAATGTT	++++++$((+*+++++++++++++&+++++++++++	MF:i:18	Aq:i:15	NM:i:5	UQ:i:40	H0:i:0	H1:i:0
+B7_593:4:28:781:723	99	chr1	676	99	36M	=	855	215	AATACCTCTACATGGCTGATTATGAAAACAATGTTC	<<<<<<<<<7<<<;;<<;;<<;<5<4<7<;7<+:<9	MF:i:18	Aq:i:70	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_81:2:27:856:401	163	chr1	679	99	35M	=	871	227	ACCTCTACATGGCTGATTATGAAAACAATGTTCCC	======6===;2==;===;=+=92=;5+=&556:6	MF:i:18	Aq:i:65	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_26:7:245:323:744	83	chr1	679	99	35M	=	499	-215	ACCTCTACATGGCTGATTATGAAAACAATGTTCCC	/.848299;&;9;9;=2.=7========;;=====	MF:i:18	Aq:i:66	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_597:7:31:948:254	99	chr1	680	99	35M	=	849	204	CCTCTACATGGCTGATTATGAAAACAATGTTCCCC	<<<<<<<<<<<<<<<<<<<;<<<<<:<<8<;;;;<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_65:6:277:590:364	83	chr1	681	99	35M	=	503	-213	CTCTACATGGCTGATTATGAAAACAATGTTCCCCA	:::<<<<;<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_32:7:201:959:19	147	chr1	681	99	35M	=	493	-223	CTCTACATGGCTGATTATTAAAACAATGTTCCCCA	;4;.9<:0&/<5<::<<9/.<<<<<<<<<<<<;<<	MF:i:18	Aq:i:41	NM:i:1	UQ:i:14	H0:i:0	H1:i:1
+EAS56_61:8:7:171:402	147	chr1	682	99	35M	=	489	-228	TCTACATGGCTGATTATGAAAACAATGTTCCCCAG	:086::::847:<7<<7<<<<<<;7<<;<<<<7<<	MF:i:18	Aq:i:70	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_610:4:67:317:249	99	chr1	683	26	35M	=	840	192	CTACATGGCTGATTATGAAATCTATGTTCCCCATA	<<<<<<;<<<<;:;<<7;<<.<&3<;;<<(;;6.<	MF:i:18	Aq:i:26	NM:i:3	UQ:i:31	H0:i:0	H1:i:0
+EAS51_64:4:189:467:475	147	chr1	683	99	35M	=	493	-225	CTACATGGCTGATTATGAAAACAATGTTCCCCAGA	*.;*;7<75<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_67:8:46:900:610	147	chr1	684	99	35M	=	491	-228	TACATGGCTGATTATGAAAACAATGTTCCCCAGAT	<;5<;<<<;<<<<<<;<<<<<<<<<<8<<<<<8<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_28:1:232:351:909	99	chr1	685	80	36M	=	843	194	ACATGGCTGATTATGAAATCAATGTTCCCCAGATGC	<<<<<99<<<<<<99<7<'<9<<<6<<+<;7;<<&;	MF:i:18	Aq:i:39	NM:i:2	UQ:i:11	H0:i:0	H1:i:1
+EAS139_11:6:11:285:1567	83	chr1	685	99	35M	=	525	-195	ACATGGCTGATTATGAAAACAATGTTCCCCAGATA	<8<4<<<;<<;<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:47	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS188_7:2:172:622:707	147	chr1	685	99	35M	=	511	-209	ACATGGCTGATTATGAAAACAATGTTCCCCAGATA	92<3996;<<<<<<<<<<<<<<<<<<<;<<<<<<<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_597:5:6:882:784	83	chr1	686	99	35M	=	496	-225	CATGGCTGATTATGAAAACAATGTTCCCCAGATAC	4;7<;64<<:<<4<<<<<;<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_71:7:80:760:490	147	chr1	686	99	35M	=	520	-201	CATGGCTGATTATGAAAACAATGTTCCCCAGATAC	%::::+<<<;<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_19:4:68:1122:79	147	chr1	687	99	40M	=	528	-199	ATGGCTGATTATGAAAACAATGTTCCCCAGATACCATCCC	::77*:1<<<<<<<<<<<<<<<:;<<<;<<<<<<8<<<<<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_93:1:264:988:663	99	chr1	688	99	35M	=	875	222	TGGCTGATTATGAAAACAATGTTCCCCAGATACCA	<<<<<<<<<<<1<4<<<4<<0<;<-<74*(<&51-	MF:i:18	Aq:i:60	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_73:5:3:233:911	163	chr1	688	99	35M	=	868	215	TGGCTGATTATGAAAACAATGTTCCCCAGATACCA	<<<<<<<<<<<<<<<<<;<<<<<<<<<<;<;<<;<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_59:6:187:925:547	99	chr1	689	99	35M	=	857	203	GGCTGATTATGAAAACAATGTTCCCAAGATACCAT	43<<<:9<;;;:7<<<<6<:<8<-4-/,81<(48:	MF:i:18	Aq:i:37	NM:i:1	UQ:i:12	H0:i:0	H1:i:1
+EAS56_65:5:75:637:650	163	chr1	691	99	35M	=	868	212	CTGATTATGAAAACAATGTTCCCCAGATACCATCC	<<<<<<<<<<<<<<<<<<<<<<<<<;<<<<<<<<:	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS192_3:3:27:973:518	147	chr1	691	99	35M	=	549	-177	CTGATTATGAAAACAATGTTCCCCAGATACCATCC	+<<<<<<9<<<<<<<<<<<;<;<<<<<<<<<<<<<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_3:6:20:492:850	147	chr1	694	10	35M	=	526	-203	AGTATGAAAACAATGTTCCCCAGATGCCGTCCCGG	:.5:+.;;&91:;79:766:1:9+6&:1&&:+:))	MF:i:18	Aq:i:10	NM:i:4	UQ:i:31	H0:i:0	H1:i:0
+EAS51_64:4:318:345:156	83	chr1	695	99	35M	=	522	-208	TTATGAAAACAATGTTCCCCAGATACCATCCCTGT	;8<8<<<<<;<<:<<;<;77<<<<<;<<;<<<<<<	MF:i:18	Aq:i:39	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_610:3:5:863:302	99	chr1	698	99	35M	=	866	203	TGAAAACAATGTTCCCCAGATACCATCCCTGTCTT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<9<<<<<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_67:4:7:526:343	147	chr1	698	99	35M	=	515	-218	TGAAAACAGTGTTCCCCAGATACCATCCCTGTCTT	(7:;;;<<;;;<1<1<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:43	NM:i:1	UQ:i:26	H0:i:0	H1:i:1
+EAS114_26:2:73:513:102	99	chr1	698	99	35M	=	868	205	TGAAAACAATGTTCCCCAGATACCATCCCTGTCTT	===========================;=======	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_11:2:6:251:1557	83	chr1	700	99	35M	=	526	-209	AAAACAATGTTCCCCAGATACCATCCCTGTCTTAC	<<<<<<<<<<<<6:<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:78	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_78:7:147:64:416	99	chr1	701	99	35M	=	870	204	AAACAATGTCCCCCAGATACCATCCCTGTCTTACT	<<<<<<<<<<<<<<<;<<<<<;<<<<;;:<;;;;;	MF:i:18	Aq:i:47	NM:i:1	UQ:i:27	H0:i:0	H1:i:1
+B7_595:3:297:637:86	163	chr1	704	99	35M	=	869	200	CAATGTTCCCCAGATACCATCCCTGTCTTACTTCC	<<<<<<<<<<<<;+<+;<;<:<<<<<9<<957<;(	MF:i:18	Aq:i:68	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_61:6:160:272:398	163	chr1	705	99	35M	=	891	221	AATGTTCCCCAGATACCATCCCTGTCTTACTTCCA	9<<<3<<<<<<<<<<<9<<;8<<<<;<+.;;89..	MF:i:18	Aq:i:68	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_1:8:4:679:110	147	chr1	705	99	35M	=	549	-191	AATGTTCCCCAGATACCATCCCTGTCTTACTTCCA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_30:6:163:312:891	147	chr1	709	99	35M	=	543	-201	TTCCCCAGATACCGTCCCTGTCTTACTTCCAGCTC	0.<;;8<<<0<<<<<<<<<<6<<<<<<8<<<<<<<	MF:i:18	Aq:i:43	NM:i:1	UQ:i:27	H0:i:0	H1:i:1
+EAS114_28:3:78:773:660	83	chr1	711	99	36M	=	534	-213	CCCCAGATACCATCCCTGTCTTACTTCCAGCTCCCC	7<;7<<<7;9<<8;<<<<<<;<<<<<<<<<<7<<<<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS218_4:5:63:875:1339	163	chr1	711	99	35M	=	879	203	CCCCAGATACCATCCCTGTCTTACTTCCAGCTCCC	<<<<<<<<<<<<<<<<<<<<<<9<<<<<<<<<<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS188_7:7:243:876:758	147	chr1	712	99	35M	=	541	-206	CCCAGATACCATCCCTGTCTTACTTCCAGCTCCCC	0%3<1;.70;3363;31;<<<<<<6<<<;<<<<<<	MF:i:18	Aq:i:47	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_593:4:104:153:698	163	chr1	713	99	36M	=	896	219	CCAGATACCATCCCTGTCTTACTTCCAGCTCCCCAG	;<<<<<<;6<<<<<<<<<<;<<<<;<;;;<.<::50	MF:i:18	Aq:i:68	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS112_34:7:86:498:373	163	chr1	716	99	35M	=	894	213	GATACCATCCCTGTCTTACTTCCAGCTCACCAGAG	<<<<<<<<<<<<<<<<<<<<<<<5:<<<:<;7+67	MF:i:18	Aq:i:69	NM:i:1	UQ:i:25	H0:i:1	H1:i:0
+EAS1_95:6:87:734:888	163	chr1	717	99	35M	=	900	218	ATACCATCCCTGTCTTACTTCCAGCTCCCCAGAGG	===========;8=========;;=;====;;3(;	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_26:5:238:31:968	147	chr1	717	99	35M	=	534	-218	ACACCATCCCTGTCTTACTTCCAGCTCCCCAGAGG	=(.7=5%===9:7==+==77===============	MF:i:18	Aq:i:69	NM:i:1	UQ:i:7	H0:i:1	H1:i:0
+EAS54_65:3:290:558:349	99	chr1	719	99	35M	=	869	185	ACCATCCCTGTCTTACTTCCAGCTCCCCAGCGGGA	<<<;<<;<;<188<<<8::<686+4:<<6:&3)*&	MF:i:18	Aq:i:59	NM:i:1	UQ:i:5	H0:i:1	H1:i:0
+EAS114_28:5:206:671:49	83	chr1	719	99	36M	=	557	-198	ACCATCCCTGTCTTACTTCCAGCTCCCCAGAGGGAA	;<<<<<<<;<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:67	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_95:2:278:918:892	147	chr1	720	99	35M	=	541	-214	CCATCCCTGTCTTACTTCCAGCTCCCCAGAGGGAA	=6=3=<===&=========================	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_591:1:191:462:705	147	chr1	721	99	36M	=	545	-212	CATCCCTGTCTTACTTCCAGCTCCCCAGAGGGAAAG	<<'<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:47	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_28:4:9:55:730	83	chr1	722	99	36M	=	540	-218	ATCCCTGTCTTACTTCCAGCTCCCCAGAGGGAAAGC	<:<;;<6<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:66	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_105:7:45:462:455	163	chr1	723	99	35M	=	874	186	TCCCTGTCTTACTTCCAGCTCCCCAGACGGAACGC	<<<<<<8<<<;<;<<<;<<<<<<<6;8&:80;733	MF:i:18	Aq:i:43	NM:i:2	UQ:i:27	H0:i:0	H1:i:1
+EAS114_28:2:149:650:44	163	chr1	726	99	36M	=	902	212	CTGTCTTACTTCCAGCTCCCCAGAGGGAAAGCTTTC	<<<<<<<<<<<<<<<<<<<<<<<<<;6<<;<<7<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_105:1:297:283:948	83	chr1	727	99	35M	=	550	-212	TGTCTTACTTCCAGCTCCCCAGAGGGAAAGCTTTC	6;;3;6<<66<<<<<;<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:68	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS219_1:3:33:1168:1762	147	chr1	728	99	35M	=	552	-211	GTCTTACTTCCAGCTCCCCAGAGGGAAAGCTTTCA	79<9;3<<<4<<<97<;;<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_57:1:228:182:717	147	chr1	729	99	35M	=	563	-201	TCTTACTTCCAGCTCCCCAGAGGGAAAGCTTTCAA	778;8;474<<<;2;;<2<<<<<<<<;<;;9<<<<	MF:i:18	Aq:i:66	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_1:8:8:1351:1986	163	chr1	729	99	35M	=	911	217	TCTTACTTCCAGATCCCCAGAGGGAAAGCTTTCAA	<<<<<<<<<<<<-<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:47	NM:i:1	UQ:i:12	H0:i:0	H1:i:1
+EAS51_64:4:163:31:455	163	chr1	730	99	35M	=	886	191	CTTACTTCCAGCTCCCCAGAGGGACAGCTNNCAAC	<+<<<<<<<;0+<<<<;06070-9(0(9<!!5)05	MF:i:18	Aq:i:31	NM:i:3	UQ:i:7	H0:i:0	H1:i:1
+EAS54_61:6:126:541:194	83	chr1	730	97	35M	=	540	-225	AGTACGACCAGCTCCCCAGAGGGAAAGCTTTCAAC	+%&:/+(46=47&71/2==;=;8====28212===	MF:i:18	Aq:i:43	NM:i:4	UQ:i:40	H0:i:1	H1:i:0
+EAS51_62:7:178:286:414	163	chr1	731	99	35M	=	907	211	TTACTTCCAGCTCCCCAGAGGGAAAGCTTTCAACG	<<<<<<<<<<<<<<<<8<<<<<<<<<1<<<1;998	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_30:3:35:361:546	163	chr1	731	99	35M	=	892	196	TTACTTCCAGCTCCCCAGAGGGAAAGCTTTCAACG	<<<<<<<<<<<<<<<<;<5<<<<<;<2<<<:<8<4	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_3:4:90:247:212	147	chr1	733	99	35M	=	567	-201	ACTTCCAGCTCCCCAGAGGGAAAGCTTTCAACGCT	7655:;87;<;;;8<<<<<<<<<<<;<<<<<<<<<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS192_3:7:149:354:667	99	chr1	734	99	35M	=	888	189	CTTCCAGCTCCCCAGAGGGAAAGCTTTCAACGCTT	<<<<<<<<<<<<<<<<<<<><<<<<<<<;<:<<<<	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_591:2:240:603:890	83	chr1	740	99	36M	=	590	-186	GCTCCCAAGAGGGAAAGCTTTCAACGCTTCTAGCCA	;+&+//&<<<<<<<<<<9<<<8<<<<9<<<<<<<<<	MF:i:18	Aq:i:66	NM:i:1	UQ:i:5	H0:i:1	H1:i:0
+B7_591:7:129:956:115	163	chr1	740	99	36M	=	927	223	GCTCCCCAGAGGGAAAGCTTTCAACGCTTCTAGCCA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;877-	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_53:4:168:528:288	83	chr1	740	99	35M	=	570	-205	GCTCCCCAGAGGGAAAGCTTTCAACGCTTCTAGCC	8<%<31;<<;<;<<<<<<<;<<<<<<<<<<;<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_65:8:275:851:240	147	chr1	743	99	35M	=	561	-217	CCCCAGAGGGAAAGCTTTCAACGTTTCTAGCCATT	66614/&3616630666&66666&66666868666	MF:i:18	Aq:i:31	NM:i:1	UQ:i:5	H0:i:0	H1:i:1
+EAS188_7:6:205:873:464	147	chr1	743	99	35M	=	552	-226	CCCCAGAGGGAAAGCTTTCAACGCTTCTAGCCATT	<-((+:+;289<--;<;-;<:;;<<<;;<<<<<<<	MF:i:18	Aq:i:63	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_65:6:37:610:260	163	chr1	745	99	35M	=	913	203	CCAGAGGGAAAGCTTTCAACGCTTCTAGCCATTTC	<<<;<;<<7<<<<<<<<<<<<<<;6<963;;;3;1	MF:i:18	Aq:i:68	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS192_3:7:93:945:176	147	chr1	745	99	35M	=	582	-198	CCAGAGGGAAAGCTTTCAACGCTTCTAGCCATTTC	6;;;8<<3<<8.<;6)<<<<<9<<<<<<<<<<<<<	MF:i:18	Aq:i:70	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_593:6:61:628:681	83	chr1	746	99	36M	=	586	-196	CAGAGGGAAAGCTTTCAACGCTTCTAGCCATTTCTT	95<<<<<<<<;<<<<;<<<:<<;;<<<<<<<<<<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_65:7:288:552:440	83	chr1	747	87	35M	=	560	-222	AGAGGGAACGCTTTCAACTCTTCTAGCCATTTCTT	9<<%'%<<.2<<<<<<<<5:<<<<<<<<<<<<<<<	MF:i:18	Aq:i:26	NM:i:2	UQ:i:33	H0:i:0	H1:i:0
+EAS56_53:2:170:265:818	163	chr1	748	10	35M	=	920	207	GAGGGGAAGCTTTCAACGCTTCTAGCACTTTCTTT	<<<<<(5/959<8.<9<8<<<2<&59&&:22:8+(	MF:i:18	Aq:i:10	NM:i:3	UQ:i:17	H0:i:0	H1:i:0
+B7_595:2:251:121:479	83	chr1	750	99	35M	=	572	-213	GGGAAAGCTTTCAACGCTTCTAGCCATTTCTTTTG	<<<<<6'..663;&<<;<<9<<<9<<<<<<<<<<<	MF:i:18	Aq:i:65	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_1:8:67:1797:1931	147	chr1	750	99	35M	=	562	-223	GGGAAAGCTTTCAACGCTTCTAGCCATTTCTTTTG	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_103:2:226:302:758	83	chr1	751	99	35M	=	556	-230	GGAAAGCTTTCAACGCTTCTAGCCATTTCTTTTGG	;<<<<9;<<<<<<<<<<7<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:33	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_32:2:163:618:570	83	chr1	751	99	35M	=	571	-215	GGAAAGCTGTCAACGCTTCTAGCCATTTCTTTTGG	<9774<88&:8<:8<8:8<8<<<<<;88<88<<<<	MF:i:18	Aq:i:41	NM:i:1	UQ:i:5	H0:i:0	H1:i:1
+EAS1_97:3:73:292:429	99	chr1	752	99	35M	=	920	203	GAAAGCTTTCAACGCTTCTAGCCATTTCTTTTTGC	<<<<<<<<<<7<<;<<<<<<<2<<<5<<<<<:%)<	MF:i:18	Aq:i:69	NM:i:1	UQ:i:4	H0:i:1	H1:i:0
+EAS1_108:3:82:356:253	99	chr1	752	99	35M	=	927	210	GAAAGCTTTCAACGCTTCTAGCCATTTCTTTTGGC	===================<========;===39=	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_30:6:62:386:959	147	chr1	752	99	35M	=	594	-193	AAAAGCTTTCAACGCTTCTAGCCATTTCTTTTGGC	%;71131((<<6<92(+<1<<;<-3<8<<;<;;<<	MF:i:18	Aq:i:57	NM:i:1	UQ:i:4	H0:i:1	H1:i:0
+EAS51_62:3:263:74:407	83	chr1	754	99	35M	=	574	-215	AAGCTTTCAACGCTTCTAGCCATTTCTTTTGGCAT	;;88<::+;<)<5<<:<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:68	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_597:3:67:620:344	99	chr1	755	99	35M	=	905	185	AGCTTTCAACGCTTCTAGCCATTTCTTTTGGCATT	<<<<2<:2<<<<<<7<<<<:<<*<<<<<<***3<<	MF:i:18	Aq:i:33	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_610:6:148:776:486	83	chr1	755	99	35M	=	578	-212	AGCTTTCAACGCTTCTAGCCATTTCTTTTGGCATT	;:<<<;<<;<<<<<;<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_61:3:150:933:810	83	chr1	755	99	35M	=	593	-197	AGCTTTCAACGCTTCTAGCCATTTCTTTTGGCATT	:89===:=:=;;==;====================	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_64:4:102:467:897	99	chr1	756	97	35M	=	940	219	GCTTTCAACGCTTCTAGCCATTTCTTTTGTCTTTT	<<<<9<<<<9<2<<<&,/</<<<<7<<;&&<$;*<	MF:i:18	Aq:i:37	NM:i:2	UQ:i:8	H0:i:1	H1:i:0
+EAS114_39:1:12:884:219	147	chr1	756	99	35M	=	584	-207	GCTTTCAACGCTTCTAGCCATTTCTTTTGGCATTT	7;::<:<<<7<<:<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_19:1:40:1596:1433	147	chr1	756	99	40M	=	587	-209	GCTTTCAACGCTTCTAGCCATTTCTTTTGGCATTTGCCTT	-:8:1841<4;<88<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:70	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_610:5:7:761:623	99	chr1	757	99	35M	=	938	216	CTTTCAACGCTTCTAGCCATTTCTTTTGGCATTTG	<<<<<<<<<<<<<8<<<<;;<0<<<<<;;<;<;;&	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_65:4:246:313:499	147	chr1	757	99	35M	=	592	-200	CTTTAAACGCTTCTAGCCATTTCTTTTGGCATTTG	+;77%;;;&:;:7;<<<<<6<:<<<<<<<<<<<<<	MF:i:18	Aq:i:65	NM:i:1	UQ:i:4	H0:i:1	H1:i:0
+EAS139_11:6:89:1151:1878	147	chr1	757	99	35M	=	587	-205	CTTTCAACGATTCTAGCCATTTCTTTTGGCATTTG	8<66,,<<<<<<:<<<<<9<<<:<<<<<<<<<<<<	MF:i:18	Aq:i:43	NM:i:1	UQ:i:27	H0:i:0	H1:i:1
+EAS54_71:4:165:397:25	83	chr1	759	99	34M	=	576	-217	TTCAACGCTTCTAGCCATTTCTTTTGGCATTTGC	&(33'60;-'+'<7;<<*3-<;;183<<<;<;<<	MF:i:18	Aq:i:54	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_3:2:59:1576:946	147	chr1	761	99	35M	=	578	-218	CAACGCTTCTAGCCATTTCTTTTGGCATTTGCCTT	9<<<9<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_32:7:256:407:470	163	chr1	762	99	35M	=	939	212	AACGCTTCTAGCCATTTCTTTTGGCATTTGCCTTC	<<<<<<<<;<;<<<<<<<<<;;<</<<;;83;7;9	MF:i:18	Aq:i:63	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_593:3:148:437:481	163	chr1	764	99	36M	=	949	221	CGCTTCTAGCCATTTCTTTTGGCATTTGCCTTCAGA	<<<<<<<<<<<<<<<<<<<<<;<<<<<;<<<<;0;8	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_65:8:140:924:923	83	chr1	767	99	35M	=	597	-205	TTTTAGCCATTTCTTTTGGCATTTGCCTTCAGACC	<<&<<;;<;<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:1	UQ:i:5	H0:i:1	H1:i:0
+EAS1_103:4:143:560:194	99	chr1	768	99	35M	=	946	213	TCTAGCCATTTCTTTTGGCATTTGCCTTCAGACCC	<<<<;;<<<<<<<<<<<6<;<<<<;;<<;9<999<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_57:2:178:192:499	83	chr1	768	99	35M	=	582	-221	TCTAGCCATTTCTTTTGGCATTTGCCTTCAGACCC	86<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:70	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS219_1:3:4:1620:413	147	chr1	768	99	35M	=	588	-215	TCTAGCCATTTCTTTTGGCATTTGCCTTCAGACCC	-<<<7<<<<<<<<<;<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:66	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_589:2:73:730:487	147	chr1	770	99	35M	=	604	-201	TAGCCATTTCTTTTGGCATTTGCCTTCAGACCCTA	<;;<<2;<;<<<;0<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_64:4:179:389:585	163	chr1	770	24	35M	=	953	218	TGGCCACTTTTTATCGCATTTCCCTTTAGAACCTA	<.4<9.4+.+'&-220<+<4<6<<20*6;<0(9<%	MF:i:130	Aq:i:24	NM:i:7	UQ:i:103	H0:i:0	H1:i:0
+B7_595:1:252:19:955	147	chr1	771	84	35M	=	596	-210	AGCCAGTTCTTTTGGCATTTGCCTTCAGACCCTCC	<8<884<<<<<<68<<<<<<<2<;<<;<+<<<;<<	MF:i:18	Aq:i:41	NM:i:2	UQ:i:46	H0:i:0	H1:i:1
+EAS54_71:4:169:862:829	83	chr1	772	99	34M	=	611	-195	GCCATTTCTTTTGGCATTTGCCTTCAGACCCTAC	,1<6<<<<<7<<<<<<<<<<<<<<<<<7<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_103:6:7:858:437	147	chr1	773	99	35M	=	593	-215	CCATTTCTTTTGGCATTTGCCTTCAGACCCTACAC	7;<4;;:;80<;<;<<<<<<:<<;<<<;;<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_30:4:183:852:253	83	chr1	773	99	35M	=	599	-209	CCATTTCTTTTGGCATTTGCCTTCAGACCCTACAC	;<9<;<<<<<<<<;<<<<<;<<<;<<<<;<<<<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_32:4:20:41:138	147	chr1	774	99	35M	=	615	-194	CATTTCTTTTGGCATTTGCCTTCAGACCCTACACG	;;;<;<<<::<<<<<<<;<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_63:5:123:998:248	83	chr1	776	99	35M	=	589	-222	TTTCTTTTGGCATTTGCCTTCAGACCCTACACGAA	;:;5;<;:<9<<<<<:<;<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_593:4:142:63:937	83	chr1	777	99	36M	=	609	-204	TTCTTTTGGCATTTGCCTTCAGACCCTACACGAATG	;;;<;<<<<;<<<<<;:<<<<<<<;<<<<<<<<<<<	MF:i:18	Aq:i:78	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_61:3:20:762:748	83	chr1	777	99	35M	=	591	-221	TTCTTTTGGCATTTGCCTTCAGACCCTACACGAAT	=:747;7=;;==7=;==7===7==7;=========	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_59:3:149:953:349	99	chr1	777	99	35M	=	915	173	TTCTTTTGGCATTTGCCTTCAGACCCTACACGAAT	<<<<<<<<;<<<<<<<<<<<;7:<:<<:<:;;::;	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_597:3:46:981:766	163	chr1	778	99	35M	=	933	190	TCTTTTGGCATTTGCCTTCAGACCCTACACGAATG	<<<<<<<<<<<<<;<<<<<-<;<<<<-<-<;-:6;	MF:i:18	Aq:i:68	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_81:6:204:779:181	83	chr1	779	99	35M	=	598	-216	CTTTTGGCATTTGCCTTCAGACCCTACACGAATGC	;:;/*<:<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:68	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_11:6:11:360:1577	147	chr1	781	99	35M	=	606	-210	TTTGGCATTTGCCTTCAGACCCTACACGAATGCGT	1<1<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_81:2:5:491:391	99	chr1	782	99	35M	=	917	170	TTGGCATTTGCCTTCAGACCCTACACGAATGCGTC	=========;===;==:4=========;3;==7;=	MF:i:18	Aq:i:62	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_78:7:186:199:927	99	chr1	783	99	35M	=	802	54	TGGCATTTGCCTTCAGACCCTACACGAATGCGTCT	<77<<<<2<;<<<<<06<<<<<<<<60<<684/6&	MF:i:18	Aq:i:57	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_67:8:19:855:491	147	chr1	783	99	35M	=	631	-187	TGGCATTTGCCTTCAGACCCTACACGAATGCGTCT	8<<<<;:<<<<:<<<<<:<;;<<<<<<<;<<<;<;	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_593:1:36:485:632	83	chr1	784	99	36M	=	610	-210	GGCATTTGCCTTCAGACCCTACACGAATGCGTCTCT	0;;;<<;<<<;<<<<<<<<<<<<<;<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_59:2:177:266:842	83	chr1	784	99	35M	=	599	-220	GGCATTTGCCTTCAGACCCTACACGAATGCGTCTC	<9<<6;9<;9;;<<<<;;;9<<<<<<<<<<<<<<<	MF:i:18	Aq:i:66	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_1:8:65:1928:1125	147	chr1	784	99	35M	=	588	-231	GGCATTTGCCTTCAGACCCTACACGAATACGTCTC	<+<<<2<4<<<0<<4<<<<<6<<<6<<<'<<<<0<	MF:i:18	Aq:i:41	NM:i:1	UQ:i:6	H0:i:0	H1:i:1
+EAS221_3:4:66:584:407	163	chr1	785	99	35M	=	954	204	GCATTTGCCTTCAGACCCTACACGAATGCGTCTCT	<<<*9<9<<<1<<<<<<<<*<59<4<)<2<<<<<<	MF:i:18	Aq:i:68	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_71:6:172:896:83	147	chr1	786	99	35M	=	604	-217	CATTTGCCTTCAGACCCTACACGAATGCGTCTCTA	;<.5.;;<+;<<<<<<<4<<<<<<<;<<<<<;<<<	MF:i:18	Aq:i:70	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:3:2:1200:1076	83	chr1	786	99	35M	=	629	-192	CATTTGCCTTCAGACCCTACACGAATGCGTCTCTA	7779779;9;:;;4;;9;;:7;<<<7;;;:<;<<;	MF:i:18	Aq:i:67	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_99:3:135:543:760	147	chr1	787	99	35M	=	619	-203	ATTTGCCTTCAGACCCTACACGAATGCGTCTCTAC	;;.;;8;<8;<<32;<<<<<7<<<<<9<<<<<<<<	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_19:3:5:538:401	147	chr1	788	99	40M	=	624	-204	TTTGCCTTCACACCCTACACGAATGCGTCTCTGCCACAGG	671&7::49:&0<<<(<::<&<<<:<<<<<<<&<<<<1<<	MF:i:18	Aq:i:39	NM:i:2	UQ:i:10	H0:i:0	H1:i:1
+EAS54_71:6:215:133:909	147	chr1	789	99	35M	=	631	-193	TTGCCTTCAGACCCTACACGAATGCGTCTCTACCA	7758;<;<;8<<<<;<;<<<<<:;<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_30:2:30:887:404	83	chr1	789	99	35M	=	600	-224	TTGCCTTCAGACCCTGCACGAATGCGTCTCTACCA	<<<<5<;::<<<;<<.<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:45	NM:i:1	UQ:i:13	H0:i:0	H1:i:1
+EAS219_1:1:5:497:687	147	chr1	789	99	35M	=	607	-217	TTGCCTTCAGACCCTACACGAATGCGTCTCTACCA	<8<<8<<<;<<<<<;<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_65:5:131:742:561	83	chr1	790	99	35M	=	620	-205	TGCCTTCAGACCCTACACGAATGCGTCTCTACCAC	<:<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:78	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_11:3:65:556:1505	83	chr1	790	99	35M	=	593	-232	TGCCTTCAGACCCTACACGAATGCGTCTCTACCAC	<6<8<<4<8;;;<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_57:4:233:478:792	147	chr1	791	99	35M	=	634	-192	GCCTTCAGACCCTACACGAATGCGTCTCTACCACA	6<;9:<<9-<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_65:6:66:257:524	99	chr1	791	99	35M	=	959	203	GCCTTCAGACCCTACACGAATGCGTCTCTACCACC	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<%	MF:i:18	Aq:i:73	NM:i:1	UQ:i:4	H0:i:1	H1:i:0
+EAS56_53:4:154:762:630	83	chr1	792	99	35M	=	604	-223	CCTTCAGACCCTACACGAATGCGTCTCTACCACAG	<<-::<91<<<<;<;<<<<;<<<<<<<<;<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS112_34:8:4:841:339	83	chr1	793	99	35M	=	646	-182	CTTCAGACCCTACACGAATGCGTCTCTACCACAGG	77-):22<<<33;<5<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:66	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS218_1:6:66:1282:1215	147	chr1	794	99	35M	=	627	-202	TTCAGACCCTACACGAATGCGTCTCTACCACAGGG	::;<;<<<<:<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_610:2:194:688:289	147	chr1	795	99	35M	=	631	-199	TCAGACCCTACACGAATGCGTCTCTACCACAGGGG	;8;%28<;<<<<<<<<;<<<<;<<<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_97:8:36:927:478	147	chr1	798	99	35M	=	610	-223	GACCCTACACGAATGCGTCTCTACCACAGGGGGCT	,6;;;3;<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_99:8:99:756:130	83	chr1	798	99	35M	=	606	-227	GACCCTACACGAATGCGTCTCTACCACAGGGGGCT	;;<<;;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_62:5:192:716:235	83	chr1	798	99	35M	=	651	-182	GACCCTACACGAATGCGTCTCTACCACAGGGGGCT	<5<<<8<:<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS219_FC30151:5:63:424:1643	83	chr1	798	99	35M	=	614	-219	GACCCTACACGAATGCGTCTCTACCACAGGGGGCT	9+<<<+7<<<<<<<<<<<<<<<<<8<<<<<<<<<<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_81:8:14:360:580	99	chr1	799	99	35M	=	963	199	ACCCTACACGAATGCGTCTCTACCACAGGGGGCGG	===========3===;5<==8;====79==.=5'5	MF:i:18	Aq:i:68	NM:i:1	UQ:i:6	H0:i:1	H1:i:0
+EAS51_78:7:186:199:927	147	chr1	802	99	35M	=	783	-54	CTACGCGAATGCGTCTCTACCACAGGGGGCTGCGC	-;++)6<*8+;&<&/<<<<7<<71<<<<<6<<<7<	MF:i:18	Aq:i:57	NM:i:1	UQ:i:8	H0:i:1	H1:i:0
+EAS139_19:3:4:1502:1911	83	chr1	802	99	40M	=	652	-190	CTACACGAATGCGTCTCTACCACAGGGGGCTGCGCGGTTT	:+:::5/;99<;<&<*<-9<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:68	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_99:3:187:791:153	99	chr1	803	99	35M	=	958	190	TACACGAATGCGTCTCTACCACAGGGGGCTGCGCG	<<<<<<<<<<<<<<<<<<<<<:+;;<;<88*6;68	MF:i:18	Aq:i:68	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_11:4:63:527:1923	99	chr1	803	99	35M	=	981	213	TACACGAATGCGTCTCTACCACAGGGGGCTGCGCG	<<<<<<<<<<<<<<<<<:<<<<3<<<<<<<<<<<<	MF:i:18	Aq:i:45	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_81:2:31:98:804	99	chr1	805	99	35M	=	982	212	CACGAATGCGTCTCTACCACAGGGGGCTGCGCGGC	=======9===;============5=;9=;=;==&	MF:i:18	Aq:i:74	NM:i:1	UQ:i:5	H0:i:1	H1:i:0
+EAS218_4:7:89:1487:520	163	chr1	805	99	35M	=	997	227	CACGAATGCGTCTCTACCACAGGGGGCTGCGCGGT	8<<<6/<<<<<<<<<:<<8<:<<3<<:668<86<3	MF:i:18	Aq:i:70	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS220_1:4:69:88:1154	99	chr1	805	99	35M	=	992	222	CACGAATGCGTCTCTACCACAGGCGGCTGCGCGGT	<<<<<<<<<<<<<<<<<<<<<<<2<<<<:<<<<<7	MF:i:18	Aq:i:47	NM:i:1	UQ:i:17	H0:i:0	H1:i:1
+EAS114_26:1:99:212:522	163	chr1	806	99	35M	=	1002	231	ACGAATGCGTCTCTACCACAGGGGGCTGCGCGGTT	================8==;====;=;===1==:8	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_610:7:35:378:681	147	chr1	812	99	35M	=	632	-215	GCGTCTCTACCACAGGGGGCTGCGCGGTTTCCCAT	:<5-<);;;<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_105:3:182:404:693	83	chr1	812	99	35M	=	646	-201	GCGTCTCTACCACAGGGGGCTGCGCGGTTTCCCAT	<;7;;4<<<<<<<7<<7<<<<<<<<<8<<<<<<<<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_57:3:119:761:239	99	chr1	813	99	35M	=	999	221	CGTCTCTACCACAGGGGGCTGCGCGGTTTCCCATC	<<<<<<<<<<<<6<<<<<<;<2<<<<;<<<<<;;<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_108:6:165:464:123	147	chr1	814	99	35M	=	650	-199	GTCTCTACCACAGGGGGCTGCGCGGTTTCCCATCA	9;<)<<%<<9<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_19:5:40:758:116	83	chr1	814	99	40M	=	632	-222	GTCTCTACCACAGGGGGCTGCGCGGTTTCCCATCATGAAG	25/8/:<75:2<<<<<<7<<;<<<<<<<88;<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_95:7:55:506:125	99	chr1	817	99	35M	=	982	200	TCTACCACAGGGGGCTGCGCGGTTTCCCATCATGA	<<<<<<<<<;<9<;<<;558<<<<5(5*<<<<<51	MF:i:18	Aq:i:35	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_105:6:162:594:858	147	chr1	818	99	35M	=	634	-219	CTACCACAGGGGGCTGCGCGGTTTCCCATCATGAA	90;<99;==99==;4=:========;=====;===	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS219_FC30151:3:55:74:1040	99	chr1	818	99	35M	=	975	192	CTACCACAGGGGGCTGCGCGGTTTCCCATCATGAA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<:<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_39:7:100:708:1984	99	chr1	819	99	35M	=	1015	231	TACCACAGGGGGCTGCGCGGTTTCCCATCATGAAG	<<<<<<<<<<<<<<<<<<<<<<<<<<;<<<<<7%:	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_11:7:92:367:1495	163	chr1	820	99	35M	=	987	202	ACCACAGGGGGCTGCGCGGTTTCCCATCATGAAGC	<<<<<<<<<<<<<<<<<<<<<<<<<<<<6<<<6<<	MF:i:18	Aq:i:78	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS218_1:6:49:905:27	163	chr1	821	68	35M	=	1000	214	CCACAGGGGGCTGCGCGGTTTCCCATCCTGAAGCA	<<;<.89<9.<2<9<:91+447.9,04&000(,+(	MF:i:18	Aq:i:31	NM:i:1	UQ:i:5	H0:i:0	H1:i:1
+EAS218_4:7:87:964:826	163	chr1	822	99	35M	=	999	212	CACAGGGGGCTGCGCGGTTTCCCATCATGAAGCAC	<<<<<<<<<<<<<<<<<<<<<<<<<<1<<8;4;;<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS220_1:8:38:1576:1923	163	chr1	822	99	35M	=	987	200	CACAGGGGGCTGCGCGGTTTCCCATCATGAAGCAC	<<<<<<<<<<<<<<<<<<<<<<<<<<;<<:;<<;<	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_589:1:122:337:968	99	chr1	823	85	35M	=	981	193	ACAGGGGGCTGCGCGGTTTCCCATCATGAAGCACT	<<<<<;<<<<<<<<<<<<<<<<<<<;<<;;<;;;;	MF:i:18	Aq:i:10	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_30:3:187:294:947	99	chr1	823	99	35M	=	1002	214	ACAGGGGGCTGCGCGGTTTCCCATCATGAAGCACT	<<<<<<<<<<<<<<<<:<<<<<&<<%:<)7;7::4	MF:i:18	Aq:i:67	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_108:2:49:271:588	83	chr1	830	99	35M	=	658	-207	GCTGCGCGGTTTCCCATCATGAAGCACTGAACTTC	:0=:===:<===;;===;=================	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_63:3:40:594:752	147	chr1	831	99	35M	=	651	-215	CTGCGCGGTTTCCCATCATGAAGCACTGAACTTCC	;7;9<;;;<;<;:<<;;<<<<<<<<<;<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_610:8:163:757:432	99	chr1	837	99	35M	=	1013	211	GGTTTCCCATCATGAAGCACTGAACTTCCACGTCT	<<<<<<<;<<<<<<<<;<;<<<<<<<<<<<<83:<	MF:i:18	Aq:i:45	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_62:4:156:857:494	83	chr1	838	99	35M	=	648	-225	GTTTCCCATCATGAAGCACTGAACTTCCACGTCTC	<<<8<:5<<;<<8<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_595:5:84:91:614	163	chr1	839	99	35M	=	1019	215	TTTCCCATCATGAAGCACTGATCTTCCACGTCTCA	;4<<<<<-84<<<;<<<<8<7.<4<<;77&:%<::	MF:i:18	Aq:i:39	NM:i:1	UQ:i:13	H0:i:0	H1:i:1
+EAS51_64:7:152:918:824	163	chr1	839	99	35M	=	1033	229	TTTCCCATCATGAAGCACTGAACTTCCACGTCTCA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<<8	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_610:4:67:317:249	147	chr1	840	26	35M	=	683	-192	TTCCCATCATGACGCACCGAACTTCCACGTCTCAT	.5;7;++;<8.;&:7<<.5<<<<7<<7<<<<<<;7	MF:i:130	Aq:i:26	NM:i:2	UQ:i:18	H0:i:0	H1:i:0
+EAS51_62:7:96:836:737	147	chr1	841	99	35M	=	642	-234	TCCCATCATGAAGCACTGAACTTCCACGTCTCATC	1<;<7;;1;8;;8:<<1<;<<;<<<<<<<<<<;<<	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_81:8:130:912:658	83	chr1	841	99	35M	=	652	-224	TCCCATCATGAAGCACTGAACTTCCACGTCTCATC	;=;;;<<<<<=55=;==<=======<=========	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_108:3:75:934:439	163	chr1	842	99	35M	=	1001	194	CCCATCATGAAGCACTGAACTTCCACGTCTCATCT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_71:7:212:329:348	163	chr1	842	99	35M	=	1020	212	CCCATCATGAAGCACTGAACTTCCACGTCTCATCT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<:;;;<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_65:6:49:183:435	163	chr1	843	99	35M	=	1005	197	CCATCATGAAGCACTGAACTTCCACGTCTCATCTA	<<<<<<<<<<<<<<<<<<<<<<<<<<;;<;:;8;:	MF:i:18	Aq:i:70	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_61:7:280:133:495	99	chr1	843	99	35M	=	1015	207	CCATCATGAAGCACTGAACTTCCACGTCTCATCTA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_28:1:232:351:909	147	chr1	843	80	36M	=	685	-194	CCATCATGAAGCGCTGAACTTCCACGTCTCATCTAG	:8%3<8====130=8==+===;=3=8===48==;3*	MF:i:18	Aq:i:39	NM:i:1	UQ:i:15	H0:i:0	H1:i:1
+EAS221_1:8:77:781:676	163	chr1	846	99	35M	=	1010	199	TCATGAAGCACTGAACTTCCACGTATCATCTAGGG	<<<<<<<5<<5<<<<<<<<<<<<13<<2<<<<<,<	MF:i:18	Aq:i:43	NM:i:1	UQ:i:18	H0:i:0	H1:i:1
+EAS1_95:2:198:691:595	83	chr1	847	99	35M	=	655	-227	CATGAAGCACTGAACTTCCACGTCTCATCTAGGGG	:=:;=;===========;=================	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_597:7:31:948:254	147	chr1	849	99	35M	=	680	-204	TGAAGCACTGAACTTCCACGTCTCATCTAGGGGAA	7;;;98<<7<<<<<<<<<<<<<<<<<<8<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_57:1:278:440:902	99	chr1	851	99	35M	=	1032	216	AAGCACTGAACTTCCACGTCTCATCTAGGGGAACA	=========<==<==============:;;=;=;;	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_589:8:74:674:124	163	chr1	854	99	35M	=	1041	222	CACTGAACTTCCACGTCTCATCTAGGGGAACAGGG	<<<<<<<<<<<<:<;<<<<;<<<<;9;<<;;.;;;	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_593:4:28:781:723	147	chr1	855	99	36M	=	676	-215	ACTGAACTTCCACGTCTCATCTAGGGGAACAGGGAG	8488<::;4;;<:;;;::<;7<<<<<<<<<<<<<<<	MF:i:18	Aq:i:70	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_28:2:28:474:566	163	chr1	855	99	36M	=	1018	199	ACTGAACTTCCACGTCTCATCTAGGGGAACAGGGAG	<<<<<<<<<<<<<<<<<<<<<<<:<;<;;<<7;8;<	MF:i:18	Aq:i:70	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_67:5:124:241:608	147	chr1	856	99	35M	=	670	-221	CTGAACTTCCACGTCTCATCTAGGGGAACAGGGAG	9;;<<;<<<;<<<;<:<<<<;<<<<<<<<<<<<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_59:6:187:925:547	147	chr1	857	99	35M	=	689	-203	TGAACTTCCACGTCTCATCTAGGGGAACAGGGAGG	((988+&8<<;<09<;<<9<<4<<-<99<<;<9<;	MF:i:18	Aq:i:37	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:7:9:512:826	99	chr1	859	99	35M	=	1021	197	AACTTCCACGTCTCATCTAGGGGAACAGGGAGGTG	67<<<;;;<;;<<;;<;<:;9;;;9;;;;<59777	MF:i:18	Aq:i:67	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_95:6:194:696:490	99	chr1	862	99	35M	=	1026	199	TTCCACGTCTCATCTAGGGGAACAGGGAGGTGCAC	<<<<<<<<<<<<<<<<<<<;5<<<<<:<1<8<<<8	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_63:5:96:788:614	83	chr1	862	99	35M	=	667	-230	TTCCACGTCTCATCTAGGGGAACAGGGAGGTGCAC	;9;;;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_57:3:81:786:340	163	chr1	863	99	35M	=	1033	205	TCCACGTCTCATCTAGGGGAACAGAGAGGTGCACT	<<<<7<<<<<<<<<<<<<<7<<;<&<<;;7<7;;;	MF:i:18	Aq:i:45	NM:i:1	UQ:i:5	H0:i:0	H1:i:1
+EAS192_3:7:298:644:697	163	chr1	863	99	35M	=	1035	207	TCCACGTCTCATCTAGGGGAACAGGGAGGTGCACT	<<<<<<<<<<<<<<<::;;;6<8:;;9;98;668;	MF:i:18	Aq:i:70	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_65:1:178:305:843	163	chr1	864	99	35M	=	1037	208	CCACGTCTCATCTAGGGGAACAGGGAGGTGCACTA	<<<<<<<<<<<<<<<<<<<:<<<<<;<<:<<:<;:	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_610:3:5:863:302	147	chr1	866	99	35M	=	698	-203	ACGTCTCATCTAGGGGAACAGGGAGGTGCACTAAT	:4:29:<<<9;<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_57:5:30:788:376	99	chr1	866	99	35M	=	1038	207	ACGTCTCATCTAGGGGAACAGGGAGGTGCACTAAT	<<<<<<<<<<<<:<<<<<<<<:<;<<(<7;7;:(;	MF:i:18	Aq:i:70	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_64:3:143:310:958	163	chr1	868	99	35M	=	1048	215	GTCTCATCTAGGGGAACAGGGAGGTGCACTAATGC	<<<<<<<<<<<8<8<<<<<;;7<<<;6;<<+4;;;	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_73:5:3:233:911	83	chr1	868	99	35M	=	688	-215	GTCTCATCTAGGGGAACAGGGAGGTGCACTAATGC	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_65:5:75:637:650	83	chr1	868	99	35M	=	691	-212	GTCTCATCTAGGGGAACAGGGAGGTGCACTAATGC	<<<<8<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_26:2:73:513:102	147	chr1	868	99	35M	=	698	-205	GTCTCATCTAGGGGAACAGGGAGGTGCACTAATGC	==::===8=>=====>=>=>>>=>>==>=>>>>>>	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_595:3:297:637:86	83	chr1	869	99	35M	=	704	-200	TCTCAGCTAGGGGAACAGGGAGGTGCACTAATGCG	<:75<;<;;<<<<<<;;<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:68	NM:i:1	UQ:i:26	H0:i:1	H1:i:0
+EAS54_65:3:290:558:349	147	chr1	869	99	35M	=	719	-185	TCTCAGCTAGGGGAACAGGGAGGTGCACTAATGCG	2;2;;'5&;<<5<<;5/<<<<<7<<;+;<<+1<8<	MF:i:18	Aq:i:59	NM:i:1	UQ:i:6	H0:i:1	H1:i:0
+EAS1_95:3:308:956:873	99	chr1	870	99	35M	=	1068	233	CTCATCTAGGGGAACAGGGAGGTGCACTAATGCGC	<<<<<<<<<<<<<;<;<;1<<<<<.<9<;<<<<+;	MF:i:18	Aq:i:31	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_78:7:147:64:416	147	chr1	870	99	35M	=	701	-204	CTCATCTAGGGGAACAGGGAGGTGCACTAATGCGC	/;49;:6<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:47	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_593:4:30:812:345	163	chr1	871	99	36M	=	1036	201	TCATCTAGGGGAACAGGGAGGTGCACTAATGCGCTC	<<<<<<<7<;<<7<;77;3<&0-;<5<;6<1'13<:	MF:i:18	Aq:i:64	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_73:7:134:243:630	163	chr1	871	99	35M	=	1052	216	TCATCTAGGGGAACAGGGAGGCGCACTAATGAGCT	<<<:<<<<</<<<-<<<<6/<-<:<5+<::-2</2	MF:i:18	Aq:i:39	NM:i:2	UQ:i:29	H0:i:0	H1:i:1
+EAS54_81:2:27:856:401	83	chr1	871	99	35M	=	679	-227	TCATCTAGGGGAACAGGGAGGTGCACTAATGCGCT	.'=.93======;;====;======;===;=;===	MF:i:18	Aq:i:65	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_105:7:45:462:455	83	chr1	874	99	35M	=	723	-186	TCTAGGGGAACAGGGAGGTGCACTAATGCGCTCCA	62*<;;;;<<;<<9;;<<<<<<<<<<<<<<<<;<<	MF:i:18	Aq:i:43	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_93:1:264:988:663	147	chr1	875	99	35M	=	688	-222	CGAGGGGAACAGGGAGGTGCACTAATGCGCTCCAC	(%<:4<4<<7<<1-:<1766<66<<<<+<:<;8;<	MF:i:18	Aq:i:60	NM:i:1	UQ:i:4	H0:i:1	H1:i:0
+EAS56_63:1:145:71:26	163	chr1	875	99	35M	=	1040	200	CTAGGGGAACAGGGAGGTGCACTAATGCGCTCCAC	<<<<<<<<<<<<<<<<<;<;;<<;<;<9<9;;99;	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_589:1:101:825:28	163	chr1	879	99	35M	=	1079	235	GGGAACAGGGGGGTGCACTAATGCGCTCCACGCCC	<<86<<;<78<<<)<;4<67<;<;<74-7;,;8,;	MF:i:18	Aq:i:39	NM:i:1	UQ:i:27	H0:i:0	H1:i:1
+EAS218_4:5:63:875:1339	83	chr1	879	99	35M	=	711	-203	GGGAACAGGGAGGTGCACTAATGCGCTCCACGCCC	;;<<<:<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_595:6:290:270:557	99	chr1	880	99	35M	=	1052	207	GGAACAGGGAGGTGCACTAATGCGCTCCACGCCCA	<<<<<<<<<<<<<;<<<<9<:;<<<<<<5<0<<;+	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_105:6:134:853:558	163	chr1	880	99	35M	=	1071	226	GGAACAGGGAGGTGCACTAATGCGCTCCACGCCCA	==========================9=9=;<;<5	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS188_4:7:282:567:481	99	chr1	880	88	35M	=	1064	219	GGAACAGGGAGGCGCACTAATGCGCTCCACGCCCA	<<<<<<<<<<<<3<7<7<<<<;<<0)<<<<<<<<3	MF:i:18	Aq:i:43	NM:i:1	UQ:i:18	H0:i:0	H1:i:1
+EAS114_30:1:154:818:165	163	chr1	881	99	35M	=	1041	195	GAACAGGGAGGTGCACTAATGCGCTCCACGCCCAA	<<<<<<<<<<<<<<<<<<<<<<<<<;<<<<:7;:;	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_95:1:301:54:240	163	chr1	882	99	35M	=	1061	214	AACAGGGAGGTGCACTAATGCGCTCCACGCCCAAG	<<<<:<9<<<<:<<<<9<<<<<<690<<6</<(83	MF:i:18	Aq:i:66	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_595:4:12:402:843	163	chr1	885	99	35M	=	1072	222	AGGGAGGTGCACTAATGCGCTCCACGCCCAAGCCC	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<;;<	MF:i:18	Aq:i:70	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_57:4:262:965:756	99	chr1	885	99	35M	=	1069	219	AGGGAGGTGCACTAATGCGCTCCACGCCCAAGCCC	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;:<9;<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS112_34:8:30:816:90	163	chr1	885	99	35M	=	1057	207	AGGGAGGTGCACTAATGCGCTCCACGCCCCAGCCC	<<<<<<<<<<<<<<<<<<<:<<<<<<::1&(1::7	MF:i:18	Aq:i:69	NM:i:1	UQ:i:5	H0:i:1	H1:i:0
+EAS188_7:4:171:104:398	163	chr1	885	99	35M	=	1066	216	AGGGAGGTGCACTAATGCGCTCCACGCCCAAGCCC	=========)===97===3===4===4==,)=/)=	MF:i:18	Aq:i:67	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_64:4:163:31:455	83	chr1	886	99	35M	=	730	-191	GGGAGGTGCACTAATGCGCTCCACGCCCAAGCCCT	8;<<;<<<78+<=</<<=;23<=<<<<<<<<<<<<	MF:i:18	Aq:i:31	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS192_3:7:149:354:667	147	chr1	888	99	35M	=	734	-189	GAGGTGCACTAATGCGCTCCACGCCCAAGCCCTTC	;<;;;<<<<;<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS219_1:7:18:571:1110	99	chr1	888	99	35M	=	1070	217	GAGGTGCACTAATGCGCTCCACGCCCAAGCCCTTC	7<<<<<<<<<<<<;<<<<<<<<<<<<788<<<;6<	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_59:6:312:837:406	163	chr1	889	99	35M	=	1048	194	AGGTGCACTAATGCGCTCCACGCCCAAGCCCTTCT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_61:6:160:272:398	83	chr1	891	99	35M	=	705	-221	GTGCACTAATGCGCTCCACGCCCAAGCCCTTCTCA	3:,<,;;<<;<<1<<<<<<<;<;<<<<<<<<<<<<	MF:i:18	Aq:i:68	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_32:4:228:587:504	99	chr1	891	65	35M	=	1050	194	GTGCACTAATGCGCTCCACGCCCAAGCCCTTCTCA	<<<<7<<7;7<<3<<<<7<<<<<*3<<<<74<:<*	MF:i:18	Aq:i:65	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_30:3:35:361:546	83	chr1	892	99	35M	=	731	-196	TGCACTAATGCGCTCCACGCCCAAGCCCTTCTCAC	:4;4;;<<;4<8<;;<;<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_19:6:84:438:1505	99	chr1	893	99	40M	=	1068	215	GCACTAATGCGCTCCACGCCCAAGCCCTTCTCACAGTTTC	35<<:;9<;<;5<<<:<3<<7:<9/<)<<:::9<&5;;+1	MF:i:18	Aq:i:41	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_66:4:277:482:316	163	chr1	894	99	35M	=	1098	239	CACTAATGCGCTCCACGCCCAAGCCCTTCTCACAG	<<<<<<<<<<<<<<;<;<<<:<;<<<<;<<<1<1;	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS112_34:7:86:498:373	83	chr1	894	99	35M	=	716	-213	CACTAATGCGCTCCACGCCCAAGCCCTTCTCACAG	):)4:<5<<<<;89<<<969<<<:<<<<<<<<<<<	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_62:5:236:498:526	163	chr1	895	99	35M	=	1048	188	ACTAATGCGCTCCACGCCCAAGCCCTTCTCACAGT	===================================	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_39:1:43:1120:878	99	chr1	895	99	35M	=	1075	215	ACTAATGCGCTCCACGCCCAAGCCCTTCTCACAGT	<<<<<<<<<<<<<<<<<<<<8<<<<<<<<<<=7;7	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_593:4:104:153:698	83	chr1	896	99	36M	=	713	-219	CTAATGCGCTCCACGCCCAAGCCCTTCTCACAGTTT	69<<)9<<:5:6<<<16:<6/<6<1<<<<<:<:<<<	MF:i:18	Aq:i:68	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_63:7:166:42:147	99	chr1	898	99	35M	=	1048	185	AATGCGCTCCACGCCCAAGCCCTTCTAACAGTTTC	<<;<<<<<<<<<<<<<<<<;6<<64;)<<7;7;;;	MF:i:18	Aq:i:43	NM:i:1	UQ:i:8	H0:i:0	H1:i:1
+B7_595:2:178:77:424	99	chr1	900	99	35M	=	1058	193	TGCGCTCCACGCCCAAGCCCTTCTCACAGTTTCTG	<<<<<<<<<<<<<<<6<<;<<<<<<<<6<;<<<<6	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_95:6:87:734:888	83	chr1	900	99	35M	=	717	-218	TGCGCTCCACGCCCAAGCCCTTCTCACAGTTTCTG	56<<86;:<<<4;<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_28:2:149:650:44	83	chr1	902	99	36M	=	726	-212	CGCTCCACGCCCAAGCCCTTCTCACAGTTTCTGCCC	;8<<</<<:<<595<<9<<<<<<<<<<<<<<3<9<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_59:2:177:552:234	99	chr1	903	99	35M	=	1094	226	GCTCCACGCCCAAGCCCTTCTCACAGTTTCTGCCC	<<<<<<<<<<<<<;<<<<<<<<9<969<<<<3<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_595:4:58:703:72	163	chr1	905	99	35M	=	1088	218	TCCACGCCCAAGCCCTTCTCACAGTTTCTGCCCCC	2<7<<<<<<<<<<<8:<<<<8<(<8<:::8.::<3	MF:i:18	Aq:i:65	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_595:7:242:4:593	99	chr1	905	99	35M	=	1086	216	TCCACGCCCAAGCCCTTCTCACAGTTTCTGCCCCC	<<<<<<<<<<<8<<<<-<<<<<88;<;<<8<;88<	MF:i:18	Aq:i:53	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_597:3:67:620:344	147	chr1	905	99	35M	=	755	-185	CCCCCGCCCAAGCCCTTCTCACAGTTTCTGCCCCC	+++*+++#++++++,++++++++,,+,&+,,,,+,	MF:i:18	Aq:i:33	NM:i:2	UQ:i:19	H0:i:1	H1:i:0
+EAS51_62:7:178:286:414	83	chr1	907	99	35M	=	731	-211	CACGCCCAAGCCCTTCTCACAGTTTCTGCCCCCAG	68;38::<<;<<8;<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_66:7:174:987:334	163	chr1	908	99	35M	=	1082	209	ACACCCAAGCCCTTCTCACAGTTTCTGCCCCCAGC	<<;4<<<<;;</4<4<+<<<<<;<<<<<</<93+2	MF:i:18	Aq:i:41	NM:i:1	UQ:i:26	H0:i:0	H1:i:1
+EAS219_FC30151:1:55:8:1412	163	chr1	910	99	35M	=	1072	197	GCCCAAGCCCTTCTCACAGTTTCTGCCCCCAGCAT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_1:8:8:1351:1986	83	chr1	911	99	35M	=	729	-217	CCCAAGCCCTTCTCACAGTTTCTGCCCCCAGCATG	<8;<<<<<<<<<<<;<<;<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:47	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_65:6:37:610:260	83	chr1	913	99	35M	=	745	-203	CAAGCCCTTCTCACAGTTTCTGCCCCCAGCATGGT	/74<.<4.&<<<:<<<<::<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:68	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_26:5:228:189:826	99	chr1	914	99	35M	=	1112	233	AAGCCCTTCTCACAGTTTCTGCCCCCCGCATGGTT	;9=========;=1======9=====1;=<3=:6;	MF:i:18	Aq:i:45	NM:i:1	UQ:i:16	H0:i:0	H1:i:1
+EAS56_59:3:149:953:349	147	chr1	915	99	35M	=	777	-173	AGCCCTTCTCACAGTTTCTGCCCCCAGCATGGTTG	2;<<;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:7:24:1374:211	99	chr1	915	99	35M	=	1064	184	AGCCCTTCTCACAGTTTCTGCCCCCAGCATGGTTG	;;:<<;<;:;;;;;;;;;;<::;;;6;;2+74917	MF:i:18	Aq:i:64	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_81:2:5:491:391	147	chr1	917	99	35M	=	782	-170	CCCTGCTCACAGTTTCTGCCCCCAGCATGGTTGTA	-/+5-.&&:5+:92=6===========9=======	MF:i:18	Aq:i:62	NM:i:1	UQ:i:12	H0:i:1	H1:i:0
+EAS114_32:2:306:119:56	99	chr1	919	99	35M	=	1083	199	CTTCTCACAGTTTCTGCCCCCAGCATGGTTGTACT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_93:1:216:381:608	163	chr1	920	99	35M	=	1075	190	TTCTCACAGTTTCTGCCCCCAGCATGGTTGTACTG	<<<<<<<<<<<<<<<<<<<<<<<<;;+<6:<;26;	MF:i:18	Aq:i:41	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_97:3:73:292:429	147	chr1	920	99	35M	=	752	-203	TTCTCACAGTTTCTGCCCCCAGCATGGTTGTACTG	;6;6;<<<<<;<<<<;<<<<<<<<7<<<<<<5<<<	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_53:2:170:265:818	83	chr1	920	73	35M	=	748	-207	TTCTCACAGTTTCTGCCCCCAGCATGGTTGTACTG	3+;%;.;;<<9+;3;;;<<<;57<1<;<<<<<<<;	MF:i:18	Aq:i:10	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_59:1:278:906:933	99	chr1	920	99	35M	=	1071	186	TTCTCACAGTTTCTGCCCCCAGCATGGTTGTACTG	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<<<.	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_63:7:190:95:706	99	chr1	920	99	35M	=	1078	193	TTCTCACAGTTTCTGCCCCCAGCATGGTTGTACTG	<<<<<<<<<<<<<<9<<<<<;;<;<;;<<;<;;<,	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_65:5:278:848:765	99	chr1	920	99	35M	=	1088	203	TTCTCACAGTTTCTGCCCCCAGCATGGTTGTACTG	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<4	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_597:6:29:249:878	163	chr1	921	99	35M	=	1077	191	TCTCACAGTTTCTGCCCCCAGCATGGTTGTACTGG	<<<<<<<<<<<<<<<<<<<<<<:<:<<=<<:<<6&	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_593:2:259:467:737	163	chr1	923	99	36M	=	1102	215	TCACAGTTTCTGCCCCCAGCATGGTTGTACTGGGCA	<<<<<<<<<<<<7<<<<<<<'<<.<<<<<<;;;<67	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_30:3:24:195:604	163	chr1	923	99	35M	=	1098	210	TCACAGTTTCTGCCCCCAGCATGGTTGTACTGTGC	<;<<<<<<<<<89<<<<<868<8;6<8;3(38&<8	MF:i:18	Aq:i:65	NM:i:1	UQ:i:5	H0:i:1	H1:i:0
+EAS114_32:4:42:923:169	163	chr1	925	99	35M	=	1099	209	ACAGTTTCTGCCCCCAGCATGGTTGTACTGGGCAA	9<<<;9<<<<<;<;<<.<<;<;6<<<<1;8<<-0;	MF:i:18	Aq:i:39	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_589:1:29:529:379	163	chr1	926	99	35M	=	1117	226	CAGTTTCTGCCCCCAGCATGGTTGTACTGGGCAAT	<<<<<<<<8<<<<<<<<<<<<<<<<<;<672;<<<	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS218_1:8:26:785:882	163	chr1	926	99	35M	=	1107	216	CAGTTTCTGCCCCAAGCATGGTTGTACTGGGCAAT	<<<0<<<<<<<<<6,<<)<<<<<<<&<<0<<,<'<	MF:i:18	Aq:i:39	NM:i:1	UQ:i:21	H0:i:0	H1:i:1
+B7_591:7:129:956:115	83	chr1	927	99	36M	=	740	-223	AGTTTCTGCCCCCAGCATGGTTGTACTGGGCAATAC	<<:<9<4<<<<7<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_108:3:82:356:253	147	chr1	927	99	35M	=	752	-210	AGTTTCTGCCCCCAGCATGGTTGTACTGGGCAATA	97;7<<;;<<<<<7;<<:<<<9<<;<<<9<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_30:1:134:379:893	99	chr1	927	99	35M	=	1095	203	AGTTTCTGCCCCCAGCATGGTTGTACTGGGCAATA	<<<<<<<<<<<<<5<<<<;<<<<<;<:5;<<4+<<	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_105:8:256:404:584	99	chr1	928	99	35M	=	1096	203	GTTTCTGCCCCCAGCATGGTTGTACTGGGCAATAC	<<<<<<<<<<<<<<<<<<<<<7<3;<:;;3:3:</	MF:i:18	Aq:i:60	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS188_7:3:76:333:905	163	chr1	929	99	35M	=	1076	182	TTTCTGCCCCCAGCATGGTTGTACTGGGCAATACA	<<<<<7;<;<<6<<6<<7<<7<)&<4+6)0+<;(0	MF:i:18	Aq:i:61	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_591:6:11:646:628	99	chr1	930	99	36M	=	1106	212	TTCTGCCCCCAGCATGGTTGTACTGGGCAATACATG	<<<<<<<<<<6<<<<<<<<<<<<</<;<<<<<<6<;	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_57:5:136:389:320	99	chr1	930	99	35M	=	1100	205	TTCTGCCCCCAGCATGGTTGTACTGGGCAATACAT	7<<<<<;<<7<6<<;;<;<;;677<6;(27;<(97	MF:i:18	Aq:i:68	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_97:6:93:334:858	99	chr1	932	99	35M	=	1106	209	CTGCCCCCAGCATGGTTGTACTTGGCAATACATGA	<<<<<<<<;<<<<;;<<9<<<<&;&<<9<9;/;&;	MF:i:18	Aq:i:41	NM:i:1	UQ:i:5	H0:i:0	H1:i:1
+B7_597:3:46:981:766	83	chr1	933	99	35M	=	778	-190	TGCCCCCAGCATGGTTGTACTGGGCAATACATGAG	/<<<;/;<<316<<<3<<<<7<<<7<<<;<<<<<7	MF:i:18	Aq:i:68	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_71:4:209:159:130	99	chr1	934	99	34M	=	1109	210	GCCCCCAGCATGGTTGTACTGGGCAATACATGAG	<<<<<<8<<<<<<&<<+7<<4<<<22<;<<<<3<	MF:i:18	Aq:i:66	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_108:1:111:796:737	99	chr1	936	99	35M	=	1112	211	CCCCAGCATGGTTGTACTGGGCAATACATGTGATT	<<<<<<<<<<<<<<<:<<;7;<<<<993<4%:%<<	MF:i:18	Aq:i:70	NM:i:1	UQ:i:4	H0:i:1	H1:i:0
+EAS218_1:4:15:856:340	99	chr1	936	99	35M	=	1093	192	CCCCAGCATGGTTGCACTGGGCAATACATGAGATT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<77<<	MF:i:18	Aq:i:47	NM:i:1	UQ:i:27	H0:i:0	H1:i:1
+B7_610:5:7:761:623	147	chr1	938	99	35M	=	757	-216	CCGGCATGGTTGTACTGGGCAATACATGAGATTAT	::';-8);<<<<;<1<<<<:<<<<<<<<<<<<<<<	MF:i:18	Aq:i:69	NM:i:1	UQ:i:6	H0:i:1	H1:i:0
+EAS1_97:5:84:927:843	99	chr1	938	99	35M	=	1138	235	CCAGCATGGTTGTACTGGGCAATACATGAGATTAT	<<<<<<<<<<<<<;9;;4;<<0<<7<<9<;<:<5<	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_65:3:273:901:459	99	chr1	938	99	35M	=	1098	195	CCAGCATGGTTGTACTGGGCAATACATGAGATTAT	<<8<<<;<;8<;<;<;7+8<788<;;22<27;77;	MF:i:18	Aq:i:59	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_32:7:256:407:470	83	chr1	939	99	35M	=	762	-212	CAGCATGGTTGTACTGGGCAATACATGAGATTATT	7.47;0;;5<4033*<<<<<9,<<<<<;<<<<<3<	MF:i:18	Aq:i:63	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS188_7:1:77:251:446	163	chr1	939	99	35M	=	1110	206	CAGCATGGTTGTACTGGGCAATACATGAGATTATT	<<9<<<<<<<<<<<<<97<<<<<<<<<96<<<+<<	MF:i:18	Aq:i:41	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_64:4:102:467:897	147	chr1	940	97	35M	=	756	-219	AGCATGGTTGTACAGGGCAATACATGAGATTATTA	83333<+02<:<.&<+<.<::7<<::<<<<:<<<<	MF:i:18	Aq:i:37	NM:i:1	UQ:i:5	H0:i:0	H1:i:1
+EAS221_1:6:92:1807:1185	99	chr1	940	99	35M	=	1119	214	AGCATGGTTGTACTGGGCAATACATGAGATTATTA	<<<<<<<<<<<<<<<:<<<<<<:<<<<;<<<;<<;	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_81:8:142:858:903	99	chr1	943	99	35M	=	1121	213	ATGGTTGTACTGGGCAATACATGAGATTATTAGGA	======;====5=======9======;===3=5=;	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_103:4:143:560:194	147	chr1	946	99	35M	=	768	-213	GTTGTACTGGGCAATACATGAGATTATTAGGAAAT	9:<;7<:::<:<;<<<<<<<<<<:<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_593:3:148:437:481	83	chr1	949	99	36M	=	764	-221	GTACTGGGCAATACATGAGATTATTAGGAAATGCTT	<<<;<<<<7<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_81:6:75:917:886	163	chr1	951	99	35M	=	1110	194	ACTGGGCAATACATGAGATTATTAGGAAATGCTTT	<<<<<<<<<<<<<<:<<<<<<<<<71<<<:6<:8<	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_99:3:118:851:285	163	chr1	953	99	35M	=	1133	215	TGGGCAATACATGAGATTATTAGGAAATGCTTTAC	<<<<<<<<<<<<<<<<<<<<<<<;;<;<:<<<<;;	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_64:4:179:389:585	83	chr1	953	24	35M	=	770	-218	TGTGAAATGAATGAGATTATTAGGAAATGCTTTAC	;<)<;*;9*+<;<<,,<,<4<4<<<<<;<4<9494	MF:i:18	Aq:i:24	NM:i:4	UQ:i:53	H0:i:0	H1:i:0
+EAS114_30:7:269:944:220	163	chr1	953	99	35M	=	1147	229	TGGGCAATACATGAGATTATTAGGAAATGCTTTAC	<<<<<<<8<<<<<<<<<<<<<<<;<<<<<;<<;81	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_63:3:93:1002:845	163	chr1	954	99	35M	=	1129	210	GGGCAATACATGAGATTATTAGGAAATGCTTTACT	<<<<<<<<<<<<<<<<<<<<<:<<;<<<;<<<</<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_3:4:66:584:407	83	chr1	954	99	35M	=	785	-204	GGGCAATACATGAGATTATTAGGAAATGCTTTACT	<<84<<<766<<<.6<<<<<<4<<7<<<<<<<7<<	MF:i:18	Aq:i:68	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_99:6:63:48:631	163	chr1	957	99	35M	=	1143	221	CAATACATGAGATTATTAGGAAATGCTTTACTGTC	<<<<<<;<<7</<<<<<<;;;<<<;<;<<7;;);<	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_99:3:187:791:153	147	chr1	958	99	35M	=	803	-190	AATACATGAGATTATTAGGAAATGCTTTACTGTCA	:;55&<99<<1<;<<8<<;<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:68	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS220_1:2:72:1809:1398	99	chr1	958	99	35M	=	1145	222	AATACATGAGATTATTAGGAAATGCTTTACTGTCA	<<<<<<<<<<<<<<<<<<::<9<<<<<<<<<6<<:	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_65:6:66:257:524	147	chr1	959	99	35M	=	791	-203	ATACATGAGATTATTAGGAAATGCTTTACTGTCAT	<;<<<<<<<<3<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_57:7:247:522:670	163	chr1	960	99	35M	=	1121	196	TACATGAGATTATTAGGAAATGCTTTACTGTCATA	<<<<<<<<<<<<<<<;<<<<<<<<<<<<<5;<<<;	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_99:7:37:400:627	163	chr1	961	99	35M	=	1154	228	ACATGAGATTATTAGGAAATGCTTTACTGTCATAA	<<<<<<7+<<<<<<2615<<6<<<<5<<1<<;:74	MF:i:18	Aq:i:65	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_105:3:329:177:267	163	chr1	962	99	35M	=	1139	212	CATGAGATTATTAGGAAATGCTTTACTGTCATAAC	<<<<<<<<<<<<<<<<<<<<<<<<<9<<<<<<<9;	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_595:7:166:203:416	163	chr1	963	99	35M	=	1136	208	ATGAGATTATTAGGAAATGCTTTACTGTCATAACT	<<<<<<<<<<<<<<<<<<;<<<<<<<;<<<<<97<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_81:8:14:360:580	147	chr1	963	99	35M	=	799	-199	ATGAGATTATTAGGAAATGCTTTACTGTCATAACT	<,1<;<;;<<<<<1<<<;<7<<6<:;;<<<<<<;;	MF:i:18	Aq:i:68	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_65:4:193:38:987	163	chr1	964	99	35M	=	1158	229	TGAGATTATTAGGAAATGCTTTACTGTCATAACTA	<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<:;:;;	MF:i:18	Aq:i:47	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_66:3:39:59:738	163	chr1	965	99	35M	=	1142	212	GAGATTATTAGGAAATGCTTTACTGTCATAATTAT	3<8.<<<<<<<-<<<<3<388;;880<0<0)-722	MF:i:18	Aq:i:43	NM:i:1	UQ:i:12	H0:i:1	H1:i:0
+EAS51_66:4:209:92:210	163	chr1	965	99	35M	=	1156	226	GAGATTATTAGGAAATGCTTTACTGTCATAACTAT	<<<<<<<<<<<<<<<<;<<<<<<<5<7<<;;;<;<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_26:7:86:308:648	99	chr1	970	99	35M	=	1161	226	TATTAGGAAATGCTTTACTGTCATAACTATGAAGA	=8=====;=8======;=======35==;=;.;25	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_65:8:206:563:262	163	chr1	971	99	35M	=	1137	201	ATTAGGAAATGCTTTACTGTCATAACTATGAAGAG	<<<<<<<<<;<<<<<<<<<<<<;<<<<<<<-;<4;	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_65:6:82:822:767	99	chr1	972	99	35M	=	1165	228	TTAGGAAATGCTTTACTGTCATAACTATGAAGAGA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<.<<.<,<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_57:5:207:926:427	163	chr1	973	99	35M	=	1159	221	TAGGAAATGCTTTACTGTCATAACTATGAAGAGAC	<<<<<<7<<<<<;<<<<<6:<;<6<&<58<<6:::	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_62:7:144:28:475	99	chr1	974	99	35M	=	1167	228	AGGAAATGCTTTACTGTCATAACTATGAAGAGACT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<:<::8<	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS219_FC30151:3:55:74:1040	147	chr1	975	99	35M	=	818	-192	GGAAATGCTTTACTGTCATAACTATGAAGAGACTA	;;;;;<<:<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_103:1:274:176:479	99	chr1	976	99	35M	=	1144	203	GAAATGCTTTACTGTCATAACTATGAAGAGACTAT	<<<<<<<<<<<<<;<<<<<<<<<<;<<9<59<<<<	MF:i:18	Aq:i:68	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_589:1:122:337:968	147	chr1	981	10	35M	=	823	-193	GCTTTACTGTCTAAACTATGAAGAGACTATTGCCA	%454<75!7<+!990<9<6<<<<6<</<<<<<<<<	MF:i:18	Aq:i:10	NM:i:3	UQ:i:24	H0:i:0	H1:i:0
+EAS114_28:7:157:786:424	99	chr1	981	99	36M	=	1171	226	GCTTTACTGTCATAACTATGAAGAGACTATTGCCAG	<<<<<<<<<<<<<;<<<<<<;<<;<<;<<<<+4:70	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_11:4:63:527:1923	147	chr1	981	99	35M	=	803	-213	GCTTTACTGTCATAACCATGAAGAGACTATTGCCA	9<<<8<-8;;8<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:45	NM:i:1	UQ:i:27	H0:i:0	H1:i:1
+EAS1_95:7:55:506:125	147	chr1	982	99	35M	=	817	-200	CTTTACTGTCATAACTATGAAGAGACTACTGCCAG	118%67;1;8,4:187<4>::1:818;;&::<>.;	MF:i:18	Aq:i:35	NM:i:1	UQ:i:5	H0:i:0	H1:i:1
+EAS54_81:2:31:98:804	147	chr1	982	99	35M	=	805	-212	CTTTACTGTCATAACTATGAAGAGACTATTGCCAG	====;========7=====================	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_103:2:235:805:373	163	chr1	983	99	35M	=	1146	198	TTTACTGTCATAACTATGAAGAGACTATTTCCAGA	<<<<<<<<<<<<<<<<<<<<;<;<<<<<<;;<99;	MF:i:18	Aq:i:74	NM:i:1	UQ:i:26	H0:i:1	H1:i:0
+EAS114_28:5:11:868:62	99	chr1	983	99	36M	=	1154	207	TTTACTGTCATAACTATGAAGAGACTATTGCCAGAT	<<<<<<<<<<<<<<<<<<<<:<<<;<<<<(7:7039	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_81:2:280:512:316	163	chr1	984	99	35M	=	1159	210	TTACTGTCATAACTATGAAGAGACTATTGCCAGCT	==<========6==4==6;;==:===;=2/:+8%6	MF:i:18	Aq:i:68	NM:i:1	UQ:i:4	H0:i:1	H1:i:0
+EAS1_93:5:292:122:666	99	chr1	985	99	35M	=	1159	209	TACTGTCATAACTATGAAGAGACTATTGTCAGATG	<<<<<<6<<<<<<<<8;<<<<<<<<<<3&9+;;(;	MF:i:18	Aq:i:68	NM:i:1	UQ:i:5	H0:i:1	H1:i:0
+EAS56_53:1:23:403:981	99	chr1	985	99	35M	=	1151	201	TACTGTCATAACTATGAAGAGACTATTGCCAGATG	<8<<<;<<<<<<;<<<<<<8;<<<9<9,3;,6(91	MF:i:18	Aq:i:65	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:7:33:1566:588	99	chr1	985	76	35M	=	1166	216	TACTGTCATAACTATGAAGAGCCTATTGCCAGATG	<;.;;;;6;;;;6;;29;;;<+9;;;.3;;73797	MF:i:18	Aq:i:37	NM:i:1	UQ:i:10	H0:i:0	H1:i:1
+EAS139_11:7:92:367:1495	83	chr1	987	99	35M	=	820	-202	CTGTCATAACTATGAAGAGACTATTGCCAGATGAA	<8<88<<<<7<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:78	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS220_1:8:38:1576:1923	83	chr1	987	99	35M	=	822	-200	CTGTCATAACTATGAAGAGACTATTGCCAGATGAA	8;<98<<<<<<<;<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_595:7:190:481:295	163	chr1	990	99	35M	=	1161	206	TCATAACTATGAAGAGACTATTGCCAGATGAACCA	<<<<<<<<<<<<<<<<<<<<<<9<<<<<9<7<2::	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS112_32:7:168:117:441	99	chr1	990	99	35M	=	1151	196	TCATAACTATGAAGAGACTATTGCCAGATGAACCA	<<3<<<<<<<<<<<<<<<<<<<+<<17;<;:<995	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_73:3:239:796:221	163	chr1	992	99	35M	=	1160	203	ATAACTATGAAGAGACTATTGCCAGCTGACCCCCC	<<<7<<7<<7<<7<;<<<<<,;;,+'<+/+99%:'	MF:i:18	Aq:i:37	NM:i:4	UQ:i:26	H0:i:0	H1:i:1
+EAS220_1:4:69:88:1154	147	chr1	992	99	35M	=	805	-222	ATAACTATGAAGAGACTATTGCCAGATGAACCACA	<<<<9<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:47	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_3:8:34:956:1309	99	chr1	994	99	35M	=	1168	209	AACTATGAAGAGACTATTGCCAGATGAACCACACA	<<<<<<7<<<<<<<<<<<6<<<<<<<<<<<:<8<8	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_108:5:229:717:121	99	chr1	995	99	35M	=	1150	190	ACTATGAAGAGACTATTGCCAGATGAACCACACAC	=================<)=<4<0=.<<<71;41&	MF:i:18	Aq:i:43	NM:i:1	UQ:i:5	H0:i:1	H1:i:0
+EAS219_1:1:67:191:668	99	chr1	995	99	35M	=	1134	174	ACTATGAAGAGACTATTGCCAGATGAACCACACCT	<<<<<<<<<<<<<<<<<6<<;<;<;<<<<<<6;%2	MF:i:18	Aq:i:74	NM:i:1	UQ:i:4	H0:i:1	H1:i:0
+EAS51_64:3:309:303:278	163	chr1	996	99	35M	=	1178	217	CTATGAAGAGACTATTGCCAGATGAACCACACATT	<<<<<<<<<<<<<<<<+<<+<<7<<<<<5<<<;;;	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_1:8:60:1020:1259	99	chr1	996	99	35M	=	1157	196	CTATGAAGAGACTATTGCCAGATGAACCACACATT	<;<<<<;<<<<<<<<<;<<<<<<<8<<<<<:<:<<	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS218_4:7:89:1487:520	83	chr1	997	99	35M	=	805	-227	TATGAAGAGACTATTGCCAGATGAACCACACATTA	4;;/<<<<<:<;<;<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:70	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_610:4:15:805:420	163	chr1	998	35	35M	=	1164	201	ATGAAGAGACTATTCACATGTGAACCACACATTTA	;73;;;;67.;1<<+*.;*&<4947<&474&*9*(	MF:i:130	Aq:i:35	NM:i:4	UQ:i:33	H0:i:0	H1:i:0
+EAS56_57:3:119:761:239	147	chr1	999	99	35M	=	813	-221	TGAAGAGACTATTGCCAGATGAACCACACATTAAT	;;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS112_34:7:142:457:584	99	chr1	999	99	35M	=	1160	196	TGAAGAGACTATTTCCAGATGAACCACACATTAAT	<<<<<<<<<<<<</<<,6<66<<<;<;;<*4744.	MF:i:18	Aq:i:41	NM:i:1	UQ:i:14	H0:i:0	H1:i:1
+EAS218_4:7:87:964:826	83	chr1	999	99	35M	=	822	-212	TGAAGAGACTATTGCCAGATGAACCACACATTAAT	)6<<<<<<:;<6<<::<<<;<<<<<<<<<<<<<<<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS218_1:6:49:905:27	83	chr1	1000	68	35M	=	821	-214	GAAGAGACTATTGCCAGTTGAACCACACATTAATA	99515<<&<<6595-56%;86&<;<<<6<<<<6;<	MF:i:18	Aq:i:31	NM:i:1	UQ:i:4	H0:i:0	H1:i:1
+EAS1_108:3:75:934:439	83	chr1	1001	99	35M	=	842	-194	AAGAGACTATTGCCAGATGAACCACACATTAATAC	==7=:=========================<====	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_26:1:99:212:522	83	chr1	1002	99	35M	=	806	-231	AGAGACTATTGCCAGATGAACCACACATTAATACT	<1<16<7<3<<;;<8<<<<<<<<<<<<;<<<<9<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_30:3:187:294:947	147	chr1	1002	99	35M	=	823	-214	AGAGACTATTGCCAGATGAACCACACATTAATACT	<<:<<8181;<8<<<<<<<<8<<<<<<<<<<<<<:	MF:i:18	Aq:i:67	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_61:2:152:860:286	163	chr1	1004	99	35M	=	1171	202	AGACTATTGCCAGATGAACCACACATTAATACTAT	<;<<<;<<0:<3<:<<2<<<<<7+<7+47<9(999	MF:i:18	Aq:i:65	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_65:6:49:183:435	83	chr1	1005	99	35M	=	843	-197	GACTATTGCCAGATGAACCACACATTAATACTATG	1<7<<<<;:<<<<<;<<<;<<<;<;<<<<<<<<<<	MF:i:18	Aq:i:70	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_73:7:63:854:610	163	chr1	1005	99	35M	=	1180	210	GACTATTGCCAGATGAACCACACATTAATACTATG	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<;<<	MF:i:18	Aq:i:70	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_3:4:12:276:1797	99	chr1	1006	99	35M	=	1190	219	ACTATTGCCAGATGAACCACACATTAATACTATGT	<<<<<<<<<<<<:</<<9<:<<<<<<<<<<<<<<<	MF:i:18	Aq:i:66	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_591:6:190:42:671	163	chr1	1008	99	36M	=	1192	220	TATTGCCAGATGAACCACACATTAATACTATGTTTC	<<<<<<<<<<<<<<9<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_65:7:67:692:110	99	chr1	1009	99	35M	=	1175	201	ATTGCCAGATGAACCACACATTAATACTATGTTTC	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_99:3:61:183:767	99	chr1	1010	99	35M	=	1195	220	TTGCCAGATGAACCACACCTTAATACTATGTTTCT	<<<<<<<<<<;<<<9<9<+<<<8<<<<<<;8<<<<	MF:i:18	Aq:i:45	NM:i:1	UQ:i:10	H0:i:0	H1:i:1
+EAS221_1:8:77:781:676	83	chr1	1010	99	35M	=	846	-199	TTGCCAGATGAACCACACATTAATACTATGTTTCT	:<;<2<<<<<<26<<<<6<;<<<<<<<<<<<<<<<	MF:i:18	Aq:i:43	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_3:4:21:132:1423	99	chr1	1012	99	35M	=	1178	201	GCCAGATGAACCACACATTAATACTATGTTTCTTA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_610:8:163:757:432	147	chr1	1013	99	35M	=	837	-211	CCAGATGAACCACACATTAATACTATGTTTCTCAT	1+<8<<<<<<;<5<;<<<<<;5<<<<<<<<<<<<<	MF:i:18	Aq:i:45	NM:i:1	UQ:i:27	H0:i:0	H1:i:1
+EAS114_30:3:302:288:657	99	chr1	1013	99	35M	=	1173	195	CCAGATGAACCACACATTAATACTATGTTTCTTAT	<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<<<;<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:7:97:1584:777	99	chr1	1013	99	35M	=	1200	222	CCAGATGAACCACACATTAATACTATGTTTCTTAT	<<;<;;;;<;<;<<;;;;;;;;;;;;;;:;79979	MF:i:18	Aq:i:66	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_61:7:280:133:495	147	chr1	1015	99	35M	=	843	-207	AGATGAACCACACATTAATACTATGTTTCTTATCT	<:<9:<<7:<6<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_39:7:100:708:1984	147	chr1	1015	99	35M	=	819	-231	AGATGAACCACACATTAATACTATGTTTCTTATCT	:8<(8<)9<;<<<<+<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_32:5:182:313:319	99	chr1	1016	99	35M	=	1180	199	GATGAACCACACATTAATACTATGTTTCTTATCTG	<<<<<<<<<<<<<<<<<<<<<<<<<<<7<<<<;<;	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_103:3:41:474:283	99	chr1	1018	99	35M	=	1182	199	TGAACCACACATTAATACTATGTTTCTTATCTGCA	<<<<<<<<<<<<<<<<<<<<<;<<<<<<<<<<+<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_28:2:28:474:566	83	chr1	1018	99	36M	=	855	-199	TGAACCACACATTAATACTATGTTTCTTATCTGCAC	;<<<+<<<<5<<<<<<;;<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:70	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_595:5:84:91:614	83	chr1	1019	99	35M	=	839	-215	GAACCACACATTAATACTATGTTTCTTATCTGCAC	<<;;<<<7<<<<<<<;<;<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:39	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_67:1:159:222:274	99	chr1	1019	99	35M	=	1189	205	GAACCACACATTAATACTATGTTTCTTATCTGCAC	=;9====;=9==59=+==9========9===5;7=	MF:i:18	Aq:i:37	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS219_1:3:62:603:1552	163	chr1	1019	99	35M	=	1180	196	GAACCACACATTAATACTATGTTTCTTATCTGCAC	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<9<;<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_71:7:212:329:348	83	chr1	1020	99	34M	=	842	-212	AACCACACATTAATACTATGTTTCTTATCTGCAC	8<6:<:<<<;<<<;<<<<;<<<<<<<<<<<<<<<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_71:4:233:97:262	99	chr1	1021	99	34M	=	1175	189	ACCACACATTAATACTATGTTTCTTATCTGCCCA	<<<<<<<<<<<;<;<<:<<<<<<<<<<<<.<&77	MF:i:18	Aq:i:72	NM:i:1	UQ:i:5	H0:i:1	H1:i:0
+EAS114_45:7:9:512:826	147	chr1	1021	99	35M	=	859	-197	ACCACACATTAATACTATGTTTCTTATCTGCACAT	76777:;;;;;;;;;;;;;;;;;;;;;;;;;:;;;	MF:i:18	Aq:i:67	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_593:4:29:794:282	163	chr1	1025	99	36M	=	1196	207	CACATTAATACTATGTTTCTTATCTGCACATTACTA	<<<<<<<<<<<<<<<<<<<<<;<<<&<<;:<<8<<8	MF:i:18	Aq:i:70	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_59:4:278:524:521	163	chr1	1025	99	35M	=	1224	234	CACATTAATACTATGTTTCTTATCTGCACATTACT	<<<;<<;<<<<<<<;<<<<<<<<<<7;5;<<<;;<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_597:3:39:966:551	99	chr1	1026	99	35M	=	1205	214	ACATTAATACTATGTTTCTTATCTGCACATTACTA	<<<<<<<<<<<<<<<<<<<<<<<<:<;<&<<&<<;	MF:i:18	Aq:i:68	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_95:6:194:696:490	147	chr1	1026	99	35M	=	862	-199	ACATTAATACTATGTTTCTTATCTGCACATTACTA	========;======;==========8==:=====	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_591:3:305:565:952	99	chr1	1030	99	36M	=	1213	219	TAATACTATGTTTCTTATCTGCACATTACTACCCTG	7<<<<<<<<<7<<<<<<<<<7<<<;;<;<;<<<<<+	MF:i:18	Aq:i:62	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_57:7:287:258:321	99	chr1	1030	99	35M	=	1194	199	TAATACTATGTTTCTTATCTGCACATTACTACCCT	<<<<<<<<<<<;<<<<<<<<42:<+<<<;<<;;;;	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_57:1:278:440:902	147	chr1	1032	99	35M	=	851	-216	ATACTATGTTTCTTATCTGCACATTACTACCCTGC	<;7;4<;<;;;<<;<;;;<<<<<9<<<;<<<<;<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_108:5:180:905:36	99	chr1	1033	99	35M	=	1212	214	TACTATGTTTCTTATCTGCACATTACTACCCTGCA	==========8===;;=========;==77%41=;	MF:i:18	Aq:i:65	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_64:7:152:918:824	83	chr1	1033	99	35M	=	839	-229	TACTATGTTTCTTATCTGCACATTACTACCCTGCA	;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_57:3:81:786:340	83	chr1	1033	99	35M	=	863	-205	TACTATGTTTCTTATCTGCACATTACTACCCTGCA	;<;<<<;<<;<<<<;<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:45	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_593:3:196:11:27	163	chr1	1035	65	36M	=	1198	199	CTATGTTTCTTATCTGCNCATTACTACCCTGCAATT	<<<<<<<<;<<<<<<<8!4<<<;+<88;8<+2,8<;	MF:i:18	Aq:i:24	NM:i:1	UQ:i:0	H0:i:0	H1:i:1
+EAS192_3:7:298:644:697	83	chr1	1035	99	35M	=	863	-207	CTATGTTTCTTATCTGCACATTACTACCCTGCAAT	8:<8;<;:7;<<;4;:+<7<<<<;<<<<<<<<<<<	MF:i:18	Aq:i:70	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_593:4:30:812:345	83	chr1	1036	99	36M	=	871	-201	TATGTTTCTTATCTGCACATTACTACCCTGCAATTA	;<;<<<<5<<<:<;<:<;<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:64	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_65:1:178:305:843	83	chr1	1037	99	35M	=	864	-208	ATGTTTCTTATCTGCACATTACTACCCTGCAATTA	<<<<<<<4<<;<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_57:5:30:788:376	147	chr1	1038	99	35M	=	866	-207	TGTTTCTTATCTGCACATTACTACCCTGCAATTAA	:5<<4:88;9<<<<<;<<<<;<8<;<<<<1<<<<<	MF:i:18	Aq:i:70	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_63:1:145:71:26	83	chr1	1040	99	35M	=	875	-200	TTTCTTATCTGCACATTACTACCCTGCAATTAATA	882;8;<;;887<<<;;<<<<;<<<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_30:6:157:42:763	163	chr1	1040	99	35M	=	1203	198	TTTCTTATCTGCACATTACTACCCTGCAATTATTA	<<;<;<<<<<;<:4<<<<<<<<<;;4<<<:;;+;+	MF:i:18	Aq:i:61	NM:i:1	UQ:i:10	H0:i:1	H1:i:0
+B7_589:8:74:674:124	83	chr1	1041	99	35M	=	854	-222	TTCTTATCTGCACATTACTACCCTGCAATTAATAT	;;;;;<<:<<:<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_30:1:154:818:165	83	chr1	1041	99	35M	=	881	-195	TTCTTATCTGCACATTACTACCCTGCAATTAATAT	;;;;<<<;<;;<;<<<<;<<;;;<<;<<<<<<<<<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_57:3:319:174:811	99	chr1	1044	99	35M	=	1242	233	TTATCTGCACATTTCTACCCTGCAATTAATATAAT	<<<<<<<<<;<<<<<<<<<;;<<<<<<<8<<;9<<	MF:i:18	Aq:i:47	NM:i:1	UQ:i:27	H0:i:0	H1:i:1
+EAS139_19:3:87:133:930	163	chr1	1044	99	40M	=	1198	194	TTATCTGCACATTACTACCCTGCAATTAATATAATTGTGT	<<<7<<<<;<<;7<<7<<;;<<<;<5;<;;;5;;<:/48:	MF:i:18	Aq:i:39	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS219_1:1:44:1466:425	163	chr1	1044	99	35M	=	1213	204	TTATCTGCACATTACTACCCTGCAATTAATATAAT	<<<<<<<<<<<<<<<<<<<<<;<<<<<<;<<<<<<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_62:5:236:498:526	83	chr1	1048	99	35M	=	895	-188	CAGCACATTACTACCCTGCAATTAATATAATTGTG	<%88<;<:8<<<<:<<<<:<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:1	UQ:i:4	H0:i:1	H1:i:0
+EAS51_64:3:143:310:958	83	chr1	1048	99	35M	=	868	-215	CTGCACATTACTACCCTGCAATTAATATAATTGTG	84<;<6<<<<;<<<;;<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_59:6:312:837:406	83	chr1	1048	99	35M	=	889	-194	CTGCACATTACTACCCTGCAATTAATATAATTGTG	;<;<<;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_63:7:166:42:147	147	chr1	1048	99	35M	=	898	-185	CTGCACATTACTACCCTGCAATTAATATAATTGTG	3.7;;;;:<<<77<<3<;<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:43	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_28:3:279:763:945	99	chr1	1048	99	36M	=	1210	198	CTGCACATTACTACCCTGCAATTAATATAATTGTGT	<<<<<<<<<<<<<<<<<<<4:<<47<:<;<<</<9<	MF:i:18	Aq:i:61	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_610:3:82:998:566	163	chr1	1050	99	35M	=	1227	212	GCACATTACTACCCTGCAATTAATATAATTGTGTC	<<<<<<<:<<0<<<<:<82<<::<4<<;<<4<4<;	MF:i:18	Aq:i:70	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_32:4:228:587:504	147	chr1	1050	65	35M	=	891	-194	GCACATTACGACCCGGCAAGGTGTATAATTGTGTC	;4;4;&&82&04+&&48;3&3&*<7<47<<;-<-8	MF:i:130	Aq:i:65	NM:i:6	UQ:i:47	H0:i:0	H1:i:0
+B7_595:6:290:270:557	147	chr1	1052	99	35M	=	880	-207	ACATTACTACCCTGCAATTAATATAATTGTGTCCA	87:9;;;<851+:5.<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_73:7:134:243:630	83	chr1	1052	99	35M	=	871	-216	ACATTACTACCCTGCAATTAATATAATTGTGTCCA	63<;37:<*&:<<<,,*<<:7<<7<<<<<<<::<<	MF:i:18	Aq:i:39	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_53:1:47:303:887	163	chr1	1052	96	35M	=	1240	223	ACATTACTACCCTGCCATTAATATACTTGTGTCCA	<<;;<+<9<<<<<9<(6<;//</<8(<<89;6084	MF:i:18	Aq:i:25	NM:i:2	UQ:i:14	H0:i:0	H1:i:0
+EAS221_3:8:74:770:1712	163	chr1	1052	99	35M	=	1208	191	ACATTACTACCCTGCAATTAATATAATTGTGTCCA	<<<<<<<<<<<<<<<<<<<5<<<<<<<<<<<<7<<	MF:i:18	Aq:i:70	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_591:6:29:575:453	163	chr1	1056	99	36M	=	1228	208	TACTACCCTGCAATTAATATAATTGTGTCCATTTAC	<<<<<<<<<<<<<<<<<<<<<<<<7<1<:<9<&<98	MF:i:18	Aq:i:72	NM:i:1	UQ:i:5	H0:i:1	H1:i:0
+EAS1_97:5:318:177:383	163	chr1	1056	99	35M	=	1251	230	TACTACCCTGCAATTAATATAATTGTGTCCATGTA	;<<<<<<<<;<<<<<<<<<<<<<<<<<<7<;1'<;	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_53:8:179:549:753	99	chr1	1056	99	35M	=	1218	197	TACTACCCTGCAATTAATATAATTGTGTCCATGTA	<<<<<<<<<<<<<<<<<<<<<<<<8<7<<<:<9<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS112_34:8:30:816:90	83	chr1	1057	99	35M	=	885	-207	ACTACCCTGCAATTAATATAATTGTGTCCATGTAC	:<3:%9299<<<<<<<<<5<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_595:2:178:77:424	147	chr1	1058	99	35M	=	900	-193	CTACCCTGCAATTAATATAATTGTGTCCATGTACA	:5:8<;<;:<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_95:1:301:54:240	83	chr1	1061	99	35M	=	882	-214	CCCTGCAATTAATATAATTGTGTCCATGTACACAC	&..*3===1=========5.5==5===4====:5=	MF:i:18	Aq:i:66	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_108:4:91:521:517	99	chr1	1061	99	35M	=	1239	213	CCCTGCAATTAATATAATTGTGTCCATGTACACAC	<<<<<<<<<<<<<<<<9<<<<<<<<<<8<<;;;<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:7:24:1374:211	147	chr1	1064	99	35M	=	915	-184	TGCAATTAATATAATTGTGTCCATGTACACACGCT	77661;;;5;;:;;:;:;;;;;;8:;;;:;;;;;:	MF:i:18	Aq:i:64	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS188_4:7:282:567:481	147	chr1	1064	88	35M	=	880	-219	TGCAATTAATATAATTGTGTCCACGTACACACGCT	<9<6<;<9<<<;<<<;<5<7<5</7<<<<<<<<<<	MF:i:18	Aq:i:43	NM:i:1	UQ:i:14	H0:i:0	H1:i:1
+EAS188_7:4:171:104:398	83	chr1	1066	99	35M	=	885	-216	CAATTAATATAATTGTGTCCATGTACACACGCTGT	79<+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:67	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_66:8:9:80:353	163	chr1	1067	99	35M	=	1233	201	AATTAATATAATTGTGTCCATGTACACACGCTGTC	<<<<<<<<<<<<<<<<<<<<<6<<<;;<<5<<2;2	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_63:6:42:920:522	163	chr1	1067	99	35M	=	1244	212	AATTAATATAATTGTGTCCATGTACACACGCTGTT	<<<<<<<<<<<<<:<<<<<<<:<<<<<<<:;;::&	MF:i:18	Aq:i:72	NM:i:1	UQ:i:5	H0:i:1	H1:i:0
+EAS1_95:3:308:956:873	147	chr1	1068	99	35M	=	870	-233	ATAAAAATAAGTGTGTCCATGTACACACGCTGTCC	91.97&9499&-1*98*19999839999.9&9799	MF:i:18	Aq:i:31	NM:i:3	UQ:i:23	H0:i:0	H1:i:1
+EAS139_19:6:84:438:1505	147	chr1	1068	99	40M	=	893	-215	ATTAATATAATTGTGTCCATGTACACACTCTGTCCTATGT	:0::413::;:::0:179::3<;<:<9<&6<<<;<019<<	MF:i:18	Aq:i:41	NM:i:1	UQ:i:5	H0:i:0	H1:i:1
+EAS51_62:3:55:340:837	163	chr1	1069	99	35M	=	1238	204	TTAATATAATTGTGTCCATGTACACACGCTGTCCT	<<;<<;<<<<<8<;<<<;<7<<<;<<<<<93+79(	MF:i:18	Aq:i:68	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_57:4:262:965:756	147	chr1	1069	99	35M	=	885	-219	TTAATATAATTGTGTCCATGTACACACGCTGTCCT	<<:<<<<<<<<:<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS219_1:7:18:571:1110	147	chr1	1070	99	35M	=	888	-217	TAATATAATTGTGTCCATGTACACACGCTGTCCTA	9<<;<;==;;=;=<;<===================	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_95:2:40:918:950	163	chr1	1071	99	35M	=	1247	211	AATATAATTGTGTCCATGTACACACGCTTTCCTTT	=========,=9=====2=7===7=0==&=+3=-=	MF:i:18	Aq:i:65	NM:i:2	UQ:i:17	H0:i:1	H1:i:0
+EAS1_97:2:59:882:980	163	chr1	1071	99	35M	=	1263	227	AATATAATTGTGTCCATGTACACACGCTGTCCTAT	<<<<<<<<<8<<<<<9<+<<<9<<<1<<77889+6	MF:i:18	Aq:i:43	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_105:6:134:853:558	83	chr1	1071	99	35M	=	880	-226	AATATAATTGTGTCCATGTACACACGCTGTCCTAT	<<<<8<<<7<<<<;;<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_59:1:278:906:933	147	chr1	1071	99	35M	=	920	-186	AATATAATTGTGTCCATGTACACACGCTGTCCTAT	<88::<<<<<<<<<;<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_595:4:12:402:843	83	chr1	1072	99	35M	=	885	-222	ATATAATTGTGTCCATGTACACACGCTGTCCTATG	<7<+<<11<9<<<<<:<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:70	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_597:5:160:434:853	163	chr1	1072	99	35M	=	1259	222	ATATAATTGTGTCCATGTACACACGCTGTCCTATG	<<<<<<<<<<<<<<<<<<<<<<,<<<<:<<<<,<:	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS219_FC30151:1:55:8:1412	83	chr1	1072	99	35M	=	910	-197	ATATAATTGTGTCCATGTACACACGCTGTCCTATG	<<<<<<<<<<<<:<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_59:1:219:294:861	163	chr1	1073	99	35M	=	1244	206	TATAATTGTGTCCATGTACACACGCTGTCCTCTGT	<<<<<<<<<<<<<9<<<5<9<<<9<<544<<'<+:	MF:i:18	Aq:i:69	NM:i:1	UQ:i:6	H0:i:1	H1:i:0
+EAS220_1:4:14:1665:1772	163	chr1	1073	84	35M	=	1263	225	TATAATGGTGTCCATGTACACACGCTGTCCTATGT	<<<<<7*<<<<<<<<<78<5<<7<<5<556<(73(	MF:i:18	Aq:i:39	NM:i:1	UQ:i:9	H0:i:0	H1:i:1
+B7_591:3:45:294:380	163	chr1	1074	80	36M	=	1233	195	ATAATTGTGTCCATGTACACACGATGTCATATGTAC	<<<<<<<<9<<<<<<<<<70<<7<6272&:3<+</%	MF:i:18	Aq:i:39	NM:i:2	UQ:i:32	H0:i:0	H1:i:1
+EAS1_108:7:222:538:267	99	chr1	1074	99	35M	=	1228	189	ATAATTGTGTCCATGTACACACGCTGTCCTATTTA	<<<<<<<<<<<<<<<<<<<<<;<<<<74;;39%6+	MF:i:18	Aq:i:67	NM:i:1	UQ:i:4	H0:i:1	H1:i:0
+EAS1_93:1:216:381:608	83	chr1	1075	99	35M	=	920	-190	TAATTGTGTCCATGTACACTCGCTGTCCTATGTAC	55<99<<<99;<;<<(<39&7<<<<<<<<<<<<<9	MF:i:18	Aq:i:41	NM:i:1	UQ:i:5	H0:i:0	H1:i:1
+EAS54_67:1:138:186:274	99	chr1	1075	99	35M	=	1231	191	TAATTGTGTCCATGTACACACGCTGTCCTATGTAC	=39====9===;=;=;=9=;=====;===-=+=-7	MF:i:18	Aq:i:67	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_39:1:43:1120:878	147	chr1	1075	99	35M	=	895	-215	TAATTGTGTCCATGTACACACGCTGTCCTATGTAC	<<<;<<;<<;<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS188_4:5:166:776:590	163	chr1	1075	99	35M	=	1252	212	TAATTGTGTCCATGTACACACGCTGTCCTATGTAC	<<<<<</<<<<<<<<<<<<<'<=<:26.</79<::	MF:i:18	Aq:i:66	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS188_7:3:76:333:905	83	chr1	1076	99	35M	=	929	-182	AATTGTGTCCATGTACACACGCTGTCCTATGTACT	<<;<<<<;7<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:61	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_597:6:29:249:878	83	chr1	1077	99	35M	=	921	-191	ATTGTGTCCATGTACACACGCTGTCCTATGTACTT	<,;<9<;<:<<<<<<<<<<<<<<<<<<<<<<><<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_63:7:190:95:706	147	chr1	1078	99	35M	=	920	-193	TTGTGTCCATGTACACACGCTGTCCTATGTACTTA	9;97437;<;;<<;<;<<<<<<;<<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_589:1:101:825:28	83	chr1	1079	99	35M	=	879	-235	TGTGTCCATGTACACACGCTGTCCTATGTACTTAT	0;0'0;<<<<<<8<;<<<<;;3<<;;<<<8<<<<<	MF:i:18	Aq:i:39	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_66:4:188:460:1000	99	chr1	1080	99	35M	=	1251	206	GTGTCCATGTACACACGCTGTCCTATGTACTTATC	<<<<<<<<<<<<<<<<7<<;:4;44<;;:8;;9;;	MF:i:18	Aq:i:70	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_95:3:268:523:511	99	chr1	1081	99	35M	=	1241	195	TGTCCATGTACACACGCTGTCCTATGTACTTATCA	<<<<<<<<<<<<<<<<<<<<;<<<<6<:9<<3<44	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_28:6:54:263:585	99	chr1	1081	99	36M	=	1254	209	TGTCCATGTACACACGCTGTCCTATGTACTTATCAT	<<<<<<<<<<<<<<<<<<<:;<<;<:;::<<;;:;4	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_66:7:174:987:334	83	chr1	1082	99	35M	=	908	-209	GTCCATGTACACACGCTGTCCTATGTACTTATCAT	,;<;;<<<&<<<1<<<<<<<<<<<<<;<<<<<<<<	MF:i:18	Aq:i:41	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_71:6:224:932:942	99	chr1	1082	99	34M	=	1250	203	GTCCATGTACACACGCTGTCCTATGTACTTATCA	<<<<<<<<<<<<<<<<<<<<<<;<<<<7<<(;3,	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:1:12:1296:358	99	chr1	1082	96	35M	=	1252	205	GTCCATGTACACACGCTGTCCTATGTACTTATCAT	;;;6;7;7;;;;;7;9;;-*1;9;699/99/7477	MF:i:18	Aq:i:37	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_32:2:306:119:56	147	chr1	1083	99	35M	=	919	-199	TCCATGTACACACGCTGTCCTATGTACTTATCATG	;;;;;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_95:4:66:179:118	163	chr1	1084	99	35M	=	1262	213	CCATGTACACACGCTGTCCTATGTACTTATCATGA	<<<<<<<<<<<<<<<<<<<<<<<<<<:<<;<<6<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_105:2:110:584:649	99	chr1	1084	99	35M	=	1266	217	CCATGTACACACGCTGTCCTATGTACTTATCATGA	<<<<<<<<<<<<<<<<<<<<<<<<;<<<<<::<38	MF:i:18	Aq:i:43	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS218_1:4:28:315:310	163	chr1	1085	99	35M	=	1242	192	CATGTACACACGCTGTCCTATGTACTTATCATGAC	<<<<<<<<<<<<<<<<<<<<<:<+.<<.<+7<*17	MF:i:18	Aq:i:68	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_595:7:242:4:593	147	chr1	1086	99	35M	=	905	-216	ATATACACACGCTGTCCTATGTACTTATCATGACT	1.%55877+8+88808887+7;7;18:8;;;.&;8	MF:i:18	Aq:i:53	NM:i:1	UQ:i:4	H0:i:1	H1:i:0
+EAS1_93:1:131:946:353	163	chr1	1087	99	35M	=	1249	197	TGTACACACGCTGTCCTATGTACTTATCATGACTC	<<<<<<<<<<<<<;<<<<;;<<<<<<<;<:52;<2	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_1:4:4:1732:88	99	chr1	1087	99	35M	=	1265	213	TGTACACACGCTGTCCTATGTACTTATCATGACTC	<<<<<<<<<<<<<<<<<2<8;8<;<8;<2;2:<:<	MF:i:18	Aq:i:45	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_595:4:58:703:72	83	chr1	1088	99	35M	=	905	-218	GTACACACGCTGTCCTATGTACTTATCATGACTCT	5&<<7;+95;7'6<<<<<.<<<<<;<<9<7<<<<<	MF:i:18	Aq:i:65	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_59:5:113:694:725	163	chr1	1088	99	35M	=	1266	213	GTACACACGCTGTCCTATGTACTTATCATGACTCT	<<<<<<<<<<<<9<<<<<:<<<<<<<<<<:;;<;;	MF:i:18	Aq:i:47	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_65:5:278:848:765	147	chr1	1088	99	35M	=	920	-203	GTACACACGCTGTCCTATGTACTTATCATGACTCT	7;;<;5<55<<;;<;<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_57:6:234:787:12	163	chr1	1092	97	35M	=	1257	200	ACACGCTGGCCTATGTACTTATAATGACTCTATCC	<;<<<9<<&+9;3;<993;<9<+94;9&41;08%9	MF:i:18	Aq:i:24	NM:i:2	UQ:i:15	H0:i:0	H1:i:0
+EAS218_1:4:15:856:340	147	chr1	1093	99	35M	=	936	-192	CACGCTGTCCTATGTACTTATCATGACTCTATCCC	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:47	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_62:2:258:266:101	163	chr1	1094	99	35M	=	1285	226	ACGCTGTCCTATGTACTTATCATGACTCTATCCCA	<<<<<<<<<<<<<<<<<<5<;,<-2<<<<;68<<6	MF:i:18	Aq:i:68	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_59:2:177:552:234	147	chr1	1094	99	35M	=	903	-226	ACGCTGTCCTATGTACTTATCATGACTCTATCCCA	::;:=;=99=====;;====;==========<===	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_30:1:134:379:893	147	chr1	1095	99	35M	=	927	-203	CGCTGTCCTATGTACTTATCATGACTCTATCCCAA	7137::;<<<<<<<;<<<<<<<<<<;<<<<<<<<<	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_105:8:256:404:584	147	chr1	1096	99	35M	=	928	-203	ACTGTCCTATGTACTTATCATGACTCTATCCCAAA	&&326+23<3<<<+:<</<<8<<<:7:<<<<<<<<	MF:i:18	Aq:i:60	NM:i:1	UQ:i:5	H0:i:1	H1:i:0
+EAS114_30:4:317:378:535	163	chr1	1096	99	35M	=	1258	197	GCTGTCCTATGTACTTATCATGACTCTATCCCAAA	<<<<<<<<<<<<:<<<<<<<<<;<<;<8<;:7:1(	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_66:4:277:482:316	83	chr1	1098	99	35M	=	894	-239	TGTCCTATGTACTTATCATGACTCTATCCCAAATT	9998;<<<<<;;<<<<<<<<<<<;<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_65:3:273:901:459	147	chr1	1098	99	35M	=	938	-195	TGTCCTATGTACTTATCATGACTCTATCCCAAATT	4;+/+7,;<8+&<;;82;;<8<8<2<;<<<<<<<<	MF:i:18	Aq:i:59	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_59:3:316:25:230	163	chr1	1098	99	35M	=	1273	210	TGTCCTATGTACTTATCATGACTCTATCCCAAATT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<);2;;	MF:i:18	Aq:i:47	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_30:3:24:195:604	83	chr1	1098	99	35M	=	923	-210	TGTCCTATGTACTTATCATGACTCTATCCCAAATT	;6<02;<<<<59<<;<;<<<<9<3<<<<<<<<<;<	MF:i:18	Aq:i:65	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_32:4:42:923:169	83	chr1	1099	99	35M	=	925	-209	TTCCTATGTACTTATCATGAATCTATCCCAAATTC	&;972<;&<9<,;;;<<<;<&99<<;<;;3<<3<<	MF:i:18	Aq:i:39	NM:i:2	UQ:i:10	H0:i:0	H1:i:1
+EAS114_45:6:59:1548:1096	163	chr1	1099	99	35M	=	1297	233	GTCCTATGTACTTATCATGACTCTATCCCAAATTC	;.;;;;;;;;6;;;;;;;;;;;;;;;73;;77777	MF:i:18	Aq:i:66	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_57:5:136:389:320	147	chr1	1100	99	35M	=	930	-205	TCCTATGTACTTATCATGACTCTATCCCAAATTCC	.5:,666<)<8<:<<:66<<<<<<<<<<5<<7<<<	MF:i:18	Aq:i:68	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_32:6:122:342:296	99	chr1	1100	99	35M	=	1256	191	TCCTATGTACTTATCATGACTCTATCCCAAATTCC	<<<<<<<<<<<<<<<<<<<<<<<<<;<<*<<<<9<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_593:2:259:467:737	83	chr1	1102	99	36M	=	923	-215	CTATGTACTTATCATGACTCTATCCCAAATTCCCAA	8<<<<<<<:<<<<<<<<;<;<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS218_1:4:71:832:743	163	chr1	1102	99	35M	=	1290	223	CTATGTACTTATCATGACTCTATCCCAAATTCCCA	<<<<<<<<<<<<<<<<<<<<<<<<<<<*<<<<<<<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_57:5:105:521:563	163	chr1	1103	72	35M	=	1267	199	TATGTACTTATCATGACTCTATCCCAAATTCCCAA	;<)<9995<9<<59<7<<<<7<7<35,0,544<3(	MF:i:18	Aq:i:10	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS192_3:6:201:195:757	163	chr1	1103	99	35M	=	1298	230	TATGTACTTATCATGACTCTATCCCAAATTCCCAA	<<<<<<<<<<<<<<;<<<<<<<<<<<<<<<;;;;8	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_593:7:6:585:132	163	chr1	1105	23	36M	=	1276	207	TGTACTTATCATGTTTCTTTCCTAATTTTTCAATTA	6666166&6)+61))646+6&)&%&-44))1'144'	MF:i:130	Aq:i:23	NM:i:7	UQ:i:59	H0:i:0	H1:i:0
+EAS1_105:2:179:532:82	99	chr1	1105	99	35M	=	1285	215	TGTACTTATCATGACTCTATCCCAAATTCCCAATT	<<<<<<<<<<<<<<<<<<<<3<;<;<<<<:<8<<<	MF:i:18	Aq:i:45	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_591:6:11:646:628	147	chr1	1106	99	36M	=	930	-212	GTACTTATCATGACTCTATCCCAAATTCCCAATTAC	<<<3<<<<<<<<<<<<<<<<<<<<<7<<<<<<<<6<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_97:6:93:334:858	147	chr1	1106	99	35M	=	932	-209	GTACTTATCATGACTCTATCCCAAATTCCCAATTA	;<;+;;<<;<<<<<;<<<<;;8<<<<8<<<<<<<<	MF:i:18	Aq:i:41	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS218_1:8:26:785:882	83	chr1	1107	99	35M	=	926	-216	TACTTATCATGACTCTATCCCAAATTCCCAATTAC	<<&5&<<<<5.;5<'<<;.76<<<<<7<7<<<<<<	MF:i:18	Aq:i:39	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_589:4:54:989:654	99	chr1	1108	99	35M	=	1296	223	ACTTATCATGACTCTATCCCAAATTCCCAATTACG	<<<<<<<<<<<<<<<9<<<<<<9<<<<<1<<<88;	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS188_4:5:202:326:680	163	chr1	1108	78	35M	=	1268	195	ACTTATCATGACTCTATCCCAAATTCTCAATTACG	<<<<<<<4<<<*<<<*<<<7..:7<3*:7.7<+.;	MF:i:18	Aq:i:37	NM:i:1	UQ:i:9	H0:i:0	H1:i:1
+B7_597:3:53:616:842	163	chr1	1109	99	35M	=	1288	214	CTTATCATGACTCTATCCCAAATTCCCACTTACGT	<<<<<<<<<<<<<<<<<<<;07<<<<<-&<<-<4;	MF:i:18	Aq:i:68	NM:i:1	UQ:i:5	H0:i:1	H1:i:0
+EAS54_71:4:209:159:130	147	chr1	1109	99	35M	=	934	-210	CTTATCATGACTCTATCCCAAATTCCCAATTACGT	;:6<:<8::;<<<;<-<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:66	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_81:6:75:917:886	83	chr1	1110	99	35M	=	951	-194	TTATCATGACTCTATCCCAAATTCCCAATTACGTC	<<<<8<<<<<<8<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_59:6:286:753:854	163	chr1	1110	99	35M	=	1288	213	TTATCATGACTCTATCCCAAATTCCCAATTACGTC	<<<<<<<<<<<<<<<<<<3<<<<<<9999<;<<9;	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_30:6:290:146:36	99	chr1	1110	99	35M	=	1280	205	TTATCATGACTCTATCCCAAATTCCCAATTACGTC	<<<<<<<<<<<<<<<<<<<<<<<8<<<<<;;<;;<	MF:i:18	Aq:i:25	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:6:93:1475:542	163	chr1	1110	99	35M	=	1254	179	TTATCATGACTCTATCCCAAATTCCCAATTACGTC	;;;;;;;;;;;;;;;;;;;;;;9;;;9;;;77777	MF:i:18	Aq:i:66	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS188_7:1:77:251:446	83	chr1	1110	99	35M	=	939	-206	TTATCATGACTCTATCCCAAATGCCCAATTACGTC	<<24,:8<<<:1<<<:35<:<:,<<<<<<:5:<<<	MF:i:18	Aq:i:41	NM:i:1	UQ:i:11	H0:i:0	H1:i:1
+EAS1_105:3:176:431:647	163	chr1	1112	99	35M	=	1285	208	ATCATGACTCTATCCCAAATTCCCAATTACGTCCT	<<<<<<<<<<<<<<<<2<<<<<<<<6<<<<9<<6<	MF:i:18	Aq:i:70	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_108:1:111:796:737	147	chr1	1112	99	35M	=	936	-211	ATCATGACTCTATCCCAAATTCCCAATTACGTCCT	<3<<<<<<<<<<<7<<<<<;<<<<<<<<<<<<<<<	MF:i:18	Aq:i:70	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_26:5:228:189:826	147	chr1	1112	99	35M	=	914	-233	ATCATGACTCTATCCCAAATTCCCAATTACGTCCT	:74=:.==1==========================	MF:i:18	Aq:i:45	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_11:1:35:631:594	163	chr1	1112	99	35M	=	1271	194	ATCATGACTCTATCCCAAATTCCCAATTACGTCCT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:45	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_589:1:29:529:379	83	chr1	1117	99	35M	=	926	-226	GACTCTATCCCAAATTCCCAATTACGTCCTATCTT	;<<<:<<<<<;<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_81:7:74:596:137	99	chr1	1119	91	35M	=	1294	210	CTCTATCCCAAATTCCCAATTACGTCCTATCTTCT	<<<<<<<<<</4<<<<<<*<:6<<<<<<<<;/3<<	MF:i:18	Aq:i:22	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_1:6:92:1807:1185	147	chr1	1119	99	35M	=	940	-214	CTCTATCCCAAATTCCCAATTACGTCCTATCTTCT	<<<<<<9<<<<<<<<<<<<<<<<<<<<<<><<<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_595:3:57:735:151	99	chr1	1121	94	35M	=	1314	228	CTATCCCAAATTCCCAATTACGTCCTATCTTCTTC	<<<<<<<<8<<8<:<<*<:<<<4<<<;,<<<<:<:	MF:i:18	Aq:i:26	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_81:8:142:858:903	147	chr1	1121	99	35M	=	943	-213	CTATCCCAAATTCCCAATTACGTCCTATCTTCTTC	<<<<<;<<<<9<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_57:7:247:522:670	83	chr1	1121	99	35M	=	960	-196	CTATCCCAAATTCCCAATTACGTCCTATCTTCTTC	;;;9;:<<<<<;<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_19:3:75:732:442	99	chr1	1121	99	40M	=	1293	212	CTATCCCAAATTCCCAATTACGTCCTATCTTCTTCTTAGG	<<<<<;<<<<<9<<<;<<;<<<5<<;8<<<<<<<<;:9%%	MF:i:18	Aq:i:60	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_99:7:183:645:699	99	chr1	1122	86	35M	=	1281	194	TATCCCAAATTCCCAATTACGTCCTATCTTCTTCT	<<9<9<<<<<<<<<;<<;<<*175;173<;;;<-/	MF:i:18	Aq:i:21	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS192_3:6:175:437:950	163	chr1	1126	99	35M	=	1298	207	CCAAATTCCCAATTACGTCCTATCTTCTTCTTAGG	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<:59	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_63:3:93:1002:845	83	chr1	1129	99	35M	=	954	-210	AATTCCCAATTACGTCCTATCTTCTTCTTAGGGAA	<<::;;;<<<<<<<<<<<<<<<<;<<<<<<<<<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_62:6:50:542:881	163	chr1	1132	99	35M	=	1324	227	TCCCAATTACGTCCTATCTTCTTCTTAGGTAAGAA	<<<<<4<09<<9<<2<<<<<<<<<<<2/.&2<%<7	MF:i:18	Aq:i:63	NM:i:1	UQ:i:5	H0:i:1	H1:i:0
+EAS1_99:3:118:851:285	83	chr1	1133	99	35M	=	953	-215	CCCAATTACGTCCTATCTTCTTCTTAGGGAAGAAC	3+7<<<;<;<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS219_1:1:67:191:668	147	chr1	1134	99	35M	=	995	-174	CCAATTACGTCCTATCTTCTTCTTAGGGAAGAACA	<<<<<7<<7<<<<<<<;<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_595:7:166:203:416	83	chr1	1136	99	35M	=	963	-208	AATTACGTCCTATCTTCTTCTTAGGGAAGAACAGC	<<<<<<<<::<<<<<<<<<;<<<<<<<<<<<<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:2:15:1497:1530	99	chr1	1136	99	35M	=	1314	213	AATTACGTCCTATCTTCTTCTTAGGGAAGAACAGC	0<;;;9;;86<;;;<<&<<.<<;)3;7;654-471	MF:i:18	Aq:i:57	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_65:8:206:563:262	83	chr1	1137	99	35M	=	971	-201	ATTACGTCCTATCTTCTTCTTAGGGAAGAACAGCT	<<<<7<<<<<<<<<<<<<<<<<<<<<<<<<<<<<7	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_26:4:40:352:151	99	chr1	1137	99	35M	=	1327	225	ATTACGTCCTATCTTCTTCTTAGGGAAGAACAGCT	<<<<<<<<<<<<<<<;<<9<<<<:<<<<;<99<3<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_593:7:67:302:762	99	chr1	1138	99	36M	=	1313	211	TTACGTCCTATCTTCTTCTTAGGGAAGAACAGCTTA	<<<<<<<<<<<<<<<<<<<<;;65;<-<;<:8<<<3	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_97:5:84:927:843	147	chr1	1138	99	35M	=	938	-235	TTACGTCCTATCTTCTTCTTAGGGAAGAACAGCTT	588;<:<<<<<<<6<<<<;<<<:/<<3<:;<*<<<	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_99:5:147:479:41	163	chr1	1139	99	35M	=	1322	218	TACGTCCTATCTTCTTCTTAGGGAAGAACAGCTTA	<<<<<<<<<<<<<<<<<<<<::6<<;<<<;;9;;6	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_105:3:329:177:267	83	chr1	1139	99	35M	=	962	-212	TACGTCCTATCTTCTTCTTAGGGAAGAACAGCTTA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_589:7:72:916:763	163	chr1	1142	99	35M	=	1340	233	GTCCTATCTTCTTCTTAGGGAAGAACAGCTTAGGT	</:8<8)<<<<:<<<<<;.89<:67<.;<<7+336	MF:i:18	Aq:i:63	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_64:6:124:128:489	99	chr1	1142	99	35M	=	1348	241	GTCCTATCTTCTTCTTAGGGAAGAACAGCTTAGGT	<<<<<<<<<<<<<<<<<6:6<<-4<::;;<<:48<	MF:i:18	Aq:i:70	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_66:3:39:59:738	83	chr1	1142	99	35M	=	965	-212	GTCCTATGTTCTTCTTAGGGAAGAACAGCTTAGGT	;.;4;<;3<<9<<9<&<<9<<<<<;<9<;<<;9<<	MF:i:18	Aq:i:43	NM:i:1	UQ:i:18	H0:i:0	H1:i:1
+EAS1_99:6:63:48:631	83	chr1	1143	99	35M	=	957	-221	TCCTATCTTCTTCTTAGGGAAGAACAGCTTAGGTA	;*:;;<2<<2779;:<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_103:1:274:176:479	147	chr1	1144	99	35M	=	976	-203	CCTATCTTCTTCTTAGGGAAGAACAGCTTAGGTAT	7)<<7<626<<7<<<<<<<<<<<<<<<<<<<3<<<	MF:i:18	Aq:i:68	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS220_1:2:72:1809:1398	147	chr1	1145	99	35M	=	958	-222	CTATCTTCTTCTTAGGGAAGAACAGCTTAGGTATC	;:;;:<7:7<:<:<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_103:2:235:805:373	83	chr1	1146	99	35M	=	983	-198	TATCTTCTTCTTAGGGAAGAACAGCTTAGGTATCA	<<;<<<<<<9<9<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_30:7:269:944:220	83	chr1	1147	99	35M	=	953	-229	ATCTTCTTCTTAGGGAAGAACAGCTTAGGTATCAA	<;<;8<<;7<<<<<;<<-<<<<<<;<<<;<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_32:7:174:597:66	163	chr1	1148	99	35M	=	1307	194	TCTTCTTCTTAGGGAAGAACAGCTTAGGTATCAAT	<<<<<<<<<<<<<<<<<<<<<<<<<;<<;<<;6;<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_108:5:229:717:121	147	chr1	1150	99	35M	=	995	-190	TTCTTCTGAGGGAAGAACAGCTTAGGTATCAATTT	6;-;7<<(<<<<<8<18<7<<<<<<<<<;<<<<<<	MF:i:18	Aq:i:43	NM:i:1	UQ:i:7	H0:i:0	H1:i:1
+EAS56_53:1:23:403:981	147	chr1	1151	99	35M	=	985	-201	TCTTCATAGGGAAGAACAGCTTAGGTATCAATTTG	(;3+<&3<</7<<<<<<;<<<<<<<<<<<<</<2<	MF:i:18	Aq:i:65	NM:i:1	UQ:i:5	H0:i:1	H1:i:0
+EAS112_32:7:168:117:441	147	chr1	1151	99	35M	=	990	-196	TCTTCTTAGGGAAGAACAGCTTAGGTATCAATTTG	;;;;3;<<<<<<<<<<<<<;<<<<<<<<<<<<<<<	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_19:6:52:1455:1212	99	chr1	1153	99	40M	=	1304	191	TTCTTAGGGAAGAACAGCTTAGGTATCAATTTGGTGTTCT	<9<<<99<;<<9<;<-<<<6<<75;;<*%<5<3+.8:*5;	MF:i:18	Aq:i:65	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_99:7:37:400:627	83	chr1	1154	99	35M	=	961	-228	TCTTAGGGAAGAACAGCTTAGGTATCAATTTGGTG	474*;<<9<;<<<;<<:<<<<<<;<<<<<<;<<;<	MF:i:18	Aq:i:65	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_28:5:11:868:62	147	chr1	1154	99	36M	=	983	-207	TCTTAGGGAAGAACAGCTTAGGTATCAATTTGGTGT	;;77;;7<<<<<<<<7<<<;<7<<<<<<<<<<<<<<	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_66:4:209:92:210	83	chr1	1156	99	35M	=	965	-226	TTAGGGAAGAACAGCTTAGGTATCAATTTGGTGTT	;9;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_81:2:128:394:455	163	chr1	1156	99	35M	=	1313	192	TTAGGGAAGAACAGCTTAGGTATCAATTTGGTGTT	======6==========;===9==;5===;==;==	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS188_7:1:316:949:122	99	chr1	1156	99	35M	=	1321	200	TTAGGGAAGAACAGCTTAGGTATCAATTTGGTGTT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<0<:<<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_1:8:60:1020:1259	147	chr1	1157	99	35M	=	996	-196	TAGGGAAGAACAGCTTAGGTATCAATTTGGTGTTC	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_65:4:193:38:987	83	chr1	1158	99	35M	=	964	-229	AGGGAAGAACAGCTTAGGTATCAATTTTGTGTTCT	<<<;<<;<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:47	NM:i:1	UQ:i:27	H0:i:0	H1:i:1
+EAS1_93:5:292:122:666	147	chr1	1159	99	35M	=	985	-209	GGGAAGAACAGCTTAGGTATCAATTTGGTGTTCTG	<;<;;<<<<<:<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:68	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_81:2:280:512:316	83	chr1	1159	99	35M	=	984	-210	GGGAAGAACAGCTTAGGTATCAATTTGGTGTTCTG	;9===;======;7==;;======;=====;====	MF:i:18	Aq:i:68	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_57:5:207:926:427	83	chr1	1159	99	35M	=	973	-221	GGGAAGAACAGCTTAGGTATCAATTTGGTGTTCTG	;;7<<;4<<<2<<;<<<<<<<<<<7<;<<<<<<<<	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_73:3:239:796:221	83	chr1	1160	99	35M	=	992	-203	GGAAGAACAGCTTAGGTATCAATTTGGTGTTCTGT	;;<<;<<;<<<+:<<<4<4<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:37	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS112_34:7:142:457:584	147	chr1	1160	99	35M	=	999	-196	GGAAGAACAGCTTAGGTATCAATTTGGTGTTCTGT	8::<:<<9<<.<:<<<<<<<<<<<7<<<<<<<<<<	MF:i:18	Aq:i:41	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_595:7:190:481:295	83	chr1	1161	99	35M	=	990	-206	GAAGAACAGCTTAGGTATCAATTTGGTGTTCTGTG	;<<:<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_26:7:86:308:648	147	chr1	1161	99	35M	=	970	-226	GAAGAACAGCTTAGGTATCAATTTGGTGTTCTGTG	<7<<<;<<<<+;<<<2<5<<<77;<<2<;;<<<<<	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_610:3:182:23:585	99	chr1	1163	99	35M	=	1336	208	AGAACAGCTTAGGTATCAATTTGGTGTTCTGTGTA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<:<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_591:4:216:650:516	99	chr1	1164	99	36M	=	1326	198	GAACAGCTTAGGTATCAATTTGGTGTTCTGTGTAAA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_610:4:15:805:420	83	chr1	1164	35	35M	=	998	-201	GAACAGTTTAGGTATCAATTTGGTGTTCTTTGTAA	<64<59&996<(64<)7).68<0<0<<7741<1:<	MF:i:18	Aq:i:35	NM:i:2	UQ:i:24	H0:i:0	H1:i:1
+EAS56_65:6:82:822:767	147	chr1	1165	99	35M	=	972	-228	AACAGCTTAGGTATCAATTTGGTGTTCTGTGTAAA	<<9<<<<<<<<<<;;<<<:<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:7:33:1566:588	147	chr1	1166	76	35M	=	985	-216	ACAGCTTAGGCATCAATTTGGTGTTCTGTGTAAAG	-6246;;97;77;;97;;;;;;9;7;79;)&;37;	MF:i:18	Aq:i:37	NM:i:1	UQ:i:22	H0:i:0	H1:i:1
+EAS1_93:1:20:635:509	163	chr1	1167	99	35M	=	1333	201	CAGCTTAGGTATCAATTTGGTGTTCTGTGTAAAGT	<<<<<<<<<;<<<<;<<<;<;;;<<<;<<<<<<(8	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_62:7:144:28:475	147	chr1	1167	99	35M	=	974	-228	CAGCTTAGGTATCAATTTGGTGTTCTGTGTAAAGT	;;;9;<<:<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_1:4:36:1402:1709	163	chr1	1168	99	35M	=	1326	193	AGCTTAGGTATCAATTTGGTGTTCTGTGTAAAGTC	<<<<<<<<<<<<<<<<<;<<<<<<<<<;<<<:9<<	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_3:8:34:956:1309	147	chr1	1168	99	35M	=	994	-209	AGCTTAGGTATCAATTTGGTGTTCTGTGTAAAGTC	9<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_62:7:157:784:936	163	chr1	1169	99	35M	=	1356	222	GCTTAGGTATCAATTTGGTGTTCTGTGTAAAGTCT	<<<<<<<<<<<<<<<<<:<<<<<<;<<<<814<4<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_61:2:152:860:286	83	chr1	1171	99	35M	=	1004	-202	TTAGGTATCAATTTGGTGTTCTGTGTAAAGTCTCA	2;5;8<<;5<<<;<2<8<<<<<<;8<;<<<<;<<<	MF:i:18	Aq:i:65	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_28:7:157:786:424	147	chr1	1171	99	36M	=	981	-226	TTAGGTATCAATTTGGTGTTCTGTGTAAAGTCTCAG	;<;2;;<<<;<;<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:1:33:1407:94	163	chr1	1172	99	35M	=	1360	223	TAGGTATCAATTTGGTGTTCTGTGTAAAGTCTCAG	;;;;;;;6:;;:::7;:;;;;:::;;;;:;47771	MF:i:18	Aq:i:66	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_30:3:302:288:657	147	chr1	1173	99	35M	=	1013	-195	AGGTATCAATTTGGTGTTCTGTGTAAAGTCTCAGG	<:5<<;;<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_71:4:233:97:262	147	chr1	1175	99	35M	=	1021	-189	GTATCAATTTGGTGTTCTGTGTAAAGTCTCAGGGA	--;;7<;<;;:;<;<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_65:7:67:692:110	147	chr1	1175	99	35M	=	1009	-201	GTATCAATTTGGTGTTCTGTGTAAAGTCTCAGGGA	;;<<8<<<<;<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_593:2:68:692:347	163	chr1	1176	99	36M	=	1351	211	TATCAATTTGGTGTTCTGTGTAAAGTCTCATGGAGC	<<<<<<<<<+6<;<<<<3<:<<<<6<8<<<&*/;*0	MF:i:18	Aq:i:64	NM:i:1	UQ:i:5	H0:i:1	H1:i:0
+EAS51_64:3:309:303:278	83	chr1	1178	99	35M	=	996	-217	TCAATTTGGTGTTCTGTGTAAAGTCTCAGGGAGCC	<:<<<:<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_3:4:21:132:1423	147	chr1	1178	99	35M	=	1012	-201	TCAATTTGGTGTTCTGTGTAAAGTCTCAGGGAGCC	:<<<<<6<<;<<;<5<;<<<<<<;<6<<<<<<<<<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_73:7:63:854:610	83	chr1	1180	99	35M	=	1005	-210	AATTTGGTGTTCTGTGTAAAGTCTCAGGGAGCCGT	:.5;2<:88<<72:<<;<<7<8;<;/<<<<<<<<<	MF:i:18	Aq:i:70	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_32:5:182:313:319	147	chr1	1180	99	35M	=	1016	-199	AATTTGGTGTTCTGTGTAAAGTCTCAGGGAGCCGT	</<;185;8<;;87<;8<<<<8<;83<<<<<<<<<	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS219_1:3:62:603:1552	83	chr1	1180	99	35M	=	1019	-196	AATTTGGTGTTCTGTGTAAAGTCTCAGGGAGCCGT	8::;:<<6<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_57:6:145:144:796	99	chr1	1181	99	35M	=	1372	226	ATTTGGTGTTCTGTGTAAAGTCTCAGGGAGCCGTC	<<<<<<<<<<<<<<;<<<<<<;<<<<<<4;4;<;/	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_103:3:41:474:283	147	chr1	1182	99	35M	=	1018	-199	TTTGGTGTTCTGTGTAAAGTCTCAGGGAGCCGTCC	6/;;;88;;<:;48<<<<<;<;<<<<<<<<<<;<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_26:2:329:458:365	99	chr1	1186	99	35M	=	1364	213	GTGTTCTGTGTAAAGTCTCAGGGAGCCGTCCGTGT	==========================9========	MF:i:18	Aq:i:78	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_67:1:159:222:274	147	chr1	1189	99	35M	=	1019	-205	GTCTGGGGAAAGTCTCAGGGAGCCGTCCGTGTCCT	''7*<&<'<<<<.<2<<<<<<<<<<+<<<8<8<<;	MF:i:18	Aq:i:37	NM:i:3	UQ:i:17	H0:i:0	H1:i:1
+EAS114_32:6:88:162:587	99	chr1	1189	99	35M	=	1372	218	TTCTGTGTAAAGTCTCAGGGAGCCGTCCGTGTCCT	<;<<<<<<<<<;<5<;<;<<7<++<<2&*:322+7	MF:i:18	Aq:i:63	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_610:3:148:340:479	99	chr1	1190	99	35M	=	1364	209	TCTGTGTAAAGTCTCAGGGAGCCGTCCGTGTCCTC	<<<<<<<<<<<<<<<<:<:<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_3:4:12:276:1797	147	chr1	1190	99	35M	=	1006	-219	TCTGTGTAAAGTCTCAGGGAGCCGTCCGTGTCCTC	)9<02)<<<<<<<<<<<<<1<<<<&<<<<9<<<<<	MF:i:18	Aq:i:66	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_591:6:190:42:671	83	chr1	1192	99	36M	=	1008	-220	TGTGTAAAGTCTCAGGGAGCCGTCCGTGTCCTCCCA	<<<<8<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_93:4:321:271:138	99	chr1	1193	99	35M	=	1394	236	GTGTAAAGTCTCAGGGAGCCGTCCGTGTCCTCCCA	<<<<<<<<<<<<<<<<<<<<<;9<<;<<;;<88;&	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_62:5:154:669:853	163	chr1	1193	99	35M	=	1371	213	GTGTAAAGTCTCAGGGAGCCGTCCGTGTCCTCCCA	============<===.====<:=<9=<<<9;:;2	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_57:7:287:258:321	147	chr1	1194	99	35M	=	1030	-199	TGTAAAGTCTCAGGGAGCCGTCCGTGTCCTCCCAT	:.<9<)<;<9<.<<:<:+5:<<<<<<<<<<<<<<<	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_99:3:61:183:767	147	chr1	1195	99	35M	=	1010	-220	GTAAAGTCTCAGGGAGCCGTCCGTGTCCTCCCATC	6&.;;<3<363<<<<<<<<8<<<6<<<<3<<<<<<	MF:i:18	Aq:i:45	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_593:4:29:794:282	83	chr1	1196	99	36M	=	1025	-207	TAAAGTCTCAGGGAGCCGTCCGTGTCCTCCCATCTG	7<<<<45::-<<<<<;<<-;<<;<<<<<<<<<<<<<	MF:i:18	Aq:i:70	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_73:3:313:827:992	99	chr1	1197	99	35M	=	1379	217	AAAGTCTCAGGGAGCCGTCCGTGTCCTCCCATCTG	<<<<6<<<<:<<<<<66<<<:33:<<<80<;6<8+	MF:i:18	Aq:i:57	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_593:3:196:11:27	83	chr1	1198	65	36M	=	1035	-199	AAGACCCAGTTAGCCGTCCGTGTCCTCCCATCTGGC	96&6<'<7:!!<,:;+7<<6:<<<<<<<<<7<7;:<	MF:i:18	Aq:i:24	NM:i:4	UQ:i:27	H0:i:0	H1:i:0
+EAS139_19:3:87:133:930	83	chr1	1198	99	40M	=	1044	-194	CAGTCTCAGGGCGCCGTCCGTTTCCTCCCATCTGGCCTCG	)8&)907)-;9&,<<9)<;<<0<;<<99<<<<<<;<<9<<	MF:i:18	Aq:i:39	NM:i:3	UQ:i:28	H0:i:0	H1:i:1
+EAS114_45:7:97:1584:777	147	chr1	1200	99	35M	=	1013	-222	GTCTCAGGGAGCCGTCCGTGTCCTCCCATCTGGCC	66746,9::9;;;;:;;;;;;;;;;;;;;;:;;;;	MF:i:18	Aq:i:66	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS112_34:6:127:153:861	99	chr1	1202	99	35M	=	1374	207	CTCAGGGAGCCGTCCGTGTCCTCCCATCTGGCCTC	<<<<<<<<<<<<<<<<<<<<<<<=<*<<<24;;::	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_30:6:157:42:763	83	chr1	1203	99	35M	=	1040	-198	TCTGGGAGCCGTCCGTGTCCTCCCATCTGGCCTCG	4++;((2(5;24<./<:<<<<<<<<;<<88<<<<9	MF:i:18	Aq:i:61	NM:i:1	UQ:i:10	H0:i:1	H1:i:0
+EAS54_65:4:91:267:655	99	chr1	1204	99	35M	=	1365	196	CAGGGAGCCGTCCGTGTCCTCCCATCTGGCCTCGT	<<<<<<<<<<<<<<<<<<<<<;:;;7<9477<74;	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_597:3:39:966:551	147	chr1	1205	99	35M	=	1026	-214	AGGGAGCCGTCCGTGTCCTCCCATCTGGCCTCGTC	8;;;;;<<6'<<<+8<<<1<<<<4<<<<<<<<<<<	MF:i:18	Aq:i:68	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_11:5:61:38:1182	163	chr1	1205	99	35M	=	1388	218	AGGGAGCCGTCCGTGTCCTCCCATCTGGCCTCGTC	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<5<<<<	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_19:1:47:352:1492	99	chr1	1205	99	40M	=	1385	220	AGGGAGCCGTCCGTGTCCTCCCATCTGGCCTCGCCCACTA	:<<<::<24<04-&<;<<2<<<&<60)&<5<<6*8:)9+*	MF:i:18	Aq:i:53	NM:i:3	UQ:i:28	H0:i:1	H1:i:0
+EAS221_3:8:74:770:1712	83	chr1	1208	99	35M	=	1052	-191	GAGCCGTCCGTGTCCTCCCATCTGGCCTCGTCCAC	3.&::6<<<9<6:<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:70	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_28:3:279:763:945	147	chr1	1210	99	36M	=	1048	-198	GCCGTCCGTGTCCTCCCATCTGGCCTCGTCCACACT	+9:-+<:1-44<<':<;<+<-<<<;:<<;;<<<<<0	MF:i:18	Aq:i:61	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_26:4:306:388:342	163	chr1	1211	99	35M	=	1398	222	CCGTCCGTGTCCTCCCATCTGGCCTCGTCCACACT	================5====:=====;==1=4==	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_108:5:180:905:36	147	chr1	1212	99	35M	=	1033	-214	CCTCCGTGTCCTCCCATCTGGCCTCGTCCACACTG	6%%<;<662<<*;<<<8<<:<<<<<<<<<<<<<<;	MF:i:18	Aq:i:65	NM:i:1	UQ:i:4	H0:i:1	H1:i:0
+EAS218_1:2:19:752:816	99	chr1	1212	99	35M	=	1394	217	CGTCCGTGTCCTCCCATCTGGCCTCGTCCACACTG	<<<<<<<<<<<<<<<<<<<8<7;<;<<767277;6	MF:i:18	Aq:i:65	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_591:3:305:565:952	147	chr1	1213	99	36M	=	1030	-219	GTCCGTGTCCTCCCATCTGGCCTCGTCCACACTGGT	5(<1<147<81<*8--8<<<7<91<<<;+<+<<<<<	MF:i:18	Aq:i:62	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS219_1:1:44:1466:425	83	chr1	1213	99	35M	=	1044	-204	GTCCGTGTCCTCCCATCTGGCCTCGTCCACACTGG	6-<<9<<:<<;<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_1:4:68:64:783	163	chr1	1214	99	35M	=	1402	223	TCCGTGTCCTCCCATCTGGCCTCGTCCACACTGGT	<<<<<<<<<<<<<<<<<;;<<<<<<;<<<9:<<:9	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_61:7:64:37:257	163	chr1	1215	99	35M	=	1389	209	CCGTGTCCTCCCATCTGGCCTCGTCCACACTGGTT	================<=====;===8;4======	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:2:20:413:1334	99	chr1	1215	99	35M	=	1370	190	CCGTGTCCTCCCATCTGGCCTCGTCCACACTGGTT	7<<;<<<.;<;67;7;;;:;;3;<59+...77677	MF:i:18	Aq:i:60	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_53:8:179:549:753	147	chr1	1218	99	35M	=	1056	-197	TGTCCTCCCATCTGGCCTCGTCCACACTGGTTCTC	:77<</<<<::<:<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_95:1:16:823:343	99	chr1	1223	99	35M	=	1403	215	TCCCATCTGGCCTCGTCCACACTGGTTCTCTTGAA	================================4==	MF:i:18	Aq:i:45	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_108:7:266:556:252	99	chr1	1224	99	35M	=	1392	203	CCCATCTGGCCTCGTCCACACTGGTTCTCTTGAAA	<<<<<<<<<<<<<<<<<;<<<<<<4;;<;;;<7;;	MF:i:18	Aq:i:67	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_59:4:278:524:521	83	chr1	1224	99	35M	=	1025	-234	CCCATCTGGCCTCGTCCACACTGGTTCTCTTGAAA	7777,<;<<7<<<<;;<<;;<<<<<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS219_FC30151:5:72:1426:1883	99	chr1	1226	99	35M	=	1405	214	CATCTGGCCTCGTCCACACTGGTTCTCTTGAAAGC	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<:<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_610:3:82:998:566	83	chr1	1227	99	35M	=	1050	-212	ATCTGGCCTCGTCCACACTGGTTCTCTTGAAAGCT	<9<9<<<<2<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:70	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_591:6:29:575:453	83	chr1	1228	99	36M	=	1056	-208	TCTGGCCTCGTCCACACTGGTTCTCTTGAAAGCTTG	;<<<;;<:<<<;<;<<<<<<<<<<<<<<;<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_108:7:222:538:267	147	chr1	1228	99	35M	=	1074	-189	TCTGGCCTCGTCCACACTGGTTCTCTTGAAAGCTT	52/8-<<7<<;<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:67	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_67:1:138:186:274	147	chr1	1231	99	35M	=	1075	-191	GGCCTCGTCCACACTGGTTCTCTTGAAAGCTTGGG	<;<<<<<6;<<<<<3<<36;3;<9<<<<<<3;<<<	MF:i:18	Aq:i:67	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_610:3:137:895:681	99	chr1	1232	99	35M	=	1418	221	GCCTCGTCCACACTGGTTCTCTTGAAAGCTTGGGC	<<<<<<<<<<<<<<<<<<<<<<<<<<<:<<<-8<<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_39:1:71:636:533	99	chr1	1232	99	35M	=	1398	201	GCCTCGTCCACACTGGTTCTCTTGAAAGCTTGGGC	<<<<<<<<<<<<<<<<<<<<<<<7<<<5<<<-847	MF:i:18	Aq:i:70	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_591:3:45:294:380	83	chr1	1233	80	36M	=	1074	-195	CCTCGTCCACACTGGTTCGCTTGAAAGCTTGGGCTG	;<+<7<<<<;7<,<7<<<+/7;<<;<<;7<<<;<<<	MF:i:18	Aq:i:39	NM:i:1	UQ:i:10	H0:i:0	H1:i:1
+EAS51_66:8:9:80:353	83	chr1	1233	99	35M	=	1067	-201	CCTCGTCCACACTGGTTCTCTTGAAAGCTTGGGCT	;;5;:8<:<:;:;<<<<;<:<<<<<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_39:1:73:302:1574	99	chr1	1233	99	35M	=	1429	231	CCTCGTCCACACTGGTTCTCTTGAAAGCTTGGGCT	<<<<<<<<<<;<<<<<<<<<<<<+:;<<;:8;<<<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_62:5:131:779:345	163	chr1	1237	99	35M	=	1399	197	GTCCACACTGGTTCTCTTGAAAGCTTGGGCTGTAA	============================9====;=	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_81:8:159:71:155	99	chr1	1237	99	35M	=	1428	226	GTCCACACTGGTTCTCTTGAAAGCTTGGGCTGTAA	=========;=<======;=:=3;==;=6<==;=;	MF:i:18	Aq:i:45	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_62:3:55:340:837	83	chr1	1238	99	35M	=	1069	-204	TCCACACTGGTTCTCTTGAAAGCTTGGGCTGTAAT	61378<::<<<5:<;;:<<<<<<<<<<<<;<<<<<	MF:i:18	Aq:i:68	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_108:4:91:521:517	147	chr1	1239	99	35M	=	1061	-213	CCACACTGGTTCTCTTGAAAGCTTGGGCTGTAATG	8;8<4=:===7===9=============<======	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_53:1:47:303:887	83	chr1	1240	96	35M	=	1052	-223	CACACTGGTTCTCTTGAAAGCTTGGGCTGTAATGA	<;<6<;<;<8<<<8<<<<;<<<.<<<<<<<8<8;<	MF:i:18	Aq:i:25	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS112_34:4:74:570:695	163	chr1	1240	99	35M	=	1436	231	CACACTGGTTCTCTTGAAAGCTTGGGCTGTAATGA	=========================7====;8<8;	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_95:3:268:523:511	147	chr1	1241	99	35M	=	1081	-195	ACACTGGTTCTCTTGAAAGCTTGGGCTGTAATGAT	8<7<99<<<<<<<<<:<<<<<<4<<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_57:3:319:174:811	147	chr1	1242	99	35M	=	1044	-233	CACTGGTTCTCTTGAAAGCTTGGGCTGTAATGATG	;7;3<<3.<<<<<<<<<<<4<<<<<<<<<<<<<0<	MF:i:18	Aq:i:47	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS218_1:4:28:315:310	83	chr1	1242	99	35M	=	1085	-192	AAACTGTTCTCTTGAAAGCTTGGGCTGTAATGATG	+%,768<<:<:<2<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:68	NM:i:4	UQ:i:70	H0:i:1	H1:i:0
+EAS1_108:1:328:614:638	99	chr1	1243	99	35M	=	1428	220	ACTGGTTCTCTTGAAAGCTTGGGCTGTAATGATGC	<<<<<<<<<<<<<<<<<<<<4/;<<9<<<<7<<*:	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_81:8:63:930:152	163	chr1	1243	99	35M	=	1410	202	ACTGGTTCTCTTGAAAGCTTGGGCTGTAATGATTC	<<<<;<<<<<<<7<<;::<<)726;)<99<)&;&+	MF:i:18	Aq:i:59	NM:i:1	UQ:i:5	H0:i:1	H1:i:0
+EAS56_59:1:219:294:861	83	chr1	1244	99	35M	=	1073	-206	CTGGTTCTCTTGAAAGCTTGGGCTGTAATGATGCC	;,;<;<<<;&<<<<<<<5<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_63:6:42:920:522	83	chr1	1244	99	35M	=	1067	-212	CTGGTTCTCTTGAAAGCTTGGGCTGTAATGATGCC	;;;;;99<;<<;<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_593:7:87:89:696	99	chr1	1245	99	36M	=	1419	210	TGGTTCTCTTGAAAGCTTGGGCTGTAATGATGCCCC	<<<<<<<<<<<<<<<<<<<<<<<<<<;<:;<<<;<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_81:7:166:979:531	163	chr1	1245	99	35M	=	1410	200	TGGTTCTCTTGAAAGCTTGGGCTGTAATGATGCCC	<<</<<<<<<<<<9<<9<<;<7<<<<9<<<9<,)6	MF:i:18	Aq:i:68	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_95:2:40:918:950	83	chr1	1247	99	35M	=	1071	-211	GTTCTCTTGAAAGCTTGGGCTGTAATGATGCCCCT	=0=&&33======;=====.===============	MF:i:18	Aq:i:65	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_93:1:131:946:353	83	chr1	1249	99	35M	=	1087	-197	TCTCTTGAAAGCTTGGGCTGTAATGATGCCCCTTG	<<:<<66<<<6<<4<<<:8<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_71:6:224:932:942	147	chr1	1250	99	35M	=	1082	-203	CTCTTGAAAGCTTGGGCTGTAATGATGCCCCTTGG	<;<<;;<<<;<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_97:5:318:177:383	83	chr1	1251	99	35M	=	1056	-230	TCTTGAAAGCTTGGGCTGTAATGATGCCCCTTGGC	5:9;7;777<<7<<<<<<<<<<<<<<<<<<<<<<4	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_66:4:188:460:1000	147	chr1	1251	99	35M	=	1080	-206	TCTTGAAAGCTTGGGCTGTAATGATGCCCCTTGGC	+;+077<7;<57<;;8<<<<<<<<<<8<<<<<<<<	MF:i:18	Aq:i:70	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:1:12:1296:358	147	chr1	1252	96	35M	=	1082	-205	CTTGAAAGCTTGGTCTGTAATGATGCCCCTTGGCC	-770074;;6;&42;:2;;;:;;;;:;;/:;;;;:	MF:i:18	Aq:i:37	NM:i:1	UQ:i:17	H0:i:0	H1:i:1
+EAS188_4:5:166:776:590	83	chr1	1252	99	35M	=	1075	-212	CTTGAAAGCTTGGGCTGTAATGATGCCCCTTGGCC	<;:;<<;<<;<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:66	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_28:6:54:263:585	147	chr1	1254	99	36M	=	1081	-209	TGAAAGCTTGGGCTGTAATGATGCCCCTTGGCCATC	1:::6<<<<;;;<4<<<<<<<<6<<<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:6:93:1475:542	83	chr1	1254	99	35M	=	1110	-179	TGAAAGCTTGGGCTGTAATGATGCCCCTTGGCCAT	98987:9:<:;:;;;;;<<;<;<;;;;<<<;;;<<	MF:i:18	Aq:i:66	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_32:6:122:342:296	147	chr1	1256	99	35M	=	1100	-191	AAAGCTTGGGCTGTAATGATGCCCCTTGGCCATCA	<:;:<<<;<2<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_57:6:234:787:12	83	chr1	1257	97	35M	=	1092	-200	AAGCTTGGGCTGTAATGATGCCCCTTGGCCATCAC	;;.<;;994<;9<<;;;<<<<<<<7<<<<<<<<<;	MF:i:18	Aq:i:24	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_30:4:317:378:535	83	chr1	1258	99	35M	=	1096	-197	AGCTTGGGCTGTAATGATGCCCCTTGGCCATCACC	;7;':<77<<;<<<;<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_597:5:160:434:853	83	chr1	1259	99	35M	=	1072	-222	GCTTGGGCTGTAATGATGCCCCTTGGCCATCACCC	;;*4;<;<<<;<<<<<<<8<<<;<<<<<<<<8<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS218_1:2:18:1498:1475	163	chr1	1260	99	35M	=	1427	202	CTTGGGCTGTAATGATGCCCCTTGGCCATCACCCG	<<<<<7<<<<<<+<<-3<<3<:<2<1<<:<<<<<+	MF:i:18	Aq:i:71	NM:i:1	UQ:i:27	H0:i:1	H1:i:0
+B7_593:2:104:744:280	99	chr1	1262	64	36M	=	1421	195	TGGGCTGTAATGATGCCCCTTGTCCATCACCCGGTC	<<<<<<<<<<<<<<;<;<<<<:4<<4<<0<;80+;:	MF:i:18	Aq:i:21	NM:i:2	UQ:i:34	H0:i:0	H1:i:1
+EAS1_95:4:66:179:118	83	chr1	1262	99	35M	=	1084	-213	TGGGCTGTAATGATGCCCCTTGGCCATCACCCAGT	<<99<<<<<<<<<<<<<<<<<<<9<<<:<<<<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_108:1:277:194:143	99	chr1	1262	99	35M	=	1444	217	TGGGCTGTAATGATGCCCCTTGGCCATCACCCGGT	<<<<<<<<<<<;<<<<<<<<<<9;<<<8</<<6<:	MF:i:18	Aq:i:72	NM:i:1	UQ:i:21	H0:i:1	H1:i:0
+EAS1_97:2:59:882:980	83	chr1	1263	99	35M	=	1071	-227	GGGCTGTAATGATGCCCCTTGGCCATCACCCGGTC	7339%<6<<<<<;<<9<<8<<<<;<<<<<<<<<<<	MF:i:18	Aq:i:43	NM:i:1	UQ:i:27	H0:i:0	H1:i:1
+EAS220_1:4:14:1665:1772	83	chr1	1263	84	35M	=	1073	-225	GGGCTGTAATGATGCCCCTTGGCCATCACCCGGTC	<&7<<:<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:39	NM:i:1	UQ:i:27	H0:i:0	H1:i:1
+EAS56_57:2:259:42:969	163	chr1	1265	99	35M	=	1426	196	GCTGTAATGATGCCCCTTGGCCATCACCCGGTCCC	<<<<<;<<;<<3<<<;9<36<<29;<<;;;</;<2	MF:i:18	Aq:i:69	NM:i:1	UQ:i:26	H0:i:1	H1:i:0
+EAS221_1:4:4:1732:88	147	chr1	1265	99	35M	=	1087	-213	GCTGTAATGATGCCCCTTGGCCATCACCCGGTCCC	:<4<:<<:<::<<<<<::<<<<<:<:<<<<<<<<<	MF:i:18	Aq:i:45	NM:i:1	UQ:i:27	H0:i:0	H1:i:1
+EAS1_105:2:110:584:649	147	chr1	1266	99	35M	=	1084	-217	CTGTAATGATGCCCCTTGGCCATCACCCGGTCCCT	++:4686<<68<;<;<;<<<:<<<<<<<<<<<<<<	MF:i:18	Aq:i:43	NM:i:1	UQ:i:27	H0:i:0	H1:i:1
+EAS56_59:5:113:694:725	83	chr1	1266	99	35M	=	1088	-213	CTGTAATGATGCCCCTTGGCCATCACCCGGTCCCT	;::<<:<:<<<<<<<<<<:<:<<<<<<;<<<<<<<	MF:i:18	Aq:i:47	NM:i:1	UQ:i:27	H0:i:0	H1:i:1
+EAS221_1:8:58:369:244	163	chr1	1266	99	35M	=	1436	205	CTGTAATGATGCCCCTTGGCCATCACCCAGTCCCT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_57:5:105:521:563	83	chr1	1267	10	35M	=	1103	-199	TGTAATGCTGCCCCTTGGCCATCCCCCGGTCCCTG	/8)-8/6(98<967<3<<979<<1<<<7<<<<7<<	MF:i:18	Aq:i:10	NM:i:3	UQ:i:45	H0:i:0	H1:i:0
+EAS188_4:5:202:326:680	83	chr1	1268	78	35M	=	1108	-195	GTAATGATGCCCCTTGGCCATCACCCGGTCCCTGC	+33<81<:*<;<;;30;<<<;<<<8<<<<<<<<<<	MF:i:18	Aq:i:37	NM:i:1	UQ:i:27	H0:i:0	H1:i:1
+EAS192_3:6:216:292:528	99	chr1	1269	99	35M	=	1438	204	TAATGATGCCCCTTGGCCATCACCCAGTCCCTGCC	<;<;<<<<<<<;<<<<<<<<;;;;:;;:<%<;1;:	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_3:2:67:1864:477	163	chr1	1270	99	35M	=	1465	230	AATGATGCCCCTTGGCCATCACCCAGTCCCTGCCC	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_11:1:35:631:594	83	chr1	1271	99	35M	=	1112	-194	ATGATGCCCCTTGGCCATCACCCGGTCCCTGCCCC	<<<<4<<<<<.<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:45	NM:i:1	UQ:i:27	H0:i:0	H1:i:1
+EAS112_34:8:103:812:255	99	chr1	1272	99	35M	=	1461	224	TGATGCCCCTTGGCCATCACCCAGTCCCTGCCCCC	<<<<<<<<<<<<<<<9<<;<<<39;;<;32:7;7+	MF:i:18	Aq:i:69	NM:i:1	UQ:i:12	H0:i:1	H1:i:0
+EAS188_7:4:259:869:641	99	chr1	1272	99	35M	=	1435	198	TGATGCCCCTTGGCCATCACCCAGTCCCTGCCCCA	<<<<<<<<<<<<<<<<<<<<<,;<:<<<<<<<<<1	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_59:3:316:25:230	83	chr1	1273	99	35M	=	1098	-210	GATGCCCCTTGGCCATCACCCGGTCCCTGCCCCAT	8;8;<<;<;;<<<<<;<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:47	NM:i:1	UQ:i:27	H0:i:0	H1:i:1
+EAS221_1:6:38:1071:155	99	chr1	1274	99	35M	=	1465	226	ATGCCCCTTGGCCATCACCCAGTCCCTGCCCCATC	<<<<<<<<<<<<<:<<<<<<<<8<<<:<<:;;8:;	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_593:7:6:585:132	83	chr1	1276	23	36M	=	1105	-207	GCCCCTTGACCACCACCCAGTCCCTGCCCCATCTCT	:<473$'<+5;7*+<7<&<37<7<<<<7;;7<<:<7	MF:i:18	Aq:i:23	NM:i:2	UQ:i:19	H0:i:0	H1:i:0
+B7_595:6:47:720:789	99	chr1	1278	90	35M	=	1455	212	CCCTTGGCCATCACCCGGTCCCGGCCCCTTCTCTT	<<72<<<<<<<<;;<7;,0<2;*7<2;<*;;<<64	MF:i:18	Aq:i:25	NM:i:3	UQ:i:44	H0:i:0	H1:i:0
+EAS192_3:6:185:868:496	163	chr1	1278	99	35M	=	1442	199	CCCTTGGCCATCACCCAGTCCCTGCCCCATCTCTT	<<<<<<<<<<<<;<<<;<<<<<<<<<<<9<<;<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_30:6:290:146:36	147	chr1	1280	99	35M	=	1110	-205	CTTTCCCATCCCCCGGTCCCTGCCCCATCTCTTGT	7;%%%<8-4<(<<<7<<<:<:<<<<<<<<<<<<<<	MF:i:18	Aq:i:25	NM:i:4	UQ:i:37	H0:i:0	H1:i:0
+B7_593:5:267:71:603	99	chr1	1281	99	36M	=	1446	201	TTGGCCATCACCCAGTCCCTGCCCCATCTCTTGTAA	<<<<<<<<<<<<<<<<<<<<<<;<<<<<<<<<<<9;	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_99:7:183:645:699	147	chr1	1281	86	35M	=	1122	-194	GTGGCCCTCCCCCATTCCCTGCCCCATCTCTTGTA	&)))2-&420<<<'--<6:6-<7<<<+:7<65<<<	MF:i:18	Aq:i:21	NM:i:4	UQ:i:37	H0:i:0	H1:i:0
+EAS1_105:2:179:532:82	147	chr1	1285	99	35M	=	1105	-215	CCATCACCCGGTCCCTGCCCCATCTCTTGTAATCT	<:96<6<<<<89<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:45	NM:i:1	UQ:i:27	H0:i:0	H1:i:1
+EAS1_105:3:176:431:647	83	chr1	1285	99	35M	=	1112	-208	CCATCACCCAGTCCCTGCCCCATCTCTTGTAATCT	<(9(<<<7;<<7<<<<<<<7<<<<<<7<<<<<<<<	MF:i:18	Aq:i:70	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_62:2:258:266:101	83	chr1	1285	99	35M	=	1094	-226	CCATCACCCAGTCCCTGCCCCATCTCTTGTAATCT	%==/7&8=======:===6================	MF:i:18	Aq:i:68	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_32:6:179:735:569	163	chr1	1286	99	35M	=	1461	210	CATCACCCGGTCCCTGCCCCATCTCTTGTAATCTC	<<<<<<<<<<<<<<<<<<<<3<<<<<<<<4/<;<<	MF:i:18	Aq:i:45	NM:i:1	UQ:i:27	H0:i:0	H1:i:1
+EAS188_7:3:200:712:439	163	chr1	1286	99	35M	=	1435	184	CGTCACCCGGTCCCTGCCCCATCTCTTGTAATCTC	<7<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:29	NM:i:2	UQ:i:49	H0:i:0	H1:i:0
+EAS1_103:5:319:165:698	99	chr1	1287	99	35M	=	1485	233	ATCACCCAGTCCCTGCCCCATATCTTGTAATCTCT	<<<<<<<<<<<<<<<<<<<3<9<<<<<<<;<<<<<	MF:i:18	Aq:i:47	NM:i:1	UQ:i:24	H0:i:0	H1:i:1
+B7_597:3:53:616:842	83	chr1	1288	99	35M	=	1109	-214	TCACCCAGTCCCTGCCCCATCTCTTGTAATCTCTC	;<;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:68	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_59:6:286:753:854	83	chr1	1288	99	35M	=	1110	-213	TCACCCAGTCCCTGCCCCATCTCTTGTAATCTCTC	;<2<<<,57:<<9<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:7:14:1256:204	99	chr1	1288	99	35M	=	1467	214	TCACCCAGTCCCTGCCCCATCTCTTGTAATCTCTC	<<<<<;;;;;;<;;;;;;;<;<;;;;<:-;79697	MF:i:18	Aq:i:64	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_591:5:289:132:526	99	chr1	1289	99	36M	=	1472	219	CACCCGGTCCCTGCCCCATCTCTTGTAATCTCTCTC	<<<<<<<<<<<<<<<<<<<<<<<<<<8<<<<<<<<<	MF:i:18	Aq:i:47	NM:i:1	UQ:i:27	H0:i:0	H1:i:1
+EAS218_1:4:71:832:743	83	chr1	1290	99	35M	=	1102	-223	ACCCAGTCCCTGCCCCATCTCTTGTAATCTCTCTC	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_66:3:102:511:946	99	chr1	1291	26	35M	=	1461	205	CCCAGTCCCTGCCCCATCTCGGGTAATCTCTCTCC	<<9<<;<<<<;<<<<;<<7;%<5<<0<<<)<.<.+	MF:i:18	Aq:i:26	NM:i:2	UQ:i:31	H0:i:0	H1:i:0
+EAS114_39:5:42:1223:1087	99	chr1	1293	99	35M	=	1479	221	CAGTCCCTGCCCCATCTCTTGTAATCTCTCTCCTT	<<<<<<<<<<<<<5<<<<<<<<;<<<<<<<<<<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_19:3:75:732:442	147	chr1	1293	99	40M	=	1121	-212	CGGTCCCTGCCCCATCTCTTGTAATCTCTCTCCTTTTTGC	7,*&28<61:88<.7<:<<:6<1<85:<:1<5<&::<<&<	MF:i:18	Aq:i:60	NM:i:1	UQ:i:11	H0:i:1	H1:i:0
+EAS54_73:3:23:502:103	163	chr1	1294	99	35M	=	1486	227	AGTCCCTGCCCCATCTCTTGTAATCTCTCTCCTTT	<2<<<<<<<<<<.<<<<<<<:1&:<<<7<<<<<<:	MF:i:18	Aq:i:66	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_81:7:74:596:137	147	chr1	1294	91	35M	=	1119	-210	GGTCCCTGCCCCATCGCTTGTAATCTCTCGCCTTT	+40778449779049'+*87489498949%89948	MF:i:18	Aq:i:22	NM:i:3	UQ:i:32	H0:i:0	H1:i:0
+EAS51_66:8:36:688:722	99	chr1	1295	99	35M	=	1469	209	GTCCCTGCCCCATCTCTTGTAATCTCTCTCCTTTT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS188_7:8:60:182:718	163	chr1	1295	99	35M	=	1485	225	GTCCCTGCCCCATCTCTTGTAATCTCTCTCCTTTT	<<<<<<<<<<<<<<<<<<<<7<<<<<<<<<;<;<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_589:4:54:989:654	147	chr1	1296	99	35M	=	1108	-223	TCCCTGCCCCATCTCTTGTAATCTCTCTCCTTTTT	,<1<2<<<;9)9<<;<<;<<<4<<<;<<<<<<<<<	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_97:2:9:203:653	163	chr1	1296	99	35M	=	1488	227	TCCCTGCCCCATCTCTTGTAATCTCTCTCCTTTTT	<<<<<<<<<<<<<<<<<<<<<<::<9<<<<<;;;<	MF:i:18	Aq:i:65	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_28:4:322:631:245	163	chr1	1297	99	36M	=	1474	213	CCCTGCCCCATCTCTTGTAATCTCTCTCCTTTTTGC	<<<<<<<<<<<<<<<<<0<<<<<<<<<<<<<<<<5;	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:6:59:1548:1096	83	chr1	1297	99	35M	=	1099	-233	CCCTGCCCCATCTCTTGTAATCTCTCTCCTTTTTG	88888;;88;;;;8;;9;;;<<<<<<<<<<<<<<;	MF:i:18	Aq:i:66	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS220_1:2:52:1779:1664	99	chr1	1297	99	35M	=	1462	200	CCCTGCCCCATCTCTTGTAATCTCTCTCCTTTTTG	<<<<<<<<<<<<<<<<<<71<<<<<<<<<<<<<<%	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_65:8:218:173:667	99	chr1	1298	99	35M	=	1448	185	CCTGCCCCATCTCTTGTAATCTCTCTCCTTTTTGC	<<<<<<<<<<<<<<<6<<<<<<<<<<<<<<<<<.<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS192_3:6:175:437:950	83	chr1	1298	99	35M	=	1126	-207	CCTGCCCCATCTCTTGTAATCTCTCTCCTTTTTGC	;;5:;;9<<:<;<;<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS192_3:6:201:195:757	83	chr1	1298	99	35M	=	1103	-230	CCTGCCCCATCTCTTGTAATCTCTCTCCTTTTTGC	:<':<:<<46<:<;:<;<;<<9<<<<<<<<;<<<<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS188_4:5:8:377:655	99	chr1	1299	99	35M	=	1473	209	CTGCCCCATCTCTTGTAATCTCTCTCCTTTTTGCT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_589:5:50:950:562	99	chr1	1301	99	35M	=	1473	207	GCCCCATCTCTTGTAATCTCTCTCCTTTTTGCTGC	<<<<<<<<<<<<<<<&<<8<<<<<<<5<:<+<:+;	MF:i:18	Aq:i:43	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_71:5:153:543:671	99	chr1	1301	99	34M	=	1465	199	GCCCCATCTCTTGTAATCTCTCTCCTTTTTGCTG	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<2<<7	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_19:2:33:1193:664	163	chr1	1301	99	40M	=	1474	213	GCCCCATCTCTTGTAATCTCTCTCCTTTTTTCTGCATCCC	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<%:<'<9:::9	MF:i:18	Aq:i:71	NM:i:1	UQ:i:4	H0:i:1	H1:i:0
+EAS1_93:1:253:59:242	99	chr1	1302	99	35M	=	1478	211	CCCCATCTCTTGTAATCTCTCTCCTTTTTGCTGCA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<</<<9;<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_19:6:52:1455:1212	147	chr1	1304	99	40M	=	1153	-191	CCATCTCTTGTAATCTCTCTCCTTTTTGCTGCATCCCTGT	6::4::;4%;9:<79)<:<;<<:4::7<<9<&+71<9;<<	MF:i:18	Aq:i:65	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_108:2:316:176:543	99	chr1	1305	99	35M	=	1469	199	CATCTCTTGTAATCTCTCTCCTTTTTGCTGCATCC	====<=9===<<<=====9====<<=3==,96==9	MF:i:18	Aq:i:62	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS219_1:7:50:1339:1154	163	chr1	1305	99	35M	=	1481	211	CATCTCTTGTAATCTCTCTCCTTTTTGCTGCATCC	==========<<==============;==7<;<<;	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_62:3:169:292:652	99	chr1	1306	99	35M	=	1510	239	ATCTCTTGTAATCTCTCTCCTTTTTGCTGCATCCC	<<<<<<<<<<<<<<<<<<<<<<<<<6<<-<<<<8<	MF:i:18	Aq:i:70	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS219_1:3:11:706:1030	99	chr1	1306	92	35M	=	1469	198	ATCTCTTGTAATCTCTCTCATCTTTGCTGCATCCC	<<<2<<2<<<<<<<<<<<<0<&<<<+<:2<4<<):	MF:i:18	Aq:i:26	NM:i:2	UQ:i:20	H0:i:0	H1:i:0
+EAS221_3:6:70:843:706	99	chr1	1306	99	35M	=	1449	178	ATCTCTTGTAATCTCTCTCCTTTTTGCTGCATCCC	<<<<<<<<<<<<<<<<<<<<<<<<<5<<5<<<<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_32:7:174:597:66	83	chr1	1307	99	35M	=	1148	-194	TCTCTTGTAATCTCTCTCCTTTTTGCTGCATCCCT	9<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS220_1:6:7:1547:1933	163	chr1	1308	99	35M	=	1497	224	CTCTTGTAATCTCTCTCCTTTTTGCTGCATCCCTG	<<<<<<<<<<<<<<<<<<<<<<<:<<8<<<<<<<<	MF:i:18	Aq:i:47	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_593:4:30:117:411	163	chr1	1309	99	36M	=	1482	209	TCTTGTAATCTCTCTCCTTTTTGCTGCATCCCTGTC	<<<<<<<<<<<<<<<<<<<<<<7<<:<<<<<<<<<:	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_95:6:53:156:845	99	chr1	1311	99	35M	=	1487	211	TTGTAATCTCTCTCCTTTTTGCTGCATCCCTGTCT	<<<<<<8<<<.<<<<.6<<--<-<<<<<<<6<<<<	MF:i:18	Aq:i:56	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:3:90:1403:1635	99	chr1	1311	99	35M	=	1480	204	TTGTAATCTCTCTCCTTTTTGCTGCATCCCTGTCT	<<;<;<<<<;<;<;;<<<<<9;<.;;<:;99.979	MF:i:18	Aq:i:66	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_593:7:67:302:762	147	chr1	1313	99	36M	=	1138	-211	GTAATCTCTCTCCTTTTTGCTGCATCCCTGTCTTCC	:8;88<;<<<;<<8<<;<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_78:7:270:448:491	99	chr1	1313	99	35M	=	1501	223	GTAATCTCTCTCCTTTTTGCTGCATCCCTGTCTTC	<<<<<<<<<<<<<<<<<<&<<.<<<<<<<:;;;<;	MF:i:18	Aq:i:68	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_71:6:82:932:400	99	chr1	1313	97	34M	=	1486	208	GTAATCTCTCTCCTCTTCGCTGCATCCCTGTCTT	<<<<<<8<1<<<<8+<<&<<<8<<<<<<<+(,/8	MF:i:18	Aq:i:25	NM:i:2	UQ:i:15	H0:i:0	H1:i:0
+EAS54_81:2:128:394:455	83	chr1	1313	99	35M	=	1156	-192	GTAATCTCTCTCCTTTTTGCTGCATCCCTGTCTTC	;=;9.=5=;=9====;;==================	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_595:3:57:735:151	147	chr1	1314	94	35M	=	1121	-228	TAAACTCTCACCTTATTGCTGCATCCCTGTCTTCC	07;+79:;<)<<9<+8<:<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:26	NM:i:3	UQ:i:28	H0:i:0	H1:i:0
+EAS114_28:6:51:506:878	163	chr1	1314	99	36M	=	1501	223	TAATCTCTCTCCTTTTTGCTGCATCCCTGTCTTCCT	<<<<<<<<<<<<<<<<<4<<<<<<<<<<0<<<<<:;	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:2:15:1497:1530	147	chr1	1314	99	35M	=	1136	-213	TAATCTCTCTCCTTTTTGCTGCATCCCTGTCTTCC	77778:;;;:;;;;:9;:;;;;;;;;;9;:;;;;;	MF:i:18	Aq:i:57	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS219_FC30151:3:9:1595:1826	99	chr1	1316	99	35M	=	1494	213	ATCTCTCTCCTTTTTGCTGCATCCCTGTCTTCCTC	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_597:3:73:273:488	163	chr1	1318	99	35M	=	1512	229	CTCTCTCCTTTTTGCTGCATCCCTGTCTTCCTCTG	<<<<<2<88<88<<<8<<1<<<<<<68<<<;<;<*	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_32:1:199:760:42	163	chr1	1318	24	35M	=	1489	206	CTCTCTAATTTTTGCTGCTTCCATGTCTTACTCTG	+2&2&2&22222220222&220-222-22-22-22	MF:i:130	Aq:i:24	NM:i:5	UQ:i:51	H0:i:0	H1:i:0
+EAS1_95:7:61:702:720	163	chr1	1320	99	35M	=	1500	215	CTCTCCTTTTTGCTGCATCCCTGTCTTCCTCTGTC	==============;=======&=========3:=	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_39:2:41:576:1016	163	chr1	1320	99	35M	=	1503	218	CTCTCCTTTTTGCTGCATCCCTGTCTTCCTCTGTC	<<<<<<<<<<<<<<;<<<;<<<<<<<<<<<4<::<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS188_7:1:115:683:296	99	chr1	1320	99	35M	=	1514	229	CTCTCCTTTTTGCTGCATCCCTGTCTTCCTCTGTC	<<<<<<<<<<<8<<<<<<<<<<6<<<<3<<<<<<<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_3:8:63:1265:820	99	chr1	1320	99	35M	=	1480	195	CTCTCCTTTTTGCTGCATCCCTGTCTTCCTCTGTC	<<<<<<<<<<27<<<<<<<<<<<<<<<<<<<<03<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_19:7:92:288:1354	163	chr1	1321	99	40M	=	1480	199	TCTCCTTTTTGCTGCATCCCTGTCTTCCTCTGTCTTGATT	<<<<<<:<<<<<<<<<<<8<<:<<<<;;<8<<<8<:8+::	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS188_7:1:316:949:122	147	chr1	1321	99	35M	=	1156	-200	TCTCCTTTTTGCTGCATCCCTGTCTTCCTCTGTCT	59899<<<<;;<<;<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS218_1:4:37:1626:862	163	chr1	1321	99	35M	=	1489	203	TCTCCTTTTTGCTGCATCCCTGTCTTCCTCTGTCT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_99:5:147:479:41	83	chr1	1322	99	35M	=	1139	-218	CTCCTTTTTGCTGCATCCCTGTCTTCCTCTGTCTT	;:;:;<::<:<<<<<:<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_19:3:73:936:1509	163	chr1	1322	99	40M	=	1502	220	CTCCTTTTTGCTGCATCCCTGTCTTCCTCTGTCTTTATTT	<<<<<<<<<7<<7<<<<<<<;<<<<<<<<<:<:<;%8:::	MF:i:18	Aq:i:75	NM:i:1	UQ:i:4	H0:i:1	H1:i:0
+EAS51_62:6:50:542:881	83	chr1	1324	99	35M	=	1132	-227	CCTTTTTGCTGCATCCCTGTCTTCCTCTGTCTTGA	+2<<<;<3;29<6<5;<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:63	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS112_34:6:71:85:629	163	chr1	1324	99	35M	=	1484	195	CCTTTTTGCTGCATCCCTGTCTTCCTCTGTCTTGA	<<<<<<<<<<9<<<<<<<<<<<<<<<<<5<9<<+6	MF:i:18	Aq:i:63	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_93:6:191:948:257	163	chr1	1325	99	35M	=	1493	203	CTTTTTGCTGCATCCCTGTCTTCCTCTGTCTTGAT	:<<<<<<<<9<:<<<<<<:<<<<;<<<<8<<<<7<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_95:1:249:986:224	99	chr1	1325	99	35M	=	1499	209	CTTTTTGCTGCATCCCTGTCTTCCTCTGTCTTGAT	=========5======7878===98==7=9==.-=	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS219_1:5:6:1067:91	163	chr1	1325	99	35M	=	1483	193	CTTTTTGCTGCATCCCTGTCTTCCTCTGTCTTGAT	<<<<<<<<<<<<<<<<<<<<<<<<<<<:<<<:8<<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_591:4:216:650:516	147	chr1	1326	99	36M	=	1164	-198	TTTTTGCTGCATCCCTGTCTTCCTCTGTCTTGATTT	;9;<<<<<<;<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_65:6:18:376:416	163	chr1	1326	99	35M	=	1510	219	TTTTTGCTGCATCCCTGTCTTCCTCTGTCTTGTTT	<<<<<<<<<<<<<<<<;<<<<<<<<<<<<<;:(<<	MF:i:18	Aq:i:70	NM:i:1	UQ:i:7	H0:i:1	H1:i:0
+EAS114_28:5:209:778:588	163	chr1	1326	99	36M	=	1514	224	TTTTTGCTGCATCCCTGTCTTCCTCTGTCTTGATTT	<<<<<<<<;<<<<<<<<<;<<<;<8<8<<<<;7;;;	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_1:4:36:1402:1709	83	chr1	1326	99	35M	=	1168	-193	TTTTTGCTGCATCCCTGTCTTCCTCTGTCTTGATT	;;;:<<<;<<<<<<<<<<<<<<<<<<<<<<;<<<<	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_26:4:40:352:151	147	chr1	1327	99	35M	=	1137	-225	TTTTGCTGCATCCCTGTCTTCCTCTGTCTTGATTT	;=;;5=:-=9=====;;==================	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_26:5:139:331:63	99	chr1	1327	99	35M	=	1486	194	TTTTGCTGCATCCCTGTCTTCCTCTGTCTTGATTT	====================<<=============	MF:i:18	Aq:i:79	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS220_1:2:11:1274:1230	163	chr1	1327	99	35M	=	1507	215	TTTTGCTGCATCCCTGTCTTCCTCTGTCTTGATTT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<7;;;;	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_63:5:36:678:316	99	chr1	1328	99	35M	=	1500	207	TTTGCTGCATCCCTGTCTTCCTCTGTCTTGATTTA	<<<<<<<<<<<<<<;<<<<<<<<<;<<<<,2<<<)	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_610:3:102:825:507	163	chr1	1330	99	35M	=	1501	206	TGCTGCATCCCTGTCTTCCTCTGTCTTGATTTACT	<<<<<<<<<<<<<<<<<<<<<<;<<<<<<<<<;;<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_593:5:171:343:758	99	chr1	1331	99	36M	=	1494	199	GCTGCATCCCTGTCTTCCTCTGTCTTGATTTACTTG	<<<<<<<<<<<<<<<<<<<<<;<<<<59<<<9;<<3	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_39:6:85:1224:625	99	chr1	1331	99	35M	=	1532	236	GCTGCATCCCTGTCTTCCTCTGTCTTGATTTCCTT	<<<<<<<<<;<<;<<7<<:<<7.<<<:&7<<.<;<	MF:i:18	Aq:i:70	NM:i:1	UQ:i:13	H0:i:1	H1:i:0
+EAS188_7:5:308:354:124	99	chr1	1331	99	35M	=	1507	211	GCTGCATCCCTGTCTTCCTCTGTCTTGATTTACTT	<<<<<<<<<<<<<<<<<<<<<;<<<<;<<<<<<<<	MF:i:18	Aq:i:70	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_53:7:22:22:934	163	chr1	1332	99	35M	=	1500	203	CTGCATCCCTGTCTTCCTCTGTCTTGATTTACTTG	<<<<<<<<<<<6<<<;<<<;84;<<48;<;6;<;)	MF:i:18	Aq:i:65	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_57:4:71:707:568	163	chr1	1332	99	35M	=	1518	221	CTGCATCCCTGTCTTCCTCTGTCTTGATTTACTTG	<<<<<<<<<<<<<<<<<<<<<<<<<<9<<<<;<;<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_595:7:123:610:472	99	chr1	1333	99	35M	=	1504	206	TGCATCCCTGTCTTCCTCTGTCTTGATTTACTTGT	<<<<<<<<<<:<<<<<<<<<<<<<+:<<<<<<<<;	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_93:1:20:635:509	83	chr1	1333	99	35M	=	1167	-201	TGCATCCCTGTCTTCCTCTGTCTTGATTTACTTGT	50<59<<9<9<<<<<<<<<<<<<<<<<<<6<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_93:1:92:213:217	99	chr1	1333	99	35M	=	1515	217	TGCATCCCTGTCTTCCTCTGTCTTGATTTACTTGT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<4<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_67:3:47:471:858	163	chr1	1335	99	35M	=	1487	187	CATCCCTGTCTTCCTCTGTCTTGATTTACTTGTTG	<<;<<<<<<<<9<<<4;;<<<<;<<<<<.<<4;<4	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_39:7:90:406:631	163	chr1	1335	99	35M	=	1525	225	CATCCCTGTCTTCCTCTGTCTTGATTTACTTGTTG	<<<<<<<<<<<<<<<<<:<<<<:;<<<<;<<8;<8	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS219_FC30151:3:81:1723:1820	99	chr1	1335	99	35M	=	1524	224	CATCCCTGTCTTCCTCTGTCTTGATTTACTTGTTG	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<:<<:	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_610:3:182:23:585	147	chr1	1336	99	35M	=	1163	-208	ATCCCTGTCTTCCTCTGTCTTGATTTACTTGTTGT	9:<<<<<<<<<<<<<<<9<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_63:8:150:508:757	163	chr1	1336	99	35M	=	1483	182	ATCCCTGTCTTCCTCTGTCTTGATTTACTTGTTGT	<<<<<<<<<<<<<<<<<<<<<<:<<<<<<<8<<,<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_95:1:261:504:780	163	chr1	1337	99	35M	=	1501	199	TCCCTGTCTTCCTCTGTCTTGATTTACTTGTTGTT	<<<<<<<<<<<<<<<<<<<</2<<<9<<<5<<,<<	MF:i:18	Aq:i:43	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_71:6:324:515:230	163	chr1	1339	99	35M	=	1512	207	CCTGTCTTCCTCTGTCTTGATTTACTTGTTGTTGG	<<;<<<<<<<<<<<<<<<:<<<<8<<<4<<4<<34	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_589:7:72:916:763	83	chr1	1340	99	35M	=	1142	-233	CTGTCTTCCTCTGTCTTGATTTACTTGTTGTTGGT	<;;:<<<<<<<;<<;;;<<<<<<<<<;;<;<<<<<	MF:i:18	Aq:i:63	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_593:3:194:168:684	99	chr1	1340	99	36M	=	1512	208	CTGTCTTCCTCTGTCTTGATTTACTTGTTGTTGGTT	<<<<<<<<<<<<<<<<<<<<<<<<<<7<<.<<6-<<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_78:7:113:43:634	163	chr1	1340	99	35M	=	1500	195	CTGTCTTCCTCTGTCTTGATTTACTTGTTGTTTTT	<<<<<<<<<<<<.<<<<<<<<<<<<</<<2;;%%;	MF:i:18	Aq:i:45	NM:i:2	UQ:i:8	H0:i:1	H1:i:0
+EAS54_71:5:16:434:204	163	chr1	1340	99	35M	=	1522	216	CTGTCTTCCTCTGTCTTGATTTACTTGTTGTTGGT	=================;)===8===:==7;<+%;	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_81:7:246:205:734	73	chr1	1340	65	35M	=	1340	0	CTGTCTTCCTCTGTCTTGATTTACTTGTTGTTGGT	<<<4<<6666<<6<:<<<3<<<:'<<:<<<<;6<+	MF:i:64	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_81:7:246:205:734	133	chr1	1340	0	*	=	1340	0	CTCCAGGGAAGTTATCTCTCATCTAGANNNNNTTG	<<<<<<:/<<<,6'</7;<-+9<<;<7!!!!!8<,	MF:i:192
+EAS54_65:3:102:884:63	163	chr1	1341	99	35M	=	1481	175	TGTCTTCCTCTGTCTTGATTTCCTTGTTGTTGGTT	<<<<<<<<<<<<<<<<<3<<<%<<<9<<9<<7+;<	MF:i:18	Aq:i:43	NM:i:1	UQ:i:4	H0:i:0	H1:i:1
+EAS51_64:3:67:782:132	99	chr1	1343	99	35M	=	1498	190	TCTTCCTCTGTCTTGATTTACTTGTTGTTGGTTTT	<<<<<<<<<<<<<<<<<<<<<<<<<<:<<;4<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS219_FC30151:5:70:348:972	163	chr1	1343	99	35M	=	1528	220	TCTTCCTCTGTCTTGATTTACTTGTTGTTGGTTTT	<.<<3+.7<<7<<:78:<<7<:<7:<3<<7.:::<	MF:i:18	Aq:i:65	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS218_4:1:9:206:901	99	chr1	1344	99	35M	=	1517	208	CTTCCTCTGTCTTGATTTACTTGTTGTTGGTTTTC	<<<<<<<<<<<<<<<<<<<<<<5<<5<<%%:<<<7	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS188_7:4:21:443:404	99	chr1	1345	99	35M	=	1529	219	TTCCTCTGTCTTGATTTACTTGTTGTTGGTTTTCT	<<<<<<<<<<<<<<<<<<<<<7<<;<<;+<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_108:1:148:286:316	163	chr1	1347	99	35M	=	1531	219	CCTCTGTCTTGATTTACTTGTTGTTGGTTTTCTGT	<<<<<<<<+<<7<<<<<<<6<<<6<142<<<6<2<	MF:i:18	Aq:i:70	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_108:6:77:48:860	99	chr1	1348	99	35M	=	1521	208	CTCTGTCTTGATTTACTTGTTGTTTGTTTTCTGTT	=========;===========9==*;5=;=;=,7=	MF:i:18	Aq:i:45	NM:i:1	UQ:i:9	H0:i:0	H1:i:1
+EAS51_64:6:124:128:489	147	chr1	1348	99	35M	=	1142	-241	CTCTGTCTTGATTTACTTGTTGTTGGTTTTCTGTT	::55<<<8<<<6<<;<<<<<<<<7<<<<<<<<<<<	MF:i:18	Aq:i:70	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_64:6:213:54:878	137	chr1	1348	99	35M	*	0	0	CTCTGTCTTGATTTACTTGTTGTTGGTTTTTTGTT	<<<<<<<<<;<<<<<<<<:<<:<<++<<<<%<%<<	MF:i:18	Aq:i:69	NM:i:1	UQ:i:4	H0:i:1	H1:i:0
+EAS218_1:4:73:42:1038	163	chr1	1349	99	35M	=	1513	199	TCTGTCTTGATTTACTTGTTGTTGGTTTTCTGTTT	<<<<<<<<<<<<<<<<<<<<<<<:<<<<<.<<<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_103:3:320:505:814	99	chr1	1350	99	35M	=	1515	200	CTGTCTTGATTTACTTGTTGTTGGTTTTCTTTTTC	<<<<<<<<<<<<<<<<;<<8<<76<<<<;<&<<<7	MF:i:18	Aq:i:72	NM:i:1	UQ:i:5	H0:i:1	H1:i:0
+B7_593:2:68:692:347	83	chr1	1351	99	36M	=	1176	-211	TGTCTTGATTTACTTGTTGTTGGTTTTCTGTTTCTT	9<;;;;<<<:<;<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:64	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_71:4:252:428:683	137	chr1	1351	99	35M	*	0	0	TGTCTTGATTTACTTGTTGTTGGTTTTCTGTTTCT	<<<<<<;<<<<<<<<7<<7<<&+<<<<:<&<<<4<	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_71:4:73:182:444	99	chr1	1354	99	34M	=	1533	214	CTTGATTTACTTGTTGTTGGTTTTCTGTTTCTTT	<<<<;;<<<<<<<<<<<<;<;<<<<<:<<<<<7<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS220_1:2:63:267:545	163	chr1	1354	99	35M	=	1524	205	CTTGATTTACTTGTTGTTGGTTTTCTGTTTCTTTG	<<<<<<<<<<<<:<<<<<::<<<<<<.<<<;;;;5	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_99:6:177:562:806	99	chr1	1356	99	35M	=	1515	194	TGATTTACTTGTTGTTGGTTTTCTGTTTCTTTTTT	<;<29<99<<;<<<9<20<9<<5;;<<<<<<<+.<	MF:i:18	Aq:i:35	NM:i:1	UQ:i:10	H0:i:1	H1:i:0
+EAS51_62:7:157:784:936	83	chr1	1356	99	35M	=	1169	-222	TGATTTACTTGTTGTTGGTTTTCTGTTTCTTTGTT	<:<<<<8<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_595:1:209:345:87	163	chr1	1360	99	35M	=	1513	188	TTACTTGTTGTTGGTTTTCTGTTTCTTTTTTTGAT	<<<<<<<<<<<<<<<<<<<<;<<<-<<<6<<<+8<	MF:i:18	Aq:i:71	NM:i:1	UQ:i:21	H0:i:1	H1:i:0
+EAS114_45:1:33:1407:94	83	chr1	1360	99	35M	=	1172	-223	TTACTTGTTGTTGGTTTTCTGTTTCTTTGTTTGAT	77477;4;;;;;44;;;;;;7;;;;;;;9;;;;;<	MF:i:18	Aq:i:66	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_589:8:2:434:715	163	chr1	1363	99	35M	=	1527	199	CTTGTTGTTGGTTTTCTGTTTCTTTGTTTGATTTT	<<<<<<<<<<<<<<<<<;<<<<<<<0<<<68<<<+	MF:i:18	Aq:i:71	NM:i:1	UQ:i:10	H0:i:1	H1:i:0
+EAS54_65:4:137:319:642	137	chr1	1363	99	35M	*	0	0	CTTGTTGTTGGTTTTCTGTTTCTTTTTTTGATTTT	<<<<<<<<<27<<<<<<<<<<<<<<&;<<&3;;<%	MF:i:18	Aq:i:41	NM:i:2	UQ:i:9	H0:i:0	H1:i:1
+B7_610:3:148:340:479	147	chr1	1364	99	35M	=	1190	-209	TTGTTGTTGGTTTTCTGTTTCTTTGTTTGATTTGG	<<;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_26:2:329:458:365	147	chr1	1364	99	35M	=	1186	-213	TTGTTGTTGGTTTTCTGTTTCTTTGTTTGATTTGG	====:==9========>==7>==9>=7=>=>>=>>	MF:i:18	Aq:i:78	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_65:4:91:267:655	147	chr1	1365	99	35M	=	1204	-196	TGTTGTTGGTTTTCTGTTTCTTTGTTTGATTTGGT	;,:;5:<6:<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_1:2:91:856:504	99	chr1	1366	99	35M	=	1520	189	GTTGTTGGTTTTCTGTTTCTTTGTTTGATTTGGTT	<<<<<<<<<<<<<<7<<<<<<<7<<<&;<<<&&<&	MF:i:18	Aq:i:68	NM:i:1	UQ:i:5	H0:i:1	H1:i:0
+EAS1_108:2:170:326:433	99	chr1	1367	99	35M	=	1535	203	TTGTTGGTTTTCTGTTTCTTTGTTTGATTTGGTGG	=====<=9===:=<:==2=======2:===9==/5	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_93:6:132:717:233	99	chr1	1368	99	35M	=	1529	196	TGTTGGTTTTCTGTTTCTTTGTTTGATTTGGTGGA	<<<<<<<<<<<<;<<<<<<<<<<<7<<<<&-<4<1	MF:i:18	Aq:i:47	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_19:1:14:420:712	99	chr1	1368	99	40M	=	1525	197	TGTTGGTTTTCTGTTTCTTTGTTTGATTTTTTTGAAGACA	<<<<<<<<<<<<;<<<<<<<;<<<-;<<<&,<&*8111:6	MF:i:18	Aq:i:66	NM:i:3	UQ:i:21	H0:i:1	H1:i:0
+EAS114_39:4:43:1047:1626	163	chr1	1369	99	35M	=	1523	189	GTTGGTTTTCTGTTTCTTTGTTTGATTTGGTGGAA	<<<<<<<<<<<<<<<<<<<:<<<:<<<<:+;-4:(	MF:i:18	Aq:i:70	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:2:20:413:1334	147	chr1	1370	99	35M	=	1215	-190	TTGGTTTTCTGTTTCTTTGTTTGATTTGGTGGAAG	88878777;:;:1:;9;;;6;;;6;9;;;;;296;	MF:i:18	Aq:i:60	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_62:5:154:669:853	83	chr1	1371	99	35M	=	1193	-213	TGGTTTTCTGTTTCTTTGTTTGATTTGGTGGAAGA	<::<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_610:7:117:857:942	99	chr1	1372	99	35M	=	1527	190	GGTTTTCTGTTTCTTTGTTTGATTTGGTGGAAGAC	<<<<<<<<<<<<<<<<<<<<<<<<<:6<;;7;9<;	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_57:6:145:144:796	147	chr1	1372	99	35M	=	1181	-226	GGTTTTCTGTTTCTTTGTTTGATTTGGTGGAAGAC	;<<<;<<<<<<<<<;<<<;<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_32:6:88:162:587	147	chr1	1372	99	35M	=	1189	-218	GGTTTTCTGTTTCTTTGTTTGATTTGGTGGAAGAC	386;;388-<8;<;68<<;;<;<6<<<8<<<<<<<	MF:i:18	Aq:i:63	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_1:8:73:108:1621	99	chr1	1373	99	35M	=	1532	194	GTTTTCTGTTTCTTTGTTTGATTTGGTGGAAGACA	<<<<<<<<71<<<<<<<<<+<<<<70:0<9<<61<	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS112_34:6:127:153:861	147	chr1	1374	99	35M	=	1202	-207	TTTTCTGTTTCTTTGTTTGATTTGGTGGAAGACAT	:;:6;9<<1;<<95<<<9<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS188_7:2:152:765:744	163	chr1	1374	99	35M	=	1534	195	TTTTCTGTTTCTTTGTTTGATTTGGTGGAAGACAT	<<<<<<<<<<<<<<<<<<:<<<<<<<<&<7293<<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_73:3:313:827:992	147	chr1	1379	99	35M	=	1197	-217	TGTTTCTTTGTTTGATTTGGTGGAAGACATAATCC	'187:1'<75<.*<<:5<..<<*<<917<<7<<17	MF:i:18	Aq:i:57	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_64:3:7:268:263	121	chr1	1381	22	35M	=	1381	0	TTGCGTTATTTGAGTTGGTGGAAGACATAATCCCA	',)*&2<$7+<<<'<-<7<<<<<<<7<<</4/;<<	MF:i:64	Aq:i:0	NM:i:4	UQ:i:22	H0:i:0	H1:i:0
+EAS51_64:3:7:268:263	181	chr1	1381	0	*	=	1381	0	TCGTACAGAAGTTTAATGGAGCCTTGGGACCTTAC	!!66'&+/&'8+2''1+'611'&6&+/&+.&+1'&	MF:i:192
+EAS139_19:1:47:352:1492	147	chr1	1385	99	40M	=	1205	-220	TTTGTTTTGTATGGTGGAAGACATAATCCCACGCTTCCTA	+7+/7+/%%1'6+3++1;:</<<5<)27<<9<)9<<9<7<	MF:i:18	Aq:i:53	NM:i:3	UQ:i:14	H0:i:1	H1:i:0
+EAS139_11:5:61:38:1182	83	chr1	1388	99	35M	=	1205	-218	GTTTGATTTGGTGGAAGACATAATCCCACGCTTCC	9:;<<<<;<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_61:7:64:37:257	83	chr1	1389	99	35M	=	1215	-209	TTTGATTTGGTGGAAGACATAATCCCACGCTTCCT	;47<<47+9<4<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_108:7:266:556:252	147	chr1	1392	99	35M	=	1224	-203	GATTTGGTGGAAGACATAATCCCACGCTTCCTATG	.8558<72<(<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:67	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_93:4:321:271:138	147	chr1	1394	99	35M	=	1193	-236	TTTGGTGGAAGACATAATCCCACGCTTCCTATGGA	261:5969==9=:=<==<=================	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS218_1:2:19:752:816	147	chr1	1394	99	35M	=	1212	-217	TTTGGTGGAAGACATAATCCCACGCTTCCTATGGA	+<<+<--/<<<<4<2<<<<45<<<:<<<<<<+<<<	MF:i:18	Aq:i:65	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_26:4:306:388:342	83	chr1	1398	99	35M	=	1211	-222	GGGGAAGACATAATCCCACGCTTCCTATGGAAAGG	9/<9;<<<;<;<<7<<<7<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:1	UQ:i:14	H0:i:1	H1:i:0
+EAS114_39:1:71:636:533	147	chr1	1398	99	35M	=	1232	-201	GTGGAAGACATAATCCCACGCTTCCTATGGAAAGG	,51(<<8<:<<<<<<<;<;<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:70	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_62:5:131:779:345	83	chr1	1399	99	35M	=	1237	-197	TGGAAGACATAATCCCACGCTTCCTATGGAAAGGT	<<7<<<<<<<<:<<<<<<<<<<<<<;<<<<<<;<<	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_1:4:68:64:783	83	chr1	1402	99	35M	=	1214	-223	AAGACATAATCCCACGCTTCCTATGGAAAGGTTGT	<<9<8<6<<<<<;<<<<;<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_95:1:16:823:343	147	chr1	1403	99	35M	=	1223	-215	AGACATAACCCCACGCTTCCTATGGAAAGGTTGTT	<<<:<<<;+;<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:45	NM:i:1	UQ:i:10	H0:i:0	H1:i:1
+EAS219_FC30151:5:72:1426:1883	147	chr1	1405	99	35M	=	1226	-214	ACATAATCCCACGCTTCCTATGGAAAGGTTGTTGG	;9<;<;0<;<;<<<<;<<<;:<<<<<<<<<<<<<<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_81:7:166:979:531	83	chr1	1410	99	35M	=	1245	-200	ATCCCACGCTTCCTATGGAAAGGTTGTTGGGAGAT	81<<<3<*<<:<<<<<<<8<<<<<<<<<<<<:<<<	MF:i:18	Aq:i:68	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_81:8:63:930:152	83	chr1	1410	99	35M	=	1243	-202	ATCCCACGCTTCCTATGGAAAGGTTGTTGGGAGAT	;:4:8;:::;=:8;=;========;=:========	MF:i:18	Aq:i:59	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_610:3:137:895:681	147	chr1	1418	99	35M	=	1232	-221	CTTCCTATGGAAAGGTTGTTGGGAGATTTTTAATG	4;5+6;<<<<<<<<<9;<4<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_593:7:87:89:696	147	chr1	1419	99	36M	=	1245	-210	TTCCTATGGAAAGGTTGTTGGGAGATTTTTAATGAT	;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_593:2:104:744:280	147	chr1	1421	64	36M	=	1262	-195	CATATGGAAAGGTTGTTGGGATTTTTTTAATGATTC	'&+74*0<'/.47:8<<<<;<7''6/1<<<.<<68<	MF:i:18	Aq:i:21	NM:i:3	UQ:i:33	H0:i:0	H1:i:0
+EAS56_57:2:259:42:969	83	chr1	1426	99	35M	=	1265	-196	GGAAAGGTTGTTGGGAGATTTTTAATGATTCCTCA	<<<6<<<<<<-<<<<<<;<<;<6<<<<<<<;<<<<	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS218_1:2:18:1498:1475	83	chr1	1427	99	35M	=	1260	-202	GAAAGGTTGTTGGGAGATTTTTAATGATTCCTCAA	:<4<*7<<<<<<<:<<:<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_108:1:328:614:638	147	chr1	1428	99	35M	=	1243	-220	AAAGGTTGTTGGGAGATTTTTAATGATTCCTCAAT	<<;;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_81:8:159:71:155	147	chr1	1428	99	35M	=	1237	-226	AAAGGTTGTTGGGAGATTTTTAATGATTCCTCGAT	5;;9<<:<;:<<<<7<<7;<3<<<:<<<;<<<<<;	MF:i:18	Aq:i:45	NM:i:1	UQ:i:27	H0:i:0	H1:i:1
+EAS114_39:1:73:302:1574	147	chr1	1429	99	35M	=	1233	-231	AAGGTTGTTGGGAGATTTTTAATGATTCCTCAATG	7<88;;<;;<;;<<<<<<<<<<<<<<<<<<<<<1<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS188_7:3:200:712:439	83	chr1	1435	99	35M	=	1286	-184	GTTGGGAGATTTTTAATGATTCCTCAATGTTAAAA	<;<<<<<<<<<<<<<<<<<<<9<<<<<<<<<<<<7	MF:i:18	Aq:i:29	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS188_7:4:259:869:641	147	chr1	1435	99	35M	=	1272	-198	GTTGGGAGATTTTTAATGATTCCTCAATGTTAAAA	99=:=9=99<=========<=<<============	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS112_34:4:74:570:695	83	chr1	1436	99	35M	=	1240	-231	TTGGGAGATTTTTAATGATTCCTCAATGTTAAAAT	.;:8<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_1:8:58:369:244	83	chr1	1436	99	35M	=	1266	-205	TTGGGAGATTTTTAATGATTCCTCAATGTTAAAAT	<<<<<<<<<<<<<<<<<<<<;<<;<<<<<<<<<<<	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS192_3:6:216:292:528	147	chr1	1438	99	35M	=	1269	-204	GGGAGATTTTTAATGATTCCTCAATGTTAAAATGT	;:;;8<<<<<<<<<<<<<:<<;<<<<<<<<<<<<<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS192_3:6:185:868:496	83	chr1	1442	99	35M	=	1278	-199	GATTTTTAATGATTCCTCAATGTTAAAATGTCTAT	:;;<;;<<<<<<<<;4<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_108:1:277:194:143	147	chr1	1444	99	35M	=	1262	-217	TTTTTAATGATTCCTCAATGTTAAAATGTCTATTT	;<<;<<<;8;<0<7<<<<<<<<<<<<7<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_593:5:267:71:603	147	chr1	1446	99	36M	=	1281	-201	TTTAATGATTCCTCAATGTTAAAATGTCTATTTTTG	9;;<;<<<;;<<<<<<<<<<<<<<<<<<<<<<<<;<	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_65:8:218:173:667	147	chr1	1448	99	35M	=	1298	-185	TAATGATTCCTCAATGTTAAAATGTCTATTTTTGT	<<<<<<;<<;<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_3:6:70:843:706	147	chr1	1449	99	35M	=	1306	-178	AATGATTCCTCAATGTTAAAATGTCTATTTTTGTC	<<<<<<<<;<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_595:6:47:720:789	147	chr1	1455	90	35M	=	1278	-212	TCCTCAATGTTAAAATGTCTATTTTTGTCTTGACA	/)040<.878<<<<;8<;<9<9;<<<<<<<<<<93	MF:i:18	Aq:i:25	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_66:3:102:511:946	147	chr1	1461	26	35M	=	1291	-205	ATGTAAAAGTGACTGTTATTGTCTTGACACCCAAC	<%-4:6<:/&46;/*;<*84<0<'<&*<2<<<<<<	MF:i:130	Aq:i:26	NM:i:5	UQ:i:78	H0:i:0	H1:i:0
+EAS112_34:8:103:812:255	147	chr1	1461	99	35M	=	1272	-224	ATGTTAAAATGTCTATTTTTGTCTTGACACCCAAC	7:777:7<<::7<7<7<<:7<7<:<<<<<<<<<7<	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_32:6:179:735:569	83	chr1	1461	99	35M	=	1286	-210	ATGTTAAAATGTCTATTTTTGTCTTGACACCCAAC	<5<3:<<<<5;8<<<55;<:</:<<<<<<<<<<<<	MF:i:18	Aq:i:45	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS220_1:2:52:1779:1664	147	chr1	1462	99	35M	=	1297	-200	TGTTAAAATGTCTATTTTTGTCTTGACACCCAACT	6;;:;<<<:<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_71:5:153:543:671	147	chr1	1465	99	35M	=	1301	-199	TAAAATGTCTATTTTTGTCTTGACACCCAACTAAT	;;;;;=;==================;=========	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_1:6:38:1071:155	147	chr1	1465	99	35M	=	1274	-226	TAAAATGTCTATTTTTGTCTTGACACCCAACTAAT	<<62<<<<<<3<<<<</<<<<<<<%<<<<<<<<<<	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_3:2:67:1864:477	83	chr1	1465	99	35M	=	1270	-230	TAAAATGTCTATTTTTGTCTTGACACCCAACTAAT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:7:14:1256:204	147	chr1	1467	99	35M	=	1288	-214	AAATGTCTATTTTTGTCTTGACACCCAACTAATAT	66777:;;37;;:;;0;:;;;;):;;:7;;;;;;;	MF:i:18	Aq:i:64	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_108:2:316:176:543	147	chr1	1469	99	35M	=	1305	-199	ATGTCTATTTTTGTCTTGACACCCAACTAATATTT	<<)/3<<<&<*<<0<<8<<82</5<<<<<88<<<<	MF:i:18	Aq:i:62	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_66:8:36:688:722	147	chr1	1469	99	35M	=	1295	-209	ATGTCTATTTTTGTCTTGACACCCAACTAATATTT	<;;<<<<<<<<<<<<<<<<:<<<<<<<<<<<<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS219_1:3:11:706:1030	147	chr1	1469	92	35M	=	1306	-198	ATGTCTATTTTTGTCTTGACACCCAACTAATATTT	+<5069+9<<<<+<;<<<<;<<77<7<<;<<;<<<	MF:i:18	Aq:i:26	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_591:5:289:132:526	147	chr1	1472	99	36M	=	1289	-219	TCTATTTTTGTCTTGACACCCAACTAATATTTGTCT	;<<<<<<<<<<<<<<<<<<<:<<<<<<<<<<<<<<<	MF:i:18	Aq:i:47	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_589:5:50:950:562	147	chr1	1473	99	35M	=	1301	-207	CTATTTTTGTCTTGACACCCTACTAATATTTGTCT	<<3<<<8<;<<<<<<+<<8<&<<<<7<<<<<<<<<	MF:i:18	Aq:i:43	NM:i:1	UQ:i:5	H0:i:0	H1:i:1
+EAS188_4:5:8:377:655	147	chr1	1473	99	35M	=	1299	-209	CTATTTTTGTCTTGACACCCAACTAATATTTGTCT	;<8;;:<;<<:<;<<<<<<<<<<<<<<<<<<<<<;	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_28:4:322:631:245	83	chr1	1474	99	36M	=	1297	-213	TATTTTTGTCTTGACACCCAACTAATATTTGTCTGA	<<<<<<<<<<<<<<<<;<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_19:2:33:1193:664	83	chr1	1474	99	40M	=	1301	-213	TATTTTTGTCTTGACACCCAACTAATATTTGTCTGAGCAA	;;;;;;<;;-9<<<:</+9<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_93:1:253:59:242	147	chr1	1478	99	35M	=	1302	-211	TTTGTCTTGACACCCAACTAATATTTGTCTGAGCA	<<<:<;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_39:5:42:1223:1087	147	chr1	1479	99	35M	=	1293	-221	TTGTCTTGACACCCAACTAATATTTGTCTGAGCAA	;:<<<:<7<<<;;<<<<<<<<<<;<<<<<<<<<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:3:90:1403:1635	147	chr1	1480	99	35M	=	1311	-204	TGTCTTGACACCCAACTAATATTTGTCTGAGCAAA	86878;;;8;788;;;;;;;;;;;;;8;5;;;;;;	MF:i:18	Aq:i:66	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_19:7:92:288:1354	83	chr1	1480	99	40M	=	1321	-199	TGTCTTGACACCCAACTAATATTTGTCTGAGCAAAACAGT	::::;;;<<<<9;<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_3:8:63:1265:820	147	chr1	1480	99	35M	=	1320	-195	TGTCTTGACACCCAACTAATATTTGTCTGAGCAAA	<<<<<<3<<1<<<<<<<7<<<<<<<<<<<<<<<+<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_65:3:102:884:63	83	chr1	1481	99	35M	=	1341	-175	GTCTTGACACCCAACTAATATTTGTCTGAGCAAAA	<;7;;<<8<;8;<<<8<<<<<<8<<<8;<<<<<<<	MF:i:18	Aq:i:43	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS219_1:7:50:1339:1154	83	chr1	1481	99	35M	=	1305	-211	GTCTTGACACCCAACTAATATTTGTCTGAGCAAAA	7;7;8;<5<:86<<;<<<<<<<<<<;<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_593:4:30:117:411	83	chr1	1482	99	36M	=	1309	-209	TCTTGACACCCAACTAATATTTGTCTGAGCAAAACA	;88<<<<<:<7<<;<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_63:8:150:508:757	83	chr1	1483	99	35M	=	1336	-182	CTTGACACCCAACTAATATTTGTCTGAGCAAAACA	6;;;<8<6;8<<8<<<<<;<<<<;<<<<;<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS219_1:5:6:1067:91	83	chr1	1483	99	35M	=	1325	-193	CTTGACACCCAACTAATATTTGTCTGAGCAAAACA	3<;<<:;9;<<7;;<;<<<;<<<;<<<<<<<<<<<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS112_34:6:71:85:629	83	chr1	1484	99	35M	=	1324	-195	TTGACACCCAACTAATATTTGTCTGAGCAAAACAG	,,1<1<7&%<9+:<<9<<9<<<<<<<<5<<<<<<<	MF:i:18	Aq:i:63	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_103:5:319:165:698	147	chr1	1485	99	35M	=	1287	-233	TGACACCCAACTAATATTTGTCTGAGCAAAACAGT	;5;2;<:;<<:<<<<<<<<<;:;<<<<<<<<<<<<	MF:i:18	Aq:i:47	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS188_7:8:60:182:718	83	chr1	1485	99	35M	=	1295	-225	TGACACCCAACTAATATTTGTCTGAGCAAAACAGT	<<<:<<;<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_71:6:82:932:400	147	chr1	1486	97	35M	=	1313	-208	GACACCCAACTAATATTTGTCTGAGCAAAACAGTC	<<;<<72<<7<<<<<<<<<<;<<<+7<<<<<<<<<	MF:i:18	Aq:i:25	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_73:3:23:502:103	83	chr1	1486	99	35M	=	1294	-227	GACACCCAACTAATATTTGTCTGAGCAAAACAGTC	4:386:6<:::<:<:4:+<::4<<<6<<<<<<<66	MF:i:18	Aq:i:66	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_26:5:139:331:63	147	chr1	1486	99	35M	=	1327	-194	GACACCCAACTAATATTTGTCTGAGCAAAACAGTC	7===================:=:============	MF:i:18	Aq:i:79	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_95:6:53:156:845	147	chr1	1487	99	35M	=	1311	-211	ACACCCAACTAATATTTGTCTGAGCAAAACAGTCT	171(*00,0;;&;7=77=;5;;(;1:=5=======	MF:i:18	Aq:i:56	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_67:3:47:471:858	83	chr1	1487	99	35M	=	1335	-187	ACACCCAACTAATATTTGTCTGAGCAAAACAGTCT	/;9<<63<<<<3<;<<<<<<<<<<<<<<<<<<<9<	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_97:2:9:203:653	83	chr1	1488	99	35M	=	1296	-227	CACCCAACTAATATTTGTCTGAGCAAAACAGTCTA	37))&<8<<<<<7<4<;<777<<:<<<<<<<<;<<	MF:i:18	Aq:i:65	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_32:1:199:760:42	83	chr1	1489	24	35M	=	1318	-206	ACCCAATTAATATTTTTCTTAGCAAAACAGTCTAG	58*5.<+<<<<,4<<**<90**9<<<<<<4<<<<<	MF:i:18	Aq:i:24	NM:i:3	UQ:i:34	H0:i:0	H1:i:0
+EAS218_1:4:37:1626:862	83	chr1	1489	99	35M	=	1321	-203	ACCCAACTAATATTTGTCTGAGCAAAACAGTCTAG	:663<<3<<<<<<<<<<:<<<<7<<<<<<<<<<<<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_93:6:191:948:257	83	chr1	1493	99	35M	=	1325	-203	AACTAATATTTGTCTGAGCAAAACAGTCTAGATGA	:;;;;<<<<<<5<5<<<<<<<<7<<<<<<<<<<<<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_593:5:171:343:758	147	chr1	1494	99	36M	=	1331	-199	ACTAATATTTGTCTGAGCAAAACAGTCTAGATGAGA	:+;;<<<<<;<;:<<<;;<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS219_FC30151:3:9:1595:1826	147	chr1	1494	99	35M	=	1316	-213	ACTAATATTTGTCTGAGCAAAACAGTCTAGATGAG	;76;;6:9<9<963;<<7<<<<<<<;<;<<<<<<<	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS220_1:6:7:1547:1933	83	chr1	1497	99	35M	=	1308	-224	AATATTTGACTGAGCAAAACAGTCTAGATGAGAGA	<<<<<<<<-<<<<<:<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:47	NM:i:1	UQ:i:12	H0:i:0	H1:i:1
+EAS51_64:3:67:782:132	147	chr1	1498	99	35M	=	1343	-190	ATATTTGTCTGAGCAAAACAGTCTAGATGAGAGAG	;;<;;;<<;;<<<;<<<;<<<;<<<<<<<<<<<<;	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_95:1:249:986:224	147	chr1	1499	99	35M	=	1325	-209	TATTTGTCTGAGCAAAACAGTCTAGATGAGAGAGA	<<<3<;<;;<<;8<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_95:7:61:702:720	83	chr1	1500	99	35M	=	1320	-215	ATTTGTCTGAGCAAAACAGTCTAGATGAGAGAGAA	<<<4<4+0;<<:<<<<<<<<-<<<<<<<<<<<<<<	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_78:7:113:43:634	83	chr1	1500	99	35M	=	1340	-195	ATTTGTCTGAGAAAAACAGTCTAGATGAGAGAGAA	;9;1;<5:<<<%<<<<;<<<;<<<<<<<<<<<<<<	MF:i:18	Aq:i:45	NM:i:1	UQ:i:4	H0:i:0	H1:i:1
+EAS56_53:7:22:22:934	83	chr1	1500	99	35M	=	1332	-203	ATTTGTCTGAGCAAAACAGTCTAGATGAGAGAGAA	<+72::72<<60<<<<<<<96<<<<0<<<<1<<<<	MF:i:18	Aq:i:65	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_63:5:36:678:316	147	chr1	1500	99	35M	=	1328	-207	ATTTGTCTGAGCAAAACAGTCTAGATGAGAGAGAA	<<72.2,;;<)6<<<<:<<;;<<<<<<<<<<<<<<	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_610:3:102:825:507	83	chr1	1501	99	35M	=	1330	-206	TTTGTCTGAGCAAAACAGTCTAGATGAGAGAGAAC	<05<<<<<<<7<<<<<<<<<<<<<7<<<<<<<<<<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_95:1:261:504:780	83	chr1	1501	99	35M	=	1337	-199	TTTGTCTGAGAAAAACAGTCTAGATGAGAGAGAAC	80;8(;0==8+====;==49===============	MF:i:18	Aq:i:43	NM:i:1	UQ:i:10	H0:i:0	H1:i:1
+EAS51_78:7:270:448:491	147	chr1	1501	99	35M	=	1313	-223	TTTGTCTGAGCAAAACAGTCTAGATGAGAGAGAAC	7;;;;+2;<<+<<<<<<<<7<<<<<<<<<<<<<<<	MF:i:18	Aq:i:68	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_28:6:51:506:878	83	chr1	1501	99	36M	=	1314	-223	TTTGTCTGAGCAAAACAGTCTAGATGAGAGAGAACT	<970;49;<;+<<<:<<<;;<<<<<<<<<<<<<<<;	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_19:3:73:936:1509	83	chr1	1502	99	40M	=	1322	-220	TTGTCTGAGCAAAACAGTCTAGATGAGAGAGAACTTCCCT	99;66:<<;-<<<<:<<<<;<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_39:2:41:576:1016	83	chr1	1503	99	35M	=	1320	-218	TGTCTGAGCAAAACAGTCTAGATGAGAGAGAACTT	:<;<<<<<6<<<<;<<<<:<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_595:7:123:610:472	147	chr1	1504	99	35M	=	1333	-206	GTCTGAGCAAAACAGTCTAGATGAGAGAGAACTTC	:<::+<<9<<9<<<<=<<<<<=<<<<<<<<?<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS188_7:5:308:354:124	147	chr1	1507	99	35M	=	1331	-211	TGAGCAAAACAGTCTAGATGAGAGAGAACTTCCCT	%+<)2<<<<<<<<8<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:70	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS220_1:2:11:1274:1230	83	chr1	1507	99	35M	=	1327	-215	TGAGCAAAACAGTCTAGATGAGAGAGAACTTCCCT	.<<<<<<<<<<<<<<<<5<<<<<<<<<<5<<<<<<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_62:3:169:292:652	147	chr1	1510	99	35M	=	1306	-239	GCAAAACAGTCTAGATGAGAGAGAACTTCCCTGGA	79919-<-<<<<<<<<<<<<<<<<<<<6<<<<<<<	MF:i:18	Aq:i:70	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_65:6:18:376:416	83	chr1	1510	99	35M	=	1326	-219	GCAAAACAGTCTAGATGAGAGAGAACTTCCCTGGA	70<<<<<<<7<7<<<2<<<<<<<<<<8<<<<<<<<	MF:i:18	Aq:i:70	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_593:3:194:168:684	147	chr1	1512	99	36M	=	1340	-208	AAAACAGTCTAGATGAGAGAGAACTTCCCTGGAGGT	;<<<<<;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_597:3:73:273:488	83	chr1	1512	99	35M	=	1318	-229	AAAACAGTCTAGATGAGAGAGAACTTCCCTGGAGG	</<<:<<9;;<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_71:6:324:515:230	83	chr1	1512	99	34M	=	1339	-207	AAAACAGTCTAGATGAGAGAGAACTTCCCTGGAG	7<<1<<<7<+<<<;<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_595:1:209:345:87	83	chr1	1513	99	35M	=	1360	-188	AAACAGTCTAGATGAGAGAGAACTTCCCTGGAGGT	<<;<<<<5<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS218_1:4:73:42:1038	83	chr1	1513	99	35M	=	1349	-199	AAACAGTCTAGATGAGAGAGAACTTCCCTGGAGGT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_28:5:209:778:588	83	chr1	1514	99	36M	=	1326	-224	AACAGTCTAGATGAGAGAGAACTTCCCTGGAGGTCT	;8;98;;;<3<<<<<<<<<;<<;<<<<<;<<<<<<<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS188_7:1:115:683:296	147	chr1	1514	99	35M	=	1320	-229	AACAGTCTAGATGAGAGAGAACTTCCCTGGAGGTC	<<<<;<;<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_93:1:92:213:217	147	chr1	1515	99	35M	=	1333	-217	ACAGTCTAGATGAGAGAGAACTTCCCTGGAGGTCT	<<<<<:<<<<<<<<<<<;<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_99:6:177:562:806	147	chr1	1515	99	35M	=	1356	-194	ACAGTGTAGATGAGAGAGACCTTCCCTGGAGGTCT	)2<9;'/:<5<<<:<<:<:&5:&<8,<<+:<&<<<	MF:i:18	Aq:i:35	NM:i:2	UQ:i:11	H0:i:0	H1:i:1
+EAS1_103:3:320:505:814	147	chr1	1515	99	35M	=	1350	-200	ACAGTCTAGATGAGAGAGAACTTCCCTGGAGGTCT	<2<;;5<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS218_4:1:9:206:901	147	chr1	1517	99	35M	=	1344	-208	AGTCTAGATGAGAGAGAACTTCCCTGGAGGTCTGA	<<<<<<<<<<<<<.<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_57:4:71:707:568	83	chr1	1518	99	35M	=	1332	-221	GTCTAGATGAGAGAGAACTTCCCTGGAGGTCTGAT	;9;<;<<<<<;<<<<<;<<<:<<<<<<<<<<<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_1:2:91:856:504	147	chr1	1520	99	35M	=	1366	-189	CTAGATGAGAGAGAACTTCCCTGGAGGTCTGATGG	:::<<:<<<<<<<<<<<<<<<<<<<<<:<:<<<<<	MF:i:18	Aq:i:68	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_108:6:77:48:860	147	chr1	1521	99	35M	=	1348	-208	TAGATGAGAGAGAACTTCCCTGGAGGTCTGATGGC	;8;8;<9<9<<<<<<<<<4<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:45	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_71:5:16:434:204	83	chr1	1522	99	34M	=	1340	-216	AGATGAGAGAGAACTTCCCTGGAGGTCTGATGGC	<:7:<<<<<<<<<<<9<<<+<<<<<<<<<<<<<<	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_39:4:43:1047:1626	83	chr1	1523	99	35M	=	1369	-189	GATGAGAGAGAACTTCCCTGGAGGTCTGATGGCGT	<<4<<<<<<<<<<<:<<<;<<<<<:<7<<;<<<<<	MF:i:18	Aq:i:70	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS219_FC30151:3:81:1723:1820	147	chr1	1524	99	35M	=	1335	-224	ATGAGAGAGAACTTCCCTGGAGGTCTGATGGCGTT	;6;;;<<<<<<<<<<<2<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS220_1:2:63:267:545	83	chr1	1524	99	35M	=	1354	-205	ATGAGAGAGAACTTCCCTGGAGGTCTGATGGCGTT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_39:7:90:406:631	83	chr1	1525	99	35M	=	1335	-225	TGAGAGAGAACTTCCCTGGAGGTCTGATGGCGTTT	<<<:<:<<<-<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_19:1:14:420:712	147	chr1	1525	99	40M	=	1368	-197	TGAGAGAGAACTTCCCTGGAGGTCTGATGGCGTTTCTCCC	1::::<<<<<<<<<<;<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:66	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_589:8:2:434:715	83	chr1	1527	99	35M	=	1363	-199	AGAGAGAACTTCCCTGGAGGTCTGATGGCGTTTCT	<<<<<<<<<:;<<<;<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_610:7:117:857:942	147	chr1	1527	99	35M	=	1372	-190	AGAGAGAACTTCCCTGGAGGTCTGATGGCGTTTCT	<<;<<<<<<<9<<<8<<<<<<<<<<;<<<<<<<<<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS219_FC30151:5:70:348:972	83	chr1	1528	99	35M	=	1343	-220	GAGAGAACTTCCCTGGAGGTCTGATGGCGTTTCTC	<99<-7<<7<<<87<<<)<<<<<<8<<<<<<<<<<	MF:i:18	Aq:i:65	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_93:6:132:717:233	147	chr1	1529	99	35M	=	1368	-196	AGAGAACTTCCCTGGAGGTCTGATGGAGTTTCTCC	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:47	NM:i:1	UQ:i:27	H0:i:0	H1:i:1
+EAS188_7:4:21:443:404	147	chr1	1529	99	35M	=	1345	-219	AGAGAACTTCCCTGGAGGTCTGATGGCGTTTCTCC	=9=9=9==:==========================	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_108:1:148:286:316	83	chr1	1531	99	35M	=	1347	-219	AGAACTTCCCTGGAGGTCTGATGGCGTTTCTCCCT	;::::;9/:<9<<<<;<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:70	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_39:6:85:1224:625	147	chr1	1532	99	35M	=	1331	-236	GAACTCCCCTGGAGGTCTGATGGCGTTTCTCCCTC	17;;7&-;<;<;:<6<<:;<<<<<<<;<<<<<<<<	MF:i:18	Aq:i:70	NM:i:1	UQ:i:5	H0:i:1	H1:i:0
+EAS221_1:8:73:108:1621	147	chr1	1532	99	35M	=	1373	-194	GAACTTCCCTGGAGGTCTGATGGCGTTTCTCCCTC	<<8<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_71:4:73:182:444	147	chr1	1533	99	35M	=	1354	-214	AACTTCCCTGGAGGTCTGATGGCGTTTCTCCCTCG	:1<4;;::<<;<<<<;<<<<<<<<<<<;<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS188_7:2:152:765:744	83	chr1	1534	99	35M	=	1374	-195	ACTTCCCTGGAGGTCTGATGGCGTTTCTCCCTCGT	6<;6<<<;<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_108:2:170:326:433	147	chr1	1535	99	35M	=	1367	-203	CTTCCCTGGAGGTCTGATGGCGTTTCTCCCTCGTC	:44<<<<<<<<<<:6<<<<<<<:<<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_591:8:4:841:340	73	chr2	1	99	36M	*	0	0	TTCAAATGAACTTCTGTAATTGAAAAATTCATTTAA	<<<<<<<<;<<<<<<<<;<<<<<;<;:<<<<<<<;;	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_67:4:142:943:582	73	chr2	1	99	35M	*	0	0	TTCAAATGAACTTCTGTAATTGAAAAATTCATTTA	<<<<<<;<<<<<<:<<;<<<<;<<<;<<<:;<<<5	MF:i:18	Aq:i:41	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_67:6:43:859:229	153	chr2	1	66	35M	*	0	0	TTCAAATGAACTTCTGTAATTGAAAAATTCATTTA	+37<=<.;<<7.;77<5<<0<<<;<<<27<<<<<<	MF:i:32	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_93:2:286:923:549	73	chr2	2	99	35M	*	0	0	TCAAATGAACTTCTGTAATTGAAAAATTCATTTAA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_99:8:117:578:853	73	chr2	5	99	35M	*	0	0	AATGAACTTCTGTAATTGAAAAATTCATTTAAGAA	<;<9<<<<<;<<;<<<<<<<<<<<,<98;<;;&92	MF:i:18	Aq:i:43	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_105:7:289:472:86	137	chr2	6	99	35M	*	0	0	ATGAACTTCTGTAATTGAAAAATTCATTTAAGAAA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;;;;	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS188_4:5:302:997:951	73	chr2	6	69	35M	*	0	0	ATGAACTTCTGTAATTGAAAAATTCATTTAAGAAA	<<<<<<<<<<;<<:<<52<<:;;<6<<;<:<2:9/	MF:i:64	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS218_1:8:13:1729:1844	73	chr2	6	99	35M	*	0	0	ATGAACTTCTGTAATTGAAAAATTCATTTAAGAAA	<<<;;<;7<<<<4<<<<762;6<<<<<<<;6;618	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_593:2:43:239:977	137	chr2	7	99	36M	*	0	0	TGAACTTCTGTAATTGAAAAATTCATTTAAGAAATT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<7;7;<;	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_66:3:233:191:520	73	chr2	7	99	35M	*	0	0	TGAACTTCTGTAATTGAAAAATTCATTTAAGAAAT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<2<8<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS218_1:4:75:555:1591	137	chr2	7	99	35M	*	0	0	TGAACTTCTGTAATTGAAAAATTCATTTAAGAAAT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<6<<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS220_1:2:43:656:1866	137	chr2	7	99	35M	*	0	0	TGAACTTCTGTAATTGAAAAATTCATTTAAGAAAT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<7;;:;	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_597:2:100:563:301	137	chr2	8	99	35M	*	0	0	GAACTTCTGTAATTGAAAAATTCATTTAAGAAATT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<:;8;;;	MF:i:18	Aq:i:54	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_59:1:126:526:276	137	chr2	8	84	35M	*	0	0	GAACTTCTGTAATTGAAAAATTCATTTAAGAAATT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<:<<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_30:3:161:366:544	137	chr2	11	99	35M	*	0	0	CTTCTGTAATTGAAAAATTCATTTAAGAAATTACA	<<<<<<<<<<<<<<<<<<<<<<<<<<;<<<<<<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_65:3:326:652:890	73	chr2	12	99	35M	*	0	0	TTCTGTAATTGAAAAATTCATTTAAGAAATTACAA	<<<<<<<<<<2<<<<<<<<<<<<<<+<8:<<9998	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS188_7:4:238:441:727	73	chr2	16	99	35M	*	0	0	GTAATTGAAAAATTCATTTAAGAAATTACAAAATA	<<<<<<<<<<<<<<<<<<<<<7<<<<<<<<<;;<<	MF:i:18	Aq:i:65	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_65:8:64:507:478	137	chr2	17	99	35M	*	0	0	TAATTGAAAAATTCATTTAAGAAATTACAAAATAT	<<<<<;<<<<<<<<<<<<<<<;;;<<<;<<8;<;<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_108:8:118:440:850	137	chr2	18	99	35M	*	0	0	AATTGAAAAATTCATTTAAGAAATTACAAAATATA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<949<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_93:7:270:995:918	137	chr2	24	84	35M	*	0	0	AAAATTCATTTAAGAAATTACAAAATATAGTTGAA	<<<<<<<<<<<<<:<<<<<<8<8<8<<<<:<;4;4	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_65:8:305:819:245	73	chr2	25	98	35M	*	0	0	AAATTCATTTAAGAAATTACAAAATATAGTTGAAA	8<<<<8<;<<<<<;<8<<8<8<<<<8<<<899<<+	MF:i:18	Aq:i:27	NM:i:0	UQ:i:0	H0:i:1	H1:i:1
+EAS114_26:7:13:172:720	73	chr2	26	99	35M	*	0	0	AATTCATTTAAGAAATTACAAAATATAGTTGAAAG	============:3<==:====<=9=3===;==83	MF:i:18	Aq:i:28	NM:i:0	UQ:i:0	H0:i:1	H1:i:1
+EAS56_63:7:34:334:825	73	chr2	30	99	35M	*	0	0	CATTTAAGAAATTACAAAATATAGTTGAAAGCTCT	<<<<<<<<<<<<<<<<<<<<<<<<3;<<<<6<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:3:32:1379:738	137	chr2	33	99	35M	*	0	0	TTAAGAAATTACAAAATATAGTTGAAAGCTCTAAC	;;;;;;;8;;;;;;;;;;;;;;;;;;;;;;88888	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:1
+EAS139_19:5:70:318:1631	137	chr2	34	99	40M	*	0	0	TAAGAAATTACAAAATATAGTTGAAAGCTCTAACAATAGA	<<<<<<;<<<<<<<<<<<<;9:<<<<<<<<<<<<<:::78	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_103:5:285:241:560	163	chr2	37	99	35M	=	200	198	GAAATTACAAAATATAGTTGAAAGCTCTAACAATA	<<<<<<<<<<;<<<<;<<<<<<<<<<<<;<;;;<.	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_28:1:168:389:889	99	chr2	37	99	36M	=	205	204	GAAATTACAAAATATAGTTGAAAGCTCTAACAATAG	<<<<<<<<<<<<<<<<<<<<;<<<<<<<;9;;<<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_71:4:127:725:381	163	chr2	39	99	35M	=	209	204	AATTACAAAATATAGTTGAAAGCTCTAACAATAGA	<<<<<<<<<<<<<<<<<<<<<;<<<<;;;;;<<8:	MF:i:18	Aq:i:54	NM:i:0	UQ:i:0	H0:i:1	H1:i:1
+EAS1_93:5:66:372:343	163	chr2	40	99	35M	=	228	223	ATTACAAAATATAGTTGAAAGATCTAACAATAGAC	<<<<<<<<<<8<<<<<6<<<8&8<<<<<58<:<::	MF:i:18	Aq:i:43	NM:i:1	UQ:i:5	H0:i:0	H1:i:1
+EAS56_65:6:67:800:450	99	chr2	41	99	35M	=	221	215	TTACAAAATATAGTTGAAAGCTCTAACAATAGACT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<5<<<	MF:i:18	Aq:i:49	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS219_FC30151:3:90:1906:1528	163	chr2	41	99	35M	=	222	216	TTACAAAATATAGTTGAAAGCTCTAACAATAGACT	<<<<<<<<<<<<<<<:<<<:<<<<;<<<<<;:7:;	MF:i:18	Aq:i:49	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_26:3:117:284:589	163	chr2	43	99	35M	=	210	202	ACAAAATATAGTTGAAAGCTCTAACAATAGACTAA	==================================0	MF:i:18	Aq:i:56	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS218_1:2:26:211:481	99	chr2	43	99	35M	=	222	214	ACAAAATATAGTTGAAAGCTCTAACAATAGACTAA	<<<<<<<<<<<<<<<<<<<<<<<7<<<<<:<7<<<	MF:i:18	Aq:i:54	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS218_4:7:85:923:726	99	chr2	43	99	35M	=	199	191	ACAAAATATAGTTGAAAGCTCTAACAATAGACTAA	<<<<<<<7<<<<<<<<<<<55<<<9<*<<<991<4	MF:i:18	Aq:i:44	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_67:6:107:395:312	163	chr2	44	99	35M	=	224	215	CAAAATATAGTTGAAAGCTCTAACAATAGACTAAA	<<<<<<<<<<<<<<<<<<<<<<<<<;<;;<:<<<<	MF:i:18	Aq:i:27	NM:i:0	UQ:i:0	H0:i:1	H1:i:1
+B7_597:7:5:753:806	163	chr2	45	99	35M	=	197	187	AAAATATAGTTGAAAGCTCTAACAATAGACTAAAC	<<<<<<<<<<<<<<<<<<<<<<<<<<7:-<;;3;;	MF:i:18	Aq:i:27	NM:i:0	UQ:i:0	H0:i:1	H1:i:1
+EAS1_103:3:277:921:474	163	chr2	45	99	35M	=	241	231	AAAATATAGTTGAAAGCTCTAACAATAGACTAAAC	<<<<<<<<<<<<<<<:<<<<<<<<<<<5<<;;;;;	MF:i:18	Aq:i:27	NM:i:0	UQ:i:0	H0:i:1	H1:i:1
+EAS56_63:4:38:28:122	163	chr2	46	99	35M	=	227	216	AAATATAGTTGAAAGCTCTAACAATAGACTAAACC	<<<<<<;<<<<<<<;<<<<6<<<<<<:<<<<;;<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:1
+EAS221_3:8:50:1203:1094	163	chr2	46	99	35M	=	223	212	AAATATAGTTGAAAGCTCTAACAATAGACTAAACC	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:1
+B7_591:2:223:583:968	99	chr2	47	88	36M	=	215	204	AATATAGTTGAAAGCTCTAACAATAGACTAAACCAA	<<<<<<<29<<<<4<<<<<<<<<<<7<<7<..<<47	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:1
+EAS114_39:1:28:350:895	163	chr2	48	95	35M	=	215	202	ATATAGTTGAAAGCTCTAACAATAGACTAAACCAA	<<<<<<<<;<;<<<<<<<<<;;<<;<<<<<;;<;8	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:1
+EAS114_45:7:69:1130:832	99	chr2	50	94	35M	=	231	216	ATAGTTGAAAGCTCTAACAATAGACTAAACCAAGC	;;2<;<;;<;9;<;;;;;;;7;8;;7;;;;77437	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:1
+EAS188_7:3:296:224:724	163	chr2	50	99	35M	=	234	219	ATAGTTGAAAGCTCTAACAATAGACTAAACCAAGC	<<<<;<<<<<<7;<<<<<6<<<06<<<<<<2(<<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:1
+B7_595:4:319:250:718	163	chr2	52	99	35M	=	240	223	AGTTGAAAGCTCTAACAATAGACTAAACCAAGCAG	<<<<<<<<<<<;<<5<5;<851;85;)9;;8594;	MF:i:18	Aq:i:53	NM:i:0	UQ:i:0	H0:i:1	H1:i:1
+EAS54_73:3:203:419:243	163	chr2	54	99	35M	=	237	218	TTGAAAGCTCTAACAATAGACTAAACCAAGCAGAA	<<<<<<<<<<<<<<<9<;<8<<<;<<<;<<<4<77	MF:i:18	Aq:i:47	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_19:6:21:1601:1666	163	chr2	56	99	40M	=	228	212	GAAAGCTCTAACAATAGACTAAACCAAGCAGAAGAAAGAG	7<<<<<<<<:<<7<<<:<<<<<<4<<44<<914<;:5:::	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_610:7:158:943:467	163	chr2	57	99	35M	=	225	203	AAAGCTCTAACAATAGACTAAACCAAGCAGAAGAA	<<<<<;<<<<<<<<<<<<<<;;<<<<<<<<<;8<<	MF:i:18	Aq:i:46	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS220_1:2:54:91:1232	99	chr2	57	99	35M	=	246	224	AAAGCTCTAACAATAGACTAAACCAAGCAGAAGAA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:47	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_73:3:29:833:612	163	chr2	58	99	35M	=	224	201	AAGCTCTAACAATAGACTAAACCAAGCAGAAGAAA	<<<<<<<<<<<<<<<<<<<<<<<<<<;<<;;<<;;	MF:i:18	Aq:i:27	NM:i:0	UQ:i:0	H0:i:1	H1:i:1
+EAS56_57:1:189:503:110	163	chr2	63	79	35M	=	229	201	CTAACAATAGACTAAACCAAGCAGAAGAAAGAGTT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<:<	MF:i:18	Aq:i:0	NM:i:1	UQ:i:25	H0:i:2	H1:i:0
+EAS114_28:2:114:938:216	99	chr2	63	99	36M	=	218	191	CTAACAATAGACTAAACCAAGCAGAAGAAAGAGGTT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<4;	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:2	H1:i:0
+EAS1_95:5:257:654:116	99	chr2	64	99	35M	=	231	202	TAACAATAGACTAAACCAAGCAGAAGAAAGAGGTT	<<<<<<<<<<<<<<<<<<<<<<;:<<<<<<<<<88	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:2	H1:i:0
+EAS1_97:3:277:144:848	163	chr2	64	99	35M	=	228	199	TAACAATAGACTAAACCAAGCAGAAGAAAGAGGTT	<<<<<<<<<;<<<<<<<<<<<<<<<<<3<<9;;6;	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:2	H1:i:0
+EAS1_108:4:75:166:463	99	chr2	64	99	35M	=	250	221	TAACAATAGACTAAACCAAGCAGAAGAAAGAGGTT	<<<<<<<<<<<<<<<<<<<<;<<<<<<<<<<<++3	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:2	H1:i:4
+B7_610:5:102:915:87	99	chr2	65	99	35M	=	222	192	AACAATAGACTAAACCAAGCAGAAGAAAGAGGTTC	<<<<<<<<<<<<<<<<<<<<;<<<<<3<<;<<<<;	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:3	H1:i:0
+EAS54_71:3:78:855:352	163	chr2	65	99	35M	=	240	209	AACAATAGACTAAACCAAGCAGAAGAAAGAGGTTC	<<<<<<<<;<<<<<<<<<;<<<<<<<<;<;<<:<:	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:3	H1:i:0
+EAS56_57:2:206:873:186	163	chr2	66	99	35M	=	227	196	ACAATAGACTAAACCAAGCAGAAGAAAGAGGTTCA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<:;53	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:2	H1:i:0
+EAS1_93:6:238:514:194	163	chr2	68	99	35M	=	265	232	AATAGACTAAACCAAGCAGAAGAAAGAGGTTCAGA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<:<;<;<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:1
+EAS56_57:3:285:489:327	99	chr2	68	99	35M	=	233	200	AATAGACTAAACCAAGCAGAAGAAAGAGGTTCAGA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:1
+EAS54_67:1:15:381:715	99	chr2	72	99	35M	=	237	200	GACTAAACCAAGCAGAAGAAAGAGGTTCAGAACTT	;=====;===9==;===9;;;=4;9=====;====	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_32:6:199:818:124	99	chr2	73	99	35M	=	266	228	ACTAAACCAAGCAGAAGAAAGAGGTTCAGAACTTG	<<<<<<<<<<<<<<<<<;<<;<<;7<<<<<<9<9;	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_59:3:182:1002:639	163	chr2	77	99	35M	=	246	204	AACCAAGCAGAAGAAAGAGGTTCAGAACTTGAAGA	<<<<<<<<<<<<<<<<<<<<<9-<<<<4<;<;;<;	MF:i:18	Aq:i:48	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_1:2:3:945:2005	163	chr2	77	99	35M	=	262	220	AACCAAGCAGAAGAAAGAGGCTCAGAACTTGAAGA	<<<<<<<<<<<<<<<<<<<<%<<<<<<;<<<<<<<	MF:i:18	Aq:i:44	NM:i:1	UQ:i:4	H0:i:0	H1:i:1
+B7_591:5:254:542:848	99	chr2	79	99	36M	=	233	190	CCAAGCAGAAGAAAGAGGTTCAGAACTTGAAGACAA	<<<;<<<<<<<<<<<<<<<;4<;8<<<;;9<9;8;9	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_95:4:71:517:742	99	chr2	81	99	35M	=	266	220	AAGCAGAAGAAAGAGGTTCAGAACTTGAAGACAAG	<<<<<<<<<<<<;<<<<<<<<<<<<<48:4<<<<3	MF:i:18	Aq:i:49	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_105:8:254:617:73	163	chr2	83	99	35M	=	266	218	GCAGAAGAAAGAGGTTCAGAACTTGAAGACAAGTC	<<<<<<<<<<<<<<<<<<<<<<<<<;<<<6;:;4%	MF:i:18	Aq:i:51	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:2:13:1507:1146	99	chr2	84	99	35M	=	278	229	CAGAAGAAAGAGGTTCAGAACTTGAAGACAAGTCT	;<9;;;;<<;;;;<<;<;;;;<;;<<;<;<99777	MF:i:18	Aq:i:49	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_11:5:32:686:735	99	chr2	84	78	35M	=	255	206	CAGAAGAAAGAGGTTCANANNNTGANGACAAGTCT	<<<<<<<<<<<<<<<<<!<!!!<<<!<<<<<<<<<	MF:i:130	Aq:i:78	NM:i:5	UQ:i:0	H0:i:0	H1:i:0
+EAS56_57:3:112:729:591	99	chr2	86	99	35M	=	283	232	GAAGAAAGAGGTTCAGAACTTGAAGACAAGTCTCT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_39:5:17:1222:783	163	chr2	87	99	35M	=	251	199	AAGAAAGAGGTTCAGAACTTGAAGACAAGTCTCGT	<<<<<<<)<<<16<<;<<<6<4<:<4<+://<7)<	MF:i:18	Aq:i:59	NM:i:1	UQ:i:8	H0:i:1	H1:i:0
+EAS188_7:6:46:122:479	99	chr2	87	99	35M	=	248	196	AAGAAAGAGGTTCAGAACTTGAAGACAAGTCTCTT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<<<<	MF:i:18	Aq:i:47	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_593:2:313:531:169	163	chr2	89	99	36M	=	250	197	GAAAGAGGTTCAGAACTTGAAGACAAGTCTCTTATG	<<<<<<<<<<<<<;<<<<<<<<<<<:<<:<;<<;<2	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_62:6:148:170:895	99	chr2	91	99	35M	=	247	191	AAGAGGTTCAGAACTTGAAGACAAGTCTCTTATGA	<<<<<<<<<<9<<<<<6<<<<<<<<<<<<<<<<6<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_39:6:34:380:815	163	chr2	91	99	35M	=	283	227	AAGAGGTTCAGAACTTGAAGACAAGTCTCTTATGA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<;:	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_64:6:210:809:735	163	chr2	93	99	35M	=	291	233	GAGGTTCAGAACTTGAAGACAAGTCTCTTATGAAT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<<5<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_81:8:40:925:442	163	chr2	93	99	35M	=	271	213	GAGGTTCAGAACTTGAAGACAAGTCTCTTATGAAT	;<;<<<<<<<<<<<3;<7;:<;;<<<;<<:<32<<	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_71:4:169:256:888	163	chr2	94	99	35M	=	270	210	AGGTTCAGAACTTGAAGACAAGTCTCTTATGAATT	<<<<<<<<<<<<<<<<<<<<<<;;<;<<;<<:;;<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_65:8:117:156:84	99	chr2	95	99	35M	=	285	225	GGTTCAGAACTTGAAGACAAGTCTCTTATGAATTA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_26:1:35:522:294	163	chr2	95	99	35M	=	272	212	GGTTCAGAACTTGAAGACAAGTCTCTTATGAATTA	===============================:=:=	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:3:41:653:1568	163	chr2	95	99	35M	=	266	206	GGTTCAGAACTTGAAGACAAGTCTCTTATGAATTA	;;;;;;;8;;;;;;;;;;;;;;;;;;;;;;88888	MF:i:18	Aq:i:67	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_28:7:178:276:693	163	chr2	96	99	36M	=	259	199	GTTCAGAACTTGAAGACAAGTCTCTTATGAATTAAC	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;;	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_73:7:223:440:667	99	chr2	97	99	35M	=	282	220	TTCAGAACTTGAAGACAAGTCTCTTATGAATTAAC	<<<<<<<<<<<<<<<<<<<;<<<<<<<<;<<<<;;	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_61:5:194:470:416	99	chr2	98	99	35M	=	265	202	TCAGAACTTGAAGACAAGTCTCTTATGAATTAACC	<<<<<<<<<<<<<<<<<<<<<<<<;<;<<<<<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_39:5:61:1000:1534	163	chr2	104	99	35M	=	286	217	CTTGAAGACAAGTCTCTTATGAATTAACCCAGTCA	<<<<4:<:<1)<<<<<<<+<:44<</7<<<)4:<)	MF:i:18	Aq:i:63	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_57:5:145:383:182	163	chr2	105	99	35M	=	291	221	TTGAAGACAAGTCTCTTATGAATTAACCCAGTCAG	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<:;;;<;	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_11:2:63:816:921	163	chr2	106	99	35M	=	291	220	TGAAGACAAGTCTCTTATGAATTAACCCAGTCAGA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<:<4<846	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_19:4:77:1780:693	99	chr2	106	99	40M	=	276	210	TGAAGACAAGTCTCTTATGAATTAACCCAGTCAGACAAAA	<<<<<<<<<<<<;<<:<<;<<<<<<<<<<<<;<<<;;:69	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_593:1:215:861:605	163	chr2	107	94	36M	=	262	191	NAAGACAAGTCTCTTATGAATTAACCCAGTCAGACA	!+++++++++++++++++++++++++++++++++++	MF:i:18	Aq:i:19	NM:i:1	UQ:i:0	H0:i:0	H1:i:1
+EAS221_3:2:22:1623:709	99	chr2	107	99	35M	=	287	215	GAAGACAAGTCTCTTATGAATTAACCCAGTCAGAC	<<<<<<<<<7<<<<<<<:<<<<<<<<:85:<:2<<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS219_FC30151:1:54:436:1452	163	chr2	108	99	35M	=	275	202	AAGACAAGTCTCTTATGAATTAACCCAGTCAGACA	<<<<<<<<<<<<<<<<<<<<<<<<<<<:<<<;<<<	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_11:2:42:333:516	163	chr2	109	99	35M	=	296	222	AGACAAGTCTCTTATGAATTAACCCAGTCAGACAA	<<<<<5<*<2<<<<<<<<<<<<<<<<<<<<<<<</	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_595:6:119:730:190	99	chr2	114	99	35M	=	301	222	AGTCTCTTATGAATTAACCCAGTCAGACAAAAATA	<<<9<;;<<<;<<<<<<<8<<<1<<918<;;;<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_97:7:63:727:203	99	chr2	114	99	35M	=	278	199	AGTCTCTTATGAATTAACCCAGTCAGACAAAAATA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<;<<;	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS192_3:5:27:577:849	163	chr2	114	99	35M	=	316	237	AGTCTCTTATGAATTAACCCAGTCAGACAAAAATA	<<<<<<<<<<<<<<<<<<<<;:<<<;<<<<<<;;;	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS219_1:5:5:259:250	99	chr2	115	99	35M	=	269	189	GTCTCTTATGAATTAACCCAGTCAGACAAAAATAA	<<<<<<<<<<<<<<<<<<<<;<<<;5<<5<;7<::	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS112_34:4:17:989:186	99	chr2	120	91	35M	=	299	214	TTATGAATTAACCCAGTCAGACAAAAATAAAGAAA	<<<<<<<<<<<<<<<<<<<<<<<<:<<;<7;::::	MF:i:18	Aq:i:20	NM:i:0	UQ:i:0	H0:i:1	H1:i:5
+EAS114_45:2:33:1445:1357	99	chr2	121	85	35M	=	299	213	TATGAATTAACCCAGTCAGACAAAAATAAAGAAAA	;;<;<<<<<<;;;<9:;:;;;;;:;:;;;;99777	MF:i:18	Aq:i:18	NM:i:0	UQ:i:0	H0:i:1	H1:i:7
+EAS221_3:4:30:1452:1563	163	chr2	122	94	35M	=	313	226	ATGAATTAACCAAGTCAGACAAAAATAAAGAAAAA	<<<<<<<<<<<<<<:<<<<1<<<<<<<<<<<<<<<	MF:i:18	Aq:i:20	NM:i:1	UQ:i:27	H0:i:0	H1:i:1
+EAS114_45:1:77:1000:1780	163	chr2	123	66	35M	=	279	191	TGAATTAACCCAGTCAGACAAAAATAAAGAAAAAA	;;;:;;;;;;;/;;;7:4;;7;;;;;;;;;77777	MF:i:18	Aq:i:0	NM:i:0	UQ:i:0	H0:i:6	H1:i:47
+EAS114_45:4:48:310:473	99	chr2	123	66	35M	=	298	210	TGAATTAACCCAGTCAGACAAAAATAAAGAAAAAA	<<<;<<;;;<<;;<;;;;;;;;;;;;;;;;89799	MF:i:18	Aq:i:0	NM:i:0	UQ:i:0	H0:i:6	H1:i:47
+B7_591:2:279:124:41	99	chr2	124	69	36M	=	307	219	GAATTAACCCAGTCAGACAAAAANNAAGAAAAAAGA	<<<<<<<7/<8<<<<<<<<<<4*!!<<7<7<<5<<3	MF:i:18	Aq:i:0	NM:i:2	UQ:i:0	H0:i:0	H1:i:0
+EAS112_32:8:89:254:332	163	chr2	124	76	35M	=	291	202	GAATTAACCCAGTCAGACAAAAATAAAGAAAAAAG	==================;=========;=7;;<;	MF:i:18	Aq:i:0	NM:i:0	UQ:i:0	H0:i:4	H1:i:36
+B7_597:7:103:731:697	99	chr2	125	72	35M	=	304	214	AATTAACCCAGTCAGACAAAAATAAAGAAAAAAGA	<<<<<<<<<<<<<<<<<<:<:<<6<<<<<<<:<;:	MF:i:18	Aq:i:0	NM:i:0	UQ:i:0	H0:i:9	H1:i:55
+EAS139_11:2:71:83:58	163	chr2	148	77	9M2I24M	=	349	236	AAAGAAAAAAGAATTTTAAAAATGAACAGAGCTTT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:130	Aq:i:77	NM:i:0	UQ:i:0	H0:i:0	H1:i:0
+EAS192_3:4:63:5:870	163	chr2	148	75	9M2I24M	=	330	217	AAAGAAAAAAGAATTTTAAAAATGAACAGAGCTTT	<<;<<<<<<<<<<<<<<<<<;<<<<<<<<<;;<<<	MF:i:130	Aq:i:75	NM:i:0	UQ:i:0	H0:i:0	H1:i:0
+EAS139_19:2:29:1822:1881	163	chr2	150	74	7M2I31M	=	328	218	AGAAAAAAGAATTTTAAAAATGAACAGAGCTTTCAAGAAG	<<<<<<<<<<<<4<<<<<<<<<<<<<<:<<<:<<;:::::	MF:i:130	Aq:i:74	NM:i:0	UQ:i:0	H0:i:0	H1:i:0
+EAS221_3:2:100:1147:124	163	chr2	150	99	35M	=	345	230	AAAAAAGAATTTTAAAAATGAACAGAGCTTTCAAG	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<9<<	MF:i:18	Aq:i:29	NM:i:2	UQ:i:54	H0:i:0	H1:i:0
+EAS192_3:8:6:104:118	163	chr2	154	99	35M	=	323	204	AAGAATTTTAAAAATGAACAGAGCTTTCAAGAAGT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<=<<<<<<	MF:i:18	Aq:i:27	NM:i:1	UQ:i:27	H0:i:0	H1:i:1
+B7_593:6:185:96:948	99	chr2	160	99	36M	=	324	200	TTTAAAAATGAACAGAGCTTTCAAGAAGTATGAGAT	<<<<<<<<<;6<<<<<<<<<;<<<;;<<<<<<<;<;	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS188_7:7:213:309:373	163	chr2	161	99	35M	=	317	191	TTAAAAATGAACAGAGCTTTCAAGAAGTATGAGAT	<;<<<<<<;<7<<<<<-<<<<<<<<<<<<<<4<7<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_93:2:30:466:652	99	chr2	163	98	35M	=	332	204	AAAAATGAACAGAGCTTTCAAGAAGTATGAGATTA	<<<<<<<<<<<<<<<<<<<<<<<<;<<<4;7<<<7	MF:i:18	Aq:i:45	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_32:4:156:21:69	163	chr2	163	99	35M	=	362	234	AAAAATGAACAGAGCTTTCAAGAAGTATGAGATTA	<<<<<<<<<<<<<<<<<<<<<<<:<4<<<:<;<;;	MF:i:18	Aq:i:54	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_93:5:197:52:58	163	chr2	165	99	35M	=	323	193	AAATGAACAGAGCTTTCAAGAAGTATGAGATTATG	<<<<<<<<<<<<<<<<<<9<<<<2<<<<<<;<<<<	MF:i:18	Aq:i:54	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_65:3:214:946:229	163	chr2	165	99	35M	=	339	209	AAATGAACAGAGCTTTCAAGAAGTATGATATTATG	<<<<<<<<<<<<<<<<<::<;;;<;<;7<:<<7<2	MF:i:18	Aq:i:65	NM:i:1	UQ:i:27	H0:i:1	H1:i:0
+EAS192_3:4:293:168:240	99	chr2	167	99	35M	=	340	208	ATGAACAGAGCTTTCAAGAAGTATGAGATTATGTA	<<<<;<<<;;;<;<<;;;<<;;<<::::<<;;+;7	MF:i:18	Aq:i:48	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_61:3:208:118:673	99	chr2	169	76	35M	=	332	198	GAACAGAGCTTTCAAGAAGTATGAGATTATGTAAA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;;<;;	MF:i:18	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_589:3:71:478:175	163	chr2	171	99	35M	=	317	181	ACAGAGCTTTCAAGAAGTATGAGATTATGTAAAGT	<<<<<<<<<<<;<<<<<;<<<<<<<<<<;<<<<<;	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_64:5:177:24:389	163	chr2	175	99	35M	=	365	225	AGCTTTCAAGAAGTATGAGATTATGTAAAGTAACT	<<<<<<<<<<<<<<<<<<<<<<<<7<;;<;9969;	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:6:14:1211:1332	163	chr2	178	99	35M	=	351	208	TTTCAAGAAGTATGAGATTATGTAAAGTAACTGAA	;;.;;;;;;;3;;;;;6;;;;;;8;;;;;;63777	MF:i:18	Aq:i:64	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_26:1:324:238:736	163	chr2	180	99	35M	=	367	222	TCAAGAAGTATGAGATTATGTAAAGTAACTGAACC	===================================	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_97:7:9:648:712	99	chr2	182	99	35M	=	358	211	AAGAAGTATGAGATTATGTAAAGTAACTGAACCTA	<9<;<<<<<<<;<<<<<8<<<<9<<;<<8)<:1<:	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_3:4:41:1308:619	163	chr2	184	99	35M	=	360	211	GAAGTATGAGATTATGTAAAGTAACTGAACCTATG	<6+<*<<<<<<<:<<<<<<<:<<&<<<<1<6<11:	MF:i:18	Aq:i:68	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_30:4:328:537:640	99	chr2	185	99	35M	=	352	202	AAGTATGAGATTATGTAAAGTAACTGAACCTATGA	<;<<<<<<;<<<<<<<<<:;<<8<<<;:<<<;<;9	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_62:5:86:697:941	163	chr2	187	99	35M	=	341	189	GTATGAGATTATGTAAAGTAACTGAACCTATGAGT	=====================<=<==<<====;=5	MF:i:18	Aq:i:27	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_95:4:224:592:744	99	chr2	188	99	35M	=	383	230	TATGAGATTATGTAAAGTAACTGAACCTATGAGTC	<<<<<<<<<<<<<<<<;<<<<<7<<<<<<<&<*<<	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_99:6:135:354:66	99	chr2	188	99	35M	=	356	203	TATGAGATTATGTAAAGTAACTGAACCTATGAGTC	<<<<<<<<<<<<<<<<;<<<<<<<<<<;<<2<;;;	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_30:7:71:311:202	163	chr2	188	99	35M	=	379	226	TATGAGATTATGTAAAGTAACTGAACCTATGAGTC	<<<<<<<<<<<<<<<<:4<<<<<<<<<<<<8;4;:	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_11:4:50:30:15	99	chr2	192	39	35M	=	358	201	AGATTATGTAAAGTAACTTAACCTATGAGTCCAAG	+:79.68872.:9&:92/.299169/5+/6/3/&2	MF:i:18	Aq:i:10	NM:i:3	UQ:i:45	H0:i:0	H1:i:1
+EAS192_3:5:287:334:110	73	chr2	196	73	35M	=	196	0	TATGTAAAGTAACTGAACCTATGAGTCACAGGTAT	<<<<<<<<<<<<<<<<<<4;<<<<<<<::6<55:.	MF:i:64	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS192_3:5:287:334:110	133	chr2	196	0	*	=	196	0	GATGAATACTAAGATTGATGTAGCAGCTTTTGCAA	.5+7)09<))&-&:33953<-./&&&)((;+3399	MF:i:192
+B7_597:7:5:753:806	83	chr2	197	99	35M	=	45	-187	ATGTAAAGTAACTGAACCTATGAGTCACAGGTATT	;:<:<<<<:<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:27	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_28:4:149:572:877	163	chr2	197	99	36M	=	334	173	ATGTAAAGTAACTGAACCTATGAGTCACAGGTATTC	=>7><>;>+>>/;>>=>=>=:>><>=<<==;)<=8;	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS218_4:7:85:923:726	147	chr2	199	99	35M	=	43	-191	GTAAAGTAACTGAACCTATGAGTCACAGGTATTCC	<:<<<%3<<1<<86<<-<<<<<<<<<<<<6<<1<<	MF:i:18	Aq:i:44	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_103:5:285:241:560	83	chr2	200	99	35M	=	37	-198	TAAAGTAACTGAACCTATGAGTCACAGGTATTCCT	:<<<<;<<,<<<<5<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_30:6:41:461:436	163	chr2	200	74	35M	=	389	224	TAAAGTAACTGAACCTATGAGTCACAGGTATTCCT	<<<<<<<<<<<<<<<<<<<:<<<<<<<<;<;;;:;	MF:i:18	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_61:6:25:949:33	99	chr2	201	99	35M	=	383	217	AAAGTAACTGAACCTATGAGTCACAGGTATTCCTG	=;===/8========*==&;6=&=&:=6&:=::67	MF:i:18	Aq:i:63	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_3:2:60:590:1760	99	chr2	201	99	35M	=	376	210	AAAGTAACTGAACCTATGAGTCACAGGTATTCCTG	<:<<<<<2<<<<:<::<<<::<<<<<6<<<<<<<6	MF:i:18	Aq:i:51	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:6:86:693:234	163	chr2	202	82	35M	=	388	221	AAGTAACTGAACCTATGAGTCACAGGTATTCCTGA	;;;;;;;;;;;;;;;;9;;;;;;;;99;;&70777	MF:i:18	Aq:i:18	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_57:6:4:223:776	163	chr2	203	93	35M	=	387	219	AGTAACTGAACCTATGAGTCACAGGTATTCCTGAG	<<<<<<<<<<<<<<<<<<<<<<<<<9<<<:;<;2<	MF:i:18	Aq:i:19	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_39:3:88:84:1558	99	chr2	203	95	35M	=	394	226	AGTAACTGAACCTATGAGTCACAGGTATTCCTGTG	<<;<<<<<<<<<<<<;;<<<<<<<::<<<<<<7&<	MF:i:18	Aq:i:22	NM:i:1	UQ:i:5	H0:i:1	H1:i:0
+B7_597:2:168:829:88	163	chr2	205	99	35M	=	369	199	TAACTGAACCTATGAGTCACAGGTATTCCTGAGGA	<<<<<<<<<<<<<<<<<<<<<<<6<<<<<<9;4;2	MF:i:18	Aq:i:68	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_28:1:168:389:889	147	chr2	205	99	36M	=	37	-204	TAACTGAACCTATGAGTCACAGGTATTCCTGAGGAA	;<<;;56;==================8========8	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_71:5:81:685:141	99	chr2	207	85	34M	=	382	210	ACTGAACCTATGAGTCACAGGTATTCCTGAGGAA	<<<<<<<<<<<<<<<<<<<<<;;<<;<<<',7,7	MF:i:18	Aq:i:17	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_19:4:26:1312:1400	99	chr2	207	99	40M	=	385	218	ACTGAACCTATGAGTCACAGGTATTCCTGAGGAAAAAGAA	<<<<;<<<:<<:<;<:<<<;:;<<<<<<:<8<1;;:::88	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_71:4:127:725:381	83	chr2	209	99	34M	=	39	-204	TGAACCTATGAGTCACAGGTATTCCTGAGGAAAA	+<<.<<;<;<<<3;<;<<<<<<6<8;<<<<<<<1	MF:i:18	Aq:i:54	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS188_7:2:19:736:559	99	chr2	209	99	35M	=	370	196	TGAACCTATGAGTCACAGGTATTCCTGAGGAAAAA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<<<<<	MF:i:18	Aq:i:70	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_26:3:117:284:589	83	chr2	210	99	35M	=	43	-202	GAACCTATGAGTCACAGGTATTCCTGAGGAAAAAG	==8==;==================;==========	MF:i:18	Aq:i:56	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_610:5:120:596:847	163	chr2	211	83	35M	=	410	234	AACCTATGAGTCACAGGTATTCCTGAGGAAAAAGA	<<<<<<<<<<<<<;<<<9<<<<<<<;:<62;58;2	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:1
+B7_610:5:51:904:391	163	chr2	212	97	35M	=	401	224	ACCTATGAGTCACAGGTATTCCTGAGGAAAAAGAA	<<<<<<<<<<<<<<<<<;<<<<<;:;<2<6;;;;;	MF:i:18	Aq:i:24	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_11:8:96:1314:1448	163	chr2	213	93	35M	=	388	210	CCTATGAGTCACAGGTATTCCTGAGGAAAAATAAA	<<<<<<<<<<<<<<<<<<<<<<<<5<4<<<<-<<<	MF:i:18	Aq:i:18	NM:i:1	UQ:i:12	H0:i:1	H1:i:0
+EAS139_19:3:73:1158:535	163	chr2	213	99	40M	=	377	204	CCTATGAGTCACAGGTATTCCTGAGGAAAAAGAAAAAGTG	<<<<<<<<<<<<<<<<<<<<<<8<;;<<<<<9<<9::8:8	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_591:2:223:583:968	147	chr2	215	88	36M	=	47	-204	TATGAGGCACAGGTATTCCTGAGGAAAAAGAAAAAG	1<';<<&%-:<<<<<:66%<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:30	NM:i:1	UQ:i:5	H0:i:1	H1:i:0
+EAS1_97:3:160:173:889	163	chr2	215	99	35M	=	379	199	TATGAGTCACAGGTATTCCTGAGGAAAAAGAAAAA	<<<<<<<<<<<<<<<<<<<<;0<7<<;<<<;7<09	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_39:1:28:350:895	83	chr2	215	95	35M	=	48	-202	TATGAGTCACAGGTATTCCTGAGGAAAAAGAAAAA	:<;<<<:;<-<<<<<4;77<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_53:4:45:707:147	163	chr2	216	99	35M	=	424	243	ATGAGTCACAGGTATTCCTGAGGAAAAAGAAAAAG	<<<<<<<<<<<<&<<<<:<<9<<<9<<<<75;;;<	MF:i:18	Aq:i:51	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS220_1:8:18:1757:95	99	chr2	216	45	35M	=	374	193	ATGAGTCGCAGGTATTCCTGAGGAAAAAGAAAAAG	<<<<<<<<<<<<<<<<<<<1<:<<<<<<:<<<;:<	MF:i:18	Aq:i:0	NM:i:1	UQ:i:27	H0:i:0	H1:i:1
+EAS51_66:6:310:747:415	163	chr2	217	99	35M	=	387	205	TGAGTCACAGGTATTCCTGAGGAAAAAGAAAAAGT	<<<<<<<<<<<<<<<<<<:<<<<<;<<<<<;<;<;	MF:i:18	Aq:i:24	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_28:2:114:938:216	147	chr2	218	99	36M	=	63	-191	GAGTCACAGGTATTCCTGAGGAAAAAGAAAAAGTGA	<<<<7<6<<<<<<<6<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_93:1:179:629:513	163	chr2	220	99	35M	=	409	224	GTCACAGGTATTCCTGAGGAAAAAGAAAAAGTGAG	<<<<<<<<<<<<<<<;<;<<<<<<<<<<<<<;<<<	MF:i:18	Aq:i:49	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:4:88:55:1187	99	chr2	220	66	35M	=	391	206	GTCACAGGTATTCCTGAGGAAAAAGAAAAAGTGAG	;;<;;;<<99<<;;<;;;;;:;49;:;;;;87898	MF:i:18	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_62:5:119:38:945	99	chr2	221	99	35M	=	428	242	TCACAGGTATTCCTGAGGAAAAAGAAAAAGTGAGA	<<<<<<<<<<<<<<<8<<<<<8<<<8<;<<7<:<<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_65:6:67:800:450	147	chr2	221	99	35M	=	41	-215	TCACAGGTATTCCTGAGGAAAAAGAAAAAGTGAGA	9-<9<;<<<<9;5<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:49	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_610:5:102:915:87	147	chr2	222	99	35M	=	65	-192	CACAGGTATTCCTGAGGAAAAAGAAAAAGTGAGAA	;<8<;;<<<<7;<<<;<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_26:1:113:367:659	163	chr2	222	72	35M	=	390	203	CACAGGTATTCCTGAGGAAAAAGAAAAAGCGAGAA	=9====8==========:=:=====9=:=&====5	MF:i:18	Aq:i:0	NM:i:1	UQ:i:5	H0:i:1	H1:i:0
+EAS218_1:2:26:211:481	147	chr2	222	99	35M	=	43	-214	CACAGGTATTCCTGAGGAAAAAGAAAAAGTGAGAA	:<:<<<<<<9:5<<<<<<<<<<<<<<:<:<<<<<<	MF:i:18	Aq:i:54	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS219_FC30151:3:90:1906:1528	83	chr2	222	99	35M	=	41	-216	CACAGGTATTCCTGAGGAAAAAGAAAAAGTGAGAA	:<<<<<<<<<3:<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:49	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_591:2:13:100:876	163	chr2	223	73	36M	=	397	210	ACAGGGATTCCTGAGGAAAAAGAAAAAGTGAGAAGT	<8<<<*<2<7<<<6<<<<<<6<<8<<<<5<<<<4<9	MF:i:18	Aq:i:30	NM:i:1	UQ:i:9	H0:i:0	H1:i:1
+EAS56_63:5:117:570:971	163	chr2	223	99	35M	=	413	225	ACAGGTATTCCTGAGGAAAAAGAAAAAGTGAGAAG	<<<<<<<<<<<<<;;;<<<<6<7;9;<:;<;<;;<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_3:8:50:1203:1094	83	chr2	223	99	35M	=	46	-212	ACAGGTATTCCTGAGGAAAAAGAAAAAGTGAGAAG	<7<<<<<5:+63<<<<<<<<<<<<<<<<2<<<<<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_67:6:107:395:312	83	chr2	224	99	35M	=	44	-215	CAGGTATTCCTGAGGAAAAAGAAAAAGTGAGAAGT	;<;;<<<<;<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:27	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_73:3:29:833:612	83	chr2	224	99	35M	=	58	-201	CAGGTATTCCTGAGGAAAAAGAAAAAGTGAGAAGT	<<;<<<;<::<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:27	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_610:7:158:943:467	83	chr2	225	99	35M	=	57	-203	AGGTATTCCTGAGGAAAAAGAAAAAGTGAGAAGTT	<:<<;;<:5<<<<<<<<<<<<<<<<<<;<<<;<<<	MF:i:18	Aq:i:46	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_59:2:201:768:529	163	chr2	225	99	35M	=	396	206	AGGTATTCCTGAGGAAAAAGAAAAAGTGAGAAGTT	==========================1=======;	MF:i:18	Aq:i:54	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS188_7:6:11:994:584	99	chr2	226	97	35M	=	417	226	GGTATTCCTGAGGAAAAAGAAAAAGTGAGAAGTTT	<<<<<<<<<<<7<<<<<<<<<<<<<6<<<<<<3<6	MF:i:18	Aq:i:24	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_57:2:206:873:186	83	chr2	227	99	35M	=	66	-196	GTATTCCTGAGGAAAAAGAAAAAGTGAGAAGTTTG	;<<;--7<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_63:4:38:28:122	83	chr2	227	99	35M	=	46	-216	GTATTCCTGAGGAAAAAGAAAAAGTGAGAAGTTTG	;9;9;-1<<<<<<<<<<<<<<<<<;<<<<<<<<<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_93:5:66:372:343	83	chr2	228	99	35M	=	40	-223	TATTCCTGAGGAAAAAGAAAAAGTGAGAAGTTTGG	;<1;89<<<<<;<9<<<<9<<<;8<9<;<<<<<;8	MF:i:18	Aq:i:43	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_97:3:277:144:848	83	chr2	228	99	35M	=	64	-199	TATTCCTGAGGAAAAAGAAAAAGTGAGAAGTTTGG	<<<)63<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_19:6:21:1601:1666	83	chr2	228	99	40M	=	56	-212	TATTACTGAGGAAAAAGAAAAAGTGAGAAGTTTGGAAAAA	-;;3&1<<<<<<<<<<<<1<<<</<<<<<</<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:1	UQ:i:5	H0:i:1	H1:i:0
+EAS56_57:1:189:503:110	83	chr2	229	79	35M	=	63	-201	ATTCCTGAGGAAAAAGAAAAAGTGAGAAGTTTGGA	=;;6:==============================	MF:i:18	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_95:5:257:654:116	147	chr2	231	99	35M	=	64	-202	TCCTGAGGAAAAAGAAAAAGTGAGAAGTTTGGAAA	0+37<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:7:69:1130:832	147	chr2	231	94	35M	=	50	-216	TCCTGAGGAAAAAGAAAAAGTGAGAAGTTTGGAAA	6)377;3;;;;;;;;;1;;;;;;;;;;;;;;;;;;	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_591:5:254:542:848	147	chr2	233	99	36M	=	79	-190	CTGAGGAAAAAGAAAAAGTGAGAAGTTTGGAAAAAC	,:4<8<<<<<<<<<<<<<;:<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_57:3:285:489:327	147	chr2	233	99	35M	=	68	-200	CTGAGGAAAAAGAAAAAGTGAGAAGTTTGGAAAAA	9;;<<8<<<<<<<<<<<<;<<<<<<<<<<<<<<;<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_108:4:163:611:211	163	chr2	234	99	35M	=	405	206	TGAGGAAAAAGAAAAAGTGAGAAGTTTGGAAAAAC	============8===============;=6;;<;	MF:i:18	Aq:i:48	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS188_7:3:296:224:724	83	chr2	234	99	35M	=	50	-219	TGAGGAAAAAGAAAAAGTGAGAAGTTTGGAAAAAC	8<<<5<<<<<<<<<<<<<<<<<<<<7<<<<<;<9<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_39:4:58:271:612	99	chr2	236	99	35M	=	415	214	AGGAAAAAGAAAAAGTGAGAAGTTTGGAAAAACTA	<;<<<<<<<<<7<<<<<<<<<<<<<<+47<<;<::	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_67:1:15:381:715	147	chr2	237	99	35M	=	72	-200	GGAAAAAGAAAAAGTGAGAAGTTTGGAAAAACTAT	<<<<<<<<<<<<<<9<<<<<<97;<<<<<<<<9<<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_73:3:203:419:243	83	chr2	237	99	35M	=	54	-218	GGAAAAAGAAAAAGTGAGAAGTTTGGAAAAACTAT	;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:47	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS218_4:3:41:1281:1785	99	chr2	237	99	35M	=	399	197	GGAAAAAGAAAAAGTGAGAAGTTTGGAAAAACTAT	<<<<<<<<<<<<<<<<<<<<<;<<<;<<<<<<<8<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_26:7:218:858:445	99	chr2	239	99	35M	=	421	217	AAAAAGAAAAAGTGAGAAGTTTGGAAAAACTATTT	;===5=;=======;==3======9;,79==;===	MF:i:18	Aq:i:27	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_595:4:319:250:718	83	chr2	240	99	35M	=	52	-223	AAAAGAAAAAGTGAGAAGTTTGGAAAAACTATTTG	<;:<<<<;<<<:<<<<<<49:<<<<<<<<<<<<<<	MF:i:18	Aq:i:53	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_64:7:92:493:891	99	chr2	240	99	35M	=	408	203	AAAAGAAAAAGTGAGAAGTTTGGAAAAACTATTTG	<<<<<<<<<<<<<<<;<<<<<<<<<<<<<<<<<<8	MF:i:18	Aq:i:49	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_71:3:78:855:352	83	chr2	240	99	34M	=	65	-209	AAAAGAAAAAGTGAGAAGTTTGGAAAAACTATTT	2<<<<<<<9<<4<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_103:3:277:921:474	83	chr2	241	99	35M	=	45	-231	AAAGAAAAAGTGAGAAGTTTGGAAAAACTATTTGA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:27	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:2:41:199:388	99	chr2	243	99	35M	=	403	195	AGAAAAAGTGAGAAGTTTGGAAAAACTATTTGAGG	;;<<<<<;;<<<<<<;;<;;<<;;<<<<<<99999	MF:i:18	Aq:i:47	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_593:7:307:481:625	99	chr2	245	99	36M	=	410	201	AAAAAGTGAGAAGTTTGGAAAAACTATTTGAGGAAG	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;;;;9<;	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_53:3:134:126:465	99	chr2	245	99	35M	=	434	224	AAAAAGTGAGAAGTTTGGAAAAACTATTTGAGGAA	<<<<<<<<<<<<<;<<<<<<<<<<<<<5<<:<<41	MF:i:18	Aq:i:56	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_57:2:44:153:969	163	chr2	245	95	35M	=	447	237	AAAAAGTGAGAAGTTTGGAAAAACTATTTGAGGAA	*:::7<77<:<<<<:<<(597:<:<9//7<529/0	MF:i:18	Aq:i:36	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_59:3:182:1002:639	83	chr2	246	99	35M	=	77	-204	AAAAGTGAGAAGTTTGGAAAAACTATTTGAGGAAG	<<;;9;9<<<<<<;<7;<;<<<<;;<<<;<<7;<<	MF:i:18	Aq:i:48	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS220_1:2:54:91:1232	147	chr2	246	99	35M	=	57	-224	AAAAGTGAGAAGTTTGGAAAAACTATTTGAGGAAG	;;;;;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:47	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_108:2:204:737:61	163	chr2	247	99	35M	=	437	225	AAAGTGAGAAGTTTGGAAAAACTATTTGAGGAAGT	<<<<<<<<<<<<<<<<<<<<<<<<<:<<9<+4:<0	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_62:6:148:170:895	147	chr2	247	99	35M	=	91	-191	AAAGTGAGAAGTTTGGAAAAACTATTTGAGGAAGT	<<9<<<<<<<<<7<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS188_7:6:46:122:479	147	chr2	248	99	35M	=	87	-196	AAGTGAGAAGTTTGGAAGAACTATTTGAGGAAGTA	<<<9<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:47	NM:i:1	UQ:i:27	H0:i:0	H1:i:1
+EAS219_1:7:16:1343:1621	99	chr2	248	99	35M	=	426	213	AAGTGAGAAGTTTGGAAAAACTATTTGAGGAAGTA	<<<<<<<<8<<<<;<<<;<;<<<<<<<:;4;71:;	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_593:2:313:531:169	83	chr2	250	99	36M	=	89	-197	GTGAGAAGTTTGGAAAAACTATTTGAGGAAGTAATT	98;<;;<<;8<<<<<<<<<<<8<<<<<<<<8<<<<<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_108:4:75:166:463	147	chr2	250	99	35M	=	64	-221	GTGAGAAGTTTGGAAAAACTATTTGAGGAAGTAAT	<<<<<==============================	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_71:7:130:260:553	99	chr2	250	99	34M	=	439	224	GTGAGAAGTTTGGAAAAACTATTTGAGGAAGCAC	<<<<<1<<<<<<<<<<6<<81</<4*2;7:+90(	MF:i:18	Aq:i:42	NM:i:2	UQ:i:31	H0:i:1	H1:i:0
+EAS56_59:2:60:677:921	99	chr2	250	96	35M	=	393	178	GTGAGAAGTTTGGAAAAACTATTTGAGGAAGTAAT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:22	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_1:6:60:1037:1146	99	chr2	250	99	35M	=	447	232	GTGAGAAGTTTGGAAAAACTATTTGAGGAAGTAAT	<<<<<<<<<<<<<<<<<<<<<<<<<;<:;;;;;;<	MF:i:18	Aq:i:53	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_39:5:17:1222:783	83	chr2	251	99	35M	=	87	-199	TGAGAAGTTTGGAAAAACTATTTGAGGAAGTAATT	6<<<8<69<8199<7<<<6<<<<<<<<<1:<:<<:	MF:i:18	Aq:i:59	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_1:6:96:491:1891	163	chr2	253	99	35M	=	409	191	AGAAGTTTGGAAAAACTATTTGAGGAAGTAATTGG	<:<<<<<::<<<<<<<<<<<<<<<<:<<::7<<:7	MF:i:18	Aq:i:46	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS112_34:6:75:615:555	99	chr2	255	99	35M	=	416	196	AAGTTTGGAAAAACTATTTGAGGAAGTAATTGGGG	<<<<<<<<<<<<<<<<<<<<<;<;<<<29<;.484	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_11:5:32:686:735	147	chr2	255	78	35M	=	84	-206	AAGTTTGGAAAAACTATTTGAGGAAGTAATTGGGG	<<<<<<<<<<<<<9<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:78	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS218_4:3:65:85:1547	163	chr2	257	99	35M	=	434	212	GTTTGGAAAAACTATTTGAGGAAGTAATTGGGGAA	<<<<<<<<<<<<<<<<<<<<;<<<<<<<<<<:<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS219_1:7:94:1655:1921	99	chr2	258	85	35M	=	447	224	TTTGGAAAAACTATTTGAGGAAGTAATTGGGGAAA	<<<8<<<<<<<<<8<<8;8<;<;<;;<<9+868<;	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:1
+B7_610:7:177:469:800	99	chr2	259	99	35M	=	433	209	TTGGAAAAACTATTTGAGGAAGTAATTGGGGAAAA	<<<<<<<<<<<<<<<<<<<<<<<<;<<;;<<<;<;	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_28:7:178:276:693	83	chr2	259	99	36M	=	96	-199	TTGGAAAAACTATTTGAGGAAGTAATTGGGGAAAAC	:;<;<<<<<<<<<<<;<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_30:3:14:697:541	99	chr2	259	99	35M	=	432	208	TTGGAAAAACTATTTGAGGAAGTAATTGGGGAAAA	<<<<<<<<<<<<<<<<<<<:<<<<<<<;;;;8;;<	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:6:37:156:134	163	chr2	261	99	35M	=	443	217	GGAAAAACTATTTGAGGAAGTAATTGGGGAAAACC	;;;;;;;;;;9;;;;;;;;;;;;;;;9;;;77679	MF:i:18	Aq:i:49	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_593:1:215:861:605	83	chr2	262	94	36M	=	107	-191	GAAAAACTATTTGAGGAAGTAATTGGGGAAAACCTC	;<<<<<;:<7:<<<;<<<<<<<;:<<<<<<<<<<<<	MF:i:18	Aq:i:19	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_1:2:3:945:2005	83	chr2	262	99	35M	=	77	-220	GAAAAACTATTTGAGGAAGTAATTGGGGAAAACCT	7<<<<;;<<;<<<<<7<<<<<<<<<;<<<<<<<<<	MF:i:18	Aq:i:44	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_595:6:52:751:360	163	chr2	263	99	35M	=	443	215	AAAAACTATTTGAGGAAGTAATTGGGGAAAACCTC	<<<<<<<<<<<<<<<<<<<<<<<:76<<<<;9:;:	MF:i:18	Aq:i:45	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_93:6:238:514:194	83	chr2	265	99	35M	=	68	-232	AAACTATTTGAGGAAGTAATTGGGGAAAACCTCTT	<<6<<<<:9<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_61:5:194:470:416	147	chr2	265	99	35M	=	98	-202	AAACTATTTGAGGAAGTAATTGGGGAAAACCTCTT	<<<7<<;<<<<<<<<<:<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_95:4:71:517:742	147	chr2	266	99	35M	=	81	-220	AACTATTTGAGGAAGTAATTGGGGAAAACCTCTTT	<<<<<<2<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:49	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_105:8:254:617:73	83	chr2	266	99	35M	=	83	-218	AACTATTTGAGGAAGTAATTGGGGAAAACCTCTTT	<<:<<<9;<<<;;<:<-<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:51	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_32:6:199:818:124	147	chr2	266	99	35M	=	73	-228	AACTATTTGAGGAAGTAATTGGGGAAAACCTCTTT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:3:41:653:1568	83	chr2	266	99	35M	=	95	-206	AACTATTTGAGGAAGTAATTGGGGAAAACCTCTTT	977979;:;<;;;;;;<<5;<;<;<<<;;;;;;;;	MF:i:18	Aq:i:67	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_65:5:211:84:84	99	chr2	268	99	35M	=	440	207	CTATTTGAGGAAGTAATTGGGGAAAACCTCTTTAG	<<<<<<<<<<<<<<<<:<<:<<:<<<44<4<<9<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_99:2:152:355:962	163	chr2	269	99	35M	=	456	222	TATTTGAGGAAGTAATTGGGGAAAACCTCTTTAGT	<;<<<<<;8<<<<<<<<<;5;;88<<3<<<<<&0;	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_66:5:285:395:450	99	chr2	269	99	35M	=	458	224	TATTTGAGGAAGTAATTGGGGAAAACCTCTTTAGT	<<<<<<<;<<<;<<<<<;:<:7<;<;7<7<<;;7<	MF:i:18	Aq:i:65	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS188_7:3:15:568:42	121	chr2	269	69	35M	=	269	0	TTTTTGAGGAAGTAATTGGGGAAAACCTCTTTAGT	!!;:<8<;<<<8<<<<<<<<8<<<<<<<<<<<<<<	MF:i:64	Aq:i:0	NM:i:2	UQ:i:0	H0:i:1	H1:i:0
+EAS188_7:3:15:568:42	181	chr2	269	0	*	=	269	0	TTTTTTTTTTTGTTTTTTTTTTTTTTTTTTTTATA	!!!!!!!!!++++!!!!!!!!!!!!!!!!!!!,!,	MF:i:192
+EAS192_3:8:6:237:885	99	chr2	269	99	35M	=	433	199	TATTTGAGGAAGTAATTGGGGAAAACCTCTTTAGT	<<<<<<<<9<<<<<<<<<<<<<<<<<<<<<;;;<;	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS219_1:5:5:259:250	147	chr2	269	99	35M	=	115	-189	TATTTGAGGAAGTAATTGGGGAAAACCTCTTTAGT	8<83;<<<<<<<<<<5<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_64:6:206:994:556	73	chr2	270	75	35M	=	270	0	ATTTGAGGAAGTAATTGGGGAAAACCTCTTTAGTC	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<4<<;<<	MF:i:64	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_64:6:206:994:556	133	chr2	270	0	*	=	270	0	NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN	!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!	MF:i:192
+EAS54_71:4:169:256:888	83	chr2	270	99	34M	=	94	-210	ATTTGAGGAAGTAATTGGGGAAAACCTCTTTAGT	&<<:<;<<;;<8<;<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_81:2:317:72:221	163	chr2	270	99	35M	=	422	187	ATTTGAGGAAGTAATTGGGGAAAACCTCTTTAGTC	===========;=======;;:==6=;=====;==	MF:i:18	Aq:i:53	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_81:8:40:925:442	83	chr2	271	99	35M	=	93	-213	TTTGAGGAAGTAATTGGGGAAAACCTCTTTAGTCT	=;=================================	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_57:2:158:909:321	163	chr2	271	99	35M	=	453	217	TTTGAGGAAGTAATTGGGGAAAACCTCTTTAGTCT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_26:1:35:522:294	83	chr2	272	99	35M	=	95	-212	TTGAGGAAGTAATTGGGGAAAACCTCTTTAGTCTT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_95:4:176:971:874	163	chr2	273	76	35M	=	432	195	TGAGGAAGTAATTGGGGAAAACCTCTTTAGTCTTG	<<<<<<<<<<<<<:<;<<<<<<<<<<<<<5<<<<7	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_81:7:226:869:36	99	chr2	273	99	35M	=	461	223	TGAGGAAGTAATTGGGGAAAACCTCTTTAGTCTTG	:<<<<,:<;:.:<<:<<717,;2171717717116	MF:i:18	Aq:i:59	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_597:6:106:595:322	163	chr2	274	99	35M	=	440	201	GAGGAAGTAATTGGGGAAAACCTCTTTAGTCTTGC	<<<<<<<<<<<<<<<<<<<<<<<<<<<<:<<<<::	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS219_FC30151:1:54:436:1452	83	chr2	275	99	35M	=	108	-202	AGGAAGTAATTGGGGAAAACCTCTTTAGTCTTGCT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_19:4:77:1780:693	147	chr2	276	99	40M	=	106	-210	GGAAGTAATTGGGGAAAACCTCTTTAGTCTTGCTAGAGAT	:**::799<<9<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_97:3:147:423:584	99	chr2	277	99	35M	=	451	209	GAAGTAATTGGGGAAAACCTCTTTAGTCTTGCTAG	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<9;;96	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_99:2:188:782:483	163	chr2	277	99	35M	=	431	189	GAAGTAATTGGGGAAAACCTCTTTAGTCTTGCTAG	<<<<<<<<<<<<<<<<<<<<<<<<<;<<<<7<;77	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_3:4:78:1314:1275	99	chr2	277	99	35M	=	469	227	GAAGTAATTGGGGAAAACCTCTTTAGTCTTGCTAG	<<<<<<<<<<<<<<<<<<<<<6<<<<<<<<<<<<8	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_97:7:63:727:203	147	chr2	278	99	35M	=	114	-199	AAGTAATTGGGGAAAACCTCTTTAGTCTTGCTAGA	<<;7<<;<<<<<<<<<;<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:2:13:1507:1146	147	chr2	278	99	35M	=	84	-229	AAGTAATTGGGGAAAACCTCTTTAGTCTTGCTAGA	88788;,;:-:2;;;;;;;;:;:;;;;;;;;;;;;	MF:i:18	Aq:i:49	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:1:77:1000:1780	83	chr2	279	66	35M	=	123	-191	AGTAATTGGGGAAAACCTCTTTAGTCTTGCTAGAG	777774;;4-7;;;;;;:;;;:;;;<;;;;<<<<;	MF:i:18	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_59:1:93:490:901	163	chr2	280	99	35M	=	445	200	GTAATTGGGGAAAACCTCTTTAGTCTTGCTAGAGA	<<<<<<<<<<<<<;<<<<<<<;<<<<<:<<1+4-8	MF:i:18	Aq:i:53	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_59:6:227:657:95	99	chr2	280	99	35M	=	458	213	GTAATTGGGGAAAACCTCTTTAGTCTTGCTAGAGA	<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<<8<85	MF:i:18	Aq:i:59	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_28:7:57:324:546	163	chr2	281	99	36M	=	458	213	TAATTGGGGAAAACCTCTTTAGTCTTGCTAGAGATT	<<<<<<<<<<<<<<<<<<<<<:<<<8:8<<;::;;;	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_73:7:223:440:667	147	chr2	282	99	35M	=	97	-220	AATTGGGGAAAACCTCTTTAGTCTTGCTAGAGATT	<<;;<;;<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_19:4:26:274:1078	163	chr2	282	99	40M	=	458	216	AATTGGGGAAAACCTCTTTAGTCTTGCTAGAGATTTAGAC	<<<2<<<<<<<<<<<<<<<<<<<<<<<<<;;:;;;:::::	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_62:7:196:511:896	163	chr2	283	99	35M	=	446	198	ATTGGGGAAAACCTCTTTAGTCTTGCTAGAGATTT	<<<<<<<<<<<<<<<<<<<<<<<<;<<<4<88;<<	MF:i:18	Aq:i:52	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_57:3:112:729:591	147	chr2	283	99	35M	=	86	-232	ATTGGGGAAAACCTCTTTAGTCTTGCTAGAGATTT	;;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_39:6:34:380:815	83	chr2	283	99	35M	=	91	-227	ATTGGGGAAAACCTCTTTAGTCTTGCTAGAGATTT	;;;;<<<<<<;<<<<;<<<<<<<<<<<<<<<<<;<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_65:8:117:156:84	147	chr2	285	99	35M	=	95	-225	TGGGGAAAACCTCTTTAGTCTTGCTAGAGATTTAG	<;;<:<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_39:5:61:1000:1534	83	chr2	286	99	35M	=	104	-217	GGGGAAAACCTCTTTAGTCTTGCTAGAGATTTAGA	<<;<<<<;;<<;6;<<<;<4;<<7<<<<<;<<<<<	MF:i:18	Aq:i:63	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_3:2:22:1623:709	147	chr2	287	99	35M	=	107	-215	GGGAAAACCTCTTTAGTCTTGCTAGAGATTTAGAC	<'<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_61:7:7:682:201	163	chr2	288	99	35M	=	452	199	GGAAAACCTCTTTAGTCTTGCTAGAGATTTAGACA	<<<<<<<7<<7<<<<77&;-9<97<76<;<<993<	MF:i:18	Aq:i:66	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:5:91:89:666	153	chr2	289	60	35M	*	0	0	GAAAACCTCTTTAGTCTTGCTAGAGATTTAGACAT	74752;;4;;;;;;;;7);;;4;;;;)4;;;;;13	MF:i:32	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_26:6:46:13:880	99	chr2	290	99	35M	=	445	190	AAAACCTCTTTAGTCTTGCTAGAGATTTAGACATC	<<<<<<<<<<<<<<<<<<<<;<7<3<<<9<+;;<9	MF:i:18	Aq:i:43	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_99:1:187:715:521	163	chr2	291	99	35M	=	451	195	AAACCTCTTTAGTCTTGCTAGAGATTTAGACATCT	<<<<<<<<<<<<<<<<<<<<:<<<<<<<;<<;<;;	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_64:6:210:809:735	83	chr2	291	99	35M	=	93	-233	AAACCTCTTTAGTCTTGCTAGAGATTTAGACATCT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_57:5:145:383:182	83	chr2	291	99	35M	=	105	-221	AAACCTCTTTAGTCTTGCTAGAGATTTAGACATCT	<<;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS112_32:8:89:254:332	83	chr2	291	76	35M	=	124	-202	AAACCTCTTTAGTCTTGCTAGAGATTTAGACATCT	<<<<<<:<;<<<<<<<<9<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_11:2:63:816:921	83	chr2	291	99	35M	=	106	-220	AAACCTCTTTAGTCTTGCTAGAGATTTAGACATCT	<<<<<<<<<4<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_105:2:280:662:939	99	chr2	294	99	35M	=	442	183	CCTCTTTAGTCTTGCTAGAGATTTAGACATCTAAA	<<<<<<<<<<<<<;<<<;;7<<<<<<<<<<<<:8<	MF:i:18	Aq:i:48	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_28:3:250:628:423	163	chr2	295	99	36M	=	489	230	CTCTTTAGTCTTGCTAGAGATTTAGACATCTAAATG	<<<<<<<<<<<<<<<<<<:;<<<<:<<<<;;;;;;4	MF:i:18	Aq:i:27	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS192_3:4:255:549:422	163	chr2	295	99	35M	=	456	196	CTCTTTAGTCTTGCTAGAGATTTAGACATCTAAAT	<<<<<<<<<<<<<<<<;<<<<<<<:<<<<<<;;;<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_3:2:2:491:1886	89	chr2	295	75	35M	*	0	0	CTCTTTAGTCTTGCTAGAGATTTAGACATCTAAAT	<<:<8:<<<:<<<<<<<<<<<9<<<<<<<<<<<<:	MF:i:32	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_71:3:267:821:860	163	chr2	296	99	35M	=	451	189	TCTTTAGTCTTGCTAGAGATTTAGACATCTAAATG	;<<<<<8<<<<<8<<;<8<<<<<5<;<<<<<2;<5	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_11:2:42:333:516	83	chr2	296	99	35M	=	109	-222	TCTTTAGTCTTGCTAGAGATTTAGACATCTAAATG	<<<<<<<<7<63<7<<<<<<<<<<<7<<<<<<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_63:2:119:161:322	99	chr2	297	99	35M	=	479	217	CTTTAGTCTTGCTAGAGATTTAGACATCTAAATGA	<<<<<<<<<<<<<<;<<<<<<<;<<<<<<<<<</6	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:4:48:310:473	147	chr2	298	66	35M	=	123	-210	TTTAGTCTTGCTAGAGATTTAGACATCTAAATGAA	77999;;6;;;;;;;;;;;;;;;9;;;;;;;;;;;	MF:i:18	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_93:6:159:273:253	153	chr2	299	76	35M	*	0	0	TTAGTCTTGCTAGAGATTTAGACATCTAAATGAAA	<<<<<<<<:<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:32	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_99:6:181:392:500	99	chr2	299	99	35M	=	470	206	TTAGTCTTGCTAGAGATTTAGACATCTAAATGAAA	<<<<<:<<<2<<<<;5<<<<29+<<)</65<7.24	MF:i:18	Aq:i:63	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS112_34:4:17:989:186	147	chr2	299	91	35M	=	120	-214	TTAGTCTTGCTAGAGATTTAGACATCTAAATGAAA	87;38$<3=/<==============9=========	MF:i:18	Aq:i:20	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:2:33:1445:1357	147	chr2	299	85	35M	=	121	-213	TTAGTCTTGCTAGAGATTTAGACATCTAAATGAAA	88888;;;;;;;:;;;;;;;:;9;;;;;;;;;;;;	MF:i:18	Aq:i:18	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_595:6:119:730:190	147	chr2	301	99	35M	=	114	-222	AGTCTTGCTAGAGATTTAGACATCTAAATGAAAGA	;;;3;<<:<<<<:<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_93:5:62:969:12	99	chr2	303	99	35M	=	464	196	TCTTGCTAGAGATTTAGACATCTAAATGAAAGAGG	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_597:7:103:731:697	147	chr2	304	72	35M	=	125	-214	CTTGCTAGAGATTTAGACATCTAAATGAAAGAGGC	:::;3:<<<<<<<:<<<<<<:<<<<<<<<<<<<<<	MF:i:18	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_30:2:111:142:21	163	chr2	304	99	35M	=	479	210	CTTGCTAGAGATTTAGACATCTAAATGAAAGAGGC	<<<<<<<<:<:<<<<<<<<<<<<<<<<<<<<;<;9	MF:i:18	Aq:i:28	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_93:7:319:280:57	99	chr2	306	99	35M	=	467	196	TGCTAGAGATTTAGACATCTAAATGAAAGAGGCTC	;==========;=====6;=========;=<;6;;	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_11:8:76:205:587	163	chr2	306	99	35M	=	483	212	TGCTAGAGATTTAGACATCTAAATGAAAGAGGCTC	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:28	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_591:2:279:124:41	147	chr2	307	69	36M	=	124	-219	GCTAGAGATTTAGACATCTAAATGAAAGAGGCTCAA	:17<8<<<:&<<<<<<:;'<<<<<<<<<<;<<<<<<	MF:i:18	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_19:3:10:349:1147	153	chr2	307	74	40M	*	0	0	GCTAGAGATTTAGACATCTAAATGAAAGAGGCTCAAAGAA	:/:::<<<<<<<<<<<<;<<<<<<<<<<<<<<<<<<<<<<	MF:i:32	Aq:i:16	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS219_1:1:22:490:2011	99	chr2	307	99	35M	=	485	213	GCTAGAGATTTAGACATCTAAATGAAAGAGGCTCA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:47	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_65:6:46:173:214	163	chr2	308	99	35M	=	487	214	CTAGAGATTTAGACATCTAAATGAAAGAGGCTCAA	<<<<<<<<<<<<<<<<<<<<<<<<<;<3<<<<<<;	MF:i:18	Aq:i:29	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_32:2:283:577:398	99	chr2	308	99	35M	=	488	215	CTAGAGATTTAGACATCTAAATGAAAGAGGCTCAA	<<<<<<<<<<<<<<<<<<<9<<<<<<<<<;<<<<<	MF:i:18	Aq:i:29	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_591:2:27:280:592	99	chr2	310	99	36M	=	484	210	AGAGATTTAGACATCTAAATGAAAGAGGCTCAAAGA	<<<<<<<<<<<<<<<<<<<<<<<<9<<<<<<<<<5<	MF:i:18	Aq:i:47	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_39:3:11:1238:1728	163	chr2	310	99	35M	=	475	200	AGAGATTTAGACATCTAAATGAAAGAGGCTCAAAG	<<7<<<<<;<<<<<<<<<<<<;<<<;<<<<<<;;<	MF:i:18	Aq:i:45	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_593:6:118:121:760	89	chr2	311	77	36M	*	0	0	GAGATTTAGACATCTAAATGAAAGAGGCTCAAAGAA	:<<<;;<<<<6<;<<<;<<<<;<<<<<<<<<<<<<<	MF:i:32	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_59:7:318:679:883	153	chr2	313	75	35M	*	0	0	GATTTAGACATCTAAATGAAAGAGGCTCAAAGAAT	<<;4<<;<:<<7<<<<<<<<<<<<<<<<<<<<<<<	MF:i:32	Aq:i:19	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_3:4:30:1452:1563	83	chr2	313	94	35M	=	122	-226	GATTTAGACATCTAAATGAAAGAGGCTCAAAGAAT	<<39<<<59<<:<<+<<<6<<:<<<<<<<<<<<<<	MF:i:18	Aq:i:20	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_57:1:189:130:136	99	chr2	314	79	35M	=	494	215	ATTTAGACATCTAAATGAAAGAGGCTCAAAGAATG	==<<=================<<====<<=;=6==	MF:i:18	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS192_3:5:27:577:849	83	chr2	316	99	35M	=	114	-237	TTAGACATCTAAATGAAAGAGGCTCAAAGAATGCC	5:<;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_589:3:71:478:175	83	chr2	317	99	35M	=	171	-181	TAGACATCTAAATGAAAGAGGCTCAAAGAATGCCA	<<<<;<96<<<<;<<<<<<<<<77<<<<<<<<<<;	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_597:4:38:999:463	99	chr2	317	39	35M	=	503	221	TAGACATCTAAATGAAAGNNGCNNNAAGAATGCCA	7<<<<<<<<:07<<:<<7!!<<!!!::<88<<<<4	MF:i:130	Aq:i:39	NM:i:5	UQ:i:0	H0:i:0	H1:i:0
+EAS54_71:8:215:830:609	89	chr2	317	71	33M	*	0	0	AAGACATCTAAATGAAAGAGGCTCAAAGAATGC	+<)<:<<:<<<<<<<<<9<<<<<;<<<<<<<<<	MF:i:32	Aq:i:0	NM:i:1	UQ:i:11	H0:i:1	H1:i:0
+EAS188_7:7:213:309:373	83	chr2	317	99	35M	=	161	-191	TAGACATCTAAATGAAAGAGGCTCAAAGAATGCCA	<<<86<82<<<<<<<<<<<<<<<9<<<<<<<<<<<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:7:45:1339:1807	153	chr2	319	64	35M	*	0	0	GACATCTAAATGAAAGAGGCTCAAAGAATGCCAGG	77797;;:;::&:;;0:;8;;4;;:;;6;;;;;;;	MF:i:32	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_93:5:197:52:58	83	chr2	323	99	35M	=	165	-193	TCTAAATGAAAGAGGCTCAAAGAATGCCAGGAAGA	<7;;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:54	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS192_3:8:6:104:118	83	chr2	323	99	35M	=	154	-204	TCTAAATGAAAGAGGCTCAAAGAATGCCAGGAAGA	;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:27	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_593:6:185:96:948	147	chr2	324	99	36M	=	160	-200	CTAAATGAAAGAGGCTCAAAGAATGCCAGGAAGATA	6<;;<;<<;<<<<<747<<<<<<<<77<<<<<<<<<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_65:4:61:346:384	163	chr2	324	68	35M	=	496	207	CTAAATGAAAGAGGCTCAAAGAATGCCAGGAAGAT	<<;<<<<<<<<9<;<<9;<6<2;<6<<<;9*558;	MF:i:18	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_81:8:177:800:714	163	chr2	324	76	35M	=	497	208	CTAAATGAAAGAGGCTCAAAGAATGCCAGGAAGAT	<<<<<<<<<<<<<<<<<<<<<;<<<;<;<<<<<;<	MF:i:18	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_591:4:329:339:408	99	chr2	325	99	36M	=	515	226	TAAATGAAAGAGGCTCAAAGAATGCCAGGAAGATAC	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<9<<<<;	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_30:6:214:565:337	99	chr2	326	99	35M	=	481	190	AAATGAAAGAGGCTCAAAGAATGCCAGGAAGATAC	<;<<<<<<<<<<<<<<;<<<<9<<<<<;;;;<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS188_4:7:296:401:60	89	chr2	327	68	35M	*	0	0	AATGAAAGAGGCTCAAAGAATGCCAGGAAGATACA	<<*<<<<7<<)<<3<<<9<<<<<<<<<<<<<<;<<	MF:i:32	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS218_1:6:88:1413:14	89	chr2	327	76	35M	*	0	0	AATGAAAGAGGCTCAAAGAATGCCAGGAAGATACA	<<<<<<<<<<<;;;<<<<<<;<;;<<<<<<<<<<<	MF:i:32	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_99:1:34:649:318	163	chr2	328	65	35M	=	481	188	ATGAAAGAGGCTCAAAGAATGCCAGGAAGATACAT	9<<3<<<9<<<<<<<<<7<<9<<0<<.0<*:77,;	MF:i:18	Aq:i:65	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_19:2:29:1822:1881	83	chr2	328	74	40M	=	150	-218	ATGAAAGAGGCTCAAAGAATGCCAGGAAGATACATTGCAA	;87;;<<<;<5<5<<<<<<<;<<<<<<<<<<<<:<<<<<<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_99:8:187:199:369	153	chr2	329	74	35M	*	0	0	TGAAAGAGGCTCAAAGAATGCCAGGAAGATACATT	;<><<<<<<<<7<<<<<<<<=<<<<<<<<<<<<<<	MF:i:32	Aq:i:19	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_57:2:23:268:529	153	chr2	329	71	35M	*	0	0	TGAAAGAGGCTCAAAGAATGCCAGGAAGATACATT	7;<<<<<<57;-<<<<<<:<77<<<<<<<;<;<<<	MF:i:32	Aq:i:28	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_26:2:315:219:7	153	chr2	330	69	35M	*	0	0	GAAAGAGGCTCAAAGAATGCCAGGAAGATACATTG	7==::<2=8<<<=====>888<=2=>==>,>,>>8	MF:i:32	Aq:i:19	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS192_3:4:63:5:870	83	chr2	330	75	35M	=	148	-217	GAAAGAGGCTCAAAGAATGCCAGGAAGATACATTG	:<;<;<<<4:;<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_591:5:243:557:560	163	chr2	331	75	36M	=	499	204	AAAGAGGCTCAAAGAATGCCAGGAAGATACATTGCA	<<<<<<<9<<<<<<<<<<<<<<<<<<;<<89<<9<;	MF:i:18	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_593:2:270:430:269	163	chr2	331	99	36M	=	519	224	AAAGAGGCTCAAAGAATGCCAGGAAGATACATTGCA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;;;7;:	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_66:6:284:442:747	89	chr2	331	75	35M	*	0	0	AAAGAGGCTCAAAGAATGCCAGGAAGATACATTGC	<;<<<<<:<;<<<<<<<<;<<<<<<<<<<<<<<<<	MF:i:32	Aq:i:29	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS218_4:7:71:31:1973	89	chr2	331	76	35M	*	0	0	AAAGAGGCTCAAAGAATGCCAGGAAGATACATTGC	<<<<<7<:<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:32	Aq:i:29	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_93:2:30:466:652	147	chr2	332	98	35M	=	163	-204	AAGAGGCTAAAAGAATGCCAGGAAGATACATTGCA	<<<<<;3;&<<<<<<<</6<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:45	NM:i:1	UQ:i:5	H0:i:0	H1:i:1
+EAS56_61:3:208:118:673	147	chr2	332	76	35M	=	169	-198	AAGAGGCTCAAAGAATGCCAGGAAGATACATTGCA	<<<<<;;<;<<<<<<<<<:<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:1:95:1530:28	163	chr2	332	74	35M	=	490	193	AAGAGGCTCAAAGAATGCCAGGAAGATACATTGCA	;;;;;;;;;;:;;;;;;;8;;;;;;;;;;;77747	MF:i:18	Aq:i:9	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_64:7:104:965:517	73	chr2	333	77	35M	=	333	0	AGAGGCTCAAAGAATGCCAGGAAGATACATTGCAA	<<<<<<<<<<<<<<<<<<<<<:<<<<<<<8<<;<<	MF:i:64	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_64:7:104:965:517	133	chr2	333	0	*	=	333	0	NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN	!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!	MF:i:192
+EAS54_65:7:155:629:357	163	chr2	333	99	35M	=	521	223	AGAGGCTCAAAGAATGCCAGGAAGATACATTGCAA	<<<<<<<<8<8<<6<<<<<<<<;<9<5<;<;;941	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_28:4:149:572:877	83	chr2	334	99	36M	=	197	-173	GAGGCTCAAAGAATGCCAGGAAGATACATTGCAAGA	6<94693<;<<<<;;<<<<<<<<<<;9<<<<<<<<<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_57:5:53:544:889	99	chr2	335	76	35M	=	495	195	AGGCTCAAAGAATGCCAGGAAGATACATTGCAAGA	<<<<<<<<;<<<<<<<<<<<<<<<<<;<<<<<;<<	MF:i:18	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_61:6:226:370:91	99	chr2	335	99	35M	=	482	182	AGGCTCAAAGAATGCCAGGAAGATACATTGCAAGA	8<<<;<8<8<;<<<8<<;7<7;8784<<,;864<&	MF:i:18	Aq:i:43	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_59:4:119:651:88	163	chr2	337	99	35M	=	527	225	GCTCAAAGAATGCCAGGAAGATACATTGCAAGACA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<9;<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_597:6:20:592:496	163	chr2	338	75	35M	=	498	195	CTCAAAGAATGCCAGGAAGATACATTGCAAGACAG	<<<<<<<<<<<<<<<<<<<<<<<<<==<<<<<<:<	MF:i:18	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_65:3:214:946:229	83	chr2	339	99	35M	=	165	-209	ACAAAGAATGCCAGGAAGATACATTGCAAGACAGA	)+<<<*<<77;8<;7<<8<4<;<88<<<<<<<<<<	MF:i:18	Aq:i:65	NM:i:1	UQ:i:8	H0:i:1	H1:i:0
+EAS188_7:5:163:982:695	99	chr2	339	77	35M	=	499	195	TCAAAGAATGCCAGGAAGATACATTGCAAGACAGA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<<;	MF:i:18	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS218_1:4:14:1872:1521	163	chr2	339	62	35M	=	500	196	TCAAAGAATGCCAGGAAGATACATTGCAAGTCAGA	7<<<<77<<<3<3<7.'<<<<<7<67<+.0%4*<4	MF:i:18	Aq:i:2	NM:i:1	UQ:i:4	H0:i:1	H1:i:0
+EAS192_3:4:293:168:240	147	chr2	340	99	35M	=	167	-208	CAAAGAATGCCAGGAAGATACATTGCAAGACAGAC	+;;;;<8<<86<<<<<<<;;8;7;<;<8<8;<<<<	MF:i:18	Aq:i:48	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_62:5:86:697:941	83	chr2	341	99	35M	=	187	-189	AAAAAAATCCCGGAAGATACATTGCAAGACAGACT	1<<%<<<1:<58<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:27	NM:i:4	UQ:i:67	H0:i:0	H1:i:0
+EAS54_71:4:14:88:306	99	chr2	341	99	34M	=	521	215	AAAGAATGCCAGGAAGATACATTGCAAGACAGAC	<<<<<<8<<<<<<;<<<3<<<8<<;<;;<15<:6	MF:i:18	Aq:i:45	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_26:6:183:697:555	163	chr2	341	84	35M	=	505	199	AAAGAATGCCAGGAAGATACATTGCCAGACAGACT	=====================:===&==:;==5;;	MF:i:18	Aq:i:37	NM:i:1	UQ:i:5	H0:i:0	H1:i:1
+EAS56_57:3:41:739:907	163	chr2	344	99	35M	=	520	211	GAATGCCAGGAAGATACATTGCAAGACAGACTTCA	<<<<<<<<<<<<<<<<<<<<<<<<;<9<<<;;;;;	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_3:2:100:1147:124	83	chr2	345	99	35M	=	150	-230	AATGCCAGGAAGATACATTGCAAGACAGACTTCAT	<<<<96<<<<<<<<<<<<<<<<<<<<<<:<<<<<<	MF:i:18	Aq:i:29	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_67:5:127:828:697	99	chr2	346	99	35M	=	552	241	ATGCCAGGAAGATACATTGCAAGACAGACTTCATC	<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<;;<;	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_63:8:62:125:888	163	chr2	347	99	35M	=	504	192	TGCCAGGAAGATACATTGCAAGACAGACTTCATCA	<<<<<<<<<<<<<<<<<<<::<<<:7<::<:;<<:	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_19:1:1:1598:843	163	chr2	347	99	40M	=	500	193	TGCCAGGAAGATACATTGCAAGACAGACTTCATCAAGATA	<<<<<<8<<<<<<<<<<<<<<<<<<<<<<<<<<8<4:8::	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_11:2:71:83:58	83	chr2	349	77	35M	=	148	-236	CCAGGAAGATACATTGCAAGACAGACTTCATCAAG	8<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS219_FC30151:1:88:1454:418	163	chr2	349	99	35M	=	522	208	CCAGGAAGATACATTGCAAGACAGACTTCATCAAG	:<<:<<<<<<<<<<<::::<:<:<9<5<<<<<<8:	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_595:5:36:649:554	163	chr2	350	99	35M	=	523	208	CAGGAAGATACATTGCAAGACAGACTTCATCAAGA	<<<<<4<<8<<<<<<8<6<<88<<<<<<<-;<;0;	MF:i:18	Aq:i:68	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_610:2:189:831:878	163	chr2	351	99	35M	=	555	239	AGGAAGATACATTGCAAGACAGACTTCATCAAGAT	:<<<2<<<<<<<<<<:8<8<<<<<<<<<<87489;	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:6:14:1211:1332	83	chr2	351	99	35M	=	178	-208	AGGAAGATACATTGCAAGACAGACTTCATCAAGAT	978961;;991;97;<;;<;<<;;;;;<;;<:8:<	MF:i:18	Aq:i:64	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_30:4:328:537:640	147	chr2	352	99	35M	=	185	-202	GGAAGATACATTGCAAGACAGACTTCATCAAGATA	;:<<;<<<<<::<:<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_593:1:85:361:418	99	chr2	353	99	36M	=	517	200	GAAGATACATTGCAAGACAGACTTCATCAAGATATG	<<<<<<<<<<<<<;<<<<<<<<<<<<<<;4;<<<<3	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_28:2:329:437:643	99	chr2	354	99	36M	=	540	222	AAGATACATTGCAAGACAGACTTCATCAAGATATGT	<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<;<<<<1	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_99:6:135:354:66	147	chr2	356	99	35M	=	188	-203	GATACATTGCAAGACAGACTTCATCAAGATATGTA	;;;;7<<<<:<<<<;<<<:<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_97:7:9:648:712	147	chr2	358	99	35M	=	182	-211	TACATTGCAAGACAGACTTCATCAAGATATGTAGT	*;0;;;95<<<<7<<<;;<<<;;<<<<;<<<<<<<	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_11:4:36:1184:994	163	chr2	358	99	35M	=	518	195	TACATTGCAAGACAGACTTCATCAAGATATGTAGT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<8<<8<	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_11:4:50:30:15	147	chr2	358	10	35M	=	192	-201	TACATTGCAAGACAGTCGTCAGCAAGATATGTAGT	1-%-22&&)&11,&/&&176<&<<<222<,6,<<<	MF:i:18	Aq:i:10	NM:i:3	UQ:i:26	H0:i:0	H1:i:0
+EAS51_66:4:322:350:374	163	chr2	360	99	35M	=	546	221	CATTGCAAGACAGACTTCATCAAGATATGTAGTCA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_61:7:41:745:603	163	chr2	360	99	35M	=	536	211	CATTGCAAGACAGACTTCATCAAGATATGTAGTCA	<<<<<<<<<<<<:<<<<<<<<<<<<<<<6<:8<<:	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_63:8:138:186:459	163	chr2	360	97	35M	=	518	193	CATTGCAAGACAGACTTCATCAAGATATGTAGTCA	<*<<7<<0<7<<+<-:<<&<:6:4:0-:<<2.:5<	MF:i:18	Aq:i:37	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_3:4:41:1308:619	83	chr2	360	99	35M	=	184	-211	CATTGCAAGACAGACTTCATCAAGATATGTAGTCA	0<9476<<<<<0<<<2<&<0<.<<<<<<<<<.<<<	MF:i:18	Aq:i:68	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_57:1:125:884:276	163	chr2	362	99	35M	=	541	214	TTGCAAGACAGACTTCATCAAGATATGTAGTCATC	<<<<<<<<<<<8<<<<<<<<<<<<<<<<<<;;<<;	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_32:4:156:21:69	83	chr2	362	99	35M	=	163	-234	TTGCAAGACAGACTTCATCAAGATATGTAGTCATC	<:3:<<;<;<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:54	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_19:5:66:1381:181	163	chr2	362	99	40M	=	544	222	TTGCAAGACAGACTTCATCAAGATATGTAGTCATCAGACT	<<6<<<<<<<<<<<<<<<<<<<<<<<<<<:<<<<<::4:7	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS219_FC30151:7:11:1261:1200	163	chr2	362	99	35M	=	558	231	TTGCAAGACAGACTTCATCAAGTTATGTAGTCATC	<<<<<<<<<<<;<<<<<<<<;<<<;<:<<8<<:<<	MF:i:18	Aq:i:47	NM:i:1	UQ:i:27	H0:i:0	H1:i:1
+EAS1_99:5:191:885:623	163	chr2	363	99	35M	=	551	223	TGCAAGACAGACTTCATCAAGATATGTAGTCATCA	<<<<<<<<<<<<<<<<<<<<<<<<<<<;;<<;;;;	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_103:7:53:783:78	99	chr2	363	99	35M	=	561	233	TGCAAGACAGACTTCATCAAGATATGTAGTCATCA	<<<<<<<<<<<<<<<<<<<<<<<<<;<<;<7;<:;	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_64:5:177:24:389	83	chr2	365	99	35M	=	175	-225	CAAGACAGACTTCATCAAGATATGTAGTCATCAGA	+<<;<9<<<9<<;<<7<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_597:5:58:684:520	99	chr2	367	99	35M	=	538	206	AGACAGACTTCATCAAGATATGTAGTCATCAGACT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<:;;<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_108:6:71:187:824	99	chr2	367	99	35M	=	534	202	AGACAGACTTCATCAAGATATGTAGTCATCAGACT	;===;======3==;==========4=;=7;;3;6	MF:i:18	Aq:i:66	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_26:1:324:238:736	83	chr2	367	99	35M	=	180	-222	AGACAGACTTCATCAAGATATGTAGTCATCAGACT	<<<9<<<70,<<4<<<<<7<4<7<<<<<0<<<<<7	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_11:6:19:306:982	99	chr2	368	99	35M	=	538	205	GACAGACTTCATCAAGATATGTAGTCATCAGACTA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<:<<<<	MF:i:18	Aq:i:78	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_597:2:168:829:88	83	chr2	369	99	35M	=	205	-199	ACAGACTTCATCAAGATATGTAGTCATCAGACTAT	<,,;<838883;;;<<<<<;<8<8;<<<<<<<<<<	MF:i:18	Aq:i:68	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_81:6:122:589:134	163	chr2	369	99	35M	=	562	228	ACAGACTTCATCAAGATATGTAGTCATCAGACTAT	<<:<<:<:<<<<<:<8<<<<<<<:<::<<<4:<;;	MF:i:18	Aq:i:68	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_95:3:303:970:243	163	chr2	370	99	35M	=	564	229	CAGACTTCATCAAGATATGTAGTCATCAGACTATC	<<<<<<<<<<<<<<<<<<<<;;<<<<<<<<<8<8<	MF:i:18	Aq:i:70	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS188_7:2:19:736:559	147	chr2	370	99	35M	=	209	-196	AAGACTTCATCAAGATATGTAGTCATCAGACTATC	)<7<2;;4<<4<<<<;<<<<<<<<<<7<<<<<<<<	MF:i:18	Aq:i:70	NM:i:1	UQ:i:8	H0:i:1	H1:i:0
+EAS51_66:3:246:711:981	99	chr2	371	99	35M	=	559	223	AGACTTCATCAAGATATGTAGTCATCAGACTATCT	<<<<<<<<;<<<<:;<<;;<:<<<4<<:4;00<;<	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_1:6:89:1164:573	99	chr2	371	99	35M	=	560	224	AGACTTCATCAAGAGATGTAGTCATCAGACTATCT	<:<<;<2<<<<<<<&:2<;<;<<<<;,+;:<<4:<	MF:i:18	Aq:i:41	NM:i:1	UQ:i:5	H0:i:0	H1:i:1
+EAS220_1:8:18:1757:95	147	chr2	374	45	35M	=	216	-193	CTTCATCAAGATATGTAGTCATCAGACTATCTAAA	<<<6<&:<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_57:2:284:597:682	99	chr2	375	99	35M	=	557	217	TTCATCAAGATATGTAGTCATCAGACTATCTAAAG	<<<<<<<9<<<<<;<<6<<<<<;<9<<<<<<1;;9	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_597:3:10:394:392	99	chr2	376	99	35M	=	542	201	TCATCAAGATATGTAGTCATCAGACTATCTAAATT	<<<<<<<<<<<<<<<<<<<:<<<<<<;<<;;:6&;	MF:i:18	Aq:i:68	NM:i:1	UQ:i:5	H0:i:1	H1:i:0
+EAS1_97:5:28:538:148	163	chr2	376	99	35M	=	557	216	TCATCAAGATATGTAGTCATCAGACTATCTAAAGT	<<<<<<<<<<<<<<<<<<<<<<:<<<<<<<+771;	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_3:2:60:590:1760	147	chr2	376	99	35M	=	201	-210	TCATCAAGATATGTAGTCATCAGACTATCTAAAGT	<8<-<<<<<<<82<<<4<<<<<<<<<<<<<8<<<<	MF:i:18	Aq:i:51	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_19:3:73:1158:535	83	chr2	377	99	40M	=	213	-204	AATAAAGATATGTAGTCATCAGACTATCTAAAGTCAACAT	+;6+;<;<<<<<<<<<0<<;<<<;<<<8<<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:2	UQ:i:20	H0:i:1	H1:i:0
+EAS188_7:3:182:104:921	99	chr2	378	99	35M	=	575	232	ATCAAGATATGTAGTCATCAGACTATCTAAAGTCA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<9<<<<<	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_97:3:160:173:889	83	chr2	379	99	35M	=	215	-199	TCAAGATATGTAGTCATCAGACTATCTAAAGTCAA	;)<</<8<<<<<<</<;<<<<;<<<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_30:7:71:311:202	83	chr2	379	99	35M	=	188	-226	TCAAGATATGTAGTCATCAGACTATCTAAAGTCAA	;6<;<<<<<<<<<<<<<<<<<<<<<;<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_593:4:315:201:673	163	chr2	381	45	36M	=	542	197	AAGATATGTAGTCATCAGACTATCTAAAGTCAACAT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<7<<<<<:;	MF:i:18	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_95:2:228:915:631	163	chr2	381	66	35M	=	547	201	AAGATATGTAGTCATCAGACTATCTAAAGTCAACA	=================;==========4======	MF:i:18	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_103:1:228:736:747	163	chr2	381	68	35M	=	542	196	AAGATATGTAGTCATCAGACTATCTAAAGTCAACA	<<<<<<<<<;<<<<<<<;;<<;<<<<;::<;;7;7	MF:i:18	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_66:3:263:689:572	99	chr2	381	68	35M	=	553	207	AAGATATGTAGTCATCAGACTATCTAAAGTCAACA	<<<<;<<<<<;<<<<<<&;;<<<;<<:<+;;7;;7	MF:i:18	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_71:5:81:685:141	147	chr2	382	85	35M	=	207	-210	AGATATGTAGTCATCAGACTATCTAAAGTCAACAT	;+;(;)..=3.1=.7=;=8;==<4====;======	MF:i:18	Aq:i:17	NM:i:0	UQ:i:0	H0:i:2	H1:i:2
+EAS114_32:1:208:971:600	163	chr2	382	99	35M	=	559	212	AGATATGTAGTCATCAGACTATCTAAAGTCAACAT	<<<<<<<<<<<<<<<<<8<<:<<<0;44<<:4<:<	MF:i:18	Aq:i:51	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_3:8:7:1864:1569	99	chr2	382	99	35M	=	561	214	AGATATGTAGTCATCAGACTATCTAAAGTCAACAT	<<<<<<<<<<<<<<<<<<<<<<<<<<:<<<8<<<<	MF:i:18	Aq:i:51	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_95:4:224:592:744	147	chr2	383	99	35M	=	188	-230	GATATGTAGTCATCAGACTATCTAAAGTCAACATG	6<6<<<<<<9+<6-<<<:<:<:<<<<<:<<<<<<<	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_61:6:25:949:33	147	chr2	383	99	35M	=	201	-217	GATATGTAGTCATCAGACTATCTAAAGTCAACATG	-<4<666<<-7<5<<<<<(<<<<<<<<<<<<<<-<	MF:i:18	Aq:i:63	NM:i:0	UQ:i:0	H0:i:2	H1:i:1
+EAS54_73:5:271:874:367	163	chr2	384	99	35M	=	560	211	ATATGTAGTCATCAGACTATCTAAAGTCAACATTA	<<<<<<<<<<<<<<4<;<;<:<;4<4<<99<7<+%	MF:i:18	Aq:i:51	NM:i:1	UQ:i:10	H0:i:1	H1:i:0
+EAS139_19:4:26:1312:1400	147	chr2	385	99	40M	=	207	-218	TATGTAGTCATCAGACTATCTAAAGTCAACATGAAGGAAA	::77:<;:+6<+<<<;<<74<<<;<<;<<<<<<<<<<<;<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:2	H1:i:2
+EAS51_66:6:310:747:415	83	chr2	387	99	35M	=	217	-205	TGTAGTCATCAGACTATCTAAAGTCAACATGAAGG	;<<<;<;<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:24	NM:i:0	UQ:i:0	H0:i:2	H1:i:6
+EAS56_57:6:4:223:776	83	chr2	387	93	35M	=	203	-219	TGTAGTCATCAGACTATCTAAAGTCAACATGAAGG	<;9<;<0<<;<<<;<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:19	NM:i:0	UQ:i:0	H0:i:2	H1:i:6
+EAS114_28:3:32:492:907	99	chr2	387	95	36M	=	571	220	TGTAGTCATCAGACTATCTAAAGTCAACATGAAGGA	<<<<<<<<<<<<<<<<<<<;<;;<<<<<<<<<<<<<	MF:i:18	Aq:i:20	NM:i:0	UQ:i:0	H0:i:1	H1:i:5
+EAS114_26:4:110:840:431	163	chr2	388	93	35M	=	567	214	GTAGTCATCAGACTATCTAAAGTCAACATGAAGGA	=====================5:======54=+3+	MF:i:18	Aq:i:21	NM:i:0	UQ:i:0	H0:i:1	H1:i:5
+EAS114_45:6:86:693:234	83	chr2	388	82	35M	=	202	-221	GTAGTCATCAGACTATCTAAAGTCAACATGAAGGA	83997;<;;;;98;;3*6<<;<:8;;;;;<;;<<<	MF:i:18	Aq:i:18	NM:i:0	UQ:i:0	H0:i:3	H1:i:13
+EAS139_11:8:96:1314:1448	83	chr2	388	93	35M	=	213	-210	GTAGTCATCAGACTATCTAAAGTCAACATGAAGGA	<<<<7<<:<<<<<<<<:<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:18	NM:i:0	UQ:i:0	H0:i:3	H1:i:8
+EAS114_30:6:41:461:436	83	chr2	389	74	35M	=	200	-224	TAGTCATCAGACTATCTAAAGTCAACATGAAGGAA	;<986<;6<<<<<<<;<<<<<<<<<;<<<<<<<<<	MF:i:18	Aq:i:0	NM:i:0	UQ:i:0	H0:i:3	H1:i:13
+EAS221_3:8:55:932:613	163	chr2	389	77	35M	=	568	214	TAGTCATCAGACTATCTAAAGTCAACATGAAGGAA	<<<<<<<<<<<<<<<<<<<<<8<<<<<<<<<<<<<	MF:i:18	Aq:i:0	NM:i:0	UQ:i:0	H0:i:3	H1:i:10
+EAS1_97:5:219:174:684	163	chr2	390	71	35M	=	560	205	AGTCATCAGACTATCTAAAGTCAACATGAAGGAAA	<<<<<<<<<<<8<8<<<7<<;<<<<<2<;&;;;;9	MF:i:18	Aq:i:0	NM:i:0	UQ:i:0	H0:i:2	H1:i:14
+EAS56_57:5:24:284:360	163	chr2	390	76	35M	=	567	212	AGTCATCAGACTATCTAAAGTCAACATGAAGGAAA	<<<<<<<<<<<<<<<<<;<<<<<<<;<9;<;99;;	MF:i:18	Aq:i:0	NM:i:0	UQ:i:0	H0:i:2	H1:i:14
+EAS114_26:1:113:367:659	83	chr2	390	72	35M	=	222	-203	AGTCATCAGACTATCTAAAGTCAACATGAAGGAAA	<<5<0&9;<3<<<<<9<<<<4<;<9<9<<<<7<3<	MF:i:18	Aq:i:0	NM:i:0	UQ:i:0	H0:i:3	H1:i:17
+EAS114_32:5:109:199:592	163	chr2	390	72	35M	=	576	221	AGTCATCAGACTATCTAAAGTCAACATGAAGGAAA	<<<<<<<<<<<;:<;;<<:;6<<;:;:<<+;;;<;	MF:i:18	Aq:i:0	NM:i:0	UQ:i:0	H0:i:2	H1:i:14
+EAS114_45:4:88:55:1187	147	chr2	391	66	35M	=	220	-206	GTCATCAGACTATCTAAAGTCAACATGAAGGAAAA	7769,7;;;;;;;;;;;;;;9;;;;;;;;;;;;;;	MF:i:18	Aq:i:0	NM:i:0	UQ:i:0	H0:i:2	H1:i:7
+EAS56_59:2:60:677:921	147	chr2	393	96	35M	=	250	-178	CATCAGACTATCTAAAGTCAACATGAAGGAAAAAA	========9==;======8==>=============	MF:i:18	Aq:i:22	NM:i:0	UQ:i:0	H0:i:4	H1:i:13
+EAS114_39:3:88:84:1558	147	chr2	394	95	35M	=	203	-226	ATCAGACTATCTAAAGTCAACATGAAGGAAAAAAA	;;<<;<<;<<5<<<<<<;<<:<<<;<<<<<<;<<<	MF:i:18	Aq:i:22	NM:i:0	UQ:i:0	H0:i:2	H1:i:3
+EAS56_59:2:201:768:529	83	chr2	396	99	35M	=	225	-206	CAGACTATCTAAAGTCAACATGAAGGAAAAAAATT	3<:<9<<;<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:54	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_591:2:13:100:876	83	chr2	397	73	36M	=	223	-210	AGAATATATAAAGTCAACATGAAGGAAAAAAATTCT	;9<$<<<$<<<<<<<<75<<<<<<<9<9<<<<<<<<	MF:i:18	Aq:i:30	NM:i:2	UQ:i:6	H0:i:1	H1:i:1
+EAS139_11:4:26:137:1382	99	chr2	397	99	35M	=	579	217	AGACTATCTAAAGTCAACATGAAGGAAAAAAATTC	<<<<<<7<<<77<<<<<<</<<+<<<<<<7<+<<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:2
+EAS54_67:3:197:261:624	99	chr2	398	99	35M	=	587	224	GACTATCTAAAGTCAACATGAAGGAAAAAAATTCT	<<<<<<<<<<<;<<<<<<<;<<;<<<<<<;<<<9<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:1
+EAS218_4:3:41:1281:1785	147	chr2	399	99	35M	=	237	-197	ACTATCTAAAGTCAACATGAAGGAAAAAAATTCTA	<6<<<6<<<<<<:<<6<:<<<<<<<<<<<<6<<<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:3
+B7_610:5:51:904:391	83	chr2	401	97	35M	=	212	-224	TATCTAAAGTCAACATGAAGGAAAAAAATTCTAAA	;<96<<<<<<7<<7<<<<<<<<<<<<<<;<<<<<<	MF:i:18	Aq:i:24	NM:i:0	UQ:i:0	H0:i:1	H1:i:2
+EAS56_63:7:137:139:248	163	chr2	401	97	35M	=	569	203	TATCTAAAGTCAACATGAAGGAAAAAAATTCTAAA	<<<<<<<<<9<<<<<<<<<<;<<<<<<<;;<;<;<	MF:i:18	Aq:i:22	NM:i:0	UQ:i:0	H0:i:3	H1:i:2
+B7_610:7:15:696:693	163	chr2	403	34	35M	=	570	202	TCTAAAGTCAACATGAAGGAAAAAAATTCTAAAAT	2:+:7<<3<<<<<6+36<<<<<<<6<<6&<<;<.7	MF:i:18	Aq:i:10	NM:i:0	UQ:i:0	H0:i:2	H1:i:1
+EAS114_45:2:41:199:388	147	chr2	403	99	35M	=	243	-195	TCTAAAGTCAACATGAAGGAAAAAAATTCTAAAAT	84898;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;	MF:i:18	Aq:i:47	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_108:4:163:611:211	83	chr2	405	99	35M	=	234	-206	TAAAGTCAACATGAAGGAAAAAAATTCTAAAATCA	<<<<9<<<<:<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:48	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS192_3:1:114:19:769	163	chr2	405	90	35M	=	572	202	TAAAGTCAACATGAAGGAAAAAAATTCTAAAATCA	<<<<<*2;6;<<<4.;;<&;;<.<40)<);5-/7;	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:2
+EAS51_64:7:92:493:891	147	chr2	408	99	35M	=	240	-203	AGTCAACATGAAGGAAAAAAATTCTAAAATCAGCA	<383<<:<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:49	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS220_1:8:5:996:2000	163	chr2	408	99	35M	=	575	202	AGTCAACATGAAGGAAAAAAATTCTAAAATCAGCA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<:	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:1
+EAS1_93:1:179:629:513	83	chr2	409	99	35M	=	220	-224	GTCAACATGAAGGAAAAAAATTCTAAAATCAGCAA	<;,<<7<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:49	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS218_4:1:84:1505:1037	99	chr2	409	99	35M	=	586	212	GTCAACATGAAGGAAAAAAATTCTAAAATCAGCAA	<<<<<<<<<<<<<<<<<:<<<<<<<<<<<<<<::)	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:1
+EAS221_1:6:96:491:1891	83	chr2	409	99	35M	=	253	-191	GTCAACATGAAGGAAAAAAATTCTAAAATCAGCAA	:;5<<7<;:<<;<<<<<<<<<<;<<<<<<<<<<<<	MF:i:18	Aq:i:46	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_593:7:307:481:625	147	chr2	410	99	36M	=	245	-201	TCAACATGAAGGAAAAAAATTCTAAAATCAGCAAGA	;4<<4<;;<<;;<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:2	H1:i:0
+B7_610:5:120:596:847	83	chr2	410	83	35M	=	211	-234	TCAACATGAAGGAAAAAAATTCTAAAATCAGCAAG	;/<<:<;<<<<<<<<<<<<<;;<<<<<;<<<<<<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:1
+EAS114_45:3:3:864:1888	99	chr2	411	99	35M	=	579	203	CAACATGAAGGAAAAAAATTCTAAAATCAGCAAGA	;<<;;<<;;;<;;<<;<;<<;<<;8<<:<;79799	MF:i:18	Aq:i:43	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS218_4:1:34:1614:558	99	chr2	411	99	35M	=	569	193	CAACATGAAGGAAAAAAATTCTAAAATCAGCAAGA	<<<<<<<<<<<7<<<<<8<<<<<<2<<<<<<<<<<	MF:i:18	Aq:i:37	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_63:5:117:570:971	83	chr2	413	99	35M	=	223	-225	ACATGAAGGAAAAAAATTCTAAAATCAGCAAGAGA	<,<9<<<<<<<<<<<<<<9<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:2	H1:i:1
+EAS112_34:8:45:800:733	163	chr2	413	99	35M	=	607	229	ACATGAAGGAAAAAAATTCTAAAATCAGCAAGAGA	<<<</<<<<<<<<<<<<<<<2<9<<<<<5*5;599	MF:i:18	Aq:i:34	NM:i:0	UQ:i:0	H0:i:1	H1:i:1
+EAS219_FC30151:7:87:1289:83	163	chr2	413	99	35M	=	585	207	ACATGAAGGAAAAAAATTCTAAAATCAGCAAGAGA	<<<<<<<<<<<<<<<<<<<<<;<<<<<;<<<<<<:	MF:i:18	Aq:i:49	NM:i:0	UQ:i:0	H0:i:1	H1:i:1
+EAS114_39:4:58:271:612	147	chr2	415	99	35M	=	236	-214	ATGAAGGAAAAAAATTCTAAAATCAGCAAGAGCAA	;:2=<<;<<<<<<:67:<<:<<<<<<<<<<<<,<<	MF:i:18	Aq:i:30	NM:i:1	UQ:i:11	H0:i:0	H1:i:2
+EAS1_108:1:33:779:821	163	chr2	416	99	35M	=	579	198	TGAAGGAAAAAAATTCTAAAATCAGCAAGAGAAAA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<;<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:3
+EAS112_34:6:75:615:555	147	chr2	416	99	35M	=	255	-196	TGAAGGAAAAAAATTCTAAAATCAGCAAGAGAAAA	;<<<;<<<<<<<<<:;<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:2	H1:i:0
+EAS188_7:6:11:994:584	147	chr2	417	97	35M	=	226	-226	GAAGGAAAAAAATTCTAAAATCAGCAAGAGAAAAG	<<<<;<<<<<<<;<:<<<<<<<<<;<<<<<<<<<<	MF:i:18	Aq:i:24	NM:i:0	UQ:i:0	H0:i:2	H1:i:0
+EAS114_26:7:218:858:445	147	chr2	421	99	35M	=	239	-217	GAAAAAAATTCTAAAATCAGCAAGAGAAAAGCATA	;<<<<<<<8;:<<<<<<;<<:<<<<<<<<<<<<;<	MF:i:18	Aq:i:27	NM:i:0	UQ:i:0	H0:i:1	H1:i:1
+EAS54_81:2:317:72:221	83	chr2	422	99	35M	=	270	-187	AAAAAAATTCTAAAATCAGCAAGAGAAAAGCATAC	=========:======;==;===============	MF:i:18	Aq:i:53	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS220_1:4:70:766:2016	163	chr2	422	99	35M	=	607	220	AAAAAAATTCTAAAATCAGCAAGAGAAAAGCATAC	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:2	H1:i:0
+EAS56_53:4:45:707:147	83	chr2	424	99	35M	=	216	-243	AAAAATTCTAAAATCAGCAAGAGAAAAGCATACAG	<<<<<<;3<<<<<4;<<;<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:51	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS219_1:7:16:1343:1621	147	chr2	426	99	35M	=	248	-213	AAATTCTAAAATCAGCAAGAGAAAAGCATACAGTC	;<<9;7=====;;==<==================<	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_595:5:184:912:258	99	chr2	428	99	35M	=	582	189	ATTCTAAAATCAGCAAGAGAAAAGCATACAGTCAT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_62:5:119:38:945	147	chr2	428	99	35M	=	221	-242	ATTCTAAAATCAGCAAGAGAAAAGCATACAGTCAT	=;;8=====:========<================	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_108:6:95:235:746	163	chr2	430	99	35M	=	598	203	TCTAAAATCAGCAAGAGAAAAGCATACAGACATCT	<<<<;<<<<<<<<79<<<<<<<<<<<<<<*;;;<9	MF:i:18	Aq:i:72	NM:i:1	UQ:i:9	H0:i:1	H1:i:0
+EAS1_99:2:188:782:483	83	chr2	431	99	35M	=	277	-189	CTAAAATCAGCAAGAGAAAAGCATACAGTCATCTA	7<<<<<<4<;;<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_30:3:39:348:594	163	chr2	431	99	35M	=	600	204	CTAAAATCAGCAAGAGAAAAGCATACAGTCATCTA	<<;<<<<<<<<<;<;;<<<<<<<<<<;<<<:<:<:	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_95:4:176:971:874	83	chr2	432	76	9M1D26M	=	273	-195	TAAAATCAGAAGAGAAAAGCATACAGTCATCTATA	<<<<<:<<<<<<<;<<<<<<<<<<<<<<<<<<<<<	MF:i:130	Aq:i:76	NM:i:0	UQ:i:0	H0:i:0	H1:i:0
+EAS114_30:3:14:697:541	147	chr2	432	99	35M	=	259	-208	TAAAAGCAGCAAGAGAAAAGCATACAGTCATCTAT	8<<<<&6<;8<<<<<<<<<<<<;<<<<;<<<<<<8	MF:i:18	Aq:i:71	NM:i:1	UQ:i:5	H0:i:1	H1:i:0
+B7_610:7:177:469:800	147	chr2	433	99	35M	=	259	-209	AAAATCAGCAAGAGAAAAGCATACAGTCATCTATA	=<<<;;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_108:1:131:518:588	163	chr2	433	99	35M	=	607	209	AAAATCAGCAAGAGAAAAGCATACAGTCATCTATA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<<1<<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS192_3:8:6:237:885	147	chr2	433	99	35M	=	269	-199	AAAATCAGCAAGAGAAAAGCATACAGTCATCTATA	<<<<1:<;:<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_53:3:134:126:465	147	chr2	434	99	35M	=	245	-224	AAATCAGCAAGAGAAAAGCATACAGTCATCTATAA	<<;:&<3)<<7<:<<<<.:<<<<<8<<<<<<<<<<	MF:i:18	Aq:i:56	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_59:2:104:402:732	163	chr2	434	99	35M	=	610	211	AAATCAGCAAGAGAAAAGCATACAGTCATCTATAA	=========================7=;===;=:=	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS218_4:3:65:85:1547	83	chr2	434	99	35M	=	257	-212	AAATCAGCAAGAGAAAAGCATACAGTCATCTATAA	<<<<<<;:<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_71:2:85:686:696	163	chr2	435	99	35M	=	594	193	AATCAGCAAGAGAAAAGCATACAGTCATCTATAAA	==================<=====:==<=<;=:==	MF:i:18	Aq:i:47	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_28:1:144:242:602	163	chr2	436	99	36M	=	611	211	ATCAGCAAGAGAAAAGCATACAGTCATCTATAAAGG	========================;=====<;;<<;	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_108:2:204:737:61	83	chr2	437	99	35M	=	247	-225	TCAGCAAGAGAAAAGCATACAGTCATCTATAAAGG	(7=72=;==2=====<===<<==============	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_81:7:124:253:889	163	chr2	437	99	35M	=	598	196	TCAGCAAGAGAAAAGCATACAGTCATCTATAAAGG	<<<<<<6<<:<<<<<<<<<<<<<;;<<;<<<<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_30:7:310:155:312	163	chr2	438	99	35M	=	606	203	CAGCAAGAGAAAAGCATACAGTCATCTATAAAGGA	;<<<;<<<8<<<<<<<<<<<<;<<<<<8<<<<8<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS192_3:7:78:692:671	99	chr2	438	99	35M	=	610	207	CAGCAAGAGAAAAGCATACAGTCATCTATAAAGGA	<<<<<<<<<<<<<;<<<<<<<:<<:<<<:8<<0;;	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_71:7:130:260:553	147	chr2	439	99	35M	=	250	-224	AGCAAGAGAAAAGCATACAGTCATCTATAAAGGAA	<*;<<7<);<<;9;<5<*<9<;<<;;<7<<<<<1<	MF:i:18	Aq:i:42	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_11:7:60:163:1612	163	chr2	439	99	35M	=	617	213	AGCAAGAGAAAAGCATACAGTCATCTATAAAGGAA	<<<<<<<<<21<<<<<<<<<3<--<+<<<+<<63<	MF:i:18	Aq:i:59	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_597:6:106:595:322	83	chr2	440	99	35M	=	274	-201	GCAAGAGAAAAGCATACAGTCATCTATAAAGGAAA	;+<<<<<<<<<<<<<<<<<<;<<7<<<<<<<<<<<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_65:5:211:84:84	147	chr2	440	99	35M	=	268	-207	GCAAGAGAAAAGCATACAGTCATCTATAAAGGAAA	6:<<:<<<<<<9<<<<<<<<<<<;<<<;;;<;<3;	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_105:2:280:662:939	147	chr2	442	99	35M	=	294	-183	AAGAGAAAAGCATACAGTCATCTATAAAGGAAATC	<<;<;<<<<<:<<<;<<<;<<;<<<<<<<<<<<;<	MF:i:18	Aq:i:48	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_595:6:52:751:360	83	chr2	443	99	35M	=	263	-215	AGAGAAAAGCATACAGTCATCTATAAAGGAAATCC	<-<9<<<<<6<<<8<<;;<<9<<<<<<<<<<<<<<	MF:i:18	Aq:i:45	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_103:2:234:167:381	163	chr2	443	99	35M	=	625	217	AGAGAAAAGCATACAGTCATCTATAAAGGAAATCC	<<<<<<<<<<<<<<<<<<<<<<<<<;<<<;;7<;;	MF:i:18	Aq:i:49	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:6:37:156:134	83	chr2	443	99	35M	=	261	-217	AGAGAAAAGCATACAGTCATCTATAAAGGAAATCC	99998<<<<:<<<<<<<;<<><<<<<<<<<<<<<<	MF:i:18	Aq:i:49	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_59:1:93:490:901	83	chr2	445	99	35M	=	280	-200	AGAAAAGCATACAGTCATCTATAAAGGAAATCCCA	<<<<<<<;<<<;<<<;<<;<<;<<<<<<<<<<<<<	MF:i:18	Aq:i:53	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS112_34:7:96:489:453	99	chr2	445	99	35M	=	625	215	AGAAAAGCATACAGTCATCTATAAAGGAAATCCCA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;;;;:	MF:i:18	Aq:i:54	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_26:6:46:13:880	147	chr2	445	99	35M	=	290	-190	AGAAAAGCATACAGTCATCTATAAAGGAAATCCCA	=&====8==========0=================	MF:i:18	Aq:i:43	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_28:2:167:905:852	163	chr2	445	99	36M	=	647	238	AGAAAAGCATACAGTCATCTATAAAGAAAATCCCAT	<<<7<<<<<<<<<<<<<<:<:<<:::&.<:<66:3<	MF:i:18	Aq:i:43	NM:i:1	UQ:i:5	H0:i:0	H1:i:1
+EAS219_FC30151:3:13:674:1717	163	chr2	445	99	35M	=	623	213	AGAAAAGCATGCAGTCATCTATAAAGGAAATCCCA	<<<<<<<<<<%<<<<<<<<<<<<<<<<<<<;:;;;	MF:i:18	Aq:i:45	NM:i:1	UQ:i:4	H0:i:0	H1:i:1
+EAS51_62:7:196:511:896	83	chr2	446	99	35M	=	283	-198	GAAAAGCATACAGTCATCTATAAAGGAAATCCCAT	8<<<<<;<<<:<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:52	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_53:1:154:118:488	163	chr2	447	99	35M	=	624	212	AAAAGCATACAGTCATCTATAAAGGAAATCCCATC	<<<<<<<<<<<<<<<<<<<<<<:7<<<<7<:;;::	MF:i:18	Aq:i:54	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_57:2:44:153:969	83	chr2	447	95	35M	=	245	-237	AAAAGCATACAGTCATCTATAAAGGAAATCCCATC	<<5<:7<72<51<7<*79<<<<<5<<<<<<<<<2<	MF:i:18	Aq:i:36	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_28:4:215:246:640	99	chr2	447	99	36M	=	624	213	AAAAGCATACAGTCATCTATAAAGGAAATCCCATCA	<<<<<<<<<<9<;<<<<<<<<<<9;<<<<<<3;<;3	MF:i:18	Aq:i:54	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS219_1:7:94:1655:1921	147	chr2	447	85	35M	=	258	-224	AAAAGCATACAGTCATCTATAAAGGAAATCCCATC	<<<<;:===<==;<==<;================;	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_1:6:60:1037:1146	147	chr2	447	99	35M	=	250	-232	AAAAGCATACAGTCATCTATAAAGGAAATCCCATC	<<<<<<<<<;<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:53	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_65:1:23:536:229	99	chr2	448	99	35M	=	614	201	AAAGCATACAGTCATCTATAAAGGAAATCCCATCA	<<<<<<<<<<<<<<<<<:<8<:<<;<<<<<<7<<<	MF:i:18	Aq:i:54	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS112_34:6:130:865:838	163	chr2	448	99	35M	=	649	236	AAAGCATACAGTCATCTATAAAGGAAATCCCATCA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;;:<;3	MF:i:18	Aq:i:54	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_59:2:239:1001:406	99	chr2	450	99	35M	=	634	219	AGCATACAGTCATCTATAAAGGAAATCCCATCAGA	<<<<<<7<<<<<<<<8<;<<<7<<<<36<<3<:33	MF:i:18	Aq:i:49	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_97:3:147:423:584	147	chr2	451	99	35M	=	277	-209	GCATACAGTCATCTATAAAGGAAATCCCATCAGAA	27<;<3<<<+<<;<<<;;-4<<<<<;<<<<<<<<<	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_99:1:187:715:521	83	chr2	451	99	35M	=	291	-195	GCATACAGTCATCTATAAAGGAAATCCCATCAGAA	<7<:<9<<<<<<<<<;<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_67:3:172:196:746	99	chr2	451	99	35M	=	620	204	GCATACAGTCATCTATAAAGGAAATCCCATCAGAA	<<<<<<<<9<<<<9<<<<<<<<<;<<<<6<<<<;<	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_71:3:267:821:860	83	chr2	451	99	34M	=	296	-189	GCATACAGTCATCTATAAAGGAAATCCCATCAGA	$&<<<.<:;6<<;<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:3
+EAS56_61:7:7:682:201	83	chr2	452	99	35M	=	288	-199	CATACAGTCATCTATAAAGGAAATCCCATCAGAAT	0:8;5<8<1:78<<<<<<<<<<<<:8<<2<<<<:<	MF:i:18	Aq:i:66	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_589:3:82:13:897	163	chr2	453	99	35M	=	606	188	ATACAGTCATCTATAAAGGAAATCCCAGCAGAATA	<<<<;<<<<<<;<;<;5<51;<1<<<<%<<<<,58	MF:i:18	Aq:i:41	NM:i:1	UQ:i:4	H0:i:0	H1:i:1
+EAS56_53:6:180:695:621	99	chr2	453	99	35M	=	637	219	ATACAGTCATCTATAAAGGAAATCCCATCAGAATA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;::<<<	MF:i:18	Aq:i:68	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_57:2:158:909:321	83	chr2	453	99	35M	=	271	-217	ATACAGTCATCTATAAAGGAAATCCCATCAGAATA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_26:2:237:497:165	99	chr2	454	99	35M	=	619	200	TACAGTCATCTATAAAGGAAATCCCATCAGAATAA	8===<8===========37=<===7=;7=8=====	MF:i:18	Aq:i:68	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_99:2:152:355:962	83	chr2	456	99	35M	=	269	-222	CAGTCATCTATAAAGGAAATCCCATCAGAATAACA	&<.9.<;+;<;<<<<<<<<<<::<<:<<<<<<<<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:2
+EAS192_3:4:255:549:422	83	chr2	456	99	35M	=	295	-196	AAGTCATCTATAAAGGAAATCCCATCAGAATAACA	&<;;+<;4;<<<<<<<<<<<;<;<<;<<<<<<<<<	MF:i:18	Aq:i:30	NM:i:1	UQ:i:5	H0:i:1	H1:i:2
+EAS220_1:4:100:20:1199	163	chr2	456	99	35M	=	614	193	CAGTCATCTATAAAGGAAATCCCATCAGAATAACA	7<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<4<<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_67:5:71:408:741	163	chr2	457	99	35M	=	637	215	AGTCATCTATAAAGGAAATCCCATCAGAATAACAA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_66:5:285:395:450	147	chr2	458	99	35M	=	269	-224	GTCATCTATAAAGGAAATCCCATCAGAATAACAAT	8)3<8+;<)<<<<<<<<97:7<<<<<<<<<<<<<<	MF:i:18	Aq:i:65	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_73:3:4:854:140	99	chr2	458	72	35M	=	638	215	GTCATCTATAAAGGAAATCCCATCAGAATAACAAT	<<<6<<<:<6<<<:36:<<<<3<<8:.6<38::4<	MF:i:18	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_59:6:227:657:95	147	chr2	458	99	35M	=	280	-213	GTCATCTATAAAGGAAATCCCATCAGAATAACAAT	;3;<);<<<<<<<<<<<<18<<<<<<<<<<<<<<<	MF:i:18	Aq:i:59	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_28:7:57:324:546	83	chr2	458	99	36M	=	281	-213	GTCATCTATAAAGGAAATCCCATCAGAATAACAATG	;;5<;,<<<;;<<<<<<<97<<<<<<<<<<9<<<<<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_19:4:26:274:1078	83	chr2	458	99	40M	=	282	-216	GTCATCTATAAAGGAAATCCCATCAGAATAACAATGGGCT	9:*:64<<;<<<<<<<<<;8;<<:<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS188_7:6:107:636:642	163	chr2	458	99	35M	=	630	207	GTCATCTATAAAGGAAATCCCATCAGAATAACAAT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_81:7:226:869:36	147	chr2	461	99	35M	=	273	-223	ATATATAAAGGAAATCCCATCAGAATAACAATGGG	<0/)</<<<:<<<<<)<<7<<<<<+55<<1<<<:<	MF:i:18	Aq:i:59	NM:i:1	UQ:i:14	H0:i:1	H1:i:0
+EAS192_3:4:312:915:751	99	chr2	461	99	35M	=	621	195	ATCTATAAAGGAAATCCCATCAGAATAACAATGGG	<2<<<<<<<8;<<<<<<<<:<<<<8<<<<<84,4:	MF:i:18	Aq:i:41	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS188_4:7:96:899:106	99	chr2	462	99	35M	=	636	209	TCTATAAAGGAAATCCCATCAGAATAACAATGGGC	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_93:5:62:969:12	147	chr2	464	99	35M	=	303	-196	TATAAAGGAAATCCCATCAGAATAACAATGGGCTT	<<;<;<::<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_65:6:67:56:806	99	chr2	464	99	35M	=	637	208	TATAAAGGAAATCCCATCAGAATAACAATGGGCTT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<;;<<:7:	MF:i:18	Aq:i:70	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_65:5:37:611:267	99	chr2	464	99	35M	=	610	181	TATAAAGGAAATCCCATAAGAATAACAATGGGCTT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:47	NM:i:1	UQ:i:27	H0:i:0	H1:i:1
+EAS1_93:7:319:280:57	147	chr2	467	99	35M	=	306	-196	AAAGGAAATCCCATCAGAATAACAATGGGCTTCTC	<<<<<<<-<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_105:8:96:720:940	163	chr2	467	99	35M	=	654	222	AAAGGAAATCCCATCAGAATAACAATGGGCTTCTC	<<<<<<;<<<<<<<<<<;9<<8<<6<;:;<;;.;;	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_53:2:59:286:290	99	chr2	467	99	35M	=	628	196	AAAGGAAATCCCATCAGAATAACAATGGGCTTCTC	<<<<<<<<;<<<;<<<<<<<<<<<<<;;;<<;7;<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_57:2:236:841:20	163	chr2	467	99	35M	=	652	220	AAAGGAAATCCCATCAGAATAACAATGGGCTTCTC	<<<<<<<<<<<<<<<<<7<<<<:<<9<<<<;<:<9	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_30:6:49:656:507	99	chr2	468	99	35M	=	637	204	AAGGAAATCCCATCAGAATAACAATGGGCTTCTCA	<<<<<<<<<<<<<<<<<<<;<<<<<<<<<<<<<;9	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_3:4:78:1314:1275	147	chr2	469	99	35M	=	277	-227	AGGAAATCCCATCAGAATAACAATGGGCTTCTCAG	<<<<<<<<6:<<<<<<<<<<<<<<<<<<<<<<<1<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_99:6:181:392:500	147	chr2	470	99	35M	=	299	-206	GGAAATCCCATCAGAATAACAATGGGCTTCTCAGC	/5<<;(88<<<;<;<<6<<<<<7<<<<<<<7<<<<	MF:i:18	Aq:i:63	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_62:2:133:8:379	163	chr2	470	99	35M	=	653	218	GGAAATCCCATCAGAATAACAATGGGCTTCTCAGC	<<<<<<<<<<<<<<<<<<<<<<<<8;<<8<<<:6<	MF:i:18	Aq:i:70	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_59:5:198:929:684	163	chr2	471	99	35M	=	624	188	GAAATCCCATCAGAATAACAATGGGCTTCTCAGCA	<7<<<<;<<<<<<<<<<<<;<<<<<:<<<<::<:7	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_30:3:181:582:435	99	chr2	471	99	35M	=	629	193	GAAATCCCATCAGAATAACAATGGGCTTCTCAGCA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<;::	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_93:1:214:784:690	99	chr2	472	99	35M	=	657	220	AAATCCCATCAGAATAACAATGGGCTTCTCAGCGG	<<<<<<<<<<<<<<<<<<<<<:<<<<<<<<<4<44	MF:i:18	Aq:i:30	NM:i:1	UQ:i:19	H0:i:1	H1:i:0
+EAS114_39:3:11:1238:1728	83	chr2	475	99	35M	=	310	-200	TCCCATCAGAATAACAATGGGCTTCTCAGCGGAAA	:677<;<<<<<<<<<<<:<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:45	NM:i:1	UQ:i:27	H0:i:0	H1:i:1
+EAS112_34:4:12:273:89	163	chr2	477	99	35M	=	631	189	CCATCAGAATAACAATGGGCTTCTCAGCGGAAACC	==========<====:=========+===4414;;	MF:i:18	Aq:i:71	NM:i:1	UQ:i:28	H0:i:1	H1:i:0
+EAS56_63:2:119:161:322	147	chr2	479	99	35M	=	297	-217	ATCAGAATAACAATGGGCTTCTCAGCAGAAACCTT	<83<;<<;<;<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:1
+EAS114_30:2:111:142:21	83	chr2	479	99	35M	=	304	-210	ATCAGAATAACAATGGGCTTCACAGCGGAAACCTT	;88<:<;;<6<;;<<<:<<<<;<<<<<<<<;<<<<	MF:i:18	Aq:i:28	NM:i:2	UQ:i:53	H0:i:0	H1:i:0
+EAS1_99:1:34:649:318	83	chr2	481	65	35M	=	328	-188	AAGAATAACAATGGGCTTCACAGCGGAACCCTTAC	)<7<<3<<<<<<+<1<;<8&<<<<<<<<<<<<<<<	MF:i:130	Aq:i:65	NM:i:3	UQ:i:59	H0:i:0	H1:i:0
+EAS114_30:6:214:565:337	147	chr2	481	99	35M	=	326	-190	CAGAATAACAATGGGCTTCTCAGCAGAAACCTTAC	;;<;<1<9<<<8<<<<<;<<<<<<8<<<;<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_61:6:226:370:91	147	chr2	482	99	35M	=	335	-182	AGAATAACAATGGGCTTCTCAGCGGAAACCTTACA	<':<6<;<<<;2<;<-7;;;<<<<<<<;;;<<7;<	MF:i:18	Aq:i:43	NM:i:1	UQ:i:27	H0:i:0	H1:i:1
+EAS139_11:6:13:682:680	99	chr2	482	99	35M	=	685	238	AGAATAACAATGGGCTTCTCAGCGGAAACCTTACA	<<<<<<<<<<<<<:<<<<<<<<<<;<;<<<<<<<<	MF:i:18	Aq:i:47	NM:i:1	UQ:i:27	H0:i:0	H1:i:1
+B7_593:2:273:348:37	163	chr2	483	99	36M	=	688	241	GAATAACAATGGGCTTCTCAGCAGAAACCTTACACG	<<<<<<<9<49<<<;<<<<*<<19<15;<</5<;.5	MF:i:18	Aq:i:41	NM:i:1	UQ:i:13	H0:i:1	H1:i:0
+EAS139_11:8:76:205:587	83	chr2	483	99	35M	=	306	-212	GAATAACAATGGGCTTCTCAGCGGAAACCTTACGA	8<<5<<<<<<<<<<<<<<<<<<<<<<<<<7<<</<	MF:i:18	Aq:i:28	NM:i:2	UQ:i:41	H0:i:0	H1:i:0
+B7_591:2:27:280:592	147	chr2	484	99	36M	=	310	-210	AATAACAATGGGCTTCTCAGCGGAAACCTTACAAGC	<<<<<<<<<<<8<<<<<<<<7<<<<<<<<<<<<<<<	MF:i:18	Aq:i:47	NM:i:1	UQ:i:27	H0:i:0	H1:i:1
+EAS1_99:7:171:196:287	163	chr2	485	99	35M	=	658	208	ATAACAATGGGCTTCTCAGCAGAAACCTTACAAGC	<<<<<<<<<<<<<<<<<<<<<;6<<<<<<2:8<0:	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_65:2:224:579:433	163	chr2	485	99	35M	=	662	212	ATAACAATGGGCTTCTCAGCAGAAACCTTACAAGC	<<<<<<<<<<<<<<<<<:<<<<<<<<<<<8<+8;:	MF:i:18	Aq:i:31	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS219_1:1:22:490:2011	147	chr2	485	99	35M	=	307	-213	ATAACAATGGGCTTCTCAGCGGAAACCTTACAAGC	<7<<<<<<<<<<<<;<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:47	NM:i:1	UQ:i:27	H0:i:0	H1:i:1
+EAS56_65:6:46:173:214	83	chr2	487	99	35M	=	308	-214	AACAATGGGCTTCTCAGCAGAAACCTTACAAGCCA	<<2<<<<<<<<<<<5<<5<7<<<<<<<<<<<<<<<	MF:i:18	Aq:i:29	NM:i:0	UQ:i:0	H0:i:4	H1:i:6
+EAS1_103:4:164:79:134	99	chr2	488	99	35M	=	656	203	ACAATGGGCTTCTCAGCGGAAACCTTACAAGCCAG	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<7<	MF:i:18	Aq:i:47	NM:i:1	UQ:i:27	H0:i:0	H1:i:1
+EAS114_32:2:283:577:398	147	chr2	488	99	35M	=	308	-215	ACAATGGGCTTCTCAGCGGAAACCTTACAAGCCAG	;8;;&<<<;<;67<;<;<<<<<<<<;<<<<<<<<<	MF:i:18	Aq:i:29	NM:i:1	UQ:i:27	H0:i:0	H1:i:2
+EAS54_67:5:149:639:910	163	chr2	489	99	35M	=	669	215	CAATGGGCTTCTCAGCAGAAACCTTACAAGCCAGA	<<<<<<<<<<<<<<<<<<<<<<<<7<;;<<;<<;<	MF:i:18	Aq:i:42	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_28:3:250:628:423	83	chr2	489	99	36M	=	295	-230	CAATGGGCTTCTCAGCGGAAACCTTACAAGCCAGAA	+<<4;;9;;7.;7<;7<;<<<;;<<<<<<<<<<<<<	MF:i:18	Aq:i:27	NM:i:1	UQ:i:27	H0:i:0	H1:i:1
+EAS1_108:1:242:419:512	163	chr2	490	94	35M	=	672	217	AATGGGCTTCTCAGCAGAAACCTTACAAGCCAGAA	<<8<<<<<<<<<<<<<<<<<<<<<<<<;<8<(<30	MF:i:18	Aq:i:24	NM:i:0	UQ:i:0	H0:i:1	H1:i:2
+EAS114_45:1:95:1530:28	83	chr2	490	74	35M	=	332	-193	AATGGGCTTCTCAGCAGAAACCTTACAAGCCAGAA	77741(9;;994;5;;4;;1;;;;;1;<;<<<<;<	MF:i:18	Aq:i:9	NM:i:0	UQ:i:0	H0:i:42	H1:i:45
+EAS192_3:6:326:887:180	163	chr2	492	73	35M	=	672	215	TGGGCTTCTCAGCAGAAACCTTACAAGCCAGAAGC	;<<<<<;<<<<<<<<<8<<<<<<<<<<<<0<;;<+	MF:i:18	Aq:i:0	NM:i:1	UQ:i:25	H0:i:3	H1:i:7
+EAS1_99:1:86:871:319	99	chr2	494	71	35M	=	651	192	GGCTTCTCAGCGGAAACCTTACAAGCCAGAAGAGA	<<<<<:<<<:<:<<<<<<<<<<<<8<<:<1;<::)	MF:i:18	Aq:i:0	NM:i:1	UQ:i:25	H0:i:0	H1:i:4
+EAS56_57:1:189:130:136	147	chr2	494	79	35M	=	314	-215	GGCTTCTCAGCAGAAACCTTACAAGCCAGAAGAGA	823;23<7<57<7<<<<<;<<;<<<<<<<<<<<<<	MF:i:18	Aq:i:0	NM:i:0	UQ:i:0	H0:i:63	H1:i:85
+EAS51_64:7:140:752:822	99	chr2	495	76	35M	=	667	207	GCTTCTCAGCGGAAACCTTACAAGCCAGAAGAGAT	<<<<<<<<<<<<<<<<<7<<<<<<<<<<<<<;<:;	MF:i:18	Aq:i:0	NM:i:1	UQ:i:27	H0:i:0	H1:i:5
+EAS56_57:5:53:544:889	147	chr2	495	76	35M	=	335	-195	GCTTCTCAGCGGAAACCTTACAAGCCAGAAGAGAT	,<;<<<;<<<<<<<<<:;;<<<<<;;<<<<<<<<<	MF:i:18	Aq:i:0	NM:i:1	UQ:i:27	H0:i:2	H1:i:32
+EAS54_65:4:61:346:384	83	chr2	496	68	35M	=	324	-207	CAACTAAGAAGAAACCTTACAAGCCAGAAGAGATT	7&$+&,<<+;;<;;<<6<<8<<<;<<;<<<<<<<<	MF:i:18	Aq:i:0	NM:i:3	UQ:i:19	H0:i:1	H1:i:53
+EAS54_81:8:177:800:714	83	chr2	497	76	35M	=	324	-208	TTCTCAGCAGAAACCTTACAAGCCAGAAGAGATTG	=;3=+=<:=<========8================	MF:i:18	Aq:i:0	NM:i:0	UQ:i:0	H0:i:29	H1:i:85
+B7_597:6:20:592:496	83	chr2	498	75	35M	=	338	-195	TCTCAGCGGAAACCTTACAAGCCAGAAGAGATTGG	97<7;<;<;<<<<;<9<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:0	NM:i:0	UQ:i:0	H0:i:5	H1:i:48
+B7_591:5:243:557:560	83	chr2	499	75	36M	=	331	-204	CTAAGCAGAAACCTTACAAGCCAGAAGAGATTGGAT	69&<;&<&<<;6.<<<+<<<;;<<<<<<<<;<<<<<	MF:i:18	Aq:i:0	NM:i:1	UQ:i:5	H0:i:1	H1:i:9
+EAS188_7:5:163:982:695	147	chr2	499	77	35M	=	339	-195	CTCAGCAGAAACCTTACAAGCCAGAAGAGATTGGA	<:<<<<<<<<<<<<<<9<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:0	NM:i:0	UQ:i:0	H0:i:7	H1:i:42
+EAS139_19:1:1:1598:843	83	chr2	500	99	40M	=	347	-193	TCAGCGGAAACCTTACAAGCCAGAAGAGATTGGATCTAAT	1)::6::<<;<98<<<<<<9<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:74	NM:i:1	UQ:i:25	H0:i:1	H1:i:0
+EAS139_19:6:78:1029:512	163	chr2	500	99	40M	=	656	196	TCAGCAGAAACCTTACAAGCCAGAAGAGATTGGATCTAAT	<0:;<<<<<<<<<:<<:;<<<;<7<<;<7;;;:6;::672	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS218_1:4:14:1872:1521	83	chr2	500	62	35M	=	339	-196	TCATCAAAAACCTTACAAGCCAGAAGAGATTGGAT	/1<%73&7<1<3577,<<<7/733<<<<<<<<1<<	MF:i:18	Aq:i:2	NM:i:2	UQ:i:9	H0:i:1	H1:i:8
+EAS221_3:6:51:1486:1131	163	chr2	500	77	35M	=	685	220	TCAGCAGAAACCTTACAAGCCAGAAGAGATTGGAT	<<<<<<<<<;<<<<<<<<<1<5<<8<<<'<;<<;1	MF:i:18	Aq:i:3	NM:i:0	UQ:i:0	H0:i:22	H1:i:22
+EAS192_3:6:45:183:25	163	chr2	501	95	35M	=	672	206	CAGCGGAAACCTTACAAGCCAGAAGAGATTGGATC	<<<<<<<<<<<<<<<<<<<<<<<<<<<<86;<;:;	MF:i:18	Aq:i:23	NM:i:1	UQ:i:27	H0:i:0	H1:i:2
+B7_597:4:38:999:463	147	chr2	503	39	35M	=	317	-221	GCGGAAACCTTACAAGCCAGAAGAGATTGGATCTA	.*:&<<0<0!<<+<<<<<<<<<<<<<0<<<<<<<<	MF:i:18	Aq:i:39	NM:i:2	UQ:i:25	H0:i:0	H1:i:1
+EAS114_45:1:30:1882:1210	163	chr2	503	82	35M	=	665	197	GCAGAAACCTTACAAGCCAGAAGAGATTGGATCTA	;;::;;;;:;;;;;:;;;;;;9;;:7;;8:77777	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:2	H1:i:0
+EAS1_108:6:222:579:961	163	chr2	504	99	35M	=	679	210	CAGAAACCTTACAAGCCAGAAGAGATTGGATCTAA	<<<<<<<<<<<<<<<<<<<<<<<<<7<<:7;;;68	MF:i:18	Aq:i:70	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_53:1:92:875:345	163	chr2	504	99	35M	=	690	221	CGGAAACCTTACAAGCCAGAAGAGATTGGATCTAA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:47	NM:i:1	UQ:i:27	H0:i:0	H1:i:1
+EAS56_63:8:62:125:888	83	chr2	504	99	35M	=	347	-192	CGGAAACCTTACAAGCCAGAAGAGATTGGATCTAA	,;3<<<8;;3<,<<<8;<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:69	NM:i:1	UQ:i:26	H0:i:1	H1:i:0
+EAS221_1:2:23:127:880	99	chr2	504	99	35M	=	686	217	CGGAAACCTTACAAGCCAGAAGAGATTGGATCTAA	<<<<<<<<<<<<<<<<<<<;;<<<<<<<<<<<<<<	MF:i:18	Aq:i:47	NM:i:1	UQ:i:27	H0:i:0	H1:i:1
+EAS51_66:8:43:972:506	163	chr2	505	99	35M	=	686	216	AGAAACCTTACAAGCCAGAAGAGATTGGATCTAAT	<;<<<<<<<<<<<<6;<;<<<<<<<<<<:;;<;<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_26:6:183:697:555	83	chr2	505	84	35M	=	341	-199	AGAAATCTTAGAAGCCAGAAGAGATTGGATCTAAT	<<<;&,.;);&96<84<<81<<&<<<9<<8<8<<1	MF:i:18	Aq:i:37	NM:i:2	UQ:i:16	H0:i:0	H1:i:1
+EAS221_3:8:65:463:703	99	chr2	506	99	35M	=	693	222	GAAACCTTACAAGCCAGAAGAGATTGGATCTAATT	<<<<<<<<<<<<<<<<<<<<<<<<<<<:<<<<<<<	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_67:7:101:752:996	163	chr2	508	99	35M	=	687	214	AACCTTACAAGCCAGAAGAGATTGGATCTAATTTT	<<<<<<<<<<<<<<<;<<<<<9<<<<<<;<<;;;;	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_105:6:267:953:459	99	chr2	509	99	35M	=	667	193	ACCTTACAAGCCAGAAGAGATTGGATCTAATTTTT	<<<<<<<<<9<<<<<<<<<<<<<<;<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_3:8:33:1240:846	99	chr2	509	99	35M	=	685	211	ACCTTACAAGCCAGAAGAGATTGGATCTAATTTTT	<<<<<<<<<<<<7<<2<;<<;<<<;<<<:6:<<<:	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS112_32:7:135:401:735	99	chr2	510	99	35M	=	703	228	CCTTACAAGCCAGAAGAGATTGGATCTAATTTTTG	<<<<<<<<<<<<<<<<<<<<<;<<<<<8<<<<<<;	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_59:6:3:186:68	99	chr2	512	99	35M	=	687	210	TTACAAGCCAGAAGAGATTGGATCTAATTTTTGTA	<<<<<<<<<<<<;<<<<<<<<<<<<;;<<<<<&%8	MF:i:18	Aq:i:71	NM:i:1	UQ:i:4	H0:i:1	H1:i:0
+EAS51_78:7:164:727:977	163	chr2	513	99	35M	=	689	211	TACAAGCCAGAAGAGATTGGATCTAATTTTTCGAC	<<<<<<<<<<<<<<<<<<<<<<<<<9<<<<;;79;	MF:i:18	Aq:i:75	NM:i:1	UQ:i:26	H0:i:1	H1:i:0
+B7_589:1:110:543:934	163	chr2	514	99	35M	=	700	221	ACAAGCCAGAAGAGATTGGATCTAATTTTTGGACT	<<<<<<<<<<<<;<<<<<;;<<<;;<<<<<,,;<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_591:4:329:339:408	147	chr2	515	99	36M	=	325	-226	CAATCCAGAAGAGATTGGATCTAATTTTTGGACTTC	7<<<7<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:76	NM:i:1	UQ:i:27	H0:i:1	H1:i:0
+EAS56_59:5:325:544:349	163	chr2	515	99	35M	=	716	236	CAAGCCAGAAGAGATTGGATCTAATTTTTGGACTT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<6;;;<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_105:1:3:903:957	99	chr2	516	99	35M	=	661	180	AAGCCAGAAGAGATTGGATCTAATTTTTGGACTTC	<<<<<<<<<<<<<<<<;;<;<;<<<<<<66<;<<;	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_593:1:85:361:418	147	chr2	517	99	36M	=	353	-200	AGCCAGAAGAGATTGGATCTAATTTTTGGACTTCTT	;;;5<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_63:8:138:186:459	83	chr2	518	97	35M	=	360	-193	GCCAGAAGAGATTGGAGCTAATTTTTGGACTTCTT	+/2/;<:<&7:7</<2&<<<&<<<<<<<<<8<<:3	MF:i:18	Aq:i:37	NM:i:1	UQ:i:5	H0:i:0	H1:i:1
+EAS139_11:4:36:1184:994	83	chr2	518	99	35M	=	358	-195	GCCAGAAGAGATTGGATCTAATTTTTGGACTTCTT	<84<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_593:2:270:430:269	83	chr2	519	99	36M	=	331	-224	CCAGAAGAGATTGGATCTAATTTTTGGACTTCTTAA	28<<;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_62:5:295:882:282	163	chr2	520	99	35M	=	691	206	CAGAAGAGATTGGATCTAATTTTTGGACTTCTTAA	========================<6<======8;	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_57:3:41:739:907	83	chr2	520	99	35M	=	344	-211	CAGAAGAGATTGGATCTAATTTTTGGACTTCTTAA	;<;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_61:5:272:240:950	163	chr2	520	97	35M	=	696	211	CAGCAGAGCTTGGATCTAATTTTTGGACTTCTTCA	6<<&:<<<&<::;&7<<<3<;<<;<:;:<8:<<(<	MF:i:18	Aq:i:25	NM:i:3	UQ:i:17	H0:i:0	H1:i:0
+EAS54_65:7:155:629:357	83	chr2	521	99	35M	=	333	-223	AGAAGAGATTGGATCTAATTTTTGGACTTCTTAAA	<<<<<<<<;<<<<<<<<<<<<6<<<<<<<<<;<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_71:4:14:88:306	147	chr2	521	99	35M	=	341	-215	AGAAGAGATTAGATCTAATTTTTGGACTTCTTAAA	<1;<;<;<4<&<<<:<<<:<<<<;<<<<<<<<<<<	MF:i:18	Aq:i:45	NM:i:1	UQ:i:5	H0:i:0	H1:i:1
+EAS1_108:5:115:193:231	163	chr2	522	99	35M	=	684	197	GAAGAGATTGGATCTAATTTTTGGACTTCTTAAAG	<<<<<<<<<<<<<<<<<<<<<<<7<<<<<<<<6<7	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS219_FC30151:1:88:1454:418	83	chr2	522	99	35M	=	349	-208	GAAGAGATTGGATCTAATTTTTGGACTTCTTAAAG	<<<<<<<<<<6<96<<<1911<<<1<<<<<<<<<1	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_595:5:36:649:554	83	chr2	523	99	35M	=	350	-208	AAGAGATTGGATCTAATTTTTGGACTTCTTAAAGA	<<<<<888;<<<;<<<;<;<8<<<<8<<<<<<<<<	MF:i:18	Aq:i:68	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_59:4:119:651:88	83	chr2	527	99	35M	=	337	-225	GATTGGATCTAATTTTTGGACTTCTTAAAGAAAAA	<<<<<<<<;<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_57:7:57:826:977	163	chr2	528	99	35M	=	693	200	ATTGGATCTAATTTTTGGACTTCTTAAAGAAAAAA	<<<<<<<<<<<<<<<<+<<<<<<<<6<9:6<<<<<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_64:3:285:417:147	99	chr2	529	99	35M	=	712	218	TTGGATCTAATTTTTGGACTTCTTAAAGAAAAAAA	<<<<<<<<<<<<<<<;8<<<<<<<<<;6<:<;<<;	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_105:8:160:130:351	99	chr2	530	99	35M	=	697	202	TGGATCTAATTTTTGGACTTCTTAAAGAAAAAAAA	<<<<<<<<<<<<<<<;<<<<4<<<<<;<<<:<<:<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_26:3:287:665:495	163	chr2	530	99	35M	=	702	207	TGGATCTAATTTTTGGACTTCTTAAAGAAAAAAAA	==========================98====8=8	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_108:6:71:187:824	147	chr2	534	99	35M	=	367	-202	TCTAATTTTTGGACTTCTTAAAGAAAAAAAAACCT	0040;<7<<<<0<7<<<;<7*<<<<<7<<771<<<	MF:i:18	Aq:i:66	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS218_1:8:70:445:1289	99	chr2	535	99	35M	=	702	202	CTAATTTTTGGACTTCTTAAAGAAAAAAAAACCTG	<<<<<<<<<<2<<<<<<<<<<:<<<<<<<;;;;<:	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_61:7:41:745:603	83	chr2	536	99	35M	=	360	-211	TAATTTTTGGACTTCTTAAAGAAAAAAAAACCTGT	;<<;;<;<8<<<<<<<<<<<;<<;<<<<<<<<<;<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_65:6:197:759:975	163	chr2	537	99	35M	=	698	196	AATTTTTGGACTTCTTAAAGAAAAAAAAACCTGTC	<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<<<<;	MF:i:18	Aq:i:78	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_26:6:140:253:322	99	chr2	537	99	35M	=	689	187	AATTTTTGGACTTCTTAAAGAAAAAAAAACCTGTC	<<<<<<<<<<<<<;<<<<<<<<<<<<<<<;;;<<;	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_597:5:58:684:520	147	chr2	538	99	35M	=	367	-206	ATTTTTGGACTTCTTAAAGAAAAAAAAACCTGTCA	<85;;:<<<7<<7<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_11:6:19:306:982	147	chr2	538	99	35M	=	368	-205	ATTTTTGGACTTCTTAAAGAAAAAAAAACCTGTCA	<<<<<<<<<9<<:<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:78	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_57:7:273:562:954	99	chr2	539	99	35M	=	722	218	TTTTTGGACTTCTTAAAGAAAAAAAAACCTGTCAA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<;;:;;;;	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_11:5:78:775:555	99	chr2	539	99	35M	=	691	187	TTTTTGGACTTCTTAAAGAAAAAAAAACCTGTCAA	6:<<<<:<<<<6:<<)::8<6<<:<<)<::63832	MF:i:18	Aq:i:68	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_81:2:49:330:699	163	chr2	540	99	35M	=	722	217	TTTTGGACTTCTTAAAGAAAAAAAAACCTGTCAAA	==;=================;======5;;;==5=	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_28:2:329:437:643	147	chr2	540	99	36M	=	354	-222	TTTTGGACTTCTTAAAGAAAAAAAAACCTGTCAAAC	885<8;;<;3,8<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_57:1:125:884:276	83	chr2	541	99	35M	=	362	-214	TTTGGACTTCTTAAAGAAAAAAAAACCTGTCAAAC	,;;3,<7<;7<<===;============;======	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_593:4:315:201:673	83	chr2	542	45	36M	=	381	-197	TTGGACTTATTAAAGAAAAAAAAACCTGTCAAACAC	;;;;<-;;&;;<<<:<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:0	NM:i:1	UQ:i:5	H0:i:0	H1:i:1
+B7_597:3:10:394:392	147	chr2	542	99	35M	=	376	-201	TTGGACTTCTTAAAGAAAAAAAAACCTGTCAAACA	28-:;0-<0<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:68	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_103:1:228:736:747	83	chr2	542	68	35M	=	381	-196	TTGGACTTCTTAAAGAAAAAAAAACCTGTCAAACA	<07<<&<;+<<<<<<<<<<<<<<<<;<<<<<<<<<	MF:i:18	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_59:4:267:394:437	163	chr2	544	99	35M	=	735	226	GGACTTCTTAAAGAAAAAAAAACCTGTCAAACACG	<<<<<<<<<<;<;<<<<<;;<<<<<;<<:;8<;<8	MF:i:18	Aq:i:66	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_19:5:66:1381:181	83	chr2	544	99	40M	=	362	-222	GGACTTCTTAAAGAAAAAAAAACCTGTCAAACACGAATGT	;;;+;;&<7<<<+<<<<<<<;<;8<<<;<<<<8<<<;<<<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_19:5:74:668:424	99	chr2	545	99	40M	=	707	202	GACTTCTTAAAGAAAAAAAAACCTGTCAAACACGAATGTT	;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;::;;	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_66:4:322:350:374	83	chr2	546	99	35M	=	360	-221	ACTTCTTAAAGAAAAAAAAACCTGTCAAACACGAA	<+;8&84<<<:<<<<<<<<<<;<<<<<<<;<<<<<	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_61:6:307:208:477	163	chr2	546	99	35M	=	710	199	ACTTCTTAAAGAAAAAAAAACCTGTCAAACACGAA	<<<<<<<;<<;<<<<<<<<<<<<<<<<;:<<<88;	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_95:2:228:915:631	83	chr2	547	66	35M	=	381	-201	ATTATTAAAGAAAAAAAAACCTGTCAAACACGAAT	&-))-*===/=========9====4==========	MF:i:18	Aq:i:0	NM:i:2	UQ:i:13	H0:i:1	H1:i:0
+EAS1_93:5:246:177:525	99	chr2	549	98	35M	=	738	224	TCTTAAAGAAAAAAAAACCTGTCAAACACGAATGT	<<<<<<<<<<<<<<<<<<<<<1<<<<<<;;;<8;;	MF:i:18	Aq:i:27	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_589:7:93:634:323	99	chr2	550	99	35M	=	721	206	CTTAAAGAAAAAAAAACCTGTCAAACACGAATGTT	<<<<<<<<<<<<<<<<<<<<7<<<<<<<<<<,<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_61:8:165:441:708	163	chr2	550	99	35M	=	737	222	CTTAAAGAAAAAAAAACCTGTCAAACACGAATGTT	=<===============================99	MF:i:18	Aq:i:54	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_99:5:191:885:623	83	chr2	551	99	35M	=	363	-223	TTAAAGAAAAAAAAACCTGTCAAACACGAATGTTA	66<<<<<<<<<<<<<2<<<<9<<<<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_67:5:127:828:697	147	chr2	552	99	35M	=	346	-241	TAAAGAAAAAAAAACCTGTCAAACACGAATGTTAT	;<<<7<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS188_7:5:115:249:673	163	chr2	552	99	35M	=	743	226	TAAAGAAAAAAAAACCTGTCAAACACGAATGTTAT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<:<6<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_66:3:263:689:572	147	chr2	553	68	35M	=	381	-207	AAAGAAAAAAAAACCTGTCAAACACGAATGTTATG	<9<2<<<<<<<<<22;;02<<<9<<;9<9<<;<<3	MF:i:18	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_19:1:99:1632:76	99	chr2	553	99	40M	=	705	192	AAAGAAAAAAAACCCTGTCAAACACGAATGTTATGCCCTG	<<<<<<<<<<<<*<<<<8<9<<<<<<<<<9;;;;<18:;:	MF:i:18	Aq:i:47	NM:i:1	UQ:i:9	H0:i:0	H1:i:1
+EAS54_71:7:250:698:842	163	chr2	554	99	35M	=	753	233	AAGAAAAAAAAACCTGTCAAACACGAATGTTATGC	<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<;<24	MF:i:18	Aq:i:39	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_11:5:41:314:1173	99	chr2	554	99	35M	=	718	199	AAGAAAAAAAAACCTGTCAAACACGAATGTTATGC	<;<<<<<<<;;<<<<<-<<<;;;<;8<*;;<<<<'	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_610:2:189:831:878	83	chr2	555	99	35M	=	351	-239	AGAAAAAAAAACCTGTCAAACACGAATGTTATGCC	<9<<<<<<<<<<;9<:<<<<<6<<<<<<<;<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_93:6:216:47:302	99	chr2	557	99	35M	=	729	207	AAAAAAAAACCTGTCAAACACGAATGTTATGCCCT	<<<<<<<<<<<7<<<<<<<<<<<<+<<<<<//6;<	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_97:5:28:538:148	83	chr2	557	99	35M	=	376	-216	AAAAAAAAACCTGTCAAACACGAATGTTATGCCCT	<<<<<<<<<<7;<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_57:2:284:597:682	147	chr2	557	99	35M	=	375	-217	AAAAAAAAACCTGTCAAACACGAATGTTATGCCCT	<<<<<<<<9;;7<;:<<<:<;<<<<<<<<;<<<<;	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS219_FC30151:7:11:1261:1200	83	chr2	558	99	35M	=	362	-231	AAAAAAAACCTGTCAAACACGAATGTTATGCCCTG	<<<<<<<:<<6<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:47	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_66:3:246:711:981	147	chr2	559	99	35M	=	371	-223	AAAAAAACCTGTCAAACACGAATGTTATGCCCTGC	;;:;7<<:5:<<:<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_32:1:208:971:600	83	chr2	559	99	35M	=	382	-212	AAAAAAACCTGTCAAACACGAATGTTATGCCCTGC	<<<<<<<3*+<4/<<<<7<<<<0<<:<8<<<<0<<	MF:i:18	Aq:i:51	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_97:5:219:174:684	83	chr2	560	71	35M	=	390	-205	AAAAAAACTGTCAAACACGAATGTTATGCCCTGCT	<<<<:;+9<<<;<<;<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:0	NM:i:1	UQ:i:10	H0:i:1	H1:i:0
+EAS51_66:7:4:234:610	163	chr2	560	84	35M	=	729	204	AAAAAACCTGTCAAACACGAATGTTATGCCCTCCT	<<<<<<<<7;<<<;7<7;7;7<;-<-<&<<<0%06	MF:i:18	Aq:i:22	NM:i:1	UQ:i:4	H0:i:1	H1:i:0
+EAS54_73:5:271:874:367	83	chr2	560	99	35M	=	384	-211	AAAAAACCTGTCAAACACGAATGTTATGCCCTGCT	<<<<<<5;<<<:<<<;<;<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:51	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:7:2:168:1878	99	chr2	560	37	35M	=	743	218	AAAAAACCTGGCAAACACGAATGTTATGACATGTN	;<:;;<:<;<;<;;;;:;<;:::&9:&:68&6&*!	MF:i:18	Aq:i:37	NM:i:5	UQ:i:61	H0:i:0	H1:i:1
+EAS221_1:6:89:1164:573	147	chr2	560	99	35M	=	371	-224	AAAAAACCTGTCAAACACGAATGTTATGCCCTGCT	3<<<6<%7<<08<<4<3<<103<1<<<<<<<<<<<	MF:i:18	Aq:i:41	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_103:7:53:783:78	147	chr2	561	99	35M	=	363	-233	AAAAACCTGTCAAACACGAATGTTATGCCCTGCTA	<;;;;<<0<,<<<<<<<<<;<<<;<;<<<<;<<<<	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_39:4:30:570:902	163	chr2	561	99	35M	=	730	204	AAAAACCTGTCAAACACGAATGTTATGCCCTGCTA	<<<<<<<<<<<;4<<:<<44<<<<<<<<<<<4<<+	MF:i:18	Aq:i:43	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_3:8:7:1864:1569	147	chr2	561	99	35M	=	382	-214	AAAAACCTGTCAAACACGAATGTTATGCCCTGCTA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:51	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_108:5:89:942:84	163	chr2	562	74	35M	=	759	232	AAAACCTGTCAAACACGAATGTTATGCCCTGCTAA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<;	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_81:6:122:589:134	83	chr2	562	99	35M	=	369	-228	AAAACCTGTCAAACACGAATGTTATGCCCTGCTAA	;<;4<<538<<;<<;<<<<';,:<<<<<<<<<<<<	MF:i:18	Aq:i:68	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS218_1:6:77:1529:522	99	chr2	562	99	35M	=	722	195	AAAACCTGTCAAACACGAATGTTATGCCCTGCTAA	<<;<<<<<<<<<<<4<<4<;;:;2:7<<<2*<;;8	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_597:8:48:805:860	99	chr2	563	78	35M	=	755	227	AAACCTGTCAAACACGAATGTTATGCCCTGCTAAA	<<<<<<<;<<<<<<<41;<<8<<<<<<<8+<4,+;	MF:i:18	Aq:i:13	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_597:4:144:492:61	99	chr2	564	99	35M	=	728	199	AACCTGTCAAACACGAATGTTATGCCCTGCTAAAC	<<<;<<<<<<<<<<<;<<<<<<7:<<<<::;9;;6	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_95:3:303:970:243	83	chr2	564	99	35M	=	370	-229	AACCTGTCAAACACGAATGTTATGCCCTGCTAAAC	<<0+<<<,<4<:<:<<<<<<<<<<<::<<<<<<<<	MF:i:18	Aq:i:70	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_19:4:78:806:800	163	chr2	564	99	40M	=	717	193	AACCTGTCAAACACGAATGTTATGCCCTGCTAAACTAAGC	<<<<<<<<<<<<<<<<<<<4<<:<1<0<;<9;<:78::::	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS219_FC30151:7:94:1440:2016	163	chr2	564	99	35M	=	751	222	AACCTGTCAAACACGAATGTTATGCCCTGCTAAAC	<<<<<<<<<<<<<<<<<<<;<<;;;<<:<8:::75	MF:i:18	Aq:i:51	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_62:3:103:443:166	163	chr2	565	99	35M	=	747	217	ACCTGTCAAACACGAATGTTATGCCCTGCTAAACT	<<<<<<<<<<<<<<<<<<<<;<<<<<<<1<-;;;<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_57:5:24:284:360	83	chr2	567	76	35M	=	390	-212	CTGTCAAACACGAATGTTATGCCCTGCTAAACTAA	:;<;:<<<;<<<<<<<<<<<<<<<<<;;<<<<<<<	MF:i:18	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_59:3:166:626:836	163	chr2	567	99	35M	=	757	225	CTGTCAAACACGAATGTTATGCCCTGCTAAACTAA	<<<<<<<<<<<<<<<<<<<<9<<<<<<<<;<;;;9	MF:i:18	Aq:i:28	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_26:4:110:840:431	83	chr2	567	93	35M	=	388	-214	CTGTCAAACACGAATGTTATGCCCTGCTAAACTAA	77<;7<<<<<<<<<4<<<<<<<:<<<<<<<<<<<<	MF:i:18	Aq:i:21	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_64:4:116:738:142	99	chr2	568	99	35M	=	722	189	TGTCAAACACGAATGTTATGCCCTGCTAAACTAAG	<<<<<<<<<<<<<<<<<<<;<<<<;<<<<<<<:;2	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_3:8:55:932:613	83	chr2	568	77	35M	=	389	-214	TGTCAAACACGAATGTTATGCCCTGCTAAACTAAG	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_63:7:137:139:248	83	chr2	569	97	35M	=	401	-203	GTCAAACACGAATGTTATGCCCTGCTAAACTAAGC	;;;99<<<;<;;<<<<<<<<<<<<;<<<<<<<<<<	MF:i:18	Aq:i:22	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS218_4:1:34:1614:558	147	chr2	569	99	35M	=	411	-193	GTCAAACACGAATGTTATGCCCTGCTAAACTAAGC	<<9<<<<<<<<<<<<9<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:37	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_610:7:15:696:693	83	chr2	570	10	35M	=	403	-202	TCAAACACGAATGTTAATCCCTGCTAAACTAATCA	)6<:7<.7<6.<0&&<&3:&7<<7<0<<<<<<<<<	MF:i:18	Aq:i:10	NM:i:3	UQ:i:50	H0:i:0	H1:i:0
+EAS114_28:3:32:492:907	147	chr2	571	95	36M	=	387	-220	CAAACACGAATGTTATGCCCTGCTAAACTAAGCATC	8<;<4<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:20	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS192_3:1:114:19:769	83	chr2	572	90	35M	=	405	-202	AAACACGAATGTTATGCCCTGCTAAACTAAGCATC	5+;+3/6;<+;/8<8*/<7/59<97147<;;9<7<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS188_7:3:182:104:921	147	chr2	575	99	35M	=	378	-232	CACGAATGTTATGCCCTGCTAAACTAAGCATCATA	;<;<<<<<<:<<<<<:<<:<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS220_1:8:5:996:2000	83	chr2	575	99	35M	=	408	-202	CACGAATGTTATGCCCTGCTAAACTAAGCATCATA	<<<<<<<<<<<<<<<<<<:<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_32:5:109:199:592	83	chr2	576	72	35M	=	390	-221	ACGAATATTATGCCCTGCTAAACTAAGCATCATAA	;9<9<:&:<<<<;;<;;<<<<<<<<<;<<<<<<<<	MF:i:18	Aq:i:0	NM:i:1	UQ:i:5	H0:i:1	H1:i:0
+EAS219_1:3:90:219:528	163	chr2	576	75	35M	=	758	217	ACGAATGTTATGCCCTGCTAAACTAAGCATCATAA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<7<<9	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_108:6:94:294:387	163	chr2	578	99	35M	=	736	193	GAATGTTATGCCCTGCTAAACTAAGCATCATAAAT	<<<<<<<;<<<<<<<<<:<<<<<<<<<<<<;)7;;	MF:i:18	Aq:i:51	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_108:1:33:779:821	83	chr2	579	99	35M	=	416	-198	AATGTTATGCCCTGCTAAACTAAGCATCATAAATG	<<730<<<<9<<<<;<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_26:5:43:114:617	163	chr2	579	99	35M	=	738	194	AATGTTATGCCCTGCTAAACTAAGCATCATAAATG	=============;=========;===========	MF:i:18	Aq:i:52	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_28:5:23:944:377	99	chr2	579	75	36M	=	757	214	AATGTTATGCCCTGCTAAACTAAGCATCATAAATGA	<<<<<<<<9<<<<;<<<<<<<<<;<7<<<<;8;<<;	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:3:3:864:1888	147	chr2	579	99	35M	=	411	-203	AATGTTATGCCCTGCTAAACTAAGCATCATAAATG	888588;;;;;;;;;;;;;;;;;;;;8;;;;;;;;	MF:i:18	Aq:i:43	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_11:4:26:137:1382	147	chr2	579	99	35M	=	397	-217	AATGTTATGCCCTGCTAAACTAAGCATCATAAATG	<<-<8<<<<<<:<<<<<<<:<<<<<<<<<<<<<<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_81:6:265:251:147	163	chr2	581	99	35M	=	754	208	TGTTATGCCCTGCTAAACTAAGCATCATAAATGAA	<<<<<<<<<<<<<<88<<<80:;<<<<<;:4;;:4	MF:i:18	Aq:i:50	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_595:5:184:912:258	147	chr2	582	99	35M	=	428	-189	GTTATGCCCTGCTAAACTAAGCATCATAAATGAAG	<;;<<<<;:<<7<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_597:3:115:646:430	99	chr2	582	45	35M	=	768	217	GTTATGCCCTGCTAAACTTAGCATCATAAATGAAG	<7<<<<<<<<<<<<;<<<<<;<7<<<<;5;<;67<	MF:i:18	Aq:i:45	NM:i:1	UQ:i:27	H0:i:0	H1:i:1
+EAS1_108:3:24:319:429	163	chr2	582	99	35M	=	740	193	GTTATGCCCTGCTAAACTAAGCATCATAAATGAAG	<<<<<<<<<<<<<<<<;<<<<<<<<1<<-6<<</<	MF:i:18	Aq:i:56	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_59:8:49:182:192	99	chr2	582	99	35M	=	750	203	GTTATGCCCTGCTAAACTGAGCATCATAAATGAAG	=====================;============<	MF:i:18	Aq:i:49	NM:i:1	UQ:i:28	H0:i:0	H1:i:1
+EAS114_45:1:100:979:1863	99	chr2	583	85	35M	=	757	209	TTATGCCCTGCTAAACTAAGCATCATAAATGAAGG	;<;;;;;;;7;;;79;;77;9;;99;974;677-6	MF:i:18	Aq:i:23	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_11:7:53:458:581	73	chr2	583	77	35M	=	583	0	TTATGCCCTGCTAAACTAAGCATCATAAATGAAGG	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:64	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_11:7:53:458:581	133	chr2	583	0	*	=	583	0	CTCAATTAATTGTTTTATAAAACCTGTGAGTTTTG	<<<<<<<<<<<<<<<<<<<<<<<<<<<<99<<<<<	MF:i:192
+B7_589:6:108:958:42	163	chr2	584	81	35M	=	755	206	TATGCCCTGCTAAACTAAGCATCATAAATGAAGGG	<<<<<<<<<<<<<<<<<<<<1<<<<<<9<<;<5<:	MF:i:18	Aq:i:9	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_59:6:89:457:591	99	chr2	585	69	35M	=	770	216	ATGCCCTGCTAAACTAAGCATCATAAATGAAGGGG	<<<<<<<<<<<4<<<<<<<<<<<<8<7/4<<<<4+	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS219_FC30151:7:87:1289:83	83	chr2	585	99	35M	=	413	-207	ATGCCCTGCTAAACTAAGCATCATAAATGAAGGGG	<<<::<<<:<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:49	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS218_4:1:84:1505:1037	147	chr2	586	99	35M	=	409	-212	TGCCCTGCTAAACTAAGCATCATAAATGAAGGGGA	<<966<<7<<<<7<<<<9<<;<<<<<<<<<<<<<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_67:3:197:261:624	147	chr2	587	99	35M	=	398	-224	GCCCTGCTAAACTAAGCATCATAAATGAAGGGGAA	866;2:/;<<<;:<<<;<;;<<<<<<<<<<<<<<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_64:6:118:41:489	163	chr2	588	76	35M	=	779	226	CCCTGCTAAACTAAGCATCATAAATGAAGGGGAAA	<<<<<<<<<<<<<<<<;<<<<<<<<<<<<<<<95:	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_597:3:157:361:309	99	chr2	589	99	35M	=	747	193	CCTGCTAAACTAAGCATCATAAATGAAGGGGAAAT	<<<<<<<<<<<<<<<<<<<<<<<<<<;<;<;<<;<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:2
+EAS114_39:6:71:644:1792	163	chr2	589	84	35M	=	754	200	CCTGCTAAACTAAGCATCATAAATGAAGGGGAAAT	<<<<<<<;<<<<<<<<<<;<<<<<<<<<;<;:<:<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:2
+B7_589:2:9:49:661	163	chr2	591	99	35M	=	747	191	TGCTAAACTAAGCATCATAAATGAAGCGGAAATAA	<<<<<<<<<<<<<<<<;<<<<<<;:<<;;;7<9;9	MF:i:18	Aq:i:45	NM:i:1	UQ:i:27	H0:i:0	H1:i:1
+EAS54_71:2:85:686:696	83	chr2	594	99	34M	=	435	-193	TAAACTAAGCATCATAAATGAAGTGGAAATAAAG	:<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:47	NM:i:1	UQ:i:27	H0:i:0	H1:i:1
+EAS188_7:1:177:522:118	69	chr2	594	0	*	=	594	0	TCTCAATTAATTGTTTTATAAAACCTGTGAGTTTT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<57<<<<	MF:i:192
+EAS188_7:1:177:522:118	137	chr2	594	49	35M	=	594	0	TAAACTAAGCATCATAAATGAAGGGGAAATAAAGT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<8<	MF:i:64	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS188_4:5:103:870:105	99	chr2	595	44	35M	=	778	214	AAACTAAGCATCATAAATGAAGGGGAAATAAAGTC	<<<<<<<<<<<<<<<<<<<<<<<<8<<<<<;<<7;	MF:i:18	Aq:i:44	NM:i:0	UQ:i:0	H0:i:1	H1:i:1
+EAS51_62:8:52:967:804	73	chr2	596	76	35M	=	596	0	AACTAAGCATCATAAATGAAGGGGAAATAAAGTCA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<:<<	MF:i:64	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_62:8:52:967:804	133	chr2	596	0	*	=	596	0	TTACCTAGTTGCTCTGTAGTCTCAATTAATTGTTT	===============<=======<<===<======	MF:i:192
+EAS1_108:6:95:235:746	83	chr2	598	99	35M	=	430	-203	CTAAGCATCATAAATGAAGGGGAAATAAAGTCAAG	==&=;===7=3===8======;=;8===8=====;	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_81:7:124:253:889	83	chr2	598	99	35M	=	437	-196	CTAAGCATCATAAATGAAGGGGAAATAAAGTCAAG	8<<<<<<<<<<<<<<<<<<<<<<<<<:<<<<<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_95:6:174:650:125	99	chr2	600	76	35M	=	770	201	AAGCATCATAAATGAAGGGGAAATAAAGTCAAGTC	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_30:3:39:348:594	83	chr2	600	99	35M	=	431	-204	AAGCATCATAAATGAAGGGGAAATAAAGTCAAGTC	<<;;<;:<;<<<;<<<<<<<<<<<<<<<<<;<<<<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS188_7:4:92:693:228	99	chr2	601	75	35M	=	770	200	AGCATCATAAATGAAGGGGAAATAAAGTCAAGTCT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;9<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS192_3:3:285:349:797	163	chr2	604	76	35M	=	773	200	ATCATAAATGAAGGGGAAATAAAGTCAAGTCTTTC	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_589:3:82:13:897	83	chr2	606	99	35M	=	453	-188	CATAAATGAAGGGGAAATAAAGTCAAGTCTTTCCT	,<2<;<<;<<<<;;;<<;<<<<<<<;;;;<<<<<<	MF:i:18	Aq:i:41	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_30:7:310:155:312	83	chr2	606	99	35M	=	438	-203	CATAAATGAAGGGGAAATAAAGTCAAGTCTTTCCT	2;<<;<<;<<;;/<<<<<<;<<<<8<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS220_1:8:45:178:1321	163	chr2	606	77	35M	=	771	196	CATAAATGAAGGGGAAATAAAGTCAAGTCTTTCCT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_97:2:193:420:78	99	chr2	607	99	35M	=	787	215	ATAAATGAAGGGGAAATAAAGTCAAGTCTTTCCTG	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;;<<;	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_108:1:131:518:588	83	chr2	607	99	35M	=	433	-209	ATAAATGAAGGGGAAATAAAGTCAAGTCTTTCCTG	<.<<<<<<<<4<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS112_34:8:45:800:733	83	chr2	607	99	35M	=	413	-229	ATAAATGAAGGGGAAATAAAGTCAAGTCTTTCCTG	<7<<7&<<9<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:34	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS220_1:4:70:766:2016	83	chr2	607	99	35M	=	422	-220	ATAAATGAAGGGGAAATAAAGTCAAGTCTTTCCTG	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_19:2:2:1217:398	163	chr2	608	99	40M	=	780	212	TAAATGAAGGGGAAATAAAGTCAAGTCTTTCCTGACAAGC	<<<<<<<<<<<<<;<<<<<<<7<<<3<<<<;<<<<9:7::	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS219_FC30151:3:73:1458:1337	163	chr2	609	99	35M	=	806	232	AAATGAAGGGGAAATAAAGTCAAGTCTTTCCTGAC	<<<<<;;;<<<<<<<<<<<<<<<<<<<;<<7;;;;	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_59:2:104:402:732	83	chr2	610	99	35M	=	434	-211	AATGAAGGGGAAATAAAGTCAAGTCTTTCCTGACA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_65:5:37:611:267	147	chr2	610	99	35M	=	464	-181	AATGAAGGGGAAATAAAGTCAAGTCTTTCCTGACA	<<4<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:47	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS192_3:7:78:692:671	147	chr2	610	99	35M	=	438	-207	AATGAAGGGGAAATAAAGTCAAGTCTTTCCTGACA	<<);<<;;<<<<<;<<<<<<<<<<<<<6<<<<<<<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_28:1:144:242:602	83	chr2	611	99	36M	=	436	-211	ATGAAGGGGAAATAAAGTCAAGTCTTTCCTGACAAG	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS219_FC30151:5:6:1243:981	69	chr2	611	0	*	=	611	0	TTACCTAGTTGCTCTGTAGTCTCAATTAATTGTTT	<<<<8<<8<<<<2<<<<<<<<8<55<<8*<<8<<<	MF:i:192
+EAS219_FC30151:5:6:1243:981	137	chr2	611	68	35M	=	611	0	ATGAAGGGGAAATAAAGTCAAGTCTTTCCTGACAA	<;<;;<<<;3;;3<<<;<<;<7%<<<.1<<<..<3	MF:i:64	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_591:3:291:404:199	163	chr2	612	76	36M	=	777	197	TGAAGGGGAAATAAAGTCAAGTCTTTCCTGACAAGC	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<:	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_108:2:266:994:429	99	chr2	612	76	35M	=	769	188	TGAAGGGGAAATAAAGTCAAGTCTTTCCTGACAAG	=====================9=======4===:=	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_65:7:159:253:353	163	chr2	613	67	35M	=	778	196	GAAGGGGAAATAAAGTCAAGTCTTTCCTGACAGGC	<<<<<<<<<<<<<<<<<<<<<<<<<<<<0,%4(+,	MF:i:18	Aq:i:67	NM:i:1	UQ:i:7	H0:i:1	H1:i:0
+EAS1_108:5:175:149:296	163	chr2	614	99	35M	=	811	232	AAGGGGAAATAAAGTCAAGCCTTTCCTGACAAGCA	<<<<<<<<<<<<<<<<<<<49<<<<<<<<<<<<;4	MF:i:18	Aq:i:45	NM:i:1	UQ:i:19	H0:i:0	H1:i:1
+EAS56_65:1:23:536:229	147	chr2	614	99	35M	=	448	-201	AAGGGGAAATAAAGTCAAGTCTTTCCTGACAAGCA	<<99<<<<<;<<<;2<<<<<<;<<<9<<<<<<<<<	MF:i:18	Aq:i:54	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS220_1:4:100:20:1199	83	chr2	614	99	35M	=	456	-193	AAGGGGAAATAAAGTCAAGTCTTTCCTGACAAGCA	:<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_59:5:181:713:140	99	chr2	615	84	35M	=	793	213	AGGGGAAATAAAGTCAAGTATTTCCTGACAAGCAA	<7<<<<<<<<<<<<7<7<6+<<<5;<;<2<;;+;;	MF:i:18	Aq:i:41	NM:i:1	UQ:i:10	H0:i:0	H1:i:1
+EAS139_19:6:82:1051:921	163	chr2	616	99	40M	=	800	224	GGGGAAATAAAGTCAAGGCTTTCCTGACAAGCAAATGCTA	<<<<<9<799<<<<7::/<<<9<7:9:;2:7552+9''66	MF:i:18	Aq:i:41	NM:i:1	UQ:i:14	H0:i:0	H1:i:1
+EAS192_3:3:309:187:267	163	chr2	616	99	35M	=	786	205	GGGGAAATAAAGTCAAGTCTTTCCTGACAAGCAAA	<<<<<<<<<<<<<<<<<<<<<<<;<;<;<;68;;8	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_593:3:115:649:259	99	chr2	617	99	36M	=	782	201	GGGAAATAAAGTCAAGTCTTTCCTGACAAGCAAATG	<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<<;<<9	MF:i:18	Aq:i:45	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_97:4:261:267:597	163	chr2	617	86	35M	=	787	205	GGGTAATAAAGTCAAGTCTTTCCTGACAAGCAAAT	<<<<<<<<<;<<<<<7<<<<<<<<<:7<7<;44:;	MF:i:18	Aq:i:41	NM:i:1	UQ:i:27	H0:i:0	H1:i:1
+EAS114_26:4:123:1001:580	163	chr2	617	43	35M	=	771	185	GGGAANTAAAGTCAAGTCTTTCCTGACAAGCAAAT	=====!=====================1.8131*=	MF:i:18	Aq:i:43	NM:i:1	UQ:i:0	H0:i:0	H1:i:1
+EAS139_11:7:60:163:1612	83	chr2	617	99	35M	=	439	-213	GGGAACTAAAGTCAAGTCTTTCCTGACAAGCAAAT	-<<<<)<<<<<<<<<<<<<<<<<<<<<8<<<<<<<	MF:i:18	Aq:i:59	NM:i:1	UQ:i:8	H0:i:1	H1:i:0
+EAS54_65:4:325:795:213	163	chr2	618	99	35M	=	790	207	GGAAATAAAGTCAAGTCTTTCCTGACAAGCAAATG	<<<<<<<;<<<<;;<<<<<<<<<<<<;:<</;/;;	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_61:3:165:665:220	163	chr2	618	76	35M	=	779	196	GGAAATAAAGTCAAGTCTTTCCTGACAAGCAAATG	<<<<<<<<<<<<<<<<<<<<<;<;;<<<;;<;<<;	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS112_34:4:22:206:150	163	chr2	619	99	35M	=	792	208	GAAATAAAGTCAAGTCTTTCCTGACAAGCAAATGC	==========================::=5&;<2<	MF:i:18	Aq:i:65	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_26:2:237:497:165	147	chr2	619	99	35M	=	454	-200	GAAATAAAGTCAAGTCTTTCCTGACAAGCAAATGC	9=:=======2=27======<>&<=,==4>4=>>=	MF:i:18	Aq:i:68	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS218_1:8:82:1540:77	163	chr2	619	99	35M	=	786	202	GAAATAAAGTCAAGTCTTTCCTGACAAGCAAATGC	<<<<<<<<<<<<<<<<<<<<<<<<<<<;;<<<<:8	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_67:3:172:196:746	147	chr2	620	99	35M	=	451	-204	AAATAAAGTCAAGTCTTTCCTGACAAGCAAATGCT	<<<;><<+<<<<:<<<<2<;<<<;<<<<<<<<<<<	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_73:7:97:892:419	163	chr2	621	99	35M	=	800	214	AATAAAGTCAAGTCTTTCCTGACAAGCAAATGCTA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS192_3:4:312:915:751	147	chr2	621	99	35M	=	461	-195	AATAAAGTCAAGTCTTTCCTGACAAGCAAAAGCTA	<:-<<<99:::);:7<4;8<<<<<<<;<2<+8<;<	MF:i:18	Aq:i:41	NM:i:1	UQ:i:10	H0:i:0	H1:i:1
+EAS1_93:4:325:352:67	163	chr2	622	99	35M	=	794	207	ATAAAGTCAAGTCTTTCCTGACAAGCAAATGCTAA	==================<========<=<;-===	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_97:4:83:731:540	99	chr2	623	99	35M	=	804	216	TAAAGTCAAGTCTTTCCTGACAAGCAAATGCTAAG	<<<<<<<<<;<<<<<<<<<<<<<:<7<*;&;<;;9	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS188_7:5:74:329:459	163	chr2	623	99	35M	=	795	207	TAAAGTCAAGTCTTTCCTGACAAGCAAATGCTAAG	<<<<<<<<<<<<<<<<<<<<<<<;<<;<<;9;599	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS219_FC30151:3:13:674:1717	83	chr2	623	99	35M	=	445	-213	TAAAGTCAAGTCTTTCCTGACAAGCAAATGCTAAG	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:45	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_105:1:141:415:738	69	chr2	624	0	*	=	624	0	TTACCTAGTTGCTCTGTAGTCTCAATTAATTGTTT	<<<<<<<<<<<<<<<<<<<<<<<;<<<<<;<8<<<	MF:i:192
+EAS1_105:1:141:415:738	137	chr2	624	76	35M	=	624	0	AAAGTCAAGTCTTTCCTGACAAGCAAATGCTAAGA	<<<<<<<<<<<<<<<<<<<<<<:<<;<<;<<<<6:	MF:i:64	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_53:1:154:118:488	83	chr2	624	99	35M	=	447	-212	AAAGTCAAGTCTTTCCTGACAAGCAAATGCTAAGA	<<<;58<<95:<<;<;<<<;<<<;;<<<<<<<<<<	MF:i:18	Aq:i:54	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_59:5:198:929:684	83	chr2	624	99	35M	=	471	-188	AAAGTCAAGTCTTTCCTGACAAGCAAATGCTAAGA	<<;<<<<<:<<<<<<<<<<<<<<<<<;<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_28:4:215:246:640	147	chr2	624	99	36M	=	447	-213	AAAGTCAAGTCTTTCCTGACAAGCAAATGCTAAGAT	;<<,<<<96<<:<:<9<6<97<<<<<9<<<<9<<9<	MF:i:18	Aq:i:54	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_103:2:234:167:381	83	chr2	625	99	35M	=	443	-217	AAGTCAAGTCTTTCCTGACAAGCAAATGCTAAGAT	<<;<;<<<<;<<<<7<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:49	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS112_34:7:96:489:453	147	chr2	625	99	35M	=	445	-215	AAGTCAAGTCTTTCCTGACAAGCAAATGCTAAGAT	;<;;;<<<<5:<<:<<<<:<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:54	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_93:3:79:879:15	99	chr2	626	99	35M	=	790	199	AGTCAAGTCTTTCCTGACAAGCAAATGCTAAGATA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<2<;<<1<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_53:2:59:286:290	147	chr2	628	99	35M	=	467	-196	TCAAGTCTTTCCTGACAAGCAAATGCTAAGATAAT	77<<<<7<<<97<<,7<<<;<<<;<9<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_95:5:263:511:936	99	chr2	629	99	35M	=	801	207	CAAGTCTTTCCTGACAAGCAAATGCTAAGATAATT	<<<<<<<<<<<<<<<<<;<<<<<;<<:<:<<<<<<	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_30:3:181:582:435	147	chr2	629	99	35M	=	471	-193	CAAGTCTTTCCTGACAAGCAAATGCTAAGATAATT	<<<<<<<<;<<<<<;<<4<<<<<<;<<<<<<<<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS188_7:6:107:636:642	83	chr2	630	99	35M	=	458	-207	AAGTCTTTCCTGACAAGCAAATGCTAAGATAATTC	<<<<<<<;<<<<<;<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS112_34:4:12:273:89	83	chr2	631	99	35M	=	477	-189	AGTCTTTCCTGACAAGCAAATGCTAAGATAATTCA	<:737<288<<<7<<<<<<<<<:9<<<<<<<<<<<	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_59:2:239:1001:406	147	chr2	634	99	35M	=	450	-219	CTTTCCTGACAAGCAAATGCTAAGATAATTCATCA	0':.71;;:9==9=;====;=;=============	MF:i:18	Aq:i:49	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS188_4:7:96:899:106	147	chr2	636	99	35M	=	462	-209	TTCCTGACAAGCAAATGCTAAGATAATTCATCATC	;;;;<<<<<<<;<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_65:6:67:56:806	147	chr2	637	99	35M	=	464	-208	TCCTGACAAGCAAATGCTAAGATAATTCATCATCA	844:8;7<88;8<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:70	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_67:5:71:408:741	83	chr2	637	99	35M	=	457	-215	TCCTGACAAGCAAATGCTAAGATAATTCATCATCA	;7;<;<0<<<<<<<<:;<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_53:6:180:695:621	147	chr2	637	99	35M	=	453	-219	TACTGAAAAGCAAATGCTAAGATAATTCATCATCA	;&377<&<<;7<<<<<7<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:68	NM:i:2	UQ:i:10	H0:i:1	H1:i:0
+EAS114_30:6:49:656:507	147	chr2	637	99	35M	=	468	-204	TCCTGACAAGCAAATGCTAAGATAATTCATCATCA	%44;;<:<<;<;<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_73:3:4:854:140	147	chr2	638	72	35M	=	458	-215	CCTGACAAGCAAATGCTAAGATAATTCATCATCAC	:9':<;<<<;<<<;<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_19:1:85:1521:58	99	chr2	639	99	40M	=	813	214	CTGACAAGCAAATGCTAAGATAATTCATCATCACTAAACC	<<<<<<<<9<<<<<<<<<<<<<7<<<<<<<<<<<<;;:7:	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_39:2:57:1064:925	137	chr2	640	76	35M	*	0	0	TGACAAGCAAATGCTAAGATAATTCATCATCACTA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<:<<<	MF:i:32	Aq:i:29	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_103:3:323:196:855	163	chr2	642	99	35M	=	809	202	ACAAGCAAATGCTAAGATAATTCATCATCACTAAA	<<<<<<<7<<<<<<:<<<<<<<<<<<<<<<<<;7:	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_67:5:117:33:262	163	chr2	642	99	35M	=	814	207	ACAAGCAAATGCTAAGATAATTCATCATCACTAAA	<<<;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_11:1:59:742:549	99	chr2	642	99	35M	=	816	209	ACAAGCAAATGCTAAGATAATTCATCATCACTAAA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<8<	MF:i:18	Aq:i:48	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_28:2:55:562:403	163	chr2	643	99	36M	=	825	218	CAAGCAAATGCTAAGATAATTCATCATCACTAAACC	<<<<<<<<<<<<<<<<<<<<<;<<;<<<<<<<;<;:	MF:i:18	Aq:i:51	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_71:7:97:743:602	163	chr2	644	99	35M	=	821	211	AAGCAAATGCTAAGATAATTCATCATCACTAAACC	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<<:	MF:i:18	Aq:i:26	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_28:2:167:905:852	83	chr2	647	99	36M	=	445	-238	CAAATGCTAAGATAATTCATCATCACTAAACCAGTC	+<<<9;7;<<+<<<<<39<;9<;9<<7<<<<<<<<<	MF:i:18	Aq:i:43	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS112_34:6:130:865:838	83	chr2	649	99	35M	=	448	-236	AATGCTAAGATAATTCATCATCACTAAACCAGTCC	;<:84<<<4<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:54	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS219_1:1:60:1420:660	163	chr2	649	99	35M	=	808	194	AATGCTAAGATAATTCATCATCACTAAACCAGTCC	<<<<<<<<<<<<<<<<<<<<<<<<<<;<<<8<<<<	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_593:3:180:89:582	99	chr2	650	99	36M	=	809	195	ATGCTAAGATAATTCATCATCACTAAACCAGTCCTA	<<<<<<<<<7<<<<<<<<<7<<<:<<<:<<::77:<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_99:1:86:871:319	147	chr2	651	71	35M	=	494	-192	TGCTAAGATAATTCATCATCACTAAACCAGTCCTA	7;+1;<:<<<<<<<<;<<;<<9<<<<<<<<<<<<<	MF:i:18	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_57:2:236:841:20	83	chr2	652	99	35M	=	467	-220	GCTAAGATAATTCATCATCACTAAACCAGTCCTAT	7;<<<;<<<<;;<<<<<<<<<<<<<<<<<<<<;<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_62:2:133:8:379	83	chr2	653	99	35M	=	470	-218	ATAAGATAATTCATCATCACTAAACCAGTCCTATA	&=========='==7==0=2====28===00====	MF:i:18	Aq:i:70	NM:i:1	UQ:i:5	H0:i:1	H1:i:0
+EAS1_105:8:96:720:940	83	chr2	654	99	35M	=	467	-222	TAAGATAATTCATCATCACTAAACCAGTCCTATAA	*<<<<;<<<9<<;,<;0<;<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_57:5:71:994:576	99	chr2	655	99	35M	=	805	185	AAGATAATTCATCATCACTAAACCAGTCCTATAAG	<<<<<<<<<<<<<<<<<<<<<<<;<<5<<<<<<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_103:4:164:79:134	147	chr2	656	99	35M	=	488	-203	AGATAATTCATCATCACTAAACCAGTCCTATAAGA	<;<;<<<;<<;<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:47	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_19:6:78:1029:512	83	chr2	656	99	40M	=	500	-196	AGATAATTCATCATCACTAAACCAGTCCTATAAGAAATGC	;;;;;<;;<<<.<<6;<<;<;8<<<<::<<<<<<<<;<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_93:1:214:784:690	147	chr2	657	99	35M	=	472	-220	GATAATTCATCATCACTAAACCAGTCCTATAAGAA	-<7<<7<:<<2<<<<;<<<<<;<<<<3<<<<<<<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:1
+EAS220_1:4:6:1178:1105	99	chr2	657	93	35M	=	830	208	GATAATTCATCATCACTAAACCAGTCCTATAAGAA	<<<<<<:<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:17	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_99:7:171:196:287	83	chr2	658	99	35M	=	485	-208	ATAATTCATCATCACTAAACCAGTCCTATAAGAAA	<;;;98;<;&<;;<<<<<<<;<<<<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_28:1:220:801:282	99	chr2	660	99	36M	=	837	213	AATTCATCATCACTAAACCAGTCCTATAAGAAATGC	<<<<<<<<<<<<<<<<<<<<<;<+<;<<<<<::<<:	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:2
+EAS221_1:2:73:955:728	163	chr2	660	44	35M	=	823	198	AATTCATCATCACTAAACCAGTCCTATAAGAAATG	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<<<<	MF:i:18	Aq:i:14	NM:i:0	UQ:i:0	H0:i:1	H1:i:2
+EAS1_105:1:3:903:957	147	chr2	661	99	35M	=	516	-180	ATTCATCATCACTAAACCAGTCCTATAAGAAATGC	<%12<&<<<;<:<<<<<<<<<7<<<<<<<<<<<<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:1
+EAS56_65:2:224:579:433	83	chr2	662	99	35M	=	485	-212	TTCATCATCACTAAACCAGTCCTATAAGAAATGCT	'<08/8<+<</<<:<<<<<8<<9<38<<<<<<<<;	MF:i:18	Aq:i:31	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_61:5:209:824:866	163	chr2	665	73	35M	=	828	198	ATCATCACTAAACCAGTCCTATAAGAAATGCTCAA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;	MF:i:18	Aq:i:19	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:1:30:1882:1210	83	chr2	665	82	35M	=	503	-197	ATCATCACTAAACCAGTCCTATAAGAAATGCTCAA	776778;5;;;;8;;7:8;;;;;;;<<<;;;;;<;	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_64:4:181:476:394	163	chr2	666	99	35M	=	847	216	TCATCACTAAACCAGTCCTATAAGAAATGCTCAAA	<<<<<<<<<<<<<<<<<<<<<<<<<;<<:<<<:;;	MF:i:18	Aq:i:54	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_105:6:267:953:459	147	chr2	667	99	35M	=	509	-193	CATCACTAAACCAGTCCTATAAGAAATGCTCAAAA	%<07<94========<<==================	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_64:7:140:752:822	147	chr2	667	76	35M	=	495	-207	CATCACTAAACCAGTCCTATAAGAAATGCTCAAAA	;<;;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS112_32:7:322:391:742	99	chr2	667	99	35M	=	847	215	CATCACTAAACCAGTCCTATAAGAAATGCTCAAAA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<;;	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_67:5:149:639:910	83	chr2	669	99	35M	=	489	-215	TCACTAAACCAGTCCTATAAGAAATGCTCAAAAGA	<;49;<<;;<<<<8;<<<<<<<<<<<<<<<<<<;<	MF:i:18	Aq:i:42	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_108:1:242:419:512	83	chr2	672	94	35M	=	490	-217	CTAAACCAGTCCTATAAGAAATGCTCAAAAGAATT	*:<<<<9<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:24	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS192_3:6:45:183:25	83	chr2	672	95	35M	=	501	-206	CTAAACCAGTCCTATAAGAAATGCTCAAAAGAATT	;1<<;<<<;;;;<<<<<+<<<<<<<<<9<<<<<<<	MF:i:18	Aq:i:23	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS192_3:6:326:887:180	83	chr2	672	73	35M	=	492	-215	CTAAACCAGTCCTATAAGAAATGCTCAAAAGAATT	8:<<:<5<<<;7<<<<<<<<<<<<;<<<<<<<<<<	MF:i:18	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_73:5:145:635:390	163	chr2	673	99	35M	=	860	222	TAAACCAGTCCTATAAGAAATGCTCAAAAGAATTG	<<<<<<<<<<<<<<<<<<:<<<<<<<8<<<::;;;	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_11:2:31:628:1820	163	chr2	675	98	35M	=	828	188	AACCAGTCCTATAAGAAATGCTCAAAAGAATTGTA	<<<<<<<<<<<<<<<<<<<<<<<<<<<9<<<<<<<	MF:i:18	Aq:i:20	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_65:7:117:452:744	163	chr2	676	99	35M	=	850	209	ACCAGTCCTATAAGAAATGCTCAAAAGAATTGTAA	<<<<<<<<<<;<<<;<<<<<<<<<<:<<<<<<<;;	MF:i:18	Aq:i:50	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_30:2:297:949:26	163	chr2	676	99	35M	=	842	201	ACCAGTCCTATAAGAAATGCTCAAAAGAATTGTAA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;	MF:i:18	Aq:i:51	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_11:8:17:437:1378	163	chr2	676	99	35M	=	847	206	ACCAGTCCTATAAGAAATGCTCAAAAGAATTGTAA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:51	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_108:6:222:579:961	83	chr2	679	99	35M	=	504	-210	AGTCCTATAAGAAATGCTCAAAAGAATTGTAAAAG	=58====;==8=======;================	MF:i:18	Aq:i:70	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_597:5:98:995:929	163	chr2	680	99	35M	=	844	199	GTCCTATAAGAAATGCTCAAAAGAATTGTAAAAGT	<;<;<8<;<<;1;<<<<<;<;;;08;<;<1&0+8<	MF:i:18	Aq:i:63	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:2:76:1765:700	163	chr2	680	99	35M	=	866	221	GTCCTATAAGAAATGCTCAAAAGAATTGTAAAAGT	;;6;;;;;;;;;6;;;;6;;;;;;;;;;;;88878	MF:i:18	Aq:i:63	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_19:5:68:306:409	99	chr2	682	99	40M	=	856	214	CCTATAAGAAATGCTCAAAAGAATTGTAAAAGTCAAAATT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<:;:;;	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_108:5:115:193:231	83	chr2	684	99	35M	=	522	-197	TATAAGAAATGCTCAAAAGAATTGTAAAAGTCAAA	=========7===========<=============	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_3:4:57:1675:720	99	chr2	684	99	35M	=	841	192	TATAAGAAATGCTCAAAAGAATTGTAAAAGTCAAA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_11:6:13:682:680	147	chr2	685	99	35M	=	482	-238	ATAAGAAATGCTCAAAAGAATTGTAAAAGTCAAAA	<<<<<<<<<<:<5<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:47	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_3:6:51:1486:1131	83	chr2	685	77	35M	=	500	-220	ATAAGAAATGCTCAAAAGAATTGTAAAAGTCAAAA	<<<<<<<<<<,<6<<<<<<<<<<<<<<<<<<7<<<	MF:i:18	Aq:i:3	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_3:8:33:1240:846	147	chr2	685	99	35M	=	509	-211	ATAAGAAATGCTCAAAAGAATTGTAAAAGTCAAAA	<<<<<<<<<<9<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_66:8:43:972:506	83	chr2	686	99	35M	=	505	-216	TAAGAAATGCTCAAAAGAATTGTAAAAGTCAAAAT	;<<<<<<<+;<;<<<<<<<<<<<<<;<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_1:2:23:127:880	147	chr2	686	99	35M	=	504	-217	TAAGAAATGCTCAAAAGAATTGTAAAAGTCAAAAT	<<<<<<<<<%<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:47	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_67:7:101:752:996	83	chr2	687	99	35M	=	508	-214	AAGAAATGCTCAAAAGAATTGTAAAAGTCAAAATT	<<<<<<<<7<7<<<<<<<<<<<<<<<<<;<<<<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_59:6:3:186:68	147	chr2	687	99	35M	=	512	-210	AAGAAATGCTCAAAAGAATTGTAAAAGTCAAAATT	<<;<<<<<&:,<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_593:2:273:348:37	83	chr2	688	99	36M	=	483	-241	AGAAATGCGCAAAAGAATTGTAAAAGTCAAAATTAA	9;7;;0<++1<<<;<7<+;;1<<<;<17<<<<<<<<	MF:i:18	Aq:i:41	NM:i:1	UQ:i:10	H0:i:0	H1:i:1
+EAS51_78:7:164:727:977	83	chr2	689	99	35M	=	513	-211	GAAATGCTCAAAAGAATTGTAAAAGTCAAAATTAA	;<;<;<:<:<<<<<<<:<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_26:6:140:253:322	147	chr2	689	99	35M	=	537	-187	GAAATGCTCAAAAGAATTGTAAAAGTCAAAATTAA	=;===;54:====================>>===>	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_105:2:146:374:692	99	chr2	690	99	35M	=	874	219	AAATGCTCAAAAGAATTGTAAAAGTCAAAATTAAA	<<<<<<<<<<<<<<<</<<<<<<<<<<<<<<<<<:	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_53:1:92:875:345	83	chr2	690	99	35M	=	504	-221	AAATGCTCAAAAGAATTGTAAAAGTCAAAATTAAA	<<<;<.;7<<<<<<<<<<<<<<<<<;<<<<<<<<<	MF:i:18	Aq:i:47	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_93:6:45:601:439	163	chr2	691	99	35M	=	864	208	AATGCTCAAAAGAATTGTAAAAGTCAAAATTAAAG	<<<<;<<<<<<<<<<<<<<<<4<<<<9<<<<<<;;	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_62:5:295:882:282	83	chr2	691	99	35M	=	520	-206	AATGCTCAAAAGAATTGTAAAAGTCAAAATTAAAG	<<:<8<-<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_11:5:78:775:555	147	chr2	691	99	35M	=	539	-187	AATGCTCAAAAGAATTGTAAAAGTCAAAATTAAAG	<<-<%4/<<<<<<<<<<<<<<<<<5<<<0<<<<<<	MF:i:18	Aq:i:68	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_73:5:255:796:239	99	chr2	692	99	35M	=	869	212	ATGCTCAAAAGAATTGTAAAAGTCAAAATTAAAGT	<<<<<<<<6<<<<<<<<<<<<<<<<;6<<<:<:<<	MF:i:18	Aq:i:43	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_57:7:57:826:977	83	chr2	693	99	35M	=	528	-200	TGCTCAAAAGAATTGTAAAAGTCAAAATTAAAGTT	875:6<<<<<<<<<<<<<<<;<<<<<<;8<<<<<<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_28:6:187:996:432	99	chr2	693	99	36M	=	860	203	TGCTCAAAAGAATTGTAAAAGTCAAAATTAAAGTTC	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<;<<;	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_3:8:65:463:703	147	chr2	693	99	35M	=	506	-222	TGCTCAAAAGAATTGTAAAAGTCAAAATTAAAGTT	<<3<9<<<<<<<8<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_57:1:288:384:444	163	chr2	696	99	35M	=	855	194	TCAAAAGAATTGTAAAAGTCAAAATTAAAGTTCAA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;;;;	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_61:5:272:240:950	83	chr2	696	97	35M	=	520	-211	TCAAAAGAATTGTAAAAGTCAAAATTAAAGTTCAA	37<<<<<<<<<<<<<<<<<<<<<<;;<;<<<<<<;	MF:i:18	Aq:i:25	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_105:8:160:130:351	147	chr2	697	99	35M	=	530	-202	CAAAAGAATTGTAAAAGTCAAAATTAAAGTTCAAT	4<;;<;<<<-<<<<<<<<<<;;<<<<;<<<<<<<<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_593:7:189:530:40	163	chr2	698	99	36M	=	883	221	AAAAGAATTGTAAAAGTCAAAATTAAAGTTCAATAC	<<<<<<<<<<;<<<<<:<<<<<<<<<<<<<<;<<<;	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_105:7:168:247:414	99	chr2	698	99	35M	=	876	213	AAAAGAATTGTAAAAGTCAAAATTAAAGTTCAATA	<<<<<<<<<<<<<<<<*<<<<<<<<<;:6<<<<<;	MF:i:18	Aq:i:67	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_65:6:197:759:975	83	chr2	698	99	35M	=	537	-196	AAAAGAATTGTAAAAGTCAAAATTAAAGTTCAATA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:78	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_19:5:29:411:1208	99	chr2	698	99	40M	=	882	224	AAAAGAATTGTAAAAGTCAAAATTAAAGTTCAATACTCAC	<<<<;<<<<<<<<<<<;<<<<<<<<<<<<<<<<<<;;;;;	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_589:1:110:543:934	83	chr2	700	99	35M	=	514	-221	AAGAATTGTAAAAGTCAAAATTAAAGTTCAATACT	<<<<<5<<;<<<<<<;<<<<<<<<<<<;<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_26:3:287:665:495	83	chr2	702	99	35M	=	530	-207	GAATTGTAAAAGTCAAAATTAAAGTTCAATACTCA	===,9=;;====7=====5===;==1=========	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS218_1:8:70:445:1289	147	chr2	702	99	35M	=	535	-202	GAATTGTAAAAGTCAAAATTAAAGTTCAATACTCA	<<<:<<<<<<<<<;<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_105:6:172:827:592	163	chr2	703	99	35M	=	899	231	AATTGTAAAAGTCAAAATTAAAGTTCAATACTCAC	=;=======;==;===:==========;==9<<.3	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS112_32:7:135:401:735	147	chr2	703	99	35M	=	510	-228	AATTGTAAAAGTCAAAATTAAAGTTCAATACTCAC	<<::7<<<<<<::<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:3:39:208:644	99	chr2	704	99	35M	=	859	190	ATTGTAAAAGTCAAAATTAAAGTTCAATACTCACC	<;<<<<<;;:<<;;<<<<<<;;;;;;.<;<79997	MF:i:18	Aq:i:67	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_19:1:99:1632:76	147	chr2	705	99	40M	=	553	-192	TTGTAAAAGTCAAAATTAAAGTTCAATACTCACCATCATA	4641::<<4<<<<<<<<<<<;<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:47	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_1:2:52:1144:509	99	chr2	706	99	35M	=	867	196	TGTAAAAGTCAAAATTAAAGTTCAATACTCACCAT	<<<<<<<<<<<<<<<<<<<;<<<<<<<;<;<<;<<	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_610:7:116:157:612	99	chr2	707	99	35M	=	889	217	GTAAAAGTCAAAATTAAAGTTCAATACTCACCATC	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_19:1:36:481:1079	163	chr2	707	99	40M	=	881	214	GTAAAAGTCAAAATTAAAGTTCAATACTCACCATCATAAA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<::::8	MF:i:18	Aq:i:70	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_19:5:74:668:424	147	chr2	707	99	40M	=	545	-202	GTAAAAGTCAAAATTAAAGTTCAATACTCACCATCATAAA	:::::<<96<<<<<;<<<;<<5<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_65:7:122:398:994	163	chr2	708	99	35M	=	871	198	TAAAAGTCAAAATTAAAGTTCAATACTCACCATCA	<:<9<<<<<<4<<<;9<<<<<98<;<<<:;<;<;7	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_11:4:36:1231:1381	99	chr2	708	99	35M	=	891	218	TAAAAGTCAAAATTAAAGTTCAATACTCACCATCA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_19:5:57:366:844	163	chr2	708	99	40M	=	877	209	TAAAAGTCAAAATTAAAGTTCAATACTCACCATCATAAAT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<::::7:	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_61:6:307:208:477	83	chr2	710	99	35M	=	546	-199	AAAGTCAAAATTAAAGTTCAATACTCACCATCATA	<<<<<.<<<<<<<<<<<<;<;<<<<<<<<<<<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_64:3:285:417:147	147	chr2	712	99	35M	=	529	-218	AGTCAAAATTAAAGTTCAATACTCACCATCATAAA	<..)<<<<;<<<<7<;-<<;<<<<<;8<<<<<<<<	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_59:5:325:544:349	83	chr2	716	99	35M	=	515	-236	AAAATTAAAGTTCAATACTCACCATCATAAATACA	<<<<57<<<7<;6<<<<;<7<7;<<7<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_63:2:33:357:858	163	chr2	716	99	35M	=	870	189	AAAATTAAAGTTCAATACTCACCATCATAAATACA	<<<<<<<<<<<<<<<<:<<<<<<:<<<<;<<<<<<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_19:4:78:806:800	83	chr2	717	99	40M	=	564	-193	AAATTAAAGTTCAATACTCACCATCATAAATACACACAAA	::;9:<<<;<<:<<<<:<.<1:<<1<<<<<<;<<<<<<<<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_11:5:41:314:1173	147	chr2	718	99	35M	=	554	-199	AATTAAAGTTCAATACTCACCATCATAAATACACA	<<2**<<82/<<<<<<<<<<9<<<<<<<<<<<<<<	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_30:2:82:963:128	163	chr2	719	99	35M	=	905	221	ATTAAAGTTCAATACTCACCATCATAAATACACAC	<<<<<<<<<<<<<<<<<<<;<<<<<<<<<<<;<<;	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_65:8:240:719:799	99	chr2	720	99	35M	=	900	215	TTAAAGTTCAATACTCACCATCATAAATACACACA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<7<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_589:7:93:634:323	147	chr2	721	99	35M	=	550	-206	TAAAGTTCAATACTCACCATCATAAATACACACAA	<<<<;<;<<<<;;<<2<:<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_19:2:12:1335:1372	163	chr2	721	99	40M	=	906	225	TAAAGTTCAATACTCACCATCATAAATACACACAAAAGTA	<<<<<<<<<<<<<<<<<<<<<<<<:<<<<<<<<<99::.:	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_64:4:116:738:142	147	chr2	722	99	35M	=	568	-189	AAAGTTCAATACTCACCATCATAAATACACACAAA	<:<7;+:<<:<<<;<<<<<;<<<<<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_81:2:49:330:699	83	chr2	722	99	35M	=	540	-217	AAAGTTCAATACTCACCATCATAAATACACACAAA	===/=;========;=;==================	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_57:7:273:562:954	147	chr2	722	99	35M	=	539	-218	AAAGTTCAATACTCACCATCATAAATACACACAAA	;<<+;95<<<;5;<<;:<<;<<<<<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS218_1:6:77:1529:522	147	chr2	722	99	35M	=	562	-195	AAAGTTCAATACTCACCATCATAAATACACACAAA	<<<;7;,<<<<<<.<,6<<6<<<<<<<;<<<<<<<	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_3:2:67:1467:1447	163	chr2	722	99	35M	=	898	211	AAAGTTCAATACTCACCATCATAAATACACACAAA	<<<<<<<<<<<<<<<<<<<<<<7<<<<<<<<<<<<	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_28:2:251:819:772	99	chr2	726	99	36M	=	881	191	TTCAATACTCACCATCATAAATACACACAAAAGTAC	<3<<<9<9<3<</<<<<<<59<3<9<<</9/++*/'	MF:i:18	Aq:i:59	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_597:4:144:492:61	147	chr2	728	99	35M	=	564	-199	AAATACTCACCATCATAAATACACACAAAAGTACA	+;;3;,:7<:;<<7<<<<<<<;;<<<<<<<<<<<<	MF:i:18	Aq:i:69	NM:i:1	UQ:i:11	H0:i:1	H1:i:0
+EAS54_73:7:200:65:291	99	chr2	728	99	35M	=	930	237	CAATACTCACCATCATAAATACACACAAAAGTACA	<<<<1<<<<<<<<<<<<<<<<<<<:<8<<<<:<;<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_26:2:130:609:467	99	chr2	728	99	35M	=	877	184	CAATACTCACCATCATAAATACACACAAAAGTACA	==8=====;==8==;=4=;;8=====;6=177.==	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_93:6:216:47:302	147	chr2	729	99	35M	=	557	-207	AATACTCACCATCATAAATACACACAAAAGTACAA	<<;<8<:<6<<<;<<<<<<<;<<<<<<<<<<<<<<	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_66:7:4:234:610	83	chr2	729	84	35M	=	560	-204	AAAAATCAACATCACAAATACACACAAAAGTACAA	<:+:'+&<+'<+'2&<:<7<2<':2<:<<7<7<<<	MF:i:18	Aq:i:22	NM:i:4	UQ:i:31	H0:i:0	H1:i:0
+EAS54_81:8:271:180:509	99	chr2	729	99	35M	=	896	202	AATACTCACCATCATAAATACACACAAAAGTACAA	=============================='====	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_81:8:41:530:663	163	chr2	730	99	35M	=	908	213	ATACTCACCATCATAAATACACACAAAATTACAAA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<7;;;;<<	MF:i:18	Aq:i:74	NM:i:1	UQ:i:22	H0:i:1	H1:i:0
+EAS114_39:4:30:570:902	83	chr2	730	99	35M	=	561	-204	ATACTCACCATCATAAATACGCACAAAAGTACAAA	<:<6:6<&:<<6<<<<<<<<.<<<<<<<<<<<<<<	MF:i:18	Aq:i:43	NM:i:1	UQ:i:13	H0:i:0	H1:i:1
+EAS1_105:1:87:430:995	99	chr2	731	67	35M	=	909	213	TACTCACCATCATAAATACACACAAAATTACAAAA	<<;<<7;;;<;<<777;7(77;;1;7;%117;,7(	MF:i:18	Aq:i:30	NM:i:1	UQ:i:4	H0:i:0	H1:i:1
+EAS114_28:7:215:863:521	163	chr2	732	99	36M	=	890	194	ACTCACCATCATAAATACACACAAAAGTACAAAACT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<<<<;	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_59:4:267:394:437	83	chr2	735	99	35M	=	544	-226	AAACATCATAAATACACACAAAAGTACAAAACTCA	&<&,<8.<;<<<;<8<8<7<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:66	NM:i:2	UQ:i:10	H0:i:1	H1:i:0
+EAS1_108:6:94:294:387	83	chr2	736	99	35M	=	578	-193	ACCATCATAAATACACACAAAAGTACAAAACTCAC	779=53=9===;=:=;=========;=========	MF:i:18	Aq:i:51	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_593:6:38:332:54	163	chr2	737	99	36M	=	904	203	CCATCATAAATACACACAAAAGTACAAAACTCACAG	<;<<<<<<<<<<<<<<<<<<<<<<<<<<<0;;;<;;	MF:i:18	Aq:i:54	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_61:8:165:441:708	83	chr2	737	99	35M	=	550	-222	CCATCATAAATACACACAAAAGTACAAAACTCACA	6+<<:<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:54	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_93:5:246:177:525	147	chr2	738	98	35M	=	549	-224	CATCATAAATACACACAAAAGTAAAAAACTCACAG	%<(4<2<<<<<:<;<:<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:27	NM:i:1	UQ:i:27	H0:i:0	H1:i:1
+EAS114_26:5:43:114:617	83	chr2	738	99	35M	=	579	-194	AATCATAAATACACACAAAAGTACAAAACTCACAG	+=22=6=================9===========	MF:i:18	Aq:i:52	NM:i:1	UQ:i:10	H0:i:1	H1:i:0
+EAS1_99:8:152:778:228	163	chr2	739	99	35M	=	915	211	ATCATAAATACACACAAAAGTACAAAACTCACAGG	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<;	MF:i:18	Aq:i:54	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_108:3:24:319:429	83	chr2	740	99	35M	=	582	-193	TAATAAATACACACAAAAGTACAAAACTCACAGGT	0%=3%=3====<=9=====89==93==9=6=====	MF:i:18	Aq:i:56	NM:i:1	UQ:i:4	H0:i:1	H1:i:0
+EAS51_66:5:210:674:911	99	chr2	740	99	35M	=	904	199	TCATAAATACACACAAAAGTACAAAACTCACAGGT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;;<;	MF:i:18	Aq:i:54	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:7:88:451:1773	99	chr2	742	99	35M	=	902	195	ATAAATACACACAAAAGTACAAAACTCACAGGTTT	;;:::<:;:<<;:6::;:;;:::;;<;;;367177	MF:i:18	Aq:i:67	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:7:2:168:1878	147	chr2	743	37	35M	=	560	-218	TAAATACACACAAAAGTAGAAAACGCACCAGTTTT	*3/6)9.;;;;;;;;5;;);;;3;(;;;+(;7.)3	MF:i:130	Aq:i:37	NM:i:4	UQ:i:32	H0:i:0	H1:i:0
+EAS188_7:5:115:249:673	83	chr2	743	99	35M	=	552	-226	TAAATACACACAAAAGTACAAAACTCACAGGTTTT	:<<<;<<<;<9<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_65:8:178:187:610	99	chr2	744	99	35M	=	903	194	AAATACACACAAAAGTACAAAACTCACAGGTTTTA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_589:2:9:49:661	83	chr2	747	99	35M	=	591	-191	TACACACAAAAGTACAAAACTCACAGGTTTTATAA	<<6<5<<<<<<<<<<<<<<<<<<<7<<<<<<<<<<	MF:i:18	Aq:i:45	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_597:3:157:361:309	147	chr2	747	99	35M	=	589	-193	TACACACAAAAGTACAAAACTCACAGGTTTTATAA	:<-<5<0<<<<<<<;<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_62:3:103:443:166	83	chr2	747	99	35M	=	565	-217	TACACACAAAAGTACAAAACTCACAGGTTTTATAA	7<4<4<:<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_59:8:49:182:192	147	chr2	750	99	35M	=	582	-203	ACACAAAAGTACAAAACTCACAGGTTTTATAAAAC	<5<;<<<<<<<<<<<:<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:49	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS218_4:3:12:630:707	99	chr2	751	99	35M	=	915	199	CACAAAAGTACAAAACTCACAGGTTTTATAAAACA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:54	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS219_FC30151:7:94:1440:2016	83	chr2	751	99	35M	=	564	-222	CACAAAAGTACAAAACTCACAGGTTTTATAAAACA	:<8<<<<9<<9<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:51	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_71:4:206:741:810	163	chr2	753	99	35M	=	929	210	CAAAAGTACAAAACTCACAGGTTTTATAAAACAAT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;:-;<<	MF:i:18	Aq:i:48	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_71:7:250:698:842	83	chr2	753	99	34M	=	554	-233	AAAAAGTACAAAACTCACAGGTTTTATAAAACAA	)<<<<<<<-<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:39	NM:i:1	UQ:i:8	H0:i:1	H1:i:0
+EAS54_81:6:265:251:147	83	chr2	754	99	35M	=	581	-208	AAAAGTACAAAACTCACAGGTTTTATAAAACAATT	<<<<::<8<<<;<;8<8<<<<<<<<:<<<<<<<<<	MF:i:18	Aq:i:50	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_39:6:71:644:1792	83	chr2	754	84	35M	=	589	-200	AAAAGTACAAAACTCACAGGTTTTATAAAACAATT	<<<<;<<<<<<:;/<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_589:6:108:958:42	83	chr2	755	81	35M	=	584	-206	AAAGTACAAAACTCACAGGTTTTATAAAACAATTA	<<<;;</<<<<;<<<<<<<<<<<<<<<<<<<<<<+	MF:i:18	Aq:i:9	NM:i:1	UQ:i:27	H0:i:0	H1:i:3
+B7_597:8:48:805:860	147	chr2	755	78	35M	=	563	-227	AAAGTACAAAACTCACAGGTTTTATAAAACAATTA	<<<;3<;7<<97<7<<<<7<4<<<<<<<<<<;8<+	MF:i:18	Aq:i:13	NM:i:1	UQ:i:27	H0:i:0	H1:i:3
+B7_591:3:179:496:161	163	chr2	756	99	36M	=	919	199	AAGTACAAAACTCACAGGTTTTATAAAACAATTAAT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<+	MF:i:18	Aq:i:49	NM:i:2	UQ:i:53	H0:i:1	H1:i:0
+EAS56_59:3:166:626:836	83	chr2	757	99	35M	=	567	-225	AGTACAAAACTCACAGGTTTTATAAAACAATTAAT	<;;7<<<<<<;<7;<<<<<<<<<<<<7<<<<<<<+	MF:i:18	Aq:i:28	NM:i:2	UQ:i:54	H0:i:0	H1:i:0
+EAS114_28:5:23:944:377	147	chr2	757	75	36M	=	579	-214	AGTACAAAACTCACAGGTTTTATAAAACAATTAATT	<;7;8<<<<:<;<:<<<<<<<<<<<<<;<<<<<<<;	MF:i:130	Aq:i:75	NM:i:0	UQ:i:0	H0:i:0	H1:i:0
+EAS114_45:1:100:979:1863	147	chr2	757	85	35M	=	583	-209	ATTACAAAACTCACAGGTTTTATAAAACAATTAAT	6&,*3;6;66;9(572692;;;79;4)9;96;59+	MF:i:18	Aq:i:23	NM:i:3	UQ:i:51	H0:i:0	H1:i:0
+EAS219_1:3:90:219:528	83	chr2	758	75	35M	=	576	-217	GTACAAAACTCACAGGTTTTATAAAACAATTAATT	;:<5<<<<<<;<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:130	Aq:i:75	NM:i:0	UQ:i:0	H0:i:0	H1:i:0
+EAS1_108:5:89:942:84	83	chr2	759	74	35M	=	562	-232	TACAAAACTCACAGGTTTTATAAAACAATTAATTG	===================>=>>>==>>===>==>	MF:i:130	Aq:i:74	NM:i:0	UQ:i:0	H0:i:0	H1:i:0
+EAS1_108:6:159:493:275	99	chr2	760	72	35M	=	939	214	ACAAAACTCACAGGTTTTATAAAACAATTAATTGA	=====3=============================	MF:i:130	Aq:i:72	NM:i:0	UQ:i:0	H0:i:0	H1:i:0
+EAS139_11:1:81:1019:558	163	chr2	760	77	35M	=	926	201	ACAAAACTCACAGGTTTTATAAAACAATTAATTGA	<<<<<<<<<<<6<<<<<<<<<<<<<<<<<<<<<7<	MF:i:130	Aq:i:77	NM:i:0	UQ:i:0	H0:i:0	H1:i:0
+EAS51_62:7:162:195:761	163	chr2	767	30	18M4I13M	=	922	190	TCACAGGTTTTATAAAACAATTAATTGAGACTACA	<<<<<<<<<<<<<<<<<<<<<<<<<<;<:<<<<;;	MF:i:130	Aq:i:30	NM:i:0	UQ:i:0	H0:i:0	H1:i:0
+B7_597:3:115:646:430	147	chr2	768	45	17M4I14M	=	582	-217	CACAGGTTTTATAAAACAATTAATTGAGACTACAG	5;5<;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:130	Aq:i:45	NM:i:0	UQ:i:0	H0:i:0	H1:i:0
+EAS114_30:6:243:209:110	163	chr2	768	48	17M4I14M	=	920	187	CACAGGTTTTATAAAACAATTAATTGAGACTACAG	<<<<<;<;<<<;<<<<<<<<<<<;<:;<<:;;+85	MF:i:130	Aq:i:48	NM:i:0	UQ:i:0	H0:i:0	H1:i:0
+EAS1_108:2:266:994:429	147	chr2	769	76	16M4I15M	=	612	-188	ACAGGTTTTATAAAACAATTAATTGAGACTACAGA	</<<<<<<<<<<<<<;<<<<<<<;<<<<<<<<<<<	MF:i:130	Aq:i:76	NM:i:0	UQ:i:0	H0:i:0	H1:i:0
+EAS114_30:5:32:461:154	99	chr2	769	71	16M4I15M	=	945	211	ACAGGTTTTATAAAACAATTAATTGAGACTACAGA	<<<<<<<<<<<<<<<:<<<<<<<<<<<<<<<+<;;	MF:i:130	Aq:i:71	NM:i:0	UQ:i:0	H0:i:0	H1:i:0
+EAS114_39:6:7:492:1088	99	chr2	769	57	16M4I15M	=	926	192	ACAGGTTTTATAAAACAATTAATTGAGACTACAGA	<<<<<<<<<<<<<<<<<<<<<<<<7<:<<<<<<6;	MF:i:130	Aq:i:57	NM:i:0	UQ:i:0	H0:i:0	H1:i:0
+EAS1_95:6:174:650:125	147	chr2	770	76	15M4I16M	=	600	-201	CAGGTTTTATAAAACAATTAATTGAGACTACAGAG	===;===============================	MF:i:130	Aq:i:76	NM:i:0	UQ:i:0	H0:i:0	H1:i:0
+EAS56_59:6:89:457:591	147	chr2	770	69	15M4I16M	=	585	-216	CAGGTTTTATAAAACAATTAATTGAGACTACATAG	797<<9<<<<<<<3<7<<<<<<<<<<)<<<<<07<	MF:i:130	Aq:i:69	NM:i:1	UQ:i:15	H0:i:0	H1:i:0
+EAS114_39:2:38:670:564	99	chr2	770	73	15M4I16M	=	930	195	CAGGTTTTATAAAACAATTAATTGAGACTACAGAG	<<<<<<<<<<<<<<<<<<<<<<<;<:<<<<;<5<;	MF:i:130	Aq:i:73	NM:i:0	UQ:i:0	H0:i:0	H1:i:0
+EAS188_7:4:92:693:228	147	chr2	770	75	14M4I17M	=	601	-200	AAGGTTTTATAAAAAAATTAATTGAGACTACAGAG	6=77=<<=======&====================	MF:i:130	Aq:i:75	NM:i:1	UQ:i:28	H0:i:0	H1:i:0
+EAS218_1:4:61:1369:440	163	chr2	770	47	15M4I16M	=	964	229	CAGGTTTTATAAAACAATTAATTGAGACTACAGAG	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<:<8	MF:i:130	Aq:i:47	NM:i:0	UQ:i:0	H0:i:0	H1:i:0
+EAS114_26:4:123:1001:580	83	chr2	771	43	14M4I17M	=	617	-185	AGGTTTTATAAAACAATTAATTGAGACTACAGAGC	<.00..3<6<<<<<<<3;<<08<<<<<6<<<<<<<	MF:i:130	Aq:i:43	NM:i:0	UQ:i:0	H0:i:0	H1:i:0
+EAS114_39:4:10:1312:1558	163	chr2	771	76	14M4I17M	=	928	192	AGGTTTTATAAAACAATTAATTGAGACTACAGAGC	5<<<<<<<<<<<<<<<<<<<<<<<;;<<<<<;8;<	MF:i:130	Aq:i:76	NM:i:0	UQ:i:0	H0:i:0	H1:i:0
+EAS220_1:8:45:178:1321	83	chr2	771	77	14M4I17M	=	606	-196	AGGTTTTATAAAACAATTAATTGAGACTACAGAGC	<<<<<<<<<<<<<<<<<:<<:<<<<<<<<<<<<<<	MF:i:130	Aq:i:77	NM:i:0	UQ:i:0	H0:i:0	H1:i:0
+EAS56_59:5:125:137:58	163	chr2	772	76	13M4I18M	=	932	195	GGTTTTATAAAACAATTAATTGAGACTACAGAGCA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<9;<	MF:i:130	Aq:i:76	NM:i:0	UQ:i:0	H0:i:0	H1:i:0
+EAS192_3:3:285:349:797	83	chr2	773	76	12M4I19M	=	604	-200	GTTTTAAAAAACCAATAATTGAGACTACAGAGCAA	;;<<<7.:<<<..<.<<<<<<<<<<<<<<<<<<<<	MF:i:130	Aq:i:76	NM:i:1	UQ:i:13	H0:i:0	H1:i:0
+EAS114_45:5:56:1757:1319	163	chr2	775	67	10M4I21M	=	957	217	TTTATAAAACAATTAATTGAGACTACAGAGCAACT	;;;;9;;;;;;;;;;;;;4;9;98;;;;;9388&7	MF:i:130	Aq:i:67	NM:i:0	UQ:i:0	H0:i:0	H1:i:0
+B7_591:3:291:404:199	83	chr2	777	76	8M4I24M	=	612	-197	TATAAAACAATTAATTGAGACTACAGAGCAACTAGG	<<<<<<<7<<9<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:130	Aq:i:76	NM:i:0	UQ:i:0	H0:i:0	H1:i:0
+EAS54_65:7:159:253:353	83	chr2	778	67	7M4I24M	=	613	-196	ATAAAACAATTAATTGAGACTACAGAGCAACTAGG	<8<<<<:<<;;<<<<<<<<<<<;<<<<<<<<<<<<	MF:i:130	Aq:i:67	NM:i:0	UQ:i:0	H0:i:0	H1:i:0
+EAS56_57:1:122:38:103	163	chr2	778	79	7M4I24M	=	972	229	ATAAAACAATTAATTGAGACTACAGAGCAACTAGG	<<<<<<<<<<<<<<<<;<<<<<<<<3<<<<9<8;<	MF:i:130	Aq:i:79	NM:i:0	UQ:i:0	H0:i:0	H1:i:0
+EAS188_4:5:103:870:105	147	chr2	778	44	7M4I24M	=	595	-214	ATAAAACAATTAATTGAGACTACAGAGCAACTAGG	<<<<<<<<<<<<<=<:<;<<<<<<<<<<*<<<<<<	MF:i:130	Aq:i:44	NM:i:0	UQ:i:0	H0:i:0	H1:i:0
+EAS1_105:8:24:718:322	163	chr2	779	23	35M	=	953	209	ACAATTAATTGAGACTACAGACCAATTATGTAAAA	5/7<3+<;<1<<1<95<.&&.&&.<&)5)1)17<%	MF:i:130	Aq:i:23	NM:i:3	UQ:i:18	H0:i:0	H1:i:0
+EAS51_64:6:118:41:489	83	chr2	779	76	35M	=	588	-226	ACAATTAATTGAGACTACAGAGCAACTAGGTAAAA	<+<<;<<<38<<<<5<<3<<<<3<<8<<<<<<<<<	MF:i:130	Aq:i:76	NM:i:0	UQ:i:0	H0:i:0	H1:i:0
+EAS56_61:3:165:665:220	83	chr2	779	76	35M	=	618	-196	ACAATTAATTGAGACTACAGAGCAACTAGGTAAAA	<:<<;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:130	Aq:i:76	NM:i:0	UQ:i:0	H0:i:0	H1:i:0
+EAS114_30:6:238:803:383	99	chr2	779	75	35M	=	954	210	ACAATTAATTGAGACTACAGAGCAACTAGGTAAAA	<<<<<<<<<<<<;<<<<<;<;<<;<<;<<<9<;<<	MF:i:130	Aq:i:75	NM:i:0	UQ:i:0	H0:i:0	H1:i:0
+EAS1_105:3:232:364:583	99	chr2	780	71	35M	=	956	211	CAATTAATTGAGACTACAGAGCAACTAGGTAAAAA	<<<<<<<<<<<<<<<<<<<<<<<<;<<<<<<<<<<	MF:i:130	Aq:i:71	NM:i:0	UQ:i:0	H0:i:0	H1:i:0
+EAS139_19:2:2:1217:398	83	chr2	780	99	40M	=	608	-212	CAATTAATTGAGACTACAGAGCAACTAGGTAAAAAATTAA	+;;:9<<66<<<;+<<7<<<<;<<+;<<<<<<<<<<<<<<	MF:i:18	Aq:i:71	NM:i:3	UQ:i:73	H0:i:1	H1:i:0
+B7_593:2:81:435:410	99	chr2	782	99	36M	=	966	220	ATTAATTGAGACTACAGAGCAACTAGGTAAAAAATT	<<<<<<<<<<<<<<<<<<<<<<<<<:<<<<<;<<;;	MF:i:18	Aq:i:29	NM:i:2	UQ:i:54	H0:i:0	H1:i:0
+B7_593:3:115:649:259	147	chr2	782	99	36M	=	617	-201	ATTAATTGAGAATACAGAGCAACTAGGTAAAAAATT	;<;<<;<<<<;&<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:45	NM:i:3	UQ:i:58	H0:i:0	H1:i:1
+EAS1_93:3:181:93:694	163	chr2	783	99	35M	=	954	206	TTAATTGAGACTACAGAGCAACTAGGTAAAAAATT	++<<<<<<;<<<<<<:;8<<;<<<5;<;<<<+<<<	MF:i:18	Aq:i:28	NM:i:2	UQ:i:54	H0:i:0	H1:i:0
+EAS114_30:1:188:863:790	163	chr2	783	98	35M	=	969	221	TTAATTGAGACTACAGAGCAACTAGGTAAAAAATT	++<;<<;;;:<<<<:<:<<:1<<1<<<6:6;4;;4	MF:i:18	Aq:i:27	NM:i:2	UQ:i:54	H0:i:0	H1:i:0
+EAS1_93:2:313:711:530	163	chr2	784	99	35M	=	968	219	TAATTGAGACTACAGAGCAACTAGGTAAAAAATTA	+<<<<<<<<<<<<<<<<<<<<<<;<<<<<<<<<<:	MF:i:18	Aq:i:47	NM:i:1	UQ:i:27	H0:i:0	H1:i:1
+B7_589:7:154:26:712	99	chr2	786	99	35M	=	959	208	ATTGAGACTACAGAGCAACTAGGTAAAAAATTAAC	<<<<<<<<<<<;<<<<<<<<<<<<<<<<<<<<<<;	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_28:6:185:87:475	163	chr2	786	99	36M	=	949	199	ATTGAGACTACAGAGCAACTAGGTAAAAAATTAACA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<6;	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_19:4:69:1593:819	163	chr2	786	99	40M	=	977	231	ATTGAGACTACAGAGCAACTAGGTAAAAAATTAACATTAC	<<<<<<<<<<<<<<;<<<<<;;<:<<<<<:<<<<<:777:	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS192_3:3:309:187:267	83	chr2	786	99	35M	=	616	-205	ATTGAGACTACAGAGCAACTAGGTAAAAAATTAAC	<:0;<;<4<<7<<<<:<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS218_1:8:82:1540:77	83	chr2	786	99	35M	=	619	-202	ATTGAGACTACAGAGCAACTAGGTAAAAAATTAAC	<48;<;</;<<<<<<:<<0<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_97:2:193:420:78	147	chr2	787	99	35M	=	607	-215	TTGAGACTACAGAGCAACTAGGTAAAAAATTAACA	81<<;<9<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_97:4:261:267:597	83	chr2	787	86	35M	=	617	-205	TTGAGAATAAAGAGCAACTAGGTAAAAAATTAACA	*-1<9<+1<+<<<<:<<;9<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:41	NM:i:2	UQ:i:20	H0:i:0	H1:i:1
+EAS56_59:4:262:928:237	99	chr2	787	99	35M	=	971	219	TTGAGACTACAGAGCAACTAGGTAAAAAATTAACA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<7<<	MF:i:18	Aq:i:47	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_65:5:262:53:888	163	chr2	787	99	35M	=	965	213	TTGAGACTACAGAGCAACTAGGTAAAAAATTAACA	<<<<<<<<;<<<<<<<<<<;<<;<;<;6<<;<;;<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_597:4:138:211:582	99	chr2	788	99	35M	=	957	204	TGAGACTACAGAGCAAATAGGTAAAAAATTAACAT	<<;<<<<<<<<<<<<<&;<;<7<<;<<<<<<<5<<	MF:i:18	Aq:i:45	NM:i:1	UQ:i:5	H0:i:0	H1:i:1
+B7_597:7:113:408:211	99	chr2	789	99	35M	=	952	198	GAGACTACAGAGCAACTAGGTAAAAAATTAACATT	<<<<<<<<<<<<<<<:&<<<&:<<<<<<<<<<;:/	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_93:3:79:879:15	147	chr2	790	99	35M	=	626	-199	AGACTACAGAGCAACTAGGTAAAAAATTAACATTA	<;;5;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_65:4:325:795:213	83	chr2	790	99	35M	=	618	-207	AGACTACAGAGCAACTAGGTAAAAAATTAACATTA	<<<0<<;<<<<;<<;:<<<<<<<<<<<;<<<<<9<	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS112_34:4:22:206:150	83	chr2	792	99	35M	=	619	-208	AAAAAAGAGCAACTAGGTAAAAAATTAACATTACA	8&)<)<<<<+<<+<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:65	NM:i:3	UQ:i:21	H0:i:1	H1:i:0
+EAS56_59:5:181:713:140	147	chr2	793	84	35M	=	615	-213	CTACAGAGCAACAAGGTAAAAAATTAACATTACAA	78<+<7<-7;;;&<5<7<<<<7<<<<<<<<<<<7<	MF:i:18	Aq:i:41	NM:i:1	UQ:i:5	H0:i:0	H1:i:1
+B7_589:7:76:306:561	163	chr2	794	89	35M	=	987	228	TACAGAGCAACTAGGTAAAAAATTAACATTACAAC	<<)<<<<<<8<<8<<<<<<<;;;<<1<<3;=7<<9	MF:i:18	Aq:i:20	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_93:4:325:352:67	83	chr2	794	99	35M	=	622	-207	TACAGAGCAACTAGGTAAAAAATTAACATTACAAC	;<8<<<;;<<7<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_66:4:310:287:420	99	chr2	794	99	35M	=	965	206	TACAGAGCAACTAGGTAAAAAATTAACATTACAAC	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<;;;	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS188_7:5:74:329:459	83	chr2	795	99	35M	=	623	-207	ACAGAGCAACTAGGTAAAAAATTAACATTACAACA	</<;<8/<<9<<<;<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_1:6:57:1342:1166	99	chr2	796	99	35M	=	964	203	CAGAGCAACTAGGTAAAAAATTAACATTACAACAG	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<;<;	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_1:2:3:542:428	163	chr2	797	99	35M	=	965	203	AGAGCAACTAGGTAAAAAATTAACATTACAACAGG	7<4<<<6<<,<9)<<<<6<,<<7<<7<<<<<<<<1	MF:i:18	Aq:i:41	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_73:7:97:892:419	83	chr2	800	99	35M	=	621	-214	GCAACTAGGTAAAAAATTAACATTACAACAGGAAC	;8<<;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_19:6:82:1051:921	83	chr2	800	99	40M	=	616	-224	GCAAATAGGTAAAAAATTAACATTACAACAGGAACAAAAC	3-::-7<;+:9<;<<<5<;9,::53-;:3<<<<9<<3<<<	MF:i:18	Aq:i:41	NM:i:1	UQ:i:12	H0:i:1	H1:i:0
+EAS1_95:5:263:511:936	147	chr2	801	99	35M	=	629	-207	CAAATAGGTAAAAAATTAACATTACAACAGGAACA	+<<%<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:71	NM:i:1	UQ:i:4	H0:i:1	H1:i:0
+EAS114_26:7:157:876:302	163	chr2	801	99	35M	=	964	198	CAACTAGGTAAAAAATTAACATTACAACACGAACA	2<<;<<<22<<<<<<77<<<<22<7<<<<%-<<1<	MF:i:18	Aq:i:66	NM:i:1	UQ:i:4	H0:i:1	H1:i:0
+EAS54_65:2:127:288:655	163	chr2	803	99	35M	=	999	231	ACTAGGTAAAAAATTAACATTACAACAGGAACAAA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<;<<;;	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_97:4:83:731:540	147	chr2	804	99	35M	=	623	-216	CTAGGTAAAAAATTAACATTACAACAGGAACAAAA	;7<:+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:5:82:843:1838	99	chr2	804	99	35M	=	999	230	CTAGGTAAAAAATTAACATTACAACAGGAACAAAA	;<<;:;;<<<;;<<<<;;<<;;;;;<;;;;68887	MF:i:18	Aq:i:67	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_57:5:71:994:576	147	chr2	805	99	35M	=	655	-185	TAGGTAAAAAATTAACATTACAACAGGAACAAAAC	<<9;;<<<<<<<<<;<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_65:8:24:415:944	99	chr2	805	99	35M	=	974	204	TAGGTAAAAAATTAACATTACAACAGGAACAAAAC	<<<<<<<<<<<<<<<<<<<<<:<<<<<<<<<<<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS219_FC30151:3:73:1458:1337	83	chr2	806	99	35M	=	609	-232	AGGTAAAAAATTAACATTACAACAGGAACAAAACC	<</<<<<<<<6:<::<<<1<<:<<<<<<<<<<<<<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_95:2:142:353:398	163	chr2	807	99	35M	=	977	205	GGTAAAAAATTAACATTACAACAGGAACAAAACCT	=================================9=	MF:i:18	Aq:i:79	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_95:7:46:522:426	163	chr2	807	99	35M	=	964	192	GGTAAAAAATTAACATTACAACAGGAACAAAACCT	=======================:==;<===78==	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_30:7:59:871:351	163	chr2	808	99	35M	=	963	190	GTAAAAAATTAACATTACAACAGGAACAAAACCTC	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<<;	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS192_3:6:235:505:553	163	chr2	808	99	35M	=	987	214	GTAAAAAATTAACATTACAACAGGAACAAAACCTC	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<;:;:	MF:i:18	Aq:i:54	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS219_1:1:60:1420:660	83	chr2	808	99	35M	=	649	-194	GTAAAAAATTAACATTACAACAGGAACAAAACCTC	99<<<<<<<<<<;<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_593:3:180:89:582	147	chr2	809	99	36M	=	650	-195	TAAAAAATTAACATTACAACAGGAACAAAACCTCAT	;<<<<<<4<<<:<<<<<<<<<6<<<<<<<<<<;<<<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_103:3:323:196:855	83	chr2	809	99	35M	=	642	-202	TAAAAAATTAACATTACAACAGGAACAAAACCTCA	&<<<<<<09<<7<7;<;<<0<<<<<;<<<<<<<<<	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS188_4:5:295:547:216	163	chr2	809	99	35M	=	970	196	TAAAAAATTAACATTACAACAGGAACAAAACCTCA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<<;	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_99:7:126:361:250	99	chr2	810	99	35M	=	1002	227	AAAAAATTAACATTACAACAGGAACAAAACCTCAT	<<<<<<;9<<<<<<<<<<<<<<;;;<<<;<664;;	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_57:5:266:133:789	99	chr2	810	99	35M	=	988	213	AAAAAATTAACATTACAACAGGAACAAAACCTCAT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_108:5:175:149:296	83	chr2	811	99	35M	=	614	-232	AAAAATTAACATTACAACAGGAACAAAACCTCATA	=;==26==;==;================7======	MF:i:18	Aq:i:45	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_610:5:136:260:254	99	chr2	813	99	35M	=	988	210	AAATTAACATTACAACAGGAACAAAACCTCATATA	<<<<<<<<<<<<<<<<<<><<<<<<<<<<<<<<<<	MF:i:18	Aq:i:54	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_19:1:85:1521:58	147	chr2	813	99	40M	=	639	-214	AAATTAACATTACAACAGGAACAAAACCTCATATATCAAT	:::86<<:<<8<<<<;<<8<<<<<<<<<<<<<<<;<<<<<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS188_7:4:164:719:947	99	chr2	813	99	35M	=	1005	227	AAATTAACATTACAACAGGAACAAAACCTCATATA	<<<<<<<<<<<<<<<<<<<;<<<<<<<<<;<<<<<	MF:i:18	Aq:i:64	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS219_1:1:50:257:341	163	chr2	813	99	35M	=	971	193	AAATTAACATTACAACAGGAACAAAACCTCATATA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<7<6<<<<	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_67:5:117:33:262	83	chr2	814	99	35M	=	642	-207	AATTAACATTACAACAGGAACAAAACCTCATATAT	<<;;<<;<:8<7<<;<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS218_1:8:90:706:1276	163	chr2	814	99	35M	=	980	201	AATTAACATTACAACAGGAACAAAACCTCATATAT	<<<<<<<<<<<<<<<<<<<<<<;<<<<<<<<:<:<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_108:2:116:966:193	163	chr2	815	99	35M	=	967	187	ATTAACATTACAACAGGAACAAAACCTCATATATC	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<<<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_11:1:59:742:549	147	chr2	816	99	35M	=	642	-209	TTAACATTACAACAGGAACAAAACCTCATATATCA	-<<<3<<<<6<<6<<<<<6<<<<6<<<<<<<<<<<	MF:i:18	Aq:i:48	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_11:7:74:213:877	99	chr2	816	99	35M	=	996	215	TTAACATTACAACAGGAACAAAACCTCATATATCA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:2
+B7_610:3:85:219:371	163	chr2	817	99	35M	=	967	185	TAACATTACAACAGGAACAAAACCTCATATATCAA	<<<<<<<<<<<<<<<<<<<<<:<<<<<<<<<<;<;	MF:i:18	Aq:i:54	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_108:2:176:653:957	163	chr2	819	82	35M	=	982	198	ACATTACAACAGGAACAAAACCTCATATATCAATA	????????????<<???@<<<<<@<<<<<<<<<<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_30:1:64:526:339	163	chr2	819	96	35M	=	1019	235	ACATTACAACAGGAACAAAACCTCATATATCAATA	<<<<<<<<;<<<<<<<<<<7<:<<<<<<<<<8:<:	MF:i:18	Aq:i:47	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_71:7:97:743:602	83	chr2	821	99	34M	=	644	-211	ATTACAACAGGAACAAAACCTCATATATCAATAT	<(&<:<<&<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:26	NM:i:0	UQ:i:0	H0:i:2	H1:i:6
+B7_610:2:75:887:149	163	chr2	823	99	35M	=	1004	216	TACAACAGGAACAAAACCTCATATATCAATATTAA	<<<<<<<<<<<<<<;<<<<<<<;<<<<<<<;<;;;	MF:i:18	Aq:i:23	NM:i:0	UQ:i:0	H0:i:1	H1:i:2
+EAS221_1:2:73:955:728	83	chr2	823	44	35M	=	660	-198	TACAACAGGAACAAAACCTCATATATCAATATTAA	;<-<<6<;<<<6<<<<;7<6<<<<<<<<<<<<<<<	MF:i:18	Aq:i:14	NM:i:0	UQ:i:0	H0:i:3	H1:i:18
+EAS1_108:2:102:543:160	163	chr2	825	99	35M	=	977	187	CAACAGGAACAAAACCTCATATATCAATATTAACT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<6<:<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:2
+EAS114_28:2:55:562:403	83	chr2	825	99	36M	=	643	-218	CAACAGGAACAAAACCTCATATATCAATATTAACTT	+<<&<<<<<<<<<<+<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:51	NM:i:0	UQ:i:0	H0:i:1	H1:i:5
+B7_593:1:19:695:59	99	chr2	826	99	36M	=	988	198	AACAGGAACAAAACCTCATATATCAATATTAACTTT	<<<<<<<<<<<;<<<<<<<<<;<<;;<;<<7<<<<;	MF:i:18	Aq:i:49	NM:i:0	UQ:i:0	H0:i:1	H1:i:3
+EAS221_1:2:8:327:522	163	chr2	826	99	35M	=	1001	210	AACAGGAACAAAACCTCATATATCAATATTAACTT	<<<<<<<<<<:<<<<<<<<<<:<<<<<<<<<:<<<	MF:i:18	Aq:i:49	NM:i:0	UQ:i:0	H0:i:1	H1:i:3
+EAS114_45:6:90:561:850	163	chr2	827	85	35M	=	1004	212	ACAGGAACAAAACCTCATATATCAATATTAACTTT	;;;;;;;;;;;;;;;;;;;;;;;;9;9;6;77777	MF:i:18	Aq:i:19	NM:i:0	UQ:i:0	H0:i:2	H1:i:25
+EAS56_61:5:209:824:866	83	chr2	828	73	35M	=	665	-198	CAGCAACAAAACCTCATATATCAATATTAACTTTG	;<:&<<:<<<<;<<;<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:19	NM:i:1	UQ:i:5	H0:i:1	H1:i:7
+EAS139_11:2:31:628:1820	83	chr2	828	98	35M	=	675	-188	CAGGAACAAAACCTCATATATCAATATTAACTTTG	<<<<<<:<<<<:6<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:20	NM:i:0	UQ:i:0	H0:i:1	H1:i:5
+EAS220_1:4:6:1178:1105	147	chr2	830	93	35M	=	657	-208	GGAACAAAACCTCATATATCAATATTAACTTTGAA	<:<<9<<<<::7<<;<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:17	NM:i:0	UQ:i:0	H0:i:1	H1:i:11
+EAS114_28:4:305:707:258	99	chr2	831	58	36M	=	992	197	GAACAAAACCTCATATATCAATATTAACTTTGAATA	9<<<<<<<<<<<<;<<-<<;;<;<<9<<;<<+99;7	MF:i:18	Aq:i:17	NM:i:0	UQ:i:0	H0:i:2	H1:i:9
+EAS54_67:3:114:736:433	163	chr2	832	63	35M	=	998	201	AACAAAACCTCATATATCAATATTAACTTTGAATA	;<<9<8;<<<<8<8<;<<;;;0<<8;<;<<47;;;	MF:i:18	Aq:i:18	NM:i:0	UQ:i:0	H0:i:1	H1:i:3
+B7_591:7:157:447:758	99	chr2	833	99	36M	=	994	197	ACAAAACCTCATATATCAATATTAACTTTGAATAAA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<<;<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:2
+B7_591:4:159:508:571	99	chr2	834	84	36M	=	989	191	CAAAACCTCATATATCAATATTAACTTTGAATAAAA	<<<<<<<<<<<<<<;<<<<<<<<<<<<<<<<<<<<;	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:3
+EAS54_65:7:68:825:405	163	chr2	835	30	35M	=	1015	215	AAAACCTCATATATCAATATTAACTTTGAATAAAA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;;;9	MF:i:18	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:5
+B7_593:3:102:856:670	99	chr2	836	99	36M	=	1025	225	AAACCTCATATATCAATATTAACTTTGAATAAAAAG	<<<<<<<;<<<;<<;:<<<<<<<<<<:;;<<;<<<7	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_61:3:260:827:289	163	chr2	836	99	35M	=	999	198	AAACCTCATATATCAATATTAACTTTGAATAAAAA	<<<<2<<<<;<<<<;<<<<<<:<<<&-<8<<88<3	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:5
+EAS114_28:1:220:801:282	147	chr2	837	99	36M	=	660	-213	AACCTCATATATCAATATTAACTTTGAATAAAAAGG	;7;87;===;==;====:===<==7===========	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_3:4:57:1675:720	147	chr2	841	99	35M	=	684	-192	TCATATATCAATATTAACTTTGAATAAAAAGGGAT	<,<<<<<<:<<<<<<<<:9<<<<<<<<;<<<<<<<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_30:2:297:949:26	83	chr2	842	99	35M	=	676	-201	CATATATCAATATTAACTTTGAATAAAAAGGGATT	5<;<;<;:<<<<<<<<;<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:51	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS219_FC30151:1:76:34:691	89	chr2	843	58	35M	*	0	0	ATATATCAATATTAACTTTGAATAAAAAGGGATTA	<<<<<<16<<<<<916<<<499<966161919<<<	MF:i:32	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_597:5:98:995:929	83	chr2	844	99	35M	=	680	-199	TATAACAATATTAACTTTGAATAAAAAGGGATTAA	&<+<'7<<+<&<<<7+4<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:63	NM:i:1	UQ:i:6	H0:i:1	H1:i:0
+EAS139_19:3:58:923:1915	163	chr2	846	99	40M	=	1007	201	TATCAATATTAACTTTGAATAAAAAGGGATTAAATTCCCC	<<<<<<<<<<<<<<<<<<<<<<<<<;<;<<<<<<<:::::	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_64:4:181:476:394	83	chr2	847	99	35M	=	666	-216	AACAATATTAACTTTGAATAAAAAGGGATTAAATT	<+;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:54	NM:i:1	UQ:i:10	H0:i:1	H1:i:0
+EAS112_32:7:322:391:742	147	chr2	847	99	35M	=	667	-215	ATCAATATTAACTTTGAATAAAAAGGGATTAAATT	<63<<<<9<<<:<;<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_11:8:17:437:1378	83	chr2	847	99	35M	=	676	-206	ATCAATATTAACTTTGAATAAAAAGGGATTAAATT	<<7<<<<<<<<:<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:51	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_66:3:155:375:623	163	chr2	849	99	35M	=	1029	215	CAATATTAACTTTGAATAAAAAGGGATTAAATTCC	0<<<<<;<<<<<<<<<<<<<4<<8<<<<<<<<;<;	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_595:2:29:729:70	163	chr2	850	51	35M	=	1009	194	ANTATTANCTTTGANNAAAAAGGGATTAAATTCCC	:!<:<<8!::::5:!!:.77::33888633:8777	MF:i:130	Aq:i:51	NM:i:3	UQ:i:0	H0:i:0	H1:i:0
+EAS54_65:7:117:452:744	83	chr2	850	99	35M	=	676	-209	AATATTAACTTTGAATAAAAAGGGATTAAATTCCC	<;;<;<<<7<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:50	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_57:1:288:384:444	83	chr2	855	99	35M	=	696	-194	TAACTTTGAATAAAAAGGGATTAAATTCCCCCACT	;=9;;<====<=;=/=9;<========<=======	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_28:7:133:514:754	163	chr2	855	63	36M	=	1036	217	TAAATTTGAATAAAAAGGGATTAAATTCCCCCACTT	***&,,,+(*,*********+*)*(***(**((*)(	MF:i:18	Aq:i:19	NM:i:1	UQ:i:5	H0:i:0	H1:i:1
+EAS139_19:5:68:306:409	147	chr2	856	99	40M	=	682	-214	AACTTTGAATAAAAAGGGATTAAATTCCCCCACTTAAGAG	::2:7<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_61:3:155:758:710	163	chr2	859	98	35M	=	1048	224	TTTGAATAAAAAGGGATTAAATTCCCCCACTTAAG	=======8================6=:7===:=:=	MF:i:18	Aq:i:22	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:3:39:208:644	147	chr2	859	99	35M	=	704	-190	TTTGAATAAAAAGGGATTAAATTCCCCCACTTAAG	78899;;;;4;;;;;;;;;;;;;;;;;;8;;8;;;	MF:i:18	Aq:i:67	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_108:1:16:438:245	89	chr2	860	65	35M	*	0	0	TTGAATAAAAAGGGATTAAATTCCCCCACTTAAGA	8*8<5'<77;;;;;7<7<<7-<;<<<;;<<<;;79	MF:i:32	Aq:i:65	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_73:5:145:635:390	83	chr2	860	99	35M	=	673	-222	TTGAATAAAAAGGGATTAAATTCCCCCACTTAAGA	+9;<<;<<<<<;;;<;<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_28:6:187:996:432	147	chr2	860	99	36M	=	693	-203	TTGAATAAAAAGGGATTAAATTCCCCCACTTAAGAG	;<<<<<<<<<<<<<<<<<<<<;<<<<<<<<<<<<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_591:2:123:924:645	163	chr2	861	84	36M	=	1045	220	TGAATAAAAAGGGATTAAATTCCCCCACTTAAGAGA	<<<<<<<<<<<<;<<<<<<;<<<<<<<6:<7<1<+<	MF:i:18	Aq:i:11	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_597:4:146:961:63	163	chr2	861	86	35M	=	1041	215	TGAATAAAAAGGGCTTAAATTCCCCCACTTAAGGG	<<+<<<<::+1<;&<<88<<<<;;.<0;;85(;(8	MF:i:18	Aq:i:37	NM:i:2	UQ:i:12	H0:i:0	H1:i:1
+EAS114_30:6:4:665:771	69	chr2	862	0	*	=	862	0	GTGCTTTATCTGATATCAATGCCGATAAACTGCCT	<<<<<<<<<<<<%<8<3:7:77<(7,:3(:&2:(0	MF:i:192
+EAS114_30:6:4:665:771	137	chr2	862	71	35M	=	862	0	GAATAAAAAGGGATTAAATTCCCCCACTTAAGAGA	<;<<;<18<;<8<<<<;<;;<<<<1<<<<6;;;;;	MF:i:64	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_93:6:45:601:439	83	chr2	864	99	35M	=	691	-208	ATAAAAAGGGATTAAATTCCCCCACTTAAGAGATA	<8<<<<<<1<<<<<<<<)<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_65:4:126:966:514	163	chr2	865	99	35M	=	1027	197	TAAAAAGGGATTAAATTCCCCCACTTAAGAGATAT	<<<<<<<<<<<<<<<<<<<<;<<<<<<<<<;<<<;	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:2:76:1765:700	83	chr2	866	99	35M	=	680	-221	AAAAAGGGATTAAATTCCCCCACTTAAGAGATATA	77777;;;;7;7;<;;;;+;;<9<<<79;<1<<77	MF:i:18	Aq:i:63	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_26:1:155:807:19	99	chr2	867	99	35M	=	1074	242	AAAAGGGATTAAATTCCCCCACTTAAGAGATATAG	<<<<<<<<<<<<<<<<9+<<<<<<9<<9;4<<<<:	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_30:2:226:885:729	99	chr2	867	98	35M	=	1037	205	AAAAGGGATTAAATTCCCCCACTTAAGAGATATAG	<<<;<<<<<<;<;<<<<<<<:;<<;4;%;<<;<<.	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_19:4:1:156:196	99	chr2	867	77	40M	=	1042	215	AAAAGGGATTAAATTCCCCCACTTAAGAGATATAGATTGG	<<<<<<<<<<<<<<<<<<;<<<<<<<<<<<<<<<<:;9:9	MF:i:18	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_1:2:52:1144:509	147	chr2	867	99	35M	=	706	-196	AAAAGGGATTAAATTCCCCCACTTAAGAGATATAG	<<<<:<<<<<<<<<<;::;:<;<<<<<<<<<<<<<	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_108:6:73:735:329	99	chr2	868	99	35M	=	1035	202	AAAGGGATTAAATTCCCCCACTTAAGAGATATAGA	================;==;====;=;=======;	MF:i:18	Aq:i:39	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_81:6:11:801:386	163	chr2	868	97	35M	=	1061	228	AAAGGGATTAAATTCCCCCACTTAAGAGATATAGA	<<<<<<<<<<8<<<<<:4<::<854:5<:::;4+4	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_65:4:150:94:843	99	chr2	868	75	35M	=	1050	217	AAAGGGATTAAATTCCCCCACTTAAGAGATATAGA	<<<<<<<<7<<<6<<<<<<<<<<<6<<62<<<<<2	MF:i:18	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_73:5:255:796:239	147	chr2	869	99	35M	=	692	-212	AAGGGATTAAATTCCCCCACTTAAGAGATAGAGAT	<<3;;<7:<<<;(7<<7;<<;<<<<<<<<<7<<<<	MF:i:18	Aq:i:43	NM:i:1	UQ:i:22	H0:i:0	H1:i:1
+B7_589:5:147:405:738	163	chr2	870	99	35M	=	1048	213	AGGGATTAAATTCCCCCACTTAAGAGATATAGATT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;;;	MF:i:18	Aq:i:24	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_63:2:33:357:858	83	chr2	870	99	35M	=	716	-189	AGGGATTAAATTCCCCCACTTAAGAGATATAGATT	<;<:<<<<<<<<<;<9<<;<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_65:7:122:398:994	83	chr2	871	99	35M	=	708	-198	GGGATTAAATTCCCCCACTTAAGAGATATAGATTG	95:<9<<<<:9<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:1
+EAS1_105:2:146:374:692	147	chr2	874	99	35M	=	690	-219	ATTAAATTCCCCCACTTAAGAGATATAGATTGGCA	<4:<<<1:<:<::<<<;<<<<<<<<<<<<<<<<<;	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_593:6:119:428:415	163	chr2	876	99	36M	=	1037	197	TAAATTCCCCCACTTAAGAGATATAGATTGGCAGAA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<9;;<;;;	MF:i:18	Aq:i:46	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_105:7:168:247:414	147	chr2	876	99	35M	=	698	-213	TAAATTCCCCCACTTAAGAGATATAGATTGGCAGA	,;;;,146<6;6<<8<<<<1<8<<<<<<<<<<;1<	MF:i:18	Aq:i:67	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_26:2:130:609:467	147	chr2	877	99	35M	=	728	-184	AAATTCCCCCACTTAAGAGATATAGATTGGCAGAA	===:2===;<====>==>=>=>=>>>==>>>=>>>	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_19:5:57:366:844	83	chr2	877	99	40M	=	708	-209	AAATTCCCCCACTTAAGAGATATAGATTGGCAGAACAGAT	;;;7:8&555<,;<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_32:3:236:475:254	163	chr2	880	99	35M	=	1051	206	TTCCCCCACTTAAGAGATATAGATTGGCAGAACAG	<<<<<<<<<<<<<<<<<<<<<<<<<:::<:;</;/	MF:i:18	Aq:i:43	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_28:2:251:819:772	147	chr2	881	99	36M	=	726	-191	TCCCCCACTTAAGAGATATAGATTGGCAGAACAGAT	6+7++1<<%<<<<<<<+<+<9<<99<9<<<<<<9<<	MF:i:18	Aq:i:59	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_19:1:36:481:1079	83	chr2	881	99	40M	=	707	-214	TCCCCCACTTAAGAGATATAGATTGGCAGAACAGATTTAA	:11+)*<4;<<<<<<<<<;;<<<<<<;<<<<<<<<<<<<<	MF:i:18	Aq:i:70	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_19:5:29:411:1208	147	chr2	882	99	40M	=	698	-224	CCCCCACTTAAGAGATATAGATTGGCAGAACAGATTTAAA	766+6<996<<<<<<<<<<<<<<<<;<<<<<<<<<<<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS219_1:7:62:1076:540	99	chr2	882	99	35M	=	1066	219	CCCCCACTTAAGAGATATAGATTGGCAGAACAGAT	<<<<<<<<<<;<<<<<<<<<<<<<<<<;;<<;<7;	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_593:7:189:530:40	83	chr2	883	99	36M	=	698	-221	CCCCACTTAAGAGATATAGATTGGCAGAACAGATTT	883;<<<<<<<<<:<<<<<<<<3<;<<<<<<<<;<<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_71:8:113:856:319	163	chr2	884	99	35M	=	1067	216	CCCACTTAAGAGATATAGATTGGCAGAACAGATTT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;;<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_11:2:55:296:1457	99	chr2	884	99	35M	=	1061	212	CCCACTTAAGAGATATAGATTGGCAGAACAGATTT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_1:8:15:881:1932	99	chr2	886	92	35M	=	1061	210	CACTTAAGAGATATAGATTGGCAGAACAGATTTAA	<<<<<<<<<<<<<<<;<<<<:<<<2<26<8<<;;.	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_610:7:116:157:612	147	chr2	889	99	35M	=	707	-217	TTAAGAGATATAGATTGGCAGTACAGATTTAAAAA	;;<<<<<<<<<<<<<<<<;<</<<<<<<<<<<<<<	MF:i:18	Aq:i:30	NM:i:1	UQ:i:14	H0:i:0	H1:i:1
+EAS114_28:7:215:863:521	83	chr2	890	99	36M	=	732	-194	TAAGAGATATAGATTGGCAGAACAGATTTAAAAACA	;<<<<<<<<<<<<<;<<;<;<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_73:7:254:572:431	163	chr2	891	97	35M	=	1048	192	AAGAGATATAGATTGGCAGAACAGATTTAAAAACA	<<<<<<<<<<<<<<<<;<<<<<<<<<<<99;;;;;	MF:i:18	Aq:i:22	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_81:6:273:424:207	163	chr2	891	99	35M	=	1066	210	AAGAGATATAGATTGGCAGAACAGATTTAAAAACA	<,<,<9<<9<<<<<<<<<<79<,599,<191<99+	MF:i:18	Aq:i:62	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_63:8:4:571:820	163	chr2	891	99	35M	=	1071	215	AAGAGATATAGATTGGCAGAACAGATTTAAAAACA	<<<<<<<<<<<9<<;9<;;;<;6;:<<<3:;;;:6	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_11:4:36:1231:1381	147	chr2	891	99	35M	=	708	-218	AAGAGATATAGATTGGCAGAACAGATTTAAAAACA	<<<<<<;<<<<<<<<<8<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_19:3:66:718:481	99	chr2	891	99	40M	=	1072	221	AAGAGATATAGATTGGCAGAACAGATTTAAAAACATGAAC	<<<<<<<<<<<<<<;<<<<<<<<;<<<<<<<;<<<:1:;:	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_591:7:22:632:176	163	chr2	894	99	36M	=	1091	233	AGATATAGATTGGCAGAACAGATTTAAAAACATGAA	<<<<<;<<<<<<;<<;<:<<<:<<:<<<;<<<;;;:	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_81:8:271:180:509	147	chr2	896	99	35M	=	729	-202	ATATAGATTGGCAGAACAGATTTAAAAACATGAAC	<<<<<<<<<9<:<<<<:<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_589:5:198:564:731	163	chr2	898	99	35M	=	1089	226	ATAGATTGGCAGAACAGATTTAAAAACATGAACTA	<<<<<;<<<<<<;<<:<<;9<<<<<<<<1;<<58<	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_3:2:67:1467:1447	83	chr2	898	99	35M	=	722	-211	ATAGATTGGCAGAACAGATTTAAAAACATGAACTA	<<<<<::<<:<<<<:<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_105:6:172:827:592	83	chr2	899	99	35M	=	703	-231	TAGATTGGCAGAACAGATTTAAAAACATGAACTAA	8<<<<;7;7<<<<;<<<<<;<<<<<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_65:8:240:719:799	147	chr2	900	99	35M	=	720	-215	AGATTGGCAGAACAGATTTAAAAACATGAACTAAC	<:<<<<<:<<<<:<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_11:7:24:1345:1627	73	chr2	900	78	35M	=	900	0	AGATTGGCAGAACAGATTTAAAAACATGAACTAAC	<<<<<<<<<<<<<<<<<<<<<<9<<<<<<<<<8<3	MF:i:64	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_11:7:24:1345:1627	133	chr2	900	0	*	=	900	0	NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN	!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!	MF:i:192
+EAS139_19:1:58:726:1746	163	chr2	900	99	40M	=	1061	201	AGATTGGCAGAACAGATTTAAAAACATGAACTAACTATAT	<<<<<<<<<<<<<<<<<<<6<<<<8<<<<<<<<:8:8:88	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:7:88:451:1773	147	chr2	902	99	35M	=	742	-195	ATTGGCAGAACAGATTTAAAAACATGAACTAACTA	973776;;;;;;;;;::;;;;;;;;;;;;;;3;;;	MF:i:18	Aq:i:67	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_65:8:178:187:610	147	chr2	903	99	35M	=	744	-194	TTGGCAGAACAGATTTAAAAACATGAACTAACTAT	66:,:<7<<<<<<<1<<<<<<<<<<<<<<<2<<<<	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_593:6:38:332:54	83	chr2	904	99	36M	=	737	-203	TGGCAGAACAGATTTAAAAACATGAACTAACTATAT	8;;&<;<<7<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:54	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_66:5:210:674:911	147	chr2	904	99	35M	=	740	-199	TGGCAGAACAGATTTAAAAACATGAACTAACTATA	27;2<;<<5<<<<;;<<<<<;<<<<<<;<<<<<<<	MF:i:18	Aq:i:54	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_30:2:82:963:128	83	chr2	905	99	35M	=	719	-221	GGCAGAACAGATTTAAAAACATGAACTAACTATAT	585<;<<:<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_19:2:12:1335:1372	83	chr2	906	99	40M	=	721	-225	GAAGAACAGATTTAAAAACATGAACTAACTATATGCTGTT	:&;;;<*<<<9<<<<<<<<<<<<<<4<<<<<<<<<<<<<<	MF:i:18	Aq:i:74	NM:i:1	UQ:i:5	H0:i:1	H1:i:0
+EAS114_39:1:98:641:1040	163	chr2	907	99	35M	=	1085	213	CAGAACAGATTTAAAAACATGAACTAACTATATGC	<<<<<<;<<<<<<<<<<<<<<<<<<<<<<<<<<<;	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_81:8:41:530:663	83	chr2	908	99	35M	=	730	-213	AGAACAGATTTAAAAACATGAACTAACTATATGCT	=8=;*=5==;;=====:=====;===;========	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_105:1:87:430:995	147	chr2	909	67	35M	=	731	-213	GAAAAGAGTTAAAAACATGAACTAACTATATGCTG	1<4%81<..1<<<<<0<<<<<0.<<9<<(<6<<6<	MF:i:18	Aq:i:30	NM:i:2	UQ:i:17	H0:i:0	H1:i:1
+B7_595:3:85:964:950	163	chr2	910	99	35M	=	1095	220	AACAGATTTAAAAACATGAACTAACTATATGCTGT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;;<;:	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_610:8:68:570:705	99	chr2	910	99	35M	=	1100	225	AACAGATTTAAAAACATGAACTAACTATATGCTGT	<<<<<<<<<<<<<<<<<<<<<<<<<<;<<<<<<8<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_67:6:198:503:669	99	chr2	912	99	35M	=	1107	230	CAGATTTAAAAACATGAACTAACTATATGCTGTTT	<<<<<<<<<<;8<<<<<;<<<<<<;<;<8<<8<<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_66:5:273:545:1001	163	chr2	913	99	35M	=	1088	210	AGATTTAAAAACATGAACTAACTATATGCTGTTTA	<<<<<<<<<<<<<<<;;<<<<<<;<8;28<8;<<8	MF:i:18	Aq:i:67	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_99:8:152:778:228	83	chr2	915	99	35M	=	739	-211	ATTTAAAAACATGAACTAACTATATGCTGTTTACA	<;;7=<<<<<<;<<<<<<<;<<<<<<<<<<<<<<<	MF:i:18	Aq:i:54	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_19:1:53:463:1132	163	chr2	915	99	40M	=	1109	234	ATTTAAAAACATGAACTAACTATATGCTGTTTACANGAAA	<<<<<<<<<<<<<<<<<<<<<;<<<8<<<<<<<8<!1488	MF:i:18	Aq:i:71	NM:i:1	UQ:i:0	H0:i:1	H1:i:0
+EAS218_4:3:12:630:707	147	chr2	915	99	35M	=	751	-199	ATTTAAAAACATGAACTAACTATATGCTGTTTACA	<:<<<<<<<;<<<<<9<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:54	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_105:8:179:119:876	163	chr2	917	60	35M	=	1112	230	TTAAAAACATGAACTAACTATATGCTGTTTACCAG	<<<<<<<7<<<<<<<8<<<6<<<<<<7<<<:0&<0	MF:i:18	Aq:i:30	NM:i:1	UQ:i:5	H0:i:1	H1:i:1
+EAS1_97:6:308:667:658	99	chr2	918	10	35M	=	1116	233	TAAAAACATGAACTAACTATATCCTTCTTACAATA	9<96<<<;<96<<9<51<<<<<1:9++<9*%4;*5	MF:i:18	Aq:i:10	NM:i:4	UQ:i:45	H0:i:0	H1:i:0
+EAS114_28:5:163:832:715	163	chr2	918	99	36M	=	1085	203	TAAAAACATGAACTAACTATATGCTGTTTACAAGAA	<<0;<9<<<<<<<<<<<<9<<<<<<<<<<<<;;;<6	MF:i:18	Aq:i:54	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_591:3:179:496:161	83	chr2	919	99	36M	=	756	-199	AAAAACATGAACTAACTATATGCTGTTTACAAGAAA	<<<<<9<<<<<7<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:49	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_93:8:13:325:483	163	chr2	919	99	35M	=	1101	217	AAAAACATGAACTAACTATATGCTGTTTACAAGAA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<;	MF:i:18	Aq:i:27	NM:i:0	UQ:i:0	H0:i:1	H1:i:1
+EAS1_103:7:139:578:951	163	chr2	919	98	35M	=	1095	211	AAAAACATGAACTAACTATATGCTGTTTACAAGAA	<<<<<<<<;<<<<<<<<<<<<;<<<<<<<<<<0;;	MF:i:18	Aq:i:26	NM:i:0	UQ:i:0	H0:i:1	H1:i:1
+EAS1_108:8:19:929:765	99	chr2	919	98	35M	=	1069	185	AAAAACATGAACTAACTATATGCTGTTTACAAGAA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<;77<	MF:i:18	Aq:i:27	NM:i:0	UQ:i:0	H0:i:1	H1:i:1
+EAS56_57:5:214:644:390	163	chr2	919	72	35M	=	1082	198	AAAAACATGAACTAACTATATGCTGTTTACAAGAA	<<<<<<<<<<<<;<<<<<<<<<<<<<<<<<<<;<;	MF:i:18	Aq:i:27	NM:i:0	UQ:i:0	H0:i:1	H1:i:1
+EAS114_30:6:243:209:110	83	chr2	920	48	35M	=	768	-187	AAAACATGAACTAACTATATGCTGTTTACAAGAAA	;<;;;:<:<:;<<;;<;<;<;7<<;<<;;<;<<<<	MF:i:18	Aq:i:48	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_32:2:247:900:123	99	chr2	920	99	35M	=	1123	238	AAAACATGAACTAACTATATGCTGTTTACAAGAAA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<9;<;	MF:i:18	Aq:i:51	NM:i:0	UQ:i:0	H0:i:1	H1:i:1
+EAS51_62:7:162:195:761	83	chr2	922	30	35M	=	767	-190	AACATGAACTAACTATATGCTGTTTACAAGAAACT	<<8<<:<<:<<<<<<<<<<:<<<<<<<<<<<<<<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:2	H1:i:0
+EAS1_103:2:184:980:396	163	chr2	923	99	35M	=	1092	204	ACATGAACTAACTATATGCTGTTTACAAGAAACTC	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<<	MF:i:18	Aq:i:54	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_59:2:162:272:415	99	chr2	923	83	35M	=	1112	224	ACATGAACTAACTATATGCTGTTTACAAGAAACTC	<<<<<<<<<<<<<<<<<<<<<<;<<<<<9;<<<<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS192_3:4:184:237:476	163	chr2	925	99	35M	=	1101	211	ATGAACTAACTATATGCTGTTTACAAGAAACTCAT	<<<<<<<<<<<<<<<<<<<<<<;<<<<<<<;<;;<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_95:1:202:341:984	99	chr2	926	99	35M	=	1094	203	TGAACTAACTATATGCTGTTTACAAGAAACTCATT	=========================4;========	MF:i:18	Aq:i:70	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_53:3:107:738:484	99	chr2	926	75	35M	=	1097	206	TGAACTAACTATATGCTGTTTACAAGAAACTCATT	<<<<<<<<<<<<<<<<<<<<<<<<<:<<<<<<<<<	MF:i:18	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_39:6:7:492:1088	147	chr2	926	57	35M	=	769	-192	TGAACTAACTATATGCTGTTTACAAGAAACTCATT	4;<<75<<::<:<<<-<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:57	NM:i:0	UQ:i:0	H0:i:1	H1:i:1
+EAS139_11:1:81:1019:558	83	chr2	926	77	35M	=	760	-201	TGAACTAACTATATGCTGTTTACAAGAAACTCATT	<<<<9<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_39:4:10:1312:1558	83	chr2	928	76	35M	=	771	-192	AACTAACTATATGCTGTTTACAAGAAACTCATTAA	<<:<<<;<<<<<<;<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_71:4:206:741:810	83	chr2	929	99	34M	=	753	-210	ACTAACTATATGCTGTTTACAAGAAACTCATTAA	<3<<;5<<<<<;:<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:48	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_73:7:200:65:291	147	chr2	930	99	35M	=	728	-237	CTAACTATATGCTGTTTACAAGAAACTCATTAATA	;9<;3<<9<7<;<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_39:2:38:670:564	147	chr2	930	73	35M	=	770	-195	CTAACTATATGCTGTTTACAAGAAACTCATTAATA	3<<<3:<<<<<:;<<<<<:<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_39:7:57:1114:2032	99	chr2	931	99	35M	=	1102	206	TAACTATATGCTGTTTACAAGAAACTCATTAATAA	<7<<<<<<<<<<<<<<<<<777<<<7<<<<<3<<7	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_59:5:125:137:58	83	chr2	932	76	35M	=	772	-195	AACTATATGCTGTTTACAAGAAACTCATTAATAAA	<<9;<<<<<;<;<<<<;<<<<<<;<<<<<<<<<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_62:1:38:250:647	163	chr2	933	71	35M	=	1100	202	ACTATATGCTGTTTACAAGAAACTCATTAATAAAT	<<<<<<<9<<9<<<<<<<6<<<<<<<<<<8<779%	MF:i:18	Aq:i:0	NM:i:1	UQ:i:4	H0:i:1	H1:i:0
+EAS192_3:6:116:464:261	99	chr2	934	99	35M	=	1107	208	CTATATGCTGTTTACAAGAAACTCATTAATAAAGA	<<<<<<<<<<<<<<<<<;<<<;<<<<<<<<<;;8<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_589:1:168:69:249	163	chr2	936	99	35M	=	1125	224	ATATGCTGTTTACAAGAAACTCATTAATAAAGACA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;;;<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_32:4:246:647:765	163	chr2	937	99	35M	=	1119	217	TATGCTGTTTACAAGAAACTCATTAATAAAGACAT	;<<<<<<<<<;<&<<3+3<<<3<<9&</:/87</8	MF:i:18	Aq:i:62	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_32:3:307:113:346	163	chr2	938	99	35M	=	1123	220	ATGCTGTTTACAAGAAACTCATTAATAAAGACATG	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;;<<8	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_108:6:159:493:275	147	chr2	939	72	35M	=	760	-214	TGCTGTTTACAAGAAACTCATTAATAAAGACATGA	4949;<<<<<<<<<<<6<;<<<<;<<<<<*<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_71:3:257:288:731	99	chr2	939	99	34M	=	1131	227	TGCTGTTTACAAGAAACTCATTAATAAAGACATG	<<<<<<<<8<8<<;<;<<<;<<<5<;;88.8<6<	MF:i:18	Aq:i:68	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_103:4:231:815:626	163	chr2	940	99	35M	=	1119	214	GCTGTTTACAAGAAACTCATTAATAAAGACATGAG	<;<<<<9<<<<<<<<<<<<<<<<<;<<;5<<<;:;	MF:i:18	Aq:i:41	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_39:4:93:77:1338	163	chr2	940	10	35M	=	1098	193	GCTGCTTACAAGAAGCGCATTAATAAAGACATGAG	<<<<*<2<<<:<4<&<6<8<4<::<8<<<<82;;7	MF:i:18	Aq:i:0	NM:i:3	UQ:i:35	H0:i:0	H1:i:0
+EAS114_45:2:54:1886:719	99	chr2	941	99	35M	=	1125	219	CTGTTTACAAGAAACTCATTAATAAAGACATGAGT	;;;9;;<;;;9;;;;;:;<9;:;;;;9;;;99799	MF:i:18	Aq:i:66	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_597:7:94:273:165	99	chr2	945	99	35M	=	1128	218	TTACAAGAAACTCATTAATAAAGACATGAGTTCAG	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<:;;:7	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_30:5:32:461:154	147	chr2	945	71	35M	=	769	-211	TTACAAGAAACTCATTAATAAAGACATGAGTTCAG	;;</<<<<<;:<.<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_593:3:303:131:673	163	chr2	947	99	36M	=	1112	201	ACAAGAAACTCATTAATAAAGACATGAGTTCAGGTA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;;<;;;	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_61:6:10:106:737	163	chr2	947	99	35M	=	1106	194	ACAAGAAACTCATTAATAAAGACATGAGTTCAGGT	<<<;<1<;<<<<<<9<<<<;;<<<<<99<<94008	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_26:2:214:950:32	163	chr2	947	99	35M	=	1132	220	ACAAGAAACTCATTAATAAAGACATGAGTTCAGGT	>>=>>>>==>=>>>==>=>=:=====;=:=6:::6	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS218_1:2:10:686:1024	163	chr2	947	99	35M	=	1103	191	ACAAGAAACTCATTAATAAAGACATGAGTTCAGGT	<:<<<<:<<<<<<<<<<:<:<<<<<<<<<<<5<<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_73:5:53:61:31	163	chr2	949	99	35M	=	1122	208	AAGAAACTCATTAATAAAGACATGAGTTCAGATAA	<<<7;<7<<<;7<;;<7<7<7<;5<73<<</%;/;	MF:i:18	Aq:i:66	NM:i:1	UQ:i:4	H0:i:1	H1:i:0
+EAS114_28:6:185:87:475	83	chr2	949	99	36M	=	786	-199	AAGAAACTCATTAATAAAGACATGAGTTCAGGTAAA	<<4<<<+<<<;<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_103:4:235:899:847	99	chr2	950	99	35M	=	1112	197	AGAAACTCATTAATAAAGACATGAGTTCAGGTAAA	<<3<;<<<<<<<<<;;<<<<<<<+<<<+6<8<3/<	MF:i:18	Aq:i:51	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_597:6:193:661:771	163	chr2	952	99	35M	=	1129	212	AAACTCATTAATAAAGACATGAGTTCAGGTAAAGG	<<<<<<<<<;<<<;;;<<<<<;<<<=;<:;5:9::	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_597:7:113:408:211	147	chr2	952	99	35M	=	789	-198	AAACTCATTAATAAAGACATGAGTTCAGGTAAAGG	<:;:;:<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_105:8:24:718:322	83	chr2	953	23	35M	=	779	-209	AACTCATTAATAATGTCATGAGTTCAGGTAAAGGG	5:+:0;**&+<00&<&<<<5<28<<;;<83<<<<<	MF:i:18	Aq:i:23	NM:i:2	UQ:i:10	H0:i:0	H1:i:0
+EAS56_61:5:263:314:696	163	chr2	953	99	35M	=	1117	199	AACTCATTAATAAAGACATGAGTTCAGGTAAAGGG	<<<<<<<<<<<<<<;<<<<<<<<<<<<:<<;<775	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_39:5:93:312:331	163	chr2	953	99	35M	=	1145	227	AACTCATTAATAAAGACATGAGTTCAGGTAAAGGG	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<=<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_93:3:181:93:694	83	chr2	954	99	35M	=	783	-206	ACTCATTAATAAAGACATGAGTTCAGGTAAAGGGG	<4;8<<+<<:<<<<<<<<<<<:<<<<<<<<<<<<<	MF:i:18	Aq:i:28	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_30:6:238:803:383	147	chr2	954	75	35M	=	779	-210	ACTCATTAATAAAGACATGAGTTCAGGTAAAGGGG	;;<;;<<<<<<<<<<<<<<<<;:<<<<<<<<<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:6:44:77:1255	163	chr2	955	99	35M	=	1113	193	CTCATTAATAAAGACATGAGTTCAGGTAAAGGGGT	;;;;;;;8;;;7;8;;;;;;;;;;886;;;76777	MF:i:18	Aq:i:67	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_105:3:232:364:583	147	chr2	956	71	35M	=	780	-211	TCATTAATAAAGACATGAGTTCAGGTAAAGGGGTG	;%;7;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_593:7:256:354:173	163	chr2	957	99	36M	=	1121	200	CATTAATAAAGACATGAGTTCAGGTAAAGGGGTGGA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<3<<;	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_597:4:138:211:582	147	chr2	957	99	35M	=	788	-204	CATTAATAAAGACATGAGTTCAGGTAAAGGGGTGG	:<8;<<<<<<<<<<<<<<;<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:45	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_95:4:61:631:567	99	chr2	957	99	35M	=	1131	209	CATTAATAAAGACATGAGTTCAGGTAAAGGGGTGG	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:5:56:1757:1319	83	chr2	957	67	35M	=	775	-217	CATTAATAAAGACATGAGTTCAGGTAAAGGGGTGG	&7778<<<<<8<;<<:::;<:<4<<:<:;8<8<;<	MF:i:18	Aq:i:67	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_589:7:154:26:712	147	chr2	959	99	35M	=	786	-208	TTAATAAAGACATGAGTTCAGGTAAAGGGGTGGAA	;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_65:8:10:975:766	163	chr2	959	99	35M	=	1166	242	TTAATAAAGACATGAGTTCAGGTAAAGGGGTGAAA	<<<<<<<<;<<<<;<:<<;<6;;<<<:6-:+1+;;	MF:i:18	Aq:i:64	NM:i:1	UQ:i:10	H0:i:1	H1:i:0
+EAS54_73:5:220:733:736	99	chr2	959	99	35M	=	1143	219	TTAATAAAGACATGAGTTCAGGTAAAGGGGTGGAA	<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<5<<;9	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS220_1:4:46:1566:668	163	chr2	959	99	35M	=	1148	224	TTAATAAAGACATGAGTTCAGGTAAAGGGGTGGAA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:78	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_30:7:59:871:351	83	chr2	963	99	35M	=	808	-190	TAAAGACATGAGTTCAGGTAAAGGGGTGGAAAAAG	;<<<<<:<;<<<4;<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_95:7:46:522:426	83	chr2	964	99	35M	=	807	-192	AAAGACATGAGTTCAGGTAAAGGGGTGGAAAAAGA	<<<<<:<<<<<<1/<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_26:7:157:876:302	83	chr2	964	99	35M	=	801	-198	AAAGACATGAGTTCAGGTAAAGGGGTGGAAAAAGA	===:=8=;==:892=,28==88==28====8=;;8	MF:i:18	Aq:i:66	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS218_1:4:61:1369:440	83	chr2	964	47	35M	=	770	-229	AAAGACATGATTTCAGGTAAAGGGGTGGAAAAAGA	<<<<<<<<<<8<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:47	NM:i:1	UQ:i:23	H0:i:0	H1:i:1
+EAS221_1:6:57:1342:1166	147	chr2	964	99	35M	=	796	-203	AAAGACATGAGTTCAGGTAAAGGGGTGGAAAAAGA	<<<<<;<<<<<<<;<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_66:4:310:287:420	147	chr2	965	99	35M	=	794	-206	AAGACATGAGTTCAGGTAAAGGGGTGGAAAAAGAT	<<<<;<;<<<<<;<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_65:5:262:53:888	83	chr2	965	99	35M	=	787	-213	AAGACATGAGTTCAGGTAAAGGGGTGGAAAAAGAT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_1:2:3:542:428	83	chr2	965	99	35M	=	797	-203	AAGACATGAGTTCAGGTACAGGGGTGGAAAAAGAT	<<876</3<8874:<8:<)<5<<<;<<<<7<<<:<	MF:i:18	Aq:i:41	NM:i:1	UQ:i:8	H0:i:0	H1:i:1
+B7_593:2:81:435:410	147	chr2	966	99	36M	=	782	-220	AGACATGAGTTCAGGTAAAGGGGTGGAAAAAGATGT	;<;;<<<<<<;<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:29	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_610:3:85:219:371	83	chr2	967	99	35M	=	817	-185	GACATGAGTTCAGGTAAAGGGGTGGAAAAAGATGT	<<7<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:54	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_108:2:116:966:193	83	chr2	967	99	35M	=	815	-187	GACATGAGTTCAGGTAAAGGGGTGGAAAAAGATGT	===================================	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_39:4:30:432:228	163	chr2	967	99	35M	=	1145	213	GACATGAGTTCAGGGAAAGGGGTGGAAAAAGATGT	<<<<<<<<<<<<<<8<<<<<<<<<<<<:<<<<<;;	MF:i:18	Aq:i:47	NM:i:1	UQ:i:23	H0:i:0	H1:i:1
+B7_610:1:12:88:200	163	chr2	968	99	35M	=	1133	200	ACATGAGTTCAGGTAAAGGGGTGGAAAAAGATGTT	<<<<<<<<<<<;<<<<<<<;<<<:<<<<<<9<<5<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_93:2:313:711:530	83	chr2	968	99	35M	=	784	-219	ACATGAGTTCAGGTAAAGGGGTGGAAAAAGATGTT	<7;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:47	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_95:7:74:866:49	163	chr2	969	99	35M	=	1143	209	CATGAGTTCAGGTAAAGGGGTGGAAAAAGATGTTC	====================9==91==<=6==;:=	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_62:7:248:17:435	99	chr2	969	99	35M	=	1139	205	CATGAGTTCAGGAAAAGGGGTGGAAAAAGATGTTC	<<<<8<<<888<+<<<<<;<:<<<<8<<<<<;3<3	MF:i:18	Aq:i:43	NM:i:1	UQ:i:10	H0:i:0	H1:i:1
+EAS114_30:1:188:863:790	83	chr2	969	98	35M	=	783	-221	CATGAGTTCAGGTAAAGGGGTGGAAAAAGATGTTC	;<7<<<55<<<<:<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:27	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_19:6:75:1503:1399	163	chr2	969	99	40M	=	1130	201	CATGAGTTCAGGTAAAGGGGTGGAAAAAGATGTTCTACGC	<<<<<<<<<<<<<<<<<<9<<<;<<<<<<;<<<<:::711	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_65:2:56:155:49	99	chr2	970	99	35M	=	1145	210	ATGAGTTCAGGTAAAGGGGTGGAAAAAGATGTTCT	<<<<<<<<<<<<<<<<<<<<<<;<<;<<<;<9<9;	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS188_4:5:295:547:216	83	chr2	970	99	35M	=	809	-196	ATGAGTTCAGGTAAAGGGGTGGAAAAAGATGTTCT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_59:4:262:928:237	147	chr2	971	99	35M	=	787	-219	TGAGTTCAGGTAAAGGTGTGGAAAAAGATGTTCTA	;<<<<<;<<<<<<<<<;<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:47	NM:i:1	UQ:i:26	H0:i:0	H1:i:1
+EAS219_1:1:50:257:341	83	chr2	971	99	35M	=	813	-193	TGAGTTCAGGTAAAGGGGTGGAAAAAGATGTTCTA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_57:1:122:38:103	83	chr2	972	79	35M	=	778	-229	GAGTTCAGGTAAAGGGGTGGAAAAAGATGTTCTAC	===;3<===:=======<=================	MF:i:18	Aq:i:79	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_59:1:82:670:302	99	chr2	973	99	35M	=	1146	208	AGTTCAGGTAAAGGGGTGGAAAAAGATGTTCTACG	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<5	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_65:8:24:415:944	147	chr2	974	99	35M	=	805	-204	GTTCAGGTAAAGGGGTGGAAAAAGATGTTCTACGC	<;;<<<<:<<<<<<<;<<<<<<<<<<<<;<<<<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_108:7:108:440:208	99	chr2	975	99	35M	=	1142	202	TTCAGGTAAAGGGGAGGAAAAAGATGTTCTACGCA	<<<;<<<<<<<<<</<<<<;<<<;<<;<;<64/:+	MF:i:18	Aq:i:43	NM:i:1	UQ:i:14	H0:i:0	H1:i:1
+B7_595:3:229:543:583	99	chr2	976	99	35M	=	1139	198	TCAGGTAAAGGGGTGGAAAAAGATGTTCTACGCAA	<<<<<<<<<<8<8<9<<<<8<<588<<<<*<2:2*	MF:i:18	Aq:i:65	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_95:2:142:353:398	83	chr2	977	99	35M	=	807	-205	CAGGTAAAGGGGTGGAAAAAGATGTTCTACGCAAA	===================================	MF:i:18	Aq:i:79	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_108:2:102:543:160	83	chr2	977	99	35M	=	825	-187	CAGGTAAAGGGGTGGAAAAAGATGTTCTACGCAAA	9==9=====;=====================<===	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_66:4:191:40:536	163	chr2	977	66	35M	=	1167	225	CAGGTAAAGGGGTGGAAAAAGATGTTCTACGCAAA	<<<<<<<<8<<;<<8<<;<;;<<8<<<<<</<74/	MF:i:18	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS112_32:7:272:328:400	163	chr2	977	99	35M	=	1151	209	CAGGTAAAGGGGTGGAAAAAGATGTTCTACGCAAA	<<<<<<<<;<<<<<<<<<<<<<<<<<<<<<7<;:7	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_19:4:69:1593:819	83	chr2	977	99	40M	=	786	-231	CAGGTAAAGGGGTGGAAAAAGATGTTCTACGCAAACAGAA	);::7<<<<:;<<<<<<<<<<<<<<<9<<9<3<<<<<<<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:1
+B7_597:3:133:707:886	99	chr2	978	99	35M	=	1146	203	AGGTAAAGGGGTGGAAAAAGATGTTCTACGCAAAC	<<<<7;<<<<<<<<<;<<<<<<<<<<<<<5<;66<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:1
+B7_591:4:92:411:955	99	chr2	979	99	36M	=	1149	206	GGTAAAGGGGTGGAAAAAGATGTTCTACGCAAACAG	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<<;	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:1
+EAS56_61:8:60:358:494	99	chr2	979	44	35M	=	1179	235	GGTAAAGGGGTGGAAAAAGATGTTCTACGCAAACA	<<<<<<<<<<<<<<<<<<<<<<<<<<:<:<<;;4;	MF:i:18	Aq:i:14	NM:i:0	UQ:i:0	H0:i:1	H1:i:1
+B7_597:7:41:34:211	163	chr2	980	99	35M	=	1164	219	GTAAAGGGGTGGAAAAAGATGTTCTACGCAAACAG	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<3:;5;	MF:i:18	Aq:i:54	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS218_1:2:40:1291:1045	99	chr2	980	99	35M	=	1167	222	GTAAAGGGGTGGAAAAAGATGTTCTACGCAACAAG	<<<<<<<<<5<<5<<<<7<<<<<<<<<5<9<&%73	MF:i:18	Aq:i:39	NM:i:2	UQ:i:9	H0:i:1	H1:i:0
+EAS218_1:8:90:706:1276	83	chr2	980	99	35M	=	814	-201	GTAAAGGGGTGGAAAAAGATGTTCTACGCAAACAG	<;<<<<<<<;<<<<<<<<<<<<<;<<<<<<<<<<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:1
+EAS114_32:4:5:396:292	163	chr2	981	99	35M	=	1155	209	TAAAGGGGTGGAAAAAGATGTTCTACGCAAACAGA	<<<<<<<<<<<<<<;;<<<<:<<<<;;<;;3/&+8	MF:i:18	Aq:i:45	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_108:2:176:653:957	83	chr2	982	82	35M	=	819	-198	AAAGGGGTGGAAAAAGATGTTCTACGCAAACAGAA	===::=============<==<====<========	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:1
+EAS54_71:6:264:705:89	99	chr2	983	99	34M	=	1155	207	AAGGGGTGGAAAAAGATGTTCTACGCAAACAGAA	<<<<<<<<<<;8<<<<<<<<<<<<<<<&<<,;;(	MF:i:18	Aq:i:54	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_61:2:66:757:918	163	chr2	985	99	35M	=	1143	193	GGGGTGGAAAAAGATGTTCTACGCAAACAGAAACC	===================================	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_61:7:114:506:971	163	chr2	986	99	35M	=	1150	199	GGGTGGAAAAAGATGTTCTACGCAAACAGAAACCA	===================================	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_30:6:220:809:850	99	chr2	986	60	35M	=	1187	236	GGGGGGAAAAAGATGTGCTACACAAAAAGATTCCA	<<;7;<<0::8<-6:<0624-*<&-93-,8+(&08	MF:i:130	Aq:i:60	NM:i:4	UQ:i:64	H0:i:0	H1:i:0
+B7_589:7:76:306:561	83	chr2	987	89	35M	=	794	-228	GGTGGAAAAAGATGTTCTACGCAAACAGAAACCAA	9<7<<9<<<<<<7<<71<71*7<<<<<<<<<<1<<	MF:i:18	Aq:i:20	NM:i:0	UQ:i:0	H0:i:1	H1:i:1
+EAS192_3:6:235:505:553	83	chr2	987	99	35M	=	808	-214	GGTGGAAAAAGATGTTCTACGCAAACAGAAACCAA	;8518<<<<<;<;<<<;<<;<.<<<<<<<<<<<<<	MF:i:18	Aq:i:54	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_593:1:19:695:59	147	chr2	988	99	36M	=	826	-198	GTGGAAAAAGATGTTCTACGCAAACAGAAACCAAAT	;+;8<<<<<<<<<<<5<<+<:<<;<<<<<<<<<<<<	MF:i:18	Aq:i:49	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_610:5:136:260:254	147	chr2	988	99	35M	=	813	-210	GTGGAAAAAGATGTTCTACGCAAACAGAAACCAAA	;:;;<<<<<<<<<<<<<<;<;<<<<<<<<<<<<<<	MF:i:18	Aq:i:54	NM:i:0	UQ:i:0	H0:i:1	H1:i:1
+EAS56_57:5:266:133:789	147	chr2	988	99	35M	=	810	-213	GTGGAAAAAGATGTTCTACGCAAACAGAAACCAAA	9;;<<<<<<<<<<<<5<<;<5<<<<<<<<<<<<<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:1
+B7_591:4:159:508:571	147	chr2	989	84	36M	=	834	-191	TGGAAAAAGATGTTCTACGCAAACAGAAACCAAATG	9<6<<<<<<<<<<<;<<;<<<<<;<<<<<<<<<<<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_103:7:166:84:766	163	chr2	990	99	35M	=	1167	212	GGAAAAAGATGTTCTACGCAAACAGAAACCAAATG	<<<<<<<<;<<<<<<<<;<<<<<<;<<<7<;::93	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:1
+EAS56_61:6:283:963:234	99	chr2	992	99	35M	=	1157	200	AAAAAGATGTTCTACGCAAACAGAAACCAAATGAG	<<<<<<<<<<<<<<<;<<<<<<<<<<<;<<;<<;<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_63:4:184:659:377	99	chr2	992	99	35M	=	1173	216	AAAAAGATGTTCTACGCAAACAGAAACCAAATGAG	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;;;;;	MF:i:18	Aq:i:70	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_28:4:305:707:258	147	chr2	992	58	36M	=	831	-197	AAAAAGATGTTCTACGCAAGCAGAAACCAAATGAGA	3<<7<,;<<<<0<66<6+<%<<<.<<<<<<<<<9<<	MF:i:18	Aq:i:17	NM:i:1	UQ:i:4	H0:i:0	H1:i:1
+EAS219_1:7:20:1444:328	99	chr2	993	99	35M	=	1149	191	AAAAGATGTTCTACGCAAACAGAAACCAAATGAGA	<<<<;<<<<<<<<;<<<<<<<<;<<<<<;<;;8:7	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_591:7:157:447:758	147	chr2	994	99	36M	=	833	-197	AAAGATGTTCTACGCAAACAGAAACCAAATGAGAGA	<<<;<<5<</<<6<5<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:7:37:763:1437	163	chr2	994	99	35M	=	1191	232	AAAGATGTTCTACGCAAACAGAAACCAAATGAGAG	;;;;;6;;;;;;;;;:;6;5;5;;;;;76;767/7	MF:i:18	Aq:i:64	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_39:6:94:1273:1462	163	chr2	995	99	35M	=	1166	206	AAGATGTTCTACGCAAACAGAAACCAAATGAGAGA	<<<<<<<<<<<<:<<<<<<<<:<<<<:6:7;744;	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_11:7:74:213:877	147	chr2	996	99	35M	=	816	-215	AGATGTTCTACGCAAACAGAAACCAAATGAGAGAA	<<<<<<<&<<-<-<<<7<<<<<77<<<<<<<<<<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_61:2:168:61:867	163	chr2	997	99	35M	=	1188	226	GATGTTCTACGCAAACAGAAACCAAATGAGAGAAG	====7====================7======6==	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_103:2:307:252:632	163	chr2	998	99	35M	=	1142	179	ATGTTCTACGCAAACAGAAACCAAATGAGAGAAGG	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<:;;<;;	MF:i:18	Aq:i:43	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_108:4:37:604:389	99	chr2	998	99	35M	=	1188	225	ATGTTCTACGCAAACAGAAACCAAATGAGAGAAGG	<<<<<<<<<3<<<<<4<<<<<9<2;949<;35:95	MF:i:18	Aq:i:67	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_65:8:147:687:428	99	chr2	998	99	35M	=	1159	196	ATGTTCTACGCAAACAGAAACCAAATGAGAGAAGG	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:36	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_67:3:114:736:433	83	chr2	998	63	35M	=	832	-201	ATGTTCTACGCAAACAGAAACCAAGTGAGAGAAGG	<9<9+9;<6<9<<;9<<<<<;<<<99<<<<<<<<<	MF:i:18	Aq:i:18	NM:i:1	UQ:i:24	H0:i:0	H1:i:1
+B7_597:8:35:118:589	163	chr2	999	99	35M	=	1188	224	TGTTCTACGCAAACAGAAACCAAATGAGAGAAGGA	<<<<<<<<<<<<<<<<<<<<<<<<<<;<:<<<<<9	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_65:2:127:288:655	83	chr2	999	99	35M	=	803	-231	TGTTCTACGCAAACAGAAACCAAATGAGAGAAGGA	<<:<3<<:<.<<<;<<<<<;<<<<<<<<<<<<<<<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_61:3:260:827:289	83	chr2	999	99	35M	=	836	-198	TGTTCTACGCAAACAGAAACCAAATGAGAGAAGGA	6;99+<<<<<<<<<<<<<<6<<<<<7<<<<<<<<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:5:82:843:1838	147	chr2	999	99	35M	=	804	-230	TGTTCTACGCAAACAGAAACCAAATGAGAGAAGGA	888829;;;;;;;;;;;;;;:;;;;;;;;;;;;;;	MF:i:18	Aq:i:67	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS188_7:8:64:350:174	163	chr2	1000	99	35M	=	1166	201	GTTCTACGCAAACAGAAACCAAATGAGAGAAGGAG	<<<<<<<<<<<<<<<<<<<<<:<<<<<6<<<<<:<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_1:2:8:327:522	83	chr2	1001	99	35M	=	826	-210	TTCTACGCAAACAGAAACCAAATGAGAGAAGGAGT	;;4;<-<-<<<7<<<<<;<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:49	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_99:7:126:361:250	147	chr2	1002	99	35M	=	810	-227	TCTACGCAAACAGAAACCAAATGAGAGAAGGAGTA	72:;7</<<<:<-7<<:<<<<<<<:<6<+:<<<<<	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_64:4:189:571:366	163	chr2	1002	99	35M	=	1194	227	TCTACGCAAACAGAAACCAAATGAGAGAAGGAGTA	<<<<<<<<<<<<<<<<<<<<<<<<<7<:<<99;;;	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_28:3:202:275:776	163	chr2	1002	99	36M	=	1196	230	TCTACGCAAACAGAAACCAAATGAGAGAAGGAGTAG	<<<<<<<<<<<<<<<<<<<<<;<<9<;;<<<;<;<;	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS188_7:6:194:998:663	163	chr2	1002	99	35M	=	1165	198	TCTACGCAAACAGAAACCAAATGAGAGAAGGAGTA	<<<<<<<<<;<<<<<<<<<<<<<<<<<<<<<<<8<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_593:5:30:599:589	99	chr2	1003	99	36M	=	1188	221	CTACGCAAACAGAAACCAAATGAGAGAAGGAGCAGC	<<<<<<<<<<<<<<<<<<<<<<<<<<;;<<;<&<<;	MF:i:18	Aq:i:72	NM:i:1	UQ:i:5	H0:i:1	H1:i:0
+EAS112_34:4:92:412:435	99	chr2	1003	89	35M	=	1184	216	CTACGCAAACAGAAACCAANTGAGAGAAGGAGTAG	<<<<<<<4<<<<<<<<<66!<<<<<<6<<77<<97	MF:i:18	Aq:i:43	NM:i:1	UQ:i:0	H0:i:0	H1:i:1
+B7_610:2:75:887:149	83	chr2	1004	99	35M	=	823	-216	TACGCAAACAGAAACCAAATGAGAGAAGGAGTAGC	:<:<0<<<;<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:23	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:1:2:1422:1820	163	chr2	1004	99	35M	=	1164	195	TACGCAAACAGAAACCAAATGAGAGAAGGAGTAGC	;7;;;;;;;;:;;;;;;;;;;;;;;;;;;;77777	MF:i:18	Aq:i:54	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:6:90:561:850	83	chr2	1004	85	35M	=	827	-212	TACGCAAACAGAAACCAAATGAGAGAAGGAGTAGC	78376<;;9<;<<;:9<<<6;<;<;;8;;<;/;;;	MF:i:18	Aq:i:19	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS188_7:4:164:719:947	147	chr2	1005	99	35M	=	813	-227	ACGCAAACAGAAACCAAATGAGAGAAGGAGTAGCT	===,=========6====)================	MF:i:18	Aq:i:64	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_97:5:154:952:558	99	chr2	1007	99	35M	=	1173	201	GCAAACAGAAACCAAATGAGAGAAGGAGTAGCTAT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<:<:<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_19:3:58:923:1915	83	chr2	1007	99	40M	=	846	-201	GCAAACAGAAACCAAATGAGAGAAGGAGTAGCTATACTTA	:+;;;8<<<<<<,<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_103:3:253:175:31	99	chr2	1008	72	35M	=	1187	214	CAAACAGAAACCAAATGAGAGAAGGAGTAGCTATA	<<<<<<<<<<<<<<<<<<<<<<:<<<<<<<:<;;;	MF:i:18	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_595:2:29:729:70	83	chr2	1009	51	35M	=	850	-194	AAACAGAAACCAAATGAGAGAAGGAGTAGCTATAC	<<<:<<<<<<7<<<<<<7<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:51	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_95:4:174:157:573	163	chr2	1012	99	35M	=	1191	214	CAGAAACCAAATGAGAGAAGGAGTAGCTATACTTA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:54	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_67:7:197:399:319	163	chr2	1012	99	35M	=	1189	212	TAGAAACCAAATGAGAGAAGGAGTAGCTATACTTA	+<<<<<<<<<<<<<<<<<;<<<<<<<<<<<;;<<;	MF:i:18	Aq:i:47	NM:i:1	UQ:i:27	H0:i:0	H1:i:1
+EAS54_65:7:68:825:405	83	chr2	1015	30	35M	=	835	-215	AAACCAAATGAGAGAAGGAGTAGCTATACTTATAT	<<<;<<<<9<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_28:4:13:701:55	99	chr2	1015	99	36M	=	1187	208	AAACCAAATGAGAGAAGGAGTAGCTATACTTATATC	<<<<<<<<<9<<<9<<<<<<6<<<<<<<6<<6<<6+	MF:i:18	Aq:i:48	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_593:2:128:555:941	153	chr2	1016	10	36M	*	0	0	AACCAAAAGAGAGAAGGAGTAGTTATACACATATCA	55--555560355$55555555.57757$7555577	MF:i:32	Aq:i:10	NM:i:4	UQ:i:58	H0:i:0	H1:i:0
+EAS219_FC30151:1:53:140:421	163	chr2	1016	99	35M	=	1185	204	AACCAAATGAGAGAAGGAGTAGCTATACTTATATC	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:48	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_30:1:64:526:339	83	chr2	1019	96	35M	=	819	-235	CAAATGAGAGAAGGAGTATCTATACTTATATCAGA	3<<<7<<;<<<<<<<<<<<;<<<<;<<<<<<<<<<	MF:i:18	Aq:i:47	NM:i:1	UQ:i:27	H0:i:0	H1:i:1
+EAS192_3:3:194:378:230	163	chr2	1022	99	35M	=	1198	211	ATGAGAGAAGGAGTAGCTATACTTATATCAGATAA	<<<<<<<<<<<<<:<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:49	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_105:1:45:239:851	163	chr2	1023	61	35M	=	1211	223	TGAGAGAAGGAGTAGCTATACTTATATCAGATAAA	<<88;<208<9<;6<<<6269;94<&401-662&2	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:6:39:956:676	163	chr2	1023	99	35M	=	1191	203	TGAGAGAAGGAGTAGCTATACTTATATCAGATAAA	;;;;;;;;;;;;9;;;;;;;;;;;;;;;9957777	MF:i:18	Aq:i:44	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS218_1:2:15:1763:1143	99	chr2	1023	99	35M	=	1193	205	TGAGAGAAGGAGTAGCTATACTTATATCAGATAAA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:46	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_57:5:309:109:987	163	chr2	1024	99	35M	=	1194	205	GAGAGAAGGAGTAGCTATACTTATATCAGATAAAG	<<<<<<<<<<<<<<<<<<<<<<<<<<9<<<;<;;;	MF:i:18	Aq:i:51	NM:i:0	UQ:i:0	H0:i:1	H1:i:2
+B7_593:3:102:856:670	147	chr2	1025	99	36M	=	836	-225	AGAGAAGGAGTAGCTATACTTATATCAGATAAAGCA	;;<<<<:<<<:<<4<<<<<<<<;<<;<<<<<<<<<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:4
+B7_610:6:107:252:533	163	chr2	1025	60	35M	=	1173	183	AGAGAAGGAGTAGCTATACTTATATCAGATAAAGC	<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<;<<;9	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:3	H1:i:3
+EAS56_65:4:126:966:514	83	chr2	1027	99	35M	=	865	-197	AGAAGAAGTAGCTATACTTATATCAGATAAAGCAC	<4<<<%<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:30	NM:i:1	UQ:i:4	H0:i:1	H1:i:1
+EAS114_26:1:171:527:247	163	chr2	1027	67	35M	=	1194	202	AGAAGGAGTAGCTAGACTTATATCAGATAAAGCAC	=4==4===8==99=&=8+9=19+.2.6'=99+999	MF:i:18	Aq:i:30	NM:i:1	UQ:i:5	H0:i:0	H1:i:3
+EAS1_105:1:234:185:359	163	chr2	1029	46	35M	=	1183	189	AAGGAGTAGCTATACTTATATCAGATAAAGCACAC	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;;9--:	MF:i:18	Aq:i:17	NM:i:0	UQ:i:0	H0:i:1	H1:i:11
+EAS51_66:3:155:375:623	83	chr2	1029	99	35M	=	849	-215	AAGGAGTAGCTATACTTATATCAGATAAAGCACAC	;;;;<<:<<<<;<<;<<<<<<;<<;<<<<<<<<<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:1
+EAS139_19:5:4:939:2021	163	chr2	1031	99	40M	=	1197	206	GGAGTAGCTATACTTATATCAGATAAAGCACACTTTAAAT	<<<<<<<<<<<<<<<<<<<<<97<<<;<<;<7;<<:48::	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:2	H1:i:2
+EAS220_1:2:50:513:882	163	chr2	1031	99	35M	=	1192	196	GGAGTAGCTATACTTATATCAGATAAAGCACACTT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;;;;;	MF:i:18	Aq:i:23	NM:i:0	UQ:i:0	H0:i:2	H1:i:14
+EAS1_103:5:188:20:592	163	chr2	1032	95	35M	=	1202	205	GAGTAGCTATACTTATATCAGATAAAGCACACTTT	<<<<<<<<<<<<<<<<<<<<;;<<<<:<<<;<;;<	MF:i:18	Aq:i:22	NM:i:0	UQ:i:0	H0:i:3	H1:i:16
+EAS114_45:3:35:896:1588	163	chr2	1032	91	35M	=	1205	208	GAGTAGCTATACTTATATCAGATAAAGCACACTTT	;;;;;;;;;;;;;;;;;;;;8;;;;;8;;;88989	MF:i:18	Aq:i:21	NM:i:0	UQ:i:0	H0:i:3	H1:i:18
+EAS1_108:6:73:735:329	147	chr2	1035	99	35M	=	868	-202	TAGCTATACTTATATCAGATAAAGCACACTTTAAA	;;;9;<<7<<<<<<<<<<<<<<<<<<<2<<<<<<<	MF:i:18	Aq:i:39	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_28:7:133:514:754	83	chr2	1036	63	36M	=	855	-217	AGCTATACTTATATCAGATAAAGCACACTTTAAATC	;;4;<;<;<<<<<<<<;<<<<<<;<<<<<<<<<<<<	MF:i:18	Aq:i:19	NM:i:0	UQ:i:0	H0:i:1	H1:i:1
+EAS218_1:4:62:561:531	163	chr2	1036	99	35M	=	1203	202	AGCTATACTTATATCAGATAAAGCACACTTTAAAT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:1
+B7_593:6:119:428:415	83	chr2	1037	99	36M	=	876	-197	GCTATACTTATATCAGATAAAGCACACTTTAAATCA	84<<<<;;<<<<<:<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:46	NM:i:0	UQ:i:0	H0:i:1	H1:i:1
+EAS114_30:2:226:885:729	147	chr2	1037	98	35M	=	867	-205	GCTGAACTTACATCAGATAAAGCACACTTTAAATC	/*220%.(;<%<3.<<<4<<<<86;<8<<8<<<<<	MF:i:18	Aq:i:30	NM:i:3	UQ:i:36	H0:i:0	H1:i:1
+EAS1_108:1:189:863:213	163	chr2	1039	99	35M	=	1202	198	TATACTTATATCAGATAAAGCACACTTTAAATCAA	<<<<<<<<<<<<<<<<<<<<;<<<;<<<<;7<9;<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:2
+B7_597:4:146:961:63	83	chr2	1041	86	35M	=	861	-215	TACTTATATCAGATAAAGCACACTTTAAATCAACA	7;;<<<<<;<<<7<<<<<<<<;;<<;<;<<;<<<7	MF:i:18	Aq:i:37	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_62:3:68:996:104	99	chr2	1041	70	35M	=	1214	208	TACTTATATCAGATAAAGCACACTTTAAATCAACA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<	MF:i:18	Aq:i:21	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:6:47:1791:444	163	chr2	1041	74	35M	=	1213	207	TACTTATATCAGATAAAGCACACTTTAAATCAACA	;3;;;;;;;;;;;;;;;;;;;;;;;;;;;877977	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_19:4:1:156:196	147	chr2	1042	77	40M	=	867	-215	ACTTATATCAGATAAAGCACACTTTAAATCAACAACAGTA	:::::<<<<<<<<<<<<<4<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_1:8:70:1349:1788	163	chr2	1043	99	35M	=	1203	195	ATTATATCAGATAAAGCACACTTTAAATCAACAAC	&<8<<<85:580;<:0-><;>588>9<>7:<0<9;	MF:i:18	Aq:i:30	NM:i:1	UQ:i:5	H0:i:0	H1:i:1
+B7_589:2:30:644:942	99	chr2	1045	83	35M	=	1229	219	TATATCAGATAAAGCACACTTTAAATCAACAACAG	<<<<<<<<<<<<<<<<<<<<<<<9<<<<<<9;<9<	MF:i:18	Aq:i:22	NM:i:0	UQ:i:0	H0:i:1	H1:i:3
+B7_591:2:123:924:645	83	chr2	1045	84	36M	=	861	-220	TATATCAGATAAAGCACACTTTAAATCAACAACAGT	;<<<<*<<<<<<</7<2<8<<<<<<<4<<<<<<<<<	MF:i:18	Aq:i:11	NM:i:0	UQ:i:0	H0:i:1	H1:i:2
+B7_589:5:147:405:738	83	chr2	1048	99	35M	=	870	-213	ATCAGATAAAGCACACTTTAAATCAACAACAGTAA	<9/<:<<<<<<<<7</<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:24	NM:i:0	UQ:i:0	H0:i:1	H1:i:2
+EAS54_61:3:155:758:710	83	chr2	1048	98	35M	=	859	-224	ATCAGATAAAGCACACTTTAAATCAACAACAGTAA	=46=4=5===:========:=7=7======11===	MF:i:18	Aq:i:22	NM:i:0	UQ:i:0	H0:i:1	H1:i:2
+EAS54_73:7:254:572:431	83	chr2	1048	97	35M	=	891	-192	ATCAGATAAAGCACACTTTAAATCAACAACAGTAA	<63<;<;<<<:7<:<7;<:<<<<:<<<<7<<<<:<	MF:i:18	Aq:i:22	NM:i:0	UQ:i:0	H0:i:1	H1:i:2
+EAS56_57:7:33:954:724	163	chr2	1049	97	35M	=	1210	196	TCAGATAAAGCACACTTTAAATCAACAACAGTAAA	;<<<<<<<<<<<<<8<<<<:<;;<<;;<;<<;;;;	MF:i:18	Aq:i:24	NM:i:0	UQ:i:0	H0:i:1	H1:i:2
+EAS56_63:6:102:816:260	99	chr2	1049	99	35M	=	1225	211	TCAGATAAAGCACACTTTAAATCAACAACAGTAAA	<<<<<<<<<;<<<<<<<<<<<<<<<<<<<<;;;;;	MF:i:18	Aq:i:23	NM:i:0	UQ:i:0	H0:i:1	H1:i:2
+EAS192_3:5:197:914:256	99	chr2	1049	97	35M	=	1204	190	TCAGATAAAGCACACTTTAAATCAACAACAGTAAA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<8;:::	MF:i:18	Aq:i:24	NM:i:0	UQ:i:0	H0:i:1	H1:i:2
+EAS56_65:4:150:94:843	147	chr2	1050	0	35M	=	868	-217	CAGATACATCCCACTTTAAATCAACCACAGTAAAA	4<9<41*747*7<:9<:7:::<72;+<;::<7<<<	MF:i:18	Aq:i:0	NM:i:4	UQ:i:47	H0:i:0	H1:i:0
+EAS1_108:5:321:712:224	163	chr2	1051	58	35M	=	1220	204	AGATAAAGCACACTTTAAATCAACAACAGAAAAAT	<<<<<<<<2<<<<<<<<<<<<<<<:<<<<(<<:<,	MF:i:18	Aq:i:28	NM:i:1	UQ:i:7	H0:i:1	H1:i:2
+EAS114_32:3:236:475:254	83	chr2	1051	99	35M	=	880	-206	AGATAAAGCACACTTTAAATCAACAACAGTAAAAT	<:<<<<<;9<7<;<<<<<<<<<<9<<<<<<<<<<<	MF:i:18	Aq:i:43	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS218_4:7:72:1288:1211	99	chr2	1052	84	35M	=	1235	218	GATAAAGCACACTTTAAATCAACAACAGTAAAATA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:2
+EAS54_65:2:264:157:150	99	chr2	1054	30	35M	=	1238	219	TAAAGCACACTTTAAATCAACAACAGTAAAATAAA	<<<<<<9<9<<<<.9;<<9&<97<;9933309605	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:2
+EAS1_95:7:310:800:761	163	chr2	1055	99	35M	=	1249	229	AAAGCACACTTTAAATCAACAACAGTAAAATAAAA	===========================+=======	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS219_1:3:88:465:1877	99	chr2	1055	99	35M	=	1212	192	AAAGCACACTTTAAATCAACAACAGTAAAATAAAA	<<<<<<<<<<;<<<<<<<<<<<<<<<<7<<<<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS192_3:7:66:891:294	163	chr2	1057	99	35M	=	1233	211	AGCACACTTTAAATCAACAACAGTAAAATAAAACA	<<<<<<<<<<<<<<<<<<<<<<<9<<<<<<;<<<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS188_7:3:100:735:530	163	chr2	1058	99	35M	=	1257	234	GCACACTTTAAATCAACAACAGTAAAATAAAACAA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_589:5:68:440:424	99	chr2	1060	99	35M	=	1237	212	ACACTTTAAATCAACAACAGTAAAATAAAACAAAG	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:2
+EAS220_1:8:66:1046:167	99	chr2	1060	99	35M	=	1241	216	ACACTTTAAATCAACAACAGTAAAATAAAACAAAG	<<<<<:<<<<<<<<<<<<<9<;77<9<7<<;<9;-	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:2
+EAS54_81:6:11:801:386	83	chr2	1061	97	35M	=	868	-228	CACTATAAATCAACAACAGTAAAATAAAACAAAGG	5<2:$6<<<38<<<<;<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:30	NM:i:1	UQ:i:3	H0:i:1	H1:i:1
+EAS114_28:2:141:7:963	163	chr2	1061	85	36M	=	1240	215	CACTTTAAATCAACAACAGTAAAATAAAACAAAGGA	<<<<<<<<<<<<;<:<<<<<<1<<&<;<;<<;,<;5	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_11:2:55:296:1457	147	chr2	1061	99	35M	=	884	-212	CACTTTAAATCAACAACAGTAAAATAAAACAAAGG	-<%63<<<<<1<<<<<5<<<<<<<<<<<<<<<7<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:1
+EAS139_19:1:58:726:1746	83	chr2	1061	99	40M	=	900	-201	CAATTTAAATCAACAACAGTAAAATAAAACAAAGGAGGTC	&:&::;<<<76<<:<<6<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:71	NM:i:1	UQ:i:5	H0:i:1	H1:i:0
+EAS221_1:8:15:881:1932	147	chr2	1061	92	35M	=	886	-210	CACTTTAAATCAACAACAGTAAAATAAAACAAAGG	)<4<<<<<<<4<<4<<4<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:1
+EAS1_95:5:284:212:932	99	chr2	1063	10	35M	=	1257	229	CTTTAAATCAACAACAATAAAAAAAAACAAAGGAG	<<9<<<<<<<<<<<<<&&<<<<5<<<<8<<<1:<:	MF:i:18	Aq:i:0	NM:i:2	UQ:i:25	H0:i:0	H1:i:0
+EAS139_19:4:18:1335:1514	99	chr2	1063	99	40M	=	1235	212	CTTTAAATCAACAACAGTAAAATAAAACAAAGGAGGTCAT	<<<;<<<<<<<<<<<<<<<;<:<<;<<<<<<;<;<;;;9;	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_81:6:273:424:207	83	chr2	1066	99	35M	=	891	-210	TAAATCAACAACAGTAAAATAAAACAAAGGAGGTC	;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:62	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS219_1:7:62:1076:540	147	chr2	1066	99	35M	=	882	-219	TAAATCAACAACAGTAAAATAAAACAAAGGAGGTC	6<<;:+=====5=:6===================2	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_71:8:113:856:319	83	chr2	1067	99	33M	=	884	-216	AAATCAACAACAGTAAAATAAAACAAAGGAGGT	<<<77<<:<<;<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_108:8:19:929:765	147	chr2	1069	98	35M	=	919	-185	ATCAACAACAGTAAAATAAAACAAAGGAGGTCATC	<3+<<;<<;<<<<<<<<<<<;<<<<<<<<<<<<<<	MF:i:18	Aq:i:27	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_67:1:88:54:900	163	chr2	1069	68	35M	=	1257	223	ATCAACAACAGAAAAATAAAACAAAGGAGGTCATC	.....&.....,.......................	MF:i:18	Aq:i:19	NM:i:1	UQ:i:11	H0:i:0	H1:i:1
+EAS56_63:7:109:22:383	163	chr2	1071	99	35M	=	1244	208	CAACAACAGTAAAATAAAACAAAGGAGGTCATCAT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<;:<<;<<	MF:i:18	Aq:i:51	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_63:8:4:571:820	83	chr2	1071	99	35M	=	891	-215	CAACAACAGTAAAATAAAACAAAGGAGGTCATCAT	&<<7<<1<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_93:6:255:441:47	99	chr2	1072	99	35M	=	1237	200	AACAACAGTAAAATAAAACAAAGGAGGTCATCATA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<6<;:<;<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_19:3:66:718:481	147	chr2	1072	99	40M	=	891	-221	AACAACAGTAAAATAAAACAAAGGAGGTCATCATACAATG	::5::1<;;<<<<<<1<<<<<<<<<<<<7<<<<<<<<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_26:1:155:807:19	147	chr2	1074	99	35M	=	867	-242	CAACAGTAAAATAAAACAAAGGAGGTCATCATACA	:==4=5:====:============:==========	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_11:3:43:1229:1855	163	chr2	1074	99	35M	=	1244	205	CAACAGTAAAATAAAACAAAGGAGGTCATCATACA	<<<<<<<<<<<<<<<<<<<<<<<<<4<<<<<<<<<	MF:i:18	Aq:i:48	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_593:2:125:875:553	99	chr2	1075	99	36M	=	1233	194	AACAGTAAAATAAAACAAAGGAGGTCATCATACAAT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<;<;	MF:i:18	Aq:i:53	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_65:7:118:775:467	163	chr2	1075	99	35M	=	1245	205	AACAGTAAAATAAAACAAAGGAGGTCATCATACAA	<<<<<<<<<<<<<<<<<<<<<<<<;<<<<<<<<<;	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_105:2:301:161:195	99	chr2	1076	75	35M	=	1239	198	ACAGTAAAATAAAACAAAGGAGGTCATCATACAAT	<<<<<<<<<<<<<<<<<<<<<<<;<<<<<<:<<<<	MF:i:18	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_64:6:54:695:952	99	chr2	1076	99	35M	=	1264	223	ACAGTAAAATAAAACAAAGGAGGTCATCATACAAT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_95:1:77:589:741	163	chr2	1078	99	35M	=	1263	220	AGTAAAATAAAACAAAGGAGGTCATCATACAATGA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<:<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_62:3:200:263:280	163	chr2	1078	99	35M	=	1236	193	AGTAAAATAAAACAAAGGAGGTCATCATACAATGA	<<<<<<<<<<<<<<<<<<<<;<<<<<<<<<;8<;1	MF:i:18	Aq:i:62	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_11:5:64:199:1288	99	chr2	1079	77	35M	=	1240	196	GTAAAATAAAACAAAGGAGGTCATCATACAATGAT	<<<<<<<<<<<<<<;<<<<<<<<<<<<<<;<<<;<	MF:i:18	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_99:8:27:228:31	99	chr2	1082	99	35M	=	1264	217	AAATAAAACAAAGGAGGTCATCATACAATGATAAA	<<<<<<<<<<<<<<<<<;9<:;<<<<<<75<<<<<	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_57:5:214:644:390	83	chr2	1082	72	35M	=	919	-198	AAATAAAACAAAGGAGGTCATGATACAATGATAAA	<<<;<<<<<<<<<<<<<<<<<&<<<<<<<<<<<<<	MF:i:18	Aq:i:27	NM:i:1	UQ:i:5	H0:i:0	H1:i:1
+EAS114_45:2:79:554:354	99	chr2	1082	63	35M	=	1242	195	AAATAAAACAAAGGAGGTCATCATACAATGATAAA	17;<;;+<<;;;;93;;:;3;;;;1;;;;<77744	MF:i:18	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_57:5:303:542:924	163	chr2	1083	76	35M	=	1242	194	AATAAAACAAAGGAGGTCATCATACAATGATAAAA	<<<;<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<;	MF:i:18	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_595:8:26:242:35	99	chr2	1084	99	35M	=	1251	202	ATAAAACAAAGGAGGTCATCATACAATGATAAAAA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<<<<;	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_28:5:163:832:715	83	chr2	1085	99	36M	=	918	-203	TAAAACAAAGGAGGTCATCATACAATGATAAAAAGA	;<<<<9<<<<<<<<;;<<7<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:54	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_39:1:98:641:1040	83	chr2	1085	99	35M	=	907	-213	TAAAACAAAGGAGGTCATCATACAATGATAAAAAG	4<<<<7<<<<<<<<<:<<;<;<<<<<<<<<<<<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_39:7:32:562:1695	99	chr2	1085	76	35M	=	1258	208	TAAAACAAAGGAGGTCATCATACAATGATAAAAAG	<<<<<<<<<<<<<<8<<<<<:<<<<<<<:<8<<<<	MF:i:18	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:7:6:758:988	163	chr2	1087	99	35M	=	1253	201	AAACAAAGGAGGTCATCATACAATGATAAAAAGAT	3+;0;0;;;0;;;;;;5;;;9;;;;90;;;57560	MF:i:18	Aq:i:51	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_66:5:273:545:1001	83	chr2	1088	99	35M	=	913	-210	AACAAAGGAGGTCATCATACAATGATAAAAAGATC	<7(<<72;<2;27<;:<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:67	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_63:2:74:656:272	163	chr2	1088	99	35M	=	1245	192	AACAAAGGAGGTCATCATACAATGATAAAAAGATC	<<<<<<<<<<<<<<<<<<<<<<<<;<<<<<<<<<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_589:5:198:564:731	83	chr2	1089	99	35M	=	898	-226	ACAAAGGAGGTCATCATACAATGATAAAAAGATCA	<6<;<<<<<<:7<<;<<<8<<+<<<<<<<<<<<<<	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_105:6:23:885:274	99	chr2	1089	99	35M	=	1289	235	ACAAAGGAGGTCATCATACAATGATAAAAAGATCA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<4<;;<	MF:i:18	Aq:i:51	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_591:7:22:632:176	83	chr2	1091	99	36M	=	894	-233	AAAGGAGGTCATCATACAATGATAAAAAGATCAATT	<9<<<<<<<-;<;<<7;6;<<<<<<<<<;<<<<<<<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_103:2:184:980:396	83	chr2	1092	99	35M	=	923	-204	AAGGAGGTCATCATACAATGATAAAAAGATCAATT	<<;;<77;;<<;<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:54	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_28:3:110:984:98	99	chr2	1092	99	36M	=	1270	214	AAGGAGGTCATCATACAATGATAAAAAGATCAATTC	98<<<<<<2<<<<<<;;<;;<<<5;5;<<;;<<<<+	MF:i:18	Aq:i:70	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_95:1:202:341:984	147	chr2	1094	99	35M	=	926	-203	GGAGGTCATCATACAATGATAAAAAGATCAATTCA	<<<(<8&<92<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:70	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_65:7:219:40:833	163	chr2	1094	99	35M	=	1278	219	GGAGGTCATCATACAATGATAAAAAGATCAATTCA	<<<<<<<<<<<<<<<<<<<<;<<<<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_39:7:23:1126:1886	99	chr2	1094	99	35M	=	1268	209	GGAGGTCATCATACAATGATAAAAAGATCAATTCA	7<<<7<<<<<<<<7<<<<<<<<<<<<<;8<;<<5<	MF:i:18	Aq:i:70	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_595:3:85:964:950	83	chr2	1095	99	35M	=	910	-220	GAGGTCATCATACAATGATAAAAAGATCAATTCAG	<<8::<<;;<<<;<<6<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_103:7:139:578:951	83	chr2	1095	98	35M	=	919	-211	GAGGTCATCATACAATGATAAAAAGATCAATTCAG	;<0;:&<:9<<<7<<<<<<<<<<<<<<;<<<<<<<	MF:i:18	Aq:i:26	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_53:3:107:738:484	147	chr2	1097	75	35M	=	926	-206	GGTCATCATACAATGATAAAAAGATCAATTCAGCA	.8/<<<7<8<<<<<<<<<<<<<<<<9<<<<<<<<<	MF:i:18	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:1
+EAS114_39:4:93:77:1338	83	chr2	1098	10	35M	=	940	-193	GTCATCATACAATGAAAAAAAGATCAATTCAGCAA	<<7<7<<<<<1<7<<&97;;<1<;1<<7<;7<<;<	MF:i:18	Aq:i:0	NM:i:1	UQ:i:5	H0:i:0	H1:i:1
+B7_610:8:68:570:705	147	chr2	1100	99	35M	=	910	-225	CATCATACAATGATAAAAAGATCAATTCAGCAAGA	4<;4<;;:<<<<<<<<;<<<<<<<<<<<<<<<<;<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:3
+EAS51_62:1:38:250:647	83	chr2	1100	71	35M	=	933	-202	AATAATAAAATGATAAAAAGATCAATTCAGCAAGA	+<&+<1<,<<7<<7<<<<<<<1,<<<<7<<2<<<<	MF:i:18	Aq:i:0	NM:i:3	UQ:i:34	H0:i:0	H1:i:3
+EAS1_93:8:13:325:483	83	chr2	1101	99	35M	=	919	-217	ATCATACAATGATAAAAAGATCAATTCAGCAAGAA	;:;<;=:========;==========;========	MF:i:18	Aq:i:27	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_59:1:128:584:952	163	chr2	1101	99	35M	=	1277	211	ATCATACAATGATAAAAAGATCAATTCAGCAAGAA	<<<<<<<<<<<<<<+<;<<<<<<;<<<;<<<+<66	MF:i:18	Aq:i:61	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS192_3:4:184:237:476	83	chr2	1101	99	35M	=	925	-211	ATCATACAATGATAAAAAGATCAATTCAGCAAGAA	<;2<;<4<<;<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:4
+EAS51_64:6:300:622:86	163	chr2	1102	99	35M	=	1264	197	TCATACAATGATAAAAAGATCAATTCAGCAAGAAG	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<:<<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_39:7:57:1114:2032	147	chr2	1102	99	35M	=	931	-206	TATTACAATGATAAAAAGATCAATTCAGCAAGAAG	;+!5<4<<<<<<<<<<<<<;<&<;7<<<<<<<<<<	MF:i:18	Aq:i:30	NM:i:2	UQ:i:10	H0:i:1	H1:i:6
+B7_593:3:310:193:629	163	chr2	1103	99	36M	=	1267	200	CATACAATGATAAAAAGATCAATTCAGCAAGAAGAT	<<<<<<<<<<<<<<<<<<<<<;<<<<<<<<<<<<<;	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_610:2:6:529:366	99	chr2	1103	99	35M	=	1291	223	CATACAATGATAAAAAGATCAATTCAGCAAGAAGA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS218_1:2:10:686:1024	83	chr2	1103	99	35M	=	947	-191	CATACAATGATAAAAAGATCAATTCAGCAAGAAGA	&<<<3<<<<<<<<<<<<<<7<<<<<<<<<<7<<<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:3
+EAS114_45:7:14:978:1296	163	chr2	1104	90	35M	=	1249	180	ATACAATGATAAAAAGATCAATTCAGCAAGAAGAT	;6;;;;;;;;;;;:;;;;;;;6;;;;;;;;77777	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:5
+EAS56_57:2:237:855:581	99	chr2	1105	87	35M	=	1271	201	TACAATGATAAAAAGATCAATTCAGCAAGAAGATA	<;4<7<<<;47<<74<:*<<2:<<7.799:2<<9:	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:4
+EAS139_19:7:85:262:751	163	chr2	1105	99	40M	=	1305	240	TACAATGATAAAAAGATCAATTCAGCAAGAAGATATAACC	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<:::92	MF:i:18	Aq:i:47	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_61:6:10:106:737	83	chr2	1106	99	35M	=	947	-194	ACAATGATAAAAAGATCAATTCAGCAAGAAGATAT	<-<<;<<<<<<<<<<<;<<<<;<<;<<<<<<<<<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:6
+B7_610:6:143:620:158	163	chr2	1107	99	35M	=	1283	211	CAATGATAAAAAGATCAATTCAGCAAGAAGATATA	<<<<<<<<<<;<<<<<<<<<<<<<<<<<<<<<;<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:3
+EAS54_67:6:198:503:669	147	chr2	1107	99	35M	=	912	-230	CAATGATAAAAAGATCAATTCAGCAAGAAGATATA	5<<:<<;<<<<<<<;;<<9<<<<<<<<;<<<<;<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:2
+EAS192_3:6:116:464:261	147	chr2	1107	99	35M	=	934	-208	CAATGATAAAAAGATCAATTCAGCAAGAAGATATA	;<<;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:2
+EAS54_73:5:263:557:988	99	chr2	1108	84	35M	=	1289	216	AATGATAAAAAGATCAATTCAGCAAGAAGATATAA	<<<<<<<<<<<<<<<<<<<<<;;<<<<<<<<;<<<	MF:i:18	Aq:i:18	NM:i:0	UQ:i:0	H0:i:1	H1:i:8
+EAS139_19:1:53:463:1132	83	chr2	1109	99	40M	=	915	-234	ATGATAAAAAGATCAATTCAGCAAGAAGATATAACCATCC	;::;:<<<<<<<<:<<;<<<<8<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS220_1:8:46:1528:799	99	chr2	1109	96	35M	=	1306	232	ATGATAAAAAGATCAATTCAGCAAGAAGATATAAC	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<	MF:i:18	Aq:i:19	NM:i:0	UQ:i:0	H0:i:1	H1:i:7
+EAS54_81:7:324:472:791	99	chr2	1110	89	35M	=	1274	199	TGATAAAAAGATCAATTCAGCAAGAAGATATAACC	<<<<<<<<:<<<<<<<<<<<<<<:<<<<<<<<<:3	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:3
+EAS54_61:8:4:173:814	163	chr2	1111	99	35M	=	1289	213	GATAAAAAGATCAATTCAGCAAGAAGATATAACCA	=====================<==========;==	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:4
+B7_593:3:303:131:673	83	chr2	1112	99	36M	=	947	-201	ATAAAAAGATCAATTCAGCAAGAAGATATAACCATC	<;<<<<<<<<:<<<<;<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_103:4:235:899:847	147	chr2	1112	99	35M	=	950	-197	ATAAAAAGATCAATTCAGCAAGAAGATATAACCAT	<7<<<<<<<<:<<<<:<</<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:51	NM:i:0	UQ:i:0	H0:i:1	H1:i:2
+EAS1_105:8:179:119:876	83	chr2	1112	60	35M	=	917	-230	ATAAAAAGATCAATTCAGCAAGAAGATATAACCAT	<<<<<<<7<<<<<<;;<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:2
+EAS56_59:2:162:272:415	147	chr2	1112	83	35M	=	923	-224	ATAAAAAGATCAATTCAGCAAGAAGATATAACCAT	=7=======;5==<<6==1==<=============	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:2
+EAS114_45:6:44:77:1255	83	chr2	1113	99	35M	=	955	-193	TAAAAAGATCAATTCAGCAAGAAGATATAACCATC	79998;;;9:;<696<;.<;;<<;<;<;<;;;<8;	MF:i:18	Aq:i:67	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_99:2:162:257:203	163	chr2	1114	99	35M	=	1301	222	AAAAAGATCAATTCAGCAAGAAGATATAACCATCC	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;;<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_39:3:55:464:146	99	chr2	1114	99	35M	=	1295	216	AAAAAGATCAATTCAGCAAGAAGATATAACCATCC	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:45	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_97:6:308:667:658	147	chr2	1116	34	35M	=	918	-233	AAAGATCACTTCAGCAATAAGATATAACCATCCTA	<9;;;45;&<;&.<5683;84+<;<;+8<;<<8;<	MF:i:18	Aq:i:10	NM:i:2	UQ:i:23	H0:i:0	H1:i:0
+EAS56_57:4:98:862:154	163	chr2	1116	99	35M	=	1290	209	AAAGATCAATTCAGCAAGAAGATATAACCATCCTA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<9<:99<;	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:2
+EAS56_61:5:263:314:696	83	chr2	1117	99	35M	=	953	-199	AAGATCAATTCAGCAAGAAGATATAACCATCCTAC	<<;<;:<<<<7<<:<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS220_1:8:83:1456:1854	163	chr2	1117	99	35M	=	1275	193	AAGATCAATTCAGCAAGAAGATATAACCATCCTAC	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<2<	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_103:4:231:815:626	83	chr2	1119	99	35M	=	940	-214	GATCAATACAGCAAGAAGATATAACCATCCTACTA	'<4%<<<22<<,<<;<<4;<<<<<<<<<<<<<<7<	MF:i:18	Aq:i:41	NM:i:1	UQ:i:17	H0:i:0	H1:i:1
+EAS114_32:4:246:647:765	83	chr2	1119	99	35M	=	937	-217	GATCAATTCAGCAAGAAGATATAACCATCCTACTA	9<+,<<&,39<,<;<<<<<<<&<<<<;0<<3;<<<	MF:i:18	Aq:i:62	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_593:7:256:354:173	83	chr2	1121	99	36M	=	957	-200	TCAATTCAGCAAGAAGATATAACCATCCTACTAAAT	-9<<:9<<;6<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_73:5:53:61:31	83	chr2	1122	99	35M	=	949	-208	CAATTCAGCAAGAAGATATAACCATCCTACTAAAT	5;;<95<<5<<<<<<<<<<:5;<<<<<<<<<<<<<	MF:i:18	Aq:i:66	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_28:3:308:509:948	99	chr2	1123	99	36M	=	1298	211	AATTCAGCAAGAAGATATAACCATCCTACTAAATAC	<9<<<<<<<;<7<<;<<<<<<<;<<<<7<<;2;<<<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_32:2:247:900:123	147	chr2	1123	99	35M	=	920	-238	AATTCAGCAAGAAGATATAACCATCCTACTAAATA	;;;;.<<4<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:51	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_32:3:307:113:346	83	chr2	1123	99	35M	=	938	-220	AATTCAGCAAGAAGATATAACCATCCTACTAAATA	<<<<9<<1<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_589:1:168:69:249	83	chr2	1125	99	35M	=	936	-224	TTCAGCAAGAAGATATAACCATCCTACTAAATACA	;0;<;;<<<<<<<<<<<<<;<<<8<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:2:54:1886:719	147	chr2	1125	99	35M	=	941	-219	TTCAGCAAGAAGATATAACCATCCTACTAAATACA	883777;;:;;;;;;;;;;;;;;;;;;;;;;;;;;	MF:i:18	Aq:i:66	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_597:7:94:273:165	147	chr2	1128	99	35M	=	945	-218	AGAAAGAAGATATAACCATCCTACTAAATACATAT	;3&;;:<<:<-<-<<8:<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:69	NM:i:1	UQ:i:5	H0:i:1	H1:i:0
+EAS1_95:7:155:530:532	163	chr2	1128	99	35M	=	1319	226	AGCAAGAAGATATAACCATCCTACTAAATACATAT	===================================	MF:i:18	Aq:i:47	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_19:5:61:1885:163	163	chr2	1128	99	40M	=	1281	193	AGCAAGAAGATATAACCATCCTACTAAATACATATGCACC	<<<<<<<<<<<<<<<<<;<<<<<<<<<<<<<<<<9::::4	MF:i:18	Aq:i:79	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_597:6:193:661:771	83	chr2	1129	99	35M	=	952	-212	GCAAGAAGATATAACCATCCTACTAAATACATATG	:&<<<<<<<<<<<<<;<<<;<<;<<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_19:6:75:1503:1399	83	chr2	1130	99	40M	=	969	-201	CAAGAAGATATAACCATCCTACTAAATACATATGCACCTA	&;;8;<<<;<<<<,6<<70<<7<<<<<<9<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_597:2:42:28:552	163	chr2	1131	99	35M	=	1294	198	AAGAAGATATAACCATCCTACTAAATACATATGCA	<<<<<<<<<<<<<<<<<<<<<<<<;<;<3<:;9;8	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_95:4:61:631:567	147	chr2	1131	99	35M	=	957	-209	AAGAAGATATAACCATCCTACTAAATACATATGCA	<<7<<<<<<<<</<<;<;<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_71:3:257:288:731	147	chr2	1131	99	35M	=	939	-227	AAGAAGATATAACCATCCTACTAAATACATATGCA	<<:<<7<<<<<;<5<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:68	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_26:2:214:950:32	83	chr2	1132	99	35M	=	947	-220	AGAAGATATAACCATCCTACTAAATACATATGCAC	=&==4======:;==6<==:===============	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_610:1:12:88:200	83	chr2	1133	99	35M	=	968	-200	GAAGATATAACCATCCTACTAAATACATATGCACC	9<<;<<<;<;6;<;:<<<7<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_93:5:256:444:399	163	chr2	1133	99	35M	=	1289	191	GAAGATATAACCATCCTACTAAATACATATGCACC	<<<<<<<<<<<<<<<<<<<<<<<<<;;<<<-;<<8	MF:i:18	Aq:i:68	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_65:4:174:753:617	99	chr2	1136	75	35M	=	1299	198	GATATAACCATCCTACTAAATACATATGCACCTAA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<;;<<<<<	MF:i:18	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_105:1:115:226:443	99	chr2	1137	99	35M	=	1314	212	ATATAACCATCCTACTAAATACATATGCACCTAAC	<<<<<<<<<<<<<<<<;<<<<<<<<<<<<;<<<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:3:26:1867:162	163	chr2	1137	70	35M	=	1299	197	ATATAACCATCCTACTAAATACATATGCACCTAAC	;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;78698	MF:i:18	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_105:3:308:66:538	99	chr2	1138	99	35M	=	1321	218	TATAACCATCCTACTAAATACATATGCACCTAACA	<<<<<<<<<<<<<<<<<<<<<<<<<;<<<<<<<;<	MF:i:18	Aq:i:45	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_595:3:229:543:583	147	chr2	1139	99	35M	=	976	-198	ATAACCATCCTACTAAATACATATGCACCTAACAC	</<;+5<855;<6<<<<;<<<<<<9<<<<<<<<<<	MF:i:18	Aq:i:65	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_99:1:17:595:863	163	chr2	1139	89	35M	=	1289	185	ATAACCATCCTACTAAATACACATGCACCTAACTC	:<4:<<1:<<<9<+<+1<%<7&&9-71<17)7</4	MF:i:18	Aq:i:33	NM:i:2	UQ:i:19	H0:i:0	H1:i:1
+EAS51_62:7:248:17:435	147	chr2	1139	99	35M	=	969	-205	ATAACCATCCTACTAAATACATATGCACCTAACAC	<1<<88++<:<<:;<;<<<:<<<;<<<<<<<<<<<	MF:i:18	Aq:i:43	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_81:6:35:186:412	99	chr2	1139	99	35M	=	1306	202	ATAACCATCCTACTAAATACATATGCACCTAACAC	<<<<<<<<4<<<<<:<<<<<<:<<<<<<<<<;;<:	MF:i:18	Aq:i:70	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_103:2:307:252:632	83	chr2	1142	99	35M	=	998	-179	ACCATCCTGCTAAATACATATGCACCTAACACAAG	<77<;,5<,9<<<<<<;<<<<<7<;<<<<<<<<<<	MF:i:18	Aq:i:43	NM:i:1	UQ:i:11	H0:i:0	H1:i:1
+EAS1_108:7:108:440:208	147	chr2	1142	99	35M	=	975	-202	CCCATCCTACTAAATACATATGCACCTAACACAAG	+35:486<<4<<<<<<<<<<<-<<<<<7<<)<<<-	MF:i:18	Aq:i:43	NM:i:1	UQ:i:12	H0:i:1	H1:i:0
+EAS1_95:7:74:866:49	83	chr2	1143	99	35M	=	969	-209	CCAACCTACTAAATACATATGCACCTAACACAAGA	:8<&<<<<7<<<<:<<<<<<8<5<<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:1	UQ:i:5	H0:i:1	H1:i:0
+EAS54_61:2:66:757:918	83	chr2	1143	99	35M	=	985	-193	CCATCCTACTAAATACATATGCACCTAACACAAGA	<9<45;<<7<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_73:5:220:733:736	147	chr2	1143	99	35M	=	959	-219	CCATCCTACTAAATACATATGCACCTAACACAAGA	:;<77;<<9<<<<<9;<<<<<<;<<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_57:6:175:289:351	99	chr2	1144	99	35M	=	1319	210	CATCCTACTAAATACATATGCACCTAACACAAGAC	<<<<<<<<<<;<<<<<<<<;<<<<<<<<<<<9<<<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_65:2:56:155:49	147	chr2	1145	99	35M	=	970	-210	ATCCTACTAAATACATATGCACCTAACACAAGACT	;:5;;<5<<<<<<<<<<<<<<<<<<<<<<<<<<<=	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_65:5:299:336:613	99	chr2	1145	99	35M	=	1293	183	ATCCTACTAAATACATATGCACCTAACACAAGACT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_39:4:30:432:228	83	chr2	1145	99	35M	=	967	-213	ATCCTACTAAATACATATGCACCTAACACAAGACT	<76<<<:<<<<<<<;<:<<<<<:<<<<<<<<<<<<	MF:i:18	Aq:i:47	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_39:5:93:312:331	83	chr2	1145	99	35M	=	953	-227	ATCCTACTAAATACATATGCACCTAACACAAGACT	<;;:;<6<<<<;<:<<<<<<<:<<<<<<<<<<<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_597:3:133:707:886	147	chr2	1146	99	35M	=	978	-203	ACCTAATAAATACATATGCACCTAACACAAGACTA	%5-2;&6<<<<<;<<<<<<<;<<<<<<<<<<<<<<	MF:i:18	Aq:i:30	NM:i:2	UQ:i:9	H0:i:1	H1:i:0
+EAS51_62:3:50:312:219	163	chr2	1146	99	35M	=	1288	177	TCCTACTAAATACATATGCACCTAACACAAGACTA	<<<<<<<<<<<;<<<<<;<;<<<;<<<<<<;;;;;	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_59:1:82:670:302	147	chr2	1146	99	35M	=	973	-208	TCCTACTAAATACATATGCACCTAACACAAGACTA	%448<7<<<<<<7<<<<<&<<7<<<<<<<<<<<<<	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS220_1:2:47:591:698	99	chr2	1146	99	35M	=	1313	202	TCCTACTAAATACATATGCACCTAACACAAGACTA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<:<<<<	MF:i:18	Aq:i:45	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_53:8:122:430:882	99	chr2	1147	99	35M	=	1338	226	CCTACTAAATACATATGCACCTAACACAAGACTAC	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<:;	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS220_1:4:46:1566:668	83	chr2	1148	99	35M	=	959	-224	CTACTAAATACATATGCACCTAACACAAGACTACC	5<<:<<<<<<<<<<<<:<:<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:78	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_591:4:92:411:955	147	chr2	1149	99	36M	=	979	-206	TACTAAATACATATGCACCTAACACAAGACTACCCA	2<+<<<<9<<<<<<<;+<;<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_97:2:96:419:327	99	chr2	1149	99	35M	=	1331	217	TACTAAATACATATGCACCTAACACAAGACTACCC	<<<<<<<<<<<<<<<<<<<<<<;<<<<<<<;;9<9	MF:i:18	Aq:i:47	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS219_1:7:20:1444:328	147	chr2	1149	99	35M	=	993	-191	TACTAAATACATATGCACCTAACACAAGACTACCC	9<3<<==;=<===;=<=====<<===========<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_610:4:198:59:675	163	chr2	1150	99	35M	=	1315	200	ACTAAATACATATGCACCTAACACAAGACTATCCT	<.<<<<<<;<<<<<<<<<<<**<;<;2<;6;&*2&	MF:i:18	Aq:i:45	NM:i:2	UQ:i:10	H0:i:1	H1:i:0
+EAS54_61:7:114:506:971	83	chr2	1150	99	35M	=	986	-199	ACTAAATACATATGCACCTAACACAAGACTACCCA	;;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_65:2:94:356:809	163	chr2	1151	99	35M	=	1334	218	CTAAATACATATGCACCTAACACAAGACTACCCAG	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<:;	MF:i:18	Aq:i:47	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_65:3:155:541:234	163	chr2	1151	99	35M	=	1319	203	CTAAATACATATGCACCTAACACAAGACTACCCAG	<<7<<<<<<<<<<<<<<<4<<<<<<<<<<<;;;08	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS112_32:7:272:328:400	83	chr2	1151	99	35M	=	977	-209	CTAAATACATATGCACCTAACACAAGACTACCCAG	4;<<<<<7<;<<<-<;<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_593:7:283:186:707	163	chr2	1154	99	36M	=	1321	203	AATACATATGCACCTAACACAAGACTACCCAGATTC	<<<<<<<<<<<<<<<<<<<<<<;<<<<<;<;<<<<8	MF:i:18	Aq:i:45	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_61:4:86:660:932	99	chr2	1154	99	35M	=	1338	219	AATACATATGCACCTAACACAAGACTACCCAGATT	================================9:=	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_71:6:264:705:89	147	chr2	1155	99	35M	=	983	-207	AAACATATGCACCTAACACAAGACTACCCAGATTC	<(<2<&<)<<<7<8<<<<<<<<<<.<<<<<<<<<<	MF:i:18	Aq:i:54	NM:i:1	UQ:i:7	H0:i:1	H1:i:0
+EAS114_32:4:5:396:292	83	chr2	1155	99	35M	=	981	-209	ATACATATGCACCTAACACAAGACTACCCAGATTC	<:<6<7<:<:;;;<<<;<7<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:45	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_32:6:178:342:866	163	chr2	1155	72	35M	=	1311	191	ATACATATGCACCTAACACAAGACTACCCAGATTC	;<<<<<;<<<8<<;<;<3<8/<<<<6<<</<8;<<	MF:i:18	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_108:1:155:809:543	163	chr2	1156	99	35M	=	1352	231	TACATATGCACCTAACACAAGACTACCCAGATTCA	<<<<<<<<<<<<<<<<7<;<<<<<<<<<<<1<;<;	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_61:1:119:880:781	99	chr2	1157	99	35M	=	1312	190	ACATATGCACCTAACACAAGACTACCCAGATTCAT	<<<<<<<<<<<<<<<<<<<<<<<<+<<<<7<<<<<	MF:i:18	Aq:i:45	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_61:6:283:963:234	147	chr2	1157	99	35M	=	992	-200	ACATATGCACCTAACACAAGACTACCCAGATTCAT	<5<;<;97;;:;<<7<;<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_105:1:28:745:352	99	chr2	1159	99	35M	=	1329	205	ATATGCACCTAACACAAGACTACCCAGATTCATAA	<<<<<9<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:45	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_65:8:147:687:428	147	chr2	1159	99	35M	=	998	-196	ATATGCACCTAACACAAGACTACCCAGATTCATAA	;1<''48;4)<<:<<<<;<<6;<<<<<<<<<<<<<	MF:i:18	Aq:i:36	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_53:3:101:809:776	99	chr2	1160	99	35M	=	1326	201	TATGCACCTAACACAAGACTACCCAGATTCATAAA	<<<<<<<<<<<<<<<<<<<<<<<<<:<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:7:35:538:1882	163	chr2	1160	98	35M	=	1337	212	TATGCACCTAACACAAGACTACCCAGATTCATAAA	;);43.50;3;93;;4;3;;;9-7.;*;;966*75	MF:i:18	Aq:i:43	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_597:7:41:34:211	83	chr2	1164	99	35M	=	980	-219	CACCTAACACAAGACTACCCAGATTCATAAAACAA	7</::<<7<<<<<<;<<<<;<<<<<<<<<<<<<<<	MF:i:18	Aq:i:54	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:1:2:1422:1820	83	chr2	1164	99	35M	=	1004	-195	CACCTAACACAAGACTACCCAGATTCATAAAACAA	*4617;;4;1;;79;/7&,4;9;;;7<;;<<<;<<	MF:i:18	Aq:i:54	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS188_7:6:194:998:663	83	chr2	1165	99	35M	=	1002	-198	ACCTAACACAAGACTACCCAGATTCATAAAACAAA	;</<<<7<<<<;<<8<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_65:8:10:975:766	83	chr2	1166	99	35M	=	959	-242	AATAACACAAGACTACCCAGATTCATAAAACAAAT	++4<<+<+<<<<8<<22;<<<<<2<<<<<<<<<<<	MF:i:18	Aq:i:64	NM:i:2	UQ:i:24	H0:i:1	H1:i:0
+EAS114_39:6:94:1273:1462	83	chr2	1166	99	35M	=	995	-206	CCTAACACAAGACTACCCAGATTCATAAAACAAAT	8.<<<;<:<<<<;<<;;;<<<;<;<;<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS188_7:8:64:350:174	83	chr2	1166	99	35M	=	1000	-201	CCTAACACAAGACTACCCAGATTCATAAAACAAAT	709<<;<;<<<<<<<;7<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_103:7:166:84:766	83	chr2	1167	99	35M	=	990	-212	ATAACACAAGACTACCCAGATTCATAAAACAAATA	%8<=+<-<<<</<<<<8<<<<<;<<<<<<<<<<<<	MF:i:18	Aq:i:30	NM:i:1	UQ:i:4	H0:i:1	H1:i:0
+EAS1_108:2:85:580:481	163	chr2	1167	99	35M	=	1359	227	CTAACACAAGACTACCCAGATTCATAAAACAAATA	<<<<<<<<<<<<<:<<<<<<<<<<<<;<<<<6:<<	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_66:4:191:40:536	83	chr2	1167	66	35M	=	977	-225	ATAAAAAAAGACTACCCAGATTCATAAAACAAATA	+1<<,<&<<:<.;<7/7<<<<;.<<<<<<<<<<<<	MF:i:18	Aq:i:0	NM:i:3	UQ:i:27	H0:i:1	H1:i:0
+EAS218_1:2:40:1291:1045	147	chr2	1167	99	35M	=	980	-222	CTAACACAAGACTACCCAGATTCATAAAACAAATA	*<<<9<<<<<<:0<9<<<<<<<;<<<<<<<<<<<<	MF:i:18	Aq:i:39	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS192_3:3:221:881:916	99	chr2	1168	96	35M	=	1327	194	TAACACAAGACTACCCAGATTCATAAAACAAATAC	<<;<<8<<;<<<<<<<;<<<<28<:<8<:;<;;;<	MF:i:18	Aq:i:24	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS219_1:7:35:392:2042	163	chr2	1168	99	35M	=	1332	199	TAACACAAGACTACCCAGATTCATAAAACNAATAC	======;==========<<=======7=;!<7;;;	MF:i:18	Aq:i:72	NM:i:1	UQ:i:0	H0:i:1	H1:i:0
+EAS54_65:4:192:714:341	163	chr2	1170	99	35M	=	1346	211	ACACAAGACTACCCAGATTCATAAAACAAATACTA	<<9<<<<<<<<<<<8<<<<<;<<;8<<<88;;;;9	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_593:1:189:876:833	163	chr2	1173	99	36M	=	1349	212	CAAGACTACCCAGATTCATAAAACAAATACTACTAG	<<<<<<<<<<<8<8<<<<<;<;;<<;<<<<<;<<<6	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_593:5:299:743:762	163	chr2	1173	99	36M	=	1345	208	CAAGACTACCCAGATTCATAAAACAAATACTACTAG	<<<;<<<<<<<<<:;<<<.<:<<<<<<<<<<;;;;;	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_610:6:107:252:533	83	chr2	1173	60	35M	=	1025	-183	CAAGACTACCCAGATTCATAAAACAAATACTACTA	3<<<<+<<96<<<<<<;<<<<<<;<<<<<<<<<<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:2	H1:i:1
+EAS1_97:5:154:952:558	147	chr2	1173	99	35M	=	1007	-201	AAAGACTACCCAGATTCATAAAACAAATACTACTA	%<<9;;<<;;;<<<<<;<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:1	UQ:i:4	H0:i:1	H1:i:0
+EAS56_63:4:184:659:377	147	chr2	1173	99	35M	=	992	-216	CAAAACTACCCAGATTCATAAAACAAATACTACTA	1;<+<;<6;66<<;<<<<;;<<<8<<<<8<<;<<<	MF:i:18	Aq:i:70	NM:i:1	UQ:i:10	H0:i:1	H1:i:0
+B7_595:6:137:811:130	163	chr2	1175	99	35M	=	1351	211	AGACTACCCAGATTCATAAAACAAATACTACTAGA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<9;;;	MF:i:18	Aq:i:47	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_65:4:124:367:72	163	chr2	1175	99	35M	=	1377	237	AGACTACCCAGATTCATAAAACAAATACTACTAGA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;;	MF:i:18	Aq:i:47	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_61:8:60:358:494	147	chr2	1179	44	35M	=	979	-235	TACCCAGATTCATAAAACAAATACTACTAGACCTA	7<77;<<<<<;<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:14	NM:i:0	UQ:i:0	H0:i:6	H1:i:36
+EAS114_30:7:319:11:255	163	chr2	1179	92	35M	=	1337	193	TACCCAGATTCATAAAACAAATACTACTAGACCTA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<:<:	MF:i:18	Aq:i:17	NM:i:0	UQ:i:0	H0:i:1	H1:i:10
+B7_610:7:26:749:174	99	chr2	1183	78	35M	=	1357	209	CAGATTCATAAAACAAATACTACTAGACCTAAGAG	<<<<<<<<<<<<<<<<<<<<<<;<9<8<<<9<;94	MF:i:18	Aq:i:11	NM:i:0	UQ:i:0	H0:i:6	H1:i:31
+EAS1_103:7:112:578:782	99	chr2	1183	89	35M	=	1366	218	CAGATTCATAAAACAAATACTACTAGACCTAAGAG	<;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<7<<<	MF:i:18	Aq:i:20	NM:i:0	UQ:i:0	H0:i:5	H1:i:25
+EAS1_105:1:234:185:359	83	chr2	1183	46	35M	=	1029	-189	CAGATTCATAAAACAAATACTACTAGACCTAAGAG	<<4<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:17	NM:i:0	UQ:i:0	H0:i:1	H1:i:9
+EAS112_34:4:92:412:435	147	chr2	1184	89	35M	=	1003	-216	AGATTCATAAAACAAATACTACTAGACCTAAGAGG	<;<52:=,====:=========<============	MF:i:18	Aq:i:43	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS220_1:6:24:105:1046	99	chr2	1184	99	35M	=	1377	228	AGATTCATAAAACAAATACTACTAGACCTAAGAGG	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:51	NM:i:0	UQ:i:0	H0:i:4	H1:i:2
+EAS1_97:2:128:629:484	163	chr2	1185	96	35M	=	1359	209	GATTCATAAAACAAATACTACTAGACCTAAGAGGG	<<49<<<<<9<<<<99<<<<<<<<<<<<+<-)7))	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:4	H1:i:45
+EAS219_FC30151:1:53:140:421	83	chr2	1185	99	35M	=	1016	-204	GATTCATAAAACAAATACTACTAGACCTAAGAGGG	<<<<:<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:48	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_595:6:99:557:427	163	chr2	1186	99	35M	=	1342	191	ATTCATAAAACAAATACTACTAGACCTAAGAGGGA	<<<<<<<<<<<<<<<<<<<<<<:<<<<+;<7:8:;	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_103:3:253:175:31	147	chr2	1187	72	35M	=	1008	-214	TTCATAAAACAAATACTACTAGACCTAAGAGGGAT	;+;<;<<<<<<<<9<<9<<<<<;<<<<<<<<<<<<	MF:i:18	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_28:4:13:701:55	147	chr2	1187	99	36M	=	1015	-208	TTCATAAAACAAATACTACTAGACCTAAGAGGGATG	0:+<7<;9<;<<<<<<<3<<<<<;;<<<:<<3<<<<	MF:i:18	Aq:i:48	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_30:6:220:809:850	147	chr2	1187	60	35M	=	986	-236	TTCATAAAACAAATACTACTAGACCTAAGAGGGAT	9+5<;*<<<2:0<<8:<*00<<<:<*<<<<<<<<&	MF:i:18	Aq:i:60	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_593:5:30:599:589	147	chr2	1188	99	36M	=	1003	-221	TCATAAAACAAATACTACTAGACCTAAGAGGGATGA	90<;<<<<<<<<+<<<;;<;<;<<<<<<<<6<<8<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_597:8:35:118:589	83	chr2	1188	99	35M	=	999	-224	TCATAAAACAAATACTACTAGACCTAAGAGGGATG	67<<<<<;<<<<<<<:7<<<<:<<<<<<<<<<<<<	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_108:4:37:604:389	147	chr2	1188	99	35M	=	998	-225	TCATAAAACAAATACTACTAGACCTAAGAGGGATG	00;:;========9========<9========<==	MF:i:18	Aq:i:67	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_61:2:168:61:867	83	chr2	1188	99	35M	=	997	-226	TCATAAAACAAATACTACTAGACCTAAGAGGGATG	;7<<<<<<<<<<<<<7<<:<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_67:7:197:399:319	83	chr2	1189	99	35M	=	1012	-212	CAAAAAACAAATACTACTAGACCTAAGAGGGATGA	&<+==<<5<<<8<89;;<<<<<<8<<<<<<<<<<<	MF:i:18	Aq:i:47	NM:i:1	UQ:i:10	H0:i:1	H1:i:0
+EAS114_32:5:267:170:250	163	chr2	1189	99	35M	=	1377	223	CATAAAACAAATACTACTAGACCTAAGAGGGATGA	<<<<<<<<<<<<<<<<<;<<<;<<<<<<<<<<<<;	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_95:4:174:157:573	83	chr2	1191	99	35M	=	1012	-214	TAAAACAAATACTACTAGACCTAAGAGGGATGAGA	8<<<<4<<<<<<<<;<<<<;<<<<<<<<<<<<<<<	MF:i:18	Aq:i:54	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:6:39:956:676	83	chr2	1191	99	35M	=	1023	-203	TAAAACAAATACTACTAGACCTAAGAGGGATGAGA	899985;;<;:9;;:9<;:9:5;<;;;<;<;<<<<	MF:i:18	Aq:i:44	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:7:37:763:1437	83	chr2	1191	99	35M	=	994	-232	TAAAACAAATACTACTAGACCTAAGAGGGATGAGA	79979;<;<;;;<;;;;;;6:;<:;<:8;<<<<;<	MF:i:18	Aq:i:64	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS220_1:2:50:513:882	83	chr2	1192	99	35M	=	1031	-196	AAAACAAATACTACTAGACCTAAGAGGGATGAGAA	<<<<:<<<<<:<<:<<<<::<<<<<<<<<<<<<<<	MF:i:18	Aq:i:23	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS218_1:2:15:1763:1143	147	chr2	1193	99	35M	=	1023	-205	AAACAAATACTACTAGACCTAAGAGGGATGAGAAA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:46	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_64:4:189:571:366	83	chr2	1194	99	35M	=	1002	-227	AACAAATACTACTAGACCTAAGAGGGATGAGAAAT	<<;<<<<<:<<<;<<<;;;<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_66:3:166:532:438	99	chr2	1194	99	35M	=	1386	227	AACAAATACTACTAGACCTAAGAGGGATGAGAAAT	<<<<<<<<<<<<<<<;<<;<<;<<<<;<;:;;<;<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_57:5:309:109:987	83	chr2	1194	99	35M	=	1024	-205	AACAAATACTACTAGACCTAAGAGGGATGAGAAAT	<<<<<<:<<;<<<<<;<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:51	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_26:1:171:527:247	83	chr2	1194	67	35M	=	1027	-202	AACAAATGCTACTAGACCTAAGAGGGATGAGAAAT	<547*9)&&7+;+<<7<<<;<<<;3<<<<<<<<<<	MF:i:18	Aq:i:30	NM:i:1	UQ:i:5	H0:i:0	H1:i:1
+B7_589:8:139:727:808	163	chr2	1195	99	35M	=	1363	203	ACAAATACTACTAGACCTAAGAGGGATGAGAAATT	<<<<<<<<<<<<<:<;<<<<<<<<9;<;9<6;<<9	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_28:3:202:275:776	83	chr2	1196	99	36M	=	1002	-230	CAAATACTACTAGACCTAAGAGGGATGAGAAATTAC	;<<<<;;<<<<<<<;<<<<<<<;<<<<<<<<<<;<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_62:6:12:484:836	163	chr2	1197	99	35M	=	1372	210	AAATACTACTAGACCTAAGAGGGATGAGAAATTAC	<<<<<<<<<<<<<<<<<7<:<<<<<<9<<<<<<<<	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_57:6:21:553:57	99	chr2	1197	99	35M	=	1358	196	AAATACTACTAGACCTAAGAGGGATGAGAAATTAC	<<<<<<<<<<<;;<<<;<<;<<;<<<;;9<;<;<9	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_19:5:4:939:2021	83	chr2	1197	99	40M	=	1031	-206	AAATACTACTAGACCTAAGAGGGATGAGAAATTACCTAAT	;;;;:8;<5:<<<7/<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS192_3:3:194:378:230	83	chr2	1198	99	35M	=	1022	-211	AATACTACTAGACCTAAGAGGGATGAGAAATTACC	<<;<8<<:<<<<:<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:49	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_591:7:68:242:834	163	chr2	1200	99	36M	=	1386	222	TACTACTAGACCTAAGAGGGATGAGAAATTACCTAA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_67:2:22:471:500	163	chr2	1200	99	35M	=	1365	200	TACTACTAGACCTAAGAGGGATGAGAAATTACCTA	=======<=<====:<2===9==;=;9;;=;;;;5	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_610:4:139:989:144	163	chr2	1201	99	35M	=	1387	221	ACTACTAGACCTAAGAGGGATGAGAAATTACCTAA	<<<<<<<<<<<<6<<<<<<<<<;<<<<<<<;;<;;	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_103:5:188:20:592	83	chr2	1202	95	35M	=	1032	-205	CTACTAGACCTAAGAGGGATGAGAAATTACCTAAT	2<<7;<<<<,;<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:22	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_108:1:189:863:213	83	chr2	1202	99	35M	=	1039	-198	CTACTAGACCTAAGAGGGATGAGAAATTACCTAAT	7:<7<<<<44;<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS218_1:4:62:561:531	83	chr2	1203	99	35M	=	1036	-202	TACTAGACCTAAGAGGGATGAGAAATTACCTAATT	<<7<<<<:<8<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_1:8:70:1349:1788	83	chr2	1203	99	35M	=	1043	-195	TACTAGACCTAAGAGGGATGAGAAATTACCTAATT	<7;<<8<74;;<1<<71<;7<;;<;<7<<<<<<<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS192_3:5:197:914:256	147	chr2	1204	97	35M	=	1049	-190	ACTAGACCTAAGAGGGATGAGAAATTACCTAATTG	<5;<8<5/;<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:24	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:3:35:896:1588	83	chr2	1205	91	35M	=	1032	-208	CTAGACCTAAGAGGGATGAGAAATTACCTAATTGG	77999:.:<<;<;;;<<;<;<<<<<;<;;<<<<;;	MF:i:18	Aq:i:21	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS112_34:6:43:47:279	163	chr2	1206	99	35M	=	1405	234	TAGACCTAAGAGGGATGAGAAGTTACCTAATTGGT	<<<<<<<<<<<<<;:<-<<<<<<<<<<<<:;;+7;	MF:i:18	Aq:i:45	NM:i:1	UQ:i:27	H0:i:0	H1:i:1
+EAS1_95:2:211:954:174	99	chr2	1207	99	35M	=	1393	221	AGACCTAAGAGGGATGAGAAATTACCTAATTGGTA	===============================777=	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_39:2:5:1219:137	99	chr2	1209	99	35M	=	1384	210	ACCTAAGAGGGATGAGAAATTACATAATTGGTACA	<<<<<<<<<<<<<<<<<<<<<<<(<<<<<<:9<;=	MF:i:18	Aq:i:45	NM:i:1	UQ:i:7	H0:i:0	H1:i:1
+EAS56_57:7:33:954:724	83	chr2	1210	97	35M	=	1049	-196	CCTAAGAGGGATGAGAAATTACCTAATTGGTACAA	;<;<;<<-7;<<;<<<<<<<<<<<<<<<<<<<<<;	MF:i:18	Aq:i:24	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_28:3:176:402:458	163	chr2	1210	99	36M	=	1376	202	CCTAAGAGGGATGAGAAATTACCTAATTGGTACAAT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<:<<<;;<;	MF:i:18	Aq:i:70	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_3:4:81:687:1379	163	chr2	1210	99	35M	=	1366	191	CCTAAGAGGGATGAGAAATTACCTAATTGGTACAA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<<<<	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_105:1:45:239:851	83	chr2	1211	61	35M	=	1023	-223	CTAAGAGGGATGAGAAATTACCTAATTGGTACAAT	*2*0<<<<<<<<<<<<<<<<9<<3<<<<<<<<<<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:1
+EAS56_65:5:312:985:871	163	chr2	1212	99	35M	=	1369	192	TAAGAGGGATGAGAAATTACCTAATTGGTACAATG	<<<<<<<<<<<<<<<<<<<<<<<<<<<:<<<<9<<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_11:4:38:557:1441	163	chr2	1212	99	35M	=	1381	204	TAAGAGGGATGAGAAATTACCTAATTGGTACAATG	<<<<<<<<<<<<<<<<<<<<<<<<<<<:<<<<<<<	MF:i:18	Aq:i:45	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS219_1:3:88:465:1877	147	chr2	1212	99	35M	=	1055	-192	TAAGAGGGATGAGAAATTACCTAATTGGTACAATG	<<<<<<<:<<<<<<<<:<<<<<<<<<<<<7;<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_595:7:149:123:265	163	chr2	1213	99	35M	=	1395	217	AAGAGGGATGAGAAATTACCTAATTGGTACAATGT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<9	MF:i:18	Aq:i:54	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:6:47:1791:444	83	chr2	1213	74	35M	=	1041	-207	AAGAGGGATGAGAAATTACCTAATTGGTACAATGT	978879;:;;<:;;<<;:<9<<<<;6;;;;<<<<;	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:6
+EAS51_62:3:68:996:104	147	chr2	1214	70	35M	=	1041	-208	AGAGGGATGAGAAATTACCTAATTGGTACAATGTA	<1<8<<<:<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:21	NM:i:0	UQ:i:0	H0:i:1	H1:i:4
+B7_593:2:68:140:542	99	chr2	1217	95	36M	=	1398	217	GGGATGAGAAATTACCTAATTGGTACAATGTACAAT	<<<8;<<;<<<<<;<<;<<<<<8;<-<8<82;;;-8	MF:i:18	Aq:i:19	NM:i:0	UQ:i:0	H0:i:1	H1:i:6
+EAS188_7:7:67:719:786	163	chr2	1218	43	35M	=	1383	200	GGATGAGAAATTACCTAATTGGTACACTGTACAAT	;;<<<<<<&<<:13&<1<<<:<<<)/&/))<'6-<	MF:i:18	Aq:i:13	NM:i:1	UQ:i:5	H0:i:0	H1:i:1
+EAS1_108:5:321:712:224	83	chr2	1220	58	35M	=	1051	-204	ATGAGAAATTACCTAATTGGTACAATGTACAATAT	=;===7;===7=========;=:;=========;=	MF:i:18	Aq:i:28	NM:i:0	UQ:i:0	H0:i:1	H1:i:1
+EAS114_26:4:100:238:596	163	chr2	1220	56	35M	=	1403	218	ATGAGAAATTACCTAATTGGTACAATGTACAATAT	======9=====;=======5===;====/=;===	MF:i:18	Aq:i:17	NM:i:0	UQ:i:0	H0:i:1	H1:i:13
+EAS51_62:7:312:236:655	163	chr2	1222	99	35M	=	1412	225	GAGAAATTACCTAATTGGTACAATGTACAATATTC	<<<<;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:5
+EAS56_63:6:102:816:260	147	chr2	1225	99	35M	=	1049	-211	AAATTACCTAATTGGTACAATGTACAATATTCTGA	<<<<<<::<<<<<<;<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:23	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_610:7:34:144:868	163	chr2	1226	76	35M	=	1412	221	AATTACCTAATTGGTACAATGTACAATATTCTGAT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<4;<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_78:7:215:516:299	99	chr2	1226	99	35M	=	1406	215	AATTACCTAATTGGTACAATGTACAATATTCTGAT	<<<<<<;<<<<;;;;<;;<<<<;<<9<;<<1;7/;	MF:i:18	Aq:i:64	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_11:3:81:12:1231	163	chr2	1228	99	35M	=	1391	198	TTACCTAATTGGTACAATGTACAATATTCTGATGA	<<<<7<<<<<<<<<<<<<<<<<<<<<<<<<<4<<6	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_589:2:30:644:942	147	chr2	1229	83	35M	=	1045	-219	TACCTAATTGGTACAATGTACAATATTCTGATGAT	85%+;<<9;<9<<;<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:22	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_1:4:41:519:609	163	chr2	1229	99	35M	=	1401	207	TACCTAATTGGTACAATGGACAATATTCTGATGAT	1<<<<<<<<<<<<<<<4<-:<+6<<<<<<<<<<<<	MF:i:18	Aq:i:43	NM:i:1	UQ:i:12	H0:i:0	H1:i:1
+B7_591:7:116:814:89	99	chr2	1231	99	36M	=	1408	213	CCTAATTGGTACAATGTACAATATTCTGATGATGGT	<<<<<<<<<<<<<<<<<<<<<<:<<<<;<<;<<66<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_73:5:169:714:644	163	chr2	1231	99	35M	=	1437	241	CCTAATTGGTACAATGTACAATATTCTGATGATGG	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<;<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_597:6:73:420:812	99	chr2	1232	66	35M	=	1414	217	CTAATTGGTACAATGTACAATATTCTGATGATGGT	<<<<<1<<<<::1<7<:<96<9<:<<:4<70:11<	MF:i:18	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_11:6:17:1179:393	99	chr2	1232	99	35M	=	1412	215	CTAATTGGTACAATGTACAATATTCTGATGATGGT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<:<<:4<	MF:i:18	Aq:i:78	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_589:8:118:829:36	99	chr2	1233	99	35M	=	1417	219	TAATTGGTACAATGTACAATATTCTGATGATGGTT	<<<<<<<<<:<2<<<<<<:<<<<<<<<<<<<71;<	MF:i:18	Aq:i:52	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_593:2:125:875:553	147	chr2	1233	99	36M	=	1075	-194	TAATTGGTACAATGTACAATATTCTGATGATGGTTA	-;<;:;<<;6<<<<<<6<;<:<<<<<<<<<<<<<<<	MF:i:18	Aq:i:53	NM:i:0	UQ:i:0	H0:i:1	H1:i:1
+EAS114_32:4:7:282:424	99	chr2	1233	83	35M	=	1397	199	TAATTGGTACAATGTACAATATTCTGATGATGGTT	<<<3<<<9<<<<3<<<<<9<<<9,<;;9;&*;3,.	MF:i:18	Aq:i:41	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS188_7:6:107:447:488	163	chr2	1233	99	35M	=	1412	214	TAATTGGTACAATGTACAATATTCTGATGATGGTT	<<<;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:53	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS192_3:7:66:891:294	83	chr2	1233	99	35M	=	1057	-211	TAATTGGTACAATGTACAATATTCTGATGATGGTT	:<<5;;<<<4<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:1
+EAS56_57:8:72:44:435	99	chr2	1235	76	35M	=	1392	192	ATTGGTACAATGTACAATATTCTGATGATGGTTAA	<<<<<<<<<<<2;<;<<;<<<;<<8<82<;22<8&	MF:i:18	Aq:i:0	NM:i:1	UQ:i:5	H0:i:1	H1:i:0
+EAS139_19:4:18:1335:1514	147	chr2	1235	99	40M	=	1063	-212	ATTGGTACAATGTACAATATTCTGATGATGGTTACACTAA	::/::<<;<<<<<<<<<<<<<;<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS218_4:7:72:1288:1211	147	chr2	1235	84	35M	=	1052	-218	ATTGGTACAATGTACAATATTCTGATGATGGTTAC	<);<:<<9<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_62:3:200:263:280	83	chr2	1236	99	35M	=	1078	-193	TTGGTACAATGTACAATATTCTGATGATGGTTACA	)<<<8<:<<<<<<<<<;<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:62	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_589:5:68:440:424	147	chr2	1237	99	35M	=	1060	-212	TGGTACAATGTACAATATTCTGATGATGGTTACAC	<<2<<<<<<<<9<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_93:6:255:441:47	147	chr2	1237	99	35M	=	1072	-200	TGGTACAATGTACAATATTCTGATGATGGTTACAC	;;7<;:<<<<<<<<<<;<<<<<<<<;<<<<<<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS112_34:8:174:557:872	163	chr2	1237	99	35M	=	1423	221	TGGTACAATGTACAATATTCTGATGATGGTTACAC	<<<<<<<<<<<<<:<<<<<<<7<<;<<6:<<2117	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:1
+EAS51_64:3:255:45:399	163	chr2	1238	99	35M	=	1404	201	GGTACAATGTACAATATTCTGATGATGGTTACACT	<<3<8<<8<0<<;<<<0<<<</+8<611<<;71;7	MF:i:18	Aq:i:57	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_65:2:264:157:150	147	chr2	1238	30	35M	=	1054	-219	GGAAAAATGGACAAGATTCTGATGAGGGTTACACT	.3%:+<<*;*<2<<1<1*,*<<7<<+<<<&<<<<<	MF:i:130	Aq:i:30	NM:i:3	UQ:i:35	H0:i:0	H1:i:0
+EAS139_19:5:95:944:247	99	chr2	1238	99	40M	=	1424	226	GGTACAATGTACAATATTCTGATGATGGTTACACTAAAAG	<<<<<<<<<<<<<<<<<<<<<<<<<<;<<<<<<<<:;:::	MF:i:18	Aq:i:78	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_105:2:301:161:195	147	chr2	1239	75	35M	=	1076	-198	GTACAATGTACAATATTCTGATGATGGTTACACTA	''6%6<6<<<4<<<<<<<<)<<<<<<<<<<<<<<<	MF:i:18	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_28:2:141:7:963	83	chr2	1240	85	36M	=	1061	-215	TACAATGTACAATATTCTGATGATGGTTACACTAAA	95+<<9<<5<;;<<;<<;'<<<<<;<<<7<9<<<<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:1
+EAS114_39:6:76:282:1668	99	chr2	1240	99	35M	=	1401	196	TACAATGTACAATATTCTGATGATGGTTACACTAA	<<<<<<<<<<<<<<<<<<;<<;<<<<<<;<;<<<8	MF:i:18	Aq:i:54	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_11:5:64:199:1288	147	chr2	1240	77	35M	=	1079	-196	TACAATGTACAATATTCTGATGATGGTTACACTAA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_108:1:49:911:980	163	chr2	1241	99	35M	=	1434	228	ACAATGTACAATATTCTGATGATGGTTACACTAAA	<<<<<<<<<<;<<<<<<<8<<<<;<;<<88-<;33	MF:i:18	Aq:i:62	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS220_1:8:66:1046:167	147	chr2	1241	99	35M	=	1060	-216	ACAATGTACAATATTCTGATGATGGTTACACTAAA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_57:5:303:542:924	83	chr2	1242	76	35M	=	1083	-194	CAATGTACAATATTCTGATGATGGTTACACTAAAA	+<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:1
+EAS114_45:2:79:554:354	147	chr2	1242	63	35M	=	1082	-195	CAATGTACAATATTCTGATGATGGTTACACTAAAA	98988;7;;;;:;;;;;;;;;;:;;;:;;;;;9;;	MF:i:18	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_59:1:248:122:558	163	chr2	1243	99	35M	=	1436	228	AATGTACAATATTCTGATGATGGTTACACTAAAAG	<<<<:<<<<<<<<<<<<<;<<<<:<6:4<<::6:6	MF:i:18	Aq:i:52	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_63:7:109:22:383	83	chr2	1244	99	35M	=	1071	-208	ATGTACAATATTCTGATGATGGTTACACTAAAAGC	<;9;<8<<<<<<;<<<<<<<<<<<<;<<<<<<<<<	MF:i:18	Aq:i:51	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_11:3:43:1229:1855	83	chr2	1244	99	35M	=	1074	-205	ATGTACAATATTCTGATGATGGTTACACTAAAAGC	8<<<<;8<<<;;5<<28<<<<<<<<<<<<7;;<<;	MF:i:18	Aq:i:48	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_63:2:74:656:272	83	chr2	1245	99	35M	=	1088	-192	TGTACAATATTCTGATGATGGTTACACTAAAAGCC	;;;</<<<<<5;<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:2
+EAS56_65:7:118:775:467	83	chr2	1245	99	35M	=	1075	-205	TGTACAATATTCTGATGATGGTTACACTAAAAGCC	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:1
+B7_593:7:15:244:876	99	chr2	1246	43	36M	=	1440	230	GTACAATATTCTGATGATGGTTACACTAAAAGCCCA	<<<<<<;<<<<<<<<;<<;;;<<<<<:<<<9;<<<;	MF:i:18	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS219_1:1:63:28:1549	163	chr2	1247	77	35M	=	1439	227	TACAATATTCTGATGATGGTTACACTAAAAGCCCA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<7;<<<<7	MF:i:18	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_95:7:310:800:761	83	chr2	1249	99	35M	=	1055	-229	CAATATTCTGATGATGGTTACACTAAAAGCCCATA	1<<:<:<:<<<<:<<<<<<<<<;<<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:7:14:978:1296	83	chr2	1249	90	35M	=	1104	-180	CAATATTCTGATGATGGTTACACTAAAAGCCCATA	77177;9;2:;;:;;(;;9;<;;;;:;;;:7;<<;	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_595:8:26:242:35	147	chr2	1251	99	35M	=	1084	-202	ATATTTTGATGATGGTTACACTAAAAGCCCATACT	<<<77!!7<;<<<;;<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:30	NM:i:2	UQ:i:0	H0:i:1	H1:i:8
+EAS114_45:7:6:758:988	83	chr2	1253	99	35M	=	1087	-201	ATTCTGATGATGGTTACACTAAAAGCCCATACTTT	3-7*73;;399:9;9;7<-(<;;<;;:;9::;;7;	MF:i:18	Aq:i:51	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_30:2:315:412:921	99	chr2	1254	99	35M	=	1424	205	TTCTGATGATGGTTACACTACAAGCCCATACTGTA	<;<;<<<<<<<;<<<<<<<<8<<<;<<:<<;;+<8	MF:i:18	Aq:i:45	NM:i:2	UQ:i:33	H0:i:0	H1:i:1
+EAS114_30:3:215:840:760	163	chr2	1256	99	35M	=	1416	195	CTGATGATGGTTACACTAAAAGCCCATACTTTCCT	<<<<<<<<<<<<<<<;<<<88<+<<:<;3585,+:	MF:i:18	Aq:i:66	NM:i:1	UQ:i:11	H0:i:1	H1:i:0
+EAS1_95:5:284:212:932	147	chr2	1257	10	35M	=	1063	-229	TGATGATGGTTACGCTAAAAGTCCATGCTTTACTG	82%<8:<-:<<:**:<-<<8<)/2/<:/<<<<<<<	MF:i:18	Aq:i:0	NM:i:3	UQ:i:42	H0:i:0	H1:i:0
+EAS1_97:4:290:121:79	163	chr2	1257	99	35M	=	1420	198	TGATGATGGTTACACTAAAAGCCCATACTTTACTG	<<<<<<<<<<<<<<<<<<<<<<<<<<<9<<<7;<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_67:1:88:54:900	83	chr2	1257	68	35M	=	1069	-223	TGATGATGGTTACACTAAAAGCCCATACTTCACTG	============;=================;9===	MF:i:18	Aq:i:19	NM:i:1	UQ:i:26	H0:i:0	H1:i:1
+EAS188_7:3:100:735:530	83	chr2	1257	99	35M	=	1058	-234	TGATGATGGTTACACTAAAAGCCCATACTTTACTG	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_39:7:32:562:1695	147	chr2	1258	76	35M	=	1085	-208	GATGATGGTTACACTAAAAGCCCATACTTTACTGC	:5:::<88/<:<<<<<<<<<7<9<<&<959<<<<<	MF:i:18	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_28:3:173:627:465	163	chr2	1260	99	36M	=	1444	220	TGATGGTTACACTAAAAGCCCATACTTTACTGCTAC	<<<<<<<<<<<<<<<<<<<<<<<;<<<<<2;;4;;7	MF:i:18	Aq:i:51	NM:i:0	UQ:i:0	H0:i:1	H1:i:1
+EAS1_95:1:77:589:741	83	chr2	1263	99	35M	=	1078	-220	TGGTTACACTAAAAGCCCATACTTTACTGCTACTC	8=;;==606;=========================	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_99:8:27:228:31	147	chr2	1264	99	35M	=	1082	-217	GGTTACACTAAAAGCCCATACTTTACTGCTACTCA	99;;;<<<<<<:<<;<;<<;<<<<;<<;<<<<<<<	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_64:6:54:695:952	147	chr2	1264	99	35M	=	1076	-223	GGTTACACTAAAAGCCCATACTTTACTGCTACTCA	277%<9<4)<<<<<<<<<;<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_64:6:300:622:86	83	chr2	1264	99	35M	=	1102	-197	GGTTACACTAAAAGCCCATACTTTACTGCTACTCA	<:<<<:<6;<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS112_34:7:71:62:254	163	chr2	1264	99	35M	=	1438	209	GGTTACACTAAAAGCCCATACTTTCCTGCTACTCA	<<<<<<7<<<<7<<<<<3<<<<<<&<<.<<::<:%	MF:i:18	Aq:i:43	NM:i:1	UQ:i:5	H0:i:0	H1:i:1
+EAS114_28:1:168:609:646	99	chr2	1264	99	36M	=	1436	208	GGTTACACTAAAAGCCCATACTTTACTGCTACTCAA	<<<<<<<<<<<;<<<<<:<8<<<<;<<<<<4<<<9<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_11:1:84:92:1246	163	chr2	1265	99	35M	=	1437	207	GTTACACTAAAAGCCCATACTTTACTGCTACTCAA	<<<<<<<<<<<<<<<<5<:<<5<<<<<<<<<<<<<	MF:i:18	Aq:i:78	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_593:3:310:193:629	83	chr2	1267	99	36M	=	1103	-200	TACACTAAAAGCCCATACTTTACTGCTACTCAATAT	9<9<6;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_610:6:111:379:700	73	chr2	1268	0	35M	=	1268	0	ACACTAAAAGCCCATACTTTACTGCTACTCAATAT	7<<:<<<<02<<6&<</<<</+9/98*<966/3/<	MF:i:64	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_610:6:111:379:700	133	chr2	1268	0	*	=	1268	0	CGCACTGGCAATATTTGTGTGTTTACTTTTTTGCA	:1+&;;6;:;918;);;):,19.9:).):::.&3(	MF:i:192
+EAS114_30:6:137:741:866	163	chr2	1268	99	35M	=	1429	196	ACACTAAAAGCCCATACTTTACTGCTACTCAATAT	<<<<8<<;;;<<<<;<<<;;;<;4<<8;<<;%<8;	MF:i:18	Aq:i:70	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_39:7:23:1126:1886	147	chr2	1268	99	35M	=	1094	-209	ACACTAAAAGCCCATACTTTACTGCTACTCAATAT	5*.:.5<<::<<<<<<<<:5<<<<<<<<<<:2<<<	MF:i:18	Aq:i:70	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_99:3:21:423:169	99	chr2	1270	99	35M	=	1468	233	ACTAAAAGCCCATACTTTACTGCTACTCAATATAT	<<<<<;<<<<<<;<<<<<;;<<<<<<<<9+:5<;;	MF:i:18	Aq:i:68	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_28:3:110:984:98	147	chr2	1270	99	36M	=	1092	-214	ACTAAAACCCCATACTTTACTGCTACTCAATATATC	:81<<<<+;;8<+<8<<<<<;<<<8;<<<<<<<<8;	MF:i:18	Aq:i:70	NM:i:1	UQ:i:10	H0:i:1	H1:i:0
+EAS219_FC30151:5:54:1351:910	99	chr2	1270	99	35M	=	1448	213	ACTAAAAGCCCATACTTTACTGCTACTCAATATAT	<<<<<<8<<<<<<<<<<<<<<<<<<<<<<18<<:<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_57:2:237:855:581	147	chr2	1271	87	35M	=	1105	-201	CTAAACGCCCATACTTTACTGCTACTCAATATATC	/+<<<&)2;66;/;;+<;;3133<3<3;9;<999<	MF:i:18	Aq:i:30	NM:i:1	UQ:i:5	H0:i:1	H1:i:0
+EAS56_59:8:80:542:549	163	chr2	1271	99	35M	=	1443	207	CTAAAAGCCCATACTTTACTGCTACTCAATATATC	<<<<<<<<;<<<<<<<<:<<<<-<;;<;7<;3;9;	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:4:7:1347:375	163	chr2	1271	99	35M	=	1436	200	CTAAAAGCCCATACTTTACTGCTACTCAATATATC	;;;;;;;;;;;;;;;;;;;;9;;;8;;;;;97777	MF:i:18	Aq:i:66	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS188_7:6:191:540:493	99	chr2	1273	99	35M	=	1432	194	AAAAGCCCATACTTTACTGCTACTCAATATATCCA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;	MF:i:18	Aq:i:78	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_81:7:324:472:791	147	chr2	1274	89	35M	=	1110	-199	AAAGCCAATACTTTACTGCTACTCAATATATCCAT	<<.)5*&;;11<<<,5<33:-<<6<<<<:<<<<<<	MF:i:18	Aq:i:30	NM:i:1	UQ:i:5	H0:i:1	H1:i:0
+EAS220_1:8:83:1456:1854	83	chr2	1275	99	35M	=	1117	-193	AAGCCCATACTTTACTGCTACTCAATATATCCATG	<<67<:<8<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_64:5:290:247:509	163	chr2	1276	99	35M	=	1450	209	AGCCCATACTTTACTGCTACTCAATATATCCATGT	<<<<<<<<<<<<<<<4<<<<<<92<;;;<;96;19	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_59:5:90:629:652	99	chr2	1276	99	35M	=	1456	215	AGCCCATACTTTACTGCTACTCAATATATCCATGT	<<<<<<<<<<<<<<<<<<<<<<<:<;<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS218_4:3:39:1671:1928	163	chr2	1276	99	35M	=	1453	212	AGCCCATACTTTACTGCTACTCAATATATCCATGT	<<<<<<<;<<<<;<<<<<4<<<;3<<<;<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_59:1:128:584:952	83	chr2	1277	99	35M	=	1101	-211	GCCCATACTTTACTGCTACTCAATATATCCATGTA	7<;9;0:<<<:<<:<<<<<:<<<<<<<<<<<<<<<	MF:i:18	Aq:i:61	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_97:7:28:979:519	163	chr2	1278	99	35M	=	1439	196	CCCATACTTTACTGCTACTCAATATATCCATGTAA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;;;;9:	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_65:7:219:40:833	83	chr2	1278	99	35M	=	1094	-219	CCCATACTTTACTGCTACTCAATATATCCATGTAA	<<*<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_66:1:289:207:323	163	chr2	1279	99	35M	=	1462	218	CCATACTTTACTGCTACTCAATATATCCATGTAAC	<<<:<<<<<:<<<<<<<<<<;<<899<<13)939;	MF:i:18	Aq:i:41	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_61:3:45:758:616	163	chr2	1280	99	35M	=	1473	228	CATACTTTACTGCTACTCAATATATCCATGTAACA	<<<<<<<<<<<<<<<<<<<<<<<<<6<<<<<<;;<	MF:i:18	Aq:i:54	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS112_32:7:42:804:114	163	chr2	1281	99	35M	=	1452	206	ATACTTTACTGCTACTCAATATATCCATGTAACAA	<<<<<<<<<<<<<<<<<<<<<<<<<<:<:<;;<;;	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_19:5:61:1885:163	83	chr2	1281	99	40M	=	1128	-193	ATACTTTACTGCTACTCAATATATCCATGTAACAAATCTG	;:;;;;<<8<<:<<:<;<<<<<<<;<<<<<<<<<<<<<<<	MF:i:18	Aq:i:79	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_62:4:282:962:46	99	chr2	1282	99	35M	=	1437	190	TACTTTACTGCTACTCAATATATCCATGTAACAAA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_610:6:143:620:158	83	chr2	1283	99	35M	=	1107	-211	ACTTTACTGCTACTCAATATATCCATGTAACAAAT	<4;<;<;<;6<<7<;<<<<<<<;<<<<<<<<<<<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_62:3:50:312:219	83	chr2	1288	99	35M	=	1146	-177	ACTGCTACTCAATATATCCATGTAACAAATCTGCG	<,;83:<::6<<<<<<<;:<;<<<<;<<<<<<<<<	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_93:5:256:444:399	83	chr2	1289	99	35M	=	1133	-191	CTGCTACTCAATATATCCATGTAACAAATCTGCGC	;+549<:<.<<<<<<<;<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:68	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_99:1:17:595:863	83	chr2	1289	89	35M	=	1139	-185	AAGCTACTCAATATATCCATGTAACAAATCTGCGC	))55))+2&<<,:5<,0657<<<<:<:<:<<<<<<	MF:i:18	Aq:i:33	NM:i:2	UQ:i:16	H0:i:1	H1:i:0
+EAS1_105:6:23:885:274	147	chr2	1289	99	35M	=	1089	-235	CTACTACTCAATATATCCATGTAACAAATCTGCGC	2+*27==;;==<<.;:<=<=<==============	MF:i:18	Aq:i:51	NM:i:1	UQ:i:9	H0:i:1	H1:i:0
+EAS54_61:8:4:173:814	83	chr2	1289	99	35M	=	1111	-213	CTGCTACTCAATATATCCATGTAACAAATCTGCGC	<<;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_73:5:263:557:988	147	chr2	1289	84	35M	=	1108	-216	CTGCTACTCAATATATCCATGTAACAAATCTGCGC	1-41:<15+<<<<<<599<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:18	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_64:2:326:153:231	163	chr2	1290	43	35M	=	1477	222	TGCTACTCAATATATCCATGTAACAAATCTGCGCT	<<<<<<<<<9<<<<<<<<<,<<<<<<8<<8.;.;4	MF:i:18	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_57:4:98:862:154	83	chr2	1290	99	35M	=	1116	-209	TGCTACTCAATATATCCATGTAACAAATCTGCGCT	856:;7<:<<9<<<9<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_610:2:6:529:366	147	chr2	1291	99	35M	=	1103	-223	GCTACTCAATATATCCATGTAACAAATCTGCGCTT	9;8;8<:<<<<<<<;<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_65:5:299:336:613	147	chr2	1293	99	35M	=	1145	-183	TACTCAATATATCCATGTAACAAATCTGCGCTTGT	1;4(+<<5<4<1<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:3
+B7_597:2:42:28:552	83	chr2	1294	99	35M	=	1131	-198	ACTCAATATATCCATGTAACAAATCTGCGCTTGTA	</8:<<:<<<;;<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:2
+EAS114_39:3:55:464:146	147	chr2	1295	99	35M	=	1114	-216	CTCAATATATCCATGTAACAAATCTGCGCTTGTAC	;(;;;;<<<<;<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:45	NM:i:0	UQ:i:0	H0:i:1	H1:i:2
+EAS54_67:6:109:953:668	99	chr2	1297	99	35M	=	1485	223	CAATATATCCATGTAACAAATCTGCGCTTGTACTT	;<<<<;<<<<<<<<<<<<<<<<<<<<<<<<8<;<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:1
+EAS139_19:1:82:946:392	163	chr2	1297	99	40M	=	1493	236	CAATATATCCATGTAACAAATCTGCGCTTGTACTTCAAAA	<<<<<<<<<<<<<<<<<<<<<<<<<8<<<8<<8<<:4488	MF:i:18	Aq:i:74	NM:i:1	UQ:i:19	H0:i:1	H1:i:0
+EAS114_28:3:308:509:948	147	chr2	1298	99	36M	=	1123	-211	AATATATCCATGTAACAAATCTGCGCTTGTACTTCT	;;+;;;.8<<;;;<<<<<<<<<<<<<8<<<<<;<<<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_65:4:174:753:617	147	chr2	1299	75	35M	=	1136	-198	ATATATCCATGTAACAAATCTGCGCTTGTACTTCT	<;<;<<<:<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:3:26:1867:162	83	chr2	1299	70	35M	=	1137	-197	ATATATCCATGTAACAAATCTGCGCTTGTACTTCT	97999:;<<9;;<:<<;;;<;;<<<<<<<;;<<<<	MF:i:18	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_99:2:162:257:203	83	chr2	1301	99	35M	=	1114	-222	ATATCCATGTAACAAATCTGCGCTTGTACTTCTAA	<;<;:<<;<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:5:62:841:1994	121	chr2	1301	70	35M	=	1301	0	ATATCCATGTAACAAATCTGCGCTTGTACTTCTAA	87878;;6:;;:<<<<:<:;;;<;<<<;<;;<;<<	MF:i:64	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:5:62:841:1994	181	chr2	1301	0	*	=	1301	0	TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT	!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!	MF:i:192
+EAS139_19:7:44:1807:833	99	chr2	1301	99	40M	=	1449	188	ATATCCATGTAACAAATCTGCGCTTGTACTTCTAAATCTA	<<<<<<<<<<<<<<<<<<<;<;<<<;<<9<<<<<89;;;:	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_95:7:280:607:113	163	chr2	1303	99	35M	=	1468	200	ATCCATGTAACAAATCTGCGCTTGTACTTCTAAAT	===================;===;=====<=7=9:	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_62:2:260:147:818	163	chr2	1303	82	35M	=	1497	229	ATCCATGTAACAAATCTGCGCTTTTACTTCTAAAT	<<<<<<3<<<<<;<<<<)<1<<<&<7<<<;<4/9<	MF:i:18	Aq:i:41	NM:i:1	UQ:i:5	H0:i:0	H1:i:1
+EAS54_71:7:194:867:616	99	chr2	1303	99	34M	=	1481	213	ATCCATGTAACAAATCTGCGCTTGTACTTCTATT	<8<<<<<<<<<<<8<<4<<<<<<8<<3<<5<&(+	MF:i:18	Aq:i:67	NM:i:2	UQ:i:23	H0:i:1	H1:i:0
+EAS139_19:7:85:262:751	83	chr2	1305	99	40M	=	1105	-240	CCATGTAACAAATCTGCGCTTGTACTTCTAAATCTATAAC	22;99;<<8<<<<<<<;<;<<<<<;<<;<<<<<<<<<<<+	MF:i:18	Aq:i:47	NM:i:1	UQ:i:27	H0:i:0	H1:i:1
+EAS54_81:6:35:186:412	147	chr2	1306	99	35M	=	1139	-202	CATGTAACAAATCTGCGCTTGTACTTCTAAATCTA	<<4:6<;<&<:4<<<<<<<<;<<<<<<<<<<<<<<	MF:i:18	Aq:i:70	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS220_1:8:46:1528:799	147	chr2	1306	96	35M	=	1109	-232	CATGTAACAAATCTGCGCTTGTACTTCTAAATCTA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:19	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_591:5:124:978:501	163	chr2	1307	99	36M	=	1499	228	ATGTAACAAATCTGCGCTTGTACTTCTAAATCTATA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS192_3:3:88:866:774	163	chr2	1307	99	35M	=	1478	206	ATGTAACAAATCTGCTCTTGTACTTCTAAATCTAT	<<<;<<<<<;<<<<<<<<<<<<<<<<<68<<<<<<	MF:i:18	Aq:i:47	NM:i:1	UQ:i:27	H0:i:0	H1:i:1
+EAS221_1:6:4:1131:104	163	chr2	1307	99	35M	=	1487	215	ATGTAACAAATCTGCGCTTGTACTTCTAAATCTAT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<;;<<<::	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_32:6:178:342:866	83	chr2	1311	72	35M	=	1155	-191	AACAAATCTGCGCTTGTACTTCTAAATCTATAAAA	<<9<<<&;;<<<<77<;<<<5;:<<<:<<<<<<<<	MF:i:18	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_61:1:119:880:781	147	chr2	1312	99	35M	=	1157	-190	ACAAATCTGCGCTTGTACTTCTAAATCTATAACAA	;8<<;<<<<:<84<<<<:<<<<<<<<<<<<<5<<<	MF:i:18	Aq:i:45	NM:i:1	UQ:i:27	H0:i:0	H1:i:1
+B7_591:2:46:220:58	99	chr2	1313	99	36M	=	1483	206	CAAATCTGCGCTTGTACTTCTAAATCTATAAAAAAA	<<<<<<<<<<<<<<<<<<<<<<9<<<<<<<<<<:<;	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS220_1:2:47:591:698	147	chr2	1313	99	35M	=	1146	-202	CAAATCTGCGCTTGTACTTCTAAATCTATAACAAA	7;;;;:<<:<:<<<<<7<<:<<<<<<<<<<<<<<<	MF:i:18	Aq:i:45	NM:i:1	UQ:i:27	H0:i:0	H1:i:1
+EAS1_105:1:115:226:443	147	chr2	1314	99	35M	=	1137	-212	AAATCTGCGCTTGTACTTCTAAATCTATAAAAAAA	<<;;<;<<<<<<<<<<<<:<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_610:4:198:59:675	83	chr2	1315	99	35M	=	1150	-200	AATCTGCGCTTGTACTTCTAAATCTATAACAAAAT	<<<<<4<4<:<<<;7<<;<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:45	NM:i:1	UQ:i:27	H0:i:0	H1:i:1
+EAS221_3:2:76:1729:813	163	chr2	1317	99	35M	=	1506	224	TCTGCGCTTGTACTTCTAAATCTATAAAAAAATTA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:36	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_597:8:147:360:141	99	chr2	1319	47	35M	=	1501	218	TGCGCTTGTACTTCTAAATCTATAACAAAATTAAA	<<<<<<<<<<7<<<<<<<<<<<<<<<<<<<<<<<7	MF:i:18	Aq:i:47	NM:i:1	UQ:i:27	H0:i:0	H1:i:1
+EAS1_95:7:155:530:532	83	chr2	1319	99	35M	=	1128	-226	TGCGCTTGTACTTCTAAATCTATAACAAAATTAAA	:<<<><<8<<<<<><<<<<><<<<<<<<<<<<<<<	MF:i:18	Aq:i:47	NM:i:1	UQ:i:27	H0:i:0	H1:i:1
+EAS51_62:4:308:614:911	99	chr2	1319	90	35M	=	1493	209	TGCGCTTGTACTTCTAAATCTATAACAAAATTAAA	<<<<<<<<<<<<<<<<<<<<<<<<<<<;;<<<<8<	MF:i:18	Aq:i:43	NM:i:1	UQ:i:27	H0:i:0	H1:i:1
+EAS54_65:3:155:541:234	83	chr2	1319	99	35M	=	1151	-203	TGCGCTTGTACTTCTAAATCTATAAAAAAATTAAA	78;<7<<<<<<<<<<<<<<;<<<<<<<<<<;<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_57:6:175:289:351	147	chr2	1319	99	35M	=	1144	-210	TGCGCTTGTACTTCTAAATCTATAAAAAAATTAAA	9;;:+<<<<<;<<:<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_593:7:283:186:707	83	chr2	1321	99	36M	=	1154	-203	CGCTTGTACTTCTAAATCTATAACAAAATTAAAATT	889;<7;<7<<7<<<<<7<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:45	NM:i:1	UQ:i:27	H0:i:0	H1:i:1
+EAS1_105:3:308:66:538	147	chr2	1321	99	35M	=	1138	-218	CGCTTGTACTTCTAAATCTATAACAAAATTAAAAT	996999;<9;<:<<<<<:<<7<<<<<<<<<<<<<<	MF:i:18	Aq:i:45	NM:i:1	UQ:i:27	H0:i:0	H1:i:1
+EAS1_108:5:11:555:330	163	chr2	1321	99	35M	=	1492	206	CGCTTGTACTTCTAAATCTATAAAAAAATTAAAAT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<4<;<	MF:i:18	Aq:i:56	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_66:7:84:411:336	73	chr2	1322	75	35M	*	0	0	GCTTGTACTTCTAAATCTATAAAAAAATTAAAATT	<<<;<<<;<<<<<<<<<<<<:<<;<<<<<<;8<;<	MF:i:32	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_11:5:52:1278:1478	163	chr2	1322	47	35M	=	1513	226	GCTTGTACTTCTAAATCTATAACAAAATTAAAATT	<<<<<<<<<<<<<<9<<<<<<<<<<<<<<<<9<<<	MF:i:18	Aq:i:0	NM:i:1	UQ:i:27	H0:i:0	H1:i:1
+EAS56_53:3:101:809:776	147	chr2	1326	99	35M	=	1160	-201	GTACTTCTAAATCTATAAAAAAATTAAAATTTAAC	<<<-<;7;<<<<:;<<<7<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS192_3:3:221:881:916	147	chr2	1327	96	35M	=	1168	-194	TAATTCTAAATCTAGAACAAAATTAAAATTTAACA	44%-4(5<;9/,:<68:1<:8<:<<84;<<<<<;<	MF:i:18	Aq:i:24	NM:i:3	UQ:i:41	H0:i:0	H1:i:0
+EAS1_105:1:28:745:352	147	chr2	1329	99	35M	=	1159	-205	CTTCTAAATCTATAACAAAATTAAAATTTAACAAA	4;;*;<<<;;<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:45	NM:i:1	UQ:i:27	H0:i:0	H1:i:1
+EAS114_45:2:23:1754:796	99	chr2	1329	99	35M	=	1488	194	CTTCTAAATCTATAAAAAAATTAAAATTTAACAAA	;<<;<;<;<;<;<<;;;;;<<<<;;<<<<<97999	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_97:2:96:419:327	147	chr2	1331	99	35M	=	1149	-217	TCTAAATCTATAACAAAATTAAAATTTAACAAAAG	;1<<<<<9<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:47	NM:i:1	UQ:i:27	H0:i:0	H1:i:1
+EAS1_97:4:274:287:423	163	chr2	1332	75	35M	=	1515	218	CTAAATCTATAAAAAAATTAAAATTTAACAAAAGT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<<	MF:i:18	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS219_1:7:35:392:2042	83	chr2	1332	99	35M	=	1168	-199	ATAAATCTATAAAAAAATTAAAATTTAACAAAAGT	+<<<<</<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:1	UQ:i:10	H0:i:1	H1:i:0
+EAS54_65:2:94:356:809	83	chr2	1334	99	35M	=	1151	-218	AAATCTATAACAAAATTAAAATTTAACAAAAGTAA	<<<<3<<<<;;<<<<<<<<<;<<<<<<<<<<<<<<	MF:i:18	Aq:i:47	NM:i:1	UQ:i:26	H0:i:0	H1:i:1
+EAS114_30:7:319:11:255	83	chr2	1337	92	35M	=	1179	-193	TCTATAAAAAAATTAAAATTTAACAAAAGTAAATA	;8<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<<	MF:i:18	Aq:i:17	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:7:35:538:1882	83	chr2	1337	98	35M	=	1160	-212	TCTATAACAAAATTAAAATTTAACAAAAGTAAATA	73797;;3<;;<6;;<<<;8:;:;<;:<:;<<;;;	MF:i:18	Aq:i:43	NM:i:1	UQ:i:18	H0:i:0	H1:i:1
+EAS51_66:1:64:182:741	153	chr2	1338	10	35M	*	0	0	AAAAAAACAAATTAAACTCTAACAAAAGTAAATAA	(+;1&(9*%0<*(*&<*5,/+<,&<&<<6<<<<<<	MF:i:32	Aq:i:10	NM:i:6	UQ:i:63	H0:i:0	H1:i:0
+EAS54_61:4:86:660:932	147	chr2	1338	99	35M	=	1154	-219	ATATAAAAAAATTAAAATTTAACAAAAGTAAATAA	&<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:71	NM:i:1	UQ:i:5	H0:i:1	H1:i:0
+EAS56_53:8:122:430:882	147	chr2	1338	99	35M	=	1147	-226	CTATAAAAAAATTAAAATTTAACAAAAGTAAATAA	0<<:<<<<<<<:3<<<<<<<<<:<<<<<<<<<<<<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_595:6:99:557:427	83	chr2	1342	99	35M	=	1186	-191	AACAAAATTAAAATTTAACAAAAGTAAATAAAACA	<<-<<<<9<<<<<:<<<<9<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:1	UQ:i:12	H0:i:1	H1:i:0
+B7_593:5:299:743:762	83	chr2	1345	99	36M	=	1173	-208	AAAATTAAAATTTAACAAAAGTAAATAAAACACATA	;<<<1<<<<<+<;<;7<<;<<<<<<<<<;<<;;<<7	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_30:2:303:428:326	99	chr2	1345	74	35M	=	1515	205	AAAATTAAAATTTAACAAAAGTAAATAAAACACAT	<<<<<<<<<<<<<<<<<<<<<<<<<<;<<<<<<<;	MF:i:18	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_65:4:192:714:341	83	chr2	1346	99	35M	=	1170	-211	AAATTAAAATTTAACAAAAGTAAATAAAACACATA	<<<3;<<<<9:<<</<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_593:1:189:876:833	83	chr2	1349	99	36M	=	1173	-212	TTAAAATTTAACAAAAGTAAATAAAACACATAGCTA	7;<<<<:;;<</<<<<<<<<<;<<<<<<<<<<<<<<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_26:7:37:79:581	163	chr2	1349	68	35M	=	1533	219	TTAAAATTTAAAAAAAGTAAATAAAACACATAGCT	<>4<>>>>;>>&>->9>9;4>->>>>,4>9>,<1>	MF:i:18	Aq:i:27	NM:i:1	UQ:i:5	H0:i:0	H1:i:1
+EAS139_19:2:82:154:1333	99	chr2	1349	77	40M	=	1511	202	TTAAAATTTAACAAAAGTAAATAAAACACACAGCTAAAAC	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;;<;;:;:	MF:i:18	Aq:i:0	NM:i:1	UQ:i:27	H0:i:1	H1:i:0
+EAS188_7:1:290:286:763	99	chr2	1349	75	35M	=	1515	201	TTAAAATTTAACAAAAGTAAATAAAACACATAGCT	<<<<<<<<<<<<<<<<7<<<<<<<<<<<<<<<8<<	MF:i:18	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_1:4:3:248:1491	73	chr2	1349	99	35M	*	0	0	TTAAAATTTAACAAAAGTAAATAAAACACATAGCT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<:8:<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_39:3:6:1064:1805	99	chr2	1350	99	35M	=	1502	187	TAAAATTTAACAAAAGTAAATAAAACACATAGCTA	<<<<<<<<<<<<<<<<<<<<<<;<<<<<<<<<<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_595:6:137:811:130	83	chr2	1351	99	35M	=	1175	-211	AAAATTTAACAAAAGTAAATAAAACACATAGCTAA	<<<<<<<<<:<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:47	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_108:1:155:809:543	83	chr2	1352	99	35M	=	1156	-231	AAATTTAACAAAAGTAAATAAAACACATAGCTAAA	<<<+0<<<9<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_63:3:41:468:459	99	chr2	1352	75	35M	=	1513	196	AAATTTAACAAAAGTAAATAAAACACATAGCTAAA	<<<<<<<<<<<<<<<<<<<<<;<<<<<<<<<<;;7	MF:i:18	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_108:4:31:622:216	73	chr2	1354	99	35M	*	0	0	ATTTAACAAAAGTAAATAAAACACATAGCTAAAAC	<<<<<<<<<<<<<<<<<<<<<<<<<<<<8<<96<7	MF:i:18	Aq:i:70	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_71:8:105:854:975	163	chr2	1354	71	35M	=	1523	202	ATTTAACAAAAGTAAATAAAACACATAGCTAAAAC	<<<<<<<<<<<<<<<<<<<<<<<<<<<7:<;;;;5	MF:i:18	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_610:7:26:749:174	147	chr2	1357	78	35M	=	1183	-209	TAACAAAAGTAAATAAAACACATAGCTAAAACTAA	(<<)<<<<6<<<<<<<<<<&:<3<<<6<<<)<:<<	MF:i:18	Aq:i:11	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_57:6:21:553:57	147	chr2	1358	99	35M	=	1197	-196	AACAAAAGTAAATAAAACACATAGCTAAAACTAAA	<<+<<<<<<<<<;<<<<8<<<<<<8<<<<<;<<<<	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_97:2:128:629:484	83	chr2	1359	96	35M	=	1185	-209	AAAAAAGTAAATAAAACACATAGCTAAAACTAAAA	:(::<</*;<<99<<<-<;<<<<4<<<<<<<<<<<	MF:i:18	Aq:i:30	NM:i:1	UQ:i:7	H0:i:1	H1:i:0
+EAS1_108:2:85:580:481	83	chr2	1359	99	35M	=	1167	-227	AAAAAAGTAAATAAAACACATAGCTAAAACTAAAA	=)====77========8=3====3===========	MF:i:18	Aq:i:71	NM:i:1	UQ:i:8	H0:i:1	H1:i:0
+B7_589:8:139:727:808	83	chr2	1363	99	35M	=	1195	-203	AAGTAAATAAAACACATAGCTAAAACTAAAAAAGC	<<;<<<<<<<<<;<;<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_67:2:22:471:500	83	chr2	1365	99	35M	=	1200	-200	GTAAATAAAACACATAGCTAAAACTAAAAAAGCAA	=9===0====;=77<==8;====;===========	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_103:7:112:578:782	147	chr2	1366	89	35M	=	1183	-218	AAAATAAAACACATAGCTAAAACTAAAAAAGCAAA	+<<<%<<<<6<;<<<<6:<<<<:<<<<<<<<<<<<	MF:i:18	Aq:i:20	NM:i:1	UQ:i:10	H0:i:1	H1:i:0
+EAS221_3:4:81:687:1379	83	chr2	1366	99	35M	=	1210	-191	TAAATAAAACACATAGCTAAAACTAAAAAAGCAAA	<<<<<<<<<<<:<<<<:<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_65:3:320:20:250	99	chr2	1367	77	35M	=	1532	200	AAATAAAACACATAGCTAAAACTAAAAAAGCAAAA	<<<<<<<<<<<<<<<<<;<<<<<<<<<;+:<;<<3	MF:i:18	Aq:i:6	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_65:5:312:985:871	83	chr2	1369	99	35M	=	1212	-192	ATAAAACACATAGCTAAAACTAAAAAAGCAAAAAC	<8<<<<.<.<<<<:<<<<<.<<<<<<<<<<<<<<<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_62:6:12:484:836	83	chr2	1372	99	35M	=	1197	-210	AAACACATAGCTAAAACTAAAAAAGCAAAAACAAA	<<<<</<4<<&7<<<<;<<<<<<<<<<<<<1<<<<	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_28:3:176:402:458	83	chr2	1376	99	36M	=	1210	-202	AAATAGCTAAAACTAAAAAAGCAAAAACAAAAACTA	</<+<4&;<<<<7<<<<<<<<;<<<<<<<<<<<<<<	MF:i:18	Aq:i:70	NM:i:1	UQ:i:14	H0:i:1	H1:i:0
+EAS139_11:7:50:1229:1313	163	chr2	1376	77	35M	=	1528	187	ACATAGCTAAAACTAAAAAAGCAAAAACAAAAACT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_65:4:124:367:72	83	chr2	1377	99	35M	=	1175	-237	CATAGCTAAAACTAAAAAAGCAAAAACAAAAACTA	,<<<8,<<<<<:<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:47	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_32:5:267:170:250	83	chr2	1377	99	35M	=	1189	-223	CATAGCTAAAACTAAAAAAGCAAAAACAAAAACTA	-<;<5-:<<<<;<<<<<<<;;<<<<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS220_1:6:24:105:1046	147	chr2	1377	99	35M	=	1184	-228	CATAGCTAAAACTAAAAAAGCAAAAACAAAAACTA	+<<<</<<<<<.<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:51	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_11:4:38:557:1441	83	chr2	1381	99	35M	=	1212	-204	GATAAAAATAAAAAAGCAAAAACAAAAACTATGCT	<&<<<<<,<<<<<<<<8<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:45	NM:i:2	UQ:i:16	H0:i:0	H1:i:1
+EAS188_7:7:67:719:786	83	chr2	1383	43	35M	=	1218	-200	TAAAAAAAAAAAAGCAAAAACAAAAACTATGCTAA	$<<;<-1<<<8<<*&<;<;,<<3<<<<33<<<33<	MF:i:18	Aq:i:13	NM:i:2	UQ:i:28	H0:i:1	H1:i:0
+EAS114_39:2:5:1219:137	147	chr2	1384	99	35M	=	1209	-210	AAAACTAAAAAAGCAAAAACAAAAACTATGCTAAG	<<<<:<<<<<<<<<<<<<<<<<<<<<<<<<<:<<<	MF:i:18	Aq:i:45	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_591:7:68:242:834	83	chr2	1386	99	36M	=	1200	-222	AAATAAAAAAGCAAAAACAAAAACTATGCTAAGTAT	<<68<<<<<<<8<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:76	NM:i:1	UQ:i:21	H0:i:1	H1:i:0
+EAS51_66:3:166:532:438	147	chr2	1386	99	35M	=	1194	-227	AACTAAAAAAGCAAAAACAAAAACTATGCTAAGTA	<<&7<<<<<<<+<<<<<:<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_610:4:139:989:144	83	chr2	1387	99	35M	=	1201	-221	ACTAAAAAAGCAAAAACAAAAACTATGCTAAGTAT	<&<<<<<<<<7<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_11:3:81:12:1231	83	chr2	1391	99	35M	=	1228	-198	AAAAAGCAAAAACAAAAACTATGCTAAGTATTGGT	<<<<<<<7<<<<<<<5<'<6/<<<5<<<<<<2<<<	MF:i:18	Aq:i:71	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_57:8:72:44:435	147	chr2	1392	76	35M	=	1235	-192	AAAAGCAAAAACAAAAACTATGCTAAGTATTGGTA	<<<<;7;<<<<;<<<<<<<<<<;<<<;<<<<<<<<	MF:i:18	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_95:2:211:954:174	147	chr2	1393	99	35M	=	1207	-221	AAAGAAAAAACAAAAACTATGCTAAGTATTGGTAA	====*=====6========================	MF:i:18	Aq:i:75	NM:i:1	UQ:i:9	H0:i:1	H1:i:0
+B7_595:7:149:123:265	83	chr2	1395	99	35M	=	1213	-217	AGCAAAAACAAAAACTATGCTAAGTATTGGTAAAG	<;&<<<<<:<<<<<<<<<<;<<<<<<<<<<<<<<<	MF:i:18	Aq:i:54	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_32:4:7:282:424	147	chr2	1397	83	35M	=	1233	-199	CAAAAACAAAAACTATGCTAAGTATTGTTAAAGAT	1<<<<<9<<<<<31<77;;;;7<3<<2+;<3<<<<	MF:i:18	Aq:i:41	NM:i:1	UQ:i:10	H0:i:0	H1:i:1
+B7_593:2:68:140:542	147	chr2	1398	95	36M	=	1217	-217	AAAAACAAAAACTATGCTAAGTATTGGTAAAGATGT	;;<<;7<<<<<<:<<<:<<<:<<<<<<<<<<<<<<<	MF:i:18	Aq:i:19	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_39:6:76:282:1668	147	chr2	1401	99	35M	=	1240	-196	AACAAAAACTATGCTAAGTATTGGTAAAGATGTGG	<<<<<:<<<8<8<<<<<::<<<<7<<<<<<2<<<8	MF:i:18	Aq:i:54	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_1:4:41:519:609	83	chr2	1401	99	35M	=	1229	-207	AACAAAAACTATGCTAAGTATTGGTAAAGATGTGG	<4;<;<<<<<<<<;4:<<;<<<<<<<<<<<;<<<<	MF:i:18	Aq:i:43	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_26:4:100:238:596	83	chr2	1403	56	35M	=	1220	-218	CAAAAACTATTCTAAGTATTGGTAAAGATGTGGGG	4<<<<;<3<3&<3<1<5<31<<3<<<<<<2<<;<,	MF:i:18	Aq:i:17	NM:i:1	UQ:i:5	H0:i:0	H1:i:1
+EAS51_64:3:255:45:399	83	chr2	1404	99	35M	=	1238	-201	AAAAACTATGCTAAGTATTGGTAAAGATGTGGGGA	<5<5<4$;;7/<<<177&7;<<<<<<;<<4<<<<<	MF:i:18	Aq:i:57	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS112_34:6:43:47:279	83	chr2	1405	99	35M	=	1206	-234	AAAACTATGCTAAGTATTGGTAAAGATGTGGGGAA	<:<<79<<<19<<<1<<9<<+<<<<<3<3<<<<<<	MF:i:18	Aq:i:45	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_78:7:215:516:299	147	chr2	1406	99	35M	=	1226	-215	AAGCTATGCTAAGTATTGGTAAAGATGTGGGGAAA	;;))7<8:855<<4<;:<<87<<<7<<;<<<*3<<	MF:i:18	Aq:i:64	NM:i:1	UQ:i:8	H0:i:1	H1:i:0
+B7_591:7:116:814:89	147	chr2	1408	99	36M	=	1231	-213	ACTATGCTAAGTATTGGTAAAGATGTGGGGAAAAAA	:38<;<;<<<<;<<<<<<<<<<<<<;<<<<<<<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_610:7:34:144:868	83	chr2	1412	76	35M	=	1226	-221	AGCTAAGGAATGGGAAAGGTGTGGGGAAAAAAGTA	&9+&7<&&0&<6<.0<<7<<<<<<<<<<<<<<<<<	MF:i:130	Aq:i:76	NM:i:4	UQ:i:50	H0:i:0	H1:i:0
+EAS51_62:7:312:236:655	83	chr2	1412	99	35M	=	1222	-225	TGCTAAGTATTGGTAAAGATGTGGGGAAAAAAGTA	<<8;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_11:6:17:1179:393	147	chr2	1412	99	35M	=	1232	-215	TGCTAAGTATTGGTAAAGATGTGGGGAAAAAAGTA	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:78	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS188_7:6:107:447:488	83	chr2	1412	99	35M	=	1233	-214	TGCTAAGTATTGGTAAAGATGTGGGGAAAAAAGTA	<<3<<<<<<6<<<<<<<<<<<<<<<<7<<<<<<<<	MF:i:18	Aq:i:53	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_597:6:73:420:812	147	chr2	1414	66	35M	=	1232	-217	CTAAGTATTGGTAAAGATGTGGGGAAAAAAGTAAA	5'<<<,<&,<<,<<<<<7<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_30:3:215:840:760	83	chr2	1416	99	35M	=	1256	-195	AAGTATTGGTAAAGATGTGGGGAAAAAAGTAAACT	<<<8<::<;;<<<:<7<7<;;;<<<<<<<<<<;<<	MF:i:18	Aq:i:66	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_589:8:118:829:36	147	chr2	1417	99	35M	=	1233	-219	AGTATTGGTAAAGATGTGGGGAAAAAAGTAAACTC	<8<<;;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:52	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_97:4:290:121:79	83	chr2	1420	99	35M	=	1257	-198	ATTGGTAAAGATGTGGGGAAAAAAGTAAACTCTCA	<1<<:<<<<<<<;<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS112_34:8:174:557:872	83	chr2	1423	99	35M	=	1237	-221	GGTAAAGATGTGGGGAAAAAAGTAAACTCTCAAAT	.77<:<9<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_30:2:315:412:921	147	chr2	1424	99	35M	=	1254	-205	GTAAAGATGTGGGGAAAAAAGTAAACTCTCAAATA	4-<79;<<<4:;:<<<<<<<<4<<<38<<;<<<<<	MF:i:18	Aq:i:45	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_19:5:95:944:247	147	chr2	1424	99	40M	=	1238	-226	GTAAAGATGTGGGGAAAAAAGTAAACTCTCAAATATTGCT	:7::;<<<<<;;<<<<<<<<<<<<<<;<<<<<<<<<<<<<	MF:i:18	Aq:i:78	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_30:6:137:741:866	83	chr2	1429	99	35M	=	1268	-196	GATGAGGGGAAAAAAGTAAACTCTCAAATATTGCT	<;0:%<:9<<<:<<<<;<<:<<;0;<<<<<::<<6	MF:i:18	Aq:i:70	NM:i:1	UQ:i:4	H0:i:1	H1:i:0
+EAS188_7:6:191:540:493	147	chr2	1432	99	35M	=	1273	-194	GTGGGGAAAAAAGTAAACTCTCAAATATTGCTAGT	<<9<1<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:78	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_108:1:49:911:980	83	chr2	1434	99	35M	=	1241	-228	GGGGAAAAAAGTAAACTCTCAAATATTGCTAGTGG	44:7<<<<<<<<<<<<<;<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:62	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_59:1:248:122:558	83	chr2	1436	99	35M	=	1243	-228	GGAAAAAAGTAAACTCTCAAATATTGCTAGTGGGA	<;<<<<<<<<<<<;<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:52	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_28:1:168:609:646	147	chr2	1436	99	36M	=	1264	-208	GGAAAAAAGTAAACTCTCAAATATTGCTAGTGGGAG	;;<<<<=======;;:;======;==<=========	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:4:7:1347:375	83	chr2	1436	99	35M	=	1271	-200	GGAAAAAAGTAAACTCTCAAATATTGCTAGTGGGA	47999<<<;;;;;;:5;:;<;;<;;;;;<;;;;;<	MF:i:18	Aq:i:66	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_62:4:282:962:46	147	chr2	1437	99	35M	=	1282	-190	GAAAAAAGTAAACTCTCAAATATTGCTAGTGGGAG	69<<<<<:<<<:<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_73:5:169:714:644	83	chr2	1437	99	35M	=	1231	-241	GAAAAAAGTAAACTCTCAAATATTGCTAGTGGGAG	;<<<<<<;<<<:<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_11:1:84:92:1246	83	chr2	1437	99	35M	=	1265	-207	GAAAAAAGTAAACTCTCAAATATTGCTAGTGGGAG	<<<<<<<<<<<<<<<8<<<<<<5<<<<<<<<<<<<	MF:i:18	Aq:i:78	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS112_34:7:71:62:254	83	chr2	1438	99	35M	=	1264	-209	AAAAAAGTAAACTCTCAAATATTGCTAGTGGGAGT	<<<<<<;8<<<<;<:<<<<<<<;<<;<<<<<<<<<	MF:i:18	Aq:i:43	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_97:7:28:979:519	83	chr2	1439	99	35M	=	1278	-196	AAAAAGTAAACTCTCAAATATTGCTAGTGGGAGTA	<<<<<6<<<<<<<<<<<<<<<8<<<<<<<<6<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS219_1:1:63:28:1549	83	chr2	1439	77	35M	=	1247	-227	AAAAAGTAAACTCTCAAATATTGCTAGTGGGAGTA	<<<<<<<<<:<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_593:7:15:244:876	147	chr2	1440	43	36M	=	1246	-230	AAAAGTAAACTCTCAAATATTGCTAGTGTGAGTATA	;<<<7<<<<<.2<-<<<<<<<<<:<<<<<<<<<2<<	MF:i:18	Aq:i:0	NM:i:1	UQ:i:27	H0:i:0	H1:i:1
+EAS56_59:8:80:542:549	83	chr2	1443	99	35M	=	1271	-207	AGTAAACTCTCAAATATTGCTAGTGGGAGTATAAA	=9====7=;=======;;==;========<=====	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_28:3:173:627:465	83	chr2	1444	99	36M	=	1260	-220	GTAAACTCTCAAATATTGCTAGTGGGAGTATAAATT	:<<<<;<;<;<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:51	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS219_FC30151:5:54:1351:910	147	chr2	1448	99	35M	=	1270	-213	ACTCTCAAATATTGCTAGTGGGAGTATAAATTGTT	<7<7;;<<<<<;<<;;<<;<<<<<<<<<<<<<<;<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS139_19:7:44:1807:833	147	chr2	1449	99	40M	=	1301	-188	CTCTCAAATATTGCTAGTGGGAGTATAAATTGTTTTCCAC	:6:9:<<<6<88<;<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_64:5:290:247:509	83	chr2	1450	99	35M	=	1276	-209	TCTCAAATATTGCTAGTGGGAGTATAAATTGTTTT	49';<<<<<8;<;;<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS112_32:7:42:804:114	83	chr2	1452	99	35M	=	1281	-206	TCAAATATTGCTAGTGGGAGTATAAATTGTTTTCC	;9<<;<<<<<<;<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS218_4:3:39:1671:1928	83	chr2	1453	99	35M	=	1276	-212	CAAATATTGCTAGTGGGAGTATAAATTGTTTTCCA	<<<<9<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_59:5:90:629:652	147	chr2	1456	99	35M	=	1276	-215	ATATTGCTAGTGGGAGTATAAATTGTTTTCCACTT	<:<7::<:<<<<<8<<<<<<<<<<<<<<<<<<<7<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_66:1:289:207:323	83	chr2	1462	99	35M	=	1279	-218	CTAGTGGGAGTATAAATTGATTTCCACTTTGGAAA	&</<7<<:<7::<<<<+3<-7<<:<7<<<<<<<<<	MF:i:18	Aq:i:41	NM:i:1	UQ:i:12	H0:i:0	H1:i:1
+EAS1_95:7:280:607:113	83	chr2	1468	99	35M	=	1303	-200	GGAGTATAAATTGTTTTCCACTTTGGAAAACAATT	18<-<<<<<<<<<<<<<8<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_99:3:21:423:169	147	chr2	1468	99	35M	=	1270	-233	GGAGTATAAATTGTTTTCCACTTTGGAAAACAATT	;376;0<<<<99<<<<<<-;<4<<<<<<<<<;<<<	MF:i:18	Aq:i:68	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS56_61:3:45:758:616	83	chr2	1473	99	35M	=	1280	-228	ATAAATTGTTTTCCACTTTGGAAAACAATTTGGTA	<<;<:<<<<<<<<<;<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:54	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_64:2:326:153:231	83	chr2	1477	43	35M	=	1290	-222	ATTGTTTTCAACTTTGGAAAACAATTTGGTAATTT	::6=68=<*$;*=========6=============	MF:i:18	Aq:i:0	NM:i:1	UQ:i:3	H0:i:0	H1:i:1
+EAS192_3:3:88:866:774	83	chr2	1478	99	35M	=	1307	-206	TTGTTTTCCACTTTGGAAAACAATTTGGTAATTTC	<<<;<<<<:<<<<<:<8<<<<<<<<<<8<<<<<<<	MF:i:18	Aq:i:47	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_71:7:194:867:616	147	chr2	1481	99	35M	=	1303	-213	TTTTCCACTTTGGAAAACAATTTGGTAATTTCGTT	38:;;:<:<<<<;<<<<<<<<<<;<<<<<<<<<<<	MF:i:18	Aq:i:67	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_591:2:46:220:58	147	chr2	1483	99	36M	=	1313	-206	TTCCACTTTGGAAAACAATTTGGTAATTTCGTTTTT	98<<<2<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS54_67:6:109:953:668	147	chr2	1485	99	35M	=	1297	-223	CCACTTTGGAAAACAATTTGGTAATTTCGTTTTTT	<:)9<<<<<<<<8:<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:30	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_1:6:4:1131:104	83	chr2	1487	99	35M	=	1307	-215	ACTTTGGAAAACAATTTGGTAATTTCGTTTTTTTT	61;;;<<<<<<<<<;:<<<:<<;<<<<;<<<<<<<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_45:2:23:1754:796	147	chr2	1488	99	35M	=	1329	-194	CTTTGGAAAACAATTTGGTAATTTCGTTTTTTTTT	88897;;;;:;:;;;;;;;;;;;;;;;;;;;;;;;	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_108:5:11:555:330	83	chr2	1492	99	35M	=	1321	-206	GGAAAACAATTTGGTAATTTCGTTTTTTTTTTTTT	6;6;9766+<<<<9:2=<===6=============	MF:i:18	Aq:i:56	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_62:4:308:614:911	147	chr2	1493	90	35M	=	1319	-209	AAAAACAATTTGGTAATTTAGTTTTTTTTTTTTTC	%<<<;:<::<6,<<<<<<:<:<<<<<<<<<<<<<<	MF:i:18	Aq:i:43	NM:i:2	UQ:i:31	H0:i:0	H1:i:1
+EAS139_19:1:82:946:392	83	chr2	1493	99	40M	=	1297	-236	GAAAACAATTTGGTAATTTCGTTTTTTTTTTTTTCTTTTC	:;:;:,::<:;<<<;;<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:74	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_62:2:260:147:818	83	chr2	1497	82	35M	=	1303	-229	AAAATTTGGTAATTTAGTTTTTTTTTTTTTCTTTT	6.=..++==6=76==&===========99======	MF:i:18	Aq:i:41	NM:i:2	UQ:i:18	H0:i:0	H1:i:1
+B7_591:5:124:978:501	83	chr2	1499	99	36M	=	1307	-228	AATTTGGTAATTTCGTTTTTTTTTTTTTCTTTTCTC	<9<;<<::<;<<;<4<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:77	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_597:8:147:360:141	147	chr2	1501	47	13M1D22M	=	1319	-218	TTTGGTAATTTAGTTTTTTTTTTTTCTTTTCTCTT	<86<<<<73<7<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:130	Aq:i:47	NM:i:1	UQ:i:27	H0:i:0	H1:i:0
+EAS114_39:3:6:1064:1805	147	chr2	1502	99	35M	=	1350	-187	TTGGTAATTTCGTTTTTTTTTTTTTCTTTTCTCTT	;88<;<;;<<;;<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS221_3:2:76:1729:813	83	chr2	1506	99	35M	=	1317	-224	TAATTTCGTTTTTTTTTTTTTCTTTTCTCTTTTTT	<+6<<<&1<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:36	NM:i:0	UQ:i:0	H0:i:2	H1:i:0
+EAS54_65:6:326:71:741	153	chr2	1509	0	35M	*	0	0	TCTCGTTTTTTTTTCTTTCTTTTCTCTTTTTTTTT	!!<66<<<<<<<<<&<<7&<<<<:<*<<<<<<<<1	MF:i:32	Aq:i:0	NM:i:2	UQ:i:22	H0:i:1	H1:i:12
+EAS112_34:6:145:144:263	73	chr2	1509	0	35M	*	0	0	TTTCGTTTTTTTTTTTTTTTTTTCCCCTTTCTTTT	<<<<<<<<<<<<<<<<+4+4&+&(&&*2&8&&&)&	MF:i:32	Aq:i:0	NM:i:4	UQ:i:29	H0:i:0	H1:i:0
+EAS1_105:1:329:407:872	73	chr2	1510	0	35M	*	0	0	TTCGTTTTTTTTTTTTTTTTTTCCCTTTTTTTTTT	<<<<<<<<<<<<<<<<<<6;<<&4::<++<(&;<<	MF:i:32	Aq:i:0	NM:i:2	UQ:i:46	H0:i:0	H1:i:0
+EAS139_19:2:82:154:1333	147	chr2	1511	77	40M	=	1349	-202	TTTTTTTTTTTTTTTTTTTTTCTTTTTTTTTTTTTTTTTT	:5'::<<<;<<<<<<</3<<<&4&7<<<<<<<<<<<<<<<	MF:i:18	Aq:i:0	NM:i:0	UQ:i:0	H0:i:85	H1:i:85
+EAS56_63:3:41:468:459	147	chr2	1513	0	35M	=	1352	-196	TTTTTTTTTTTTTTTTTTTCTTTTTTTTTTTTTTT	+;<<<<<<<<<<<;&<<;;88&<<<<<<<<<<<<<	MF:i:18	Aq:i:0	NM:i:0	UQ:i:0	H0:i:85	H1:i:85
+EAS114_28:6:11:151:750	153	chr2	1513	5	36M	*	0	0	GTTTTTATTTTTTTCCTCTCTCTTTTTTTTTTTTTT	:'1:%4;4<<<+;6;&9+6;/<<<<<<<<<<<<<<<	MF:i:32	Aq:i:5	NM:i:3	UQ:i:41	H0:i:0	H1:i:3
+EAS139_11:5:52:1278:1478	83	chr2	1513	47	35M	=	1322	-226	GTTTTTTTTTTTTTCTTTTCTCTTTTTTTTTTTTT	.8::<<<<<<<;<<<<<;<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:0	NM:i:0	UQ:i:0	H0:i:9	H1:i:85
+B7_591:2:309:798:997	153	chr2	1514	0	36M	*	0	0	TTTTTTTTTTTTTTTTTTCTCTTTTTTTTTTTTTTT	466;<<744077+&7097&%&4<9<<<9<<<::<<<	MF:i:32	Aq:i:0	NM:i:1	UQ:i:5	H0:i:12	H1:i:85
+EAS1_93:6:218:144:794	121	chr2	1514	0	35M	=	1514	0	TTTTTTTTTTTTTCTTTTCTCTTTTTTTTTTTTTT	;92/;5:<6)+<5)67</9<&<&<<<:<<<57<<<	MF:i:64	Aq:i:0	NM:i:0	UQ:i:0	H0:i:22	H1:i:85
+EAS1_93:6:218:144:794	181	chr2	1514	0	*	=	1514	0	GGGTGCATTGCTATGTTGCGGTCGCTTTGCCTCCT	++(3:&)5<9035<3):-<53<+&&-+)<<&)&<6	MF:i:192
+EAS1_97:6:222:305:337	153	chr2	1514	0	35M	*	0	0	TTTTTTTTTTTTTTTTTTCCCTTTTTTTTTTTTTT	;;;;;<<';<<<<*;<<<78;7<7<;<<<<<<<<<	MF:i:32	Aq:i:0	NM:i:2	UQ:i:32	H0:i:0	H1:i:37
+EAS1_105:3:7:35:528	89	chr2	1514	0	35M	*	0	0	TTTTTTTTTTGTTCTTTACTCTTTTTTTTTTTTTT	<<<<<<<<<<5<<<(<<%<<-8<<<<<<<<<8<<<	MF:i:32	Aq:i:0	NM:i:2	UQ:i:24	H0:i:0	H1:i:0
+EAS54_65:2:182:924:833	137	chr2	1514	0	35M	*	0	0	TTTTTTTTTTTTTATTTGCGCTTTTTTTTTTTTTT	<<<<<<<<<<<<<)7<<)3/:07<<9<9<<==<7<	MF:i:32	Aq:i:0	NM:i:3	UQ:i:30	H0:i:0	H1:i:0
+EAS54_81:8:78:735:536	153	chr2	1514	0	35M	*	0	0	TTTTTTTTTTTTTCATTTCTCTTTTTTTTTTTTTT	;9<<<<<<<.7<9'%1<<)2::<<<<<<<<<<<<<	MF:i:32	Aq:i:0	NM:i:1	UQ:i:4	H0:i:0	H1:i:15
+EAS56_59:5:232:336:46	137	chr2	1514	0	35M	*	0	0	ATTTTTTTTTTTTCTTTTCTCTTGTTTCTTTTTTT	+<<<<<<<<<<<<6<<<<;<6<<&&<,3<<<<3,,	MF:i:32	Aq:i:0	NM:i:3	UQ:i:50	H0:i:0	H1:i:0
+EAS188_4:5:308:552:77	89	chr2	1514	0	35M	*	0	0	TTTTCTTTTTTTTCTTTTCTCTTTTTTTTTTTTTT	1;-<%<;8<<<<<&<5-<58:5:<<<<<<<<<<<<	MF:i:32	Aq:i:0	NM:i:1	UQ:i:4	H0:i:30	H1:i:85
+B7_597:5:125:957:753	137	chr2	1515	0	35M	*	0	0	TTTTTTTTTTTTCTCTCCTCTTTTTTTTTTTTTTT	<8<<<;<8;8//++(,(+++&++(/+008880;;/	MF:i:32	Aq:i:0	NM:i:2	UQ:i:14	H0:i:0	H1:i:1
+EAS1_97:4:274:287:423	83	chr2	1515	0	35M	=	1332	-218	TTTTTTTTTTTTTTTTTCTCTTTTTTTTTTTTTTT	7<<<<9<<9<<<.<<<<90-<<<<<<<<<<<<<<<	MF:i:18	Aq:i:0	NM:i:0	UQ:i:0	H0:i:12	H1:i:85
+EAS54_71:8:234:21:950	89	chr2	1515	0	33M	*	0	0	TTTTTTTTTTTTCTCCTCTCTTTTTTTTTTTTT	<<<<<<<<<&<;2;&-<,<+;<<<7<<<;<;<;	MF:i:32	Aq:i:0	NM:i:2	UQ:i:17	H0:i:0	H1:i:7
+EAS56_61:6:256:67:461	117	chr2	1515	0	*	=	1515	0	TCATGTTTGTGTCTTTCTATGCATTTTTTTTTTTT	!!7181!63:6-:!-163(-1%-18<<4<<<<<<<	MF:i:192
+EAS56_61:6:256:67:461	185	chr2	1515	0	35M	=	1515	0	TTGTTTTTTCTTCTTTTCTCTTTTTTTTTTTTTTT	*.%53.:)1+9;3397;1795507+335;.&51)5	MF:i:64	Aq:i:0	NM:i:2	UQ:i:14	H0:i:2	H1:i:85
+EAS56_65:8:317:83:500	153	chr2	1515	0	35M	*	0	0	TTTTTTTTTTTTCTTTTCTCCTTTTTTTTTTGTTT	;;;;;<<<<<<<3<<<)-;31<<)97<;9<<:<<<	MF:i:32	Aq:i:0	NM:i:2	UQ:i:41	H0:i:0	H1:i:0
+EAS114_30:2:303:428:326	147	chr2	1515	0	35M	=	1345	-205	TTTTTTTTTTTTTTTTTCTCTTTTTTTTTTTTTTT	4<;<<;<;<4<<8;;;;.8+;<<;<8<;<;<<<<<	MF:i:18	Aq:i:0	NM:i:0	UQ:i:0	H0:i:11	H1:i:85
+EAS188_7:1:290:286:763	147	chr2	1515	75	35M	=	1349	-201	TTTTTTTTTTTTCTTTTCTCTTTTTTTTTTTTTTT	<<<<;<<<<<<<&<<<<&77<<<<<<<<<<<<<<<	MF:i:18	Aq:i:0	NM:i:0	UQ:i:0	H0:i:29	H1:i:85
+B7_591:7:89:67:709	89	chr2	1516	0	36M	*	0	0	TTTTTTTTTTTGTCTTCTCTTTTTTTTTTTTTTTTT	:7:::9:7:<<7<'<<477<<<<<<<<<:<<<<<:<	MF:i:32	Aq:i:0	NM:i:2	UQ:i:28	H0:i:0	H1:i:17
+EAS56_65:3:47:64:359	89	chr2	1516	0	35M	*	0	0	TTTTTTTTTTTCTCTCCTCTTTTTTTTTTTTTTTT	<<<6<<<<<<<4<4</9<4@<<;<<<<<<<<<<<<	MF:i:32	Aq:i:0	NM:i:2	UQ:i:33	H0:i:0	H1:i:6
+EAS56_65:4:296:78:421	121	chr2	1518	0	35M	=	1518	0	TCTTTTTTTCTTTTCTCTTTTTTTTTTTTTTTTTT	!!<<<:<<<<..<::<<<<<<<<<<<<<<<<<<<<	MF:i:64	Aq:i:0	NM:i:1	UQ:i:4	H0:i:85	H1:i:85
+EAS56_65:4:296:78:421	181	chr2	1518	0	*	=	1518	0	TGTTGGTGTTCGTTTTTTCTCCTGTTTCTTTTTCT	<<*<4<<<;:<0<<<<<<<<+;<9<<1<<;<<<+:	MF:i:192
+EAS1_95:4:238:124:196	89	chr2	1519	0	35M	*	0	0	TTTTTTTTCTTTTCTCTTTTTTTTTTTTTTTTTTT	<0<9.<5.5<<<<9<1<<5<<85<5<<<9<:<<<<	MF:i:32	Aq:i:0	NM:i:0	UQ:i:0	H0:i:85	H1:i:85
+EAS54_65:7:56:57:985	117	chr2	1519	0	*	=	1519	0	TTCTGTCTTCTCTCCTGTCTTCTTTTCTCTTCTTT	<9'<.<7<<2<<;77<7<<<<7<7<<<<7<<<2<<	MF:i:192
+EAS54_65:7:56:57:985	185	chr2	1519	0	35M	=	1519	0	TTTTTTCTCTTTTCTCTTTTTTTTTTTTTTTTTTT	666666*6&1666+64666666666&266666666	MF:i:64	Aq:i:0	NM:i:1	UQ:i:9	H0:i:85	H1:i:85
+EAS56_61:3:5:45:441	89	chr2	1519	0	35M	*	0	0	TTTTTTTTCTTTTCTCTTTTTTTTTTTTTTTTTTT	;;58:<:<(:<<11<&<1<<;<<<<><<<<<<<<<	MF:i:32	Aq:i:0	NM:i:0	UQ:i:0	H0:i:82	H1:i:85
+B7_589:6:33:356:636	73	chr2	1520	0	35M	*	0	0	TTTTTTTCTTTTCTCTTTTTTTTTTTTTTTTTTTT	<<<<<<<8;<<<<<<<<<<<<<7<<<<<<<;;3&3	MF:i:32	Aq:i:0	NM:i:0	UQ:i:0	H0:i:14	H1:i:85
+EAS114_45:6:86:859:1779	137	chr2	1520	0	35M	*	0	0	TTTTTTTCATTTCTCTTTTTTTTTTTTTTTTTTTT	;;;;;;;;;;;;;;;;;;;;;;;;;;;8;;)7699	MF:i:32	Aq:i:0	NM:i:1	UQ:i:26	H0:i:0	H1:i:15
+EAS54_71:8:105:854:975	83	chr2	1523	71	33M	=	1354	-202	TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTG	<<<<;<:<<;<&<;<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:0	NM:i:0	UQ:i:0	H0:i:85	H1:i:85
+EAS51_62:4:187:907:145	153	chr2	1524	28	35M	*	0	0	TTTCTTCTCTCTCTTTTTTTTTTTTTTTATTGCAT	<<<+;;,6<<<<6<<<<<<<<<<<<<<<<<<<<<<	MF:i:32	Aq:i:28	NM:i:3	UQ:i:59	H0:i:0	H1:i:0
+EAS54_71:4:284:269:882	73	chr2	1524	0	34M	*	0	0	TTTCTTTTCTCTTTTTTTTTTTTTTGTTTTTGCA	<;<<<<<8<7<8;<<<;<7<<<<<;272;73&&)	MF:i:32	Aq:i:0	NM:i:1	UQ:i:17	H0:i:0	H1:i:85
+EAS56_63:4:141:9:811	137	chr2	1524	10	35M	*	0	0	TTTCTTTTCTCCTTTTTTTTTTTTTTTTTCTACAT	<<<;<<<<<<<;<;<:<<<;<<<<<<<<..));;.	MF:i:32	Aq:i:0	NM:i:3	UQ:i:47	H0:i:2	H1:i:27
+EAS114_30:6:277:397:932	73	chr2	1524	0	35M	*	0	0	TTTCTTTTCACTTTTTTTTTTTTTTTTTTTTACTT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<:8(,0%(	MF:i:32	Aq:i:0	NM:i:3	UQ:i:42	H0:i:2	H1:i:85
+EAS139_11:7:50:1229:1313	83	chr2	1528	77	35M	=	1376	-187	TTTTTTCTTTTTTTTTTTTTTTTTTTTGCATGCCA	<<<<,<&<7<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:18	Aq:i:0	NM:i:1	UQ:i:11	H0:i:3	H1:i:7
+EAS54_65:3:320:20:250	147	chr2	1532	77	35M	=	1367	-200	TTTTTTTTTTTTTTTTTTTTTTTGCATGCCAGAAA	+'''/<<<<7:;+<;::<<<;;<<<<<<<<<<<<<	MF:i:18	Aq:i:6	NM:i:2	UQ:i:24	H0:i:1	H1:i:2
+EAS114_26:7:37:79:581	83	chr2	1533	68	35M	=	1349	-219	TTTTTTTTTTTTTTTTTTTTTTTCATGCCAGAAAA	3,,,===6===<===<;=====-============	MF:i:18	Aq:i:27	NM:i:2	UQ:i:23	H0:i:0	H1:i:1
diff --git a/tests/pysam_data/softclip.sam b/tests/pysam_data/softclip.sam
new file mode 100644
index 0000000..b285471
--- /dev/null
+++ b/tests/pysam_data/softclip.sam
@@ -0,0 +1,6 @@
+@HD	VN:1.5	SO:coordinate
+@SQ	SN:ref	LN:45
+r001	0	ref	9	30	3S6M1P1I4M	*	0	0	AAAAGATAAGGATA	*
+r002	0	ref	9	30	5S6M	*	0	0	GCCTAAGCTAA	01234567890
+r003	0	ref	9	30	6M5S	*	0	0	GCCTAAGCTAA	01234567890
+r004	2064	ref	29	17	6H5M	*	0	0	TAGGC	01234
diff --git a/tests/pysam_data/tag_bug.sam b/tests/pysam_data/tag_bug.sam
new file mode 100644
index 0000000..9c0b1cc
--- /dev/null
+++ b/tests/pysam_data/tag_bug.sam
@@ -0,0 +1,16 @@
+@SQ	SN:2L	LN:23011544
+@SQ	SN:2LHet	LN:368872
+@SQ	SN:2R	LN:21146708
+@SQ	SN:2RHet	LN:3288761
+@SQ	SN:3L	LN:24543557
+@SQ	SN:3LHet	LN:2555491
+@SQ	SN:3R	LN:27905053
+@SQ	SN:3RHet	LN:2517507
+@SQ	SN:4	LN:1351857
+@SQ	SN:U	LN:10049037
+@SQ	SN:Uextra	LN:29004656
+@SQ	SN:X	LN:22422827
+@SQ	SN:XHet	LN:204112
+@SQ	SN:YHet	LN:347038
+@SQ	SN:dmel_mitochondrion_genome	LN:19517
+HWI-EAS241:138:4:17:7389-21153#0	256	2L	8878	3	36M	*	0	0	CGCTGGACTCGCAAAGTGGACTTGTTCAGCAAGGAC	FEAAEDBEEFEDGDGGG@88GBEED:BB<BGDGG<F	NM:i:0	NH:i:2	CC:A:X	CP:f:1.90973e+07	HI:i:0	XC:i:1
diff --git a/tests/pysam_data/test.gtf b/tests/pysam_data/test.gtf
new file mode 100644
index 0000000..39b2938
--- /dev/null
+++ b/tests/pysam_data/test.gtf
@@ -0,0 +1,10 @@
+X	pseudogene	exon	170410	170513	.	+	.	 gene_id "ENSG00000228572"; transcript_id "ENST00000431238"; exon_number "1"; gene_name "NCRNA00108"; transcript_name "NCRNA00108-001";
+X	pseudogene	exon	171604	171758	.	+	.	 gene_id "ENSG00000228572"; transcript_id "ENST00000431238"; exon_number "2"; gene_name "NCRNA00108"; transcript_name "NCRNA00108-001";
+X	pseudogene	exon	172682	172712	.	+	.	 gene_id "ENSG00000228572"; transcript_id "ENST00000431238"; exon_number "3"; gene_name "NCRNA00108"; transcript_name "NCRNA00108-001";
+X	protein_coding	exon	192989	193061	.	+	.	 gene_id "ENSG00000182378"; transcript_id "ENST00000399012"; exon_number "1"; gene_name "PLCXD1"; transcript_name "PLCXD1-001";
+X	protein_coding	exon	198149	198351	.	+	.	 gene_id "ENSG00000182378"; transcript_id "ENST00000399012"; exon_number "2"; gene_name "PLCXD1"; transcript_name "PLCXD1-001";
+X	protein_coding	exon	200834	200981	.	+	.	 gene_id "ENSG00000182378"; transcript_id "ENST00000399012"; exon_number "3"; gene_name "PLCXD1"; transcript_name "PLCXD1-001";
+X	protein_coding	CDS	200855	200981	.	+	0	 gene_id "ENSG00000182378"; transcript_id "ENST00000399012"; exon_number "3"; gene_name "PLCXD1"; transcript_name "PLCXD1-001"; protein_id "ENSP00000381976";
+X	protein_coding	start_codon	200855	200857	.	+	0	 gene_id "ENSG00000182378"; transcript_id "ENST00000399012"; exon_number "3"; gene_name "PLCXD1"; transcript_name "PLCXD1-001";
+X	protein_coding	exon	205400	205536	.	+	.	 gene_id "ENSG00000182378"; transcript_id "ENST00000399012"; exon_number "4"; gene_name "PLCXD1"; transcript_name "PLCXD1-001";
+X	protein_coding	CDS	205400	205536	.	+	2	 gene_id "ENSG00000182378"; transcript_id "ENST00000399012"; exon_number "4"; gene_name "PLCXD1"; transcript_name "PLCXD1-001"; protein_id "ENSP00000381976";
diff --git a/tests/pysam_data/test.gtf.gz b/tests/pysam_data/test.gtf.gz
new file mode 100644
index 0000000000000000000000000000000000000000..047ef93cb04335ed2d2b8b7f42f493276800bc24
GIT binary patch
literal 311
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zTG-EDq87Gd=V5_P&_~SU<$LnXgJY*pRkPPd2l}%y0Vco^ToA~D$Kc-Hq1!I%DvX}9
z?F+bzNQ#7_RoJ(s>2_^>?9U1BLjq?=OxgrjwJ@i{hi=0N?Tew9DGxe~vh*!`0zi;I
zD_!nB*k`o5%V)G019u@2(z}+tYbloGLW1O7%l@iun_kzZ*fmvc_LEqVlF9}KF<uv=
zB$miu#7rqbT9}5-YnrcdPCM=_NF{P7l}z}Tl1C{4NXA{TWbabuN1Cp;15}9bP`EWT
zJTs>QHsb*jRT9s&(e-89yT$a~$9C-R^*`FVIw67sxFA^UeL}d;3Au#Qt)UAO@&z_S
J$a?Vx004wXnCt)m

literal 0
HcmV?d00001

diff --git a/tests/pysam_data/test_mapped_unmapped.sam b/tests/pysam_data/test_mapped_unmapped.sam
new file mode 100644
index 0000000..f5ca805
--- /dev/null
+++ b/tests/pysam_data/test_mapped_unmapped.sam
@@ -0,0 +1,28 @@
+@HD	VN:1.0
+@SQ	SN:chr1	LN:100
+@SQ	SN:chr2	LN:100
+@CO	Test counting of mapped/unmapped reads
+read1_mapped	0	chr1	21	20	10M1D25M	=	200	167	AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG	<<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<<	NM:i:1
+read2_unmapped	4	chr1	21	20	10M1D25M	=	200	167	AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG	<<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<<	NM:i:1
+read3_unmapped	20	chr1	21	20	10M1D25M	=	200	167	AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG	<<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<<	NM:i:1
+pair1a_mapped	67	chr1	21	20	10M1D25M	=	200	167	AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG	<<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<<	NM:i:1
+pair1b_mapped	131	chr1	21	20	10M1D25M	=	200	167	AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG	<<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<<	NM:i:1
+pair2a_unmapped	71	chr1	21	20	10M1D25M	=	200	167	AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG	<<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<<	NM:i:1
+pair2b_mapped	139	chr1	21	20	10M1D25M	=	200	167	AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG	<<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<<	NM:i:1
+pair3a_unmapped	77	chr1	21	20	10M1D25M	=	200	167	AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG	<<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<<	NM:i:1
+pair3b_unmapped	141	chr1	21	20	10M1D25M	=	200	167	AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG	<<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<<	NM:i:1
+noseq2b_mapped	139	chr1	21	20	10M1D25M	=	200	167	AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG	<<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<<	NM:i:1
+bread1_mapped	0	chr2	21	20	10M1D25M	=	200	167	AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG	<<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<<	NM:i:1
+bread2_unmapped	4	chr2	21	20	10M1D25M	=	200	167	AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG	<<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<<	NM:i:1
+bread3_unmapped	20	chr2	21	20	10M1D25M	=	200	167	AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG	<<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<<	NM:i:1
+bpair1a_mapped	67	chr2	21	20	10M1D25M	=	200	167	AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG	<<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<<	NM:i:1
+bpair1b_mapped	131	chr2	21	20	10M1D25M	=	200	167	AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG	<<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<<	NM:i:1
+bpair2a_unmapped	71	chr2	21	20	10M1D25M	=	200	167	AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG	<<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<<	NM:i:1
+bpair2b_mapped	139	chr2	21	20	10M1D25M	=	200	167	AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG	<<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<<	NM:i:1
+bpair3a_unmapped	77	chr2	21	20	10M1D25M	=	200	167	AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG	<<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<<	NM:i:1
+bpair3b_unmapped	141	chr2	21	20	10M1D25M	=	200	167	AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG	<<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<<	NM:i:1
+bnoseq2b_mapped	139	chr2	21	20	10M1D25M	=	200	167	AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG	<<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<<	NM:i:1
+noseq1_unmapped	4	*	0	20	*	=	200	167	AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG	<<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<<	NM:i:1
+noseq2a_unmapped	71	*	0	20	*	=	200	167	AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG	<<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<<	NM:i:1
+pair3a_unmapped	77	*	0	20	*	=	200	167	AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG	<<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<<	NM:i:1
+pair3b_unmapped	141	*	0	20	*	=	200	167	AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG	<<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<<	NM:i:1
diff --git a/tests/pysam_data/test_query_position.sam b/tests/pysam_data/test_query_position.sam
new file mode 100644
index 0000000..5e8d2d1
--- /dev/null
+++ b/tests/pysam_data/test_query_position.sam
@@ -0,0 +1,9 @@
+@HD	VN:1.0
+@SQ	SN:chr1	LN:100
+@SQ	SN:chr2	LN:100
+@SQ	SN:chr3	LN:100
+@SQ	SN:chr4	LN:100
+read1	0	chr1	21	20	10M1D25M	=	200	167	AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG	<<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<<	NM:i:1
+read2	0	chr2	21	30	10M2D25M	=	500	412	ACCTATATCTTGGCCTTGGCCGATGCGGCCTTGCA	<<<<<;<<<<7;:<<<6;<<<<<<<<<<<<7<<<<	MF:i:18
+read1	16	chr3	21	20	10M1D25M	=	200	167	AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG	<<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<<	NM:i:1
+read2	16	chr4	21	30	10M2D25M	=	500	412	ACCTATATCTTGGCCTTGGCCGATGCGGCCTTGCA	<<<<<;<<<<7;:<<<6;<<<<<<<<<<<<7<<<<	MF:i:18
diff --git a/tests/pysam_data/test_unaligned.sam b/tests/pysam_data/test_unaligned.sam
new file mode 100644
index 0000000..3cbb20a
--- /dev/null
+++ b/tests/pysam_data/test_unaligned.sam
@@ -0,0 +1,6 @@
+@HD	VN:1.0	SO:queryname
+@RG	ID:myid	PL:illumina	PU:P123456	LB:L123456	DT:2013-03-20T21:00:00-0700	SM:S123456	CN:MYCN
+B123456:6:1101:10000:137074	77	*	0	0	*	*	0	0	CATGTGTATCACCCAGTACAATGCCTGACACACAGCAGTCACTTAAAGAGTGCTATTGCTATTATACAGTCATACT	HHHHHHHHHHHHHHHHFHHHHHHHHHHGHHHHHHHBHHEFFHHHHHHHHHDHHHFHFHHHHHFHHEHFB@CDCCDE	RG:Z:myid	AM:i:0	SM:i:0
+B123456:6:1101:10000:137074	141	*	0	0	*	*	0	0	CAAGGAACTTTACAGTTCAGGGGAGTTTTCCAGTGGCAGAAAGTGGGAAGATGATGCTCCCAAGGAAGAAGTAGAT	HHHHHHHHHHHGHHHHHHHHHHHHHHHHHHHHHFHGHFHDFEF?EFEDEFFHHHFHDFHHHFHHHEFBBHD@D=C#	RG:Z:myid	AM:i:0	SM:i:0
+B123456:6:1101:10000:171579	589	*	0	0	*	*	0	0	GAAGCATAGGACATGTCAATGATGGCCAGGTGTGTGAGGAAGAAGTACATGGGGGTGTGAAGCTTAGAGTCCAGGC	############################################################################	RG:Z:myid	AM:i:0	SM:i:0
+B123456:6:1101:10000:171579	653	*	0	0	*	*	0	0	ACCCTGCTGGGGAATGGGGTCATCTTTGGGATTATCTGCCTGGACTCTAAGCTTCACACACCCATGTACTTCTTCC	8BBBB>6<C<53679<:6<@95>><937964@?:@@B;A@8>=<>CB=CD##########################	RG:Z:myid	AM:i:0	SM:i:23
diff --git a/tests/refactoring.pl b/tests/refactoring.pl
new file mode 100644
index 0000000..3300111
--- /dev/null
+++ b/tests/refactoring.pl
@@ -0,0 +1,60 @@
+while (<STDIN>) {
+    # Samfile refactoring
+    s/Samfile/AlignmentFile/g;
+
+    # AlignedRead refactoring
+    s/AlignedRead/AlignedSegment/g;
+    
+    # Do these patterns first as they match
+    # the new names
+    s/\.query/\.query_alignment_sequence/g;
+    s/\.positions/\.getReferencePositions()/g;
+
+    # Tabixfile, etc
+    s/Tabixfile/TabixFile/g;
+    s/Fastafile/FastaFile/g;
+    s/Fastqfile/FastqFile/g;
+
+    # basic attributes
+    s/\.qname/\.query_name/g;
+    s/\.tid/\.reference_id/g;
+    s/\.pos/\.reference_start/g;
+    s/\.mapq/\.mapping_quality/g;
+    s/\.rnext/\.next_reference_id/g;
+    s/\.pnext/\.next_reference_start/g;
+    s/\.tlen/\.query_length/g;
+    s/\.seq/\.query_sequence/g;
+    if (/\.qual =/) {
+	s/([[\].0-9a-zA-Z]*)\.qual = (\S*)/$1.query_qualities = pysam.fromQualityString($2)/g;
+    } else {
+	s/([[\].0-9a-zA-Z]*)\.qual/pysam.toQualityString($1\.query_qualities)/g;
+    }
+    s/\.alen/\.reference_length/g;
+    s/\.aend/\.reference_end/g;
+    s/\.rlen/\.query_alignment_length/g;
+    s/([[\].0-9a-zA-Z]*)\.qqual/pysam.toQualityString($1\.query_alignment_qualities)/g;
+    s/\.qstart/\.query_alignment_start/g;
+    s/\.qend/\.query_alignment_end/g;
+    s/\.qlen/\.query_alignment_length/g;
+    s/\.mrnm/\.next_reference_id/g;
+    s/\.rnext/\.next_reference_id/g;
+    s/\.mpos/\.next_reference_start/g;
+    s/\.rname/\.reference_id/g;
+    s/\.isize/\.query_length/g;
+    s/\.cigar/\.cigartuples/g unless (/\.cigarstring/);
+
+    s/\.blocks/\.getBlocks()/g;
+    s/\.aligned_pairs/\.getAlignedPairs()/g;
+    s/\.inferred_length/\.getInferredQueryLength()/g;
+
+    s/\.overlap()/\.getOverlap()/g;
+
+    # PileupProxy
+    s/\.n([^a-zA-Z])/\.nsegments$1/g;
+    
+    # if (/\.mrnm/ || /\.rnext/ || /\.mpos/ || /\.rname/)
+    # { 
+    #     warn "Deprecated tag $& at line $.\n";
+    # }
+    print;
+}
diff --git a/tests/refactoring.txt b/tests/refactoring.txt
new file mode 100644
index 0000000..bc7d086
--- /dev/null
+++ b/tests/refactoring.txt
@@ -0,0 +1,198 @@
+;; This buffer is for notes you don't want to save, and for Lisp evaluation.
+;; If you want to create a file, visit that file with C-x C-f,
+;; then enter the text in that file's own buffer.
+
+Samfile -> AlignmentFile
+AlignedRead -> AlignedSegment
+Tabixfile -> TabixFile
+Fastafile -> FastaFile
+Fastqfile -> FastqFile
+
+Changes to the AlignedSegment.API:
+
+Basic attributes
+================
+
+qname -> query_name
+tid -> reference_id
+pos -> reference_start
+mapq -> mapping_quality
+rnext -> next_reference_id
+pnext -> next_reference_start
+cigar = alignment (now returns CigarAlignment object)
+cigarstring = cigarstring
+tlen -> query_length
+seq -> query_sequence
+qual -> query_qualities, now returns array
+tags = tags (now returns Tags object)
+
+
+Derived simple attributes
+=========================
+
+alen -> reference_length, reference is always "alignment", so removed
+aend -> reference_end
+rlen -> query_length 
+query -> query_alignment_sequence
+qqual -> query_alignment_qualities, now returns array
+qstart -> query_alignment_start
+qend -> query_alignment_end
+qlen -> query_alignment_length, kept, because can be computed without fetching the sequence
+mrnm -> next_reference_id   
+mpos -> next_reference_start
+rname -> reference_id
+isize -> query_length
+
+
+Complex attributes - functions
+===============================
+
+blocks -> getBlocks()
+aligned_pairs -> getAlignedPairs()
+inferred_length -> inferQueryLength()
+positions -> getReferencePositions()
+overlap() -> getOverlap()
+
+
+Backwards incompatible changes:
+================================
+
+1. Empty cigarstring now returns None (instead of '')
+
+2. Empty cigar now returns None (instead of [])
+
+3. When using the extension classes in cython modules, AlignedRead
+   needs to be substituted with AlignedSegment. Automatic casting
+   of the base class to the derived class seems not to work?
+
+4. fancy_str() has been removed
+
+
+=====================================================
+
+Kevin's suggestions:
+
+
+* smarter file opener
+* CRAM support
+* CSI index support (create and use)
+* better attribute and property names
+* remove deprecated names
+* add object oriented CIGAR and tag handling
+* fetch query that recruits mate pairs that overlap query region
+* other commonly re-invented functionality
+
+        qname -> template_name
+        pos -> reference_start
+        aend -> reference_stop
+        alen -> reference_length
+        tid -> ref_id
+        qname -> template_name (not a high priority, but would be clearer)
+        qstart -> query_start (really segment_align_start)
+        qend -> query_stop (really segment_align_stop)
+        qlen -> query_length (really segment_align_length)
+        qqual -> query_qual (really segment_align_qual)
+        rlen -> drop in favor of len(align.seq)
+        inferred_length -> inferred_query_length
+        is_* -> replace with flag object that is a subclass of int
+        cigarstring -> str(align.cigar)
+        tags -> opts object with a mapping-like interface
+    Non-backward compatible:
+        rname, mrnm, mpos, isize -> remove
+        cigar -> CigarSequence object (or something similar)
+        All coordinate and length queries return None when a value is not available (currently some return None, some 0)
+        Store qualities as an array or bytes type
+
+
+Marcel's suggestions:
+
+    I recently sent in a pull request (which was merged) that improves the pysam doc a bit. While preparing that, I also wrote down some ways in which the API itself could be improved. I think the API is ok, but for someone like me who uses pysam not every day, some of the details are hard to remember and every time I do very basic things I end up looking them up again in the docs. I can recommend this article, written for C++, but many points still apply:
+    http://qt-project.org/wiki/API_Design_Principles .
+
+    Originally, I wanted to convert at least some of these suggestions to pull requests, but I'm not sure I have the time for that in the near future. So before I forget about this completely, I thought it's best to at least send this to the list. I'm concentrating on issues I found in Samfile and AlignedRead here.
+
+    - The terminology is inconsistent - often two words are used
+      to describe the same thing: opt vs. tag, query vs. read,
+      reference vs. target. My suggestion is to consistently use
+      the same terms as in the SAM spec: tag, query,
+      reference. This applies both to documentation and
+      function/property names.
+
+    - In line with the document linked to above (see the
+      section "The Art of Naming"): Do not abbreviate function
+      and property names. For example, tlen -> template_length,
+      pos -> position, mapq -> mapping_quality etc.
+
+    - Be consistent with multiword function and variable names. I
+      suggest to use the PEP8 convention. This isn't so visible
+      to the user in Samfile and AlignedRead, it seems, but there
+      are things like convertBinaryTagToList which could be
+      renamed to convert_binary_tag_to_list.
+
+    - Don't make functions that are not setters or getters a
+      property. This applies to
+      AlignedRead.positions/.inferred_length/.aligned_pairs/.blocks
+      and currently also Samfile.references, for example. Making
+      these a property implies to the user that access requires
+      constant time. This is important in code like this:
+
+    for i in range(n):
+     do_something_with(read.positions[i])
+
+    This looks inconspicuous, but is possibly inefficient since
+    .positions actually builds up the result it returns each time
+    it's accessed.
+
+    - Update the examples in the docs to use context manager
+      syntax.
+
+    Particular to Samfile:
+
+    - Deprecate Samfile.nreferences: propose to use
+      len(samfile.references) instead. Cache Samfile.references
+      so it's not re-created every time.
+
+    - Move Samfile.mapped/.unmapped/.nocoordinate into a .stats
+      attribute (Samfile.stats.mapped/.unmapped/.noocordinate).
+
+    Particular to AlignedRead:
+
+    - When read is an AlignedRead, print(read) should print out a
+      properly formatted SAM line.
+
+    - Force assignment to .qual/.seq to go through a function
+      that sets both at the same time. This avoids the problem
+      that they must be set in a particular order, which is easy
+      to forget and only 'enforced' through documentation.
+
+    - Deprecate rlen, use len(read.seq) instead.
+
+    - Handling of tags is a little awkward. Would be cool if this
+      worked:
+
+    read.tags['XK'] = 'hello'  # add a new tag if it doesn't exist
+    read.tags['AS'] += 17      # update the value of a tag
+    del read.tags['AS']
+    if 'AS' in read.tags: ...
+
+    - Add a property AlignedRead.qualities that behaves like a
+      Py3-bytes object in both Py2 and Py3. That is, accessing
+      read.qualities[0] gives you an int value that represents
+      the quality. The fact that qualities are encoded as
+      ASCII(q+33) is an implementation detail that can be hidden.
+
+      Done      
+
+    - And finally: Add a Cigar class. I guess this is already
+      what 'improved CIGAR string handling' refers to in the
+      roadmap. AlignedRead.cigar would then return a Cigar object
+      that can be printed, compared and concatenated to others,
+      whose length can be measured etc. The .unclipped and
+      .inferred length properties can also be moved here. Or
+      perhaps: Make this an Alignment class that even knows about
+      the two strings it is aligning. One could then also iterate
+      over all columns of the alignment. But I guess this goes
+      too far since that's what the AlignedRead itself should be.
+
+    Regards,
+    Marcel
diff --git a/tests/samtools_test.py b/tests/samtools_test.py
new file mode 100644
index 0000000..7c40237
--- /dev/null
+++ b/tests/samtools_test.py
@@ -0,0 +1,425 @@
+#!/usr/bin/env python
+'''unit testing code for pysam.
+
+Execute in the :file:`tests` directory as it requires the Makefile
+and data files located there.
+'''
+
+import warnings
+import unittest
+import os
+import re
+import glob
+import sys
+import subprocess
+import shutil
+import pysam
+import pysam.samtools
+import pysam.bcftools
+from TestUtils import checkBinaryEqual, check_lines_equal, \
+    check_samtools_view_equal, get_temp_filename, force_bytes, WORKDIR, \
+    make_data_files, BAM_DATADIR
+
+
+IS_PYTHON3 = sys.version_info[0] >= 3
+
+
+def setUpModule():
+    make_data_files(BAM_DATADIR)
+
+
+def run_command(cmd):
+    '''run a samtools command'''
+    try:
+        retcode = subprocess.call(cmd, shell=True,
+                                  stderr=subprocess.PIPE)
+        if retcode < 0:
+            print("Child was terminated by signal", -retcode)
+    except OSError as e:
+        print("Execution failed:", e)
+
+
+def get_version(executable):
+    '''return samtools/bcftools version'''
+
+    with subprocess.Popen(executable, shell=True,
+                          stderr=subprocess.PIPE).stderr as pipe:
+        lines = b"".join(pipe.readlines())
+
+    if IS_PYTHON3:
+        lines = lines.decode('ascii')
+    try:
+        x = re.search(r"Version:\s+(\S+)", lines).groups()[0]
+    except AttributeError:
+        raise ValueError("could not get version from %s" % lines)
+    return x
+
+
+class SamtoolsTest(unittest.TestCase):
+
+    '''test samtools command line commands and compare
+    against pysam commands.
+
+    Tests fail, if the output is not binary identical.
+    '''
+
+    requisites = [
+        "ex1.fa", "ex1.fa.fai",
+        "ex1.sam.gz",
+        "ex1.bam", "ex1.bam.bai",
+        "ex1.sam",
+        "ex1.sam",
+        "ex2.bam",
+        "ex2.sam",
+        "ex1.bed"]
+
+    # a list of statements to test
+    # should contain at least one %(out)s component indicating
+    # an output file.
+    statements = [
+        "view ex1.bam > %(out)s_ex1.view",
+        "view -c ex1.bam > %(out)s_ex1.count",
+        # ("view -bT ex1.fa -o %(out)s_ex1.view2 ex1.sam",
+        "sort ex1.bam -o %(out)s_ex1.sort.bam",
+        "mpileup ex1.bam > %(out)s_ex1.pileup",
+        "depth ex1.bam > %(out)s_ex1.depth",
+        # TODO: issues with file naming
+        # "faidx ex1.fa; %(out)s_ex1.fa.fai",
+        "index ex1.bam %(out)s_ex1.bam.fai",
+        "index -@2 ex1.bam %(out)s_ex1.bam.fai",
+        "idxstats ex1.bam > %(out)s_ex1.idxstats",
+        "fixmate ex1.bam %(out)s_ex1.fixmate.bam",
+        "flagstat ex1.bam > %(out)s_ex1.flagstat",
+        # Fails python 3.3 on linux, passes on OsX and when
+        # run locally
+        "calmd ex1.bam ex1.fa > %(out)s_ex1.calmd.bam",
+        # use -s option, otherwise the following error in samtools 1.2:
+        # Samtools-htslib-API: bam_get_library() not yet implemented
+        # causes downstream problems
+        # TODO: The following cause subsequent commands to fail
+        # unknown option
+        # "rmdup -s ex1.bam %(out)s_ex1.rmdup.bam",
+        # "merge -f %(out)s_ex1.merge.bam ex1.bam ex1.bam",
+        "reheader ex2.sam ex1.bam > %(out)s_ex1.reheader.bam",
+        "cat -o %(out)s_ex1.cat.bam ex1.bam ex1.bam",
+        "targetcut ex1.bam > %(out)s_ex1.targetcut",
+        "phase ex1.bam > %(out)s_ex1.phase",
+        "view -bt ex1.fa.fai ex1.sam.gz > %(out)s_ex1.bam",
+        "bam2fq ex1.bam > %(out)s_ex1.bam2fq",
+        # TODO: not the same
+        # "pad2unpad -T ex1.fa ex2.bam > %(out)s_ex2.unpad",
+        # TODO: command line option problem
+        # "bamshuf ex1.bam -O --output-fmt SAM > %(out)s_ex1.bamshuf.sam",
+        # "collate ex1.bam %(out)s_ex1.collate",
+        "bedcov ex1.bed ex1.bam > %(out)s_ex1.bedcov",
+        "stats ex1.bam > %(out)s_ex1.stats",
+        "dict ex1.bam > %(out)s_ex1.dict",
+        # TODO: not the same
+        # ("addreplacerg -r 'RG\tID:ga\tSM:hs' ex1.bam > %(out)s_ex1.addreplacerg",
+    ]
+
+    map_command = {
+    }
+
+    executable = "samtools"
+
+    module = pysam.samtools
+
+    def check_version(self):
+
+        samtools_version = get_version(self.executable)
+
+        def _r(s):
+            # patch - remove any of the alpha/beta suffixes, i.e., 0.1.12a ->
+            # 0.1.12
+            if s.count('-') > 0:
+                s = s[0:s.find('-')]
+            return re.sub("[^0-9.]", "", s)
+
+        if _r(samtools_version) != _r(pysam.__samtools_version__):
+            warnings.warn(
+                "versions of pysam.%s and %s differ: %s != %s" %
+                (self.executable,
+                 self.executable,
+                 pysam.__samtools_version__,
+                 samtools_version))
+
+    def setUp(self):
+        '''setup tests.
+
+        For setup, all commands will be run before the first test is
+        executed. Individual tests will then just compare the output
+        files.
+
+        '''
+        self.check_version()
+
+        self.workdir = os.path.join(WORKDIR, "samtools_test")
+        
+        if not os.path.exists(self.workdir):
+            os.makedirs(self.workdir)
+
+        for f in self.requisites:
+            shutil.copy(os.path.join(BAM_DATADIR, f),
+                        os.path.join(self.workdir, f))
+
+        self.savedir = os.getcwd()
+        os.chdir(self.workdir)
+
+        return
+
+    def get_command(self, statement, map_to_internal=True):
+        """return samtools command from statement"""
+        parts = statement.split(" ")
+        command = parts[0]
+        if map_to_internal:
+            return self.map_command.get(command, command)
+        else:
+            return command
+
+    def check_statement(self, statement):
+
+        parts = statement.split(" ")
+        r_samtools = {"out": self.executable}
+        r_pysam = {"out": "pysam"}
+
+        command = self.get_command(statement)
+
+        # self.assertTrue(command in pysam.SAMTOOLS_DISPATCH)
+
+        targets = [x for x in parts if "%(out)s" in x]
+        samtools_targets = [x % r_samtools for x in targets]
+        pysam_targets = [x % r_pysam for x in targets]
+
+        pysam_method = getattr(self.module, command)
+
+        # run samtools
+        full_statement = re.sub(r"%\(out\)s", self.executable, statement)
+        run_command(" ".join((self.executable, full_statement)))
+        # sys.stdout.write("%s %s ok" % (command, self.executable))
+
+        # run pysam
+        if ">" in statement:
+            assert parts[-2] == ">"
+            parts = parts[:-2]
+
+        # avoid interpolation to preserve string quoting, tab chars, etc.
+        pysam_parts = [re.sub(r"%\(out\)s", "pysam", x) for x in parts[1:]]
+        output = pysam_method(*pysam_parts,
+                              raw=True,
+                              catch_stdout=True)
+        # sys.stdout.write(" pysam ok\n")
+        if ">" in statement:
+            with open(pysam_targets[-1], "wb") as outfile:
+                if output is not None:
+                    outfile.write(force_bytes(output))
+        for samtools_target, pysam_target in zip(samtools_targets,
+                                                 pysam_targets):
+            if os.path.isdir(samtools_target):
+                samtools_files = glob.glob(os.path.join(
+                    samtools_target, "*"))
+                pysam_files = glob.glob(os.path.join(pysam_target, "*"))
+                self.assertEqual(len(samtools_files), len(pysam_files))
+                # need to be able to exclude files like README, etc.
+                continue
+            else:
+                samtools_files = [samtools_target]
+                pysam_files = [pysam_target]
+
+            for s, p in zip(samtools_files, pysam_files):
+                binary_equal = checkBinaryEqual(s, p)
+                error_msg = "%s failed: files %s and %s are not the same" % (
+                    command, s, p)
+                if binary_equal:
+                    continue
+                elif s.endswith(".bam"):
+                    self.assertTrue(
+                        check_samtools_view_equal(
+                            s, p, without_header=True),
+                        error_msg)
+                else:
+                    check_lines_equal(
+                        self, s, p,
+                        filter_f=lambda x: x.startswith("#"),
+                        msg=error_msg)
+
+    def testStatements(self):
+        for statement in self.statements:
+            command = self.get_command(statement, map_to_internal=False)
+            # bam2fq differs between version 1.5 and 1.6 - re-enable if
+            # bioconda samtools will be available.
+            # flagstat differs between version <=1.12 and >=1.13
+            if command in ("bedcov", "stats", "dict", "bam2fq", "flagstat"):
+                continue
+
+            if (command == "calmd" and
+                    list(sys.version_info[:2]) == [3, 3]):
+                # skip calmd test, fails only on python 3.3.5
+                # in linux (empty output). Works in OsX and passes
+                # for 3.4 and 3.5, see issue #293
+                continue
+            self.check_statement(statement)
+
+    @unittest.skipIf(sys.platform == "darwin", "not supported, pattern does not match")
+    @unittest.skipIf(not sys.stdin.isatty(), "skipping usage tests, stdin is not a tty")
+    def testUsage(self):
+        if self.executable == "bcftools":
+            # bcftools usage messages end with exit(1)
+            return
+
+        for statement in self.statements:
+            command = self.get_command(statement, map_to_internal=False)
+            # ignore commands that exit or cause other failures
+            # TODO: check - if reheader or phase is run in testStatements, sort fails
+            # here
+            if command in ("view", "sort", "bam2fq", "flagstat", "reheader",
+                           "stats", "idxstats"):
+                continue
+            mapped_command = self.get_command(statement, map_to_internal=True)
+            pysam_method = getattr(self.module, mapped_command)
+            usage_msg = pysam_method.usage()
+            expected = r"Usage:\s+{} {}".format(self.executable, command)
+            self.assertTrue(re.search(expected, usage_msg) is not None)
+
+    def tearDown(self):
+        if os.path.exists(self.workdir):
+            shutil.rmtree(self.workdir)
+        os.chdir(self.savedir)
+
+
+class EmptyIndexTest(unittest.TestCase):
+
+    def testEmptyIndex(self):
+        self.assertRaises(IOError, pysam.samtools.index,
+                          "exdoesntexist.bam")
+
+    def testEmptyIndexWithExtraFlag(self):
+        self.assertRaises(IOError, pysam.samtools.index,
+                          "-c",
+                          "exdoesntexist.bam")
+
+    def testEmptyIndexWithExtraArg(self):
+        self.assertRaises(IOError, pysam.samtools.index,
+                          "-c",
+                          "-m",
+                          "14",
+                          "exdoesntexist.bam")
+
+
+if sys.platform != "darwin":
+    # fails with segfault with htslib 1.5 on Osx, an issue with flockfile
+    # issue seems to be with repeated calls to interface
+
+    class TestReturnType(unittest.TestCase):
+
+        def testReturnValueString(self):
+            retval = pysam.idxstats(os.path.join(BAM_DATADIR, "ex1.bam"))
+            if IS_PYTHON3:
+                self.assertFalse(isinstance(retval, bytes))
+                self.assertTrue(isinstance(retval, str))
+            else:
+                self.assertTrue(isinstance(retval, bytes))
+                self.assertTrue(isinstance(retval, basestring))
+
+        def testReturnValueData(self):
+            args = "-O BAM {}".format(os.path.join(BAM_DATADIR,
+                                                   "ex1.bam")).split(" ")
+            retval = pysam.view(*args)
+
+            if IS_PYTHON3:
+                self.assertTrue(isinstance(retval, bytes))
+                self.assertFalse(isinstance(retval, str))
+            else:
+                self.assertTrue(isinstance(retval, bytes))
+                self.assertTrue(isinstance(retval, basestring))
+
+    class StdoutTest(unittest.TestCase):
+        '''test if stdout can be redirected.'''
+
+        def testWithRedirectedStdout(self):
+            r = pysam.samtools.flagstat(
+                os.path.join(BAM_DATADIR, "ex1.bam"))
+            self.assertTrue(len(r) > 0)
+
+        def testWithoutRedirectedStdout(self):
+            r = pysam.samtools.flagstat(
+                os.path.join(BAM_DATADIR, "ex1.bam"),
+                catch_stdout=False)
+            self.assertEqual(r, None)
+
+        def testDoubleCalling(self):
+            # The following would fail if there is an
+            # issue with stdout being improperly caught.
+            retvals = pysam.idxstats(
+                os.path.join(BAM_DATADIR, "ex1.bam"))
+            retvals = pysam.idxstats(
+                os.path.join(BAM_DATADIR, "ex1.bam"))
+
+        def testSaveStdout(self):
+            outfile = get_temp_filename(suffix=".tsv")
+            r = pysam.samtools.flagstat(
+                os.path.join(BAM_DATADIR, "ex1.bam"),
+                save_stdout=outfile)
+            self.assertEqual(r, None)
+            with open(outfile) as inf:
+                r = inf.read()
+            self.assertTrue(len(r) > 0)
+
+    class PysamTest(SamtoolsTest):
+        """check access to samtools command in the pysam
+        main package.
+
+        This is for backwards capability.
+        """
+
+        module = pysam
+
+# class BcftoolsTest(SamtoolsTest):
+
+#     requisites = [
+#         "ex1.fa",
+#         "ex1.vcf.gz",
+#         "ex1.vcf.gz.tbi",
+#     ]
+#     # a list of statements to test
+#     # should contain at least one %(out)s component indicating
+#     # an output file.
+#     statements = [
+#         # "index -n ex1.vcf.gz > %(out)s_ex1.index",
+
+#         "annotate -x ID ex1.vcf.gz > %(out)s_ex1.annotate",
+#         "concat -a ex1.vcf.gz ex1.vcf.gz > %(out)s_ex1.concat",
+#         "isec -p %(out)s_ex1.isec ex1.vcf.gz ex1.vcf.gz",
+#         "merge --force-samples ex1.vcf.gz ex1.vcf.gz > %(out)s_ex1.norm",
+#         "norm -m +both ex1.vcf.gz > %(out)s_ex1.norm",
+
+#         # "plugin",
+#         # "query -f '%CHROM\n' ex1.vcf.gz > %(out)s_ex1.query",
+#         # "reheader -s A > %(out)s_ex1.reheader",
+#         # "view ex1.vcf.gz > %(out)s_ex1.view",
+#         # "call -m ex1.vcf.gz > %(out)s_ex1.call",
+#         # bad file descriptor
+#         # "consensus -f ex1.fa ex1.vcf.gz  > %(out)s_ex1.consensus"
+#         # need appropriate VCF file
+#         # "cnv",
+#         # segfault
+#         # "filter -s A ex1.vcf.gz  > %(out)s_ex1.filter",
+#         # exit
+#         # "gtcheck -s A ex1.vcf.gz  > %(out)s_ex1.gtcheck",
+#         # segfault, used to work with bcftools 1.3
+#         # "roh -s A ex1.vcf.gz > %(out)s_ex1.roh",
+#         "stats ex1.vcf.gz > %(out)s_ex1.stats",
+#     ]
+
+#     map_command = {
+#     }
+
+#     executable = "bcftools"
+
+#     module = pysam.bcftools
+
+
+if __name__ == "__main__":
+    print("starting tests")
+    unittest.main()
+    print("completed tests")
diff --git a/tests/tabix_bench.py b/tests/tabix_bench.py
new file mode 100644
index 0000000..ce7077d
--- /dev/null
+++ b/tests/tabix_bench.py
@@ -0,0 +1,180 @@
+import gzip
+import os
+import pysam
+
+from TestUtils import TABIX_DATADIR
+
+FN_COMPRESSED = "example.bed.gz"
+FN_UNCOMPRESSED = "example.bed"
+FN_LARGE_COMPRESSED = "example_large.bed.gz"
+FN_LARGE_UNCOMPRESSED = "example_large.bed"
+
+
+def read_python_compressed(fn):
+    '''iterate through with python.'''
+    with gzip.open(fn, mode="r") as f:
+        return len([x.split(b"\t") for x in f])
+
+
+def read_python_uncompressed(fn):
+    with open(fn) as f:
+        return len([x.split("\t") for x in f])
+
+
+def fetch_plain(fn):
+    with pysam.Tabixfile(fn) as f:
+        return len(list(f.fetch()))
+
+
+def fetch_parsed(fn):
+    with pysam.Tabixfile(fn) as f:
+        return len(list(f.fetch(parser=pysam.asBed())))
+
+
+def iterate_generic_compressed(fn):
+    with gzip.open(fn) as f:
+        return len(list(pysam.tabix_generic_iterator(f, parser=pysam.asBed())))
+
+
+def iterate_generic_uncompressed(fn):
+    with open(fn) as f:
+        return len(list(pysam.tabix_generic_iterator(f, parser=pysam.asBed())))
+
+
+def iterate_parsed_compressed(fn):
+    with gzip.open(fn) as f:
+        return len(list(pysam.tabix_iterator(f, parser=pysam.asBed())))
+
+
+def iterate_parsed_uncompressed(fn):
+    with open(fn) as f:
+        return len(list(pysam.tabix_iterator(f, parser=pysam.asBed())))
+
+
+def iterate_file_compressed(fn):
+    with gzip.open(fn) as f:
+        return len(list(pysam.tabix_file_iterator(f, parser=pysam.asBed())))
+
+
+def iterate_file_uncompressed(fn):
+    with open(fn) as f:
+        return len(list(pysam.tabix_file_iterator(f, parser=pysam.asBed())))
+
+
+def test_read_python_compressed(benchmark):
+    result = benchmark(read_python_compressed,
+                       os.path.join(TABIX_DATADIR, FN_COMPRESSED))
+    assert result == 164
+
+
+def test_read_python_uncompressed(benchmark):
+    result = benchmark(read_python_uncompressed,
+                       os.path.join(TABIX_DATADIR, FN_UNCOMPRESSED))
+    assert result == 164
+
+
+def test_fetch_plain(benchmark):
+    result = benchmark(fetch_plain, os.path.join(TABIX_DATADIR, FN_COMPRESSED))
+    assert result == 164
+
+
+def test_fetch_parsed(benchmark):
+    result = benchmark(fetch_parsed, os.path.join(
+        TABIX_DATADIR, FN_COMPRESSED))
+    assert result == 164
+
+
+def test_iterate_generic_compressed(benchmark):
+    result = benchmark(iterate_generic_compressed,
+                       os.path.join(TABIX_DATADIR, FN_COMPRESSED))
+    assert result == 164
+
+
+def test_iterate_generic_uncompressed(benchmark):
+    result = benchmark(iterate_generic_uncompressed,
+                       os.path.join(TABIX_DATADIR, FN_UNCOMPRESSED))
+    assert result == 164
+
+
+def test_iterate_parsed_compressed(benchmark):
+    result = benchmark(iterate_parsed_compressed,
+                       os.path.join(TABIX_DATADIR, FN_COMPRESSED))
+    assert result == 164
+
+
+def test_iterate_parsed_uncompressed(benchmark):
+    result = benchmark(iterate_parsed_uncompressed,
+                       os.path.join(TABIX_DATADIR, FN_UNCOMPRESSED))
+    assert result == 164
+
+
+def test_iterate_file_compressed(benchmark):
+    result = benchmark(iterate_file_compressed,
+                       os.path.join(TABIX_DATADIR, FN_COMPRESSED))
+    assert result == 164
+
+
+def test_iterate_file_uncompressed(benchmark):
+    result = benchmark(iterate_file_uncompressed,
+                       os.path.join(TABIX_DATADIR, FN_UNCOMPRESSED))
+    assert result == 164
+
+
+def test_read_python_large_compressed(benchmark):
+    result = benchmark(read_python_compressed, os.path.join(
+        TABIX_DATADIR, FN_LARGE_COMPRESSED))
+    assert result == 100000
+
+
+def test_read_python_large_uncompressed(benchmark):
+    result = benchmark(read_python_uncompressed, os.path.join(
+        TABIX_DATADIR, FN_LARGE_UNCOMPRESSED))
+    assert result == 100000
+
+
+def test_fetch_plain(benchmark):
+    result = benchmark(fetch_plain, os.path.join(
+        TABIX_DATADIR, FN_LARGE_COMPRESSED))
+    assert result == 100000
+
+
+def test_fetch_parsed(benchmark):
+    result = benchmark(fetch_parsed, os.path.join(
+        TABIX_DATADIR, FN_LARGE_COMPRESSED))
+    assert result == 100000
+
+
+def test_iterate_generic_large_compressed(benchmark):
+    result = benchmark(iterate_generic_compressed, os.path.join(
+        TABIX_DATADIR, FN_LARGE_COMPRESSED))
+    assert result == 100000
+
+
+def test_iterate_generic_large_uncompressed(benchmark):
+    result = benchmark(iterate_generic_uncompressed, os.path.join(
+        TABIX_DATADIR, FN_LARGE_UNCOMPRESSED))
+    assert result == 100000
+
+
+def test_iterate_parsed_large_compressed(benchmark):
+    result = benchmark(iterate_parsed_compressed, os.path.join(
+        TABIX_DATADIR, FN_LARGE_COMPRESSED))
+    assert result == 100000
+
+
+def test_iterate_parsed_large_uncompressed(benchmark):
+    result = benchmark(iterate_parsed_uncompressed, os.path.join(
+        TABIX_DATADIR, FN_LARGE_UNCOMPRESSED))
+    assert result == 100000
+
+
+def test_iterate_file_large_compressed(benchmark):
+    result = benchmark(iterate_file_compressed, os.path.join(
+        TABIX_DATADIR, FN_LARGE_COMPRESSED))
+    assert result == 100000
+
+
+def test_iterate_file_large_uncompressed(benchmark):
+    result = benchmark(iterate_file_uncompressed, os.path.join(
+        TABIX_DATADIR, FN_LARGE_UNCOMPRESSED))
+    assert result == 100000
diff --git a/tests/tabix_data/Makefile b/tests/tabix_data/Makefile
new file mode 100644
index 0000000..19812df
--- /dev/null
+++ b/tests/tabix_data/Makefile
@@ -0,0 +1,40 @@
+all: all.stamp
+
+DERIVED_FILES = \
+	empty.bed.gz.tbi \
+	example.bed.gz example.bed.gz.tbi \
+	example.gff2.gz.tbi \
+	example.gff3.gz.tbi \
+	example.sam.gz.tbi \
+	example.vcf.gz.tbi \
+	example_badcomments.bed.gz.tbi \
+	example_badcomments.gtf.gz.tbi \
+	example_badcomments.sam.gz.tbi \
+	example_badcomments.vcf.gz.tbi \
+	example_comments.bed.gz.tbi \
+	example_comments.gtf.gz.tbi \
+	example_comments.sam.gz.tbi \
+	example_comments.vcf.gz.tbi \
+	example_large.bed.gz.tbi \
+	fivecolumns.bed.gz fivecolumns.bed.gz.tbi
+
+all.stamp: $(DERIVED_FILES)
+	touch $@
+
+%.gz: %
+	bgzip -c $< > $@
+
+%.gff2.gz.tbi: %.gff2.gz
+	tabix -p gff $<
+
+%.gff3.gz.tbi: %.gff3.gz
+	tabix -p gff $<
+
+%.gtf.gz.tbi: %.gtf.gz
+	tabix -p gff $<
+
+%.gz.tbi: %.gz
+	tabix -p $(subst .,,$(suffix $*)) $<
+
+clean:
+	-rm -f all.stamp $(DERIVED_FILES)
diff --git a/tests/tabix_data/empty.bed.gz b/tests/tabix_data/empty.bed.gz
new file mode 100644
index 0000000000000000000000000000000000000000..a776e8d995dc9c98882e0db160c0453d340e7fe8
GIT binary patch
literal 28
bcmb2|=3rp}f&Xj_PR>jW(hSUCE{FgCFhK%g

literal 0
HcmV?d00001

diff --git a/tests/tabix_data/example.bed b/tests/tabix_data/example.bed
new file mode 100644
index 0000000..544e42d
--- /dev/null
+++ b/tests/tabix_data/example.bed
@@ -0,0 +1,164 @@
+chr1	1737	2090
+chr1	1737	4275
+chr1	1873	1920
+chr1	1873	3533
+chr1	2042	2090
+chr1	2476	2560
+chr1	2476	2584
+chr1	2838	2915
+chr1	3084	3237
+chr1	3084	4021
+chr1	3084	4275
+chr1	3316	3533
+chr1	4022	4024
+chr1	4022	4249
+chr1	4226	4561
+chr1	4226	4692
+chr1	4226	19233
+chr1	4226	19433
+chr1	4250	4252
+chr1	4250	4275
+chr1	4267	4364
+chr1	4267	19433
+chr1	4559	4561
+chr1	4562	4692
+chr1	4833	4901
+chr1	4868	4901
+chr1	5659	5764
+chr1	5659	5810
+chr1	5767	5810
+chr1	6470	6628
+chr1	6717	6918
+chr1	6721	6918
+chr1	7096	7141
+chr1	7096	7227
+chr1	7096	7231
+chr1	7139	7141
+chr1	7142	7231
+chr1	7414	7416
+chr1	7414	7605
+chr1	7414	19206
+chr1	7417	7605
+chr1	7465	7605
+chr1	7469	7605
+chr1	7778	7924
+chr1	8131	8226
+chr1	8131	8229
+chr1	8227	8229
+chr1	8776	8868
+chr1	8776	8938
+chr1	8866	8868
+chr1	8869	8938
+chr1	14601	14706
+chr1	14601	14754
+chr1	14704	14706
+chr1	14707	14754
+chr1	19184	19206
+chr1	19184	19233
+chr1	19397	19433
+chr1	19417	19902
+chr1	19417	20960
+chr1	19417	20972
+chr1	20130	20530
+chr1	20130	20972
+chr1	20229	20366
+chr1	20427	20530
+chr1	20839	20960
+chr1	20839	20972
+chr1	24417	25003
+chr1	24417	25037
+chr1	24417	25944
+chr1	25001	25003
+chr1	25004	25037
+chr1	25108	25344
+chr1	25108	25936
+chr1	25140	25344
+chr1	25584	25599
+chr1	25584	25936
+chr1	25584	25944
+chr1	25597	25599
+chr1	25600	25944
+chr1	42912	42930
+chr1	42912	44799
+chr1	44693	44796
+chr1	44693	44799
+chr1	44797	44799
+chr1	52811	53750
+chr1	58918	58953
+chr1	58918	59971
+chr1	58954	58956
+chr1	58954	59868
+chr1	59869	59871
+chr1	59869	59971
+chr1	79158	81492
+chr1	79158	110795
+chr1	79158	123429
+chr1	79414	79913
+chr1	79414	80968
+chr1	80150	80968
+chr1	81954	82103
+chr1	82093	82103
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diff --git a/tests/tabix_data/example.gff2.gz b/tests/tabix_data/example.gff2.gz
new file mode 100644
index 0000000000000000000000000000000000000000..4084a744555d0da52c679778938d60bfd3aa2cd2
GIT binary patch
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diff --git a/tests/tabix_data/example.gff3.gz b/tests/tabix_data/example.gff3.gz
new file mode 100644
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diff --git a/tests/tabix_data/example.gtf.gz.tbi b/tests/tabix_data/example.gtf.gz.tbi
new file mode 100644
index 0000000000000000000000000000000000000000..aa5009d670651dcf2d21e9c62982396099705b52
GIT binary patch
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diff --git a/tests/tabix_data/example.sam.gz b/tests/tabix_data/example.sam.gz
new file mode 100644
index 0000000000000000000000000000000000000000..9d7cb5f31df05bc9716d1ac6185329acf10eb82a
GIT binary patch
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diff --git a/tests/tabix_data/example.vcf.gz b/tests/tabix_data/example.vcf.gz
new file mode 100644
index 0000000000000000000000000000000000000000..277bd7bce7ff60ded736f4df4ccf77a1bef6f210
GIT binary patch
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literal 0
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diff --git a/tests/tabix_data/example.vcf40 b/tests/tabix_data/example.vcf40
new file mode 100644
index 0000000..07e0746
--- /dev/null
+++ b/tests/tabix_data/example.vcf40
@@ -0,0 +1,23 @@
+##fileformat=VCFv4.0
+##fileDate=20090805
+##source=myImputationProgramV3.1
+##reference=1000GenomesPilot-NCBI36
+##phasing=partial
+##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
+##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency">
+##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele">
+##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129">
+##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership">
+##FILTER=<ID=q10,Description="Quality below 10">
+##FILTER=<ID=s50,Description="Less than 50% of samples have data">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
+##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA00001	NA00002	NA00003
+M	1230237	.	T	.	47	PASS	NS=3;DP=13;AA=T	GT:GQ:DP:HQ	0|0:54:7:56,60	0|0:48:4:51,51	0/0:61:2
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GIT binary patch
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diff --git a/tests/tabix_data/example_0v23.bed.gz.tbi b/tests/tabix_data/example_0v23.bed.gz.tbi
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GIT binary patch
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diff --git a/tests/tabix_data/example_0v23.vcf.gz b/tests/tabix_data/example_0v23.vcf.gz
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GIT binary patch
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diff --git a/tests/tabix_data/example_0v23.vcf.gz.tbi b/tests/tabix_data/example_0v23.vcf.gz.tbi
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GIT binary patch
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diff --git a/tests/tabix_data/example_0v26.bed.gz b/tests/tabix_data/example_0v26.bed.gz
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GIT binary patch
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diff --git a/tests/tabix_data/example_0v26.bed.gz.tbi b/tests/tabix_data/example_0v26.bed.gz.tbi
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GIT binary patch
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diff --git a/tests/tabix_data/example_0v26.vcf.gz.tbi b/tests/tabix_data/example_0v26.vcf.gz.tbi
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diff --git a/tests/tabix_data/example_badcomments.bed.gz b/tests/tabix_data/example_badcomments.bed.gz
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diff --git a/tests/tabix_data/example_badcomments.gtf.gz b/tests/tabix_data/example_badcomments.gtf.gz
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new file mode 100644
index 0000000000000000000000000000000000000000..9d7cb5f31df05bc9716d1ac6185329acf10eb82a
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diff --git a/tests/tabix_data/example_badcomments.vcf.gz b/tests/tabix_data/example_badcomments.vcf.gz
new file mode 100644
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diff --git a/tests/tabix_data/example_comments.bed.gz b/tests/tabix_data/example_comments.bed.gz
new file mode 100644
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diff --git a/tests/tabix_data/example_large.bed.gz b/tests/tabix_data/example_large.bed.gz
new file mode 100644
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literal 0
HcmV?d00001

diff --git a/tests/tabix_data/example_unicode.vcf b/tests/tabix_data/example_unicode.vcf
new file mode 100644
index 0000000..4512a8f
--- /dev/null
+++ b/tests/tabix_data/example_unicode.vcf
@@ -0,0 +1,23 @@
+##fileformat=VCFv4.0
+##fileDate=20090805
+##source=myImputationProgramV3.1
+##reference=1000GenomesPilot-NCBI36
+##phasing=partial
+##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
+##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency">
+##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele">
+##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129">
+##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership">
+##FILTER=<ID=q10,Description="Quality below 10">
+##FILTER=<ID=s50,Description="Less than 50% of samples have data">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
+##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	Reneé	Grün	Señor
+M	1230237	.	T	.	47	PASS	NS=3;DP=13;AA=T	GT:GQ:DP:HQ	0|0:54:7:56,60	0|0:48:4:51,51	0/0:61:2
+17	14370	Reneé	G	A	29	PASS	NS=3;DP=14;AF=0.5;DB;H2	GT:GQ:DP:HQ	0|0:48:1:51,51	1|0:48:8:51,51	1/1:43:5:.,.
+20	17330	.	T	A	3	q10	NS=3;DP=11;AF=0.017	GT:GQ:DP:HQ	0|0:49:3:58,50	0|1:3:5:65,3	0/0:41:3
+20	1110696	Grün	A	G,T	67	PASS	NS=2;DP=10;AF=0.333,0.667;AA=T;DB	GT:GQ:DP:HQ	1|2:21:6:23,27	2|1:2:0:18,2	2/2:35:4
+20	1234567	Señor	GTCT	G,GTACT	50	PASS	NS=3;DP=9;AA=G	GT:GQ:DP	0/1:35:4	0/2:17:2	1/1:40:3
diff --git a/tests/tabix_data/fivecolumns.bed b/tests/tabix_data/fivecolumns.bed
new file mode 100644
index 0000000..2ba7294
--- /dev/null
+++ b/tests/tabix_data/fivecolumns.bed
@@ -0,0 +1,4 @@
+chr1	100	200	one	apple
+chr1	300	400	two	banana
+chr2	100	600	three	carrot
+chr2	700	800	four	durian
diff --git a/tests/tabix_data/gtf_toofew_fields.gtf.gz b/tests/tabix_data/gtf_toofew_fields.gtf.gz
new file mode 100644
index 0000000000000000000000000000000000000000..42b924d544c3880238198054da2c6d396f3f4cbc
GIT binary patch
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literal 0
HcmV?d00001

diff --git a/tests/tabix_data/gtf_toomany_fields.gtf.gz b/tests/tabix_data/gtf_toomany_fields.gtf.gz
new file mode 100644
index 0000000000000000000000000000000000000000..901dc1e92ca2ae444a7b6bebee06b77cc4850413
GIT binary patch
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literal 0
HcmV?d00001

diff --git a/tests/tabix_data/gtf_wrong_fields.gtf.gz b/tests/tabix_data/gtf_wrong_fields.gtf.gz
new file mode 100644
index 0000000000000000000000000000000000000000..901dc1e92ca2ae444a7b6bebee06b77cc4850413
GIT binary patch
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literal 0
HcmV?d00001

diff --git a/tests/tabix_data/vcf/10.vcf b/tests/tabix_data/vcf/10.vcf
new file mode 100644
index 0000000..4ec2daf
--- /dev/null
+++ b/tests/tabix_data/vcf/10.vcf
@@ -0,0 +1,84 @@
+##fileformat=VCFv4.0
+##FILTER=<ID=HardyWeinbergViolation,Description="The validation is in Hardy-Weinberg violation">
+##FILTER=<ID=HighNoCallRate,Description="The validation no-call rate is too high">
+##FILTER=<ID=TooManyHomVars,Description="The validation homozygous variant rate is too high">
+##INFO=<ID=AC,Number=1,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##INFO=<ID=HW,Number=1,Type=Float,Description="Phred-scaled Hardy-Weinberg violation p-value">
+##INFO=<ID=HetPct,Number=1,Type=Float,Description="Percent of heterozygous genotypes">
+##INFO=<ID=HomRefPct,Number=1,Type=Float,Description="Percent of homozygous reference genotypes">
+##INFO=<ID=HomVarPct,Number=1,Type=Float,Description="Percent homozygous variant genotypes">
+##INFO=<ID=NoCallPct,Number=1,Type=Float,Description="Percent of no-calls">
+##ValidationMetrics_HardyWeinbergViolations="25 (8%)"
+##ValidationMetrics_HomVarViolations="0 (0%)"
+##ValidationMetrics_NoCallViolations="13 (4%)"
+##ValidationMetrics_PolymorphicPassingRecords="195 (75%)"
+##ValidationMetrics_RecordsPassingFilters="258 (87%)"
+##ValidationMetrics_RecordsProcessed=296
+##ValidationMetrics_SamplesAssayed=383
+##VariantValidationAssessor="analysis_type=VariantValidationAssessor input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=null excludeIntervals=null reference_sequence=/humgen/1kg/reference/human_g1k_v37.fasta rodBind=[rawData/plink.renamed.sorted.fixed.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub maxHardy=20.0 maxNoCall=0.05 maxHomVar=1.1"
+##source=PLINK
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diff --git a/tests/tabix_data/vcf/11.vcf b/tests/tabix_data/vcf/11.vcf
new file mode 100644
index 0000000..fe190df
--- /dev/null
+++ b/tests/tabix_data/vcf/11.vcf
@@ -0,0 +1,216 @@
+##fileformat=VCFv4.0
+##FILTER=<ID=HardyWeinbergViolation,Description="The validation is in Hardy-Weinberg violation">
+##FILTER=<ID=HighNoCallRate,Description="The validation no-call rate is too high">
+##FILTER=<ID=TooManyHomVars,Description="The validation homozygous variant rate is too high">
+##INFO=<ID=AC,Number=1,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##INFO=<ID=HW,Number=1,Type=Float,Description="Phred-scaled Hardy-Weinberg violation p-value">
+##INFO=<ID=HetPct,Number=1,Type=Float,Description="Percent of heterozygous genotypes">
+##INFO=<ID=HomRefPct,Number=1,Type=Float,Description="Percent of homozygous reference genotypes">
+##INFO=<ID=HomVarPct,Number=1,Type=Float,Description="Percent homozygous variant genotypes">
+##INFO=<ID=NoCallPct,Number=1,Type=Float,Description="Percent of no-calls">
+##ValidationMetrics_HardyWeinbergViolations="25 (8%)"
+##ValidationMetrics_HomVarViolations="0 (0%)"
+##ValidationMetrics_NoCallViolations="13 (4%)"
+##ValidationMetrics_PolymorphicPassingRecords="195 (75%)"
+##ValidationMetrics_RecordsPassingFilters="258 (87%)"
+##ValidationMetrics_RecordsProcessed=296
+##ValidationMetrics_SamplesAssayed=383
+##VariantValidationAssessor="analysis_type=VariantValidationAssessor input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=null excludeIntervals=null reference_sequence=/humgen/1kg/reference/human_g1k_v37.fasta rodBind=[rawData/plink.renamed.sorted.fixed.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub maxHardy=20.0 maxNoCall=0.05 maxHomVar=1.1"
+##source=PLINK
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+20	669442	.	TG	T	.	PASS	AC=54;AN=766;HW=6.74;HetPct=12.0;HomRefPct=86.9;HomVarPct=1.0;NoCallPct=0.0	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/0	1/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
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diff --git a/tests/tabix_data/vcf/12.vcf b/tests/tabix_data/vcf/12.vcf
new file mode 100644
index 0000000..e0d112c
--- /dev/null
+++ b/tests/tabix_data/vcf/12.vcf
@@ -0,0 +1,1000 @@
+##fileformat=VCFv4.0
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	DNA_pool_A
+chr1	1281168	.	A	G	14	.	DP=37;AF1=0.6243;CI95=0.5,1;DP4=4,0,6,0;MQ=15;PV4=1,0.027,1,1	PL:GT:GQ	43,0,4:0/1:6
+chr1	1281205	.	T	C	26	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=41	PL:GT:GQ	58,9,0:1/1:63
+chr1	1281206	.	G	C	25	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=41	PL:GT:GQ	57,9,0:1/1:63
+chr1	1922737	.	G	C	13.2	.	DP=21;AF1=1;CI95=1,1;DP4=0,0,0,21;MQ=22	PL:GT:GQ	46,63,0:1/1:99
+chr1	21197513	.	A	G	55.1	.	DP=9;AF1=1;CI95=1,1;DP4=0,0,0,7;MQ=41	PL:GT:GQ	88,21,0:1/1:84
+chr1	21343209	.	T	C	5.45	.	DP=17;AF1=1;CI95=1,1;DP4=0,0,17,0;MQ=14	PL:GT:GQ	37,51,0:1/1:99
+chr1	22097362	.	T	C	4.75	.	DP=10;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=30	PL:GT:GQ	35,9,0:1/1:63
+chr1	22254012	.	A	G	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=50	PL:GT:GQ	40,6,0:1/1:49
+chr1	22650927	.	G	A	48.1	.	DP=11;AF1=1;CI95=1,1;DP4=0,0,0,7;MQ=24	PL:GT:GQ	81,21,0:1/1:84
+chr1	23535401	.	C	T	40.4	.	DP=25;AF1=1;CI95=0.5,1;DP4=0,16,0,5;MQ=19;PV4=1,0.2,1,1	PL:GT:GQ	73,13,0:1/1:65
+chr1	23543855	.	T	C	49.1	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=44	PL:GT:GQ	82,18,0:1/1:90
+chr1	24245107	.	C	G	32	.	DP=4;AF1=0.5001;CI95=0.5,0.5;DP4=0,2,0,2;MQ=36;PV4=1,1,1,1	PL:GT:GQ	62,0,35:0/1:38
+chr1	24274412	.	G	C	39.5	.	DP=7;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=32	PL:GT:GQ	72,12,0:1/1:72
+chr1	36529832	.	C	T	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=46	PL:GT:GQ	73,6,0:1/1:49
+chr1	37788090	.	A	G	89.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=49	PL:GT:GQ	122,12,0:1/1:72
+chr1	43120440	.	C	T	34	.	DP=3;AF1=0.5002;CI95=0.5,0.5;DP4=0,1,0,2;MQ=49;PV4=1,1,1,1	PL:GT:GQ	64,0,31:0/1:34
+chr1	43980466	.	C	T	43	.	DP=16;AF1=1;CI95=1,1;DP4=0,0,0,15;MQ=19	PL:GT:GQ	76,45,0:1/1:99
+chr1	46047795	.	T	C	29.1	.	DP=7;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=31	PL:GT:GQ	62,18,0:1/1:90
+chr1	48860309	.	C	T	99	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=46	PL:GT:GQ	141,18,0:1/1:90
+chr1	49415599	.	T	C	4.61	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=34	PL:GT:GQ	34,6,0:1/1:49
+chr1	51601816	.	G	T	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=50	PL:GT:GQ	40,6,0:1/1:49
+chr1	51955459	.	G	C	89.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=49	PL:GT:GQ	122,12,0:1/1:72
+chr1	68479569	.	T	G	12	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48	PL:GT:GQ	43,6,0:1/1:49
+chr1	69032455	.	A	G	15.1	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=29	PL:GT:GQ	47,9,0:1/1:63
+chr1	71888225	.	G	T	9.31	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=43	PL:GT:GQ	40,6,0:1/1:49
+chr1	72381528	.	T	C	44	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=41	PL:GT:GQ	76,9,0:1/1:63
+chr1	82004013	.	A	G	37.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=50	PL:GT:GQ	70,12,0:1/1:72
+chr1	86289622	.	C	T	18	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=42	PL:GT:GQ	50,9,0:1/1:63
+chr1	90267663	.	A	G	22	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=45	PL:GT:GQ	54,9,0:1/1:63
+chr1	92699542	.	A	G	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=45	PL:GT:GQ	40,6,0:1/1:49
+chr1	94867317	.	G	A	26.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=45	PL:GT:GQ	58,6,0:1/1:49
+chr1	96428713	.	C	G	3.98	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=27	PL:GT:GQ	33,6,0:1/1:49
+chr1	100466329	.	G	C	4.85	.	DP=16;AF1=1;CI95=1,1;DP4=0,0,0,6;MQ=22	PL:GT:GQ	36,18,0:1/1:90
+chr1	101909281	.	G	A	70	.	DP=11;AF1=0.5;CI95=0.5,0.5;DP4=4,0,5,0;MQ=46;PV4=1,1,0.096,1	PL:GT:GQ	100,0,88:0/1:91
+chr1	106216572	.	T	A	22	.	DP=18;AF1=1;CI95=1,1;DP4=0,0,16,0;MQ=21	PL:GT:GQ	55,48,0:1/1:99
+chr1	107901770	.	T	C	9.31	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35	PL:GT:GQ	40,6,0:1/1:49
+chr1	108431179	.	A	G	99	.	DP=8;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=41	PL:GT:GQ	155,24,0:1/1:96
+chr1	112005344	.	C	T	99	.	DP=52;AF1=1;CI95=1,1;DP4=7,0,27,0;MQ=44;PV4=1,1,1,1	PL:GT:GQ	196,25,0:1/1:99
+chr1	116625452	.	C	T	36	.	DP=44;AF1=0.5;CI95=0.5,0.5;DP4=0,23,0,20;MQ=49;PV4=1,2.3e-69,0.42,1	PL:GT:GQ	66,0,179:0/1:69
+chr1	118060710	.	G	T	6.98	.	DP=8;AF1=0.4999;CI95=0.5,0.5;DP4=4,0,3,0;MQ=47;PV4=1,0.0071,1,1	PL:GT:GQ	36,0,73:0/1:39
+chr1	118198177	.	A	G	15.9	.	DP=23;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=43	PL:GT:GQ	47,6,0:1/1:49
+chr1	118586346	.	T	C	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49	PL:GT:GQ	40,6,0:1/1:49
+chr1	120809555	.	G	A	20	.	DP=8;AF1=0.5;CI95=0.5,0.5;DP4=6,0,2,0;MQ=46;PV4=1,1,1,1	PL:GT:GQ	50,0,106:0/1:53
+chr1	130723110	.	C	A	20.7	.	DP=8;AF1=0.5939;CI95=0.5,1;DP4=0,6,0,2;MQ=26;PV4=1,1,1,1	PL:GT:GQ	50,0,5:0/1:7
+chr1	133979895	.	T	C	14.9	.	DP=7;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=43	PL:GT:GQ	46,6,0:1/1:49
+chr1	134977940	.	C	T	30	.	DP=3;AF1=0.5002;CI95=0.5,0.5;DP4=0,1,0,2;MQ=38;PV4=1,1,0.26,1	PL:GT:GQ	60,0,31:0/1:34
+chr1	141768589	.	G	A	18.1	.	DP=15;AF1=0.5;CI95=0.5,0.5;DP4=4,0,4,0;MQ=51;PV4=1,2.7e-05,1,1	PL:GT:GQ	48,0,100:0/1:51
+chr1	141768590	.	G	A	22	.	DP=15;AF1=0.5;CI95=0.5,0.5;DP4=2,0,4,0;MQ=50;PV4=1,0.0033,1,1	PL:GT:GQ	52,0,40:0/1:43
+chr1	146506051	.	T	C	44	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=43	PL:GT:GQ	76,9,0:1/1:63
+chr1	150997009	.	G	A	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47	PL:GT:GQ	40,6,0:1/1:49
+chr1	162915612	.	G	C	13.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35	PL:GT:GQ	45,6,0:1/1:49
+chr1	168455400	.	A	G	4.12	.	DP=28;AF1=1;CI95=1,1;DP4=0,0,0,27;MQ=10	PL:GT:GQ	35,81,0:1/1:99
+chr1	172784744	.	T	C	17.8	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=48	PL:GT:GQ	49,6,0:1/1:49
+chr1	183627307	.	G	A	13.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35	PL:GT:GQ	45,6,0:1/1:49
+chr1	185789457	.	T	C	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=50	PL:GT:GQ	73,6,0:1/1:49
+chr1	187081827	.	T	C	4.77	.	DP=10;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=17	PL:GT:GQ	36,30,0:1/1:99
+chr1	188468339	.	C	T	33	.	DP=25;AF1=1;CI95=1,1;DP4=0,0,0,13;MQ=24	PL:GT:GQ	66,39,0:1/1:99
+chr1	188595435	.	C	T	41.8	.	DP=8;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49	PL:GT:GQ	73,6,0:1/1:49
+chr1	188670561	.	G	C	3.55	.	DP=22;AF1=1;CI95=1,1;DP4=0,0,0,9;MQ=18	PL:GT:GQ	34,27,0:1/1:99
+chr1	188924877	.	G	A	6.2	.	DP=10;AF1=0.9999;CI95=0.5,1;DP4=2,0,3,0;MQ=21;PV4=1,1,1,0.3	PL:GT:GQ	35,3,0:1/1:41
+chr1	190536295	.	G	A	68	.	DP=38;AF1=1;CI95=1,1;DP4=0,0,36,0;MQ=18	PL:GT:GQ	101,108,0:1/1:99
+chr1	191129408	.	T	A	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=48	PL:GT:GQ	40,6,0:1/1:49
+chr1	195937816	.	T	C	13	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35	PL:GT:GQ	44,6,0:1/1:49
+chr1	198857619	.	T	C	89	.	DP=61;AF1=0.5;CI95=0.5,0.5;DP4=0,38,0,17;MQ=30;PV4=1,0.032,1,1	PL:GT:GQ	119,0,139:0/1:99
+chr1	199057483	.	T	C	13	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=32	PL:GT:GQ	44,6,0:1/1:49
+chr1	200133619	.	G	C	5.83	.	DP=49;AF1=1;CI95=0.5,1;DP4=2,0,8,0;MQ=17;PV4=1,0.059,1,0.2	PL:GT:GQ	37,12,0:1/1:72
+chr1	200729661	.	A	T	36	.	DP=15;AF1=1;CI95=1,1;DP4=0,0,14,0;MQ=27	PL:GT:GQ	69,42,0:1/1:99
+chr1	201374519	.	T	C	69.5	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=39	PL:GT:GQ	102,12,0:1/1:72
+chr1	202811668	.	G	A	20.2	.	DP=4;AF1=0.5163;CI95=0.5,1;DP4=0,1,0,3;MQ=24;PV4=1,1,1,1	PL:GT:GQ	50,0,12:0/1:15
+chr1	202960650	.	C	T	16.6	.	DP=8;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=27	PL:GT:GQ	49,12,0:1/1:72
+chr1	205686638	.	C	T	11.3	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=42	PL:GT:GQ	43,9,0:1/1:63
+chr1	205949857	.	A	G	3.14	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=21	PL:GT:GQ	33,15,0:1/1:75
+chr1	209806643	.	A	G	13.2	.	DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=21	PL:GT:GQ	46,24,0:1/1:96
+chr1	209871501	.	C	T	25	.	DP=12;AF1=0.5;CI95=0.5,0.5;DP4=5,0,4,0;MQ=41;PV4=1,7.7e-06,1,1	PL:GT:GQ	55,0,84:0/1:58
+chr1	211051323	.	G	A	99	.	DP=14;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=49	PL:GT:GQ	176,24,0:1/1:96
+chr1	211389716	.	C	T	12	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=32	PL:GT:GQ	43,6,0:1/1:49
+chr1	211868415	.	G	A	3.54	.	DP=11;AF1=1;CI95=1,1;DP4=0,0,0,11;MQ=14	PL:GT:GQ	34,33,0:1/1:99
+chr1	211914531	.	C	T	84.5	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,1,0,4;MQ=46;PV4=1,1,1,1	PL:GT:GQ	116,7,0:1/1:57
+chr1	214691313	.	A	G	22	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=49	PL:GT:GQ	54,9,0:1/1:63
+chr1	215184650	.	C	T	40.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=46	PL:GT:GQ	72,6,0:1/1:49
+chr1	215995258	.	A	G	68	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=50	PL:GT:GQ	100,9,0:1/1:63
+chr1	217031394	.	G	C	13.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35	PL:GT:GQ	45,6,0:1/1:49
+chr1	217986960	.	T	C	44	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=36	PL:GT:GQ	76,9,0:1/1:63
+chr1	218086681	.	A	G	99	.	DP=10;AF1=1;CI95=1,1;DP4=0,0,0,9;MQ=34	PL:GT:GQ	142,27,0:1/1:99
+chr1	218546019	.	A	G	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=50	PL:GT:GQ	40,6,0:1/1:49
+chr1	218632417	.	G	T	17.1	.	DP=19;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=26	PL:GT:GQ	50,21,0:1/1:84
+chr1	218833355	.	C	G	23	.	DP=7;AF1=0.5;CI95=0.5,0.5;DP4=5,0,2,0;MQ=39;PV4=1,1,1,1	PL:GT:GQ	53,0,63:0/1:56
+chr1	219303186	.	T	C	7.79	.	DP=25;AF1=1;CI95=1,1;DP4=0,0,0,25;MQ=12	PL:GT:GQ	40,75,0:1/1:99
+chr1	219517634	.	G	A	26.5	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=42	PL:GT:GQ	59,12,0:1/1:72
+chr1	219590158	.	T	C	3.27	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=25	PL:GT:GQ	33,12,0:1/1:72
+chr1	219709853	.	A	T	99	.	DP=124;AF1=0.5;CI95=0.5,0.5;DP4=80,0,41,0;MQ=44;PV4=1,0.26,1,1	PL:GT:GQ	143,0,156:0/1:99
+chr1	222457988	.	A	G	11.1	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=23	PL:GT:GQ	42,6,0:1/1:49
+chr1	222477914	.	A	G	11.3	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=39	PL:GT:GQ	43,9,0:1/1:63
+chr1	223010233	.	A	G	18.6	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=25	PL:GT:GQ	51,12,0:1/1:72
+chr1	223796360	.	G	A	6.79	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=21	PL:GT:GQ	37,6,0:1/1:49
+chr1	224273784	.	A	T	14.2	.	DP=18;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=15	PL:GT:GQ	47,30,0:1/1:99
+chr1	224454685	.	C	T	46.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=32	PL:GT:GQ	79,15,0:1/1:75
+chr1	224514706	.	G	C	21	.	DP=38;AF1=1;CI95=1,1;DP4=0,0,38,0;MQ=19	PL:GT:GQ	54,114,0:1/1:99
+chr1	224515793	.	C	T	99	.	DP=26;AF1=1;CI95=1,1;DP4=0,0,26,0;MQ=45	PL:GT:GQ	211,78,0:1/1:99
+chr1	224692969	.	C	A	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=36	PL:GT:GQ	40,6,0:1/1:49
+chr1	225607249	.	A	G	34	.	DP=3;AF1=0.5002;CI95=0.5,0.5;DP4=1,0,2,0;MQ=45;PV4=1,1,0,1	PL:GT:GQ	64,0,31:0/1:34
+chr1	226923918	.	C	A	29.1	.	DP=52;AF1=1;CI95=0.5,1;DP4=0,2,0,10;MQ=27;PV4=1,1,1,1	PL:GT:GQ	62,18,0:1/1:90
+chr1	227125189	.	T	C	56.5	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=41	PL:GT:GQ	89,12,0:1/1:72
+chr1	227133712	.	A	T	20.1	.	DP=26;AF1=0.5;CI95=0.5,0.5;DP4=11,0,10,0;MQ=23;PV4=1,1,0.48,1	PL:GT:GQ	50,0,39:0/1:42
+chr1	227943954	.	G	C	47	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=37	PL:GT:GQ	79,9,0:1/1:63
+chr1	227943974	.	G	A	33.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=34	PL:GT:GQ	66,12,0:1/1:72
+chr1	228067480	.	A	G	42.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=45	PL:GT:GQ	75,15,0:1/1:75
+chr1	228067510	.	A	G	99	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=45	PL:GT:GQ	140,15,0:1/1:75
+chr1	228088778	.	C	T	6.79	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=23	PL:GT:GQ	37,6,0:1/1:49
+chr1	228117888	.	A	C	13.9	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=40	PL:GT:GQ	45,6,0:1/1:49
+chr1	228139641	.	T	C	44.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=35	PL:GT:GQ	77,12,0:1/1:72
+chr1	228577146	.	T	C	26	.	DP=41;AF1=0.5;CI95=0.5,0.5;DP4=0,25,0,14;MQ=22;PV4=1,1,1,0.027	PL:GT:GQ	56,0,77:0/1:59
+chr1	229001369	.	C	A	45	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=41	PL:GT:GQ	77,9,0:1/1:63
+chr1	229001386	.	C	T	8.44	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=42	PL:GT:GQ	39,6,0:1/1:49
+chr1	229348080	.	T	C	18.1	.	DP=3;AF1=0.5002;CI95=0.5,0.5;DP4=0,1,0,2;MQ=40;PV4=1,0.33,0.17,0.33	PL:GT:GQ	48,0,31:0/1:34
+chr1	229439710	.	C	T	33.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=32	PL:GT:GQ	66,12,0:1/1:72
+chr1	229655149	.	T	C	30	.	DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=30	PL:GT:GQ	63,24,0:1/1:96
+chr1	229660873	.	C	G	81	.	DP=28;AF1=0.5;CI95=0.5,0.5;DP4=0,20,0,7;MQ=36;PV4=1,1,1,1	PL:GT:GQ	111,0,120:0/1:99
+chr2a	3661005	.	C	G	24	.	DP=13;AF1=0.5001;CI95=0.5,0.5;DP4=7,0,4,0;MQ=27;PV4=1,1.1e-05,1,1	PL:GT:GQ	54,0,34:0/1:37
+chr2a	4140063	.	G	A	81	.	DP=26;AF1=0.6671;CI95=0.5,1;DP4=18,0,8,0;MQ=24;PV4=1,8.3e-09,1,1	PL:GT:GQ	110,0,3:0/1:5
+chr2a	4248440	.	T	C	20	.	DP=28;AF1=0.5;CI95=0.5,0.5;DP4=11,0,7,0;MQ=25;PV4=1,1,0.47,1	PL:GT:GQ	50,0,92:0/1:53
+chr2a	4707656	.	A	G	63	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=49	PL:GT:GQ	95,9,0:1/1:63
+chr2a	5194801	.	G	A	7.59	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=24	PL:GT:GQ	38,6,0:1/1:49
+chr2a	14111103	.	A	G	7.84	.	DP=7;AF1=1;CI95=1,1;DP4=0,0,0,7;MQ=20	PL:GT:GQ	40,21,0:1/1:84
+chr2a	17799746	.	A	G	11.3	.	DP=5;AF1=0.5001;CI95=0.5,0.5;DP4=0,3,0,2;MQ=32;PV4=1,1,1,1	PL:GT:GQ	41,0,35:0/1:37
+chr2a	24728910	.	G	A	45.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=28	PL:GT:GQ	78,15,0:1/1:75
+chr2a	29627939	.	G	T	5.44	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=27	PL:GT:GQ	36,9,0:1/1:63
+chr2a	31373164	.	C	T	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=44	PL:GT:GQ	73,6,0:1/1:49
+chr2a	33935228	.	T	C	41.8	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=51	PL:GT:GQ	73,6,0:1/1:49
+chr2a	36311856	.	G	A	99	.	DP=30;AF1=1;CI95=1,1;DP4=0,0,0,29;MQ=44	PL:GT:GQ	213,87,0:1/1:99
+chr2a	39281204	.	T	C	68	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=49	PL:GT:GQ	100,9,0:1/1:63
+chr2a	41087565	.	C	T	74.5	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=38	PL:GT:GQ	107,12,0:1/1:72
+chr2a	45574768	.	C	A	11.3	.	DP=8;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=18	PL:GT:GQ	43,9,0:1/1:63
+chr2a	55464464	.	T	C	26.1	.	DP=7;AF1=0.9966;CI95=0.5,1;DP4=5,0,2,0;MQ=26;PV4=1,1,1,1	PL:GT:GQ	55,1,0:1/1:23
+chr2a	63107673	.	T	A	70.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=34	PL:GT:GQ	103,12,0:1/1:72
+chr2a	63141732	.	A	T	22.8	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=42	PL:GT:GQ	54,6,0:1/1:49
+chr2a	63141910	.	G	A	3.41	.	DP=16;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=32	PL:GT:GQ	32,6,0:1/1:49
+chr2a	63141911	.	C	T	9.55	.	DP=16;AF1=0.5031;CI95=0.5,0.5;DP4=0,2,0,3;MQ=33;PV4=1,0.43,1,1	PL:GT:GQ	39,0,19:0/1:22
+chr2a	63143543	.	C	T	28	.	DP=18;AF1=1;CI95=1,1;DP4=0,1,0,17;MQ=16;PV4=1,1,1,1	PL:GT:GQ	61,42,0:1/1:99
+chr2a	66419805	.	G	A	3.69	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=23	PL:GT:GQ	34,15,0:1/1:75
+chr2a	66563922	.	C	T	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=51	PL:GT:GQ	40,6,0:1/1:49
+chr2a	67719136	.	C	T	39.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=50	PL:GT:GQ	71,6,0:1/1:49
+chr2a	72781453	.	A	C	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=50	PL:GT:GQ	73,6,0:1/1:49
+chr2a	76733211	.	G	A	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47	PL:GT:GQ	40,6,0:1/1:49
+chr2a	78190502	.	A	C	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47	PL:GT:GQ	40,6,0:1/1:49
+chr2a	85021209	.	A	G	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49	PL:GT:GQ	40,6,0:1/1:49
+chr2a	88554861	.	A	T	39	.	DP=74;AF1=0.5;CI95=0.5,0.5;DP4=0,7,0,4;MQ=46;PV4=1,1,1,1	PL:GT:GQ	69,0,92:0/1:72
+chr2a	88554877	.	A	G	92	.	DP=90;AF1=0.5;CI95=0.5,0.5;DP4=0,23,0,13;MQ=41;PV4=1,0.3,1,1	PL:GT:GQ	122,0,128:0/1:99
+chr2a	88824857	.	G	A	13.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=37	PL:GT:GQ	45,6,0:1/1:49
+chr2a	93546675	.	C	T	26	.	DP=6;AF1=0.5;CI95=0.5,0.5;DP4=4,0,2,0;MQ=46;PV4=1,1,1,1	PL:GT:GQ	56,0,87:0/1:59
+chr2a	94788853	.	A	G	34.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=43	PL:GT:GQ	67,15,0:1/1:75
+chr2a	96738146	.	T	C	11.3	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=40	PL:GT:GQ	43,9,0:1/1:63
+chr2a	102737384	.	A	G	12.3	.	DP=18;AF1=1;CI95=1,1;DP4=0,0,18,0;MQ=11	PL:GT:GQ	45,54,0:1/1:99
+chr2a	103407172	.	A	G	35	.	DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=19	PL:GT:GQ	68,24,0:1/1:96
+chr2a	105774580	.	T	G	99	.	DP=13;AF1=1;CI95=1,1;DP4=0,0,13,0;MQ=30	PL:GT:GQ	135,39,0:1/1:99
+chr2a	106376301	.	C	G	24.1	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=19	PL:GT:GQ	57,18,0:1/1:90
+chr2a	106376315	.	C	T	8.75	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=19	PL:GT:GQ	41,18,0:1/1:90
+chr2a	112422267	.	C	T	30	.	DP=20;AF1=0.5;CI95=0.5,0.5;DP4=14,0,5,0;MQ=39;PV4=1,1,1,1	PL:GT:GQ	60,0,131:0/1:63
+chr2b	3049384	.	A	C	14.9	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=42	PL:GT:GQ	46,6,0:1/1:49
+chr2b	3049385	.	G	C	14.9	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=42	PL:GT:GQ	46,6,0:1/1:49
+chr2b	3049406	.	C	G	99	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=36	PL:GT:GQ	135,18,0:1/1:90
+chr2b	4213802	.	T	C	89.5	.	DP=10;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=49	PL:GT:GQ	122,12,0:1/1:72
+chr2b	5022895	.	G	A	66	.	DP=10;AF1=1;CI95=1,1;DP4=0,0,0,10;MQ=49	PL:GT:GQ	99,30,0:1/1:99
+chr2b	6037666	.	G	T	56	.	DP=18;AF1=1;CI95=1,1;DP4=0,0,0,13;MQ=17	PL:GT:GQ	89,39,0:1/1:99
+chr2b	13656952	.	G	A	19.2	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=21	PL:GT:GQ	52,18,0:1/1:90
+chr2b	15026944	.	A	G	6.79	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=32	PL:GT:GQ	37,6,0:1/1:49
+chr2b	23362613	.	A	G	5.64	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=22	PL:GT:GQ	37,15,0:1/1:75
+chr2b	45947861	.	C	G	68	.	DP=11;AF1=1;CI95=1,1;DP4=0,0,0,11;MQ=50	PL:GT:GQ	101,33,0:1/1:99
+chr2b	46597824	.	T	C	65.6	.	DP=39;AF1=0.5939;CI95=0.5,1;DP4=23,0,10,0;MQ=22;PV4=1,0.014,1,1	PL:GT:GQ	95,0,5:0/1:7
+chr2b	49665191	.	G	T	34.1	.	DP=7;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=37	PL:GT:GQ	67,21,0:1/1:84
+chr2b	61001546	.	A	G	48	.	DP=9;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=26	PL:GT:GQ	81,24,0:1/1:96
+chr2b	88502851	.	T	C	4.77	.	DP=4;AF1=0.5;CI95=0.5,0.5;DP4=0,2,0,2;MQ=37;PV4=1,1,0.46,1	PL:GT:GQ	33,0,34:0/1:33
+chr2b	91675431	.	C	T	30	.	DP=14;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=27	PL:GT:GQ	63,24,0:1/1:96
+chr2b	91870148	.	T	G	67	.	DP=14;AF1=1;CI95=1,1;DP4=0,1,0,13;MQ=47;PV4=1,1,1,1	PL:GT:GQ	100,31,0:1/1:99
+chr2b	97066826	.	G	A	20.1	.	DP=9;AF1=0.5001;CI95=0.5,0.5;DP4=0,6,0,2;MQ=31;PV4=1,1,1,1	PL:GT:GQ	50,0,35:0/1:38
+chr2b	97670822	.	G	A	4.85	.	DP=6;AF1=1;CI95=1,1;DP4=0,0,0,6;MQ=18	PL:GT:GQ	36,18,0:1/1:90
+chr2b	102773175	.	A	G	17.1	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=38	PL:GT:GQ	49,9,0:1/1:63
+chr2b	109805532	.	T	C	99	.	DP=8;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=45	PL:GT:GQ	176,24,0:1/1:96
+chr2b	110841448	.	A	G	11.1	.	DP=20;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=44	PL:GT:GQ	42,6,0:1/1:49
+chr2b	123217025	.	T	C	31.5	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=37	PL:GT:GQ	64,12,0:1/1:72
+chr2b	123263214	.	A	G	11.3	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=35	PL:GT:GQ	43,9,0:1/1:63
+chr2b	127747292	.	C	T	68	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=52	PL:GT:GQ	100,9,0:1/1:63
+chr2b	130121958	.	A	G	89.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=43	PL:GT:GQ	122,15,0:1/1:75
+chr2b	130253633	.	A	G	14.9	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=42	PL:GT:GQ	46,6,0:1/1:49
+chr2b	130692761	.	C	T	49.1	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=51	PL:GT:GQ	82,18,0:1/1:90
+chr2b	130743365	.	A	G	99	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=42	PL:GT:GQ	140,15,0:1/1:75
+chr2b	131553874	.	A	C	11.3	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=37	PL:GT:GQ	43,9,0:1/1:63
+chr2b	131716894	.	A	G	99	.	DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=40	PL:GT:GQ	137,24,0:1/1:96
+chr2b	131716936	.	G	A	99	.	DP=14;AF1=1;CI95=1,1;DP4=0,0,0,12;MQ=36	PL:GT:GQ	173,36,0:1/1:99
+chr2b	131716952	.	A	G	99	.	DP=22;AF1=0.5;CI95=0.5,0.5;DP4=0,7,0,14;MQ=36;PV4=1,1,1,1	PL:GT:GQ	152,0,43:0/1:46
+chr2b	133360184	.	C	T	99	.	DP=20;AF1=1;CI95=1,1;DP4=0,0,0,20;MQ=32	PL:GT:GQ	163,60,0:1/1:99
+chr2b	133644741	.	T	A	16.4	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=27	PL:GT:GQ	49,15,0:1/1:75
+chr2b	133720595	.	T	C	41	.	DP=15;AF1=1;CI95=1,1;DP4=0,0,0,12;MQ=29	PL:GT:GQ	74,36,0:1/1:99
+chr2b	133727192	.	C	T	19.3	.	DP=8;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=23	PL:GT:GQ	52,15,0:1/1:75
+chr2b	133727260	.	G	A	3.56	.	DP=8;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=18	PL:GT:GQ	34,24,0:1/1:95
+chr2b	133800294	.	A	G	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=23	PL:GT:GQ	40,6,0:1/1:49
+chr2b	134582754	.	A	C	56.1	.	DP=37;AF1=1;CI95=1,1;DP4=0,0,0,7;MQ=36	PL:GT:GQ	89,21,0:1/1:84
+chr2b	134582763	.	G	C	78	.	DP=37;AF1=1;CI95=1,1;DP4=0,0,0,36;MQ=34	PL:GT:GQ	111,108,0:1/1:99
+chr2b	134809668	.	G	A	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49	PL:GT:GQ	40,6,0:1/1:49
+chr3	527814	.	C	G	46	.	DP=9;AF1=0.5;CI95=0.5,0.5;DP4=6,0,3,0;MQ=43;PV4=1,1,1,1	PL:GT:GQ	76,0,106:0/1:79
+chr3	559510	.	G	A	38	.	DP=27;AF1=0.5;CI95=0.5,0.5;DP4=10,0,17,0;MQ=28;PV4=1,1,0.014,1	PL:GT:GQ	68,0,111:0/1:71
+chr3	879433	.	T	G	32	.	DP=4;AF1=0.5001;CI95=0.5,0.5;DP4=2,0,2,0;MQ=43;PV4=1,1,1,1	PL:GT:GQ	62,0,34:0/1:37
+chr3	1809645	.	A	G	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=51	PL:GT:GQ	73,6,0:1/1:49
+chr3	3235812	.	C	T	7.59	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=45	PL:GT:GQ	38,6,0:1/1:49
+chr3	3250176	.	A	G	83	.	DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=32	PL:GT:GQ	116,24,0:1/1:96
+chr3	5049073	.	T	A	99	.	DP=25;AF1=0.5;CI95=0.5,0.5;DP4=16,0,9,0;MQ=39;PV4=1,1,1,1	PL:GT:GQ	136,0,129:0/1:99
+chr3	5142874	.	G	A	99	.	DP=38;AF1=1;CI95=1,1;DP4=0,0,38,0;MQ=28	PL:GT:GQ	179,114,0:1/1:99
+chr3	5554864	.	T	C	3.54	.	DP=7;AF1=0.4999;CI95=0.5,0.5;DP4=0,4,0,3;MQ=27;PV4=1,1,1,1	PL:GT:GQ	31,0,35:0/1:33
+chr3	5749648	.	G	A	21.2	.	DP=26;AF1=0.7303;CI95=0.5,1;DP4=0,7,0,7;MQ=26;PV4=1,0.16,1,0.17	PL:GT:GQ	50,0,2:0/1:3
+chr3	16451708	.	A	T	71.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=38	PL:GT:GQ	104,15,0:1/1:75
+chr3	23410276	.	G	A	99	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=45	PL:GT:GQ	140,15,0:1/1:75
+chr3	51368824	.	A	G	28	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=48	PL:GT:GQ	60,9,0:1/1:63
+chr3	53000453	.	A	G	54	.	DP=10;AF1=1;CI95=1,1;DP4=0,0,0,10;MQ=19	PL:GT:GQ	87,30,0:1/1:99
+chr3	53000463	.	A	G	54	.	DP=10;AF1=1;CI95=1,1;DP4=0,0,0,10;MQ=19	PL:GT:GQ	87,30,0:1/1:99
+chr3	59077423	.	C	T	77.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=33	PL:GT:GQ	110,15,0:1/1:75
+chr3	60040501	.	T	C	11.3	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=35	PL:GT:GQ	43,9,0:1/1:63
+chr3	64203481	.	A	G	33.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=49	PL:GT:GQ	66,12,0:1/1:72
+chr3	67947441	.	C	T	17.6	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=25	PL:GT:GQ	50,12,0:1/1:72
+chr3	76372631	.	A	G	44	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=36	PL:GT:GQ	76,9,0:1/1:63
+chr3	80611316	.	C	G	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49	PL:GT:GQ	40,6,0:1/1:49
+chr3	81554381	.	G	T	17.6	.	DP=24;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=26	PL:GT:GQ	50,12,0:1/1:72
+chr3	87614647	.	A	G	13.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=34	PL:GT:GQ	45,6,0:1/1:49
+chr3	93900455	.	A	T	11.6	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=13	PL:GT:GQ	44,15,0:1/1:75
+chr3	96174457	.	A	G	4.11	.	DP=8;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=24	PL:GT:GQ	34,9,0:1/1:63
+chr3	96215569	.	A	C	3.41	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=32	PL:GT:GQ	32,6,0:1/1:49
+chr3	96587998	.	A	C	7.08	.	DP=9;AF1=1;CI95=1,1;DP4=0,0,6,0;MQ=17	PL:GT:GQ	39,18,0:1/1:90
+chr3	99711220	.	A	C	12.8	.	DP=11;AF1=0.9998;CI95=0.5,1;DP4=1,0,2,0;MQ=35;PV4=1,1,1,1	PL:GT:GQ	42,2,0:1/1:37
+chr3	99789741	.	C	G	99	.	DP=18;AF1=1;CI95=1,1;DP4=0,0,17,0;MQ=47	PL:GT:GQ	210,51,0:1/1:99
+chr3	103667651	.	A	C	3.98	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=37	PL:GT:GQ	33,6,0:1/1:49
+chr3	104604896	.	G	C	55	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=50	PL:GT:GQ	87,9,0:1/1:63
+chr3	104997217	.	G	A	33.1	.	DP=18;AF1=1;CI95=1,1;DP4=1,0,16,0;MQ=34;PV4=1,3e-10,0.17,0.36	PL:GT:GQ	66,19,0:1/1:76
+chr3	106097816	.	A	G	28	.	DP=15;AF1=1;CI95=1,1;DP4=0,0,0,15;MQ=26	PL:GT:GQ	61,45,0:1/1:99
+chr3	106822259	.	G	C	99	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=50	PL:GT:GQ	140,15,0:1/1:75
+chr3	109946413	.	G	A	13	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=34	PL:GT:GQ	44,6,0:1/1:49
+chr3	121238963	.	T	C	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=51	PL:GT:GQ	40,6,0:1/1:49
+chr3	126248567	.	A	G	13.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=33	PL:GT:GQ	45,6,0:1/1:49
+chr3	129733836	.	A	G	6.2	.	DP=4;AF1=0.5003;CI95=0.5,0.5;DP4=1,0,3,0;MQ=43;PV4=1,0.02,0.31,1	PL:GT:GQ	35,0,28:0/1:30
+chr3	131372785	.	C	T	44	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=34	PL:GT:GQ	76,9,0:1/1:63
+chr3	132290987	.	C	T	22	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=45	PL:GT:GQ	54,9,0:1/1:63
+chr3	136054421	.	C	T	73	.	DP=82;AF1=1;CI95=1,1;DP4=0,0,78,0;MQ=28	PL:GT:GQ	106,235,0:1/1:99
+chr3	141075246	.	G	A	30.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=41	PL:GT:GQ	62,6,0:1/1:49
+chr3	141075262	.	T	G	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=41	PL:GT:GQ	73,6,0:1/1:49
+chr3	141430649	.	G	T	81.8	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,1,0,4;MQ=41;PV4=1,0.34,1,0.25	PL:GT:GQ	113,6,0:1/1:49
+chr3	143617747	.	G	T	22	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=29	PL:GT:GQ	54,9,0:1/1:63
+chr3	163576128	.	C	T	5.6	.	DP=4;AF1=0.7302;CI95=0.5,1;DP4=2,0,2,0;MQ=23;PV4=1,1,1,1	PL:GT:GQ	33,0,2:0/1:3
+chr3	163839828	.	A	G	4.45	.	DP=7;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=26	PL:GT:GQ	35,12,0:1/1:72
+chr3	175839340	.	G	T	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=51	PL:GT:GQ	40,6,0:1/1:49
+chr3	190193258	.	G	T	3.98	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35	PL:GT:GQ	33,6,0:1/1:49
+chr3	190777007	.	G	A	13	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35	PL:GT:GQ	44,6,0:1/1:49
+chr3	190970350	.	A	G	61	.	DP=11;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=37	PL:GT:GQ	94,30,0:1/1:99
+chr3	198686408	.	G	A	36.6	.	DP=17;AF1=1;CI95=0.5,1;DP4=0,1,0,16;MQ=25;PV4=1,1,0.026,1	PL:GT:GQ	69,11,0:1/1:66
+chr3	199277478	.	T	C	3.61	.	DP=6;AF1=1;CI95=1,1;DP4=0,0,0,6;MQ=21	PL:GT:GQ	34,18,0:1/1:90
+chr3	199780181	.	G	T	77	.	DP=45;AF1=0.5;CI95=0.5,0.5;DP4=0,35,0,10;MQ=33;PV4=1,1,1,1	PL:GT:GQ	107,0,114:0/1:99
+chr3	199889335	.	A	C	9.54	.	DP=16;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=18	PL:GT:GQ	42,24,0:1/1:96
+chr3	200018161	.	A	G	13.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=31	PL:GT:GQ	45,6,0:1/1:49
+chr4	195475	.	A	G	13	.	DP=13;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47	PL:GT:GQ	44,6,0:1/1:49
+chr4	639141	.	C	A	14.9	.	DP=10;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=42	PL:GT:GQ	46,6,0:1/1:49
+chr4	639152	.	C	T	15.2	.	DP=17;AF1=0.5016;CI95=0.5,0.5;DP4=0,2,0,2;MQ=33;PV4=1,1,1,1	PL:GT:GQ	45,0,22:0/1:25
+chr4	986497	.	G	T	99	.	DP=10;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=33	PL:GT:GQ	163,30,0:1/1:99
+chr4	986516	.	C	T	55.1	.	DP=8;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=37	PL:GT:GQ	88,21,0:1/1:84
+chr4	1207485	.	A	C	14.9	.	DP=22;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=45	PL:GT:GQ	46,6,0:1/1:49
+chr4	1323502	.	G	A	13.2	.	DP=13;AF1=1;CI95=1,1;DP4=0,0,11,0;MQ=22	PL:GT:GQ	46,33,0:1/1:99
+chr4	1613521	.	G	A	89	.	DP=16;AF1=1;CI95=1,1;DP4=0,0,16,0;MQ=32	PL:GT:GQ	122,48,0:1/1:99
+chr4	1748790	.	C	T	38	.	DP=21;AF1=0.5005;CI95=0.5,0.5;DP4=6,0,8,0;MQ=40;PV4=1,0.09,1,1	PL:GT:GQ	68,0,27:0/1:30
+chr4	2255732	.	T	C	99	.	DP=29;AF1=1;CI95=1,1;DP4=0,0,28,0;MQ=31	PL:GT:GQ	186,84,0:1/1:99
+chr4	3010159	.	C	T	13.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=31	PL:GT:GQ	45,6,0:1/1:49
+chr4	3545023	.	A	G	99	.	DP=9;AF1=1;CI95=1,1;DP4=0,0,0,9;MQ=38	PL:GT:GQ	145,27,0:1/1:99
+chr4	3586344	.	C	T	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=44	PL:GT:GQ	73,6,0:1/1:49
+chr4	3879337	.	A	G	16.6	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=25	PL:GT:GQ	49,12,0:1/1:72
+chr4	3940733	.	A	G	47.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=31	PL:GT:GQ	80,15,0:1/1:75
+chr4	4410338	.	T	C	13.5	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=31	PL:GT:GQ	46,15,0:1/1:75
+chr4	4796408	.	T	C	41	.	DP=16;AF1=1;CI95=1,1;DP4=0,0,0,16;MQ=17	PL:GT:GQ	74,48,0:1/1:99
+chr4	4796414	.	A	G	11.3	.	DP=16;AF1=1;CI95=1,1;DP4=0,0,0,15;MQ=17	PL:GT:GQ	44,45,0:1/1:99
+chr4	6436959	.	T	C	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=50	PL:GT:GQ	40,6,0:1/1:49
+chr4	9494256	.	T	C	3.41	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=37	PL:GT:GQ	32,6,0:1/1:49
+chr4	24881479	.	G	A	14.1	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=42	PL:GT:GQ	46,9,0:1/1:63
+chr4	26128644	.	A	G	23	.	DP=18;AF1=0.5006;CI95=0.5,0.5;DP4=8,0,10,0;MQ=22;PV4=1,1,1,1	PL:GT:GQ	53,0,26:0/1:29
+chr4	42109100	.	G	A	17.1	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=48	PL:GT:GQ	49,9,0:1/1:63
+chr4	42309652	.	C	T	68	.	DP=17;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=50	PL:GT:GQ	100,9,0:1/1:63
+chr4	46913966	.	C	T	9.08	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=16	PL:GT:GQ	41,12,0:1/1:72
+chr4	50335142	.	A	G	44	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=41	PL:GT:GQ	76,9,0:1/1:63
+chr4	51658550	.	C	A	13	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=48	PL:GT:GQ	44,6,0:1/1:49
+chr4	58258023	.	T	C	26	.	DP=5;AF1=0.5002;CI95=0.5,0.5;DP4=0,3,0,2;MQ=34;PV4=1,1,1,0.05	PL:GT:GQ	56,0,32:0/1:35
+chr4	59219112	.	C	A	42.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=50	PL:GT:GQ	75,12,0:1/1:72
+chr4	62746067	.	C	T	13.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35	PL:GT:GQ	45,6,0:1/1:49
+chr4	67404338	.	G	T	33.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=39	PL:GT:GQ	66,12,0:1/1:72
+chr4	73353380	.	A	G	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49	PL:GT:GQ	73,6,0:1/1:49
+chr4	73946294	.	G	C	4.77	.	DP=51;AF1=0.4999;CI95=0.5,0.5;DP4=0,5,0,3;MQ=40;PV4=1,0.19,0.37,0.11	PL:GT:GQ	33,0,64:0/1:36
+chr4	79607484	.	A	G	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49	PL:GT:GQ	40,6,0:1/1:49
+chr4	82337365	.	G	C	90	.	DP=54;AF1=1;CI95=1,1;DP4=0,0,0,16;MQ=28	PL:GT:GQ	123,48,0:1/1:99
+chr4	82653801	.	A	G	4.11	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=29	PL:GT:GQ	34,9,0:1/1:63
+chr4	87130164	.	C	T	11.3	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=26	PL:GT:GQ	43,9,0:1/1:63
+chr4	87130176	.	G	A	11.3	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=26	PL:GT:GQ	43,9,0:1/1:63
+chr4	91459729	.	C	A	13	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35	PL:GT:GQ	44,6,0:1/1:49
+chr4	96130778	.	G	C	99	.	DP=19;AF1=1;CI95=1,1;DP4=0,0,0,19;MQ=45	PL:GT:GQ	211,57,0:1/1:99
+chr4	100709417	.	A	G	45.1	.	DP=16;AF1=0.505;CI95=0.5,0.5;DP4=12,0,4,0;MQ=24;PV4=1,1,1,1	PL:GT:GQ	75,0,17:0/1:20
+chr4	107276770	.	C	T	70	.	DP=15;AF1=0.5;CI95=0.5,0.5;DP4=0,9,0,6;MQ=31;PV4=1,1,1,1	PL:GT:GQ	100,0,97:0/1:98
+chr4	115327550	.	G	C	42	.	DP=67;AF1=1;CI95=1,1;DP4=0,1,0,66;MQ=35;PV4=1,3.2e-24,0.13,1	PL:GT:GQ	75,162,0:1/1:99
+chr4	136558502	.	A	G	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49	PL:GT:GQ	40,6,0:1/1:49
+chr4	159572459	.	G	A	15.1	.	DP=126;AF1=0.5;CI95=0.5,0.5;DP4=0,69,0,57;MQ=39;PV4=1,4.1e-96,0.077,1	PL:GT:GQ	45,0,175:0/1:48
+chr4	174968484	.	G	C	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=42	PL:GT:GQ	40,6,0:1/1:49
+chr4	175030633	.	T	C	14.3	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=29	PL:GT:GQ	47,18,0:1/1:90
+chr4	183410027	.	G	T	6.2	.	DP=31;AF1=0.5003;CI95=0.5,0.5;DP4=2,0,2,0;MQ=45;PV4=1,0.035,1,0.21	PL:GT:GQ	35,0,28:0/1:30
+chr4	190907368	.	T	C	33.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=50	PL:GT:GQ	66,12,0:1/1:72
+chr4	192175690	.	A	G	76.8	.	DP=7;AF1=0.95;CI95=0.5,1;DP4=0,3,0,4;MQ=35;PV4=1,1,1,1	PL:GT:GQ	105,0,0:1/1:10
+chr4	192673268	.	G	A	14.2	.	DP=9;AF1=1;CI95=1,1;DP4=0,0,9,0;MQ=22	PL:GT:GQ	47,27,0:1/1:99
+chr4	192943966	.	T	C	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=44	PL:GT:GQ	73,6,0:1/1:49
+chr4	195460104	.	C	G	23.1	.	DP=8;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=19	PL:GT:GQ	56,24,0:1/1:96
+chr4	198277830	.	A	G	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49	PL:GT:GQ	40,6,0:1/1:49
+chr5	170098	.	A	G	13	.	DP=12;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=30	PL:GT:GQ	44,6,0:1/1:49
+chr5	395814	.	T	C	4.77	.	DP=4;AF1=0.5;CI95=0.5,0.5;DP4=0,2,0,2;MQ=36;PV4=1,1,0.48,1	PL:GT:GQ	33,0,33:0/1:33
+chr5	414024	.	T	A	10.4	.	DP=17;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=20	PL:GT:GQ	42,9,0:1/1:63
+chr5	496767	.	T	C	13.9	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=36	PL:GT:GQ	45,6,0:1/1:49
+chr5	805676	.	C	G	45	.	DP=17;AF1=1;CI95=1,1;DP4=0,0,17,0;MQ=32	PL:GT:GQ	78,51,0:1/1:99
+chr5	1252896	.	A	G	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49	PL:GT:GQ	40,6,0:1/1:49
+chr5	1418370	.	G	A	3.65	.	DP=8;AF1=0.7301;CI95=0.5,1;DP4=4,0,4,0;MQ=13;PV4=1,1,1,1	PL:GT:GQ	30,0,2:0/1:3
+chr5	1494911	.	G	C	62	.	DP=9;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=46	PL:GT:GQ	95,24,0:1/1:96
+chr5	1494932	.	C	T	6.98	.	DP=8;AF1=0.5001;CI95=0.5,0.5;DP4=1,0,2,0;MQ=46;PV4=1,0.1,0.077,1	PL:GT:GQ	36,0,31:0/1:33
+chr5	1506037	.	T	C	24.1	.	DP=24;AF1=1;CI95=0.5,1;DP4=11,0,13,0;MQ=16;PV4=1,1,1,1	PL:GT:GQ	55,5,0:1/1:46
+chr5	1509406	.	A	G	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=47	PL:GT:GQ	73,6,0:1/1:49
+chr5	1733649	.	A	G	99	.	DP=25;AF1=1;CI95=1,1;DP4=0,0,0,25;MQ=47	PL:GT:GQ	212,75,0:1/1:99
+chr5	1747304	.	A	G	12.3	.	DP=12;AF1=1;CI95=1,1;DP4=0,0,0,12;MQ=19	PL:GT:GQ	45,36,0:1/1:99
+chr5	1747308	.	C	A	44	.	DP=12;AF1=1;CI95=1,1;DP4=0,0,0,12;MQ=19	PL:GT:GQ	77,36,0:1/1:99
+chr5	3519783	.	C	T	21.1	.	DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=18	PL:GT:GQ	54,24,0:1/1:96
+chr5	4101593	.	A	G	69.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=43	PL:GT:GQ	102,12,0:1/1:72
+chr5	7204332	.	T	A	4.61	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=24	PL:GT:GQ	34,6,0:1/1:49
+chr5	11510398	.	A	C	34	.	DP=3;AF1=0.5002;CI95=0.5,0.5;DP4=1,0,2,0;MQ=51;PV4=1,1,0,1	PL:GT:GQ	64,0,31:0/1:34
+chr5	15406720	.	T	C	6.02	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=51	PL:GT:GQ	36,6,0:1/1:49
+chr5	25152417	.	C	A	10.9	.	DP=28;AF1=0.5718;CI95=0.5,1;DP4=0,2,0,6;MQ=25;PV4=1,1,0.21,1	PL:GT:GQ	40,0,6:0/1:8
+chr5	39072637	.	A	G	35.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=50	PL:GT:GQ	68,15,0:1/1:75
+chr5	46022699	.	G	A	44	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=35	PL:GT:GQ	76,9,0:1/1:63
+chr5	55664181	.	C	G	10.4	.	DP=8;AF1=0.9999;CI95=0.5,1;DP4=3,0,5,0;MQ=18;PV4=1,1,1,1	PL:GT:GQ	40,3,0:1/1:41
+chr5	56253386	.	T	C	50.1	.	DP=7;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=36	PL:GT:GQ	83,21,0:1/1:84
+chr5	56253447	.	C	T	42.5	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=45	PL:GT:GQ	75,12,0:1/1:72
+chr5	71950166	.	G	T	11.3	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=40	PL:GT:GQ	43,9,0:1/1:63
+chr5	72703090	.	C	T	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=46	PL:GT:GQ	40,6,0:1/1:49
+chr5	73570280	.	G	T	5.45	.	DP=41;AF1=1;CI95=1,1;DP4=0,0,41,0;MQ=15	PL:GT:GQ	37,123,0:1/1:99
+chr5	73701762	.	G	T	40.8	.	DP=13;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=43	PL:GT:GQ	72,6,0:1/1:49
+chr5	76956867	.	T	C	10.2	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=46	PL:GT:GQ	41,6,0:1/1:49
+chr5	79097961	.	C	G	22	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=40	PL:GT:GQ	54,9,0:1/1:63
+chr5	87026167	.	T	C	22	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=49	PL:GT:GQ	54,9,0:1/1:63
+chr5	97680525	.	T	C	3.27	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=23	PL:GT:GQ	33,12,0:1/1:72
+chr5	100674737	.	C	T	13.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35	PL:GT:GQ	45,6,0:1/1:49
+chr5	105389966	.	T	C	3.52	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=15	PL:GT:GQ	33,9,0:1/1:63
+chr5	109998341	.	A	C	12.7	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=35	PL:GT:GQ	45,12,0:1/1:72
+chr5	120629105	.	C	T	6.79	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48	PL:GT:GQ	37,6,0:1/1:49
+chr5	128383954	.	C	T	23	.	DP=10;AF1=0.5;CI95=0.5,0.5;DP4=0,5,0,5;MQ=48;PV4=1,3.3e-07,1,1	PL:GT:GQ	53,0,98:0/1:56
+chr5	133925142	.	A	G	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49	PL:GT:GQ	73,6,0:1/1:49
+chr5	135375404	.	T	C	11.8	.	DP=6;AF1=1;CI95=0.5,1;DP4=1,0,3,0;MQ=31;PV4=1,0.03,1,1	PL:GT:GQ	42,4,0:1/1:45
+chr5	136498281	.	T	G	13.9	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=37	PL:GT:GQ	45,6,0:1/1:49
+chr5	136717285	.	A	G	82.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=48	PL:GT:GQ	115,12,0:1/1:72
+chr5	136910734	.	G	A	62	.	DP=19;AF1=1;CI95=1,1;DP4=0,1,0,13;MQ=23;PV4=1,1,1,1	PL:GT:GQ	95,31,0:1/1:99
+chr5	141208149	.	C	G	13	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35	PL:GT:GQ	44,6,0:1/1:49
+chr5	148056348	.	C	A	37.1	.	DP=4;AF1=0.9966;CI95=0.5,1;DP4=1,0,2,0;MQ=38;PV4=1,1,1,1	PL:GT:GQ	66,1,0:1/1:23
+chr5	151941534	.	G	T	46.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=34	PL:GT:GQ	79,12,0:1/1:72
+chr5	159967229	.	G	C	22.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=35	PL:GT:GQ	55,12,0:1/1:72
+chr5	174024541	.	T	G	29.5	.	DP=3;AF1=0.9998;CI95=0.5,1;DP4=0,1,0,2;MQ=32;PV4=1,1,1,1	PL:GT:GQ	59,2,0:1/1:37
+chr5	175525290	.	A	G	3.27	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=20	PL:GT:GQ	33,12,0:1/1:72
+chr5	175988954	.	A	C	14.2	.	DP=23;AF1=0.5;CI95=0.5,0.5;DP4=0,6,0,4;MQ=47;PV4=1,1,0.2,1	PL:GT:GQ	44,0,76:0/1:47
+chr5	176782226	.	T	C	9.31	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=43	PL:GT:GQ	40,6,0:1/1:49
+chr5	179132834	.	C	G	99	.	DP=28;AF1=1;CI95=1,1;DP4=0,0,0,28;MQ=41	PL:GT:GQ	207,84,0:1/1:99
+chr5	180155809	.	G	C	3.01	.	DP=36;AF1=0.4997;CI95=0.5,0.5;DP4=25,0,9,0;MQ=35;PV4=1,1e-15,1,1	PL:GT:GQ	30,0,121:0/1:33
+chr5	181282819	.	T	G	38.3	.	DP=11;AF1=1;CI95=0.5,1;DP4=0,2,0,9;MQ=23;PV4=1,1,1,1	PL:GT:GQ	71,14,0:1/1:70
+chr5	182426125	.	G	C	29	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=26	PL:GT:GQ	61,9,0:1/1:63
+chr5	182443682	.	G	A	3.69	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=21	PL:GT:GQ	34,15,0:1/1:75
+chr5	183008993	.	C	T	22	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=49	PL:GT:GQ	54,9,0:1/1:63
+chr5	183312016	.	G	T	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=47	PL:GT:GQ	40,6,0:1/1:49
+chr6_cox_hap1	519146	.	G	A	17.1	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=30	PL:GT:GQ	49,9,0:1/1:63
+chr6_cox_hap1	687497	.	A	G	33	.	DP=6;AF1=0.9999;CI95=0.5,1;DP4=2,0,4,0;MQ=35;PV4=1,0.0016,1,1	PL:GT:GQ	63,3,0:1/1:41
+chr6_qbl_hap2	120066	.	T	C	99	.	DP=12;AF1=1;CI95=1,1;DP4=0,0,0,9;MQ=37	PL:GT:GQ	139,27,0:1/1:99
+chr6	277954	.	C	T	53	.	DP=41;AF1=1;CI95=1,1;DP4=4,0,37,0;MQ=19;PV4=1,1,0.3,1	PL:GT:GQ	86,49,0:1/1:99
+chr6	593158	.	A	G	4.61	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=32	PL:GT:GQ	34,6,0:1/1:49
+chr6	2865562	.	T	G	25	.	DP=9;AF1=1;CI95=1,1;DP4=0,0,9,0;MQ=23	PL:GT:GQ	58,27,0:1/1:99
+chr6	3751403	.	G	A	42.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=32	PL:GT:GQ	75,15,0:1/1:75
+chr6	3884989	.	A	G	13.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=36	PL:GT:GQ	45,6,0:1/1:49
+chr6	4127278	.	A	T	13.9	.	DP=8;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35	PL:GT:GQ	45,6,0:1/1:49
+chr6	5887783	.	C	G	99	.	DP=7;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=34	PL:GT:GQ	142,21,0:1/1:84
+chr6	5887811	.	C	T	55.1	.	DP=7;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=34	PL:GT:GQ	88,21,0:1/1:84
+chr6	6937170	.	G	C	99	.	DP=47;AF1=1;CI95=1,1;DP4=0,0,0,47;MQ=28	PL:GT:GQ	157,141,0:1/1:99
+chr6	7262317	.	C	T	13.2	.	DP=50;AF1=0.5;CI95=0.5,0.5;DP4=21,0,9,0;MQ=36;PV4=1,4e-05,0.17,0.26	PL:GT:GQ	43,0,158:0/1:46
+chr6	7533214	.	A	G	10.4	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=26	PL:GT:GQ	42,9,0:1/1:63
+chr6	20979907	.	A	G	44	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=38	PL:GT:GQ	76,9,0:1/1:63
+chr6	22321632	.	A	G	41	.	DP=5;AF1=0.5004;CI95=0.5,0.5;DP4=1,0,3,0;MQ=46;PV4=1,0.24,0.19,0.33	PL:GT:GQ	71,0,28:0/1:31
+chr6	25352296	.	G	A	7.8	.	DP=4;AF1=0.5003;CI95=0.5,0.5;DP4=0,1,0,3;MQ=38;PV4=1,1,0.16,1	PL:GT:GQ	37,0,28:0/1:30
+chr6	26298040	.	T	A	34	.	DP=3;AF1=0.5002;CI95=0.5,0.5;DP4=0,1,0,2;MQ=48;PV4=1,1,0.21,0.33	PL:GT:GQ	64,0,31:0/1:34
+chr6	33428755	.	G	A	70	.	DP=14;AF1=1;CI95=1,1;DP4=0,0,9,0;MQ=32	PL:GT:GQ	103,27,0:1/1:99
+chr6	39512099	.	G	A	55.1	.	DP=7;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=50	PL:GT:GQ	88,21,0:1/1:84
+chr6	39961094	.	G	A	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49	PL:GT:GQ	73,6,0:1/1:49
+chr6	40452120	.	A	G	40.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=42	PL:GT:GQ	72,6,0:1/1:49
+chr6	43204766	.	A	G	99	.	DP=8;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=51	PL:GT:GQ	176,24,0:1/1:96
+chr6	52696512	.	C	T	70	.	DP=76;AF1=0.5;CI95=0.5,0.5;DP4=0,34,0,42;MQ=18;PV4=1,0.11,1,1	PL:GT:GQ	100,0,51:0/1:54
+chr6	53785550	.	A	G	99	.	DP=20;AF1=1;CI95=1,1;DP4=0,0,0,10;MQ=46	PL:GT:GQ	190,30,0:1/1:99
+chr6	53897484	.	C	T	13.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=36	PL:GT:GQ	45,6,0:1/1:49
+chr6	57038290	.	C	T	10.2	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=36	PL:GT:GQ	41,6,0:1/1:49
+chr6	62925087	.	G	C	35	.	DP=5;AF1=0.5008;CI95=0.5,0.5;DP4=1,0,4,0;MQ=36;PV4=1,1,0.2,1	PL:GT:GQ	65,0,25:0/1:28
+chr6	62925094	.	T	C	25.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=36	PL:GT:GQ	58,15,0:1/1:75
+chr6	70834405	.	G	A	72.1	.	DP=13;AF1=1;CI95=1,1;DP4=0,0,0,7;MQ=29	PL:GT:GQ	105,21,0:1/1:84
+chr6	71026058	.	C	T	48.1	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=42	PL:GT:GQ	81,18,0:1/1:90
+chr6	74420752	.	T	C	44	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=39	PL:GT:GQ	76,9,0:1/1:63
+chr6	77498624	.	T	C	16.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=33	PL:GT:GQ	48,6,0:1/1:49
+chr6	80416836	.	T	C	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=50	PL:GT:GQ	40,6,0:1/1:49
+chr6	113611590	.	A	G	68	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=46	PL:GT:GQ	100,9,0:1/1:63
+chr6	119308431	.	T	C	38.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=40	PL:GT:GQ	71,12,0:1/1:72
+chr6	151758592	.	T	C	3.07	.	DP=17;AF1=0.9966;CI95=0.5,1;DP4=0,8,0,9;MQ=13;PV4=1,1,1,1	PL:GT:GQ	29,1,0:1/1:23
+chr6	151759358	.	A	G	99	.	DP=27;AF1=0.5;CI95=0.5,0.5;DP4=12,0,15,0;MQ=44;PV4=1,1,1,0.19	PL:GT:GQ	171,0,128:0/1:99
+chr6	154741755	.	G	A	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=50	PL:GT:GQ	40,6,0:1/1:49
+chr6	161061053	.	C	A	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=52	PL:GT:GQ	40,6,0:1/1:49
+chr6	161474189	.	C	T	6.02	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49	PL:GT:GQ	36,6,0:1/1:49
+chr6	164304657	.	C	T	10.4	.	DP=63;AF1=0.5;CI95=0.5,0.5;DP4=0,29,0,19;MQ=22;PV4=1,7.7e-11,1,0.049	PL:GT:GQ	40,0,37:0/1:38
+chr6	164703105	.	T	C	99	.	DP=11;AF1=1;CI95=1,1;DP4=0,0,0,10;MQ=40	PL:GT:GQ	165,30,0:1/1:99
+chr6	167518328	.	A	G	78	.	DP=41;AF1=0.5;CI95=0.5,0.5;DP4=27,0,14,0;MQ=33;PV4=1,0.026,0.43,0.056	PL:GT:GQ	108,0,149:0/1:99
+chr6	169906323	.	G	A	41.8	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49	PL:GT:GQ	73,6,0:1/1:49
+chr6	171893912	.	G	A	69.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=33	PL:GT:GQ	102,15,0:1/1:75
+chr6	173631604	.	A	G	6.98	.	DP=7;AF1=0.5;CI95=0.5,0.5;DP4=4,0,3,0;MQ=37;PV4=1,0.069,1,1	PL:GT:GQ	36,0,34:0/1:35
+chr7	835856	.	C	T	27.5	.	DP=13;AF1=0.9998;CI95=0.5,1;DP4=4,0,6,0;MQ=23;PV4=1,0.46,1,1	PL:GT:GQ	57,2,0:1/1:37
+chr7	1046005	.	C	T	11.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=36	PL:GT:GQ	43,9,0:1/1:63
+chr7	1564339	.	C	T	71	.	DP=66;AF1=0.5;CI95=0.5,0.5;DP4=36,0,24,0;MQ=29;PV4=1,1,0.35,1	PL:GT:GQ	101,0,134:0/1:99
+chr7	1806266	.	C	T	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48	PL:GT:GQ	73,6,0:1/1:49
+chr7	1936013	.	G	T	7.77	.	DP=7;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=17	PL:GT:GQ	39,9,0:1/1:63
+chr7	2319532	.	C	A	4.11	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=14	PL:GT:GQ	34,9,0:1/1:63
+chr7	2682121	.	C	T	13	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=33	PL:GT:GQ	44,6,0:1/1:49
+chr7	3248116	.	T	C	36.5	.	DP=3;AF1=0.9998;CI95=0.5,1;DP4=0,1,0,2;MQ=37;PV4=1,1,1,1	PL:GT:GQ	66,2,0:1/1:37
+chr7	3624766	.	C	T	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=41	PL:GT:GQ	40,6,0:1/1:49
+chr7	5291140	.	G	C	13.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=37	PL:GT:GQ	45,6,0:1/1:49
+chr7	5314457	.	C	A	3.56	.	DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=18	PL:GT:GQ	34,24,0:1/1:95
+chr7	5595072	.	T	A	79	.	DP=13;AF1=0.5;CI95=0.5,0.5;DP4=8,0,5,0;MQ=31;PV4=1,1,1,1	PL:GT:GQ	109,0,57:0/1:60
+chr7	5646060	.	G	C	7.79	.	DP=11;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=10	PL:GT:GQ	40,30,0:1/1:99
+chr7	6056816	.	C	G	7.08	.	DP=6;AF1=0.9966;CI95=0.5,1;DP4=0,2,0,3;MQ=23;PV4=1,1,1,1	PL:GT:GQ	35,1,0:1/1:23
+chr7	6412641	.	C	T	40	.	DP=11;AF1=1;CI95=1,1;DP4=0,0,11,0;MQ=33	PL:GT:GQ	73,33,0:1/1:99
+chr7	6766874	.	A	G	34.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=43	PL:GT:GQ	67,15,0:1/1:75
+chr7	8482729	.	C	T	5.08	.	DP=16;AF1=0.8276;CI95=0.5,1;DP4=3,0,3,0;MQ=22;PV4=1,1,1,0.19	PL:GT:GQ	32,0,1:1/1:5
+chr7	9238362	.	G	A	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49	PL:GT:GQ	40,6,0:1/1:49
+chr7	9687781	.	G	A	33	.	DP=29;AF1=0.5;CI95=0.5,0.5;DP4=0,16,0,12;MQ=48;PV4=1,6.5e-38,1,1	PL:GT:GQ	63,0,170:0/1:66
+chr7	9752803	.	A	T	14.2	.	DP=17;AF1=1;CI95=1,1;DP4=0,0,9,0;MQ=18	PL:GT:GQ	47,27,0:1/1:99
+chr7	10240910	.	T	C	45.5	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=35	PL:GT:GQ	78,12,0:1/1:72
+chr7	11046187	.	C	T	86.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=47	PL:GT:GQ	119,12,0:1/1:72
+chr7	11548207	.	C	G	14.6	.	DP=13;AF1=1;CI95=0.5,1;DP4=6,1,0,5;MQ=18;PV4=0.015,1,1,1	PL:GT:GQ	46,7,0:1/1:57
+chr7	11580317	.	C	T	42	.	DP=12;AF1=1;CI95=1,1;DP4=0,1,0,10;MQ=22;PV4=1,1,1,1	PL:GT:GQ	75,23,0:1/1:92
+chr7	11585384	.	G	A	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=46	PL:GT:GQ	73,6,0:1/1:49
+chr7	13498356	.	A	G	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=47	PL:GT:GQ	73,6,0:1/1:49
+chr7	13500887	.	G	A	15.1	.	DP=11;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=22	PL:GT:GQ	48,30,0:1/1:99
+chr7	13827079	.	C	T	6.02	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47	PL:GT:GQ	36,6,0:1/1:49
+chr7	14403976	.	T	G	59	.	DP=30;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=39	PL:GT:GQ	92,24,0:1/1:96
+chr7	14756588	.	A	G	44	.	DP=15;AF1=0.5;CI95=0.5,0.5;DP4=5,0,10,0;MQ=44;PV4=1,5.3e-18,1,1	PL:GT:GQ	74,0,70:0/1:72
+chr7	14756619	.	T	G	44	.	DP=15;AF1=0.5;CI95=0.5,0.5;DP4=5,0,10,0;MQ=44;PV4=1,6.4e-10,1,1	PL:GT:GQ	74,0,70:0/1:72
+chr7	36734598	.	A	C	11.1	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=40	PL:GT:GQ	42,6,0:1/1:49
+chr7	36734599	.	A	T	11.1	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=40	PL:GT:GQ	42,6,0:1/1:49
+chr7	36734603	.	G	C	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=40	PL:GT:GQ	40,6,0:1/1:49
+chr7	40634921	.	A	C	55	.	DP=13;AF1=1;CI95=1,1;DP4=0,0,13,0;MQ=39	PL:GT:GQ	88,39,0:1/1:99
+chr7	48271285	.	A	T	73	.	DP=15;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=25	PL:GT:GQ	106,30,0:1/1:99
+chr7	56264700	.	G	A	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=51	PL:GT:GQ	40,6,0:1/1:49
+chr7	62326003	.	C	A	26.1	.	DP=35;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=28	PL:GT:GQ	59,18,0:1/1:90
+chr7	109468934	.	T	G	5.13	.	DP=10;AF1=0.9998;CI95=0.5,1;DP4=0,1,0,2;MQ=39;PV4=1,0.031,1,1	PL:GT:GQ	33,2,0:1/1:37
+chr7	110208327	.	C	G	16.9	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=44	PL:GT:GQ	48,6,0:1/1:49
+chr7	125654934	.	A	G	4.11	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=27	PL:GT:GQ	34,9,0:1/1:63
+chr7	125770209	.	A	C	32	.	DP=31;AF1=0.5;CI95=0.5,0.5;DP4=11,0,13,0;MQ=34;PV4=1,0.00017,0.16,0.22	PL:GT:GQ	62,0,105:0/1:65
+chr7	125770265	.	G	C	36	.	DP=16;AF1=0.5;CI95=0.5,0.5;DP4=0,5,0,5;MQ=48;PV4=1,0.0047,0.016,0.035	PL:GT:GQ	66,0,110:0/1:69
+chr7	126687042	.	A	G	21.1	.	DP=36;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=22	PL:GT:GQ	54,21,0:1/1:84
+chr7	132292897	.	G	T	99	.	DP=7;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=43	PL:GT:GQ	167,21,0:1/1:84
+chr7	132334562	.	A	C	23	.	DP=16;AF1=1;CI95=1,1;DP4=0,0,0,10;MQ=23	PL:GT:GQ	56,30,0:1/1:99
+chr7	132431838	.	C	T	13.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=1,0,4,0;MQ=23;PV4=1,1,1,1	PL:GT:GQ	44,5,0:1/1:46
+chr7	136324945	.	T	C	13.7	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=35	PL:GT:GQ	46,12,0:1/1:72
+chr7	136957634	.	G	A	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=43	PL:GT:GQ	40,6,0:1/1:49
+chr7	141746871	.	G	A	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=42	PL:GT:GQ	40,6,0:1/1:49
+chr7	146831870	.	C	T	4.77	.	DP=14;AF1=0.5003;CI95=0.5,0.5;DP4=1,0,3,0;MQ=37;PV4=1,0.0029,0.28,1	PL:GT:GQ	33,0,28:0/1:30
+chr7	147142770	.	T	C	45	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=31	PL:GT:GQ	77,9,0:1/1:63
+chr7	147713906	.	C	T	4.77	.	DP=8;AF1=0.5002;CI95=0.5,0.5;DP4=2,0,4,0;MQ=35;PV4=1,8.9e-06,0.48,0.27	PL:GT:GQ	33,0,29:0/1:31
+chr7	148742642	.	G	A	68	.	DP=14;AF1=0.5032;CI95=0.5,0.5;DP4=4,0,10,0;MQ=28;PV4=1,1,1,1	PL:GT:GQ	98,0,19:0/1:22
+chr7	148879148	.	C	T	22	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=48	PL:GT:GQ	54,9,0:1/1:63
+chr7	149484407	.	A	G	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=45	PL:GT:GQ	73,6,0:1/1:49
+chr7	152444478	.	A	G	13	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=36	PL:GT:GQ	44,6,0:1/1:49
+chr7	154106613	.	C	T	68	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=51	PL:GT:GQ	100,9,0:1/1:63
+chr7	154776891	.	G	T	14.4	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=31	PL:GT:GQ	47,15,0:1/1:75
+chr7	155882061	.	A	C	29	.	DP=24;AF1=0.502;CI95=0.5,0.5;DP4=0,1,0,4;MQ=46;PV4=1,0.018,0.15,0.29	PL:GT:GQ	59,0,21:0/1:24
+chr7	155956844	.	G	C	23	.	DP=11;AF1=0.5;CI95=0.5,0.5;DP4=0,7,0,4;MQ=38;PV4=1,1,0.38,1	PL:GT:GQ	53,0,103:0/1:56
+chr7	156277694	.	G	A	62	.	DP=9;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=46	PL:GT:GQ	95,24,0:1/1:96
+chr7	156720588	.	T	C	16.1	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=29	PL:GT:GQ	48,9,0:1/1:63
+chr7	156807649	.	T	C	3.01	.	DP=30;AF1=0.4997;CI95=0.5,0.5;DP4=0,4,0,3;MQ=43;PV4=1,0.16,0.15,1	PL:GT:GQ	30,0,72:0/1:33
+chr7	157331292	.	G	T	43.1	.	DP=7;AF1=1;CI95=1,1;DP4=0,0,0,7;MQ=34	PL:GT:GQ	76,21,0:1/1:84
+chr7	157382957	.	T	C	33.5	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=43	PL:GT:GQ	66,12,0:1/1:72
+chr8	556382	.	A	G	37.1	.	DP=5;AF1=0.9966;CI95=0.5,1;DP4=2,0,3,0;MQ=31;PV4=1,1,1,1	PL:GT:GQ	66,1,0:1/1:23
+chr8	1661673	.	T	C	9.31	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49	PL:GT:GQ	40,6,0:1/1:49
+chr8	7379751	.	C	A	6.24	.	DP=8;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=19	PL:GT:GQ	38,21,0:1/1:84
+chr8	8160505	.	A	T	68.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=35	PL:GT:GQ	101,12,0:1/1:72
+chr8	8160508	.	C	T	24.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=35	PL:GT:GQ	57,12,0:1/1:72
+chr8	16781011	.	A	G	55.5	.	DP=9;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=34	PL:GT:GQ	88,12,0:1/1:72
+chr8	18716499	.	A	T	20	.	DP=10;AF1=0.5;CI95=0.5,0.5;DP4=0,4,0,2;MQ=29;PV4=1,1,1,1	PL:GT:GQ	50,0,52:0/1:51
+chr8	23326483	.	A	G	60	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=47	PL:GT:GQ	92,9,0:1/1:63
+chr8	25842819	.	T	A	12	.	DP=18;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=47	PL:GT:GQ	43,6,0:1/1:49
+chr8	26300279	.	T	C	34	.	DP=44;AF1=1;CI95=1,1;DP4=0,0,41,0;MQ=21	PL:GT:GQ	67,123,0:1/1:99
+chr8	29673470	.	A	G	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=41	PL:GT:GQ	73,6,0:1/1:49
+chr8	29673473	.	C	G	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=41	PL:GT:GQ	40,6,0:1/1:49
+chr8	31685466	.	C	T	34	.	DP=17;AF1=0.5;CI95=0.5,0.5;DP4=10,0,5,0;MQ=28;PV4=1,0.072,1,0.36	PL:GT:GQ	64,0,50:0/1:53
+chr8	37378739	.	C	T	13.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=34	PL:GT:GQ	45,6,0:1/1:49
+chr8	51325952	.	G	A	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49	PL:GT:GQ	40,6,0:1/1:49
+chr8	59221963	.	G	A	16.1	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=29	PL:GT:GQ	48,9,0:1/1:63
+chr8	62764995	.	T	G	20	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=32	PL:GT:GQ	52,9,0:1/1:63
+chr8	63157426	.	C	G	41.6	.	DP=22;AF1=1;CI95=0.5,1;DP4=0,7,0,15;MQ=19;PV4=1,1,1,0.25	PL:GT:GQ	74,11,0:1/1:66
+chr8	68710444	.	G	A	30	.	DP=5;AF1=0.6671;CI95=0.5,1;DP4=3,0,2,0;MQ=32;PV4=1,1,1,1	PL:GT:GQ	59,0,3:0/1:5
+chr8	76416560	.	G	A	89.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=46	PL:GT:GQ	122,12,0:1/1:72
+chr8	81425275	.	T	G	68	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=50	PL:GT:GQ	100,9,0:1/1:63
+chr8	89842286	.	G	C	4.61	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=30	PL:GT:GQ	34,6,0:1/1:49
+chr8	100926281	.	G	A	38	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=41	PL:GT:GQ	70,9,0:1/1:63
+chr8	102746002	.	G	C	13.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35	PL:GT:GQ	45,6,0:1/1:49
+chr8	107850176	.	C	T	43.1	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=45	PL:GT:GQ	76,18,0:1/1:90
+chr8	109966441	.	T	C	27.3	.	DP=9;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=38	PL:GT:GQ	60,15,0:1/1:75
+chr8	118811716	.	G	T	99	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=50	PL:GT:GQ	155,18,0:1/1:90
+chr8	119440254	.	A	T	58.5	.	DP=5;AF1=0.8277;CI95=0.5,1;DP4=2,0,3,0;MQ=34;PV4=1,1,1,0.14	PL:GT:GQ	87,0,1:1/1:5
+chr8	121236024	.	G	A	39.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=48	PL:GT:GQ	71,6,0:1/1:49
+chr8	125489079	.	C	T	13	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35	PL:GT:GQ	44,6,0:1/1:49
+chr8	128502549	.	A	G	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=45	PL:GT:GQ	73,6,0:1/1:49
+chr8	128502551	.	A	G	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=45	PL:GT:GQ	73,6,0:1/1:49
+chr8	130951113	.	G	A	4.61	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=19	PL:GT:GQ	34,6,0:1/1:49
+chr8	135307123	.	G	A	6.02	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=45	PL:GT:GQ	36,6,0:1/1:49
+chr8	138814155	.	C	T	57.1	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=46	PL:GT:GQ	90,18,0:1/1:90
+chr8	140566111	.	A	G	18.1	.	DP=12;AF1=1;CI95=1,1;DP4=0,0,0,12;MQ=15	PL:GT:GQ	51,36,0:1/1:99
+chr8	141586480	.	T	G	44	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=40	PL:GT:GQ	76,9,0:1/1:63
+chr8	143376712	.	A	G	13	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35	PL:GT:GQ	44,6,0:1/1:49
+chr8	150662729	.	T	C	9.31	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47	PL:GT:GQ	40,6,0:1/1:49
+chr8	150741294	.	A	G	25.1	.	DP=7;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=34	PL:GT:GQ	58,18,0:1/1:90
+chr8	150975618	.	A	G	9.31	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48	PL:GT:GQ	40,6,0:1/1:49
+chr8	151580103	.	T	C	6.02	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=20	PL:GT:GQ	36,6,0:1/1:49
+chr8	151634410	.	G	T	48	.	DP=17;AF1=0.5;CI95=0.5,0.5;DP4=0,12,0,5;MQ=39;PV4=1,0.072,1,1	PL:GT:GQ	78,0,125:0/1:81
+chr8	151709267	.	G	A	91.1	.	DP=8;AF1=0.5064;CI95=0.5,0.5;DP4=0,1,0,7;MQ=40;PV4=1,1,0.28,0.37	PL:GT:GQ	121,0,16:0/1:19
+chr8	152636420	.	G	A	8.75	.	DP=3;AF1=0.9966;CI95=0.5,1;DP4=0,1,0,2;MQ=30;PV4=1,1,1,1	PL:GT:GQ	37,1,0:1/1:23
+chr8	152706967	.	G	A	3.01	.	DP=10;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=16	PL:GT:GQ	33,30,0:1/1:99
+chr8	152786522	.	T	C	80.1	.	DP=16;AF1=0.5102;CI95=0.5,0.5;DP4=0,4,0,12;MQ=31;PV4=1,0.25,1,1	PL:GT:GQ	110,0,14:0/1:17
+chr8	152863132	.	T	G	5.44	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=30	PL:GT:GQ	36,9,0:1/1:63
+chr9	23235268	.	C	T	12	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=32	PL:GT:GQ	43,6,0:1/1:49
+chr9	26391176	.	T	C	15.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35	PL:GT:GQ	47,6,0:1/1:49
+chr9	26868232	.	C	G	63	.	DP=20;AF1=0.5025;CI95=0.5,0.5;DP4=7,0,13,0;MQ=22;PV4=1,0.2,1,0.44	PL:GT:GQ	93,0,20:0/1:23
+chr9	34223668	.	C	T	22	.	DP=16;AF1=0.5;CI95=0.5,0.5;DP4=0,9,0,7;MQ=27;PV4=1,0.14,0.34,1	PL:GT:GQ	52,0,79:0/1:55
+chr9	39696645	.	G	A	11.3	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=41	PL:GT:GQ	43,9,0:1/1:63
+chr9	40654130	.	T	G	13	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48	PL:GT:GQ	44,6,0:1/1:49
+chr9	41145321	.	T	G	46.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=33	PL:GT:GQ	79,12,0:1/1:72
+chr9	42273483	.	G	A	9.31	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49	PL:GT:GQ	40,6,0:1/1:49
+chr9	55633192	.	C	T	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49	PL:GT:GQ	73,6,0:1/1:49
+chr9	58705807	.	T	C	70	.	DP=10;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=24	PL:GT:GQ	103,30,0:1/1:99
+chr9	61697149	.	C	G	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49	PL:GT:GQ	73,6,0:1/1:49
+chr9	63152790	.	A	C	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48	PL:GT:GQ	40,6,0:1/1:49
+chr9	63703913	.	C	G	90.1	.	DP=7;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=38	PL:GT:GQ	123,21,0:1/1:84
+chr9	65116068	.	T	C	70	.	DP=13;AF1=1;CI95=1,1;DP4=0,0,0,13;MQ=49	PL:GT:GQ	103,39,0:1/1:99
+chr9	71266598	.	C	A	3.98	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35	PL:GT:GQ	33,6,0:1/1:49
+chr9	73188677	.	G	T	52	.	DP=294;AF1=1;CI95=1,1;DP4=44,0,245,0;MQ=33;PV4=1,0.28,0.0092,1	PL:GT:GQ	85,147,0:1/1:99
+chr9	78854179	.	G	T	22	.	DP=97;AF1=0.5;CI95=0.5,0.5;DP4=21,0,12,0;MQ=44;PV4=1,0.02,0.032,0.0033	PL:GT:GQ	52,0,158:0/1:55
+chr9	82964679	.	A	C	13.2	.	DP=19;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=36	PL:GT:GQ	45,9,0:1/1:63
+chr9	84124545	.	G	T	57	.	DP=11;AF1=0.5;CI95=0.5,0.5;DP4=2,0,3,0;MQ=49;PV4=1,1,0.024,1	PL:GT:GQ	87,0,59:0/1:62
+chr9	86552862	.	C	T	14.4	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=26	PL:GT:GQ	47,15,0:1/1:75
+chr9	87548941	.	A	G	22	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=49	PL:GT:GQ	54,9,0:1/1:63
+chr9	89021101	.	G	A	89.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=49	PL:GT:GQ	122,12,0:1/1:72
+chr9	90447825	.	G	A	9.31	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=46	PL:GT:GQ	40,6,0:1/1:49
+chr9	92462035	.	C	A	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=36	PL:GT:GQ	40,6,0:1/1:49
+chr9	93077294	.	T	G	5.44	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=31	PL:GT:GQ	36,9,0:1/1:63
+chr9	93998137	.	G	A	68	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=46	PL:GT:GQ	100,9,0:1/1:63
+chr9	93998148	.	C	T	21.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=36	PL:GT:GQ	54,15,0:1/1:75
+chr9	95028964	.	C	A	99	.	DP=83;AF1=0.5;CI95=0.5,0.5;DP4=0,57,0,26;MQ=32;PV4=1,9.3e-08,1,0.092	PL:GT:GQ	134,0,120:0/1:99
+chr9	103829155	.	A	G	33	.	DP=96;AF1=1;CI95=1,1;DP4=0,0,96,0;MQ=16	PL:GT:GQ	66,255,0:1/1:99
+chr9	104981331	.	C	T	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=43	PL:GT:GQ	73,6,0:1/1:49
+chr9	111070656	.	G	A	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49	PL:GT:GQ	73,6,0:1/1:49
+chr9	117395657	.	T	C	16.4	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=23	PL:GT:GQ	49,15,0:1/1:75
+chr9	117718907	.	A	G	46.1	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=29	PL:GT:GQ	79,18,0:1/1:90
+chr9	119149161	.	T	C	3.14	.	DP=65;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=22	PL:GT:GQ	33,15,0:1/1:75
+chr9	124528802	.	G	A	78	.	DP=23;AF1=1;CI95=1,1;DP4=0,0,13,0;MQ=25	PL:GT:GQ	111,39,0:1/1:99
+chr9	126707903	.	G	A	26	.	DP=37;AF1=0.5;CI95=0.5,0.5;DP4=0,21,0,8;MQ=46;PV4=1,2.6e-07,0.21,0.42	PL:GT:GQ	56,0,175:0/1:59
+chr9	128700686	.	C	G	33.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=50	PL:GT:GQ	66,12,0:1/1:72
+chr9	129084077	.	G	A	11.3	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=41	PL:GT:GQ	43,9,0:1/1:63
+chr9	129116900	.	A	T	20	.	DP=13;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=30	PL:GT:GQ	52,9,0:1/1:63
+chr9	130290720	.	C	G	21.8	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=42	PL:GT:GQ	53,6,0:1/1:49
+chr9	130306057	.	C	G	71	.	DP=14;AF1=1;CI95=1,1;DP4=0,0,14,0;MQ=28	PL:GT:GQ	104,42,0:1/1:99
+chr9	130528990	.	G	A	99	.	DP=31;AF1=1;CI95=1,1;DP4=0,0,31,0;MQ=27	PL:GT:GQ	174,93,0:1/1:99
+chr9	130529002	.	A	T	7.79	.	DP=30;AF1=1;CI95=1,1;DP4=0,0,11,0;MQ=15	PL:GT:GQ	40,33,0:1/1:99
+chr9	130639996	.	A	G	8.44	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=51	PL:GT:GQ	39,6,0:1/1:49
+chr9	130704890	.	A	G	3.27	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=26	PL:GT:GQ	33,12,0:1/1:72
+chr9	130708345	.	G	A	13.3	.	DP=11;AF1=0.9966;CI95=0.5,1;DP4=0,2,0,3;MQ=38;PV4=1,0.096,1,1	PL:GT:GQ	42,1,0:1/1:23
+chr9	131001601	.	T	A	3.98	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=31	PL:GT:GQ	33,6,0:1/1:49
+chr9	131058539	.	T	A	13	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=44	PL:GT:GQ	44,6,0:1/1:49
+chr9	131808965	.	C	T	42	.	DP=9;AF1=1;CI95=1,1;DP4=0,0,0,9;MQ=37	PL:GT:GQ	75,27,0:1/1:99
+chr9	132551867	.	C	T	17.1	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=25	PL:GT:GQ	49,9,0:1/1:63
+chr9	132685120	.	A	G	4.75	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=25	PL:GT:GQ	35,9,0:1/1:63
+chr9	133175050	.	A	G	18.1	.	DP=30;AF1=1;CI95=1,1;DP4=0,0,17,0;MQ=20	PL:GT:GQ	51,51,0:1/1:99
+chr9	133584978	.	A	G	99	.	DP=25;AF1=1;CI95=1,1;DP4=0,0,25,0;MQ=45	PL:GT:GQ	212,75,0:1/1:99
+chr9	133661895	.	A	G	99	.	DP=17;AF1=1;CI95=1,1;DP4=0,0,14,0;MQ=31	PL:GT:GQ	138,42,0:1/1:99
+chr9	133670376	.	T	C	68	.	DP=19;AF1=1;CI95=1,1;DP4=0,1,0,16;MQ=39;PV4=1,1.4e-20,1,1	PL:GT:GQ	101,39,0:1/1:99
+chr9	133843777	.	T	C	99	.	DP=9;AF1=0.5129;CI95=0.5,0.5;DP4=1,0,8,0;MQ=43;PV4=1,1,1,1	PL:GT:GQ	154,0,13:0/1:16
+chr9	134017265	.	G	C	3.27	.	DP=10;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=13	PL:GT:GQ	33,12,0:1/1:72
+chr9	134105563	.	T	C	34.1	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=39	PL:GT:GQ	67,18,0:1/1:90
+chr9	134608906	.	C	T	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=46	PL:GT:GQ	73,6,0:1/1:49
+chr9	134861929	.	T	A	9.49	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=30	PL:GT:GQ	41,9,0:1/1:63
+chr10	796662	.	A	G	22	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=46	PL:GT:GQ	54,9,0:1/1:63
+chr10	1216716	.	T	A	18.6	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=25	PL:GT:GQ	51,12,0:1/1:72
+chr10	1220781	.	G	A	21	.	DP=9;AF1=1;CI95=1,1;DP4=0,0,9,0;MQ=18	PL:GT:GQ	54,27,0:1/1:99
+chr10	1225208	.	T	C	68	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=47	PL:GT:GQ	100,9,0:1/1:63
+chr10	1727946	.	T	C	14.2	.	DP=8;AF1=1;CI95=1,1;DP4=0,0,0,7;MQ=27	PL:GT:GQ	47,21,0:1/1:84
+chr10	5986542	.	T	C	83	.	DP=93;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=39	PL:GT:GQ	116,30,0:1/1:99
+chr10	6436277	.	G	A	6.02	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47	PL:GT:GQ	36,6,0:1/1:49
+chr10	7704114	.	C	A	35	.	DP=6;AF1=0.9999;CI95=0.5,1;DP4=0,2,0,4;MQ=29;PV4=1,0.27,1,0.27	PL:GT:GQ	65,3,0:1/1:41
+chr10	10881734	.	A	G	9.52	.	DP=9;AF1=0.5;CI95=0.5,0.5;DP4=4,0,5,0;MQ=42;PV4=1,0.0026,0.14,1	PL:GT:GQ	39,0,91:0/1:42
+chr10	13099383	.	G	A	27.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=48	PL:GT:GQ	60,12,0:1/1:72
+chr10	15764077	.	G	C	11.3	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=40	PL:GT:GQ	43,9,0:1/1:63
+chr10	18091502	.	T	C	47	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=38	PL:GT:GQ	79,9,0:1/1:63
+chr10	19645913	.	A	T	15.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=43	PL:GT:GQ	47,6,0:1/1:49
+chr10	22845062	.	C	T	18.1	.	DP=8;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=18	PL:GT:GQ	51,21,0:1/1:84
+chr10	28282802	.	T	C	69	.	DP=12;AF1=1;CI95=1,1;DP4=0,0,12,0;MQ=42	PL:GT:GQ	102,36,0:1/1:99
+chr10	28496872	.	T	G	8.44	.	DP=11;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=45	PL:GT:GQ	39,6,0:1/1:49
+chr10	32746793	.	G	A	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=46	PL:GT:GQ	73,6,0:1/1:49
+chr10	41437604	.	T	G	11.3	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=39	PL:GT:GQ	43,9,0:1/1:63
+chr10	43051239	.	C	T	6.98	.	DP=3;AF1=0.5001;CI95=0.5,0.5;DP4=1,0,2,0;MQ=40;PV4=1,0.33,0.33,1	PL:GT:GQ	36,0,31:0/1:33
+chr10	44455192	.	C	T	4.41	.	DP=6;AF1=0.8276;CI95=0.5,1;DP4=0,3,0,3;MQ=21;PV4=1,1,1,1	PL:GT:GQ	31,0,1:1/1:5
+chr10	48387336	.	A	G	13	.	DP=7;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35	PL:GT:GQ	44,6,0:1/1:49
+chr10	51561705	.	A	G	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=45	PL:GT:GQ	40,6,0:1/1:49
+chr10	51561712	.	C	G	39.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=45	PL:GT:GQ	71,6,0:1/1:49
+chr10	55617954	.	G	A	8.44	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=31	PL:GT:GQ	39,6,0:1/1:49
+chr10	55718281	.	T	A	3.41	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=32	PL:GT:GQ	32,6,0:1/1:49
+chr10	55888771	.	T	C	23.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=43	PL:GT:GQ	56,12,0:1/1:72
+chr10	56025569	.	C	G	34.1	.	DP=3;AF1=0.5064;CI95=0.5,0.5;DP4=0,1,0,2;MQ=39;PV4=1,1,1,1	PL:GT:GQ	64,0,16:0/1:19
+chr10	57384943	.	G	T	84	.	DP=29;AF1=0.5;CI95=0.5,0.5;DP4=16,0,13,0;MQ=26;PV4=1,0.015,1,1	PL:GT:GQ	114,0,110:0/1:99
+chr10	59873077	.	T	G	49	.	DP=8;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=42	PL:GT:GQ	82,24,0:1/1:96
+chr10	61329572	.	C	T	15.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48	PL:GT:GQ	47,6,0:1/1:49
+chr10	63790636	.	T	G	32.1	.	DP=19;AF1=1;CI95=1,1;DP4=1,0,10,0;MQ=28;PV4=1,0.14,1,1	PL:GT:GQ	65,22,0:1/1:88
+chr10	64466048	.	C	G	18.2	.	DP=7;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=28	PL:GT:GQ	51,18,0:1/1:90
+chr10	65053440	.	G	T	99	.	DP=10;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=39	PL:GT:GQ	153,30,0:1/1:99
+chr10	65407358	.	C	G	84.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=45	PL:GT:GQ	117,15,0:1/1:75
+chr10	65605291	.	G	A	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=51	PL:GT:GQ	73,6,0:1/1:49
+chr10	66104447	.	T	C	99	.	DP=47;AF1=0.5;CI95=0.5,0.5;DP4=0,25,0,21;MQ=34;PV4=1,1,0.15,1	PL:GT:GQ	136,0,162:0/1:99
+chr10	82160859	.	G	C	99	.	DP=17;AF1=1;CI95=1,1;DP4=0,0,0,13;MQ=36	PL:GT:GQ	153,39,0:1/1:99
+chr10	82198579	.	C	T	9.31	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47	PL:GT:GQ	40,6,0:1/1:49
+chr10	87086290	.	A	G	4.13	.	DP=9;AF1=1;CI95=1,1;DP4=0,0,0,9;MQ=17	PL:GT:GQ	35,27,0:1/1:99
+chr10	89550621	.	T	G	74	.	DP=47;AF1=1;CI95=1,1;DP4=0,0,0,45;MQ=45	PL:GT:GQ	107,135,0:1/1:99
+chr10	92325046	.	G	A	42.3	.	DP=18;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=45	PL:GT:GQ	75,15,0:1/1:75
+chr10	94488050	.	A	G	5.46	.	DP=4;AF1=0.5;CI95=0.5,0.5;DP4=2,0,2,0;MQ=43;PV4=1,0.16,1,1	PL:GT:GQ	34,0,34:0/1:34
+chr10	95024815	.	C	T	13.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=36	PL:GT:GQ	45,6,0:1/1:49
+chr10	95466306	.	G	A	53	.	DP=7;AF1=0.6671;CI95=0.5,1;DP4=0,4,0,3;MQ=33;PV4=1,1,1,1	PL:GT:GQ	82,0,3:0/1:5
+chr10	100256777	.	T	G	3.83	.	DP=7;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=23	PL:GT:GQ	34,12,0:1/1:72
+chr10	101510485	.	T	C	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49	PL:GT:GQ	40,6,0:1/1:49
+chr10	101530760	.	C	T	13.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35	PL:GT:GQ	45,6,0:1/1:49
+chr10	101879744	.	T	C	22	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=44	PL:GT:GQ	54,9,0:1/1:63
+chr10	102147276	.	G	C	11.3	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=33	PL:GT:GQ	43,9,0:1/1:63
+chr10	102642248	.	T	G	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49	PL:GT:GQ	40,6,0:1/1:49
+chr10	107666616	.	T	C	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=43	PL:GT:GQ	40,6,0:1/1:49
+chr10	108319945	.	C	G	11.3	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=29	PL:GT:GQ	43,9,0:1/1:63
+chr10	109734371	.	G	A	12.7	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=35	PL:GT:GQ	45,12,0:1/1:72
+chr10	112870604	.	C	T	46.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=36	PL:GT:GQ	79,12,0:1/1:72
+chr10	115304673	.	T	C	11.3	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=42	PL:GT:GQ	43,9,0:1/1:63
+chr10	119380588	.	G	A	14.2	.	DP=4;AF1=0.502;CI95=0.5,0.5;DP4=1,0,3,0;MQ=43;PV4=1,0.18,0.32,1	PL:GT:GQ	44,0,21:0/1:24
+chr10	123063756	.	C	T	14.1	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=23	PL:GT:GQ	46,9,0:1/1:63
+chr10	128424770	.	T	G	13.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=30	PL:GT:GQ	45,6,0:1/1:49
+chr10	131229204	.	T	C	44	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=40	PL:GT:GQ	76,9,0:1/1:63
+chr10	132420570	.	G	C	89.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=49	PL:GT:GQ	122,12,0:1/1:72
+chr10	132528066	.	C	T	99	.	DP=19;AF1=1;CI95=1,1;DP4=0,0,19,0;MQ=42	PL:GT:GQ	213,57,0:1/1:99
+chr10	132644619	.	G	A	19.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=23	PL:GT:GQ	52,15,0:1/1:75
+chr10	132707581	.	G	C	9.11	.	DP=51;AF1=0.9998;CI95=0.5,1;DP4=1,0,2,0;MQ=25;PV4=1,1,1,1	PL:GT:GQ	38,2,0:1/1:37
+chr10	133026892	.	T	C	55.1	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=44	PL:GT:GQ	88,18,0:1/1:90
+chr11	768033	.	T	C	33.5	.	DP=4;AF1=0.8277;CI95=0.5,1;DP4=0,2,0,2;MQ=32;PV4=1,1,1,1	PL:GT:GQ	62,0,1:1/1:5
+chr11	768042	.	T	C	33.5	.	DP=6;AF1=0.8277;CI95=0.5,1;DP4=0,2,0,2;MQ=32;PV4=1,1,1,1	PL:GT:GQ	62,0,1:1/1:5
+chr11	874568	.	G	C	33.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=33	PL:GT:GQ	66,12,0:1/1:72
+chr11	1009210	.	T	C	4	.	DP=70;AF1=0.6241;CI95=0.5,1;DP4=0,3,0,8;MQ=24;PV4=1,1,0.5,1	PL:GT:GQ	31,0,4:0/1:6
+chr11	1016692	.	C	T	27	.	DP=39;AF1=1;CI95=1,1;DP4=0,0,0,38;MQ=22	PL:GT:GQ	60,114,0:1/1:99
+chr11	1034477	.	A	G	66	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=42	PL:GT:GQ	98,9,0:1/1:63
+chr11	1074037	.	G	A	4.13	.	DP=9;AF1=0.5001;CI95=0.5,0.5;DP4=4,0,5,0;MQ=24;PV4=1,1,0.43,1	PL:GT:GQ	32,0,30:0/1:31
+chr11	1556298	.	G	A	11.8	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=33	PL:GT:GQ	44,12,0:1/1:72
+chr11	1824777	.	T	C	27	.	DP=10;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=28	PL:GT:GQ	60,30,0:1/1:99
+chr11	3395801	.	C	T	22	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=49	PL:GT:GQ	54,9,0:1/1:63
+chr11	3411901	.	G	A	4.75	.	DP=17;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=29	PL:GT:GQ	35,9,0:1/1:63
+chr11	3731606	.	A	C	11.3	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=39	PL:GT:GQ	43,9,0:1/1:63
+chr11	3783855	.	C	T	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=44	PL:GT:GQ	40,6,0:1/1:49
+chr11	3967636	.	A	G	4.29	.	DP=20;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=24	PL:GT:GQ	35,15,0:1/1:75
+chr11	4385618	.	C	T	13.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=31	PL:GT:GQ	45,6,0:1/1:49
+chr11	4424365	.	T	A	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49	PL:GT:GQ	73,6,0:1/1:49
+chr11	5295586	.	C	T	3.01	.	DP=52;AF1=0.4997;CI95=0.5,0.5;DP4=33,0,10,0;MQ=29;PV4=1,0.0045,0.3,0.17	PL:GT:GQ	30,0,131:0/1:33
+chr11	6157144	.	C	G	45.1	.	DP=14;AF1=1;CI95=1,1;DP4=0,0,0,7;MQ=35	PL:GT:GQ	78,21,0:1/1:84
+chr11	6352044	.	C	T	18	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=31	PL:GT:GQ	50,9,0:1/1:63
+chr11	6767356	.	T	C	9.63	.	DP=3;AF1=0.9966;CI95=0.5,1;DP4=1,0,2,0;MQ=29;PV4=1,1,1,1	PL:GT:GQ	38,1,0:1/1:23
+chr11	6999404	.	G	C	21	.	DP=8;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=37	PL:GT:GQ	53,9,0:1/1:63
+chr11	9120930	.	C	G	17.6	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=25	PL:GT:GQ	50,12,0:1/1:72
+chr11	9373125	.	T	C	19.8	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48	PL:GT:GQ	51,6,0:1/1:49
+chr11	9585101	.	C	T	67	.	DP=16;AF1=1;CI95=1,1;DP4=0,0,14,0;MQ=45	PL:GT:GQ	100,42,0:1/1:99
+chr11	10266192	.	A	C	14.3	.	DP=22;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=27	PL:GT:GQ	47,18,0:1/1:90
+chr11	10303263	.	T	C	8.64	.	DP=17;AF1=1;CI95=1,1;DP4=0,0,0,17;MQ=18	PL:GT:GQ	41,51,0:1/1:99
+chr11	10420170	.	T	C	35	.	DP=17;AF1=1;CI95=1,1;DP4=0,1,0,15;MQ=28;PV4=1,0.12,1,0.4	PL:GT:GQ	68,36,0:1/1:99
+chr11	10912169	.	G	A	99	.	DP=7;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=49	PL:GT:GQ	155,18,0:1/1:90
+chr11	11315826	.	T	G	6.29	.	DP=27;AF1=1;CI95=1,1;DP4=0,0,0,6;MQ=19	PL:GT:GQ	38,18,0:1/1:90
+chr11	11603859	.	A	C	22	.	DP=15;AF1=0.5;CI95=0.5,0.5;DP4=0,9,0,6;MQ=34;PV4=1,9.5e-13,0.22,1	PL:GT:GQ	52,0,115:0/1:55
+chr11	11700034	.	C	T	33	.	DP=11;AF1=1;CI95=1,1;DP4=0,0,9,0;MQ=30	PL:GT:GQ	66,27,0:1/1:99
+chr11	11822758	.	G	A	15.1	.	DP=15;AF1=0.5;CI95=0.5,0.5;DP4=0,7,0,3;MQ=38;PV4=1,0.18,1,1	PL:GT:GQ	45,0,88:0/1:48
+chr11	11976636	.	C	T	22	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=24	PL:GT:GQ	54,9,0:1/1:63
+chr11	14380517	.	C	G	16.1	.	DP=10;AF1=0.5;CI95=0.5,0.5;DP4=5,0,5,0;MQ=48;PV4=1,2.1e-05,0.13,1	PL:GT:GQ	46,0,113:0/1:49
+chr11	14419212	.	A	G	91.1	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=38	PL:GT:GQ	124,18,0:1/1:90
+chr11	14846792	.	A	G	55	.	DP=11;AF1=1;CI95=1,1;DP4=0,0,0,11;MQ=19	PL:GT:GQ	88,33,0:1/1:99
+chr11	15494556	.	C	T	99	.	DP=38;AF1=0.5;CI95=0.5,0.5;DP4=22,0,14,0;MQ=34;PV4=1,0.0071,1,1	PL:GT:GQ	146,0,159:0/1:99
+chr11	16262879	.	A	C	16.1	.	DP=4;AF1=0.5004;CI95=0.5,0.5;DP4=0,1,0,3;MQ=43;PV4=1,0.061,0.24,0.33	PL:GT:GQ	46,0,28:0/1:31
+chr11	21514947	.	T	C	24.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=41	PL:GT:GQ	57,12,0:1/1:72
+chr11	22532576	.	C	G	28	.	DP=17;AF1=1;CI95=1,1;DP4=0,0,0,17;MQ=17	PL:GT:GQ	61,51,0:1/1:99
+chr11	23529238	.	G	T	4.29	.	DP=13;AF1=0.5334;CI95=0.5,1;DP4=1,0,3,0;MQ=37;PV4=1,1,0.34,0.21	PL:GT:GQ	32,0,9:0/1:12
+chr11	24249554	.	A	G	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=48	PL:GT:GQ	73,6,0:1/1:49
+chr11	24853167	.	A	G	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=51	PL:GT:GQ	73,6,0:1/1:49
+chr11	33353903	.	T	C	24.3	.	DP=8;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=36	PL:GT:GQ	57,15,0:1/1:75
+chr11	35126569	.	T	C	24.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=43	PL:GT:GQ	57,12,0:1/1:72
+chr11	35132248	.	C	T	18.6	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=25	PL:GT:GQ	51,12,0:1/1:72
+chr11	35155482	.	T	C	68	.	DP=22;AF1=1;CI95=1,1;DP4=0,0,22,0;MQ=46	PL:GT:GQ	101,66,0:1/1:99
+chr11	52494088	.	T	C	99	.	DP=9;AF1=1;CI95=1,1;DP4=0,0,0,9;MQ=37	PL:GT:GQ	140,27,0:1/1:99
+chr11	57899943	.	C	G	13	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35	PL:GT:GQ	44,6,0:1/1:49
+chr11	62261460	.	G	T	19.1	.	DP=15;AF1=0.5;CI95=0.5,0.5;DP4=0,7,0,5;MQ=27;PV4=1,1.1e-06,1,1	PL:GT:GQ	49,0,58:0/1:51
+chr11	67456049	.	C	T	39.1	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=19	PL:GT:GQ	72,18,0:1/1:90
+chr11	68509708	.	C	G	3.65	.	DP=9;AF1=0.7301;CI95=0.5,1;DP4=0,5,0,4;MQ=17;PV4=1,1,1,1	PL:GT:GQ	30,0,2:0/1:3
+chr11	70115115	.	T	A	99	.	DP=7;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=49	PL:GT:GQ	140,15,0:1/1:75
+chr11	72643951	.	T	C	70	.	DP=23;AF1=1;CI95=1,1;DP4=0,0,22,0;MQ=39	PL:GT:GQ	103,66,0:1/1:99
+chr11	72647930	.	G	A	36	.	DP=4;AF1=0.5004;CI95=0.5,0.5;DP4=0,1,0,3;MQ=41;PV4=1,1,0.3,1	PL:GT:GQ	66,0,28:0/1:31
+chr11	73330148	.	C	T	13	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35	PL:GT:GQ	44,6,0:1/1:49
+chr11	81720893	.	A	G	5.83	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=19	PL:GT:GQ	37,12,0:1/1:72
+chr11	83813797	.	A	G	23.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=43	PL:GT:GQ	56,12,0:1/1:72
+chr11	85949488	.	C	A	54	.	DP=17;AF1=1;CI95=1,1;DP4=0,0,14,0;MQ=37	PL:GT:GQ	87,42,0:1/1:99
+chr11	87634829	.	G	A	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=51	PL:GT:GQ	40,6,0:1/1:49
+chr11	90913093	.	A	T	35.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=46	PL:GT:GQ	67,6,0:1/1:49
+chr11	93793348	.	G	A	99	.	DP=8;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=31	PL:GT:GQ	139,24,0:1/1:96
+chr11	100802294	.	T	C	16.6	.	DP=21;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=35	PL:GT:GQ	49,12,0:1/1:72
+chr11	107455449	.	C	T	8.44	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=26	PL:GT:GQ	39,6,0:1/1:49
+chr11	111344355	.	A	G	69.5	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=43	PL:GT:GQ	102,12,0:1/1:72
+chr11	111611115	.	C	T	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49	PL:GT:GQ	73,6,0:1/1:49
+chr11	113050466	.	G	C	6.02	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=30	PL:GT:GQ	36,6,0:1/1:49
+chr11	114332544	.	T	C	3.54	.	DP=17;AF1=0.4999;CI95=0.5,0.5;DP4=0,4,0,5;MQ=37;PV4=1,0.32,0.13,1	PL:GT:GQ	31,0,37:0/1:33
+chr11	114332549	.	G	A	3.54	.	DP=17;AF1=0.4998;CI95=0.5,0.5;DP4=0,9,0,8;MQ=36;PV4=1,3.1e-10,0.088,1	PL:GT:GQ	31,0,127:0/1:34
+chr11	114843578	.	G	C	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=50	PL:GT:GQ	73,6,0:1/1:49
+chr11	115580279	.	A	G	99	.	DP=15;AF1=1;CI95=1,1;DP4=0,0,15,0;MQ=48	PL:GT:GQ	190,45,0:1/1:99
+chr11	116434328	.	G	A	17.6	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=25	PL:GT:GQ	50,12,0:1/1:72
+chr11	125914161	.	A	G	20.8	.	DP=7;AF1=0.95;CI95=0.5,1;DP4=3,0,4,0;MQ=38;PV4=1,0.074,1,1	PL:GT:GQ	49,0,0:1/1:10
+chr11	125917089	.	C	T	12.3	.	DP=41;AF1=0.5;CI95=0.5,0.5;DP4=0,28,0,12;MQ=44;PV4=1,4.7e-25,1,1	PL:GT:GQ	42,0,167:0/1:45
+chr11	127194100	.	A	G	60	.	DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=49	PL:GT:GQ	93,24,0:1/1:96
+chr12	70856	.	G	A	27.5	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=49	PL:GT:GQ	60,12,0:1/1:72
+chr12	153693	.	T	C	52.3	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=38	PL:GT:GQ	85,15,0:1/1:75
+chr12	924547	.	C	G	37.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=50	PL:GT:GQ	69,6,0:1/1:49
+chr12	1555916	.	G	A	7.18	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=23	PL:GT:GQ	39,15,0:1/1:75
+chr12	1919860	.	G	T	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49	PL:GT:GQ	40,6,0:1/1:49
+chr12	2283756	.	G	A	13.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=34	PL:GT:GQ	45,6,0:1/1:49
+chr12	2805983	.	G	C	12.7	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=35	PL:GT:GQ	45,12,0:1/1:72
+chr12	6088203	.	T	C	72.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=37	PL:GT:GQ	105,15,0:1/1:75
+chr12	7099460	.	G	C	10.8	.	DP=6;AF1=0.8277;CI95=0.5,1;DP4=3,0,3,0;MQ=26;PV4=1,0.027,1,1	PL:GT:GQ	39,0,1:1/1:5
+chr12	7099464	.	G	A	13.3	.	DP=6;AF1=0.9966;CI95=0.5,1;DP4=2,0,3,0;MQ=28;PV4=1,0.16,1,1	PL:GT:GQ	42,1,0:1/1:23
+chr12	7198516	.	T	G	4.61	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35	PL:GT:GQ	34,6,0:1/1:49
+chr12	23331895	.	C	T	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49	PL:GT:GQ	40,6,0:1/1:49
+chr12	28209020	.	T	G	14.4	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=31	PL:GT:GQ	47,15,0:1/1:75
+chr12	30074073	.	C	T	32.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35	PL:GT:GQ	64,6,0:1/1:49
+chr12	30563452	.	T	C	25	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=46	PL:GT:GQ	57,9,0:1/1:63
+chr12	30563453	.	A	G	25	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=46	PL:GT:GQ	57,9,0:1/1:63
+chr12	30563464	.	C	A	78.8	.	DP=8;AF1=1;CI95=0.5,1;DP4=0,2,0,5;MQ=34;PV4=1,0.29,1,1	PL:GT:GQ	110,6,0:1/1:49
+chr12	31505085	.	G	A	13.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35	PL:GT:GQ	45,6,0:1/1:49
+chr12	34041336	.	G	A	5.46	.	DP=5;AF1=0.5;CI95=0.5,0.5;DP4=2,0,2,0;MQ=36;PV4=1,1,0.48,0.21	PL:GT:GQ	34,0,34:0/1:34
+chr12	49003648	.	C	G	42	.	DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=39	PL:GT:GQ	75,24,0:1/1:96
+chr12	51280690	.	G	A	69	.	DP=98;AF1=0.5;CI95=0.5,0.5;DP4=13,0,18,0;MQ=45;PV4=1,1,0.051,1	PL:GT:GQ	99,0,84:0/1:87
+chr12	69206633	.	T	C	17.1	.	DP=12;AF1=1;CI95=1,1;DP4=0,0,0,11;MQ=17	PL:GT:GQ	50,33,0:1/1:99
+chr12	80417253	.	T	C	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=48	PL:GT:GQ	73,6,0:1/1:49
+chr12	86633033	.	C	T	34	.	DP=3;AF1=0.5002;CI95=0.5,0.5;DP4=0,1,0,2;MQ=43;PV4=1,1,0.33,1	PL:GT:GQ	64,0,31:0/1:34
+chr12	98097274	.	C	T	47.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=31	PL:GT:GQ	80,15,0:1/1:75
+chr12	105269319	.	C	T	19	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=26	PL:GT:GQ	51,9,0:1/1:63
+chr12	109053425	.	G	A	9.53	.	DP=8;AF1=0.5012;CI95=0.5,0.5;DP4=2,0,6,0;MQ=25;PV4=1,1,0.19,1	PL:GT:GQ	39,0,23:0/1:26
+chr12	111904540	.	A	G	3.41	.	DP=65;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=31	PL:GT:GQ	32,6,0:1/1:49
+chr12	115038686	.	T	C	15.2	.	DP=7;AF1=1;CI95=1,1;DP4=0,0,0,7;MQ=27	PL:GT:GQ	48,21,0:1/1:84
+chr12	115039419	.	A	G	4.11	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=30	PL:GT:GQ	34,9,0:1/1:63
+chr12	115103890	.	G	A	66	.	DP=39;AF1=1;CI95=1,1;DP4=0,0,0,38;MQ=49	PL:GT:GQ	99,114,0:1/1:99
+chr12	115833830	.	G	A	68	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=49	PL:GT:GQ	100,9,0:1/1:63
+chr12	116361873	.	T	G	6.34	.	DP=5;AF1=0.7302;CI95=0.5,1;DP4=0,2,0,2;MQ=23;PV4=1,1,1,1	PL:GT:GQ	34,0,2:0/1:3
+chr12	123583527	.	G	A	14.1	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=25	PL:GT:GQ	46,9,0:1/1:63
+chr12	124115330	.	A	G	44	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=38	PL:GT:GQ	76,9,0:1/1:63
+chr12	125062296	.	G	A	41.8	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=50	PL:GT:GQ	73,6,0:1/1:49
+chr12	126718106	.	A	G	8.76	.	DP=50;AF1=0.5163;CI95=0.5,1;DP4=2,0,6,0;MQ=26;PV4=1,0.33,0.37,1	PL:GT:GQ	38,0,12:0/1:15
+chr12	133348311	.	G	A	24	.	DP=18;AF1=0.5;CI95=0.5,0.5;DP4=14,0,3,0;MQ=35;PV4=1,1,1,1	PL:GT:GQ	54,0,118:0/1:57
+chr12	134494475	.	C	T	28	.	DP=18;AF1=0.6671;CI95=0.5,1;DP4=8,0,10,0;MQ=18;PV4=1,1,1,1	PL:GT:GQ	57,0,3:0/1:5
+chr12	134831761	.	C	T	41.3	.	DP=10;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=27	PL:GT:GQ	74,15,0:1/1:75
+chr12	134992770	.	A	C,T	84	.	DP=47;AF1=1;CI95=1,1;DP4=0,0,26,0;MQ=29	PL:GT:GQ	117,72,114,0,44,114:1/1:99
+chr12	135261117	.	G	A	49.1	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=46	PL:GT:GQ	82,18,0:1/1:90
+chr12	135261144	.	A	G	99	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=46	PL:GT:GQ	155,18,0:1/1:90
+chr12	135460302	.	G	A	99	.	DP=25;AF1=1;CI95=1,1;DP4=0,0,23,0;MQ=40	PL:GT:GQ	198,69,0:1/1:99
+chr12	135463758	.	A	G	83	.	DP=16;AF1=1;CI95=1,1;DP4=0,0,0,16;MQ=26	PL:GT:GQ	116,48,0:1/1:99
+chr12	135523325	.	G	A	99	.	DP=23;AF1=1;CI95=1,1;DP4=0,0,22,0;MQ=26	PL:GT:GQ	136,66,0:1/1:99
+chr12	135782401	.	T	C	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49	PL:GT:GQ	73,6,0:1/1:49
+chr12	135795472	.	G	T	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48	PL:GT:GQ	40,6,0:1/1:49
+chr13	18040027	.	G	C	42	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=33	PL:GT:GQ	74,9,0:1/1:63
+chr13	19494625	.	G	T	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48	PL:GT:GQ	73,6,0:1/1:49
+chr13	20121126	.	A	G	15.1	.	DP=36;AF1=0.5;CI95=0.5,0.5;DP4=25,0,9,0;MQ=36;PV4=1,1,0.13,1	PL:GT:GQ	45,0,153:0/1:48
+chr13	21536703	.	A	G	9.31	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49	PL:GT:GQ	40,6,0:1/1:49
+chr13	23160035	.	G	T	3.98	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=36	PL:GT:GQ	33,6,0:1/1:49
+chr13	23476554	.	C	A	6.79	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=52	PL:GT:GQ	37,6,0:1/1:49
+chr13	26632967	.	C	G	32	.	DP=9;AF1=1;CI95=1,1;DP4=0,0,0,9;MQ=34	PL:GT:GQ	65,27,0:1/1:99
+chr13	26790010	.	T	C	89.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=35	PL:GT:GQ	122,15,0:1/1:75
+chr13	36083571	.	T	C	43	.	DP=84;AF1=1;CI95=1,1;DP4=1,0,37,0;MQ=16;PV4=1,1,1,0.3	PL:GT:GQ	76,99,0:1/1:99
+chr13	44432419	.	C	T	3.58	.	DP=7;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=19	PL:GT:GQ	34,21,0:1/1:84
+chr13	46592359	.	T	C	16.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47	PL:GT:GQ	48,6,0:1/1:49
+chr13	52764657	.	A	T	3.14	.	DP=32;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=22	PL:GT:GQ	33,15,0:1/1:75
+chr13	53084193	.	C	T	9.11	.	DP=3;AF1=0.9998;CI95=0.5,1;DP4=0,1,0,2;MQ=29;PV4=1,1,1,1	PL:GT:GQ	38,2,0:1/1:37
+chr13	57763228	.	C	T	45	.	DP=555;AF1=1;CI95=1,1;DP4=2,0,21,0;MQ=23;PV4=1,0.00021,1,0.3	PL:GT:GQ	78,45,0:1/1:99
+chr13	73857921	.	G	C	31	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=49	PL:GT:GQ	63,9,0:1/1:63
+chr13	76718001	.	G	A	59	.	DP=4;AF1=0.5004;CI95=0.5,0.5;DP4=1,0,3,0;MQ=45;PV4=1,1,0.12,1	PL:GT:GQ	89,0,28:0/1:31
+chr13	100912695	.	A	T	23	.	DP=22;AF1=0.5;CI95=0.5,0.5;DP4=0,16,0,6;MQ=31;PV4=1,0.029,1,0.35	PL:GT:GQ	53,0,103:0/1:56
+chr13	101332001	.	G	C	21	.	DP=23;AF1=1;CI95=1,1;DP4=0,0,23,0;MQ=21	PL:GT:GQ	54,69,0:1/1:99
+chr13	102637334	.	C	T	68	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=49	PL:GT:GQ	100,9,0:1/1:63
+chr13	102895627	.	C	T	63	.	DP=9;AF1=1;CI95=1,1;DP4=0,0,9,0;MQ=48	PL:GT:GQ	96,27,0:1/1:99
+chr13	103830322	.	T	C	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=50	PL:GT:GQ	73,6,0:1/1:49
+chr13	112842448	.	G	A	39	.	DP=18;AF1=1;CI95=1,1;DP4=0,0,0,9;MQ=27	PL:GT:GQ	72,27,0:1/1:99
+chr13	113310291	.	C	T	33.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=43	PL:GT:GQ	66,12,0:1/1:72
+chr13	114775162	.	A	G	80	.	DP=17;AF1=1;CI95=1,1;DP4=0,0,17,0;MQ=21	PL:GT:GQ	113,51,0:1/1:99
+chr13	115267482	.	A	G	16.1	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=29	PL:GT:GQ	48,9,0:1/1:63
+chr13	116068676	.	C	T	3.83	.	DP=8;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=27	PL:GT:GQ	34,12,0:1/1:72
+chr13	116455918	.	A	G	33	.	DP=29;AF1=0.5;CI95=0.5,0.5;DP4=13,0,15,0;MQ=42;PV4=1,1.8e-20,0.3,1	PL:GT:GQ	63,0,146:0/1:66
+chr13	116765012	.	G	A	30.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49	PL:GT:GQ	62,6,0:1/1:49
+chr13	116779773	.	C	T	17.1	.	DP=38;AF1=0.5;CI95=0.5,0.5;DP4=27,0,11,0;MQ=24;PV4=1,4.5e-35,1,1	PL:GT:GQ	47,0,106:0/1:50
+chr13	116779791	.	C	T	57	.	DP=38;AF1=0.5;CI95=0.5,0.5;DP4=24,0,14,0;MQ=24;PV4=1,1,1,1	PL:GT:GQ	87,0,103:0/1:90
+chr14	20159250	.	C	T	11.3	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=39	PL:GT:GQ	43,9,0:1/1:63
+chr14	23510676	.	T	C	52	.	DP=22;AF1=1;CI95=1,1;DP4=0,0,22,0;MQ=32	PL:GT:GQ	85,66,0:1/1:99
+chr14	24735256	.	G	A	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49	PL:GT:GQ	40,6,0:1/1:49
+chr14	29525577	.	G	A	21	.	DP=10;AF1=1;CI95=1,1;DP4=0,0,9,0;MQ=16	PL:GT:GQ	54,27,0:1/1:99
+chr14	36186389	.	C	T	6.79	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=20	PL:GT:GQ	37,6,0:1/1:49
+chr14	36186394	.	A	G	6.79	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=20	PL:GT:GQ	37,6,0:1/1:49
+chr14	37440609	.	A	G	13	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=33	PL:GT:GQ	44,6,0:1/1:49
+chr14	40432807	.	A	G	18.6	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=23	PL:GT:GQ	51,12,0:1/1:72
+chr14	59466268	.	T	C	15.1	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=25	PL:GT:GQ	47,9,0:1/1:63
+chr14	61368162	.	G	T	7.18	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=17	PL:GT:GQ	39,15,0:1/1:75
+chr14	65152922	.	G	A	92	.	DP=33;AF1=0.5;CI95=0.5,0.5;DP4=0,18,0,15;MQ=36;PV4=1,0.059,0.35,1	PL:GT:GQ	122,0,144:0/1:99
+chr14	69749148	.	G	T	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=25	PL:GT:GQ	40,6,0:1/1:49
+chr14	74877658	.	C	T	45	.	DP=48;AF1=1;CI95=1,1;DP4=0,1,0,12;MQ=36;PV4=1,0.02,1,0.39	PL:GT:GQ	78,28,0:1/1:99
+chr14	75546678	.	C	T	19.2	.	DP=7;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=17	PL:GT:GQ	52,18,0:1/1:90
+chr14	76439185	.	T	C	67.1	.	DP=7;AF1=0.505;CI95=0.5,0.5;DP4=0,1,0,6;MQ=33;PV4=1,1,0.056,0.29	PL:GT:GQ	97,0,17:0/1:20
+chr14	77313295	.	T	A	99	.	DP=12;AF1=1;CI95=1,1;DP4=0,0,0,10;MQ=48	PL:GT:GQ	191,30,0:1/1:99
+chr14	77673422	.	G	A	11.5	.	DP=7;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=24	PL:GT:GQ	44,18,0:1/1:90
+chr14	78646125	.	T	C	99	.	DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=40	PL:GT:GQ	153,24,0:1/1:96
+chr14	91702449	.	A	G	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47	PL:GT:GQ	40,6,0:1/1:49
+chr14	91769842	.	G	A	63	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=47	PL:GT:GQ	95,9,0:1/1:63
+chr14	91775899	.	C	G	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=45	PL:GT:GQ	73,6,0:1/1:49
+chr14	91775924	.	A	G	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=45	PL:GT:GQ	40,6,0:1/1:49
+chr14	93482918	.	A	C	68	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=49	PL:GT:GQ	100,9,0:1/1:63
+chr14	93665819	.	C	T	75	.	DP=7;AF1=0.5002;CI95=0.5,0.5;DP4=0,3,0,4;MQ=42;PV4=1,1,1,1	PL:GT:GQ	105,0,31:0/1:34
+chr14	95422276	.	A	G	55.1	.	DP=7;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=45	PL:GT:GQ	88,21,0:1/1:84
+chr14	95731986	.	C	T	68	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=49	PL:GT:GQ	100,9,0:1/1:63
+chr14	96045464	.	A	G	13	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=33	PL:GT:GQ	44,6,0:1/1:49
+chr14	97172020	.	C	T	68	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=51	PL:GT:GQ	100,9,0:1/1:63
+chr14	100515480	.	A	G	6.98	.	DP=3;AF1=0.5002;CI95=0.5,0.5;DP4=1,0,2,0;MQ=45;PV4=1,0.14,0.085,0.33	PL:GT:GQ	36,0,30:0/1:32
+chr14	100770214	.	A	T	8.69	.	DP=20;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=16	PL:GT:GQ	41,21,0:1/1:84
+chr14	101258303	.	G	A	82	.	DP=15;AF1=1;CI95=1,1;DP4=0,0,15,0;MQ=26	PL:GT:GQ	115,45,0:1/1:99
+chr14	101701492	.	C	G	66	.	DP=10;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=49	PL:GT:GQ	99,30,0:1/1:99
+chr14	102113772	.	T	C	3.98	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=30	PL:GT:GQ	33,6,0:1/1:49
+chr14	102751431	.	A	C	36.5	.	DP=3;AF1=0.9998;CI95=0.5,1;DP4=1,0,2,0;MQ=35;PV4=1,1,1,1	PL:GT:GQ	66,2,0:1/1:37
+chr14	103708033	.	A	G	99	.	DP=13;AF1=1;CI95=1,1;DP4=0,0,0,12;MQ=27	PL:GT:GQ	141,36,0:1/1:99
+chr14	104744582	.	G	A	3.52	.	DP=8;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=25	PL:GT:GQ	33,9,0:1/1:63
+chr14	105989100	.	C	T	3.14	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=23	PL:GT:GQ	33,15,0:1/1:75
+chr14	105989162	.	C	T	3.65	.	DP=12;AF1=0.7301;CI95=0.5,1;DP4=0,6,0,6;MQ=15;PV4=1,1,1,1	PL:GT:GQ	30,0,2:0/1:3
+chr14	106234810	.	G	A	25.3	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=39	PL:GT:GQ	58,15,0:1/1:75
+chr14	106995572	.	A	G	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49	PL:GT:GQ	40,6,0:1/1:49
+chr14	107283057	.	T	C	5.5	.	DP=8;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=20	PL:GT:GQ	37,21,0:1/1:84
+chr14	107285319	.	T	C	33	.	DP=36;AF1=1;CI95=1,1;DP4=0,0,0,35;MQ=22	PL:GT:GQ	66,105,0:1/1:99
+chr14	107640449	.	A	G	11.8	.	DP=7;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=36	PL:GT:GQ	44,12,0:1/1:72
+chr15	20082092	.	T	G	18.3	.	DP=10;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=24	PL:GT:GQ	51,15,0:1/1:75
+chr15	22955884	.	T	C	67	.	DP=12;AF1=1;CI95=1,1;DP4=0,0,12,0;MQ=48	PL:GT:GQ	100,36,0:1/1:99
+chr15	22971987	.	A	G	5.29	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=22	PL:GT:GQ	35,6,0:1/1:49
+chr15	23233324	.	C	A	47	.	DP=16;AF1=1;CI95=1,1;DP4=0,0,14,0;MQ=31	PL:GT:GQ	80,42,0:1/1:99
+chr15	25175286	.	C	T	36.5	.	DP=3;AF1=0.9998;CI95=0.5,1;DP4=1,0,2,0;MQ=42;PV4=1,1,1,1	PL:GT:GQ	66,2,0:1/1:37
+chr15	25385709	.	G	A	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=48	PL:GT:GQ	40,6,0:1/1:49
+chr15	27372396	.	A	G	44	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=40	PL:GT:GQ	76,9,0:1/1:63
+chr15	35998093	.	C	T	9.53	.	DP=9;AF1=1;CI95=1,1;DP4=0,0,9,0;MQ=17	PL:GT:GQ	42,27,0:1/1:99
+chr15	36716538	.	C	G	13.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=36	PL:GT:GQ	45,6,0:1/1:49
+chr15	36793360	.	G	T	44	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=42	PL:GT:GQ	76,9,0:1/1:63
+chr15	53783097	.	A	G	10.5	.	DP=31;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=16	PL:GT:GQ	43,21,0:1/1:84
+chr15	54180175	.	C	T	10.4	.	DP=7;AF1=0.5001;CI95=0.5,0.5;DP4=4,0,3,0;MQ=27;PV4=1,1.2e-05,1,1	PL:GT:GQ	40,0,32:0/1:34
+chr15	54939306	.	C	T	99	.	DP=34;AF1=0.5;CI95=0.5,0.5;DP4=0,18,0,16;MQ=49;PV4=1,1,0.18,1	PL:GT:GQ	172,0,181:0/1:99
+chr15	59377916	.	C	T	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=50	PL:GT:GQ	73,6,0:1/1:49
+chr15	59685961	.	G	C	68	.	DP=11;AF1=1;CI95=1,1;DP4=0,0,0,11;MQ=36	PL:GT:GQ	101,33,0:1/1:99
+chr15	60306384	.	A	G	18.6	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=25	PL:GT:GQ	51,12,0:1/1:72
+chr15	60345642	.	G	C	14.9	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35	PL:GT:GQ	46,6,0:1/1:49
+chr15	60367387	.	G	A	13.2	.	DP=6;AF1=0.5001;CI95=0.5,0.5;DP4=3,0,3,0;MQ=34;PV4=1,0.098,0.24,1	PL:GT:GQ	43,0,35:0/1:37
+chr15	60367446	.	C	T	44	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=41	PL:GT:GQ	76,9,0:1/1:63
+chr15	61763755	.	G	A	68	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=45	PL:GT:GQ	100,9,0:1/1:63
+chr15	61831362	.	C	G	11.3	.	DP=5;AF1=0.5;CI95=0.5,0.5;DP4=0,2,0,3;MQ=30;PV4=1,0.00077,0.47,1	PL:GT:GQ	41,0,42:0/1:41
+chr15	63978880	.	G	C	60	.	DP=6;AF1=0.9999;CI95=0.5,1;DP4=2,0,4,0;MQ=35;PV4=1,1,1,1	PL:GT:GQ	90,3,0:1/1:41
+chr15	64342445	.	A	G	12.2	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=18	PL:GT:GQ	44,9,0:1/1:63
+chr15	65424859	.	T	C	11.3	.	DP=10;AF1=1;CI95=1,1;DP4=0,0,0,10;MQ=21	PL:GT:GQ	44,30,0:1/1:99
+chr15	65603698	.	C	T	60	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=49	PL:GT:GQ	92,9,0:1/1:63
+chr15	67005078	.	G	A	13.9	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35	PL:GT:GQ	45,6,0:1/1:49
+chr15	71133512	.	G	C	22.3	.	DP=19;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=25	PL:GT:GQ	55,15,0:1/1:75
+chr15	72619009	.	A	G	22	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=48	PL:GT:GQ	54,9,0:1/1:63
+chr15	73272688	.	C	T	70.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=39	PL:GT:GQ	103,15,0:1/1:75
+chr15	73699335	.	T	A	99	.	DP=9;AF1=1;CI95=1,1;DP4=0,0,0,9;MQ=45	PL:GT:GQ	175,27,0:1/1:99
+chr15	74513352	.	C	T	99	.	DP=10;AF1=1;CI95=1,1;DP4=0,0,0,10;MQ=37	PL:GT:GQ	139,30,0:1/1:99
+chr15	75540536	.	G	A	9.31	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=44	PL:GT:GQ	40,6,0:1/1:49
+chr15	75822537	.	C	A	17.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=23	PL:GT:GQ	50,15,0:1/1:75
+chr15	78554005	.	T	C	12	.	DP=18;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=46	PL:GT:GQ	43,6,0:1/1:49
+chr15	80089369	.	G	A	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=28	PL:GT:GQ	40,6,0:1/1:49
+chr15	83089149	.	C	G	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=33	PL:GT:GQ	40,6,0:1/1:49
+chr15	86839307	.	T	C	90.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=43	PL:GT:GQ	123,15,0:1/1:75
+chr15	89836258	.	T	C	99	.	DP=10;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=39	PL:GT:GQ	141,24,0:1/1:96
+chr15	89837706	.	G	A	4.13	.	DP=8;AF1=0.4998;CI95=0.5,0.5;DP4=0,4,0,4;MQ=30;PV4=1,1,0.25,1	PL:GT:GQ	32,0,59:0/1:35
+chr15	89857648	.	T	C	99	.	DP=27;AF1=0.5;CI95=0.5,0.5;DP4=8,0,8,0;MQ=40;PV4=1,1,0.3,1	PL:GT:GQ	133,0,130:0/1:99
+chr15	89864228	.	A	C	32	.	DP=4;AF1=0.5002;CI95=0.5,0.5;DP4=2,0,2,0;MQ=42;PV4=1,1,1,1	PL:GT:GQ	62,0,31:0/1:34
+chr15	91261235	.	G	A	7.8	.	DP=4;AF1=0.5002;CI95=0.5,0.5;DP4=1,0,2,0;MQ=44;PV4=1,1,0.32,1	PL:GT:GQ	37,0,30:0/1:32
+chr16	256990	.	A	C	10.4	.	DP=16;AF1=0.5008;CI95=0.5,0.5;DP4=4,0,3,0;MQ=23;PV4=1,0.34,1,1	PL:GT:GQ	40,0,25:0/1:28
+chr16	260794	.	T	C	3.01	.	DP=19;AF1=0.4999;CI95=0.5,0.5;DP4=13,0,2,0;MQ=24;PV4=1,1,1,1	PL:GT:GQ	30,0,32:0/1:31
+chr16	419905	.	A	G	7.9	.	DP=5;AF1=0.9966;CI95=0.5,1;DP4=0,2,0,3;MQ=22;PV4=1,1,1,1	PL:GT:GQ	36,1,0:1/1:23
+chr16	824086	.	T	C	22	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=48	PL:GT:GQ	54,9,0:1/1:63
+chr16	1085063	.	C	T	52	.	DP=12;AF1=0.5;CI95=0.5,0.5;DP4=6,0,6,0;MQ=42;PV4=1,1,0.014,1	PL:GT:GQ	82,0,128:0/1:85
+chr16	1221305	.	T	C	54	.	DP=7;AF1=0.5;CI95=0.5,0.5;DP4=0,3,0,3;MQ=40;PV4=1,1,1,1	PL:GT:GQ	84,0,60:0/1:63
+chr16	1411728	.	A	G	32.3	.	DP=11;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=35	PL:GT:GQ	65,15,0:1/1:75
+chr16	1443197	.	C	G	64	.	DP=26;AF1=1;CI95=1,1;DP4=0,0,25,0;MQ=36	PL:GT:GQ	97,75,0:1/1:99
+chr16	1478746	.	A	T	32	.	DP=20;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=28	PL:GT:GQ	65,24,0:1/1:96
+chr16	1514438	.	A	C	45	.	DP=49;AF1=1;CI95=1,1;DP4=0,0,48,0;MQ=26	PL:GT:GQ	78,144,0:1/1:99
+chr16	1601989	.	T	C	99	.	DP=13;AF1=1;CI95=1,1;DP4=0,0,13,0;MQ=29	PL:GT:GQ	133,39,0:1/1:99
+chr16	2043883	.	C	T	30	.	DP=33;AF1=1;CI95=1,1;DP4=0,0,0,33;MQ=14	PL:GT:GQ	63,99,0:1/1:99
+chr16	2137470	.	A	C	39	.	DP=38;AF1=0.5016;CI95=0.5,0.5;DP4=4,0,6,0;MQ=34;PV4=1,0.02,1,1	PL:GT:GQ	69,0,22:0/1:25
+chr16	2537260	.	A	G	99	.	DP=11;AF1=1;CI95=1,1;DP4=0,0,11,0;MQ=40	PL:GT:GQ	177,33,0:1/1:99
+chr16	2564737	.	T	C	99	.	DP=25;AF1=1;CI95=1,1;DP4=0,0,0,22;MQ=41	PL:GT:GQ	199,66,0:1/1:99
+chr16	2612605	.	A	T	62.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=28	PL:GT:GQ	95,15,0:1/1:75
+chr16	2704518	.	G	A	41	.	DP=48;AF1=0.5;CI95=0.5,0.5;DP4=0,17,0,12;MQ=48;PV4=1,1.9e-23,0.24,0.034	PL:GT:GQ	71,0,175:0/1:74
+chr16	3274307	.	G	T	68	.	DP=39;AF1=0.5;CI95=0.5,0.5;DP4=0,30,0,8;MQ=37;PV4=1,1,1,1	PL:GT:GQ	98,0,138:0/1:99
+chr16	5467292	.	G	C	37.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49	PL:GT:GQ	69,6,0:1/1:49
+chr16	10079145	.	A	G	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49	PL:GT:GQ	73,6,0:1/1:49
+chr16	11483702	.	A	G	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=44	PL:GT:GQ	40,6,0:1/1:49
+chr16	12038227	.	A	T	23	.	DP=47;AF1=0.5;CI95=0.5,0.5;DP4=0,22,0,23;MQ=32;PV4=1,4.4e-66,0.47,0.028	PL:GT:GQ	53,0,135:0/1:56
+chr16	21336880	.	G	C	55	.	DP=35;AF1=0.5;CI95=0.5,0.5;DP4=0,12,0,19;MQ=47;PV4=1,5.6e-21,1,1	PL:GT:GQ	85,0,121:0/1:88
+chr16	21980241	.	C	T	16.1	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=29	PL:GT:GQ	48,9,0:1/1:63
+chr16	23275383	.	C	G	13	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47	PL:GT:GQ	44,6,0:1/1:49
+chr16	27546495	.	G	T	25	.	DP=35;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=43	PL:GT:GQ	57,9,0:1/1:63
+chr16	27700399	.	A	T	17.6	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=17	PL:GT:GQ	50,12,0:1/1:72
+chr16	28021935	.	A	G	18.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=23	PL:GT:GQ	51,15,0:1/1:75
+chr16	29070016	.	G	T	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47	PL:GT:GQ	40,6,0:1/1:49
+chr16	29478618	.	C	T	11.3	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=42	PL:GT:GQ	43,9,0:1/1:63
+chr16	29718140	.	C	T	46.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=31	PL:GT:GQ	79,15,0:1/1:75
+chr16	30700759	.	T	C	17.1	.	DP=14;AF1=1;CI95=1,1;DP4=0,0,0,14;MQ=14	PL:GT:GQ	50,42,0:1/1:99
+chr16	35139103	.	A	G	46.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=37	PL:GT:GQ	79,12,0:1/1:72
+chr16	35473348	.	G	A	3.83	.	DP=11;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=25	PL:GT:GQ	34,12,0:1/1:72
+chr16	36213667	.	A	G	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49	PL:GT:GQ	73,6,0:1/1:49
+chr16	36705528	.	G	A	14.4	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=32	PL:GT:GQ	47,15,0:1/1:75
+chr16	43831353	.	C	T	69.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=42	PL:GT:GQ	102,12,0:1/1:72
+chr16	44715166	.	A	C	25	.	DP=18;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=32	PL:GT:GQ	58,24,0:1/1:96
+chr16	44957661	.	T	C	7.03	.	DP=23;AF1=1;CI95=1,1;DP4=0,0,0,7;MQ=18	PL:GT:GQ	39,21,0:1/1:84
+chr16	44958698	.	C	T	42.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=49	PL:GT:GQ	75,15,0:1/1:75
+chr16	44959163	.	T	C	33.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=48	PL:GT:GQ	66,12,0:1/1:72
+chr16	45167959	.	C	T	4.45	.	DP=16;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=24	PL:GT:GQ	35,12,0:1/1:72
+chr16	50254956	.	C	T	13.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=36	PL:GT:GQ	45,6,0:1/1:49
+chr16	52383122	.	A	C	46.5	.	DP=19;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=42	PL:GT:GQ	79,12,0:1/1:72
+chr16	55978159	.	C	T	10.7	.	DP=20;AF1=0.5336;CI95=0.5,1;DP4=2,0,5,0;MQ=35;PV4=1,0.038,1,0.059	PL:GT:GQ	40,0,9:0/1:12
+chr16	61358878	.	T	A	15.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=32	PL:GT:GQ	47,6,0:1/1:49
+chr16	61392487	.	G	A	13	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=31	PL:GT:GQ	44,6,0:1/1:49
+chr16	61621603	.	G	T	6.59	.	DP=10;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=22	PL:GT:GQ	38,12,0:1/1:72
+chr16	69120890	.	G	C	51.3	.	DP=36;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=42	PL:GT:GQ	84,15,0:1/1:75
+chr16	70778219	.	A	G	21.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=39	PL:GT:GQ	53,6,0:1/1:49
+chr16	71899519	.	T	C	40	.	DP=11;AF1=1;CI95=1,1;DP4=0,0,11,0;MQ=33	PL:GT:GQ	73,33,0:1/1:99
+chr16	72079251	.	A	G	11.3	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=41	PL:GT:GQ	43,9,0:1/1:63
+chr16	72093003	.	G	C	9.31	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49	PL:GT:GQ	40,6,0:1/1:49
+chr16	72672428	.	A	G	68	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=49	PL:GT:GQ	100,9,0:1/1:63
+chr16	72864515	.	A	G	13.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35	PL:GT:GQ	45,6,0:1/1:49
+chr16	72890560	.	G	A	47.1	.	DP=10;AF1=0.5064;CI95=0.5,0.5;DP4=0,1,0,7;MQ=49;PV4=1,0.0019,0.0033,1	PL:GT:GQ	77,0,16:0/1:19
+chr16	73048929	.	A	G	6.29	.	DP=4;AF1=0.9966;CI95=0.5,1;DP4=1,0,2,0;MQ=27;PV4=1,1,1,0.33	PL:GT:GQ	34,1,0:1/1:23
+chr16	73177179	.	A	G	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49	PL:GT:GQ	40,6,0:1/1:49
+chr16	73191468	.	C	T	69.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=40	PL:GT:GQ	102,12,0:1/1:72
+chr16	73367439	.	A	C	7.41	.	DP=36;AF1=1;CI95=0.5,1;DP4=0,2,0,13;MQ=26;PV4=1,1,0.027,1	PL:GT:GQ	37,4,0:1/1:45
+chr16	74259316	.	C	T	89.5	.	DP=13;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=49	PL:GT:GQ	122,12,0:1/1:72
+chr16	75271450	.	C	G	6.99	.	DP=15;AF1=0.5015;CI95=0.5,0.5;DP4=0,1,0,3;MQ=44;PV4=1,0.065,0.31,1	PL:GT:GQ	36,0,22:0/1:25
+chr16	76199870	.	G	A	26	.	DP=14;AF1=0.5;CI95=0.5,0.5;DP4=8,0,6,0;MQ=47;PV4=1,1.2e-06,0.32,1	PL:GT:GQ	56,0,141:0/1:59
+chr16	77723692	.	A	G	89.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=50	PL:GT:GQ	122,12,0:1/1:72
+chr17	165875	.	G	A	40.8	.	DP=11;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=42	PL:GT:GQ	72,6,0:1/1:49
+chr17	1443809	.	C	G	9.31	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=50	PL:GT:GQ	40,6,0:1/1:49
+chr17	1618253	.	C	T	22	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=39	PL:GT:GQ	54,9,0:1/1:63
+chr17	2815309	.	T	G	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49	PL:GT:GQ	40,6,0:1/1:49
+chr17	3537486	.	T	G	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=50	PL:GT:GQ	73,6,0:1/1:49
+chr17	3734367	.	C	A	23.5	.	DP=10;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=36	PL:GT:GQ	56,12,0:1/1:72
+chr17	5634764	.	T	C	13	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35	PL:GT:GQ	44,6,0:1/1:49
+chr17	6408090	.	C	G	3.54	.	DP=5;AF1=0.4998;CI95=0.5,0.5;DP4=3,0,2,0;MQ=40;PV4=1,1,0.36,1	PL:GT:GQ	31,0,66:0/1:34
+chr17	7089723	.	A	G	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=47	PL:GT:GQ	40,6,0:1/1:49
+chr17	8731503	.	G	C	11.1	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=46	PL:GT:GQ	42,6,0:1/1:49
+chr17	9282935	.	T	C,G	24.5	.	DP=10;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=40	PL:GT:GQ	57,12,61,0,3,61:1/1:72
+chr17	17284831	.	T	C	29	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=25	PL:GT:GQ	61,9,0:1/1:63
+chr17	18439515	.	G	A	4.11	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=25	PL:GT:GQ	34,9,0:1/1:63
+chr17	18602146	.	C	T	4.76	.	DP=20;AF1=1;CI95=1,1;DP4=0,0,0,11;MQ=16	PL:GT:GQ	36,33,0:1/1:99
+chr17	19427888	.	C	T	57	.	DP=104;AF1=0.5;CI95=0.5,0.5;DP4=45,0,29,0;MQ=39;PV4=1,2.2e-12,1,1	PL:GT:GQ	87,0,131:0/1:90
+chr17	19604159	.	T	C	9.31	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=45	PL:GT:GQ	40,6,0:1/1:49
+chr17	19610366	.	C	T	13	.	DP=13;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48	PL:GT:GQ	44,6,0:1/1:49
+chr17	20484706	.	C	G	51	.	DP=35;AF1=0.5001;CI95=0.5,0.5;DP4=0,11,0,21;MQ=21;PV4=1,0.39,0.49,1	PL:GT:GQ	81,0,36:0/1:39
+chr17	20555720	.	A	G	26.3	.	DP=8;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=28	PL:GT:GQ	59,15,0:1/1:75
+chr17	24328984	.	A	C	15.4	.	DP=34;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=25	PL:GT:GQ	48,15,0:1/1:75
+chr17	26237090	.	G	A	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=44	PL:GT:GQ	73,6,0:1/1:49
+chr17	28394766	.	C	A	13.9	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=31	PL:GT:GQ	45,6,0:1/1:49
+chr17	31218277	.	A	G	3.62	.	DP=38;AF1=0.5161;CI95=0.5,0.5;DP4=0,1,0,2;MQ=38;PV4=1,0.26,1,1	PL:GT:GQ	31,0,12:0/1:15
+chr17	31254021	.	C	T	15.1	.	DP=10;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=35	PL:GT:GQ	47,9,0:1/1:63
+chr17	32516798	.	G	A	37.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49	PL:GT:GQ	69,6,0:1/1:49
+chr17	32600253	.	A	G	16.6	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=25	PL:GT:GQ	49,12,0:1/1:72
+chr17	34255214	.	G	C	19.2	.	DP=8;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=21	PL:GT:GQ	52,18,0:1/1:90
+chr17	34365900	.	T	C	93.1	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=38	PL:GT:GQ	126,18,0:1/1:90
+chr17	35380386	.	A	T	6.79	.	DP=44;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=46	PL:GT:GQ	37,6,0:1/1:49
+chr17	41993344	.	C	T	64	.	DP=41;AF1=1;CI95=1,1;DP4=0,0,0,41;MQ=16	PL:GT:GQ	97,123,0:1/1:99
+chr17	42128201	.	A	G	4.13	.	DP=5;AF1=0.4998;CI95=0.5,0.5;DP4=0,2,0,2;MQ=52;PV4=1,0.0041,1,1	PL:GT:GQ	32,0,62:0/1:35
+chr17	42984490	.	C	A	56	.	DP=33;AF1=0.5001;CI95=0.5,0.5;DP4=6,0,12,0;MQ=42;PV4=1,0.004,1,1	PL:GT:GQ	86,0,34:0/1:37
+chr17	43419457	.	G	A	99	.	DP=16;AF1=1;CI95=1,1;DP4=0,0,0,14;MQ=45	PL:GT:GQ	185,42,0:1/1:99
+chr17	43421225	.	A	G	65.1	.	DP=31;AF1=1;CI95=0.5,1;DP4=0,6,0,17;MQ=43;PV4=1,0.004,1,1	PL:GT:GQ	98,18,0:1/1:90
+chr17	45206897	.	G	A	22	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=47	PL:GT:GQ	54,9,0:1/1:63
+chr17	45381302	.	T	C	18.6	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=25	PL:GT:GQ	51,12,0:1/1:72
+chr17	45530812	.	C	A	3.54	.	DP=6;AF1=0.4998;CI95=0.5,0.5;DP4=0,3,0,2;MQ=40;PV4=1,1,0.37,1	PL:GT:GQ	31,0,58:0/1:34
+chr17	50242633	.	G	A	44	.	DP=42;AF1=0.5;CI95=0.5,0.5;DP4=0,25,0,13;MQ=32;PV4=1,0.084,0.14,1	PL:GT:GQ	74,0,154:0/1:77
+chr17	51275317	.	G	A	14.9	.	DP=10;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=31	PL:GT:GQ	46,6,0:1/1:49
+chr17	52325530	.	C	T	29	.	DP=19;AF1=1;CI95=1,1;DP4=0,0,0,18;MQ=24	PL:GT:GQ	62,54,0:1/1:99
+chr17	52411748	.	T	G	18.6	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=25	PL:GT:GQ	51,12,0:1/1:72
+chr17	53190746	.	C	G	62.1	.	DP=20;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=40	PL:GT:GQ	95,18,0:1/1:90
+chr17	58289916	.	T	C	18.2	.	DP=8;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=22	PL:GT:GQ	51,18,0:1/1:90
+chr17	59796875	.	C	T	42	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=35	PL:GT:GQ	74,9,0:1/1:63
diff --git a/tests/tabix_data/vcf/13.vcf b/tests/tabix_data/vcf/13.vcf
new file mode 100644
index 0000000..08b54e0
--- /dev/null
+++ b/tests/tabix_data/vcf/13.vcf
@@ -0,0 +1,220 @@
+##fileformat=VCFv4.0
+##fileDate=2011-10-11
+##source=Platypus_Version_0.1.5
+##INFO=<ID=func,Number=1,Type=String,Description="Functional category: exnoic, intergenic etc">
+##INFO=<ID=gene,Number=2,Type=String,Description="RefSeq gene name">
+##INFO=<ID=exon_func,Number=1,Type=String,Description="Exonic function of the variant">
+##INFO=<ID=AAchange,Number=1,Type=String,Description="Amino Acid change">
+##INFO=<ID=cons46,Number=1,Type=String,Description="UCSC 46 species conservation score">
+##INFO=<ID=segdup,Number=1,Type=Float,Description="UCSC segment duplication score">
+##INFO=<ID=1000g,Number=1,Type=Float,Description="1000 genomes allelic frequency">
+##INFO=<ID=dbsnp,Number=1,Type=String,Description="dbSNP ID">
+##INFO=<ID=sift,Number=1,Type=Float,Description="SIFT score">
+##INFO=<ID=pp2,Number=1,Type=Float,Description="PolyPhen2 score">
+##INFO=<ID=phylop,Number=1,Type=Float,Description="Phylop score">
+##INFO=<ID=mutT,Number=1,Type=Float,Description="Mutation Taster score">
+##INFO=<ID=LRT,Number=1,Type=Float,Description="LRT score">
+##INFO=<ID=FR,Number=0,Type=Float,Description="Estimated population frequency">
+##INFO=<ID=RPV,Number=0,Type=Float,Description="Median minimum base quality for bases around variant">
+##INFO=<ID=RPV,Number=0,Type=Float,Description="Reverse strand p-value">
+##INFO=<ID=TCR,Number=0,Type=Integer,Description="Total reverse strand coverage at this locus">
+##INFO=<ID=HP,Number=1,Type=Integer,Description="Homopolmer run length">
+##INFO=<ID=ABPV,Number=0,Type=Float,Description="Allele-bias p-value. Testing for low variant coverage">
+##INFO=<ID=TR,Number=0,Type=Integer,Description="Total number of reads containing this variant">
+##INFO=<ID=PP,Number=0,Type=Float,Description="Posterior probability (phred scaled) that this variant segregates">
+##INFO=<ID=NF,Number=0,Type=Integer,Description="Total number of forward reads containing this variant">
+##INFO=<ID=SC,Number=1,Type=String,Description="Genomic sequence 10 bases either side of variant position">
+##INFO=<ID=FPV,Number=0,Type=Float,Description="Forward strand p-value">
+##INFO=<ID=TCF,Number=0,Type=Integer,Description="Total forward strand coverage at this locus">
+##INFO=<ID=NR,Number=0,Type=Integer,Description="Total number of reverse reads containing this variant">
+##INFO=<ID=RMP,Number=0,Type=Float,Description="RMS Position in reads of Variant">
+##INFO=<ID=TC,Number=0,Type=Integer,Description="Total coverage at this locus">
+##FILTER=<ID=sb,Description="Variant fails strand-bias filter">
+##FILTER=<ID=ab,Description="Variant fails allele-bias filter">
+##FILTER=<ID=badReads,Description="Variant supported only by reads with low quality bases close to variant position, and not present on both strands.">
+##FILTER=<ID=hp10,Description="Flanking sequence contains homopolymer of length 10 or greater">
+##FORMAT=<ID=GL,Number=.,Type=Float,Description="Genotype log-likelihoods (log10) for AA,AB and BB genotypes, where A = ref and B = variant. Only applicable for bi-allelic sites">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Unphased genotypes">
+##FORMAT=<ID=NR,Number=1,Type=Integer,Description="Number of reads covering variant in this sample">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype quality, as Phred score">
+##FORMAT=<ID=GT:GL:GQ:NR,Number=.,Type=String,Description="(Undefined tag)">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	WTCHG_27173_05.bam	WTCHG_27173_04.bam
+chr1	1451489	.	T	C	103	PASS	ABPV=1.00e+00;FPV=7.56e-01;FR=0.2501;HP=7;MMLQ=30;NF=2;NR=18;PP=103;RMP=57.54;RPV=1.00e-00;SC=CCGGTGTGGGTGGGGAGGCCG;TC=42;TCF=7;TCR=35;TR=20;func=intronic;gene=ATAD3A;segdup=0.91;1000g=0.36;dbsnp=rs76717221	GT:GL:GQ:NR	0/0:-43.28,-51.0,-125.34:35:18	1/0:-135.58,-103.29,-138.87:100:24
+chr1	1451490	.	G	A	73	PASS	ABPV=1.00e+00;FPV=9.29e-01;FR=0.2501;HP=3;MMLQ=30;NF=3;NR=16;PP=73;RMP=58.79;RPV=9.98e-01;SC=CGGTGTGGGTGGGGAGGCCGG;TC=42;TCF=7;TCR=35;TR=19;func=intronic;gene=ATAD3A;segdup=0.91;1000g=0.33;dbsnp=rs9439460	GT:GL:GQ:NR	0/0:-43.28,-50.99,-127.79:35:18	0/1:-135.58,-110.35,-146.87:100:24
+chr1	12939904	.	A	C	109	PASS	ABPV=1.00e+00;FPV=7.66e-01;FR=0.2500;HP=1;MMLQ=37;NF=22;NR=1;PP=109;RMP=45.66;RPV=4.46e-06;SC=ATTGTGAGGAACTTTAACGAG;TC=132;TCF=79;TCR=53;TR=23	GT:GL:GQ:NR	0/0:-40.31,-50.48,-301.89:45:53	0/1:-121.0,-87.39,-396.61:100:79
+chr1	16902943	.	T	C	50	PASS	ABPV=1.00e+00;FPV=2.90e-01;FR=0.2506;HP=2;MMLQ=34;NF=30;NR=18;PP=50;RMP=46.42;RPV=8.84e-01;SC=GGGTCAGCTCTCGTTCCTGAG;TC=191;TCF=133;TCR=58;TR=48	GT:GL:GQ:NR	0/0:-337.26,-342.92,-618.53:26:93	0/1:-428.71,-408.75,-668.15:84:98
+chr1	16902982	.	G	T	41	PASS	ABPV=1.00e+00;FPV=5.26e-02;FR=0.2500;HP=1;MMLQ=36;NF=29;NR=10;PP=41;RMP=55.68;RPV=1.90e-02;SC=ATTGCCTAAGGTGAGACGGTA;TC=223;TCF=152;TCR=71;TR=39	GT:GL:GQ:NR	0/0:-282.16,-293.75,-760.18:52:108	0/1:-308.83,-290.99,-786.16:75:115
+chr1	16918180	.	C	T	200	PASS	ABPV=1.00e+00;FPV=7.60e-05;FR=0.2500;HP=1;MMLQ=37;NF=8;NR=11;PP=200;RMP=57.84;RPV=6.15e-01;SC=TACTTTGGTACCTCTGTCTTC;TC=134;TCF=91;TCR=43;TR=19	GT:GL:GQ:NR	0/0:-48.3,-68.7,-289.28:90:47	0/1:-194.28,-132.13,-452.09:100:87
+chr1	17083652	.	C	T	200	PASS	ABPV=3.06e-02;FPV=6.38e-13;FR=0.2500;HP=2;MMLQ=36;NF=29;NR=3;PP=200;RMP=38.16;RPV=2.05e-02;SC=AAATCTCAACCTTGAGTACAA;TC=350;TCF=317;TCR=33;TR=32;func=ncRNA;gene=MST1P9;cons46=632 Name=lod=492;segdup=0.99;1000g=0.37;dbsnp=rs113710576	GT:GL:GQ:NR	0/0:-547.14,-559.85,-1017.76:56:159	0/1:-723.35,-656.42,-1167.76:100:191
+chr1	17083776	.	C	A	79	PASS	ABPV=1.08e-01;FPV=7.38e-01;FR=0.2500;HP=1;MMLQ=35;NF=1;NR=22;PP=79;RMP=76.99;RPV=1.13e-09;SC=CACAGAGACACGCGTGAAGAC;TC=238;TCF=4;TCR=234;TR=23;func=ncRNA;gene=MST1P9;cons46=632 Name=lod=492;segdup=0.99;1000g=0.20;dbsnp=rs56318124	GT:GL:GQ:NR	0/0:-442.45,-455.85,-790.66:59:121	0/1:-451.84,-425.21,-717.41:100:117
+chr1	17575714	.	G	A	59	PASS	ABPV=2.52e-01;FPV=3.10e-02;FR=0.2500;HP=1;MMLQ=31;NF=1;NR=4;PP=59;RMP=43.35;RPV=1.94e-02;SC=GACCCTCGTGGACATTTATGG;TC=58;TCF=19;TCR=39;TR=5	GT:GL:GQ:NR	0/0:-14.49,-33.87,-234.95:85:32	0/1:-39.36,-17.32,-168.9:93:26
+chr1	21751228	.	T	TCGCGCCCGGC	66	PASS	ABPV=3.86e-06;FPV=8.03e-37;FR=0.2500;HP=4;NF=1;NR=1;PP=66;RMP=15.56;RPV=1.98e-06;SC=CTCAAATGAGTAAAAGGCACT;TC=133;TCF=77;TCR=56;TR=2	GT:GL:GQ:NR	0/0:-178.34,-190.57,-398.5:54:72	0/1:-308.3,-271.14,-540.05:100:98
+chr1	21755539	.	C	A	27	PASS	ABPV=1.00e+00;FPV=9.84e-01;FR=0.2503;HP=1;MMLQ=31;NF=2;NR=1;PP=27;RMP=65.83;RPV=4.98e-02;SC=GGCCAACAACCGCCAGGTGCG;TC=20;TCF=3;TCR=17;TR=3;func=intergenic;gene=ECE1(dist=83505) NBPF3(dist=11092);cons46=807 Name=lod=2532;segdup=0.99;1000g=0.80;dbsnp=rs3855556	GT:GL:GQ:NR	0/0:0.0,-6.22,-62.68:28:10	1/0:-21.51,-6.92,-52.98:61:10
+chr1	40798730	.	A	AT	59	PASS	ABPV=1.00e+00;FPV=6.06e-01;FR=0.2504;HP=10;NF=7;NR=1;PP=59;RMP=50.29;RPV=7.38e-01;SC=GAAGTCTTCTATTTTTTTTTA;TC=28;TCF=24;TCR=4;TR=8;func=intergenic;gene=COL9A2(dist=15791) SMAP2(dist=40648);dbsnp=rs34372767	GT:GL:GQ:NR	0/0:0.0,-6.13,-39.37:28:12	0/1:-35.97,-10.49,-31.53:98:16
+chr1	142803580	.	TA	T	145	PASS	ABPV=1.00e+00;FPV=6.35e-02;FR=0.2500;HP=6;NF=1;NR=11;PP=145;RMP=65.89;RPV=8.29e-02;SC=TTCATAGATTTAAAAAATTAT;TC=81;TCF=16;TCR=65;TR=12	GT:GL:GQ:NR	0/0:-39.18,-49.93,-242.54:48:33	1/0:-80.12,-35.74,-249.72:100:48
+chr1	144854799	.	C	T	50	PASS	ABPV=1.00e+00;FPV=9.37e-01;FR=0.2504;HP=1;MMLQ=34;NF=1;NR=19;PP=50;RMP=60.89;RPV=9.86e-01;SC=GCCTCGGATACCTCCAGCTGA;TC=52;TCF=2;TCR=50;TR=20;func=intronic;gene=PDE4DIP;segdup=0.96;dbsnp=rs5004097	GT:GL:GQ:NR	0/0:-89.24,-95.22,-205.12:27:25	0/1:-177.25,-157.18,-246.67:85:27
+chr1	145116027	.	T	C	127	PASS	ABPV=1.00e+00;FPV=1.00e+00;FR=0.2501;HP=2;MMLQ=34;NF=0;NR=7;PP=127;RMP=54.07;RPV=5.14e-01;SC=AAAAGAGATGTCCTGAAAATG;TC=30;TCF=0;TCR=30;TR=7;func=UTR3;gene=SEC22B;cons46=340 Name=lod=32;1000g=0.45;dbsnp=rs7550440	GT:GL:GQ:NR	0/0:0.0,-7.61,-92.94:34:11	0/1:-56.84,-19.14,-106.99:100:19
+chr1	146554532	.	C	T	57	PASS	ABPV=1.00e+00;FPV=5.18e-01;FR=0.2501;HP=12;MMLQ=31;NF=4;NR=5;PP=57;RMP=66.19;RPV=4.68e-01;SC=CTTCTTCTTTCTTTTTTTTTA;TC=41;TCF=18;TCR=23;TR=9;func=intergenic;gene=LOC728989(dist=39933) PRKAB2(dist=72153);segdup=0.93;dbsnp=rs9662613	GT:GL:GQ:NR	0/0:-13.82,-21.42,-95.53:34:13	0/1:-131.76,-110.18,-223.87:91:28
+chr1	148344564	.	T	C	34	PASS	ABPV=3.69e-01;FPV=1.16e-03;FR=0.2500;HP=2;MMLQ=36;NF=24;NR=1;PP=34;RMP=22.65;RPV=1.98e-06;SC=TTCGTTCTTATTTCTCCCCGC;TC=218;TCF=162;TCR=56;TR=25	GT:GL:GQ:NR	0/0:-210.1,-224.84,-651.44:65:104	0/1:-232.74,-216.41,-586.14:69:114
+chr1	148853862	.	G	T	37	PASS	ABPV=3.79e-01;FPV=1.94e-02;FR=0.2500;HP=3;MMLQ=31;NF=6;NR=2;PP=37;RMP=50.34;RPV=2.58e-02;SC=CGCTCCTGGAGCCCAGCCCGG;TC=76;TCF=50;TCR=26;TR=8	GT:GL:GQ:NR	0/0:-247.75,-257.0,-317.61:41:35	1/0:-179.5,-162.62,-280.47:71:41
+chr1	148854004	.	C	T	32	PASS	ABPV=1.83e-01;FPV=3.17e-02;FR=0.2500;HP=1;MMLQ=34;NF=0;NR=3;PP=32;RMP=93.74;RPV=2.52e-02;SC=GCCCGCACTGCTGCAGCGCCC;TC=44;TCF=12;TCR=32;TR=3	GT:GL:GQ:NR	0/0:-75.02,-87.66,-197.34:56:26	1/0:-55.07,-39.25,-94.0:66:18
+chr1	152187606	.	G	A	200	PASS	ABPV=3.64e-01;FPV=4.08e-07;FR=0.2500;HP=2;MMLQ=32;NF=7;NR=16;PP=200;RMP=30.4;RPV=4.89e-02;SC=GAAGACTGACGGGAGCCAGAC;TC=202;TCF=109;TCR=93;TR=23;func=exonic;gene=HRNR;exon_func=nonsynonymous SNV;AAchange=NM_001009931:c.C6499T:p.R2167C;segdup=0.98;1000g=0.05;sift=0.2;pp2=0.269490;phylop=0.009549;mutT=0.062064;LRT=0.589002	GT:GL:GQ:NR	0/0:-190.82,-206.2,-650.62:68:98	0/1:-306.73,-239.37,-605.74:100:104
+chr1	152281007	.	A	G	38	PASS	ABPV=1.00e+00;FPV=2.01e-01;FR=0.2500;HP=1;MMLQ=31;NF=37;NR=62;PP=38;RMP=56.83;RPV=9.75e-01;SC=GCCTGATCATAATGGGATCCT;TC=370;TCF=169;TCR=201;TR=99	GT:GL:GQ:NR	0/0:-830.31,-842.03,-1695.93:52:178	0/1:-1104.87,-1087.65,-1851.72:72:192
+chr1	152281008	.	A	G	56	PASS	ABPV=1.00e+00;FPV=2.26e-01;FR=0.2500;HP=1;MMLQ=31;NF=37;NR=62;PP=56;RMP=57.69;RPV=9.75e-01;SC=CCTGATCATAATGGGATCCTT;TC=368;TCF=167;TCR=201;TR=99	GT:GL:GQ:NR	0/0:-836.29,-850.28,-1704.3:62:178	1/0:-1097.96,-1076.67,-1811.19:90:190
+chr1	152281466	.	C	T	200	PASS	ABPV=1.00e+00;FPV=3.99e-04;FR=0.2500;HP=2;MMLQ=33;NF=26;NR=66;PP=200;RMP=66.62;RPV=7.23e-01;SC=TGCCCGTGACCGGCTCTGTCT;TC=430;TCF=180;TCR=250;TR=92	GT:GL:GQ:NR	0/0:-912.94,-966.99,-1954.85:100:223	1/0:-939.3,-872.22,-1720.42:100:207
+chr1	168549565	.	T	C	28	PASS	ABPV=1.00e+00;FPV=1.00e+00;FR=0.2504;HP=2;MMLQ=37;NF=0;NR=8;PP=28;RMP=72.28;RPV=1.34e-01;SC=TCCTTATCAATCATGTCTTTC;TC=47;TCF=0;TCR=47;TR=8	GT:GL:GQ:NR	0/0:-27.57,-33.72,-167.32:28:21	1/0:-34.62,-19.62,-182.0:63:26
+chr1	236647542	.	G	T	46	PASS	ABPV=1.00e+00;FPV=9.99e-01;FR=0.2500;HP=3;MMLQ=34;NF=16;NR=40;PP=46;RMP=62.31;RPV=1.00e-00;SC=GTGCAAGCTGGCCCAGGCCAA;TC=104;TCF=32;TCR=72;TR=56	GT:GL:GQ:NR	0/0:-318.17,-328.23,-521.3:45:54	1/0:-498.22,-479.17,-572.27:80:50
+chr1	236647562	.	T	C	73	PASS	ABPV=1.00e+00;FPV=9.95e-01;FR=0.2503;HP=2;MMLQ=37;NF=11;NR=36;PP=73;RMP=64.25;RPV=1.00e-00;SC=ATGGTTGGTGTGTCATGGTGC;TC=85;TCF=23;TCR=62;TR=47	GT:GL:GQ:NR	0/0:-240.39,-246.81,-405.51:29:42	0/1:-421.95,-396.59,-483.66:100:43
+chr1	236700807	.	T	A	130	PASS	ABPV=1.00e+00;FPV=5.12e-01;FR=0.2502;HP=2;MMLQ=33;NF=8;NR=7;PP=130;RMP=47.87;RPV=8.70e-01;SC=GTAATCCCGTTTGTTGGCACC;TC=55;TCF=34;TCR=21;TR=15;func=exonic;gene=LGALS8;exon_func=nonsynonymous SNV;AAchange=NM_201544:c.T56A:p.F19Y;cons46=463 Name=lod=102;1000g=0.62;dbsnp=rs2737713;pp2=0.0;phylop=0.983932;mutT=4.6E-5;LRT=0.999982	GT:GL:GQ:NR	0/0:-41.35,-48.14,-183.02:31:21	0/1:-204.57,-166.19,-295.14:100:34
+chr1	236700823	.	T	C	200	PASS	ABPV=1.00e+00;FPV=6.24e-01;FR=0.2504;HP=2;MMLQ=32;NF=9;NR=8;PP=200;RMP=58.62;RPV=8.49e-01;SC=GCACCATTCCTGATCAGCTGG;TC=60;TCF=35;TCR=25;TR=17;func=exonic;gene=LGALS8;exon_func=synonymous SNV;AAchange=NM_201544:c.T72C:p.P24P;cons46=463 Name=lod=102;1000g=0.61;dbsnp=rs1041934	GT:GL:GQ:NR	0/0:-41.35,-47.43,-173.43:28:22	1/0:-232.08,-183.12,-325.41:100:38
+chr1	241663902	.	TGA	T	37	PASS	ABPV=2.57e-03;FPV=3.07e-05;FR=0.2507;HP=2;NF=0;NR=3;PP=37;RMP=44.45;RPV=2.39e-06;SC=TTTGAGTGAGTGAGAGAGAGA;TC=90;TCF=18;TCR=72;TR=3;func=intronic;gene=FH	GT:GL:GQ:NR	0/0:-115.58,-120.99,-206.17:25:29	1/0:-208.1,-188.38,-347.52:83:62
+chr10	52420020	.	G	A	135	PASS	ABPV=1.00e+00;FPV=2.24e-01;FR=0.2502;HP=2;MMLQ=35;NF=3;NR=3;PP=135;RMP=58.04;RPV=7.75e-01;SC=GAGAACTTCCGGCTGCAGTAC;TC=30;TCF=20;TCR=10;TR=6	GT:GL:GQ:NR	0/0:-65.01,-71.52,-138.01:30:16	0/1:-83.86,-44.38,-74.93:100:14
+chr10	118380701	.	G	A	77	PASS	ABPV=1.00e+00;FPV=5.15e-01;FR=0.2503;HP=3;MMLQ=32;NF=5;NR=0;PP=77;RMP=22.32;RPV=5.62e-01;SC=CCGGGTTGCGGGGCGTCTGTT;TC=24;TCF=22;TCR=2;TR=5	GT:GL:GQ:NR	0/0:-4.14,-10.38,-77.71:28:10	0/1:-51.41,-25.11,-83.53:100:14
+chr11	1651169	.	T	C	84	PASS	ABPV=1.00e+00;FPV=9.98e-01;FR=0.2502;HP=2;MMLQ=33;NF=8;NR=26;PP=84;RMP=71.99;RPV=1.00e-00;SC=GCTGTGGCTCTGGCTGTGGGG;TC=71;TCF=14;TCR=57;TR=34;func=exonic;gene=KRTAP5-5;exon_func=synonymous SNV;AAchange=NM_001001480:c.T99C:p.S33S;1000g=0.29;dbsnp=rs71454095	GT:GL:GQ:NR	0/0:-199.38,-206.33,-365.55:31:38	0/1:-226.68,-198.86,-282.14:100:33
+chr11	3431576	.	G	A	33	PASS	ABPV=4.46e-01;FPV=4.99e-05;FR=0.2500;HP=1;MMLQ=30;NF=13;NR=10;PP=33;RMP=62.67;RPV=1.90e-02;SC=TCGTGTGTGAGTCCTACAGTG;TC=194;TCF=123;TCR=71;TR=23	GT:GL:GQ:NR	0/0:-71.93,-106.62,-693.75:100:102	1/0:-110.6,-94.58,-543.82:67:92
+chr11	43918703	.	C	CTTTTCATATTAT	36	PASS	ABPV=4.61e-02;FPV=1.12e-04;FR=0.2500;HP=3;NF=2;NR=0;PP=36;RMP=5.0;RPV=1.00e+00;SC=CTGACAGTGGCTTTATATATA;TC=49;TCF=49;TCR=0;TR=2	GT:GL:GQ:NR	0/0:-14.5,-34.6,-394.96:89:42	1/0:-47.66,-15.24,-223.69:100:36
+chr11	48366812	.	A	C	48	PASS	ABPV=1.00e+00;FPV=9.80e-01;FR=0.2502;HP=1;MMLQ=35;NF=16;NR=2;PP=48;RMP=45.69;RPV=1.00e+00;SC=AGATAATTGAATGTCCCAAGT;TC=44;TCF=42;TCR=2;TR=18	GT:GL:GQ:NR	0/0:-92.79,-99.69,-183.18:31:18	0/1:-133.87,-114.4,-228.26:82:26
+chr11	48387506	.	A	G	48	PASS	ABPV=1.00e+00;FPV=6.15e-01;FR=0.2500;HP=3;MMLQ=34;NF=28;NR=52;PP=48;RMP=59.69;RPV=1.00e-00;SC=AAATCCCCCGACCCATGCCAT;TC=227;TCF=109;TCR=118;TR=80;func=intergenic;gene=OR4C45(dist=13507) OR4A47(dist=122839);dbsnp=rs72898882;sift=0.42	GT:GL:GQ:NR	0/0:-665.75,-691.04,-1124.95:100:117	0/1:-697.01,-677.56,-1037.3:82:110
+chr11	56143357	.	G	A	91	PASS	ABPV=1.00e+00;FPV=9.70e-04;FR=0.2500;HP=3;MMLQ=36;NF=7;NR=60;PP=91;RMP=66.63;RPV=1.00e-00;SC=GGAATTTCTTGTACAAACAAA;TC=221;TCF=72;TCR=149;TR=67;func=exonic;gene=OR8U1 OR8U8;exon_func=synonymous SNV;AAchange=NM_001005204:c.G258A:p.L86L;dbsnp=rs76949582	GT:GL:GQ:NR	0/0:-538.52,-560.54,-1080.28:97:104	1/0:-924.01,-894.57,-1497.61:100:131
+chr11	56468493	.	A	G	86	PASS	ABPV=1.00e+00;FPV=1.31e-03;FR=0.2500;HP=1;MMLQ=30;NF=23;NR=16;PP=86;RMP=49.16;RPV=3.74e-01;SC=TCTGCCCCGCAGTGCTCATCC;TC=227;TCF=156;TCR=71;TR=39	GT:GL:GQ:NR	0/0:-212.22,-234.78,-819.52:99:105	0/1:-472.13,-443.86,-1063.46:100:122
+chr11	92592540	.	T	G	22	PASS	ABPV=9.72e-03;FPV=5.62e-02;FR=0.2501;HP=3;MMLQ=35;NF=0;NR=3;PP=22;RMP=99.66;RPV=8.62e-06;SC=GTTAGTGTTTTGGCTCTTGGA;TC=77;TCF=10;TCR=67;TR=3	GT:GL:GQ:NR	0/0:-302.47,-309.64,-322.1:32:36	0/1:-338.7,-325.07,-335.6:52:41
+chr11	123504959	.	C	G	200	PASS	ABPV=1.00e+00;FPV=4.20e-01;FR=0.2508;HP=2;MMLQ=40;NF=0;NR=7;PP=200;RMP=63.62;RPV=9.72e-01;SC=CAGTGCCCAGCGTGGGAACAC;TC=19;TCF=3;TCR=16;TR=7;func=intronic;gene=SCN3B;1000g=0.72;dbsnp=rs1148110	GT:GL:GQ:NR	0/0:-1.61,-6.93,-61.43:24:8	1/0:-66.0,-7.62,-36.11:100:11
+chr12	92675	.	C	T	152	PASS	ABPV=1.00e+00;FPV=7.38e-01;FR=0.2500;HP=1;MMLQ=37;NF=1;NR=7;PP=152;RMP=66.0;RPV=3.57e-01;SC=GGACTGTTTCCTGCTTGTAGC;TC=38;TCF=4;TCR=34;TR=8	GT:GL:GQ:NR	0/0:-41.61,-49.75,-120.62:37:14	1/0:-68.65,-25.34,-113.9:100:24
+chr12	11183642	.	A	G	154	PASS	ABPV=1.00e+00;FPV=8.37e-01;FR=0.2500;HP=1;MMLQ=34;NF=47;NR=62;PP=154;RMP=57.25;RPV=1.00e-00;SC=GCTAGTAGCAAGCCAGTTGCT;TC=311;TCF=168;TCR=143;TR=109;func=exonic;gene=TAS2R31;exon_func=nonsynonymous SNV;AAchange=NM_176885:c.T293C:p.L98P;segdup=0.93;dbsnp=rs73049067	GT:GL:GQ:NR	0/0:-561.52,-579.71,-1246.3:80:152	0/1:-826.02,-782.04,-1401.37:100:159
+chr12	29908580	.	A	ATTGTT	200	PASS	ABPV=1.00e+00;FPV=9.78e-01;FR=0.2507;HP=3;NF=10;NR=0;PP=200;RMP=36.19;RPV=1.00e+00;SC=TTTGGAAACTATTAAGTAATT;TC=24;TCF=24;TCR=0;TR=10;func=intronic;gene=TMTC1;dbsnp=rs3830194	GT:GL:GQ:NR	0/0:0.0,-5.55,-96.69:25:9	1/0:-151.5,-15.23,-76.28:100:17
+chr12	31282765	.	A	T	21	PASS	ABPV=1.00e+00;FPV=8.68e-01;FR=0.2502;HP=2;MMLQ=35;NF=12;NR=5;PP=21;RMP=46.72;RPV=8.51e-01;SC=AATGAATACAAATTTTTTCAT;TC=53;TCF=38;TCR=15;TR=17	GT:GL:GQ:NR	0/0:-83.08,-89.72,-221.87:30:27	1/0:-63.64,-50.39,-170.59:55:26
+chr12	52843779	.	T	C	52	PASS	ABPV=1.00e+00;FPV=1.21e-05;FR=0.2500;HP=4;MMLQ=20;NF=8;NR=16;PP=52;RMP=64.54;RPV=6.52e-01;SC=TTTGAACCCCTGGCTTCATCT;TC=161;TCF=100;TCR=61;TR=24;func=intronic;gene=KRT6B;segdup=0.93;dbsnp=rs380379	GT:GL:GQ:NR	0/0:-109.82,-139.81,-567.08:100:82	0/1:-186.27,-165.75,-481.84:87:79
+chr12	65471467	.	A	G	200	PASS	ABPV=1.00e+00;FPV=6.42e-01;FR=0.2501;HP=2;MMLQ=36;NF=7;NR=0;PP=200;RMP=38.97;RPV=4.22e-01;SC=TGCATCTTAAATATTCTTATC;TC=30;TCF=27;TCR=3;TR=7;func=intronic;gene=WIF1;1000g=0.27;dbsnp=rs2289936	GT:GL:GQ:NR	0/0:0.0,-7.62,-98.02:34:12	1/0:-69.82,-23.48,-105.09:100:18
+chr12	99175091	.	AAC	A	86	PASS	ABPV=3.61e-01;FPV=7.09e-04;FR=0.2503;HP=1;NF=4;NR=0;PP=86;RMP=34.87;RPV=9.95e-03;SC=AAACAACAACAACACACACAC;TC=43;TCF=27;TCR=16;TR=4;func=intronic;gene=ANKS1B	GT:GL:GQ:NR	0/0:-4.37,-10.61,-100.0:28:17	0/1:-72.08,-41.09,-136.47:100:27
+chr12	104378526	.	G	GACACAGAAACT	200	PASS	ABPV=2.37e-01;FPV=8.53e-03;FR=0.2500;HP=1;NF=5;NR=0;PP=200;RMP=8.25;RPV=5.63e-02;SC=TGTGATTCTAGCTCTGCTATG;TC=59;TCF=49;TCR=10;TR=5	GT:GL:GQ:NR	0/0:0.0,-15.25,-297.25:67:32	1/0:-137.95,-64.82,-429.82:100:44
+chr13	25169091	.	A	G	41	PASS	ABPV=1.00e+00;FPV=1.23e-02;FR=0.2501;HP=3;MMLQ=35;NF=18;NR=1;PP=41;RMP=17.52;RPV=3.10e-02;SC=AATAACCAAAACAGTTTTTTA;TC=133;TCF=114;TCR=19;TR=19	GT:GL:GQ:NR	0/0:-140.13,-147.81,-405.22:35:57	0/1:-204.4,-186.51,-512.07:75:76
+chr13	37795039	.	G	T	20	PASS	ABPV=5.69e-01;FPV=5.25e-01;FR=0.2502;HP=1;MMLQ=40;NF=2;NR=0;PP=20;RMP=33.0;RPV=7.49e-02;SC=TCCTTGGCCTGAGCTTCTTTG;TC=19;TCF=10;TCR=9;TR=2	GT:GL:GQ:NR	0/0:0.0,-6.93,-89.94:31:11	1/0:-22.03,-9.0,-57.23:54:8
+chr13	100517209	.	G	A	21	PASS	ABPV=2.00e-01;FPV=2.14e-03;FR=0.2500;HP=2;MMLQ=35;NF=6;NR=7;PP=21;RMP=94.07;RPV=9.71e-04;SC=GTGTGTGTGTGTATATGTGTG;TC=134;TCF=62;TCR=72;TR=13	GT:GL:GQ:NR	0/0:-265.23,-279.13,-623.6:62:70	1/0:-308.0,-294.6,-524.58:56:64
+chr13	114540947	.	C	CTCTGCTCTT	45	PASS	ABPV=1.42e-01;FPV=3.34e-03;FR=0.2500;HP=2;NF=2;NR=0;PP=45;RMP=1.0;RPV=5.62e-01;SC=CCACAGGAACCCAGCCAGCAG;TC=37;TCF=35;TCR=2;TR=2	GT:GL:GQ:NR	0/0:0.0,-11.09,-214.96:49:19	1/0:-74.37,-43.34,-288.0:100:27
+chr14	19118192	.	A	G	200	PASS	ABPV=1.00e+00;FPV=1.32e-05;FR=0.2507;HP=2;MMLQ=32;NF=68;NR=76;PP=200;RMP=53.85;RPV=5.74e-02;SC=TGCTTGCCATATGTCATGGAT;TC=771;TCF=415;TCR=356;TR=144;func=intergenic;gene=NONE(dist=NONE) OR11H12(dist=259402);segdup=0.96;dbsnp=rs77434589	GT:GL:GQ:NR	0/0:-730.61,-736.03,-2441.78:25:349	1/0:-997.51,-891.65,-2847.93:100:422
+chr14	19500081	.	A	G	22	PASS	ABPV=1.00e+00;FPV=1.61e-01;FR=0.2505;HP=3;MMLQ=22;NF=3;NR=0;PP=22;RMP=47.77;RPV=1.00e+00;SC=GGTGCACACCACTGTGGACGT;TC=22;TCF=22;TCR=0;TR=3	GT:GL:GQ:NR	0/0:-15.46,-21.36,-64.18:27:10	0/1:-27.84,-14.25,-57.82:57:12
+chr14	20137380	.	C	T	33	PASS	ABPV=1.24e-02;FPV=1.12e-09;FR=0.2500;HP=1;MMLQ=31;NF=8;NR=17;PP=33;RMP=61.98;RPV=3.46e-06;SC=TCACTGCCCTCGCCGCATGCA;TC=303;TCF=142;TCR=161;TR=25	GT:GL:GQ:NR	0/0:-373.48,-389.86,-1035.03:72:144	0/1:-475.48,-459.41,-1121.57:68:159
+chr14	64496872	.	G	C	96	PASS	ABPV=1.00e+00;FPV=1.00e+00;FR=0.2503;HP=1;MMLQ=37;NF=0;NR=4;PP=96;RMP=55.12;RPV=5.17e-01;SC=AGAAATTCCAGTGGTATTCAG;TC=18;TCF=0;TCR=18;TR=4;func=intronic;gene=SYNE2;1000g=0.90;dbsnp=rs3866737	GT:GL:GQ:NR	0/0:0.0,-6.24,-83.73:28:9	0/1:-36.8,-6.24,-45.77:100:9
+chr14	106881425	.	A	G	71	PASS	ABPV=1.00e+00;FPV=1.15e-01;FR=0.2500;HP=1;MMLQ=32;NF=4;NR=10;PP=71;RMP=49.71;RPV=2.88e-01;SC=CCATCCACTCAAGCCCTTGTC;TC=78;TCF=29;TCR=49;TR=14	GT:GL:GQ:NR	0/0:-39.35,-48.57,-258.02:41:30	1/0:-231.62,-206.72,-399.17:100:48
+chr14	106881452	.	T	C	66	PASS	ABPV=1.00e+00;FPV=3.03e-01;FR=0.2509;HP=1;MMLQ=27;NF=3;NR=10;PP=66;RMP=65.33;RPV=1.89e-01;SC=CTGGTCACACTGAATTCATAC;TC=71;TCF=18;TCR=53;TR=13	GT:GL:GQ:NR	0/0:-57.13,-62.37,-258.3:24:30	0/1:-168.08,-144.38,-338.93:100:41
+chr14	107034967	.	T	C	105	PASS	ABPV=1.00e+00;FPV=6.54e-01;FR=0.2500;HP=1;MMLQ=34;NF=6;NR=9;PP=105;RMP=58.51;RPV=6.64e-01;SC=ACAGGAGATCTTCAGAGACTC;TC=57;TCF=23;TCR=34;TR=15	GT:GL:GQ:NR	0/0:-163.23,-172.19,-255.57:40:20	1/0:-379.46,-346.84,-445.34:100:39
+chr15	20083754	.	G	A	54	PASS	ABPV=1.00e+00;FPV=5.67e-01;FR=0.2500;HP=2;MMLQ=36;NF=33;NR=5;PP=54;RMP=47.07;RPV=4.22e-01;SC=AAATCATTATGTGCTTTGAGA;TC=155;TCF=131;TCR=24;TR=38	GT:GL:GQ:NR	0/0:-122.79,-137.29,-483.11:64:64	1/0:-176.25,-155.43,-655.46:88:91
+chr15	20446256	.	G	C	57	PASS	ABPV=1.00e+00;FPV=1.00e+00;FR=0.2500;HP=2;MMLQ=34;NF=1;NR=7;PP=57;RMP=71.88;RPV=4.32e-01;SC=CATGCAAGAAGCTGGAAAGCC;TC=33;TCF=1;TCR=32;TR=8;func=intergenic;gene=NONE(dist=NONE) LOC646096(dist=41741);segdup=0.97;dbsnp=rs3907011	GT:GL:GQ:NR	0/0:-13.82,-23.14,-131.81:42:16	0/1:-45.04,-23.56,-104.26:91:17
+chr15	20875055	.	C	G	154	PASS	ABPV=1.00e+00;FPV=7.50e-01;FR=0.2504;HP=3;MMLQ=37;NF=0;NR=12;PP=154;RMP=60.19;RPV=1.71e-01;SC=AATTTAAACGCAAATTAGTAA;TC=64;TCF=1;TCR=63;TR=12;func=ncRNA;gene=NBEAP1;segdup=0.93;1000g=0.26;dbsnp=rs7496378	GT:GL:GQ:NR	0/0:-9.2,-15.25,-188.16:27:22	0/1:-137.96,-94.13,-342.43:100:42
+chr15	20875100	.	A	G	21	PASS	ABPV=1.00e+00;FPV=7.50e-01;FR=0.2502;HP=4;MMLQ=35;NF=0;NR=6;PP=21;RMP=81.39;RPV=2.77e-01;SC=AGAGGTTAAAAATAACTTTCT;TC=33;TCF=1;TCR=32;TR=6;func=ncRNA;gene=NBEAP1;cons46=243 Name=lod=13;segdup=0.93;1000g=0.28;dbsnp=rs7497715	GT:GL:GQ:NR	0/0:-7.83,-14.75,-92.12:31:10	1/0:-92.65,-79.35,-211.07:56:23
+chr15	21140945	.	C	T	26	PASS	ABPV=1.00e+00;FPV=1.00e-01;FR=0.2506;HP=2;MMLQ=33;NF=1;NR=3;PP=26;RMP=65.04;RPV=7.12e-01;SC=ACATGTACAGCGCCACACTTC;TC=25;TCF=14;TCR=11;TR=4;func=intergenic;gene=NF1P2(dist=6320) LOC348120(dist=4822);cons46=679 Name=lod=765;segdup=1.00;1000g=0.24;dbsnp=rs12324229	GT:GL:GQ:NR	0/0:-16.95,-22.6,-60.18:26:13	0/1:-36.66,-22.19,-44.85:61:12
+chr15	28900400	.	G	T	133	PASS	ABPV=1.00e+00;FPV=6.31e-01;FR=0.2502;HP=3;MMLQ=34;NF=14;NR=0;PP=133;RMP=36.99;RPV=4.21e-01;SC=GCTTGTCATTGTAAATTTTCT;TC=57;TCF=54;TCR=3;TR=14	GT:GL:GQ:NR	0/0:-26.38,-32.94,-192.24:30:27	1/0:-71.34,-32.36,-180.89:100:30
+chr15	75656200	.	G	A	75	PASS	ABPV=1.00e+00;FPV=6.28e-01;FR=0.2507;HP=6;MMLQ=37;NF=4;NR=0;PP=75;RMP=47.43;RPV=1.00e+00;SC=CCAGCCCCCCGGCCCCGTTTT;TC=16;TCF=16;TCR=0;TR=4	GT:GL:GQ:NR	0/0:-7.14,-12.68,-76.44:25:8	0/1:-34.75,-8.99,-31.71:100:8
+chr15	76075732	.	A	C	29	PASS	ABPV=1.00e+00;FPV=9.97e-01;FR=0.2501;HP=2;MMLQ=34;NF=11;NR=15;PP=29;RMP=61.41;RPV=9.58e-01;SC=ATCCCTATCTATCCAGGCCTT;TC=64;TCF=22;TCR=42;TR=26	GT:GL:GQ:NR	0/0:-89.15,-96.33,-237.9:32:31	1/0:-134.14,-119.09,-238.26:63:33
+chr15	100340178	.	C	G	52	PASS	ABPV=1.00e+00;FPV=1.76e-01;FR=0.2500;HP=1;MMLQ=31;NF=5;NR=5;PP=52;RMP=87.78;RPV=1.32e-01;SC=AGTGTCTTCTCGTTCCCACGC;TC=64;TCF=31;TCR=33;TR=10;func=ncRNA;gene=DNM1P46;cons46=699 Name=lod=923;segdup=0.97;sift=0.27	GT:GL:GQ:NR	0/0:-139.12,-149.96,-310.47:37:36	1/0:-206.67,-186.19,-317.68:87:38
+chr15	102303399	.	C	T	65	PASS	ABPV=1.00e+00;FPV=4.32e-02;FR=0.2500;HP=2;MMLQ=34;NF=5;NR=30;PP=65;RMP=65.58;RPV=1.00e-00;SC=AGAGCTGCTGCCCAACCTGCA;TC=90;TCF=40;TCR=50;TR=35;func=intergenic;gene=TARSL2(dist=38754) OR4F6(dist=42524);cons46=920 Name=lod=7327;segdup=0.98;1000g=0.50;dbsnp=rs71416239	GT:GL:GQ:NR	0/0:-129.26,-138.34,-250.21:41:46	0/1:-118.78,-95.27,-224.48:100:44
+chr15	102506389	.	C	T	50	PASS	ABPV=6.29e-01;FPV=1.27e-01;FR=0.2500;HP=1;MMLQ=34;NF=1;NR=3;PP=50;RMP=67.19;RPV=2.63e-01;SC=GGATGCCCTGCAGTACCTGCA;TC=32;TCF=13;TCR=19;TR=4	GT:GL:GQ:NR	0/0:-3.9,-15.65,-133.88:52:17	0/1:-31.25,-11.29,-72.06:84:15
+chr16	9250260	.	T	G	22	PASS	ABPV=1.00e+00;FPV=1.00e-02;FR=0.2500;HP=2;MMLQ=29;NF=0;NR=4;PP=22;RMP=37.36;RPV=8.85e-01;SC=CACCTATTATTCCATGAATTC;TC=27;TCF=16;TCR=11;TR=4;func=intergenic;gene=C16orf72(dist=36705) MIR548X(dist=78514);cons46=749 Name=lod=1471;1000g=0.73;dbsnp=rs12929693	GT:GL:GQ:NR	0/0:-1.84,-10.83,-100.69:40:14	0/1:-25.85,-12.37,-70.66:56:13
+chr16	21747662	.	G	A	36	PASS	ABPV=1.00e+00;FPV=2.01e-01;FR=0.2500;HP=1;MMLQ=34;NF=16;NR=6;PP=36;RMP=40.34;RPV=5.40e-05;SC=CTGTCTTTCAGTCTGTTCGGA;TC=159;TCF=79;TCR=80;TR=22	GT:GL:GQ:NR	0/0:-69.29,-88.69,-470.14:85:75	1/0:-171.53,-154.82,-534.35:70:84
+chr16	28618446	.	T	C	36	PASS	ABPV=1.00e+00;FPV=8.61e-01;FR=0.2500;HP=3;MMLQ=32;NF=6;NR=14;PP=36;RMP=63.74;RPV=5.40e-01;SC=ACACAGCCTGTCCCAGGCCAG;TC=75;TCF=18;TCR=57;TR=20	GT:GL:GQ:NR	0/0:-33.24,-41.67,-205.86:38:27	0/1:-113.92,-97.17,-312.83:70:48
+chr16	33390329	.	G	C	24	PASS	ABPV=6.16e-01;FPV=4.32e-02;FR=0.2500;HP=2;MMLQ=34;NF=5;NR=0;PP=24;RMP=54.47;RPV=1.00e+00;SC=TTAGAAACAGGTTCACAATTG;TC=40;TCF=40;TCR=0;TR=5;func=intergenic;gene=LOC390705(dist=91627) LINC00273(dist=570723);segdup=0.97;1000g=0.32;dbsnp=rs12232434	GT:GL:GQ:NR	0/0:-6.09,-14.55,-170.95:38:21	0/1:-47.14,-33.16,-147.34:58:19
+chr16	33401967	.	G	A	116	PASS	ABPV=1.00e+00;FPV=1.64e-02;FR=0.2500;HP=2;MMLQ=34;NF=16;NR=15;PP=116;RMP=51.2;RPV=2.96e-01;SC=GAGGTCTGCCGACAGCTGCAC;TC=172;TCF=102;TCR=70;TR=31;func=intergenic;gene=LOC390705(dist=103265) LINC00273(dist=559085);cons46=611 Name=lod=406;segdup=0.97;dbsnp=rs8047578	GT:GL:GQ:NR	0/0:-133.55,-144.14,-490.22:47:76	1/0:-209.17,-173.99,-648.51:100:96
+chr16	33407954	.	C	G	34	PASS	ABPV=1.00e+00;FPV=4.21e-01;FR=0.2507;HP=3;MMLQ=34;NF=0;NR=3;PP=34;RMP=61.08;RPV=5.19e-01;SC=GAAATTGTCTCGGGCCTGAAG;TC=17;TCF=3;TCR=14;TR=3	GT:GL:GQ:NR	0/0:-10.82,-16.36,-77.44:25:9	1/0:-63.55,-47.37,-59.15:58:8
+chr16	46405120	.	C	G	37	PASS	ABPV=3.94e-02;FPV=4.07e-03;FR=0.2510;HP=2;MMLQ=40;NF=2;NR=1;PP=37;RMP=51.27;RPV=3.18e-03;SC=CGATTCCATTCGATAATGATT;TC=62;TCF=34;TCR=28;TR=3	GT:GL:GQ:NR	0/0:-129.24,-134.38,-161.33:24:28	0/1:-205.7,-188.69,-196.8:42:34
+chr16	58148083	.	C	CACACGCAGGTACA	31	PASS	ABPV=1.69e-01;FPV=1.00e+00;FR=0.2500;HP=2;NF=0;NR=2;PP=31;RMP=88.0;RPV=3.34e-03;SC=CAGGGAAGCACCCACCCTTGT;TC=35;TCF=0;TCR=35;TR=2	GT:GL:GQ:NR	0/0:-11.28,-21.68,-223.8:46:16	0/1:-62.86,-30.44,-243.59:100:20
+chr17	5036281	.	G	C	48	PASS	ABPV=1.00e+00;FPV=8.00e-01;FR=0.2500;HP=1;MMLQ=32;NF=14;NR=49;PP=48;RMP=47.67;RPV=9.22e-01;SC=AAGCACAGTAGCAAAGTAATG;TC=214;TCF=48;TCR=166;TR=63	GT:GL:GQ:NR	0/0:-506.02,-514.23,-1090.2:37:117	0/1:-460.03,-440.62,-871.14:82:97
+chr17	6328747	.	T	G	200	PASS	ABPV=1.00e+00;FPV=8.77e-01;FR=0.2507;HP=4;MMLQ=32;NF=8;NR=5;PP=200;RMP=59.22;RPV=9.45e-01;SC=GGCCACTTGCTCCCTGCCTGG;TC=36;TCF=24;TCR=12;TR=13	GT:GL:GQ:NR	0/0:-4.84,-10.37,-69.24:25:8	0/1:-116.1,-23.7,-86.84:100:28
+chr17	14140191	.	G	A	125	PASS	ABPV=1.00e+00;FPV=3.98e-02;FR=0.2500;HP=1;MMLQ=34;NF=2;NR=11;PP=125;RMP=71.76;RPV=3.84e-02;SC=AGCTGTTTACGGCGCTGACTC;TC=95;TCF=24;TCR=71;TR=13;func=upstream;gene=CDRT15;segdup=0.99;1000g=0.17;dbsnp=rs28533558	GT:GL:GQ:NR	0/0:-146.51,-156.3,-338.05:44:40	0/1:-162.79,-125.58,-384.62:100:55
+chr17	21904955	.	G	A	29	PASS	ABPV=1.46e-01;FPV=3.00e-01;FR=0.2500;HP=2;MMLQ=33;NF=1;NR=7;PP=29;RMP=77.08;RPV=5.90e-05;SC=GTGGCACGGCGCTGTATCCTG;TC=95;TCF=9;TCR=86;TR=8	GT:GL:GQ:NR	0/0:-95.23,-110.26,-302.39:67:42	0/1:-104.15,-88.94,-334.7:64:53
+chr17_gl000205_random	114392	.	G	GC	200	PASS	ABPV=1.00e+00;FPV=1.00e+00;FR=0.2503;HP=1;NF=1;NR=9;PP=200;RMP=62.13;RPV=8.86e-01;SC=GAGCTTCTATGAGGCGTGGGG;TC=28;TCF=1;TCR=27;TR=10;func=intergenic;gene=NONE(dist=NONE) MGC70870(dist=2231)	GT:GL:GQ:NR	0/0:0.0,-6.24,-93.01:28:9	0/1:-137.06,-63.68,-124.76:100:19
+chr17_gl000205_random	118186	.	TCGC	T	157	PASS	ABPV=1.00e+00;FPV=4.85e-02;FR=0.2506;HP=1;NF=4;NR=5;PP=157;RMP=51.77;RPV=1.51e-01;SC=CCATCATAAGTCGCATCCCGG;TC=55;TCF=23;TCR=32;TR=9;func=ncRNA;gene=MGC70870;cons46=824 Name=lod=2972;segdup=0.90	GT:GL:GQ:NR	0/0:-80.93,-86.51,-246.22:26:23	0/1:-151.92,-104.34,-309.99:100:34
+chr17_gl000205_random	118289	.	G	A	30	PASS	ABPV=1.00e+00;FPV=2.43e-02;FR=0.2500;HP=1;MMLQ=38;NF=1;NR=4;PP=30;RMP=51.3;RPV=5.18e-01;SC=TGAGCTCAGTGGTGCTACCTA;TC=38;TCF=20;TCR=18;TR=5	GT:GL:GQ:NR	0/0:-92.27,-100.53,-170.2:37:15	0/1:-193.59,-178.31,-262.43:64:23
+chr17_gl000205_random	122791	.	T	C	124	PASS	ABPV=1.00e+00;FPV=6.72e-01;FR=0.2504;HP=1;MMLQ=34;NF=8;NR=0;PP=124;RMP=54.5;RPV=1.00e+00;SC=GATATAAACTTCTAAAATTCA;TC=30;TCF=30;TCR=0;TR=8;func=intergenic;gene=MGC70870(dist=3059) NONE(dist=NONE)	GT:GL:GQ:NR	0/0:-33.82,-39.98,-100.64:28:10	1/0:-177.82,-140.79,-190.46:100:20
+chr18	14183747	.	T	C	115	PASS	ABPV=1.00e+00;FPV=9.72e-01;FR=0.2500;HP=5;MMLQ=36;NF=49;NR=88;PP=115;RMP=54.47;RPV=9.86e-01;SC=ACAAAGAAAATAGAACGCCTT;TC=444;TCF=156;TCR=288;TR=137	GT:GL:GQ:NR	0/0:-919.95,-948.86,-1765.89:100:211	0/1:-1189.4,-1154.37,-1918.79:100:233
+chr19	3611146	.	A	G	30	PASS	ABPV=1.00e+00;FPV=5.15e-01;FR=0.2501;HP=1;MMLQ=24;NF=6;NR=1;PP=30;RMP=42.3;RPV=2.44e-01;SC=CCCTGTGCTCAGAGGTGGGGG;TC=36;TCF=26;TCR=10;TR=7;func=ncRNA;gene=C19orf29-AS1;1000g=0.56;dbsnp=rs2074786	GT:GL:GQ:NR	0/0:-27.63,-35.13,-121.04:34:15	0/1:-69.97,-54.53,-137.67:65:21
+chr19	12543121	.	C	G	200	PASS	ABPV=1.00e+00;FPV=7.14e-01;FR=0.2502;HP=7;MMLQ=40;NF=11;NR=0;PP=200;RMP=33.87;RPV=7.50e-01;SC=TTCTTTGCTTCTTTTTAAATT;TC=41;TCF=40;TCR=1;TR=11;func=intronic;gene=ZNF443;segdup=0.96;dbsnp=rs74181652	GT:GL:GQ:NR	0/0:-8.47,-15.46,-153.74:32:20	0/1:-71.21,-15.46,-97.4:100:21
+chr19	15014189	.	T	C	90	PASS	ABPV=1.00e+00;FPV=1.97e-01;FR=0.2500;HP=4;MMLQ=100;NF=2;NR=5;PP=90;RMP=90.56;RPV=4.68e-01;SC=GAGTGAGTTGTGGGTTGCAGC;TC=39;TCF=16;TCR=23;TR=7	GT:GL:GQ:NR	0/0:-190.71,-200.49,-255.11:44:24	1/0:-174.95,-145.84,-178.61:100:15
+chr19	41515263	.	A	G	88	PASS	ABPV=3.76e-01;FPV=1.82e-01;FR=0.2500;HP=2;MMLQ=33;NF=7;NR=3;PP=88;RMP=64.16;RPV=2.48e-04;SC=AGCGCCCCCAAGGACCTCATC;TC=93;TCF=40;TCR=53;TR=10;func=exonic;gene=CYP2B6;exon_func=nonsynonymous SNV;AAchange=NM_000767:c.A785G:p.K262R;segdup=0.92;1000g=0.20;dbsnp=rs2279343;pp2=0.0;phylop=0.086093;mutT=1.0E-6;LRT=0.999974	GT:GL:GQ:NR	0/0:-4.81,-28.32,-273.38:100:41	0/1:-65.82,-37.11,-263.4:100:52
+chr19	42188037	.	C	T	114	PASS	ABPV=1.00e+00;FPV=6.06e-02;FR=0.2500;HP=4;MMLQ=34;NF=2;NR=8;PP=114;RMP=98.9;RPV=1.54e-02;SC=GTGTGGCCCCCTTGGTTCCCC;TC=73;TCF=11;TCR=62;TR=10	GT:GL:GQ:NR	0/0:-205.49,-214.25,-251.15:29:29	0/1:-379.34,-343.91,-357.8:15:44
+chr19	50474708	.	T	G	61	PASS	ABPV=1.00e+00;FPV=7.17e-01;FR=0.2501;HP=2;MMLQ=30;NF=5;NR=1;PP=61;RMP=67.96;RPV=3.09e-02;SC=CTGGGCTCAGTGTCCCAGAGC;TC=37;TCF=18;TCR=19;TR=6	GT:GL:GQ:NR	0/0:-86.34,-93.74,-137.77:33:15	0/1:-129.81,-107.4,-147.05:95:22
+chr19	52977823	.	A	G	102	PASS	ABPV=1.00e+00;FPV=3.15e-01;FR=0.2507;HP=2;MMLQ=35;NF=0;NR=4;PP=102;RMP=41.58;RPV=8.84e-01;SC=GTTTCTCTCCAGTATGAATTC;TC=15;TCF=4;TCR=11;TR=4;func=intronic;gene=ZNF578;cons46=395 Name=lod=54;1000g=0.94;dbsnp=rs1673901	GT:GL:GQ:NR	0/0:0.0,-5.54,-65.87:25:9	1/0:-36.12,-4.16,-18.86:71:6
+chr19	54726711	.	G	T	43	PASS	ABPV=1.00e+00;FPV=1.00e-00;FR=0.2504;HP=3;MMLQ=31;NF=22;NR=2;PP=43;RMP=52.84;RPV=6.78e-01;SC=GTCCCCGCCCGGGTGCCTCCT;TC=53;TCF=45;TCR=8;TR=24	GT:GL:GQ:NR	0/0:-47.88,-54.03,-95.64:28:18	1/0:-164.89,-146.64,-206.88:77:35
+chr2	905553	.	G	C	76	PASS	ABPV=1.62e-02;FPV=5.75e-08;FR=0.2500;HP=2;MMLQ=31;NF=1;NR=7;PP=76;RMP=95.73;RPV=1.04e-02;SC=GCCTGCACTGGGTCTGGTGTT;TC=128;TCF=69;TCR=59;TR=8	GT:GL:GQ:NR	0/0:-314.19,-325.21,-450.94:49:57	0/1:-390.34,-364.48,-513.78:100:71
+chr2	905595	.	G	C	24	PASS	ABPV=1.21e-01;FPV=1.79e-02;FR=0.2500;HP=2;MMLQ=35;NF=5;NR=1;PP=24;RMP=13.0;RPV=6.96e-04;SC=GCCTGCACTGGGTCTGGTGTT;TC=79;TCF=45;TCR=34;TR=6	GT:GL:GQ:NR	0/0:-210.22,-219.58,-290.19:42:42	1/0:-197.49,-183.47,-250.46:59:38
+chr2	91885842	.	G	A	37	PASS	ABPV=1.00e+00;FPV=2.46e-01;FR=0.2502;HP=1;MMLQ=36;NF=4;NR=0;PP=37;RMP=71.85;RPV=4.22e-01;SC=CCAACATTACGGAATTTGGAT;TC=27;TCF=24;TCR=3;TR=4	GT:GL:GQ:NR	0/0:-11.45,-18.39,-83.47:31:11	0/1:-59.01,-41.99,-86.53:72:16
+chr2	96525556	.	C	T	37	PASS	ABPV=1.00e+00;FPV=1.00e-00;FR=0.2503;HP=1;MMLQ=37;NF=60;NR=2;PP=37;RMP=45.25;RPV=9.49e-01;SC=TCTCCTTATACGTCTTTAATA;TC=91;TCF=87;TCR=4;TR=62	GT:GL:GQ:NR	0/0:-304.4,-310.82,-406.42:29:43	0/1:-411.62,-394.62,-459.09:72:48
+chr2	107042620	.	C	T	45	PASS	ABPV=1.00e+00;FPV=7.50e-01;FR=0.2500;HP=4;MMLQ=33;NF=0;NR=10;PP=45;RMP=77.64;RPV=2.94e-02;SC=GCAAGAGCTACAAATACAAAA;TC=69;TCF=1;TCR=68;TR=10;func=intronic;gene=RGPD3;cons46=333 Name=lod=30;segdup=0.99;dbsnp=rs2433787	GT:GL:GQ:NR	0/0:-9.17,-23.45,-154.19:63:21	1/0:-107.84,-88.96,-294.09:80:48
+chr2	132860931	.	G	A	113	PASS	ABPV=1.00e+00;FPV=5.61e-01;FR=0.2507;HP=1;MMLQ=38;NF=0;NR=8;PP=113;RMP=69.43;RPV=9.58e-01;SC=GAAGAATGTGGTAAAGCCTTT;TC=22;TCF=2;TCR=20;TR=8	GT:GL:GQ:NR	0/0:-12.66,-18.1,-56.72:25:9	1/0:-57.64,-23.24,-50.67:100:13
+chr2	133020074	.	G	A	33	PASS	ABPV=1.00e+00;FPV=9.94e-01;FR=0.2501;HP=2;MMLQ=36;NF=45;NR=12;PP=33;RMP=47.59;RPV=9.08e-01;SC=ATTTCAGAAGGGAAAATATCC;TC=167;TCF=131;TCR=36;TR=57;func=intergenic;gene=ANKRD30BL(dist=4532) GPR39(dist=154073);cons46=762 Name=lod=1662;segdup=0.91;dbsnp=rs111959326	GT:GL:GQ:NR	0/0:-698.84,-706.52,-798.38:35:80	1/0:-786.87,-770.7,-903.5:68:87
+chr2	133020186	.	T	C	66	PASS	ABPV=1.00e+00;FPV=1.55e-01;FR=0.2500;HP=1;MMLQ=34;NF=52;NR=51;PP=66;RMP=46.69;RPV=9.65e-01;SC=TAGCTTTGTGTTCATACCACT;TC=402;TCF=237;TCR=165;TR=103;func=intergenic;gene=ANKRD30BL(dist=4644) GPR39(dist=153961);cons46=762 Name=lod=1662;segdup=0.91;dbsnp=rs112259198	GT:GL:GQ:NR	0/0:-1712.52,-1737.48,-1975.72:100:192	1/0:-1974.59,-1950.96,-2276.74:100:211
+chr2	133020542	.	G	A	50	PASS	ABPV=1.00e+00;FPV=1.14e-01;FR=0.2503;HP=1;MMLQ=32;NF=3;NR=6;PP=50;RMP=53.94;RPV=7.08e-02;SC=CTATCCAAGTGGATCCAAATT;TC=66;TCF=24;TCR=42;TR=9;func=intergenic;gene=ANKRD30BL(dist=5000) GPR39(dist=153605);cons46=762 Name=lod=1662;segdup=0.93;dbsnp=rs2257591	GT:GL:GQ:NR	0/0:-181.04,-187.42,-271.44:29:29	1/0:-243.98,-224.07,-313.1:84:37
+chr2	166801924	.	C	G	78	PASS	ABPV=1.00e+00;FPV=5.71e-01;FR=0.2507;HP=3;MMLQ=34;NF=4;NR=0;PP=78;RMP=67.75;RPV=7.49e-01;SC=TATTTACAAACTGGCAATAGA;TC=18;TCF=17;TCR=1;TR=4;func=ncRNA;gene=LOC100506134;1000g=0.64;dbsnp=rs6432853	GT:GL:GQ:NR	0/0:-34.05,-39.57,-91.24:25:8	1/0:-42.79,-16.34,-58.89:100:10
+chr2	204055943	.	T	C	59	PASS	ABPV=2.58e-01;FPV=8.29e-02;FR=0.2500;HP=2;MMLQ=33;NF=11;NR=2;PP=59;RMP=61.13;RPV=3.22e-06;SC=ATGGCCGCCATCCTCATGACA;TC=128;TCF=65;TCR=63;TR=13;func=intronic;gene=NBEAL1;cons46=702 Name=lod=950;dbsnp=rs4561645	GT:GL:GQ:NR	0/0:-41.52,-53.03,-440.53:51:70	1/0:-89.56,-67.55,-350.54:93:58
+chr2	210594540	.	A	G	200	PASS	ABPV=1.00e+00;FPV=9.70e-01;FR=0.2507;HP=1;MMLQ=30;NF=10;NR=1;PP=200;RMP=52.61;RPV=9.37e-01;SC=CGAATGCAAGATATAGTTAAA;TC=27;TCF=25;TCR=2;TR=11;func=intronic;gene=MAP2;1000g=0.88;dbsnp=rs4673486	GT:GL:GQ:NR	0/0:0.0,-5.54,-62.54:25:8	0/1:-93.19,-14.77,-63.29:100:19
+chr2	211444533	.	GGT	G	32	PASS	ABPV=1.78e-01;FPV=1.96e-01;FR=0.2503;HP=2;NF=1;NR=3;PP=32;RMP=50.82;RPV=2.40e-03;SC=TGTTTCTTCGGGTGTGTGTGT;TC=54;TCF=11;TCR=43;TR=4	GT:GL:GQ:NR	0/0:-4.14,-10.38,-103.02:28:17	1/0:-41.6,-23.06,-172.26:78:37
+chr2	227659818	.	T	TCAAGTGAGGA	93	PASS	ABPV=3.68e-02;FPV=2.37e-01;FR=0.2500;HP=1;NF=0;NR=3;PP=93;RMP=91.0;RPV=7.64e-05;SC=CTCTCACCGCTGCCCAGGGGT;TC=63;TCF=5;TCR=58;TR=3	GT:GL:GQ:NR	0/0:-17.96,-35.28,-330.9:77:30	0/1:-94.07,-50.73,-458.79:100:41
+chr2	227954599	.	G	A	200	PASS	ABPV=1.00e+00;FPV=9.19e-01;FR=0.2507;HP=2;MMLQ=31;NF=6;NR=4;PP=200;RMP=46.35;RPV=9.51e-01;SC=TCTCCTTTTGGGCCTCTTCCT;TC=25;TCF=16;TCR=9;TR=10;func=exonic;gene=COL4A4;exon_func=nonsynonymous SNV;AAchange=NM_000092:c.C1444T:p.P482S;1000g=0.55;dbsnp=rs2229814;sift=0.44;pp2=0.0;phylop=0.897442;mutT=9.0E-5;LRT=0.824593	GT:GL:GQ:NR	0/0:0.0,-5.54,-68.56:25:9	0/1:-80.77,-11.53,-34.97:100:16
+chr2	233273018	.	G	A	32	PASS	ABPV=1.00e+00;FPV=3.62e-01;FR=0.2500;HP=3;MMLQ=34;NF=13;NR=4;PP=32;RMP=56.47;RPV=8.89e-03;SC=TTCCCATGGGGACCCCAGACC;TC=102;TCF=59;TCR=43;TR=17	GT:GL:GQ:NR	0/0:-50.24,-59.48,-309.03:41:45	0/1:-159.89,-144.07,-409.74:66:57
+chr20	29633938	.	A	G	28	PASS	ABPV=1.00e+00;FPV=1.27e-01;FR=0.2500;HP=2;MMLQ=34;NF=16;NR=24;PP=28;RMP=56.91;RPV=2.94e-01;SC=AAATGACTGGAATTTTTGTTT;TC=192;TCF=84;TCR=108;TR=40;func=ncRNA;gene=FRG1B;cons46=514 Name=lod=163;segdup=0.96;dbsnp=rs4006818	GT:GL:GQ:NR	0/0:-963.63,-978.07,-1139.59:64:101	1/0:-1046.34,-1031.41,-1112.07:63:91
+chr20	33356511	.	C	T	44	PASS	ABPV=1.00e+00;FPV=7.49e-01;FR=0.2507;HP=1;MMLQ=37;NF=0;NR=4;PP=44;RMP=57.46;RPV=6.28e-01;SC=AGTTTACCACCAGAAAAATGG;TC=17;TCF=1;TCR=16;TR=4;func=intronic;gene=NCOA6;cons46=243 Name=lod=13;1000g=0.36;dbsnp=rs2295353	GT:GL:GQ:NR	0/0:0.0,-5.54,-70.65:25:8	0/1:-49.75,-31.07,-63.51:79:9
+chr21	14424170	.	C	G	200	PASS	ABPV=1.00e+00;FPV=7.37e-05;FR=0.2502;HP=1;MMLQ=31;NF=51;NR=68;PP=200;RMP=55.06;RPV=7.01e-02;SC=GGAAAGAACACCTGACACGGC;TC=637;TCF=318;TCR=319;TR=119	GT:GL:GQ:NR	0/0:-1068.97,-1075.78,-2090.04:31:272	1/0:-1608.82,-1559.51,-2814.14:100:365
+chr22	16256578	.	G	T	200	PASS	ABPV=2.18e-01;FPV=6.87e-08;FR=0.2502;HP=4;MMLQ=34;NF=19;NR=8;PP=200;RMP=40.16;RPV=2.46e-02;SC=TGGCTCTGATGTTTCATTATG;TC=253;TCF=194;TCR=59;TR=27	GT:GL:GQ:NR	0/0:-139.12,-145.98,-745.94:31:118	0/1:-324.53,-220.54,-788.14:100:135
+chr22	24640438	.	TCA	T	58	PASS	ABPV=5.57e-01;FPV=3.19e-02;FR=0.2503;HP=2;NF=2;NR=1;PP=58;RMP=48.68;RPV=9.37e-01;SC=ATACATTCACTCACACACACA;TC=27;TCF=25;TCR=2;TR=3	GT:GL:GQ:NR	0/0:-4.37,-10.61,-107.94:28:12	0/1:-47.48,-22.82,-120.6:100:15
+chr22	42524924	.	A	G	32	PASS	ABPV=1.00e+00;FPV=1.78e-02;FR=0.2500;HP=2;MMLQ=35;NF=0;NR=4;PP=32;RMP=71.83;RPV=5.74e-01;SC=TGTCCAAGAGACCGTTGGGGC;TC=31;TCF=14;TCR=17;TR=4	GT:GL:GQ:NR	0/0:-1.84,-12.87,-112.28:49:17	1/0:-35.2,-19.47,-73.62:66:14
+chr3	6522043	.	G	A	62	PASS	ABPV=1.00e+00;FPV=5.16e-01;FR=0.2507;HP=3;MMLQ=37;NF=4;NR=0;PP=62;RMP=44.82;RPV=7.49e-01;SC=TAACTGCAAAGTAGGAACACG;TC=19;TCF=18;TCR=1;TR=4	GT:GL:GQ:NR	0/0:0.0,-5.54,-65.36:25:9	1/0:-46.21,-23.49,-68.33:96:10
+chr3	135742089	.	GAAAATA	G	56	PASS	ABPV=2.53e-02;FPV=5.62e-01;FR=0.2500;HP=4;NF=0;NR=2;PP=56;RMP=97.0;RPV=4.10e-05;SC=GTTTTGTTTTGAAAATATTTT;TC=55;TCF=2;TCR=53;TR=2	GT:GL:GQ:NR	0/0:-171.19,-180.69,-401.53:43:27	1/0:-163.7,-138.73,-368.83:100:28
+chr3	195453014	.	G	A	73	PASS	ABPV=1.00e+00;FPV=9.99e-01;FR=0.2500;HP=3;MMLQ=31;NF=44;NR=44;PP=73;RMP=52.04;RPV=1.00e-00;SC=GACAGCACCCGGGGCCACGAC;TC=210;TCF=115;TCR=95;TR=88	GT:GL:GQ:NR	0/0:-596.82,-608.68,-929.74:53:99	0/1:-825.59,-800.41,-1040.36:100:111
+chr3	195453412	.	C	T	21	PASS	ABPV=1.00e+00;FPV=1.25e-02;FR=0.2502;HP=2;MMLQ=25;NF=13;NR=52;PP=21;RMP=62.2;RPV=1.00e-00;SC=CCACGACTGCCCGGACGAGGC;TC=219;TCF=89;TCR=130;TR=65	GT:GL:GQ:NR	0/0:-275.62,-282.43,-681.47:31:103	0/1:-362.65,-349.41,-719.87:55:117
+chr3	195506775	.	G	A	87	PASS	ABPV=1.00e+00;FPV=8.81e-01;FR=0.2500;HP=1;MMLQ=34;NF=11;NR=4;PP=87;RMP=30.23;RPV=4.10e-02;SC=AGGAAGTGTCGGTGACAGGAA;TC=69;TCF=34;TCR=35;TR=15;func=exonic;gene=MUC4;exon_func=synonymous SNV;AAchange=NM_018406:c.C11676T:p.H3892H;cons46=381 Name=lod=47;segdup=0.92;1000g=0.48;dbsnp=rs79609066	GT:GL:GQ:NR	0/0:-215.78,-225.62,-329.97:44:31	0/1:-253.55,-225.09,-324.19:100:38
+chr3	195507372	.	C	A	72	PASS	ABPV=1.00e+00;FPV=9.50e-01;FR=0.2510;HP=1;MMLQ=31;NF=12;NR=10;PP=72;RMP=82.02;RPV=4.71e-01;SC=GAGGGGTGGCCTGACCTGTGG;TC=76;TCF=33;TCR=43;TR=22	GT:GL:GQ:NR	0/0:-85.59,-90.71,-175.03:23:27	0/1:-302.0,-277.02,-435.24:100:49
+chr3	195509974	.	A	G	107	PASS	ABPV=1.00e+00;FPV=4.52e-02;FR=0.2501;HP=1;MMLQ=33;NF=7;NR=15;PP=107;RMP=66.83;RPV=1.62e-01;SC=ATGACCTGTGAACACTGAGGA;TC=127;TCF=50;TCR=77;TR=22	GT:GL:GQ:NR	0/0:-281.04,-289.1,-469.31:36:51	0/1:-474.46,-441.44,-679.46:100:76
+chr4	3589510	.	G	A	82	PASS	ABPV=1.00e+00;FPV=1.00e-00;FR=0.2500;HP=1;MMLQ=35;NF=28;NR=15;PP=82;RMP=39.79;RPV=1.00e-00;SC=ACTTCCAGATGAGACTTCCTG;TC=89;TCF=62;TCR=27;TR=43;func=ncRNA;gene=FLJ35424	GT:GL:GQ:NR	0/0:-202.17,-216.0,-372.38:61:36	0/1:-618.94,-591.66,-690.1:100:53
+chr4	5747131	.	C	A	40	PASS	ABPV=1.00e+00;FPV=6.32e-01;FR=0.2502;HP=2;MMLQ=33;NF=1;NR=19;PP=40;RMP=63.27;RPV=9.99e-01;SC=AAATTGGCTACATTAGAGAGA;TC=45;TCF=5;TCR=40;TR=20	GT:GL:GQ:NR	0/0:-175.23,-182.17,-227.63:31:19	1/0:-264.71,-246.95,-301.81:75:26
+chr4	70261725	.	G	A	25	PASS	ABPV=1.00e+00;FPV=8.43e-01;FR=0.2503;HP=3;MMLQ=36;NF=1;NR=5;PP=25;RMP=77.58;RPV=8.09e-01;SC=TGTGGCCCTGGGGTAGTTACT;TC=19;TCF=3;TCR=16;TR=6	GT:GL:GQ:NR	0/0:-25.09,-31.31,-100.1:28:11	1/0:-62.48,-48.33,-68.8:59:8
+chr5	837488	.	C	A	84	PASS	ABPV=3.03e-01;FPV=2.26e-02;FR=0.2502;HP=2;MMLQ=35;NF=22;NR=3;PP=84;RMP=67.65;RPV=4.45e-09;SC=ACCTGGAGAACTCCTTTGTCC;TC=225;TCF=128;TCR=97;TR=25	GT:GL:GQ:NR	0/0:-71.02,-77.56,-596.34:30:92	0/1:-157.13,-129.33,-794.35:100:133
+chr5	34192944	.	A	G	136	PASS	ABPV=3.53e-01;FPV=1.29e-04;FR=0.2500;HP=1;MMLQ=31;NF=17;NR=13;PP=136;RMP=51.73;RPV=7.15e-05;SC=GCAGTGGATGAAGGCCCCTCA;TC=261;TCF=140;TCR=121;TR=30	GT:GL:GQ:NR	0/0:-120.41,-138.2,-806.35:79:120	0/1:-199.6,-159.91,-913.41:100:141
+chr5	36200413	.	G	A	33	PASS	ABPV=1.25e-02;FPV=1.03e-02;FR=0.2511;HP=3;MMLQ=34;NF=2;NR=4;PP=33;RMP=98.68;RPV=2.69e-06;SC=GAAAATGTATGTTATAAATAT;TC=109;TCF=30;TCR=79;TR=6	GT:GL:GQ:NR	0/0:-295.77,-300.82,-490.03:23:53	1/0:-290.08,-274.08,-469.93:67:56
+chr5	41909830	.	C	T	27	PASS	ABPV=5.28e-01;FPV=2.35e-03;FR=0.2504;HP=18;MMLQ=0;NF=0;NR=3;PP=27;RMP=14.14;RPV=9.29e-01;SC=AGATATCTTTCTTTTTTTTTT;TC=28;TCF=21;TCR=7;TR=3	GT:GL:GQ:NR	0/0:-4.61,-10.58,-40.73:26:11	0/1:-41.44,-26.72,-53.62:62:17
+chr5	54329850	.	C	CTGCTTTACTTA	68	PASS	ABPV=5.01e-01;FPV=1.00e+00;FR=0.2503;HP=1;NF=0;NR=2;PP=68;RMP=90.0;RPV=7.41e-02;SC=CATATGGGGTCCATTTTTGCA;TC=21;TCF=0;TCR=21;TR=2	GT:GL:GQ:NR	0/0:0.0,-6.24,-122.94:28:9	1/0:-45.59,-6.93,-110.5:100:12
+chr5	58121059	.	G	A	112	PASS	ABPV=1.00e+00;FPV=4.22e-01;FR=0.2501;HP=2;MMLQ=35;NF=0;NR=5;PP=112;RMP=75.51;RPV=4.68e-01;SC=TACAGAGTCCGAGCTAATTGT;TC=26;TCF=3;TCR=23;TR=5	GT:GL:GQ:NR	0/0:-31.77,-39.38,-124.25:34:12	0/1:-43.94,-9.7,-79.61:100:15
+chr5	169535734	.	C	A	20	PASS	ABPV=1.00e+00;FPV=1.00e+00;FR=0.2507;HP=1;MMLQ=34;NF=0;NR=2;PP=20;RMP=68.72;RPV=3.31e-01;SC=CAGGAGCCTCCGAGGAATCCA;TC=13;TCF=0;TCR=13;TR=2;func=UTR3;gene=FOXI1;1000g=0.35;dbsnp=rs6873124	GT:GL:GQ:NR	0/0:-5.3,-10.84,-76.27:25:8	1/0:-15.88,-2.77,-16.56:54:5
+chr5	175467765	.	A	C	34	PASS	ABPV=1.00e+00;FPV=6.86e-01;FR=0.2503;HP=3;MMLQ=37;NF=4;NR=7;PP=34;RMP=58.23;RPV=9.60e-01;SC=AGGAAAGCAGATTTGTACATC;TC=32;TCF=15;TCR=17;TR=11	GT:GL:GQ:NR	0/0:-48.25,-54.62,-116.89:29:16	0/1:-64.43,-48.26,-102.15:68:18
+chr5	180047739	.	CGT	C	40	PASS	ABPV=3.01e-01;FPV=4.20e-02;FR=0.2503;HP=3;NF=0;NR=2;PP=40;RMP=66.37;RPV=1.63e-01;SC=AAGGGGCCGGCGTGTGTGTGT;TC=28;TCF=11;TCR=17;TR=2	GT:GL:GQ:NR	0/0:-15.43,-21.66,-115.16:28:17	0/1:-35.79,-15.44,-86.67:86:11
+chr6	26370657	.	A	G	26	PASS	ABPV=1.00e+00;FPV=9.98e-01;FR=0.2500;HP=1;MMLQ=34;NF=25;NR=18;PP=26;RMP=46.67;RPV=9.65e-01;SC=ACAGTGGAGCAACGCCAAGGG;TC=112;TCF=61;TCR=51;TR=43	GT:GL:GQ:NR	0/0:-408.78,-416.97,-671.27:37:70	1/0:-270.25,-255.76,-422.39:61:42
+chr6	26370659	.	C	T	32	PASS	ABPV=1.00e+00;FPV=9.98e-01;FR=0.2500;HP=2;MMLQ=34;NF=25;NR=17;PP=32;RMP=48.69;RPV=9.08e-01;SC=AGTGGAGCAACGCCAAGGGAG;TC=114;TCF=61;TCR=53;TR=42	GT:GL:GQ:NR	0/0:-408.78,-419.23,-664.68:47:70	1/0:-278.07,-262.18,-440.62:67:44
+chr6	35838820	.	A	ATTCTTACTTGG	44	PASS	ABPV=1.42e-01;FPV=7.50e-01;FR=0.2500;HP=1;NF=0;NR=2;PP=44;RMP=90.0;RPV=2.64e-03;SC=CTCTACCAGAATGAAAAGTCT;TC=37;TCF=1;TCR=36;TR=2	GT:GL:GQ:NR	0/0:-22.8,-33.89,-243.84:49:19	1/0:-50.19,-17.08,-221.97:100:21
+chr6	58777098	.	A	T	42	PASS	ABPV=1.00e+00;FPV=2.57e-03;FR=0.2500;HP=2;MMLQ=34;NF=14;NR=25;PP=42;RMP=50.5;RPV=1.85e-01;SC=GTAACTCTAGATTGAAGAATT;TC=224;TCF=105;TCR=119;TR=39;func=intergenic;gene=GUSBP4(dist=489374) NONE(dist=NONE);dbsnp=rs4330557	GT:GL:GQ:NR	0/0:-1161.42,-1180.18,-1411.53:83:106	0/1:-1283.78,-1265.72,-1460.11:76:119
+chr6	116774635	.	C	G	38	PASS	ABPV=1.00e+00;FPV=3.66e-01;FR=0.2504;HP=1;MMLQ=36;NF=4;NR=12;PP=38;RMP=76.7;RPV=4.76e-01;SC=CTTTTTCCACCACAAATTCTT;TC=72;TCF=21;TCR=51;TR=16	GT:GL:GQ:NR	0/0:-45.72,-51.81,-228.46:28:30	0/1:-179.58,-162.43,-353.98:72:42
+chr6	136599000	.	T	TCATCTGTGA	73	PASS	ABPV=2.21e-05;FPV=2.55e-09;FR=0.2505;HP=4;NF=2;NR=0;PP=73;RMP=1.41;RPV=3.11e-04;SC=TTTTAGTTTTTACCTTTTTAA;TC=118;TCF=90;TCR=28;TR=2;func=intronic;gene=BCLAF1;cons46=573 Name=lod=284;segdup=0.97	GT:GL:GQ:NR	0/0:-44.16,-49.89,-603.4:26:61	1/0:-105.25,-67.59,-750.95:100:79
+chr6	155757781	.	T	A	106	PASS	ABPV=1.00e+00;FPV=3.16e-01;FR=0.2504;HP=2;MMLQ=36;NF=0;NR=5;PP=106;RMP=66.42;RPV=6.16e-01;SC=TACAGTGAGCTCTGAAATATC;TC=24;TCF=4;TCR=20;TR=5;func=intronic;gene=NOX3;1000g=0.22;dbsnp=rs231961	GT:GL:GQ:NR	0/0:0.0,-6.09,-69.03:28:9	0/1:-48.54,-15.69,-84.63:100:15
+chr7	65159983	.	A	G	128	PASS	ABPV=1.00e+00;FPV=5.13e-01;FR=0.2500;HP=2;MMLQ=33;NF=9;NR=0;PP=128;RMP=42.05;RPV=1.33e-01;SC=TTGCTTAGTTACCAGGTAGAA;TC=45;TCF=38;TCR=7;TR=9;func=ncRNA;gene=INTS4L2 LOC441242;cons46=439 Name=lod=81;segdup=0.99;1000g=0.26;dbsnp=rs2949280	GT:GL:GQ:NR	0/0:0.0,-9.67,-99.87:43:16	0/1:-63.32,-25.43,-98.84:100:29
+chr7	100552044	.	T	G	46	PASS	ABPV=1.00e+00;FPV=1.00e-00;FR=0.2500;HP=1;MMLQ=33;NF=133;NR=185;PP=46;RMP=54.24;RPV=1.00e-00;SC=CTGTTCCTTCTTCACCATACA;TC=776;TCF=387;TCR=389;TR=318	GT:GL:GQ:NR	0/0:-2768.08,-2799.9,-3980.82:100:373	0/1:-3148.55,-3129.5,-4372.1:80:403
+chr7	102319079	.	G	A	34	PASS	ABPV=4.40e-01;FPV=1.00e+00;FR=0.2500;HP=1;MMLQ=38;NF=0;NR=6;PP=34;RMP=53.53;RPV=6.65e-03;SC=TGTGAGATGCGTGTGAAAATG;TC=56;TCF=0;TCR=56;TR=6;func=intergenic;gene=POLR2J2(dist=6903) FAM185A(dist=70320);segdup=1.00;1000g=0.17;dbsnp=rs62458736	GT:GL:GQ:NR	0/0:-9.39,-20.95,-166.2:51:26	0/1:-46.26,-30.07,-176.58:68:30
+chr7	106272259	.	C	T	200	PASS	ABPV=1.00e+00;FPV=1.51e-04;FR=0.2501;HP=2;MMLQ=31;NF=27;NR=25;PP=200;RMP=18.87;RPV=1.08e-05;SC=CTCATTCCAACCTCTGCTTCC;TC=391;TCF=192;TCR=199;TR=52	GT:GL:GQ:NR	0/0:-1599.11,-1606.25,-1841.06:32:195	0/1:-1703.84,-1621.18,-1787.33:100:196
+chr7	128492558	.	G	A	32	PASS	ABPV=1.00e+00;FPV=9.80e-01;FR=0.2501;HP=6;MMLQ=35;NF=15;NR=1;PP=32;RMP=45.11;RPV=5.34e-01;SC=TGAGTCCAGGGGGGGCTGCTC;TC=45;TCF=39;TCR=6;TR=16	GT:GL:GQ:NR	0/0:-82.82,-89.89,-214.44:32:24	0/1:-137.27,-121.35,-194.99:67:21
+chr7	142223942	.	A	G	200	PASS	ABPV=1.00e+00;FPV=1.00e-00;FR=0.2500;HP=1;MMLQ=33;NF=86;NR=42;PP=200;RMP=48.5;RPV=9.93e-01;SC=ACTGTGAATCATCTACTACAC;TC=282;TCF=160;TCR=122;TR=128	GT:GL:GQ:NR	0/0:-840.21,-856.54,-1228.56:72:124	1/0:-1069.18,-1023.08,-1489.98:100:158
+chr7	142498735	.	A	C	51	PASS	ABPV=1.00e+00;FPV=9.39e-01;FR=0.2500;HP=4;MMLQ=34;NF=23;NR=20;PP=51;RMP=54.1;RPV=9.74e-01;SC=AGGACCTGAAAAACGTGTTCC;TC=127;TCF=71;TCR=56;TR=43;func=intergenic;gene=TRY6(dist=16336) EPHB6(dist=54057);sift=0.35	GT:GL:GQ:NR	0/0:-407.53,-415.97,-666.18:38:67	0/1:-407.94,-387.73,-626.55:86:62
+chr7	143295456	.	A	C	200	PASS	ABPV=1.00e+00;FPV=7.75e-01;FR=0.2500;HP=1;MMLQ=26;NF=24;NR=7;PP=200;RMP=70.65;RPV=6.11e-02;SC=GCCTCCTCGCAGTGGGGGGCA;TC=135;TCF=87;TCR=48;TR=31	GT:GL:GQ:NR	0/0:-28.78,-39.63,-253.37:48:66	0/1:-158.76,-57.73,-187.94:100:69
+chr7	143453710	.	T	A	66	PASS	ABPV=1.00e+00;FPV=5.62e-01;FR=0.2501;HP=3;MMLQ=36;NF=0;NR=15;PP=66;RMP=54.55;RPV=5.68e-01;SC=TCTTCCTTTGTTTTGTCCACT;TC=62;TCF=2;TCR=60;TR=15	GT:GL:GQ:NR	0/0:-65.41,-73.41,-216.2:36:31	0/1:-102.8,-79.18,-187.97:100:31
+chr7	143956461	.	T	C	37	PASS	ABPV=1.00e+00;FPV=8.34e-02;FR=0.2500;HP=2;MMLQ=31;NF=5;NR=0;PP=37;RMP=48.38;RPV=1.00e+00;SC=TGGGCTTGGCTGGATGCAGGA;TC=36;TCF=36;TCR=0;TR=5	GT:GL:GQ:NR	0/0:-6.63,-15.42,-125.53:39:20	1/0:-33.93,-16.96,-77.4:71:16
+chr7	157367205	.	TGA	T	52	PASS	ABPV=3.26e-01;FPV=5.62e-01;FR=0.2503;HP=2;NF=0;NR=2;PP=52;RMP=55.44;RPV=3.19e-02;SC=AGAGTAATAATGAGAGAGAGA;TC=27;TCF=2;TCR=25;TR=2;func=intronic;gene=PTPRN2	GT:GL:GQ:NR	0/0:-10.36,-16.59,-113.87:28:16	1/0:-39.42,-16.12,-59.64:99:12
+chr8	8095880	.	C	T	131	PASS	ABPV=1.00e+00;FPV=2.37e-01;FR=0.2500;HP=3;MMLQ=37;NF=0;NR=10;PP=131;RMP=64.63;RPV=8.71e-01;SC=GCCACATGGCCCCAGGCCCAA;TC=36;TCF=5;TCR=31;TR=10;func=ncRNA;gene=FLJ10661;segdup=0.98	GT:GL:GQ:NR	0/0:-78.8,-87.2,-171.27:38:18	0/1:-81.81,-43.3,-81.08:100:18
+chr8	12236123	.	T	G	111	PASS	ABPV=1.00e+00;FPV=1.38e-39;FR=0.2500;HP=2;MMLQ=30;NF=16;NR=9;PP=111;RMP=18.14;RPV=9.45e-01;SC=GTATTTGTGTTTGTGTGTGTG;TC=103;TCF=79;TCR=24;TR=25	GT:GL:GQ:NR	0/0:-265.16,-270.76,-457.35:100:49	1/0:-317.4,-305.02,-585.97:25:76
+chr8	12428634	.	C	T	69	PASS	ABPV=1.00e+00;FPV=7.50e-01;FR=0.2500;HP=1;MMLQ=36;NF=0;NR=5;PP=69;RMP=63.98;RPV=2.03e-01;SC=TCTTAACAACCGCCATGGTGC;TC=31;TCF=1;TCR=30;TR=5	GT:GL:GQ:NR	0/0:-10.77,-21.63,-134.62:48:17	1/0:-41.03,-16.59,-80.89:100:14
+chr8	35608374	.	T	C	24	PASS	ABPV=1.00e+00;FPV=6.32e-01;FR=0.2502;HP=2;MMLQ=34;NF=1;NR=34;PP=24;RMP=69.53;RPV=1.00e-00;SC=TGAAAGTGTGTGTTTTCCAAA;TC=62;TCF=5;TCR=57;TR=35	GT:GL:GQ:NR	0/0:-248.65,-255.21,-376.27:30:35	1/0:-265.91,-251.92,-307.04:58:27
+chr8	121500323	.	A	AGTGGGATTGC	40	PASS	ABPV=2.19e-01;FPV=8.43e-03;FR=0.2500;HP=2;NF=2;NR=0;PP=40;RMP=1.0;RPV=7.50e-01;SC=ATTATATCCTATGGATCAAAT;TC=32;TCF=31;TCR=1;TR=2	GT:GL:GQ:NR	0/0:-2.07,-11.08,-162.96:40:13	1/0:-47.66,-16.63,-264.67:100:25
+chr9	14510	.	CTGT	C	200	PASS	ABPV=2.20e-01;FPV=4.66e-14;FR=0.2500;HP=1;NF=12;NR=0;PP=200;RMP=43.31;RPV=1.00e-02;SC=TAAAAGCACACTGTTGGTTTC;TC=123;TCF=107;TCR=16;TR=12	GT:GL:GQ:NR	0/0:-22.04,-38.67,-350.71:73:53	0/1:-133.83,-67.48,-425.73:100:75
+chr9	34724786	.	G	A	54	PASS	ABPV=1.00e+00;FPV=5.46e-01;FR=0.2503;HP=2;MMLQ=31;NF=10;NR=18;PP=54;RMP=64.11;RPV=9.71e-01;SC=GGATTTCCACGGGACTAGGCT;TC=91;TCF=41;TCR=50;TR=28	GT:GL:GQ:NR	0/0:-77.92,-84.2,-224.15:29:46	1/0:-101.32,-80.48,-207.58:88:45
+chr9	44118498	.	G	C	200	PASS	ABPV=1.00e+00;FPV=9.49e-01;FR=0.2503;HP=2;MMLQ=34;NF=2;NR=7;PP=200;RMP=65.44;RPV=6.41e-01;SC=GAGGGCAGCTGCCTGTCACCT;TC=31;TCF=4;TCR=27;TR=9;func=intergenic;gene=CNTNAP3B(dist=196025) FAM27C(dist=871738);segdup=0.98;1000g=0.77;dbsnp=rs28610048	GT:GL:GQ:NR	0/0:-11.97,-18.32,-91.33:29:13	0/1:-73.63,-27.61,-81.59:100:18
+chr9	67281836	.	T	G	200	PASS	ABPV=1.00e+00;FPV=3.12e-01;FR=0.2500;HP=2;MMLQ=34;NF=6;NR=21;PP=200;RMP=63.02;RPV=5.58e-01;SC=GTGGACCTGATACAGTGGCCC;TC=115;TCF=31;TCR=84;TR=27;func=ncRNA;gene=AQP7P1;segdup=0.99;1000g=0.26;dbsnp=rs75812522	GT:GL:GQ:NR	0/0:-227.43,-240.42,-365.47:58:50	0/1:-353.09,-303.78,-464.7:100:65
+chr9	67293649	.	T	G	200	PASS	ABPV=1.00e+00;FPV=2.40e-02;FR=0.2509;HP=2;MMLQ=32;NF=8;NR=20;PP=200;RMP=65.85;RPV=6.29e-01;SC=GTGTGCCAAGTGACTTCATCT;TC=136;TCF=59;TCR=77;TR=28	GT:GL:GQ:NR	0/0:-52.46,-57.7,-399.51:24:62	0/1:-141.44,-82.05,-400.07:100:74
+chr9	68358140	.	T	C	101	PASS	ABPV=1.00e+00;FPV=4.09e-01;FR=0.2501;HP=2;MMLQ=31;NF=10;NR=13;PP=101;RMP=52.55;RPV=9.14e-01;SC=CCGCTTCAGATAGTGAAGAAG;TC=84;TCF=45;TCR=39;TR=23;func=intergenic;gene=ANKRD20A3(dist=387847) LOC642236(dist=69643);cons46=780 Name=lod=1967;segdup=0.98;dbsnp=rs62544188	GT:GL:GQ:NR	0/0:-99.49,-107.4,-306.63:36:46	0/1:-122.69,-91.06,-221.21:100:38
+chr9	92995102	.	C	T	25	PASS	ABPV=1.74e-02;FPV=2.34e-06;FR=0.2500;HP=3;MMLQ=33;NF=11;NR=10;PP=25;RMP=36.17;RPV=2.75e-07;SC=ATAAAATTGTCCCCTCCATTC;TC=258;TCF=127;TCR=131;TR=21;func=intergenic;gene=LOC286370(dist=191321) LOC340515(dist=229612);segdup=0.96	GT:GL:GQ:NR	0/0:-127.8,-170.89,-839.43:100:127	1/0:-164.37,-150.07,-829.28:60:131
+chr9	139572068	.	C	G	44	PASS	ABPV=1.00e+00;FPV=4.21e-01;FR=0.2507;HP=2;MMLQ=29;NF=0;NR=3;PP=44;RMP=57.58;RPV=7.11e-01;SC=GGCTGGGGCGCGAAGGCCTGG;TC=14;TCF=3;TCR=11;TR=3;func=intronic;gene=AGPAT2;1000g=0.57;dbsnp=rs2236514	GT:GL:GQ:NR	0/0:0.0,-5.54,-62.14:25:9	1/0:-29.67,-11.06,-23.48:61:5
+chr9	140777194	.	A	AGAGCGGCT	200	PASS	ABPV=7.76e-05;FPV=4.77e-24;FR=0.2500;HP=2;NF=2;NR=1;PP=200;RMP=4.36;RPV=2.92e-05;SC=CGCTTCTCCTAGGACGACACG;TC=123;TCF=77;TCR=46;TR=3;func=splicing;gene=CACNA1B(NM_000718:c.390-2->CATGTCCGAGCGGCT NM_001243812:c.390-2->CATGTCCGAGCGGCT);cons46=573 Name=lod=285	GT:GL:GQ:NR	0/0:-260.4,-275.23,-819.04:71:85	0/1:-510.15,-408.95,-886.86:3:93
+chrUn_gl000214	53458	.	T	A	82	PASS	ABPV=4.34e-01;FPV=7.36e-06;FR=0.2500;HP=4;MMLQ=34;NF=22;NR=0;PP=82;RMP=47.4;RPV=5.62e-01;SC=AAACACTATATAAATATAATT;TC=187;TCF=185;TCR=2;TR=22;func=intergenic;gene=NONE(dist=NONE) NONE(dist=NONE);segdup=0.98	GT:GL:GQ:NR	0/0:-154.3,-180.61,-694.01:100:88	1/0:-304.62,-277.18,-752.95:100:99
+chrUn_gl000214	61035	.	A	G	25	PASS	ABPV=2.68e-01;FPV=1.27e-06;FR=0.2500;HP=2;MMLQ=34;NF=20;NR=0;PP=25;RMP=60.63;RPV=4.22e-01;SC=ATGTTTACCTATATAACAAAC;TC=187;TCF=184;TCR=3;TR=20	GT:GL:GQ:NR	0/0:-517.15,-538.58,-910.78:94:80	0/1:-812.82,-798.54,-1242.08:60:107
+chrUn_gl000214	74804	.	T	C	45	PASS	ABPV=5.69e-01;FPV=4.33e-02;FR=0.2500;HP=2;MMLQ=35;NF=5;NR=0;PP=45;RMP=36.66;RPV=5.62e-01;SC=ATCACTTGAATGCAGTAGGCA;TC=42;TCF=40;TCR=2;TR=5	GT:GL:GQ:NR	0/0:-65.35,-75.06,-177.61:43:16	0/1:-180.67,-161.94,-279.38:79:26
+chrUn_gl000220	121703	.	T	C	75	PASS	ABPV=9.31e-02;FPV=1.94e-05;FR=0.2500;HP=2;MMLQ=31;NF=5;NR=8;PP=75;RMP=52.13;RPV=2.81e-03;SC=GTGGGCACGGTACGCTCTGGT;TC=150;TCF=78;TCR=72;TR=13	GT:GL:GQ:NR	0/0:-64.92,-78.18,-505.13:59:80	1/0:-102.59,-76.78,-453.86:100:70
+chrUn_gl000220	128026	.	C	T	73	PASS	ABPV=1.00e+00;FPV=1.39e-05;FR=0.2500;HP=1;MMLQ=37;NF=12;NR=5;PP=73;RMP=48.23;RPV=2.65e-03;SC=TCTCTGTCTCCGTCTCTGTCT;TC=117;TCF=62;TCR=55;TR=17	GT:GL:GQ:NR	0/0:-175.58,-193.94,-521.81:81:62	1/0:-151.61,-126.36,-397.61:100:57
+chrUn_gl000220	132074	.	G	A	200	PASS	ABPV=1.00e+00;FPV=2.39e-03;FR=0.2500;HP=2;MMLQ=34;NF=10;NR=11;PP=200;RMP=61.51;RPV=6.72e-03;SC=CTCTCTGTCCGTCTCTGTCTT;TC=167;TCF=84;TCR=83;TR=21;func=intergenic;gene=LOC100507412(dist=5378) RN5-8S1(dist=23923);segdup=0.95	GT:GL:GQ:NR	0/0:-248.2,-257.69,-615.12:42:77	0/1:-290.71,-234.79,-658.31:100:90
+chrUn_gl000220	145002	.	C	T	28	PASS	ABPV=3.17e-02;FPV=7.56e-08;FR=0.2500;HP=4;MMLQ=31;NF=1;NR=3;PP=28;RMP=65.86;RPV=4.70e-03;SC=ACTAGCCGGGCGCGGTGGCAC;TC=76;TCF=36;TCR=40;TR=4	GT:GL:GQ:NR	0/0:-17.73,-43.17,-320.69:100:46	1/0:-67.96,-52.99,-236.43:63:37
+chrUn_gl000220	145368	.	T	C	30	PASS	ABPV=1.09e-01;FPV=1.31e-02;FR=0.2500;HP=1;MMLQ=29;NF=8;NR=2;PP=30;RMP=72.81;RPV=1.92e-05;SC=AGCCGGGCGCTGTGCTGTGCT;TC=119;TCF=63;TCR=56;TR=10;func=intergenic;gene=LOC100507412(dist=18672) RN5-8S1(dist=10629);dbsnp=rs3878955	GT:GL:GQ:NR	0/0:-48.56,-59.69,-409.13:50:53	0/1:-66.74,-51.46,-448.03:64:66
+chrUn_gl000225	30398	.	C	T	29	PASS	ABPV=1.13e-01;FPV=3.15e-04;FR=0.2502;HP=1;MMLQ=33;NF=1;NR=5;PP=29;RMP=58.12;RPV=2.55e-02;SC=CCTGCTCCTCCGAGCCTTTGA;TC=80;TCF=37;TCR=43;TR=6	GT:GL:GQ:NR	0/0:-195.73,-202.53,-342.72:31:35	1/0:-230.45,-215.31,-371.74:63:45
+chrUn_gl000225	43193	.	C	T	46	PASS	ABPV=1.00e+00;FPV=7.84e-02;FR=0.2507;HP=3;MMLQ=31;NF=8;NR=12;PP=46;RMP=44.42;RPV=4.19e-02;SC=GCCAGAGAGACGGGCCTCCCG;TC=126;TCF=51;TCR=75;TR=20	GT:GL:GQ:NR	0/0:-577.5,-583.01,-743.98:25:63	1/0:-604.31,-585.16,-703.98:81:63
+chrX	106390898	.	G	A	65	PASS	ABPV=4.78e-01;FPV=1.49e-02;FR=0.2500;HP=1;MMLQ=39;NF=5;NR=0;PP=65;RMP=43.16;RPV=1.00e+00;SC=GTTTGGTCATGGAGCATACAA;TC=46;TCF=46;TCR=0;TR=5	GT:GL:GQ:NR	0/0:0.0,-11.78,-148.84:52:17	1/0:-49.23,-25.85,-211.17:99:29
diff --git a/tests/tabix_data/vcf/15.vcf b/tests/tabix_data/vcf/15.vcf
new file mode 100644
index 0000000..9df9a1e
--- /dev/null
+++ b/tests/tabix_data/vcf/15.vcf
@@ -0,0 +1,317 @@
+##fileformat=VCFv4.0
+##FILTER=<ID=HardyWeinbergViolation,Description="The validation is in Hardy-Weinberg violation">
+##FILTER=<ID=HighNoCallRate,Description="The validation no-call rate is too high">
+##FILTER=<ID=TooManyHomVars,Description="The validation homozygous variant rate is too high">
+##INFO=<ID=AC,Number=1,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##INFO=<ID=HW,Number=1,Type=Float,Description="Phred-scaled Hardy-Weinberg violation p-value">
+##INFO=<ID=HetPct,Number=1,Type=Float,Description="Percent of heterozygous genotypes">
+##INFO=<ID=HomRefPct,Number=1,Type=Float,Description="Percent of homozygous reference genotypes">
+##INFO=<ID=HomVarPct,Number=1,Type=Float,Description="Percent homozygous variant genotypes">
+##INFO=<ID=NoCallPct,Number=1,Type=Float,Description="Percent of no-calls">
+##ValidationMetrics_HardyWeinbergViolations="25 (8%)"
+##ValidationMetrics_HomVarViolations="0 (0%)"
+##ValidationMetrics_NoCallViolations="13 (4%)"
+##ValidationMetrics_PolymorphicPassingRecords="195 (75%)"
+##ValidationMetrics_RecordsPassingFilters="258 (87%)"
+##ValidationMetrics_RecordsProcessed=296
+##ValidationMetrics_SamplesAssayed=383
+##VariantValidationAssessor="analysis_type=VariantValidationAssessor input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=null excludeIntervals=null reference_sequence=/humgen/1kg/reference/human_g1k_v37.fasta rodBind=[rawData/plink.renamed.sorted.fixed.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub maxHardy=20.0 maxNoCall=0.05 maxHomVar=1.1"
+##source=PLINK
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+20	2263095	.	TG	T	.	HardyWeinbergViolation	AC=358;AN=766;HW=812.29;HetPct=93.5;HomRefPct=6.5;HomVarPct=0.0;NoCallPct=0.0	GT	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1
+20	2426886	.	G	GAATT	.	HighNoCallRate	AC=11;AN=680;HW=0.00;HetPct=2.9;HomRefPct=85.9;HomVarPct=0.0;NoCallPct=11.2	GT	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	.	.	.	.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	.	.	.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	.	0/0	0/0	0/0	0/0	0/0	0/0	.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	.	.	.	.	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	.	.	0/0	0/0	0/0	0/1	.	0/1	.	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	.	.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	.	.	.	0/0	0/0	.	0/0	0/0	0/0	0/0	.	.	.	0/1	.	.	0/0	0/0	.	0/0	0/0	0/0	.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	.	0/0	0/0	0/0	.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	.	.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	.	0/0
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+20	8233352	.	TACTC	T	.	PASS	AC=56;AN=764;HW=1.84;HetPct=13.1;HomRefPct=85.9;HomVarPct=0.8;NoCallPct=0.3	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	1/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0
+20	8504000	.	TAG	T	.	PASS	AC=5;AN=762;HW=0.00;HetPct=1.3;HomRefPct=98.2;HomVarPct=0.0;NoCallPct=0.5	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	.	0/0	.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+20	8779672	.	TG	T	.	HighNoCallRate	AC=0;AN=86;HW=0.00;HetPct=0.0;HomRefPct=11.2;HomVarPct=0.0;NoCallPct=88.8	GT	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0/0	.	.	.	.	.	.	.	.	.	.	.	0/0	.	.	.	.	.	.	.	.	.	.	0/0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0/0	0/0	.	.	.	0/0	.	0/0	.	.	.	0/0	.	.	.	.	.	.	.	0/0	.	0/0	0/0	.	0/0	.	0/0	0/0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0/0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0/0	0/0	0/0	0/0	.	.	.	0/0	.	.	.	.	.	0/0	0/0	.	.	.	.	0/0	.	.	0/0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0/0	.	.	.	.	.	.	.	.	.	.	.	0/0	.	.	.	.	0/0	.	.	.	.	.	.	.	.	.	0/0	.	0/0	.	0/0	0/0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0/0	.	.	.	.	.	.	0/0	.	.	.	.	.	.	.	0/0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0/0	0/0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0/0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0/0	0/0	.	0/0	.	.	0/0	.	.	.	0/0	.	.	.	.	.	.	.	.	.	.	.	0/0	.	.	.	.	.	.	.	.	.	.	.
+20	8794142	.	AG	A	.	HardyWeinbergViolation	AC=52;AN=756;HW=57.86;HetPct=8.4;HomRefPct=87.7;HomVarPct=2.6;NoCallPct=1.3	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	.	1/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	1/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	1/1	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	.	0/0	.	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	1/1	0/0	0/0	1/1	0/1	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	.	0/0	0/0	0/0	0/0	0/0	0/0	.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0
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+20	9900218	.	C	CT	.	HardyWeinbergViolation	AC=3;AN=766;HW=21.06;HetPct=0.3;HomRefPct=99.5;HomVarPct=0.3;NoCallPct=0.0	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
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+20	22655862	.	TATC	T	.	PASS	AC=6;AN=766;HW=0.00;HetPct=1.6;HomRefPct=98.4;HomVarPct=0.0;NoCallPct=0.0	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
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+20	62871860	.	C	CCCGCA	.	PASS	AC=27;AN=764;HW=17.87;HetPct=5.5;HomRefPct=93.5;HomVarPct=0.8;NoCallPct=0.3	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
diff --git a/tests/tabix_data/vcf/16.vcf b/tests/tabix_data/vcf/16.vcf
new file mode 100644
index 0000000..d36970e
--- /dev/null
+++ b/tests/tabix_data/vcf/16.vcf
@@ -0,0 +1,369 @@
+##fileformat=VCFv4.0
+##ApplyRecalibration="analysis_type=ApplyRecalibration input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=[20] excludeIntervals=null reference_sequence=/humgen/1kg/reference/human_g1k_v37.fasta rodBind=[/humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110608VQSRConsensus/calls/combined.phase1.chr20.raw.indels.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false recal_file=/humgen/gsa-scr1/delangel/VQSRIndels/data/trainMills75_truthMills75_p15_12_12_pctb0.05_std12.0_mG8_QD_FS_HS_RP_IC.recal tranches_file=/humgen/gsa-scr1/delangel/VQSRIndels/data/trainMills75_truthMills75_p15_12_12_pctb0.05_std12.0_mG8_QD_FS_HS_RP_IC.tranches out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub ts_filter_level=93.0 ignore_filter=null mode=INDEL"
+##CombineVariants="analysis_type=CombineVariants input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=[20:41000001-42000000] excludeIntervals=null reference_sequence=/humgen/1kg/reference/human_g1k_v37.fasta rodBind=[/humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110608VQSRConsensus/calls/chr20/AFR/AFR.phase1.chr20.42.raw.indels.vcf, /humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110608VQSRConsensus/calls/chr20/ASN/ASN.phase1.chr20.42.raw.indels.vcf, /humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110608VQSRConsensus/calls/chr20/AMR/AMR.phase1.chr20.42.raw.indels.vcf, /humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110608VQSRConsensus/calls/chr20/EUR/EUR.phase1.chr20.42.raw.indels.vcf, /humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110608VQSRConsensus/calls/chr20/AFR.admix/AFR.admix.phase1.chr20.42.raw.indels.vcf, /humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110608VQSRConsensus/calls/chr20/ASN.admix/ASN.admix.phase1.chr20.42.raw.indels.vcf, /humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110608VQSRConsensus/calls/chr20/AMR.admix/AMR.admix.phase1.chr20.42.raw.indels.vcf, /humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110608VQSRConsensus/calls/chr20/EUR.admix/EUR.admix.phase1.chr20.42.raw.indels.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub genotypemergeoption=PRIORITIZE filteredrecordsmergetype=KEEP_IF_ANY_UNFILTERED rod_priority_list=AFR.admix,AMR.admix,EUR.admix,ASN.admix,AFR,AMR,EUR,ASN printComplexMerges=false filteredAreUncalled=false minimalVCF=false setKey=set assumeIdenticalSamples=false minimumN=1 masterMerge=false mergeInfoWithMaxAC=true"
+##FILTER=<ID=BothStrands,Description="Variant not seen on both strands">
+##FILTER=<ID=HARD_TO_VALIDATE,Description="MQ0 >= 4 && (MQ0 / (1.0 * DP)) > 0.1">
+##FILTER=<ID=HP10,Description="Variant occurs in long homopolymer run (>10)">
+##FILTER=<ID=HaplotypeScore,Description="HaplotypeScore>20.0">
+##FILTER=<ID=HighCoverage,Description="Coverage at variant site is > 7500">
+##FILTER=<ID=HomopolymerRun,Description="HRun>=15">
+##FILTER=<ID=LongRepeat,Description="Variant occurs in long tandem repeat (as defined by 1kg phase one filters)">
+##FILTER=<ID=LowQual,Description="QUAL<30.0">
+##FILTER=<ID=PP20,Description="Variant posterior phred is < 20">
+##FILTER=<ID=QualByDepth,Description="QD<1.0">
+##FILTER=<ID=StrandBias,Description="SB>=-1.0">
+##FILTER=<ID=TruthSensitivityTranche93.00to94.00,Description="Truth sensitivity tranche level at VSQ Lod: 3.9628 <= x < 4.1824">
+##FILTER=<ID=TruthSensitivityTranche94.00to95.00,Description="Truth sensitivity tranche level at VSQ Lod: 3.7129 <= x < 3.9628">
+##FILTER=<ID=TruthSensitivityTranche95.00to96.00,Description="Truth sensitivity tranche level at VSQ Lod: 3.3717 <= x < 3.7129">
+##FILTER=<ID=TruthSensitivityTranche96.00to97.00,Description="Truth sensitivity tranche level at VSQ Lod: 2.8762 <= x < 3.3717">
+##FILTER=<ID=TruthSensitivityTranche97.00to98.00,Description="Truth sensitivity tranche level at VSQ Lod: 2.2618 <= x < 2.8762">
+##FILTER=<ID=TruthSensitivityTranche98.00to99.00+,Description="Truth sensitivity tranche level at VQS Lod < 1.2907">
+##FILTER=<ID=TruthSensitivityTranche98.00to99.00,Description="Truth sensitivity tranche level at VSQ Lod: 1.2907 <= x < 2.2618">
+##FORMAT=<ID=AA,Number=1,Type=Integer,Description="Alternate allele observations">
+##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth (only filtered reads used for calling)">
+##FORMAT=<ID=FT,Number=1,Type=String,Description="Sample Genotype Filter">
+##FORMAT=<ID=GL,Number=3,Type=Integer,Description="Genotype Likelihood, log-scaled likeilhoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy">
+##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=HQ,Number=.,Type=Integer,Description="Haplotype Quality">
+##FORMAT=<ID=PL,Number=3,Type=Float,Description="Normalized, Phred-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; not applicable if site is not biallelic">
+##FORMAT=<ID=RA,Number=1,Type=Integer,Description="Reference allele observations">
+##FORMAT=<ID=SA,Number=1,Type=Integer,Description="Number of alternate observations by strand, delimited by |: [forward]|[reverse]">
+##FORMAT=<ID=SP,Number=1,Type=Integer,Description="Phred-scaled strand bias P-value">
+##FORMAT=<ID=SR,Number=1,Type=Integer,Description="Number of reference observations by strand, delimited by |: [forward]|[reverse]">
+##INFO=<ID=AA,Number=1,Type=Integer,Description="Alternate allele observations">
+##INFO=<ID=AB,Number=1,Type=Float,Description="Allele balance at heterozygous sites: a number between 0 and 1 representing the ratio of reads showing the reference allele to all reads, considering only reads from individuals called as heterozygous">
+##INFO=<ID=ABA,Number=1,Type=Integer,Description="Alternate allele balance count: the number of sequence reads from apparent heterozygotes supporting the alternate allele">
+##INFO=<ID=ABP,Number=1,Type=Float,Description="Allele balance probability at heterozygous sites: Phred-scaled upper-bounds estimate of the probability of observing the deviation between ABR and ABA given E(ABR/ABA) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=ABR,Number=1,Type=Integer,Description="Reference allele balance count: the number of sequence reads from apparent heterozygotes supporting the reference allele">
+##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
+##INFO=<ID=AF1,Number=1,Type=Float,Description="Max-likelihood estimate of the site allele frequency of the first ALT allele">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##INFO=<ID=BL,Number=1,Type=Integer,Description="Base Pairs Left: number of base pairs in reads supporting the alternate to the left (5') of the alternate allele">
+##INFO=<ID=BR,Number=1,Type=Integer,Description="Base Pairs Right: number of base pairs in reads supporting the alternate to the right (3') of the alternate allele">
+##INFO=<ID=BVAR,Number=0,Type=Flag,Description="The best genotype combination in the posterior is variant (non homozygous).">
+##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
+##INFO=<ID=CI95,Number=2,Type=Float,Description="Equal-tail Bayesian credible interval of the site allele frequency at the 95% level">
+##INFO=<ID=CpG,Number=0,Type=Flag,Description="CpG site (either CpG, TpG or CpA)">
+##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership">
+##INFO=<ID=DEL,Number=0,Type=Flag,Description="deletion allele">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Filtered Depth">
+##INFO=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
+##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">
+##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions">
+##INFO=<ID=EL,Number=1,Type=Integer,Description="Allele End Left: number of observations of the alternate where the alternate occurs in the left end of the read">
+##INFO=<ID=EPP,Number=1,Type=Float,Description="End Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=ER,Number=1,Type=Integer,Description="Allele End Right: number of observations of the alternate where the alternate occurs in the right end of the read">
+##INFO=<ID=FQ,Number=1,Type=Float,Description="Phred probability that sample chromosomes are not all the same">
+##INFO=<ID=FR,Number=0,Type=Float,Description="Estimated population frequency">
+##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
+##INFO=<ID=HETAR,Number=1,Type=Integer,Description="Number of individuals heterozygous alternate / reference">
+##INFO=<ID=HOMA,Number=1,Type=Integer,Description="Number of individuals homozygous for the alternate">
+##INFO=<ID=HOMR,Number=1,Type=Integer,Description="Number of individuals homozygous for the reference">
+##INFO=<ID=HP,Number=1,Type=Integer,Description="Homopolmer run length">
+##INFO=<ID=HPLen,Number=1,Type=Integer,Description="Homopolymer length">
+##INFO=<ID=HR,Number=1,Type=Integer,Description="Homopolymer run length">
+##INFO=<ID=HRun,Number=1,Type=Integer,Description="Largest Contiguous Homopolymer Run of Variant Allele In Either Direction">
+##INFO=<ID=HU,Number=1,Type=String,Description="Homopolymer run unit (stranded)">
+##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes">
+##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Not provided in original VCF header">
+##INFO=<ID=INS,Number=0,Type=Flag,Description="insertion allele">
+##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">
+##INFO=<ID=KGPilot123,Number=0,Type=Flag,Description="1000 Genome discovery all pilots 2010(1,2,3)">
+##INFO=<ID=LEN,Number=1,Type=Integer,Description="allele length">
+##INFO=<ID=LRB,Number=1,Type=Float,Description="((max(BR, BL) / (BR + BL)) - 0.5) * 2 : The proportion of base pairs in reads on one side of the alternate allele relative to total bases, scaled from [0.5,1] to [0,1]">
+##INFO=<ID=LRBP,Number=1,Type=Float,Description="Left-Right Balance Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between BL and BR given E(BR/BL) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=MNP,Number=0,Type=Flag,Description="MNP allele">
+##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
+##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
+##INFO=<ID=MQ0Fraction,Number=1,Type=Float,Description="Fraction of Mapping Quality Zero Reads">
+##INFO=<ID=MQM,Number=1,Type=Float,Description="Mean mapping quality of observed alternate alleles">
+##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
+##INFO=<ID=NF,Number=0,Type=Integer,Description="Total number of forward reads containing this variant">
+##INFO=<ID=NR,Number=0,Type=Integer,Description="Total number of reads containing this variant">
+##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data">
+##INFO=<ID=PP,Number=0,Type=Float,Description="Posterior probability (phred scaled) that this variant segregates">
+##INFO=<ID=PV4,Number=4,Type=Float,Description="P-values for strand bias, baseQ bias, mapQ bias and tail distance bias">
+##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
+##INFO=<ID=RA,Number=1,Type=Integer,Description="Reference allele observations">
+##INFO=<ID=RL,Number=1,Type=Integer,Description="Reads Placed Left: number of reads supporting the alternate balanced to the left (5') of the alternate allele">
+##INFO=<ID=RPP,Number=1,Type=Float,Description="Read Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=RR,Number=1,Type=Integer,Description="Reads Placed Right: number of reads supporting the alternate balanced to the right (3') of the alternate allele">
+##INFO=<ID=RUN,Number=1,Type=Integer,Description="Homopolymer run length: the number of consecutive nucleotides in the reference genome matching the alternate allele prior to the current position">
+##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
+##INFO=<ID=SAB,Number=1,Type=Float,Description="Strand bias for the alternate allele: SAF / ( SAF + SAR )">
+##INFO=<ID=SAF,Number=1,Type=Integer,Description="Number of alternate observations on the forward strand">
+##INFO=<ID=SAP,Number=1,Type=Float,Description="Strand balance probability for the alternate allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SAF and SAR given E(SAF/SAR) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=SAR,Number=1,Type=Integer,Description="Number of alternate observations on the reverse strand">
+##INFO=<ID=SB,Number=1,Type=Float,Description="Strand Bias">
+##INFO=<ID=SC,Number=1,Type=String,Description="Genomic sequence 10 bases either side of variant position">
+##INFO=<ID=SNP,Number=0,Type=Flag,Description="SNP allele">
+##INFO=<ID=SRB,Number=1,Type=Float,Description="Strand bias for the reference allele: SRF / ( SRF + SRR )">
+##INFO=<ID=SRF,Number=1,Type=Integer,Description="Number of reference observations on the forward strand">
+##INFO=<ID=SRP,Number=1,Type=Float,Description="Strand balance probability for the reference allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SRF and SRR given E(SRF/SRR) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=SRR,Number=1,Type=Integer,Description="Number of reference observations on the reverse strand">
+##INFO=<ID=TC,Number=0,Type=Integer,Description="Total coverage">
+##INFO=<ID=TR,Number=1,Type=Integer,Description="Tandem repeat run length (bp)">
+##INFO=<ID=TS,Number=0,Type=Flag,Description="transition SNP">
+##INFO=<ID=TU,Number=1,Type=String,Description="tandem repeat run unit (stranded)">
+##INFO=<ID=TV,Number=0,Type=Flag,Description="transversion SNP">
+##INFO=<ID=VLD,Number=0,Type=Flag,Description="Is Validated.  This bit is set if the snp has 2+ minor allele count based on frequency or genotype data.">
+##INFO=<ID=VQSLOD,Number=1,Type=Float,Description="Log odds ratio of being a true variant versus being false under the trained gaussian mixture model">
+##INFO=<ID=dbSNP,Number=1,Type=Integer,Description="First SNP Build for RS">
+##INFO=<ID=set,Number=1,Type=String,Description="Source VCF for the merged record in CombineVariants">
+##LeftAlignVariants="analysis_type=LeftAlignVariants input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=[20] excludeIntervals=null reference_sequence=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta rodBind=[/humgen/gsa-scr1/ebanks/ALL.chr20.Oxford.20110407.indels.genotypes.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub"
+##SelectVariants="analysis_type=SelectVariants input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=[20] excludeIntervals=null reference_sequence=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta rodBind=[/humgen/gsa-scr1/delangel/officialCalls/20110201_chr20_phase1_indels/dindel/20110208.chr20.dindel2.ALL.sites.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sample=null select_expressions=[] excludeNonVariants=false excludeFiltered=false discordance= concordance= family_structure= mendelianViolation=false mendelianViolationQualThreshold=0.0 select_random_number=0 select_random_fraction=0.0 selectSNPs=false selectIndels=true"
+##UnifiedGenotyper="analysis_type=UnifiedGenotyper input_file=[/broad/shptmp/delangel/calls/chr20/CHB.phase1.chr20.42.cleaned.bam, /broad/shptmp/delangel/calls/chr20/CHS.phase1.chr20.42.cleaned.bam, /broad/shptmp/delangel/calls/chr20/CLM.phase1.chr20.42.cleaned.bam, /broad/shptmp/delangel/calls/chr20/JPT.phase1.chr20.42.cleaned.bam, /broad/shptmp/delangel/calls/chr20/MXL.phase1.chr20.42.cleaned.bam, /broad/shptmp/delangel/calls/chr20/PUR.phase1.chr20.42.cleaned.bam] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=[20:41000001-42000000] excludeIntervals=null reference_sequence=/humgen/1kg/reference/human_g1k_v37.fasta rodBind=[/humgen/gsa-scr1/delangel/otherIndelCallerAnalysis/ALL.indels.combined.chr20.vcf, /humgen/gsa-hpprojects/GATK/data/dbsnp_132_b37.leftAligned.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=50 baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=8 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false genotype_likelihoods_model=INDEL p_nonref_model=EXACT heterozygosity=0.0010 pcr_error_rate=1.0E-4 genotyping_mode=GENOTYPE_GIVEN_ALLELES output_mode=EMIT_ALL_SITES standard_min_confidence_threshold_for_calling=4.0 standard_min_confidence_threshold_for_emitting=4.0 noSLOD=false assume_single_sample_reads=null abort_at_too_much_coverage=-1 min_base_quality_score=17 min_mapping_quality_score=20 max_deletion_fraction=0.05 min_indel_count_for_genotyping=5 indel_heterozygosity=1.25E-4 indelGapContinuationPenalty=10.0 indelGapOpenPenalty=45.0 indelHaplotypeSize=80 doContextDependentGapPenalties=true getGapPenaltiesFromData=false indel_recal_file=indel.recal_data.csv indelDebug=false dovit=false GSA_PRODUCTION_ONLY=false exactCalculation=LINEAR_EXPERIMENTAL ignoreSNPAlleles=true output_all_callable_bases=false genotype=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub debug_file=null metrics_file=null annotation=[MappingQualityZeroFraction]"
+##VariantFiltration="analysis_type=VariantFiltration input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=[/humgen/1kg/processing/pipeline_test_bams/chr22_chunked.hg19.intervals] excludeIntervals=null reference_sequence=/humgen/1kg/reference/human_g1k_v37.fasta rodBind=[/broad/shptmp/rpoplin/ALL.phase1.chr22.raw.indels.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false enable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null quiet_output_mode=false debug_mode=false help=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub filterExpression=[MQ0 >= 4 && (MQ0 / (1.0 * DP)) > 0.1, QUAL<30.0, SB>=-1.0, QD<1.0, HRun>=15, HaplotypeScore>20.0] filterName=[HARD_TO_VALIDATE, LowQual, StrandBias, QualByDepth, HomopolymerRun, HaplotypeScore] genotypeFilterExpression=[] genotypeFilterName=[] clusterSize=3 clusterWindowSize=0 maskName=Mask missingValuesInExpressionsShouldEvaluateAsFailing=false"
+##commandline="/share/software/freebayes/bin/freebayes --stdin --min-alternate-count 2 --genotype-combo-step-max 20 --genotype-variant-threshold 4 --no-marginals --pvar 0.0001 --indels --mnps --no-filters --binomial-obs-priors --allele-balance-priors --region 20:0..100000 --vcf /d1/data/1000G/20101123/populations/finalised.phase1/integrated/including454/wg/ALL/Pipeline/none//freebayes/freebayes.20:0-100000.baq.20110328.vcf --fasta-reference /d2/data/references/build_37/human_reference_v37.fa"
+##fileDate=2011-03-28
+##filedate=2011-02-08
+##filter="( SNP | MNP ) & ( MQM > 65 | QUAL > 1 ) & ABP < 30 & AB < 0.9 | ( INS | DEL ) & QUAL > 500"
+##phasing=none
+##platypusOptions={'bamFiles': ['/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA06984', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA06985', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA06986', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA06989', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA06994', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA07000', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA07037', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA07048', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA07051', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA07056', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA07346', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA07347', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA07357', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA10847', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA10851', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11829', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11830', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11831', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11832', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11843', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11881', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11892', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11893', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11894', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11918', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11919', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11920', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11930', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11931', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11932', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11933', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11992', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11993', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11994', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11995', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12003', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12004', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12005', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12006', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12043', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12044', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12045', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12046', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12058', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12144', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12154', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12155', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12156', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12234', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12249', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12272', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12273', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12275', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12282', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12283', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12286', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12287', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12340', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12341', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12342', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12347', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12348', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12383', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12399', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12400', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12413', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12414', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12489', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12546', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12716', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12717', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12718', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12748', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12749', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12750', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12751', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12761', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12763', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12775', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12776', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12777', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12778', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12813', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12827', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12828', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12829', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12830', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12842', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12843', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12889', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12890', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18486', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18487', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18488', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18489', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18498', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18499', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18501', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18502', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18504', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18505', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18507', 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'/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00380', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00403', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00404', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00418', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00419', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00421', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00422', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00427', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00428', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00436', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00437', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00442', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00443', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00448', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00449', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00463', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00464', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00472', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00473', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00475', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00476', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00478', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00479', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00500', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00501', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00512', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00513', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00524', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00525', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00530', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00531', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00533', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00534', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00536', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00537', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00542', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00543', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00551', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00553', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00554', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00556', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00557', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00559', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00560', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00565', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00566', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00577', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00578', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00580', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00581', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00583', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00584', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00589', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00590', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00592', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00593', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00595', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00596', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00607', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00608', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00610', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00611', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00613', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00614', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00619', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00620', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00625', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00626', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00628', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00629', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00634', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00635', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00637', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00638', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00640', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00641', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00650', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00651', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00653', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00654', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00656', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00657', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00662', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00663', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00671', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00672', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00683', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00684', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00689', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00690', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00692', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00693', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00698', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00699', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00701', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00702', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00704', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00705', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00707', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00708', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00731', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00732', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00734', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00736', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00737', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00739', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG00740', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01047', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01048', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01051', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01052', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01055', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01060', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01061', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01066', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01067', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01069', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01070', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01072', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01073', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01075', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01079', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01080', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01082', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01083', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01094', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01095', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01097', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01098', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01101', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01102', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01107', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01108', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01110', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01111', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01112', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01113', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01124', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01125', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01133', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01134', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01136', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01137', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01140', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01148', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01149', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01167', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01168', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01170', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01171', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01173', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01174', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01176', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01177', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01182', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01183', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01187', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01188', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01190', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01191', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01197', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01198', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01204', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01250', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01251', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01253', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01254', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01334', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01342', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01350', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01351', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01353', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01354', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01356', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01357', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01359', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01360', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01365', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01366', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01374', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01375', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01377', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01378', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01383', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01384', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01389', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01390', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01437', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01440', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01441', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01455', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01456', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01461', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01462', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01464', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01465', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01488', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01489', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01491', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01492', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01494', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01495', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01497', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01498', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01515', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01516', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01518', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01519', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01521', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01522', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01550', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01551'], 'minReads': 2, 'refFile': '/scratch/rimmer/Genomes/human_g1k_v37_ebv.fa', 'maxHaplotypes': 64, 'maxSize': 100, 'ploidy': 2, 'maxRegionSize': 10000, 'nCPU': 1, 'minFlank': 3, 'logFileName': 'LogsAllPhaseOne/ThousandGenomesPhaseOneCalls_20:1-100001.log', 'regions': ['20:1-100001'], 'maxVariants': 6, 'genIndels': 1, 'labels': None, 'dataType': 'population', 'minMapQual': 20, 'rlen': 100, 'nInd': 994, 'getVariantsFromBAMs': 1, 'genSNPs': 1, 'minReadQual': 20, 'maxCoverage': 1000000.0, 'verbosity': 2, 'sourceFile': None, 'callOnlyIndels': 1, 'output': 'VariantCallsAllPhaseOne/ThousandGenomesPhaseOneCalls_20:1-100001.vcf'}
+##reference=/lustre/scratch105/projects/g1k/ref/main_project/human_g1k_v37.fasta
+##source=Dindel2
+##source=SelectVariants
+##source_20110031.1=/nfs/users/nfs_p/pd3/cvs/vcftools/perl/vcf-annotate -d /nfs/users/nfs_p/pd3/sandbox/hapmap/dbSNP-b132/non-1kg-vld.desc -a /nfs/users/nfs_p/pd3/sandbox/hapmap/dbSNP-b132/non-1kg-vld.tab.gz -c CHROM,FROM,INFO/VLD,INFO/KGPilot123,INFO/dbSNP
+##vcfCTools=filter
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freebayes.20:2100000-2200000.baq.20110328.vcf, freebayes.20:2200000-2300000.baq.20110328.vcf, freebayes.20:2300000-2400000.baq.20110328.vcf, freebayes.20:2400000-2500000.baq.20110328.vcf, freebayes.20:2500000-2600000.baq.20110328.vcf, freebayes.20:2600000-2700000.baq.20110328.vcf, freebayes.20:2700000-2800000.baq.20110328.vcf, freebayes.20:2800000-2900000.baq.20110328.vcf, freebayes.20:2900000-3000000.baq.20110328.vcf, freebayes.20:3000000-3100000.baq.20110328.vcf, freebayes.20:3100000-3200000.baq.20110328.vcf, freebayes.20:3200000-3300000.baq.20110328.vcf, freebayes.20:3300000-3400000.baq.20110328.vcf, freebayes.20:3400000-3500000.baq.20110328.vcf, freebayes.20:3500000-3600000.baq.20110328.vcf, freebayes.20:3600000-3700000.baq.20110328.vcf, freebayes.20:3700000-3800000.baq.20110328.vcf, freebayes.20:3800000-3900000.baq.20110328.vcf, freebayes.20:3900000-4000000.baq.20110328.vcf, freebayes.20:4000000-4100000.baq.20110328.vcf, freebayes.20:4100000-4200000.baq.20110328.vcf, 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+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
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+20	539571	.	TG	T	18546	PASS	AA=71;AB=0.92482;ABA=63;ABP=1316.6;ABR=775;AC=42;AF=0.03512;AN=1196;BL=3915;BR=252;BVAR;BaseQRankSum=0.556;DEL;DP=10073;Dels=0.01;EL=47;EPP=19.189;ER=24;FS=2.124;HETAR=290;HOMA=156;HOMR=570;HRun=1;InbreedingCoeff=0.0620;LEN=1;LRB=0.87905;LRBP=6995.1;MQ0=0;MQ0Fraction=0.0000;MQM=127.99;MQRankSum=0.410;NS=1016;RA=3090;RL=71;RPP=157.18;RR=0;RUN=1;ReadPosRankSum=-11.038;SAB=0.66197;SAF=47;SAP=19.189;SAR=24;SRB=0.55016;SRF=1700;SRP=70.544;SRR=1390;VQSLOD=2.6772;set=filterInVQSR-2of5;sumGLbyD=4.71
+20	573764	.	TA	T	591.51	PASS	AC=91;AF=0.1987;AN=458;BaseQRankSum=0.137;DP=519;FS=3.153;HRun=1;HaplotypeScore=14.0744;InbreedingCoeff=0.1460;MQ=48.16;MQ0=26;MQ0Fraction=0.0501;MQRankSum=-1.636;QD=3.63;ReadPosRankSum=-4.140;SB=-408.14;VQSLOD=5.2458;set=VQSR
+20	766143	.	C	A,CATCTGGTA	5521.70	PASS	AA=24;AB=0.5;ABA=18;ABP=3.0103;ABR=18;AC=14;AF=0.0289;AF1=0.02038;AN=484;BL=655;BR=1542;BVAR;BaseQRankSum=3.801;CI95=0.01549,0.02655;DP=11749;DP4=2222,1998,14,8;Dels=0.00;EL=9;EPP=6.2675;ER=15;FQ=999;FR;FS=2.941;HETAR=9;HOMA=4;HOMR=901;HP=2;HPLen=2;HR=1;HRun=0;HU=A;INDEL;INS;InbreedingCoeff=0.0515;LEN=8;LRB=0.40373;LRBP=780.64;MQ=56.81;MQ0Fraction=0.0253;MQM=22.167;MQRankSum=-4.809;NF;NR;NS=914;PP;PV4=0.39,1,5.8e-07,1;RA=3093;RL=6;RPP=16.039;RR=18;RUN=1;ReadPosRankSum=-2.827;SAB=0.625;SAF=15;SAP=6.2675;SAR=9;SC=GCTTTAAATTCATCTGGTACT;SRB=0.61623;SRF=1906;SRP=365.95;SRR=1187;TC;TR=1;TU=A;VQSLOD=7.0268;set=Intersection;sumGLbyD=50.23
+20	997076	rs11467490	CTG	C	15379.78	PASS	AA=195;AB=0.59878;ABA=132;ABP=30.896;ABR=197;AC=173;AF=0.14562;AN=1188;BL=7664;BR=7309;BVAR;BaseQRankSum=21.853;DB;DEL;DP=27127;DP4=1801,2002,241,282;Dels=0.13;EL=100;EPP=3.2887;ER=95;FQ=999;FR;FS=6.591;HETAR=77;HOMA=42;HOMR=815;HP=1;HPLen=1;HR=1;HRun=0;HU=T;INDEL;InbreedingCoeff=0.1284;LEN=2;LRB=0.023709;LRBP=21.287;MQ=61.18;MQ0Fraction=0.0214;MQM=43.041;MQRankSum=6.886;NF;NR;NS=934;PP;PV4=0.61,1.5e-78,1,1;RA=2800;RL=120;RPP=25.56;RR=75;RUN=1;ReadPosRankSum=4.504;SAB=0.62051;SAF=121;SAP=27.609;SAR=74;SC=CAGCTAATTACTGTATTTTTA;SRB=0.49821;SRF=1395;SRP=3.0879;SRR=1405;TC;TR=1;TU=T;VQSLOD=8.9396;set=Intersection;sumGLbyD=16.76
+20	1042261	rs10597473	CCCTG	C	168658.05	PASS	AA=4481;AB=0.29043;ABA=2128;ABP=1147.1;ABR=871;AC=1172;AF=0.97830;AN=1198;BL=169975;BR=194027;BVAR;BaseQRankSum=4.599;DB;DEL;DP=29418;DP4=29,47,1441,2403;Dels=0.84;EL=2358;EPP=29.772;ER=2123;FR;FS=9.122;HETAR=482;HOMA=559;HOMR=30;HP=2;HPLen=3;HR=3;HRun=0;HU=C;INDEL;InbreedingCoeff=0.0470;LEN=4;LRB=0.066077;LRBP=3454.1;MQ=104.58;MQ0=4;MQ0Fraction=0.0014;MQM=58.257;MQRankSum=-3.368;NF;NR;NS=1071;PP;PV4=0.91,6.8e-09,2.8e-05,1;RA=1039;RL=2088;RPP=48.09;RR=2393;RUN=1;ReadPosRankSum=5.288;SAB=0.41442;SAF=1857;SAP=288.09;SAR=2624;SC=CCAAACCCAACCCTGCCTGGC;SRB=0.48893;SRF=508;SRP=4.1159;SRR=531;TC;TR=8;TU=CCTG;VQSLOD=8.5148;dbSNP=120;set=Intersection;sumGLbyD=59.79
+20	1046297	rs33956316	C	CT,CTT,CTTT	17698	PASS	ABR=408;AC=432,79,230;AF=0.39779,0.07274,0.21179;BVAR;BaseQRankSum=-8.413;DB;DP=15649;DP4=147,199,534,436;FR;FS=11.580;HOMA=97;HOMR=457;HP=20;HR=16;HU=T;HaplotypeScore=16.0590;INDEL;INS;InbreedingCoeff=0.6018;KGPilot123;MQ0=19;MQ0Fraction=0.0093;MQRankSum=7.992;NF;NR;NS=767;PP;PV4=6e-05,1,1,1;QD=8.18;RA=1183;RUN=1;ReadPosRankSum=2.684;SB=-6384.08;SC=GGAAAATTTTCTTTTTTTTTT;SRB=0.40913;SRF=484;SRP=87.859;SRR=699;TC;TR=16;TU=T;VQSLOD=8.4941;dbSNP=132;set=Intersection
+20	1405740	.	T	TA	257.28	PASS	AF=0.0188;BaseQRankSum=-0.745;DP=3769;Dels=0.00;FS=0.742;HPLen=9;HRun=9;InbreedingCoeff=0.0462;MQ0Fraction=0.0151;MQRankSum=-0.090;ReadPosRankSum=-1.582;VQSLOD=5.6502;set=Intersection;sumGLbyD=6.94
+20	1690501	.	TC	T	27928	PASS	AA=108;AB=0.91372;ABA=100;ABP=1726.1;ABR=1059;AC=35;AF=0.02966;AN=1180;BL=593;BR=6973;BVAR;BaseQRankSum=7.567;DEL;DP=10612;Dels=0.01;EL=50;EPP=4.2971;ER=58;FS=0.000;HETAR=378;HOMA=184;HOMR=477;HRun=1;InbreedingCoeff=0.0495;LEN=1;LRB=0.84325;LRBP=11685;MQ0=0;MQ0Fraction=0.0000;MQM=87.361;MQRankSum=4.088;NS=1045;RA=3125;RL=3;RPP=212.2;RR=105;RUN=1;ReadPosRankSum=-13.096;SAB=0.56481;SAF=61;SAP=6.9511;SAR=47;SRB=0.51776;SRF=1618;SRP=11.572;SRR=1507;VQSLOD=3.9824;set=filterInVQSR-2of5;sumGLbyD=4.07
+20	1948787	.	GTC	G,GTCTC	78.70	PASS	AC=18,18;AF=0.01466,0.01466;AN=1228;BaseQRankSum=3.894;DP=19030;DP4=1874,1916,21,20;FR;FS=0.767;HP=2;HPLen=1;HR=1;HU=T;HaplotypeScore=16.5619;INDEL;InbreedingCoeff=0.2332;MQ0=0;MQ0Fraction=0.0000;MQRankSum=2.080;NF;NR;PP;PV4=0.88,1,0.094,0.47;QD=0.28;ReadPosRankSum=0.822;SB=-172.46;SC=CTCGACCCCTGTCTCTCTCTC;TC;TR=13;TU=CT;VQSLOD=3.7405;set=filterInVQSR-2of5
+20	1991285	rs113891396	TAA	T,TA,TAAA,TAAAAA,TAAAAAA,TAAAAAAA,TAAAAAAAA	39235.36	PASS	AC=5,251,20,39,188,52,79;AF=0.0056,0.2789,0.0222,0.0433,0.2089,0.0578,0.0878;AN=900;BVAR;BaseQRankSum=1.124;DB;DEL;DP=54393;DP4=906,772,824,579;Dels=0.21;FR;FS=37.525;HP=12;HR=12;HRun=12;HU=A;INDEL;INS;InbreedingCoeff=0.6891;MQ=76.81;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-6.593;NF;NR;PP;PV4=0.0087,1,6.3e-19,1;RUN=1;ReadPosRankSum=-2.184;SC=ATCTGCCACTTAAAAAAAAAA;TC;TR=12;TU=A;VQSLOD=9.0007;dbSNP=132;set=Intersection;sumGLbyD=11.45
+20	2355911	.	TA	T	11723	PASS	AA=79;AB=0.9393;ABA=57;ABP=1577;ABR=882;AC=38;AF=0.0411;AN=924;BL=644;BR=5536;BVAR;BaseQRankSum=2.434;DEL;DP=9687;Dels=0.00;EL=45;EPP=6.3362;ER=34;FS=3.043;HETAR=321;HOMA=182;HOMR=555;HRun=5;InbreedingCoeff=0.0412;LEN=1;LRB=0.79159;LRBP=8411.9;MQ0=0;MQ0Fraction=0.0000;MQM=70.848;MQRankSum=0.137;NS=1058;RA=3415;RL=3;RPP=149.49;RR=76;RUN=1;ReadPosRankSum=-12.116;SAB=0.44304;SAF=35;SAP=5.2367;SAR=44;SRB=0.43572;SRF=1488;SRP=125.55;SRR=1927;VQSLOD=3.8910;set=filterInVQSR-2of5;sumGLbyD=4.88
+20	2512346	.	A	AC	11046.11	PASS	AC=673;AF=0.57034;AN=1180;BaseQRankSum=19.890;DP=2717;FS=26.809;HRun=0;HaplotypeScore=19.0575;InbreedingCoeff=0.3068;MQ=61.07;MQ0=25;MQ0Fraction=0.0092;MQRankSum=2.745;QD=5.80;ReadPosRankSum=3.139;SB=-4564.39;VQSLOD=4.3252;set=VQSR
+20	2597210	rs71329387	TAAAG	T	32206.62	PASS	AA=689;AB=0.5805;ABA=542;ABP=75.724;ABR=750;AC=253;AF=0.20738;BL=29921;BR=30215;BVAR;BaseQRankSum=20.638;DB;DEL;DP=29293;DP4=1750,1070,405,274;Dels=0.18;EL=345;EPP=3.0135;ER=344;FQ=999;FR;FS=1.827;HETAR=225;HOMA=55;HOMR=783;HP=7;HPLen=4;HR=3;HRun=0;HU=A;INDEL;InbreedingCoeff=0.1419;LEN=4;LRB=0.0048889;LRBP=6.1314;MQ=66.96;MQ0=0;MQ0Fraction=0.0000;MQM=42.925;MQRankSum=-7.105;NF;NR;NS=1063;PP;PV4=0.25,1,9e-20,1;RA=4619;RL=345;RPP=3.0135;RR=344;RUN=1;ReadPosRankSum=2.719;SAB=0.53556;SAF=369;SAP=10.577;SAR=320;SC=GAAAGGAAAATAAAGAAGGAG;SRB=0.52414;SRF=2421;SRP=26.389;SRR=2198;TC;TR=3;TU=A;VQSLOD=9.7974;dbSNP=130;set=Intersection;sumGLbyD=33.30
+20	2771621	rs11479849	GT	G,GTT	1605.60	PASS	AA=80;AB=0.79825;ABA=69;ABP=267.24;ABR=273;AC=79,91;AF=0.06551,0.07546;AN=1206;BL=2593;BR=3805;BVAR;BaseQRankSum=7.825;DB;DP=9790;Dels=0.04;EL=37;EPP=3.9875;ER=43;FR;FS=4.751;HETAR=62;HOMA=5;HOMR=958;HP=11;HR=11;HRun=11;HU=T;INS;InbreedingCoeff=0.2646;LEN=1;LRB=0.18943;LRBP=501.57;MQ0=0;MQ0Fraction=0.0000;MQM=52.45;MQRankSum=-0.560;NF;NR;NS=1025;PP;RA=3949;RL=29;RPP=16.148;RR=51;RUN=1;ReadPosRankSum=-2.397;SAB=0.525;SAF=42;SAP=3.4446;SAR=38;SC=TCATTTTAACGTTTTTTTTTT;SRB=0.54368;SRF=2147;SRP=68.46;SRR=1802;TC;TR=11;TU=T;VQSLOD=3.5989;set=filterInVQSR-2of5;sumGLbyD=3.92
+20	2891235	.	G	GT,GTTT	2869.87	PASS	AC=236,246;AF=0.2803,0.2922;AN=842;BaseQRankSum=8.979;DP=1067;FS=3.911;HaplotypeScore=20.3595;InbreedingCoeff=0.6511;MQ=44.86;MQ0=114;MQ0Fraction=0.1068;MQRankSum=-2.273;QD=4.00;ReadPosRankSum=-6.601;SB=-991.85;VQSLOD=5.4379;set=VQSR
+20	3033550	.	TGAG	T	2005.90	PASS	AA=34;AB=0.51429;ABA=34;ABP=3.1344;ABR=36;AC=22;AF=0.0332;AN=662;BL=1374;BR=1649;BVAR;BaseQRankSum=5.192;DEL;DP=14639;DP4=2271,1492,12,21;Dels=0.02;EL=19;EPP=4.0322;ER=15;FR;FS=16.657;HETAR=17;HOMA=0;HOMR=914;HP=1;HPLen=1;HR=1;HRun=0;HU=G;INDEL;InbreedingCoeff=-0.0454;LEN=3;LRB=0.090969;LRBP=57.333;MQ=53.99;MQ0Fraction=0.0304;MQM=46.735;MQRankSum=1.938;NF;NR;NS=931;PP;PV4=0.0068,9.4e-05,1,1;RA=2985;RL=11;RPP=12.207;RR=23;RUN=1;ReadPosRankSum=-0.466;SAB=0.41176;SAF=14;SAP=5.3095;SAR=20;SC=CTTGGGAGGCTGAGGTGGGAG;SRB=0.62781;SRF=1874;SRP=426.52;SRR=1111;TC;TR=1;TU=G;VQSLOD=8.9194;set=Intersection;sumGLbyD=24.41
+20	3635363	.	T	TG	999	PASS	AA=16;AB=0.61905;ABA=16;ABP=8.1805;ABR=26;AF=0.0141;AF1=0.01726;AN=708;BL=614;BR=523;BVAR;BaseQRankSum=2.337;CI95=0.01106,0.02434;DP=14594;DP4=2128,2038,6,10;Dels=0.00;EL=7;EPP=3.5532;ER=9;FQ=999;FR;FS=5.579;HETAR=8;HOMA=0;HOMR=1055;HP=3;HPLen=3;HR=3;HRun=3;HU=G;INDEL;INS;InbreedingCoeff=0.0633;LEN=1;LRB=0.080035;LRBP=18.826;MQ=100.74;MQ0=0;MQ0Fraction=0.0000;MQM=51.312;MQRankSum=2.569;NF;NR;NS=1063;PP;PV4=0.32,1,1,1;RA=5628;RL=9;RPP=3.5532;RR=7;RUN=1;ReadPosRankSum=-1.941;SAB=0.375;SAF=6;SAP=5.1818;SAR=10;SC=AAGGTTCGCTTGGGTGTGGAG;SRB=0.4984;SRF=2805;SRP=3.1353;SRR=2823;TC;TR=3;TU=G;VQSLOD=9.3275;set=Intersection;sumGLbyD=11.68
+20	3873327	rs61519218	A	AAG	683.85	PASS	AC=25;AF=0.0313;AN=800;BaseQRankSum=4.839;DB;DP=1718;FS=4.265;HRun=0;HaplotypeScore=20.5789;InbreedingCoeff=0.1055;MQ=53.70;MQ0=37;MQ0Fraction=0.0215;MQRankSum=2.468;QD=6.30;ReadPosRankSum=4.254;SB=-403.21;VQSLOD=6.1858;set=VQSR
+20	4028835	.	GC	G	2511.30	PASS	AA=66;AB=0.56954;ABA=65;ABP=9.3521;ABR=86;AC=22;AF=0.01836;AN=1198;BL=2303;BR=2463;BVAR;BaseQRankSum=7.621;DEL;DP=22795;DP4=1714,2774,22,37;Dels=0.02;EL=34;EPP=3.1419;ER=32;FQ=999;FR;FS=2.095;HETAR=21;HOMA=0;HOMR=1050;HP=2;HPLen=2;HR=2;HRun=2;HU=C;INDEL;InbreedingCoeff=0.0125;LEN=1;LRB=0.033571;LRBP=14.674;MQ=108.09;MQ0=0;MQ0Fraction=0.0000;MQM=53.318;MQRankSum=5.257;NF;NR;NS=1071;PP;PV4=1,5.4e-13,1,0.075;RA=6185;RL=36;RPP=4.1947;RR=30;RUN=1;ReadPosRankSum=-1.059;SAB=0.45455;SAF=30;SAP=4.1947;SAR=36;SC=TGCTGTCACTGCCTTCTCCTA;SRB=0.42118;SRF=2605;SRP=336.76;SRR=3580;TC;TR=2;TU=C;VQSLOD=10.2409;set=Intersection;sumGLbyD=12.71
+20	4039609	rs67812039	G	GA	43457	PASS	AA=909;AB=0.54639;ABA=572;ABP=26.583;ABR=689;AC=302;AF=0.3455;AN=874;BL=37070;BR=38211;BVAR;BaseQRankSum=20.147;DB;DP=25595;DP4=1483,1374,528,542;Dels=0.00;EL=467;EPP=4.5033;ER=442;FQ=999;FR;FS=5.441;HETAR=243;HOMA=127;HOMR=608;HP=4;HPLen=3;HR=3;HRun=3;HU=A;INDEL;INS;InbreedingCoeff=0.1388;LEN=1;LRB=0.015157;LRBP=40.563;MQ=119.50;MQ0=0;MQ0Fraction=0.0000;MQM=83.197;MQRankSum=1.080;NF;NR;NS=978;PP;PV4=0.16,1,3.6e-12,1;RA=3033;RL=443;RPP=4.274;RR=466;RUN=1;ReadPosRankSum=-1.000;SAB=0.32233;SAF=293;SAP=252.24;SAR=616;SC=TATGTTGGGAGAAATATCAGT;SRB=0.38378;SRF=1164;SRP=358.85;SRR=1869;TC;TR=4;TU=AG;VQSLOD=9.9146;dbSNP=130;set=Intersection;sumGLbyD=16.79
+20	4390056	.	TC	T	49312	PASS	AA=91;AB=0.94353;ABA=86;ABP=2605.4;ABR=1437;AC=39;AF=0.03160;AN=1234;BL=6823;BR=731;BVAR;BaseQRankSum=2.727;DEL;DP=13149;Dels=0.00;EL=41;EPP=4.9431;ER=50;FS=4.002;HETAR=465;HOMA=313;HOMR=292;HRun=3;InbreedingCoeff=0.0326;LEN=1;LRB=0.80646;LRBP=10671;MQ0=0;MQ0Fraction=0.0000;MQM=69.824;MQRankSum=-0.903;NS=1073;RA=3078;RL=89;RPP=183.62;RR=2;RUN=1;ReadPosRankSum=-12.526;SAB=0.45055;SAF=41;SAP=4.9431;SAR=50;SRB=0.52567;SRF=1618;SRP=20.622;SRR=1460;VQSLOD=4.3235;set=Intersection;sumGLbyD=3.53
+20	4474622	.	TA	AA,T,TAA,TAAA,TAAAA	94522.28	PASS	ABR=114;AC=38,68,16,900;AF=0.03333,0.05965,0.01404,0.78947;AN=1140;BVAR;BaseQRankSum=9.741;DB;DP=16656;Dels=0.00;FR;FS=2.355;HOMA=3;HOMR=936;HP=10;HPLen=10;HR=10;HRun=10;HU=A;INS;InbreedingCoeff=0.4516;MQ0=2;MQ0Fraction=0.0008;MQRankSum=-4.096;NF;NR;NS=980;PP;RA=3766;RUN=1;ReadPosRankSum=2.380;SC=AGAAAAAAATTAAAAAAAAAA;SRB=0.49734;SRF=1873;SRP=3.2409;SRR=1893;TC;TR=10;TU=A;VQSLOD=8.8186;set=Intersection;sumGLbyD=38.79
+20	4824911	.	AC	A	41998.70	PASS	AC=1172;AF=0.97342;AN=1204;BaseQRankSum=8.604;DP=3615;FS=9.934;HRun=1;HaplotypeScore=39.6843;InbreedingCoeff=0.0980;MQ=129.80;MQ0=1;MQ0Fraction=0.0003;MQRankSum=3.378;QD=11.62;ReadPosRankSum=6.967;SB=-16955.28;VQSLOD=4.2689;set=VQSR
+20	4839897	rs35881880	TAA	T,TA,TAAA,TAAAAA	3906.80	PASS	AC=12,95,137,189;AF=0.01024,0.08106,0.11689,0.16126;AN=1172;BVAR;BaseQRankSum=15.271;DB;DEL;DP=15105;Dels=0.04;FR;FS=43.567;HP=19;HR=13;HRun=13;HU=A;INS;InbreedingCoeff=0.5716;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-2.569;NF;NR;PP;RUN=1;ReadPosRankSum=-13.794;SC=TGTTAAAAAATAAAAAAAAAA;TC;TR=13;TU=A;VQSLOD=8.1773;set=Intersection;sumGLbyD=3.77
+20	5071386	.	AT	A	45200.27	PASS	AC=685;AF=0.7495;AN=914;BaseQRankSum=11.006;DP=2725;FS=8.133;HRun=3;HaplotypeScore=50.5496;InbreedingCoeff=0.2364;MQ=81.40;MQ0=0;MQ0Fraction=0.0000;MQRankSum=2.411;QD=18.51;ReadPosRankSum=3.429;SB=-22405.85;VQSLOD=4.2872;set=VQSR
+20	5507414	.	G	GCC	439.08	PASS	AC=23;AF=0.01876;AN=1226;BaseQRankSum=3.051;DP=3023;FS=3.636;HRun=1;HaplotypeScore=30.3104;InbreedingCoeff=0.0204;MQ=112.09;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-2.065;QD=2.85;ReadPosRankSum=-2.709;SB=-302.22;VQSLOD=4.4311;set=VQSR
+20	5609676	.	GA	G,GAA	799.89	PASS	AA=42;AB=0.79096;ABA=37;ABP=133.16;ABR=140;AC=43,65;AF=0.03607,0.05453;AF1=0.02826;AN=1192;BL=1360;BR=2334;BVAR;BaseQRankSum=5.069;CI95=0.01242,0.04037;DP=15610;DP4=1548,2441,21,30;Dels=0.02;EL=18;EPP=4.8716;ER=24;FQ=12.1;FR;FS=0.000;HETAR=36;HOMA=1;HOMR=991;HP=13;HPLen=10;HR=10;HRun=10;HU=A;INDEL;INS;InbreedingCoeff=0.2001;LEN=1;LRB=0.26367;LRBP=560.68;MQ=63.29;MQ0Fraction=0.0003;MQM=44.143;MQRankSum=1.755;NF;NR;NS=1028;PP;PV4=0.77,1,0.0087,0.0053;RA=4114;RL=15;RPP=10.455;RR=27;RUN=1;ReadPosRankSum=-2.978;SAB=0.5;SAF=21;SAP=3.0103;SAR=21;SC=AAAAAAGAAAGAAAAAAAAAA;SRB=0.39742;SRF=1635;SRP=379;SRR=2479;TC;TR=11;TU=AAAG;VQSLOD=4.1229;set=filterInVQSR-2of5;sumGLbyD=7.95
+20	5736211	rs35303106	CT	C,CTT	4384.40	PASS	AA=117;AB=0.71499;ABA=116;ABP=166.4;ABR=291;AC=32,145;AF=0.02712,0.12288;AN=1180;BL=5556;BR=4901;BVAR;BaseQRankSum=2.708;DB;DP=9157;Dels=0.01;EL=54;EPP=4.5136;ER=63;FR;FS=2.802;HETAR=79;HOMA=1;HOMR=837;HP=16;HR=11;HRun=11;HU=T;INS;InbreedingCoeff=0.1903;LEN=1;LRB=0.062637;LRBP=92.1;MQ0Fraction=0.0273;MQM=48.932;MQRankSum=3.654;NF;NR;NS=917;PP;RA=2785;RL=79;RPP=34.209;RR=38;RUN=1;ReadPosRankSum=0.795;SAB=0.5641;SAF=66;SAP=7.1862;SAR=51;SC=TTTTCTTTTTCTTTTTTTTTT;SRB=0.41795;SRF=1164;SRP=165.85;SRR=1621;TC;TR=11;TU=T;VQSLOD=5.0895;set=Intersection;sumGLbyD=4.66
+20	5898626	rs34483659	CAAA	C,CA,CAA,CAAAAA	1140.16	PASS	ABR=34;AC=19,98,56,199;AF=0.0227,0.1172,0.0670,0.2380;AF1=0.08519;BVAR;BaseQRankSum=5.049;CI95=0.03727,0.1273;DB;DEL;DP=5091;DP4=539,408,121,123;FQ=4.43;FR;FS=5.701;HOMA=64;HOMR=156;HP=19;HR=18;HU=A;HaplotypeScore=11.5333;INDEL;InbreedingCoeff=0.7405;MQ0=117;MQ0Fraction=0.0986;MQRankSum=6.290;NF;NR;NS=240;PP;PV4=0.043,1,1,0.0087;QD=1.22;RA=204;RUN=1;ReadPosRankSum=-2.684;SB=-1015.09;SC=ACTAAAAATACAAAAAAAAAA;SRB=0.35294;SRF=72;SRP=41.33;SRR=132;TC;TR=18;TU=A;VQSLOD=4.1696;set=filterInVQSR-2of5
+20	5975126	rs10541892	C	CAG	504.78	PASS	AC=79;AF=0.07004;AN=1128;BaseQRankSum=10.498;DB;DP=2050;FS=38.228;HRun=0;HaplotypeScore=14.1426;InbreedingCoeff=-0.0053;MQ=60.40;MQ0=80;MQ0Fraction=0.0390;MQRankSum=5.098;QD=1.63;ReadPosRankSum=-4.851;SB=-590.69;VQSLOD=4.8517;set=VQSR
+20	5992611	.	G	GT	799.56	PASS	AA=39;AB=0.8301;ABA=35;ABP=197.98;ABR=171;AC=13;AF=0.0183;AN=712;BL=1164;BR=1566;BVAR;BaseQRankSum=1.914;DP=9561;Dels=0.01;EL=16;EPP=5.7386;ER=23;FS=0.739;HETAR=32;HOMA=0;HOMR=1024;HRun=9;INS;InbreedingCoeff=0.0339;LEN=1;LRB=0.14725;LRBP=131.55;MQ0=0;MQ0Fraction=0.0000;MQM=97.231;MQRankSum=0.764;NS=1056;RA=5204;RL=16;RPP=5.7386;RR=23;RUN=1;ReadPosRankSum=-1.169;SAB=0.69231;SAF=27;SAP=15.538;SAR=12;SRB=0.56399;SRF=2935;SRP=188.09;SRR=2269;VQSLOD=4.6516;set=Intersection;sumGLbyD=5.96
+20	6040983	rs11087710	A	AAAAAAGAG,AAAAAGAG,AAAAGAG,AAAAGAGAG,AAAGAG,AAAGAGAG,AAGAG,AAGAGAG,AG,AGAG,AGAGAG	66894.55	PASS	ABR=468;AC=80,9,20,136,31,91,33,29,9,3,5;AF=0.0980,0.0110,0.0245,0.1667,0.0380,0.1115,0.0404,0.0355,0.0110,0.0037,0.0061;AN=816;BVAR;BaseQRankSum=-12.470;DB;DP=38726;DP4=426,611,310,472;Dels=0.00;FQ=999;FR;FS=6.635;HOMA=110;HOMR=506;HP=14;HR=15;HRun=0;HU=A;INDEL;INS;InbreedingCoeff=0.8291;KGPilot123;MQ=54.22;MQ0Fraction=0.0168;MQRankSum=-5.329;NF;NR;NS=861;PP;PV4=0.56,1,6.9e-09,0.31;RA=1828;RUN=1;ReadPosRankSum=-7.857;SC=AAAAAAAAAAAAGAGAGAGAG;SRB=0.62418;SRF=1141;SRP=247.85;SRR=687;TC;TR=15;TU=A;VQSLOD=9.0574;dbSNP=131;set=Intersection;sumGLbyD=36.72
+20	6903392	.	TC	CC,T	999	PASS	AF=0.0000;AF1=0.01192;CI95=0.008547,0.01709;DP=10440;DP4=2544,2062,9,11;Dels=0.01;FQ=999;FR;HP=2;HPLen=3;HR=3;HRun=2;HU=T;INDEL;InbreedingCoeff=0.0324;MQ=62.78;MQ0=2;MQ0Fraction=0.0009;NF;NR;PP;PV4=0.38,0.0069,0.36,0.41;QD=8.05;SB=-320.13;SC=TTATTTTCTTTCCAATTTTTA;TC;TR=8;TU=CTTT;set=filterInVQSR-2of5;sumGLbyD=13.22
+20	7024548	.	G	GAT	5041.27	PASS	AC=123;AF=0.10336;AN=1190;BaseQRankSum=23.097;DP=3045;FS=7.979;HRun=0;HaplotypeScore=15.6967;InbreedingCoeff=0.1062;MQ=119.29;MQ0=2;MQ0Fraction=0.0007;MQRankSum=-3.725;QD=8.97;ReadPosRankSum=-1.636;SB=-2257.45;VQSLOD=5.9332;set=VQSR
+20	7484554	.	A	AT	5.09	PASS	AC=0;AF=0.0000;AN=710;BaseQRankSum=-0.696;DP=1862;FS=2.835;HRun=9;HaplotypeScore=13.5425;InbreedingCoeff=0.0567;MQ=76.92;MQ0=0;MQ0Fraction=0.0000;MQRankSum=1.932;ReadPosRankSum=-1.701;VQSLOD=4.3156;set=VQSR
+20	7632194	rs77286341	GAA	AAA,G	5324	PASS	AC=0;AF=0.0000;AN=700;BaseQRankSum=-1.741;DB;DP=1772;FR;HP=4;HPLen=3;HR=3;HRun=0;HU=A;HaplotypeScore=60.1795;InbreedingCoeff=0.0017;MQ=70.69;MQ0=13;MQ0Fraction=0.0073;MQRankSum=-1.315;NF;NR;PP;ReadPosRankSum=-3.650;SC=GAGAGAGAGAGAAAGGTGTAA;TC;TR=13;TU=AG;set=filterInVQSR-2of5
+20	7767508	rs71329674	G	GA	17914	PASS	AA=415;AB=0.61617;ABA=337;ABP=105.94;ABR=541;AC=141;AF=0.11614;AN=1214;BL=15187;BR=20323;BVAR;BaseQRankSum=-13.946;DB;DP=28222;Dels=0.00;EL=184;EPP=14.569;ER=231;FQ=999;FR;FS=13.296;HETAR=178;HOMA=35;HOMR=822;HP=14;HPLen=9;HR=9;HRun=9;HU=A;INDEL;INS;InbreedingCoeff=0.0714;LEN=1;LRB=0.14464;LRBP=1616.1;MQ=89.69;MQ0=1;MQ0Fraction=0.0003;MQM=51.667;MQRankSum=0.664;NF;NR;NS=1035;PP;RA=3707;RL=171;RPP=30.894;RR=244;RUN=1;ReadPosRankSum=-1.120;SAB=0.45301;SAF=188;SAP=10.969;SAR=227;SC=ATTCTAAAAAGAAAAAAAAAT;SRB=0.38495;SRF=1427;SRP=429.23;SRR=2280;TC;TR=9;TU=A;VQSLOD=9.0748;set=Intersection;sumGLbyD=11.09
+20	7920261	.	TA	T,TAA	802.15	PASS	AA=28;AB=0.8;ABA=28;ABP=112.45;ABR=112;AC=22,39;AF=0.01836,0.03255;AN=1198;BL=943;BR=1487;BVAR;BaseQRankSum=2.233;DP=10645;Dels=0.01;EL=11;EPP=5.8022;ER=17;FR;FS=1.691;HETAR=20;HOMA=0;HOMR=1007;HP=10;HPLen=9;HR=9;HRun=9;HU=A;INS;InbreedingCoeff=0.2256;LEN=1;LRB=0.22387;LRBP=267.46;MQ0=0;MQ0Fraction=0.0000;MQM=57.571;MQRankSum=0.940;NF;NR;NS=1027;PP;RA=4776;RL=8;RPP=14.178;RR=20;RUN=1;ReadPosRankSum=-1.567;SAB=0.53571;SAF=15;SAP=3.3205;SAR=13;SC=GTAACTGCTATAAAAAAAAAC;SRB=0.48576;SRF=2320;SRP=11.42;SRR=2456;TC;TR=9;TU=A;VQSLOD=4.0815;set=filterInVQSR-2of5;sumGLbyD=5.37
+20	8012465	rs10595338	TATGA	T	2104.41	PASS	AF=0.03339;BaseQRankSum=10.662;DB;DP=11772;DS;Dels=0.01;FR;FS=7.678;HP=1;HPLen=1;HR=1;HRun=0;HU=A;InbreedingCoeff=0.0266;MQ0Fraction=0.0731;MQRankSum=0.603;NF;NR;PP;ReadPosRankSum=1.276;SC=TGTATGTATGTATGATGTATG;TC;TR=19;TU=ATGT;VQSLOD=4.1376;set=filterInVQSR-2of5;sumGLbyD=6.53
+20	8573999	.	CGTGT	C,CGT,CGTGTGT,TGTGT	45865.96	PASS	AC=458,0,731;AF=0.37727,0.00000,0.60214;AN=1214;BVAR;BaseQRankSum=-6.703;DEL;DP=37714;Dels=0.03;FR;FS=11.079;HP=2;HPLen=1;HR=1;HRun=0;HU=G;INDEL;INS;InbreedingCoeff=0.7632;LEN=2;MQ0Fraction=0.0026;MQRankSum=-1.394;NF;NR;PP;RUN=1;ReadPosRankSum=-2.102;SC=TGTGTGTGCGCGTGTGTGTGT;TC;TR=18;TU=GT;VQSLOD=6.1435;set=Intersection;sumGLbyD=3.53
+20	8610455	rs10571111	TTTTC	T	11763.51	PASS	AC=190;AF=0.17056;AN=1114;BaseQRankSum=-14.397;DB;DP=2323;FS=2.321;HRun=0;HaplotypeScore=39.8020;InbreedingCoeff=0.2502;MQ=53.39;MQ0=104;MQ0Fraction=0.0448;MQRankSum=3.519;QD=19.07;ReadPosRankSum=4.150;SB=-4067.02;VQSLOD=5.0554;set=VQSR
+20	9139079	.	ATT	A,AT,ATTT,ATTTT,ATTTTT	8777.90	PASS	AC=23,140,114,69,113;AF=0.01993,0.12132,0.09879,0.05979,0.09792;AN=1154;BVAR;BaseQRankSum=-0.022;DEL;DP=25109;DP4=502,657,278,313;FR;FS=11.929;HP=16;HR=16;HU=T;HaplotypeScore=20.2361;INDEL;INS;InbreedingCoeff=0.5704;MQ0=16;MQ0Fraction=0.0067;MQRankSum=2.624;NF;NR;PP;PV4=0.14,1,1,1;QD=1.48;RUN=1;ReadPosRankSum=-0.480;SB=-2354.28;SC=CACCTGGCTAATTTTTTTTTT;TC;TR=16;TU=T;VQSLOD=6.9180;set=Intersection
+20	9862448	.	CT	C	49312	PASS	AA=60;AB=0.96003;ABA=53;ABP=2440.4;ABR=1273;AC=18;AF=0.01461;AN=1232;BL=3516;BR=140;BVAR;BaseQRankSum=-2.056;DEL;DP=11893;Dels=0.01;EL=35;EPP=6.6294;ER=25;FS=1.787;HETAR=396;HOMA=344;HOMR=334;HRun=1;InbreedingCoeff=0.0379;LEN=1;LRB=0.92341;LRBP=6772.5;MQ0Fraction=0.0006;MQM=54.267;MQRankSum=-0.907;NS=1074;RA=2990;RL=60;RPP=133.3;RR=0;RUN=1;ReadPosRankSum=-10.579;SAB=0.58333;SAF=35;SAP=6.6294;SAR=25;SRB=0.47826;SRF=1430;SRP=15.284;SRR=1560;VQSLOD=3.0237;set=filterInVQSR-2of5;sumGLbyD=2.84
+20	9863736	rs73618103	G	GT	50570.21	PASS	AA=2247;AB=0.48878;ABA=1412;ABP=6.0324;ABR=1350;AC=546;AF=0.44463;AN=1228;BL=86886;BR=95862;BVAR;BaseQRankSum=-23.978;DB;DP=32517;DP4=1125,1133,1017,1048;Dels=0.00;EL=1089;EPP=7.6113;ER=1158;FQ=999;FR;FS=2.529;HETAR=445;HOMA=201;HOMR=393;HP=4;HPLen=4;HR=4;HRun=4;HU=T;INDEL;INS;InbreedingCoeff=0.1393;KGPilot123;LEN=1;LRB=0.049117;LRBP=960.35;MQ=68.10;MQ0=2;MQ0Fraction=0.0006;MQM=50.931;MQRankSum=-1.580;NF;NR;NS=1039;PP;PV4=0.71,1,0.11,1;RA=3139;RL=1089;RPP=7.6113;RR=1158;RUN=1;ReadPosRankSum=0.846;SAB=0.54161;SAF=1217;SAP=36.804;SAR=1030;SC=TGATTGTATGGTTTTGTCCTT;SRB=0.53425;SRF=1677;SRP=34.987;SRR=1462;TC;TR=4;TU=T;VLD;VQSLOD=10.1800;dbSNP=131;set=Intersection;sumGLbyD=18.20
+20	10640876	.	TA	T	42819	PASS	AA=86;AB=0.92316;ABA=75;ABP=1521;ABR=901;AC=40;AF=0.0447;AN=894;BL=6265;BR=415;BVAR;BaseQRankSum=-0.850;DEL;DP=8223;Dels=0.00;EL=41;EPP=3.4143;ER=45;FS=3.190;HETAR=336;HOMA=384;HOMR=290;HRun=1;InbreedingCoeff=0.0173;LEN=1;LRB=0.87575;LRBP=11128;MQ0=0;MQ0Fraction=0.0000;MQM=76.163;MQRankSum=1.314;NS=1034;RA=2046;RL=83;RPP=164.61;RR=3;RUN=1;ReadPosRankSum=-12.060;SAB=0.46512;SAF=40;SAP=3.9193;SAR=46;SRB=0.5523;SRF=1130;SRP=51.615;SRR=916;VQSLOD=3.9183;set=filterInVQSR-2of5;sumGLbyD=4.00
+20	10926959	.	AG	A	12239	PASS	AA=65;AB=0.92801;ABA=64;ABP=1417.6;ABR=825;AC=24;AF=0.0264;AN=908;BL=616;BR=3782;BVAR;BaseQRankSum=9.990;DEL;DP=10708;Dels=0.01;EL=37;EPP=5.7163;ER=28;FS=1.652;HETAR=275;HOMA=70;HOMR=724;HRun=1;InbreedingCoeff=0.0102;LEN=1;LRB=0.71987;LRBP=4952;MQ0=1;MQ0Fraction=0.0004;MQM=118.82;MQRankSum=1.018;NS=1069;RA=4746;RL=5;RPP=104.07;RR=60;RUN=1;ReadPosRankSum=-12.039;SAB=0.41538;SAF=27;SAP=7.0526;SAR=38;SRB=0.4764;SRF=2261;SRP=25.968;SRR=2485;VQSLOD=2.9713;set=filterInVQSR-2of5;sumGLbyD=4.10
+20	11299648	.	TG	T	49315	PASS	AA=62;AB=0.95292;ABA=54;ABP=2046.7;ABR=1093;AC=28;AF=0.0373;AN=750;BL=3126;BR=528;BVAR;BaseQRankSum=-4.929;DEL;DP=10764;Dels=0.01;EL=26;EPP=6.5127;ER=36;FS=3.851;HETAR=366;HOMA=383;HOMR=304;HRun=1;InbreedingCoeff=0.0267;LEN=1;LRB=0.711;LRBP=4014.1;MQ0=1;MQ0Fraction=0.0005;MQM=76.468;MQRankSum=1.327;NS=1070;RA=2588;RL=54;RPP=77.121;RR=8;RUN=1;ReadPosRankSum=-12.507;SAB=0.48387;SAF=30;SAP=3.1504;SAR=32;SRB=0.47643;SRF=1233;SRP=15.499;SRR=1355;VQSLOD=3.8673;set=filterInVQSR-2of5;sumGLbyD=3.00
+20	11561096	.	CTA	C	999	PASS	AC=2;AF=0.0029;AF1=0.005602;BaseQRankSum=3.190;CI95=0.004425,0.01106;DP=7521;DP4=1998,1794,2,4;Dels=0.00;FQ=999;FR;FS=5.422;HP=3;HPLen=2;HR=1;HRun=0;HU=T;INDEL;InbreedingCoeff=0.0056;MQ=113.88;MQ0=0;MQ0Fraction=0.0000;MQRankSum=0.297;NF;NR;PP;PV4=0.43,0.024,1,1;ReadPosRankSum=1.406;SC=CAATAGTATTCTATGTCAGTC;TC;TR=1;TU=T;VQSLOD=8.6243;set=Intersection;sumGLbyD=21.89
+20	11723671	.	C	CA	1096.60	PASS	AA=35;AB=0.69565;ABA=35;ABP=41.247;ABR=80;AC=10;AF=0.0141;AN=710;BL=2005;BR=1702;BVAR;BaseQRankSum=-3.427;DP=9819;Dels=0.00;EL=20;EPP=4.5614;ER=15;FR;FS=3.814;HETAR=20;HOMA=0;HOMR=1034;HP=8;HPLen=7;HR=7;HRun=7;HU=A;INS;InbreedingCoeff=0.0323;LEN=1;LRB=0.081737;LRBP=56.79;MQ0=0;MQ0Fraction=0.0000;MQM=81.057;MQRankSum=0.050;NF;NR;NS=1054;PP;RA=5562;RL=22;RPP=8.0357;RR=13;RUN=1;ReadPosRankSum=-2.012;SAB=0.71429;SAF=25;SAP=16.97;SAR=10;SC=ATATTGAAGACAAAAAAACAG;SRB=0.49371;SRF=2746;SRP=4.9233;SRR=2816;TC;TR=7;TU=A;VQSLOD=7.4342;set=Intersection;sumGLbyD=8.30
+20	11767787	.	CA	C	1382.10	PASS	AA=24;AB=0.56667;ABA=13;ABP=4.1684;ABR=17;AC=10;AF=0.00810;AN=1234;BL=967;BR=819;BVAR;BaseQRankSum=1.629;DEL;DP=22318;DP4=2190,2491,8,14;Dels=0.01;EL=16;EPP=8.8009;ER=8;FQ=999;FR;FS=2.536;HETAR=6;HOMA=3;HOMR=1051;HP=2;HPLen=1;HR=1;HRun=1;HU=A;INDEL;InbreedingCoeff=0.0823;LEN=1;LRB=0.082867;LRBP=29.642;MQ=65.44;MQ0Fraction=0.0032;MQM=50.583;MQRankSum=0.931;NF;NR;NS=1060;PP;PV4=0.39,0.018,1,0.37;RA=5568;RL=11;RPP=3.3722;RR=13;RUN=1;ReadPosRankSum=-0.694;SAB=0.375;SAF=9;SAP=6.2675;SAR=15;SC=TGAACATGTACAGACTTGGTT;SRB=0.44325;SRF=2468;SRP=158.78;SRR=3100;TC;TR=1;TU=A;VQSLOD=9.9622;set=Intersection;sumGLbyD=15.42
+20	12021825	.	A	AG	1063.30	PASS	AA=26;AB=0.53704;ABA=25;ABP=3.6537;ABR=29;AC=12;AF=0.0214;AN=562;BL=1077;BR=815;BVAR;BaseQRankSum=-3.787;DP=22049;DP4=2650,2464,13,12;Dels=0.00;EL=18;EPP=11.362;ER=8;FR;FS=0.735;HETAR=12;HOMA=1;HOMR=1064;HP=1;HR=1;HRun=1;HU=G;INDEL;INS;InbreedingCoeff=0.0876;LEN=1;LRB=0.13848;LRBP=81.794;MQ=102.78;MQ0=0;MQ0Fraction=0.0000;MQM=85.538;MQRankSum=-0.126;NF;NR;NS=1077;PP;PV4=1,1,0.19,0.2;RA=6457;RL=17;RPP=8.3555;RR=9;RUN=1;ReadPosRankSum=-1.941;SAB=0.57692;SAF=15;SAP=4.3466;SAR=11;SC=GTAGTTTAACAGTTTATCAGG;SRB=0.5182;SRF=3346;SRP=21.582;SRR=3111;TC;TR=1;TU=G;VQSLOD=8.0483;set=Intersection;sumGLbyD=13.94
+20	12238835	rs113904674	CTCTTCATGGTCT	C	1813.44	PASS	AA=7;AB=0.73077;ABA=7;ABP=15.037;ABR=19;AC=4;AF=0.0056;AN=712;BL=360;BR=368;BVAR;BaseQRankSum=3.891;DB;DEL;DP=10309;Dels=0.00;EL=4;EPP=3.3205;ER=3;FR;FS=0.000;HETAR=3;HOMA=0;HOMR=1076;HP=1;HPLen=2;HR=2;HRun=0;HU=C;InbreedingCoeff=-0.0381;LEN=12;LRB=0.010989;LRBP=3.2012;MQ0=0;MQ0Fraction=0.0000;MQM=37;MQRankSum=-3.793;NF;NR;NS=1079;PP;RA=6085;RL=4;RPP=3.3205;RR=3;RUN=1;ReadPosRankSum=1.319;SAB=0.42857;SAF=3;SAP=3.3205;SAR=4;SC=CTTAATGCTCCTCTTCATGGT;SRB=0.51257;SRF=3119;SRP=11.364;SRR=2966;TC;TR=6;TU=CCT;VQSLOD=5.7551;set=Intersection;sumGLbyD=69.48
+20	12602812	.	AT	A	12344	PASS	AA=47;AB=0.94372;ABA=43;ABP=1309.5;ABR=721;AC=14;AF=0.0196;AN=716;BL=2714;BR=217;BVAR;BaseQRankSum=1.424;DEL;DP=10743;Dels=0.00;EL=24;EPP=3.0565;ER=23;FS=0.629;HETAR=228;HOMA=65;HOMR=769;HRun=1;InbreedingCoeff=0.0233;LEN=1;LRB=0.85193;LRBP=4622.3;MQ0Fraction=0.0000;MQM=99.574;MQRankSum=1.901;NS=1080;RA=4839;RL=46;RPP=96.568;RR=1;RUN=1;ReadPosRankSum=-9.906;SAB=0.53191;SAF=25;SAP=3.4261;SAR=22;SRB=0.51106;SRF=2473;SRP=8.148;SRR=2366;VQSLOD=2.8161;set=filterInVQSR-2of5;sumGLbyD=3.67
+20	13600884	.	CTG	C,CTGTG	1278.10	PASS	AA=85;AB=0.77994;ABA=79;ABP=247.38;ABR=280;AC=71,22;AF=0.05907,0.01830;AN=1202;BL=3279;BR=3205;BVAR;BaseQRankSum=8.852;DEL;DP=24185;DP4=1317,931,52,49;Dels=0.03;EL=45;EPP=3.649;ER=40;FQ=999;FR;FS=31.826;HETAR=75;HOMA=4;HOMR=926;HP=2;HPLen=1;HR=1;HRun=0;HU=T;INDEL;InbreedingCoeff=0.1566;LEN=2;LRB=0.011413;LRBP=4.8442;MQ=65.06;MQ0Fraction=0.0012;MQM=48.671;MQRankSum=-0.511;NF;NR;NS=1005;PP;PV4=0.18,1,0.39,0.27;RA=3342;RL=35;RPP=8.7583;RR=50;RUN=1;ReadPosRankSum=-2.329;SAB=0.43529;SAF=37;SAP=6.1015;SAR=48;SC=TCCCTTTACTCTGTGTGTGTG;SRB=0.59066;SRF=1974;SRP=241.62;SRR=1368;TC;TR=15;TU=GT;VQSLOD=3.8635;set=filterInVQSR-2of5;sumGLbyD=4.23
+20	13666265	.	T	TATAG	556.88	PASS	AC=21;AF=0.01959;AN=1072;BaseQRankSum=24.958;DP=2706;FS=2.581;HRun=0;HaplotypeScore=25.9952;InbreedingCoeff=0.1419;MQ=72.43;MQ0=0;MQ0Fraction=0.0000;MQRankSum=2.888;QD=4.38;ReadPosRankSum=2.552;SB=-417.04;VQSLOD=7.3380;set=VQSR
+20	13861245	rs72422273	C	CTCA	2685.46	PASS	AC=140;AF=0.11589;AN=1208;BaseQRankSum=24.355;DB;DP=2910;FS=6.808;HRun=0;HaplotypeScore=19.3095;InbreedingCoeff=-0.0991;MQ=78.25;MQ0=22;MQ0Fraction=0.0076;MQRankSum=3.225;QD=3.64;ReadPosRankSum=2.607;SB=-1861.38;VQSLOD=4.1974;set=VQSR
+20	13865746	.	T	TA,TAA	1416.23	PASS	AA=63;AB=0.80417;ABA=47;ABP=195.87;ABR=193;AC=122,21;AF=0.10133,0.01744;AN=1204;BL=3673;BR=1145;BVAR;BaseQRankSum=-3.336;DP=10513;Dels=0.00;EL=62;EPP=131.27;ER=1;FR;FS=716.583;HETAR=45;HOMA=1;HOMR=998;HP=2;HR=1;HRun=1;HU=A;INS;InbreedingCoeff=0.0814;LEN=1;LRB=0.5247;LRBP=2883.3;MQ0=0;MQ0Fraction=0.0000;MQM=56.143;MQRankSum=-1.197;NF;NR;NS=1044;PP;RA=4529;RL=62;RPP=131.27;RR=1;RUN=1;ReadPosRankSum=-12.295;SAB=1;SAF=63;SAP=139.81;SAR=0;SC=GGAACATGGATACCCCCCTGC;SRB=0.52462;SRF=2376;SRP=26.853;SRR=2153;TC;TR=1;TU=A;VQSLOD=-4.2308;set=filterInVQSR-2of5;sumGLbyD=4.77
+20	13881703	.	CTT	C	152.85	PASS	AC=8;AF=0.0093;AN=862;BaseQRankSum=3.941;DP=2063;FS=0.962;HRun=5;HaplotypeScore=24.0313;InbreedingCoeff=0.0790;MQ=55.05;MQ0=49;MQ0Fraction=0.0238;MQRankSum=-1.418;QD=3.47;ReadPosRankSum=-0.605;SB=-93.04;VQSLOD=5.3874;set=VQSR
+20	14033345	.	A	AT	2718.30	PASS	AA=91;AB=0.80899;ABA=85;ABP=372.04;ABR=360;AC=43;AF=0.03895;AN=1104;BL=3916;BR=4753;BVAR;BaseQRankSum=-6.609;DP=8350;Dels=0.02;EL=46;EPP=3.0342;ER=45;FR;FS=0.498;HETAR=70;HOMA=1;HOMR=871;HP=11;HR=11;HRun=11;HU=T;INS;InbreedingCoeff=0.0952;LEN=1;LRB=0.096551;LRBP=178.49;MQ0=0;MQ0Fraction=0.0000;MQM=54.879;MQRankSum=2.164;NF;NR;NS=942;PP;RA=3717;RL=37;RPP=9.9065;RR=54;RUN=1;ReadPosRankSum=-1.447;SAB=0.48352;SAF=44;SAP=3.2251;SAR=47;SC=TTGCAAACAGATTTTTTTTTT;SRB=0.45252;SRF=1682;SRP=75.807;SRR=2035;TC;TR=11;TU=T;VQSLOD=3.8299;set=filterInVQSR-2of5;sumGLbyD=3.88
+20	14260090	rs73619828	A	AT	27935	PASS	AA=596;AB=0.59484;ABA=487;ABP=96.922;ABR=715;AC=204;AF=0.17000;AN=1200;BL=21718;BR=28458;BVAR;BaseQRankSum=0.756;DB;DP=23629;DP4=1385,1492,287,328;Dels=0.00;EL=299;EPP=3.0249;ER=297;FQ=999;FR;FS=6.187;HETAR=218;HOMA=38;HOMR=788;HP=9;HPLen=9;HR=9;HRun=9;HU=T;INDEL;INS;InbreedingCoeff=0.0797;LEN=1;LRB=0.13433;LRBP=1969;MQ=100.81;MQ0=0;MQ0Fraction=0.0000;MQM=57.084;MQRankSum=2.224;NF;NR;NS=1044;PP;PV4=0.53,1,1.2e-11,1;RA=4143;RL=238;RPP=55.475;RR=358;RUN=1;ReadPosRankSum=0.198;SAB=0.46812;SAF=279;SAP=8.2714;SAR=317;SC=CCTTAAGTTGATTTTTTTTTC;SRB=0.50374;SRF=2087;SRP=3.514;SRR=2056;TC;TR=9;TU=T;VQSLOD=9.0018;set=Intersection;sumGLbyD=10.82
+20	14260558	.	AC	A	238	PASS	AC=1;AF=0.0014;AF1=0.003368;BaseQRankSum=2.868;CI95=0.003106,0.006211;DP=9724;DP4=2075,2329,1,7;Dels=0.00;FQ=106;FR;FS=10.678;HP=1;HPLen=2;HR=2;HRun=1;HU=A;INDEL;InbreedingCoeff=-0.0406;MQ=114.37;MQ0=0;MQ0Fraction=0.0000;MQRankSum=0.862;NF;NR;PP;PV4=0.074,0.0096,0.017,1;ReadPosRankSum=-0.042;SC=ATCAGGAATAACTGTGTGACC;TC;TR=2;TU=A;VQSLOD=8.1618;set=Intersection;sumGLbyD=18.65
+20	14425481	.	GTA	G,GTATA	148.85	PASS	AC=43,23;AF=0.03473,0.01858;AN=1238;BaseQRankSum=6.289;DP=25167;DP4=1800,2021,38,49;FR;FS=9.416;HP=2;HPLen=1;HR=1;HU=T;HaplotypeScore=17.7453;INDEL;InbreedingCoeff=0.0995;MQ0=21;MQ0Fraction=0.0058;MQRankSum=-0.200;NF;NR;PP;PV4=0.59,1,0.04,0.023;QD=0.35;ReadPosRankSum=-1.689;SB=-367.50;SC=CTGTGTGTGTGTATATATATA;TC;TR=13;TU=AT;VQSLOD=3.5796;set=filterInVQSR-2of5
+20	14943522	rs11478299	GA	AA,G	1761.24	PASS	AA=117;AB=0.68142;ABA=108;ABP=99.919;ABR=231;AC=0;AF=0.0000;AF1=0.04204;AN=712;BL=4931;BR=5802;BVAR;BaseQRankSum=9.118;CI95=0.02876,0.05752;DB;DEL;DP=13717;DP4=1908,1684,59,58;Dels=0.05;EL=60;EPP=3.1773;ER=57;FQ=81.9;FR;HETAR=56;HOMA=1;HOMR=1011;HP=8;HPLen=8;HR=8;HU=A;INDEL;InbreedingCoeff=0.1264;LEN=1;LRB=0.081152;LRBP=156.5;MQ=106.93;MQ0=0;MQ0Fraction=0.0000;MQM=96.855;MQRankSum=1.619;NF;NR;NS=1068;PP;PV4=0.57,1,0.0003,1;QD=7.40;RA=5080;RL=56;RPP=3.4743;RR=61;RUN=1;ReadPosRankSum=0.814;SAB=0.52137;SAF=61;SAP=3.4743;SAR=56;SB=-1122.51;SC=GTTGTTTGGGGAAAAAAAACT;SRB=0.51083;SRF=2595;SRP=8.1825;SRR=2485;TC;TR=8;TU=A;set=filterInVQSR-2of5;sumGLbyD=9.81
+20	14974486	.	A	AG	4101.40	PASS	AA=57;AB=0.57143;ABA=51;ABP=8.2839;ABR=68;AC=22;AF=0.01846;AN=1192;BL=2286;BR=2834;BVAR;BaseQRankSum=8.711;DP=20538;DP4=2172,2100,19,13;Dels=0.00;EL=32;EPP=4.877;ER=25;FS=0.517;HETAR=20;HOMA=4;HOMR=1027;HRun=1;INDEL;INS;InbreedingCoeff=0.0677;LEN=1;LRB=0.10703;LRBP=130.37;MQ=126.07;MQ0=0;MQ0Fraction=0.0000;MQM=56.088;MQRankSum=-10.756;NS=1051;PV4=0.38,3.5e-51,7.9e-34,1;RA=5203;RL=26;RPP=3.9627;RR=31;RUN=1;ReadPosRankSum=1.283;SAB=0.54386;SAF=31;SAP=3.9627;SAR=26;SRB=0.51816;SRF=2696;SRP=17.918;SRR=2507;VQSLOD=8.0072;set=Intersection;sumGLbyD=25.60
+20	15111137	.	GA	G	13533	PASS	AA=98;AB=0.84864;ABA=89;ABP=623.8;ABR=499;AC=47;AF=0.03796;AN=1238;BL=5324;BR=856;BVAR;BaseQRankSum=-11.577;DEL;DP=13384;Dels=0.01;EL=53;EPP=4.4284;ER=45;FS=6.099;HETAR=219;HOMA=845;HOMR=18;HRun=1;InbreedingCoeff=-0.0056;LEN=1;LRB=0.72298;LRBP=7017.4;MQ0Fraction=0.0003;MQM=90.449;MQRankSum=1.408;NS=1083;RA=590;RL=87;RPP=130.99;RR=11;RUN=1;ReadPosRankSum=-18.074;SAB=0.55102;SAF=54;SAP=5.2261;SAR=44;SRB=0.52373;SRF=309;SRP=5.8958;SRR=281;VQSLOD=4.1054;set=filterInVQSR-2of5;sumGLbyD=3.06
+20	15283028	.	A	AC,ACACACACACACAC	140844.83	PASS	AA=180;AB=0.61442;ABA=123;ABP=39.285;ABR=196;AC=13,817;AF=0.01111,0.69829;AN=1170;BL=4453;BR=11407;BVAR;BaseQRankSum=24.686;DP=6365;Dels=0.00;EL=124;EPP=58.793;ER=56;FR;FS=10.912;HETAR=87;HOMA=48;HOMR=683;HP=1;HR=1;HRun=1;HU=T;INS;InbreedingCoeff=0.2074;LEN=1;LRB=0.43846;LRBP=6624;MQ0Fraction=0.0558;MQM=38.211;MQRankSum=-21.111;NF;NR;NS=818;PP;RA=1732;RL=0;RPP=393.88;RR=180;RUN=1;ReadPosRankSum=-7.620;SAB=0.31111;SAF=56;SAP=58.793;SAR=124;SC=ACACACACACATACACACATA;SRB=0.54042;SRF=936;SRP=27.584;SRR=796;TC;TR=21;TU=AC;VQSLOD=4.7569;set=Intersection;sumGLbyD=18.36
+20	15361056	.	ATAACT	A	4892.81	PASS	AA=59;AB=0.63576;ABA=55;ABP=27.184;ABR=96;AC=34;AF=0.0487;AN=698;BL=3164;BR=1999;BVAR;BaseQRankSum=3.391;DEL;DP=7080;Dels=0.03;EL=27;EPP=3.9304;ER=32;FR;FS=4.816;HETAR=35;HOMA=6;HOMR=966;HP=2;HPLen=3;HR=3;HRun=0;HU=A;InbreedingCoeff=0.0785;LEN=5;LRB=0.22564;LRBP=573.84;MQ0=0;MQ0Fraction=0.0000;MQM=70.034;MQRankSum=-8.732;NF;NR;NS=1008;PP;RA=3915;RL=42;RPP=26.013;RR=17;RUN=1;ReadPosRankSum=-0.735;SAB=0.44068;SAF=26;SAP=4.8137;SAR=33;SC=AGATTAGGAAATAACTTAGGG;SRB=0.42682;SRF=1671;SRP=185.12;SRR=2244;TC;TR=3;TU=A;VQSLOD=7.0900;set=Intersection;sumGLbyD=43.38
+20	15579507	.	AATTAGTC	A,TATTAGTC	1936.38	PASS	AA=16;AB=0.58974;ABA=16;ABP=5.7386;ABR=23;AC=64;AF=0.05229;AN=1224;BL=699;BR=775;BVAR;BaseQRankSum=-21.390;DEL;DP=21920;DP4=2099,2403,6,6;Dels=0.00;EL=8;EPP=3.0103;ER=8;FR;FS=2.920;HETAR=5;HOMA=0;HOMR=1063;HP=3;HPLen=4;HR=4;HU=A;INDEL;InbreedingCoeff=-0.0143;LEN=7;LRB=0.05156;LRBP=11.519;MQ=129.49;MQ0=0;MQ0Fraction=0.0000;MQM=51.938;MQRankSum=3.331;NF;NR;NS=1068;PP;PV4=1,0.019,1.3e-07,1;RA=5334;RL=5;RPP=7.8961;RR=11;RUN=1;ReadPosRankSum=-16.901;SAB=0.4375;SAF=7;SAP=3.5532;SAR=9;SC=CATACTACAAAATTAGTCATT;SRB=0.41695;SRF=2224;SRP=322.58;SRR=3110;TC;TR=4;TU=A;VQSLOD=3.2237;set=filterInVQSR-2of5;sumGLbyD=43.57
+20	15752535	.	CT	C,GT	3775.20	PASS	AA=92;AB=0.78636;ABA=47;ABP=159.71;ABR=173;AC=0;AF=0.0000;AN=608;BL=4955;BR=2380;BVAR;BaseQRankSum=2.910;DEL;DP=3429;Dels=0.04;EL=13;EPP=105.82;ER=79;FR;HETAR=92;HOMA=95;HOMR=544;HP=2;HPLen=2;HR=2;HU=T;InbreedingCoeff=0.0483;LEN=1;LRB=0.35106;LRBP=1966;MQ0Fraction=0.0232;MQM=35.293;MQRankSum=-2.199;NF;NR;NS=732;PP;QD=4.91;RA=1272;RL=81;RPP=118.66;RR=11;RUN=1;ReadPosRankSum=-1.077;SAB=0.021739;SAF=2;SAP=185.79;SAR=90;SB=-59.51;SC=CAAGACCATCCTTGGCTAACA;SRB=0.14623;SRF=186;SRP=1385.8;SRR=1086;TC;TR=2;TU=T;set=filterInVQSR-2of5;sumGLbyD=9.70
+20	15883060	rs73619850	A	AT	1325.60	PASS	AA=38;AB=0.59302;ABA=35;ABP=9.4742;ABR=51;AC=14;AF=0.0156;AN=896;BL=1078;BR=1638;BVAR;BaseQRankSum=-4.526;DB;DP=19854;DP4=1632,1800,15,20;Dels=0.00;EL=18;EPP=3.2389;ER=20;FR;FS=0.000;HETAR=14;HOMA=1;HOMR=1014;HP=1;HPLen=1;HR=1;HRun=1;HU=T;INDEL;INS;InbreedingCoeff=-0.0131;LEN=1;LRB=0.20619;LRBP=253.74;MQ=118.40;MQ0=0;MQ0Fraction=0.0000;MQM=56.526;MQRankSum=0.892;NF;NR;NS=1029;PP;PV4=0.61,1,0.25,0.14;RA=4439;RL=14;RPP=8.7247;RR=24;RUN=1;ReadPosRankSum=-2.061;SAB=0.42105;SAF=16;SAP=5.0675;SAR=22;SC=GGATTGGCAGATAAAAAATGG;SRB=0.46429;SRF=2061;SRP=52.168;SRR=2378;TC;TR=1;TU=T;VQSLOD=9.7576;set=Intersection;sumGLbyD=15.69
+20	16073315	rs111824749	GA	G,GAA,GAAA	6400.63	PASS	AC=138,47,20;AF=0.11577,0.03943,0.01678;AN=1192;BVAR;BaseQRankSum=11.377;DB;DEL;DP=35284;DP4=1695,1547,60,56;Dels=0.08;FR;FS=9.576;HP=11;HPLen=10;HR=10;HRun=10;HU=A;INDEL;INS;InbreedingCoeff=0.2137;MQ=106.87;MQ0=1;MQ0Fraction=0.0003;MQRankSum=0.773;NF;NR;PP;PV4=0.92,1,0.024,0.45;RUN=1;ReadPosRankSum=-2.224;SC=TATTTGAGGAGAAAAAAAAAA;TC;TR=10;TU=A;VQSLOD=9.3264;set=Intersection;sumGLbyD=8.64
+20	16122099	.	GA	G	12914	PASS	AA=85;AB=0.85915;ABA=80;ABP=639.4;ABR=488;AC=19;AF=0.01542;AN=1232;BL=805;BR=5457;BVAR;BaseQRankSum=-6.084;DEL;DP=13592;Dels=0.00;EL=45;EPP=3.649;ER=40;FS=0.935;HETAR=218;HOMA=841;HOMR=14;HRun=2;InbreedingCoeff=0.0250;LEN=1;LRB=0.74289;LRBP=7507.5;MQ0=0;MQ0Fraction=0.0000;MQM=103.01;MQRankSum=2.843;NS=1075;RA=541;RL=2;RPP=170.62;RR=83;RUN=1;ReadPosRankSum=-16.222;SAB=0.49412;SAF=42;SAP=3.0358;SAR=43;SRB=0.44917;SRF=243;SRP=15.152;SRR=298;VQSLOD=3.9745;set=filterInVQSR-2of5;sumGLbyD=2.97
+20	16828509	.	G	GT	843.62	PASS	AA=30;AB=0.70103;ABA=29;ABP=37.06;ABR=68;AC=10;AF=0.0140;AN=714;BL=1368;BR=1786;BVAR;BaseQRankSum=-4.061;DP=8682;Dels=0.01;EL=14;EPP=3.2998;ER=16;FR;FS=2.681;HETAR=22;HOMA=1;HOMR=1020;HP=8;HPLen=8;HR=8;HRun=8;HU=T;INS;InbreedingCoeff=0.1389;LEN=1;LRB=0.13253;LRBP=123.3;MQ0=0;MQ0Fraction=0.0000;MQM=62.8;MQRankSum=-1.491;NF;NR;NS=1043;PP;RA=4416;RL=11;RPP=7.6428;RR=19;RUN=1;ReadPosRankSum=-1.718;SAB=0.76667;SAF=23;SAP=21.54;SAR=7;SC=CCTTCAAAAGGTTTTTTTTGG;SRB=0.5745;SRF=2537;SRP=215.91;SRR=1879;TC;TR=8;TU=T;VQSLOD=7.6258;set=Intersection;sumGLbyD=10.77
+20	17470034	.	GC	G	46975	PASS	AA=57;AB=0.96043;ABA=52;ABP=2422.5;ABR=1262;AC=34;AF=0.02773;AN=1226;BL=418;BR=3446;BVAR;BaseQRankSum=-6.250;DEL;DP=12035;Dels=0.00;EL=22;EPP=9.4485;ER=35;FS=1.350;HETAR=416;HOMA=409;HOMR=244;HRun=1;InbreedingCoeff=0.0083;LEN=1;LRB=0.78364;LRBP=5155.6;MQ0=0;MQ0Fraction=0.0000;MQM=99.509;MQRankSum=2.192;NS=1076;RA=2396;RL=5;RPP=87.164;RR=52;RUN=1;ReadPosRankSum=-15.199;SAB=0.5614;SAF=32;SAP=4.877;SAR=25;SRB=0.52963;SRF=1269;SRP=21.285;SRR=1127;VQSLOD=3.8440;set=filterInVQSR-2of5;sumGLbyD=3.06
+20	17471374	.	AGCGGC	A	850.03	PASS	AC=6;AF=0.0085;AF1=0.01301;AN=704;BaseQRankSum=6.259;CI95=0.00885,0.01991;DP=8180;DP4=2215,1878,4,5;Dels=0.01;FQ=131;FS=0.000;HRun=0;INDEL;InbreedingCoeff=0.0009;MQ=104.41;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-5.521;PV4=0.74,0.37,0.0005,1;ReadPosRankSum=2.468;VQSLOD=6.8773;set=Intersection;sumGLbyD=30.85
+20	18433202	rs35582929	G	GA	2506.90	PASS	AA=55;AB=0.5812;ABA=49;ABP=9.7103;ABR=68;AC=20;AF=0.0218;AN=918;BL=2263;BR=2175;BVAR;BaseQRankSum=-6.639;DB;DP=19467;DP4=1845,2365,27,26;Dels=0.00;EL=21;EPP=9.6826;ER=34;FQ=999;FR;FS=5.633;HETAR=16;HOMA=3;HOMR=1045;HP=2;HPLen=3;HR=3;HRun=1;HU=G;INDEL;INS;InbreedingCoeff=0.0700;LEN=1;LRB=0.019829;LRBP=6.7994;MQ=114.03;MQ0=0;MQ0Fraction=0.0000;MQM=83.345;MQRankSum=1.610;NF;NR;NS=1064;PP;PV4=0.33,1,1,1;RA=5380;RL=28;RPP=3.0498;RR=27;RUN=1;ReadPosRankSum=0.873;SAB=0.47273;SAF=26;SAP=3.3656;SAR=29;SC=TATTTCATGGGAGCATTAAAA;SRB=0.42862;SRF=2306;SRP=241.07;SRR=3074;TC;TR=3;TU=G;VQSLOD=10.0372;dbSNP=126;set=Intersection;sumGLbyD=13.10
+20	18551314	rs10659122	CA	C,CAA,CAAA,CAAAA,CAAAAA	18810.74	PASS	ABR=243;AC=19,169,216,164,188;AF=0.01816,0.16157,0.20650,0.15679,0.17973;BVAR;BaseQRankSum=-5.742;DB;DP=17637;DP4=136,77,560,237;FR;FS=2.693;HOMA=177;HOMR=299;HP=17;HR=17;HU=A;HaplotypeScore=15.5048;INDEL;INS;InbreedingCoeff=0.8901;MQ0=11;MQ0Fraction=0.0069;MQRankSum=1.845;NF;NR;NS=658;PP;PV4=0.08,1,1,1;QD=12.66;RA=673;RUN=1;ReadPosRankSum=0.283;SB=-3514.45;SC=GATTCCATCTCAAAAAAAAAA;SRB=0.63596;SRF=428;SRP=111.06;SRR=245;TC;TR=17;TU=A;VQSLOD=10.6964;dbSNP=130;set=Intersection
+20	18785519	.	G	GTC	415.55	PASS	AC=28;AF=0.0400;AN=700;BaseQRankSum=10.889;DP=1929;FS=8.778;HRun=0;HaplotypeScore=27.6448;InbreedingCoeff=0.0510;MQ=61.99;MQ0=36;MQ0Fraction=0.0187;MQRankSum=4.508;QD=3.08;ReadPosRankSum=8.080;SB=-437.03;VQSLOD=4.9313;set=VQSR
+20	19149501	.	A	AG	17.85	PASS	AC=1;AF=0.0015;AN=670;BaseQRankSum=0.769;DP=1635;FS=9.858;HRun=0;HaplotypeScore=12.1949;InbreedingCoeff=-0.0381;MQ=102.63;MQ0=0;MQ0Fraction=0.0000;MQRankSum=1.200;QD=3.23;ReadPosRankSum=0.292;SB=-7.06;VQSLOD=4.4695;set=VQSR
+20	19540281	.	AC	A	19710	PASS	AA=145;AB=0.81843;ABA=134;ABP=652.98;ABR=604;AC=115;AF=0.09583;AN=1200;BL=9637;BR=817;BVAR;BaseQRankSum=-13.669;DEL;DP=10963;Dels=0.01;EL=66;EPP=5.5412;ER=79;FS=1.252;HETAR=305;HOMA=681;HOMR=59;HRun=1;InbreedingCoeff=0.0298;LEN=1;LRB=0.8437;LRBP=16162;MQ0=0;MQ0Fraction=0.0000;MQM=118.51;MQRankSum=-2.194;NS=1046;RA=823;RL=141;RPP=284.09;RR=4;RUN=1;ReadPosRankSum=-20.775;SAB=0.45517;SAF=66;SAP=5.5412;SAR=79;SRB=0.452;SRF=372;SRP=19.477;SRR=451;VQSLOD=3.9584;set=filterInVQSR-2of5;sumGLbyD=3.29
+20	20015051	.	TGAGGGTGG	T	1820.73	PASS	AF=0.0112;AF1=0.01638;AN=714;BaseQRankSum=6.652;CI95=0.01106,0.02212;DP=9910;DP4=2812,1912,6,11;Dels=0.01;FQ=999;FR;FS=6.147;HP=1;HPLen=2;HR=2;HRun=0;HU=T;INDEL;InbreedingCoeff=0.0077;MQ=129.13;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-3.195;NF;NR;PP;PV4=0.049,1,5.5e-05,0.006;ReadPosRankSum=-1.989;SC=TTGGTGGAGTTGAGGGTGGGA;TC;TR=2;TU=T;VQSLOD=6.5963;set=Intersection;sumGLbyD=33.49
+20	20301041	rs35451634	ATATG	A	200.42	PASS	AC=21;AF=0.0449;AN=468;BaseQRankSum=5.251;DB;DP=579;FS=24.013;HRun=0;HaplotypeScore=27.8977;InbreedingCoeff=0.0113;MQ=78.47;MQ0=26;MQ0Fraction=0.0449;MQRankSum=-5.284;QD=3.06;ReadPosRankSum=1.793;SB=-55.76;VQSLOD=5.0981;set=VQSR
+20	20378174	.	TC	T	245.55	PASS	AC=23;AF=0.01879;AN=1224;BaseQRankSum=0.990;DP=3225;FS=10.413;HRun=1;HaplotypeScore=22.6109;InbreedingCoeff=0.0244;MQ=93.70;MQ0=3;MQ0Fraction=0.0009;MQRankSum=-3.349;QD=1.86;ReadPosRankSum=-7.227;SB=-188.62;VQSLOD=4.2553;set=VQSR
+20	20809160	rs10571503	TAA	AAA,T	3496	PASS	AC=0;AF=0.0000;AN=612;BaseQRankSum=1.968;DB;DP=1092;FR;HP=4;HPLen=3;HR=3;HRun=0;HU=A;HaplotypeScore=26.1253;InbreedingCoeff=0.0603;MQ=68.98;MQ0=1;MQ0Fraction=0.0009;MQRankSum=1.520;NF;NR;PP;ReadPosRankSum=-4.042;SC=TATATATATATAAATTTAAAT;TC;TR=13;TU=AT;set=filterInVQSR-2of5
+20	22508765	.	CT	C	53877.84	PASS	AA=187;AB=0.78077;ABA=171;ABP=537.09;ABR=609;AC=1017;AF=0.91787;AN=1108;BL=12690;BR=1718;BVAR;BaseQRankSum=13.773;DEL;DP=7430;Dels=0.02;EL=73;EPP=22.53;ER=114;FR;FS=16.352;HETAR=152;HOMA=9;HOMR=786;HP=8;HR=4;HRun=4;HU=T;InbreedingCoeff=0.3885;LEN=1;LRB=0.76152;LRBP=18147;MQ0=0;MQ0Fraction=0.0000;MQM=46.086;MQRankSum=0.971;NF;NR;NS=947;PP;RA=2868;RL=177;RPP=326.86;RR=10;RUN=1;ReadPosRankSum=9.951;SAB=0.34759;SAF=65;SAP=40.738;SAR=122;SC=AAAAAATTTTCTTTTGAACTG;SRB=0.46269;SRF=1327;SRP=37.684;SRR=1541;TC;TR=4;TU=T;VQSLOD=5.1182;set=Intersection;sumGLbyD=25.15
+20	22555082	rs11477526	AT	A	11503	PASS	AA=530;AB=0.50816;ABA=422;ABP=3.5063;ABR=436;AF=0.1614;AN=700;BL=21453;BR=23313;BVAR;BaseQRankSum=17.562;DB;DEL;DP=25587;DP4=1869,1600,283,201;Dels=0.14;EL=259;EPP=3.6003;ER=271;FQ=999;FR;FS=14.595;HETAR=159;HOMA=41;HOMR=846;HP=3;HPLen=3;HR=3;HRun=3;HU=T;INDEL;InbreedingCoeff=0.0995;LEN=1;LRB=0.041549;LRBP=170.83;MQ=95.89;MQ0=0;MQ0Fraction=0.0000;MQM=72.162;MQRankSum=2.564;NF;NR;NS=1046;PP;PV4=0.058,6.6e-129,0.04,1;RA=4303;RL=264;RPP=3.0267;RR=266;RUN=1;ReadPosRankSum=0.176;SAB=0.58679;SAF=311;SAP=37.688;SAR=219;SC=GGGAAAGCTGATTTACTGATT;SRB=0.54892;SRF=2362;SRP=92.453;SRR=1941;TC;TR=3;TU=T;VQSLOD=8.7746;dbSNP=120;set=Intersection;sumGLbyD=15.27
+20	22590907	.	A	AC	4204.88	PASS	AA=67;AB=0.592;ABA=51;ABP=12.2;ABR=74;AF=0.0554;AF1=0.0468;AN=560;BL=2277;BR=2389;BVAR;BaseQRankSum=10.968;CI95=0.03759,0.05639;DP=14380;DP4=2514,2018,33,33;Dels=0.00;EL=22;EPP=20.155;ER=45;FQ=999;FR;FS=3.846;HETAR=25;HOMA=4;HOMR=1049;HP=4;HPLen=5;HR=5;HRun=0;HU=A;INDEL;INS;InbreedingCoeff=0.0719;LEN=1;LRB=0.024003;LRBP=8.8481;MQ=110.68;MQ0=0;MQ0Fraction=0.0000;MQM=96.149;MQRankSum=2.668;NF;NR;NS=1078;PP;PV4=0.39,1,0.46,0.36;RA=5468;RL=33;RPP=3.0427;RR=34;RUN=1;ReadPosRankSum=-1.097;SAB=0.50746;SAF=34;SAP=3.0427;SAR=33;SC=TCATATCAAAAACATTACGTT;SRB=0.54389;SRF=2974;SRP=94.508;SRR=2494;TC;TR=5;TU=A;VQSLOD=10.0712;set=Intersection;sumGLbyD=27.69
+20	22806326	rs11468890	ATTCCATCAC	A	105320.99	PASS	AC=567;AF=0.48795;AN=1162;BVAR;BaseQRankSum=32.858;DB;DEL;DP=26278;DP4=727,796,554,587;Dels=0.30;FQ=999;FR;FS=1.923;HP=3;HPLen=3;HR=2;HRun=0;HU=T;INDEL;InbreedingCoeff=0.2548;LEN=9;MQ=89.42;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-23.545;NF;NR;PP;PV4=0.7,1,1.3e-167,1;RUN=1;ReadPosRankSum=4.384;SC=GGCTGCTCCCATTCCATCACT;TC;TR=2;TU=T;VQSLOD=8.2594;set=Intersection;sumGLbyD=69.81
+20	22999898	rs55966257	CAGGA	C	8019.97	PASS	AA=23;AB=0.57778;ABA=19;ABP=5.3748;ABR=26;AC=214;AF=0.18838;AN=1136;BL=1143;BR=1040;BVAR;BaseQRankSum=29.294;DB;DEL;DP=8216;Dels=0.02;EL=11;EPP=3.1047;ER=12;FS=14.938;HETAR=14;HOMA=2;HOMR=948;HRun=0;InbreedingCoeff=0.0797;LEN=4;LRB=0.047183;LRBP=13.563;MQ0=0;MQ0Fraction=0.0000;MQM=34.783;MQRankSum=-20.301;NS=964;RA=3637;RL=13;RPP=3.86;RR=10;RUN=1;ReadPosRankSum=-24.607;SAB=0.47826;SAF=11;SAP=3.1047;SAR=12;SRB=0.49024;SRF=1783;SRP=6.02;SRR=1854;VQSLOD=7.9163;set=Intersection;sumGLbyD=9.43
+20	23385964	rs57723772	GAA	G	8170.95	PASS	AC=257;AF=0.20928;AN=1228;BaseQRankSum=32.220;DB;DP=3291;FS=1.688;HRun=3;HaplotypeScore=22.6739;InbreedingCoeff=0.0171;MQ=58.44;MQ0=32;MQ0Fraction=0.0097;MQRankSum=-4.893;QD=6.55;ReadPosRankSum=-35.524;SB=-3631.67;VQSLOD=5.6549;set=VQSR
+20	23534530	.	TA	T	3542.10	PASS	AA=45;AB=0.75658;ABA=37;ABP=89.926;ABR=115;AC=35;AF=0.02991;AN=1170;BL=3090;BR=270;BVAR;BaseQRankSum=-6.892;DEL;DP=8108;Dels=0.00;EL=19;EPP=5.3748;ER=26;FS=1.026;HETAR=76;HOMA=896;HOMR=18;HRun=1;InbreedingCoeff=0.0551;LEN=1;LRB=0.83929;LRBP=5142.4;MQ0Fraction=0.0017;MQM=41.578;MQRankSum=0.818;NS=991;RA=203;RL=43;RPP=84.127;RR=2;RUN=1;ReadPosRankSum=-12.923;SAB=0.37778;SAF=17;SAP=8.8491;SAR=28;SRB=0.5665;SRF=115;SRP=10.808;SRR=88;VQSLOD=4.2093;set=Intersection;sumGLbyD=3.49
+20	23976810	rs5841018	A	ATATTAAT	1782.38	PASS	AF=0.1387;AF1=0.01507;BaseQRankSum=3.717;CI95=0.00188,0.03947;DB;DP=1712;DP4=357,376,7,2;Dels=0.00;FQ=31.1;FS=14.489;HPLen=2;HRun=0;INDEL;InbreedingCoeff=0.1123;MQ=49.53;MQ0=2;MQ0Fraction=0.0055;MQRankSum=-4.928;PV4=0.1,1,0.00085,0.016;ReadPosRankSum=-4.456;VQSLOD=5.3140;dbSNP=116;set=Intersection;sumGLbyD=19.98
+20	24222100	.	CTTTTA	C	4219.36	PASS	AA=57;AB=0.59434;ABA=43;ABP=11.205;ABR=63;AF=0.01803;AF1=0.01547;AN=1220;BL=2073;BR=2345;BVAR;BaseQRankSum=7.990;CI95=0.0114,0.02137;DEL;DP=17536;DP4=2140,2346,7,12;Dels=0.01;EL=32;EPP=4.877;ER=25;FQ=104;FS=0.614;HETAR=21;HOMA=4;HOMR=1042;HRun=0;INDEL;InbreedingCoeff=0.1941;LEN=5;LRB=0.061566;LRBP=39.374;MQ=73.32;MQ0Fraction=0.0021;MQM=39.614;MQRankSum=-5.728;NS=1067;PV4=0.37,1.1e-39,3.5e-09,1;RA=5527;RL=28;RPP=3.0484;RR=29;RUN=1;ReadPosRankSum=0.214;SAB=0.54386;SAF=31;SAP=3.9627;SAR=26;SRB=0.49267;SRF=2723;SRP=5.588;SRR=2804;VQSLOD=7.5428;set=Intersection;sumGLbyD=38.08
+20	24395018	.	AT	A	49310	PASS	AA=146;AB=0.91198;ABA=130;ABP=2180.5;ABR=1347;AC=50;AF=0.04045;AN=1236;BL=587;BR=9625;BVAR;BaseQRankSum=-4.610;DEL;DP=12793;Dels=0.01;EL=54;EPP=24.487;ER=92;FS=22.108;HETAR=485;HOMA=384;HOMR=210;HRun=2;InbreedingCoeff=0.0374;LEN=1;LRB=0.88504;LRBP=17373;MQ0=0;MQ0Fraction=0.0000;MQM=102.26;MQRankSum=2.256;NS=1080;RA=2377;RL=1;RPP=311.42;RR=145;RUN=1;ReadPosRankSum=-16.347;SAB=0.63699;SAF=93;SAP=26.807;SAR=53;SRB=0.52167;SRF=1240;SRP=12.702;SRR=1137;VQSLOD=3.2421;set=filterInVQSR-2of5;sumGLbyD=3.80
+20	24411517	.	C	CA	246.18	PASS	AF=0.01546;AF1=0.01095;BaseQRankSum=7.832;CI95=0.005698,0.01709;DP=7981;DP4=983,2037,7,7;Dels=0.00;FQ=27.9;FS=18.815;HPLen=3;HRun=3;INDEL;InbreedingCoeff=0.0175;MQ=60.28;MQ0Fraction=0.0137;MQRankSum=-7.243;PV4=0.25,1,2.7e-05,1;ReadPosRankSum=-0.143;VQSLOD=4.3701;set=Intersection;sumGLbyD=6.56
+20	24421169	.	AG	A	27480	PASS	AA=182;AB=0.8303;ABA=149;ABP=835;ABR=729;AC=89;AF=0.07224;AN=1232;BL=11276;BR=2214;BVAR;BaseQRankSum=-5.447;DEL;DP=11717;Dels=0.01;EL=103;EPP=9.8827;ER=79;FR;FS=15.492;HETAR=343;HOMA=607;HOMR=114;HP=4;HR=1;HRun=1;HU=G;InbreedingCoeff=0.0353;LEN=1;LRB=0.67176;LRBP=13222;MQ0=0;MQ0Fraction=0.0000;MQM=88.324;MQRankSum=2.221;NF;NR;NS=1071;PP;RA=1226;RL=169;RPP=293.37;RR=13;RUN=1;ReadPosRankSum=-19.711;SAB=0.54945;SAF=100;SAP=6.876;SAR=82;SC=CCTTAGCCCCAGAAAACATCT;SRB=0.44535;SRF=546;SRP=34.814;SRR=680;TC;TR=1;TU=G;VQSLOD=4.2669;set=Intersection;sumGLbyD=3.91
+20	24765537	rs71841337	ATTT	A,AT,ATT,ATTTT,ATTTTT	37852	PASS	AC=13,120,527,51,92;AF=0.01102,0.10169,0.44661,0.04322,0.07797;AN=1180;BVAR;BaseQRankSum=8.172;DB;DEL;DP=39116;DP4=200,331,851,1169;FR;FS=2.394;HP=15;HR=15;HU=T;HaplotypeScore=20.8091;INDEL;INS;InbreedingCoeff=0.4815;MQ0=1;MQ0Fraction=0.0003;MQRankSum=4.344;NF;NR;PP;PV4=0.067,1,1,0.1;QD=7.90;RUN=1;ReadPosRankSum=1.798;SB=-8371.96;SC=CTCTGCAACAATTTTTTTTTT;TC;TR=15;TU=T;VQSLOD=9.9679;dbSNP=120;set=Intersection
+20	25500689	.	A	AATTT	84980.72	PASS	AC=1005;AF=0.89096;AN=1128;BaseQRankSum=17.400;DP=2324;FS=6.721;HRun=0;HaplotypeScore=25.3376;InbreedingCoeff=0.2148;MQ=75.19;MQ0=1;MQ0Fraction=0.0004;MQRankSum=-8.221;QD=38.28;ReadPosRankSum=4.504;SB=-34833.07;VQSLOD=4.6038;set=VQSR
+20	25550373	.	GA	G	11251.31	PASS	AA=246;AB=0.42963;ABA=154;ABP=14.624;ABR=116;AC=566;AF=0.6521;AN=868;BL=5230;BR=11845;BVAR;BaseQRankSum=7.418;DEL;DP=8885;Dels=0.02;EL=99;EPP=23.348;ER=147;FR;FS=50.357;HETAR=150;HOMA=849;HOMR=14;HP=1;HR=2;HRun=1;HU=G;InbreedingCoeff=0.1365;LEN=1;LRB=0.38741;LRBP=5567.9;MQ0=0;MQ0Fraction=0.0000;MQM=97.561;MQRankSum=0.050;NF;NR;NS=1013;PP;RA=269;RL=75;RPP=84.361;RR=171;RUN=1;ReadPosRankSum=-7.128;SAB=0.52846;SAF=130;SAP=4.7404;SAR=116;SC=CACGGAGGCGGAGGAAGCAGC;SRB=0.42379;SRF=114;SRP=16.58;SRR=155;TC;TR=6;TU=AGG;VQSLOD=4.0103;set=filterInVQSR-2of5;sumGLbyD=4.58
+20	25903865	.	TTC	T	7459.23	PASS	AC=277;AF=0.23316;AN=1188;BaseQRankSum=31.479;DP=2969;FS=137.723;HRun=0;HaplotypeScore=37.3300;InbreedingCoeff=-0.1755;MQ=53.49;MQ0=50;MQ0Fraction=0.0168;MQRankSum=-25.506;QD=4.70;ReadPosRankSum=-5.913;SB=-1747.98;VQSLOD=5.4731;set=VQSR
+20	25934237	.	C	CCACTT	771.36	PASS	AC=37;AF=0.0426;AN=868;BaseQRankSum=16.331;DP=2253;FS=4.545;HRun=0;HaplotypeScore=29.9764;InbreedingCoeff=-0.0685;MQ=48.12;MQ0=87;MQ0Fraction=0.0386;MQRankSum=-12.497;QD=3.37;ReadPosRankSum=-8.428;SB=-297.70;VQSLOD=4.2324;set=VQSR
+20	26054751	rs112967123	TATC	T	33244	PASS	AA=1863;AB=0.79012;ABA=1788;ABP=6231;ABR=6731;AC=227;AF=0.18218;AN=1246;BL=74924;BR=72452;BVAR;BaseQRankSum=32.258;DB;DEL;DP=36404;DS;Dels=0.05;EL=931;EPP=3.0115;ER=932;FR;FS=265.752;HETAR=527;HOMA=2;HOMR=565;HP=1;HR=2;HRun=0;HU=T;InbreedingCoeff=-0.2137;LEN=3;LRB=0.016773;LRBP=93.048;MQ0Fraction=0.0127;MQM=28.797;MQRankSum=-5.329;NF;NR;NS=1094;PP;RA=14604;RL=1014;RPP=34.743;RR=849;RUN=1;ReadPosRankSum=8.394;SAB=0.65486;SAF=1220;SAP=391.07;SAR=643;SC=TCACCATCATTATCATCATTA;SRB=0.56717;SRF=8283;SRP=575.39;SRR=6321;TC;TR=8;TU=ATC;VQSLOD=1.0486;set=filterInVQSR-2of5;sumGLbyD=6.54
+20	26075169	.	CTTCATT	C	34603	PASS	AA=311;AB=0.88905;ABA=298;ABP=3534.4;ABR=2388;AC=235;AF=0.18921;AN=1242;BL=17537;BR=5525;BVAR;BaseQRankSum=33.761;DEL;DP=20706;DS;Dels=0.01;EL=206;EPP=74.236;ER=105;FR;FS=94.549;HETAR=596;HOMA=99;HOMR=336;HP=3;HR=2;HRun=0;HU=T;InbreedingCoeff=-0.2083;LEN=6;LRB=0.52086;LRBP=13589;MQ0Fraction=0.0426;MQM=14.524;MQRankSum=-37.199;NF;NR;NS=1038;PP;RA=3600;RL=311;RPP=678.34;RR=0;RUN=1;ReadPosRankSum=-27.333;SAB=0.66238;SAF=206;SAP=74.236;SAR=105;SC=TCACCATCATCTTCATTATCA;SRB=0.55833;SRF=2010;SRP=109.41;SRR=1590;TC;TR=7;TU=ATC;VQSLOD=1.4394;set=filterInVQSR-2of5;sumGLbyD=4.96
+20	26120452	.	CAG	C	7863.19	PASS	AA=163;AB=0.70489;ABA=157;ABP=196.99;ABR=375;AC=171;AF=0.1908;AN=896;BL=3455;BR=4877;BVAR;BaseQRankSum=25.536;DEL;DP=7014;Dels=0.10;EL=58;EPP=32.438;ER=105;FS=231.723;HETAR=90;HOMA=5;HOMR=387;HRun=0;InbreedingCoeff=-0.1966;LEN=2;LRB=0.17067;LRBP=530;MQ0Fraction=0.0470;MQM=21.951;MQRankSum=-23.449;NS=482;RA=1117;RL=62;RPP=23.273;RR=101;RUN=1;ReadPosRankSum=1.904;SAB=0.37423;SAF=61;SAP=25.404;SAR=102;SRB=0.41719;SRF=466;SRP=69.544;SRR=651;VQSLOD=-0.9395;set=filterInVQSR-2of5;sumGLbyD=5.06
+20	26136208	.	A	AT	17172.04	PASS	AA=252;AB=0.73593;ABA=183;ABP=338.07;ABR=510;AC=381;AF=0.30775;AN=1238;BL=8304;BR=14158;BVAR;BaseQRankSum=41.520;DP=40036;DP4=2448,2564,317,366;Dels=0.00;EL=163;EPP=50.197;ER=89;FQ=999;FS=6.531;HETAR=149;HOMA=52;HOMR=708;HRun=1;INDEL;INS;InbreedingCoeff=-0.3996;LEN=1;LRB=0.26062;LRBP=3315.9;MQ=64.20;MQ0=22;MQ0Fraction=0.0048;MQM=25.706;MQRankSum=-29.318;NS=909;PV4=0.24,1.1e-119,3.2e-281,1;RA=2939;RL=58;RPP=162.39;RR=194;RUN=1;ReadPosRankSum=0.592;SAB=0.24206;SAF=61;SAP=148.64;SAR=191;SRB=0.4852;SRF=1426;SRP=8.6026;SRR=1513;VQSLOD=0.5981;set=filterInVQSR-2of5;sumGLbyD=5.77
+20	26185812	.	AG	A	322.58	PASS	AF=0.0342;BaseQRankSum=3.668;DP=3014;Dels=0.01;FR;FS=10.238;HP=8;HPLen=6;HR=6;HRun=6;HU=G;InbreedingCoeff=0.1504;MQ0Fraction=0.0473;MQRankSum=-5.464;NF;NR;PP;ReadPosRankSum=0.536;SC=GGGTGGGTGGAGGGGGGAGGG;TC;TR=6;TU=G;VQSLOD=5.0767;set=Intersection;sumGLbyD=8.46
+20	30963468	.	AGTTT	A	2041.12	PASS	AA=38;AB=0.75694;ABA=35;ABP=85.587;ABR=109;AC=34;AF=0.0377;AN=902;BL=1974;BR=668;BVAR;BaseQRankSum=3.060;DEL;DP=22806;DP4=1997,1747,28,36;Dels=0.02;EL=17;EPP=3.9246;ER=21;FR;FS=16.034;HETAR=29;HOMA=1;HOMR=1009;HP=1;HPLen=1;HR=1;HRun=0;HU=G;INDEL;InbreedingCoeff=0.0752;LEN=4;LRB=0.49432;LRBP=1404.9;MQ=87.17;MQ0Fraction=0.0013;MQM=98.079;MQRankSum=6.021;NF;NR;NS=1039;PP;PV4=0.13,1.5e-07,1,0.051;RA=4052;RL=36;RPP=69.069;RR=2;RUN=1;ReadPosRankSum=-1.847;SAB=0.5;SAF=19;SAP=3.0103;SAR=19;SC=AGAAGTAAGTAGTTTGTTTTT;SRB=0.53776;SRF=2179;SRP=53.19;SRR=1873;TC;TR=9;TU=AAGT;VQSLOD=7.3578;set=Intersection;sumGLbyD=14.03
+20	31963212	.	AAAAAAAAAAAAG	A	727.15	PASS	AC=5;AF=0.0080;AN=622;BaseQRankSum=4.037;DP=1480;FS=0.000;HRun=0;HaplotypeScore=43.3793;InbreedingCoeff=0.0350;MQ=51.77;MQ0=59;MQ0Fraction=0.0399;MQRankSum=-1.799;QD=22.72;ReadPosRankSum=3.591;SB=-364.04;VQSLOD=5.3166;set=VQSR
+20	31997272	.	CT	C,CTT,CTTT	1837.10	PASS	AA=63;AB=0.77559;ABA=57;ABP=170.57;ABR=197;AC=79,49,30;AF=0.06594,0.04090,0.02504;AN=1198;BL=2372;BR=2640;BVAR;BaseQRankSum=3.277;DP=9050;Dels=0.03;EL=24;EPP=10.766;ER=39;FR;FS=0.303;HETAR=45;HOMA=1;HOMR=981;HP=10;HPLen=10;HR=10;HRun=10;HU=T;INS;InbreedingCoeff=0.2796;LEN=1;LRB=0.053472;LRBP=34.128;MQ0Fraction=0.0000;MQM=50.889;MQRankSum=0.610;NF;NR;NS=1027;PP;RA=3776;RL=30;RPP=3.3205;RR=33;RUN=1;ReadPosRankSum=-0.800;SAB=0.39683;SAF=25;SAP=8.8354;SAR=38;SC=ACCCAACTTCCTTTTTTTTTT;SRB=0.46213;SRF=1745;SRP=50.049;SRR=2031;TC;TR=10;TU=T;VQSLOD=4.1189;set=filterInVQSR-2of5;sumGLbyD=3.66
+20	33446974	rs113250263	TAA	T,TA,TAAA	17130.16	PASS	AC=65,417,184;AF=0.05941,0.38117,0.16819;AN=1094;BVAR;BaseQRankSum=3.400;DB;DEL;DP=22362;DP4=221,247,418,524;Dels=0.33;FR;FS=15.409;HP=15;HR=14;HRun=14;HU=A;INDEL;INS;InbreedingCoeff=0.5215;MQ=61.32;MQ0Fraction=0.0021;MQRankSum=0.481;NF;NR;PP;PV4=0.33,1,1,1;RUN=1;ReadPosRankSum=-0.056;SC=CTCCGTCTCATAAAAAAAAAA;TC;TR=14;TU=A;VQSLOD=8.0974;dbSNP=132;set=Intersection;sumGLbyD=12.78
+20	33877149	.	C	CT	1784.40	PASS	AA=58;AB=0.73096;ABA=53;ABP=94.289;ABR=144;AC=65;AF=0.05682;AN=1144;BL=3298;BR=1935;BVAR;BaseQRankSum=-2.066;DP=8074;Dels=0.02;EL=22;EPP=10.348;ER=36;FR;FS=11.452;HETAR=47;HOMA=3;HOMR=754;HP=16;HR=12;HRun=12;HU=T;INS;InbreedingCoeff=0.1178;LEN=1;LRB=0.26046;LRBP=773.91;MQ0Fraction=0.0165;MQM=52.259;MQRankSum=0.734;NF;NR;NS=804;PP;RA=2141;RL=43;RPP=32.363;RR=15;RUN=1;ReadPosRankSum=-1.273;SAB=0.46552;SAF=27;SAP=3.6093;SAR=31;SC=ATTTTCTTTTCTTTTTTTTTT;SRB=0.37553;SRF=804;SRP=291.14;SRR=1337;TC;TR=12;TU=T;VQSLOD=3.1540;set=filterInVQSR-2of5;sumGLbyD=2.84
+20	34358698	.	A	AAAAAAT	583.61	PASS	AC=27;AF=0.02542;AN=1062;BaseQRankSum=5.228;DP=1997;FS=3.765;HRun=0;HaplotypeScore=27.7123;InbreedingCoeff=0.0566;MQ=55.50;MQ0=14;MQ0Fraction=0.0070;MQRankSum=-3.961;QD=5.21;ReadPosRankSum=0.862;SB=-399.69;VQSLOD=4.3826;set=VQSR
+20	34387589	rs112431805	CT	C,CTT	4039.10	PASS	AA=121;AB=0.75368;ABA=117;ABP=268.53;ABR=358;AC=84,139;AF=0.07047,0.11661;AN=1192;BL=5557;BR=3901;BVAR;BaseQRankSum=2.693;DB;DP=10157;Dels=0.03;EL=47;EPP=16.093;ER=74;FR;FS=7.639;HETAR=89;HOMA=2;HOMR=913;HP=13;HR=11;HRun=11;HU=T;INS;InbreedingCoeff=0.2097;LEN=1;LRB=0.17509;LRBP=632.63;MQ0Fraction=0.0000;MQM=49.802;MQRankSum=-0.801;NF;NR;NS=1004;PP;RA=3789;RL=77;RPP=22.554;RR=44;RUN=1;ReadPosRankSum=-2.691;SAB=0.3719;SAF=45;SAP=20.256;SAR=76;SC=AAGAAGTGTTCTTTTTTTTTT;SRB=0.40987;SRF=1553;SRP=270.35;SRR=2236;TC;TR=11;TU=T;VQSLOD=4.0473;set=filterInVQSR-2of5;sumGLbyD=4.64
+20	34493409	rs73621682	C	CAG	62288.93	PASS	AA=1069;AB=0.54863;ABA=826;ABP=40.606;ABR=1004;AC=257;AF=0.3640;AN=706;BL=41524;BR=47039;BVAR;BaseQRankSum=-24.248;DB;DP=30195;DP4=1743,1636,614,487;Dels=0.00;EL=582;EPP=21.343;ER=487;FQ=999;FR;FS=5.080;HETAR=298;HOMA=63;HOMR=712;HP=1;HPLen=1;HR=1;HRun=0;HU=A;INDEL;INS;InbreedingCoeff=0.1437;LEN=2;LRB=0.062272;LRBP=748.76;MQ=77.99;MQ0=3;MQ0Fraction=0.0015;MQM=54.446;MQRankSum=0.160;NF;NR;NS=1073;PP;PV4=0.016,1,0.01,1;RA=4461;RL=526;RPP=3.5973;RR=543;RUN=1;ReadPosRankSum=-1.716;SAB=0.57343;SAF=613;SAP=53.08;SAR=456;SC=AGGAAGAGATCAGAGCTCCCC;SRB=0.52634;SRF=2348;SRP=29.892;SRR=2113;TC;TR=4;TU=AG;VQSLOD=8.7047;dbSNP=130;set=Intersection;sumGLbyD=49.82
+20	35086229	rs112534255	G	GAT	6109.24	PASS	AA=14;AB=0.71795;ABA=11;ABP=19.101;ABR=28;AC=35;AF=0.0509;AN=688;BL=846;BR=517;BVAR;BaseQRankSum=-7.153;DB;DP=15775;DP4=2064,2212,31,22;Dels=0.00;EL=7;EPP=3.0103;ER=7;FR;FS=0.000;HETAR=10;HOMA=2;HOMR=914;HP=3;HPLen=4;HR=4;HRun=0;HU=G;INDEL;INS;InbreedingCoeff=0.1170;LEN=2;LRB=0.24138;LRBP=175.46;MQ=54.65;MQ0Fraction=0.0118;MQM=45.643;MQRankSum=1.614;NF;NR;NS=926;PP;PV4=0.17,1,1,1;RA=2867;RL=11;RPP=12.937;RR=3;RUN=1;ReadPosRankSum=-0.520;SAB=0.71429;SAF=10;SAP=8.5941;SAR=4;SC=TTTTAGTAAAGGGGATTTCAC;SRB=0.58249;SRF=1670;SRP=172.46;SRR=1197;TC;TR=4;TU=G;VQSLOD=10.3126;set=Intersection;sumGLbyD=42.13
+20	35575895	rs67189278	AGTGT	A,AGT,AGTGTGT,TGTGT	43809.26	PASS	AC=593,3,481;AF=0.53327,0.00270,0.43255;AN=1112;BVAR;BaseQRankSum=-8.327;DB;DEL;DP=8989;Dels=0.04;FR;FS=9.400;HP=2;HPLen=1;HR=1;HRun=0;HU=G;INS;InbreedingCoeff=0.7735;LEN=2;MQ0Fraction=0.0400;MQRankSum=-2.719;NF;NR;PP;RUN=1;ReadPosRankSum=-9.301;SC=TGTGTGTGTGAGTGTGTGTGT;TC;TR=22;TU=GT;VQSLOD=8.6440;set=Intersection;sumGLbyD=6.01
+20	35957317	.	CTGACT	C,CGACT	4370.96	PASS	ABR=81;AC=22,1;AF=0.0321,0.0015;AF1=0.04523;AN=686;BVAR;BaseQRankSum=7.969;CI95=0.0354,0.05752;DEL;DP=16632;DP4=1942,1815,17,21;Dels=0.03;FQ=999;FR;FS=0.531;HOMA=1;HOMR=998;HP=2;HPLen=1;HR=1;HRun=0;HU=T;INDEL;InbreedingCoeff=0.0587;MQ=83.38;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-7.201;NF;NR;NS=1020;PP;PV4=0.42,0.00017,4.5e-12,1;RA=4620;RUN=1;ReadPosRankSum=-1.007;SC=CCTCTCAGCTCTGACTGAGTC;SRB=0.50043;SRF=2312;SRP=3.0178;SRR=2308;TC;TR=8;TU=ACTG;VQSLOD=9.9778;dbSNP=130;set=Intersection;sumGLbyD=36.45
+20	36136198	.	GTGTC	G	2078.76	PASS	AA=35;AB=0.54167;ABA=33;ABP=4.096;ABR=39;AC=17;AF=0.01384;AN=1228;BL=1212;BR=1523;BVAR;BaseQRankSum=6.900;DEL;DP=22483;DP4=1696,2291,9,16;Dels=0.01;EL=9;EPP=20.94;ER=26;FQ=999;FR;FS=3.023;HETAR=13;HOMA=1;HOMR=1061;HP=1;HPLen=1;HR=1;HRun=0;HU=T;INDEL;InbreedingCoeff=0.1113;LEN=4;LRB=0.11371;LRBP=79.803;MQ=93.98;MQ0=1;MQ0Fraction=0.0003;MQM=83.686;MQRankSum=-1.683;NF;NR;NS=1075;PP;PV4=0.55,1,0.0083,1;RA=5771;RL=19;RPP=3.5687;RR=16;RUN=1;ReadPosRankSum=0.618;SAB=0.37143;SAF=13;SAP=8.0357;SAR=22;SC=TATCATTTTAGTGTCTGTCTG;SRB=0.44966;SRF=2595;SRP=130.03;SRR=3176;TC;TR=11;TU=CTGT;VQSLOD=10.1935;set=Intersection;sumGLbyD=31.66
+20	36250522	.	CA	C	37933	PASS	AA=51;AB=0.95582;ABA=44;ABP=1800.5;ABR=952;AC=23;AF=0.01885;AN=1220;BL=691;BR=3464;BVAR;BaseQRankSum=-2.418;DEL;DP=11998;Dels=0.00;EL=18;EPP=12.59;ER=33;FS=2.307;HETAR=348;HOMA=534;HOMR=164;HRun=1;InbreedingCoeff=0.0763;LEN=1;LRB=0.66739;LRBP=4021.7;MQ0=2;MQ0Fraction=0.0006;MQM=53.647;MQRankSum=1.083;NS=1047;RA=1663;RL=2;RPP=97.065;RR=49;RUN=1;ReadPosRankSum=-12.726;SAB=0.68627;SAF=35;SAP=18.381;SAR=16;SRB=0.59651;SRF=992;SRP=137.56;SRR=671;VQSLOD=4.1346;set=filterInVQSR-2of5;sumGLbyD=3.29
+20	36285033	rs34715186	AT	A	39417	PASS	AA=530;AB=0.5406;ABA=447;ABP=16.939;ABR=526;AC=88;AF=0.0950;AN=926;BL=20722;BR=20406;BVAR;BaseQRankSum=15.611;DB;DEL;DP=36713;DP4=2551,2475,236,218;Dels=0.09;EL=241;EPP=12.45;ER=289;FQ=999;FR;FS=1.290;HETAR=141;HOMA=16;HOMR=926;HP=2;HPLen=3;HR=3;HRun=1;HU=A;INDEL;InbreedingCoeff=0.0742;LEN=1;LRB=0.0076833;LRBP=8.2825;MQ=104.81;MQ0=0;MQ0Fraction=0.0000;MQM=84.285;MQRankSum=-0.702;NF;NR;NS=1083;PP;PV4=0.62,1,1,1;RA=6562;RL=263;RPP=3.0759;RR=267;RUN=1;ReadPosRankSum=0.090;SAB=0.55849;SAF=296;SAP=18.76;SAR=234;SC=AAAAACACAAATCAGATCGTG;SRB=0.51707;SRF=3393;SRP=19.614;SRR=3169;TC;TR=3;TU=A;VQSLOD=10.5533;dbSNP=126;set=Intersection;sumGLbyD=14.15
+20	36384872	.	CTG	C	43532.41	PASS	AC=1213;AF=0.99589;AN=1218;BaseQRankSum=0.802;DP=3208;FS=9.727;HRun=0;HaplotypeScore=46.6153;InbreedingCoeff=0.1085;MQ=58.37;MQ0=50;MQ0Fraction=0.0156;MQRankSum=-1.672;QD=13.57;ReadPosRankSum=2.063;SB=-18894.12;VQSLOD=4.7353;set=VQSR
+20	36542802	.	GTA	G	31310.15	PASS	AA=1481;AB=0.67546;ABA=1378;ABP=1138.4;ABR=2868;AC=437;AF=0.35938;AN=1216;BL=25719;BR=95500;BVAR;BaseQRankSum=9.478;DEL;DP=18068;DS;Dels=0.10;EL=889;EPP=132.34;ER=592;FS=320.726;HETAR=591;HOMA=44;HOMR=378;HRun=0;InbreedingCoeff=-0.4197;LEN=2;LRB=0.57566;LRBP=87231;MQ0Fraction=0.0091;MQM=29.319;MQRankSum=-3.409;NS=1013;RA=4037;RL=3;RPP=3193;RR=1478;RUN=1;ReadPosRankSum=-6.687;SAB=0.40041;SAF=593;SAP=130.61;SAR=888;SRB=0.39014;SRF=1575;SRP=426.21;SRR=2462;VQSLOD=-1.6586;set=filterInVQSR-2of5;sumGLbyD=5.49
+20	36985025	.	CCA	C	4.57	PASS	AC=0;AF=0.0000;AN=682;BaseQRankSum=4.199;DP=1504;FS=1.036;HRun=0;HaplotypeScore=18.5241;InbreedingCoeff=0.0460;MQ=57.04;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-1.774;ReadPosRankSum=-2.105;VQSLOD=6.7455;set=VQSR
+20	37139725	.	CAG	C	250.77	PASS	AF=0.0084;AF1=0.0139;BaseQRankSum=4.131;CI95=0.00885,0.01991;DP=7973;DP4=1808,1990,2,7;Dels=0.01;FQ=104;FR;FS=11.160;HP=3;HPLen=2;HR=1;HRun=0;HU=A;INDEL;InbreedingCoeff=-0.0001;MQ=103.71;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-3.378;NF;NR;PP;PV4=0.18,0.0011,0.041,1;ReadPosRankSum=0.605;SC=AGATGGGGAACAGAGAGCAAG;TC;TR=6;TU=AG;VQSLOD=7.0630;set=Intersection;sumGLbyD=12.13
+20	37213224	.	G	GTA	3230.05	PASS	AA=32;AB=0.50769;ABA=32;ABP=3.0437;ABR=33;AC=12;AF=0.0168;AF1=0.02635;AN=714;BL=1271;BR=1743;BVAR;BaseQRankSum=-7.288;CI95=0.02212,0.03319;DP=14304;DP4=2180,2256,13,21;Dels=0.00;EL=20;EPP=7.3532;ER=12;FQ=999;FR;FS=7.863;HETAR=9;HOMA=0;HOMR=1043;HP=1;HPLen=1;HR=1;HRun=0;HU=T;INDEL;INS;InbreedingCoeff=0.0410;LEN=2;LRB=0.1566;LRBP=163.52;MQ=95.56;MQ0=1;MQ0Fraction=0.0005;MQM=51.562;MQRankSum=0.420;NF;NR;NS=1052;PP;PV4=0.23,1,0.03,0.33;RA=5138;RL=11;RPP=9.7962;RR=21;RUN=1;ReadPosRankSum=-1.122;SAB=0.28125;SAF=9;SAP=16.311;SAR=23;SC=TTTGCATCCAGTAGCACCACT;SRB=0.42293;SRF=2173;SRP=268.11;SRR=2965;TC;TR=1;TU=T;VQSLOD=9.7315;set=Intersection;sumGLbyD=36.69
+20	37282014	.	ATGG	A	2518.52	PASS	AF=0.03519;BaseQRankSum=11.994;DP=24592;DP4=415,3804,8,49;DS;Dels=0.01;FQ=999;FR;FS=2.049;HP=1;HPLen=1;HR=1;HRun=0;HU=T;INDEL;InbreedingCoeff=0.1028;MQ=51.01;MQ0Fraction=0.0139;MQRankSum=-5.912;NF;NR;PP;PV4=0.27,1,0.22,0.015;ReadPosRankSum=1.781;SC=GGTGGTGATGATGGTGGTGGT;TC;TR=17;TU=GGT;VQSLOD=2.1183;set=filterInVQSR-2of5;sumGLbyD=9.05
+20	37532218	.	GTCCGTCCA	ATCCGTCCA,G	76120.88	PASS	AC=998;AF=0.92924;AN=1074;BaseQRankSum=-2.877;DP=3087;FR;FS=9.889;HP=2;HPLen=2;HR=1;HRun=0;HU=T;HaplotypeScore=71.6244;InbreedingCoeff=-0.0027;MQ=52.68;MQ0=543;MQ0Fraction=0.1759;MQRankSum=-1.750;NF;NR;PP;QD=24.98;ReadPosRankSum=-0.850;SB=-36635.43;SC=CCGTCCGTCCGTCCGTCCATC;TC;TR=19;TU=CCGT;VQSLOD=5.3068;set=Intersection
+20	37712193	.	AAG	A	2670.33	PASS	AA=106;AB=0.62821;ABA=87;ABP=36.418;ABR=147;AC=53;AF=0.0759;AN=698;BL=4672;BR=4303;BVAR;BaseQRankSum=13.696;DEL;DP=15155;DP4=1340,1852,32,52;Dels=0.06;EL=57;EPP=4.3214;ER=49;FR;FS=0.824;HETAR=43;HOMA=7;HOMR=982;HP=1;HPLen=2;HR=2;HRun=0;HU=A;INDEL;InbreedingCoeff=0.0861;LEN=2;LRB=0.041114;LRBP=35.954;MQ=86.12;MQ0=0;MQ0Fraction=0.0000;MQM=54.236;MQRankSum=-5.745;NF;NR;NS=1034;PP;PV4=0.5,7.3e-26,1.1e-10,1;RA=4423;RL=58;RPP=5.0589;RR=48;RUN=1;ReadPosRankSum=2.617;SAB=0.38679;SAF=41;SAP=14.81;SAR=65;SC=GAAAATTCTGAAGAGAGTCAG;SRB=0.43093;SRF=1906;SRP=186.29;SRR=2517;TC;TR=6;TU=AG;VQSLOD=9.8131;set=Intersection;sumGLbyD=14.20
+20	37739002	.	T	TCA	1395.38	PASS	AA=16;AB=0.48387;ABA=16;ABP=3.0803;ABR=15;AC=11;AF=0.00950;AN=1158;BL=504;BR=630;BVAR;BaseQRankSum=-3.257;DP=13617;DP4=1660,883,7,5;Dels=0.00;EL=7;EPP=3.5532;ER=9;FR;FS=1.114;HETAR=9;HOMA=0;HOMR=991;HP=1;HPLen=2;HR=2;HRun=0;HU=T;INDEL;INS;InbreedingCoeff=0.0527;LEN=2;LRB=0.11111;LRBP=33.411;MQ=88.41;MQ0=0;MQ0Fraction=0.0000;MQM=83.75;MQRankSum=1.713;NF;NR;NS=1000;PP;PV4=0.76,1,1,0.5;RA=3257;RL=6;RPP=5.1818;RR=10;RUN=1;ReadPosRankSum=1.190;SAB=0.6875;SAF=11;SAP=7.8961;SAR=5;SC=CCTTTTTTGTTCATTTCTGCA;SRB=0.68806;SRF=2241;SRP=1003.5;SRR=1016;TC;TR=2;TU=T;VQSLOD=10.2220;set=Intersection;sumGLbyD=41.32
+20	38122459	.	T	TG,TGG	1346.40	PASS	ABR=339;AC=37,26;AF=0.02989,0.02100;BVAR;BaseQRankSum=10.222;DP=16425;FS=601.551;HOMA=0;HOMR=1008;HaplotypeScore=20.6522;INS;InbreedingCoeff=0.0829;MQ=105.78;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-4.295;NS=1079;QD=0.40;RA=6208;RUN=1;ReadPosRankSum=-14.427;SAB=1;SAR=0;SB=-368.88;SRB=0.34907;SRF=2167;SRP=1231.4;SRR=4041;VQSLOD=-3.3455;set=filterInVQSR-2of5
+20	38395256	.	TTGAG	T	633.19	PASS	AF=0.0028;BaseQRankSum=5.667;DP=3839;Dels=0.00;FR;FS=10.238;HP=2;HPLen=3;HR=3;HRun=0;HU=T;InbreedingCoeff=-0.0097;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-1.276;NF;NR;PP;ReadPosRankSum=-1.016;SC=ATGTGTTTGTTTGAGTATGTT;TC;TR=10;TU=GTTT;VQSLOD=6.4906;set=Intersection;sumGLbyD=10.83
+20	38882632	rs72004513	AGTGTGTGTGT	A,AGT,AGTGT,AGTGTGT,AGTGTGTGT,AGTGTGTGTGTGT	12304.47	PASS	AC=57,24,51,78,89,186;AF=0.04664,0.01964,0.04173,0.06383,0.07283,0.15221;AN=1222;BVAR;BaseQRankSum=3.183;DB;DEL;DP=49261;DP4=144,106,104,101;Dels=0.05;FQ=999;FR;FS=5.209;HP=1;HPLen=2;HR=2;HRun=0;HU=A;INDEL;InbreedingCoeff=0.9090;MQ=87.48;MQ0Fraction=0.0071;MQRankSum=-0.897;NF;NR;PP;PV4=0.16,1,0.19,1;RUN=1;ReadPosRankSum=3.551;SC=TAACTCCTCAAGTGTGTGTGT;TC;TR=47;TU=GT;VQSLOD=9.9069;set=Intersection;sumGLbyD=5.30
+20	39345038	.	CTGAACCATAATGTG	C,CCCATAATGTG	60744.52	PASS	AA=23;AB=0.67143;ABA=23;ABP=20.878;ABR=47;AC=232,2;AF=0.19366,0.00167;AN=1198;BL=1607;BR=1843;BVAR;BaseQRankSum=30.955;DEL;DP=31490;DP4=1729,2100,265,278;Dels=0.13;EL=6;EPP=14.434;ER=17;FQ=999;FR;FS=1.767;HETAR=18;HOMA=0;HOMR=1015;HP=1;HPLen=2;HR=2;HRun=0;HU=C;INDEL;InbreedingCoeff=0.1991;LEN=14;LRB=0.068406;LRBP=38.066;MQ=104.60;MQ0=0;MQ0Fraction=0.0000;MQM=189.83;MQRankSum=-16.579;NF;NR;NS=1033;PP;PV4=0.12,1,5.5e-137,1;RA=5286;RL=14;RPP=5.3706;RR=9;RUN=1;ReadPosRankSum=4.323;SAB=0.56522;SAF=13;SAP=3.86;SAR=10;SC=TGGGCTGGACCTGAACCATAA;SRB=0.46311;SRF=2448;SRP=65.493;SRR=2838;TC;TR=2;TU=C;VQSLOD=6.2643;dbSNP=130;set=Intersection;sumGLbyD=65.43
+20	39418008	.	AG	A	46796	PASS	AA=113;AB=0.9511;ABA=80;ABP=2894.6;ABR=1556;AC=30;AF=0.02412;AN=1244;BL=638;BR=6936;BVAR;BaseQRankSum=7.280;DEL;DP=14307;Dels=0.00;EL=50;EPP=6.2579;ER=63;FR;FS=5.707;HETAR=473;HOMA=361;HOMR=246;HP=3;HR=3;HRun=3;HU=G;InbreedingCoeff=0.0272;LEN=1;LRB=0.83153;LRBP=11375;MQ0=0;MQ0Fraction=0.0000;MQM=62.398;MQRankSum=3.530;NF;NR;NS=1089;PP;RA=3000;RL=3;RPP=223.02;RR=110;RUN=1;ReadPosRankSum=-18.601;SAB=0.58407;SAF=66;SAP=9.9475;SAR=47;SC=ACTGGGGGAAAGGGATTCTAG;SRB=0.494;SRF=1482;SRP=3.9484;SRR=1518;TC;TR=3;TU=G;VQSLOD=4.5834;set=Intersection;sumGLbyD=3.06
+20	39876961	.	GT	G,GTT,GTTT	2302.10	PASS	ABR=496;AC=45,51,45;AF=0.03664,0.04153,0.03664;AN=1228;BVAR;BaseQRankSum=4.462;DP=37649;DP4=1457,1975,57,59;Dels=0.02;FR;FS=9.938;HOMA=0;HOMR=978;HP=10;HPLen=10;HR=10;HRun=10;HU=T;INDEL;INS;InbreedingCoeff=0.2583;MQ=97.28;MQ0=0;MQ0Fraction=0.0000;MQRankSum=0.246;NF;NR;NS=1063;PP;PV4=0.15,1,1.9e-09,0.016;RA=5185;RUN=1;ReadPosRankSum=-4.954;SC=AGTTTCTCCGGTTTTTTTTTT;SRB=0.47464;SRF=2461;SRP=31.978;SRR=2724;TC;TR=10;TU=T;VQSLOD=4.9752;set=Intersection;sumGLbyD=4.39
+20	41013333	.	TC	T	20681	PASS	AA=137;AB=0.89211;ABA=134;ABP=1661.6;ABR=1108;AC=68;AF=0.05601;AN=1214;BL=1091;BR=8981;BVAR;BaseQRankSum=1.354;DEL;DP=12998;Dels=0.01;EL=57;EPP=11.395;ER=80;FS=0.758;HETAR=359;HOMA=100;HOMR=610;HRun=1;InbreedingCoeff=0.0104;LEN=1;LRB=0.78336;LRBP=13424;MQ0=1;MQ0Fraction=0.0003;MQM=67.745;MQRankSum=2.563;NS=1072;RA=4447;RL=5;RPP=258.66;RR=132;RUN=1;ReadPosRankSum=-14.092;SAB=0.59124;SAF=81;SAP=12.917;SAR=56;SRB=0.54194;SRF=2410;SRP=70.947;SRR=2037;VQSLOD=3.7531;set=filterInVQSR-2of5;sumGLbyD=4.14
+20	41453533	rs112736557	T	TA	1734.60	PASS	AA=44;AB=0.58025;ABA=34;ABP=7.5409;ABR=47;AC=23;AF=0.0345;AN=666;BL=2061;BR=2408;BVAR;BaseQRankSum=5.768;DB;DP=7437;Dels=0.00;EL=25;EPP=4.787;ER=19;FR;FS=3.680;HETAR=17;HOMA=5;HOMR=975;HP=7;HPLen=6;HR=6;HRun=6;HU=A;INS;InbreedingCoeff=0.1712;LEN=1;LRB=0.077646;LRBP=61.517;MQ0=0;MQ0Fraction=0.0000;MQM=75.614;MQRankSum=-4.976;NF;NR;NS=997;PP;RA=4229;RL=21;RPP=3.2077;RR=23;RUN=1;ReadPosRankSum=-0.039;SAB=0.5;SAF=22;SAP=3.0103;SAR=22;SC=CCTTTCTCCATAAAAAAGCTT;SRB=0.46299;SRF=1958;SRP=53.315;SRR=2271;TC;TR=6;TU=A;VQSLOD=7.8972;set=Intersection;sumGLbyD=13.16
+20	41659532	.	GC	G	40544	PASS	AA=42;AB=0.97149;ABA=39;ABP=2644.5;ABR=1329;AC=15;AF=0.0209;AN=716;BL=2531;BR=135;BVAR;BaseQRankSum=-2.537;DEL;DP=12219;Dels=0.00;EL=25;EPP=6.3192;ER=17;FS=2.656;HETAR=374;HOMA=155;HOMR=551;HRun=1;InbreedingCoeff=-0.0270;LEN=1;LRB=0.89872;LRBP=4678.9;MQ0=0;MQ0Fraction=0.0000;MQM=103.31;MQRankSum=2.828;NS=1088;RA=4736;RL=41;RPP=85.733;RR=1;RUN=1;ReadPosRankSum=-9.702;SAB=0.57143;SAF=24;SAP=4.8716;SAR=18;SRB=0.5625;SRF=2664;SRP=163.7;SRR=2072;VQSLOD=4.3267;set=Intersection;sumGLbyD=3.22
+20	41687456	.	A	AT	19682	PASS	AA=446;AB=0.61202;ABA=426;ABP=122.69;ABR=672;AC=162;AF=0.13214;AN=1226;BL=15293;BR=20484;BVAR;BaseQRankSum=2.364;DP=29324;DP4=1993,1785,261,252;Dels=0.01;EL=214;EPP=4.5878;ER=232;FQ=999;FR;FS=1.923;HETAR=170;HOMA=7;HOMR=897;HP=11;HPLen=9;HR=9;HRun=9;HU=T;INDEL;INS;InbreedingCoeff=0.0769;LEN=1;LRB=0.14509;LRBP=1638.5;MQ=91.55;MQ0=0;MQ0Fraction=0.0000;MQM=57.168;MQRankSum=-0.764;NF;NR;NS=1074;PP;PV4=0.45,1,3.5e-08,1;RA=5437;RL=179;RPP=40.714;RR=267;RUN=1;ReadPosRankSum=0.356;SAB=0.51794;SAF=231;SAP=4.2567;SAR=215;SC=AGAAAACCTTATTTTTTTTTC;SRB=0.51094;SRF=2778;SRP=8.666;SRR=2659;TC;TR=9;TU=T;VQSLOD=9.6786;set=Intersection;sumGLbyD=10.93
+20	41845580	.	GA	G	49310	PASS	AA=83;AB=0.95258;ABA=69;ABP=2591.6;ABR=1386;AC=46;AF=0.03740;AN=1230;BL=1320;BR=5150;BVAR;BaseQRankSum=-1.121;DEL;DP=13336;Dels=0.00;EL=36;EPP=6.1759;ER=47;FR;FS=0.372;HETAR=442;HOMA=341;HOMR=295;HP=2;HR=3;HRun=1;HU=G;InbreedingCoeff=0.0238;LEN=1;LRB=0.59196;LRBP=4926.2;MQ0=0;MQ0Fraction=0.0000;MQM=89.048;MQRankSum=0.897;NF;NR;NS=1080;PP;RA=3006;RL=5;RPP=142.43;RR=78;RUN=1;ReadPosRankSum=-15.412;SAB=0.55422;SAF=46;SAP=5.1294;SAR=37;SC=CCAGCTGTGGGAGAGAAACAT;SRB=0.47971;SRF=1442;SRP=13.762;SRR=1564;TC;TR=6;TU=AG;VQSLOD=4.4669;set=Intersection;sumGLbyD=3.65
+20	42209428	.	GC	G	13163	PASS	AA=89;AB=0.86677;ABA=83;ABP=730.96;ABR=540;AC=39;AF=0.03218;AN=1212;BL=950;BR=5334;BVAR;BaseQRankSum=-10.119;DEL;DP=10692;Dels=0.01;EL=48;EPP=4.2058;ER=41;FS=0.000;HETAR=259;HOMA=727;HOMR=54;HRun=1;InbreedingCoeff=0.0448;LEN=1;LRB=0.69764;LRBP=6644.4;MQ0=0;MQ0Fraction=0.0000;MQM=126.55;MQRankSum=4.223;NS=1040;RA=723;RL=12;RPP=106.09;RR=77;RUN=1;ReadPosRankSum=-17.362;SAB=0.39326;SAF=35;SAP=11.818;SAR=54;SRB=0.37898;SRF=274;SRP=94.99;SRR=449;VQSLOD=3.7157;set=filterInVQSR-2of5;sumGLbyD=3.48
+20	42281109	.	T	TAG	2321.12	PASS	AC=181;AF=0.3740;AN=484;BaseQRankSum=8.977;DP=435;FS=17.001;HRun=0;HaplotypeScore=14.6734;InbreedingCoeff=0.2340;MQ=53.88;MQ0=47;MQ0Fraction=0.1080;MQRankSum=0.762;QD=12.41;ReadPosRankSum=3.399;SB=-1299.73;VQSLOD=4.8926;set=VQSR
+20	42436117	.	TC	T	38933	PASS	AA=18;AB=0.98435;ABA=17;ABP=2215.9;ABR=1069;AC=15;AF=0.01223;AN=1226;BL=498;BR=428;BVAR;BaseQRankSum=-7.224;DEL;DP=12436;Dels=0.00;EL=1;EPP=33.893;ER=17;FS=2.469;HETAR=303;HOMA=614;HOMR=123;HRun=1;InbreedingCoeff=0.0439;LEN=1;LRB=0.075594;LRBP=14.501;MQ0=0;MQ0Fraction=0.0000;MQM=98.611;MQRankSum=1.086;NS=1075;RA=1656;RL=10;RPP=3.4928;RR=8;RUN=1;ReadPosRankSum=-17.765;SAB=0.5;SAF=9;SAP=3.0103;SAR=9;SRB=0.49879;SRF=826;SRP=3.0313;SRR=830;VQSLOD=4.0821;set=filterInVQSR-2of5;sumGLbyD=3.04
+20	42682214	.	C	A,CAT	3904.51	PASS	AA=24;AB=0.6383;ABA=17;ABP=10.818;ABR=30;AC=0;AF=0.0000;AN=636;BL=1119;BR=949;BVAR;BaseQRankSum=1.426;DP=6509;Dels=0.00;EL=9;EPP=6.2675;ER=15;FR;HETAR=12;HOMA=3;HOMR=876;HP=2;HPLen=1;HR=1;HRun=0;HU=A;INS;InbreedingCoeff=0.0006;LEN=2;LRB=0.082205;LRBP=33.356;MQ0Fraction=0.0046;MQM=40.792;MQRankSum=-0.296;NF;NR;NS=891;PP;QD=32.81;RA=2679;RL=15;RPP=6.2675;RR=9;RUN=1;ReadPosRankSum=-1.806;SAB=0.75;SAF=18;SAP=16.039;SAR=6;SB=-924.23;SC=TATACACACACATATATATAC;SRB=0.66293;SRF=1776;SRP=620.76;SRR=903;TC;TR=9;TU=AC;set=filterInVQSR-2of5;sumGLbyD=32.75
+20	42973456	.	CA	C,CAA,CAAA	2675	PASS	AA=90;AB=0.79177;ABA=86;ABP=308.39;ABR=327;AC=77,61,39;AF=0.06492,0.05143,0.03288;AN=1186;BL=2983;BR=4446;BVAR;BaseQRankSum=2.422;DP=9416;Dels=0.03;EL=39;EPP=6.4847;ER=51;FR;FS=31.555;HETAR=75;HOMA=1;HOMR=888;HP=11;HR=11;HRun=11;HU=A;INS;InbreedingCoeff=0.2696;LEN=1;LRB=0.19693;LRBP=628.63;MQ0=0;MQ0Fraction=0.0000;MQM=55.567;MQRankSum=1.777;NF;NR;NS=964;PP;RA=3601;RL=37;RPP=9.1869;RR=53;RUN=1;ReadPosRankSum=-4.991;SAB=0.55556;SAF=50;SAP=5.423;SAR=40;SC=TAGTGACTGTCAAAAAAAAAA;SRB=0.60622;SRF=2183;SRP=355.91;SRR=1418;TC;TR=11;TU=A;VQSLOD=1.0763;set=filterInVQSR-2of5;sumGLbyD=4.05
+20	43091870	.	TC	T	2455.60	PASS	AA=120;AB=0.10619;ABA=101;ABP=155.22;ABR=12;AC=42;AF=0.03825;AN=1098;BL=573;BR=8744;BVAR;BaseQRankSum=-13.513;DEL;DP=9139;Dels=0.00;EL=64;EPP=4.1684;ER=56;FS=9.856;HETAR=118;HOMA=820;HOMR=0;HRun=1;InbreedingCoeff=0.0833;LEN=1;LRB=0.877;LRBP=15564;MQ0Fraction=0.0017;MQM=45.1;MQRankSum=2.266;NS=938;RA=24;RL=1;RPP=254.97;RR=119;RUN=1;ReadPosRankSum=-15.803;SAB=0.475;SAF=57;SAP=3.6617;SAR=63;SRB=0.54167;SRF=13;SRP=3.3722;SRR=11;VQSLOD=3.9930;set=filterInVQSR-2of5;sumGLbyD=3.09
+20	43233648	rs74585029	GA	G,GAA	1504.40	PASS	AA=113;AB=0.78652;ABA=95;ABP=320.31;ABR=350;AC=41,65;AF=0.03394,0.05381;AF1=0.0115;AN=1208;BL=4677;BR=5548;BVAR;BaseQRankSum=6.744;CI95=0.004274,0.01852;DB;DEL;DP=13996;DP4=1736,1549,15,17;Dels=0.03;EL=69;EPP=15.021;ER=44;FQ=14;FR;FS=12.174;HETAR=119;HOMA=15;HOMR=892;HP=11;HPLen=10;HR=10;HRun=10;HU=A;INDEL;InbreedingCoeff=0.2359;LEN=1;LRB=0.085183;LRBP=164.12;MQ=89.12;MQ0Fraction=0.0000;MQM=69.867;MQRankSum=2.513;NF;NR;NS=1027;PP;PV4=0.59,1,0.065,0.33;RA=3845;RL=46;RPP=11.485;RR=67;RUN=1;ReadPosRankSum=-4.957;SAB=0.33628;SAF=38;SAP=29.318;SAR=75;SC=AAAACAGCCAGAAAAAAAAAA;SRB=0.43667;SRF=1679;SRP=136.95;SRR=2166;TC;TR=10;TU=A;VQSLOD=4.5121;set=Intersection;sumGLbyD=8.22
+20	43246548	.	AC	A,CC	41579.13	PASS	AA=382;AB=0.72402;ABA=316;ABP=502.11;ABR=829;AC=1197;AF=0.99254;AN=1206;BL=9889;BR=14293;BVAR;BaseQRankSum=1.373;DEL;DP=10477;DS;Dels=0.05;EL=243;EPP=64.494;ER=139;FS=29.162;HETAR=291;HOMA=85;HOMR=624;HPLen=10;InbreedingCoeff=0.1392;LEN=1;LRB=0.18212;LRBP=1744.6;MQ0Fraction=0.0024;MQM=48.471;MQRankSum=5.726;NS=1001;RA=3138;RL=174;RPP=9.5816;RR=208;RUN=1;ReadPosRankSum=5.755;SAB=0.79843;SAF=305;SAP=298.51;SAR=77;SRB=0.70363;SRF=2208;SRP=1133.2;SRR=930;VQSLOD=5.6318;set=Intersection;sumGLbyD=5.22
+20	43258646	.	T	TT	1107.17	PASS	AC=97;AF=0.08420;AN=1152;BaseQRankSum=4.525;DP=2345;FS=19.308;HRun=9;HaplotypeScore=13.6276;InbreedingCoeff=0.1299;MQ=76.70;MQ0=0;MQ0Fraction=0.0000;MQRankSum=1.395;QD=2.67;ReadPosRankSum=-4.696;SB=-899.41;VQSLOD=5.4523;set=VQSR
+20	43718299	.	ATTACT	A	5497.06	PASS	AA=56;AB=0.51818;ABA=53;ABP=3.3262;ABR=57;AC=18;AF=0.0251;AF1=0.03729;AN=718;BL=2321;BR=2591;BVAR;BaseQRankSum=11.142;CI95=0.03319,0.04425;DEL;DP=17576;DP4=2460,2692,31,22;Dels=0.02;EL=28;EPP=3.0103;ER=28;FQ=999;FR;FS=9.689;HETAR=15;HOMA=1;HOMR=1068;HP=2;HPLen=2;HR=2;HRun=0;HU=T;INDEL;InbreedingCoeff=0.0448;LEN=5;LRB=0.054967;LRBP=35.238;MQ=96.55;MQ0=0;MQ0Fraction=0.0000;MQM=50.286;MQRankSum=-5.149;NF;NR;NS=1084;PP;PV4=0.13,1,1.2e-12,1;RA=6745;RL=28;RPP=3.0103;RR=28;RUN=1;ReadPosRankSum=0.828;SAB=0.5;SAF=28;SAP=3.0103;SAR=28;SC=ATGACAGTGGATTACTTTAGT;SRB=0.46835;SRF=3159;SRP=61.709;SRR=3586;TC;TR=2;TU=T;VQSLOD=7.8832;set=Intersection;sumGLbyD=46.60
+20	43981749	.	A	AAAAAAC,AC	20899.71	PASS	ABR=192;AC=91,0;AF=0.1285,0.0000;AN=708;BVAR;BaseQRankSum=7.858;DP=23372;DP4=1554,1457,55,42;Dels=0.00;FR;FS=0.000;HOMA=4;HOMR=995;HP=6;HPLen=7;HR=7;HRun=0;HU=A;INDEL;INS;InbreedingCoeff=0.2109;MQ=95.59;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-12.081;NF;NR;NS=1051;PP;PV4=0.35,1,8.9e-73,1;RA=5027;RUN=1;ReadPosRankSum=-1.359;SC=TACACTAGCAAAAAAACAAAA;SRB=0.48518;SRF=2439;SRP=12.6;SRR=2588;TC;TR=7;TU=A;VQSLOD=8.0916;set=Intersection;sumGLbyD=54.33
+20	43999274	.	TCAAA	T	2948.85	PASS	AA=59;AB=0.59441;ABA=58;ABP=14.08;ABR=85;AC=20;AF=0.0290;AF1=0.04249;AN=690;BL=2277;BR=2436;BVAR;BaseQRankSum=9.320;CI95=0.0354,0.05088;DEL;DP=14599;DP4=2052,2303,21,22;Dels=0.03;EL=32;EPP=3.9304;ER=27;FQ=999;FR;FS=0.000;HETAR=21;HOMA=0;HOMR=1043;HP=2;HPLen=1;HR=1;HRun=0;HU=C;INDEL;InbreedingCoeff=-0.0037;LEN=4;LRB=0.033736;LRBP=14.658;MQ=90.05;MQ0=0;MQ0Fraction=0.0000;MQM=75.339;MQRankSum=-1.294;NF;NR;NS=1064;PP;PV4=0.88,1,0.0026,1;RA=5732;RL=27;RPP=3.9304;RR=32;RUN=1;ReadPosRankSum=-0.915;SAB=0.47458;SAF=28;SAP=3.3415;SAR=31;SC=GGTACACAGCTCAAACAGTCT;SRB=0.4836;SRF=2772;SRP=16.4;SRR=2960;TC;TR=1;TU=C;VQSLOD=9.8086;set=Intersection;sumGLbyD=27.09
+20	44098622	.	C	CG	1092.40	PASS	AA=129;AB=0.77301;ABA=74;ABP=214.06;ABR=252;AC=45;AF=0.0455;AN=988;BL=6586;BR=3029;BVAR;BaseQRankSum=2.802;DP=5177;Dels=0.00;EL=122;EPP=225.63;ER=7;FR;FS=355.273;HETAR=66;HOMA=11;HOMR=734;HP=6;HR=4;HRun=4;HU=G;INS;InbreedingCoeff=0.1759;LEN=1;LRB=0.36994;LRBP=2860.4;MQ0=0;MQ0Fraction=0.0000;MQM=52.395;MQRankSum=1.946;NF;NR;NS=811;PP;RA=1981;RL=121;RPP=217.95;RR=8;RUN=1;ReadPosRankSum=-6.413;SAB=0.99225;SAF=128;SAP=274.51;SAR=1;SC=GCGGAAGTGGCGGGGACCCTT;SRB=0.41242;SRF=817;SRP=135;SRR=1164;TC;TR=4;TU=G;VQSLOD=-2.2690;set=filterInVQSR-2of5;sumGLbyD=4.04
+20	44327637	.	A	AG,AGGGGGG	14351.23	PASS	AC=9,211;AF=0.0103,0.2409;AN=876;BaseQRankSum=15.517;DP=1704;FS=6.768;HaplotypeScore=31.5906;InbreedingCoeff=0.1538;MQ=54.64;MQ0=4;MQ0Fraction=0.0023;MQRankSum=-12.691;QD=20.83;ReadPosRankSum=-3.583;SB=-6278.99;VQSLOD=5.1556;set=VQSR
+20	45202636	.	GA	G	13269	PASS	AA=25;AB=0.96162;ABA=18;ABP=871.09;ABR=451;AC=24;AF=0.02013;AN=1192;BL=567;BR=1728;BVAR;BaseQRankSum=-5.361;DEL;DP=10873;Dels=0.00;EL=10;EPP=5.1818;ER=15;FS=0.928;HETAR=169;HOMA=831;HOMR=45;HRun=1;InbreedingCoeff=0.0999;LEN=1;LRB=0.50588;LRBP=1278.4;MQ0=0;MQ0Fraction=0.0000;MQM=170.56;MQRankSum=0.161;NS=1049;RA=632;RL=2;RPP=41.315;RR=23;RUN=1;ReadPosRankSum=-14.760;SAB=0.68;SAF=17;SAP=10.046;SAR=8;SRB=0.51424;SRF=325;SRP=4.1235;SRR=307;VQSLOD=3.9290;set=filterInVQSR-2of5;sumGLbyD=3.90
+20	45417828	.	TGAGC	T,TGC	4672.90	PASS	ABR=317;AC=69,104;AF=0.05712,0.08609;BVAR;BaseQRankSum=18.527;DEL;DP=11835;DS;FS=184.873;HOMA=48;HOMR=575;HaplotypeScore=65.5875;InbreedingCoeff=0.0599;MQ=29.78;MQ0=2988;MQ0Fraction=0.3629;MQRankSum=5.052;NS=713;QD=1.11;RA=1581;RUN=1;ReadPosRankSum=6.574;SB=-2116.87;SRB=0.47502;SRF=751;SRP=11.582;SRR=830;VQSLOD=0.0651;set=filterInVQSR-2of5
+20	45525657	rs66759083	TA	AA,T	49315	PASS	AA=2361;AB=0.45241;ABA=1398;ABP=53.235;ABR=1155;AC=20;AF=0.01701;AN=1176;BL=94913;BR=100886;BVAR;BaseQRankSum=0.740;DB;DEL;DP=30636;DP4=1258,881,1206,999;Dels=0.48;EL=1133;EPP=11.311;ER=1228;FQ=999;FR;FS=7.072;HETAR=503;HOMA=310;HOMR=218;HP=6;HPLen=7;HR=7;HU=T;INDEL;InbreedingCoeff=0.2271;LEN=1;LRB=0.030506;LRBP=398.68;MQ=102.24;MQ0=0;MQ0Fraction=0.0000;MQM=75.359;MQRankSum=0.148;NF;NR;NS=1031;PP;PV4=0.0064,0,4.6e-23,0.47;RA=2042;RL=1183;RPP=3.0333;RR=1178;RUN=1;ReadPosRankSum=-2.999;SAB=0.52139;SAF=1231;SAP=12.392;SAR=1130;SC=AGGATTTTTTTAAAAAGTTTT;SRB=0.55093;SRF=1125;SRP=49.017;SRR=917;TC;TR=7;TU=T;VQSLOD=7.1651;dbSNP=114;set=Intersection;sumGLbyD=18.51
+20	45783456	.	T	TG	2355.68	PASS	AA=64;AB=0.78521;ABA=61;ABP=203.67;ABR=223;AC=15;AF=0.0165;AN=910;BL=815;BR=5486;BVAR;BaseQRankSum=8.593;DP=10348;Dels=0.00;EL=48;EPP=37.754;ER=16;FS=77.861;HETAR=56;HOMA=1;HOMR=970;HRun=1;INS;InbreedingCoeff=-0.0549;LEN=1;LRB=0.74131;LRBP=7522.1;MQ0Fraction=0.0122;MQM=44.562;MQRankSum=-1.258;NS=1027;RA=4750;RL=0;RPP=141.98;RR=64;RUN=1;ReadPosRankSum=-7.047;SAB=0.25;SAF=16;SAP=37.754;SAR=48;SRB=0.6;SRF=2850;SRP=415.59;SRR=1900;VQSLOD=1.3146;set=filterInVQSR-2of5;sumGLbyD=6.03
+20	46384744	.	CT	C	17791	PASS	AA=51;AB=0.94826;ABA=49;ABP=1655.8;ABR=898;AC=23;AF=0.01867;AN=1232;BL=120;BR=3678;BVAR;BaseQRankSum=-0.185;DEL;DP=13879;Dels=0.00;EL=23;EPP=4.0747;ER=28;FS=2.864;HETAR=262;HOMA=78;HOMR=722;HRun=2;InbreedingCoeff=0.0193;LEN=1;LRB=0.93681;LRBP=7240.9;MQ0=0;MQ0Fraction=0.0000;MQM=66.667;MQRankSum=1.031;NS=1079;RA=5295;RL=0;RPP=113.76;RR=51;RUN=1;ReadPosRankSum=-12.934;SAB=0.54902;SAF=28;SAP=4.0747;SAR=23;SRB=0.54674;SRF=2895;SRP=103.49;SRR=2400;VQSLOD=3.0419;set=filterInVQSR-2of5;sumGLbyD=3.47
+20	46517110	.	C	CT	868.55	PASS	AC=15;AF=0.0218;AN=688;BaseQRankSum=8.522;DP=1752;FS=6.570;HRun=0;HaplotypeScore=14.9548;InbreedingCoeff=0.0452;MQ=77.73;MQ0=0;MQ0Fraction=0.0000;MQRankSum=3.874;QD=10.98;ReadPosRankSum=-0.733;SB=-396.78;VQSLOD=6.7740;set=VQSR
+20	46629361	.	TTTCTTTC	T,TTTTC	13000.91	PASS	AC=188,107;AF=0.2212,0.1259;AN=850;BaseQRankSum=7.214;DP=1846;FS=14.502;HaplotypeScore=40.8481;InbreedingCoeff=0.3210;MQ=50.74;MQ0=79;MQ0Fraction=0.0428;MQRankSum=-6.348;QD=13.59;ReadPosRankSum=3.943;SB=-3581.20;VQSLOD=5.9412;set=VQSR
+20	46951099	.	G	GT	1662.30	PASS	AA=55;AB=0.7713;ABA=51;ABP=145.58;ABR=172;AC=47;AF=0.03923;AN=1198;BL=3288;BR=2434;BVAR;BaseQRankSum=-4.014;DP=27423;DP4=1483,1590,58,42;Dels=0.01;EL=21;EPP=9.6826;ER=34;FR;FS=9.565;HETAR=48;HOMA=0;HOMR=913;HP=16;HPLen=10;HR=10;HRun=10;HU=T;INDEL;INS;InbreedingCoeff=0.0952;LEN=1;LRB=0.14925;LRBP=279.78;MQ=70.36;MQ0Fraction=0.0124;MQM=52.545;MQRankSum=0.717;NF;NR;NS=961;PP;PV4=0.067,1,1,0.17;RA=3035;RL=38;RPP=20.422;RR=17;RUN=1;ReadPosRankSum=-3.014;SAB=0.47273;SAF=26;SAP=3.3656;SAR=29;SC=TTTGTTTTTTGTTTTTTTTTT;SRB=0.36013;SRF=1093;SRP=518.73;SRR=1942;TC;TR=10;TU=T;VQSLOD=5.4779;set=Intersection;sumGLbyD=3.49
+20	47201076	rs58052846	C	CT	982.16	PASS	AC=50;AF=0.0551;AN=908;BaseQRankSum=12.598;DB;DP=2449;FS=35.648;HRun=0;HaplotypeScore=29.4602;InbreedingCoeff=-0.0542;MQ=63.54;MQ0=0;MQ0Fraction=0.0000;MQRankSum=2.196;QD=3.16;ReadPosRankSum=-13.833;SB=-488.19;VQSLOD=6.0429;set=VQSR
+20	47965974	rs60011158	G	GA	999	PASS	AA=21;AB=0.57143;ABA=21;ABP=5.1818;ABR=28;AC=7;AF=0.0101;AF1=0.02061;AN=690;BL=1043;BR=577;BVAR;BaseQRankSum=-3.087;CI95=0.01549,0.02655;DB;DP=14578;DP4=1554,3055,6,17;Dels=0.00;EL=11;EPP=3.1137;ER=10;FQ=999;FR;FS=5.982;HETAR=7;HOMA=0;HOMR=1041;HP=2;HPLen=1;HR=1;HRun=1;HU=A;INDEL;INS;InbreedingCoeff=0.0356;LEN=1;LRB=0.28765;LRBP=294.09;MQ=80.17;MQ0=0;MQ0Fraction=0.0000;MQM=64.19;MQRankSum=2.137;NF;NR;NS=1048;PP;PV4=0.51,1,1,1;RA=5224;RL=16;RPP=15.522;RR=5;RUN=1;ReadPosRankSum=0.236;SAB=0.38095;SAF=8;SAP=5.5954;SAR=13;SC=TTCATGTACAGAGCTGCTGTG;SRB=0.31183;SRF=1629;SRP=1609.6;SRR=3595;TC;TR=4;TU=AG;VQSLOD=9.5466;dbSNP=129;set=Intersection;sumGLbyD=13.83
+20	48402974	rs57331436	GA	G	27741	PASS	AA=401;AB=0.5372;ABA=311;ABP=11.089;ABR=361;AC=84;AF=0.1186;AN=708;BL=16591;BR=14776;BVAR;BaseQRankSum=14.621;DB;DEL;DP=30607;DP4=1928,2310,195,225;Dels=0.11;EL=189;EPP=5.8749;ER=212;FQ=999;FR;FS=15.568;HETAR=110;HOMA=30;HOMR=923;HP=4;HPLen=3;HR=1;HRun=3;HU=A;INDEL;InbreedingCoeff=0.1263;KGPilot123;LEN=1;LRB=0.057863;LRBP=231.06;MQ=106.68;MQ0=0;MQ0Fraction=0.0000;MQM=63.005;MQRankSum=-2.010;NF;NR;NS=1063;PP;PV4=0.72,1,0.001,1;RA=5258;RL=223;RPP=13.976;RR=178;RUN=1;ReadPosRankSum=1.337;SAB=0.37656;SAF=151;SAP=56.084;SAR=250;SC=TGCCCTCAAAGAGAAAAAGGA;SRB=0.38075;SRF=2002;SRP=652.44;SRR=3256;TC;TR=5;TU=AG;VQSLOD=8.7259;dbSNP=132;set=Intersection;sumGLbyD=15.86
+20	48519434	rs56747320	TA	T,TAA	26754	PASS	AC=91,355;AF=0.07738,0.30187;AN=1176;BVAR;BaseQRankSum=-5.499;DB;DEL;DP=24872;DP4=726,883,443,502;Dels=0.04;FR;FS=1.430;HP=12;HR=12;HRun=12;HU=A;INDEL;INS;InbreedingCoeff=0.2576;LEN=1;MQ=71.86;MQ0=1;MQ0Fraction=0.0004;MQRankSum=-0.526;NF;NR;PP;PV4=0.41,1,0.00077,1;RUN=1;ReadPosRankSum=-4.130;SC=CGTCTTAAACTAAAAAAAAAA;TC;TR=12;TU=A;VQSLOD=7.3200;set=Intersection;sumGLbyD=10.43
+20	49086519	rs111404890	CA	C,CAA	1379.10	PASS	AA=43;AB=0.672;ABA=41;ABP=35.131;ABR=84;AC=7,14;AF=0.0100,0.0201;AN=698;BL=1097;BR=2286;BVAR;BaseQRankSum=-2.656;DB;DP=9319;Dels=0.00;EL=22;EPP=3.0608;ER=21;FR;FS=1.147;HETAR=20;HOMA=0;HOMR=1029;HP=11;HPLen=8;HR=8;HRun=8;HU=A;INS;InbreedingCoeff=0.0760;LEN=1;LRB=0.35146;LRBP=910.45;MQ0=0;MQ0Fraction=0.0000;MQM=47.674;MQRankSum=2.682;NF;NR;NS=1049;PP;RA=5237;RL=10;RPP=29.724;RR=33;RUN=1;ReadPosRankSum=-2.367;SAB=0.48837;SAF=21;SAP=3.0608;SAR=22;SC=GTAAAACAAACAAAAAAAATG;SRB=0.48635;SRF=2547;SRP=11.489;SRR=2690;TC;TR=11;TU=AAAC;VQSLOD=7.3084;set=Intersection;sumGLbyD=9.84
+20	49101936	.	C	CT	404.46	PASS	AC=40;AF=0.03559;AN=1124;BaseQRankSum=0.750;DP=2162;FS=14.291;HRun=2;HaplotypeScore=30.9513;InbreedingCoeff=-0.0082;MQ=49.78;MQ0=113;MQ0Fraction=0.0523;MQRankSum=-1.289;QD=1.94;ReadPosRankSum=-2.041;SB=-385.48;VQSLOD=4.6365;set=VQSR
+20	49681276	.	TC	T	40042	PASS	AA=72;AB=0.93908;ABA=70;ABP=1927.1;ABR=1079;AC=18;AF=0.0196;AN=918;BL=514;BR=4340;BVAR;BaseQRankSum=0.869;DEL;DP=10368;Dels=0.00;EL=33;EPP=4.096;ER=39;FS=17.302;HETAR=389;HOMA=269;HOMR=405;HRun=1;InbreedingCoeff=0.0626;LEN=1;LRB=0.78822;LRBP=6551.6;MQ0=0;MQ0Fraction=0.0000;MQM=123.06;MQRankSum=-1.047;NS=1064;RA=3095;RL=3;RPP=134.38;RR=69;RUN=1;ReadPosRankSum=-10.928;SAB=0.58333;SAF=42;SAP=7.3532;SAR=30;SRB=0.57738;SRF=1787;SRP=163.99;SRR=1308;VQSLOD=2.8517;set=filterInVQSR-2of5;sumGLbyD=3.69
+20	49690436	.	GT	G	473.74	PASS	AF=0.0263;AF1=0.02287;BaseQRankSum=3.830;CI95=0.01327,0.03319;DP=7473;DP4=2241,1740,14,12;Dels=0.01;FQ=129;FR;FS=0.000;HP=4;HPLen=4;HR=4;HRun=4;HU=T;INDEL;InbreedingCoeff=0.1310;MQ=51.71;MQ0Fraction=0.0407;MQRankSum=1.792;NF;NR;PP;PV4=0.84,5.7e-10,0.22,1;ReadPosRankSum=0.973;SC=GTAGGACGGGGTTTTACCATG;TC;TR=4;TU=T;VQSLOD=7.4809;set=Intersection;sumGLbyD=10.96
+20	49731218	.	ATTTTATTTTTTATT	A,ATTTTATT	8398.93	PASS	AF=0.0656,0.0156;AF1=0.0996;BaseQRankSum=13.996;CI95=0.07743,0.1239;DP=6308;DP4=951,1311,23,35;Dels=0.05;FQ=999;FR;FS=12.503;HP=7;HPLen=4;HR=4;HRun=0;HU=T;INDEL;InbreedingCoeff=0.1892;MQ=57.61;MQ0Fraction=0.0145;MQRankSum=-5.208;NF;NR;PP;PV4=0.79,1,6.3e-06,0.16;ReadPosRankSum=-2.239;SC=TATTTTATTTATTTTATTTTT;TC;TR=11;TU=ATTT;VQSLOD=4.3191;set=Intersection;sumGLbyD=42.27
+20	49894989	.	TA	T	172.25	PASS	AF=0.0140;BaseQRankSum=7.220;DP=3882;Dels=0.00;FS=17.217;HPLen=2;HRun=1;InbreedingCoeff=0.0531;MQ0Fraction=0.0214;MQRankSum=-0.661;ReadPosRankSum=-0.592;VQSLOD=3.0905;set=filterInVQSR-2of5;sumGLbyD=6.60
+20	50010923	rs66516522	C	CT,CTGG	35851	PASS	ABR=555;AC=310,11;AF=0.26451,0.00939;BVAR;BaseQRankSum=10.662;DB;DP=8188;FR;FS=34.411;HOMA=261;HOMR=399;HP=5;HR=6;HU=C;HaplotypeScore=45.1715;INS;InbreedingCoeff=0.2090;MQ=72.80;MQ0=0;MQ0Fraction=0.0000;MQRankSum=9.015;NF;NR;NS=831;PP;QD=9.69;RA=1986;RUN=1;ReadPosRankSum=-24.284;SB=-6038.55;SC=TGTCTGTCCCCCCTCAGCACT;SRB=0.45972;SRF=913;SRP=31.001;SRR=1073;TC;TR=6;TU=C;VQSLOD=6.1824;set=Intersection
+20	50059710	.	C	CCA	4175.86	PASS	AA=28;AB=0.62963;ABA=20;ABP=10.892;ABR=34;AC=36;AF=0.0738;AN=488;BL=1050;BR=1273;BVAR;BaseQRankSum=3.198;DP=9138;Dels=0.00;EL=10;EPP=7.9737;ER=18;FR;FS=19.190;HETAR=10;HOMA=2;HOMR=1053;HP=6;HPLen=7;HR=7;HRun=0;HU=C;INS;InbreedingCoeff=0.1390;LEN=2;LRB=0.095997;LRBP=49.496;MQ0=0;MQ0Fraction=0.0000;MQM=57.464;MQRankSum=-1.875;NF;NR;NS=1065;PP;RA=5745;RL=12;RPP=4.2511;RR=16;RUN=1;ReadPosRankSum=-2.894;SAB=0.5;SAF=14;SAP=3.0103;SAR=14;SC=GGAGACCCCCCCTTCATCCTA;SRB=0.48129;SRF=2765;SRP=20.482;SRR=2980;TC;TR=7;TU=C;VQSLOD=5.1567;set=Intersection;sumGLbyD=11.49
+20	50228709	rs71192536	TG	T	20517	PASS	AA=924;AB=0.50203;ABA=735;ABP=3.0633;ABR=741;AC=200;AF=0.16502;AN=1212;BL=35460;BR=34197;BVAR;BaseQRankSum=13.810;DB;DEL;DP=32402;DP4=1760,2065,395,449;Dels=0.16;EL=439;EPP=7.9831;ER=485;FQ=999;FR;FS=0.558;HETAR=242;HOMA=63;HOMR=764;HP=5;HPLen=3;HR=3;HRun=3;HU=G;INDEL;InbreedingCoeff=0.1050;LEN=1;LRB=0.018132;LRBP=52.738;MQ=105.83;MQ0=0;MQ0Fraction=0.0000;MQM=75.87;MQRankSum=3.895;NF;NR;NS=1069;PP;PV4=0.7,1.5e-173,1,1;RA=4708;RL=486;RPP=8.4249;RR=438;RUN=1;ReadPosRankSum=1.586;SAB=0.43615;SAF=403;SAP=35.733;SAR=521;SC=GTTTTCCAGGTGGGAAGACCG;SRB=0.44074;SRF=2075;SRP=146.62;SRR=2633;TC;TR=3;TU=G;VQSLOD=10.4820;dbSNP=120;set=Intersection;sumGLbyD=15.35
+20	50236115	.	AGG	A,ACGGG,AG,AGGG	7429.57	PASS	AC=192,13,221,183;AF=0.2115,0.0143,0.2434,0.2015;AN=908;BaseQRankSum=1.045;DP=1177;FS=13.479;HaplotypeScore=11.8294;InbreedingCoeff=0.7959;MQ=52.98;MQ0=6;MQ0Fraction=0.0051;MQRankSum=-1.482;QD=7.28;ReadPosRankSum=-2.380;SB=-1229.31;VQSLOD=8.3762;set=VQSR
+20	51589568	.	TAAAC	AAAAC,T	12477.52	PASS	AF=0.27949;BaseQRankSum=-28.122;DP=3777;Dels=0.00;FR;FS=31.799;HP=7;HPLen=4;HR=3;HRun=0;HU=A;InbreedingCoeff=-0.1429;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-1.196;NF;NR;PP;ReadPosRankSum=-16.483;SC=AAATTCAAAATAAACAAACAA;TC;TR=18;TU=AAAC;VQSLOD=3.9201;set=filterInVQSR-2of5;sumGLbyD=52.43
+20	51617742	.	TGC	T,TGCGC	1374.91	PASS	AF=0.06000,0.02000;BaseQRankSum=12.051;DP=6231;Dels=0.00;FS=189.609;HPLen=1;HRun=0;InbreedingCoeff=0.0862;MQ0Fraction=0.0180;MQRankSum=-2.959;ReadPosRankSum=-5.090;VQSLOD=-2.8715;set=filterInVQSR-2of5;sumGLbyD=3.97
+20	51770354	.	AG	A	1010.90	PASS	AA=26;AB=0.52727;ABA=26;ABP=3.3656;ABR=29;AC=7;AF=0.0097;AF1=0.01637;AN=718;BL=1034;BR=964;BVAR;BaseQRankSum=5.588;CI95=0.01327,0.02212;DEL;DP=16259;DP4=2785,2239,15,10;Dels=0.01;EL=11;EPP=4.3466;ER=15;FQ=999;FR;FS=3.367;HETAR=8;HOMA=0;HOMR=1064;HP=2;HPLen=2;HR=2;HRun=2;HU=G;INDEL;InbreedingCoeff=0.0557;LEN=1;LRB=0.035035;LRBP=8.3357;MQ=90.48;MQ0=0;MQ0Fraction=0.0000;MQM=61.346;MQRankSum=-0.019;NF;NR;NS=1072;PP;PV4=0.69,2.1e-08,0.078,1;RA=6173;RL=13;RPP=3.0103;RR=13;RUN=1;ReadPosRankSum=-0.460;SAB=0.61538;SAF=16;SAP=6.017;SAR=10;SC=GTGGTCCTGCAGGTCAATAAT;SRB=0.56342;SRF=3478;SRP=218.68;SRR=2695;TC;TR=2;TU=G;VQSLOD=10.1601;set=Intersection;sumGLbyD=14.60
+20	51848430	.	AT	A,ATT	999	PASS	AA=39;AB=0.83408;ABA=37;ABP=219.19;ABR=186;AC=14,33;AF=0.0153,0.0359;AF1=0.03062;AN=918;BL=1676;BR=1732;BVAR;BaseQRankSum=3.338;CI95=0.02212,0.03982;DP=14886;DP4=1970,1762,22,31;Dels=0.01;EL=18;EPP=3.5114;ER=21;FQ=999;FR;FS=3.004;HETAR=31;HOMA=0;HOMR=1040;HP=10;HPLen=9;HR=9;HRun=9;HU=T;INDEL;INS;InbreedingCoeff=0.1629;LEN=1;LRB=0.016432;LRBP=5.0085;MQ=80.05;MQ0=0;MQ0Fraction=0.0000;MQM=56.667;MQRankSum=0.325;NF;NR;NS=1071;PP;PV4=0.13,1,0.0095,0.064;RA=5318;RL=21;RPP=3.5114;RR=18;RUN=1;ReadPosRankSum=-0.493;SAB=0.46154;SAF=18;SAP=3.5114;SAR=21;SC=ACAAAACAATATTTTTTTTTC;SRB=0.4968;SRF=2642;SRP=3.4823;SRR=2676;TC;TR=9;TU=T;VQSLOD=5.7417;set=Intersection;sumGLbyD=7.57
+20	51897203	.	T	TG	8427.20	PASS	AA=237;AB=0.69846;ABA=215;ABP=246.92;ABR=498;AC=117;AF=0.1662;AN=704;BL=14961;BR=5990;BVAR;BaseQRankSum=22.203;DP=9710;Dels=0.00;EL=83;EPP=49.198;ER=154;FR;FS=9.450;HETAR=123;HOMA=9;HOMR=895;HP=5;HPLen=6;HR=6;HRun=0;HU=T;INS;InbreedingCoeff=-0.0513;LEN=1;LRB=0.42819;LRBP=8344.3;MQ0Fraction=0.0291;MQM=45.861;MQRankSum=-10.426;NF;NR;NS=1027;PP;RA=4919;RL=210;RPP=309.85;RR=27;RUN=1;ReadPosRankSum=-1.843;SAB=0.29536;SAF=70;SAP=89.219;SAR=167;SC=TTTGTTTGTTTTTTGTTGTTG;SRB=0.47794;SRF=2351;SRP=23.798;SRR=2568;TC;TR=23;TU=GTTT;VQSLOD=6.2670;set=Intersection;sumGLbyD=8.99
+20	52274070	.	AAG	A	1400.37	PASS	AA=30;AB=0.74227;ABA=25;ABP=52.462;ABR=72;AC=21;AF=0.01756;AN=1196;BL=412;BR=1966;BVAR;BaseQRankSum=6.660;DEL;DP=9362;Dels=0.01;EL=16;EPP=3.2998;ER=14;FS=1.485;HETAR=18;HOMA=2;HOMR=1004;HRun=0;InbreedingCoeff=0.0317;LEN=2;LRB=0.65349;LRBP=2208.2;MQ0Fraction=0.0022;MQM=46.133;MQRankSum=-4.743;NS=1024;RA=3931;RL=2;RPP=51.941;RR=28;RUN=1;ReadPosRankSum=-4.152;SAB=0.4;SAF=12;SAP=5.6161;SAR=18;SRB=0.49784;SRF=1957;SRP=3.1699;SRR=1974;VQSLOD=5.6452;set=Intersection;sumGLbyD=11.11
+20	52351501	.	TAC	T	199.59	PASS	AC=22;AF=0.0238;AN=926;BaseQRankSum=7.874;DP=22911;DP4=2146,1691,26,22;FR;FS=2.898;HP=4;HPLen=3;HR=1;HRun=0;HU=A;HaplotypeScore=18.6111;INDEL;InbreedingCoeff=-0.0326;MQ0=2;MQ0Fraction=0.0007;MQRankSum=1.011;NF;NR;PP;PV4=0.88,0.14,0.16,0.24;QD=1.10;ReadPosRankSum=-1.053;SB=-306.09;SC=GACACACAAATACACACACAC;TC;TR=13;TU=AC;VQSLOD=4.0486;set=filterInVQSR-2of5
+20	52447173	.	CA	C	503.89	PASS	AC=23;AF=0.01891;AN=1216;BaseQRankSum=0.801;DP=3266;FS=2.606;HRun=2;HaplotypeScore=22.1543;InbreedingCoeff=-0.0097;MQ=118.02;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-1.309;QD=2.65;ReadPosRankSum=-7.872;SB=-279.27;VQSLOD=4.1900;set=VQSR
+20	52498650	.	GT	G	24069	PASS	AA=74;AB=0.90594;ABA=57;ABP=870.4;ABR=549;AC=28;AF=0.02333;AN=1200;BL=505;BR=4514;BVAR;BaseQRankSum=-3.837;DEL;DP=9798;Dels=0.01;EL=41;EPP=4.8883;ER=33;FS=4.085;HETAR=209;HOMA=663;HOMR=121;HRun=1;InbreedingCoeff=0.0334;LEN=1;LRB=0.79876;LRBP=6956.6;MQ0=2;MQ0Fraction=0.0007;MQM=57.784;MQRankSum=-2.951;NS=995;RA=957;RL=8;RPP=101.72;RR=66;RUN=1;ReadPosRankSum=-14.806;SAB=0.39189;SAF=29;SAP=10.522;SAR=45;SRB=0.39916;SRF=382;SRP=87.53;SRR=575;VQSLOD=3.8710;set=filterInVQSR-2of5;sumGLbyD=2.90
+20	52823602	rs11469056	CAAA	C,CA,CAA,CAAAA,CAAAAA,CAAAAAA,CAAAAAAA,CAAAAAAAA,CAAAAAAAAA,CAAAAAAAAAA	14515.17	PASS	AC=24,83,246,109,83,19,10,16,22,59;AF=0.02128,0.07358,0.21809,0.09663,0.07358,0.01684,0.00887,0.01418,0.01950,0.05230;AN=1128;BVAR;BaseQRankSum=4.150;DB;DEL;DP=28279;FR;FS=2.021;HP=17;HR=17;HU=A;HaplotypeScore=27.8032;INS;InbreedingCoeff=0.7740;MQ=69.00;MQ0=0;MQ0Fraction=0.0000;MQRankSum=1.418;NF;NR;PP;QD=7.90;RUN=1;ReadPosRankSum=-3.864;SB=-3244.40;SC=GGTCCTAAGGCAAAAAAAAAA;TC;TR=17;TU=A;VQSLOD=14.1033;set=Intersection
+20	53308906	.	CT	C,CTT	2276	PASS	AA=92;AB=0.84453;ABA=81;ABP=540.17;ABR=440;AC=53,81;AF=0.04351,0.06650;AN=1218;BL=3561;BR=4796;BVAR;BaseQRankSum=3.000;DP=11804;Dels=0.02;EL=48;EPP=3.3879;ER=44;FR;FS=13.197;HETAR=69;HOMA=3;HOMR=993;HP=11;HR=10;HRun=10;HU=T;INS;InbreedingCoeff=0.2297;LEN=1;LRB=0.14778;LRBP=399.32;MQ0=1;MQ0Fraction=0.0003;MQM=56.348;MQRankSum=3.154;NF;NR;NS=1065;PP;RA=5520;RL=39;RPP=7.6365;RR=53;RUN=1;ReadPosRankSum=-2.140;SAB=0.57609;SAF=53;SAP=7.6365;SAR=39;SC=AATCCAAAGTCTTTTTTTTTT;SRB=0.51576;SRF=2847;SRP=14.92;SRR=2673;TC;TR=10;TU=T;VQSLOD=2.4753;set=filterInVQSR-2of5;sumGLbyD=4.42
+20	53334602	.	T	TG,TGG	905.13	PASS	ABR=325;AC=44,22;AF=0.03624,0.01812;BVAR;BaseQRankSum=-4.608;DP=15015;FR;FS=494.901;HOMA=0;HOMR=1004;HP=1;HR=1;HU=G;HaplotypeScore=20.5023;INS;InbreedingCoeff=0.0799;MQ=116.70;MQ0=0;MQ0Fraction=0.0000;MQRankSum=8.022;NF;NR;NS=1064;PP;QD=0.35;RA=5690;RUN=1;ReadPosRankSum=-14.522;SB=-311.57;SC=AGCCATTGGCTGTTTCACTGA;SRB=0.40738;SRF=2318;SRP=426.97;SRR=3372;TC;TR=1;TU=G;VQSLOD=-2.3042;set=filterInVQSR-2of5
+20	53729115	.	T	TG	15.48	PASS	AC=1;AF=0.0015;AN=668;BaseQRankSum=-1.001;DP=1711;FS=9.048;HRun=2;HaplotypeScore=12.4681;InbreedingCoeff=-0.0320;MQ=131.36;MQ0=0;MQ0Fraction=0.0000;MQRankSum=0.193;QD=4.57;ReadPosRankSum=0.407;SB=-5.35;VQSLOD=4.8071;set=VQSR
+20	53960980	.	GC	G	588.40	PASS	AA=32;AB=0.78632;ABA=25;ABP=86.324;ABR=92;AF=0.0275;AF1=0.01689;AN=690;BL=1047;BR=1108;BVAR;BaseQRankSum=3.049;CI95=0.006637,0.02876;DEL;DP=11389;DP4=1514,1481,16,12;Dels=0.02;EL=27;EPP=35.854;ER=5;FQ=17.6;FS=0.652;HETAR=27;HOMA=3;HOMR=1006;HRun=1;INDEL;InbreedingCoeff=0.0473;LEN=1;LRB=0.028306;LRBP=6.7597;MQ=106.54;MQ0=0;MQ0Fraction=0.0000;MQM=115.53;MQRankSum=1.395;NS=1036;PV4=0.57,0.0057,0.46,0.22;RA=4207;RL=14;RPP=4.096;RR=18;RUN=1;ReadPosRankSum=-5.581;SAB=0.40625;SAF=13;SAP=5.4532;SAR=19;SRB=0.48586;SRF=2044;SRP=10.32;SRR=2163;VQSLOD=6.0155;set=Intersection;sumGLbyD=7.94
+20	54033830	.	GTATTTTAAAATCA	G	2220.86	PASS	AF=0.0113;BaseQRankSum=5.506;DP=2577;Dels=0.01;FR;FS=6.533;HP=5;HPLen=4;HR=1;HRun=0;HU=T;InbreedingCoeff=0.0032;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-2.969;NF;NR;PP;ReadPosRankSum=1.322;SC=TCAATATTTTGTATTTTAAAA;TC;TR=1;TU=T;VQSLOD=5.5145;set=Intersection;sumGLbyD=95.65
+20	54375236	.	GT	G	626.13	PASS	AA=40;AB=0.63551;ABA=39;ABP=20.078;ABR=68;AC=18;AF=0.0256;AN=702;BL=1331;BR=1743;BVAR;BaseQRankSum=9.346;DEL;DP=8568;Dels=0.02;EL=26;EPP=10.828;ER=14;FS=0.610;HETAR=21;HOMA=1;HOMR=1035;HRun=1;InbreedingCoeff=-0.0056;LEN=1;LRB=0.13403;LRBP=122.92;MQ0=0;MQ0Fraction=0.0000;MQM=67.125;MQRankSum=-2.537;NS=1058;RA=4870;RL=17;RPP=4.9646;RR=23;RUN=1;ReadPosRankSum=-1.229;SAB=0.525;SAF=21;SAP=3.2274;SAR=19;SRB=0.5271;SRF=2567;SRP=34.087;SRR=2303;VQSLOD=7.9228;set=Intersection;sumGLbyD=10.77
+20	54457331	.	G	GA	1793.40	PASS	AA=77;AB=0.66667;ABA=74;ABP=56.573;ABR=148;AC=33;AF=0.02687;AN=1228;BL=3834;BR=1154;BVAR;BaseQRankSum=10.572;DP=10230;Dels=0.00;EL=77;EPP=170.21;ER=0;FS=139.433;HETAR=44;HOMA=1;HOMR=1001;HRun=1;INS;InbreedingCoeff=0.0023;LEN=1;LRB=0.53729;LRBP=3129.8;MQ0Fraction=0.0095;MQM=4.7013;MQRankSum=-8.116;NS=1046;RA=4009;RL=77;RPP=170.21;RR=0;RUN=1;ReadPosRankSum=-6.026;SAB=1;SAF=77;SAP=170.21;SAR=0;SRB=0.57022;SRF=2286;SRP=174.7;SRR=1723;VQSLOD=1.1887;set=filterInVQSR-2of5;sumGLbyD=5.90
+20	54469810	.	CA	C	1697.62	PASS	AA=93;AB=0.63855;ABA=90;ABP=44.53;ABR=159;AC=34;AF=0.0374;AF1=0.01719;AN=908;BL=3242;BR=5839;BVAR;BaseQRankSum=10.425;CI95=0.009317,0.02795;DEL;DP=15197;DP4=2134,1896,56,46;Dels=0.03;EL=34;EPP=17.604;ER=59;FQ=16;FR;FS=9.985;HETAR=41;HOMA=1;HOMR=1011;HP=9;HPLen=8;HR=8;HRun=8;HU=A;INDEL;InbreedingCoeff=-0.0472;LEN=1;LRB=0.28598;LRBP=1615.8;MQ=83.37;MQ0=1;MQ0Fraction=0.0004;MQM=64.075;MQRankSum=3.036;NF;NR;NS=1053;PP;PV4=0.76,1,0.31,0.22;RA=5150;RL=28;RPP=34.975;RR=65;RUN=1;ReadPosRankSum=-0.252;SAB=0.5914;SAF=55;SAP=9.7582;SAR=38;SC=ATTGCTAAGACAAAAAAAAGA;SRB=0.50621;SRF=2607;SRP=4.7374;SRR=2543;TC;TR=8;TU=A;VQSLOD=8.3677;set=Intersection;sumGLbyD=9.90
+20	54542453	.	GTATA	G,GTA	5109.66	PASS	ABR=112;AC=66,56;AF=0.0682,0.0579;AN=968;BVAR;BaseQRankSum=17.089;DB;DEL;DP=5519;DS;Dels=0.06;FS=99.502;HOMA=15;HOMR=409;HRun=0;InbreedingCoeff=0.1584;MQ0Fraction=0.0178;MQRankSum=-6.854;NS=460;RA=864;RUN=1;ReadPosRankSum=0.855;SRB=0.79282;SRF=685;SRP=646.5;SRR=179;VQSLOD=0.6375;set=filterInVQSR-2of5;sumGLbyD=8.53
+20	54629773	.	CA	C	1799.50	PASS	AA=49;AB=0.82707;ABA=46;ABP=250.17;ABR=220;AC=9;AF=0.00746;AN=1206;BL=173;BR=2277;BVAR;BaseQRankSum=5.240;DEL;DP=8557;Dels=0.01;EL=49;EPP=109.41;ER=0;FS=32.359;HETAR=35;HOMA=1;HOMR=325;HRun=1;InbreedingCoeff=0.0892;LEN=1;LRB=0.85878;LRBP=3926.6;MQ0Fraction=0.0602;MQM=32.163;MQRankSum=-3.926;NS=361;RA=1091;RL=0;RPP=109.41;RR=49;RUN=1;ReadPosRankSum=-4.512;SAB=0;SAF=0;SAP=109.41;SAR=49;SRB=0.49404;SRF=539;SRP=3.3467;SRR=552;VQSLOD=1.1233;set=filterInVQSR-2of5;sumGLbyD=3.54
+20	54710245	.	TA	T	999	PASS	AF=0.0084;AF1=0.0148;BaseQRankSum=3.954;CI95=0.00885,0.02212;DP=8043;DP4=2000,1849,10,7;Dels=0.01;FQ=999;FR;FS=0.000;HP=9;HPLen=6;HR=3;HRun=6;HU=A;INDEL;InbreedingCoeff=0.1181;MQ=78.51;MQ0=0;MQ0Fraction=0.0000;MQRankSum=0.095;NF;NR;PP;PV4=0.63,0.00056,1,1;ReadPosRankSum=-0.448;SC=CAACAAAAAATAAATAAATAA;TC;TR=15;TU=AAAT;VQSLOD=7.8129;set=Intersection;sumGLbyD=19.02
+20	54968173	.	A	AAT,AATAT,AT,ATAT	89535.82	PASS	ABR=994;AC=561,278,2,3;AF=0.50179,0.24866,0.00179,0.00268;AN=1118;BVAR;BaseQRankSum=-2.699;DB;DP=27837;DP4=168,177,1045,866;Dels=0.00;FQ=999;FR;FS=12.472;HOMA=71;HOMR=455;HP=3;HPLen=4;HR=4;HRun=0;HU=A;INDEL;INS;InbreedingCoeff=0.6391;KGPilot123;MQ=80.36;MQ0Fraction=0.0055;MQRankSum=-1.512;NF;NR;NS=913;PP;PV4=0.046,1,1,1;RA=2015;RUN=1;ReadPosRankSum=1.015;SC=GGCCACTTAAAATATATATAT;SRB=0.44864;SRF=904;SRP=49.187;SRR=1111;TC;TR=15;TU=AT;VQSLOD=9.0092;dbSNP=132;set=Intersection;sumGLbyD=42.33
+20	55176688	.	TA	T	421.84	PASS	AF=0.01322;AF1=0.01845;BaseQRankSum=5.383;CI95=0.01282,0.02564;DP=10531;DP4=1975,2017,16,14;Dels=0.01;FQ=91.2;FR;FS=7.401;HP=6;HPLen=5;HR=5;HRun=5;HU=A;INDEL;InbreedingCoeff=0.0829;MQ=75.80;MQ0=1;MQ0Fraction=0.0003;MQRankSum=-0.471;NF;NR;PP;PV4=0.72,1,1,1;ReadPosRankSum=0.223;SC=CTGCAAAATATAAAAATTAGG;TC;TR=5;TU=A;VQSLOD=6.6000;set=Intersection;sumGLbyD=12.15
+20	55664086	.	GTT	ATT,G,GT,GTTT	5622.44	PASS	AC=6,71,136;AF=0.00498,0.05887,0.11277;AN=1206;BVAR;BaseQRankSum=3.173;DB;DEL;DP=40384;DP4=1567,1317,54,29;Dels=0.05;FR;FS=1.949;HP=14;HR=11;HRun=11;HU=T;INDEL;INS;InbreedingCoeff=0.3490;MQ=77.90;MQ0=0;MQ0Fraction=0.0000;MQRankSum=0.052;NF;NR;PP;PV4=0.057,1,0.2,1.2e-05;RUN=1;ReadPosRankSum=-13.646;SC=AATTTTATTTGTTTTTTTTTT;TC;TR=11;TU=T;VQSLOD=11.7964;set=Intersection;sumGLbyD=8.09
+20	56045006	.	TG	T	342.15	PASS	AC=72;AF=0.0940;AN=766;BaseQRankSum=4.992;DP=1238;FS=1.460;HRun=7;HaplotypeScore=20.2784;InbreedingCoeff=0.1795;MQ=66.42;MQ0=1;MQ0Fraction=0.0008;MQRankSum=-0.937;QD=1.84;ReadPosRankSum=-4.385;SB=-320.83;VQSLOD=5.2383;set=VQSR
+20	56158711	.	AG	A	922.47	PASS	AA=18;AB=0.575;ABA=17;ABP=4.9646;ABR=23;AC=2;AF=0.0028;AN=714;BL=953;BR=808;BVAR;BaseQRankSum=3.129;DEL;DP=10462;Dels=0.01;EL=9;EPP=3.0103;ER=9;FR;FS=8.724;HETAR=4;HOMA=0;HOMR=1058;HP=1;HPLen=2;HR=2;HRun=1;HU=A;InbreedingCoeff=0.0262;LEN=1;LRB=0.08234;LRBP=28.936;MQ0=0;MQ0Fraction=0.0000;MQM=55.889;MQRankSum=2.052;NF;NR;NS=1062;PP;RA=6300;RL=9;RPP=3.0103;RR=9;RUN=1;ReadPosRankSum=-0.317;SAB=0.66667;SAF=12;SAP=7.3532;SAR=6;SC=TGGCCTAGCAAGCATCGTGAC;SRB=0.48143;SRF=3033;SRP=21.883;SRR=3267;TC;TR=8;TU=AAGC;VQSLOD=8.3252;set=Intersection;sumGLbyD=13.22
+20	56258618	rs113670927	T	C,TGC,TGTGC,TGTGTGC	37834.99	PASS	ABR=441;AC=11,100,43;AF=0.0123,0.1119,0.0481;AN=894;BVAR;BaseQRankSum=19.514;DB;DP=23173;DP4=541,920,413,579;Dels=0.00;FQ=999;FR;FS=1.238;HOMA=28;HOMR=808;HP=2;HPLen=1;HR=1;HRun=0;HU=G;INDEL;INS;InbreedingCoeff=0.2154;MQ=57.25;MQ0Fraction=0.0275;MQRankSum=-6.684;NF;NR;NS=976;PP;PV4=0.023,1,1,1;RA=3294;RUN=1;ReadPosRankSum=11.873;SC=TGCGTGTGTGTGTGTGTGTGT;SRB=0.42441;SRF=1398;SRP=166.5;SRR=1896;TC;TR=30;TU=GT;VQSLOD=6.7457;dbSNP=114;set=Intersection;sumGLbyD=21.27
+20	56395857	.	T	TAGGCAG	6614.22	PASS	AA=30;AB=0.63415;ABA=30;ABP=15.827;ABR=52;AC=14;AF=0.0197;AF1=0.03154;AN=710;BL=991;BR=1813;BVAR;BaseQRankSum=-4.589;CI95=0.02434,0.04204;DP=13879;DP4=1543,1833,12,14;Dels=0.00;EL=14;EPP=3.2998;ER=16;FQ=999;FR;FS=1.482;HETAR=11;HOMA=0;HOMR=1051;HP=1;HPLen=2;HR=2;HRun=0;HU=T;INDEL;INS;InbreedingCoeff=0.0774;LEN=6;LRB=0.29315;LRBP=526.27;MQ=90.42;MQ0=0;MQ0Fraction=0.0000;MQM=39.433;MQRankSum=-7.011;NF;NR;NS=1062;PP;PV4=1,1,3.7e-09,1;RA=5322;RL=9;RPP=13.433;RR=21;RUN=1;ReadPosRankSum=0.679;SAB=0.43333;SAF=13;SAP=4.1684;SAR=17;SC=AAGAGCATCTTAGGCAGAGGC;SRB=0.47294;SRF=2517;SRP=36.853;SRR=2805;TC;TR=2;TU=T;VQSLOD=8.3045;set=Intersection;sumGLbyD=68.22
+20	56969289	.	GTTTGT	G	600.69	PASS	AF=0.0056;AF1=0.007726;BaseQRankSum=2.907;CI95=0.004425,0.01327;DP=9643;DP4=1892,1749,6,3;Dels=0.00;FQ=117;FR;FS=16.601;HP=5;HPLen=3;HR=3;HRun=0;HU=T;INDEL;InbreedingCoeff=0.0236;MQ=92.59;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-2.134;NF;NR;PP;PV4=0.51,1,0.07,0.3;ReadPosRankSum=0.236;SC=TAAGGACGTTGTTTGTTTTGT;TC;TR=10;TU=GTTT;VQSLOD=5.8458;set=Intersection;sumGLbyD=39.51
+20	57187557	.	AG	A,AGG	1486.69	PASS	AA=130;AB=0.55446;ABA=90;ABP=8.2132;ABR=112;AC=56,26;AF=0.0574,0.0266;AN=976;BL=3817;BR=5968;BVAR;BaseQRankSum=5.517;DEL;DP=14174;DP4=925,721,59,48;Dels=0.05;EL=52;EPP=14.302;ER=78;FR;FS=0.917;HETAR=44;HOMA=17;HOMR=864;HP=4;HPLen=4;HR=4;HRun=4;HU=G;INDEL;InbreedingCoeff=0.2856;LEN=1;LRB=0.21983;LRBP=1029.8;MQ=91.56;MQ0=0;MQ0Fraction=0.0000;MQM=63.631;MQRankSum=1.900;NF;NR;NS=925;PP;PV4=0.84,1,1,0.39;RA=2746;RL=44;RPP=32.476;RR=86;RUN=1;ReadPosRankSum=-0.639;SAB=0.44615;SAF=58;SAP=6.2842;SAR=72;SC=TCAGGCCCGCAGGGGTCAGGG;SRB=0.5772;SRF=1585;SRP=145.17;SRR=1161;TC;TR=4;TU=G;VQSLOD=7.7167;set=Intersection;sumGLbyD=14.85
+20	57282771	.	T	TG	506.43	PASS	AA=34;AB=0.70312;ABA=19;ABP=25.946;ABR=45;AC=34;AF=0.0373;AN=912;BL=886;BR=1938;BVAR;BaseQRankSum=3.744;DP=4276;Dels=0.00;EL=18;EPP=3.2658;ER=16;FR;FS=0.639;HETAR=17;HOMA=9;HOMR=737;HP=9;HR=8;HRun=8;HU=G;INS;InbreedingCoeff=0.2149;LEN=1;LRB=0.37252;LRBP=853.99;MQ0=0;MQ0Fraction=0.0000;MQM=49.706;MQRankSum=-0.051;NF;NR;NS=763;PP;RA=1822;RL=9;RPP=19.36;RR=25;RUN=1;ReadPosRankSum=-2.111;SAB=0.55882;SAF=19;SAP=4.0322;SAR=15;SC=TCGGGGGGCGTGGGGGGGGTG;SRB=0.51098;SRF=931;SRP=4.9172;SRR=891;TC;TR=8;TU=G;VQSLOD=5.7772;set=Intersection;sumGLbyD=7.95
+20	57419740	rs11481507	A	AT	82613.57	PASS	AA=3850;AB=0.41404;ABA=1786;ABP=198.63;ABR=1262;AC=919;AF=0.75328;AN=1220;BL=140665;BR=151383;BVAR;BaseQRankSum=-27.490;DB;DP=31794;DP4=588,585,1571,1721;Dels=0.00;EL=1924;EPP=3.0126;ER=1926;FQ=999;FR;FS=2.191;HETAR=482;HOMA=454;HOMR=135;HP=3;HPLen=3;HR=3;HRun=3;HU=T;INDEL;INS;InbreedingCoeff=0.0861;LEN=1;LRB=0.036699;LRBP=857.15;MQ=123.92;MQ0=0;MQ0Fraction=0.0000;MQM=91.654;MQRankSum=3.016;NF;NR;NS=1071;PP;PV4=0.16,1,0.12,1;RA=1850;RL=1874;RPP=8.8784;RR=1976;RUN=1;ReadPosRankSum=-0.685;SAB=0.47636;SAF=1834;SAP=21.693;SAR=2016;SC=TACACTAGTGATTTAACCCTA;SRB=0.49027;SRF=907;SRP=4.5315;SRR=943;TC;TR=3;TU=T;VQSLOD=9.2768;dbSNP=126;set=Intersection;sumGLbyD=22.78
+20	57529209	.	TA	AA,T	1285.20	PASS	AA=52;AB=0.89572;ABA=39;ABP=511.72;ABR=335;AC=0;AF=0.0000;AN=694;BL=1317;BR=3667;BVAR;BaseQRankSum=1.788;DEL;DP=8008;Dels=0.00;EL=30;EPP=5.6829;ER=22;FR;HETAR=151;HOMA=83;HOMR=752;HP=7;HR=7;HU=A;InbreedingCoeff=0.1368;LEN=1;LRB=0.47151;LRBP=2409.1;MQ0=0;MQ0Fraction=0.0000;MQM=58.288;MQRankSum=-0.490;NF;NR;NS=987;PP;QD=2.29;RA=2909;RL=4;RPP=83.856;RR=48;RUN=1;ReadPosRankSum=0.513;SAB=0.46154;SAF=24;SAP=3.6784;SAR=28;SB=-361.38;SC=CATAATTTTTTAAAAAAATAG;SRB=0.46855;SRF=1363;SRP=28.009;SRR=1546;TC;TR=7;TU=A;set=filterInVQSR-2of5;sumGLbyD=5.59
+20	57558194	.	CT	C,CTT,CTTT	6470.30	PASS	ABR=451;AC=104,161,177;AF=0.08919,0.13808,0.15180;BVAR;BaseQRankSum=1.172;DP=7985;FR;FS=2.202;HOMA=19;HOMR=778;HP=22;HR=15;HU=T;HaplotypeScore=16.1921;INS;InbreedingCoeff=0.6440;MQ=69.24;MQ0=27;MQ0Fraction=0.0109;MQRankSum=-0.003;NF;NR;NS=943;PP;QD=2.22;RA=2531;RUN=1;ReadPosRankSum=-0.104;SB=-2096.85;SC=GCCTTTTTTTCTTTTTTTTTT;SRB=0.34848;SRF=882;SRP=507.73;SRR=1649;TC;TR=15;TU=T;VQSLOD=6.5151;set=Intersection
+20	57693627	.	AG	A	1991.90	PASS	AA=52;AB=0.49462;ABA=47;ABP=3.0336;ABR=46;AC=15;AF=0.01227;AN=1222;BL=1902;BR=1478;BVAR;BaseQRankSum=-6.121;DEL;DP=26459;DP4=2647,2873,16,20;Dels=0.01;EL=25;EPP=3.1773;ER=27;FR;FS=3.135;HETAR=15;HOMA=1;HOMR=1064;HP=2;HPLen=3;HR=3;HRun=2;HU=A;INDEL;InbreedingCoeff=0.0866;LEN=1;LRB=0.12544;LRBP=118.51;MQ=116.26;MQ0=0;MQ0Fraction=0.0000;MQM=114.65;MQRankSum=1.942;NF;NR;NS=1080;PP;PV4=0.74,6.9e-08,1,0.38;RA=6781;RL=33;RPP=11.195;RR=19;RUN=1;ReadPosRankSum=-1.795;SAB=0.5;SAF=26;SAP=3.0103;SAR=26;SC=ATTGGAGGAAAGGCTTTTTCA;SRB=0.46247;SRF=3136;SRP=85.976;SRR=3645;TC;TR=3;TU=A;VQSLOD=8.6672;set=Intersection;sumGLbyD=13.55
+20	57716287	.	A	AT	66.47	PASS	AC=6;AF=0.00506;AN=1186;BaseQRankSum=1.369;DP=2744;FS=3.834;HRun=8;HaplotypeScore=11.2046;InbreedingCoeff=0.1196;MQ=73.00;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-0.086;QD=2.14;ReadPosRankSum=-2.588;SB=-53.80;VQSLOD=4.2080;set=VQSR
+20	58121928	rs73625057	T	TGG	6649.17	PASS	AA=132;AB=0.57854;ABA=110;ABP=16.996;ABR=151;AC=57;AF=0.0617;AN=924;BL=4530;BR=4790;BVAR;BaseQRankSum=-13.456;DB;DP=30353;DP4=2107,2168,61,66;Dels=0.00;EL=67;EPP=3.0761;ER=65;FR;FS=0.708;HETAR=46;HOMA=8;HOMR=1023;HP=3;HPLen=2;HR=2;HRun=2;HU=G;INDEL;INS;InbreedingCoeff=0.1241;LEN=2;LRB=0.027897;LRBP=18.76;MQ=109.61;MQ0=1;MQ0Fraction=0.0004;MQM=79.833;MQRankSum=-0.699;NF;NR;NS=1077;PP;PV4=0.79,1,0.49,0.036;RA=5754;RL=61;RPP=4.6554;RR=71;RUN=1;ReadPosRankSum=-3.309;SAB=0.45455;SAF=60;SAP=5.3792;SAR=72;SC=GATTAGAATGTGGATATCTTT;SRB=0.48836;SRF=2810;SRP=9.7866;SRR=2944;TC;TR=4;TU=GT;VQSLOD=8.5770;set=Intersection;sumGLbyD=27.19
+20	58287008	.	T	TC	23.57	PASS	AC=1;AF=0.0015;AN=678;BaseQRankSum=1.500;DP=1783;FS=0.000;HRun=1;HaplotypeScore=13.0585;InbreedingCoeff=0.0243;MQ=98.37;MQ0=0;MQ0Fraction=0.0000;MQRankSum=1.259;QD=5.43;ReadPosRankSum=1.115;SB=-40.33;VQSLOD=4.9523;set=VQSR
+20	58418087	.	TAC	T	1908.26	PASS	AA=64;AB=0.58667;ABA=62;ABP=12.796;ABR=88;AC=24;AF=0.0337;AN=712;BL=2841;BR=2706;BVAR;BaseQRankSum=12.276;DEL;DP=21427;DP4=2243,2398,22,31;Dels=0.03;EL=29;EPP=4.2318;ER=35;FQ=999;FR;FS=0.961;HETAR=21;HOMA=1;HOMR=1050;HP=2;HPLen=1;HR=1;HRun=0;HU=A;INDEL;InbreedingCoeff=0.0008;LEN=2;LRB=0.024337;LRBP=10.145;MQ=93.02;MQ0=0;MQ0Fraction=0.0000;MQM=51.109;MQRankSum=-3.746;NF;NR;NS=1072;PP;PV4=0.34,1.8e-11,2.3e-08,1;RA=6247;RL=37;RPP=6.4032;RR=27;RUN=1;ReadPosRankSum=0.418;SAB=0.4375;SAF=28;SAP=5.1818;SAR=36;SC=AGCCATAGGATACACAAAATC;SRB=0.47911;SRF=2993;SRP=26.689;SRR=3254;TC;TR=5;TU=AC;VQSLOD=10.5463;set=Intersection;sumGLbyD=12.25
+20	58468826	.	ACAAG	A	999	PASS	AF=0.0014;AF1=0.003429;BaseQRankSum=4.082;CI95=0.003106,0.006211;DP=8461;DP4=2500,1817,8,2;Dels=0.01;FQ=999;FR;FS=5.034;HP=2;HPLen=1;HR=1;HRun=0;HU=C;INDEL;InbreedingCoeff=-0.0183;MQ=120.69;MQ0=0;MQ0Fraction=0.0000;MQRankSum=0.141;NF;NR;PP;PV4=0.21,1,0.054,1;ReadPosRankSum=2.096;SC=ATCCTGAAACACAAGAAGAAA;TC;TR=5;TU=AC;VQSLOD=7.4928;set=Intersection;sumGLbyD=29.17
+20	58731262	.	TC	T	999	PASS	AA=21;AB=0.48649;ABA=19;ABP=3.069;ABR=18;AC=7;AF=0.0101;AF1=0.01493;AN=694;BL=939;BR=848;BVAR;BaseQRankSum=4.205;CI95=0.01106,0.02212;DEL;DP=12598;DP4=1766,1428,11,15;Dels=0.01;EL=13;EPP=5.5954;ER=8;FQ=999;FR;FS=1.796;HETAR=8;HOMA=1;HOMR=1031;HP=7;HPLen=8;HR=8;HRun=2;HU=T;INDEL;InbreedingCoeff=-0.0030;LEN=1;LRB=0.050923;LRBP=13.073;MQ=124.57;MQ0=0;MQ0Fraction=0.0000;MQM=67.905;MQRankSum=1.103;NF;NR;NS=1040;PP;PV4=0.23,1,1,1;RA=4884;RL=10;RPP=3.1137;RR=11;RUN=1;ReadPosRankSum=-0.091;SAB=0.47619;SAF=10;SAP=3.1137;SAR=11;SC=TCATTTTTTTTCCTTGAAACT;SRB=0.58006;SRF=2833;SRP=274.9;SRR=2051;TC;TR=8;TU=T;VQSLOD=10.8783;set=Intersection;sumGLbyD=15.11
+20	59181229	rs11476579	CTT	C,CT,CTTT,CTTTT	7787.17	PASS	AC=19,195,104,91;AF=0.01599,0.16414,0.08754,0.07660;AF1=0.2124;AN=1188;BVAR;BaseQRankSum=6.347;CI95=0.146,0.2743;DB;DEL;DP=26140;DP4=932,880,352,375;Dels=0.13;FQ=85.6;FR;FS=11.914;HP=14;HR=14;HRun=14;HU=T;INDEL;INS;InbreedingCoeff=0.4183;MQ=86.88;MQ0=0;MQ0Fraction=0.0000;MQRankSum=1.469;NF;NR;PP;PV4=0.17,1,1,1;RUN=1;ReadPosRankSum=-1.055;SC=GGTGAGAAAGCTTTTTTTTTT;TC;TR=14;TU=T;VQSLOD=7.4340;dbSNP=120;set=Intersection;sumGLbyD=7.02
+20	59213979	rs112141381	G	GC	9068	PASS	AA=131;AB=0.47115;ABA=110;ABP=4.5136;ABR=98;AF=0.0586;AN=700;BL=5395;BR=5816;BVAR;BaseQRankSum=15.453;DB;DP=23381;DP4=2191,2184,71,49;Dels=0.00;EL=66;EPP=3.0269;ER=65;FR;FS=7.907;HETAR=35;HOMA=5;HOMR=1019;HP=2;HPLen=3;HR=3;HRun=0;HU=G;INDEL;INS;InbreedingCoeff=0.0283;LEN=1;LRB=0.037552;LRBP=37.34;MQ=72.13;MQ0=0;MQ0Fraction=0.0000;MQM=54.496;MQRankSum=0.897;NF;NR;NS=1059;PP;PV4=0.052,1,0.066,1;RA=4976;RL=59;RPP=5.8117;RR=72;RUN=1;ReadPosRankSum=-0.811;SAB=0.58015;SAF=76;SAP=10.32;SAR=55;SC=GATGGACTGGGACAGTGACTC;SRB=0.49457;SRF=2461;SRP=4.2828;SRR=2515;TC;TR=3;TU=G;VQSLOD=9.3917;set=Intersection;sumGLbyD=28.58
+20	59252945	.	CT	C,CTT	557.18	PASS	AA=24;AB=0.84868;ABA=23;ABP=163.53;ABR=129;AC=21,29;AF=0.01759,0.02429;BL=1217;BR=1336;BVAR;BaseQRankSum=5.135;DP=9970;Dels=0.01;EL=13;EPP=3.3722;ER=11;FS=2.302;HETAR=21;HOMA=1;HOMR=1012;HRun=9;INS;InbreedingCoeff=0.1549;LEN=1;LRB=0.046612;LRBP=15.055;MQ0=0;MQ0Fraction=0.0000;MQM=67.208;MQRankSum=0.086;NS=1034;RA=4421;RL=11;RPP=3.3722;RR=13;RUN=1;ReadPosRankSum=-1.826;SAB=0.41667;SAF=10;SAP=4.4579;SAR=14;SRB=0.49649;SRF=2195;SRP=3.4823;SRR=2226;VQSLOD=2.8923;set=filterInVQSR-2of5;sumGLbyD=5.47
+20	60016966	.	CT	C	42650	PASS	AA=37;AB=0.97834;ABA=31;ABP=2847;ABR=1400;AC=15;AF=0.0163;AN=920;BL=2596;BR=778;BVAR;BaseQRankSum=-0.632;DEL;DP=10967;Dels=0.00;EL=14;EPP=7.7641;ER=23;FS=4.094;HETAR=421;HOMA=256;HOMR=385;HRun=1;InbreedingCoeff=-0.0051;LEN=1;LRB=0.53883;LRBP=2130.2;MQ0=0;MQ0Fraction=0.0000;MQM=120.3;MQRankSum=-0.911;NS=1072;RA=3413;RL=31;RPP=39.691;RR=6;RUN=1;ReadPosRankSum=-12.062;SAB=0.48649;SAF=18;SAP=3.069;SAR=19;SRB=0.47407;SRF=1618;SRP=22.943;SRR=1795;VQSLOD=3.3758;set=filterInVQSR-2of5;sumGLbyD=3.27
+20	60188651	.	AG	A	17624.52	PASS	AA=462;AB=0.76548;ABA=409;ABP=1070.7;ABR=1335;AC=403;AF=0.34444;AN=1170;BL=13877;BR=25909;BVAR;BaseQRankSum=6.180;DEL;DP=9900;Dels=0.08;EL=353;EPP=282.84;ER=109;FR;FS=2699.057;HETAR=346;HOMA=26;HOMR=633;HP=3;HR=4;HRun=1;HU=A;InbreedingCoeff=-0.2900;LEN=1;LRB=0.30242;LRBP=7904.3;MQ0Fraction=0.0004;MQM=56.119;MQRankSum=1.644;NF;NR;NS=1005;PP;RA=3521;RL=112;RPP=269.25;RR=350;RUN=1;ReadPosRankSum=2.490;SAB=0.0064935;SAF=3;SAP=980.34;SAR=459;SC=AGGCTTCAAAAGAAAAAAAAA;SRB=0.55978;SRF=1971;SRP=112.32;SRR=1550;TC;TR=4;TU=A;VQSLOD=-34.0667;set=filterInVQSR-2of5;sumGLbyD=7.81
+20	60195570	.	GTACATACATACA	ATACATACATACA,G,GTACATACA	20140	PASS	ABR=102;AC=105,2;AF=0.08794,0.00168;AN=1194;BVAR;BaseQRankSum=-28.899;DB;DEL;DP=14347;Dels=0.02;FR;FS=52.125;HOMA=1;HOMR=1006;HP=1;HPLen=1;HR=1;HRun=0;HU=T;InbreedingCoeff=0.0695;MQ0Fraction=0.0007;MQRankSum=1.957;NF;NR;NS=1035;PP;RA=4759;RUN=1;ReadPosRankSum=-22.252;SAB=0.5;SAP=3.0103;SC=TGATAGATTCGTACATACATA;SRB=0.47615;SRF=2266;SRP=26.522;SRR=2493;TC;TR=21;TU=ACAT;VQSLOD=2.7673;set=filterInVQSR-2of5;sumGLbyD=19.14
+20	60670601	rs72127450	AT	A,ATT	6401.59	PASS	AC=177,79;AF=0.16239,0.07248;AF1=0.1602;AN=1090;BVAR;BaseQRankSum=8.618;CI95=0.1106,0.2058;DB;DEL;DP=17508;DP4=1285,1094,313,259;Dels=0.10;FQ=94.1;FR;FS=0.000;HP=12;HR=12;HRun=12;HU=T;INDEL;INS;InbreedingCoeff=0.1076;LEN=1;MQ=64.73;MQ0=0;MQ0Fraction=0.0000;MQRankSum=0.620;NF;NR;PP;PV4=0.78,1,0.012,1;RUN=1;ReadPosRankSum=-1.294;SC=AGCCAGGCACATTTTTTTTTT;TC;TR=12;TU=T;VQSLOD=6.1650;dbSNP=130;set=Intersection;sumGLbyD=5.80
+20	60685780	.	TC	T	1123.58	PASS	AC=79;AF=0.07655;AN=1032;BaseQRankSum=14.949;DP=2084;FS=23.521;HRun=1;HaplotypeScore=19.7117;InbreedingCoeff=0.1356;MQ=53.57;MQ0=61;MQ0Fraction=0.0293;MQRankSum=-7.958;QD=4.35;ReadPosRankSum=-13.757;SB=-791.28;VQSLOD=6.3549;set=VQSR
+20	60744906	rs113528167	CG	C	422.53	PASS	AC=48;AF=0.0732;AN=656;BaseQRankSum=17.669;DB;DP=1189;FS=0.356;HRun=1;HaplotypeScore=15.1808;InbreedingCoeff=0.2111;MQ=82.83;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-10.455;QD=2.71;ReadPosRankSum=-16.887;SB=-326.46;VQSLOD=7.1707;set=VQSR
+20	60848742	.	CGT	C,CGTGT	999	PASS	AF=0.00980,0.01225;BaseQRankSum=5.597;DP=17065;DP4=1928,2188,17,13;Dels=0.01;FR;HP=1;HPLen=2;HR=2;HRun=0;HU=C;INDEL;InbreedingCoeff=0.2094;MQ=115.78;MQ0=0;MQ0Fraction=0.0000;MQRankSum=0.281;NF;NR;PP;PV4=0.36,0.4,0.12,0.12;ReadPosRankSum=-1.465;SB=-157.35;SC=TAGACGCTTCCGTGTGTGTGT;TC;TR=11;TU=GT;VQSLOD=1.7100;set=filterInVQSR-2of5;sumGLbyD=16.39
+20	61023668	rs57452309	G	GAGC	6896.67	PASS	AC=115;AF=0.1445;AN=796;BaseQRankSum=12.146;DB;DP=1423;FS=5.070;HRun=0;HaplotypeScore=29.8897;InbreedingCoeff=0.0740;MQ=77.02;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-9.005;QD=19.16;ReadPosRankSum=-17.440;SB=-3045.82;VQSLOD=4.5788;set=VQSR
+20	61180519	.	C	CA,CT	1774.30	PASS	ABR=135;AC=27,15;AF=0.02538,0.01410;BVAR;BaseQRankSum=-2.189;DP=8393;FR;FS=27.692;HOMA=2;HOMR=825;HP=6;HPLen=3;HR=3;HU=T;HaplotypeScore=19.5313;INS;InbreedingCoeff=0.0868;LEN=1;MQ=56.11;MQ0=172;MQ0Fraction=0.0667;MQRankSum=2.605;NF;NR;NS=854;PP;QD=1.99;RA=2868;RUN=1;ReadPosRankSum=-7.324;SB=-385.54;SC=TTCTTTCTTTCTTTCTTTCTT;SRB=0.32741;SRF=939;SRP=745.08;SRR=1929;TC;TR=69;TU=CTTT;VQSLOD=3.4398;set=filterInVQSR-2of5
+20	61184281	.	AC	A	9798.10	PASS	AA=24;AB=0.96507;ABA=16;ABP=863.43;ABR=442;AC=4;AF=0.00341;AN=1174;BL=349;BR=1039;BVAR;BaseQRankSum=2.048;DEL;DP=10073;Dels=0.00;EL=11;EPP=3.3722;ER=13;FS=2.097;HETAR=141;HOMA=69;HOMR=829;HRun=1;InbreedingCoeff=0.0697;LEN=1;LRB=0.49712;LRBP=747.85;MQ0=0;MQ0Fraction=0.0000;MQM=98.042;MQRankSum=1.881;NS=1042;RA=3625;RL=5;RPP=20.744;RR=19;RUN=1;ReadPosRankSum=-8.009;SAB=0.75;SAF=18;SAP=16.039;SAR=6;SRB=0.52662;SRF=1909;SRP=25.323;SRR=1716;VQSLOD=1.8117;set=filterInVQSR-2of5;sumGLbyD=5.55
+20	62067246	.	T	TCGA	60869.60	PASS	AC=1024;AF=0.88889;AN=1152;BaseQRankSum=17.328;DP=2144;FS=2.378;HRun=0;HaplotypeScore=22.0069;InbreedingCoeff=0.1400;MQ=86.75;MQ0=6;MQ0Fraction=0.0028;MQRankSum=-5.536;QD=29.45;ReadPosRankSum=1.266;SB=-24220.18;VQSLOD=6.4647;set=VQSR
+20	62074219	.	C	CTAT,CTGT	2328	PASS	ABR=99;AC=20,6;AF=0.01754,0.00526;BVAR;BaseQRankSum=11.221;DP=9498;DS;FS=4.510;HOMA=15;HOMR=645;HaplotypeScore=82.8868;INS;InbreedingCoeff=0.0880;LEN=3;MQ=29.88;MQ0=1378;MQ0Fraction=0.2286;MQRankSum=-5.309;NS=689;QD=0.77;RA=1679;RUN=1;ReadPosRankSum=-3.510;SAR=1;SB=-93.21;SRB=0.70697;SRF=1187;SRP=627.71;SRR=492;VQSLOD=1.8325;set=filterInVQSR-2of5
+20	62304449	.	CA	C,CAA	6680.17	PASS	AC=141,69;AF=0.12567,0.06150;AF1=0.08178;AN=1122;BVAR;BaseQRankSum=9.754;CI95=0.05088,0.1128;DEL;DP=15867;DP4=1252,1289,232,208;Dels=0.10;FQ=52.6;FR;FS=6.576;HP=11;HR=11;HRun=11;HU=A;INDEL;INS;InbreedingCoeff=0.1950;LEN=1;MQ=60.48;MQ0Fraction=0.0004;MQRankSum=-0.049;NF;NR;PP;PV4=0.2,1,1,1;RUN=1;ReadPosRankSum=-2.137;SC=GATTCTGTGTCAAAAAAAAAA;TC;TR=11;TU=A;VQSLOD=7.4714;set=Intersection;sumGLbyD=8.36
+20	62804895	rs57769591	CCTT	C	1148	PASS	AC=8;AF=0.0085;AF1=0.002839;AN=938;BaseQRankSum=4.952;CI95=0.002212,0.006637;DB;DP=8889;DP4=2574,1668,4,8;FQ=12.3;FS=2.289;HPLen=3;HRun=0;HaplotypeScore=29.4184;INDEL;InbreedingCoeff=-0.0270;MQ0=876;MQ0Fraction=0.2674;MQRankSum=-0.641;PV4=0.074,1,1,1;QD=1.03;ReadPosRankSum=0.118;SB=-65.30;VQSLOD=6.4881;dbSNP=126;set=Intersection
+20	62907688	.	AAT	A	6629.57	PASS	AC=164;AF=0.13735;AN=1194;BaseQRankSum=27.368;DP=2746;FS=5.985;HRun=0;HaplotypeScore=14.7748;InbreedingCoeff=0.1433;MQ=96.65;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-3.318;QD=10.81;ReadPosRankSum=0.789;SB=-2662.16;VQSLOD=6.1473;set=VQSR
+20	62952465	.	G	GT	9149.70	PASS	AA=156;AB=0.66667;ABA=110;ABP=82.631;ABR=220;AC=8;AF=0.00768;AN=1042;BL=6618;BR=3296;BVAR;BaseQRankSum=-0.466;DP=6244;Dels=0.00;EL=70;EPP=6.5737;ER=86;FS=2.927;HETAR=88;HOMA=34;HOMR=664;HRun=0;INS;InbreedingCoeff=0.0711;LEN=1;LRB=0.33508;LRBP=2420.2;MQ0Fraction=0.0431;MQM=29.506;MQRankSum=-3.251;NS=786;RA=1722;RL=146;RPP=260.47;RR=10;RUN=1;ReadPosRankSum=-2.554;SAB=0.47436;SAF=74;SAP=3.9012;SAR=82;SRB=0.50523;SRF=870;SRP=3.4189;SRR=852;VQSLOD=6.1217;set=Intersection;sumGLbyD=16.58
diff --git a/tests/tabix_data/vcf/18.vcf b/tests/tabix_data/vcf/18.vcf
new file mode 100644
index 0000000..e0d112c
--- /dev/null
+++ b/tests/tabix_data/vcf/18.vcf
@@ -0,0 +1,1000 @@
+##fileformat=VCFv4.0
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	DNA_pool_A
+chr1	1281168	.	A	G	14	.	DP=37;AF1=0.6243;CI95=0.5,1;DP4=4,0,6,0;MQ=15;PV4=1,0.027,1,1	PL:GT:GQ	43,0,4:0/1:6
+chr1	1281205	.	T	C	26	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=41	PL:GT:GQ	58,9,0:1/1:63
+chr1	1281206	.	G	C	25	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=41	PL:GT:GQ	57,9,0:1/1:63
+chr1	1922737	.	G	C	13.2	.	DP=21;AF1=1;CI95=1,1;DP4=0,0,0,21;MQ=22	PL:GT:GQ	46,63,0:1/1:99
+chr1	21197513	.	A	G	55.1	.	DP=9;AF1=1;CI95=1,1;DP4=0,0,0,7;MQ=41	PL:GT:GQ	88,21,0:1/1:84
+chr1	21343209	.	T	C	5.45	.	DP=17;AF1=1;CI95=1,1;DP4=0,0,17,0;MQ=14	PL:GT:GQ	37,51,0:1/1:99
+chr1	22097362	.	T	C	4.75	.	DP=10;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=30	PL:GT:GQ	35,9,0:1/1:63
+chr1	22254012	.	A	G	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=50	PL:GT:GQ	40,6,0:1/1:49
+chr1	22650927	.	G	A	48.1	.	DP=11;AF1=1;CI95=1,1;DP4=0,0,0,7;MQ=24	PL:GT:GQ	81,21,0:1/1:84
+chr1	23535401	.	C	T	40.4	.	DP=25;AF1=1;CI95=0.5,1;DP4=0,16,0,5;MQ=19;PV4=1,0.2,1,1	PL:GT:GQ	73,13,0:1/1:65
+chr1	23543855	.	T	C	49.1	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=44	PL:GT:GQ	82,18,0:1/1:90
+chr1	24245107	.	C	G	32	.	DP=4;AF1=0.5001;CI95=0.5,0.5;DP4=0,2,0,2;MQ=36;PV4=1,1,1,1	PL:GT:GQ	62,0,35:0/1:38
+chr1	24274412	.	G	C	39.5	.	DP=7;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=32	PL:GT:GQ	72,12,0:1/1:72
+chr1	36529832	.	C	T	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=46	PL:GT:GQ	73,6,0:1/1:49
+chr1	37788090	.	A	G	89.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=49	PL:GT:GQ	122,12,0:1/1:72
+chr1	43120440	.	C	T	34	.	DP=3;AF1=0.5002;CI95=0.5,0.5;DP4=0,1,0,2;MQ=49;PV4=1,1,1,1	PL:GT:GQ	64,0,31:0/1:34
+chr1	43980466	.	C	T	43	.	DP=16;AF1=1;CI95=1,1;DP4=0,0,0,15;MQ=19	PL:GT:GQ	76,45,0:1/1:99
+chr1	46047795	.	T	C	29.1	.	DP=7;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=31	PL:GT:GQ	62,18,0:1/1:90
+chr1	48860309	.	C	T	99	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=46	PL:GT:GQ	141,18,0:1/1:90
+chr1	49415599	.	T	C	4.61	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=34	PL:GT:GQ	34,6,0:1/1:49
+chr1	51601816	.	G	T	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=50	PL:GT:GQ	40,6,0:1/1:49
+chr1	51955459	.	G	C	89.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=49	PL:GT:GQ	122,12,0:1/1:72
+chr1	68479569	.	T	G	12	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48	PL:GT:GQ	43,6,0:1/1:49
+chr1	69032455	.	A	G	15.1	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=29	PL:GT:GQ	47,9,0:1/1:63
+chr1	71888225	.	G	T	9.31	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=43	PL:GT:GQ	40,6,0:1/1:49
+chr1	72381528	.	T	C	44	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=41	PL:GT:GQ	76,9,0:1/1:63
+chr1	82004013	.	A	G	37.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=50	PL:GT:GQ	70,12,0:1/1:72
+chr1	86289622	.	C	T	18	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=42	PL:GT:GQ	50,9,0:1/1:63
+chr1	90267663	.	A	G	22	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=45	PL:GT:GQ	54,9,0:1/1:63
+chr1	92699542	.	A	G	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=45	PL:GT:GQ	40,6,0:1/1:49
+chr1	94867317	.	G	A	26.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=45	PL:GT:GQ	58,6,0:1/1:49
+chr1	96428713	.	C	G	3.98	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=27	PL:GT:GQ	33,6,0:1/1:49
+chr1	100466329	.	G	C	4.85	.	DP=16;AF1=1;CI95=1,1;DP4=0,0,0,6;MQ=22	PL:GT:GQ	36,18,0:1/1:90
+chr1	101909281	.	G	A	70	.	DP=11;AF1=0.5;CI95=0.5,0.5;DP4=4,0,5,0;MQ=46;PV4=1,1,0.096,1	PL:GT:GQ	100,0,88:0/1:91
+chr1	106216572	.	T	A	22	.	DP=18;AF1=1;CI95=1,1;DP4=0,0,16,0;MQ=21	PL:GT:GQ	55,48,0:1/1:99
+chr1	107901770	.	T	C	9.31	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35	PL:GT:GQ	40,6,0:1/1:49
+chr1	108431179	.	A	G	99	.	DP=8;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=41	PL:GT:GQ	155,24,0:1/1:96
+chr1	112005344	.	C	T	99	.	DP=52;AF1=1;CI95=1,1;DP4=7,0,27,0;MQ=44;PV4=1,1,1,1	PL:GT:GQ	196,25,0:1/1:99
+chr1	116625452	.	C	T	36	.	DP=44;AF1=0.5;CI95=0.5,0.5;DP4=0,23,0,20;MQ=49;PV4=1,2.3e-69,0.42,1	PL:GT:GQ	66,0,179:0/1:69
+chr1	118060710	.	G	T	6.98	.	DP=8;AF1=0.4999;CI95=0.5,0.5;DP4=4,0,3,0;MQ=47;PV4=1,0.0071,1,1	PL:GT:GQ	36,0,73:0/1:39
+chr1	118198177	.	A	G	15.9	.	DP=23;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=43	PL:GT:GQ	47,6,0:1/1:49
+chr1	118586346	.	T	C	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49	PL:GT:GQ	40,6,0:1/1:49
+chr1	120809555	.	G	A	20	.	DP=8;AF1=0.5;CI95=0.5,0.5;DP4=6,0,2,0;MQ=46;PV4=1,1,1,1	PL:GT:GQ	50,0,106:0/1:53
+chr1	130723110	.	C	A	20.7	.	DP=8;AF1=0.5939;CI95=0.5,1;DP4=0,6,0,2;MQ=26;PV4=1,1,1,1	PL:GT:GQ	50,0,5:0/1:7
+chr1	133979895	.	T	C	14.9	.	DP=7;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=43	PL:GT:GQ	46,6,0:1/1:49
+chr1	134977940	.	C	T	30	.	DP=3;AF1=0.5002;CI95=0.5,0.5;DP4=0,1,0,2;MQ=38;PV4=1,1,0.26,1	PL:GT:GQ	60,0,31:0/1:34
+chr1	141768589	.	G	A	18.1	.	DP=15;AF1=0.5;CI95=0.5,0.5;DP4=4,0,4,0;MQ=51;PV4=1,2.7e-05,1,1	PL:GT:GQ	48,0,100:0/1:51
+chr1	141768590	.	G	A	22	.	DP=15;AF1=0.5;CI95=0.5,0.5;DP4=2,0,4,0;MQ=50;PV4=1,0.0033,1,1	PL:GT:GQ	52,0,40:0/1:43
+chr1	146506051	.	T	C	44	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=43	PL:GT:GQ	76,9,0:1/1:63
+chr1	150997009	.	G	A	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47	PL:GT:GQ	40,6,0:1/1:49
+chr1	162915612	.	G	C	13.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35	PL:GT:GQ	45,6,0:1/1:49
+chr1	168455400	.	A	G	4.12	.	DP=28;AF1=1;CI95=1,1;DP4=0,0,0,27;MQ=10	PL:GT:GQ	35,81,0:1/1:99
+chr1	172784744	.	T	C	17.8	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=48	PL:GT:GQ	49,6,0:1/1:49
+chr1	183627307	.	G	A	13.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35	PL:GT:GQ	45,6,0:1/1:49
+chr1	185789457	.	T	C	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=50	PL:GT:GQ	73,6,0:1/1:49
+chr1	187081827	.	T	C	4.77	.	DP=10;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=17	PL:GT:GQ	36,30,0:1/1:99
+chr1	188468339	.	C	T	33	.	DP=25;AF1=1;CI95=1,1;DP4=0,0,0,13;MQ=24	PL:GT:GQ	66,39,0:1/1:99
+chr1	188595435	.	C	T	41.8	.	DP=8;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49	PL:GT:GQ	73,6,0:1/1:49
+chr1	188670561	.	G	C	3.55	.	DP=22;AF1=1;CI95=1,1;DP4=0,0,0,9;MQ=18	PL:GT:GQ	34,27,0:1/1:99
+chr1	188924877	.	G	A	6.2	.	DP=10;AF1=0.9999;CI95=0.5,1;DP4=2,0,3,0;MQ=21;PV4=1,1,1,0.3	PL:GT:GQ	35,3,0:1/1:41
+chr1	190536295	.	G	A	68	.	DP=38;AF1=1;CI95=1,1;DP4=0,0,36,0;MQ=18	PL:GT:GQ	101,108,0:1/1:99
+chr1	191129408	.	T	A	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=48	PL:GT:GQ	40,6,0:1/1:49
+chr1	195937816	.	T	C	13	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35	PL:GT:GQ	44,6,0:1/1:49
+chr1	198857619	.	T	C	89	.	DP=61;AF1=0.5;CI95=0.5,0.5;DP4=0,38,0,17;MQ=30;PV4=1,0.032,1,1	PL:GT:GQ	119,0,139:0/1:99
+chr1	199057483	.	T	C	13	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=32	PL:GT:GQ	44,6,0:1/1:49
+chr1	200133619	.	G	C	5.83	.	DP=49;AF1=1;CI95=0.5,1;DP4=2,0,8,0;MQ=17;PV4=1,0.059,1,0.2	PL:GT:GQ	37,12,0:1/1:72
+chr1	200729661	.	A	T	36	.	DP=15;AF1=1;CI95=1,1;DP4=0,0,14,0;MQ=27	PL:GT:GQ	69,42,0:1/1:99
+chr1	201374519	.	T	C	69.5	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=39	PL:GT:GQ	102,12,0:1/1:72
+chr1	202811668	.	G	A	20.2	.	DP=4;AF1=0.5163;CI95=0.5,1;DP4=0,1,0,3;MQ=24;PV4=1,1,1,1	PL:GT:GQ	50,0,12:0/1:15
+chr1	202960650	.	C	T	16.6	.	DP=8;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=27	PL:GT:GQ	49,12,0:1/1:72
+chr1	205686638	.	C	T	11.3	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=42	PL:GT:GQ	43,9,0:1/1:63
+chr1	205949857	.	A	G	3.14	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=21	PL:GT:GQ	33,15,0:1/1:75
+chr1	209806643	.	A	G	13.2	.	DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=21	PL:GT:GQ	46,24,0:1/1:96
+chr1	209871501	.	C	T	25	.	DP=12;AF1=0.5;CI95=0.5,0.5;DP4=5,0,4,0;MQ=41;PV4=1,7.7e-06,1,1	PL:GT:GQ	55,0,84:0/1:58
+chr1	211051323	.	G	A	99	.	DP=14;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=49	PL:GT:GQ	176,24,0:1/1:96
+chr1	211389716	.	C	T	12	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=32	PL:GT:GQ	43,6,0:1/1:49
+chr1	211868415	.	G	A	3.54	.	DP=11;AF1=1;CI95=1,1;DP4=0,0,0,11;MQ=14	PL:GT:GQ	34,33,0:1/1:99
+chr1	211914531	.	C	T	84.5	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,1,0,4;MQ=46;PV4=1,1,1,1	PL:GT:GQ	116,7,0:1/1:57
+chr1	214691313	.	A	G	22	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=49	PL:GT:GQ	54,9,0:1/1:63
+chr1	215184650	.	C	T	40.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=46	PL:GT:GQ	72,6,0:1/1:49
+chr1	215995258	.	A	G	68	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=50	PL:GT:GQ	100,9,0:1/1:63
+chr1	217031394	.	G	C	13.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35	PL:GT:GQ	45,6,0:1/1:49
+chr1	217986960	.	T	C	44	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=36	PL:GT:GQ	76,9,0:1/1:63
+chr1	218086681	.	A	G	99	.	DP=10;AF1=1;CI95=1,1;DP4=0,0,0,9;MQ=34	PL:GT:GQ	142,27,0:1/1:99
+chr1	218546019	.	A	G	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=50	PL:GT:GQ	40,6,0:1/1:49
+chr1	218632417	.	G	T	17.1	.	DP=19;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=26	PL:GT:GQ	50,21,0:1/1:84
+chr1	218833355	.	C	G	23	.	DP=7;AF1=0.5;CI95=0.5,0.5;DP4=5,0,2,0;MQ=39;PV4=1,1,1,1	PL:GT:GQ	53,0,63:0/1:56
+chr1	219303186	.	T	C	7.79	.	DP=25;AF1=1;CI95=1,1;DP4=0,0,0,25;MQ=12	PL:GT:GQ	40,75,0:1/1:99
+chr1	219517634	.	G	A	26.5	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=42	PL:GT:GQ	59,12,0:1/1:72
+chr1	219590158	.	T	C	3.27	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=25	PL:GT:GQ	33,12,0:1/1:72
+chr1	219709853	.	A	T	99	.	DP=124;AF1=0.5;CI95=0.5,0.5;DP4=80,0,41,0;MQ=44;PV4=1,0.26,1,1	PL:GT:GQ	143,0,156:0/1:99
+chr1	222457988	.	A	G	11.1	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=23	PL:GT:GQ	42,6,0:1/1:49
+chr1	222477914	.	A	G	11.3	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=39	PL:GT:GQ	43,9,0:1/1:63
+chr1	223010233	.	A	G	18.6	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=25	PL:GT:GQ	51,12,0:1/1:72
+chr1	223796360	.	G	A	6.79	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=21	PL:GT:GQ	37,6,0:1/1:49
+chr1	224273784	.	A	T	14.2	.	DP=18;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=15	PL:GT:GQ	47,30,0:1/1:99
+chr1	224454685	.	C	T	46.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=32	PL:GT:GQ	79,15,0:1/1:75
+chr1	224514706	.	G	C	21	.	DP=38;AF1=1;CI95=1,1;DP4=0,0,38,0;MQ=19	PL:GT:GQ	54,114,0:1/1:99
+chr1	224515793	.	C	T	99	.	DP=26;AF1=1;CI95=1,1;DP4=0,0,26,0;MQ=45	PL:GT:GQ	211,78,0:1/1:99
+chr1	224692969	.	C	A	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=36	PL:GT:GQ	40,6,0:1/1:49
+chr1	225607249	.	A	G	34	.	DP=3;AF1=0.5002;CI95=0.5,0.5;DP4=1,0,2,0;MQ=45;PV4=1,1,0,1	PL:GT:GQ	64,0,31:0/1:34
+chr1	226923918	.	C	A	29.1	.	DP=52;AF1=1;CI95=0.5,1;DP4=0,2,0,10;MQ=27;PV4=1,1,1,1	PL:GT:GQ	62,18,0:1/1:90
+chr1	227125189	.	T	C	56.5	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=41	PL:GT:GQ	89,12,0:1/1:72
+chr1	227133712	.	A	T	20.1	.	DP=26;AF1=0.5;CI95=0.5,0.5;DP4=11,0,10,0;MQ=23;PV4=1,1,0.48,1	PL:GT:GQ	50,0,39:0/1:42
+chr1	227943954	.	G	C	47	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=37	PL:GT:GQ	79,9,0:1/1:63
+chr1	227943974	.	G	A	33.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=34	PL:GT:GQ	66,12,0:1/1:72
+chr1	228067480	.	A	G	42.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=45	PL:GT:GQ	75,15,0:1/1:75
+chr1	228067510	.	A	G	99	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=45	PL:GT:GQ	140,15,0:1/1:75
+chr1	228088778	.	C	T	6.79	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=23	PL:GT:GQ	37,6,0:1/1:49
+chr1	228117888	.	A	C	13.9	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=40	PL:GT:GQ	45,6,0:1/1:49
+chr1	228139641	.	T	C	44.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=35	PL:GT:GQ	77,12,0:1/1:72
+chr1	228577146	.	T	C	26	.	DP=41;AF1=0.5;CI95=0.5,0.5;DP4=0,25,0,14;MQ=22;PV4=1,1,1,0.027	PL:GT:GQ	56,0,77:0/1:59
+chr1	229001369	.	C	A	45	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=41	PL:GT:GQ	77,9,0:1/1:63
+chr1	229001386	.	C	T	8.44	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=42	PL:GT:GQ	39,6,0:1/1:49
+chr1	229348080	.	T	C	18.1	.	DP=3;AF1=0.5002;CI95=0.5,0.5;DP4=0,1,0,2;MQ=40;PV4=1,0.33,0.17,0.33	PL:GT:GQ	48,0,31:0/1:34
+chr1	229439710	.	C	T	33.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=32	PL:GT:GQ	66,12,0:1/1:72
+chr1	229655149	.	T	C	30	.	DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=30	PL:GT:GQ	63,24,0:1/1:96
+chr1	229660873	.	C	G	81	.	DP=28;AF1=0.5;CI95=0.5,0.5;DP4=0,20,0,7;MQ=36;PV4=1,1,1,1	PL:GT:GQ	111,0,120:0/1:99
+chr2a	3661005	.	C	G	24	.	DP=13;AF1=0.5001;CI95=0.5,0.5;DP4=7,0,4,0;MQ=27;PV4=1,1.1e-05,1,1	PL:GT:GQ	54,0,34:0/1:37
+chr2a	4140063	.	G	A	81	.	DP=26;AF1=0.6671;CI95=0.5,1;DP4=18,0,8,0;MQ=24;PV4=1,8.3e-09,1,1	PL:GT:GQ	110,0,3:0/1:5
+chr2a	4248440	.	T	C	20	.	DP=28;AF1=0.5;CI95=0.5,0.5;DP4=11,0,7,0;MQ=25;PV4=1,1,0.47,1	PL:GT:GQ	50,0,92:0/1:53
+chr2a	4707656	.	A	G	63	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=49	PL:GT:GQ	95,9,0:1/1:63
+chr2a	5194801	.	G	A	7.59	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=24	PL:GT:GQ	38,6,0:1/1:49
+chr2a	14111103	.	A	G	7.84	.	DP=7;AF1=1;CI95=1,1;DP4=0,0,0,7;MQ=20	PL:GT:GQ	40,21,0:1/1:84
+chr2a	17799746	.	A	G	11.3	.	DP=5;AF1=0.5001;CI95=0.5,0.5;DP4=0,3,0,2;MQ=32;PV4=1,1,1,1	PL:GT:GQ	41,0,35:0/1:37
+chr2a	24728910	.	G	A	45.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=28	PL:GT:GQ	78,15,0:1/1:75
+chr2a	29627939	.	G	T	5.44	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=27	PL:GT:GQ	36,9,0:1/1:63
+chr2a	31373164	.	C	T	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=44	PL:GT:GQ	73,6,0:1/1:49
+chr2a	33935228	.	T	C	41.8	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=51	PL:GT:GQ	73,6,0:1/1:49
+chr2a	36311856	.	G	A	99	.	DP=30;AF1=1;CI95=1,1;DP4=0,0,0,29;MQ=44	PL:GT:GQ	213,87,0:1/1:99
+chr2a	39281204	.	T	C	68	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=49	PL:GT:GQ	100,9,0:1/1:63
+chr2a	41087565	.	C	T	74.5	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=38	PL:GT:GQ	107,12,0:1/1:72
+chr2a	45574768	.	C	A	11.3	.	DP=8;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=18	PL:GT:GQ	43,9,0:1/1:63
+chr2a	55464464	.	T	C	26.1	.	DP=7;AF1=0.9966;CI95=0.5,1;DP4=5,0,2,0;MQ=26;PV4=1,1,1,1	PL:GT:GQ	55,1,0:1/1:23
+chr2a	63107673	.	T	A	70.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=34	PL:GT:GQ	103,12,0:1/1:72
+chr2a	63141732	.	A	T	22.8	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=42	PL:GT:GQ	54,6,0:1/1:49
+chr2a	63141910	.	G	A	3.41	.	DP=16;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=32	PL:GT:GQ	32,6,0:1/1:49
+chr2a	63141911	.	C	T	9.55	.	DP=16;AF1=0.5031;CI95=0.5,0.5;DP4=0,2,0,3;MQ=33;PV4=1,0.43,1,1	PL:GT:GQ	39,0,19:0/1:22
+chr2a	63143543	.	C	T	28	.	DP=18;AF1=1;CI95=1,1;DP4=0,1,0,17;MQ=16;PV4=1,1,1,1	PL:GT:GQ	61,42,0:1/1:99
+chr2a	66419805	.	G	A	3.69	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=23	PL:GT:GQ	34,15,0:1/1:75
+chr2a	66563922	.	C	T	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=51	PL:GT:GQ	40,6,0:1/1:49
+chr2a	67719136	.	C	T	39.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=50	PL:GT:GQ	71,6,0:1/1:49
+chr2a	72781453	.	A	C	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=50	PL:GT:GQ	73,6,0:1/1:49
+chr2a	76733211	.	G	A	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47	PL:GT:GQ	40,6,0:1/1:49
+chr2a	78190502	.	A	C	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47	PL:GT:GQ	40,6,0:1/1:49
+chr2a	85021209	.	A	G	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49	PL:GT:GQ	40,6,0:1/1:49
+chr2a	88554861	.	A	T	39	.	DP=74;AF1=0.5;CI95=0.5,0.5;DP4=0,7,0,4;MQ=46;PV4=1,1,1,1	PL:GT:GQ	69,0,92:0/1:72
+chr2a	88554877	.	A	G	92	.	DP=90;AF1=0.5;CI95=0.5,0.5;DP4=0,23,0,13;MQ=41;PV4=1,0.3,1,1	PL:GT:GQ	122,0,128:0/1:99
+chr2a	88824857	.	G	A	13.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=37	PL:GT:GQ	45,6,0:1/1:49
+chr2a	93546675	.	C	T	26	.	DP=6;AF1=0.5;CI95=0.5,0.5;DP4=4,0,2,0;MQ=46;PV4=1,1,1,1	PL:GT:GQ	56,0,87:0/1:59
+chr2a	94788853	.	A	G	34.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=43	PL:GT:GQ	67,15,0:1/1:75
+chr2a	96738146	.	T	C	11.3	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=40	PL:GT:GQ	43,9,0:1/1:63
+chr2a	102737384	.	A	G	12.3	.	DP=18;AF1=1;CI95=1,1;DP4=0,0,18,0;MQ=11	PL:GT:GQ	45,54,0:1/1:99
+chr2a	103407172	.	A	G	35	.	DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=19	PL:GT:GQ	68,24,0:1/1:96
+chr2a	105774580	.	T	G	99	.	DP=13;AF1=1;CI95=1,1;DP4=0,0,13,0;MQ=30	PL:GT:GQ	135,39,0:1/1:99
+chr2a	106376301	.	C	G	24.1	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=19	PL:GT:GQ	57,18,0:1/1:90
+chr2a	106376315	.	C	T	8.75	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=19	PL:GT:GQ	41,18,0:1/1:90
+chr2a	112422267	.	C	T	30	.	DP=20;AF1=0.5;CI95=0.5,0.5;DP4=14,0,5,0;MQ=39;PV4=1,1,1,1	PL:GT:GQ	60,0,131:0/1:63
+chr2b	3049384	.	A	C	14.9	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=42	PL:GT:GQ	46,6,0:1/1:49
+chr2b	3049385	.	G	C	14.9	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=42	PL:GT:GQ	46,6,0:1/1:49
+chr2b	3049406	.	C	G	99	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=36	PL:GT:GQ	135,18,0:1/1:90
+chr2b	4213802	.	T	C	89.5	.	DP=10;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=49	PL:GT:GQ	122,12,0:1/1:72
+chr2b	5022895	.	G	A	66	.	DP=10;AF1=1;CI95=1,1;DP4=0,0,0,10;MQ=49	PL:GT:GQ	99,30,0:1/1:99
+chr2b	6037666	.	G	T	56	.	DP=18;AF1=1;CI95=1,1;DP4=0,0,0,13;MQ=17	PL:GT:GQ	89,39,0:1/1:99
+chr2b	13656952	.	G	A	19.2	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=21	PL:GT:GQ	52,18,0:1/1:90
+chr2b	15026944	.	A	G	6.79	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=32	PL:GT:GQ	37,6,0:1/1:49
+chr2b	23362613	.	A	G	5.64	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=22	PL:GT:GQ	37,15,0:1/1:75
+chr2b	45947861	.	C	G	68	.	DP=11;AF1=1;CI95=1,1;DP4=0,0,0,11;MQ=50	PL:GT:GQ	101,33,0:1/1:99
+chr2b	46597824	.	T	C	65.6	.	DP=39;AF1=0.5939;CI95=0.5,1;DP4=23,0,10,0;MQ=22;PV4=1,0.014,1,1	PL:GT:GQ	95,0,5:0/1:7
+chr2b	49665191	.	G	T	34.1	.	DP=7;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=37	PL:GT:GQ	67,21,0:1/1:84
+chr2b	61001546	.	A	G	48	.	DP=9;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=26	PL:GT:GQ	81,24,0:1/1:96
+chr2b	88502851	.	T	C	4.77	.	DP=4;AF1=0.5;CI95=0.5,0.5;DP4=0,2,0,2;MQ=37;PV4=1,1,0.46,1	PL:GT:GQ	33,0,34:0/1:33
+chr2b	91675431	.	C	T	30	.	DP=14;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=27	PL:GT:GQ	63,24,0:1/1:96
+chr2b	91870148	.	T	G	67	.	DP=14;AF1=1;CI95=1,1;DP4=0,1,0,13;MQ=47;PV4=1,1,1,1	PL:GT:GQ	100,31,0:1/1:99
+chr2b	97066826	.	G	A	20.1	.	DP=9;AF1=0.5001;CI95=0.5,0.5;DP4=0,6,0,2;MQ=31;PV4=1,1,1,1	PL:GT:GQ	50,0,35:0/1:38
+chr2b	97670822	.	G	A	4.85	.	DP=6;AF1=1;CI95=1,1;DP4=0,0,0,6;MQ=18	PL:GT:GQ	36,18,0:1/1:90
+chr2b	102773175	.	A	G	17.1	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=38	PL:GT:GQ	49,9,0:1/1:63
+chr2b	109805532	.	T	C	99	.	DP=8;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=45	PL:GT:GQ	176,24,0:1/1:96
+chr2b	110841448	.	A	G	11.1	.	DP=20;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=44	PL:GT:GQ	42,6,0:1/1:49
+chr2b	123217025	.	T	C	31.5	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=37	PL:GT:GQ	64,12,0:1/1:72
+chr2b	123263214	.	A	G	11.3	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=35	PL:GT:GQ	43,9,0:1/1:63
+chr2b	127747292	.	C	T	68	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=52	PL:GT:GQ	100,9,0:1/1:63
+chr2b	130121958	.	A	G	89.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=43	PL:GT:GQ	122,15,0:1/1:75
+chr2b	130253633	.	A	G	14.9	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=42	PL:GT:GQ	46,6,0:1/1:49
+chr2b	130692761	.	C	T	49.1	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=51	PL:GT:GQ	82,18,0:1/1:90
+chr2b	130743365	.	A	G	99	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=42	PL:GT:GQ	140,15,0:1/1:75
+chr2b	131553874	.	A	C	11.3	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=37	PL:GT:GQ	43,9,0:1/1:63
+chr2b	131716894	.	A	G	99	.	DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=40	PL:GT:GQ	137,24,0:1/1:96
+chr2b	131716936	.	G	A	99	.	DP=14;AF1=1;CI95=1,1;DP4=0,0,0,12;MQ=36	PL:GT:GQ	173,36,0:1/1:99
+chr2b	131716952	.	A	G	99	.	DP=22;AF1=0.5;CI95=0.5,0.5;DP4=0,7,0,14;MQ=36;PV4=1,1,1,1	PL:GT:GQ	152,0,43:0/1:46
+chr2b	133360184	.	C	T	99	.	DP=20;AF1=1;CI95=1,1;DP4=0,0,0,20;MQ=32	PL:GT:GQ	163,60,0:1/1:99
+chr2b	133644741	.	T	A	16.4	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=27	PL:GT:GQ	49,15,0:1/1:75
+chr2b	133720595	.	T	C	41	.	DP=15;AF1=1;CI95=1,1;DP4=0,0,0,12;MQ=29	PL:GT:GQ	74,36,0:1/1:99
+chr2b	133727192	.	C	T	19.3	.	DP=8;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=23	PL:GT:GQ	52,15,0:1/1:75
+chr2b	133727260	.	G	A	3.56	.	DP=8;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=18	PL:GT:GQ	34,24,0:1/1:95
+chr2b	133800294	.	A	G	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=23	PL:GT:GQ	40,6,0:1/1:49
+chr2b	134582754	.	A	C	56.1	.	DP=37;AF1=1;CI95=1,1;DP4=0,0,0,7;MQ=36	PL:GT:GQ	89,21,0:1/1:84
+chr2b	134582763	.	G	C	78	.	DP=37;AF1=1;CI95=1,1;DP4=0,0,0,36;MQ=34	PL:GT:GQ	111,108,0:1/1:99
+chr2b	134809668	.	G	A	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49	PL:GT:GQ	40,6,0:1/1:49
+chr3	527814	.	C	G	46	.	DP=9;AF1=0.5;CI95=0.5,0.5;DP4=6,0,3,0;MQ=43;PV4=1,1,1,1	PL:GT:GQ	76,0,106:0/1:79
+chr3	559510	.	G	A	38	.	DP=27;AF1=0.5;CI95=0.5,0.5;DP4=10,0,17,0;MQ=28;PV4=1,1,0.014,1	PL:GT:GQ	68,0,111:0/1:71
+chr3	879433	.	T	G	32	.	DP=4;AF1=0.5001;CI95=0.5,0.5;DP4=2,0,2,0;MQ=43;PV4=1,1,1,1	PL:GT:GQ	62,0,34:0/1:37
+chr3	1809645	.	A	G	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=51	PL:GT:GQ	73,6,0:1/1:49
+chr3	3235812	.	C	T	7.59	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=45	PL:GT:GQ	38,6,0:1/1:49
+chr3	3250176	.	A	G	83	.	DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=32	PL:GT:GQ	116,24,0:1/1:96
+chr3	5049073	.	T	A	99	.	DP=25;AF1=0.5;CI95=0.5,0.5;DP4=16,0,9,0;MQ=39;PV4=1,1,1,1	PL:GT:GQ	136,0,129:0/1:99
+chr3	5142874	.	G	A	99	.	DP=38;AF1=1;CI95=1,1;DP4=0,0,38,0;MQ=28	PL:GT:GQ	179,114,0:1/1:99
+chr3	5554864	.	T	C	3.54	.	DP=7;AF1=0.4999;CI95=0.5,0.5;DP4=0,4,0,3;MQ=27;PV4=1,1,1,1	PL:GT:GQ	31,0,35:0/1:33
+chr3	5749648	.	G	A	21.2	.	DP=26;AF1=0.7303;CI95=0.5,1;DP4=0,7,0,7;MQ=26;PV4=1,0.16,1,0.17	PL:GT:GQ	50,0,2:0/1:3
+chr3	16451708	.	A	T	71.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=38	PL:GT:GQ	104,15,0:1/1:75
+chr3	23410276	.	G	A	99	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=45	PL:GT:GQ	140,15,0:1/1:75
+chr3	51368824	.	A	G	28	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=48	PL:GT:GQ	60,9,0:1/1:63
+chr3	53000453	.	A	G	54	.	DP=10;AF1=1;CI95=1,1;DP4=0,0,0,10;MQ=19	PL:GT:GQ	87,30,0:1/1:99
+chr3	53000463	.	A	G	54	.	DP=10;AF1=1;CI95=1,1;DP4=0,0,0,10;MQ=19	PL:GT:GQ	87,30,0:1/1:99
+chr3	59077423	.	C	T	77.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=33	PL:GT:GQ	110,15,0:1/1:75
+chr3	60040501	.	T	C	11.3	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=35	PL:GT:GQ	43,9,0:1/1:63
+chr3	64203481	.	A	G	33.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=49	PL:GT:GQ	66,12,0:1/1:72
+chr3	67947441	.	C	T	17.6	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=25	PL:GT:GQ	50,12,0:1/1:72
+chr3	76372631	.	A	G	44	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=36	PL:GT:GQ	76,9,0:1/1:63
+chr3	80611316	.	C	G	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49	PL:GT:GQ	40,6,0:1/1:49
+chr3	81554381	.	G	T	17.6	.	DP=24;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=26	PL:GT:GQ	50,12,0:1/1:72
+chr3	87614647	.	A	G	13.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=34	PL:GT:GQ	45,6,0:1/1:49
+chr3	93900455	.	A	T	11.6	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=13	PL:GT:GQ	44,15,0:1/1:75
+chr3	96174457	.	A	G	4.11	.	DP=8;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=24	PL:GT:GQ	34,9,0:1/1:63
+chr3	96215569	.	A	C	3.41	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=32	PL:GT:GQ	32,6,0:1/1:49
+chr3	96587998	.	A	C	7.08	.	DP=9;AF1=1;CI95=1,1;DP4=0,0,6,0;MQ=17	PL:GT:GQ	39,18,0:1/1:90
+chr3	99711220	.	A	C	12.8	.	DP=11;AF1=0.9998;CI95=0.5,1;DP4=1,0,2,0;MQ=35;PV4=1,1,1,1	PL:GT:GQ	42,2,0:1/1:37
+chr3	99789741	.	C	G	99	.	DP=18;AF1=1;CI95=1,1;DP4=0,0,17,0;MQ=47	PL:GT:GQ	210,51,0:1/1:99
+chr3	103667651	.	A	C	3.98	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=37	PL:GT:GQ	33,6,0:1/1:49
+chr3	104604896	.	G	C	55	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=50	PL:GT:GQ	87,9,0:1/1:63
+chr3	104997217	.	G	A	33.1	.	DP=18;AF1=1;CI95=1,1;DP4=1,0,16,0;MQ=34;PV4=1,3e-10,0.17,0.36	PL:GT:GQ	66,19,0:1/1:76
+chr3	106097816	.	A	G	28	.	DP=15;AF1=1;CI95=1,1;DP4=0,0,0,15;MQ=26	PL:GT:GQ	61,45,0:1/1:99
+chr3	106822259	.	G	C	99	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=50	PL:GT:GQ	140,15,0:1/1:75
+chr3	109946413	.	G	A	13	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=34	PL:GT:GQ	44,6,0:1/1:49
+chr3	121238963	.	T	C	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=51	PL:GT:GQ	40,6,0:1/1:49
+chr3	126248567	.	A	G	13.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=33	PL:GT:GQ	45,6,0:1/1:49
+chr3	129733836	.	A	G	6.2	.	DP=4;AF1=0.5003;CI95=0.5,0.5;DP4=1,0,3,0;MQ=43;PV4=1,0.02,0.31,1	PL:GT:GQ	35,0,28:0/1:30
+chr3	131372785	.	C	T	44	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=34	PL:GT:GQ	76,9,0:1/1:63
+chr3	132290987	.	C	T	22	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=45	PL:GT:GQ	54,9,0:1/1:63
+chr3	136054421	.	C	T	73	.	DP=82;AF1=1;CI95=1,1;DP4=0,0,78,0;MQ=28	PL:GT:GQ	106,235,0:1/1:99
+chr3	141075246	.	G	A	30.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=41	PL:GT:GQ	62,6,0:1/1:49
+chr3	141075262	.	T	G	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=41	PL:GT:GQ	73,6,0:1/1:49
+chr3	141430649	.	G	T	81.8	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,1,0,4;MQ=41;PV4=1,0.34,1,0.25	PL:GT:GQ	113,6,0:1/1:49
+chr3	143617747	.	G	T	22	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=29	PL:GT:GQ	54,9,0:1/1:63
+chr3	163576128	.	C	T	5.6	.	DP=4;AF1=0.7302;CI95=0.5,1;DP4=2,0,2,0;MQ=23;PV4=1,1,1,1	PL:GT:GQ	33,0,2:0/1:3
+chr3	163839828	.	A	G	4.45	.	DP=7;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=26	PL:GT:GQ	35,12,0:1/1:72
+chr3	175839340	.	G	T	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=51	PL:GT:GQ	40,6,0:1/1:49
+chr3	190193258	.	G	T	3.98	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35	PL:GT:GQ	33,6,0:1/1:49
+chr3	190777007	.	G	A	13	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35	PL:GT:GQ	44,6,0:1/1:49
+chr3	190970350	.	A	G	61	.	DP=11;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=37	PL:GT:GQ	94,30,0:1/1:99
+chr3	198686408	.	G	A	36.6	.	DP=17;AF1=1;CI95=0.5,1;DP4=0,1,0,16;MQ=25;PV4=1,1,0.026,1	PL:GT:GQ	69,11,0:1/1:66
+chr3	199277478	.	T	C	3.61	.	DP=6;AF1=1;CI95=1,1;DP4=0,0,0,6;MQ=21	PL:GT:GQ	34,18,0:1/1:90
+chr3	199780181	.	G	T	77	.	DP=45;AF1=0.5;CI95=0.5,0.5;DP4=0,35,0,10;MQ=33;PV4=1,1,1,1	PL:GT:GQ	107,0,114:0/1:99
+chr3	199889335	.	A	C	9.54	.	DP=16;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=18	PL:GT:GQ	42,24,0:1/1:96
+chr3	200018161	.	A	G	13.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=31	PL:GT:GQ	45,6,0:1/1:49
+chr4	195475	.	A	G	13	.	DP=13;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47	PL:GT:GQ	44,6,0:1/1:49
+chr4	639141	.	C	A	14.9	.	DP=10;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=42	PL:GT:GQ	46,6,0:1/1:49
+chr4	639152	.	C	T	15.2	.	DP=17;AF1=0.5016;CI95=0.5,0.5;DP4=0,2,0,2;MQ=33;PV4=1,1,1,1	PL:GT:GQ	45,0,22:0/1:25
+chr4	986497	.	G	T	99	.	DP=10;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=33	PL:GT:GQ	163,30,0:1/1:99
+chr4	986516	.	C	T	55.1	.	DP=8;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=37	PL:GT:GQ	88,21,0:1/1:84
+chr4	1207485	.	A	C	14.9	.	DP=22;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=45	PL:GT:GQ	46,6,0:1/1:49
+chr4	1323502	.	G	A	13.2	.	DP=13;AF1=1;CI95=1,1;DP4=0,0,11,0;MQ=22	PL:GT:GQ	46,33,0:1/1:99
+chr4	1613521	.	G	A	89	.	DP=16;AF1=1;CI95=1,1;DP4=0,0,16,0;MQ=32	PL:GT:GQ	122,48,0:1/1:99
+chr4	1748790	.	C	T	38	.	DP=21;AF1=0.5005;CI95=0.5,0.5;DP4=6,0,8,0;MQ=40;PV4=1,0.09,1,1	PL:GT:GQ	68,0,27:0/1:30
+chr4	2255732	.	T	C	99	.	DP=29;AF1=1;CI95=1,1;DP4=0,0,28,0;MQ=31	PL:GT:GQ	186,84,0:1/1:99
+chr4	3010159	.	C	T	13.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=31	PL:GT:GQ	45,6,0:1/1:49
+chr4	3545023	.	A	G	99	.	DP=9;AF1=1;CI95=1,1;DP4=0,0,0,9;MQ=38	PL:GT:GQ	145,27,0:1/1:99
+chr4	3586344	.	C	T	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=44	PL:GT:GQ	73,6,0:1/1:49
+chr4	3879337	.	A	G	16.6	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=25	PL:GT:GQ	49,12,0:1/1:72
+chr4	3940733	.	A	G	47.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=31	PL:GT:GQ	80,15,0:1/1:75
+chr4	4410338	.	T	C	13.5	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=31	PL:GT:GQ	46,15,0:1/1:75
+chr4	4796408	.	T	C	41	.	DP=16;AF1=1;CI95=1,1;DP4=0,0,0,16;MQ=17	PL:GT:GQ	74,48,0:1/1:99
+chr4	4796414	.	A	G	11.3	.	DP=16;AF1=1;CI95=1,1;DP4=0,0,0,15;MQ=17	PL:GT:GQ	44,45,0:1/1:99
+chr4	6436959	.	T	C	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=50	PL:GT:GQ	40,6,0:1/1:49
+chr4	9494256	.	T	C	3.41	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=37	PL:GT:GQ	32,6,0:1/1:49
+chr4	24881479	.	G	A	14.1	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=42	PL:GT:GQ	46,9,0:1/1:63
+chr4	26128644	.	A	G	23	.	DP=18;AF1=0.5006;CI95=0.5,0.5;DP4=8,0,10,0;MQ=22;PV4=1,1,1,1	PL:GT:GQ	53,0,26:0/1:29
+chr4	42109100	.	G	A	17.1	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=48	PL:GT:GQ	49,9,0:1/1:63
+chr4	42309652	.	C	T	68	.	DP=17;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=50	PL:GT:GQ	100,9,0:1/1:63
+chr4	46913966	.	C	T	9.08	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=16	PL:GT:GQ	41,12,0:1/1:72
+chr4	50335142	.	A	G	44	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=41	PL:GT:GQ	76,9,0:1/1:63
+chr4	51658550	.	C	A	13	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=48	PL:GT:GQ	44,6,0:1/1:49
+chr4	58258023	.	T	C	26	.	DP=5;AF1=0.5002;CI95=0.5,0.5;DP4=0,3,0,2;MQ=34;PV4=1,1,1,0.05	PL:GT:GQ	56,0,32:0/1:35
+chr4	59219112	.	C	A	42.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=50	PL:GT:GQ	75,12,0:1/1:72
+chr4	62746067	.	C	T	13.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35	PL:GT:GQ	45,6,0:1/1:49
+chr4	67404338	.	G	T	33.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=39	PL:GT:GQ	66,12,0:1/1:72
+chr4	73353380	.	A	G	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49	PL:GT:GQ	73,6,0:1/1:49
+chr4	73946294	.	G	C	4.77	.	DP=51;AF1=0.4999;CI95=0.5,0.5;DP4=0,5,0,3;MQ=40;PV4=1,0.19,0.37,0.11	PL:GT:GQ	33,0,64:0/1:36
+chr4	79607484	.	A	G	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49	PL:GT:GQ	40,6,0:1/1:49
+chr4	82337365	.	G	C	90	.	DP=54;AF1=1;CI95=1,1;DP4=0,0,0,16;MQ=28	PL:GT:GQ	123,48,0:1/1:99
+chr4	82653801	.	A	G	4.11	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=29	PL:GT:GQ	34,9,0:1/1:63
+chr4	87130164	.	C	T	11.3	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=26	PL:GT:GQ	43,9,0:1/1:63
+chr4	87130176	.	G	A	11.3	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=26	PL:GT:GQ	43,9,0:1/1:63
+chr4	91459729	.	C	A	13	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35	PL:GT:GQ	44,6,0:1/1:49
+chr4	96130778	.	G	C	99	.	DP=19;AF1=1;CI95=1,1;DP4=0,0,0,19;MQ=45	PL:GT:GQ	211,57,0:1/1:99
+chr4	100709417	.	A	G	45.1	.	DP=16;AF1=0.505;CI95=0.5,0.5;DP4=12,0,4,0;MQ=24;PV4=1,1,1,1	PL:GT:GQ	75,0,17:0/1:20
+chr4	107276770	.	C	T	70	.	DP=15;AF1=0.5;CI95=0.5,0.5;DP4=0,9,0,6;MQ=31;PV4=1,1,1,1	PL:GT:GQ	100,0,97:0/1:98
+chr4	115327550	.	G	C	42	.	DP=67;AF1=1;CI95=1,1;DP4=0,1,0,66;MQ=35;PV4=1,3.2e-24,0.13,1	PL:GT:GQ	75,162,0:1/1:99
+chr4	136558502	.	A	G	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49	PL:GT:GQ	40,6,0:1/1:49
+chr4	159572459	.	G	A	15.1	.	DP=126;AF1=0.5;CI95=0.5,0.5;DP4=0,69,0,57;MQ=39;PV4=1,4.1e-96,0.077,1	PL:GT:GQ	45,0,175:0/1:48
+chr4	174968484	.	G	C	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=42	PL:GT:GQ	40,6,0:1/1:49
+chr4	175030633	.	T	C	14.3	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=29	PL:GT:GQ	47,18,0:1/1:90
+chr4	183410027	.	G	T	6.2	.	DP=31;AF1=0.5003;CI95=0.5,0.5;DP4=2,0,2,0;MQ=45;PV4=1,0.035,1,0.21	PL:GT:GQ	35,0,28:0/1:30
+chr4	190907368	.	T	C	33.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=50	PL:GT:GQ	66,12,0:1/1:72
+chr4	192175690	.	A	G	76.8	.	DP=7;AF1=0.95;CI95=0.5,1;DP4=0,3,0,4;MQ=35;PV4=1,1,1,1	PL:GT:GQ	105,0,0:1/1:10
+chr4	192673268	.	G	A	14.2	.	DP=9;AF1=1;CI95=1,1;DP4=0,0,9,0;MQ=22	PL:GT:GQ	47,27,0:1/1:99
+chr4	192943966	.	T	C	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=44	PL:GT:GQ	73,6,0:1/1:49
+chr4	195460104	.	C	G	23.1	.	DP=8;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=19	PL:GT:GQ	56,24,0:1/1:96
+chr4	198277830	.	A	G	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49	PL:GT:GQ	40,6,0:1/1:49
+chr5	170098	.	A	G	13	.	DP=12;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=30	PL:GT:GQ	44,6,0:1/1:49
+chr5	395814	.	T	C	4.77	.	DP=4;AF1=0.5;CI95=0.5,0.5;DP4=0,2,0,2;MQ=36;PV4=1,1,0.48,1	PL:GT:GQ	33,0,33:0/1:33
+chr5	414024	.	T	A	10.4	.	DP=17;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=20	PL:GT:GQ	42,9,0:1/1:63
+chr5	496767	.	T	C	13.9	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=36	PL:GT:GQ	45,6,0:1/1:49
+chr5	805676	.	C	G	45	.	DP=17;AF1=1;CI95=1,1;DP4=0,0,17,0;MQ=32	PL:GT:GQ	78,51,0:1/1:99
+chr5	1252896	.	A	G	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49	PL:GT:GQ	40,6,0:1/1:49
+chr5	1418370	.	G	A	3.65	.	DP=8;AF1=0.7301;CI95=0.5,1;DP4=4,0,4,0;MQ=13;PV4=1,1,1,1	PL:GT:GQ	30,0,2:0/1:3
+chr5	1494911	.	G	C	62	.	DP=9;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=46	PL:GT:GQ	95,24,0:1/1:96
+chr5	1494932	.	C	T	6.98	.	DP=8;AF1=0.5001;CI95=0.5,0.5;DP4=1,0,2,0;MQ=46;PV4=1,0.1,0.077,1	PL:GT:GQ	36,0,31:0/1:33
+chr5	1506037	.	T	C	24.1	.	DP=24;AF1=1;CI95=0.5,1;DP4=11,0,13,0;MQ=16;PV4=1,1,1,1	PL:GT:GQ	55,5,0:1/1:46
+chr5	1509406	.	A	G	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=47	PL:GT:GQ	73,6,0:1/1:49
+chr5	1733649	.	A	G	99	.	DP=25;AF1=1;CI95=1,1;DP4=0,0,0,25;MQ=47	PL:GT:GQ	212,75,0:1/1:99
+chr5	1747304	.	A	G	12.3	.	DP=12;AF1=1;CI95=1,1;DP4=0,0,0,12;MQ=19	PL:GT:GQ	45,36,0:1/1:99
+chr5	1747308	.	C	A	44	.	DP=12;AF1=1;CI95=1,1;DP4=0,0,0,12;MQ=19	PL:GT:GQ	77,36,0:1/1:99
+chr5	3519783	.	C	T	21.1	.	DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=18	PL:GT:GQ	54,24,0:1/1:96
+chr5	4101593	.	A	G	69.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=43	PL:GT:GQ	102,12,0:1/1:72
+chr5	7204332	.	T	A	4.61	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=24	PL:GT:GQ	34,6,0:1/1:49
+chr5	11510398	.	A	C	34	.	DP=3;AF1=0.5002;CI95=0.5,0.5;DP4=1,0,2,0;MQ=51;PV4=1,1,0,1	PL:GT:GQ	64,0,31:0/1:34
+chr5	15406720	.	T	C	6.02	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=51	PL:GT:GQ	36,6,0:1/1:49
+chr5	25152417	.	C	A	10.9	.	DP=28;AF1=0.5718;CI95=0.5,1;DP4=0,2,0,6;MQ=25;PV4=1,1,0.21,1	PL:GT:GQ	40,0,6:0/1:8
+chr5	39072637	.	A	G	35.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=50	PL:GT:GQ	68,15,0:1/1:75
+chr5	46022699	.	G	A	44	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=35	PL:GT:GQ	76,9,0:1/1:63
+chr5	55664181	.	C	G	10.4	.	DP=8;AF1=0.9999;CI95=0.5,1;DP4=3,0,5,0;MQ=18;PV4=1,1,1,1	PL:GT:GQ	40,3,0:1/1:41
+chr5	56253386	.	T	C	50.1	.	DP=7;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=36	PL:GT:GQ	83,21,0:1/1:84
+chr5	56253447	.	C	T	42.5	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=45	PL:GT:GQ	75,12,0:1/1:72
+chr5	71950166	.	G	T	11.3	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=40	PL:GT:GQ	43,9,0:1/1:63
+chr5	72703090	.	C	T	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=46	PL:GT:GQ	40,6,0:1/1:49
+chr5	73570280	.	G	T	5.45	.	DP=41;AF1=1;CI95=1,1;DP4=0,0,41,0;MQ=15	PL:GT:GQ	37,123,0:1/1:99
+chr5	73701762	.	G	T	40.8	.	DP=13;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=43	PL:GT:GQ	72,6,0:1/1:49
+chr5	76956867	.	T	C	10.2	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=46	PL:GT:GQ	41,6,0:1/1:49
+chr5	79097961	.	C	G	22	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=40	PL:GT:GQ	54,9,0:1/1:63
+chr5	87026167	.	T	C	22	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=49	PL:GT:GQ	54,9,0:1/1:63
+chr5	97680525	.	T	C	3.27	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=23	PL:GT:GQ	33,12,0:1/1:72
+chr5	100674737	.	C	T	13.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35	PL:GT:GQ	45,6,0:1/1:49
+chr5	105389966	.	T	C	3.52	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=15	PL:GT:GQ	33,9,0:1/1:63
+chr5	109998341	.	A	C	12.7	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=35	PL:GT:GQ	45,12,0:1/1:72
+chr5	120629105	.	C	T	6.79	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48	PL:GT:GQ	37,6,0:1/1:49
+chr5	128383954	.	C	T	23	.	DP=10;AF1=0.5;CI95=0.5,0.5;DP4=0,5,0,5;MQ=48;PV4=1,3.3e-07,1,1	PL:GT:GQ	53,0,98:0/1:56
+chr5	133925142	.	A	G	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49	PL:GT:GQ	73,6,0:1/1:49
+chr5	135375404	.	T	C	11.8	.	DP=6;AF1=1;CI95=0.5,1;DP4=1,0,3,0;MQ=31;PV4=1,0.03,1,1	PL:GT:GQ	42,4,0:1/1:45
+chr5	136498281	.	T	G	13.9	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=37	PL:GT:GQ	45,6,0:1/1:49
+chr5	136717285	.	A	G	82.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=48	PL:GT:GQ	115,12,0:1/1:72
+chr5	136910734	.	G	A	62	.	DP=19;AF1=1;CI95=1,1;DP4=0,1,0,13;MQ=23;PV4=1,1,1,1	PL:GT:GQ	95,31,0:1/1:99
+chr5	141208149	.	C	G	13	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35	PL:GT:GQ	44,6,0:1/1:49
+chr5	148056348	.	C	A	37.1	.	DP=4;AF1=0.9966;CI95=0.5,1;DP4=1,0,2,0;MQ=38;PV4=1,1,1,1	PL:GT:GQ	66,1,0:1/1:23
+chr5	151941534	.	G	T	46.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=34	PL:GT:GQ	79,12,0:1/1:72
+chr5	159967229	.	G	C	22.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=35	PL:GT:GQ	55,12,0:1/1:72
+chr5	174024541	.	T	G	29.5	.	DP=3;AF1=0.9998;CI95=0.5,1;DP4=0,1,0,2;MQ=32;PV4=1,1,1,1	PL:GT:GQ	59,2,0:1/1:37
+chr5	175525290	.	A	G	3.27	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=20	PL:GT:GQ	33,12,0:1/1:72
+chr5	175988954	.	A	C	14.2	.	DP=23;AF1=0.5;CI95=0.5,0.5;DP4=0,6,0,4;MQ=47;PV4=1,1,0.2,1	PL:GT:GQ	44,0,76:0/1:47
+chr5	176782226	.	T	C	9.31	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=43	PL:GT:GQ	40,6,0:1/1:49
+chr5	179132834	.	C	G	99	.	DP=28;AF1=1;CI95=1,1;DP4=0,0,0,28;MQ=41	PL:GT:GQ	207,84,0:1/1:99
+chr5	180155809	.	G	C	3.01	.	DP=36;AF1=0.4997;CI95=0.5,0.5;DP4=25,0,9,0;MQ=35;PV4=1,1e-15,1,1	PL:GT:GQ	30,0,121:0/1:33
+chr5	181282819	.	T	G	38.3	.	DP=11;AF1=1;CI95=0.5,1;DP4=0,2,0,9;MQ=23;PV4=1,1,1,1	PL:GT:GQ	71,14,0:1/1:70
+chr5	182426125	.	G	C	29	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=26	PL:GT:GQ	61,9,0:1/1:63
+chr5	182443682	.	G	A	3.69	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=21	PL:GT:GQ	34,15,0:1/1:75
+chr5	183008993	.	C	T	22	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=49	PL:GT:GQ	54,9,0:1/1:63
+chr5	183312016	.	G	T	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=47	PL:GT:GQ	40,6,0:1/1:49
+chr6_cox_hap1	519146	.	G	A	17.1	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=30	PL:GT:GQ	49,9,0:1/1:63
+chr6_cox_hap1	687497	.	A	G	33	.	DP=6;AF1=0.9999;CI95=0.5,1;DP4=2,0,4,0;MQ=35;PV4=1,0.0016,1,1	PL:GT:GQ	63,3,0:1/1:41
+chr6_qbl_hap2	120066	.	T	C	99	.	DP=12;AF1=1;CI95=1,1;DP4=0,0,0,9;MQ=37	PL:GT:GQ	139,27,0:1/1:99
+chr6	277954	.	C	T	53	.	DP=41;AF1=1;CI95=1,1;DP4=4,0,37,0;MQ=19;PV4=1,1,0.3,1	PL:GT:GQ	86,49,0:1/1:99
+chr6	593158	.	A	G	4.61	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=32	PL:GT:GQ	34,6,0:1/1:49
+chr6	2865562	.	T	G	25	.	DP=9;AF1=1;CI95=1,1;DP4=0,0,9,0;MQ=23	PL:GT:GQ	58,27,0:1/1:99
+chr6	3751403	.	G	A	42.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=32	PL:GT:GQ	75,15,0:1/1:75
+chr6	3884989	.	A	G	13.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=36	PL:GT:GQ	45,6,0:1/1:49
+chr6	4127278	.	A	T	13.9	.	DP=8;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35	PL:GT:GQ	45,6,0:1/1:49
+chr6	5887783	.	C	G	99	.	DP=7;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=34	PL:GT:GQ	142,21,0:1/1:84
+chr6	5887811	.	C	T	55.1	.	DP=7;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=34	PL:GT:GQ	88,21,0:1/1:84
+chr6	6937170	.	G	C	99	.	DP=47;AF1=1;CI95=1,1;DP4=0,0,0,47;MQ=28	PL:GT:GQ	157,141,0:1/1:99
+chr6	7262317	.	C	T	13.2	.	DP=50;AF1=0.5;CI95=0.5,0.5;DP4=21,0,9,0;MQ=36;PV4=1,4e-05,0.17,0.26	PL:GT:GQ	43,0,158:0/1:46
+chr6	7533214	.	A	G	10.4	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=26	PL:GT:GQ	42,9,0:1/1:63
+chr6	20979907	.	A	G	44	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=38	PL:GT:GQ	76,9,0:1/1:63
+chr6	22321632	.	A	G	41	.	DP=5;AF1=0.5004;CI95=0.5,0.5;DP4=1,0,3,0;MQ=46;PV4=1,0.24,0.19,0.33	PL:GT:GQ	71,0,28:0/1:31
+chr6	25352296	.	G	A	7.8	.	DP=4;AF1=0.5003;CI95=0.5,0.5;DP4=0,1,0,3;MQ=38;PV4=1,1,0.16,1	PL:GT:GQ	37,0,28:0/1:30
+chr6	26298040	.	T	A	34	.	DP=3;AF1=0.5002;CI95=0.5,0.5;DP4=0,1,0,2;MQ=48;PV4=1,1,0.21,0.33	PL:GT:GQ	64,0,31:0/1:34
+chr6	33428755	.	G	A	70	.	DP=14;AF1=1;CI95=1,1;DP4=0,0,9,0;MQ=32	PL:GT:GQ	103,27,0:1/1:99
+chr6	39512099	.	G	A	55.1	.	DP=7;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=50	PL:GT:GQ	88,21,0:1/1:84
+chr6	39961094	.	G	A	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49	PL:GT:GQ	73,6,0:1/1:49
+chr6	40452120	.	A	G	40.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=42	PL:GT:GQ	72,6,0:1/1:49
+chr6	43204766	.	A	G	99	.	DP=8;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=51	PL:GT:GQ	176,24,0:1/1:96
+chr6	52696512	.	C	T	70	.	DP=76;AF1=0.5;CI95=0.5,0.5;DP4=0,34,0,42;MQ=18;PV4=1,0.11,1,1	PL:GT:GQ	100,0,51:0/1:54
+chr6	53785550	.	A	G	99	.	DP=20;AF1=1;CI95=1,1;DP4=0,0,0,10;MQ=46	PL:GT:GQ	190,30,0:1/1:99
+chr6	53897484	.	C	T	13.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=36	PL:GT:GQ	45,6,0:1/1:49
+chr6	57038290	.	C	T	10.2	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=36	PL:GT:GQ	41,6,0:1/1:49
+chr6	62925087	.	G	C	35	.	DP=5;AF1=0.5008;CI95=0.5,0.5;DP4=1,0,4,0;MQ=36;PV4=1,1,0.2,1	PL:GT:GQ	65,0,25:0/1:28
+chr6	62925094	.	T	C	25.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=36	PL:GT:GQ	58,15,0:1/1:75
+chr6	70834405	.	G	A	72.1	.	DP=13;AF1=1;CI95=1,1;DP4=0,0,0,7;MQ=29	PL:GT:GQ	105,21,0:1/1:84
+chr6	71026058	.	C	T	48.1	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=42	PL:GT:GQ	81,18,0:1/1:90
+chr6	74420752	.	T	C	44	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=39	PL:GT:GQ	76,9,0:1/1:63
+chr6	77498624	.	T	C	16.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=33	PL:GT:GQ	48,6,0:1/1:49
+chr6	80416836	.	T	C	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=50	PL:GT:GQ	40,6,0:1/1:49
+chr6	113611590	.	A	G	68	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=46	PL:GT:GQ	100,9,0:1/1:63
+chr6	119308431	.	T	C	38.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=40	PL:GT:GQ	71,12,0:1/1:72
+chr6	151758592	.	T	C	3.07	.	DP=17;AF1=0.9966;CI95=0.5,1;DP4=0,8,0,9;MQ=13;PV4=1,1,1,1	PL:GT:GQ	29,1,0:1/1:23
+chr6	151759358	.	A	G	99	.	DP=27;AF1=0.5;CI95=0.5,0.5;DP4=12,0,15,0;MQ=44;PV4=1,1,1,0.19	PL:GT:GQ	171,0,128:0/1:99
+chr6	154741755	.	G	A	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=50	PL:GT:GQ	40,6,0:1/1:49
+chr6	161061053	.	C	A	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=52	PL:GT:GQ	40,6,0:1/1:49
+chr6	161474189	.	C	T	6.02	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49	PL:GT:GQ	36,6,0:1/1:49
+chr6	164304657	.	C	T	10.4	.	DP=63;AF1=0.5;CI95=0.5,0.5;DP4=0,29,0,19;MQ=22;PV4=1,7.7e-11,1,0.049	PL:GT:GQ	40,0,37:0/1:38
+chr6	164703105	.	T	C	99	.	DP=11;AF1=1;CI95=1,1;DP4=0,0,0,10;MQ=40	PL:GT:GQ	165,30,0:1/1:99
+chr6	167518328	.	A	G	78	.	DP=41;AF1=0.5;CI95=0.5,0.5;DP4=27,0,14,0;MQ=33;PV4=1,0.026,0.43,0.056	PL:GT:GQ	108,0,149:0/1:99
+chr6	169906323	.	G	A	41.8	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49	PL:GT:GQ	73,6,0:1/1:49
+chr6	171893912	.	G	A	69.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=33	PL:GT:GQ	102,15,0:1/1:75
+chr6	173631604	.	A	G	6.98	.	DP=7;AF1=0.5;CI95=0.5,0.5;DP4=4,0,3,0;MQ=37;PV4=1,0.069,1,1	PL:GT:GQ	36,0,34:0/1:35
+chr7	835856	.	C	T	27.5	.	DP=13;AF1=0.9998;CI95=0.5,1;DP4=4,0,6,0;MQ=23;PV4=1,0.46,1,1	PL:GT:GQ	57,2,0:1/1:37
+chr7	1046005	.	C	T	11.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=36	PL:GT:GQ	43,9,0:1/1:63
+chr7	1564339	.	C	T	71	.	DP=66;AF1=0.5;CI95=0.5,0.5;DP4=36,0,24,0;MQ=29;PV4=1,1,0.35,1	PL:GT:GQ	101,0,134:0/1:99
+chr7	1806266	.	C	T	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48	PL:GT:GQ	73,6,0:1/1:49
+chr7	1936013	.	G	T	7.77	.	DP=7;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=17	PL:GT:GQ	39,9,0:1/1:63
+chr7	2319532	.	C	A	4.11	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=14	PL:GT:GQ	34,9,0:1/1:63
+chr7	2682121	.	C	T	13	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=33	PL:GT:GQ	44,6,0:1/1:49
+chr7	3248116	.	T	C	36.5	.	DP=3;AF1=0.9998;CI95=0.5,1;DP4=0,1,0,2;MQ=37;PV4=1,1,1,1	PL:GT:GQ	66,2,0:1/1:37
+chr7	3624766	.	C	T	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=41	PL:GT:GQ	40,6,0:1/1:49
+chr7	5291140	.	G	C	13.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=37	PL:GT:GQ	45,6,0:1/1:49
+chr7	5314457	.	C	A	3.56	.	DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=18	PL:GT:GQ	34,24,0:1/1:95
+chr7	5595072	.	T	A	79	.	DP=13;AF1=0.5;CI95=0.5,0.5;DP4=8,0,5,0;MQ=31;PV4=1,1,1,1	PL:GT:GQ	109,0,57:0/1:60
+chr7	5646060	.	G	C	7.79	.	DP=11;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=10	PL:GT:GQ	40,30,0:1/1:99
+chr7	6056816	.	C	G	7.08	.	DP=6;AF1=0.9966;CI95=0.5,1;DP4=0,2,0,3;MQ=23;PV4=1,1,1,1	PL:GT:GQ	35,1,0:1/1:23
+chr7	6412641	.	C	T	40	.	DP=11;AF1=1;CI95=1,1;DP4=0,0,11,0;MQ=33	PL:GT:GQ	73,33,0:1/1:99
+chr7	6766874	.	A	G	34.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=43	PL:GT:GQ	67,15,0:1/1:75
+chr7	8482729	.	C	T	5.08	.	DP=16;AF1=0.8276;CI95=0.5,1;DP4=3,0,3,0;MQ=22;PV4=1,1,1,0.19	PL:GT:GQ	32,0,1:1/1:5
+chr7	9238362	.	G	A	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49	PL:GT:GQ	40,6,0:1/1:49
+chr7	9687781	.	G	A	33	.	DP=29;AF1=0.5;CI95=0.5,0.5;DP4=0,16,0,12;MQ=48;PV4=1,6.5e-38,1,1	PL:GT:GQ	63,0,170:0/1:66
+chr7	9752803	.	A	T	14.2	.	DP=17;AF1=1;CI95=1,1;DP4=0,0,9,0;MQ=18	PL:GT:GQ	47,27,0:1/1:99
+chr7	10240910	.	T	C	45.5	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=35	PL:GT:GQ	78,12,0:1/1:72
+chr7	11046187	.	C	T	86.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=47	PL:GT:GQ	119,12,0:1/1:72
+chr7	11548207	.	C	G	14.6	.	DP=13;AF1=1;CI95=0.5,1;DP4=6,1,0,5;MQ=18;PV4=0.015,1,1,1	PL:GT:GQ	46,7,0:1/1:57
+chr7	11580317	.	C	T	42	.	DP=12;AF1=1;CI95=1,1;DP4=0,1,0,10;MQ=22;PV4=1,1,1,1	PL:GT:GQ	75,23,0:1/1:92
+chr7	11585384	.	G	A	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=46	PL:GT:GQ	73,6,0:1/1:49
+chr7	13498356	.	A	G	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=47	PL:GT:GQ	73,6,0:1/1:49
+chr7	13500887	.	G	A	15.1	.	DP=11;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=22	PL:GT:GQ	48,30,0:1/1:99
+chr7	13827079	.	C	T	6.02	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47	PL:GT:GQ	36,6,0:1/1:49
+chr7	14403976	.	T	G	59	.	DP=30;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=39	PL:GT:GQ	92,24,0:1/1:96
+chr7	14756588	.	A	G	44	.	DP=15;AF1=0.5;CI95=0.5,0.5;DP4=5,0,10,0;MQ=44;PV4=1,5.3e-18,1,1	PL:GT:GQ	74,0,70:0/1:72
+chr7	14756619	.	T	G	44	.	DP=15;AF1=0.5;CI95=0.5,0.5;DP4=5,0,10,0;MQ=44;PV4=1,6.4e-10,1,1	PL:GT:GQ	74,0,70:0/1:72
+chr7	36734598	.	A	C	11.1	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=40	PL:GT:GQ	42,6,0:1/1:49
+chr7	36734599	.	A	T	11.1	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=40	PL:GT:GQ	42,6,0:1/1:49
+chr7	36734603	.	G	C	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=40	PL:GT:GQ	40,6,0:1/1:49
+chr7	40634921	.	A	C	55	.	DP=13;AF1=1;CI95=1,1;DP4=0,0,13,0;MQ=39	PL:GT:GQ	88,39,0:1/1:99
+chr7	48271285	.	A	T	73	.	DP=15;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=25	PL:GT:GQ	106,30,0:1/1:99
+chr7	56264700	.	G	A	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=51	PL:GT:GQ	40,6,0:1/1:49
+chr7	62326003	.	C	A	26.1	.	DP=35;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=28	PL:GT:GQ	59,18,0:1/1:90
+chr7	109468934	.	T	G	5.13	.	DP=10;AF1=0.9998;CI95=0.5,1;DP4=0,1,0,2;MQ=39;PV4=1,0.031,1,1	PL:GT:GQ	33,2,0:1/1:37
+chr7	110208327	.	C	G	16.9	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=44	PL:GT:GQ	48,6,0:1/1:49
+chr7	125654934	.	A	G	4.11	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=27	PL:GT:GQ	34,9,0:1/1:63
+chr7	125770209	.	A	C	32	.	DP=31;AF1=0.5;CI95=0.5,0.5;DP4=11,0,13,0;MQ=34;PV4=1,0.00017,0.16,0.22	PL:GT:GQ	62,0,105:0/1:65
+chr7	125770265	.	G	C	36	.	DP=16;AF1=0.5;CI95=0.5,0.5;DP4=0,5,0,5;MQ=48;PV4=1,0.0047,0.016,0.035	PL:GT:GQ	66,0,110:0/1:69
+chr7	126687042	.	A	G	21.1	.	DP=36;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=22	PL:GT:GQ	54,21,0:1/1:84
+chr7	132292897	.	G	T	99	.	DP=7;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=43	PL:GT:GQ	167,21,0:1/1:84
+chr7	132334562	.	A	C	23	.	DP=16;AF1=1;CI95=1,1;DP4=0,0,0,10;MQ=23	PL:GT:GQ	56,30,0:1/1:99
+chr7	132431838	.	C	T	13.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=1,0,4,0;MQ=23;PV4=1,1,1,1	PL:GT:GQ	44,5,0:1/1:46
+chr7	136324945	.	T	C	13.7	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=35	PL:GT:GQ	46,12,0:1/1:72
+chr7	136957634	.	G	A	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=43	PL:GT:GQ	40,6,0:1/1:49
+chr7	141746871	.	G	A	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=42	PL:GT:GQ	40,6,0:1/1:49
+chr7	146831870	.	C	T	4.77	.	DP=14;AF1=0.5003;CI95=0.5,0.5;DP4=1,0,3,0;MQ=37;PV4=1,0.0029,0.28,1	PL:GT:GQ	33,0,28:0/1:30
+chr7	147142770	.	T	C	45	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=31	PL:GT:GQ	77,9,0:1/1:63
+chr7	147713906	.	C	T	4.77	.	DP=8;AF1=0.5002;CI95=0.5,0.5;DP4=2,0,4,0;MQ=35;PV4=1,8.9e-06,0.48,0.27	PL:GT:GQ	33,0,29:0/1:31
+chr7	148742642	.	G	A	68	.	DP=14;AF1=0.5032;CI95=0.5,0.5;DP4=4,0,10,0;MQ=28;PV4=1,1,1,1	PL:GT:GQ	98,0,19:0/1:22
+chr7	148879148	.	C	T	22	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=48	PL:GT:GQ	54,9,0:1/1:63
+chr7	149484407	.	A	G	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=45	PL:GT:GQ	73,6,0:1/1:49
+chr7	152444478	.	A	G	13	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=36	PL:GT:GQ	44,6,0:1/1:49
+chr7	154106613	.	C	T	68	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=51	PL:GT:GQ	100,9,0:1/1:63
+chr7	154776891	.	G	T	14.4	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=31	PL:GT:GQ	47,15,0:1/1:75
+chr7	155882061	.	A	C	29	.	DP=24;AF1=0.502;CI95=0.5,0.5;DP4=0,1,0,4;MQ=46;PV4=1,0.018,0.15,0.29	PL:GT:GQ	59,0,21:0/1:24
+chr7	155956844	.	G	C	23	.	DP=11;AF1=0.5;CI95=0.5,0.5;DP4=0,7,0,4;MQ=38;PV4=1,1,0.38,1	PL:GT:GQ	53,0,103:0/1:56
+chr7	156277694	.	G	A	62	.	DP=9;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=46	PL:GT:GQ	95,24,0:1/1:96
+chr7	156720588	.	T	C	16.1	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=29	PL:GT:GQ	48,9,0:1/1:63
+chr7	156807649	.	T	C	3.01	.	DP=30;AF1=0.4997;CI95=0.5,0.5;DP4=0,4,0,3;MQ=43;PV4=1,0.16,0.15,1	PL:GT:GQ	30,0,72:0/1:33
+chr7	157331292	.	G	T	43.1	.	DP=7;AF1=1;CI95=1,1;DP4=0,0,0,7;MQ=34	PL:GT:GQ	76,21,0:1/1:84
+chr7	157382957	.	T	C	33.5	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=43	PL:GT:GQ	66,12,0:1/1:72
+chr8	556382	.	A	G	37.1	.	DP=5;AF1=0.9966;CI95=0.5,1;DP4=2,0,3,0;MQ=31;PV4=1,1,1,1	PL:GT:GQ	66,1,0:1/1:23
+chr8	1661673	.	T	C	9.31	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49	PL:GT:GQ	40,6,0:1/1:49
+chr8	7379751	.	C	A	6.24	.	DP=8;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=19	PL:GT:GQ	38,21,0:1/1:84
+chr8	8160505	.	A	T	68.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=35	PL:GT:GQ	101,12,0:1/1:72
+chr8	8160508	.	C	T	24.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=35	PL:GT:GQ	57,12,0:1/1:72
+chr8	16781011	.	A	G	55.5	.	DP=9;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=34	PL:GT:GQ	88,12,0:1/1:72
+chr8	18716499	.	A	T	20	.	DP=10;AF1=0.5;CI95=0.5,0.5;DP4=0,4,0,2;MQ=29;PV4=1,1,1,1	PL:GT:GQ	50,0,52:0/1:51
+chr8	23326483	.	A	G	60	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=47	PL:GT:GQ	92,9,0:1/1:63
+chr8	25842819	.	T	A	12	.	DP=18;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=47	PL:GT:GQ	43,6,0:1/1:49
+chr8	26300279	.	T	C	34	.	DP=44;AF1=1;CI95=1,1;DP4=0,0,41,0;MQ=21	PL:GT:GQ	67,123,0:1/1:99
+chr8	29673470	.	A	G	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=41	PL:GT:GQ	73,6,0:1/1:49
+chr8	29673473	.	C	G	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=41	PL:GT:GQ	40,6,0:1/1:49
+chr8	31685466	.	C	T	34	.	DP=17;AF1=0.5;CI95=0.5,0.5;DP4=10,0,5,0;MQ=28;PV4=1,0.072,1,0.36	PL:GT:GQ	64,0,50:0/1:53
+chr8	37378739	.	C	T	13.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=34	PL:GT:GQ	45,6,0:1/1:49
+chr8	51325952	.	G	A	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49	PL:GT:GQ	40,6,0:1/1:49
+chr8	59221963	.	G	A	16.1	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=29	PL:GT:GQ	48,9,0:1/1:63
+chr8	62764995	.	T	G	20	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=32	PL:GT:GQ	52,9,0:1/1:63
+chr8	63157426	.	C	G	41.6	.	DP=22;AF1=1;CI95=0.5,1;DP4=0,7,0,15;MQ=19;PV4=1,1,1,0.25	PL:GT:GQ	74,11,0:1/1:66
+chr8	68710444	.	G	A	30	.	DP=5;AF1=0.6671;CI95=0.5,1;DP4=3,0,2,0;MQ=32;PV4=1,1,1,1	PL:GT:GQ	59,0,3:0/1:5
+chr8	76416560	.	G	A	89.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=46	PL:GT:GQ	122,12,0:1/1:72
+chr8	81425275	.	T	G	68	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=50	PL:GT:GQ	100,9,0:1/1:63
+chr8	89842286	.	G	C	4.61	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=30	PL:GT:GQ	34,6,0:1/1:49
+chr8	100926281	.	G	A	38	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=41	PL:GT:GQ	70,9,0:1/1:63
+chr8	102746002	.	G	C	13.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35	PL:GT:GQ	45,6,0:1/1:49
+chr8	107850176	.	C	T	43.1	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=45	PL:GT:GQ	76,18,0:1/1:90
+chr8	109966441	.	T	C	27.3	.	DP=9;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=38	PL:GT:GQ	60,15,0:1/1:75
+chr8	118811716	.	G	T	99	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=50	PL:GT:GQ	155,18,0:1/1:90
+chr8	119440254	.	A	T	58.5	.	DP=5;AF1=0.8277;CI95=0.5,1;DP4=2,0,3,0;MQ=34;PV4=1,1,1,0.14	PL:GT:GQ	87,0,1:1/1:5
+chr8	121236024	.	G	A	39.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=48	PL:GT:GQ	71,6,0:1/1:49
+chr8	125489079	.	C	T	13	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35	PL:GT:GQ	44,6,0:1/1:49
+chr8	128502549	.	A	G	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=45	PL:GT:GQ	73,6,0:1/1:49
+chr8	128502551	.	A	G	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=45	PL:GT:GQ	73,6,0:1/1:49
+chr8	130951113	.	G	A	4.61	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=19	PL:GT:GQ	34,6,0:1/1:49
+chr8	135307123	.	G	A	6.02	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=45	PL:GT:GQ	36,6,0:1/1:49
+chr8	138814155	.	C	T	57.1	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=46	PL:GT:GQ	90,18,0:1/1:90
+chr8	140566111	.	A	G	18.1	.	DP=12;AF1=1;CI95=1,1;DP4=0,0,0,12;MQ=15	PL:GT:GQ	51,36,0:1/1:99
+chr8	141586480	.	T	G	44	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=40	PL:GT:GQ	76,9,0:1/1:63
+chr8	143376712	.	A	G	13	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35	PL:GT:GQ	44,6,0:1/1:49
+chr8	150662729	.	T	C	9.31	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47	PL:GT:GQ	40,6,0:1/1:49
+chr8	150741294	.	A	G	25.1	.	DP=7;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=34	PL:GT:GQ	58,18,0:1/1:90
+chr8	150975618	.	A	G	9.31	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48	PL:GT:GQ	40,6,0:1/1:49
+chr8	151580103	.	T	C	6.02	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=20	PL:GT:GQ	36,6,0:1/1:49
+chr8	151634410	.	G	T	48	.	DP=17;AF1=0.5;CI95=0.5,0.5;DP4=0,12,0,5;MQ=39;PV4=1,0.072,1,1	PL:GT:GQ	78,0,125:0/1:81
+chr8	151709267	.	G	A	91.1	.	DP=8;AF1=0.5064;CI95=0.5,0.5;DP4=0,1,0,7;MQ=40;PV4=1,1,0.28,0.37	PL:GT:GQ	121,0,16:0/1:19
+chr8	152636420	.	G	A	8.75	.	DP=3;AF1=0.9966;CI95=0.5,1;DP4=0,1,0,2;MQ=30;PV4=1,1,1,1	PL:GT:GQ	37,1,0:1/1:23
+chr8	152706967	.	G	A	3.01	.	DP=10;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=16	PL:GT:GQ	33,30,0:1/1:99
+chr8	152786522	.	T	C	80.1	.	DP=16;AF1=0.5102;CI95=0.5,0.5;DP4=0,4,0,12;MQ=31;PV4=1,0.25,1,1	PL:GT:GQ	110,0,14:0/1:17
+chr8	152863132	.	T	G	5.44	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=30	PL:GT:GQ	36,9,0:1/1:63
+chr9	23235268	.	C	T	12	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=32	PL:GT:GQ	43,6,0:1/1:49
+chr9	26391176	.	T	C	15.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35	PL:GT:GQ	47,6,0:1/1:49
+chr9	26868232	.	C	G	63	.	DP=20;AF1=0.5025;CI95=0.5,0.5;DP4=7,0,13,0;MQ=22;PV4=1,0.2,1,0.44	PL:GT:GQ	93,0,20:0/1:23
+chr9	34223668	.	C	T	22	.	DP=16;AF1=0.5;CI95=0.5,0.5;DP4=0,9,0,7;MQ=27;PV4=1,0.14,0.34,1	PL:GT:GQ	52,0,79:0/1:55
+chr9	39696645	.	G	A	11.3	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=41	PL:GT:GQ	43,9,0:1/1:63
+chr9	40654130	.	T	G	13	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48	PL:GT:GQ	44,6,0:1/1:49
+chr9	41145321	.	T	G	46.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=33	PL:GT:GQ	79,12,0:1/1:72
+chr9	42273483	.	G	A	9.31	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49	PL:GT:GQ	40,6,0:1/1:49
+chr9	55633192	.	C	T	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49	PL:GT:GQ	73,6,0:1/1:49
+chr9	58705807	.	T	C	70	.	DP=10;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=24	PL:GT:GQ	103,30,0:1/1:99
+chr9	61697149	.	C	G	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49	PL:GT:GQ	73,6,0:1/1:49
+chr9	63152790	.	A	C	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48	PL:GT:GQ	40,6,0:1/1:49
+chr9	63703913	.	C	G	90.1	.	DP=7;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=38	PL:GT:GQ	123,21,0:1/1:84
+chr9	65116068	.	T	C	70	.	DP=13;AF1=1;CI95=1,1;DP4=0,0,0,13;MQ=49	PL:GT:GQ	103,39,0:1/1:99
+chr9	71266598	.	C	A	3.98	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35	PL:GT:GQ	33,6,0:1/1:49
+chr9	73188677	.	G	T	52	.	DP=294;AF1=1;CI95=1,1;DP4=44,0,245,0;MQ=33;PV4=1,0.28,0.0092,1	PL:GT:GQ	85,147,0:1/1:99
+chr9	78854179	.	G	T	22	.	DP=97;AF1=0.5;CI95=0.5,0.5;DP4=21,0,12,0;MQ=44;PV4=1,0.02,0.032,0.0033	PL:GT:GQ	52,0,158:0/1:55
+chr9	82964679	.	A	C	13.2	.	DP=19;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=36	PL:GT:GQ	45,9,0:1/1:63
+chr9	84124545	.	G	T	57	.	DP=11;AF1=0.5;CI95=0.5,0.5;DP4=2,0,3,0;MQ=49;PV4=1,1,0.024,1	PL:GT:GQ	87,0,59:0/1:62
+chr9	86552862	.	C	T	14.4	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=26	PL:GT:GQ	47,15,0:1/1:75
+chr9	87548941	.	A	G	22	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=49	PL:GT:GQ	54,9,0:1/1:63
+chr9	89021101	.	G	A	89.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=49	PL:GT:GQ	122,12,0:1/1:72
+chr9	90447825	.	G	A	9.31	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=46	PL:GT:GQ	40,6,0:1/1:49
+chr9	92462035	.	C	A	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=36	PL:GT:GQ	40,6,0:1/1:49
+chr9	93077294	.	T	G	5.44	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=31	PL:GT:GQ	36,9,0:1/1:63
+chr9	93998137	.	G	A	68	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=46	PL:GT:GQ	100,9,0:1/1:63
+chr9	93998148	.	C	T	21.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=36	PL:GT:GQ	54,15,0:1/1:75
+chr9	95028964	.	C	A	99	.	DP=83;AF1=0.5;CI95=0.5,0.5;DP4=0,57,0,26;MQ=32;PV4=1,9.3e-08,1,0.092	PL:GT:GQ	134,0,120:0/1:99
+chr9	103829155	.	A	G	33	.	DP=96;AF1=1;CI95=1,1;DP4=0,0,96,0;MQ=16	PL:GT:GQ	66,255,0:1/1:99
+chr9	104981331	.	C	T	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=43	PL:GT:GQ	73,6,0:1/1:49
+chr9	111070656	.	G	A	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49	PL:GT:GQ	73,6,0:1/1:49
+chr9	117395657	.	T	C	16.4	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=23	PL:GT:GQ	49,15,0:1/1:75
+chr9	117718907	.	A	G	46.1	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=29	PL:GT:GQ	79,18,0:1/1:90
+chr9	119149161	.	T	C	3.14	.	DP=65;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=22	PL:GT:GQ	33,15,0:1/1:75
+chr9	124528802	.	G	A	78	.	DP=23;AF1=1;CI95=1,1;DP4=0,0,13,0;MQ=25	PL:GT:GQ	111,39,0:1/1:99
+chr9	126707903	.	G	A	26	.	DP=37;AF1=0.5;CI95=0.5,0.5;DP4=0,21,0,8;MQ=46;PV4=1,2.6e-07,0.21,0.42	PL:GT:GQ	56,0,175:0/1:59
+chr9	128700686	.	C	G	33.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=50	PL:GT:GQ	66,12,0:1/1:72
+chr9	129084077	.	G	A	11.3	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=41	PL:GT:GQ	43,9,0:1/1:63
+chr9	129116900	.	A	T	20	.	DP=13;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=30	PL:GT:GQ	52,9,0:1/1:63
+chr9	130290720	.	C	G	21.8	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=42	PL:GT:GQ	53,6,0:1/1:49
+chr9	130306057	.	C	G	71	.	DP=14;AF1=1;CI95=1,1;DP4=0,0,14,0;MQ=28	PL:GT:GQ	104,42,0:1/1:99
+chr9	130528990	.	G	A	99	.	DP=31;AF1=1;CI95=1,1;DP4=0,0,31,0;MQ=27	PL:GT:GQ	174,93,0:1/1:99
+chr9	130529002	.	A	T	7.79	.	DP=30;AF1=1;CI95=1,1;DP4=0,0,11,0;MQ=15	PL:GT:GQ	40,33,0:1/1:99
+chr9	130639996	.	A	G	8.44	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=51	PL:GT:GQ	39,6,0:1/1:49
+chr9	130704890	.	A	G	3.27	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=26	PL:GT:GQ	33,12,0:1/1:72
+chr9	130708345	.	G	A	13.3	.	DP=11;AF1=0.9966;CI95=0.5,1;DP4=0,2,0,3;MQ=38;PV4=1,0.096,1,1	PL:GT:GQ	42,1,0:1/1:23
+chr9	131001601	.	T	A	3.98	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=31	PL:GT:GQ	33,6,0:1/1:49
+chr9	131058539	.	T	A	13	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=44	PL:GT:GQ	44,6,0:1/1:49
+chr9	131808965	.	C	T	42	.	DP=9;AF1=1;CI95=1,1;DP4=0,0,0,9;MQ=37	PL:GT:GQ	75,27,0:1/1:99
+chr9	132551867	.	C	T	17.1	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=25	PL:GT:GQ	49,9,0:1/1:63
+chr9	132685120	.	A	G	4.75	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=25	PL:GT:GQ	35,9,0:1/1:63
+chr9	133175050	.	A	G	18.1	.	DP=30;AF1=1;CI95=1,1;DP4=0,0,17,0;MQ=20	PL:GT:GQ	51,51,0:1/1:99
+chr9	133584978	.	A	G	99	.	DP=25;AF1=1;CI95=1,1;DP4=0,0,25,0;MQ=45	PL:GT:GQ	212,75,0:1/1:99
+chr9	133661895	.	A	G	99	.	DP=17;AF1=1;CI95=1,1;DP4=0,0,14,0;MQ=31	PL:GT:GQ	138,42,0:1/1:99
+chr9	133670376	.	T	C	68	.	DP=19;AF1=1;CI95=1,1;DP4=0,1,0,16;MQ=39;PV4=1,1.4e-20,1,1	PL:GT:GQ	101,39,0:1/1:99
+chr9	133843777	.	T	C	99	.	DP=9;AF1=0.5129;CI95=0.5,0.5;DP4=1,0,8,0;MQ=43;PV4=1,1,1,1	PL:GT:GQ	154,0,13:0/1:16
+chr9	134017265	.	G	C	3.27	.	DP=10;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=13	PL:GT:GQ	33,12,0:1/1:72
+chr9	134105563	.	T	C	34.1	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=39	PL:GT:GQ	67,18,0:1/1:90
+chr9	134608906	.	C	T	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=46	PL:GT:GQ	73,6,0:1/1:49
+chr9	134861929	.	T	A	9.49	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=30	PL:GT:GQ	41,9,0:1/1:63
+chr10	796662	.	A	G	22	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=46	PL:GT:GQ	54,9,0:1/1:63
+chr10	1216716	.	T	A	18.6	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=25	PL:GT:GQ	51,12,0:1/1:72
+chr10	1220781	.	G	A	21	.	DP=9;AF1=1;CI95=1,1;DP4=0,0,9,0;MQ=18	PL:GT:GQ	54,27,0:1/1:99
+chr10	1225208	.	T	C	68	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=47	PL:GT:GQ	100,9,0:1/1:63
+chr10	1727946	.	T	C	14.2	.	DP=8;AF1=1;CI95=1,1;DP4=0,0,0,7;MQ=27	PL:GT:GQ	47,21,0:1/1:84
+chr10	5986542	.	T	C	83	.	DP=93;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=39	PL:GT:GQ	116,30,0:1/1:99
+chr10	6436277	.	G	A	6.02	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47	PL:GT:GQ	36,6,0:1/1:49
+chr10	7704114	.	C	A	35	.	DP=6;AF1=0.9999;CI95=0.5,1;DP4=0,2,0,4;MQ=29;PV4=1,0.27,1,0.27	PL:GT:GQ	65,3,0:1/1:41
+chr10	10881734	.	A	G	9.52	.	DP=9;AF1=0.5;CI95=0.5,0.5;DP4=4,0,5,0;MQ=42;PV4=1,0.0026,0.14,1	PL:GT:GQ	39,0,91:0/1:42
+chr10	13099383	.	G	A	27.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=48	PL:GT:GQ	60,12,0:1/1:72
+chr10	15764077	.	G	C	11.3	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=40	PL:GT:GQ	43,9,0:1/1:63
+chr10	18091502	.	T	C	47	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=38	PL:GT:GQ	79,9,0:1/1:63
+chr10	19645913	.	A	T	15.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=43	PL:GT:GQ	47,6,0:1/1:49
+chr10	22845062	.	C	T	18.1	.	DP=8;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=18	PL:GT:GQ	51,21,0:1/1:84
+chr10	28282802	.	T	C	69	.	DP=12;AF1=1;CI95=1,1;DP4=0,0,12,0;MQ=42	PL:GT:GQ	102,36,0:1/1:99
+chr10	28496872	.	T	G	8.44	.	DP=11;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=45	PL:GT:GQ	39,6,0:1/1:49
+chr10	32746793	.	G	A	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=46	PL:GT:GQ	73,6,0:1/1:49
+chr10	41437604	.	T	G	11.3	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=39	PL:GT:GQ	43,9,0:1/1:63
+chr10	43051239	.	C	T	6.98	.	DP=3;AF1=0.5001;CI95=0.5,0.5;DP4=1,0,2,0;MQ=40;PV4=1,0.33,0.33,1	PL:GT:GQ	36,0,31:0/1:33
+chr10	44455192	.	C	T	4.41	.	DP=6;AF1=0.8276;CI95=0.5,1;DP4=0,3,0,3;MQ=21;PV4=1,1,1,1	PL:GT:GQ	31,0,1:1/1:5
+chr10	48387336	.	A	G	13	.	DP=7;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35	PL:GT:GQ	44,6,0:1/1:49
+chr10	51561705	.	A	G	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=45	PL:GT:GQ	40,6,0:1/1:49
+chr10	51561712	.	C	G	39.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=45	PL:GT:GQ	71,6,0:1/1:49
+chr10	55617954	.	G	A	8.44	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=31	PL:GT:GQ	39,6,0:1/1:49
+chr10	55718281	.	T	A	3.41	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=32	PL:GT:GQ	32,6,0:1/1:49
+chr10	55888771	.	T	C	23.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=43	PL:GT:GQ	56,12,0:1/1:72
+chr10	56025569	.	C	G	34.1	.	DP=3;AF1=0.5064;CI95=0.5,0.5;DP4=0,1,0,2;MQ=39;PV4=1,1,1,1	PL:GT:GQ	64,0,16:0/1:19
+chr10	57384943	.	G	T	84	.	DP=29;AF1=0.5;CI95=0.5,0.5;DP4=16,0,13,0;MQ=26;PV4=1,0.015,1,1	PL:GT:GQ	114,0,110:0/1:99
+chr10	59873077	.	T	G	49	.	DP=8;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=42	PL:GT:GQ	82,24,0:1/1:96
+chr10	61329572	.	C	T	15.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48	PL:GT:GQ	47,6,0:1/1:49
+chr10	63790636	.	T	G	32.1	.	DP=19;AF1=1;CI95=1,1;DP4=1,0,10,0;MQ=28;PV4=1,0.14,1,1	PL:GT:GQ	65,22,0:1/1:88
+chr10	64466048	.	C	G	18.2	.	DP=7;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=28	PL:GT:GQ	51,18,0:1/1:90
+chr10	65053440	.	G	T	99	.	DP=10;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=39	PL:GT:GQ	153,30,0:1/1:99
+chr10	65407358	.	C	G	84.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=45	PL:GT:GQ	117,15,0:1/1:75
+chr10	65605291	.	G	A	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=51	PL:GT:GQ	73,6,0:1/1:49
+chr10	66104447	.	T	C	99	.	DP=47;AF1=0.5;CI95=0.5,0.5;DP4=0,25,0,21;MQ=34;PV4=1,1,0.15,1	PL:GT:GQ	136,0,162:0/1:99
+chr10	82160859	.	G	C	99	.	DP=17;AF1=1;CI95=1,1;DP4=0,0,0,13;MQ=36	PL:GT:GQ	153,39,0:1/1:99
+chr10	82198579	.	C	T	9.31	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47	PL:GT:GQ	40,6,0:1/1:49
+chr10	87086290	.	A	G	4.13	.	DP=9;AF1=1;CI95=1,1;DP4=0,0,0,9;MQ=17	PL:GT:GQ	35,27,0:1/1:99
+chr10	89550621	.	T	G	74	.	DP=47;AF1=1;CI95=1,1;DP4=0,0,0,45;MQ=45	PL:GT:GQ	107,135,0:1/1:99
+chr10	92325046	.	G	A	42.3	.	DP=18;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=45	PL:GT:GQ	75,15,0:1/1:75
+chr10	94488050	.	A	G	5.46	.	DP=4;AF1=0.5;CI95=0.5,0.5;DP4=2,0,2,0;MQ=43;PV4=1,0.16,1,1	PL:GT:GQ	34,0,34:0/1:34
+chr10	95024815	.	C	T	13.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=36	PL:GT:GQ	45,6,0:1/1:49
+chr10	95466306	.	G	A	53	.	DP=7;AF1=0.6671;CI95=0.5,1;DP4=0,4,0,3;MQ=33;PV4=1,1,1,1	PL:GT:GQ	82,0,3:0/1:5
+chr10	100256777	.	T	G	3.83	.	DP=7;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=23	PL:GT:GQ	34,12,0:1/1:72
+chr10	101510485	.	T	C	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49	PL:GT:GQ	40,6,0:1/1:49
+chr10	101530760	.	C	T	13.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35	PL:GT:GQ	45,6,0:1/1:49
+chr10	101879744	.	T	C	22	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=44	PL:GT:GQ	54,9,0:1/1:63
+chr10	102147276	.	G	C	11.3	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=33	PL:GT:GQ	43,9,0:1/1:63
+chr10	102642248	.	T	G	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49	PL:GT:GQ	40,6,0:1/1:49
+chr10	107666616	.	T	C	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=43	PL:GT:GQ	40,6,0:1/1:49
+chr10	108319945	.	C	G	11.3	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=29	PL:GT:GQ	43,9,0:1/1:63
+chr10	109734371	.	G	A	12.7	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=35	PL:GT:GQ	45,12,0:1/1:72
+chr10	112870604	.	C	T	46.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=36	PL:GT:GQ	79,12,0:1/1:72
+chr10	115304673	.	T	C	11.3	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=42	PL:GT:GQ	43,9,0:1/1:63
+chr10	119380588	.	G	A	14.2	.	DP=4;AF1=0.502;CI95=0.5,0.5;DP4=1,0,3,0;MQ=43;PV4=1,0.18,0.32,1	PL:GT:GQ	44,0,21:0/1:24
+chr10	123063756	.	C	T	14.1	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=23	PL:GT:GQ	46,9,0:1/1:63
+chr10	128424770	.	T	G	13.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=30	PL:GT:GQ	45,6,0:1/1:49
+chr10	131229204	.	T	C	44	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=40	PL:GT:GQ	76,9,0:1/1:63
+chr10	132420570	.	G	C	89.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=49	PL:GT:GQ	122,12,0:1/1:72
+chr10	132528066	.	C	T	99	.	DP=19;AF1=1;CI95=1,1;DP4=0,0,19,0;MQ=42	PL:GT:GQ	213,57,0:1/1:99
+chr10	132644619	.	G	A	19.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=23	PL:GT:GQ	52,15,0:1/1:75
+chr10	132707581	.	G	C	9.11	.	DP=51;AF1=0.9998;CI95=0.5,1;DP4=1,0,2,0;MQ=25;PV4=1,1,1,1	PL:GT:GQ	38,2,0:1/1:37
+chr10	133026892	.	T	C	55.1	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=44	PL:GT:GQ	88,18,0:1/1:90
+chr11	768033	.	T	C	33.5	.	DP=4;AF1=0.8277;CI95=0.5,1;DP4=0,2,0,2;MQ=32;PV4=1,1,1,1	PL:GT:GQ	62,0,1:1/1:5
+chr11	768042	.	T	C	33.5	.	DP=6;AF1=0.8277;CI95=0.5,1;DP4=0,2,0,2;MQ=32;PV4=1,1,1,1	PL:GT:GQ	62,0,1:1/1:5
+chr11	874568	.	G	C	33.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=33	PL:GT:GQ	66,12,0:1/1:72
+chr11	1009210	.	T	C	4	.	DP=70;AF1=0.6241;CI95=0.5,1;DP4=0,3,0,8;MQ=24;PV4=1,1,0.5,1	PL:GT:GQ	31,0,4:0/1:6
+chr11	1016692	.	C	T	27	.	DP=39;AF1=1;CI95=1,1;DP4=0,0,0,38;MQ=22	PL:GT:GQ	60,114,0:1/1:99
+chr11	1034477	.	A	G	66	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=42	PL:GT:GQ	98,9,0:1/1:63
+chr11	1074037	.	G	A	4.13	.	DP=9;AF1=0.5001;CI95=0.5,0.5;DP4=4,0,5,0;MQ=24;PV4=1,1,0.43,1	PL:GT:GQ	32,0,30:0/1:31
+chr11	1556298	.	G	A	11.8	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=33	PL:GT:GQ	44,12,0:1/1:72
+chr11	1824777	.	T	C	27	.	DP=10;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=28	PL:GT:GQ	60,30,0:1/1:99
+chr11	3395801	.	C	T	22	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=49	PL:GT:GQ	54,9,0:1/1:63
+chr11	3411901	.	G	A	4.75	.	DP=17;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=29	PL:GT:GQ	35,9,0:1/1:63
+chr11	3731606	.	A	C	11.3	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=39	PL:GT:GQ	43,9,0:1/1:63
+chr11	3783855	.	C	T	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=44	PL:GT:GQ	40,6,0:1/1:49
+chr11	3967636	.	A	G	4.29	.	DP=20;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=24	PL:GT:GQ	35,15,0:1/1:75
+chr11	4385618	.	C	T	13.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=31	PL:GT:GQ	45,6,0:1/1:49
+chr11	4424365	.	T	A	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49	PL:GT:GQ	73,6,0:1/1:49
+chr11	5295586	.	C	T	3.01	.	DP=52;AF1=0.4997;CI95=0.5,0.5;DP4=33,0,10,0;MQ=29;PV4=1,0.0045,0.3,0.17	PL:GT:GQ	30,0,131:0/1:33
+chr11	6157144	.	C	G	45.1	.	DP=14;AF1=1;CI95=1,1;DP4=0,0,0,7;MQ=35	PL:GT:GQ	78,21,0:1/1:84
+chr11	6352044	.	C	T	18	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=31	PL:GT:GQ	50,9,0:1/1:63
+chr11	6767356	.	T	C	9.63	.	DP=3;AF1=0.9966;CI95=0.5,1;DP4=1,0,2,0;MQ=29;PV4=1,1,1,1	PL:GT:GQ	38,1,0:1/1:23
+chr11	6999404	.	G	C	21	.	DP=8;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=37	PL:GT:GQ	53,9,0:1/1:63
+chr11	9120930	.	C	G	17.6	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=25	PL:GT:GQ	50,12,0:1/1:72
+chr11	9373125	.	T	C	19.8	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48	PL:GT:GQ	51,6,0:1/1:49
+chr11	9585101	.	C	T	67	.	DP=16;AF1=1;CI95=1,1;DP4=0,0,14,0;MQ=45	PL:GT:GQ	100,42,0:1/1:99
+chr11	10266192	.	A	C	14.3	.	DP=22;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=27	PL:GT:GQ	47,18,0:1/1:90
+chr11	10303263	.	T	C	8.64	.	DP=17;AF1=1;CI95=1,1;DP4=0,0,0,17;MQ=18	PL:GT:GQ	41,51,0:1/1:99
+chr11	10420170	.	T	C	35	.	DP=17;AF1=1;CI95=1,1;DP4=0,1,0,15;MQ=28;PV4=1,0.12,1,0.4	PL:GT:GQ	68,36,0:1/1:99
+chr11	10912169	.	G	A	99	.	DP=7;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=49	PL:GT:GQ	155,18,0:1/1:90
+chr11	11315826	.	T	G	6.29	.	DP=27;AF1=1;CI95=1,1;DP4=0,0,0,6;MQ=19	PL:GT:GQ	38,18,0:1/1:90
+chr11	11603859	.	A	C	22	.	DP=15;AF1=0.5;CI95=0.5,0.5;DP4=0,9,0,6;MQ=34;PV4=1,9.5e-13,0.22,1	PL:GT:GQ	52,0,115:0/1:55
+chr11	11700034	.	C	T	33	.	DP=11;AF1=1;CI95=1,1;DP4=0,0,9,0;MQ=30	PL:GT:GQ	66,27,0:1/1:99
+chr11	11822758	.	G	A	15.1	.	DP=15;AF1=0.5;CI95=0.5,0.5;DP4=0,7,0,3;MQ=38;PV4=1,0.18,1,1	PL:GT:GQ	45,0,88:0/1:48
+chr11	11976636	.	C	T	22	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=24	PL:GT:GQ	54,9,0:1/1:63
+chr11	14380517	.	C	G	16.1	.	DP=10;AF1=0.5;CI95=0.5,0.5;DP4=5,0,5,0;MQ=48;PV4=1,2.1e-05,0.13,1	PL:GT:GQ	46,0,113:0/1:49
+chr11	14419212	.	A	G	91.1	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=38	PL:GT:GQ	124,18,0:1/1:90
+chr11	14846792	.	A	G	55	.	DP=11;AF1=1;CI95=1,1;DP4=0,0,0,11;MQ=19	PL:GT:GQ	88,33,0:1/1:99
+chr11	15494556	.	C	T	99	.	DP=38;AF1=0.5;CI95=0.5,0.5;DP4=22,0,14,0;MQ=34;PV4=1,0.0071,1,1	PL:GT:GQ	146,0,159:0/1:99
+chr11	16262879	.	A	C	16.1	.	DP=4;AF1=0.5004;CI95=0.5,0.5;DP4=0,1,0,3;MQ=43;PV4=1,0.061,0.24,0.33	PL:GT:GQ	46,0,28:0/1:31
+chr11	21514947	.	T	C	24.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=41	PL:GT:GQ	57,12,0:1/1:72
+chr11	22532576	.	C	G	28	.	DP=17;AF1=1;CI95=1,1;DP4=0,0,0,17;MQ=17	PL:GT:GQ	61,51,0:1/1:99
+chr11	23529238	.	G	T	4.29	.	DP=13;AF1=0.5334;CI95=0.5,1;DP4=1,0,3,0;MQ=37;PV4=1,1,0.34,0.21	PL:GT:GQ	32,0,9:0/1:12
+chr11	24249554	.	A	G	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=48	PL:GT:GQ	73,6,0:1/1:49
+chr11	24853167	.	A	G	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=51	PL:GT:GQ	73,6,0:1/1:49
+chr11	33353903	.	T	C	24.3	.	DP=8;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=36	PL:GT:GQ	57,15,0:1/1:75
+chr11	35126569	.	T	C	24.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=43	PL:GT:GQ	57,12,0:1/1:72
+chr11	35132248	.	C	T	18.6	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=25	PL:GT:GQ	51,12,0:1/1:72
+chr11	35155482	.	T	C	68	.	DP=22;AF1=1;CI95=1,1;DP4=0,0,22,0;MQ=46	PL:GT:GQ	101,66,0:1/1:99
+chr11	52494088	.	T	C	99	.	DP=9;AF1=1;CI95=1,1;DP4=0,0,0,9;MQ=37	PL:GT:GQ	140,27,0:1/1:99
+chr11	57899943	.	C	G	13	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35	PL:GT:GQ	44,6,0:1/1:49
+chr11	62261460	.	G	T	19.1	.	DP=15;AF1=0.5;CI95=0.5,0.5;DP4=0,7,0,5;MQ=27;PV4=1,1.1e-06,1,1	PL:GT:GQ	49,0,58:0/1:51
+chr11	67456049	.	C	T	39.1	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=19	PL:GT:GQ	72,18,0:1/1:90
+chr11	68509708	.	C	G	3.65	.	DP=9;AF1=0.7301;CI95=0.5,1;DP4=0,5,0,4;MQ=17;PV4=1,1,1,1	PL:GT:GQ	30,0,2:0/1:3
+chr11	70115115	.	T	A	99	.	DP=7;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=49	PL:GT:GQ	140,15,0:1/1:75
+chr11	72643951	.	T	C	70	.	DP=23;AF1=1;CI95=1,1;DP4=0,0,22,0;MQ=39	PL:GT:GQ	103,66,0:1/1:99
+chr11	72647930	.	G	A	36	.	DP=4;AF1=0.5004;CI95=0.5,0.5;DP4=0,1,0,3;MQ=41;PV4=1,1,0.3,1	PL:GT:GQ	66,0,28:0/1:31
+chr11	73330148	.	C	T	13	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35	PL:GT:GQ	44,6,0:1/1:49
+chr11	81720893	.	A	G	5.83	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=19	PL:GT:GQ	37,12,0:1/1:72
+chr11	83813797	.	A	G	23.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=43	PL:GT:GQ	56,12,0:1/1:72
+chr11	85949488	.	C	A	54	.	DP=17;AF1=1;CI95=1,1;DP4=0,0,14,0;MQ=37	PL:GT:GQ	87,42,0:1/1:99
+chr11	87634829	.	G	A	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=51	PL:GT:GQ	40,6,0:1/1:49
+chr11	90913093	.	A	T	35.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=46	PL:GT:GQ	67,6,0:1/1:49
+chr11	93793348	.	G	A	99	.	DP=8;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=31	PL:GT:GQ	139,24,0:1/1:96
+chr11	100802294	.	T	C	16.6	.	DP=21;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=35	PL:GT:GQ	49,12,0:1/1:72
+chr11	107455449	.	C	T	8.44	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=26	PL:GT:GQ	39,6,0:1/1:49
+chr11	111344355	.	A	G	69.5	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=43	PL:GT:GQ	102,12,0:1/1:72
+chr11	111611115	.	C	T	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49	PL:GT:GQ	73,6,0:1/1:49
+chr11	113050466	.	G	C	6.02	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=30	PL:GT:GQ	36,6,0:1/1:49
+chr11	114332544	.	T	C	3.54	.	DP=17;AF1=0.4999;CI95=0.5,0.5;DP4=0,4,0,5;MQ=37;PV4=1,0.32,0.13,1	PL:GT:GQ	31,0,37:0/1:33
+chr11	114332549	.	G	A	3.54	.	DP=17;AF1=0.4998;CI95=0.5,0.5;DP4=0,9,0,8;MQ=36;PV4=1,3.1e-10,0.088,1	PL:GT:GQ	31,0,127:0/1:34
+chr11	114843578	.	G	C	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=50	PL:GT:GQ	73,6,0:1/1:49
+chr11	115580279	.	A	G	99	.	DP=15;AF1=1;CI95=1,1;DP4=0,0,15,0;MQ=48	PL:GT:GQ	190,45,0:1/1:99
+chr11	116434328	.	G	A	17.6	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=25	PL:GT:GQ	50,12,0:1/1:72
+chr11	125914161	.	A	G	20.8	.	DP=7;AF1=0.95;CI95=0.5,1;DP4=3,0,4,0;MQ=38;PV4=1,0.074,1,1	PL:GT:GQ	49,0,0:1/1:10
+chr11	125917089	.	C	T	12.3	.	DP=41;AF1=0.5;CI95=0.5,0.5;DP4=0,28,0,12;MQ=44;PV4=1,4.7e-25,1,1	PL:GT:GQ	42,0,167:0/1:45
+chr11	127194100	.	A	G	60	.	DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=49	PL:GT:GQ	93,24,0:1/1:96
+chr12	70856	.	G	A	27.5	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=49	PL:GT:GQ	60,12,0:1/1:72
+chr12	153693	.	T	C	52.3	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=38	PL:GT:GQ	85,15,0:1/1:75
+chr12	924547	.	C	G	37.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=50	PL:GT:GQ	69,6,0:1/1:49
+chr12	1555916	.	G	A	7.18	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=23	PL:GT:GQ	39,15,0:1/1:75
+chr12	1919860	.	G	T	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49	PL:GT:GQ	40,6,0:1/1:49
+chr12	2283756	.	G	A	13.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=34	PL:GT:GQ	45,6,0:1/1:49
+chr12	2805983	.	G	C	12.7	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=35	PL:GT:GQ	45,12,0:1/1:72
+chr12	6088203	.	T	C	72.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=37	PL:GT:GQ	105,15,0:1/1:75
+chr12	7099460	.	G	C	10.8	.	DP=6;AF1=0.8277;CI95=0.5,1;DP4=3,0,3,0;MQ=26;PV4=1,0.027,1,1	PL:GT:GQ	39,0,1:1/1:5
+chr12	7099464	.	G	A	13.3	.	DP=6;AF1=0.9966;CI95=0.5,1;DP4=2,0,3,0;MQ=28;PV4=1,0.16,1,1	PL:GT:GQ	42,1,0:1/1:23
+chr12	7198516	.	T	G	4.61	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35	PL:GT:GQ	34,6,0:1/1:49
+chr12	23331895	.	C	T	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49	PL:GT:GQ	40,6,0:1/1:49
+chr12	28209020	.	T	G	14.4	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=31	PL:GT:GQ	47,15,0:1/1:75
+chr12	30074073	.	C	T	32.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35	PL:GT:GQ	64,6,0:1/1:49
+chr12	30563452	.	T	C	25	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=46	PL:GT:GQ	57,9,0:1/1:63
+chr12	30563453	.	A	G	25	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=46	PL:GT:GQ	57,9,0:1/1:63
+chr12	30563464	.	C	A	78.8	.	DP=8;AF1=1;CI95=0.5,1;DP4=0,2,0,5;MQ=34;PV4=1,0.29,1,1	PL:GT:GQ	110,6,0:1/1:49
+chr12	31505085	.	G	A	13.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35	PL:GT:GQ	45,6,0:1/1:49
+chr12	34041336	.	G	A	5.46	.	DP=5;AF1=0.5;CI95=0.5,0.5;DP4=2,0,2,0;MQ=36;PV4=1,1,0.48,0.21	PL:GT:GQ	34,0,34:0/1:34
+chr12	49003648	.	C	G	42	.	DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=39	PL:GT:GQ	75,24,0:1/1:96
+chr12	51280690	.	G	A	69	.	DP=98;AF1=0.5;CI95=0.5,0.5;DP4=13,0,18,0;MQ=45;PV4=1,1,0.051,1	PL:GT:GQ	99,0,84:0/1:87
+chr12	69206633	.	T	C	17.1	.	DP=12;AF1=1;CI95=1,1;DP4=0,0,0,11;MQ=17	PL:GT:GQ	50,33,0:1/1:99
+chr12	80417253	.	T	C	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=48	PL:GT:GQ	73,6,0:1/1:49
+chr12	86633033	.	C	T	34	.	DP=3;AF1=0.5002;CI95=0.5,0.5;DP4=0,1,0,2;MQ=43;PV4=1,1,0.33,1	PL:GT:GQ	64,0,31:0/1:34
+chr12	98097274	.	C	T	47.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=31	PL:GT:GQ	80,15,0:1/1:75
+chr12	105269319	.	C	T	19	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=26	PL:GT:GQ	51,9,0:1/1:63
+chr12	109053425	.	G	A	9.53	.	DP=8;AF1=0.5012;CI95=0.5,0.5;DP4=2,0,6,0;MQ=25;PV4=1,1,0.19,1	PL:GT:GQ	39,0,23:0/1:26
+chr12	111904540	.	A	G	3.41	.	DP=65;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=31	PL:GT:GQ	32,6,0:1/1:49
+chr12	115038686	.	T	C	15.2	.	DP=7;AF1=1;CI95=1,1;DP4=0,0,0,7;MQ=27	PL:GT:GQ	48,21,0:1/1:84
+chr12	115039419	.	A	G	4.11	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=30	PL:GT:GQ	34,9,0:1/1:63
+chr12	115103890	.	G	A	66	.	DP=39;AF1=1;CI95=1,1;DP4=0,0,0,38;MQ=49	PL:GT:GQ	99,114,0:1/1:99
+chr12	115833830	.	G	A	68	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=49	PL:GT:GQ	100,9,0:1/1:63
+chr12	116361873	.	T	G	6.34	.	DP=5;AF1=0.7302;CI95=0.5,1;DP4=0,2,0,2;MQ=23;PV4=1,1,1,1	PL:GT:GQ	34,0,2:0/1:3
+chr12	123583527	.	G	A	14.1	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=25	PL:GT:GQ	46,9,0:1/1:63
+chr12	124115330	.	A	G	44	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=38	PL:GT:GQ	76,9,0:1/1:63
+chr12	125062296	.	G	A	41.8	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=50	PL:GT:GQ	73,6,0:1/1:49
+chr12	126718106	.	A	G	8.76	.	DP=50;AF1=0.5163;CI95=0.5,1;DP4=2,0,6,0;MQ=26;PV4=1,0.33,0.37,1	PL:GT:GQ	38,0,12:0/1:15
+chr12	133348311	.	G	A	24	.	DP=18;AF1=0.5;CI95=0.5,0.5;DP4=14,0,3,0;MQ=35;PV4=1,1,1,1	PL:GT:GQ	54,0,118:0/1:57
+chr12	134494475	.	C	T	28	.	DP=18;AF1=0.6671;CI95=0.5,1;DP4=8,0,10,0;MQ=18;PV4=1,1,1,1	PL:GT:GQ	57,0,3:0/1:5
+chr12	134831761	.	C	T	41.3	.	DP=10;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=27	PL:GT:GQ	74,15,0:1/1:75
+chr12	134992770	.	A	C,T	84	.	DP=47;AF1=1;CI95=1,1;DP4=0,0,26,0;MQ=29	PL:GT:GQ	117,72,114,0,44,114:1/1:99
+chr12	135261117	.	G	A	49.1	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=46	PL:GT:GQ	82,18,0:1/1:90
+chr12	135261144	.	A	G	99	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=46	PL:GT:GQ	155,18,0:1/1:90
+chr12	135460302	.	G	A	99	.	DP=25;AF1=1;CI95=1,1;DP4=0,0,23,0;MQ=40	PL:GT:GQ	198,69,0:1/1:99
+chr12	135463758	.	A	G	83	.	DP=16;AF1=1;CI95=1,1;DP4=0,0,0,16;MQ=26	PL:GT:GQ	116,48,0:1/1:99
+chr12	135523325	.	G	A	99	.	DP=23;AF1=1;CI95=1,1;DP4=0,0,22,0;MQ=26	PL:GT:GQ	136,66,0:1/1:99
+chr12	135782401	.	T	C	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49	PL:GT:GQ	73,6,0:1/1:49
+chr12	135795472	.	G	T	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48	PL:GT:GQ	40,6,0:1/1:49
+chr13	18040027	.	G	C	42	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=33	PL:GT:GQ	74,9,0:1/1:63
+chr13	19494625	.	G	T	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48	PL:GT:GQ	73,6,0:1/1:49
+chr13	20121126	.	A	G	15.1	.	DP=36;AF1=0.5;CI95=0.5,0.5;DP4=25,0,9,0;MQ=36;PV4=1,1,0.13,1	PL:GT:GQ	45,0,153:0/1:48
+chr13	21536703	.	A	G	9.31	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49	PL:GT:GQ	40,6,0:1/1:49
+chr13	23160035	.	G	T	3.98	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=36	PL:GT:GQ	33,6,0:1/1:49
+chr13	23476554	.	C	A	6.79	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=52	PL:GT:GQ	37,6,0:1/1:49
+chr13	26632967	.	C	G	32	.	DP=9;AF1=1;CI95=1,1;DP4=0,0,0,9;MQ=34	PL:GT:GQ	65,27,0:1/1:99
+chr13	26790010	.	T	C	89.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=35	PL:GT:GQ	122,15,0:1/1:75
+chr13	36083571	.	T	C	43	.	DP=84;AF1=1;CI95=1,1;DP4=1,0,37,0;MQ=16;PV4=1,1,1,0.3	PL:GT:GQ	76,99,0:1/1:99
+chr13	44432419	.	C	T	3.58	.	DP=7;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=19	PL:GT:GQ	34,21,0:1/1:84
+chr13	46592359	.	T	C	16.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47	PL:GT:GQ	48,6,0:1/1:49
+chr13	52764657	.	A	T	3.14	.	DP=32;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=22	PL:GT:GQ	33,15,0:1/1:75
+chr13	53084193	.	C	T	9.11	.	DP=3;AF1=0.9998;CI95=0.5,1;DP4=0,1,0,2;MQ=29;PV4=1,1,1,1	PL:GT:GQ	38,2,0:1/1:37
+chr13	57763228	.	C	T	45	.	DP=555;AF1=1;CI95=1,1;DP4=2,0,21,0;MQ=23;PV4=1,0.00021,1,0.3	PL:GT:GQ	78,45,0:1/1:99
+chr13	73857921	.	G	C	31	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=49	PL:GT:GQ	63,9,0:1/1:63
+chr13	76718001	.	G	A	59	.	DP=4;AF1=0.5004;CI95=0.5,0.5;DP4=1,0,3,0;MQ=45;PV4=1,1,0.12,1	PL:GT:GQ	89,0,28:0/1:31
+chr13	100912695	.	A	T	23	.	DP=22;AF1=0.5;CI95=0.5,0.5;DP4=0,16,0,6;MQ=31;PV4=1,0.029,1,0.35	PL:GT:GQ	53,0,103:0/1:56
+chr13	101332001	.	G	C	21	.	DP=23;AF1=1;CI95=1,1;DP4=0,0,23,0;MQ=21	PL:GT:GQ	54,69,0:1/1:99
+chr13	102637334	.	C	T	68	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=49	PL:GT:GQ	100,9,0:1/1:63
+chr13	102895627	.	C	T	63	.	DP=9;AF1=1;CI95=1,1;DP4=0,0,9,0;MQ=48	PL:GT:GQ	96,27,0:1/1:99
+chr13	103830322	.	T	C	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=50	PL:GT:GQ	73,6,0:1/1:49
+chr13	112842448	.	G	A	39	.	DP=18;AF1=1;CI95=1,1;DP4=0,0,0,9;MQ=27	PL:GT:GQ	72,27,0:1/1:99
+chr13	113310291	.	C	T	33.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=43	PL:GT:GQ	66,12,0:1/1:72
+chr13	114775162	.	A	G	80	.	DP=17;AF1=1;CI95=1,1;DP4=0,0,17,0;MQ=21	PL:GT:GQ	113,51,0:1/1:99
+chr13	115267482	.	A	G	16.1	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=29	PL:GT:GQ	48,9,0:1/1:63
+chr13	116068676	.	C	T	3.83	.	DP=8;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=27	PL:GT:GQ	34,12,0:1/1:72
+chr13	116455918	.	A	G	33	.	DP=29;AF1=0.5;CI95=0.5,0.5;DP4=13,0,15,0;MQ=42;PV4=1,1.8e-20,0.3,1	PL:GT:GQ	63,0,146:0/1:66
+chr13	116765012	.	G	A	30.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49	PL:GT:GQ	62,6,0:1/1:49
+chr13	116779773	.	C	T	17.1	.	DP=38;AF1=0.5;CI95=0.5,0.5;DP4=27,0,11,0;MQ=24;PV4=1,4.5e-35,1,1	PL:GT:GQ	47,0,106:0/1:50
+chr13	116779791	.	C	T	57	.	DP=38;AF1=0.5;CI95=0.5,0.5;DP4=24,0,14,0;MQ=24;PV4=1,1,1,1	PL:GT:GQ	87,0,103:0/1:90
+chr14	20159250	.	C	T	11.3	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=39	PL:GT:GQ	43,9,0:1/1:63
+chr14	23510676	.	T	C	52	.	DP=22;AF1=1;CI95=1,1;DP4=0,0,22,0;MQ=32	PL:GT:GQ	85,66,0:1/1:99
+chr14	24735256	.	G	A	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49	PL:GT:GQ	40,6,0:1/1:49
+chr14	29525577	.	G	A	21	.	DP=10;AF1=1;CI95=1,1;DP4=0,0,9,0;MQ=16	PL:GT:GQ	54,27,0:1/1:99
+chr14	36186389	.	C	T	6.79	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=20	PL:GT:GQ	37,6,0:1/1:49
+chr14	36186394	.	A	G	6.79	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=20	PL:GT:GQ	37,6,0:1/1:49
+chr14	37440609	.	A	G	13	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=33	PL:GT:GQ	44,6,0:1/1:49
+chr14	40432807	.	A	G	18.6	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=23	PL:GT:GQ	51,12,0:1/1:72
+chr14	59466268	.	T	C	15.1	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=25	PL:GT:GQ	47,9,0:1/1:63
+chr14	61368162	.	G	T	7.18	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=17	PL:GT:GQ	39,15,0:1/1:75
+chr14	65152922	.	G	A	92	.	DP=33;AF1=0.5;CI95=0.5,0.5;DP4=0,18,0,15;MQ=36;PV4=1,0.059,0.35,1	PL:GT:GQ	122,0,144:0/1:99
+chr14	69749148	.	G	T	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=25	PL:GT:GQ	40,6,0:1/1:49
+chr14	74877658	.	C	T	45	.	DP=48;AF1=1;CI95=1,1;DP4=0,1,0,12;MQ=36;PV4=1,0.02,1,0.39	PL:GT:GQ	78,28,0:1/1:99
+chr14	75546678	.	C	T	19.2	.	DP=7;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=17	PL:GT:GQ	52,18,0:1/1:90
+chr14	76439185	.	T	C	67.1	.	DP=7;AF1=0.505;CI95=0.5,0.5;DP4=0,1,0,6;MQ=33;PV4=1,1,0.056,0.29	PL:GT:GQ	97,0,17:0/1:20
+chr14	77313295	.	T	A	99	.	DP=12;AF1=1;CI95=1,1;DP4=0,0,0,10;MQ=48	PL:GT:GQ	191,30,0:1/1:99
+chr14	77673422	.	G	A	11.5	.	DP=7;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=24	PL:GT:GQ	44,18,0:1/1:90
+chr14	78646125	.	T	C	99	.	DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=40	PL:GT:GQ	153,24,0:1/1:96
+chr14	91702449	.	A	G	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47	PL:GT:GQ	40,6,0:1/1:49
+chr14	91769842	.	G	A	63	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=47	PL:GT:GQ	95,9,0:1/1:63
+chr14	91775899	.	C	G	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=45	PL:GT:GQ	73,6,0:1/1:49
+chr14	91775924	.	A	G	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=45	PL:GT:GQ	40,6,0:1/1:49
+chr14	93482918	.	A	C	68	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=49	PL:GT:GQ	100,9,0:1/1:63
+chr14	93665819	.	C	T	75	.	DP=7;AF1=0.5002;CI95=0.5,0.5;DP4=0,3,0,4;MQ=42;PV4=1,1,1,1	PL:GT:GQ	105,0,31:0/1:34
+chr14	95422276	.	A	G	55.1	.	DP=7;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=45	PL:GT:GQ	88,21,0:1/1:84
+chr14	95731986	.	C	T	68	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=49	PL:GT:GQ	100,9,0:1/1:63
+chr14	96045464	.	A	G	13	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=33	PL:GT:GQ	44,6,0:1/1:49
+chr14	97172020	.	C	T	68	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=51	PL:GT:GQ	100,9,0:1/1:63
+chr14	100515480	.	A	G	6.98	.	DP=3;AF1=0.5002;CI95=0.5,0.5;DP4=1,0,2,0;MQ=45;PV4=1,0.14,0.085,0.33	PL:GT:GQ	36,0,30:0/1:32
+chr14	100770214	.	A	T	8.69	.	DP=20;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=16	PL:GT:GQ	41,21,0:1/1:84
+chr14	101258303	.	G	A	82	.	DP=15;AF1=1;CI95=1,1;DP4=0,0,15,0;MQ=26	PL:GT:GQ	115,45,0:1/1:99
+chr14	101701492	.	C	G	66	.	DP=10;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=49	PL:GT:GQ	99,30,0:1/1:99
+chr14	102113772	.	T	C	3.98	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=30	PL:GT:GQ	33,6,0:1/1:49
+chr14	102751431	.	A	C	36.5	.	DP=3;AF1=0.9998;CI95=0.5,1;DP4=1,0,2,0;MQ=35;PV4=1,1,1,1	PL:GT:GQ	66,2,0:1/1:37
+chr14	103708033	.	A	G	99	.	DP=13;AF1=1;CI95=1,1;DP4=0,0,0,12;MQ=27	PL:GT:GQ	141,36,0:1/1:99
+chr14	104744582	.	G	A	3.52	.	DP=8;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=25	PL:GT:GQ	33,9,0:1/1:63
+chr14	105989100	.	C	T	3.14	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=23	PL:GT:GQ	33,15,0:1/1:75
+chr14	105989162	.	C	T	3.65	.	DP=12;AF1=0.7301;CI95=0.5,1;DP4=0,6,0,6;MQ=15;PV4=1,1,1,1	PL:GT:GQ	30,0,2:0/1:3
+chr14	106234810	.	G	A	25.3	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=39	PL:GT:GQ	58,15,0:1/1:75
+chr14	106995572	.	A	G	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49	PL:GT:GQ	40,6,0:1/1:49
+chr14	107283057	.	T	C	5.5	.	DP=8;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=20	PL:GT:GQ	37,21,0:1/1:84
+chr14	107285319	.	T	C	33	.	DP=36;AF1=1;CI95=1,1;DP4=0,0,0,35;MQ=22	PL:GT:GQ	66,105,0:1/1:99
+chr14	107640449	.	A	G	11.8	.	DP=7;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=36	PL:GT:GQ	44,12,0:1/1:72
+chr15	20082092	.	T	G	18.3	.	DP=10;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=24	PL:GT:GQ	51,15,0:1/1:75
+chr15	22955884	.	T	C	67	.	DP=12;AF1=1;CI95=1,1;DP4=0,0,12,0;MQ=48	PL:GT:GQ	100,36,0:1/1:99
+chr15	22971987	.	A	G	5.29	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=22	PL:GT:GQ	35,6,0:1/1:49
+chr15	23233324	.	C	A	47	.	DP=16;AF1=1;CI95=1,1;DP4=0,0,14,0;MQ=31	PL:GT:GQ	80,42,0:1/1:99
+chr15	25175286	.	C	T	36.5	.	DP=3;AF1=0.9998;CI95=0.5,1;DP4=1,0,2,0;MQ=42;PV4=1,1,1,1	PL:GT:GQ	66,2,0:1/1:37
+chr15	25385709	.	G	A	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=48	PL:GT:GQ	40,6,0:1/1:49
+chr15	27372396	.	A	G	44	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=40	PL:GT:GQ	76,9,0:1/1:63
+chr15	35998093	.	C	T	9.53	.	DP=9;AF1=1;CI95=1,1;DP4=0,0,9,0;MQ=17	PL:GT:GQ	42,27,0:1/1:99
+chr15	36716538	.	C	G	13.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=36	PL:GT:GQ	45,6,0:1/1:49
+chr15	36793360	.	G	T	44	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=42	PL:GT:GQ	76,9,0:1/1:63
+chr15	53783097	.	A	G	10.5	.	DP=31;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=16	PL:GT:GQ	43,21,0:1/1:84
+chr15	54180175	.	C	T	10.4	.	DP=7;AF1=0.5001;CI95=0.5,0.5;DP4=4,0,3,0;MQ=27;PV4=1,1.2e-05,1,1	PL:GT:GQ	40,0,32:0/1:34
+chr15	54939306	.	C	T	99	.	DP=34;AF1=0.5;CI95=0.5,0.5;DP4=0,18,0,16;MQ=49;PV4=1,1,0.18,1	PL:GT:GQ	172,0,181:0/1:99
+chr15	59377916	.	C	T	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=50	PL:GT:GQ	73,6,0:1/1:49
+chr15	59685961	.	G	C	68	.	DP=11;AF1=1;CI95=1,1;DP4=0,0,0,11;MQ=36	PL:GT:GQ	101,33,0:1/1:99
+chr15	60306384	.	A	G	18.6	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=25	PL:GT:GQ	51,12,0:1/1:72
+chr15	60345642	.	G	C	14.9	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35	PL:GT:GQ	46,6,0:1/1:49
+chr15	60367387	.	G	A	13.2	.	DP=6;AF1=0.5001;CI95=0.5,0.5;DP4=3,0,3,0;MQ=34;PV4=1,0.098,0.24,1	PL:GT:GQ	43,0,35:0/1:37
+chr15	60367446	.	C	T	44	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=41	PL:GT:GQ	76,9,0:1/1:63
+chr15	61763755	.	G	A	68	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=45	PL:GT:GQ	100,9,0:1/1:63
+chr15	61831362	.	C	G	11.3	.	DP=5;AF1=0.5;CI95=0.5,0.5;DP4=0,2,0,3;MQ=30;PV4=1,0.00077,0.47,1	PL:GT:GQ	41,0,42:0/1:41
+chr15	63978880	.	G	C	60	.	DP=6;AF1=0.9999;CI95=0.5,1;DP4=2,0,4,0;MQ=35;PV4=1,1,1,1	PL:GT:GQ	90,3,0:1/1:41
+chr15	64342445	.	A	G	12.2	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=18	PL:GT:GQ	44,9,0:1/1:63
+chr15	65424859	.	T	C	11.3	.	DP=10;AF1=1;CI95=1,1;DP4=0,0,0,10;MQ=21	PL:GT:GQ	44,30,0:1/1:99
+chr15	65603698	.	C	T	60	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=49	PL:GT:GQ	92,9,0:1/1:63
+chr15	67005078	.	G	A	13.9	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35	PL:GT:GQ	45,6,0:1/1:49
+chr15	71133512	.	G	C	22.3	.	DP=19;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=25	PL:GT:GQ	55,15,0:1/1:75
+chr15	72619009	.	A	G	22	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=48	PL:GT:GQ	54,9,0:1/1:63
+chr15	73272688	.	C	T	70.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=39	PL:GT:GQ	103,15,0:1/1:75
+chr15	73699335	.	T	A	99	.	DP=9;AF1=1;CI95=1,1;DP4=0,0,0,9;MQ=45	PL:GT:GQ	175,27,0:1/1:99
+chr15	74513352	.	C	T	99	.	DP=10;AF1=1;CI95=1,1;DP4=0,0,0,10;MQ=37	PL:GT:GQ	139,30,0:1/1:99
+chr15	75540536	.	G	A	9.31	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=44	PL:GT:GQ	40,6,0:1/1:49
+chr15	75822537	.	C	A	17.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=23	PL:GT:GQ	50,15,0:1/1:75
+chr15	78554005	.	T	C	12	.	DP=18;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=46	PL:GT:GQ	43,6,0:1/1:49
+chr15	80089369	.	G	A	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=28	PL:GT:GQ	40,6,0:1/1:49
+chr15	83089149	.	C	G	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=33	PL:GT:GQ	40,6,0:1/1:49
+chr15	86839307	.	T	C	90.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=43	PL:GT:GQ	123,15,0:1/1:75
+chr15	89836258	.	T	C	99	.	DP=10;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=39	PL:GT:GQ	141,24,0:1/1:96
+chr15	89837706	.	G	A	4.13	.	DP=8;AF1=0.4998;CI95=0.5,0.5;DP4=0,4,0,4;MQ=30;PV4=1,1,0.25,1	PL:GT:GQ	32,0,59:0/1:35
+chr15	89857648	.	T	C	99	.	DP=27;AF1=0.5;CI95=0.5,0.5;DP4=8,0,8,0;MQ=40;PV4=1,1,0.3,1	PL:GT:GQ	133,0,130:0/1:99
+chr15	89864228	.	A	C	32	.	DP=4;AF1=0.5002;CI95=0.5,0.5;DP4=2,0,2,0;MQ=42;PV4=1,1,1,1	PL:GT:GQ	62,0,31:0/1:34
+chr15	91261235	.	G	A	7.8	.	DP=4;AF1=0.5002;CI95=0.5,0.5;DP4=1,0,2,0;MQ=44;PV4=1,1,0.32,1	PL:GT:GQ	37,0,30:0/1:32
+chr16	256990	.	A	C	10.4	.	DP=16;AF1=0.5008;CI95=0.5,0.5;DP4=4,0,3,0;MQ=23;PV4=1,0.34,1,1	PL:GT:GQ	40,0,25:0/1:28
+chr16	260794	.	T	C	3.01	.	DP=19;AF1=0.4999;CI95=0.5,0.5;DP4=13,0,2,0;MQ=24;PV4=1,1,1,1	PL:GT:GQ	30,0,32:0/1:31
+chr16	419905	.	A	G	7.9	.	DP=5;AF1=0.9966;CI95=0.5,1;DP4=0,2,0,3;MQ=22;PV4=1,1,1,1	PL:GT:GQ	36,1,0:1/1:23
+chr16	824086	.	T	C	22	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=48	PL:GT:GQ	54,9,0:1/1:63
+chr16	1085063	.	C	T	52	.	DP=12;AF1=0.5;CI95=0.5,0.5;DP4=6,0,6,0;MQ=42;PV4=1,1,0.014,1	PL:GT:GQ	82,0,128:0/1:85
+chr16	1221305	.	T	C	54	.	DP=7;AF1=0.5;CI95=0.5,0.5;DP4=0,3,0,3;MQ=40;PV4=1,1,1,1	PL:GT:GQ	84,0,60:0/1:63
+chr16	1411728	.	A	G	32.3	.	DP=11;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=35	PL:GT:GQ	65,15,0:1/1:75
+chr16	1443197	.	C	G	64	.	DP=26;AF1=1;CI95=1,1;DP4=0,0,25,0;MQ=36	PL:GT:GQ	97,75,0:1/1:99
+chr16	1478746	.	A	T	32	.	DP=20;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=28	PL:GT:GQ	65,24,0:1/1:96
+chr16	1514438	.	A	C	45	.	DP=49;AF1=1;CI95=1,1;DP4=0,0,48,0;MQ=26	PL:GT:GQ	78,144,0:1/1:99
+chr16	1601989	.	T	C	99	.	DP=13;AF1=1;CI95=1,1;DP4=0,0,13,0;MQ=29	PL:GT:GQ	133,39,0:1/1:99
+chr16	2043883	.	C	T	30	.	DP=33;AF1=1;CI95=1,1;DP4=0,0,0,33;MQ=14	PL:GT:GQ	63,99,0:1/1:99
+chr16	2137470	.	A	C	39	.	DP=38;AF1=0.5016;CI95=0.5,0.5;DP4=4,0,6,0;MQ=34;PV4=1,0.02,1,1	PL:GT:GQ	69,0,22:0/1:25
+chr16	2537260	.	A	G	99	.	DP=11;AF1=1;CI95=1,1;DP4=0,0,11,0;MQ=40	PL:GT:GQ	177,33,0:1/1:99
+chr16	2564737	.	T	C	99	.	DP=25;AF1=1;CI95=1,1;DP4=0,0,0,22;MQ=41	PL:GT:GQ	199,66,0:1/1:99
+chr16	2612605	.	A	T	62.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=28	PL:GT:GQ	95,15,0:1/1:75
+chr16	2704518	.	G	A	41	.	DP=48;AF1=0.5;CI95=0.5,0.5;DP4=0,17,0,12;MQ=48;PV4=1,1.9e-23,0.24,0.034	PL:GT:GQ	71,0,175:0/1:74
+chr16	3274307	.	G	T	68	.	DP=39;AF1=0.5;CI95=0.5,0.5;DP4=0,30,0,8;MQ=37;PV4=1,1,1,1	PL:GT:GQ	98,0,138:0/1:99
+chr16	5467292	.	G	C	37.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49	PL:GT:GQ	69,6,0:1/1:49
+chr16	10079145	.	A	G	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49	PL:GT:GQ	73,6,0:1/1:49
+chr16	11483702	.	A	G	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=44	PL:GT:GQ	40,6,0:1/1:49
+chr16	12038227	.	A	T	23	.	DP=47;AF1=0.5;CI95=0.5,0.5;DP4=0,22,0,23;MQ=32;PV4=1,4.4e-66,0.47,0.028	PL:GT:GQ	53,0,135:0/1:56
+chr16	21336880	.	G	C	55	.	DP=35;AF1=0.5;CI95=0.5,0.5;DP4=0,12,0,19;MQ=47;PV4=1,5.6e-21,1,1	PL:GT:GQ	85,0,121:0/1:88
+chr16	21980241	.	C	T	16.1	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=29	PL:GT:GQ	48,9,0:1/1:63
+chr16	23275383	.	C	G	13	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47	PL:GT:GQ	44,6,0:1/1:49
+chr16	27546495	.	G	T	25	.	DP=35;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=43	PL:GT:GQ	57,9,0:1/1:63
+chr16	27700399	.	A	T	17.6	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=17	PL:GT:GQ	50,12,0:1/1:72
+chr16	28021935	.	A	G	18.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=23	PL:GT:GQ	51,15,0:1/1:75
+chr16	29070016	.	G	T	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47	PL:GT:GQ	40,6,0:1/1:49
+chr16	29478618	.	C	T	11.3	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=42	PL:GT:GQ	43,9,0:1/1:63
+chr16	29718140	.	C	T	46.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=31	PL:GT:GQ	79,15,0:1/1:75
+chr16	30700759	.	T	C	17.1	.	DP=14;AF1=1;CI95=1,1;DP4=0,0,0,14;MQ=14	PL:GT:GQ	50,42,0:1/1:99
+chr16	35139103	.	A	G	46.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=37	PL:GT:GQ	79,12,0:1/1:72
+chr16	35473348	.	G	A	3.83	.	DP=11;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=25	PL:GT:GQ	34,12,0:1/1:72
+chr16	36213667	.	A	G	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49	PL:GT:GQ	73,6,0:1/1:49
+chr16	36705528	.	G	A	14.4	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=32	PL:GT:GQ	47,15,0:1/1:75
+chr16	43831353	.	C	T	69.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=42	PL:GT:GQ	102,12,0:1/1:72
+chr16	44715166	.	A	C	25	.	DP=18;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=32	PL:GT:GQ	58,24,0:1/1:96
+chr16	44957661	.	T	C	7.03	.	DP=23;AF1=1;CI95=1,1;DP4=0,0,0,7;MQ=18	PL:GT:GQ	39,21,0:1/1:84
+chr16	44958698	.	C	T	42.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=49	PL:GT:GQ	75,15,0:1/1:75
+chr16	44959163	.	T	C	33.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=48	PL:GT:GQ	66,12,0:1/1:72
+chr16	45167959	.	C	T	4.45	.	DP=16;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=24	PL:GT:GQ	35,12,0:1/1:72
+chr16	50254956	.	C	T	13.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=36	PL:GT:GQ	45,6,0:1/1:49
+chr16	52383122	.	A	C	46.5	.	DP=19;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=42	PL:GT:GQ	79,12,0:1/1:72
+chr16	55978159	.	C	T	10.7	.	DP=20;AF1=0.5336;CI95=0.5,1;DP4=2,0,5,0;MQ=35;PV4=1,0.038,1,0.059	PL:GT:GQ	40,0,9:0/1:12
+chr16	61358878	.	T	A	15.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=32	PL:GT:GQ	47,6,0:1/1:49
+chr16	61392487	.	G	A	13	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=31	PL:GT:GQ	44,6,0:1/1:49
+chr16	61621603	.	G	T	6.59	.	DP=10;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=22	PL:GT:GQ	38,12,0:1/1:72
+chr16	69120890	.	G	C	51.3	.	DP=36;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=42	PL:GT:GQ	84,15,0:1/1:75
+chr16	70778219	.	A	G	21.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=39	PL:GT:GQ	53,6,0:1/1:49
+chr16	71899519	.	T	C	40	.	DP=11;AF1=1;CI95=1,1;DP4=0,0,11,0;MQ=33	PL:GT:GQ	73,33,0:1/1:99
+chr16	72079251	.	A	G	11.3	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=41	PL:GT:GQ	43,9,0:1/1:63
+chr16	72093003	.	G	C	9.31	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49	PL:GT:GQ	40,6,0:1/1:49
+chr16	72672428	.	A	G	68	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=49	PL:GT:GQ	100,9,0:1/1:63
+chr16	72864515	.	A	G	13.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35	PL:GT:GQ	45,6,0:1/1:49
+chr16	72890560	.	G	A	47.1	.	DP=10;AF1=0.5064;CI95=0.5,0.5;DP4=0,1,0,7;MQ=49;PV4=1,0.0019,0.0033,1	PL:GT:GQ	77,0,16:0/1:19
+chr16	73048929	.	A	G	6.29	.	DP=4;AF1=0.9966;CI95=0.5,1;DP4=1,0,2,0;MQ=27;PV4=1,1,1,0.33	PL:GT:GQ	34,1,0:1/1:23
+chr16	73177179	.	A	G	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49	PL:GT:GQ	40,6,0:1/1:49
+chr16	73191468	.	C	T	69.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=40	PL:GT:GQ	102,12,0:1/1:72
+chr16	73367439	.	A	C	7.41	.	DP=36;AF1=1;CI95=0.5,1;DP4=0,2,0,13;MQ=26;PV4=1,1,0.027,1	PL:GT:GQ	37,4,0:1/1:45
+chr16	74259316	.	C	T	89.5	.	DP=13;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=49	PL:GT:GQ	122,12,0:1/1:72
+chr16	75271450	.	C	G	6.99	.	DP=15;AF1=0.5015;CI95=0.5,0.5;DP4=0,1,0,3;MQ=44;PV4=1,0.065,0.31,1	PL:GT:GQ	36,0,22:0/1:25
+chr16	76199870	.	G	A	26	.	DP=14;AF1=0.5;CI95=0.5,0.5;DP4=8,0,6,0;MQ=47;PV4=1,1.2e-06,0.32,1	PL:GT:GQ	56,0,141:0/1:59
+chr16	77723692	.	A	G	89.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=50	PL:GT:GQ	122,12,0:1/1:72
+chr17	165875	.	G	A	40.8	.	DP=11;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=42	PL:GT:GQ	72,6,0:1/1:49
+chr17	1443809	.	C	G	9.31	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=50	PL:GT:GQ	40,6,0:1/1:49
+chr17	1618253	.	C	T	22	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=39	PL:GT:GQ	54,9,0:1/1:63
+chr17	2815309	.	T	G	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49	PL:GT:GQ	40,6,0:1/1:49
+chr17	3537486	.	T	G	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=50	PL:GT:GQ	73,6,0:1/1:49
+chr17	3734367	.	C	A	23.5	.	DP=10;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=36	PL:GT:GQ	56,12,0:1/1:72
+chr17	5634764	.	T	C	13	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35	PL:GT:GQ	44,6,0:1/1:49
+chr17	6408090	.	C	G	3.54	.	DP=5;AF1=0.4998;CI95=0.5,0.5;DP4=3,0,2,0;MQ=40;PV4=1,1,0.36,1	PL:GT:GQ	31,0,66:0/1:34
+chr17	7089723	.	A	G	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=47	PL:GT:GQ	40,6,0:1/1:49
+chr17	8731503	.	G	C	11.1	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=46	PL:GT:GQ	42,6,0:1/1:49
+chr17	9282935	.	T	C,G	24.5	.	DP=10;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=40	PL:GT:GQ	57,12,61,0,3,61:1/1:72
+chr17	17284831	.	T	C	29	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=25	PL:GT:GQ	61,9,0:1/1:63
+chr17	18439515	.	G	A	4.11	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=25	PL:GT:GQ	34,9,0:1/1:63
+chr17	18602146	.	C	T	4.76	.	DP=20;AF1=1;CI95=1,1;DP4=0,0,0,11;MQ=16	PL:GT:GQ	36,33,0:1/1:99
+chr17	19427888	.	C	T	57	.	DP=104;AF1=0.5;CI95=0.5,0.5;DP4=45,0,29,0;MQ=39;PV4=1,2.2e-12,1,1	PL:GT:GQ	87,0,131:0/1:90
+chr17	19604159	.	T	C	9.31	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=45	PL:GT:GQ	40,6,0:1/1:49
+chr17	19610366	.	C	T	13	.	DP=13;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48	PL:GT:GQ	44,6,0:1/1:49
+chr17	20484706	.	C	G	51	.	DP=35;AF1=0.5001;CI95=0.5,0.5;DP4=0,11,0,21;MQ=21;PV4=1,0.39,0.49,1	PL:GT:GQ	81,0,36:0/1:39
+chr17	20555720	.	A	G	26.3	.	DP=8;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=28	PL:GT:GQ	59,15,0:1/1:75
+chr17	24328984	.	A	C	15.4	.	DP=34;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=25	PL:GT:GQ	48,15,0:1/1:75
+chr17	26237090	.	G	A	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=44	PL:GT:GQ	73,6,0:1/1:49
+chr17	28394766	.	C	A	13.9	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=31	PL:GT:GQ	45,6,0:1/1:49
+chr17	31218277	.	A	G	3.62	.	DP=38;AF1=0.5161;CI95=0.5,0.5;DP4=0,1,0,2;MQ=38;PV4=1,0.26,1,1	PL:GT:GQ	31,0,12:0/1:15
+chr17	31254021	.	C	T	15.1	.	DP=10;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=35	PL:GT:GQ	47,9,0:1/1:63
+chr17	32516798	.	G	A	37.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49	PL:GT:GQ	69,6,0:1/1:49
+chr17	32600253	.	A	G	16.6	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=25	PL:GT:GQ	49,12,0:1/1:72
+chr17	34255214	.	G	C	19.2	.	DP=8;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=21	PL:GT:GQ	52,18,0:1/1:90
+chr17	34365900	.	T	C	93.1	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=38	PL:GT:GQ	126,18,0:1/1:90
+chr17	35380386	.	A	T	6.79	.	DP=44;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=46	PL:GT:GQ	37,6,0:1/1:49
+chr17	41993344	.	C	T	64	.	DP=41;AF1=1;CI95=1,1;DP4=0,0,0,41;MQ=16	PL:GT:GQ	97,123,0:1/1:99
+chr17	42128201	.	A	G	4.13	.	DP=5;AF1=0.4998;CI95=0.5,0.5;DP4=0,2,0,2;MQ=52;PV4=1,0.0041,1,1	PL:GT:GQ	32,0,62:0/1:35
+chr17	42984490	.	C	A	56	.	DP=33;AF1=0.5001;CI95=0.5,0.5;DP4=6,0,12,0;MQ=42;PV4=1,0.004,1,1	PL:GT:GQ	86,0,34:0/1:37
+chr17	43419457	.	G	A	99	.	DP=16;AF1=1;CI95=1,1;DP4=0,0,0,14;MQ=45	PL:GT:GQ	185,42,0:1/1:99
+chr17	43421225	.	A	G	65.1	.	DP=31;AF1=1;CI95=0.5,1;DP4=0,6,0,17;MQ=43;PV4=1,0.004,1,1	PL:GT:GQ	98,18,0:1/1:90
+chr17	45206897	.	G	A	22	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=47	PL:GT:GQ	54,9,0:1/1:63
+chr17	45381302	.	T	C	18.6	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=25	PL:GT:GQ	51,12,0:1/1:72
+chr17	45530812	.	C	A	3.54	.	DP=6;AF1=0.4998;CI95=0.5,0.5;DP4=0,3,0,2;MQ=40;PV4=1,1,0.37,1	PL:GT:GQ	31,0,58:0/1:34
+chr17	50242633	.	G	A	44	.	DP=42;AF1=0.5;CI95=0.5,0.5;DP4=0,25,0,13;MQ=32;PV4=1,0.084,0.14,1	PL:GT:GQ	74,0,154:0/1:77
+chr17	51275317	.	G	A	14.9	.	DP=10;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=31	PL:GT:GQ	46,6,0:1/1:49
+chr17	52325530	.	C	T	29	.	DP=19;AF1=1;CI95=1,1;DP4=0,0,0,18;MQ=24	PL:GT:GQ	62,54,0:1/1:99
+chr17	52411748	.	T	G	18.6	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=25	PL:GT:GQ	51,12,0:1/1:72
+chr17	53190746	.	C	G	62.1	.	DP=20;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=40	PL:GT:GQ	95,18,0:1/1:90
+chr17	58289916	.	T	C	18.2	.	DP=8;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=22	PL:GT:GQ	51,18,0:1/1:90
+chr17	59796875	.	C	T	42	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=35	PL:GT:GQ	74,9,0:1/1:63
diff --git a/tests/tabix_data/vcf/2.vcf b/tests/tabix_data/vcf/2.vcf
new file mode 100644
index 0000000..1b338fc
--- /dev/null
+++ b/tests/tabix_data/vcf/2.vcf
@@ -0,0 +1,334 @@
+##fileformat=VCFv4.0
+##ApplyRecalibration="analysis_type=ApplyRecalibration input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=[20] excludeIntervals=null reference_sequence=/humgen/1kg/reference/human_g1k_v37.fasta rodBind=[/humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110608VQSRConsensus/calls/combined.phase1.chr20.raw.indels.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false recal_file=/humgen/gsa-scr1/delangel/VQSRIndels/data/trainMills75_truthMills75_p15_12_12_pctb0.05_std12.0_mG8_QD_FS_HS_RP_IC.recal tranches_file=/humgen/gsa-scr1/delangel/VQSRIndels/data/trainMills75_truthMills75_p15_12_12_pctb0.05_std12.0_mG8_QD_FS_HS_RP_IC.tranches out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub ts_filter_level=93.0 ignore_filter=null mode=INDEL"
+##CombineVariants="analysis_type=CombineVariants input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=[20:41000001-42000000] excludeIntervals=null reference_sequence=/humgen/1kg/reference/human_g1k_v37.fasta rodBind=[/humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110608VQSRConsensus/calls/chr20/AFR/AFR.phase1.chr20.42.raw.indels.vcf, /humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110608VQSRConsensus/calls/chr20/ASN/ASN.phase1.chr20.42.raw.indels.vcf, /humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110608VQSRConsensus/calls/chr20/AMR/AMR.phase1.chr20.42.raw.indels.vcf, /humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110608VQSRConsensus/calls/chr20/EUR/EUR.phase1.chr20.42.raw.indels.vcf, /humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110608VQSRConsensus/calls/chr20/AFR.admix/AFR.admix.phase1.chr20.42.raw.indels.vcf, /humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110608VQSRConsensus/calls/chr20/ASN.admix/ASN.admix.phase1.chr20.42.raw.indels.vcf, /humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110608VQSRConsensus/calls/chr20/AMR.admix/AMR.admix.phase1.chr20.42.raw.indels.vcf, /humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110608VQSRConsensus/calls/chr20/EUR.admix/EUR.admix.phase1.chr20.42.raw.indels.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub genotypemergeoption=PRIORITIZE filteredrecordsmergetype=KEEP_IF_ANY_UNFILTERED rod_priority_list=AFR.admix,AMR.admix,EUR.admix,ASN.admix,AFR,AMR,EUR,ASN printComplexMerges=false filteredAreUncalled=false minimalVCF=false setKey=set assumeIdenticalSamples=false minimumN=1 masterMerge=false mergeInfoWithMaxAC=true"
+##FILTER=<ID=BothStrands,Description="Variant not seen on both strands">
+##FILTER=<ID=HARD_TO_VALIDATE,Description="MQ0 >= 4 && (MQ0 / (1.0 * DP)) > 0.1">
+##FILTER=<ID=HP10,Description="Variant occurs in long homopolymer run (>10)">
+##FILTER=<ID=HaplotypeScore,Description="HaplotypeScore>20.0">
+##FILTER=<ID=HighCoverage,Description="Coverage at variant site is > 7500">
+##FILTER=<ID=HomopolymerRun,Description="HRun>=15">
+##FILTER=<ID=LongRepeat,Description="Variant occurs in long tandem repeat (as defined by 1kg phase one filters)">
+##FILTER=<ID=LowQual,Description="QUAL<30.0">
+##FILTER=<ID=PP20,Description="Variant posterior phred is < 20">
+##FILTER=<ID=QualByDepth,Description="QD<1.0">
+##FILTER=<ID=StrandBias,Description="SB>=-1.0">
+##FILTER=<ID=TruthSensitivityTranche93.00to94.00,Description="Truth sensitivity tranche level at VSQ Lod: 3.9628 <= x < 4.1824">
+##FILTER=<ID=TruthSensitivityTranche94.00to95.00,Description="Truth sensitivity tranche level at VSQ Lod: 3.7129 <= x < 3.9628">
+##FILTER=<ID=TruthSensitivityTranche95.00to96.00,Description="Truth sensitivity tranche level at VSQ Lod: 3.3717 <= x < 3.7129">
+##FILTER=<ID=TruthSensitivityTranche96.00to97.00,Description="Truth sensitivity tranche level at VSQ Lod: 2.8762 <= x < 3.3717">
+##FILTER=<ID=TruthSensitivityTranche97.00to98.00,Description="Truth sensitivity tranche level at VSQ Lod: 2.2618 <= x < 2.8762">
+##FILTER=<ID=TruthSensitivityTranche98.00to99.00+,Description="Truth sensitivity tranche level at VQS Lod < 1.2907">
+##FILTER=<ID=TruthSensitivityTranche98.00to99.00,Description="Truth sensitivity tranche level at VSQ Lod: 1.2907 <= x < 2.2618">
+##FORMAT=<ID=AA,Number=1,Type=Integer,Description="Alternate allele observations">
+##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth (only filtered reads used for calling)">
+##FORMAT=<ID=FT,Number=1,Type=String,Description="Sample Genotype Filter">
+##FORMAT=<ID=GL,Number=3,Type=Integer,Description="Genotype Likelihood, log-scaled likeilhoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy">
+##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=HQ,Number=.,Type=Integer,Description="Haplotype Quality">
+##FORMAT=<ID=PL,Number=3,Type=Float,Description="Normalized, Phred-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; not applicable if site is not biallelic">
+##FORMAT=<ID=RA,Number=1,Type=Integer,Description="Reference allele observations">
+##FORMAT=<ID=SA,Number=1,Type=Integer,Description="Number of alternate observations by strand, delimited by |: [forward]|[reverse]">
+##FORMAT=<ID=SP,Number=1,Type=Integer,Description="Phred-scaled strand bias P-value">
+##FORMAT=<ID=SR,Number=1,Type=Integer,Description="Number of reference observations by strand, delimited by |: [forward]|[reverse]">
+##INFO=<ID=AA,Number=1,Type=Integer,Description="Alternate allele observations">
+##INFO=<ID=AB,Number=1,Type=Float,Description="Allele balance at heterozygous sites: a number between 0 and 1 representing the ratio of reads showing the reference allele to all reads, considering only reads from individuals called as heterozygous">
+##INFO=<ID=ABA,Number=1,Type=Integer,Description="Alternate allele balance count: the number of sequence reads from apparent heterozygotes supporting the alternate allele">
+##INFO=<ID=ABP,Number=1,Type=Float,Description="Allele balance probability at heterozygous sites: Phred-scaled upper-bounds estimate of the probability of observing the deviation between ABR and ABA given E(ABR/ABA) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=ABR,Number=1,Type=Integer,Description="Reference allele balance count: the number of sequence reads from apparent heterozygotes supporting the reference allele">
+##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
+##INFO=<ID=AF1,Number=1,Type=Float,Description="Max-likelihood estimate of the site allele frequency of the first ALT allele">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##INFO=<ID=BL,Number=1,Type=Integer,Description="Base Pairs Left: number of base pairs in reads supporting the alternate to the left (5') of the alternate allele">
+##INFO=<ID=BR,Number=1,Type=Integer,Description="Base Pairs Right: number of base pairs in reads supporting the alternate to the right (3') of the alternate allele">
+##INFO=<ID=BVAR,Number=0,Type=Flag,Description="The best genotype combination in the posterior is variant (non homozygous).">
+##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
+##INFO=<ID=CI95,Number=2,Type=Float,Description="Equal-tail Bayesian credible interval of the site allele frequency at the 95% level">
+##INFO=<ID=CpG,Number=0,Type=Flag,Description="CpG site (either CpG, TpG or CpA)">
+##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership">
+##INFO=<ID=DEL,Number=0,Type=Flag,Description="deletion allele">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Filtered Depth">
+##INFO=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
+##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">
+##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions">
+##INFO=<ID=EL,Number=1,Type=Integer,Description="Allele End Left: number of observations of the alternate where the alternate occurs in the left end of the read">
+##INFO=<ID=EPP,Number=1,Type=Float,Description="End Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=ER,Number=1,Type=Integer,Description="Allele End Right: number of observations of the alternate where the alternate occurs in the right end of the read">
+##INFO=<ID=FQ,Number=1,Type=Float,Description="Phred probability that sample chromosomes are not all the same">
+##INFO=<ID=FR,Number=0,Type=Float,Description="Estimated population frequency">
+##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
+##INFO=<ID=HETAR,Number=1,Type=Integer,Description="Number of individuals heterozygous alternate / reference">
+##INFO=<ID=HOMA,Number=1,Type=Integer,Description="Number of individuals homozygous for the alternate">
+##INFO=<ID=HOMR,Number=1,Type=Integer,Description="Number of individuals homozygous for the reference">
+##INFO=<ID=HP,Number=1,Type=Integer,Description="Homopolmer run length">
+##INFO=<ID=HPLen,Number=1,Type=Integer,Description="Homopolymer length">
+##INFO=<ID=HR,Number=1,Type=Integer,Description="Homopolymer run length">
+##INFO=<ID=HRun,Number=1,Type=Integer,Description="Largest Contiguous Homopolymer Run of Variant Allele In Either Direction">
+##INFO=<ID=HU,Number=1,Type=String,Description="Homopolymer run unit (stranded)">
+##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes">
+##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Not provided in original VCF header">
+##INFO=<ID=INS,Number=0,Type=Flag,Description="insertion allele">
+##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">
+##INFO=<ID=IndelType,Number=1,Type=String,Description="Indel type description">
+##INFO=<ID=KGPilot123,Number=0,Type=Flag,Description="1000 Genome discovery all pilots 2010(1,2,3)">
+##INFO=<ID=LEN,Number=1,Type=Integer,Description="allele length">
+##INFO=<ID=LRB,Number=1,Type=Float,Description="((max(BR, BL) / (BR + BL)) - 0.5) * 2 : The proportion of base pairs in reads on one side of the alternate allele relative to total bases, scaled from [0.5,1] to [0,1]">
+##INFO=<ID=LRBP,Number=1,Type=Float,Description="Left-Right Balance Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between BL and BR given E(BR/BL) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=MNP,Number=0,Type=Flag,Description="MNP allele">
+##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
+##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
+##INFO=<ID=MQ0Fraction,Number=1,Type=Float,Description="Fraction of Mapping Quality Zero Reads">
+##INFO=<ID=MQM,Number=1,Type=Float,Description="Mean mapping quality of observed alternate alleles">
+##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
+##INFO=<ID=NF,Number=0,Type=Integer,Description="Total number of forward reads containing this variant">
+##INFO=<ID=NR,Number=0,Type=Integer,Description="Total number of reads containing this variant">
+##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data">
+##INFO=<ID=PP,Number=0,Type=Float,Description="Posterior probability (phred scaled) that this variant segregates">
+##INFO=<ID=PV4,Number=4,Type=Float,Description="P-values for strand bias, baseQ bias, mapQ bias and tail distance bias">
+##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
+##INFO=<ID=RA,Number=1,Type=Integer,Description="Reference allele observations">
+##INFO=<ID=RL,Number=1,Type=Integer,Description="Reads Placed Left: number of reads supporting the alternate balanced to the left (5') of the alternate allele">
+##INFO=<ID=RPP,Number=1,Type=Float,Description="Read Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=RR,Number=1,Type=Integer,Description="Reads Placed Right: number of reads supporting the alternate balanced to the right (3') of the alternate allele">
+##INFO=<ID=RUN,Number=1,Type=Integer,Description="Homopolymer run length: the number of consecutive nucleotides in the reference genome matching the alternate allele prior to the current position">
+##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
+##INFO=<ID=SAB,Number=1,Type=Float,Description="Strand bias for the alternate allele: SAF / ( SAF + SAR )">
+##INFO=<ID=SAF,Number=1,Type=Integer,Description="Number of alternate observations on the forward strand">
+##INFO=<ID=SAP,Number=1,Type=Float,Description="Strand balance probability for the alternate allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SAF and SAR given E(SAF/SAR) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=SAR,Number=1,Type=Integer,Description="Number of alternate observations on the reverse strand">
+##INFO=<ID=SB,Number=1,Type=Float,Description="Strand Bias">
+##INFO=<ID=SC,Number=1,Type=String,Description="Genomic sequence 10 bases either side of variant position">
+##INFO=<ID=SNP,Number=0,Type=Flag,Description="SNP allele">
+##INFO=<ID=SRB,Number=1,Type=Float,Description="Strand bias for the reference allele: SRF / ( SRF + SRR )">
+##INFO=<ID=SRF,Number=1,Type=Integer,Description="Number of reference observations on the forward strand">
+##INFO=<ID=SRP,Number=1,Type=Float,Description="Strand balance probability for the reference allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SRF and SRR given E(SRF/SRR) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=SRR,Number=1,Type=Integer,Description="Number of reference observations on the reverse strand">
+##INFO=<ID=TC,Number=0,Type=Integer,Description="Total coverage">
+##INFO=<ID=TR,Number=1,Type=Integer,Description="Tandem repeat run length (bp)">
+##INFO=<ID=TS,Number=0,Type=Flag,Description="transition SNP">
+##INFO=<ID=TU,Number=1,Type=String,Description="tandem repeat run unit (stranded)">
+##INFO=<ID=TV,Number=0,Type=Flag,Description="transversion SNP">
+##INFO=<ID=VLD,Number=0,Type=Flag,Description="Is Validated.  This bit is set if the snp has 2+ minor allele count based on frequency or genotype data.">
+##INFO=<ID=VQSLOD,Number=1,Type=Float,Description="Log odds ratio of being a true variant versus being false under the trained gaussian mixture model">
+##INFO=<ID=dbSNP,Number=1,Type=Integer,Description="First SNP Build for RS">
+##INFO=<ID=set,Number=1,Type=String,Description="Source VCF for the merged record in CombineVariants">
+##LeftAlignVariants="analysis_type=LeftAlignVariants input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=[20] excludeIntervals=null reference_sequence=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta rodBind=[/humgen/gsa-scr1/ebanks/ALL.chr20.Oxford.20110407.indels.genotypes.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub"
+##SelectVariants="analysis_type=SelectVariants input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=[20] excludeIntervals=null reference_sequence=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta rodBind=[/humgen/gsa-scr1/delangel/officialCalls/20110201_chr20_phase1_indels/dindel/20110208.chr20.dindel2.ALL.sites.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sample=null select_expressions=[] excludeNonVariants=false excludeFiltered=false discordance= concordance= family_structure= mendelianViolation=false mendelianViolationQualThreshold=0.0 select_random_number=0 select_random_fraction=0.0 selectSNPs=false selectIndels=true"
+##UnifiedGenotyper="analysis_type=UnifiedGenotyper input_file=[/broad/shptmp/delangel/calls/chr20/CHB.phase1.chr20.42.cleaned.bam, /broad/shptmp/delangel/calls/chr20/CHS.phase1.chr20.42.cleaned.bam, /broad/shptmp/delangel/calls/chr20/CLM.phase1.chr20.42.cleaned.bam, /broad/shptmp/delangel/calls/chr20/JPT.phase1.chr20.42.cleaned.bam, /broad/shptmp/delangel/calls/chr20/MXL.phase1.chr20.42.cleaned.bam, /broad/shptmp/delangel/calls/chr20/PUR.phase1.chr20.42.cleaned.bam] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=[20:41000001-42000000] excludeIntervals=null reference_sequence=/humgen/1kg/reference/human_g1k_v37.fasta rodBind=[/humgen/gsa-scr1/delangel/otherIndelCallerAnalysis/ALL.indels.combined.chr20.vcf, /humgen/gsa-hpprojects/GATK/data/dbsnp_132_b37.leftAligned.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=50 baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=8 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false genotype_likelihoods_model=INDEL p_nonref_model=EXACT heterozygosity=0.0010 pcr_error_rate=1.0E-4 genotyping_mode=GENOTYPE_GIVEN_ALLELES output_mode=EMIT_ALL_SITES standard_min_confidence_threshold_for_calling=4.0 standard_min_confidence_threshold_for_emitting=4.0 noSLOD=false assume_single_sample_reads=null abort_at_too_much_coverage=-1 min_base_quality_score=17 min_mapping_quality_score=20 max_deletion_fraction=0.05 min_indel_count_for_genotyping=5 indel_heterozygosity=1.25E-4 indelGapContinuationPenalty=10.0 indelGapOpenPenalty=45.0 indelHaplotypeSize=80 doContextDependentGapPenalties=true getGapPenaltiesFromData=false indel_recal_file=indel.recal_data.csv indelDebug=false dovit=false GSA_PRODUCTION_ONLY=false exactCalculation=LINEAR_EXPERIMENTAL ignoreSNPAlleles=true output_all_callable_bases=false genotype=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub debug_file=null metrics_file=null annotation=[MappingQualityZeroFraction]"
+##VariantAnnotator="analysis_type=VariantAnnotator input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=null excludeIntervals=null reference_sequence=/humgen/1kg/reference/human_g1k_v37.fasta rodBind=[./ALL.chr20.vqsr_2of5_union_sites_for_validation_boosted.vcf] rodToIntervalTrackName=variant BTI_merge_rule=UNION nonDeterministicRandomSeed=false DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sampleName=null annotation=[IndelType] group=[] expression=[] useAllAnnotations=false list=false assume_single_sample_reads=null vcfContainsOnlyIndels=false"
+##VariantFiltration="analysis_type=VariantFiltration input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=[/humgen/1kg/processing/pipeline_test_bams/chr22_chunked.hg19.intervals] excludeIntervals=null reference_sequence=/humgen/1kg/reference/human_g1k_v37.fasta rodBind=[/broad/shptmp/rpoplin/ALL.phase1.chr22.raw.indels.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false enable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null quiet_output_mode=false debug_mode=false help=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub filterExpression=[MQ0 >= 4 && (MQ0 / (1.0 * DP)) > 0.1, QUAL<30.0, SB>=-1.0, QD<1.0, HRun>=15, HaplotypeScore>20.0] filterName=[HARD_TO_VALIDATE, LowQual, StrandBias, QualByDepth, HomopolymerRun, HaplotypeScore] genotypeFilterExpression=[] genotypeFilterName=[] clusterSize=3 clusterWindowSize=0 maskName=Mask missingValuesInExpressionsShouldEvaluateAsFailing=false"
+##commandline="/share/software/freebayes/bin/freebayes --stdin --min-alternate-count 2 --genotype-combo-step-max 20 --genotype-variant-threshold 4 --no-marginals --pvar 0.0001 --indels --mnps --no-filters --binomial-obs-priors --allele-balance-priors --region 20:0..100000 --vcf /d1/data/1000G/20101123/populations/finalised.phase1/integrated/including454/wg/ALL/Pipeline/none//freebayes/freebayes.20:0-100000.baq.20110328.vcf --fasta-reference /d2/data/references/build_37/human_reference_v37.fa"
+##fileDate=2011-03-28
+##filedate=2011-02-08
+##filter="( SNP | MNP ) & ( MQM > 65 | QUAL > 1 ) & ABP < 30 & AB < 0.9 | ( INS | DEL ) & QUAL > 500"
+##phasing=none
+##platypusOptions={'bamFiles': ['/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA06984', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA06985', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA06986', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA06989', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA06994', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA07000', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA07037', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA07048', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA07051', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA07056', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA07346', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA07347', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA07357', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA10847', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA10851', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11829', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11830', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11831', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11832', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11843', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11881', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11892', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11893', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11894', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11918', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11919', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11920', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11930', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11931', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11932', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11933', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11992', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11993', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11994', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11995', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12003', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12004', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12005', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12006', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12043', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12044', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12045', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12046', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12058', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12144', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12154', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12155', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12156', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12234', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12249', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12272', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12273', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12275', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12282', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12283', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12286', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12287', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12340', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12341', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12342', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12347', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12348', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12383', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12399', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12400', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12413', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12414', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12489', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12546', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12716', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12717', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12718', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12748', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12749', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12750', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12751', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12761', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12763', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12775', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12776', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12777', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12778', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12813', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12827', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12828', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12829', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12830', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12842', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12843', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12889', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA12890', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18486', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18487', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18488', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18489', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18498', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18499', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18501', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18502', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18504', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18505', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18507', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18508', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18510', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18511', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18516', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18517', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18519', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18520', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18522', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18523', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18526', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18530', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18532', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18533', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18534', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18535', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18536', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18537', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18538', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18539', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18541', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18542', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18543', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18544', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18545', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18546', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18547', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18548', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18549', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18550', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18552', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18553', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18555', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18557', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18558', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18559', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18560', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18561', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18562', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18563', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18564', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18565', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18566', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18567', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18570', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18571', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18572', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18573', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18574', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18576', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18577', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18579', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18582', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18592', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18593', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18595', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18596', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18597', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18599', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18602', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18603', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18605', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18606', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18608', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18609', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18610', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18611', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18612', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18613', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18614', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18615', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18616', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18617', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18618', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18619', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18620', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18621', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18622', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18623', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18624', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18625', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18626', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18627', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18628', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18630', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18631', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18632', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18633', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18634', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18635', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18636', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18637', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18638', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18853', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18856', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18858', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18861', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18867', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18868', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18870', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18871', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18873', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18874', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18907', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18908', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18909', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18910', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18912', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18916', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18917', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18923', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18924', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18933', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18934', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18940', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18941', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18942', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18943', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18944', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18945', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18947', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18948', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18949', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18950', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18951', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18952', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18953', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18956', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18959', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18960', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18961', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18963', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18964', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18965', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18967', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18968', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA18971', 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'/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01113', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01124', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01125', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01133', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01134', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01136', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01137', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01140', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01148', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01149', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01167', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01168', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01170', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01171', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01173', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01174', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01176', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01177', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01182', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01183', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01187', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01188', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01190', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01191', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01197', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01198', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01204', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01250', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01251', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01253', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01254', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01334', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01342', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01350', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01351', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01353', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01354', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01356', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01357', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01359', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01360', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01365', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01366', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01374', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01375', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01377', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01378', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01383', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01384', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01389', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01390', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01437', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01440', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01441', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01455', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01456', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01461', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01462', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01464', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01465', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01488', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01489', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01491', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01492', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01494', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01495', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01497', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01498', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01515', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01516', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01518', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01519', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01521', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01522', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01550', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01551'], 'minReads': 2, 'refFile': '/scratch/rimmer/Genomes/human_g1k_v37_ebv.fa', 'maxHaplotypes': 64, 'maxSize': 100, 'ploidy': 2, 'maxRegionSize': 10000, 'nCPU': 1, 'minFlank': 3, 'logFileName': 'LogsAllPhaseOne/ThousandGenomesPhaseOneCalls_20:1-100001.log', 'regions': ['20:1-100001'], 'maxVariants': 6, 'genIndels': 1, 'labels': None, 'dataType': 'population', 'minMapQual': 20, 'rlen': 100, 'nInd': 994, 'getVariantsFromBAMs': 1, 'genSNPs': 1, 'minReadQual': 20, 'maxCoverage': 1000000.0, 'verbosity': 2, 'sourceFile': None, 'callOnlyIndels': 1, 'output': 'VariantCallsAllPhaseOne/ThousandGenomesPhaseOneCalls_20:1-100001.vcf'}
+##reference=/lustre/scratch105/projects/g1k/ref/main_project/human_g1k_v37.fasta
+##source=Dindel2
+##source=SelectVariants
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+##vcfCTools=filter
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freebayes.20:60500000-60600000.baq.20110328.vcf, freebayes.20:60600000-60700000.baq.20110328.vcf, freebayes.20:60700000-60800000.baq.20110328.vcf, freebayes.20:60800000-60900000.baq.20110328.vcf, freebayes.20:60900000-61000000.baq.20110328.vcf, freebayes.20:61000000-61100000.baq.20110328.vcf, freebayes.20:61100000-61200000.baq.20110328.vcf, freebayes.20:61200000-61300000.baq.20110328.vcf, freebayes.20:61300000-61400000.baq.20110328.vcf, freebayes.20:61400000-61500000.baq.20110328.vcf, freebayes.20:61500000-61600000.baq.20110328.vcf, freebayes.20:61600000-61700000.baq.20110328.vcf, freebayes.20:61700000-61800000.baq.20110328.vcf, freebayes.20:61800000-61900000.baq.20110328.vcf, freebayes.20:61900000-62000000.baq.20110328.vcf, freebayes.20:62000000-62100000.baq.20110328.vcf, freebayes.20:62100000-62200000.baq.20110328.vcf, freebayes.20:62200000-62300000.baq.20110328.vcf, freebayes.20:62300000-62400000.baq.20110328.vcf, freebayes.20:62400000-62500000.baq.20110328.vcf, 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+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
+20	458502	.	G	GA	4567.01	PASS	AA=20;AB=0.61111;ABA=14;ABP=6.8707;ABR=22;AC=38;AF=0.0544;AN=698;BL=374;BR=1129;BVAR;BaseQRankSum=13.364;DP=15979;DP4=1882,2188,45,37;Dels=0.00;EL=5;EPP=13.868;ER=15;FR;FS=6.503;HETAR=11;HOMA=2;HOMR=985;HP=1;HPLen=2;HR=2;HRun=0;HU=G;INDEL;INS;InbreedingCoeff=0.0157;IndelType=INS.NOVEL_1.Novel_A.;LEN=1;LRB=0.50233;LRBP=826.56;MQ=66.16;MQ0Fraction=0.0110;MQM=70.5;MQRankSum=-3.158;NF;NR;NS=998;PP;PV4=0.15,1,0.42,0.15;RA=3173;RL=1;RPP=38.188;RR=19;RUN=1;ReadPosRankSum=-2.346;SAB=0.7;SAF=14;SAP=9.959;SAR=6;SC=GGGCGTGGTGGTGCATGTAAT;SRB=0.50047;SRF=1588;SRP=3.0165;SRR=1585;TC;TR=9;TU=GGT;VQSLOD=10.0079;set=Intersection;sumGLbyD=23.94
+20	573764	.	TA	T	591.51	PASS	AC=91;AF=0.1987;AN=458;BaseQRankSum=0.137;DP=519;FS=3.153;HRun=1;HaplotypeScore=14.0744;InbreedingCoeff=0.1460;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_A.;MQ=48.16;MQ0=26;MQ0Fraction=0.0501;MQRankSum=-1.636;QD=3.63;ReadPosRankSum=-4.140;SB=-408.14;VQSLOD=5.2458;set=VQSR
+20	766143	.	C	CATCTGGTA	5521.70	PASS	AA=24;AB=0.5;ABA=18;ABP=3.0103;ABR=18;AC=14;AF=0.0289;AF1=0.02038;AN=484;BL=655;BR=1542;BVAR;BaseQRankSum=3.801;CI95=0.01549,0.02655;DP=11749;DP4=2222,1998,14,8;Dels=0.00;EL=9;EPP=6.2675;ER=15;FQ=999;FR;FS=2.941;HETAR=9;HOMA=4;HOMR=901;HP=2;HPLen=2;HR=1;HRun=0;HU=A;INDEL;INS;InbreedingCoeff=0.0515;IndelType=INS.NumRepetitions_1.EventLength_8.;LEN=8;LRB=0.40373;LRBP=780.64;MQ=56.81;MQ0Fraction=0.0253;MQM=22.167;MQRankSum=-4.809;NF;NR;NS=914;PP;PV4=0.39,1,5.8e-07,1;RA=3093;RL=6;RPP=16.039;RR=18;RUN=1;ReadPosRankSum=-2.827;SAB=0.625;SAF=15;SAP=6.2675;SAR=9;SC=GCTTTAAATTCATCTGGTACT;SRB=0.61623;SRF=1906;SRP=365.95;SRR=1187;TC;TR=1;TU=A;VQSLOD=7.0268;set=Intersection;sumGLbyD=50.23
+20	997076	rs11467490	CTG	C	15379.78	PASS	AA=195;AB=0.59878;ABA=132;ABP=30.896;ABR=197;AC=173;AF=0.14562;AN=1188;BL=7664;BR=7309;BVAR;BaseQRankSum=21.853;DB;DEL;DP=27127;DP4=1801,2002,241,282;Dels=0.13;EL=100;EPP=3.2887;ER=95;FQ=999;FR;FS=6.591;HETAR=77;HOMA=42;HOMR=815;HP=1;HPLen=1;HR=1;HRun=0;HU=T;INDEL;InbreedingCoeff=0.1284;IndelType=DEL.NumRepetitions_1.EventLength_2.RepeatExpansion_TG.;LEN=2;LRB=0.023709;LRBP=21.287;MQ=61.18;MQ0Fraction=0.0214;MQM=43.041;MQRankSum=6.886;NF;NR;NS=934;PP;PV4=0.61,1.5e-78,1,1;RA=2800;RL=120;RPP=25.56;RR=75;RUN=1;ReadPosRankSum=4.504;SAB=0.62051;SAF=121;SAP=27.609;SAR=74;SC=CAGCTAATTACTGTATTTTTA;SRB=0.49821;SRF=1395;SRP=3.0879;SRR=1405;TC;TR=1;TU=T;VQSLOD=8.9396;set=Intersection;sumGLbyD=16.76
+20	1042261	rs10597473	CCCTG	C	168658.05	PASS	AA=4481;AB=0.29043;ABA=2128;ABP=1147.1;ABR=871;AC=1172;AF=0.97830;AN=1198;BL=169975;BR=194027;BVAR;BaseQRankSum=4.599;DB;DEL;DP=29418;DP4=29,47,1441,2403;Dels=0.84;EL=2358;EPP=29.772;ER=2123;FR;FS=9.122;HETAR=482;HOMA=559;HOMR=30;HP=2;HPLen=3;HR=3;HRun=0;HU=C;INDEL;InbreedingCoeff=0.0470;IndelType=DEL.NumRepetitions_2.EventLength_4.;LEN=4;LRB=0.066077;LRBP=3454.1;MQ=104.58;MQ0=4;MQ0Fraction=0.0014;MQM=58.257;MQRankSum=-3.368;NF;NR;NS=1071;PP;PV4=0.91,6.8e-09,2.8e-05,1;RA=1039;RL=2088;RPP=48.09;RR=2393;RUN=1;ReadPosRankSum=5.288;SAB=0.41442;SAF=1857;SAP=288.09;SAR=2624;SC=CCAAACCCAACCCTGCCTGGC;SRB=0.48893;SRF=508;SRP=4.1159;SRR=531;TC;TR=8;TU=CCTG;VQSLOD=8.5148;dbSNP=120;set=Intersection;sumGLbyD=59.79
+20	1046297	rs33956316	C	CT,CTT,CTTT	17698	PASS	ABR=408;AC=432,79,230;AF=0.39779,0.07274,0.21179;BVAR;BaseQRankSum=-8.413;DB;DP=15649;DP4=147,199,534,436;FR;FS=11.580;HOMA=97;HOMR=457;HP=20;HR=16;HU=T;HaplotypeScore=16.0590;INDEL;INS;InbreedingCoeff=0.6018;IndelType=MULTIALLELIC_INDEL;KGPilot123;MQ0=19;MQ0Fraction=0.0093;MQRankSum=7.992;NF;NR;NS=767;PP;PV4=6e-05,1,1,1;QD=8.18;RA=1183;RUN=1;ReadPosRankSum=2.684;SB=-6384.08;SC=GGAAAATTTTCTTTTTTTTTT;SRB=0.40913;SRF=484;SRP=87.859;SRR=699;TC;TR=16;TU=T;VQSLOD=8.4941;dbSNP=132;set=Intersection
+20	1405740	.	T	TA	257.28	PASS	AF=0.0188;BaseQRankSum=-0.745;DP=3769;Dels=0.00;FS=0.742;HPLen=9;HRun=9;InbreedingCoeff=0.0462;IndelType=INS.NumRepetitions_9.EventLength_1.RepeatExpansion_A.;MQ0Fraction=0.0151;MQRankSum=-0.090;ReadPosRankSum=-1.582;VQSLOD=5.6502;set=Intersection;sumGLbyD=6.94
+20	1690501	.	TC	T	27928	PASS	AA=108;AB=0.91372;ABA=100;ABP=1726.1;ABR=1059;AC=35;AF=0.02966;AN=1180;BL=593;BR=6973;BVAR;BaseQRankSum=7.567;DEL;DP=10612;Dels=0.01;EL=50;EPP=4.2971;ER=58;FS=0.000;HETAR=378;HOMA=184;HOMR=477;HRun=1;InbreedingCoeff=0.0495;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;LEN=1;LRB=0.84325;LRBP=11685;MQ0=0;MQ0Fraction=0.0000;MQM=87.361;MQRankSum=4.088;NS=1045;RA=3125;RL=3;RPP=212.2;RR=105;RUN=1;ReadPosRankSum=-13.096;SAB=0.56481;SAF=61;SAP=6.9511;SAR=47;SRB=0.51776;SRF=1618;SRP=11.572;SRR=1507;VQSLOD=3.9824;set=filterInVQSR-2of5;sumGLbyD=4.07
+20	1991285	rs113891396	TAA	T,TA,TAAA,TAAAAA,TAAAAAA,TAAAAAAA,TAAAAAAAA	39235.36	PASS	AC=5,251,20,39,188,52,79;AF=0.0056,0.2789,0.0222,0.0433,0.2089,0.0578,0.0878;AN=900;BVAR;BaseQRankSum=1.124;DB;DEL;DP=54393;DP4=906,772,824,579;Dels=0.21;FR;FS=37.525;HP=12;HR=12;HRun=12;HU=A;INDEL;INS;InbreedingCoeff=0.6891;IndelType=MULTIALLELIC_INDEL;MQ=76.81;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-6.593;NF;NR;PP;PV4=0.0087,1,6.3e-19,1;RUN=1;ReadPosRankSum=-2.184;SC=ATCTGCCACTTAAAAAAAAAA;TC;TR=12;TU=A;VQSLOD=9.0007;dbSNP=132;set=Intersection;sumGLbyD=11.45
+20	2355911	.	TA	T	11723	PASS	AA=79;AB=0.9393;ABA=57;ABP=1577;ABR=882;AC=38;AF=0.0411;AN=924;BL=644;BR=5536;BVAR;BaseQRankSum=2.434;DEL;DP=9687;Dels=0.00;EL=45;EPP=6.3362;ER=34;FS=3.043;HETAR=321;HOMA=182;HOMR=555;HRun=5;InbreedingCoeff=0.0412;IndelType=DEL.NumRepetitions_5.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.79159;LRBP=8411.9;MQ0=0;MQ0Fraction=0.0000;MQM=70.848;MQRankSum=0.137;NS=1058;RA=3415;RL=3;RPP=149.49;RR=76;RUN=1;ReadPosRankSum=-12.116;SAB=0.44304;SAF=35;SAP=5.2367;SAR=44;SRB=0.43572;SRF=1488;SRP=125.55;SRR=1927;VQSLOD=3.8910;set=filterInVQSR-2of5;sumGLbyD=4.88
+20	2771621	rs11479849	GT	G,GTT	1605.60	PASS	AA=80;AB=0.79825;ABA=69;ABP=267.24;ABR=273;AC=79,91;AF=0.06551,0.07546;AN=1206;BL=2593;BR=3805;BVAR;BaseQRankSum=7.825;DB;DP=9790;Dels=0.04;EL=37;EPP=3.9875;ER=43;FR;FS=4.751;HETAR=62;HOMA=5;HOMR=958;HP=11;HR=11;HRun=11;HU=T;INS;InbreedingCoeff=0.2646;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.18943;LRBP=501.57;MQ0=0;MQ0Fraction=0.0000;MQM=52.45;MQRankSum=-0.560;NF;NR;NS=1025;PP;RA=3949;RL=29;RPP=16.148;RR=51;RUN=1;ReadPosRankSum=-2.397;SAB=0.525;SAF=42;SAP=3.4446;SAR=38;SC=TCATTTTAACGTTTTTTTTTT;SRB=0.54368;SRF=2147;SRP=68.46;SRR=1802;TC;TR=11;TU=T;VQSLOD=3.5989;set=filterInVQSR-2of5;sumGLbyD=3.92
+20	2891235	.	G	GT,GTTT	2869.87	PASS	AC=236,246;AF=0.2803,0.2922;AN=842;BaseQRankSum=8.979;DP=1067;FS=3.911;HaplotypeScore=20.3595;InbreedingCoeff=0.6511;IndelType=MULTIALLELIC_INDEL;MQ=44.86;MQ0=114;MQ0Fraction=0.1068;MQRankSum=-2.273;QD=4.00;ReadPosRankSum=-6.601;SB=-991.85;VQSLOD=5.4379;set=VQSR
+20	3033550	.	TGAG	T	2005.90	PASS	AA=34;AB=0.51429;ABA=34;ABP=3.1344;ABR=36;AC=22;AF=0.0332;AN=662;BL=1374;BR=1649;BVAR;BaseQRankSum=5.192;DEL;DP=14639;DP4=2271,1492,12,21;Dels=0.02;EL=19;EPP=4.0322;ER=15;FR;FS=16.657;HETAR=17;HOMA=0;HOMR=914;HP=1;HPLen=1;HR=1;HRun=0;HU=G;INDEL;InbreedingCoeff=-0.0454;IndelType=DEL.NumRepetitions_1.EventLength_3.;LEN=3;LRB=0.090969;LRBP=57.333;MQ=53.99;MQ0Fraction=0.0304;MQM=46.735;MQRankSum=1.938;NF;NR;NS=931;PP;PV4=0.0068,9.4e-05,1,1;RA=2985;RL=11;RPP=12.207;RR=23;RUN=1;ReadPosRankSum=-0.466;SAB=0.41176;SAF=14;SAP=5.3095;SAR=20;SC=CTTGGGAGGCTGAGGTGGGAG;SRB=0.62781;SRF=1874;SRP=426.52;SRR=1111;TC;TR=1;TU=G;VQSLOD=8.9194;set=Intersection;sumGLbyD=24.41
+20	3873327	rs61519218	A	AAG	683.85	PASS	AC=25;AF=0.0313;AN=800;BaseQRankSum=4.839;DB;DP=1718;FS=4.265;HRun=0;HaplotypeScore=20.5789;InbreedingCoeff=0.1055;IndelType=INS.NOVEL_2.;MQ=53.70;MQ0=37;MQ0Fraction=0.0215;MQRankSum=2.468;QD=6.30;ReadPosRankSum=4.254;SB=-403.21;VQSLOD=6.1858;set=VQSR
+20	4028835	.	GC	G	2511.30	PASS	AA=66;AB=0.56954;ABA=65;ABP=9.3521;ABR=86;AC=22;AF=0.01836;AN=1198;BL=2303;BR=2463;BVAR;BaseQRankSum=7.621;DEL;DP=22795;DP4=1714,2774,22,37;Dels=0.02;EL=34;EPP=3.1419;ER=32;FQ=999;FR;FS=2.095;HETAR=21;HOMA=0;HOMR=1050;HP=2;HPLen=2;HR=2;HRun=2;HU=C;INDEL;InbreedingCoeff=0.0125;IndelType=DEL.NumRepetitions_2.EventLength_1.RepeatExpansion_C.;LEN=1;LRB=0.033571;LRBP=14.674;MQ=108.09;MQ0=0;MQ0Fraction=0.0000;MQM=53.318;MQRankSum=5.257;NF;NR;NS=1071;PP;PV4=1,5.4e-13,1,0.075;RA=6185;RL=36;RPP=4.1947;RR=30;RUN=1;ReadPosRankSum=-1.059;SAB=0.45455;SAF=30;SAP=4.1947;SAR=36;SC=TGCTGTCACTGCCTTCTCCTA;SRB=0.42118;SRF=2605;SRP=336.76;SRR=3580;TC;TR=2;TU=C;VQSLOD=10.2409;set=Intersection;sumGLbyD=12.71
+20	4039609	rs67812039	G	GA	43457	PASS	AA=909;AB=0.54639;ABA=572;ABP=26.583;ABR=689;AC=302;AF=0.3455;AN=874;BL=37070;BR=38211;BVAR;BaseQRankSum=20.147;DB;DP=25595;DP4=1483,1374,528,542;Dels=0.00;EL=467;EPP=4.5033;ER=442;FQ=999;FR;FS=5.441;HETAR=243;HOMA=127;HOMR=608;HP=4;HPLen=3;HR=3;HRun=3;HU=A;INDEL;INS;InbreedingCoeff=0.1388;IndelType=INS.NumRepetitions_3.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.015157;LRBP=40.563;MQ=119.50;MQ0=0;MQ0Fraction=0.0000;MQM=83.197;MQRankSum=1.080;NF;NR;NS=978;PP;PV4=0.16,1,3.6e-12,1;RA=3033;RL=443;RPP=4.274;RR=466;RUN=1;ReadPosRankSum=-1.000;SAB=0.32233;SAF=293;SAP=252.24;SAR=616;SC=TATGTTGGGAGAAATATCAGT;SRB=0.38378;SRF=1164;SRP=358.85;SRR=1869;TC;TR=4;TU=AG;VQSLOD=9.9146;dbSNP=130;set=Intersection;sumGLbyD=16.79
+20	4390056	.	TC	T	49312	PASS	AA=91;AB=0.94353;ABA=86;ABP=2605.4;ABR=1437;AC=39;AF=0.03160;AN=1234;BL=6823;BR=731;BVAR;BaseQRankSum=2.727;DEL;DP=13149;Dels=0.00;EL=41;EPP=4.9431;ER=50;FS=4.002;HETAR=465;HOMA=313;HOMR=292;HRun=3;InbreedingCoeff=0.0326;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;LEN=1;LRB=0.80646;LRBP=10671;MQ0=0;MQ0Fraction=0.0000;MQM=69.824;MQRankSum=-0.903;NS=1073;RA=3078;RL=89;RPP=183.62;RR=2;RUN=1;ReadPosRankSum=-12.526;SAB=0.45055;SAF=41;SAP=4.9431;SAR=50;SRB=0.52567;SRF=1618;SRP=20.622;SRR=1460;VQSLOD=4.3235;set=Intersection;sumGLbyD=3.53
+20	4474622	.	TA	T,TAA,TAAA,TAAAA	94522.28	PASS	ABR=114;AC=38,68,16,900;AF=0.03333,0.05965,0.01404,0.78947;AN=1140;BVAR;BaseQRankSum=9.741;DB;DP=16656;Dels=0.00;FR;FS=2.355;HOMA=3;HOMR=936;HP=10;HPLen=10;HR=10;HRun=10;HU=A;INS;InbreedingCoeff=0.4516;IndelType=MULTIALLELIC_INDEL;MQ0=2;MQ0Fraction=0.0008;MQRankSum=-4.096;NF;NR;NS=980;PP;RA=3766;RUN=1;ReadPosRankSum=2.380;SC=AGAAAAAAATTAAAAAAAAAA;SRB=0.49734;SRF=1873;SRP=3.2409;SRR=1893;TC;TR=10;TU=A;VQSLOD=8.8186;set=Intersection;sumGLbyD=38.79
+20	4824911	.	AC	A	41998.70	PASS	AC=1172;AF=0.97342;AN=1204;BaseQRankSum=8.604;DP=3615;FS=9.934;HRun=1;HaplotypeScore=39.6843;InbreedingCoeff=0.0980;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;MQ=129.80;MQ0=1;MQ0Fraction=0.0003;MQRankSum=3.378;QD=11.62;ReadPosRankSum=6.967;SB=-16955.28;VQSLOD=4.2689;set=VQSR
+20	4839897	rs35881880	TAA	T,TA,TAAA,TAAAAA	3906.80	PASS	AC=12,95,137,189;AF=0.01024,0.08106,0.11689,0.16126;AN=1172;BVAR;BaseQRankSum=15.271;DB;DEL;DP=15105;Dels=0.04;FR;FS=43.567;HP=19;HR=13;HRun=13;HU=A;INS;InbreedingCoeff=0.5716;IndelType=MULTIALLELIC_INDEL;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-2.569;NF;NR;PP;RUN=1;ReadPosRankSum=-13.794;SC=TGTTAAAAAATAAAAAAAAAA;TC;TR=13;TU=A;VQSLOD=8.1773;set=Intersection;sumGLbyD=3.77
+20	5507414	.	G	GCC	439.08	PASS	AC=23;AF=0.01876;AN=1226;BaseQRankSum=3.051;DP=3023;FS=3.636;HRun=1;HaplotypeScore=30.3104;InbreedingCoeff=0.0204;IndelType=INS.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;MQ=112.09;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-2.065;QD=2.85;ReadPosRankSum=-2.709;SB=-302.22;VQSLOD=4.4311;set=VQSR
+20	5609676	.	GA	G,GAA	799.89	PASS	AA=42;AB=0.79096;ABA=37;ABP=133.16;ABR=140;AC=43,65;AF=0.03607,0.05453;AF1=0.02826;AN=1192;BL=1360;BR=2334;BVAR;BaseQRankSum=5.069;CI95=0.01242,0.04037;DP=15610;DP4=1548,2441,21,30;Dels=0.02;EL=18;EPP=4.8716;ER=24;FQ=12.1;FR;FS=0.000;HETAR=36;HOMA=1;HOMR=991;HP=13;HPLen=10;HR=10;HRun=10;HU=A;INDEL;INS;InbreedingCoeff=0.2001;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.26367;LRBP=560.68;MQ=63.29;MQ0Fraction=0.0003;MQM=44.143;MQRankSum=1.755;NF;NR;NS=1028;PP;PV4=0.77,1,0.0087,0.0053;RA=4114;RL=15;RPP=10.455;RR=27;RUN=1;ReadPosRankSum=-2.978;SAB=0.5;SAF=21;SAP=3.0103;SAR=21;SC=AAAAAAGAAAGAAAAAAAAAA;SRB=0.39742;SRF=1635;SRP=379;SRR=2479;TC;TR=11;TU=AAAG;VQSLOD=4.1229;set=filterInVQSR-2of5;sumGLbyD=7.95
+20	5736211	rs35303106	CT	C,CTT	4384.40	PASS	AA=117;AB=0.71499;ABA=116;ABP=166.4;ABR=291;AC=32,145;AF=0.02712,0.12288;AN=1180;BL=5556;BR=4901;BVAR;BaseQRankSum=2.708;DB;DP=9157;Dels=0.01;EL=54;EPP=4.5136;ER=63;FR;FS=2.802;HETAR=79;HOMA=1;HOMR=837;HP=16;HR=11;HRun=11;HU=T;INS;InbreedingCoeff=0.1903;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.062637;LRBP=92.1;MQ0Fraction=0.0273;MQM=48.932;MQRankSum=3.654;NF;NR;NS=917;PP;RA=2785;RL=79;RPP=34.209;RR=38;RUN=1;ReadPosRankSum=0.795;SAB=0.5641;SAF=66;SAP=7.1862;SAR=51;SC=TTTTCTTTTTCTTTTTTTTTT;SRB=0.41795;SRF=1164;SRP=165.85;SRR=1621;TC;TR=11;TU=T;VQSLOD=5.0895;set=Intersection;sumGLbyD=4.66
+20	5898626	rs34483659	CAAA	C,CA,CAA,CAAAAA	1140.16	PASS	ABR=34;AC=19,98,56,199;AF=0.0227,0.1172,0.0670,0.2380;AF1=0.08519;BVAR;BaseQRankSum=5.049;CI95=0.03727,0.1273;DB;DEL;DP=5091;DP4=539,408,121,123;FQ=4.43;FR;FS=5.701;HOMA=64;HOMR=156;HP=19;HR=18;HU=A;HaplotypeScore=11.5333;INDEL;InbreedingCoeff=0.7405;IndelType=MULTIALLELIC_INDEL;MQ0=117;MQ0Fraction=0.0986;MQRankSum=6.290;NF;NR;NS=240;PP;PV4=0.043,1,1,0.0087;QD=1.22;RA=204;RUN=1;ReadPosRankSum=-2.684;SB=-1015.09;SC=ACTAAAAATACAAAAAAAAAA;SRB=0.35294;SRF=72;SRP=41.33;SRR=132;TC;TR=18;TU=A;VQSLOD=4.1696;set=filterInVQSR-2of5
+20	5975126	rs10541892	C	CAG	504.78	PASS	AC=79;AF=0.07004;AN=1128;BaseQRankSum=10.498;DB;DP=2050;FS=38.228;HRun=0;HaplotypeScore=14.1426;InbreedingCoeff=-0.0053;IndelType=INS.NOVEL_2.;MQ=60.40;MQ0=80;MQ0Fraction=0.0390;MQRankSum=5.098;QD=1.63;ReadPosRankSum=-4.851;SB=-590.69;VQSLOD=4.8517;set=VQSR
+20	6040983	rs11087710	A	AAAAAAGAG,AAAAAGAG,AAAAGAG,AAAAGAGAG,AAAGAG,AAAGAGAG,AAGAG,AAGAGAG,AG,AGAG,AGAGAG	66894.55	PASS	ABR=468;AC=80,9,20,136,31,91,33,29,9,3,5;AF=0.0980,0.0110,0.0245,0.1667,0.0380,0.1115,0.0404,0.0355,0.0110,0.0037,0.0061;AN=816;BVAR;BaseQRankSum=-12.470;DB;DP=38726;DP4=426,611,310,472;Dels=0.00;FQ=999;FR;FS=6.635;HOMA=110;HOMR=506;HP=14;HR=15;HRun=0;HU=A;INDEL;INS;InbreedingCoeff=0.8291;IndelType=MULTIALLELIC_INDEL;KGPilot123;MQ=54.22;MQ0Fraction=0.0168;MQRankSum=-5.329;NF;NR;NS=861;PP;PV4=0.56,1,6.9e-09,0.31;RA=1828;RUN=1;ReadPosRankSum=-7.857;SC=AAAAAAAAAAAAGAGAGAGAG;SRB=0.62418;SRF=1141;SRP=247.85;SRR=687;TC;TR=15;TU=A;VQSLOD=9.0574;dbSNP=131;set=Intersection;sumGLbyD=36.72
+20	7024548	.	G	GAT	5041.27	PASS	AC=123;AF=0.10336;AN=1190;BaseQRankSum=23.097;DP=3045;FS=7.979;HRun=0;HaplotypeScore=15.6967;InbreedingCoeff=0.1062;IndelType=INS.NumRepetitions_5.EventLength_2.RepeatExpansion_AT.;MQ=119.29;MQ0=2;MQ0Fraction=0.0007;MQRankSum=-3.725;QD=8.97;ReadPosRankSum=-1.636;SB=-2257.45;VQSLOD=5.9332;set=VQSR
+20	7484554	.	A	AT	5.09	PASS	AC=0;AF=0.0000;AN=710;BaseQRankSum=-0.696;DP=1862;FS=2.835;HRun=9;HaplotypeScore=13.5425;InbreedingCoeff=0.0567;IndelType=INS.NumRepetitions_9.EventLength_1.RepeatExpansion_T.;MQ=76.92;MQ0=0;MQ0Fraction=0.0000;MQRankSum=1.932;ReadPosRankSum=-1.701;VQSLOD=4.3156;set=VQSR
+20	7632194	rs77286341	GAA	AAA,G	5324	PASS	AC=0;AF=0.0000;AN=700;BaseQRankSum=-1.741;DB;DP=1772;FR;HP=4;HPLen=3;HR=3;HRun=0;HU=A;HaplotypeScore=60.1795;InbreedingCoeff=0.0017;IndelType=MIXED;MQ=70.69;MQ0=13;MQ0Fraction=0.0073;MQRankSum=-1.315;NF;NR;PP;ReadPosRankSum=-3.650;SC=GAGAGAGAGAGAAAGGTGTAA;TC;TR=13;TU=AG;set=filterInVQSR-2of5
+20	7767508	rs71329674	G	GA	17914	PASS	AA=415;AB=0.61617;ABA=337;ABP=105.94;ABR=541;AC=141;AF=0.11614;AN=1214;BL=15187;BR=20323;BVAR;BaseQRankSum=-13.946;DB;DP=28222;Dels=0.00;EL=184;EPP=14.569;ER=231;FQ=999;FR;FS=13.296;HETAR=178;HOMA=35;HOMR=822;HP=14;HPLen=9;HR=9;HRun=9;HU=A;INDEL;INS;InbreedingCoeff=0.0714;IndelType=INS.NumRepetitions_9.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.14464;LRBP=1616.1;MQ=89.69;MQ0=1;MQ0Fraction=0.0003;MQM=51.667;MQRankSum=0.664;NF;NR;NS=1035;PP;RA=3707;RL=171;RPP=30.894;RR=244;RUN=1;ReadPosRankSum=-1.120;SAB=0.45301;SAF=188;SAP=10.969;SAR=227;SC=ATTCTAAAAAGAAAAAAAAAT;SRB=0.38495;SRF=1427;SRP=429.23;SRR=2280;TC;TR=9;TU=A;VQSLOD=9.0748;set=Intersection;sumGLbyD=11.09
+20	7920261	.	TA	T,TAA	802.15	PASS	AA=28;AB=0.8;ABA=28;ABP=112.45;ABR=112;AC=22,39;AF=0.01836,0.03255;AN=1198;BL=943;BR=1487;BVAR;BaseQRankSum=2.233;DP=10645;Dels=0.01;EL=11;EPP=5.8022;ER=17;FR;FS=1.691;HETAR=20;HOMA=0;HOMR=1007;HP=10;HPLen=9;HR=9;HRun=9;HU=A;INS;InbreedingCoeff=0.2256;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.22387;LRBP=267.46;MQ0=0;MQ0Fraction=0.0000;MQM=57.571;MQRankSum=0.940;NF;NR;NS=1027;PP;RA=4776;RL=8;RPP=14.178;RR=20;RUN=1;ReadPosRankSum=-1.567;SAB=0.53571;SAF=15;SAP=3.3205;SAR=13;SC=GTAACTGCTATAAAAAAAAAC;SRB=0.48576;SRF=2320;SRP=11.42;SRR=2456;TC;TR=9;TU=A;VQSLOD=4.0815;set=filterInVQSR-2of5;sumGLbyD=5.37
+20	8012465	rs10595338	TATGA	T	2104.41	PASS	AF=0.03339;BaseQRankSum=10.662;DB;DP=11772;DS;Dels=0.01;FR;FS=7.678;HP=1;HPLen=1;HR=1;HRun=0;HU=A;InbreedingCoeff=0.0266;IndelType=DEL.NumRepetitions_1.EventLength_4.;MQ0Fraction=0.0731;MQRankSum=0.603;NF;NR;PP;ReadPosRankSum=1.276;SC=TGTATGTATGTATGATGTATG;TC;TR=19;TU=ATGT;VQSLOD=4.1376;set=filterInVQSR-2of5;sumGLbyD=6.53
+20	8573999	.	CGTGT	C,CGT,CGTGTGT,TGTGT	45865.96	PASS	AC=458,0,731;AF=0.37727,0.00000,0.60214;AN=1214;BVAR;BaseQRankSum=-6.703;DEL;DP=37714;Dels=0.03;FR;FS=11.079;HP=2;HPLen=1;HR=1;HRun=0;HU=G;INDEL;INS;InbreedingCoeff=0.7632;IndelType=MIXED;LEN=2;MQ0Fraction=0.0026;MQRankSum=-1.394;NF;NR;PP;RUN=1;ReadPosRankSum=-2.102;SC=TGTGTGTGCGCGTGTGTGTGT;TC;TR=18;TU=GT;VQSLOD=6.1435;set=Intersection;sumGLbyD=3.53
+20	8610455	rs10571111	TTTTC	T	11763.51	PASS	AC=190;AF=0.17056;AN=1114;BaseQRankSum=-14.397;DB;DP=2323;FS=2.321;HRun=0;HaplotypeScore=39.8020;InbreedingCoeff=0.2502;IndelType=DEL.NumRepetitions_2.EventLength_4.;MQ=53.39;MQ0=104;MQ0Fraction=0.0448;MQRankSum=3.519;QD=19.07;ReadPosRankSum=4.150;SB=-4067.02;VQSLOD=5.0554;set=VQSR
+20	9139079	.	ATT	A,AT,ATTT,ATTTT,ATTTTT	8777.90	PASS	AC=23,140,114,69,113;AF=0.01993,0.12132,0.09879,0.05979,0.09792;AN=1154;BVAR;BaseQRankSum=-0.022;DEL;DP=25109;DP4=502,657,278,313;FR;FS=11.929;HP=16;HR=16;HU=T;HaplotypeScore=20.2361;INDEL;INS;InbreedingCoeff=0.5704;IndelType=MULTIALLELIC_INDEL;MQ0=16;MQ0Fraction=0.0067;MQRankSum=2.624;NF;NR;PP;PV4=0.14,1,1,1;QD=1.48;RUN=1;ReadPosRankSum=-0.480;SB=-2354.28;SC=CACCTGGCTAATTTTTTTTTT;TC;TR=16;TU=T;VQSLOD=6.9180;set=Intersection
+20	9862448	.	CT	C	49312	PASS	AA=60;AB=0.96003;ABA=53;ABP=2440.4;ABR=1273;AC=18;AF=0.01461;AN=1232;BL=3516;BR=140;BVAR;BaseQRankSum=-2.056;DEL;DP=11893;Dels=0.01;EL=35;EPP=6.6294;ER=25;FS=1.787;HETAR=396;HOMA=344;HOMR=334;HRun=1;InbreedingCoeff=0.0379;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.92341;LRBP=6772.5;MQ0Fraction=0.0006;MQM=54.267;MQRankSum=-0.907;NS=1074;RA=2990;RL=60;RPP=133.3;RR=0;RUN=1;ReadPosRankSum=-10.579;SAB=0.58333;SAF=35;SAP=6.6294;SAR=25;SRB=0.47826;SRF=1430;SRP=15.284;SRR=1560;VQSLOD=3.0237;set=filterInVQSR-2of5;sumGLbyD=2.84
+20	9863736	rs73618103	G	GT	50570.21	PASS	AA=2247;AB=0.48878;ABA=1412;ABP=6.0324;ABR=1350;AC=546;AF=0.44463;AN=1228;BL=86886;BR=95862;BVAR;BaseQRankSum=-23.978;DB;DP=32517;DP4=1125,1133,1017,1048;Dels=0.00;EL=1089;EPP=7.6113;ER=1158;FQ=999;FR;FS=2.529;HETAR=445;HOMA=201;HOMR=393;HP=4;HPLen=4;HR=4;HRun=4;HU=T;INDEL;INS;InbreedingCoeff=0.1393;IndelType=INS.NumRepetitions_4.EventLength_1.RepeatExpansion_T.;KGPilot123;LEN=1;LRB=0.049117;LRBP=960.35;MQ=68.10;MQ0=2;MQ0Fraction=0.0006;MQM=50.931;MQRankSum=-1.580;NF;NR;NS=1039;PP;PV4=0.71,1,0.11,1;RA=3139;RL=1089;RPP=7.6113;RR=1158;RUN=1;ReadPosRankSum=0.846;SAB=0.54161;SAF=1217;SAP=36.804;SAR=1030;SC=TGATTGTATGGTTTTGTCCTT;SRB=0.53425;SRF=1677;SRP=34.987;SRR=1462;TC;TR=4;TU=T;VLD;VQSLOD=10.1800;dbSNP=131;set=Intersection;sumGLbyD=18.20
+20	10926959	.	AG	A	12239	PASS	AA=65;AB=0.92801;ABA=64;ABP=1417.6;ABR=825;AC=24;AF=0.0264;AN=908;BL=616;BR=3782;BVAR;BaseQRankSum=9.990;DEL;DP=10708;Dels=0.01;EL=37;EPP=5.7163;ER=28;FS=1.652;HETAR=275;HOMA=70;HOMR=724;HRun=1;InbreedingCoeff=0.0102;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_G.;LEN=1;LRB=0.71987;LRBP=4952;MQ0=1;MQ0Fraction=0.0004;MQM=118.82;MQRankSum=1.018;NS=1069;RA=4746;RL=5;RPP=104.07;RR=60;RUN=1;ReadPosRankSum=-12.039;SAB=0.41538;SAF=27;SAP=7.0526;SAR=38;SRB=0.4764;SRF=2261;SRP=25.968;SRR=2485;VQSLOD=2.9713;set=filterInVQSR-2of5;sumGLbyD=4.10
+20	11299648	.	TG	T	49315	PASS	AA=62;AB=0.95292;ABA=54;ABP=2046.7;ABR=1093;AC=28;AF=0.0373;AN=750;BL=3126;BR=528;BVAR;BaseQRankSum=-4.929;DEL;DP=10764;Dels=0.01;EL=26;EPP=6.5127;ER=36;FS=3.851;HETAR=366;HOMA=383;HOMR=304;HRun=1;InbreedingCoeff=0.0267;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_G.;LEN=1;LRB=0.711;LRBP=4014.1;MQ0=1;MQ0Fraction=0.0005;MQM=76.468;MQRankSum=1.327;NS=1070;RA=2588;RL=54;RPP=77.121;RR=8;RUN=1;ReadPosRankSum=-12.507;SAB=0.48387;SAF=30;SAP=3.1504;SAR=32;SRB=0.47643;SRF=1233;SRP=15.499;SRR=1355;VQSLOD=3.8673;set=filterInVQSR-2of5;sumGLbyD=3.00
+20	11561096	.	CTA	C	999	PASS	AC=2;AF=0.0029;AF1=0.005602;BaseQRankSum=3.190;CI95=0.004425,0.01106;DP=7521;DP4=1998,1794,2,4;Dels=0.00;FQ=999;FR;FS=5.422;HP=3;HPLen=2;HR=1;HRun=0;HU=T;INDEL;InbreedingCoeff=0.0056;IndelType=DEL.NumRepetitions_1.EventLength_2.RepeatExpansion_TA.;MQ=113.88;MQ0=0;MQ0Fraction=0.0000;MQRankSum=0.297;NF;NR;PP;PV4=0.43,0.024,1,1;ReadPosRankSum=1.406;SC=CAATAGTATTCTATGTCAGTC;TC;TR=1;TU=T;VQSLOD=8.6243;set=Intersection;sumGLbyD=21.89
+20	11723671	.	C	CA	1096.60	PASS	AA=35;AB=0.69565;ABA=35;ABP=41.247;ABR=80;AC=10;AF=0.0141;AN=710;BL=2005;BR=1702;BVAR;BaseQRankSum=-3.427;DP=9819;Dels=0.00;EL=20;EPP=4.5614;ER=15;FR;FS=3.814;HETAR=20;HOMA=0;HOMR=1034;HP=8;HPLen=7;HR=7;HRun=7;HU=A;INS;InbreedingCoeff=0.0323;IndelType=INS.NumRepetitions_7.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.081737;LRBP=56.79;MQ0=0;MQ0Fraction=0.0000;MQM=81.057;MQRankSum=0.050;NF;NR;NS=1054;PP;RA=5562;RL=22;RPP=8.0357;RR=13;RUN=1;ReadPosRankSum=-2.012;SAB=0.71429;SAF=25;SAP=16.97;SAR=10;SC=ATATTGAAGACAAAAAAACAG;SRB=0.49371;SRF=2746;SRP=4.9233;SRR=2816;TC;TR=7;TU=A;VQSLOD=7.4342;set=Intersection;sumGLbyD=8.30
+20	12238835	rs113904674	CTCTTCATGGTCT	C	1813.44	PASS	AA=7;AB=0.73077;ABA=7;ABP=15.037;ABR=19;AC=4;AF=0.0056;AN=712;BL=360;BR=368;BVAR;BaseQRankSum=3.891;DB;DEL;DP=10309;Dels=0.00;EL=4;EPP=3.3205;ER=3;FR;FS=0.000;HETAR=3;HOMA=0;HOMR=1076;HP=1;HPLen=2;HR=2;HRun=0;HU=C;InbreedingCoeff=-0.0381;IndelType=DEL.NumRepetitions_1.EventLength_10orMore.;LEN=12;LRB=0.010989;LRBP=3.2012;MQ0=0;MQ0Fraction=0.0000;MQM=37;MQRankSum=-3.793;NF;NR;NS=1079;PP;RA=6085;RL=4;RPP=3.3205;RR=3;RUN=1;ReadPosRankSum=1.319;SAB=0.42857;SAF=3;SAP=3.3205;SAR=4;SC=CTTAATGCTCCTCTTCATGGT;SRB=0.51257;SRF=3119;SRP=11.364;SRR=2966;TC;TR=6;TU=CCT;VQSLOD=5.7551;set=Intersection;sumGLbyD=69.48
+20	12602812	.	AT	A	12344	PASS	AA=47;AB=0.94372;ABA=43;ABP=1309.5;ABR=721;AC=14;AF=0.0196;AN=716;BL=2714;BR=217;BVAR;BaseQRankSum=1.424;DEL;DP=10743;Dels=0.00;EL=24;EPP=3.0565;ER=23;FS=0.629;HETAR=228;HOMA=65;HOMR=769;HRun=1;InbreedingCoeff=0.0233;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.85193;LRBP=4622.3;MQ0Fraction=0.0000;MQM=99.574;MQRankSum=1.901;NS=1080;RA=4839;RL=46;RPP=96.568;RR=1;RUN=1;ReadPosRankSum=-9.906;SAB=0.53191;SAF=25;SAP=3.4261;SAR=22;SRB=0.51106;SRF=2473;SRP=8.148;SRR=2366;VQSLOD=2.8161;set=filterInVQSR-2of5;sumGLbyD=3.67
+20	13600884	.	CTG	C,CTGTG	1278.10	PASS	AA=85;AB=0.77994;ABA=79;ABP=247.38;ABR=280;AC=71,22;AF=0.05907,0.01830;AN=1202;BL=3279;BR=3205;BVAR;BaseQRankSum=8.852;DEL;DP=24185;DP4=1317,931,52,49;Dels=0.03;EL=45;EPP=3.649;ER=40;FQ=999;FR;FS=31.826;HETAR=75;HOMA=4;HOMR=926;HP=2;HPLen=1;HR=1;HRun=0;HU=T;INDEL;InbreedingCoeff=0.1566;IndelType=MULTIALLELIC_INDEL;LEN=2;LRB=0.011413;LRBP=4.8442;MQ=65.06;MQ0Fraction=0.0012;MQM=48.671;MQRankSum=-0.511;NF;NR;NS=1005;PP;PV4=0.18,1,0.39,0.27;RA=3342;RL=35;RPP=8.7583;RR=50;RUN=1;ReadPosRankSum=-2.329;SAB=0.43529;SAF=37;SAP=6.1015;SAR=48;SC=TCCCTTTACTCTGTGTGTGTG;SRB=0.59066;SRF=1974;SRP=241.62;SRR=1368;TC;TR=15;TU=GT;VQSLOD=3.8635;set=filterInVQSR-2of5;sumGLbyD=4.23
+20	13666265	.	T	TATAG	556.88	PASS	AC=21;AF=0.01959;AN=1072;BaseQRankSum=24.958;DP=2706;FS=2.581;HRun=0;HaplotypeScore=25.9952;InbreedingCoeff=0.1419;IndelType=INS.NOVEL_4.;MQ=72.43;MQ0=0;MQ0Fraction=0.0000;MQRankSum=2.888;QD=4.38;ReadPosRankSum=2.552;SB=-417.04;VQSLOD=7.3380;set=VQSR
+20	13861245	rs72422273	C	CTCA	2685.46	PASS	AC=140;AF=0.11589;AN=1208;BaseQRankSum=24.355;DB;DP=2910;FS=6.808;HRun=0;HaplotypeScore=19.3095;InbreedingCoeff=-0.0991;IndelType=INS.NumRepetitions_1.EventLength_3.;MQ=78.25;MQ0=22;MQ0Fraction=0.0076;MQRankSum=3.225;QD=3.64;ReadPosRankSum=2.607;SB=-1861.38;VQSLOD=4.1974;set=VQSR
+20	13865746	.	T	TA,TAA	1416.23	PASS	AA=63;AB=0.80417;ABA=47;ABP=195.87;ABR=193;AC=122,21;AF=0.10133,0.01744;AN=1204;BL=3673;BR=1145;BVAR;BaseQRankSum=-3.336;DP=10513;Dels=0.00;EL=62;EPP=131.27;ER=1;FR;FS=716.583;HETAR=45;HOMA=1;HOMR=998;HP=2;HR=1;HRun=1;HU=A;INS;InbreedingCoeff=0.0814;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.5247;LRBP=2883.3;MQ0=0;MQ0Fraction=0.0000;MQM=56.143;MQRankSum=-1.197;NF;NR;NS=1044;PP;RA=4529;RL=62;RPP=131.27;RR=1;RUN=1;ReadPosRankSum=-12.295;SAB=1;SAF=63;SAP=139.81;SAR=0;SC=GGAACATGGATACCCCCCTGC;SRB=0.52462;SRF=2376;SRP=26.853;SRR=2153;TC;TR=1;TU=A;VQSLOD=-4.2308;set=filterInVQSR-2of5;sumGLbyD=4.77
+20	13881703	.	CTT	C	152.85	PASS	AC=8;AF=0.0093;AN=862;BaseQRankSum=3.941;DP=2063;FS=0.962;HRun=5;HaplotypeScore=24.0313;InbreedingCoeff=0.0790;IndelType=DEL.NumRepetitions_5.EventLength_1.RepeatExpansion_T.;MQ=55.05;MQ0=49;MQ0Fraction=0.0238;MQRankSum=-1.418;QD=3.47;ReadPosRankSum=-0.605;SB=-93.04;VQSLOD=5.3874;set=VQSR
+20	14260090	rs73619828	A	AT	27935	PASS	AA=596;AB=0.59484;ABA=487;ABP=96.922;ABR=715;AC=204;AF=0.17000;AN=1200;BL=21718;BR=28458;BVAR;BaseQRankSum=0.756;DB;DP=23629;DP4=1385,1492,287,328;Dels=0.00;EL=299;EPP=3.0249;ER=297;FQ=999;FR;FS=6.187;HETAR=218;HOMA=38;HOMR=788;HP=9;HPLen=9;HR=9;HRun=9;HU=T;INDEL;INS;InbreedingCoeff=0.0797;IndelType=INS.NumRepetitions_9.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.13433;LRBP=1969;MQ=100.81;MQ0=0;MQ0Fraction=0.0000;MQM=57.084;MQRankSum=2.224;NF;NR;NS=1044;PP;PV4=0.53,1,1.2e-11,1;RA=4143;RL=238;RPP=55.475;RR=358;RUN=1;ReadPosRankSum=0.198;SAB=0.46812;SAF=279;SAP=8.2714;SAR=317;SC=CCTTAAGTTGATTTTTTTTTC;SRB=0.50374;SRF=2087;SRP=3.514;SRR=2056;TC;TR=9;TU=T;VQSLOD=9.0018;set=Intersection;sumGLbyD=10.82
+20	14260558	.	AC	A	238	PASS	AC=1;AF=0.0014;AF1=0.003368;BaseQRankSum=2.868;CI95=0.003106,0.006211;DP=9724;DP4=2075,2329,1,7;Dels=0.00;FQ=106;FR;FS=10.678;HP=1;HPLen=2;HR=2;HRun=1;HU=A;INDEL;InbreedingCoeff=-0.0406;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;MQ=114.37;MQ0=0;MQ0Fraction=0.0000;MQRankSum=0.862;NF;NR;PP;PV4=0.074,0.0096,0.017,1;ReadPosRankSum=-0.042;SC=ATCAGGAATAACTGTGTGACC;TC;TR=2;TU=A;VQSLOD=8.1618;set=Intersection;sumGLbyD=18.65
+20	14425481	.	GTA	G,GTATA	148.85	PASS	AC=43,23;AF=0.03473,0.01858;AN=1238;BaseQRankSum=6.289;DP=25167;DP4=1800,2021,38,49;FR;FS=9.416;HP=2;HPLen=1;HR=1;HU=T;HaplotypeScore=17.7453;INDEL;InbreedingCoeff=0.0995;IndelType=MULTIALLELIC_INDEL;MQ0=21;MQ0Fraction=0.0058;MQRankSum=-0.200;NF;NR;PP;PV4=0.59,1,0.04,0.023;QD=0.35;ReadPosRankSum=-1.689;SB=-367.50;SC=CTGTGTGTGTGTATATATATA;TC;TR=13;TU=AT;VQSLOD=3.5796;set=filterInVQSR-2of5
+20	14943522	rs11478299	GA	AA,G	1761.24	PASS	AA=117;AB=0.68142;ABA=108;ABP=99.919;ABR=231;AC=0;AF=0.0000;AF1=0.04204;AN=712;BL=4931;BR=5802;BVAR;BaseQRankSum=9.118;CI95=0.02876,0.05752;DB;DEL;DP=13717;DP4=1908,1684,59,58;Dels=0.05;EL=60;EPP=3.1773;ER=57;FQ=81.9;FR;HETAR=56;HOMA=1;HOMR=1011;HP=8;HPLen=8;HR=8;HU=A;INDEL;InbreedingCoeff=0.1264;IndelType=MIXED;LEN=1;LRB=0.081152;LRBP=156.5;MQ=106.93;MQ0=0;MQ0Fraction=0.0000;MQM=96.855;MQRankSum=1.619;NF;NR;NS=1068;PP;PV4=0.57,1,0.0003,1;QD=7.40;RA=5080;RL=56;RPP=3.4743;RR=61;RUN=1;ReadPosRankSum=0.814;SAB=0.52137;SAF=61;SAP=3.4743;SAR=56;SB=-1122.51;SC=GTTGTTTGGGGAAAAAAAACT;SRB=0.51083;SRF=2595;SRP=8.1825;SRR=2485;TC;TR=8;TU=A;set=filterInVQSR-2of5;sumGLbyD=9.81
+20	14974486	.	A	AG	4101.40	PASS	AA=57;AB=0.57143;ABA=51;ABP=8.2839;ABR=68;AC=22;AF=0.01846;AN=1192;BL=2286;BR=2834;BVAR;BaseQRankSum=8.711;DP=20538;DP4=2172,2100,19,13;Dels=0.00;EL=32;EPP=4.877;ER=25;FS=0.517;HETAR=20;HOMA=4;HOMR=1027;HRun=1;INDEL;INS;InbreedingCoeff=0.0677;IndelType=INS.NOVEL_1.Novel_G.;LEN=1;LRB=0.10703;LRBP=130.37;MQ=126.07;MQ0=0;MQ0Fraction=0.0000;MQM=56.088;MQRankSum=-10.756;NS=1051;PV4=0.38,3.5e-51,7.9e-34,1;RA=5203;RL=26;RPP=3.9627;RR=31;RUN=1;ReadPosRankSum=1.283;SAB=0.54386;SAF=31;SAP=3.9627;SAR=26;SRB=0.51816;SRF=2696;SRP=17.918;SRR=2507;VQSLOD=8.0072;set=Intersection;sumGLbyD=25.60
+20	15111137	.	GA	G	13533	PASS	AA=98;AB=0.84864;ABA=89;ABP=623.8;ABR=499;AC=47;AF=0.03796;AN=1238;BL=5324;BR=856;BVAR;BaseQRankSum=-11.577;DEL;DP=13384;Dels=0.01;EL=53;EPP=4.4284;ER=45;FS=6.099;HETAR=219;HOMA=845;HOMR=18;HRun=1;InbreedingCoeff=-0.0056;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.72298;LRBP=7017.4;MQ0Fraction=0.0003;MQM=90.449;MQRankSum=1.408;NS=1083;RA=590;RL=87;RPP=130.99;RR=11;RUN=1;ReadPosRankSum=-18.074;SAB=0.55102;SAF=54;SAP=5.2261;SAR=44;SRB=0.52373;SRF=309;SRP=5.8958;SRR=281;VQSLOD=4.1054;set=filterInVQSR-2of5;sumGLbyD=3.06
+20	15283028	.	A	AC,ACACACACACACAC	140844.83	PASS	AA=180;AB=0.61442;ABA=123;ABP=39.285;ABR=196;AC=13,817;AF=0.01111,0.69829;AN=1170;BL=4453;BR=11407;BVAR;BaseQRankSum=24.686;DP=6365;Dels=0.00;EL=124;EPP=58.793;ER=56;FR;FS=10.912;HETAR=87;HOMA=48;HOMR=683;HP=1;HR=1;HRun=1;HU=T;INS;InbreedingCoeff=0.2074;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.43846;LRBP=6624;MQ0Fraction=0.0558;MQM=38.211;MQRankSum=-21.111;NF;NR;NS=818;PP;RA=1732;RL=0;RPP=393.88;RR=180;RUN=1;ReadPosRankSum=-7.620;SAB=0.31111;SAF=56;SAP=58.793;SAR=124;SC=ACACACACACATACACACATA;SRB=0.54042;SRF=936;SRP=27.584;SRR=796;TC;TR=21;TU=AC;VQSLOD=4.7569;set=Intersection;sumGLbyD=18.36
+20	15361056	.	ATAACT	A	4892.81	PASS	AA=59;AB=0.63576;ABA=55;ABP=27.184;ABR=96;AC=34;AF=0.0487;AN=698;BL=3164;BR=1999;BVAR;BaseQRankSum=3.391;DEL;DP=7080;Dels=0.03;EL=27;EPP=3.9304;ER=32;FR;FS=4.816;HETAR=35;HOMA=6;HOMR=966;HP=2;HPLen=3;HR=3;HRun=0;HU=A;InbreedingCoeff=0.0785;IndelType=DEL.NumRepetitions_1.EventLength_5.;LEN=5;LRB=0.22564;LRBP=573.84;MQ0=0;MQ0Fraction=0.0000;MQM=70.034;MQRankSum=-8.732;NF;NR;NS=1008;PP;RA=3915;RL=42;RPP=26.013;RR=17;RUN=1;ReadPosRankSum=-0.735;SAB=0.44068;SAF=26;SAP=4.8137;SAR=33;SC=AGATTAGGAAATAACTTAGGG;SRB=0.42682;SRF=1671;SRP=185.12;SRR=2244;TC;TR=3;TU=A;VQSLOD=7.0900;set=Intersection;sumGLbyD=43.38
+20	15579507	.	AATTAGTC	A,TATTAGTC	1936.38	PASS	AA=16;AB=0.58974;ABA=16;ABP=5.7386;ABR=23;AC=64;AF=0.05229;AN=1224;BL=699;BR=775;BVAR;BaseQRankSum=-21.390;DEL;DP=21920;DP4=2099,2403,6,6;Dels=0.00;EL=8;EPP=3.0103;ER=8;FR;FS=2.920;HETAR=5;HOMA=0;HOMR=1063;HP=3;HPLen=4;HR=4;HU=A;INDEL;InbreedingCoeff=-0.0143;IndelType=MIXED;LEN=7;LRB=0.05156;LRBP=11.519;MQ=129.49;MQ0=0;MQ0Fraction=0.0000;MQM=51.938;MQRankSum=3.331;NF;NR;NS=1068;PP;PV4=1,0.019,1.3e-07,1;RA=5334;RL=5;RPP=7.8961;RR=11;RUN=1;ReadPosRankSum=-16.901;SAB=0.4375;SAF=7;SAP=3.5532;SAR=9;SC=CATACTACAAAATTAGTCATT;SRB=0.41695;SRF=2224;SRP=322.58;SRR=3110;TC;TR=4;TU=A;VQSLOD=3.2237;set=filterInVQSR-2of5;sumGLbyD=43.57
+20	15752535	.	CT	C,GT	3775.20	PASS	AA=92;AB=0.78636;ABA=47;ABP=159.71;ABR=173;AC=0;AF=0.0000;AN=608;BL=4955;BR=2380;BVAR;BaseQRankSum=2.910;DEL;DP=3429;Dels=0.04;EL=13;EPP=105.82;ER=79;FR;HETAR=92;HOMA=95;HOMR=544;HP=2;HPLen=2;HR=2;HU=T;InbreedingCoeff=0.0483;IndelType=MIXED;LEN=1;LRB=0.35106;LRBP=1966;MQ0Fraction=0.0232;MQM=35.293;MQRankSum=-2.199;NF;NR;NS=732;PP;QD=4.91;RA=1272;RL=81;RPP=118.66;RR=11;RUN=1;ReadPosRankSum=-1.077;SAB=0.021739;SAF=2;SAP=185.79;SAR=90;SB=-59.51;SC=CAAGACCATCCTTGGCTAACA;SRB=0.14623;SRF=186;SRP=1385.8;SRR=1086;TC;TR=2;TU=T;set=filterInVQSR-2of5;sumGLbyD=9.70
+20	15883060	rs73619850	A	AT	1325.60	PASS	AA=38;AB=0.59302;ABA=35;ABP=9.4742;ABR=51;AC=14;AF=0.0156;AN=896;BL=1078;BR=1638;BVAR;BaseQRankSum=-4.526;DB;DP=19854;DP4=1632,1800,15,20;Dels=0.00;EL=18;EPP=3.2389;ER=20;FR;FS=0.000;HETAR=14;HOMA=1;HOMR=1014;HP=1;HPLen=1;HR=1;HRun=1;HU=T;INDEL;INS;InbreedingCoeff=-0.0131;IndelType=INS.NumRepetitions_1.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.20619;LRBP=253.74;MQ=118.40;MQ0=0;MQ0Fraction=0.0000;MQM=56.526;MQRankSum=0.892;NF;NR;NS=1029;PP;PV4=0.61,1,0.25,0.14;RA=4439;RL=14;RPP=8.7247;RR=24;RUN=1;ReadPosRankSum=-2.061;SAB=0.42105;SAF=16;SAP=5.0675;SAR=22;SC=GGATTGGCAGATAAAAAATGG;SRB=0.46429;SRF=2061;SRP=52.168;SRR=2378;TC;TR=1;TU=T;VQSLOD=9.7576;set=Intersection;sumGLbyD=15.69
+20	16122099	.	GA	G	12914	PASS	AA=85;AB=0.85915;ABA=80;ABP=639.4;ABR=488;AC=19;AF=0.01542;AN=1232;BL=805;BR=5457;BVAR;BaseQRankSum=-6.084;DEL;DP=13592;Dels=0.00;EL=45;EPP=3.649;ER=40;FS=0.935;HETAR=218;HOMA=841;HOMR=14;HRun=2;InbreedingCoeff=0.0250;IndelType=DEL.NumRepetitions_2.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.74289;LRBP=7507.5;MQ0=0;MQ0Fraction=0.0000;MQM=103.01;MQRankSum=2.843;NS=1075;RA=541;RL=2;RPP=170.62;RR=83;RUN=1;ReadPosRankSum=-16.222;SAB=0.49412;SAF=42;SAP=3.0358;SAR=43;SRB=0.44917;SRF=243;SRP=15.152;SRR=298;VQSLOD=3.9745;set=filterInVQSR-2of5;sumGLbyD=2.97
+20	16828509	.	G	GT	843.62	PASS	AA=30;AB=0.70103;ABA=29;ABP=37.06;ABR=68;AC=10;AF=0.0140;AN=714;BL=1368;BR=1786;BVAR;BaseQRankSum=-4.061;DP=8682;Dels=0.01;EL=14;EPP=3.2998;ER=16;FR;FS=2.681;HETAR=22;HOMA=1;HOMR=1020;HP=8;HPLen=8;HR=8;HRun=8;HU=T;INS;InbreedingCoeff=0.1389;IndelType=INS.NumRepetitions_8.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.13253;LRBP=123.3;MQ0=0;MQ0Fraction=0.0000;MQM=62.8;MQRankSum=-1.491;NF;NR;NS=1043;PP;RA=4416;RL=11;RPP=7.6428;RR=19;RUN=1;ReadPosRankSum=-1.718;SAB=0.76667;SAF=23;SAP=21.54;SAR=7;SC=CCTTCAAAAGGTTTTTTTTGG;SRB=0.5745;SRF=2537;SRP=215.91;SRR=1879;TC;TR=8;TU=T;VQSLOD=7.6258;set=Intersection;sumGLbyD=10.77
+20	17470034	.	GC	G	46975	PASS	AA=57;AB=0.96043;ABA=52;ABP=2422.5;ABR=1262;AC=34;AF=0.02773;AN=1226;BL=418;BR=3446;BVAR;BaseQRankSum=-6.250;DEL;DP=12035;Dels=0.00;EL=22;EPP=9.4485;ER=35;FS=1.350;HETAR=416;HOMA=409;HOMR=244;HRun=1;InbreedingCoeff=0.0083;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;LEN=1;LRB=0.78364;LRBP=5155.6;MQ0=0;MQ0Fraction=0.0000;MQM=99.509;MQRankSum=2.192;NS=1076;RA=2396;RL=5;RPP=87.164;RR=52;RUN=1;ReadPosRankSum=-15.199;SAB=0.5614;SAF=32;SAP=4.877;SAR=25;SRB=0.52963;SRF=1269;SRP=21.285;SRR=1127;VQSLOD=3.8440;set=filterInVQSR-2of5;sumGLbyD=3.06
+20	17471374	.	AGCGGC	A	850.03	PASS	AC=6;AF=0.0085;AF1=0.01301;AN=704;BaseQRankSum=6.259;CI95=0.00885,0.01991;DP=8180;DP4=2215,1878,4,5;Dels=0.01;FQ=131;FS=0.000;HRun=0;INDEL;InbreedingCoeff=0.0009;IndelType=DEL.NumRepetitions_1.EventLength_5.;MQ=104.41;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-5.521;PV4=0.74,0.37,0.0005,1;ReadPosRankSum=2.468;VQSLOD=6.8773;set=Intersection;sumGLbyD=30.85
+20	18433202	rs35582929	G	GA	2506.90	PASS	AA=55;AB=0.5812;ABA=49;ABP=9.7103;ABR=68;AC=20;AF=0.0218;AN=918;BL=2263;BR=2175;BVAR;BaseQRankSum=-6.639;DB;DP=19467;DP4=1845,2365,27,26;Dels=0.00;EL=21;EPP=9.6826;ER=34;FQ=999;FR;FS=5.633;HETAR=16;HOMA=3;HOMR=1045;HP=2;HPLen=3;HR=3;HRun=1;HU=G;INDEL;INS;InbreedingCoeff=0.0700;IndelType=INS.NumRepetitions_1.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.019829;LRBP=6.7994;MQ=114.03;MQ0=0;MQ0Fraction=0.0000;MQM=83.345;MQRankSum=1.610;NF;NR;NS=1064;PP;PV4=0.33,1,1,1;RA=5380;RL=28;RPP=3.0498;RR=27;RUN=1;ReadPosRankSum=0.873;SAB=0.47273;SAF=26;SAP=3.3656;SAR=29;SC=TATTTCATGGGAGCATTAAAA;SRB=0.42862;SRF=2306;SRP=241.07;SRR=3074;TC;TR=3;TU=G;VQSLOD=10.0372;dbSNP=126;set=Intersection;sumGLbyD=13.10
+20	18551314	rs10659122	CA	C,CAA,CAAA,CAAAA,CAAAAA	18810.74	PASS	ABR=243;AC=19,169,216,164,188;AF=0.01816,0.16157,0.20650,0.15679,0.17973;BVAR;BaseQRankSum=-5.742;DB;DP=17637;DP4=136,77,560,237;FR;FS=2.693;HOMA=177;HOMR=299;HP=17;HR=17;HU=A;HaplotypeScore=15.5048;INDEL;INS;InbreedingCoeff=0.8901;IndelType=MULTIALLELIC_INDEL;MQ0=11;MQ0Fraction=0.0069;MQRankSum=1.845;NF;NR;NS=658;PP;PV4=0.08,1,1,1;QD=12.66;RA=673;RUN=1;ReadPosRankSum=0.283;SB=-3514.45;SC=GATTCCATCTCAAAAAAAAAA;SRB=0.63596;SRF=428;SRP=111.06;SRR=245;TC;TR=17;TU=A;VQSLOD=10.6964;dbSNP=130;set=Intersection
+20	18785519	.	G	GTC	415.55	PASS	AC=28;AF=0.0400;AN=700;BaseQRankSum=10.889;DP=1929;FS=8.778;HRun=0;HaplotypeScore=27.6448;InbreedingCoeff=0.0510;IndelType=INS.NOVEL_2.;MQ=61.99;MQ0=36;MQ0Fraction=0.0187;MQRankSum=4.508;QD=3.08;ReadPosRankSum=8.080;SB=-437.03;VQSLOD=4.9313;set=VQSR
+20	20301041	rs35451634	ATATG	A	200.42	PASS	AC=21;AF=0.0449;AN=468;BaseQRankSum=5.251;DB;DP=579;FS=24.013;HRun=0;HaplotypeScore=27.8977;InbreedingCoeff=0.0113;IndelType=DEL.NumRepetitions_1.EventLength_4.;MQ=78.47;MQ0=26;MQ0Fraction=0.0449;MQRankSum=-5.284;QD=3.06;ReadPosRankSum=1.793;SB=-55.76;VQSLOD=5.0981;set=VQSR
+20	20378174	.	TC	T	245.55	PASS	AC=23;AF=0.01879;AN=1224;BaseQRankSum=0.990;DP=3225;FS=10.413;HRun=1;HaplotypeScore=22.6109;InbreedingCoeff=0.0244;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;MQ=93.70;MQ0=3;MQ0Fraction=0.0009;MQRankSum=-3.349;QD=1.86;ReadPosRankSum=-7.227;SB=-188.62;VQSLOD=4.2553;set=VQSR
+20	20809160	rs10571503	TAA	AAA,T	3496	PASS	AC=0;AF=0.0000;AN=612;BaseQRankSum=1.968;DB;DP=1092;FR;HP=4;HPLen=3;HR=3;HRun=0;HU=A;HaplotypeScore=26.1253;InbreedingCoeff=0.0603;IndelType=MIXED;MQ=68.98;MQ0=1;MQ0Fraction=0.0009;MQRankSum=1.520;NF;NR;PP;ReadPosRankSum=-4.042;SC=TATATATATATAAATTTAAAT;TC;TR=13;TU=AT;set=filterInVQSR-2of5
+20	22508765	.	CT	C	53877.84	PASS	AA=187;AB=0.78077;ABA=171;ABP=537.09;ABR=609;AC=1017;AF=0.91787;AN=1108;BL=12690;BR=1718;BVAR;BaseQRankSum=13.773;DEL;DP=7430;Dels=0.02;EL=73;EPP=22.53;ER=114;FR;FS=16.352;HETAR=152;HOMA=9;HOMR=786;HP=8;HR=4;HRun=4;HU=T;InbreedingCoeff=0.3885;IndelType=DEL.NumRepetitions_4.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.76152;LRBP=18147;MQ0=0;MQ0Fraction=0.0000;MQM=46.086;MQRankSum=0.971;NF;NR;NS=947;PP;RA=2868;RL=177;RPP=326.86;RR=10;RUN=1;ReadPosRankSum=9.951;SAB=0.34759;SAF=65;SAP=40.738;SAR=122;SC=AAAAAATTTTCTTTTGAACTG;SRB=0.46269;SRF=1327;SRP=37.684;SRR=1541;TC;TR=4;TU=T;VQSLOD=5.1182;set=Intersection;sumGLbyD=25.15
+20	22555082	rs11477526	AT	A	11503	PASS	AA=530;AB=0.50816;ABA=422;ABP=3.5063;ABR=436;AF=0.1614;AN=700;BL=21453;BR=23313;BVAR;BaseQRankSum=17.562;DB;DEL;DP=25587;DP4=1869,1600,283,201;Dels=0.14;EL=259;EPP=3.6003;ER=271;FQ=999;FR;FS=14.595;HETAR=159;HOMA=41;HOMR=846;HP=3;HPLen=3;HR=3;HRun=3;HU=T;INDEL;InbreedingCoeff=0.0995;IndelType=DEL.NumRepetitions_3.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.041549;LRBP=170.83;MQ=95.89;MQ0=0;MQ0Fraction=0.0000;MQM=72.162;MQRankSum=2.564;NF;NR;NS=1046;PP;PV4=0.058,6.6e-129,0.04,1;RA=4303;RL=264;RPP=3.0267;RR=266;RUN=1;ReadPosRankSum=0.176;SAB=0.58679;SAF=311;SAP=37.688;SAR=219;SC=GGGAAAGCTGATTTACTGATT;SRB=0.54892;SRF=2362;SRP=92.453;SRR=1941;TC;TR=3;TU=T;VQSLOD=8.7746;dbSNP=120;set=Intersection;sumGLbyD=15.27
+20	22590907	.	A	AC	4204.88	PASS	AA=67;AB=0.592;ABA=51;ABP=12.2;ABR=74;AF=0.0554;AF1=0.0468;AN=560;BL=2277;BR=2389;BVAR;BaseQRankSum=10.968;CI95=0.03759,0.05639;DP=14380;DP4=2514,2018,33,33;Dels=0.00;EL=22;EPP=20.155;ER=45;FQ=999;FR;FS=3.846;HETAR=25;HOMA=4;HOMR=1049;HP=4;HPLen=5;HR=5;HRun=0;HU=A;INDEL;INS;InbreedingCoeff=0.0719;IndelType=INS.NOVEL_1.Novel_C.;LEN=1;LRB=0.024003;LRBP=8.8481;MQ=110.68;MQ0=0;MQ0Fraction=0.0000;MQM=96.149;MQRankSum=2.668;NF;NR;NS=1078;PP;PV4=0.39,1,0.46,0.36;RA=5468;RL=33;RPP=3.0427;RR=34;RUN=1;ReadPosRankSum=-1.097;SAB=0.50746;SAF=34;SAP=3.0427;SAR=33;SC=TCATATCAAAAACATTACGTT;SRB=0.54389;SRF=2974;SRP=94.508;SRR=2494;TC;TR=5;TU=A;VQSLOD=10.0712;set=Intersection;sumGLbyD=27.69
+20	22806326	rs11468890	ATTCCATCAC	A	105320.99	PASS	AC=567;AF=0.48795;AN=1162;BVAR;BaseQRankSum=32.858;DB;DEL;DP=26278;DP4=727,796,554,587;Dels=0.30;FQ=999;FR;FS=1.923;HP=3;HPLen=3;HR=2;HRun=0;HU=T;INDEL;InbreedingCoeff=0.2548;IndelType=DEL.NumRepetitions_2.EventLength_9.;LEN=9;MQ=89.42;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-23.545;NF;NR;PP;PV4=0.7,1,1.3e-167,1;RUN=1;ReadPosRankSum=4.384;SC=GGCTGCTCCCATTCCATCACT;TC;TR=2;TU=T;VQSLOD=8.2594;set=Intersection;sumGLbyD=69.81
+20	22999898	rs55966257	CAGGA	C	8019.97	PASS	AA=23;AB=0.57778;ABA=19;ABP=5.3748;ABR=26;AC=214;AF=0.18838;AN=1136;BL=1143;BR=1040;BVAR;BaseQRankSum=29.294;DB;DEL;DP=8216;Dels=0.02;EL=11;EPP=3.1047;ER=12;FS=14.938;HETAR=14;HOMA=2;HOMR=948;HRun=0;InbreedingCoeff=0.0797;IndelType=DEL.NumRepetitions_1.EventLength_4.;LEN=4;LRB=0.047183;LRBP=13.563;MQ0=0;MQ0Fraction=0.0000;MQM=34.783;MQRankSum=-20.301;NS=964;RA=3637;RL=13;RPP=3.86;RR=10;RUN=1;ReadPosRankSum=-24.607;SAB=0.47826;SAF=11;SAP=3.1047;SAR=12;SRB=0.49024;SRF=1783;SRP=6.02;SRR=1854;VQSLOD=7.9163;set=Intersection;sumGLbyD=9.43
+20	23385964	rs57723772	GAA	G	8170.95	PASS	AC=257;AF=0.20928;AN=1228;BaseQRankSum=32.220;DB;DP=3291;FS=1.688;HRun=3;HaplotypeScore=22.6739;InbreedingCoeff=0.0171;IndelType=DEL.NumRepetitions_3.EventLength_1.RepeatExpansion_A.;MQ=58.44;MQ0=32;MQ0Fraction=0.0097;MQRankSum=-4.893;QD=6.55;ReadPosRankSum=-35.524;SB=-3631.67;VQSLOD=5.6549;set=VQSR
+20	23534530	.	TA	T	3542.10	PASS	AA=45;AB=0.75658;ABA=37;ABP=89.926;ABR=115;AC=35;AF=0.02991;AN=1170;BL=3090;BR=270;BVAR;BaseQRankSum=-6.892;DEL;DP=8108;Dels=0.00;EL=19;EPP=5.3748;ER=26;FS=1.026;HETAR=76;HOMA=896;HOMR=18;HRun=1;InbreedingCoeff=0.0551;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.83929;LRBP=5142.4;MQ0Fraction=0.0017;MQM=41.578;MQRankSum=0.818;NS=991;RA=203;RL=43;RPP=84.127;RR=2;RUN=1;ReadPosRankSum=-12.923;SAB=0.37778;SAF=17;SAP=8.8491;SAR=28;SRB=0.5665;SRF=115;SRP=10.808;SRR=88;VQSLOD=4.2093;set=Intersection;sumGLbyD=3.49
+20	23976810	rs5841018	A	ATATTAAT	1782.38	PASS	AF=0.1387;AF1=0.01507;BaseQRankSum=3.717;CI95=0.00188,0.03947;DB;DP=1712;DP4=357,376,7,2;Dels=0.00;FQ=31.1;FS=14.489;HPLen=2;HRun=0;INDEL;InbreedingCoeff=0.1123;IndelType=INS.NumRepetitions_1.EventLength_7.;MQ=49.53;MQ0=2;MQ0Fraction=0.0055;MQRankSum=-4.928;PV4=0.1,1,0.00085,0.016;ReadPosRankSum=-4.456;VQSLOD=5.3140;dbSNP=116;set=Intersection;sumGLbyD=19.98
+20	24222100	.	CTTTTA	C	4219.36	PASS	AA=57;AB=0.59434;ABA=43;ABP=11.205;ABR=63;AF=0.01803;AF1=0.01547;AN=1220;BL=2073;BR=2345;BVAR;BaseQRankSum=7.990;CI95=0.0114,0.02137;DEL;DP=17536;DP4=2140,2346,7,12;Dels=0.01;EL=32;EPP=4.877;ER=25;FQ=104;FS=0.614;HETAR=21;HOMA=4;HOMR=1042;HRun=0;INDEL;InbreedingCoeff=0.1941;IndelType=DEL.NumRepetitions_2.EventLength_5.;LEN=5;LRB=0.061566;LRBP=39.374;MQ=73.32;MQ0Fraction=0.0021;MQM=39.614;MQRankSum=-5.728;NS=1067;PV4=0.37,1.1e-39,3.5e-09,1;RA=5527;RL=28;RPP=3.0484;RR=29;RUN=1;ReadPosRankSum=0.214;SAB=0.54386;SAF=31;SAP=3.9627;SAR=26;SRB=0.49267;SRF=2723;SRP=5.588;SRR=2804;VQSLOD=7.5428;set=Intersection;sumGLbyD=38.08
+20	24395018	.	AT	A	49310	PASS	AA=146;AB=0.91198;ABA=130;ABP=2180.5;ABR=1347;AC=50;AF=0.04045;AN=1236;BL=587;BR=9625;BVAR;BaseQRankSum=-4.610;DEL;DP=12793;Dels=0.01;EL=54;EPP=24.487;ER=92;FS=22.108;HETAR=485;HOMA=384;HOMR=210;HRun=2;InbreedingCoeff=0.0374;IndelType=DEL.NumRepetitions_2.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.88504;LRBP=17373;MQ0=0;MQ0Fraction=0.0000;MQM=102.26;MQRankSum=2.256;NS=1080;RA=2377;RL=1;RPP=311.42;RR=145;RUN=1;ReadPosRankSum=-16.347;SAB=0.63699;SAF=93;SAP=26.807;SAR=53;SRB=0.52167;SRF=1240;SRP=12.702;SRR=1137;VQSLOD=3.2421;set=filterInVQSR-2of5;sumGLbyD=3.80
+20	24411517	.	C	CA	246.18	PASS	AF=0.01546;AF1=0.01095;BaseQRankSum=7.832;CI95=0.005698,0.01709;DP=7981;DP4=983,2037,7,7;Dels=0.00;FQ=27.9;FS=18.815;HPLen=3;HRun=3;INDEL;InbreedingCoeff=0.0175;IndelType=INS.NumRepetitions_3.EventLength_1.RepeatExpansion_A.;MQ=60.28;MQ0Fraction=0.0137;MQRankSum=-7.243;PV4=0.25,1,2.7e-05,1;ReadPosRankSum=-0.143;VQSLOD=4.3701;set=Intersection;sumGLbyD=6.56
+20	24421169	.	AG	A	27480	PASS	AA=182;AB=0.8303;ABA=149;ABP=835;ABR=729;AC=89;AF=0.07224;AN=1232;BL=11276;BR=2214;BVAR;BaseQRankSum=-5.447;DEL;DP=11717;Dels=0.01;EL=103;EPP=9.8827;ER=79;FR;FS=15.492;HETAR=343;HOMA=607;HOMR=114;HP=4;HR=1;HRun=1;HU=G;InbreedingCoeff=0.0353;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_G.;LEN=1;LRB=0.67176;LRBP=13222;MQ0=0;MQ0Fraction=0.0000;MQM=88.324;MQRankSum=2.221;NF;NR;NS=1071;PP;RA=1226;RL=169;RPP=293.37;RR=13;RUN=1;ReadPosRankSum=-19.711;SAB=0.54945;SAF=100;SAP=6.876;SAR=82;SC=CCTTAGCCCCAGAAAACATCT;SRB=0.44535;SRF=546;SRP=34.814;SRR=680;TC;TR=1;TU=G;VQSLOD=4.2669;set=Intersection;sumGLbyD=3.91
+20	24765537	rs71841337	ATTT	A,AT,ATT,ATTTT,ATTTTT	37852	PASS	AC=13,120,527,51,92;AF=0.01102,0.10169,0.44661,0.04322,0.07797;AN=1180;BVAR;BaseQRankSum=8.172;DB;DEL;DP=39116;DP4=200,331,851,1169;FR;FS=2.394;HP=15;HR=15;HU=T;HaplotypeScore=20.8091;INDEL;INS;InbreedingCoeff=0.4815;IndelType=MULTIALLELIC_INDEL;MQ0=1;MQ0Fraction=0.0003;MQRankSum=4.344;NF;NR;PP;PV4=0.067,1,1,0.1;QD=7.90;RUN=1;ReadPosRankSum=1.798;SB=-8371.96;SC=CTCTGCAACAATTTTTTTTTT;TC;TR=15;TU=T;VQSLOD=9.9679;dbSNP=120;set=Intersection
+20	25500689	.	A	AATTT	84980.72	PASS	AC=1005;AF=0.89096;AN=1128;BaseQRankSum=17.400;DP=2324;FS=6.721;HRun=0;HaplotypeScore=25.3376;InbreedingCoeff=0.2148;IndelType=INS.NumRepetitions_1.EventLength_4.;MQ=75.19;MQ0=1;MQ0Fraction=0.0004;MQRankSum=-8.221;QD=38.28;ReadPosRankSum=4.504;SB=-34833.07;VQSLOD=4.6038;set=VQSR
+20	25550373	.	GA	G	11251.31	PASS	AA=246;AB=0.42963;ABA=154;ABP=14.624;ABR=116;AC=566;AF=0.6521;AN=868;BL=5230;BR=11845;BVAR;BaseQRankSum=7.418;DEL;DP=8885;Dels=0.02;EL=99;EPP=23.348;ER=147;FR;FS=50.357;HETAR=150;HOMA=849;HOMR=14;HP=1;HR=2;HRun=1;HU=G;InbreedingCoeff=0.1365;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.38741;LRBP=5567.9;MQ0=0;MQ0Fraction=0.0000;MQM=97.561;MQRankSum=0.050;NF;NR;NS=1013;PP;RA=269;RL=75;RPP=84.361;RR=171;RUN=1;ReadPosRankSum=-7.128;SAB=0.52846;SAF=130;SAP=4.7404;SAR=116;SC=CACGGAGGCGGAGGAAGCAGC;SRB=0.42379;SRF=114;SRP=16.58;SRR=155;TC;TR=6;TU=AGG;VQSLOD=4.0103;set=filterInVQSR-2of5;sumGLbyD=4.58
+20	25903865	.	TTC	T	7459.23	PASS	AC=277;AF=0.23316;AN=1188;BaseQRankSum=31.479;DP=2969;FS=137.723;HRun=0;HaplotypeScore=37.3300;InbreedingCoeff=-0.1755;IndelType=DEL.NumRepetitions_1.EventLength_2.RepeatExpansion_TC.;MQ=53.49;MQ0=50;MQ0Fraction=0.0168;MQRankSum=-25.506;QD=4.70;ReadPosRankSum=-5.913;SB=-1747.98;VQSLOD=5.4731;set=VQSR
+20	25934237	.	C	CCACTT	771.36	PASS	AC=37;AF=0.0426;AN=868;BaseQRankSum=16.331;DP=2253;FS=4.545;HRun=0;HaplotypeScore=29.9764;InbreedingCoeff=-0.0685;IndelType=INS.NOVEL_5.;MQ=48.12;MQ0=87;MQ0Fraction=0.0386;MQRankSum=-12.497;QD=3.37;ReadPosRankSum=-8.428;SB=-297.70;VQSLOD=4.2324;set=VQSR
+20	26054751	rs112967123	TATC	T	33244	PASS	AA=1863;AB=0.79012;ABA=1788;ABP=6231;ABR=6731;AC=227;AF=0.18218;AN=1246;BL=74924;BR=72452;BVAR;BaseQRankSum=32.258;DB;DEL;DP=36404;DS;Dels=0.05;EL=931;EPP=3.0115;ER=932;FR;FS=265.752;HETAR=527;HOMA=2;HOMR=565;HP=1;HR=2;HRun=0;HU=T;InbreedingCoeff=-0.2137;IndelType=DEL.NumRepetitions_2.EventLength_3.;LEN=3;LRB=0.016773;LRBP=93.048;MQ0Fraction=0.0127;MQM=28.797;MQRankSum=-5.329;NF;NR;NS=1094;PP;RA=14604;RL=1014;RPP=34.743;RR=849;RUN=1;ReadPosRankSum=8.394;SAB=0.65486;SAF=1220;SAP=391.07;SAR=643;SC=TCACCATCATTATCATCATTA;SRB=0.56717;SRF=8283;SRP=575.39;SRR=6321;TC;TR=8;TU=ATC;VQSLOD=1.0486;set=filterInVQSR-2of5;sumGLbyD=6.54
+20	26120452	.	CAG	C	7863.19	PASS	AA=163;AB=0.70489;ABA=157;ABP=196.99;ABR=375;AC=171;AF=0.1908;AN=896;BL=3455;BR=4877;BVAR;BaseQRankSum=25.536;DEL;DP=7014;Dels=0.10;EL=58;EPP=32.438;ER=105;FS=231.723;HETAR=90;HOMA=5;HOMR=387;HRun=0;InbreedingCoeff=-0.1966;IndelType=DEL.NumRepetitions_1.EventLength_2.RepeatExpansion_AG.;LEN=2;LRB=0.17067;LRBP=530;MQ0Fraction=0.0470;MQM=21.951;MQRankSum=-23.449;NS=482;RA=1117;RL=62;RPP=23.273;RR=101;RUN=1;ReadPosRankSum=1.904;SAB=0.37423;SAF=61;SAP=25.404;SAR=102;SRB=0.41719;SRF=466;SRP=69.544;SRR=651;VQSLOD=-0.9395;set=filterInVQSR-2of5;sumGLbyD=5.06
+20	26185812	.	AG	A	322.58	PASS	AF=0.0342;BaseQRankSum=3.668;DP=3014;Dels=0.01;FR;FS=10.238;HP=8;HPLen=6;HR=6;HRun=6;HU=G;InbreedingCoeff=0.1504;IndelType=DEL.NumRepetitions_6.EventLength_1.RepeatExpansion_G.;MQ0Fraction=0.0473;MQRankSum=-5.464;NF;NR;PP;ReadPosRankSum=0.536;SC=GGGTGGGTGGAGGGGGGAGGG;TC;TR=6;TU=G;VQSLOD=5.0767;set=Intersection;sumGLbyD=8.46
+20	30963468	.	AGTTT	A	2041.12	PASS	AA=38;AB=0.75694;ABA=35;ABP=85.587;ABR=109;AC=34;AF=0.0377;AN=902;BL=1974;BR=668;BVAR;BaseQRankSum=3.060;DEL;DP=22806;DP4=1997,1747,28,36;Dels=0.02;EL=17;EPP=3.9246;ER=21;FR;FS=16.034;HETAR=29;HOMA=1;HOMR=1009;HP=1;HPLen=1;HR=1;HRun=0;HU=G;INDEL;InbreedingCoeff=0.0752;IndelType=DEL.NumRepetitions_2.EventLength_4.;LEN=4;LRB=0.49432;LRBP=1404.9;MQ=87.17;MQ0Fraction=0.0013;MQM=98.079;MQRankSum=6.021;NF;NR;NS=1039;PP;PV4=0.13,1.5e-07,1,0.051;RA=4052;RL=36;RPP=69.069;RR=2;RUN=1;ReadPosRankSum=-1.847;SAB=0.5;SAF=19;SAP=3.0103;SAR=19;SC=AGAAGTAAGTAGTTTGTTTTT;SRB=0.53776;SRF=2179;SRP=53.19;SRR=1873;TC;TR=9;TU=AAGT;VQSLOD=7.3578;set=Intersection;sumGLbyD=14.03
+20	31963212	.	AAAAAAAAAAAAG	A	727.15	PASS	AC=5;AF=0.0080;AN=622;BaseQRankSum=4.037;DP=1480;FS=0.000;HRun=0;HaplotypeScore=43.3793;InbreedingCoeff=0.0350;IndelType=DEL.NumRepetitions_1.EventLength_10orMore.;MQ=51.77;MQ0=59;MQ0Fraction=0.0399;MQRankSum=-1.799;QD=22.72;ReadPosRankSum=3.591;SB=-364.04;VQSLOD=5.3166;set=VQSR
+20	31997272	.	CT	C,CTT,CTTT	1837.10	PASS	AA=63;AB=0.77559;ABA=57;ABP=170.57;ABR=197;AC=79,49,30;AF=0.06594,0.04090,0.02504;AN=1198;BL=2372;BR=2640;BVAR;BaseQRankSum=3.277;DP=9050;Dels=0.03;EL=24;EPP=10.766;ER=39;FR;FS=0.303;HETAR=45;HOMA=1;HOMR=981;HP=10;HPLen=10;HR=10;HRun=10;HU=T;INS;InbreedingCoeff=0.2796;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.053472;LRBP=34.128;MQ0Fraction=0.0000;MQM=50.889;MQRankSum=0.610;NF;NR;NS=1027;PP;RA=3776;RL=30;RPP=3.3205;RR=33;RUN=1;ReadPosRankSum=-0.800;SAB=0.39683;SAF=25;SAP=8.8354;SAR=38;SC=ACCCAACTTCCTTTTTTTTTT;SRB=0.46213;SRF=1745;SRP=50.049;SRR=2031;TC;TR=10;TU=T;VQSLOD=4.1189;set=filterInVQSR-2of5;sumGLbyD=3.66
+20	33446974	rs113250263	TAA	T,TA,TAAA	17130.16	PASS	AC=65,417,184;AF=0.05941,0.38117,0.16819;AN=1094;BVAR;BaseQRankSum=3.400;DB;DEL;DP=22362;DP4=221,247,418,524;Dels=0.33;FR;FS=15.409;HP=15;HR=14;HRun=14;HU=A;INDEL;INS;InbreedingCoeff=0.5215;IndelType=MULTIALLELIC_INDEL;MQ=61.32;MQ0Fraction=0.0021;MQRankSum=0.481;NF;NR;PP;PV4=0.33,1,1,1;RUN=1;ReadPosRankSum=-0.056;SC=CTCCGTCTCATAAAAAAAAAA;TC;TR=14;TU=A;VQSLOD=8.0974;dbSNP=132;set=Intersection;sumGLbyD=12.78
+20	33877149	.	C	CT	1784.40	PASS	AA=58;AB=0.73096;ABA=53;ABP=94.289;ABR=144;AC=65;AF=0.05682;AN=1144;BL=3298;BR=1935;BVAR;BaseQRankSum=-2.066;DP=8074;Dels=0.02;EL=22;EPP=10.348;ER=36;FR;FS=11.452;HETAR=47;HOMA=3;HOMR=754;HP=16;HR=12;HRun=12;HU=T;INS;InbreedingCoeff=0.1178;IndelType=INS.NumRepetitions_10orMore.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.26046;LRBP=773.91;MQ0Fraction=0.0165;MQM=52.259;MQRankSum=0.734;NF;NR;NS=804;PP;RA=2141;RL=43;RPP=32.363;RR=15;RUN=1;ReadPosRankSum=-1.273;SAB=0.46552;SAF=27;SAP=3.6093;SAR=31;SC=ATTTTCTTTTCTTTTTTTTTT;SRB=0.37553;SRF=804;SRP=291.14;SRR=1337;TC;TR=12;TU=T;VQSLOD=3.1540;set=filterInVQSR-2of5;sumGLbyD=2.84
+20	34387589	rs112431805	CT	C,CTT	4039.10	PASS	AA=121;AB=0.75368;ABA=117;ABP=268.53;ABR=358;AC=84,139;AF=0.07047,0.11661;AN=1192;BL=5557;BR=3901;BVAR;BaseQRankSum=2.693;DB;DP=10157;Dels=0.03;EL=47;EPP=16.093;ER=74;FR;FS=7.639;HETAR=89;HOMA=2;HOMR=913;HP=13;HR=11;HRun=11;HU=T;INS;InbreedingCoeff=0.2097;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.17509;LRBP=632.63;MQ0Fraction=0.0000;MQM=49.802;MQRankSum=-0.801;NF;NR;NS=1004;PP;RA=3789;RL=77;RPP=22.554;RR=44;RUN=1;ReadPosRankSum=-2.691;SAB=0.3719;SAF=45;SAP=20.256;SAR=76;SC=AAGAAGTGTTCTTTTTTTTTT;SRB=0.40987;SRF=1553;SRP=270.35;SRR=2236;TC;TR=11;TU=T;VQSLOD=4.0473;set=filterInVQSR-2of5;sumGLbyD=4.64
+20	34493409	rs73621682	C	CAG	62288.93	PASS	AA=1069;AB=0.54863;ABA=826;ABP=40.606;ABR=1004;AC=257;AF=0.3640;AN=706;BL=41524;BR=47039;BVAR;BaseQRankSum=-24.248;DB;DP=30195;DP4=1743,1636,614,487;Dels=0.00;EL=582;EPP=21.343;ER=487;FQ=999;FR;FS=5.080;HETAR=298;HOMA=63;HOMR=712;HP=1;HPLen=1;HR=1;HRun=0;HU=A;INDEL;INS;InbreedingCoeff=0.1437;IndelType=INS.NumRepetitions_2.EventLength_2.RepeatExpansion_AG.;LEN=2;LRB=0.062272;LRBP=748.76;MQ=77.99;MQ0=3;MQ0Fraction=0.0015;MQM=54.446;MQRankSum=0.160;NF;NR;NS=1073;PP;PV4=0.016,1,0.01,1;RA=4461;RL=526;RPP=3.5973;RR=543;RUN=1;ReadPosRankSum=-1.716;SAB=0.57343;SAF=613;SAP=53.08;SAR=456;SC=AGGAAGAGATCAGAGCTCCCC;SRB=0.52634;SRF=2348;SRP=29.892;SRR=2113;TC;TR=4;TU=AG;VQSLOD=8.7047;dbSNP=130;set=Intersection;sumGLbyD=49.82
+20	35957317	.	CTGACT	C,CGACT	4370.96	PASS	ABR=81;AC=22,1;AF=0.0321,0.0015;AF1=0.04523;AN=686;BVAR;BaseQRankSum=7.969;CI95=0.0354,0.05752;DEL;DP=16632;DP4=1942,1815,17,21;Dels=0.03;FQ=999;FR;FS=0.531;HOMA=1;HOMR=998;HP=2;HPLen=1;HR=1;HRun=0;HU=T;INDEL;InbreedingCoeff=0.0587;IndelType=MULTIALLELIC_INDEL;MQ=83.38;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-7.201;NF;NR;NS=1020;PP;PV4=0.42,0.00017,4.5e-12,1;RA=4620;RUN=1;ReadPosRankSum=-1.007;SC=CCTCTCAGCTCTGACTGAGTC;SRB=0.50043;SRF=2312;SRP=3.0178;SRR=2308;TC;TR=8;TU=ACTG;VQSLOD=9.9778;dbSNP=130;set=Intersection;sumGLbyD=36.45
+20	36136198	.	GTGTC	G	2078.76	PASS	AA=35;AB=0.54167;ABA=33;ABP=4.096;ABR=39;AC=17;AF=0.01384;AN=1228;BL=1212;BR=1523;BVAR;BaseQRankSum=6.900;DEL;DP=22483;DP4=1696,2291,9,16;Dels=0.01;EL=9;EPP=20.94;ER=26;FQ=999;FR;FS=3.023;HETAR=13;HOMA=1;HOMR=1061;HP=1;HPLen=1;HR=1;HRun=0;HU=T;INDEL;InbreedingCoeff=0.1113;IndelType=DEL.NumRepetitions_2.EventLength_4.;LEN=4;LRB=0.11371;LRBP=79.803;MQ=93.98;MQ0=1;MQ0Fraction=0.0003;MQM=83.686;MQRankSum=-1.683;NF;NR;NS=1075;PP;PV4=0.55,1,0.0083,1;RA=5771;RL=19;RPP=3.5687;RR=16;RUN=1;ReadPosRankSum=0.618;SAB=0.37143;SAF=13;SAP=8.0357;SAR=22;SC=TATCATTTTAGTGTCTGTCTG;SRB=0.44966;SRF=2595;SRP=130.03;SRR=3176;TC;TR=11;TU=CTGT;VQSLOD=10.1935;set=Intersection;sumGLbyD=31.66
+20	36250522	.	CA	C	37933	PASS	AA=51;AB=0.95582;ABA=44;ABP=1800.5;ABR=952;AC=23;AF=0.01885;AN=1220;BL=691;BR=3464;BVAR;BaseQRankSum=-2.418;DEL;DP=11998;Dels=0.00;EL=18;EPP=12.59;ER=33;FS=2.307;HETAR=348;HOMA=534;HOMR=164;HRun=1;InbreedingCoeff=0.0763;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.66739;LRBP=4021.7;MQ0=2;MQ0Fraction=0.0006;MQM=53.647;MQRankSum=1.083;NS=1047;RA=1663;RL=2;RPP=97.065;RR=49;RUN=1;ReadPosRankSum=-12.726;SAB=0.68627;SAF=35;SAP=18.381;SAR=16;SRB=0.59651;SRF=992;SRP=137.56;SRR=671;VQSLOD=4.1346;set=filterInVQSR-2of5;sumGLbyD=3.29
+20	36285033	rs34715186	AT	A	39417	PASS	AA=530;AB=0.5406;ABA=447;ABP=16.939;ABR=526;AC=88;AF=0.0950;AN=926;BL=20722;BR=20406;BVAR;BaseQRankSum=15.611;DB;DEL;DP=36713;DP4=2551,2475,236,218;Dels=0.09;EL=241;EPP=12.45;ER=289;FQ=999;FR;FS=1.290;HETAR=141;HOMA=16;HOMR=926;HP=2;HPLen=3;HR=3;HRun=1;HU=A;INDEL;InbreedingCoeff=0.0742;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.0076833;LRBP=8.2825;MQ=104.81;MQ0=0;MQ0Fraction=0.0000;MQM=84.285;MQRankSum=-0.702;NF;NR;NS=1083;PP;PV4=0.62,1,1,1;RA=6562;RL=263;RPP=3.0759;RR=267;RUN=1;ReadPosRankSum=0.090;SAB=0.55849;SAF=296;SAP=18.76;SAR=234;SC=AAAAACACAAATCAGATCGTG;SRB=0.51707;SRF=3393;SRP=19.614;SRR=3169;TC;TR=3;TU=A;VQSLOD=10.5533;dbSNP=126;set=Intersection;sumGLbyD=14.15
+20	36384872	.	CTG	C	43532.41	PASS	AC=1213;AF=0.99589;AN=1218;BaseQRankSum=0.802;DP=3208;FS=9.727;HRun=0;HaplotypeScore=46.6153;InbreedingCoeff=0.1085;IndelType=DEL.NumRepetitions_7.EventLength_2.RepeatExpansion_TG.;MQ=58.37;MQ0=50;MQ0Fraction=0.0156;MQRankSum=-1.672;QD=13.57;ReadPosRankSum=2.063;SB=-18894.12;VQSLOD=4.7353;set=VQSR
+20	36542802	.	GTA	G	31310.15	PASS	AA=1481;AB=0.67546;ABA=1378;ABP=1138.4;ABR=2868;AC=437;AF=0.35938;AN=1216;BL=25719;BR=95500;BVAR;BaseQRankSum=9.478;DEL;DP=18068;DS;Dels=0.10;EL=889;EPP=132.34;ER=592;FS=320.726;HETAR=591;HOMA=44;HOMR=378;HRun=0;InbreedingCoeff=-0.4197;IndelType=DEL.NumRepetitions_1.EventLength_2.RepeatExpansion_TA.;LEN=2;LRB=0.57566;LRBP=87231;MQ0Fraction=0.0091;MQM=29.319;MQRankSum=-3.409;NS=1013;RA=4037;RL=3;RPP=3193;RR=1478;RUN=1;ReadPosRankSum=-6.687;SAB=0.40041;SAF=593;SAP=130.61;SAR=888;SRB=0.39014;SRF=1575;SRP=426.21;SRR=2462;VQSLOD=-1.6586;set=filterInVQSR-2of5;sumGLbyD=5.49
+20	36985025	.	CCA	C	4.57	PASS	AC=0;AF=0.0000;AN=682;BaseQRankSum=4.199;DP=1504;FS=1.036;HRun=0;HaplotypeScore=18.5241;InbreedingCoeff=0.0460;IndelType=DEL.NumRepetitions_6.EventLength_2.RepeatExpansion_CA.;MQ=57.04;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-1.774;ReadPosRankSum=-2.105;VQSLOD=6.7455;set=VQSR
+20	37139725	.	CAG	C	250.77	PASS	AF=0.0084;AF1=0.0139;BaseQRankSum=4.131;CI95=0.00885,0.01991;DP=7973;DP4=1808,1990,2,7;Dels=0.01;FQ=104;FR;FS=11.160;HP=3;HPLen=2;HR=1;HRun=0;HU=A;INDEL;InbreedingCoeff=-0.0001;IndelType=DEL.NumRepetitions_3.EventLength_2.RepeatExpansion_AG.;MQ=103.71;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-3.378;NF;NR;PP;PV4=0.18,0.0011,0.041,1;ReadPosRankSum=0.605;SC=AGATGGGGAACAGAGAGCAAG;TC;TR=6;TU=AG;VQSLOD=7.0630;set=Intersection;sumGLbyD=12.13
+20	37213224	.	G	GTA	3230.05	PASS	AA=32;AB=0.50769;ABA=32;ABP=3.0437;ABR=33;AC=12;AF=0.0168;AF1=0.02635;AN=714;BL=1271;BR=1743;BVAR;BaseQRankSum=-7.288;CI95=0.02212,0.03319;DP=14304;DP4=2180,2256,13,21;Dels=0.00;EL=20;EPP=7.3532;ER=12;FQ=999;FR;FS=7.863;HETAR=9;HOMA=0;HOMR=1043;HP=1;HPLen=1;HR=1;HRun=0;HU=T;INDEL;INS;InbreedingCoeff=0.0410;IndelType=INS.NumRepetitions_1.EventLength_2.RepeatExpansion_TA.;LEN=2;LRB=0.1566;LRBP=163.52;MQ=95.56;MQ0=1;MQ0Fraction=0.0005;MQM=51.562;MQRankSum=0.420;NF;NR;NS=1052;PP;PV4=0.23,1,0.03,0.33;RA=5138;RL=11;RPP=9.7962;RR=21;RUN=1;ReadPosRankSum=-1.122;SAB=0.28125;SAF=9;SAP=16.311;SAR=23;SC=TTTGCATCCAGTAGCACCACT;SRB=0.42293;SRF=2173;SRP=268.11;SRR=2965;TC;TR=1;TU=T;VQSLOD=9.7315;set=Intersection;sumGLbyD=36.69
+20	37282014	.	ATGG	A	2518.52	PASS	AF=0.03519;BaseQRankSum=11.994;DP=24592;DP4=415,3804,8,49;DS;Dels=0.01;FQ=999;FR;FS=2.049;HP=1;HPLen=1;HR=1;HRun=0;HU=T;INDEL;InbreedingCoeff=0.1028;IndelType=DEL.NumRepetitions_5.EventLength_3.;MQ=51.01;MQ0Fraction=0.0139;MQRankSum=-5.912;NF;NR;PP;PV4=0.27,1,0.22,0.015;ReadPosRankSum=1.781;SC=GGTGGTGATGATGGTGGTGGT;TC;TR=17;TU=GGT;VQSLOD=2.1183;set=filterInVQSR-2of5;sumGLbyD=9.05
+20	37532218	.	GTCCGTCCA	ATCCGTCCA,G	76120.88	PASS	AC=998;AF=0.92924;AN=1074;BaseQRankSum=-2.877;DP=3087;FR;FS=9.889;HP=2;HPLen=2;HR=1;HRun=0;HU=T;HaplotypeScore=71.6244;InbreedingCoeff=-0.0027;IndelType=MIXED;MQ=52.68;MQ0=543;MQ0Fraction=0.1759;MQRankSum=-1.750;NF;NR;PP;QD=24.98;ReadPosRankSum=-0.850;SB=-36635.43;SC=CCGTCCGTCCGTCCGTCCATC;TC;TR=19;TU=CCGT;VQSLOD=5.3068;set=Intersection
+20	37712193	.	AAG	A	2670.33	PASS	AA=106;AB=0.62821;ABA=87;ABP=36.418;ABR=147;AC=53;AF=0.0759;AN=698;BL=4672;BR=4303;BVAR;BaseQRankSum=13.696;DEL;DP=15155;DP4=1340,1852,32,52;Dels=0.06;EL=57;EPP=4.3214;ER=49;FR;FS=0.824;HETAR=43;HOMA=7;HOMR=982;HP=1;HPLen=2;HR=2;HRun=0;HU=A;INDEL;InbreedingCoeff=0.0861;IndelType=DEL.NumRepetitions_3.EventLength_2.RepeatExpansion_AG.;LEN=2;LRB=0.041114;LRBP=35.954;MQ=86.12;MQ0=0;MQ0Fraction=0.0000;MQM=54.236;MQRankSum=-5.745;NF;NR;NS=1034;PP;PV4=0.5,7.3e-26,1.1e-10,1;RA=4423;RL=58;RPP=5.0589;RR=48;RUN=1;ReadPosRankSum=2.617;SAB=0.38679;SAF=41;SAP=14.81;SAR=65;SC=GAAAATTCTGAAGAGAGTCAG;SRB=0.43093;SRF=1906;SRP=186.29;SRR=2517;TC;TR=6;TU=AG;VQSLOD=9.8131;set=Intersection;sumGLbyD=14.20
+20	37739002	.	T	TCA	1395.38	PASS	AA=16;AB=0.48387;ABA=16;ABP=3.0803;ABR=15;AC=11;AF=0.00950;AN=1158;BL=504;BR=630;BVAR;BaseQRankSum=-3.257;DP=13617;DP4=1660,883,7,5;Dels=0.00;EL=7;EPP=3.5532;ER=9;FR;FS=1.114;HETAR=9;HOMA=0;HOMR=991;HP=1;HPLen=2;HR=2;HRun=0;HU=T;INDEL;INS;InbreedingCoeff=0.0527;IndelType=INS.NumRepetitions_1.EventLength_2.RepeatExpansion_CA.;LEN=2;LRB=0.11111;LRBP=33.411;MQ=88.41;MQ0=0;MQ0Fraction=0.0000;MQM=83.75;MQRankSum=1.713;NF;NR;NS=1000;PP;PV4=0.76,1,1,0.5;RA=3257;RL=6;RPP=5.1818;RR=10;RUN=1;ReadPosRankSum=1.190;SAB=0.6875;SAF=11;SAP=7.8961;SAR=5;SC=CCTTTTTTGTTCATTTCTGCA;SRB=0.68806;SRF=2241;SRP=1003.5;SRR=1016;TC;TR=2;TU=T;VQSLOD=10.2220;set=Intersection;sumGLbyD=41.32
+20	38395256	.	TTGAG	T	633.19	PASS	AF=0.0028;BaseQRankSum=5.667;DP=3839;Dels=0.00;FR;FS=10.238;HP=2;HPLen=3;HR=3;HRun=0;HU=T;InbreedingCoeff=-0.0097;IndelType=DEL.NumRepetitions_1.EventLength_4.;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-1.276;NF;NR;PP;ReadPosRankSum=-1.016;SC=ATGTGTTTGTTTGAGTATGTT;TC;TR=10;TU=GTTT;VQSLOD=6.4906;set=Intersection;sumGLbyD=10.83
+20	39345038	.	CTGAACCATAATGTG	C,CCCATAATGTG	60744.52	PASS	AA=23;AB=0.67143;ABA=23;ABP=20.878;ABR=47;AC=232,2;AF=0.19366,0.00167;AN=1198;BL=1607;BR=1843;BVAR;BaseQRankSum=30.955;DEL;DP=31490;DP4=1729,2100,265,278;Dels=0.13;EL=6;EPP=14.434;ER=17;FQ=999;FR;FS=1.767;HETAR=18;HOMA=0;HOMR=1015;HP=1;HPLen=2;HR=2;HRun=0;HU=C;INDEL;InbreedingCoeff=0.1991;IndelType=MULTIALLELIC_INDEL;LEN=14;LRB=0.068406;LRBP=38.066;MQ=104.60;MQ0=0;MQ0Fraction=0.0000;MQM=189.83;MQRankSum=-16.579;NF;NR;NS=1033;PP;PV4=0.12,1,5.5e-137,1;RA=5286;RL=14;RPP=5.3706;RR=9;RUN=1;ReadPosRankSum=4.323;SAB=0.56522;SAF=13;SAP=3.86;SAR=10;SC=TGGGCTGGACCTGAACCATAA;SRB=0.46311;SRF=2448;SRP=65.493;SRR=2838;TC;TR=2;TU=C;VQSLOD=6.2643;dbSNP=130;set=Intersection;sumGLbyD=65.43
+20	39418008	.	AG	A	46796	PASS	AA=113;AB=0.9511;ABA=80;ABP=2894.6;ABR=1556;AC=30;AF=0.02412;AN=1244;BL=638;BR=6936;BVAR;BaseQRankSum=7.280;DEL;DP=14307;Dels=0.00;EL=50;EPP=6.2579;ER=63;FR;FS=5.707;HETAR=473;HOMA=361;HOMR=246;HP=3;HR=3;HRun=3;HU=G;InbreedingCoeff=0.0272;IndelType=DEL.NumRepetitions_3.EventLength_1.RepeatExpansion_G.;LEN=1;LRB=0.83153;LRBP=11375;MQ0=0;MQ0Fraction=0.0000;MQM=62.398;MQRankSum=3.530;NF;NR;NS=1089;PP;RA=3000;RL=3;RPP=223.02;RR=110;RUN=1;ReadPosRankSum=-18.601;SAB=0.58407;SAF=66;SAP=9.9475;SAR=47;SC=ACTGGGGGAAAGGGATTCTAG;SRB=0.494;SRF=1482;SRP=3.9484;SRR=1518;TC;TR=3;TU=G;VQSLOD=4.5834;set=Intersection;sumGLbyD=3.06
+20	39876961	.	GT	G,GTT,GTTT	2302.10	PASS	ABR=496;AC=45,51,45;AF=0.03664,0.04153,0.03664;AN=1228;BVAR;BaseQRankSum=4.462;DP=37649;DP4=1457,1975,57,59;Dels=0.02;FR;FS=9.938;HOMA=0;HOMR=978;HP=10;HPLen=10;HR=10;HRun=10;HU=T;INDEL;INS;InbreedingCoeff=0.2583;IndelType=MULTIALLELIC_INDEL;MQ=97.28;MQ0=0;MQ0Fraction=0.0000;MQRankSum=0.246;NF;NR;NS=1063;PP;PV4=0.15,1,1.9e-09,0.016;RA=5185;RUN=1;ReadPosRankSum=-4.954;SC=AGTTTCTCCGGTTTTTTTTTT;SRB=0.47464;SRF=2461;SRP=31.978;SRR=2724;TC;TR=10;TU=T;VQSLOD=4.9752;set=Intersection;sumGLbyD=4.39
+20	41013333	.	TC	T	20681	PASS	AA=137;AB=0.89211;ABA=134;ABP=1661.6;ABR=1108;AC=68;AF=0.05601;AN=1214;BL=1091;BR=8981;BVAR;BaseQRankSum=1.354;DEL;DP=12998;Dels=0.01;EL=57;EPP=11.395;ER=80;FS=0.758;HETAR=359;HOMA=100;HOMR=610;HRun=1;InbreedingCoeff=0.0104;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;LEN=1;LRB=0.78336;LRBP=13424;MQ0=1;MQ0Fraction=0.0003;MQM=67.745;MQRankSum=2.563;NS=1072;RA=4447;RL=5;RPP=258.66;RR=132;RUN=1;ReadPosRankSum=-14.092;SAB=0.59124;SAF=81;SAP=12.917;SAR=56;SRB=0.54194;SRF=2410;SRP=70.947;SRR=2037;VQSLOD=3.7531;set=filterInVQSR-2of5;sumGLbyD=4.14
+20	41659532	.	GC	G	40544	PASS	AA=42;AB=0.97149;ABA=39;ABP=2644.5;ABR=1329;AC=15;AF=0.0209;AN=716;BL=2531;BR=135;BVAR;BaseQRankSum=-2.537;DEL;DP=12219;Dels=0.00;EL=25;EPP=6.3192;ER=17;FS=2.656;HETAR=374;HOMA=155;HOMR=551;HRun=1;InbreedingCoeff=-0.0270;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;LEN=1;LRB=0.89872;LRBP=4678.9;MQ0=0;MQ0Fraction=0.0000;MQM=103.31;MQRankSum=2.828;NS=1088;RA=4736;RL=41;RPP=85.733;RR=1;RUN=1;ReadPosRankSum=-9.702;SAB=0.57143;SAF=24;SAP=4.8716;SAR=18;SRB=0.5625;SRF=2664;SRP=163.7;SRR=2072;VQSLOD=4.3267;set=Intersection;sumGLbyD=3.22
+20	41845580	.	GA	G	49310	PASS	AA=83;AB=0.95258;ABA=69;ABP=2591.6;ABR=1386;AC=46;AF=0.03740;AN=1230;BL=1320;BR=5150;BVAR;BaseQRankSum=-1.121;DEL;DP=13336;Dels=0.00;EL=36;EPP=6.1759;ER=47;FR;FS=0.372;HETAR=442;HOMA=341;HOMR=295;HP=2;HR=3;HRun=1;HU=G;InbreedingCoeff=0.0238;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.59196;LRBP=4926.2;MQ0=0;MQ0Fraction=0.0000;MQM=89.048;MQRankSum=0.897;NF;NR;NS=1080;PP;RA=3006;RL=5;RPP=142.43;RR=78;RUN=1;ReadPosRankSum=-15.412;SAB=0.55422;SAF=46;SAP=5.1294;SAR=37;SC=CCAGCTGTGGGAGAGAAACAT;SRB=0.47971;SRF=1442;SRP=13.762;SRR=1564;TC;TR=6;TU=AG;VQSLOD=4.4669;set=Intersection;sumGLbyD=3.65
+20	42209428	.	GC	G	13163	PASS	AA=89;AB=0.86677;ABA=83;ABP=730.96;ABR=540;AC=39;AF=0.03218;AN=1212;BL=950;BR=5334;BVAR;BaseQRankSum=-10.119;DEL;DP=10692;Dels=0.01;EL=48;EPP=4.2058;ER=41;FS=0.000;HETAR=259;HOMA=727;HOMR=54;HRun=1;InbreedingCoeff=0.0448;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;LEN=1;LRB=0.69764;LRBP=6644.4;MQ0=0;MQ0Fraction=0.0000;MQM=126.55;MQRankSum=4.223;NS=1040;RA=723;RL=12;RPP=106.09;RR=77;RUN=1;ReadPosRankSum=-17.362;SAB=0.39326;SAF=35;SAP=11.818;SAR=54;SRB=0.37898;SRF=274;SRP=94.99;SRR=449;VQSLOD=3.7157;set=filterInVQSR-2of5;sumGLbyD=3.48
+20	42281109	.	T	TAG	2321.12	PASS	AC=181;AF=0.3740;AN=484;BaseQRankSum=8.977;DP=435;FS=17.001;HRun=0;HaplotypeScore=14.6734;InbreedingCoeff=0.2340;IndelType=INS.NOVEL_2.;MQ=53.88;MQ0=47;MQ0Fraction=0.1080;MQRankSum=0.762;QD=12.41;ReadPosRankSum=3.399;SB=-1299.73;VQSLOD=4.8926;set=VQSR
+20	42436117	.	TC	T	38933	PASS	AA=18;AB=0.98435;ABA=17;ABP=2215.9;ABR=1069;AC=15;AF=0.01223;AN=1226;BL=498;BR=428;BVAR;BaseQRankSum=-7.224;DEL;DP=12436;Dels=0.00;EL=1;EPP=33.893;ER=17;FS=2.469;HETAR=303;HOMA=614;HOMR=123;HRun=1;InbreedingCoeff=0.0439;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;LEN=1;LRB=0.075594;LRBP=14.501;MQ0=0;MQ0Fraction=0.0000;MQM=98.611;MQRankSum=1.086;NS=1075;RA=1656;RL=10;RPP=3.4928;RR=8;RUN=1;ReadPosRankSum=-17.765;SAB=0.5;SAF=9;SAP=3.0103;SAR=9;SRB=0.49879;SRF=826;SRP=3.0313;SRR=830;VQSLOD=4.0821;set=filterInVQSR-2of5;sumGLbyD=3.04
+20	42682214	.	C	A,CAT	3904.51	PASS	AA=24;AB=0.6383;ABA=17;ABP=10.818;ABR=30;AC=0;AF=0.0000;AN=636;BL=1119;BR=949;BVAR;BaseQRankSum=1.426;DP=6509;Dels=0.00;EL=9;EPP=6.2675;ER=15;FR;HETAR=12;HOMA=3;HOMR=876;HP=2;HPLen=1;HR=1;HRun=0;HU=A;INS;InbreedingCoeff=0.0006;IndelType=MIXED;LEN=2;LRB=0.082205;LRBP=33.356;MQ0Fraction=0.0046;MQM=40.792;MQRankSum=-0.296;NF;NR;NS=891;PP;QD=32.81;RA=2679;RL=15;RPP=6.2675;RR=9;RUN=1;ReadPosRankSum=-1.806;SAB=0.75;SAF=18;SAP=16.039;SAR=6;SB=-924.23;SC=TATACACACACATATATATAC;SRB=0.66293;SRF=1776;SRP=620.76;SRR=903;TC;TR=9;TU=AC;set=filterInVQSR-2of5;sumGLbyD=32.75
+20	42973456	.	CA	C,CAA,CAAA	2675	PASS	AA=90;AB=0.79177;ABA=86;ABP=308.39;ABR=327;AC=77,61,39;AF=0.06492,0.05143,0.03288;AN=1186;BL=2983;BR=4446;BVAR;BaseQRankSum=2.422;DP=9416;Dels=0.03;EL=39;EPP=6.4847;ER=51;FR;FS=31.555;HETAR=75;HOMA=1;HOMR=888;HP=11;HR=11;HRun=11;HU=A;INS;InbreedingCoeff=0.2696;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.19693;LRBP=628.63;MQ0=0;MQ0Fraction=0.0000;MQM=55.567;MQRankSum=1.777;NF;NR;NS=964;PP;RA=3601;RL=37;RPP=9.1869;RR=53;RUN=1;ReadPosRankSum=-4.991;SAB=0.55556;SAF=50;SAP=5.423;SAR=40;SC=TAGTGACTGTCAAAAAAAAAA;SRB=0.60622;SRF=2183;SRP=355.91;SRR=1418;TC;TR=11;TU=A;VQSLOD=1.0763;set=filterInVQSR-2of5;sumGLbyD=4.05
+20	43091870	.	TC	T	2455.60	PASS	AA=120;AB=0.10619;ABA=101;ABP=155.22;ABR=12;AC=42;AF=0.03825;AN=1098;BL=573;BR=8744;BVAR;BaseQRankSum=-13.513;DEL;DP=9139;Dels=0.00;EL=64;EPP=4.1684;ER=56;FS=9.856;HETAR=118;HOMA=820;HOMR=0;HRun=1;InbreedingCoeff=0.0833;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;LEN=1;LRB=0.877;LRBP=15564;MQ0Fraction=0.0017;MQM=45.1;MQRankSum=2.266;NS=938;RA=24;RL=1;RPP=254.97;RR=119;RUN=1;ReadPosRankSum=-15.803;SAB=0.475;SAF=57;SAP=3.6617;SAR=63;SRB=0.54167;SRF=13;SRP=3.3722;SRR=11;VQSLOD=3.9930;set=filterInVQSR-2of5;sumGLbyD=3.09
+20	43233648	rs74585029	GA	G,GAA	1504.40	PASS	AA=113;AB=0.78652;ABA=95;ABP=320.31;ABR=350;AC=41,65;AF=0.03394,0.05381;AF1=0.0115;AN=1208;BL=4677;BR=5548;BVAR;BaseQRankSum=6.744;CI95=0.004274,0.01852;DB;DEL;DP=13996;DP4=1736,1549,15,17;Dels=0.03;EL=69;EPP=15.021;ER=44;FQ=14;FR;FS=12.174;HETAR=119;HOMA=15;HOMR=892;HP=11;HPLen=10;HR=10;HRun=10;HU=A;INDEL;InbreedingCoeff=0.2359;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.085183;LRBP=164.12;MQ=89.12;MQ0Fraction=0.0000;MQM=69.867;MQRankSum=2.513;NF;NR;NS=1027;PP;PV4=0.59,1,0.065,0.33;RA=3845;RL=46;RPP=11.485;RR=67;RUN=1;ReadPosRankSum=-4.957;SAB=0.33628;SAF=38;SAP=29.318;SAR=75;SC=AAAACAGCCAGAAAAAAAAAA;SRB=0.43667;SRF=1679;SRP=136.95;SRR=2166;TC;TR=10;TU=A;VQSLOD=4.5121;set=Intersection;sumGLbyD=8.22
+20	43246548	.	AC	A,CC	41579.13	PASS	AA=382;AB=0.72402;ABA=316;ABP=502.11;ABR=829;AC=1197;AF=0.99254;AN=1206;BL=9889;BR=14293;BVAR;BaseQRankSum=1.373;DEL;DP=10477;DS;Dels=0.05;EL=243;EPP=64.494;ER=139;FS=29.162;HETAR=291;HOMA=85;HOMR=624;HPLen=10;InbreedingCoeff=0.1392;IndelType=MIXED;LEN=1;LRB=0.18212;LRBP=1744.6;MQ0Fraction=0.0024;MQM=48.471;MQRankSum=5.726;NS=1001;RA=3138;RL=174;RPP=9.5816;RR=208;RUN=1;ReadPosRankSum=5.755;SAB=0.79843;SAF=305;SAP=298.51;SAR=77;SRB=0.70363;SRF=2208;SRP=1133.2;SRR=930;VQSLOD=5.6318;set=Intersection;sumGLbyD=5.22
+20	43258646	.	T	TT	1107.17	PASS	AC=97;AF=0.08420;AN=1152;BaseQRankSum=4.525;DP=2345;FS=19.308;HRun=9;HaplotypeScore=13.6276;InbreedingCoeff=0.1299;IndelType=INS.NumRepetitions_10orMore.EventLength_1.RepeatExpansion_T.;MQ=76.70;MQ0=0;MQ0Fraction=0.0000;MQRankSum=1.395;QD=2.67;ReadPosRankSum=-4.696;SB=-899.41;VQSLOD=5.4523;set=VQSR
+20	43718299	.	ATTACT	A	5497.06	PASS	AA=56;AB=0.51818;ABA=53;ABP=3.3262;ABR=57;AC=18;AF=0.0251;AF1=0.03729;AN=718;BL=2321;BR=2591;BVAR;BaseQRankSum=11.142;CI95=0.03319,0.04425;DEL;DP=17576;DP4=2460,2692,31,22;Dels=0.02;EL=28;EPP=3.0103;ER=28;FQ=999;FR;FS=9.689;HETAR=15;HOMA=1;HOMR=1068;HP=2;HPLen=2;HR=2;HRun=0;HU=T;INDEL;InbreedingCoeff=0.0448;IndelType=DEL.NumRepetitions_1.EventLength_5.;LEN=5;LRB=0.054967;LRBP=35.238;MQ=96.55;MQ0=0;MQ0Fraction=0.0000;MQM=50.286;MQRankSum=-5.149;NF;NR;NS=1084;PP;PV4=0.13,1,1.2e-12,1;RA=6745;RL=28;RPP=3.0103;RR=28;RUN=1;ReadPosRankSum=0.828;SAB=0.5;SAF=28;SAP=3.0103;SAR=28;SC=ATGACAGTGGATTACTTTAGT;SRB=0.46835;SRF=3159;SRP=61.709;SRR=3586;TC;TR=2;TU=T;VQSLOD=7.8832;set=Intersection;sumGLbyD=46.60
+20	43981749	.	A	AAAAAAC,AC	20899.71	PASS	ABR=192;AC=91,0;AF=0.1285,0.0000;AN=708;BVAR;BaseQRankSum=7.858;DP=23372;DP4=1554,1457,55,42;Dels=0.00;FR;FS=0.000;HOMA=4;HOMR=995;HP=6;HPLen=7;HR=7;HRun=0;HU=A;INDEL;INS;InbreedingCoeff=0.2109;IndelType=MULTIALLELIC_INDEL;MQ=95.59;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-12.081;NF;NR;NS=1051;PP;PV4=0.35,1,8.9e-73,1;RA=5027;RUN=1;ReadPosRankSum=-1.359;SC=TACACTAGCAAAAAAACAAAA;SRB=0.48518;SRF=2439;SRP=12.6;SRR=2588;TC;TR=7;TU=A;VQSLOD=8.0916;set=Intersection;sumGLbyD=54.33
+20	43999274	.	TCAAA	T	2948.85	PASS	AA=59;AB=0.59441;ABA=58;ABP=14.08;ABR=85;AC=20;AF=0.0290;AF1=0.04249;AN=690;BL=2277;BR=2436;BVAR;BaseQRankSum=9.320;CI95=0.0354,0.05088;DEL;DP=14599;DP4=2052,2303,21,22;Dels=0.03;EL=32;EPP=3.9304;ER=27;FQ=999;FR;FS=0.000;HETAR=21;HOMA=0;HOMR=1043;HP=2;HPLen=1;HR=1;HRun=0;HU=C;INDEL;InbreedingCoeff=-0.0037;IndelType=DEL.NumRepetitions_1.EventLength_4.;LEN=4;LRB=0.033736;LRBP=14.658;MQ=90.05;MQ0=0;MQ0Fraction=0.0000;MQM=75.339;MQRankSum=-1.294;NF;NR;NS=1064;PP;PV4=0.88,1,0.0026,1;RA=5732;RL=27;RPP=3.9304;RR=32;RUN=1;ReadPosRankSum=-0.915;SAB=0.47458;SAF=28;SAP=3.3415;SAR=31;SC=GGTACACAGCTCAAACAGTCT;SRB=0.4836;SRF=2772;SRP=16.4;SRR=2960;TC;TR=1;TU=C;VQSLOD=9.8086;set=Intersection;sumGLbyD=27.09
+20	44098622	.	C	CG	1092.40	PASS	AA=129;AB=0.77301;ABA=74;ABP=214.06;ABR=252;AC=45;AF=0.0455;AN=988;BL=6586;BR=3029;BVAR;BaseQRankSum=2.802;DP=5177;Dels=0.00;EL=122;EPP=225.63;ER=7;FR;FS=355.273;HETAR=66;HOMA=11;HOMR=734;HP=6;HR=4;HRun=4;HU=G;INS;InbreedingCoeff=0.1759;IndelType=INS.NumRepetitions_4.EventLength_1.RepeatExpansion_G.;LEN=1;LRB=0.36994;LRBP=2860.4;MQ0=0;MQ0Fraction=0.0000;MQM=52.395;MQRankSum=1.946;NF;NR;NS=811;PP;RA=1981;RL=121;RPP=217.95;RR=8;RUN=1;ReadPosRankSum=-6.413;SAB=0.99225;SAF=128;SAP=274.51;SAR=1;SC=GCGGAAGTGGCGGGGACCCTT;SRB=0.41242;SRF=817;SRP=135;SRR=1164;TC;TR=4;TU=G;VQSLOD=-2.2690;set=filterInVQSR-2of5;sumGLbyD=4.04
+20	44327637	.	A	AG,AGGGGGG	14351.23	PASS	AC=9,211;AF=0.0103,0.2409;AN=876;BaseQRankSum=15.517;DP=1704;FS=6.768;HaplotypeScore=31.5906;InbreedingCoeff=0.1538;IndelType=MULTIALLELIC_INDEL;MQ=54.64;MQ0=4;MQ0Fraction=0.0023;MQRankSum=-12.691;QD=20.83;ReadPosRankSum=-3.583;SB=-6278.99;VQSLOD=5.1556;set=VQSR
+20	45202636	.	GA	G	13269	PASS	AA=25;AB=0.96162;ABA=18;ABP=871.09;ABR=451;AC=24;AF=0.02013;AN=1192;BL=567;BR=1728;BVAR;BaseQRankSum=-5.361;DEL;DP=10873;Dels=0.00;EL=10;EPP=5.1818;ER=15;FS=0.928;HETAR=169;HOMA=831;HOMR=45;HRun=1;InbreedingCoeff=0.0999;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.50588;LRBP=1278.4;MQ0=0;MQ0Fraction=0.0000;MQM=170.56;MQRankSum=0.161;NS=1049;RA=632;RL=2;RPP=41.315;RR=23;RUN=1;ReadPosRankSum=-14.760;SAB=0.68;SAF=17;SAP=10.046;SAR=8;SRB=0.51424;SRF=325;SRP=4.1235;SRR=307;VQSLOD=3.9290;set=filterInVQSR-2of5;sumGLbyD=3.90
+20	45417828	.	TGAGC	T,TGC	4672.90	PASS	ABR=317;AC=69,104;AF=0.05712,0.08609;BVAR;BaseQRankSum=18.527;DEL;DP=11835;DS;FS=184.873;HOMA=48;HOMR=575;HaplotypeScore=65.5875;InbreedingCoeff=0.0599;IndelType=MULTIALLELIC_INDEL;MQ=29.78;MQ0=2988;MQ0Fraction=0.3629;MQRankSum=5.052;NS=713;QD=1.11;RA=1581;RUN=1;ReadPosRankSum=6.574;SB=-2116.87;SRB=0.47502;SRF=751;SRP=11.582;SRR=830;VQSLOD=0.0651;set=filterInVQSR-2of5
+20	45525657	rs66759083	TA	AA,T	49315	PASS	AA=2361;AB=0.45241;ABA=1398;ABP=53.235;ABR=1155;AC=20;AF=0.01701;AN=1176;BL=94913;BR=100886;BVAR;BaseQRankSum=0.740;DB;DEL;DP=30636;DP4=1258,881,1206,999;Dels=0.48;EL=1133;EPP=11.311;ER=1228;FQ=999;FR;FS=7.072;HETAR=503;HOMA=310;HOMR=218;HP=6;HPLen=7;HR=7;HU=T;INDEL;InbreedingCoeff=0.2271;IndelType=MIXED;LEN=1;LRB=0.030506;LRBP=398.68;MQ=102.24;MQ0=0;MQ0Fraction=0.0000;MQM=75.359;MQRankSum=0.148;NF;NR;NS=1031;PP;PV4=0.0064,0,4.6e-23,0.47;RA=2042;RL=1183;RPP=3.0333;RR=1178;RUN=1;ReadPosRankSum=-2.999;SAB=0.52139;SAF=1231;SAP=12.392;SAR=1130;SC=AGGATTTTTTTAAAAAGTTTT;SRB=0.55093;SRF=1125;SRP=49.017;SRR=917;TC;TR=7;TU=T;VQSLOD=7.1651;dbSNP=114;set=Intersection;sumGLbyD=18.51
+20	45783456	.	T	TG	2355.68	PASS	AA=64;AB=0.78521;ABA=61;ABP=203.67;ABR=223;AC=15;AF=0.0165;AN=910;BL=815;BR=5486;BVAR;BaseQRankSum=8.593;DP=10348;Dels=0.00;EL=48;EPP=37.754;ER=16;FS=77.861;HETAR=56;HOMA=1;HOMR=970;HRun=1;INS;InbreedingCoeff=-0.0549;IndelType=INS.NOVEL_1.Novel_G.;LEN=1;LRB=0.74131;LRBP=7522.1;MQ0Fraction=0.0122;MQM=44.562;MQRankSum=-1.258;NS=1027;RA=4750;RL=0;RPP=141.98;RR=64;RUN=1;ReadPosRankSum=-7.047;SAB=0.25;SAF=16;SAP=37.754;SAR=48;SRB=0.6;SRF=2850;SRP=415.59;SRR=1900;VQSLOD=1.3146;set=filterInVQSR-2of5;sumGLbyD=6.03
+20	46517110	.	C	CT	868.55	PASS	AC=15;AF=0.0218;AN=688;BaseQRankSum=8.522;DP=1752;FS=6.570;HRun=0;HaplotypeScore=14.9548;InbreedingCoeff=0.0452;IndelType=INS.NOVEL_1.Novel_T.;MQ=77.73;MQ0=0;MQ0Fraction=0.0000;MQRankSum=3.874;QD=10.98;ReadPosRankSum=-0.733;SB=-396.78;VQSLOD=6.7740;set=VQSR
+20	46629361	.	TTTCTTTC	T,TTTTC	13000.91	PASS	AC=188,107;AF=0.2212,0.1259;AN=850;BaseQRankSum=7.214;DP=1846;FS=14.502;HaplotypeScore=40.8481;InbreedingCoeff=0.3210;IndelType=MULTIALLELIC_INDEL;MQ=50.74;MQ0=79;MQ0Fraction=0.0428;MQRankSum=-6.348;QD=13.59;ReadPosRankSum=3.943;SB=-3581.20;VQSLOD=5.9412;set=VQSR
+20	46951099	.	G	GT	1662.30	PASS	AA=55;AB=0.7713;ABA=51;ABP=145.58;ABR=172;AC=47;AF=0.03923;AN=1198;BL=3288;BR=2434;BVAR;BaseQRankSum=-4.014;DP=27423;DP4=1483,1590,58,42;Dels=0.01;EL=21;EPP=9.6826;ER=34;FR;FS=9.565;HETAR=48;HOMA=0;HOMR=913;HP=16;HPLen=10;HR=10;HRun=10;HU=T;INDEL;INS;InbreedingCoeff=0.0952;IndelType=INS.NumRepetitions_10orMore.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.14925;LRBP=279.78;MQ=70.36;MQ0Fraction=0.0124;MQM=52.545;MQRankSum=0.717;NF;NR;NS=961;PP;PV4=0.067,1,1,0.17;RA=3035;RL=38;RPP=20.422;RR=17;RUN=1;ReadPosRankSum=-3.014;SAB=0.47273;SAF=26;SAP=3.3656;SAR=29;SC=TTTGTTTTTTGTTTTTTTTTT;SRB=0.36013;SRF=1093;SRP=518.73;SRR=1942;TC;TR=10;TU=T;VQSLOD=5.4779;set=Intersection;sumGLbyD=3.49
+20	47201076	rs58052846	C	CT	982.16	PASS	AC=50;AF=0.0551;AN=908;BaseQRankSum=12.598;DB;DP=2449;FS=35.648;HRun=0;HaplotypeScore=29.4602;InbreedingCoeff=-0.0542;IndelType=INS.NOVEL_1.Novel_T.;MQ=63.54;MQ0=0;MQ0Fraction=0.0000;MQRankSum=2.196;QD=3.16;ReadPosRankSum=-13.833;SB=-488.19;VQSLOD=6.0429;set=VQSR
+20	47965974	rs60011158	G	GA	999	PASS	AA=21;AB=0.57143;ABA=21;ABP=5.1818;ABR=28;AC=7;AF=0.0101;AF1=0.02061;AN=690;BL=1043;BR=577;BVAR;BaseQRankSum=-3.087;CI95=0.01549,0.02655;DB;DP=14578;DP4=1554,3055,6,17;Dels=0.00;EL=11;EPP=3.1137;ER=10;FQ=999;FR;FS=5.982;HETAR=7;HOMA=0;HOMR=1041;HP=2;HPLen=1;HR=1;HRun=1;HU=A;INDEL;INS;InbreedingCoeff=0.0356;IndelType=INS.NumRepetitions_1.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.28765;LRBP=294.09;MQ=80.17;MQ0=0;MQ0Fraction=0.0000;MQM=64.19;MQRankSum=2.137;NF;NR;NS=1048;PP;PV4=0.51,1,1,1;RA=5224;RL=16;RPP=15.522;RR=5;RUN=1;ReadPosRankSum=0.236;SAB=0.38095;SAF=8;SAP=5.5954;SAR=13;SC=TTCATGTACAGAGCTGCTGTG;SRB=0.31183;SRF=1629;SRP=1609.6;SRR=3595;TC;TR=4;TU=AG;VQSLOD=9.5466;dbSNP=129;set=Intersection;sumGLbyD=13.83
+20	48402974	rs57331436	GA	G	27741	PASS	AA=401;AB=0.5372;ABA=311;ABP=11.089;ABR=361;AC=84;AF=0.1186;AN=708;BL=16591;BR=14776;BVAR;BaseQRankSum=14.621;DB;DEL;DP=30607;DP4=1928,2310,195,225;Dels=0.11;EL=189;EPP=5.8749;ER=212;FQ=999;FR;FS=15.568;HETAR=110;HOMA=30;HOMR=923;HP=4;HPLen=3;HR=1;HRun=3;HU=A;INDEL;InbreedingCoeff=0.1263;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_A.;KGPilot123;LEN=1;LRB=0.057863;LRBP=231.06;MQ=106.68;MQ0=0;MQ0Fraction=0.0000;MQM=63.005;MQRankSum=-2.010;NF;NR;NS=1063;PP;PV4=0.72,1,0.001,1;RA=5258;RL=223;RPP=13.976;RR=178;RUN=1;ReadPosRankSum=1.337;SAB=0.37656;SAF=151;SAP=56.084;SAR=250;SC=TGCCCTCAAAGAGAAAAAGGA;SRB=0.38075;SRF=2002;SRP=652.44;SRR=3256;TC;TR=5;TU=AG;VQSLOD=8.7259;dbSNP=132;set=Intersection;sumGLbyD=15.86
+20	49101936	.	C	CT	404.46	PASS	AC=40;AF=0.03559;AN=1124;BaseQRankSum=0.750;DP=2162;FS=14.291;HRun=2;HaplotypeScore=30.9513;InbreedingCoeff=-0.0082;IndelType=INS.NumRepetitions_2.EventLength_1.RepeatExpansion_T.;MQ=49.78;MQ0=113;MQ0Fraction=0.0523;MQRankSum=-1.289;QD=1.94;ReadPosRankSum=-2.041;SB=-385.48;VQSLOD=4.6365;set=VQSR
+20	49731218	.	ATTTTATTTTTTATT	A,ATTTTATT	8398.93	PASS	AF=0.0656,0.0156;AF1=0.0996;BaseQRankSum=13.996;CI95=0.07743,0.1239;DP=6308;DP4=951,1311,23,35;Dels=0.05;FQ=999;FR;FS=12.503;HP=7;HPLen=4;HR=4;HRun=0;HU=T;INDEL;InbreedingCoeff=0.1892;IndelType=MULTIALLELIC_INDEL;MQ=57.61;MQ0Fraction=0.0145;MQRankSum=-5.208;NF;NR;PP;PV4=0.79,1,6.3e-06,0.16;ReadPosRankSum=-2.239;SC=TATTTTATTTATTTTATTTTT;TC;TR=11;TU=ATTT;VQSLOD=4.3191;set=Intersection;sumGLbyD=42.27
+20	49894989	.	TA	T	172.25	PASS	AF=0.0140;BaseQRankSum=7.220;DP=3882;Dels=0.00;FS=17.217;HPLen=2;HRun=1;InbreedingCoeff=0.0531;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_A.;MQ0Fraction=0.0214;MQRankSum=-0.661;ReadPosRankSum=-0.592;VQSLOD=3.0905;set=filterInVQSR-2of5;sumGLbyD=6.60
+20	50010923	rs66516522	C	CT,CTGG	35851	PASS	ABR=555;AC=310,11;AF=0.26451,0.00939;BVAR;BaseQRankSum=10.662;DB;DP=8188;FR;FS=34.411;HOMA=261;HOMR=399;HP=5;HR=6;HU=C;HaplotypeScore=45.1715;INS;InbreedingCoeff=0.2090;IndelType=MULTIALLELIC_INDEL;MQ=72.80;MQ0=0;MQ0Fraction=0.0000;MQRankSum=9.015;NF;NR;NS=831;PP;QD=9.69;RA=1986;RUN=1;ReadPosRankSum=-24.284;SB=-6038.55;SC=TGTCTGTCCCCCCTCAGCACT;SRB=0.45972;SRF=913;SRP=31.001;SRR=1073;TC;TR=6;TU=C;VQSLOD=6.1824;set=Intersection
+20	50228709	rs71192536	TG	T	20517	PASS	AA=924;AB=0.50203;ABA=735;ABP=3.0633;ABR=741;AC=200;AF=0.16502;AN=1212;BL=35460;BR=34197;BVAR;BaseQRankSum=13.810;DB;DEL;DP=32402;DP4=1760,2065,395,449;Dels=0.16;EL=439;EPP=7.9831;ER=485;FQ=999;FR;FS=0.558;HETAR=242;HOMA=63;HOMR=764;HP=5;HPLen=3;HR=3;HRun=3;HU=G;INDEL;InbreedingCoeff=0.1050;IndelType=DEL.NumRepetitions_3.EventLength_1.RepeatExpansion_G.;LEN=1;LRB=0.018132;LRBP=52.738;MQ=105.83;MQ0=0;MQ0Fraction=0.0000;MQM=75.87;MQRankSum=3.895;NF;NR;NS=1069;PP;PV4=0.7,1.5e-173,1,1;RA=4708;RL=486;RPP=8.4249;RR=438;RUN=1;ReadPosRankSum=1.586;SAB=0.43615;SAF=403;SAP=35.733;SAR=521;SC=GTTTTCCAGGTGGGAAGACCG;SRB=0.44074;SRF=2075;SRP=146.62;SRR=2633;TC;TR=3;TU=G;VQSLOD=10.4820;dbSNP=120;set=Intersection;sumGLbyD=15.35
+20	50236115	.	AGG	A,ACGGG,AG,AGGG	7429.57	PASS	AC=192,13,221,183;AF=0.2115,0.0143,0.2434,0.2015;AN=908;BaseQRankSum=1.045;DP=1177;FS=13.479;HaplotypeScore=11.8294;InbreedingCoeff=0.7959;IndelType=MULTIALLELIC_INDEL;MQ=52.98;MQ0=6;MQ0Fraction=0.0051;MQRankSum=-1.482;QD=7.28;ReadPosRankSum=-2.380;SB=-1229.31;VQSLOD=8.3762;set=VQSR
+20	51589568	.	TAAAC	AAAAC,T	12477.52	PASS	AF=0.27949;BaseQRankSum=-28.122;DP=3777;Dels=0.00;FR;FS=31.799;HP=7;HPLen=4;HR=3;HRun=0;HU=A;InbreedingCoeff=-0.1429;IndelType=MIXED;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-1.196;NF;NR;PP;ReadPosRankSum=-16.483;SC=AAATTCAAAATAAACAAACAA;TC;TR=18;TU=AAAC;VQSLOD=3.9201;set=filterInVQSR-2of5;sumGLbyD=52.43
+20	51617742	.	TGC	T,TGCGC	1374.91	PASS	AF=0.06000,0.02000;BaseQRankSum=12.051;DP=6231;Dels=0.00;FS=189.609;HPLen=1;HRun=0;InbreedingCoeff=0.0862;IndelType=MULTIALLELIC_INDEL;MQ0Fraction=0.0180;MQRankSum=-2.959;ReadPosRankSum=-5.090;VQSLOD=-2.8715;set=filterInVQSR-2of5;sumGLbyD=3.97
+20	51770354	.	AG	A	1010.90	PASS	AA=26;AB=0.52727;ABA=26;ABP=3.3656;ABR=29;AC=7;AF=0.0097;AF1=0.01637;AN=718;BL=1034;BR=964;BVAR;BaseQRankSum=5.588;CI95=0.01327,0.02212;DEL;DP=16259;DP4=2785,2239,15,10;Dels=0.01;EL=11;EPP=4.3466;ER=15;FQ=999;FR;FS=3.367;HETAR=8;HOMA=0;HOMR=1064;HP=2;HPLen=2;HR=2;HRun=2;HU=G;INDEL;InbreedingCoeff=0.0557;IndelType=DEL.NumRepetitions_2.EventLength_1.RepeatExpansion_G.;LEN=1;LRB=0.035035;LRBP=8.3357;MQ=90.48;MQ0=0;MQ0Fraction=0.0000;MQM=61.346;MQRankSum=-0.019;NF;NR;NS=1072;PP;PV4=0.69,2.1e-08,0.078,1;RA=6173;RL=13;RPP=3.0103;RR=13;RUN=1;ReadPosRankSum=-0.460;SAB=0.61538;SAF=16;SAP=6.017;SAR=10;SC=GTGGTCCTGCAGGTCAATAAT;SRB=0.56342;SRF=3478;SRP=218.68;SRR=2695;TC;TR=2;TU=G;VQSLOD=10.1601;set=Intersection;sumGLbyD=14.60
+20	51848430	.	AT	A,ATT	999	PASS	AA=39;AB=0.83408;ABA=37;ABP=219.19;ABR=186;AC=14,33;AF=0.0153,0.0359;AF1=0.03062;AN=918;BL=1676;BR=1732;BVAR;BaseQRankSum=3.338;CI95=0.02212,0.03982;DP=14886;DP4=1970,1762,22,31;Dels=0.01;EL=18;EPP=3.5114;ER=21;FQ=999;FR;FS=3.004;HETAR=31;HOMA=0;HOMR=1040;HP=10;HPLen=9;HR=9;HRun=9;HU=T;INDEL;INS;InbreedingCoeff=0.1629;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.016432;LRBP=5.0085;MQ=80.05;MQ0=0;MQ0Fraction=0.0000;MQM=56.667;MQRankSum=0.325;NF;NR;NS=1071;PP;PV4=0.13,1,0.0095,0.064;RA=5318;RL=21;RPP=3.5114;RR=18;RUN=1;ReadPosRankSum=-0.493;SAB=0.46154;SAF=18;SAP=3.5114;SAR=21;SC=ACAAAACAATATTTTTTTTTC;SRB=0.4968;SRF=2642;SRP=3.4823;SRR=2676;TC;TR=9;TU=T;VQSLOD=5.7417;set=Intersection;sumGLbyD=7.57
+20	51897203	.	T	TG	8427.20	PASS	AA=237;AB=0.69846;ABA=215;ABP=246.92;ABR=498;AC=117;AF=0.1662;AN=704;BL=14961;BR=5990;BVAR;BaseQRankSum=22.203;DP=9710;Dels=0.00;EL=83;EPP=49.198;ER=154;FR;FS=9.450;HETAR=123;HOMA=9;HOMR=895;HP=5;HPLen=6;HR=6;HRun=0;HU=T;INS;InbreedingCoeff=-0.0513;IndelType=INS.NOVEL_1.Novel_G.;LEN=1;LRB=0.42819;LRBP=8344.3;MQ0Fraction=0.0291;MQM=45.861;MQRankSum=-10.426;NF;NR;NS=1027;PP;RA=4919;RL=210;RPP=309.85;RR=27;RUN=1;ReadPosRankSum=-1.843;SAB=0.29536;SAF=70;SAP=89.219;SAR=167;SC=TTTGTTTGTTTTTTGTTGTTG;SRB=0.47794;SRF=2351;SRP=23.798;SRR=2568;TC;TR=23;TU=GTTT;VQSLOD=6.2670;set=Intersection;sumGLbyD=8.99
+20	52274070	.	AAG	A	1400.37	PASS	AA=30;AB=0.74227;ABA=25;ABP=52.462;ABR=72;AC=21;AF=0.01756;AN=1196;BL=412;BR=1966;BVAR;BaseQRankSum=6.660;DEL;DP=9362;Dels=0.01;EL=16;EPP=3.2998;ER=14;FS=1.485;HETAR=18;HOMA=2;HOMR=1004;HRun=0;InbreedingCoeff=0.0317;IndelType=DEL.NumRepetitions_1.EventLength_2.RepeatExpansion_AG.;LEN=2;LRB=0.65349;LRBP=2208.2;MQ0Fraction=0.0022;MQM=46.133;MQRankSum=-4.743;NS=1024;RA=3931;RL=2;RPP=51.941;RR=28;RUN=1;ReadPosRankSum=-4.152;SAB=0.4;SAF=12;SAP=5.6161;SAR=18;SRB=0.49784;SRF=1957;SRP=3.1699;SRR=1974;VQSLOD=5.6452;set=Intersection;sumGLbyD=11.11
+20	52351501	.	TAC	T	199.59	PASS	AC=22;AF=0.0238;AN=926;BaseQRankSum=7.874;DP=22911;DP4=2146,1691,26,22;FR;FS=2.898;HP=4;HPLen=3;HR=1;HRun=0;HU=A;HaplotypeScore=18.6111;INDEL;InbreedingCoeff=-0.0326;IndelType=DEL.NumRepetitions_6.EventLength_2.RepeatExpansion_AC.;MQ0=2;MQ0Fraction=0.0007;MQRankSum=1.011;NF;NR;PP;PV4=0.88,0.14,0.16,0.24;QD=1.10;ReadPosRankSum=-1.053;SB=-306.09;SC=GACACACAAATACACACACAC;TC;TR=13;TU=AC;VQSLOD=4.0486;set=filterInVQSR-2of5
+20	52447173	.	CA	C	503.89	PASS	AC=23;AF=0.01891;AN=1216;BaseQRankSum=0.801;DP=3266;FS=2.606;HRun=2;HaplotypeScore=22.1543;InbreedingCoeff=-0.0097;IndelType=DEL.NumRepetitions_2.EventLength_1.RepeatExpansion_A.;MQ=118.02;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-1.309;QD=2.65;ReadPosRankSum=-7.872;SB=-279.27;VQSLOD=4.1900;set=VQSR
+20	52498650	.	GT	G	24069	PASS	AA=74;AB=0.90594;ABA=57;ABP=870.4;ABR=549;AC=28;AF=0.02333;AN=1200;BL=505;BR=4514;BVAR;BaseQRankSum=-3.837;DEL;DP=9798;Dels=0.01;EL=41;EPP=4.8883;ER=33;FS=4.085;HETAR=209;HOMA=663;HOMR=121;HRun=1;InbreedingCoeff=0.0334;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.79876;LRBP=6956.6;MQ0=2;MQ0Fraction=0.0007;MQM=57.784;MQRankSum=-2.951;NS=995;RA=957;RL=8;RPP=101.72;RR=66;RUN=1;ReadPosRankSum=-14.806;SAB=0.39189;SAF=29;SAP=10.522;SAR=45;SRB=0.39916;SRF=382;SRP=87.53;SRR=575;VQSLOD=3.8710;set=filterInVQSR-2of5;sumGLbyD=2.90
+20	52823602	rs11469056	CAAA	C,CA,CAA,CAAAA,CAAAAA,CAAAAAA,CAAAAAAA,CAAAAAAAA,CAAAAAAAAA,CAAAAAAAAAA	14515.17	PASS	AC=24,83,246,109,83,19,10,16,22,59;AF=0.02128,0.07358,0.21809,0.09663,0.07358,0.01684,0.00887,0.01418,0.01950,0.05230;AN=1128;BVAR;BaseQRankSum=4.150;DB;DEL;DP=28279;FR;FS=2.021;HP=17;HR=17;HU=A;HaplotypeScore=27.8032;INS;InbreedingCoeff=0.7740;IndelType=MULTIALLELIC_INDEL;MQ=69.00;MQ0=0;MQ0Fraction=0.0000;MQRankSum=1.418;NF;NR;PP;QD=7.90;RUN=1;ReadPosRankSum=-3.864;SB=-3244.40;SC=GGTCCTAAGGCAAAAAAAAAA;TC;TR=17;TU=A;VQSLOD=14.1033;set=Intersection
+20	53308906	.	CT	C,CTT	2276	PASS	AA=92;AB=0.84453;ABA=81;ABP=540.17;ABR=440;AC=53,81;AF=0.04351,0.06650;AN=1218;BL=3561;BR=4796;BVAR;BaseQRankSum=3.000;DP=11804;Dels=0.02;EL=48;EPP=3.3879;ER=44;FR;FS=13.197;HETAR=69;HOMA=3;HOMR=993;HP=11;HR=10;HRun=10;HU=T;INS;InbreedingCoeff=0.2297;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.14778;LRBP=399.32;MQ0=1;MQ0Fraction=0.0003;MQM=56.348;MQRankSum=3.154;NF;NR;NS=1065;PP;RA=5520;RL=39;RPP=7.6365;RR=53;RUN=1;ReadPosRankSum=-2.140;SAB=0.57609;SAF=53;SAP=7.6365;SAR=39;SC=AATCCAAAGTCTTTTTTTTTT;SRB=0.51576;SRF=2847;SRP=14.92;SRR=2673;TC;TR=10;TU=T;VQSLOD=2.4753;set=filterInVQSR-2of5;sumGLbyD=4.42
+20	53334602	.	T	TG,TGG	905.13	PASS	ABR=325;AC=44,22;AF=0.03624,0.01812;BVAR;BaseQRankSum=-4.608;DP=15015;FR;FS=494.901;HOMA=0;HOMR=1004;HP=1;HR=1;HU=G;HaplotypeScore=20.5023;INS;InbreedingCoeff=0.0799;IndelType=MULTIALLELIC_INDEL;MQ=116.70;MQ0=0;MQ0Fraction=0.0000;MQRankSum=8.022;NF;NR;NS=1064;PP;QD=0.35;RA=5690;RUN=1;ReadPosRankSum=-14.522;SB=-311.57;SC=AGCCATTGGCTGTTTCACTGA;SRB=0.40738;SRF=2318;SRP=426.97;SRR=3372;TC;TR=1;TU=G;VQSLOD=-2.3042;set=filterInVQSR-2of5
+20	53729115	.	T	TG	15.48	PASS	AC=1;AF=0.0015;AN=668;BaseQRankSum=-1.001;DP=1711;FS=9.048;HRun=2;HaplotypeScore=12.4681;InbreedingCoeff=-0.0320;IndelType=INS.NumRepetitions_2.EventLength_1.RepeatExpansion_G.;MQ=131.36;MQ0=0;MQ0Fraction=0.0000;MQRankSum=0.193;QD=4.57;ReadPosRankSum=0.407;SB=-5.35;VQSLOD=4.8071;set=VQSR
+20	54033830	.	GTATTTTAAAATCA	G	2220.86	PASS	AF=0.0113;BaseQRankSum=5.506;DP=2577;Dels=0.01;FR;FS=6.533;HP=5;HPLen=4;HR=1;HRun=0;HU=T;InbreedingCoeff=0.0032;IndelType=DEL.NumRepetitions_1.EventLength_10orMore.;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-2.969;NF;NR;PP;ReadPosRankSum=1.322;SC=TCAATATTTTGTATTTTAAAA;TC;TR=1;TU=T;VQSLOD=5.5145;set=Intersection;sumGLbyD=95.65
+20	54375236	.	GT	G	626.13	PASS	AA=40;AB=0.63551;ABA=39;ABP=20.078;ABR=68;AC=18;AF=0.0256;AN=702;BL=1331;BR=1743;BVAR;BaseQRankSum=9.346;DEL;DP=8568;Dels=0.02;EL=26;EPP=10.828;ER=14;FS=0.610;HETAR=21;HOMA=1;HOMR=1035;HRun=1;InbreedingCoeff=-0.0056;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.13403;LRBP=122.92;MQ0=0;MQ0Fraction=0.0000;MQM=67.125;MQRankSum=-2.537;NS=1058;RA=4870;RL=17;RPP=4.9646;RR=23;RUN=1;ReadPosRankSum=-1.229;SAB=0.525;SAF=21;SAP=3.2274;SAR=19;SRB=0.5271;SRF=2567;SRP=34.087;SRR=2303;VQSLOD=7.9228;set=Intersection;sumGLbyD=10.77
+20	54457331	.	G	GA	1793.40	PASS	AA=77;AB=0.66667;ABA=74;ABP=56.573;ABR=148;AC=33;AF=0.02687;AN=1228;BL=3834;BR=1154;BVAR;BaseQRankSum=10.572;DP=10230;Dels=0.00;EL=77;EPP=170.21;ER=0;FS=139.433;HETAR=44;HOMA=1;HOMR=1001;HRun=1;INS;InbreedingCoeff=0.0023;IndelType=INS.NOVEL_1.Novel_A.;LEN=1;LRB=0.53729;LRBP=3129.8;MQ0Fraction=0.0095;MQM=4.7013;MQRankSum=-8.116;NS=1046;RA=4009;RL=77;RPP=170.21;RR=0;RUN=1;ReadPosRankSum=-6.026;SAB=1;SAF=77;SAP=170.21;SAR=0;SRB=0.57022;SRF=2286;SRP=174.7;SRR=1723;VQSLOD=1.1887;set=filterInVQSR-2of5;sumGLbyD=5.90
+20	54469810	.	CA	C	1697.62	PASS	AA=93;AB=0.63855;ABA=90;ABP=44.53;ABR=159;AC=34;AF=0.0374;AF1=0.01719;AN=908;BL=3242;BR=5839;BVAR;BaseQRankSum=10.425;CI95=0.009317,0.02795;DEL;DP=15197;DP4=2134,1896,56,46;Dels=0.03;EL=34;EPP=17.604;ER=59;FQ=16;FR;FS=9.985;HETAR=41;HOMA=1;HOMR=1011;HP=9;HPLen=8;HR=8;HRun=8;HU=A;INDEL;InbreedingCoeff=-0.0472;IndelType=DEL.NumRepetitions_8.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.28598;LRBP=1615.8;MQ=83.37;MQ0=1;MQ0Fraction=0.0004;MQM=64.075;MQRankSum=3.036;NF;NR;NS=1053;PP;PV4=0.76,1,0.31,0.22;RA=5150;RL=28;RPP=34.975;RR=65;RUN=1;ReadPosRankSum=-0.252;SAB=0.5914;SAF=55;SAP=9.7582;SAR=38;SC=ATTGCTAAGACAAAAAAAAGA;SRB=0.50621;SRF=2607;SRP=4.7374;SRR=2543;TC;TR=8;TU=A;VQSLOD=8.3677;set=Intersection;sumGLbyD=9.90
+20	54542453	.	GTATA	G,GTA	5109.66	PASS	ABR=112;AC=66,56;AF=0.0682,0.0579;AN=968;BVAR;BaseQRankSum=17.089;DB;DEL;DP=5519;DS;Dels=0.06;FS=99.502;HOMA=15;HOMR=409;HRun=0;InbreedingCoeff=0.1584;IndelType=MULTIALLELIC_INDEL;MQ0Fraction=0.0178;MQRankSum=-6.854;NS=460;RA=864;RUN=1;ReadPosRankSum=0.855;SRB=0.79282;SRF=685;SRP=646.5;SRR=179;VQSLOD=0.6375;set=filterInVQSR-2of5;sumGLbyD=8.53
+20	54629773	.	CA	C	1799.50	PASS	AA=49;AB=0.82707;ABA=46;ABP=250.17;ABR=220;AC=9;AF=0.00746;AN=1206;BL=173;BR=2277;BVAR;BaseQRankSum=5.240;DEL;DP=8557;Dels=0.01;EL=49;EPP=109.41;ER=0;FS=32.359;HETAR=35;HOMA=1;HOMR=325;HRun=1;InbreedingCoeff=0.0892;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.85878;LRBP=3926.6;MQ0Fraction=0.0602;MQM=32.163;MQRankSum=-3.926;NS=361;RA=1091;RL=0;RPP=109.41;RR=49;RUN=1;ReadPosRankSum=-4.512;SAB=0;SAF=0;SAP=109.41;SAR=49;SRB=0.49404;SRF=539;SRP=3.3467;SRR=552;VQSLOD=1.1233;set=filterInVQSR-2of5;sumGLbyD=3.54
+20	54710245	.	TA	T	999	PASS	AF=0.0084;AF1=0.0148;BaseQRankSum=3.954;CI95=0.00885,0.02212;DP=8043;DP4=2000,1849,10,7;Dels=0.01;FQ=999;FR;FS=0.000;HP=9;HPLen=6;HR=3;HRun=6;HU=A;INDEL;InbreedingCoeff=0.1181;IndelType=DEL.NumRepetitions_3.EventLength_1.RepeatExpansion_A.;MQ=78.51;MQ0=0;MQ0Fraction=0.0000;MQRankSum=0.095;NF;NR;PP;PV4=0.63,0.00056,1,1;ReadPosRankSum=-0.448;SC=CAACAAAAAATAAATAAATAA;TC;TR=15;TU=AAAT;VQSLOD=7.8129;set=Intersection;sumGLbyD=19.02
+20	54968173	.	A	AAT,AATAT,AT,ATAT	89535.82	PASS	ABR=994;AC=561,278,2,3;AF=0.50179,0.24866,0.00179,0.00268;AN=1118;BVAR;BaseQRankSum=-2.699;DB;DP=27837;DP4=168,177,1045,866;Dels=0.00;FQ=999;FR;FS=12.472;HOMA=71;HOMR=455;HP=3;HPLen=4;HR=4;HRun=0;HU=A;INDEL;INS;InbreedingCoeff=0.6391;IndelType=MULTIALLELIC_INDEL;KGPilot123;MQ=80.36;MQ0Fraction=0.0055;MQRankSum=-1.512;NF;NR;NS=913;PP;PV4=0.046,1,1,1;RA=2015;RUN=1;ReadPosRankSum=1.015;SC=GGCCACTTAAAATATATATAT;SRB=0.44864;SRF=904;SRP=49.187;SRR=1111;TC;TR=15;TU=AT;VQSLOD=9.0092;dbSNP=132;set=Intersection;sumGLbyD=42.33
+20	55176688	.	TA	T	421.84	PASS	AF=0.01322;AF1=0.01845;BaseQRankSum=5.383;CI95=0.01282,0.02564;DP=10531;DP4=1975,2017,16,14;Dels=0.01;FQ=91.2;FR;FS=7.401;HP=6;HPLen=5;HR=5;HRun=5;HU=A;INDEL;InbreedingCoeff=0.0829;IndelType=DEL.NumRepetitions_5.EventLength_1.RepeatExpansion_A.;MQ=75.80;MQ0=1;MQ0Fraction=0.0003;MQRankSum=-0.471;NF;NR;PP;PV4=0.72,1,1,1;ReadPosRankSum=0.223;SC=CTGCAAAATATAAAAATTAGG;TC;TR=5;TU=A;VQSLOD=6.6000;set=Intersection;sumGLbyD=12.15
+20	55664086	.	GTT	ATT,G,GT,GTTT	5622.44	PASS	AC=6,71,136;AF=0.00498,0.05887,0.11277;AN=1206;BVAR;BaseQRankSum=3.173;DB;DEL;DP=40384;DP4=1567,1317,54,29;Dels=0.05;FR;FS=1.949;HP=14;HR=11;HRun=11;HU=T;INDEL;INS;InbreedingCoeff=0.3490;IndelType=MIXED;MQ=77.90;MQ0=0;MQ0Fraction=0.0000;MQRankSum=0.052;NF;NR;PP;PV4=0.057,1,0.2,1.2e-05;RUN=1;ReadPosRankSum=-13.646;SC=AATTTTATTTGTTTTTTTTTT;TC;TR=11;TU=T;VQSLOD=11.7964;set=Intersection;sumGLbyD=8.09
+20	56045006	.	TG	T	342.15	PASS	AC=72;AF=0.0940;AN=766;BaseQRankSum=4.992;DP=1238;FS=1.460;HRun=7;HaplotypeScore=20.2784;InbreedingCoeff=0.1795;IndelType=DEL.NumRepetitions_7.EventLength_1.RepeatExpansion_G.;MQ=66.42;MQ0=1;MQ0Fraction=0.0008;MQRankSum=-0.937;QD=1.84;ReadPosRankSum=-4.385;SB=-320.83;VQSLOD=5.2383;set=VQSR
+20	56158711	.	AG	A	922.47	PASS	AA=18;AB=0.575;ABA=17;ABP=4.9646;ABR=23;AC=2;AF=0.0028;AN=714;BL=953;BR=808;BVAR;BaseQRankSum=3.129;DEL;DP=10462;Dels=0.01;EL=9;EPP=3.0103;ER=9;FR;FS=8.724;HETAR=4;HOMA=0;HOMR=1058;HP=1;HPLen=2;HR=2;HRun=1;HU=A;InbreedingCoeff=0.0262;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_G.;LEN=1;LRB=0.08234;LRBP=28.936;MQ0=0;MQ0Fraction=0.0000;MQM=55.889;MQRankSum=2.052;NF;NR;NS=1062;PP;RA=6300;RL=9;RPP=3.0103;RR=9;RUN=1;ReadPosRankSum=-0.317;SAB=0.66667;SAF=12;SAP=7.3532;SAR=6;SC=TGGCCTAGCAAGCATCGTGAC;SRB=0.48143;SRF=3033;SRP=21.883;SRR=3267;TC;TR=8;TU=AAGC;VQSLOD=8.3252;set=Intersection;sumGLbyD=13.22
+20	56258618	rs113670927	T	C,TGC,TGTGC,TGTGTGC	37834.99	PASS	ABR=441;AC=11,100,43;AF=0.0123,0.1119,0.0481;AN=894;BVAR;BaseQRankSum=19.514;DB;DP=23173;DP4=541,920,413,579;Dels=0.00;FQ=999;FR;FS=1.238;HOMA=28;HOMR=808;HP=2;HPLen=1;HR=1;HRun=0;HU=G;INDEL;INS;InbreedingCoeff=0.2154;IndelType=MIXED;MQ=57.25;MQ0Fraction=0.0275;MQRankSum=-6.684;NF;NR;NS=976;PP;PV4=0.023,1,1,1;RA=3294;RUN=1;ReadPosRankSum=11.873;SC=TGCGTGTGTGTGTGTGTGTGT;SRB=0.42441;SRF=1398;SRP=166.5;SRR=1896;TC;TR=30;TU=GT;VQSLOD=6.7457;dbSNP=114;set=Intersection;sumGLbyD=21.27
+20	56395857	.	T	TAGGCAG	6614.22	PASS	AA=30;AB=0.63415;ABA=30;ABP=15.827;ABR=52;AC=14;AF=0.0197;AF1=0.03154;AN=710;BL=991;BR=1813;BVAR;BaseQRankSum=-4.589;CI95=0.02434,0.04204;DP=13879;DP4=1543,1833,12,14;Dels=0.00;EL=14;EPP=3.2998;ER=16;FQ=999;FR;FS=1.482;HETAR=11;HOMA=0;HOMR=1051;HP=1;HPLen=2;HR=2;HRun=0;HU=T;INDEL;INS;InbreedingCoeff=0.0774;IndelType=INS.NumRepetitions_2.EventLength_6.;LEN=6;LRB=0.29315;LRBP=526.27;MQ=90.42;MQ0=0;MQ0Fraction=0.0000;MQM=39.433;MQRankSum=-7.011;NF;NR;NS=1062;PP;PV4=1,1,3.7e-09,1;RA=5322;RL=9;RPP=13.433;RR=21;RUN=1;ReadPosRankSum=0.679;SAB=0.43333;SAF=13;SAP=4.1684;SAR=17;SC=AAGAGCATCTTAGGCAGAGGC;SRB=0.47294;SRF=2517;SRP=36.853;SRR=2805;TC;TR=2;TU=T;VQSLOD=8.3045;set=Intersection;sumGLbyD=68.22
+20	56969289	.	GTTTGT	G	600.69	PASS	AF=0.0056;AF1=0.007726;BaseQRankSum=2.907;CI95=0.004425,0.01327;DP=9643;DP4=1892,1749,6,3;Dels=0.00;FQ=117;FR;FS=16.601;HP=5;HPLen=3;HR=3;HRun=0;HU=T;INDEL;InbreedingCoeff=0.0236;IndelType=DEL.NumRepetitions_3.EventLength_5.;MQ=92.59;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-2.134;NF;NR;PP;PV4=0.51,1,0.07,0.3;ReadPosRankSum=0.236;SC=TAAGGACGTTGTTTGTTTTGT;TC;TR=10;TU=GTTT;VQSLOD=5.8458;set=Intersection;sumGLbyD=39.51
+20	57187557	.	AG	A,AGG	1486.69	PASS	AA=130;AB=0.55446;ABA=90;ABP=8.2132;ABR=112;AC=56,26;AF=0.0574,0.0266;AN=976;BL=3817;BR=5968;BVAR;BaseQRankSum=5.517;DEL;DP=14174;DP4=925,721,59,48;Dels=0.05;EL=52;EPP=14.302;ER=78;FR;FS=0.917;HETAR=44;HOMA=17;HOMR=864;HP=4;HPLen=4;HR=4;HRun=4;HU=G;INDEL;InbreedingCoeff=0.2856;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.21983;LRBP=1029.8;MQ=91.56;MQ0=0;MQ0Fraction=0.0000;MQM=63.631;MQRankSum=1.900;NF;NR;NS=925;PP;PV4=0.84,1,1,0.39;RA=2746;RL=44;RPP=32.476;RR=86;RUN=1;ReadPosRankSum=-0.639;SAB=0.44615;SAF=58;SAP=6.2842;SAR=72;SC=TCAGGCCCGCAGGGGTCAGGG;SRB=0.5772;SRF=1585;SRP=145.17;SRR=1161;TC;TR=4;TU=G;VQSLOD=7.7167;set=Intersection;sumGLbyD=14.85
+20	57282771	.	T	TG	506.43	PASS	AA=34;AB=0.70312;ABA=19;ABP=25.946;ABR=45;AC=34;AF=0.0373;AN=912;BL=886;BR=1938;BVAR;BaseQRankSum=3.744;DP=4276;Dels=0.00;EL=18;EPP=3.2658;ER=16;FR;FS=0.639;HETAR=17;HOMA=9;HOMR=737;HP=9;HR=8;HRun=8;HU=G;INS;InbreedingCoeff=0.2149;IndelType=INS.NumRepetitions_8.EventLength_1.RepeatExpansion_G.;LEN=1;LRB=0.37252;LRBP=853.99;MQ0=0;MQ0Fraction=0.0000;MQM=49.706;MQRankSum=-0.051;NF;NR;NS=763;PP;RA=1822;RL=9;RPP=19.36;RR=25;RUN=1;ReadPosRankSum=-2.111;SAB=0.55882;SAF=19;SAP=4.0322;SAR=15;SC=TCGGGGGGCGTGGGGGGGGTG;SRB=0.51098;SRF=931;SRP=4.9172;SRR=891;TC;TR=8;TU=G;VQSLOD=5.7772;set=Intersection;sumGLbyD=7.95
+20	57419740	rs11481507	A	AT	82613.57	PASS	AA=3850;AB=0.41404;ABA=1786;ABP=198.63;ABR=1262;AC=919;AF=0.75328;AN=1220;BL=140665;BR=151383;BVAR;BaseQRankSum=-27.490;DB;DP=31794;DP4=588,585,1571,1721;Dels=0.00;EL=1924;EPP=3.0126;ER=1926;FQ=999;FR;FS=2.191;HETAR=482;HOMA=454;HOMR=135;HP=3;HPLen=3;HR=3;HRun=3;HU=T;INDEL;INS;InbreedingCoeff=0.0861;IndelType=INS.NumRepetitions_3.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.036699;LRBP=857.15;MQ=123.92;MQ0=0;MQ0Fraction=0.0000;MQM=91.654;MQRankSum=3.016;NF;NR;NS=1071;PP;PV4=0.16,1,0.12,1;RA=1850;RL=1874;RPP=8.8784;RR=1976;RUN=1;ReadPosRankSum=-0.685;SAB=0.47636;SAF=1834;SAP=21.693;SAR=2016;SC=TACACTAGTGATTTAACCCTA;SRB=0.49027;SRF=907;SRP=4.5315;SRR=943;TC;TR=3;TU=T;VQSLOD=9.2768;dbSNP=126;set=Intersection;sumGLbyD=22.78
+20	57558194	.	CT	C,CTT,CTTT	6470.30	PASS	ABR=451;AC=104,161,177;AF=0.08919,0.13808,0.15180;BVAR;BaseQRankSum=1.172;DP=7985;FR;FS=2.202;HOMA=19;HOMR=778;HP=22;HR=15;HU=T;HaplotypeScore=16.1921;INS;InbreedingCoeff=0.6440;IndelType=MULTIALLELIC_INDEL;MQ=69.24;MQ0=27;MQ0Fraction=0.0109;MQRankSum=-0.003;NF;NR;NS=943;PP;QD=2.22;RA=2531;RUN=1;ReadPosRankSum=-0.104;SB=-2096.85;SC=GCCTTTTTTTCTTTTTTTTTT;SRB=0.34848;SRF=882;SRP=507.73;SRR=1649;TC;TR=15;TU=T;VQSLOD=6.5151;set=Intersection
+20	57693627	.	AG	A	1991.90	PASS	AA=52;AB=0.49462;ABA=47;ABP=3.0336;ABR=46;AC=15;AF=0.01227;AN=1222;BL=1902;BR=1478;BVAR;BaseQRankSum=-6.121;DEL;DP=26459;DP4=2647,2873,16,20;Dels=0.01;EL=25;EPP=3.1773;ER=27;FR;FS=3.135;HETAR=15;HOMA=1;HOMR=1064;HP=2;HPLen=3;HR=3;HRun=2;HU=A;INDEL;InbreedingCoeff=0.0866;IndelType=DEL.NumRepetitions_2.EventLength_1.RepeatExpansion_G.;LEN=1;LRB=0.12544;LRBP=118.51;MQ=116.26;MQ0=0;MQ0Fraction=0.0000;MQM=114.65;MQRankSum=1.942;NF;NR;NS=1080;PP;PV4=0.74,6.9e-08,1,0.38;RA=6781;RL=33;RPP=11.195;RR=19;RUN=1;ReadPosRankSum=-1.795;SAB=0.5;SAF=26;SAP=3.0103;SAR=26;SC=ATTGGAGGAAAGGCTTTTTCA;SRB=0.46247;SRF=3136;SRP=85.976;SRR=3645;TC;TR=3;TU=A;VQSLOD=8.6672;set=Intersection;sumGLbyD=13.55
+20	57716287	.	A	AT	66.47	PASS	AC=6;AF=0.00506;AN=1186;BaseQRankSum=1.369;DP=2744;FS=3.834;HRun=8;HaplotypeScore=11.2046;InbreedingCoeff=0.1196;IndelType=INS.NumRepetitions_8.EventLength_1.RepeatExpansion_T.;MQ=73.00;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-0.086;QD=2.14;ReadPosRankSum=-2.588;SB=-53.80;VQSLOD=4.2080;set=VQSR
+20	58121928	rs73625057	T	TGG	6649.17	PASS	AA=132;AB=0.57854;ABA=110;ABP=16.996;ABR=151;AC=57;AF=0.0617;AN=924;BL=4530;BR=4790;BVAR;BaseQRankSum=-13.456;DB;DP=30353;DP4=2107,2168,61,66;Dels=0.00;EL=67;EPP=3.0761;ER=65;FR;FS=0.708;HETAR=46;HOMA=8;HOMR=1023;HP=3;HPLen=2;HR=2;HRun=2;HU=G;INDEL;INS;InbreedingCoeff=0.1241;IndelType=INS.NumRepetitions_2.EventLength_1.RepeatExpansion_G.;LEN=2;LRB=0.027897;LRBP=18.76;MQ=109.61;MQ0=1;MQ0Fraction=0.0004;MQM=79.833;MQRankSum=-0.699;NF;NR;NS=1077;PP;PV4=0.79,1,0.49,0.036;RA=5754;RL=61;RPP=4.6554;RR=71;RUN=1;ReadPosRankSum=-3.309;SAB=0.45455;SAF=60;SAP=5.3792;SAR=72;SC=GATTAGAATGTGGATATCTTT;SRB=0.48836;SRF=2810;SRP=9.7866;SRR=2944;TC;TR=4;TU=GT;VQSLOD=8.5770;set=Intersection;sumGLbyD=27.19
+20	58468826	.	ACAAG	A	999	PASS	AF=0.0014;AF1=0.003429;BaseQRankSum=4.082;CI95=0.003106,0.006211;DP=8461;DP4=2500,1817,8,2;Dels=0.01;FQ=999;FR;FS=5.034;HP=2;HPLen=1;HR=1;HRun=0;HU=C;INDEL;InbreedingCoeff=-0.0183;IndelType=DEL.NumRepetitions_1.EventLength_4.;MQ=120.69;MQ0=0;MQ0Fraction=0.0000;MQRankSum=0.141;NF;NR;PP;PV4=0.21,1,0.054,1;ReadPosRankSum=2.096;SC=ATCCTGAAACACAAGAAGAAA;TC;TR=5;TU=AC;VQSLOD=7.4928;set=Intersection;sumGLbyD=29.17
+20	58731262	.	TC	T	999	PASS	AA=21;AB=0.48649;ABA=19;ABP=3.069;ABR=18;AC=7;AF=0.0101;AF1=0.01493;AN=694;BL=939;BR=848;BVAR;BaseQRankSum=4.205;CI95=0.01106,0.02212;DEL;DP=12598;DP4=1766,1428,11,15;Dels=0.01;EL=13;EPP=5.5954;ER=8;FQ=999;FR;FS=1.796;HETAR=8;HOMA=1;HOMR=1031;HP=7;HPLen=8;HR=8;HRun=2;HU=T;INDEL;InbreedingCoeff=-0.0030;IndelType=DEL.NumRepetitions_2.EventLength_1.RepeatExpansion_C.;LEN=1;LRB=0.050923;LRBP=13.073;MQ=124.57;MQ0=0;MQ0Fraction=0.0000;MQM=67.905;MQRankSum=1.103;NF;NR;NS=1040;PP;PV4=0.23,1,1,1;RA=4884;RL=10;RPP=3.1137;RR=11;RUN=1;ReadPosRankSum=-0.091;SAB=0.47619;SAF=10;SAP=3.1137;SAR=11;SC=TCATTTTTTTTCCTTGAAACT;SRB=0.58006;SRF=2833;SRP=274.9;SRR=2051;TC;TR=8;TU=T;VQSLOD=10.8783;set=Intersection;sumGLbyD=15.11
+20	59181229	rs11476579	CTT	C,CT,CTTT,CTTTT	7787.17	PASS	AC=19,195,104,91;AF=0.01599,0.16414,0.08754,0.07660;AF1=0.2124;AN=1188;BVAR;BaseQRankSum=6.347;CI95=0.146,0.2743;DB;DEL;DP=26140;DP4=932,880,352,375;Dels=0.13;FQ=85.6;FR;FS=11.914;HP=14;HR=14;HRun=14;HU=T;INDEL;INS;InbreedingCoeff=0.4183;IndelType=MULTIALLELIC_INDEL;MQ=86.88;MQ0=0;MQ0Fraction=0.0000;MQRankSum=1.469;NF;NR;PP;PV4=0.17,1,1,1;RUN=1;ReadPosRankSum=-1.055;SC=GGTGAGAAAGCTTTTTTTTTT;TC;TR=14;TU=T;VQSLOD=7.4340;dbSNP=120;set=Intersection;sumGLbyD=7.02
+20	59213979	rs112141381	G	GC	9068	PASS	AA=131;AB=0.47115;ABA=110;ABP=4.5136;ABR=98;AF=0.0586;AN=700;BL=5395;BR=5816;BVAR;BaseQRankSum=15.453;DB;DP=23381;DP4=2191,2184,71,49;Dels=0.00;EL=66;EPP=3.0269;ER=65;FR;FS=7.907;HETAR=35;HOMA=5;HOMR=1019;HP=2;HPLen=3;HR=3;HRun=0;HU=G;INDEL;INS;InbreedingCoeff=0.0283;IndelType=INS.NOVEL_1.Novel_C.;LEN=1;LRB=0.037552;LRBP=37.34;MQ=72.13;MQ0=0;MQ0Fraction=0.0000;MQM=54.496;MQRankSum=0.897;NF;NR;NS=1059;PP;PV4=0.052,1,0.066,1;RA=4976;RL=59;RPP=5.8117;RR=72;RUN=1;ReadPosRankSum=-0.811;SAB=0.58015;SAF=76;SAP=10.32;SAR=55;SC=GATGGACTGGGACAGTGACTC;SRB=0.49457;SRF=2461;SRP=4.2828;SRR=2515;TC;TR=3;TU=G;VQSLOD=9.3917;set=Intersection;sumGLbyD=28.58
+20	59252945	.	CT	C,CTT	557.18	PASS	AA=24;AB=0.84868;ABA=23;ABP=163.53;ABR=129;AC=21,29;AF=0.01759,0.02429;BL=1217;BR=1336;BVAR;BaseQRankSum=5.135;DP=9970;Dels=0.01;EL=13;EPP=3.3722;ER=11;FS=2.302;HETAR=21;HOMA=1;HOMR=1012;HRun=9;INS;InbreedingCoeff=0.1549;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.046612;LRBP=15.055;MQ0=0;MQ0Fraction=0.0000;MQM=67.208;MQRankSum=0.086;NS=1034;RA=4421;RL=11;RPP=3.3722;RR=13;RUN=1;ReadPosRankSum=-1.826;SAB=0.41667;SAF=10;SAP=4.4579;SAR=14;SRB=0.49649;SRF=2195;SRP=3.4823;SRR=2226;VQSLOD=2.8923;set=filterInVQSR-2of5;sumGLbyD=5.47
+20	60016966	.	CT	C	42650	PASS	AA=37;AB=0.97834;ABA=31;ABP=2847;ABR=1400;AC=15;AF=0.0163;AN=920;BL=2596;BR=778;BVAR;BaseQRankSum=-0.632;DEL;DP=10967;Dels=0.00;EL=14;EPP=7.7641;ER=23;FS=4.094;HETAR=421;HOMA=256;HOMR=385;HRun=1;InbreedingCoeff=-0.0051;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.53883;LRBP=2130.2;MQ0=0;MQ0Fraction=0.0000;MQM=120.3;MQRankSum=-0.911;NS=1072;RA=3413;RL=31;RPP=39.691;RR=6;RUN=1;ReadPosRankSum=-12.062;SAB=0.48649;SAF=18;SAP=3.069;SAR=19;SRB=0.47407;SRF=1618;SRP=22.943;SRR=1795;VQSLOD=3.3758;set=filterInVQSR-2of5;sumGLbyD=3.27
+20	60188651	.	AG	A	17624.52	PASS	AA=462;AB=0.76548;ABA=409;ABP=1070.7;ABR=1335;AC=403;AF=0.34444;AN=1170;BL=13877;BR=25909;BVAR;BaseQRankSum=6.180;DEL;DP=9900;Dels=0.08;EL=353;EPP=282.84;ER=109;FR;FS=2699.057;HETAR=346;HOMA=26;HOMR=633;HP=3;HR=4;HRun=1;HU=A;InbreedingCoeff=-0.2900;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_G.;LEN=1;LRB=0.30242;LRBP=7904.3;MQ0Fraction=0.0004;MQM=56.119;MQRankSum=1.644;NF;NR;NS=1005;PP;RA=3521;RL=112;RPP=269.25;RR=350;RUN=1;ReadPosRankSum=2.490;SAB=0.0064935;SAF=3;SAP=980.34;SAR=459;SC=AGGCTTCAAAAGAAAAAAAAA;SRB=0.55978;SRF=1971;SRP=112.32;SRR=1550;TC;TR=4;TU=A;VQSLOD=-34.0667;set=filterInVQSR-2of5;sumGLbyD=7.81
+20	60195570	.	GTACATACATACA	ATACATACATACA,G,GTACATACA	20140	PASS	ABR=102;AC=105,2;AF=0.08794,0.00168;AN=1194;BVAR;BaseQRankSum=-28.899;DB;DEL;DP=14347;Dels=0.02;FR;FS=52.125;HOMA=1;HOMR=1006;HP=1;HPLen=1;HR=1;HRun=0;HU=T;InbreedingCoeff=0.0695;IndelType=MIXED;MQ0Fraction=0.0007;MQRankSum=1.957;NF;NR;NS=1035;PP;RA=4759;RUN=1;ReadPosRankSum=-22.252;SAB=0.5;SAP=3.0103;SC=TGATAGATTCGTACATACATA;SRB=0.47615;SRF=2266;SRP=26.522;SRR=2493;TC;TR=21;TU=ACAT;VQSLOD=2.7673;set=filterInVQSR-2of5;sumGLbyD=19.14
+20	60670601	rs72127450	AT	A,ATT	6401.59	PASS	AC=177,79;AF=0.16239,0.07248;AF1=0.1602;AN=1090;BVAR;BaseQRankSum=8.618;CI95=0.1106,0.2058;DB;DEL;DP=17508;DP4=1285,1094,313,259;Dels=0.10;FQ=94.1;FR;FS=0.000;HP=12;HR=12;HRun=12;HU=T;INDEL;INS;InbreedingCoeff=0.1076;IndelType=MULTIALLELIC_INDEL;LEN=1;MQ=64.73;MQ0=0;MQ0Fraction=0.0000;MQRankSum=0.620;NF;NR;PP;PV4=0.78,1,0.012,1;RUN=1;ReadPosRankSum=-1.294;SC=AGCCAGGCACATTTTTTTTTT;TC;TR=12;TU=T;VQSLOD=6.1650;dbSNP=130;set=Intersection;sumGLbyD=5.80
+20	60685780	.	TC	T	1123.58	PASS	AC=79;AF=0.07655;AN=1032;BaseQRankSum=14.949;DP=2084;FS=23.521;HRun=1;HaplotypeScore=19.7117;InbreedingCoeff=0.1356;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;MQ=53.57;MQ0=61;MQ0Fraction=0.0293;MQRankSum=-7.958;QD=4.35;ReadPosRankSum=-13.757;SB=-791.28;VQSLOD=6.3549;set=VQSR
+20	60744906	rs113528167	CG	C	422.53	PASS	AC=48;AF=0.0732;AN=656;BaseQRankSum=17.669;DB;DP=1189;FS=0.356;HRun=1;HaplotypeScore=15.1808;InbreedingCoeff=0.2111;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_G.;MQ=82.83;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-10.455;QD=2.71;ReadPosRankSum=-16.887;SB=-326.46;VQSLOD=7.1707;set=VQSR
+20	60848742	.	CGT	C,CGTGT	999	PASS	AF=0.00980,0.01225;BaseQRankSum=5.597;DP=17065;DP4=1928,2188,17,13;Dels=0.01;FR;HP=1;HPLen=2;HR=2;HRun=0;HU=C;INDEL;InbreedingCoeff=0.2094;IndelType=MULTIALLELIC_INDEL;MQ=115.78;MQ0=0;MQ0Fraction=0.0000;MQRankSum=0.281;NF;NR;PP;PV4=0.36,0.4,0.12,0.12;ReadPosRankSum=-1.465;SB=-157.35;SC=TAGACGCTTCCGTGTGTGTGT;TC;TR=11;TU=GT;VQSLOD=1.7100;set=filterInVQSR-2of5;sumGLbyD=16.39
+20	61023668	rs57452309	G	GAGC	6896.67	PASS	AC=115;AF=0.1445;AN=796;BaseQRankSum=12.146;DB;DP=1423;FS=5.070;HRun=0;HaplotypeScore=29.8897;InbreedingCoeff=0.0740;IndelType=INS.NOVEL_3.;MQ=77.02;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-9.005;QD=19.16;ReadPosRankSum=-17.440;SB=-3045.82;VQSLOD=4.5788;set=VQSR
+20	61180519	.	C	CA,CT	1774.30	PASS	ABR=135;AC=27,15;AF=0.02538,0.01410;BVAR;BaseQRankSum=-2.189;DP=8393;FR;FS=27.692;HOMA=2;HOMR=825;HP=6;HPLen=3;HR=3;HU=T;HaplotypeScore=19.5313;INS;InbreedingCoeff=0.0868;IndelType=MULTIALLELIC_INDEL;LEN=1;MQ=56.11;MQ0=172;MQ0Fraction=0.0667;MQRankSum=2.605;NF;NR;NS=854;PP;QD=1.99;RA=2868;RUN=1;ReadPosRankSum=-7.324;SB=-385.54;SC=TTCTTTCTTTCTTTCTTTCTT;SRB=0.32741;SRF=939;SRP=745.08;SRR=1929;TC;TR=69;TU=CTTT;VQSLOD=3.4398;set=filterInVQSR-2of5
+20	61184281	.	AC	A	9798.10	PASS	AA=24;AB=0.96507;ABA=16;ABP=863.43;ABR=442;AC=4;AF=0.00341;AN=1174;BL=349;BR=1039;BVAR;BaseQRankSum=2.048;DEL;DP=10073;Dels=0.00;EL=11;EPP=3.3722;ER=13;FS=2.097;HETAR=141;HOMA=69;HOMR=829;HRun=1;InbreedingCoeff=0.0697;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;LEN=1;LRB=0.49712;LRBP=747.85;MQ0=0;MQ0Fraction=0.0000;MQM=98.042;MQRankSum=1.881;NS=1042;RA=3625;RL=5;RPP=20.744;RR=19;RUN=1;ReadPosRankSum=-8.009;SAB=0.75;SAF=18;SAP=16.039;SAR=6;SRB=0.52662;SRF=1909;SRP=25.323;SRR=1716;VQSLOD=1.8117;set=filterInVQSR-2of5;sumGLbyD=5.55
+20	62074219	.	C	CTAT,CTGT	2328	PASS	ABR=99;AC=20,6;AF=0.01754,0.00526;BVAR;BaseQRankSum=11.221;DP=9498;DS;FS=4.510;HOMA=15;HOMR=645;HaplotypeScore=82.8868;INS;InbreedingCoeff=0.0880;IndelType=MULTIALLELIC_INDEL;LEN=3;MQ=29.88;MQ0=1378;MQ0Fraction=0.2286;MQRankSum=-5.309;NS=689;QD=0.77;RA=1679;RUN=1;ReadPosRankSum=-3.510;SAR=1;SB=-93.21;SRB=0.70697;SRF=1187;SRP=627.71;SRR=492;VQSLOD=1.8325;set=filterInVQSR-2of5
+20	62304449	.	CA	C,CAA	6680.17	PASS	AC=141,69;AF=0.12567,0.06150;AF1=0.08178;AN=1122;BVAR;BaseQRankSum=9.754;CI95=0.05088,0.1128;DEL;DP=15867;DP4=1252,1289,232,208;Dels=0.10;FQ=52.6;FR;FS=6.576;HP=11;HR=11;HRun=11;HU=A;INDEL;INS;InbreedingCoeff=0.1950;IndelType=MULTIALLELIC_INDEL;LEN=1;MQ=60.48;MQ0Fraction=0.0004;MQRankSum=-0.049;NF;NR;PP;PV4=0.2,1,1,1;RUN=1;ReadPosRankSum=-2.137;SC=GATTCTGTGTCAAAAAAAAAA;TC;TR=11;TU=A;VQSLOD=7.4714;set=Intersection;sumGLbyD=8.36
+20	62804895	rs57769591	CCTT	C	1148	PASS	AC=8;AF=0.0085;AF1=0.002839;AN=938;BaseQRankSum=4.952;CI95=0.002212,0.006637;DB;DP=8889;DP4=2574,1668,4,8;FQ=12.3;FS=2.289;HPLen=3;HRun=0;HaplotypeScore=29.4184;INDEL;InbreedingCoeff=-0.0270;IndelType=DEL.NumRepetitions_1.EventLength_3.;MQ0=876;MQ0Fraction=0.2674;MQRankSum=-0.641;PV4=0.074,1,1,1;QD=1.03;ReadPosRankSum=0.118;SB=-65.30;VQSLOD=6.4881;dbSNP=126;set=Intersection
+20	62907688	.	AAT	A	6629.57	PASS	AC=164;AF=0.13735;AN=1194;BaseQRankSum=27.368;DP=2746;FS=5.985;HRun=0;HaplotypeScore=14.7748;InbreedingCoeff=0.1433;IndelType=DEL.NumRepetitions_2.EventLength_2.RepeatExpansion_AT.;MQ=96.65;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-3.318;QD=10.81;ReadPosRankSum=0.789;SB=-2662.16;VQSLOD=6.1473;set=VQSR
diff --git a/tests/tabix_data/vcf/20.vcf b/tests/tabix_data/vcf/20.vcf
new file mode 100644
index 0000000..5e33de1
--- /dev/null
+++ b/tests/tabix_data/vcf/20.vcf
@@ -0,0 +1,307 @@
+##fileformat=VCFv4.1
+##INFO=<ID=PacBio,Number=1,Type=String,Description="Status of PacBio for this site">
+##INFO=<ID=Sqnm,Number=1,Type=String,Description="Status of Sequenom for this site">
+##INFO=<ID=Sanger,Number=1,Type=String,Description="Status of Sanger Sequencing for this site">
+##INFO=<ID=NotCalledInValidationSamples,Number=.,Type=Flag,Description="Was not called polymorphic in sequencing for any of the passing validation samples; could still be polymorphic">
+##reference=file:///humgen/1kg/reference/human_g1k_v37.fasta
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
+20	207414	.	G	A	.	.	PacBio=NoCall;Sqnm=NoCall
+20	792106	.	C	G	.	.	PacBio=Poly;Sqnm=NoCall
+20	894031	.	G	A	.	.	PacBio=Poly;Sqnm=Poly
+20	1508892	.	A	G	.	.	PacBio=Poly;Sqnm=Poly
+20	1686745	.	G	A	.	.	PacBio=Poly;Sqnm=NoCall
+20	1818886	.	C	T	.	.	PacBio=Poly;Sqnm=Poly
+20	2062981	.	A	G	.	.	PacBio=Poly;Sqnm=Poly
+20	2773229	.	A	G	.	.	PacBio=Poly;Sqnm=Poly
+20	2817761	.	T	C	.	.	PacBio=Poly;Sqnm=Poly
+20	2994966	.	G	T	.	.	PacBio=Poly;Sqnm=Poly
+20	3126723	.	C	T	.	.	PacBio=Poly;Sqnm=Poly
+20	3523369	.	G	A	.	.	PacBio=Poly;Sqnm=Poly
+20	3635082	.	A	G	.	.	PacBio=Poly;Sqnm=Poly
+20	3714080	.	C	G	.	.	PacBio=Poly;Sqnm=Poly
+20	3905791	.	G	A	.	.	PacBio=Poly;Sqnm=NoCall
+20	3907250	.	A	G	.	.	PacBio=Poly;Sqnm=Poly
+20	4171994	.	C	T	.	.	PacBio=Poly;Sqnm=Poly
+20	4246375	.	T	C	.	.	PacBio=Poly;Sqnm=NoCall
+20	4375206	.	C	T	.	.	PacBio=Poly;Sqnm=Poly
+20	4434727	.	A	T	.	.	PacBio=NoCall;Sqnm=Mono;Sanger=Mono
+20	4495199	.	G	C	.	.	PacBio=Poly;Sqnm=Poly
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+20	60559594	.	C	T	.	.	PacBio=NoCall;Sqnm=Poly
+20	60745115	.	G	A	.	.	PacBio=Poly;Sqnm=Poly
+20	60831300	.	G	A	.	.	PacBio=Poly;Sqnm=Poly
+20	60907675	.	G	A	.	.	PacBio=Poly;Sqnm=Poly
+20	61458191	.	G	A	.	.	PacBio=Poly;Sqnm=Poly
+20	61717607	.	C	T	.	.	PacBio=Mono;Sqnm=Poly
+20	61771154	.	G	A	.	.	PacBio=Poly;Sqnm=Poly
+20	61950497	.	G	A	.	.	PacBio=Poly;Sqnm=Poly
+20	62000091	.	C	T	.	.	PacBio=Poly;Sqnm=Poly
+20	62550780	.	C	T	.	.	PacBio=NoCall;Sqnm=NoCall
+20	62558259	.	T	C	.	.	PacBio=Poly;Sqnm=Poly
+20	62727205	.	C	T	.	.	PacBio=Poly;Sqnm=Poly
diff --git a/tests/tabix_data/vcf/21.vcf b/tests/tabix_data/vcf/21.vcf
new file mode 100644
index 0000000..db6cec6
--- /dev/null
+++ b/tests/tabix_data/vcf/21.vcf
@@ -0,0 +1,310 @@
+##fileformat=VCFv4.1
+##INFO=<ID=Consensus,Number=1,Type=String,Description="Consensus validation result">
+##INFO=<ID=PacBio,Number=1,Type=String,Description="Status of PacBio for this site">
+##INFO=<ID=Sqnm,Number=1,Type=String,Description="Status of Sequenom for this site">
+##INFO=<ID=Sanger,Number=1,Type=String,Description="Status of Sanger Sequencing for this site">
+##INFO=<ID=NotCalledInValidationSamples,Number=.,Type=Flag,Description="Was not called polymorphic in sequencing for any of the passing validation samples; could still be polymorphic">
+##INFO=<ID=pcr454_ss,Number=1,Type=String,Description="Status of PCR-Roche 454 single-sample experiment for this site">
+##INFO=<ID=pcr454_ps,Number=1,Type=String,Description="Status of PCR-Roche 454 pooled-samples experiment for this site">
+##reference=file:///humgen/1kg/reference/human_g1k_v37.fasta
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
+20	207414	.	G	A	0	.	Consensus=Poly;PacBio=NoCall;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly
+20	792106	.	C	G	0	.	Consensus=Poly;PacBio=Poly;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly
+20	894031	.	G	A	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	1508892	.	A	G	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	1686745	.	G	A	0	.	Consensus=Poly;PacBio=Poly;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly
+20	1818886	.	C	T	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	2062981	.	A	G	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	2773229	.	A	G	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	2817761	.	T	C	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	2994966	.	G	T	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	3126723	.	C	T	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=NoCall;pcr454_ps=NoCall
+20	3523369	.	G	A	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	3635082	.	A	G	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	3714080	.	C	G	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	3905791	.	G	A	0	.	Consensus=Poly;PacBio=Poly;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly
+20	3907250	.	A	G	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	4171994	.	C	T	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	4246375	.	T	C	0	.	Consensus=Poly;PacBio=Poly;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly
+20	4375206	.	C	T	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	4434727	.	A	T	0	.	Consensus=Mono;PacBio=Mono;Sqnm=Mono;Sanger=Mono;pcr454_ss=NoCall;pcr454_ps=Poly
+20	4495199	.	G	C	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	4835415	.	C	T	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	4915769	.	T	C	0	.	Consensus=Poly;PacBio=Poly;Sqnm=NoCall;pcr454_ss=NoCall;pcr454_ps=NoCall
+20	4983198	.	T	C	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	5441171	.	C	T	0	.	Consensus=Poly;PacBio=Poly;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly
+20	5978029	.	T	C	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	6061317	.	C	A	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Mono;pcr454_ps=Poly
+20	6328925	.	C	A	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	6675461	.	C	T	0	.	Consensus=Poly;PacBio=Poly;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly
+20	6976115	.	C	T	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	7013349	.	G	A	0	.	Consensus=Poly;PacBio=NoCall;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly
+20	7039302	.	C	T	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	7638704	.	C	A	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	7688381	.	G	A	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	7726350	.	G	T	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=NoCall;pcr454_ps=NoCall
+20	7733957	.	C	T	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	7850516	.	T	C	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	8095059	.	G	A	0	.	Consensus=Mono;PacBio=NoCall;Sqnm=NoCall;pcr454_ss=NoCall;pcr454_ps=NoCall
+20	8232012	.	T	A	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	8415290	.	A	C	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	8438535	.	T	C	0	.	Consensus=Poly;PacBio=Poly;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly
+20	8815233	.	G	A	0	.	Consensus=Poly;PacBio=Mono;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly
+20	8953629	.	C	G	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Mono;pcr454_ps=Poly
+20	9237267	.	T	A	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=NoCall;pcr454_ps=NoCall
+20	9744549	.	T	C	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	9780416	.	C	A	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	10252552	.	T	C	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	10314038	.	C	G	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	10757416	.	T	C	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	11087688	.	A	G	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	11094107	.	G	A	0	.	Consensus=Poly;PacBio=NoCall;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly
+20	11098680	.	G	A	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	11353163	.	G	C	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	11510559	.	A	G	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	11787224	.	C	T	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	11821024	.	T	C	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=NoCall;pcr454_ps=NoCall
+20	11932295	.	A	G	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	11965311	.	G	T	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	12023599	.	C	T	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	12505523	.	G	T	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	12570054	.	A	C	0	.	Consensus=Poly;PacBio=NoCall;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	12667452	.	A	G	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=NoCall;pcr454_ps=NoCall
+20	12678271	.	G	A	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Mono;pcr454_ss=Poly;pcr454_ps=Poly
+20	12704885	.	T	C	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	12733996	.	C	T	0	.	Consensus=Poly;PacBio=Poly;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly
+20	12737269	.	C	T	0	.	Consensus=Poly;PacBio=NoCall;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly
+20	12788981	.	G	A	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	12828594	.	T	C	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	12999157	.	T	C	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	13083804	.	C	G	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	13197077	.	G	T	0	.	Consensus=Poly;PacBio=Poly;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly
+20	13217896	.	A	G	0	.	Consensus=Poly;PacBio=NoCall;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	13276778	.	G	A	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	13375116	.	G	A	0	.	Consensus=Mono;PacBio=Mono;Sqnm=NoCall;NotCalledInValidationSamples;pcr454_ss=Mono;pcr454_ps=Mono
+20	13648056	.	T	C	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	13672895	.	C	T	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	14160159	.	C	G	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	14266815	.	T	A	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	14865143	.	C	T	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	14882868	.	T	G	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	15244725	.	C	A	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	15277072	.	G	A	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=NoCall;pcr454_ps=NoCall
+20	15390867	.	C	T	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	15785205	.	T	C	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	15833020	.	A	G	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	15847620	.	C	T	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	15953253	.	G	A	0	.	Consensus=Poly;PacBio=Poly;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly
+20	15964434	.	G	C	0	.	Consensus=NoCall;PacBio=NoCall;Sqnm=NoCall;pcr454_ss=NoCall;pcr454_ps=NoCall
+20	16183922	.	G	A	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	16190824	.	A	G	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	16557779	.	A	G	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=NoCall;pcr454_ps=NoCall
+20	16730061	.	C	T	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	16794015	.	T	C	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	17048741	.	G	A	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	17299827	.	G	A	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=NoCall;pcr454_ps=NoCall
+20	17299845	.	C	T	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	17390323	.	G	A	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=NoCall;pcr454_ps=NoCall
+20	17624973	.	C	G	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	17666040	.	G	A	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	17735813	.	T	C	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	17794990	.	A	G	0	.	Consensus=Mono;PacBio=Mono;Sqnm=Mono;NotCalledInValidationSamples;pcr454_ss=NoCall;pcr454_ps=NoCall
+20	17809418	.	G	A	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	17860794	.	C	T	0	.	Consensus=Poly;PacBio=Mono;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly
+20	17881936	.	A	G	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	17893097	.	C	G	0	.	Consensus=Mono;PacBio=NoCall;Sqnm=NoCall;pcr454_ss=Mono;pcr454_ps=Mono
+20	18188883	.	A	G	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=NoCall;pcr454_ps=NoCall
+20	18199319	.	G	A	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	18233699	.	C	T	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	18536869	.	G	A	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	18637785	.	T	C	0	.	Consensus=Mono;PacBio=NoCall;Sqnm=Mono;Sanger=Mono;NotCalledInValidationSamples;pcr454_ss=Mono;pcr454_ps=Mono
+20	18763166	.	G	A	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	19102715	.	A	G	0	.	Consensus=Mono;PacBio=NoCall;Sqnm=NoCall;pcr454_ss=Mono;pcr454_ps=Mono
+20	19244609	.	C	T	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	19573719	.	C	T	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	19815613	.	A	G	0	.	Consensus=Poly;PacBio=NoCall;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	20511479	.	C	T	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;Sanger=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	20639358	.	T	C	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	21278490	.	T	C	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	21297718	.	C	G	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=NoCall;pcr454_ps=NoCall
+20	21418269	.	A	T	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	21560553	.	A	T	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	21618451	.	G	A	0	.	Consensus=NoCall;PacBio=NoCall;Sqnm=NoCall;pcr454_ss=NoCall;pcr454_ps=NoCall
+20	21705723	.	C	A	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	22076189	.	A	G	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	22118677	.	T	A	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	22320721	.	C	T	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	22368918	.	C	A	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	23020003	.	A	G	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	23214163	.	G	A	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	23273877	.	T	C	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	23335790	.	C	T	0	.	Consensus=Poly;PacBio=Poly;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Mono
+20	23790659	.	C	T	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	23830388	.	T	C	0	.	Consensus=Poly;PacBio=Poly;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly
+20	23837678	.	C	G	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	23901081	.	A	C	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	23946361	.	C	T	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	23949242	.	A	G	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	24539119	.	A	G	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=NoCall;pcr454_ps=NoCall
+20	24986457	.	C	T	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	25183729	.	G	A	0	.	Consensus=Mono;PacBio=NoCall;Sqnm=NoCall;pcr454_ss=Mono;pcr454_ps=Mono
+20	25277133	.	C	T	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	25292464	.	C	T	0	.	Consensus=Poly;PacBio=Poly;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly
+20	25528915	.	G	C	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	25851836	.	A	G	0	.	Consensus=Poly;PacBio=NoCall;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly
+20	25970163	.	C	T	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	29920798	.	C	T	0	.	Consensus=Poly;PacBio=NoCall;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly
+20	30007713	.	T	C	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	30051768	.	T	C	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	30183598	.	T	C	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	30604408	.	G	A	0	.	Consensus=Poly;PacBio=NoCall;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly
+20	30759940	.	G	T	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	30881454	.	G	T	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=NoCall;pcr454_ps=Poly
+20	31356560	.	C	T	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	31450036	.	A	G	0	.	Consensus=Poly;PacBio=NoCall;Sqnm=Mono;pcr454_ss=Poly;pcr454_ps=Poly
+20	31589920	.	A	T	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	31922121	.	C	T	0	.	Consensus=Poly;PacBio=NoCall;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly
+20	32801430	.	G	C	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	32943975	.	G	T	0	.	Consensus=Mono;PacBio=Mono;Sqnm=Mono;pcr454_ss=NoCall;pcr454_ps=NoCall
+20	33155812	.	C	A	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	34090682	.	C	T	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	34254080	.	C	T	0	.	Consensus=Mono;PacBio=Mono;Sqnm=NoCall;NotCalledInValidationSamples;pcr454_ss=Mono;pcr454_ps=Mono
+20	34312126	.	C	T	0	.	Consensus=Poly;PacBio=Poly;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly
+20	34481504	.	G	A	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	34694577	.	G	A	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	35026572	.	T	C	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=NoCall;pcr454_ps=NoCall
+20	35472344	.	T	G	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=NoCall;pcr454_ps=NoCall
+20	35882698	.	G	A	0	.	Consensus=Poly;PacBio=Poly;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly
+20	36044719	.	G	A	0	.	Consensus=Poly;PacBio=Poly;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly
+20	36047623	.	C	A	0	.	Consensus=Poly;PacBio=NoCall;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly
+20	36204890	.	C	T	0	.	Consensus=Poly;PacBio=Poly;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly
+20	36469514	.	G	C	0	.	Consensus=Poly;PacBio=NoCall;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	36840217	.	T	C	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=NoCall;pcr454_ps=NoCall
+20	37460945	.	C	T	0	.	Consensus=Poly;PacBio=Mono;Sqnm=Poly;pcr454_ss=NoCall;pcr454_ps=NoCall
+20	37665246	.	G	A	0	.	Consensus=Poly;PacBio=Poly;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly
+20	37732397	.	A	G	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	37874645	.	G	T	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	37958191	.	T	C	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	37996273	.	C	T	0	.	Consensus=Mono;PacBio=Mono;Sqnm=NoCall;NotCalledInValidationSamples;pcr454_ss=Mono;pcr454_ps=Mono
+20	38016547	.	C	T	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	38435682	.	A	G	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=NoCall;pcr454_ps=NoCall
+20	38505534	.	A	T	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	38803278	.	A	G	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	38963803	.	G	C	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	38971986	.	A	G	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	39269586	.	G	A	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	39289390	.	C	A	0	.	Consensus=Mono;PacBio=Mono;Sqnm=Mono;NotCalledInValidationSamples;pcr454_ss=NoCall;pcr454_ps=NoCall
+20	39318956	.	T	A	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=NoCall;pcr454_ps=Poly
+20	39736197	.	A	G	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	40241339	.	T	C	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	41473555	.	G	A	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	41878576	.	T	G	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	42022716	.	A	G	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=NoCall;pcr454_ps=NoCall
+20	42033671	.	A	C	0	.	Consensus=Poly;PacBio=NoCall;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly
+20	42270334	.	C	T	0	.	Consensus=NoCall;PacBio=NoCall;Sqnm=NoCall;pcr454_ss=NoCall;pcr454_ps=NoCall
+20	42449590	.	C	T	0	.	Consensus=Poly;PacBio=Poly;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly
+20	42521157	.	T	G	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	42624300	.	C	A	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	42984548	.	G	A	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	43200148	.	G	C	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	43425384	.	T	G	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	43521990	.	C	G	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	43565804	.	G	A	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	43591237	.	T	C	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	43805929	.	C	T	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	43866692	.	A	G	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	43902088	.	C	T	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=NoCall;pcr454_ps=NoCall
+20	44478507	.	C	A	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=NoCall;pcr454_ps=NoCall
+20	44768810	.	C	T	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	45151582	.	G	A	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	45414003	.	G	A	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Mono;pcr454_ps=Mono
+20	45776825	.	G	C	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=NoCall;pcr454_ps=NoCall
+20	46454905	.	G	A	0	.	Consensus=Poly;PacBio=Poly;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly
+20	46823642	.	C	T	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	47001376	.	C	T	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	47079360	.	G	C	0	.	Consensus=Poly;PacBio=Poly;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly
+20	47248953	.	G	A	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	47480655	.	C	T	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	47529099	.	T	C	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	47703355	.	A	C	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	47919541	.	A	G	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	48126120	.	A	C	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	48157380	.	G	A	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	48233077	.	C	T	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=NoCall;pcr454_ps=NoCall
+20	48488571	.	G	A	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	48534468	.	G	A	0	.	Consensus=Poly;PacBio=Poly;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly
+20	48631385	.	G	C	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	48654970	.	G	A	0	.	Consensus=Poly;PacBio=Poly;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly
+20	48708007	.	C	T	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	48979827	.	C	A	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	49100106	.	G	A	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	49509102	.	G	A	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	49631170	.	G	A	0	.	Consensus=Mono;PacBio=Mono;Sqnm=Mono;NotCalledInValidationSamples;pcr454_ss=Mono;pcr454_ps=Mono
+20	50210361	.	C	T	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	50309600	.	C	A	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	50681296	.	T	C	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	50750138	.	A	G	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	51639257	.	G	A	0	.	Consensus=Poly;PacBio=Mono;Sqnm=Poly;pcr454_ss=Mono;pcr454_ps=Mono
+20	51814664	.	T	C	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	51891088	.	C	T	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	52299250	.	A	G	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	52363435	.	G	A	0	.	Consensus=Poly;PacBio=Poly;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly
+20	52583941	.	C	T	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	52787584	.	C	T	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	53256945	.	G	A	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	54155398	.	A	G	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	54172374	.	G	T	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=NoCall;pcr454_ps=Poly
+20	54209446	.	A	G	0	.	Consensus=Poly;PacBio=Mono;Sqnm=Mono;NotCalledInValidationSamples;Sanger=Poly;pcr454_ss=Mono;pcr454_ps=Mono
+20	54317862	.	C	T	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	54852735	.	C	T	0	.	Consensus=Poly;PacBio=Poly;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly
+20	54889864	.	G	A	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	55208711	.	G	A	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	55220477	.	G	T	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	55224856	.	G	T	0	.	Consensus=NoCall;PacBio=NoCall;Sqnm=NoCall;pcr454_ss=NoCall;pcr454_ps=NoCall
+20	55441530	.	C	T	0	.	Consensus=Poly;PacBio=Poly;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly
+20	55585710	.	C	T	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	55630163	.	C	T	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	56031994	.	A	G	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	56316071	.	T	G	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=NoCall;pcr454_ps=NoCall
+20	56366198	.	C	T	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	56703987	.	G	A	0	.	Consensus=Poly;PacBio=Mono;Sqnm=Mono;NotCalledInValidationSamples;Sanger=Poly;pcr454_ss=Mono;pcr454_ps=Mono
+20	56794829	.	G	C	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	56797026	.	G	A	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	56922427	.	A	G	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	57025102	.	A	T	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	57104529	.	G	A	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	57360225	.	C	T	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	57630386	.	T	A	0	.	Consensus=Poly;PacBio=NoCall;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly
+20	57754033	.	G	A	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=NoCall;pcr454_ps=NoCall
+20	57956631	.	C	T	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=NoCall;pcr454_ps=NoCall
+20	57997801	.	C	T	0	.	Consensus=Poly;PacBio=Poly;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly
+20	58046279	.	C	G	0	.	Consensus=Poly;PacBio=NoCall;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly
+20	58186723	.	A	G	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	58214460	.	C	T	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	58317759	.	A	G	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	58491642	.	A	C	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	58560045	.	C	T	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	58629232	.	C	T	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	58805192	.	G	T	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	58869523	.	A	G	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	59337535	.	T	C	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	59441596	.	G	A	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	59445223	.	G	A	0	.	Consensus=Poly;PacBio=NoCall;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly
+20	59605846	.	C	T	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	59864395	.	G	C	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=NoCall;pcr454_ps=NoCall
+20	60099821	.	G	T	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	60290551	.	A	G	0	.	Consensus=Poly;PacBio=Mono;Sqnm=Mono;NotCalledInValidationSamples;Sanger=Poly;pcr454_ss=Mono;pcr454_ps=Mono
+20	60362527	.	G	C	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	60516358	.	C	T	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	60559594	.	C	T	0	.	Consensus=Poly;PacBio=NoCall;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	60745115	.	G	A	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	60831300	.	G	A	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	60907675	.	G	A	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	61458191	.	G	A	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	61717607	.	C	T	0	.	Consensus=Poly;PacBio=Mono;Sqnm=Poly;pcr454_ss=Mono;pcr454_ps=Mono
+20	61771154	.	G	A	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	61950497	.	G	A	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	62000091	.	C	T	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	62550780	.	C	T	0	.	Consensus=NoCall;PacBio=NoCall;Sqnm=NoCall;pcr454_ss=NoCall;pcr454_ps=NoCall
+20	62558259	.	T	C	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
+20	62727205	.	C	T	0	.	Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly
diff --git a/tests/tabix_data/vcf/22.vcf b/tests/tabix_data/vcf/22.vcf
new file mode 100644
index 0000000..ffb2fce
--- /dev/null
+++ b/tests/tabix_data/vcf/22.vcf
@@ -0,0 +1,1000 @@
+##fileformat=VCFv4.0
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FilterLiftedVariants="analysis_type=FilterLiftedVariants input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=null excludeIntervals=null reference_sequence=/local/sequence/reference/BWA_ref/hg19/hg19.fasta rodBind=[/local/scratch/xyliu/0.915136538286792.sorted.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false enable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null quiet_output_mode=false debug_mode=false help=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub"
+##INFO=<ID=VC,Number=1,Type=String,Description="Variation Class">
+##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA15029	NA15036	NA15038	NA15056b	NA15072	NA15144C	NA15213_006	NA15215A	NA15216_A2	NA15221b	NA15223_6v2	NA15224_4	NA15226A	NA15227b	NA15236_6	NA15242_005	NA15245v2	NA15268	NA15324_A1	NA15385b	NA15386A	NA15510_A1	NA15590_4	NA15594_005	NA18500b	NA18501	NA18502	NA18503	NA18504	NA18505	NA18506	NA18507	NA18508	NA18515	NA18516	NA18517	NA18521	NA18522	NA18523	NA18524_B1	NA18526_B2	NA18529_B1	NA18532_B1	NA18537_B1	NA18540_B1	NA18542_B1	NA18545_5	NA18547_B1	NA18550_B1	NA18555_A2	NA18561_A3	NA18562_B1	NA18563	NA18564_4	NA18566_3	NA18570_3	NA18571_3	NA18572_3	NA18573_B3	NA18576_4	NA18577_B1	NA18579_B1	NA18582_B1	NA18592_2	NA18593_B1	NA18594_B1	NA18603_B1	NA18605_B1	NA18608_B1	NA18609_B1	NA18611_B1	NA18612_B1	NA18620_3	NA18621_B1	NA18622_B1	NA18623_B1	NA18624	NA18632_3	NA18635_A1	NA18637_2	NA18852	NA18853	NA18854	NA18855	NA18856	NA18857	NA18858	NA18859	NA18860	NA18861	NA18862	NA18863	NA18870	NA18871	NA18872	NA18912	NA18913	NA18914	NA18940_3	NA19092	NA19093	NA19094	NA19098	NA19099	NA19100	NA19101	NA19102	NA19103	NA19116	NA19119b	NA19120	NA19127	NA19128	NA19129	NA19130b	NA19131	NA19132b	NA19137	NA19138	NA19139	NA19140b	NA19141	NA19142	NA19143	NA19144	NA19145	NA19152	NA19153	NA19154	NA19159	NA19160	NA19161	NA19171	NA19172	NA19173	NA19192	NA19193	NA19194	NA19200	NA19201	NA19202	NA19203	NA19204	NA19205	NA19206	NA19207	NA19208v2	NA19209	NA19210	NA19211	NA19221	NA19222	NA19223	NA19238	NA19239	NA19240	NA_pos103a	NS12911_1
+chr1	5911136	.	T	TGCCATTCCAAAGAGGCACTCA	.	PASS	VC=INDEL;AC=28;AF=0.09;AN=316	GT	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	1/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0
+chr1	17054990	.	G	GA	.	PASS	VC=INDEL;AC=25;AF=0.12;AN=200	GT	./.	./.	0/1	./.	0/0	./.	./.	./.	./.	0/0	0/1	./.	./.	0/0	./.	./.	0/1	./.	./.	./.	./.	0/0	0/1	./.	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/1	./.	./.	./.	0/0	0/0	./.	0/0	0/0	./.	0/0	./.	0/0	./.	./.	./.	./.	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/1	./.	0/1	./.	0/1	./.	0/0	0/0	0/0	./.	0/1	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	./.	./.	0/0	0/0	0/0	0/1	./.	./.	./.	0/1	0/1	./.	0/1	0/1	0/1	0/0	0/0	./.	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/0	./.	./.	./.	0/1	./.	./.	0/0	./.	./.	./.	./.	./.	./.	./.	0/1	0/1	./.
+chr1	17390953	.	CT	C	.	PASS	VC=INDEL;AC=118;AF=0.37;AN=316	GT	0/1	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	0/1	0/1	1/1	1/1	0/0	1/1	0/1	0/0	0/1	0/0	0/1	1/1	0/0	1/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	1/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	1/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/0	1/1	1/1	0/1	0/1	1/1	1/1	0/0	0/1	0/1	1/1	0/1	1/1	0/1	0/0	0/1	0/0	0/0	1/1	0/1	0/0	0/1	0/1	1/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	1/1	0/0	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/0	1/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/1	0/1
+chr1	17754916	.	CCT	C	.	PASS	VC=INDEL;AC=66;AF=0.21;AN=316;refseq.name=NM_018715;refseq.positionType=intron	GT	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	1/1	0/0	0/1	0/1	1/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	1/1	0/0	0/0	0/0	1/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	1/1	0/1
+chr1	18293100	.	C	CCTC	.	PASS	VC=INDEL;AC=263;AF=0.84;AN=314	GT	1/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/0	1/1	0/0	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/0	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/0	1/1	1/1	0/1	0/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1	0/1	0/1	0/1	1/1	1/1	0/1	1/1	0/0	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	1/1	0/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1
+chr1	18823397	.	T	TTAAT	.	PASS	VC=INDEL;AC=87;AF=0.28;AN=316	GT	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	1/1	0/0	0/0	0/1	0/1	1/1	0/1	0/1	1/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	1/1	0/1	1/1	0/0	0/1	0/1	0/0	0/0	1/1	1/1	1/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	1/1	0/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	1/1	0/1	0/0	0/1	0/0	1/1	0/1	0/1	0/1	0/1	0/1	1/1	0/0	0/1	0/1	0/1	0/1	1/1	0/1	1/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	1/1	1/1	1/1	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	19215209	.	G	GAG	.	PASS	VC=INDEL;AC=2;AF=0.01;AN=316;refseq.name=NM_003748;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1
+chr1	19943821	.	CACAG	C	.	PASS	VC=INDEL;AC=12;AF=0.04;AN=308;refseq.name=NM_001032363;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	./.	0/1	0/0	0/0	0/0	./.	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	20092486	.	GAAG	G	.	PASS	VC=INDEL;AC=7;AF=0.02;AN=314;refseq.name=NM_181719;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	20977854	.	A	ATTC	.	PASS	VC=INDEL;AC=152;AF=0.52;AN=292;refseq.name=NM_032409;refseq.positionType=exon	GT	0/1	1/1	1/1	0/1	0/0	0/0	0/1	1/1	0/1	0/0	./.	0/1	0/1	1/1	0/1	0/1	./.	0/0	1/1	1/1	0/1	0/1	0/0	1/1	0/0	0/0	0/0	0/1	0/0	1/1	0/1	1/1	0/1	0/1	0/1	0/0	0/1	1/1	0/0	1/1	1/1	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/0	1/1	1/1	1/1	0/1	0/1	0/1	0/1	1/1	0/0	0/1	0/0	0/1	./.	0/0	0/1	0/1	0/1	0/0	0/0	1/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/0	1/1	1/1	0/1	1/1	1/1	./.	./.	0/0	0/0	1/1	0/1	0/0	0/1	0/0	0/0	0/1	0/0	1/1	0/1	0/0	0/1	0/1	1/1	1/1	0/0	0/0	0/0	1/1	0/1	1/1	0/0	0/0	./.	0/0	./.	0/0	1/1	1/1	1/1	0/1	0/0	0/1	0/0	0/1	0/1	1/1	0/1	0/1	0/1	0/1	1/1	./.	0/1	1/1	1/1	0/0	0/1	0/1	1/1	./.	./.	0/1	0/0	0/0	0/0	./.	1/1	0/1	1/1	0/0	./.	0/1	1/1	1/1	1/1	1/1	0/0	0/1	0/1	1/1
+chr1	21275058	.	CTTTG	C	.	PASS	VC=INDEL;AC=30;AF=0.1;AN=296;refseq.name=NM_003760;refseq.positionType=intron	GT	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/1	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	./.	0/0	./.	0/0	0/1	0/1	0/0	0/0	0/0	./.	./.	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/1	0/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	1/1	0/1	0/0	0/0
+chr1	22642904	.	A	AAC	.	PASS	VC=INDEL;AC=255;AF=0.85;AN=300	GT	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	1/1	0/1	1/1	./.	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	1/1	0/0	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	1/1	0/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	./.	1/1	0/1	1/1	1/1	1/1	./.	0/1	0/1	0/1	1/1	1/1	1/1	./.	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	./.	1/1	0/1	0/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1
+chr1	22844297	.	ATCT	A	.	PASS	VC=INDEL;AC=162;AF=0.51;AN=316;refseq.name=NM_001083621;refseq.positionType=intron	GT	0/1	0/0	0/0	0/1	0/1	0/0	0/0	1/1	0/0	0/0	0/1	0/1	0/1	0/1	0/0	1/1	0/0	0/1	1/1	0/0	0/0	0/1	1/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/0	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/0	1/1	0/0	0/0	1/1	0/0	0/0	0/0	1/1	0/1	0/0	1/1	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/0	1/1	0/1	0/1	1/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	1/1	0/1	1/1	0/1	0/1	1/1	0/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/1	1/1	0/0	0/1	1/1	0/1	0/1	1/1	1/1	1/1	0/0	0/1	0/1	1/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/0	1/1	0/1	1/1	0/1	0/0	0/0	1/1	0/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/0
+chr1	22844299	.	CTTC	C	.	PASS	VC=INDEL;AC=160;AF=0.51;AN=314;refseq.name=NM_001083621;refseq.positionType=intron	GT	0/1	0/0	0/0	0/1	0/1	0/0	0/0	1/1	0/0	0/0	0/1	0/1	0/1	0/1	0/0	1/1	0/0	0/1	1/1	0/0	0/0	0/1	1/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/0	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/0	1/1	0/0	0/0	1/1	0/0	0/0	0/0	1/1	0/1	0/0	1/1	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/0	1/1	0/1	0/1	1/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	1/1	0/1	1/1	0/1	0/1	1/1	0/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/1	1/1	0/0	0/1	1/1	0/1	0/1	1/1	1/1	1/1	0/0	0/1	0/1	1/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/0	1/1	0/1	1/1	0/1	0/0	0/0	1/1	0/1	1/1	0/1	1/1	1/1	0/1	./.	1/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/0
+chr1	23162393	.	AA	A	.	PASS	VC=INDEL;AC=44;AF=0.14;AN=316;refseq.name=NM_004442;refseq.positionType=intron	GT	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	1/1	0/1	0/0	0/0	0/0	0/0	1/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1
+chr1	23882634	.	T	TAGGTG	.	PASS	VC=INDEL;AC=24;AF=0.08;AN=284	GT	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	./.	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/0	1/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	./.	0/1	0/1	./.	0/1	0/0	0/0	1/1	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	./.	0/0	./.	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0
+chr1	25799681	.	CTCTG	C	.	PASS	VC=INDEL;AC=49;AF=0.21;AN=230;refseq.name=NM_018202;refseq.positionType=intron	GT	0/1	./.	1/1	./.	0/1	./.	0/1	0/0	0/0	./.	0/0	0/0	0/0	0/1	0/1	1/1	0/1	./.	./.	0/1	1/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	./.	./.	1/1	./.	1/1	0/0	0/1	1/1	./.	0/1	./.	0/1	./.	0/1	0/1	0/0	1/1	0/1	./.	./.	0/1	./.	1/1	0/1	./.	0/1	1/1	./.	./.	0/1	./.	0/1	./.	./.	1/1	./.	0/1	./.	1/1	./.	0/0	./.	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	./.	./.	0/0	./.	./.	0/0	./.	./.	./.	./.	./.	0/0	0/0	0/0	./.	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	./.	./.	0/0	0/0	./.	./.	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1
+chr1	26081170	.	CA	C	.	PASS	VC=INDEL;AC=17;AF=0.06;AN=308;refseq.name=NM_020379;refseq.positionType=intron	GT	0/0	./.	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	1/1	0/1	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	1/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	26240086	.	GAT	G	.	PASS	VC=INDEL;AC=31;AF=0.1;AN=316	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0
+chr1	26725650	.	A	ATGAAG	.	PASS	VC=INDEL;AC=300;AF=0.95;AN=316	GT	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/0	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1
+chr1	26725655	.	G	GTGAAG	.	PASS	VC=INDEL;AC=300;AF=0.95;AN=316	GT	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/0	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1
+chr1	27425097	.	CTGG	C	.	PASS	VC=INDEL;AC=40;AF=0.16;AN=248;refseq.name=NM_003047;refseq.positionType=terminator	GT	1/1	0/1	0/0	./.	0/0	0/0	./.	0/0	0/0	./.	./.	0/0	0/0	./.	./.	0/0	0/1	0/1	0/0	0/0	0/1	0/0	0/0	./.	0/1	./.	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	./.	./.	0/0	0/0	./.	./.	./.	./.	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	./.	0/1	0/0	0/0	0/0	0/0	./.	./.	0/0	./.	./.	./.	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	./.	0/0	0/1	0/1	0/1	0/1	./.	0/1	./.	0/0	0/0	0/0	0/1	0/0	./.	0/0	0/0	0/0	0/1	0/0	0/0	./.	0/1	0/1	0/1	./.	./.	0/0	0/1	0/0	./.	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/0	./.	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	./.	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	1/1	./.	0/0	0/0	./.	0/0	0/0	./.	0/0
+chr1	27737240	.	A	AT	.	PASS	VC=INDEL;AC=0;AF=0;AN=316;refseq.name=NM_006990;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	27744410	.	GATCCATG	G	.	PASS	VC=INDEL;AC=166;AF=0.56;AN=296;refseq.name=NM_006990;refseq.positionType=intron	GT	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/1	1/1	0/1	0/0	1/1	0/1	0/0	0/0	1/1	./.	0/1	0/0	./.	0/0	./.	0/1	0/1	0/1	1/1	1/1	0/1	1/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	0/0	0/0	0/0	1/1	0/0	0/0	0/1	0/0	0/0	0/0	1/1	1/1	0/0	0/0	./.	1/1	0/1	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/1	1/1	0/0	0/1	0/1	0/0	1/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	0/0	0/1	0/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	0/1	./.	1/1	0/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	./.	1/1	0/1	1/1	./.	0/1	1/1	1/1	1/1	0/1	0/1	0/1	0/0	1/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	0/0	0/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	0/0	./.	0/1	0/1	1/1	1/1	0/1	0/1	0/1	0/1	./.	./.
+chr1	28156589	.	G	GGATG	.	PASS	VC=INDEL;AC=127;AF=0.4;AN=314;refseq.name=NM_002713;refseq.positionType=promoter	GT	0/0	0/0	1/1	0/0	0/1	0/1	0/0	0/0	0/1	0/0	1/1	0/0	0/0	1/1	0/0	0/0	0/0	1/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/1	1/1	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	0/1	0/0	0/1	0/0	1/1	1/1	1/1	1/1	0/1	0/1	0/0	0/1	1/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	1/1	0/1	0/1	./.	0/1	0/1	1/1	0/1	0/1	0/0	0/1	0/0	1/1	0/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	0/1	0/1	1/1	0/1	1/1	0/1	0/1	1/1	1/1	0/0	0/1	1/1	0/1	1/1	0/0	1/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/0
+chr1	28721777	.	TA	T	.	PASS	VC=INDEL;AC=287;AF=0.91;AN=316;refseq.name=NM_001048183;refseq.positionType=intron	GT	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	0/1	0/0	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1
+chr1	28721778	.	AA	A	.	PASS	VC=INDEL;AC=287;AF=0.91;AN=316;refseq.name=NM_001048183;refseq.positionType=intron	GT	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	0/1	0/0	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1
+chr1	28907201	.	GT	G	.	PASS	VC=INDEL;AC=3;AF=0.01;AN=224	GT	0/0	./.	0/0	0/0	./.	./.	0/0	./.	./.	0/0	0/0	./.	./.	0/0	./.	./.	0/0	./.	./.	0/0	./.	./.	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	./.	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	./.	./.	./.	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	./.	0/0	0/0	0/0	./.	./.	0/0	0/1	0/1	./.	./.	0/0	./.	./.	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	./.	./.	0/0	0/0	0/0	0/0	0/0	./.	./.	0/0	0/0	0/0	./.	0/0	0/0	./.	0/0	0/1	./.	./.	./.	./.
+chr1	29223339	.	G	GTGAG	.	PASS	VC=INDEL;AC=203;AF=0.7;AN=292;refseq.name=NM_004437;refseq.positionType=intron	GT	1/1	1/1	./.	1/1	1/1	1/1	1/1	0/1	0/1	0/0	1/1	1/1	0/1	0/1	./.	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/0	1/1	0/1	1/1	0/0	1/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	./.	1/1	0/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	1/1	1/1	1/1	1/1	1/1	1/1	./.	0/1	1/1	1/1	./.	1/1	1/1	0/1	1/1	0/1	./.	1/1	0/1	0/0	0/0	0/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	0/0	1/1	1/1	0/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	0/1	1/1	0/1	0/1	0/0	0/0	./.	./.	0/1	0/0	0/1	0/0	0/1	0/1	0/0	1/1	0/1	1/1	1/1	0/1	0/1	0/0	0/0	0/0	1/1	0/1	./.	0/0	0/1	0/1	1/1	1/1	1/1	0/0	0/1	0/0	0/1	1/1	0/1	0/0	1/1	0/0	0/0	0/0	0/0	1/1	1/1	./.	1/1	0/1
+chr1	29223342	.	A	AGCAA	.	PASS	VC=INDEL;AC=71;AF=0.29;AN=242;refseq.name=NM_004437;refseq.positionType=intron	GT	0/1	0/1	1/1	./.	0/1	0/1	0/1	0/0	./.	0/0	0/1	./.	0/0	0/0	1/1	0/1	0/1	0/0	0/1	0/0	0/1	./.	1/1	0/1	./.	./.	0/1	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/0	1/1	0/1	0/0	1/1	0/1	0/1	1/1	0/1	0/1	0/1	./.	0/1	./.	0/1	./.	0/1	0/1	./.	0/1	0/1	./.	./.	0/1	./.	./.	./.	./.	0/1	./.	0/0	./.	./.	./.	0/1	0/1	0/0	0/1	0/0	0/1	./.	0/0	0/0	0/0	./.	0/1	0/1	0/1	0/0	0/0	./.	0/0	./.	0/1	0/1	0/0	0/0	0/0	0/0	./.	0/0	0/1	0/1	0/0	0/1	./.	./.	0/0	0/0	./.	0/1	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	./.	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/1	./.	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	./.	0/1	0/0	0/0	0/1	0/0	0/0	./.	0/0	./.	0/1	./.	./.	0/0
+chr1	29865521	.	G	GCTCCGT	.	PASS	VC=INDEL;AC=115;AF=0.36;AN=316	GT	0/0	1/1	0/0	0/1	0/1	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/0	1/1	0/0	1/1	0/1	0/1	1/1	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	1/1	0/1	0/0	0/1	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/1	1/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/1	0/1	0/0	1/1	0/1	0/0	0/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	1/1	1/1	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	1/1	0/0	0/1	1/1	0/0	0/1	0/1	0/0	0/0	1/1	0/0	0/1	0/1	1/1	1/1	0/1	0/1	1/1	0/1	1/1	1/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	1/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/0
+chr1	31128790	.	C	CT	.	PASS	VC=INDEL;AC=0;AF=0;AN=316	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	31135886	.	A	AG	.	PASS	VC=INDEL;AC=246;AF=0.92;AN=268	GT	./.	1/1	0/1	1/1	0/1	./.	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	./.	1/1	1/1	1/1	1/1	./.	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	./.	./.	./.	1/1	./.	1/1	0/1	0/1	0/1	./.	1/1	1/1	./.	./.	0/1	1/1	1/1	./.	1/1	1/1	./.	0/1	1/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	./.	1/1	1/1	1/1	./.	0/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	./.	./.	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.
+chr1	31503645	.	AAAAGA	A	.	PASS	VC=INDEL;AC=5;AF=0.02;AN=314;refseq.name=NM_001020658;refseq.positionType=intron	GT	0/1	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	31504005	.	C	CAT	.	PASS	VC=INDEL;AC=84;AF=0.27;AN=316;refseq.name=NM_001020658;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/0
+chr1	31731414	.	CCTCT	C	.	PASS	VC=INDEL;AC=40;AF=0.13;AN=314	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	1/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	./.	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	31775152	.	A	ACTA	.	PASS	VC=INDEL;AC=47;AF=0.15;AN=308;refseq.name=NM_016505;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	./.	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	1/1	0/1	1/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	./.	./.	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	1/1	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	31882582	.	G	GGCCTCA	.	PASS	VC=INDEL;AC=163;AF=0.59;AN=274	GT	1/1	1/1	0/0	0/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	0/0	1/1	1/1	./.	1/1	0/1	0/1	0/0	1/1	0/1	0/1	1/1	0/1	./.	0/1	1/1	0/1	1/1	0/0	1/1	0/1	0/1	0/0	0/1	./.	0/1	1/1	0/1	0/1	1/1	0/1	./.	0/1	1/1	0/1	0/1	1/1	1/1	0/0	0/1	1/1	0/0	1/1	1/1	1/1	1/1	0/1	./.	1/1	0/1	1/1	1/1	0/1	./.	./.	./.	1/1	./.	1/1	0/1	0/1	0/1	0/0	0/1	1/1	1/1	0/1	1/1	0/1	0/0	./.	0/0	1/1	0/0	0/1	0/1	1/1	1/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/0	./.	0/1	0/1	1/1	0/1	0/0	1/1	0/1	1/1	./.	1/1	0/1	./.	0/1	0/1	0/1	./.	1/1	0/1	1/1	1/1	0/1	1/1	0/1	0/0	./.	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/0	./.	0/1	0/1	0/1	./.	./.	0/1	0/1	./.	0/0	0/1	./.	0/1	./.	1/1	1/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	1/1	0/1	0/1	1/1
+chr1	32010706	.	GG	G	.	PASS	VC=INDEL;AC=312;AF=1;AN=312	GT	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1
+chr1	32078865	.	G	GT	.	PASS	VC=INDEL;AC=78;AF=0.25;AN=316	GT	0/1	0/0	0/1	0/1	0/0	0/0	1/1	0/0	0/1	1/1	0/0	0/0	0/1	0/0	0/0	1/1	1/1	0/0	0/1	1/1	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	1/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	1/1	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/0	1/1	1/1	1/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/0	1/1	0/1	1/1	0/1	0/0	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	1/1	0/1
+chr1	33422344	.	G	GAA	.	PASS	VC=INDEL;AC=123;AF=0.39;AN=316;refseq.name=NM_153341;refseq.positionType=intron	GT	1/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	1/1	0/1	0/0	0/0	0/0	1/1	0/0	1/1	0/1	0/0	0/1	0/0	1/1	0/0	0/0	0/0	1/1	0/1	1/1	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	0/1	1/1	1/1	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	1/1	1/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	1/1	0/1	1/1	0/0	0/1	0/1	1/1	1/1	0/0	0/1	0/0	0/1	0/0	1/1	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	1/1	0/1	1/1	0/1	1/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	0/0	0/1	0/1	1/1	0/1	0/1	0/1
+chr1	33634618	.	TC	T	.	PASS	VC=INDEL;AC=238;AF=0.75;AN=316;refseq.name=NM_018207;refseq.positionType=intron	GT	0/0	0/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	0/0	1/1	0/0	1/1	1/1	0/1	0/1	0/0	1/1	1/1	1/1	1/1	1/1	1/1	0/0	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	0/1	0/1	0/0	1/1	1/1	0/1	1/1	1/1	0/1	1/1	0/1	0/1	0/1	0/0	0/1	1/1	0/1	1/1	0/0	0/1	0/1	1/1	0/1	0/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1	0/1	0/1	1/1	1/1	0/1	0/1	0/1	0/1	0/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/0	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/0	1/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1	0/1
+chr1	33965999	.	CCCAGTTC	C	.	PASS	VC=INDEL;AC=203;AF=0.65;AN=314	GT	0/1	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/1	1/1	1/1	0/1	1/1	1/1	0/1	0/0	1/1	1/1	0/1	1/1	0/0	0/0	0/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/0	1/1	./.	0/1	1/1	0/0	0/1	0/0	0/0	0/0	1/1	0/0	0/0	0/1	0/0	0/1	0/0	0/0	1/1	0/0	1/1	0/0	0/1	0/0	0/1	0/1	1/1	0/0	0/1	0/0	0/0	0/1	0/0	0/0	1/1	0/0	0/0	0/0	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	0/0	1/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	0/1	1/1	0/0	1/1	0/1	1/1	1/1	0/1	1/1	0/1	1/1	0/0	0/1
+chr1	34176371	.	GAAACATAAG	G	.	PASS	VC=INDEL;AC=252;AF=0.95;AN=266;refseq.name=NM_052896;refseq.positionType=intron	GT	0/0	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	./.	./.	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	./.	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	./.	0/1	1/1	./.	./.	./.	0/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	./.	0/1	1/1	./.	0/1	0/1	1/1	./.	./.	1/1	1/1	0/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	./.	1/1
+chr1	34931817	.	AT	A	.	PASS	VC=INDEL;AC=38;AF=0.12;AN=316	GT	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	1/1	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	1/1	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/1
+chr1	35879227	.	CAT	C	.	PASS	VC=INDEL;AC=31;AF=0.1;AN=316;refseq.name=NM_005095;refseq.positionType=intron	GT	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0
+chr1	36429590	.	A	AG	.	PASS	VC=INDEL;AC=181;AF=0.57;AN=316;refseq.name=NM_024852;refseq.positionType=intron	GT	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	1/1	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	0/1	0/1	0/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	0/1	0/1	1/1	0/0	0/1	0/0	0/0	0/1	1/1	0/1	0/1	0/0	0/0	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	0/1	1/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	0/0	1/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1	0/1	1/1	0/0	0/1	1/1	0/0	0/1	0/1	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/0
+chr1	36558240	.	C	CAC	.	PASS	VC=INDEL;AC=11;AF=0.03;AN=316;refseq.name=NM_017825;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0
+chr1	37034721	.	ATACT	A	.	PASS	VC=INDEL;AC=44;AF=0.16;AN=282	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/1	1/1	0/0	0/0	./.	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	./.	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	1/1	0/1	0/1	0/0	./.	./.	./.	0/1	0/1	0/0	./.	0/0	0/1	0/0	0/0	./.	0/0	0/1	0/0	./.	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	./.	0/0	0/0	0/0	0/0	0/1	./.	./.	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/0
+chr1	37142202	.	AATA	A	.	PASS	VC=INDEL;AC=24;AF=0.08;AN=314	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/1	1/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	37169424	.	TA	T	.	PASS	VC=INDEL;AC=176;AF=0.56;AN=316	GT	0/0	0/1	0/1	0/0	0/0	0/1	0/0	1/1	0/1	0/1	1/1	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	1/1	0/1	0/0	0/0	1/1	0/1	0/0	0/0	0/1	0/0	0/0	1/1	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	1/1	0/0	1/1	0/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	0/1	1/1	0/1	1/1	0/0	0/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/0	1/1	0/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/0	1/1	0/1	0/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	0/0	0/0	0/0	0/1	0/1	1/1	0/1	1/1	1/1	0/1	0/1	1/1	0/1	1/1	1/1	0/0	0/0
+chr1	37169427	.	AA	A	.	PASS	VC=INDEL;AC=173;AF=0.56;AN=308	GT	0/0	0/1	0/1	0/0	0/0	0/1	0/0	1/1	0/1	0/1	1/1	0/0	0/1	./.	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	1/1	0/1	0/0	0/0	1/1	0/1	0/0	0/0	0/1	0/0	0/0	1/1	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/1	./.	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	1/1	0/0	1/1	0/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	0/1	1/1	0/1	1/1	0/0	0/1	1/1	0/1	1/1	./.	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/0	1/1	0/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/0	1/1	0/1	0/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	0/0	0/0	./.	0/1	0/1	1/1	0/1	1/1	1/1	0/1	0/1	1/1	0/1	1/1	1/1	0/0	0/0
+chr1	37638341	.	T	TAT	.	PASS	VC=INDEL;AC=11;AF=0.05;AN=222	GT	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/1	./.	0/0	0/0	./.	0/0	0/0	./.	0/0	0/0	0/0	0/1	0/0	./.	0/0	0/1	./.	0/0	./.	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	./.	0/0	0/0	0/0	./.	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	./.	0/1	./.	0/0	0/0	./.	./.	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	./.	0/0	./.	./.	0/0	./.	./.	./.	0/0	0/1	./.	./.	./.	./.	./.	./.	./.	./.	./.	0/0	0/0	0/0	0/0	0/1	0/0	./.	./.	0/0	0/0	0/1	0/0	./.	0/1	./.	./.	0/0	./.	./.	./.	./.	0/0	0/0	0/1	./.	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	./.	./.	./.	0/0
+chr1	38077349	.	CTTATCCCCATACTAGTTATTATCGAAACCATCAGCCTACTCATTCAACCAATAGCCCTGGCCGTACGCCTA	C	.	PASS	VC=INDEL;AC=209;AF=0.77;AN=272;refseq.name=NM_001038633;refseq.positionType=intron	GT	0/1	1/1	1/1	1/1	1/1	./.	0/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	0/1	0/1	0/1	0/0	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/0	0/0	0/1	1/1	./.	1/1	./.	0/1	1/1	1/1	1/1	./.	./.	1/1	1/1	1/1	./.	1/1	1/1	1/1	./.	1/1	1/1	1/1	./.	./.	1/1	1/1	./.	0/1	./.	1/1	1/1	0/1	0/1	1/1	./.	1/1	1/1	1/1	0/1	1/1	./.	./.	./.	1/1	0/1	1/1	0/1	0/1	0/0	1/1	0/1	./.	1/1	0/1	1/1	0/1	0/1	0/1	0/1	1/1	./.	1/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	./.	1/1	0/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	1/1	0/0	0/1	1/1	./.	1/1	0/0	0/1	0/0	1/1	1/1	1/1	./.	./.	0/1	1/1	1/1	1/1	0/0	0/0	0/0	./.	1/1	0/1	1/1	0/1
+chr1	38392549	.	AT	A	.	PASS	VC=INDEL;AC=0;AF=0;AN=316;refseq.name=NM_005540;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	38664242	.	TA	T	.	PASS	VC=INDEL;AC=93;AF=0.29;AN=316	GT	0/1	1/1	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/0	1/1	0/0	1/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	1/1	0/0	0/1	0/1	1/1	1/1	1/1	0/1	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/0	1/1	0/0	0/1	1/1	0/1	1/1	0/0	0/1	0/1	0/1	0/0	0/0	0/0	1/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	1/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/1	1/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	1/1	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/0
+chr1	38739177	.	GTG	G	.	PASS	VC=INDEL;AC=32;AF=0.1;AN=316	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/0	1/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/1	1/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	1/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0
+chr1	39288395	.	CTTC	C	.	PASS	VC=INDEL;AC=36;AF=0.12;AN=306	GT	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	1/1	0/1	0/0	1/1	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	./.	0/0	0/0	0/1	0/1	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/1
+chr1	39615407	.	C	CGATAT	.	PASS	VC=INDEL;AC=192;AF=0.63;AN=306;refseq.name=NM_012090;refseq.positionType=intron	GT	1/1	1/1	1/1	1/1	0/1	0/0	0/1	1/1	0/0	1/1	0/1	1/1	1/1	0/1	0/1	1/1	1/1	0/0	0/1	0/1	0/0	0/1	0/1	1/1	0/0	0/0	0/0	1/1	1/1	0/1	0/1	0/1	0/0	0/0	0/0	0/1	1/1	1/1	0/1	0/1	0/1	0/1	0/1	1/1	1/1	./.	0/1	1/1	0/0	0/0	0/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/0	0/0	0/1	0/1	0/0	1/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	0/0	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1	0/0	1/1	0/0	0/1	0/1	0/1	1/1	1/1	1/1	0/0	0/1	0/0	1/1	0/1	1/1	0/1	0/1	0/1	0/1	1/1	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	1/1	./.	0/1	1/1	0/1	1/1	1/1	0/1	1/1	./.	1/1	1/1	1/1	0/1	0/1	./.	0/1	0/0	0/0	1/1	1/1	1/1	0/1	1/1	1/1	0/1	0/0	0/1	1/1	1/1	./.	0/0	1/1	0/1	1/1	1/1
+chr1	39615412	.	T	TGATAT	.	PASS	VC=INDEL;AC=200;AF=0.63;AN=316;refseq.name=NM_012090;refseq.positionType=intron	GT	1/1	1/1	1/1	1/1	0/1	0/0	0/1	1/1	0/0	1/1	0/1	1/1	1/1	0/1	0/1	1/1	1/1	0/0	0/1	0/1	0/0	0/1	0/1	1/1	0/0	0/0	0/0	1/1	1/1	0/1	0/1	0/1	0/0	0/0	0/0	0/1	1/1	1/1	0/1	0/1	0/1	0/1	0/1	1/1	1/1	0/0	0/1	1/1	0/0	0/0	0/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/0	0/0	0/1	0/1	0/0	1/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	0/0	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1	0/0	1/1	0/0	0/1	0/1	0/1	1/1	1/1	1/1	0/0	0/1	0/0	1/1	0/1	1/1	0/1	0/1	0/1	0/1	1/1	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	0/0	0/0	1/1	1/1	1/1	0/1	1/1	1/1	0/1	0/0	0/1	1/1	1/1	1/1	0/0	1/1	0/1	1/1	1/1
+chr1	39736467	.	T	TATAT	.	PASS	VC=INDEL;AC=27;AF=0.09;AN=316;refseq.name=NM_012090;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/1	1/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	1/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	39936801	.	GTG	G	.	PASS	VC=INDEL;AC=23;AF=0.07;AN=314;refseq.name=NM_012090;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/1	1/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/0	0/1	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	40525320	.	AACACAAGAAC	A	.	PASS	VC=INDEL;AC=21;AF=0.11;AN=196;refseq.name=NM_006367;refseq.positionType=intron	GT	./.	./.	0/0	./.	0/0	0/0	0/0	0/0	./.	./.	0/1	0/0	0/0	0/1	1/1	1/1	0/1	./.	1/1	./.	0/0	1/1	0/0	1/1	0/0	0/0	0/0	./.	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	./.	./.	./.	0/1	./.	0/0	./.	./.	./.	0/0	0/0	./.	./.	0/0	./.	./.	./.	./.	./.	./.	./.	0/0	0/0	./.	./.	./.	0/1	0/1	0/0	./.	./.	./.	./.	./.	0/0	./.	./.	./.	./.	./.	./.	0/0	./.	0/0	./.	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/1	0/0	0/0	./.	./.	0/0	0/0	0/0	0/0	0/0	0/1	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	./.	0/0	0/0	./.	./.	./.	0/0	./.	0/0	0/0	./.	0/0	./.	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/1	0/0	./.	./.	0/1	0/0	0/0	./.	0/0	0/0	0/0	./.
+chr1	40728529	.	TA	T	.	PASS	VC=INDEL;AC=216;AF=0.68;AN=316;refseq.name=NM_005857;refseq.positionType=intron	GT	0/1	0/0	1/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	1/1	0/1	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/0	1/1	1/1	1/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/0	1/1	0/1	0/1	0/1	1/1	0/1	0/1	1/1	1/1	0/1	0/0	1/1	0/1	0/0	1/1	0/1	0/0	0/1	0/1	0/0	1/1	0/0	0/0	0/0	1/1	0/1	1/1	1/1	0/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	0/0	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/0	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	0/1	0/1	1/1	0/1	1/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/0	1/1	0/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1
+chr1	41281719	.	CT	C	.	PASS	VC=INDEL;AC=142;AF=0.45;AN=316;refseq.name=NM_004700;refseq.positionType=intron	GT	0/1	1/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/1	1/1	0/1	0/1	1/1	0/1	0/1	0/1	1/1	0/1	0/0	0/1	1/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	1/1	1/1	0/1	0/1	0/1	0/1	1/1	0/0	0/0	0/1	0/1	0/0	1/1	0/0	0/1	0/0	1/1	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/1	1/1	0/1	0/0	0/1	0/1	1/1	0/1	0/0	0/0	0/0	0/0	0/1	1/1	0/1	0/0	1/1	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/1	1/1	1/1	0/0	0/1	0/1	0/0	0/0	0/0	0/1	1/1	0/1	0/1	0/0	0/0	1/1	0/1	0/1	0/1	0/1	0/0	1/1	0/0	0/1	1/1	1/1	1/1	1/1	0/1	1/1	0/0	0/1	0/1	0/1	0/1	1/1	0/1	0/1	1/1	0/1	1/1	0/1	0/1	0/1	1/1	1/1	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/0	0/0	1/1	0/1	0/1	1/1	1/1	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0
+chr1	41808814	.	CT	C	.	PASS	VC=INDEL;AC=32;AF=0.1;AN=308	GT	0/0	0/0	0/1	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	1/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	1/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/0	1/1	0/0	1/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	1/1	./.	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	./.	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1
+chr1	41991662	.	CCA	C	.	PASS	VC=INDEL;AC=17;AF=0.06;AN=304;refseq.name=NM_024503;refseq.positionType=intron	GT	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/0	./.	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/1	./.
+chr1	42083551	.	C	CT	.	PASS	VC=INDEL;AC=139;AF=0.44;AN=316;refseq.name=NM_024503;refseq.positionType=intron	GT	0/1	1/1	1/1	0/1	1/1	0/0	0/1	0/1	1/1	1/1	1/1	0/1	0/0	1/1	1/1	0/1	0/1	1/1	0/0	0/1	1/1	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/0	1/1	1/1	0/1	0/1	0/1	0/1	1/1	0/1	1/1	0/0	1/1	0/1	1/1	0/0	1/1	0/0	0/0	0/0	0/1	1/1	0/1	0/1	0/0	0/1	1/1	0/1	0/0	0/0	1/1	0/1	0/0	0/1	0/1	1/1	0/1	1/1	0/1	0/0	1/1	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/0	1/1	0/1	1/1	1/1	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	1/1	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/0	1/1	0/1	1/1	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	1/1	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/0	1/1	0/1	0/1	0/0	0/1	1/1	1/1	1/1	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/0
+chr1	42531504	.	G	GATAG	.	PASS	VC=INDEL;AC=199;AF=0.66;AN=302	GT	0/1	0/1	0/1	1/1	0/0	0/1	0/0	0/1	1/1	1/1	0/1	0/1	0/0	0/1	0/1	0/0	0/1	1/1	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/0	1/1	1/1	1/1	0/0	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/0	1/1	1/1	1/1	./.	0/0	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	1/1	0/1	0/1	0/1	1/1	0/1	./.	1/1	1/1	1/1	./.	0/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	0/1	0/0	./.	0/1	0/1	0/1	0/0	./.	0/1	1/1	1/1	0/1	0/0	0/1	0/1	1/1	0/1	0/0	0/1	0/0	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	0/1	0/1	0/0	0/1	1/1	1/1	0/0	0/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/0	1/1	1/1	1/1	1/1	0/1
+chr1	42835720	.	C	CTTG	.	PASS	VC=INDEL;AC=297;AF=0.94;AN=316	GT	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1
+chr1	42835723	.	G	GTTG	.	PASS	VC=INDEL;AC=297;AF=0.94;AN=316	GT	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1
+chr1	42880843	.	A	ACA	.	PASS	VC=INDEL;AC=179;AF=0.57;AN=316;refseq.name=NM_173642;refseq.positionType=exon	GT	0/1	0/0	0/1	0/1	0/0	0/0	1/1	0/1	1/1	1/1	0/0	1/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/0	1/1	0/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	0/0	1/1	0/1	1/1	1/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/0	1/1	0/0	0/1	0/1	0/1	0/0	0/0	0/1	0/1	1/1	0/0	1/1	0/0	0/1	0/0	0/0	1/1	1/1	1/1	0/1	1/1	0/0	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/0	1/1	1/1	1/1	0/0	0/0	0/0	1/1	0/1	1/1	0/1	0/1	0/1	0/0	0/0	1/1	0/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	1/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	0/0	0/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	0/0	0/1	0/0	0/1	0/1	1/1	1/1	0/1
+chr1	44114854	.	C	CGC	.	PASS	VC=INDEL;AC=107;AF=0.45;AN=238;refseq.name=NM_014663;refseq.positionType=promoter	GT	0/0	1/1	1/1	./.	0/0	./.	./.	0/0	0/1	0/0	1/1	0/0	0/0	0/1	0/0	1/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/1	0/1	1/1	0/0	./.	0/1	1/1	./.	0/1	0/1	0/1	0/0	0/1	0/1	./.	./.	0/0	0/0	./.	0/1	0/0	0/1	1/1	./.	1/1	0/1	0/1	0/1	./.	0/1	0/0	0/1	./.	0/1	0/1	./.	0/0	0/0	0/1	0/0	0/0	1/1	./.	0/0	0/0	0/1	0/1	./.	./.	./.	0/0	0/0	0/1	0/1	./.	0/0	0/1	0/1	0/1	0/1	0/0	1/1	0/1	./.	0/1	./.	0/1	0/0	0/0	0/1	1/1	1/1	1/1	0/0	0/0	0/0	1/1	./.	0/1	0/1	0/1	./.	./.	./.	0/1	./.	0/1	./.	1/1	./.	1/1	1/1	1/1	1/1	./.	./.	./.	1/1	./.	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	./.	./.	0/1	1/1	0/1	./.	0/0	0/1	1/1	0/1	0/1	./.	./.	1/1	0/1	1/1	0/1	0/1	./.	./.	./.	0/1	./.	0/0	0/1
+chr1	44231607	.	CA	C	.	PASS	VC=INDEL;AC=216;AF=0.69;AN=314;refseq.name=NM_006279;refseq.positionType=intron	GT	1/1	1/1	1/1	0/1	0/1	1/1	0/1	1/1	0/1	0/1	0/1	0/1	0/0	1/1	0/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	0/0	0/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	0/0	0/1	0/1	1/1	1/1	0/1	0/0	1/1	0/1	0/0	0/1	1/1	0/0	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	0/1	1/1	1/1	0/0	0/1	1/1	1/1	0/1	0/0	0/1	1/1	0/1	1/1	0/1	0/0	1/1	0/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	0/0	1/1	0/1	0/1	0/1	0/1	1/1	0/0	0/1	1/1	1/1	1/1	1/1	0/0	0/0	0/0	1/1	./.	0/1	0/1	1/1	0/1	0/1	1/1	1/1	0/0	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	0/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	0/1	0/1	1/1	0/1	1/1	0/1	0/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	0/1
+chr1	44231608	.	AA	A	.	PASS	VC=INDEL;AC=215;AF=0.68;AN=314;refseq.name=NM_006279;refseq.positionType=intron	GT	1/1	1/1	1/1	0/1	0/1	1/1	0/1	1/1	0/1	0/1	0/1	0/1	0/0	1/1	0/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	0/0	0/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	0/0	0/1	0/1	1/1	1/1	0/1	0/0	1/1	0/1	0/0	0/1	1/1	0/0	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	./.	0/1	1/1	1/1	0/0	0/1	1/1	1/1	0/1	0/0	0/1	1/1	0/1	1/1	0/1	0/0	1/1	0/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	0/0	1/1	0/1	0/1	0/1	0/1	1/1	0/0	0/1	1/1	1/1	1/1	1/1	0/0	0/0	0/0	1/1	0/0	0/1	0/1	1/1	0/1	0/1	1/1	1/1	0/0	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	0/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	0/1	0/1	1/1	0/1	1/1	0/1	0/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	0/1
+chr1	44327106	.	GCTGTCAGGACTTGTATAGA	G	.	PASS	VC=INDEL;AC=193;AF=0.66;AN=294;refseq.name=NM_006279;refseq.positionType=intron	GT	1/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	./.	0/0	0/1	1/1	1/1	0/0	0/1	0/1	1/1	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/0	1/1	0/1	1/1	0/1	0/1	0/1	0/1	0/1	0/1	1/1	1/1	0/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	0/1	0/1	./.	1/1	1/1	1/1	1/1	./.	0/1	1/1	1/1	0/1	0/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	0/1	1/1	0/1	0/1	0/0	./.	1/1	./.	1/1	1/1	0/1	1/1	1/1	0/1	0/1	0/0	1/1	0/1	0/1	0/0	0/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	./.	0/1	./.	1/1	0/1	1/1	0/1	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/1	1/1	1/1	1/1	0/1	0/1	0/1	0/0	0/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/1	./.	0/0	1/1	0/1	0/1	0/1	0/1	./.	0/1	./.	1/1	1/1
+chr1	44730823	.	G	GGAGA	.	PASS	VC=INDEL;AC=295;AF=0.96;AN=306;refseq.name=NM_024066;refseq.positionType=intron	GT	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	./.	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1
+chr1	44881687	.	GCAT	G	.	PASS	VC=INDEL;AC=29;AF=0.09;AN=314;refseq.name=NM_018150;refseq.positionType=intron	GT	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	1/1	0/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/1	1/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	1/1	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0
+chr1	45223909	.	GATTAGCTG	G	.	PASS	VC=INDEL;AC=167;AF=0.55;AN=306;refseq.name=NM_006845;refseq.positionType=intron	GT	0/1	0/0	0/0	0/0	0/1	0/1	0/1	1/1	0/0	1/1	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	0/1	0/0	0/1	1/1	0/1	1/1	0/1	1/1	0/0	1/1	0/1	0/1	0/1	1/1	0/0	0/1	0/1	1/1	1/1	0/1	0/0	0/1	0/0	0/0	0/0	1/1	0/1	0/1	0/0	0/0	0/1	0/1	0/1	1/1	0/0	0/1	0/1	1/1	0/0	0/1	1/1	1/1	1/1	1/1	0/0	0/1	0/1	1/1	0/0	0/1	0/1	1/1	0/1	1/1	1/1	0/1	0/1	0/0	./.	0/1	./.	0/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	./.	./.	0/1	1/1	1/1	./.	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	1/1	1/1	0/0	1/1	0/1	1/1	0/1	1/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	0/1	0/1	0/0	0/1	0/1	1/1	0/1	0/1	1/1	0/1	0/1	1/1	0/1	0/1	0/0	0/1	0/1	0/1
+chr1	46900444	.	T	TGTGGGAATGC	.	PASS	VC=INDEL;AC=2;AF=0.01;AN=296	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	./.	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0
+chr1	46900720	.	C	CTT	.	PASS	VC=INDEL;AC=244;AF=0.79;AN=308	GT	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	0/0	0/1	1/1	0/1	0/1	1/1	0/1	0/1	0/1	0/0	1/1	1/1	0/1	0/0	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	0/1	1/1	0/1	0/0	1/1	0/1	1/1	0/0	0/1	0/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/0	0/1	1/1	1/1	./.	1/1	./.	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	0/1	0/0	0/0	0/1	0/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	0/1	1/1	1/1	0/0	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1
+chr1	46900721	.	T	TTT	.	PASS	VC=INDEL;AC=241;AF=0.79;AN=304	GT	1/1	1/1	1/1	1/1	1/1	./.	0/1	0/1	0/1	0/1	0/0	0/1	1/1	0/1	0/1	1/1	0/1	0/1	0/1	0/0	1/1	1/1	0/1	0/0	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	0/1	1/1	0/1	0/0	1/1	0/1	1/1	0/0	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/0	0/1	1/1	1/1	./.	1/1	./.	1/1	0/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	0/1	0/0	0/0	0/1	0/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	./.	1/1	1/1	0/0	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1
+chr1	47052336	.	TGAAA	T	.	PASS	VC=INDEL;AC=76;AF=0.24;AN=316;refseq.name=NM_003684;refseq.positionType=intron	GT	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/0	1/1	0/0	0/1	0/1	0/0	1/1	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/0	1/1	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	1/1	1/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	1/1	0/0	0/0
+chr1	47167062	.	TT	T	.	PASS	VC=INDEL;AC=174;AF=0.64;AN=272;refseq.name=NM_014774;refseq.positionType=intron	GT	./.	0/1	0/1	0/1	./.	0/0	0/0	1/1	1/1	0/1	1/1	0/1	./.	./.	0/1	0/1	0/1	0/1	0/1	0/0	1/1	0/0	0/0	1/1	0/1	0/1	0/0	0/0	0/0	0/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	./.	0/1	0/1	1/1	0/1	0/1	0/1	./.	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	./.	0/1	1/1	0/1	1/1	1/1	0/1	./.	0/1	0/1	1/1	1/1	1/1	1/1	./.	0/1	0/1	0/0	0/1	./.	1/1	1/1	1/1	./.	./.	0/0	./.	0/1	0/1	1/1	1/1	1/1	1/1	0/1	0/0	./.	0/1	1/1	./.	0/1	0/1	1/1	1/1	0/0	0/1	1/1	1/1	./.	1/1	1/1	1/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	0/1	0/1	0/0	0/0	./.	1/1	./.	1/1	0/1	0/1	1/1	0/1	0/1	0/0	./.	0/1	./.	0/1	1/1	0/1	1/1	./.	1/1	./.	0/0
+chr1	47324578	.	CTACTACAAA	C	.	PASS	VC=INDEL;AC=150;AF=0.65;AN=232	GT	1/1	./.	./.	./.	./.	0/1	0/0	0/1	0/0	./.	./.	1/1	0/1	1/1	0/0	0/1	./.	0/1	0/1	0/0	0/1	./.	0/1	0/0	./.	0/0	1/1	1/1	./.	0/1	1/1	1/1	./.	0/1	0/0	0/1	1/1	1/1	./.	0/1	./.	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	0/1	./.	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	./.	1/1	./.	1/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	./.	1/1	1/1	./.	1/1	1/1	1/1	0/1	0/1	0/1	0/1	0/1	1/1	1/1	0/0	0/1	0/1	1/1	0/1	./.	./.	0/1	0/1	0/1	./.	1/1	0/1	0/0	0/1	./.	0/1	1/1	0/1	./.	0/1	1/1	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	./.	0/0	0/0	./.	1/1	./.	0/0	0/1	0/0	./.	1/1	1/1	1/1	./.	./.	1/1	./.	./.	0/0	./.	0/1	0/1	./.	./.	1/1	1/1	1/1	0/1	0/1	0/1	1/1	./.	./.	./.	0/1	./.	0/1	0/1	0/1	./.	0/1
+chr1	47325281	.	CA	C	.	PASS	VC=INDEL;AC=0;AF=0;AN=316	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	47891688	.	AT	A	.	PASS	VC=INDEL;AC=84;AF=0.29;AN=294	GT	1/1	0/0	0/1	0/0	1/1	0/1	0/0	0/0	0/0	1/1	0/0	1/1	./.	0/0	./.	0/0	./.	0/0	1/1	1/1	0/1	0/1	0/1	./.	1/1	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/1	./.	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	1/1	0/0	0/0	0/1	./.	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/1	./.	0/0	0/1	1/1	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	./.	0/1	0/1	0/1	./.	./.	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0
+chr1	47931769	.	TTCTC	T	.	PASS	VC=INDEL;AC=2;AF=0.01;AN=316	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1
+chr1	48000154	.	G	GTTT	.	PASS	VC=INDEL;AC=11;AF=0.05;AN=232	GT	./.	0/1	./.	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	./.	0/0	0/1	./.	0/0	0/0	./.	./.	0/0	./.	0/0	./.	0/0	./.	0/0	0/0	0/0	./.	./.	./.	0/0	./.	./.	0/0	0/0	0/1	0/0	0/1	./.	0/1	0/1	./.	0/0	./.	0/0	0/0	0/0	0/0	./.	0/0	0/0	./.	./.	0/0	./.	./.	0/1	0/1	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	./.	./.	./.	0/0	0/0	0/0	0/1	0/0	0/0	./.	0/1	./.	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	./.	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	./.	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	./.	0/0	./.	0/0	0/0
+chr1	48146050	.	CCTGA	C	.	PASS	VC=INDEL;AC=28;AF=0.09;AN=316	GT	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/0	1/1	0/0	1/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/1	1/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	48520865	.	CAGGGTGAGTAGGCCTGGGCAG	C	.	PASS	VC=INDEL;AC=4;AF=0.01;AN=316	GT	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	48520886	.	GAG	G	.	PASS	VC=INDEL;AC=31;AF=0.14;AN=216	GT	./.	0/0	0/1	0/0	0/0	./.	./.	0/0	0/1	0/0	1/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	./.	./.	./.	0/0	./.	./.	0/0	0/1	0/0	0/0	0/0	0/0	0/1	./.	0/1	0/0	0/0	./.	0/0	0/0	0/0	./.	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	./.	0/1	0/0	./.	./.	./.	0/0	./.	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	./.	./.	0/0	./.	0/0	0/0	0/1	0/0	0/1	0/0	0/1	./.	0/0	0/0	0/0	./.	./.	0/0	0/0	0/0	./.	0/0	0/0	./.	0/0	0/0	0/0	0/0	./.	./.	./.	./.	./.	./.	0/0	./.	0/1	0/1	./.	0/1	0/0	0/1	0/1	0/1	./.	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/1	./.	./.	0/0	./.	./.	./.	0/0	1/1	0/0	0/1	./.	./.	0/0	./.	0/0	0/0	0/1	./.	0/1	0/1	0/0	./.	./.	./.
+chr1	48544917	.	G	GTGTT	.	PASS	VC=INDEL;AC=43;AF=0.14;AN=314	GT	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	0/0	0/1	1/1	0/0	0/1	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	./.	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	49109456	.	AGAGC	A	.	PASS	VC=INDEL;AC=31;AF=0.14;AN=226;refseq.name=NM_032785;refseq.positionType=intron	GT	0/0	0/1	0/1	./.	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	./.	./.	0/0	0/0	0/1	0/0	./.	./.	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	./.	./.	0/0	./.	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	./.	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	./.	./.	0/1	0/0	0/1	0/0	./.	0/0	0/0	./.	0/0	0/1	./.	./.	0/0	0/1	./.	./.	./.	./.	0/1	0/0	./.	0/0	./.	0/0	0/0	0/0	./.	./.	./.	0/0	./.	0/0	./.	./.	./.	./.	0/0	./.	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	./.	0/0	0/0	./.	0/0	./.	0/0	0/0	0/0	0/0	./.	./.	0/0	./.	./.	0/0	0/0	0/1	./.	./.	./.	0/1	0/1	0/1
+chr1	49124365	.	C	CGAG	.	PASS	VC=INDEL;AC=93;AF=0.29;AN=316;refseq.name=NM_032785;refseq.positionType=intron	GT	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	1/1	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	1/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/0	1/1	0/1	0/1	0/0	0/0	0/1	0/1	1/1	0/1	1/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/1	1/1	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	1/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	1/1	0/0	0/1	0/1	1/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	1/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/1	1/1	1/1	1/1
+chr1	49124368	.	G	GGAG	.	PASS	VC=INDEL;AC=93;AF=0.29;AN=316;refseq.name=NM_032785;refseq.positionType=intron	GT	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	1/1	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	1/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/0	1/1	0/1	0/1	0/0	0/0	0/1	0/1	1/1	0/1	1/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/1	1/1	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	1/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	1/1	0/0	0/1	0/1	1/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	1/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/1	1/1	1/1	1/1
+chr1	49126514	.	C	CTG	.	PASS	VC=INDEL;AC=89;AF=0.3;AN=296;refseq.name=NM_032785;refseq.positionType=intron	GT	0/1	0/1	0/1	1/1	0/0	1/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/1	0/1	1/1	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	1/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	./.	0/0	0/1	0/1	0/0	0/1	./.	0/0	0/0	0/0	1/1	0/1	./.	0/0	0/0	0/1	0/1	0/1	0/1	1/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	./.	0/0	./.	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/1	1/1	0/1	0/1	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/0	./.	0/1	./.	0/0	./.	0/0	0/1	0/0	0/1	1/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	1/1	0/0	0/1	0/1	1/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	1/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/1	1/1	1/1	1/1
+chr1	50107735	.	G	GA	.	PASS	VC=INDEL;AC=68;AF=0.22;AN=312	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/1	./.	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	./.	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0
+chr1	50539498	.	T	TCT	.	PASS	VC=INDEL;AC=312;AF=0.99;AN=316	GT	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1
+chr1	50652516	.	A	AGAA	.	PASS	VC=INDEL;AC=247;AF=0.78;AN=316;refseq.name=NM_021952;refseq.positionType=intron	GT	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1	1/1	1/1	0/1	0/1	0/1	1/1	0/0	0/0	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/0	0/1	0/0	0/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	0/1	1/1	1/1	0/0	0/1	1/1	0/1	0/0	0/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/0	1/1	0/1	0/1	0/1	1/1	0/0	0/1	0/0	0/1	0/1	0/1	1/1	0/0	0/1	1/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	0/0	0/1	0/1	0/1	1/1	1/1
+chr1	51315116	.	ACTG	A	.	PASS	VC=INDEL;AC=13;AF=0.04;AN=316;refseq.name=NM_007051;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0
+chr1	52336500	.	TAATACA	T	.	PASS	VC=INDEL;AC=17;AF=0.07;AN=230;refseq.name=NM_002525;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	./.	0/0	0/0	./.	0/1	./.	./.	./.	0/0	./.	./.	0/0	./.	./.	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	./.	./.	0/1	0/0	0/1	0/0	./.	0/0	0/0	0/1	0/0	./.	./.	./.	0/1	0/0	0/0	0/0	./.	0/0	./.	0/0	0/0	0/1	0/1	0/1	./.	0/0	0/0	0/0	./.	./.	./.	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/1	./.	0/0	./.	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	./.	0/0	0/0	0/1	0/0	./.	0/0	./.	./.	./.	0/0	0/0	0/0	0/1	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	./.	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/1	0/0	0/0	./.	0/0	./.	./.	0/0	./.	0/0	0/0	./.	./.	./.	0/1	0/0	0/0	0/0	0/0	0/0	0/0	./.
+chr1	52798171	.	A	AT	.	PASS	VC=INDEL;AC=307;AF=0.97;AN=316;refseq.name=NM_004799;refseq.positionType=intron	GT	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1
+chr1	53554533	.	A	AT	.	PASS	VC=INDEL;AC=33;AF=0.11;AN=294;refseq.name=NM_006671;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	./.	0/0	./.	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	./.	0/1	0/0	0/0	./.	0/1	./.	0/1	0/0	./.	0/0	0/1	0/0	0/0	0/0	0/0	./.	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/0	1/1	0/1	0/0	0/0	0/1	0/1	0/0	./.	./.	0/1
+chr1	53986946	.	TG	T	.	PASS	VC=INDEL;AC=188;AF=0.59;AN=316;refseq.name=NM_147193;refseq.positionType=intron	GT	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	1/1	0/1	0/1	0/1	0/0	0/0	0/0	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/1	0/0	0/1	0/1	1/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	1/1	0/1	1/1	0/0	0/1	0/0	0/1	0/0	0/0	1/1	0/1	0/0	0/0	0/0	1/1	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	1/1	0/1	1/1	0/1	0/1	0/1	0/1	0/1	0/0	1/1	0/1	0/1	0/0	0/0	0/0	1/1	1/1
+chr1	54168427	.	C	CTCTG	.	PASS	VC=INDEL;AC=109;AF=0.35;AN=308;refseq.name=NM_147193;refseq.positionType=intron	GT	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	1/1	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/1	1/1	0/0	0/1	0/1	0/1	0/1	1/1	0/0	0/0	0/1	0/0	0/1	1/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/0	1/1	0/1	1/1	0/1	0/0	0/0	0/1	0/1	0/0	1/1	0/1	0/1	0/1	0/1	0/1	0/1	./.	0/1	0/0	0/0	0/1	1/1	0/1	0/1	0/1	1/1	0/0	0/0	0/0	0/0	1/1	0/1	1/1	1/1	./.	1/1	0/0	0/0	./.	1/1	0/1	0/1	0/0	./.	0/1	0/0	0/0	0/0	0/0	0/1	0/0	1/1	1/1	1/1	0/0	0/1	0/0	1/1	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/1	1/1	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0
+chr1	54558546	.	T	TAGAC	.	PASS	VC=INDEL;AC=66;AF=0.21;AN=316;refseq.name=NM_153035;refseq.positionType=intron	GT	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/0	1/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	1/1	0/0	0/1	0/0	0/0	0/0	0/0	1/1	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/1	1/1	1/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	1/1	0/1	1/1	0/0	0/0	0/0	1/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	1/1	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/1	0/1	1/1	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0
+chr1	54558548	.	G	GACAG	.	PASS	VC=INDEL;AC=66;AF=0.21;AN=316;refseq.name=NM_153035;refseq.positionType=intron	GT	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/0	1/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	1/1	0/0	0/1	0/0	0/0	0/0	0/0	1/1	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/1	1/1	1/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	1/1	0/1	1/1	0/0	0/0	0/0	1/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	1/1	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/1	0/1	1/1	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0
+chr1	54619996	.	AC	A	.	PASS	VC=INDEL;AC=193;AF=0.64;AN=302;refseq.name=NM_201546;refseq.positionType=promoter	GT	1/1	0/0	1/1	1/1	0/1	1/1	0/1	1/1	1/1	0/1	0/0	0/1	1/1	0/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	0/1	1/1	0/0	0/1	0/1	1/1	0/1	0/1	0/1	./.	0/0	0/0	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	0/0	0/1	0/1	0/1	0/1	0/1	1/1	1/1	0/1	0/1	1/1	0/1	0/1	0/1	1/1	0/0	0/1	0/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	0/0	1/1	0/1	0/1	1/1	1/1	0/1	0/0	0/0	1/1	0/1	0/1	0/1	./.	1/1	0/1	1/1	1/1	0/0	0/1	0/0	1/1	0/1	./.	0/1	0/0	0/1	0/0	0/1	0/1	0/1	1/1	1/1	1/1	./.	./.	0/1	0/1	0/0	0/0	1/1	0/1	1/1	0/1	0/1	./.	0/1	0/0	0/1	./.	1/1	0/0	0/0	0/1	0/1	0/1	0/0	0/0	1/1
+chr1	54757161	.	C	CCA	.	PASS	VC=INDEL;AC=186;AF=0.59;AN=314;refseq.name=NM_001009955;refseq.positionType=intron	GT	0/1	0/1	1/1	1/1	0/1	0/1	1/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	1/1	1/1	0/1	0/1	1/1	0/1	0/1	1/1	1/1	0/1	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	0/0	1/1	0/1	0/1	1/1	0/1	0/0	1/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	1/1	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	1/1	0/0	0/1	1/1	0/1	0/1	1/1	0/1	1/1	0/1	0/1	1/1	0/0	0/0	0/0	0/1	0/0	0/0	./.	1/1	1/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	1/1	1/1	0/1	0/1	1/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/1
+chr1	54757166	.	C	CAC	.	PASS	VC=INDEL;AC=185;AF=0.59;AN=312;refseq.name=NM_001009955;refseq.positionType=intron	GT	0/1	0/1	1/1	1/1	0/1	0/1	1/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	1/1	1/1	0/1	0/1	1/1	0/1	0/1	1/1	1/1	0/1	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	./.	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	0/0	1/1	0/1	0/1	1/1	0/1	0/0	1/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	1/1	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/0	./.	1/1	0/0	0/1	1/1	0/1	0/1	1/1	0/1	1/1	0/1	0/1	1/1	0/0	0/0	0/0	0/1	0/0	0/0	0/1	1/1	1/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	1/1	1/1	0/1	0/1	1/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/1
+chr1	55566411	.	TTAGTC	T	.	PASS	VC=INDEL;AC=207;AF=0.66;AN=316;refseq.name=NM_015306;refseq.positionType=intron	GT	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	0/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	0/0	0/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	1/1	0/0	0/0	0/1	0/0	1/1	0/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	0/1	0/1	0/0	0/1	1/1	0/1	0/0	0/1	0/1	1/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	1/1	0/1	0/1	1/1	0/0	0/1	0/1	0/0	0/0	0/1	0/1	1/1	0/1	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	0/0	1/1	0/1	0/0	0/1	0/0	0/1	1/1	0/0	0/1	0/1	1/1	0/1	1/1
+chr1	55743440	.	C	CCT	.	PASS	VC=INDEL;AC=261;AF=0.84;AN=312	GT	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/0	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	./.	1/1	1/1	0/0	1/1	0/1	0/1	1/1	0/1	0/1	1/1	1/1	0/0	0/1	./.	1/1	0/0	0/1	1/1	0/1	1/1	0/1	0/1	1/1	1/1	0/0	0/1	1/1	0/0	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	0/1
+chr1	55888273	.	T	TC	.	PASS	VC=INDEL;AC=265;AF=0.88;AN=302	GT	0/0	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	./.	0/1	./.	0/1	0/1	1/1	1/1	0/1	1/1	0/1	1/1	./.	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	./.	1/1	1/1	1/1	1/1	./.	1/1	0/1	0/1	1/1	./.	1/1	0/1	0/1	1/1	1/1	0/1	0/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1
+chr1	55888274	.	C	CC	.	PASS	VC=INDEL;AC=271;AF=0.89;AN=306	GT	0/0	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	./.	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	0/1	0/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	./.	./.	1/1	1/1	1/1	0/1	0/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	./.	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1
+chr1	55892282	.	T	TAGAAAA	.	PASS	VC=INDEL;AC=0;AF=0;AN=316	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	55998244	.	CGCACGCTC	C	.	PASS	VC=INDEL;AC=265;AF=0.84;AN=314	GT	1/1	0/1	1/1	0/0	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	1/1	0/1	0/0	1/1	1/1	1/1	0/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	1/1	1/1	0/0	1/1	0/1	0/1	0/1	1/1	0/1	./.	1/1	0/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1	1/1	1/1
+chr1	56495367	.	CTGAG	C	.	PASS	VC=INDEL;AC=76;AF=0.24;AN=316	GT	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	1/1	0/1	1/1	0/1	0/0	0/1	0/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	1/1	0/0	0/1	0/0	0/1	0/0	1/1	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	1/1	1/1	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/0	1/1	0/0	0/1	0/1	0/0	0/0	1/1	0/0	0/1	0/0	1/1	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	1/1	0/1	1/1	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	57353886	.	C	CTA	.	PASS	VC=INDEL;AC=0;AF=0;AN=316;refseq.name=NM_000562;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	57854490	.	AAT	A	.	PASS	VC=INDEL;AC=24;AF=0.08;AN=312;refseq.name=NM_021080;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/0	./.	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	58391942	.	G	GAAA	.	PASS	VC=INDEL;AC=10;AF=0.03;AN=314;refseq.name=NM_021080;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1
+chr1	58413348	.	A	AG	.	PASS	VC=INDEL;AC=50;AF=0.22;AN=226;refseq.name=NM_021080;refseq.positionType=intron	GT	0/0	./.	./.	0/1	0/0	./.	0/1	0/1	0/1	1/1	0/0	./.	./.	0/0	0/1	0/1	0/0	0/0	1/1	0/1	1/1	0/0	0/0	0/1	0/0	./.	./.	0/1	./.	./.	0/1	0/0	0/0	0/0	./.	./.	./.	1/1	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	./.	0/0	0/0	0/0	./.	1/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/1	0/0	0/0	0/0	./.	./.	./.	./.	0/1	0/1	./.	0/0	0/0	0/0	./.	0/0	0/0	0/0	./.	./.	./.	0/1	0/1	0/0	./.	0/0	0/0	0/0	0/1	0/1	0/1	./.	./.	./.	./.	./.	./.	0/1	0/1	./.	0/1	0/0	1/1	0/0	0/1	0/0	0/0	./.	./.	0/0	0/0	0/1	./.	./.	0/0	0/0	0/0	0/0	0/1	0/1	0/0	./.	0/1	1/1	0/0	0/1	0/0	./.	0/0	0/0	0/1	0/0	./.	0/0	0/0	./.	0/1	./.	0/1	./.	1/1	./.	1/1
+chr1	58550673	.	CT	C	.	PASS	VC=INDEL;AC=0;AF=0;AN=316;refseq.name=NM_021080;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	58629900	.	CAGA	C	.	PASS	VC=INDEL;AC=15;AF=0.05;AN=316;refseq.name=NM_021080;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/1	1/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	58999156	.	AT	A	.	PASS	VC=INDEL;AC=151;AF=0.53;AN=286;refseq.name=NM_145243;refseq.positionType=intron	GT	./.	1/1	1/1	0/1	0/1	0/0	1/1	./.	0/1	1/1	0/1	1/1	0/1	0/0	1/1	1/1	0/1	0/0	1/1	1/1	0/1	0/1	1/1	1/1	0/0	0/0	0/0	0/1	0/1	0/0	1/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	./.	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/0	1/1	1/1	1/1	1/1	0/0	1/1	./.	0/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	./.	0/1	0/0	0/0	0/1	0/0	0/1	0/1	./.	1/1	0/0	0/0	0/0	0/1	1/1	./.	1/1	0/1	0/0	0/0	./.	0/0	0/0	0/1	1/1	0/1	./.	0/0	0/1	0/0	0/1	0/1	0/0	./.	0/0	0/1	0/0	0/1	./.	0/1	0/1	1/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	./.	0/0	0/1	0/0	./.	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/1	./.	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	1/1	1/1
+chr1	59009401	.	T	TT	.	PASS	VC=INDEL;AC=0;AF=0;AN=316;refseq.name=NM_145243;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	59104181	.	GA	G	.	PASS	VC=INDEL;AC=271;AF=0.89;AN=304	GT	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	./.	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	./.	1/1	1/1	./.	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/0	0/1	0/1	1/1	0/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1
+chr1	59319761	.	AG	A	.	PASS	VC=INDEL;AC=195;AF=0.67;AN=290	GT	0/0	0/1	0/0	0/0	./.	1/1	1/1	0/1	1/1	0/1	1/1	0/0	1/1	1/1	0/1	0/1	1/1	0/0	1/1	1/1	0/1	0/1	0/1	0/1	0/1	1/1	0/0	0/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	0/0	0/1	0/0	1/1	0/1	1/1	0/0	1/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1	0/0	0/1	0/1	./.	0/0	0/0	0/1	1/1	1/1	1/1	0/1	0/1	1/1	0/0	0/1	1/1	1/1	0/1	0/1	0/0	1/1	0/1	./.	1/1	0/1	1/1	1/1	1/1	0/1	./.	0/1	1/1	0/1	./.	0/1	1/1	1/1	0/0	1/1	0/1	0/1	1/1	1/1	0/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	0/1	1/1	0/1	1/1	./.	1/1	1/1	./.	1/1	0/0	1/1	0/1	0/0	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1	0/1	0/1	0/0	./.	./.	1/1	1/1	1/1	1/1	0/1	0/1	0/0	./.	1/1	1/1	0/1	0/1	0/1	0/1	0/1	0/1	./.	1/1	1/1	1/1	0/1
+chr1	59319762	.	GG	G	.	PASS	VC=INDEL;AC=200;AF=0.68;AN=296	GT	0/0	0/1	0/0	0/0	0/1	1/1	1/1	0/1	1/1	0/1	1/1	0/0	1/1	1/1	0/1	0/1	1/1	./.	1/1	1/1	0/1	0/1	0/1	0/1	0/1	1/1	0/0	0/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	0/0	0/1	0/0	1/1	0/1	1/1	0/0	./.	1/1	0/1	0/1	0/1	1/1	./.	1/1	0/1	1/1	1/1	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/1	1/1	1/1	1/1	0/1	0/1	1/1	0/0	0/1	1/1	1/1	0/1	0/1	0/0	1/1	0/1	0/1	1/1	./.	1/1	1/1	1/1	0/1	./.	0/1	1/1	0/1	1/1	0/1	1/1	1/1	0/0	1/1	0/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	0/0	1/1	0/1	0/0	1/1	0/1	./.	1/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1	0/1	0/1	0/0	1/1	1/1	./.	1/1	./.	1/1	0/1	0/1	0/0	1/1	1/1	1/1	0/1	0/1	0/1	0/1	0/1	0/1	./.	1/1	1/1	1/1	0/1
+chr1	59630873	.	CT	C	.	PASS	VC=INDEL;AC=155;AF=0.49;AN=316	GT	1/1	0/1	1/1	0/1	1/1	0/1	0/1	1/1	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	1/1	0/1	0/1	1/1	0/1	1/1	1/1	0/1	0/0	0/1	0/1	1/1	1/1	1/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/0	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	0/0	1/1	1/1	0/1	1/1	0/0	1/1	1/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	1/1	1/1	0/1	0/1	0/1	0/0	1/1	0/1	1/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	1/1	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/1	1/1	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/1	0/1	0/1	1/1	0/1	0/1	0/1	1/1	0/0	0/1	0/0	0/0
+chr1	59635600	.	TAT	T	.	PASS	VC=INDEL;AC=287;AF=0.91;AN=316	GT	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	1/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	0/1	1/1	0/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1
+chr1	60128716	.	G	GC	.	PASS	VC=INDEL;AC=309;AF=0.98;AN=316;refseq.name=NM_018291;refseq.positionType=intron	GT	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1
+chr1	60128717	.	C	CC	.	PASS	VC=INDEL;AC=309;AF=0.98;AN=316;refseq.name=NM_018291;refseq.positionType=intron	GT	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1
+chr1	60228311	.	T	TCT	.	PASS	VC=INDEL;AC=250;AF=0.8;AN=314;refseq.name=NM_018291;refseq.positionType=exon	GT	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/0	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/0	0/1	0/1	1/1	0/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/0	1/1	0/1	1/1	0/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	0/1	0/1	1/1	0/1	0/0	0/1	0/1	0/0	1/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	1/1	0/1	0/0	0/1	0/1	1/1	./.	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	0/0	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1
+chr1	60460874	.	A	ACTA	.	PASS	VC=INDEL;AC=316;AF=1;AN=316;refseq.name=NM_152377;refseq.positionType=intron	GT	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1
+chr1	61786308	.	ATCTTA	A	.	PASS	VC=INDEL;AC=126;AF=0.4;AN=316;refseq.name=NM_005595;refseq.positionType=intron	GT	0/1	1/1	1/1	0/1	0/1	0/1	0/1	0/1	1/1	0/0	0/0	0/1	1/1	0/0	0/1	0/1	1/1	0/0	1/1	1/1	0/1	0/1	0/1	1/1	0/0	0/1	0/1	1/1	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	1/1	1/1	0/1	0/0	1/1	0/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	0/1	0/1	1/1	1/1	0/1	1/1	0/1	0/1	1/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/0	1/1	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	1/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0
+chr1	62087979	.	T	TGACCTACTGTGCT	.	PASS	VC=INDEL;AC=194;AF=0.63;AN=310	GT	1/1	1/1	1/1	0/0	1/1	0/1	1/1	0/1	0/0	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	0/1	0/0	0/1	1/1	0/0	1/1	0/1	0/1	0/1	0/0	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	0/0	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	./.	0/1	0/0	0/0	0/0	0/1	0/1	1/1	0/1	1/1	0/1	0/0	0/0	0/0	./.	0/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	1/1	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/0	./.	1/1	0/0	0/1	1/1	0/0	0/1	1/1	0/0	0/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1
+chr1	62128942	.	CTTGCACA	C	.	PASS	VC=INDEL;AC=123;AF=0.39;AN=316	GT	0/0	1/1	1/1	0/0	0/1	1/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1	1/1	0/0	1/1	0/0	0/1	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/0	1/1	1/1	0/1	1/1	1/1	0/1	1/1	0/0	1/1	0/1	1/1	1/1	1/1	0/1	0/1	1/1	0/0	1/1	1/1	1/1	0/1	0/1	1/1	0/1	0/0	0/0	0/0	0/1	1/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/0	1/1	0/1	0/0	1/1	0/1	0/1	0/0	0/0	0/0	1/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	1/1	0/1	0/1	0/1	0/0	1/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/1	0/0	0/0	0/0	0/1	1/1	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/0	1/1	0/1	1/1	0/1	0/0
+chr1	62940266	.	T	TG	.	PASS	VC=INDEL;AC=133;AF=0.43;AN=312;refseq.name=NM_033407;refseq.positionType=intron	GT	0/0	0/1	1/1	0/0	0/1	0/0	1/1	0/0	0/1	0/1	0/0	0/1	0/1	1/1	0/1	0/1	1/1	0/0	0/1	0/1	0/0	1/1	0/1	./.	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/1	1/1	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/1	0/0	0/1	0/0	0/0	0/0	0/1	1/1	1/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	./.	0/0	0/0	0/0	0/0	0/1	0/0	0/0	1/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	1/1
+chr1	63331690	.	TA	T	.	PASS	VC=INDEL;AC=234;AF=0.74;AN=316	GT	1/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	0/0	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/0	0/1	1/1	0/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/0	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	0/0	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1	1/1	0/0	1/1	1/1	0/1	0/1	1/1	0/0	0/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	0/1	0/0	1/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	0/0	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	0/1	0/1	1/1	0/1	0/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	0/1	1/1	0/1	0/1	0/1	1/1
+chr1	63331691	.	AA	A	.	PASS	VC=INDEL;AC=232;AF=0.74;AN=314	GT	1/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	0/0	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/0	0/1	1/1	0/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/0	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	0/0	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1	1/1	0/0	1/1	1/1	0/1	0/1	1/1	0/0	0/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	0/1	0/0	1/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	1/1	1/1	./.	1/1	0/1	0/1	0/0	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	0/1	0/1	1/1	0/1	0/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	0/1	1/1	0/1	0/1	0/1	1/1
+chr1	63423181	.	T	TCAT	.	PASS	VC=INDEL;AC=0;AF=0;AN=316	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	63907866	.	A	AATGTTT	.	PASS	VC=INDEL;AC=229;AF=0.76;AN=300;refseq.name=NM_014288;refseq.positionType=intron	GT	1/1	1/1	1/1	1/1	0/1	0/1	0/0	1/1	1/1	0/0	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/0	1/1	1/1	1/1	0/0	1/1	1/1	1/1	0/1	0/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	0/1	0/0	1/1	./.	0/1	0/1	0/0	1/1	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	0/0	1/1	1/1	1/1	1/1	1/1	0/1	./.	0/1	1/1	1/1	0/1	0/0	0/1	1/1	0/0	1/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	0/0	0/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	./.	1/1	1/1	0/1	0/1	./.	1/1	./.	1/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	./.	1/1	0/0	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	0/1	0/1
+chr1	63907868	.	T	TGTTTAT	.	PASS	VC=INDEL;AC=229;AF=0.77;AN=298;refseq.name=NM_014288;refseq.positionType=intron	GT	./.	1/1	1/1	1/1	0/1	0/1	0/0	1/1	1/1	0/0	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/0	1/1	1/1	1/1	0/0	1/1	1/1	1/1	0/1	0/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	0/1	0/0	1/1	./.	./.	0/1	0/0	1/1	0/1	0/0	0/1	0/0	./.	0/0	0/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	0/0	1/1	./.	1/1	1/1	1/1	0/1	./.	0/1	1/1	1/1	0/1	0/0	0/1	1/1	0/0	1/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	./.	1/1	1/1	0/1	0/0	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	./.	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	0/0	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1
+chr1	63985884	.	ATCAT	A	.	PASS	VC=INDEL;AC=91;AF=0.31;AN=298;refseq.name=NM_014288;refseq.positionType=intron	GT	./.	0/0	0/1	0/1	0/0	0/0	0/0	1/1	1/1	0/0	0/0	0/0	0/1	1/1	0/0	0/1	0/0	1/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	./.	0/1	0/0	0/0	0/0	1/1	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	./.	0/0	0/1	0/0	0/1	1/1	./.	1/1	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	./.	0/1	0/1	0/1	1/1	0/0	0/1	0/0	0/0	./.	0/1	1/1	0/1	1/1	0/1	1/1	1/1	0/0	1/1	0/1	1/1	1/1	1/1	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/1	1/1	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/0	./.	0/1	0/1	./.	0/0	0/0	./.	0/1
+chr1	63987096	.	ATG	A	.	PASS	VC=INDEL;AC=37;AF=0.18;AN=202;refseq.name=NM_014288;refseq.positionType=intron	GT	./.	0/0	0/1	./.	./.	./.	0/0	0/1	./.	./.	./.	0/0	./.	0/1	0/0	0/1	0/0	./.	0/0	./.	./.	0/1	0/0	0/0	0/0	0/0	0/0	./.	./.	0/1	0/0	./.	0/0	./.	0/1	0/0	./.	0/0	0/0	0/0	0/0	./.	./.	0/0	0/1	0/1	./.	./.	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	./.	0/1	./.	0/0	0/0	./.	./.	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	./.	0/0	0/1	0/0	0/1	0/0	./.	0/1	./.	./.	./.	./.	0/0	./.	./.	./.	0/0	./.	0/0	0/0	./.	./.	0/0	0/0	./.	./.	0/1	0/0	0/1	./.	./.	0/1	0/0	0/1	./.	./.	0/1	0/0	0/1	0/0	./.	./.	0/0	0/0	./.	0/0	0/0	0/1	./.	0/1	0/1	./.	0/0	0/0	0/0	./.	0/0	0/0	./.	0/0	0/1	./.	./.	./.	0/0	./.	0/0	0/1	./.	0/0	0/1	0/0	0/1	./.	./.	0/0	0/1	./.	0/1	0/0	0/1	0/1	0/1	0/1
+chr1	64264921	.	TTGTGTCAT	T	.	PASS	VC=INDEL;AC=136;AF=0.46;AN=298;refseq.name=NM_005012;refseq.positionType=intron	GT	0/0	0/0	0/1	0/1	0/0	1/1	0/0	0/1	0/0	0/0	0/1	0/1	1/1	0/1	0/0	0/0	0/0	0/1	0/1	1/1	0/0	0/0	0/0	0/0	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	1/1	1/1	./.	1/1	0/1	1/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	./.	0/0	./.	0/0	0/0	0/0	0/1	0/0	0/1	0/0	./.	0/0	0/1	0/0	0/1	0/1	./.	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/1	1/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	0/0	0/1	./.	0/1	./.	1/1	0/1	0/1	0/1	1/1	0/1	0/1	0/1	0/1	./.	./.	0/1	1/1	0/0	1/1	0/1	0/0	0/1	0/0	1/1	0/1	1/1	0/0	1/1	0/1	1/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/1	1/1	1/1	1/1	1/1	0/0	0/1	0/1	1/1	1/1	0/1	0/0	0/1	0/1	1/1	0/1	0/1	0/1	0/1	0/0	0/1
+chr1	64463351	.	GT	G	.	PASS	VC=INDEL;AC=244;AF=0.77;AN=316;refseq.name=NM_005012;refseq.positionType=intron	GT	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	0/1	0/1	0/0	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/0	0/1	0/1	1/1	1/1	0/1	1/1	0/1	0/1	1/1	1/1	0/1	0/1	0/1	0/0	0/0	0/0	1/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	1/1	1/1	0/0	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1	1/1	0/1	0/1	0/1	0/0	0/0	0/0	0/1	1/1	0/1	0/1	1/1	0/1	0/0	0/1	0/1	1/1	1/1
+chr1	64627261	.	A	AAA	.	PASS	VC=INDEL;AC=79;AF=0.25;AN=316;refseq.name=NM_005012;refseq.positionType=intron	GT	0/0	1/1	0/1	1/1	0/0	1/1	0/0	0/0	0/1	0/1	0/0	0/1	0/0	1/1	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/0	1/1	0/1	1/1	0/1	0/1	0/1	0/1	0/0	0/1	1/1	1/1	0/1	0/0	0/0	1/1	0/1	0/0	0/0	0/1	0/1	1/1	0/1	0/1	1/1	0/0	0/0	0/0	0/0	0/1	1/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/0	1/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	65237568	.	G	GGTTA	.	PASS	VC=INDEL;AC=237;AF=0.75;AN=316;refseq.name=NM_018211;refseq.positionType=intron	GT	0/0	0/1	0/1	0/0	0/0	0/0	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	0/1	0/1	0/1	0/0	0/0	1/1	0/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	1/1	0/1	0/1	0/1	0/1	0/0	1/1	0/1	1/1	1/1	0/0	0/1	1/1	0/1	1/1	0/1	0/1	0/1	0/0	0/1	1/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/0	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	0/0	0/1
+chr1	65299673	.	T	TTAAG	.	PASS	VC=INDEL;AC=10;AF=0.03;AN=314;refseq.name=NM_002227;refseq.positionType=exon	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	65545194	.	A	AT	.	PASS	VC=INDEL;AC=316;AF=1;AN=316	GT	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1
+chr1	65545195	.	T	TT	.	PASS	VC=INDEL;AC=316;AF=1;AN=316	GT	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1
+chr1	66063617	.	ATGT	A	.	PASS	VC=INDEL;AC=212;AF=0.67;AN=316;refseq.name=NM_002303;refseq.positionType=intron	GT	0/0	0/0	1/1	0/0	1/1	0/0	0/1	0/0	0/1	0/1	1/1	0/1	0/1	0/0	1/1	0/0	1/1	0/1	0/0	0/1	0/1	1/1	0/1	1/1	1/1	0/1	1/1	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/0	1/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	1/1	0/1	0/1	0/1	0/1	0/0	1/1	0/1	0/1	1/1	0/1	1/1	1/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/0	0/1	0/1	0/0	0/0	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	0/1	0/1	0/1	0/1	0/1	1/1	1/1
+chr1	66198019	.	A	ACCATCCA	.	PASS	VC=INDEL;AC=76;AF=0.26;AN=296	GT	0/1	0/1	0/1	1/1	0/1	0/1	0/0	0/0	0/0	0/0	1/1	0/1	0/0	0/1	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	1/1	0/1	./.	1/1	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	1/1	0/1	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	1/1	0/0	0/1	0/0	./.	./.	0/1	0/1	0/1	0/0	0/0	0/1	1/1	0/0	0/0	1/1	0/0	./.	0/0	./.	./.	1/1	0/1	0/0	0/1	./.	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/1	./.	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	1/1	0/1	1/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	./.	0/0	0/1
+chr1	66460193	.	T	TC	.	PASS	VC=INDEL;AC=301;AF=0.95;AN=316;refseq.name=NM_001037341;refseq.positionType=intron	GT	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/0	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1
+chr1	66801086	.	TGT	T	.	PASS	VC=INDEL;AC=19;AF=0.06;AN=316;refseq.name=NM_001037341;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	1/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	66952677	.	A	ATC	.	PASS	VC=INDEL;AC=158;AF=0.65;AN=244	GT	0/1	1/1	1/1	0/0	1/1	./.	./.	0/1	0/0	0/1	./.	1/1	0/1	0/1	1/1	0/1	0/1	0/1	1/1	1/1	0/0	./.	0/1	1/1	0/1	0/1	0/1	0/1	1/1	./.	1/1	0/1	0/1	0/1	1/1	./.	0/0	0/0	0/0	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	0/0	0/1	0/0	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	./.	1/1	./.	1/1	1/1	./.	1/1	1/1	0/1	0/1	1/1	0/1	./.	0/0	0/0	1/1	0/1	1/1	./.	0/1	0/1	0/1	./.	0/1	./.	0/1	./.	./.	1/1	0/1	./.	./.	0/1	0/1	0/1	./.	1/1	0/1	0/1	0/1	0/1	0/1	./.	0/1	./.	0/1	0/1	1/1	./.	./.	0/1	0/1	0/1	1/1	1/1	./.	0/1	0/0	./.	0/1	./.	0/1	0/0	0/0	0/1	0/1	0/0	./.	0/0	0/1	./.	1/1	0/1	0/1	./.	./.	0/1	./.	0/1	./.	0/1	1/1	1/1	0/1	./.	0/1	0/1	./.	0/1	1/1
+chr1	67152254	.	ATAATTTCACGA	A	.	PASS	VC=INDEL;AC=9;AF=0.03;AN=316;refseq.name=NM_032291;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	67206037	.	AATTG	A	.	PASS	VC=INDEL;AC=50;AF=0.19;AN=268;refseq.name=NM_032291;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	./.	0/1	0/0	0/1	./.	0/0	0/0	0/1	0/1	./.	0/0	0/1	0/0	0/0	0/1	./.	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/0	./.	./.	0/0	0/1	./.	./.	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	./.	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/1	0/0	./.	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	./.	./.	0/1	0/0	./.	./.	0/1	0/1	0/1	0/0	0/0	0/0	0/0	./.	0/0	0/1	0/0	0/0	0/1	0/1	./.	./.	0/1	0/1	0/1	./.	0/0	0/1	0/0	./.	0/1	1/1	0/0	0/0	0/0	0/0	./.	0/0	0/1	0/1	0/1	0/1	0/1
+chr1	67459726	.	T	TT	.	PASS	VC=INDEL;AC=54;AF=0.18;AN=300	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/1	./.	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/0	./.	0/1	0/1	0/0	0/1	./.	./.	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/0	./.	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	./.	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/0	./.
+chr1	68038796	.	ACA	A	.	PASS	VC=INDEL;AC=21;AF=0.08;AN=264	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/1	0/1	0/0	./.	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	./.	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	./.	0/0	./.	0/0	0/1	./.	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	./.	0/1	0/0	./.	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	./.	0/0	0/0	0/0	./.	0/0	0/0	0/1	0/0	0/1	./.	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/1	0/0	./.	0/0	./.	0/0	0/0	0/0	./.	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	./.	0/0	./.	0/0	0/0
+chr1	68291788	.	GC	G	.	PASS	VC=INDEL;AC=19;AF=0.06;AN=316;refseq.name=NM_018841;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0
+chr1	68570194	.	CCCT	C	.	PASS	VC=INDEL;AC=110;AF=0.35;AN=310;refseq.name=NM_001002292;refseq.positionType=intron	GT	0/0	0/1	0/1	0/0	0/1	0/0	1/1	0/1	1/1	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	1/1	0/1	0/0	0/1	0/0	1/1	1/1	0/1	0/1	0/0	0/1	./.	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	1/1	1/1	0/0	0/1	1/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/1	./.	0/1	0/0	0/1	0/0	0/1	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/0	1/1	0/1	1/1	0/1	1/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	0/0	0/1	0/1	0/1	1/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0
+chr1	69008683	.	C	CA	.	PASS	VC=INDEL;AC=68;AF=0.3;AN=230	GT	0/0	./.	0/0	./.	0/0	./.	0/1	0/0	./.	./.	0/0	1/1	./.	1/1	0/0	0/0	0/0	0/1	0/1	./.	0/1	1/1	./.	./.	1/1	0/1	1/1	0/0	0/1	0/0	1/1	0/0	0/1	1/1	1/1	1/1	0/1	0/0	1/1	0/0	0/0	./.	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	./.	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	./.	0/0	0/0	./.	0/1	0/1	0/0	./.	./.	./.	1/1	0/1	1/1	0/0	./.	1/1	0/1	./.	0/1	0/0	./.	0/0	0/1	./.	0/1	0/0	0/0	./.	0/1	0/0	./.	./.	1/1	./.	./.	0/0	0/0	0/1	0/1	0/1	1/1	./.	1/1	1/1	./.	0/1	0/0	1/1	./.	./.	./.	0/0	./.	1/1	./.	./.	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/0	./.	0/1	./.	./.	./.	0/1	0/1	./.	0/1	0/0	0/0	0/0	0/1	./.
+chr1	69398928	.	CAAC	C	.	PASS	VC=INDEL;AC=66;AF=0.21;AN=316	GT	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	1/1	0/1	1/1	0/0	1/1	0/0	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	1/1	1/1	0/1	0/1	1/1	0/1	0/1	1/1	0/0	1/1	0/1	0/0	1/1	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1	1/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	1/1	0/1	1/1	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0
+chr1	69424885	.	AG	A	.	PASS	VC=INDEL;AC=257;AF=0.81;AN=316	GT	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	0/0	1/1	0/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/0	0/1	0/1	1/1	1/1	1/1	0/1	0/0	0/1	0/1	0/0	1/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	1/1	1/1	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1	0/0	0/1	0/0	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1
+chr1	69424886	.	GG	G	.	PASS	VC=INDEL;AC=257;AF=0.81;AN=316	GT	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	0/0	1/1	0/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/0	0/1	0/1	1/1	1/1	1/1	0/1	0/0	0/1	0/1	0/0	1/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	1/1	1/1	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1	0/0	0/1	0/0	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1
+chr1	69702172	.	T	TT	.	PASS	VC=INDEL;AC=186;AF=0.59;AN=316	GT	1/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	0/1	0/1	0/0	1/1	1/1	1/1	1/1	1/1	0/0	0/1	0/1	0/1	1/1	0/1	1/1	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/1	0/0	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1	1/1	0/1	0/1	0/0	0/1	1/1	1/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	1/1	1/1	0/1	1/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	0/1	0/0	0/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	0/1	0/1	0/0	1/1	0/1	0/1	0/1	0/1	1/1	1/1	0/1	0/1	1/1	0/0	0/1	0/1	0/0	0/0	1/1	0/1	1/1	0/1	0/0	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/0	1/1	0/1	0/1	0/1	1/1	0/1	0/0	0/1	0/1	0/0	0/0	0/1	0/1	1/1	0/1	0/1	0/0	0/1	0/1	1/1	0/1	0/0	0/0	0/0	0/0	0/0	1/1	1/1	0/1	1/1	0/1	0/1	1/1	1/1
+chr1	69947085	.	T	TT	.	PASS	VC=INDEL;AC=199;AF=0.87;AN=230	GT	./.	1/1	1/1	0/1	0/1	0/0	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	./.	1/1	0/1	1/1	0/0	1/1	0/1	./.	./.	./.	0/0	./.	1/1	1/1	1/1	1/1	./.	./.	1/1	./.	1/1	1/1	1/1	0/0	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	0/1	0/1	0/1	1/1	1/1	./.	1/1	./.	1/1	1/1	1/1	./.	1/1	./.	1/1	1/1	1/1	./.	./.	0/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	./.	1/1	1/1	./.	1/1	1/1	1/1	0/1	./.	0/0	./.	./.	1/1	./.	1/1	./.	./.	1/1	0/1	./.	0/1	./.	1/1	1/1	./.	1/1	./.	0/1	0/0	1/1	./.	1/1	1/1	0/1	1/1	1/1	1/1	1/1	./.	./.	1/1	1/1	./.	./.	./.	./.	./.	./.	1/1	1/1	1/1	0/1	1/1	1/1	./.	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	./.	./.	1/1	1/1
+chr1	70116412	.	T	TAAT	.	PASS	VC=INDEL;AC=236;AF=0.77;AN=308	GT	0/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	0/0	1/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	0/1	0/1	1/1	./.	1/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	0/0	1/1	1/1	0/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	1/1	0/1	0/1	0/1	0/0	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	0/1	0/1	0/1	0/1	1/1	./.	1/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	0/1	./.	1/1	1/1	0/1	0/1
+chr1	70794740	.	AAAAC	A	.	PASS	VC=INDEL;AC=49;AF=0.17;AN=288;refseq.name=NM_030816;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	./.	0/0	0/0	0/1	0/0	0/0	./.	0/1	0/0	0/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	1/1	0/1	0/0	0/0	0/0	./.	0/0	0/0	0/1	0/0	0/1	0/0	./.	./.	0/1	./.	0/0	0/1	0/1	0/0	0/1	./.	./.	./.	0/0	0/1	./.	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/1	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	./.	0/0	0/1	0/0	0/0	0/1	0/0	0/0	./.	0/0	./.	0/1	1/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	70796576	.	TTACTT	T	.	PASS	VC=INDEL;AC=0;AF=0;AN=316;refseq.name=NM_030816;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	71101845	.	TG	T	.	PASS	VC=INDEL;AC=38;AF=0.12;AN=310	GT	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/0	./.	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	./.	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	71353307	.	AT	A	.	PASS	VC=INDEL;AC=88;AF=0.28;AN=310;refseq.name=NM_000957;refseq.positionType=intron	GT	0/1	0/0	0/0	1/1	0/1	0/0	0/1	0/0	0/0	0/1	0/1	1/1	0/0	0/1	1/1	1/1	1/1	0/0	0/0	0/1	./.	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/0	./.	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	./.	0/1	0/0	0/1	1/1	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/1	1/1	1/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	1/1	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/1	1/1	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1
+chr1	71366228	.	AA	A	.	PASS	VC=INDEL;AC=123;AF=0.39;AN=314;refseq.name=NM_000957;refseq.positionType=intron	GT	1/1	1/1	0/0	1/1	1/1	0/0	1/1	./.	0/0	1/1	0/0	0/1	0/0	1/1	1/1	0/1	1/1	0/0	0/0	1/1	0/0	0/1	0/1	0/0	1/1	0/1	1/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	1/1	0/1	0/0	0/1	1/1	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/1	0/1	0/1	1/1	0/0	0/0	0/0	1/1	0/1	0/0	1/1	1/1	0/1	0/0	0/0	0/1	1/1	0/1	0/1	0/1	1/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/1	1/1	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/0	1/1	0/1	0/1	1/1	1/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/1	1/1	1/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/1	1/1	1/1	0/1	0/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	1/1	1/1	0/0	0/1
+chr1	71366595	.	A	AAGTG	.	PASS	VC=INDEL;AC=108;AF=0.34;AN=316;refseq.name=NM_000957;refseq.positionType=intron	GT	0/1	0/1	0/0	1/1	1/1	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/1	1/1	0/1	1/1	0/0	0/0	0/1	0/0	0/1	0/1	0/0	1/1	0/1	1/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	1/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/1	0/1	0/1	1/1	0/0	0/0	0/0	1/1	0/1	0/0	0/1	1/1	0/1	0/0	0/0	0/1	1/1	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/1	1/1	1/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/1	1/1	1/1	0/1	0/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1
+chr1	71366598	.	T	TGAGT	.	PASS	VC=INDEL;AC=109;AF=0.34;AN=316;refseq.name=NM_000957;refseq.positionType=intron	GT	0/1	0/1	0/0	1/1	1/1	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/1	1/1	0/1	1/1	0/0	0/0	0/1	0/0	0/1	0/1	0/0	1/1	0/1	1/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	1/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/1	0/1	0/1	1/1	0/0	0/0	0/0	1/1	0/1	0/0	0/1	1/1	0/1	0/0	0/0	0/1	1/1	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/1	1/1	1/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/1	1/1	1/1	0/1	0/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	1/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1
+chr1	71693491	.	TGAG	T	.	PASS	VC=INDEL;AC=32;AF=0.1;AN=312	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	1/1	0/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/0	./.	0/1	1/1	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	71693493	.	AGGA	A	.	PASS	VC=INDEL;AC=34;AF=0.11;AN=316	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	1/1	0/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/1	1/1	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	72053145	.	AG	A	.	PASS	VC=INDEL;AC=229;AF=0.72;AN=316;refseq.name=NM_173808;refseq.positionType=intron	GT	1/1	0/1	1/1	1/1	1/1	0/1	1/1	0/1	0/0	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	0/0	0/1	0/1	0/1	0/1	0/0	1/1	0/1	0/1	1/1	0/1	0/1	1/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/0	0/0	1/1	0/1	0/1	0/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	0/1	0/1	1/1	0/1	0/1	1/1	1/1	0/1	1/1	0/0	0/0	0/0	0/1	1/1	1/1	0/1	1/1	0/1	0/1	1/1	0/1	1/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	0/0	1/1	0/1	1/1	1/1
+chr1	72321086	.	AA	A	.	PASS	VC=INDEL;AC=54;AF=0.17;AN=314;refseq.name=NM_173808;refseq.positionType=intron	GT	0/1	1/1	0/1	0/0	1/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	1/1	0/0	1/1	1/1	0/0	0/1	1/1	0/1	1/1	0/1	0/1	1/1	1/1	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/0	1/1	0/0	0/0	0/1	1/1	0/1	0/1	0/1	0/1	0/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/1
+chr1	73854019	.	T	TTTTA	.	PASS	VC=INDEL;AC=181;AF=0.59;AN=308	GT	0/1	0/1	0/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	0/1	1/1	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/1	1/1	0/1	0/0	1/1	0/1	0/1	0/0	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	0/0	1/1	0/0	0/1	0/1	1/1	0/1	1/1	0/1	0/1	0/1	1/1	./.	0/1	0/1	1/1	1/1	1/1	1/1	0/0	1/1	0/1	0/1	0/1	1/1	0/1	1/1	0/1	0/1	0/1	0/1	0/1	0/1	1/1	0/0	0/1	0/1	1/1	0/1	0/1	0/0	1/1	0/1	0/0	0/0	0/0	1/1	0/1	1/1	0/1	1/1	0/1	1/1	0/0	0/1	0/1	0/1	1/1	0/1	0/0	0/0	0/0	0/1	./.	0/1	0/1	1/1	1/1	0/1	0/1	0/0	0/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	0/0	0/0	0/1	0/0	0/1	./.	0/1	0/1	0/0	0/0	1/1	1/1	1/1	1/1	1/1	1/1	0/1	./.	0/0	0/1	0/0	0/1	0/1	0/1	0/1	1/1	0/1
+chr1	74227801	.	AG	A	.	PASS	VC=INDEL;AC=2;AF=0.01;AN=316	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1
+chr1	74404505	.	TTT	T	.	PASS	VC=INDEL;AC=23;AF=0.07;AN=316	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/1	1/1	1/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0
+chr1	74892891	.	AG	A	.	PASS	VC=INDEL;AC=75;AF=0.24;AN=316;refseq.name=NM_001112808;refseq.positionType=intron	GT	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/0	1/1	0/0	0/1	0/0	0/1	0/1	1/1	0/0	0/0	1/1	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	1/1	0/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	0/1	0/1	0/1	0/0	0/1	1/1	1/1	0/1	1/1	0/0	1/1	1/1	1/1	0/0	0/1	0/0	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1
+chr1	74896404	.	ACTCAA	A	.	PASS	VC=INDEL;AC=26;AF=0.08;AN=316;refseq.name=NM_001112808;refseq.positionType=intron	GT	0/1	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	1/1	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	1/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	75049490	.	C	CT	.	PASS	VC=INDEL;AC=0;AF=0;AN=316;refseq.name=NM_001002912;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	75156563	.	GCTT	G	.	PASS	VC=INDEL;AC=259;AF=0.82;AN=316	GT	0/1	1/1	1/1	0/1	1/1	1/1	0/0	1/1	1/1	0/1	0/1	0/0	0/1	1/1	0/1	0/0	0/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	0/0	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	0/0	1/1	0/1	0/1	1/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1	0/0	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1
+chr1	75661521	.	TTCTT	T	.	PASS	VC=INDEL;AC=7;AF=0.02;AN=312	GT	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/1	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	76005746	.	A	AC	.	PASS	VC=INDEL;AC=184;AF=0.58;AN=316;refseq.name=NM_152697;refseq.positionType=intron	GT	0/1	0/0	0/1	1/1	0/0	0/1	0/0	0/0	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	0/0	0/1	0/1	0/1	0/1	0/0	1/1	0/1	1/1	1/1	1/1	1/1	0/1	0/0	1/1	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	1/1	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	0/0	0/1	1/1	1/1	1/1	0/0	1/1	1/1	1/1	0/1	0/1	1/1	0/1	1/1	0/1	0/1	1/1	0/1	0/0	0/1	0/0	0/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/0	1/1	0/1	0/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	0/0
+chr1	76054645	.	AT	A	.	PASS	VC=INDEL;AC=14;AF=0.05;AN=290;refseq.name=NM_152697;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/1	0/0	./.	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/1	0/0	0/0	0/0	./.	0/0	0/0	./.	0/1	./.	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/1	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	./.	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	./.	0/0
+chr1	76110056	.	ATCAT	A	.	PASS	VC=INDEL;AC=202;AF=0.7;AN=290	GT	0/0	1/1	1/1	0/1	1/1	0/1	0/0	1/1	0/0	0/0	1/1	0/1	0/0	0/1	0/1	0/0	0/1	0/0	1/1	0/0	0/1	0/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	0/1	./.	1/1	./.	0/1	0/0	0/1	0/1	1/1	0/0	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	0/1	0/0	0/0	0/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	0/1	0/0	1/1	0/1	1/1	1/1	./.	1/1	0/1	0/0	1/1	0/1	1/1	0/1	0/1	0/1	0/1	./.	0/0	0/0	0/0	0/1	0/1	./.	0/1	0/1	1/1	./.	1/1	1/1	0/0	0/1	0/0	1/1	0/1	./.	1/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	0/0	./.	0/1	0/0	1/1	0/1	1/1	1/1	1/1	0/1	0/1	0/1	./.	1/1
+chr1	76110059	.	ATTCA	A	.	PASS	VC=INDEL;AC=198;AF=0.68;AN=290	GT	./.	1/1	1/1	0/1	1/1	0/1	0/0	1/1	./.	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/0	./.	1/1	0/0	0/1	0/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	./.	0/1	1/1	0/1	0/1	0/0	0/1	0/1	1/1	0/0	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	./.	1/1	1/1	1/1	0/1	0/0	0/0	./.	0/1	0/1	./.	1/1	0/1	./.	1/1	1/1	1/1	1/1	1/1	0/1	./.	0/0	1/1	0/1	1/1	1/1	0/0	1/1	0/1	0/0	1/1	0/1	1/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	./.	0/1	0/1	0/1	./.	1/1	1/1	1/1	1/1	0/0	0/1	0/0	1/1	0/1	0/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	0/0	0/1	0/1	0/0	1/1	0/1	./.	1/1	1/1	0/1	0/1	0/1	0/0	1/1
+chr1	76603385	.	A	AA	.	PASS	VC=INDEL;AC=45;AF=0.14;AN=316;refseq.name=NM_152996;refseq.positionType=intron	GT	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	1/1	0/1	1/1	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0
+chr1	76647177	.	T	TA	.	PASS	VC=INDEL;AC=44;AF=0.15;AN=292;refseq.name=NM_152996;refseq.positionType=intron	GT	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	./.	0/1	0/1	0/0	0/1	./.	./.	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	./.	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/1	./.	0/0	./.	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/1	0/1	1/1	0/1	./.	0/0	0/0	0/0	./.	0/0	./.	./.	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/1	1/1	0/0	0/0
+chr1	76772246	.	TAG	T	.	PASS	VC=INDEL;AC=71;AF=0.22;AN=316;refseq.name=NM_152996;refseq.positionType=intron	GT	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/0	1/1	0/0	1/1	0/0	0/1	0/1	0/1	1/1	1/1	0/1	0/1	0/0	0/1	0/1	1/1	0/1	0/1	0/1	0/1	1/1	0/0	0/0	0/1	1/1	0/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	1/1	0/1
+chr1	77019040	.	G	GA	.	PASS	VC=INDEL;AC=123;AF=0.39;AN=316;refseq.name=NM_152996;refseq.positionType=intron	GT	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	1/1	0/0	0/1	0/0	1/1	0/1	0/1	0/0	1/1	0/0	0/1	0/0	1/1	1/1	0/1	1/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	1/1	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/0	1/1	0/1	0/1	0/0	0/1	0/1	1/1	0/1	0/1	0/1	1/1	0/1	0/0	0/1	1/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	1/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	1/1	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/1	1/1	0/0	0/1	0/1	0/1	0/1	1/1	0/1	1/1	0/1	0/1	1/1	0/0	0/1
+chr1	77019568	.	TTCTG	T	.	PASS	VC=INDEL;AC=72;AF=0.23;AN=316;refseq.name=NM_152996;refseq.positionType=intron	GT	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	1/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1	1/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	1/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/1	1/1	1/1	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	1/1	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/1	1/1	0/1	0/0	0/0	0/0	1/1	0/0	0/1	0/0	0/1
+chr1	77147457	.	T	TG	.	PASS	VC=INDEL;AC=307;AF=0.97;AN=316	GT	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1
+chr1	77154589	.	T	TA	.	PASS	VC=INDEL;AC=300;AF=0.95;AN=316	GT	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1
+chr1	77350958	.	GT	G	.	PASS	VC=INDEL;AC=0;AF=0;AN=316;refseq.name=NM_030965;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	77412672	.	T	TCAAA	.	PASS	VC=INDEL;AC=183;AF=0.58;AN=316;refseq.name=NM_030965;refseq.positionType=intron	GT	0/1	0/1	0/0	1/1	1/1	0/1	0/1	1/1	1/1	0/1	0/1	0/1	0/0	1/1	0/1	0/0	0/1	0/1	1/1	0/1	1/1	0/0	1/1	1/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/1	1/1	0/0	0/1	0/1	0/0	0/1	0/1	1/1	1/1	0/1	0/0	0/1	0/0	1/1	0/1	1/1	0/1	0/1	0/1	0/0	1/1	0/1	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	1/1	0/0	0/0	0/0	1/1	1/1	0/0	0/0	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	1/1	1/1	0/1	1/1	0/1	0/0	0/1	0/0	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	0/0	0/0	1/1	1/1	1/1	0/1	0/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	0/1	0/1	0/0	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	0/1	0/1	0/1	0/0	0/1	0/1
+chr1	77412677	.	C	CAAAC	.	PASS	VC=INDEL;AC=183;AF=0.58;AN=316;refseq.name=NM_030965;refseq.positionType=intron	GT	0/1	0/1	0/0	1/1	1/1	0/1	0/1	1/1	1/1	0/1	0/1	0/1	0/0	1/1	0/1	0/0	0/1	0/1	1/1	0/1	1/1	0/0	1/1	1/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/1	1/1	0/0	0/1	0/1	0/0	0/1	0/1	1/1	1/1	0/1	0/0	0/1	0/0	1/1	0/1	1/1	0/1	0/1	0/1	0/0	1/1	0/1	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	1/1	0/0	0/0	0/0	1/1	1/1	0/0	0/0	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	1/1	1/1	0/1	1/1	0/1	0/0	0/1	0/0	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	0/0	0/0	1/1	1/1	1/1	0/1	0/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	0/1	0/1	0/0	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	0/1	0/1	0/1	0/0	0/1	0/1
+chr1	77761353	.	ATTCT	A	.	PASS	VC=INDEL;AC=87;AF=0.28;AN=310;refseq.name=NM_174858;refseq.positionType=intron	GT	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/1	1/1	0/0	1/1	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	./.	0/1	0/1	0/0	1/1	0/1	0/0	0/0	0/0	0/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	1/1	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	./.	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	1/1	0/1	0/1	0/0	0/1	0/1	./.	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	1/1	0/1	0/0	0/1	0/0	0/0	0/1	0/1	1/1	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/0	0/1	0/1	1/1	0/1	0/1
+chr1	78436001	.	T	TCT	.	PASS	VC=INDEL;AC=139;AF=0.45;AN=308;refseq.name=NM_003902;refseq.positionType=intron	GT	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	1/1	0/1	0/1	0/0	0/0	0/1	0/1	0/0	0/0	1/1	0/1	./.	0/0	0/1	0/1	0/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/0	1/1	0/1	0/0	0/1	0/1	0/1	0/0	1/1	0/1	0/1	0/0	0/0	0/0	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	0/1	0/0	1/1	0/1	1/1	0/0	0/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	0/0	1/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	0/0	0/1	0/0	0/1	0/1	0/1	1/1	0/1	1/1	0/1	0/1	0/0	0/1	0/1	0/1	1/1	0/1	1/1	0/0	0/1	0/1	0/0	1/1	0/1	1/1	0/0	0/1	0/1	./.	1/1	1/1	./.	1/1	./.	0/1	0/0	0/0	0/0
+chr1	78477804	.	T	TAAGAC	.	PASS	VC=INDEL;AC=294;AF=0.93;AN=316;refseq.name=NM_007034;refseq.positionType=intron	GT	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1
+chr1	78533885	.	CAG	C	.	PASS	VC=INDEL;AC=126;AF=0.4;AN=316;refseq.name=NM_017655;refseq.positionType=intron	GT	0/1	0/0	0/1	1/1	0/1	1/1	1/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	1/1	0/1	1/1	0/0	1/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/1	1/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	1/1	0/1	1/1	0/1	0/1	1/1	0/0	0/0	0/1	0/1	0/0	0/1	1/1	1/1	1/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	1/1	0/0	0/1	0/1	0/1	1/1	0/1	1/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	1/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	1/1	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	1/1	0/0	0/1	0/1	1/1
+chr1	78533886	.	AGA	A	.	PASS	VC=INDEL;AC=126;AF=0.4;AN=316;refseq.name=NM_017655;refseq.positionType=intron	GT	0/1	0/0	0/1	1/1	0/1	1/1	1/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	1/1	0/1	1/1	0/0	1/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/1	1/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	1/1	0/1	1/1	0/1	0/1	1/1	0/0	0/0	0/1	0/1	0/0	0/1	1/1	1/1	1/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	1/1	0/0	0/1	0/1	0/1	1/1	0/1	1/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	1/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	1/1	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	1/1	0/0	0/1	0/1	1/1
+chr1	78752617	.	TC	T	.	PASS	VC=INDEL;AC=160;AF=0.51;AN=314	GT	0/1	1/1	0/0	0/0	1/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	1/1	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/1	0/1	1/1	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/0	0/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	0/1	0/0	1/1	0/1	1/1	0/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	0/1	0/1	1/1	0/1	1/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	0/0	0/1	0/0	1/1	0/1	0/1	0/1	./.	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/0	1/1	0/1	0/1	0/0	0/0	0/0	1/1	0/1	1/1	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	1/1	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/1	1/1	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/1
+chr1	79595269	.	T	TC	.	PASS	VC=INDEL;AC=37;AF=0.12;AN=312	GT	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	./.	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	./.	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1
+chr1	79694557	.	CTTGT	C	.	PASS	VC=INDEL;AC=173;AF=0.68;AN=254	GT	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	1/1	./.	./.	0/0	0/1	./.	0/0	0/0	0/0	0/1	0/1	0/0	0/0	1/1	./.	0/1	0/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/0	./.	./.	./.	./.	0/0	0/1	0/1	./.	0/1	0/1	./.	0/0	0/1	./.	./.	0/1	1/1	0/1	0/1	./.	0/1	0/1	./.	./.	0/1	./.	1/1	./.	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	./.	./.	1/1	./.	1/1	1/1	1/1	0/1	1/1	./.	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	1/1	1/1	./.	0/1	1/1	1/1	0/1	1/1	1/1	0/1	0/0	./.	./.	1/1	0/1	1/1	./.	1/1	./.	1/1	1/1	1/1	1/1	1/1	0/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	./.	0/1	0/1	./.	1/1	0/1	1/1	1/1	1/1	1/1	./.	0/1	0/1	0/1	1/1	0/1	1/1	1/1	./.	1/1	1/1	1/1	0/1	1/1	1/1	0/1	0/0
+chr1	80133716	.	CA	C	.	PASS	VC=INDEL;AC=74;AF=0.27;AN=276	GT	0/1	0/1	0/0	0/1	1/1	0/0	0/0	0/1	0/1	0/0	./.	0/0	./.	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	1/1	0/1	0/1	0/1	./.	./.	0/0	0/0	./.	0/1	0/0	0/1	1/1	./.	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	./.	0/0	0/0	./.	0/1	0/0	0/1	0/1	0/0	0/1	0/0	./.	0/1	./.	0/0	0/0	0/0	0/1	0/0	0/0	./.	0/0	0/1	1/1	0/1	1/1	0/1	1/1	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/0	1/1	0/1	0/0	./.	0/1	0/0	0/1	0/1	1/1	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/1	0/1	0/1	0/1	0/0	1/1	0/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	./.	./.	0/1	./.	1/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	./.	0/1	./.	0/1	0/1	0/0	1/1	0/1	0/0	0/0
+chr1	80193527	.	CA	C	.	PASS	VC=INDEL;AC=0;AF=0;AN=314	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	80279810	.	T	TT	.	PASS	VC=INDEL;AC=69;AF=0.22;AN=314	GT	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	1/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	1/1	1/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	1/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	1/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	1/1	1/1	0/1	1/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	1/1	1/1	./.	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	1/1	1/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	1/1	0/0	0/1	0/1	0/1	0/1	0/1
+chr1	80415715	.	C	CATGTCTATTAT	.	PASS	VC=INDEL;AC=197;AF=0.62;AN=316	GT	0/1	0/0	1/1	1/1	0/0	1/1	0/1	0/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	0/0	0/1	0/0	1/1	0/0	0/1	0/0	1/1	1/1	0/1	0/1	0/0	0/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/0	1/1	1/1	1/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	0/0	0/1	0/1	1/1	1/1	0/0	1/1	0/1	1/1	0/1	0/1	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/1	1/1	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/0	1/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	0/0	0/1	0/0	0/1	0/0	0/1	1/1	1/1	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	1/1	0/0	0/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/0	1/1	0/1	0/1	1/1
+chr1	80415717	.	T	TGTCTATTATAT	.	PASS	VC=INDEL;AC=197;AF=0.62;AN=316	GT	0/1	0/0	1/1	1/1	0/0	1/1	0/1	0/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	0/0	0/1	0/0	1/1	0/0	0/1	0/0	1/1	1/1	0/1	0/1	0/0	0/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/0	1/1	1/1	1/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	0/0	0/1	0/1	1/1	1/1	0/0	1/1	0/1	1/1	0/1	0/1	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/1	1/1	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/0	1/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	0/0	0/1	0/0	0/1	0/0	0/1	1/1	1/1	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	1/1	0/0	0/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/0	1/1	0/1	0/1	1/1
+chr1	80606020	.	GTAGGC	G	.	PASS	VC=INDEL;AC=282;AF=0.89;AN=316	GT	1/1	0/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	1/1	0/1	1/1	0/0	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/0	1/1	1/1	1/1	0/1	1/1
+chr1	80684057	.	A	AA	.	PASS	VC=INDEL;AC=217;AF=0.69;AN=316	GT	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	0/0	0/1	0/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	1/1	0/1	1/1	0/0	1/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	0/0	0/1	0/0	0/1	1/1	1/1	0/1	0/1	1/1	1/1	0/0	0/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	1/1	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	0/0	0/1	1/1	1/1	1/1	0/1	0/1	0/0	1/1	0/1	1/1	1/1	0/1	1/1	0/1	0/0	0/0	1/1	1/1
+chr1	80857688	.	AAATA	A	.	PASS	VC=INDEL;AC=97;AF=0.31;AN=316	GT	0/0	0/1	0/0	1/1	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/0	1/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	1/1	0/0	0/1	0/0	0/1	1/1	1/1	0/1	0/1	0/1	0/1	0/1	1/1	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/1	1/1	1/1	0/0	1/1	0/1	0/1	1/1	1/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	1/1	1/1	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/1	1/1	0/0	0/1	0/1	1/1	0/0
+chr1	81007659	.	A	AC	.	PASS	VC=INDEL;AC=185;AF=0.59;AN=312	GT	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	1/1	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	0/0	0/0	0/1	0/0	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/0	0/1	0/1	0/1	1/1	0/1	1/1	0/0	1/1	0/1	0/1	1/1	0/1	0/1	0/1	1/1	1/1	0/0	1/1	1/1	1/1	0/0	0/1	0/1	0/1	0/1	1/1	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/0	1/1	0/1	0/1	0/1	1/1	0/1	1/1	0/1	0/1	0/1	0/1	1/1	0/0	0/1	0/1	1/1	1/1	./.	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/0	1/1	1/1	1/1	0/1	1/1	1/1	0/1	./.	0/0	0/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	0/1	0/1	0/1	0/1	1/1	0/1	0/0	0/1	0/0	1/1	0/1	1/1	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/1	1/1	0/1	0/0	1/1	0/1	0/0	0/1	0/0	0/1	1/1	0/1	0/1	0/0	1/1	1/1	1/1	1/1	0/0	0/0
+chr1	81007660	.	C	CC	.	PASS	VC=INDEL;AC=185;AF=0.59;AN=314	GT	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	1/1	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	0/0	0/0	0/1	0/0	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/0	0/1	0/1	0/1	1/1	0/1	1/1	0/0	1/1	0/1	0/1	1/1	0/1	0/1	0/1	1/1	1/1	0/0	1/1	1/1	1/1	0/0	0/1	0/1	0/1	0/1	1/1	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/0	1/1	0/1	0/1	0/1	1/1	0/1	1/1	0/1	0/1	0/1	0/1	1/1	0/0	0/1	0/1	1/1	1/1	./.	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/0	1/1	1/1	1/1	0/1	1/1	1/1	0/1	0/0	0/0	0/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	0/1	0/1	0/1	0/1	1/1	0/1	0/0	0/1	0/0	1/1	0/1	1/1	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/1	1/1	0/1	0/0	1/1	0/1	0/0	0/1	0/0	0/1	1/1	0/1	0/1	0/0	1/1	1/1	1/1	1/1	0/0	0/0
+chr1	81912884	.	C	CT	.	PASS	VC=INDEL;AC=15;AF=0.05;AN=298	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	./.	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	./.	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	./.	0/1	0/0	0/0	0/0	./.	0/0	0/0
+chr1	82042397	.	TCTT	T	.	PASS	VC=INDEL;AC=5;AF=0.02;AN=316	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	82264610	.	TG	T	.	PASS	VC=INDEL;AC=167;AF=0.54;AN=312;refseq.name=NM_012302;refseq.positionType=promoter	GT	0/1	1/1	0/1	1/1	1/1	0/1	0/1	0/0	0/1	0/1	0/0	1/1	0/1	0/1	1/1	0/1	1/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	0/1	./.	0/1	0/0	1/1	0/0	0/1	0/0	1/1	0/1	1/1	0/0	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	0/0	0/0	0/1	1/1	0/1	1/1	0/1	0/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	0/0	0/1	0/1	0/1	0/0	0/1	1/1	0/1	1/1	0/0	0/1	0/1	1/1	1/1	0/1	0/0	0/1	0/1	0/0	1/1	0/0	1/1	1/1	1/1	0/0	0/1	0/0	1/1	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	1/1	0/1	0/1	0/1	1/1	0/0	0/0	0/1	0/1	0/1	1/1	1/1	0/1	0/1	0/1	0/0	1/1	0/1	0/0	0/1	0/0	0/0	1/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	./.	0/1	0/1	0/0
+chr1	82264994	.	G	GGTAG	.	PASS	VC=INDEL;AC=49;AF=0.16;AN=316;refseq.name=NM_012302;refseq.positionType=promoter	GT	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/0	1/1	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/0	1/1	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/0
+chr1	82280496	.	ATGT	A	.	PASS	VC=INDEL;AC=84;AF=0.27;AN=316;refseq.name=NM_012302;refseq.positionType=intron	GT	0/1	1/1	0/1	0/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/1	0/1	0/0	1/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	0/0	0/0	0/1	1/1	0/1	1/1	0/1	0/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	1/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	82315714	.	G	GAGTG	.	PASS	VC=INDEL;AC=38;AF=0.12;AN=306;refseq.name=NM_012302;refseq.positionType=intron	GT	0/1	0/0	0/1	0/0	0/0	./.	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/0	0/1	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1
+chr1	82316526	.	TT	T	.	PASS	VC=INDEL;AC=209;AF=0.67;AN=312;refseq.name=NM_012302;refseq.positionType=intron	GT	0/1	1/1	0/1	1/1	1/1	0/1	0/1	0/1	0/1	0/0	0/1	1/1	1/1	0/1	1/1	0/1	./.	0/1	0/1	0/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1	1/1	0/1	0/1	0/0	1/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	0/0	0/0	0/1	1/1	0/1	1/1	0/1	0/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	0/0	0/1	1/1	1/1	1/1	0/1	0/0	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/0	0/0	0/0	1/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/0	1/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	0/0	1/1	0/1	0/1	1/1	0/1	0/1	0/1	./.	1/1	1/1	1/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	1/1	0/1	0/1	0/0
+chr1	82329993	.	CATAT	C	.	PASS	VC=INDEL;AC=305;AF=0.97;AN=316;refseq.name=NM_012302;refseq.positionType=intron	GT	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	1/1	0/1	1/1	1/1
+chr1	82710650	.	AA	A	.	PASS	VC=INDEL;AC=297;AF=0.96;AN=310	GT	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	0/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1
+chr1	83144930	.	TC	T	.	PASS	VC=INDEL;AC=153;AF=0.55;AN=278	GT	1/1	1/1	0/1	1/1	0/1	0/0	1/1	1/1	0/0	1/1	0/1	0/0	0/1	./.	0/1	0/0	1/1	0/1	0/0	0/1	0/0	0/0	./.	./.	0/1	1/1	0/0	0/1	0/1	0/1	0/1	./.	1/1	0/1	./.	1/1	0/1	0/1	0/1	0/1	0/1	./.	0/1	0/1	./.	0/1	0/1	1/1	1/1	0/1	0/0	0/1	./.	0/0	0/1	1/1	0/1	0/1	0/1	0/1	1/1	1/1	0/0	1/1	0/1	0/0	./.	0/1	0/0	0/1	1/1	0/1	1/1	0/1	0/0	0/0	0/0	0/0	1/1	1/1	1/1	1/1	1/1	0/1	0/1	./.	1/1	0/0	./.	0/1	0/1	0/0	0/1	./.	0/0	0/1	1/1	0/1	1/1	./.	0/0	0/0	./.	0/1	0/0	./.	1/1	0/1	1/1	0/1	1/1	0/1	0/1	0/0	1/1	0/0	0/1	0/0	1/1	0/1	1/1	0/0	0/1	1/1	0/0	./.	0/0	1/1	./.	./.	1/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	1/1	0/0	0/1	./.	0/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1
+chr1	83208212	.	C	CAGAT	.	PASS	VC=INDEL;AC=0;AF=0;AN=316	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	83208213	.	A	AGATA	.	PASS	VC=INDEL;AC=0;AF=0;AN=316	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	83581070	.	C	CCAGA	.	PASS	VC=INDEL;AC=188;AF=0.74;AN=254	GT	./.	./.	1/1	0/1	./.	0/1	1/1	0/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	0/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	./.	./.	1/1	0/1	./.	./.	./.	1/1	1/1	./.	0/0	0/1	0/1	1/1	./.	0/1	1/1	0/1	0/1	./.	0/0	1/1	0/1	0/1	./.	./.	0/1	1/1	./.	1/1	0/1	0/1	./.	./.	1/1	1/1	0/1	1/1	1/1	0/1	1/1	0/1	1/1	./.	0/1	0/1	0/1	0/1	0/1	0/1	1/1	1/1	0/1	./.	0/1	0/0	0/1	./.	0/1	1/1	1/1	1/1	0/1	./.	1/1	0/1	0/1	./.	./.	./.	0/1	1/1	./.	0/1	1/1	0/1	1/1	0/1	0/1	0/1	1/1	0/0	0/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	./.	0/1	0/1	./.	1/1	0/1	1/1	./.	./.	0/1	1/1	1/1	1/1	./.	1/1	1/1	0/1	1/1	0/1	0/1	0/1	1/1	./.	1/1
+chr1	84127066	.	TCT	T	.	PASS	VC=INDEL;AC=71;AF=0.22;AN=316	GT	1/1	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/1	1/1	0/1	0/1	0/0	1/1	0/0	1/1	0/0	1/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	0/1	1/1	0/0	0/1	0/1	0/1	0/1	0/1	1/1	1/1	0/1	0/0	0/0	1/1	0/1	0/1	1/1	1/1	0/1	1/1	0/0	0/1	0/0	1/1	0/1	0/0	1/1	1/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1
+chr1	84822658	.	TCAATTAAAACTCACAG	T	.	PASS	VC=INDEL;AC=45;AF=0.16;AN=286	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/1	1/1	./.	0/1	1/1	0/0	0/0	./.	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	./.	0/1	0/1	1/1	0/1	0/1	0/0	0/1	0/1	./.	0/1	0/0	0/1	0/1	0/1	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	./.	0/0	./.	./.	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	./.	0/1	0/1	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	1/1	0/1	0/0	0/0
+chr1	85570521	.	GTTC	G	.	PASS	VC=INDEL;AC=166;AF=0.53;AN=316;refseq.name=NM_145172;refseq.positionType=intron	GT	0/1	0/0	0/0	0/1	0/1	0/1	1/1	1/1	0/1	0/0	0/1	1/1	1/1	0/1	0/0	1/1	1/1	1/1	0/1	0/1	0/1	1/1	0/0	0/0	0/1	0/0	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/0	0/1	0/1	0/1	1/1	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	1/1	1/1	0/0	0/1	1/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	1/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1	0/1	0/1	1/1	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1	0/0	1/1	0/0	0/1	1/1	1/1	1/1	0/1	0/1	0/1	0/0	1/1	0/1	1/1	0/1	0/1	0/1	0/0	0/0	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	0/1	0/1	1/1	0/1	1/1	0/0	0/0	0/1	1/1	0/1	0/1	0/1	0/1
+chr1	86565855	.	T	TCT	.	PASS	VC=INDEL;AC=20;AF=0.06;AN=316;refseq.name=NM_152890;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0
+chr1	86714492	.	T	TA	.	PASS	VC=INDEL;AC=263;AF=0.88;AN=300	GT	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	./.	./.	1/1	1/1	1/1	./.	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/0	0/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	0/0	0/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	./.	1/1	1/1	./.	1/1	0/1	0/1	0/1	0/1	0/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	./.	1/1	1/1
+chr1	86786541	.	CAG	C	.	PASS	VC=INDEL;AC=7;AF=0.02;AN=316	GT	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	86839425	.	TACTT	T	.	PASS	VC=INDEL;AC=15;AF=0.05;AN=280;refseq.name=NM_001007022;refseq.positionType=intron	GT	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	./.	0/0	./.	0/0	0/1	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	./.	0/0	0/0	./.	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	./.	0/0	./.	./.	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	./.	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0
+chr1	87558067	.	CACATAC	C	.	PASS	VC=INDEL;AC=285;AF=0.97;AN=294;refseq.name=NM_012262;refseq.positionType=intron	GT	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	./.	1/1	0/1	1/1	1/1	1/1	1/1	0/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	./.	./.	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	./.	./.	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	./.	0/1	1/1	1/1
+chr1	88184554	.	T	TCA	.	PASS	VC=INDEL;AC=40;AF=0.14;AN=276	GT	0/0	0/0	0/0	0/0	./.	./.	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	1/1	0/1	0/0	0/1	1/1	./.	0/1	0/1	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	1/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	./.	0/0	0/0	0/1	0/0	0/0	0/1	./.	0/0	./.	./.	0/0	./.	0/0	0/1	0/1	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/1	0/0	./.	0/0	0/0	0/0	0/1	0/0	./.	./.	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/1	0/0	0/0	0/0	./.	0/0	./.	0/0	./.	0/1	0/1
+chr1	88351056	.	A	AGT	.	PASS	VC=INDEL;AC=222;AF=0.7;AN=316	GT	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/1	1/1	0/0	1/1	0/0	1/1	0/1	0/1	0/1	0/0	1/1	1/1	0/1	0/1	0/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/0	0/0	0/1	0/0	0/0	0/1	1/1	0/0	0/1	0/1	0/1	0/1	0/1	1/1	0/0	0/1	0/0	1/1	0/0	0/1	0/1	0/0	0/1	1/1	1/1	1/1	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	1/1	0/1	0/1	0/1	0/0	0/0	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0
+chr1	88391828	.	C	CCTT	.	PASS	VC=INDEL;AC=216;AF=0.7;AN=310	GT	0/1	0/0	0/1	1/1	1/1	1/1	0/0	0/1	1/1	0/0	0/1	0/0	1/1	1/1	0/1	0/0	0/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/0	1/1	0/1	0/1	0/0	./.	0/1	1/1	0/0	0/0	0/0	0/1	0/0	1/1	0/1	0/1	0/0	0/0	./.	0/0	0/1	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	1/1	1/1	1/1	1/1	0/1	0/1	1/1	./.	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1
+chr1	88391834	.	T	TCTT	.	PASS	VC=INDEL;AC=219;AF=0.69;AN=316	GT	0/1	0/0	0/1	1/1	1/1	1/1	0/0	0/1	1/1	0/0	0/1	0/0	1/1	1/1	0/1	0/0	0/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/0	1/1	0/1	0/1	0/0	0/1	0/1	1/1	0/0	0/0	0/0	0/1	0/0	1/1	0/1	0/1	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1
+chr1	88423056	.	T	TA	.	PASS	VC=INDEL;AC=210;AF=0.8;AN=262	GT	1/1	0/0	1/1	./.	0/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	./.	./.	./.	1/1	1/1	./.	0/1	0/1	0/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	./.	0/1	1/1	0/1	0/1	./.	./.	0/1	0/1	1/1	0/1	0/1	0/1	0/1	./.	./.	./.	1/1	0/0	0/1	0/0	0/1	0/0	0/1	1/1	0/0	0/1	0/0	0/1	0/0	0/0	0/1	1/1	0/0	0/1	0/1	./.	1/1	./.	0/0	0/1	1/1	./.	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	0/0	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	0/1	1/1	1/1	1/1	1/1	./.	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	./.	./.	1/1	1/1	./.	1/1	0/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	./.	1/1	1/1	1/1	1/1	1/1	0/1	0/1
+chr1	88878932	.	TGAAG	T	.	PASS	VC=INDEL;AC=222;AF=0.71;AN=314	GT	0/1	1/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/0	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/0	1/1	0/1	1/1	1/1	0/1	1/1	1/1	0/1	0/0	0/0	1/1	1/1	0/1	0/0	1/1	1/1	0/0	1/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/1	1/1	0/0	0/1	0/1	0/0	0/1	0/1	1/1	0/1	0/1	0/1	0/0	1/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	0/0	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	0/0	1/1	0/1	1/1	0/1	0/1	1/1	0/1	0/1	1/1	0/1	1/1	1/1	0/1	0/1	1/1	0/0	0/1	0/1	0/1	0/1	1/1	0/1	0/1	1/1	0/0	0/1	1/1	./.	1/1	1/1	1/1	1/1	0/0	1/1	0/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1
+chr1	88934449	.	T	TA	.	PASS	VC=INDEL;AC=215;AF=0.71;AN=304	GT	0/1	0/1	0/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	./.	0/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	0/0	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	0/0	1/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	1/1	0/1	0/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	0/1	0/1	0/0	0/1	0/1	1/1	1/1	1/1	1/1	0/1	./.	0/1	0/1	0/1	0/1	0/0	0/1	0/0	1/1	0/0	0/1	1/1	0/0	0/1	0/0	0/1	0/1	1/1	0/1	1/1	1/1	0/0	./.	0/1	0/0	0/1	0/1	1/1	0/0	0/1	0/0	0/0	0/1	0/0	0/1	1/1	1/1	1/1	0/0	1/1	0/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	0/0	1/1	0/0
+chr1	89147233	.	C	CTG	.	PASS	VC=INDEL;AC=270;AF=0.94;AN=288;refseq.name=NM_006256;refseq.positionType=promoter	GT	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	0/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	./.	1/1	./.	./.	1/1	1/1	0/1	0/1	./.	1/1	1/1	1/1	./.	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	./.	./.	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	./.	1/1	1/1	1/1	1/1	./.	0/1	1/1	0/0	0/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1
+chr1	89147234	.	T	TGT	.	PASS	VC=INDEL;AC=193;AF=0.91;AN=212;refseq.name=NM_006256;refseq.positionType=promoter	GT	./.	1/1	1/1	1/1	./.	./.	1/1	1/1	./.	1/1	./.	./.	1/1	1/1	./.	1/1	./.	./.	./.	./.	./.	1/1	1/1	./.	0/1	1/1	0/1	./.	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	0/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	./.	./.	./.	1/1	1/1	./.	0/1	./.	1/1	1/1	1/1	./.	0/1	1/1	1/1	1/1	1/1	./.	./.	./.	./.	./.	./.	./.	1/1	./.	1/1	./.	./.	./.	0/1	./.	1/1	./.	./.	1/1	1/1	1/1	./.	1/1	1/1	1/1	./.	./.	1/1	1/1	./.	1/1	0/1	0/1	./.	0/0	0/1	./.	./.	./.	./.	0/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	./.	1/1	1/1	1/1	./.	./.	1/1	./.	./.	./.	1/1
+chr1	90055475	.	TT	T	.	PASS	VC=INDEL;AC=35;AF=0.11;AN=316;refseq.name=NM_015350;refseq.positionType=intron	GT	0/1	0/0	0/0	1/1	0/0	0/1	1/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/0	1/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	1/1	0/1	0/1	0/0	0/1	1/1	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0
+chr1	90055577	.	TATG	T	.	PASS	VC=INDEL;AC=0;AF=0;AN=316;refseq.name=NM_015350;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	90305331	.	G	GA	.	PASS	VC=INDEL;AC=301;AF=0.95;AN=316;refseq.name=NM_018103;refseq.positionType=intron	GT	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	0/0	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	0/0	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1
+chr1	91238816	.	G	GT	.	PASS	VC=INDEL;AC=86;AF=0.29;AN=296	GT	0/0	0/0	./.	1/1	0/0	0/0	0/1	./.	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	1/1	0/1	0/0	0/0	./.	0/1	0/0	0/1	0/1	0/0	1/1	0/0	0/0	0/0	1/1	0/1	0/1	0/0	0/0	0/0	1/1	0/0	1/1	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/0	./.	0/1	0/0	0/1	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/1	0/0	0/1	0/1	./.	0/1	1/1	0/0	0/0	0/0	0/1	0/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	./.	0/0	0/1	0/0	0/1	0/0	0/1	1/1	1/1	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/0	1/1	0/0	0/0	0/0	1/1	1/1	1/1	0/0	1/1	./.	0/0	0/0	0/0	0/1	0/1	1/1	0/1	0/0	1/1	0/1	0/1	0/1	./.	0/0	0/0	1/1	0/1	1/1	1/1	0/0	0/0	./.	0/0	0/1	0/1	0/1	0/0	./.	0/1
+chr1	91308113	.	GC	G	.	PASS	VC=INDEL;AC=8;AF=0.03;AN=282	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	./.	0/0	./.	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	./.	./.	0/0	0/0	./.	0/0	0/0	./.	0/0	0/0	0/1	0/1	./.	0/0	0/0	./.	0/0	./.	./.	0/0	0/0
+chr1	91354296	.	TT	T	.	PASS	VC=INDEL;AC=252;AF=0.83;AN=304	GT	1/1	0/0	0/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	./.	1/1	0/0	0/0	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/0	0/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	./.	./.	1/1	1/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/0	0/1	0/1	1/1	0/1	0/1	./.	0/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	0/0	0/1	1/1	0/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1
+chr1	91544957	.	ACT	A	.	PASS	VC=INDEL;AC=99;AF=0.32;AN=314	GT	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/1	0/0	0/0	0/0	0/0	0/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	1/1	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/1	1/1	1/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/0	1/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	1/1	1/1	0/1	0/1	1/1	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/1	0/1	1/1	0/1	0/0	0/1	0/1	1/1	1/1	0/1	0/0	0/1	0/0	0/0	0/0	1/1	0/1	0/1	1/1	0/1	1/1	1/1	0/1	0/1	0/1	0/0	1/1	0/0	0/1	0/1	0/0	0/0
+chr1	91566585	.	GTTA	G	.	PASS	VC=INDEL;AC=139;AF=0.45;AN=312	GT	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	0/0	0/0	1/1	0/1	0/0	0/1	0/0	0/0	0/1	1/1	0/1	0/1	0/0	1/1	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/1	1/1	1/1	1/1	0/1	0/1	0/1	0/0	0/1	0/0	1/1	0/0	0/1	0/0	0/1	1/1	1/1	1/1	0/0	0/0	0/1	0/1	1/1	0/0	0/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	0/0	1/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	0/0	0/1	0/0	0/1	0/1	0/1	0/1	1/1	0/1	0/0	0/1	0/1	1/1	0/1	./.	0/1	0/0	0/0	0/1	0/0	0/1	0/1	1/1	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/0	./.	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	1/1	0/1	0/1	1/1	1/1	0/1	0/1	0/1	0/1	0/0	0/1	1/1	0/1	1/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/1
+chr1	92219769	.	C	CTCCTCAA	.	PASS	VC=INDEL;AC=54;AF=0.17;AN=314;refseq.name=NM_003243;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	1/1	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/1	1/1	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/1	1/1	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/1	0/0	0/0	./.	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	1/1	0/0	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0
+chr1	93167519	.	C	CTG	.	PASS	VC=INDEL;AC=276;AF=1;AN=276;refseq.name=NM_005665;refseq.positionType=intron	GT	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	./.	1/1	./.	1/1	./.	1/1	1/1	1/1	./.	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	./.	./.	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1
+chr1	93628710	.	TACTC	T	.	PASS	VC=INDEL;AC=94;AF=0.31;AN=304;refseq.name=NM_016040;refseq.positionType=intron	GT	0/1	1/1	0/1	1/1	1/1	0/1	0/1	0/1	0/0	1/1	0/0	0/1	0/0	0/0	0/1	0/1	./.	0/0	0/1	1/1	0/1	1/1	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	1/1	0/0	0/1	0/1	0/1	0/1	0/1	1/1	1/1	0/1	0/0	0/1	1/1	1/1	1/1	1/1	0/1	0/1	0/0	1/1	1/1	0/0	./.	0/1	1/1	1/1	1/1	1/1	1/1	0/1	0/0	0/1	0/1	0/1	0/1	1/1	1/1	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	1/1	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	./.	0/0	0/1	0/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	./.	0/0	0/1
+chr1	93704043	.	T	TCTAGAAAAATC	.	PASS	VC=INDEL;AC=7;AF=0.02;AN=306;refseq.name=NM_206886;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	./.	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	./.	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0
+chr1	94443843	.	G	GAGAG	.	PASS	VC=INDEL;AC=88;AF=0.3;AN=292	GT	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	1/1	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/1	./.	0/1	0/1	0/1	0/0	0/1	0/1	0/0	1/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	./.	0/1	0/0	0/1	0/1	0/0	0/0	0/0	./.	0/0	0/0	0/1	0/0	0/0	0/0	./.	0/0	0/0	0/1	./.	0/0	0/0	0/1	./.	0/1	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/1	1/1	0/1	1/1	1/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/0	./.	1/1	0/1	0/1	0/1	0/1	1/1	0/1	0/0	0/1	0/0	0/0	./.	0/0	0/1	0/0	0/0	0/0	0/0	0/1	1/1	1/1	0/0	0/0	./.	0/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	./.	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/1	1/1	0/0	0/1	0/0	./.	0/0
+chr1	94634727	.	TGAGT	T	.	PASS	VC=INDEL;AC=0;AF=0;AN=316;refseq.name=NM_004815;refseq.positionType=exon	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	95103314	.	AGCATCCTAAA	A	.	PASS	VC=INDEL;AC=6;AF=0.03;AN=240	GT	./.	./.	0/0	0/0	0/0	./.	./.	0/1	0/0	./.	0/0	./.	0/0	0/0	./.	./.	./.	0/0	0/0	./.	0/0	./.	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	./.	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	./.	./.	0/0	0/0	0/0	0/0	./.	0/0	0/1	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	./.	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	./.	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	./.	./.	0/0	0/0	0/0	0/0	0/0	./.	./.	0/0	./.	./.	0/0	0/0	./.	0/0	0/0	./.	0/1	0/1	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	95167241	.	TTAAC	T	.	PASS	VC=INDEL;AC=115;AF=0.36;AN=316	GT	0/1	0/1	0/1	1/1	0/0	0/1	0/1	0/1	0/0	1/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	1/1	0/1	0/0	0/0	0/1	0/1	1/1	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/0	1/1	0/0	0/1	0/1	0/1	1/1	0/0	1/1	0/1	0/1	0/1	0/0	0/0	1/1	1/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/0	1/1	0/0	0/1	0/1	1/1	0/0	0/0	0/1	1/1	0/0	1/1	0/0	1/1	0/1	0/1	1/1	0/0	0/0	0/0	0/1	0/0	0/1	1/1	0/0	0/1	0/0	0/1	0/0	0/0	1/1	0/1	0/1	0/1	1/1	0/1	0/1	1/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	1/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	1/1	0/1	0/0	0/0	0/0	1/1
+chr1	95167244	.	ACTAA	A	.	PASS	VC=INDEL;AC=116;AF=0.37;AN=316	GT	0/1	0/1	0/1	1/1	0/0	0/1	0/1	0/1	0/0	1/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	1/1	0/1	0/0	0/0	0/1	0/1	1/1	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/0	1/1	0/0	0/1	0/1	0/1	1/1	0/0	1/1	0/1	0/1	0/1	0/0	0/0	1/1	1/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/0	1/1	0/0	0/1	0/1	1/1	0/0	0/0	0/1	1/1	0/0	1/1	0/0	1/1	0/1	0/1	1/1	0/0	0/0	0/0	0/1	0/0	0/1	1/1	0/0	0/1	0/0	0/1	0/0	0/0	1/1	0/1	0/1	0/1	1/1	0/1	0/1	1/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/1	1/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	1/1	0/1	0/0	0/0	0/0	1/1
+chr1	95266356	.	A	AAAATAAGAATCCA	.	PASS	VC=INDEL;AC=212;AF=0.83;AN=256	GT	1/1	./.	1/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	0/1	./.	1/1	1/1	1/1	./.	./.	./.	0/0	1/1	0/0	0/1	./.	0/1	0/1	1/1	1/1	1/1	./.	0/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	./.	0/1	1/1	0/1	0/0	0/1	1/1	1/1	./.	1/1	./.	1/1	0/1	1/1	0/1	1/1	./.	./.	0/1	./.	0/1	1/1	0/1	0/1	0/1	./.	0/1	./.	1/1	0/1	0/1	1/1	1/1	1/1	0/1	0/0	0/0	./.	1/1	0/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	1/1	0/1	1/1	0/0	0/1	1/1	1/1	./.	./.	./.	0/1	0/1	1/1	./.	0/1	1/1	0/1	0/1	0/1	1/1	1/1	./.	0/1	./.	1/1	./.	./.	./.
+chr1	95349846	.	G	GG	.	PASS	VC=INDEL;AC=195;AF=0.65;AN=302;refseq.name=NM_001114106;refseq.positionType=intron	GT	1/1	1/1	0/0	1/1	1/1	1/1	0/1	0/1	0/1	1/1	./.	1/1	0/1	1/1	0/1	1/1	1/1	0/1	0/1	0/1	0/1	1/1	1/1	0/1	0/1	0/1	1/1	0/1	0/0	1/1	0/1	0/1	0/0	1/1	1/1	1/1	0/1	0/0	0/1	1/1	0/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1	0/1	0/0	0/1	1/1	./.	1/1	0/1	0/1	0/1	0/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	0/0	0/1	0/0	0/1	0/1	./.	1/1	0/1	./.	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	1/1	1/1	0/1	1/1	1/1	0/0	1/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	0/0	0/0	0/1	0/0	0/1	1/1	0/0	0/1	0/1	1/1	./.	0/0	0/1	0/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	1/1	1/1	0/1	1/1	0/1	./.	0/0	0/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	./.	0/1	0/1	0/1	1/1	1/1
+chr1	95638470	.	GTAG	G	.	PASS	VC=INDEL;AC=9;AF=0.03;AN=306;refseq.name=NM_152487;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	96578762	.	CAG	C	.	PASS	VC=INDEL;AC=78;AF=0.25;AN=314	GT	1/1	0/0	0/0	0/1	1/1	0/1	0/0	1/1	0/0	1/1	0/1	1/1	1/1	0/0	0/1	1/1	0/1	0/0	0/1	0/1	0/1	1/1	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	1/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	./.	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/1	1/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/1	1/1
+chr1	97069290	.	G	GT	.	PASS	VC=INDEL;AC=57;AF=0.18;AN=316	GT	0/0	0/1	1/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	1/1	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	1/1	1/1	0/0	0/1	0/0	0/0	0/1	0/0	0/1	1/1	1/1	0/0	0/0	0/1	0/0	1/1	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0
+chr1	97352585	.	A	AGA	.	PASS	VC=INDEL;AC=167;AF=0.53;AN=316	GT	0/0	0/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/0	0/0	1/1	1/1	0/1	1/1	0/0	0/1	0/1	1/1	1/1	0/1	1/1	0/1	0/1	0/1	0/0	1/1	0/1	0/1	1/1	0/1	0/1	0/1	0/1	0/1	1/1	1/1	0/1	0/0	0/1	0/1	0/1	0/0	1/1	0/1	0/1	0/1	1/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	1/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	1/1	0/0	1/1	0/1	1/1	0/1	0/1	0/1	0/0	0/0	0/0	1/1	1/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	0/1	1/1	1/1	0/0	0/0	0/0	1/1	0/0	0/1	1/1	0/0	0/0	0/0	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	0/0	0/1	0/1	0/0	0/1	0/0	1/1	1/1	1/1	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/0	0/1	0/1	0/1	1/1	0/1	0/0	0/0	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/1	0/1	0/1
+chr1	97471673	.	T	TTA	.	PASS	VC=INDEL;AC=39;AF=0.16;AN=238	GT	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/1	0/0	0/0	0/1	0/0	./.	0/1	0/0	1/1	./.	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/1	0/0	1/1	./.	0/1	./.	1/1	0/1	0/1	0/0	0/0	./.	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/0	./.	./.	0/1	0/0	0/0	0/1	./.	0/1	1/1	1/1	0/0	0/1	0/0	0/1	0/1	0/0	0/0	./.	./.	0/0	./.	./.	./.	0/0	0/0	0/0	./.	0/1	./.	0/0	./.	0/1	0/0	0/0	0/0	0/0	./.	./.	0/0	0/0	./.	0/0	0/0	./.	./.	./.	./.	0/0	0/1	./.	./.	./.	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	./.	0/0	0/0	0/0	0/0	./.	0/0	./.	./.	0/1	0/0	0/1	0/0	./.	0/0	./.	0/0	./.	0/0	./.	0/0	0/1
+chr1	97654513	.	GTTAT	G	.	PASS	VC=INDEL;AC=17;AF=0.06;AN=302;refseq.name=NM_000110;refseq.positionType=intron	GT	./.	0/0	0/0	0/0	./.	0/0	./.	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/1	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	./.	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	97728316	.	AATA	A	.	PASS	VC=INDEL;AC=15;AF=0.05;AN=316;refseq.name=NM_000110;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	1/1	0/1	0/0	0/0
+chr1	97862494	.	TCCT	T	.	PASS	VC=INDEL;AC=47;AF=0.18;AN=256;refseq.name=NM_000110;refseq.positionType=intron	GT	0/0	0/1	./.	0/1	0/0	0/1	./.	0/0	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/0	./.	./.	0/1	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/1	0/1	0/0	0/0	0/0	0/0	./.	0/0	0/1	./.	0/1	1/1	0/0	0/0	./.	./.	0/1	0/1	0/1	0/1	1/1	0/1	0/1	0/0	0/0	0/0	./.	0/0	0/0	./.	0/0	0/0	0/0	0/0	./.	0/0	./.	0/1	0/1	0/0	./.	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	./.	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	./.	0/1	0/1	./.	./.	0/1	0/0	./.	0/1	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/1	0/0	./.	0/0	0/0	0/0	./.	0/1	0/0	0/0	0/1	0/1	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	1/1	./.	0/1	0/1	0/1	./.	0/1	0/1	0/1	0/0	./.	0/0	./.	0/1	0/0	0/0	0/0	0/0	0/0	./.
+chr1	97940369	.	TAACT	T	.	PASS	VC=INDEL;AC=37;AF=0.12;AN=306;refseq.name=NM_000110;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	./.	0/0	0/0	0/0	0/1	0/1	0/1	0/1	1/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	./.	0/1	0/1	0/0	0/1	0/0	./.	./.	0/1	0/1	0/0	./.	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0
+chr1	98400957	.	C	CGATAT	.	PASS	VC=INDEL;AC=290;AF=0.92;AN=316	GT	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/0	0/0	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1
+chr1	99032443	.	T	TTC	.	PASS	VC=INDEL;AC=230;AF=0.79;AN=292	GT	0/1	0/1	0/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	0/1	0/0	1/1	1/1	1/1	./.	1/1	1/1	1/1	0/0	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	0/1	1/1	1/1	0/1	0/1	1/1	1/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/0	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	0/1	./.	./.	./.	./.	1/1	1/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	0/0	1/1	0/1	1/1	1/1	1/1	0/1	0/1	./.	0/1	1/1	1/1	1/1	./.	1/1	1/1	0/0	0/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1	./.	0/1	0/1	0/0	1/1	1/1	1/1	1/1	0/0	0/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	0/0	0/1	0/1	1/1	0/1	./.	0/0	1/1
+chr1	99032444	.	T	TCT	.	PASS	VC=INDEL;AC=236;AF=0.8;AN=296	GT	0/1	0/1	0/1	1/1	1/1	./.	0/1	0/1	1/1	0/1	0/1	0/0	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	0/1	0/1	1/1	1/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	./.	./.	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/0	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	./.	0/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	./.	1/1	1/1	1/1	1/1	0/1	0/0	1/1	0/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	0/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1	0/0	0/1	0/1	0/0	1/1	1/1	./.	1/1	0/0	0/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	0/1	0/1	1/1	0/1	1/1	0/0	1/1
+chr1	99662955	.	A	AAGA	.	PASS	VC=INDEL;AC=146;AF=0.46;AN=316	GT	0/1	0/1	0/0	0/1	0/1	0/1	1/1	1/1	1/1	0/0	0/1	0/1	1/1	0/1	1/1	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	0/0	0/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	1/1	0/0	0/1	0/0	0/0	1/1	1/1	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	1/1	1/1	0/0	0/1	0/1	1/1	0/1	1/1	1/1	0/1	1/1	0/0	0/0	0/0	0/1	0/0	0/1	1/1	1/1	0/1	1/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	1/1	1/1	0/1	0/0	0/1	1/1	0/0	0/1	0/0	0/1	0/1	1/1	0/0	0/1	0/1	0/1	0/1	1/1	0/0	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/0	1/1	0/1	0/1	0/1	0/0	0/0	1/1	0/1	0/1	0/1	0/0	0/0	0/1	0/0	1/1	0/1	0/1	0/1	0/1	0/1	0/0	0/0
+chr1	99714941	.	GTTACAG	G	.	PASS	VC=INDEL;AC=6;AF=0.02;AN=316	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0
+chr1	99848725	.	AT	A	.	PASS	VC=INDEL;AC=50;AF=0.16;AN=316	GT	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	1/1	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/0	1/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	100194878	.	C	CCT	.	PASS	VC=INDEL;AC=248;AF=0.78;AN=316;refseq.name=NM_001013660;refseq.positionType=intron	GT	1/1	0/0	0/1	0/1	0/1	0/1	0/0	1/1	1/1	0/1	1/1	1/1	0/1	1/1	0/0	1/1	0/1	1/1	1/1	0/1	0/1	0/1	1/1	0/0	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/0	0/1	0/0	1/1	0/0	1/1	0/1	0/0	1/1	0/1	0/1	0/0	0/0	1/1	1/1	0/1	1/1	0/0	1/1	0/0	0/1	0/1	1/1	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/0	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1
+chr1	100194903	.	C	CT	.	PASS	VC=INDEL;AC=7;AF=0.02;AN=316;refseq.name=NM_001013660;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	100567908	.	C	CT	.	PASS	VC=INDEL;AC=43;AF=0.14;AN=300;refseq.name=NM_194292;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	1/1	0/0	0/0	0/0	0/1	./.	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	1/1	0/1	./.	0/0	0/1	0/0	0/0	0/0	0/0	0/0	1/1	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	./.	./.	1/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/0	./.	0/0	0/0	0/1	0/0	0/1	1/1	0/0	0/1	0/0	./.	0/0	0/1	0/1	0/1	0/0	0/0
+chr1	100793875	.	CACTC	C	.	PASS	VC=INDEL;AC=105;AF=0.38;AN=274	GT	0/0	0/1	0/1	./.	0/1	1/1	0/0	./.	0/0	1/1	0/1	0/0	0/1	0/0	0/0	0/0	./.	./.	0/0	0/1	0/1	0/1	1/1	./.	0/0	0/0	0/0	0/0	0/1	0/0	1/1	0/0	0/1	1/1	1/1	1/1	0/0	0/0	0/1	0/0	1/1	0/0	0/0	0/1	1/1	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/0	1/1	0/1	0/1	0/0	./.	0/1	0/1	0/0	./.	0/1	./.	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/1	0/0	0/0	./.	0/1	0/1	0/1	0/1	./.	./.	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/1	0/1	1/1	0/0	1/1	./.	0/1	0/1	./.	0/1	0/1	0/0	./.	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	1/1	0/1	1/1	0/1	1/1	./.	0/1	1/1	0/1	0/0	0/0	./.	0/0	0/1	./.	0/0	1/1	0/1	0/1	0/0	0/1	0/1	0/0	0/1	./.	1/1	0/1	./.	./.	0/1	0/1	0/1	0/1	./.	0/1	0/1	0/1	0/0
+chr1	100808351	.	TT	T	.	PASS	VC=INDEL;AC=27;AF=0.09;AN=294	GT	./.	0/0	0/0	1/1	0/0	0/0	1/1	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	./.	0/0	1/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	1/1	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	1/1	0/0	0/0	0/0	0/0	1/1	./.	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	./.	./.	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	100856872	.	T	TT	.	PASS	VC=INDEL;AC=79;AF=0.25;AN=316;refseq.name=NM_003672;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	1/1	1/1	1/1	0/0	1/1	0/1	0/0	0/0	0/0	1/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/1	1/1	0/1	0/0	1/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/0	1/1	1/1	1/1	0/1	0/0	0/1	0/0	1/1	0/1	0/0	0/1	0/0	0/1	0/1	0/1	1/1	0/0	0/1	1/1	0/0	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/1	1/1	0/1	0/0	1/1	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/1	1/1	0/0	0/0
+chr1	101093845	.	TTCTGTAGTCAC	T	.	PASS	VC=INDEL;AC=24;AF=0.08;AN=316	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1
+chr1	101295925	.	CTA	C	.	PASS	VC=INDEL;AC=82;AF=0.26;AN=314	GT	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/1	1/1	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/0	1/1	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/0	1/1	0/1	0/0	1/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/0	./.	0/0	0/1	1/1	0/1	0/1	0/1	0/0	0/1	0/0	0/0	1/1	0/0	1/1	1/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	1/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	1/1	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	1/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1
+chr1	101442572	.	T	TT	.	PASS	VC=INDEL;AC=99;AF=0.31;AN=316;refseq.name=NM_133496;refseq.positionType=exon	GT	0/0	1/1	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	1/1	0/1	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/0	1/1	1/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	1/1	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/1	1/1	0/1	1/1	0/0	0/0	0/0	1/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/1	0/1	0/0	1/1	0/1	0/1	1/1	0/1	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/1	1/1	1/1	0/0	0/1	0/1	1/1	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/0	0/0	1/1	0/1	1/1	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/1
+chr1	101482924	.	CTGTG	C	.	PASS	VC=INDEL;AC=32;AF=0.1;AN=316;refseq.name=NM_001077394;refseq.positionType=intron	GT	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1
+chr1	101859015	.	G	GA	.	PASS	VC=INDEL;AC=107;AF=0.34;AN=316	GT	1/1	1/1	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	1/1	0/1	0/0	1/1	0/1	0/1	0/0	0/0	0/1	1/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	1/1	0/0	0/1	0/0	0/1	0/0	0/1	0/1	1/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	1/1	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/1	1/1	0/0	1/1	0/1	0/1	0/0	0/0	0/1	0/0	0/0	1/1	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/1	1/1	0/1	0/1	0/0	0/0	0/0	0/0	1/1	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	1/1	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/1	1/1	0/1	0/1	1/1	0/0	0/1	0/1	0/0
+chr1	102315705	.	A	ATCTC	.	PASS	VC=INDEL;AC=185;AF=0.59;AN=316;refseq.name=NM_058170;refseq.positionType=intron	GT	0/1	1/1	0/1	0/1	0/0	0/1	1/1	1/1	1/1	0/0	0/1	0/1	0/1	0/0	0/1	0/0	1/1	0/1	0/1	1/1	0/0	0/1	0/1	0/0	1/1	0/1	1/1	0/1	0/1	0/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	0/0	0/0	0/1	0/0	1/1	0/0	0/0	0/1	1/1	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/1	0/1	1/1	0/1	0/0	0/1	0/1	1/1	0/1	1/1	1/1	0/1	0/1	0/1	0/0	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	0/1	1/1	0/1	0/1	1/1	1/1	0/0	0/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	0/0	0/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	0/1	0/1	0/1	0/1	1/1	0/0	0/1	1/1	1/1	0/1	0/1
+chr1	102315708	.	T	TCTCT	.	PASS	VC=INDEL;AC=185;AF=0.59;AN=316;refseq.name=NM_058170;refseq.positionType=intron	GT	0/1	1/1	0/1	0/1	0/0	0/1	1/1	1/1	1/1	0/0	0/1	0/1	0/1	0/0	0/1	0/0	1/1	0/1	0/1	1/1	0/0	0/1	0/1	0/0	1/1	0/1	1/1	0/1	0/1	0/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	0/0	0/0	0/1	0/0	1/1	0/0	0/0	0/1	1/1	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/1	0/1	1/1	0/1	0/0	0/1	0/1	1/1	0/1	1/1	1/1	0/1	0/1	0/1	0/0	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	0/1	1/1	0/1	0/1	1/1	1/1	0/0	0/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	0/0	0/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	0/1	0/1	0/1	0/1	1/1	0/0	0/1	1/1	1/1	0/1	0/1
+chr1	103391817	.	TTA	T	.	PASS	VC=INDEL;AC=0;AF=0;AN=244;refseq.name=NM_001854;refseq.positionType=intron	GT	0/0	./.	0/0	./.	0/0	0/0	./.	0/0	./.	0/0	0/0	0/0	0/0	0/0	./.	./.	0/0	0/0	0/0	0/0	./.	0/0	./.	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	./.	./.	./.	0/0	0/0	0/0	0/0	./.	0/0	./.	0/0	0/0	./.	0/0	0/0	./.	0/0	0/0	./.	0/0	0/0	./.	0/0	0/0	./.	./.	0/0	0/0	./.	./.	./.	./.	./.	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	./.	0/0	0/0	./.	0/0	0/0	0/0	0/0	./.	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	./.	./.	./.	0/0	0/0
+chr1	103722297	.	TGT	T	.	PASS	VC=INDEL;AC=32;AF=0.1;AN=316	GT	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	1/1	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0
+chr1	104533187	.	A	AGTT	.	PASS	VC=INDEL;AC=148;AF=0.47;AN=316	GT	0/0	0/1	0/1	0/1	0/0	1/1	1/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	0/1	0/1	0/1	1/1	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	1/1	0/0	0/1	0/1	0/0	0/0	0/1	1/1	0/1	0/1	1/1	1/1	1/1	0/0	0/1	0/0	0/0	0/0	1/1	0/1	0/1	0/1	0/0	0/1	0/0	1/1	0/0	0/1	0/0	0/0	0/0	1/1	0/0	0/0	0/0	1/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/1	1/1	0/1	0/0	0/0	0/0	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	0/0	0/0	1/1	0/0	0/1	0/1	1/1	1/1	1/1	0/0	0/1	0/1	0/1	0/1	0/1	1/1	1/1	0/1	0/1	0/1	0/0	1/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/1	1/1	1/1	0/1	0/1	1/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/0	0/0	0/0	0/1	0/1	0/1	1/1	0/1
+chr1	104896267	.	GAG	G	.	PASS	VC=INDEL;AC=48;AF=0.15;AN=312	GT	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	1/1	0/0	0/1	1/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	./.	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	./.	0/0	0/1	0/0	1/1	1/1	1/1	0/0	0/1	0/0	1/1	0/1	0/1	1/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/1	1/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0
+chr1	104896390	.	ATATT	A	.	PASS	VC=INDEL;AC=38;AF=0.14;AN=268	GT	0/0	0/1	0/1	0/0	./.	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	./.	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	1/1	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/0	0/0	0/1	./.	./.	0/0	1/1	0/0	./.	0/1	1/1	./.	1/1	0/0	0/0	0/0	./.	0/0	0/1	./.	0/0	./.	0/1	0/0	0/0	1/1	0/1	0/1	1/1	0/0	1/1	0/0	1/1	0/1	0/1	0/0	1/1	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	./.	1/1	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	./.	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	./.	./.	0/0	./.	0/1	0/0
+chr1	105259435	.	CACTAAACGTGCC	C	.	PASS	VC=INDEL;AC=6;AF=0.02;AN=250	GT	./.	0/0	./.	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	./.	0/0	./.	0/0	0/0	./.	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	./.	0/1	0/0	0/0	0/0	./.	./.	0/0	0/0	./.	0/0	./.	0/0	0/0	0/0	0/0	./.	0/0	0/0	./.	./.	./.	0/0	./.	./.	0/0	0/0	./.	./.	0/1	0/0	./.	./.	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	./.	0/0	0/0	0/1	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	./.	./.	0/0	0/1	./.	0/0
+chr1	105451424	.	A	ATCTAGT	.	PASS	VC=INDEL;AC=98;AF=0.31;AN=316	GT	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/0	1/1	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/1	1/1	0/1	1/1	1/1	0/1	0/1	0/1	0/0	1/1	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/1	0/1	0/0	0/1	1/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	1/1	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/1	1/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/0	1/1	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/1	1/1	1/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/1	1/1
+chr1	105504523	.	C	CTTT	.	PASS	VC=INDEL;AC=82;AF=0.29;AN=282	GT	./.	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/1	1/1	0/1	0/0	1/1	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/1	1/1	0/1	1/1	1/1	0/0	0/1	0/1	0/0	./.	0/0	0/0	0/0	./.	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/0	./.	0/1	0/0	./.	0/1	0/1	0/1	./.	1/1	0/0	0/1	0/0	./.	1/1	0/1	0/0	0/1	1/1	0/0	0/1	0/1	./.	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	./.	./.	0/1	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/1	./.	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	./.	./.	0/0	0/0	0/1	0/1	0/1	0/0	0/1	./.	0/0	1/1	0/1	0/0	0/1	0/1	0/0	./.	0/0	0/1	./.	1/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/1	0/0	0/1	1/1
+chr1	105837170	.	T	TAA	.	PASS	VC=INDEL;AC=67;AF=0.24;AN=280	GT	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	./.	0/0	0/1	./.	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	1/1	1/1	0/1	0/1	./.	0/0	0/1	1/1	1/1	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	./.	0/1	0/1	0/0	0/1	./.	./.	0/1	0/1	0/0	0/1	0/1	0/1	0/1	1/1	0/1	1/1	./.	0/1	1/1	0/1	1/1	./.	./.	./.	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	./.	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/1	./.	0/1	./.	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	./.	./.	0/0
+chr1	105868766	.	ATACTT	A	.	PASS	VC=INDEL;AC=92;AF=0.34;AN=274	GT	./.	0/1	0/1	0/1	0/0	0/1	1/1	1/1	0/0	0/1	0/0	0/0	1/1	0/0	0/1	0/1	1/1	1/1	0/1	0/0	0/1	./.	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	./.	0/1	0/1	1/1	0/1	0/0	0/0	0/0	0/0	0/0	1/1	1/1	1/1	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/1	1/1	0/1	0/1	0/0	0/1	0/0	0/0	1/1	1/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	./.	0/1	0/0	0/0	0/0	0/0	./.	0/0	1/1	0/1	0/0	./.	1/1	./.	1/1	0/1	1/1	0/0	./.	./.	./.	0/0	0/1	0/1	./.	0/1	0/0	0/0	0/0	0/0	0/1	./.	./.	./.	0/0	0/0	0/0	1/1	0/1	0/1	0/0	./.	1/1	0/1	./.	0/1	./.	1/1	0/0	0/0	0/0	./.	0/1	0/0	0/0	1/1	0/1	0/0	0/0	0/0	0/0	0/0	./.	0/1	0/1	0/0	0/1	0/0	./.	0/0	0/0	0/0	0/0	0/1	0/0	0/1	1/1	0/0	./.	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	1/1	1/1
+chr1	106762526	.	AACT	A	.	PASS	VC=INDEL;AC=87;AF=0.28;AN=316	GT	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/1	1/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/1	1/1	1/1	0/1	0/1	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/1	1/1	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/1	0/1	1/1	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/1	1/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	1/1	0/0	0/1	0/1	0/1	1/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0
+chr1	106908645	.	AC	A	.	PASS	VC=INDEL;AC=25;AF=0.08;AN=316	GT	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	1/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/1
+chr1	107217236	.	A	AGGATCA	.	PASS	VC=INDEL;AC=240;AF=0.79;AN=302	GT	1/1	1/1	./.	1/1	0/0	1/1	1/1	1/1	1/1	1/1	0/0	1/1	./.	1/1	1/1	./.	1/1	0/0	1/1	1/1	1/1	1/1	0/1	./.	1/1	1/1	1/1	0/0	0/0	0/0	0/0	1/1	1/1	0/0	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	0/0	0/0	1/1	./.	0/0	0/0	0/0	1/1	1/1	0/0	1/1	1/1	1/1	1/1	0/0	1/1	0/0	0/0	1/1	1/1	0/0	1/1	0/0	0/0	0/0	1/1	1/1	0/0	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/0	./.	1/1	1/1	1/1	1/1	0/0	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	0/0	1/1	1/1	1/1	0/0	1/1	1/1	1/1	1/1	1/1	1/1	0/0	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1
+chr1	107979567	.	TT	T	.	PASS	VC=INDEL;AC=150;AF=0.55;AN=274;refseq.name=NM_001113226;refseq.positionType=intron	GT	1/1	0/1	0/0	1/1	0/1	0/0	0/0	0/1	0/0	1/1	0/1	./.	1/1	0/1	0/1	0/1	0/0	0/0	1/1	1/1	0/1	0/1	./.	./.	0/1	0/1	0/0	1/1	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/1	1/1	0/1	0/1	0/1	1/1	0/1	0/1	0/1	./.	0/1	0/0	1/1	./.	./.	0/1	1/1	1/1	1/1	0/0	1/1	./.	1/1	0/1	0/1	0/1	0/1	0/1	0/1	./.	0/0	1/1	./.	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/1	1/1	0/1	./.	0/1	./.	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	1/1	0/0	1/1	0/1	0/0	1/1	./.	1/1	0/0	1/1	0/1	1/1	1/1	1/1	0/1	./.	1/1	0/1	0/1	0/1	0/1	0/1	./.	0/1	0/1	./.	0/1	0/1	0/0	0/1	./.	1/1	./.	1/1	1/1	0/1	0/1	0/1	0/0	1/1	0/1	0/1	0/0	./.	0/0	1/1	0/1	./.	0/1	1/1	0/0	1/1	0/1	0/1	1/1	./.	0/1	0/1	0/1	./.	1/1	1/1	0/1	1/1
+chr1	108737087	.	GG	G	.	PASS	VC=INDEL;AC=99;AF=0.32;AN=308;refseq.name=NM_013386;refseq.positionType=intron	GT	1/1	0/1	0/1	0/0	0/0	0/0	1/1	0/1	0/0	0/0	./.	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/1	1/1	0/0	0/0	0/0	0/1	0/1	1/1	0/1	1/1	0/0	0/1	0/0	0/1	1/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	./.	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	1/1	1/1	0/0	0/1	0/1	1/1	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/1	0/0	./.	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/0	1/1	0/1	0/1	1/1	0/1	0/0	1/1	0/1	0/1	0/0	0/0	0/0	1/1	0/1	1/1	0/1	1/1	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	1/1	./.	1/1	0/0	0/1	0/0	0/1	1/1	0/1	0/0	0/0	0/0	0/1	0/1
+chr1	109186604	.	A	ATA	.	PASS	VC=INDEL;AC=3;AF=0.01;AN=316	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	109295950	.	TA	T	.	PASS	VC=INDEL;AC=54;AF=0.17;AN=312;refseq.name=NM_007269;refseq.positionType=intron	GT	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	./.	0/1	0/1	0/0	0/1	0/0	0/0	0/0	./.	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0
+chr1	109295955	.	TTA	T	.	PASS	VC=INDEL;AC=57;AF=0.18;AN=310;refseq.name=NM_007269;refseq.positionType=intron	GT	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	./.	0/1	0/0	0/0	0/1	0/0	0/0	0/1	./.	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/1	./.	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0
+chr1	109303951	.	GTATAG	G	.	PASS	VC=INDEL;AC=89;AF=0.28;AN=316;refseq.name=NM_007269;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	1/1	0/1	0/1	1/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	1/1	0/1	0/1	1/1	0/0	0/0	1/1	0/0	0/1	0/0	1/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	1/1	1/1	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	1/1	0/1	0/1	0/0	0/0	0/1	0/1	1/1	0/0	1/1	0/1	0/0	0/0	0/0	0/1	0/1	1/1	0/0	0/1	0/1	1/1	0/1	0/1	1/1	0/0	0/1	1/1	0/1	0/1	0/1	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/0	1/1	0/1	0/1	0/1	1/1	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/1
+chr1	109429108	.	G	GGAGAAAT	.	PASS	VC=INDEL;AC=33;AF=0.14;AN=234;refseq.name=NM_013296;refseq.positionType=intron	GT	0/1	./.	./.	0/0	0/0	0/0	0/0	0/1	./.	0/1	0/0	./.	0/1	./.	./.	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	./.	./.	0/1	./.	./.	0/1	./.	0/1	0/1	./.	./.	./.	0/1	./.	0/1	./.	0/1	0/1	./.	./.	0/1	./.	0/1	0/1	./.	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	./.	./.	./.	0/1	./.	0/1	./.	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	./.	./.	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/1	0/0	./.	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/1	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	./.	./.	0/1	0/0	0/0	0/0	0/0	0/0	./.	0/1
+chr1	109565068	.	C	CTC	.	PASS	VC=INDEL;AC=304;AF=0.96;AN=316;refseq.name=NM_014969;refseq.positionType=intron	GT	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1
+chr1	110418161	.	CTTAG	C	.	PASS	VC=INDEL;AC=56;AF=0.18;AN=316	GT	0/0	0/1	0/1	0/0	0/0	0/0	0/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/0	1/1	1/1	0/1	1/1	1/1	0/1	0/1	0/1	0/0	0/1	1/1	0/1	0/1	1/1	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/0	0/1	1/1	1/1	0/0	0/1	1/1	1/1	0/1	0/0	0/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/1
+chr1	110911466	.	AT	A	.	PASS	VC=INDEL;AC=67;AF=0.22;AN=310;refseq.name=NM_004696;refseq.positionType=intron	GT	0/0	0/0	0/0	1/1	0/0	0/0	0/1	0/1	0/1	1/1	0/1	1/1	0/1	0/0	0/1	0/1	0/0	0/0	1/1	0/1	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	1/1	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/1	1/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	./.	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/1
+chr1	111820993	.	TTAAG	T	.	PASS	VC=INDEL;AC=46;AF=0.2;AN=232	GT	0/1	./.	1/1	./.	0/0	./.	0/1	0/1	./.	0/0	0/0	./.	0/0	0/0	./.	0/1	0/0	0/0	0/1	1/1	./.	0/1	0/0	0/1	0/0	0/0	./.	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	./.	0/0	0/0	0/1	./.	./.	./.	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	./.	0/0	0/1	./.	./.	0/0	0/1	0/1	0/1	0/1	0/0	0/0	./.	./.	0/1	./.	./.	0/0	0/1	./.	0/0	./.	0/1	./.	0/0	./.	0/1	0/1	0/1	0/0	0/1	0/1	0/1	./.	0/0	0/0	0/0	0/1	0/0	./.	./.	0/0	0/0	0/0	0/0	0/0	0/1	./.	0/1	0/0	./.	./.	./.	0/0	0/0	0/1	0/0	0/1	0/1	./.	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	./.	./.	./.	0/0	0/0	0/0	./.	0/0	./.	0/1	0/1	./.	./.	./.
+chr1	111894729	.	C	CATG	.	PASS	VC=INDEL;AC=32;AF=0.11;AN=302;refseq.name=NM_181643;refseq.positionType=exon	GT	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	1/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	./.	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	./.	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	./.	0/0	0/0	0/1	0/1	0/1	0/0
+chr1	112384059	.	G	GG	.	PASS	VC=INDEL;AC=111;AF=0.35;AN=314;refseq.name=NM_004980;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	1/1	0/0	0/0	1/1	0/0	0/1	1/1	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	1/1	1/1	0/1	0/0	0/1	0/0	0/0	0/1	1/1	0/1	0/0	1/1	0/1	1/1	0/1	0/1	1/1	1/1	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	1/1	0/1	0/1	1/1	1/1	0/1	0/0	0/1	0/1	0/0	0/0	0/1	0/1	0/1	1/1	./.	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/0	1/1	0/0	0/0	0/0	0/1	0/1	1/1	0/1	0/0	0/1	0/0	1/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	1/1	0/1	1/1	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/1	1/1	0/1	0/0	0/1	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	1/1	0/1	0/1	0/0	1/1
+chr1	112440856	.	A	ACTTA	.	PASS	VC=INDEL;AC=138;AF=0.44;AN=312;refseq.name=NM_004980;refseq.positionType=intron	GT	1/1	1/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	./.	1/1	0/1	0/1	0/1	0/1	1/1	0/1	1/1	0/1	0/0	1/1	1/1	0/1	1/1	1/1	0/1	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	1/1	0/1	1/1	0/0	0/0	0/1	0/1	1/1	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/1	1/1	0/0	0/1	1/1	0/1	0/1	0/1	0/1	0/1	0/1	1/1	1/1	0/0	1/1	0/0	0/1	0/1	1/1	1/1	0/1	1/1	0/1	0/0	0/0	0/0	1/1	1/1	1/1	0/1	./.	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	1/1	0/1	0/1	0/1	1/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	1/1	1/1	1/1	0/1	0/1	0/0	0/1	0/1	0/1	1/1	1/1	0/1	0/1	1/1	1/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0
+chr1	112896532	.	CTAAC	C	.	PASS	VC=INDEL;AC=1;AF=0;AN=316	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1
+chr1	112896636	.	CA	C	.	PASS	VC=INDEL;AC=199;AF=0.64;AN=312	GT	0/1	0/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	0/1	0/0	0/0	0/1	1/1	0/0	0/0	1/1	0/1	0/1	0/0	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	0/1	0/1	0/1	0/0	1/1	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/1	1/1	0/0	0/1	0/1	0/1	1/1	0/1	0/0	0/0	1/1	0/1	0/1	1/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	0/1	1/1	0/0	0/0	0/1	1/1	0/1	0/0	0/1	0/1	1/1	0/1	1/1	0/1	0/1	0/1	1/1	0/1	0/0	0/0	0/0	1/1	1/1	1/1	0/0	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	./.	1/1	0/0	0/1	1/1	0/1	1/1	0/0	1/1	0/1	1/1	1/1	1/1	0/1	0/1	0/0	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	./.	1/1
+chr1	112896637	.	AA	A	.	PASS	VC=INDEL;AC=199;AF=0.63;AN=316	GT	0/1	0/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	0/1	0/0	0/0	0/1	1/1	0/0	0/0	1/1	0/1	0/1	0/0	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	0/1	0/1	0/1	0/0	1/1	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/1	1/1	0/0	0/1	0/1	0/1	1/1	0/1	0/0	0/0	1/1	0/1	0/1	1/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	0/1	1/1	0/0	0/0	0/1	1/1	0/1	0/0	0/1	0/1	1/1	0/1	1/1	0/1	0/1	0/1	1/1	0/1	0/0	0/0	0/0	1/1	1/1	1/1	0/0	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	0/0	1/1	0/0	0/1	1/1	0/1	1/1	0/0	1/1	0/1	1/1	1/1	1/1	0/1	0/1	0/0	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	0/0	1/1
+chr1	113322895	.	TTCTA	T	.	PASS	VC=INDEL;AC=73;AF=0.3;AN=246	GT	0/0	./.	0/1	0/0	./.	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/1	0/1	1/1	./.	0/1	0/1	0/1	0/1	0/1	0/0	1/1	0/0	0/0	0/0	0/0	./.	0/0	0/1	1/1	0/1	0/0	0/0	0/0	./.	./.	./.	1/1	0/0	1/1	1/1	0/1	0/1	1/1	./.	./.	./.	0/0	0/1	1/1	0/0	0/1	./.	./.	0/0	./.	0/1	1/1	0/1	0/0	0/1	0/1	./.	0/1	0/0	1/1	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/0	1/1	./.	0/0	0/0	./.	./.	./.	0/0	0/0	0/0	0/0	0/1	./.	./.	./.	./.	./.	0/0	0/1	1/1	./.	0/0	0/0	0/0	./.	0/0	0/1	./.	0/1	0/0	0/0	./.	0/1	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/1	0/1	0/0	0/1	./.	0/0	0/0	1/1	0/0	0/1	0/0	0/0	./.	./.	0/0	./.	0/0	./.	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/1	./.	0/0	./.	0/0	0/0
+chr1	113467083	.	CC	C	.	PASS	VC=INDEL;AC=1;AF=0;AN=316;refseq.name=NM_003051;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1
+chr1	113635187	.	C	CTTTG	.	PASS	VC=INDEL;AC=261;AF=0.83;AN=316;refseq.name=NM_014813;refseq.positionType=intron	GT	1/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/0	1/1	1/1	1/1	1/1	1/1	1/1	0/0	0/0	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/0	0/1	0/0	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/1	1/1	1/1	0/0	0/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	0/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1
+chr1	113635190	.	T	TGTTT	.	PASS	VC=INDEL;AC=261;AF=0.83;AN=316;refseq.name=NM_014813;refseq.positionType=intron	GT	1/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/0	1/1	1/1	1/1	1/1	1/1	1/1	0/0	0/0	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/0	0/1	0/0	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/1	1/1	1/1	0/0	0/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	0/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1
+chr1	113640553	.	GA	G	.	PASS	VC=INDEL;AC=111;AF=0.35;AN=314;refseq.name=NM_014813;refseq.positionType=intron	GT	0/1	0/0	0/1	0/1	1/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	1/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	1/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	1/1	1/1	0/1	0/0	0/0	0/1	0/1	0/0	1/1	1/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/0	0/1	0/0	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	1/1	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/1	1/1	0/0	1/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/1	./.	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	1/1	0/1
+chr1	113640556	.	AA	A	.	PASS	VC=INDEL;AC=112;AF=0.35;AN=316;refseq.name=NM_014813;refseq.positionType=intron	GT	0/1	0/0	0/1	0/1	1/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	1/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	1/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	1/1	1/1	0/1	0/0	0/0	0/1	0/1	0/0	1/1	1/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/0	0/1	0/0	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	1/1	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/1	1/1	0/0	1/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	1/1	0/1
+chr1	113689905	.	GAG	G	.	PASS	VC=INDEL;AC=41;AF=0.13;AN=316	GT	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	1/1	1/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	1/1	1/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	1/1	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	1/1	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	114240320	.	A	AA	.	PASS	VC=INDEL;AC=229;AF=0.72;AN=316;refseq.name=NM_006608;refseq.positionType=exon	GT	0/1	0/1	0/0	0/1	0/1	0/1	0/1	1/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1	0/1	0/0	0/1	1/1	0/0	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	1/1	0/0	0/0	0/1	0/0	1/1	0/1	0/1	0/1	0/0	1/1	0/1	0/1	0/0	0/0	0/0	1/1	0/0	1/1	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/1	0/0	0/1	1/1	0/0	0/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	0/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1
+chr1	114339956	.	C	CTAAA	.	PASS	VC=INDEL;AC=210;AF=0.78;AN=270;refseq.name=NM_018364;refseq.positionType=intron	GT	1/1	0/1	0/0	0/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	./.	./.	1/1	0/1	0/0	0/1	1/1	0/0	0/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	0/0	1/1	0/0	0/0	0/1	0/0	1/1	0/1	1/1	0/1	./.	1/1	./.	./.	0/0	0/0	0/0	1/1	0/0	1/1	0/1	0/1	0/1	0/0	0/1	./.	./.	./.	0/0	0/1	0/1	./.	./.	0/0	0/1	0/0	0/1	./.	0/0	./.	0/1	0/1	1/1	./.	1/1	./.	1/1	1/1	1/1	1/1	0/1	0/1	./.	1/1	1/1	1/1	./.	1/1	1/1	0/0	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	0/1	0/1	./.	1/1	0/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1
+chr1	114565357	.	CGGAGG	C	.	PASS	VC=INDEL;AC=0;AF=0;AN=316	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	116298599	.	A	ACTT	.	PASS	VC=INDEL;AC=54;AF=0.17;AN=316;refseq.name=NM_001232;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	1/1	1/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	1/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	1/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/0	1/1	0/0	0/1	0/0	0/1	0/1	1/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0
+chr1	116435014	.	ATAACCGA	A	.	PASS	VC=INDEL;AC=66;AF=0.26;AN=250	GT	1/1	1/1	./.	1/1	0/1	0/1	0/1	./.	0/0	0/0	./.	0/1	0/1	0/0	0/0	0/1	1/1	0/0	0/0	1/1	0/0	0/1	0/1	1/1	./.	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	./.	0/0	0/0	./.	0/1	0/1	./.	0/0	0/0	0/1	0/0	1/1	0/0	./.	./.	0/1	0/0	0/0	0/0	0/1	./.	1/1	./.	0/0	0/1	0/1	0/0	0/0	0/1	./.	1/1	1/1	0/1	0/1	./.	0/0	1/1	./.	0/0	1/1	0/1	1/1	./.	1/1	0/0	./.	1/1	0/1	./.	./.	0/0	0/0	0/0	0/0	./.	0/0	./.	0/0	./.	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	./.	./.	./.	0/0	0/0	0/1	0/0	0/0	0/0	./.	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	./.	0/1	0/1	0/0	0/0	0/0	./.	0/0	./.	0/0	0/0	0/0	0/0	./.	0/0	./.	0/0	0/0	./.	0/0	0/0	./.	0/1	0/1	0/0	0/0	./.	0/1	0/1
+chr1	116551982	.	T	TTAAAGC	.	PASS	VC=INDEL;AC=31;AF=0.1;AN=304;refseq.name=NM_018420;refseq.positionType=intron	GT	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	./.	0/0	0/0	0/0	0/0	0/0	0/1	0/0	./.	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	./.	0/1	0/0	0/0	0/1	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	116662025	.	T	TGA	.	PASS	VC=INDEL;AC=55;AF=0.17;AN=316;refseq.name=NM_152367;refseq.positionType=intron	GT	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	1/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/0	1/1	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/0	1/1	0/1	0/0	0/0	0/0	0/0
+chr1	116662028	.	G	GAG	.	PASS	VC=INDEL;AC=55;AF=0.17;AN=316;refseq.name=NM_152367;refseq.positionType=intron	GT	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	1/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/0	1/1	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/0	1/1	0/1	0/0	0/0	0/0	0/0
+chr1	117459931	.	AAC	A	.	PASS	VC=INDEL;AC=90;AF=0.28;AN=316;refseq.name=NM_020440;refseq.positionType=intron	GT	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	1/1	0/1	1/1	0/1	0/1	0/0	0/1	1/1	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	1/1	0/0	0/1	0/1	0/1	0/1	0/1	1/1	1/1	0/0	1/1	0/1	1/1	0/0	0/1	0/1	0/1	1/1	0/0	1/1	0/0	0/1	0/1	0/1	0/0	1/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	1/1	0/1	0/1	0/0	0/0	0/0	0/1	1/1	0/1	1/1	0/1	0/1	1/1	0/0	0/1	0/1	1/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/0	1/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0
+chr1	117459932	.	ACA	A	.	PASS	VC=INDEL;AC=90;AF=0.28;AN=316;refseq.name=NM_020440;refseq.positionType=intron	GT	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	1/1	0/1	1/1	0/1	0/1	0/0	0/1	1/1	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	1/1	0/0	0/1	0/1	0/1	0/1	0/1	1/1	1/1	0/0	1/1	0/1	1/1	0/0	0/1	0/1	0/1	1/1	0/0	1/1	0/0	0/1	0/1	0/1	0/0	1/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	1/1	0/1	0/1	0/0	0/0	0/0	0/1	1/1	0/1	1/1	0/1	0/1	1/1	0/0	0/1	0/1	1/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/0	1/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0
+chr1	117592136	.	TTG	T	.	PASS	VC=INDEL;AC=24;AF=0.08;AN=300	GT	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/1	0/1	0/0	0/0	0/1	1/1	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.
+chr1	117722836	.	C	CA	.	PASS	VC=INDEL;AC=36;AF=0.11;AN=316;refseq.name=NM_024626;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	1/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/1	0/0	0/0
+chr1	120034138	.	TCTAT	T	.	PASS	VC=INDEL;AC=99;AF=0.35;AN=284	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	./.	0/0	0/0	0/0	0/0	0/1	0/0	0/1	./.	0/0	./.	0/0	0/0	./.	0/0	0/1	0/0	./.	0/0	0/1	1/1	0/1	0/1	1/1	0/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	./.	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	1/1	1/1	1/1	0/1	0/1	0/0	./.	0/1	0/1	0/1	./.	0/1	0/1	0/1	./.	0/1	0/1	0/0	1/1	0/1	1/1	./.	0/1	0/1	0/1	0/1	0/1	1/1	1/1	./.	0/1	0/1	0/1	0/1	1/1	1/1	0/0	0/1	0/1	1/1	1/1	1/1	1/1	./.	./.	0/0	0/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	0/0	0/0	./.	0/1	0/0	0/0	1/1	1/1	1/1	0/1	1/1	1/1	0/0	./.	0/1	0/0	0/0	0/1	./.	1/1	1/1	0/0	0/0
+chr1	120185496	.	G	GGATT	.	PASS	VC=INDEL;AC=264;AF=0.84;AN=314;refseq.name=NM_001080470;refseq.positionType=intron	GT	0/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	0/0	1/1	0/1	0/1	0/1	1/1	0/1	0/1	1/1	1/1	0/0	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	0/0	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1
+chr1	120280730	.	TAA	T	.	PASS	VC=INDEL;AC=73;AF=0.23;AN=314;refseq.name=NM_006623;refseq.positionType=intron	GT	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/1	1/1	1/1	1/1	0/0	0/0	0/0	0/1	0/1	0/0	1/1	0/1	1/1	0/1	1/1	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	1/1	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/1	./.	0/0	0/1	1/1	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/1	1/1	0/1	0/1	0/0	0/0	0/0	0/0
+chr1	144995277	.	AG	A	.	PASS	VC=INDEL;AC=41;AF=0.16;AN=258;refseq.name=NM_014644;refseq.positionType=promoter	GT	0/0	0/0	0/0	./.	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/0	./.	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	./.	0/1	0/0	./.	0/1	./.	./.	0/0	./.	0/1	0/0	0/0	0/1	0/0	0/0	0/0	./.	0/1	0/0	./.	0/1	0/1	0/1	0/0	./.	./.	./.	0/0	./.	./.	0/0	0/1	0/1	./.	0/1	0/1	0/0	0/0	./.	./.	./.	0/1	0/0	./.	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/1	./.	0/1	./.	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	./.	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/1	0/0	0/1	0/0	0/0	0/0	0/0	./.	./.	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0
+chr1	145060382	.	A	AG	.	PASS	VC=INDEL;AC=316;AF=1;AN=316;refseq.name=NM_022359;refseq.positionType=intron	GT	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1
+chr1	146556039	.	CCAAC	C	.	PASS	VC=INDEL;AC=64;AF=0.21;AN=310	GT	0/0	0/0	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	1/1	1/1	0/1	1/1	0/0	0/1	0/0	1/1	0/0	0/1	0/0	0/0	1/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	1/1	0/0	1/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/1	./.	0/0	0/0	0/0	0/1	0/1	0/1	1/1	0/0	./.	./.	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/1	1/1	1/1	1/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	1/1	0/0	0/0	0/0	0/0	0/0
+chr1	146768690	.	TC	T	.	PASS	VC=INDEL;AC=289;AF=0.91;AN=316	GT	0/1	0/1	0/1	1/1	1/1	0/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	0/0	1/1	1/1	0/0	0/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1
+chr1	146979526	.	CCT	C	.	PASS	VC=INDEL;AC=63;AF=0.2;AN=316	GT	1/1	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/0	1/1	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	1/1	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0
+chr1	147047674	.	AA	A	.	PASS	VC=INDEL;AC=101;AF=0.32;AN=314;refseq.name=NM_004326;refseq.positionType=intron	GT	0/1	0/1	0/0	1/1	1/1	0/0	1/1	0/0	0/0	0/1	0/0	1/1	0/1	0/1	0/1	0/1	1/1	0/0	0/1	1/1	1/1	1/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	0/1	1/1	1/1	0/1	0/1	0/1	1/1	0/0	0/1	1/1	1/1	0/0	1/1	1/1	1/1	0/1	1/1	1/1	0/0	0/1	0/0	1/1	0/1	0/1	1/1	1/1	0/0	1/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	1/1	1/1
+chr1	147108091	.	A	AC	.	PASS	VC=INDEL;AC=227;AF=0.72;AN=314	GT	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	0/0	1/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/0	0/1	0/1	1/1	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/0	1/1	0/1	1/1	1/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	1/1	0/1	1/1	1/1	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/1	0/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1	0/0	0/1	./.	1/1
+chr1	147392223	.	CATGGCTC	C	.	PASS	VC=INDEL;AC=0;AF=0;AN=316	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	147393527	.	A	AAGAA	.	PASS	VC=INDEL;AC=10;AF=0.05;AN=218	GT	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	./.	0/1	0/0	./.	./.	0/0	0/0	0/1	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	./.	./.	0/1	0/0	./.	0/0	0/0	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	./.	0/0	0/0	./.	0/0	./.	./.	./.	./.	0/0	0/1	./.	./.	./.	./.	0/0	0/0	0/0	0/1	./.	0/1	./.	./.	./.	0/0	./.	0/0	0/0	0/0	0/0	0/0	./.	./.	0/0	0/0	./.	0/0	0/0	0/0	./.	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/1	0/0	0/0	0/0	0/0	./.	0/1	./.	0/0	0/0	0/0	0/0	./.	./.	./.	0/0	0/0	./.	0/0	./.	0/0	0/0
+chr1	147823728	.	A	AC	.	PASS	VC=INDEL;AC=2;AF=0.01;AN=266	GT	0/0	0/0	./.	0/0	0/0	./.	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	./.	./.	0/0	0/0	./.	./.	0/0	./.	./.	./.	./.	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	./.	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	./.	0/0	0/0	0/0	0/0	./.	./.	0/0	./.	0/0	0/0
+chr1	151094921	.	T	TA	.	PASS	VC=INDEL;AC=0;AF=0;AN=316	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	151094936	.	CCTTA	C	.	PASS	VC=INDEL;AC=0;AF=0;AN=316	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	151743871	.	AA	A	.	PASS	VC=INDEL;AC=98;AF=0.32;AN=308;refseq.name=NM_016178;refseq.positionType=terminator	GT	1/1	0/1	./.	0/0	0/1	0/0	1/1	0/0	0/1	1/1	0/0	0/0	0/1	0/0	0/0	0/0	1/1	0/1	0/0	0/1	./.	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/1	0/0	1/1	./.	0/1	0/0	1/1	0/0	0/0	0/0	1/1	0/0	0/1	0/0	0/1	0/1	0/1	1/1	0/1	1/1	./.	0/0	0/1	1/1	1/1	0/0	1/1	0/1	0/0	0/0	1/1	0/0	0/1	1/1	0/1	1/1	0/0	0/0	1/1	1/1	0/0	0/0	1/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	1/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	1/1	1/1	0/0	0/1	1/1	0/1
+chr1	152348228	.	TTAT	T	.	PASS	VC=INDEL;AC=9;AF=0.03;AN=316	GT	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	152442163	.	AAACA	A	.	PASS	VC=INDEL;AC=212;AF=0.68;AN=310	GT	0/1	./.	0/0	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	0/0	0/1	1/1	1/1	0/0	0/1	1/1	0/1	0/0	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/0	1/1	0/0	0/0	0/1	1/1	0/1	0/1	1/1	1/1	0/0	1/1	0/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	0/0	0/1	1/1	1/1	1/1	0/0	1/1	0/1	0/1	0/1	1/1	1/1	0/1	0/0	1/1	./.	0/1	0/1	0/0	1/1	0/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1	0/1	0/1	0/0	0/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/0	0/1	0/0	./.	0/0	0/0	0/1	0/1	0/1	0/0	1/1	0/1	1/1	0/1	0/1	1/1	0/1	0/1	0/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	0/1	1/1	0/1	0/1	0/1
+chr1	152572426	.	G	GT	.	PASS	VC=INDEL;AC=70;AF=0.25;AN=280;refseq.name=NM_178434;refseq.positionType=promoter	GT	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	./.	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	1/1	0/0	0/0	0/1	0/1	0/0	1/1	0/0	0/0	1/1	0/1	1/1	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	./.	0/0	1/1	0/0	0/1	./.	0/0	./.	0/1	0/0	0/0	0/0	./.	./.	0/1	0/1	0/1	0/1	./.	0/0	0/0	0/0	0/1	0/1	./.	0/1	./.	0/0	./.	./.	0/1	0/1	./.	1/1	./.	0/0	0/1	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	1/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	./.	0/0	./.	0/1	0/0	0/0	1/1	./.	1/1	0/1	0/1	./.	0/1	0/1	0/1	0/0	0/0	0/0	0/0	./.	1/1	0/1	0/0
+chr1	152797773	.	C	CC	.	PASS	VC=INDEL;AC=0;AF=0;AN=316;refseq.name=NM_178348;refseq.positionType=promoter	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	153703019	.	TGTGTCTCTGCTT	T	.	PASS	VC=INDEL;AC=1;AF=0;AN=316;refseq.name=NM_023015;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	154741714	.	TAT	T	.	PASS	VC=INDEL;AC=1;AF=0;AN=316;refseq.name=NM_002249;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1
+chr1	155303581	.	AT	A	.	PASS	VC=INDEL;AC=0;AF=0;AN=316	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	155559888	.	C	CTTAT	.	PASS	VC=INDEL;AC=0;AF=0;AN=316	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	156565049	.	A	AAC	.	PASS	VC=INDEL;AC=314;AF=0.99;AN=316;refseq.name=NM_015590;refseq.positionType=exon	GT	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1
+chr1	156572952	.	T	TGAA	.	PASS	VC=INDEL;AC=39;AF=0.12;AN=312;refseq.name=NM_015590;refseq.positionType=promoter	GT	0/0	0/0	1/1	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	./.	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/1	0/1	1/1	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	156859572	.	C	CCT	.	PASS	VC=INDEL;AC=219;AF=0.73;AN=300	GT	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/0	1/1	1/1	1/1	1/1	0/0	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	0/0	0/0	1/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	./.	1/1	1/1	0/1	1/1	0/1	0/1	0/1	0/1	./.	0/0	0/1	0/0	0/0	1/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	./.	1/1	0/1	1/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	0/0	0/1	1/1	1/1	1/1	0/0	1/1	0/1	0/1	0/0	0/1	./.	0/0	./.	0/1	0/0	0/0	0/0	./.	./.	1/1	0/1	1/1	0/0	0/1	0/1	0/1	1/1	0/1	0/1	0/1	0/1	1/1	1/1
+chr1	156910892	.	GCTCGTCTT	G	.	PASS	VC=INDEL;AC=39;AF=0.14;AN=270;refseq.name=NM_014784;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	./.	0/0	./.	0/0	0/1	0/0	./.	./.	0/0	0/1	./.	./.	0/1	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	./.	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	./.	0/1	0/0	0/0	0/1	0/1	./.	0/1	0/0	0/0	0/1	0/0	0/0	0/0	./.	./.	./.	0/0	0/1	./.	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/0	./.	./.	0/0	0/1	0/1	0/1	0/1	0/1	./.	0/1	0/0	0/1	./.	./.	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	./.	0/0	0/1	0/1	0/0	0/0	0/0	0/0
+chr1	157531425	.	CA	C	.	PASS	VC=INDEL;AC=16;AF=0.06;AN=260	GT	0/1	0/1	./.	0/1	0/0	0/0	0/1	0/0	0/0	./.	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	./.	0/0	./.	0/0	./.	0/0	0/0	./.	./.	0/1	./.	./.	0/1	./.	0/0	./.	0/0	0/0	0/0	./.	0/1	./.	0/0	0/1	./.	0/1	0/0	0/1	0/1	0/0	0/0	0/0	./.	0/0	0/0	./.	./.	./.	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	./.	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	./.	0/0
+chr1	157807166	.	TGTTA	T	.	PASS	VC=INDEL;AC=250;AF=0.81;AN=310;refseq.name=NM_005894;refseq.positionType=intron	GT	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/0	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	0/1	0/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/0	1/1	0/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	0/1	1/1	0/1	1/1	1/1	1/1	0/1	0/0	0/1	0/0	1/1	0/1	1/1	0/1	0/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	0/0	1/1	0/1	0/1	0/1	0/0	1/1	0/1	1/1	1/1	0/0	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	0/0	0/0	0/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/0
+chr1	157818429	.	AC	A	.	PASS	VC=INDEL;AC=0;AF=0;AN=316	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	157924621	.	ATAAG	A	.	PASS	VC=INDEL;AC=24;AF=0.08;AN=316	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	1/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0
+chr1	157932325	.	T	TT	.	PASS	VC=INDEL;AC=0;AF=0;AN=316	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	158154060	.	CT	C	.	PASS	VC=INDEL;AC=0;AF=0;AN=316;refseq.name=NM_001766;refseq.positionType=exon	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	158684734	.	CA	C	.	PASS	VC=INDEL;AC=90;AF=0.28;AN=316	GT	0/1	1/1	1/1	0/1	0/1	0/0	1/1	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/1	1/1	0/0	0/0	0/0	1/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/1	1/1	1/1	1/1	0/1	0/0	0/0	0/0	1/1	0/1	0/0	0/1	0/1	0/1	0/1	0/0	1/1	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/1	1/1	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	1/1	0/1	1/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1
+chr1	158886780	.	A	AAGAT	.	PASS	VC=INDEL;AC=241;AF=0.76;AN=316	GT	0/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	0/1	1/1	0/1	0/1	1/1	0/1	0/1	1/1	0/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	0/1	1/1	0/1	0/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	1/1	1/1	0/1	1/1	1/1	0/0	0/0	0/0	0/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	1/1	0/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/0	0/1	0/1	0/1	1/1	1/1
+chr1	158886783	.	A	ATAGA	.	PASS	VC=INDEL;AC=240;AF=0.76;AN=314	GT	0/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	./.	1/1	0/1	0/1	1/1	0/1	0/1	1/1	0/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	0/1	1/1	0/1	0/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	1/1	1/1	0/1	1/1	1/1	0/0	0/0	0/0	0/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	1/1	0/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/0	0/1	0/1	0/1	1/1	1/1
+chr1	158984187	.	G	GAGGC	.	PASS	VC=INDEL;AC=26;AF=0.13;AN=198;refseq.name=NM_005531;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	1/1	1/1	./.	./.	0/0	0/0	0/0	1/1	0/0	1/1	./.	0/0	0/0	0/0	0/0	./.	./.	0/0	./.	0/0	0/0	./.	./.	./.	0/0	0/0	./.	0/0	./.	./.	0/0	0/0	0/0	./.	0/0	0/0	./.	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	./.	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	./.	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	./.	1/1	./.	./.	0/0	./.	0/0	./.	./.	0/0	./.	0/0	0/0	0/0	0/0	./.	0/0	./.	./.	0/0	./.	./.	0/0	./.	./.	./.	0/0	./.	./.	./.	1/1	1/1	1/1	./.	1/1	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	./.	./.	./.	0/0	1/1	1/1	./.	0/0	./.	0/0	./.	./.	0/0	./.	./.	./.	0/0	0/0	./.	./.	0/0	0/0	./.	./.	./.	./.	./.	1/1	1/1
+chr1	158984259	.	AATT	A	.	PASS	VC=INDEL;AC=130;AF=0.49;AN=266;refseq.name=NM_005531;refseq.positionType=intron	GT	./.	1/1	1/1	1/1	0/1	0/1	0/1	0/1	0/0	1/1	./.	1/1	0/1	0/0	0/1	1/1	0/1	0/1	1/1	0/1	./.	1/1	1/1	0/1	./.	0/0	0/0	0/1	0/0	0/1	0/0	./.	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/1	1/1	1/1	0/0	./.	0/1	0/1	0/1	0/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	0/0	1/1	0/1	./.	0/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/0	1/1	0/0	0/1	0/1	0/0	0/1	0/0	0/1	./.	0/1	./.	1/1	0/0	0/1	0/1	1/1	0/1	./.	./.	0/0	0/0	./.	0/1	1/1	0/1	0/1	1/1	./.	./.	0/0	0/1	0/0	0/1	1/1	./.	0/1	0/1	./.	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/1	1/1	0/1	0/1	0/0	./.	0/0	0/1	0/0	./.	0/0	0/1	0/1	./.	0/1	0/1	./.	./.	./.	./.	./.	0/1	0/1	1/1	0/1	0/1	0/1	./.	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/0
+chr1	159500234	.	CT	C	.	PASS	VC=INDEL;AC=19;AF=0.06;AN=316	GT	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1
+chr1	159741079	.	TGT	T	.	PASS	VC=INDEL;AC=163;AF=0.52;AN=314	GT	0/1	1/1	1/1	1/1	1/1	0/1	0/1	0/0	0/1	0/0	0/1	1/1	0/0	0/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	./.	0/0	0/0	1/1	0/1	0/1	0/0	0/0	0/0	1/1	0/1	1/1	0/1	0/0	0/1	1/1	0/1	1/1	1/1	1/1	0/0	1/1	0/1	0/1	0/1	1/1	0/1	1/1	0/1	0/1	0/0	1/1	0/1	0/0	0/0	1/1	1/1	0/1	0/0	0/1	0/1	0/1	1/1	1/1	1/1	0/1	0/0	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/0	0/1	0/1	1/1	1/1	0/1	0/0	0/1	0/1	0/0	0/0	1/1	0/0	0/1	1/1	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/1	1/1	0/0	0/1	0/1	1/1	0/1	1/1	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/0	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	1/1	0/1	0/1	1/1	1/1	0/1	0/0	0/1	0/0	0/1	0/0	1/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1
+chr1	160004099	.	GATGTAGATAG	G	.	PASS	VC=INDEL;AC=3;AF=0.01;AN=314;refseq.name=NM_145167;refseq.positionType=promoter	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	160081222	.	TGAAAAG	T	.	PASS	VC=INDEL;AC=5;AF=0.02;AN=312	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	160430789	.	C	CAG	.	PASS	VC=INDEL;AC=51;AF=0.16;AN=314	GT	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	1/1	0/1	1/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/1	1/1	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/1	1/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/1	1/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0
+chr1	160464965	.	AGTGAATTTTAGA	A	.	PASS	VC=INDEL;AC=12;AF=0.06;AN=214;refseq.name=NM_052931;refseq.positionType=intron	GT	./.	0/0	0/0	./.	./.	./.	./.	0/0	./.	0/0	0/0	0/0	./.	0/0	./.	./.	0/0	./.	./.	0/0	./.	./.	0/0	./.	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	./.	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	./.	./.	0/1	./.	0/0	0/0	./.	0/1	0/0	./.	0/0	0/0	./.	0/0	./.	0/0	0/0	./.	./.	0/0	./.	./.	0/0	0/0	./.	./.	./.	./.	0/1	0/1	0/1	./.	./.	0/1	./.	0/0	0/0	./.	./.	./.	0/1	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	./.	0/0	./.	./.	0/0	0/0	0/1	0/0	./.	0/0	0/0	0/0	./.	./.	0/0	0/0	./.	0/0	0/0	0/0	./.	./.	0/1	./.	0/1	./.	0/1
+chr1	160578541	.	C	CA	.	PASS	VC=INDEL;AC=277;AF=0.88;AN=316	GT	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	0/0	0/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/0	1/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1	1/1	0/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1
+chr1	161765879	.	T	TCTT	.	PASS	VC=INDEL;AC=77;AF=0.25;AN=310;refseq.name=NM_007348;refseq.positionType=intron	GT	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/0	1/1	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/0	1/1	0/1	1/1	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/1	1/1	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/0	./.	0/1	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	1/1	1/1	0/0	0/0	0/0	0/1	0/1	1/1	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/1	1/1	0/1	./.	0/1	0/1	1/1	0/1	0/0	0/0	0/1	./.	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/0
+chr1	161826110	.	TT	T	.	PASS	VC=INDEL;AC=0;AF=0;AN=308;refseq.name=NM_007348;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	162354200	.	AACAC	A	.	PASS	VC=INDEL;AC=32;AF=0.12;AN=262;refseq.name=NM_001085375;refseq.positionType=exon	GT	0/1	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	1/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	1/1	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/0	./.	0/0	0/0	0/0	0/0	0/1	./.	0/0	0/0	0/0	0/0	1/1	0/0	0/0	./.	./.	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	./.	0/0	./.	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	1/1	./.	0/0	0/0	./.	0/1	./.	0/0	./.	./.	0/0	0/1	./.	./.	./.	./.	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	./.	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	./.	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/1	1/1
+chr1	162629796	.	C	CGTT	.	PASS	VC=INDEL;AC=238;AF=0.75;AN=316;refseq.name=NM_001014796;refseq.positionType=intron	GT	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	0/1	0/1	1/1	0/0	1/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/1	1/1	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	1/1	0/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	0/0	0/0	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	1/1	0/0	1/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1
+chr1	163132415	.	TCCTGAACA	T	.	PASS	VC=INDEL;AC=7;AF=0.02;AN=314;refseq.name=NM_003617;refseq.positionType=intron	GT	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1
+chr1	163135904	.	C	CAGA	.	PASS	VC=INDEL;AC=217;AF=0.84;AN=258;refseq.name=NM_003617;refseq.positionType=intron	GT	1/1	1/1	1/1	./.	0/1	1/1	1/1	0/1	1/1	0/1	0/1	0/1	1/1	0/1	0/1	1/1	./.	0/1	0/0	./.	0/1	0/0	./.	1/1	./.	0/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	./.	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	0/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	./.	1/1	./.	1/1	0/1	./.	0/1	./.	1/1	1/1	1/1	0/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	./.	./.	./.	1/1	1/1	0/1	1/1	0/1	1/1	./.	./.	0/1	./.	0/1	./.	0/1	./.	1/1	1/1	1/1	0/1	./.	./.	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	0/1	1/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	./.	0/1	0/1	0/1	0/1	1/1	0/1	1/1	0/1	0/1	./.	1/1
+chr1	163136054	.	T	TTC	.	PASS	VC=INDEL;AC=266;AF=0.84;AN=316;refseq.name=NM_003617;refseq.positionType=intron	GT	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	0/1	0/1	0/1	1/1	0/1	0/1	1/1	0/1	0/1	0/0	0/1	0/1	0/0	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	0/0	0/0	0/1	0/0	0/1	1/1	0/1	1/1	0/1	0/1	1/1	1/1
+chr1	163136055	.	T	TCT	.	PASS	VC=INDEL;AC=265;AF=0.84;AN=314;refseq.name=NM_003617;refseq.positionType=intron	GT	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	0/1	0/1	0/1	1/1	0/1	0/1	1/1	1/1	0/1	0/0	0/1	0/1	0/0	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	0/0	0/0	0/1	0/0	0/1	1/1	0/1	1/1	0/1	0/1	1/1	1/1
+chr1	164351168	.	ATTG	A	.	PASS	VC=INDEL;AC=261;AF=0.83;AN=316	GT	1/1	0/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	0/0	0/1	0/1	1/1	1/1	0/1	0/0	0/1	1/1	0/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	0/1	1/1	0/0	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	0/0	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	1/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1
+chr1	164448310	.	AAAC	A	.	PASS	VC=INDEL;AC=236;AF=0.75;AN=316	GT	0/1	1/1	0/0	0/1	0/1	1/1	0/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	1/1	0/1	1/1	0/0	0/0	0/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/0	0/1	1/1	0/0	1/1	0/1	0/0	1/1	0/1	0/1	0/1	0/1	0/1	0/0	1/1	0/1	0/1	0/1	0/1	1/1	1/1	0/0	0/1	0/1	0/1	0/1	1/1	1/1	0/1	0/1	0/1	0/0	0/0	0/1	1/1	0/1	0/0	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1
+chr1	164548574	.	TT	T	.	PASS	VC=INDEL;AC=11;AF=0.04;AN=308;refseq.name=NM_002585;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	./.	0/0	./.	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0
+chr1	164790567	.	C	CT	.	PASS	VC=INDEL;AC=164;AF=0.52;AN=314;refseq.name=NM_002585;refseq.positionType=intron	GT	1/1	0/0	0/0	0/1	0/0	1/1	0/1	1/1	0/0	0/0	1/1	1/1	0/0	0/1	1/1	0/0	0/0	1/1	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/1	1/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/0	1/1	0/1	0/1	0/0	0/0	0/1	0/0	1/1	0/0	0/1	0/1	0/1	0/1	1/1	0/1	0/0	0/0	0/0	0/1	0/1	0/0	1/1	0/0	0/0	0/1	0/1	0/1	1/1	0/1	0/1	0/0	1/1	0/1	0/1	1/1	0/1	0/1	1/1	0/1	0/1	0/0	0/1	0/1	1/1	0/1	0/1	0/1	1/1	0/1	0/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1	1/1	0/1	0/1	./.	1/1	0/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/0	0/1	0/1	0/1	0/1	0/0	1/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	0/0	0/1	1/1	1/1	1/1	1/1	0/0	0/1	1/1	1/1	1/1	0/1	1/1	0/0	1/1	0/1	1/1	0/1	0/0
+chr1	165207456	.	TAGA	T	.	PASS	VC=INDEL;AC=17;AF=0.05;AN=316;refseq.name=NM_177398;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1
+chr1	165218477	.	AGAGATTACTCTG	A	.	PASS	VC=INDEL;AC=79;AF=0.28;AN=280;refseq.name=NM_177398;refseq.positionType=intron	GT	0/1	1/1	0/1	0/0	0/1	0/1	0/1	0/1	0/0	1/1	0/0	0/1	0/0	0/0	0/0	0/0	1/1	0/0	0/0	0/0	0/1	0/0	0/1	0/1	./.	1/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	./.	0/0	1/1	0/1	0/0	0/0	1/1	./.	1/1	1/1	0/0	0/1	./.	./.	1/1	0/0	1/1	0/1	0/1	./.	0/1	1/1	1/1	./.	0/1	0/1	1/1	./.	0/0	0/1	./.	0/1	1/1	0/1	1/1	1/1	./.	1/1	./.	0/1	1/1	0/1	0/0	./.	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	./.	./.	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	./.	0/0	0/0	0/1	0/1	0/1	0/1
+chr1	165261980	.	TA	T	.	PASS	VC=INDEL;AC=129;AF=0.42;AN=308;refseq.name=NM_177398;refseq.positionType=intron	GT	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/1	1/1	./.	0/1	0/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/0	./.	0/1	1/1	0/1	0/0	0/1	0/1	1/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	1/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	1/1	0/0	0/1	1/1	./.	1/1	0/0	0/0	0/0	1/1	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	1/1	./.	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/0	1/1	0/1	1/1	0/1	0/1	0/0	0/0	0/0	1/1	0/0	0/1	1/1	0/0	0/1	0/1	0/0	0/1	1/1	0/0	0/1	1/1	1/1	1/1	0/0	0/1	0/0	1/1	0/1	1/1	0/1	0/1	1/1	1/1	0/1	0/1	0/1	0/1	0/1	0/0	1/1	0/1	0/1	1/1	0/1	0/1	1/1	0/1	0/1	0/1
+chr1	165286489	.	AA	A	.	PASS	VC=INDEL;AC=23;AF=0.07;AN=314;refseq.name=NM_177398;refseq.positionType=intron	GT	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1
+chr1	165349359	.	G	GT	.	PASS	VC=INDEL;AC=130;AF=0.42;AN=306	GT	0/1	./.	1/1	1/1	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/0	1/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/0	0/1	0/1	1/1	0/0	1/1	0/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	0/0	0/0	0/1	0/1	0/1	1/1	1/1	0/1	0/1	1/1	0/0	1/1	1/1	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/1	1/1	0/1	0/1	0/1	0/0	./.	0/0	0/1	0/1	0/0	0/0	0/0	0/0	1/1	0/0	0/1	0/1	1/1	0/1	./.	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/1	0/0	./.	0/0	0/1	0/1	0/1	0/1	1/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	1/1	0/1	1/1	0/0	0/0	0/0	0/0	0/1	0/0	1/1	0/0	0/1	0/1	0/1	0/1	1/1	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/0	1/1	0/1	0/1	1/1	1/1	./.	0/1	0/1
+chr1	165475542	.	CT	C	.	PASS	VC=INDEL;AC=157;AF=0.5;AN=316	GT	0/1	1/1	0/1	0/1	0/1	1/1	1/1	0/0	0/0	1/1	0/1	0/1	1/1	0/0	0/1	1/1	0/1	0/0	0/0	1/1	0/1	0/1	1/1	0/1	0/1	0/1	1/1	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	1/1	0/1	0/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	0/1	1/1	0/1	0/0	0/1	0/0	0/0	0/0	1/1	0/1	1/1	0/0	0/0	0/0	0/1	0/0	0/0	1/1	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	1/1	1/1	0/0	0/1	0/0	0/1	1/1	1/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/1	0/0	0/0	0/0	0/1	0/1	1/1	0/1	0/1	1/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/1	1/1	0/1	0/1	0/1	0/1	0/0	1/1
+chr1	165627134	.	AT	A	.	PASS	VC=INDEL;AC=144;AF=0.46;AN=314	GT	0/0	1/1	0/1	0/1	1/1	0/0	0/0	0/1	0/1	0/0	1/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	1/1	0/1	1/1	0/1	0/1	0/1	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/0	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	./.	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/1	1/1	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	1/1	0/1	0/0	0/0	0/0	0/1	1/1	0/1	0/1	0/1	0/0	0/1	0/1	1/1	0/1	0/0	0/0	0/0	1/1	0/1	0/1	0/1	1/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/1	0/0	1/1	1/1	0/1	0/1	0/0	0/0	0/0	1/1
+chr1	165652540	.	GTTAA	G	.	PASS	VC=INDEL;AC=202;AF=0.66;AN=304;refseq.name=NM_000696;refseq.positionType=intron	GT	0/1	1/1	1/1	1/1	1/1	0/0	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	0/1	0/0	0/1	0/0	1/1	0/1	0/1	0/0	0/0	0/0	0/1	0/1	1/1	0/0	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	0/1	0/1	0/0	0/1	0/0	0/1	1/1	1/1	1/1	0/1	0/1	1/1	0/0	0/1	0/1	0/1	0/1	1/1	1/1	0/1	0/1	0/1	./.	./.	1/1	0/1	1/1	0/0	./.	0/1	0/0	0/1	0/0	0/1	./.	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/1	1/1	0/1	0/1	0/1	0/1	0/1	0/1	1/1	1/1	0/1	0/1	0/0	0/1	1/1	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/0	1/1	1/1	1/1	0/0	0/0	0/0	./.	1/1
+chr1	165685796	.	GGCACAGAT	G	.	PASS	VC=INDEL;AC=155;AF=0.49;AN=314	GT	0/0	0/1	0/0	0/0	1/1	0/0	0/0	1/1	0/0	0/0	0/1	0/0	0/1	0/1	0/1	1/1	0/0	1/1	0/0	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/1	1/1	0/1	1/1	0/1	0/1	0/1	0/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	0/0	1/1	0/0	0/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	0/1	./.	0/1	1/1	0/1	1/1	0/0	1/1	0/0	1/1	0/1	1/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	1/1	0/1	0/1	1/1	0/1	0/1	0/1	0/1	0/0	1/1	0/1	1/1	0/0	0/1	1/1	0/1	0/1	1/1	0/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	0/0	0/1	1/1	0/0	0/1	0/0	1/1	0/1	1/1	0/1	1/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	1/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	1/1	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	1/1	0/1	0/1	1/1	0/1	0/0
+chr1	165686450	.	TAGG	T	.	PASS	VC=INDEL;AC=144;AF=0.46;AN=316	GT	0/1	0/1	1/1	0/1	0/0	1/1	1/1	0/0	1/1	1/1	0/1	0/1	0/0	0/0	0/1	0/0	1/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	1/1	0/0	1/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/1	1/1	0/0	1/1	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/0	1/1	0/1	1/1	0/0	0/1	0/0	1/1	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	1/1	0/1	1/1	0/0	0/1	0/0	0/0	0/0	0/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	1/1	0/1	1/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/1
+chr1	165686452	.	GGAG	G	.	PASS	VC=INDEL;AC=145;AF=0.46;AN=316	GT	1/1	0/1	1/1	0/1	0/0	1/1	1/1	0/0	1/1	1/1	0/1	0/1	0/0	0/0	0/1	0/0	1/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	1/1	0/0	1/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/1	1/1	0/0	1/1	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/0	1/1	0/1	1/1	0/0	0/1	0/0	1/1	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	1/1	0/1	1/1	0/0	0/1	0/0	0/0	0/0	0/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	1/1	0/1	1/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/1
+chr1	166083223	.	CCAC	C	.	PASS	VC=INDEL;AC=0;AF=0;AN=316;refseq.name=NM_001017961;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	166602705	.	TTGT	T	.	PASS	VC=INDEL;AC=73;AF=0.23;AN=316	GT	0/0	0/0	0/0	0/1	0/0	1/1	0/1	0/1	0/0	0/0	0/0	1/1	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/1	0/1	0/1	0/1	0/0	1/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/1	1/1	1/1	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/1	1/1	1/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/1	1/1	0/0	0/1	0/1	1/1	0/0	0/1	1/1	0/1	1/1	0/0	1/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0
+chr1	166639248	.	A	AAT	.	PASS	VC=INDEL;AC=289;AF=0.91;AN=316	GT	0/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	0/1	0/1	0/0	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	0/1
+chr1	166708316	.	G	GTAG	.	PASS	VC=INDEL;AC=102;AF=0.32;AN=316	GT	0/1	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/1	1/1	0/0	0/0	0/0	0/0	0/0	0/1	1/1	0/1	1/1	0/0	0/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	1/1	1/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	1/1	0/1	1/1	1/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/1	1/1	0/0	1/1	0/1	0/0	0/1	0/0	0/1	1/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/1	1/1	0/0	0/0	0/0	1/1	1/1	1/1	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	1/1	0/0	0/1	0/1	0/0	0/0	0/1	0/0	0/0	1/1	0/1	1/1	0/1	0/0	0/0	0/0	0/0
+chr1	167512714	.	TTCCAAAACCGA	T	.	PASS	VC=INDEL;AC=7;AF=0.02;AN=316;refseq.name=NM_003851;refseq.positionType=intron	GT	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1
+chr1	167513042	.	CA	C	.	PASS	VC=INDEL;AC=7;AF=0.02;AN=316;refseq.name=NM_003851;refseq.positionType=intron	GT	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1
+chr1	167516739	.	T	TAA	.	PASS	VC=INDEL;AC=1;AF=0;AN=316;refseq.name=NM_003851;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1
+chr1	167675717	.	T	TTC	.	PASS	VC=INDEL;AC=22;AF=0.07;AN=296;refseq.name=NM_052862;refseq.positionType=terminator	GT	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	./.	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	./.	0/1	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	./.	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/0	./.	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	167682039	.	CCAAA	C	.	PASS	VC=INDEL;AC=68;AF=0.22;AN=316	GT	0/0	0/1	1/1	0/0	0/0	0/1	1/1	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/0	1/1	0/0	0/0	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1	1/1	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	1/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/1	1/1	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/1
+chr1	167682041	.	AAACA	A	.	PASS	VC=INDEL;AC=68;AF=0.22;AN=316	GT	0/0	0/1	1/1	0/0	0/0	0/1	1/1	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/0	1/1	0/0	0/0	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1	1/1	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	1/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/1	1/1	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/1
+chr1	167697899	.	GTG	G	.	PASS	VC=INDEL;AC=50;AF=0.16;AN=316;refseq.name=NM_003953;refseq.positionType=intron	GT	0/0	0/1	1/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0
+chr1	167985326	.	TG	T	.	PASS	VC=INDEL;AC=144;AF=0.49;AN=294;refseq.name=NM_001017977;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/1	0/1	./.	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	1/1	0/0	0/1	0/1	1/1	1/1	0/0	0/1	0/1	1/1	./.	0/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	1/1	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/1	1/1	0/0	0/0	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	0/0	1/1	1/1	./.	1/1	1/1	0/1	0/1	0/0	1/1	0/1	0/0	1/1	1/1	1/1	0/0	1/1	0/1	1/1	./.	./.	1/1	0/1	0/1	1/1	0/1	./.	0/1	0/1	0/0	1/1	0/0	0/1	1/1	0/1	1/1	0/1	1/1	0/1	0/1	1/1	0/1	./.	1/1	./.	0/1	1/1	0/1	0/0	./.	0/1	0/0	0/0	0/0	1/1	0/1	1/1	1/1	1/1	1/1	0/1	0/0	1/1	1/1	1/1	0/1	0/1	./.	0/1	1/1	0/1
+chr1	168053859	.	ACTCA	A	.	PASS	VC=INDEL;AC=11;AF=0.03;AN=316;refseq.name=NM_153832;refseq.positionType=terminator	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0
+chr1	168133510	.	CCTAAC	C	.	PASS	VC=INDEL;AC=96;AF=0.3;AN=316	GT	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/1	0/0	0/1	1/1	0/0	0/0	1/1	0/0	0/1	0/1	1/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/0	1/1	0/0	0/0	0/0	0/1	0/1	1/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/0	1/1	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/1	0/1	1/1	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/0	1/1	0/1	0/1	1/1	1/1	0/0	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/1	1/1	1/1	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/1	0/0	0/0	0/0	1/1	0/0	0/1	0/1	0/1
+chr1	168200152	.	GT	G	.	PASS	VC=INDEL;AC=135;AF=0.43;AN=316;refseq.name=NM_199344;refseq.positionType=intron	GT	1/1	0/0	1/1	0/0	0/1	0/1	0/1	1/1	0/0	1/1	0/0	1/1	1/1	0/1	0/0	0/1	1/1	0/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	0/1	0/1	1/1	1/1	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/1	1/1	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/1	1/1	0/1	0/1	0/0	0/1	1/1	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/0	1/1	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	1/1	0/1	0/1	1/1	0/1	0/1	0/1	1/1	0/0	1/1	0/1	1/1	0/1	1/1	0/0	0/1	0/0	0/0	0/1	1/1	0/1	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/1	1/1	1/1	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/1	0/0	1/1	1/1	1/1	0/0	1/1	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/0
+chr1	168423776	.	AGC	A	.	PASS	VC=INDEL;AC=4;AF=0.01;AN=316	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1
+chr1	169066627	.	T	TC	.	PASS	VC=INDEL;AC=301;AF=0.95;AN=316	GT	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	1/1	0/1	1/1	1/1	0/1	1/1	0/0	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	0/0
+chr1	169066629	.	C	CC	.	PASS	VC=INDEL;AC=301;AF=0.95;AN=316	GT	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	1/1	0/1	1/1	1/1	0/1	1/1	0/0	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	0/0
+chr1	169095586	.	T	TAT	.	PASS	VC=INDEL;AC=165;AF=0.52;AN=316;refseq.name=NM_001001787;refseq.positionType=intron	GT	0/0	1/1	1/1	0/0	1/1	0/1	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	0/0	1/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	0/1	0/1	0/0	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	0/1	0/1	1/1	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	1/1	0/0	0/1	0/0	0/1	0/1	1/1	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	1/1	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/0	0/1	0/0	1/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	1/1
+chr1	169214437	.	CA	C	.	PASS	VC=INDEL;AC=10;AF=0.03;AN=316;refseq.name=NM_013330;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	169875635	.	AG	A	.	PASS	VC=INDEL;AC=2;AF=0.01;AN=314	GT	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	170054566	.	CAAAT	C	.	PASS	VC=INDEL;AC=2;AF=0.01;AN=316	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	170213713	.	C	CA	.	PASS	VC=INDEL;AC=302;AF=0.96;AN=314	GT	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1
+chr1	170231599	.	C	CA	.	PASS	VC=INDEL;AC=178;AF=0.57;AN=314	GT	0/1	0/1	0/0	1/1	1/1	0/0	0/1	1/1	0/0	0/1	0/0	0/1	0/1	0/1	1/1	1/1	0/1	0/1	0/0	0/0	0/1	0/1	0/1	1/1	0/0	0/0	0/0	0/1	0/1	0/0	1/1	1/1	1/1	0/1	0/0	1/1	0/1	0/0	0/1	1/1	0/1	0/0	1/1	1/1	0/0	1/1	0/1	0/1	0/1	0/1	1/1	0/0	0/1	0/1	0/1	1/1	0/0	1/1	1/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/1	1/1	0/1	0/0	1/1	1/1	0/1	0/0	0/1	1/1	0/1	1/1	1/1	0/1	0/1	1/1	0/1	1/1	0/1	0/1	0/0	0/1	0/0	1/1	0/1	0/0	0/1	0/1	0/1	1/1	0/1	0/0	0/1	0/1	1/1	0/0	1/1	0/1	1/1	1/1	1/1	1/1	1/1	./.	0/0	0/1	0/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/1	1/1	0/1	0/1	0/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1	0/0	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	0/1	0/0	0/1	0/1	0/0	0/1	1/1	0/1
+chr1	170412385	.	A	AA	.	PASS	VC=INDEL;AC=247;AF=0.79;AN=312	GT	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/0	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	0/1	0/1	1/1	1/1	0/1	0/1	1/1	0/1	0/0	0/1	0/0	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/0	1/1	0/0	0/1	0/1	0/1	0/1	0/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1	1/1	1/1	0/0	1/1	0/1	0/1	0/1	0/0	0/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/0	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	0/1	0/0	./.	0/0	1/1	1/1	1/1	0/1	0/1	0/0	1/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1
+chr1	171564547	.	T	TT	.	PASS	VC=INDEL;AC=141;AF=0.68;AN=206	GT	1/1	1/1	1/1	./.	0/1	./.	1/1	0/1	./.	0/1	./.	./.	./.	1/1	1/1	./.	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	./.	1/1	./.	1/1	1/1	./.	./.	./.	0/1	0/1	./.	./.	./.	0/1	0/1	./.	1/1	0/1	./.	0/1	1/1	./.	1/1	./.	./.	0/1	./.	0/1	./.	./.	./.	./.	0/1	./.	1/1	./.	0/1	1/1	0/1	0/1	1/1	1/1	0/0	./.	./.	./.	./.	./.	0/1	0/1	1/1	0/1	./.	0/1	1/1	./.	0/1	0/1	0/1	./.	0/1	0/1	0/0	1/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	./.	0/0	0/1	./.	0/1	0/1	1/1	./.	1/1	1/1	./.	0/1	1/1	0/1	0/1	./.	1/1	0/1	0/1	0/1	0/1	0/1	0/0	0/0	./.	./.	./.	./.	1/1	./.	./.	0/1	1/1	1/1	./.	0/1	1/1	./.	./.	0/1	./.	./.	0/1	./.	0/1	./.	./.	1/1	./.	1/1	1/1	1/1	0/1
+chr1	171668398	.	C	CATC	.	PASS	VC=INDEL;AC=42;AF=0.13;AN=316	GT	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	1/1	1/1	1/1	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0
+chr1	171779854	.	AAAG	A	.	PASS	VC=INDEL;AC=128;AF=0.46;AN=278	GT	0/1	1/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	./.	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	1/1	1/1	0/1	1/1	0/1	1/1	0/1	./.	0/0	0/0	0/1	0/0	0/1	0/0	1/1	0/1	1/1	0/0	0/1	./.	0/1	0/1	./.	./.	./.	1/1	0/1	./.	0/1	1/1	0/1	0/1	1/1	0/1	./.	0/1	1/1	0/1	0/1	1/1	0/1	0/1	0/1	0/0	./.	0/0	0/1	1/1	0/1	1/1	1/1	./.	1/1	0/1	0/1	1/1	./.	0/1	1/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	0/0	1/1	0/1	./.	0/0	0/1	0/0	./.	0/0	0/1	0/0	0/1	./.	1/1	./.	0/1	0/1	0/1	0/0	1/1	0/1	./.	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	1/1	0/0	0/1	1/1	0/1	0/1	0/1	0/1	0/1	0/0	./.	0/1	0/1	0/1	0/0	0/0	0/0	0/1	./.	1/1	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/1	./.	0/1	0/1
+chr1	171799766	.	A	ACT	.	PASS	VC=INDEL;AC=48;AF=0.18;AN=268	GT	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/0	./.	0/1	./.	0/0	0/1	0/0	0/0	./.	0/0	0/1	0/0	./.	0/1	0/1	0/1	0/1	0/0	0/1	0/0	./.	0/1	./.	0/0	0/1	./.	0/1	0/1	0/0	0/0	./.	0/1	0/1	0/1	0/1	0/0	0/0	./.	0/0	0/1	0/0	./.	0/0	0/0	0/1	0/0	./.	0/0	0/0	0/0	./.	0/0	./.	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	./.	0/0	0/0	0/0	./.	0/1	./.	0/1	0/1	0/1	0/1	0/0	./.	0/0	0/1	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/1	0/0	./.	./.	0/0	0/0	./.	0/0	0/0	0/0	0/0	./.	./.	0/1	0/1	0/0	0/0
+chr1	171806532	.	C	CAT	.	PASS	VC=INDEL;AC=14;AF=0.05;AN=308	GT	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0
+chr1	172312482	.	AAG	A	.	PASS	VC=INDEL;AC=5;AF=0.02;AN=316;refseq.name=NM_015569;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0
+chr1	172415351	.	GA	G	.	PASS	VC=INDEL;AC=75;AF=0.24;AN=316;refseq.name=NM_139240;refseq.positionType=intron	GT	0/0	0/1	1/1	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/0	1/1	1/1	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/0	1/1	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/1	1/1	0/1	0/1	0/1	0/0	0/1	1/1	1/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	0/1	0/1	1/1	1/1	0/1	1/1	0/0	1/1	1/1	0/1	0/1	1/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	1/1
+chr1	172620138	.	A	ACT	.	PASS	VC=INDEL;AC=134;AF=0.42;AN=316	GT	0/0	0/0	0/1	0/0	0/1	1/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	1/1	0/1	1/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/1	1/1	0/1	0/0	1/1	0/1	1/1	0/1	1/1	1/1	0/1	1/1	0/0	0/0	0/1	0/0	1/1	0/0	0/1	0/0	1/1	1/1	0/1	0/1	0/1	0/0	0/1	0/1	0/0	1/1	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/1	1/1	0/0	0/0	0/0	0/0	0/1	0/0	1/1	0/1	0/0	0/1	1/1	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	1/1	0/1	1/1	0/0	0/1	0/0	1/1	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	0/0	1/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	1/1	0/1	0/1	0/1	0/1	1/1	0/1	0/0	0/1	0/0	0/1	0/1	0/1	1/1	1/1
+chr1	172620139	.	C	CTC	.	PASS	VC=INDEL;AC=134;AF=0.43;AN=314	GT	0/0	0/0	0/1	0/0	0/1	1/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	1/1	0/1	1/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/1	1/1	0/1	0/0	1/1	0/1	1/1	0/1	1/1	1/1	0/1	1/1	0/0	0/0	0/1	0/0	1/1	0/0	0/1	0/0	1/1	1/1	0/1	0/1	0/1	0/0	0/1	0/1	0/0	1/1	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/1	1/1	0/0	0/0	0/0	0/0	0/1	0/0	1/1	0/1	./.	0/1	1/1	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	1/1	0/1	1/1	0/0	0/1	0/0	1/1	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	0/0	1/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	1/1	0/1	0/1	0/1	0/1	1/1	0/1	0/0	0/1	0/0	0/1	0/1	0/1	1/1	1/1
+chr1	173063473	.	A	ATGTC	.	PASS	VC=INDEL;AC=124;AF=0.62;AN=200	GT	0/0	0/1	0/1	./.	0/1	./.	./.	1/1	0/1	0/0	0/1	./.	0/1	1/1	./.	./.	0/0	0/1	0/1	./.	1/1	1/1	0/1	1/1	0/0	1/1	0/0	1/1	./.	1/1	0/0	1/1	1/1	./.	./.	./.	./.	./.	./.	1/1	./.	0/1	./.	1/1	0/1	1/1	./.	1/1	./.	0/1	./.	0/1	1/1	./.	1/1	0/1	./.	0/1	0/1	./.	./.	0/1	0/1	./.	./.	0/1	./.	0/1	./.	./.	0/1	./.	1/1	0/1	./.	1/1	./.	./.	0/1	./.	1/1	1/1	./.	1/1	0/1	./.	./.	0/0	./.	0/1	1/1	1/1	./.	1/1	1/1	0/0	./.	./.	0/1	0/0	./.	./.	1/1	1/1	1/1	1/1	1/1	0/1	./.	1/1	0/1	0/1	./.	./.	0/1	0/1	0/1	0/0	./.	./.	0/0	1/1	1/1	1/1	0/0	0/0	./.	0/0	0/0	1/1	1/1	1/1	0/0	0/1	0/1	1/1	0/0	0/1	1/1	./.	./.	1/1	0/0	./.	0/1	./.	./.	1/1	0/0	./.	./.	./.	1/1	0/1	./.	0/1	1/1	./.
+chr1	173541560	.	CAA	C	.	PASS	VC=INDEL;AC=233;AF=0.74;AN=316;refseq.name=NM_178527;refseq.positionType=intron	GT	0/0	0/1	1/1	0/0	1/1	1/1	0/1	1/1	1/1	0/0	1/1	1/1	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	0/1	1/1	0/1	0/1	1/1	0/0	1/1	0/0	1/1	1/1	1/1	0/1	0/1	0/1	0/1	0/1	1/1	0/0	0/0	0/1	1/1	0/1	0/1	0/0	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/0	0/1	0/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/0	1/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	0/1	0/1	1/1	1/1	1/1	0/1	0/0
+chr1	173749093	.	T	TC	.	PASS	VC=INDEL;AC=316;AF=1;AN=316;refseq.name=NM_014458;refseq.positionType=intron	GT	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1
+chr1	173755936	.	T	TGAAG	.	PASS	VC=INDEL;AC=182;AF=0.58;AN=316;refseq.name=NM_014458;refseq.positionType=terminator	GT	0/0	0/1	0/1	0/0	0/1	0/1	0/0	1/1	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/1	0/1	1/1	0/1	0/0	0/0	0/0	1/1	1/1	1/1	0/0	0/1	0/0	1/1	0/1	1/1	0/0	0/1	0/0	1/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/0	0/1	0/1	0/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/1	1/1	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/1	1/1	0/1	0/1	0/1	0/0	0/1	0/1	1/1	1/1	1/1	0/1	0/0	0/0	0/0	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	1/1	0/1	0/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	0/1	0/1	0/1	0/0	1/1	0/1	1/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	0/0
+chr1	173870326	.	ACTA	A	.	PASS	VC=INDEL;AC=235;AF=0.74;AN=316	GT	0/0	0/1	0/1	0/0	0/1	0/1	0/0	1/1	1/1	0/1	1/1	0/1	0/0	1/1	0/1	0/0	0/0	0/1	0/1	1/1	0/1	0/0	0/0	0/0	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	0/0	0/1	0/1	0/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/1	1/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	0/0
+chr1	174411392	.	T	TTGTAT	.	PASS	VC=INDEL;AC=251;AF=0.8;AN=314;refseq.name=NM_014857;refseq.positionType=intron	GT	0/0	0/1	0/1	0/0	0/1	0/1	0/0	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	0/0	0/1	0/1	0/1	1/1	1/1	0/1	0/0	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/0
+chr1	174524160	.	T	TAT	.	PASS	VC=INDEL;AC=212;AF=0.67;AN=316;refseq.name=NM_014857;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/1	0/0	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	0/0	0/1	0/1	0/1	0/1	1/1	0/1	0/0	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	0/1	0/0	1/1	0/1	0/0	1/1	0/0	1/1	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/1	1/1	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/0	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	0/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/0
+chr1	175131961	.	GA	G	.	PASS	VC=INDEL;AC=85;AF=0.28;AN=306	GT	1/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	1/1	0/0	0/0	0/1	0/0	0/1	0/1	1/1	1/1	0/0	0/0	0/0	0/1	0/1	0/0	./.	1/1	0/1	0/0	0/1	0/0	0/0	1/1	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/0	./.	0/1	0/1	1/1	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/1	./.	0/1	1/1	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/1	0/1	1/1	./.	0/1	0/1	1/1	./.	0/1	0/0	0/1
+chr1	175299777	.	CAT	C	.	PASS	VC=INDEL;AC=18;AF=0.06;AN=316;refseq.name=NM_003285;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	1/1	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/0
+chr1	175355790	.	GG	G	.	PASS	VC=INDEL;AC=199;AF=0.74;AN=270;refseq.name=NM_003285;refseq.positionType=intron	GT	1/1	0/1	1/1	1/1	1/1	./.	1/1	0/1	1/1	0/1	1/1	0/0	1/1	1/1	0/1	1/1	0/0	0/0	0/1	0/0	1/1	1/1	1/1	1/1	1/1	0/1	0/1	./.	0/1	0/1	1/1	0/1	0/1	0/1	./.	./.	1/1	0/1	1/1	1/1	1/1	1/1	./.	./.	1/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/0	1/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	./.	0/0	./.	0/1	0/0	0/0	0/0	./.	./.	1/1	1/1	1/1	1/1	0/1	1/1	1/1	./.	0/1	1/1	1/1	0/1	./.	0/1	1/1	1/1	1/1	0/0	1/1	0/1	0/1	0/1	./.	1/1	./.	./.	0/1	1/1	0/1	1/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	./.	0/1	1/1	0/1	1/1	1/1	1/1	./.	1/1	1/1	0/1	1/1	1/1	0/1	1/1	./.	./.	0/0	0/1	./.	0/1
+chr1	175418807	.	A	AACA	.	PASS	VC=INDEL;AC=118;AF=0.37;AN=316;refseq.name=NM_003285;refseq.positionType=intron	GT	0/1	0/0	0/0	0/1	1/1	0/0	0/0	1/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	1/1	0/0	0/1	0/0	0/0	1/1	1/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	1/1	0/0	0/0	0/0	1/1	0/0	0/1	0/1	1/1	0/0	0/1	0/0	0/1	1/1	1/1	0/1	1/1	0/1	0/1	0/1	0/0	0/1	0/0	1/1	0/0	1/1	0/1	0/1	1/1	1/1	0/1	0/1	0/0	0/1	0/0	0/1	1/1	1/1	1/1	0/1	0/1	0/0	0/1	1/1	1/1	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/1	0/1	1/1	0/0	1/1	0/1	0/1	0/0	0/0	0/0	0/1	1/1	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	1/1	0/1	0/1	0/1	0/1	1/1	0/0	0/1	1/1	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/1
+chr1	175420618	.	A	AG	.	PASS	VC=INDEL;AC=0;AF=0;AN=316;refseq.name=NM_003285;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	175443036	.	AGGAGA	A	.	PASS	VC=INDEL;AC=1;AF=0;AN=316;refseq.name=NM_003285;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	175472120	.	C	CTAATCAGGATCTTGACATGTGACACAAGATCCTTGAG	.	PASS	VC=INDEL;AC=14;AF=0.04;AN=316;refseq.name=NM_003285;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	175584762	.	CT	C	.	PASS	VC=INDEL;AC=45;AF=0.14;AN=314;refseq.name=NM_003285;refseq.positionType=intron	GT	0/0	0/0	0/1	0/0	0/0	0/1	1/1	0/1	0/1	0/0	1/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	1/1	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	1/1
+chr1	177236388	.	C	CG	.	PASS	VC=INDEL;AC=167;AF=0.54;AN=312;refseq.name=NM_021165;refseq.positionType=intron	GT	1/1	0/1	0/0	0/1	0/1	0/1	1/1	0/1	1/1	0/1	0/1	0/0	1/1	1/1	0/1	1/1	0/1	0/1	0/0	0/1	1/1	1/1	0/1	1/1	0/1	0/0	1/1	0/1	1/1	0/0	0/1	1/1	1/1	1/1	1/1	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	0/1	1/1	0/0	0/0	1/1	0/0	0/1	0/1	0/1	1/1	0/1	0/1	1/1	1/1	0/0	0/1	1/1	0/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	0/1	1/1	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	1/1	0/1	1/1	0/1	0/0	0/1	0/1	0/1	0/1	1/1	0/0	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/1	1/1	0/1	0/0	./.	0/1	./.	0/0	1/1	1/1	1/1	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/0	0/1	1/1	1/1	1/1	0/1	0/1	0/0	0/0	0/0	0/0	1/1	0/1	0/0	1/1	0/1	1/1	0/0	0/1	0/0	1/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	0/0	0/0	0/0	1/1	0/1
+chr1	177236389	.	G	GG	.	PASS	VC=INDEL;AC=166;AF=0.53;AN=316;refseq.name=NM_021165;refseq.positionType=intron	GT	1/1	0/1	0/0	0/1	0/1	0/1	1/1	0/1	1/1	0/1	0/1	0/0	1/1	1/1	0/1	1/1	0/1	0/1	0/0	0/1	1/1	1/1	0/1	1/1	0/1	0/0	1/1	0/1	1/1	0/0	0/1	1/1	1/1	1/1	1/1	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	0/1	1/1	0/0	0/0	1/1	0/0	0/1	0/1	0/1	1/1	0/1	0/1	1/1	1/1	0/0	0/1	1/1	0/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	0/1	1/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	1/1	0/1	1/1	0/1	0/0	0/1	0/1	0/1	0/1	1/1	0/0	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/1	1/1	0/1	0/0	0/0	0/1	0/0	0/0	1/1	1/1	1/1	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/0	0/1	1/1	1/1	1/1	0/1	0/1	0/0	0/0	0/0	0/0	1/1	0/1	0/0	1/1	0/1	1/1	0/0	0/1	0/0	1/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	0/0	0/0	0/0	1/1	0/1
+chr1	177558539	.	G	GAGA	.	PASS	VC=INDEL;AC=7;AF=0.02;AN=290	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	./.	0/0	0/0	./.	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/1	./.	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	177558541	.	G	GAAG	.	PASS	VC=INDEL;AC=10;AF=0.03;AN=296	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/1	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	./.	0/0	0/0	./.	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	178521563	.	TAAGAC	T	.	PASS	VC=INDEL;AC=21;AF=0.09;AN=246	GT	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	./.	0/0	0/0	./.	./.	0/0	0/0	./.	./.	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	./.	./.	0/1	0/0	0/0	./.	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	./.	0/0	0/1	0/0	0/0	0/0	0/0	./.	1/1	1/1	./.	./.	0/0	./.	0/0	./.	./.	./.	0/0	0/0	./.	./.	0/0	0/0	./.	0/0	0/0	./.	0/1	0/0	0/1	./.	./.	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	./.	0/0	0/0	0/0	./.	0/0	0/1	0/1	0/0	0/0	./.	./.	./.	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	./.	1/1	0/0	1/1	0/1	0/0	0/0
+chr1	179038241	.	GT	G	.	PASS	VC=INDEL;AC=0;AF=0;AN=316;refseq.name=NM_014864;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	179293907	.	CAA	C	.	PASS	VC=INDEL;AC=34;AF=0.11;AN=314;refseq.name=NM_003101;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	./.	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/1	0/1	0/0	0/0	0/0	0/0	1/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	1/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1
+chr1	179724329	.	G	GG	.	PASS	VC=INDEL;AC=307;AF=0.97;AN=316;refseq.name=NM_173509;refseq.positionType=intron	GT	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1
+chr1	179762445	.	GT	G	.	PASS	VC=INDEL;AC=85;AF=0.27;AN=316;refseq.name=NM_173509;refseq.positionType=intron	GT	0/1	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/1	1/1	0/1	1/1	1/1	1/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/0	1/1	0/1	1/1	1/1	1/1	0/0	0/1	0/1	0/0	1/1	1/1	1/1	0/0	0/1	0/1	0/1	0/0	0/0	1/1	1/1	1/1	0/0	0/0	0/0	0/1	0/1	1/1	0/1	1/1	0/1	0/1	0/0	0/0	1/1	0/0	0/1	0/0	1/1	0/1	0/1	1/1	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0
+chr1	179762446	.	TT	T	.	PASS	VC=INDEL;AC=85;AF=0.27;AN=316;refseq.name=NM_173509;refseq.positionType=intron	GT	0/1	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/1	1/1	0/1	1/1	1/1	1/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/0	1/1	0/1	1/1	1/1	1/1	0/0	0/1	0/1	0/0	1/1	1/1	1/1	0/0	0/1	0/1	0/1	0/0	0/0	1/1	1/1	1/1	0/0	0/0	0/0	0/1	0/1	1/1	0/1	1/1	0/1	0/1	0/0	0/0	1/1	0/0	0/1	0/0	1/1	0/1	0/1	1/1	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0
+chr1	179773170	.	CTTGTC	C	.	PASS	VC=INDEL;AC=77;AF=0.28;AN=274;refseq.name=NM_173509;refseq.positionType=intron	GT	1/1	0/0	0/1	0/1	0/0	0/0	1/1	1/1	./.	0/0	0/0	0/0	./.	0/0	1/1	0/0	1/1	0/0	0/0	1/1	0/0	1/1	0/0	0/1	./.	0/1	0/0	0/1	0/0	1/1	0/1	0/0	./.	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	./.	./.	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	./.	0/0	0/1	0/0	0/0	./.	1/1	./.	./.	./.	0/0	0/0	./.	0/0	0/1	0/1	0/1	./.	0/1	1/1	1/1	0/0	./.	0/0	0/1	0/1	0/0	0/1	0/1	1/1	0/0	0/0	./.	0/1	0/1	0/0	0/1	0/1	./.	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/0	./.	0/1	0/0	0/1	0/0	0/1	0/1	0/1	1/1	0/1	./.	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	./.	1/1	0/1
+chr1	180108217	.	T	TTATC	.	PASS	VC=INDEL;AC=229;AF=0.72;AN=316	GT	1/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/0	1/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	0/0	1/1	0/1	1/1	0/1	0/1	1/1	0/1	1/1	1/1	0/1	0/1	0/1	0/1	1/1	1/1	0/1	0/0	0/0	1/1	0/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	0/0	1/1	0/1	1/1	0/0	0/1	0/1	0/0	0/0	0/1	1/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	0/1	0/0	0/1	0/1	1/1	0/1	0/0	0/1	0/0	0/1	0/1	1/1	1/1	0/0	0/1	1/1	0/1	0/1	0/1	0/1	0/1	0/0	1/1	0/1	1/1	1/1
+chr1	180722815	.	TACTC	T	.	PASS	VC=INDEL;AC=4;AF=0.01;AN=316;refseq.name=NM_004736;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	180722816	.	ACTCA	A	.	PASS	VC=INDEL;AC=5;AF=0.02;AN=316;refseq.name=NM_004736;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	180762626	.	CAT	C	.	PASS	VC=INDEL;AC=12;AF=0.04;AN=296;refseq.name=NM_004736;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	./.	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/1	./.	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/1
+chr1	180866670	.	CCC	C	.	PASS	VC=INDEL;AC=73;AF=0.29;AN=256	GT	0/0	0/1	0/1	0/0	./.	0/0	./.	0/1	./.	0/0	./.	0/1	./.	0/1	0/0	0/0	0/0	0/1	0/0	0/0	./.	./.	0/0	./.	0/1	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	./.	0/1	0/0	0/1	0/1	0/1	0/0	./.	0/1	1/1	0/1	0/1	0/0	0/1	0/1	0/1	0/0	1/1	1/1	./.	0/1	0/1	0/1	./.	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/1	1/1	0/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	./.	0/1	0/1	0/0	0/1	./.	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	./.	0/0	./.	0/0	0/0	0/1	0/0	0/1	0/0	./.	0/1	./.	0/1	./.	0/1	./.	./.	0/0	0/0	0/0	0/1	./.	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/1	0/0	./.	0/0	0/0	0/0	0/1	0/1	0/0	./.	0/1	./.	0/0	0/0	0/0	0/0	./.	./.	./.	0/1	0/1	0/1	0/1
+chr1	180974402	.	A	AA	.	PASS	VC=INDEL;AC=0;AF=0;AN=298;refseq.name=NM_005819;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	./.	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	./.	0/0	0/0
+chr1	181233905	.	AA	A	.	PASS	VC=INDEL;AC=1;AF=0;AN=266	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	./.	0/0	./.	0/0	0/0	./.	./.	./.	0/0	./.	./.	0/0	0/0	0/0	0/0	0/0	./.	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	./.	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	./.	./.	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	./.	0/0
+chr1	181456872	.	CC	C	.	PASS	VC=INDEL;AC=2;AF=0.01;AN=300;refseq.name=NM_000721;refseq.positionType=intron	GT	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	./.	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	181610646	.	CT	C	.	PASS	VC=INDEL;AC=58;AF=0.18;AN=314;refseq.name=NM_000721;refseq.positionType=intron	GT	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	./.	0/1	0/1	0/1	0/0	0/1	0/0	0/1	1/1	0/0	0/1	0/0	0/0	0/0	1/1	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	1/1	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/0	1/1	0/1	0/0	0/0
+chr1	182087446	.	G	GTCT	.	PASS	VC=INDEL;AC=198;AF=0.68;AN=292	GT	0/1	1/1	1/1	0/1	0/1	0/0	0/1	0/1	1/1	1/1	1/1	0/1	0/1	1/1	./.	1/1	0/1	0/1	0/1	./.	0/1	./.	./.	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	./.	1/1	0/1	0/1	0/1	1/1	./.	1/1	1/1	1/1	0/1	0/1	./.	1/1	0/1	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/0	1/1	0/1	0/1	0/1	0/1	0/1	0/0	1/1	0/0	0/1	1/1	./.	0/1	0/1	0/1	0/0	0/0	1/1	1/1	0/1	0/1	1/1	0/1	0/1	./.	1/1	./.	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	0/1	0/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	0/1	0/1	0/1	1/1	0/1	0/1	0/1	0/1	0/1	1/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/0	1/1	0/1	./.	1/1	0/1	1/1	0/0	0/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	0/0	0/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	0/0
+chr1	182739634	.	TAAGA	T	.	PASS	VC=INDEL;AC=65;AF=0.21;AN=316	GT	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/0	1/1	0/1	0/1	0/1	0/1	0/0	0/1	0/1	1/1	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	1/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1
+chr1	182951675	.	AGA	A	.	PASS	VC=INDEL;AC=78;AF=0.25;AN=316	GT	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	1/1	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/1	1/1	0/0	0/1	1/1	0/0	0/1	1/1	0/1	1/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	1/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	1/1	1/1	0/1	0/0	0/1	0/0	1/1	0/1	0/1	0/1	1/1	0/1	0/0	0/1	0/1	0/1	0/0	0/1	1/1	1/1	0/0	0/0
+chr1	183032447	.	C	CTAAG	.	PASS	VC=INDEL;AC=125;AF=0.4;AN=316;refseq.name=NM_002293;refseq.positionType=intron	GT	0/1	1/1	1/1	0/0	0/1	0/0	1/1	0/0	1/1	1/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	1/1	1/1	0/0	1/1	0/1	1/1	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/1	1/1	0/0	1/1	1/1	0/1	0/1	0/1	1/1	0/0	0/1	0/0	0/1	1/1	0/1	0/1	1/1	0/0	1/1	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/1	1/1	0/0	0/0	0/1	1/1	1/1	0/1	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	1/1	0/0	0/1	0/1	1/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	1/1	0/0	1/1	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	1/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	1/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/1	1/1	0/1	0/1	0/0	0/1	0/1	0/1
+chr1	183073109	.	T	TTG	.	PASS	VC=INDEL;AC=125;AF=0.4;AN=316;refseq.name=NM_002293;refseq.positionType=intron	GT	0/1	1/1	1/1	0/0	0/1	0/0	1/1	0/0	1/1	1/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	1/1	1/1	0/0	1/1	0/1	1/1	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/1	1/1	0/0	1/1	1/1	0/1	0/1	0/1	1/1	0/0	0/1	0/0	0/1	1/1	0/1	0/1	1/1	0/0	1/1	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/1	1/1	0/0	0/0	0/1	1/1	1/1	0/1	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	1/1	0/0	0/1	0/1	1/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	1/1	0/0	1/1	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	1/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	1/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/1	1/1	0/1	0/1	0/0	0/1	0/1	0/1
+chr1	183073111	.	G	GTG	.	PASS	VC=INDEL;AC=125;AF=0.4;AN=316;refseq.name=NM_002293;refseq.positionType=intron	GT	0/1	1/1	1/1	0/0	0/1	0/0	1/1	0/0	1/1	1/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	1/1	1/1	0/0	1/1	0/1	1/1	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/1	1/1	0/0	1/1	1/1	0/1	0/1	0/1	1/1	0/0	0/1	0/0	0/1	1/1	0/1	0/1	1/1	0/0	1/1	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/1	1/1	0/0	0/0	0/1	1/1	1/1	0/1	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	1/1	0/0	0/1	0/1	1/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	1/1	0/0	1/1	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	1/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	1/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/1	1/1	0/1	0/1	0/0	0/1	0/1	0/1
+chr1	183077296	.	A	AG	.	PASS	VC=INDEL;AC=126;AF=0.4;AN=316;refseq.name=NM_002293;refseq.positionType=intron	GT	0/1	1/1	1/1	0/0	0/1	0/0	1/1	0/0	1/1	1/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	1/1	1/1	0/0	1/1	0/1	1/1	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/1	1/1	0/0	1/1	1/1	0/1	0/1	0/1	1/1	0/0	0/1	0/0	0/1	1/1	0/1	0/1	1/1	0/0	1/1	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/1	1/1	0/0	0/0	0/1	1/1	1/1	0/1	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	1/1	0/0	0/1	0/1	1/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	1/1	0/0	1/1	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	1/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	1/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/1	1/1	0/1	0/1	0/0	0/1	0/1	0/1
+chr1	183097956	.	G	GTTA	.	PASS	VC=INDEL;AC=127;AF=0.4;AN=314;refseq.name=NM_002293;refseq.positionType=intron	GT	0/1	1/1	1/1	0/0	0/1	0/0	1/1	0/0	1/1	1/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	1/1	1/1	0/0	1/1	0/1	1/1	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/1	1/1	0/0	1/1	1/1	0/1	0/1	0/1	1/1	0/0	0/1	0/0	0/1	1/1	0/1	0/1	1/1	0/0	1/1	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/1	1/1	0/0	0/0	0/1	1/1	1/1	0/1	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	1/1	0/0	0/1	0/1	1/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	./.	0/1	0/1	1/1	0/0	1/1	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	1/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	1/1	0/1	0/0	0/1	0/1	0/1	0/1	1/1	0/1	0/1	0/1	0/0	0/1	0/1	1/1	0/1	0/1	0/0	0/1	0/1	0/1
+chr1	183145207	.	G	GTAG	.	PASS	VC=INDEL;AC=35;AF=0.11;AN=312	GT	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/1	0/0	0/0	./.	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0
+chr1	183180446	.	GG	G	.	PASS	VC=INDEL;AC=54;AF=0.17;AN=316;refseq.name=NM_005562;refseq.positionType=intron	GT	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/1	1/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	1/1	0/1	1/1	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0
+chr1	183330737	.	TAA	T	.	PASS	VC=INDEL;AC=197;AF=0.63;AN=312;refseq.name=NM_015039;refseq.positionType=intron	GT	0/1	1/1	1/1	0/1	1/1	0/0	1/1	0/0	0/1	0/1	./.	1/1	0/1	0/1	1/1	0/1	1/1	1/1	0/1	0/1	0/1	0/1	1/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	1/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/0	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	./.	0/0	0/0	0/1	1/1	1/1	0/0	0/1	0/0	0/0	0/1	0/0	1/1	1/1	1/1	0/1	0/1	0/1	1/1	0/0	0/1	0/1	0/0	0/1	0/0	0/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	1/1	0/0	0/1	0/0	0/1	0/0	0/1	1/1	0/0	0/1	1/1	1/1	1/1	0/0	0/1	0/0	1/1	0/1	0/1	0/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	0/1	1/1	0/0	0/1	0/0	1/1	0/1	1/1	0/0	0/0	0/1	0/1	0/1	1/1	0/1	1/1
+chr1	183589923	.	A	ATCTT	.	PASS	VC=INDEL;AC=117;AF=0.37;AN=314	GT	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/0	1/1	0/1	0/1	0/1	1/1	0/0	0/0	0/1	0/0	0/1	0/1	1/1	1/1	0/1	0/1	1/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	0/0	0/1	0/0	0/1	0/0	1/1	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	1/1	1/1	0/1	0/1	./.	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/1	1/1	0/1	0/0	0/0	0/0	1/1	0/1	1/1	0/1	0/1	1/1	0/1	0/1	0/0	0/1	0/1	1/1	0/0	0/1	0/0	1/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	0/1	0/0	1/1	0/0	0/1	0/0	1/1	0/1	0/1	1/1	1/1	0/1	1/1	0/0	0/0	0/1	0/0	0/1	0/0
+chr1	183712910	.	AC	A	.	PASS	VC=INDEL;AC=131;AF=0.42;AN=312;refseq.name=NM_015149;refseq.positionType=intron	GT	1/1	1/1	0/1	0/0	0/1	0/1	1/1	0/0	0/1	1/1	0/0	0/1	0/0	0/0	0/0	0/1	1/1	0/1	1/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	1/1	0/0	1/1	0/0	0/0	0/1	0/0	0/0	0/0	1/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	0/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	./.	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/1	1/1
+chr1	183806728	.	T	TG	.	PASS	VC=INDEL;AC=229;AF=0.85;AN=270;refseq.name=NM_015149;refseq.positionType=intron	GT	1/1	./.	1/1	./.	./.	0/1	0/1	./.	1/1	1/1	0/1	1/1	0/1	./.	1/1	0/1	1/1	1/1	0/1	./.	0/1	1/1	1/1	0/1	1/1	1/1	./.	./.	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	./.	0/1	./.	./.	0/0	./.	1/1	1/1	0/0	1/1	./.	1/1	0/0	1/1	./.	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	./.	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	./.	0/1	1/1	0/1	1/1	1/1	1/1	./.	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	./.	0/1	1/1	1/1	1/1	0/0	1/1	./.	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	1/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	0/0	1/1	./.	1/1	1/1	1/1	1/1	0/0	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1
+chr1	183996005	.	C	CTATTA	.	PASS	VC=INDEL;AC=27;AF=0.09;AN=316;refseq.name=NM_015101;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	184391018	.	C	CTA	.	PASS	VC=INDEL;AC=68;AF=0.22;AN=312;refseq.name=NM_030806;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/0	1/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	1/1	0/1	0/1	0/1	0/0	0/1	1/1	0/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/1	./.	0/1	1/1	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/1	0/0	1/1	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	1/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/1	./.	0/1	0/1	0/0	0/1	0/0	0/1	0/1	1/1	1/1	1/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/0
+chr1	184561827	.	CAGA	C	.	PASS	VC=INDEL;AC=47;AF=0.15;AN=316;refseq.name=NM_030806;refseq.positionType=intron	GT	0/0	0/1	1/1	0/0	1/1	0/0	0/1	0/0	0/0	1/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	1/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	1/1	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	184577643	.	T	TC	.	PASS	VC=INDEL;AC=0;AF=0;AN=316;refseq.name=NM_030806;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	185540897	.	T	TCCAG	.	PASS	VC=INDEL;AC=136;AF=0.48;AN=286	GT	0/0	0/1	0/0	0/1	0/0	./.	0/1	0/1	0/1	0/1	0/0	0/1	./.	1/1	./.	0/1	0/1	0/1	0/0	0/1	./.	0/1	0/1	0/0	1/1	0/1	0/1	1/1	1/1	0/1	0/1	1/1	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	./.	0/1	0/1	./.	0/0	0/1	0/0	./.	0/0	0/0	./.	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/1	0/0	0/1	./.	0/0	0/0	0/1	0/1	1/1	1/1	0/1	./.	0/1	1/1	1/1	1/1	./.	0/1	1/1	./.	0/1	0/1	0/1	1/1	1/1	0/0	1/1	0/1	0/1	0/1	1/1	1/1	0/1	0/1	./.	0/0	0/0	./.	0/1	1/1	1/1	0/0	1/1	0/1	0/0	0/1	0/1	1/1	0/0	0/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	0/0	1/1	0/1	0/1	1/1	1/1	1/1	0/0	0/1	0/0	0/1	0/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	0/0
+chr1	185865550	.	C	CAT	.	PASS	VC=INDEL;AC=53;AF=0.17;AN=310;refseq.name=NM_031935;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	./.	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/1	0/0	./.	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0
+chr1	186378142	.	CAGTT	C	.	PASS	VC=INDEL;AC=55;AF=0.21;AN=266;refseq.name=NM_017847;refseq.positionType=intron	GT	0/1	0/0	0/0	0/0	./.	0/1	0/0	0/0	0/1	0/0	./.	0/1	1/1	0/1	./.	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/1	./.	0/1	0/0	0/1	./.	0/0	0/0	0/0	1/1	0/1	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	./.	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	./.	0/1	0/0	1/1	0/0	0/0	0/0	0/0	./.	0/1	0/0	0/0	./.	0/0	0/0	0/1	0/1	1/1	0/0	0/1	0/1	./.	./.	0/0	0/0	0/1	0/1	0/0	1/1	./.	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/1	./.	./.	0/0	0/1	./.	./.	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	1/1	./.	0/1	0/0	0/0	./.	./.	0/0	0/1	0/0	0/0	0/0	0/0	./.	./.	0/0	./.	0/0	./.	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/0
+chr1	186769215	.	T	TA	.	PASS	VC=INDEL;AC=45;AF=0.14;AN=316	GT	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	1/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	1/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/1	0/0	0/0	0/0	1/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	186933480	.	T	TTAAT	.	PASS	VC=INDEL;AC=135;AF=0.43;AN=316;refseq.name=NM_024420;refseq.positionType=intron	GT	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1	1/1	0/0	1/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	1/1	0/1	0/1	0/1	1/1	0/1	0/1	0/0	1/1	1/1	1/1	0/1	1/1	0/1	0/1	1/1	0/1	0/0	1/1	0/0	0/1	0/1	1/1	0/1	0/1	0/1	0/0	1/1	0/1	0/1	1/1	0/1	1/1	0/1	0/0	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	0/0	0/1	0/1	1/1	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	0/0	0/0
+chr1	187372829	.	AGGCTT	A	.	PASS	VC=INDEL;AC=34;AF=0.11;AN=304	GT	./.	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	1/1	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	./.	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	./.	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/1
+chr1	187372830	.	GGCTTG	G	.	PASS	VC=INDEL;AC=32;AF=0.1;AN=306	GT	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	./.	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/1
+chr1	187685847	.	CAATT	C	.	PASS	VC=INDEL;AC=112;AF=0.36;AN=314	GT	0/1	1/1	1/1	0/1	1/1	0/0	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/1	1/1	0/1	0/1	1/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/1	1/1	0/1	0/1	0/0	0/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	0/0	1/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	0/1	0/0	1/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	0/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	./.	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	1/1	0/0	0/1	0/0	0/1
+chr1	187781028	.	C	CT	.	PASS	VC=INDEL;AC=278;AF=0.9;AN=310	GT	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/0	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	./.	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1
+chr1	187815820	.	A	ACAA	.	PASS	VC=INDEL;AC=21;AF=0.07;AN=314	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	1/1	1/1	0/1	0/0	0/0	1/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0
+chr1	187899550	.	AAA	A	.	PASS	VC=INDEL;AC=65;AF=0.21;AN=314	GT	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/1	1/1	1/1	1/1	1/1	0/1	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	1/1	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0
+chr1	188075358	.	GTAAG	G	.	PASS	VC=INDEL;AC=63;AF=0.2;AN=316	GT	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/0	1/1	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/1	1/1	0/0	0/1	0/0	0/0	0/0	1/1	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	1/1	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/1	1/1	0/0	0/0	0/0	0/1	0/1	0/0	1/1	0/0	0/1	0/0	0/0
+chr1	188110355	.	C	CT	.	PASS	VC=INDEL;AC=222;AF=0.71;AN=312	GT	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/0	0/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/0	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	0/1	1/1	0/1	0/1	1/1	0/0	./.	0/1	0/0	1/1	0/1	1/1	0/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	0/1	0/0	0/1	0/1	1/1	1/1	0/1	0/1	0/0	1/1	0/1	0/1	0/1	1/1	1/1	./.	0/0	0/0	0/0	1/1	0/1	1/1	0/0	0/1	0/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	0/1	1/1	0/0	1/1	0/1	0/0	0/0	0/0	0/1	0/1	1/1	1/1	0/0	0/1	0/1	1/1	0/1	1/1	0/0	0/1	1/1	1/1
+chr1	188372559	.	CAAG	C	.	PASS	VC=INDEL;AC=230;AF=0.73;AN=314	GT	0/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	0/1	0/0	1/1	0/0	0/1	0/1	1/1	0/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	0/1	0/0	0/0	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	0/1	0/1	1/1	1/1	0/1	0/0	0/1	1/1	0/0	0/1	0/1	0/0	1/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	1/1	0/1	1/1	0/0	0/1	0/1	0/0	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	1/1	0/0	0/1	0/1	1/1	./.	0/1	0/1	0/1	1/1	0/1	0/0	0/1	1/1	0/1	1/1	1/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/0	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1
+chr1	188397016	.	C	CA	.	PASS	VC=INDEL;AC=9;AF=0.03;AN=316	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0
+chr1	188526820	.	C	CT	.	PASS	VC=INDEL;AC=262;AF=0.91;AN=288	GT	1/1	1/1	1/1	1/1	./.	0/1	./.	1/1	0/1	1/1	./.	1/1	1/1	./.	1/1	0/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	./.	0/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1	0/1	0/1	1/1	1/1	0/1	0/0	./.	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	./.	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1
+chr1	188533586	.	G	GTTCT	.	PASS	VC=INDEL;AC=290;AF=0.92;AN=316	GT	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1	0/1	0/1	1/1	1/1	0/1	0/0	0/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1
+chr1	188628449	.	CAACT	C	.	PASS	VC=INDEL;AC=100;AF=0.32;AN=314	GT	0/1	0/0	0/0	0/0	1/1	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/1	0/0	0/0	1/1	0/1	0/0	0/0	0/1	0/0	0/1	0/0	./.	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	1/1	1/1	1/1	0/1	0/1	1/1	0/0	0/1	1/1	0/1	0/1	0/1	1/1	0/0	0/0	0/0	0/1	0/0	1/1	0/0	0/1	0/1	0/1	1/1	0/1	0/1	0/1	0/1	0/0	0/1	0/1	1/1	0/0	1/1	0/1	0/1	1/1	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/1	1/1	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/0	0/0	1/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/1	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1
+chr1	189027168	.	C	CTG	.	PASS	VC=INDEL;AC=146;AF=0.69;AN=212	GT	1/1	./.	./.	./.	./.	./.	0/1	1/1	0/1	0/1	./.	0/1	./.	0/1	./.	0/1	1/1	0/1	0/0	1/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	./.	./.	./.	0/1	0/1	0/1	0/0	1/1	1/1	0/1	1/1	0/1	0/1	1/1	./.	./.	1/1	./.	1/1	1/1	0/0	1/1	0/0	./.	1/1	1/1	1/1	1/1	0/1	1/1	0/1	./.	0/1	1/1	1/1	0/1	0/1	0/1	./.	./.	1/1	1/1	1/1	0/1	0/1	0/0	./.	0/1	0/1	./.	./.	0/1	./.	1/1	./.	./.	./.	0/1	0/1	0/1	./.	1/1	0/1	./.	0/1	0/1	0/0	0/1	./.	0/1	./.	1/1	./.	1/1	1/1	0/1	0/1	1/1	1/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	./.	1/1	1/1	0/1	./.	./.	1/1	./.	./.	1/1	0/1	0/0	1/1	0/1	0/1	0/1	./.	./.	./.	./.	./.	1/1	0/1	./.	./.	./.	./.	1/1	1/1	./.	./.	1/1	1/1	1/1	./.	./.	1/1	./.	./.	./.
+chr1	189046798	.	C	CA	.	PASS	VC=INDEL;AC=86;AF=0.27;AN=316	GT	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/1
+chr1	189087000	.	TTA	T	.	PASS	VC=INDEL;AC=159;AF=0.53;AN=302	GT	0/1	0/1	0/0	1/1	0/1	1/1	0/1	1/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	1/1	0/1	0/1	1/1	0/1	0/1	0/0	1/1	0/1	0/1	0/1	1/1	0/0	0/1	0/1	1/1	0/0	0/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	0/0	1/1	0/0	0/1	1/1	0/1	1/1	1/1	0/1	0/1	0/1	1/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	0/0	1/1	1/1	1/1	0/1	0/1	0/0	0/1	0/1	0/1	0/0	1/1	0/1	0/0	0/1	0/1	1/1	0/1	1/1	./.	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/1	./.	1/1	1/1	0/1	0/1	0/1	0/0	0/1	0/1	0/0	./.	0/0	0/0	./.	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/0	1/1	0/1	0/0	0/1	0/0	./.	0/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	0/1	1/1	0/1	1/1	0/1	0/1	0/1	1/1	1/1	0/1	./.	0/0	0/1	./.	0/0	0/1	1/1
+chr1	189190273	.	AT	A	.	PASS	VC=INDEL;AC=2;AF=0.01;AN=316	GT	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1
+chr1	189547870	.	A	AAT	.	PASS	VC=INDEL;AC=194;AF=0.79;AN=246	GT	0/1	./.	./.	1/1	0/1	1/1	1/1	1/1	1/1	0/0	1/1	0/1	0/0	1/1	./.	0/1	0/1	0/1	1/1	1/1	0/1	./.	./.	0/1	./.	0/0	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	./.	./.	1/1	0/1	0/1	1/1	1/1	1/1	1/1	0/0	./.	./.	./.	1/1	1/1	1/1	1/1	0/1	1/1	0/0	1/1	./.	0/1	./.	./.	0/1	1/1	0/0	./.	1/1	1/1	./.	./.	./.	0/0	1/1	./.	./.	1/1	./.	0/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	./.	0/0	1/1	./.	0/1	1/1	1/1	1/1	./.	./.	1/1	1/1	1/1	0/1	0/1	0/1	0/1	0/1	0/1	1/1	./.	./.	0/1	./.	1/1	0/1	1/1	./.	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	./.	./.	0/1	1/1	1/1	./.	0/1	1/1	0/1	0/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	0/0	0/1
+chr1	189629285	.	A	ATAACT	.	PASS	VC=INDEL;AC=158;AF=0.59;AN=266	GT	0/1	1/1	0/0	1/1	./.	0/1	1/1	0/1	0/0	0/0	1/1	0/1	./.	1/1	./.	0/1	./.	0/1	0/1	1/1	0/1	./.	./.	0/1	0/0	./.	0/0	0/1	0/0	0/1	1/1	1/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	./.	0/1	./.	0/0	0/0	1/1	0/1	./.	0/1	1/1	0/1	0/1	0/0	1/1	0/1	0/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	0/1	0/1	0/0	./.	1/1	0/1	0/1	0/0	0/1	./.	0/1	1/1	0/1	0/1	0/0	1/1	0/1	0/0	0/1	0/0	0/1	./.	./.	0/1	1/1	1/1	1/1	0/1	./.	1/1	0/1	0/0	0/1	1/1	1/1	1/1	0/0	0/1	0/1	./.	0/1	0/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1	./.	./.	0/0	./.	0/1	./.	0/1	0/1	./.	0/1	0/1	0/1	0/1	0/0	0/1	1/1	./.	./.	1/1	1/1	1/1	./.	0/1	0/1	1/1	1/1	1/1	0/0	1/1	0/1	0/1	1/1	0/1	1/1	0/1	0/1	0/1	0/0	0/0	./.	0/1	0/1	1/1	1/1	1/1	0/1	0/1
+chr1	189867802	.	G	GC	.	PASS	VC=INDEL;AC=23;AF=0.07;AN=316	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/0
+chr1	190095126	.	CTAACA	C	.	PASS	VC=INDEL;AC=143;AF=0.45;AN=316;refseq.name=NM_199051;refseq.positionType=intron	GT	0/1	0/0	0/1	0/0	1/1	0/1	1/1	1/1	0/0	1/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	1/1	0/0	1/1	0/0	0/1	0/0	0/0	0/1	0/0	1/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	0/1	0/0	0/0	0/0	0/1	1/1	0/0	0/0	0/1	0/0	0/0	0/0	1/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	1/1	0/1	0/1	1/1	1/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	1/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/0	1/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	0/0	1/1	0/1	0/1	1/1	0/1	0/1	1/1	0/1	1/1	0/1	0/1	1/1	0/1	0/1	1/1	0/1	1/1	0/0	0/1	0/1	1/1	1/1	1/1	0/1	0/1	1/1	0/0	1/1	0/1	1/1	1/1	1/1	0/1	0/0	0/1	0/0	1/1	0/1	0/1	1/1
+chr1	190095129	.	ACATAA	A	.	PASS	VC=INDEL;AC=143;AF=0.45;AN=316;refseq.name=NM_199051;refseq.positionType=intron	GT	0/1	0/0	0/1	0/0	1/1	0/1	1/1	1/1	0/0	1/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	1/1	0/0	1/1	0/0	0/1	0/0	0/0	0/1	0/0	1/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	0/1	0/0	0/0	0/0	0/1	1/1	0/0	0/0	0/1	0/0	0/0	0/0	1/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	1/1	0/1	0/1	1/1	1/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	1/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/0	1/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	0/0	1/1	0/1	0/1	1/1	0/1	0/1	1/1	0/1	1/1	0/1	0/1	1/1	0/1	0/1	1/1	0/1	1/1	0/0	0/1	0/1	1/1	1/1	1/1	0/1	0/1	1/1	0/0	1/1	0/1	1/1	1/1	1/1	0/1	0/0	0/1	0/0	1/1	0/1	0/1	1/1
+chr1	190636901	.	C	CTAA	.	PASS	VC=INDEL;AC=131;AF=0.42;AN=314	GT	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/1	1/1	0/1	0/1	1/1	0/1	0/1	0/1	1/1	1/1	0/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	1/1	0/1	0/1	0/0	1/1	0/1	0/1	1/1	0/1	0/1	0/1	0/1	0/0	1/1	1/1	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/1	1/1	0/1	0/1	0/1	0/1	1/1	0/1	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/1	1/1	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/1	0/0	1/1	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/1	0/0	0/1	1/1	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/1	1/1	0/1	0/1	0/1	1/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1	0/1	1/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/1	1/1	0/0	0/0
+chr1	190886420	.	AA	A	.	PASS	VC=INDEL;AC=76;AF=0.26;AN=292	GT	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	./.	0/1	0/0	1/1	0/0	0/1	0/0	0/0	0/1	0/0	1/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	1/1	0/0	./.	0/1	0/1	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/0	0/1	0/0	0/0	./.	0/0	0/0	1/1	0/1	0/0	0/1	0/0	0/1	0/0	./.	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	./.	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/1	./.	0/1	./.	0/0	0/0	0/1	0/1	./.	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	./.	0/0	0/0	0/0	./.	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	./.	./.	0/0	0/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	0/1
+chr1	191196527	.	A	AAT	.	PASS	VC=INDEL;AC=191;AF=0.6;AN=316	GT	0/0	0/1	1/1	1/1	1/1	0/0	1/1	0/0	0/1	1/1	0/0	0/1	1/1	0/0	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	0/0	1/1	0/0	0/1	0/1	1/1	1/1	1/1	0/1	1/1	0/0	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	0/1	0/0	0/1	1/1	0/1	0/0	1/1	1/1	0/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	0/1	0/0	0/1	0/1	1/1	1/1	0/1	0/1	0/0	0/1	0/1	0/0	1/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	1/1	1/1	0/0	1/1	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/1	0/0	1/1	0/1	0/1	1/1	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	1/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	0/1	1/1	0/0	0/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1
+chr1	191340485	.	TTAGA	T	.	PASS	VC=INDEL;AC=175;AF=0.59;AN=296	GT	1/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	0/0	0/1	./.	0/1	1/1	1/1	1/1	./.	0/1	1/1	1/1	0/1	0/1	0/0	0/1	0/1	1/1	0/0	1/1	0/1	0/1	0/1	0/0	0/0	0/1	0/0	1/1	1/1	0/1	0/1	0/0	0/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	0/0	0/1	1/1	0/0	1/1	0/1	0/1	0/1	0/0	0/1	1/1	0/1	0/0	0/1	0/1	1/1	0/1	0/1	0/1	0/0	1/1	1/1	0/1	1/1	0/1	0/1	1/1	0/1	1/1	0/1	0/1	./.	0/0	./.	1/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	1/1	0/0	1/1	0/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	./.	0/1	./.	./.	0/1	0/0	0/1	1/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	0/1	0/1	0/0	1/1	0/1	1/1	0/1	1/1	1/1	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/1	1/1	0/1	0/1	./.	0/1	0/0	0/1	0/1	0/1	./.	0/1	0/1	0/0	0/1	./.	0/1	0/1	0/1	0/1	1/1	0/1
+chr1	191464816	.	A	ATTA	.	PASS	VC=INDEL;AC=213;AF=0.7;AN=306	GT	0/0	0/0	0/0	0/1	0/0	1/1	1/1	1/1	1/1	0/0	1/1	0/1	0/1	1/1	0/0	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/0	0/1	1/1	0/1	0/0	1/1	0/0	1/1	./.	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/1	0/1	0/0	1/1	0/0	0/1	0/1	0/1	0/1	0/0	0/1	./.	0/0	0/1	1/1	0/1	0/1	0/0	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	./.	0/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	0/0	1/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/0
+chr1	191588586	.	C	CA	.	PASS	VC=INDEL;AC=190;AF=0.61;AN=310	GT	1/1	0/0	0/1	0/1	0/1	1/1	0/0	1/1	0/1	0/0	./.	0/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	0/0	0/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	0/1	1/1	0/0	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	1/1	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	1/1	0/1	0/0	0/1	0/0	1/1	1/1	0/1	0/1	0/0	1/1	0/1	1/1	0/0	1/1	1/1	0/0	0/0	1/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	1/1	0/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	0/0	0/1	0/0	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	1/1	0/1	1/1	0/1	0/1	0/0	0/0	./.	1/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	0/1	1/1
+chr1	191588587	.	A	AA	.	PASS	VC=INDEL;AC=186;AF=0.61;AN=304	GT	1/1	0/0	0/1	0/1	0/1	1/1	0/0	1/1	0/1	0/0	0/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	0/0	0/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	0/1	1/1	0/0	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	1/1	0/0	0/0	0/1	0/0	0/0	0/1	./.	0/1	0/0	0/0	0/0	0/1	0/1	1/1	0/1	0/0	0/1	0/0	1/1	1/1	0/1	0/1	0/0	1/1	0/1	1/1	0/0	1/1	1/1	0/0	0/0	1/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	./.	0/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	0/1	0/1	./.	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	0/0	0/0	./.	0/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	0/0	0/1	0/0	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	1/1	0/1	1/1	0/1	0/1	0/0	0/0	./.	1/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	0/1	1/1
+chr1	191752595	.	T	TCTTT	.	PASS	VC=INDEL;AC=132;AF=0.42;AN=316	GT	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/0	1/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/1	1/1	0/0	0/1	0/0	1/1	0/1	1/1	0/0	0/1	1/1	0/0	0/1	1/1	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/0	1/1	0/0	0/1	0/1	0/0	0/0	0/1	1/1	0/1	1/1	0/1	0/0	0/1	0/1	0/0	0/0	1/1	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/0	1/1	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	1/1	1/1	1/1	0/0	0/1	0/1	0/1	0/1	1/1	0/1	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/0	1/1	0/1	0/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/0	1/1	0/1	1/1	0/0	0/0	0/0	1/1	0/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	0/1	0/1	0/0	1/1	1/1	1/1	0/0	0/0
+chr1	192047581	.	TT	T	.	PASS	VC=INDEL;AC=1;AF=0;AN=314	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	192460381	.	T	TT	.	PASS	VC=INDEL;AC=0;AF=0;AN=316	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	192612585	.	T	TCA	.	PASS	VC=INDEL;AC=80;AF=0.25;AN=316;refseq.name=NM_002927;refseq.positionType=intron	GT	0/0	0/1	0/1	0/0	1/1	0/0	1/1	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/1	1/1	0/0	1/1	1/1	0/0	1/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	0/1	0/0	0/0	1/1	1/1	1/1	1/1	0/1	0/0	1/1	0/1	1/1	0/1	1/1	0/1	0/0	1/1	0/1	1/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	1/1	0/0
+chr1	192726770	.	C	CT	.	PASS	VC=INDEL;AC=121;AF=0.39;AN=314	GT	0/0	0/0	0/0	0/0	0/1	0/0	1/1	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/0	1/1	1/1	1/1	0/1	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/1	1/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	1/1	0/0	0/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	1/1	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/0	1/1	0/1	0/1	1/1	0/1	0/1	0/1	1/1	0/1	0/1	0/1	1/1	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/0	1/1	0/0	0/1	0/1	0/1	1/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	./.	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/1	1/1	1/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	1/1	1/1
+chr1	193118950	.	AGACT	A	.	PASS	VC=INDEL;AC=7;AF=0.02;AN=316;refseq.name=NM_024529;refseq.positionType=intron	GT	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	193158515	.	CTG	C	.	PASS	VC=INDEL;AC=7;AF=0.02;AN=316;refseq.name=NM_003783;refseq.positionType=promoter	GT	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	193261423	.	AAAGTA	A	.	PASS	VC=INDEL;AC=7;AF=0.02;AN=316	GT	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	193421510	.	A	ATCT	.	PASS	VC=INDEL;AC=102;AF=0.33;AN=310	GT	0/1	1/1	0/1	0/1	1/1	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	./.	0/0	0/1	0/1	1/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	0/1	0/0	0/0	0/1	1/1	0/1	1/1	1/1	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/1	1/1	0/0	0/1	1/1	./.	0/1	0/1	0/1	0/0	0/1	0/1	0/0	1/1	0/1	0/1	0/1	0/0	0/1	1/1	0/0	1/1	./.	0/0	0/1	0/0	0/0	0/1	0/0	0/0	1/1	0/1	0/1	1/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	1/1	0/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	1/1	0/0	0/1	0/0	0/0	0/0
+chr1	193482947	.	CAA	C	.	PASS	VC=INDEL;AC=71;AF=0.22;AN=316	GT	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	1/1	1/1	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/1	1/1	0/1	1/1	0/0	1/1	0/0	1/1	0/1	1/1	0/0	1/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/1	0/1	0/1	1/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	1/1	1/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	1/1	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	1/1	1/1
+chr1	193569090	.	C	CG	.	PASS	VC=INDEL;AC=85;AF=0.27;AN=312	GT	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/0	./.	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/0
+chr1	193877310	.	GG	G	.	PASS	VC=INDEL;AC=106;AF=0.34;AN=316	GT	0/1	0/0	1/1	0/1	0/0	0/1	0/0	0/1	0/0	0/1	1/1	0/1	0/1	1/1	0/1	1/1	0/0	0/1	1/1	0/1	0/0	0/1	1/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	1/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	0/0	0/1	1/1	0/0	0/1	0/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/1	1/1	0/1	1/1	0/0	0/1	1/1	0/1	1/1	0/1	0/1	0/1	1/1	0/0	0/1	0/1	1/1	0/0	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0
+chr1	193881567	.	T	TT	.	PASS	VC=INDEL;AC=4;AF=0.01;AN=314	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1
+chr1	194004698	.	TCTT	T	.	PASS	VC=INDEL;AC=34;AF=0.11;AN=314	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	1/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1
+chr1	194047765	.	TAT	T	.	PASS	VC=INDEL;AC=48;AF=0.2;AN=238	GT	./.	0/0	0/1	./.	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	./.	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/1	./.	0/1	0/1	0/0	0/0	0/0	0/0	1/1	0/0	./.	0/1	0/0	0/1	0/0	0/1	./.	0/0	0/1	0/1	0/0	0/0	0/0	./.	./.	0/0	./.	0/1	0/1	0/0	0/1	./.	./.	0/0	./.	./.	0/1	0/1	0/0	0/0	./.	./.	./.	0/0	0/0	0/1	0/0	./.	0/1	./.	0/1	0/0	0/0	./.	0/0	0/0	0/1	0/1	0/0	./.	0/1	0/0	0/1	0/0	0/0	0/0	0/0	./.	./.	0/0	0/1	0/0	0/0	0/1	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	./.	./.	./.	0/0	./.	0/0	0/1	0/0	0/1	./.	0/1	0/0	0/1	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/1	0/0	0/1	./.	0/0	0/0	0/0	./.	./.	0/1	0/1	0/1	1/1	0/1	0/1	0/0	0/0	./.	0/1	./.	1/1	0/1	./.	0/0	./.	0/0	./.	0/0	0/0	./.	0/0	0/1
+chr1	194160203	.	TTAGT	T	.	PASS	VC=INDEL;AC=25;AF=0.12;AN=206	GT	0/1	0/0	0/1	0/0	./.	0/1	0/0	./.	./.	./.	0/1	./.	0/0	./.	0/1	./.	0/0	0/1	0/1	0/1	./.	0/0	./.	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/1	./.	./.	./.	0/0	0/0	0/0	0/0	./.	0/0	0/1	0/1	0/0	./.	./.	0/1	0/0	./.	./.	./.	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	./.	0/1	./.	0/0	0/0	./.	./.	0/0	./.	0/0	./.	./.	./.	./.	0/1	./.	0/1	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	./.	0/0	0/0	0/0	./.	0/0	0/0	./.	0/0	0/0	0/1	./.	0/0	./.	0/0	./.	0/0	0/0	./.	0/0	./.	0/0	./.	0/0	0/0	0/1	./.	./.	0/0	./.	0/0	0/0	./.	./.	0/1	./.	./.	0/1	0/1	./.	0/1	0/0	0/0	0/0	0/0	./.	./.	0/0	0/0	0/0	0/0	./.	0/0	0/0	./.	0/0	0/0	./.	0/0	0/0	./.	0/0	0/0	./.	0/1
+chr1	194193740	.	A	AG	.	PASS	VC=INDEL;AC=316;AF=1;AN=316	GT	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1
+chr1	194339262	.	ATGT	A	.	PASS	VC=INDEL;AC=67;AF=0.21;AN=316	GT	0/0	0/1	0/0	0/0	0/0	0/0	1/1	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	1/1	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	1/1	0/1	0/1	1/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/1	1/1	0/1	1/1	0/1	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/0	1/1	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/0
+chr1	194487871	.	C	CCTAT	.	PASS	VC=INDEL;AC=302;AF=0.97;AN=312	GT	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1
+chr1	194520551	.	GG	G	.	PASS	VC=INDEL;AC=0;AF=0;AN=316	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	194563981	.	TAAT	T	.	PASS	VC=INDEL;AC=169;AF=0.53;AN=316	GT	1/1	0/0	0/1	0/1	1/1	0/0	0/0	0/1	0/1	1/1	0/0	0/1	0/1	1/1	0/1	0/1	1/1	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/1	1/1	1/1	0/1	0/1	0/0	0/0	0/1	1/1	0/0	0/0	0/0	0/1	0/1	0/1	1/1	0/0	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	0/0	0/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	1/1	0/0	0/1	0/0	1/1	0/1	1/1	1/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	1/1	0/1	0/1	0/0	1/1	0/1	0/0	0/0	0/0	0/1	1/1	0/1	1/1	0/1	1/1	0/1	0/1	0/1	0/0	0/1	0/1	1/1	0/0	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/1	1/1	0/1	1/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/1	1/1
+chr1	194738670	.	T	TTT	.	PASS	VC=INDEL;AC=0;AF=0;AN=316	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	194763917	.	CATG	C	.	PASS	VC=INDEL;AC=267;AF=0.84;AN=316	GT	1/1	1/1	1/1	0/0	1/1	0/1	0/0	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/1	1/1	0/1	0/1	0/1	0/1	0/1	0/0	1/1	1/1	1/1	0/1	1/1	1/1	0/1	0/0	0/1	1/1	0/1	0/1	0/1	0/0	0/1	1/1	1/1	0/0	0/0	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	0/1
+chr1	195047681	.	GG	G	.	PASS	VC=INDEL;AC=29;AF=0.1;AN=278	GT	0/0	0/0	./.	0/0	0/0	0/0	1/1	1/1	0/0	./.	0/0	1/1	0/0	0/0	./.	0/0	0/1	./.	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	./.	0/1	./.	./.	./.	0/1	./.	0/0	./.	0/0	0/0	./.	0/0	0/0	0/1	0/0	./.	./.	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/1	./.	0/1	0/0	0/1	0/0	1/1	1/1
+chr1	195637390	.	TA	T	.	PASS	VC=INDEL;AC=90;AF=0.29;AN=314	GT	1/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	1/1	0/0	1/1	1/1	0/1	0/1	1/1	1/1	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	1/1	0/1	0/0	1/1	1/1	0/0	0/0	1/1	1/1	0/1	0/1	0/1	0/1	0/1	0/0	1/1	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/1	1/1	1/1	0/1	0/0	1/1	0/0	0/1	0/0	1/1	1/1	0/1	0/1	0/0	1/1	1/1	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	1/1	0/1
+chr1	195637391	.	AA	A	.	PASS	VC=INDEL;AC=89;AF=0.28;AN=316	GT	1/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	1/1	0/0	1/1	1/1	0/1	0/1	1/1	1/1	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	1/1	0/1	0/0	1/1	1/1	0/0	0/0	1/1	1/1	0/1	0/1	0/1	0/1	0/1	0/0	1/1	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/1	1/1	0/1	0/0	1/1	0/0	0/1	0/0	1/1	1/1	0/1	0/1	0/0	1/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	1/1	0/1
+chr1	195877296	.	T	TAA	.	PASS	VC=INDEL;AC=232;AF=0.73;AN=316	GT	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	1/1	0/0	0/1	1/1	0/1	1/1	0/1	0/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	0/1	0/0	1/1	0/1	1/1	0/1	0/1	1/1	0/0	0/1	0/1	0/0	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	0/1	0/1	0/1	0/0	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/0	1/1	0/1	0/0	0/1	0/0	1/1	0/1	1/1	1/1	0/1	0/1	0/1	0/1	1/1	0/1	1/1	0/1	0/1	0/1	0/1	1/1	0/1	1/1	0/1	0/1	0/1	1/1	0/0	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/1	1/1	1/1	0/1	1/1	0/0	0/0	0/1	0/1	0/1	1/1	1/1	1/1
+chr1	195877297	.	A	AAA	.	PASS	VC=INDEL;AC=232;AF=0.73;AN=316	GT	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	1/1	0/0	0/1	1/1	0/1	1/1	0/1	0/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	0/1	0/0	1/1	0/1	1/1	0/1	0/1	1/1	0/0	0/1	0/1	0/0	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	0/1	0/1	0/1	0/0	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/0	1/1	0/1	0/0	0/1	0/0	1/1	0/1	1/1	1/1	0/1	0/1	0/1	0/1	1/1	0/1	1/1	0/1	0/1	0/1	0/1	1/1	0/1	1/1	0/1	0/1	0/1	1/1	0/0	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/1	1/1	1/1	0/1	1/1	0/0	0/0	0/1	0/1	0/1	1/1	1/1	1/1
+chr1	195934123	.	CCTAT	C	.	PASS	VC=INDEL;AC=185;AF=0.59;AN=312	GT	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/0	0/0	0/1	0/1	0/1	1/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	1/1	1/1	0/1	1/1	0/0	0/1	0/0	0/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/0	0/1	0/1	1/1	0/0	0/1	0/0	./.	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/1	./.	1/1	0/1	1/1	0/0	0/1	0/1	0/0	0/0	0/0	1/1	0/1	1/1	0/1	1/1	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/1	1/1	0/1	0/0
+chr1	195934125	.	TATCT	T	.	PASS	VC=INDEL;AC=184;AF=0.59;AN=312	GT	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/0	0/0	0/1	./.	0/1	1/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	1/1	1/1	0/1	1/1	0/0	0/1	0/0	0/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/0	0/1	0/1	1/1	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/1	./.	1/1	0/1	1/1	0/0	0/1	0/1	0/0	0/0	0/0	1/1	0/1	1/1	0/1	1/1	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/1	1/1	0/1	0/0
+chr1	196163677	.	TT	T	.	PASS	VC=INDEL;AC=284;AF=0.9;AN=316	GT	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	0/0	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	0/1	1/1	1/1
+chr1	196344374	.	C	CA	.	PASS	VC=INDEL;AC=153;AF=0.53;AN=290;refseq.name=NM_198503;refseq.positionType=intron	GT	0/0	0/0	0/0	./.	0/0	./.	0/0	1/1	1/1	0/0	1/1	0/0	0/0	1/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	1/1	1/1	0/1	1/1	1/1	0/1	0/1	0/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	0/1	0/0	0/0	0/1	./.	0/0	0/1	0/0	./.	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/0	0/0	1/1	0/1	0/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	0/1	./.	0/1	0/1	0/1	0/1	./.	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	./.	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	0/1	./.	./.	0/0
+chr1	196448625	.	ATG	A	.	PASS	VC=INDEL;AC=7;AF=0.03;AN=266;refseq.name=NM_198503;refseq.positionType=intron	GT	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	./.	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	./.	0/1	0/0	0/0	0/0	./.	./.	0/0	0/0	0/0	./.	0/0	./.	0/0	./.	0/1	./.	0/0	0/0	0/0	./.	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	./.	0/0	0/0	0/0	./.	./.	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	./.	0/0	0/1	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	./.	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	./.	0/0
+chr1	196448626	.	TGTA	T	.	PASS	VC=INDEL;AC=8;AF=0.03;AN=302;refseq.name=NM_198503;refseq.positionType=intron	GT	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0
+chr1	197406760	.	GAA	G	.	PASS	VC=INDEL;AC=78;AF=0.25;AN=312;refseq.name=NM_201253;refseq.positionType=intron	GT	0/1	0/0	1/1	0/1	0/1	0/0	0/1	0/0	0/0	1/1	./.	0/1	0/1	0/0	0/0	1/1	0/1	0/1	1/1	0/1	0/0	0/1	0/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	1/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	0/0	0/1	1/1	0/1	0/1	1/1	0/1	0/1	1/1	0/1	0/0	1/1	1/1	0/1	1/1	0/1	0/1	0/1	1/1	1/1	0/1	0/1	1/1	0/0	0/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0
+chr1	197613756	.	ACCT	A	.	PASS	VC=INDEL;AC=25;AF=0.08;AN=316;refseq.name=NM_144977;refseq.positionType=intron	GT	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1
+chr1	197690664	.	T	TG	.	PASS	VC=INDEL;AC=291;AF=0.92;AN=316;refseq.name=NM_144977;refseq.positionType=intron	GT	1/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1
+chr1	198792990	.	T	TG	.	PASS	VC=INDEL;AC=131;AF=0.41;AN=316	GT	0/1	0/1	0/0	1/1	1/1	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/1	1/1	1/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	1/1	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/0	1/1	0/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1	0/1	0/1	1/1	0/1	0/0	0/1	0/1	0/1	1/1	1/1	0/1	0/1	1/1	0/0	0/1	0/1	0/1	0/1	0/1	1/1	1/1	0/1	1/1	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	1/1	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/1	1/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	1/1	0/1	1/1	0/0	0/1	0/0	1/1	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/1	1/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0
+chr1	198940301	.	C	CCTT	.	PASS	VC=INDEL;AC=258;AF=0.82;AN=316	GT	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	1/1	0/1	0/0	0/1	0/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	0/0	1/1	0/1	1/1	0/1	1/1	0/1	0/1	0/1	0/0	1/1	1/1	1/1	0/0	1/1
+chr1	198940306	.	T	TTCT	.	PASS	VC=INDEL;AC=258;AF=0.82;AN=316	GT	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	1/1	0/1	0/0	0/1	0/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	0/0	1/1	0/1	1/1	0/1	1/1	0/1	0/1	0/1	0/0	1/1	1/1	1/1	0/0	1/1
+chr1	199277515	.	AC	A	.	PASS	VC=INDEL;AC=36;AF=0.11;AN=316	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0
+chr1	200575750	.	AAATA	A	.	PASS	VC=INDEL;AC=97;AF=0.31;AN=314;refseq.name=NM_014875;refseq.positionType=intron	GT	0/0	0/0	1/1	1/1	0/0	0/1	0/1	0/0	0/0	0/1	0/0	1/1	0/0	0/1	1/1	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	1/1	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/1	./.	0/1	0/0	0/1	0/1	0/1	0/0	1/1	0/0	0/1	1/1	0/0	0/1	1/1	0/1	1/1	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	1/1	0/1	0/1	0/0	0/0	0/1	1/1	1/1	1/1	0/0	0/1	1/1	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/1
+chr1	201173407	.	AA	A	.	PASS	VC=INDEL;AC=56;AF=0.18;AN=314	GT	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	1/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/0	1/1	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	./.	0/0
+chr1	201288249	.	TATC	T	.	PASS	VC=INDEL;AC=209;AF=0.66;AN=316;refseq.name=NM_000299;refseq.positionType=intron	GT	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/0	1/1	0/0	1/1	1/1	0/0	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/0	0/0	0/0	0/1	0/1	0/1	0/1	1/1	0/1	0/0	0/0	0/1	0/0	0/1	0/0	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	0/1	0/0	1/1	1/1	1/1	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/1	0/0	0/1	0/1	0/1	1/1	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/1	1/1	1/1	0/1	0/1	0/1	0/1	0/0	0/1	0/0	1/1	0/1	0/1	1/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/1	1/1	1/1	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1
+chr1	201457641	.	AA	A	.	PASS	VC=INDEL;AC=55;AF=0.18;AN=310;refseq.name=NM_004078;refseq.positionType=intron	GT	1/1	0/0	0/0	0/1	0/0	0/1	1/1	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/1	1/1	1/1	0/1	0/1	0/1	1/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	./.	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	1/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	1/1	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	1/1	1/1
+chr1	201587178	.	CA	C	.	PASS	VC=INDEL;AC=145;AF=0.47;AN=310	GT	0/0	0/0	0/0	0/0	0/0	0/1	0/0	1/1	1/1	0/0	0/1	0/1	0/1	0/0	1/1	0/0	0/0	0/1	0/1	0/0	1/1	0/1	1/1	0/0	1/1	1/1	0/1	0/1	1/1	0/0	0/1	0/1	0/1	0/1	0/0	1/1	1/1	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	1/1	0/0	0/0	1/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	1/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	0/0	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	./.	0/1	1/1	./.	0/1	0/0	0/0	0/0	0/1	1/1	0/1	0/1	1/1	0/1	0/1	1/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1	0/0	0/1	0/1	0/1	0/0	1/1	0/1	1/1	0/1	1/1	0/1	0/1	0/0
+chr1	201733889	.	G	GG	.	PASS	VC=INDEL;AC=46;AF=0.15;AN=316;refseq.name=NM_020443;refseq.positionType=intron	GT	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	1/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	1/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	1/1	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	1/1	0/1	0/1	0/1	0/1	0/1
+chr1	203792216	.	AA	A	.	PASS	VC=INDEL;AC=265;AF=0.93;AN=286;refseq.name=NM_014827;refseq.positionType=intron	GT	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	./.	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	./.	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	0/1	./.	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	0/1	0/1	./.	1/1	./.	./.	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	./.	0/1	0/1	1/1	0/1	1/1	0/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	0/1	1/1	./.	./.	1/1
+chr1	203829389	.	CTCAAC	C	.	PASS	VC=INDEL;AC=195;AF=0.62;AN=316;refseq.name=NM_003094;refseq.positionType=promoter	GT	0/1	1/1	0/1	0/1	0/0	0/1	0/1	1/1	1/1	0/0	1/1	1/1	0/1	0/0	1/1	0/1	0/1	0/1	1/1	0/1	0/0	0/1	0/1	0/0	0/1	0/1	1/1	0/1	1/1	0/1	0/1	0/1	1/1	0/1	0/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	0/0	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	0/1	0/1	1/1	1/1	0/1	0/1	1/1	0/0	1/1	0/1	1/1	1/1	1/1	0/1	0/0	0/1	0/0	0/1	0/1	0/1	0/1	1/1	0/0	0/1	0/0	0/1	0/1	0/1	1/1	1/1	0/0	1/1	0/1	1/1	0/1	1/1	1/1	0/1	1/1	0/1	0/0	0/1	0/1	0/0	0/1	0/0	1/1	1/1	1/1	0/1	1/1	1/1	0/1	0/0	0/0	0/1	0/0	0/1	0/1	1/1	1/1	0/1	1/1	0/1	0/1	1/1	0/1	0/1	0/1	1/1	1/1	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/1	1/1	0/1	0/1	0/0	1/1	0/1	0/1	0/1	0/1	1/1	0/0	0/1	1/1	0/1
+chr1	203848383	.	C	CTT	.	PASS	VC=INDEL;AC=275;AF=0.87;AN=316	GT	0/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	0/1	0/1	0/0	0/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	0/1	1/1	1/1	0/1
+chr1	203848384	.	T	TTT	.	PASS	VC=INDEL;AC=275;AF=0.87;AN=316	GT	0/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	0/1	0/1	0/0	0/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	0/1	1/1	1/1	0/1
+chr1	204049028	.	T	TG	.	PASS	VC=INDEL;AC=0;AF=0;AN=316;refseq.name=NM_005686;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	204452618	.	T	TGT	.	PASS	VC=INDEL;AC=141;AF=0.47;AN=300;refseq.name=NM_002646;refseq.positionType=intron	GT	1/1	0/0	0/1	1/1	1/1	0/1	0/1	1/1	0/1	1/1	0/0	0/1	0/1	1/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1	1/1	0/1	1/1	0/1	0/0	0/1	0/1	1/1	0/1	0/1	./.	0/0	0/0	0/1	1/1	0/1	0/1	0/1	./.	1/1	0/1	0/1	1/1	1/1	./.	1/1	0/1	0/0	1/1	0/0	1/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1	1/1	./.	1/1	0/0	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/0	1/1	0/1	0/0	0/0	0/0	0/1	./.	0/1	0/1	0/1	0/1	./.	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	./.	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	1/1	1/1	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	./.	1/1	0/1	0/0	0/1	0/0	1/1	1/1
+chr1	205036040	.	T	TG	.	PASS	VC=INDEL;AC=69;AF=0.23;AN=302;refseq.name=NM_005076;refseq.positionType=intron	GT	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/0	1/1	./.	1/1	0/1	0/1	0/1	0/1	1/1	1/1	0/0	0/1	0/0	0/1	0/0	0/1	./.	0/0	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	./.	0/0	0/1	0/0	0/0	0/1	0/1	1/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/1	./.	0/0	0/0	0/1	0/1	0/1	./.	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	1/1	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/1
+chr1	205036041	.	G	GG	.	PASS	VC=INDEL;AC=71;AF=0.23;AN=310;refseq.name=NM_005076;refseq.positionType=intron	GT	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/0	1/1	0/1	1/1	0/1	0/1	0/1	0/1	1/1	1/1	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	1/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/1	./.	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	1/1	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/1
+chr1	206303222	.	C	CAGCCTAGCT	.	PASS	VC=INDEL;AC=105;AF=0.33;AN=316	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	1/1	0/0	0/0	1/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/1	1/1	1/1	0/1	0/1	0/1	1/1	0/1	0/1	1/1	0/0	0/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	1/1	1/1	0/0	1/1	0/1	0/1	1/1	1/1	0/1	1/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	1/1	1/1	0/1	1/1	0/1	0/1	0/1	1/1	0/0	0/1	0/0	1/1	0/1	0/1	0/0	0/1	0/1	0/1	1/1	1/1	0/1	0/0	0/0	1/1	0/1	1/1	1/1	0/1	1/1	0/1	0/0	0/0	0/1	0/0	0/1	0/1	0/1	1/1	0/1	1/1	1/1	0/0	1/1	0/1	0/0	0/1	0/0	0/1	0/1	1/1	0/0	1/1	0/1	0/0	0/0
+chr1	206571046	.	G	GA	.	PASS	VC=INDEL;AC=2;AF=0.01;AN=290;refseq.name=NM_015326;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/1	./.	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/1	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	./.	./.	0/0	./.
+chr1	206862605	.	G	GA	.	PASS	VC=INDEL;AC=0;AF=0;AN=316;refseq.name=NM_004759;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	206955760	.	TGTAA	T	.	PASS	VC=INDEL;AC=95;AF=0.31;AN=310	GT	0/1	0/1	0/1	0/1	0/0	1/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	1/1	0/0	0/0	1/1	0/1	1/1	0/1	1/1	0/0	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	0/1	0/0	0/0	1/1	0/1	1/1	1/1	1/1	0/0	0/0	0/1	0/0	0/1	1/1	1/1	0/1	1/1	0/0	1/1	0/1	1/1	1/1	1/1	0/1	0/0	./.	0/1	1/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/0	0/0	0/0	1/1	0/1	0/0	0/0	0/0	0/0	0/0	./.	0/0	./.	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	1/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/1
+chr1	207260285	.	T	TCAATTCACAGGAGTATGTGA	.	PASS	VC=INDEL;AC=197;AF=0.62;AN=316;refseq.name=NM_001017365;refseq.positionType=promoter	GT	1/1	0/1	1/1	0/0	1/1	0/1	1/1	0/1	1/1	0/1	0/1	0/1	1/1	0/0	0/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	0/1	0/1	0/0	0/1	0/0	1/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	0/1	1/1	1/1	0/1	0/0	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	0/1	0/0	0/0	1/1	0/1	1/1	0/0	0/0	0/0	0/0	0/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1	0/0	0/1	0/0	1/1	0/1	1/1	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	1/1	0/1	0/0	0/1	0/1	1/1	0/1	0/1	1/1	0/1	0/1	0/1	0/1	1/1	0/0	0/0	0/0	1/1	0/0	0/1	1/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1
+chr1	207277350	.	CC	C	.	PASS	VC=INDEL;AC=201;AF=0.64;AN=316;refseq.name=NM_000715;refseq.positionType=promoter	GT	0/0	0/1	0/0	0/1	0/1	0/1	0/1	1/1	0/1	0/0	1/1	0/0	0/1	1/1	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/0	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/0	0/0
+chr1	207641329	.	TTAAG	T	.	PASS	VC=INDEL;AC=13;AF=0.06;AN=216;refseq.name=NM_001006658;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	./.	./.	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	./.	./.	./.	./.	./.	./.	./.	0/0	./.	0/0	0/1	0/0	./.	0/0	./.	./.	./.	./.	0/0	./.	0/1	./.	0/0	0/0	./.	./.	./.	./.	0/0	0/0	0/1	./.	./.	./.	0/0	0/0	./.	0/0	0/0	./.	0/0	./.	0/0	0/0	0/0	./.	0/0	0/0	0/0	./.	0/1	0/0	0/0	0/1	./.	0/0	0/0	0/0	0/0	0/1	./.	0/0	./.	./.	0/0	0/0	0/0	0/1	0/0	./.	0/0	0/0	1/1	./.	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	./.	0/0	0/0	./.	./.	0/0	./.	0/0	./.	./.	0/0	0/0	0/0	./.	./.	0/0	0/0	0/0	./.	0/0	./.	./.	0/0	./.
+chr1	207824638	.	A	AATTC	.	PASS	VC=INDEL;AC=153;AF=0.48;AN=316;refseq.name=NM_175710;refseq.positionType=intron	GT	0/0	0/1	0/0	1/1	0/0	0/1	0/1	1/1	0/1	0/1	1/1	1/1	0/0	0/0	0/0	0/1	0/1	1/1	0/1	0/0	0/0	0/1	0/1	0/0	1/1	1/1	0/1	0/1	1/1	0/1	0/0	1/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	1/1	0/0	0/0	0/1	0/0	0/1	0/0	1/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	1/1	0/1	0/0	1/1	0/0	0/0	0/0	0/1	0/0	0/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	1/1	1/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	1/1	0/1	0/0	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/0	0/1	0/0	0/0	0/0	0/1	1/1	0/1	0/1	1/1	0/1	0/1	1/1	0/1	0/1	1/1
+chr1	208201207	.	GT	G	.	PASS	VC=INDEL;AC=0;AF=0;AN=316;refseq.name=NM_025179;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	208514674	.	GTTAC	G	.	PASS	VC=INDEL;AC=165;AF=0.53;AN=314	GT	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	1/1	0/0	1/1	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	1/1	0/1	0/1	0/0	1/1	0/0	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	0/0	1/1	1/1	1/1	0/0	0/1	0/0	0/1	1/1	0/1	0/1	0/1	0/0	0/1	0/0	1/1	0/1	0/0	1/1	0/0	0/0	0/0	0/0	1/1	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/0	1/1	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/1	1/1	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	1/1	0/1	1/1	1/1	0/1	1/1	0/1	0/1	0/0	0/0	1/1	0/0	0/1	0/0	0/1	0/0	0/1	1/1	1/1	1/1	1/1	1/1	0/0	1/1	0/1	0/1	./.	0/1	0/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/0	0/1	0/0	0/0
+chr1	208514676	.	TACTT	T	.	PASS	VC=INDEL;AC=166;AF=0.53;AN=314	GT	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	1/1	0/0	1/1	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	1/1	0/1	0/1	0/0	1/1	0/0	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	0/0	1/1	1/1	1/1	0/0	0/1	0/0	0/1	1/1	0/1	0/1	0/1	0/0	0/1	0/0	1/1	0/1	0/0	1/1	0/0	0/0	0/0	0/0	1/1	0/0	0/1	0/1	0/1	0/1	0/0	0/0	./.	1/1	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/1	1/1	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	1/1	0/1	1/1	1/1	0/1	1/1	0/1	0/1	0/0	0/0	1/1	0/0	0/1	0/0	0/1	0/0	0/1	1/1	1/1	1/1	1/1	1/1	0/0	1/1	0/1	0/1	0/1	0/1	0/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/0	0/1	0/0	0/0
+chr1	208609280	.	GGAAG	G	.	PASS	VC=INDEL;AC=55;AF=0.21;AN=256	GT	0/0	./.	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	./.	0/0	0/1	0/1	1/1	0/1	./.	0/1	./.	1/1	0/1	./.	0/1	./.	0/0	0/0	0/0	0/0	./.	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	./.	0/0	0/1	1/1	0/1	0/1	1/1	0/0	0/1	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/1	./.	1/1	0/0	1/1	0/1	./.	./.	0/1	1/1	./.	./.	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/1	1/1	./.	0/0	0/0	0/0	0/0	0/0	./.	./.	0/1	0/0	0/0	0/0	0/0	./.	0/0	0/1	0/0	0/0	1/1	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	./.	./.	0/0	./.	0/0	0/1	0/0	./.	0/0	./.	./.	0/0	0/0	./.	./.	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/1	0/0	0/1	0/0	0/1	0/0	./.	0/0	0/0	0/0	./.	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	1/1
+chr1	208643013	.	CA	C	.	PASS	VC=INDEL;AC=36;AF=0.12;AN=310	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	./.	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	./.	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	./.	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	1/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	1/1	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1
+chr1	208643015	.	AA	A	.	PASS	VC=INDEL;AC=39;AF=0.12;AN=316	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	1/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	1/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	1/1	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1
+chr1	208763800	.	C	CA	.	PASS	VC=INDEL;AC=175;AF=0.55;AN=316	GT	1/1	1/1	0/1	1/1	1/1	0/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	0/0	1/1	1/1	0/1	0/1	1/1	1/1	0/1	1/1	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/1	1/1	0/1	0/0	0/0	0/1	0/1	0/1	1/1	0/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	0/0	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	0/0	0/1	0/0	1/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/0	0/1	0/1	1/1	0/0	1/1	0/1	1/1	1/1	0/1	1/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	1/1	0/1	0/1	1/1	0/0	0/0	0/0	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/1	0/1	1/1	1/1	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	1/1	1/1
+chr1	209124169	.	T	TA	.	PASS	VC=INDEL;AC=226;AF=0.72;AN=316	GT	0/1	0/1	0/1	0/1	0/1	0/1	1/1	1/1	0/1	0/0	0/1	0/0	1/1	1/1	1/1	0/1	0/0	0/0	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/0	0/1	0/1	1/1	1/1	1/1	0/0	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/0	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	0/0	0/1	0/0	1/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	0/1	1/1	0/1	1/1	0/0	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	0/0	0/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/0	0/1
+chr1	209124171	.	A	AA	.	PASS	VC=INDEL;AC=226;AF=0.72;AN=316	GT	0/1	0/1	0/1	0/1	0/1	0/1	1/1	1/1	0/1	0/0	0/1	0/0	1/1	1/1	1/1	0/1	0/0	0/0	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/0	0/1	0/1	1/1	1/1	1/1	0/0	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/0	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	0/0	0/1	0/0	1/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	0/1	1/1	0/1	1/1	0/0	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	0/0	0/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/0	0/1
+chr1	209639686	.	A	AG	.	PASS	VC=INDEL;AC=203;AF=0.64;AN=316	GT	0/0	0/1	0/1	0/1	1/1	0/1	0/0	1/1	1/1	0/1	1/1	0/0	0/0	0/1	0/0	0/0	0/1	1/1	0/1	0/0	1/1	0/1	0/0	1/1	0/1	0/0	0/1	0/1	0/0	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	0/1	0/1	1/1	0/1	0/0	1/1	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	1/1	0/0	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/1	1/1	0/0	0/1	0/1	0/0	0/0	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/0	0/1	0/1	1/1	0/1	0/1	0/1	1/1	1/1	0/0	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	0/1
+chr1	209662878	.	T	TG	.	PASS	VC=INDEL;AC=205;AF=0.65;AN=316	GT	0/0	0/1	0/1	0/1	1/1	0/1	0/0	1/1	1/1	0/1	1/1	0/0	0/0	0/1	0/0	0/1	0/1	1/1	0/1	0/0	1/1	0/1	0/0	1/1	0/1	0/1	0/1	0/1	0/0	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	0/1	0/1	1/1	0/1	0/0	1/1	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	1/1	0/0	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/1	1/1	0/0	0/1	0/1	0/0	0/0	0/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/0	0/1	0/1	1/1	0/1	0/1	0/1	1/1	1/1	0/0	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/0	0/1
+chr1	209936964	.	T	TCA	.	PASS	VC=INDEL;AC=184;AF=0.58;AN=316;refseq.name=NM_025228;refseq.positionType=intron	GT	0/0	0/1	0/1	0/1	0/1	0/1	0/0	0/1	1/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/1	1/1	1/1	0/1	0/1	0/0	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/1	1/1	0/0	0/1	0/0	1/1	1/1	0/1	1/1	0/1	0/0	0/1	0/1	0/1	0/1	1/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	1/1	0/1	0/1	0/0	0/0	0/0	1/1	0/1	1/1	1/1	1/1	1/1	0/0	0/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	0/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	0/1	1/1	0/1	0/1	1/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	0/1	0/0	0/1	1/1	1/1	1/1	1/1	1/1	0/0	1/1	0/1	0/1	1/1	0/1	0/1	1/1	0/1	0/0	0/0
+chr1	210007940	.	TCT	T	.	PASS	VC=INDEL;AC=190;AF=0.6;AN=316;refseq.name=NM_014388;refseq.positionType=intron	GT	1/1	0/1	0/1	1/1	0/1	0/0	0/1	1/1	1/1	0/1	0/0	1/1	1/1	1/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	0/0	0/0	0/1	0/0	0/1	1/1	1/1	1/1	0/0	0/1	0/1	0/0	0/0	0/0	1/1	0/1	0/1	1/1	0/1	1/1	0/1	0/1	0/0	0/1	0/1	0/0	0/1	1/1	0/0	0/1	1/1	0/1	0/1	1/1	0/1	0/1	0/1	0/1	0/0	0/0	1/1	0/0	0/1	0/1	0/1	1/1	0/1	1/1	0/0	0/1	1/1	0/0	0/0	1/1	0/1	0/0	1/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1	0/1	0/1	0/0	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/0	1/1	0/1	0/1	0/1	0/0	1/1	1/1	1/1	1/1	0/1	0/1
+chr1	210483472	.	TG	T	.	PASS	VC=INDEL;AC=13;AF=0.04;AN=316	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/0	1/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	210485101	.	A	AGGAC	.	PASS	VC=INDEL;AC=232;AF=0.8;AN=290	GT	0/0	1/1	1/1	0/1	1/1	0/1	0/1	0/1	0/1	./.	1/1	0/1	0/1	1/1	1/1	1/1	./.	./.	0/1	0/1	0/1	0/1	./.	1/1	0/1	1/1	0/0	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	./.	0/0	1/1	0/1	0/0	./.	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	0/0	1/1	0/0	1/1	0/1	1/1	1/1	0/1	1/1	1/1	./.	0/1	./.	1/1	0/1	0/0	0/1	1/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	0/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	1/1	0/1	1/1	0/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	./.
+chr1	210713503	.	TT	T	.	PASS	VC=INDEL;AC=303;AF=0.96;AN=316;refseq.name=NM_018194;refseq.positionType=intron	GT	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1
+chr1	211710916	.	CC	C	.	PASS	VC=INDEL;AC=55;AF=0.17;AN=316	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	1/1	0/1	0/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	1/1	0/1	0/1	1/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/0	1/1	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	1/1	0/1	1/1	0/0	0/1	0/1	0/1	0/1	0/1	1/1	1/1	0/1	0/0	0/0	0/0	0/0	0/0
+chr1	211786200	.	TA	T	.	PASS	VC=INDEL;AC=147;AF=0.56;AN=264	GT	./.	1/1	1/1	1/1	1/1	0/0	1/1	0/0	0/0	./.	0/0	1/1	1/1	0/0	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	./.	./.	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	0/1	0/0	./.	./.	./.	0/0	0/0	0/1	0/0	./.	0/0	0/0	./.	0/0	./.	1/1	0/0	0/1	1/1	0/0	0/0	0/0	./.	0/0	0/0	./.	./.	./.	0/0	./.	0/1	0/1	./.	./.	0/0	./.	0/0	1/1	0/0	0/1	0/0	1/1	0/1	0/1	0/0	0/0	1/1	0/0	0/1	./.	0/0	0/0	0/1	0/0	1/1	0/0	0/0	0/0	0/1	./.	./.	0/0	./.	0/0	0/1	0/0	0/0	0/0	0/1	0/1	./.	1/1	0/0	0/0	1/1	./.	1/1	0/1
+chr1	212767202	.	TTT	T	.	PASS	VC=INDEL;AC=63;AF=0.2;AN=316;refseq.name=NM_001030287;refseq.positionType=intron	GT	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/1	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	1/1	0/0	0/0	0/0	0/0	1/1	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/0	1/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	1/1	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0
+chr1	213150090	.	T	TGT	.	PASS	VC=INDEL;AC=64;AF=0.21;AN=300;refseq.name=NM_024749;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	./.	1/1	0/1	0/1	0/1	0/1	0/0	0/1	0/1	./.	0/1	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/1	./.	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/1	./.	1/1	0/1	0/0	0/1	0/1	0/1	./.	0/1	0/0	./.	./.	0/0
+chr1	213160084	.	A	AG	.	PASS	VC=INDEL;AC=129;AF=0.41;AN=312;refseq.name=NM_024749;refseq.positionType=intron	GT	0/1	0/1	0/1	0/0	1/1	0/1	0/1	0/0	0/0	0/1	0/1	0/0	0/0	1/1	1/1	1/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	1/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/0	1/1	1/1	0/0	0/1	0/1	0/0	0/0	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/1	1/1	0/1	0/1	0/1	0/0	0/1	1/1	0/0	1/1	0/1	0/1	1/1	0/1	0/0	0/1	0/0	0/1	0/0	0/1	1/1	./.	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	1/1	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	1/1	0/0	0/1	0/0	0/1	0/1	0/1	./.	0/1	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/0	1/1	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/0	1/1	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/1	1/1	1/1	0/0	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/1	1/1	0/1	0/0	0/1
+chr1	213160085	.	G	GG	.	PASS	VC=INDEL;AC=129;AF=0.41;AN=314;refseq.name=NM_024749;refseq.positionType=intron	GT	0/1	0/1	0/1	0/0	1/1	0/1	0/1	0/0	0/0	0/1	0/1	0/0	0/0	1/1	1/1	1/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	1/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/0	1/1	1/1	0/0	0/1	0/1	0/0	0/0	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/1	1/1	0/1	0/1	0/1	0/0	0/1	1/1	0/0	1/1	0/1	0/1	1/1	0/1	0/0	0/1	0/0	0/1	0/0	0/1	1/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	1/1	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	1/1	0/0	0/1	0/0	0/1	0/1	0/1	./.	0/1	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/0	1/1	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/0	1/1	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/1	1/1	1/1	0/0	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/1	1/1	0/1	0/0	0/1
+chr1	213393510	.	AG	A	.	PASS	VC=INDEL;AC=62;AF=0.2;AN=316;refseq.name=NM_012424;refseq.positionType=intron	GT	0/1	0/1	0/1	1/1	0/0	0/0	1/1	0/0	0/0	0/1	0/0	0/1	1/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/0	1/1	0/1	0/1	1/1	1/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	1/1	0/1	0/1	1/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	1/1	0/0	0/0	0/1	0/0	0/1	1/1	0/1	1/1	0/1	1/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/1
+chr1	213790399	.	C	CGA	.	PASS	VC=INDEL;AC=2;AF=0.01;AN=316	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	214136369	.	CTTC	C	.	PASS	VC=INDEL;AC=93;AF=0.29;AN=316	GT	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/0	1/1	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/0	1/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/1	1/1	0/0	0/1	0/1	0/1	0/0	0/0	0/1	0/0	0/1	0/1	0/0	1/1	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/0	1/1	1/1	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/0	1/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/1	1/1	0/1	0/1	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0
+chr1	214365999	.	C	CTG	.	PASS	VC=INDEL;AC=164;AF=0.59;AN=278	GT	1/1	0/1	1/1	0/0	0/1	./.	1/1	0/1	0/1	0/1	1/1	1/1	0/1	0/0	0/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	0/0	0/1	./.	0/1	0/0	0/1	1/1	0/1	1/1	1/1	0/1	0/1	0/1	1/1	0/0	1/1	./.	0/0	0/1	1/1	0/0	0/0	0/0	./.	1/1	0/1	0/1	0/0	0/1	0/1	1/1	0/1	0/1	0/1	./.	0/0	0/0	0/1	0/1	1/1	0/1	1/1	0/1	./.	0/1	1/1	0/0	0/1	0/0	0/1	1/1	0/1	0/0	0/1	0/1	0/1	./.	0/1	0/1	./.	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/0	0/0	1/1	0/1	1/1	0/0	./.	0/1	0/1	./.	./.	./.	1/1	./.	./.	1/1	0/1	./.	1/1	1/1	1/1	0/1	./.	0/1	0/0	0/1	0/0	./.	1/1	1/1	0/0	0/0	0/0	0/1	1/1	0/1	1/1	1/1	1/1	0/0	0/1	./.	0/1	0/0	0/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	./.	0/1	1/1	1/1	0/1	0/0	0/1	0/1	0/1	0/1	1/1	0/1
+chr1	214573392	.	G	GTTC	.	PASS	VC=INDEL;AC=271;AF=0.86;AN=316;refseq.name=NM_005401;refseq.positionType=intron	GT	1/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/0	1/1	0/1	0/0	0/1	1/1	1/1	1/1	0/1	0/0	0/1	1/1	1/1	0/0	1/1	0/1	0/1	0/1	0/1	0/1	1/1	1/1	0/0	0/1	0/1	0/1	0/0	0/1	1/1	0/1	0/1	0/1	0/1	1/1	1/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1
+chr1	215120715	.	AA	A	.	PASS	VC=INDEL;AC=36;AF=0.12;AN=312	GT	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/1	0/1	./.	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	1/1	0/0	0/1	0/0	1/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	1/1	0/0	0/0	0/0	./.	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0
+chr1	216179286	.	T	TCAAT	.	PASS	VC=INDEL;AC=30;AF=0.09;AN=316;refseq.name=NM_206933;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0
+chr1	216298294	.	C	CAG	.	PASS	VC=INDEL;AC=113;AF=0.36;AN=316;refseq.name=NM_206933;refseq.positionType=intron	GT	0/0	1/1	1/1	0/1	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/0	1/1	0/1	1/1	0/1	0/1	0/0	0/1	0/1	1/1	1/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	0/1	0/1	0/1	0/1	1/1	0/1	1/1	0/0	0/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	0/1	0/1	1/1	1/1	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	1/1	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/0	1/1	0/1	0/1	0/0	0/0	0/0	0/1	1/1
+chr1	216298296	.	G	GAG	.	PASS	VC=INDEL;AC=112;AF=0.35;AN=316;refseq.name=NM_206933;refseq.positionType=intron	GT	0/0	1/1	1/1	0/1	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/0	1/1	0/1	1/1	0/1	0/0	0/0	0/1	0/1	1/1	1/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	0/1	0/1	0/1	0/1	1/1	0/1	1/1	0/0	0/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	0/1	0/1	1/1	1/1	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	1/1	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/0	1/1	0/1	0/1	0/0	0/0	0/0	0/1	1/1
+chr1	216454053	.	A	AACA	.	PASS	VC=INDEL;AC=224;AF=0.71;AN=316;refseq.name=NM_206933;refseq.positionType=intron	GT	0/0	1/1	0/1	0/1	0/1	1/1	0/0	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1	0/0	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	0/1	0/1	0/1	1/1	1/1	0/1	0/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	1/1	1/1	0/1	0/0	0/0	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	1/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	0/0	0/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	0/0	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/1	1/1	1/1	0/1	1/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	1/1	1/1
+chr1	216780749	.	C	CC	.	PASS	VC=INDEL;AC=10;AF=0.03;AN=316;refseq.name=NM_206594;refseq.positionType=intron	GT	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0
+chr1	216835074	.	A	AGTTT	.	PASS	VC=INDEL;AC=89;AF=0.28;AN=316;refseq.name=NM_206594;refseq.positionType=intron	GT	0/0	0/0	0/1	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	1/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/1	0/1	0/0	0/0	0/1	1/1	0/0	0/1	0/1	1/1	0/0	0/1	0/0	0/1	1/1	0/0	0/1	0/1	0/1	1/1	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	1/1	0/1	0/1	0/1	0/1	1/1	0/0	0/1	0/1	0/0	0/0	0/0	1/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	1/1	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	1/1	0/1	1/1	0/0	0/1	0/1	0/1	0/1	0/0	1/1	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	1/1	0/1	0/1	0/0	0/1
+chr1	217026745	.	AA	A	.	PASS	VC=INDEL;AC=13;AF=0.04;AN=304;refseq.name=NM_206594;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	./.	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0
+chr1	217057204	.	G	GC	.	PASS	VC=INDEL;AC=231;AF=0.73;AN=316;refseq.name=NM_206594;refseq.positionType=intron	GT	0/1	0/1	0/0	1/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	1/1	1/1	0/1	0/1	0/1	0/1	1/1	0/0	1/1	1/1	0/0	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	0/1	0/0	0/1	0/1	0/0	0/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	0/1	0/0	0/1	0/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	0/0	0/1	0/0	1/1	0/1	0/1	1/1	0/0	0/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	0/0	0/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/0	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1
+chr1	217363476	.	CTATT	C	.	PASS	VC=INDEL;AC=40;AF=0.19;AN=212	GT	0/0	1/1	1/1	0/0	0/1	./.	./.	0/0	0/1	0/0	0/0	0/0	0/0	./.	0/0	0/1	0/0	0/0	0/0	0/0	./.	./.	0/0	0/1	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/1	./.	0/1	0/0	0/0	0/0	1/1	0/0	1/1	0/1	0/0	./.	0/0	./.	0/0	0/1	0/0	1/1	0/0	1/1	1/1	0/0	./.	1/1	1/1	./.	./.	./.	0/0	0/0	./.	1/1	0/0	./.	0/1	0/0	0/0	./.	0/1	0/0	./.	./.	./.	./.	./.	./.	./.	0/0	0/0	./.	0/0	0/1	0/0	./.	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	./.	0/0	0/1	0/0	./.	./.	./.	0/0	./.	./.	0/0	0/0	./.	0/1	0/1	1/1	0/0	0/1	0/1	0/0	0/0	./.	0/0	0/0	0/0	0/0	./.	./.	0/0	0/0	0/0	0/0	./.	0/1	0/0	0/0	./.	0/0	./.	./.	0/0	0/0	0/0	0/0	0/0	0/0	./.	./.	./.	0/0	./.	./.	0/0	./.	./.	./.	./.	./.	./.	./.
+chr1	218217904	.	C	CG	.	PASS	VC=INDEL;AC=130;AF=0.43;AN=302	GT	0/1	0/1	0/1	./.	1/1	0/1	./.	0/1	0/0	1/1	0/0	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/0	0/1	1/1	0/1	0/1	0/0	1/1	0/0	0/0	0/0	0/0	1/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	1/1	0/1	0/0	0/1	0/1	./.	1/1	1/1	0/1	0/1	0/0	1/1	1/1	1/1	1/1	./.	1/1	0/1	0/1	0/0	0/1	1/1	0/1	0/1	1/1	0/0	0/1	1/1	./.	1/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	1/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/0	1/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	./.	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/0	1/1	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/1	1/1	0/1	1/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	./.
+chr1	218473680	.	CGAG	C	.	PASS	VC=INDEL;AC=16;AF=0.05;AN=316;refseq.name=NM_016052;refseq.positionType=intron	GT	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1
+chr1	218574584	.	A	AT	.	PASS	VC=INDEL;AC=21;AF=0.09;AN=236;refseq.name=NM_003238;refseq.positionType=intron	GT	0/0	./.	./.	0/0	0/0	0/0	0/0	0/1	./.	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/1	./.	./.	0/0	0/0	./.	0/0	0/1	0/1	0/1	0/0	0/0	./.	0/0	0/1	0/0	0/0	0/0	./.	0/1	0/0	0/0	0/0	0/0	0/1	./.	0/1	./.	0/0	./.	0/1	0/1	0/1	0/0	./.	0/1	0/0	0/1	0/0	0/0	./.	0/0	0/0	./.	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	./.	./.	./.	0/1	0/0	./.	0/0	./.	0/0	0/0	./.	0/0	./.	0/0	./.	./.	0/0	0/0	./.	0/1	0/0	0/0	0/0	./.	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	./.	0/0	./.	0/1	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/1	./.	./.	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	./.	./.	0/0	./.	0/0	0/0	./.	0/1	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	218845277	.	TTTGT	T	.	PASS	VC=INDEL;AC=97;AF=0.31;AN=314	GT	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/1	1/1	0/1	0/0	0/0	0/0	1/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	1/1	0/1	0/0	1/1	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/1	1/1	1/1	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/1	1/1	1/1	0/0	0/1	0/1	1/1	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/1	1/1	1/1	0/0	0/1	1/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/1	./.	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0
+chr1	219001503	.	T	TC	.	PASS	VC=INDEL;AC=176;AF=0.56;AN=316	GT	1/1	0/1	0/0	0/1	1/1	0/1	0/1	1/1	1/1	0/1	1/1	0/0	0/1	1/1	0/1	0/1	1/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	1/1	1/1	0/1	0/1	1/1	0/1	0/1	0/0	1/1	1/1	1/1	1/1	0/1	1/1	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	0/0	0/1	0/1	0/1	0/0	0/0	0/0	1/1	0/1	0/1	0/1	1/1	0/1	1/1	0/0	0/1	1/1	0/0	0/0	0/1	0/1	1/1	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	1/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	0/1	0/0	0/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	1/1	1/1	1/1	0/1	0/1	0/0	0/1	0/0	0/0	1/1	0/1	0/0	0/0	0/0	0/1	0/1	1/1	0/1	1/1	0/1	0/1	1/1	0/1	0/1	0/1	0/1	1/1	0/1	1/1	0/0	1/1	0/1	0/1	1/1
+chr1	219293844	.	A	ACT	.	PASS	VC=INDEL;AC=274;AF=0.89;AN=308	GT	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	0/0	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/0	1/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	0/1	1/1	0/1	0/1	1/1	0/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1	./.	0/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1	1/1	./.	1/1	0/0	1/1	1/1	1/1	1/1	1/1
+chr1	219293846	.	T	TCT	.	PASS	VC=INDEL;AC=199;AF=0.9;AN=222	GT	1/1	1/1	./.	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	1/1	1/1	1/1	./.	./.	./.	1/1	1/1	./.	1/1	1/1	1/1	./.	0/1	./.	./.	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	./.	./.	1/1	./.	./.	./.	1/1	1/1	./.	1/1	./.	1/1	./.	./.	0/1	0/0	1/1	./.	1/1	1/1	./.	./.	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	./.	1/1	1/1	0/1	./.	0/1	./.	1/1	0/1	0/1	1/1	0/1	0/1	./.	1/1	1/1	0/1	./.	1/1	1/1	1/1	./.	1/1	./.	./.	1/1	1/1	./.	./.	0/1	./.	1/1	1/1	1/1	1/1	1/1	./.	./.	./.	1/1	./.	1/1	1/1	1/1	./.	0/1	1/1	./.	0/1	./.	1/1	0/1	./.	0/0	./.	1/1	./.	1/1	./.
+chr1	219467766	.	AAC	A	.	PASS	VC=INDEL;AC=102;AF=0.32;AN=314	GT	0/0	1/1	1/1	0/0	1/1	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/0	1/1	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	1/1	0/1	1/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/1	0/1	0/0	0/1	0/0	1/1	1/1	0/0	0/1	0/0	0/0	0/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	0/1	1/1	0/0	1/1	0/1	0/1	0/1	1/1	1/1	1/1	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	./.	0/1	1/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	1/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	1/1	0/0	0/0	0/0	0/0	0/1	0/1
+chr1	219839015	.	C	CATGG	.	PASS	VC=INDEL;AC=73;AF=0.24;AN=306	GT	1/1	0/0	0/0	1/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	1/1	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	1/1	0/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	1/1	0/0	0/1	1/1	0/0	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	0/1	0/1	1/1	1/1	0/1	0/0	0/0	1/1	1/1	0/1	1/1	0/1	0/1	0/1	0/1	0/1	0/0	./.	0/1	0/1	0/0	1/1	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/1	0/1	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	1/1	0/1
+chr1	221137225	.	T	TCTT	.	PASS	VC=INDEL;AC=159;AF=0.61;AN=262	GT	0/0	./.	0/1	0/1	0/1	./.	1/1	1/1	./.	0/1	1/1	1/1	0/1	./.	0/1	0/1	0/1	1/1	1/1	0/1	0/1	0/1	0/1	1/1	0/1	1/1	0/1	0/0	0/0	0/1	1/1	0/1	./.	0/1	0/1	0/1	0/1	1/1	./.	0/1	0/1	0/0	0/1	0/1	./.	./.	0/1	0/0	0/1	0/1	./.	1/1	0/1	1/1	./.	0/1	1/1	0/0	0/1	./.	./.	./.	0/1	./.	0/1	./.	0/1	1/1	0/1	0/1	./.	0/1	0/1	0/0	0/0	./.	0/1	./.	0/1	0/1	1/1	0/1	1/1	0/0	1/1	./.	1/1	1/1	./.	0/1	0/1	0/0	./.	0/1	0/1	0/1	1/1	1/1	0/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	./.	1/1	0/1	1/1	0/1	1/1	./.	1/1	0/1	1/1	0/1	0/1	0/1	0/0	1/1	1/1	1/1	1/1	1/1	1/1	0/0	0/1	0/0	0/1	0/1	0/1	1/1	1/1	1/1	0/1	0/1	0/0	1/1	./.	1/1	0/1	0/1	0/1	./.	0/1	0/0	1/1	./.	./.	1/1	1/1	1/1	1/1	0/0	0/1	0/1	0/0
+chr1	221202698	.	GA	G	.	PASS	VC=INDEL;AC=82;AF=0.26;AN=310	GT	0/0	./.	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/1	0/0	0/1	1/1	./.	0/1	0/0	0/0	0/0	1/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/1	0/1	1/1	0/0	0/0	0/0	1/1	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/0	0/0	1/1	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/1	1/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/1	0/1	1/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	1/1	0/1	0/1	1/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0
+chr1	221279126	.	CC	C	.	PASS	VC=INDEL;AC=0;AF=0;AN=312	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	221315912	.	TTCT	T	.	PASS	VC=INDEL;AC=94;AF=0.3;AN=312	GT	1/1	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/1	1/1	0/0	0/0	0/1	0/1	0/0	1/1	0/1	1/1	0/0	0/0	0/0	1/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	1/1	0/0	0/1	0/0	0/0	0/1	0/0	1/1	0/1	0/1	0/0	0/0	0/1	0/1	1/1	0/0	0/1	0/0	0/1	1/1	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/1	1/1	0/1	1/1	0/0	0/1	0/1	0/0	0/0	1/1	./.	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	1/1	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/0	0/1	./.	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	1/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	1/1	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	1/1	0/1	0/1	0/0
+chr1	222205539	.	AATTGACC	A	.	PASS	VC=INDEL;AC=90;AF=0.29;AN=310	GT	1/1	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	./.	0/0	0/1	./.	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/1	1/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	1/1	0/1	./.	0/0	0/1	0/1	0/0	1/1	0/1	0/1	0/1	1/1	1/1	0/1	0/1	0/1	1/1	0/1	0/1	0/1	1/1	0/1	0/0	0/1	0/0	0/0	0/0	1/1	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/1	1/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/1
+chr1	222493300	.	T	TGA	.	PASS	VC=INDEL;AC=310;AF=0.98;AN=316	GT	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1
+chr1	222493301	.	G	GAG	.	PASS	VC=INDEL;AC=310;AF=0.98;AN=316	GT	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1
+chr1	222990213	.	ATTTG	A	.	PASS	VC=INDEL;AC=9;AF=0.04;AN=254	GT	0/1	0/0	0/0	0/0	./.	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	./.	./.	0/0	0/1	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	./.	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	./.	./.	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/1	./.	./.	./.	./.	0/1	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	./.	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	./.	./.	./.	0/0	./.	0/0	0/0	0/0	./.	./.	./.	./.	0/0	0/0	0/1
+chr1	223387015	.	CTG	C	.	PASS	VC=INDEL;AC=6;AF=0.02;AN=316	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	223657734	.	A	ATGAG	.	PASS	VC=INDEL;AC=231;AF=0.99;AN=234	GT	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	./.	./.	1/1	./.	1/1	1/1	./.	1/1	1/1	1/1	./.	./.	1/1	0/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	./.	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	./.	./.	./.	1/1	1/1	./.	1/1	1/1	./.	1/1	./.	1/1	1/1	./.	1/1	./.	./.	0/1	./.	1/1	./.	1/1	1/1	1/1	1/1	./.	1/1	0/1	./.	1/1	1/1	1/1	./.	1/1	./.	./.	1/1	1/1	1/1	./.	1/1	./.	1/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	./.	./.	1/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	./.	./.	1/1	1/1	1/1	1/1	1/1
+chr1	223984835	.	G	GAA	.	PASS	VC=INDEL;AC=194;AF=0.63;AN=306;refseq.name=NM_001031685;refseq.positionType=intron	GT	./.	1/1	0/1	./.	0/1	1/1	1/1	1/1	1/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	./.	0/1	0/0	./.	0/1	0/0	0/0	0/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	0/1	1/1	0/1	0/0	./.	0/0	0/1	0/0	0/1	0/1	0/0	1/1	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	1/1	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/0	1/1	0/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	0/0	0/0
+chr1	224264255	.	A	AG	.	PASS	VC=INDEL;AC=150;AF=0.66;AN=228	GT	0/1	1/1	0/1	0/1	1/1	./.	0/1	./.	1/1	1/1	./.	./.	./.	1/1	./.	0/1	0/0	./.	./.	0/1	1/1	0/1	0/1	0/1	./.	0/1	1/1	1/1	1/1	1/1	0/1	./.	1/1	./.	0/1	0/1	0/0	1/1	0/0	1/1	1/1	1/1	./.	1/1	./.	0/1	1/1	./.	0/1	1/1	1/1	1/1	1/1	1/1	./.	0/1	./.	1/1	1/1	0/1	1/1	1/1	./.	0/1	1/1	0/1	1/1	./.	1/1	./.	0/1	1/1	0/0	./.	1/1	1/1	./.	./.	1/1	1/1	0/1	./.	0/0	0/1	0/1	./.	0/0	1/1	0/1	0/1	1/1	./.	1/1	./.	./.	1/1	0/0	0/1	./.	1/1	0/0	./.	0/1	0/0	0/1	./.	./.	1/1	1/1	0/1	0/1	0/1	0/1	0/0	1/1	0/1	0/1	0/1	./.	0/0	0/1	0/1	1/1	0/1	./.	0/0	1/1	./.	./.	./.	./.	1/1	./.	1/1	0/1	0/1	1/1	0/1	0/1	1/1	./.	1/1	./.	./.	0/1	0/1	0/0	0/0	1/1	0/1	0/1	0/1	./.	0/1	0/1	0/1	./.	./.
+chr1	224264346	.	TGAG	T	.	PASS	VC=INDEL;AC=154;AF=0.63;AN=244	GT	0/1	1/1	0/1	0/1	1/1	./.	./.	1/1	./.	1/1	0/0	1/1	1/1	./.	0/1	./.	0/1	./.	1/1	0/1	1/1	0/1	0/1	./.	0/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	./.	0/1	0/1	0/0	./.	0/0	1/1	1/1	1/1	0/1	1/1	./.	0/1	1/1	./.	0/1	1/1	1/1	1/1	1/1	1/1	./.	0/1	./.	1/1	1/1	0/1	1/1	1/1	0/1	0/1	./.	./.	./.	0/1	./.	1/1	0/1	./.	0/0	./.	./.	1/1	0/1	./.	1/1	./.	0/1	./.	0/0	0/1	0/1	./.	0/0	1/1	0/1	0/1	./.	1/1	./.	0/1	0/1	1/1	0/0	0/1	./.	1/1	0/0	0/0	0/1	0/0	0/1	1/1	1/1	1/1	1/1	./.	0/1	0/1	0/1	0/0	1/1	0/1	./.	0/1	0/1	./.	0/1	0/1	./.	0/1	0/0	0/0	1/1	./.	0/1	1/1	0/1	./.	0/1	1/1	0/1	./.	1/1	0/1	0/1	./.	0/1	1/1	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/1	1/1	0/1	0/1	./.	1/1	0/1
+chr1	224833844	.	A	AAGACGTAAGACAGT	.	PASS	VC=INDEL;AC=215;AF=0.68;AN=314;refseq.name=NM_152495;refseq.positionType=intron	GT	0/0	0/0	0/1	0/1	1/1	0/1	0/1	0/1	0/1	0/0	1/1	0/1	0/0	1/1	1/1	0/1	1/1	0/0	0/0	0/1	0/1	0/0	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	0/1	0/1	0/1	0/1	0/1	1/1	1/1	0/1	0/1	0/1	0/1	1/1	0/0	1/1	0/0	1/1	1/1	0/1	1/1	0/1	0/1	0/1	1/1	1/1	0/1	0/0	1/1	0/1	1/1	1/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	./.	0/0	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	0/1	1/1	0/1	0/1	0/0	1/1	0/1	0/1	1/1	0/1	0/1	0/1	0/0	0/0	1/1	0/1	0/1	1/1	1/1	1/1	0/0	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/0
+chr1	225662220	.	CT	C	.	PASS	VC=INDEL;AC=203;AF=0.66;AN=306	GT	0/1	1/1	0/1	0/1	1/1	0/1	./.	0/0	./.	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/0	1/1	0/1	1/1	1/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	1/1	0/1	1/1	0/0	0/0	1/1	1/1	1/1	0/1	0/1	0/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	./.	0/1	0/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	0/0	1/1	1/1	1/1	1/1	1/1	1/1	./.	0/1	1/1	0/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	./.	0/0	0/1	1/1	0/1	0/0	1/1	0/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	0/1	0/0	0/1	1/1	1/1	1/1	1/1	0/0	0/1	0/1	0/0	0/1	0/1	0/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	0/1	0/1	0/0	0/1	0/0	0/1	1/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1
+chr1	225974486	.	T	TG	.	PASS	VC=INDEL;AC=187;AF=0.6;AN=310;refseq.name=NM_003133;refseq.positionType=intron	GT	0/1	0/1	0/0	1/1	0/1	0/1	0/0	1/1	0/0	0/1	0/1	0/1	0/1	1/1	0/0	1/1	0/1	1/1	0/1	0/0	0/0	1/1	1/1	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/0	0/1	0/1	1/1	1/1	0/1	0/1	0/0	1/1	0/0	0/1	0/0	./.	1/1	1/1	0/1	1/1	0/1	0/1	0/1	1/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	0/0	1/1	1/1	1/1	0/1	0/1	./.	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	0/1	1/1	0/1	0/1	0/1	1/1	1/1	0/0	0/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	0/1	./.	1/1	0/1	0/1	1/1	0/1	1/1	0/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/0	1/1	0/1	1/1	0/1	1/1	1/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1
+chr1	225974487	.	G	GG	.	PASS	VC=INDEL;AC=189;AF=0.6;AN=314;refseq.name=NM_003133;refseq.positionType=intron	GT	0/1	0/1	0/0	1/1	0/1	0/1	0/0	1/1	0/0	0/1	0/1	0/1	0/1	1/1	0/0	1/1	0/0	1/1	0/1	0/0	0/0	1/1	1/1	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/0	0/1	0/1	1/1	1/1	0/1	0/1	0/0	1/1	0/0	0/1	0/0	1/1	1/1	1/1	0/1	1/1	0/1	0/1	0/1	1/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	0/0	1/1	1/1	1/1	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	0/1	1/1	0/1	0/1	0/1	1/1	1/1	0/0	0/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	0/1	./.	1/1	0/1	0/1	1/1	0/1	1/1	0/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/0	1/1	0/1	1/1	0/1	1/1	1/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1
+chr1	226014266	.	ATGG	A	.	PASS	VC=INDEL;AC=30;AF=0.1;AN=310;refseq.name=NM_000120;refseq.positionType=intron	GT	0/0	0/1	1/1	0/0	0/1	./.	0/0	0/0	0/0	0/0	./.	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	1/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/1	1/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.
+chr1	226014267	.	TGGT	T	.	PASS	VC=INDEL;AC=31;AF=0.1;AN=316;refseq.name=NM_000120;refseq.positionType=intron	GT	0/0	0/1	1/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	1/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/1	1/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1
+chr1	226878226	.	ACTC	A	.	PASS	VC=INDEL;AC=45;AF=0.15;AN=306;refseq.name=NM_002221;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	1/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	./.	1/1	0/0	0/0	0/0	0/1	1/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	./.	./.	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	1/1	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/1	0/0	0/0	0/0	1/1	./.	0/0	0/0	0/0	1/1	0/0	0/0	0/1	0/1	0/1	1/1	1/1	1/1	0/0	0/1	0/1	1/1	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0
+chr1	226878233	.	CTAC	C	.	PASS	VC=INDEL;AC=60;AF=0.21;AN=292;refseq.name=NM_002221;refseq.positionType=intron	GT	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	1/1	1/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/1	1/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	1/1	0/1	0/1	0/1	./.	./.	1/1	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/1	./.	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	./.	0/1	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/1	0/0	1/1	0/0	0/1	0/0	0/0	./.	1/1	./.	./.	0/0	0/0	0/0	1/1	0/0	0/1	0/1	./.	0/0	./.	0/0	0/0	0/1	0/1	0/0	./.	0/0	./.	0/1	0/0
+chr1	226913049	.	GCCA	G	.	PASS	VC=INDEL;AC=14;AF=0.05;AN=302;refseq.name=NM_002221;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	./.	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	./.	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	./.	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0
+chr1	226913051	.	CACC	C	.	PASS	VC=INDEL;AC=6;AF=0.02;AN=280;refseq.name=NM_002221;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	./.	0/0	./.	0/0	0/0	0/0	0/1	./.	0/1	0/0	0/0	0/0	0/0	0/0	0/0	./.	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	./.	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	./.	0/0	./.	0/0	0/0	./.	0/0	0/1	0/0	0/0	0/0	0/0	0/0
+chr1	227051261	.	G	GC	.	PASS	VC=INDEL;AC=21;AF=0.07;AN=314	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	227252431	.	TTTC	T	.	PASS	VC=INDEL;AC=21;AF=0.07;AN=316;refseq.name=NM_003607;refseq.positionType=intron	GT	0/1	1/1	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1
+chr1	227401072	.	GC	G	.	PASS	VC=INDEL;AC=122;AF=0.39;AN=316;refseq.name=NM_003607;refseq.positionType=intron	GT	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	1/1	0/1	0/0	0/0	0/1	1/1	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	1/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/1	1/1	1/1	0/1	1/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/1	1/1	1/1	1/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/1	1/1	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	1/1	1/1	0/1	0/1	0/0	0/1	0/1	1/1	1/1	0/1	1/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	1/1	0/1	0/0	0/0
+chr1	227560279	.	G	GTCATAG	.	PASS	VC=INDEL;AC=316;AF=1;AN=316	GT	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1
+chr1	228479392	.	ATG	A	.	PASS	VC=INDEL;AC=12;AF=0.04;AN=316;refseq.name=NM_001098623;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	229074693	.	TAGAGG	T	.	PASS	VC=INDEL;AC=102;AF=0.32;AN=316	GT	0/1	0/1	0/1	1/1	0/1	1/1	1/1	0/0	0/0	0/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	0/1	1/1	0/1	0/0	0/1	0/1	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/0	1/1	0/0	1/1	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/1	1/1	0/1	0/1	1/1	0/1	0/0	0/0	0/0	1/1	0/1	0/1	1/1	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	1/1	1/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	1/1	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	1/1	1/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/1	1/1	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/1
+chr1	229075090	.	ATAGCCTG	A	.	PASS	VC=INDEL;AC=30;AF=0.11;AN=264	GT	1/1	0/0	0/0	./.	0/0	./.	./.	0/0	0/0	0/0	0/0	./.	./.	./.	0/0	0/0	./.	0/0	0/0	./.	./.	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/1	./.	0/0	./.	0/1	0/0	0/1	0/0	0/1	0/0	./.	0/0	0/0	0/1	./.	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	./.	0/0	0/1	0/0	0/0	0/1	0/0	0/0	./.	0/0	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/1	./.	./.	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/1	0/0	0/0	./.	0/0	./.	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	./.	./.
+chr1	229336842	.	CATTT	C	.	PASS	VC=INDEL;AC=19;AF=0.06;AN=300	GT	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	./.	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	./.	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	./.	0/1	0/1	0/1	./.	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/0	./.	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0
+chr1	229631495	.	A	AC	.	PASS	VC=INDEL;AC=0;AF=0;AN=316;refseq.name=NM_018230;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	229922597	.	CCTT	C	.	PASS	VC=INDEL;AC=144;AF=0.46;AN=316	GT	0/1	0/1	1/1	0/1	0/1	0/1	1/1	0/0	0/0	0/1	0/0	1/1	1/1	0/1	1/1	1/1	0/1	0/1	1/1	0/0	0/1	1/1	0/1	1/1	0/0	0/1	0/1	0/0	0/1	0/1	1/1	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/0	1/1	0/1	0/1	0/0	0/1	0/1	1/1	0/1	0/1	0/1	1/1	1/1	0/1	1/1	0/1	0/1	1/1	0/1	0/1	0/0	0/1	0/0	1/1	0/1	1/1	0/0	0/1	0/1	0/1	0/1	1/1	1/1	0/1	0/1	0/0	1/1	1/1	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/1	1/1	0/1	0/1	1/1	0/1	0/0	0/0	0/1	0/1	1/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/0	1/1	0/0	0/1	0/0	1/1	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/1	1/1	0/1	1/1
+chr1	229922599	.	TTCT	T	.	PASS	VC=INDEL;AC=142;AF=0.45;AN=314	GT	0/1	0/1	1/1	0/1	0/1	0/1	1/1	0/0	0/0	0/1	0/0	1/1	1/1	0/1	1/1	1/1	0/1	0/1	1/1	0/0	0/1	1/1	0/1	1/1	0/0	0/1	0/1	0/0	0/1	0/1	1/1	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/0	1/1	0/1	0/1	0/0	0/1	0/1	1/1	0/1	0/1	0/1	1/1	1/1	0/1	1/1	0/1	0/1	1/1	0/1	0/1	0/0	0/1	0/0	1/1	0/1	1/1	0/0	0/1	0/1	0/1	0/1	1/1	1/1	0/1	0/1	0/0	1/1	1/1	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/1	1/1	0/1	0/1	./.	0/1	0/0	0/0	0/1	0/1	1/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/0	1/1	0/0	0/1	0/0	1/1	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/1	1/1	0/1	1/1
+chr1	230272407	.	GAG	G	.	PASS	VC=INDEL;AC=15;AF=0.05;AN=314;refseq.name=NM_004481;refseq.positionType=intron	GT	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	./.	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	230625946	.	T	TGA	.	PASS	VC=INDEL;AC=302;AF=0.96;AN=316	GT	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1
+chr1	230626726	.	CTTTAAGTCCTGT	C	.	PASS	VC=INDEL;AC=59;AF=0.19;AN=314	GT	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	1/1	1/1	1/1	1/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	1/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	1/1	0/1	0/0	0/0	0/0	0/0
+chr1	230626728	.	TTAAGTCCTGTTT	T	.	PASS	VC=INDEL;AC=59;AF=0.19;AN=316	GT	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	1/1	1/1	1/1	1/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	1/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	1/1	0/1	0/0	0/0	0/0	0/0
+chr1	230697057	.	ACA	A	.	PASS	VC=INDEL;AC=152;AF=0.48;AN=316	GT	0/1	1/1	1/1	0/0	1/1	0/0	1/1	0/0	0/0	1/1	1/1	1/1	0/0	0/1	1/1	0/1	1/1	0/1	0/1	1/1	0/0	1/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	1/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/1	1/1	0/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/0	1/1	0/1	0/1	0/1	0/1	0/1	1/1	1/1	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/1	1/1	0/1	0/0	0/0	0/1	0/1	0/1	1/1	0/1	1/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	1/1	0/1	0/1	1/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	1/1	0/1	0/1	0/1	1/1	0/1	1/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	1/1	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	1/1	0/0
+chr1	230952100	.	GG	G	.	PASS	VC=INDEL;AC=34;AF=0.11;AN=316	GT	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	1/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	1/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1
+chr1	232200072	.	CGACT	C	.	PASS	VC=INDEL;AC=86;AF=0.28;AN=312	GT	0/0	0/1	0/0	0/1	0/0	0/1	0/0	1/1	0/0	0/1	0/0	1/1	0/1	0/0	0/0	0/1	./.	1/1	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	1/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	./.	0/1	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/1	1/1	0/1	0/1	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/0	1/1	0/1	1/1	0/1	1/1	0/0	0/0	0/0	0/1	0/1	1/1	0/1	0/1	1/1	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/1
+chr1	232606995	.	GTCTG	G	.	PASS	VC=INDEL;AC=54;AF=0.17;AN=316;refseq.name=NM_020808;refseq.positionType=intron	GT	0/0	0/0	0/0	1/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	1/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	1/1	0/1	1/1
+chr1	232883964	.	G	GTT	.	PASS	VC=INDEL;AC=279;AF=0.88;AN=316	GT	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	0/1	0/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	0/0	0/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	0/1	1/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	1/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1
+chr1	232883965	.	T	TTT	.	PASS	VC=INDEL;AC=279;AF=0.88;AN=316	GT	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	0/1	0/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	0/0	0/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	0/1	1/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	1/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1
+chr1	232944224	.	AAGAA	A	.	PASS	VC=INDEL;AC=17;AF=0.05;AN=316;refseq.name=NM_019090;refseq.positionType=exon	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	1/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	233013835	.	C	CT	.	PASS	VC=INDEL;AC=38;AF=0.18;AN=214	GT	0/0	./.	0/0	./.	0/0	0/0	0/0	0/1	./.	./.	0/1	0/0	./.	0/0	0/0	0/0	./.	./.	0/0	0/0	0/0	./.	0/0	./.	0/1	1/1	./.	./.	./.	1/1	0/0	./.	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	./.	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/1	./.	0/0	0/0	0/0	0/1	1/1	1/1	0/1	./.	./.	0/0	./.	0/0	0/0	0/0	./.	./.	0/1	0/0	./.	./.	./.	0/1	./.	0/1	0/1	./.	./.	./.	0/0	0/1	./.	0/1	0/0	0/0	./.	./.	0/0	0/0	0/0	0/0	0/1	0/0	./.	./.	0/0	0/0	./.	1/1	0/1	./.	1/1	0/1	0/0	./.	0/0	1/1	./.	./.	0/0	1/1	./.	./.	0/0	./.	1/1	./.	1/1	./.	./.	0/0	./.	./.
+chr1	233013837	.	T	TT	.	PASS	VC=INDEL;AC=78;AF=0.25;AN=310	GT	0/1	./.	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/0	./.	0/1	0/0	0/0	1/1	1/1	0/1	0/1	0/1	1/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	1/1	0/1	0/1	0/0	0/0	0/0	0/1	1/1	1/1	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/1	1/1	0/1	0/1	1/1	0/1	0/0	0/1	0/0	1/1	0/1	0/1	0/0	1/1	0/1	0/1	0/1	0/1	1/1	0/1	1/1	0/0	0/0	0/0	0/0	0/0
+chr1	233458691	.	ACAC	A	.	PASS	VC=INDEL;AC=18;AF=0.06;AN=314	GT	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	./.	0/0	0/1
+chr1	233593090	.	TT	T	.	PASS	VC=INDEL;AC=257;AF=0.82;AN=312	GT	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	./.	1/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	0/0	1/1	1/1	1/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	0/0	0/0	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	0/0	0/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	0/0	0/1	1/1	0/1	0/1	0/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/0	1/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	0/0	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1
+chr1	233991847	.	T	TCA	.	PASS	VC=INDEL;AC=220;AF=0.72;AN=306	GT	1/1	1/1	./.	1/1	0/1	1/1	0/1	0/1	0/1	0/1	1/1	0/0	0/1	1/1	1/1	0/1	1/1	0/0	0/1	1/1	1/1	./.	0/1	0/0	1/1	1/1	1/1	0/1	1/1	0/1	1/1	0/0	0/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/0	0/0	1/1	0/1	1/1	1/1	1/1	0/0	1/1	1/1	./.	1/1	1/1	1/1	0/1	0/1	1/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	0/1	0/0	1/1	1/1	1/1	0/1	0/0	0/0	0/1	0/1	0/1	1/1	1/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	0/1	0/1	0/1	0/0	0/1	1/1	1/1	0/1	0/1	./.	0/1	0/1	0/1	1/1	1/1	1/1	1/1	./.	0/1	0/1	1/1	0/1	0/0	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/0	0/1	0/0	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	0/1
+chr1	234635298	.	G	GT	.	PASS	VC=INDEL;AC=205;AF=0.65;AN=316	GT	0/1	0/0	0/0	0/1	0/0	1/1	0/0	1/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	0/0	1/1	1/1	1/1	0/0	1/1	1/1	1/1	1/1	1/1	1/1	0/0	1/1	0/1	0/1	0/0	1/1	1/1	0/1	1/1	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/1	1/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/0	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/0	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	0/0
+chr1	234704346	.	TCT	T	.	PASS	VC=INDEL;AC=36;AF=0.12;AN=312	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/1	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	1/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	./.	0/1	0/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0
+chr1	235770627	.	AATTA	A	.	PASS	VC=INDEL;AC=56;AF=0.18;AN=316;refseq.name=NM_004485;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/1	1/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/1	1/1	0/0	1/1	0/1	0/0	0/0	0/0	0/1	1/1	1/1	1/1	0/0	0/1	0/0	0/1	0/1	0/1	1/1	1/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	236043714	.	ATCCTGTGTTGATTTA	A	.	PASS	VC=INDEL;AC=6;AF=0.02;AN=294	GT	./.	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	./.	0/0	./.	0/0	./.	0/0	0/0	0/0	0/0	./.	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	236043717	.	CTGTGTTGATTTATTA	C	.	PASS	VC=INDEL;AC=5;AF=0.02;AN=316	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	236118487	.	TT	T	.	PASS	VC=INDEL;AC=12;AF=0.04;AN=316	GT	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0
+chr1	236195380	.	GTG	G	.	PASS	VC=INDEL;AC=163;AF=0.52;AN=316;refseq.name=NM_002508;refseq.positionType=intron	GT	0/1	1/1	0/1	0/1	0/1	0/0	0/0	0/1	0/0	1/1	0/1	0/0	0/0	0/1	0/1	0/0	1/1	0/0	0/1	0/1	0/0	1/1	0/0	0/1	0/0	0/1	0/0	1/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/1	1/1	1/1	0/1	0/1	1/1	0/1	1/1	0/1	0/1	1/1	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/1	1/1	0/1	0/1	0/0	1/1	0/0	1/1	0/0	0/1	1/1	0/1	0/1	1/1	0/1	0/0	1/1	1/1	1/1	1/1	1/1	0/0	1/1	0/1	1/1	1/1	1/1	0/0	1/1	0/1	0/1	1/1	0/1	1/1	0/0	0/1	0/0	0/1	0/1	1/1	0/1	0/0	0/0	1/1	0/0	0/1	0/0	1/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	1/1	0/1	1/1	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/0	0/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	0/1	1/1	0/0	0/1
+chr1	236375505	.	T	TG	.	PASS	VC=INDEL;AC=130;AF=0.42;AN=310	GT	0/0	./.	0/0	0/0	0/0	1/1	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	1/1	1/1	0/1	1/1	0/1	0/1	0/1	0/1	0/0	0/1	1/1	0/0	0/0	0/1	0/1	0/1	0/1	0/0	./.	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/0	./.	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/0	1/1	1/1	1/1	0/1	0/1	0/1	0/1	0/0	0/0	0/1	1/1	0/1	0/0	0/1	0/1	1/1	0/0	1/1	0/1	0/0	1/1	0/1	0/1	1/1	0/1	0/1	0/0	0/0	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	0/0	1/1	0/1	0/1	0/0	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	1/1	0/1	0/1	0/1	0/1	0/0	0/0
+chr1	236555148	.	T	TA	.	PASS	VC=INDEL;AC=3;AF=0.01;AN=316;refseq.name=NM_145861;refseq.positionType=promoter	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0
+chr1	236723352	.	CGACCTCGCTCAGACTCTGTGAGGTGCTGAATAAGCAACA	C	.	PASS	VC=INDEL;AC=72;AF=0.23;AN=314;refseq.name=NM_018072;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	1/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	1/1	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/1	1/1	1/1	0/1	1/1	0/1	0/1	1/1	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	1/1	0/1	0/0	1/1	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0
+chr1	236723354	.	ACCTCGCTCAGACTCTGTGAGGTGCTGAATAAGCAACAGA	A	.	PASS	VC=INDEL;AC=72;AF=0.23;AN=312;refseq.name=NM_018072;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	./.	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	1/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	1/1	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/1	1/1	1/1	0/1	1/1	0/1	0/1	1/1	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	1/1	0/1	0/0	1/1	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0
+chr1	236848307	.	A	AG	.	PASS	VC=INDEL;AC=62;AF=0.21;AN=300;refseq.name=NM_001103;refseq.positionType=promoter	GT	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	./.	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	./.	./.	0/0	1/1	0/0	1/1	0/0	0/0	0/0	0/1	0/0	1/1	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	1/1	1/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	./.	0/1	./.	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	./.	0/1	./.	0/1	0/0	0/0	0/0	./.	0/0	0/0	0/0	1/1	0/1	0/1	0/0	0/0	0/1	0/0	1/1	0/0	0/0	0/0	0/0	0/0
+chr1	237009685	.	TAGC	T	.	PASS	VC=INDEL;AC=6;AF=0.02;AN=292;refseq.name=NM_000254;refseq.positionType=intron	GT	0/1	0/0	0/0	./.	0/1	0/0	0/0	./.	0/0	0/0	./.	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/1	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	237009687	.	GCAG	G	.	PASS	VC=INDEL;AC=3;AF=0.01;AN=304;refseq.name=NM_000254;refseq.positionType=intron	GT	0/1	0/0	0/0	0/0	./.	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	237055125	.	CA	C	.	PASS	VC=INDEL;AC=9;AF=0.03;AN=284;refseq.name=NM_000254;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	./.	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/1	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/1	0/0	./.	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/1	./.	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	./.	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	237277023	.	C	CA	.	PASS	VC=INDEL;AC=18;AF=0.06;AN=312;refseq.name=NM_001035;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1
+chr1	237535965	.	AA	A	.	PASS	VC=INDEL;AC=0;AF=0;AN=280;refseq.name=NM_001035;refseq.positionType=intron	GT	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	./.	./.	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	./.	0/0
+chr1	237539975	.	GCTTGA	G	.	PASS	VC=INDEL;AC=3;AF=0.01;AN=316;refseq.name=NM_001035;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0
+chr1	237649833	.	C	CTCTT	.	PASS	VC=INDEL;AC=140;AF=0.45;AN=312;refseq.name=NM_001035;refseq.positionType=intron	GT	1/1	0/1	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/1	1/1	1/1	0/1	1/1	0/1	0/0	0/1	0/0	0/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	1/1	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/0	0/1	0/1	0/0	1/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	1/1	0/1	0/0	0/1	0/1	0/1	0/1	1/1	0/0	0/1	0/0	1/1	0/1	0/1	0/1	1/1	0/1	0/0	0/1	1/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	1/1	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/0	1/1	0/1	0/0	./.	0/0	1/1	0/1	./.	1/1	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/0	1/1	0/1	0/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/0	1/1	0/1	0/1	1/1	0/1	1/1	0/1	0/1
+chr1	237649835	.	C	CTTTC	.	PASS	VC=INDEL;AC=138;AF=0.44;AN=312;refseq.name=NM_001035;refseq.positionType=intron	GT	1/1	0/1	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/1	1/1	1/1	0/1	1/1	0/1	0/0	0/1	0/0	0/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	1/1	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/0	0/1	0/1	0/0	1/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	1/1	0/1	0/0	0/1	0/1	0/1	0/1	1/1	0/0	0/1	0/0	1/1	0/1	0/1	0/1	1/1	0/1	0/0	0/1	1/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	1/1	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/0	1/1	0/1	0/0	0/0	0/0	1/1	0/1	./.	1/1	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/0	1/1	0/1	0/1	1/1	1/1	0/1	0/1	1/1	./.	1/1	1/1	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/0	1/1	0/1	0/1	1/1	0/1	1/1	0/1	0/1
+chr1	237995162	.	T	TTTGA	.	PASS	VC=INDEL;AC=301;AF=0.96;AN=312;refseq.name=NM_001035;refseq.positionType=intron	GT	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/0	1/1	0/1	1/1	1/1	./.	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1
+chr1	238017296	.	T	TCT	.	PASS	VC=INDEL;AC=80;AF=0.25;AN=316	GT	0/0	0/0	0/0	0/1	0/0	0/1	1/1	0/0	1/1	0/0	0/0	0/0	0/0	1/1	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/1	1/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/0	1/1	0/1	0/1	0/0	1/1	0/1	1/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	1/1	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/1	1/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	1/1	1/1	1/1	0/1	0/1	0/0	0/1	1/1	1/1	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/1	1/1	0/1	0/0
+chr1	238125441	.	AGA	A	.	PASS	VC=INDEL;AC=26;AF=0.08;AN=316	GT	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1
+chr1	238152842	.	C	CGTAA	.	PASS	VC=INDEL;AC=165;AF=0.52;AN=316	GT	0/1	0/0	0/1	0/0	0/1	0/1	0/1	1/1	1/1	0/0	0/1	0/1	0/1	0/1	1/1	0/0	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/0	1/1	1/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/1	1/1	0/1	0/1	0/1	1/1	0/1	0/0	0/1	0/1	1/1	0/1	0/0	0/0	1/1	0/1	0/1	1/1	1/1	1/1	0/0	0/1	1/1	0/1	0/1	0/0	0/0	1/1	1/1	0/1	0/1	0/0	0/1	1/1	0/1	1/1	0/0	0/1	0/0	1/1	1/1	0/0	0/1	1/1	0/0	0/1	1/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/0	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	0/0	0/0	0/1	1/1	0/1	0/1	1/1	0/1	0/1	0/1	0/0	0/1	1/1	0/1	0/1	0/1	1/1	0/0	0/0	0/0	0/0	1/1	0/1	1/1	0/0	0/1	0/1	0/0	0/0	0/0	1/1	0/1	0/0	1/1	0/1	1/1	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/0	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	0/1	1/1	0/0
+chr1	238152845	.	A	AAGTA	.	PASS	VC=INDEL;AC=166;AF=0.53;AN=316	GT	0/1	0/0	0/1	0/0	0/1	0/1	0/1	1/1	1/1	0/0	0/1	0/1	0/1	0/1	1/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/0	1/1	1/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/1	1/1	0/1	0/1	0/1	1/1	0/1	0/0	0/1	0/1	1/1	0/1	0/0	0/0	1/1	0/1	0/1	1/1	1/1	1/1	0/0	0/1	1/1	0/1	0/1	0/0	0/0	1/1	1/1	0/1	0/1	0/0	0/1	1/1	0/1	1/1	0/0	0/1	0/0	1/1	1/1	0/0	0/1	1/1	0/0	0/1	1/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/0	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	0/0	0/0	0/1	1/1	0/1	0/1	1/1	0/1	0/1	0/1	0/0	0/1	1/1	0/1	0/1	0/1	1/1	0/0	0/0	0/0	0/0	1/1	0/1	1/1	0/0	0/1	0/1	0/0	0/0	0/0	1/1	0/1	0/0	1/1	0/1	1/1	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/0	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	0/1	1/1	0/0
+chr1	238257585	.	TGAT	T	.	PASS	VC=INDEL;AC=159;AF=0.61;AN=262	GT	1/1	1/1	1/1	0/1	1/1	0/1	0/1	0/0	0/1	1/1	0/1	1/1	1/1	./.	1/1	0/1	./.	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	1/1	1/1	0/1	0/1	1/1	0/1	./.	0/0	1/1	1/1	1/1	0/1	1/1	0/0	1/1	1/1	1/1	1/1	1/1	./.	0/1	./.	1/1	1/1	0/1	./.	1/1	1/1	1/1	1/1	./.	1/1	1/1	./.	0/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	0/1	0/1	0/1	0/1	1/1	1/1	0/1	0/1	0/1	0/0	0/1	0/0	./.	0/0	0/1	./.	0/0	0/0	0/1	./.	0/1	0/1	0/0	0/0	1/1	./.	0/1	0/1	./.	0/1	./.	0/1	./.	0/1	0/0	./.	0/0	0/1	0/1	1/1	0/1	0/1	1/1	0/1	0/1	./.	0/1	1/1	1/1	1/1	0/1	1/1	0/0	0/1	./.	1/1	0/1	1/1	./.	./.	0/0	1/1	0/1	./.	0/0	0/0	0/0	0/0	0/1	0/0	./.	0/0	0/1	0/1	./.	./.	./.	0/1	0/1	./.	./.	0/1	1/1	1/1
+chr1	238476744	.	A	ATCTA	.	PASS	VC=INDEL;AC=283;AF=0.98;AN=290	GT	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	0/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	./.	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	./.	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	./.	1/1	./.	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	./.	1/1
+chr1	238497833	.	G	GAGAA	.	PASS	VC=INDEL;AC=232;AF=0.76;AN=304	GT	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	0/1	1/1	0/0	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/0	1/1	1/1	0/0	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/0	0/1	1/1	1/1	1/1	0/0	0/0	0/0	0/1	1/1	1/1	./.	1/1	1/1	0/1	0/0	0/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	0/0	0/0	1/1	1/1	1/1	0/1	1/1	0/1	0/1	1/1	./.	0/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	./.	1/1	0/0	0/1	0/0	0/0	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	./.	0/0	./.	./.	0/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	0/1
+chr1	238623394	.	C	CTTGA	.	PASS	VC=INDEL;AC=178;AF=0.58;AN=308	GT	0/0	1/1	1/1	0/1	1/1	0/0	1/1	0/0	0/1	0/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/0	0/0	0/1	1/1	0/0	0/1	0/1	1/1	0/1	1/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/0	1/1	1/1	1/1	0/0	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	0/1	0/1	0/0	0/1	0/1	0/0	1/1	./.	0/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	./.	./.	0/1	0/1	0/0	0/1	0/1	1/1	0/0	0/1	0/1	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/1	./.	0/1	1/1	0/0	0/1	0/1	0/1	1/1	0/0	1/1	0/1	0/1	1/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/0	1/1	1/1
+chr1	238699979	.	T	TATCT	.	PASS	VC=INDEL;AC=97;AF=0.31;AN=314	GT	0/0	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/0	0/0	0/0	1/1	1/1	0/1	0/1	0/0	1/1	0/0	1/1	0/1	1/1	0/1	1/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	1/1	0/1	0/1	1/1	0/1	1/1	0/1	./.	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	0/1	0/0	0/1	0/1	0/0	1/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	0/0	1/1	1/1	0/0	1/1	0/0	0/1	1/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1
+chr1	238921290	.	CATTCAT	C	.	PASS	VC=INDEL;AC=188;AF=0.59;AN=316	GT	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/1	1/1	0/1	0/1	0/1	0/0	0/1	0/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	0/0	0/0	0/0	0/1	0/1	1/1	0/1	0/1	1/1	0/1	0/0	0/1	0/0	1/1	1/1	0/1	0/0	0/0	0/0	1/1	0/0	0/0	1/1	0/1	0/0	0/1	1/1	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/1	1/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	0/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	0/0	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	0/0	1/1	0/1	0/1	0/0
+chr1	238933453	.	C	CA	.	PASS	VC=INDEL;AC=26;AF=0.08;AN=314	GT	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/1	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	238933454	.	A	AA	.	PASS	VC=INDEL;AC=25;AF=0.08;AN=314	GT	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	239644576	.	C	CAA	.	PASS	VC=INDEL;AC=46;AF=0.15;AN=300	GT	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	1/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/1	./.	./.	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/1	./.	1/1	0/0	0/1	0/1	0/0	./.	0/1	0/0	0/0	0/0	0/0	1/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	./.	0/0	0/0	./.	0/0	0/0	0/0	0/1	0/0	./.	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/0	./.	0/0	0/1	0/1	0/0	0/0	0/0	0/0
+chr1	240115184	.	GAAG	G	.	PASS	VC=INDEL;AC=62;AF=0.2;AN=316	GT	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	1/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	1/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	1/1	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	1/1	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	1/1	0/1	0/1	0/0	0/1	0/1	0/0	0/1
+chr1	240170484	.	ATCA	A	.	PASS	VC=INDEL;AC=30;AF=0.1;AN=310	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	./.	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/0	./.	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/0
+chr1	240469105	.	A	ACT	.	PASS	VC=INDEL;AC=44;AF=0.14;AN=308;refseq.name=NM_020066;refseq.positionType=intron	GT	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	./.	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0
+chr1	240556294	.	A	AG	.	PASS	VC=INDEL;AC=180;AF=0.73;AN=248;refseq.name=NM_020066;refseq.positionType=intron	GT	./.	0/1	1/1	./.	1/1	0/1	1/1	1/1	./.	0/1	1/1	0/1	1/1	0/1	./.	0/0	1/1	1/1	0/0	0/1	1/1	1/1	1/1	0/0	1/1	1/1	1/1	./.	./.	./.	0/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	./.	0/1	0/1	0/1	./.	0/1	1/1	0/0	1/1	0/1	1/1	0/0	1/1	0/1	0/0	0/1	./.	1/1	1/1	1/1	0/1	0/1	1/1	0/0	1/1	./.	0/0	0/0	0/1	./.	0/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	0/0	0/1	0/1	1/1	0/1	./.	./.	./.	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	./.	0/1	1/1	0/1	./.	1/1	1/1	./.	1/1	0/1	./.	./.	0/1	./.	1/1	1/1	0/0	0/1	1/1	1/1	1/1	./.	./.	1/1	0/1	1/1	./.	./.	./.	./.	1/1	1/1	1/1	./.	./.	1/1	1/1	1/1	1/1	./.	0/1	0/1	0/0	./.	0/0	0/1	./.	0/1	1/1	0/1
+chr1	240750353	.	A	AT	.	PASS	VC=INDEL;AC=1;AF=0;AN=208;refseq.name=NM_022469;refseq.positionType=intron	GT	0/0	0/0	./.	./.	0/0	0/0	./.	./.	./.	0/0	./.	0/0	0/0	0/0	./.	0/0	./.	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	./.	./.	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	./.	./.	./.	./.	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	./.	./.	0/0	./.	0/0	./.	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	./.	./.	0/0	0/0	0/0	0/0	0/0	0/0	./.	./.	0/0	./.	0/0	./.	0/0	0/0	0/0	./.	./.	0/0	0/0	0/0	./.	./.	0/0	0/0	0/0	./.	0/0	0/0	./.	./.	0/0	./.	0/0	0/0	./.	0/0	./.	0/0	./.	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/1	./.	0/0	0/0	0/0	0/0	0/0	./.	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	./.	./.	./.	0/0	0/0	0/0	0/0	./.	./.	0/0	0/0	0/0	0/0	./.	0/0	0/0	./.	0/0	./.	0/0	0/0	0/0	0/0	./.
+chr1	241292738	.	CGAC	C	.	PASS	VC=INDEL;AC=16;AF=0.06;AN=254;refseq.name=NM_002924;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	./.	0/0	1/1	0/0	0/0	0/1	0/0	0/0	./.	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/1	./.	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	./.	0/1	./.	./.	0/0	./.	./.	./.	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/1	./.	./.	0/1	./.	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	./.	./.	0/0	./.	./.	0/0	0/0	./.	0/1	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	./.	./.	./.	0/0	./.	0/1	0/1	0/0	0/0
+chr1	241342365	.	TTCAA	T	.	PASS	VC=INDEL;AC=54;AF=0.18;AN=308;refseq.name=NM_002924;refseq.positionType=intron	GT	0/1	0/1	0/1	1/1	1/1	0/1	0/0	0/0	0/0	0/0	./.	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	1/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	1/1	0/0	1/1	0/1	0/1	0/1	0/0	0/1	0/1	0/0	1/1	0/0	./.	1/1	0/0	0/1	0/1	1/1	0/1	0/0	0/1	0/0	0/0	1/1	./.	0/1	0/0	0/1	0/1	0/1	0/1	0/0	1/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	1/1	0/1
+chr1	241864983	.	A	AGTCAAAC	.	PASS	VC=INDEL;AC=235;AF=0.75;AN=314;refseq.name=NM_144625;refseq.positionType=intron	GT	0/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	0/1	0/1	0/1	0/1	1/1	0/0	0/0	0/0	1/1	0/1	1/1	1/1	1/1	0/0	0/1	0/1	1/1	0/1	0/1	1/1	0/0	0/1	0/1	1/1	1/1	0/0	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/0	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	0/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/0
+chr1	241901460	.	ACTG	A	.	PASS	VC=INDEL;AC=126;AF=0.4;AN=316;refseq.name=NM_144625;refseq.positionType=intron	GT	0/0	0/0	0/1	0/1	0/1	0/0	0/0	1/1	1/1	0/1	0/1	0/1	0/1	1/1	0/0	1/1	0/1	0/0	0/1	1/1	0/1	1/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	1/1	0/1	1/1	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/1	1/1	0/0	0/0	1/1	1/1	1/1	0/0	0/0	1/1	0/1	0/1	0/1	0/1	1/1	0/1	0/0	0/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	1/1	0/0	0/1	0/1	0/1	1/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/1	1/1	0/1	0/1	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	1/1	1/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	1/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	1/1	0/1	0/0	0/0
+chr1	241920499	.	TGTAG	T	.	PASS	VC=INDEL;AC=5;AF=0.02;AN=316;refseq.name=NM_144625;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1
+chr1	241920501	.	TAGGT	T	.	PASS	VC=INDEL;AC=5;AF=0.02;AN=316;refseq.name=NM_144625;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1
+chr1	242055743	.	C	CTG	.	PASS	VC=INDEL;AC=47;AF=0.15;AN=314	GT	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	1/1	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	./.	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	1/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	1/1	0/0
+chr1	242257290	.	TC	T	.	PASS	VC=INDEL;AC=59;AF=0.22;AN=270;refseq.name=NM_152666;refseq.positionType=intron	GT	0/1	./.	0/1	0/0	0/0	0/1	0/1	0/1	1/1	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	./.	0/0	0/1	0/0	0/1	0/0	0/1	./.	./.	./.	0/1	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	./.	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/1	0/1	./.	./.	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/1	./.	0/0	./.	0/1	0/1	0/0	./.	0/1	0/0	./.	0/0	0/0	0/1	0/0	./.	0/0	0/0	./.	0/1	./.	0/0	0/0	0/0	0/1	./.	0/1	0/1	0/0	0/1	1/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	./.	0/1	./.	0/0	1/1	0/1	1/1	0/0	0/0	0/0	./.	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/1	./.	0/1	0/1	0/1	0/0
+chr1	242281287	.	T	TCT	.	PASS	VC=INDEL;AC=296;AF=0.95;AN=312;refseq.name=NM_152666;refseq.positionType=intron	GT	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	0/1	0/0	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1
+chr1	242328018	.	CATTACACTACTTTT	C	.	PASS	VC=INDEL;AC=97;AF=0.4;AN=244;refseq.name=NM_152666;refseq.positionType=intron	GT	1/1	0/1	0/1	./.	1/1	0/0	0/1	0/0	1/1	0/1	./.	0/0	./.	0/1	0/0	0/1	0/1	./.	0/1	0/0	1/1	0/0	0/1	./.	0/0	0/1	1/1	1/1	0/1	./.	0/0	0/1	1/1	0/1	1/1	0/0	./.	0/0	./.	1/1	0/0	0/1	0/1	0/0	0/1	0/1	./.	./.	./.	0/1	0/1	./.	0/0	1/1	0/1	0/1	0/1	0/1	./.	0/1	./.	1/1	./.	0/0	0/0	1/1	0/1	0/1	./.	1/1	0/1	1/1	0/1	./.	./.	1/1	0/1	0/1	0/1	./.	./.	0/0	1/1	0/1	./.	0/0	0/0	./.	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/1	0/1	./.	./.	0/1	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/1	./.	./.	0/0	0/1	0/1	0/1	./.	1/1	0/1	0/0	0/0	0/1	0/1	1/1	0/1	0/0	./.	0/0	0/1	0/0	0/1	0/0	0/1	./.	./.	0/1	1/1	0/0	0/1	0/0	0/1	1/1	0/0	0/1	./.	./.	./.	0/1	0/1	0/0	0/0	0/1	0/0	0/1	0/1	1/1	./.	0/0	0/0
+chr1	242602261	.	CC	C	.	PASS	VC=INDEL;AC=51;AF=0.16;AN=316;refseq.name=NM_152666;refseq.positionType=intron	GT	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	1/1	0/1	1/1	0/0	0/1	1/1	0/0	0/1	0/0	1/1	0/1	0/0	0/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1
+chr1	243409926	.	AAGTT	A	.	PASS	VC=INDEL;AC=99;AF=0.32;AN=312;refseq.name=NM_014812;refseq.positionType=intron	GT	1/1	1/1	0/0	0/1	0/1	1/1	0/0	0/1	0/0	0/1	0/0	0/1	0/0	1/1	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/1	1/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	1/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/1	1/1	0/0	0/1	0/0	1/1	1/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	1/1	0/0	0/1	0/1	0/0	1/1	1/1	0/0	0/1	0/0	1/1	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	./.	0/0	1/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	1/1
+chr1	243410210	.	G	GTAT	.	PASS	VC=INDEL;AC=137;AF=0.43;AN=316;refseq.name=NM_014812;refseq.positionType=intron	GT	0/1	0/1	1/1	1/1	1/1	0/0	1/1	0/0	0/0	1/1	0/0	1/1	0/1	0/0	1/1	0/1	1/1	0/0	0/1	1/1	1/1	1/1	1/1	1/1	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	1/1	0/0	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	1/1	1/1	1/1	1/1	1/1	1/1	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	1/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/1
+chr1	243435760	.	CATT	C	.	PASS	VC=INDEL;AC=26;AF=0.1;AN=272;refseq.name=NM_006642;refseq.positionType=intron	GT	0/1	0/0	0/0	0/0	./.	./.	0/0	0/0	0/0	0/0	./.	0/0	0/0	./.	0/0	0/1	./.	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	./.	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/1	0/0	./.	0/1	0/1	0/0	0/0	0/0	0/0	./.	0/0	0/0	./.	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	./.	0/0	0/1	./.	1/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/0	./.	0/0	0/0	0/0	0/0	0/1	./.	0/1	0/1	1/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	./.	./.
+chr1	244015225	.	GTCTG	G	.	PASS	VC=INDEL;AC=70;AF=0.22;AN=316	GT	0/0	1/1	0/1	0/1	0/0	0/1	0/1	0/1	0/0	1/1	0/0	0/1	0/1	0/1	1/1	0/1	0/1	0/0	0/0	0/1	0/0	0/1	0/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/1	1/1	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/0	1/1	0/1	1/1	0/0	1/1	0/1	0/0	0/0	0/0	0/0	0/1	1/1	0/1	0/0	0/1	1/1	0/0	0/1	0/1	0/1	1/1	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	1/1
+chr1	244033256	.	GTTGA	G	.	PASS	VC=INDEL;AC=18;AF=0.06;AN=316	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	244186794	.	T	TT	.	PASS	VC=INDEL;AC=0;AF=0;AN=316	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	244216819	.	T	TA	.	PASS	VC=INDEL;AC=79;AF=0.25;AN=316;refseq.name=NM_006352;refseq.positionType=exon	GT	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	1/1	0/0	0/1	0/0	0/0	0/1	0/0	1/1	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/0	1/1	1/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/1	0/0	1/1	0/1	0/1	0/1	0/1	1/1	0/1	1/1	0/0	0/1	0/0	1/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0
+chr1	244216822	.	A	AA	.	PASS	VC=INDEL;AC=79;AF=0.25;AN=312;refseq.name=NM_006352;refseq.positionType=exon	GT	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	1/1	0/0	0/1	0/0	0/0	0/1	0/0	1/1	1/1	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	./.	0/0	0/0	0/0	0/0	0/1	0/1	0/0	1/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/0	1/1	1/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/1	0/0	1/1	0/1	0/1	0/1	0/1	1/1	0/1	1/1	0/0	0/1	0/0	1/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0
+chr1	244371962	.	CAACTGGTCAAC	C	.	PASS	VC=INDEL;AC=2;AF=0.01;AN=314	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	244372739	.	C	CTA	.	PASS	VC=INDEL;AC=70;AF=0.22;AN=312	GT	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/0	1/1	0/0	0/1	0/0	0/0	1/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	./.	0/0	0/0	0/1	1/1	0/0	0/1	1/1	0/1	1/1	0/0	0/0	1/1	0/0	1/1	0/0	0/1	0/0	1/1	1/1	0/1	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	0/0	0/0	0/0	0/0	0/1	1/1	0/1	0/1	0/0	0/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	1/1	0/0	1/1	1/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/1
+chr1	244517491	.	A	AG	.	PASS	VC=INDEL;AC=229;AF=0.72;AN=316;refseq.name=NM_001012970;refseq.positionType=intron	GT	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	0/1	0/0	0/1	1/1	1/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	0/1	0/1	1/1	1/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/0	1/1	1/1	0/0	0/1	1/1	0/0	0/1	0/1	0/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	0/0	1/1	0/1	0/1	1/1	1/1	0/0	0/1	0/0	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/0	0/0	0/1	0/1	1/1	0/0	0/0	0/0	1/1	0/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	0/1
+chr1	244552134	.	CATTT	C	.	PASS	VC=INDEL;AC=41;AF=0.13;AN=314;refseq.name=NM_001012970;refseq.positionType=intron	GT	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/1	0/0	0/0	1/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	1/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/0	./.	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	244794244	.	T	TAAC	.	PASS	VC=INDEL;AC=2;AF=0.01;AN=316;refseq.name=NM_173807;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	245242885	.	A	ATT	.	PASS	VC=INDEL;AC=3;AF=0.01;AN=316;refseq.name=NM_032328;refseq.positionType=intron	GT	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1
+chr1	245242887	.	T	TTT	.	PASS	VC=INDEL;AC=3;AF=0.01;AN=316;refseq.name=NM_032328;refseq.positionType=intron	GT	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1
+chr1	245310839	.	T	TTAAAG	.	PASS	VC=INDEL;AC=156;AF=0.59;AN=266	GT	0/1	./.	0/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1	./.	1/1	1/1	1/1	0/0	0/1	0/1	./.	1/1	1/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	1/1	./.	1/1	0/0	0/0	0/1	./.	0/1	0/1	0/1	0/0	0/0	1/1	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/1	./.	./.	0/0	0/1	0/1	0/0	0/0	./.	0/1	./.	0/0	./.	./.	./.	1/1	0/1	0/1	0/0	0/1	0/0	0/0	0/1	1/1	0/1	1/1	./.	1/1	1/1	./.	0/1	0/1	1/1	1/1	0/0	./.	0/0	1/1	0/0	0/1	0/0	0/1	0/1	1/1	0/1	1/1	0/1	./.	1/1	./.	1/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	./.	./.	0/1	./.	0/1	0/0	0/1	0/0	1/1	0/0	0/1	./.	./.	./.	0/1	./.	1/1	1/1	1/1	0/1	0/1	0/1	1/1	./.	1/1
+chr1	245453003	.	G	GCCAA	.	PASS	VC=INDEL;AC=80;AF=0.26;AN=308;refseq.name=NM_018012;refseq.positionType=intron	GT	0/0	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/0	./.	0/0	0/1	./.	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/1	./.	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	./.	0/1	0/1	0/0	0/1
+chr1	245709104	.	A	AGTCAAC	.	PASS	VC=INDEL;AC=221;AF=0.7;AN=316;refseq.name=NM_018012;refseq.positionType=intron	GT	1/1	0/1	1/1	0/1	0/1	1/1	0/0	1/1	0/1	1/1	0/0	1/1	0/1	0/1	0/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1	1/1	1/1	0/1	0/1	1/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	0/1	1/1	0/1	0/1	1/1	0/0	0/0	1/1	0/1	0/1	0/1	0/0	1/1	0/1	1/1	0/1	1/1	1/1	1/1	0/0	0/1	0/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	0/0	0/1	1/1	0/1	0/1	0/1	0/1	0/0	1/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1	1/1	0/1	0/1	1/1	0/1	0/0	0/1	0/0	0/1	0/1	0/1	1/1	0/1	0/0	1/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	0/0	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1
+chr1	245868167	.	G	GTCTT	.	PASS	VC=INDEL;AC=138;AF=0.44;AN=316	GT	0/1	0/0	0/0	1/1	0/1	1/1	1/1	0/0	0/0	0/0	1/1	0/0	1/1	0/1	0/1	1/1	0/1	0/0	1/1	0/1	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/1	1/1	0/1	0/0	0/1	0/1	1/1	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/0	1/1	0/0	0/1	0/0	0/1	1/1	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/1	1/1	0/1	0/1	0/0	0/0	1/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/0	1/1	0/1	0/1	1/1	1/1	0/0	1/1	0/1	0/1	0/1	1/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/1	1/1	0/1	0/1	0/0	1/1	0/1	0/0	0/0	0/0	0/1	1/1	1/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/0	0/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	0/1	0/1	1/1	0/1	0/0	0/0
+chr1	245868172	.	T	TCTTT	.	PASS	VC=INDEL;AC=137;AF=0.43;AN=316	GT	0/1	0/0	0/0	1/1	0/1	1/1	1/1	0/0	0/0	0/0	1/1	0/0	1/1	0/1	0/1	1/1	0/1	0/0	1/1	0/1	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/1	1/1	0/1	0/0	0/1	0/1	1/1	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/0	1/1	0/0	0/1	0/0	0/1	1/1	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/1	1/1	0/1	0/1	0/0	0/0	1/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/0	1/1	0/1	0/1	0/1	1/1	0/0	1/1	0/1	0/1	0/1	1/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/1	1/1	0/1	0/1	0/0	1/1	0/1	0/0	0/0	0/0	0/1	1/1	1/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/0	0/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	0/1	0/1	1/1	0/1	0/0	0/0
+chr1	246124841	.	A	AAACAGAAG	.	PASS	VC=INDEL;AC=316;AF=1;AN=316;refseq.name=NM_022743;refseq.positionType=intron	GT	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1
+chr1	246124843	.	A	ACAGAAGAA	.	PASS	VC=INDEL;AC=316;AF=1;AN=316;refseq.name=NM_022743;refseq.positionType=intron	GT	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1
+chr1	246149511	.	C	CT	.	PASS	VC=INDEL;AC=69;AF=0.32;AN=214;refseq.name=NM_022743;refseq.positionType=intron	GT	1/1	./.	0/1	0/1	1/1	./.	0/1	1/1	0/0	./.	./.	1/1	./.	./.	./.	0/1	./.	0/0	./.	./.	1/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	./.	./.	./.	0/1	./.	1/1	0/1	./.	./.	./.	1/1	0/1	./.	./.	1/1	./.	1/1	0/1	1/1	./.	0/1	0/1	1/1	./.	0/1	1/1	0/1	./.	0/1	0/1	0/0	0/0	0/1	./.	0/1	1/1	./.	./.	1/1	./.	1/1	0/1	./.	0/1	0/1	./.	0/1	0/1	0/0	./.	0/1	./.	0/0	0/1	./.	0/1	0/1	0/0	0/0	./.	./.	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/1	0/0	0/0	0/0	./.	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	./.	0/1	0/0	0/0	0/0	./.	0/0	./.	0/0	0/0	0/0	./.	./.	0/0	0/1	./.	0/1	0/0	0/0	0/0	./.	./.	./.	0/1	0/0	0/1	0/1	0/1	0/0	0/0	./.	./.	0/0	./.	./.	0/1	./.
+chr1	246152615	.	GC	G	.	PASS	VC=INDEL;AC=164;AF=0.52;AN=316;refseq.name=NM_022743;refseq.positionType=intron	GT	1/1	0/1	1/1	1/1	1/1	0/1	0/1	1/1	0/0	1/1	0/0	1/1	1/1	0/1	1/1	0/1	0/1	0/0	1/1	1/1	1/1	1/1	1/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	0/0	1/1	0/1	1/1	1/1	0/1	1/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	0/0	0/1	1/1	0/1	1/1	1/1	0/1	0/1	0/1	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/1	1/1	0/1	1/1	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/0	1/1	0/0	0/1	0/0	0/1	0/1	0/1	1/1	1/1	1/1	0/0	0/1	1/1	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/1	1/1
+chr1	247110970	.	T	TCA	.	PASS	VC=INDEL;AC=157;AF=0.5;AN=316	GT	0/0	0/1	0/1	0/0	0/1	0/1	0/0	1/1	0/0	1/1	0/0	0/1	1/1	0/0	0/1	0/1	1/1	0/0	0/1	0/1	0/1	1/1	0/1	1/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/1	0/0	0/1	1/1	0/1	1/1	1/1	1/1	0/0	1/1	1/1	0/1	0/1	0/1	0/1	0/0	0/1	1/1	0/1	0/1	0/1	0/0	0/0	1/1	1/1	1/1	0/1	0/1	0/1	0/1	0/1	0/0	1/1	1/1	0/1	0/1	0/1	0/0	0/1	1/1	0/0	1/1	0/1	0/1	0/0	1/1	1/1	1/1	0/1	1/1	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	1/1	0/1	0/0	0/1	0/0	0/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	0/0	0/1	0/0	1/1	0/1	1/1	0/1	1/1	0/0	0/0	0/0	0/0	0/1	0/0	1/1	0/1	1/1	1/1	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/1	1/1	1/1	0/1	0/1	1/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	1/1	0/1	0/1	0/1	1/1
+chr1	247340579	.	TTTCTT	T	.	PASS	VC=INDEL;AC=232;AF=0.74;AN=312	GT	1/1	0/0	0/1	0/1	0/0	1/1	0/1	1/1	0/1	0/0	1/1	0/0	0/0	1/1	0/1	0/0	1/1	1/1	./.	0/0	0/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/0	0/1	0/0	0/0	1/1	0/1	1/1	0/1	0/0	1/1	0/0	0/1	1/1	0/1	0/0	0/1	1/1	0/1	0/1	1/1	0/1	1/1	0/0	1/1	0/1	0/1	0/0	1/1	1/1	1/1	0/1	0/0	1/1	0/0	0/1	0/1	0/1	1/1	./.	0/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/0	0/1	1/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1
+chr1	247694106	.	C	CTCCGTGGCCTAAACGGGCAGCCGAGCCCG	.	PASS	VC=INDEL;AC=124;AF=0.62;AN=200;refseq.name=NM_198074;refseq.positionType=exon	GT	./.	./.	1/1	1/1	1/1	0/1	./.	1/1	0/1	./.	1/1	1/1	0/1	0/1	./.	0/1	./.	1/1	./.	1/1	1/1	./.	1/1	./.	0/1	0/1	./.	0/1	0/1	./.	0/1	0/1	0/1	./.	0/1	./.	./.	0/1	0/1	./.	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	./.	0/1	0/1	0/1	./.	0/1	0/1	0/1	0/1	./.	0/1	./.	0/1	0/1	./.	0/1	0/1	./.	0/1	0/1	0/1	0/1	0/1	0/1	./.	0/1	0/1	./.	./.	./.	0/1	./.	./.	./.	0/1	0/1	1/1	0/1	./.	0/1	0/1	0/1	0/1	./.	0/1	0/1	./.	1/1	0/1	./.	./.	./.	1/1	0/1	1/1	./.	./.	1/1	0/1	1/1	./.	1/1	1/1	1/1	./.	./.	./.	./.	./.	./.	./.	0/1	0/1	./.	0/1	./.	0/1	0/1	0/1	0/1	0/1	./.	0/1	0/1	0/1	./.	0/1	./.	./.	./.	0/1	./.	0/1	./.	./.	0/1	./.	./.	1/1	./.	1/1	1/1	1/1	1/1	./.
+chr1	248807991	.	TATGA	T	.	PASS	VC=INDEL;AC=85;AF=0.34;AN=252	GT	0/0	./.	0/1	0/1	./.	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/0	1/1	0/0	1/1	0/0	0/1	0/1	./.	./.	1/1	0/1	1/1	0/1	0/1	1/1	0/1	0/0	0/0	0/0	0/0	./.	0/1	0/0	./.	0/0	1/1	0/0	./.	0/1	0/1	./.	./.	0/0	0/1	0/0	./.	./.	0/1	./.	0/1	./.	0/1	0/1	0/0	1/1	./.	./.	1/1	0/1	1/1	0/1	0/0	1/1	./.	0/1	1/1	0/0	./.	./.	0/1	./.	0/0	0/1	0/0	0/0	0/1	./.	0/1	./.	0/0	./.	0/1	0/1	1/1	0/1	./.	./.	0/0	1/1	0/1	0/0	0/1	./.	0/1	0/1	0/0	1/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	./.	0/1	0/1	./.	0/0	0/1	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	./.	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/1	0/1	0/0	1/1	0/1	1/1	./.	1/1	0/1	0/1	./.	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/1
+chr1	248809274	.	GAACA	G	.	PASS	VC=INDEL;AC=79;AF=0.26;AN=304	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/1	./.	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	1/1	1/1	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	1/1	0/0	1/1	0/0	0/0	./.	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	./.	./.	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	./.	0/1	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/0	./.	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/1
+chr1	248809275	.	AACAA	A	.	PASS	VC=INDEL;AC=79;AF=0.26;AN=306	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/1	./.	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	1/1	1/1	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	1/1	0/0	1/1	0/0	0/0	./.	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	./.	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	./.	0/1	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/0	./.	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/1
+chr1	248809277	.	C	CAATT	.	PASS	VC=INDEL;AC=9;AF=0.03;AN=316	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr1	249122808	.	C	CAT	.	PASS	VC=INDEL;AC=176;AF=0.58;AN=304;refseq.name=NM_030645;refseq.positionType=promoter	GT	0/1	1/1	0/0	0/1	1/1	1/1	0/0	0/0	0/1	0/0	1/1	0/0	0/1	1/1	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/0	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	1/1	0/0	./.	0/1	0/1	1/1	0/0	0/1	0/1	0/0	0/1	./.	0/0	1/1	0/0	0/1	0/1	0/0	0/0	1/1	1/1	0/1	0/0	1/1	0/0	0/1	0/0	0/1	./.	1/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	0/1	0/1	0/0	1/1	0/1	1/1	0/1	0/1	1/1	0/1	0/1	0/1	1/1	0/0	0/1	0/1	0/1	0/1	1/1	0/1	1/1	0/1	0/1	1/1	1/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	./.	1/1	0/1	0/1	0/0	1/1	./.	0/1	1/1	0/0	0/1	1/1	1/1	./.	1/1	0/1	1/1	1/1	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/1	1/1	0/1	1/1	0/1	0/1	1/1	0/1	0/0	0/0	0/1	1/1	1/1	0/1	1/1	1/1	0/0	0/1	0/1	0/1	0/1	1/1	0/1	0/1
+chr1	249129038	.	GCCTCTAACTT	G	.	PASS	VC=INDEL;AC=2;AF=0.01;AN=316	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr2	311906	.	TA	T	.	PASS	VC=INDEL;AC=148;AF=0.48;AN=308	GT	0/1	0/1	0/1	1/1	0/0	1/1	1/1	0/1	0/1	1/1	./.	1/1	0/1	1/1	0/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/0	1/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	0/0	0/0	0/1	0/0	1/1	0/0	0/0	1/1	0/1	1/1	0/1	0/1	0/1	0/0	0/0	1/1	0/1	1/1	0/1	0/0	0/1	0/0	0/1	1/1	0/1	1/1	0/1	0/1	0/0	0/1	0/0	0/1	1/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	1/1	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/1	./.	0/0	0/0	0/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	0/1	0/0	1/1	0/1	1/1	0/1	1/1	1/1	0/0	0/1	0/1	1/1	0/1	0/1	0/0	0/1	0/1	0/0	0/1	./.	0/0	0/1	0/1	0/0	0/1	0/1	1/1	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	1/1	0/1	1/1	1/1
+chr2	341060	.	TC	T	.	PASS	VC=INDEL;AC=52;AF=0.17;AN=314	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	./.	1/1	1/1	0/0	0/0	0/0	0/0	0/0	1/1	1/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/0	1/1	0/1	1/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	1/1	0/0	0/1	1/1	0/0	1/1	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/0
+chr2	623863	.	GTTC	G	.	PASS	VC=INDEL;AC=278;AF=0.9;AN=310	GT	1/1	0/1	1/1	1/1	1/1	0/0	1/1	1/1	1/1	1/1	./.	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/0	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	./.	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	0/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1
+chr2	623869	.	CTTC	C	.	PASS	VC=INDEL;AC=283;AF=0.9;AN=314	GT	1/1	0/1	1/1	1/1	1/1	0/0	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/0	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	0/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1
+chr2	872231	.	G	GCC	.	PASS	VC=INDEL;AC=46;AF=0.16;AN=284	GT	1/1	0/1	0/0	1/1	0/0	1/1	1/1	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	./.	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/0	1/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	./.	./.	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	./.	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/1	./.	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	./.	0/1	./.	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	./.	0/0	0/1	./.	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/0	./.	0/0	0/0	0/0	0/0
+chr2	872234	.	C	CCC	.	PASS	VC=INDEL;AC=53;AF=0.21;AN=248	GT	1/1	0/1	0/0	1/1	0/0	1/1	1/1	0/1	./.	0/0	0/1	0/1	./.	0/0	0/0	./.	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/0	1/1	0/1	0/1	0/0	0/0	0/0	0/0	./.	./.	0/1	./.	./.	./.	0/0	0/0	./.	./.	./.	0/0	./.	0/0	0/1	0/0	0/0	0/0	0/1	./.	./.	0/0	0/0	0/0	0/0	./.	./.	0/0	0/1	0/0	0/0	0/1	./.	0/0	0/0	./.	0/0	0/0	0/1	./.	0/1	0/0	./.	0/1	0/1	0/1	0/0	0/0	0/0	./.	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	./.	0/1	./.	./.	./.	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	./.	./.	0/1	./.	0/0	0/0	0/0	0/0	0/0	./.	./.	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/0	./.	0/0	./.	0/0	./.
+chr2	1131016	.	TTTAGG	T	.	PASS	VC=INDEL;AC=189;AF=0.6;AN=316;refseq.name=NM_018968;refseq.positionType=intron	GT	0/0	1/1	0/1	0/1	0/0	1/1	0/1	0/0	0/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	0/0	1/1	0/1	0/0	0/1	1/1	0/1	1/1	1/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	1/1	0/1	1/1	0/0	1/1	1/1	1/1	0/0	1/1	1/1	1/1	1/1	0/1	0/1	0/0	1/1	1/1	0/1	0/1	0/1	0/1	1/1	0/1	0/0	0/1	1/1	0/1	0/1	0/1	0/1	0/1	0/0	1/1	1/1	1/1	0/1	0/0	1/1	1/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	1/1	1/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/0	1/1	1/1	1/1	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1	0/1	1/1	1/1	0/1	1/1	1/1	0/0	1/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	0/0	0/1	0/1	1/1	0/0	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/1	1/1	1/1	1/1	0/0	0/1
+chr2	1146399	.	T	TA	.	PASS	VC=INDEL;AC=280;AF=0.89;AN=316;refseq.name=NM_018968;refseq.positionType=intron	GT	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1
+chr2	1146400	.	A	AA	.	PASS	VC=INDEL;AC=280;AF=0.89;AN=316;refseq.name=NM_018968;refseq.positionType=intron	GT	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1
+chr2	1184342	.	CAACTT	C	.	PASS	VC=INDEL;AC=94;AF=0.3;AN=316;refseq.name=NM_018968;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	1/1	0/1	0/1	1/1	0/1	0/0	0/1	1/1	0/1	1/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	1/1	0/1	1/1	0/1	0/0	0/1	0/1	0/0	0/0	0/1	0/1	1/1	0/0	1/1	0/1	0/1	1/1	1/1	0/0	0/0	1/1	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/1	1/1	1/1	0/1	1/1	0/0	1/1	0/1	1/1	1/1	1/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/0	1/1	0/1	0/1	0/1	1/1	0/1	0/0	0/1	0/0	0/1
+chr2	1369823	.	AGC	A	.	PASS	VC=INDEL;AC=243;AF=0.77;AN=316;refseq.name=NM_018968;refseq.positionType=intron	GT	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/0	0/1	0/0	1/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	0/0	0/1	0/0	1/1	1/1	0/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	0/0	0/1	0/1	1/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/0	0/1	0/0	1/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	0/0	0/1	0/1	1/1	1/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/0
+chr2	1371776	.	T	TTTAA	.	PASS	VC=INDEL;AC=50;AF=0.16;AN=312;refseq.name=NM_018968;refseq.positionType=terminator	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	1/1	0/1	1/1	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	1/1	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	1/1	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/0	./.	0/0	0/0	1/1	0/1	0/1	0/0	0/0	1/1	0/0	0/1	./.	1/1	1/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0
+chr2	1371779	.	A	AATTA	.	PASS	VC=INDEL;AC=38;AF=0.13;AN=282;refseq.name=NM_018968;refseq.positionType=terminator	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/1	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	1/1	0/1	1/1	0/0	0/0	0/0	./.	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	./.	0/1	./.	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	./.	0/0	1/1	0/1	0/1	0/0	./.	./.	0/0	0/1	0/0	0/0	./.	./.	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/1	./.	0/0	0/0	1/1	0/0	0/1	./.	./.	1/1	0/1	./.	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	./.
+chr2	1379755	.	A	AA	.	PASS	VC=INDEL;AC=5;AF=0.02;AN=316	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr2	1789405	.	A	AT	.	PASS	VC=INDEL;AC=63;AF=0.2;AN=316	GT	0/0	0/0	0/0	1/1	0/0	0/0	1/1	0/0	0/0	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	1/1	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/0	1/1	0/0	0/1	0/1	0/1	0/1	1/1	0/1	1/1	0/1	0/1	0/1	0/1	0/0	0/0	1/1	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	1/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1
+chr2	2440845	.	A	AA	.	PASS	VC=INDEL;AC=87;AF=0.32;AN=272	GT	./.	0/1	0/0	0/1	0/1	1/1	0/1	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/1	1/1	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/0	1/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	./.	0/0	0/0	0/0	./.	0/0	0/0	./.	./.	0/1	0/0	0/0	0/0	0/1	0/1	./.	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	1/1	./.	0/0	0/0	0/0	0/0	0/1	0/1	./.	1/1	0/1	1/1	./.	0/0	0/1	0/1	0/0	0/0	1/1	0/1	1/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	./.	./.	./.	0/1	./.	0/1	./.	0/0	./.	0/0	1/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	1/1	0/0	0/1	0/0	1/1	0/1	0/0	0/1	0/0	./.	0/1	0/1	0/0	1/1	0/1	./.	0/1	./.	0/1	./.	1/1	1/1	./.	0/1	./.	1/1	0/1	0/1	0/1	./.	0/0	0/1
+chr2	2656901	.	TG	T	.	PASS	VC=INDEL;AC=278;AF=0.9;AN=310	GT	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	./.	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1
+chr2	3126017	.	G	GG	.	PASS	VC=INDEL;AC=0;AF=0;AN=316	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr2	3424142	.	CGCTGAC	C	.	PASS	VC=INDEL;AC=112;AF=0.46;AN=244;refseq.name=NM_016030;refseq.positionType=intron	GT	0/1	0/1	./.	0/0	0/1	./.	1/1	0/1	0/1	0/0	./.	1/1	0/0	0/1	./.	./.	0/1	0/0	0/0	0/1	./.	0/1	1/1	./.	0/0	0/1	./.	1/1	0/1	0/1	0/1	./.	./.	0/0	0/0	./.	1/1	1/1	1/1	0/0	0/0	0/0	1/1	0/0	0/1	./.	0/0	0/0	0/1	0/0	0/0	0/0	0/0	1/1	0/1	0/1	0/0	0/0	./.	0/0	0/0	0/0	0/0	1/1	0/0	0/1	1/1	0/0	1/1	0/1	1/1	./.	0/0	1/1	0/0	0/0	0/0	0/1	0/0	0/0	./.	0/1	./.	./.	./.	0/1	0/1	1/1	1/1	./.	1/1	./.	0/0	./.	0/1	0/0	1/1	./.	./.	1/1	./.	0/1	0/0	0/1	./.	0/1	./.	0/1	1/1	0/1	1/1	0/1	0/1	0/1	./.	0/1	0/1	0/1	./.	0/0	0/1	./.	./.	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	1/1	1/1	./.	0/1	1/1	0/1	0/1	./.	0/0	0/1	./.	./.	0/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	0/1	1/1	1/1	./.
+chr2	3658789	.	ACAAA	A	.	PASS	VC=INDEL;AC=95;AF=0.33;AN=284;refseq.name=NM_024027;refseq.positionType=intron	GT	0/1	0/1	0/0	0/1	0/1	0/1	0/1	./.	0/0	0/1	0/0	0/0	0/1	0/0	./.	0/1	0/1	./.	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/1	./.	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/1	./.	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	./.	0/1	0/0	./.	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/1	./.	0/1	0/0	./.	0/0	0/1	./.	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	./.	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/0	./.	0/1	0/1	0/1	0/0	0/1	0/1	0/1	./.	0/0	./.	0/0	./.	0/1
+chr2	3749151	.	GGAA	G	.	PASS	VC=INDEL;AC=163;AF=0.53;AN=310;refseq.name=NM_018436;refseq.positionType=exon	GT	0/0	0/1	0/1	0/1	0/0	0/1	0/1	1/1	0/0	0/0	0/1	0/1	0/0	1/1	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/0	1/1	1/1	1/1	0/1	0/1	1/1	0/1	1/1	0/0	0/0	0/1	0/1	0/1	0/0	1/1	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/1	1/1	0/1	0/1	0/1	0/1	1/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/0	1/1	0/1	1/1	1/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	./.	1/1	0/1	0/1	0/1	0/0	1/1	0/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	0/0	0/1	0/1	1/1	0/0	0/1	1/1	0/1	1/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	0/0	0/1	1/1	./.	0/1	0/1	0/0	0/0	0/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	0/0	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	0/1	0/1	0/1
+chr2	3749158	.	GAAG	G	.	PASS	VC=INDEL;AC=164;AF=0.53;AN=308;refseq.name=NM_018436;refseq.positionType=exon	GT	0/0	0/1	0/1	0/1	0/0	0/1	0/1	1/1	0/0	0/0	0/1	0/1	0/0	1/1	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/0	1/1	1/1	1/1	0/1	0/1	1/1	0/1	1/1	0/0	0/0	0/1	0/1	0/1	0/0	1/1	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/1	1/1	0/1	0/1	0/1	0/1	1/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/0	1/1	0/1	1/1	1/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	./.	1/1	0/1	0/1	./.	0/0	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	0/1	0/1	1/1	0/0	0/1	1/1	0/1	1/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	./.	0/1	1/1	0/0	0/1	0/1	0/0	0/0	0/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	0/0	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	0/0	0/1	./.	0/1	0/0	0/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	0/1	0/1	0/1
+chr2	4140967	.	G	GA	.	PASS	VC=INDEL;AC=125;AF=0.4;AN=312	GT	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	1/1	1/1	0/0	0/1	1/1	1/1	0/1	0/0	0/1	1/1	1/1	0/0	1/1	0/1	0/1	1/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	./.	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	1/1	1/1	1/1	0/0	1/1	0/1	0/1	0/0	0/1	0/0	1/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	0/0	1/1	0/1	0/1	0/0	1/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/0	1/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	0/1	0/0	0/0	1/1	0/1	1/1	0/0	1/1	0/1	0/1	0/0	0/0	0/1	1/1	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/0	1/1	1/1	1/1	1/1	0/0	0/1	1/1	0/1	0/1	0/1	./.	1/1	1/1	0/1
+chr2	4184693	.	AGAG	A	.	PASS	VC=INDEL;AC=60;AF=0.22;AN=274	GT	1/1	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/1	0/1	0/1	./.	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	./.	./.	0/0	0/0	./.	./.	./.	./.	./.	0/0	0/1	0/1	0/0	0/1	./.	0/0	0/0	./.	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/1	./.	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/1	0/0	./.	0/0	0/1	0/0	0/1	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/1	./.	1/1	0/0	./.	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	./.	0/1	0/1	1/1	0/0	0/1	0/1	./.	0/0	0/0	0/1	0/1	0/1	./.	0/0
+chr2	4296243	.	ACCTGGCCTTTT	A	.	PASS	VC=INDEL;AC=19;AF=0.06;AN=312	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/0	./.	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0
+chr2	4604536	.	ATCTG	A	.	PASS	VC=INDEL;AC=82;AF=0.27;AN=308	GT	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/1	0/0	./.	1/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/1	1/1	1/1	0/1	0/1	0/1	0/1	0/0	1/1	0/1	0/0	0/0	1/1	0/1	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/1	1/1	0/0	1/1	1/1	1/1	0/0	1/1	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/1	./.	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/0	./.	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	1/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	1/1	0/0	0/1	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/1
+chr2	4607815	.	TAT	T	.	PASS	VC=INDEL;AC=90;AF=0.28;AN=316	GT	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	1/1	0/1	0/0	0/1	0/0	0/1	1/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/1	1/1	1/1	0/1	0/1	0/1	0/1	0/0	1/1	0/1	0/0	0/0	1/1	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/1	1/1	0/0	1/1	1/1	1/1	0/0	1/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/1	1/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/0	1/1	0/1	1/1	0/0	0/1	0/0	0/0	0/1	0/0	1/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	1/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	1/1	0/0	0/0	0/0	0/1	0/1
+chr2	4874174	.	CAT	C	.	PASS	VC=INDEL;AC=203;AF=0.64;AN=316	GT	1/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	0/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1	0/0	0/1	0/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	0/0	0/1	1/1	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/1	1/1	0/1	1/1	0/0	1/1	1/1	1/1	1/1	0/1	0/0	0/0	0/1	0/1	0/1	0/1	0/0	1/1	0/1	1/1	1/1	0/1	0/0	0/0	1/1	0/1	0/0	0/1	0/1	0/1	0/0	1/1	0/1	0/1	1/1	0/1	0/1	0/1	0/0	1/1	0/1	1/1	0/1	1/1	0/1	1/1	0/0	0/1	0/0	1/1	1/1	1/1	1/1	1/1	1/1	0/0	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	1/1	0/1	0/0	1/1	0/1	0/1	1/1	0/1	0/1	1/1	0/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	0/0	0/1	0/1	0/1	1/1	1/1	0/1	0/0
+chr2	4933418	.	GATC	G	.	PASS	VC=INDEL;AC=86;AF=0.28;AN=304	GT	1/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	1/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	0/1	0/1	0/0	1/1	0/1	0/1	1/1	0/1	1/1	1/1	0/0	1/1	1/1	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	1/1	0/0	0/1	0/1	0/1	1/1	0/1	0/1	1/1	1/1	0/1	./.	0/1	0/1	0/0	./.	0/0	0/0	0/0	0/0	./.	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/1	0/0
+chr2	4987676	.	A	ACT	.	PASS	VC=INDEL;AC=100;AF=0.32;AN=316	GT	0/0	0/1	0/1	0/0	0/0	0/1	1/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/1	1/1	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	1/1	0/0	0/1	0/1	0/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	0/1	1/1	0/1	1/1	0/1	0/1	1/1	0/0	1/1	1/1	0/1	1/1	0/1	0/1	0/1	0/1	0/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	1/1	0/1	0/0
+chr2	4994909	.	G	GT	.	PASS	VC=INDEL;AC=122;AF=0.41;AN=294	GT	0/1	0/0	1/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	1/1	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/0	./.	0/1	1/1	0/0	0/1	0/1	0/1	0/1	0/0	./.	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	0/1	0/0	1/1	0/1	0/0	1/1	0/0	0/1	0/0	0/0	0/1	1/1	0/0	0/1	0/1	0/1	1/1	0/1	./.	1/1	0/1	1/1	0/0	0/1	0/1	0/1	0/1	1/1	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	./.	0/1	0/1	0/1	0/1	./.	0/0	0/0	0/1	0/1	./.	0/1	1/1	0/1	1/1	0/1	0/1	1/1	0/1	0/1	./.	0/0	./.	0/1	./.	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/0	1/1	0/1	0/0	0/1	0/0	0/1	1/1	./.	0/1	0/0	0/1	0/1	0/0	0/1	1/1	0/1	1/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	./.	0/1	0/1	0/1	1/1	0/1	0/1	0/1	0/1	0/1	1/1	0/0	0/0
+chr2	5222830	.	CTGTT	C	.	PASS	VC=INDEL;AC=127;AF=0.4;AN=314	GT	0/0	0/0	0/0	0/1	0/1	1/1	0/0	0/1	1/1	0/0	1/1	0/1	0/1	0/1	0/0	0/0	1/1	0/1	1/1	0/0	0/0	0/1	0/0	1/1	0/1	0/0	1/1	0/1	0/1	0/1	0/0	1/1	0/0	0/1	1/1	0/1	0/1	0/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/1	0/0	1/1	0/0	1/1	0/0	1/1	0/1	0/1	0/0	0/1	0/1	1/1	1/1	0/0	0/1	0/1	0/1	./.	0/0	0/1	0/1	1/1	1/1	1/1	1/1	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	1/1	1/1	1/1	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	1/1	0/1	0/1	0/1	0/1	0/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/1
+chr2	5418395	.	T	TAA	.	PASS	VC=INDEL;AC=147;AF=0.47;AN=314	GT	1/1	0/0	0/0	1/1	0/1	0/0	0/1	0/1	1/1	1/1	0/0	0/1	0/1	0/1	0/1	0/1	1/1	0/1	1/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	1/1	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/0	1/1	0/1	1/1	0/1	0/0	1/1	0/0	0/1	0/0	0/0	0/1	1/1	1/1	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/1	1/1	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	1/1	0/1	0/1	1/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	1/1	1/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	0/1	0/1	0/0	1/1	0/1	1/1	0/1	0/1	0/1	0/1	0/0	1/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	./.	0/1	0/0	0/1	0/0	0/0	0/1	0/0	1/1	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/1	1/1	1/1
+chr2	5821332	.	TTCAGTCCCCCTAATGCC	T	.	PASS	VC=INDEL;AC=261;AF=0.83;AN=316	GT	0/0	1/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	1/1	0/0	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/0	0/1	1/1	0/1	1/1	0/0	0/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	0/1	0/0	1/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1
+chr2	5821334	.	CAGTCCCCCTAATGCCTC	C	.	PASS	VC=INDEL;AC=261;AF=0.83;AN=316	GT	0/0	1/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	1/1	0/0	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/0	0/1	1/1	0/1	1/1	0/0	0/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	0/1	0/0	1/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1
+chr2	7238500	.	A	ACTT	.	PASS	VC=INDEL;AC=184;AF=0.58;AN=316	GT	0/0	0/0	1/1	1/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	1/1	1/1	0/1	1/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1	0/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	1/1	0/1	0/1	0/1	1/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	1/1	1/1	0/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	0/1	1/1	0/1	0/0	0/1	0/1	1/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/0	1/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/0	1/1	0/1	0/1	1/1	0/1	0/1	1/1	0/1	0/0	0/0
+chr2	7238505	.	T	TTCT	.	PASS	VC=INDEL;AC=184;AF=0.58;AN=316	GT	0/0	0/0	1/1	1/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	1/1	1/1	0/1	1/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1	0/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	1/1	0/1	0/1	0/1	1/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	1/1	1/1	0/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	0/1	1/1	0/1	0/0	0/1	0/1	1/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/0	1/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/0	1/1	0/1	0/1	1/1	0/1	0/1	1/1	0/1	0/0	0/0
+chr2	7616680	.	C	CA	.	PASS	VC=INDEL;AC=196;AF=0.62;AN=314	GT	./.	1/1	0/0	0/1	0/0	0/1	0/1	1/1	1/1	0/1	0/1	0/0	0/1	0/0	0/1	1/1	0/1	0/0	0/1	0/1	0/1	0/0	0/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	0/1	0/0	1/1	0/0	0/0	0/0	0/0	0/1	1/1	1/1	0/1	0/1	0/1	0/1	1/1	0/0	1/1	0/1	0/0	0/1	0/0	0/1	0/1	0/1	0/1	1/1	1/1	0/0	0/1	1/1	0/1	0/1	0/1	0/1	0/0	1/1	1/1	0/0	1/1	0/0	0/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	1/1	0/1	0/1	0/0	0/0	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	1/1	0/1	0/1	0/0	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	1/1	1/1	0/0	0/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	1/1	0/0	0/1
+chr2	10714143	.	CAA	C	.	PASS	VC=INDEL;AC=143;AF=0.47;AN=306;refseq.name=NM_024894;refseq.positionType=intron	GT	0/0	1/1	0/1	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/0	1/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/0	1/1	0/1	0/1	1/1	0/1	0/1	0/1	1/1	0/1	0/1	1/1	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/0	1/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	0/0	1/1	1/1	0/1	0/1	0/0	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	./.	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/1	1/1	0/1	0/1	1/1	./.	1/1	0/1	0/1	0/1	0/0	0/0	1/1	0/1	0/1	0/1	0/1	0/1	0/1	./.	0/1	./.	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	1/1	0/0	0/0	0/0	0/1	0/1	1/1	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/1	1/1	1/1	./.	0/1
+chr2	11163207	.	TCA	T	.	PASS	VC=INDEL;AC=63;AF=0.2;AN=316	GT	0/0	1/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	1/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/1	1/1	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/1	1/1	0/1	0/1	1/1	0/0	0/0	1/1	1/1	0/1	0/0	0/1	0/0	0/1	1/1	0/1	1/1	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr2	11163209	.	ACA	A	.	PASS	VC=INDEL;AC=63;AF=0.2;AN=316	GT	0/0	1/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	1/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/1	1/1	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/1	1/1	0/1	0/1	1/1	0/0	0/0	1/1	1/1	0/1	0/0	0/1	0/0	0/1	1/1	0/1	1/1	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr2	11454443	.	TTGTC	T	.	PASS	VC=INDEL;AC=85;AF=0.27;AN=310;refseq.name=NM_004850;refseq.positionType=intron	GT	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/1	0/0	0/0	1/1	1/1	0/1	0/0	0/1	1/1	0/1	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/1	1/1	0/1	0/0	0/1	0/1	0/0	0/1	0/1	1/1	0/1	0/1	0/1	0/1	1/1	0/0	0/0	0/0	./.	0/1	1/1	0/1	0/0	0/1	1/1	0/0	0/1	0/1	0/1	0/0	1/1	0/1	0/1	1/1	0/1	0/1	0/1	0/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1
+chr2	11600452	.	TT	T	.	PASS	VC=INDEL;AC=316;AF=1;AN=316;refseq.name=NM_198256;refseq.positionType=intron	GT	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1
+chr2	11843046	.	C	CAACT	.	PASS	VC=INDEL;AC=157;AF=0.5;AN=316	GT	0/0	0/1	0/0	0/1	0/1	0/1	0/0	1/1	0/0	0/0	0/1	0/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	0/1	0/0	0/0	1/1	0/1	0/0	0/1	0/1	0/1	0/1	1/1	0/1	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/1	1/1	0/1	0/0	0/1	1/1	0/1	0/1	1/1	1/1	0/0	0/1	0/0	1/1	0/0	0/0	0/1	0/1	0/0	0/1	1/1	1/1	0/0	0/1	0/1	0/1	0/1	0/1	1/1	0/1	0/0	0/1	0/1	0/1	0/0	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	0/0	0/1	0/1	0/1	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/0	1/1	0/0	0/1	0/1	1/1	0/1	0/1	0/0	0/0	0/0	1/1	1/1	1/1	0/1	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	1/1	1/1	0/1	0/1	0/1	0/0	0/1	0/0	1/1	0/1	1/1	0/1	0/1	0/0	0/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	0/1	0/0	0/0	0/1	0/0
+chr2	11843047	.	A	AACTA	.	PASS	VC=INDEL;AC=157;AF=0.5;AN=316	GT	0/0	0/1	0/0	0/1	0/1	0/1	0/0	1/1	0/0	0/0	0/1	0/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	0/1	0/0	0/0	1/1	0/1	0/0	0/1	0/1	0/1	0/1	1/1	0/1	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/1	1/1	0/1	0/0	0/1	1/1	0/1	0/1	1/1	1/1	0/0	0/1	0/0	1/1	0/0	0/0	0/1	0/1	0/0	0/1	1/1	1/1	0/0	0/1	0/1	0/1	0/1	0/1	1/1	0/1	0/0	0/1	0/1	0/1	0/0	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	0/0	0/1	0/1	0/1	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/0	1/1	0/0	0/1	0/1	1/1	0/1	0/1	0/0	0/0	0/0	1/1	1/1	1/1	0/1	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	1/1	1/1	0/1	0/1	0/1	0/0	0/1	0/0	1/1	0/1	1/1	0/1	0/1	0/0	0/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	0/1	0/0	0/0	0/1	0/0
+chr2	12317135	.	T	TT	.	PASS	VC=INDEL;AC=2;AF=0.01;AN=316	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr2	12787834	.	GT	G	.	PASS	VC=INDEL;AC=0;AF=0;AN=314	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr2	12877501	.	G	GA	.	PASS	VC=INDEL;AC=241;AF=0.76;AN=316;refseq.name=NM_021643;refseq.positionType=intron	GT	1/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	0/0	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	0/0	0/1	1/1	0/1	0/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	0/1	0/1	1/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	1/1	0/0	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	0/1	0/0	0/1	0/1	0/0	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	0/1	0/1	1/1	0/0	0/1	0/1	0/1	0/1	1/1	0/1	0/1	1/1	0/1	0/1	0/1	1/1	0/0	0/1	0/1	0/1	0/1	1/1
+chr2	13123234	.	A	ACTTA	.	PASS	VC=INDEL;AC=273;AF=0.89;AN=308	GT	./.	0/0	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	./.	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	./.	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/0	1/1
+chr2	13297277	.	GC	G	.	PASS	VC=INDEL;AC=23;AF=0.07;AN=314	GT	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/1	0/0	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr2	13446741	.	T	TCACT	.	PASS	VC=INDEL;AC=105;AF=0.41;AN=256	GT	0/0	0/0	0/1	0/0	0/1	0/0	1/1	0/1	1/1	0/1	1/1	./.	./.	0/1	0/1	0/0	0/0	./.	0/1	0/0	0/0	0/0	0/0	0/0	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	0/0	0/1	0/0	0/1	1/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	./.	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/0	./.	./.	0/1	0/0	0/0	./.	0/0	0/1	1/1	0/1	0/0	0/0	0/0	1/1	./.	0/1	./.	./.	0/1	./.	0/1	0/0	0/1	./.	1/1	1/1	0/0	0/1	0/1	1/1	./.	0/1	0/1	./.	./.	0/1	0/1	0/0	0/1	./.	./.	0/0	0/0	./.	0/0	0/1	0/1	./.	0/0	./.	0/1	0/1	./.	0/1	0/1	./.	0/1	./.	1/1	0/1	1/1	0/1	./.	0/1	1/1	1/1	./.	0/1	1/1	0/1	0/0	0/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	1/1	0/1	0/1	0/1	0/1	./.	./.	0/0	0/1	1/1	./.	./.	0/0
+chr2	13637137	.	TTGCTG	T	.	PASS	VC=INDEL;AC=19;AF=0.06;AN=308	GT	0/0	./.	0/1	0/0	0/0	0/0	./.	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	./.	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1
+chr2	13829513	.	T	TT	.	PASS	VC=INDEL;AC=91;AF=0.29;AN=314	GT	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/1	1/1	0/0	0/1	0/1	0/1	1/1	0/1	0/1	0/1	1/1	1/1	0/1	0/1	0/0	./.	0/0	0/1	0/1	0/0	0/1	0/1	0/0	1/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/1	1/1	1/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	1/1	1/1	0/1	0/0	0/0	0/0	0/1	0/1	1/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/1	1/1	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	1/1	0/0	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	1/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1
+chr2	13967190	.	TAGAT	T	.	PASS	VC=INDEL;AC=22;AF=0.07;AN=316	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	1/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0
+chr2	14096044	.	AAA	A	.	PASS	VC=INDEL;AC=47;AF=0.16;AN=298	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/1	1/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	1/1	1/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	./.	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/1	./.	0/0	./.	0/0	0/1	0/1	0/1	0/1	0/0	./.	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	./.	0/0	0/0	1/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/1	./.	1/1	0/0	0/0
+chr2	14214846	.	C	CT	.	PASS	VC=INDEL;AC=40;AF=0.13;AN=316	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	1/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	1/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	1/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/1	0/0	0/0
+chr2	14381137	.	A	ATC	.	PASS	VC=INDEL;AC=0;AF=0;AN=280	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	./.	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	./.	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	./.	0/0	0/0	./.	0/0	0/0	0/0	./.	0/0	./.	./.	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	./.	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr2	14428427	.	G	GC	.	PASS	VC=INDEL;AC=242;AF=0.77;AN=316	GT	1/1	1/1	0/1	0/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/0	1/1	0/1	1/1	0/1	1/1	0/0	0/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	0/1	0/1	0/1	0/0	1/1	1/1	1/1	0/1	0/0	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/0	1/1	0/1	1/1	0/1	0/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	1/1	0/1	1/1	0/0	0/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	1/1	1/1	0/0	1/1
+chr2	14428428	.	C	CC	.	PASS	VC=INDEL;AC=241;AF=0.77;AN=314	GT	1/1	1/1	0/1	0/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/0	1/1	0/1	1/1	0/1	1/1	0/0	0/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	0/1	0/1	0/1	0/0	1/1	1/1	1/1	0/1	0/0	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/0	1/1	0/1	1/1	0/1	0/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	1/1	0/1	1/1	0/0	0/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	1/1	1/1	0/0	1/1
+chr2	14685393	.	C	CTTC	.	PASS	VC=INDEL;AC=29;AF=0.09;AN=316	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/0
+chr2	15208721	.	A	AC	.	PASS	VC=INDEL;AC=116;AF=0.38;AN=304	GT	0/1	0/1	0/1	0/1	0/0	0/1	1/1	0/0	0/1	1/1	0/1	1/1	./.	1/1	0/1	1/1	0/1	0/1	0/1	0/0	1/1	0/0	1/1	1/1	0/1	./.	1/1	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/1	0/1	0/0	0/0	0/0	0/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	0/1	1/1	1/1	0/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	1/1	0/0	0/1	0/1	1/1	0/0	0/0	1/1	0/0	0/1	1/1	0/1	1/1	0/1	1/1	0/0	0/1	1/1	0/1	1/1	1/1	0/0	0/0	./.	1/1	./.	0/0	0/0	0/1	0/0	0/0	0/0	0/0	1/1	1/1	1/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	1/1	0/0	./.	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	1/1	1/1	./.	1/1	0/1
+chr2	15263072	.	A	AAGGA	.	PASS	VC=INDEL;AC=86;AF=0.33;AN=262	GT	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	1/1	0/0	0/1	0/0	0/0	0/1	0/0	0/0	./.	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/1	1/1	./.	0/0	./.	./.	0/0	0/0	0/0	./.	1/1	./.	1/1	1/1	0/1	0/0	0/0	0/0	0/1	0/1	./.	0/1	0/0	0/1	1/1	0/0	0/0	1/1	0/1	0/0	0/0	0/0	0/1	0/1	./.	0/0	0/1	./.	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/1	./.	0/1	0/1	0/0	0/0	./.	1/1	0/0	0/0	0/0	./.	./.	0/1	0/1	0/1	./.	0/0	./.	0/1	1/1	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	./.	0/0	./.	0/0	0/0	./.	0/1	0/1	1/1	0/1	0/0	0/1	0/1	0/1	0/1	./.	0/0	0/1	0/1	0/1	0/1	0/1	./.	0/0	0/0	0/0	1/1	0/1	0/0	0/0	0/0	0/1	0/1	1/1	0/1	./.	0/0	1/1	./.	0/1	0/0	1/1	./.	0/1	0/1	0/1	./.	1/1	0/1	1/1	0/1	0/1	./.	./.	0/1	0/0	0/0
+chr2	15744484	.	CT	C	.	PASS	VC=INDEL;AC=48;AF=0.15;AN=314;refseq.name=NM_004939;refseq.positionType=intron	GT	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	./.	0/1	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	1/1	0/0	0/0	0/0	0/1	1/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	1/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/1	1/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0
+chr2	15907161	.	G	GACTG	.	PASS	VC=INDEL;AC=60;AF=0.19;AN=314	GT	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	./.	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	1/1	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/1	1/1	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	1/1	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/0
+chr2	16916657	.	T	TAGAA	.	PASS	VC=INDEL;AC=153;AF=0.51;AN=298	GT	0/0	0/0	0/0	0/1	0/0	0/1	0/0	1/1	0/0	0/1	1/1	0/1	0/0	0/1	0/0	0/0	./.	0/0	0/0	0/1	0/1	0/0	0/0	0/0	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	./.	0/1	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/1	0/0	1/1	0/0	0/1	0/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	./.	0/1	1/1	0/1	1/1	1/1	1/1	./.	0/1	1/1	1/1	1/1	./.	1/1	0/1	0/1	1/1	1/1	0/1	1/1	0/0	0/0
+chr2	16916659	.	G	GAAAG	.	PASS	VC=INDEL;AC=145;AF=0.49;AN=294	GT	0/0	0/0	0/0	0/1	0/0	0/1	0/0	1/1	0/0	0/1	1/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	0/1	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	./.	./.	0/1	./.	0/1	1/1	1/1	1/1	./.	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/0	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	./.	1/1	./.	1/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	0/1	0/1	0/1	1/1	./.	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	./.	./.	./.	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	0/1	1/1	0/0	0/0
+chr2	17460258	.	C	CC	.	PASS	VC=INDEL;AC=54;AF=0.17;AN=316	GT	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	1/1	0/1	0/1	0/0	0/0	0/0	0/0	1/1	1/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/0	1/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/1
+chr2	18018674	.	TAT	T	.	PASS	VC=INDEL;AC=71;AF=0.23;AN=314	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	1/1	0/1	0/1	1/1	0/0	0/1	0/0	1/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/0	./.	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	1/1	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/1	1/1	1/1	1/1	1/1	0/0	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	1/1	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	1/1	1/1	1/1	0/1	0/0	0/1	0/0	0/0	0/1	1/1	0/0	0/1	0/0	0/0
+chr2	18139969	.	T	TT	.	PASS	VC=INDEL;AC=0;AF=0;AN=316	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr2	18291829	.	TCT	T	.	PASS	VC=INDEL;AC=276;AF=0.87;AN=316	GT	0/1	0/1	0/1	1/1	0/1	1/1	0/0	1/1	0/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	0/0	0/0	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/0
+chr2	18382578	.	G	GC	.	PASS	VC=INDEL;AC=304;AF=0.97;AN=314	GT	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1
+chr2	18386046	.	ACAGA	A	.	PASS	VC=INDEL;AC=1;AF=0;AN=314	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr2	18673070	.	CT	C	.	PASS	VC=INDEL;AC=0;AF=0;AN=314	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr2	18704268	.	C	CCATGACAAGAACTGCT	.	PASS	VC=INDEL;AC=210;AF=0.66;AN=316	GT	1/1	0/0	0/0	1/1	0/1	0/1	0/1	0/1	1/1	0/0	0/1	0/1	0/1	0/1	0/0	1/1	0/1	0/1	1/1	1/1	0/1	0/1	1/1	0/0	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1	1/1	0/0	0/1	0/1	0/1	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	1/1	0/0	0/1	0/1	0/1	1/1	0/0	0/0	0/1	0/0	0/0	1/1	1/1	0/0	0/0	0/1	0/1	0/0	0/1	0/0	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	0/0	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/0	0/0	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1
+chr2	18954606	.	T	TGTA	.	PASS	VC=INDEL;AC=272;AF=0.87;AN=314	GT	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	0/0	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	0/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	0/0	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	1/1
+chr2	19229223	.	A	AG	.	PASS	VC=INDEL;AC=230;AF=0.82;AN=280	GT	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	./.	1/1	1/1	./.	1/1	1/1	0/1	1/1	0/1	1/1	0/1	./.	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	0/1	./.	0/1	0/1	0/1	0/1	0/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	0/1	0/1	./.	0/1	0/1	0/1	1/1	0/1	0/1	0/1	0/1	./.	0/1	./.	0/1	0/1	./.	0/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	./.	0/1	1/1	0/1	./.	1/1	0/1	1/1	0/1	0/1	1/1	0/1	./.	0/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	./.	0/1	1/1	./.	./.	1/1
+chr2	19416083	.	CAAT	C	.	PASS	VC=INDEL;AC=26;AF=0.08;AN=312	GT	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	./.	0/1	0/1	1/1	0/0	0/0	1/1	0/0	1/1	0/1	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr2	19486700	.	C	CGT	.	PASS	VC=INDEL;AC=200;AF=0.9;AN=222	GT	0/1	./.	./.	./.	0/1	0/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	./.	1/1	0/1	1/1	./.	1/1	1/1	./.	1/1	1/1	1/1	./.	1/1	1/1	0/1	./.	1/1	1/1	1/1	1/1	0/1	1/1	./.	./.	./.	0/1	./.	1/1	./.	0/1	./.	0/1	0/1	0/1	./.	1/1	./.	./.	./.	./.	0/1	1/1	./.	./.	0/1	1/1	1/1	0/1	1/1	./.	0/1	1/1	0/1	1/1	./.	0/1	0/1	0/1	0/1	1/1	1/1	1/1	./.	./.	./.	1/1	1/1	./.	./.	1/1	1/1	1/1	1/1	./.	./.	./.	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	./.	./.	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	0/1	./.	1/1	1/1	1/1	1/1	1/1	./.	./.	./.	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	./.
+chr2	19792293	.	AAA	A	.	PASS	VC=INDEL;AC=92;AF=0.29;AN=316	GT	0/1	0/0	1/1	0/1	0/0	0/0	1/1	0/0	0/1	1/1	1/1	0/1	0/0	0/0	0/1	1/1	0/1	0/1	0/0	0/1	0/0	1/1	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	1/1	1/1	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	1/1	0/1	1/1	1/1	0/1	1/1	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	1/1	0/0	0/1	0/0	0/1	0/1	1/1	0/1	0/0	0/1	0/1	0/0	0/1	0/0	1/1	0/0	0/1	1/1	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/1
+chr2	19850365	.	ATA	A	.	PASS	VC=INDEL;AC=17;AF=0.06;AN=302	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/1	0/1	0/0	./.	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0
+chr2	20061297	.	A	AATCA	.	PASS	VC=INDEL;AC=10;AF=0.03;AN=316	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr2	20902911	.	G	GC	.	PASS	VC=INDEL;AC=0;AF=0;AN=316;refseq.name=NM_021925;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr2	21209314	.	GTG	G	.	PASS	VC=INDEL;AC=13;AF=0.04;AN=316	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr2	21319809	.	GACAA	G	.	PASS	VC=INDEL;AC=64;AF=0.2;AN=316	GT	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/0	1/1	1/1	0/1	1/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	0/1	0/1	1/1	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr2	21692599	.	AA	A	.	PASS	VC=INDEL;AC=78;AF=0.25;AN=314	GT	0/1	0/0	0/1	0/0	0/1	1/1	0/0	0/0	0/1	0/0	1/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/0	1/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/1	0/1	./.	0/1	0/1	1/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	1/1	0/1	0/1	1/1	0/1	0/1	0/1	0/1	0/0	0/1	1/1	0/1	0/1	1/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/0
+chr2	22508039	.	GCCT	G	.	PASS	VC=INDEL;AC=70;AF=0.23;AN=300	GT	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	./.	0/0	0/1	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	1/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	1/1	1/1	0/0	0/1	0/1	0/1	0/0	0/0	./.	0/1	1/1	1/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	1/1	0/0	0/1	0/1	./.	0/1	0/0	0/1	./.	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/0	1/1	0/1	./.	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	./.	0/1	1/1	0/1	0/1	1/1	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/1	./.	0/0	0/1	0/1	0/0	0/0
+chr2	23055890	.	CTT	C	.	PASS	VC=INDEL;AC=32;AF=0.1;AN=310	GT	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	./.	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0
+chr2	23059421	.	CC	C	.	PASS	VC=INDEL;AC=0;AF=0;AN=316	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr2	23080285	.	C	CC	.	PASS	VC=INDEL;AC=0;AF=0;AN=316	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr2	23252488	.	T	TGTTT	.	PASS	VC=INDEL;AC=261;AF=0.83;AN=314	GT	0/1	0/1	1/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	0/0	0/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	0/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	0/1	./.	1/1	1/1	0/0	0/1	0/0	1/1	0/1	0/0	0/1	0/0	1/1	1/1	0/0	1/1	0/1	1/1	0/0	0/0	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1
+chr2	23656105	.	CT	C	.	PASS	VC=INDEL;AC=78;AF=0.25;AN=314	GT	0/0	0/0	0/0	1/1	0/0	0/1	0/0	0/1	1/1	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	1/1	0/0	0/1	0/1	0/0	0/1	0/1	1/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	./.	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	1/1	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	1/1	0/1	1/1	0/1	0/1	1/1	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/1	1/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/1	0/0	0/0	0/0	0/0	1/1	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr2	23929327	.	T	TAACT	.	PASS	VC=INDEL;AC=0;AF=0;AN=316	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr2	25136190	.	TC	T	.	PASS	VC=INDEL;AC=190;AF=0.68;AN=280;refseq.name=NM_004036;refseq.positionType=intron	GT	0/1	1/1	1/1	0/1	0/1	1/1	0/0	1/1	0/0	0/1	1/1	0/1	0/1	1/1	1/1	0/1	0/0	1/1	1/1	0/0	0/0	0/0	0/1	0/0	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	./.	0/1	1/1	0/0	0/1	0/0	0/1	0/0	1/1	0/0	0/1	0/0	0/1	./.	0/0	0/1	0/1	1/1	0/1	0/0	0/0	0/1	1/1	0/0	0/0	0/1	./.	1/1	0/1	1/1	0/1	0/0	0/1	./.	0/0	0/0	0/0	0/0	0/1	0/0	./.	0/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	0/0	0/1	./.	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	./.	./.	./.	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	./.	1/1	1/1	./.	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	./.	1/1	1/1	0/1	0/1	./.	./.	./.	./.	0/1	0/1
+chr2	25696290	.	CA	C	.	PASS	VC=INDEL;AC=7;AF=0.02;AN=314;refseq.name=NM_021907;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1
+chr2	25971939	.	A	AGTAAA	.	PASS	VC=INDEL;AC=90;AF=0.28;AN=316;refseq.name=NM_018263;refseq.positionType=intron	GT	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/1	0/0	1/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	1/1	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	1/1	0/1	0/1	0/1	1/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1	1/1	0/1	0/1	1/1	0/0	0/1	0/0	0/1	0/1	1/1	0/1	0/1	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/1
+chr2	26471341	.	T	TTTC	.	PASS	VC=INDEL;AC=10;AF=0.03;AN=316;refseq.name=NM_000183;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	1/1	0/0	0/0
+chr2	26547936	.	GAC	G	.	PASS	VC=INDEL;AC=69;AF=0.22;AN=308;refseq.name=NM_153835;refseq.positionType=intron	GT	0/0	0/0	1/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	1/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/0	1/1	0/1	0/1	0/1	0/1	0/1	./.	0/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	0/1	0/1	0/1	0/1	0/1	1/1	0/0	1/1	0/0	0/1	./.	./.	1/1	0/1	0/1	1/1	0/1	1/1	1/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0
+chr2	26849198	.	ACGGTT	A	.	PASS	VC=INDEL;AC=85;AF=0.28;AN=308;refseq.name=NM_001029881;refseq.positionType=intron	GT	1/1	0/1	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/1	1/1	0/0	0/1	0/0	1/1	1/1	0/1	0/1	1/1	0/1	1/1	0/1	0/1	0/0	0/1	0/0	0/1	0/0	1/1	0/0	1/1	0/1	0/1	0/0	0/0	0/1	0/1	1/1	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	1/1	0/0	0/1	1/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	./.	1/1	./.	0/1	0/0	0/0	0/0	0/1	0/1	0/1	1/1	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	1/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	1/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	./.	0/1	./.	0/0	0/1
+chr2	26849199	.	CGGTTC	C	.	PASS	VC=INDEL;AC=83;AF=0.27;AN=302;refseq.name=NM_001029881;refseq.positionType=intron	GT	1/1	0/1	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/1	1/1	0/0	0/1	0/0	1/1	1/1	0/1	0/1	1/1	0/1	1/1	0/1	0/1	0/0	0/1	0/0	0/1	0/0	1/1	0/0	1/1	0/1	0/1	0/0	0/0	0/1	0/1	1/1	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	./.	1/1	0/0	0/1	./.	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	./.	1/1	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/1	1/1	0/1	0/1	0/1	0/0	./.	./.	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	1/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	1/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	./.	0/1	./.	0/0	0/1
+chr2	27134249	.	ATA	A	.	PASS	VC=INDEL;AC=100;AF=0.32;AN=316;refseq.name=NM_020134;refseq.positionType=intron	GT	0/0	0/0	0/1	0/1	0/1	0/0	1/1	0/0	0/0	0/1	1/1	0/0	0/1	0/0	0/0	0/1	0/0	0/1	1/1	0/0	0/0	1/1	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/0	1/1	0/0	0/0	0/0	0/0	0/0	1/1	1/1	0/0	1/1	0/1	0/0	0/1	1/1	0/1	1/1	0/1	0/1	0/0	0/1	1/1	0/0	0/1	0/0	0/1	1/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	1/1	1/1	0/0	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/0	0/0	1/1	0/1	0/0	0/1	0/1	0/0	1/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	1/1	0/1	1/1	0/1	0/0	0/0	1/1	0/1	1/1	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/1	1/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1
+chr2	27787778	.	AAATTAAAATTCTAC	A	.	PASS	VC=INDEL;AC=10;AF=0.03;AN=316	GT	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr2	28368075	.	CACAG	C	.	PASS	VC=INDEL;AC=0;AF=0;AN=306;refseq.name=NM_199193;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr2	28792105	.	A	AATA	.	PASS	VC=INDEL;AC=100;AF=0.32;AN=308;refseq.name=NM_153021;refseq.positionType=intron	GT	0/1	0/1	0/0	0/1	0/0	0/0	1/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	1/1	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	1/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/1	0/1	0/0	0/0	0/1	1/1	0/0	0/1	0/1	0/1	0/0	0/0	0/1	0/0	0/1	0/0	1/1	./.	1/1	./.	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	1/1	1/1	1/1	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/1	./.	0/1	1/1	0/1	0/1	1/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	1/1	0/0	0/1	0/1	0/0	1/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/1	./.	1/1	0/1
+chr2	29191749	.	GA	G	.	PASS	VC=INDEL;AC=87;AF=0.28;AN=316	GT	0/1	0/0	0/0	1/1	0/0	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/1	1/1	0/1	1/1	1/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	1/1	0/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	1/1	0/1	1/1	0/1	1/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	1/1	0/1	1/1	0/1	0/0	0/0	0/1	0/1	1/1	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	1/1	1/1	0/0	0/0	0/0	1/1	0/0	0/1	1/1	0/1	0/1	0/0	1/1	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	1/1	0/0	0/1	0/0	0/1
+chr2	29191750	.	AA	A	.	PASS	VC=INDEL;AC=86;AF=0.27;AN=316	GT	0/1	0/0	0/0	1/1	0/0	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/1	1/1	0/1	1/1	1/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	1/1	0/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	1/1	0/1	1/1	0/1	1/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	1/1	0/1	1/1	0/1	0/0	0/0	0/1	0/1	1/1	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	1/1	1/1	0/0	0/0	0/0	1/1	0/0	0/1	1/1	0/1	0/1	0/0	1/1	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	1/1	0/0	0/1	0/0	0/1
+chr2	29738576	.	TA	T	.	PASS	VC=INDEL;AC=284;AF=0.9;AN=316;refseq.name=NM_004304;refseq.positionType=intron	GT	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	0/0	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/0	0/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	0/0	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1
+chr2	29738577	.	AA	A	.	PASS	VC=INDEL;AC=284;AF=0.9;AN=316;refseq.name=NM_004304;refseq.positionType=intron	GT	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	0/0	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/0	0/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	0/0	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1
+chr2	30158127	.	C	CA	.	PASS	VC=INDEL;AC=192;AF=0.61;AN=316	GT	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	1/1	0/0	0/1	0/0	0/0	0/0	0/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	0/1	0/1	0/0	0/0	0/1	1/1	0/1	0/1	0/1	1/1	1/1	0/1	0/1	1/1	1/1	0/1	0/1	1/1	0/0	0/1	0/0	0/1	1/1	1/1	0/0	0/1	1/1	0/1	0/1	0/0	1/1	1/1	0/0	1/1	1/1	0/1	1/1	0/1	0/1	0/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	0/0	0/1	1/1	0/0	0/1	1/1	0/1	0/1	0/0	0/1	0/1	1/1	0/1	0/1	0/1	0/1	0/1	1/1	1/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/0	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	0/1	0/0	0/0	0/1	0/0	1/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/1	1/1	1/1	0/1	0/0	0/0	1/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	0/0	0/0
+chr2	30158129	.	A	AA	.	PASS	VC=INDEL;AC=192;AF=0.61;AN=316	GT	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	1/1	0/0	0/1	0/0	0/0	0/0	0/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	0/1	0/1	0/0	0/0	0/1	1/1	0/1	0/1	0/1	1/1	1/1	0/1	0/1	1/1	1/1	0/1	0/1	1/1	0/0	0/1	0/0	0/1	1/1	1/1	0/0	0/1	1/1	0/1	0/1	0/0	1/1	1/1	0/0	1/1	1/1	0/1	1/1	0/1	0/1	0/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	0/0	0/1	1/1	0/0	0/1	1/1	0/1	0/1	0/0	0/1	0/1	1/1	0/1	0/1	0/1	0/1	0/1	1/1	1/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/0	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	0/1	0/0	0/0	0/1	0/0	1/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/1	1/1	1/1	0/1	0/0	0/0	1/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	0/0	0/0
+chr2	30645653	.	A	AAGCTTTTCTAATGAACATCTACAAGACTGTTGTG	.	PASS	VC=INDEL;AC=303;AF=0.96;AN=316	GT	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	0/1
+chr2	30727159	.	C	CAGTCTATATGCC	.	PASS	VC=INDEL;AC=189;AF=0.6;AN=316;refseq.name=NM_182551;refseq.positionType=intron	GT	0/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	1/1	0/1	0/1	0/1	0/0	1/1	0/1	0/0	0/1	0/1	0/0	0/0	0/1	1/1	1/1	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/1	1/1	0/0	0/1	0/0	0/0	0/1	0/1	1/1	0/1	0/1	1/1	0/0	0/1	0/1	0/0	0/0	0/1	1/1	0/1	0/1	0/1	0/0	1/1	1/1	1/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	1/1	0/0	0/0	0/0	0/0	0/1
+chr2	30727390	.	GTTG	G	.	PASS	VC=INDEL;AC=31;AF=0.1;AN=314;refseq.name=NM_182551;refseq.positionType=intron	GT	0/0	0/0	0/0	0/1	0/0	0/0	1/1	0/1	0/1	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0
+chr2	30855218	.	CCATGGGA	C	.	PASS	VC=INDEL;AC=0;AF=0;AN=316;refseq.name=NM_182551;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr2	30937800	.	GATTTT	G	.	PASS	VC=INDEL;AC=14;AF=0.06;AN=244	GT	0/0	./.	./.	./.	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	./.	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	./.	0/0	0/1	0/0	0/0	./.	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	./.	0/0	0/1	./.	./.	./.	0/0	0/1	0/0	./.	0/1	0/1	0/1	./.	./.	0/1	./.	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	./.	./.	./.	0/0	0/1	./.	0/0	0/0	0/0	0/0	0/0	0/1	./.	0/0	0/1	0/0	0/0	0/0	./.	0/1	./.	./.	0/1	./.	./.
+chr2	31084461	.	AATAAAATACAG	A	.	PASS	VC=INDEL;AC=36;AF=0.11;AN=316	GT	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/0	0/0	0/0	1/1	0/0	1/1	0/0	0/0	0/0	1/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/0	1/1	1/1	0/0	1/1	0/0	0/0	0/0	0/0	1/1	1/1	1/1	1/1	0/0	1/1	0/0	0/0	0/0	0/0	0/0
+chr2	31249797	.	ATATC	A	.	PASS	VC=INDEL;AC=34;AF=0.11;AN=316;refseq.name=NM_024572;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1
+chr2	31249799	.	ATCTA	A	.	PASS	VC=INDEL;AC=47;AF=0.16;AN=302;refseq.name=NM_024572;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	1/1	0/0	0/0	./.	0/0	0/0	0/1	0/0	1/1	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/0	./.	0/0	0/0	0/0	1/1	1/1	0/0	0/0	0/0	0/0	1/1	./.	0/0	0/0	0/0	0/0	0/0	0/0	1/1	1/1	1/1	0/0	1/1	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	1/1	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	1/1	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	1/1	1/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1
+chr2	31374768	.	AGTA	A	.	PASS	VC=INDEL;AC=13;AF=0.05;AN=278	GT	0/0	0/0	0/0	./.	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	./.	0/0	0/1	0/0	0/0	0/0	0/0	0/0	./.	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	./.	0/0	./.	0/0	0/1	./.	0/0	0/0	0/0	0/0	0/1	0/0	0/1	./.	0/0	0/0	0/1	0/0	0/0	./.	0/0	0/0	0/0	./.	0/0	./.	0/0	0/1	./.	./.	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0
+chr2	31499486	.	C	CC	.	PASS	VC=INDEL;AC=11;AF=0.03;AN=316	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr2	32845664	.	A	AT	.	PASS	VC=INDEL;AC=138;AF=0.44;AN=316	GT	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/0	1/1	1/1	1/1	1/1	0/0	0/1	1/1	0/0	1/1	1/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/1	1/1	1/1	1/1	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/1	1/1	1/1	0/1	1/1	0/1	0/0	0/1	0/0	1/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	1/1	0/1	1/1	0/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	1/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/1	1/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	1/1	1/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	1/1	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/1	1/1	1/1	0/1	0/0	0/1	0/0	1/1	0/1	0/1	0/1	1/1	0/0	0/0	0/0	0/1	0/1	1/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	1/1	0/1	0/0	1/1
+chr2	32845666	.	T	TT	.	PASS	VC=INDEL;AC=138;AF=0.44;AN=316	GT	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/0	1/1	1/1	1/1	1/1	0/0	0/1	1/1	0/0	1/1	1/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/1	1/1	1/1	1/1	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/1	1/1	1/1	0/1	1/1	0/1	0/0	0/1	0/0	1/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	1/1	0/1	1/1	0/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	1/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/1	1/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	1/1	1/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	1/1	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/1	1/1	1/1	0/1	0/0	0/1	0/0	1/1	0/1	0/1	0/1	1/1	0/0	0/0	0/0	0/1	0/1	1/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	1/1	0/1	0/0	1/1
+chr2	33393523	.	AGCAA	A	.	PASS	VC=INDEL;AC=10;AF=0.03;AN=308;refseq.name=NM_206943;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr2	33403610	.	ATTG	A	.	PASS	VC=INDEL;AC=46;AF=0.15;AN=316;refseq.name=NM_206943;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	1/1	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	1/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/0
+chr2	33478311	.	TGAGT	T	.	PASS	VC=INDEL;AC=2;AF=0.01;AN=314;refseq.name=NM_206943;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr2	33542959	.	TT	T	.	PASS	VC=INDEL;AC=258;AF=0.82;AN=316;refseq.name=NM_206943;refseq.positionType=intron	GT	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	0/0	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	0/0	0/1	0/0	0/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	0/0	0/0	0/0	1/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	0/1	0/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	0/1	0/1	0/1	0/0	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1
+chr2	33760624	.	C	CC	.	PASS	VC=INDEL;AC=5;AF=0.02;AN=216;refseq.name=NM_170672;refseq.positionType=intron	GT	0/1	./.	0/0	0/0	0/0	0/0	./.	0/0	./.	0/1	0/0	0/0	0/1	0/0	0/0	./.	0/0	./.	0/0	0/0	0/0	0/1	./.	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	./.	./.	0/0	0/0	./.	./.	0/0	./.	./.	./.	0/0	./.	0/0	./.	0/0	./.	0/0	./.	0/0	0/0	./.	0/0	0/0	0/0	./.	./.	0/0	./.	0/0	0/0	./.	./.	0/0	0/0	./.	./.	0/0	./.	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	./.	0/0	0/0	0/0	0/0	./.	0/0	0/0	./.	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	./.	0/0	0/0	0/0	./.	0/0	0/0	./.	0/0	0/0	./.	./.	./.	0/0	./.	0/0	./.	0/0	./.	0/0	./.	0/0	./.	0/0	0/0	./.	./.	0/0	0/0	0/0	./.	0/0	0/0
+chr2	33899643	.	G	GGAG	.	PASS	VC=INDEL;AC=261;AF=0.83;AN=316	GT	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	0/1	0/1	1/1	0/0	0/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	0/1	0/1	1/1	0/0	0/0	0/1	0/1	0/1	0/0	1/1	0/0	1/1	0/1	0/1	0/1	0/0	1/1	1/1	0/1	0/1	0/1	1/1	0/1	0/0	0/1	1/1	1/1	1/1	0/0	1/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0
+chr2	34119549	.	A	AA	.	PASS	VC=INDEL;AC=45;AF=0.14;AN=316	GT	1/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	1/1	0/0	1/1	0/1	0/0	1/1	0/1	0/1	0/0	0/0	0/1	1/1	1/1	1/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	1/1	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	1/1	0/0	0/0	1/1	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/1	1/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	1/1
+chr2	34427438	.	A	AT	.	PASS	VC=INDEL;AC=175;AF=0.76;AN=230	GT	0/1	0/1	./.	0/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	./.	./.	0/1	1/1	./.	./.	./.	./.	0/0	0/1	0/1	./.	./.	./.	0/1	1/1	0/1	0/1	0/1	1/1	./.	0/1	1/1	./.	1/1	./.	1/1	0/1	./.	./.	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	./.	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	./.	1/1	1/1	0/1	0/1	1/1	./.	1/1	1/1	0/1	0/1	0/1	1/1	./.	1/1	1/1	./.	0/1	1/1	./.	0/1	./.	./.	./.	./.	1/1	1/1	./.	1/1	1/1	./.	1/1	1/1	0/1	./.	1/1	0/1	0/1	1/1	./.	0/1	1/1	0/1	./.	0/1	1/1	1/1	0/1	0/0	0/0	0/1	./.	1/1	./.	1/1	1/1	1/1	./.	1/1	1/1	0/0	0/0	0/1	0/1	1/1	0/0	./.	./.	1/1	1/1	./.	1/1	0/1	0/1	./.	1/1	./.	0/1	0/1	0/1	1/1	./.	./.	0/1	0/1	./.	1/1	0/0	1/1	1/1	0/1
+chr2	34841691	.	TGAAT	T	.	PASS	VC=INDEL;AC=165;AF=0.79;AN=210	GT	./.	./.	./.	1/1	./.	./.	./.	0/1	./.	1/1	0/1	./.	1/1	./.	./.	1/1	1/1	1/1	1/1	1/1	0/1	./.	./.	./.	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	./.	0/0	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	./.	1/1	1/1	./.	./.	1/1	1/1	./.	./.	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	0/1	0/1	0/0	./.	./.	./.	./.	1/1	./.	0/1	1/1	./.	0/1	0/1	0/0	1/1	1/1	1/1	./.	1/1	1/1	1/1	0/1	0/0	./.	./.	./.	0/1	./.	./.	1/1	0/1	./.	./.	0/1	./.	./.	0/1	0/1	1/1	./.	0/1	./.	./.	./.	0/1	./.	0/1	0/0	1/1	./.	0/1	./.	0/1	0/1	./.	0/1	0/0	0/1	1/1	1/1	./.	0/1	1/1	0/0	1/1	0/1	1/1	0/1	0/1	1/1	./.	./.	0/1	1/1	0/1	./.	./.
+chr2	35025338	.	G	GG	.	PASS	VC=INDEL;AC=227;AF=0.72;AN=314	GT	0/1	0/0	1/1	0/1	1/1	1/1	0/0	1/1	0/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	0/0	1/1	1/1	0/1	1/1	0/1	0/0	0/1	0/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1	0/1	0/1	1/1	0/0	1/1	0/0	1/1	0/1	0/1	0/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1	0/0	1/1	1/1	0/1	1/1	1/1	0/0	0/0	1/1	1/1	0/1	0/0	1/1	0/1	1/1	./.	0/1	1/1	0/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	0/1	0/1	1/1	1/1	0/1	0/0	0/1	1/1	1/1	1/1	1/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	0/0	1/1	0/1	1/1	1/1	0/0
+chr2	35255151	.	TCT	T	.	PASS	VC=INDEL;AC=29;AF=0.09;AN=316	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	1/1	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr2	35667838	.	A	AGG	.	PASS	VC=INDEL;AC=54;AF=0.21;AN=252	GT	0/0	./.	./.	./.	0/1	0/1	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	./.	./.	0/0	./.	0/0	0/0	./.	./.	0/1	0/0	0/0	0/0	./.	0/0	0/0	0/1	0/0	./.	./.	./.	./.	./.	0/1	0/0	0/1	./.	0/1	0/1	0/1	0/0	./.	0/1	0/1	0/1	./.	0/1	0/0	0/0	0/1	0/1	0/0	0/1	./.	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/0	0/1	./.	0/1	./.	0/1	0/0	0/1	0/0	0/0	0/0	0/0	./.	0/1	./.	0/1	0/1	./.	0/0	0/1	0/0	0/0	./.	0/0	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	./.	0/1	./.	0/0	0/0	0/0	0/1	0/0	0/0	0/0	./.	0/1	0/1	0/0	0/0	0/0	0/1	./.	0/0	./.	./.	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	./.	0/0	0/0	0/0	0/1	0/0	0/0	0/0
+chr2	35668564	.	A	AG	.	PASS	VC=INDEL;AC=275;AF=0.87;AN=316	GT	0/1	1/1	1/1	1/1	1/1	1/1	0/0	1/1	1/1	1/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	0/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	1/1	1/1
+chr2	36779604	.	C	CTT	.	PASS	VC=INDEL;AC=130;AF=0.44;AN=298;refseq.name=NM_001042548;refseq.positionType=exon	GT	1/1	0/0	1/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	./.	0/0	./.	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	1/1	0/1	1/1	0/1	0/1	1/1	1/1	0/1	1/1	0/0	0/1	0/0	0/1	1/1	0/1	0/1	1/1	0/1	0/1	1/1	0/0	0/1	0/1	0/0	0/0	0/0	1/1	0/1	0/1	1/1	0/0	1/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	0/0	./.	0/0	0/1	0/1	0/1	1/1	0/1	0/1	0/1	0/0	0/1	1/1	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/0	./.	1/1	0/1	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	./.	0/0	0/0	0/1	0/1	./.	0/1	1/1	1/1	0/1	1/1	1/1	0/0	0/1	0/1	0/0	0/1	0/1	1/1	1/1	1/1	0/0	./.	0/0	1/1	1/1	1/1	0/0	0/0	0/0	./.	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	./.	0/1	1/1	0/1	1/1	1/1	0/1	0/0	1/1	1/1	1/1	0/1	0/0
+chr2	37233064	.	ACT	A	.	PASS	VC=INDEL;AC=48;AF=0.16;AN=302;refseq.name=NM_019024;refseq.positionType=intron	GT	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	./.	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/0	./.	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/1	1/1	0/0	0/1	0/1	0/0	0/1	0/1	0/0	./.	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	./.	0/0	0/0	./.	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	./.	0/0
+chr2	37865906	.	GA	G	.	PASS	VC=INDEL;AC=161;AF=0.51;AN=314	GT	0/0	1/1	0/1	0/1	0/1	0/0	0/0	1/1	1/1	0/1	0/1	0/0	0/1	0/1	0/0	1/1	0/0	1/1	1/1	0/1	0/1	0/1	0/1	1/1	0/0	0/0	0/1	1/1	1/1	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	1/1	0/0	0/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	0/0	0/0	1/1	0/1	0/0	0/1	0/1	0/1	1/1	0/1	0/1	0/1	1/1	1/1	0/0	0/1	0/1	0/1	0/0	1/1	0/1	1/1	0/1	./.	1/1	1/1	0/1	1/1	1/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/0	1/1	0/1	1/1	0/0	0/1	0/0	0/1	0/1	0/0	0/1	1/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	1/1	0/1	0/1	0/0	0/0	1/1	0/1	0/1	0/0	0/1	1/1	0/1	0/1	1/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/0
+chr2	37960289	.	A	AG	.	PASS	VC=INDEL;AC=1;AF=0;AN=302	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	./.
+chr2	38003881	.	T	TAGA	.	PASS	VC=INDEL;AC=312;AF=0.99;AN=316	GT	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1
+chr2	38079466	.	CAT	C	.	PASS	VC=INDEL;AC=93;AF=0.3;AN=308	GT	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	1/1	0/0	0/1	0/0	0/1	0/1	1/1	0/1	0/1	0/1	0/1	1/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/1	1/1	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/1	1/1	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	./.	0/0	0/0	1/1	0/1	0/1	0/1	0/1	0/1	1/1	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/1	1/1	0/0	0/0	0/1	0/0	./.	0/0	0/1	0/1	0/0	1/1	0/1	0/1	1/1	1/1	1/1	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	./.	0/0	0/0	0/0	0/1	1/1	0/0	0/0	0/0	./.	0/1	0/0
+chr2	38476518	.	T	TCA	.	PASS	VC=INDEL;AC=179;AF=0.57;AN=316	GT	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	1/1	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/1	0/1	1/1	1/1	0/1	1/1	0/1	0/1	1/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	1/1	0/0	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	0/0	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/0	1/1	0/1	0/1	1/1	0/1	0/1	1/1	1/1	0/1	0/0	0/1	0/1	0/0	0/0	1/1	1/1	1/1	0/1	0/0	0/1	0/0	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/0	0/0	0/1	0/0	0/0	0/1	1/1	1/1	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/1	1/1	1/1	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/1	1/1	1/1	1/1	0/1	0/1	0/1	0/0	0/0	1/1	1/1	0/1	0/1	0/0	0/0	0/0	0/1
+chr2	38682923	.	T	TTTCTCTCT	.	PASS	VC=INDEL;AC=35;AF=0.11;AN=316	GT	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	1/1	0/0
+chr2	38990657	.	C	CACTT	.	PASS	VC=INDEL;AC=241;AF=0.76;AN=316	GT	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1	1/1	0/0	0/1	0/1	0/1	1/1	0/1	0/1	0/0	0/1	0/1	0/0	1/1	0/1	1/1	0/0	0/1	0/1	1/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1	0/1	0/1	1/1	0/0	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	0/1	0/1	0/1	1/1	1/1	0/0	0/1	0/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/0	0/1	1/1	1/1	1/1	0/1	0/1	0/0	1/1	0/1	1/1	0/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1
+chr2	39202671	.	TCAC	T	.	PASS	VC=INDEL;AC=68;AF=0.22;AN=314	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	1/1	0/1	0/0	0/1	1/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/1	1/1	0/1	0/1	1/1	0/0	0/0	0/0	1/1	0/1	1/1	0/0	0/1	1/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	1/1	0/0	0/0	0/0	1/1	0/1	0/1	0/0	0/1	0/0	./.	1/1	1/1	0/1	1/1	1/1	0/0	0/0	0/1	0/1	1/1	0/1	0/0	0/0
+chr2	39848964	.	GACTA	G	.	PASS	VC=INDEL;AC=92;AF=0.3;AN=304	GT	0/0	0/1	0/1	0/1	0/0	1/1	0/1	0/0	0/0	1/1	0/1	0/0	0/1	0/0	1/1	0/1	0/0	1/1	0/1	0/0	./.	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	1/1	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/1	1/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	1/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/1	./.	0/0	0/1	0/1	0/1	0/0	1/1	0/1	0/1	./.	0/1	0/0	0/1	1/1	1/1	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/0	./.	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	./.	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	1/1	1/1
+chr2	40095196	.	TCTT	T	.	PASS	VC=INDEL;AC=22;AF=0.07;AN=316	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr2	40207026	.	AA	A	.	PASS	VC=INDEL;AC=1;AF=0;AN=314	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1
+chr2	40328669	.	A	ATC	.	PASS	VC=INDEL;AC=182;AF=0.58;AN=316	GT	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/0	1/1	1/1	0/0	0/1	1/1	0/1	0/1	0/0	1/1	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/1	1/1	1/1	1/1	0/0	0/1	0/0	1/1	0/1	1/1	0/0	0/1	0/1	1/1	1/1	0/1	1/1	0/1	0/0	0/1	0/1	1/1	1/1	0/1	1/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	0/0	0/0	1/1	0/1	0/1	0/1	1/1	0/1	0/1	0/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	0/0	1/1	0/1	0/1	1/1	0/1	0/0	0/1	0/1	1/1	0/1	0/1	1/1	0/1	0/1	0/1	0/0	0/1	1/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	1/1	1/1	0/1	0/0	0/1	1/1	0/1	0/1	1/1	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/0	1/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/1	1/1	1/1
+chr2	40396501	.	G	GTCAG	.	PASS	VC=INDEL;AC=13;AF=0.04;AN=310;refseq.name=NM_001112802;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	./.	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0
+chr2	40446174	.	T	TCTACCTGCAACCCTTGATTGGCCTC	.	PASS	VC=INDEL;AC=196;AF=0.62;AN=314;refseq.name=NM_001112802;refseq.positionType=intron	GT	1/1	0/1	0/1	0/1	0/0	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/0	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	1/1	1/1	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	1/1	0/1	0/0	0/1	0/1	0/0	0/0	1/1	0/1	0/1	./.	0/0	1/1	1/1	1/1	0/0	0/1	0/0	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	0/0	0/0	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/0	1/1	0/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	0/0	1/1	0/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	0/1	0/0	1/1	1/1
+chr2	40527545	.	T	TGC	.	PASS	VC=INDEL;AC=69;AF=0.22;AN=316;refseq.name=NM_001112802;refseq.positionType=intron	GT	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/0	1/1	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/1	1/1	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	1/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	1/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	1/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0
+chr2	40764424	.	TATG	T	.	PASS	VC=INDEL;AC=6;AF=0.02;AN=314	GT	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr2	40840587	.	A	ATTG	.	PASS	VC=INDEL;AC=15;AF=0.06;AN=242	GT	./.	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	./.	./.	./.	./.	0/0	0/0	0/0	0/0	0/0	./.	./.	0/0	0/0	0/0	0/0	0/0	./.	0/0	./.	./.	0/0	0/0	./.	0/0	0/0	./.	0/0	0/0	./.	0/1	0/0	./.	./.	./.	./.	0/0	./.	./.	0/0	0/1	0/0	0/1	./.	0/0	./.	1/1	0/0	./.	0/1	0/0	0/1	./.	./.	./.	./.	./.	./.	0/0	0/0	0/0	0/0	0/0	./.	1/1	0/0	1/1	0/0	0/0	0/1	./.	0/0	0/1	./.	./.	./.	0/0	0/0
+chr2	41367520	.	A	AT	.	PASS	VC=INDEL;AC=187;AF=0.6;AN=314	GT	1/1	1/1	0/0	0/0	0/0	0/1	1/1	0/1	1/1	0/0	1/1	0/1	0/0	1/1	0/1	0/1	0/0	1/1	0/1	0/1	1/1	0/0	0/1	1/1	0/1	1/1	0/1	0/1	0/0	1/1	1/1	1/1	0/1	0/0	0/1	0/1	1/1	1/1	1/1	0/0	0/0	0/0	0/1	0/0	0/1	1/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	1/1	1/1	0/1	1/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	0/0	1/1	0/1	1/1	1/1	1/1	0/1	0/0	0/1	0/1	1/1	0/0	0/1	0/1	0/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	0/1	0/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1
+chr2	41554849	.	TCAGA	T	.	PASS	VC=INDEL;AC=231;AF=0.74;AN=314	GT	./.	1/1	1/1	0/1	1/1	0/1	0/1	0/1	1/1	0/1	0/1	1/1	1/1	0/1	0/1	1/1	0/0	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	0/0	1/1	0/1	1/1	0/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	0/0	1/1	0/1	0/1	0/1	0/0	1/1	0/1	0/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	0/1	0/1	0/0	0/0	1/1	0/1	0/0	1/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/0	1/1	1/1
+chr2	41554851	.	AGACA	A	.	PASS	VC=INDEL;AC=233;AF=0.74;AN=316	GT	1/1	1/1	1/1	0/1	1/1	0/1	0/1	0/1	1/1	0/1	0/1	1/1	1/1	0/1	0/1	1/1	0/0	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	0/0	1/1	0/1	1/1	0/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	0/0	1/1	0/1	0/1	0/1	0/0	1/1	0/1	0/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	0/1	0/1	0/0	0/0	1/1	0/1	0/0	1/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/0	1/1	1/1
+chr2	41628974	.	G	GA	.	PASS	VC=INDEL;AC=282;AF=0.9;AN=314	GT	0/1	1/1	1/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	0/0	1/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	0/1	1/1	1/1	0/0	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/0	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1
+chr2	41628975	.	A	AA	.	PASS	VC=INDEL;AC=281;AF=0.9;AN=312	GT	0/1	1/1	1/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	0/0	1/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	./.	0/1	0/1	1/1	1/1	0/1	1/1	1/1	0/0	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/0	1/1	1/1	1/1	1/1	1/1	./.	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1
+chr2	41838136	.	GGC	G	.	PASS	VC=INDEL;AC=0;AF=0;AN=316	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr2	42604189	.	CTTATGGGTTAC	C	.	PASS	VC=INDEL;AC=3;AF=0.01;AN=316	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr2	42773644	.	C	CC	.	PASS	VC=INDEL;AC=111;AF=0.35;AN=316	GT	0/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	0/0	0/0	1/1	0/1	1/1	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	1/1	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/0	1/1	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/1	0/0	1/1	0/1	0/1	1/1	1/1	0/1	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	1/1	0/1	0/0	0/1	0/1	0/1	1/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	1/1	0/1	0/0	1/1
+chr2	43140881	.	TA	T	.	PASS	VC=INDEL;AC=0;AF=0;AN=316	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr2	43205232	.	A	AAG	.	PASS	VC=INDEL;AC=287;AF=0.91;AN=316	GT	0/1	1/1	1/1	0/1	0/1	1/1	0/0	1/1	1/1	0/0	1/1	0/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1
+chr2	43324908	.	C	CA	.	PASS	VC=INDEL;AC=316;AF=1;AN=316	GT	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1
+chr2	43570900	.	TCT	T	.	PASS	VC=INDEL;AC=84;AF=0.27;AN=316;refseq.name=NM_022065;refseq.positionType=intron	GT	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	1/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/1	1/1	0/1	1/1	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	1/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	1/1	1/1	0/1	1/1	0/0	0/1	0/0	0/1	0/0	1/1	0/1	0/0	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	0/0	0/0	1/1	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	1/1	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/1	1/1	0/1	0/0
+chr2	44397082	.	AAGAGTA	A	.	PASS	VC=INDEL;AC=39;AF=0.12;AN=316;refseq.name=NM_177968;refseq.positionType=intron	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	1/1	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	1/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	1/1	0/0	0/0	0/0	0/1	0/1	1/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0
+chr2	44735716	.	TAAAC	T	.	PASS	VC=INDEL;AC=189;AF=0.6;AN=316;refseq.name=NM_024766;refseq.positionType=intron	GT	1/1	0/0	0/0	1/1	0/1	0/0	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	0/0	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	0/1	0/1	0/1	0/1	0/1	1/1	0/1	1/1	0/1	0/1	0/1	0/1	0/0	0/1	1/1	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/0	1/1	0/0	0/1	0/1	1/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	0/0	0/1	0/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1	0/0	1/1	1/1	1/1	0/1	1/1	0/1	0/0	1/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	0/0	0/1	0/1	1/1	0/1	1/1	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/1	1/1	0/1	1/1	0/1	0/1	1/1	0/1	1/1	1/1	0/1
+chr2	45472533	.	T	TATA	.	PASS	VC=INDEL;AC=284;AF=0.92;AN=308	GT	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	./.	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1
+chr2	45472535	.	T	TAAT	.	PASS	VC=INDEL;AC=291;AF=0.92;AN=316	GT	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1
+chr2	47399270	.	TCA	T	.	PASS	VC=INDEL;AC=140;AF=0.44;AN=316;refseq.name=NM_001743;refseq.positionType=intron	GT	1/1	0/1	1/1	0/0	1/1	0/1	0/1	0/0	1/1	1/1	0/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	0/1	0/1	1/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/1	0/1	0/1	0/0	0/1	0/1	0/0	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	0/1	1/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	1/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	1/1	0/1
+chr2	48032874	.	ACTAT	A	.	PASS	VC=INDEL;AC=254;AF=0.8;AN=316;refseq.name=NM_000179;refseq.positionType=intron	GT	0/0	1/1	0/1	0/0	1/1	1/1	0/1	1/1	0/1	0/1	1/1	1/1	0/1	1/1	1/1	0/0	0/1	0/1	1/1	1/1	0/0	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/0	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	1/1	1/1	0/1	0/0	1/1	1/1	0/1	1/1	1/1	0/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/0	1/1	1/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/0	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1	1/1	0/0
+chr2	49026643	.	A	AA	.	PASS	VC=INDEL;AC=0;AF=0;AN=316	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr2	49468159	.	C	CTCTT	.	PASS	VC=INDEL;AC=57;AF=0.18;AN=316	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	1/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/1	1/1	0/0	0/1	0/0	1/1	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/1	0/1	1/1	1/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/0	1/1	0/1	0/1	1/1	0/0	0/1	0/0	1/1	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/0	1/1	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0
+chr2	49514324	.	GAAGAA	G	.	PASS	VC=INDEL;AC=179;AF=0.58;AN=310	GT	1/1	0/1	1/1	0/1	0/1	0/1	1/1	1/1	0/1	1/1	0/1	0/1	0/1	0/1	0/0	0/0	./.	1/1	0/1	1/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	0/0	0/1	0/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1	0/1	1/1	0/1	0/1	0/0	1/1	1/1	1/1	0/0	0/1	0/0	0/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	0/1	0/0	1/1	0/1	1/1	0/1	0/1	0/1	1/1	0/1	0/0	1/1	0/1	0/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	0/0	1/1	0/1	0/1	0/1	0/1	./.	0/0	0/0	0/0	1/1	0/1	./.	1/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	1/1	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/0	1/1	1/1	1/1	0/1	0/1	0/0	0/1	1/1	1/1	1/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/0	1/1	0/1	0/1	0/0	1/1	0/1	0/0	0/1	0/0	1/1
+chr2	49982314	.	T	TT	.	PASS	VC=INDEL;AC=196;AF=0.64;AN=304	GT	1/1	0/1	1/1	1/1	0/0	./.	0/0	0/1	1/1	1/1	0/1	0/1	1/1	0/1	0/0	0/1	0/1	0/1	0/1	1/1	0/0	0/0	0/1	0/0	1/1	1/1	1/1	0/1	0/1	0/1	0/1	1/1	0/1	0/0	0/0	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	0/0	1/1	0/1	0/0	1/1	0/0	0/0	1/1	1/1	0/1	1/1	1/1	0/1	0/0	1/1	0/1	1/1	0/1	1/1	0/1	0/1	1/1	1/1	0/0	0/1	1/1	0/1	0/1	0/0	1/1	0/1	1/1	0/0	0/1	0/1	0/1	0/1	0/1	./.	./.	0/1	0/1	0/0	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/1	1/1	0/1	1/1	./.	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	0/1	0/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	0/1	0/0	0/1	0/1	1/1	0/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	0/1	0/0	1/1	1/1	0/1	1/1	1/1	0/1
+chr2	50152899	.	TTTTC	T	.	PASS	VC=INDEL;AC=26;AF=0.1;AN=268;refseq.name=NM_004801;refseq.positionType=intron	GT	./.	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	./.	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	./.	./.	0/0	0/0	./.	0/1	./.	0/0	0/1	0/1	0/0	./.	0/0	0/1	0/1	0/0	0/0	0/0	./.	0/0	0/1	./.	./.	./.	0/1	0/0	0/1	./.	0/0	0/1	0/1	0/0	0/1	./.	0/0	0/0	0/0	./.	0/0	./.	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	./.	0/1	./.	0/1	0/0	0/0	0/1	0/0	0/0	0/0
+chr2	50693504	.	AAC	A	.	PASS	VC=INDEL;AC=193;AF=0.63;AN=306;refseq.name=NM_004801;refseq.positionType=intron	GT	0/0	1/1	1/1	0/1	1/1	0/0	0/1	0/1	1/1	1/1	0/1	1/1	0/0	0/1	1/1	0/0	0/0	0/1	0/0	1/1	0/0	0/0	0/1	0/0	1/1	1/1	1/1	0/0	0/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/0	0/1	1/1	0/1	0/1	1/1	1/1	0/0	0/0	1/1	0/0	0/0	0/1	1/1	1/1	1/1	0/1	./.	0/0	1/1	0/1	0/1	1/1	1/1	1/1	0/0	./.	1/1	0/1	./.	./.	0/1	0/0	0/1	0/1	0/0	0/1	0/0	1/1	0/1	0/1	0/1	0/0	0/0	1/1	0/0	0/1	0/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	0/1	./.	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/0	1/1	0/1	1/1	1/1	1/1	0/1	0/0	0/0	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	0/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	0/1	0/0	0/1	0/0	1/1	1/1	0/1	0/1	1/1	0/1
+chr2	50703696	.	C	CTG	.	PASS	VC=INDEL;AC=287;AF=0.91;AN=314;refseq.name=NM_004801;refseq.positionType=intron	GT	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	0/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	1/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1
+chr2	50703699	.	T	TGT	.	PASS	VC=INDEL;AC=285;AF=0.9;AN=316;refseq.name=NM_004801;refseq.positionType=intron	GT	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	0/1	0/0	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	1/1	0/1	0/0	0/1	0/1	0/0	0/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1
+chr2	51260591	.	T	TAT	.	PASS	VC=INDEL;AC=0;AF=0;AN=316;refseq.name=NM_004801;refseq.positionType=promoter	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr2	51281539	.	TT	T	.	PASS	VC=INDEL;AC=252;AF=0.8;AN=316	GT	0/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	0/1	0/1	0/0	1/1	0/1	1/1	1/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	0/0	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	0/1	0/1	0/1	0/0	1/1	0/1	0/1	1/1	0/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	0/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/0	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/0	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1
+chr2	51315220	.	A	ATT	.	PASS	VC=INDEL;AC=55;AF=0.19;AN=292	GT	0/0	0/1	0/1	0/1	1/1	0/1	0/1	1/1	0/0	0/1	./.	0/1	0/0	0/0	1/1	0/1	0/1	0/0	0/0	0/0	./.	1/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	1/1	0/0	./.	0/1	0/1	0/0	0/1	1/1	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/1	./.	0/0	0/1	0/1	1/1	0/1	0/1	0/0	0/0	./.	0/1	0/1	1/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	./.	./.	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	./.	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/1	0/1
+chr2	51315221	.	T	TTT	.	PASS	VC=INDEL;AC=56;AF=0.19;AN=300	GT	0/0	0/1	0/1	0/1	1/1	0/1	0/1	1/1	0/0	0/1	0/1	0/1	0/0	0/0	./.	0/1	0/1	0/0	0/0	0/0	0/0	1/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	1/1	0/0	0/1	0/1	0/1	0/0	0/1	1/1	0/0	0/1	0/0	0/0	0/1	0/0	./.	0/1	0/1	0/0	0/1	0/1	1/1	0/1	0/1	0/0	0/0	0/1	0/1	0/1	1/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	./.	0/1	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1
+chr2	51355364	.	TTT	T	.	PASS	VC=INDEL;AC=30;AF=0.1;AN=304	GT	0/0	0/1	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/1	0/1	1/1	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	./.	0/0	0/0
+chr2	52397945	.	A	ATGCTATTCCAATATCTCAG	.	PASS	VC=INDEL;AC=33;AF=0.15;AN=214	GT	0/1	./.	0/0	0/0	0/1	0/0	0/0	0/0	./.	./.	./.	0/1	./.	./.	./.	0/1	./.	0/1	0/1	./.	0/1	0/1	./.	0/1	./.	0/0	0/1	0/0	./.	0/0	./.	./.	0/0	0/0	./.	0/0	./.	./.	0/0	0/0	0/0	0/0	./.	./.	0/0	0/0	0/0	./.	0/0	0/0	./.	0/0	./.	0/0	./.	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	./.	0/0	0/0	0/0	./.	./.	0/0	0/0	0/0	0/1	./.	./.	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/1	./.	0/0	0/0	./.	./.	0/1	0/0	./.	0/1	./.	./.	0/1	0/0	0/1	0/1	./.	0/0	0/0	0/0	0/1	0/0	0/1	0/0	./.	./.	0/1	./.	0/1	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/1	0/1	./.	./.	./.	0/0	0/0	0/0	0/1	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	./.	0/0	./.	0/0	./.	0/0	0/1	./.	./.	0/0	0/0	./.	0/1	0/0	0/1	0/0	0/1
+chr2	52643648	.	G	GAG	.	PASS	VC=INDEL;AC=140;AF=0.53;AN=266	GT	0/1	./.	0/0	0/1	0/1	1/1	0/0	0/0	1/1	./.	0/1	0/1	0/1	0/1	0/1	0/1	./.	0/0	0/1	0/0	0/0	0/1	0/1	0/0	./.	./.	0/1	0/0	0/1	0/0	0/1	1/1	./.	0/0	0/1	0/0	1/1	1/1	1/1	0/1	0/0	./.	1/1	1/1	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/1	1/1	0/0	0/0	0/1	0/0	1/1	0/0	./.	./.	./.	0/0	./.	1/1	0/1	0/1	0/0	0/1	./.	0/0	0/0	0/1	0/0	1/1	0/1	0/1	0/1	0/1	./.	1/1	1/1	0/1	./.	1/1	1/1	1/1	0/1	0/0	./.	0/1	0/1	1/1	./.	./.	./.	0/1	1/1	./.	1/1	0/1	./.	./.	0/0	1/1	0/1	0/1	1/1	0/1	0/1	0/0	0/1	1/1	1/1	1/1	0/1	0/0	0/1	0/0	0/1	0/1	0/1	1/1	0/1	0/0	./.	0/1	1/1	./.	0/1	1/1	1/1	./.	0/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	0/1	1/1	1/1	0/1	1/1	./.	0/0	1/1	0/0	1/1	0/1	0/0	1/1
+chr2	53056176	.	G	GAG	.	PASS	VC=INDEL;AC=131;AF=0.49;AN=270	GT	1/1	0/0	0/1	./.	./.	0/0	./.	1/1	0/1	0/1	0/1	./.	./.	./.	./.	0/1	1/1	0/1	./.	0/1	./.	0/1	./.	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	./.	0/0	./.	0/1	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/0	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	1/1	./.	1/1	./.	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	0/0	0/0	0/0	./.	0/1	0/1	0/1	0/1	./.	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/1	./.	0/1	0/1	0/1	0/1	0/1	0/1	0/0	./.	0/1	0/0	./.	0/0	0/1	0/1	./.	0/1	0/1	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/1	./.	0/1	0/0	0/1	0/0	0/1	0/1	1/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/0	./.	1/1
+chr2	53674036	.	AA	A	.	PASS	VC=INDEL;AC=106;AF=0.34;AN=310	GT	0/0	0/1	0/1	0/0	0/0	0/0	1/1	0/1	0/1	0/0	0/0	1/1	0/0	1/1	0/1	0/1	0/0	0/1	0/0	0/0	1/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	1/1	0/0	0/1	0/1	1/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/0	1/1	0/0	0/0	0/1	0/0	0/1	1/1	1/1	1/1	0/0	0/1	0/1	0/1	0/0	1/1	0/1	0/1	1/1	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/1	./.	1/1	0/1	0/0	0/0	0/0	0/1	0/0	0/1	./.	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/1	1/1	1/1	0/0	0/1	0/0	0/0	0/0	1/1	0/1	0/1	0/1	0/0	0/0	0/1	0/0	0/1	0/1	1/1	0/0	0/1	0/1	0/0	0/1	0/0	1/1	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/1	./.	0/0	0/0	0/1	0/1	1/1	0/0	0/1	1/1	0/0	0/1	0/1	0/0	0/1	1/1	0/1	0/1	0/0	0/0	0/0	0/1	0/1
+chr2	53737951	.	AGGAT	A	.	PASS	VC=INDEL;AC=107;AF=0.35;AN=302	GT	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/1	0/1	0/0	0/1	./.	0/0	./.	0/0	0/1	0/0	1/1	0/1	0/1	0/0	0/1	1/1	0/1	0/1	1/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	./.	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	1/1	0/1	0/1	0/0	0/1	0/0	0/1	0/1	./.	1/1	1/1	0/1	0/0	./.	0/1	0/0	0/0	0/0	0/0	1/1	./.	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/1	1/1	1/1	0/1	0/0	0/1	./.	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	0/1	0/0	0/1	0/0	0/1	0/1	0/1	1/1	1/1	0/1	0/1	0/1	0/0	1/1	0/1	0/1	1/1	1/1	0/1	0/0	0/1	0/1	0/1	1/1	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0
+chr2	54573230	.	AACA	A	.	PASS	VC=INDEL;AC=62;AF=0.2;AN=316;refseq.name=NM_001100396;refseq.positionType=intron	GT	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	1/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	1/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/1	0/1	0/0	0/1	0/0	1/1	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/1	1/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/0	1/1	0/0	0/0	0/0	0/0	0/1
+chr2	54726113	.	G	GA	.	PASS	VC=INDEL;AC=269;AF=0.87;AN=308;refseq.name=NM_003128;refseq.positionType=intron	GT	1/1	0/0	1/1	0/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	0/0	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	0/0	0/1	0/1	0/1	1/1	1/1	0/1	0/1	0/0	1/1	./.	0/1	1/1	0/1	1/1	0/1	0/1	0/1	0/1	0/1	./.	0/1	1/1	1/1	0/0	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1
+chr2	54726287	.	T	TGTTA	.	PASS	VC=INDEL;AC=269;AF=0.85;AN=316;refseq.name=NM_003128;refseq.positionType=intron	GT	1/1	0/0	1/1	0/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	0/0	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	0/0	0/1	0/1	0/1	1/1	1/1	0/1	0/1	0/0	1/1	1/1	0/1	1/1	0/1	1/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	1/1	1/1	0/0	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1
+chr2	54783793	.	C	CTT	.	PASS	VC=INDEL;AC=270;AF=0.85;AN=316;refseq.name=NM_003128;refseq.positionType=intron	GT	0/1	0/0	1/1	0/1	0/1	0/1	0/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1	1/1	1/1	0/0	0/1	0/1	0/1	1/1	0/1	0/1	0/1	0/0	1/1	0/1	0/1	1/1	0/1	1/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	1/1	1/1	0/0	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1
+chr2	55080611	.	GCTTT	G	.	PASS	VC=INDEL;AC=3;AF=0.01;AN=310	GT	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	./.	0/0	0/0	./.	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr2	55174675	.	AC	A	.	PASS	VC=INDEL;AC=6;AF=0.02;AN=306	GT	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	./.	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.
+chr2	55208953	.	A	ATATGAATCACATACAAGCTAAGAAAC	.	PASS	VC=INDEL;AC=211;AF=0.67;AN=316;refseq.name=NM_020532;refseq.positionType=intron	GT	1/1	0/1	0/1	0/1	0/1	1/1	1/1	0/0	0/0	0/1	1/1	0/1	0/1	1/1	0/1	0/1	0/1	0/0	0/0	0/1	0/1	1/1	1/1	1/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	0/0	1/1	0/0	1/1	0/1	0/0	1/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	0/0	0/0	0/0	1/1	1/1	0/1	0/0	1/1	1/1	0/1	0/0	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	0/1	0/0	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	0/0	1/1	0/1	0/1	0/1	1/1	1/1	0/1	1/1	1/1	0/0	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	0/0	0/0	1/1	0/1	0/0	1/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1
+chr2	55208955	.	A	ATGAATCACATACAAGCTAAGAAACTA	.	PASS	VC=INDEL;AC=211;AF=0.67;AN=316;refseq.name=NM_020532;refseq.positionType=intron	GT	1/1	0/1	0/1	0/1	0/1	1/1	1/1	0/0	0/0	0/1	1/1	0/1	0/1	1/1	0/1	0/1	0/1	0/0	0/0	0/1	0/1	1/1	1/1	1/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	0/0	1/1	0/0	1/1	0/1	0/0	1/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	0/0	0/0	0/0	1/1	1/1	0/1	0/0	1/1	1/1	0/1	0/0	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	0/1	0/0	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	0/0	1/1	0/1	0/1	0/1	1/1	1/1	0/1	1/1	1/1	0/0	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	0/0	0/0	1/1	0/1	0/0	1/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1
+chr2	55284481	.	AA	A	.	PASS	VC=INDEL;AC=90;AF=0.28;AN=316	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/1	1/1	0/0	0/1	1/1	1/1	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/1	1/1	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/1	1/1	0/1	0/1	0/0	0/0	0/1	0/1	0/0	1/1	0/1	0/1	0/1	1/1	0/1	0/0	0/1	1/1	0/0	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/1	0/0	1/1	1/1	1/1	0/1	0/1	0/1	0/1	1/1	0/1	0/1	0/0
+chr2	55355370	.	CTG	C	.	PASS	VC=INDEL;AC=0;AF=0;AN=316	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr2	55473492	.	AA	A	.	PASS	VC=INDEL;AC=27;AF=0.11;AN=236;refseq.name=NM_002453;refseq.positionType=exon	GT	0/1	./.	0/0	./.	0/0	0/1	0/1	0/0	0/0	0/0	0/0	./.	./.	0/0	0/0	0/0	./.	0/0	0/1	./.	0/1	0/0	./.	./.	0/0	0/0	0/0	./.	0/0	0/0	0/0	./.	./.	0/0	0/0	./.	0/1	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	./.	0/0	./.	0/1	0/1	./.	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/1	./.	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	./.	0/0	0/1	0/0	./.	0/0	0/0	0/1	0/0	./.	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/1	0/0	0/1	./.	./.	0/0	0/0	0/0	0/0	./.	./.	0/0	./.	0/0	0/0	./.	0/0	0/1	0/0	./.	./.	0/0	./.	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	./.	./.	0/1	0/0	0/1	./.	0/0	0/1	0/0	0/0	./.	0/0	0/1	0/0	0/0	0/0	0/1	./.	0/0	0/0	0/0	./.	0/0	0/0	0/0	./.
+chr2	56088199	.	TA	T	.	PASS	VC=INDEL;AC=21;AF=0.07;AN=316	GT	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	1/1	0/1	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+chr2	56603301	.	G	GT	.	PASS	VC=INDEL;AC=118;AF=0.39;AN=306;refseq.name=NM_001080433;refseq.positionType=intron	GT	1/1	0/0	0/0	0/0	0/0	0/1	0/1	1/1	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/0	./.	1/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	1/1	0/0	1/1	0/1	0/1	0/1	1/1	1/1	1/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	1/1	0/1	0/0	1/1	0/1	1/1	1/1	1/1	1/1	0/0	0/1	1/1	1/1	1/1	./.	1/1	0/0	0/1	0/1	1/1	./.	0/1	0/1	0/1	1/1	0/0	0/1	0/1	0/1	0/1	1/1	0/0	0/1	0/1	1/1	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/0	1/1	0/1	1/1	1/1	0/1	0/1	1/1	0/0	0/1	1/1	0/1	1/1	0/1	1/1	1/1	0/0	0/1	0/1	0/0	0/1	0/0	1/1	1/1	1/1	1/1	0/0	0/1	1/1	0/0
+chr2	57161556	.	CCTT	C	.	PASS	VC=INDEL;AC=24;AF=0.1;AN=230	GT	0/1	./.	./.	0/0	0/0	./.	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	./.	./.	0/1	./.	0/0	0/0	./.	./.	./.	./.	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	./.	0/1	./.	0/0	0/0	0/1	0/0	./.	./.	./.	./.	0/0	./.	0/0	0/0	0/0	0/0	0/1	./.	0/0	./.	./.	./.	0/0	./.	0/1	0/1	./.	0/1	./.	0/1	0/1	./.	./.	./.	0/1	0/0	0/0	0/1	0/0	./.	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/1	./.	0/0	0/0	0/1	./.	0/0	0/0	./.	0/0	./.	0/1	./.	0/1	0/0	0/0	./.	./.	./.	0/1	./.	./.	./.	./.	0/0
+chr2	58167700	.	AA	A	.	PASS	VC=INDEL;AC=220;AF=0.73;AN=300	GT	0/1	1/1	0/1	0/0	1/1	1/1	0/0	1/1	0/0	1/1	./.	1/1	0/1	1/1	0/1	0/1	1/1	1/1	0/0	0/1	1/1	0/1	0/0	0/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	0/0	0/1	0/1	1/1	0/1	./.	1/1	0/1	1/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	./.	0/1	1/1	0/1	1/1	0/1	1/1	0/0	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	./.	0/1	0/1	1/1	0/1	1/1	0/1	0/1	0/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	./.	1/1	1/1	./.	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/0	0/0	0/1	1/1	0/1	0/1	0/0	0/1	1/1	0/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	./.	0/1	1/1
+chr2	58193832	.	A	ACAA	.	PASS	VC=INDEL;AC=35;AF=0.16;AN=222	GT	0/1	0/1	./.	0/0	./.	./.	0/0	0/0	0/0	./.	0/1	0/0	./.	./.	0/1	1/1	./.	./.	./.	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	0/1	./.	0/1	0/0	0/0	0/0	0/0	1/1	./.	0/0	0/0	./.	./.	0/0	./.	0/0	0/1	1/1	0/0	./.	0/0	./.	0/0	./.	0/0	./.	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	0/0	./.	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/0	./.	0/1	./.	./.	0/0	0/1	./.	0/0	./.	0/0	0/0	0/1	0/0	./.	0/1	./.	./.	0/0	./.	0/1	./.	./.	./.	./.	./.	0/0	0/0	0/0	0/0	0/1	0/0	0/1	./.	0/0	./.	0/1	0/0	0/0	./.	0/0	0/0	0/0	0/0	./.	0/0	./.	./.	1/1	0/0	0/1	0/0	./.	0/1	./.	0/1	0/0	0/0	./.	0/0	0/0	0/0	0/1	./.	0/0	./.	0/0	0/0
+chr2	58274884	.	C	CAGG	.	PASS	VC=INDEL;AC=125;AF=0.4;AN=314;refseq.name=NM_006296;refseq.positionType=intron	GT	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/1	0/1	1/1	0/0	0/1	0/0	0/1	1/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/1	1/1	1/1	1/1	0/0	1/1	0/1	0/1	0/0	0/1	1/1	1/1	1/1	0/0	1/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	1/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/0	0/0	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	0/0	0/1	0/1	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/1	./.	0/0	0/1	1/1	1/1	0/0	0/1	0/1	0/0	0/1	0/1	1/1	0/0	0/1	0/1	0/0	0/1	0/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	0/0	0/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	0/0	1/1	0/1	0/1	0/0	0/1	0/1	0/0	1/1	0/1	0/1	1/1	0/0	0/0
+chr2	58274891	.	A	AGGA	.	PASS	VC=INDEL;AC=123;AF=0.4;AN=308;refseq.name=NM_006296;refseq.positionType=intron	GT	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/1	0/1	1/1	0/0	0/1	0/0	0/1	1/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/1	1/1	1/1	1/1	0/0	./.	0/1	0/1	0/0	0/1	1/1	1/1	1/1	0/0	1/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	1/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	./.	0/0	0/0	0/0	0/0	1/1	0/0	0/0	0/0	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	0/0	0/1	0/1	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/1	./.	0/1	0/1	1/1	1/1	0/0	0/1	0/1	0/0	0/1	0/1	1/1	0/0	0/1	0/1	0/0	0/1	0/1	1/1	1/1	./.	0/1	1/1	1/1	1/1	1/1	0/1	0/1	0/0	0/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	0/0	1/1	0/1	0/1	0/0	0/1	0/1	0/0	1/1	0/1	0/1	1/1	0/0	0/0
+chr2	58283746	.	A	ACT	.	PASS	VC=INDEL;AC=268;AF=0.88;AN=304;refseq.name=NM_006296;refseq.positionType=intron	GT	0/1	1/1	0/1	0/1	1/1	1/1	0/1	0/1	./.	1/1	./.	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	./.	0/1	1/1	0/1	0/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	./.	1/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1
+chr2	58283749	.	C	CTC	.	PASS	VC=INDEL;AC=266;AF=0.86;AN=308;refseq.name=NM_006296;refseq.positionType=intron	GT	0/1	1/1	0/1	0/0	1/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/0	1/1	1/1	0/1	0/0	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	1/1	0/1	0/1	0/1	0/1	0/1	0/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	0/0	1/1	1/1	1/1	1/1	0/1	1/1	./.	0/1	0/1	./.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	./.	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	./.	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1
+chr2	58385305	.	T	TCTTA	.	PASS	VC=INDEL;AC=79;AF=0.25;AN=316;refseq.name=NM_006296;refseq.positionType=intron	GT	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	1/1	0/1	0/0	0/1	1/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/0	0/1	0/0	1/1	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/1	0/1	1/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	1/1	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	1/1	1/1	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/0
+chr2	58385307	.	T	TTACT	.	PASS	VC=INDEL;AC=79;AF=0.25;AN=316;refseq.name=NM_006296;refseq.positionType=intron	GT	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	1/1	0/1	0/0	0/1	1/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/0	0/1	0/0	1/1	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/1	0/1	1/1	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/0	1/1	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	1/1	1/1	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/0	0/1	0/1	0/1	0/1	0/0
diff --git a/tests/tabix_data/vcf/23.vcf b/tests/tabix_data/vcf/23.vcf
new file mode 100644
index 0000000..153bad6
--- /dev/null
+++ b/tests/tabix_data/vcf/23.vcf
@@ -0,0 +1,419 @@
+##fileformat=VCFv4.1
+##ApplyRecalibration="analysis_type=ApplyRecalibration input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=[20] excludeIntervals=null reference_sequence=/humgen/1kg/reference/human_g1k_v37.fasta rodBind=[/humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110608VQSRConsensus/calls/combined.phase1.chr20.raw.indels.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false recal_file=/humgen/gsa-scr1/delangel/VQSRIndels/data/trainMills75_truthMills75_p15_12_12_pctb0.05_std12.0_mG8_QD_FS_HS_RP_IC.recal tranches_file=/humgen/gsa-scr1/delangel/VQSRIndels/data/trainMills75_truthMills75_p15_12_12_pctb0.05_std12.0_mG8_QD_FS_HS_RP_IC.tranches out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub ts_filter_level=93.0 ignore_filter=null mode=INDEL"
+##CombineVariants="analysis_type=CombineVariants input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=[20:41000001-42000000] excludeIntervals=null reference_sequence=/humgen/1kg/reference/human_g1k_v37.fasta rodBind=[/humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110608VQSRConsensus/calls/chr20/AFR/AFR.phase1.chr20.42.raw.indels.vcf, /humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110608VQSRConsensus/calls/chr20/ASN/ASN.phase1.chr20.42.raw.indels.vcf, /humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110608VQSRConsensus/calls/chr20/AMR/AMR.phase1.chr20.42.raw.indels.vcf, /humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110608VQSRConsensus/calls/chr20/EUR/EUR.phase1.chr20.42.raw.indels.vcf, /humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110608VQSRConsensus/calls/chr20/AFR.admix/AFR.admix.phase1.chr20.42.raw.indels.vcf, /humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110608VQSRConsensus/calls/chr20/ASN.admix/ASN.admix.phase1.chr20.42.raw.indels.vcf, /humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110608VQSRConsensus/calls/chr20/AMR.admix/AMR.admix.phase1.chr20.42.raw.indels.vcf, /humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110608VQSRConsensus/calls/chr20/EUR.admix/EUR.admix.phase1.chr20.42.raw.indels.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub genotypemergeoption=PRIORITIZE filteredrecordsmergetype=KEEP_IF_ANY_UNFILTERED rod_priority_list=AFR.admix,AMR.admix,EUR.admix,ASN.admix,AFR,AMR,EUR,ASN printComplexMerges=false filteredAreUncalled=false minimalVCF=false setKey=set assumeIdenticalSamples=false minimumN=1 masterMerge=false mergeInfoWithMaxAC=true"
+##FILTER=<ID=BothStrands,Description="Variant not seen on both strands">
+##FILTER=<ID=HARD_TO_VALIDATE,Description="MQ0 >= 4 && (MQ0 / (1.0 * DP)) > 0.1">
+##FILTER=<ID=HP10,Description="Variant occurs in long homopolymer run (>10)">
+##FILTER=<ID=HaplotypeScore,Description="HaplotypeScore>20.0">
+##FILTER=<ID=HighCoverage,Description="Coverage at variant site is > 7500">
+##FILTER=<ID=HomopolymerRun,Description="HRun>=15">
+##FILTER=<ID=LongRepeat,Description="Variant occurs in long tandem repeat (as defined by 1kg phase one filters)">
+##FILTER=<ID=LowQual,Description="QUAL<30.0">
+##FILTER=<ID=PP20,Description="Variant posterior phred is < 20">
+##FILTER=<ID=QualByDepth,Description="QD<1.0">
+##FILTER=<ID=StrandBias,Description="SB>=-1.0">
+##FILTER=<ID=TruthSensitivityTranche93.00to94.00,Description="Truth sensitivity tranche level at VSQ Lod: 3.9628 <= x < 4.1824">
+##FILTER=<ID=TruthSensitivityTranche94.00to95.00,Description="Truth sensitivity tranche level at VSQ Lod: 3.7129 <= x < 3.9628">
+##FILTER=<ID=TruthSensitivityTranche95.00to96.00,Description="Truth sensitivity tranche level at VSQ Lod: 3.3717 <= x < 3.7129">
+##FILTER=<ID=TruthSensitivityTranche96.00to97.00,Description="Truth sensitivity tranche level at VSQ Lod: 2.8762 <= x < 3.3717">
+##FILTER=<ID=TruthSensitivityTranche97.00to98.00,Description="Truth sensitivity tranche level at VSQ Lod: 2.2618 <= x < 2.8762">
+##FILTER=<ID=TruthSensitivityTranche98.00to99.00+,Description="Truth sensitivity tranche level at VQS Lod < 1.2907">
+##FILTER=<ID=TruthSensitivityTranche98.00to99.00,Description="Truth sensitivity tranche level at VSQ Lod: 1.2907 <= x < 2.2618">
+##FORMAT=<ID=AA,Number=1,Type=Integer,Description="Alternate allele observations">
+##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth (only filtered reads used for calling)">
+##FORMAT=<ID=FT,Number=1,Type=String,Description="Sample Genotype Filter">
+##FORMAT=<ID=GL,Number=3,Type=Integer,Description="Genotype Likelihood, log-scaled likeilhoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy">
+##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=HQ,Number=.,Type=Integer,Description="Haplotype Quality">
+##FORMAT=<ID=PL,Number=3,Type=Float,Description="Normalized, Phred-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; not applicable if site is not biallelic">
+##FORMAT=<ID=RA,Number=1,Type=Integer,Description="Reference allele observations">
+##FORMAT=<ID=SA,Number=1,Type=Integer,Description="Number of alternate observations by strand, delimited by |: [forward]|[reverse]">
+##FORMAT=<ID=SP,Number=1,Type=Integer,Description="Phred-scaled strand bias P-value">
+##FORMAT=<ID=SR,Number=1,Type=Integer,Description="Number of reference observations by strand, delimited by |: [forward]|[reverse]">
+##INFO=<ID=AA,Number=1,Type=Integer,Description="Alternate allele observations">
+##INFO=<ID=AB,Number=1,Type=Float,Description="Allele balance at heterozygous sites: a number between 0 and 1 representing the ratio of reads showing the reference allele to all reads, considering only reads from individuals called as heterozygous">
+##INFO=<ID=ABA,Number=1,Type=Integer,Description="Alternate allele balance count: the number of sequence reads from apparent heterozygotes supporting the alternate allele">
+##INFO=<ID=ABP,Number=1,Type=Float,Description="Allele balance probability at heterozygous sites: Phred-scaled upper-bounds estimate of the probability of observing the deviation between ABR and ABA given E(ABR/ABA) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=ABR,Number=1,Type=Integer,Description="Reference allele balance count: the number of sequence reads from apparent heterozygotes supporting the reference allele">
+##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
+##INFO=<ID=AF1,Number=1,Type=Float,Description="Max-likelihood estimate of the site allele frequency of the first ALT allele">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##INFO=<ID=BL,Number=1,Type=Integer,Description="Base Pairs Left: number of base pairs in reads supporting the alternate to the left (5') of the alternate allele">
+##INFO=<ID=BR,Number=1,Type=Integer,Description="Base Pairs Right: number of base pairs in reads supporting the alternate to the right (3') of the alternate allele">
+##INFO=<ID=BVAR,Number=0,Type=Flag,Description="The best genotype combination in the posterior is variant (non homozygous).">
+##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
+##INFO=<ID=CI95,Number=2,Type=Float,Description="Equal-tail Bayesian credible interval of the site allele frequency at the 95% level">
+##INFO=<ID=CpG,Number=0,Type=Flag,Description="CpG site (either CpG, TpG or CpA)">
+##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership">
+##INFO=<ID=DEL,Number=0,Type=Flag,Description="deletion allele">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Filtered Depth">
+##INFO=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
+##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">
+##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions">
+##INFO=<ID=EL,Number=1,Type=Integer,Description="Allele End Left: number of observations of the alternate where the alternate occurs in the left end of the read">
+##INFO=<ID=EPP,Number=1,Type=Float,Description="End Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=ER,Number=1,Type=Integer,Description="Allele End Right: number of observations of the alternate where the alternate occurs in the right end of the read">
+##INFO=<ID=FQ,Number=1,Type=Float,Description="Phred probability that sample chromosomes are not all the same">
+##INFO=<ID=FR,Number=0,Type=Float,Description="Estimated population frequency">
+##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
+##INFO=<ID=HETAR,Number=1,Type=Integer,Description="Number of individuals heterozygous alternate / reference">
+##INFO=<ID=HOMA,Number=1,Type=Integer,Description="Number of individuals homozygous for the alternate">
+##INFO=<ID=HOMR,Number=1,Type=Integer,Description="Number of individuals homozygous for the reference">
+##INFO=<ID=HP,Number=1,Type=Integer,Description="Homopolmer run length">
+##INFO=<ID=HPLen,Number=1,Type=Integer,Description="Homopolymer length">
+##INFO=<ID=HR,Number=1,Type=Integer,Description="Homopolymer run length">
+##INFO=<ID=HRun,Number=1,Type=Integer,Description="Largest Contiguous Homopolymer Run of Variant Allele In Either Direction">
+##INFO=<ID=HU,Number=1,Type=String,Description="Homopolymer run unit (stranded)">
+##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes">
+##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Not provided in original VCF header">
+##INFO=<ID=INS,Number=0,Type=Flag,Description="insertion allele">
+##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">
+##INFO=<ID=IndelType,Number=1,Type=String,Description="Indel type description">
+##INFO=<ID=KGPilot123,Number=0,Type=Flag,Description="1000 Genome discovery all pilots 2010(1,2,3)">
+##INFO=<ID=LEN,Number=1,Type=Integer,Description="allele length">
+##INFO=<ID=LRB,Number=1,Type=Float,Description="((max(BR, BL) / (BR + BL)) - 0.5) * 2 : The proportion of base pairs in reads on one side of the alternate allele relative to total bases, scaled from [0.5,1] to [0,1]">
+##INFO=<ID=LRBP,Number=1,Type=Float,Description="Left-Right Balance Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between BL and BR given E(BR/BL) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=MNP,Number=0,Type=Flag,Description="MNP allele">
+##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
+##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
+##INFO=<ID=MQ0Fraction,Number=1,Type=Float,Description="Fraction of Mapping Quality Zero Reads">
+##INFO=<ID=MQM,Number=1,Type=Float,Description="Mean mapping quality of observed alternate alleles">
+##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
+##INFO=<ID=NF,Number=0,Type=Integer,Description="Total number of forward reads containing this variant">
+##INFO=<ID=NR,Number=0,Type=Integer,Description="Total number of reads containing this variant">
+##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data">
+##INFO=<ID=PP,Number=0,Type=Float,Description="Posterior probability (phred scaled) that this variant segregates">
+##INFO=<ID=PV4,Number=4,Type=Float,Description="P-values for strand bias, baseQ bias, mapQ bias and tail distance bias">
+##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
+##INFO=<ID=RA,Number=1,Type=Integer,Description="Reference allele observations">
+##INFO=<ID=RL,Number=1,Type=Integer,Description="Reads Placed Left: number of reads supporting the alternate balanced to the left (5') of the alternate allele">
+##INFO=<ID=RPP,Number=1,Type=Float,Description="Read Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=RR,Number=1,Type=Integer,Description="Reads Placed Right: number of reads supporting the alternate balanced to the right (3') of the alternate allele">
+##INFO=<ID=RUN,Number=1,Type=Integer,Description="Homopolymer run length: the number of consecutive nucleotides in the reference genome matching the alternate allele prior to the current position">
+##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
+##INFO=<ID=SAB,Number=1,Type=Float,Description="Strand bias for the alternate allele: SAF / ( SAF + SAR )">
+##INFO=<ID=SAF,Number=1,Type=Integer,Description="Number of alternate observations on the forward strand">
+##INFO=<ID=SAP,Number=1,Type=Float,Description="Strand balance probability for the alternate allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SAF and SAR given E(SAF/SAR) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=SAR,Number=1,Type=Integer,Description="Number of alternate observations on the reverse strand">
+##INFO=<ID=SB,Number=1,Type=Float,Description="Strand Bias">
+##INFO=<ID=SC,Number=1,Type=String,Description="Genomic sequence 10 bases either side of variant position">
+##INFO=<ID=SET_INTEGRATION,Number=0,Type=Flag,Description="SET_INTEGRATION Membership">
+##INFO=<ID=SET_WGVQSR,Number=0,Type=Flag,Description="SET_WGVQSR Membership">
+##INFO=<ID=SNP,Number=0,Type=Flag,Description="SNP allele">
+##INFO=<ID=SRB,Number=1,Type=Float,Description="Strand bias for the reference allele: SRF / ( SRF + SRR )">
+##INFO=<ID=SRF,Number=1,Type=Integer,Description="Number of reference observations on the forward strand">
+##INFO=<ID=SRP,Number=1,Type=Float,Description="Strand balance probability for the reference allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SRF and SRR given E(SRF/SRR) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=SRR,Number=1,Type=Integer,Description="Number of reference observations on the reverse strand">
+##INFO=<ID=TC,Number=0,Type=Integer,Description="Total coverage">
+##INFO=<ID=TR,Number=1,Type=Integer,Description="Tandem repeat run length (bp)">
+##INFO=<ID=TS,Number=0,Type=Flag,Description="transition SNP">
+##INFO=<ID=TU,Number=1,Type=String,Description="tandem repeat run unit (stranded)">
+##INFO=<ID=TV,Number=0,Type=Flag,Description="transversion SNP">
+##INFO=<ID=VLD,Number=0,Type=Flag,Description="Is Validated.  This bit is set if the snp has 2+ minor allele count based on frequency or genotype data.">
+##INFO=<ID=VQSLOD,Number=1,Type=Float,Description="Log odds ratio of being a true variant versus being false under the trained gaussian mixture model">
+##INFO=<ID=dbSNP,Number=1,Type=Integer,Description="First SNP Build for RS">
+##INFO=<ID=set,Number=1,Type=String,Description="Source VCF for the merged record in CombineVariants">
+##LeftAlignVariants="analysis_type=LeftAlignVariants input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=[20] excludeIntervals=null reference_sequence=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta rodBind=[/humgen/gsa-scr1/ebanks/ALL.chr20.Oxford.20110407.indels.genotypes.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub"
+##SelectVariants="analysis_type=SelectVariants input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=[20] excludeIntervals=null reference_sequence=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta rodBind=[/humgen/gsa-scr1/delangel/officialCalls/20110201_chr20_phase1_indels/dindel/20110208.chr20.dindel2.ALL.sites.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sample=null select_expressions=[] excludeNonVariants=false excludeFiltered=false discordance= concordance= family_structure= mendelianViolation=false mendelianViolationQualThreshold=0.0 select_random_number=0 select_random_fraction=0.0 selectSNPs=false selectIndels=true"
+##UnifiedGenotyper="analysis_type=UnifiedGenotyper input_file=[/broad/shptmp/delangel/calls/chr20/CHB.phase1.chr20.42.cleaned.bam, /broad/shptmp/delangel/calls/chr20/CHS.phase1.chr20.42.cleaned.bam, /broad/shptmp/delangel/calls/chr20/CLM.phase1.chr20.42.cleaned.bam, /broad/shptmp/delangel/calls/chr20/JPT.phase1.chr20.42.cleaned.bam, /broad/shptmp/delangel/calls/chr20/MXL.phase1.chr20.42.cleaned.bam, /broad/shptmp/delangel/calls/chr20/PUR.phase1.chr20.42.cleaned.bam] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=[20:41000001-42000000] excludeIntervals=null reference_sequence=/humgen/1kg/reference/human_g1k_v37.fasta rodBind=[/humgen/gsa-scr1/delangel/otherIndelCallerAnalysis/ALL.indels.combined.chr20.vcf, /humgen/gsa-hpprojects/GATK/data/dbsnp_132_b37.leftAligned.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=50 baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=8 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false genotype_likelihoods_model=INDEL p_nonref_model=EXACT heterozygosity=0.0010 pcr_error_rate=1.0E-4 genotyping_mode=GENOTYPE_GIVEN_ALLELES output_mode=EMIT_ALL_SITES standard_min_confidence_threshold_for_calling=4.0 standard_min_confidence_threshold_for_emitting=4.0 noSLOD=false assume_single_sample_reads=null abort_at_too_much_coverage=-1 min_base_quality_score=17 min_mapping_quality_score=20 max_deletion_fraction=0.05 min_indel_count_for_genotyping=5 indel_heterozygosity=1.25E-4 indelGapContinuationPenalty=10.0 indelGapOpenPenalty=45.0 indelHaplotypeSize=80 doContextDependentGapPenalties=true getGapPenaltiesFromData=false indel_recal_file=indel.recal_data.csv indelDebug=false dovit=false GSA_PRODUCTION_ONLY=false exactCalculation=LINEAR_EXPERIMENTAL ignoreSNPAlleles=true output_all_callable_bases=false genotype=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub debug_file=null metrics_file=null annotation=[MappingQualityZeroFraction]"
+##VariantAnnotator="analysis_type=VariantAnnotator input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=null excludeIntervals=null reference_sequence=/humgen/1kg/reference/human_g1k_v37.fasta rodBind=[./ALL.chr20.vqsr_2of5_union_sites_for_validation_boosted.vcf] rodToIntervalTrackName=variant BTI_merge_rule=UNION nonDeterministicRandomSeed=false DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sampleName=null annotation=[IndelType] group=[] expression=[] useAllAnnotations=false list=false assume_single_sample_reads=null vcfContainsOnlyIndels=false"
+##VariantFiltration="analysis_type=VariantFiltration input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=[/humgen/1kg/processing/pipeline_test_bams/chr22_chunked.hg19.intervals] excludeIntervals=null reference_sequence=/humgen/1kg/reference/human_g1k_v37.fasta rodBind=[/broad/shptmp/rpoplin/ALL.phase1.chr22.raw.indels.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false enable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null quiet_output_mode=false debug_mode=false help=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub filterExpression=[MQ0 >= 4 && (MQ0 / (1.0 * DP)) > 0.1, QUAL<30.0, SB>=-1.0, QD<1.0, HRun>=15, HaplotypeScore>20.0] filterName=[HARD_TO_VALIDATE, LowQual, StrandBias, QualByDepth, HomopolymerRun, HaplotypeScore] genotypeFilterExpression=[] genotypeFilterName=[] clusterSize=3 clusterWindowSize=0 maskName=Mask missingValuesInExpressionsShouldEvaluateAsFailing=false"
+##commandline="/share/software/freebayes/bin/freebayes --stdin --min-alternate-count 2 --genotype-combo-step-max 20 --genotype-variant-threshold 4 --no-marginals --pvar 0.0001 --indels --mnps --no-filters --binomial-obs-priors --allele-balance-priors --region 20:0..100000 --vcf /d1/data/1000G/20101123/populations/finalised.phase1/integrated/including454/wg/ALL/Pipeline/none//freebayes/freebayes.20:0-100000.baq.20110328.vcf --fasta-reference /d2/data/references/build_37/human_reference_v37.fa"
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+##fileDate=2011-03-28
+##filedate=2011-02-08
+##filter="( SNP | MNP ) & ( MQM > 65 | QUAL > 1 ) & ABP < 30 & AB < 0.9 | ( INS | DEL ) & QUAL > 500"
+##phasing=none
+##reference=/lustre/scratch105/projects/g1k/ref/main_project/human_g1k_v37.fasta
+##reference=file:///humgen/1kg/reference/human_g1k_v37.fasta
+##source=Dindel2
+##source=SelectVariants
+##source_20110031.1=/nfs/users/nfs_p/pd3/cvs/vcftools/perl/vcf-annotate -d /nfs/users/nfs_p/pd3/sandbox/hapmap/dbSNP-b132/non-1kg-vld.desc -a /nfs/users/nfs_p/pd3/sandbox/hapmap/dbSNP-b132/non-1kg-vld.tab.gz -c CHROM,FROM,INFO/VLD,INFO/KGPilot123,INFO/dbSNP
+##vcfCTools=filter
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
+20	458502	.	G	GA	4567.01	PASS	AA=20;AB=0.61111;ABA=14;ABP=6.8707;ABR=22;AC=38;AF=0.0544;AN=698;BL=374;BR=1129;BVAR;BaseQRankSum=13.364;DP=15979;DP4=1882,2188,45,37;Dels=0.00;EL=5;EPP=13.868;ER=15;FR;FS=6.503;HETAR=11;HOMA=2;HOMR=985;HP=1;HPLen=2;HR=2;HRun=0;HU=G;INDEL;INS;InbreedingCoeff=0.0157;IndelType=INS.NOVEL_1.Novel_A.;LEN=1;LRB=0.50233;LRBP=826.56;MQ=66.16;MQ0Fraction=0.0110;MQM=70.5;MQRankSum=-3.158;NF;NR;NS=998;PP;PV4=0.15,1,0.42,0.15;RA=3173;RL=1;RPP=38.188;RR=19;RUN=1;ReadPosRankSum=-2.346;SAB=0.7;SAF=14;SAP=9.959;SAR=6;SC=GGGCGTGGTGGTGCATGTAAT;SET_INTEGRATION;SET_WGVQSR;SRB=0.50047;SRF=1588;SRP=3.0165;SRR=1585;TC;TR=9;TU=GGT;VQSLOD=10.0079;set=Intersection;sumGLbyD=23.94
+20	573764	.	TA	T	591.51	PASS	AC=91;AF=0.1987;AN=458;BaseQRankSum=0.137;DP=519;FS=3.153;HRun=1;HaplotypeScore=14.0744;InbreedingCoeff=0.1460;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_A.;MQ=48.16;MQ0=26;MQ0Fraction=0.0501;MQRankSum=-1.636;QD=3.63;ReadPosRankSum=-4.140;SB=-408.14;SET_INTEGRATION;SET_WGVQSR;VQSLOD=5.2458;set=VQSR
+20	766143	.	C	CATCTGGTA	5521.70	PASS	AA=24;AB=0.5;ABA=18;ABP=3.0103;ABR=18;AC=14;AF=0.0289;AF1=0.02038;AN=484;BL=655;BR=1542;BVAR;BaseQRankSum=3.801;CI95=0.01549,0.02655;DP=11749;DP4=2222,1998,14,8;Dels=0.00;EL=9;EPP=6.2675;ER=15;FQ=999;FR;FS=2.941;HETAR=9;HOMA=4;HOMR=901;HP=2;HPLen=2;HR=1;HRun=0;HU=A;INDEL;INS;InbreedingCoeff=0.0515;IndelType=INS.NumRepetitions_1.EventLength_8.;LEN=8;LRB=0.40373;LRBP=780.64;MQ=56.81;MQ0Fraction=0.0253;MQM=22.167;MQRankSum=-4.809;NF;NR;NS=914;PP;PV4=0.39,1,5.8e-07,1;RA=3093;RL=6;RPP=16.039;RR=18;RUN=1;ReadPosRankSum=-2.827;SAB=0.625;SAF=15;SAP=6.2675;SAR=9;SC=GCTTTAAATTCATCTGGTACT;SET_INTEGRATION;SET_WGVQSR;SRB=0.61623;SRF=1906;SRP=365.95;SRR=1187;TC;TR=1;TU=A;VQSLOD=7.0268;set=Intersection;sumGLbyD=50.23
+20	997076	rs11467490	CTG	C	15379.78	PASS	AA=195;AB=0.59878;ABA=132;ABP=30.896;ABR=197;AC=173;AF=0.14562;AN=1188;BL=7664;BR=7309;BVAR;BaseQRankSum=21.853;DB;DEL;DP=27127;DP4=1801,2002,241,282;Dels=0.13;EL=100;EPP=3.2887;ER=95;FQ=999;FR;FS=6.591;HETAR=77;HOMA=42;HOMR=815;HP=1;HPLen=1;HR=1;HRun=0;HU=T;INDEL;InbreedingCoeff=0.1284;IndelType=DEL.NumRepetitions_1.EventLength_2.RepeatExpansion_TG.;LEN=2;LRB=0.023709;LRBP=21.287;MQ=61.18;MQ0Fraction=0.0214;MQM=43.041;MQRankSum=6.886;NF;NR;NS=934;PP;PV4=0.61,1.5e-78,1,1;RA=2800;RL=120;RPP=25.56;RR=75;RUN=1;ReadPosRankSum=4.504;SAB=0.62051;SAF=121;SAP=27.609;SAR=74;SC=CAGCTAATTACTGTATTTTTA;SET_INTEGRATION;SET_WGVQSR;SRB=0.49821;SRF=1395;SRP=3.0879;SRR=1405;TC;TR=1;TU=T;VQSLOD=8.9396;set=Intersection;sumGLbyD=16.76
+20	1042261	rs10597473	CCCTG	C	168658.05	PASS	AA=4481;AB=0.29043;ABA=2128;ABP=1147.1;ABR=871;AC=1172;AF=0.97830;AN=1198;BL=169975;BR=194027;BVAR;BaseQRankSum=4.599;DB;DEL;DP=29418;DP4=29,47,1441,2403;Dels=0.84;EL=2358;EPP=29.772;ER=2123;FR;FS=9.122;HETAR=482;HOMA=559;HOMR=30;HP=2;HPLen=3;HR=3;HRun=0;HU=C;INDEL;InbreedingCoeff=0.0470;IndelType=DEL.NumRepetitions_2.EventLength_4.;LEN=4;LRB=0.066077;LRBP=3454.1;MQ=104.58;MQ0=4;MQ0Fraction=0.0014;MQM=58.257;MQRankSum=-3.368;NF;NR;NS=1071;PP;PV4=0.91,6.8e-09,2.8e-05,1;RA=1039;RL=2088;RPP=48.09;RR=2393;RUN=1;ReadPosRankSum=5.288;SAB=0.41442;SAF=1857;SAP=288.09;SAR=2624;SC=CCAAACCCAACCCTGCCTGGC;SET_INTEGRATION;SET_WGVQSR;SRB=0.48893;SRF=508;SRP=4.1159;SRR=531;TC;TR=8;TU=CCTG;VQSLOD=8.5148;dbSNP=120;set=Intersection;sumGLbyD=59.79
+20	1046297	rs33956316	C	CT,CTT,CTTT	17698	PASS	ABR=408;AC=432,79,230;AF=0.39779,0.07274,0.21179;BVAR;BaseQRankSum=-8.413;DB;DP=15649;DP4=147,199,534,436;FR;FS=11.580;HOMA=97;HOMR=457;HP=20;HR=16;HU=T;HaplotypeScore=16.0590;INDEL;INS;InbreedingCoeff=0.6018;IndelType=MULTIALLELIC_INDEL;KGPilot123;MQ0=19;MQ0Fraction=0.0093;MQRankSum=7.992;NF;NR;NS=767;PP;PV4=6e-05,1,1,1;QD=8.18;RA=1183;RUN=1;ReadPosRankSum=2.684;SB=-6384.08;SC=GGAAAATTTTCTTTTTTTTTT;SET_WGVQSR;SRB=0.40913;SRF=484;SRP=87.859;SRR=699;TC;TR=16;TU=T;VQSLOD=8.4941;dbSNP=132;set=Intersection
+20	1405740	.	T	TA	257.28	PASS	AF=0.0188;BaseQRankSum=-0.745;DP=3769;Dels=0.00;FS=0.742;HPLen=9;HRun=9;InbreedingCoeff=0.0462;IndelType=INS.NumRepetitions_9.EventLength_1.RepeatExpansion_A.;MQ0Fraction=0.0151;MQRankSum=-0.090;ReadPosRankSum=-1.582;SET_INTEGRATION;SET_WGVQSR;VQSLOD=5.6502;set=Intersection;sumGLbyD=6.94
+20	1690501	.	TC	T	27928	PASS	AA=108;AB=0.91372;ABA=100;ABP=1726.1;ABR=1059;AC=35;AF=0.02966;AN=1180;BL=593;BR=6973;BVAR;BaseQRankSum=7.567;DEL;DP=10612;Dels=0.01;EL=50;EPP=4.2971;ER=58;FS=0.000;HETAR=378;HOMA=184;HOMR=477;HRun=1;InbreedingCoeff=0.0495;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;LEN=1;LRB=0.84325;LRBP=11685;MQ0=0;MQ0Fraction=0.0000;MQM=87.361;MQRankSum=4.088;NS=1045;RA=3125;RL=3;RPP=212.2;RR=105;RUN=1;ReadPosRankSum=-13.096;SAB=0.56481;SAF=61;SAP=6.9511;SAR=47;SRB=0.51776;SRF=1618;SRP=11.572;SRR=1507;VQSLOD=3.9824;set=filterInVQSR-2of5;sumGLbyD=4.07
+20	1991285	rs113891396	TAA	T,TA,TAAA,TAAAAA,TAAAAAA,TAAAAAAA,TAAAAAAAA	39235.36	PASS	AC=5,251,20,39,188,52,79;AF=0.0056,0.2789,0.0222,0.0433,0.2089,0.0578,0.0878;AN=900;BVAR;BaseQRankSum=1.124;DB;DEL;DP=54393;DP4=906,772,824,579;Dels=0.21;FR;FS=37.525;HP=12;HR=12;HRun=12;HU=A;INDEL;INS;InbreedingCoeff=0.6891;IndelType=MULTIALLELIC_INDEL;MQ=76.81;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-6.593;NF;NR;PP;PV4=0.0087,1,6.3e-19,1;RUN=1;ReadPosRankSum=-2.184;SC=ATCTGCCACTTAAAAAAAAAA;SET_WGVQSR;TC;TR=12;TU=A;VQSLOD=9.0007;dbSNP=132;set=Intersection;sumGLbyD=11.45
+20	2355911	.	TA	T	11723	PASS	AA=79;AB=0.9393;ABA=57;ABP=1577;ABR=882;AC=38;AF=0.0411;AN=924;BL=644;BR=5536;BVAR;BaseQRankSum=2.434;DEL;DP=9687;Dels=0.00;EL=45;EPP=6.3362;ER=34;FS=3.043;HETAR=321;HOMA=182;HOMR=555;HRun=5;InbreedingCoeff=0.0412;IndelType=DEL.NumRepetitions_5.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.79159;LRBP=8411.9;MQ0=0;MQ0Fraction=0.0000;MQM=70.848;MQRankSum=0.137;NS=1058;RA=3415;RL=3;RPP=149.49;RR=76;RUN=1;ReadPosRankSum=-12.116;SAB=0.44304;SAF=35;SAP=5.2367;SAR=44;SRB=0.43572;SRF=1488;SRP=125.55;SRR=1927;VQSLOD=3.8910;set=filterInVQSR-2of5;sumGLbyD=4.88
+20	2771621	rs11479849	GT	G,GTT	1605.60	PASS	AA=80;AB=0.79825;ABA=69;ABP=267.24;ABR=273;AC=79,91;AF=0.06551,0.07546;AN=1206;BL=2593;BR=3805;BVAR;BaseQRankSum=7.825;DB;DP=9790;Dels=0.04;EL=37;EPP=3.9875;ER=43;FR;FS=4.751;HETAR=62;HOMA=5;HOMR=958;HP=11;HR=11;HRun=11;HU=T;INS;InbreedingCoeff=0.2646;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.18943;LRBP=501.57;MQ0=0;MQ0Fraction=0.0000;MQM=52.45;MQRankSum=-0.560;NF;NR;NS=1025;PP;RA=3949;RL=29;RPP=16.148;RR=51;RUN=1;ReadPosRankSum=-2.397;SAB=0.525;SAF=42;SAP=3.4446;SAR=38;SC=TCATTTTAACGTTTTTTTTTT;SET_WGVQSR;SRB=0.54368;SRF=2147;SRP=68.46;SRR=1802;TC;TR=11;TU=T;VQSLOD=3.5989;set=filterInVQSR-2of5;sumGLbyD=3.92
+20	2891235	.	G	GT,GTTT	2869.87	PASS	AC=236,246;AF=0.2803,0.2922;AN=842;BaseQRankSum=8.979;DP=1067;FS=3.911;HaplotypeScore=20.3595;InbreedingCoeff=0.6511;IndelType=MULTIALLELIC_INDEL;MQ=44.86;MQ0=114;MQ0Fraction=0.1068;MQRankSum=-2.273;QD=4.00;ReadPosRankSum=-6.601;SB=-991.85;SET_INTEGRATION;SET_WGVQSR;VQSLOD=5.4379;set=VQSR
+20	3033550	.	TGAG	T	2005.90	PASS	AA=34;AB=0.51429;ABA=34;ABP=3.1344;ABR=36;AC=22;AF=0.0332;AN=662;BL=1374;BR=1649;BVAR;BaseQRankSum=5.192;DEL;DP=14639;DP4=2271,1492,12,21;Dels=0.02;EL=19;EPP=4.0322;ER=15;FR;FS=16.657;HETAR=17;HOMA=0;HOMR=914;HP=1;HPLen=1;HR=1;HRun=0;HU=G;INDEL;InbreedingCoeff=-0.0454;IndelType=DEL.NumRepetitions_1.EventLength_3.;LEN=3;LRB=0.090969;LRBP=57.333;MQ=53.99;MQ0Fraction=0.0304;MQM=46.735;MQRankSum=1.938;NF;NR;NS=931;PP;PV4=0.0068,9.4e-05,1,1;RA=2985;RL=11;RPP=12.207;RR=23;RUN=1;ReadPosRankSum=-0.466;SAB=0.41176;SAF=14;SAP=5.3095;SAR=20;SC=CTTGGGAGGCTGAGGTGGGAG;SET_INTEGRATION;SET_WGVQSR;SRB=0.62781;SRF=1874;SRP=426.52;SRR=1111;TC;TR=1;TU=G;VQSLOD=8.9194;set=Intersection;sumGLbyD=24.41
+20	3873327	rs61519218	A	AAG	683.85	PASS	AC=25;AF=0.0313;AN=800;BaseQRankSum=4.839;DB;DP=1718;FS=4.265;HRun=0;HaplotypeScore=20.5789;InbreedingCoeff=0.1055;IndelType=INS.NOVEL_2.;MQ=53.70;MQ0=37;MQ0Fraction=0.0215;MQRankSum=2.468;QD=6.30;ReadPosRankSum=4.254;SB=-403.21;SET_INTEGRATION;SET_WGVQSR;VQSLOD=6.1858;set=VQSR
+20	4028835	.	GC	G	2511.30	PASS	AA=66;AB=0.56954;ABA=65;ABP=9.3521;ABR=86;AC=22;AF=0.01836;AN=1198;BL=2303;BR=2463;BVAR;BaseQRankSum=7.621;DEL;DP=22795;DP4=1714,2774,22,37;Dels=0.02;EL=34;EPP=3.1419;ER=32;FQ=999;FR;FS=2.095;HETAR=21;HOMA=0;HOMR=1050;HP=2;HPLen=2;HR=2;HRun=2;HU=C;INDEL;InbreedingCoeff=0.0125;IndelType=DEL.NumRepetitions_2.EventLength_1.RepeatExpansion_C.;LEN=1;LRB=0.033571;LRBP=14.674;MQ=108.09;MQ0=0;MQ0Fraction=0.0000;MQM=53.318;MQRankSum=5.257;NF;NR;NS=1071;PP;PV4=1,5.4e-13,1,0.075;RA=6185;RL=36;RPP=4.1947;RR=30;RUN=1;ReadPosRankSum=-1.059;SAB=0.45455;SAF=30;SAP=4.1947;SAR=36;SC=TGCTGTCACTGCCTTCTCCTA;SET_INTEGRATION;SET_WGVQSR;SRB=0.42118;SRF=2605;SRP=336.76;SRR=3580;TC;TR=2;TU=C;VQSLOD=10.2409;set=Intersection;sumGLbyD=12.71
+20	4039609	rs67812039	G	GA	43457	PASS	AA=909;AB=0.54639;ABA=572;ABP=26.583;ABR=689;AC=302;AF=0.3455;AN=874;BL=37070;BR=38211;BVAR;BaseQRankSum=20.147;DB;DP=25595;DP4=1483,1374,528,542;Dels=0.00;EL=467;EPP=4.5033;ER=442;FQ=999;FR;FS=5.441;HETAR=243;HOMA=127;HOMR=608;HP=4;HPLen=3;HR=3;HRun=3;HU=A;INDEL;INS;InbreedingCoeff=0.1388;IndelType=INS.NumRepetitions_3.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.015157;LRBP=40.563;MQ=119.50;MQ0=0;MQ0Fraction=0.0000;MQM=83.197;MQRankSum=1.080;NF;NR;NS=978;PP;PV4=0.16,1,3.6e-12,1;RA=3033;RL=443;RPP=4.274;RR=466;RUN=1;ReadPosRankSum=-1.000;SAB=0.32233;SAF=293;SAP=252.24;SAR=616;SC=TATGTTGGGAGAAATATCAGT;SET_INTEGRATION;SET_WGVQSR;SRB=0.38378;SRF=1164;SRP=358.85;SRR=1869;TC;TR=4;TU=AG;VQSLOD=9.9146;dbSNP=130;set=Intersection;sumGLbyD=16.79
+20	4390056	.	TC	T	49312	PASS	AA=91;AB=0.94353;ABA=86;ABP=2605.4;ABR=1437;AC=39;AF=0.03160;AN=1234;BL=6823;BR=731;BVAR;BaseQRankSum=2.727;DEL;DP=13149;Dels=0.00;EL=41;EPP=4.9431;ER=50;FS=4.002;HETAR=465;HOMA=313;HOMR=292;HRun=3;InbreedingCoeff=0.0326;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;LEN=1;LRB=0.80646;LRBP=10671;MQ0=0;MQ0Fraction=0.0000;MQM=69.824;MQRankSum=-0.903;NS=1073;RA=3078;RL=89;RPP=183.62;RR=2;RUN=1;ReadPosRankSum=-12.526;SAB=0.45055;SAF=41;SAP=4.9431;SAR=50;SRB=0.52567;SRF=1618;SRP=20.622;SRR=1460;VQSLOD=4.3235;set=Intersection;sumGLbyD=3.53
+20	4474622	.	TA	T,TAA,TAAA,TAAAA	94522.28	PASS	ABR=114;AC=38,68,16,900;AF=0.03333,0.05965,0.01404,0.78947;AN=1140;BVAR;BaseQRankSum=9.741;DB;DP=16656;Dels=0.00;FR;FS=2.355;HOMA=3;HOMR=936;HP=10;HPLen=10;HR=10;HRun=10;HU=A;INS;InbreedingCoeff=0.4516;IndelType=MULTIALLELIC_INDEL;MQ0=2;MQ0Fraction=0.0008;MQRankSum=-4.096;NF;NR;NS=980;PP;RA=3766;RUN=1;ReadPosRankSum=2.380;SC=AGAAAAAAATTAAAAAAAAAA;SET_WGVQSR;SRB=0.49734;SRF=1873;SRP=3.2409;SRR=1893;TC;TR=10;TU=A;VQSLOD=8.8186;set=Intersection;sumGLbyD=38.79
+20	4824911	.	AC	A	41998.70	PASS	AC=1172;AF=0.97342;AN=1204;BaseQRankSum=8.604;DP=3615;FS=9.934;HRun=1;HaplotypeScore=39.6843;InbreedingCoeff=0.0980;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;MQ=129.80;MQ0=1;MQ0Fraction=0.0003;MQRankSum=3.378;QD=11.62;ReadPosRankSum=6.967;SB=-16955.28;VQSLOD=4.2689;set=VQSR
+20	4839897	rs35881880	TAA	T,TA,TAAA,TAAAAA	3906.80	PASS	AC=12,95,137,189;AF=0.01024,0.08106,0.11689,0.16126;AN=1172;BVAR;BaseQRankSum=15.271;DB;DEL;DP=15105;Dels=0.04;FR;FS=43.567;HP=19;HR=13;HRun=13;HU=A;INS;InbreedingCoeff=0.5716;IndelType=MULTIALLELIC_INDEL;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-2.569;NF;NR;PP;RUN=1;ReadPosRankSum=-13.794;SC=TGTTAAAAAATAAAAAAAAAA;TC;TR=13;TU=A;VQSLOD=8.1773;set=Intersection;sumGLbyD=3.77
+20	5507414	.	G	GCC	439.08	PASS	AC=23;AF=0.01876;AN=1226;BaseQRankSum=3.051;DP=3023;FS=3.636;HRun=1;HaplotypeScore=30.3104;InbreedingCoeff=0.0204;IndelType=INS.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;MQ=112.09;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-2.065;QD=2.85;ReadPosRankSum=-2.709;SB=-302.22;VQSLOD=4.4311;set=VQSR
+20	5609676	.	GA	G,GAA	799.89	PASS	AA=42;AB=0.79096;ABA=37;ABP=133.16;ABR=140;AC=43,65;AF=0.03607,0.05453;AF1=0.02826;AN=1192;BL=1360;BR=2334;BVAR;BaseQRankSum=5.069;CI95=0.01242,0.04037;DP=15610;DP4=1548,2441,21,30;Dels=0.02;EL=18;EPP=4.8716;ER=24;FQ=12.1;FR;FS=0.000;HETAR=36;HOMA=1;HOMR=991;HP=13;HPLen=10;HR=10;HRun=10;HU=A;INDEL;INS;InbreedingCoeff=0.2001;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.26367;LRBP=560.68;MQ=63.29;MQ0Fraction=0.0003;MQM=44.143;MQRankSum=1.755;NF;NR;NS=1028;PP;PV4=0.77,1,0.0087,0.0053;RA=4114;RL=15;RPP=10.455;RR=27;RUN=1;ReadPosRankSum=-2.978;SAB=0.5;SAF=21;SAP=3.0103;SAR=21;SC=AAAAAAGAAAGAAAAAAAAAA;SET_WGVQSR;SRB=0.39742;SRF=1635;SRP=379;SRR=2479;TC;TR=11;TU=AAAG;VQSLOD=4.1229;set=filterInVQSR-2of5;sumGLbyD=7.95
+20	5736211	rs35303106	CT	C,CTT	4384.40	PASS	AA=117;AB=0.71499;ABA=116;ABP=166.4;ABR=291;AC=32,145;AF=0.02712,0.12288;AN=1180;BL=5556;BR=4901;BVAR;BaseQRankSum=2.708;DB;DP=9157;Dels=0.01;EL=54;EPP=4.5136;ER=63;FR;FS=2.802;HETAR=79;HOMA=1;HOMR=837;HP=16;HR=11;HRun=11;HU=T;INS;InbreedingCoeff=0.1903;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.062637;LRBP=92.1;MQ0Fraction=0.0273;MQM=48.932;MQRankSum=3.654;NF;NR;NS=917;PP;RA=2785;RL=79;RPP=34.209;RR=38;RUN=1;ReadPosRankSum=0.795;SAB=0.5641;SAF=66;SAP=7.1862;SAR=51;SC=TTTTCTTTTTCTTTTTTTTTT;SET_INTEGRATION;SET_WGVQSR;SRB=0.41795;SRF=1164;SRP=165.85;SRR=1621;TC;TR=11;TU=T;VQSLOD=5.0895;set=Intersection;sumGLbyD=4.66
+20	5898626	rs34483659	CAAA	C,CA,CAA,CAAAAA	1140.16	PASS	ABR=34;AC=19,98,56,199;AF=0.0227,0.1172,0.0670,0.2380;AF1=0.08519;BVAR;BaseQRankSum=5.049;CI95=0.03727,0.1273;DB;DEL;DP=5091;DP4=539,408,121,123;FQ=4.43;FR;FS=5.701;HOMA=64;HOMR=156;HP=19;HR=18;HU=A;HaplotypeScore=11.5333;INDEL;InbreedingCoeff=0.7405;IndelType=MULTIALLELIC_INDEL;MQ0=117;MQ0Fraction=0.0986;MQRankSum=6.290;NF;NR;NS=240;PP;PV4=0.043,1,1,0.0087;QD=1.22;RA=204;RUN=1;ReadPosRankSum=-2.684;SB=-1015.09;SC=ACTAAAAATACAAAAAAAAAA;SET_WGVQSR;SRB=0.35294;SRF=72;SRP=41.33;SRR=132;TC;TR=18;TU=A;VQSLOD=4.1696;set=filterInVQSR-2of5
+20	5975126	rs10541892	C	CAG	504.78	PASS	AC=79;AF=0.07004;AN=1128;BaseQRankSum=10.498;DB;DP=2050;FS=38.228;HRun=0;HaplotypeScore=14.1426;InbreedingCoeff=-0.0053;IndelType=INS.NOVEL_2.;MQ=60.40;MQ0=80;MQ0Fraction=0.0390;MQRankSum=5.098;QD=1.63;ReadPosRankSum=-4.851;SB=-590.69;VQSLOD=4.8517;set=VQSR
+20	6040983	rs11087710	A	AAAAAAGAG,AAAAAGAG,AAAAGAG,AAAAGAGAG,AAAGAG,AAAGAGAG,AAGAG,AAGAGAG,AG,AGAG,AGAGAG	66894.55	PASS	ABR=468;AC=80,9,20,136,31,91,33,29,9,3,5;AF=0.0980,0.0110,0.0245,0.1667,0.0380,0.1115,0.0404,0.0355,0.0110,0.0037,0.0061;AN=816;BVAR;BaseQRankSum=-12.470;DB;DP=38726;DP4=426,611,310,472;Dels=0.00;FQ=999;FR;FS=6.635;HOMA=110;HOMR=506;HP=14;HR=15;HRun=0;HU=A;INDEL;INS;InbreedingCoeff=0.8291;IndelType=MULTIALLELIC_INDEL;KGPilot123;MQ=54.22;MQ0Fraction=0.0168;MQRankSum=-5.329;NF;NR;NS=861;PP;PV4=0.56,1,6.9e-09,0.31;RA=1828;RUN=1;ReadPosRankSum=-7.857;SC=AAAAAAAAAAAAGAGAGAGAG;SET_WGVQSR;SRB=0.62418;SRF=1141;SRP=247.85;SRR=687;TC;TR=15;TU=A;VQSLOD=9.0574;dbSNP=131;set=Intersection;sumGLbyD=36.72
+20	7024548	.	G	GAT	5041.27	PASS	AC=123;AF=0.10336;AN=1190;BaseQRankSum=23.097;DP=3045;FS=7.979;HRun=0;HaplotypeScore=15.6967;InbreedingCoeff=0.1062;IndelType=INS.NumRepetitions_5.EventLength_2.RepeatExpansion_AT.;MQ=119.29;MQ0=2;MQ0Fraction=0.0007;MQRankSum=-3.725;QD=8.97;ReadPosRankSum=-1.636;SB=-2257.45;SET_INTEGRATION;SET_WGVQSR;VQSLOD=5.9332;set=VQSR
+20	7484554	.	A	AT	5.09	PASS	AC=0;AF=0.0000;AN=710;BaseQRankSum=-0.696;DP=1862;FS=2.835;HRun=9;HaplotypeScore=13.5425;InbreedingCoeff=0.0567;IndelType=INS.NumRepetitions_9.EventLength_1.RepeatExpansion_T.;MQ=76.92;MQ0=0;MQ0Fraction=0.0000;MQRankSum=1.932;ReadPosRankSum=-1.701;VQSLOD=4.3156;set=VQSR
+20	7632194	rs77286341	GAA	AAA,G	5324	PASS	AC=0;AF=0.0000;AN=700;BaseQRankSum=-1.741;DB;DP=1772;FR;HP=4;HPLen=3;HR=3;HRun=0;HU=A;HaplotypeScore=60.1795;InbreedingCoeff=0.0017;IndelType=MIXED;MQ=70.69;MQ0=13;MQ0Fraction=0.0073;MQRankSum=-1.315;NF;NR;PP;ReadPosRankSum=-3.650;SC=GAGAGAGAGAGAAAGGTGTAA;TC;TR=13;TU=AG;set=filterInVQSR-2of5
+20	7767508	rs71329674	G	GA	17914	PASS	AA=415;AB=0.61617;ABA=337;ABP=105.94;ABR=541;AC=141;AF=0.11614;AN=1214;BL=15187;BR=20323;BVAR;BaseQRankSum=-13.946;DB;DP=28222;Dels=0.00;EL=184;EPP=14.569;ER=231;FQ=999;FR;FS=13.296;HETAR=178;HOMA=35;HOMR=822;HP=14;HPLen=9;HR=9;HRun=9;HU=A;INDEL;INS;InbreedingCoeff=0.0714;IndelType=INS.NumRepetitions_9.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.14464;LRBP=1616.1;MQ=89.69;MQ0=1;MQ0Fraction=0.0003;MQM=51.667;MQRankSum=0.664;NF;NR;NS=1035;PP;RA=3707;RL=171;RPP=30.894;RR=244;RUN=1;ReadPosRankSum=-1.120;SAB=0.45301;SAF=188;SAP=10.969;SAR=227;SC=ATTCTAAAAAGAAAAAAAAAT;SET_INTEGRATION;SET_WGVQSR;SRB=0.38495;SRF=1427;SRP=429.23;SRR=2280;TC;TR=9;TU=A;VQSLOD=9.0748;set=Intersection;sumGLbyD=11.09
+20	7920261	.	TA	T,TAA	802.15	PASS	AA=28;AB=0.8;ABA=28;ABP=112.45;ABR=112;AC=22,39;AF=0.01836,0.03255;AN=1198;BL=943;BR=1487;BVAR;BaseQRankSum=2.233;DP=10645;Dels=0.01;EL=11;EPP=5.8022;ER=17;FR;FS=1.691;HETAR=20;HOMA=0;HOMR=1007;HP=10;HPLen=9;HR=9;HRun=9;HU=A;INS;InbreedingCoeff=0.2256;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.22387;LRBP=267.46;MQ0=0;MQ0Fraction=0.0000;MQM=57.571;MQRankSum=0.940;NF;NR;NS=1027;PP;RA=4776;RL=8;RPP=14.178;RR=20;RUN=1;ReadPosRankSum=-1.567;SAB=0.53571;SAF=15;SAP=3.3205;SAR=13;SC=GTAACTGCTATAAAAAAAAAC;SET_WGVQSR;SRB=0.48576;SRF=2320;SRP=11.42;SRR=2456;TC;TR=9;TU=A;VQSLOD=4.0815;set=filterInVQSR-2of5;sumGLbyD=5.37
+20	8012465	rs10595338	TATGA	T	2104.41	PASS	AF=0.03339;BaseQRankSum=10.662;DB;DP=11772;DS;Dels=0.01;FR;FS=7.678;HP=1;HPLen=1;HR=1;HRun=0;HU=A;InbreedingCoeff=0.0266;IndelType=DEL.NumRepetitions_1.EventLength_4.;MQ0Fraction=0.0731;MQRankSum=0.603;NF;NR;PP;ReadPosRankSum=1.276;SC=TGTATGTATGTATGATGTATG;TC;TR=19;TU=ATGT;VQSLOD=4.1376;set=filterInVQSR-2of5;sumGLbyD=6.53
+20	8573999	.	CGTGT	C,CGT,CGTGTGT,TGTGT	45865.96	PASS	AC=458,0,731;AF=0.37727,0.00000,0.60214;AN=1214;BVAR;BaseQRankSum=-6.703;DEL;DP=37714;Dels=0.03;FR;FS=11.079;HP=2;HPLen=1;HR=1;HRun=0;HU=G;INDEL;INS;InbreedingCoeff=0.7632;IndelType=MIXED;LEN=2;MQ0Fraction=0.0026;MQRankSum=-1.394;NF;NR;PP;RUN=1;ReadPosRankSum=-2.102;SC=TGTGTGTGCGCGTGTGTGTGT;SET_INTEGRATION;SET_WGVQSR;TC;TR=18;TU=GT;VQSLOD=6.1435;set=Intersection;sumGLbyD=3.53
+20	8610455	rs10571111	TTTTC	T	11763.51	PASS	AC=190;AF=0.17056;AN=1114;BaseQRankSum=-14.397;DB;DP=2323;FS=2.321;HRun=0;HaplotypeScore=39.8020;InbreedingCoeff=0.2502;IndelType=DEL.NumRepetitions_2.EventLength_4.;MQ=53.39;MQ0=104;MQ0Fraction=0.0448;MQRankSum=3.519;QD=19.07;ReadPosRankSum=4.150;SB=-4067.02;SET_INTEGRATION;SET_WGVQSR;VQSLOD=5.0554;set=VQSR
+20	9139079	.	ATT	A,AT,ATTT,ATTTT,ATTTTT	8777.90	PASS	AC=23,140,114,69,113;AF=0.01993,0.12132,0.09879,0.05979,0.09792;AN=1154;BVAR;BaseQRankSum=-0.022;DEL;DP=25109;DP4=502,657,278,313;FR;FS=11.929;HP=16;HR=16;HU=T;HaplotypeScore=20.2361;INDEL;INS;InbreedingCoeff=0.5704;IndelType=MULTIALLELIC_INDEL;MQ0=16;MQ0Fraction=0.0067;MQRankSum=2.624;NF;NR;PP;PV4=0.14,1,1,1;QD=1.48;RUN=1;ReadPosRankSum=-0.480;SB=-2354.28;SC=CACCTGGCTAATTTTTTTTTT;SET_WGVQSR;TC;TR=16;TU=T;VQSLOD=6.9180;set=Intersection
+20	9862448	.	CT	C	49312	PASS	AA=60;AB=0.96003;ABA=53;ABP=2440.4;ABR=1273;AC=18;AF=0.01461;AN=1232;BL=3516;BR=140;BVAR;BaseQRankSum=-2.056;DEL;DP=11893;Dels=0.01;EL=35;EPP=6.6294;ER=25;FS=1.787;HETAR=396;HOMA=344;HOMR=334;HRun=1;InbreedingCoeff=0.0379;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.92341;LRBP=6772.5;MQ0Fraction=0.0006;MQM=54.267;MQRankSum=-0.907;NS=1074;RA=2990;RL=60;RPP=133.3;RR=0;RUN=1;ReadPosRankSum=-10.579;SAB=0.58333;SAF=35;SAP=6.6294;SAR=25;SRB=0.47826;SRF=1430;SRP=15.284;SRR=1560;VQSLOD=3.0237;set=filterInVQSR-2of5;sumGLbyD=2.84
+20	9863736	rs73618103	G	GT	50570.21	PASS	AA=2247;AB=0.48878;ABA=1412;ABP=6.0324;ABR=1350;AC=546;AF=0.44463;AN=1228;BL=86886;BR=95862;BVAR;BaseQRankSum=-23.978;DB;DP=32517;DP4=1125,1133,1017,1048;Dels=0.00;EL=1089;EPP=7.6113;ER=1158;FQ=999;FR;FS=2.529;HETAR=445;HOMA=201;HOMR=393;HP=4;HPLen=4;HR=4;HRun=4;HU=T;INDEL;INS;InbreedingCoeff=0.1393;IndelType=INS.NumRepetitions_4.EventLength_1.RepeatExpansion_T.;KGPilot123;LEN=1;LRB=0.049117;LRBP=960.35;MQ=68.10;MQ0=2;MQ0Fraction=0.0006;MQM=50.931;MQRankSum=-1.580;NF;NR;NS=1039;PP;PV4=0.71,1,0.11,1;RA=3139;RL=1089;RPP=7.6113;RR=1158;RUN=1;ReadPosRankSum=0.846;SAB=0.54161;SAF=1217;SAP=36.804;SAR=1030;SC=TGATTGTATGGTTTTGTCCTT;SET_INTEGRATION;SET_WGVQSR;SRB=0.53425;SRF=1677;SRP=34.987;SRR=1462;TC;TR=4;TU=T;VLD;VQSLOD=10.1800;dbSNP=131;set=Intersection;sumGLbyD=18.20
+20	10926959	.	AG	A	12239	PASS	AA=65;AB=0.92801;ABA=64;ABP=1417.6;ABR=825;AC=24;AF=0.0264;AN=908;BL=616;BR=3782;BVAR;BaseQRankSum=9.990;DEL;DP=10708;Dels=0.01;EL=37;EPP=5.7163;ER=28;FS=1.652;HETAR=275;HOMA=70;HOMR=724;HRun=1;InbreedingCoeff=0.0102;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_G.;LEN=1;LRB=0.71987;LRBP=4952;MQ0=1;MQ0Fraction=0.0004;MQM=118.82;MQRankSum=1.018;NS=1069;RA=4746;RL=5;RPP=104.07;RR=60;RUN=1;ReadPosRankSum=-12.039;SAB=0.41538;SAF=27;SAP=7.0526;SAR=38;SRB=0.4764;SRF=2261;SRP=25.968;SRR=2485;VQSLOD=2.9713;set=filterInVQSR-2of5;sumGLbyD=4.10
+20	11299648	.	TG	T	49315	PASS	AA=62;AB=0.95292;ABA=54;ABP=2046.7;ABR=1093;AC=28;AF=0.0373;AN=750;BL=3126;BR=528;BVAR;BaseQRankSum=-4.929;DEL;DP=10764;Dels=0.01;EL=26;EPP=6.5127;ER=36;FS=3.851;HETAR=366;HOMA=383;HOMR=304;HRun=1;InbreedingCoeff=0.0267;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_G.;LEN=1;LRB=0.711;LRBP=4014.1;MQ0=1;MQ0Fraction=0.0005;MQM=76.468;MQRankSum=1.327;NS=1070;RA=2588;RL=54;RPP=77.121;RR=8;RUN=1;ReadPosRankSum=-12.507;SAB=0.48387;SAF=30;SAP=3.1504;SAR=32;SRB=0.47643;SRF=1233;SRP=15.499;SRR=1355;VQSLOD=3.8673;set=filterInVQSR-2of5;sumGLbyD=3.00
+20	11561096	.	CTA	C	999	PASS	AC=2;AF=0.0029;AF1=0.005602;BaseQRankSum=3.190;CI95=0.004425,0.01106;DP=7521;DP4=1998,1794,2,4;Dels=0.00;FQ=999;FR;FS=5.422;HP=3;HPLen=2;HR=1;HRun=0;HU=T;INDEL;InbreedingCoeff=0.0056;IndelType=DEL.NumRepetitions_1.EventLength_2.RepeatExpansion_TA.;MQ=113.88;MQ0=0;MQ0Fraction=0.0000;MQRankSum=0.297;NF;NR;PP;PV4=0.43,0.024,1,1;ReadPosRankSum=1.406;SC=CAATAGTATTCTATGTCAGTC;SET_INTEGRATION;SET_WGVQSR;TC;TR=1;TU=T;VQSLOD=8.6243;set=Intersection;sumGLbyD=21.89
+20	11723671	.	C	CA	1096.60	PASS	AA=35;AB=0.69565;ABA=35;ABP=41.247;ABR=80;AC=10;AF=0.0141;AN=710;BL=2005;BR=1702;BVAR;BaseQRankSum=-3.427;DP=9819;Dels=0.00;EL=20;EPP=4.5614;ER=15;FR;FS=3.814;HETAR=20;HOMA=0;HOMR=1034;HP=8;HPLen=7;HR=7;HRun=7;HU=A;INS;InbreedingCoeff=0.0323;IndelType=INS.NumRepetitions_7.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.081737;LRBP=56.79;MQ0=0;MQ0Fraction=0.0000;MQM=81.057;MQRankSum=0.050;NF;NR;NS=1054;PP;RA=5562;RL=22;RPP=8.0357;RR=13;RUN=1;ReadPosRankSum=-2.012;SAB=0.71429;SAF=25;SAP=16.97;SAR=10;SC=ATATTGAAGACAAAAAAACAG;SET_INTEGRATION;SET_WGVQSR;SRB=0.49371;SRF=2746;SRP=4.9233;SRR=2816;TC;TR=7;TU=A;VQSLOD=7.4342;set=Intersection;sumGLbyD=8.30
+20	12238835	rs113904674	CTCTTCATGGTCT	C	1813.44	PASS	AA=7;AB=0.73077;ABA=7;ABP=15.037;ABR=19;AC=4;AF=0.0056;AN=712;BL=360;BR=368;BVAR;BaseQRankSum=3.891;DB;DEL;DP=10309;Dels=0.00;EL=4;EPP=3.3205;ER=3;FR;FS=0.000;HETAR=3;HOMA=0;HOMR=1076;HP=1;HPLen=2;HR=2;HRun=0;HU=C;InbreedingCoeff=-0.0381;IndelType=DEL.NumRepetitions_1.EventLength_10orMore.;LEN=12;LRB=0.010989;LRBP=3.2012;MQ0=0;MQ0Fraction=0.0000;MQM=37;MQRankSum=-3.793;NF;NR;NS=1079;PP;RA=6085;RL=4;RPP=3.3205;RR=3;RUN=1;ReadPosRankSum=1.319;SAB=0.42857;SAF=3;SAP=3.3205;SAR=4;SC=CTTAATGCTCCTCTTCATGGT;SET_INTEGRATION;SET_WGVQSR;SRB=0.51257;SRF=3119;SRP=11.364;SRR=2966;TC;TR=6;TU=CCT;VQSLOD=5.7551;set=Intersection;sumGLbyD=69.48
+20	12602812	.	AT	A	12344	PASS	AA=47;AB=0.94372;ABA=43;ABP=1309.5;ABR=721;AC=14;AF=0.0196;AN=716;BL=2714;BR=217;BVAR;BaseQRankSum=1.424;DEL;DP=10743;Dels=0.00;EL=24;EPP=3.0565;ER=23;FS=0.629;HETAR=228;HOMA=65;HOMR=769;HRun=1;InbreedingCoeff=0.0233;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.85193;LRBP=4622.3;MQ0Fraction=0.0000;MQM=99.574;MQRankSum=1.901;NS=1080;RA=4839;RL=46;RPP=96.568;RR=1;RUN=1;ReadPosRankSum=-9.906;SAB=0.53191;SAF=25;SAP=3.4261;SAR=22;SRB=0.51106;SRF=2473;SRP=8.148;SRR=2366;VQSLOD=2.8161;set=filterInVQSR-2of5;sumGLbyD=3.67
+20	13600884	.	CTG	C,CTGTG	1278.10	PASS	AA=85;AB=0.77994;ABA=79;ABP=247.38;ABR=280;AC=71,22;AF=0.05907,0.01830;AN=1202;BL=3279;BR=3205;BVAR;BaseQRankSum=8.852;DEL;DP=24185;DP4=1317,931,52,49;Dels=0.03;EL=45;EPP=3.649;ER=40;FQ=999;FR;FS=31.826;HETAR=75;HOMA=4;HOMR=926;HP=2;HPLen=1;HR=1;HRun=0;HU=T;INDEL;InbreedingCoeff=0.1566;IndelType=MULTIALLELIC_INDEL;LEN=2;LRB=0.011413;LRBP=4.8442;MQ=65.06;MQ0Fraction=0.0012;MQM=48.671;MQRankSum=-0.511;NF;NR;NS=1005;PP;PV4=0.18,1,0.39,0.27;RA=3342;RL=35;RPP=8.7583;RR=50;RUN=1;ReadPosRankSum=-2.329;SAB=0.43529;SAF=37;SAP=6.1015;SAR=48;SC=TCCCTTTACTCTGTGTGTGTG;SET_INTEGRATION;SET_WGVQSR;SRB=0.59066;SRF=1974;SRP=241.62;SRR=1368;TC;TR=15;TU=GT;VQSLOD=3.8635;set=filterInVQSR-2of5;sumGLbyD=4.23
+20	13666265	.	T	TATAG	556.88	PASS	AC=21;AF=0.01959;AN=1072;BaseQRankSum=24.958;DP=2706;FS=2.581;HRun=0;HaplotypeScore=25.9952;InbreedingCoeff=0.1419;IndelType=INS.NOVEL_4.;MQ=72.43;MQ0=0;MQ0Fraction=0.0000;MQRankSum=2.888;QD=4.38;ReadPosRankSum=2.552;SB=-417.04;SET_INTEGRATION;SET_WGVQSR;VQSLOD=7.3380;set=VQSR
+20	13861245	rs72422273	C	CTCA	2685.46	PASS	AC=140;AF=0.11589;AN=1208;BaseQRankSum=24.355;DB;DP=2910;FS=6.808;HRun=0;HaplotypeScore=19.3095;InbreedingCoeff=-0.0991;IndelType=INS.NumRepetitions_1.EventLength_3.;MQ=78.25;MQ0=22;MQ0Fraction=0.0076;MQRankSum=3.225;QD=3.64;ReadPosRankSum=2.607;SB=-1861.38;VQSLOD=4.1974;set=VQSR
+20	13865746	.	T	TA,TAA	1416.23	PASS	AA=63;AB=0.80417;ABA=47;ABP=195.87;ABR=193;AC=122,21;AF=0.10133,0.01744;AN=1204;BL=3673;BR=1145;BVAR;BaseQRankSum=-3.336;DP=10513;Dels=0.00;EL=62;EPP=131.27;ER=1;FR;FS=716.583;HETAR=45;HOMA=1;HOMR=998;HP=2;HR=1;HRun=1;HU=A;INS;InbreedingCoeff=0.0814;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.5247;LRBP=2883.3;MQ0=0;MQ0Fraction=0.0000;MQM=56.143;MQRankSum=-1.197;NF;NR;NS=1044;PP;RA=4529;RL=62;RPP=131.27;RR=1;RUN=1;ReadPosRankSum=-12.295;SAB=1;SAF=63;SAP=139.81;SAR=0;SC=GGAACATGGATACCCCCCTGC;SRB=0.52462;SRF=2376;SRP=26.853;SRR=2153;TC;TR=1;TU=A;VQSLOD=-4.2308;set=filterInVQSR-2of5;sumGLbyD=4.77
+20	13881703	.	CTT	C	152.85	PASS	AC=8;AF=0.0093;AN=862;BaseQRankSum=3.941;DP=2063;FS=0.962;HRun=5;HaplotypeScore=24.0313;InbreedingCoeff=0.0790;IndelType=DEL.NumRepetitions_5.EventLength_1.RepeatExpansion_T.;MQ=55.05;MQ0=49;MQ0Fraction=0.0238;MQRankSum=-1.418;QD=3.47;ReadPosRankSum=-0.605;SB=-93.04;SET_INTEGRATION;SET_WGVQSR;VQSLOD=5.3874;set=VQSR
+20	14260090	rs73619828	A	AT	27935	PASS	AA=596;AB=0.59484;ABA=487;ABP=96.922;ABR=715;AC=204;AF=0.17000;AN=1200;BL=21718;BR=28458;BVAR;BaseQRankSum=0.756;DB;DP=23629;DP4=1385,1492,287,328;Dels=0.00;EL=299;EPP=3.0249;ER=297;FQ=999;FR;FS=6.187;HETAR=218;HOMA=38;HOMR=788;HP=9;HPLen=9;HR=9;HRun=9;HU=T;INDEL;INS;InbreedingCoeff=0.0797;IndelType=INS.NumRepetitions_9.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.13433;LRBP=1969;MQ=100.81;MQ0=0;MQ0Fraction=0.0000;MQM=57.084;MQRankSum=2.224;NF;NR;NS=1044;PP;PV4=0.53,1,1.2e-11,1;RA=4143;RL=238;RPP=55.475;RR=358;RUN=1;ReadPosRankSum=0.198;SAB=0.46812;SAF=279;SAP=8.2714;SAR=317;SC=CCTTAAGTTGATTTTTTTTTC;SET_INTEGRATION;SET_WGVQSR;SRB=0.50374;SRF=2087;SRP=3.514;SRR=2056;TC;TR=9;TU=T;VQSLOD=9.0018;set=Intersection;sumGLbyD=10.82
+20	14260558	.	AC	A	238	PASS	AC=1;AF=0.0014;AF1=0.003368;BaseQRankSum=2.868;CI95=0.003106,0.006211;DP=9724;DP4=2075,2329,1,7;Dels=0.00;FQ=106;FR;FS=10.678;HP=1;HPLen=2;HR=2;HRun=1;HU=A;INDEL;InbreedingCoeff=-0.0406;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;MQ=114.37;MQ0=0;MQ0Fraction=0.0000;MQRankSum=0.862;NF;NR;PP;PV4=0.074,0.0096,0.017,1;ReadPosRankSum=-0.042;SC=ATCAGGAATAACTGTGTGACC;SET_INTEGRATION;SET_WGVQSR;TC;TR=2;TU=A;VQSLOD=8.1618;set=Intersection;sumGLbyD=18.65
+20	14425481	.	GTA	G,GTATA	148.85	PASS	AC=43,23;AF=0.03473,0.01858;AN=1238;BaseQRankSum=6.289;DP=25167;DP4=1800,2021,38,49;FR;FS=9.416;HP=2;HPLen=1;HR=1;HU=T;HaplotypeScore=17.7453;INDEL;InbreedingCoeff=0.0995;IndelType=MULTIALLELIC_INDEL;MQ0=21;MQ0Fraction=0.0058;MQRankSum=-0.200;NF;NR;PP;PV4=0.59,1,0.04,0.023;QD=0.35;ReadPosRankSum=-1.689;SB=-367.50;SC=CTGTGTGTGTGTATATATATA;SET_WGVQSR;TC;TR=13;TU=AT;VQSLOD=3.5796;set=filterInVQSR-2of5
+20	14943522	rs11478299	GA	AA,G	1761.24	PASS	AA=117;AB=0.68142;ABA=108;ABP=99.919;ABR=231;AC=0;AF=0.0000;AF1=0.04204;AN=712;BL=4931;BR=5802;BVAR;BaseQRankSum=9.118;CI95=0.02876,0.05752;DB;DEL;DP=13717;DP4=1908,1684,59,58;Dels=0.05;EL=60;EPP=3.1773;ER=57;FQ=81.9;FR;HETAR=56;HOMA=1;HOMR=1011;HP=8;HPLen=8;HR=8;HU=A;INDEL;InbreedingCoeff=0.1264;IndelType=MIXED;LEN=1;LRB=0.081152;LRBP=156.5;MQ=106.93;MQ0=0;MQ0Fraction=0.0000;MQM=96.855;MQRankSum=1.619;NF;NR;NS=1068;PP;PV4=0.57,1,0.0003,1;QD=7.40;RA=5080;RL=56;RPP=3.4743;RR=61;RUN=1;ReadPosRankSum=0.814;SAB=0.52137;SAF=61;SAP=3.4743;SAR=56;SB=-1122.51;SC=GTTGTTTGGGGAAAAAAAACT;SET_WGVQSR;SRB=0.51083;SRF=2595;SRP=8.1825;SRR=2485;TC;TR=8;TU=A;set=filterInVQSR-2of5;sumGLbyD=9.81
+20	14974486	.	A	AG	4101.40	PASS	AA=57;AB=0.57143;ABA=51;ABP=8.2839;ABR=68;AC=22;AF=0.01846;AN=1192;BL=2286;BR=2834;BVAR;BaseQRankSum=8.711;DP=20538;DP4=2172,2100,19,13;Dels=0.00;EL=32;EPP=4.877;ER=25;FS=0.517;HETAR=20;HOMA=4;HOMR=1027;HRun=1;INDEL;INS;InbreedingCoeff=0.0677;IndelType=INS.NOVEL_1.Novel_G.;LEN=1;LRB=0.10703;LRBP=130.37;MQ=126.07;MQ0=0;MQ0Fraction=0.0000;MQM=56.088;MQRankSum=-10.756;NS=1051;PV4=0.38,3.5e-51,7.9e-34,1;RA=5203;RL=26;RPP=3.9627;RR=31;RUN=1;ReadPosRankSum=1.283;SAB=0.54386;SAF=31;SAP=3.9627;SAR=26;SET_INTEGRATION;SET_WGVQSR;SRB=0.51816;SRF=2696;SRP=17.918;SRR=2507;VQSLOD=8.0072;set=Intersection;sumGLbyD=25.60
+20	15111137	.	GA	G	13533	PASS	AA=98;AB=0.84864;ABA=89;ABP=623.8;ABR=499;AC=47;AF=0.03796;AN=1238;BL=5324;BR=856;BVAR;BaseQRankSum=-11.577;DEL;DP=13384;Dels=0.01;EL=53;EPP=4.4284;ER=45;FS=6.099;HETAR=219;HOMA=845;HOMR=18;HRun=1;InbreedingCoeff=-0.0056;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.72298;LRBP=7017.4;MQ0Fraction=0.0003;MQM=90.449;MQRankSum=1.408;NS=1083;RA=590;RL=87;RPP=130.99;RR=11;RUN=1;ReadPosRankSum=-18.074;SAB=0.55102;SAF=54;SAP=5.2261;SAR=44;SRB=0.52373;SRF=309;SRP=5.8958;SRR=281;VQSLOD=4.1054;set=filterInVQSR-2of5;sumGLbyD=3.06
+20	15283028	.	A	AC,ACACACACACACAC	140844.83	PASS	AA=180;AB=0.61442;ABA=123;ABP=39.285;ABR=196;AC=13,817;AF=0.01111,0.69829;AN=1170;BL=4453;BR=11407;BVAR;BaseQRankSum=24.686;DP=6365;Dels=0.00;EL=124;EPP=58.793;ER=56;FR;FS=10.912;HETAR=87;HOMA=48;HOMR=683;HP=1;HR=1;HRun=1;HU=T;INS;InbreedingCoeff=0.2074;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.43846;LRBP=6624;MQ0Fraction=0.0558;MQM=38.211;MQRankSum=-21.111;NF;NR;NS=818;PP;RA=1732;RL=0;RPP=393.88;RR=180;RUN=1;ReadPosRankSum=-7.620;SAB=0.31111;SAF=56;SAP=58.793;SAR=124;SC=ACACACACACATACACACATA;SRB=0.54042;SRF=936;SRP=27.584;SRR=796;TC;TR=21;TU=AC;VQSLOD=4.7569;set=Intersection;sumGLbyD=18.36
+20	15361056	.	ATAACT	A	4892.81	PASS	AA=59;AB=0.63576;ABA=55;ABP=27.184;ABR=96;AC=34;AF=0.0487;AN=698;BL=3164;BR=1999;BVAR;BaseQRankSum=3.391;DEL;DP=7080;Dels=0.03;EL=27;EPP=3.9304;ER=32;FR;FS=4.816;HETAR=35;HOMA=6;HOMR=966;HP=2;HPLen=3;HR=3;HRun=0;HU=A;InbreedingCoeff=0.0785;IndelType=DEL.NumRepetitions_1.EventLength_5.;LEN=5;LRB=0.22564;LRBP=573.84;MQ0=0;MQ0Fraction=0.0000;MQM=70.034;MQRankSum=-8.732;NF;NR;NS=1008;PP;RA=3915;RL=42;RPP=26.013;RR=17;RUN=1;ReadPosRankSum=-0.735;SAB=0.44068;SAF=26;SAP=4.8137;SAR=33;SC=AGATTAGGAAATAACTTAGGG;SET_INTEGRATION;SET_WGVQSR;SRB=0.42682;SRF=1671;SRP=185.12;SRR=2244;TC;TR=3;TU=A;VQSLOD=7.0900;set=Intersection;sumGLbyD=43.38
+20	15579507	.	AATTAGTC	A,TATTAGTC	1936.38	PASS	AA=16;AB=0.58974;ABA=16;ABP=5.7386;ABR=23;AC=64;AF=0.05229;AN=1224;BL=699;BR=775;BVAR;BaseQRankSum=-21.390;DEL;DP=21920;DP4=2099,2403,6,6;Dels=0.00;EL=8;EPP=3.0103;ER=8;FR;FS=2.920;HETAR=5;HOMA=0;HOMR=1063;HP=3;HPLen=4;HR=4;HU=A;INDEL;InbreedingCoeff=-0.0143;IndelType=MIXED;LEN=7;LRB=0.05156;LRBP=11.519;MQ=129.49;MQ0=0;MQ0Fraction=0.0000;MQM=51.938;MQRankSum=3.331;NF;NR;NS=1068;PP;PV4=1,0.019,1.3e-07,1;RA=5334;RL=5;RPP=7.8961;RR=11;RUN=1;ReadPosRankSum=-16.901;SAB=0.4375;SAF=7;SAP=3.5532;SAR=9;SC=CATACTACAAAATTAGTCATT;SET_INTEGRATION;SET_WGVQSR;SRB=0.41695;SRF=2224;SRP=322.58;SRR=3110;TC;TR=4;TU=A;VQSLOD=3.2237;set=filterInVQSR-2of5;sumGLbyD=43.57
+20	15752535	.	CT	C,GT	3775.20	PASS	AA=92;AB=0.78636;ABA=47;ABP=159.71;ABR=173;AC=0;AF=0.0000;AN=608;BL=4955;BR=2380;BVAR;BaseQRankSum=2.910;DEL;DP=3429;Dels=0.04;EL=13;EPP=105.82;ER=79;FR;HETAR=92;HOMA=95;HOMR=544;HP=2;HPLen=2;HR=2;HU=T;InbreedingCoeff=0.0483;IndelType=MIXED;LEN=1;LRB=0.35106;LRBP=1966;MQ0Fraction=0.0232;MQM=35.293;MQRankSum=-2.199;NF;NR;NS=732;PP;QD=4.91;RA=1272;RL=81;RPP=118.66;RR=11;RUN=1;ReadPosRankSum=-1.077;SAB=0.021739;SAF=2;SAP=185.79;SAR=90;SB=-59.51;SC=CAAGACCATCCTTGGCTAACA;SET_INTEGRATION;SET_WGVQSR;SRB=0.14623;SRF=186;SRP=1385.8;SRR=1086;TC;TR=2;TU=T;set=filterInVQSR-2of5;sumGLbyD=9.70
+20	15883060	rs73619850	A	AT	1325.60	PASS	AA=38;AB=0.59302;ABA=35;ABP=9.4742;ABR=51;AC=14;AF=0.0156;AN=896;BL=1078;BR=1638;BVAR;BaseQRankSum=-4.526;DB;DP=19854;DP4=1632,1800,15,20;Dels=0.00;EL=18;EPP=3.2389;ER=20;FR;FS=0.000;HETAR=14;HOMA=1;HOMR=1014;HP=1;HPLen=1;HR=1;HRun=1;HU=T;INDEL;INS;InbreedingCoeff=-0.0131;IndelType=INS.NumRepetitions_1.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.20619;LRBP=253.74;MQ=118.40;MQ0=0;MQ0Fraction=0.0000;MQM=56.526;MQRankSum=0.892;NF;NR;NS=1029;PP;PV4=0.61,1,0.25,0.14;RA=4439;RL=14;RPP=8.7247;RR=24;RUN=1;ReadPosRankSum=-2.061;SAB=0.42105;SAF=16;SAP=5.0675;SAR=22;SC=GGATTGGCAGATAAAAAATGG;SET_INTEGRATION;SET_WGVQSR;SRB=0.46429;SRF=2061;SRP=52.168;SRR=2378;TC;TR=1;TU=T;VQSLOD=9.7576;set=Intersection;sumGLbyD=15.69
+20	16122099	.	GA	G	12914	PASS	AA=85;AB=0.85915;ABA=80;ABP=639.4;ABR=488;AC=19;AF=0.01542;AN=1232;BL=805;BR=5457;BVAR;BaseQRankSum=-6.084;DEL;DP=13592;Dels=0.00;EL=45;EPP=3.649;ER=40;FS=0.935;HETAR=218;HOMA=841;HOMR=14;HRun=2;InbreedingCoeff=0.0250;IndelType=DEL.NumRepetitions_2.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.74289;LRBP=7507.5;MQ0=0;MQ0Fraction=0.0000;MQM=103.01;MQRankSum=2.843;NS=1075;RA=541;RL=2;RPP=170.62;RR=83;RUN=1;ReadPosRankSum=-16.222;SAB=0.49412;SAF=42;SAP=3.0358;SAR=43;SRB=0.44917;SRF=243;SRP=15.152;SRR=298;VQSLOD=3.9745;set=filterInVQSR-2of5;sumGLbyD=2.97
+20	16828509	.	G	GT	843.62	PASS	AA=30;AB=0.70103;ABA=29;ABP=37.06;ABR=68;AC=10;AF=0.0140;AN=714;BL=1368;BR=1786;BVAR;BaseQRankSum=-4.061;DP=8682;Dels=0.01;EL=14;EPP=3.2998;ER=16;FR;FS=2.681;HETAR=22;HOMA=1;HOMR=1020;HP=8;HPLen=8;HR=8;HRun=8;HU=T;INS;InbreedingCoeff=0.1389;IndelType=INS.NumRepetitions_8.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.13253;LRBP=123.3;MQ0=0;MQ0Fraction=0.0000;MQM=62.8;MQRankSum=-1.491;NF;NR;NS=1043;PP;RA=4416;RL=11;RPP=7.6428;RR=19;RUN=1;ReadPosRankSum=-1.718;SAB=0.76667;SAF=23;SAP=21.54;SAR=7;SC=CCTTCAAAAGGTTTTTTTTGG;SET_INTEGRATION;SET_WGVQSR;SRB=0.5745;SRF=2537;SRP=215.91;SRR=1879;TC;TR=8;TU=T;VQSLOD=7.6258;set=Intersection;sumGLbyD=10.77
+20	17470034	.	GC	G	46975	PASS	AA=57;AB=0.96043;ABA=52;ABP=2422.5;ABR=1262;AC=34;AF=0.02773;AN=1226;BL=418;BR=3446;BVAR;BaseQRankSum=-6.250;DEL;DP=12035;Dels=0.00;EL=22;EPP=9.4485;ER=35;FS=1.350;HETAR=416;HOMA=409;HOMR=244;HRun=1;InbreedingCoeff=0.0083;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;LEN=1;LRB=0.78364;LRBP=5155.6;MQ0=0;MQ0Fraction=0.0000;MQM=99.509;MQRankSum=2.192;NS=1076;RA=2396;RL=5;RPP=87.164;RR=52;RUN=1;ReadPosRankSum=-15.199;SAB=0.5614;SAF=32;SAP=4.877;SAR=25;SRB=0.52963;SRF=1269;SRP=21.285;SRR=1127;VQSLOD=3.8440;set=filterInVQSR-2of5;sumGLbyD=3.06
+20	17471374	.	AGCGGC	A	850.03	PASS	AC=6;AF=0.0085;AF1=0.01301;AN=704;BaseQRankSum=6.259;CI95=0.00885,0.01991;DP=8180;DP4=2215,1878,4,5;Dels=0.01;FQ=131;FS=0.000;HRun=0;INDEL;InbreedingCoeff=0.0009;IndelType=DEL.NumRepetitions_1.EventLength_5.;MQ=104.41;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-5.521;PV4=0.74,0.37,0.0005,1;ReadPosRankSum=2.468;SET_INTEGRATION;SET_WGVQSR;VQSLOD=6.8773;set=Intersection;sumGLbyD=30.85
+20	18433202	rs35582929	G	GA	2506.90	PASS	AA=55;AB=0.5812;ABA=49;ABP=9.7103;ABR=68;AC=20;AF=0.0218;AN=918;BL=2263;BR=2175;BVAR;BaseQRankSum=-6.639;DB;DP=19467;DP4=1845,2365,27,26;Dels=0.00;EL=21;EPP=9.6826;ER=34;FQ=999;FR;FS=5.633;HETAR=16;HOMA=3;HOMR=1045;HP=2;HPLen=3;HR=3;HRun=1;HU=G;INDEL;INS;InbreedingCoeff=0.0700;IndelType=INS.NumRepetitions_1.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.019829;LRBP=6.7994;MQ=114.03;MQ0=0;MQ0Fraction=0.0000;MQM=83.345;MQRankSum=1.610;NF;NR;NS=1064;PP;PV4=0.33,1,1,1;RA=5380;RL=28;RPP=3.0498;RR=27;RUN=1;ReadPosRankSum=0.873;SAB=0.47273;SAF=26;SAP=3.3656;SAR=29;SC=TATTTCATGGGAGCATTAAAA;SET_INTEGRATION;SET_WGVQSR;SRB=0.42862;SRF=2306;SRP=241.07;SRR=3074;TC;TR=3;TU=G;VQSLOD=10.0372;dbSNP=126;set=Intersection;sumGLbyD=13.10
+20	18551314	rs10659122	CA	C,CAA,CAAA,CAAAA,CAAAAA	18810.74	PASS	ABR=243;AC=19,169,216,164,188;AF=0.01816,0.16157,0.20650,0.15679,0.17973;BVAR;BaseQRankSum=-5.742;DB;DP=17637;DP4=136,77,560,237;FR;FS=2.693;HOMA=177;HOMR=299;HP=17;HR=17;HU=A;HaplotypeScore=15.5048;INDEL;INS;InbreedingCoeff=0.8901;IndelType=MULTIALLELIC_INDEL;MQ0=11;MQ0Fraction=0.0069;MQRankSum=1.845;NF;NR;NS=658;PP;PV4=0.08,1,1,1;QD=12.66;RA=673;RUN=1;ReadPosRankSum=0.283;SB=-3514.45;SC=GATTCCATCTCAAAAAAAAAA;SET_WGVQSR;SRB=0.63596;SRF=428;SRP=111.06;SRR=245;TC;TR=17;TU=A;VQSLOD=10.6964;dbSNP=130;set=Intersection
+20	18785519	.	G	GTC	415.55	PASS	AC=28;AF=0.0400;AN=700;BaseQRankSum=10.889;DP=1929;FS=8.778;HRun=0;HaplotypeScore=27.6448;InbreedingCoeff=0.0510;IndelType=INS.NOVEL_2.;MQ=61.99;MQ0=36;MQ0Fraction=0.0187;MQRankSum=4.508;QD=3.08;ReadPosRankSum=8.080;SB=-437.03;SET_INTEGRATION;SET_WGVQSR;VQSLOD=4.9313;set=VQSR
+20	20301041	rs35451634	ATATG	A	200.42	PASS	AC=21;AF=0.0449;AN=468;BaseQRankSum=5.251;DB;DP=579;FS=24.013;HRun=0;HaplotypeScore=27.8977;InbreedingCoeff=0.0113;IndelType=DEL.NumRepetitions_1.EventLength_4.;MQ=78.47;MQ0=26;MQ0Fraction=0.0449;MQRankSum=-5.284;QD=3.06;ReadPosRankSum=1.793;SB=-55.76;SET_INTEGRATION;SET_WGVQSR;VQSLOD=5.0981;set=VQSR
+20	20378174	.	TC	T	245.55	PASS	AC=23;AF=0.01879;AN=1224;BaseQRankSum=0.990;DP=3225;FS=10.413;HRun=1;HaplotypeScore=22.6109;InbreedingCoeff=0.0244;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;MQ=93.70;MQ0=3;MQ0Fraction=0.0009;MQRankSum=-3.349;QD=1.86;ReadPosRankSum=-7.227;SB=-188.62;VQSLOD=4.2553;set=VQSR
+20	20809160	rs10571503	TAA	AAA,T	3496	PASS	AC=0;AF=0.0000;AN=612;BaseQRankSum=1.968;DB;DP=1092;FR;HP=4;HPLen=3;HR=3;HRun=0;HU=A;HaplotypeScore=26.1253;InbreedingCoeff=0.0603;IndelType=MIXED;MQ=68.98;MQ0=1;MQ0Fraction=0.0009;MQRankSum=1.520;NF;NR;PP;ReadPosRankSum=-4.042;SC=TATATATATATAAATTTAAAT;TC;TR=13;TU=AT;set=filterInVQSR-2of5
+20	22508765	.	CT	C	53877.84	PASS	AA=187;AB=0.78077;ABA=171;ABP=537.09;ABR=609;AC=1017;AF=0.91787;AN=1108;BL=12690;BR=1718;BVAR;BaseQRankSum=13.773;DEL;DP=7430;Dels=0.02;EL=73;EPP=22.53;ER=114;FR;FS=16.352;HETAR=152;HOMA=9;HOMR=786;HP=8;HR=4;HRun=4;HU=T;InbreedingCoeff=0.3885;IndelType=DEL.NumRepetitions_4.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.76152;LRBP=18147;MQ0=0;MQ0Fraction=0.0000;MQM=46.086;MQRankSum=0.971;NF;NR;NS=947;PP;RA=2868;RL=177;RPP=326.86;RR=10;RUN=1;ReadPosRankSum=9.951;SAB=0.34759;SAF=65;SAP=40.738;SAR=122;SC=AAAAAATTTTCTTTTGAACTG;SET_INTEGRATION;SET_WGVQSR;SRB=0.46269;SRF=1327;SRP=37.684;SRR=1541;TC;TR=4;TU=T;VQSLOD=5.1182;set=Intersection;sumGLbyD=25.15
+20	22555082	rs11477526	AT	A	11503	PASS	AA=530;AB=0.50816;ABA=422;ABP=3.5063;ABR=436;AF=0.1614;AN=700;BL=21453;BR=23313;BVAR;BaseQRankSum=17.562;DB;DEL;DP=25587;DP4=1869,1600,283,201;Dels=0.14;EL=259;EPP=3.6003;ER=271;FQ=999;FR;FS=14.595;HETAR=159;HOMA=41;HOMR=846;HP=3;HPLen=3;HR=3;HRun=3;HU=T;INDEL;InbreedingCoeff=0.0995;IndelType=DEL.NumRepetitions_3.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.041549;LRBP=170.83;MQ=95.89;MQ0=0;MQ0Fraction=0.0000;MQM=72.162;MQRankSum=2.564;NF;NR;NS=1046;PP;PV4=0.058,6.6e-129,0.04,1;RA=4303;RL=264;RPP=3.0267;RR=266;RUN=1;ReadPosRankSum=0.176;SAB=0.58679;SAF=311;SAP=37.688;SAR=219;SC=GGGAAAGCTGATTTACTGATT;SET_INTEGRATION;SET_WGVQSR;SRB=0.54892;SRF=2362;SRP=92.453;SRR=1941;TC;TR=3;TU=T;VQSLOD=8.7746;dbSNP=120;set=Intersection;sumGLbyD=15.27
+20	22590907	.	A	AC	4204.88	PASS	AA=67;AB=0.592;ABA=51;ABP=12.2;ABR=74;AF=0.0554;AF1=0.0468;AN=560;BL=2277;BR=2389;BVAR;BaseQRankSum=10.968;CI95=0.03759,0.05639;DP=14380;DP4=2514,2018,33,33;Dels=0.00;EL=22;EPP=20.155;ER=45;FQ=999;FR;FS=3.846;HETAR=25;HOMA=4;HOMR=1049;HP=4;HPLen=5;HR=5;HRun=0;HU=A;INDEL;INS;InbreedingCoeff=0.0719;IndelType=INS.NOVEL_1.Novel_C.;LEN=1;LRB=0.024003;LRBP=8.8481;MQ=110.68;MQ0=0;MQ0Fraction=0.0000;MQM=96.149;MQRankSum=2.668;NF;NR;NS=1078;PP;PV4=0.39,1,0.46,0.36;RA=5468;RL=33;RPP=3.0427;RR=34;RUN=1;ReadPosRankSum=-1.097;SAB=0.50746;SAF=34;SAP=3.0427;SAR=33;SC=TCATATCAAAAACATTACGTT;SET_INTEGRATION;SET_WGVQSR;SRB=0.54389;SRF=2974;SRP=94.508;SRR=2494;TC;TR=5;TU=A;VQSLOD=10.0712;set=Intersection;sumGLbyD=27.69
+20	22806326	rs11468890	ATTCCATCAC	A	105320.99	PASS	AC=567;AF=0.48795;AN=1162;BVAR;BaseQRankSum=32.858;DB;DEL;DP=26278;DP4=727,796,554,587;Dels=0.30;FQ=999;FR;FS=1.923;HP=3;HPLen=3;HR=2;HRun=0;HU=T;INDEL;InbreedingCoeff=0.2548;IndelType=DEL.NumRepetitions_2.EventLength_9.;LEN=9;MQ=89.42;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-23.545;NF;NR;PP;PV4=0.7,1,1.3e-167,1;RUN=1;ReadPosRankSum=4.384;SC=GGCTGCTCCCATTCCATCACT;SET_INTEGRATION;SET_WGVQSR;TC;TR=2;TU=T;VQSLOD=8.2594;set=Intersection;sumGLbyD=69.81
+20	22999898	rs55966257	CAGGA	C	8019.97	PASS	AA=23;AB=0.57778;ABA=19;ABP=5.3748;ABR=26;AC=214;AF=0.18838;AN=1136;BL=1143;BR=1040;BVAR;BaseQRankSum=29.294;DB;DEL;DP=8216;Dels=0.02;EL=11;EPP=3.1047;ER=12;FS=14.938;HETAR=14;HOMA=2;HOMR=948;HRun=0;InbreedingCoeff=0.0797;IndelType=DEL.NumRepetitions_1.EventLength_4.;LEN=4;LRB=0.047183;LRBP=13.563;MQ0=0;MQ0Fraction=0.0000;MQM=34.783;MQRankSum=-20.301;NS=964;RA=3637;RL=13;RPP=3.86;RR=10;RUN=1;ReadPosRankSum=-24.607;SAB=0.47826;SAF=11;SAP=3.1047;SAR=12;SRB=0.49024;SRF=1783;SRP=6.02;SRR=1854;VQSLOD=7.9163;set=Intersection;sumGLbyD=9.43
+20	23385964	rs57723772	GAA	G	8170.95	PASS	AC=257;AF=0.20928;AN=1228;BaseQRankSum=32.220;DB;DP=3291;FS=1.688;HRun=3;HaplotypeScore=22.6739;InbreedingCoeff=0.0171;IndelType=DEL.NumRepetitions_3.EventLength_1.RepeatExpansion_A.;MQ=58.44;MQ0=32;MQ0Fraction=0.0097;MQRankSum=-4.893;QD=6.55;ReadPosRankSum=-35.524;SB=-3631.67;VQSLOD=5.6549;set=VQSR
+20	23534530	.	TA	T	3542.10	PASS	AA=45;AB=0.75658;ABA=37;ABP=89.926;ABR=115;AC=35;AF=0.02991;AN=1170;BL=3090;BR=270;BVAR;BaseQRankSum=-6.892;DEL;DP=8108;Dels=0.00;EL=19;EPP=5.3748;ER=26;FS=1.026;HETAR=76;HOMA=896;HOMR=18;HRun=1;InbreedingCoeff=0.0551;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.83929;LRBP=5142.4;MQ0Fraction=0.0017;MQM=41.578;MQRankSum=0.818;NS=991;RA=203;RL=43;RPP=84.127;RR=2;RUN=1;ReadPosRankSum=-12.923;SAB=0.37778;SAF=17;SAP=8.8491;SAR=28;SRB=0.5665;SRF=115;SRP=10.808;SRR=88;VQSLOD=4.2093;set=Intersection;sumGLbyD=3.49
+20	23976810	rs5841018	A	ATATTAAT	1782.38	PASS	AF=0.1387;AF1=0.01507;BaseQRankSum=3.717;CI95=0.00188,0.03947;DB;DP=1712;DP4=357,376,7,2;Dels=0.00;FQ=31.1;FS=14.489;HPLen=2;HRun=0;INDEL;InbreedingCoeff=0.1123;IndelType=INS.NumRepetitions_1.EventLength_7.;MQ=49.53;MQ0=2;MQ0Fraction=0.0055;MQRankSum=-4.928;PV4=0.1,1,0.00085,0.016;ReadPosRankSum=-4.456;VQSLOD=5.3140;dbSNP=116;set=Intersection;sumGLbyD=19.98
+20	24222100	.	CTTTTA	C	4219.36	PASS	AA=57;AB=0.59434;ABA=43;ABP=11.205;ABR=63;AF=0.01803;AF1=0.01547;AN=1220;BL=2073;BR=2345;BVAR;BaseQRankSum=7.990;CI95=0.0114,0.02137;DEL;DP=17536;DP4=2140,2346,7,12;Dels=0.01;EL=32;EPP=4.877;ER=25;FQ=104;FS=0.614;HETAR=21;HOMA=4;HOMR=1042;HRun=0;INDEL;InbreedingCoeff=0.1941;IndelType=DEL.NumRepetitions_2.EventLength_5.;LEN=5;LRB=0.061566;LRBP=39.374;MQ=73.32;MQ0Fraction=0.0021;MQM=39.614;MQRankSum=-5.728;NS=1067;PV4=0.37,1.1e-39,3.5e-09,1;RA=5527;RL=28;RPP=3.0484;RR=29;RUN=1;ReadPosRankSum=0.214;SAB=0.54386;SAF=31;SAP=3.9627;SAR=26;SET_INTEGRATION;SET_WGVQSR;SRB=0.49267;SRF=2723;SRP=5.588;SRR=2804;VQSLOD=7.5428;set=Intersection;sumGLbyD=38.08
+20	24395018	.	AT	A	49310	PASS	AA=146;AB=0.91198;ABA=130;ABP=2180.5;ABR=1347;AC=50;AF=0.04045;AN=1236;BL=587;BR=9625;BVAR;BaseQRankSum=-4.610;DEL;DP=12793;Dels=0.01;EL=54;EPP=24.487;ER=92;FS=22.108;HETAR=485;HOMA=384;HOMR=210;HRun=2;InbreedingCoeff=0.0374;IndelType=DEL.NumRepetitions_2.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.88504;LRBP=17373;MQ0=0;MQ0Fraction=0.0000;MQM=102.26;MQRankSum=2.256;NS=1080;RA=2377;RL=1;RPP=311.42;RR=145;RUN=1;ReadPosRankSum=-16.347;SAB=0.63699;SAF=93;SAP=26.807;SAR=53;SRB=0.52167;SRF=1240;SRP=12.702;SRR=1137;VQSLOD=3.2421;set=filterInVQSR-2of5;sumGLbyD=3.80
+20	24411517	.	C	CA	246.18	PASS	AF=0.01546;AF1=0.01095;BaseQRankSum=7.832;CI95=0.005698,0.01709;DP=7981;DP4=983,2037,7,7;Dels=0.00;FQ=27.9;FS=18.815;HPLen=3;HRun=3;INDEL;InbreedingCoeff=0.0175;IndelType=INS.NumRepetitions_3.EventLength_1.RepeatExpansion_A.;MQ=60.28;MQ0Fraction=0.0137;MQRankSum=-7.243;PV4=0.25,1,2.7e-05,1;ReadPosRankSum=-0.143;VQSLOD=4.3701;set=Intersection;sumGLbyD=6.56
+20	24421169	.	AG	A	27480	PASS	AA=182;AB=0.8303;ABA=149;ABP=835;ABR=729;AC=89;AF=0.07224;AN=1232;BL=11276;BR=2214;BVAR;BaseQRankSum=-5.447;DEL;DP=11717;Dels=0.01;EL=103;EPP=9.8827;ER=79;FR;FS=15.492;HETAR=343;HOMA=607;HOMR=114;HP=4;HR=1;HRun=1;HU=G;InbreedingCoeff=0.0353;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_G.;LEN=1;LRB=0.67176;LRBP=13222;MQ0=0;MQ0Fraction=0.0000;MQM=88.324;MQRankSum=2.221;NF;NR;NS=1071;PP;RA=1226;RL=169;RPP=293.37;RR=13;RUN=1;ReadPosRankSum=-19.711;SAB=0.54945;SAF=100;SAP=6.876;SAR=82;SC=CCTTAGCCCCAGAAAACATCT;SRB=0.44535;SRF=546;SRP=34.814;SRR=680;TC;TR=1;TU=G;VQSLOD=4.2669;set=Intersection;sumGLbyD=3.91
+20	24765537	rs71841337	ATTT	A,AT,ATT,ATTTT,ATTTTT	37852	PASS	AC=13,120,527,51,92;AF=0.01102,0.10169,0.44661,0.04322,0.07797;AN=1180;BVAR;BaseQRankSum=8.172;DB;DEL;DP=39116;DP4=200,331,851,1169;FR;FS=2.394;HP=15;HR=15;HU=T;HaplotypeScore=20.8091;INDEL;INS;InbreedingCoeff=0.4815;IndelType=MULTIALLELIC_INDEL;MQ0=1;MQ0Fraction=0.0003;MQRankSum=4.344;NF;NR;PP;PV4=0.067,1,1,0.1;QD=7.90;RUN=1;ReadPosRankSum=1.798;SB=-8371.96;SC=CTCTGCAACAATTTTTTTTTT;SET_WGVQSR;TC;TR=15;TU=T;VQSLOD=9.9679;dbSNP=120;set=Intersection
+20	25500689	.	A	AATTT	84980.72	PASS	AC=1005;AF=0.89096;AN=1128;BaseQRankSum=17.400;DP=2324;FS=6.721;HRun=0;HaplotypeScore=25.3376;InbreedingCoeff=0.2148;IndelType=INS.NumRepetitions_1.EventLength_4.;MQ=75.19;MQ0=1;MQ0Fraction=0.0004;MQRankSum=-8.221;QD=38.28;ReadPosRankSum=4.504;SB=-34833.07;SET_INTEGRATION;SET_WGVQSR;VQSLOD=4.6038;set=VQSR
+20	25550373	.	GA	G	11251.31	PASS	AA=246;AB=0.42963;ABA=154;ABP=14.624;ABR=116;AC=566;AF=0.6521;AN=868;BL=5230;BR=11845;BVAR;BaseQRankSum=7.418;DEL;DP=8885;Dels=0.02;EL=99;EPP=23.348;ER=147;FR;FS=50.357;HETAR=150;HOMA=849;HOMR=14;HP=1;HR=2;HRun=1;HU=G;InbreedingCoeff=0.1365;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.38741;LRBP=5567.9;MQ0=0;MQ0Fraction=0.0000;MQM=97.561;MQRankSum=0.050;NF;NR;NS=1013;PP;RA=269;RL=75;RPP=84.361;RR=171;RUN=1;ReadPosRankSum=-7.128;SAB=0.52846;SAF=130;SAP=4.7404;SAR=116;SC=CACGGAGGCGGAGGAAGCAGC;SRB=0.42379;SRF=114;SRP=16.58;SRR=155;TC;TR=6;TU=AGG;VQSLOD=4.0103;set=filterInVQSR-2of5;sumGLbyD=4.58
+20	25903865	.	TTC	T	7459.23	PASS	AC=277;AF=0.23316;AN=1188;BaseQRankSum=31.479;DP=2969;FS=137.723;HRun=0;HaplotypeScore=37.3300;InbreedingCoeff=-0.1755;IndelType=DEL.NumRepetitions_1.EventLength_2.RepeatExpansion_TC.;MQ=53.49;MQ0=50;MQ0Fraction=0.0168;MQRankSum=-25.506;QD=4.70;ReadPosRankSum=-5.913;SB=-1747.98;VQSLOD=5.4731;set=VQSR
+20	25934237	.	C	CCACTT	771.36	PASS	AC=37;AF=0.0426;AN=868;BaseQRankSum=16.331;DP=2253;FS=4.545;HRun=0;HaplotypeScore=29.9764;InbreedingCoeff=-0.0685;IndelType=INS.NOVEL_5.;MQ=48.12;MQ0=87;MQ0Fraction=0.0386;MQRankSum=-12.497;QD=3.37;ReadPosRankSum=-8.428;SB=-297.70;VQSLOD=4.2324;set=VQSR
+20	26054751	rs112967123	TATC	T	33244	PASS	AA=1863;AB=0.79012;ABA=1788;ABP=6231;ABR=6731;AC=227;AF=0.18218;AN=1246;BL=74924;BR=72452;BVAR;BaseQRankSum=32.258;DB;DEL;DP=36404;DS;Dels=0.05;EL=931;EPP=3.0115;ER=932;FR;FS=265.752;HETAR=527;HOMA=2;HOMR=565;HP=1;HR=2;HRun=0;HU=T;InbreedingCoeff=-0.2137;IndelType=DEL.NumRepetitions_2.EventLength_3.;LEN=3;LRB=0.016773;LRBP=93.048;MQ0Fraction=0.0127;MQM=28.797;MQRankSum=-5.329;NF;NR;NS=1094;PP;RA=14604;RL=1014;RPP=34.743;RR=849;RUN=1;ReadPosRankSum=8.394;SAB=0.65486;SAF=1220;SAP=391.07;SAR=643;SC=TCACCATCATTATCATCATTA;SRB=0.56717;SRF=8283;SRP=575.39;SRR=6321;TC;TR=8;TU=ATC;VQSLOD=1.0486;set=filterInVQSR-2of5;sumGLbyD=6.54
+20	26120452	.	CAG	C	7863.19	PASS	AA=163;AB=0.70489;ABA=157;ABP=196.99;ABR=375;AC=171;AF=0.1908;AN=896;BL=3455;BR=4877;BVAR;BaseQRankSum=25.536;DEL;DP=7014;Dels=0.10;EL=58;EPP=32.438;ER=105;FS=231.723;HETAR=90;HOMA=5;HOMR=387;HRun=0;InbreedingCoeff=-0.1966;IndelType=DEL.NumRepetitions_1.EventLength_2.RepeatExpansion_AG.;LEN=2;LRB=0.17067;LRBP=530;MQ0Fraction=0.0470;MQM=21.951;MQRankSum=-23.449;NS=482;RA=1117;RL=62;RPP=23.273;RR=101;RUN=1;ReadPosRankSum=1.904;SAB=0.37423;SAF=61;SAP=25.404;SAR=102;SRB=0.41719;SRF=466;SRP=69.544;SRR=651;VQSLOD=-0.9395;set=filterInVQSR-2of5;sumGLbyD=5.06
+20	26185812	.	AG	A	322.58	PASS	AF=0.0342;BaseQRankSum=3.668;DP=3014;Dels=0.01;FR;FS=10.238;HP=8;HPLen=6;HR=6;HRun=6;HU=G;InbreedingCoeff=0.1504;IndelType=DEL.NumRepetitions_6.EventLength_1.RepeatExpansion_G.;MQ0Fraction=0.0473;MQRankSum=-5.464;NF;NR;PP;ReadPosRankSum=0.536;SC=GGGTGGGTGGAGGGGGGAGGG;SET_WGVQSR;TC;TR=6;TU=G;VQSLOD=5.0767;set=Intersection;sumGLbyD=8.46
+20	30963468	.	AGTTT	A	2041.12	PASS	AA=38;AB=0.75694;ABA=35;ABP=85.587;ABR=109;AC=34;AF=0.0377;AN=902;BL=1974;BR=668;BVAR;BaseQRankSum=3.060;DEL;DP=22806;DP4=1997,1747,28,36;Dels=0.02;EL=17;EPP=3.9246;ER=21;FR;FS=16.034;HETAR=29;HOMA=1;HOMR=1009;HP=1;HPLen=1;HR=1;HRun=0;HU=G;INDEL;InbreedingCoeff=0.0752;IndelType=DEL.NumRepetitions_2.EventLength_4.;LEN=4;LRB=0.49432;LRBP=1404.9;MQ=87.17;MQ0Fraction=0.0013;MQM=98.079;MQRankSum=6.021;NF;NR;NS=1039;PP;PV4=0.13,1.5e-07,1,0.051;RA=4052;RL=36;RPP=69.069;RR=2;RUN=1;ReadPosRankSum=-1.847;SAB=0.5;SAF=19;SAP=3.0103;SAR=19;SC=AGAAGTAAGTAGTTTGTTTTT;SET_INTEGRATION;SET_WGVQSR;SRB=0.53776;SRF=2179;SRP=53.19;SRR=1873;TC;TR=9;TU=AAGT;VQSLOD=7.3578;set=Intersection;sumGLbyD=14.03
+20	31963212	.	AAAAAAAAAAAAG	A	727.15	PASS	AC=5;AF=0.0080;AN=622;BaseQRankSum=4.037;DP=1480;FS=0.000;HRun=0;HaplotypeScore=43.3793;InbreedingCoeff=0.0350;IndelType=DEL.NumRepetitions_1.EventLength_10orMore.;MQ=51.77;MQ0=59;MQ0Fraction=0.0399;MQRankSum=-1.799;QD=22.72;ReadPosRankSum=3.591;SB=-364.04;VQSLOD=5.3166;set=VQSR
+20	31997272	.	CT	C,CTT,CTTT	1837.10	PASS	AA=63;AB=0.77559;ABA=57;ABP=170.57;ABR=197;AC=79,49,30;AF=0.06594,0.04090,0.02504;AN=1198;BL=2372;BR=2640;BVAR;BaseQRankSum=3.277;DP=9050;Dels=0.03;EL=24;EPP=10.766;ER=39;FR;FS=0.303;HETAR=45;HOMA=1;HOMR=981;HP=10;HPLen=10;HR=10;HRun=10;HU=T;INS;InbreedingCoeff=0.2796;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.053472;LRBP=34.128;MQ0Fraction=0.0000;MQM=50.889;MQRankSum=0.610;NF;NR;NS=1027;PP;RA=3776;RL=30;RPP=3.3205;RR=33;RUN=1;ReadPosRankSum=-0.800;SAB=0.39683;SAF=25;SAP=8.8354;SAR=38;SC=ACCCAACTTCCTTTTTTTTTT;SET_WGVQSR;SRB=0.46213;SRF=1745;SRP=50.049;SRR=2031;TC;TR=10;TU=T;VQSLOD=4.1189;set=filterInVQSR-2of5;sumGLbyD=3.66
+20	33446974	rs113250263	TAA	T,TA,TAAA	17130.16	PASS	AC=65,417,184;AF=0.05941,0.38117,0.16819;AN=1094;BVAR;BaseQRankSum=3.400;DB;DEL;DP=22362;DP4=221,247,418,524;Dels=0.33;FR;FS=15.409;HP=15;HR=14;HRun=14;HU=A;INDEL;INS;InbreedingCoeff=0.5215;IndelType=MULTIALLELIC_INDEL;MQ=61.32;MQ0Fraction=0.0021;MQRankSum=0.481;NF;NR;PP;PV4=0.33,1,1,1;RUN=1;ReadPosRankSum=-0.056;SC=CTCCGTCTCATAAAAAAAAAA;SET_WGVQSR;TC;TR=14;TU=A;VQSLOD=8.0974;dbSNP=132;set=Intersection;sumGLbyD=12.78
+20	33877149	.	C	CT	1784.40	PASS	AA=58;AB=0.73096;ABA=53;ABP=94.289;ABR=144;AC=65;AF=0.05682;AN=1144;BL=3298;BR=1935;BVAR;BaseQRankSum=-2.066;DP=8074;Dels=0.02;EL=22;EPP=10.348;ER=36;FR;FS=11.452;HETAR=47;HOMA=3;HOMR=754;HP=16;HR=12;HRun=12;HU=T;INS;InbreedingCoeff=0.1178;IndelType=INS.NumRepetitions_10orMore.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.26046;LRBP=773.91;MQ0Fraction=0.0165;MQM=52.259;MQRankSum=0.734;NF;NR;NS=804;PP;RA=2141;RL=43;RPP=32.363;RR=15;RUN=1;ReadPosRankSum=-1.273;SAB=0.46552;SAF=27;SAP=3.6093;SAR=31;SC=ATTTTCTTTTCTTTTTTTTTT;SET_INTEGRATION;SET_WGVQSR;SRB=0.37553;SRF=804;SRP=291.14;SRR=1337;TC;TR=12;TU=T;VQSLOD=3.1540;set=filterInVQSR-2of5;sumGLbyD=2.84
+20	34387589	rs112431805	CT	C,CTT	4039.10	PASS	AA=121;AB=0.75368;ABA=117;ABP=268.53;ABR=358;AC=84,139;AF=0.07047,0.11661;AN=1192;BL=5557;BR=3901;BVAR;BaseQRankSum=2.693;DB;DP=10157;Dels=0.03;EL=47;EPP=16.093;ER=74;FR;FS=7.639;HETAR=89;HOMA=2;HOMR=913;HP=13;HR=11;HRun=11;HU=T;INS;InbreedingCoeff=0.2097;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.17509;LRBP=632.63;MQ0Fraction=0.0000;MQM=49.802;MQRankSum=-0.801;NF;NR;NS=1004;PP;RA=3789;RL=77;RPP=22.554;RR=44;RUN=1;ReadPosRankSum=-2.691;SAB=0.3719;SAF=45;SAP=20.256;SAR=76;SC=AAGAAGTGTTCTTTTTTTTTT;SET_WGVQSR;SRB=0.40987;SRF=1553;SRP=270.35;SRR=2236;TC;TR=11;TU=T;VQSLOD=4.0473;set=filterInVQSR-2of5;sumGLbyD=4.64
+20	34493409	rs73621682	C	CAG	62288.93	PASS	AA=1069;AB=0.54863;ABA=826;ABP=40.606;ABR=1004;AC=257;AF=0.3640;AN=706;BL=41524;BR=47039;BVAR;BaseQRankSum=-24.248;DB;DP=30195;DP4=1743,1636,614,487;Dels=0.00;EL=582;EPP=21.343;ER=487;FQ=999;FR;FS=5.080;HETAR=298;HOMA=63;HOMR=712;HP=1;HPLen=1;HR=1;HRun=0;HU=A;INDEL;INS;InbreedingCoeff=0.1437;IndelType=INS.NumRepetitions_2.EventLength_2.RepeatExpansion_AG.;LEN=2;LRB=0.062272;LRBP=748.76;MQ=77.99;MQ0=3;MQ0Fraction=0.0015;MQM=54.446;MQRankSum=0.160;NF;NR;NS=1073;PP;PV4=0.016,1,0.01,1;RA=4461;RL=526;RPP=3.5973;RR=543;RUN=1;ReadPosRankSum=-1.716;SAB=0.57343;SAF=613;SAP=53.08;SAR=456;SC=AGGAAGAGATCAGAGCTCCCC;SET_INTEGRATION;SET_WGVQSR;SRB=0.52634;SRF=2348;SRP=29.892;SRR=2113;TC;TR=4;TU=AG;VQSLOD=8.7047;dbSNP=130;set=Intersection;sumGLbyD=49.82
+20	35957317	.	CTGACT	C,CGACT	4370.96	PASS	ABR=81;AC=22,1;AF=0.0321,0.0015;AF1=0.04523;AN=686;BVAR;BaseQRankSum=7.969;CI95=0.0354,0.05752;DEL;DP=16632;DP4=1942,1815,17,21;Dels=0.03;FQ=999;FR;FS=0.531;HOMA=1;HOMR=998;HP=2;HPLen=1;HR=1;HRun=0;HU=T;INDEL;InbreedingCoeff=0.0587;IndelType=MULTIALLELIC_INDEL;MQ=83.38;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-7.201;NF;NR;NS=1020;PP;PV4=0.42,0.00017,4.5e-12,1;RA=4620;RUN=1;ReadPosRankSum=-1.007;SC=CCTCTCAGCTCTGACTGAGTC;SET_WGVQSR;SRB=0.50043;SRF=2312;SRP=3.0178;SRR=2308;TC;TR=8;TU=ACTG;VQSLOD=9.9778;dbSNP=130;set=Intersection;sumGLbyD=36.45
+20	36136198	.	GTGTC	G	2078.76	PASS	AA=35;AB=0.54167;ABA=33;ABP=4.096;ABR=39;AC=17;AF=0.01384;AN=1228;BL=1212;BR=1523;BVAR;BaseQRankSum=6.900;DEL;DP=22483;DP4=1696,2291,9,16;Dels=0.01;EL=9;EPP=20.94;ER=26;FQ=999;FR;FS=3.023;HETAR=13;HOMA=1;HOMR=1061;HP=1;HPLen=1;HR=1;HRun=0;HU=T;INDEL;InbreedingCoeff=0.1113;IndelType=DEL.NumRepetitions_2.EventLength_4.;LEN=4;LRB=0.11371;LRBP=79.803;MQ=93.98;MQ0=1;MQ0Fraction=0.0003;MQM=83.686;MQRankSum=-1.683;NF;NR;NS=1075;PP;PV4=0.55,1,0.0083,1;RA=5771;RL=19;RPP=3.5687;RR=16;RUN=1;ReadPosRankSum=0.618;SAB=0.37143;SAF=13;SAP=8.0357;SAR=22;SC=TATCATTTTAGTGTCTGTCTG;SET_INTEGRATION;SET_WGVQSR;SRB=0.44966;SRF=2595;SRP=130.03;SRR=3176;TC;TR=11;TU=CTGT;VQSLOD=10.1935;set=Intersection;sumGLbyD=31.66
+20	36250522	.	CA	C	37933	PASS	AA=51;AB=0.95582;ABA=44;ABP=1800.5;ABR=952;AC=23;AF=0.01885;AN=1220;BL=691;BR=3464;BVAR;BaseQRankSum=-2.418;DEL;DP=11998;Dels=0.00;EL=18;EPP=12.59;ER=33;FS=2.307;HETAR=348;HOMA=534;HOMR=164;HRun=1;InbreedingCoeff=0.0763;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.66739;LRBP=4021.7;MQ0=2;MQ0Fraction=0.0006;MQM=53.647;MQRankSum=1.083;NS=1047;RA=1663;RL=2;RPP=97.065;RR=49;RUN=1;ReadPosRankSum=-12.726;SAB=0.68627;SAF=35;SAP=18.381;SAR=16;SRB=0.59651;SRF=992;SRP=137.56;SRR=671;VQSLOD=4.1346;set=filterInVQSR-2of5;sumGLbyD=3.29
+20	36285033	rs34715186	AT	A	39417	PASS	AA=530;AB=0.5406;ABA=447;ABP=16.939;ABR=526;AC=88;AF=0.0950;AN=926;BL=20722;BR=20406;BVAR;BaseQRankSum=15.611;DB;DEL;DP=36713;DP4=2551,2475,236,218;Dels=0.09;EL=241;EPP=12.45;ER=289;FQ=999;FR;FS=1.290;HETAR=141;HOMA=16;HOMR=926;HP=2;HPLen=3;HR=3;HRun=1;HU=A;INDEL;InbreedingCoeff=0.0742;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.0076833;LRBP=8.2825;MQ=104.81;MQ0=0;MQ0Fraction=0.0000;MQM=84.285;MQRankSum=-0.702;NF;NR;NS=1083;PP;PV4=0.62,1,1,1;RA=6562;RL=263;RPP=3.0759;RR=267;RUN=1;ReadPosRankSum=0.090;SAB=0.55849;SAF=296;SAP=18.76;SAR=234;SC=AAAAACACAAATCAGATCGTG;SET_INTEGRATION;SET_WGVQSR;SRB=0.51707;SRF=3393;SRP=19.614;SRR=3169;TC;TR=3;TU=A;VQSLOD=10.5533;dbSNP=126;set=Intersection;sumGLbyD=14.15
+20	36384872	.	CTG	C	43532.41	PASS	AC=1213;AF=0.99589;AN=1218;BaseQRankSum=0.802;DP=3208;FS=9.727;HRun=0;HaplotypeScore=46.6153;InbreedingCoeff=0.1085;IndelType=DEL.NumRepetitions_7.EventLength_2.RepeatExpansion_TG.;MQ=58.37;MQ0=50;MQ0Fraction=0.0156;MQRankSum=-1.672;QD=13.57;ReadPosRankSum=2.063;SB=-18894.12;VQSLOD=4.7353;set=VQSR
+20	36542802	.	GTA	G	31310.15	PASS	AA=1481;AB=0.67546;ABA=1378;ABP=1138.4;ABR=2868;AC=437;AF=0.35938;AN=1216;BL=25719;BR=95500;BVAR;BaseQRankSum=9.478;DEL;DP=18068;DS;Dels=0.10;EL=889;EPP=132.34;ER=592;FS=320.726;HETAR=591;HOMA=44;HOMR=378;HRun=0;InbreedingCoeff=-0.4197;IndelType=DEL.NumRepetitions_1.EventLength_2.RepeatExpansion_TA.;LEN=2;LRB=0.57566;LRBP=87231;MQ0Fraction=0.0091;MQM=29.319;MQRankSum=-3.409;NS=1013;RA=4037;RL=3;RPP=3193;RR=1478;RUN=1;ReadPosRankSum=-6.687;SAB=0.40041;SAF=593;SAP=130.61;SAR=888;SRB=0.39014;SRF=1575;SRP=426.21;SRR=2462;VQSLOD=-1.6586;set=filterInVQSR-2of5;sumGLbyD=5.49
+20	36985025	.	CCA	C	4.57	PASS	AC=0;AF=0.0000;AN=682;BaseQRankSum=4.199;DP=1504;FS=1.036;HRun=0;HaplotypeScore=18.5241;InbreedingCoeff=0.0460;IndelType=DEL.NumRepetitions_6.EventLength_2.RepeatExpansion_CA.;MQ=57.04;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-1.774;ReadPosRankSum=-2.105;VQSLOD=6.7455;set=VQSR
+20	37139725	.	CAG	C	250.77	PASS	AF=0.0084;AF1=0.0139;BaseQRankSum=4.131;CI95=0.00885,0.01991;DP=7973;DP4=1808,1990,2,7;Dels=0.01;FQ=104;FR;FS=11.160;HP=3;HPLen=2;HR=1;HRun=0;HU=A;INDEL;InbreedingCoeff=-0.0001;IndelType=DEL.NumRepetitions_3.EventLength_2.RepeatExpansion_AG.;MQ=103.71;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-3.378;NF;NR;PP;PV4=0.18,0.0011,0.041,1;ReadPosRankSum=0.605;SC=AGATGGGGAACAGAGAGCAAG;SET_INTEGRATION;SET_WGVQSR;TC;TR=6;TU=AG;VQSLOD=7.0630;set=Intersection;sumGLbyD=12.13
+20	37213224	.	G	GTA	3230.05	PASS	AA=32;AB=0.50769;ABA=32;ABP=3.0437;ABR=33;AC=12;AF=0.0168;AF1=0.02635;AN=714;BL=1271;BR=1743;BVAR;BaseQRankSum=-7.288;CI95=0.02212,0.03319;DP=14304;DP4=2180,2256,13,21;Dels=0.00;EL=20;EPP=7.3532;ER=12;FQ=999;FR;FS=7.863;HETAR=9;HOMA=0;HOMR=1043;HP=1;HPLen=1;HR=1;HRun=0;HU=T;INDEL;INS;InbreedingCoeff=0.0410;IndelType=INS.NumRepetitions_1.EventLength_2.RepeatExpansion_TA.;LEN=2;LRB=0.1566;LRBP=163.52;MQ=95.56;MQ0=1;MQ0Fraction=0.0005;MQM=51.562;MQRankSum=0.420;NF;NR;NS=1052;PP;PV4=0.23,1,0.03,0.33;RA=5138;RL=11;RPP=9.7962;RR=21;RUN=1;ReadPosRankSum=-1.122;SAB=0.28125;SAF=9;SAP=16.311;SAR=23;SC=TTTGCATCCAGTAGCACCACT;SET_INTEGRATION;SET_WGVQSR;SRB=0.42293;SRF=2173;SRP=268.11;SRR=2965;TC;TR=1;TU=T;VQSLOD=9.7315;set=Intersection;sumGLbyD=36.69
+20	37282014	.	ATGG	A	2518.52	PASS	AF=0.03519;BaseQRankSum=11.994;DP=24592;DP4=415,3804,8,49;DS;Dels=0.01;FQ=999;FR;FS=2.049;HP=1;HPLen=1;HR=1;HRun=0;HU=T;INDEL;InbreedingCoeff=0.1028;IndelType=DEL.NumRepetitions_5.EventLength_3.;MQ=51.01;MQ0Fraction=0.0139;MQRankSum=-5.912;NF;NR;PP;PV4=0.27,1,0.22,0.015;ReadPosRankSum=1.781;SC=GGTGGTGATGATGGTGGTGGT;TC;TR=17;TU=GGT;VQSLOD=2.1183;set=filterInVQSR-2of5;sumGLbyD=9.05
+20	37532218	.	GTCCGTCCA	ATCCGTCCA,G	76120.88	PASS	AC=998;AF=0.92924;AN=1074;BaseQRankSum=-2.877;DP=3087;FR;FS=9.889;HP=2;HPLen=2;HR=1;HRun=0;HU=T;HaplotypeScore=71.6244;InbreedingCoeff=-0.0027;IndelType=MIXED;MQ=52.68;MQ0=543;MQ0Fraction=0.1759;MQRankSum=-1.750;NF;NR;PP;QD=24.98;ReadPosRankSum=-0.850;SB=-36635.43;SC=CCGTCCGTCCGTCCGTCCATC;TC;TR=19;TU=CCGT;VQSLOD=5.3068;set=Intersection
+20	37712193	.	AAG	A	2670.33	PASS	AA=106;AB=0.62821;ABA=87;ABP=36.418;ABR=147;AC=53;AF=0.0759;AN=698;BL=4672;BR=4303;BVAR;BaseQRankSum=13.696;DEL;DP=15155;DP4=1340,1852,32,52;Dels=0.06;EL=57;EPP=4.3214;ER=49;FR;FS=0.824;HETAR=43;HOMA=7;HOMR=982;HP=1;HPLen=2;HR=2;HRun=0;HU=A;INDEL;InbreedingCoeff=0.0861;IndelType=DEL.NumRepetitions_3.EventLength_2.RepeatExpansion_AG.;LEN=2;LRB=0.041114;LRBP=35.954;MQ=86.12;MQ0=0;MQ0Fraction=0.0000;MQM=54.236;MQRankSum=-5.745;NF;NR;NS=1034;PP;PV4=0.5,7.3e-26,1.1e-10,1;RA=4423;RL=58;RPP=5.0589;RR=48;RUN=1;ReadPosRankSum=2.617;SAB=0.38679;SAF=41;SAP=14.81;SAR=65;SC=GAAAATTCTGAAGAGAGTCAG;SET_INTEGRATION;SET_WGVQSR;SRB=0.43093;SRF=1906;SRP=186.29;SRR=2517;TC;TR=6;TU=AG;VQSLOD=9.8131;set=Intersection;sumGLbyD=14.20
+20	37739002	.	T	TCA	1395.38	PASS	AA=16;AB=0.48387;ABA=16;ABP=3.0803;ABR=15;AC=11;AF=0.00950;AN=1158;BL=504;BR=630;BVAR;BaseQRankSum=-3.257;DP=13617;DP4=1660,883,7,5;Dels=0.00;EL=7;EPP=3.5532;ER=9;FR;FS=1.114;HETAR=9;HOMA=0;HOMR=991;HP=1;HPLen=2;HR=2;HRun=0;HU=T;INDEL;INS;InbreedingCoeff=0.0527;IndelType=INS.NumRepetitions_1.EventLength_2.RepeatExpansion_CA.;LEN=2;LRB=0.11111;LRBP=33.411;MQ=88.41;MQ0=0;MQ0Fraction=0.0000;MQM=83.75;MQRankSum=1.713;NF;NR;NS=1000;PP;PV4=0.76,1,1,0.5;RA=3257;RL=6;RPP=5.1818;RR=10;RUN=1;ReadPosRankSum=1.190;SAB=0.6875;SAF=11;SAP=7.8961;SAR=5;SC=CCTTTTTTGTTCATTTCTGCA;SET_INTEGRATION;SET_WGVQSR;SRB=0.68806;SRF=2241;SRP=1003.5;SRR=1016;TC;TR=2;TU=T;VQSLOD=10.2220;set=Intersection;sumGLbyD=41.32
+20	38395256	.	TTGAG	T	633.19	PASS	AF=0.0028;BaseQRankSum=5.667;DP=3839;Dels=0.00;FR;FS=10.238;HP=2;HPLen=3;HR=3;HRun=0;HU=T;InbreedingCoeff=-0.0097;IndelType=DEL.NumRepetitions_1.EventLength_4.;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-1.276;NF;NR;PP;ReadPosRankSum=-1.016;SC=ATGTGTTTGTTTGAGTATGTT;SET_INTEGRATION;SET_WGVQSR;TC;TR=10;TU=GTTT;VQSLOD=6.4906;set=Intersection;sumGLbyD=10.83
+20	39345038	.	CTGAACCATAATGTG	C,CCCATAATGTG	60744.52	PASS	AA=23;AB=0.67143;ABA=23;ABP=20.878;ABR=47;AC=232,2;AF=0.19366,0.00167;AN=1198;BL=1607;BR=1843;BVAR;BaseQRankSum=30.955;DEL;DP=31490;DP4=1729,2100,265,278;Dels=0.13;EL=6;EPP=14.434;ER=17;FQ=999;FR;FS=1.767;HETAR=18;HOMA=0;HOMR=1015;HP=1;HPLen=2;HR=2;HRun=0;HU=C;INDEL;InbreedingCoeff=0.1991;IndelType=MULTIALLELIC_INDEL;LEN=14;LRB=0.068406;LRBP=38.066;MQ=104.60;MQ0=0;MQ0Fraction=0.0000;MQM=189.83;MQRankSum=-16.579;NF;NR;NS=1033;PP;PV4=0.12,1,5.5e-137,1;RA=5286;RL=14;RPP=5.3706;RR=9;RUN=1;ReadPosRankSum=4.323;SAB=0.56522;SAF=13;SAP=3.86;SAR=10;SC=TGGGCTGGACCTGAACCATAA;SET_WGVQSR;SRB=0.46311;SRF=2448;SRP=65.493;SRR=2838;TC;TR=2;TU=C;VQSLOD=6.2643;dbSNP=130;set=Intersection;sumGLbyD=65.43
+20	39418008	.	AG	A	46796	PASS	AA=113;AB=0.9511;ABA=80;ABP=2894.6;ABR=1556;AC=30;AF=0.02412;AN=1244;BL=638;BR=6936;BVAR;BaseQRankSum=7.280;DEL;DP=14307;Dels=0.00;EL=50;EPP=6.2579;ER=63;FR;FS=5.707;HETAR=473;HOMA=361;HOMR=246;HP=3;HR=3;HRun=3;HU=G;InbreedingCoeff=0.0272;IndelType=DEL.NumRepetitions_3.EventLength_1.RepeatExpansion_G.;LEN=1;LRB=0.83153;LRBP=11375;MQ0=0;MQ0Fraction=0.0000;MQM=62.398;MQRankSum=3.530;NF;NR;NS=1089;PP;RA=3000;RL=3;RPP=223.02;RR=110;RUN=1;ReadPosRankSum=-18.601;SAB=0.58407;SAF=66;SAP=9.9475;SAR=47;SC=ACTGGGGGAAAGGGATTCTAG;SRB=0.494;SRF=1482;SRP=3.9484;SRR=1518;TC;TR=3;TU=G;VQSLOD=4.5834;set=Intersection;sumGLbyD=3.06
+20	39876961	.	GT	G,GTT,GTTT	2302.10	PASS	ABR=496;AC=45,51,45;AF=0.03664,0.04153,0.03664;AN=1228;BVAR;BaseQRankSum=4.462;DP=37649;DP4=1457,1975,57,59;Dels=0.02;FR;FS=9.938;HOMA=0;HOMR=978;HP=10;HPLen=10;HR=10;HRun=10;HU=T;INDEL;INS;InbreedingCoeff=0.2583;IndelType=MULTIALLELIC_INDEL;MQ=97.28;MQ0=0;MQ0Fraction=0.0000;MQRankSum=0.246;NF;NR;NS=1063;PP;PV4=0.15,1,1.9e-09,0.016;RA=5185;RUN=1;ReadPosRankSum=-4.954;SC=AGTTTCTCCGGTTTTTTTTTT;SET_WGVQSR;SRB=0.47464;SRF=2461;SRP=31.978;SRR=2724;TC;TR=10;TU=T;VQSLOD=4.9752;set=Intersection;sumGLbyD=4.39
+20	41013333	.	TC	T	20681	PASS	AA=137;AB=0.89211;ABA=134;ABP=1661.6;ABR=1108;AC=68;AF=0.05601;AN=1214;BL=1091;BR=8981;BVAR;BaseQRankSum=1.354;DEL;DP=12998;Dels=0.01;EL=57;EPP=11.395;ER=80;FS=0.758;HETAR=359;HOMA=100;HOMR=610;HRun=1;InbreedingCoeff=0.0104;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;LEN=1;LRB=0.78336;LRBP=13424;MQ0=1;MQ0Fraction=0.0003;MQM=67.745;MQRankSum=2.563;NS=1072;RA=4447;RL=5;RPP=258.66;RR=132;RUN=1;ReadPosRankSum=-14.092;SAB=0.59124;SAF=81;SAP=12.917;SAR=56;SRB=0.54194;SRF=2410;SRP=70.947;SRR=2037;VQSLOD=3.7531;set=filterInVQSR-2of5;sumGLbyD=4.14
+20	41659532	.	GC	G	40544	PASS	AA=42;AB=0.97149;ABA=39;ABP=2644.5;ABR=1329;AC=15;AF=0.0209;AN=716;BL=2531;BR=135;BVAR;BaseQRankSum=-2.537;DEL;DP=12219;Dels=0.00;EL=25;EPP=6.3192;ER=17;FS=2.656;HETAR=374;HOMA=155;HOMR=551;HRun=1;InbreedingCoeff=-0.0270;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;LEN=1;LRB=0.89872;LRBP=4678.9;MQ0=0;MQ0Fraction=0.0000;MQM=103.31;MQRankSum=2.828;NS=1088;RA=4736;RL=41;RPP=85.733;RR=1;RUN=1;ReadPosRankSum=-9.702;SAB=0.57143;SAF=24;SAP=4.8716;SAR=18;SRB=0.5625;SRF=2664;SRP=163.7;SRR=2072;VQSLOD=4.3267;set=Intersection;sumGLbyD=3.22
+20	41845580	.	GA	G	49310	PASS	AA=83;AB=0.95258;ABA=69;ABP=2591.6;ABR=1386;AC=46;AF=0.03740;AN=1230;BL=1320;BR=5150;BVAR;BaseQRankSum=-1.121;DEL;DP=13336;Dels=0.00;EL=36;EPP=6.1759;ER=47;FR;FS=0.372;HETAR=442;HOMA=341;HOMR=295;HP=2;HR=3;HRun=1;HU=G;InbreedingCoeff=0.0238;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.59196;LRBP=4926.2;MQ0=0;MQ0Fraction=0.0000;MQM=89.048;MQRankSum=0.897;NF;NR;NS=1080;PP;RA=3006;RL=5;RPP=142.43;RR=78;RUN=1;ReadPosRankSum=-15.412;SAB=0.55422;SAF=46;SAP=5.1294;SAR=37;SC=CCAGCTGTGGGAGAGAAACAT;SRB=0.47971;SRF=1442;SRP=13.762;SRR=1564;TC;TR=6;TU=AG;VQSLOD=4.4669;set=Intersection;sumGLbyD=3.65
+20	42209428	.	GC	G	13163	PASS	AA=89;AB=0.86677;ABA=83;ABP=730.96;ABR=540;AC=39;AF=0.03218;AN=1212;BL=950;BR=5334;BVAR;BaseQRankSum=-10.119;DEL;DP=10692;Dels=0.01;EL=48;EPP=4.2058;ER=41;FS=0.000;HETAR=259;HOMA=727;HOMR=54;HRun=1;InbreedingCoeff=0.0448;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;LEN=1;LRB=0.69764;LRBP=6644.4;MQ0=0;MQ0Fraction=0.0000;MQM=126.55;MQRankSum=4.223;NS=1040;RA=723;RL=12;RPP=106.09;RR=77;RUN=1;ReadPosRankSum=-17.362;SAB=0.39326;SAF=35;SAP=11.818;SAR=54;SRB=0.37898;SRF=274;SRP=94.99;SRR=449;VQSLOD=3.7157;set=filterInVQSR-2of5;sumGLbyD=3.48
+20	42281109	.	T	TAG	2321.12	PASS	AC=181;AF=0.3740;AN=484;BaseQRankSum=8.977;DP=435;FS=17.001;HRun=0;HaplotypeScore=14.6734;InbreedingCoeff=0.2340;IndelType=INS.NOVEL_2.;MQ=53.88;MQ0=47;MQ0Fraction=0.1080;MQRankSum=0.762;QD=12.41;ReadPosRankSum=3.399;SB=-1299.73;SET_INTEGRATION;VQSLOD=4.8926;set=VQSR
+20	42436117	.	TC	T	38933	PASS	AA=18;AB=0.98435;ABA=17;ABP=2215.9;ABR=1069;AC=15;AF=0.01223;AN=1226;BL=498;BR=428;BVAR;BaseQRankSum=-7.224;DEL;DP=12436;Dels=0.00;EL=1;EPP=33.893;ER=17;FS=2.469;HETAR=303;HOMA=614;HOMR=123;HRun=1;InbreedingCoeff=0.0439;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;LEN=1;LRB=0.075594;LRBP=14.501;MQ0=0;MQ0Fraction=0.0000;MQM=98.611;MQRankSum=1.086;NS=1075;RA=1656;RL=10;RPP=3.4928;RR=8;RUN=1;ReadPosRankSum=-17.765;SAB=0.5;SAF=9;SAP=3.0103;SAR=9;SRB=0.49879;SRF=826;SRP=3.0313;SRR=830;VQSLOD=4.0821;set=filterInVQSR-2of5;sumGLbyD=3.04
+20	42682214	.	C	A,CAT	3904.51	PASS	AA=24;AB=0.6383;ABA=17;ABP=10.818;ABR=30;AC=0;AF=0.0000;AN=636;BL=1119;BR=949;BVAR;BaseQRankSum=1.426;DP=6509;Dels=0.00;EL=9;EPP=6.2675;ER=15;FR;HETAR=12;HOMA=3;HOMR=876;HP=2;HPLen=1;HR=1;HRun=0;HU=A;INS;InbreedingCoeff=0.0006;IndelType=MIXED;LEN=2;LRB=0.082205;LRBP=33.356;MQ0Fraction=0.0046;MQM=40.792;MQRankSum=-0.296;NF;NR;NS=891;PP;QD=32.81;RA=2679;RL=15;RPP=6.2675;RR=9;RUN=1;ReadPosRankSum=-1.806;SAB=0.75;SAF=18;SAP=16.039;SAR=6;SB=-924.23;SC=TATACACACACATATATATAC;SET_INTEGRATION;SET_WGVQSR;SRB=0.66293;SRF=1776;SRP=620.76;SRR=903;TC;TR=9;TU=AC;set=filterInVQSR-2of5;sumGLbyD=32.75
+20	42973456	.	CA	C,CAA,CAAA	2675	PASS	AA=90;AB=0.79177;ABA=86;ABP=308.39;ABR=327;AC=77,61,39;AF=0.06492,0.05143,0.03288;AN=1186;BL=2983;BR=4446;BVAR;BaseQRankSum=2.422;DP=9416;Dels=0.03;EL=39;EPP=6.4847;ER=51;FR;FS=31.555;HETAR=75;HOMA=1;HOMR=888;HP=11;HR=11;HRun=11;HU=A;INS;InbreedingCoeff=0.2696;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.19693;LRBP=628.63;MQ0=0;MQ0Fraction=0.0000;MQM=55.567;MQRankSum=1.777;NF;NR;NS=964;PP;RA=3601;RL=37;RPP=9.1869;RR=53;RUN=1;ReadPosRankSum=-4.991;SAB=0.55556;SAF=50;SAP=5.423;SAR=40;SC=TAGTGACTGTCAAAAAAAAAA;SET_WGVQSR;SRB=0.60622;SRF=2183;SRP=355.91;SRR=1418;TC;TR=11;TU=A;VQSLOD=1.0763;set=filterInVQSR-2of5;sumGLbyD=4.05
+20	43091870	.	TC	T	2455.60	PASS	AA=120;AB=0.10619;ABA=101;ABP=155.22;ABR=12;AC=42;AF=0.03825;AN=1098;BL=573;BR=8744;BVAR;BaseQRankSum=-13.513;DEL;DP=9139;Dels=0.00;EL=64;EPP=4.1684;ER=56;FS=9.856;HETAR=118;HOMA=820;HOMR=0;HRun=1;InbreedingCoeff=0.0833;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;LEN=1;LRB=0.877;LRBP=15564;MQ0Fraction=0.0017;MQM=45.1;MQRankSum=2.266;NS=938;RA=24;RL=1;RPP=254.97;RR=119;RUN=1;ReadPosRankSum=-15.803;SAB=0.475;SAF=57;SAP=3.6617;SAR=63;SRB=0.54167;SRF=13;SRP=3.3722;SRR=11;VQSLOD=3.9930;set=filterInVQSR-2of5;sumGLbyD=3.09
+20	43233648	rs74585029	GA	G,GAA	1504.40	PASS	AA=113;AB=0.78652;ABA=95;ABP=320.31;ABR=350;AC=41,65;AF=0.03394,0.05381;AF1=0.0115;AN=1208;BL=4677;BR=5548;BVAR;BaseQRankSum=6.744;CI95=0.004274,0.01852;DB;DEL;DP=13996;DP4=1736,1549,15,17;Dels=0.03;EL=69;EPP=15.021;ER=44;FQ=14;FR;FS=12.174;HETAR=119;HOMA=15;HOMR=892;HP=11;HPLen=10;HR=10;HRun=10;HU=A;INDEL;InbreedingCoeff=0.2359;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.085183;LRBP=164.12;MQ=89.12;MQ0Fraction=0.0000;MQM=69.867;MQRankSum=2.513;NF;NR;NS=1027;PP;PV4=0.59,1,0.065,0.33;RA=3845;RL=46;RPP=11.485;RR=67;RUN=1;ReadPosRankSum=-4.957;SAB=0.33628;SAF=38;SAP=29.318;SAR=75;SC=AAAACAGCCAGAAAAAAAAAA;SET_INTEGRATION;SET_WGVQSR;SRB=0.43667;SRF=1679;SRP=136.95;SRR=2166;TC;TR=10;TU=A;VQSLOD=4.5121;set=Intersection;sumGLbyD=8.22
+20	43246548	.	AC	A,CC	41579.13	PASS	AA=382;AB=0.72402;ABA=316;ABP=502.11;ABR=829;AC=1197;AF=0.99254;AN=1206;BL=9889;BR=14293;BVAR;BaseQRankSum=1.373;DEL;DP=10477;DS;Dels=0.05;EL=243;EPP=64.494;ER=139;FS=29.162;HETAR=291;HOMA=85;HOMR=624;HPLen=10;InbreedingCoeff=0.1392;IndelType=MIXED;LEN=1;LRB=0.18212;LRBP=1744.6;MQ0Fraction=0.0024;MQM=48.471;MQRankSum=5.726;NS=1001;RA=3138;RL=174;RPP=9.5816;RR=208;RUN=1;ReadPosRankSum=5.755;SAB=0.79843;SAF=305;SAP=298.51;SAR=77;SET_INTEGRATION;SET_WGVQSR;SRB=0.70363;SRF=2208;SRP=1133.2;SRR=930;VQSLOD=5.6318;set=Intersection;sumGLbyD=5.22
+20	43258646	.	T	TT	1107.17	PASS	AC=97;AF=0.08420;AN=1152;BaseQRankSum=4.525;DP=2345;FS=19.308;HRun=9;HaplotypeScore=13.6276;InbreedingCoeff=0.1299;IndelType=INS.NumRepetitions_10orMore.EventLength_1.RepeatExpansion_T.;MQ=76.70;MQ0=0;MQ0Fraction=0.0000;MQRankSum=1.395;QD=2.67;ReadPosRankSum=-4.696;SB=-899.41;VQSLOD=5.4523;set=VQSR
+20	43718299	.	ATTACT	A	5497.06	PASS	AA=56;AB=0.51818;ABA=53;ABP=3.3262;ABR=57;AC=18;AF=0.0251;AF1=0.03729;AN=718;BL=2321;BR=2591;BVAR;BaseQRankSum=11.142;CI95=0.03319,0.04425;DEL;DP=17576;DP4=2460,2692,31,22;Dels=0.02;EL=28;EPP=3.0103;ER=28;FQ=999;FR;FS=9.689;HETAR=15;HOMA=1;HOMR=1068;HP=2;HPLen=2;HR=2;HRun=0;HU=T;INDEL;InbreedingCoeff=0.0448;IndelType=DEL.NumRepetitions_1.EventLength_5.;LEN=5;LRB=0.054967;LRBP=35.238;MQ=96.55;MQ0=0;MQ0Fraction=0.0000;MQM=50.286;MQRankSum=-5.149;NF;NR;NS=1084;PP;PV4=0.13,1,1.2e-12,1;RA=6745;RL=28;RPP=3.0103;RR=28;RUN=1;ReadPosRankSum=0.828;SAB=0.5;SAF=28;SAP=3.0103;SAR=28;SC=ATGACAGTGGATTACTTTAGT;SET_INTEGRATION;SET_WGVQSR;SRB=0.46835;SRF=3159;SRP=61.709;SRR=3586;TC;TR=2;TU=T;VQSLOD=7.8832;set=Intersection;sumGLbyD=46.60
+20	43981749	.	A	AAAAAAC,AC	20899.71	PASS	ABR=192;AC=91,0;AF=0.1285,0.0000;AN=708;BVAR;BaseQRankSum=7.858;DP=23372;DP4=1554,1457,55,42;Dels=0.00;FR;FS=0.000;HOMA=4;HOMR=995;HP=6;HPLen=7;HR=7;HRun=0;HU=A;INDEL;INS;InbreedingCoeff=0.2109;IndelType=MULTIALLELIC_INDEL;MQ=95.59;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-12.081;NF;NR;NS=1051;PP;PV4=0.35,1,8.9e-73,1;RA=5027;RUN=1;ReadPosRankSum=-1.359;SC=TACACTAGCAAAAAAACAAAA;SET_WGVQSR;SRB=0.48518;SRF=2439;SRP=12.6;SRR=2588;TC;TR=7;TU=A;VQSLOD=8.0916;set=Intersection;sumGLbyD=54.33
+20	43999274	.	TCAAA	T	2948.85	PASS	AA=59;AB=0.59441;ABA=58;ABP=14.08;ABR=85;AC=20;AF=0.0290;AF1=0.04249;AN=690;BL=2277;BR=2436;BVAR;BaseQRankSum=9.320;CI95=0.0354,0.05088;DEL;DP=14599;DP4=2052,2303,21,22;Dels=0.03;EL=32;EPP=3.9304;ER=27;FQ=999;FR;FS=0.000;HETAR=21;HOMA=0;HOMR=1043;HP=2;HPLen=1;HR=1;HRun=0;HU=C;INDEL;InbreedingCoeff=-0.0037;IndelType=DEL.NumRepetitions_1.EventLength_4.;LEN=4;LRB=0.033736;LRBP=14.658;MQ=90.05;MQ0=0;MQ0Fraction=0.0000;MQM=75.339;MQRankSum=-1.294;NF;NR;NS=1064;PP;PV4=0.88,1,0.0026,1;RA=5732;RL=27;RPP=3.9304;RR=32;RUN=1;ReadPosRankSum=-0.915;SAB=0.47458;SAF=28;SAP=3.3415;SAR=31;SC=GGTACACAGCTCAAACAGTCT;SET_INTEGRATION;SET_WGVQSR;SRB=0.4836;SRF=2772;SRP=16.4;SRR=2960;TC;TR=1;TU=C;VQSLOD=9.8086;set=Intersection;sumGLbyD=27.09
+20	44098622	.	C	CG	1092.40	PASS	AA=129;AB=0.77301;ABA=74;ABP=214.06;ABR=252;AC=45;AF=0.0455;AN=988;BL=6586;BR=3029;BVAR;BaseQRankSum=2.802;DP=5177;Dels=0.00;EL=122;EPP=225.63;ER=7;FR;FS=355.273;HETAR=66;HOMA=11;HOMR=734;HP=6;HR=4;HRun=4;HU=G;INS;InbreedingCoeff=0.1759;IndelType=INS.NumRepetitions_4.EventLength_1.RepeatExpansion_G.;LEN=1;LRB=0.36994;LRBP=2860.4;MQ0=0;MQ0Fraction=0.0000;MQM=52.395;MQRankSum=1.946;NF;NR;NS=811;PP;RA=1981;RL=121;RPP=217.95;RR=8;RUN=1;ReadPosRankSum=-6.413;SAB=0.99225;SAF=128;SAP=274.51;SAR=1;SC=GCGGAAGTGGCGGGGACCCTT;SRB=0.41242;SRF=817;SRP=135;SRR=1164;TC;TR=4;TU=G;VQSLOD=-2.2690;set=filterInVQSR-2of5;sumGLbyD=4.04
+20	44327637	.	A	AG,AGGGGGG	14351.23	PASS	AC=9,211;AF=0.0103,0.2409;AN=876;BaseQRankSum=15.517;DP=1704;FS=6.768;HaplotypeScore=31.5906;InbreedingCoeff=0.1538;IndelType=MULTIALLELIC_INDEL;MQ=54.64;MQ0=4;MQ0Fraction=0.0023;MQRankSum=-12.691;QD=20.83;ReadPosRankSum=-3.583;SB=-6278.99;VQSLOD=5.1556;set=VQSR
+20	45202636	.	GA	G	13269	PASS	AA=25;AB=0.96162;ABA=18;ABP=871.09;ABR=451;AC=24;AF=0.02013;AN=1192;BL=567;BR=1728;BVAR;BaseQRankSum=-5.361;DEL;DP=10873;Dels=0.00;EL=10;EPP=5.1818;ER=15;FS=0.928;HETAR=169;HOMA=831;HOMR=45;HRun=1;InbreedingCoeff=0.0999;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.50588;LRBP=1278.4;MQ0=0;MQ0Fraction=0.0000;MQM=170.56;MQRankSum=0.161;NS=1049;RA=632;RL=2;RPP=41.315;RR=23;RUN=1;ReadPosRankSum=-14.760;SAB=0.68;SAF=17;SAP=10.046;SAR=8;SRB=0.51424;SRF=325;SRP=4.1235;SRR=307;VQSLOD=3.9290;set=filterInVQSR-2of5;sumGLbyD=3.90
+20	45417828	.	TGAGC	T,TGC	4672.90	PASS	ABR=317;AC=69,104;AF=0.05712,0.08609;BVAR;BaseQRankSum=18.527;DEL;DP=11835;DS;FS=184.873;HOMA=48;HOMR=575;HaplotypeScore=65.5875;InbreedingCoeff=0.0599;IndelType=MULTIALLELIC_INDEL;MQ=29.78;MQ0=2988;MQ0Fraction=0.3629;MQRankSum=5.052;NS=713;QD=1.11;RA=1581;RUN=1;ReadPosRankSum=6.574;SB=-2116.87;SRB=0.47502;SRF=751;SRP=11.582;SRR=830;VQSLOD=0.0651;set=filterInVQSR-2of5
+20	45525657	rs66759083	TA	AA,T	49315	PASS	AA=2361;AB=0.45241;ABA=1398;ABP=53.235;ABR=1155;AC=20;AF=0.01701;AN=1176;BL=94913;BR=100886;BVAR;BaseQRankSum=0.740;DB;DEL;DP=30636;DP4=1258,881,1206,999;Dels=0.48;EL=1133;EPP=11.311;ER=1228;FQ=999;FR;FS=7.072;HETAR=503;HOMA=310;HOMR=218;HP=6;HPLen=7;HR=7;HU=T;INDEL;InbreedingCoeff=0.2271;IndelType=MIXED;LEN=1;LRB=0.030506;LRBP=398.68;MQ=102.24;MQ0=0;MQ0Fraction=0.0000;MQM=75.359;MQRankSum=0.148;NF;NR;NS=1031;PP;PV4=0.0064,0,4.6e-23,0.47;RA=2042;RL=1183;RPP=3.0333;RR=1178;RUN=1;ReadPosRankSum=-2.999;SAB=0.52139;SAF=1231;SAP=12.392;SAR=1130;SC=AGGATTTTTTTAAAAAGTTTT;SET_INTEGRATION;SET_WGVQSR;SRB=0.55093;SRF=1125;SRP=49.017;SRR=917;TC;TR=7;TU=T;VQSLOD=7.1651;dbSNP=114;set=Intersection;sumGLbyD=18.51
+20	45783456	.	T	TG	2355.68	PASS	AA=64;AB=0.78521;ABA=61;ABP=203.67;ABR=223;AC=15;AF=0.0165;AN=910;BL=815;BR=5486;BVAR;BaseQRankSum=8.593;DP=10348;Dels=0.00;EL=48;EPP=37.754;ER=16;FS=77.861;HETAR=56;HOMA=1;HOMR=970;HRun=1;INS;InbreedingCoeff=-0.0549;IndelType=INS.NOVEL_1.Novel_G.;LEN=1;LRB=0.74131;LRBP=7522.1;MQ0Fraction=0.0122;MQM=44.562;MQRankSum=-1.258;NS=1027;RA=4750;RL=0;RPP=141.98;RR=64;RUN=1;ReadPosRankSum=-7.047;SAB=0.25;SAF=16;SAP=37.754;SAR=48;SRB=0.6;SRF=2850;SRP=415.59;SRR=1900;VQSLOD=1.3146;set=filterInVQSR-2of5;sumGLbyD=6.03
+20	46517110	.	C	CT	868.55	PASS	AC=15;AF=0.0218;AN=688;BaseQRankSum=8.522;DP=1752;FS=6.570;HRun=0;HaplotypeScore=14.9548;InbreedingCoeff=0.0452;IndelType=INS.NOVEL_1.Novel_T.;MQ=77.73;MQ0=0;MQ0Fraction=0.0000;MQRankSum=3.874;QD=10.98;ReadPosRankSum=-0.733;SB=-396.78;SET_INTEGRATION;SET_WGVQSR;VQSLOD=6.7740;set=VQSR
+20	46629361	.	TTTCTTTC	T,TTTTC	13000.91	PASS	AC=188,107;AF=0.2212,0.1259;AN=850;BaseQRankSum=7.214;DP=1846;FS=14.502;HaplotypeScore=40.8481;InbreedingCoeff=0.3210;IndelType=MULTIALLELIC_INDEL;MQ=50.74;MQ0=79;MQ0Fraction=0.0428;MQRankSum=-6.348;QD=13.59;ReadPosRankSum=3.943;SB=-3581.20;VQSLOD=5.9412;set=VQSR
+20	46951099	.	G	GT	1662.30	PASS	AA=55;AB=0.7713;ABA=51;ABP=145.58;ABR=172;AC=47;AF=0.03923;AN=1198;BL=3288;BR=2434;BVAR;BaseQRankSum=-4.014;DP=27423;DP4=1483,1590,58,42;Dels=0.01;EL=21;EPP=9.6826;ER=34;FR;FS=9.565;HETAR=48;HOMA=0;HOMR=913;HP=16;HPLen=10;HR=10;HRun=10;HU=T;INDEL;INS;InbreedingCoeff=0.0952;IndelType=INS.NumRepetitions_10orMore.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.14925;LRBP=279.78;MQ=70.36;MQ0Fraction=0.0124;MQM=52.545;MQRankSum=0.717;NF;NR;NS=961;PP;PV4=0.067,1,1,0.17;RA=3035;RL=38;RPP=20.422;RR=17;RUN=1;ReadPosRankSum=-3.014;SAB=0.47273;SAF=26;SAP=3.3656;SAR=29;SC=TTTGTTTTTTGTTTTTTTTTT;SET_INTEGRATION;SET_WGVQSR;SRB=0.36013;SRF=1093;SRP=518.73;SRR=1942;TC;TR=10;TU=T;VQSLOD=5.4779;set=Intersection;sumGLbyD=3.49
+20	47201076	rs58052846	C	CT	982.16	PASS	AC=50;AF=0.0551;AN=908;BaseQRankSum=12.598;DB;DP=2449;FS=35.648;HRun=0;HaplotypeScore=29.4602;InbreedingCoeff=-0.0542;IndelType=INS.NOVEL_1.Novel_T.;MQ=63.54;MQ0=0;MQ0Fraction=0.0000;MQRankSum=2.196;QD=3.16;ReadPosRankSum=-13.833;SB=-488.19;VQSLOD=6.0429;set=VQSR
+20	47965974	rs60011158	G	GA	999	PASS	AA=21;AB=0.57143;ABA=21;ABP=5.1818;ABR=28;AC=7;AF=0.0101;AF1=0.02061;AN=690;BL=1043;BR=577;BVAR;BaseQRankSum=-3.087;CI95=0.01549,0.02655;DB;DP=14578;DP4=1554,3055,6,17;Dels=0.00;EL=11;EPP=3.1137;ER=10;FQ=999;FR;FS=5.982;HETAR=7;HOMA=0;HOMR=1041;HP=2;HPLen=1;HR=1;HRun=1;HU=A;INDEL;INS;InbreedingCoeff=0.0356;IndelType=INS.NumRepetitions_1.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.28765;LRBP=294.09;MQ=80.17;MQ0=0;MQ0Fraction=0.0000;MQM=64.19;MQRankSum=2.137;NF;NR;NS=1048;PP;PV4=0.51,1,1,1;RA=5224;RL=16;RPP=15.522;RR=5;RUN=1;ReadPosRankSum=0.236;SAB=0.38095;SAF=8;SAP=5.5954;SAR=13;SC=TTCATGTACAGAGCTGCTGTG;SET_INTEGRATION;SET_WGVQSR;SRB=0.31183;SRF=1629;SRP=1609.6;SRR=3595;TC;TR=4;TU=AG;VQSLOD=9.5466;dbSNP=129;set=Intersection;sumGLbyD=13.83
+20	48402974	rs57331436	GA	G	27741	PASS	AA=401;AB=0.5372;ABA=311;ABP=11.089;ABR=361;AC=84;AF=0.1186;AN=708;BL=16591;BR=14776;BVAR;BaseQRankSum=14.621;DB;DEL;DP=30607;DP4=1928,2310,195,225;Dels=0.11;EL=189;EPP=5.8749;ER=212;FQ=999;FR;FS=15.568;HETAR=110;HOMA=30;HOMR=923;HP=4;HPLen=3;HR=1;HRun=3;HU=A;INDEL;InbreedingCoeff=0.1263;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_A.;KGPilot123;LEN=1;LRB=0.057863;LRBP=231.06;MQ=106.68;MQ0=0;MQ0Fraction=0.0000;MQM=63.005;MQRankSum=-2.010;NF;NR;NS=1063;PP;PV4=0.72,1,0.001,1;RA=5258;RL=223;RPP=13.976;RR=178;RUN=1;ReadPosRankSum=1.337;SAB=0.37656;SAF=151;SAP=56.084;SAR=250;SC=TGCCCTCAAAGAGAAAAAGGA;SET_INTEGRATION;SET_WGVQSR;SRB=0.38075;SRF=2002;SRP=652.44;SRR=3256;TC;TR=5;TU=AG;VQSLOD=8.7259;dbSNP=132;set=Intersection;sumGLbyD=15.86
+20	49101936	.	C	CT	404.46	PASS	AC=40;AF=0.03559;AN=1124;BaseQRankSum=0.750;DP=2162;FS=14.291;HRun=2;HaplotypeScore=30.9513;InbreedingCoeff=-0.0082;IndelType=INS.NumRepetitions_2.EventLength_1.RepeatExpansion_T.;MQ=49.78;MQ0=113;MQ0Fraction=0.0523;MQRankSum=-1.289;QD=1.94;ReadPosRankSum=-2.041;SB=-385.48;VQSLOD=4.6365;set=VQSR
+20	49731218	.	ATTTTATTTTTTATT	A,ATTTTATT	8398.93	PASS	AF=0.0656,0.0156;AF1=0.0996;BaseQRankSum=13.996;CI95=0.07743,0.1239;DP=6308;DP4=951,1311,23,35;Dels=0.05;FQ=999;FR;FS=12.503;HP=7;HPLen=4;HR=4;HRun=0;HU=T;INDEL;InbreedingCoeff=0.1892;IndelType=MULTIALLELIC_INDEL;MQ=57.61;MQ0Fraction=0.0145;MQRankSum=-5.208;NF;NR;PP;PV4=0.79,1,6.3e-06,0.16;ReadPosRankSum=-2.239;SC=TATTTTATTTATTTTATTTTT;TC;TR=11;TU=ATTT;VQSLOD=4.3191;set=Intersection;sumGLbyD=42.27
+20	49894989	.	TA	T	172.25	PASS	AF=0.0140;BaseQRankSum=7.220;DP=3882;Dels=0.00;FS=17.217;HPLen=2;HRun=1;InbreedingCoeff=0.0531;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_A.;MQ0Fraction=0.0214;MQRankSum=-0.661;ReadPosRankSum=-0.592;SET_INTEGRATION;SET_WGVQSR;VQSLOD=3.0905;set=filterInVQSR-2of5;sumGLbyD=6.60
+20	50010923	rs66516522	C	CT,CTGG	35851	PASS	ABR=555;AC=310,11;AF=0.26451,0.00939;BVAR;BaseQRankSum=10.662;DB;DP=8188;FR;FS=34.411;HOMA=261;HOMR=399;HP=5;HR=6;HU=C;HaplotypeScore=45.1715;INS;InbreedingCoeff=0.2090;IndelType=MULTIALLELIC_INDEL;MQ=72.80;MQ0=0;MQ0Fraction=0.0000;MQRankSum=9.015;NF;NR;NS=831;PP;QD=9.69;RA=1986;RUN=1;ReadPosRankSum=-24.284;SB=-6038.55;SC=TGTCTGTCCCCCCTCAGCACT;SRB=0.45972;SRF=913;SRP=31.001;SRR=1073;TC;TR=6;TU=C;VQSLOD=6.1824;set=Intersection
+20	50228709	rs71192536	TG	T	20517	PASS	AA=924;AB=0.50203;ABA=735;ABP=3.0633;ABR=741;AC=200;AF=0.16502;AN=1212;BL=35460;BR=34197;BVAR;BaseQRankSum=13.810;DB;DEL;DP=32402;DP4=1760,2065,395,449;Dels=0.16;EL=439;EPP=7.9831;ER=485;FQ=999;FR;FS=0.558;HETAR=242;HOMA=63;HOMR=764;HP=5;HPLen=3;HR=3;HRun=3;HU=G;INDEL;InbreedingCoeff=0.1050;IndelType=DEL.NumRepetitions_3.EventLength_1.RepeatExpansion_G.;LEN=1;LRB=0.018132;LRBP=52.738;MQ=105.83;MQ0=0;MQ0Fraction=0.0000;MQM=75.87;MQRankSum=3.895;NF;NR;NS=1069;PP;PV4=0.7,1.5e-173,1,1;RA=4708;RL=486;RPP=8.4249;RR=438;RUN=1;ReadPosRankSum=1.586;SAB=0.43615;SAF=403;SAP=35.733;SAR=521;SC=GTTTTCCAGGTGGGAAGACCG;SET_INTEGRATION;SET_WGVQSR;SRB=0.44074;SRF=2075;SRP=146.62;SRR=2633;TC;TR=3;TU=G;VQSLOD=10.4820;dbSNP=120;set=Intersection;sumGLbyD=15.35
+20	50236115	.	AGG	A,ACGGG,AG,AGGG	7429.57	PASS	AC=192,13,221,183;AF=0.2115,0.0143,0.2434,0.2015;AN=908;BaseQRankSum=1.045;DP=1177;FS=13.479;HaplotypeScore=11.8294;InbreedingCoeff=0.7959;IndelType=MULTIALLELIC_INDEL;MQ=52.98;MQ0=6;MQ0Fraction=0.0051;MQRankSum=-1.482;QD=7.28;ReadPosRankSum=-2.380;SB=-1229.31;SET_WGVQSR;VQSLOD=8.3762;set=VQSR
+20	51589568	.	TAAAC	AAAAC,T	12477.52	PASS	AF=0.27949;BaseQRankSum=-28.122;DP=3777;Dels=0.00;FR;FS=31.799;HP=7;HPLen=4;HR=3;HRun=0;HU=A;InbreedingCoeff=-0.1429;IndelType=MIXED;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-1.196;NF;NR;PP;ReadPosRankSum=-16.483;SC=AAATTCAAAATAAACAAACAA;SET_INTEGRATION;SET_WGVQSR;TC;TR=18;TU=AAAC;VQSLOD=3.9201;set=filterInVQSR-2of5;sumGLbyD=52.43
+20	51617742	.	TGC	T,TGCGC	1374.91	PASS	AF=0.06000,0.02000;BaseQRankSum=12.051;DP=6231;Dels=0.00;FS=189.609;HPLen=1;HRun=0;InbreedingCoeff=0.0862;IndelType=MULTIALLELIC_INDEL;MQ0Fraction=0.0180;MQRankSum=-2.959;ReadPosRankSum=-5.090;VQSLOD=-2.8715;set=filterInVQSR-2of5;sumGLbyD=3.97
+20	51770354	.	AG	A	1010.90	PASS	AA=26;AB=0.52727;ABA=26;ABP=3.3656;ABR=29;AC=7;AF=0.0097;AF1=0.01637;AN=718;BL=1034;BR=964;BVAR;BaseQRankSum=5.588;CI95=0.01327,0.02212;DEL;DP=16259;DP4=2785,2239,15,10;Dels=0.01;EL=11;EPP=4.3466;ER=15;FQ=999;FR;FS=3.367;HETAR=8;HOMA=0;HOMR=1064;HP=2;HPLen=2;HR=2;HRun=2;HU=G;INDEL;InbreedingCoeff=0.0557;IndelType=DEL.NumRepetitions_2.EventLength_1.RepeatExpansion_G.;LEN=1;LRB=0.035035;LRBP=8.3357;MQ=90.48;MQ0=0;MQ0Fraction=0.0000;MQM=61.346;MQRankSum=-0.019;NF;NR;NS=1072;PP;PV4=0.69,2.1e-08,0.078,1;RA=6173;RL=13;RPP=3.0103;RR=13;RUN=1;ReadPosRankSum=-0.460;SAB=0.61538;SAF=16;SAP=6.017;SAR=10;SC=GTGGTCCTGCAGGTCAATAAT;SET_INTEGRATION;SET_WGVQSR;SRB=0.56342;SRF=3478;SRP=218.68;SRR=2695;TC;TR=2;TU=G;VQSLOD=10.1601;set=Intersection;sumGLbyD=14.60
+20	51848430	.	AT	A,ATT	999	PASS	AA=39;AB=0.83408;ABA=37;ABP=219.19;ABR=186;AC=14,33;AF=0.0153,0.0359;AF1=0.03062;AN=918;BL=1676;BR=1732;BVAR;BaseQRankSum=3.338;CI95=0.02212,0.03982;DP=14886;DP4=1970,1762,22,31;Dels=0.01;EL=18;EPP=3.5114;ER=21;FQ=999;FR;FS=3.004;HETAR=31;HOMA=0;HOMR=1040;HP=10;HPLen=9;HR=9;HRun=9;HU=T;INDEL;INS;InbreedingCoeff=0.1629;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.016432;LRBP=5.0085;MQ=80.05;MQ0=0;MQ0Fraction=0.0000;MQM=56.667;MQRankSum=0.325;NF;NR;NS=1071;PP;PV4=0.13,1,0.0095,0.064;RA=5318;RL=21;RPP=3.5114;RR=18;RUN=1;ReadPosRankSum=-0.493;SAB=0.46154;SAF=18;SAP=3.5114;SAR=21;SC=ACAAAACAATATTTTTTTTTC;SET_WGVQSR;SRB=0.4968;SRF=2642;SRP=3.4823;SRR=2676;TC;TR=9;TU=T;VQSLOD=5.7417;set=Intersection;sumGLbyD=7.57
+20	51897203	.	T	TG	8427.20	PASS	AA=237;AB=0.69846;ABA=215;ABP=246.92;ABR=498;AC=117;AF=0.1662;AN=704;BL=14961;BR=5990;BVAR;BaseQRankSum=22.203;DP=9710;Dels=0.00;EL=83;EPP=49.198;ER=154;FR;FS=9.450;HETAR=123;HOMA=9;HOMR=895;HP=5;HPLen=6;HR=6;HRun=0;HU=T;INS;InbreedingCoeff=-0.0513;IndelType=INS.NOVEL_1.Novel_G.;LEN=1;LRB=0.42819;LRBP=8344.3;MQ0Fraction=0.0291;MQM=45.861;MQRankSum=-10.426;NF;NR;NS=1027;PP;RA=4919;RL=210;RPP=309.85;RR=27;RUN=1;ReadPosRankSum=-1.843;SAB=0.29536;SAF=70;SAP=89.219;SAR=167;SC=TTTGTTTGTTTTTTGTTGTTG;SET_INTEGRATION;SET_WGVQSR;SRB=0.47794;SRF=2351;SRP=23.798;SRR=2568;TC;TR=23;TU=GTTT;VQSLOD=6.2670;set=Intersection;sumGLbyD=8.99
+20	52274070	.	AAG	A	1400.37	PASS	AA=30;AB=0.74227;ABA=25;ABP=52.462;ABR=72;AC=21;AF=0.01756;AN=1196;BL=412;BR=1966;BVAR;BaseQRankSum=6.660;DEL;DP=9362;Dels=0.01;EL=16;EPP=3.2998;ER=14;FS=1.485;HETAR=18;HOMA=2;HOMR=1004;HRun=0;InbreedingCoeff=0.0317;IndelType=DEL.NumRepetitions_1.EventLength_2.RepeatExpansion_AG.;LEN=2;LRB=0.65349;LRBP=2208.2;MQ0Fraction=0.0022;MQM=46.133;MQRankSum=-4.743;NS=1024;RA=3931;RL=2;RPP=51.941;RR=28;RUN=1;ReadPosRankSum=-4.152;SAB=0.4;SAF=12;SAP=5.6161;SAR=18;SET_INTEGRATION;SET_WGVQSR;SRB=0.49784;SRF=1957;SRP=3.1699;SRR=1974;VQSLOD=5.6452;set=Intersection;sumGLbyD=11.11
+20	52351501	.	TAC	T	199.59	PASS	AC=22;AF=0.0238;AN=926;BaseQRankSum=7.874;DP=22911;DP4=2146,1691,26,22;FR;FS=2.898;HP=4;HPLen=3;HR=1;HRun=0;HU=A;HaplotypeScore=18.6111;INDEL;InbreedingCoeff=-0.0326;IndelType=DEL.NumRepetitions_6.EventLength_2.RepeatExpansion_AC.;MQ0=2;MQ0Fraction=0.0007;MQRankSum=1.011;NF;NR;PP;PV4=0.88,0.14,0.16,0.24;QD=1.10;ReadPosRankSum=-1.053;SB=-306.09;SC=GACACACAAATACACACACAC;SET_INTEGRATION;SET_WGVQSR;TC;TR=13;TU=AC;VQSLOD=4.0486;set=filterInVQSR-2of5
+20	52447173	.	CA	C	503.89	PASS	AC=23;AF=0.01891;AN=1216;BaseQRankSum=0.801;DP=3266;FS=2.606;HRun=2;HaplotypeScore=22.1543;InbreedingCoeff=-0.0097;IndelType=DEL.NumRepetitions_2.EventLength_1.RepeatExpansion_A.;MQ=118.02;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-1.309;QD=2.65;ReadPosRankSum=-7.872;SB=-279.27;VQSLOD=4.1900;set=VQSR
+20	52498650	.	GT	G	24069	PASS	AA=74;AB=0.90594;ABA=57;ABP=870.4;ABR=549;AC=28;AF=0.02333;AN=1200;BL=505;BR=4514;BVAR;BaseQRankSum=-3.837;DEL;DP=9798;Dels=0.01;EL=41;EPP=4.8883;ER=33;FS=4.085;HETAR=209;HOMA=663;HOMR=121;HRun=1;InbreedingCoeff=0.0334;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.79876;LRBP=6956.6;MQ0=2;MQ0Fraction=0.0007;MQM=57.784;MQRankSum=-2.951;NS=995;RA=957;RL=8;RPP=101.72;RR=66;RUN=1;ReadPosRankSum=-14.806;SAB=0.39189;SAF=29;SAP=10.522;SAR=45;SRB=0.39916;SRF=382;SRP=87.53;SRR=575;VQSLOD=3.8710;set=filterInVQSR-2of5;sumGLbyD=2.90
+20	52823602	rs11469056	CAAA	C,CA,CAA,CAAAA,CAAAAA,CAAAAAA,CAAAAAAA,CAAAAAAAA,CAAAAAAAAA,CAAAAAAAAAA	14515.17	PASS	AC=24,83,246,109,83,19,10,16,22,59;AF=0.02128,0.07358,0.21809,0.09663,0.07358,0.01684,0.00887,0.01418,0.01950,0.05230;AN=1128;BVAR;BaseQRankSum=4.150;DB;DEL;DP=28279;FR;FS=2.021;HP=17;HR=17;HU=A;HaplotypeScore=27.8032;INS;InbreedingCoeff=0.7740;IndelType=MULTIALLELIC_INDEL;MQ=69.00;MQ0=0;MQ0Fraction=0.0000;MQRankSum=1.418;NF;NR;PP;QD=7.90;RUN=1;ReadPosRankSum=-3.864;SB=-3244.40;SC=GGTCCTAAGGCAAAAAAAAAA;SET_WGVQSR;TC;TR=17;TU=A;VQSLOD=14.1033;set=Intersection
+20	53308906	.	CT	C,CTT	2276	PASS	AA=92;AB=0.84453;ABA=81;ABP=540.17;ABR=440;AC=53,81;AF=0.04351,0.06650;AN=1218;BL=3561;BR=4796;BVAR;BaseQRankSum=3.000;DP=11804;Dels=0.02;EL=48;EPP=3.3879;ER=44;FR;FS=13.197;HETAR=69;HOMA=3;HOMR=993;HP=11;HR=10;HRun=10;HU=T;INS;InbreedingCoeff=0.2297;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.14778;LRBP=399.32;MQ0=1;MQ0Fraction=0.0003;MQM=56.348;MQRankSum=3.154;NF;NR;NS=1065;PP;RA=5520;RL=39;RPP=7.6365;RR=53;RUN=1;ReadPosRankSum=-2.140;SAB=0.57609;SAF=53;SAP=7.6365;SAR=39;SC=AATCCAAAGTCTTTTTTTTTT;SET_WGVQSR;SRB=0.51576;SRF=2847;SRP=14.92;SRR=2673;TC;TR=10;TU=T;VQSLOD=2.4753;set=filterInVQSR-2of5;sumGLbyD=4.42
+20	53334602	.	T	TG,TGG	905.13	PASS	ABR=325;AC=44,22;AF=0.03624,0.01812;BVAR;BaseQRankSum=-4.608;DP=15015;FR;FS=494.901;HOMA=0;HOMR=1004;HP=1;HR=1;HU=G;HaplotypeScore=20.5023;INS;InbreedingCoeff=0.0799;IndelType=MULTIALLELIC_INDEL;MQ=116.70;MQ0=0;MQ0Fraction=0.0000;MQRankSum=8.022;NF;NR;NS=1064;PP;QD=0.35;RA=5690;RUN=1;ReadPosRankSum=-14.522;SB=-311.57;SC=AGCCATTGGCTGTTTCACTGA;SRB=0.40738;SRF=2318;SRP=426.97;SRR=3372;TC;TR=1;TU=G;VQSLOD=-2.3042;set=filterInVQSR-2of5
+20	53729115	.	T	TG	15.48	PASS	AC=1;AF=0.0015;AN=668;BaseQRankSum=-1.001;DP=1711;FS=9.048;HRun=2;HaplotypeScore=12.4681;InbreedingCoeff=-0.0320;IndelType=INS.NumRepetitions_2.EventLength_1.RepeatExpansion_G.;MQ=131.36;MQ0=0;MQ0Fraction=0.0000;MQRankSum=0.193;QD=4.57;ReadPosRankSum=0.407;SB=-5.35;SET_INTEGRATION;SET_WGVQSR;VQSLOD=4.8071;set=VQSR
+20	54033830	.	GTATTTTAAAATCA	G	2220.86	PASS	AF=0.0113;BaseQRankSum=5.506;DP=2577;Dels=0.01;FR;FS=6.533;HP=5;HPLen=4;HR=1;HRun=0;HU=T;InbreedingCoeff=0.0032;IndelType=DEL.NumRepetitions_1.EventLength_10orMore.;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-2.969;NF;NR;PP;ReadPosRankSum=1.322;SC=TCAATATTTTGTATTTTAAAA;SET_INTEGRATION;SET_WGVQSR;TC;TR=1;TU=T;VQSLOD=5.5145;set=Intersection;sumGLbyD=95.65
+20	54375236	.	GT	G	626.13	PASS	AA=40;AB=0.63551;ABA=39;ABP=20.078;ABR=68;AC=18;AF=0.0256;AN=702;BL=1331;BR=1743;BVAR;BaseQRankSum=9.346;DEL;DP=8568;Dels=0.02;EL=26;EPP=10.828;ER=14;FS=0.610;HETAR=21;HOMA=1;HOMR=1035;HRun=1;InbreedingCoeff=-0.0056;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.13403;LRBP=122.92;MQ0=0;MQ0Fraction=0.0000;MQM=67.125;MQRankSum=-2.537;NS=1058;RA=4870;RL=17;RPP=4.9646;RR=23;RUN=1;ReadPosRankSum=-1.229;SAB=0.525;SAF=21;SAP=3.2274;SAR=19;SET_INTEGRATION;SET_WGVQSR;SRB=0.5271;SRF=2567;SRP=34.087;SRR=2303;VQSLOD=7.9228;set=Intersection;sumGLbyD=10.77
+20	54457331	.	G	GA	1793.40	PASS	AA=77;AB=0.66667;ABA=74;ABP=56.573;ABR=148;AC=33;AF=0.02687;AN=1228;BL=3834;BR=1154;BVAR;BaseQRankSum=10.572;DP=10230;Dels=0.00;EL=77;EPP=170.21;ER=0;FS=139.433;HETAR=44;HOMA=1;HOMR=1001;HRun=1;INS;InbreedingCoeff=0.0023;IndelType=INS.NOVEL_1.Novel_A.;LEN=1;LRB=0.53729;LRBP=3129.8;MQ0Fraction=0.0095;MQM=4.7013;MQRankSum=-8.116;NS=1046;RA=4009;RL=77;RPP=170.21;RR=0;RUN=1;ReadPosRankSum=-6.026;SAB=1;SAF=77;SAP=170.21;SAR=0;SRB=0.57022;SRF=2286;SRP=174.7;SRR=1723;VQSLOD=1.1887;set=filterInVQSR-2of5;sumGLbyD=5.90
+20	54469810	.	CA	C	1697.62	PASS	AA=93;AB=0.63855;ABA=90;ABP=44.53;ABR=159;AC=34;AF=0.0374;AF1=0.01719;AN=908;BL=3242;BR=5839;BVAR;BaseQRankSum=10.425;CI95=0.009317,0.02795;DEL;DP=15197;DP4=2134,1896,56,46;Dels=0.03;EL=34;EPP=17.604;ER=59;FQ=16;FR;FS=9.985;HETAR=41;HOMA=1;HOMR=1011;HP=9;HPLen=8;HR=8;HRun=8;HU=A;INDEL;InbreedingCoeff=-0.0472;IndelType=DEL.NumRepetitions_8.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.28598;LRBP=1615.8;MQ=83.37;MQ0=1;MQ0Fraction=0.0004;MQM=64.075;MQRankSum=3.036;NF;NR;NS=1053;PP;PV4=0.76,1,0.31,0.22;RA=5150;RL=28;RPP=34.975;RR=65;RUN=1;ReadPosRankSum=-0.252;SAB=0.5914;SAF=55;SAP=9.7582;SAR=38;SC=ATTGCTAAGACAAAAAAAAGA;SET_INTEGRATION;SET_WGVQSR;SRB=0.50621;SRF=2607;SRP=4.7374;SRR=2543;TC;TR=8;TU=A;VQSLOD=8.3677;set=Intersection;sumGLbyD=9.90
+20	54542453	.	GTATA	G,GTA	5109.66	PASS	ABR=112;AC=66,56;AF=0.0682,0.0579;AN=968;BVAR;BaseQRankSum=17.089;DB;DEL;DP=5519;DS;Dels=0.06;FS=99.502;HOMA=15;HOMR=409;HRun=0;InbreedingCoeff=0.1584;IndelType=MULTIALLELIC_INDEL;MQ0Fraction=0.0178;MQRankSum=-6.854;NS=460;RA=864;RUN=1;ReadPosRankSum=0.855;SRB=0.79282;SRF=685;SRP=646.5;SRR=179;VQSLOD=0.6375;set=filterInVQSR-2of5;sumGLbyD=8.53
+20	54629773	.	CA	C	1799.50	PASS	AA=49;AB=0.82707;ABA=46;ABP=250.17;ABR=220;AC=9;AF=0.00746;AN=1206;BL=173;BR=2277;BVAR;BaseQRankSum=5.240;DEL;DP=8557;Dels=0.01;EL=49;EPP=109.41;ER=0;FS=32.359;HETAR=35;HOMA=1;HOMR=325;HRun=1;InbreedingCoeff=0.0892;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.85878;LRBP=3926.6;MQ0Fraction=0.0602;MQM=32.163;MQRankSum=-3.926;NS=361;RA=1091;RL=0;RPP=109.41;RR=49;RUN=1;ReadPosRankSum=-4.512;SAB=0;SAF=0;SAP=109.41;SAR=49;SRB=0.49404;SRF=539;SRP=3.3467;SRR=552;VQSLOD=1.1233;set=filterInVQSR-2of5;sumGLbyD=3.54
+20	54710245	.	TA	T	999	PASS	AF=0.0084;AF1=0.0148;BaseQRankSum=3.954;CI95=0.00885,0.02212;DP=8043;DP4=2000,1849,10,7;Dels=0.01;FQ=999;FR;FS=0.000;HP=9;HPLen=6;HR=3;HRun=6;HU=A;INDEL;InbreedingCoeff=0.1181;IndelType=DEL.NumRepetitions_3.EventLength_1.RepeatExpansion_A.;MQ=78.51;MQ0=0;MQ0Fraction=0.0000;MQRankSum=0.095;NF;NR;PP;PV4=0.63,0.00056,1,1;ReadPosRankSum=-0.448;SC=CAACAAAAAATAAATAAATAA;SET_INTEGRATION;SET_WGVQSR;TC;TR=15;TU=AAAT;VQSLOD=7.8129;set=Intersection;sumGLbyD=19.02
+20	54968173	.	A	AAT,AATAT,AT,ATAT	89535.82	PASS	ABR=994;AC=561,278,2,3;AF=0.50179,0.24866,0.00179,0.00268;AN=1118;BVAR;BaseQRankSum=-2.699;DB;DP=27837;DP4=168,177,1045,866;Dels=0.00;FQ=999;FR;FS=12.472;HOMA=71;HOMR=455;HP=3;HPLen=4;HR=4;HRun=0;HU=A;INDEL;INS;InbreedingCoeff=0.6391;IndelType=MULTIALLELIC_INDEL;KGPilot123;MQ=80.36;MQ0Fraction=0.0055;MQRankSum=-1.512;NF;NR;NS=913;PP;PV4=0.046,1,1,1;RA=2015;RUN=1;ReadPosRankSum=1.015;SC=GGCCACTTAAAATATATATAT;SET_WGVQSR;SRB=0.44864;SRF=904;SRP=49.187;SRR=1111;TC;TR=15;TU=AT;VQSLOD=9.0092;dbSNP=132;set=Intersection;sumGLbyD=42.33
+20	55176688	.	TA	T	421.84	PASS	AF=0.01322;AF1=0.01845;BaseQRankSum=5.383;CI95=0.01282,0.02564;DP=10531;DP4=1975,2017,16,14;Dels=0.01;FQ=91.2;FR;FS=7.401;HP=6;HPLen=5;HR=5;HRun=5;HU=A;INDEL;InbreedingCoeff=0.0829;IndelType=DEL.NumRepetitions_5.EventLength_1.RepeatExpansion_A.;MQ=75.80;MQ0=1;MQ0Fraction=0.0003;MQRankSum=-0.471;NF;NR;PP;PV4=0.72,1,1,1;ReadPosRankSum=0.223;SC=CTGCAAAATATAAAAATTAGG;SET_INTEGRATION;SET_WGVQSR;TC;TR=5;TU=A;VQSLOD=6.6000;set=Intersection;sumGLbyD=12.15
+20	55664086	.	GTT	ATT,G,GT,GTTT	5622.44	PASS	AC=6,71,136;AF=0.00498,0.05887,0.11277;AN=1206;BVAR;BaseQRankSum=3.173;DB;DEL;DP=40384;DP4=1567,1317,54,29;Dels=0.05;FR;FS=1.949;HP=14;HR=11;HRun=11;HU=T;INDEL;INS;InbreedingCoeff=0.3490;IndelType=MIXED;MQ=77.90;MQ0=0;MQ0Fraction=0.0000;MQRankSum=0.052;NF;NR;PP;PV4=0.057,1,0.2,1.2e-05;RUN=1;ReadPosRankSum=-13.646;SC=AATTTTATTTGTTTTTTTTTT;SET_INTEGRATION;SET_WGVQSR;TC;TR=11;TU=T;VQSLOD=11.7964;set=Intersection;sumGLbyD=8.09
+20	56045006	.	TG	T	342.15	PASS	AC=72;AF=0.0940;AN=766;BaseQRankSum=4.992;DP=1238;FS=1.460;HRun=7;HaplotypeScore=20.2784;InbreedingCoeff=0.1795;IndelType=DEL.NumRepetitions_7.EventLength_1.RepeatExpansion_G.;MQ=66.42;MQ0=1;MQ0Fraction=0.0008;MQRankSum=-0.937;QD=1.84;ReadPosRankSum=-4.385;SB=-320.83;VQSLOD=5.2383;set=VQSR
+20	56158711	.	AG	A	922.47	PASS	AA=18;AB=0.575;ABA=17;ABP=4.9646;ABR=23;AC=2;AF=0.0028;AN=714;BL=953;BR=808;BVAR;BaseQRankSum=3.129;DEL;DP=10462;Dels=0.01;EL=9;EPP=3.0103;ER=9;FR;FS=8.724;HETAR=4;HOMA=0;HOMR=1058;HP=1;HPLen=2;HR=2;HRun=1;HU=A;InbreedingCoeff=0.0262;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_G.;LEN=1;LRB=0.08234;LRBP=28.936;MQ0=0;MQ0Fraction=0.0000;MQM=55.889;MQRankSum=2.052;NF;NR;NS=1062;PP;RA=6300;RL=9;RPP=3.0103;RR=9;RUN=1;ReadPosRankSum=-0.317;SAB=0.66667;SAF=12;SAP=7.3532;SAR=6;SC=TGGCCTAGCAAGCATCGTGAC;SET_INTEGRATION;SET_WGVQSR;SRB=0.48143;SRF=3033;SRP=21.883;SRR=3267;TC;TR=8;TU=AAGC;VQSLOD=8.3252;set=Intersection;sumGLbyD=13.22
+20	56258618	rs113670927	T	C,TGC,TGTGC,TGTGTGC	37834.99	PASS	ABR=441;AC=11,100,43;AF=0.0123,0.1119,0.0481;AN=894;BVAR;BaseQRankSum=19.514;DB;DP=23173;DP4=541,920,413,579;Dels=0.00;FQ=999;FR;FS=1.238;HOMA=28;HOMR=808;HP=2;HPLen=1;HR=1;HRun=0;HU=G;INDEL;INS;InbreedingCoeff=0.2154;IndelType=MIXED;MQ=57.25;MQ0Fraction=0.0275;MQRankSum=-6.684;NF;NR;NS=976;PP;PV4=0.023,1,1,1;RA=3294;RUN=1;ReadPosRankSum=11.873;SC=TGCGTGTGTGTGTGTGTGTGT;SRB=0.42441;SRF=1398;SRP=166.5;SRR=1896;TC;TR=30;TU=GT;VQSLOD=6.7457;dbSNP=114;set=Intersection;sumGLbyD=21.27
+20	56395857	.	T	TAGGCAG	6614.22	PASS	AA=30;AB=0.63415;ABA=30;ABP=15.827;ABR=52;AC=14;AF=0.0197;AF1=0.03154;AN=710;BL=991;BR=1813;BVAR;BaseQRankSum=-4.589;CI95=0.02434,0.04204;DP=13879;DP4=1543,1833,12,14;Dels=0.00;EL=14;EPP=3.2998;ER=16;FQ=999;FR;FS=1.482;HETAR=11;HOMA=0;HOMR=1051;HP=1;HPLen=2;HR=2;HRun=0;HU=T;INDEL;INS;InbreedingCoeff=0.0774;IndelType=INS.NumRepetitions_2.EventLength_6.;LEN=6;LRB=0.29315;LRBP=526.27;MQ=90.42;MQ0=0;MQ0Fraction=0.0000;MQM=39.433;MQRankSum=-7.011;NF;NR;NS=1062;PP;PV4=1,1,3.7e-09,1;RA=5322;RL=9;RPP=13.433;RR=21;RUN=1;ReadPosRankSum=0.679;SAB=0.43333;SAF=13;SAP=4.1684;SAR=17;SC=AAGAGCATCTTAGGCAGAGGC;SET_INTEGRATION;SET_WGVQSR;SRB=0.47294;SRF=2517;SRP=36.853;SRR=2805;TC;TR=2;TU=T;VQSLOD=8.3045;set=Intersection;sumGLbyD=68.22
+20	56969289	.	GTTTGT	G	600.69	PASS	AF=0.0056;AF1=0.007726;BaseQRankSum=2.907;CI95=0.004425,0.01327;DP=9643;DP4=1892,1749,6,3;Dels=0.00;FQ=117;FR;FS=16.601;HP=5;HPLen=3;HR=3;HRun=0;HU=T;INDEL;InbreedingCoeff=0.0236;IndelType=DEL.NumRepetitions_3.EventLength_5.;MQ=92.59;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-2.134;NF;NR;PP;PV4=0.51,1,0.07,0.3;ReadPosRankSum=0.236;SC=TAAGGACGTTGTTTGTTTTGT;SET_INTEGRATION;SET_WGVQSR;TC;TR=10;TU=GTTT;VQSLOD=5.8458;set=Intersection;sumGLbyD=39.51
+20	57187557	.	AG	A,AGG	1486.69	PASS	AA=130;AB=0.55446;ABA=90;ABP=8.2132;ABR=112;AC=56,26;AF=0.0574,0.0266;AN=976;BL=3817;BR=5968;BVAR;BaseQRankSum=5.517;DEL;DP=14174;DP4=925,721,59,48;Dels=0.05;EL=52;EPP=14.302;ER=78;FR;FS=0.917;HETAR=44;HOMA=17;HOMR=864;HP=4;HPLen=4;HR=4;HRun=4;HU=G;INDEL;InbreedingCoeff=0.2856;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.21983;LRBP=1029.8;MQ=91.56;MQ0=0;MQ0Fraction=0.0000;MQM=63.631;MQRankSum=1.900;NF;NR;NS=925;PP;PV4=0.84,1,1,0.39;RA=2746;RL=44;RPP=32.476;RR=86;RUN=1;ReadPosRankSum=-0.639;SAB=0.44615;SAF=58;SAP=6.2842;SAR=72;SC=TCAGGCCCGCAGGGGTCAGGG;SET_INTEGRATION;SET_WGVQSR;SRB=0.5772;SRF=1585;SRP=145.17;SRR=1161;TC;TR=4;TU=G;VQSLOD=7.7167;set=Intersection;sumGLbyD=14.85
+20	57282771	.	T	TG	506.43	PASS	AA=34;AB=0.70312;ABA=19;ABP=25.946;ABR=45;AC=34;AF=0.0373;AN=912;BL=886;BR=1938;BVAR;BaseQRankSum=3.744;DP=4276;Dels=0.00;EL=18;EPP=3.2658;ER=16;FR;FS=0.639;HETAR=17;HOMA=9;HOMR=737;HP=9;HR=8;HRun=8;HU=G;INS;InbreedingCoeff=0.2149;IndelType=INS.NumRepetitions_8.EventLength_1.RepeatExpansion_G.;LEN=1;LRB=0.37252;LRBP=853.99;MQ0=0;MQ0Fraction=0.0000;MQM=49.706;MQRankSum=-0.051;NF;NR;NS=763;PP;RA=1822;RL=9;RPP=19.36;RR=25;RUN=1;ReadPosRankSum=-2.111;SAB=0.55882;SAF=19;SAP=4.0322;SAR=15;SC=TCGGGGGGCGTGGGGGGGGTG;SET_INTEGRATION;SET_WGVQSR;SRB=0.51098;SRF=931;SRP=4.9172;SRR=891;TC;TR=8;TU=G;VQSLOD=5.7772;set=Intersection;sumGLbyD=7.95
+20	57419740	rs11481507	A	AT	82613.57	PASS	AA=3850;AB=0.41404;ABA=1786;ABP=198.63;ABR=1262;AC=919;AF=0.75328;AN=1220;BL=140665;BR=151383;BVAR;BaseQRankSum=-27.490;DB;DP=31794;DP4=588,585,1571,1721;Dels=0.00;EL=1924;EPP=3.0126;ER=1926;FQ=999;FR;FS=2.191;HETAR=482;HOMA=454;HOMR=135;HP=3;HPLen=3;HR=3;HRun=3;HU=T;INDEL;INS;InbreedingCoeff=0.0861;IndelType=INS.NumRepetitions_3.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.036699;LRBP=857.15;MQ=123.92;MQ0=0;MQ0Fraction=0.0000;MQM=91.654;MQRankSum=3.016;NF;NR;NS=1071;PP;PV4=0.16,1,0.12,1;RA=1850;RL=1874;RPP=8.8784;RR=1976;RUN=1;ReadPosRankSum=-0.685;SAB=0.47636;SAF=1834;SAP=21.693;SAR=2016;SC=TACACTAGTGATTTAACCCTA;SET_INTEGRATION;SET_WGVQSR;SRB=0.49027;SRF=907;SRP=4.5315;SRR=943;TC;TR=3;TU=T;VQSLOD=9.2768;dbSNP=126;set=Intersection;sumGLbyD=22.78
+20	57558194	.	CT	C,CTT,CTTT	6470.30	PASS	ABR=451;AC=104,161,177;AF=0.08919,0.13808,0.15180;BVAR;BaseQRankSum=1.172;DP=7985;FR;FS=2.202;HOMA=19;HOMR=778;HP=22;HR=15;HU=T;HaplotypeScore=16.1921;INS;InbreedingCoeff=0.6440;IndelType=MULTIALLELIC_INDEL;MQ=69.24;MQ0=27;MQ0Fraction=0.0109;MQRankSum=-0.003;NF;NR;NS=943;PP;QD=2.22;RA=2531;RUN=1;ReadPosRankSum=-0.104;SB=-2096.85;SC=GCCTTTTTTTCTTTTTTTTTT;SET_WGVQSR;SRB=0.34848;SRF=882;SRP=507.73;SRR=1649;TC;TR=15;TU=T;VQSLOD=6.5151;set=Intersection
+20	57693627	.	AG	A	1991.90	PASS	AA=52;AB=0.49462;ABA=47;ABP=3.0336;ABR=46;AC=15;AF=0.01227;AN=1222;BL=1902;BR=1478;BVAR;BaseQRankSum=-6.121;DEL;DP=26459;DP4=2647,2873,16,20;Dels=0.01;EL=25;EPP=3.1773;ER=27;FR;FS=3.135;HETAR=15;HOMA=1;HOMR=1064;HP=2;HPLen=3;HR=3;HRun=2;HU=A;INDEL;InbreedingCoeff=0.0866;IndelType=DEL.NumRepetitions_2.EventLength_1.RepeatExpansion_G.;LEN=1;LRB=0.12544;LRBP=118.51;MQ=116.26;MQ0=0;MQ0Fraction=0.0000;MQM=114.65;MQRankSum=1.942;NF;NR;NS=1080;PP;PV4=0.74,6.9e-08,1,0.38;RA=6781;RL=33;RPP=11.195;RR=19;RUN=1;ReadPosRankSum=-1.795;SAB=0.5;SAF=26;SAP=3.0103;SAR=26;SC=ATTGGAGGAAAGGCTTTTTCA;SET_INTEGRATION;SET_WGVQSR;SRB=0.46247;SRF=3136;SRP=85.976;SRR=3645;TC;TR=3;TU=A;VQSLOD=8.6672;set=Intersection;sumGLbyD=13.55
+20	57716287	.	A	AT	66.47	PASS	AC=6;AF=0.00506;AN=1186;BaseQRankSum=1.369;DP=2744;FS=3.834;HRun=8;HaplotypeScore=11.2046;InbreedingCoeff=0.1196;IndelType=INS.NumRepetitions_8.EventLength_1.RepeatExpansion_T.;MQ=73.00;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-0.086;QD=2.14;ReadPosRankSum=-2.588;SB=-53.80;SET_INTEGRATION;SET_WGVQSR;VQSLOD=4.2080;set=VQSR
+20	58121928	rs73625057	T	TGG	6649.17	PASS	AA=132;AB=0.57854;ABA=110;ABP=16.996;ABR=151;AC=57;AF=0.0617;AN=924;BL=4530;BR=4790;BVAR;BaseQRankSum=-13.456;DB;DP=30353;DP4=2107,2168,61,66;Dels=0.00;EL=67;EPP=3.0761;ER=65;FR;FS=0.708;HETAR=46;HOMA=8;HOMR=1023;HP=3;HPLen=2;HR=2;HRun=2;HU=G;INDEL;INS;InbreedingCoeff=0.1241;IndelType=INS.NumRepetitions_2.EventLength_1.RepeatExpansion_G.;LEN=2;LRB=0.027897;LRBP=18.76;MQ=109.61;MQ0=1;MQ0Fraction=0.0004;MQM=79.833;MQRankSum=-0.699;NF;NR;NS=1077;PP;PV4=0.79,1,0.49,0.036;RA=5754;RL=61;RPP=4.6554;RR=71;RUN=1;ReadPosRankSum=-3.309;SAB=0.45455;SAF=60;SAP=5.3792;SAR=72;SC=GATTAGAATGTGGATATCTTT;SET_INTEGRATION;SET_WGVQSR;SRB=0.48836;SRF=2810;SRP=9.7866;SRR=2944;TC;TR=4;TU=GT;VQSLOD=8.5770;set=Intersection;sumGLbyD=27.19
+20	58468826	.	ACAAG	A	999	PASS	AF=0.0014;AF1=0.003429;BaseQRankSum=4.082;CI95=0.003106,0.006211;DP=8461;DP4=2500,1817,8,2;Dels=0.01;FQ=999;FR;FS=5.034;HP=2;HPLen=1;HR=1;HRun=0;HU=C;INDEL;InbreedingCoeff=-0.0183;IndelType=DEL.NumRepetitions_1.EventLength_4.;MQ=120.69;MQ0=0;MQ0Fraction=0.0000;MQRankSum=0.141;NF;NR;PP;PV4=0.21,1,0.054,1;ReadPosRankSum=2.096;SC=ATCCTGAAACACAAGAAGAAA;SET_INTEGRATION;SET_WGVQSR;TC;TR=5;TU=AC;VQSLOD=7.4928;set=Intersection;sumGLbyD=29.17
+20	58731262	.	TC	T	999	PASS	AA=21;AB=0.48649;ABA=19;ABP=3.069;ABR=18;AC=7;AF=0.0101;AF1=0.01493;AN=694;BL=939;BR=848;BVAR;BaseQRankSum=4.205;CI95=0.01106,0.02212;DEL;DP=12598;DP4=1766,1428,11,15;Dels=0.01;EL=13;EPP=5.5954;ER=8;FQ=999;FR;FS=1.796;HETAR=8;HOMA=1;HOMR=1031;HP=7;HPLen=8;HR=8;HRun=2;HU=T;INDEL;InbreedingCoeff=-0.0030;IndelType=DEL.NumRepetitions_2.EventLength_1.RepeatExpansion_C.;LEN=1;LRB=0.050923;LRBP=13.073;MQ=124.57;MQ0=0;MQ0Fraction=0.0000;MQM=67.905;MQRankSum=1.103;NF;NR;NS=1040;PP;PV4=0.23,1,1,1;RA=4884;RL=10;RPP=3.1137;RR=11;RUN=1;ReadPosRankSum=-0.091;SAB=0.47619;SAF=10;SAP=3.1137;SAR=11;SC=TCATTTTTTTTCCTTGAAACT;SET_INTEGRATION;SET_WGVQSR;SRB=0.58006;SRF=2833;SRP=274.9;SRR=2051;TC;TR=8;TU=T;VQSLOD=10.8783;set=Intersection;sumGLbyD=15.11
+20	59181229	rs11476579	CTT	C,CT,CTTT,CTTTT	7787.17	PASS	AC=19,195,104,91;AF=0.01599,0.16414,0.08754,0.07660;AF1=0.2124;AN=1188;BVAR;BaseQRankSum=6.347;CI95=0.146,0.2743;DB;DEL;DP=26140;DP4=932,880,352,375;Dels=0.13;FQ=85.6;FR;FS=11.914;HP=14;HR=14;HRun=14;HU=T;INDEL;INS;InbreedingCoeff=0.4183;IndelType=MULTIALLELIC_INDEL;MQ=86.88;MQ0=0;MQ0Fraction=0.0000;MQRankSum=1.469;NF;NR;PP;PV4=0.17,1,1,1;RUN=1;ReadPosRankSum=-1.055;SC=GGTGAGAAAGCTTTTTTTTTT;SET_WGVQSR;TC;TR=14;TU=T;VQSLOD=7.4340;dbSNP=120;set=Intersection;sumGLbyD=7.02
+20	59213979	rs112141381	G	GC	9068	PASS	AA=131;AB=0.47115;ABA=110;ABP=4.5136;ABR=98;AF=0.0586;AN=700;BL=5395;BR=5816;BVAR;BaseQRankSum=15.453;DB;DP=23381;DP4=2191,2184,71,49;Dels=0.00;EL=66;EPP=3.0269;ER=65;FR;FS=7.907;HETAR=35;HOMA=5;HOMR=1019;HP=2;HPLen=3;HR=3;HRun=0;HU=G;INDEL;INS;InbreedingCoeff=0.0283;IndelType=INS.NOVEL_1.Novel_C.;LEN=1;LRB=0.037552;LRBP=37.34;MQ=72.13;MQ0=0;MQ0Fraction=0.0000;MQM=54.496;MQRankSum=0.897;NF;NR;NS=1059;PP;PV4=0.052,1,0.066,1;RA=4976;RL=59;RPP=5.8117;RR=72;RUN=1;ReadPosRankSum=-0.811;SAB=0.58015;SAF=76;SAP=10.32;SAR=55;SC=GATGGACTGGGACAGTGACTC;SET_INTEGRATION;SET_WGVQSR;SRB=0.49457;SRF=2461;SRP=4.2828;SRR=2515;TC;TR=3;TU=G;VQSLOD=9.3917;set=Intersection;sumGLbyD=28.58
+20	59252945	.	CT	C,CTT	557.18	PASS	AA=24;AB=0.84868;ABA=23;ABP=163.53;ABR=129;AC=21,29;AF=0.01759,0.02429;BL=1217;BR=1336;BVAR;BaseQRankSum=5.135;DP=9970;Dels=0.01;EL=13;EPP=3.3722;ER=11;FS=2.302;HETAR=21;HOMA=1;HOMR=1012;HRun=9;INS;InbreedingCoeff=0.1549;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.046612;LRBP=15.055;MQ0=0;MQ0Fraction=0.0000;MQM=67.208;MQRankSum=0.086;NS=1034;RA=4421;RL=11;RPP=3.3722;RR=13;RUN=1;ReadPosRankSum=-1.826;SAB=0.41667;SAF=10;SAP=4.4579;SAR=14;SET_WGVQSR;SRB=0.49649;SRF=2195;SRP=3.4823;SRR=2226;VQSLOD=2.8923;set=filterInVQSR-2of5;sumGLbyD=5.47
+20	60016966	.	CT	C	42650	PASS	AA=37;AB=0.97834;ABA=31;ABP=2847;ABR=1400;AC=15;AF=0.0163;AN=920;BL=2596;BR=778;BVAR;BaseQRankSum=-0.632;DEL;DP=10967;Dels=0.00;EL=14;EPP=7.7641;ER=23;FS=4.094;HETAR=421;HOMA=256;HOMR=385;HRun=1;InbreedingCoeff=-0.0051;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.53883;LRBP=2130.2;MQ0=0;MQ0Fraction=0.0000;MQM=120.3;MQRankSum=-0.911;NS=1072;RA=3413;RL=31;RPP=39.691;RR=6;RUN=1;ReadPosRankSum=-12.062;SAB=0.48649;SAF=18;SAP=3.069;SAR=19;SRB=0.47407;SRF=1618;SRP=22.943;SRR=1795;VQSLOD=3.3758;set=filterInVQSR-2of5;sumGLbyD=3.27
+20	60188651	.	AG	A	17624.52	PASS	AA=462;AB=0.76548;ABA=409;ABP=1070.7;ABR=1335;AC=403;AF=0.34444;AN=1170;BL=13877;BR=25909;BVAR;BaseQRankSum=6.180;DEL;DP=9900;Dels=0.08;EL=353;EPP=282.84;ER=109;FR;FS=2699.057;HETAR=346;HOMA=26;HOMR=633;HP=3;HR=4;HRun=1;HU=A;InbreedingCoeff=-0.2900;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_G.;LEN=1;LRB=0.30242;LRBP=7904.3;MQ0Fraction=0.0004;MQM=56.119;MQRankSum=1.644;NF;NR;NS=1005;PP;RA=3521;RL=112;RPP=269.25;RR=350;RUN=1;ReadPosRankSum=2.490;SAB=0.0064935;SAF=3;SAP=980.34;SAR=459;SC=AGGCTTCAAAAGAAAAAAAAA;SRB=0.55978;SRF=1971;SRP=112.32;SRR=1550;TC;TR=4;TU=A;VQSLOD=-34.0667;set=filterInVQSR-2of5;sumGLbyD=7.81
+20	60195570	.	GTACATACATACA	ATACATACATACA,G,GTACATACA	20140	PASS	ABR=102;AC=105,2;AF=0.08794,0.00168;AN=1194;BVAR;BaseQRankSum=-28.899;DB;DEL;DP=14347;Dels=0.02;FR;FS=52.125;HOMA=1;HOMR=1006;HP=1;HPLen=1;HR=1;HRun=0;HU=T;InbreedingCoeff=0.0695;IndelType=MIXED;MQ0Fraction=0.0007;MQRankSum=1.957;NF;NR;NS=1035;PP;RA=4759;RUN=1;ReadPosRankSum=-22.252;SAB=0.5;SAP=3.0103;SC=TGATAGATTCGTACATACATA;SET_INTEGRATION;SRB=0.47615;SRF=2266;SRP=26.522;SRR=2493;TC;TR=21;TU=ACAT;VQSLOD=2.7673;set=filterInVQSR-2of5;sumGLbyD=19.14
+20	60670601	rs72127450	AT	A,ATT	6401.59	PASS	AC=177,79;AF=0.16239,0.07248;AF1=0.1602;AN=1090;BVAR;BaseQRankSum=8.618;CI95=0.1106,0.2058;DB;DEL;DP=17508;DP4=1285,1094,313,259;Dels=0.10;FQ=94.1;FR;FS=0.000;HP=12;HR=12;HRun=12;HU=T;INDEL;INS;InbreedingCoeff=0.1076;IndelType=MULTIALLELIC_INDEL;LEN=1;MQ=64.73;MQ0=0;MQ0Fraction=0.0000;MQRankSum=0.620;NF;NR;PP;PV4=0.78,1,0.012,1;RUN=1;ReadPosRankSum=-1.294;SC=AGCCAGGCACATTTTTTTTTT;SET_WGVQSR;TC;TR=12;TU=T;VQSLOD=6.1650;dbSNP=130;set=Intersection;sumGLbyD=5.80
+20	60685780	.	TC	T	1123.58	PASS	AC=79;AF=0.07655;AN=1032;BaseQRankSum=14.949;DP=2084;FS=23.521;HRun=1;HaplotypeScore=19.7117;InbreedingCoeff=0.1356;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;MQ=53.57;MQ0=61;MQ0Fraction=0.0293;MQRankSum=-7.958;QD=4.35;ReadPosRankSum=-13.757;SB=-791.28;VQSLOD=6.3549;set=VQSR
+20	60744906	rs113528167	CG	C	422.53	PASS	AC=48;AF=0.0732;AN=656;BaseQRankSum=17.669;DB;DP=1189;FS=0.356;HRun=1;HaplotypeScore=15.1808;InbreedingCoeff=0.2111;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_G.;MQ=82.83;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-10.455;QD=2.71;ReadPosRankSum=-16.887;SB=-326.46;VQSLOD=7.1707;set=VQSR
+20	60848742	.	CGT	C,CGTGT	999	PASS	AF=0.00980,0.01225;BaseQRankSum=5.597;DP=17065;DP4=1928,2188,17,13;Dels=0.01;FR;HP=1;HPLen=2;HR=2;HRun=0;HU=C;INDEL;InbreedingCoeff=0.2094;IndelType=MULTIALLELIC_INDEL;MQ=115.78;MQ0=0;MQ0Fraction=0.0000;MQRankSum=0.281;NF;NR;PP;PV4=0.36,0.4,0.12,0.12;ReadPosRankSum=-1.465;SB=-157.35;SC=TAGACGCTTCCGTGTGTGTGT;SET_INTEGRATION;SET_WGVQSR;TC;TR=11;TU=GT;VQSLOD=1.7100;set=filterInVQSR-2of5;sumGLbyD=16.39
+20	61023668	rs57452309	G	GAGC	6896.67	PASS	AC=115;AF=0.1445;AN=796;BaseQRankSum=12.146;DB;DP=1423;FS=5.070;HRun=0;HaplotypeScore=29.8897;InbreedingCoeff=0.0740;IndelType=INS.NOVEL_3.;MQ=77.02;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-9.005;QD=19.16;ReadPosRankSum=-17.440;SB=-3045.82;VQSLOD=4.5788;set=VQSR
+20	61180519	.	C	CA,CT	1774.30	PASS	ABR=135;AC=27,15;AF=0.02538,0.01410;BVAR;BaseQRankSum=-2.189;DP=8393;FR;FS=27.692;HOMA=2;HOMR=825;HP=6;HPLen=3;HR=3;HU=T;HaplotypeScore=19.5313;INS;InbreedingCoeff=0.0868;IndelType=MULTIALLELIC_INDEL;LEN=1;MQ=56.11;MQ0=172;MQ0Fraction=0.0667;MQRankSum=2.605;NF;NR;NS=854;PP;QD=1.99;RA=2868;RUN=1;ReadPosRankSum=-7.324;SB=-385.54;SC=TTCTTTCTTTCTTTCTTTCTT;SRB=0.32741;SRF=939;SRP=745.08;SRR=1929;TC;TR=69;TU=CTTT;VQSLOD=3.4398;set=filterInVQSR-2of5
+20	61184281	.	AC	A	9798.10	PASS	AA=24;AB=0.96507;ABA=16;ABP=863.43;ABR=442;AC=4;AF=0.00341;AN=1174;BL=349;BR=1039;BVAR;BaseQRankSum=2.048;DEL;DP=10073;Dels=0.00;EL=11;EPP=3.3722;ER=13;FS=2.097;HETAR=141;HOMA=69;HOMR=829;HRun=1;InbreedingCoeff=0.0697;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;LEN=1;LRB=0.49712;LRBP=747.85;MQ0=0;MQ0Fraction=0.0000;MQM=98.042;MQRankSum=1.881;NS=1042;RA=3625;RL=5;RPP=20.744;RR=19;RUN=1;ReadPosRankSum=-8.009;SAB=0.75;SAF=18;SAP=16.039;SAR=6;SRB=0.52662;SRF=1909;SRP=25.323;SRR=1716;VQSLOD=1.8117;set=filterInVQSR-2of5;sumGLbyD=5.55
+20	62074219	.	C	CTAT,CTGT	2328	PASS	ABR=99;AC=20,6;AF=0.01754,0.00526;BVAR;BaseQRankSum=11.221;DP=9498;DS;FS=4.510;HOMA=15;HOMR=645;HaplotypeScore=82.8868;INS;InbreedingCoeff=0.0880;IndelType=MULTIALLELIC_INDEL;LEN=3;MQ=29.88;MQ0=1378;MQ0Fraction=0.2286;MQRankSum=-5.309;NS=689;QD=0.77;RA=1679;RUN=1;ReadPosRankSum=-3.510;SAR=1;SB=-93.21;SRB=0.70697;SRF=1187;SRP=627.71;SRR=492;VQSLOD=1.8325;set=filterInVQSR-2of5
+20	62304449	.	CA	C,CAA	6680.17	PASS	AC=141,69;AF=0.12567,0.06150;AF1=0.08178;AN=1122;BVAR;BaseQRankSum=9.754;CI95=0.05088,0.1128;DEL;DP=15867;DP4=1252,1289,232,208;Dels=0.10;FQ=52.6;FR;FS=6.576;HP=11;HR=11;HRun=11;HU=A;INDEL;INS;InbreedingCoeff=0.1950;IndelType=MULTIALLELIC_INDEL;LEN=1;MQ=60.48;MQ0Fraction=0.0004;MQRankSum=-0.049;NF;NR;PP;PV4=0.2,1,1,1;RUN=1;ReadPosRankSum=-2.137;SC=GATTCTGTGTCAAAAAAAAAA;SET_WGVQSR;TC;TR=11;TU=A;VQSLOD=7.4714;set=Intersection;sumGLbyD=8.36
+20	62804895	rs57769591	CCTT	C	1148	PASS	AC=8;AF=0.0085;AF1=0.002839;AN=938;BaseQRankSum=4.952;CI95=0.002212,0.006637;DB;DP=8889;DP4=2574,1668,4,8;FQ=12.3;FS=2.289;HPLen=3;HRun=0;HaplotypeScore=29.4184;INDEL;InbreedingCoeff=-0.0270;IndelType=DEL.NumRepetitions_1.EventLength_3.;MQ0=876;MQ0Fraction=0.2674;MQRankSum=-0.641;PV4=0.074,1,1,1;QD=1.03;ReadPosRankSum=0.118;SB=-65.30;SET_INTEGRATION;SET_WGVQSR;VQSLOD=6.4881;dbSNP=126;set=Intersection
+20	62907688	.	AAT	A	6629.57	PASS	AC=164;AF=0.13735;AN=1194;BaseQRankSum=27.368;DP=2746;FS=5.985;HRun=0;HaplotypeScore=14.7748;InbreedingCoeff=0.1433;IndelType=DEL.NumRepetitions_2.EventLength_2.RepeatExpansion_AT.;MQ=96.65;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-3.318;QD=10.81;ReadPosRankSum=0.789;SB=-2662.16;SET_INTEGRATION;SET_WGVQSR;VQSLOD=6.1473;set=VQSR
diff --git a/tests/tabix_data/vcf/24.vcf b/tests/tabix_data/vcf/24.vcf
new file mode 100644
index 0000000..a62e424
--- /dev/null
+++ b/tests/tabix_data/vcf/24.vcf
@@ -0,0 +1,724 @@
+##fileformat=VCFv4.1
+##INFO=<ID=Sample,Number=1,Type=String,Description="Sample picked for single sample pooled 454-PCR validation">
+##INFO=<ID=GT,Number=1,Type=String,Description="Genotype">
+##INFO=<ID=PCR_454_AR,Number=1,Type=Integer,Description="Number of alternative reads in 454-PCR sequencing data">
+##INFO=<ID=PCR_454_RR,Number=1,Type=Integer,Description="Number of reference reads in 454-PCR sequencing data">
+##reference=file:///humgen/1kg/reference/human_g1k_v37.fasta
+#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO
+20	256726	.	T	A	.	.	Sample=HG00097;GT=0/1;PCR_454_AR=739;PCR_454_RR=885
+20	256726	.	T	A	.	.	Sample=HG00099;GT=0/1;PCR_454_AR=723;PCR_454_RR=714
+20	256726	.	T	A	.	.	Sample=HG00106;GT=0/1;PCR_454_AR=1092;PCR_454_RR=1102
+20	256726	.	T	A	.	.	Sample=HG00112;GT=0/1;PCR_454_AR=947;PCR_454_RR=1005
+20	256726	.	T	A	.	.	Sample=HG00104;GT=1/1;PCR_454_AR=1970;PCR_454_RR=52
+20	257977	.	G	C	.	.	Sample=NA19438;GT=0/1;PCR_454_AR=1312;PCR_454_RR=1123
+20	330407	.	C	G	.	.	Sample=HG00134;GT=0/1;PCR_454_AR=1034;PCR_454_RR=1037
+20	330407	.	C	G	.	.	Sample=HG00148;GT=0/1;PCR_454_AR=840;PCR_454_RR=820
+20	330407	.	C	G	.	.	Sample=HG00151;GT=0/1;PCR_454_AR=952;PCR_454_RR=982
+20	330407	.	C	G	.	.	Sample=HG00358;GT=0/1;PCR_454_AR=880;PCR_454_RR=957
+20	330407	.	C	G	.	.	Sample=HG01277;GT=0/1;PCR_454_AR=914;PCR_454_RR=984
+20	368826	.	G	A	.	.	Sample=NA20346;GT=0/1;PCR_454_AR=632;PCR_454_RR=591
+20	371957	.	G	A	.	.	Sample=HG00150;GT=0/1;PCR_454_AR=403;PCR_454_RR=424
+20	371957	.	G	A	.	.	Sample=NA12287;GT=0/1;PCR_454_AR=401;PCR_454_RR=435
+20	467031	.	T	A	.	.	Sample=NA20510;GT=0/0;PCR_454_AR=5;PCR_454_RR=1763
+20	741858	.	G	A	.	.	Sample=NA18634;GT=0/1;PCR_454_AR=1273;PCR_454_RR=1301
+20	947853	.	C	T	.	.	Sample=HG00578;GT=0/0;PCR_454_AR=0;PCR_454_RR=197
+20	947853	.	C	T	.	.	Sample=NA18861;GT=0/1;PCR_454_AR=40;PCR_454_RR=39
+20	947853	.	C	T	.	.	Sample=NA18868;GT=0/1;PCR_454_AR=88;PCR_454_RR=80
+20	947853	.	C	T	.	.	Sample=NA18870;GT=0/1;PCR_454_AR=66;PCR_454_RR=99
+20	947853	.	C	T	.	.	Sample=NA18917;GT=0/1;PCR_454_AR=96;PCR_454_RR=111
+20	947908	.	C	T	.	.	Sample=NA11993;GT=0/1;PCR_454_AR=598;PCR_454_RR=2114
+20	947908	.	C	T	.	.	Sample=NA18501;GT=0/1;PCR_454_AR=392;PCR_454_RR=1687
+20	947908	.	C	T	.	.	Sample=NA18504;GT=0/1;PCR_454_AR=635;PCR_454_RR=2218
+20	947908	.	C	T	.	.	Sample=NA18505;GT=0/1;PCR_454_AR=1312;PCR_454_RR=1429
+20	947908	.	C	T	.	.	Sample=NA18507;GT=0/1;PCR_454_AR=598;PCR_454_RR=2127
+20	948715	.	T	G	.	.	Sample=NA06989;GT=0/0;PCR_454_AR=4;PCR_454_RR=1252
+20	1144999	.	C	T	.	.	Sample=NA18510;GT=0/1;PCR_454_AR=450;PCR_454_RR=447
+20	1144999	.	C	T	.	.	Sample=NA19172;GT=0/1;PCR_454_AR=541;PCR_454_RR=531
+20	1285858	.	A	C	.	.	Sample=NA19311;GT=0/1;PCR_454_AR=1210;PCR_454_RR=1315
+20	1285932	.	G	A	.	.	Sample=HG00097;GT=0/1;PCR_454_AR=868;PCR_454_RR=867
+20	1285932	.	G	A	.	.	Sample=HG00106;GT=0/1;PCR_454_AR=745;PCR_454_RR=680
+20	1285932	.	G	A	.	.	Sample=HG00126;GT=0/1;PCR_454_AR=780;PCR_454_RR=838
+20	1285932	.	G	A	.	.	Sample=HG00134;GT=0/1;PCR_454_AR=978;PCR_454_RR=944
+20	1285932	.	G	A	.	.	Sample=HG00128;GT=1/1;PCR_454_AR=1499;PCR_454_RR=14
+20	1286090	.	A	G	.	.	Sample=HG00235;GT=0/1;PCR_454_AR=1223;PCR_454_RR=1352
+20	1286090	.	A	G	.	.	Sample=HG00351;GT=0/1;PCR_454_AR=799;PCR_454_RR=823
+20	1286090	.	A	G	.	.	Sample=HG01125;GT=0/1;PCR_454_AR=1167;PCR_454_RR=1149
+20	1286090	.	A	G	.	.	Sample=NA19773;GT=0/1;PCR_454_AR=1070;PCR_454_RR=1130
+20	1546804	.	G	A	.	.	Sample=HG00141;GT=0/1;PCR_454_AR=1174;PCR_454_RR=1231
+20	1546804	.	G	A	.	.	Sample=HG00149;GT=0/1;PCR_454_AR=1029;PCR_454_RR=1050
+20	1546804	.	G	A	.	.	Sample=HG00151;GT=0/1;PCR_454_AR=1135;PCR_454_RR=1034
+20	1546804	.	G	A	.	.	Sample=HG00177;GT=0/1;PCR_454_AR=1063;PCR_454_RR=1118
+20	1546804	.	G	A	.	.	Sample=HG00179;GT=0/1;PCR_454_AR=1118;PCR_454_RR=954
+20	1551579	.	T	G	.	.	Sample=NA20515;GT=0/0;PCR_454_AR=5;PCR_454_RR=1812
+20	1551579	.	T	G	.	.	Sample=NA19466;GT=0/1;PCR_454_AR=1011;PCR_454_RR=1042
+20	1559334	.	C	T	.	.	Sample=NA18941;GT=0/0;PCR_454_AR=1;PCR_454_RR=1193
+20	1615980	.	G	A	.	.	Sample=NA19914;GT=0/1;PCR_454_AR=441;PCR_454_RR=492
+20	1616047	.	C	G	.	.	Sample=NA07048;GT=0/1;PCR_454_AR=508;PCR_454_RR=813
+20	1629751	.	T	C	.	.	Sample=HG00156;GT=0/1;PCR_454_AR=285;PCR_454_RR=282
+20	1896011	.	C	T	.	.	Sample=NA18639;GT=0/0;PCR_454_AR=0;PCR_454_RR=29
+20	1896011	.	C	T	.	.	Sample=NA19314;GT=0/0;PCR_454_AR=0;PCR_454_RR=47
+20	2291684	.	T	C	.	.	Sample=NA19036;GT=0/1;PCR_454_AR=873;PCR_454_RR=1025
+20	2291684	.	T	C	.	.	Sample=NA19347;GT=0/1;PCR_454_AR=1116;PCR_454_RR=1217
+20	2375127	.	G	A	.	.	Sample=NA18615;GT=0/1;PCR_454_AR=1016;PCR_454_RR=1016
+20	2777844	.	T	C	.	.	Sample=NA20819;GT=0/1;PCR_454_AR=908;PCR_454_RR=970
+20	2844678	.	G	A	.	.	Sample=HG00360;GT=0/1;PCR_454_AR=1081;PCR_454_RR=1071
+20	2944927	.	A	T	.	.	Sample=NA12347;GT=0/1;PCR_454_AR=704;PCR_454_RR=752
+20	2969014	.	C	G	.	.	Sample=HG00151;GT=0/1;PCR_454_AR=684;PCR_454_RR=809
+20	2969014	.	C	G	.	.	Sample=NA18511;GT=0/1;PCR_454_AR=666;PCR_454_RR=704
+20	2969014	.	C	G	.	.	Sample=NA18523;GT=0/1;PCR_454_AR=767;PCR_454_RR=802
+20	2969014	.	C	G	.	.	Sample=NA18549;GT=0/1;PCR_454_AR=772;PCR_454_RR=838
+20	2969014	.	C	G	.	.	Sample=NA18858;GT=1/1;PCR_454_AR=1313;PCR_454_RR=8
+20	3026344	.	A	C	.	.	Sample=NA18640;GT=0/1;PCR_454_AR=1652;PCR_454_RR=1336
+20	3128885	.	G	A	.	.	Sample=NA19473;GT=0/1;PCR_454_AR=620;PCR_454_RR=669
+20	3128950	.	G	A	.	.	Sample=NA18624;GT=0/1;PCR_454_AR=570;PCR_454_RR=517
+20	3128950	.	G	A	.	.	Sample=NA18953;GT=0/1;PCR_454_AR=685;PCR_454_RR=700
+20	3128950	.	G	A	.	.	Sample=NA18998;GT=0/1;PCR_454_AR=606;PCR_454_RR=638
+20	3128950	.	G	A	.	.	Sample=NA19076;GT=0/1;PCR_454_AR=663;PCR_454_RR=643
+20	3128950	.	G	A	.	.	Sample=NA19088;GT=0/1;PCR_454_AR=492;PCR_454_RR=472
+20	3171356	.	T	C	.	.	Sample=NA12003;GT=0/0;PCR_454_AR=6;PCR_454_RR=1919
+20	3171356	.	T	C	.	.	Sample=NA12872;GT=0/0;PCR_454_AR=6;PCR_454_RR=2324
+20	3193990	.	G	T	.	.	Sample=NA12815;GT=0/0;PCR_454_AR=0;PCR_454_RR=1570
+20	3193990	.	G	T	.	.	Sample=NA18505;GT=0/0;PCR_454_AR=0;PCR_454_RR=1586
+20	3204083	.	G	A	.	.	Sample=HG00104;GT=0/1;PCR_454_AR=1059;PCR_454_RR=982
+20	3204083	.	G	A	.	.	Sample=HG00118;GT=0/1;PCR_454_AR=1190;PCR_454_RR=1178
+20	3204083	.	G	A	.	.	Sample=HG00122;GT=0/1;PCR_454_AR=1156;PCR_454_RR=1277
+20	3204083	.	G	A	.	.	Sample=HG00099;GT=1/1;PCR_454_AR=2171;PCR_454_RR=12
+20	3204083	.	G	A	.	.	Sample=HG00106;GT=1/1;PCR_454_AR=2027;PCR_454_RR=19
+20	3214580	.	C	T	.	.	Sample=HG00097;GT=0/1;PCR_454_AR=852;PCR_454_RR=784
+20	3214580	.	C	T	.	.	Sample=HG00099;GT=0/1;PCR_454_AR=628;PCR_454_RR=682
+20	3214580	.	C	T	.	.	Sample=HG00129;GT=0/1;PCR_454_AR=869;PCR_454_RR=844
+20	3214580	.	C	T	.	.	Sample=HG00130;GT=0/1;PCR_454_AR=651;PCR_454_RR=767
+20	3214580	.	C	T	.	.	Sample=HG00128;GT=1/1;PCR_454_AR=1378;PCR_454_RR=3
+20	3214802	.	T	C	.	.	Sample=NA18526;GT=0/1;PCR_454_AR=969;PCR_454_RR=1018
+20	3235915	.	T	C	.	.	Sample=HG00560;GT=0/1;PCR_454_AR=795;PCR_454_RR=798
+20	3235915	.	T	C	.	.	Sample=HG00566;GT=0/1;PCR_454_AR=688;PCR_454_RR=650
+20	3235915	.	T	C	.	.	Sample=HG00596;GT=0/1;PCR_454_AR=863;PCR_454_RR=935
+20	3235915	.	T	C	.	.	Sample=HG01124;GT=0/1;PCR_454_AR=802;PCR_454_RR=836
+20	3235915	.	T	C	.	.	Sample=NA18487;GT=0/1;PCR_454_AR=942;PCR_454_RR=968
+20	3274851	.	C	T	.	.	Sample=NA19704;GT=0/1;PCR_454_AR=486;PCR_454_RR=479
+20	3274851	.	C	T	.	.	Sample=NA20334;GT=0/1;PCR_454_AR=512;PCR_454_RR=512
+20	3274851	.	C	T	.	.	Sample=NA20336;GT=0/1;PCR_454_AR=510;PCR_454_RR=440
+20	3324372	.	G	C	.	.	Sample=NA19003;GT=0/1;PCR_454_AR=1902;PCR_454_RR=1898
+20	3362102	.	T	G	.	.	Sample=NA06994;GT=0/0;PCR_454_AR=0;PCR_454_RR=526
+20	3362102	.	T	G	.	.	Sample=NA12249;GT=0/0;PCR_454_AR=0;PCR_454_RR=465
+20	3515923	.	G	A	.	.	Sample=HG00122;GT=0/1;PCR_454_AR=237;PCR_454_RR=261
+20	3515923	.	G	A	.	.	Sample=HG00126;GT=0/1;PCR_454_AR=299;PCR_454_RR=293
+20	3515923	.	G	A	.	.	Sample=HG00130;GT=0/1;PCR_454_AR=307;PCR_454_RR=279
+20	3515923	.	G	A	.	.	Sample=HG00128;GT=1/1;PCR_454_AR=633;PCR_454_RR=4
+20	3515923	.	G	A	.	.	Sample=HG00129;GT=1/1;PCR_454_AR=580;PCR_454_RR=2
+20	3641233	.	G	T	.	.	Sample=NA20773;GT=0/0;PCR_454_AR=3;PCR_454_RR=1477
+20	3650204	.	G	A	.	.	Sample=HG00118;GT=0/1;PCR_454_AR=737;PCR_454_RR=771
+20	3650204	.	G	A	.	.	Sample=HG00126;GT=0/1;PCR_454_AR=518;PCR_454_RR=552
+20	3650204	.	G	A	.	.	Sample=HG00141;GT=0/1;PCR_454_AR=643;PCR_454_RR=668
+20	3650204	.	G	A	.	.	Sample=HG00143;GT=0/1;PCR_454_AR=549;PCR_454_RR=613
+20	3650204	.	G	A	.	.	Sample=HG00148;GT=0/1;PCR_454_AR=708;PCR_454_RR=830
+20	3652397	.	G	A	.	.	Sample=NA18635;GT=0/1;PCR_454_AR=1604;PCR_454_RR=1658
+20	3672827	.	A	T	.	.	Sample=HG00130;GT=0/0;PCR_454_AR=0;PCR_454_RR=941
+20	3672827	.	A	T	.	.	Sample=HG00349;GT=0/0;PCR_454_AR=2;PCR_454_RR=943
+20	3675119	.	G	T	.	.	Sample=NA20544;GT=0/1;PCR_454_AR=577;PCR_454_RR=657
+20	3687329	.	T	C	.	.	Sample=NA18532;GT=0/1;PCR_454_AR=702;PCR_454_RR=746
+20	3842125	.	C	G	.	.	Sample=NA12155;GT=0/1;PCR_454_AR=1193;PCR_454_RR=1178
+20	4680289	.	G	A	.	.	Sample=NA18856;GT=0/1;PCR_454_AR=1335;PCR_454_RR=1278
+20	4680289	.	G	A	.	.	Sample=NA19130;GT=0/1;PCR_454_AR=1273;PCR_454_RR=1286
+20	4680289	.	G	A	.	.	Sample=NA19213;GT=0/1;PCR_454_AR=1305;PCR_454_RR=1241
+20	4680289	.	G	A	.	.	Sample=NA19311;GT=0/1;PCR_454_AR=1332;PCR_454_RR=1400
+20	4680289	.	G	A	.	.	Sample=NA19332;GT=0/1;PCR_454_AR=1272;PCR_454_RR=1275
+20	4848511	.	G	A	.	.	Sample=NA19440;GT=0/0;PCR_454_AR=8;PCR_454_RR=2951
+20	4848511	.	G	A	.	.	Sample=NA19448;GT=0/1;PCR_454_AR=1278;PCR_454_RR=1434
+20	4848511	.	G	A	.	.	Sample=NA19461;GT=0/1;PCR_454_AR=1412;PCR_454_RR=1478
+20	5099300	.	A	G	.	.	Sample=NA19138;GT=0/1;PCR_454_AR=511;PCR_454_RR=496
+20	5903387	.	A	C	.	.	Sample=HG00566;GT=0/1;PCR_454_AR=1400;PCR_454_RR=1384
+20	5903387	.	A	C	.	.	Sample=HG01124;GT=0/1;PCR_454_AR=856;PCR_454_RR=1007
+20	5903387	.	A	C	.	.	Sample=HG01125;GT=0/1;PCR_454_AR=891;PCR_454_RR=816
+20	5903387	.	A	C	.	.	Sample=HG01149;GT=0/1;PCR_454_AR=1011;PCR_454_RR=959
+20	5903387	.	A	C	.	.	Sample=HG01278;GT=0/1;PCR_454_AR=1077;PCR_454_RR=1049
+20	5923222	.	C	T	.	.	Sample=HG00592;GT=0/1;PCR_454_AR=968;PCR_454_RR=950
+20	5923222	.	C	T	.	.	Sample=NA18567;GT=0/1;PCR_454_AR=678;PCR_454_RR=728
+20	5923222	.	C	T	.	.	Sample=NA18602;GT=0/1;PCR_454_AR=926;PCR_454_RR=988
+20	5923222	.	C	T	.	.	Sample=NA18624;GT=0/1;PCR_454_AR=991;PCR_454_RR=963
+20	5923222	.	C	T	.	.	Sample=NA18632;GT=0/1;PCR_454_AR=892;PCR_454_RR=906
+20	5943955	.	G	C	.	.	Sample=HG00565;GT=0/1;PCR_454_AR=259;PCR_454_RR=227
+20	5943955	.	G	C	.	.	Sample=HG00566;GT=0/1;PCR_454_AR=245;PCR_454_RR=235
+20	5943955	.	G	C	.	.	Sample=HG00577;GT=0/1;PCR_454_AR=264;PCR_454_RR=305
+20	5943955	.	G	C	.	.	Sample=HG00578;GT=0/1;PCR_454_AR=210;PCR_454_RR=261
+20	5943955	.	G	C	.	.	Sample=HG00593;GT=0/1;PCR_454_AR=261;PCR_454_RR=238
+20	6015109	.	G	A	.	.	Sample=NA20796;GT=0/1;PCR_454_AR=440;PCR_454_RR=500
+20	6060150	.	C	T	.	.	Sample=NA18961;GT=0/1;PCR_454_AR=384;PCR_454_RR=464
+20	7967973	.	G	A	.	.	Sample=NA19371;GT=0/1;PCR_454_AR=281;PCR_454_RR=506
+20	7967973	.	G	A	.	.	Sample=NA19390;GT=0/1;PCR_454_AR=410;PCR_454_RR=538
+20	8665657	.	G	A	.	.	Sample=NA19740;GT=0/1;PCR_454_AR=724;PCR_454_RR=703
+20	9453955	.	C	A	.	.	Sample=NA20314;GT=0/1;PCR_454_AR=1048;PCR_454_RR=1147
+20	9520132	.	G	A	.	.	Sample=HG00143;GT=0/1;PCR_454_AR=472;PCR_454_RR=583
+20	9520132	.	G	A	.	.	Sample=HG01624;GT=0/1;PCR_454_AR=589;PCR_454_RR=589
+20	9520132	.	G	A	.	.	Sample=NA12046;GT=0/1;PCR_454_AR=688;PCR_454_RR=708
+20	9520132	.	G	A	.	.	Sample=NA18517;GT=0/1;PCR_454_AR=566;PCR_454_RR=585
+20	9520132	.	G	A	.	.	Sample=NA18858;GT=0/1;PCR_454_AR=550;PCR_454_RR=561
+20	9543621	.	C	T	.	.	Sample=HG00097;GT=0/1;PCR_454_AR=499;PCR_454_RR=480
+20	9543621	.	C	T	.	.	Sample=HG00104;GT=0/1;PCR_454_AR=524;PCR_454_RR=480
+20	9543621	.	C	T	.	.	Sample=HG00112;GT=0/1;PCR_454_AR=467;PCR_454_RR=406
+20	9543621	.	C	T	.	.	Sample=HG00099;GT=1/1;PCR_454_AR=1321;PCR_454_RR=9
+20	9543621	.	C	T	.	.	Sample=HG00106;GT=1/1;PCR_454_AR=802;PCR_454_RR=6
+20	9547022	.	G	A	.	.	Sample=NA18924;GT=0/1;PCR_454_AR=853;PCR_454_RR=944
+20	9560813	.	T	C	.	.	Sample=NA12761;GT=0/1;PCR_454_AR=692;PCR_454_RR=734
+20	10030206	.	C	T	.	.	Sample=NA19175;GT=0/1;PCR_454_AR=784;PCR_454_RR=759
+20	10030206	.	C	T	.	.	Sample=NA19380;GT=0/1;PCR_454_AR=781;PCR_454_RR=739
+20	10030206	.	C	T	.	.	Sample=NA19446;GT=0/1;PCR_454_AR=533;PCR_454_RR=540
+20	13098183	.	A	C	.	.	Sample=NA19453;GT=0/1;PCR_454_AR=857;PCR_454_RR=1146
+20	16253907	.	C	A	.	.	Sample=NA19087;GT=0/1;PCR_454_AR=868;PCR_454_RR=854
+20	16254032	.	G	A	.	.	Sample=NA19651;GT=0/1;PCR_454_AR=299;PCR_454_RR=263
+20	16485159	.	T	G	.	.	Sample=NA18625;GT=0/1;PCR_454_AR=160;PCR_454_RR=1004
+20	17474781	.	G	A	.	.	Sample=NA18870;GT=0/1;PCR_454_AR=496;PCR_454_RR=536
+20	17585255	.	C	G	.	.	Sample=NA18528;GT=0/1;PCR_454_AR=370;PCR_454_RR=390
+20	17923814	.	C	T	.	.	Sample=HG00104;GT=0/0;PCR_454_AR=1;PCR_454_RR=1854
+20	17923814	.	C	T	.	.	Sample=HG00126;GT=0/0;PCR_454_AR=1;PCR_454_RR=1724
+20	17928182	.	T	G	.	.	Sample=NA18522;GT=0/1;PCR_454_AR=222;PCR_454_RR=1564
+20	17931030	.	C	G	.	.	Sample=NA20508;GT=0/1;PCR_454_AR=495;PCR_454_RR=446
+20	17933265	.	G	A	.	.	Sample=NA19137;GT=0/1;PCR_454_AR=300;PCR_454_RR=315
+20	17968811	.	C	G	.	.	Sample=NA19222;GT=0/1;PCR_454_AR=150;PCR_454_RR=189
+20	18123396	.	A	G	.	.	Sample=NA20507;GT=0/0;PCR_454_AR=5;PCR_454_RR=2239
+20	18125941	.	T	C	.	.	Sample=NA12006;GT=0/0;PCR_454_AR=2;PCR_454_RR=2354
+20	18125941	.	T	C	.	.	Sample=NA12762;GT=0/0;PCR_454_AR=4;PCR_454_RR=1116
+20	18374912	.	T	A	.	.	Sample=NA19189;GT=0/1;PCR_454_AR=896;PCR_454_RR=888
+20	18440904	.	G	C	.	.	Sample=NA19058;GT=0/1;PCR_454_AR=685;PCR_454_RR=881
+20	19698200	.	C	T	.	.	Sample=NA18574;GT=0/1;PCR_454_AR=1012;PCR_454_RR=1086
+20	20020489	.	T	C	.	.	Sample=NA19000;GT=0/1;PCR_454_AR=459;PCR_454_RR=436
+20	20028425	.	C	T	.	.	Sample=NA20787;GT=0/1;PCR_454_AR=687;PCR_454_RR=739
+20	20033171	.	G	A	.	.	Sample=NA19468;GT=0/0;PCR_454_AR=109;PCR_454_RR=1866
+20	20051634	.	A	G	.	.	Sample=NA19711;GT=0/1;PCR_454_AR=659;PCR_454_RR=2324
+20	20051634	.	A	G	.	.	Sample=NA20126;GT=0/1;PCR_454_AR=687;PCR_454_RR=2379
+20	20177371	.	T	C	.	.	Sample=NA19713;GT=0/1;PCR_454_AR=882;PCR_454_RR=785
+20	21346240	.	C	T	.	.	Sample=HG01125;GT=0/1;PCR_454_AR=707;PCR_454_RR=711
+20	21346240	.	C	T	.	.	Sample=NA18489;GT=0/1;PCR_454_AR=670;PCR_454_RR=648
+20	21346240	.	C	T	.	.	Sample=NA18498;GT=0/1;PCR_454_AR=706;PCR_454_RR=667
+20	21346240	.	C	T	.	.	Sample=NA18502;GT=0/1;PCR_454_AR=698;PCR_454_RR=678
+20	21346240	.	C	T	.	.	Sample=NA18505;GT=1/1;PCR_454_AR=1096;PCR_454_RR=2
+20	21494183	.	C	T	.	.	Sample=HG00128;GT=0/1;PCR_454_AR=556;PCR_454_RR=605
+20	21494183	.	C	T	.	.	Sample=HG00151;GT=0/1;PCR_454_AR=465;PCR_454_RR=425
+20	21494183	.	C	T	.	.	Sample=HG00234;GT=0/1;PCR_454_AR=583;PCR_454_RR=487
+20	21494183	.	C	T	.	.	Sample=HG00355;GT=0/1;PCR_454_AR=608;PCR_454_RR=521
+20	21494183	.	C	T	.	.	Sample=HG00362;GT=0/1;PCR_454_AR=518;PCR_454_RR=577
+20	21687304	.	C	T	.	.	Sample=NA19657;GT=0/1;PCR_454_AR=804;PCR_454_RR=862
+20	23028428	.	C	T	.	.	Sample=NA18970;GT=0/1;PCR_454_AR=360;PCR_454_RR=418
+20	23028637	.	C	G	.	.	Sample=NA18517;GT=0/1;PCR_454_AR=358;PCR_454_RR=374
+20	23028637	.	C	G	.	.	Sample=NA19118;GT=0/1;PCR_454_AR=502;PCR_454_RR=432
+20	23420987	.	G	T	.	.	Sample=NA19076;GT=0/0;PCR_454_AR=20;PCR_454_RR=1732
+20	23420993	.	C	G	.	.	Sample=NA19076;GT=0/0;PCR_454_AR=40;PCR_454_RR=3495
+20	23424637	.	C	T	.	.	Sample=HG00126;GT=0/1;PCR_454_AR=766;PCR_454_RR=721
+20	23424637	.	C	T	.	.	Sample=HG00150;GT=0/1;PCR_454_AR=444;PCR_454_RR=435
+20	23424637	.	C	T	.	.	Sample=HG00247;GT=0/1;PCR_454_AR=510;PCR_454_RR=486
+20	23424637	.	C	T	.	.	Sample=HG00565;GT=0/1;PCR_454_AR=684;PCR_454_RR=609
+20	23424637	.	C	T	.	.	Sample=HG00593;GT=0/1;PCR_454_AR=640;PCR_454_RR=676
+20	23545657	.	A	C	.	.	Sample=NA18924;GT=0/1;PCR_454_AR=767;PCR_454_RR=780
+20	23548918	.	T	C	.	.	Sample=NA18501;GT=0/1;PCR_454_AR=1397;PCR_454_RR=1168
+20	23548918	.	T	C	.	.	Sample=NA18502;GT=0/1;PCR_454_AR=1373;PCR_454_RR=1383
+20	23548918	.	T	C	.	.	Sample=NA18856;GT=0/1;PCR_454_AR=1376;PCR_454_RR=1446
+20	23548918	.	T	C	.	.	Sample=NA18907;GT=0/1;PCR_454_AR=1522;PCR_454_RR=1533
+20	23548918	.	T	C	.	.	Sample=NA19036;GT=0/1;PCR_454_AR=1549;PCR_454_RR=1624
+20	23667793	.	G	T	.	.	Sample=NA11994;GT=0/0;PCR_454_AR=135;PCR_454_RR=1637
+20	23667793	.	G	T	.	.	Sample=NA12400;GT=0/1;PCR_454_AR=651;PCR_454_RR=619
+20	23667793	.	G	T	.	.	Sample=NA18527;GT=0/1;PCR_454_AR=816;PCR_454_RR=732
+20	23667793	.	G	T	.	.	Sample=NA18566;GT=0/1;PCR_454_AR=928;PCR_454_RR=2446
+20	23667793	.	G	T	.	.	Sample=NA19064;GT=0/1;PCR_454_AR=892;PCR_454_RR=2346
+20	23667834	.	A	C	.	.	Sample=NA18510;GT=0/0;PCR_454_AR=27;PCR_454_RR=622
+20	23667834	.	A	C	.	.	Sample=NA18858;GT=0/0;PCR_454_AR=32;PCR_454_RR=615
+20	23731469	.	G	T	.	.	Sample=NA20544;GT=0/1;PCR_454_AR=292;PCR_454_RR=376
+20	23804690	.	A	C	.	.	Sample=NA19749;GT=0/1;PCR_454_AR=1141;PCR_454_RR=1145
+20	23807156	.	G	C	.	.	Sample=HG00129;GT=0/0;PCR_454_AR=0;PCR_454_RR=1447
+20	23807156	.	G	C	.	.	Sample=HG00130;GT=0/0;PCR_454_AR=0;PCR_454_RR=1603
+20	23860201	.	C	T	.	.	Sample=NA18553;GT=0/1;PCR_454_AR=722;PCR_454_RR=657
+20	23965921	.	G	A	.	.	Sample=NA18549;GT=0/0;PCR_454_AR=21;PCR_454_RR=582
+20	23965921	.	G	A	.	.	Sample=NA19000;GT=0/0;PCR_454_AR=19;PCR_454_RR=337
+20	24523782	.	G	A	.	.	Sample=NA19921;GT=0/1;PCR_454_AR=933;PCR_454_RR=1005
+20	24523986	.	C	A	.	.	Sample=HG00104;GT=0/1;PCR_454_AR=1056;PCR_454_RR=1346
+20	24954343	.	G	A	.	.	Sample=NA19146;GT=0/1;PCR_454_AR=1208;PCR_454_RR=1132
+20	25058490	.	T	G	.	.	Sample=NA11830;GT=0/0;PCR_454_AR=5;PCR_454_RR=1757
+20	25187224	.	A	G	.	.	Sample=NA19137;GT=0/1;PCR_454_AR=69;PCR_454_RR=566
+20	25203611	.	T	C	.	.	Sample=NA12006;GT=0/1;PCR_454_AR=1326;PCR_454_RR=1209
+20	25252066	.	A	G	.	.	Sample=NA18637;GT=0/1;PCR_454_AR=1208;PCR_454_RR=1230
+20	25262768	.	G	A	.	.	Sample=HG00099;GT=0/1;PCR_454_AR=920;PCR_454_RR=727
+20	25262768	.	G	A	.	.	Sample=HG00106;GT=0/1;PCR_454_AR=733;PCR_454_RR=613
+20	25262768	.	G	A	.	.	Sample=HG00112;GT=0/1;PCR_454_AR=756;PCR_454_RR=723
+20	25262768	.	G	A	.	.	Sample=HG00130;GT=0/1;PCR_454_AR=854;PCR_454_RR=827
+20	25262768	.	G	A	.	.	Sample=HG00152;GT=0/1;PCR_454_AR=798;PCR_454_RR=764
+20	25277132	.	C	T	.	.	Sample=NA18861;GT=0/1;PCR_454_AR=415;PCR_454_RR=446
+20	25434162	.	C	T	.	.	Sample=NA19346;GT=0/1;PCR_454_AR=566;PCR_454_RR=613
+20	25434162	.	C	T	.	.	Sample=NA19395;GT=0/1;PCR_454_AR=504;PCR_454_RR=531
+20	25439088	.	C	T	.	.	Sample=NA19095;GT=0/0;PCR_454_AR=1;PCR_454_RR=1220
+20	25439088	.	C	T	.	.	Sample=NA19923;GT=0/1;PCR_454_AR=575;PCR_454_RR=834
+20	25457145	.	G	A	.	.	Sample=NA12842;GT=0/1;PCR_454_AR=333;PCR_454_RR=438
+20	25457559	.	G	A	.	.	Sample=NA19159;GT=0/1;PCR_454_AR=1225;PCR_454_RR=1285
+20	25457665	.	C	T	.	.	Sample=NA20341;GT=0/1;PCR_454_AR=627;PCR_454_RR=1348
+20	25459659	.	T	C	.	.	Sample=NA18647;GT=0/0;PCR_454_AR=5;PCR_454_RR=2809
+20	25459659	.	T	C	.	.	Sample=NA18748;GT=0/0;PCR_454_AR=5;PCR_454_RR=2184
+20	25459659	.	T	C	.	.	Sample=HG01274;GT=0/1;PCR_454_AR=1246;PCR_454_RR=1375
+20	25459659	.	T	C	.	.	Sample=NA12275;GT=0/1;PCR_454_AR=1183;PCR_454_RR=1148
+20	25459659	.	T	C	.	.	Sample=NA12718;GT=0/1;PCR_454_AR=1017;PCR_454_RR=1225
+20	25478961	.	G	A	.	.	Sample=HG00104;GT=0/0;PCR_454_AR=1;PCR_454_RR=1933
+20	25478961	.	G	A	.	.	Sample=HG00234;GT=0/0;PCR_454_AR=0;PCR_454_RR=1964
+20	25478961	.	G	A	.	.	Sample=HG00364;GT=0/0;PCR_454_AR=2;PCR_454_RR=1909
+20	25478961	.	G	A	.	.	Sample=HG00593;GT=0/0;PCR_454_AR=2;PCR_454_RR=2173
+20	25478961	.	G	A	.	.	Sample=HG01271;GT=0/0;PCR_454_AR=0;PCR_454_RR=2082
+20	30407977	.	A	G	.	.	Sample=NA12287;GT=0/1;PCR_454_AR=1313;PCR_454_RR=1488
+20	30432438	.	C	T	.	.	Sample=NA19352;GT=0/1;PCR_454_AR=1043;PCR_454_RR=964
+20	30432438	.	C	T	.	.	Sample=NA19654;GT=0/1;PCR_454_AR=937;PCR_454_RR=1465
+20	30432570	.	T	C	.	.	Sample=NA18510;GT=0/1;PCR_454_AR=1224;PCR_454_RR=1413
+20	30432570	.	T	C	.	.	Sample=NA18858;GT=0/1;PCR_454_AR=1050;PCR_454_RR=1052
+20	30432570	.	T	C	.	.	Sample=NA18868;GT=0/1;PCR_454_AR=1087;PCR_454_RR=966
+20	30432570	.	T	C	.	.	Sample=NA18871;GT=0/1;PCR_454_AR=1178;PCR_454_RR=1344
+20	30432570	.	T	C	.	.	Sample=NA18522;GT=1/1;PCR_454_AR=1873;PCR_454_RR=7
+20	30602754	.	C	T	.	.	Sample=NA19749;GT=0/1;PCR_454_AR=63;PCR_454_RR=409
+20	30729618	.	G	A	.	.	Sample=NA11994;GT=0/0;PCR_454_AR=0;PCR_454_RR=1866
+20	30729618	.	G	A	.	.	Sample=NA07037;GT=0/1;PCR_454_AR=1373;PCR_454_RR=1435
+20	30729618	.	G	A	.	.	Sample=NA12058;GT=0/1;PCR_454_AR=963;PCR_454_RR=990
+20	30729618	.	G	A	.	.	Sample=NA12144;GT=0/1;PCR_454_AR=1419;PCR_454_RR=1136
+20	30729618	.	G	A	.	.	Sample=NA12282;GT=0/1;PCR_454_AR=1353;PCR_454_RR=1148
+20	30789767	.	G	A	.	.	Sample=HG00350;GT=0/0;PCR_454_AR=36;PCR_454_RR=553
+20	30897726	.	G	A	.	.	Sample=NA20507;GT=0/0;PCR_454_AR=239;PCR_454_RR=2404
+20	30918043	.	C	T	.	.	Sample=NA19707;GT=0/1;PCR_454_AR=1147;PCR_454_RR=1123
+20	30918043	.	C	T	.	.	Sample=NA20775;GT=0/1;PCR_454_AR=1234;PCR_454_RR=1140
+20	31021429	.	G	C	.	.	Sample=NA18870;GT=0/1;PCR_454_AR=747;PCR_454_RR=929
+20	31021429	.	G	C	.	.	Sample=NA19319;GT=0/1;PCR_454_AR=585;PCR_454_RR=657
+20	31021429	.	G	C	.	.	Sample=NA19445;GT=0/1;PCR_454_AR=531;PCR_454_RR=553
+20	31021429	.	G	C	.	.	Sample=NA20127;GT=0/1;PCR_454_AR=661;PCR_454_RR=679
+20	31021429	.	G	C	.	.	Sample=NA20317;GT=0/1;PCR_454_AR=874;PCR_454_RR=917
+20	31022764	.	C	T	.	.	Sample=NA18498;GT=0/1;PCR_454_AR=1455;PCR_454_RR=1259
+20	31022764	.	C	T	.	.	Sample=NA18507;GT=0/1;PCR_454_AR=1020;PCR_454_RR=972
+20	31022764	.	C	T	.	.	Sample=NA18511;GT=0/1;PCR_454_AR=1339;PCR_454_RR=1297
+20	31022764	.	C	T	.	.	Sample=NA18856;GT=0/1;PCR_454_AR=1582;PCR_454_RR=1572
+20	31022764	.	C	T	.	.	Sample=NA18870;GT=0/1;PCR_454_AR=1642;PCR_454_RR=1613
+20	31024033	.	G	A	.	.	Sample=HG01356;GT=0/1;PCR_454_AR=1045;PCR_454_RR=1002
+20	31024033	.	G	A	.	.	Sample=NA18537;GT=0/1;PCR_454_AR=794;PCR_454_RR=788
+20	31024033	.	G	A	.	.	Sample=NA18557;GT=0/1;PCR_454_AR=830;PCR_454_RR=795
+20	31024033	.	G	A	.	.	Sample=NA18558;GT=0/1;PCR_454_AR=833;PCR_454_RR=878
+20	31024033	.	G	A	.	.	Sample=NA18637;GT=1/1;PCR_454_AR=1528;PCR_454_RR=6
+20	31040782	.	G	A	.	.	Sample=HG00097;GT=0/1;PCR_454_AR=978;PCR_454_RR=1231
+20	31040782	.	G	A	.	.	Sample=HG00179;GT=0/1;PCR_454_AR=1054;PCR_454_RR=993
+20	31040782	.	G	A	.	.	Sample=HG01620;GT=0/1;PCR_454_AR=1091;PCR_454_RR=1111
+20	31040782	.	G	A	.	.	Sample=NA12273;GT=0/1;PCR_454_AR=1073;PCR_454_RR=1182
+20	31040782	.	G	A	.	.	Sample=NA12341;GT=0/1;PCR_454_AR=1102;PCR_454_RR=1318
+20	31375167	.	G	A	.	.	Sample=NA18486;GT=0/1;PCR_454_AR=563;PCR_454_RR=523
+20	31375167	.	G	A	.	.	Sample=NA19113;GT=0/1;PCR_454_AR=628;PCR_454_RR=620
+20	31388076	.	C	T	.	.	Sample=NA18504;GT=0/1;PCR_454_AR=809;PCR_454_RR=773
+20	31388076	.	C	T	.	.	Sample=NA18519;GT=0/1;PCR_454_AR=683;PCR_454_RR=752
+20	31388076	.	C	T	.	.	Sample=NA18856;GT=0/1;PCR_454_AR=1012;PCR_454_RR=1073
+20	31388076	.	C	T	.	.	Sample=NA18917;GT=0/1;PCR_454_AR=888;PCR_454_RR=931
+20	31388076	.	C	T	.	.	Sample=NA18522;GT=1/1;PCR_454_AR=1422;PCR_454_RR=2
+20	31424592	.	C	T	.	.	Sample=NA19146;GT=0/1;PCR_454_AR=237;PCR_454_RR=257
+20	31434427	.	A	G	.	.	Sample=NA11995;GT=0/1;PCR_454_AR=325;PCR_454_RR=325
+20	31604884	.	A	G	.	.	Sample=NA12748;GT=0/1;PCR_454_AR=1098;PCR_454_RR=1153
+20	31606483	.	G	C	.	.	Sample=NA18740;GT=0/1;PCR_454_AR=595;PCR_454_RR=964
+20	31606907	.	G	A	.	.	Sample=NA19753;GT=0/0;PCR_454_AR=0;PCR_454_RR=1627
+20	31606907	.	G	A	.	.	Sample=NA19747;GT=0/1;PCR_454_AR=952;PCR_454_RR=884
+20	31622899	.	A	G	.	.	Sample=NA19038;GT=0/1;PCR_454_AR=196;PCR_454_RR=111
+20	31626754	.	G	A	.	.	Sample=NA18579;GT=0/1;PCR_454_AR=941;PCR_454_RR=902
+20	31643241	.	A	C	.	.	Sample=NA18622;GT=0/1;PCR_454_AR=832;PCR_454_RR=877
+20	31659074	.	G	A	.	.	Sample=NA19449;GT=0/1;PCR_454_AR=915;PCR_454_RR=863
+20	31672711	.	A	G	.	.	Sample=NA20754;GT=0/1;PCR_454_AR=762;PCR_454_RR=820
+20	31680333	.	C	T	.	.	Sample=HG00156;GT=0/1;PCR_454_AR=446;PCR_454_RR=438
+20	31680333	.	C	T	.	.	Sample=HG00235;GT=0/1;PCR_454_AR=525;PCR_454_RR=435
+20	31680333	.	C	T	.	.	Sample=HG01125;GT=0/1;PCR_454_AR=433;PCR_454_RR=415
+20	31680333	.	C	T	.	.	Sample=NA12043;GT=0/1;PCR_454_AR=559;PCR_454_RR=477
+20	31680333	.	C	T	.	.	Sample=NA12046;GT=0/1;PCR_454_AR=364;PCR_454_RR=330
+20	31695565	.	C	T	.	.	Sample=NA19054;GT=0/1;PCR_454_AR=988;PCR_454_RR=944
+20	31889182	.	T	C	.	.	Sample=HG01277;GT=0/1;PCR_454_AR=594;PCR_454_RR=639
+20	31889182	.	T	C	.	.	Sample=HG01278;GT=0/1;PCR_454_AR=533;PCR_454_RR=540
+20	31889182	.	T	C	.	.	Sample=HG01623;GT=0/1;PCR_454_AR=703;PCR_454_RR=668
+20	31889182	.	T	C	.	.	Sample=NA18487;GT=0/1;PCR_454_AR=644;PCR_454_RR=647
+20	31889182	.	T	C	.	.	Sample=NA18486;GT=1/1;PCR_454_AR=1419;PCR_454_RR=15
+20	31890796	.	G	A	.	.	Sample=NA18595;GT=0/1;PCR_454_AR=36;PCR_454_RR=49
+20	31967485	.	T	C	.	.	Sample=NA18757;GT=0/0;PCR_454_AR=4;PCR_454_RR=1506
+20	32162066	.	G	C	.	.	Sample=HG00099;GT=0/1;PCR_454_AR=98;PCR_454_RR=92
+20	32162066	.	G	C	.	.	Sample=NA12282;GT=0/1;PCR_454_AR=72;PCR_454_RR=74
+20	32162066	.	G	C	.	.	Sample=NA12342;GT=0/1;PCR_454_AR=105;PCR_454_RR=134
+20	32162066	.	G	C	.	.	Sample=NA12778;GT=0/1;PCR_454_AR=94;PCR_454_RR=122
+20	32162066	.	G	C	.	.	Sample=NA19773;GT=0/1;PCR_454_AR=84;PCR_454_RR=115
+20	32295637	.	A	G	.	.	Sample=NA19204;GT=0/1;PCR_454_AR=1263;PCR_454_RR=1230
+20	32298533	.	G	A	.	.	Sample=HG01125;GT=0/1;PCR_454_AR=1577;PCR_454_RR=1574
+20	32298533	.	G	A	.	.	Sample=NA18510;GT=0/1;PCR_454_AR=1537;PCR_454_RR=1597
+20	32298533	.	G	A	.	.	Sample=NA18520;GT=0/1;PCR_454_AR=1689;PCR_454_RR=1754
+20	32298533	.	G	A	.	.	Sample=NA19099;GT=0/1;PCR_454_AR=1900;PCR_454_RR=1940
+20	32298533	.	G	A	.	.	Sample=NA19129;GT=0/1;PCR_454_AR=1900;PCR_454_RR=1840
+20	32336754	.	G	A	.	.	Sample=HG00358;GT=0/1;PCR_454_AR=1185;PCR_454_RR=1161
+20	32336754	.	G	A	.	.	Sample=HG00565;GT=0/1;PCR_454_AR=1018;PCR_454_RR=958
+20	32336754	.	G	A	.	.	Sample=HG00595;GT=0/1;PCR_454_AR=1201;PCR_454_RR=1222
+20	32336754	.	G	A	.	.	Sample=NA18532;GT=0/1;PCR_454_AR=1204;PCR_454_RR=1235
+20	32336754	.	G	A	.	.	Sample=NA18542;GT=1/1;PCR_454_AR=2997;PCR_454_RR=11
+20	32358043	.	A	T	.	.	Sample=NA18955;GT=0/1;PCR_454_AR=1050;PCR_454_RR=1022
+20	32881901	.	T	C	.	.	Sample=NA19257;GT=0/1;PCR_454_AR=1007;PCR_454_RR=966
+20	33328321	.	C	T	.	.	Sample=NA18487;GT=0/1;PCR_454_AR=637;PCR_454_RR=629
+20	33328321	.	C	T	.	.	Sample=NA18516;GT=0/1;PCR_454_AR=613;PCR_454_RR=605
+20	33328321	.	C	T	.	.	Sample=NA19044;GT=0/1;PCR_454_AR=629;PCR_454_RR=661
+20	33328321	.	C	T	.	.	Sample=NA19102;GT=0/1;PCR_454_AR=680;PCR_454_RR=625
+20	33328321	.	C	T	.	.	Sample=NA19175;GT=0/1;PCR_454_AR=652;PCR_454_RR=703
+20	33330691	.	C	G	.	.	Sample=NA19189;GT=0/1;PCR_454_AR=604;PCR_454_RR=575
+20	33433247	.	G	A	.	.	Sample=NA11919;GT=0/1;PCR_454_AR=196;PCR_454_RR=195
+20	33447313	.	C	T	.	.	Sample=HG01125;GT=0/1;PCR_454_AR=260;PCR_454_RR=285
+20	33447313	.	C	T	.	.	Sample=NA18504;GT=0/1;PCR_454_AR=231;PCR_454_RR=217
+20	33447313	.	C	T	.	.	Sample=NA18517;GT=0/1;PCR_454_AR=298;PCR_454_RR=311
+20	33447313	.	C	T	.	.	Sample=NA18520;GT=0/1;PCR_454_AR=254;PCR_454_RR=256
+20	33447313	.	C	T	.	.	Sample=NA18522;GT=0/1;PCR_454_AR=286;PCR_454_RR=277
+20	33517251	.	C	T	.	.	Sample=HG00126;GT=0/1;PCR_454_AR=685;PCR_454_RR=676
+20	33517301	.	G	A	.	.	Sample=NA20282;GT=0/1;PCR_454_AR=1082;PCR_454_RR=1076
+20	33523396	.	A	C	.	.	Sample=NA18910;GT=0/1;PCR_454_AR=879;PCR_454_RR=933
+20	33572880	.	C	T	.	.	Sample=NA20516;GT=0/1;PCR_454_AR=935;PCR_454_RR=847
+20	33575007	.	C	T	.	.	Sample=NA19118;GT=0/1;PCR_454_AR=793;PCR_454_RR=659
+20	33575043	.	C	T	.	.	Sample=NA19036;GT=0/1;PCR_454_AR=972;PCR_454_RR=919
+20	33575043	.	C	T	.	.	Sample=NA19308;GT=0/1;PCR_454_AR=801;PCR_454_RR=728
+20	33575043	.	C	T	.	.	Sample=NA19434;GT=0/1;PCR_454_AR=825;PCR_454_RR=915
+20	33575043	.	C	T	.	.	Sample=NA19439;GT=0/1;PCR_454_AR=1001;PCR_454_RR=1073
+20	33575043	.	C	T	.	.	Sample=NA19466;GT=0/1;PCR_454_AR=936;PCR_454_RR=931
+20	33583330	.	A	G	.	.	Sample=HG00097;GT=1/1;PCR_454_AR=651;PCR_454_RR=5
+20	33583330	.	A	G	.	.	Sample=HG00099;GT=1/1;PCR_454_AR=326;PCR_454_RR=0
+20	33583330	.	A	G	.	.	Sample=HG00104;GT=1/1;PCR_454_AR=430;PCR_454_RR=2
+20	33583330	.	A	G	.	.	Sample=HG00106;GT=1/1;PCR_454_AR=613;PCR_454_RR=3
+20	33583330	.	A	G	.	.	Sample=HG00112;GT=1/1;PCR_454_AR=632;PCR_454_RR=6
+20	33584196	.	C	T	.	.	Sample=NA12286;GT=0/1;PCR_454_AR=989;PCR_454_RR=1638
+20	33584196	.	C	T	.	.	Sample=NA12750;GT=0/1;PCR_454_AR=886;PCR_454_RR=1206
+20	33584196	.	C	T	.	.	Sample=NA19750;GT=0/1;PCR_454_AR=1179;PCR_454_RR=1155
+20	33584196	.	C	T	.	.	Sample=NA20807;GT=0/1;PCR_454_AR=1089;PCR_454_RR=1724
+20	33584196	.	C	T	.	.	Sample=NA20826;GT=0/1;PCR_454_AR=1373;PCR_454_RR=1259
+20	33587399	.	G	A	.	.	Sample=NA19328;GT=0/1;PCR_454_AR=893;PCR_454_RR=754
+20	33711732	.	T	A	.	.	Sample=NA19347;GT=0/1;PCR_454_AR=887;PCR_454_RR=946
+20	33874473	.	C	A	.	.	Sample=NA18626;GT=0/1;PCR_454_AR=1001;PCR_454_RR=1012
+20	33874719	.	C	T	.	.	Sample=HG00099;GT=0/1;PCR_454_AR=585;PCR_454_RR=542
+20	33874719	.	C	T	.	.	Sample=HG00141;GT=0/1;PCR_454_AR=499;PCR_454_RR=508
+20	33874719	.	C	T	.	.	Sample=HG00142;GT=0/1;PCR_454_AR=541;PCR_454_RR=540
+20	33874719	.	C	T	.	.	Sample=HG00143;GT=0/1;PCR_454_AR=699;PCR_454_RR=604
+20	33874719	.	C	T	.	.	Sample=HG00156;GT=0/1;PCR_454_AR=722;PCR_454_RR=617
+20	34092317	.	C	A	.	.	Sample=HG00128;GT=0/0;PCR_454_AR=0;PCR_454_RR=1205
+20	34092317	.	C	A	.	.	Sample=HG00266;GT=0/0;PCR_454_AR=3;PCR_454_RR=3354
+20	34218898	.	A	G	.	.	Sample=NA12763;GT=0/1;PCR_454_AR=295;PCR_454_RR=291
+20	34292440	.	T	C	.	.	Sample=NA18639;GT=0/1;PCR_454_AR=481;PCR_454_RR=572
+20	34317286	.	G	A	.	.	Sample=NA19204;GT=0/1;PCR_454_AR=665;PCR_454_RR=705
+20	34611604	.	C	T	.	.	Sample=NA11893;GT=0/1;PCR_454_AR=1180;PCR_454_RR=1243
+20	35060852	.	G	A	.	.	Sample=NA12283;GT=0/1;PCR_454_AR=433;PCR_454_RR=444
+20	35060852	.	G	A	.	.	Sample=NA19676;GT=0/1;PCR_454_AR=368;PCR_454_RR=421
+20	35068262	.	A	C	.	.	Sample=NA20759;GT=0/1;PCR_454_AR=1272;PCR_454_RR=1190
+20	35075140	.	C	T	.	.	Sample=NA19444;GT=0/1;PCR_454_AR=1174;PCR_454_RR=605
+20	35075140	.	C	T	.	.	Sample=NA19448;GT=0/1;PCR_454_AR=1574;PCR_454_RR=932
+20	35075309	.	G	A	.	.	Sample=NA18549;GT=0/1;PCR_454_AR=923;PCR_454_RR=1559
+20	35075309	.	G	A	.	.	Sample=NA19391;GT=0/1;PCR_454_AR=1114;PCR_454_RR=1064
+20	35075309	.	G	A	.	.	Sample=NA19397;GT=0/1;PCR_454_AR=1198;PCR_454_RR=1233
+20	35176551	.	A	G	.	.	Sample=NA20289;GT=0/1;PCR_454_AR=532;PCR_454_RR=1682
+20	35207263	.	G	A	.	.	Sample=HG00234;GT=0/1;PCR_454_AR=235;PCR_454_RR=221
+20	35219406	.	G	C	.	.	Sample=HG00105;GT=0/0;PCR_454_AR=57;PCR_454_RR=585
+20	35219406	.	G	C	.	.	Sample=HG00130;GT=0/0;PCR_454_AR=58;PCR_454_RR=574
+20	35438474	.	G	A	.	.	Sample=NA18642;GT=0/1;PCR_454_AR=1030;PCR_454_RR=1093
+20	35507540	.	G	A	.	.	Sample=NA19740;GT=0/1;PCR_454_AR=466;PCR_454_RR=584
+20	35539699	.	T	C	.	.	Sample=NA12717;GT=0/1;PCR_454_AR=336;PCR_454_RR=421
+20	35812756	.	C	T	.	.	Sample=NA19726;GT=0/1;PCR_454_AR=1085;PCR_454_RR=1070
+20	35944759	.	A	C	.	.	Sample=NA11831;GT=0/0;PCR_454_AR=1;PCR_454_RR=1726
+20	35944759	.	A	C	.	.	Sample=NA11832;GT=0/0;PCR_454_AR=3;PCR_454_RR=1809
+20	36024598	.	C	T	.	.	Sample=NA19682;GT=0/1;PCR_454_AR=677;PCR_454_RR=797
+20	36024598	.	C	T	.	.	Sample=NA20528;GT=0/1;PCR_454_AR=691;PCR_454_RR=703
+20	36030944	.	T	C	.	.	Sample=NA18618;GT=0/0;PCR_454_AR=0;PCR_454_RR=985
+20	36030944	.	T	C	.	.	Sample=NA18626;GT=0/0;PCR_454_AR=2;PCR_454_RR=778
+20	36030944	.	T	C	.	.	Sample=NA18916;GT=0/1;PCR_454_AR=454;PCR_454_RR=444
+20	36030944	.	T	C	.	.	Sample=NA19150;GT=0/1;PCR_454_AR=471;PCR_454_RR=509
+20	36488331	.	A	G	.	.	Sample=NA20340;GT=0/1;PCR_454_AR=1388;PCR_454_RR=1472
+20	36640610	.	C	G	.	.	Sample=NA18508;GT=0/1;PCR_454_AR=985;PCR_454_RR=1026
+20	36641870	.	G	A	.	.	Sample=HG00106;GT=0/1;PCR_454_AR=1062;PCR_454_RR=1095
+20	36641870	.	G	A	.	.	Sample=NA11893;GT=0/1;PCR_454_AR=976;PCR_454_RR=1033
+20	36641870	.	G	A	.	.	Sample=NA12399;GT=0/1;PCR_454_AR=971;PCR_454_RR=973
+20	36641870	.	G	A	.	.	Sample=NA12489;GT=0/1;PCR_454_AR=1107;PCR_454_RR=1037
+20	36641870	.	G	A	.	.	Sample=NA12749;GT=0/1;PCR_454_AR=947;PCR_454_RR=885
+20	36775155	.	A	G	.	.	Sample=NA19067;GT=0/1;PCR_454_AR=771;PCR_454_RR=772
+20	36775233	.	G	A	.	.	Sample=NA19352;GT=0/1;PCR_454_AR=732;PCR_454_RR=723
+20	36784261	.	G	A	.	.	Sample=NA19171;GT=0/1;PCR_454_AR=1197;PCR_454_RR=1200
+20	36841848	.	C	T	.	.	Sample=NA19449;GT=0/1;PCR_454_AR=402;PCR_454_RR=394
+20	36869075	.	G	A	.	.	Sample=NA19185;GT=0/1;PCR_454_AR=1430;PCR_454_RR=1382
+20	36869206	.	C	T	.	.	Sample=NA20287;GT=0/1;PCR_454_AR=584;PCR_454_RR=626
+20	36979308	.	T	A	.	.	Sample=NA11894;GT=0/1;PCR_454_AR=973;PCR_454_RR=1087
+20	37001736	.	C	T	.	.	Sample=NA18987;GT=0/1;PCR_454_AR=122;PCR_454_RR=88
+20	39798902	.	C	T	.	.	Sample=NA18994;GT=0/1;PCR_454_AR=1212;PCR_454_RR=1202
+20	39981307	.	G	T	.	.	Sample=NA18595;GT=0/1;PCR_454_AR=1273;PCR_454_RR=1102
+20	39981307	.	G	T	.	.	Sample=NA18622;GT=0/1;PCR_454_AR=635;PCR_454_RR=623
+20	39981307	.	G	T	.	.	Sample=NA18977;GT=0/1;PCR_454_AR=1251;PCR_454_RR=1141
+20	39981307	.	G	T	.	.	Sample=NA18978;GT=0/1;PCR_454_AR=1286;PCR_454_RR=1331
+20	39981307	.	G	T	.	.	Sample=NA18998;GT=0/1;PCR_454_AR=1174;PCR_454_RR=1225
+20	39986913	.	G	A	.	.	Sample=NA20317;GT=0/1;PCR_454_AR=627;PCR_454_RR=535
+20	39987386	.	G	A	.	.	Sample=NA19437;GT=0/1;PCR_454_AR=989;PCR_454_RR=971
+20	39992390	.	G	A	.	.	Sample=NA18636;GT=0/1;PCR_454_AR=925;PCR_454_RR=969
+20	39993723	.	C	T	.	.	Sample=NA18489;GT=0/1;PCR_454_AR=677;PCR_454_RR=819
+20	39993723	.	C	T	.	.	Sample=NA18505;GT=0/1;PCR_454_AR=603;PCR_454_RR=578
+20	39993723	.	C	T	.	.	Sample=NA18517;GT=0/1;PCR_454_AR=791;PCR_454_RR=747
+20	39993723	.	C	T	.	.	Sample=NA19380;GT=0/1;PCR_454_AR=869;PCR_454_RR=972
+20	39993790	.	G	A	.	.	Sample=NA18871;GT=0/1;PCR_454_AR=2297;PCR_454_RR=2512
+20	40033848	.	A	G	.	.	Sample=HG00559;GT=0/0;PCR_454_AR=6;PCR_454_RR=2130
+20	40050233	.	T	G	.	.	Sample=HG01133;GT=0/0;PCR_454_AR=2;PCR_454_RR=1613
+20	40050233	.	T	G	.	.	Sample=NA18502;GT=0/0;PCR_454_AR=4;PCR_454_RR=1967
+20	40162202	.	T	C	.	.	Sample=NA12874;GT=0/1;PCR_454_AR=171;PCR_454_RR=157
+20	42143783	.	A	G	.	.	Sample=NA20334;GT=0/1;PCR_454_AR=1011;PCR_454_RR=632
+20	42143783	.	A	G	.	.	Sample=NA20336;GT=0/1;PCR_454_AR=1556;PCR_454_RR=492
+20	42196587	.	G	A	.	.	Sample=NA19312;GT=0/1;PCR_454_AR=522;PCR_454_RR=486
+20	42196587	.	G	A	.	.	Sample=NA19383;GT=0/1;PCR_454_AR=693;PCR_454_RR=821
+20	42333997	.	C	T	.	.	Sample=NA19058;GT=0/1;PCR_454_AR=994;PCR_454_RR=994
+20	42680115	.	G	A	.	.	Sample=NA18611;GT=0/1;PCR_454_AR=1042;PCR_454_RR=1086
+20	42747246	.	C	T	.	.	Sample=HG00097;GT=0/1;PCR_454_AR=1132;PCR_454_RR=1174
+20	42747246	.	C	T	.	.	Sample=HG00106;GT=0/1;PCR_454_AR=899;PCR_454_RR=983
+20	42747246	.	C	T	.	.	Sample=HG00112;GT=0/1;PCR_454_AR=901;PCR_454_RR=960
+20	42747246	.	C	T	.	.	Sample=HG00135;GT=0/1;PCR_454_AR=677;PCR_454_RR=680
+20	42747246	.	C	T	.	.	Sample=HG00142;GT=0/1;PCR_454_AR=928;PCR_454_RR=956
+20	42939738	.	C	T	.	.	Sample=NA18611;GT=0/1;PCR_454_AR=1131;PCR_454_RR=984
+20	43243299	.	G	C	.	.	Sample=NA18633;GT=0/1;PCR_454_AR=1194;PCR_454_RR=1277
+20	43255152	.	G	A	.	.	Sample=HG00130;GT=0/0;PCR_454_AR=0;PCR_454_RR=2287
+20	43255152	.	G	A	.	.	Sample=HG00234;GT=0/0;PCR_454_AR=1;PCR_454_RR=2172
+20	43255152	.	G	A	.	.	Sample=NA18618;GT=0/0;PCR_454_AR=2;PCR_454_RR=2266
+20	43255152	.	G	A	.	.	Sample=NA18956;GT=0/0;PCR_454_AR=0;PCR_454_RR=2152
+20	43255152	.	G	A	.	.	Sample=NA19083;GT=0/1;PCR_454_AR=986;PCR_454_RR=974
+20	43723672	.	G	A	.	.	Sample=NA18530;GT=0/1;PCR_454_AR=356;PCR_454_RR=401
+20	43723672	.	G	A	.	.	Sample=NA18622;GT=0/1;PCR_454_AR=449;PCR_454_RR=391
+20	43739354	.	G	A	.	.	Sample=NA18504;GT=0/1;PCR_454_AR=455;PCR_454_RR=1477
+20	43934213	.	G	T	.	.	Sample=HG01345;GT=0/1;PCR_454_AR=1327;PCR_454_RR=1169
+20	44190750	.	T	G	.	.	Sample=HG00143;GT=0/1;PCR_454_AR=898;PCR_454_RR=938
+20	44190750	.	T	G	.	.	Sample=NA12340;GT=0/1;PCR_454_AR=882;PCR_454_RR=872
+20	44424037	.	G	A	.	.	Sample=HG00152;GT=0/1;PCR_454_AR=603;PCR_454_RR=593
+20	44469565	.	C	T	.	.	Sample=NA18549;GT=0/1;PCR_454_AR=999;PCR_454_RR=246
+20	44485866	.	T	A	.	.	Sample=NA12890;GT=0/1;PCR_454_AR=536;PCR_454_RR=596
+20	44506417	.	G	A	.	.	Sample=HG00099;GT=0/1;PCR_454_AR=1320;PCR_454_RR=1305
+20	44506417	.	G	A	.	.	Sample=HG00118;GT=0/1;PCR_454_AR=1559;PCR_454_RR=1533
+20	44506417	.	G	A	.	.	Sample=HG00097;GT=1/1;PCR_454_AR=3211;PCR_454_RR=20
+20	44506417	.	G	A	.	.	Sample=HG00112;GT=1/1;PCR_454_AR=2632;PCR_454_RR=20
+20	44506417	.	G	A	.	.	Sample=HG00122;GT=1/1;PCR_454_AR=2875;PCR_454_RR=6
+20	44506987	.	G	C	.	.	Sample=NA19117;GT=0/1;PCR_454_AR=1387;PCR_454_RR=1532
+20	44511253	.	C	T	.	.	Sample=NA20799;GT=0/1;PCR_454_AR=1286;PCR_454_RR=1280
+20	44519372	.	G	A	.	.	Sample=NA19437;GT=0/0;PCR_454_AR=0;PCR_454_RR=2075
+20	44519372	.	G	A	.	.	Sample=NA19917;GT=0/1;PCR_454_AR=1243;PCR_454_RR=1234
+20	44576246	.	G	A	.	.	Sample=NA18912;GT=0/1;PCR_454_AR=458;PCR_454_RR=2154
+20	44576246	.	G	A	.	.	Sample=NA18924;GT=0/1;PCR_454_AR=1131;PCR_454_RR=1078
+20	44576246	.	G	A	.	.	Sample=NA20276;GT=0/1;PCR_454_AR=860;PCR_454_RR=852
+20	44576246	.	G	A	.	.	Sample=NA20289;GT=0/1;PCR_454_AR=492;PCR_454_RR=2174
+20	44580998	.	T	C	.	.	Sample=NA18566;GT=0/1;PCR_454_AR=877;PCR_454_RR=925
+20	44680318	.	C	G	.	.	Sample=HG00592;GT=0/0;PCR_454_AR=0;PCR_454_RR=3602
+20	44680318	.	C	G	.	.	Sample=HG01139;GT=0/0;PCR_454_AR=1;PCR_454_RR=3510
+20	44856207	.	G	A	.	.	Sample=NA11995;GT=0/1;PCR_454_AR=127;PCR_454_RR=17
+20	44980779	.	G	A	.	.	Sample=NA18553;GT=0/1;PCR_454_AR=993;PCR_454_RR=1022
+20	45919012	.	C	T	.	.	Sample=NA19445;GT=0/1;PCR_454_AR=265;PCR_454_RR=525
+20	46271051	.	C	G	.	.	Sample=NA18486;GT=0/1;PCR_454_AR=754;PCR_454_RR=749
+20	47262594	.	C	A	.	.	Sample=NA20291;GT=0/1;PCR_454_AR=1210;PCR_454_RR=1153
+20	47558430	.	C	T	.	.	Sample=NA20296;GT=0/1;PCR_454_AR=699;PCR_454_RR=682
+20	47733688	.	T	C	.	.	Sample=NA18630;GT=0/0;PCR_454_AR=0;PCR_454_RR=806
+20	47739668	.	G	A	.	.	Sample=NA19036;GT=0/0;PCR_454_AR=1;PCR_454_RR=2292
+20	47886859	.	C	T	.	.	Sample=NA18956;GT=0/0;PCR_454_AR=1;PCR_454_RR=2153
+20	47990798	.	C	G	.	.	Sample=HG00105;GT=0/0;PCR_454_AR=0;PCR_454_RR=387
+20	47990798	.	C	G	.	.	Sample=HG00122;GT=0/0;PCR_454_AR=0;PCR_454_RR=534
+20	48124475	.	C	T	.	.	Sample=NA19257;GT=0/1;PCR_454_AR=628;PCR_454_RR=644
+20	48273201	.	A	C	.	.	Sample=NA19914;GT=0/1;PCR_454_AR=338;PCR_454_RR=323
+20	48713355	.	T	C	.	.	Sample=NA12155;GT=0/0;PCR_454_AR=8;PCR_454_RR=1686
+20	48713355	.	T	C	.	.	Sample=NA12815;GT=0/0;PCR_454_AR=10;PCR_454_RR=1607
+20	49218698	.	C	T	.	.	Sample=NA19338;GT=0/1;PCR_454_AR=776;PCR_454_RR=682
+20	49218698	.	C	T	.	.	Sample=NA19457;GT=0/1;PCR_454_AR=803;PCR_454_RR=759
+20	49219065	.	C	T	.	.	Sample=NA18599;GT=0/1;PCR_454_AR=1018;PCR_454_RR=1080
+20	49354597	.	A	G	.	.	Sample=HG00177;GT=0/1;PCR_454_AR=580;PCR_454_RR=617
+20	49354597	.	A	G	.	.	Sample=NA11829;GT=0/1;PCR_454_AR=778;PCR_454_RR=869
+20	49354597	.	A	G	.	.	Sample=NA20510;GT=0/1;PCR_454_AR=518;PCR_454_RR=631
+20	49354597	.	A	G	.	.	Sample=NA20512;GT=0/1;PCR_454_AR=238;PCR_454_RR=333
+20	49354597	.	A	G	.	.	Sample=NA20586;GT=0/1;PCR_454_AR=562;PCR_454_RR=642
+20	50048925	.	G	C	.	.	Sample=NA20507;GT=0/1;PCR_454_AR=774;PCR_454_RR=809
+20	50051804	.	C	T	.	.	Sample=NA19102;GT=0/1;PCR_454_AR=136;PCR_454_RR=155
+20	50071136	.	C	T	.	.	Sample=NA18637;GT=0/1;PCR_454_AR=334;PCR_454_RR=349
+20	50140178	.	G	A	.	.	Sample=NA18924;GT=0/1;PCR_454_AR=540;PCR_454_RR=481
+20	50140178	.	G	A	.	.	Sample=NA19321;GT=0/1;PCR_454_AR=481;PCR_454_RR=652
+20	50235576	.	G	A	.	.	Sample=HG00106;GT=0/1;PCR_454_AR=982;PCR_454_RR=886
+20	50235576	.	G	A	.	.	Sample=HG00122;GT=0/1;PCR_454_AR=838;PCR_454_RR=717
+20	50235576	.	G	A	.	.	Sample=HG00126;GT=0/1;PCR_454_AR=795;PCR_454_RR=769
+20	50235576	.	G	A	.	.	Sample=HG00135;GT=0/1;PCR_454_AR=972;PCR_454_RR=930
+20	50235576	.	G	A	.	.	Sample=HG00148;GT=0/1;PCR_454_AR=933;PCR_454_RR=931
+20	50310567	.	C	T	.	.	Sample=NA19152;GT=0/1;PCR_454_AR=689;PCR_454_RR=773
+20	50310567	.	C	T	.	.	Sample=NA19377;GT=0/1;PCR_454_AR=736;PCR_454_RR=683
+20	50406859	.	G	A	.	.	Sample=NA19921;GT=0/1;PCR_454_AR=1045;PCR_454_RR=930
+20	50407501	.	A	C	.	.	Sample=HG00118;GT=0/1;PCR_454_AR=569;PCR_454_RR=608
+20	50407508	.	C	T	.	.	Sample=NA20534;GT=0/1;PCR_454_AR=753;PCR_454_RR=2120
+20	50408613	.	A	G	.	.	Sample=NA18487;GT=0/1;PCR_454_AR=637;PCR_454_RR=634
+20	50408613	.	A	G	.	.	Sample=NA18502;GT=0/1;PCR_454_AR=561;PCR_454_RR=553
+20	50408613	.	A	G	.	.	Sample=NA18519;GT=0/1;PCR_454_AR=571;PCR_454_RR=554
+20	50408613	.	A	G	.	.	Sample=NA18908;GT=0/1;PCR_454_AR=731;PCR_454_RR=791
+20	50408613	.	A	G	.	.	Sample=NA18909;GT=0/1;PCR_454_AR=683;PCR_454_RR=634
+20	50803476	.	G	A	.	.	Sample=NA19046;GT=0/1;PCR_454_AR=692;PCR_454_RR=685
+20	50803476	.	G	A	.	.	Sample=NA19375;GT=0/1;PCR_454_AR=735;PCR_454_RR=803
+20	50803476	.	G	A	.	.	Sample=NA19376;GT=0/1;PCR_454_AR=892;PCR_454_RR=831
+20	51872037	.	G	A	.	.	Sample=NA18502;GT=0/1;PCR_454_AR=602;PCR_454_RR=654
+20	51872037	.	G	A	.	.	Sample=NA18504;GT=0/1;PCR_454_AR=717;PCR_454_RR=760
+20	51872037	.	G	A	.	.	Sample=NA18507;GT=0/1;PCR_454_AR=790;PCR_454_RR=822
+20	51872037	.	G	A	.	.	Sample=NA18508;GT=0/1;PCR_454_AR=868;PCR_454_RR=914
+20	51872037	.	G	A	.	.	Sample=NA18501;GT=1/1;PCR_454_AR=1687;PCR_454_RR=5
+20	52192483	.	T	C	.	.	Sample=HG00266;GT=0/1;PCR_454_AR=1044;PCR_454_RR=1029
+20	52198279	.	G	A	.	.	Sample=NA19065;GT=0/1;PCR_454_AR=1001;PCR_454_RR=1070
+20	52561468	.	A	G	.	.	Sample=HG00118;GT=0/1;PCR_454_AR=398;PCR_454_RR=501
+20	52561468	.	A	G	.	.	Sample=HG00126;GT=0/1;PCR_454_AR=228;PCR_454_RR=250
+20	52561468	.	A	G	.	.	Sample=HG00130;GT=0/1;PCR_454_AR=472;PCR_454_RR=535
+20	52561468	.	A	G	.	.	Sample=HG00134;GT=0/1;PCR_454_AR=462;PCR_454_RR=543
+20	52561468	.	A	G	.	.	Sample=HG00143;GT=0/1;PCR_454_AR=355;PCR_454_RR=404
+20	52779394	.	G	T	.	.	Sample=NA20540;GT=0/1;PCR_454_AR=470;PCR_454_RR=557
+20	53205268	.	T	C	.	.	Sample=NA19038;GT=0/1;PCR_454_AR=447;PCR_454_RR=421
+20	53226967	.	G	A	.	.	Sample=NA19462;GT=0/1;PCR_454_AR=770;PCR_454_RR=792
+20	54961540	.	A	T	.	.	Sample=HG00106;GT=0/1;PCR_454_AR=457;PCR_454_RR=411
+20	54961540	.	A	T	.	.	Sample=HG00112;GT=0/1;PCR_454_AR=466;PCR_454_RR=483
+20	54961540	.	A	T	.	.	Sample=HG00134;GT=0/1;PCR_454_AR=480;PCR_454_RR=467
+20	54961540	.	A	T	.	.	Sample=HG00143;GT=0/1;PCR_454_AR=522;PCR_454_RR=458
+20	54961540	.	A	T	.	.	Sample=HG00097;GT=1/1;PCR_454_AR=937;PCR_454_RR=4
+20	54970682	.	C	T	.	.	Sample=NA18912;GT=0/1;PCR_454_AR=683;PCR_454_RR=745
+20	54970682	.	C	T	.	.	Sample=NA19171;GT=0/1;PCR_454_AR=819;PCR_454_RR=792
+20	55021021	.	G	A	.	.	Sample=NA19087;GT=0/1;PCR_454_AR=1018;PCR_454_RR=1144
+20	55108414	.	G	A	.	.	Sample=NA20756;GT=1/1;PCR_454_AR=1220;PCR_454_RR=3
+20	55206884	.	C	T	.	.	Sample=NA19726;GT=0/1;PCR_454_AR=806;PCR_454_RR=864
+20	55206884	.	C	T	.	.	Sample=NA19738;GT=0/1;PCR_454_AR=988;PCR_454_RR=1033
+20	56087684	.	C	T	.	.	Sample=NA18599;GT=0/1;PCR_454_AR=1158;PCR_454_RR=1234
+20	56089789	.	C	T	.	.	Sample=HG01277;GT=0/1;PCR_454_AR=737;PCR_454_RR=779
+20	56137833	.	A	G	.	.	Sample=HG00099;GT=0/1;PCR_454_AR=794;PCR_454_RR=777
+20	56137833	.	A	G	.	.	Sample=HG00106;GT=0/1;PCR_454_AR=1272;PCR_454_RR=1196
+20	56137833	.	A	G	.	.	Sample=HG00097;GT=1/1;PCR_454_AR=1763;PCR_454_RR=4
+20	56137833	.	A	G	.	.	Sample=HG00104;GT=1/1;PCR_454_AR=1726;PCR_454_RR=5
+20	56137833	.	A	G	.	.	Sample=HG00112;GT=1/1;PCR_454_AR=1821;PCR_454_RR=3
+20	57036354	.	C	T	.	.	Sample=NA19080;GT=0/1;PCR_454_AR=1722;PCR_454_RR=1581
+20	57036538	.	C	T	.	.	Sample=NA19248;GT=0/1;PCR_454_AR=1224;PCR_454_RR=902
+20	57415535	.	C	T	.	.	Sample=NA19722;GT=0/1;PCR_454_AR=291;PCR_454_RR=1503
+20	57415601	.	G	A	.	.	Sample=NA20296;GT=0/1;PCR_454_AR=1262;PCR_454_RR=350
+20	57428947	.	G	T	.	.	Sample=NA19311;GT=0/1;PCR_454_AR=1304;PCR_454_RR=553
+20	57572729	.	C	T	.	.	Sample=NA19707;GT=0/1;PCR_454_AR=840;PCR_454_RR=1015
+20	57576684	.	T	G	.	.	Sample=NA18747;GT=0/0;PCR_454_AR=3;PCR_454_RR=1578
+20	57597952	.	C	T	.	.	Sample=NA20529;GT=0/1;PCR_454_AR=816;PCR_454_RR=883
+20	57768304	.	G	A	.	.	Sample=NA20818;GT=0/1;PCR_454_AR=710;PCR_454_RR=535
+20	57769546	.	C	T	.	.	Sample=NA18917;GT=0/0;PCR_454_AR=61;PCR_454_RR=810
+20	57769738	.	A	G	.	.	Sample=NA18527;GT=0/1;PCR_454_AR=799;PCR_454_RR=792
+20	57769738	.	A	G	.	.	Sample=NA18530;GT=0/1;PCR_454_AR=558;PCR_454_RR=527
+20	57769738	.	A	G	.	.	Sample=NA18532;GT=0/1;PCR_454_AR=734;PCR_454_RR=719
+20	57769738	.	A	G	.	.	Sample=NA18545;GT=0/1;PCR_454_AR=524;PCR_454_RR=502
+20	57769738	.	A	G	.	.	Sample=NA18593;GT=0/1;PCR_454_AR=809;PCR_454_RR=835
+20	58444902	.	C	T	.	.	Sample=NA19095;GT=0/1;PCR_454_AR=164;PCR_454_RR=144
+20	58467100	.	C	T	.	.	Sample=NA19324;GT=0/1;PCR_454_AR=312;PCR_454_RR=301
+20	58560056	.	C	T	.	.	Sample=HG00593;GT=0/1;PCR_454_AR=1491;PCR_454_RR=1378
+20	58560056	.	C	T	.	.	Sample=NA18553;GT=0/1;PCR_454_AR=1226;PCR_454_RR=1216
+20	58564005	.	G	A	.	.	Sample=NA19355;GT=0/0;PCR_454_AR=0;PCR_454_RR=2602
+20	58567458	.	A	C	.	.	Sample=HG00143;GT=0/0;PCR_454_AR=1;PCR_454_RR=878
+20	58567458	.	A	C	.	.	Sample=HG00149;GT=0/0;PCR_454_AR=0;PCR_454_RR=883
+20	58571705	.	C	T	.	.	Sample=NA19319;GT=0/1;PCR_454_AR=342;PCR_454_RR=265
+20	60504808	.	C	T	.	.	Sample=NA18639;GT=0/1;PCR_454_AR=1079;PCR_454_RR=1027
+20	60504808	.	C	T	.	.	Sample=NA19921;GT=0/1;PCR_454_AR=914;PCR_454_RR=890
+20	60701482	.	T	A	.	.	Sample=NA19651;GT=0/1;PCR_454_AR=540;PCR_454_RR=612
+20	60708462	.	T	C	.	.	Sample=NA18962;GT=0/1;PCR_454_AR=891;PCR_454_RR=784
+20	60738559	.	G	A	.	.	Sample=NA18965;GT=0/1;PCR_454_AR=1072;PCR_454_RR=896
+20	60838713	.	C	T	.	.	Sample=NA20506;GT=0/1;PCR_454_AR=618;PCR_454_RR=642
+20	60866830	.	A	C	.	.	Sample=NA18923;GT=0/0;PCR_454_AR=0;PCR_454_RR=211
+20	60868936	.	C	T	.	.	Sample=NA19119;GT=0/1;PCR_454_AR=1424;PCR_454_RR=1554
+20	60878814	.	G	A	.	.	Sample=NA18638;GT=0/1;PCR_454_AR=223;PCR_454_RR=1299
+20	60884465	.	G	A	.	.	Sample=NA19681;GT=0/1;PCR_454_AR=928;PCR_454_RR=1002
+20	60885810	.	C	T	.	.	Sample=HG00134;GT=0/0;PCR_454_AR=2;PCR_454_RR=2017
+20	60885810	.	C	T	.	.	Sample=HG00350;GT=0/0;PCR_454_AR=4;PCR_454_RR=1963
+20	60886712	.	T	C	.	.	Sample=NA19438;GT=0/1;PCR_454_AR=929;PCR_454_RR=721
+20	60891010	.	C	T	.	.	Sample=NA19700;GT=0/1;PCR_454_AR=334;PCR_454_RR=389
+20	60893610	.	C	T	.	.	Sample=HG00359;GT=0/0;PCR_454_AR=2;PCR_454_RR=2041
+20	60893610	.	C	T	.	.	Sample=NA19758;GT=0/1;PCR_454_AR=1173;PCR_454_RR=1158
+20	60893636	.	C	T	.	.	Sample=NA20520;GT=0/1;PCR_454_AR=847;PCR_454_RR=1197
+20	60893636	.	C	T	.	.	Sample=NA20540;GT=0/1;PCR_454_AR=776;PCR_454_RR=1355
+20	60893960	.	C	T	.	.	Sample=NA19236;GT=0/1;PCR_454_AR=1310;PCR_454_RR=1388
+20	60897486	.	C	T	.	.	Sample=HG00099;GT=0/1;PCR_454_AR=454;PCR_454_RR=403
+20	60897486	.	C	T	.	.	Sample=HG00122;GT=0/1;PCR_454_AR=465;PCR_454_RR=352
+20	60897486	.	C	T	.	.	Sample=HG00097;GT=1/1;PCR_454_AR=849;PCR_454_RR=3
+20	60897486	.	C	T	.	.	Sample=HG00104;GT=1/1;PCR_454_AR=925;PCR_454_RR=4
+20	60897486	.	C	T	.	.	Sample=HG00118;GT=1/1;PCR_454_AR=799;PCR_454_RR=7
+20	60907674	.	G	A	.	.	Sample=HG00104;GT=0/1;PCR_454_AR=279;PCR_454_RR=228
+20	60907674	.	G	A	.	.	Sample=HG00106;GT=0/1;PCR_454_AR=334;PCR_454_RR=295
+20	60907674	.	G	A	.	.	Sample=HG00097;GT=1/1;PCR_454_AR=739;PCR_454_RR=4
+20	60907674	.	G	A	.	.	Sample=HG00099;GT=1/1;PCR_454_AR=395;PCR_454_RR=3
+20	60907674	.	G	A	.	.	Sample=HG00112;GT=1/1;PCR_454_AR=980;PCR_454_RR=6
+20	60911433	.	A	C	.	.	Sample=NA11920;GT=0/1;PCR_454_AR=341;PCR_454_RR=380
+20	60911433	.	A	C	.	.	Sample=NA20278;GT=0/1;PCR_454_AR=398;PCR_454_RR=444
+20	60913173	.	C	T	.	.	Sample=NA18522;GT=0/1;PCR_454_AR=1062;PCR_454_RR=1032
+20	60920914	.	T	C	.	.	Sample=NA18530;GT=0/1;PCR_454_AR=937;PCR_454_RR=877
+20	60920914	.	T	C	.	.	Sample=NA18873;GT=0/1;PCR_454_AR=791;PCR_454_RR=836
+20	60920914	.	T	C	.	.	Sample=NA19038;GT=0/1;PCR_454_AR=895;PCR_454_RR=857
+20	60920914	.	T	C	.	.	Sample=NA19099;GT=0/1;PCR_454_AR=1115;PCR_454_RR=1150
+20	60920914	.	T	C	.	.	Sample=NA19317;GT=0/1;PCR_454_AR=1165;PCR_454_RR=1206
+20	60927411	.	G	A	.	.	Sample=HG00099;GT=0/1;PCR_454_AR=330;PCR_454_RR=345
+20	60927411	.	G	A	.	.	Sample=HG00112;GT=0/1;PCR_454_AR=389;PCR_454_RR=468
+20	60927411	.	G	A	.	.	Sample=HG00118;GT=0/1;PCR_454_AR=1434;PCR_454_RR=538
+20	60927411	.	G	A	.	.	Sample=HG00097;GT=1/1;PCR_454_AR=993;PCR_454_RR=7
+20	60927411	.	G	A	.	.	Sample=HG00104;GT=1/1;PCR_454_AR=837;PCR_454_RR=8
+20	60937543	.	A	G	.	.	Sample=HG00115;GT=0/0;PCR_454_AR=2;PCR_454_RR=3444
+20	60963387	.	C	T	.	.	Sample=NA18992;GT=0/1;PCR_454_AR=689;PCR_454_RR=728
+20	60986026	.	T	C	.	.	Sample=NA18511;GT=0/1;PCR_454_AR=510;PCR_454_RR=522
+20	60986026	.	T	C	.	.	Sample=NA18520;GT=0/1;PCR_454_AR=384;PCR_454_RR=403
+20	60986026	.	T	C	.	.	Sample=NA18861;GT=0/1;PCR_454_AR=372;PCR_454_RR=432
+20	60986026	.	T	C	.	.	Sample=NA18908;GT=0/1;PCR_454_AR=428;PCR_454_RR=386
+20	60989186	.	G	T	.	.	Sample=HG00351;GT=0/0;PCR_454_AR=0;PCR_454_RR=299
+20	60989186	.	G	T	.	.	Sample=HG00099;GT=0/1;PCR_454_AR=1182;PCR_454_RR=966
+20	60989186	.	G	T	.	.	Sample=HG01344;GT=0/1;PCR_454_AR=654;PCR_454_RR=302
+20	60989186	.	G	T	.	.	Sample=NA12045;GT=0/1;PCR_454_AR=504;PCR_454_RR=534
+20	60989186	.	G	T	.	.	Sample=HG00130;GT=1/1;PCR_454_AR=76;PCR_454_RR=2
+20	60992370	.	C	T	.	.	Sample=NA18917;GT=0/1;PCR_454_AR=598;PCR_454_RR=363
+20	60992370	.	C	T	.	.	Sample=NA19453;GT=0/1;PCR_454_AR=541;PCR_454_RR=677
+20	61288592	.	G	A	.	.	Sample=HG01625;GT=0/1;PCR_454_AR=852;PCR_454_RR=871
+20	61288592	.	G	A	.	.	Sample=NA12383;GT=0/1;PCR_454_AR=794;PCR_454_RR=737
+20	61288592	.	G	A	.	.	Sample=NA19780;GT=0/1;PCR_454_AR=1012;PCR_454_RR=880
+20	61288592	.	G	A	.	.	Sample=NA20508;GT=0/1;PCR_454_AR=913;PCR_454_RR=773
+20	61512157	.	C	T	.	.	Sample=NA18933;GT=0/1;PCR_454_AR=1227;PCR_454_RR=1206
+20	61512157	.	C	T	.	.	Sample=NA18934;GT=0/1;PCR_454_AR=1110;PCR_454_RR=1182
+20	61512157	.	C	T	.	.	Sample=NA19771;GT=0/1;PCR_454_AR=1250;PCR_454_RR=1148
+20	61512982	.	T	A	.	.	Sample=NA18559;GT=0/1;PCR_454_AR=1255;PCR_454_RR=1117
+20	61513433	.	T	C	.	.	Sample=NA20810;GT=0/0;PCR_454_AR=1;PCR_454_RR=550
+20	61525226	.	G	A	.	.	Sample=NA19428;GT=0/1;PCR_454_AR=719;PCR_454_RR=719
+20	61542496	.	G	C	.	.	Sample=NA19648;GT=0/1;PCR_454_AR=237;PCR_454_RR=1305
+20	61574860	.	C	T	.	.	Sample=NA19762;GT=0/1;PCR_454_AR=703;PCR_454_RR=488
+20	61591950	.	T	G	.	.	Sample=HG00106;GT=0/0;PCR_454_AR=2;PCR_454_RR=1219
+20	61591950	.	T	G	.	.	Sample=HG00122;GT=0/0;PCR_454_AR=0;PCR_454_RR=1227
+20	61833992	.	G	A	.	.	Sample=NA18489;GT=0/1;PCR_454_AR=738;PCR_454_RR=786
+20	61833992	.	G	A	.	.	Sample=NA19093;GT=0/1;PCR_454_AR=839;PCR_454_RR=739
+20	61834856	.	G	A	.	.	Sample=NA19041;GT=0/1;PCR_454_AR=389;PCR_454_RR=374
+20	61834856	.	G	A	.	.	Sample=NA19095;GT=0/1;PCR_454_AR=383;PCR_454_RR=364
+20	61834856	.	G	A	.	.	Sample=NA19113;GT=0/1;PCR_454_AR=322;PCR_454_RR=325
+20	61834856	.	G	A	.	.	Sample=NA19318;GT=0/1;PCR_454_AR=434;PCR_454_RR=399
+20	61834856	.	G	A	.	.	Sample=NA19334;GT=0/1;PCR_454_AR=380;PCR_454_RR=343
+20	61943307	.	G	C	.	.	Sample=NA19201;GT=0/1;PCR_454_AR=920;PCR_454_RR=890
+20	61943346	.	G	A	.	.	Sample=NA19758;GT=0/1;PCR_454_AR=683;PCR_454_RR=705
+20	62187372	.	C	G	.	.	Sample=NA19117;GT=0/0;PCR_454_AR=0;PCR_454_RR=963
+20	62187668	.	C	T	.	.	Sample=NA12154;GT=0/1;PCR_454_AR=905;PCR_454_RR=664
+20	62194106	.	C	T	.	.	Sample=NA18910;GT=0/1;PCR_454_AR=1083;PCR_454_RR=1040
+20	62194106	.	C	T	.	.	Sample=NA19338;GT=0/1;PCR_454_AR=784;PCR_454_RR=854
+20	62194106	.	C	T	.	.	Sample=NA19346;GT=0/1;PCR_454_AR=757;PCR_454_RR=817
+20	62194106	.	C	T	.	.	Sample=NA19376;GT=0/1;PCR_454_AR=1152;PCR_454_RR=962
+20	62194106	.	C	T	.	.	Sample=NA19439;GT=0/1;PCR_454_AR=1387;PCR_454_RR=1456
+20	62194211	.	C	A	.	.	Sample=HG00156;GT=0/1;PCR_454_AR=1116;PCR_454_RR=536
+20	62194211	.	C	A	.	.	Sample=NA07051;GT=0/1;PCR_454_AR=2089;PCR_454_RR=259
+20	62194211	.	C	A	.	.	Sample=NA12003;GT=0/1;PCR_454_AR=1330;PCR_454_RR=796
+20	62194290	.	C	T	.	.	Sample=NA19346;GT=0/1;PCR_454_AR=1000;PCR_454_RR=751
+20	62194290	.	C	T	.	.	Sample=NA19351;GT=0/1;PCR_454_AR=901;PCR_454_RR=771
+20	62198552	.	G	C	.	.	Sample=NA20542;GT=0/1;PCR_454_AR=1527;PCR_454_RR=1010
+20	62198883	.	C	T	.	.	Sample=NA19346;GT=0/1;PCR_454_AR=1447;PCR_454_RR=1455
+20	62198883	.	C	T	.	.	Sample=NA19351;GT=0/1;PCR_454_AR=903;PCR_454_RR=1401
+20	62198883	.	C	T	.	.	Sample=NA20340;GT=0/1;PCR_454_AR=843;PCR_454_RR=892
+20	62198960	.	G	A	.	.	Sample=NA20534;GT=0/1;PCR_454_AR=1223;PCR_454_RR=864
+20	62200240	.	G	A	.	.	Sample=NA18910;GT=0/1;PCR_454_AR=1221;PCR_454_RR=1347
+20	62226984	.	G	C	.	.	Sample=HG00559;GT=0/0;PCR_454_AR=2;PCR_454_RR=1774
+20	62226984	.	G	C	.	.	Sample=NA12003;GT=0/0;PCR_454_AR=1;PCR_454_RR=1871
+20	62250734	.	C	T	.	.	Sample=NA19473;GT=0/1;PCR_454_AR=607;PCR_454_RR=722
+20	62297382	.	A	T	.	.	Sample=NA11993;GT=0/0;PCR_454_AR=3;PCR_454_RR=2573
+20	62297382	.	A	T	.	.	Sample=NA19117;GT=0/0;PCR_454_AR=5;PCR_454_RR=1753
+20	62305427	.	G	A	.	.	Sample=HG00104;GT=0/0;PCR_454_AR=10;PCR_454_RR=803
+20	62305427	.	G	A	.	.	Sample=HG00122;GT=0/0;PCR_454_AR=28;PCR_454_RR=1300
+20	62319912	.	G	T	.	.	Sample=HG00128;GT=0/0;PCR_454_AR=1;PCR_454_RR=1911
+20	62319912	.	G	T	.	.	Sample=HG00560;GT=0/0;PCR_454_AR=0;PCR_454_RR=2111
+20	62324258	.	C	G	.	.	Sample=NA18562;GT=0/1;PCR_454_AR=1126;PCR_454_RR=1126
+20	62324622	.	C	G	.	.	Sample=NA18574;GT=0/1;PCR_454_AR=1153;PCR_454_RR=1158
+20	62325731	.	G	A	.	.	Sample=NA18548;GT=0/1;PCR_454_AR=779;PCR_454_RR=2199
+20	62325821	.	G	A	.	.	Sample=NA20278;GT=0/1;PCR_454_AR=819;PCR_454_RR=764
+20	62325821	.	G	A	.	.	Sample=NA20507;GT=0/1;PCR_454_AR=1163;PCR_454_RR=1060
+20	62326150	.	G	A	.	.	Sample=NA18870;GT=0/1;PCR_454_AR=1080;PCR_454_RR=892
+20	62326234	.	C	T	.	.	Sample=HG00128;GT=0/0;PCR_454_AR=0;PCR_454_RR=761
+20	62326234	.	C	T	.	.	Sample=HG00179;GT=0/0;PCR_454_AR=1;PCR_454_RR=1158
+20	62326811	.	G	T	.	.	Sample=HG00149;GT=0/0;PCR_454_AR=0;PCR_454_RR=1467
+20	62326811	.	G	T	.	.	Sample=HG00151;GT=0/0;PCR_454_AR=1;PCR_454_RR=1492
+20	62407154	.	C	T	.	.	Sample=NA18987;GT=0/0;PCR_454_AR=181;PCR_454_RR=2041
+20	62421536	.	C	T	.	.	Sample=NA20521;GT=0/1;PCR_454_AR=856;PCR_454_RR=910
+20	62421536	.	C	T	.	.	Sample=NA20543;GT=0/1;PCR_454_AR=865;PCR_454_RR=854
+20	62593676	.	C	T	.	.	Sample=NA20291;GT=0/1;PCR_454_AR=1038;PCR_454_RR=995
+20	62594479	.	C	T	.	.	Sample=NA19746;GT=0/1;PCR_454_AR=349;PCR_454_RR=347
+20	62595981	.	C	T	.	.	Sample=NA19172;GT=0/1;PCR_454_AR=440;PCR_454_RR=415
+20	62630426	.	C	T	.	.	Sample=NA19428;GT=0/1;PCR_454_AR=1246;PCR_454_RR=1277
+20	62632542	.	C	T	.	.	Sample=NA18501;GT=0/1;PCR_454_AR=1203;PCR_454_RR=1150
+20	62657404	.	C	T	.	.	Sample=NA18612;GT=0/1;PCR_454_AR=1480;PCR_454_RR=1071
+20	62700725	.	G	A	.	.	Sample=NA19020;GT=0/1;PCR_454_AR=832;PCR_454_RR=815
+20	62700725	.	G	A	.	.	Sample=NA19036;GT=0/1;PCR_454_AR=1024;PCR_454_RR=966
+20	62729481	.	C	T	.	.	Sample=NA20276;GT=0/1;PCR_454_AR=401;PCR_454_RR=408
+20	62899302	.	T	C	.	.	Sample=HG00104;GT=0/0;PCR_454_AR=10;PCR_454_RR=871
+20	62899302	.	T	C	.	.	Sample=HG00128;GT=0/0;PCR_454_AR=2;PCR_454_RR=950
diff --git a/tests/tabix_data/vcf/3.vcf b/tests/tabix_data/vcf/3.vcf
new file mode 100644
index 0000000..a3f2e0f
--- /dev/null
+++ b/tests/tabix_data/vcf/3.vcf
@@ -0,0 +1,1000 @@
+##fileformat=VCFv4.0
+##filedate=2010-06-21
+##reference=NCBI36
+##INFO=<ID=GC, Number=0, Type=Flag, Description="Overlap with Gencode CCDS coding sequence">
+##INFO=<ID=DP, Number=1, Type=Integer, Description="Total number of reads in haplotype window">
+##INFO=<ID=AF, Number=1, Type=Float, Description="Dindel estimated population allele frequency">
+##INFO=<ID=CA, Number=1, Type=String, Description="Pilot 1 callability mask">
+##INFO=<ID=HP, Number=1, Type=Integer, Description="Reference homopolymer tract length">
+##INFO=<ID=NS, Number=1, Type=Integer, Description="Number of samples with data">
+##INFO=<ID=DB, Number=0, Type=Flag, Description="dbSNP membership build 129 - type match and indel sequence length match within 25 bp">
+##INFO=<ID=NR, Number=1, Type=Integer, Description="Number of reads covering non-ref variant on reverse strand">
+##INFO=<ID=NF, Number=1, Type=Integer, Description="Number of reads covering non-ref variant on forward strand">
+##FILTER=<ID=NoQCALL, Description="Variant called by Dindel but not confirmed by QCALL">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
+1	1000153	.	TCACAC	TC	100	PASS	AF=0.115095;HP=1;NF=16;NR=13;NS=52;CA=0;DP=615
+1	1000906	.	CAG	CG	48	PASS	AF=0.0772696;HP=1;NF=2;NR=9;NS=51;CA=0;DP=281
+1	1000950	rs60561655;-/G	CGG	CG	100	PASS	AF=0.447771;HP=5;DB;NF=10;NR=20;NS=50;CA=M;DP=291
+1	1010786	rs36095298;-/G,mills,venter	AC	AGC	100	PASS	AF=0.774334;HP=1;DB;NF=21;NR=27;NS=51;CA=0;DP=306
+1	1026158	.	TG	TGGGGGG	100	PASS	AF=0.115637;HP=1;NF=5;NR=2;NS=52;CA=0;DP=591
+1	1028860	mills,venter	ACTCC	AC	10	PASS	AF=0.0107751;HP=1;NF=5;NR=4;NS=52;CA=0;DP=522
+1	1040517	.	CA	CAA	100	PASS	AF=0.0577672;HP=1;NF=7;NR=4;NS=52;CA=0;DP=426
+1	1043690	rs5772037;-/G,venter	TG	TGG	100	PASS	AF=0.065857;HP=3;DB;NF=5;NR=8;NS=51;CA=0;DP=427
+1	1049375	.	TA	TACACACCTGAGCACACACACCTGTGCA	100	PASS	AF=0.0808078;HP=1;NF=1;NR=1;NS=51;CA=M;DP=643
+1	1055459	venter	ACC	AC	100	PASS	AF=0.936429;HP=2;NF=13;NR=24;NS=51;CA=M;DP=342
+1	1056251	rs34287831;-/A,venter	CT	CTT	100	PASS	AF=0.725164;HP=1;DB;NF=31;NR=20;NS=52;CA=0;DP=375
+1	1057459	rs55853944;-/AG,venter	CAGG	CG	100	PASS	AF=0.525146;HP=1;DB;NF=16;NR=18;NS=51;CA=0;DP=331
+1	1057537	rs35574593;-/CC,watson	TG	TGGG	100	PASS	AF=0.591248;HP=1;DB;NF=30;NR=12;NS=50;CA=0;DP=341
+1	1058532	rs34990026;-/A	GTT	GT	100	PASS	AF=0.702381;HP=4;DB;NF=29;NR=32;NS=52;CA=0;DP=405
+1	1058695	rs56086046;-/GCCTGCCTGCCCGGCC,watson	CGCCGCCTGCCTGCCCGG	CG	100	PASS	AF=0.601284;HP=1;DB;NF=24;NR=23;NS=51;CA=0;DP=365
+1	1073880	.	AC	ACC	13	PASS	AF=0.0555821;HP=2;NF=1;NR=6;NS=52;CA=0;DP=457
+1	1087270	mills,venter,watson	CCCCAC	CC	100	PASS	AF=0.990156;HP=4;NF=32;NR=27;NS=50;CA=0;DP=339
+1	1088683	rs5772039;-/C,venter	TCC	TC	100	PASS	AF=0.957928;HP=9;DB;NF=31;NR=26;NS=49;CA=0;DP=336
+1	1093553	.	TC	TCAC	100	PASS	AF=0.962343;HP=5;NF=44;NR=17;NS=51;CA=0;DP=324
+1	1111698	rs57346441;-/TG,watson	CA	CTGA	100	PASS	AF=0.0986662;HP=1;DB;NF=8;NR=5;NS=52;CA=0;DP=528
+1	1117471	.	GT	GTT	48	PASS	AF=0.04843;HP=6;NF=20;NR=8;NS=52;CA=0;DP=510
+1	1118641	.	CT	CTTAT	38	PASS	AF=0.0574453;HP=1;NF=5;NR=1;NS=51;CA=0;DP=424
+1	1119225	rs60117456;-/C	AC	ACC	50	PASS	AF=0.0255886;HP=4;DB;NF=8;NR=5;NS=52;CA=0;DP=522
+1	1121774	.	GCTGTTCAGACCTG	GG	100	PASS	AF=0.0749767;HP=1;NF=6;NR=6;NS=51;CA=0;DP=508
+1	1123178	.	AACA	AA	14	PASS	AF=0.0195065;HP=3;NF=2;NR=3;NS=49;CA=0;DP=329
+1	1134362	.	GGAG	GG	100	PASS	AF=0.142028;HP=2;NF=12;NR=17;NS=51;CA=0;DP=407
+1	1140087	.	TCA	TA	19	PASS	AF=0.0635822;HP=1;NF=2;NR=5;NS=51;CA=0;DP=446
+1	1141951	.	CTG	CG	100	PASS	AF=0.100135;HP=1;NF=7;NR=7;NS=52;CA=0;DP=463
+1	1148304	rs34808371;-/GT,venter	GCAC	GC	100	PASS	AF=0.0786699;HP=1;DB;NF=11;NR=18;NS=52;CA=0;DP=687
+1	1148425	rs57524763;-/AC	AACA	AA	100	PASS	AF=0.0744913;HP=2;DB;NF=17;NR=8;NS=51;CA=0;DP=647
+1	1149524	.	GTTTTAT	GT	100	PASS	AF=0.0475567;HP=4;NF=19;NR=14;NS=50;CA=0;DP=395
+1	1150963	.	CGCCACAGACACGGGCCACACACTCCACATG	CG	100	PASS	AF=0.111384;HP=1;NF=46;NR=28;NS=50;CA=0;DP=510
+1	1151863	.	GT	GCT	100	PASS	AF=0.126132;HP=1;NF=8;NR=7;NS=52;CA=0;DP=416
+1	1153674	rs3831195;-/ACAG	GG	GGACAG	18	PASS	AF=0.0388728;HP=2;DB;NF=3;NR=2;NS=51;CA=0;DP=418
+1	1154612	.	GT	GCT	100	PASS	AF=0.0630518;HP=1;NF=7;NR=4;NS=52;CA=0;DP=531
+1	1155143	.	GCAC	GC	100	PASS	AF=0.0991605;HP=1;NF=25;NR=23;NS=52;CA=0;DP=540
+1	1155183	.	CATG	CG	100	PASS	AF=0.0714383;HP=1;NF=5;NR=8;NS=52;CA=0;DP=527
+1	1156953	rs57672822;-/ACCCCGGGA	CCCCCGGGAAC	CC	59	PASS	AF=0.0847102;HP=5;DB;NF=5;NR=8;NS=50;CA=0;DP=312
+1	1164370	.	AA	AACATGCATCCA	100	PASS	AF=0.0550752;HP=2;NF=2;NR=1;NS=51;CA=0;DP=481
+1	1166826	.	AC	ACC	11	PASS	AF=0.0735648;HP=1;NF=1;NR=10;NS=52;CA=0;DP=379
+1	1167781	rs3835300;-/T	CTG	CG	100	PASS	AF=0.0719128;HP=1;DB;NF=3;NR=3;NS=50;CA=0;DP=360
+1	1180776	rs35025185;-/T,mills	CTT	CT	15	PASS	AF=0.0182173;HP=3;DB;NF=5;NR=1;NS=52;CA=0;DP=526
+1	1184391	.	GC	GCAC	16	PASS	AF=0.0187867;HP=1;NF=2;NR=6;NS=51;CA=M;DP=521
+1	1204971	.	TGG	TG	100	PASS	AF=0.0564084;HP=6;NF=11;NR=6;NS=50;CA=0;DP=419
+1	1207801	rs35647244;-/GT,watson	CC	CCAC	100	PASS	AF=0.034013;HP=2;DB;NF=9;NR=4;NS=52;CA=0;DP=624
+1	1213486	.	GTCT	GT	100	PASS	AF=0.504039;HP=1;NF=9;NR=5;NS=50;CA=M;DP=372
+1	1217527	rs3831920;-/CTCA,watson	TTGAGT	TT	100	PASS	AF=0.098042;HP=2;DB;NF=11;NR=14;NS=51;CA=0;DP=444
+1	1224625	.	AGG	AG	40	PASS	AF=0.0395551;HP=5;NF=4;NR=4;NS=51;CA=0;DP=406
+1	1228918	rs35156558;-/GGA,venter	CC	CCCTC	100	PASS	AF=0.999996;HP=5;DB;NF=24;NR=30;NS=49;CA=0;DP=268
+1	1232491	.	CTACCTGACCTTC	CC	13	PASS	AF=0.0510512;HP=1;NF=5;NR=5;NS=52;CA=0;DP=510
+1	1236119	.	CGGCTCTGGGTCACAGGTG	CG	17	PASS	AF=0.0581287;HP=2;NF=6;NR=8;NS=49;CA=M;DP=277
+1	1245266	rs5772041;-/G,venter	TGG	TG	100	PASS	AF=0.928175;HP=4;DB;NF=39;NR=39;NS=52;CA=0;DP=431
+1	1286232	venter,watson	GACA	GA	100	PASS	AF=0.878082;HP=1;NF=31;NR=15;NS=50;CA=0;DP=249
+1	1292184	watson	TG	TGTGTGCAG	100	PASS	AF=0.92351;HP=1;NF=36;NR=17;NS=51;CA=0;DP=633
+1	1475307	rs35008066;-/G,venter	GCC	GC	59	PASS	AF=0.0854422;HP=2;DB;NF=2;NR=3;NS=52;CA=0;DP=372
+1	1476800	rs3835461;-/C	AG	AGG	100	PASS	AF=0.239098;HP=1;DB;NF=13;NR=18;NS=52;CA=0;DP=491
+1	1482738	rs34962853;-/AT,watson	CATA	CA	100	PASS	AF=0.1747;HP=1;DB;NF=28;NR=14;NS=51;CA=0;DP=441
+1	1483969	rs3835460;-/T,mills	CG	CAG	100	PASS	AF=0.180671;HP=5;DB;NF=6;NR=13;NS=52;CA=0;DP=512
+1	1484993	rs35384209;-/CT	CA	CAGA	100	PASS	AF=0.182804;HP=1;DB;NF=9;NR=15;NS=52;CA=0;DP=441
+1	1485720	.	TC	TCGTAC	39	PASS	AF=0.0207216;HP=1;NF=1;NR=3;NS=51;CA=0;DP=498
+1	1487504	rs35885836;-/AGAA,venter,watson	TTTTCT	TT	100	PASS	AF=0.210263;HP=4;DB;NF=16;NR=20;NS=52;CA=0;DP=574
+1	1490348	rs3835459;-/CATGATCCGCCTGCCTT	CAAGGCAGGCGGATCATGA	CA	59	PASS	AF=0.230233;HP=2;DB;NF=5;NR=66;NS=51;CA=M;DP=377
+1	1490873	.	GT	GGGCCCGACGGTGCT	100	PASS	AF=0.133846;HP=1;NF=8;NR=3;NS=52;CA=0;DP=572
+1	1495811	venter	ACC	AC	100	PASS	AF=0.232263;HP=8;NF=12;NR=29;NS=52;CA=0;DP=481
+1	1502734	rs35576478;-/G,venter	AC	ACC	100	PASS	AF=0.221604;HP=4;DB;NF=16;NR=9;NS=51;CA=0;DP=388
+1	1507556	.	AC	ACC	42	PASS	AF=0.0176775;HP=1;NF=1;NR=4;NS=51;CA=0;DP=511
+1	1508235	.	CT	CTT	100	PASS	AF=0.2555;HP=1;NF=18;NR=15;NS=51;CA=0;DP=535
+1	1508689	.	CG	CGG	100	PASS	AF=0.0922424;HP=5;NF=19;NR=17;NS=51;CA=0;DP=568
+1	1510533	.	TTTTGT	TT	100	PASS	AF=0.423696;HP=7;NF=37;NR=39;NS=52;CA=0;DP=387
+1	1511216	.	TA	TAATAATAATAAAA	39	PASS	AF=0.542394;HP=2;NF=7;NR=3;NS=51;CA=0;DP=331
+1	1512041	.	CAAAAGTAAA	CA	33	PASS	AF=0.0333379;HP=4;NF=12;NR=13;NS=52;CA=0;DP=440
+1	1514403	.	TTTTAT	TT	100	PASS	AF=0.771875;HP=5;NF=24;NR=58;NS=50;CA=0;DP=243
+1	1520133	rs34595829;-/GT,venter	GA	GACA	100	PASS	AF=0.432871;HP=1;DB;NF=24;NR=19;NS=52;CA=0;DP=966
+1	1520238	venter,watson	TG	TGAGACAG	100	PASS	AF=0.606404;HP=1;NF=52;NR=36;NS=52;CA=M;DP=847
+1	1520271	.	CA	CAGA	100	PASS	AF=0.169509;HP=1;NF=48;NR=39;NS=52;CA=M;DP=736
+1	1520357	.	CAGAGAGA	CA	100	PASS	AF=0.218715;HP=1;NF=44;NR=30;NS=52;CA=M;DP=708
+1	1520549	.	CAGA	CA	100	PASS	AF=0.257166;HP=1;NF=41;NR=40;NS=52;CA=0;DP=790
+1	1520595	.	CAGA	CA	100	PASS	AF=0.107822;HP=1;NF=52;NR=44;NS=52;CA=M;DP=804
+1	1520983	.	GA	GAGAGAGACA	34	PASS	AF=0.0372679;HP=1;NF=2;NR=3;NS=52;CA=0;DP=610
+1	1521139	.	GA	GAGACA	100	PASS	AF=0.667375;HP=1;NF=10;NR=7;NS=52;CA=M;DP=537
+1	1521387	.	GAGACA	GA	100	PASS	AF=0.361313;HP=1;NF=13;NR=34;NS=52;CA=M;DP=598
+1	1521833	.	GACA	GA	100	PASS	AF=0.193306;HP=1;NF=23;NR=17;NS=52;CA=0;DP=737
+1	1522371	.	CC	CCCTCAGCTGGACTC	100	PASS	AF=0.480499;HP=3;NF=11;NR=12;NS=51;CA=0;DP=535
+1	1530305	.	AG	AGG	15	PASS	AF=0.0737746;HP=3;NF=13;NR=4;NS=51;CA=0;DP=569
+1	1536491	rs36101309;-/GA	ATCT	AT	100	PASS	AF=0.128408;HP=1;DB;NF=22;NR=14;NS=51;CA=0;DP=621
+1	1537805	venter	TT	TCT	100	PASS	AF=0.350404;HP=8;NF=3;NR=18;NS=52;CA=M;DP=419
+1	1539301	.	CAAAAGA	CA	56	PASS	AF=0.0156055;HP=4;NF=9;NR=2;NS=51;CA=0;DP=577
+1	1549566	venter	ATT	AT	100	PASS	AF=0.505899;HP=3;NF=25;NR=27;NS=52;CA=0;DP=451
+1	1554815	.	TGG	TG	100	PASS	AF=0.158582;HP=6;NF=12;NR=6;NS=48;CA=0;DP=271
+1	1575329	.	GCAAC	GC	12	PASS	AF=0.0174116;HP=1;NF=27;NR=21;NS=52;CA=0;DP=554
+1	1575977	rs35072492;-/A	TCC	TC	100	PASS	AF=0.626664;HP=3;DB;NF=23;NR=50;NS=51;CA=0;DP=361
+1	1577203	venter,watson	AA	AAAACA	100	PASS	AF=0.979791;HP=4;NF=59;NR=37;NS=52;CA=0;DP=498
+1	1584062	rs5772057;-/T,venter	CT	CTT	100	PASS	AF=0.992883;HP=1;DB;NF=34;NR=22;NS=46;CA=0;DP=291
+1	1589954	.	TTGT	TT	100	PASS	AF=0.0452889;HP=8;NF=5;NR=13;NS=51;CA=0;DP=424
+1	1611607	venter	ATA	AA	100	PASS	AF=0.528232;HP=1;NF=7;NR=10;NS=50;CA=M;DP=243
+1	1615408	venter	AC	ACGC	100	PASS	AF=0.553544;HP=9;NF=16;NR=20;NS=51;CA=M;DP=247
+1	1618248	.	CTGA	CA	100	PASS	AF=0.0412633;HP=1;NF=5;NR=2;NS=51;CA=0;DP=789
+1	1637509	venter	CG	CTG	100	PASS	AF=0.956642;HP=1;NF=57;NR=41;NS=52;CA=M;DP=533
+1	1637828	rs34259364;-/AT,mills	CG	CATG	100	PASS	AF=0.24683;HP=1;DB;NF=5;NR=57;NS=52;CA=0;DP=744
+1	1638199	.	GA	GATGTTAA	100	PASS	AF=0.962724;HP=1;NF=22;NR=22;NS=52;CA=0;DP=480
+1	1638366	venter	AT	ATT	100	PASS	AF=0.471703;HP=4;NF=50;NR=16;NS=52;CA=0;DP=738
+1	1638469	rs34392519;-/AGC,mills	GA	GAGCA	100	PASS	AF=0.428728;HP=1;DB;NF=34;NR=23;NS=52;CA=0;DP=804
+1	1639339	rs36127854;-/CT,venter	TA	TAGA	100	PASS	AF=0.27562;HP=1;DB;NF=10;NR=15;NS=52;CA=0;DP=961
+1	1639610	.	ATTCTC	AC	59	PASS	AF=0.0697107;HP=2;NF=31;NR=24;NS=52;CA=M;DP=817
+1	1640937	venter	CG	CTCGCTCTGTCACCCAGGCTG	100	PASS	AF=0.639983;HP=2;NF=4;NR=3;NS=52;CA=M;DP=638
+1	1641995	rs34986248;-/ATT,venter,watson	CT	CTTAT	100	PASS	AF=0.924551;HP=2;DB;NF=33;NR=29;NS=52;CA=0;DP=414
+1	1654133	rs34171153;-/ATCG	TA	TATCGA	100	PASS	AF=0.2409;HP=1;DB;NF=10;NR=13;NS=52;CA=0;DP=463
+1	1656307	rs35516110;-/GTTT,venter	GT	GGTTTT	100	PASS	AF=0.686901;HP=6;DB;NF=22;NR=20;NS=51;CA=0;DP=293
+1	1674207	venter	CC	CCCTC	100	PASS	AF=0.303909;HP=3;NF=26;GC;NR=29;NS=52;CA=0;DP=534
+1	1675781	.	TCCCTGGGACCGAAGTCGCCCCAC	TC	100	PASS	AF=0.270579;HP=3;NF=25;NR=24;NS=52;CA=0;DP=473
+1	1679986	rs35357728;-/TG,mills,venter,watson	AA	AACA	100	PASS	AF=0.956895;HP=4;DB;NF=60;NR=58;NS=52;CA=0;DP=520
+1	1684058	.	AAATGA	AA	100	PASS	AF=0.508762;HP=4;NF=48;NR=55;NS=52;CA=0;DP=471
+1	1684177	.	TG	TGGGGGGGG	100	PASS	AF=0.126497;HP=1;NF=5;NR=3;NS=51;CA=0;DP=449
+1	1691268	rs35459537;-/AAAAACAAAAAC,mills,venter	CAAAACAAAAACAA	CA	100	PASS	AF=0.305762;HP=4;DB;NF=54;NR=62;NS=51;CA=0;DP=443
+1	1697760	mills,venter	GAAACA	GA	100	PASS	AF=0.276545;HP=3;NF=21;NR=43;NS=52;CA=0;DP=564
+1	1700966	rs34974144;-/AT,venter	TT	TTGT	100	PASS	AF=0.37365;HP=3;DB;NF=34;NR=30;NS=52;CA=0;DP=445
+1	1715347	.	TG	TGGGGGG	24	PASS	AF=0.0415083;HP=1;NF=4;NR=5;NS=52;CA=0;DP=519
+1	1717050	rs56070879;-/ACAAAAAA,venter	TC	TCAAAAAAAC	100	PASS	AF=0.90619;HP=1;DB;NF=11;NR=7;NS=52;CA=0;DP=442
+1	1729683	.	ACT	AT	100	PASS	AF=0.104273;HP=1;NF=9;NR=11;NS=52;CA=0;DP=587
+1	1729941	rs55730045;-/TTTG,watson	TTTTGT	TT	100	PASS	AF=0.270089;HP=5;DB;NF=25;NR=44;NS=52;CA=M;DP=458
+1	1733706	rs4012956;-/GT,mills,venter	TA	TACA	100	PASS	AF=0.737658;HP=1;DB;NF=58;NR=26;NS=52;CA=M;DP=547
+1	1750193	rs34820549;-/TG,venter	TA	TACA	100	PASS	AF=0.417596;HP=1;DB;NF=42;NR=29;NS=52;CA=0;DP=495
+1	1761838	.	GCAC	GC	17	PASS	AF=0.0186129;HP=1;NF=23;NR=23;NS=52;CA=0;DP=566
+1	1767123	.	TACACACACACACACACACACACACACACACA	TA	100	PASS	AF=0.205885;HP=1;NF=32;NR=32;NS=52;CA=0;DP=560
+1	1767308	.	AG	ATG	12	PASS	AF=0.363076;HP=2;NF=25;NR=12;NS=52;CA=0;DP=611
+1	1768358	.	ACA	AA	11	NoQCALL	AF=0.0311546;HP=1;NF=1;NR=4;NS=52;CA=0;DP=502
+1	1768592	.	AC	ACAACAAAATCCCTTTTTC	100	PASS	AF=0.0974177;HP=1;NF=2;NR=5;NS=52;CA=0;DP=597
+1	1769336	rs34011234;-/TA,venter,watson	CT	CTAT	100	PASS	AF=0.385782;HP=1;DB;NF=21;NR=42;NS=52;CA=0;DP=534
+1	1769673	rs56979938;-/A,venter	AGA	AA	21	PASS	AF=0.232442;HP=1;DB;NF=9;NR=3;NS=52;CA=0;DP=465
+1	1771291	.	TG	TGG	100	PASS	AF=0.18937;HP=2;NF=5;NR=15;NS=52;CA=0;DP=590
+1	1778545	.	TA	TAAA	100	PASS	AF=0.155668;HP=3;NF=5;NR=12;NS=52;CA=0;DP=621
+1	1778604	rs34483468;-/AGCC,venter	GG	GGGCTG	100	PASS	AF=0.135521;HP=4;DB;NF=22;NR=28;NS=52;CA=0;DP=629
+1	1786587	watson	ACCA	AA	26	PASS	AF=0.0677562;HP=2;NF=15;NR=22;NS=52;CA=M;DP=404
+1	1797136	rs59528461;-/C,venter	TCC	TC	100	PASS	AF=0.94689;HP=10;DB;NF=58;NR=57;NS=52;CA=0;DP=531
+1	1797791	rs35226472;-/CT,venter	CG	CGAG	100	PASS	AF=0.383219;HP=1;DB;NF=64;NR=38;NS=52;CA=0;DP=673
+1	1802225	rs34339560;-/A,mills,venter	CAA	CA	100	PASS	AF=0.973419;HP=2;DB;NF=64;NR=71;NS=52;CA=0;DP=635
+1	1802305	.	GGAG	GG	100	PASS	AF=0.273326;HP=2;NF=41;NR=34;NS=52;CA=0;DP=695
+1	1806743	.	TTAGAT	TT	100	PASS	AF=0.179706;HP=2;NF=9;NR=6;NS=52;CA=0;DP=377
+1	1809681	.	AG	AGG	21	PASS	AF=0.133833;HP=2;NF=7;NR=3;NS=52;CA=0;DP=482
+1	1810283	.	AC	ACC	30	PASS	AF=0.0430128;HP=2;NF=4;NR=11;NS=52;CA=0;DP=523
+1	1810555	.	CTTAAT	CT	100	PASS	AF=0.0498379;HP=2;NF=9;NR=7;NS=52;CA=0;DP=521
+1	1812953	rs34135959;-/TCTC	CA	CAGAGA	100	PASS	AF=0.311555;HP=1;DB;NF=6;NR=8;NS=42;CA=0;DP=242
+1	1819911	.	CATG	CG	100	PASS	AF=0.0319085;HP=1;NF=3;NR=6;NS=52;CA=0;DP=765
+1	1819947	rs60517384;-/AAGTTGGATATACACACAT	CACACACATAAGTTGGATATA	CA	100	PASS	AF=0.0935091;HP=1;DB;NF=59;NR=69;NS=52;CA=0;DP=854
+1	1825723	venter	AA	AAAATAAATAAATA	100	PASS	AF=0.348026;HP=4;NF=9;NR=10;NS=52;CA=0;DP=373
+1	1835530	.	GTGAGAGTTGTTG	GG	100	PASS	AF=0.15298;HP=1;NF=12;NR=1;NS=51;CA=0;DP=528
+1	1838692	rs5772055;-/AC,mills	AA	AACA	100	PASS	AF=0.0441449;HP=3;DB;NF=2;NR=3;NS=51;CA=0;DP=360
+1	1843475	rs3039777;-/ACTG,venter,watson	TC	TCTGAC	100	PASS	AF=0.999998;HP=1;DB;NF=38;NR=39;NS=50;CA=0;DP=422
+1	1850674	.	AGG	AG	100	PASS	AF=0.474687;HP=3;NF=7;NR=1;NS=49;CA=0;DP=271
+1	1855740	watson	GT	GTGTAT	100	PASS	AF=0.646893;HP=1;NF=42;NR=28;NS=51;CA=0;DP=653
+1	1856762	.	CACAGG	CG	14	PASS	AF=0.0324715;HP=1;NF=1;NR=2;NS=50;CA=M;DP=379
+1	1857166	.	TACA	TA	100	PASS	AF=0.0531955;HP=1;NF=39;NR=29;NS=52;CA=0;DP=634
+1	1859140	mills	ACACCAGGTCCACCTCTGGACACAGGTCCACCC	AC	100	PASS	AF=0.180806;HP=1;NF=26;NR=15;NS=52;CA=0;DP=672
+1	1859353	rs35385292;-/TC,venter	ACTC	AC	100	PASS	AF=0.493919;HP=1;DB;NF=26;NR=38;NS=52;CA=M;DP=641
+1	1859424	rs34242289;-/CA,venter	TCAG	TG	100	PASS	AF=0.3962;HP=1;DB;NF=40;NR=32;NS=52;CA=M;DP=695
+1	1859520	.	TCAC	TC	100	PASS	AF=0.234548;HP=1;NF=26;NR=23;NS=52;CA=0;DP=729
+1	1859631	rs35205487;-/GA,venter	AC	ACTC	100	PASS	AF=0.347295;HP=1;DB;NF=15;NR=28;NS=52;CA=0;DP=710
+1	1859792	rs34050188;-/AT,watson	CG	CATG	100	PASS	AF=0.715253;HP=1;DB;NF=35;NR=44;NS=52;CA=0;DP=590
+1	1864576	.	CG	CGG	13	PASS	AF=0.0158703;HP=1;NF=3;NR=2;NS=51;CA=0;DP=556
+1	1867274	rs34832935;-/C	TGG	TG	100	PASS	AF=0.304336;HP=8;DB;NF=38;NR=23;NS=51;CA=0;DP=538
+1	1869711	rs56005703;-/ATAT,watson	AA	AATATA	100	PASS	AF=0.652198;HP=3;DB;NF=16;NR=16;NS=51;CA=0;DP=349
+1	1870233	.	TC	TCCCTCCCTTCTTTCCTTCCCTTTCCCTCC	100	PASS	AF=0.408049;HP=2;NF=11;NR=9;NS=52;CA=0;DP=814
+1	1870305	.	CC	CCTTTCCCTCCCTTACTCCTTCCTTCCTTC	100	PASS	AF=0.121733;HP=4;NF=1;NR=5;NS=52;CA=0;DP=680
+1	1870363	.	CT	CTT	100	PASS	AF=0.11398;HP=2;NF=4;NR=6;NS=52;CA=0;DP=680
+1	1870863	rs35875775;-/C,venter	TT	TGT	100	PASS	AF=0.744276;HP=2;DB;NF=43;NR=22;NS=52;CA=0;DP=455
+1	1873164	.	GT	GTT	100	PASS	AF=0.387355;HP=3;NF=20;NR=18;NS=52;CA=0;DP=523
+1	1873889	rs58267869;-/AAGA	AA	AAAAGA	100	PASS	AF=0.252999;HP=5;DB;NF=57;NR=31;NS=52;CA=0;DP=536
+1	1874122	rs35595511;-/T	TAA	TA	100	PASS	AF=0.338059;HP=9;DB;NF=38;NR=38;NS=51;CA=0;DP=519
+1	1876064	watson	AG	AGAGTG	100	PASS	AF=0.0829624;HP=1;NF=6;NR=5;NS=52;CA=0;DP=465
+1	1876204	.	AC	ACAGC	100	PASS	AF=0.256855;HP=1;NF=14;NR=10;NS=52;CA=0;DP=483
+1	1876616	.	GC	GCTGGTGCGCGTC	100	PASS	AF=0.0656988;HP=1;NF=5;NR=2;NS=51;CA=0;DP=420
+1	1876971	rs3838975;-/G	GCC	GC	21	PASS	AF=0.201137;HP=2;DB;NF=15;NR=6;NS=52;CA=0;DP=439
+1	1877704	.	CCTGC	CC	19	PASS	AF=0.0183173;HP=2;NF=7;NR=13;NS=52;CA=0;DP=436
+1	1884832	rs34937714;-/T	CA	CAA	100	PASS	AF=0.254902;HP=3;DB;NF=27;NR=6;NS=52;CA=0;DP=449
+1	1886549	rs3838974;-/T	GG	GAG	100	PASS	AF=0.153123;HP=4;DB;NF=11;NR=10;NS=52;CA=0;DP=456
+1	1889260	rs55954278;-/ATGA	GT	GTGAAT	100	PASS	AF=0.630203;HP=1;DB;NF=12;NR=17;NS=52;CA=0;DP=656
+1	1889311	.	GTGAAT	GT	100	PASS	AF=0.167491;HP=1;NF=33;NR=18;NS=52;CA=0;DP=606
+1	1889402	rs34520694;-/GTGA	AT	ATGAGT	100	PASS	AF=0.306146;HP=1;DB;NF=24;NR=32;NS=52;CA=0;DP=916
+1	1889884	rs56985589;-/G	TGC	TC	100	PASS	AF=0.347999;HP=1;DB;NF=20;NR=28;NS=51;CA=0;DP=537
+1	1889966	rs61233860;-/CCT,watson	TC	TCTCC	100	PASS	AF=0.211403;HP=1;DB;NF=12;NR=14;NS=52;CA=0;DP=554
+1	1892548	.	ACTC	AC	21	PASS	AF=0.0207771;HP=1;NF=4;NR=3;NS=52;CA=0;DP=750
+1	1900826	.	AACA	AA	100	PASS	AF=0.122368;HP=2;NF=13;NR=6;NS=52;CA=M;DP=435
+1	1908846	venter	CT	CTT	100	PASS	AF=0.30139;HP=10;NF=11;NR=28;NS=51;CA=0;DP=350
+1	1910458	.	TGAG	TG	15	PASS	AF=0.0208928;HP=1;NF=23;NR=12;NS=52;CA=0;DP=514
+1	1927207	rs61162553;-/GTTCTCTCTCTCTCTCTCTC,venter	CTCTCTCTCTCTCTCTCTCGTT	CT	100	PASS	AF=0.399955;HP=1;DB;NF=34;NR=47;NS=51;CA=0;DP=427
+1	1929307	rs36066718;-/T	CAA	CA	30	PASS	AF=0.114706;HP=10;DB;NF=24;NR=15;NS=52;CA=0;DP=520
+1	1933578	.	CA	CAAAATAAAATA	100	PASS	AF=0.562689;HP=4;NF=21;NR=28;NS=52;CA=0;DP=359
+1	1947079	rs3831907;-/C	CGG	CG	100	PASS	AF=0.131218;HP=3;DB;NF=4;NR=10;NS=52;CA=0;DP=316
+1	1949721	rs35354651;-/G	GC	GCC	100	PASS	AF=0.218024;HP=1;DB;NF=11;NR=5;NS=51;CA=0;DP=306
+1	1965555	rs56225932;-/CA,venter	TACA	TA	100	PASS	AF=0.743144;HP=1;DB;NF=50;NR=67;NS=52;CA=0;DP=679
+1	1966402	venter,watson	GC	GCCGCC	100	PASS	AF=0.988372;HP=2;NF=36;NR=16;NS=46;CA=0;DP=232
+1	1989567	.	AC	ACC	12	PASS	AF=0.0334278;HP=6;NF=10;NR=9;NS=52;CA=0;DP=367
+1	1992350	.	CA	CACCTGGGCGTGTGA	56	PASS	AF=0.19029;HP=1;NF=6;NR=3;NS=52;CA=0;DP=412
+1	1993852	rs34106910;-/G,venter	GCC	GC	100	PASS	AF=0.178292;HP=2;DB;NF=15;NR=7;NS=51;CA=0;DP=388
+1	1996153	.	GT	GTT	59	PASS	AF=0.126167;HP=8;NF=7;NR=14;NS=51;CA=0;DP=436
+1	2010531	rs35300904;-/C,venter	CA	CGA	100	PASS	AF=0.2131;HP=1;DB;NF=18;NR=7;NS=52;CA=0;DP=418
+1	2019409	rs55716481;-/AGTGACTAAGGTGACCAGG,venter	CA	CAGGTGACCAGGAGTGACTAA	100	PASS	AF=0.901172;HP=1;DB;NF=17;NR=16;NS=52;CA=0;DP=600
+1	2019867	rs58602729;-/CT	CCTC	CC	100	PASS	AF=0.15521;HP=3;DB;NF=6;NR=12;NS=52;CA=0;DP=542
+1	2019961	mills	CGTTTTGTTTTG	CG	100	PASS	AF=0.239816;HP=1;NF=44;NR=59;NS=52;CA=0;DP=513
+1	2027926	.	CT	CTT	100	PASS	AF=0.591615;HP=1;NF=7;NR=4;NS=51;CA=M;DP=262
+1	2028042	.	CT	CTT	100	PASS	AF=0.242884;HP=1;NF=28;NR=12;NS=51;CA=M;DP=738
+1	2031773	.	GA	GGGTA	100	PASS	AF=0.197429;HP=1;NF=15;NR=7;NS=51;CA=0;DP=405
+1	2036771	.	AC	ACCCC	100	PASS	AF=0.173415;HP=3;NF=1;NR=5;NS=52;CA=0;DP=532
+1	2040362	venter	CT	CTT	100	PASS	AF=0.61548;HP=3;NF=31;NR=33;NS=52;CA=0;DP=522
+1	2042747	.	CG	CGGGGG	100	PASS	AF=0.132985;HP=2;NF=11;NR=6;NS=51;CA=0;DP=880
+1	2042976	.	GT	GTTATT	100	PASS	AF=0.225391;HP=2;NF=13;NR=25;NS=51;CA=M;DP=882
+1	2045297	.	GT	GTAGTTATT	36	PASS	AF=0.513037;HP=2;NF=5;NR=16;NS=46;CA=M;DP=269
+1	2048642	rs56348719;-/A	CAG	CG	100	PASS	AF=0.626672;HP=1;DB;NF=15;NR=37;NS=51;CA=0;DP=337
+1	2055895	watson	AT	AATT	100	PASS	AF=0.183323;HP=1;NF=10;NR=14;NS=52;CA=0;DP=511
+1	2058884	watson	GCCTC	GC	100	PASS	AF=0.258368;HP=2;NF=23;NR=18;NS=51;CA=0;DP=533
+1	2068674	.	CTCTAT	CT	100	PASS	AF=0.0693035;HP=1;NF=7;NR=5;NS=52;CA=0;DP=600
+1	2076576	.	GTGAT	GT	100	PASS	AF=0.0691863;HP=1;NF=32;NR=24;NS=52;CA=0;DP=918
+1	2076741	.	GTGAT	GT	49	PASS	AF=0.200249;HP=1;NF=13;NR=21;NS=51;CA=0;DP=758
+1	2076895	.	GTGAT	GT	100	PASS	AF=0.134423;HP=1;NF=21;NR=19;NS=51;CA=0;DP=658
+1	2076954	rs60433546;-/ATG	AA	AATGA	100	PASS	AF=0.310432;HP=2;DB;NF=12;NR=27;NS=52;CA=0;DP=664
+1	2079377	rs3835418;-/T	CT	CTT	100	PASS	AF=0.201153;HP=1;DB;NF=13;NR=15;NS=52;CA=0;DP=451
+1	2081537	rs56068331;-/GTGT	CGTGTG	CG	13	PASS	AF=0.276967;HP=1;DB;NF=58;NR=66;NS=52;CA=0;DP=516
+1	2085600	rs3835419;-/CTGGGCCAACCC	GA	GACCCCTGGGCCAA	100	PASS	AF=0.243746;HP=1;DB;NF=11;NR=6;NS=52;CA=0;DP=535
+1	2087974	.	GCC	GC	15	PASS	AF=0.0623565;HP=8;NF=7;NR=14;NS=52;CA=0;DP=325
+1	2089182	rs34571180;-/CTC,mills,venter	GCCTC	GC	100	PASS	AF=0.116512;HP=2;DB;NF=9;NR=4;NS=51;CA=0;DP=440
+1	2089950	.	CG	CGGGG	100	PASS	AF=0.178382;HP=2;NF=20;NR=7;NS=51;CA=0;DP=444
+1	2091793	rs56317708;-/GATA,venter,watson	AA	AAGATA	100	PASS	AF=0.896718;HP=2;DB;NF=37;NR=55;NS=52;CA=0;DP=525
+1	2094394	watson	TCCACC	TC	100	PASS	AF=0.191274;HP=2;NF=15;NR=11;NS=52;CA=0;DP=554
+1	2099298	.	TG	TGG	100	PASS	AF=0.234547;HP=1;NF=15;NR=4;NS=51;CA=0;DP=434
+1	2101678	.	AGACG	AG	100	PASS	AF=0.0220699;HP=1;NF=10;NR=4;NS=51;CA=0;DP=533
+1	2104518	rs55672189;-/CGTCTC,venter	AG	AGTCTCCG	32	PASS	AF=0.0318159;HP=1;DB;NF=1;NR=2;NS=51;CA=0;DP=303
+1	2110593	rs34825103;-/C	TG	TGG	100	PASS	AF=0.0674605;HP=1;DB;NF=1;NR=4;NS=52;CA=M;DP=336
+1	2114205	.	TT	TTTGT	14	PASS	AF=0.0440601;HP=4;NF=24;NR=27;NS=52;CA=0;DP=414
+1	2118677	rs35613376;-/T,venter	GA	GAA	100	PASS	AF=0.110597;HP=1;DB;NF=4;NR=6;NS=51;CA=0;DP=395
+1	2129208	venter	CGTGTGTGTGTGTGTGTGTGTG	CG	100	PASS	AF=0.312577;HP=1;NF=50;NR=42;NS=51;CA=0;DP=395
+1	2136104	rs34745034;-/AC,venter,watson	CTGT	CT	100	PASS	AF=0.148774;HP=1;DB;NF=9;NR=15;NS=51;CA=0;DP=394
+1	2147798	.	CGG	CG	100	PASS	AF=0.069257;HP=5;NF=3;NR=7;NS=51;CA=0;DP=433
+1	2156467	rs34646035;-/A,venter	GG	GTG	100	PASS	AF=0.0650203;HP=2;DB;NF=3;NR=2;NS=51;CA=0;DP=299
+1	2163248	rs34969427;-/CA,venter,watson	CT	CTGT	59	PASS	AF=0.323344;HP=1;DB;NF=36;NR=42;NS=52;CA=0;DP=622
+1	2168152	rs34184068;-/C	TG	TGG	100	PASS	AF=0.267631;HP=8;DB;NF=12;NR=25;NS=52;CA=0;DP=462
+1	2173905	rs59705675;-/C,venter	GCC	GC	100	PASS	AF=0.519185;HP=4;DB;NF=28;NR=31;NS=52;CA=0;DP=472
+1	2178426	.	ATCTCT	AT	59	PASS	AF=0.0153899;HP=1;NF=1;NR=2;NS=52;CA=0;DP=558
+1	2180516	.	TG	TGGG	15	PASS	AF=0.10873;HP=1;NF=7;NR=3;NS=52;CA=0;DP=495
+1	2193017	rs35691128;-/C,venter	TG	TGG	100	PASS	AF=0.296206;HP=9;DB;NF=9;NR=11;NS=52;CA=0;DP=367
+1	2204648	.	AGGGG	AG	100	PASS	AF=0.0847086;HP=8;NF=9;NR=7;NS=52;CA=0;DP=441
+1	2211603	.	TG	TGGGGGGGGGG	100	PASS	AF=0.176;HP=1;NF=5;NR=9;NS=52;CA=0;DP=507
+1	2211835	rs35471620;-/C,venter	CG	CGG	100	PASS	AF=0.403922;HP=3;DB;NF=20;NR=20;NS=51;CA=0;DP=363
+1	2213004	rs35841716;-/G,mills,venter	TGG	TG	100	PASS	AF=0.938006;HP=7;DB;NF=35;NR=9;NS=52;CA=0;DP=297
+1	2214726	.	GC	GCC	100	PASS	AF=0.415474;HP=9;NF=18;NR=19;NS=51;CA=0;DP=416
+1	2220552	rs35472917;-/C,venter	AGG	AG	100	PASS	AF=0.609848;HP=9;DB;NF=24;NR=22;NS=51;CA=0;DP=385
+1	2221276	.	GC	GCC	23	PASS	AF=0.0895016;HP=2;NF=1;NR=11;NS=50;CA=0;DP=396
+1	2222657	.	AC	ACC	16	PASS	AF=0.0530452;HP=2;NF=1;NR=3;NS=51;CA=0;DP=404
+1	2223900	.	CAGGA	CA	100	PASS	AF=0.105506;HP=1;NF=9;NR=6;NS=52;CA=0;DP=517
+1	2232109	.	CAGG	CG	100	PASS	AF=0.220422;HP=1;NF=14;NR=13;NS=51;CA=0;DP=430
+1	2233476	rs34394327;-/CGTTT,mills,venter,watson	CC	CCGTTTC	100	PASS	AF=0.982218;HP=3;DB;NF=18;NR=31;NS=52;CA=0;DP=378
+1	2238242	rs56200665;-/C,mills	GG	GCG	100	PASS	AF=0.745403;HP=4;DB;NF=37;NR=40;NS=51;CA=0;DP=419
+1	2242260	rs34121936;-/C	AGG	AG	100	PASS	AF=0.107749;HP=4;DB;NF=7;NR=6;NS=51;CA=0;DP=427
+1	2246276	rs61120130;-/TGC,venter	GG	GGCTG	100	PASS	AF=0.447977;HP=3;DB;NF=13;NR=17;NS=51;CA=0;DP=403
+1	2246469	.	TT	TTCCCTCCCTTCCTTCCTTCCCTCCCT	100	PASS	AF=0.0710328;HP=3;NF=8;NR=6;NS=51;CA=B;DP=731
+1	2246586	rs59175712;-/CT	CC	CCTC	100	PASS	AF=0.378253;HP=2;DB;NF=33;NR=29;NS=50;CA=0;DP=515
+1	2248450	rs61135926;-/CACA	AA	AACACA	100	PASS	AF=0.367115;HP=3;DB;NF=24;NR=19;NS=51;CA=0;DP=445
+1	2248486	.	CAGA	CA	100	PASS	AF=0.108968;HP=1;NF=14;NR=11;NS=51;CA=M;DP=382
+1	2248806	rs59142249;-/A	CA	CAA	100	PASS	AF=0.0756571;HP=1;DB;NF=4;NR=12;NS=51;CA=0;DP=728
+1	2255198	.	TGCTGGAAAGAACAG	TG	100	PASS	AF=0.115149;HP=1;NF=9;NR=12;NS=51;CA=0;DP=470
+1	2267148	.	ACACACAGA	AA	100	PASS	AF=0.128331;HP=1;NF=4;NR=6;NS=51;CA=0;DP=681
+1	2268675	.	TG	TGG	10	PASS	AF=0.0406249;HP=1;NF=7;NR=3;NS=52;CA=0;DP=508
+1	2269958	.	GCACGCACACGCAC	GC	40	PASS	AF=0.0297002;HP=1;NF=6;NR=7;NS=50;CA=0;DP=288
+1	2270248	.	CCTG	CG	100	PASS	AF=0.21901;HP=4;NF=14;NR=17;NS=52;CA=0;DP=478
+1	2272049	.	AGGGGTGGCACGG	AG	100	PASS	AF=0.0657391;HP=4;NF=20;NR=19;NS=52;CA=0;DP=465
+1	2272576	rs35424701;-/T	TA	TAA	100	PASS	AF=0.0794139;HP=1;DB;NF=5;NR=5;NS=51;CA=0;DP=426
+1	2273487	.	TAA	TA	10	PASS	AF=0.0158231;HP=10;NF=25;NR=9;NS=51;CA=0;DP=564
+1	2282631	rs59328016;-/G	AG	AGG	100	PASS	AF=0.230902;HP=1;DB;NF=1;NR=6;NS=52;CA=M;DP=310
+1	2282847	rs34534255;-/AG	AC	ACTC	100	PASS	AF=0.108076;HP=1;DB;NF=5;NR=4;NS=50;CA=0;DP=293
+1	2284162	.	CA	CAA	12	PASS	AF=0.0508845;HP=10;NF=7;NR=7;NS=52;CA=0;DP=406
+1	2285124	.	TAAAAA	TA	100	PASS	AF=0.226133;HP=8;NF=14;NR=5;NS=52;CA=0;DP=315
+1	2288255	rs56670882;-/TACATAGAAAAA,venter,watson	CAAAATACATAGAA	CA	100	PASS	AF=0.154865;HP=4;DB;NF=46;NR=50;NS=51;CA=0;DP=466
+1	2291012	venter	ATAATT	AT	100	PASS	AF=0.140631;HP=1;NF=7;NR=9;NS=51;CA=0;DP=365
+1	2292525	rs60502597;-/CACAACAAC,venter	CA	CACAACCACAA	100	PASS	AF=0.411828;HP=1;DB;NF=18;NR=3;NS=52;CA=0;DP=515
+1	2305015	rs35699260;-/T,venter	CAG	CG	100	PASS	AF=0.283002;HP=1;DB;NF=14;NR=17;NS=51;CA=0;DP=451
+1	2310430	.	AA	AAAGA	100	PASS	AF=0.382413;HP=6;NF=20;NR=11;NS=52;CA=0;DP=408
+1	2314333	venter	CG	CGGACGCCAGGCAGAGGACTTCATCCCAGGCTTCAGTGCTCCTG	100	PASS	AF=0.736856;HP=2;NF=1;NR=2;NS=52;CA=0;DP=679
+1	2319273	rs57204595;-/C	ACC	AC	100	PASS	AF=0.125223;HP=2;DB;NF=7;NR=13;NS=52;CA=0;DP=523
+1	2322519	.	TCCT	TT	100	PASS	AF=0.200476;HP=2;NF=2;NR=10;NS=50;CA=0;DP=413
+1	2322562	.	TCCACCCTCC	TC	100	PASS	AF=0.3747;HP=2;NF=8;NR=15;NS=51;CA=0;DP=325
+1	2322680	.	CT	CTT	100	PASS	AF=0.284453;HP=1;NF=26;NR=24;NS=52;CA=M;DP=388
+1	2323804	venter	TC	TCC	100	PASS	AF=0.865363;HP=3;NF=38;NR=47;NS=50;CA=0;DP=438
+1	2325452	.	CG	CGG	39	PASS	AF=0.0242463;HP=3;NF=5;NR=8;NS=51;CA=0;DP=547
+1	2332518	.	GA	GAA	100	PASS	AF=0.0862532;HP=1;NF=5;NR=13;NS=51;CA=0;DP=414
+1	2337697	rs55744642;-/CGACA,venter,watson	GG	GGGACAG	100	PASS	AF=0.867582;HP=3;DB;NF=16;NR=23;NS=51;CA=0;DP=383
+1	2338712	rs34210450;-/AGCTTCCC,mills,venter	GC	GCCCAGCTTC	100	PASS	AF=0.431742;HP=3;DB;NF=24;NR=15;NS=52;CA=0;DP=504
+1	2341261	.	TCC	TC	20	PASS	AF=0.13716;HP=9;NF=4;NR=20;NS=51;CA=0;DP=258
+1	2343280	rs60532031;-/AAAAG,watson	GA	GAAGAAA	100	PASS	AF=0.0544808;HP=2;DB;NF=2;NR=10;NS=49;CA=0;DP=348
+1	2343570	venter	AA	AAAACA	100	PASS	AF=0.0882931;HP=6;NF=28;NR=18;NS=52;CA=0;DP=434
+1	2344468	.	TTTTGT	TT	100	PASS	AF=0.233529;HP=7;NF=49;NR=55;NS=52;CA=0;DP=493
+1	2345597	rs35560781;-/T,venter	TAA	TA	100	PASS	AF=0.501718;HP=6;DB;NF=36;NR=26;NS=52;CA=0;DP=532
+1	2352446	.	CGTG	CG	16	PASS	AF=0.0185013;HP=1;NF=10;NR=25;NS=52;CA=0;DP=432
+1	2352629	rs35263617;-/CA,venter	CG	CGTG	100	PASS	AF=0.4693;HP=1;DB;NF=44;NR=38;NS=51;CA=0;DP=539
+1	2355283	rs35314501;-/G	TC	TCC	100	PASS	AF=0.408524;HP=4;DB;NF=21;NR=18;NS=52;CA=0;DP=436
+1	2356275	rs34090130;-/G,mills	AGG	AG	100	PASS	AF=0.172214;HP=6;DB;NF=16;NR=9;NS=51;CA=0;DP=415
+1	2356753	rs58056215;-/TGGAGGC	TGGCTGGAG	TG	100	PASS	AF=0.178356;HP=2;DB;NF=43;NR=59;NS=51;CA=0;DP=429
+1	2357119	.	TGG	TG	100	PASS	AF=0.179635;HP=6;NF=12;NR=18;NS=52;CA=0;DP=495
+1	2357323	.	TCCCT	TT	100	PASS	AF=0.0931072;HP=3;NF=8;NR=9;NS=52;CA=0;DP=484
+1	2357636	.	CTCCACCTTT	CT	100	PASS	AF=0.252701;HP=1;NF=11;NR=9;NS=47;CA=M;DP=266
+1	2358758	.	CAA	CA	26	PASS	AF=0.0241071;HP=3;NF=1;NR=3;NS=51;CA=0;DP=486
+1	2360543	rs34299371;-/G,venter	GCC	GC	100	PASS	AF=0.460241;HP=7;DB;NF=18;NR=28;NS=51;CA=0;DP=403
+1	2365835	rs35499456;-/A	GT	GTT	100	PASS	AF=0.299753;HP=3;DB;NF=19;NR=20;NS=52;CA=0;DP=431
+1	2370798	.	AAACCA	AA	100	PASS	AF=0.315002;HP=4;NF=56;NR=52;NS=52;CA=0;DP=505
+1	2379981	rs35697743;-/C,venter	TGC	TC	100	PASS	AF=0.0396508;HP=1;DB;NF=1;NR=5;NS=50;CA=0;DP=425
+1	2383170	rs35931789;-/T,venter	CC	CAC	100	PASS	AF=0.441832;HP=7;DB;NF=24;NR=21;NS=52;CA=0;DP=453
+1	2383775	.	ACC	AC	19	PASS	AF=0.0298335;HP=5;NF=6;NR=2;NS=52;CA=0;DP=442
+1	2388741	watson	GCCTTCCTCAC	GC	100	PASS	AF=0.134128;HP=2;NF=6;NR=9;NS=47;CA=0;DP=257
+1	2394261	rs34886292;-/T,venter	CA	CAA	100	PASS	AF=0.640008;HP=1;DB;NF=28;NR=33;NS=51;CA=0;DP=459
+1	2395694	venter	AGG	AG	100	PASS	AF=0.518622;HP=3;NF=29;NR=23;NS=50;CA=0;DP=387
+1	2406522	rs35886782;-/CTCTGGACGCT,venter,watson	TG	TGCTCTCTGGACG	100	PASS	AF=0.531691;HP=1;DB;NF=12;NR=19;NS=51;CA=0;DP=452
+1	2429911	rs3831090;-/AT,mills	TT	TTAT	100	PASS	AF=0.138967;HP=3;DB;NF=24;NR=13;NS=52;CA=0;DP=328
+1	2458287	.	CGTG	CG	100	PASS	AF=0.0696687;HP=1;NF=38;NR=32;NS=52;CA=0;DP=613
+1	2458465	.	AGTG	AG	31	PASS	AF=0.0212179;HP=1;NF=18;NR=32;NS=51;CA=0;DP=600
+1	2460527	.	TG	TGCGGCCCATCTCAG	51	PASS	AF=0.164756;HP=1;NF=1;NR=4;NS=51;CA=0;DP=496
+1	2477778	.	AC	ACCC	100	PASS	AF=0.157812;HP=2;NF=2;NR=11;NS=51;CA=0;DP=389
+1	2501833	rs34000217;-/ATT	AA	AAATA	100	PASS	AF=0.437274;HP=5;DB;NF=19;NR=23;NS=51;CA=0;DP=337
+1	2503512	rs59345997;-/CAAA	AAAACA	AA	100	PASS	AF=0.46764;HP=4;DB;NF=44;NR=29;NS=52;CA=0;DP=456
+1	2506681	.	TG	TGGG	46	PASS	AF=0.310909;HP=9;NF=14;NR=8;NS=51;CA=0;DP=273
+1	2513520	rs5772070;-/G,mills	CGG	CG	100	PASS	AF=0.652792;HP=8;DB;NF=8;NR=34;NS=51;CA=0;DP=275
+1	2517761	.	TGC	TC	100	PASS	AF=0.0839269;HP=1;NF=3;NR=6;NS=50;CA=0;DP=359
+1	2520201	rs34705971;-/C,venter	AG	AGG	100	PASS	AF=0.612406;HP=1;DB;NF=42;NR=46;NS=52;CA=0;DP=518
+1	2521983	.	TCAAACAAACAAAC	TC	100	PASS	AF=0.365407;HP=1;NF=35;NR=29;NS=52;CA=0;DP=501
+1	2522019	.	CT	CTGTT	100	PASS	AF=0.523695;HP=1;NF=28;NR=12;NS=52;CA=0;DP=410
+1	2522313	rs34791736;-/A,venter	CT	CTT	100	PASS	AF=0.621139;HP=1;DB;NF=47;NR=24;NS=52;CA=0;DP=472
+1	2524952	rs35090174;-/CT	ACTC	AC	100	PASS	AF=0.224915;HP=1;DB;NF=19;NR=15;NS=51;CA=0;DP=517
+1	2529806	.	CATA	CA	100	PASS	AF=0.236462;HP=1;NF=22;NR=13;NS=51;CA=0;DP=625
+1	2529841	.	CACATA	CA	100	PASS	AF=0.190786;HP=1;NF=20;NR=19;NS=51;CA=0;DP=663
+1	2530205	rs61132608;-/CATATA,watson	CA	CACATATA	100	PASS	AF=0.547698;HP=1;DB;NF=20;NR=28;NS=52;CA=0;DP=660
+1	2543402	rs5772073;-/GAG,mills	TAGGA	TA	100	PASS	AF=0.24689;HP=1;DB;NF=12;NR=31;NS=52;CA=0;DP=543
+1	2547236	rs58240187;-/AGA,venter,watson	GG	GGAAG	100	PASS	AF=0.531939;HP=2;DB;NF=25;NR=25;NS=52;CA=0;DP=444
+1	2551119	rs35955733;-/CCC,venter,watson	GCCCC	GC	100	PASS	AF=0.606107;HP=9;DB;NF=24;NR=35;NS=52;CA=0;DP=492
+1	2551885	rs36036408;-/AC,venter	CGTG	CG	100	PASS	AF=0.356574;HP=1;DB;NF=39;NR=38;NS=52;CA=0;DP=803
+1	2552076	.	CGTG	CG	100	PASS	AF=0.066645;HP=1;NF=25;NR=15;NS=51;CA=0;DP=782
+1	2552384	.	CTGT	CT	12	PASS	AF=0.0121638;HP=1;NF=13;NR=25;NS=52;CA=0;DP=612
+1	2556252	.	ACACTC	AC	59	PASS	AF=0.143579;HP=1;NF=12;NR=9;NS=49;CA=0;DP=331
+1	2578474	.	CCACACCCCCAG	CG	100	PASS	AF=0.930867;HP=3;NF=16;NR=12;NS=51;CA=M;DP=281
+1	2688911	rs34425096;-/TC,venter	TTCT	TT	100	PASS	AF=0.26327;HP=5;DB;NF=17;NR=12;NS=52;CA=0;DP=451
+1	2691366	rs36213670;-/CTCTGGGCCA,mills,venter	GCTCTGGGCCAC	GC	39	PASS	AF=0.191253;HP=1;DB;NF=21;NR=36;NS=52;CA=0;DP=344
+1	2691723	rs57511628;-/ACCCCAGGAGATCCCTGC	TA	TACCCCAGGAGATCCCTGCA	100	PASS	AF=0.332823;HP=1;DB;NF=6;NR=7;NS=52;CA=0;DP=453
+1	2703254	.	CA	CAA	100	PASS	AF=0.111948;HP=3;NF=8;NR=13;NS=51;CA=0;DP=502
+1	2703885	.	AC	ACC	100	PASS	AF=0.0959517;HP=6;NF=24;NR=11;NS=51;CA=0;DP=531
+1	2725125	rs34936518;-/C,venter	GCT	GT	100	PASS	AF=0.375093;HP=1;DB;NF=33;NR=32;NS=52;CA=0;DP=621
+1	2725735	.	AACACA	AA	24	PASS	AF=0.0139746;HP=2;NF=16;NR=4;NS=51;CA=0;DP=639
+1	2726135	rs34620269;-/CA	GCAC	GC	100	PASS	AF=0.0410325;HP=1;DB;NF=28;NR=22;NS=52;CA=0;DP=626
+1	2726213	.	GC	GCAC	13	PASS	AF=0.0257105;HP=1;NF=8;NR=9;NS=52;CA=0;DP=552
+1	2746483	.	AC	ACC	40	PASS	AF=0.0544668;HP=1;NF=4;NR=12;NS=51;CA=0;DP=544
+1	2747281	.	TG	TGAGAG	100	PASS	AF=0.152256;HP=1;NF=11;NR=8;NS=52;CA=0;DP=855
+1	2754002	rs36202379;-/CTGCTTGT,mills,watson	ATTGTCTGCT	AT	100	PASS	AF=0.260861;HP=2;DB;NF=32;NR=35;NS=52;CA=0;DP=496
+1	2755160	rs34916159;-/A	TA	TAA	100	PASS	AF=0.532865;HP=7;DB;NF=10;NR=34;NS=52;CA=0;DP=533
+1	2755983	.	GCC	GC	100	PASS	AF=0.106339;HP=3;NF=18;NR=26;NS=52;CA=M;DP=700
+1	2765711	.	AA	AAGGAAGGA	100	PASS	AF=0.686149;HP=2;NF=11;NR=8;NS=50;CA=0;DP=364
+1	2765863	.	AG	AGG	100	PASS	AF=0.999885;HP=1;NF=14;NR=36;NS=49;CA=0;DP=364
+1	2765952	.	AG	AGG	100	PASS	AF=0.0789769;HP=1;NF=29;NR=29;NS=51;CA=B;DP=851
+1	2779479	.	TTTTCTTCTCTTTCT	TT	100	PASS	AF=0.712577;HP=4;NF=29;NR=22;NS=50;CA=0;DP=322
+1	2794338	rs34131736;-/T	CTG	CG	100	PASS	AF=0.089184;HP=1;DB;NF=7;NR=4;NS=51;CA=0;DP=440
+1	2801123	.	TCCTCCCCACCCTGAC	TC	48	PASS	AF=0.0412327;HP=2;NF=13;NR=18;NS=51;CA=0;DP=343
+1	2803308	watson	CATG	CG	100	PASS	AF=0.160766;HP=1;NF=23;NR=20;NS=52;CA=0;DP=816
+1	2805468	rs56260225;-/ACAA	AAAACA	AA	100	PASS	AF=0.859977;HP=4;DB;NF=62;NR=35;NS=51;CA=0;DP=433
+1	2806441	rs34966309;-/G	CG	CGG	100	PASS	AF=0.211987;HP=4;DB;NF=20;NR=11;NS=52;CA=0;DP=441
+1	2810388	.	GCC	GC	100	PASS	AF=0.11183;HP=2;NF=8;NR=5;NS=51;CA=0;DP=431
+1	2822166	.	TACATGCACACA	TA	100	PASS	AF=0.150719;HP=1;NF=43;NR=52;NS=52;CA=0;DP=844
+1	2822270	rs59677991;-/GC	GGCG	GG	18	NoQCALL	AF=0.0194725;HP=2;DB;NF=15;NR=5;NS=52;CA=0;DP=806
+1	2822473	.	CACACAC	CC	100	PASS	AF=0.138944;HP=1;NF=6;NR=7;NS=52;CA=0;DP=951
+1	2827616	.	CAAGC	CC	52	PASS	AF=0.132317;HP=2;NF=8;NR=4;NS=51;CA=0;DP=300
+1	2828576	.	CG	CTG	100	PASS	AF=0.168378;HP=1;NF=8;NR=2;NS=52;CA=0;DP=325
+1	2829365	rs35758696;-/A	TAA	TA	100	PASS	AF=0.216995;HP=6;DB;NF=20;NR=20;NS=51;CA=0;DP=531
+1	2833106	.	TG	TGTTGGG	100	PASS	AF=0.237115;HP=1;NF=11;NR=4;NS=52;CA=0;DP=336
+1	2834384	.	AC	ACC	32	PASS	AF=0.0617917;HP=1;NF=3;NR=5;NS=52;CA=0;DP=592
+1	2835704	rs35824541;-/G	AGG	AG	100	PASS	AF=0.188967;HP=3;DB;NF=15;NR=11;NS=52;CA=0;DP=691
+1	2836635	rs56691957;-/AT	CATG	CG	100	PASS	AF=0.126742;HP=1;DB;NF=8;NR=13;NS=52;CA=0;DP=611
+1	2851063	.	ATGTGTGTCT	AT	100	PASS	AF=0.224053;HP=1;NF=34;NR=32;NS=52;CA=0;DP=798
+1	2859183	rs34869376;-/CT	ACTC	AC	100	PASS	AF=0.228335;HP=1;DB;NF=11;NR=14;NS=52;CA=0;DP=446
+1	2859269	rs34009406;-/C	AC	ACC	100	PASS	AF=0.168197;HP=2;DB;NF=8;NR=14;NS=52;CA=0;DP=460
+1	2862455	rs34488344;-/T	GT	GTT	100	PASS	AF=0.140555;HP=10;DB;NF=25;NR=16;NS=52;CA=0;DP=484
+1	2866073	.	AC	ACC	56	PASS	AF=0.0758065;HP=1;NF=2;NR=11;NS=51;CA=0;DP=513
+1	2871504	.	TA	TACTAA	100	PASS	AF=0.128765;HP=1;NF=11;NR=12;NS=52;CA=0;DP=676
+1	2871601	rs60410855;-/TCCA	CC	CCCATC	100	PASS	AF=0.11635;HP=3;DB;NF=19;NR=14;NS=52;CA=0;DP=682
+1	2874709	.	GT	GTT	100	PASS	AF=0.138394;HP=9;NF=8;NR=12;NS=51;CA=0;DP=534
+1	2876814	rs5772089;-/A,mills,venter	GG	GAG	100	PASS	AF=0.999994;HP=10;DB;NF=39;NR=42;NS=50;CA=0;DP=343
+1	2877421	rs35085736;-/C,venter	GC	GCC	100	PASS	AF=0.582204;HP=6;DB;NF=29;NR=37;NS=50;CA=0;DP=426
+1	2881114	.	GG	GTG	100	PASS	AF=0.586283;HP=5;NF=16;NR=5;NS=47;CA=M;DP=256
+1	2883970	.	GG	GCG	16	PASS	AF=0.516075;HP=4;NF=6;NR=2;NS=51;CA=M;DP=332
+1	2885504	.	TCC	TC	29	PASS	AF=0.140908;HP=9;NF=12;NR=8;NS=51;CA=0;DP=353
+1	2886983	.	AG	AGG	50	PASS	AF=0.0436199;HP=3;NF=7;NR=2;NS=50;CA=0;DP=401
+1	2887864	rs57379840;-/T,venter	CG	CTG	100	PASS	AF=0.770236;HP=2;DB;NF=41;NR=25;NS=51;CA=0;DP=375
+1	2892284	.	CAT	CT	100	PASS	AF=0.0885935;HP=1;NF=23;NR=17;NS=52;CA=0;DP=685
+1	2892433	venter	AT	ATCCATCCTCCATCCT	100	PASS	AF=0.814532;HP=1;NF=13;NR=12;NS=52;CA=0;DP=620
+1	2892472	.	CCCATC	CC	100	PASS	AF=0.181828;HP=3;NF=50;NR=61;NS=52;CA=0;DP=633
+1	2899352	.	CTA	CA	100	PASS	AF=0.0433393;HP=1;NF=5;NR=2;NS=51;CA=0;DP=512
+1	2902379	.	TAGA	TA	40	PASS	AF=0.0165292;HP=1;NF=3;NR=2;NS=51;CA=0;DP=476
+1	2903930	rs36097640;-/A	TAA	TA	12	PASS	AF=0.0522384;HP=8;DB;NF=13;NR=15;NS=51;CA=0;DP=535
+1	2907194	rs35693840;-/G	AG	AGG	100	PASS	AF=0.136995;HP=5;DB;NF=14;NR=8;NS=52;CA=0;DP=516
+1	2916313	.	AC	ACC	40	PASS	AF=0.0606632;HP=1;NF=1;NR=13;NS=52;CA=0;DP=529
+1	2923107	.	GA	GGGGGGAA	35	PASS	AF=0.311458;HP=1;NF=1;NR=2;NS=50;CA=0;DP=285
+1	2923994	.	AAGGA	AA	100	PASS	AF=0.136914;HP=3;NF=4;NR=16;NS=52;CA=0;DP=475
+1	2926544	rs58065168;-/G	TG	TGG	100	PASS	AF=0.231871;HP=7;DB;NF=23;NR=13;NS=51;CA=0;DP=445
+1	2927774	.	GTCT	GT	100	PASS	AF=0.039848;HP=1;NF=24;NR=39;NS=52;CA=0;DP=466
+1	2928267	rs4013154;-/TCT	CAGAA	CA	100	PASS	AF=0.176094;HP=1;DB;NF=10;GC;NR=20;NS=52;CA=0;DP=390
+1	2931584	.	GTGGTGTTTTCATT	GT	100	PASS	AF=0.171247;HP=1;NF=23;NR=10;NS=52;CA=0;DP=486
+1	2932462	.	GT	GTGAT	56	PASS	AF=0.766604;HP=1;NF=33;NR=13;NS=52;CA=M;DP=790
+1	2932531	.	GT	GTGGTGAT	56	PASS	AF=0.365205;HP=1;NF=19;NR=4;NS=52;CA=M;DP=738
+1	2938240	rs57953122;-/AAGCC	AC	ACCAAGC	100	PASS	AF=0.229942;HP=2;DB;NF=5;NR=7;NS=52;CA=0;DP=387
+1	2939820	rs35035410;-/C,venter	GCC	GC	100	PASS	AF=0.270114;HP=6;DB;NF=15;NR=21;NS=52;CA=0;DP=477
+1	2940602	.	GA	GAA	100	PASS	AF=0.245189;HP=10;NF=31;NR=30;NS=52;CA=0;DP=516
+1	2941986	.	ACCC	AC	100	PASS	AF=0.242307;HP=10;NF=20;NR=20;NS=52;CA=0;DP=471
+1	2943041	rs34450334;-/G,mills	CGG	CG	100	PASS	AF=0.212427;HP=8;DB;NF=13;NR=12;NS=52;CA=0;DP=523
+1	2943605	rs5772091;-/C,mills	GC	GCC	100	PASS	AF=0.155328;HP=1;DB;NF=7;NR=7;NS=52;CA=0;DP=349
+1	2946559	.	TT	TTGT	100	PASS	AF=0.174249;HP=3;NF=13;NR=14;NS=52;CA=0;DP=596
+1	2948391	.	TT	TTTTTCT	100	PASS	AF=0.137955;HP=5;NF=19;NR=16;NS=52;CA=0;DP=557
+1	2949076	rs33910396;-/G,mills	CG	CGG	100	PASS	AF=0.102902;HP=1;DB;NF=3;NR=8;NS=52;CA=0;DP=413
+1	2950056	.	TC	TCAAACAAAC	100	PASS	AF=0.133966;HP=1;NF=9;NR=9;NS=51;CA=0;DP=587
+1	2950689	rs60031908;-/A	CAA	CA	100	PASS	AF=0.200188;HP=8;DB;NF=20;NR=25;NS=51;CA=0;DP=517
+1	2958314	.	CC	CCCATC	100	PASS	AF=0.190271;HP=3;NF=39;NR=18;NS=52;CA=M;DP=454
+1	2961502	rs60708459;-/T	AT	ATT	100	PASS	AF=0.219472;HP=3;DB;NF=14;NR=16;NS=52;CA=0;DP=460
+1	2968615	.	AG	AGG	100	PASS	AF=0.288912;HP=2;NF=11;NR=13;NS=51;CA=0;DP=324
+1	2982005	.	GT	GGGTT	100	PASS	AF=0.189932;HP=5;NF=6;NR=5;NS=52;CA=0;DP=460
+1	2984462	rs34471979;-/C,venter	TCC	TC	100	PASS	AF=0.423837;HP=2;DB;NF=20;NR=27;NS=51;CA=0;DP=459
+1	2985828	rs5772093;-/TTCGGGG,mills,venter,watson	CT	CTTCGGGGT	100	PASS	AF=0.888966;HP=1;DB;NF=22;NR=15;NS=49;CA=0;DP=372
+1	2987353	.	AGTG	AG	39	PASS	AF=0.0534166;HP=1;NF=13;NR=12;NS=51;CA=0;DP=341
+1	2990018	.	TC	TGC	51	PASS	AF=0.347647;HP=1;NF=9;NR=5;NS=52;CA=0;DP=328
+1	2992552	rs55740340;-/TTGT,mills,venter,watson	CT	CTGTTT	100	PASS	AF=0.633228;HP=1;DB;NF=31;NR=31;NS=52;CA=0;DP=471
+1	2994869	.	TT	TTTAT	48	PASS	AF=0.246512;HP=4;NF=8;NR=15;NS=49;CA=0;DP=238
+1	2996339	rs60239912;-/TCATTCAT	CT	CTCATTCATT	100	PASS	AF=0.288255;HP=1;DB;NF=27;NR=24;NS=52;CA=0;DP=550
+1	2996940	.	TG	TGGG	52	PASS	AF=0.252534;HP=1;NF=5;NR=3;NS=51;CA=0;DP=485
+1	2997430	rs58914207;-/TC	TTCT	TT	17	PASS	AF=0.0239916;HP=3;DB;NF=1;NR=3;NS=51;CA=0;DP=533
+1	2998548	rs3067411;-/GC,mills,watson	TT	TGCT	100	PASS	AF=0.513959;HP=2;DB;NF=16;NR=33;NS=51;CA=0;DP=457
+1	2998746	rs33948447;-/CTGAGGGTAT,mills,watson	CCTGAGGGTATC	CC	100	PASS	AF=0.567187;HP=2;DB;NF=32;NR=26;NS=51;CA=0;DP=446
+1	2998922	rs3067390;-/CA,mills,watson	CTGT	CT	100	PASS	AF=0.344398;HP=1;DB;NF=25;NR=25;NS=52;CA=0;DP=544
+1	3001309	.	TCTTCC	TC	100	PASS	AF=0.122521;HP=1;NF=13;NR=16;NS=51;CA=0;DP=463
+1	3003643	rs34727240;-/A	CA	CAA	100	PASS	AF=0.30407;HP=4;DB;NF=23;NR=14;NS=51;CA=0;DP=462
+1	3003980	.	ATTCT	AT	100	PASS	AF=0.0770408;HP=2;NF=12;NR=8;NS=51;CA=0;DP=436
+1	3015507	rs36215320;-/AATAAT,mills	AAATAATA	AA	100	PASS	AF=0.341849;HP=4;DB;NF=19;NR=21;NS=52;CA=M;DP=287
+1	3020627	.	GC	GCGCGCAC	45	PASS	AF=0.0864166;HP=1;NF=3;NR=4;NS=52;CA=0;DP=675
+1	3020729	.	GCAC	GC	100	PASS	AF=0.270815;HP=1;NF=26;NR=22;NS=52;CA=0;DP=511
+1	3020780	.	GCAC	GC	100	PASS	AF=0.0529136;HP=1;NF=14;NR=13;NS=52;CA=0;DP=580
+1	3020851	rs36140038;-/G,venter	CC	CGC	100	PASS	AF=0.0570603;HP=2;DB;NF=7;NR=8;NS=52;CA=0;DP=580
+1	3020930	.	GCAC	GC	100	PASS	AF=0.0608239;HP=1;NF=21;NR=20;NS=52;CA=0;DP=662
+1	3020996	.	ACT	AT	100	PASS	AF=0.0376658;HP=1;NF=4;NR=2;NS=52;CA=0;DP=646
+1	3021049	rs58793198;-/CA	AA	AACA	100	PASS	AF=0.0822964;HP=2;DB;NF=19;NR=18;NS=52;CA=0;DP=756
+1	3024532	.	TGTGTGCG	TG	100	PASS	AF=0.0453628;HP=1;NF=12;NR=35;NS=51;CA=0;DP=585
+1	3035092	venter,watson	CTCCCACCATGCTACTGGAGACCAT	CT	100	PASS	AF=0.175148;HP=1;NF=41;NR=54;NS=51;CA=0;DP=464
+1	3035605	rs56967751;-/TG,venter,watson	AG	AGTG	100	PASS	AF=0.387697;HP=1;DB;NF=30;NR=25;NS=51;CA=0;DP=671
+1	3035812	.	CGTG	CG	100	PASS	AF=0.051827;HP=1;NF=28;NR=20;NS=51;CA=0;DP=643
+1	3035887	.	ATGT	AT	50	PASS	AF=0.0421027;HP=1;NF=24;NR=34;NS=52;CA=0;DP=556
+1	3036291	rs36033160;-/CCG	CT	CCCGT	100	PASS	AF=0.0605711;HP=1;DB;NF=3;NR=5;NS=51;CA=0;DP=428
+1	3037949	rs34840011;-/A,venter	TA	TAA	100	PASS	AF=0.096326;HP=8;DB;NF=5;NR=6;NS=52;CA=0;DP=462
+1	3046082	rs35271327;-/T	AT	ATT	19	PASS	AF=0.0473995;HP=7;DB;NF=9;NR=8;NS=52;CA=0;DP=430
+1	3049499	.	ACC	AC	27	PASS	AF=0.0269129;HP=3;NF=3;NR=1;NS=51;CA=0;DP=373
+1	3053337	.	TGG	TG	100	PASS	AF=0.205181;HP=7;NF=15;NR=19;NS=52;CA=0;DP=424
+1	3058772	.	TCATCC	TC	100	PASS	AF=0.716787;HP=1;NF=61;NR=51;NS=52;CA=0;DP=435
+1	3069377	.	CATGGT	CT	100	PASS	AF=0.42044;HP=1;NF=3;NR=14;NS=48;CA=M;DP=257
+1	3076481	rs35945121;-/T,mills	ATT	AT	100	PASS	AF=0.33892;HP=10;DB;NF=9;NR=38;NS=52;CA=0;DP=438
+1	3079028	.	TA	TCA	100	PASS	AF=0.0528803;HP=1;NF=5;NR=3;NS=51;CA=0;DP=475
+1	3084256	watson	AGTTTAGATACTG	AG	100	PASS	AF=0.123981;HP=1;NF=18;NR=14;NS=52;CA=0;DP=554
+1	3087172	rs34468831;-/A	GAA	GA	100	PASS	AF=0.0618762;HP=3;DB;NF=2;NR=5;NS=50;CA=0;DP=475
+1	3087517	.	CACACGCAGTCTTA	CA	100	PASS	AF=0.637316;HP=1;NF=41;NR=37;NS=52;CA=0;DP=973
+1	3087777	.	TA	TACA	100	PASS	AF=0.377666;HP=1;NF=43;NR=55;NS=52;CA=M;DP=966
+1	3087871	.	CACGGTCTTA	CA	100	PASS	AF=0.589214;HP=1;NF=16;NR=14;NS=51;CA=0;DP=710
+1	3087938	.	AG	AGTCTTACACAAGCGG	100	PASS	AF=0.469462;HP=1;NF=28;NR=29;NS=52;CA=M;DP=816
+1	3088154	.	GG	GCAG	100	PASS	AF=0.0511127;HP=2;NF=11;NR=10;NS=52;CA=M;DP=894
+1	3088232	rs35125658;-/TT	GG	GCAG	100	PASS	AF=0.0967781;HP=2;DB;NF=3;NR=24;NS=51;CA=M;DP=938
+1	3088301	.	CT	CTTGCACACGCAGTTT	47	PASS	AF=0.0188781;HP=2;NF=5;NR=2;NS=51;CA=M;DP=684
+1	3105704	rs35372326;-/G,mills	CGG	CG	100	PASS	AF=0.0956114;HP=2;DB;NF=6;NR=4;NS=52;CA=0;DP=378
+1	3107408	rs5772098;-/G,mills	AG	AGG	100	PASS	AF=0.107417;HP=5;DB;NF=19;NR=15;NS=52;CA=0;DP=504
+1	3107714	rs34461209;-/G,venter	TG	TGG	100	PASS	AF=0.61875;HP=3;DB;NF=21;NR=28;NS=52;CA=0;DP=454
+1	3108534	rs59512254;-/GA	GGAG	GG	100	PASS	AF=0.184609;HP=2;DB;NF=17;NR=11;NS=52;CA=0;DP=510
+1	3121064	.	TG	TGAG	59	PASS	AF=0.0221492;HP=1;NF=7;NR=3;NS=52;CA=0;DP=555
+1	3131583	rs57750843;-/A	GAA	GA	100	PASS	AF=0.166149;HP=9;DB;NF=21;NR=20;NS=52;CA=0;DP=490
+1	3131742	.	GT	GGGGGGGGGTT	27	PASS	AF=0.243052;HP=3;NF=2;NR=1;NS=49;CA=0;DP=394
+1	3135855	rs34340862;-/TAA,mills	CT	CTAAT	100	PASS	AF=0.183257;HP=1;DB;NF=11;NR=9;NS=51;CA=0;DP=520
+1	3146366	.	GGAG	GG	100	PASS	AF=0.040688;HP=4;NF=13;NR=14;NS=51;CA=0;DP=434
+1	3152159	.	AT	ATT	100	PASS	AF=0.0396994;HP=4;NF=8;NR=9;NS=52;CA=0;DP=489
+1	3157729	venter,watson	AG	AGGGGTGAGGTG	100	PASS	AF=0.830079;HP=4;NF=30;NR=23;NS=51;CA=0;DP=548
+1	3158807	.	AGG	AG	100	PASS	AF=0.705976;HP=6;NF=35;NR=30;NS=52;CA=0;DP=371
+1	3158885	.	CATG	CG	100	PASS	AF=0.09216;HP=1;NF=6;NR=6;NS=51;CA=0;DP=375
+1	3163280	.	CAAAATA	CA	100	PASS	AF=0.148526;HP=4;NF=13;NR=1;NS=49;CA=M;DP=326
+1	3164018	rs5772100;-/A,mills,venter	TAA	TA	100	PASS	AF=0.999998;HP=3;DB;NF=67;NR=69;NS=52;CA=0;DP=511
+1	3174387	.	CAGG	CG	17	PASS	AF=0.0141709;HP=1;NF=1;NR=2;NS=51;CA=0;DP=428
+1	3176024	.	GACAGTCCCAGAGGAGCA	GA	44	PASS	AF=0.0444872;HP=1;NF=3;NR=10;NS=52;CA=M;DP=480
+1	3177102	.	AG	AGAGGAGGACAGTCGGGGAGGACAGTCCCGG	100	PASS	AF=0.346135;HP=1;NF=8;NR=13;NS=52;CA=0;DP=550
+1	3179862	rs35987870;-/GTGG	ATGTGT	AT	100	PASS	AF=0.0762534;HP=1;DB;NF=17;NR=17;NS=51;CA=0;DP=618
+1	3183094	rs33953525;-/GGTGCCGTGAACAGAGCCAGCGAGG,mills	AG	AGGTGCCGTGAACAGAGCCAGCGAGGG	100	PASS	AF=0.665581;HP=2;DB;NF=15;NR=15;NS=52;CA=0;DP=424
+1	3183166	rs35451643;-/C,venter	TCC	TC	100	PASS	AF=0.123295;HP=4;DB;NF=12;NR=6;NS=52;CA=0;DP=460
+1	3184208	rs59663829;-/GCACACACAA	TA	TGCACACACAAA	100	PASS	AF=0.152939;HP=1;DB;NF=4;NR=4;NS=52;CA=0;DP=733
+1	3186299	.	ACC	AC	100	PASS	AF=0.951135;HP=8;NF=16;NR=14;NS=51;CA=0;DP=311
+1	3202609	.	TG	TGGGGGGG	11	PASS	AF=0.122471;HP=1;NF=3;NR=3;NS=52;CA=0;DP=479
+1	3292566	.	TC	TCGGGGTGCCC	12	PASS	AF=0.209628;HP=1;NF=22;NR=17;NS=51;CA=0;DP=462
+1	3292669	.	AAGA	AA	100	PASS	AF=0.312194;HP=8;NF=13;NR=14;NS=51;CA=0;DP=483
+1	3293018	rs35846516;-/A,venter	GAA	GA	100	PASS	AF=0.791047;HP=9;DB;NF=59;NR=44;NS=51;CA=0;DP=507
+1	3293422	rs34150215;-/A,mills,venter	TA	TAA	100	PASS	AF=0.418316;HP=7;DB;NF=27;NR=18;NS=52;CA=0;DP=481
+1	3307979	rs35082175;-/A,venter	CAT	CT	100	PASS	AF=0.379363;HP=1;DB;NF=36;NR=25;NS=52;CA=0;DP=659
+1	3308056	.	CATA	CA	100	PASS	AF=0.0313721;HP=1;NF=4;NR=5;NS=52;CA=0;DP=699
+1	3308306	rs34659426;-/AA	CAAA	CA	100	PASS	AF=0.238591;HP=3;DB;NF=23;NR=22;NS=52;CA=0;DP=732
+1	3308692	.	GC	GCC	100	PASS	AF=0.610676;HP=6;NF=23;NR=26;NS=52;CA=0;DP=447
+1	3309461	.	ACCCTCCTCTGAGTCTTCCTCCCCTTCCCGTGC	AC	100	PASS	AF=0.218197;HP=3;NF=28;NR=41;NS=51;CA=0;DP=430
+1	3313004	.	ATT	AT	18	PASS	AF=0.117282;HP=10;NF=22;NR=12;NS=51;CA=0;DP=407
+1	3315219	rs35154920;-/GT	CG	CGTG	100	PASS	AF=0.407055;HP=1;DB;NF=23;NR=17;NS=52;CA=0;DP=498
+1	3315279	rs34306698;-/AT	CG	CATG	100	PASS	AF=0.27165;HP=1;DB;NF=18;NR=10;NS=51;CA=0;DP=460
+1	3315552	rs61650876;-/ATGT	CATGTG	CG	100	PASS	AF=0.074251;HP=1;DB;NF=10;NR=7;NS=52;CA=0;DP=612
+1	3315608	.	CGTG	CG	44	PASS	AF=0.0200264;HP=1;NF=15;NR=25;NS=52;CA=0;DP=622
+1	3316180	rs34769314;-/GTGA	TGTGAG	TG	100	PASS	AF=0.13026;HP=1;DB;NF=29;NR=21;NS=52;CA=0;DP=930
+1	3316258	rs57503175;-/TGTATGTGCGTGTGTGTGGTGTG	GG	GGTGTGTGGTGTGTGTATGTGCGTG	100	PASS	AF=0.277124;HP=3;DB;NF=3;NR=11;NS=52;CA=0;DP=898
+1	3316338	rs34133894;-/GT	GGTG	GG	100	PASS	AF=0.121606;HP=2;DB;NF=18;NR=27;NS=52;CA=0;DP=901
+1	3316408	.	TGG	TG	100	PASS	AF=0.153074;HP=7;NF=23;NR=10;NS=52;CA=0;DP=898
+1	3316476	rs60842130;-/GTG	TGTGG	TG	43	PASS	AF=0.0151943;HP=1;DB;NF=4;NR=1;NS=52;CA=0;DP=732
+1	3317481	rs34240659;-/AT	CATA	CA	100	PASS	AF=0.127605;HP=1;DB;NF=14;NR=8;NS=52;CA=0;DP=538
+1	3319964	.	ACC	AC	100	PASS	AF=0.0511239;HP=5;NF=12;NR=4;NS=52;CA=0;DP=505
+1	3327173	rs56093721;-/A,venter	TAA	TA	100	PASS	AF=0.89527;HP=9;DB;NF=37;NR=68;NS=52;CA=0;DP=540
+1	3328302	.	AG	AGGGGGG	53	PASS	AF=0.124625;HP=2;NF=13;NR=2;NS=52;CA=0;DP=585
+1	3335208	.	CGG	CG	100	PASS	AF=0.0438559;HP=2;NF=3;NR=3;NS=52;CA=0;DP=448
+1	3335551	rs34869178;-/T	CTC	CC	100	PASS	AF=0.0947355;HP=1;DB;NF=4;NR=8;NS=52;CA=0;DP=487
+1	3342021	rs34485545;-/A	TA	TAA	100	PASS	AF=0.154806;HP=9;DB;NF=25;NR=23;NS=52;CA=0;DP=444
+1	3347098	venter	CG	CAG	100	PASS	AF=0.931731;HP=1;NF=49;NR=54;NS=52;CA=0;DP=497
+1	3348129	rs55866341;-/G,venter	CG	CGG	100	PASS	AF=0.883294;HP=1;DB;NF=55;NR=55;NS=52;CA=0;DP=521
+1	3352897	.	AA	ACA	46	PASS	AF=0.0385898;HP=6;NF=2;NR=6;NS=51;CA=0;DP=407
+1	3353821	rs34792713;-/T	AT	ATT	36	PASS	AF=0.0290672;HP=1;DB;NF=3;NR=3;NS=52;CA=0;DP=428
+1	3356271	.	TTCCT	TT	15	PASS	AF=0.00990969;HP=3;NF=1;NR=1;NS=52;CA=0;DP=537
+1	3356391	rs4018597;-/TA	TT	TTAT	100	PASS	AF=0.0517593;HP=2;DB;NF=13;NR=11;NS=52;CA=0;DP=475
+1	3356436	rs5772104;-/GT	CGTG	CG	100	PASS	AF=0.82813;HP=1;DB;NF=59;NR=53;NS=51;CA=0;DP=449
+1	3356871	.	CATG	CG	26	PASS	AF=0.0193592;HP=1;NF=1;NR=3;NS=51;CA=0;DP=430
+1	3359412	rs34037774;-/G,venter	TGG	TG	59	PASS	AF=0.0301496;HP=2;DB;NF=4;NR=5;NS=52;CA=0;DP=451
+1	3370575	rs35597752;-/TG,venter,watson	CTGT	CT	100	PASS	AF=0.760154;HP=1;DB;NF=43;NR=36;NS=52;CA=0;DP=405
+1	3372018	rs34109718;-/G,venter	CGG	CG	100	PASS	AF=0.891318;HP=3;DB;NF=46;NR=36;NS=51;CA=0;DP=349
+1	3383745	rs57207202;-/C	AC	ACC	100	PASS	AF=0.182529;HP=4;DB;NF=9;NR=7;NS=47;CA=D;DP=229
+1	3384084	rs5772105;-/G,mills,venter	CG	CGG	100	PASS	AF=0.937697;HP=2;DB;NF=49;NR=47;NS=50;CA=0;DP=457
+1	3385833	rs5772106;-/CC,mills,venter,watson	ACCC	AC	100	PASS	AF=0.778535;HP=5;DB;NF=33;NR=14;NS=51;CA=0;DP=418
+1	3387275	rs56102150;-/TC,venter	CC	CCTC	100	PASS	AF=0.999995;HP=4;DB;NF=16;NR=36;NS=50;CA=0;DP=364
+1	3388739	rs58188396;-/GGGGGGCGGGTAGCC	GG	GGGGGGGCGGGTAGCCG	40	PASS	AF=0.263678;HP=7;DB;NF=3;NR=2;NS=48;CA=0;DP=326
+1	3393157	.	AAAAAATA	AA	100	PASS	AF=0.0549314;HP=6;NF=23;NR=18;NS=51;CA=0;DP=468
+1	3393524	.	GGTGTG	GG	23	PASS	AF=0.017751;HP=2;NF=1;NR=19;NS=49;CA=0;DP=266
+1	3409800	.	AAGA	AA	100	PASS	AF=0.0431791;HP=3;NF=1;NR=8;NS=51;CA=0;DP=643
+1	3410131	rs58666986;-/GTGT	ATGTGT	AT	100	PASS	AF=0.0433727;HP=1;DB;NF=7;NR=13;NS=52;CA=0;DP=603
+1	3411485	rs60864742;-/ACACCGGTAGCAAGGCA,mills	ACACCGGTAGCAAGGCACC	AC	100	PASS	AF=0.0858716;HP=1;DB;NF=8;NR=17;NS=52;CA=0;DP=523
+1	3417374	.	GCACACGCCCCCACCC	GC	20	PASS	AF=0.0294079;HP=1;NF=4;NR=3;NS=50;CA=0;DP=447
+1	3429498	rs56204236;-/G	CG	CGG	100	PASS	AF=0.596026;HP=10;DB;NF=6;NR=7;NS=51;CA=0;DP=322
+1	3435396	.	CACAGA	CA	100	PASS	AF=0.0433621;HP=1;NF=2;NR=6;NS=52;CA=0;DP=457
+1	3442767	rs36106109;-/G	CG	CGG	100	PASS	AF=0.112939;HP=5;DB;NF=5;NR=6;NS=50;CA=0;DP=369
+1	3451064	rs36030995;-/C	GC	GCC	100	PASS	AF=0.385449;HP=5;DB;NF=22;NR=12;NS=50;CA=0;DP=388
+1	3456931	rs35289361;-/G	AG	AGG	100	PASS	AF=0.0676076;HP=4;DB;NF=11;NR=9;NS=52;CA=0;DP=554
+1	3467274	watson	GGGCTG	GG	100	PASS	AF=0.132596;HP=3;NF=16;NR=12;NS=51;CA=0;DP=428
+1	3475422	rs61428836;-/G	TG	TGG	100	PASS	AF=0.0480433;HP=3;DB;NF=6;NR=10;NS=52;CA=0;DP=468
+1	3482055	.	CA	CGTCTTATA	100	PASS	AF=0.593516;HP=1;NF=10;NR=11;NS=49;CA=M;DP=256
+1	3482413	mills,watson	TCTCC	TC	100	PASS	AF=0.414589;HP=1;NF=24;NR=32;NS=51;CA=0;DP=496
+1	3485140	venter,watson	CCAAC	CC	100	PASS	AF=0.714294;HP=2;NF=21;NR=32;NS=52;CA=0;DP=460
+1	3486991	rs35452084;-/G,venter	AGG	AG	100	PASS	AF=0.744909;HP=4;DB;NF=15;NR=35;NS=50;CA=0;DP=363
+1	3492812	.	CGTG	CG	14	PASS	AF=0.0148914;HP=1;NF=22;NR=26;NS=51;CA=0;DP=585
+1	3494290	.	AC	ACAGGACCGGCC	100	PASS	AF=0.117184;HP=1;NF=2;NR=22;NS=52;CA=0;DP=464
+1	3496820	rs34860893;-/C,mills,venter	ACC	AC	100	PASS	AF=0.924032;HP=7;DB;NF=33;NR=48;NS=52;CA=0;DP=386
+1	3504928	rs36094767;-/C,venter	TC	TCC	100	PASS	AF=0.786142;HP=4;DB;NF=23;NR=43;NS=51;CA=0;DP=405
+1	3511572	rs3072238;-/TCAC,venter	ACACTC	AC	100	PASS	AF=0.160871;HP=1;DB;NF=22;NR=22;NS=52;CA=0;DP=824
+1	3511789	rs59801836;-/CTCA,watson	ACACTC	AC	100	PASS	AF=0.620819;HP=1;DB;NF=54;NR=52;NS=52;CA=0;DP=740
+1	3511919	.	TACA	TA	100	PASS	AF=0.049568;HP=1;NF=20;NR=22;NS=52;CA=0;DP=729
+1	3511980	rs57128321;-/ACTC,venter,watson	AC	ACACTC	100	PASS	AF=0.937206;HP=1;DB;NF=63;NR=38;NS=52;CA=0;DP=712
+1	3512089	rs61705210;-/TCACAC,venter,watson	AACTCACA	AA	100	PASS	AF=0.658764;HP=3;DB;NF=65;NR=52;NS=52;CA=0;DP=808
+1	3516936	rs60239345;-/CA,venter	CG	CCAG	100	PASS	AF=0.999997;HP=1;DB;NF=52;NR=26;NS=52;CA=0;DP=391
+1	3519155	rs35740208;-/G,venter	AGG	AG	100	PASS	AF=0.108418;HP=3;DB;NF=7;NR=11;NS=51;CA=0;DP=505
+1	3523781	rs56339243;-/GGCTCC,venter,watson	AC	ACCGGCTC	100	PASS	AF=0.603986;HP=3;DB;NF=20;NR=23;NS=52;CA=0;DP=449
+1	3526023	.	GGCACTTCCCGCCCCCGTCACCCCTGCCGCCATG	GG	100	PASS	AF=0.227609;HP=2;NF=10;NR=15;NS=52;CA=0;DP=454
+1	3526486	rs35020651;-/C,venter	TC	TCC	100	PASS	AF=0.389171;HP=3;DB;NF=32;NR=20;NS=52;CA=0;DP=470
+1	3530060	.	TGG	TG	100	PASS	AF=0.033793;HP=3;NF=6;NR=1;NS=52;CA=0;DP=540
+1	3531966	rs3838971;-/C	TG	TGG	100	PASS	AF=0.155382;HP=6;DB;NF=14;NR=11;NS=49;CA=0;DP=292
+1	3534095	rs35816205;-/A,mills,venter	TAA	TA	100	PASS	AF=0.160054;HP=3;DB;NF=9;NR=10;NS=52;CA=0;DP=455
+1	3535035	rs58849058;-/TCTGGGAGCTCCTCCCCCT,venter,watson	GTTCTGGGAGCTCCTCCCCCT	GT	100	PASS	AF=0.609724;HP=2;DB;NF=50;NR=48;NS=52;CA=0;DP=487
+1	3535985	.	CCAAAC	CC	100	PASS	AF=0.116123;HP=2;NF=10;NR=13;NS=51;CA=0;DP=553
+1	3536124	rs55905548;-/GGCG,venter,watson	CCGGGC	CC	100	PASS	AF=0.45742;HP=3;DB;NF=28;NR=31;NS=51;CA=0;DP=499
+1	3543853	.	TC	TCC	100	PASS	AF=0.156605;HP=6;NF=12;NR=13;NS=52;CA=0;DP=527
+1	3549495	.	AC	ACCCCC	34	PASS	AF=0.0959154;HP=1;NF=1;NR=3;NS=52;CA=0;DP=496
+1	3553372	rs34514629;-/C,venter	GCA	GA	100	PASS	AF=0.652107;HP=1;DB;NF=45;NR=47;NS=52;CA=0;DP=551
+1	3556485	rs3831025;-/CAGCCTGC,venter,watson	AGCAGGCTGC	AC	100	PASS	AF=0.38103;HP=1;DB;NF=13;NR=9;NS=49;CA=0;DP=292
+1	3556883	.	CA	CATA	14	PASS	AF=0.0221011;HP=1;NF=9;NR=13;NS=50;CA=0;DP=436
+1	3563429	.	CG	CGGGGG	56	PASS	AF=0.17049;HP=2;NF=3;NR=7;NS=52;CA=0;DP=586
+1	3564334	rs3034639;-/GT,mills	GA	GACA	100	PASS	AF=0.227635;HP=1;DB;NF=10;NR=13;NS=50;CA=0;DP=364
+1	3564964	rs5772113;-/G	TGG	TG	100	PASS	AF=0.220888;HP=2;DB;NF=11;NR=18;NS=50;CA=0;DP=408
+1	3565238	venter	GGTCTCCTACAGTCATATTTTGGGGTGACGTATTCTAG	GG	100	PASS	AF=0.145422;HP=2;NF=1;NR=10;NS=52;CA=M;DP=323
+1	3566253	rs57149403;-/GTCCAGC	AC	ACGTCCAGC	100	PASS	AF=0.0476733;HP=1;DB;NF=3;NR=3;NS=52;CA=0;DP=363
+1	3567114	.	ATG	AG	100	PASS	AF=0.0358982;HP=1;NF=3;NR=5;NS=52;CA=0;DP=555
+1	3568146	rs3034606;-/TA	GTAT	GT	100	PASS	AF=0.533957;HP=1;DB;NF=12;NR=29;NS=51;CA=0;DP=247
+1	3570893	rs34305694;-/C	TCC	TC	100	PASS	AF=0.0467251;HP=2;DB;NF=5;NR=3;NS=52;CA=0;DP=443
+1	3574939	.	CG	CGTGTGTG	23	PASS	AF=0.401022;HP=1;NF=46;NR=32;NS=52;CA=0;DP=481
+1	3586002	.	ACTC	AC	100	PASS	AF=0.157197;HP=1;NF=17;NR=24;NS=52;CA=0;DP=691
+1	3586231	rs61542341;-/GTCTCT	CTCTCTGT	CT	12	PASS	AF=0.0310208;HP=1;DB;NF=1;NR=11;NS=52;CA=M;DP=400
+1	3586281	.	CTTT	CT	21	PASS	AF=0.115475;HP=3;NF=1;NR=3;NS=51;CA=M;DP=469
+1	3589610	rs57492244;-/G	TGG	TG	100	PASS	AF=0.0691843;HP=7;DB;NF=11;NR=8;NS=51;CA=0;DP=527
+1	3593995	rs57765962;-/AT,watson	AATG	AG	100	PASS	AF=0.127015;HP=2;DB;NF=10;NR=8;NS=52;CA=0;DP=423
+1	3603570	.	GCGGGGCCCACCTCGCACCCGCGGCCCACGTCGCACCC	GC	100	PASS	AF=0.0758905;HP=1;NF=8;NR=12;NS=51;CA=0;DP=414
+1	3606881	rs5772119;-/A,venter	TAG	TG	100	PASS	AF=0.333638;HP=1;DB;NF=12;NR=36;NS=51;CA=0;DP=522
+1	3618309	rs3841787;-/TG,watson	CATG	CG	100	PASS	AF=0.219932;HP=1;DB;NF=14;NR=14;NS=50;CA=0;DP=449
+1	3619353	venter	GCCCCTGCC	GC	100	PASS	AF=0.290838;HP=4;NF=18;NR=8;NS=51;CA=0;DP=322
+1	3629994	rs35939665;-/CTGC,mills,venter,watson	TCTGCC	TC	100	PASS	AF=0.953969;HP=1;DB;NF=43;NR=31;NS=51;CA=0;DP=364
+1	3630547	rs35380007;-/A,venter	TA	TAA	100	PASS	AF=0.373122;HP=2;DB;NF=20;NR=12;NS=51;CA=0;DP=293
+1	3632819	rs61728692;-/CGGA	GT	GCGGAT	100	PASS	AF=0.63605;HP=1;DB;NF=18;NR=3;NS=48;CA=0;DP=238
+1	3632891	.	GGATTG	GG	46	PASS	AF=0.024415;HP=2;NF=4;NR=2;NS=49;CA=0;DP=381
+1	3633325	.	CG	CGATGGATGGGTGG	100	PASS	AF=0.870192;HP=1;NF=3;NR=4;NS=52;CA=0;DP=751
+1	3635416	rs3034587;-/CTCTCT,mills,venter	AA	AAGAGAGA	100	PASS	AF=0.707697;HP=3;DB;NF=37;NR=27;NS=52;CA=0;DP=538
+1	3643833	.	AC	ACCC	25	PASS	AF=0.0664372;HP=1;NF=3;NR=3;NS=51;CA=0;DP=511
+1	3648954	rs3216059;-/G	AG	AGG	100	PASS	AF=0.42719;HP=4;DB;NF=35;NR=35;NS=51;CA=0;DP=551
+1	3660684	.	GA	GCA	100	PASS	AF=0.136632;HP=1;NF=2;NR=10;NS=49;CA=0;DP=480
+1	3663009	rs35440871;-/AA	CAAG	CG	100	PASS	AF=0.2595;HP=2;DB;NF=19;NR=14;NS=51;CA=0;DP=498
+1	3665663	rs60798590;-/TATTTAAAAAT,watson	CA	CAATTATTTAAAA	33	PASS	AF=0.0338921;HP=2;DB;NF=8;NR=3;NS=51;CA=0;DP=388
+1	3665995	.	TTTGAAACT	TT	33	PASS	AF=0.00986571;HP=4;NF=1;NR=3;NS=52;CA=0;DP=507
+1	3668078	.	AGG	AG	100	PASS	AF=0.341281;HP=8;NF=21;NR=29;NS=52;CA=0;DP=467
+1	3677245	rs36002367;-/AG	AAGA	AA	100	PASS	AF=0.137474;HP=3;DB;NF=6;NR=10;NS=52;CA=0;DP=521
+1	3680208	.	TG	TGG	10	PASS	AF=0.0239017;HP=1;NF=7;NR=5;NS=51;CA=0;DP=448
+1	3681294	venter	CC	CGCAC	100	PASS	AF=0.200075;HP=8;NF=7;NR=2;NS=50;CA=0;DP=245
+1	3682989	rs35616712;-/C	TCC	TC	100	PASS	AF=0.0813904;HP=3;DB;NF=9;NR=3;NS=51;CA=0;DP=447
+1	3684305	venter	CG	CGG	100	PASS	AF=0.0596707;HP=3;NF=4;NR=6;NS=51;CA=0;DP=416
+1	3686623	rs35661250;-/AG	CA	CAGA	100	PASS	AF=0.0609898;HP=1;DB;NF=5;NR=6;NS=52;CA=0;DP=626
+1	3691009	rs35756038;-/A,venter	CAA	CA	100	PASS	AF=0.444393;HP=2;DB;NF=24;NR=32;NS=52;CA=0;DP=562
+1	3696676	.	CCTG	CG	100	PASS	AF=0.102585;HP=4;NF=7;NR=6;NS=52;CA=0;DP=502
+1	3697316	rs34679063;-/C,venter	GC	GCC	100	PASS	AF=0.8246;HP=1;DB;NF=51;NR=32;NS=52;CA=0;DP=438
+1	3704105	.	TT	TTAATTTTTATATTAACCGTGTTAATAT	100	PASS	AF=0.377269;HP=2;NF=17;NR=26;NS=52;CA=0;DP=476
+1	3708451	watson	TG	TGGAGG	43	PASS	AF=0.0406373;HP=2;NF=3;NR=4;NS=52;CA=0;DP=587
+1	3710853	rs35447451;-/G,venter	AG	AGG	100	PASS	AF=0.272856;HP=4;DB;NF=25;NR=31;NS=52;CA=0;DP=507
+1	3711553	rs36007194;-/T	AT	ATT	100	PASS	AF=0.093968;HP=10;DB;NF=11;NR=13;NS=52;CA=0;DP=515
+1	3712668	rs35364504;-/GA,venter	GGAG	GG	100	PASS	AF=0.369523;HP=5;DB;NF=18;NR=34;NS=51;CA=0;DP=320
+1	3713867	venter	TTTTATTTAT	TT	100	PASS	AF=0.301438;HP=5;NF=21;NR=36;NS=49;CA=0;DP=294
+1	3714365	rs58666367;-/CTCAT,venter,watson	GA	GATCTCA	100	PASS	AF=0.431722;HP=1;DB;NF=24;NR=17;NS=52;CA=0;DP=484
+1	3721514	rs3838969;-/A,venter	CG	CTG	100	PASS	AF=0.472733;HP=2;DB;NF=27;NR=26;NS=52;CA=0;DP=461
+1	3726918	rs34085838;-/G	CG	CGG	100	PASS	AF=0.242958;HP=1;DB;NF=17;NR=14;NS=52;CA=0;DP=479
+1	3728638	rs61301856;-/GA,venter,watson	TGAG	TG	100	PASS	AF=0.446341;HP=1;DB;NF=54;NR=33;NS=52;CA=0;DP=666
+1	3729131	rs56900717;-/A	TT	TAT	100	PASS	AF=0.489357;HP=2;DB;NF=33;NR=22;NS=52;CA=0;DP=466
+1	3733293	rs5772126;-/G,venter	TG	TGG	100	PASS	AF=0.701257;HP=2;DB;NF=17;NR=26;NS=51;CA=0;DP=451
+1	3733413	.	CA	CAA	100	PASS	AF=0.107016;HP=5;NF=12;NR=16;NS=52;CA=0;DP=523
+1	3735276	venter	TA	TAAA	100	PASS	AF=0.491527;HP=1;NF=29;NR=33;NS=52;CA=0;DP=477
+1	3737219	rs61056063;-/A	AGA	AA	11	PASS	AF=0.205567;HP=1;DB;NF=13;NR=6;NS=51;CA=0;DP=431
+1	3740075	rs35801288;-/C	ACA	AA	100	PASS	AF=0.438207;HP=1;DB;NF=35;NR=12;NS=52;CA=0;DP=395
+1	3741588	rs34966926;-/T,venter	GT	GTT	100	PASS	AF=0.212825;HP=10;DB;NF=21;NR=22;NS=51;CA=0;DP=541
+1	3748510	mills	TTTTTTAT	TT	53	PASS	AF=0.0323102;HP=7;NF=21;NR=15;NS=51;CA=0;DP=420
+1	3759325	.	CG	CGGCCAAGGAG	100	PASS	AF=0.391954;HP=2;NF=19;NR=18;NS=52;CA=0;DP=465
+1	3759824	.	CG	CGGG	22	PASS	AF=0.0355289;HP=5;NF=4;NR=8;NS=52;CA=0;DP=591
+1	3760224	rs61309375;-/A,venter	CAG	CG	100	PASS	AF=0.303624;HP=1;DB;NF=27;NR=13;NS=51;CA=0;DP=447
+1	3773150	.	CTT	CT	12	NoQCALL	AF=0.0786801;HP=2;NF=1;NR=9;NS=52;CA=0;DP=540
+1	3774838	.	GT	GTT	11	PASS	AF=0.0109686;HP=1;NF=2;NR=1;NS=52;CA=0;DP=492
+1	3774974	venter	CG	CTG	100	PASS	AF=0.552417;HP=1;NF=26;NR=38;NS=52;CA=0;DP=559
+1	3776839	.	TGG	TG	100	PASS	AF=0.0926011;HP=3;NF=5;NR=5;NS=52;CA=0;DP=441
+1	3780438	venter	CT	CTTT	100	PASS	AF=0.113197;HP=2;NF=10;NR=13;NS=52;CA=0;DP=654
+1	3780687	rs34664006;-/G	TGT	TT	50	PASS	AF=0.0614825;HP=1;DB;NF=4;NR=8;NS=50;CA=M;DP=299
+1	3784253	venter	ACTGTGCCGGCTTTCTATTC	AC	100	PASS	AF=0.0567473;HP=1;NF=81;NR=75;NS=52;CA=0;DP=627
+1	3786092	.	TACTCA	TA	100	PASS	AF=0.0330531;HP=1;NF=1;NR=6;NS=52;CA=0;DP=497
+1	3788460	rs35600694;-/ATA,watson	CA	CAATA	100	PASS	AF=0.42686;HP=1;DB;NF=20;NR=17;NS=51;CA=0;DP=533
+1	3788666	rs34172576;-/T,venter	GT	GTT	100	PASS	AF=0.481873;HP=1;DB;NF=26;NR=12;NS=52;CA=0;DP=409
+1	3804956	rs60302317;-/CAACA	AACAACA	AA	46	PASS	AF=0.0866272;HP=2;DB;NF=6;NR=2;NS=52;CA=M;DP=556
+1	3805210	rs58663935;-/AAAG	CA	CAAAGA	100	PASS	AF=0.0920558;HP=3;DB;NF=9;NR=2;NS=52;CA=0;DP=523
+1	3805480	.	GAA	GA	55	PASS	AF=0.0675729;HP=8;NF=13;NR=11;NS=52;CA=0;DP=539
+1	3805914	.	CCAGACACTGGCACCCCCCTTC	CC	100	PASS	AF=0.0288464;HP=2;NF=5;NR=4;NS=52;CA=0;DP=613
+1	3806447	rs35704040;-/C,mills	GCC	GC	100	PASS	AF=0.0700176;HP=6;DB;NF=4;NR=8;NS=52;CA=0;DP=350
+1	3807398	rs35759189;-/G,venter	AGG	AG	100	PASS	AF=0.324114;HP=3;DB;NF=21;NR=8;NS=50;CA=0;DP=355
+1	3808303	venter	GT	GTTCTTTTCTTT	100	PASS	AF=0.475205;HP=2;NF=19;NR=9;NS=52;CA=0;DP=264
+1	3809301	.	TACA	TA	100	PASS	AF=0.028676;HP=1;NF=26;NR=22;NS=52;CA=0;DP=553
+1	3813066	rs34938659;-/T	ATT	AT	100	PASS	AF=0.131264;HP=2;DB;NF=8;NR=6;NS=52;CA=0;DP=521
+1	3814885	.	TCACACACACACACACAC	TC	34	PASS	AF=0.149965;HP=1;NF=6;NR=2;NS=52;CA=M;DP=644
+1	3818483	.	AC	ACC	29	PASS	AF=0.0676027;HP=3;NF=1;NR=7;NS=50;CA=0;DP=412
+1	3820456	.	TGG	TG	12	PASS	AF=0.0215117;HP=4;NF=5;NR=1;NS=51;CA=0;DP=417
+1	3824944	.	GCTC	GC	100	PASS	AF=0.174164;HP=1;NF=9;NR=17;NS=50;CA=0;DP=277
+1	3825911	.	CG	CGGGGGG	100	PASS	AF=0.29134;HP=2;NF=24;NR=12;NS=52;CA=0;DP=514
+1	3827024	.	TTCCCT	TT	16	PASS	AF=0.0318298;HP=2;NF=34;NR=70;NS=51;CA=M;DP=394
+1	3827604	.	TG	TGG	40	PASS	AF=0.0159039;HP=1;NF=2;NR=5;NS=52;CA=0;DP=571
+1	3833062	watson	TC	TCCACC	100	PASS	AF=0.312659;HP=2;NF=17;NR=16;NS=52;CA=0;DP=463
+1	3833266	venter,watson	AT	ATCAGT	100	PASS	AF=0.497122;HP=1;NF=10;NR=19;NS=51;CA=0;DP=412
+1	3833395	.	CTATCTT	CT	24	PASS	AF=0.0218407;HP=1;NF=7;NR=3;NS=50;CA=0;DP=400
+1	3833485	.	GTCTAT	GT	100	PASS	AF=0.417779;HP=1;NF=11;NR=12;NS=50;CA=0;DP=323
+1	3833578	watson	TTATCT	TT	100	PASS	AF=0.329625;HP=2;NF=27;NR=26;NS=51;CA=0;DP=388
+1	3833880	watson	CA	CATCTA	100	PASS	AF=0.347946;HP=1;NF=11;NR=13;NS=52;CA=0;DP=458
+1	3906706	.	TGG	TG	100	PASS	AF=0.149111;HP=3;NF=11;NR=9;NS=52;CA=0;DP=498
+1	3907565	rs34088401;-/C,mills	TCC	TC	100	PASS	AF=0.191109;HP=6;DB;NF=11;NR=14;NS=51;CA=0;DP=478
+1	3909253	.	AC	ACC	100	PASS	AF=0.0974891;HP=2;NF=10;NR=9;NS=52;CA=0;DP=591
+1	3909917	rs35302885;-/T,venter	CTT	CT	100	PASS	AF=0.766256;HP=7;DB;NF=45;NR=61;NS=52;CA=0;DP=605
+1	3916501	rs55698528;-/A,venter	GA	GAA	100	PASS	AF=0.624637;HP=1;DB;NF=37;NR=28;NS=52;CA=0;DP=488
+1	3920626	rs59758170;-/TAAATAAATA	AATAAATAAATA	AA	100	PASS	AF=0.276985;HP=3;DB;NF=6;NR=6;NS=50;CA=M;DP=308
+1	3923069	.	TCG	TG	100	PASS	AF=0.224119;HP=1;NF=23;NR=7;NS=52;CA=0;DP=488
+1	3925431	rs34400281;-/T,venter	CTT	CT	100	PASS	AF=0.372459;HP=2;DB;NF=14;NR=10;NS=51;CA=0;DP=500
+1	3933527	.	ATTCCCCACAGTGTCTATGGGGACTCTAGCACGGTCAGGGACCCT	AT	100	PASS	AF=0.0367516;HP=2;NF=29;NR=33;NS=51;CA=0;DP=622
+1	3934862	venter	GCAC	GC	100	PASS	AF=0.565308;HP=1;NF=47;NR=42;NS=51;CA=0;DP=648
+1	3935044	.	TCAC	TC	40	PASS	AF=0.0156518;HP=1;NF=25;NR=8;NS=52;CA=0;DP=717
+1	3937578	rs56700097;-/A,venter	TG	TAG	100	PASS	AF=0.540707;HP=1;DB;NF=40;NR=17;NS=52;CA=0;DP=392
+1	3938627	rs58820377;-/ATAG	TTAGAT	TT	100	PASS	AF=0.0846429;HP=2;DB;NF=10;NR=11;NS=52;CA=0;DP=489
+1	3945777	.	CAGA	CA	100	PASS	AF=0.442957;HP=1;NF=49;NR=35;NS=52;CA=M;DP=511
+1	3967107	venter	GAGAA	GA	100	PASS	AF=0.226936;HP=1;NF=10;NR=15;NS=52;CA=0;DP=543
+1	3971955	rs56102422;-/T	AT	ATT	100	PASS	AF=0.275646;HP=10;DB;NF=12;NR=15;NS=52;CA=0;DP=477
+1	3973109	rs56883229;-/T,venter	ATT	AT	100	PASS	AF=0.374332;HP=8;DB;NF=7;NR=38;NS=52;CA=0;DP=398
+1	3974590	.	ATT	AT	100	PASS	AF=0.373956;HP=8;NF=19;NR=19;NS=51;CA=0;DP=352
+1	3976220	.	TTCCAGCTGTTGGACTGGCAAACAGT	TT	100	PASS	AF=0.155908;HP=3;NF=51;NR=67;NS=52;CA=0;DP=702
+1	3983232	.	GC	GCC	100	PASS	AF=0.153929;HP=3;NF=2;NR=12;NS=51;CA=0;DP=479
+1	3989673	rs34117538;-/T	CTT	CT	100	PASS	AF=0.138005;HP=7;DB;NF=10;NR=16;NS=52;CA=0;DP=480
+1	3991472	.	GT	GTT	41	PASS	AF=0.0921994;HP=10;NF=23;NR=19;NS=52;CA=0;DP=490
+1	3995340	.	GAATA	GA	100	PASS	AF=0.126804;HP=2;NF=18;NR=25;NS=51;CA=0;DP=456
+1	3995701	rs35842317;-/A	GA	GAA	100	PASS	AF=0.287765;HP=3;DB;NF=16;NR=28;NS=52;CA=0;DP=515
+1	3998289	rs34690250;-/C	AT	ATT	31	PASS	AF=0.0505667;HP=1;DB;NF=5;NR=6;NS=50;CA=0;DP=373
+1	3998556	rs35439065;-/C,venter	AC	ACC	100	PASS	AF=0.152989;HP=1;DB;NF=17;NR=4;NS=52;CA=0;DP=565
+1	4003805	.	CCCTTC	CC	100	PASS	AF=0.497734;HP=3;NF=13;NR=9;NS=52;CA=M;DP=357
+1	4004467	.	TA	TAA	100	PASS	AF=0.178845;HP=10;NF=39;NR=12;NS=52;CA=0;DP=482
+1	4005161	.	AAGA	AA	10	PASS	AF=0.109604;HP=8;NF=5;NR=3;NS=52;CA=0;DP=418
+1	4009724	.	GGAGAGGGAGAAG	GG	100	PASS	AF=0.0443217;HP=4;NF=7;NR=9;NS=51;CA=0;DP=347
+1	4010638	rs59300943;-/T	CT	CTT	100	PASS	AF=0.238748;HP=5;DB;NF=17;NR=13;NS=52;CA=0;DP=424
+1	4018608	.	GGGAG	GG	14	PASS	AF=0.0210215;HP=3;NF=11;NR=22;NS=52;CA=0;DP=439
+1	4020045	rs60135555;-/AAA,venter	TA	TAAAA	55	PASS	AF=0.669408;HP=9;DB;NF=19;NR=3;NS=52;CA=0;DP=315
+1	4021381	.	CTGGGAAC	CC	26	PASS	AF=0.0682584;HP=1;NF=1;NR=7;NS=52;CA=0;DP=500
+1	4022270	.	TG	TCG	59	PASS	AF=0.0269606;HP=6;NF=2;NR=3;NS=52;CA=0;DP=522
+1	4022431	rs58149124;-/CC,watson	TC	TCCC	100	PASS	AF=0.833755;HP=1;DB;NF=29;NR=41;NS=52;CA=0;DP=574
+1	4024133	rs56013829;-/GTCA,venter	ACAGTC	AC	100	PASS	AF=0.444062;HP=1;DB;NF=29;NR=25;NS=52;CA=0;DP=599
+1	4024168	rs56372495;-/AC,venter	TCAC	TC	100	PASS	AF=0.370935;HP=1;DB;NF=14;NR=39;NS=52;CA=0;DP=645
+1	4024408	rs55816119;-/TT,watson	TC	TCAC	100	PASS	AF=0.479654;HP=1;DB;NF=17;NR=29;NS=52;CA=0;DP=726
+1	4024524	.	ACTC	AC	100	PASS	AF=0.220192;HP=1;NF=11;NR=5;NS=52;CA=0;DP=721
+1	4024673	.	TT	TTCACT	100	PASS	AF=0.173855;HP=2;NF=11;NR=13;NS=52;CA=0;DP=887
+1	4024704	.	TCAG	TG	100	PASS	AF=0.0291681;HP=1;NF=6;NR=1;NS=52;CA=0;DP=750
+1	4024735	venter	TC	TCAC	100	PASS	AF=0.247468;HP=1;NF=19;NR=5;NS=52;CA=0;DP=775
+1	4024928	.	CTCAGT	CT	100	PASS	AF=0.0974879;HP=1;NF=11;NR=7;NS=52;CA=0;DP=919
+1	4025065	.	TCAC	TC	100	PASS	AF=0.273013;HP=1;NF=7;NR=12;NS=52;CA=0;DP=714
+1	4025127	.	ACTC	AC	100	PASS	AF=0.380734;HP=1;NF=17;NR=20;NS=52;CA=M;DP=574
+1	4025165	.	TC	TCACTCAC	100	PASS	AF=0.0820414;HP=1;NF=1;NR=9;NS=52;CA=M;DP=574
+1	4025232	watson	TC	TCAC	100	PASS	AF=0.631924;HP=1;NF=15;NR=11;NS=52;CA=M;DP=459
+1	4025339	.	TTCACT	TT	53	PASS	AF=0.159738;HP=2;NF=17;NR=14;NS=51;CA=0;DP=609
+1	4025399	.	CA	CATA	100	PASS	AF=0.0862676;HP=1;NF=4;NR=7;NS=52;CA=0;DP=506
+1	4025472	.	CA	CATTTA	39	PASS	AF=0.0270865;HP=1;NF=2;NR=1;NS=52;CA=0;DP=538
+1	4025543	venter,watson	TC	TCAC	100	PASS	AF=0.26036;HP=1;NF=9;NR=12;NS=52;CA=0;DP=482
+1	4025589	.	AC	ACTC	53	PASS	AF=0.0696821;HP=1;NF=1;NR=1;NS=52;CA=0;DP=575
+1	4025678	watson	TACTCA	TA	100	PASS	AF=0.299176;HP=1;NF=14;NR=7;NS=52;CA=0;DP=549
+1	4025718	.	CATT	CT	100	PASS	AF=0.0815807;HP=1;NF=8;NR=6;NS=52;CA=0;DP=570
+1	4025810	watson	TC	TCAC	100	PASS	AF=0.240222;HP=1;NF=8;NR=8;NS=52;CA=0;DP=442
+1	4025920	.	ACTCACACTC	AC	15	PASS	AF=0.0440807;HP=1;NF=5;NR=6;NS=52;CA=0;DP=439
+1	4025988	.	ATCACT	AT	100	PASS	AF=0.115745;HP=1;NF=7;NR=3;NS=52;CA=M;DP=409
+1	4026021	.	ATTCGC	AC	19	PASS	AF=0.0230633;HP=2;NF=4;NR=4;NS=52;CA=0;DP=408
+1	4026091	.	ACAGTC	AC	100	PASS	AF=0.239672;HP=1;NF=10;NR=12;NS=52;CA=0;DP=418
+1	4026188	.	GTCACTCGTT	GT	100	PASS	AF=0.0942528;HP=1;NF=17;NR=15;NS=51;CA=M;DP=704
+1	4026243	.	AC	ACTCACTC	100	PASS	AF=0.0701669;HP=1;NF=8;NR=2;NS=52;CA=0;DP=852
+1	4026341	.	AC	ACTC	100	PASS	AF=0.180464;HP=1;NF=7;NR=12;NS=52;CA=0;DP=797
+1	4026433	.	AC	ACTCACAGTC	100	PASS	AF=0.0755971;HP=1;NF=10;NR=4;NS=52;CA=0;DP=727
+1	4026489	.	CCACTC	CC	100	PASS	AF=0.152175;HP=2;NF=20;NR=14;NS=52;CA=0;DP=896
+1	4026521	.	AT	ACT	18	PASS	AF=0.0348752;HP=1;NF=8;NR=8;NS=52;CA=0;DP=896
+1	4026676	.	ACACTC	AC	100	PASS	AF=0.345964;HP=1;NF=25;NR=27;NS=52;CA=0;DP=805
+1	4026745	.	ACTC	AC	100	PASS	AF=0.277096;HP=1;NF=6;NR=11;NS=52;CA=0;DP=625
+1	4026831	.	AC	ACTC	100	PASS	AF=0.158736;HP=1;NF=13;NR=9;NS=52;CA=0;DP=585
+1	4026904	.	TACTCA	TA	59	PASS	AF=0.094457;HP=1;NF=7;NR=4;NS=52;CA=0;DP=594
+1	4026996	.	TT	TTCACT	100	PASS	AF=0.0816069;HP=2;NF=19;NR=16;NS=52;CA=0;DP=668
+1	4027100	watson	GT	GTCACT	100	PASS	AF=0.51624;HP=1;NF=22;NR=20;NS=52;CA=0;DP=958
+1	4027153	.	AC	ACTCACACTC	100	PASS	AF=0.221157;HP=1;NF=11;NR=7;NS=52;CA=0;DP=694
+1	4027249	.	ACACTCGCTCAGTC	AC	100	PASS	AF=0.191741;HP=1;NF=20;NR=16;NS=52;CA=0;DP=528
+1	4027301	.	TCAC	TC	100	PASS	AF=0.21653;HP=1;NF=6;NR=9;NS=52;CA=0;DP=511
+1	4027378	.	TT	TTCACT	100	PASS	AF=0.23813;HP=2;NF=19;NR=16;NS=52;CA=0;DP=565
+1	4027440	.	TT	TTCACT	100	PASS	AF=0.351897;HP=2;NF=28;NR=13;NS=52;CA=0;DP=736
+1	4031776	venter,watson	GC	GCTGCTCC	100	PASS	AF=0.57914;HP=1;NF=17;NR=13;NS=52;CA=0;DP=475
+1	4046995	rs60127181;-/ATG,watson	GC	GGATC	100	PASS	AF=0.863384;HP=1;DB;NF=37;NR=32;NS=51;CA=0;DP=427
+1	4053051	.	AC	AACC	10	PASS	AF=0.0731381;HP=1;NF=2;NR=3;NS=52;CA=0;DP=453
+1	4056743	rs57501900;-/T,venter	ATT	AT	100	PASS	AF=0.863012;HP=6;DB;NF=63;NR=45;NS=52;CA=0;DP=485
+1	4078234	venter,watson	CTGCCTGTGTGAGCAAGAT	CT	100	PASS	AF=0.308447;HP=1;NF=26;NR=18;NS=52;CA=0;DP=484
+1	4080449	rs35774756;-/T	GTT	GT	100	PASS	AF=0.285891;HP=2;DB;NF=20;NR=24;NS=51;CA=0;DP=526
+1	4082493	rs35701497;-/G	CGG	CG	100	PASS	AF=0.277913;HP=4;DB;NF=14;NR=16;NS=52;CA=0;DP=416
+1	4086137	.	CA	CTA	100	PASS	AF=0.0260425;HP=1;NF=4;NR=2;NS=52;CA=0;DP=569
+1	4088196	.	TTCT	TT	100	PASS	AF=0.0658972;HP=3;NF=67;NR=77;NS=51;CA=B;DP=647
+1	4091673	rs56198003;-/TTA	GTTAT	GT	100	PASS	AF=0.0274099;HP=2;DB;NF=4;NR=7;NS=52;CA=0;DP=489
+1	4093407	rs35442233;-/G,venter	TGG	TG	100	PASS	AF=0.056726;HP=4;DB;NF=4;NR=5;NS=51;CA=0;DP=432
+1	4097902	rs5772141;-/ATT,mills,venter,watson	CA	CATTA	100	PASS	AF=0.999995;HP=1;DB;NF=38;NR=34;NS=52;CA=0;DP=432
+1	4106716	.	AC	ACACACACACACGC	100	PASS	AF=0.316911;HP=1;NF=1;NR=1;NS=52;CA=0;DP=601
+1	4114274	rs60603556;-/CAT,watson	AATCA	AA	100	PASS	AF=0.135224;HP=3;DB;NF=17;NR=9;NS=51;CA=0;DP=587
+1	4114592	rs56285575;-/ACA,venter	AAACA	AA	100	PASS	AF=0.254759;HP=3;DB;NF=21;NR=18;NS=52;CA=0;DP=554
+1	4114812	.	TTAT	TT	33	PASS	AF=0.14738;HP=3;NF=5;NR=4;NS=52;CA=0;DP=411
+1	4114996	.	AA	AATTATTA	11	PASS	AF=0.228122;HP=2;NF=26;NR=29;NS=49;CA=0;DP=276
+1	4120825	.	GAA	GA	43	PASS	AF=0.147904;HP=2;NF=11;NR=17;NS=51;CA=0;DP=328
+1	4121802	.	ATGT	AT	11	PASS	AF=0.0113836;HP=1;NF=24;NR=16;NS=52;CA=0;DP=570
+1	4131826	.	ATTGTTT	AT	100	PASS	AF=0.999996;HP=2;NF=38;NR=35;NS=52;CA=0;DP=456
+1	4134659	rs35271731;-/G	TG	TGG	100	PASS	AF=0.417516;HP=5;DB;NF=21;NR=19;NS=52;CA=0;DP=429
+1	4139315	rs35859581;-/T,venter	GT	GTT	100	PASS	AF=0.371694;HP=2;DB;NF=12;NR=16;NS=52;CA=0;DP=444
+1	4144542	.	CAA	CA	100	PASS	AF=0.0915309;HP=2;NF=7;NR=8;NS=52;CA=M;DP=461
+1	4149378	rs35644791;-/CCT,venter,watson	AC	ACCTC	100	PASS	AF=0.955034;HP=2;DB;NF=35;NR=24;NS=52;CA=0;DP=461
+1	4150078	.	ATC	AC	100	PASS	AF=0.0248618;HP=1;NF=3;NR=1;NS=52;CA=0;DP=489
+1	4158176	rs61115653;-/A	CA	CAA	100	PASS	AF=0.109858;HP=9;DB;NF=9;NR=8;NS=52;CA=0;DP=480
+1	4158371	rs35550030;-/G	AGA	AA	100	PASS	AF=0.282272;HP=1;DB;NF=22;NR=13;NS=52;CA=0;DP=508
+1	4160853	.	AG	AGTG	100	PASS	AF=0.883963;HP=1;NF=52;NR=40;NS=52;CA=0;DP=475
+1	4163479	rs35439066;-/T,venter	ATT	AT	100	PASS	AF=0.421487;HP=7;DB;NF=35;NR=40;NS=52;CA=0;DP=580
+1	4165518	rs5772143;-/A,mills	CAT	CT	100	PASS	AF=0.0997002;HP=1;DB;NF=8;NR=9;NS=52;CA=0;DP=569
+1	4168412	.	TG	TGG	100	PASS	AF=0.0597927;HP=5;NF=7;NR=5;NS=50;CA=0;DP=411
+1	4174019	.	CCTTTC	CC	100	PASS	AF=0.223832;HP=2;NF=5;NR=11;NS=51;CA=M;DP=369
+1	4176371	rs5772145;-/GGGCT,mills,venter,watson	GG	GGGGCTG	100	PASS	AF=0.965127;HP=4;DB;NF=37;NR=39;NS=51;CA=0;DP=577
+1	4180359	rs35134459;-/T,venter	CG	CTG	100	PASS	AF=0.994644;HP=2;DB;NF=70;NR=40;NS=52;CA=0;DP=510
+1	4198168	.	GCCATTTACATCCCACC	GC	100	PASS	AF=0.0947023;HP=2;NF=47;NR=53;NS=52;CA=0;DP=625
+1	4203370	.	TCAC	TC	22	PASS	AF=0.151126;HP=1;NF=40;NR=22;NS=51;CA=0;DP=481
+1	4224147	.	ATGT	AT	100	PASS	AF=0.459042;HP=1;NF=45;NR=57;NS=52;CA=0;DP=508
+1	4236168	venter,watson	GT	GTCCTGTT	100	PASS	AF=0.465028;HP=1;NF=21;NR=21;NS=51;CA=0;DP=473
+1	4238553	.	TAG	TG	100	PASS	AF=0.0884036;HP=1;NF=3;NR=3;NS=52;CA=0;DP=313
+1	4243904	.	TG	TGGGGG	28	PASS	AF=0.177328;HP=1;NF=6;NR=9;NS=52;CA=0;DP=598
+1	4252300	.	AATTTA	AA	27	PASS	AF=0.0160294;HP=2;NF=16;NR=12;NS=52;CA=0;DP=550
+1	4256051	.	CC	CCTCAC	100	PASS	AF=0.423907;HP=2;NF=10;NR=6;NS=52;CA=M;DP=450
+1	4256251	rs56817136;-/AATCCATC	TC	TCATCAATCC	27	PASS	AF=0.483921;HP=1;DB;NF=24;NR=28;NS=52;CA=M;DP=501
+1	4256338	rs59859709;-/CCAT	CCCATC	CC	100	PASS	AF=0.420087;HP=3;DB;NF=47;NR=73;NS=52;CA=0;DP=510
+1	4258560	rs35749795;-/G,venter	TGG	TG	100	PASS	AF=0.563751;HP=3;DB;NF=30;NR=43;NS=52;CA=0;DP=533
+1	4270968	rs5772150;-/A,mills,venter	TAA	TA	100	PASS	AF=0.863858;HP=2;DB;NF=66;NR=65;NS=52;CA=0;DP=554
+1	4272781	rs34523387;-/CA,venter,watson	TCAC	TC	100	PASS	AF=0.221206;HP=1;DB;NF=55;NR=32;NS=52;CA=0;DP=555
+1	4276688	rs56762609;-/A	CA	CAA	25	PASS	AF=0.0168189;HP=4;DB;NF=5;NR=7;NS=52;CA=0;DP=567
+1	4278344	rs33957131;-/A,mills	TAT	TT	100	PASS	AF=0.260307;HP=1;DB;NF=13;NR=14;NS=52;CA=M;DP=390
+1	4280264	rs35972891;-/G,venter	TG	TGG	100	PASS	AF=0.36321;HP=6;DB;NF=16;NR=21;NS=52;CA=0;DP=487
+1	4280920	rs3058085;-/AGA,mills,venter,watson	AT	ATCTT	100	PASS	AF=0.75024;HP=1;DB;NF=34;NR=50;NS=52;CA=0;DP=518
+1	4281851	rs59086076;-/TTGT	CTGTTT	CT	100	PASS	AF=0.15371;HP=1;DB;NF=12;NR=13;NS=52;CA=0;DP=454
+1	4287207	rs3986843;-/CCT	CA	CAGGA	100	PASS	AF=0.100002;HP=1;DB;NF=8;NR=1;NS=52;CA=0;DP=451
+1	4289708	.	GTGTTAG	GG	37	PASS	AF=0.0904846;HP=1;NF=3;NR=9;NS=52;CA=0;DP=447
+1	4291813	.	CGC	CC	41	PASS	AF=0.05598;HP=1;NF=1;NR=9;NS=52;CA=0;DP=504
+1	4291856	rs33950418;-/C,mills	ACA	AA	53	PASS	AF=0.0424203;HP=1;DB;NF=2;NR=10;NS=52;CA=M;DP=504
+1	4292024	rs33982329;-/CA,mills	CG	CATG	100	PASS	AF=0.0974178;HP=1;DB;NF=14;NR=14;NS=52;CA=0;DP=697
+1	4296830	.	CTT	CT	100	PASS	AF=0.101792;HP=2;NF=15;NR=4;NS=52;CA=0;DP=805
+1	4298115	rs34054009;-/G,venter	AG	AGG	100	PASS	AF=0.314255;HP=2;DB;NF=25;NR=10;NS=52;CA=0;DP=565
+1	4310246	rs35999105;-/A	TA	TAA	100	PASS	AF=0.229765;HP=5;DB;NF=23;NR=13;NS=52;CA=0;DP=488
+1	4310305	venter	GA	GAA	39	PASS	AF=0.078696;HP=9;NF=15;NR=5;NS=52;CA=0;DP=455
+1	4312461	.	GAAAGAAA	GA	24	PASS	AF=0.0372797;HP=3;NF=23;NR=6;NS=52;CA=M;DP=401
+1	4313453	.	GG	GTG	23	PASS	AF=0.026167;HP=2;NF=2;NR=5;NS=52;CA=0;DP=614
+1	4315016	rs34078493;-/T,venter	CT	CTT	100	PASS	AF=0.459017;HP=1;DB;NF=25;NR=37;NS=52;CA=0;DP=493
+1	4316236	rs35864764;-/TC	ATCT	AT	100	PASS	AF=0.164629;HP=1;DB;NF=18;NR=15;NS=52;CA=0;DP=434
+1	4317119	rs35907112;-/AG	AAGA	AA	100	PASS	AF=0.210583;HP=3;DB;NF=19;NR=13;NS=52;CA=0;DP=652
+1	4319781	rs34098980;-/AAAAA,mills,venter	CC	CAAAAAC	100	PASS	AF=0.451406;HP=2;DB;NF=9;NR=1;NS=52;CA=0;DP=605
+1	4323411	.	GT	GTT	41	PASS	AF=0.0448346;HP=6;NF=4;NR=5;NS=52;CA=0;DP=498
+1	4326343	.	CG	CGGGGGGGGGGG	100	PASS	AF=0.212625;HP=2;NF=5;NR=11;NS=52;CA=0;DP=475
+1	4329138	.	GTGAT	GT	47	PASS	AF=0.0168095;HP=1;NF=35;NR=37;NS=52;CA=0;DP=675
+1	4329500	venter	ATGGTGATGGT	AT	100	PASS	AF=0.0491;HP=1;NF=35;NR=49;NS=52;CA=0;DP=718
+1	4333035	.	CCACTC	CC	100	PASS	AF=0.0536691;HP=2;NF=18;NR=17;NS=52;CA=0;DP=614
+1	4333090	.	CCCATC	CC	100	PASS	AF=0.896174;HP=3;NF=52;NR=56;NS=52;CA=0;DP=564
+1	4333868	rs34013096;-/CCAT	AC	ACCATC	100	PASS	AF=0.411752;HP=2;DB;NF=63;NR=59;NS=52;CA=0;DP=556
+1	4352929	.	TAA	TA	100	PASS	AF=0.0606075;HP=5;NF=10;NR=5;NS=51;CA=0;DP=422
+1	4360308	.	CAA	CA	100	PASS	AF=0.160821;HP=3;NF=12;NR=13;NS=52;CA=0;DP=502
+1	4360675	rs55750624;-/A	GAA	GA	100	PASS	AF=0.209252;HP=2;DB;NF=18;NR=10;NS=52;CA=0;DP=456
+1	4362123	rs57250327;-/AAATT	TA	TAATTAA	100	PASS	AF=0.202867;HP=2;DB;NF=23;NR=24;NS=52;CA=0;DP=404
+1	4372014	rs34773421;-/A,venter	TAA	TA	100	PASS	AF=0.507594;HP=2;DB;NF=43;NR=31;NS=52;CA=0;DP=496
+1	4373092	.	CATTTA	CA	100	PASS	AF=0.155807;HP=1;NF=19;NR=10;NS=52;CA=0;DP=440
+1	4375952	.	TCT	TT	100	PASS	AF=0.0215948;HP=1;NF=3;NR=2;NS=52;CA=0;DP=530
+1	4376164	rs57973702;-/TG,venter	CG	CGTG	100	PASS	AF=0.555727;HP=1;DB;NF=33;NR=60;NS=52;CA=0;DP=552
+1	4382255	.	GT	GTT	100	PASS	AF=0.134524;HP=8;NF=12;NR=14;NS=52;CA=0;DP=445
+1	4382929	.	CG	CGCCGTGCCCTGCTCAG	100	PASS	AF=0.293977;HP=1;NF=3;NR=1;NS=52;CA=0;DP=423
+1	4386769	rs34696074;-/G	TGG	TG	100	PASS	AF=0.524405;HP=3;DB;NF=43;NR=31;NS=51;CA=0;DP=586
+1	4386900	rs35831569;-/GTGA,watson	TG	TGTGAG	100	PASS	AF=0.786341;HP=1;DB;NF=49;NR=47;NS=52;CA=0;DP=728
+1	4387089	rs35106948;-/GA,venter,watson	TGAG	TG	100	PASS	AF=0.76407;HP=1;DB;NF=42;NR=48;NS=52;CA=0;DP=730
+1	4398343	rs56075652;-/AGCTAG,mills,venter,watson	GGAGCTAG	GG	100	PASS	AF=0.850798;HP=2;DB;NF=51;NR=52;NS=52;CA=0;DP=535
+1	4403445	.	ATC	AC	100	PASS	AF=0.0257077;HP=1;NF=3;NR=3;NS=52;CA=0;DP=579
+1	4413424	.	GGAAG	GG	100	PASS	AF=0.0911622;HP=2;NF=13;NR=11;NS=52;CA=0;DP=539
+1	4415363	rs35655214;-/A,mills,venter	CAA	CA	100	PASS	AF=0.279808;HP=10;DB;NF=16;NR=13;NS=52;CA=0;DP=623
+1	4419729	rs34301403;-/T,venter	CT	CTT	100	PASS	AF=0.276688;HP=3;DB;NF=23;NR=17;NS=52;CA=0;DP=491
+1	4429935	.	ACC	AC	100	PASS	AF=0.121066;HP=2;NF=8;NR=7;NS=52;CA=0;DP=509
+1	4432975	rs35185885;-/TTAT,venter	TT	TTTTAT	100	PASS	AF=0.370788;HP=4;DB;NF=7;NR=50;NS=51;CA=0;DP=329
+1	4433724	.	AC	ACC	100	PASS	AF=0.191535;HP=2;NF=16;NR=17;NS=52;CA=0;DP=609
+1	4434361	.	GA	GATGATATTGAAA	100	PASS	AF=0.175787;HP=1;NF=8;NR=5;NS=52;CA=0;DP=496
+1	4439328	rs55695069;-/TGTG,watson	TGTGAG	TG	100	PASS	AF=0.115075;HP=1;DB;NF=13;NR=10;NS=51;CA=0;DP=510
+1	4444447	.	GC	GCC	100	PASS	AF=0.126735;HP=1;NF=8;NR=6;NS=52;CA=0;DP=442
+1	4444562	watson	TTCG	TG	100	PASS	AF=0.167206;HP=3;NF=13;NR=9;NS=52;CA=0;DP=477
+1	4448379	rs55971665;-/A,venter	GAA	GA	100	PASS	AF=0.999997;HP=5;DB;NF=29;NR=34;NS=51;CA=0;DP=398
+1	4456774	rs34368344;-/CTCA,watson	TCTCAC	TC	100	PASS	AF=0.4985;HP=1;DB;NF=46;NR=35;NS=52;CA=0;DP=679
+1	4456823	.	TT	TTTTCTCTCT	100	PASS	AF=0.281015;HP=3;NF=18;NR=7;NS=52;CA=0;DP=566
+1	4460399	.	CAGA	CA	17	PASS	AF=0.0162627;HP=1;NF=4;NR=1;NS=52;CA=0;DP=437
+1	4461064	.	TG	TGGG	100	PASS	AF=0.136493;HP=8;NF=11;NR=12;NS=52;CA=0;DP=516
+1	4461120	.	GAGTCA	GA	100	PASS	AF=0.106497;HP=1;NF=4;NR=10;NS=52;CA=0;DP=513
+1	4462914	rs35786528;-/T,venter	GTT	GT	100	PASS	AF=0.636288;HP=9;DB;NF=46;NR=44;NS=52;CA=0;DP=457
+1	4464201	rs35933446;-/G	AGC	AC	100	PASS	AF=0.0422945;HP=1;DB;NF=3;NR=5;NS=52;CA=0;DP=559
+1	4465553	rs33984734;-/C,mills,venter	GCC	GC	100	PASS	AF=0.832437;HP=3;DB;NF=43;NR=36;NS=52;CA=0;DP=507
+1	4465878	rs55781312;-/GAACA,watson	TACAGAA	TA	100	PASS	AF=0.547352;HP=1;DB;NF=48;NR=55;NS=52;CA=0;DP=612
+1	4466414	rs34356738;-/T,venter	AT	ATT	100	PASS	AF=0.0343632;HP=4;DB;NF=5;NR=2;NS=52;CA=0;DP=523
+1	4468803	.	CT	CTTTTCTTTTCTTT	100	PASS	AF=0.185641;HP=2;NF=2;NR=1;NS=51;CA=0;DP=271
+1	4469024	.	TT	TTGTGT	26	PASS	AF=0.65093;HP=2;NF=51;NR=54;NS=51;CA=0;DP=465
+1	4470162	rs34280110;-/T,venter	CT	CTT	100	PASS	AF=0.19103;HP=3;DB;NF=13;NR=16;NS=52;CA=0;DP=581
+1	4472390	rs35540877;-/AAG	TAAGA	TA	100	PASS	AF=0.0513799;HP=2;DB;NF=4;NR=3;NS=52;CA=0;DP=531
+1	4481812	rs34806922;-/A,venter	GAA	GA	100	PASS	AF=0.0356083;HP=3;DB;NF=4;NR=4;NS=52;CA=0;DP=576
+1	4482705	.	CA	CATCTA	100	PASS	AF=0.203301;HP=1;NF=34;NR=52;NS=50;CA=M;DP=382
+1	4482808	.	CTA	CA	16	PASS	AF=0.0550307;HP=1;NF=1;NR=1;NS=51;CA=M;DP=356
+1	4482848	rs5772166;-/TCTCTCTC,mills	ATCTCTCTCT	AT	100	PASS	AF=0.561639;HP=1;DB;NF=52;NR=17;NS=51;CA=M;DP=311
+1	4484471	rs3059158;-/CT,mills,watson	AG	ACTG	100	PASS	AF=0.497825;HP=1;DB;NF=31;NR=34;NS=52;CA=0;DP=538
+1	4486660	rs34976033;-/CCCT,mills,venter,watson	GCTCCC	GC	100	PASS	AF=0.593551;HP=1;DB;NF=42;NR=55;NS=52;CA=0;DP=566
+1	4486840	rs35808993;-/A,venter	GAT	GT	100	PASS	AF=0.0446408;HP=1;DB;NF=4;NR=4;NS=52;CA=0;DP=539
+1	4495865	watson	TGACCT	TT	100	PASS	AF=0.477912;HP=1;NF=15;NR=22;NS=52;CA=0;DP=386
+1	4498895	.	TAAACTCA	TA	100	PASS	AF=0.365307;HP=3;NF=30;NR=28;NS=52;CA=0;DP=561
+1	4499763	.	TT	TTTTAGTTTAGTTTAGTTTAGTTTAGT	15	PASS	AF=0.437504;HP=4;NF=5;NR=8;NS=51;CA=0;DP=440
+1	4500994	rs57293099;-/A,venter	GG	GAG	19	PASS	AF=0.533167;HP=5;DB;NF=26;NR=15;NS=51;CA=0;DP=466
+1	4501978	rs34937816;-/T,mills,venter	GT	GTT	100	PASS	AF=0.677682;HP=1;DB;NF=47;NR=42;NS=52;CA=0;DP=475
+1	4504724	venter,watson	TAGACA	TA	100	PASS	AF=0.381777;HP=1;NF=34;NR=33;NS=52;CA=0;DP=728
+1	4504861	venter	TACAGAGAGAGACAGAGAGA	TA	100	PASS	AF=0.208225;HP=1;NF=42;NR=31;NS=52;CA=0;DP=820
+1	4506249	rs56013880;-/T,mills,venter	GC	GTC	100	PASS	AF=0.652109;HP=2;DB;NF=41;NR=48;NS=52;CA=0;DP=522
+1	4506287	venter	TAG	TG	100	PASS	AF=0.348604;HP=1;NF=23;NR=27;NS=52;CA=0;DP=534
+1	4510123	rs35963445;-/C,venter	TC	TCC	100	PASS	AF=0.750939;HP=6;DB;NF=32;NR=50;NS=52;CA=0;DP=488
+1	4511427	rs34235356;-/T,venter	AT	ATT	100	PASS	AF=0.559297;HP=8;DB;NF=40;NR=27;NS=52;CA=0;DP=549
+1	4512561	rs57315980;-/GAG	TGGAG	TG	100	PASS	AF=0.0276885;HP=2;DB;NF=7;NR=4;NS=52;CA=0;DP=581
+1	4512788	rs56318426;-/GGATAGTGTG	TC	TGTGTGGGATAC	100	PASS	AF=0.145759;HP=1;DB;NF=7;NR=6;NS=52;CA=0;DP=570
+1	4513234	rs5772168;-/ATCA,venter,watson	TA	TATCAA	100	PASS	AF=0.761132;HP=1;DB;NF=45;NR=38;NS=52;CA=0;DP=478
+1	4513552	rs34248962;-/G,venter	CTC	CC	100	PASS	AF=0.397344;HP=1;DB;NF=19;NR=21;NS=52;CA=0;DP=502
+1	4518079	.	CTTTATGTCAAC	CC	31	PASS	AF=0.0537494;HP=3;NF=13;NR=6;NS=52;CA=0;DP=567
+1	4519870	.	CATAA	CA	100	PASS	AF=0.156873;HP=1;NF=25;NR=19;NS=52;CA=0;DP=518
+1	4520552	venter,watson	ATATT	AT	100	PASS	AF=0.0454741;HP=1;NF=13;NR=21;NS=52;CA=0;DP=523
+1	4524683	rs60936673;-/A,venter	GAC	GC	100	PASS	AF=0.0433734;HP=1;DB;NF=5;NR=1;NS=51;CA=0;DP=407
+1	4531795	.	CG	CGAGCAGATAG	100	PASS	AF=0.0529244;HP=1;NF=2;NR=3;NS=52;CA=0;DP=598
+1	4533811	rs61232512;-/TCCCTCCTGGACAGCCAGG,watson	TCCTCCTGGACAGCCAGGTCC	TC	100	PASS	AF=0.455665;HP=2;DB;NF=9;NR=12;NS=52;CA=0;DP=455
+1	4535415	rs34971058;-/C,mills,venter	GC	GCC	100	PASS	AF=0.872856;HP=1;DB;NF=71;NR=50;NS=52;CA=0;DP=585
+1	4540778	rs5772169;-/T,mills	CTG	CG	100	PASS	AF=0.129616;HP=1;DB;NF=9;NR=6;NS=52;CA=0;DP=518
+1	4541031	.	TT	TTTTCT	100	PASS	AF=0.0665496;HP=6;NF=18;NR=24;NS=51;CA=0;DP=371
+1	4541492	rs5772170;-/G,mills,venter	TG	TGG	100	PASS	AF=0.912727;HP=3;DB;NF=57;NR=39;NS=52;CA=0;DP=454
+1	4542962	.	CC	CCTCTCTCTCTC	100	PASS	AF=0.767807;HP=2;NF=57;NR=35;NS=52;CA=0;DP=481
+1	4544333	rs3059964;-/CT,venter	ACTC	AC	100	PASS	AF=0.941425;HP=1;DB;NF=54;NR=73;NS=52;CA=0;DP=591
+1	4547027	rs34146010;-/C	ACC	AC	100	PASS	AF=0.974502;HP=2;DB;NF=55;NR=74;NS=52;CA=0;DP=535
+1	4547927	rs34056554;-/T,venter	ATT	AT	100	PASS	AF=0.867021;HP=3;DB;NF=7;NR=12;NS=51;CA=0;DP=398
+1	4551259	rs34018288;-/TG,venter,watson	CT	CTGT	100	PASS	AF=0.964821;HP=1;DB;NF=25;NR=27;NS=52;CA=0;DP=445
+1	4552887	.	GT	GTCT	100	PASS	AF=0.155774;HP=1;NF=6;NR=7;NS=52;CA=0;DP=507
+1	4556585	rs3833958;-/GGGCT,venter	GA	GAGCCCA	100	PASS	AF=0.248571;HP=1;DB;NF=9;NR=9;NS=52;CA=0;DP=416
+1	4558195	rs58248788;-/T,venter	ATT	AT	100	PASS	AF=0.949748;HP=4;DB;NF=38;NR=18;NS=51;CA=0;DP=446
+1	4558625	.	AGA	AA	100	PASS	AF=0.105248;HP=1;NF=12;NR=4;NS=52;CA=0;DP=526
+1	4570630	.	GT	GGGTTT	14	PASS	AF=0.0570941;HP=1;NF=4;NR=2;NS=52;CA=0;DP=480
+1	4574298	.	GC	GAC	41	PASS	AF=0.0333335;HP=2;NF=1;NR=4;NS=52;CA=0;DP=497
+1	4574507	.	TT	TTCCTCTAATGCT	100	PASS	AF=0.406213;HP=2;NF=13;NR=8;NS=52;CA=0;DP=437
+1	4577694	rs33988719;-/G,mills,venter	TG	TGG	100	PASS	AF=0.999997;HP=1;DB;NF=52;NR=28;NS=52;CA=0;DP=381
+1	4578235	.	TAT	TT	26	PASS	AF=0.292482;HP=1;NF=8;NR=14;NS=51;CA=0;DP=330
+1	4580634	.	ATAAAATA	AA	100	PASS	AF=0.328083;HP=1;NF=11;NR=4;NS=51;CA=M;DP=372
+1	4581760	.	CTT	CT	100	PASS	AF=0.0551414;HP=2;NF=4;NR=7;NS=52;CA=0;DP=578
+1	4583153	rs35427335;-/CA,venter,watson	GCAC	GC	100	PASS	AF=0.0310016;HP=1;DB;NF=3;NR=4;NS=52;CA=0;DP=483
+1	4586257	rs34899280;-/T	GTC	GC	100	PASS	AF=0.311452;HP=1;DB;NF=16;NR=8;NS=51;CA=0;DP=441
+1	4589959	venter,watson	GG	GGGCCTG	100	PASS	AF=0.0494854;HP=3;NF=3;NR=4;NS=52;CA=0;DP=469
+1	4590830	rs34057361;-/GCAAAGC,mills,venter,watson	TGCAAAGCG	TG	100	PASS	AF=0.739178;HP=1;DB;NF=42;NR=52;NS=50;CA=0;DP=465
+1	4595540	rs56784481;-/T	TCT	TT	53	PASS	AF=0.154234;HP=1;DB;NF=7;NR=21;NS=52;CA=0;DP=439
+1	4596270	.	AC	ACGCTGAGGCTGCAGCACCCCTCGTGGAGC	100	PASS	AF=0.171201;HP=1;NF=6;NR=1;NS=52;CA=0;DP=498
+1	4600396	rs36042545;-/AT,venter	CATA	CA	100	PASS	AF=0.185579;HP=1;DB;NF=24;NR=23;NS=52;CA=0;DP=357
+1	4603645	rs60786353;-/C,venter	AC	ACC	100	PASS	AF=0.999998;HP=1;DB;NF=76;NR=57;NS=52;CA=0;DP=571
+1	4607282	.	GTGAT	GT	100	PASS	AF=0.287968;HP=1;NF=38;NR=26;NS=52;CA=0;DP=810
+1	4607435	.	GTGAT	GT	100	PASS	AF=0.347474;HP=1;NF=39;NR=53;NS=52;CA=0;DP=674
+1	4611309	.	CGTGTG	CG	100	PASS	AF=0.311775;HP=1;NF=38;NR=31;NS=52;CA=0;DP=486
+1	4621966	rs35610947;-/GT	TTGT	TT	100	PASS	AF=0.252136;HP=3;DB;NF=41;NR=42;NS=52;CA=0;DP=612
+1	4623256	rs59174221;-/CTCCAGAAAGCAC	GGAAAGCACCTCCAG	GG	100	PASS	AF=0.248792;HP=2;DB;NF=24;NR=28;NS=52;CA=0;DP=458
+1	4623618	rs60584333;-/GTGTCGGGAGCAGAGACTG,venter	GC	GCTGGTGTCGGGAGCAGAGAC	100	PASS	AF=0.624955;HP=1;DB;NF=8;NR=16;NS=51;CA=0;DP=518
+1	4628242	rs56871532;-/TG,venter,watson	CTGT	CT	100	PASS	AF=0.630417;HP=1;DB;NF=46;NR=41;NS=52;CA=0;DP=605
+1	4631325	watson	GAGGACATA	GA	100	PASS	AF=0.0694082;HP=1;NF=14;NR=10;NS=51;CA=0;DP=388
+1	4633949	.	TCC	TC	100	PASS	AF=0.223776;HP=7;NF=13;NR=4;NS=51;CA=0;DP=492
+1	4637510	.	TAAA	TA	18	PASS	AF=0.0428857;HP=9;NF=13;NR=6;NS=52;CA=0;DP=456
+1	4639728	.	GGTGTGTGTGTGTGTG	GG	56	PASS	AF=0.223403;HP=3;NF=39;NR=66;NS=51;CA=0;DP=466
+1	4645583	rs59275910;-/G,venter	AG	AGG	100	PASS	AF=0.999998;HP=1;DB;NF=41;NR=59;NS=51;CA=0;DP=416
+1	4649824	.	CTT	CT	100	PASS	AF=0.0615007;HP=2;NF=3;NR=3;NS=52;CA=0;DP=371
+1	4653490	.	GAG	GG	19	PASS	AF=0.016501;HP=1;NF=1;NR=2;NS=52;CA=0;DP=448
+1	4654099	rs3086606;-/GTCTGCA,mills	CC	CCAGTCTGC	100	PASS	AF=0.299705;HP=2;DB;NF=11;NR=10;NS=52;CA=0;DP=440
+1	4655877	rs58828516;-/G	TG	TGG	100	PASS	AF=0.083803;HP=6;DB;NF=13;NR=14;NS=52;CA=0;DP=553
+1	4656096	rs34592768;-/G,mills	TGG	TG	100	PASS	AF=0.0586852;HP=2;DB;NF=6;NR=4;NS=52;CA=0;DP=486
+1	4656943	.	GGTGTG	GG	53	PASS	AF=0.0156574;HP=2;NF=15;NR=18;NS=52;CA=0;DP=804
+1	4668803	.	CTT	CT	39	PASS	AF=0.0748695;HP=8;NF=8;NR=6;NS=52;CA=0;DP=401
+1	4670089	rs34058244;-/AC,venter	GA	GACA	100	PASS	AF=0.471432;HP=1;DB;NF=47;NR=39;NS=52;CA=0;DP=789
+1	4670383	rs35737766;-/TCAC,watson	ACACTC	AC	100	PASS	AF=0.331554;HP=1;DB;NF=20;NR=35;NS=52;CA=0;DP=609
+1	4676654	.	AGATG	AG	10	PASS	AF=0.011049;HP=1;NF=15;NR=18;NS=52;CA=0;DP=617
+1	4684590	.	TCCTGCACCTGCTGTGCCCCTGGCTCCCAGCACC	TC	100	PASS	AF=0.0368566;HP=2;NF=13;NR=7;NS=52;CA=0;DP=543
+1	4689505	.	TC	TCTGTCCTCTCTCCTAGCTCTGGTGCCCTGAGATGC	100	PASS	AF=0.355136;HP=1;NF=2;NR=3;NS=52;CA=0;DP=597
+1	4693342	rs3835539;-/TTCA	CC	CCATTC	100	PASS	AF=0.307703;HP=2;DB;NF=60;NR=61;NS=52;CA=0;DP=594
+1	4695582	venter	TGTGAGG	TG	100	PASS	AF=0.630317;HP=1;NF=17;NR=29;NS=52;CA=0;DP=408
+1	4700273	.	GCCT	GT	51	PASS	AF=0.154012;HP=2;NF=3;NR=3;NS=52;CA=0;DP=402
+1	4700727	rs34897087;-/A,venter	CG	CGG	13	PASS	AF=0.0702045;HP=8;DB;NF=22;NR=6;NS=51;CA=M;DP=305
+1	4702014	rs34592315;-/AA,venter	TAAA	TA	100	PASS	AF=0.183045;HP=3;DB;NF=9;NR=20;NS=52;CA=0;DP=551
+1	4702135	.	GCC	GC	100	PASS	AF=0.132917;HP=5;NF=18;NR=10;NS=52;CA=0;DP=561
+1	4702842	rs3835540;-/GAC	TGACG	TG	100	PASS	AF=0.333162;HP=1;DB;NF=25;NR=19;NS=52;CA=0;DP=517
+1	4703849	rs35422518;-/TCTCCAGGC,mills,venter,watson	AGCTCTCCAGG	AG	100	PASS	AF=0.461699;HP=1;DB;NF=52;NR=39;NS=52;CA=0;DP=558
+1	4704242	.	ATT	AT	100	PASS	AF=0.124811;HP=6;NF=16;NR=12;NS=52;CA=0;DP=518
+1	4704545	.	GCACAC	GC	43	PASS	AF=0.374122;HP=1;NF=68;NR=46;NS=52;CA=0;DP=586
+1	4709952	rs55677440;-/GT	TT	TTGT	100	PASS	AF=0.111566;HP=3;DB;NF=37;NR=55;NS=52;CA=0;DP=757
+1	4712998	rs35177072;-/CTC,mills,venter,watson	TCTCC	TC	100	PASS	AF=0.409205;HP=1;DB;NF=23;NR=30;NS=52;CA=0;DP=527
+1	4714785	rs3835541;-/A,venter	CAA	CA	100	PASS	AF=0.207747;HP=2;DB;NF=12;NR=9;NS=52;CA=0;DP=525
+1	4715739	.	GT	GTT	100	PASS	AF=0.0593871;HP=1;NF=4;NR=4;NS=52;CA=0;DP=486
+1	4717874	rs33969697;-/C,mills,venter	TCA	TA	100	PASS	AF=0.644689;HP=1;DB;NF=37;NR=47;NS=52;CA=0;DP=521
+1	4720164	rs5772181;-/GA,mills,venter,watson	TG	TGAG	100	PASS	AF=0.660601;HP=1;DB;NF=60;NR=61;NS=52;CA=0;DP=723
+1	4725394	venter	AG	AGAGAGACATGAGTGAAGAAGG	100	PASS	AF=0.486541;HP=1;NF=34;NR=40;NS=52;CA=0;DP=600
+1	4726136	rs35816653;-/T,venter	CT	CTT	100	PASS	AF=0.325542;HP=7;DB;NF=25;NR=33;NS=52;CA=0;DP=561
+1	4728249	rs35594902;-/TGTT	CT	CTGTTT	100	PASS	AF=0.236832;HP=1;DB;NF=16;NR=16;NS=52;CA=0;DP=595
+1	4730619	rs56688128;-/AAGGC,venter,watson	ACAAGGC	AC	100	PASS	AF=0.197783;HP=1;DB;NF=14;NR=10;NS=52;CA=0;DP=450
+1	4738491	.	ATCTCTCTCTCTCTCTCTCTCT	AT	100	PASS	AF=0.109332;HP=1;NF=34;NR=36;NS=52;CA=0;DP=556
+1	4743143	rs34960969;-/T,venter	ATT	AT	100	PASS	AF=0.443382;HP=2;DB;NF=27;NR=29;NS=51;CA=0;DP=521
+1	4750482	.	AC	ACC	44	PASS	AF=0.0773717;HP=1;NF=1;NR=10;NS=52;CA=0;DP=532
+1	4751808	.	CC	CTC	100	PASS	AF=0.287743;HP=6;NF=22;NR=19;NS=52;CA=0;DP=549
+1	4753639	rs56735073;-/G	AG	AGG	100	PASS	AF=0.354197;HP=6;DB;NF=26;NR=25;NS=52;CA=0;DP=499
+1	4756338	.	TGG	TG	100	PASS	AF=0.145276;HP=6;NF=12;NR=22;NS=52;CA=0;DP=505
+1	4756654	.	CTGT	CT	100	PASS	AF=0.0253358;HP=1;NF=2;NR=3;NS=52;CA=0;DP=502
+1	4768227	rs34482713;-/A,venter	CAC	CC	100	PASS	AF=0.624286;HP=1;DB;NF=16;NR=29;NS=52;CA=0;DP=382
+1	4769408	rs3030792;-/CA,venter	TC	TCAC	100	PASS	AF=0.564397;HP=1;DB;NF=37;NR=45;NS=51;CA=0;DP=550
+1	4771107	rs59952959;-/TTATCGGTGGTTT	ATTATCGGTGGTTTC	AC	100	PASS	AF=0.43732;HP=2;DB;NF=24;NR=26;NS=52;CA=0;DP=437
+1	4771150	.	AGGCAGAGGATTTAGGGGGCAGTGAAACTA	AA	100	PASS	AF=0.365014;HP=2;NF=25;NR=17;NS=51;CA=0;DP=446
+1	4773228	.	AACA	AA	100	PASS	AF=0.358433;HP=4;NF=49;NR=37;NS=51;CA=0;DP=403
+1	4779293	rs35799766;-/A,venter	GAA	GA	100	PASS	AF=0.620558;HP=4;DB;NF=40;NR=44;NS=52;CA=0;DP=539
+1	4783405	.	TACGTATATACATATACA	TA	100	PASS	AF=0.346752;HP=1;NF=20;NR=40;NS=52;CA=0;DP=331
+1	4784171	.	TA	TAAGA	100	PASS	AF=0.058761;HP=2;NF=4;NR=4;NS=52;CA=0;DP=522
+1	4787548	rs35350740;-/CA,mills	AACA	AA	100	PASS	AF=0.294238;HP=3;DB;NF=43;NR=40;NS=52;CA=0;DP=565
+1	4790642	rs5772184;-/T,venter	ATT	AT	100	PASS	AF=0.360239;HP=10;DB;NF=23;NR=25;NS=52;CA=0;DP=544
+1	4794867	.	AATA	AA	59	PASS	AF=0.0541594;HP=2;NF=6;NR=24;NS=52;CA=0;DP=316
+1	4794934	.	CT	CTCTCTTT	21	PASS	AF=0.322809;HP=1;NF=7;NR=9;NS=50;CA=M;DP=241
+1	4800829	rs35005833;-/C,venter	TC	TCC	100	PASS	AF=0.404199;HP=5;DB;NF=48;NR=15;NS=52;CA=0;DP=479
+1	4806476	.	GC	GCC	100	PASS	AF=0.0973173;HP=6;NF=8;NR=8;NS=52;CA=M;DP=398
+1	4808450	rs34573971;-/A,venter	GAA	GA	100	PASS	AF=0.332411;HP=9;DB;NF=26;NR=22;NS=52;CA=0;DP=474
+1	4809140	rs60726929;-/TCCA,venter,watson	TC	TCATCC	100	PASS	AF=0.348085;HP=1;DB;NF=49;NR=32;NS=52;CA=0;DP=579
+1	4810276	rs3030822;-/TAGT,watson	ATAGTT	AT	100	PASS	AF=0.242205;HP=1;DB;NF=27;NR=13;NS=52;CA=0;DP=582
+1	4831434	.	TA	TACCACACACACA	100	PASS	AF=0.49717;HP=1;NF=18;NR=17;NS=52;CA=0;DP=675
+1	4831567	rs34042090;-/CA	CCAC	CC	100	PASS	AF=0.535527;HP=4;DB;NF=52;NR=45;NS=52;CA=0;DP=738
+1	4833596	rs35226825;-/T	AT	ATT	100	PASS	AF=0.237481;HP=5;DB;NF=19;NR=19;NS=52;CA=0;DP=498
+1	4839967	.	TCCTGCCAGCCGGGGGC	TC	100	PASS	AF=0.0394386;HP=2;NF=5;NR=2;NS=52;CA=0;DP=565
+1	4840948	rs59349393;-/AAACCACATCCCTTGAACT	GACTAAACCACATCCCTTGAA	GA	100	PASS	AF=0.144437;HP=1;DB;NF=16;NR=17;NS=52;CA=0;DP=578
+1	4846284	rs36118323;-/T,venter	CT	CTT	100	PASS	AF=0.130437;HP=7;DB;NF=12;NR=15;NS=52;CA=0;DP=415
+1	4855247	venter	GA	GACACA	100	PASS	AF=0.301971;HP=1;NF=19;NR=3;NS=52;CA=0;DP=635
+1	4864897	venter	AT	ATT	100	PASS	AF=0.215684;HP=6;NF=17;NR=20;NS=52;CA=0;DP=450
+1	4865373	rs34273857;-/A,venter	CA	CAA	100	PASS	AF=0.169967;HP=6;DB;NF=17;NR=15;NS=52;CA=0;DP=533
diff --git a/tests/tabix_data/vcf/4.vcf b/tests/tabix_data/vcf/4.vcf
new file mode 100644
index 0000000..65ed14e
--- /dev/null
+++ b/tests/tabix_data/vcf/4.vcf
@@ -0,0 +1,318 @@
+##fileformat=VCFv4.1
+##INFO=<ID=BCM.AC,Number=1,Type=Integer,Description="Allele count from BCM's (sequencing-based) genotypes subsetted to the 383 validation samples">
+##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership">
+##INFO=<ID=SEQUENOM.AC,Number=1,Type=Integer,Description="Allele count from Sequenom genotyping">
+##INFO=<ID=SRC,Number=1,Type=String,Description="Type of SNPs submitted for validation; VQSR refers to preliminary consensus set, not the final one">
+##INFO=<ID=PQ,Number=1,Type=Integer,Description="BWA mapping quality of the PCR primers">
+##FILTER=<ID=AMBIGUOUS_SEQUENOM_CALLS,Description="Possible Sequenom miscalls based on manual review of cluster plots">
+##FILTER=<ID=HIGH_NO_CALL_RATE,Description="Extremely high no-call rate">
+##FILTER=<ID=INCORRECT_SEQUENOM_CALLS,Description="Clear Sequenom miscalls that cannot easily be fixed based on manual review of cluster plots">
+##FILTER=<ID=NOT_DESIGNED,Description="Primer not designed">
+##FILTER=<ID=NOT_TYPED,Description="Not typed">
+##FILTER=<ID=POLYMORPHIC_SAMPLES_FAILED,Description="All polymorphic samples from sequencing were no-called">
+##FILTER=<ID=POSSIBLE_PROBE_FAILURE,Description="Suspicious genotyping based on nearby SNPs">
+##FILTER=<ID=PQ10,Description="PQ<10">
+##fileDate=20110524
+##reference=ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz
+##source=EricBanksValidationQC;fromGoncaloAbecasisValidationSelection
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	HG00127	HG00128	HG00136	HG00137	HG00138	HG00139	HG00152	HG00156	HG00234	HG00235	HG00237	HG00242	HG00244	HG00262	HG01055	HG01079	NA19138	NA18974	NA18523	NA12717	NA19209	NA18577	NA18973	NA18943	NA12873	NA18623	NA18622	NA18948	NA19171	NA19204	NA06994	NA18563	NA18547	NA18861	NA18608	NA12282	NA12751	NA18959	NA19331	NA19453	NA20537	NA12046	NA20515	NA20516	NA20521	NA20524	NA20528	NA20759	NA20768	NA20769	NA20774	NA20775	NA20783	NA20787	NA20790	NA20800	NA20819	NA20812	NA20505	NA20530	NA20540	NA20538	NA20581	NA20815	NA20544	NA20810	NA20807	NA20816	NA20504	NA20753	NA20502	NA12342	NA19150	NA19468	NA20336	NA19395	NA19257	NA19360	NA19700	NA18867	NA20317	NA18968	NA19107	HG00111	HG00108	NA19077	NA19684	NA18511	NA12044	NA19382	NA19457	NA18933	NA18923	NA18965	HG00141	NA20341	NA18740	HG00537	HG00346	HG01173	HG00702	HG00313	HG00150	NA18612	HG00339	NA12273	HG00250	NA18593	NA18621	HG00478	HG00251	HG01070	NA19160	NA18995	NA10851	NA18976	NA18603	NA19200	HG01204	HG01191	HG01101	HG00146	HG00306	NA18985	HG00160	HG00635	HG00372	HG00357	HG00634	NA18541	NA18950	NA19759	HG00351	HG00257	HG00118	HG00336	HG00448	HG01354	NA18609	HG00428	HG00326	NA11894	NA18956	HG00173	HG00117	NA11893	HG01251	HG01441	HG01437	HG00182	HG00330	HG01060	HG00329	NA18960	NA18856	NA07346	NA18871	NA19057	NA18868	NA18636	NA12830	NA19007	NA18910	NA18874	NA19056	NA19064	NA19066	NA18487	NA18642	NA19236	NA07056	NA18637	NA19235	NA19309	NA19311	NA19334	NA19346	NA19347	NA19372	NA19376	NA19383	NA19384	NA19394	NA19428	NA19430	NA19451	NA19466	NA19313	NA19321	NA19324	NA19332	HG00479	HG00608	NA18573	HG00375	NA19248	NA19093	HG01170	HG00534	HG01171	HG01522	NA18624	HG00683	HG01521	NA19005	NA20412	NA18971	HG00446	NA12748	HG00530	HG00690	HG01356	HG01516	NA20532	HG00344	HG00328	NA18542	HG00254	HG00321	HG00577	HG00656	HG00342	HG00524	HG00650	HG00557	HG00319	HG00457	HG00125	HG00578	HG00543	HG00638	HG00171	HG00699	HG00595	HG00187	HG00704	HG00533	HG00596	HG00268	HG01083	HG00651	HG01133	HG00671	HG00327	HG01148	HG00246	HG00672	HG00556	HG00436	HG00554	NA18633	NA20344	NA11993	NA07037	NA11930	HG01366	HG01389	HG00620	NA19740	HG00190	HG00419	NA18535	HG01495	NA18592	HG01497	HG00174	HG01140	NA12287	HG00689	HG01550	HG00334	HG01375	HG00637	NA18507	HG01113	NA18550	NA19129	HG01551	HG01462	HG00331	NA12413	HG01456	HG01360	HG00708	HG01350	HG00684	NA19099	HG00284	NA12399	NA12286	NA12777	HG00277	HG00266	NA19985	HG00353	HG01102	NA07347	NA07051	NA19900	NA18984	NA07048	HG00640	HG01066	NA12812	HG01174	HG01188	NA19390	NA19436	NA19439	NA19440	NA19463	NA19470	NA19471	NA19472	NA19676	NA19660	NA19661	NA19663	NA19722	NA19725	NA19728	NA19729	NA19731	NA19749	NA19755	NA19756	NA19758	NA19770	NA19773	NA19777	NA19780	NA19783	NA20525	NA20589	NA20765	NA20802	NA20804	NA18544	NA18602	NA18546	NA18610	NA18957	NA18615	NA18616	NA19010	NA18638	NA18639	NA18627	NA19072	NA18630	NA19074	NA19080	NA19081	NA19083	NA19085	NA19088	NA20287	NA19835	NA20276	NA19818	NA20278	NA20282	NA20342	NA20296	NA20314	NA20346	NA19712	NA19198	NA19108	NA18934	NA18916	NA18907	NA18917	NA06989	NA12058	NA12341	NA12546	NA12489	HG01197	NA18983	NA11843	NA11892	NA12749
+20	82176	rs11906362	T	C	318	NOT_TYPED;PQ10	BCM.AC=16;DB;SRC=VQSR+2-OF-7;PQ=0
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+20	688672	rs116071340	C	T	56	PASS	BCM.AC=1;DB;SEQUENOM.AC=2;SRC=VQSR+2-OF-7;PQ=52	GT	.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	.	0/0	.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
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+20	62888718	.	T	C	57	POLYMORPHIC_SAMPLES_FAILED	BCM.AC=1;SEQUENOM.AC=0;SRC=VQSR+2-OF-7;PQ=60	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	.	0/0	.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+20	62918298	.	G	A	33	NOT_DESIGNED	SRC=VQSR+2-OF-7
+20	62961477	.	T	C	17	AMBIGUOUS_SEQUENOM_CALLS;PQ10	SEQUENOM.AC=0;SRC=VQSR+2-OF-7;PQ=0	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
diff --git a/tests/tabix_data/vcf/5.vcf b/tests/tabix_data/vcf/5.vcf
new file mode 100644
index 0000000..a23ed89
--- /dev/null
+++ b/tests/tabix_data/vcf/5.vcf
@@ -0,0 +1,1000 @@
+##fileformat=VCFv4.0
+##fileDate=2011-07-18
+##source=Platypus_Version_0.1
+##platypusOptions={'bamFiles': ['/data/lindah/illumina_projects/rimmer_indels/AllData.bam'], 'labels': None, 'refFile': '/ib/groups/bsg/scratch/rimmer/Genomes/human_g1k_v37_ebv.fa', 'maxHaplotypes': 256, 'maxSize': 250, 'parseNCBI': 0, 'ploidy': 2, 'bufferSize': 1000000, 'nCPU': 1, 'minFlank': 3, 'minPosterior': 5, 'logFileName': 'log.txt', 'regions': ['20'], 'processRegionSize': 30000000, 'maxVariants': 8, 'maxReads': 5000000, 'genIndels': 1, 'minReads': 2, 'dataType': 'population', 'minMapQual': 20, 'rlen': 150, 'nInd': 1, 'getVariantsFromBAMs': 1, 'genSNPs': 1, 'strandFilter': 0, 'verbosity': 2, 'sourceFile': None, 'callOnlyIndels': 0, 'output': 'test.vcf', 'minBaseQual': 20}
+##INFO=<ID=FR,Number=0,Type=Float,Description="Estimated population frequency">
+##INFO=<ID=HP,Number=1,Type=Integer,Description="Homopolmer run length">
+##INFO=<ID=TR,Number=0,Type=Integer,Description="Total number of reads containing this variant">
+##INFO=<ID=PP,Number=0,Type=Float,Description="Posterior probability (phred scaled) that this variant segregates">
+##INFO=<ID=NF,Number=0,Type=Integer,Description="Total number of forward reads containing this variant">
+##INFO=<ID=SC,Number=1,Type=String,Description="Genomic sequence 10 bases either side of variant position">
+##INFO=<ID=NR,Number=0,Type=Integer,Description="Total number of reverse reads containing this variant">
+##INFO=<ID=TC,Number=0,Type=Integer,Description="Total coverage at this locus">
+##FILTER=<ID=sb,Description="Variant not seen at least once on both strands">
+##FILTER=<ID=pp10,Description="Posterior probability phred-score is less than 10">
+##FILTER=<ID=pp5,Description="Posterior probability phred-score is less than 5">
+##FILTER=<ID=hp10,Description="Inside a homopolymer of length greater than 10">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Unphased genotypes">
+##FORMAT=<ID=FT,Number=1,Type=String,Description="Sample Genotype Filter">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype quality, as Phred score">
+##FORMAT=<ID=HQ,Number=.,Type=Integer,Description="Haplotype Quality">
+##FORMAT=<ID=GL,Number=.,Type=Float,Description="Genotype log-likelihoods (log10) for AA,AB and BB genotypes, where A = ref and B = variant. Only applicable for bi-allelic sites">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth at this position for this sample">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	AllData.bam
+20	67500	.	T	TTGGTATCTAG	.	PASS	FR=0.5;HP=2;NF=6;NR=2;PP=100.0;SC=CCTGATTTCCTTGGTATTAAA;TC=20;TR=8	GT:GL:GQ	0/1:-198.02,-21.47,-166.02:100
+20	69506	.	G	GAC,GACACAC	.	PASS	FR=0.5,0.5;HP=1;NF=1,3;NR=1,0;PP=44.0,72.0;SC=TGGACACGTGGACACACACAC;TC=20;TR=2,3	GT:GL:GQ	1/2:-1.0,-1.0,-1.0:100
+20	70484	.	CTCTT	C	.	PASS	FR=0.5;HP=2;NF=13;NR=3;PP=100.0;SC=GTCTATGTCTCTCTTTCTCTT;TC=31;TR=16	GT:GL:GQ	0/1:-189.04,-24.53,-147.47:100
+20	72104	.	TA	T	.	PASS	FR=0.5;HP=4;NF=9;NR=10;PP=100.0;SC=TTTAAGTCTGTAAAACCATAC;TC=39;TR=19	GT:GL:GQ	0/1:-173.69,-34.04,-169.85:100
+20	74729	.	G	GT	.	PASS	FR=0.5;HP=9;NF=4;NR=4;PP=100.0;SC=AAGTTTTTTGGTTTTTTTTTA;TC=29;TR=8	GT:GL:GQ	0/1:-83.86,-25.71,-59.16:100
+20	117309	.	G	GCAGGATTTCAT	.	PASS	FR=0.5;HP=1;NF=4;NR=4;PP=100.0;SC=CAGGATTTCTGCAGGATTTCA;TC=25;TR=8	GT:GL:GQ	0/1:-259.57,-46.67,-146.18:100
+20	119645	.	G	GT	.	PASS	FR=1.0;HP=5;NF=6;NR=5;PP=100.0;SC=TTGTTTGTTTGTTGTTGTTGT;TC=16;TR=11	GT:GL:GQ	1/1:-157.48,-18.84,-7.1:77
+20	120122	.	A	AAG	.	PASS	FR=1.0;HP=6;NF=10;NR=8;PP=100.0;SC=ATAAAGAAAAAAATTTTAAAA;TC=27;TR=18	GT:GL:GQ	1/1:-266.98,-24.1,-5.49:100
+20	120750	.	C	CAATT	.	PASS	FR=1.0;HP=6;NF=10;NR=10;PP=100.0;SC=TTTTATAAAACAATTGAGACT;TC=21;TR=20	GT:GL:GQ	1/1:-319.22,-18.71,-2.07:100
+20	122806	.	T	TTA	.	PASS	FR=0.5;HP=2;NF=8;NR=7;PP=100.0;SC=CAGAAAAGAATTATATATATA;TC=29;TR=15	GT:GL:GQ	0/1:-181.3,-19.86,-96.14:100
+20	126155	.	GCAAA	G	.	PASS	FR=0.5;HP=1;NF=5;NR=5;PP=100.0;SC=GCAATGTGCGGCAAACAAAGG;TC=32;TR=10	GT:GL:GQ	0/1:-122.73,-27.0,-209.16:100
+20	126310	.	ACC	A	.	PASS	FR=0.5;HP=5;NF=3;NR=8;PP=100.0;SC=GATGGCTCCTACCCCCGTTTC;TC=26;TR=11	GT:GL:GQ	0/1:-153.97,-42.91,-110.82:100
+20	131505	.	CTCT	C	.	PASS	FR=1.0;HP=2;NF=11;NR=11;PP=100.0;SC=TACTTGTGATCTCTTGTCTTT;TC=24;TR=22	GT:GL:GQ	1/1:-487.46,-251.24,-235.3:100
+20	131948	.	C	CCA	.	PASS	FR=1.0;HP=1;NF=2;NR=11;PP=100.0;SC=TTATCTTACACCACACACACA;TC=27;TR=13	GT:GL:GQ	1/1:-201.6,-36.32,-23.94:100
+20	135116	.	T	TTTGCATTCACAGGAAGACTATAAATA	.	PASS	FR=1.0;HP=2;NF=2;NR=1;PP=100.0;SC=TCTAGAGAAGTGCTCTCCAAT;TC=15;TR=3	GT:GL:GQ	1/1:-603.73,-461.77,-448.12:100
+20	135119	.	TC	T	.	PASS	FR=1.0;HP=2;NF=2;NR=2;PP=100.0;SC=AGAGAAGTGCTCTCCAATAGA;TC=21;TR=4	GT:GL:GQ	1/1:-603.73,-576.89,-572.06:100
+20	137518	.	GTA	G	.	PASS	FR=0.5005;HP=2;NF=5;NR=5;PP=100.0;SC=GTGTGTGTGTGTATATATATA;TC=21;TR=10	GT:GL:GQ	1/0:-210.61,-46.97,-32.7:29
+20	138178	.	GC	G	.	PASS	FR=1.0;HP=3;NF=21;NR=5;PP=100.0;SC=CTTCTGGAAAGCCTGGCCATG;TC=29;TR=26	GT:GL:GQ	1/1:-267.55,-29.21,-9.21:100
+20	138570	.	ATATGTGTGTG	ATG,A	.	PASS	FR=0.5,0.5;HP=2;NF=6,2;NR=9,2;PP=100.0,10.0;SC=TCAAATATATATATGTGTGTG;TC=28;TR=15,4	GT:GL:GQ	1/2:-1.0,-1.0,-1.0:65
+20	140396	.	TTTG	T	.	PASS	FR=1.0;HP=2;NF=15;NR=4;PP=100.0;SC=AGGTTTTTGCTTTGTTGTTGT;TC=34;TR=19	GT:GL:GQ	1/1:-246.82,-30.67,-15.42:100
+20	144832	.	C	CT	.	PASS	FR=1.0;HP=3;NF=12;NR=22;PP=100.0;SC=TCCTAAAACTCTTGTAATATC;TC=35;TR=34	GT:GL:GQ	1/1:-541.89,-322.78,-299.72:100
+20	144884	.	CCTT	C	.	PASS	FR=1.0;HP=1;NF=9;NR=16;PP=100.0;SC=TGTAATGACACCTTCTTTTTC;TC=29;TR=25	GT:GL:GQ	1/1:-590.4,-430.25,-411.02:100
+20	145257	.	G	GC	.	PASS	FR=1.0;HP=2;NF=11;NR=8;PP=100.0;SC=ATGGTGGCAGGGCCTGTAATC;TC=21;TR=19	GT:GL:GQ	1/1:-258.74,-106.61,-91.83:100
+20	153298	.	T	TTC	.	PASS	FR=1.0;HP=2;NF=13;NR=17;PP=100.0;SC=CAGGATTTCTTTGTTTTAAGA;TC=34;TR=30	GT:GL:GQ	1/1:-447.58,-228.67,-205.19:100
+20	160111	.	A	AT	.	PASS	FR=1.0;HP=10;NF=8;NR=9;PP=100.0;SC=GAGCTCTTGAATTTTTTTTTT;TC=25;TR=17	GT:GL:GQ	1/1:-115.49,-38.32,-28.08:85
+20	163607	.	A	AAT	.	PASS	FR=1.0;HP=2;NF=12;NR=14;PP=100.0;SC=ACATTAAATGATTCAAATGAT;TC=31;TR=26	GT:GL:GQ	1/1:-308.34,-35.98,-14.5:100
+20	163741	.	T	TACACAC	.	PASS	FR=0.5243;HP=1;NF=13;NR=6;PP=100.0;SC=GAACCCTCTGTACACACACAC;TC=28;TR=19	GT:GL:GQ	0/1:-416.01,-75.48,-55.48:13
+20	164279	.	G	GAAAAC	.	PASS	FR=0.5;HP=8;NF=1;NR=1;PP=100.0;SC=GAAAAGAAAAGAAAAGAAAAC;TC=34;TR=2	GT:GL:GQ	0/1:-492.01,-428.61,-448.28:100
+20	164284	.	G	GAAAAC,C	.	PASS	FR=0.5,0.5;HP=8;NF=5,10;NR=11,9;PP=100.0,100.0;SC=GAAAAGAAAAGAAAACTCATC;TC=33;TR=16,19	GT:GL:GQ	1/2:-1.0,-1.0,-1.0:100
+20	176386	.	CGTGTGT	C	.	PASS	FR=1.0;HP=2;NF=3;NR=2;PP=100.0;SC=TAATCCCATTCGTGTGTGTGT;TC=25;TR=5	GT:GL:GQ	1/1:-176.18,-68.1,-61.92:77
+20	179735	.	TTAAAA	T	.	PASS	FR=0.5;HP=1;NF=4;NR=4;PP=100.0;SC=ACCTTTGATCTTAAAATAAAA;TC=27;TR=8	GT:GL:GQ	0/1:-142.0,-61.37,-164.64:100
+20	218255	.	A	AG	.	PASS	FR=0.5;HP=1;NF=5;NR=3;PP=100.0;SC=TGCTCACTGCAATAAAAAGAA;TC=17;TR=8	GT:GL:GQ	0/1:-99.61,-20.66,-85.67:100
+20	222539	.	C	CA	.	PASS	FR=0.5;HP=2;NF=1;NR=9;PP=100.0;SC=TACCCAGCTACTTCTCTTAAG;TC=31;TR=10	GT:GL:GQ	0/1:-113.51,-40.72,-197.06:100
+20	230058	.	CAT	C	.	PASS	FR=0.5;HP=1;NF=6;NR=2;PP=100.0;SC=GACTCCATCTCATAAAAAAAA;TC=33;TR=8	GT:GL:GQ	0/1:-215.64,-148.07,-177.0:100
+20	236459	.	G	GAT	.	PASS	FR=0.5001;HP=2;NF=1;NR=1;PP=100.0;SC=TTGGAATACAGATATATATAT;TC=14;TR=2	GT:GL:GQ	0/1:-82.0,-46.74,-54.25:35
+20	237649	.	CAGAT	C	.	PASS	FR=0.5;HP=2;NF=1;NR=1;PP=79.0;SC=AGATAGATGACAGATAGATAG;TC=23;TR=2	GT:GL:GQ	0/1:-209.52,-180.44,-254.54:100
+20	237816	.	A	AT	.	PASS	FR=0.5;HP=4;NF=4;NR=7;PP=100.0;SC=CATTTTCATCATTTTAATAAC;TC=32;TR=11	GT:GL:GQ	0/1:-124.3,-28.61,-145.84:100
+20	243223	.	C	CT	.	PASS	FR=0.5;HP=1;NF=12;NR=4;PP=100.0;SC=ATCTGTGTGACTGTGATCAAA;TC=33;TR=16	GT:GL:GQ	0/1:-191.55,-34.68,-144.05:100
+20	246483	.	T	TTAAA	.	PASS	FR=0.5;HP=1;NF=3;NR=4;PP=100.0;SC=AGACTCCATCTTAAATAAATA;TC=25;TR=7	GT:GL:GQ	0/1:-110.34,-17.05,-40.1:100
+20	251373	.	ACTT	A	.	PASS	FR=0.5;HP=2;NF=1;NR=4;PP=100.0;SC=TTGCTCCAGCACTTCTTCTGG;TC=19;TR=5	GT:GL:GQ	0/1:-99.2,-52.91,-150.48:100
+20	271135	.	G	GC	.	PASS	FR=1.0;HP=2;NF=3;NR=4;PP=100.0;SC=AAGACCGAGGGCGACCTCGAG;TC=16;TR=7	GT:GL:GQ	1/1:-163.65,-94.48,-85.08:78
+20	286648	.	TAAATA	T	.	PASS	FR=0.5;HP=6;NF=5;NR=5;PP=100.0;SC=TCTAAATAAATAAATAAAAGG;TC=22;TR=10	GT:GL:GQ	0/1:-240.51,-100.72,-176.05:100
+20	299585	.	AC	A	.	PASS	FR=1.0;HP=2;NF=4;NR=7;PP=21.0;SC=ACAGGGAGAGACCTTGTCGAA;TC=14;TR=11	GT:GL:GQ	1/1:-152.36,-140.91,-138.05:46
+20	334317	.	TC	T	.	PASS	FR=1.0;HP=6;NF=9;NR=8;PP=100.0;SC=CCTGGATCCTTCCCCCCTTCT;TC=24;TR=17	GT:GL:GQ	1/1:-177.37,-48.79,-33.34:100
+20	337392	.	ACC	A	.	PASS	FR=0.5;HP=6;NF=5;NR=1;PP=100.0;SC=CCTTGTTACCACCCCTCCCTG;TC=19;TR=6	GT:GL:GQ	0/1:-91.61,-45.67,-115.7:100
+20	340044	.	GCAC	G	.	PASS	FR=0.5;HP=1;NF=2;NR=5;PP=100.0;SC=ATGAAGGCTGGCACCACCAGT;TC=22;TR=7	GT:GL:GQ	0/1:-122.54,-28.81,-115.11:100
+20	343323	.	A	ATG	.	PASS	FR=0.5;HP=2;NF=8;NR=4;PP=100.0;SC=GATAAACAGGATGTCCACCAG;TC=23;TR=12	GT:GL:GQ	0/1:-150.99,-48.03,-125.5:100
+20	346702	.	AGCCTCCCAAAGGAG	A	.	PASS	FR=0.5;HP=1;NF=4;NR=3;PP=100.0;SC=CACCCACCTCAGCCTCCCAAA;TC=17;TR=7	GT:GL:GQ	0/1:-191.1,-120.01,-173.49:100
+20	347858	.	A	AAAACAAAC	.	PASS	FR=0.5;HP=4;NF=2;NR=1;PP=100.0;SC=TCCGTCTCCAAAAACAAACAA;TC=22;TR=3	GT:GL:GQ	0/1:-270.04,-201.07,-226.88:100
+20	347878	.	A	AAAAC	.	PASS	FR=0.5;HP=3;NF=2;NR=1;PP=100.0;SC=AAAAAACAAAACAAACAAACA;TC=22;TR=3	GT:GL:GQ	0/1:-258.23,-262.98,-327.72:100
+20	348365	.	G	GT	.	PASS	FR=0.5;HP=2;NF=5;NR=4;PP=100.0;SC=ACGGCCCATGGGATCGAATAG;TC=19;TR=9	GT:GL:GQ	0/1:-127.12,-35.07,-72.46:100
+20	349321	.	ACT	A	.	PASS	FR=0.5;HP=3;NF=10;NR=3;PP=100.0;SC=CCAGGCCTCCACTCTCTGCTG;TC=20;TR=13	GT:GL:GQ	0/1:-183.61,-95.19,-129.48:100
+20	355549	.	A	AC	.	PASS	FR=1.0;HP=10;NF=12;NR=9;PP=100.0;SC=AACAACAACAAAAAAAAAAAC;TC=24;TR=21	GT:GL:GQ	1/1:-171.74,-97.15,-84.12:100
+20	356670	.	T	TCAAA	.	PASS	FR=0.5;HP=3;NF=4;NR=2;PP=100.0;SC=AGACACTGCCTCAAAAAAACA;TC=16;TR=6	GT:GL:GQ	0/1:-204.44,-131.78,-155.8:100
+20	356675	.	A	AAAAC	.	PASS	FR=1.0;HP=6;NF=2;NR=3;PP=100.0;SC=CTGCCTCAAAAAAACAAACAA;TC=17;TR=5	GT:GL:GQ	1/1:-201.68,-85.68,-76.1:85
+20	358147	.	CA	C	.	PASS	FR=1.0;HP=4;NF=10;NR=5;PP=100.0;SC=TGGGATTTGACAAACCCAGCT;TC=18;TR=15	GT:GL:GQ	1/1:-150.87,-32.16,-20.25:100
+20	360927	.	TAA	T	.	PASS	FR=1.0;HP=7;NF=4;NR=7;PP=100.0;SC=ATGTGCTTTATAAAAAAGGGG;TC=18;TR=11	GT:GL:GQ	1/1:-185.94,-114.38,-104.3:84
+20	380790	.	C	CT	.	PASS	FR=1.0;HP=3;NF=16;NR=12;PP=100.0;SC=CACCACACCCCGACCCTAATT;TC=32;TR=28	GT:GL:GQ	1/1:-323.67,-24.71,-1.84:100
+20	385989	.	T	TA	.	PASS	FR=0.5;HP=7;NF=7;NR=4;PP=100.0;SC=AGATTTTTTTTAAAAAACTCT;TC=29;TR=11	GT:GL:GQ	0/1:-131.67,-23.75,-80.28:100
+20	386575	.	GTTCT	G	.	PASS	FR=0.5;HP=3;NF=2;NR=3;PP=100.0;SC=TGATAAGAATGTTCTTTCTTT;TC=24;TR=5	GT:GL:GQ	0/1:-109.28,-29.71,-86.14:100
+20	387657	.	G	GA	.	PASS	FR=1.0;HP=8;NF=13;NR=19;PP=100.0;SC=ATGCTGAGAAGAAAAAATGAA;TC=38;TR=32	GT:GL:GQ	1/1:-284.64,-52.81,-28.53:100
+20	396023	.	A	AAAAC	.	PASS	FR=1.0;HP=4;NF=9;NR=9;PP=100.0;SC=AAAAAAAACAAAAACAAACAA;TC=25;TR=18	GT:GL:GQ	1/1:-279.26,-33.44,-17.73:100
+20	403158	.	GA	G	.	PASS	FR=0.5;HP=2;NF=4;NR=7;PP=89.0;SC=ATCTATGAAGGAAGGACAGCA;TC=20;TR=11	GT:GL:GQ	0/1:-137.87,-107.23,-160.58:100
+20	405057	.	A	AC	.	PASS	FR=0.5;HP=2;NF=5;NR=4;PP=100.0;SC=AAACACATACACAGACCTCCT;TC=25;TR=9	GT:GL:GQ	0/1:-136.78,-33.82,-124.47:100
+20	421805	.	T	TCCA	.	PASS	FR=0.5;HP=2;NF=2;NR=4;PP=100.0;SC=AGAACACATTTCCAACTAAAC;TC=29;TR=6	GT:GL:GQ	0/1:-108.14,-30.52,-185.93:100
+20	425206	.	GTTTT	G	.	PASS	FR=0.5;HP=7;NF=2;NR=7;PP=100.0;SC=TTGTTTGTTTGTTTTGTTTTT;TC=25;TR=9	GT:GL:GQ	0/1:-158.57,-21.01,-100.22:100
+20	430158	.	GA	G	.	PASS	FR=0.5;HP=3;NF=2;NR=4;PP=100.0;SC=AGAGTCGCTTGAAACCCAGGA;TC=16;TR=6	GT:GL:GQ	0/1:-74.97,-35.93,-74.51:100
+20	434939	.	G	GA	.	PASS	FR=0.5;HP=10;NF=6;NR=2;PP=100.0;SC=AAGAAAAAAGGAAAAAAAAAA;TC=22;TR=8	GT:GL:GQ	0/1:-99.4,-65.02,-85.64:92
+20	436981	.	TTTCATCCA	T	.	PASS	FR=0.5;HP=2;NF=1;NR=2;PP=100.0;SC=AGGTGTGTCCTTTCATCCATT;TC=27;TR=3	GT:GL:GQ	0/1:-88.19,-26.08,-154.96:100
+20	525046	.	G	GT	.	PASS	FR=0.5;HP=10;NF=5;NR=8;PP=100.0;SC=AAAATACAGTGTTTTTTTTTC;TC=33;TR=13	GT:GL:GQ	0/1:-160.44,-103.25,-141.37:100
+20	538639	.	C	CA	.	PASS	FR=1.0;HP=9;NF=14;NR=9;PP=100.0;SC=ACCACCACAACAAAAAAACCC;TC=36;TR=23	GT:GL:GQ	1/1:-261.69,-66.02,-42.16:100
+20	539756	.	G	GT	.	PASS	FR=0.5;HP=1;NF=6;NR=2;PP=100.0;SC=AATGTGAGCAGTCTAGGTAAA;TC=24;TR=8	GT:GL:GQ	0/1:-130.62,-70.51,-165.77:100
+20	540198	.	T	TG	.	PASS	FR=1.0;HP=1;NF=9;NR=16;PP=100.0;SC=AGAGTCGCTGTTATTAAAACC;TC=26;TR=25	GT:GL:GQ	1/1:-262.05,-37.69,-19.11:100
+20	545849	.	A	AT	.	PASS	FR=1.0;HP=9;NF=6;NR=13;PP=100.0;SC=CTCTGGACTGATTTTTTTTTA;TC=24;TR=19	GT:GL:GQ	1/1:-225.47,-140.74,-126.39:100
+20	555243	.	C	CT	.	PASS	FR=0.5;HP=1;NF=3;NR=4;PP=100.0;SC=TTGGGGCCTCCTGGGTCCCAG;TC=23;TR=7	GT:GL:GQ	0/1:-124.01,-59.66,-144.99:100
+20	559298	.	TACAC	T	.	PASS	FR=0.5081;HP=1;NF=1;NR=1;PP=100.0;SC=GGCACACATGTACACACACAC;TC=20;TR=2	GT:GL:GQ	0/1:-95.31,-59.31,-62.75:17
+20	570945	.	A	AACAC	.	PASS	FR=1.0;HP=1;NF=7;NR=2;PP=100.0;SC=AGAAGGCAATAACACACACAC;TC=28;TR=9	GT:GL:GQ	1/1:-281.44,-73.27,-58.53:100
+20	576287	.	T	TTTA	.	PASS	FR=1.0;HP=3;NF=2;NR=9;PP=100.0;SC=CTGGAAAAGTTTTATTATTAT;TC=26;TR=11	GT:GL:GQ	1/1:-188.46,-27.21,-14.74:100
+20	593205	.	AG	A	.	PASS	FR=0.5;HP=6;NF=2;NR=2;PP=100.0;SC=GGGAGTGCGGAGGGGACTCCT;TC=14;TR=4	GT:GL:GQ	0/1:-90.79,-21.16,-46.9:100
+20	635817	.	C	CAGAAAAAAA	.	PASS	FR=1.0;HP=1;NF=6;NR=7;PP=100.0;SC=GAGACTCTCTCAGAAAAAAAA;TC=23;TR=13	GT:GL:GQ	1/1:-318.1,-28.61,-13.35:100
+20	666340	.	AAATAATAATAAT	AAATAAT,A	.	PASS	FR=0.5,0.5;HP=2;NF=1,2;NR=3,3;PP=100.0,100.0;SC=ATACAAATACAAATAATAATA;TC=16;TR=4,5	GT:GL:GQ	1/2:-1.0,-1.0,-1.0:100
+20	671463	.	AGTGT	A	.	PASS	FR=1.0;HP=1;NF=6;NR=2;PP=100.0;SC=CATGCATGCAAGTGTGTGTGT;TC=25;TR=8	GT:GL:GQ	1/1:-248.41,-147.67,-140.04:63
+20	675799	.	G	GTA	.	PASS	FR=0.5;HP=2;NF=7;NR=3;PP=100.0;SC=TAATGAACATGTATATATACA;TC=20;TR=10	GT:GL:GQ	0/1:-154.12,-35.67,-66.33:100
+20	704073	.	CTCT	C	.	PASS	FR=0.5;HP=3;NF=3;NR=3;PP=100.0;SC=CTTCATTCTTCTCTTTTCTTT;TC=20;TR=6	GT:GL:GQ	0/1:-159.89,-91.96,-171.96:100
+20	704111	.	C	CTTTCT	.	PASS	FR=0.5;HP=4;NF=2;NR=3;PP=100.0;SC=TTCCTCCTCTCTTTGTCTAGT;TC=20;TR=5	GT:GL:GQ	0/1:-189.74,-115.92,-237.08:100
+20	714136	.	TA	T	.	PASS	FR=1.0;HP=2;NF=12;NR=13;PP=100.0;SC=CTGTGGTTGTTAACTGTAGTC;TC=30;TR=25	GT:GL:GQ	1/1:-253.68,-26.24,-6.67:100
+20	715254	.	G	GGT,GGTGTGT	.	PASS	FR=0.5,0.5;HP=1;NF=3,4;NR=0,1;PP=57.0,100.0;SC=ATAGTTTATAGGTGTGTGTGT;TC=23;TR=3,5	GT:GL:GQ	1/2:-1.0,-1.0,-1.0:100
+20	715847	.	C	CA	.	PASS	FR=1.0;HP=7;NF=10;NR=6;PP=100.0;SC=GGCTCCGTCTCAAAAAAATAA;TC=26;TR=16	GT:GL:GQ	1/1:-157.25,-40.0,-26.17:100
+20	718268	.	A	AAATAAT	.	PASS	FR=0.5;HP=3;NF=1;NR=1;PP=81.0;SC=AAAAAATACAAAATAATAATA;TC=15;TR=2	GT:GL:GQ	0/1:-64.86,-29.69,-87.73:100
+20	724447	.	A	AG	.	PASS	FR=0.5;HP=2;NF=12;NR=9;PP=100.0;SC=GGGTGTTGTGAGACTGATTGA;TC=42;TR=21	GT:GL:GQ	0/1:-229.53,-40.83,-188.06:100
+20	726275	.	CAGA	C	.	PASS	FR=0.5;HP=3;NF=10;NR=10;PP=100.0;SC=ACATATATAACAGAAGGAGAG;TC=41;TR=20	GT:GL:GQ	0/1:-286.26,-52.94,-197.08:100
+20	728851	.	CT	C	.	PASS	FR=0.5;HP=1;NF=5;NR=1;PP=21.0;SC=GATCACACCACTGCAGTCCAG;TC=22;TR=6	GT:GL:GQ	0/1:-200.76,-185.85,-212.48:67
+20	732117	.	CTTTATTTTAT	C	.	PASS	FR=0.9998;HP=4;NF=1;NR=1;PP=80.0;SC=TCAGGTATGTCTTTATTTTAT;TC=14;TR=2	GT:GL:GQ	1/1:-96.6,-68.07,-66.69:34
+20	739616	.	CGTGTGTGT	C	.	PASS	FR=1.0;HP=1;NF=4;NR=4;PP=100.0;SC=TAAAAGTGCTCGTGTGTGTGT;TC=20;TR=8	GT:GL:GQ	1/1:-222.59,-24.43,-16.81:63
+20	744662	.	A	ACAGGTCAAT	.	PASS	FR=0.5;HP=1;NF=3;NR=4;PP=100.0;SC=AAAGGACAAGACAGATCCCTG;TC=16;TR=7	GT:GL:GQ	0/1:-105.45,-32.23,-150.03:100
+20	746855	.	A	AG	.	PASS	FR=1.0;HP=1;NF=9;NR=5;PP=100.0;SC=CTGGGATTACAGTGTGAGCCA;TC=22;TR=14	GT:GL:GQ	1/1:-242.45,-177.27,-167.62:80
+20	747680	.	A	ATAG	.	PASS	FR=0.5;HP=1;NF=3;NR=3;PP=100.0;SC=CTTGTTGGTAATAGCAAGTTA;TC=17;TR=6	GT:GL:GQ	0/1:-177.8,-96.72,-120.09:100
+20	755106	.	C	CA	.	PASS	FR=1.0;HP=3;NF=7;NR=15;PP=100.0;SC=GCTGAGAGGTCAAACCACAAA;TC=27;TR=22	GT:GL:GQ	1/1:-255.81,-41.84,-23.33:100
+20	757564	.	T	TG	.	PASS	FR=0.5;HP=3;NF=3;NR=1;PP=78.0;SC=GGTGGAGCCATGGGTGTCAAA;TC=10;TR=4	GT:GL:GQ	0/1:-67.44,-38.36,-58.29:89
+20	757919	.	A	AC	.	PASS	FR=0.5;HP=9;NF=3;NR=9;PP=100.0;SC=AAAAAACAAAAAAAAAACACC;TC=27;TR=12	GT:GL:GQ	0/1:-172.2,-112.42,-144.61:100
+20	762893	.	G	GA	.	PASS	FR=1.0;HP=6;NF=8;NR=9;PP=100.0;SC=TCTTGGGGGGGAAAAAATGGG;TC=24;TR=17	GT:GL:GQ	1/1:-215.19,-64.36,-48.0:100
+20	782496	.	CAAATAAAT	C	.	PASS	FR=0.5;HP=3;NF=2;NR=1;PP=100.0;SC=GACTCTGCCTCAAATAAATAA;TC=17;TR=3	GT:GL:GQ	0/1:-87.5,-27.65,-92.5:100
+20	786252	.	AAG	A	.	PASS	FR=1.0;HP=5;NF=4;NR=13;PP=100.0;SC=TTAATTAAAAAAGATATTGCA;TC=19;TR=17	GT:GL:GQ	1/1:-216.25,-31.31,-17.45:100
+20	786764	.	T	TA	.	PASS	FR=1.0;HP=3;NF=17;NR=12;PP=100.0;SC=ACTATATATATAATATATTTT;TC=33;TR=29	GT:GL:GQ	1/1:-388.27,-147.23,-125.36:100
+20	787870	.	T	TTTTATTTATTTATTTATTTA	.	PASS	FR=1.0;HP=3;NF=2;NR=1;PP=100.0;SC=ATATCAAGCATTTTATTTATT;TC=19;TR=3	GT:GL:GQ	1/1:-317.88,-65.36,-53.59:99
+20	787893	.	T	TATTTATTTA	.	PASS	FR=0.5;HP=4;NF=1;NR=1;PP=100.0;SC=TTTATTTATTTTTGAGATGGA;TC=20;TR=2	GT:GL:GQ	0/1:-356.98,-227.18,-263.76:5
+20	789767	.	T	TA	.	PASS	FR=1.0;HP=10;NF=8;NR=5;PP=100.0;SC=CAAAGCCAATTAAAAAAAAAA;TC=29;TR=13	GT:GL:GQ	1/1:-124.57,-44.47,-30.25:100
+20	795148	.	T	TTTTA	.	PASS	FR=1.0;HP=4;NF=9;NR=1;PP=100.0;SC=ATAAGTTTATTTTTATTTATT;TC=16;TR=10	GT:GL:GQ	1/1:-136.44,-12.46,-4.83:63
+20	797336	.	GA	G	.	PASS	FR=1.0;HP=10;NF=18;NR=11;PP=100.0;SC=CCATTTATGTGAAAAAAAAAA;TC=35;TR=29	GT:GL:GQ	1/1:-156.82,-42.02,-20.72:100
+20	801157	.	T	TTTC	.	PASS	FR=1.0;HP=6;NF=1;NR=6;PP=100.0;SC=CTTCTCTTTCTTTTTTTCTTT;TC=13;TR=7	GT:GL:GQ	1/1:-142.57,-41.24,-32.92:92
+20	825082	.	TGCCCAGGTC	T	.	PASS	FR=0.5;HP=1;NF=5;NR=1;PP=100.0;SC=CTGCTCAGGTTGCCCAGGTCG;TC=8;TR=6	GT:GL:GQ	1/0:-180.72,-60.67,-71.61:61
+20	833239	.	ACT	A	.	PASS	FR=0.5;HP=1;NF=3;NR=5;PP=100.0;SC=GGAGAAATAGACTCTCTCTCT;TC=21;TR=8	GT:GL:GQ	0/1:-96.13,-31.34,-89.12:100
+20	835500	.	TTGTG	T	.	PASS	FR=1.0;HP=2;NF=8;NR=2;PP=100.0;SC=GTGTTTGTGTTTGTGTGTGTG;TC=29;TR=10	GT:GL:GQ	1/1:-258.26,-62.01,-52.79:77
+20	855678	.	TC	T	.	PASS	FR=0.5;HP=2;NF=3;NR=5;PP=100.0;SC=TCTTTTTCTTTCTTTTTTTTC;TC=28;TR=8	GT:GL:GQ	0/1:-124.38,-62.93,-124.85:100
+20	860945	.	A	AG	.	PASS	FR=0.5;HP=6;NF=2;NR=6;PP=100.0;SC=GTATATTAAGAGGGGGTGAAA;TC=23;TR=8	GT:GL:GQ	0/1:-96.52,-33.16,-85.46:100
+20	863148	.	C	CTAT	.	PASS	FR=0.5;HP=2;NF=3;NR=12;PP=100.0;SC=CCAGAGAAGGCTATTGCTCTC;TC=37;TR=15	GT:GL:GQ	0/1:-223.19,-48.7,-208.9:100
+20	899789	.	CTCTT	C	.	PASS	FR=0.5;HP=3;NF=1;NR=3;PP=100.0;SC=TTTCCTTCTTCTCTTTCTTTC;TC=21;TR=4	GT:GL:GQ	0/1:-62.34,-23.94,-85.48:100
+20	900698	.	T	TC	.	PASS	FR=1.0;HP=4;NF=11;NR=5;PP=100.0;SC=AGGAAGGCAGTCCCCTTTCCT;TC=29;TR=16	GT:GL:GQ	1/1:-292.54,-113.13,-95.49:100
+20	902060	.	T	TG,G	.	PASS	FR=0.5,0.5;HP=5;NF=2,7;NR=2,4;PP=100.0,100.0;SC=TTGACTGCCCTCCTCCACTTT;TC=19;TR=4,11	GT:GL:GQ	1/2:-1.0,-1.0,-1.0:100
+20	909945	.	TTATGG	TTGG,T	.	PASS	FR=0.5,0.5;HP=2;NF=10,8;NR=5,5;PP=100.0,100.0;SC=TTAGTTTAGTTTATGGTATCC;TC=32;TR=15,13	GT:GL:GQ	1/2:-1.0,-1.0,-1.0:100
+20	913303	.	A	AT	.	PASS	FR=1.0;HP=10;NF=9;NR=4;PP=100.0;SC=AGATTTAAAGATTTTTTTTTT;TC=21;TR=13	GT:GL:GQ	1/1:-227.97,-180.37,-171.35:75
+20	922916	.	A	AT	.	PASS	FR=1.0;HP=6;NF=2;NR=1;PP=27.0;SC=TTATTTATTTATTTATTTTTT;TC=7;TR=3	GT:GL:GQ	1/1:-68.71,-54.63,-52.11:41
+20	933970	.	GTTAT	G	.	PASS	FR=1.0;HP=4;NF=5;NR=5;PP=100.0;SC=CAGGCTAATTGTTATTTATTT;TC=24;TR=10	GT:GL:GQ	1/1:-169.08,-10.86,-0.46:87
+20	934153	.	A	AT	.	PASS	FR=1.0;HP=7;NF=4;NR=5;PP=100.0;SC=ATTTTTTTGTATTTTTTAATA;TC=11;TR=9	GT:GL:GQ	1/1:-123.08,-66.05,-59.03:57
+20	945474	.	CAT	C	.	PASS	FR=1.0;HP=2;NF=2;NR=6;PP=100.0;SC=CACACACACACATATATATAT;TC=31;TR=8	GT:GL:GQ	1/1:-229.9,-58.37,-41.73:100
+20	954102	.	A	ATTGT	.	PASS	FR=0.5;HP=6;NF=4;NR=1;PP=100.0;SC=TGTTTGTTTTATTGTTTGTTT;TC=30;TR=5	GT:GL:GQ	0/1:-77.28,-28.19,-134.91:100
+20	972071	.	A	AT	.	PASS	FR=0.5;HP=8;NF=7;NR=5;PP=100.0;SC=ATTAAAAAAGATTTTTTTTGT;TC=27;TR=12	GT:GL:GQ	0/1:-76.99,-19.47,-57.49:100
+20	995685	.	CAAAT	C	.	PASS	FR=1.0;HP=3;NF=3;NR=2;PP=100.0;SC=AACTCTATCTCAAATAAATAA;TC=15;TR=5	GT:GL:GQ	1/1:-96.06,-12.82,-6.68:77
+20	1000562	.	TTTCA	T	.	PASS	FR=0.5;HP=2;NF=10;NR=1;PP=100.0;SC=TCACCCTTTCTTTCATTCACT;TC=23;TR=11	GT:GL:GQ	0/1:-127.76,-31.92,-110.25:100
+20	1005659	.	CTCAG	C	.	PASS	FR=1.0;HP=3;NF=15;NR=6;PP=100.0;SC=AACAAACAAACTCAGTCTGTC;TC=34;TR=21	GT:GL:GQ	1/1:-379.32,-49.71,-26.34:100
+20	1018266	.	CAAT	C	.	PASS	FR=1.0;HP=4;NF=10;NR=7;PP=100.0;SC=GAAGTAACAACAATAATAATA;TC=26;TR=17	GT:GL:GQ	1/1:-307.78,-61.51,-42.82:100
+20	1023817	.	C	CCCT	.	PASS	FR=1.0;HP=3;NF=7;NR=3;PP=100.0;SC=CAGTGCCCACCCCTCCTCTCC;TC=22;TR=10	GT:GL:GQ	1/1:-230.45,-50.55,-37.14:100
+20	1024121	.	A	AT	.	PASS	FR=1.0;HP=6;NF=5;NR=3;PP=100.0;SC=CGGGTCAGGCATTTTTTATCA;TC=16;TR=8	GT:GL:GQ	1/1:-95.55,-28.09,-20.26:65
+20	1042261	.	CCCTG	C	.	PASS	FR=1.0;HP=2;NF=10;NR=10;PP=100.0;SC=CCAAACCCAACCCTGCCTGGC;TC=25;TR=20	GT:GL:GQ	1/1:-365.29,-133.94,-117.57:100
+20	1050585	.	AT	A	.	PASS	FR=1.0;HP=10;NF=9;NR=15;PP=100.0;SC=TTCTAATTCCATTTTTTTTTT;TC=33;TR=24	GT:GL:GQ	1/1:-288.37,-205.98,-189.27:100
+20	1059991	.	G	GAATT	.	PASS	FR=1.0;HP=2;NF=10;NR=6;PP=100.0;SC=AACATTTGTTGAATTAATTAA;TC=25;TR=16	GT:GL:GQ	1/1:-290.89,-32.75,-16.81:100
+20	1072882	.	CAG	C	.	PASS	FR=0.5;HP=6;NF=5;NR=6;PP=100.0;SC=ATCAGAAAAACAGAGACCACA;TC=23;TR=11	GT:GL:GQ	0/1:-124.42,-26.5,-135.46:100
+20	1084744	.	TG	T	.	PASS	FR=1.0;HP=5;NF=9;NR=12;PP=100.0;SC=ACCATAAATGTGGGGCTACTG;TC=23;TR=21	GT:GL:GQ	1/1:-326.86,-192.89,-179.07:100
+20	1100621	.	TAG	T	.	PASS	FR=0.5;HP=4;NF=6;NR=3;PP=100.0;SC=GCTTCTCAAATAGAGTCTTAA;TC=23;TR=9	GT:GL:GQ	0/1:-166.5,-71.13,-124.84:100
+20	1105206	.	C	CAT	.	PASS	FR=1.0;HP=1;NF=15;NR=11;PP=100.0;SC=AATTTATCCACGTGTACCAGA;TC=32;TR=26	GT:GL:GQ	1/1:-427.57,-192.92,-171.28:100
+20	1114638	.	C	CTCTT	.	PASS	FR=1.0;HP=4;NF=9;NR=17;PP=100.0;SC=TGTGTCCTCTCTTTGTATTTG;TC=34;TR=26	GT:GL:GQ	1/1:-420.88,-72.2,-49.92:100
+20	1118278	.	GAA	G	.	PASS	FR=1.0;HP=5;NF=13;NR=8;PP=100.0;SC=AGAAAAGGGAGAAAAGGAGGC;TC=24;TR=21	GT:GL:GQ	1/1:-206.9,-16.17,-0.92:100
+20	1127807	.	TCATCATCATCATCAC	T	.	PASS	FR=0.5;HP=1;NF=2;NR=3;PP=100.0;SC=ATCATCATCATCATCATCATC;TC=18;TR=5	GT:GL:GQ	1/0:-246.11,-143.41,-171.3:100
+20	1133620	.	GC	G	.	PASS	FR=1.0;HP=3;NF=17;NR=8;PP=100.0;SC=TAAGGACCAAGCCCTGTTTAT;TC=28;TR=25	GT:GL:GQ	1/1:-266.52,-52.99,-34.3:100
+20	1162839	.	AG	A	.	PASS	FR=0.5;HP=10;NF=1;NR=6;PP=100.0;SC=GGGGTGGGGGAGGGGGTAGAA;TC=27;TR=7	GT:GL:GQ	0/1:-154.34,-117.72,-158.43:100
+20	1165265	.	TACAC	T	.	PASS	FR=1.0;HP=1;NF=2;NR=1;PP=100.0;SC=CACACGCGCGTACACACACAC;TC=13;TR=3	GT:GL:GQ	1/1:-65.7,-24.93,-20.64:52
+20	1168799	.	T	TAC	.	PASS	FR=0.5;HP=3;NF=1;NR=3;PP=100.0;SC=ATATATATAATACACACACAC;TC=33;TR=4	GT:GL:GQ	0/1:-146.28,-74.63,-149.77:100
+20	1194678	.	A	AT	.	PASS	FR=1.0;HP=8;NF=13;NR=12;PP=100.0;SC=TACAAGATTAATTTTTTTTGT;TC=37;TR=25	GT:GL:GQ	1/1:-428.37,-300.25,-279.55:89
+20	1195705	.	AAAG	A	.	PASS	FR=1.0;HP=2;NF=10;NR=12;PP=100.0;SC=AGAGATGGCCAAAGAAGACAT;TC=27;TR=22	GT:GL:GQ	1/1:-481.8,-237.54,-219.64:100
+20	1200593	.	GA	G	.	PASS	FR=0.5;HP=5;NF=7;NR=5;PP=100.0;SC=TTTTTTAAAAGATCAACAAAA;TC=31;TR=12	GT:GL:GQ	0/1:-291.7,-258.36,-302.47:100
+20	1202056	.	C	CT	.	PASS	FR=0.5;HP=6;NF=2;NR=1;PP=73.0;SC=TTCTTTCTTTCTTTCTTTCTT;TC=17;TR=3	GT:GL:GQ	0/1:-78.02,-50.24,-96.3:100
+20	1217230	.	C	CT	.	PASS	FR=0.5;HP=3;NF=6;NR=7;PP=100.0;SC=TGAATCTGAACTTTCTCTATT;TC=29;TR=13	GT:GL:GQ	0/1:-136.34,-37.11,-139.78:100
+20	1238533	.	TATC	T	.	PASS	FR=0.5;HP=1;NF=6;NR=8;PP=100.0;SC=ATTCCCTTATTATCCTTTTAA;TC=32;TR=14	GT:GL:GQ	0/1:-203.0,-27.66,-145.09:100
+20	1258183	.	GTGTC	G	.	PASS	FR=0.5;HP=2;NF=9;NR=7;PP=100.0;SC=CTGTGCATGTGTGTCTGTGTG;TC=40;TR=16	GT:GL:GQ	0/1:-393.66,-270.04,-334.02:100
+20	1258199	.	C	CTG	.	PASS	FR=1.0;HP=2;NF=10;NR=8;PP=100.0;SC=GTGTGTGTATCTGTGTGTGTG;TC=39;TR=18	GT:GL:GQ	1/1:-443.43,-273.82,-255.93:100
+20	1258268	.	C	CTG	.	PASS	FR=1.0;HP=1;NF=14;NR=7;PP=100.0;SC=GTATGTGTGCCTGTGTGTGTG;TC=36;TR=21	GT:GL:GQ	1/1:-385.28,-210.98,-205.13:73
+20	1258437	.	GTGTGCCTGTGTGTGTC	G	.	PASS	FR=0.5;HP=2;NF=3;NR=4;PP=100.0;SC=GCCTGTGTATGTGTGCCTGTG;TC=40;TR=7	GT:GL:GQ	0/1:-300.85,-170.75,-363.46:100
+20	1258704	.	C	CTGTT	.	PASS	FR=0.5;HP=2;NF=6;NR=3;PP=100.0;SC=GTGTGTGTGTCTGTGTGTGTA;TC=34;TR=9	GT:GL:GQ	0/1:-182.12,-58.28,-233.67:100
+20	1270442	.	CA	C	.	PASS	FR=1.0;HP=2;NF=5;NR=12;PP=100.0;SC=CACTGCACTCCAAGCCTAGGT;TC=17;TR=17	GT:GL:GQ	1/1:-162.61,-26.2,-14.46:98
+20	1272295	.	CTCTGT	C	.	PASS	FR=1.0;HP=1;NF=13;NR=7;PP=100.0;SC=CCAAGTTCTGCTCTGTTGATT;TC=25;TR=20	GT:GL:GQ	1/1:-389.78,-103.27,-85.17:100
+20	1272815	.	C	CATAG	.	PASS	FR=1.0;HP=2;NF=11;NR=10;PP=100.0;SC=TAGTCTAAGGCATAGCATCCT;TC=27;TR=21	GT:GL:GQ	1/1:-368.78,-50.48,-32.46:100
+20	1291149	.	GCAA	G	.	PASS	FR=0.5;HP=1;NF=2;NR=3;PP=100.0;SC=CCTGGATACAGCAACAACAGT;TC=25;TR=5	GT:GL:GQ	0/1:-151.35,-93.7,-185.23:100
+20	1292033	.	C	CTTGT	.	PASS	FR=0.5;HP=2;NF=7;NR=5;PP=100.0;SC=CTTACATTTGCTTGTTTGATA;TC=29;TR=12	GT:GL:GQ	0/1:-444.32,-314.49,-337.3:100
+20	1292718	.	GT	G	.	PASS	FR=1.0;HP=8;NF=9;NR=3;PP=100.0;SC=TAATTTTTTAGTTTTTTTTGT;TC=17;TR=12	GT:GL:GQ	1/1:-140.26,-85.11,-76.3:73
+20	1292776	.	T	TA	.	PASS	FR=1.0;HP=1;NF=14;NR=10;PP=100.0;SC=CTCCTGGACTTAGTGATCCTC;TC=25;TR=24	GT:GL:GQ	1/1:-310.19,-119.02,-102.21:100
+20	1303648	.	A	AG	.	PASS	FR=0.5;HP=4;NF=6;NR=2;PP=100.0;SC=GGCAACACTCACCCGGCTGAG;TC=19;TR=8	GT:GL:GQ	0/1:-115.57,-32.83,-76.0:100
+20	1312294	.	A	AT	.	PASS	FR=1.0;HP=7;NF=5;NR=6;PP=100.0;SC=CACCTGGCTAATTTTTTTATT;TC=17;TR=11	GT:GL:GQ	1/1:-196.82,-109.27,-98.21:93
+20	1318554	.	TCCCACAGAGAAGTCC	T	.	PASS	FR=1.0;HP=3;NF=5;NR=4;PP=100.0;SC=ACCTAAGCATTCCCACAGAGA;TC=12;TR=9	GT:GL:GQ	1/1:-228.16,-15.45,-7.14:62
+20	1322791	.	G	GCACACA,GCACACACA	.	PASS	FR=0.5,0.5;HP=1;NF=3,3;NR=0,4;PP=43.0,100.0;SC=GAGAACAAATGCACACACACA;TC=18;TR=3,7	GT:GL:GQ	1/2:-1.0,-1.0,-1.0:100
+20	1333430	.	C	CT	.	PASS	FR=1.0;HP=2;NF=18;NR=9;PP=100.0;SC=ATGAAGGTGACTTCTCAGGTG;TC=32;TR=27	GT:GL:GQ	1/1:-276.34,-27.55,-7.09:100
+20	1342649	.	AT	A	.	PASS	FR=1.0;HP=6;NF=17;NR=10;PP=100.0;SC=AGTGTATGAGATTTTTTGTTA;TC=29;TR=27	GT:GL:GQ	1/1:-209.72,-24.22,-4.14:100
+20	1349439	.	C	CCCT	.	PASS	FR=0.5;HP=4;NF=2;NR=6;PP=100.0;SC=CCCACATTCCCCCTCCTCTGA;TC=22;TR=8	GT:GL:GQ	0/1:-157.47,-56.31,-133.86:100
+20	1358694	.	C	CAGTTTGGGCACTAACACCTACTT	.	PASS	FR=0.5;HP=1;NF=4;NR=1;PP=100.0;SC=CTATACGGGTCAGTTTGGGCA;TC=19;TR=5	GT:GL:GQ	0/1:-272.45,-105.91,-212.24:100
+20	1364390	.	G	GA	.	PASS	FR=1.0;HP=2;NF=9;NR=6;PP=100.0;SC=GATCAAGTGGGAGATCACTTG;TC=25;TR=15	GT:GL:GQ	1/1:-334.68,-154.31,-139.66:100
+20	1369478	.	CG	C	.	PASS	FR=0.5;HP=2;NF=7;NR=4;PP=100.0;SC=TAAAAACCAACGAGGCTCCAC;TC=23;TR=11	GT:GL:GQ	0/1:-184.87,-113.86,-180.77:100
+20	1372404	.	GA	G	.	PASS	FR=1.0;HP=7;NF=8;NR=5;PP=100.0;SC=GAGGGAGTGGGAAAAAAAGAG;TC=17;TR=13	GT:GL:GQ	1/1:-147.21,-77.38,-68.31:75
+20	1379453	.	C	CTG	.	PASS	FR=1.0;HP=2;NF=4;NR=11;PP=100.0;SC=TGCCAGGACTCTCCTCGCTGT;TC=19;TR=15	GT:GL:GQ	1/1:-192.19,-47.83,-35.2:100
+20	1381135	.	AG	A	.	PASS	FR=0.5;HP=2;NF=3;NR=5;PP=100.0;SC=CTTGAGGACAAGGCATTATAG;TC=26;TR=8	GT:GL:GQ	0/1:-99.07,-46.56,-212.4:100
+20	1386382	.	AGAG	A	.	PASS	FR=0.5;HP=3;NF=7;NR=1;PP=100.0;SC=ACTAATTAAAAGAGAACCCTG;TC=26;TR=8	GT:GL:GQ	0/1:-184.22,-117.09,-276.56:100
+20	1389225	.	CGTGTGT	C	.	PASS	FR=1.0;HP=1;NF=1;NR=1;PP=100.0;SC=TATGAAGACTCGTGTGTGTGT;TC=12;TR=2	GT:GL:GQ	1/1:-80.8,-37.12,-33.18:48
+20	1392633	.	AT	A	.	PASS	FR=0.5;HP=9;NF=8;NR=5;PP=100.0;SC=AAGCCAACACATTTTTTTTTC;TC=29;TR=13	GT:GL:GQ	0/1:-142.17,-103.31,-156.4:100
+20	1399660	.	A	AAAAAC	.	PASS	FR=0.5;HP=2;NF=1;NR=7;PP=100.0;SC=TGTTTATGTTAGAAACAAAAC;TC=28;TR=8	GT:GL:GQ	0/1:-237.24,-123.87,-245.2:100
+20	1401887	.	T	TC	.	PASS	FR=0.5;HP=6;NF=3;NR=5;PP=100.0;SC=TGACTTTTTTTCTCCCTGAGA;TC=26;TR=8	GT:GL:GQ	0/1:-140.81,-26.64,-103.7:100
+20	1403888	.	G	GT	.	PASS	FR=0.5;HP=1;NF=3;NR=5;PP=100.0;SC=CAGAGAGGGCGTAAGATTGGA;TC=18;TR=8	GT:GL:GQ	0/1:-134.33,-94.6,-144.84:100
+20	1411174	.	G	GT	.	PASS	FR=1.0;HP=1;NF=14;NR=18;PP=100.0;SC=TTCCAACAGTGACAAGGGTTT;TC=34;TR=32	GT:GL:GQ	1/1:-370.91,-42.86,-18.85:100
+20	1411544	.	TG	T	.	PASS	FR=0.5;HP=4;NF=7;NR=2;PP=36.0;SC=ATTTATAAAATGTTTTTGTTG;TC=28;TR=9	GT:GL:GQ	0/1:-275.92,-257.59,-310.84:82
+20	1420200	.	CT	C	.	PASS	FR=1.0;HP=2;NF=13;NR=7;PP=100.0;SC=AAGATGGAACCTTAAGTTCAA;TC=24;TR=20	GT:GL:GQ	1/1:-229.24,-45.08,-29.19:100
+20	1421627	.	GC	G	.	PASS	FR=1.0;HP=4;NF=12;NR=6;PP=100.0;SC=GGAGCCCAACGCCCATTTAAA;TC=24;TR=18	GT:GL:GQ	1/1:-219.35,-32.03,-15.65:100
+20	1428402	.	A	ATCTAT	.	PASS	FR=0.5;HP=2;NF=6;NR=3;PP=100.0;SC=AATAGCTGATATCAGTTAAGG;TC=30;TR=9	GT:GL:GQ	0/1:-414.87,-348.43,-419.1:100
+20	1428454	.	TC	T	.	PASS	FR=0.5;HP=2;NF=11;NR=7;PP=100.0;SC=TTACACCGACTCTGTGCAGGT;TC=37;TR=18	GT:GL:GQ	0/1:-456.05,-415.06,-465.1:100
+20	1448428	.	AC	A	.	PASS	FR=1.0;HP=2;NF=12;NR=6;PP=100.0;SC=ACGGTAAACAACCTTCCCGCG;TC=21;TR=18	GT:GL:GQ	1/1:-289.43,-190.83,-179.1:98
+20	1450561	.	A	AAATAAT	.	PASS	FR=1.0;HP=8;NF=6;NR=4;PP=100.0;SC=CTGTCTCAAAAAAAAATAATA;TC=23;TR=10	GT:GL:GQ	1/1:-324.02,-170.06,-160.02:94
+20	1454025	.	GCACACACGCA	G	.	PASS	FR=1.0;HP=1;NF=5;NR=3;PP=100.0;SC=ACGCACACATGCACACACGCA;TC=23;TR=8	GT:GL:GQ	1/1:-298.98,-49.31,-43.52:72
+20	1455718	.	AC	A	.	PASS	FR=0.5;HP=8;NF=5;NR=3;PP=100.0;SC=TGGTGGTAGCACCCCCCCAGG;TC=26;TR=8	GT:GL:GQ	0/1:-122.23,-68.33,-113.23:100
+20	1466298	.	C	CCA	.	PASS	FR=0.5;HP=1;NF=3;NR=2;PP=100.0;SC=CACACACACACCACACACACA;TC=25;TR=5	GT:GL:GQ	0/1:-174.97,-31.68,-40.82:42
+20	1470727	.	TG	T	.	PASS	FR=1.0;HP=4;NF=9;NR=10;PP=100.0;SC=CAACAATCATTGGGGAATATT;TC=24;TR=19	GT:GL:GQ	1/1:-243.08,-66.7,-50.7:100
+20	1473489	.	ATAATT	A	.	PASS	FR=0.5;HP=2;NF=13;NR=9;PP=100.0;SC=TTACTTACAAATAATTTTATT;TC=35;TR=22	GT:GL:GQ	0/1:-297.03,-26.79,-121.41:100
+20	1475430	.	C	CTCT	.	PASS	FR=0.5;HP=3;NF=5;NR=7;PP=100.0;SC=CTCATTTCTTCTCTTTTCATT;TC=31;TR=12	GT:GL:GQ	0/1:-179.5,-26.21,-143.42:100
+20	1477952	.	AGTCTACACGT	A	.	PASS	FR=0.5;HP=1;NF=1;NR=2;PP=100.0;SC=TTGTCTTTTCAGTCTACACGT;TC=26;TR=3	GT:GL:GQ	0/1:-132.31,-83.49,-272.8:100
+20	1485444	.	TGAGAGAGA	T	.	PASS	FR=0.5;HP=2;NF=1;NR=2;PP=100.0;SC=TGTGTGTGTGTGAGAGAGAGA;TC=17;TR=3	GT:GL:GQ	1/0:-294.27,-239.82,-244.87:100
+20	1498426	.	G	GA	.	PASS	FR=1.0;HP=6;NF=18;NR=13;PP=100.0;SC=TACAACGGAAGAAAAGCCTAA;TC=33;TR=31	GT:GL:GQ	1/1:-335.62,-79.86,-57.15:100
+20	1499276	.	TGAGA	T	.	PASS	FR=0.5;HP=2;NF=4;NR=2;PP=100.0;SC=TCAAAGTGAATGAGAGAGAGG;TC=23;TR=6	GT:GL:GQ	0/1:-190.39,-128.87,-245.46:100
+20	1500650	.	A	AG	.	PASS	FR=1.0;HP=1;NF=9;NR=8;PP=100.0;SC=AAGGAGCAGCAGTTCTGAGAG;TC=19;TR=17	GT:GL:GQ	1/1:-187.24,-32.97,-19.25:100
+20	1510246	.	CA	C	.	PASS	FR=1.0;HP=10;NF=15;NR=6;PP=100.0;SC=AACTCTGTCTCAAAAAAAAAA;TC=29;TR=21	GT:GL:GQ	1/1:-113.89,-25.37,-8.27:100
+20	1510966	.	C	CTA	.	PASS	FR=1.0;HP=2;NF=10;NR=3;PP=100.0;SC=TTTTATCTCTCTGTGTCATTT;TC=21;TR=13	GT:GL:GQ	1/1:-215.34,-14.55,0.0:100
+20	1512623	.	TTGTC	T	.	PASS	FR=0.5;HP=1;NF=2;NR=7;PP=100.0;SC=ACTCCATAGATTGTCTGGGTA;TC=27;TR=9	GT:GL:GQ	0/1:-204.17,-64.36,-220.46:100
+20	1516154	.	A	AAG	.	PASS	FR=0.5;HP=1;NF=9;NR=1;PP=100.0;SC=GTTTTATAAGAAGAGAGAGAG;TC=28;TR=10	GT:GL:GQ	0/1:-197.81,-103.51,-159.44:100
+20	1524117	.	G	GTGA	.	PASS	FR=1.0;HP=2;NF=12;NR=14;PP=100.0;SC=TGGGATCAGGGTATTCCCTTC;TC=27;TR=26	GT:GL:GQ	1/1:-368.49,-35.51,-15.43:100
+20	1525024	.	CT	C	.	PASS	FR=0.5;HP=7;NF=3;NR=3;PP=96.0;SC=CCTTCTTTGTCTTTTTTGATC;TC=18;TR=6	GT:GL:GQ	0/1:-53.12,-20.94,-98.55:100
+20	1525853	.	G	GT	.	PASS	FR=0.5;HP=5;NF=7;NR=4;PP=100.0;SC=CCTGAAGTGTGTTTTCCAACT;TC=29;TR=11	GT:GL:GQ	0/1:-133.05,-52.13,-148.67:100
+20	1597255	.	TG	T	.	PASS	FR=0.5;HP=2;NF=13;NR=3;PP=100.0;SC=GTAAAAGTACTGGAAGAAAAG;TC=39;TR=16	GT:GL:GQ	0/1:-269.31,-182.14,-334.79:100
+20	1627288	.	ATTTGT	A	.	PASS	FR=0.5;HP=3;NF=4;NR=2;PP=100.0;SC=ACTTTTTTTCATTTGTTTTGT;TC=20;TR=6	GT:GL:GQ	0/1:-133.15,-70.66,-175.26:100
+20	1629280	.	T	TAATAAAATAA	.	PASS	FR=0.5;HP=3;NF=1;NR=4;PP=100.0;SC=ACTTAAAGTATAATAAAATAA;TC=18;TR=5	GT:GL:GQ	0/1:-155.63,-27.66,-95.67:100
+20	1648829	.	CTTTCTTTTTCTTTTCT	C	.	PASS	FR=0.5;HP=6;NF=1;NR=1;PP=74.0;SC=TTCTTTCTTTCTTTCTTTTTC;TC=20;TR=2	GT:GL:GQ	0/1:-191.4,-160.88,-232.59:100
+20	1653387	.	T	TTTG	.	PASS	FR=0.5;HP=2;NF=2;NR=7;PP=100.0;SC=CGGCCAATCATTTGTTGTTGT;TC=25;TR=9	GT:GL:GQ	0/1:-189.9,-54.75,-106.65:100
+20	1656519	.	GT	G	.	PASS	FR=0.5;HP=9;NF=4;NR=5;PP=100.0;SC=GAGCTGCACTGTTTTTTTTCT;TC=20;TR=9	GT:GL:GQ	0/1:-62.34,-19.97,-47.7:100
+20	1658890	.	ACT	A	.	PASS	FR=0.5;HP=2;NF=6;NR=2;PP=100.0;SC=CATGTGATACACTGTGGGCCC;TC=27;TR=8	GT:GL:GQ	0/1:-198.65,-163.08,-324.51:100
+20	1660493	.	AT	A	.	PASS	FR=0.5;HP=1;NF=6;NR=5;PP=100.0;SC=CATTTGGGAGATGCTATTACC;TC=31;TR=11	GT:GL:GQ	0/1:-160.86,-59.8,-177.36:100
+20	1661355	.	TG	T	.	PASS	FR=0.5;HP=1;NF=6;NR=7;PP=100.0;SC=GAAAAACACATGATTATCCAT;TC=34;TR=13	GT:GL:GQ	0/1:-171.31,-99.84,-269.81:100
+20	1661478	.	G	GT	.	PASS	FR=0.5;HP=9;NF=7;NR=5;PP=100.0;SC=ATACTTTCTTGTTTTTTTGGC;TC=35;TR=12	GT:GL:GQ	0/1:-150.06,-61.16,-108.32:100
+20	1661816	.	C	CA	.	PASS	FR=0.5;HP=1;NF=1;NR=6;PP=100.0;SC=AATTTGCAATCATACAGAAAG;TC=24;TR=7	GT:GL:GQ	0/1:-96.53,-29.07,-136.56:100
+20	1662592	.	GATATAACTA	G	.	PASS	FR=0.5;HP=1;NF=4;NR=5;PP=100.0;SC=TATGGATATGGATATAACTAA;TC=23;TR=9	GT:GL:GQ	0/1:-238.09,-62.84,-220.35:100
+20	1665050	.	A	ATG	.	PASS	FR=0.5;HP=2;NF=6;NR=6;PP=100.0;SC=ATACACACATATATATATGTA;TC=34;TR=12	GT:GL:GQ	0/1:-151.91,-67.61,-244.28:100
+20	1667770	.	TG	T	.	PASS	FR=0.5;HP=6;NF=5;NR=5;PP=100.0;SC=AGGGTTATGATGGGGGGAGAA;TC=29;TR=10	GT:GL:GQ	0/1:-75.51,-17.52,-115.09:100
+20	1674714	.	A	AT	.	PASS	FR=1.0;HP=6;NF=12;NR=9;PP=100.0;SC=AAGGAGAATCATTTTTTCTTA;TC=26;TR=21	GT:GL:GQ	1/1:-198.16,-29.36,-11.98:100
+20	1679689	.	TACACAC	TACACACACAC,T	.	PASS	FR=0.5,0.5;HP=3;NF=2,1;NR=0,1;PP=100.0,100.0;SC=TTAGATGCCCTACACACACAC;TC=23;TR=2,2	GT:GL:GQ	1/2:-1.0,-1.0,-1.0:100
+20	1680048	.	G	GA	.	PASS	FR=0.5;HP=9;NF=4;NR=9;PP=100.0;SC=GAAAACAACAGAAAAAAAACT;TC=30;TR=13	GT:GL:GQ	0/1:-157.3,-90.19,-130.66:100
+20	1680109	.	GA	G	.	PASS	FR=0.5;HP=4;NF=9;NR=8;PP=100.0;SC=AACAGCAAGAGAAATTATAAA;TC=32;TR=17	GT:GL:GQ	0/1:-210.03,-97.05,-217.17:100
+20	1682621	.	A	AT	.	PASS	FR=1.0;HP=3;NF=18;NR=11;PP=100.0;SC=AATATATCATATTACACAGTG;TC=31;TR=29	GT:GL:GQ	1/1:-304.45,-32.07,-10.59:100
+20	1683112	.	T	TC	.	PASS	FR=1.0;HP=2;NF=6;NR=11;PP=100.0;SC=CAAACCCTCTTCCTATACCAC;TC=23;TR=17	GT:GL:GQ	1/1:-265.19,-181.47,-172.55:74
+20	1683153	.	CA	C	.	PASS	FR=0.5;HP=2;NF=5;NR=7;PP=100.0;SC=GCAGCAGCTGCAAGAAGTCTC;TC=22;TR=12	GT:GL:GQ	0/1:-291.99,-237.27,-279.09:100
+20	1683250	.	ATAGCTCTACCAGT	A	.	PASS	FR=0.5;HP=1;NF=5;NR=4;PP=100.0;SC=AGTTCGAATCATAGCTCTACC;TC=22;TR=9	GT:GL:GQ	0/1:-267.9,-88.45,-154.18:100
+20	1683813	.	C	CT	.	PASS	FR=0.5;HP=6;NF=12;NR=13;PP=100.0;SC=AAGAGAATGTCTTTTTAAAAT;TC=53;TR=25	GT:GL:GQ	0/1:-327.36,-122.23,-224.07:100
+20	1683959	.	C	CA	.	PASS	FR=0.5;HP=8;NF=4;NR=9;PP=100.0;SC=TCAACAATGACAAAAAAAGCA;TC=24;TR=13	GT:GL:GQ	0/1:-130.55,-27.62,-42.34:66
+20	1684576	.	A	AATGTATAATAC	.	PASS	FR=0.5;HP=2;NF=5;NR=4;PP=96.0;SC=ATACTGTTTAAATATTTCCTG;TC=24;TR=9	GT:GL:GQ	0/1:-370.23,-353.25,-494.05:100
+20	1688002	.	AAAAC	A	.	PASS	FR=1.0;HP=3;NF=4;NR=6;PP=100.0;SC=ACTCCCTCTCAAAACAAACAA;TC=22;TR=10	GT:GL:GQ	1/1:-132.2,-18.69,-9.78:74
+20	1690549	.	CCT	C	.	PASS	FR=0.5;HP=3;NF=6;NR=6;PP=100.0;SC=GAAATCTTCCCCTGTCTGTGA;TC=32;TR=12	GT:GL:GQ	0/1:-184.81,-148.16,-332.53:100
+20	1694183	.	CT	C	.	PASS	FR=0.5;HP=3;NF=8;NR=5;PP=100.0;SC=TATACAAAGACTTTATAACCA;TC=29;TR=13	GT:GL:GQ	0/1:-144.04,-44.56,-141.78:100
+20	1699510	.	T	TCCCA	.	PASS	FR=0.5;HP=3;NF=10;NR=2;PP=100.0;SC=AATGTCTCATTCCCACATCCT;TC=19;TR=12	GT:GL:GQ	0/1:-164.23,-17.54,-74.37:100
+20	1701571	.	TTAAAATAAAA	T	.	PASS	FR=0.5;HP=4;NF=5;NR=2;PP=100.0;SC=CATCTCAAAATTAAAATAAAA;TC=21;TR=7	GT:GL:GQ	0/1:-177.13,-95.66,-194.53:100
+20	1716144	.	A	AGTGT	.	PASS	FR=0.5;HP=8;NF=3;NR=4;PP=100.0;SC=GGTTTTTTTTAGTGTGTGTGT;TC=23;TR=7	GT:GL:GQ	0/1:-151.21,-52.44,-109.8:100
+20	1719870	.	TG	T	.	PASS	FR=0.5;HP=1;NF=3;NR=11;PP=100.0;SC=ATCAAACCTCTGTGGGAGAGA;TC=27;TR=14	GT:GL:GQ	0/1:-146.54,-22.92,-111.48:100
+20	1721789	.	GT	G	.	PASS	FR=0.5;HP=9;NF=6;NR=4;PP=100.0;SC=GCACTTGGGAGTTTTTTTTTC;TC=23;TR=10	GT:GL:GQ	0/1:-60.27,-22.43,-60.17:100
+20	1722316	.	CCTTT	C	.	PASS	FR=1.0;HP=2;NF=2;NR=1;PP=100.0;SC=TTTCTCTCTTCCTTTCTTTCT;TC=7;TR=3	GT:GL:GQ	1/1:-85.7,-30.24,-25.46:57
+20	1727042	.	T	TA	.	PASS	FR=1.0;HP=2;NF=10;NR=8;PP=100.0;SC=AATTAAATTATATAGAGGAAG;TC=20;TR=18	GT:GL:GQ	1/1:-223.19,-104.73,-92.26:100
+20	1728298	.	G	GT	.	PASS	FR=1.0;HP=4;NF=11;NR=14;PP=100.0;SC=AAGAACAGAGGTTTTAAGCAT;TC=28;TR=25	GT:GL:GQ	1/1:-297.24,-94.99,-75.97:100
+20	1730788	.	T	TGATA	.	PASS	FR=1.0;HP=3;NF=3;NR=6;PP=100.0;SC=AGATGATAAATGATAGATAGA;TC=36;TR=9	GT:GL:GQ	1/1:-190.89,-23.51,-13.12:87
+20	1731625	.	CA	C	.	PASS	FR=1.0;HP=9;NF=5;NR=8;PP=100.0;SC=GACTCCATCTCAAAAAAAAAG;TC=23;TR=13	GT:GL:GQ	1/1:-93.68,-29.69,-18.4:95
+20	1734082	.	AAAAAT	A	.	PASS	FR=0.5;HP=4;NF=6;NR=3;PP=100.0;SC=CAATAGCTATAAAAATAAAAT;TC=38;TR=9	GT:GL:GQ	0/1:-124.98,-23.78,-220.83:100
+20	1738324	.	T	TC	.	PASS	FR=1.0;HP=3;NF=7;NR=10;PP=100.0;SC=ACACTCCTTTTCCTTCATGAT;TC=22;TR=17	GT:GL:GQ	1/1:-213.69,-47.59,-33.85:100
+20	1738519	.	A	AG	.	PASS	FR=1.0;HP=1;NF=13;NR=11;PP=100.0;SC=CTGTCAAACTAGCCTCTGGCT;TC=29;TR=24	GT:GL:GQ	1/1:-269.52,-42.45,-23.17:100
+20	1741051	.	T	TAA	.	PASS	FR=1.0;HP=1;NF=12;NR=12;PP=100.0;SC=TAAATATATATGACTATTTTT;TC=35;TR=24	GT:GL:GQ	1/1:-395.96,-52.09,-26.1:100
+20	1745352	.	A	ACAATAATCACATCAAAGAT	.	PASS	FR=1.0;HP=2;NF=4;NR=8;PP=100.0;SC=CAAGACCATTACACTAATCAC;TC=17;TR=12	GT:GL:GQ	1/1:-425.27,-43.37,-23.58:100
+20	1746606	.	GTA	G	.	PASS	FR=1.0;HP=2;NF=1;NR=4;PP=100.0;SC=ATATATATGTGTATATATATA;TC=9;TR=5	GT:GL:GQ	1/1:-98.72,-49.48,-45.34:50
+20	1768362	.	G	GAA	.	PASS	FR=1.0;HP=2;NF=7;NR=14;PP=100.0;SC=TAGAGTGATGGAAGAGACTGG;TC=27;TR=21	GT:GL:GQ	1/1:-269.69,-41.32,-23.11:100
+20	1778684	.	A	AGTGCTT	.	PASS	FR=0.5;HP=2;NF=1;NR=1;PP=83.0;SC=ATTGCCCTCCATTGGAGGCTG;TC=14;TR=2	GT:GL:GQ	1/0:-256.33,-220.54,-244.27:69
+20	1833292	.	TA	T	.	PASS	FR=0.5;HP=3;NF=5;NR=5;PP=100.0;SC=ATATTATGTATAATCTCAATT;TC=25;TR=10	GT:GL:GQ	0/1:-147.42,-89.75,-210.06:100
+20	1848829	.	CTTTTCT	C	.	PASS	FR=1.0;HP=8;NF=6;NR=15;PP=100.0;SC=CTTTTCTTTTCTTTTCTTTTC;TC=25;TR=21	GT:GL:GQ	1/1:-409.42,-172.01,-156.56:100
+20	1848853	.	CTT	C	.	PASS	FR=0.5;HP=4;NF=3;NR=4;PP=100.0;SC=CTTTCTTTCTCTTTCTTTCTT;TC=26;TR=7	GT:GL:GQ	0/1:-469.4,-397.68,-416.1:83
+20	1848877	.	C	CTT	.	PASS	FR=0.9999;HP=4;NF=2;NR=1;PP=100.0;SC=TTCTTTCTTTCTCTTTCTTTC;TC=26;TR=3	GT:GL:GQ	1/1:-373.17,-284.63,-280.27:37
+20	1852149	.	CCA	C	.	PASS	FR=0.5;HP=1;NF=4;NR=1;PP=100.0;SC=CACCCCCTCTCCACACACACA;TC=23;TR=5	GT:GL:GQ	0/1:-139.51,-90.17,-161.53:100
+20	1855569	.	AACACAC	A	.	PASS	FR=1.0;HP=1;NF=7;NR=3;PP=100.0;SC=GTCACTCTACAACACACACAC;TC=14;TR=10	GT:GL:GQ	1/1:-159.46,-18.21,-11.49:84
+20	1857852	.	TC	T	.	PASS	FR=1.0;HP=6;NF=4;NR=19;PP=100.0;SC=CCCGTGTCCATCCCCCCTGTA;TC=58;TR=23	GT:GL:GQ	1/1:-667.45,-637.23,-632.11:63
+20	1857976	.	G	GT	.	PASS	FR=1.0;HP=5;NF=12;NR=1;PP=100.0;SC=GCTTTGTTTTGTCAGTTGTTT;TC=22;TR=13	GT:GL:GQ	1/1:-196.6,-28.45,-14.03:100
+20	1872437	.	AT	A	.	PASS	FR=0.5;HP=2;NF=2;NR=4;PP=100.0;SC=TCCCTGGCTAATTCCCCCCAC;TC=23;TR=6	GT:GL:GQ	0/1:-111.11,-55.77,-134.66:100
+20	1890990	.	CTT	C	.	PASS	FR=1.0;HP=5;NF=11;NR=12;PP=100.0;SC=TGTTTCATTACTTTTTAACTT;TC=24;TR=23	GT:GL:GQ	1/1:-245.45,-38.39,-20.54:100
+20	1895466	.	T	TATAG	.	PASS	FR=1.0;HP=1;NF=11;NR=5;PP=100.0;SC=AGATTAGAATTAGCCCAGCTC;TC=24;TR=16	GT:GL:GQ	1/1:-500.31,-454.72,-448.18:79
+20	1895484	.	ACT	A	.	PASS	FR=1.0;HP=1;NF=14;NR=4;PP=52.0;SC=CTCAGATGTGACTCTTCCAGA;TC=23;TR=18	GT:GL:GQ	1/1:-454.69,-436.37,-433.13:53
+20	1912065	.	AC	A	.	PASS	FR=0.5;HP=2;NF=7;NR=8;PP=100.0;SC=TGCCTTCATCACTGTTCCCAT;TC=25;TR=15	GT:GL:GQ	0/1:-166.95,-40.53,-113.76:100
+20	1930288	.	TAAG	T	.	PASS	FR=0.5;HP=2;NF=9;NR=4;PP=100.0;SC=TATAAGTTGTTAAGAAGAAAA;TC=31;TR=13	GT:GL:GQ	0/1:-196.67,-58.02,-140.92:100
+20	1940722	.	GTT	G	.	PASS	FR=0.5;HP=2;NF=6;NR=7;PP=100.0;SC=AAAAACCCAGGTTATATATAC;TC=25;TR=13	GT:GL:GQ	0/1:-178.3,-32.72,-93.72:100
+20	1940980	.	G	GA	.	PASS	FR=0.5;HP=3;NF=5;NR=3;PP=100.0;SC=AACTACTCAGGGGCTGAGATG;TC=20;TR=8	GT:GL:GQ	0/1:-91.81,-43.36,-126.02:100
+20	1941170	.	A	AC	.	PASS	FR=0.5;HP=1;NF=10;NR=2;PP=100.0;SC=ATACCTGTATAGAAAAAAAGT;TC=31;TR=12	GT:GL:GQ	0/1:-250.35,-208.27,-291.77:100
+20	1943171	.	T	TG	.	PASS	FR=0.5;HP=7;NF=1;NR=1;PP=56.0;SC=AGGGGAAGCCTGGGGGGGTTG;TC=19;TR=2	GT:GL:GQ	0/1:-65.38,-41.58,-85.08:100
+20	1949783	.	C	CT	.	PASS	FR=0.5;HP=10;NF=3;NR=4;PP=100.0;SC=GTGCTGAGCCCTTTTTTTTTT;TC=26;TR=7	GT:GL:GQ	0/1:-82.34,-46.95,-63.27:73
+20	1959266	.	A	ATG	.	PASS	FR=0.5;HP=2;NF=3;NR=4;PP=100.0;SC=CAACCTGAATATGTGTGTGTG;TC=24;TR=7	GT:GL:GQ	0/1:-140.42,-42.47,-66.02:100
+20	1967894	.	GATGA	G	.	PASS	FR=0.5;HP=2;NF=2;NR=4;PP=100.0;SC=TTGAGTGATTGATGAATGAAT;TC=24;TR=6	GT:GL:GQ	0/1:-113.7,-41.87,-83.28:100
+20	1977448	.	A	ACACACACACG	.	PASS	FR=0.5;HP=1;NF=1;NR=1;PP=100.0;SC=ACACACACACATAGAAGGCCA;TC=32;TR=2	GT:GL:GQ	0/1:-253.96,-71.96,-163.76:100
+20	1996777	.	CT	C	.	PASS	FR=0.5;HP=2;NF=4;NR=7;PP=100.0;SC=GTGTTTTAGGCTGTTATTTCA;TC=21;TR=11	GT:GL:GQ	0/1:-127.06,-33.79,-125.68:100
+20	1997708	.	CAT	C	.	PASS	FR=0.5;HP=2;NF=5;NR=4;PP=100.0;SC=CACACACACACATACAAAATA;TC=31;TR=9	GT:GL:GQ	0/1:-145.15,-85.85,-245.36:100
+20	2004765	.	T	TG	.	PASS	FR=0.5;HP=1;NF=2;NR=2;PP=76.0;SC=AGGATTTTTCTATCAGTCCAC;TC=12;TR=4	GT:GL:GQ	0/1:-54.31,-25.7,-84.4:100
+20	2034931	.	G	GTTC	.	PASS	FR=0.5;HP=2;NF=6;NR=4;PP=100.0;SC=AGATAGGTAAGTTCTTCCCCA;TC=24;TR=10	GT:GL:GQ	0/1:-162.21,-52.77,-146.87:100
+20	2035677	.	AACACAC	AAC,A	.	PASS	FR=0.5,0.5;HP=2;NF=2,3;NR=0,2;PP=39.0,100.0;SC=TTTTATAATAAACACACACAC;TC=29;TR=2,5	GT:GL:GQ	1/2:-1.0,-1.0,-1.0:88
+20	2050099	.	AATTG	A	.	PASS	FR=0.5;HP=2;NF=10;NR=5;PP=100.0;SC=TCTTATTCTTAATTGATCTAA;TC=35;TR=15	GT:GL:GQ	0/1:-259.54,-91.86,-224.89:100
+20	2052246	.	AC	A	.	PASS	FR=0.5;HP=1;NF=3;NR=6;PP=100.0;SC=GGTCCCAGCTACTCAGGAGGC;TC=19;TR=9	GT:GL:GQ	0/1:-113.96,-44.77,-115.57:100
+20	2053863	.	C	CA	.	PASS	FR=0.5;HP=9;NF=3;NR=4;PP=96.0;SC=ACTAAAAATACAAAAAAAATA;TC=16;TR=7	GT:GL:GQ	0/1:-46.07,-13.04,-34.97:98
+20	2054845	.	AAAGAGGAAAAAG	A	.	PASS	FR=0.5;HP=4;NF=7;NR=1;PP=100.0;SC=AAAAGAGGAAAAAGAGGAAAA;TC=27;TR=8	GT:GL:GQ	0/1:-251.05,-86.54,-294.87:100
+20	2055452	.	AAAGG	A	.	PASS	FR=0.5;HP=4;NF=4;NR=4;PP=100.0;SC=AAGAAAAGAAAAAGGAAGGAA;TC=27;TR=8	GT:GL:GQ	0/1:-227.92,-152.39,-281.38:100
+20	2077127	.	AAC	A	.	PASS	FR=0.5;HP=3;NF=1;NR=3;PP=97.0;SC=TCTCTACTAAAACACACACAC;TC=17;TR=4	GT:GL:GQ	0/1:-57.31,-24.65,-94.33:100
+20	2078747	.	CCT	C	.	PASS	FR=0.5;HP=3;NF=3;NR=2;PP=100.0;SC=AGAAAATTCCCCTGTGGCCCT;TC=15;TR=5	GT:GL:GQ	0/1:-78.54,-32.73,-103.05:100
+20	2120509	.	AAAGGT	A	.	PASS	FR=0.5;HP=2;NF=8;NR=1;PP=100.0;SC=CTGAAATGAGAAAGGTAAGGA;TC=19;TR=9	GT:GL:GQ	0/1:-189.27,-90.48,-174.84:100
+20	2122413	.	CT	C	.	PASS	FR=0.5;HP=4;NF=3;NR=8;PP=100.0;SC=GTAACCTACCCTTTTCCACCT;TC=23;TR=11	GT:GL:GQ	0/1:-132.75,-34.8,-69.03:100
+20	2126052	.	T	TCTATGTGA	.	PASS	FR=0.5;HP=2;NF=3;NR=1;PP=100.0;SC=CATTTCCGTTTCTATGTGACC;TC=22;TR=4	GT:GL:GQ	0/1:-179.74,-76.1,-178.95:100
+20	2131707	.	T	TGG	.	PASS	FR=0.5;HP=2;NF=7;NR=1;PP=100.0;SC=CCCTGTTGCCTGACCTGAGCC;TC=20;TR=8	GT:GL:GQ	0/1:-145.56,-92.76,-163.87:100
+20	2153043	.	C	CTTTATTTA	.	PASS	FR=0.5;HP=3;NF=1;NR=2;PP=100.0;SC=GGTGACATCACTTTATTTATT;TC=21;TR=3	GT:GL:GQ	0/1:-97.11,-28.78,-48.32:87
+20	2155932	.	C	CAT	.	PASS	FR=0.5;HP=7;NF=4;NR=3;PP=100.0;SC=AATTAAAAAACATATATATAT;TC=32;TR=7	GT:GL:GQ	0/1:-176.17,-66.01,-150.43:100
+20	2160585	.	AT	A	.	PASS	FR=0.5;HP=7;NF=9;NR=11;PP=100.0;SC=GTTTTTAAATATTTTTTAATT;TC=41;TR=20	GT:GL:GQ	0/1:-237.9,-137.73,-264.06:100
+20	2162113	.	A	ATT	.	PASS	FR=0.5;HP=1;NF=2;NR=4;PP=100.0;SC=TATCAGGAATAATTTTTTTTT;TC=25;TR=6	GT:GL:GQ	0/1:-145.37,-128.61,-213.61:100
+20	2165761	.	GTTAT	G	.	PASS	FR=0.5;HP=3;NF=4;NR=1;PP=100.0;SC=CTAATAACCTGTTATTTATTT;TC=28;TR=5	GT:GL:GQ	0/1:-79.63,-28.99,-73.78:100
+20	2171122	.	CAAACA	C	.	PASS	FR=0.5;HP=4;NF=4;NR=1;PP=100.0;SC=AACAAACAGACAAACAAAACA;TC=18;TR=5	GT:GL:GQ	0/1:-113.12,-57.95,-91.54:100
+20	2171346	.	TA	T	.	PASS	FR=0.5;HP=8;NF=4;NR=5;PP=100.0;SC=AATTTTTTTTTAAAATCCTTA;TC=20;TR=9	GT:GL:GQ	0/1:-174.43,-122.88,-194.49:100
+20	2171402	.	T	TA	.	PASS	FR=0.5;HP=2;NF=3;NR=1;PP=92.0;SC=TGATTGATCCTAACTTAATGA;TC=23;TR=4	GT:GL:GQ	0/1:-112.12,-79.99,-224.63:100
+20	2198337	.	AAG	A	.	PASS	FR=0.5;HP=2;NF=17;NR=3;PP=100.0;SC=CAACCAAAGAAAGAATGGGAG;TC=38;TR=20	GT:GL:GQ	0/1:-234.35,-51.22,-161.95:100
+20	2199055	.	G	GCCACACACTTCTAAA	.	PASS	FR=0.5;HP=2;NF=2;NR=5;PP=100.0;SC=AGGGGGAAGTGCCATCAGATG;TC=20;TR=7	GT:GL:GQ	0/1:-318.25,-129.11,-238.35:100
+20	2199168	.	T	TG	.	PASS	FR=0.5;HP=9;NF=3;NR=6;PP=100.0;SC=TGAGATTTGGTGGGGGGGACA;TC=37;TR=9	GT:GL:GQ	0/1:-144.44,-70.03,-129.92:100
+20	2209336	.	A	AGTG	.	PASS	FR=0.5;HP=1;NF=4;NR=1;PP=100.0;SC=GCTGGAGTGCAGTGGTACAAT;TC=18;TR=5	GT:GL:GQ	0/1:-105.48,-46.83,-99.81:100
+20	2215492	.	T	TA	.	PASS	FR=1.0;HP=1;NF=17;NR=16;PP=100.0;SC=TGGATGAACGTATTTATTTAA;TC=37;TR=33	GT:GL:GQ	1/1:-589.49,-315.53,-293.02:100
+20	2215506	.	G	GT	.	PASS	FR=1.0;HP=3;NF=18;NR=13;PP=100.0;SC=TATTTAACCAGTTTCTCTTGA;TC=36;TR=31	GT:GL:GQ	1/1:-602.79,-346.63,-325.98:100
+20	2216792	.	CAG	C	.	PASS	FR=0.5;HP=1;NF=6;NR=7;PP=100.0;SC=TGCGTTCATGCAGTTTATGGG;TC=25;TR=13	GT:GL:GQ	0/1:-181.42,-37.01,-108.03:100
+20	2217535	.	CCT	C	.	PASS	FR=0.5;HP=1;NF=6;NR=6;PP=100.0;SC=CATTGCATCACCTGCCTCTGA;TC=32;TR=12	GT:GL:GQ	0/1:-224.94,-75.19,-157.78:100
+20	2218702	.	CA	C	.	PASS	FR=0.5;HP=1;NF=3;NR=5;PP=100.0;SC=AATCACGACTCATTGTAGCCT;TC=18;TR=8	GT:GL:GQ	0/1:-111.7,-55.95,-90.25:100
+20	2221607	.	TTTTCTTTCTTTCTTTTTCC	T	.	PASS	FR=0.5;HP=4;NF=4;NR=2;PP=100.0;SC=AAAGTTTTCTTTTTCTTTCTT;TC=29;TR=6	GT:GL:GQ	0/1:-196.61,-29.28,-142.76:100
+20	2241427	.	AAAAC	A	.	PASS	FR=1.0;HP=4;NF=4;NR=3;PP=100.0;SC=CTTGTCTCTAAAAACAAACAA;TC=19;TR=7	GT:GL:GQ	1/1:-166.73,-37.97,-27.83:84
+20	2263098	.	TG	T	.	PASS	FR=1.0;HP=4;NF=5;NR=5;PP=100.0;SC=TGACGGATGGTGGAGTGAGAA;TC=12;TR=10	GT:GL:GQ	1/1:-115.83,-17.15,-8.29:71
+20	2278675	.	A	ATGAATGGCACT	.	PASS	FR=1.0;HP=4;NF=8;NR=9;PP=100.0;SC=ACTCTGAAAAATGGTCACAGA;TC=18;TR=17	GT:GL:GQ	1/1:-567.99,-218.0,-199.44:100
+20	2280081	.	C	CT	.	PASS	FR=1.0;HP=3;NF=15;NR=9;PP=100.0;SC=TAACTTCATGCGGCTCCACCC;TC=30;TR=24	GT:GL:GQ	1/1:-287.69,-60.5,-41.43:100
+20	2280751	.	TA	T	.	PASS	FR=1.0;HP=10;NF=11;NR=3;PP=100.0;SC=AGACTCCATTTAAAAAAAAAA;TC=22;TR=14	GT:GL:GQ	1/1:-139.24,-88.42,-77.92:88
+20	2280882	.	A	AAAAG	.	PASS	FR=1.0;HP=6;NF=2;NR=2;PP=100.0;SC=AAGAAAGAAAAAAAGAAAGAA;TC=21;TR=4	GT:GL:GQ	1/1:-160.24,-78.2,-70.5:63
+20	2285898	.	AGTCACTG	A	.	PASS	FR=1.0;HP=1;NF=9;NR=3;PP=100.0;SC=CCAAGTCTCTAGTCACTGGTT;TC=19;TR=12	GT:GL:GQ	1/1:-272.68,-30.42,-16.26:99
+20	2287002	.	TAAG	T	.	PASS	FR=1.0;HP=2;NF=12;NR=8;PP=100.0;SC=GAAAAATCTCTAAGAAGGCTC;TC=24;TR=20	GT:GL:GQ	1/1:-245.61,-20.38,-4.14:100
+20	2294297	.	A	ACT	.	PASS	FR=1.0;HP=2;NF=5;NR=3;PP=100.0;SC=AATCACACACACTCTCTCTCT;TC=24;TR=8	GT:GL:GQ	1/1:-199.54,-41.84,-28.04:100
+20	2297084	.	AT	A	.	PASS	FR=1.0;HP=2;NF=10;NR=7;PP=100.0;SC=GGTGGCACGCATTAACACCAG;TC=18;TR=17	GT:GL:GQ	1/1:-184.14,-27.34,-14.78:100
+20	2297605	.	CT	C	.	PASS	FR=0.5;HP=3;NF=4;NR=6;PP=100.0;SC=CAATCATGGCCTTTGGCTTCC;TC=24;TR=10	GT:GL:GQ	0/1:-137.24,-29.13,-84.17:100
+20	2298589	.	C	CAT,T	.	PASS	FR=0.5,0.5;HP=1;NF=5,2;NR=2,3;PP=100.0,100.0;SC=ATATATATATCATATATATAT;TC=23;TR=7,5	GT:GL:GQ	1/2:-1.0,-1.0,-1.0:100
+20	2316853	.	G	GC	.	PASS	FR=1.0;HP=4;NF=3;NR=6;PP=100.0;SC=TCACCCTGTAGCCCCTGTGCC;TC=15;TR=9	GT:GL:GQ	1/1:-147.72,-38.92,-28.94:83
+20	2318317	.	GATCACACC	G	.	PASS	FR=1.0;HP=2;NF=8;NR=8;PP=100.0;SC=AGTGAGCCGAGATCACACCAC;TC=22;TR=16	GT:GL:GQ	1/1:-356.42,-104.52,-90.96:100
+20	2318716	.	AG	A	.	PASS	FR=1.0;HP=3;NF=13;NR=4;PP=100.0;SC=CACTCAGAGCAGGGCACCGAT;TC=26;TR=17	GT:GL:GQ	1/1:-256.21,-181.8,-170.54:94
+20	2323655	.	A	AT	.	PASS	FR=1.0;HP=8;NF=11;NR=9;PP=100.0;SC=AGGAAAAAAAAACACTGATGT;TC=31;TR=20	GT:GL:GQ	1/1:-290.56,-28.0,-5.91:100
+20	2326944	.	G	GA	.	PASS	FR=1.0;HP=5;NF=6;NR=12;PP=100.0;SC=AGATACAGAGGAAAAATGAAG;TC=25;TR=18	GT:GL:GQ	1/1:-204.47,-32.24,-15.14:100
+20	2329825	.	T	TC	.	PASS	FR=1.0;HP=1;NF=16;NR=4;PP=100.0;SC=ATATGGGTTGTCTTTGAGACT;TC=22;TR=20	GT:GL:GQ	1/1:-212.37,-32.28,-17.55:100
+20	2334719	.	CTAT	C	.	PASS	FR=1.0;HP=3;NF=14;NR=16;PP=100.0;SC=TTCCCAGGTTCTATTATGTAG;TC=36;TR=30	GT:GL:GQ	1/1:-368.57,-33.34,-9.9:100
+20	2335944	.	C	CTG	.	PASS	FR=1.0;HP=4;NF=10;NR=19;PP=100.0;SC=GCTGAGAAAACTATATCCAAA;TC=34;TR=29	GT:GL:GQ	1/1:-370.96,-31.85,-8.29:100
+20	2340299	.	TTGTC	T	.	PASS	FR=1.0;HP=2;NF=10;NR=15;PP=100.0;SC=ATCCTGTAGGTTGTCTGTTTA;TC=27;TR=25	GT:GL:GQ	1/1:-327.39,-42.17,-22.8:100
+20	2342117	.	T	TG	.	PASS	FR=1.0;HP=5;NF=14;NR=14;PP=100.0;SC=TGCTTATTTTTTCCACTTAAT;TC=32;TR=28	GT:GL:GQ	1/1:-450.6,-326.69,-308.08:100
+20	2344369	.	TAAG	T	.	PASS	FR=1.0;HP=2;NF=13;NR=10;PP=100.0;SC=TGAGAGGTGGTAAGAAGAAGA;TC=36;TR=23	GT:GL:GQ	1/1:-351.7,-76.99,-56.29:100
+20	2344451	.	G	GAGGA	.	PASS	FR=1.0;HP=2;NF=12;NR=3;PP=100.0;SC=ACACCCAACAGAGGAAGGTTA;TC=20;TR=15	GT:GL:GQ	1/1:-372.02,-158.89,-145.61:100
+20	2344539	.	T	TTTTGTTTG	.	PASS	FR=1.0;HP=3;NF=8;NR=4;PP=100.0;SC=ACTACCCCAGTTTTGTTTGTT;TC=23;TR=12	GT:GL:GQ	1/1:-243.77,-36.7,-24.92:99
+20	2345269	.	TCCTGGC	T	.	PASS	FR=1.0;HP=2;NF=7;NR=13;PP=100.0;SC=ATCGAGACCATCCTGGCTAAC;TC=21;TR=20	GT:GL:GQ	1/1:-260.12,-24.22,-9.67:100
+20	2346660	.	T	TAATAAATAAATAAATA	.	PASS	FR=1.0;HP=3;NF=3;NR=4;PP=100.0;SC=CAATTCCTTATAATAAATAAA;TC=13;TR=7	GT:GL:GQ	1/1:-305.93,-18.69,-7.6:93
+20	2352930	.	AC	A	.	PASS	FR=1.0;HP=2;NF=10;NR=8;PP=100.0;SC=TTTCAGGCCTACCTCTCAAGC;TC=21;TR=18	GT:GL:GQ	1/1:-216.23,-90.38,-78.46:100
+20	2362643	.	C	CTG	.	PASS	FR=1.0;HP=3;NF=11;NR=8;PP=100.0;SC=AAGAACTTGTCTTAGATGCTG;TC=21;TR=19	GT:GL:GQ	1/1:-259.19,-87.0,-72.75:100
+20	2379170	.	TC	T	.	PASS	FR=0.5;HP=4;NF=1;NR=3;PP=99.0;SC=AGCTTGGGCTTCCCCACAATA;TC=23;TR=4	GT:GL:GQ	0/1:-84.89,-51.93,-137.5:100
+20	2401510	.	ATGT	A	.	PASS	FR=0.5;HP=2;NF=2;NR=4;PP=100.0;SC=CATTATATGGATGTACACAGT;TC=23;TR=6	GT:GL:GQ	0/1:-138.83,-80.65,-217.86:100
+20	2406090	.	AACT	A	.	PASS	FR=0.5;HP=3;NF=8;NR=7;PP=100.0;SC=GTTGCCACAAAACTTCAATTT;TC=36;TR=15	GT:GL:GQ	0/1:-277.31,-158.31,-369.27:100
+20	2407722	.	A	AT	.	PASS	FR=0.5;HP=9;NF=4;NR=11;PP=100.0;SC=AATTGCTATAATTTTTTTTTC;TC=38;TR=15	GT:GL:GQ	0/1:-112.13,-34.3,-69.71:100
+20	2409340	.	C	CAATA	.	PASS	FR=0.5;HP=2;NF=4;NR=3;PP=100.0;SC=CATAATAAATCAATCAATAAA;TC=22;TR=7	GT:GL:GQ	0/1:-189.45,-43.56,-132.72:100
+20	2409613	.	G	GCA	.	PASS	FR=0.5;HP=1;NF=6;NR=4;PP=57.0;SC=GGGATTATAGGCACAACACCA;TC=25;TR=10	GT:GL:GQ	0/1:-231.71,-206.44,-319.84:100
+20	2411731	.	CAG	C	.	PASS	FR=0.5;HP=1;NF=1;NR=2;PP=36.0;SC=GTGGATGAGCCAGAGAGAAGT;TC=13;TR=3	GT:GL:GQ	0/1:-55.56,-36.89,-120.4:84
+20	2414786	.	G	GA	.	PASS	FR=1.0;HP=8;NF=8;NR=10;PP=100.0;SC=GAAGCTTTCAGAAAAAAACCC;TC=23;TR=18	GT:GL:GQ	1/1:-173.45,-78.53,-65.46:100
+20	2418166	.	GTGTT	G	.	PASS	FR=0.5;HP=1;NF=1;NR=4;PP=100.0;SC=CACCTGGCTAGTGTTTGTTTG;TC=21;TR=5	GT:GL:GQ	0/1:-134.79,-72.62,-117.78:100
+20	2425523	.	A	ATTTATTTTATTTTAT	.	PASS	FR=0.5;HP=7;NF=3;NR=2;PP=100.0;SC=ATTTTATTTTATTTATTTTAT;TC=23;TR=5	GT:GL:GQ	0/1:-149.61,-12.23,-46.02:100
+20	2425934	.	T	TA	.	PASS	FR=0.5;HP=8;NF=8;NR=4;PP=67.0;SC=TTAATCAATTTAAAAAAAATG;TC=25;TR=12	GT:GL:GQ	0/1:-160.28,-133.72,-162.95:100
+20	2430943	.	ATGTG	A	.	PASS	FR=0.5;HP=1;NF=1;NR=1;PP=100.0;SC=GTGCGTGTGCATGTGTGTGTG;TC=29;TR=2	GT:GL:GQ	0/1:-164.1,-78.49,-99.2:92
+20	2433931	.	TC	T	.	PASS	FR=0.5;HP=5;NF=1;NR=1;PP=26.0;SC=CCCTGGAAGCTCCCCTTTGTG;TC=10;TR=2	GT:GL:GQ	0/1:-34.79,-18.58,-53.81:73
+20	2436455	.	A	AAAAAAG,AAAAAG	.	PASS	FR=0.5,0.5;HP=9;NF=3,3;NR=1,4;PP=50.0,100.0;SC=CTACCAAAAAAAAAAGAAAAG;TC=25;TR=4,7	GT:GL:GQ	1/2:-1.0,-1.0,-1.0:100
+20	2436835	.	A	AC	.	PASS	FR=0.5;HP=1;NF=7;NR=8;PP=100.0;SC=ACAATGATGTACATTTTTCAG;TC=37;TR=15	GT:GL:GQ	0/1:-177.52,-36.56,-198.23:100
+20	2448573	.	CCT	C	.	PASS	FR=0.5;HP=2;NF=6;NR=5;PP=100.0;SC=CCCATGCCACCCTGTTTTAGC;TC=34;TR=11	GT:GL:GQ	0/1:-159.22,-114.6,-320.68:100
+20	2450954	.	CA	C	.	PASS	FR=0.5;HP=2;NF=1;NR=4;PP=100.0;SC=CAAACTTCCGCAAGTCTGAGC;TC=22;TR=5	GT:GL:GQ	0/1:-106.22,-51.15,-126.38:100
+20	2452700	.	TAAAAAAGAA	T	.	PASS	FR=0.5;HP=6;NF=4;NR=5;PP=100.0;SC=TTTCTTGGATTAAAAAAGAAA;TC=32;TR=9	GT:GL:GQ	0/1:-216.2,-29.76,-153.35:100
+20	2458350	.	G	GA	.	PASS	FR=0.5;HP=3;NF=4;NR=6;PP=100.0;SC=CAAGGTGGGAGAATTGCTTGA;TC=27;TR=10	GT:GL:GQ	0/1:-156.97,-38.22,-122.55:100
+20	2477736	.	A	AT	.	PASS	FR=0.5;HP=10;NF=4;NR=3;PP=100.0;SC=AAAAAAAAAAATTTTACCATC;TC=23;TR=7	GT:GL:GQ	0/1:-89.51,-39.15,-127.81:100
+20	2498012	.	GTA	G	.	PASS	FR=0.5;HP=2;NF=3;NR=6;PP=100.0;SC=GTATATGTGTGTATATATATA;TC=22;TR=9	GT:GL:GQ	0/1:-140.02,-17.32,-103.73:100
+20	2516178	.	GA	G	.	PASS	FR=0.5;HP=8;NF=3;NR=5;PP=100.0;SC=GTTTAATTGGGAAAAAAAATA;TC=17;TR=8	GT:GL:GQ	0/1:-52.67,-14.95,-45.28:100
+20	2520604	.	T	TAGCA	.	PASS	FR=0.5;HP=4;NF=4;NR=3;PP=100.0;SC=CTCCCGCAAATAGCACACAAG;TC=20;TR=7	GT:GL:GQ	0/1:-194.0,-75.16,-105.67:100
+20	2522684	.	G	GA	.	PASS	FR=0.5;HP=7;NF=5;NR=6;PP=83.0;SC=TTTCTTATTTGAAAAAAACTT;TC=31;TR=11	GT:GL:GQ	0/1:-153.71,-123.52,-187.08:100
+20	2523586	.	T	TA	.	PASS	FR=1.0;HP=4;NF=11;NR=6;PP=100.0;SC=TTTTTCTTTTTAAAACAAAAT;TC=23;TR=17	GT:GL:GQ	1/1:-179.22,-18.0,-3.45:100
+20	2526468	.	GAAGA	G	.	PASS	FR=0.5001;HP=2;NF=2;NR=4;PP=100.0;SC=AGAGGAAGAGGAAGAAAGAAA;TC=25;TR=6	GT:GL:GQ	0/1:-210.76,-128.72,-136.62:37
+20	2526552	.	A	AAG	.	PASS	FR=0.5;HP=6;NF=5;NR=8;PP=100.0;SC=GAAAGAAAGAAAAAAAGAAAG;TC=30;TR=13	GT:GL:GQ	0/1:-215.19,-78.8,-144.35:100
+20	2527129	.	G	GTTGGGCATAAGCTGTAGATC	.	PASS	FR=0.5;HP=2;NF=3;NR=1;PP=100.0;SC=AACCTGCAGAGTTGGGCATAA;TC=18;TR=4	GT:GL:GQ	0/1:-243.57,-136.91,-199.82:100
+20	2534184	.	T	TGTTTTGTGTGAC	.	PASS	FR=0.5;HP=1;NF=5;NR=9;PP=100.0;SC=GATACAGGTCTGTTTTTGTCT;TC=31;TR=14	GT:GL:GQ	0/1:-444.44,-61.75,-181.17:100
+20	2546156	.	TGG	T	.	PASS	FR=0.5;HP=3;NF=4;NR=12;PP=100.0;SC=CCCAAAGTGCTGGGATTACAG;TC=31;TR=16	GT:GL:GQ	0/1:-172.01,-63.37,-146.93:100
+20	2568176	.	G	GT	.	PASS	FR=1.0;HP=10;NF=12;NR=9;PP=100.0;SC=ATTTGGGAATGTTTTTTTTTA;TC=27;TR=21	GT:GL:GQ	1/1:-116.08,-18.72,-6.68:100
+20	2577356	.	A	AAT	.	PASS	FR=0.5;HP=6;NF=1;NR=2;PP=100.0;SC=ATCAGAAAAAAATATATATGT;TC=26;TR=3	GT:GL:GQ	0/1:-199.48,-88.19,-98.9:49
+20	2579040	.	C	CTTTATTTA	.	PASS	FR=0.5;HP=3;NF=1;NR=2;PP=100.0;SC=CTTGCCTCTACTTTATTTATT;TC=16;TR=3	GT:GL:GQ	0/1:-103.59,-10.59,-52.57:100
+20	2586119	.	GGA	G	.	PASS	FR=0.5;HP=1;NF=2;NR=1;PP=30.0;SC=GCATGTGCATGGAGAGAGAGA;TC=23;TR=3	GT:GL:GQ	0/1:-35.49,-18.23,-170.44:77
+20	2594696	.	A	AT	.	PASS	FR=0.5;HP=8;NF=2;NR=7;PP=100.0;SC=TTTCTGTCACATTTTTTTTCG;TC=24;TR=9	GT:GL:GQ	0/1:-70.9,-30.05,-77.99:100
+20	2597210	.	TAAAG	T	.	PASS	FR=0.5;HP=7;NF=2;NR=2;PP=100.0;SC=GAAAGGAAAATAAAGAAGGAG;TC=20;TR=4	GT:GL:GQ	0/1:-85.33,-27.89,-144.98:100
+20	2611781	.	A	ATATCT	.	PASS	FR=0.5;HP=1;NF=8;NR=8;PP=100.0;SC=ATTATAATTAATATAACAAAC;TC=31;TR=16	GT:GL:GQ	0/1:-408.96,-183.07,-309.58:100
+20	2613623	.	T	TTTG	.	PASS	FR=0.5;HP=3;NF=2;NR=2;PP=100.0;SC=CTTCCATGGGTTTGTTGTTGT;TC=18;TR=4	GT:GL:GQ	0/1:-165.53,-112.66,-139.53:100
+20	2613971	.	TA	T	.	PASS	FR=0.5;HP=4;NF=4;NR=7;PP=100.0;SC=CTTGGACACATAAACAGCCCT;TC=27;TR=11	GT:GL:GQ	0/1:-121.36,-29.89,-140.29:100
+20	2614405	.	T	TGGGTAGG	.	PASS	FR=0.5;HP=3;NF=2;NR=2;PP=52.0;SC=ACTACAGAACTGGGTAGGGGA;TC=30;TR=4	GT:GL:GQ	0/1:-185.89,-156.26,-363.71:100
+20	2616002	.	C	CT	.	PASS	FR=0.5;HP=4;NF=5;NR=5;PP=100.0;SC=ACCTCCACCTCCCCCTCTCAG;TC=22;TR=10	GT:GL:GQ	0/1:-182.46,-117.29,-171.16:100
+20	2617861	.	C	CCT	.	PASS	FR=0.5;HP=2;NF=2;NR=5;PP=100.0;SC=ATGGTGAACCCGTCTCTACTA;TC=17;TR=7	GT:GL:GQ	0/1:-111.22,-36.32,-97.76:100
+20	2625967	.	TGAG	T	.	PASS	FR=0.5;HP=1;NF=2;NR=3;PP=100.0;SC=CTGAGTAGGCTGAGGAGGAGG;TC=15;TR=5	GT:GL:GQ	0/1:-133.1,-85.47,-137.74:100
+20	2627766	.	TTTTATTTA	T	.	PASS	FR=0.5;HP=3;NF=1;NR=1;PP=86.0;SC=ACTGAATTTATTTTATTTATT;TC=19;TR=2	GT:GL:GQ	0/1:-102.46,-70.95,-132.69:100
+20	2630436	.	T	TACC	.	PASS	FR=0.5;HP=2;NF=6;NR=5;PP=100.0;SC=ACATGCCAGGTACACCATTGT;TC=23;TR=11	GT:GL:GQ	0/1:-159.47,-31.83,-143.4:100
+20	2634285	.	CTG	C	.	PASS	FR=0.5;HP=1;NF=3;NR=15;PP=100.0;SC=CTTGTGGGCACTGTAGTGACA;TC=29;TR=18	GT:GL:GQ	0/1:-229.42,-26.07,-86.72:100
+20	2641823	.	C	CTG	.	PASS	FR=0.5;HP=5;NF=2;NR=2;PP=100.0;SC=ATTGCATTTTCTGTGTGTGTG;TC=21;TR=4	GT:GL:GQ	0/1:-96.78,-48.19,-99.13:100
+20	2643833	.	G	GAAATGCAAT	.	PASS	FR=0.5;HP=4;NF=9;NR=2;PP=100.0;SC=TGGTATTCCAGAAATGCAATG;TC=31;TR=11	GT:GL:GQ	0/1:-379.88,-109.48,-180.95:100
+20	2650007	.	T	TACACACACACACACACAC	.	PASS	FR=1.0;HP=1;NF=3;NR=1;PP=100.0;SC=ACCCTTTTCTTACACACACAC;TC=19;TR=4	GT:GL:GQ	1/1:-231.82,-84.82,-75.66:76
+20	2650235	.	C	CT	.	PASS	FR=1.0;HP=9;NF=12;NR=9;PP=100.0;SC=TTTATTGGGCCTTTTTTTTTG;TC=28;TR=21	GT:GL:GQ	1/1:-325.44,-296.08,-289.77:79
+20	2656886	.	AT	A	.	PASS	FR=1.0;HP=6;NF=17;NR=6;PP=100.0;SC=ATAAATAATAATTTTTTAAAA;TC=29;TR=23	GT:GL:GQ	1/1:-339.94,-246.4,-231.12:100
+20	2663020	.	G	GGAA	.	PASS	FR=1.0;HP=1;NF=8;NR=7;PP=100.0;SC=AAGAGGAAGAGGAAGAAGACA;TC=28;TR=15	GT:GL:GQ	1/1:-408.26,-206.61,-189.41:100
+20	2665268	.	TA	T	.	PASS	FR=1.0;HP=8;NF=2;NR=1;PP=43.0;SC=TATGCAGCCATAAAAAAATGA;TC=4;TR=3	GT:GL:GQ	1/1:-20.74,-4.04,-1.38:43
+20	2665956	.	AG	A	.	PASS	FR=1.0;HP=1;NF=9;NR=5;PP=100.0;SC=CCCAGGCTATAGTGCAGTGGC;TC=16;TR=14	GT:GL:GQ	1/1:-156.94,-33.67,-23.62:84
+20	2666401	.	TA	T	.	PASS	FR=0.5;HP=2;NF=8;NR=7;PP=100.0;SC=ACTTTTCTATTAAGAAACGCA;TC=38;TR=15	GT:GL:GQ	0/1:-158.74,-28.32,-160.06:100
+20	2668149	.	A	ATG	.	PASS	FR=0.5;HP=2;NF=1;NR=2;PP=100.0;SC=ATATATATATATGTGTGTGTG;TC=17;TR=3	GT:GL:GQ	0/1:-54.4,-18.57,-68.0:100
+20	2671350	.	GTA	G	.	PASS	FR=1.0;HP=2;NF=8;NR=5;PP=100.0;SC=ATATATATGTGTATATATATA;TC=23;TR=13	GT:GL:GQ	1/1:-348.62,-348.37,-348.16:60
+20	2676135	.	C	CAG	.	PASS	FR=0.5;HP=1;NF=6;NR=2;PP=100.0;SC=TGCTGGGATGCAGAGGGCTTC;TC=17;TR=8	GT:GL:GQ	0/1:-189.45,-108.27,-131.01:100
+20	2678198	.	A	AAAAG	.	PASS	FR=1.0;HP=10;NF=1;NR=2;PP=100.0;SC=CTCAAAAAAAAAAAGAAAGAA;TC=16;TR=3	GT:GL:GQ	1/1:-113.89,-62.27,-58.08:51
+20	2691794	.	AAAT	A	.	PASS	FR=1.0;HP=3;NF=2;NR=4;PP=100.0;SC=ACCCTGTCTAAAATAATAATA;TC=12;TR=6	GT:GL:GQ	1/1:-83.97,-10.76,-5.22:69
+20	2713483	.	C	CAG	.	PASS	FR=0.5;HP=2;NF=7;NR=1;PP=100.0;SC=TTTTTTGAGACGGAATTATAA;TC=28;TR=8	GT:GL:GQ	0/1:-114.91,-36.16,-205.08:100
+20	2717474	.	A	ACAAAGGTCTC	.	PASS	FR=1.0;HP=2;NF=9;NR=5;PP=100.0;SC=AGTCATAAGGACAAAGGACCC;TC=17;TR=14	GT:GL:GQ	1/1:-343.26,-32.05,-17.5:94
+20	2724519	.	AG	A	.	PASS	FR=0.5;HP=3;NF=6;NR=7;PP=100.0;SC=CCAGATATTTAGGGTGTCCAT;TC=28;TR=13	GT:GL:GQ	0/1:-149.48,-35.03,-149.61:100
+20	2734607	.	C	CCCCCTTGGTTTTGAAACTTT	.	PASS	FR=1.0;HP=4;NF=2;NR=4;PP=100.0;SC=TCTGTGGGCACCCCCTTGGGC;TC=12;TR=6	GT:GL:GQ	1/1:-301.3,-108.37,-98.31:100
+20	2742852	.	C	CCAGCAATCCTCAGT	.	PASS	FR=0.5;HP=1;NF=1;NR=5;PP=100.0;SC=CTCAATAGCACCTGAGGATGA;TC=16;TR=6	GT:GL:GQ	0/1:-233.59,-35.77,-130.91:100
+20	2766949	.	C	CT	.	PASS	FR=1.0;HP=10;NF=5;NR=10;PP=100.0;SC=ACTTCATTCCCTTTTTTTTTT;TC=28;TR=15	GT:GL:GQ	1/1:-134.68,-37.76,-21.4:100
+20	2782855	.	AC	A	.	PASS	FR=1.0;HP=4;NF=3;NR=8;PP=100.0;SC=AATCACTTGTACCCCGGGGGC;TC=25;TR=11	GT:GL:GQ	1/1:-262.64,-187.36,-174.92:100
+20	2789088	.	AC	A	.	PASS	FR=1.0;HP=9;NF=1;NR=4;PP=100.0;SC=CAAAAAAAAAACCAAAAAACA;TC=13;TR=5	GT:GL:GQ	1/1:-119.81,-36.46,-27.82:89
+20	2796485	.	C	CCTTTT	.	PASS	FR=0.5;HP=4;NF=1;NR=4;PP=100.0;SC=CATCAGGCCCCCTTTTCTCCT;TC=18;TR=5	GT:GL:GQ	0/1:-128.25,-42.55,-123.81:100
+20	2797764	.	AG	A	.	PASS	FR=1.0;HP=3;NF=1;NR=4;PP=100.0;SC=CTGCCTTGGCAGGGCCCAGAC;TC=14;TR=5	GT:GL:GQ	1/1:-134.46,-67.08,-59.42:63
+20	2834884	.	T	TAC	.	PASS	FR=0.5;HP=1;NF=2;NR=1;PP=100.0;SC=ACCCCGTCTCTACACACACAC;TC=22;TR=3	GT:GL:GQ	0/1:-64.62,-28.32,-80.82:100
+20	2849974	.	AT	A	.	PASS	FR=0.5;HP=10;NF=4;NR=6;PP=99.0;SC=TTGGTTTGCAATTTTTTTTTT;TC=36;TR=10	GT:GL:GQ	0/1:-66.95,-34.01,-107.66:100
+20	2850721	.	ACT	A	.	PASS	FR=0.5;HP=1;NF=4;NR=4;PP=100.0;SC=CCAGTGAAAGACTCTTGGGGT;TC=17;TR=8	GT:GL:GQ	0/1:-88.06,-17.99,-74.67:100
+20	2858849	.	GT	G	.	PASS	FR=0.5;HP=8;NF=1;NR=5;PP=52.0;SC=GACAGCTGTAGTTTTTTTTAA;TC=15;TR=6	GT:GL:GQ	0/1:-33.96,-11.94,-50.39:98
+20	2867547	.	AT	A	.	PASS	FR=0.5;HP=6;NF=5;NR=6;PP=100.0;SC=AAATAAAAAAATGTAGTATCT;TC=32;TR=11	GT:GL:GQ	0/1:-115.49,-28.1,-161.94:100
+20	2880787	.	C	CCT	.	PASS	FR=0.5;HP=1;NF=4;NR=5;PP=100.0;SC=GAAAAATCTGCCTCCTTTTTT;TC=27;TR=9	GT:GL:GQ	0/1:-140.77,-68.5,-172.28:100
+20	2890657	.	C	CAT	.	PASS	FR=0.5003;HP=1;NF=2;NR=1;PP=100.0;SC=TATCATATATCATATATAATC;TC=5;TR=3	GT:GL:GQ	0/1:-44.82,-3.47,-10.33:32
+20	2890805	.	CAT	C	.	PASS	FR=0.5017;HP=1;NF=1;NR=6;PP=100.0;SC=TACTATACGTCATATATAATA;TC=9;TR=7	GT:GL:GQ	0/1:-87.98,-14.06,-19.03:24
+20	2894312	.	CTTATT	C	.	PASS	FR=0.5;HP=4;NF=3;NR=5;PP=100.0;SC=GTGCTGTGTTCTTATTTTATC;TC=22;TR=8	GT:GL:GQ	0/1:-141.94,-29.98,-159.98:100
+20	2896142	.	T	TTATC	.	PASS	FR=1.0;HP=2;NF=9;NR=10;PP=100.0;SC=TAAGAGTTCTTTATTCTGATA;TC=30;TR=19	GT:GL:GQ	1/1:-399.17,-94.52,-74.73:100
+20	2912364	.	T	TTG	.	PASS	FR=0.5004;HP=1;NF=1;NR=1;PP=75.0;SC=GGGTCTTGGCTTGTGTGTGTG;TC=20;TR=2	GT:GL:GQ	0/1:-121.99,-92.59,-99.11:31
+20	2926228	.	GGTGTGTGT	G	.	PASS	FR=0.5;HP=1;NF=1;NR=9;PP=100.0;SC=ATAATTGGCAGGTGTGTGTGT;TC=27;TR=10	GT:GL:GQ	0/1:-233.62,-33.54,-77.33:100
+20	2937307	.	AAAATAAAT	A	.	PASS	FR=0.5;HP=4;NF=3;NR=3;PP=100.0;SC=TCAGTAAATAAAAATAAATAA;TC=17;TR=6	GT:GL:GQ	0/1:-165.86,-12.93,-101.78:100
+20	2950624	.	T	TAATA,TAATAAATAAATA	.	PASS	FR=0.5,0.5;HP=5;NF=5,2;NR=2,2;PP=100.0,100.0;SC=TCTAAATAAATAATAAATAAA;TC=24;TR=7,4	GT:GL:GQ	1/2:-1.0,-1.0,-1.0:100
+20	2966530	.	CTTGTTTGT	CTTGT,C	.	PASS	FR=0.5,0.5;HP=2;NF=1,1;NR=2,1;PP=100.0,27.0;SC=CAGCTGTCTCCTTGTTTGTTT;TC=22;TR=3,2	GT:GL:GQ	1/2:-1.0,-1.0,-1.0:80
+20	2973326	.	T	TTTAGGGTTTTTC	.	PASS	FR=0.5;HP=4;NF=1;NR=5;PP=100.0;SC=CATATCCAAATATTACGATTC;TC=15;TR=6	GT:GL:GQ	0/0:-275.74,-159.4,-213.4:3
+20	2977781	.	CATAT	C	.	PASS	FR=0.5;HP=5;NF=3;NR=6;PP=100.0;SC=TGTGAGAAAACATATGTGGGA;TC=26;TR=9	GT:GL:GQ	0/1:-131.98,-30.22,-206.04:100
+20	2979576	.	T	TTATTA	.	PASS	FR=0.5;HP=2;NF=2;NR=5;PP=100.0;SC=TATTTATAATTTATTATATAT;TC=21;TR=7	GT:GL:GQ	0/1:-148.89,-17.32,-97.42:100
+20	2982245	.	CT	C	.	PASS	FR=0.5;HP=3;NF=8;NR=4;PP=100.0;SC=CTGTGGAAATCTTATGTGAAG;TC=27;TR=12	GT:GL:GQ	0/1:-126.56,-21.8,-132.46:100
+20	2982823	.	CA	C	.	PASS	FR=1.0;HP=7;NF=10;NR=9;PP=100.0;SC=TTCCATCTGACAAAAAATTGG;TC=21;TR=19	GT:GL:GQ	1/1:-196.74,-95.2,-82.42:100
+20	2989926	.	AT	A	.	PASS	FR=0.5;HP=10;NF=2;NR=5;PP=29.0;SC=GAGTTGTGTGATTTTTTTTTT;TC=36;TR=7	GT:GL:GQ	0/1:-66.0,-49.11,-118.97:76
+20	3005541	.	TC	T	.	PASS	FR=0.5;HP=5;NF=7;NR=7;PP=100.0;SC=AGCAGTTTTTTCTGTAAGAGC;TC=32;TR=14	GT:GL:GQ	0/1:-167.85,-53.03,-186.47:100
+20	3007694	.	A	AGGT	.	PASS	FR=0.5;HP=3;NF=4;NR=5;PP=100.0;SC=CCAGGGCCTGAGGTGGGAGCA;TC=22;TR=9	GT:GL:GQ	0/1:-162.22,-42.91,-117.4:100
+20	3012419	.	C	CTGTT	.	PASS	FR=0.5;HP=2;NF=5;NR=3;PP=100.0;SC=CCTCCTTACTCTGTGTGTTTT;TC=26;TR=8	GT:GL:GQ	0/1:-154.4,-24.26,-143.38:100
+20	3022136	.	GAATT	G	.	PASS	FR=0.5;HP=7;NF=8;NR=1;PP=100.0;SC=AAAAGAAAAAGAATTAATTAA;TC=20;TR=9	GT:GL:GQ	1/0:-190.17,-78.0,-90.9:100
+20	3039218	.	GT	G	.	PASS	FR=1.0;HP=5;NF=12;NR=13;PP=100.0;SC=TGTTGTTGTTGTTTGTTTGTT;TC=29;TR=25	GT:GL:GQ	1/1:-226.7,-48.88,-31.11:100
+20	3042034	.	T	TA	.	PASS	FR=1.0;HP=10;NF=5;NR=14;PP=100.0;SC=AAGACACTGATAAAAAAAAAT;TC=25;TR=19	GT:GL:GQ	1/1:-125.74,-31.3,-15.65:100
+20	3047853	.	A	ATTCCCCCATT	.	PASS	FR=0.5;HP=2;NF=6;NR=1;PP=100.0;SC=ACTCCCTCTCATTCCCCCATT;TC=20;TR=7	GT:GL:GQ	0/1:-258.31,-36.83,-99.91:100
+20	3050529	.	A	AT	.	PASS	FR=0.5;HP=10;NF=4;NR=1;PP=23.0;SC=GCAAAAAAAAAAATTTTTATT;TC=22;TR=5	GT:GL:GQ	0/1:-257.11,-262.46,-292.84:73
+20	3050531	.	A	ATTT,T	.	PASS	FR=0.5,0.5;HP=10;NF=3,13;NR=0,6;PP=97.0,100.0;SC=AAAAAAAAAAATTTTTATTTT;TC=22;TR=3,19	GT:GL:GQ	1/2:-1.0,-1.0,-1.0:100
+20	3051123	.	A	AT	.	PASS	FR=0.5;HP=6;NF=2;NR=1;PP=69.0;SC=TCAAGAAAAAAATATATATAT;TC=17;TR=3	GT:GL:GQ	0/1:-107.95,-81.12,-160.4:100
+20	3058938	.	C	CTT	.	PASS	FR=1.0;HP=2;NF=19;NR=9;PP=100.0;SC=ACTGGATACTCTGAACTCCTA;TC=30;TR=28	GT:GL:GQ	1/1:-404.4,-115.7,-94.26:100
+20	3060201	.	C	CAAT	.	PASS	FR=0.5;HP=4;NF=13;NR=9;PP=100.0;SC=ACAAAGTCAACAATAATTCAT;TC=44;TR=22	GT:GL:GQ	0/1:-325.42,-43.13,-189.79:100
+20	3062903	.	T	TC	.	PASS	FR=0.5;HP=3;NF=1;NR=5;PP=94.0;SC=TCCAGGCCTTTCCCTCTCTGC;TC=19;TR=6	GT:GL:GQ	0/1:-95.35,-62.58,-147.62:100
+20	3072606	.	A	AAGG	.	PASS	FR=1.0;HP=5;NF=4;NR=4;PP=100.0;SC=CCAAGTAAAAAAGGGCGGGGG;TC=22;TR=8	GT:GL:GQ	1/1:-220.94,-78.12,-65.62:100
+20	3126086	.	CCT	TCT,C	.	PASS	FR=0.5,0.5;HP=7;NF=1,1;NR=3,1;PP=8.0,36.0;SC=GCCTTTTTTTCCTTTTTTTTT;TC=19;TR=4,2	GT:GL:GQ	2/1:-1.0,-1.0,-1.0:42
+20	3159346	.	C	CA	.	PASS	FR=1.0;HP=2;NF=3;NR=12;PP=100.0;SC=GCTGGGACTACGGCATTTACT;TC=15;TR=15	GT:GL:GQ	1/1:-149.15,-11.32,-0.92:87
+20	3161722	.	C	CAGAT,CAGATAGAT	.	PASS	FR=0.5,0.5;HP=2;NF=2,1;NR=2,2;PP=35.0,42.0;SC=GATAGATAGACAGATAGATAG;TC=18;TR=4,3	GT:GL:GQ	1/2:-1.0,-1.0,-1.0:99
+20	3161783	.	CTA	C	.	PASS	FR=1.0;HP=2;NF=9;NR=7;PP=100.0;SC=TTTTATATATCTATATATATA;TC=25;TR=16	GT:GL:GQ	1/1:-263.89,-139.12,-127.54:97
+20	3162560	.	CAT	C	.	PASS	FR=0.5369;HP=2;NF=1;NR=3;PP=100.0;SC=CACACACACACATGGTCCATG;TC=6;TR=4	GT:GL:GQ	0/1:-84.99,-50.52,-52.5:11
+20	3169476	.	T	TTTG	.	PASS	FR=0.5;HP=3;NF=5;NR=9;PP=100.0;SC=AATGTTTACTTTTAATAAACT;TC=35;TR=14	GT:GL:GQ	0/1:-273.66,-64.07,-202.46:100
+20	3169541	.	A	AT	.	PASS	FR=0.5;HP=7;NF=5;NR=9;PP=100.0;SC=AGGATCATAGATTTTTTTCCT;TC=23;TR=14	GT:GL:GQ	0/1:-204.2,-123.3,-145.94:100
+20	3172618	.	GACAC	G	.	PASS	FR=0.7893;HP=1;NF=3;NR=1;PP=100.0;SC=TTGCTCCCCTGACACACACAC;TC=16;TR=4	GT:GL:GQ	1/1:-154.29,-100.95,-101.25:3
+20	3172771	.	C	CAT	.	PASS	FR=1.0;HP=1;NF=13;NR=6;PP=100.0;SC=CCGAGACACACGAGTGGTAAT;TC=24;TR=19	GT:GL:GQ	1/1:-267.07,-44.87,-28.98:100
+20	3177159	.	T	TA	.	PASS	FR=1.0;HP=5;NF=6;NR=3;PP=87.0;SC=CTGTCTCCACTAAAAATACAA;TC=15;TR=9	GT:GL:GQ	1/1:-169.92,-142.98,-139.57:56
+20	3177517	.	C	CAT	.	PASS	FR=1.0;HP=2;NF=15;NR=10;PP=100.0;SC=TAATAAATAACGTTACTGGAT;TC=26;TR=25	GT:GL:GQ	1/1:-294.64,-37.59,-18.88:100
+20	3188342	.	A	AAACAACAACAACAAC	.	PASS	FR=0.5;HP=3;NF=2;NR=2;PP=100.0;SC=CTCCATCTCAAAACAACAACA;TC=17;TR=4	GT:GL:GQ	0/1:-131.35,-46.51,-82.74:100
+20	3192138	.	T	TTTTGTTTGTTTG	.	PASS	FR=0.5;HP=3;NF=3;NR=1;PP=99.0;SC=TTTTGTTTTGTTTTGTTTGTT;TC=17;TR=4	GT:GL:GQ	0/1:-79.23,-33.31,-124.52:100
+20	3192798	.	C	CAG	.	PASS	FR=0.5;HP=2;NF=2;NR=6;PP=100.0;SC=GCCTGGGTGACAGAGAGAGAG;TC=20;TR=8	GT:GL:GQ	0/1:-108.84,-41.85,-123.5:100
+20	3198551	.	G	GTT	.	PASS	FR=0.5;HP=2;NF=1;NR=2;PP=63.0;SC=AGTTTTTGTGGGTTTTTTTTT;TC=22;TR=3	GT:GL:GQ	0/1:-111.88,-112.41,-193.71:91
+20	3202220	.	GTGGC	G	.	PASS	FR=0.5;HP=2;NF=2;NR=5;PP=100.0;SC=TGTCCCGGGTGTGGCTGGCGA;TC=19;TR=7	GT:GL:GQ	0/1:-150.53,-63.82,-136.14:100
+20	3276659	.	CT	C	.	PASS	FR=1.0;HP=3;NF=5;NR=6;PP=100.0;SC=ACATCGGGAACTTTCGGTTTC;TC=16;TR=11	GT:GL:GQ	1/1:-135.26,-24.21,-14.73:79
+20	3290980	.	A	AAAAG	.	PASS	FR=0.9998;HP=4;NF=1;NR=1;PP=30.0;SC=AAGAGAAAGAAAAAGAAAGAA;TC=7;TR=2	GT:GL:GQ	1/1:-37.89,-18.65,-17.26:34
+20	3313547	.	G	GGTGT	.	PASS	FR=1.0;HP=1;NF=1;NR=3;PP=100.0;SC=GTGTGCGTGTGGTGTGTGTGT;TC=20;TR=4	GT:GL:GQ	1/1:-194.22,-148.74,-144.19:56
+20	3314333	.	G	GT	.	PASS	FR=1.0;HP=10;NF=9;NR=9;PP=100.0;SC=CTTATTAAAGGTTTTTTTTTT;TC=34;TR=18	GT:GL:GQ	1/1:-126.24,-28.85,-19.8:75
+20	3317061	.	G	GT	.	PASS	FR=1.0;HP=10;NF=5;NR=7;PP=100.0;SC=GTTTTGTTCAGTTTTTTTTTT;TC=20;TR=12	GT:GL:GQ	1/1:-81.13,-22.72,-13.12:80
+20	3318622	.	TATAAAATATATAATAC	T	.	PASS	FR=0.5;HP=2;NF=3;NR=5;PP=100.0;SC=ATATATAATATATAAAATATA;TC=21;TR=8	GT:GL:GQ	1/0:-309.41,-50.93,-55.49:45
+20	3320964	.	AGTTT	A	.	PASS	FR=1.0;HP=1;NF=6;NR=12;PP=100.0;SC=AATCATACCTAGTTTGTACTA;TC=22;TR=18	GT:GL:GQ	1/1:-403.07,-167.86,-153.33:100
+20	3320971	.	A	AC	.	PASS	FR=1.0;HP=1;NF=6;NR=13;PP=100.0;SC=CCTAGTTTGTACTATAAAAAA;TC=19;TR=19	GT:GL:GQ	1/1:-403.07,-261.66,-248.63:100
+20	3323678	.	AT	A	.	PASS	FR=1.0;HP=5;NF=3;NR=1;PP=100.0;SC=TCTGATGATTATTTCTATTGC;TC=28;TR=4	GT:GL:GQ	1/1:-575.25,-570.95,-570.67:100
+20	3323683	.	T	TAAA	.	PASS	FR=1.0;HP=1;NF=13;NR=11;PP=100.0;SC=TGATTATTTCTATTGCTGTGC;TC=29;TR=24	GT:GL:GQ	1/1:-597.36,-560.99,-550.34:86
+20	3323709	.	T	TA	.	PASS	FR=1.0;HP=2;NF=16;NR=21;PP=100.0;SC=CATGTTCATTTGTTAGGTCCC;TC=38;TR=37	GT:GL:GQ	1/1:-694.83,-570.91,-558.14:100
+20	3325237	.	TACACACAC	T	.	PASS	FR=1.0;HP=2;NF=4;NR=2;PP=100.0;SC=TACACACACATACACACACAC;TC=33;TR=6	GT:GL:GQ	1/1:-276.44,-185.04,-177.42:63
+20	3332481	.	TTTTA	T	.	PASS	FR=1.0;HP=3;NF=7;NR=10;PP=100.0;SC=GTTTGTGTTATTTTATTTATT;TC=28;TR=17	GT:GL:GQ	1/1:-276.75,-43.8,-27.83:100
+20	3333166	.	TCA	T	.	PASS	FR=1.0;HP=1;NF=9;NR=10;PP=100.0;SC=TGGCTGTCATTCACATTCCAG;TC=22;TR=19	GT:GL:GQ	1/1:-222.99,-23.7,-9.78:100
+20	3333493	.	T	TTA	.	PASS	FR=1.0;HP=2;NF=6;NR=7;PP=100.0;SC=TTCAAAATATTTATATATATA;TC=27;TR=13	GT:GL:GQ	1/1:-272.96,-96.81,-86.7:65
+20	3336192	.	G	GC	.	PASS	FR=1.0;HP=2;NF=5;NR=10;PP=100.0;SC=CTGCACTCCAGCCTGGGTGAC;TC=18;TR=15	GT:GL:GQ	1/1:-163.64,-31.05,-19.12:100
+20	3338276	.	G	GCTTAT	.	PASS	FR=1.0;HP=1;NF=8;NR=10;PP=100.0;SC=CACCCATCCAGCTTTATCTTT;TC=23;TR=18	GT:GL:GQ	1/1:-329.33,-26.75,-8.74:100
+20	3345587	.	C	CT	.	PASS	FR=1.0;HP=6;NF=1;NR=10;PP=100.0;SC=CCTTCTTTTCCTTTTTTCTTT;TC=27;TR=11	GT:GL:GQ	1/1:-267.74,-155.91,-141.96:100
+20	3346020	.	TTTTATTTA	T	.	PASS	FR=1.0;HP=3;NF=7;NR=6;PP=100.0;SC=TTTGATAACATTTTATTTATT;TC=29;TR=13	GT:GL:GQ	1/1:-347.46,-36.68,-23.65:100
+20	3349612	.	T	TA	.	PASS	FR=1.0;HP=2;NF=8;NR=3;PP=100.0;SC=ACCCCATTTCTCTAAAAATAC;TC=11;TR=11	GT:GL:GQ	1/1:-135.85,-60.43,-52.97:61
+20	3377965	.	G	GTTTTGTT	.	PASS	FR=1.0;HP=8;NF=3;NR=2;PP=100.0;SC=TTTTTGTTTTGTTTTGTTTTT;TC=16;TR=5	GT:GL:GQ	1/1:-157.49,-62.9,-56.59:79
+20	3378366	.	TG	T	.	PASS	FR=1.0;HP=10;NF=6;NR=4;PP=100.0;SC=AGATTTTTTTTGGGGGGGGGG;TC=22;TR=10	GT:GL:GQ	1/1:-84.99,-30.32,-19.67:66
+20	3382249	.	T	TA	.	PASS	FR=1.0;HP=2;NF=7;NR=9;PP=100.0;SC=AATTATTATCTTTCATTCAAT;TC=19;TR=16	GT:GL:GQ	1/1:-178.1,-44.13,-31.76:100
+20	3382515	.	TC	T	.	PASS	FR=1.0;HP=6;NF=2;NR=10;PP=100.0;SC=TGGGGAGGGCTCCCCCGCCCC;TC=19;TR=12	GT:GL:GQ	1/1:-132.42,-42.62,-32.12:88
+20	3398847	.	T	TAC	.	PASS	FR=0.5;HP=2;NF=2;NR=1;PP=82.0;SC=AATAACAACATACACACACAC;TC=26;TR=3	GT:GL:GQ	0/1:-87.09,-56.01,-103.69:100
+20	3418279	.	TACACACACAC	T	.	PASS	FR=0.5;HP=3;NF=2;NR=1;PP=100.0;SC=CACACGAGGGTACACACACAC;TC=17;TR=3	GT:GL:GQ	0/1:-117.7,-66.19,-77.13:50
+20	3419562	.	TACAC	T	.	PASS	FR=0.5;HP=2;NF=2;NR=2;PP=100.0;SC=TCAAAATACATACACACACAC;TC=29;TR=4	GT:GL:GQ	0/1:-141.17,-79.46,-166.16:100
+20	3426771	.	T	TC	.	PASS	FR=1.0;HP=1;NF=13;NR=10;PP=100.0;SC=TTGCAGAAACTGACAAAATAG;TC=25;TR=23	GT:GL:GQ	1/1:-297.92,-207.29,-192.68:100
+20	3439128	.	AT	A	.	PASS	FR=1.0;HP=4;NF=4;NR=3;PP=100.0;SC=TGTCTCAAAAATATATATATA;TC=13;TR=7	GT:GL:GQ	1/1:-127.06,-48.08,-43.43:57
+20	3439712	.	CATTTATTTATTT	CATTTATTT,C	.	PASS	FR=0.5,0.5;HP=1;NF=2,5;NR=1,1;PP=100.0,100.0;SC=AACATAAAATCATTTATTTAT;TC=23;TR=3,6	GT:GL:GQ	1/2:-1.0,-1.0,-1.0:100
+20	3441674	.	G	GA	.	PASS	FR=0.5;HP=7;NF=13;NR=3;PP=100.0;SC=TTCTTATTAGGAAAAAAACCA;TC=23;TR=16	GT:GL:GQ	0/1:-122.74,-20.86,-35.93:68
+20	3456629	.	CA	C	.	PASS	FR=0.5;HP=8;NF=3;NR=5;PP=100.0;SC=TCCTCACTACCAAAAAAAAGA;TC=22;TR=8	GT:GL:GQ	0/1:-62.73,-25.03,-67.91:100
+20	3462307	.	A	ATTC	.	PASS	FR=0.5;HP=2;NF=7;NR=2;PP=100.0;SC=TAAATTTTTAATTAAGTTTTC;TC=17;TR=9	GT:GL:GQ	0/1:-213.54,-117.72,-169.88:100
+20	3465413	.	G	GTTA	.	PASS	FR=0.5;HP=3;NF=4;NR=7;PP=100.0;SC=TATATTTCCAGTTTAGGTCTC;TC=32;TR=11	GT:GL:GQ	0/1:-171.48,-39.39,-198.21:100
+20	3465556	.	AATT	A	.	PASS	FR=0.5;HP=3;NF=3;NR=3;PP=100.0;SC=TGGATTTTAAAATTATTATTA;TC=23;TR=6	GT:GL:GQ	0/1:-128.2,-26.49,-64.94:100
+20	3467027	.	TTTTCC	T	.	PASS	FR=0.5;HP=3;NF=3;NR=10;PP=100.0;SC=GTTGTTTTTCTTTTCCTTTTT;TC=35;TR=13	GT:GL:GQ	0/1:-205.57,-36.22,-212.27:100
+20	3468732	.	AT	A	.	PASS	FR=0.5;HP=1;NF=7;NR=3;PP=100.0;SC=GTTGGCTAACATGTTCCCTGC;TC=24;TR=10	GT:GL:GQ	0/1:-129.57,-23.07,-107.21:100
+20	3472426	.	T	TA	.	PASS	FR=0.5;HP=1;NF=4;NR=5;PP=100.0;SC=CCCCAAAACTTATCTAAGTAT;TC=30;TR=9	GT:GL:GQ	0/1:-164.9,-36.91,-163.8:100
+20	3473769	.	TTGTGTGTGTG	TTGTGTGTG,T	.	PASS	FR=0.5,0.5;HP=2;NF=3,2;NR=1,0;PP=100.0,100.0;SC=GTACGTTTGTTTGTGTGTGTG;TC=10;TR=4,2	GT:GL:GQ	1/2:-1.0,-1.0,-1.0:100
+20	3489906	.	C	CAG	.	PASS	FR=0.5;HP=3;NF=7;NR=5;PP=100.0;SC=TGTAATGAGTCAAATATTGAA;TC=30;TR=12	GT:GL:GQ	0/1:-218.47,-143.39,-285.84:100
+20	3495915	.	T	TG	.	PASS	FR=0.5;HP=1;NF=8;NR=2;PP=100.0;SC=GTGTTACCATTCTAGAGATGA;TC=24;TR=10	GT:GL:GQ	0/1:-170.31,-150.44,-250.52:100
+20	3509359	.	CTAAAA	C	.	PASS	FR=0.5;HP=1;NF=7;NR=9;PP=100.0;SC=CCCCTTGAACCTAAAATAAAA;TC=36;TR=16	GT:GL:GQ	0/1:-259.32,-75.45,-201.38:100
+20	3516100	.	GA	G	.	PASS	FR=0.5;HP=2;NF=4;NR=5;PP=100.0;SC=AACATTACTTGATAACCTTTC;TC=24;TR=9	GT:GL:GQ	0/1:-89.87,-17.09,-134.48:100
+20	3517232	.	T	TA	.	PASS	FR=0.5;HP=4;NF=5;NR=10;PP=100.0;SC=TTTATTCATTTAAAAGCAACA;TC=33;TR=15	GT:GL:GQ	0/1:-148.46,-23.56,-134.17:100
+20	3518135	.	TTG	T	.	PASS	FR=0.5;HP=1;NF=2;NR=7;PP=100.0;SC=TATTTTTTTCTTGTTTTTTTT;TC=24;TR=9	GT:GL:GQ	0/1:-164.48,-76.63,-118.93:100
+20	3520111	.	TGAGAAACAGAAA	T	.	PASS	FR=0.5;HP=1;NF=6;NR=4;PP=100.0;SC=GTCAAATACTTGAGAAACAGA;TC=30;TR=10	GT:GL:GQ	0/1:-291.42,-56.72,-205.51:100
+20	3533082	.	C	CTA	.	PASS	FR=0.5;HP=6;NF=5;NR=7;PP=100.0;SC=CCAGATGTCCCCCCCAGTTAA;TC=28;TR=12	GT:GL:GQ	0/1:-172.54,-164.36,-281.23:100
+20	3536203	.	CA	C	.	PASS	FR=0.5;HP=5;NF=5;NR=1;PP=100.0;SC=TGGTAGACCACAAAACAAAAT;TC=20;TR=6	GT:GL:GQ	0/1:-93.07,-22.5,-78.34:100
+20	3549166	.	A	AT	.	PASS	FR=0.5;HP=7;NF=6;NR=5;PP=100.0;SC=ACTCAAAAAAAATATATTTCA;TC=27;TR=11	GT:GL:GQ	0/1:-132.66,-26.81,-119.92:100
+20	3550790	.	AT	A	.	PASS	FR=0.5;HP=10;NF=9;NR=3;PP=100.0;SC=AATTGTCTCAATTTTTTTTTT;TC=36;TR=12	GT:GL:GQ	0/1:-95.8,-54.46,-109.39:100
+20	3554405	.	TTTTA	T	.	PASS	FR=0.5;HP=3;NF=5;NR=3;PP=100.0;SC=TTTTATTTTATTTTATTTATT;TC=28;TR=8	GT:GL:GQ	0/1:-169.52,-76.02,-126.65:100
+20	3557342	.	G	GTCTATCTATCTATCTATCTA,GTCTGTCTGTCTATCTA	.	PASS	FR=0.5,0.5;HP=2;NF=0,1;NR=2,1;PP=100.0,100.0;SC=CTGTCTGTCTGTCTATCTATC;TC=14;TR=2,2	GT:GL:GQ	1/2:-1.0,-1.0,-1.0:100
+20	3577359	.	AACTTT	A	.	PASS	FR=0.5;HP=3;NF=8;NR=4;PP=100.0;SC=GTTCTCTTAAAACTTTACTTT;TC=28;TR=12	GT:GL:GQ	0/1:-187.21,-26.31,-190.0:100
+20	3587084	.	A	ACT	.	PASS	FR=0.5;HP=2;NF=5;NR=2;PP=100.0;SC=TTCTCTCTTCACTGTTTCCTG;TC=27;TR=7	GT:GL:GQ	0/1:-175.39,-93.87,-225.08:100
+20	3587106	.	TGTG	T	.	PASS	FR=0.5;HP=1;NF=4;NR=3;PP=100.0;SC=ATGTGGGACTTGTGGTGCCAC;TC=26;TR=7	GT:GL:GQ	0/1:-197.29,-142.58,-281.02:100
+20	3597598	.	AT	A	.	PASS	FR=0.5;HP=5;NF=5;NR=7;PP=29.0;SC=CAAGGATCGCATTTTTATCCC;TC=39;TR=12	GT:GL:GQ	0/1:-225.54,-208.64,-370.51:76
+20	3599489	.	G	GGTT	.	PASS	FR=0.5;HP=1;NF=6;NR=4;PP=100.0;SC=TGGTGGTGGTGGTTTTGTTTC;TC=28;TR=10	GT:GL:GQ	0/1:-173.69,-38.78,-110.57:100
+20	3601166	.	T	TAC	.	PASS	FR=0.5;HP=1;NF=1;NR=5;PP=100.0;SC=GTACTGGGATTAGGCGTGAGC;TC=23;TR=6	GT:GL:GQ	0/1:-99.56,-38.65,-114.14:100
+20	3607044	.	TAAAAA	T	.	PASS	FR=0.5;HP=5;NF=6;NR=1;PP=100.0;SC=TTTTCTCTCTTAAAAAGAAAA;TC=23;TR=7	GT:GL:GQ	0/1:-96.17,-24.47,-167.72:100
+20	3608928	.	A	AAG	.	PASS	FR=0.5;HP=2;NF=6;NR=2;PP=100.0;SC=GAAAACTAGAAAGAAACTTCT;TC=32;TR=8	GT:GL:GQ	0/1:-96.19,-24.02,-201.47:100
+20	3610589	.	G	GT	.	PASS	FR=0.5;HP=7;NF=7;NR=8;PP=100.0;SC=ATCATTCTGAGTTTTTTTATT;TC=36;TR=15	GT:GL:GQ	0/1:-148.28,-61.67,-123.51:100
+20	3612124	.	A	AC	.	PASS	FR=0.5;HP=1;NF=5;NR=1;PP=100.0;SC=GTCTGTTGAGACTGTGTCCTA;TC=17;TR=6	GT:GL:GQ	0/1:-86.01,-27.19,-97.39:100
+20	3627840	.	C	CA	.	PASS	FR=0.5;HP=6;NF=4;NR=7;PP=100.0;SC=CTCAACTGTGCAAAAAACAAA;TC=27;TR=11	GT:GL:GQ	0/1:-99.01,-25.59,-91.79:100
+20	3627925	.	A	ATTAAC	.	PASS	FR=0.5;HP=2;NF=2;NR=9;PP=100.0;SC=AGTCAGATGAATTGTTTTCAT;TC=29;TR=11	GT:GL:GQ	0/1:-210.42,-38.37,-176.36:100
+20	3635158	.	A	AT	.	PASS	FR=0.5;HP=2;NF=8;NR=5;PP=100.0;SC=CAAGAAAGCCATAGACCGGAA;TC=23;TR=13	GT:GL:GQ	0/1:-191.76,-111.36,-148.51:100
+20	3642221	.	TTC	T	.	PASS	FR=1.0;HP=2;NF=12;NR=3;PP=100.0;SC=TCGCCACCATTTCTCCAGAAC;TC=20;TR=15	GT:GL:GQ	1/1:-312.08,-172.82,-161.67:43
+20	3643129	.	TC	T	.	PASS	FR=1.0;HP=9;NF=4;NR=4;PP=100.0;SC=CGGGGTGGTATCCCCCCCCCA;TC=20;TR=8	GT:GL:GQ	1/1:-89.01,-45.99,-37.4:71
+20	3645120	.	AAAAC	A	.	PASS	FR=1.0;HP=5;NF=1;NR=4;PP=100.0;SC=TTTTTTTTAAAAAACAAACAA;TC=18;TR=5	GT:GL:GQ	1/1:-88.2,-13.8,-7.58:77
+20	3650540	.	A	ACACCACC	.	PASS	FR=1.0;HP=1;NF=3;NR=4;PP=100.0;SC=CCAGGCTCTGACAGCAGCCTG;TC=12;TR=7	GT:GL:GQ	1/1:-183.63,-21.64,-13.12:68
+20	3664603	.	AG	A	.	PASS	FR=1.0;HP=6;NF=3;NR=9;PP=100.0;SC=TTCTGTAGACAGGGGGGTCTC;TC=16;TR=12	GT:GL:GQ	1/1:-110.02,-26.49,-16.31:85
+20	3667748	.	C	CG	.	PASS	FR=1.0;HP=2;NF=12;NR=5;PP=100.0;SC=AAAGTTCACCCGCCCCCAACT;TC=24;TR=17	GT:GL:GQ	1/1:-221.42,-44.79,-28.21:100
+20	3677095	.	T	TGCTG	.	PASS	FR=1.0;HP=1;NF=4;NR=13;PP=100.0;SC=GGAGGCCTTCTGCTGGCTGGA;TC=22;TR=17	GT:GL:GQ	1/1:-297.16,-58.83,-44.05:100
+20	3685444	.	A	AT	.	PASS	FR=1.0;HP=7;NF=6;NR=4;PP=100.0;SC=TTGTTTTTTAATTTTTTTGTA;TC=15;TR=10	GT:GL:GQ	1/1:-93.4,-15.67,-6.68:75
+20	3699376	.	AAAAT	A	.	PASS	FR=1.0;HP=5;NF=4;NR=2;PP=100.0;SC=CAAAAAATAAAAAATAAATAA;TC=21;TR=6	GT:GL:GQ	1/1:-124.16,-19.34,-11.28:66
+20	3700024	.	TTTAC	T	.	PASS	FR=0.5;HP=2;NF=3;NR=4;PP=100.0;SC=TATTTATTTATTTACTTACTT;TC=22;TR=7	GT:GL:GQ	0/1:-142.54,-24.82,-34.29:44
+20	3702676	.	C	CT	.	PASS	FR=1.0;HP=9;NF=9;NR=6;PP=100.0;SC=ATATGTTGAACTTTTTTTTTA;TC=20;TR=15	GT:GL:GQ	1/1:-102.25,-23.87,-11.51:100
+20	3703373	.	GAATA	G	.	PASS	FR=1.0;HP=3;NF=3;NR=4;PP=100.0;SC=TATACATGGAGAATAAATAAA;TC=24;TR=7	GT:GL:GQ	1/1:-129.84,-26.73,-19.11:63
+20	3705235	.	G	GGAAA	.	PASS	FR=1.0;HP=3;NF=3;NR=2;PP=100.0;SC=AAGAAAGAAAGGAAAGAAATA;TC=24;TR=5	GT:GL:GQ	1/1:-319.51,-157.83,-145.36:98
+20	3717704	.	AAAATAAATAAATAAAT	AAAATAAATAAAT,A	.	PASS	FR=0.5,0.5;HP=4;NF=1,0;NR=1,2;PP=100.0,55.0;SC=CTCTGCCTCAAAAATAAATAA;TC=12;TR=2,2	GT:GL:GQ	1/2:-1.0,-1.0,-1.0:100
+20	3719488	.	AGT	A	.	PASS	FR=0.5;HP=2;NF=4;NR=6;PP=100.0;SC=TCTGTGAGTGAGTGTGTGTGT;TC=28;TR=10	GT:GL:GQ	0/1:-149.53,-25.54,-102.21:100
+20	3736407	.	CCCCCAGCCCAGTGG	C	.	PASS	FR=0.5;HP=4;NF=3;NR=1;PP=100.0;SC=AGCTGATCGACCCCCAGCCCA;TC=22;TR=4	GT:GL:GQ	0/1:-177.03,-114.74,-207.47:100
+20	3740620	.	GCA	G	.	PASS	FR=1.0;HP=1;NF=4;NR=6;PP=100.0;SC=ACTCACACATGCACACACACA;TC=17;TR=10	GT:GL:GQ	1/1:-154.32,-36.11,-25.75:86
+20	3751453	.	G	GT	.	PASS	FR=1.0;HP=6;NF=1;NR=1;PP=100.0;SC=CAAACACACGGTTTTTTGTTT;TC=25;TR=2	GT:GL:GQ	1/1:-234.3,-199.49,-191.92:62
+20	3752464	.	A	AACAC,AACACAC	.	PASS	FR=0.5,0.5;HP=3;NF=4,3;NR=3,3;PP=100.0,100.0;SC=AAAAAGAGAAAACACACACAC;TC=29;TR=7,6	GT:GL:GQ	1/2:-1.0,-1.0,-1.0:100
+20	3755004	.	G	GACA	.	PASS	FR=1.0;HP=2;NF=1;NR=7;PP=100.0;SC=GACAGAGTGAGACATCTCATA;TC=13;TR=8	GT:GL:GQ	1/1:-134.63,-25.28,-17.61:63
+20	3768789	.	A	AAAAG	.	PASS	FR=0.5;HP=8;NF=4;NR=3;PP=100.0;SC=ATCTCAAAAAAAAAGAAAGAA;TC=28;TR=7	GT:GL:GQ	0/1:-141.47,-38.74,-119.72:100
+20	3770324	.	T	TAATAATA	.	PASS	FR=0.5;HP=8;NF=1;NR=2;PP=29.0;SC=GGCCAAAAAATAATAATAAAT;TC=11;TR=3	GT:GL:GQ	0/1:-67.44,-43.02,-52.14:42
+20	3774219	.	AATTTT	A	.	PASS	FR=0.5;HP=1;NF=2;NR=3;PP=100.0;SC=GGTTTTAGAGAATTTTATTTT;TC=20;TR=5	GT:GL:GQ	0/1:-126.4,-91.22,-154.58:100
+20	3775162	.	GTT	G	.	PASS	FR=0.5;HP=10;NF=3;NR=6;PP=100.0;SC=TCTCGGGGCAGTTTTTTTTTT;TC=26;TR=9	GT:GL:GQ	0/1:-103.9,-68.26,-117.09:100
+20	3776005	.	C	CA	.	PASS	FR=0.5;HP=8;NF=1;NR=4;PP=23.0;SC=GACTCCATCCCAAAAAAAACA;TC=14;TR=5	GT:GL:GQ	0/1:-145.51,-129.15,-148.62:73
+20	3776021	.	AAAC	A	.	PASS	FR=0.5;HP=3;NF=3;NR=1;PP=100.0;SC=AAACAAAACAAAACAAAAAGA;TC=21;TR=4	GT:GL:GQ	0/1:-163.41,-119.44,-232.96:100
+20	3780857	.	T	TGGACTGGAGACCTGGTGCTAG	.	PASS	FR=0.5;HP=6;NF=4;NR=1;PP=100.0;SC=TACTCCCCCCTGGACTGGGGG;TC=10;TR=5	GT:GL:GQ	0/1:-153.98,-19.16,-34.72:70
+20	3786892	.	C	CT	.	PASS	FR=1.0;HP=4;NF=10;NR=2;PP=100.0;SC=CTTGTCCCTTCTTCTCCCAAT;TC=16;TR=12	GT:GL:GQ	1/1:-171.33,-64.44,-53.38:92
+20	3787614	.	CAT	C	.	PASS	FR=1.0;HP=2;NF=11;NR=13;PP=100.0;SC=AGTGCACACACATGTCAGGCA;TC=30;TR=24	GT:GL:GQ	1/1:-451.43,-312.17,-297.5:100
+20	3789927	.	C	CCCG	.	PASS	FR=1.0;HP=2;NF=2;NR=10;PP=100.0;SC=AGTTACCACGCGCTCTCTTTC;TC=17;TR=12	GT:GL:GQ	1/1:-241.99,-120.76,-110.7:78
+20	3790246	.	ATATAT	A	.	PASS	FR=1.0;HP=8;NF=5;NR=2;PP=92.0;SC=TCAAAAAAAAATATATATATA;TC=14;TR=7	GT:GL:GQ	1/1:-198.37,-176.0,-172.1:52
+20	3795480	.	AGGCGTGAGCCACCGCGCCC	A	.	PASS	FR=0.5;HP=2;NF=2;NR=2;PP=100.0;SC=CTGGGATTACAGGCGTGAGCC;TC=12;TR=4	GT:GL:GQ	0/1:-109.14,-46.17,-99.46:100
+20	3824585	.	TTTTAC	T	.	PASS	FR=1.0;HP=3;NF=18;NR=4;PP=100.0;SC=AGATGATTTATTTTACTTTAT;TC=28;TR=22	GT:GL:GQ	1/1:-337.35,-36.39,-16.32:100
+20	3843259	.	A	AT	.	PASS	FR=0.5;HP=10;NF=3;NR=7;PP=100.0;SC=AGTTTTCCAAATTTTTTTTTT;TC=31;TR=10	GT:GL:GQ	0/1:-80.23,-37.02,-73.45:100
+20	3859483	.	TCACACACACA	TCA,T	.	PASS	FR=0.5,0.5;HP=1;NF=1,2;NR=1,1;PP=100.0,85.0;SC=TGAGACTCTGTCACACACACA;TC=21;TR=2,3	GT:GL:GQ	1/2:-1.0,-1.0,-1.0:100
+20	3860757	.	AAAAC	A	.	PASS	FR=0.5;HP=4;NF=5;NR=2;PP=100.0;SC=GTCTCTACTAAAAACAAACAA;TC=18;TR=7	GT:GL:GQ	0/1:-108.81,-21.22,-75.5:100
+20	3860858	.	GC	G	.	PASS	FR=0.5;HP=1;NF=5;NR=1;PP=100.0;SC=AACCCAGGAGGCGGAGCTTGT;TC=16;TR=6	GT:GL:GQ	0/1:-84.65,-31.03,-99.29:100
+20	3865910	.	A	AGGC	.	PASS	FR=0.5;HP=3;NF=8;NR=4;PP=100.0;SC=TCTGTCACCCAGGCTCAAGTT;TC=27;TR=12	GT:GL:GQ	0/1:-249.42,-106.14,-180.19:100
+20	3873092	.	TTTTA	T	.	PASS	FR=1.0;HP=5;NF=6;NR=8;PP=100.0;SC=ACTAAATCTTTTTTATTTATT;TC=25;TR=14	GT:GL:GQ	1/1:-225.87,-50.85,-37.99:100
+20	3879882	.	AGT	A	.	PASS	FR=1.0;HP=1;NF=4;NR=4;PP=100.0;SC=GCAGTGATGTAGTGTAGGCTC;TC=17;TR=8	GT:GL:GQ	1/1:-213.63,-128.83,-121.45:61
+20	3882311	.	TTTTG	T	.	PASS	FR=1.0;HP=3;NF=15;NR=11;PP=100.0;SC=AAGTCAGTACTTTTGTTTATT;TC=29;TR=26	GT:GL:GQ	1/1:-341.87,-21.25,-0.46:100
+20	3883619	.	GACACACACACACACAC	G	.	PASS	FR=0.5013;HP=2;NF=4;NR=1;PP=100.0;SC=GATGTGTATAGACACACACAC;TC=14;TR=5	GT:GL:GQ	0/1:-204.43,-28.1,-33.39:25
+20	3885810	.	GACTGCACC	G	.	PASS	FR=1.0;HP=1;NF=4;NR=7;PP=100.0;SC=CATCGCTTGTGACTGCACCAC;TC=19;TR=11	GT:GL:GQ	1/1:-301.58,-43.69,-32.0:95
+20	3899973	.	T	TTGA	.	PASS	FR=1.0;HP=3;NF=18;NR=6;PP=100.0;SC=AGAAAAACCCTTGAACATTCC;TC=30;TR=24	GT:GL:GQ	1/1:-376.13,-29.44,-7.6:100
+20	3900864	.	T	TA	.	PASS	FR=1.0;HP=10;NF=11;NR=11;PP=100.0;SC=AAGTTAACCTTAAAAAAAAAA;TC=30;TR=22	GT:GL:GQ	1/1:-160.94,-53.86,-35.6:100
+20	3929292	.	G	GA	.	PASS	FR=1.0;HP=1;NF=16;NR=6;PP=100.0;SC=TACATACCAGGATAACTGTTG;TC=29;TR=22	GT:GL:GQ	1/1:-330.17,-190.24,-173.09:100
+20	3930806	.	T	TGACTGG	.	PASS	FR=1.0;HP=2;NF=7;NR=14;PP=100.0;SC=CCTTGTATAGTGATGAATGTG;TC=26;TR=21	GT:GL:GQ	1/1:-450.24,-61.65,-40.95:100
+20	3945171	.	A	AT	.	PASS	FR=1.0;HP=10;NF=7;NR=12;PP=100.0;SC=TTTTCAAGTAATTTTTTTTTT;TC=29;TR=19	GT:GL:GQ	1/1:-126.38,-32.45,-22.97:79
+20	3956227	.	C	CA	.	PASS	FR=1.0;HP=5;NF=12;NR=13;PP=100.0;SC=ATTGTGTTCTCAAAAAGATAT;TC=28;TR=25	GT:GL:GQ	1/1:-249.31,-33.1,-13.35:100
+20	3965697	.	AACC	A	.	PASS	FR=1.0;HP=1;NF=9;NR=9;PP=100.0;SC=GAACAACAACAACCACAACAA;TC=26;TR=18	GT:GL:GQ	1/1:-461.94,-340.35,-326.48:100
+20	3971557	.	G	GTTCCATGATAACAT	.	PASS	FR=1.0;HP=2;NF=12;NR=8;PP=100.0;SC=ATTTGGCACAGTTCCATGATA;TC=27;TR=20	GT:GL:GQ	1/1:-553.38,-41.98,-23.08:100
+20	3990695	.	CACAAACAA	C	.	PASS	FR=1.0;HP=1;NF=6;NR=4;PP=100.0;SC=GAGACCCTGTCACAAACAAAC;TC=23;TR=10	GT:GL:GQ	1/1:-176.37,-39.86,-31.94:65
+20	3995386	.	GCACACA	G	.	PASS	FR=1.0;HP=2;NF=1;NR=1;PP=100.0;SC=ACTTGAATGCGCACACACACA;TC=18;TR=2	GT:GL:GQ	1/1:-95.82,-46.66,-41.67:61
+20	4008931	.	C	CTCTT	.	PASS	FR=1.0;HP=2;NF=1;NR=4;PP=100.0;SC=TCTCATCTCTCTGTCTTTCTC;TC=9;TR=5	GT:GL:GQ	1/1:-127.43,-46.42,-40.22:77
+20	4021562	.	C	CGA	.	PASS	FR=1.0;HP=2;NF=8;NR=2;PP=100.0;SC=GAAGAGAAAGCGAGAGAGAGA;TC=21;TR=10	GT:GL:GQ	1/1:-216.37,-85.41,-73.73:98
+20	4025709	.	TGA	T	.	PASS	FR=1.0;HP=2;NF=12;NR=9;PP=100.0;SC=AAATACATAATGAGAGAGAGA;TC=26;TR=21	GT:GL:GQ	1/1:-247.4,-21.57,-4.6:100
+20	4035810	.	T	TGTTTGTATTACA	.	PASS	FR=1.0;HP=2;NF=10;NR=4;PP=100.0;SC=TAGCTGGGCATGGTGGCGGGT;TC=15;TR=14	GT:GL:GQ	1/1:-361.94,-174.62,-163.57:92
+20	4042278	.	A	AT	.	PASS	FR=1.0;HP=2;NF=7;NR=15;PP=100.0;SC=AAACACATAAATCTCTCTCTC;TC=29;TR=22	GT:GL:GQ	1/1:-269.48,-66.17,-47.18:100
+20	4044153	.	C	CA	.	PASS	FR=1.0;HP=6;NF=8;NR=10;PP=100.0;SC=GCCCCAGGGACGGGGGGCTGG;TC=21;TR=18	GT:GL:GQ	1/1:-167.11,-27.75,-13.35:100
+20	4048870	.	AGAGTTATCTTGCCTGAG	A	.	PASS	FR=0.5;HP=4;NF=9;NR=5;PP=100.0;SC=CACGTGCCCCAGAGTTATCTT;TC=24;TR=14	GT:GL:GQ	1/0:-626.63,-331.02,-449.96:74
+20	4050067	.	A	AT	.	PASS	FR=1.0;HP=8;NF=14;NR=11;PP=100.0;SC=TAAGTTTTAAATTTTTTTTGT;TC=36;TR=25	GT:GL:GQ	1/1:-400.71,-316.84,-301.94:100
+20	4052527	.	A	AT	.	PASS	FR=1.0;HP=1;NF=15;NR=9;PP=100.0;SC=CTAAGCATGAAGTGGTCTCAG;TC=27;TR=24	GT:GL:GQ	1/1:-335.51,-240.21,-229.69:88
+20	4057207	.	G	GT	.	PASS	FR=1.0;HP=3;NF=17;NR=11;PP=100.0;SC=TAGATTATTTGGTTTTTTTTT;TC=40;TR=28	GT:GL:GQ	1/1:-398.27,-278.49,-261.61:100
+20	4057861	.	T	TTTCC	.	PASS	FR=1.0;HP=4;NF=8;NR=13;PP=100.0;SC=CTGATGATTTTTATGTTTTCT;TC=33;TR=21	GT:GL:GQ	1/1:-430.04,-131.81,-113.85:100
+20	4058335	.	T	TATTA	.	PASS	FR=1.0;HP=2;NF=14;NR=5;PP=100.0;SC=TTAATATGTTTATTATACATA;TC=19;TR=19	GT:GL:GQ	1/1:-424.99,-369.88,-364.34:69
+20	4060198	.	CTCTT	C	.	PASS	FR=0.5;HP=3;NF=8;NR=6;PP=100.0;SC=TTCTATTGTTCTCTTTGTTTT;TC=37;TR=14	GT:GL:GQ	0/1:-273.47,-128.98,-306.0:100
+20	4060592	.	C	CTTTA	.	PASS	FR=0.5;HP=3;NF=4;NR=8;PP=100.0;SC=ATAATTTTTGCTTTATTTATT;TC=31;TR=12	GT:GL:GQ	0/1:-163.9,-38.86,-129.26:100
+20	4070170	.	GTA	G	.	PASS	FR=0.5;HP=2;NF=3;NR=2;PP=100.0;SC=GTGTGTGTGTGTATATATATA;TC=25;TR=5	GT:GL:GQ	0/1:-276.88,-237.9,-267.79:100
+20	4070252	.	A	ATGTATATATG	.	PASS	FR=1.0;HP=2;NF=3;NR=1;PP=100.0;SC=GTGTGTATATATGTATATATG;TC=16;TR=4	GT:GL:GQ	1/1:-231.61,-30.38,-18.61:81
+20	4070382	.	ATATGTGTGTGTG	A	.	PASS	FR=1.0;HP=2;NF=1;NR=2;PP=100.0;SC=ATGTGTATATATATGTGTGTG;TC=25;TR=3	GT:GL:GQ	1/1:-347.8,-231.66,-223.35:51
+20	4070396	.	GTGTGTGTGTGTGTATATATATATATA	G	.	PASS	FR=0.5;HP=2;NF=4;NR=4;PP=100.0;SC=GTGTGTGTGTGTGTGTGTGTG;TC=18;TR=8	GT:GL:GQ	1/0:-384.34,-235.32,-225.8:62
+20	4071341	.	CA	C	.	PASS	FR=0.5026;HP=9;NF=5;NR=5;PP=100.0;SC=CTGATTATGGCAAAAAAAAAC;TC=20;TR=10	GT:GL:GQ	0/1:-155.5,-119.13,-123.71:22
+20	4071895	.	G	GT	.	PASS	FR=0.5;HP=8;NF=3;NR=3;PP=72.0;SC=TGGGACCTTTGTTTTTGCAAA;TC=22;TR=6	GT:GL:GQ	0/1:-127.95,-100.32,-170.75:100
+20	4074739	.	G	GA	.	PASS	FR=0.5;HP=9;NF=2;NR=4;PP=75.0;SC=ACTACATCTCGAAAAAAAAAG;TC=16;TR=6	GT:GL:GQ	0/1:-104.75,-76.46,-99.49:100
+20	4077346	.	ATATTAT	A	.	PASS	FR=0.5;HP=1;NF=2;NR=2;PP=100.0;SC=TATGAGGACAATATTATTATT;TC=23;TR=4	GT:GL:GQ	0/1:-62.56,-10.62,-98.18:100
+20	4092195	.	G	GTCAGCCAGAGAGGCTC	.	PASS	FR=1.0;HP=1;NF=7;NR=5;PP=100.0;SC=AGGTAAGACAGTCAGCCAGAG;TC=21;TR=12	GT:GL:GQ	1/1:-408.88,-45.59,-29.88:100
+20	4092421	.	A	AT	.	PASS	FR=0.5;HP=4;NF=5;NR=6;PP=100.0;SC=CTGGCAGCAGATTTTCCCTTA;TC=31;TR=11	GT:GL:GQ	0/1:-137.54,-52.61,-154.29:100
+20	4095639	.	T	TATAC	.	PASS	FR=0.5;HP=2;NF=3;NR=6;PP=100.0;SC=TATATATATATACACACACAT;TC=30;TR=9	GT:GL:GQ	0/1:-239.61,-67.33,-166.02:100
+20	4096614	.	T	TG	.	PASS	FR=0.5;HP=1;NF=3;NR=8;PP=100.0;SC=TTTGATGGCTTGTGAAGCCCA;TC=42;TR=11	GT:GL:GQ	0/1:-166.13,-48.49,-243.23:100
+20	4099234	.	C	CTCT	.	PASS	FR=1.0;HP=1;NF=2;NR=7;PP=100.0;SC=CTTCTTCTTCCTCTTCTTCCT;TC=17;TR=9	GT:GL:GQ	1/1:-213.81,-121.18,-113.85:91
+20	4106279	.	C	CA	.	PASS	FR=1.0;HP=4;NF=9;NR=14;PP=100.0;SC=ATGATCCACCCCCTTGGCCTC;TC=27;TR=23	GT:GL:GQ	1/1:-261.7,-33.57,-14.72:100
+20	4106498	.	AC	A	.	PASS	FR=0.5;HP=3;NF=4;NR=6;PP=100.0;SC=ACCCGCCACCACGTCAAGCTA;TC=17;TR=10	GT:GL:GQ	0/1:-151.03,-63.2,-86.55:100
+20	4107003	.	T	TCTAA	.	PASS	FR=0.5;HP=2;NF=4;NR=9;PP=100.0;SC=TGGAGGTAACTCTAGGACATA;TC=28;TR=13	GT:GL:GQ	0/1:-216.14,-60.6,-196.15:100
+20	4108348	.	A	AC	.	PASS	FR=1.0;HP=3;NF=9;NR=6;PP=100.0;SC=TTCTATGGAAAAGAGCAGTCA;TC=22;TR=15	GT:GL:GQ	1/1:-263.65,-164.58,-152.76:96
+20	4111438	.	CA	C	.	PASS	FR=1.0;HP=2;NF=13;NR=9;PP=100.0;SC=GGTGATCACACAGGGGCATGG;TC=27;TR=22	GT:GL:GQ	1/1:-393.14,-310.63,-301.96:68
+20	4111530	.	T	TG	.	PASS	FR=1.0;HP=1;NF=13;NR=14;PP=100.0;SC=CATCAAAACTTGCAGAAGTAT;TC=30;TR=27	GT:GL:GQ	1/1:-576.34,-531.28,-526.81:55
+20	4112367	.	TA	T	.	PASS	FR=0.5;HP=2;NF=7;NR=2;PP=100.0;SC=AGACTTTAGTTAATAATAATA;TC=25;TR=9	GT:GL:GQ	0/1:-105.53,-48.17,-185.05:100
+20	4124037	.	TACAC	TAC,T	.	PASS	FR=0.5,0.5;HP=2;NF=0,1;NR=6,6;PP=100.0,100.0;SC=TGTATGTGTATACACACACAC;TC=29;TR=6,7	GT:GL:GQ	1/2:-1.0,-1.0,-1.0:100
+20	4165244	.	C	CAG	.	PASS	FR=0.5;HP=3;NF=9;NR=7;PP=100.0;SC=TAAAACTCAACAGTTATATTT;TC=28;TR=16	GT:GL:GQ	0/1:-164.36,-34.34,-133.84:100
+20	4189405	.	A	AGTGTTCT	.	PASS	FR=1.0;HP=1;NF=8;NR=19;PP=100.0;SC=TGATCACAGAAGTGTTGAATG;TC=31;TR=27	GT:GL:GQ	1/1:-510.65,-52.94,-31.94:100
+20	4193006	.	T	TA	.	PASS	FR=1.0;HP=9;NF=5;NR=11;PP=100.0;SC=TGTGTTTGATTAAAAAAAAAT;TC=25;TR=16	GT:GL:GQ	1/1:-189.06,-113.86,-103.2:89
+20	4204545	.	CAACAGGTTT	C	.	PASS	FR=0.5;HP=3;NF=5;NR=5;PP=100.0;SC=TTTCAATTTACAACAGGTTTA;TC=29;TR=10	GT:GL:GQ	0/1:-264.93,-66.16,-208.86:100
+20	4210072	.	T	TA	.	PASS	FR=0.5;HP=5;NF=7;NR=3;PP=100.0;SC=GGAAGGAAGATGGGGGCGAGT;TC=33;TR=10	GT:GL:GQ	0/1:-169.78,-122.55,-232.56:100
+20	4211685	.	T	TTTTCTTTC	.	PASS	FR=1.0;HP=4;NF=3;NR=1;PP=100.0;SC=CTTTCTTTCTTTTTCTTTCTT;TC=17;TR=4	GT:GL:GQ	1/1:-163.69,-62.85,-59.76:50
+20	4222606	.	TG	T,AG	.	PASS	FR=0.5,0.5;HP=2;NF=14,3;NR=8,0;PP=72.0,7.0;SC=CAGCACAGCCTGATGGCTCTG;TC=29;TR=22,3	GT:GL:GQ	1/2:-1.0,-1.0,-1.0:41
+20	4223993	.	CG	C	.	PASS	FR=1.0;HP=4;NF=10;NR=1;PP=100.0;SC=CTGGGCTCCTCGGGGCATCCG;TC=14;TR=11	GT:GL:GQ	1/1:-180.73,-119.68,-111.91:64
+20	4255571	.	TGAAA	T	.	PASS	FR=1.0;HP=1;NF=5;NR=4;PP=100.0;SC=AGGTATGCTCTGAAAGGAAGA;TC=15;TR=9	GT:GL:GQ	1/1:-155.75,-66.2,-58.38:79
+20	4260218	.	C	CA	.	PASS	FR=0.5;HP=3;NF=1;NR=9;PP=100.0;SC=CTGGTCTCCCCAGCATCTAGT;TC=27;TR=10	GT:GL:GQ	0/1:-138.73,-38.26,-150.01:100
+20	4280077	.	G	GTGA	.	PASS	FR=0.5;HP=1;NF=2;NR=4;PP=100.0;SC=GATGTCTTTGGTGATGATGAT;TC=23;TR=6	GT:GL:GQ	0/1:-118.58,-26.45,-67.22:100
+20	4300671	.	G	GT	.	PASS	FR=1.0;HP=9;NF=9;NR=7;PP=100.0;SC=TATTTTTTAAGTTTTTTTTTC;TC=22;TR=16	GT:GL:GQ	1/1:-112.49,-30.96,-17.5:100
+20	4305010	.	C	CCTGT	.	PASS	FR=1.0;HP=1;NF=9;NR=14;PP=100.0;SC=AGGTTTGGCTCCTGTCTGACA;TC=27;TR=23	GT:GL:GQ	1/1:-478.98,-124.12,-105.32:100
+20	4306264	.	GT	G	.	PASS	FR=0.5;HP=3;NF=7;NR=4;PP=100.0;SC=ACAATATAAGGTTTACTTCAA;TC=24;TR=11	GT:GL:GQ	0/1:-115.0,-27.63,-111.62:100
+20	4310291	.	T	TC	.	PASS	FR=1.0;HP=1;NF=20;NR=9;PP=100.0;SC=CTCCTACGTGTCATGCCAGCT;TC=32;TR=29	GT:GL:GQ	1/1:-333.81,-66.33,-44.4:100
+20	4310977	.	GC	G	.	PASS	FR=0.5;HP=1;NF=14;NR=6;PP=100.0;SC=CCTGAAACTGGCGTAATTTAT;TC=41;TR=20	GT:GL:GQ	0/1:-231.9,-39.91,-159.66:100
+20	4321071	.	A	AG	.	PASS	FR=0.5;HP=5;NF=3;NR=2;PP=100.0;SC=AAGTCAAATCAGGGGGAGGAA;TC=19;TR=5	GT:GL:GQ	0/1:-50.11,-15.88,-71.26:100
+20	4322091	.	CA	C	.	PASS	FR=0.5;HP=1;NF=11;NR=7;PP=100.0;SC=GCCGTGTGTCCAGCCAAAACT;TC=33;TR=18	GT:GL:GQ	0/1:-210.17,-46.06,-156.61:100
+20	4329185	.	TC	T	.	PASS	FR=0.5;HP=1;NF=8;NR=2;PP=100.0;SC=AATTCTAGGTTCTTTCTCTCA;TC=28;TR=10	GT:GL:GQ	0/1:-148.46,-71.81,-182.2:100
+20	4330761	.	GGTGTGTGT	G	.	PASS	FR=1.0;HP=3;NF=1;NR=3;PP=100.0;SC=TAATTCATGGGGTGTGTGTGT;TC=30;TR=4	GT:GL:GQ	1/1:-224.07,-44.24,-35.58:72
+20	4332044	.	TG	T	.	PASS	FR=1.0;HP=6;NF=5;NR=2;PP=57.0;SC=TTTGTTTTTTTGTTTTTTTTT;TC=24;TR=7	GT:GL:GQ	1/1:-226.96,-113.86,-100.61:42
+20	4343821	.	TA	T	.	PASS	FR=0.5;HP=8;NF=5;NR=8;PP=100.0;SC=CATTTTTTTTTAAAATTTTTG;TC=35;TR=13	GT:GL:GQ	1/0:-274.8,-111.87,-90.41:100
+20	4349378	.	A	AT	.	PASS	FR=0.5;HP=3;NF=11;NR=7;PP=100.0;SC=TTTTGAAGGCATTTCCAGGGT;TC=27;TR=18	GT:GL:GQ	0/1:-181.47,-28.52,-69.89:100
+20	4366637	.	AAAAC	A	.	PASS	FR=1.0;HP=3;NF=8;NR=10;PP=100.0;SC=AAAACAAAACAAAACAAACAA;TC=29;TR=18	GT:GL:GQ	1/1:-255.42,-38.69,-23.59:100
+20	4378952	.	A	AAAC	.	PASS	FR=1.0;HP=2;NF=5;NR=8;PP=100.0;SC=CAAAACAAACAAACAACAACA;TC=26;TR=13	GT:GL:GQ	1/1:-242.03,-34.58,-19.38:100
+20	4380979	.	CACAT	C	.	PASS	FR=1.0;HP=2;NF=6;NR=6;PP=100.0;SC=CACACACACACACATACAAGC;TC=29;TR=12	GT:GL:GQ	1/1:-310.99,-41.83,-21.18:100
+20	4381267	.	T	TGTGTATTGTGGA	.	PASS	FR=1.0;HP=2;NF=4;NR=9;PP=100.0;SC=GACAGCCTCCTTCAACAAAAA;TC=23;TR=13	GT:GL:GQ	1/1:-573.3,-462.6,-447.82:96
+20	4381268	.	TC	T	.	PASS	FR=1.0;HP=1;NF=4;NR=9;PP=100.0;SC=ACAGCCTCCTTCAACAAAAAA;TC=27;TR=13	GT:GL:GQ	1/1:-573.3,-567.48,-566.42:96
+20	4384878	.	TAGAC	T	.	PASS	FR=0.5;HP=4;NF=7;NR=6;PP=100.0;SC=ATGGAAGAAATAGACAGAGAG;TC=32;TR=13	GT:GL:GQ	0/1:-215.18,-58.15,-186.03:100
+20	4390996	.	ACT	A	.	PASS	FR=0.5;HP=1;NF=5;NR=4;PP=100.0;SC=AACACTCGAGACTCTCCAGCT;TC=25;TR=9	GT:GL:GQ	0/1:-160.6,-43.63,-115.25:100
+20	4392384	.	T	TTG	.	PASS	FR=0.5;HP=1;NF=2;NR=1;PP=100.0;SC=GGGAATATAGTTGTGTGTGTG;TC=26;TR=3	GT:GL:GQ	0/1:-141.31,-92.22,-156.97:100
+20	4403198	.	CGT	CGTGT,C	.	PASS	FR=0.5,0.5;HP=2;NF=3,3;NR=2,0;PP=100.0,91.0;SC=TGTGTGTGTGCGTGTGTGTGT;TC=16;TR=5,3	GT:GL:GQ	1/2:-1.0,-1.0,-1.0:100
+20	4418283	.	TCC	T	.	PASS	FR=1.0;HP=5;NF=9;NR=17;PP=100.0;SC=TGAAAAATGCTCCCCAGGTTT;TC=26;TR=26	GT:GL:GQ	1/1:-235.22,-17.92,0.0:100
+20	4422138	.	A	AAGAGGCAAGGCTTCCCCACATGCTCAGAATGG,G	.	PASS	FR=0.5,0.5;HP=1;NF=2,3;NR=0,5;PP=100.0,87.0;SC=CTACAGAAAGATGATGGAGGT;TC=14;TR=2,8	GT:GL:GQ	1/2:-1.0,-1.0,-1.0:23
+20	4422142	.	T	TG	.	PASS	FR=1.0;HP=2;NF=8;NR=6;PP=100.0;SC=AGAAAGATGATGGAGGTACTA;TC=19;TR=14	GT:GL:GQ	1/1:-319.37,-289.62,-286.77:23
+20	4427312	.	A	AGCTTCTAT	.	PASS	FR=0.5;HP=2;NF=1;NR=1;PP=100.0;SC=TGTATAATAGAGTCCAGAGTC;TC=11;TR=2	GT:GL:GQ	1/0:-513.43,-441.06,-437.62:42
+20	4431651	.	TA	T	.	PASS	FR=0.5;HP=5;NF=9;NR=13;PP=100.0;SC=TCTAGACCCTTAAAAATAACA;TC=34;TR=22	GT:GL:GQ	0/1:-196.04,-30.01,-107.67:100
+20	4438168	.	T	TTACACAAATGTAACCTATGTAACAA	.	PASS	FR=0.5;HP=1;NF=2;NR=3;PP=100.0;SC=CCTGCACATGTACCCTTGAAC;TC=16;TR=5	GT:GL:GQ	0/1:-418.07,-256.53,-367.22:100
+20	4439599	.	GT	G	.	PASS	FR=0.5;HP=2;NF=11;NR=12;PP=100.0;SC=TGTGGGGAGAGTTAGCAAGAG;TC=36;TR=23	GT:GL:GQ	0/1:-329.81,-228.22,-300.4:100
+20	4442338	.	CTTTATTTTATTTTAT	CTTTATTTTAT,C	.	PASS	FR=0.5,0.5;HP=3;NF=2,1;NR=0,3;PP=100.0,100.0;SC=AAGTATCTAACTTTATTTTAT;TC=21;TR=2,4	GT:GL:GQ	1/2:-1.0,-1.0,-1.0:100
+20	4445547	.	T	TAA	.	PASS	FR=1.0;HP=1;NF=18;NR=22;PP=100.0;SC=TGTTTCCAGTTGTTATACTTT;TC=39;TR=40	GT:GL:GQ	1/1:-459.22,-244.89,-221.84:100
+20	4452980	.	TACAC	T	.	PASS	FR=1.0;HP=2;NF=1;NR=2;PP=100.0;SC=TTAATTCTTATACACACACAC;TC=21;TR=3	GT:GL:GQ	1/1:-75.87,-32.41,-30.31:43
+20	4460649	.	G	GA	.	PASS	FR=0.5;HP=9;NF=5;NR=8;PP=100.0;SC=TTTCCTCGGAGAAAAAAAACA;TC=39;TR=13	GT:GL:GQ	0/1:-191.57,-119.31,-159.65:100
+20	4462152	.	GGTCAATGTTATAAACTTTGC	G	.	PASS	FR=0.5;HP=2;NF=6;NR=5;PP=100.0;SC=CTACTTCTTGGGTCAATGTTA;TC=18;TR=11	GT:GL:GQ	1/0:-501.72,-174.1,-171.31:67
+20	4462516	.	T	TTC	.	PASS	FR=0.5;HP=1;NF=16;NR=1;PP=100.0;SC=GGGTTTAAAGTTCTCTAATGA;TC=41;TR=17	GT:GL:GQ	0/1:-181.56,-38.08,-223.18:100
+20	4462799	.	C	CTT	.	PASS	FR=0.5;HP=1;NF=1;NR=1;PP=100.0;SC=TCTTCTTCGTCCTTTTTTTTT;TC=36;TR=2	GT:GL:GQ	0/1:-520.7,-504.74,-499.84:81
+20	4465737	.	TG	T	.	PASS	FR=1.0;HP=2;NF=9;NR=18;PP=100.0;SC=CTCCTTGACATGGACTGAGAA;TC=27;TR=27	GT:GL:GQ	1/1:-258.03,-34.15,-15.14:100
+20	4468340	.	TA	T	.	PASS	FR=0.5;HP=10;NF=5;NR=2;PP=57.0;SC=ATATATATATTAAAAAAAAAA;TC=21;TR=7	GT:GL:GQ	0/1:-41.89,-18.73,-52.45:100
+20	4469569	.	C	CT	.	PASS	FR=0.5;HP=4;NF=3;NR=6;PP=100.0;SC=CAAGTAAAGACTTTTGATTGT;TC=23;TR=9	GT:GL:GQ	0/1:-113.7,-24.95,-84.55:100
+20	4474613	.	GA	G	.	PASS	FR=0.5;HP=8;NF=4;NR=6;PP=100.0;SC=ATTAGGAACAGAAAAAAATTA;TC=37;TR=10	GT:GL:GQ	0/1:-311.99,-245.02,-353.92:100
+20	4474629	.	A	AAAT	.	PASS	FR=0.5;HP=9;NF=11;NR=5;PP=100.0;SC=AATTAAAAAAAAAATATACAC;TC=32;TR=16	GT:GL:GQ	0/1:-322.36,-111.27,-187.62:100
+20	4475883	.	AT	A	.	PASS	FR=0.5;HP=5;NF=1;NR=3;PP=100.0;SC=AAATATATATATTTTAATATA;TC=14;TR=4	GT:GL:GQ	0/1:-74.26,-40.07,-92.44:100
+20	4481373	.	A	AG	.	PASS	FR=1.0;HP=1;NF=5;NR=6;PP=100.0;SC=TCTTTTTTCAAGTTTTTAGCT;TC=13;TR=11	GT:GL:GQ	1/1:-84.43,-9.42,-0.46:74
+20	4484587	.	T	TA	.	PASS	FR=0.5;HP=9;NF=4;NR=9;PP=100.0;SC=TCTCTGATTTTAAAAAAAAAG;TC=46;TR=13	GT:GL:GQ	0/1:-163.36,-92.55,-141.98:100
+20	4487527	.	TG	T	.	PASS	FR=0.5006;HP=5;NF=8;NR=7;PP=100.0;SC=TACTAGGGGCTGGGGGCAGGG;TC=34;TR=15	GT:GL:GQ	0/1:-421.09,-350.88,-356.92:29
+20	4492336	.	C	CA	.	PASS	FR=1.0;HP=1;NF=11;NR=14;PP=100.0;SC=ACATTCTTGCCACCTTTGGTA;TC=27;TR=25	GT:GL:GQ	1/1:-281.59,-90.33,-72.03:100
+20	4493592	.	C	CG	.	PASS	FR=1.0;HP=2;NF=20;NR=17;PP=100.0;SC=GCATTTTGGACATCTCACCCT;TC=39;TR=37	GT:GL:GQ	1/1:-454.89,-182.56,-157.87:100
+20	4497462	.	TTA	T	.	PASS	FR=0.5;HP=2;NF=2;NR=2;PP=88.0;SC=TAAATCAACTTTATATATATA;TC=14;TR=4	GT:GL:GQ	1/0:-149.41,-117.69,-112.45:46
+20	4500613	.	G	GC	.	PASS	FR=1.0;HP=2;NF=12;NR=13;PP=100.0;SC=ATGCCCAAGGGTGTCCCAGAG;TC=29;TR=25	GT:GL:GQ	1/1:-293.02,-49.83,-29.64:100
+20	4502874	.	CT	C	.	PASS	FR=1.0;HP=4;NF=11;NR=7;PP=100.0;SC=TACAGCCCTTCTTGGGAGCCC;TC=24;TR=18	GT:GL:GQ	1/1:-204.97,-36.44,-20.43:100
+20	4512447	.	AAAACAAAC	AAAAC,A	.	PASS	FR=0.5,0.5;HP=3;NF=3,4;NR=0,1;PP=100.0,100.0;SC=ACTCCATCTCAAAACAAACAA;TC=20;TR=3,5	GT:GL:GQ	1/2:-1.0,-1.0,-1.0:100
+20	4519983	.	GA	G	.	PASS	FR=0.5;HP=3;NF=7;NR=13;PP=100.0;SC=TCCAAACTAAGACAGGTATTA;TC=36;TR=20	GT:GL:GQ	0/1:-201.76,-27.24,-148.43:100
+20	4524299	.	AGTGTGT	A	.	PASS	FR=0.5;HP=3;NF=2;NR=1;PP=100.0;SC=TCTGTGCTTTAGTGTGTGTGT;TC=28;TR=3	GT:GL:GQ	0/1:-144.55,-75.64,-138.78:100
+20	4530940	.	CTT	C	.	PASS	FR=0.5002;HP=6;NF=2;NR=9;PP=80.0;SC=TTCTTTCTTTCTTTCTCTCTC;TC=25;TR=11	GT:GL:GQ	0/1:-323.77,-294.9,-301.87:33
+20	4541935	.	A	AGAG	.	PASS	FR=0.5;HP=2;NF=8;NR=4;PP=100.0;SC=GTGGCAGATTAGAGGAGACAT;TC=32;TR=12	GT:GL:GQ	0/1:-211.5,-48.19,-198.54:100
+20	4547067	.	G	GA	.	PASS	FR=0.5116;HP=10;NF=5;NR=1;PP=100.0;SC=TATAGAGAGAGAAAAAAAAAC;TC=18;TR=6	GT:GL:GQ	0/1:-156.12,-119.31,-122.4:16
+20	4553580	.	GT	G	.	PASS	FR=0.5;HP=10;NF=1;NR=1;PP=71.0;SC=TTTTGTTTTTGTTTTTGTTTT;TC=17;TR=2	GT:GL:GQ	1/0:-197.42,-152.57,-154.01:100
+20	4553925	.	T	TC	.	PASS	FR=1.0;HP=1;NF=7;NR=5;PP=100.0;SC=CGGCCCCTCTTCACTTTTAAG;TC=16;TR=12	GT:GL:GQ	1/1:-135.25,-18.29,-7.82:87
+20	4560578	.	C	CCTTA	.	PASS	FR=1.0;HP=1;NF=11;NR=12;PP=100.0;SC=ATGTTATATACCTTTTAGAGA;TC=32;TR=23	GT:GL:GQ	1/1:-416.23,-42.65,-19.11:100
+20	4566007	.	G	GC	.	PASS	FR=0.5;HP=1;NF=9;NR=3;PP=100.0;SC=AGCTGGGGCTGACTCATCTGA;TC=27;TR=12	GT:GL:GQ	0/1:-150.18,-87.47,-213.89:100
+20	4572622	.	T	TA	.	PASS	FR=0.5;HP=1;NF=5;NR=4;PP=100.0;SC=AAAGGGGTGCTAGGAATTCCA;TC=21;TR=9	GT:GL:GQ	0/1:-105.47,-33.77,-107.56:100
+20	4580659	.	ATTG	A	.	PASS	FR=0.5;HP=3;NF=9;NR=11;PP=100.0;SC=AATAATTTATATTGTTATTAT;TC=41;TR=20	GT:GL:GQ	0/1:-343.69,-136.17,-313.1:100
+20	4580822	.	AAC	A	.	PASS	FR=0.5;HP=1;NF=7;NR=7;PP=100.0;SC=TATCTTACATAACAGTGTATC;TC=27;TR=14	GT:GL:GQ	0/1:-159.59,-31.47,-183.78:100
+20	4589159	.	TAC	T	.	PASS	FR=0.5;HP=1;NF=5;NR=5;PP=100.0;SC=CACACACACGTACACACACAC;TC=25;TR=10	GT:GL:GQ	0/1:-134.67,-33.29,-88.29:100
+20	4590266	.	T	TCTGGCC	.	PASS	FR=0.5;HP=3;NF=3;NR=4;PP=100.0;SC=GCTGGCAGCCTCTGGCCCTGG;TC=20;TR=7	GT:GL:GQ	0/1:-180.62,-56.12,-103.3:100
+20	4613873	.	T	TATA	.	PASS	FR=0.5;HP=3;NF=6;NR=2;PP=100.0;SC=CTCTTTCTTTTATAATAATAA;TC=26;TR=8	GT:GL:GQ	0/1:-121.23,-16.51,-65.45:100
+20	4616453	.	G	GAGTAGA	.	PASS	FR=0.5;HP=3;NF=5;NR=7;PP=100.0;SC=CACAGAGTAGGGGTTCAATAA;TC=22;TR=12	GT:GL:GQ	0/1:-211.56,-25.38,-113.94:100
+20	4617264	.	G	GAGAA	.	PASS	FR=0.5;HP=2;NF=3;NR=1;PP=100.0;SC=GAAAGCAAGAGAGAAAGAAGA;TC=22;TR=4	GT:GL:GQ	0/1:-126.22,-46.88,-138.67:100
+20	4617272	.	AG	A	.	PASS	FR=0.5;HP=1;NF=1;NR=3;PP=20.0;SC=GAGAGAAAGAAGAGAAGAGAA;TC=22;TR=4	GT:GL:GQ	0/1:-134.04,-119.35,-223.11:66
+20	4617303	.	G	GAGGA	.	PASS	FR=0.5;HP=2;NF=2;NR=3;PP=100.0;SC=GGGAGGGAGAGAGGAAGGAAG;TC=19;TR=5	GT:GL:GQ	0/1:-154.78,-90.63,-135.29:100
+20	4655424	.	G	GA	.	PASS	FR=0.5;HP=8;NF=13;NR=4;PP=100.0;SC=GTTCTTTAGAGAAAAAAAGAT;TC=30;TR=17	GT:GL:GQ	0/1:-186.33,-114.25,-152.75:100
+20	4668235	.	AT	A	.	PASS	FR=0.5;HP=10;NF=12;NR=5;PP=100.0;SC=TAGGAAATAGATTTTTTTTTT;TC=33;TR=17	GT:GL:GQ	0/1:-91.71,-31.87,-60.05:100
+20	4673330	.	C	CTTT	.	PASS	FR=0.5;HP=5;NF=6;NR=8;PP=100.0;SC=TGAAGAAAATCTTTTCTTCCT;TC=24;TR=14	GT:GL:GQ	0/1:-183.35,-23.94,-71.42:100
+20	4684173	.	TG	T	.	PASS	FR=0.5;HP=1;NF=5;NR=1;PP=100.0;SC=CAGGCACAGTTGCTCACGCCT;TC=17;TR=6	GT:GL:GQ	0/1:-81.87,-25.35,-94.89:100
+20	4691383	.	CA	C	.	PASS	FR=1.0;HP=2;NF=14;NR=12;PP=100.0;SC=TGGGGTCATCCAAGCATGGCT;TC=29;TR=26	GT:GL:GQ	1/1:-259.65,-39.57,-19.54:100
+20	4692075	.	C	CA	.	PASS	FR=0.5;HP=9;NF=5;NR=3;PP=95.0;SC=AGTAATTGGACAAAAAAAACA;TC=26;TR=8	GT:GL:GQ	0/1:-67.83,-34.9,-96.78:100
+20	4704696	.	A	ATG	.	PASS	FR=0.5;HP=2;NF=5;NR=3;PP=100.0;SC=ATATGTATATATGTGTGTGTA;TC=30;TR=8	GT:GL:GQ	0/1:-168.25,-105.64,-257.19:100
+20	4706654	.	GTGCCATCA	G	.	PASS	FR=1.0;HP=2;NF=7;NR=4;PP=100.0;SC=TTACAGGTGTGTGCCATCATG;TC=17;TR=11	GT:GL:GQ	1/1:-236.92,-30.58,-21.39:67
+20	4727159	.	C	CATTTTATTTT	.	PASS	FR=1.0;HP=1;NF=2;NR=4;PP=100.0;SC=ATAGCATTTGCATTTTATTTT;TC=27;TR=6	GT:GL:GQ	1/1:-510.26,-402.24,-397.15:63
+20	4735780	.	T	TTTCTTTCTTTCTTTCTTTCTTTCTTTC,C	.	PASS	FR=0.5,0.5;HP=3;NF=0,5;NR=3,16;PP=100.0,100.0;SC=CCTTTCTTTCTTTTCTTTCTT;TC=27;TR=3,21	GT:GL:GQ	1/2:-1.0,-1.0,-1.0:100
+20	4737530	.	T	TA	.	PASS	FR=1.0;HP=1;NF=11;NR=14;PP=100.0;SC=TTAAATGTATTGAGGCTCATT;TC=26;TR=25	GT:GL:GQ	1/1:-245.38,-21.97,-3.97:100
+20	4737701	.	T	TTGA	.	PASS	FR=1.0;HP=1;NF=12;NR=7;PP=100.0;SC=ACTTTCTGTCTTGACCTGTCT;TC=19;TR=19	GT:GL:GQ	1/1:-227.02,-18.69,-5.52:100
+20	4741155	.	G	GGA	.	PASS	FR=1.0;HP=1;NF=5;NR=11;PP=100.0;SC=AACACACCAGGTGTGTCAAAA;TC=22;TR=16	GT:GL:GQ	1/1:-218.41,-31.08,-15.98:100
+20	4743693	.	G	GTTAA	.	PASS	FR=1.0;HP=2;NF=6;NR=7;PP=100.0;SC=AGCCCAGGAGGTTAAGTCTGC;TC=16;TR=13	GT:GL:GQ	1/1:-225.23,-59.89,-50.88:75
+20	4743774	.	A	AAAATAAAT	.	PASS	FR=1.0;HP=5;NF=4;NR=3;PP=100.0;SC=AAAAGGAGAAAAAATAAATAA;TC=16;TR=7	GT:GL:GQ	1/1:-319.93,-209.77,-203.54:78
+20	4748739	.	A	ACTAT	.	PASS	FR=1.0;HP=1;NF=12;NR=7;PP=100.0;SC=TCTTTCACCAACTATTTTCAC;TC=23;TR=19	GT:GL:GQ	1/1:-501.66,-334.66,-319.16:100
+20	4761877	.	T	TG	.	PASS	FR=0.5;HP=8;NF=1;NR=4;PP=100.0;SC=ACAGATATTTTGGGGGGGGCA;TC=23;TR=5	GT:GL:GQ	0/1:-97.23,-58.4,-90.76:100
+20	4768475	.	A	AAGGGACT	.	PASS	FR=1.0;HP=2;NF=7;NR=8;PP=100.0;SC=CAGGGGTCCAAAGGCACCTTA;TC=23;TR=15	GT:GL:GQ	1/1:-372.13,-36.56,-17.94:100
+20	4783543	.	CATAT	C	.	PASS	FR=0.5;HP=2;NF=1;NR=2;PP=100.0;SC=TATATATATACATATATATAT;TC=23;TR=3	GT:GL:GQ	0/1:-115.71,-29.18,-62.14:100
+20	4794428	.	CGT	C	.	PASS	FR=0.5;HP=3;NF=3;NR=2;PP=100.0;SC=CAGTGTGTGGCGTGTGTGTGT;TC=28;TR=5	GT:GL:GQ	0/1:-119.46,-68.74,-106.78:100
+20	4796034	.	TACC	T	.	PASS	FR=0.5;HP=1;NF=7;NR=5;PP=100.0;SC=TATCTGAGGCTACCACCACCC;TC=27;TR=12	GT:GL:GQ	0/1:-222.6,-98.55,-189.77:100
+20	4802486	.	G	GCC	.	PASS	FR=0.5;HP=2;NF=5;NR=4;PP=100.0;SC=GACTGCCACAGCCTAGGCATC;TC=24;TR=9	GT:GL:GQ	0/1:-135.36,-38.11,-126.44:100
+20	4803072	.	CT	C	.	PASS	FR=0.5;HP=1;NF=1;NR=5;PP=100.0;SC=GTGCACGCAGCTGTTGAGAGG;TC=15;TR=6	GT:GL:GQ	0/1:-82.81,-37.85,-91.55:100
+20	4823348	.	AT	A	.	PASS	FR=1.0;HP=8;NF=17;NR=7;PP=100.0;SC=AATATTTTCCATTTTTTTTGA;TC=32;TR=24	GT:GL:GQ	1/1:-298.64,-180.3,-160.97:100
+20	4850186	.	GAC	G	.	PASS	FR=0.5;HP=1;NF=3;NR=2;PP=49.0;SC=ATCTCCAAATGACACACACAC;TC=34;TR=5	GT:GL:GQ	0/1:-186.75,-165.14,-349.63:96
+20	4880132	.	AGCTCAATGCCTTCTGC	A	.	PASS	FR=1.0;HP=1;NF=3;NR=4;PP=100.0;SC=CAAACGGCGCAGCTCAATGCC;TC=17;TR=7	GT:GL:GQ	1/1:-255.52,-55.88,-53.61:44
+20	4883735	.	G	GGA	.	PASS	FR=1.0;HP=1;NF=13;NR=18;PP=100.0;SC=GGTGAAAAGAGTAATTCTAAA;TC=34;TR=31	GT:GL:GQ	1/1:-361.9,-346.05,-342.67:97
+20	4886527	.	GA	G	.	PASS	FR=0.5;HP=3;NF=5;NR=6;PP=100.0;SC=ACTCTACTGAGAAGAACAGAT;TC=19;TR=11	GT:GL:GQ	0/1:-166.67,-86.72,-123.24:100
+20	4892485	.	AATTT	A	.	PASS	FR=0.5;HP=1;NF=2;NR=7;PP=100.0;SC=TTTATTTATGAATTTATTTAT;TC=34;TR=9	GT:GL:GQ	0/1:-148.07,-23.75,-121.86:100
+20	4922648	.	CTAAACTAACT	C	.	PASS	FR=0.5;HP=5;NF=1;NR=10;PP=100.0;SC=TCTATATTTTCTAAACTAACT;TC=33;TR=11	GT:GL:GQ	0/1:-284.06,-37.14,-228.78:100
+20	4942899	.	C	CA	.	PASS	FR=0.5;HP=7;NF=4;NR=3;PP=100.0;SC=ACCCCCGCCCCAAAAAAACAG;TC=28;TR=7	GT:GL:GQ	0/1:-99.42,-46.78,-95.55:100
+20	4947451	.	G	GTTTGA	.	PASS	FR=0.5;HP=4;NF=4;NR=4;PP=100.0;SC=ACTTTTGATAGTTTTACACAC;TC=18;TR=8	GT:GL:GQ	0/1:-283.81,-185.62,-217.52:100
+20	4947582	.	TG	T	.	PASS	FR=0.5;HP=4;NF=9;NR=4;PP=100.0;SC=GATTACATGATGGGGAGCAGG;TC=22;TR=13	GT:GL:GQ	0/1:-139.84,-55.72,-119.49:100
+20	4947775	.	T	TA	.	PASS	FR=0.5;HP=6;NF=8;NR=4;PP=100.0;SC=GAAATCTAAATAAACACAGGG;TC=24;TR=12	GT:GL:GQ	0/1:-128.76,-21.0,-91.02:100
+20	4949766	.	CTT	C	.	PASS	FR=0.5;HP=3;NF=8;NR=4;PP=100.0;SC=GAGTTTCCCTCTTGTTACCCA;TC=25;TR=12	GT:GL:GQ	0/1:-147.72,-32.95,-112.56:100
+20	4954109	.	G	GGACTT	.	PASS	FR=0.5;HP=2;NF=4;NR=8;PP=100.0;SC=ATGGCTGGAAGGACTTAACTA;TC=30;TR=12	GT:GL:GQ	0/1:-203.74,-23.32,-169.48:100
+20	4965192	.	C	CT	.	PASS	FR=0.5;HP=2;NF=5;NR=3;PP=100.0;SC=GAGCAAGACTCTGTCTCAAAA;TC=26;TR=8	GT:GL:GQ	0/1:-134.47,-59.87,-111.38:100
+20	4969015	.	AG	A	.	PASS	FR=1.0;HP=8;NF=4;NR=5;PP=100.0;SC=TGGGAAACCGAGGGGGGGCCA;TC=12;TR=9	GT:GL:GQ	1/1:-67.79,-12.99,-5.52:61
+20	4970270	.	C	CTTAATAT	.	PASS	FR=0.5;HP=1;NF=4;NR=1;PP=100.0;SC=TGCAGTGAGCCATGATCTTGC;TC=22;TR=5	GT:GL:GQ	0/1:-247.44,-164.56,-281.24:100
+20	4972366	.	TCA	TCACACA,T	.	PASS	FR=0.5,0.5;HP=2;NF=1,0;NR=1,2;PP=100.0,49.0;SC=AGACTCCGTTTCACACACACA;TC=15;TR=2,2	GT:GL:GQ	1/2:-1.0,-1.0,-1.0:97
+20	4979252	.	ATGAGG	A	.	PASS	FR=0.5;HP=1;NF=5;NR=2;PP=100.0;SC=AAATGAATTAATGAGGTGAGG;TC=24;TR=7	GT:GL:GQ	0/1:-146.48,-63.04,-172.38:100
+20	4985646	.	A	AAAAT	.	PASS	FR=0.5;HP=4;NF=2;NR=1;PP=100.0;SC=CTCCGTCTCAAAAATAAATAA;TC=22;TR=3	GT:GL:GQ	0/1:-69.57,-20.73,-73.7:100
+20	4987193	.	T	TTTTA	.	PASS	FR=1.0;HP=3;NF=5;NR=7;PP=100.0;SC=GTAAAAGCCATTTTATTTATT;TC=33;TR=12	GT:GL:GQ	1/1:-198.93,-19.38,-8.29:93
+20	5003823	.	C	CA	.	PASS	FR=1.0;HP=2;NF=2;NR=1;PP=69.0;SC=CTCAGCCTCCCAGTAGCTGGG;TC=5;TR=3	GT:GL:GQ	1/1:-35.46,-12.52,-9.15:55
+20	5006924	.	GTATATATATGTGTA	G	.	PASS	FR=0.5;HP=2;NF=3;NR=1;PP=100.0;SC=ATGTATATATGTATATATATG;TC=17;TR=4	GT:GL:GQ	0/1:-102.23,-17.74,-69.04:100
+20	5019857	.	C	CT	.	PASS	FR=1.0;HP=1;NF=5;NR=1;PP=100.0;SC=CACCCCTGCACTCCAGCCTGG;TC=10;TR=6	GT:GL:GQ	1/1:-78.84,-38.79,-34.59:51
+20	5021323	.	T	TC	.	PASS	FR=1.0;HP=10;NF=8;NR=5;PP=100.0;SC=CTTTTTTTTTTTCAATGGCAA;TC=18;TR=13	GT:GL:GQ	1/1:-164.3,-19.64,-6.44:82
+20	5021471	.	G	GA	.	PASS	FR=1.0;HP=1;NF=11;NR=14;PP=100.0;SC=ACATAATGCTGGTTAAAGAGG;TC=33;TR=25	GT:GL:GQ	1/1:-406.51,-306.39,-293.23:100
+20	5033824	.	G	GTATA	.	PASS	FR=1.0;HP=8;NF=6;NR=6;PP=100.0;SC=CCAAAAAAAAGTATATATATA;TC=19;TR=12	GT:GL:GQ	1/1:-293.31,-92.78,-80.65:100
+20	5034013	.	GGCAT	G	.	PASS	FR=1.0;HP=1;NF=8;NR=10;PP=100.0;SC=ATGACAGCCAGGCATGGGGGC;TC=24;TR=18	GT:GL:GQ	1/1:-275.61,-34.13,-17.26:100
+20	5044461	.	A	AAATTTTTAT	.	PASS	FR=1.0;HP=4;NF=13;NR=12;PP=100.0;SC=GTTAACTTGGAAAAATTTCTA;TC=29;TR=25	GT:GL:GQ	1/1:-660.59,-158.53,-137.22:100
+20	5058110	.	G	GGGGGCT	.	PASS	FR=1.0;HP=2;NF=6;NR=6;PP=100.0;SC=CAACATTTTGGGAGGTGGGTG;TC=14;TR=12	GT:GL:GQ	1/1:-206.1,-87.92,-82.33:69
+20	5062840	.	AAAG	A	.	PASS	FR=1.0;HP=4;NF=12;NR=4;PP=100.0;SC=AATTTTTTAAAAAGAAGAAGA;TC=21;TR=16	GT:GL:GQ	1/1:-217.23,-55.74,-43.97:99
+20	5079870	.	AAATAAATAAATCAATC	A	.	PASS	FR=0.5;HP=2;NF=4;NR=6;PP=100.0;SC=ATAAATAAATAAATAAATAAA;TC=24;TR=10	GT:GL:GQ	1/0:-419.18,-202.82,-208.38:27
+20	5094493	.	T	TA	.	PASS	FR=1.0;HP=1;NF=7;NR=16;PP=100.0;SC=AAAATGAACTTACTACTGGAC;TC=26;TR=23	GT:GL:GQ	1/1:-300.98,-148.38,-131.87:100
+20	5097837	.	AC	A	.	PASS	FR=1.0;HP=1;NF=15;NR=5;PP=100.0;SC=TAAAGGTTATACGCCTAACTT;TC=25;TR=20	GT:GL:GQ	1/1:-243.65,-32.97,-15.65:100
+20	5100990	.	AAG	A	.	PASS	FR=1.0;HP=1;NF=10;NR=6;PP=100.0;SC=TTGCAGCCTGAAGAGAGTACA;TC=18;TR=16	GT:GL:GQ	1/1:-198.64,-18.46,-5.29:100
+20	5105482	.	C	CATTTTAGG	.	PASS	FR=1.0;HP=2;NF=6;NR=11;PP=100.0;SC=GTTCAGACCACATGTTATCCA;TC=22;TR=17	GT:GL:GQ	1/1:-471.45,-181.5,-164.38:100
+20	5118209	.	A	AT	.	PASS	FR=0.5;HP=8;NF=3;NR=2;PP=100.0;SC=TTTAAGTCTTATTTTTTCAAA;TC=16;TR=5	GT:GL:GQ	0/1:-55.51,-21.15,-68.35:100
+20	5145860	.	A	AC	.	PASS	FR=0.5;HP=5;NF=6;NR=2;PP=100.0;SC=TTTTTTGGAAACCCCCGTATT;TC=29;TR=8	GT:GL:GQ	0/1:-81.29,-28.9,-130.37:100
+20	5150896	.	G	GC	.	PASS	FR=0.5;HP=3;NF=2;NR=5;PP=100.0;SC=ACCTCGCTGTGCCCAGAGGAG;TC=17;TR=7	GT:GL:GQ	0/1:-79.22,-17.13,-53.13:100
+20	5156258	.	CCT	C	.	PASS	FR=0.5093;HP=2;NF=6;NR=6;PP=100.0;SC=ATGGTGAAACCCTGTCTCTAC;TC=16;TR=12	GT:GL:GQ	0/1:-101.9,-26.13,-29.44:17
+20	5156432	.	AAAAC	A	.	PASS	FR=0.5;HP=3;NF=5;NR=3;PP=100.0;SC=ACTCCATCTCAAAACAAACAA;TC=23;TR=8	GT:GL:GQ	0/1:-98.71,-15.69,-97.38:100
+20	5173014	.	C	CA	.	PASS	FR=1.0;HP=2;NF=8;NR=13;PP=100.0;SC=GAAGGGGGGTCTAGGAAGCCG;TC=22;TR=21	GT:GL:GQ	1/1:-250.84,-61.97,-47.15:100
+20	5178081	.	C	CCT	.	PASS	FR=0.5;HP=1;NF=5;NR=6;PP=100.0;SC=AGAGGTCAGCCGTGTCTGCCC;TC=22;TR=11	GT:GL:GQ	0/1:-193.35,-72.27,-102.13:100
+20	5181165	.	C	CA	.	PASS	FR=0.5;HP=8;NF=1;NR=6;PP=91.0;SC=TTAGACACAACAAAAAAGAGA;TC=22;TR=7	GT:GL:GQ	0/1:-61.45,-29.38,-90.08:100
+20	5187401	.	A	AC	.	PASS	FR=0.5;HP=6;NF=4;NR=3;PP=100.0;SC=TTTTCATGTCACCCCCGAGGT;TC=17;TR=7	GT:GL:GQ	0/1:-139.03,-104.99,-121.15:73
+20	5187831	.	G	GAATC	.	PASS	FR=0.5;HP=5;NF=5;NR=3;PP=100.0;SC=TGAAAGGAAAGAAGCATGTTT;TC=22;TR=8	GT:GL:GQ	0/1:-144.73,-26.29,-132.63:100
+20	5192127	.	A	AATT	.	PASS	FR=0.5;HP=3;NF=2;NR=7;PP=100.0;SC=AATGTGTTAAAATTATATAAG;TC=32;TR=9	GT:GL:GQ	0/1:-228.5,-119.37,-283.27:100
+20	5212592	.	TA	T	.	PASS	FR=1.0;HP=9;NF=20;NR=10;PP=100.0;SC=CCTGCCATATTAAAAAAAAAC;TC=39;TR=30	GT:GL:GQ	1/1:-191.03,-64.37,-41.93:100
+20	5223122	.	TA	T	.	PASS	FR=0.5;HP=2;NF=2;NR=4;PP=100.0;SC=GAATAAGACCTAGTATTTGCT;TC=11;TR=6	GT:GL:GQ	0/1:-63.8,-25.4,-69.29:100
+20	5234499	.	AAC	A	.	PASS	FR=0.5;HP=1;NF=1;NR=1;PP=25.0;SC=GTGCCTTCACAACACACACAC;TC=26;TR=2	GT:GL:GQ	0/1:-75.14,-59.09,-216.84:72
+20	5236854	.	A	AATTAT	.	PASS	FR=1.0;HP=1;NF=17;NR=9;PP=100.0;SC=AAAAGACATGAATTATCATTA;TC=29;TR=26	GT:GL:GQ	1/1:-427.74,-26.55,-5.07:100
+20	5240296	.	CT	C	.	PASS	FR=0.5;HP=1;NF=7;NR=6;PP=100.0;SC=AATTGATACACTACAATGGCC;TC=39;TR=13	GT:GL:GQ	0/1:-220.75,-129.27,-297.86:100
+20	5242946	.	A	AC	.	PASS	FR=0.5;HP=3;NF=6;NR=5;PP=100.0;SC=AGCTGGAACCACTGTTGTGGA;TC=22;TR=11	GT:GL:GQ	0/1:-141.29,-37.29,-109.65:100
+20	5246342	.	GC	G	.	PASS	FR=0.5;HP=7;NF=6;NR=8;PP=100.0;SC=AACCGAGACAGCCCCCCCTTT;TC=21;TR=14	GT:GL:GQ	0/1:-107.74,-25.34,-35.96:49
+20	5247531	.	T	TTGCAGTAGAGAAACTCCC	.	PASS	FR=0.5;HP=1;NF=3;NR=5;PP=100.0;SC=TTGCAGGTTATTGCAGTAGAG;TC=31;TR=8	GT:GL:GQ	0/1:-296.8,-101.13,-189.63:100
+20	5251109	.	ACTCTCTCTCTCTCTCTCT	A	.	PASS	FR=0.5;HP=1;NF=3;NR=2;PP=37.0;SC=CATCCAGTGTACTCTCTCTCT;TC=27;TR=5	GT:GL:GQ	0/1:-322.05,-299.54,-356.33:100
+20	5251154	.	G	GTGTA	.	PASS	FR=0.5;HP=2;NF=1;NR=4;PP=100.0;SC=CTCTGTGTGTGTGTATGTGTG;TC=19;TR=5	GT:GL:GQ	0/1:-297.98,-257.24,-280.47:100
+20	5256228	.	GAAAAAC	G	.	PASS	FR=0.5;HP=5;NF=8;NR=3;PP=100.0;SC=CAAATGTTTTGAAAAACAAAA;TC=29;TR=11	GT:GL:GQ	0/1:-159.47,-21.9,-134.38:100
+20	5256836	.	CT	C	.	PASS	FR=0.5;HP=10;NF=4;NR=7;PP=58.0;SC=TCTCAACTCACTTTTTTTTTT;TC=23;TR=11	GT:GL:GQ	0/1:-145.3,-121.72,-154.45:100
+20	5260631	.	G	GA	.	PASS	FR=0.5;HP=9;NF=6;NR=2;PP=100.0;SC=TTTAATGAAGGAAAAAAAAAT;TC=25;TR=8	GT:GL:GQ	0/1:-133.97,-86.93,-109.55:100
+20	5261161	.	ACT	A	.	PASS	FR=0.5;HP=2;NF=9;NR=8;PP=100.0;SC=CTTGAATGAAACTTATCTAAC;TC=33;TR=17	GT:GL:GQ	0/1:-246.04,-189.54,-319.81:100
+20	5275657	.	CAAAATAACTATTACAAATAACA	C	.	PASS	FR=0.5;HP=6;NF=2;NR=1;PP=100.0;SC=TCAAACATAACAAAATAACTA;TC=27;TR=3	GT:GL:GQ	0/1:-135.83,-52.75,-276.31:100
+20	5277471	.	C	CCTT	.	PASS	FR=0.5;HP=1;NF=11;NR=5;PP=100.0;SC=GTATCCATGTCCTAGGGTACA;TC=27;TR=16	GT:GL:GQ	0/1:-278.16,-87.4,-130.16:100
+20	5278336	.	TA	T	.	PASS	FR=0.5;HP=4;NF=3;NR=6;PP=100.0;SC=TTGAACTCTTTAAAAGTTTGA;TC=24;TR=9	GT:GL:GQ	0/1:-132.29,-83.79,-178.99:100
+20	5280465	.	TTG	T	.	PASS	FR=0.5;HP=4;NF=6;NR=8;PP=100.0;SC=GATGGGGTTTTTGGCCATGTT;TC=30;TR=14	GT:GL:GQ	0/1:-161.14,-49.68,-168.09:100
+20	5280839	.	T	TATA	.	PASS	FR=0.5;HP=1;NF=9;NR=3;PP=100.0;SC=ACCACAAATGTATAATACAAA;TC=30;TR=12	GT:GL:GQ	0/1:-228.47,-89.38,-201.59:100
+20	5285786	.	T	TG	.	PASS	FR=0.5;HP=1;NF=3;NR=2;PP=21.0;SC=GGCTAATCAGTTCACTCTAAG;TC=24;TR=5	GT:GL:GQ	0/1:-80.46,-64.62,-184.45:71
+20	5289619	.	GA	G	.	PASS	FR=0.5;HP=1;NF=9;NR=5;PP=100.0;SC=GAAGATCTAGGATGAAGCTGG;TC=22;TR=14	GT:GL:GQ	0/1:-219.59,-148.82,-190.02:100
+20	5291220	.	TGATCA	T	.	PASS	FR=0.5;HP=2;NF=6;NR=6;PP=100.0;SC=GTTTAGAACCTGATCAGAGAA;TC=27;TR=12	GT:GL:GQ	0/1:-284.71,-179.16,-294.64:100
+20	5291304	.	G	GACTTATGGGGAGCTGGGGTATAAATACCCCAGCTCCCTCCT	.	PASS	FR=0.5;HP=1;NF=1;NR=1;PP=100.0;SC=CCTCATCAATGACCTCCCACC;TC=8;TR=2	GT:GL:GQ	0/1:-488.84,-441.13,-506.41:71
+20	5293792	.	ATG	A	.	PASS	FR=0.5;HP=3;NF=6;NR=12;PP=100.0;SC=TACAATTATTATGTGTCAATT;TC=42;TR=18	GT:GL:GQ	0/1:-201.09,-30.39,-231.82:100
+20	5303337	.	CAGCT	C	.	PASS	FR=0.5;HP=2;NF=7;NR=7;PP=100.0;SC=AAATGTCACACAGCTAGCTGG;TC=32;TR=14	GT:GL:GQ	0/1:-273.85,-111.21,-258.62:100
+20	5313928	.	TA	T	.	PASS	FR=0.5;HP=10;NF=9;NR=8;PP=100.0;SC=ATACAGTTGATAAAAAAAAAC;TC=39;TR=17	GT:GL:GQ	0/1:-100.8,-36.94,-107.23:100
+20	5316589	.	GT	G	.	PASS	FR=1.0;HP=2;NF=7;NR=11;PP=100.0;SC=GAATATCTGGGTAAAATTTAA;TC=22;TR=18	GT:GL:GQ	1/1:-227.4,-66.98,-52.55:100
+20	5320851	.	AT	A	.	PASS	FR=0.5;HP=6;NF=5;NR=10;PP=100.0;SC=ATCTCAATAGATTTTTTAAAA;TC=39;TR=15	GT:GL:GQ	0/1:-177.77,-103.88,-250.39:100
+20	5323468	.	GA	G	.	PASS	FR=0.5;HP=10;NF=2;NR=4;PP=85.0;SC=GGCAACAAAAGAAAAAATAGA;TC=23;TR=6	GT:GL:GQ	0/1:-61.27,-31.53,-121.44:100
+20	5326511	.	G	GT	.	PASS	FR=0.5;HP=9;NF=11;NR=2;PP=100.0;SC=TTGATTCAAAGTTTTTTTTTA;TC=29;TR=13	GT:GL:GQ	0/1:-178.07,-139.61,-153.82:64
+20	5326660	.	T	TA	.	PASS	FR=0.5;HP=8;NF=4;NR=6;PP=100.0;SC=CTTTATCCTTTAAAAAAAATC;TC=26;TR=10	GT:GL:GQ	0/1:-181.43,-128.15,-159.02:100
+20	5328799	.	CA	C	.	PASS	FR=1.0;HP=4;NF=10;NR=6;PP=100.0;SC=AACCACCTTCCAAAATGTGGA;TC=20;TR=16	GT:GL:GQ	1/1:-179.33,-21.23,-7.37:100
+20	5351875	.	T	TACACACAC	.	PASS	FR=0.5;HP=6;NF=1;NR=1;PP=38.0;SC=ATCTTAAAAATACACACACAC;TC=12;TR=2	GT:GL:GQ	0/1:-48.31,-20.86,-63.23:100
+20	5354510	.	G	GGC	.	PASS	FR=0.5;HP=1;NF=5;NR=5;PP=100.0;SC=CCTCCTCCCTGCAGAGCTCCT;TC=28;TR=10	GT:GL:GQ	0/1:-148.18,-38.3,-173.54:100
+20	5373349	.	A	AATTT	.	PASS	FR=0.5;HP=6;NF=1;NR=2;PP=96.0;SC=CTAATTTTTTAATTTTTTTTT;TC=20;TR=3	GT:GL:GQ	0/1:-100.6,-64.12,-96.6:100
+20	5390447	.	C	CA	.	PASS	FR=0.5;HP=6;NF=4;NR=5;PP=100.0;SC=CATTAGCATACAAAAACCATC;TC=26;TR=9	GT:GL:GQ	0/1:-88.65,-28.46,-120.44:100
+20	5408475	.	AAAAC	A	.	PASS	FR=0.5;HP=4;NF=4;NR=5;PP=100.0;SC=CTCTGTCTCAAAAACAAACAA;TC=29;TR=9	GT:GL:GQ	0/1:-128.94,-29.02,-144.52:100
+20	5410361	.	G	GA	.	PASS	FR=1.0;HP=9;NF=6;NR=7;PP=100.0;SC=CTGGGTTGGGGAAAAAAAAAG;TC=25;TR=13	GT:GL:GQ	1/1:-119.78,-34.18,-19.33:100
+20	5419440	.	CTCCCTGTG	C	.	PASS	FR=0.5;HP=3;NF=1;NR=4;PP=100.0;SC=TGTTGTTCCCCTCCCTGTGTC;TC=19;TR=5	GT:GL:GQ	0/1:-128.97,-30.52,-125.82:100
+20	5432204	.	A	AG	.	PASS	FR=0.5;HP=8;NF=2;NR=3;PP=100.0;SC=AAAGAAAGAGAAAAAAAAAGG;TC=19;TR=5	GT:GL:GQ	0/1:-83.51,-76.05,-116.49:100
+20	5432394	.	G	GT	.	PASS	FR=1.0;HP=5;NF=9;NR=14;PP=100.0;SC=TTCCTCAATTGAAAAATCTTA;TC=26;TR=23	GT:GL:GQ	1/1:-328.05,-211.91,-196.14:100
+20	5435136	.	GAGAAAA	G	.	PASS	FR=0.5;HP=3;NF=3;NR=6;PP=44.0;SC=AAAAAAAGGGGAGAAAAAGAA;TC=24;TR=9	GT:GL:GQ	0/1:-190.59,-169.15,-271.82:96
+20	5435153	.	A	ATTT	.	PASS	FR=0.5;HP=8;NF=4;NR=10;PP=100.0;SC=AGAAAAAAAAATTTTAATGTT;TC=22;TR=14	GT:GL:GQ	0/1:-325.96,-275.2,-333.88:100
+20	5435908	.	G	GTTAAT	.	PASS	FR=0.5;HP=2;NF=5;NR=2;PP=100.0;SC=ACCAGGCCCAGTTATTTTTTG;TC=16;TR=7	GT:GL:GQ	0/1:-176.12,-112.78,-176.63:100
+20	5443418	.	A	ACAGGGGCAC	.	PASS	FR=0.5;HP=4;NF=3;NR=1;PP=100.0;SC=GCTTTGTCCCACAGCCTGATG;TC=15;TR=4	GT:GL:GQ	0/1:-94.87,-42.4,-160.11:100
+20	5443724	.	C	CT	.	PASS	FR=0.5;HP=3;NF=6;NR=4;PP=38.0;SC=GTTACCTTTCCCCTGAGATGC;TC=20;TR=10	GT:GL:GQ	0/1:-163.73,-143.91,-199.73:89
+20	5452897	.	G	GA	.	PASS	FR=0.5;HP=10;NF=2;NR=2;PP=26.0;SC=TCAGTCAGAAGAAAAAAAATT;TC=15;TR=4	GT:GL:GQ	0/1:-34.37,-17.3,-53.75:77
+20	5460271	.	C	CA	.	PASS	FR=0.5;HP=10;NF=2;NR=2;PP=67.0;SC=ACCCCTGTCTCAAAAAAAAAA;TC=21;TR=4	GT:GL:GQ	0/1:-56.83,-30.33,-56.83:100
+20	5473577	.	A	AGT	.	PASS	FR=0.5;HP=2;NF=2;NR=8;PP=100.0;SC=AACTGAGCAGAGTTCCTTTTT;TC=29;TR=10	GT:GL:GQ	0/1:-165.26,-86.94,-217.65:100
+20	5475853	.	CTTATTTAT	CTTATTTATTTAT,C	.	PASS	FR=0.5,0.5;HP=4;NF=1,1;NR=2,2;PP=100.0,100.0;SC=GAAGGCTCTTCTTATTTATTT;TC=18;TR=3,3	GT:GL:GQ	1/2:-1.0,-1.0,-1.0:100
+20	5485434	.	C	CT	.	PASS	FR=0.5001;HP=10;NF=4;NR=1;PP=63.0;SC=TTTTTATCTTCTTTTTTTTCC;TC=9;TR=5	GT:GL:GQ	0/1:-37.99,-12.58,-20.26:36
+20	5518456	.	C	CG	.	PASS	FR=0.5;HP=7;NF=7;NR=6;PP=100.0;SC=GTGACAAATGCGGGGGGTCTT;TC=27;TR=13	GT:GL:GQ	0/1:-115.32,-28.55,-76.08:100
+20	5546352	.	A	AAG	.	PASS	FR=1.0;HP=1;NF=13;NR=12;PP=100.0;SC=AAGTAGTCACAAGCTGTGATT;TC=26;TR=25	GT:GL:GQ	1/1:-322.1,-20.79,0.0:100
+20	5596481	.	TTATG	T	.	PASS	FR=1.0;HP=2;NF=4;NR=4;PP=100.0;SC=TGCTACTGGTTTATGTATGTA;TC=20;TR=8	GT:GL:GQ	1/1:-167.17,-32.77,-22.47:86
+20	5596891	.	ATGTGTGTG	A	.	PASS	FR=1.0;HP=2;NF=3;NR=4;PP=100.0;SC=AATTTGGGGTATGTGTGTGTG;TC=23;TR=7	GT:GL:GQ	1/1:-241.36,-45.12,-34.38:90
+20	5600458	.	A	AG	.	PASS	FR=1.0;HP=2;NF=3;NR=3;PP=100.0;SC=TCTTGACCTGAGTGATACACC;TC=16;TR=6	GT:GL:GQ	1/1:-146.08,-65.05,-55.59:79
+20	5613790	.	GA	G	.	PASS	FR=1.0;HP=4;NF=11;NR=9;PP=100.0;SC=CATGATTTCTGAAAACAAGCT;TC=26;TR=20	GT:GL:GQ	1/1:-222.44,-43.9,-26.57:100
+20	5624959	.	C	CCTCCTTACCCT	.	PASS	FR=0.5;HP=1;NF=1;NR=1;PP=100.0;SC=AACTTGTCCACCTCCATTACC;TC=28;TR=2	GT:GL:GQ	0/1:-225.26,-176.16,-303.27:100
+20	5627592	.	AT	A	.	PASS	FR=0.5;HP=6;NF=4;NR=3;PP=100.0;SC=TCTCAAAAAAATAATAAAGTT;TC=19;TR=7	GT:GL:GQ	0/1:-112.89,-28.55,-78.51:100
+20	5629324	.	T	TTAC	.	PASS	FR=0.5;HP=1;NF=3;NR=3;PP=100.0;SC=ATTATTACTATTATTATTATT;TC=26;TR=6	GT:GL:GQ	1/0:-227.05,-75.82,-72.8:100
+20	5635153	.	TGGAATATGAAAGAG	T	.	PASS	FR=1.0;HP=2;NF=7;NR=11;PP=100.0;SC=CAAGCCTGTTTGGAATATGAA;TC=27;TR=18	GT:GL:GQ	1/1:-490.0,-56.65,-38.89:100
+20	5635246	.	T	TTGTGTG,TTGTGTGTG	.	PASS	FR=0.5,0.5;HP=1;NF=2,0;NR=2,3;PP=100.0,100.0;SC=AAAATGAATATTGTGTGTGTG;TC=22;TR=4,3	GT:GL:GQ	1/2:-1.0,-1.0,-1.0:100
+20	5644716	.	GTCTCTCTCTCTC	G	.	PASS	FR=1.0;HP=1;NF=1;NR=6;PP=100.0;SC=ATGAGACCTCGTCTCTCTCTC;TC=22;TR=7	GT:GL:GQ	1/1:-261.18,-61.24,-58.02:52
+20	5654462	.	C	CGTGTGTGTGTGTGT	.	PASS	FR=0.5;HP=1;NF=3;NR=1;PP=100.0;SC=TATACATATACGTGTGTGTGT;TC=16;TR=4	GT:GL:GQ	0/1:-129.11,-28.26,-136.2:100
+20	5654661	.	AAAAAAATTTTTTTTGCTT	A	.	PASS	FR=0.5;HP=6;NF=7;NR=3;PP=100.0;SC=ATTTTTTGCCAAAAAAATTTT;TC=21;TR=10	GT:GL:GQ	0/1:-264.68,-158.41,-268.38:100
+20	5655925	.	ACG	A	.	PASS	FR=0.5047;HP=2;NF=4;NR=3;PP=100.0;SC=TTGCATGCGCACGCGCGCACA;TC=34;TR=7	GT:GL:GQ	0/1:-234.34,-106.46,-110.43:20
+20	5674501	.	T	TTTTG	.	PASS	FR=0.5;HP=4;NF=2;NR=2;PP=100.0;SC=AGATTTAGATTTTTGTTTGTT;TC=22;TR=4	GT:GL:GQ	0/1:-64.3,-21.33,-64.69:100
+20	5691054	.	A	AC	.	PASS	FR=0.5;HP=6;NF=4;NR=5;PP=100.0;SC=GTATAGTGAGACCCCCCATCT;TC=18;TR=9	GT:GL:GQ	0/1:-137.75,-89.82,-120.86:100
+20	5696589	.	AAAG	A	.	PASS	FR=0.5;HP=2;NF=3;NR=9;PP=100.0;SC=AGAAAACCATAAAGAAGAGAA;TC=35;TR=12	GT:GL:GQ	0/1:-142.07,-32.31,-238.04:100
+20	5706639	.	T	TA	.	PASS	FR=0.5;HP=9;NF=5;NR=2;PP=98.0;SC=TTGTCTCAATTAAAAAAAAAT;TC=31;TR=7	GT:GL:GQ	0/1:-60.75,-27.2,-75.24:100
+20	5707109	.	A	ATTTTTCCC	.	PASS	FR=0.5;HP=7;NF=2;NR=2;PP=100.0;SC=TGCCCAGCTGATTTTTTTAAA;TC=15;TR=4	GT:GL:GQ	0/1:-95.63,-40.43,-104.52:100
+20	5740635	.	T	TAC,TACAC	.	PASS	FR=0.5,0.5;HP=2;NF=3,1;NR=7,4;PP=100.0,100.0;SC=TGTATTTTTATACACACACAC;TC=23;TR=10,5	GT:GL:GQ	1/2:-1.0,-1.0,-1.0:100
+20	5747768	.	ATTTTC	ATTTTCTTTTC,A	.	PASS	FR=0.5,0.5;HP=4;NF=1,4;NR=1,1;PP=100.0,100.0;SC=CTCCATTCACATTTTCTTTTC;TC=17;TR=2,5	GT:GL:GQ	1/2:-1.0,-1.0,-1.0:100
+20	5754003	.	A	AT	.	PASS	FR=0.5;HP=9;NF=6;NR=4;PP=100.0;SC=AGAGAGTGGAATTTTTTTTTG;TC=33;TR=10	GT:GL:GQ	0/1:-69.42,-30.04,-87.94:100
+20	5762289	.	A	AT	.	PASS	FR=0.5;HP=8;NF=2;NR=3;PP=95.0;SC=CTGCCCAGCTATTTTTTTGTA;TC=13;TR=5	GT:GL:GQ	0/1:-43.82,-10.94,-28.53:79
+20	5767540	.	AGATCATTT	A	.	PASS	FR=1.0;HP=2;NF=5;NR=6;PP=100.0;SC=TTCTCAAGCCAGATCATTTGA;TC=16;TR=11	GT:GL:GQ	1/1:-333.85,-224.08,-215.75:69
+20	5768941	.	AGTT	A	.	PASS	FR=0.5;HP=1;NF=4;NR=9;PP=100.0;SC=TATATTCAGTAGTTGTTGTTT;TC=21;TR=13	GT:GL:GQ	0/1:-159.07,-13.83,-29.97:73
+20	5771896	.	CAAATAAATA	C	.	PASS	FR=1.0;HP=3;NF=11;NR=5;PP=100.0;SC=AAAATCTTAGCAAATAAATAA;TC=26;TR=16	GT:GL:GQ	1/1:-433.86,-58.29,-43.98:62
+20	5778212	.	AAAG	A	.	PASS	FR=1.0;HP=5;NF=6;NR=12;PP=100.0;SC=CCATCTCAAAAAAGAAGAAGA;TC=23;TR=18	GT:GL:GQ	1/1:-251.53,-37.12,-21.87:100
+20	5781503	.	GCGTA	G	.	PASS	FR=1.0;HP=1;NF=9;NR=6;PP=100.0;SC=GTGTGTGTGTGCGTATGTCTA;TC=23;TR=15	GT:GL:GQ	1/1:-450.31,-256.77,-243.2:93
+20	5788895	.	C	CAGCCTGGGTGACAG	.	PASS	FR=1.0;HP=1;NF=3;NR=6;PP=100.0;SC=CACTGCACTCCAGCAAGACTC;TC=11;TR=9	GT:GL:GQ	1/1:-304.26,-23.03,-12.43:73
+20	5798352	.	CTGGCATTA	C	.	PASS	FR=0.5;HP=1;NF=1;NR=3;PP=100.0;SC=CTGGCTGTGCCTGGCATTATG;TC=29;TR=4	GT:GL:GQ	1/0:-390.33,-302.72,-305.99:100
+20	5798359	.	T	TGC	.	PASS	FR=0.5;HP=1;NF=6;NR=6;PP=100.0;SC=TGCCTGGCATTATGACTTAGT;TC=26;TR=12	GT:GL:GQ	0/1:-390.33,-366.98,-362.46:100
+20	5807781	.	T	TG	.	PASS	FR=1.0;HP=3;NF=7;NR=3;PP=100.0;SC=TGAGTGGGCGTGGCACCCACA;TC=10;TR=10	GT:GL:GQ	1/1:-98.15,-11.06,-4.14:57
+20	5808542	.	C	CT	.	PASS	FR=1.0;HP=3;NF=16;NR=16;PP=100.0;SC=ATCATTCACTCTTGTGGGTAG;TC=33;TR=32	GT:GL:GQ	1/1:-408.08,-203.57,-182.32:100
+20	5808967	.	T	TGTGTAGTAG	.	PASS	FR=1.0;HP=2;NF=7;NR=18;PP=100.0;SC=CTTAGAACAGTGTGATAGGTC;TC=28;TR=25	GT:GL:GQ	1/1:-678.96,-93.79,-70.92:100
+20	5809144	.	TTGA	T	.	PASS	FR=1.0;HP=1;NF=10;NR=16;PP=100.0;SC=GAGTCATTTCTTGATGACTCC;TC=34;TR=26	GT:GL:GQ	1/1:-408.43,-70.02,-46.73:100
+20	5809747	.	CCTGGGCTCA	C	.	PASS	FR=1.0;HP=1;NF=13;NR=15;PP=100.0;SC=GGTCTCAACTCCTGGGCTCAA;TC=33;TR=28	GT:GL:GQ	1/1:-583.71,-71.8,-56.82:48
+20	5810527	.	G	GA	.	PASS	FR=1.0;HP=9;NF=9;NR=9;PP=100.0;SC=TCTTCTTTAGGAAAAAAAAAC;TC=26;TR=18	GT:GL:GQ	1/1:-296.92,-216.99,-203.12:100
+20	5820132	.	A	AAGATAGAT,AAGATAGATAGAT	.	PASS	FR=0.5,0.5;HP=2;NF=4,2;NR=2,6;PP=100.0,100.0;SC=ATTAGATAGAAAGATAGATAG;TC=36;TR=6,8	GT:GL:GQ	1/2:-1.0,-1.0,-1.0:100
+20	5822610	.	A	AAAG	.	PASS	FR=0.5;HP=2;NF=4;NR=6;PP=100.0;SC=GACTATGGAGAAAGAGAACAT;TC=30;TR=10	GT:GL:GQ	0/1:-160.25,-33.5,-176.54:100
+20	5830758	.	C	CAATAATAAT	.	PASS	FR=1.0;HP=2;NF=2;NR=2;PP=100.0;SC=GACCCCGTCTCAATAATAATA;TC=8;TR=4	GT:GL:GQ	1/1:-112.77,-19.78,-14.93:60
+20	5848219	.	C	CAAAAT	.	PASS	FR=1.0;HP=7;NF=10;NR=13;PP=100.0;SC=ATTAAACACTCAAAAAAATAA;TC=29;TR=23	GT:GL:GQ	1/1:-431.75,-125.0,-103.09:100
+20	5848530	.	A	AAT	.	PASS	FR=1.0;HP=1;NF=13;NR=10;PP=100.0;SC=ATATATATAGAATATATATAT;TC=33;TR=23	GT:GL:GQ	1/1:-409.72,-328.74,-317.3:96
+20	5850230	.	A	AT	.	PASS	FR=1.0;HP=6;NF=1;NR=1;PP=100.0;SC=TAATTTTTGCATTTTTTGTTT;TC=22;TR=2	GT:GL:GQ	1/1:-134.01,-105.23,-98.33:86
+20	5854908	.	A	AATTTTATTTT	.	PASS	FR=1.0;HP=3;NF=3;NR=7;PP=100.0;SC=CATATACTTTAATTTTATTTT;TC=28;TR=10	GT:GL:GQ	1/1:-352.01,-27.1,-12.2:100
+20	5856355	.	CTAAA	C	.	PASS	FR=1.0;HP=4;NF=2;NR=2;PP=100.0;SC=GACCCTATTTCTAAATAAATA;TC=15;TR=4	GT:GL:GQ	1/1:-57.0,-6.23,-2.76:42
+20	5860647	.	TGAG	T	.	PASS	FR=1.0;HP=4;NF=8;NR=6;PP=100.0;SC=AGAAAGAAAATGAGGAGCGAA;TC=18;TR=14	GT:GL:GQ	1/1:-182.28,-15.91,-4.13:99
+20	5879792	.	CAA	C	.	PASS	FR=1.0;HP=10;NF=14;NR=15;PP=100.0;SC=ACAATAACATCAAAAAAAAAA;TC=39;TR=29	GT:GL:GQ	1/1:-170.66,-28.34,-5.76:100
+20	5898748	.	GAA	G	.	PASS	FR=1.0;HP=2;NF=5;NR=5;PP=100.0;SC=AGCCAAGATTGAACTCCATTG;TC=13;TR=10	GT:GL:GQ	1/1:-132.95,-97.25,-91.93:66
+20	5900669	.	G	GC	.	PASS	FR=0.5;HP=1;NF=4;NR=2;PP=100.0;SC=CATGACAGATGCATTTCCCTG;TC=15;TR=6	GT:GL:GQ	0/1:-72.42,-12.46,-72.17:100
+20	5911588	.	TCA	T	.	PASS	FR=0.5;HP=2;NF=6;NR=1;PP=100.0;SC=CTGGCAAATCTCACACACACA;TC=19;TR=7	GT:GL:GQ	0/1:-115.11,-26.04,-76.51:100
+20	5923828	.	CAGAGAGAATACATGCTTA	C	.	PASS	FR=0.5;HP=1;NF=3;NR=5;PP=100.0;SC=TGTATTCTTCCAGAGAGAATA;TC=22;TR=8	GT:GL:GQ	0/1:-297.99,-115.43,-361.46:100
+20	5928403	.	T	TA	.	PASS	FR=0.5;HP=2;NF=3;NR=2;PP=100.0;SC=ACCTAGGTGCTTTGAAACACT;TC=18;TR=5	GT:GL:GQ	0/1:-52.7,-18.59,-121.61:100
+20	5930573	.	A	AG	.	PASS	FR=0.5;HP=3;NF=4;NR=4;PP=100.0;SC=ACAGGTGATTAGGGTGTGGAG;TC=26;TR=8	GT:GL:GQ	0/1:-121.38,-46.04,-144.61:100
+20	5932104	.	C	CT	.	PASS	FR=0.5;HP=2;NF=5;NR=6;PP=100.0;SC=TCTTTATTTACTTGTATACTT;TC=20;TR=11	GT:GL:GQ	0/1:-138.34,-48.83,-107.16:100
+20	5934084	.	GGTGT	GGT,G	.	PASS	FR=0.5,0.5;HP=3;NF=1,2;NR=3,2;PP=100.0,100.0;SC=TCTCATGAGGGGTGTGTGTGT;TC=32;TR=4,4	GT:GL:GQ	1/2:-1.0,-1.0,-1.0:100
+20	5938650	.	A	AT	.	PASS	FR=0.5;HP=3;NF=3;NR=6;PP=100.0;SC=TTTTCCTTAAATTTCTTTTTT;TC=36;TR=9	GT:GL:GQ	0/1:-182.01,-137.8,-289.15:100
+20	5939638	.	G	GT	.	PASS	FR=0.5;HP=7;NF=8;NR=7;PP=100.0;SC=ATTAGTGTCTGTTTTTTACCT;TC=37;TR=15	GT:GL:GQ	0/1:-244.24,-166.31,-240.23:100
+20	5946414	.	TTTTACTTCTTAGAGTATGC	T	.	PASS	FR=0.5;HP=3;NF=2;NR=4;PP=100.0;SC=TAAGTGCTGGTTTTACTTCTT;TC=34;TR=6	GT:GL:GQ	0/1:-213.07,-102.23,-466.92:100
+20	5948421	.	CATT	C	.	PASS	FR=0.5;HP=1;NF=6;NR=8;PP=100.0;SC=CTAGTTGAGTCATTGTAGGGA;TC=25;TR=14	GT:GL:GQ	0/1:-180.5,-26.28,-114.93:100
+20	5958367	.	TATA	T	.	PASS	FR=0.5;HP=2;NF=1;NR=12;PP=100.0;SC=TAAATCAGGATATAATAATAC;TC=28;TR=13	GT:GL:GQ	0/1:-168.03,-21.02,-138.69:100
+20	5958971	.	AT	A	.	PASS	FR=0.5;HP=8;NF=7;NR=10;PP=100.0;SC=ATTTGTGATCATTTTTTTTAA;TC=36;TR=17	GT:GL:GQ	0/1:-190.15,-122.85,-187.1:100
+20	5972522	.	TC	T	.	PASS	FR=0.5;HP=2;NF=3;NR=8;PP=100.0;SC=AGTTTTCATCTCTTCAGCTTC;TC=35;TR=11	GT:GL:GQ	0/1:-138.05,-67.95,-261.75:100
+20	5974701	.	T	TTTTG	.	PASS	FR=0.5;HP=6;NF=12;NR=8;PP=100.0;SC=TTAGCTTGATTTTTTTCAGCT;TC=40;TR=20	GT:GL:GQ	0/1:-282.01,-46.13,-199.33:100
+20	5979818	.	CTA	C	.	PASS	FR=0.5;HP=1;NF=4;NR=2;PP=100.0;SC=CACACACACACTATATAGAGT;TC=23;TR=6	GT:GL:GQ	0/1:-148.54,-97.12,-217.3:100
+20	5979861	.	T	TAG	.	PASS	FR=0.5;HP=1;NF=1;NR=6;PP=100.0;SC=GTATATATACTAGTGTGTATA;TC=23;TR=7	GT:GL:GQ	0/1:-206.33,-148.87,-246.11:100
+20	5979921	.	ATATATATTATATATAC	A	.	PASS	FR=0.5;HP=2;NF=2;NR=3;PP=100.0;SC=TCTATAAAGTATATATATTAT;TC=15;TR=5	GT:GL:GQ	0/1:-143.6,-52.22,-114.36:100
+20	5980041	.	CTATA	C	.	PASS	FR=0.5;HP=1;NF=6;NR=4;PP=100.0;SC=TATATATACACTATATATAGT;TC=35;TR=10	GT:GL:GQ	0/1:-130.29,-26.74,-240.87:100
+20	5982833	.	CTT	C	.	PASS	FR=0.5;HP=5;NF=2;NR=5;PP=100.0;SC=GCAATGCACTCTTTTGCTTAC;TC=22;TR=7	GT:GL:GQ	0/1:-154.07,-87.47,-142.2:100
+20	5984269	.	CTT	C	.	PASS	FR=0.5;HP=5;NF=6;NR=7;PP=100.0;SC=AATCCTTTCTCTTTTCACGTT;TC=31;TR=13	GT:GL:GQ	0/1:-161.92,-47.17,-162.99:100
+20	5986173	.	A	ATAATT	.	PASS	FR=0.5;HP=3;NF=9;NR=5;PP=100.0;SC=AAAATTTAAAATAAAAACTAT;TC=31;TR=14	GT:GL:GQ	0/1:-275.95,-89.41,-205.85:100
+20	5997120	.	T	TGTGTGA	.	PASS	FR=0.5;HP=2;NF=2;NR=2;PP=100.0;SC=TGTGTGTGTGTGAGTTTTCTT;TC=20;TR=4	GT:GL:GQ	0/1:-128.89,-41.21,-139.69:100
+20	5999929	.	G	GTTA	.	PASS	FR=0.5;HP=5;NF=7;NR=6;PP=100.0;SC=CTTTTGACCAGTTTTTAAGTT;TC=34;TR=13	GT:GL:GQ	0/1:-145.72,-26.46,-192.55:100
+20	6013970	.	C	CG	.	PASS	FR=0.5;HP=4;NF=4;NR=1;PP=100.0;SC=TTAGTAGAGACGGGGTTTCAC;TC=18;TR=5	GT:GL:GQ	0/1:-76.07,-30.4,-70.18:100
+20	6019907	.	TTGTGTGTGTGTGTGTG	T	.	PASS	FR=0.5;HP=2;NF=1;NR=1;PP=100.0;SC=GCAGTTTTGTTTGTGTGTGTG;TC=27;TR=2	GT:GL:GQ	0/1:-146.39,-89.3,-170.65:100
+20	6052252	.	CT	C	.	PASS	FR=1.0;HP=2;NF=5;NR=9;PP=100.0;SC=ATCCCCAGCCCTTCCTGGCTT;TC=21;TR=14	GT:GL:GQ	1/1:-166.42,-15.59,-2.3:100
+20	6054897	.	T	TG	.	PASS	FR=1.0;HP=3;NF=4;NR=7;PP=100.0;SC=TGGGCAAGGCTGGGAAGGAAG;TC=16;TR=11	GT:GL:GQ	1/1:-170.6,-33.42,-22.33:90
+20	6056042	.	T	TA	.	PASS	FR=1.0;HP=2;NF=8;NR=17;PP=100.0;SC=ACATCAAGTATATACGGTACA;TC=29;TR=25	GT:GL:GQ	1/1:-301.61,-48.56,-28.73:100
+20	6163149	.	CATTT	C	.	PASS	FR=1.0;HP=1;NF=11;NR=10;PP=100.0;SC=AACCTCTGAGCATTTATTTCA;TC=24;TR=21	GT:GL:GQ	1/1:-265.47,-16.86,-0.92:100
+20	6169158	.	C	CT	.	PASS	FR=1.0;HP=1;NF=11;NR=21;PP=100.0;SC=AATTGCAAGACCTTAAGAACC;TC=38;TR=32	GT:GL:GQ	1/1:-377.27,-55.22,-28.98:100
+20	6186522	.	G	GC	.	PASS	FR=1.0;HP=6;NF=10;NR=10;PP=100.0;SC=TAAAAAATGTGTTTTTAATCA;TC=21;TR=20	GT:GL:GQ	1/1:-309.42,-177.87,-163.8:100
+20	6186628	.	C	CA	.	PASS	FR=0.5;HP=3;NF=5;NR=12;PP=100.0;SC=TTCATCACCTCAAACATTTAT;TC=33;TR=17	GT:GL:GQ	0/1:-173.72,-30.0,-131.16:100
+20	6189872	.	C	CCTT	.	PASS	FR=0.5;HP=1;NF=1;NR=10;PP=100.0;SC=CTTCCTCCCTCCTTTCCCTCT;TC=26;TR=11	GT:GL:GQ	0/1:-217.8,-111.28,-184.18:100
+20	6190124	.	C	CTT	.	PASS	FR=0.5;HP=2;NF=2;NR=4;PP=92.0;SC=TCCTGCCTCTCTCTTTCCTCC;TC=16;TR=6	GT:GL:GQ	0/1:-129.79,-96.5,-151.55:100
+20	6190921	.	A	AT	.	PASS	FR=0.5;HP=2;NF=5;NR=4;PP=100.0;SC=CCATAAGTACATTAAAAAAAA;TC=24;TR=9	GT:GL:GQ	0/1:-121.19,-85.53,-104.7:86
+20	6202427	.	C	CT	.	PASS	FR=1.0;HP=6;NF=6;NR=13;PP=100.0;SC=GAAATCCTTTCTTTCCCCCTA;TC=20;TR=19	GT:GL:GQ	1/1:-165.74,-14.09,-0.92:100
+20	6211244	.	GT	G	.	PASS	FR=0.5;HP=10;NF=5;NR=6;PP=100.0;SC=TTGATTTCCAGTTTTTTTTTT;TC=33;TR=11	GT:GL:GQ	0/1:-97.67,-63.78,-117.4:100
+20	6217057	.	T	TA	.	PASS	FR=0.5;HP=2;NF=4;NR=7;PP=100.0;SC=TCTCTACAACTAACCATCAAC;TC=33;TR=11	GT:GL:GQ	0/1:-151.16,-56.84,-189.09:100
+20	6227811	.	TTTTTCTTTTC	T	.	PASS	FR=0.5;HP=6;NF=3;NR=2;PP=100.0;SC=TATACTGCTTTTTTTCTTTTC;TC=28;TR=5	GT:GL:GQ	0/1:-171.28,-80.47,-279.48:100
+20	6228139	.	TA	T	.	PASS	FR=0.5;HP=8;NF=6;NR=7;PP=100.0;SC=ACTGGTTGTTTAAAAAAAACA;TC=27;TR=13	GT:GL:GQ	0/1:-101.53,-37.68,-71.46:100
+20	6229361	.	G	GTA	.	PASS	FR=0.5;HP=2;NF=7;NR=5;PP=100.0;SC=TGCTTTTGAAGTATACCTTTA;TC=28;TR=12	GT:GL:GQ	0/1:-168.24,-128.05,-263.48:100
+20	6232719	.	T	TA	.	PASS	FR=1.0;HP=4;NF=10;NR=14;PP=100.0;SC=CGTACCTCAATAAGTACTGTT;TC=26;TR=24	GT:GL:GQ	1/1:-246.13,-19.86,-1.84:100
+20	6235756	.	T	TA	.	PASS	FR=0.5;HP=10;NF=4;NR=2;PP=51.0;SC=ATATAAAAGTTAAAAAAAAAA;TC=22;TR=6	GT:GL:GQ	0/1:-59.89,-37.16,-67.02:100
+20	6242610	.	GCAGACC	G	.	PASS	FR=0.5;HP=1;NF=7;NR=3;PP=100.0;SC=ACTGGGAGAGGCAGACCCACC;TC=27;TR=10	GT:GL:GQ	0/1:-180.6,-46.65,-174.85:100
+20	6245977	.	A	AT	.	PASS	FR=0.5;HP=6;NF=7;NR=5;PP=100.0;SC=CTTAGTTTTCATTTTTTAGCA;TC=29;TR=12	GT:GL:GQ	0/1:-149.75,-66.4,-136.45:100
+20	6258987	.	CT	C	.	PASS	FR=0.5;HP=6;NF=4;NR=10;PP=100.0;SC=GTATGTTCTTCTTTTGTCCCC;TC=34;TR=14	GT:GL:GQ	0/1:-185.84,-121.45,-268.81:100
+20	6272029	.	T	TA	.	PASS	FR=0.5;HP=3;NF=4;NR=9;PP=100.0;SC=TAATAGCTGGTAAACCCAACC;TC=39;TR=13	GT:GL:GQ	0/1:-151.49,-56.11,-226.05:100
+20	6293812	.	G	GA	.	PASS	FR=1.0;HP=7;NF=15;NR=12;PP=100.0;SC=GGAAAAGAAAGAAAAGAAAAA;TC=35;TR=27	GT:GL:GQ	1/1:-393.29,-260.24,-242.04:100
+20	6296458	.	T	TA	.	PASS	FR=1.0;HP=8;NF=5;NR=17;PP=100.0;SC=GAAAGCACAATTTTTTTTTCT;TC=39;TR=22	GT:GL:GQ	1/1:-284.36,-128.48,-104.71:100
+20	6304002	.	A	ATG	.	PASS	FR=1.0;HP=2;NF=6;NR=5;PP=100.0;SC=ATATATATATATATGTGTGTG;TC=30;TR=11	GT:GL:GQ	1/1:-328.64,-256.07,-245.8:100
+20	6307745	.	GTA	G	.	PASS	FR=1.0;HP=3;NF=4;NR=7;PP=100.0;SC=TATATATGTTGTATATATATA;TC=16;TR=11	GT:GL:GQ	1/1:-114.94,-15.25,-6.19:75
+20	6307849	.	TATATATATGGTATATATATC	T	.	PASS	FR=0.5034;HP=1;NF=2;NR=2;PP=100.0;SC=ATATATGGTGTATATATATGG;TC=11;TR=4	GT:GL:GQ	0/1:-108.24,-70.67,-74.96:21
+20	6307908	.	TG	T	.	PASS	FR=0.5;HP=2;NF=3;NR=4;PP=100.0;SC=ATATCATATATGGTGTATATA;TC=21;TR=7	GT:GL:GQ	0/1:-127.13,-92.55,-148.07:100
+20	6308166	.	G	GTA,GTATA	.	PASS	FR=0.5,0.5;HP=2;NF=2,1;NR=0,3;PP=86.0,100.0;SC=GTGTGTGTGTGTATATATATA;TC=16;TR=2,4	GT:GL:GQ	1/2:-1.0,-1.0,-1.0:100
+20	6308279	.	G	GTA	.	PASS	FR=1.0;HP=2;NF=5;NR=4;PP=100.0;SC=TATATATGGTGTATATATATA;TC=12;TR=9	GT:GL:GQ	1/1:-129.24,-92.18,-87.75:54
+20	6308322	.	GTGTGTGTATATATATATATATATA	G	.	PASS	FR=1.0;HP=2;NF=1;NR=2;PP=88.0;SC=ATGTATGTGTGTGTGTGTATA;TC=16;TR=3	GT:GL:GQ	1/1:-227.62,-141.11,-132.99:40
+20	6319701	.	G	GGT	.	PASS	FR=0.5;HP=1;NF=1;NR=5;PP=100.0;SC=GAGTCTATGTGGTGTGTGTGT;TC=19;TR=6	GT:GL:GQ	0/1:-99.44,-38.84,-115.36:100
+20	6345189	.	G	GT	.	PASS	FR=0.5;HP=8;NF=8;NR=3;PP=100.0;SC=ATTGTTTTCAGTTTTTTTTCT;TC=31;TR=11	GT:GL:GQ	0/1:-92.31,-34.03,-73.88:100
+20	6346428	.	C	CTCTGTATG	.	PASS	FR=0.5;HP=4;NF=5;NR=1;PP=45.0;SC=TATTCTCTATCTTTAATTTAA;TC=31;TR=6	GT:GL:GQ	0/1:-234.84,-191.03,-405.18:86
+20	6349738	.	TAC	T	.	PASS	FR=0.5;HP=1;NF=2;NR=1;PP=86.0;SC=GACACATACGTACACACACAC;TC=15;TR=3	GT:GL:GQ	0/1:-95.85,-65.71,-99.67:100
+20	6364214	.	ACTCTT	A	.	PASS	FR=0.5;HP=3;NF=5;NR=10;PP=100.0;SC=TCTTTACAAAACTCTTCTAGA;TC=36;TR=15	GT:GL:GQ	0/1:-210.3,-34.68,-236.21:100
+20	6373382	.	TCTACCTAC	T	.	PASS	FR=1.0;HP=1;NF=9;NR=8;PP=100.0;SC=ATTTCCTCTATCTACCTACCT;TC=38;TR=17	GT:GL:GQ	1/1:-510.97,-41.39,-20.72:100
+20	6384835	.	TACACACAC	TAC,T	.	PASS	FR=0.5,0.5;HP=2;NF=2,2;NR=7,1;PP=100.0,51.0;SC=GGATGACACATACACACACAC;TC=32;TR=9,3	GT:GL:GQ	1/2:-1.0,-1.0,-1.0:100
+20	6390974	.	TAA	T	.	PASS	FR=1.0;HP=3;NF=19;NR=16;PP=100.0;SC=CTGCCTACCTTAAACACATAA;TC=42;TR=35	GT:GL:GQ	1/1:-376.88,-34.87,-5.52:100
+20	6401100	.	A	AT	.	PASS	FR=1.0;HP=9;NF=15;NR=9;PP=100.0;SC=TTCAAAAAGCATTTTTTTTTG;TC=34;TR=24	GT:GL:GQ	1/1:-148.27,-28.49,-8.51:100
+20	6406758	.	C	CT	.	PASS	FR=1.0;HP=7;NF=4;NR=16;PP=100.0;SC=TCTCTCCCCTCTTTTTTCTCC;TC=31;TR=20	GT:GL:GQ	1/1:-235.73,-83.65,-66.42:100
+20	6410888	.	CAGGGCTTGGCCCTGGAGT	C	.	PASS	FR=0.5;HP=1;NF=2;NR=4;PP=100.0;SC=TTCTCCACTCCAGGGCTTGGC;TC=24;TR=6	GT:GL:GQ	0/1:-188.53,-25.15,-199.92:100
+20	6426272	.	T	TCTC,TTTC	.	PASS	FR=0.5,0.5;HP=1;NF=11,6;NR=5,5;PP=100.0,100.0;SC=TTAAAAATTATCTCATTTCCT;TC=28;TR=16,11	GT:GL:GQ	1/2:-1.0,-1.0,-1.0:100
+20	6428681	.	CA	C	.	PASS	FR=0.5009;HP=2;NF=4;NR=5;PP=100.0;SC=GGTGGGCCACCAACAGTGTCT;TC=20;TR=9	GT:GL:GQ	0/1:-312.7,-243.18,-248.77:27
+20	6430456	.	A	AT	.	PASS	FR=0.5;HP=10;NF=10;NR=6;PP=100.0;SC=TAATATTTAAATTTTTTTTTT;TC=35;TR=16	GT:GL:GQ	0/1:-143.54,-83.39,-119.6:100
+20	6438083	.	TA	T	.	PASS	FR=0.5;HP=7;NF=2;NR=8;PP=100.0;SC=AACAGATATATAAAAAATGCT;TC=21;TR=10	GT:GL:GQ	0/1:-86.86,-14.54,-78.87:100
+20	6441903	.	C	CT	.	PASS	FR=0.5;HP=9;NF=10;NR=11;PP=100.0;SC=AAATTAAATACTTTTTTTTTA;TC=43;TR=21	GT:GL:GQ	0/1:-221.48,-121.14,-137.31:73
+20	6443155	.	TTA	T	.	PASS	FR=0.5005;HP=5;NF=2;NR=2;PP=100.0;SC=AAACAGTTTTTTATATATATA;TC=14;TR=4	GT:GL:GQ	0/1:-162.1,-119.94,-126.23:30
+20	6443546	.	G	GTA	.	PASS	FR=0.5;HP=2;NF=1;NR=2;PP=100.0;SC=ATATATATGTGTATATATATA;TC=14;TR=3	GT:GL:GQ	0/1:-156.72,-103.24,-116.61:61
+20	6447485	.	C	CA	.	PASS	FR=0.5;HP=3;NF=4;NR=13;PP=100.0;SC=TTTTGAATTTCAAATATTTTC;TC=38;TR=17	GT:GL:GQ	0/1:-255.09,-105.01,-200.26:100
+20	6448179	.	TAATAA	T	.	PASS	FR=0.5;HP=5;NF=3;NR=4;PP=100.0;SC=TATCTCGAAATAATAAAATAA;TC=36;TR=7	GT:GL:GQ	0/1:-185.97,-96.1,-256.82:100
+20	6456952	.	ATT	AT,A	.	PASS	FR=0.5,0.5;HP=10;NF=7,8;NR=4,5;PP=100.0,100.0;SC=CAATGATGTCATTTTTTTTTT;TC=27;TR=11,13	GT:GL:GQ	1/2:-1.0,-1.0,-1.0:100
+20	6458185	.	GA	G	.	PASS	FR=0.5;HP=10;NF=11;NR=4;PP=100.0;SC=AAATAAAAATGAAAAAAAAAA;TC=48;TR=15	GT:GL:GQ	0/1:-255.96,-202.85,-273.91:100
+20	6459292	.	G	GA	.	PASS	FR=0.5;HP=10;NF=2;NR=6;PP=49.0;SC=TATCCTATCAGAAAAAAAAAC;TC=30;TR=8	GT:GL:GQ	0/1:-83.74,-61.52,-111.1:99
+20	6473904	.	TAGGTGAAATTTTCTTTTCTGTTTTTTTAA	T	.	PASS	FR=0.5;HP=1;NF=2;NR=1;PP=100.0;SC=TCCCTAATTCTAGGTGAAATT;TC=25;TR=3	GT:GL:GQ	0/1:-202.85,-99.33,-502.66:100
+20	6481086	.	T	TTGTC	.	PASS	FR=1.0;HP=2;NF=7;NR=5;PP=100.0;SC=TTGTTCCTCTTTGTCAGAGCA;TC=21;TR=12	GT:GL:GQ	1/1:-268.34,-19.84,-4.6:100
+20	6488178	.	CTTG	C	.	PASS	FR=1.0;HP=2;NF=13;NR=13;PP=100.0;SC=AAGCTACTTGCTTGTTGTTGA;TC=32;TR=26	GT:GL:GQ	1/1:-335.98,-26.27,-4.81:100
+20	6520175	.	C	CTT	.	PASS	FR=1.0;HP=3;NF=12;NR=17;PP=100.0;SC=TTACTTAAGACTTTCTATTGA;TC=35;TR=29	GT:GL:GQ	1/1:-362.42,-32.47,-7.59:100
+20	6524976	.	GACTAC	G	.	PASS	FR=1.0;HP=2;NF=12;NR=13;PP=100.0;SC=CTATGAAATTGACTACACTAC;TC=32;TR=25	GT:GL:GQ	1/1:-403.49,-65.81,-45.47:100
+20	6531643	.	GT	G	.	PASS	FR=1.0;HP=4;NF=17;NR=11;PP=100.0;SC=CAGATAAAGTGTTTAATTCAT;TC=31;TR=28	GT:GL:GQ	1/1:-281.56,-58.08,-38.11:100
+20	6544912	.	CAGAT	CAGATAGATAGATAGAT,C	.	PASS	FR=0.5,0.5;HP=1;NF=1,1;NR=4,1;PP=100.0,100.0;SC=TATTCACTGCCAGATAGATAG;TC=24;TR=5,2	GT:GL:GQ	1/2:-1.0,-1.0,-1.0:100
+20	6548435	.	A	AAGAG	.	PASS	FR=1.0;HP=2;NF=5;NR=8;PP=100.0;SC=GAGAAACAGAAAGAGAGAGAG;TC=33;TR=13	GT:GL:GQ	1/1:-316.58,-47.12,-29.98:100
+20	6549783	.	C	CTT	.	PASS	FR=1.0;HP=9;NF=3;NR=10;PP=100.0;SC=TGGTCCAGGCCTTTTTTTTTG;TC=24;TR=13	GT:GL:GQ	1/1:-145.52,-61.65,-53.62:66
+20	6553955	.	TTATA	T	.	PASS	FR=1.0;HP=3;NF=12;NR=6;PP=100.0;SC=ATTTTACATTTTATATATATA;TC=30;TR=18	GT:GL:GQ	1/1:-272.92,-35.6,-20.34:100
+20	6563467	.	CTAGGTAGGTAGG	C	.	PASS	FR=1.0;HP=1;NF=3;NR=6;PP=100.0;SC=ACATGCATTCCTAGGTAGGTA;TC=22;TR=9	GT:GL:GQ	1/1:-367.98,-150.14,-139.95:85
+20	6565618	.	CGTGT	C	.	PASS	FR=1.0;HP=2;NF=4;NR=3;PP=100.0;SC=TGTGTGTGTTCGTGTGTGTGT;TC=19;TR=7	GT:GL:GQ	1/1:-220.73,-126.68,-119.85:85
+20	6565651	.	G	GTA	.	PASS	FR=0.5286;HP=2;NF=3;NR=2;PP=100.0;SC=GTGTATATGTGTATATATATA;TC=16;TR=5	GT:GL:GQ	0/1:-258.66,-193.34,-195.57:12
+20	6585232	.	C	CT	.	PASS	FR=1.0;HP=2;NF=15;NR=16;PP=100.0;SC=ACAAACCCATCTCCTAAAATC;TC=33;TR=31	GT:GL:GQ	1/1:-314.24,-29.76,-6.91:100
+20	6590623	.	C	CCTGCTT	.	PASS	FR=1.0;HP=1;NF=17;NR=14;PP=100.0;SC=AGAGTTATCTCCTGCTGTCAT;TC=32;TR=31	GT:GL:GQ	1/1:-527.33,-38.07,-14.51:100
+20	6603635	.	C	CA	.	PASS	FR=1.0;HP=4;NF=12;NR=8;PP=100.0;SC=TTAGTCAAGCCAAAATCACAT;TC=27;TR=20	GT:GL:GQ	1/1:-325.58,-214.53,-199.34:100
+20	6609608	.	CTT	C	.	PASS	FR=1.0;HP=3;NF=10;NR=9;PP=100.0;SC=TGTTTTGATGCTTTCTGGCTT;TC=27;TR=19	GT:GL:GQ	1/1:-576.75,-576.47,-576.51:100
+20	6609611	.	T	TGGAGGAGGA	.	PASS	FR=1.0;HP=2;NF=9;NR=9;PP=100.0;SC=TTTGATGCTTTCTGGCTTGGA;TC=23;TR=18	GT:GL:GQ	1/1:-576.75,-311.9,-294.35:100
+20	6644452	.	C	CTGTAG	.	PASS	FR=1.0;HP=1;NF=14;NR=16;PP=100.0;SC=ATAAAAGGCACTGTAGCATAG;TC=35;TR=30	GT:GL:GQ	1/1:-563.91,-35.77,-9.44:100
+20	6647434	.	A	ATC	.	PASS	FR=1.0;HP=2;NF=4;NR=14;PP=100.0;SC=GGATACTGAGATTCTAAGTAG;TC=21;TR=18	GT:GL:GQ	1/1:-241.28,-23.07,-7.83:100
+20	6655343	.	T	TG	.	PASS	FR=1.0;HP=6;NF=6;NR=9;PP=100.0;SC=AGTCTAAAGATTTTTTTCTGG;TC=18;TR=15	GT:GL:GQ	1/1:-141.83,-27.31,-14.91:95
+20	6655876	.	GTATATA	GTA,G	.	PASS	FR=0.5,0.5;HP=1;NF=8,2;NR=11,1;PP=100.0,58.0;SC=TACATATATAGTATATATATA;TC=31;TR=19,3	GT:GL:GQ	1/2:-1.0,-1.0,-1.0:100
+20	6664331	.	C	CTG	.	PASS	FR=1.0;HP=5;NF=5;NR=10;PP=100.0;SC=GGTTTAAAAACTGTGTGTGTG;TC=30;TR=15	GT:GL:GQ	1/1:-232.49,-35.13,-29.16:74
+20	6668238	.	CT	C	.	PASS	FR=1.0;HP=10;NF=7;NR=15;PP=100.0;SC=ACTGGAGAAACTTTTTTTTTT;TC=30;TR=22	GT:GL:GQ	1/1:-332.94,-279.88,-269.29:89
+20	6677392	.	CTGTGTG	C	.	PASS	FR=0.5;HP=2;NF=1;NR=6;PP=100.0;SC=GTGTGTGGCCCTGTGTGTGTG;TC=24;TR=7	GT:GL:GQ	0/1:-156.67,-56.12,-128.5:100
+20	6687137	.	CAT	C	.	PASS	FR=1.0;HP=2;NF=12;NR=13;PP=100.0;SC=ATAAGATCCACATGAGACAAT;TC=26;TR=25	GT:GL:GQ	1/1:-279.85,-22.16,-4.14:100
+20	6690400	.	T	TG	.	PASS	FR=1.0;HP=2;NF=22;NR=8;PP=100.0;SC=TTAATACATTTGTATGCCCTG;TC=31;TR=30	GT:GL:GQ	1/1:-315.1,-40.57,-19.1:100
+20	6694813	.	GAA	G	.	PASS	FR=1.0;HP=6;NF=5;NR=4;PP=100.0;SC=AAGAAAGAAAGAAAGAGAAAG;TC=13;TR=9	GT:GL:GQ	1/1:-119.78,-18.28,-9.43:64
+20	6717401	.	G	GA	.	PASS	FR=1.0;HP=10;NF=14;NR=6;PP=100.0;SC=CTCTCTTAAGGAAAAAAAAAA;TC=27;TR=20	GT:GL:GQ	1/1:-134.21,-33.86,-20.0:100
+20	6723994	.	A	AAC	.	PASS	FR=1.0;HP=4;NF=10;NR=3;PP=100.0;SC=CACATACAAAAACACACACAC;TC=23;TR=13	GT:GL:GQ	1/1:-174.48,-22.71,-13.76:74
+20	6746236	.	C	CTTAT	.	PASS	FR=0.5;HP=2;NF=2;NR=4;PP=100.0;SC=CTGGAGACTACTTATTTATTT;TC=23;TR=6	GT:GL:GQ	0/1:-115.46,-26.87,-109.86:100
+20	6759758	.	A	AAT	.	PASS	FR=0.5;HP=2;NF=2;NR=3;PP=100.0;SC=TAAATACATAAATATATATAT;TC=21;TR=5	GT:GL:GQ	0/1:-98.2,-23.97,-51.3:100
+20	6765134	.	A	AACAC	.	PASS	FR=0.5;HP=1;NF=2;NR=5;PP=100.0;SC=TTGAGAATCTAACACACACAC;TC=25;TR=7	GT:GL:GQ	0/1:-145.56,-56.64,-151.12:100
diff --git a/tests/tabix_data/vcf/6.vcf b/tests/tabix_data/vcf/6.vcf
new file mode 100644
index 0000000..fa039b1
--- /dev/null
+++ b/tests/tabix_data/vcf/6.vcf
@@ -0,0 +1,278 @@
+##fileformat=VCFv4.1
+##INFO=<ID=CallsetAC,Number=.,Type=Integer,Description="">
+##INFO=<ID=CallsetAC2,Number=.,Type=Integer,Description="">
+##INFO=<ID=HW_VIOLATION,Number=0,Type=Flag,Description="Genotypes violate Hardy-Weinberg">
+##INFO=<ID=SEQUENCING.AC,Number=1,Type=Integer,Description="Allele count from sequencing-based genotypes over all samples">
+##INFO=<ID=SEQUENOM.AC,Number=1,Type=Integer,Description="Allele count from Sequenom genotyping">
+##INFO=<ID=Groups,Number=.,Type=String,Description="Center that called this variant">
+##INFO=<ID=HR,Number=1,Type=Integer,Description="Homopolymer run length">
+##INFO=<ID=TR,Number=1,Type=Integer,Description="Tandem repeat run length (bp)">
+##INFO=<ID=TU,Number=1,Type=String,Description="tandem repeat run unit (stranded)">
+##INFO=<ID=HU,Number=1,Type=String,Description="Homopolymer run unit (stranded)">
+##INFO=<ID=IH,Number=1,Type=Character,Description="Indel hotspot: estimated local rate exceeds SNP rate">
+##INFO=<ID=Set,Number=1,Type=String,Description="Set from which this site was chosen for validation">
+##FILTER=<ID=AMBIGUOUS_SEQUENOM_CALLS,Description="Possible Sequenom miscalls based on manual review of cluster plots">
+##FILTER=<ID=INCORRECT_SEQUENOM_CALLS,Description="Clear Sequenom miscalls based on manual review of cluster plots">
+##FILTER=<ID=TOO_MANY_ALT_ALLELES,Description="Extremely high value (many times more or greater than 700) for SEQUENOM.AC given the SEQUENCING.AC">
+##fileDate=20110531
+##reference=ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz
+##source=EricBanksValidationQC;fromGertonLunterValidationSelection
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	HG00127	HG00128	HG00136	HG00137	HG00138	HG00139	HG00152	HG00156	HG00234	HG00235	HG00237	HG00242	HG00244	HG00262	HG01055	HG01079	NA19138	NA18974	NA18523	NA12717	NA19209	NA18577	NA18973	NA18943	NA12873	NA18623	NA18622	NA18948	NA19171	NA19204	NA06994	NA18563	NA18547	NA18861	NA18608	NA18995	NA10851	NA18976	NA18603	NA19200	HG01204	HG01191	HG01101	HG00146	HG00306	NA18985	HG00160	HG00635	HG00372	HG00357	HG00634	NA18541	NA18950	NA19759	HG00351	HG00257	HG00118	HG00336	HG00448	HG01354	NA18609	HG00428	HG00326	NA11894	NA18956	HG00173	HG00117	NA11893	HG01251	HG01441	HG01437	HG00182	HG00330	HG01060	HG00329	NA18960	NA18856	NA07346	NA18871	NA19057	NA18868	NA18636	NA12830	NA19007	NA18910	NA18874	NA19056	NA19064	NA19066	NA18487	NA18642	NA19236	NA07056	NA18637	NA19235	NA19309	NA19311	NA19334	NA19346	NA19347	NA19372	NA19376	NA19383	NA19384	NA19394	NA19428	NA19430	NA19451	NA19466	NA19313	NA19321	NA19324	NA19332	NA19390	NA19436	NA19439	NA19440	NA19463	NA19470	NA19471	NA19472	NA19676	NA19660	NA19661	NA19663	NA19722	NA19725	NA19728	NA19729	NA19731	NA19749	NA19755	NA19756	NA19758	NA19770	NA19773	NA19777	NA19780	NA19783	NA20525	NA20589	NA20765	NA20802	NA20804	NA18544	NA18602	NA18546	NA18610	NA18957	NA18615	NA18616	NA19010	NA18638	NA18639	NA18627	NA19072	NA18630	NA19074	NA19080	NA19081	NA19083	NA19085	NA19088	NA20287	NA19835	NA20276	NA19818	NA20278	NA20282	NA20342	NA20296	NA20314	NA20346	NA19712	NA19198	NA19108	NA18934	NA18916	NA18907	NA18917	NA06989	NA12058	NA12341	NA12546	NA12489	HG01197	NA18983	NA11843	NA11892	NA12749	NA12282	NA12751	NA18959	NA19331	NA19453	NA20537	NA12046	NA20515	NA20516	NA20521	NA20524	NA20528	NA20759	NA20768	NA20769	NA20774	NA20775	NA20783	NA20787	NA20790	NA20800	NA20819	NA20812	NA20505	NA20530	NA20540	NA20538	NA20581	NA20815	NA20544	NA20810	NA20807	NA20816	NA20504	NA20753	NA20502	NA12342	NA19150	NA19468	NA20336	NA19395	NA19257	NA19360	NA19700	NA18867	NA20317	NA18968	NA19107	HG00111	HG00108	NA19077	NA19684	NA18511	NA12044	NA19382	NA19457	NA18933	NA18923	NA18965	HG00141	NA20341	NA18740	HG00537	HG00346	HG01173	HG00702	HG00313	HG00150	NA18612	HG00339	NA12273	HG00250	NA18593	NA18621	HG00478	HG00251	HG01070	NA19160	HG00479	HG00608	NA18573	HG00375	NA19248	NA19093	HG01170	HG00534	HG01171	HG01522	NA18624	HG00683	HG01521	NA19005	NA20412	NA18971	HG00446	NA12748	HG00530	HG00690	HG01356	HG01516	NA20532	HG00344	HG00328	NA18542	HG00254	HG00321	HG00577	HG00656	HG00342	HG00524	HG00650	HG00557	HG00319	HG00457	HG00125	HG00578	HG00543	HG00638	HG00171	HG00699	HG00595	HG00187	HG00704	HG00533	HG00596	HG00268	HG01083	HG00651	HG01133	HG00671	HG00327	HG01148	HG00246	HG00672	HG00556	HG00436	HG00554	NA18633	NA20344	NA11993	NA07037	NA11930	HG01366	HG01389	HG00620	NA19740	HG00190	HG00419	NA18535	HG01495	NA18592	HG01497	HG00174	HG01140	NA12287	HG00689	HG01550	HG00334	HG01375	HG00637	NA18507	HG01113	NA18550	NA19129	HG01551	HG01462	HG00331	NA12413	HG01456	HG01360	HG00708	HG01350	HG00684	NA19099	HG00284	NA12399	NA12286	NA12777	HG00277	HG00266	NA19985	HG00353	HG01102	NA07347	NA07051	NA19900	NA18984	NA07048	HG00640	HG01066	NA12812	HG01174	HG01188
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+20	4363519	.	CATT	C	99	PASS	SEQUENCING.AC=15;CallSetAC=18,20,15,14,16;CallSetAC2=0,1,0,0,0;Groups=BC,BI,DINDEL,OX,SAMTOOLS;HR=1;HU=A;IH=0;TR=1;TU=A;Set=SAMTOOLS;SEQUENOM.AC=7	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
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+20	4641550	.	CCTTGA	C	99	PASS	SEQUENCING.AC=3;CallSetAC=0,0,13,4,3;CallSetAC2=0,0,2,1,1;Groups=DINDEL,OX,SAMTOOLS;HR=2;HU=C;IH=0;TR=2;TU=C;Set=SAMTOOLS;SEQUENOM.AC=3	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
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+20	12114989	.	CTA	C	99	PASS	SEQUENCING.AC=3;CallSetAC=0,4,4,3,4;CallSetAC2=0,1,1,1,1;Groups=BI,DINDEL,OX,SAMTOOLS;HR=1;HU=T;IH=0;TR=1;TU=T;Set=BI;SEQUENOM.AC=4	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
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+20	13287841	.	CAT	C	99	TOO_MANY_ALT_ALLELES	SEQUENCING.AC=36;CallSetAC=0,64,0,38,18;CallSetAC2=0,1,0,0,0;Groups=BI,OX,SAMTOOLS;HR=1;HU=A;IH=0;TR=1;TU=A;Set=BI;SEQUENOM.AC=626	GT	0/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/0	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/0	1/1	0/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	0/0	1/1	1/1	1/1	0/0	0/1	0/1	.	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/0	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	0/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	1/1	0/0	1/1	0/0	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	0/1	0/1	0/1	1/1	0/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	0/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	0/0	1/1	0/0	0/1	1/1	1/1	0/1	.	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	1/1	1/1	1/1	1/1	1/1	1/1	0/1	0/1	1/1	0/1	1/1	1/1	0/1	1/1	1/1	0/0	0/1	0/1	0/1	0/1	1/1	1/1	0/1	0/1	1/1	0/1	1/1	1/1	0/1	1/1	.	1/1	1/1	1/1	0/1	0/1	1/1	1/1	0/1	0/1	1/1	0/1	1/1	0/1	0/1	0/1	1/1	1/1	1/1	1/1	1/1	0/1	1/1	0/1	0/1	0/1	1/1	0/1	0/1	1/1	0/0	1/1	1/1	0/1	0/1	0/1	1/1	1/1	0/1	1/1	1/1	1/1	1/1	0/1	1/1
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+20	25905250	.	GT	G	99	TOO_MANY_ALT_ALLELES	SEQUENCING.AC=56;CallSetAC=0,58,57,0,0;CallSetAC2=0,1,1,0,0;Groups=BI,DINDEL;HR=6;HU=T;IH=1;TR=6;TU=T;Set=DINDEL;SEQUENOM.AC=764	GT	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	.	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1	1/1
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+20	41964672	.	A	AT	99	PASS	SEQUENCING.AC=243;CallSetAC=0,0,0,253,0;CallSetAC2=0,0,0,1,0;Groups=OX;HR=2;HU=T;IH=0;TR=2;TU=T;Set=OX;SEQUENOM.AC=0	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	.	0/0	.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
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+20	42159695	.	GC	G	99	TOO_MANY_ALT_ALLELES	SEQUENCING.AC=6;CallSetAC=7,0,0,0,0;CallSetAC2=1,0,0,0,0;Groups=BC;HR=3;HU=G;IH=0;TR=3;TU=G;Set=BC;SEQUENOM.AC=87	GT	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/1	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	1/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	.	0/0	.	0/1	0/0	0/1	0/1	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1
+20	42261635	.	C	CATTT	99	PASS	SEQUENCING.AC=54;CallSetAC=62,75,76,57,58;CallSetAC2=1,1,1,1,1;Groups=BC,BI,DINDEL,OX,SAMTOOLS;HR=1;HU=A;IH=0;TR=5;TU=AC;Set=DINDEL;SEQUENOM.AC=24	GT	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
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+20	44071585	.	C	CT	99	PASS	SEQUENCING.AC=293;CallSetAC=310,351,323,302,335;CallSetAC2=0,1,0,1,1;Groups=BC,BI,DINDEL,OX,SAMTOOLS;HR=1;HU=T;IH=0;TR=4;TU=CT;Set=SAMTOOLS;SEQUENOM.AC=132	GT	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/1	1/1	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/1	0/1	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	1/1	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	.	0/0	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	1/1	0/0	0/0	0/1	1/1	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	1/1	0/1	0/1	0/0	0/1	0/1	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/1	0/0	0/1	0/0	1/1	0/0	0/1	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	1/1	0/1	0/0	0/0	1/1	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/1	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1
+20	44220528	.	T	TC	99	PASS	SEQUENCING.AC=29;CallSetAC=34,38,0,0,18;CallSetAC2=0,1,0,0,0;Groups=BC,BI,SAMTOOLS;HR=5;HU=T;IH=0;TR=5;TU=T;Set=BI;SEQUENOM.AC=59	GT	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/1	0/0	0/1	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/1	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0
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diff --git a/tests/tabix_data/vcf/7.vcf b/tests/tabix_data/vcf/7.vcf
new file mode 100644
index 0000000..33e3ca7
--- /dev/null
+++ b/tests/tabix_data/vcf/7.vcf
@@ -0,0 +1,317 @@
+##fileformat=VCFv4.1
+##INFO=<ID=BCM.AC,Number=1,Type=Integer,Description="Allele count from BCM's (sequencing-based) genotypes subsetted to the 383 validation samples">
+##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership">
+##INFO=<ID=HW_VIOLATION,Number=0,Type=Flag,Description="Genotypes violate Hardy-Weinberg">
+##INFO=<ID=SEQUENOM.AC,Number=1,Type=Integer,Description="Allele count from Sequenom genotyping">
+##INFO=<ID=SRC,Number=1,Type=String,Description="Type of SNPs submitted for validation; VQSR refers to preliminary consensus set, not the final one">
+##FILTER=<ID=AMBIGUOUS_SEQUENOM_CALLS,Description="Possible Sequenom miscalls based on manual review of cluster plots">
+##FILTER=<ID=DUPLICATE_MAPPING,Description="Site did not map uniquely in the genome">
+##FILTER=<ID=HIGH_NO_CALL_RATE,Description="Extremely high no-call rate">
+##FILTER=<ID=INCORRECT_SEQUENOM_CALLS,Description="Clear Sequenom miscalls that cannot easily be fixed based on manual review of cluster plots">
+##FILTER=<ID=NOT_DESIGNED,Description="Site did not design or genotype">
+##FILTER=<ID=POLYMORPHIC_SAMPLES_FAILED,Description="All polymorphic samples from sequencing were no-called">
+##FILTER=<ID=POSSIBLE_PROBE_FAILURE,Description="Suspicious genotyping based on nearby SNPs">
+##fileDate=20110524
+##reference=ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz
+##source=EricBanksValidationQC;fromGoncaloAbecasisValidationSelection
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+20	82176	rs11906362	T	C	318	NOT_DESIGNED	BCM.AC=16;DB;SRC=VQSR+2-OF-7
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+20	688672	rs116071340	C	T	56	PASS	BCM.AC=1;DB;SEQUENOM.AC=2;SRC=VQSR+2-OF-7	GT	.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	.	0/0	.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0
+20	987773	rs6077519	T	G	474	PASS	DB;HW_VIOLATION;SEQUENOM.AC=73;SRC=VQSR-ONLY	GT	.	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	.	0/0	1/1	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	.	0/0	.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	1/1	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	.	0/0	1/1	1/1	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/0	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/1	0/0	0/0	0/0	1/1	1/1	0/0	1/1	0/0	0/0	0/0	0/0	1/1	1/1	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/0	0/0	0/0	1/1	0/0	0/0	0/0	1/1	0/0	0/0	.	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	.	0/0	0/1	.	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/1	0/0	0/0	.	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	1/1	0/0	0/0	0/1	0/0	0/0	0/0	0/0	0/0	0/0	1/1	0/0	0/0	0/0	.	0/0	0/0	0/0	0/0	0/0	0/0
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diff --git a/tests/tabix_data/vcf/8.vcf b/tests/tabix_data/vcf/8.vcf
new file mode 100644
index 0000000..4ec2daf
--- /dev/null
+++ b/tests/tabix_data/vcf/8.vcf
@@ -0,0 +1,84 @@
+##fileformat=VCFv4.0
+##FILTER=<ID=HardyWeinbergViolation,Description="The validation is in Hardy-Weinberg violation">
+##FILTER=<ID=HighNoCallRate,Description="The validation no-call rate is too high">
+##FILTER=<ID=TooManyHomVars,Description="The validation homozygous variant rate is too high">
+##INFO=<ID=AC,Number=1,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##INFO=<ID=HW,Number=1,Type=Float,Description="Phred-scaled Hardy-Weinberg violation p-value">
+##INFO=<ID=HetPct,Number=1,Type=Float,Description="Percent of heterozygous genotypes">
+##INFO=<ID=HomRefPct,Number=1,Type=Float,Description="Percent of homozygous reference genotypes">
+##INFO=<ID=HomVarPct,Number=1,Type=Float,Description="Percent homozygous variant genotypes">
+##INFO=<ID=NoCallPct,Number=1,Type=Float,Description="Percent of no-calls">
+##ValidationMetrics_HardyWeinbergViolations="25 (8%)"
+##ValidationMetrics_HomVarViolations="0 (0%)"
+##ValidationMetrics_NoCallViolations="13 (4%)"
+##ValidationMetrics_PolymorphicPassingRecords="195 (75%)"
+##ValidationMetrics_RecordsPassingFilters="258 (87%)"
+##ValidationMetrics_RecordsProcessed=296
+##ValidationMetrics_SamplesAssayed=383
+##VariantValidationAssessor="analysis_type=VariantValidationAssessor input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=null excludeIntervals=null reference_sequence=/humgen/1kg/reference/human_g1k_v37.fasta rodBind=[rawData/plink.renamed.sorted.fixed.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub maxHardy=20.0 maxNoCall=0.05 maxHomVar=1.1"
+##source=PLINK
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	HG00127	HG00128	HG00136	HG00137	HG00138	HG00139	HG00152	HG00156	HG00234	HG00235	HG00237	HG00242	HG00244	HG00262	HG01055	HG01079	NA19138	NA18974	NA18523	NA12717	NA19209	NA18577	NA18973	NA18943	NA12873	NA18623	NA18622	NA18948	NA19171	NA19204	NA06994	NA18563	NA18547	NA18861	NA18608	NA18995	NA10851	NA18976	NA18603	NA19200	HG01204	HG01191	HG01101	HG00146	HG00306	NA18985	HG00160	HG00635	HG00372	HG00357	HG00634	NA18541	NA18950	NA19759	HG00351	HG00257	HG00118	HG00336	HG00448	HG01354	NA18609	HG00428	HG00326	NA11894	NA18956	HG00173	HG00117	NA11893	HG01251	HG01441	HG01437	HG00182	HG00330	HG01060	HG00329	NA18960	NA18856	NA07346	NA18871	NA19057	NA18868	NA18636	NA12830	NA19007	NA18910	NA18874	NA19056	NA19064	NA19066	NA18487	NA18642	NA19236	NA07056	NA18637	NA19235	NA19309	NA19311	NA19334	NA19346	NA19347	NA19372	NA19376	NA19383	NA19384	NA19394	NA19428	NA19430	NA19451	NA19466	NA19313	NA19321	NA19324	NA19332	NA19390	NA19436	NA19439	NA19440	NA19463	NA19470	NA19471	NA19472	NA19676	NA19660	NA19661	NA19663	NA19722	NA19725	NA19728	NA19729	NA19731	NA19749	NA19755	NA19756	NA19758	NA19770	NA19773	NA19777	NA19780	NA19783	NA20525	NA20589	NA20765	NA20802	NA20804	NA18544	NA18602	NA18546	NA18610	NA18957	NA18615	NA18616	NA19010	NA18638	NA18639	NA18627	NA19072	NA18630	NA19074	NA19080	NA19081	NA19083	NA19085	NA19088	NA20287	NA19835	NA20276	NA19818	NA20278	NA20282	NA20342	NA20296	NA20314	NA20346	NA19712	NA19198	NA19108	NA18934	NA18916	NA18907	NA18917	NA06989	NA12058	NA12341	NA12546	NA12489	HG01197	NA18983	NA11843	NA11892	NA12749	NA12282	NA12751	NA18959	NA19331	NA19453	NA20537	NA12046	NA20515	NA20516	NA20521	NA20524	NA20528	NA20759	NA20768	NA20769	NA20774	NA20775	NA20783	NA20787	NA20790	NA20800	NA20819	NA20812	NA20505	NA20530	NA20540	NA20538	NA20581	NA20815	NA20544	NA20810	NA20807	NA20816	NA20504	NA20753	NA20502	NA12342	NA19150	NA19468	NA20336	NA19395	NA19257	NA19360	NA19700	NA18867	NA20317	NA18968	NA19107	HG00111	HG00108	NA19077	NA19684	NA18511	NA12044	NA19382	NA19457	NA18933	NA18923	NA18965	HG00141	NA20341	NA18740	HG00537	HG00346	HG01173	HG00702	HG00313	HG00150	NA18612	HG00339	NA12273	HG00250	NA18593	NA18621	HG00478	HG00251	HG01070	NA19160	HG00479	HG00608	NA18573	HG00375	NA19248	NA19093	HG01170	HG00534	HG01171	HG01522	NA18624	HG00683	HG01521	NA19005	NA20412	NA18971	HG00446	NA12748	HG00530	HG00690	HG01356	HG01516	NA20532	HG00344	HG00328	NA18542	HG00254	HG00321	HG00577	HG00656	HG00342	HG00524	HG00650	HG00557	HG00319	HG00457	HG00125	HG00578	HG00543	HG00638	HG00171	HG00699	HG00595	HG00187	HG00704	HG00533	HG00596	HG00268	HG01083	HG00651	HG01133	HG00671	HG00327	HG01148	HG00246	HG00672	HG00556	HG00436	HG00554	NA18633	NA20344	NA11993	NA07037	NA11930	HG01366	HG01389	HG00620	NA19740	HG00190	HG00419	NA18535	HG01495	NA18592	HG01497	HG00174	HG01140	NA12287	HG00689	HG01550	HG00334	HG01375	HG00637	NA18507	HG01113	NA18550	NA19129	HG01551	HG01462	HG00331	NA12413	HG01456	HG01360	HG00708	HG01350	HG00684	NA19099	HG00284	NA12399	NA12286	NA12777	HG00277	HG00266	NA19985	HG00353	HG01102	NA07347	NA07051	NA19900	NA18984	NA07048	HG00640	HG01066	NA12812	HG01174	HG01188
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diff --git a/tests/tabix_data/vcf/9.vcf b/tests/tabix_data/vcf/9.vcf
new file mode 100644
index 0000000..e0d112c
--- /dev/null
+++ b/tests/tabix_data/vcf/9.vcf
@@ -0,0 +1,1000 @@
+##fileformat=VCFv4.0
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	DNA_pool_A
+chr1	1281168	.	A	G	14	.	DP=37;AF1=0.6243;CI95=0.5,1;DP4=4,0,6,0;MQ=15;PV4=1,0.027,1,1	PL:GT:GQ	43,0,4:0/1:6
+chr1	1281205	.	T	C	26	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=41	PL:GT:GQ	58,9,0:1/1:63
+chr1	1281206	.	G	C	25	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=41	PL:GT:GQ	57,9,0:1/1:63
+chr1	1922737	.	G	C	13.2	.	DP=21;AF1=1;CI95=1,1;DP4=0,0,0,21;MQ=22	PL:GT:GQ	46,63,0:1/1:99
+chr1	21197513	.	A	G	55.1	.	DP=9;AF1=1;CI95=1,1;DP4=0,0,0,7;MQ=41	PL:GT:GQ	88,21,0:1/1:84
+chr1	21343209	.	T	C	5.45	.	DP=17;AF1=1;CI95=1,1;DP4=0,0,17,0;MQ=14	PL:GT:GQ	37,51,0:1/1:99
+chr1	22097362	.	T	C	4.75	.	DP=10;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=30	PL:GT:GQ	35,9,0:1/1:63
+chr1	22254012	.	A	G	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=50	PL:GT:GQ	40,6,0:1/1:49
+chr1	22650927	.	G	A	48.1	.	DP=11;AF1=1;CI95=1,1;DP4=0,0,0,7;MQ=24	PL:GT:GQ	81,21,0:1/1:84
+chr1	23535401	.	C	T	40.4	.	DP=25;AF1=1;CI95=0.5,1;DP4=0,16,0,5;MQ=19;PV4=1,0.2,1,1	PL:GT:GQ	73,13,0:1/1:65
+chr1	23543855	.	T	C	49.1	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=44	PL:GT:GQ	82,18,0:1/1:90
+chr1	24245107	.	C	G	32	.	DP=4;AF1=0.5001;CI95=0.5,0.5;DP4=0,2,0,2;MQ=36;PV4=1,1,1,1	PL:GT:GQ	62,0,35:0/1:38
+chr1	24274412	.	G	C	39.5	.	DP=7;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=32	PL:GT:GQ	72,12,0:1/1:72
+chr1	36529832	.	C	T	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=46	PL:GT:GQ	73,6,0:1/1:49
+chr1	37788090	.	A	G	89.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=49	PL:GT:GQ	122,12,0:1/1:72
+chr1	43120440	.	C	T	34	.	DP=3;AF1=0.5002;CI95=0.5,0.5;DP4=0,1,0,2;MQ=49;PV4=1,1,1,1	PL:GT:GQ	64,0,31:0/1:34
+chr1	43980466	.	C	T	43	.	DP=16;AF1=1;CI95=1,1;DP4=0,0,0,15;MQ=19	PL:GT:GQ	76,45,0:1/1:99
+chr1	46047795	.	T	C	29.1	.	DP=7;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=31	PL:GT:GQ	62,18,0:1/1:90
+chr1	48860309	.	C	T	99	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=46	PL:GT:GQ	141,18,0:1/1:90
+chr1	49415599	.	T	C	4.61	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=34	PL:GT:GQ	34,6,0:1/1:49
+chr1	51601816	.	G	T	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=50	PL:GT:GQ	40,6,0:1/1:49
+chr1	51955459	.	G	C	89.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=49	PL:GT:GQ	122,12,0:1/1:72
+chr1	68479569	.	T	G	12	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48	PL:GT:GQ	43,6,0:1/1:49
+chr1	69032455	.	A	G	15.1	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=29	PL:GT:GQ	47,9,0:1/1:63
+chr1	71888225	.	G	T	9.31	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=43	PL:GT:GQ	40,6,0:1/1:49
+chr1	72381528	.	T	C	44	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=41	PL:GT:GQ	76,9,0:1/1:63
+chr1	82004013	.	A	G	37.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=50	PL:GT:GQ	70,12,0:1/1:72
+chr1	86289622	.	C	T	18	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=42	PL:GT:GQ	50,9,0:1/1:63
+chr1	90267663	.	A	G	22	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=45	PL:GT:GQ	54,9,0:1/1:63
+chr1	92699542	.	A	G	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=45	PL:GT:GQ	40,6,0:1/1:49
+chr1	94867317	.	G	A	26.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=45	PL:GT:GQ	58,6,0:1/1:49
+chr1	96428713	.	C	G	3.98	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=27	PL:GT:GQ	33,6,0:1/1:49
+chr1	100466329	.	G	C	4.85	.	DP=16;AF1=1;CI95=1,1;DP4=0,0,0,6;MQ=22	PL:GT:GQ	36,18,0:1/1:90
+chr1	101909281	.	G	A	70	.	DP=11;AF1=0.5;CI95=0.5,0.5;DP4=4,0,5,0;MQ=46;PV4=1,1,0.096,1	PL:GT:GQ	100,0,88:0/1:91
+chr1	106216572	.	T	A	22	.	DP=18;AF1=1;CI95=1,1;DP4=0,0,16,0;MQ=21	PL:GT:GQ	55,48,0:1/1:99
+chr1	107901770	.	T	C	9.31	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35	PL:GT:GQ	40,6,0:1/1:49
+chr1	108431179	.	A	G	99	.	DP=8;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=41	PL:GT:GQ	155,24,0:1/1:96
+chr1	112005344	.	C	T	99	.	DP=52;AF1=1;CI95=1,1;DP4=7,0,27,0;MQ=44;PV4=1,1,1,1	PL:GT:GQ	196,25,0:1/1:99
+chr1	116625452	.	C	T	36	.	DP=44;AF1=0.5;CI95=0.5,0.5;DP4=0,23,0,20;MQ=49;PV4=1,2.3e-69,0.42,1	PL:GT:GQ	66,0,179:0/1:69
+chr1	118060710	.	G	T	6.98	.	DP=8;AF1=0.4999;CI95=0.5,0.5;DP4=4,0,3,0;MQ=47;PV4=1,0.0071,1,1	PL:GT:GQ	36,0,73:0/1:39
+chr1	118198177	.	A	G	15.9	.	DP=23;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=43	PL:GT:GQ	47,6,0:1/1:49
+chr1	118586346	.	T	C	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49	PL:GT:GQ	40,6,0:1/1:49
+chr1	120809555	.	G	A	20	.	DP=8;AF1=0.5;CI95=0.5,0.5;DP4=6,0,2,0;MQ=46;PV4=1,1,1,1	PL:GT:GQ	50,0,106:0/1:53
+chr1	130723110	.	C	A	20.7	.	DP=8;AF1=0.5939;CI95=0.5,1;DP4=0,6,0,2;MQ=26;PV4=1,1,1,1	PL:GT:GQ	50,0,5:0/1:7
+chr1	133979895	.	T	C	14.9	.	DP=7;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=43	PL:GT:GQ	46,6,0:1/1:49
+chr1	134977940	.	C	T	30	.	DP=3;AF1=0.5002;CI95=0.5,0.5;DP4=0,1,0,2;MQ=38;PV4=1,1,0.26,1	PL:GT:GQ	60,0,31:0/1:34
+chr1	141768589	.	G	A	18.1	.	DP=15;AF1=0.5;CI95=0.5,0.5;DP4=4,0,4,0;MQ=51;PV4=1,2.7e-05,1,1	PL:GT:GQ	48,0,100:0/1:51
+chr1	141768590	.	G	A	22	.	DP=15;AF1=0.5;CI95=0.5,0.5;DP4=2,0,4,0;MQ=50;PV4=1,0.0033,1,1	PL:GT:GQ	52,0,40:0/1:43
+chr1	146506051	.	T	C	44	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=43	PL:GT:GQ	76,9,0:1/1:63
+chr1	150997009	.	G	A	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47	PL:GT:GQ	40,6,0:1/1:49
+chr1	162915612	.	G	C	13.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35	PL:GT:GQ	45,6,0:1/1:49
+chr1	168455400	.	A	G	4.12	.	DP=28;AF1=1;CI95=1,1;DP4=0,0,0,27;MQ=10	PL:GT:GQ	35,81,0:1/1:99
+chr1	172784744	.	T	C	17.8	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=48	PL:GT:GQ	49,6,0:1/1:49
+chr1	183627307	.	G	A	13.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35	PL:GT:GQ	45,6,0:1/1:49
+chr1	185789457	.	T	C	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=50	PL:GT:GQ	73,6,0:1/1:49
+chr1	187081827	.	T	C	4.77	.	DP=10;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=17	PL:GT:GQ	36,30,0:1/1:99
+chr1	188468339	.	C	T	33	.	DP=25;AF1=1;CI95=1,1;DP4=0,0,0,13;MQ=24	PL:GT:GQ	66,39,0:1/1:99
+chr1	188595435	.	C	T	41.8	.	DP=8;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49	PL:GT:GQ	73,6,0:1/1:49
+chr1	188670561	.	G	C	3.55	.	DP=22;AF1=1;CI95=1,1;DP4=0,0,0,9;MQ=18	PL:GT:GQ	34,27,0:1/1:99
+chr1	188924877	.	G	A	6.2	.	DP=10;AF1=0.9999;CI95=0.5,1;DP4=2,0,3,0;MQ=21;PV4=1,1,1,0.3	PL:GT:GQ	35,3,0:1/1:41
+chr1	190536295	.	G	A	68	.	DP=38;AF1=1;CI95=1,1;DP4=0,0,36,0;MQ=18	PL:GT:GQ	101,108,0:1/1:99
+chr1	191129408	.	T	A	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=48	PL:GT:GQ	40,6,0:1/1:49
+chr1	195937816	.	T	C	13	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35	PL:GT:GQ	44,6,0:1/1:49
+chr1	198857619	.	T	C	89	.	DP=61;AF1=0.5;CI95=0.5,0.5;DP4=0,38,0,17;MQ=30;PV4=1,0.032,1,1	PL:GT:GQ	119,0,139:0/1:99
+chr1	199057483	.	T	C	13	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=32	PL:GT:GQ	44,6,0:1/1:49
+chr1	200133619	.	G	C	5.83	.	DP=49;AF1=1;CI95=0.5,1;DP4=2,0,8,0;MQ=17;PV4=1,0.059,1,0.2	PL:GT:GQ	37,12,0:1/1:72
+chr1	200729661	.	A	T	36	.	DP=15;AF1=1;CI95=1,1;DP4=0,0,14,0;MQ=27	PL:GT:GQ	69,42,0:1/1:99
+chr1	201374519	.	T	C	69.5	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=39	PL:GT:GQ	102,12,0:1/1:72
+chr1	202811668	.	G	A	20.2	.	DP=4;AF1=0.5163;CI95=0.5,1;DP4=0,1,0,3;MQ=24;PV4=1,1,1,1	PL:GT:GQ	50,0,12:0/1:15
+chr1	202960650	.	C	T	16.6	.	DP=8;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=27	PL:GT:GQ	49,12,0:1/1:72
+chr1	205686638	.	C	T	11.3	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=42	PL:GT:GQ	43,9,0:1/1:63
+chr1	205949857	.	A	G	3.14	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=21	PL:GT:GQ	33,15,0:1/1:75
+chr1	209806643	.	A	G	13.2	.	DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=21	PL:GT:GQ	46,24,0:1/1:96
+chr1	209871501	.	C	T	25	.	DP=12;AF1=0.5;CI95=0.5,0.5;DP4=5,0,4,0;MQ=41;PV4=1,7.7e-06,1,1	PL:GT:GQ	55,0,84:0/1:58
+chr1	211051323	.	G	A	99	.	DP=14;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=49	PL:GT:GQ	176,24,0:1/1:96
+chr1	211389716	.	C	T	12	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=32	PL:GT:GQ	43,6,0:1/1:49
+chr1	211868415	.	G	A	3.54	.	DP=11;AF1=1;CI95=1,1;DP4=0,0,0,11;MQ=14	PL:GT:GQ	34,33,0:1/1:99
+chr1	211914531	.	C	T	84.5	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,1,0,4;MQ=46;PV4=1,1,1,1	PL:GT:GQ	116,7,0:1/1:57
+chr1	214691313	.	A	G	22	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=49	PL:GT:GQ	54,9,0:1/1:63
+chr1	215184650	.	C	T	40.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=46	PL:GT:GQ	72,6,0:1/1:49
+chr1	215995258	.	A	G	68	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=50	PL:GT:GQ	100,9,0:1/1:63
+chr1	217031394	.	G	C	13.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35	PL:GT:GQ	45,6,0:1/1:49
+chr1	217986960	.	T	C	44	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=36	PL:GT:GQ	76,9,0:1/1:63
+chr1	218086681	.	A	G	99	.	DP=10;AF1=1;CI95=1,1;DP4=0,0,0,9;MQ=34	PL:GT:GQ	142,27,0:1/1:99
+chr1	218546019	.	A	G	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=50	PL:GT:GQ	40,6,0:1/1:49
+chr1	218632417	.	G	T	17.1	.	DP=19;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=26	PL:GT:GQ	50,21,0:1/1:84
+chr1	218833355	.	C	G	23	.	DP=7;AF1=0.5;CI95=0.5,0.5;DP4=5,0,2,0;MQ=39;PV4=1,1,1,1	PL:GT:GQ	53,0,63:0/1:56
+chr1	219303186	.	T	C	7.79	.	DP=25;AF1=1;CI95=1,1;DP4=0,0,0,25;MQ=12	PL:GT:GQ	40,75,0:1/1:99
+chr1	219517634	.	G	A	26.5	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=42	PL:GT:GQ	59,12,0:1/1:72
+chr1	219590158	.	T	C	3.27	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=25	PL:GT:GQ	33,12,0:1/1:72
+chr1	219709853	.	A	T	99	.	DP=124;AF1=0.5;CI95=0.5,0.5;DP4=80,0,41,0;MQ=44;PV4=1,0.26,1,1	PL:GT:GQ	143,0,156:0/1:99
+chr1	222457988	.	A	G	11.1	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=23	PL:GT:GQ	42,6,0:1/1:49
+chr1	222477914	.	A	G	11.3	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=39	PL:GT:GQ	43,9,0:1/1:63
+chr1	223010233	.	A	G	18.6	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=25	PL:GT:GQ	51,12,0:1/1:72
+chr1	223796360	.	G	A	6.79	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=21	PL:GT:GQ	37,6,0:1/1:49
+chr1	224273784	.	A	T	14.2	.	DP=18;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=15	PL:GT:GQ	47,30,0:1/1:99
+chr1	224454685	.	C	T	46.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=32	PL:GT:GQ	79,15,0:1/1:75
+chr1	224514706	.	G	C	21	.	DP=38;AF1=1;CI95=1,1;DP4=0,0,38,0;MQ=19	PL:GT:GQ	54,114,0:1/1:99
+chr1	224515793	.	C	T	99	.	DP=26;AF1=1;CI95=1,1;DP4=0,0,26,0;MQ=45	PL:GT:GQ	211,78,0:1/1:99
+chr1	224692969	.	C	A	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=36	PL:GT:GQ	40,6,0:1/1:49
+chr1	225607249	.	A	G	34	.	DP=3;AF1=0.5002;CI95=0.5,0.5;DP4=1,0,2,0;MQ=45;PV4=1,1,0,1	PL:GT:GQ	64,0,31:0/1:34
+chr1	226923918	.	C	A	29.1	.	DP=52;AF1=1;CI95=0.5,1;DP4=0,2,0,10;MQ=27;PV4=1,1,1,1	PL:GT:GQ	62,18,0:1/1:90
+chr1	227125189	.	T	C	56.5	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=41	PL:GT:GQ	89,12,0:1/1:72
+chr1	227133712	.	A	T	20.1	.	DP=26;AF1=0.5;CI95=0.5,0.5;DP4=11,0,10,0;MQ=23;PV4=1,1,0.48,1	PL:GT:GQ	50,0,39:0/1:42
+chr1	227943954	.	G	C	47	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=37	PL:GT:GQ	79,9,0:1/1:63
+chr1	227943974	.	G	A	33.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=34	PL:GT:GQ	66,12,0:1/1:72
+chr1	228067480	.	A	G	42.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=45	PL:GT:GQ	75,15,0:1/1:75
+chr1	228067510	.	A	G	99	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=45	PL:GT:GQ	140,15,0:1/1:75
+chr1	228088778	.	C	T	6.79	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=23	PL:GT:GQ	37,6,0:1/1:49
+chr1	228117888	.	A	C	13.9	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=40	PL:GT:GQ	45,6,0:1/1:49
+chr1	228139641	.	T	C	44.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=35	PL:GT:GQ	77,12,0:1/1:72
+chr1	228577146	.	T	C	26	.	DP=41;AF1=0.5;CI95=0.5,0.5;DP4=0,25,0,14;MQ=22;PV4=1,1,1,0.027	PL:GT:GQ	56,0,77:0/1:59
+chr1	229001369	.	C	A	45	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=41	PL:GT:GQ	77,9,0:1/1:63
+chr1	229001386	.	C	T	8.44	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=42	PL:GT:GQ	39,6,0:1/1:49
+chr1	229348080	.	T	C	18.1	.	DP=3;AF1=0.5002;CI95=0.5,0.5;DP4=0,1,0,2;MQ=40;PV4=1,0.33,0.17,0.33	PL:GT:GQ	48,0,31:0/1:34
+chr1	229439710	.	C	T	33.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=32	PL:GT:GQ	66,12,0:1/1:72
+chr1	229655149	.	T	C	30	.	DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=30	PL:GT:GQ	63,24,0:1/1:96
+chr1	229660873	.	C	G	81	.	DP=28;AF1=0.5;CI95=0.5,0.5;DP4=0,20,0,7;MQ=36;PV4=1,1,1,1	PL:GT:GQ	111,0,120:0/1:99
+chr2a	3661005	.	C	G	24	.	DP=13;AF1=0.5001;CI95=0.5,0.5;DP4=7,0,4,0;MQ=27;PV4=1,1.1e-05,1,1	PL:GT:GQ	54,0,34:0/1:37
+chr2a	4140063	.	G	A	81	.	DP=26;AF1=0.6671;CI95=0.5,1;DP4=18,0,8,0;MQ=24;PV4=1,8.3e-09,1,1	PL:GT:GQ	110,0,3:0/1:5
+chr2a	4248440	.	T	C	20	.	DP=28;AF1=0.5;CI95=0.5,0.5;DP4=11,0,7,0;MQ=25;PV4=1,1,0.47,1	PL:GT:GQ	50,0,92:0/1:53
+chr2a	4707656	.	A	G	63	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=49	PL:GT:GQ	95,9,0:1/1:63
+chr2a	5194801	.	G	A	7.59	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=24	PL:GT:GQ	38,6,0:1/1:49
+chr2a	14111103	.	A	G	7.84	.	DP=7;AF1=1;CI95=1,1;DP4=0,0,0,7;MQ=20	PL:GT:GQ	40,21,0:1/1:84
+chr2a	17799746	.	A	G	11.3	.	DP=5;AF1=0.5001;CI95=0.5,0.5;DP4=0,3,0,2;MQ=32;PV4=1,1,1,1	PL:GT:GQ	41,0,35:0/1:37
+chr2a	24728910	.	G	A	45.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=28	PL:GT:GQ	78,15,0:1/1:75
+chr2a	29627939	.	G	T	5.44	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=27	PL:GT:GQ	36,9,0:1/1:63
+chr2a	31373164	.	C	T	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=44	PL:GT:GQ	73,6,0:1/1:49
+chr2a	33935228	.	T	C	41.8	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=51	PL:GT:GQ	73,6,0:1/1:49
+chr2a	36311856	.	G	A	99	.	DP=30;AF1=1;CI95=1,1;DP4=0,0,0,29;MQ=44	PL:GT:GQ	213,87,0:1/1:99
+chr2a	39281204	.	T	C	68	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=49	PL:GT:GQ	100,9,0:1/1:63
+chr2a	41087565	.	C	T	74.5	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=38	PL:GT:GQ	107,12,0:1/1:72
+chr2a	45574768	.	C	A	11.3	.	DP=8;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=18	PL:GT:GQ	43,9,0:1/1:63
+chr2a	55464464	.	T	C	26.1	.	DP=7;AF1=0.9966;CI95=0.5,1;DP4=5,0,2,0;MQ=26;PV4=1,1,1,1	PL:GT:GQ	55,1,0:1/1:23
+chr2a	63107673	.	T	A	70.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=34	PL:GT:GQ	103,12,0:1/1:72
+chr2a	63141732	.	A	T	22.8	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=42	PL:GT:GQ	54,6,0:1/1:49
+chr2a	63141910	.	G	A	3.41	.	DP=16;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=32	PL:GT:GQ	32,6,0:1/1:49
+chr2a	63141911	.	C	T	9.55	.	DP=16;AF1=0.5031;CI95=0.5,0.5;DP4=0,2,0,3;MQ=33;PV4=1,0.43,1,1	PL:GT:GQ	39,0,19:0/1:22
+chr2a	63143543	.	C	T	28	.	DP=18;AF1=1;CI95=1,1;DP4=0,1,0,17;MQ=16;PV4=1,1,1,1	PL:GT:GQ	61,42,0:1/1:99
+chr2a	66419805	.	G	A	3.69	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=23	PL:GT:GQ	34,15,0:1/1:75
+chr2a	66563922	.	C	T	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=51	PL:GT:GQ	40,6,0:1/1:49
+chr2a	67719136	.	C	T	39.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=50	PL:GT:GQ	71,6,0:1/1:49
+chr2a	72781453	.	A	C	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=50	PL:GT:GQ	73,6,0:1/1:49
+chr2a	76733211	.	G	A	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47	PL:GT:GQ	40,6,0:1/1:49
+chr2a	78190502	.	A	C	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47	PL:GT:GQ	40,6,0:1/1:49
+chr2a	85021209	.	A	G	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49	PL:GT:GQ	40,6,0:1/1:49
+chr2a	88554861	.	A	T	39	.	DP=74;AF1=0.5;CI95=0.5,0.5;DP4=0,7,0,4;MQ=46;PV4=1,1,1,1	PL:GT:GQ	69,0,92:0/1:72
+chr2a	88554877	.	A	G	92	.	DP=90;AF1=0.5;CI95=0.5,0.5;DP4=0,23,0,13;MQ=41;PV4=1,0.3,1,1	PL:GT:GQ	122,0,128:0/1:99
+chr2a	88824857	.	G	A	13.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=37	PL:GT:GQ	45,6,0:1/1:49
+chr2a	93546675	.	C	T	26	.	DP=6;AF1=0.5;CI95=0.5,0.5;DP4=4,0,2,0;MQ=46;PV4=1,1,1,1	PL:GT:GQ	56,0,87:0/1:59
+chr2a	94788853	.	A	G	34.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=43	PL:GT:GQ	67,15,0:1/1:75
+chr2a	96738146	.	T	C	11.3	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=40	PL:GT:GQ	43,9,0:1/1:63
+chr2a	102737384	.	A	G	12.3	.	DP=18;AF1=1;CI95=1,1;DP4=0,0,18,0;MQ=11	PL:GT:GQ	45,54,0:1/1:99
+chr2a	103407172	.	A	G	35	.	DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=19	PL:GT:GQ	68,24,0:1/1:96
+chr2a	105774580	.	T	G	99	.	DP=13;AF1=1;CI95=1,1;DP4=0,0,13,0;MQ=30	PL:GT:GQ	135,39,0:1/1:99
+chr2a	106376301	.	C	G	24.1	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=19	PL:GT:GQ	57,18,0:1/1:90
+chr2a	106376315	.	C	T	8.75	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=19	PL:GT:GQ	41,18,0:1/1:90
+chr2a	112422267	.	C	T	30	.	DP=20;AF1=0.5;CI95=0.5,0.5;DP4=14,0,5,0;MQ=39;PV4=1,1,1,1	PL:GT:GQ	60,0,131:0/1:63
+chr2b	3049384	.	A	C	14.9	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=42	PL:GT:GQ	46,6,0:1/1:49
+chr2b	3049385	.	G	C	14.9	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=42	PL:GT:GQ	46,6,0:1/1:49
+chr2b	3049406	.	C	G	99	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=36	PL:GT:GQ	135,18,0:1/1:90
+chr2b	4213802	.	T	C	89.5	.	DP=10;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=49	PL:GT:GQ	122,12,0:1/1:72
+chr2b	5022895	.	G	A	66	.	DP=10;AF1=1;CI95=1,1;DP4=0,0,0,10;MQ=49	PL:GT:GQ	99,30,0:1/1:99
+chr2b	6037666	.	G	T	56	.	DP=18;AF1=1;CI95=1,1;DP4=0,0,0,13;MQ=17	PL:GT:GQ	89,39,0:1/1:99
+chr2b	13656952	.	G	A	19.2	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=21	PL:GT:GQ	52,18,0:1/1:90
+chr2b	15026944	.	A	G	6.79	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=32	PL:GT:GQ	37,6,0:1/1:49
+chr2b	23362613	.	A	G	5.64	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=22	PL:GT:GQ	37,15,0:1/1:75
+chr2b	45947861	.	C	G	68	.	DP=11;AF1=1;CI95=1,1;DP4=0,0,0,11;MQ=50	PL:GT:GQ	101,33,0:1/1:99
+chr2b	46597824	.	T	C	65.6	.	DP=39;AF1=0.5939;CI95=0.5,1;DP4=23,0,10,0;MQ=22;PV4=1,0.014,1,1	PL:GT:GQ	95,0,5:0/1:7
+chr2b	49665191	.	G	T	34.1	.	DP=7;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=37	PL:GT:GQ	67,21,0:1/1:84
+chr2b	61001546	.	A	G	48	.	DP=9;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=26	PL:GT:GQ	81,24,0:1/1:96
+chr2b	88502851	.	T	C	4.77	.	DP=4;AF1=0.5;CI95=0.5,0.5;DP4=0,2,0,2;MQ=37;PV4=1,1,0.46,1	PL:GT:GQ	33,0,34:0/1:33
+chr2b	91675431	.	C	T	30	.	DP=14;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=27	PL:GT:GQ	63,24,0:1/1:96
+chr2b	91870148	.	T	G	67	.	DP=14;AF1=1;CI95=1,1;DP4=0,1,0,13;MQ=47;PV4=1,1,1,1	PL:GT:GQ	100,31,0:1/1:99
+chr2b	97066826	.	G	A	20.1	.	DP=9;AF1=0.5001;CI95=0.5,0.5;DP4=0,6,0,2;MQ=31;PV4=1,1,1,1	PL:GT:GQ	50,0,35:0/1:38
+chr2b	97670822	.	G	A	4.85	.	DP=6;AF1=1;CI95=1,1;DP4=0,0,0,6;MQ=18	PL:GT:GQ	36,18,0:1/1:90
+chr2b	102773175	.	A	G	17.1	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=38	PL:GT:GQ	49,9,0:1/1:63
+chr2b	109805532	.	T	C	99	.	DP=8;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=45	PL:GT:GQ	176,24,0:1/1:96
+chr2b	110841448	.	A	G	11.1	.	DP=20;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=44	PL:GT:GQ	42,6,0:1/1:49
+chr2b	123217025	.	T	C	31.5	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=37	PL:GT:GQ	64,12,0:1/1:72
+chr2b	123263214	.	A	G	11.3	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=35	PL:GT:GQ	43,9,0:1/1:63
+chr2b	127747292	.	C	T	68	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=52	PL:GT:GQ	100,9,0:1/1:63
+chr2b	130121958	.	A	G	89.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=43	PL:GT:GQ	122,15,0:1/1:75
+chr2b	130253633	.	A	G	14.9	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=42	PL:GT:GQ	46,6,0:1/1:49
+chr2b	130692761	.	C	T	49.1	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=51	PL:GT:GQ	82,18,0:1/1:90
+chr2b	130743365	.	A	G	99	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=42	PL:GT:GQ	140,15,0:1/1:75
+chr2b	131553874	.	A	C	11.3	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=37	PL:GT:GQ	43,9,0:1/1:63
+chr2b	131716894	.	A	G	99	.	DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=40	PL:GT:GQ	137,24,0:1/1:96
+chr2b	131716936	.	G	A	99	.	DP=14;AF1=1;CI95=1,1;DP4=0,0,0,12;MQ=36	PL:GT:GQ	173,36,0:1/1:99
+chr2b	131716952	.	A	G	99	.	DP=22;AF1=0.5;CI95=0.5,0.5;DP4=0,7,0,14;MQ=36;PV4=1,1,1,1	PL:GT:GQ	152,0,43:0/1:46
+chr2b	133360184	.	C	T	99	.	DP=20;AF1=1;CI95=1,1;DP4=0,0,0,20;MQ=32	PL:GT:GQ	163,60,0:1/1:99
+chr2b	133644741	.	T	A	16.4	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=27	PL:GT:GQ	49,15,0:1/1:75
+chr2b	133720595	.	T	C	41	.	DP=15;AF1=1;CI95=1,1;DP4=0,0,0,12;MQ=29	PL:GT:GQ	74,36,0:1/1:99
+chr2b	133727192	.	C	T	19.3	.	DP=8;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=23	PL:GT:GQ	52,15,0:1/1:75
+chr2b	133727260	.	G	A	3.56	.	DP=8;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=18	PL:GT:GQ	34,24,0:1/1:95
+chr2b	133800294	.	A	G	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=23	PL:GT:GQ	40,6,0:1/1:49
+chr2b	134582754	.	A	C	56.1	.	DP=37;AF1=1;CI95=1,1;DP4=0,0,0,7;MQ=36	PL:GT:GQ	89,21,0:1/1:84
+chr2b	134582763	.	G	C	78	.	DP=37;AF1=1;CI95=1,1;DP4=0,0,0,36;MQ=34	PL:GT:GQ	111,108,0:1/1:99
+chr2b	134809668	.	G	A	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49	PL:GT:GQ	40,6,0:1/1:49
+chr3	527814	.	C	G	46	.	DP=9;AF1=0.5;CI95=0.5,0.5;DP4=6,0,3,0;MQ=43;PV4=1,1,1,1	PL:GT:GQ	76,0,106:0/1:79
+chr3	559510	.	G	A	38	.	DP=27;AF1=0.5;CI95=0.5,0.5;DP4=10,0,17,0;MQ=28;PV4=1,1,0.014,1	PL:GT:GQ	68,0,111:0/1:71
+chr3	879433	.	T	G	32	.	DP=4;AF1=0.5001;CI95=0.5,0.5;DP4=2,0,2,0;MQ=43;PV4=1,1,1,1	PL:GT:GQ	62,0,34:0/1:37
+chr3	1809645	.	A	G	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=51	PL:GT:GQ	73,6,0:1/1:49
+chr3	3235812	.	C	T	7.59	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=45	PL:GT:GQ	38,6,0:1/1:49
+chr3	3250176	.	A	G	83	.	DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=32	PL:GT:GQ	116,24,0:1/1:96
+chr3	5049073	.	T	A	99	.	DP=25;AF1=0.5;CI95=0.5,0.5;DP4=16,0,9,0;MQ=39;PV4=1,1,1,1	PL:GT:GQ	136,0,129:0/1:99
+chr3	5142874	.	G	A	99	.	DP=38;AF1=1;CI95=1,1;DP4=0,0,38,0;MQ=28	PL:GT:GQ	179,114,0:1/1:99
+chr3	5554864	.	T	C	3.54	.	DP=7;AF1=0.4999;CI95=0.5,0.5;DP4=0,4,0,3;MQ=27;PV4=1,1,1,1	PL:GT:GQ	31,0,35:0/1:33
+chr3	5749648	.	G	A	21.2	.	DP=26;AF1=0.7303;CI95=0.5,1;DP4=0,7,0,7;MQ=26;PV4=1,0.16,1,0.17	PL:GT:GQ	50,0,2:0/1:3
+chr3	16451708	.	A	T	71.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=38	PL:GT:GQ	104,15,0:1/1:75
+chr3	23410276	.	G	A	99	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=45	PL:GT:GQ	140,15,0:1/1:75
+chr3	51368824	.	A	G	28	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=48	PL:GT:GQ	60,9,0:1/1:63
+chr3	53000453	.	A	G	54	.	DP=10;AF1=1;CI95=1,1;DP4=0,0,0,10;MQ=19	PL:GT:GQ	87,30,0:1/1:99
+chr3	53000463	.	A	G	54	.	DP=10;AF1=1;CI95=1,1;DP4=0,0,0,10;MQ=19	PL:GT:GQ	87,30,0:1/1:99
+chr3	59077423	.	C	T	77.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=33	PL:GT:GQ	110,15,0:1/1:75
+chr3	60040501	.	T	C	11.3	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=35	PL:GT:GQ	43,9,0:1/1:63
+chr3	64203481	.	A	G	33.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=49	PL:GT:GQ	66,12,0:1/1:72
+chr3	67947441	.	C	T	17.6	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=25	PL:GT:GQ	50,12,0:1/1:72
+chr3	76372631	.	A	G	44	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=36	PL:GT:GQ	76,9,0:1/1:63
+chr3	80611316	.	C	G	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49	PL:GT:GQ	40,6,0:1/1:49
+chr3	81554381	.	G	T	17.6	.	DP=24;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=26	PL:GT:GQ	50,12,0:1/1:72
+chr3	87614647	.	A	G	13.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=34	PL:GT:GQ	45,6,0:1/1:49
+chr3	93900455	.	A	T	11.6	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=13	PL:GT:GQ	44,15,0:1/1:75
+chr3	96174457	.	A	G	4.11	.	DP=8;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=24	PL:GT:GQ	34,9,0:1/1:63
+chr3	96215569	.	A	C	3.41	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=32	PL:GT:GQ	32,6,0:1/1:49
+chr3	96587998	.	A	C	7.08	.	DP=9;AF1=1;CI95=1,1;DP4=0,0,6,0;MQ=17	PL:GT:GQ	39,18,0:1/1:90
+chr3	99711220	.	A	C	12.8	.	DP=11;AF1=0.9998;CI95=0.5,1;DP4=1,0,2,0;MQ=35;PV4=1,1,1,1	PL:GT:GQ	42,2,0:1/1:37
+chr3	99789741	.	C	G	99	.	DP=18;AF1=1;CI95=1,1;DP4=0,0,17,0;MQ=47	PL:GT:GQ	210,51,0:1/1:99
+chr3	103667651	.	A	C	3.98	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=37	PL:GT:GQ	33,6,0:1/1:49
+chr3	104604896	.	G	C	55	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=50	PL:GT:GQ	87,9,0:1/1:63
+chr3	104997217	.	G	A	33.1	.	DP=18;AF1=1;CI95=1,1;DP4=1,0,16,0;MQ=34;PV4=1,3e-10,0.17,0.36	PL:GT:GQ	66,19,0:1/1:76
+chr3	106097816	.	A	G	28	.	DP=15;AF1=1;CI95=1,1;DP4=0,0,0,15;MQ=26	PL:GT:GQ	61,45,0:1/1:99
+chr3	106822259	.	G	C	99	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=50	PL:GT:GQ	140,15,0:1/1:75
+chr3	109946413	.	G	A	13	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=34	PL:GT:GQ	44,6,0:1/1:49
+chr3	121238963	.	T	C	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=51	PL:GT:GQ	40,6,0:1/1:49
+chr3	126248567	.	A	G	13.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=33	PL:GT:GQ	45,6,0:1/1:49
+chr3	129733836	.	A	G	6.2	.	DP=4;AF1=0.5003;CI95=0.5,0.5;DP4=1,0,3,0;MQ=43;PV4=1,0.02,0.31,1	PL:GT:GQ	35,0,28:0/1:30
+chr3	131372785	.	C	T	44	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=34	PL:GT:GQ	76,9,0:1/1:63
+chr3	132290987	.	C	T	22	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=45	PL:GT:GQ	54,9,0:1/1:63
+chr3	136054421	.	C	T	73	.	DP=82;AF1=1;CI95=1,1;DP4=0,0,78,0;MQ=28	PL:GT:GQ	106,235,0:1/1:99
+chr3	141075246	.	G	A	30.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=41	PL:GT:GQ	62,6,0:1/1:49
+chr3	141075262	.	T	G	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=41	PL:GT:GQ	73,6,0:1/1:49
+chr3	141430649	.	G	T	81.8	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,1,0,4;MQ=41;PV4=1,0.34,1,0.25	PL:GT:GQ	113,6,0:1/1:49
+chr3	143617747	.	G	T	22	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=29	PL:GT:GQ	54,9,0:1/1:63
+chr3	163576128	.	C	T	5.6	.	DP=4;AF1=0.7302;CI95=0.5,1;DP4=2,0,2,0;MQ=23;PV4=1,1,1,1	PL:GT:GQ	33,0,2:0/1:3
+chr3	163839828	.	A	G	4.45	.	DP=7;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=26	PL:GT:GQ	35,12,0:1/1:72
+chr3	175839340	.	G	T	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=51	PL:GT:GQ	40,6,0:1/1:49
+chr3	190193258	.	G	T	3.98	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35	PL:GT:GQ	33,6,0:1/1:49
+chr3	190777007	.	G	A	13	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35	PL:GT:GQ	44,6,0:1/1:49
+chr3	190970350	.	A	G	61	.	DP=11;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=37	PL:GT:GQ	94,30,0:1/1:99
+chr3	198686408	.	G	A	36.6	.	DP=17;AF1=1;CI95=0.5,1;DP4=0,1,0,16;MQ=25;PV4=1,1,0.026,1	PL:GT:GQ	69,11,0:1/1:66
+chr3	199277478	.	T	C	3.61	.	DP=6;AF1=1;CI95=1,1;DP4=0,0,0,6;MQ=21	PL:GT:GQ	34,18,0:1/1:90
+chr3	199780181	.	G	T	77	.	DP=45;AF1=0.5;CI95=0.5,0.5;DP4=0,35,0,10;MQ=33;PV4=1,1,1,1	PL:GT:GQ	107,0,114:0/1:99
+chr3	199889335	.	A	C	9.54	.	DP=16;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=18	PL:GT:GQ	42,24,0:1/1:96
+chr3	200018161	.	A	G	13.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=31	PL:GT:GQ	45,6,0:1/1:49
+chr4	195475	.	A	G	13	.	DP=13;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47	PL:GT:GQ	44,6,0:1/1:49
+chr4	639141	.	C	A	14.9	.	DP=10;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=42	PL:GT:GQ	46,6,0:1/1:49
+chr4	639152	.	C	T	15.2	.	DP=17;AF1=0.5016;CI95=0.5,0.5;DP4=0,2,0,2;MQ=33;PV4=1,1,1,1	PL:GT:GQ	45,0,22:0/1:25
+chr4	986497	.	G	T	99	.	DP=10;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=33	PL:GT:GQ	163,30,0:1/1:99
+chr4	986516	.	C	T	55.1	.	DP=8;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=37	PL:GT:GQ	88,21,0:1/1:84
+chr4	1207485	.	A	C	14.9	.	DP=22;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=45	PL:GT:GQ	46,6,0:1/1:49
+chr4	1323502	.	G	A	13.2	.	DP=13;AF1=1;CI95=1,1;DP4=0,0,11,0;MQ=22	PL:GT:GQ	46,33,0:1/1:99
+chr4	1613521	.	G	A	89	.	DP=16;AF1=1;CI95=1,1;DP4=0,0,16,0;MQ=32	PL:GT:GQ	122,48,0:1/1:99
+chr4	1748790	.	C	T	38	.	DP=21;AF1=0.5005;CI95=0.5,0.5;DP4=6,0,8,0;MQ=40;PV4=1,0.09,1,1	PL:GT:GQ	68,0,27:0/1:30
+chr4	2255732	.	T	C	99	.	DP=29;AF1=1;CI95=1,1;DP4=0,0,28,0;MQ=31	PL:GT:GQ	186,84,0:1/1:99
+chr4	3010159	.	C	T	13.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=31	PL:GT:GQ	45,6,0:1/1:49
+chr4	3545023	.	A	G	99	.	DP=9;AF1=1;CI95=1,1;DP4=0,0,0,9;MQ=38	PL:GT:GQ	145,27,0:1/1:99
+chr4	3586344	.	C	T	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=44	PL:GT:GQ	73,6,0:1/1:49
+chr4	3879337	.	A	G	16.6	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=25	PL:GT:GQ	49,12,0:1/1:72
+chr4	3940733	.	A	G	47.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=31	PL:GT:GQ	80,15,0:1/1:75
+chr4	4410338	.	T	C	13.5	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=31	PL:GT:GQ	46,15,0:1/1:75
+chr4	4796408	.	T	C	41	.	DP=16;AF1=1;CI95=1,1;DP4=0,0,0,16;MQ=17	PL:GT:GQ	74,48,0:1/1:99
+chr4	4796414	.	A	G	11.3	.	DP=16;AF1=1;CI95=1,1;DP4=0,0,0,15;MQ=17	PL:GT:GQ	44,45,0:1/1:99
+chr4	6436959	.	T	C	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=50	PL:GT:GQ	40,6,0:1/1:49
+chr4	9494256	.	T	C	3.41	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=37	PL:GT:GQ	32,6,0:1/1:49
+chr4	24881479	.	G	A	14.1	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=42	PL:GT:GQ	46,9,0:1/1:63
+chr4	26128644	.	A	G	23	.	DP=18;AF1=0.5006;CI95=0.5,0.5;DP4=8,0,10,0;MQ=22;PV4=1,1,1,1	PL:GT:GQ	53,0,26:0/1:29
+chr4	42109100	.	G	A	17.1	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=48	PL:GT:GQ	49,9,0:1/1:63
+chr4	42309652	.	C	T	68	.	DP=17;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=50	PL:GT:GQ	100,9,0:1/1:63
+chr4	46913966	.	C	T	9.08	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=16	PL:GT:GQ	41,12,0:1/1:72
+chr4	50335142	.	A	G	44	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=41	PL:GT:GQ	76,9,0:1/1:63
+chr4	51658550	.	C	A	13	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=48	PL:GT:GQ	44,6,0:1/1:49
+chr4	58258023	.	T	C	26	.	DP=5;AF1=0.5002;CI95=0.5,0.5;DP4=0,3,0,2;MQ=34;PV4=1,1,1,0.05	PL:GT:GQ	56,0,32:0/1:35
+chr4	59219112	.	C	A	42.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=50	PL:GT:GQ	75,12,0:1/1:72
+chr4	62746067	.	C	T	13.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35	PL:GT:GQ	45,6,0:1/1:49
+chr4	67404338	.	G	T	33.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=39	PL:GT:GQ	66,12,0:1/1:72
+chr4	73353380	.	A	G	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49	PL:GT:GQ	73,6,0:1/1:49
+chr4	73946294	.	G	C	4.77	.	DP=51;AF1=0.4999;CI95=0.5,0.5;DP4=0,5,0,3;MQ=40;PV4=1,0.19,0.37,0.11	PL:GT:GQ	33,0,64:0/1:36
+chr4	79607484	.	A	G	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49	PL:GT:GQ	40,6,0:1/1:49
+chr4	82337365	.	G	C	90	.	DP=54;AF1=1;CI95=1,1;DP4=0,0,0,16;MQ=28	PL:GT:GQ	123,48,0:1/1:99
+chr4	82653801	.	A	G	4.11	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=29	PL:GT:GQ	34,9,0:1/1:63
+chr4	87130164	.	C	T	11.3	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=26	PL:GT:GQ	43,9,0:1/1:63
+chr4	87130176	.	G	A	11.3	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=26	PL:GT:GQ	43,9,0:1/1:63
+chr4	91459729	.	C	A	13	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35	PL:GT:GQ	44,6,0:1/1:49
+chr4	96130778	.	G	C	99	.	DP=19;AF1=1;CI95=1,1;DP4=0,0,0,19;MQ=45	PL:GT:GQ	211,57,0:1/1:99
+chr4	100709417	.	A	G	45.1	.	DP=16;AF1=0.505;CI95=0.5,0.5;DP4=12,0,4,0;MQ=24;PV4=1,1,1,1	PL:GT:GQ	75,0,17:0/1:20
+chr4	107276770	.	C	T	70	.	DP=15;AF1=0.5;CI95=0.5,0.5;DP4=0,9,0,6;MQ=31;PV4=1,1,1,1	PL:GT:GQ	100,0,97:0/1:98
+chr4	115327550	.	G	C	42	.	DP=67;AF1=1;CI95=1,1;DP4=0,1,0,66;MQ=35;PV4=1,3.2e-24,0.13,1	PL:GT:GQ	75,162,0:1/1:99
+chr4	136558502	.	A	G	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49	PL:GT:GQ	40,6,0:1/1:49
+chr4	159572459	.	G	A	15.1	.	DP=126;AF1=0.5;CI95=0.5,0.5;DP4=0,69,0,57;MQ=39;PV4=1,4.1e-96,0.077,1	PL:GT:GQ	45,0,175:0/1:48
+chr4	174968484	.	G	C	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=42	PL:GT:GQ	40,6,0:1/1:49
+chr4	175030633	.	T	C	14.3	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=29	PL:GT:GQ	47,18,0:1/1:90
+chr4	183410027	.	G	T	6.2	.	DP=31;AF1=0.5003;CI95=0.5,0.5;DP4=2,0,2,0;MQ=45;PV4=1,0.035,1,0.21	PL:GT:GQ	35,0,28:0/1:30
+chr4	190907368	.	T	C	33.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=50	PL:GT:GQ	66,12,0:1/1:72
+chr4	192175690	.	A	G	76.8	.	DP=7;AF1=0.95;CI95=0.5,1;DP4=0,3,0,4;MQ=35;PV4=1,1,1,1	PL:GT:GQ	105,0,0:1/1:10
+chr4	192673268	.	G	A	14.2	.	DP=9;AF1=1;CI95=1,1;DP4=0,0,9,0;MQ=22	PL:GT:GQ	47,27,0:1/1:99
+chr4	192943966	.	T	C	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=44	PL:GT:GQ	73,6,0:1/1:49
+chr4	195460104	.	C	G	23.1	.	DP=8;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=19	PL:GT:GQ	56,24,0:1/1:96
+chr4	198277830	.	A	G	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49	PL:GT:GQ	40,6,0:1/1:49
+chr5	170098	.	A	G	13	.	DP=12;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=30	PL:GT:GQ	44,6,0:1/1:49
+chr5	395814	.	T	C	4.77	.	DP=4;AF1=0.5;CI95=0.5,0.5;DP4=0,2,0,2;MQ=36;PV4=1,1,0.48,1	PL:GT:GQ	33,0,33:0/1:33
+chr5	414024	.	T	A	10.4	.	DP=17;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=20	PL:GT:GQ	42,9,0:1/1:63
+chr5	496767	.	T	C	13.9	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=36	PL:GT:GQ	45,6,0:1/1:49
+chr5	805676	.	C	G	45	.	DP=17;AF1=1;CI95=1,1;DP4=0,0,17,0;MQ=32	PL:GT:GQ	78,51,0:1/1:99
+chr5	1252896	.	A	G	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49	PL:GT:GQ	40,6,0:1/1:49
+chr5	1418370	.	G	A	3.65	.	DP=8;AF1=0.7301;CI95=0.5,1;DP4=4,0,4,0;MQ=13;PV4=1,1,1,1	PL:GT:GQ	30,0,2:0/1:3
+chr5	1494911	.	G	C	62	.	DP=9;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=46	PL:GT:GQ	95,24,0:1/1:96
+chr5	1494932	.	C	T	6.98	.	DP=8;AF1=0.5001;CI95=0.5,0.5;DP4=1,0,2,0;MQ=46;PV4=1,0.1,0.077,1	PL:GT:GQ	36,0,31:0/1:33
+chr5	1506037	.	T	C	24.1	.	DP=24;AF1=1;CI95=0.5,1;DP4=11,0,13,0;MQ=16;PV4=1,1,1,1	PL:GT:GQ	55,5,0:1/1:46
+chr5	1509406	.	A	G	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=47	PL:GT:GQ	73,6,0:1/1:49
+chr5	1733649	.	A	G	99	.	DP=25;AF1=1;CI95=1,1;DP4=0,0,0,25;MQ=47	PL:GT:GQ	212,75,0:1/1:99
+chr5	1747304	.	A	G	12.3	.	DP=12;AF1=1;CI95=1,1;DP4=0,0,0,12;MQ=19	PL:GT:GQ	45,36,0:1/1:99
+chr5	1747308	.	C	A	44	.	DP=12;AF1=1;CI95=1,1;DP4=0,0,0,12;MQ=19	PL:GT:GQ	77,36,0:1/1:99
+chr5	3519783	.	C	T	21.1	.	DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=18	PL:GT:GQ	54,24,0:1/1:96
+chr5	4101593	.	A	G	69.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=43	PL:GT:GQ	102,12,0:1/1:72
+chr5	7204332	.	T	A	4.61	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=24	PL:GT:GQ	34,6,0:1/1:49
+chr5	11510398	.	A	C	34	.	DP=3;AF1=0.5002;CI95=0.5,0.5;DP4=1,0,2,0;MQ=51;PV4=1,1,0,1	PL:GT:GQ	64,0,31:0/1:34
+chr5	15406720	.	T	C	6.02	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=51	PL:GT:GQ	36,6,0:1/1:49
+chr5	25152417	.	C	A	10.9	.	DP=28;AF1=0.5718;CI95=0.5,1;DP4=0,2,0,6;MQ=25;PV4=1,1,0.21,1	PL:GT:GQ	40,0,6:0/1:8
+chr5	39072637	.	A	G	35.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=50	PL:GT:GQ	68,15,0:1/1:75
+chr5	46022699	.	G	A	44	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=35	PL:GT:GQ	76,9,0:1/1:63
+chr5	55664181	.	C	G	10.4	.	DP=8;AF1=0.9999;CI95=0.5,1;DP4=3,0,5,0;MQ=18;PV4=1,1,1,1	PL:GT:GQ	40,3,0:1/1:41
+chr5	56253386	.	T	C	50.1	.	DP=7;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=36	PL:GT:GQ	83,21,0:1/1:84
+chr5	56253447	.	C	T	42.5	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=45	PL:GT:GQ	75,12,0:1/1:72
+chr5	71950166	.	G	T	11.3	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=40	PL:GT:GQ	43,9,0:1/1:63
+chr5	72703090	.	C	T	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=46	PL:GT:GQ	40,6,0:1/1:49
+chr5	73570280	.	G	T	5.45	.	DP=41;AF1=1;CI95=1,1;DP4=0,0,41,0;MQ=15	PL:GT:GQ	37,123,0:1/1:99
+chr5	73701762	.	G	T	40.8	.	DP=13;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=43	PL:GT:GQ	72,6,0:1/1:49
+chr5	76956867	.	T	C	10.2	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=46	PL:GT:GQ	41,6,0:1/1:49
+chr5	79097961	.	C	G	22	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=40	PL:GT:GQ	54,9,0:1/1:63
+chr5	87026167	.	T	C	22	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=49	PL:GT:GQ	54,9,0:1/1:63
+chr5	97680525	.	T	C	3.27	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=23	PL:GT:GQ	33,12,0:1/1:72
+chr5	100674737	.	C	T	13.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35	PL:GT:GQ	45,6,0:1/1:49
+chr5	105389966	.	T	C	3.52	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=15	PL:GT:GQ	33,9,0:1/1:63
+chr5	109998341	.	A	C	12.7	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=35	PL:GT:GQ	45,12,0:1/1:72
+chr5	120629105	.	C	T	6.79	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48	PL:GT:GQ	37,6,0:1/1:49
+chr5	128383954	.	C	T	23	.	DP=10;AF1=0.5;CI95=0.5,0.5;DP4=0,5,0,5;MQ=48;PV4=1,3.3e-07,1,1	PL:GT:GQ	53,0,98:0/1:56
+chr5	133925142	.	A	G	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49	PL:GT:GQ	73,6,0:1/1:49
+chr5	135375404	.	T	C	11.8	.	DP=6;AF1=1;CI95=0.5,1;DP4=1,0,3,0;MQ=31;PV4=1,0.03,1,1	PL:GT:GQ	42,4,0:1/1:45
+chr5	136498281	.	T	G	13.9	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=37	PL:GT:GQ	45,6,0:1/1:49
+chr5	136717285	.	A	G	82.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=48	PL:GT:GQ	115,12,0:1/1:72
+chr5	136910734	.	G	A	62	.	DP=19;AF1=1;CI95=1,1;DP4=0,1,0,13;MQ=23;PV4=1,1,1,1	PL:GT:GQ	95,31,0:1/1:99
+chr5	141208149	.	C	G	13	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35	PL:GT:GQ	44,6,0:1/1:49
+chr5	148056348	.	C	A	37.1	.	DP=4;AF1=0.9966;CI95=0.5,1;DP4=1,0,2,0;MQ=38;PV4=1,1,1,1	PL:GT:GQ	66,1,0:1/1:23
+chr5	151941534	.	G	T	46.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=34	PL:GT:GQ	79,12,0:1/1:72
+chr5	159967229	.	G	C	22.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=35	PL:GT:GQ	55,12,0:1/1:72
+chr5	174024541	.	T	G	29.5	.	DP=3;AF1=0.9998;CI95=0.5,1;DP4=0,1,0,2;MQ=32;PV4=1,1,1,1	PL:GT:GQ	59,2,0:1/1:37
+chr5	175525290	.	A	G	3.27	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=20	PL:GT:GQ	33,12,0:1/1:72
+chr5	175988954	.	A	C	14.2	.	DP=23;AF1=0.5;CI95=0.5,0.5;DP4=0,6,0,4;MQ=47;PV4=1,1,0.2,1	PL:GT:GQ	44,0,76:0/1:47
+chr5	176782226	.	T	C	9.31	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=43	PL:GT:GQ	40,6,0:1/1:49
+chr5	179132834	.	C	G	99	.	DP=28;AF1=1;CI95=1,1;DP4=0,0,0,28;MQ=41	PL:GT:GQ	207,84,0:1/1:99
+chr5	180155809	.	G	C	3.01	.	DP=36;AF1=0.4997;CI95=0.5,0.5;DP4=25,0,9,0;MQ=35;PV4=1,1e-15,1,1	PL:GT:GQ	30,0,121:0/1:33
+chr5	181282819	.	T	G	38.3	.	DP=11;AF1=1;CI95=0.5,1;DP4=0,2,0,9;MQ=23;PV4=1,1,1,1	PL:GT:GQ	71,14,0:1/1:70
+chr5	182426125	.	G	C	29	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=26	PL:GT:GQ	61,9,0:1/1:63
+chr5	182443682	.	G	A	3.69	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=21	PL:GT:GQ	34,15,0:1/1:75
+chr5	183008993	.	C	T	22	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=49	PL:GT:GQ	54,9,0:1/1:63
+chr5	183312016	.	G	T	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=47	PL:GT:GQ	40,6,0:1/1:49
+chr6_cox_hap1	519146	.	G	A	17.1	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=30	PL:GT:GQ	49,9,0:1/1:63
+chr6_cox_hap1	687497	.	A	G	33	.	DP=6;AF1=0.9999;CI95=0.5,1;DP4=2,0,4,0;MQ=35;PV4=1,0.0016,1,1	PL:GT:GQ	63,3,0:1/1:41
+chr6_qbl_hap2	120066	.	T	C	99	.	DP=12;AF1=1;CI95=1,1;DP4=0,0,0,9;MQ=37	PL:GT:GQ	139,27,0:1/1:99
+chr6	277954	.	C	T	53	.	DP=41;AF1=1;CI95=1,1;DP4=4,0,37,0;MQ=19;PV4=1,1,0.3,1	PL:GT:GQ	86,49,0:1/1:99
+chr6	593158	.	A	G	4.61	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=32	PL:GT:GQ	34,6,0:1/1:49
+chr6	2865562	.	T	G	25	.	DP=9;AF1=1;CI95=1,1;DP4=0,0,9,0;MQ=23	PL:GT:GQ	58,27,0:1/1:99
+chr6	3751403	.	G	A	42.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=32	PL:GT:GQ	75,15,0:1/1:75
+chr6	3884989	.	A	G	13.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=36	PL:GT:GQ	45,6,0:1/1:49
+chr6	4127278	.	A	T	13.9	.	DP=8;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35	PL:GT:GQ	45,6,0:1/1:49
+chr6	5887783	.	C	G	99	.	DP=7;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=34	PL:GT:GQ	142,21,0:1/1:84
+chr6	5887811	.	C	T	55.1	.	DP=7;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=34	PL:GT:GQ	88,21,0:1/1:84
+chr6	6937170	.	G	C	99	.	DP=47;AF1=1;CI95=1,1;DP4=0,0,0,47;MQ=28	PL:GT:GQ	157,141,0:1/1:99
+chr6	7262317	.	C	T	13.2	.	DP=50;AF1=0.5;CI95=0.5,0.5;DP4=21,0,9,0;MQ=36;PV4=1,4e-05,0.17,0.26	PL:GT:GQ	43,0,158:0/1:46
+chr6	7533214	.	A	G	10.4	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=26	PL:GT:GQ	42,9,0:1/1:63
+chr6	20979907	.	A	G	44	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=38	PL:GT:GQ	76,9,0:1/1:63
+chr6	22321632	.	A	G	41	.	DP=5;AF1=0.5004;CI95=0.5,0.5;DP4=1,0,3,0;MQ=46;PV4=1,0.24,0.19,0.33	PL:GT:GQ	71,0,28:0/1:31
+chr6	25352296	.	G	A	7.8	.	DP=4;AF1=0.5003;CI95=0.5,0.5;DP4=0,1,0,3;MQ=38;PV4=1,1,0.16,1	PL:GT:GQ	37,0,28:0/1:30
+chr6	26298040	.	T	A	34	.	DP=3;AF1=0.5002;CI95=0.5,0.5;DP4=0,1,0,2;MQ=48;PV4=1,1,0.21,0.33	PL:GT:GQ	64,0,31:0/1:34
+chr6	33428755	.	G	A	70	.	DP=14;AF1=1;CI95=1,1;DP4=0,0,9,0;MQ=32	PL:GT:GQ	103,27,0:1/1:99
+chr6	39512099	.	G	A	55.1	.	DP=7;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=50	PL:GT:GQ	88,21,0:1/1:84
+chr6	39961094	.	G	A	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49	PL:GT:GQ	73,6,0:1/1:49
+chr6	40452120	.	A	G	40.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=42	PL:GT:GQ	72,6,0:1/1:49
+chr6	43204766	.	A	G	99	.	DP=8;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=51	PL:GT:GQ	176,24,0:1/1:96
+chr6	52696512	.	C	T	70	.	DP=76;AF1=0.5;CI95=0.5,0.5;DP4=0,34,0,42;MQ=18;PV4=1,0.11,1,1	PL:GT:GQ	100,0,51:0/1:54
+chr6	53785550	.	A	G	99	.	DP=20;AF1=1;CI95=1,1;DP4=0,0,0,10;MQ=46	PL:GT:GQ	190,30,0:1/1:99
+chr6	53897484	.	C	T	13.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=36	PL:GT:GQ	45,6,0:1/1:49
+chr6	57038290	.	C	T	10.2	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=36	PL:GT:GQ	41,6,0:1/1:49
+chr6	62925087	.	G	C	35	.	DP=5;AF1=0.5008;CI95=0.5,0.5;DP4=1,0,4,0;MQ=36;PV4=1,1,0.2,1	PL:GT:GQ	65,0,25:0/1:28
+chr6	62925094	.	T	C	25.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=36	PL:GT:GQ	58,15,0:1/1:75
+chr6	70834405	.	G	A	72.1	.	DP=13;AF1=1;CI95=1,1;DP4=0,0,0,7;MQ=29	PL:GT:GQ	105,21,0:1/1:84
+chr6	71026058	.	C	T	48.1	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=42	PL:GT:GQ	81,18,0:1/1:90
+chr6	74420752	.	T	C	44	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=39	PL:GT:GQ	76,9,0:1/1:63
+chr6	77498624	.	T	C	16.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=33	PL:GT:GQ	48,6,0:1/1:49
+chr6	80416836	.	T	C	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=50	PL:GT:GQ	40,6,0:1/1:49
+chr6	113611590	.	A	G	68	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=46	PL:GT:GQ	100,9,0:1/1:63
+chr6	119308431	.	T	C	38.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=40	PL:GT:GQ	71,12,0:1/1:72
+chr6	151758592	.	T	C	3.07	.	DP=17;AF1=0.9966;CI95=0.5,1;DP4=0,8,0,9;MQ=13;PV4=1,1,1,1	PL:GT:GQ	29,1,0:1/1:23
+chr6	151759358	.	A	G	99	.	DP=27;AF1=0.5;CI95=0.5,0.5;DP4=12,0,15,0;MQ=44;PV4=1,1,1,0.19	PL:GT:GQ	171,0,128:0/1:99
+chr6	154741755	.	G	A	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=50	PL:GT:GQ	40,6,0:1/1:49
+chr6	161061053	.	C	A	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=52	PL:GT:GQ	40,6,0:1/1:49
+chr6	161474189	.	C	T	6.02	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49	PL:GT:GQ	36,6,0:1/1:49
+chr6	164304657	.	C	T	10.4	.	DP=63;AF1=0.5;CI95=0.5,0.5;DP4=0,29,0,19;MQ=22;PV4=1,7.7e-11,1,0.049	PL:GT:GQ	40,0,37:0/1:38
+chr6	164703105	.	T	C	99	.	DP=11;AF1=1;CI95=1,1;DP4=0,0,0,10;MQ=40	PL:GT:GQ	165,30,0:1/1:99
+chr6	167518328	.	A	G	78	.	DP=41;AF1=0.5;CI95=0.5,0.5;DP4=27,0,14,0;MQ=33;PV4=1,0.026,0.43,0.056	PL:GT:GQ	108,0,149:0/1:99
+chr6	169906323	.	G	A	41.8	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49	PL:GT:GQ	73,6,0:1/1:49
+chr6	171893912	.	G	A	69.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=33	PL:GT:GQ	102,15,0:1/1:75
+chr6	173631604	.	A	G	6.98	.	DP=7;AF1=0.5;CI95=0.5,0.5;DP4=4,0,3,0;MQ=37;PV4=1,0.069,1,1	PL:GT:GQ	36,0,34:0/1:35
+chr7	835856	.	C	T	27.5	.	DP=13;AF1=0.9998;CI95=0.5,1;DP4=4,0,6,0;MQ=23;PV4=1,0.46,1,1	PL:GT:GQ	57,2,0:1/1:37
+chr7	1046005	.	C	T	11.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=36	PL:GT:GQ	43,9,0:1/1:63
+chr7	1564339	.	C	T	71	.	DP=66;AF1=0.5;CI95=0.5,0.5;DP4=36,0,24,0;MQ=29;PV4=1,1,0.35,1	PL:GT:GQ	101,0,134:0/1:99
+chr7	1806266	.	C	T	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48	PL:GT:GQ	73,6,0:1/1:49
+chr7	1936013	.	G	T	7.77	.	DP=7;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=17	PL:GT:GQ	39,9,0:1/1:63
+chr7	2319532	.	C	A	4.11	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=14	PL:GT:GQ	34,9,0:1/1:63
+chr7	2682121	.	C	T	13	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=33	PL:GT:GQ	44,6,0:1/1:49
+chr7	3248116	.	T	C	36.5	.	DP=3;AF1=0.9998;CI95=0.5,1;DP4=0,1,0,2;MQ=37;PV4=1,1,1,1	PL:GT:GQ	66,2,0:1/1:37
+chr7	3624766	.	C	T	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=41	PL:GT:GQ	40,6,0:1/1:49
+chr7	5291140	.	G	C	13.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=37	PL:GT:GQ	45,6,0:1/1:49
+chr7	5314457	.	C	A	3.56	.	DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=18	PL:GT:GQ	34,24,0:1/1:95
+chr7	5595072	.	T	A	79	.	DP=13;AF1=0.5;CI95=0.5,0.5;DP4=8,0,5,0;MQ=31;PV4=1,1,1,1	PL:GT:GQ	109,0,57:0/1:60
+chr7	5646060	.	G	C	7.79	.	DP=11;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=10	PL:GT:GQ	40,30,0:1/1:99
+chr7	6056816	.	C	G	7.08	.	DP=6;AF1=0.9966;CI95=0.5,1;DP4=0,2,0,3;MQ=23;PV4=1,1,1,1	PL:GT:GQ	35,1,0:1/1:23
+chr7	6412641	.	C	T	40	.	DP=11;AF1=1;CI95=1,1;DP4=0,0,11,0;MQ=33	PL:GT:GQ	73,33,0:1/1:99
+chr7	6766874	.	A	G	34.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=43	PL:GT:GQ	67,15,0:1/1:75
+chr7	8482729	.	C	T	5.08	.	DP=16;AF1=0.8276;CI95=0.5,1;DP4=3,0,3,0;MQ=22;PV4=1,1,1,0.19	PL:GT:GQ	32,0,1:1/1:5
+chr7	9238362	.	G	A	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49	PL:GT:GQ	40,6,0:1/1:49
+chr7	9687781	.	G	A	33	.	DP=29;AF1=0.5;CI95=0.5,0.5;DP4=0,16,0,12;MQ=48;PV4=1,6.5e-38,1,1	PL:GT:GQ	63,0,170:0/1:66
+chr7	9752803	.	A	T	14.2	.	DP=17;AF1=1;CI95=1,1;DP4=0,0,9,0;MQ=18	PL:GT:GQ	47,27,0:1/1:99
+chr7	10240910	.	T	C	45.5	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=35	PL:GT:GQ	78,12,0:1/1:72
+chr7	11046187	.	C	T	86.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=47	PL:GT:GQ	119,12,0:1/1:72
+chr7	11548207	.	C	G	14.6	.	DP=13;AF1=1;CI95=0.5,1;DP4=6,1,0,5;MQ=18;PV4=0.015,1,1,1	PL:GT:GQ	46,7,0:1/1:57
+chr7	11580317	.	C	T	42	.	DP=12;AF1=1;CI95=1,1;DP4=0,1,0,10;MQ=22;PV4=1,1,1,1	PL:GT:GQ	75,23,0:1/1:92
+chr7	11585384	.	G	A	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=46	PL:GT:GQ	73,6,0:1/1:49
+chr7	13498356	.	A	G	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=47	PL:GT:GQ	73,6,0:1/1:49
+chr7	13500887	.	G	A	15.1	.	DP=11;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=22	PL:GT:GQ	48,30,0:1/1:99
+chr7	13827079	.	C	T	6.02	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47	PL:GT:GQ	36,6,0:1/1:49
+chr7	14403976	.	T	G	59	.	DP=30;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=39	PL:GT:GQ	92,24,0:1/1:96
+chr7	14756588	.	A	G	44	.	DP=15;AF1=0.5;CI95=0.5,0.5;DP4=5,0,10,0;MQ=44;PV4=1,5.3e-18,1,1	PL:GT:GQ	74,0,70:0/1:72
+chr7	14756619	.	T	G	44	.	DP=15;AF1=0.5;CI95=0.5,0.5;DP4=5,0,10,0;MQ=44;PV4=1,6.4e-10,1,1	PL:GT:GQ	74,0,70:0/1:72
+chr7	36734598	.	A	C	11.1	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=40	PL:GT:GQ	42,6,0:1/1:49
+chr7	36734599	.	A	T	11.1	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=40	PL:GT:GQ	42,6,0:1/1:49
+chr7	36734603	.	G	C	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=40	PL:GT:GQ	40,6,0:1/1:49
+chr7	40634921	.	A	C	55	.	DP=13;AF1=1;CI95=1,1;DP4=0,0,13,0;MQ=39	PL:GT:GQ	88,39,0:1/1:99
+chr7	48271285	.	A	T	73	.	DP=15;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=25	PL:GT:GQ	106,30,0:1/1:99
+chr7	56264700	.	G	A	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=51	PL:GT:GQ	40,6,0:1/1:49
+chr7	62326003	.	C	A	26.1	.	DP=35;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=28	PL:GT:GQ	59,18,0:1/1:90
+chr7	109468934	.	T	G	5.13	.	DP=10;AF1=0.9998;CI95=0.5,1;DP4=0,1,0,2;MQ=39;PV4=1,0.031,1,1	PL:GT:GQ	33,2,0:1/1:37
+chr7	110208327	.	C	G	16.9	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=44	PL:GT:GQ	48,6,0:1/1:49
+chr7	125654934	.	A	G	4.11	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=27	PL:GT:GQ	34,9,0:1/1:63
+chr7	125770209	.	A	C	32	.	DP=31;AF1=0.5;CI95=0.5,0.5;DP4=11,0,13,0;MQ=34;PV4=1,0.00017,0.16,0.22	PL:GT:GQ	62,0,105:0/1:65
+chr7	125770265	.	G	C	36	.	DP=16;AF1=0.5;CI95=0.5,0.5;DP4=0,5,0,5;MQ=48;PV4=1,0.0047,0.016,0.035	PL:GT:GQ	66,0,110:0/1:69
+chr7	126687042	.	A	G	21.1	.	DP=36;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=22	PL:GT:GQ	54,21,0:1/1:84
+chr7	132292897	.	G	T	99	.	DP=7;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=43	PL:GT:GQ	167,21,0:1/1:84
+chr7	132334562	.	A	C	23	.	DP=16;AF1=1;CI95=1,1;DP4=0,0,0,10;MQ=23	PL:GT:GQ	56,30,0:1/1:99
+chr7	132431838	.	C	T	13.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=1,0,4,0;MQ=23;PV4=1,1,1,1	PL:GT:GQ	44,5,0:1/1:46
+chr7	136324945	.	T	C	13.7	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=35	PL:GT:GQ	46,12,0:1/1:72
+chr7	136957634	.	G	A	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=43	PL:GT:GQ	40,6,0:1/1:49
+chr7	141746871	.	G	A	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=42	PL:GT:GQ	40,6,0:1/1:49
+chr7	146831870	.	C	T	4.77	.	DP=14;AF1=0.5003;CI95=0.5,0.5;DP4=1,0,3,0;MQ=37;PV4=1,0.0029,0.28,1	PL:GT:GQ	33,0,28:0/1:30
+chr7	147142770	.	T	C	45	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=31	PL:GT:GQ	77,9,0:1/1:63
+chr7	147713906	.	C	T	4.77	.	DP=8;AF1=0.5002;CI95=0.5,0.5;DP4=2,0,4,0;MQ=35;PV4=1,8.9e-06,0.48,0.27	PL:GT:GQ	33,0,29:0/1:31
+chr7	148742642	.	G	A	68	.	DP=14;AF1=0.5032;CI95=0.5,0.5;DP4=4,0,10,0;MQ=28;PV4=1,1,1,1	PL:GT:GQ	98,0,19:0/1:22
+chr7	148879148	.	C	T	22	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=48	PL:GT:GQ	54,9,0:1/1:63
+chr7	149484407	.	A	G	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=45	PL:GT:GQ	73,6,0:1/1:49
+chr7	152444478	.	A	G	13	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=36	PL:GT:GQ	44,6,0:1/1:49
+chr7	154106613	.	C	T	68	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=51	PL:GT:GQ	100,9,0:1/1:63
+chr7	154776891	.	G	T	14.4	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=31	PL:GT:GQ	47,15,0:1/1:75
+chr7	155882061	.	A	C	29	.	DP=24;AF1=0.502;CI95=0.5,0.5;DP4=0,1,0,4;MQ=46;PV4=1,0.018,0.15,0.29	PL:GT:GQ	59,0,21:0/1:24
+chr7	155956844	.	G	C	23	.	DP=11;AF1=0.5;CI95=0.5,0.5;DP4=0,7,0,4;MQ=38;PV4=1,1,0.38,1	PL:GT:GQ	53,0,103:0/1:56
+chr7	156277694	.	G	A	62	.	DP=9;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=46	PL:GT:GQ	95,24,0:1/1:96
+chr7	156720588	.	T	C	16.1	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=29	PL:GT:GQ	48,9,0:1/1:63
+chr7	156807649	.	T	C	3.01	.	DP=30;AF1=0.4997;CI95=0.5,0.5;DP4=0,4,0,3;MQ=43;PV4=1,0.16,0.15,1	PL:GT:GQ	30,0,72:0/1:33
+chr7	157331292	.	G	T	43.1	.	DP=7;AF1=1;CI95=1,1;DP4=0,0,0,7;MQ=34	PL:GT:GQ	76,21,0:1/1:84
+chr7	157382957	.	T	C	33.5	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=43	PL:GT:GQ	66,12,0:1/1:72
+chr8	556382	.	A	G	37.1	.	DP=5;AF1=0.9966;CI95=0.5,1;DP4=2,0,3,0;MQ=31;PV4=1,1,1,1	PL:GT:GQ	66,1,0:1/1:23
+chr8	1661673	.	T	C	9.31	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49	PL:GT:GQ	40,6,0:1/1:49
+chr8	7379751	.	C	A	6.24	.	DP=8;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=19	PL:GT:GQ	38,21,0:1/1:84
+chr8	8160505	.	A	T	68.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=35	PL:GT:GQ	101,12,0:1/1:72
+chr8	8160508	.	C	T	24.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=35	PL:GT:GQ	57,12,0:1/1:72
+chr8	16781011	.	A	G	55.5	.	DP=9;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=34	PL:GT:GQ	88,12,0:1/1:72
+chr8	18716499	.	A	T	20	.	DP=10;AF1=0.5;CI95=0.5,0.5;DP4=0,4,0,2;MQ=29;PV4=1,1,1,1	PL:GT:GQ	50,0,52:0/1:51
+chr8	23326483	.	A	G	60	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=47	PL:GT:GQ	92,9,0:1/1:63
+chr8	25842819	.	T	A	12	.	DP=18;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=47	PL:GT:GQ	43,6,0:1/1:49
+chr8	26300279	.	T	C	34	.	DP=44;AF1=1;CI95=1,1;DP4=0,0,41,0;MQ=21	PL:GT:GQ	67,123,0:1/1:99
+chr8	29673470	.	A	G	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=41	PL:GT:GQ	73,6,0:1/1:49
+chr8	29673473	.	C	G	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=41	PL:GT:GQ	40,6,0:1/1:49
+chr8	31685466	.	C	T	34	.	DP=17;AF1=0.5;CI95=0.5,0.5;DP4=10,0,5,0;MQ=28;PV4=1,0.072,1,0.36	PL:GT:GQ	64,0,50:0/1:53
+chr8	37378739	.	C	T	13.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=34	PL:GT:GQ	45,6,0:1/1:49
+chr8	51325952	.	G	A	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49	PL:GT:GQ	40,6,0:1/1:49
+chr8	59221963	.	G	A	16.1	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=29	PL:GT:GQ	48,9,0:1/1:63
+chr8	62764995	.	T	G	20	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=32	PL:GT:GQ	52,9,0:1/1:63
+chr8	63157426	.	C	G	41.6	.	DP=22;AF1=1;CI95=0.5,1;DP4=0,7,0,15;MQ=19;PV4=1,1,1,0.25	PL:GT:GQ	74,11,0:1/1:66
+chr8	68710444	.	G	A	30	.	DP=5;AF1=0.6671;CI95=0.5,1;DP4=3,0,2,0;MQ=32;PV4=1,1,1,1	PL:GT:GQ	59,0,3:0/1:5
+chr8	76416560	.	G	A	89.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=46	PL:GT:GQ	122,12,0:1/1:72
+chr8	81425275	.	T	G	68	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=50	PL:GT:GQ	100,9,0:1/1:63
+chr8	89842286	.	G	C	4.61	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=30	PL:GT:GQ	34,6,0:1/1:49
+chr8	100926281	.	G	A	38	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=41	PL:GT:GQ	70,9,0:1/1:63
+chr8	102746002	.	G	C	13.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35	PL:GT:GQ	45,6,0:1/1:49
+chr8	107850176	.	C	T	43.1	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=45	PL:GT:GQ	76,18,0:1/1:90
+chr8	109966441	.	T	C	27.3	.	DP=9;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=38	PL:GT:GQ	60,15,0:1/1:75
+chr8	118811716	.	G	T	99	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=50	PL:GT:GQ	155,18,0:1/1:90
+chr8	119440254	.	A	T	58.5	.	DP=5;AF1=0.8277;CI95=0.5,1;DP4=2,0,3,0;MQ=34;PV4=1,1,1,0.14	PL:GT:GQ	87,0,1:1/1:5
+chr8	121236024	.	G	A	39.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=48	PL:GT:GQ	71,6,0:1/1:49
+chr8	125489079	.	C	T	13	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35	PL:GT:GQ	44,6,0:1/1:49
+chr8	128502549	.	A	G	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=45	PL:GT:GQ	73,6,0:1/1:49
+chr8	128502551	.	A	G	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=45	PL:GT:GQ	73,6,0:1/1:49
+chr8	130951113	.	G	A	4.61	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=19	PL:GT:GQ	34,6,0:1/1:49
+chr8	135307123	.	G	A	6.02	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=45	PL:GT:GQ	36,6,0:1/1:49
+chr8	138814155	.	C	T	57.1	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=46	PL:GT:GQ	90,18,0:1/1:90
+chr8	140566111	.	A	G	18.1	.	DP=12;AF1=1;CI95=1,1;DP4=0,0,0,12;MQ=15	PL:GT:GQ	51,36,0:1/1:99
+chr8	141586480	.	T	G	44	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=40	PL:GT:GQ	76,9,0:1/1:63
+chr8	143376712	.	A	G	13	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35	PL:GT:GQ	44,6,0:1/1:49
+chr8	150662729	.	T	C	9.31	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47	PL:GT:GQ	40,6,0:1/1:49
+chr8	150741294	.	A	G	25.1	.	DP=7;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=34	PL:GT:GQ	58,18,0:1/1:90
+chr8	150975618	.	A	G	9.31	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48	PL:GT:GQ	40,6,0:1/1:49
+chr8	151580103	.	T	C	6.02	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=20	PL:GT:GQ	36,6,0:1/1:49
+chr8	151634410	.	G	T	48	.	DP=17;AF1=0.5;CI95=0.5,0.5;DP4=0,12,0,5;MQ=39;PV4=1,0.072,1,1	PL:GT:GQ	78,0,125:0/1:81
+chr8	151709267	.	G	A	91.1	.	DP=8;AF1=0.5064;CI95=0.5,0.5;DP4=0,1,0,7;MQ=40;PV4=1,1,0.28,0.37	PL:GT:GQ	121,0,16:0/1:19
+chr8	152636420	.	G	A	8.75	.	DP=3;AF1=0.9966;CI95=0.5,1;DP4=0,1,0,2;MQ=30;PV4=1,1,1,1	PL:GT:GQ	37,1,0:1/1:23
+chr8	152706967	.	G	A	3.01	.	DP=10;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=16	PL:GT:GQ	33,30,0:1/1:99
+chr8	152786522	.	T	C	80.1	.	DP=16;AF1=0.5102;CI95=0.5,0.5;DP4=0,4,0,12;MQ=31;PV4=1,0.25,1,1	PL:GT:GQ	110,0,14:0/1:17
+chr8	152863132	.	T	G	5.44	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=30	PL:GT:GQ	36,9,0:1/1:63
+chr9	23235268	.	C	T	12	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=32	PL:GT:GQ	43,6,0:1/1:49
+chr9	26391176	.	T	C	15.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35	PL:GT:GQ	47,6,0:1/1:49
+chr9	26868232	.	C	G	63	.	DP=20;AF1=0.5025;CI95=0.5,0.5;DP4=7,0,13,0;MQ=22;PV4=1,0.2,1,0.44	PL:GT:GQ	93,0,20:0/1:23
+chr9	34223668	.	C	T	22	.	DP=16;AF1=0.5;CI95=0.5,0.5;DP4=0,9,0,7;MQ=27;PV4=1,0.14,0.34,1	PL:GT:GQ	52,0,79:0/1:55
+chr9	39696645	.	G	A	11.3	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=41	PL:GT:GQ	43,9,0:1/1:63
+chr9	40654130	.	T	G	13	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48	PL:GT:GQ	44,6,0:1/1:49
+chr9	41145321	.	T	G	46.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=33	PL:GT:GQ	79,12,0:1/1:72
+chr9	42273483	.	G	A	9.31	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49	PL:GT:GQ	40,6,0:1/1:49
+chr9	55633192	.	C	T	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49	PL:GT:GQ	73,6,0:1/1:49
+chr9	58705807	.	T	C	70	.	DP=10;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=24	PL:GT:GQ	103,30,0:1/1:99
+chr9	61697149	.	C	G	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49	PL:GT:GQ	73,6,0:1/1:49
+chr9	63152790	.	A	C	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48	PL:GT:GQ	40,6,0:1/1:49
+chr9	63703913	.	C	G	90.1	.	DP=7;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=38	PL:GT:GQ	123,21,0:1/1:84
+chr9	65116068	.	T	C	70	.	DP=13;AF1=1;CI95=1,1;DP4=0,0,0,13;MQ=49	PL:GT:GQ	103,39,0:1/1:99
+chr9	71266598	.	C	A	3.98	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35	PL:GT:GQ	33,6,0:1/1:49
+chr9	73188677	.	G	T	52	.	DP=294;AF1=1;CI95=1,1;DP4=44,0,245,0;MQ=33;PV4=1,0.28,0.0092,1	PL:GT:GQ	85,147,0:1/1:99
+chr9	78854179	.	G	T	22	.	DP=97;AF1=0.5;CI95=0.5,0.5;DP4=21,0,12,0;MQ=44;PV4=1,0.02,0.032,0.0033	PL:GT:GQ	52,0,158:0/1:55
+chr9	82964679	.	A	C	13.2	.	DP=19;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=36	PL:GT:GQ	45,9,0:1/1:63
+chr9	84124545	.	G	T	57	.	DP=11;AF1=0.5;CI95=0.5,0.5;DP4=2,0,3,0;MQ=49;PV4=1,1,0.024,1	PL:GT:GQ	87,0,59:0/1:62
+chr9	86552862	.	C	T	14.4	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=26	PL:GT:GQ	47,15,0:1/1:75
+chr9	87548941	.	A	G	22	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=49	PL:GT:GQ	54,9,0:1/1:63
+chr9	89021101	.	G	A	89.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=49	PL:GT:GQ	122,12,0:1/1:72
+chr9	90447825	.	G	A	9.31	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=46	PL:GT:GQ	40,6,0:1/1:49
+chr9	92462035	.	C	A	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=36	PL:GT:GQ	40,6,0:1/1:49
+chr9	93077294	.	T	G	5.44	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=31	PL:GT:GQ	36,9,0:1/1:63
+chr9	93998137	.	G	A	68	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=46	PL:GT:GQ	100,9,0:1/1:63
+chr9	93998148	.	C	T	21.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=36	PL:GT:GQ	54,15,0:1/1:75
+chr9	95028964	.	C	A	99	.	DP=83;AF1=0.5;CI95=0.5,0.5;DP4=0,57,0,26;MQ=32;PV4=1,9.3e-08,1,0.092	PL:GT:GQ	134,0,120:0/1:99
+chr9	103829155	.	A	G	33	.	DP=96;AF1=1;CI95=1,1;DP4=0,0,96,0;MQ=16	PL:GT:GQ	66,255,0:1/1:99
+chr9	104981331	.	C	T	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=43	PL:GT:GQ	73,6,0:1/1:49
+chr9	111070656	.	G	A	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49	PL:GT:GQ	73,6,0:1/1:49
+chr9	117395657	.	T	C	16.4	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=23	PL:GT:GQ	49,15,0:1/1:75
+chr9	117718907	.	A	G	46.1	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=29	PL:GT:GQ	79,18,0:1/1:90
+chr9	119149161	.	T	C	3.14	.	DP=65;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=22	PL:GT:GQ	33,15,0:1/1:75
+chr9	124528802	.	G	A	78	.	DP=23;AF1=1;CI95=1,1;DP4=0,0,13,0;MQ=25	PL:GT:GQ	111,39,0:1/1:99
+chr9	126707903	.	G	A	26	.	DP=37;AF1=0.5;CI95=0.5,0.5;DP4=0,21,0,8;MQ=46;PV4=1,2.6e-07,0.21,0.42	PL:GT:GQ	56,0,175:0/1:59
+chr9	128700686	.	C	G	33.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=50	PL:GT:GQ	66,12,0:1/1:72
+chr9	129084077	.	G	A	11.3	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=41	PL:GT:GQ	43,9,0:1/1:63
+chr9	129116900	.	A	T	20	.	DP=13;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=30	PL:GT:GQ	52,9,0:1/1:63
+chr9	130290720	.	C	G	21.8	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=42	PL:GT:GQ	53,6,0:1/1:49
+chr9	130306057	.	C	G	71	.	DP=14;AF1=1;CI95=1,1;DP4=0,0,14,0;MQ=28	PL:GT:GQ	104,42,0:1/1:99
+chr9	130528990	.	G	A	99	.	DP=31;AF1=1;CI95=1,1;DP4=0,0,31,0;MQ=27	PL:GT:GQ	174,93,0:1/1:99
+chr9	130529002	.	A	T	7.79	.	DP=30;AF1=1;CI95=1,1;DP4=0,0,11,0;MQ=15	PL:GT:GQ	40,33,0:1/1:99
+chr9	130639996	.	A	G	8.44	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=51	PL:GT:GQ	39,6,0:1/1:49
+chr9	130704890	.	A	G	3.27	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=26	PL:GT:GQ	33,12,0:1/1:72
+chr9	130708345	.	G	A	13.3	.	DP=11;AF1=0.9966;CI95=0.5,1;DP4=0,2,0,3;MQ=38;PV4=1,0.096,1,1	PL:GT:GQ	42,1,0:1/1:23
+chr9	131001601	.	T	A	3.98	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=31	PL:GT:GQ	33,6,0:1/1:49
+chr9	131058539	.	T	A	13	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=44	PL:GT:GQ	44,6,0:1/1:49
+chr9	131808965	.	C	T	42	.	DP=9;AF1=1;CI95=1,1;DP4=0,0,0,9;MQ=37	PL:GT:GQ	75,27,0:1/1:99
+chr9	132551867	.	C	T	17.1	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=25	PL:GT:GQ	49,9,0:1/1:63
+chr9	132685120	.	A	G	4.75	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=25	PL:GT:GQ	35,9,0:1/1:63
+chr9	133175050	.	A	G	18.1	.	DP=30;AF1=1;CI95=1,1;DP4=0,0,17,0;MQ=20	PL:GT:GQ	51,51,0:1/1:99
+chr9	133584978	.	A	G	99	.	DP=25;AF1=1;CI95=1,1;DP4=0,0,25,0;MQ=45	PL:GT:GQ	212,75,0:1/1:99
+chr9	133661895	.	A	G	99	.	DP=17;AF1=1;CI95=1,1;DP4=0,0,14,0;MQ=31	PL:GT:GQ	138,42,0:1/1:99
+chr9	133670376	.	T	C	68	.	DP=19;AF1=1;CI95=1,1;DP4=0,1,0,16;MQ=39;PV4=1,1.4e-20,1,1	PL:GT:GQ	101,39,0:1/1:99
+chr9	133843777	.	T	C	99	.	DP=9;AF1=0.5129;CI95=0.5,0.5;DP4=1,0,8,0;MQ=43;PV4=1,1,1,1	PL:GT:GQ	154,0,13:0/1:16
+chr9	134017265	.	G	C	3.27	.	DP=10;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=13	PL:GT:GQ	33,12,0:1/1:72
+chr9	134105563	.	T	C	34.1	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=39	PL:GT:GQ	67,18,0:1/1:90
+chr9	134608906	.	C	T	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=46	PL:GT:GQ	73,6,0:1/1:49
+chr9	134861929	.	T	A	9.49	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=30	PL:GT:GQ	41,9,0:1/1:63
+chr10	796662	.	A	G	22	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=46	PL:GT:GQ	54,9,0:1/1:63
+chr10	1216716	.	T	A	18.6	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=25	PL:GT:GQ	51,12,0:1/1:72
+chr10	1220781	.	G	A	21	.	DP=9;AF1=1;CI95=1,1;DP4=0,0,9,0;MQ=18	PL:GT:GQ	54,27,0:1/1:99
+chr10	1225208	.	T	C	68	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=47	PL:GT:GQ	100,9,0:1/1:63
+chr10	1727946	.	T	C	14.2	.	DP=8;AF1=1;CI95=1,1;DP4=0,0,0,7;MQ=27	PL:GT:GQ	47,21,0:1/1:84
+chr10	5986542	.	T	C	83	.	DP=93;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=39	PL:GT:GQ	116,30,0:1/1:99
+chr10	6436277	.	G	A	6.02	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47	PL:GT:GQ	36,6,0:1/1:49
+chr10	7704114	.	C	A	35	.	DP=6;AF1=0.9999;CI95=0.5,1;DP4=0,2,0,4;MQ=29;PV4=1,0.27,1,0.27	PL:GT:GQ	65,3,0:1/1:41
+chr10	10881734	.	A	G	9.52	.	DP=9;AF1=0.5;CI95=0.5,0.5;DP4=4,0,5,0;MQ=42;PV4=1,0.0026,0.14,1	PL:GT:GQ	39,0,91:0/1:42
+chr10	13099383	.	G	A	27.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=48	PL:GT:GQ	60,12,0:1/1:72
+chr10	15764077	.	G	C	11.3	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=40	PL:GT:GQ	43,9,0:1/1:63
+chr10	18091502	.	T	C	47	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=38	PL:GT:GQ	79,9,0:1/1:63
+chr10	19645913	.	A	T	15.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=43	PL:GT:GQ	47,6,0:1/1:49
+chr10	22845062	.	C	T	18.1	.	DP=8;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=18	PL:GT:GQ	51,21,0:1/1:84
+chr10	28282802	.	T	C	69	.	DP=12;AF1=1;CI95=1,1;DP4=0,0,12,0;MQ=42	PL:GT:GQ	102,36,0:1/1:99
+chr10	28496872	.	T	G	8.44	.	DP=11;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=45	PL:GT:GQ	39,6,0:1/1:49
+chr10	32746793	.	G	A	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=46	PL:GT:GQ	73,6,0:1/1:49
+chr10	41437604	.	T	G	11.3	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=39	PL:GT:GQ	43,9,0:1/1:63
+chr10	43051239	.	C	T	6.98	.	DP=3;AF1=0.5001;CI95=0.5,0.5;DP4=1,0,2,0;MQ=40;PV4=1,0.33,0.33,1	PL:GT:GQ	36,0,31:0/1:33
+chr10	44455192	.	C	T	4.41	.	DP=6;AF1=0.8276;CI95=0.5,1;DP4=0,3,0,3;MQ=21;PV4=1,1,1,1	PL:GT:GQ	31,0,1:1/1:5
+chr10	48387336	.	A	G	13	.	DP=7;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35	PL:GT:GQ	44,6,0:1/1:49
+chr10	51561705	.	A	G	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=45	PL:GT:GQ	40,6,0:1/1:49
+chr10	51561712	.	C	G	39.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=45	PL:GT:GQ	71,6,0:1/1:49
+chr10	55617954	.	G	A	8.44	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=31	PL:GT:GQ	39,6,0:1/1:49
+chr10	55718281	.	T	A	3.41	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=32	PL:GT:GQ	32,6,0:1/1:49
+chr10	55888771	.	T	C	23.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=43	PL:GT:GQ	56,12,0:1/1:72
+chr10	56025569	.	C	G	34.1	.	DP=3;AF1=0.5064;CI95=0.5,0.5;DP4=0,1,0,2;MQ=39;PV4=1,1,1,1	PL:GT:GQ	64,0,16:0/1:19
+chr10	57384943	.	G	T	84	.	DP=29;AF1=0.5;CI95=0.5,0.5;DP4=16,0,13,0;MQ=26;PV4=1,0.015,1,1	PL:GT:GQ	114,0,110:0/1:99
+chr10	59873077	.	T	G	49	.	DP=8;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=42	PL:GT:GQ	82,24,0:1/1:96
+chr10	61329572	.	C	T	15.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48	PL:GT:GQ	47,6,0:1/1:49
+chr10	63790636	.	T	G	32.1	.	DP=19;AF1=1;CI95=1,1;DP4=1,0,10,0;MQ=28;PV4=1,0.14,1,1	PL:GT:GQ	65,22,0:1/1:88
+chr10	64466048	.	C	G	18.2	.	DP=7;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=28	PL:GT:GQ	51,18,0:1/1:90
+chr10	65053440	.	G	T	99	.	DP=10;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=39	PL:GT:GQ	153,30,0:1/1:99
+chr10	65407358	.	C	G	84.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=45	PL:GT:GQ	117,15,0:1/1:75
+chr10	65605291	.	G	A	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=51	PL:GT:GQ	73,6,0:1/1:49
+chr10	66104447	.	T	C	99	.	DP=47;AF1=0.5;CI95=0.5,0.5;DP4=0,25,0,21;MQ=34;PV4=1,1,0.15,1	PL:GT:GQ	136,0,162:0/1:99
+chr10	82160859	.	G	C	99	.	DP=17;AF1=1;CI95=1,1;DP4=0,0,0,13;MQ=36	PL:GT:GQ	153,39,0:1/1:99
+chr10	82198579	.	C	T	9.31	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47	PL:GT:GQ	40,6,0:1/1:49
+chr10	87086290	.	A	G	4.13	.	DP=9;AF1=1;CI95=1,1;DP4=0,0,0,9;MQ=17	PL:GT:GQ	35,27,0:1/1:99
+chr10	89550621	.	T	G	74	.	DP=47;AF1=1;CI95=1,1;DP4=0,0,0,45;MQ=45	PL:GT:GQ	107,135,0:1/1:99
+chr10	92325046	.	G	A	42.3	.	DP=18;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=45	PL:GT:GQ	75,15,0:1/1:75
+chr10	94488050	.	A	G	5.46	.	DP=4;AF1=0.5;CI95=0.5,0.5;DP4=2,0,2,0;MQ=43;PV4=1,0.16,1,1	PL:GT:GQ	34,0,34:0/1:34
+chr10	95024815	.	C	T	13.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=36	PL:GT:GQ	45,6,0:1/1:49
+chr10	95466306	.	G	A	53	.	DP=7;AF1=0.6671;CI95=0.5,1;DP4=0,4,0,3;MQ=33;PV4=1,1,1,1	PL:GT:GQ	82,0,3:0/1:5
+chr10	100256777	.	T	G	3.83	.	DP=7;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=23	PL:GT:GQ	34,12,0:1/1:72
+chr10	101510485	.	T	C	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49	PL:GT:GQ	40,6,0:1/1:49
+chr10	101530760	.	C	T	13.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35	PL:GT:GQ	45,6,0:1/1:49
+chr10	101879744	.	T	C	22	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=44	PL:GT:GQ	54,9,0:1/1:63
+chr10	102147276	.	G	C	11.3	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=33	PL:GT:GQ	43,9,0:1/1:63
+chr10	102642248	.	T	G	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49	PL:GT:GQ	40,6,0:1/1:49
+chr10	107666616	.	T	C	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=43	PL:GT:GQ	40,6,0:1/1:49
+chr10	108319945	.	C	G	11.3	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=29	PL:GT:GQ	43,9,0:1/1:63
+chr10	109734371	.	G	A	12.7	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=35	PL:GT:GQ	45,12,0:1/1:72
+chr10	112870604	.	C	T	46.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=36	PL:GT:GQ	79,12,0:1/1:72
+chr10	115304673	.	T	C	11.3	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=42	PL:GT:GQ	43,9,0:1/1:63
+chr10	119380588	.	G	A	14.2	.	DP=4;AF1=0.502;CI95=0.5,0.5;DP4=1,0,3,0;MQ=43;PV4=1,0.18,0.32,1	PL:GT:GQ	44,0,21:0/1:24
+chr10	123063756	.	C	T	14.1	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=23	PL:GT:GQ	46,9,0:1/1:63
+chr10	128424770	.	T	G	13.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=30	PL:GT:GQ	45,6,0:1/1:49
+chr10	131229204	.	T	C	44	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=40	PL:GT:GQ	76,9,0:1/1:63
+chr10	132420570	.	G	C	89.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=49	PL:GT:GQ	122,12,0:1/1:72
+chr10	132528066	.	C	T	99	.	DP=19;AF1=1;CI95=1,1;DP4=0,0,19,0;MQ=42	PL:GT:GQ	213,57,0:1/1:99
+chr10	132644619	.	G	A	19.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=23	PL:GT:GQ	52,15,0:1/1:75
+chr10	132707581	.	G	C	9.11	.	DP=51;AF1=0.9998;CI95=0.5,1;DP4=1,0,2,0;MQ=25;PV4=1,1,1,1	PL:GT:GQ	38,2,0:1/1:37
+chr10	133026892	.	T	C	55.1	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=44	PL:GT:GQ	88,18,0:1/1:90
+chr11	768033	.	T	C	33.5	.	DP=4;AF1=0.8277;CI95=0.5,1;DP4=0,2,0,2;MQ=32;PV4=1,1,1,1	PL:GT:GQ	62,0,1:1/1:5
+chr11	768042	.	T	C	33.5	.	DP=6;AF1=0.8277;CI95=0.5,1;DP4=0,2,0,2;MQ=32;PV4=1,1,1,1	PL:GT:GQ	62,0,1:1/1:5
+chr11	874568	.	G	C	33.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=33	PL:GT:GQ	66,12,0:1/1:72
+chr11	1009210	.	T	C	4	.	DP=70;AF1=0.6241;CI95=0.5,1;DP4=0,3,0,8;MQ=24;PV4=1,1,0.5,1	PL:GT:GQ	31,0,4:0/1:6
+chr11	1016692	.	C	T	27	.	DP=39;AF1=1;CI95=1,1;DP4=0,0,0,38;MQ=22	PL:GT:GQ	60,114,0:1/1:99
+chr11	1034477	.	A	G	66	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=42	PL:GT:GQ	98,9,0:1/1:63
+chr11	1074037	.	G	A	4.13	.	DP=9;AF1=0.5001;CI95=0.5,0.5;DP4=4,0,5,0;MQ=24;PV4=1,1,0.43,1	PL:GT:GQ	32,0,30:0/1:31
+chr11	1556298	.	G	A	11.8	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=33	PL:GT:GQ	44,12,0:1/1:72
+chr11	1824777	.	T	C	27	.	DP=10;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=28	PL:GT:GQ	60,30,0:1/1:99
+chr11	3395801	.	C	T	22	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=49	PL:GT:GQ	54,9,0:1/1:63
+chr11	3411901	.	G	A	4.75	.	DP=17;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=29	PL:GT:GQ	35,9,0:1/1:63
+chr11	3731606	.	A	C	11.3	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=39	PL:GT:GQ	43,9,0:1/1:63
+chr11	3783855	.	C	T	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=44	PL:GT:GQ	40,6,0:1/1:49
+chr11	3967636	.	A	G	4.29	.	DP=20;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=24	PL:GT:GQ	35,15,0:1/1:75
+chr11	4385618	.	C	T	13.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=31	PL:GT:GQ	45,6,0:1/1:49
+chr11	4424365	.	T	A	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49	PL:GT:GQ	73,6,0:1/1:49
+chr11	5295586	.	C	T	3.01	.	DP=52;AF1=0.4997;CI95=0.5,0.5;DP4=33,0,10,0;MQ=29;PV4=1,0.0045,0.3,0.17	PL:GT:GQ	30,0,131:0/1:33
+chr11	6157144	.	C	G	45.1	.	DP=14;AF1=1;CI95=1,1;DP4=0,0,0,7;MQ=35	PL:GT:GQ	78,21,0:1/1:84
+chr11	6352044	.	C	T	18	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=31	PL:GT:GQ	50,9,0:1/1:63
+chr11	6767356	.	T	C	9.63	.	DP=3;AF1=0.9966;CI95=0.5,1;DP4=1,0,2,0;MQ=29;PV4=1,1,1,1	PL:GT:GQ	38,1,0:1/1:23
+chr11	6999404	.	G	C	21	.	DP=8;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=37	PL:GT:GQ	53,9,0:1/1:63
+chr11	9120930	.	C	G	17.6	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=25	PL:GT:GQ	50,12,0:1/1:72
+chr11	9373125	.	T	C	19.8	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48	PL:GT:GQ	51,6,0:1/1:49
+chr11	9585101	.	C	T	67	.	DP=16;AF1=1;CI95=1,1;DP4=0,0,14,0;MQ=45	PL:GT:GQ	100,42,0:1/1:99
+chr11	10266192	.	A	C	14.3	.	DP=22;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=27	PL:GT:GQ	47,18,0:1/1:90
+chr11	10303263	.	T	C	8.64	.	DP=17;AF1=1;CI95=1,1;DP4=0,0,0,17;MQ=18	PL:GT:GQ	41,51,0:1/1:99
+chr11	10420170	.	T	C	35	.	DP=17;AF1=1;CI95=1,1;DP4=0,1,0,15;MQ=28;PV4=1,0.12,1,0.4	PL:GT:GQ	68,36,0:1/1:99
+chr11	10912169	.	G	A	99	.	DP=7;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=49	PL:GT:GQ	155,18,0:1/1:90
+chr11	11315826	.	T	G	6.29	.	DP=27;AF1=1;CI95=1,1;DP4=0,0,0,6;MQ=19	PL:GT:GQ	38,18,0:1/1:90
+chr11	11603859	.	A	C	22	.	DP=15;AF1=0.5;CI95=0.5,0.5;DP4=0,9,0,6;MQ=34;PV4=1,9.5e-13,0.22,1	PL:GT:GQ	52,0,115:0/1:55
+chr11	11700034	.	C	T	33	.	DP=11;AF1=1;CI95=1,1;DP4=0,0,9,0;MQ=30	PL:GT:GQ	66,27,0:1/1:99
+chr11	11822758	.	G	A	15.1	.	DP=15;AF1=0.5;CI95=0.5,0.5;DP4=0,7,0,3;MQ=38;PV4=1,0.18,1,1	PL:GT:GQ	45,0,88:0/1:48
+chr11	11976636	.	C	T	22	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=24	PL:GT:GQ	54,9,0:1/1:63
+chr11	14380517	.	C	G	16.1	.	DP=10;AF1=0.5;CI95=0.5,0.5;DP4=5,0,5,0;MQ=48;PV4=1,2.1e-05,0.13,1	PL:GT:GQ	46,0,113:0/1:49
+chr11	14419212	.	A	G	91.1	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=38	PL:GT:GQ	124,18,0:1/1:90
+chr11	14846792	.	A	G	55	.	DP=11;AF1=1;CI95=1,1;DP4=0,0,0,11;MQ=19	PL:GT:GQ	88,33,0:1/1:99
+chr11	15494556	.	C	T	99	.	DP=38;AF1=0.5;CI95=0.5,0.5;DP4=22,0,14,0;MQ=34;PV4=1,0.0071,1,1	PL:GT:GQ	146,0,159:0/1:99
+chr11	16262879	.	A	C	16.1	.	DP=4;AF1=0.5004;CI95=0.5,0.5;DP4=0,1,0,3;MQ=43;PV4=1,0.061,0.24,0.33	PL:GT:GQ	46,0,28:0/1:31
+chr11	21514947	.	T	C	24.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=41	PL:GT:GQ	57,12,0:1/1:72
+chr11	22532576	.	C	G	28	.	DP=17;AF1=1;CI95=1,1;DP4=0,0,0,17;MQ=17	PL:GT:GQ	61,51,0:1/1:99
+chr11	23529238	.	G	T	4.29	.	DP=13;AF1=0.5334;CI95=0.5,1;DP4=1,0,3,0;MQ=37;PV4=1,1,0.34,0.21	PL:GT:GQ	32,0,9:0/1:12
+chr11	24249554	.	A	G	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=48	PL:GT:GQ	73,6,0:1/1:49
+chr11	24853167	.	A	G	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=51	PL:GT:GQ	73,6,0:1/1:49
+chr11	33353903	.	T	C	24.3	.	DP=8;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=36	PL:GT:GQ	57,15,0:1/1:75
+chr11	35126569	.	T	C	24.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=43	PL:GT:GQ	57,12,0:1/1:72
+chr11	35132248	.	C	T	18.6	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=25	PL:GT:GQ	51,12,0:1/1:72
+chr11	35155482	.	T	C	68	.	DP=22;AF1=1;CI95=1,1;DP4=0,0,22,0;MQ=46	PL:GT:GQ	101,66,0:1/1:99
+chr11	52494088	.	T	C	99	.	DP=9;AF1=1;CI95=1,1;DP4=0,0,0,9;MQ=37	PL:GT:GQ	140,27,0:1/1:99
+chr11	57899943	.	C	G	13	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35	PL:GT:GQ	44,6,0:1/1:49
+chr11	62261460	.	G	T	19.1	.	DP=15;AF1=0.5;CI95=0.5,0.5;DP4=0,7,0,5;MQ=27;PV4=1,1.1e-06,1,1	PL:GT:GQ	49,0,58:0/1:51
+chr11	67456049	.	C	T	39.1	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=19	PL:GT:GQ	72,18,0:1/1:90
+chr11	68509708	.	C	G	3.65	.	DP=9;AF1=0.7301;CI95=0.5,1;DP4=0,5,0,4;MQ=17;PV4=1,1,1,1	PL:GT:GQ	30,0,2:0/1:3
+chr11	70115115	.	T	A	99	.	DP=7;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=49	PL:GT:GQ	140,15,0:1/1:75
+chr11	72643951	.	T	C	70	.	DP=23;AF1=1;CI95=1,1;DP4=0,0,22,0;MQ=39	PL:GT:GQ	103,66,0:1/1:99
+chr11	72647930	.	G	A	36	.	DP=4;AF1=0.5004;CI95=0.5,0.5;DP4=0,1,0,3;MQ=41;PV4=1,1,0.3,1	PL:GT:GQ	66,0,28:0/1:31
+chr11	73330148	.	C	T	13	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35	PL:GT:GQ	44,6,0:1/1:49
+chr11	81720893	.	A	G	5.83	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=19	PL:GT:GQ	37,12,0:1/1:72
+chr11	83813797	.	A	G	23.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=43	PL:GT:GQ	56,12,0:1/1:72
+chr11	85949488	.	C	A	54	.	DP=17;AF1=1;CI95=1,1;DP4=0,0,14,0;MQ=37	PL:GT:GQ	87,42,0:1/1:99
+chr11	87634829	.	G	A	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=51	PL:GT:GQ	40,6,0:1/1:49
+chr11	90913093	.	A	T	35.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=46	PL:GT:GQ	67,6,0:1/1:49
+chr11	93793348	.	G	A	99	.	DP=8;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=31	PL:GT:GQ	139,24,0:1/1:96
+chr11	100802294	.	T	C	16.6	.	DP=21;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=35	PL:GT:GQ	49,12,0:1/1:72
+chr11	107455449	.	C	T	8.44	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=26	PL:GT:GQ	39,6,0:1/1:49
+chr11	111344355	.	A	G	69.5	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=43	PL:GT:GQ	102,12,0:1/1:72
+chr11	111611115	.	C	T	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49	PL:GT:GQ	73,6,0:1/1:49
+chr11	113050466	.	G	C	6.02	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=30	PL:GT:GQ	36,6,0:1/1:49
+chr11	114332544	.	T	C	3.54	.	DP=17;AF1=0.4999;CI95=0.5,0.5;DP4=0,4,0,5;MQ=37;PV4=1,0.32,0.13,1	PL:GT:GQ	31,0,37:0/1:33
+chr11	114332549	.	G	A	3.54	.	DP=17;AF1=0.4998;CI95=0.5,0.5;DP4=0,9,0,8;MQ=36;PV4=1,3.1e-10,0.088,1	PL:GT:GQ	31,0,127:0/1:34
+chr11	114843578	.	G	C	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=50	PL:GT:GQ	73,6,0:1/1:49
+chr11	115580279	.	A	G	99	.	DP=15;AF1=1;CI95=1,1;DP4=0,0,15,0;MQ=48	PL:GT:GQ	190,45,0:1/1:99
+chr11	116434328	.	G	A	17.6	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=25	PL:GT:GQ	50,12,0:1/1:72
+chr11	125914161	.	A	G	20.8	.	DP=7;AF1=0.95;CI95=0.5,1;DP4=3,0,4,0;MQ=38;PV4=1,0.074,1,1	PL:GT:GQ	49,0,0:1/1:10
+chr11	125917089	.	C	T	12.3	.	DP=41;AF1=0.5;CI95=0.5,0.5;DP4=0,28,0,12;MQ=44;PV4=1,4.7e-25,1,1	PL:GT:GQ	42,0,167:0/1:45
+chr11	127194100	.	A	G	60	.	DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=49	PL:GT:GQ	93,24,0:1/1:96
+chr12	70856	.	G	A	27.5	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=49	PL:GT:GQ	60,12,0:1/1:72
+chr12	153693	.	T	C	52.3	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=38	PL:GT:GQ	85,15,0:1/1:75
+chr12	924547	.	C	G	37.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=50	PL:GT:GQ	69,6,0:1/1:49
+chr12	1555916	.	G	A	7.18	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=23	PL:GT:GQ	39,15,0:1/1:75
+chr12	1919860	.	G	T	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49	PL:GT:GQ	40,6,0:1/1:49
+chr12	2283756	.	G	A	13.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=34	PL:GT:GQ	45,6,0:1/1:49
+chr12	2805983	.	G	C	12.7	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=35	PL:GT:GQ	45,12,0:1/1:72
+chr12	6088203	.	T	C	72.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=37	PL:GT:GQ	105,15,0:1/1:75
+chr12	7099460	.	G	C	10.8	.	DP=6;AF1=0.8277;CI95=0.5,1;DP4=3,0,3,0;MQ=26;PV4=1,0.027,1,1	PL:GT:GQ	39,0,1:1/1:5
+chr12	7099464	.	G	A	13.3	.	DP=6;AF1=0.9966;CI95=0.5,1;DP4=2,0,3,0;MQ=28;PV4=1,0.16,1,1	PL:GT:GQ	42,1,0:1/1:23
+chr12	7198516	.	T	G	4.61	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35	PL:GT:GQ	34,6,0:1/1:49
+chr12	23331895	.	C	T	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49	PL:GT:GQ	40,6,0:1/1:49
+chr12	28209020	.	T	G	14.4	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=31	PL:GT:GQ	47,15,0:1/1:75
+chr12	30074073	.	C	T	32.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35	PL:GT:GQ	64,6,0:1/1:49
+chr12	30563452	.	T	C	25	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=46	PL:GT:GQ	57,9,0:1/1:63
+chr12	30563453	.	A	G	25	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=46	PL:GT:GQ	57,9,0:1/1:63
+chr12	30563464	.	C	A	78.8	.	DP=8;AF1=1;CI95=0.5,1;DP4=0,2,0,5;MQ=34;PV4=1,0.29,1,1	PL:GT:GQ	110,6,0:1/1:49
+chr12	31505085	.	G	A	13.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35	PL:GT:GQ	45,6,0:1/1:49
+chr12	34041336	.	G	A	5.46	.	DP=5;AF1=0.5;CI95=0.5,0.5;DP4=2,0,2,0;MQ=36;PV4=1,1,0.48,0.21	PL:GT:GQ	34,0,34:0/1:34
+chr12	49003648	.	C	G	42	.	DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=39	PL:GT:GQ	75,24,0:1/1:96
+chr12	51280690	.	G	A	69	.	DP=98;AF1=0.5;CI95=0.5,0.5;DP4=13,0,18,0;MQ=45;PV4=1,1,0.051,1	PL:GT:GQ	99,0,84:0/1:87
+chr12	69206633	.	T	C	17.1	.	DP=12;AF1=1;CI95=1,1;DP4=0,0,0,11;MQ=17	PL:GT:GQ	50,33,0:1/1:99
+chr12	80417253	.	T	C	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=48	PL:GT:GQ	73,6,0:1/1:49
+chr12	86633033	.	C	T	34	.	DP=3;AF1=0.5002;CI95=0.5,0.5;DP4=0,1,0,2;MQ=43;PV4=1,1,0.33,1	PL:GT:GQ	64,0,31:0/1:34
+chr12	98097274	.	C	T	47.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=31	PL:GT:GQ	80,15,0:1/1:75
+chr12	105269319	.	C	T	19	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=26	PL:GT:GQ	51,9,0:1/1:63
+chr12	109053425	.	G	A	9.53	.	DP=8;AF1=0.5012;CI95=0.5,0.5;DP4=2,0,6,0;MQ=25;PV4=1,1,0.19,1	PL:GT:GQ	39,0,23:0/1:26
+chr12	111904540	.	A	G	3.41	.	DP=65;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=31	PL:GT:GQ	32,6,0:1/1:49
+chr12	115038686	.	T	C	15.2	.	DP=7;AF1=1;CI95=1,1;DP4=0,0,0,7;MQ=27	PL:GT:GQ	48,21,0:1/1:84
+chr12	115039419	.	A	G	4.11	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=30	PL:GT:GQ	34,9,0:1/1:63
+chr12	115103890	.	G	A	66	.	DP=39;AF1=1;CI95=1,1;DP4=0,0,0,38;MQ=49	PL:GT:GQ	99,114,0:1/1:99
+chr12	115833830	.	G	A	68	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=49	PL:GT:GQ	100,9,0:1/1:63
+chr12	116361873	.	T	G	6.34	.	DP=5;AF1=0.7302;CI95=0.5,1;DP4=0,2,0,2;MQ=23;PV4=1,1,1,1	PL:GT:GQ	34,0,2:0/1:3
+chr12	123583527	.	G	A	14.1	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=25	PL:GT:GQ	46,9,0:1/1:63
+chr12	124115330	.	A	G	44	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=38	PL:GT:GQ	76,9,0:1/1:63
+chr12	125062296	.	G	A	41.8	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=50	PL:GT:GQ	73,6,0:1/1:49
+chr12	126718106	.	A	G	8.76	.	DP=50;AF1=0.5163;CI95=0.5,1;DP4=2,0,6,0;MQ=26;PV4=1,0.33,0.37,1	PL:GT:GQ	38,0,12:0/1:15
+chr12	133348311	.	G	A	24	.	DP=18;AF1=0.5;CI95=0.5,0.5;DP4=14,0,3,0;MQ=35;PV4=1,1,1,1	PL:GT:GQ	54,0,118:0/1:57
+chr12	134494475	.	C	T	28	.	DP=18;AF1=0.6671;CI95=0.5,1;DP4=8,0,10,0;MQ=18;PV4=1,1,1,1	PL:GT:GQ	57,0,3:0/1:5
+chr12	134831761	.	C	T	41.3	.	DP=10;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=27	PL:GT:GQ	74,15,0:1/1:75
+chr12	134992770	.	A	C,T	84	.	DP=47;AF1=1;CI95=1,1;DP4=0,0,26,0;MQ=29	PL:GT:GQ	117,72,114,0,44,114:1/1:99
+chr12	135261117	.	G	A	49.1	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=46	PL:GT:GQ	82,18,0:1/1:90
+chr12	135261144	.	A	G	99	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=46	PL:GT:GQ	155,18,0:1/1:90
+chr12	135460302	.	G	A	99	.	DP=25;AF1=1;CI95=1,1;DP4=0,0,23,0;MQ=40	PL:GT:GQ	198,69,0:1/1:99
+chr12	135463758	.	A	G	83	.	DP=16;AF1=1;CI95=1,1;DP4=0,0,0,16;MQ=26	PL:GT:GQ	116,48,0:1/1:99
+chr12	135523325	.	G	A	99	.	DP=23;AF1=1;CI95=1,1;DP4=0,0,22,0;MQ=26	PL:GT:GQ	136,66,0:1/1:99
+chr12	135782401	.	T	C	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49	PL:GT:GQ	73,6,0:1/1:49
+chr12	135795472	.	G	T	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48	PL:GT:GQ	40,6,0:1/1:49
+chr13	18040027	.	G	C	42	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=33	PL:GT:GQ	74,9,0:1/1:63
+chr13	19494625	.	G	T	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48	PL:GT:GQ	73,6,0:1/1:49
+chr13	20121126	.	A	G	15.1	.	DP=36;AF1=0.5;CI95=0.5,0.5;DP4=25,0,9,0;MQ=36;PV4=1,1,0.13,1	PL:GT:GQ	45,0,153:0/1:48
+chr13	21536703	.	A	G	9.31	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49	PL:GT:GQ	40,6,0:1/1:49
+chr13	23160035	.	G	T	3.98	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=36	PL:GT:GQ	33,6,0:1/1:49
+chr13	23476554	.	C	A	6.79	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=52	PL:GT:GQ	37,6,0:1/1:49
+chr13	26632967	.	C	G	32	.	DP=9;AF1=1;CI95=1,1;DP4=0,0,0,9;MQ=34	PL:GT:GQ	65,27,0:1/1:99
+chr13	26790010	.	T	C	89.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=35	PL:GT:GQ	122,15,0:1/1:75
+chr13	36083571	.	T	C	43	.	DP=84;AF1=1;CI95=1,1;DP4=1,0,37,0;MQ=16;PV4=1,1,1,0.3	PL:GT:GQ	76,99,0:1/1:99
+chr13	44432419	.	C	T	3.58	.	DP=7;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=19	PL:GT:GQ	34,21,0:1/1:84
+chr13	46592359	.	T	C	16.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47	PL:GT:GQ	48,6,0:1/1:49
+chr13	52764657	.	A	T	3.14	.	DP=32;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=22	PL:GT:GQ	33,15,0:1/1:75
+chr13	53084193	.	C	T	9.11	.	DP=3;AF1=0.9998;CI95=0.5,1;DP4=0,1,0,2;MQ=29;PV4=1,1,1,1	PL:GT:GQ	38,2,0:1/1:37
+chr13	57763228	.	C	T	45	.	DP=555;AF1=1;CI95=1,1;DP4=2,0,21,0;MQ=23;PV4=1,0.00021,1,0.3	PL:GT:GQ	78,45,0:1/1:99
+chr13	73857921	.	G	C	31	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=49	PL:GT:GQ	63,9,0:1/1:63
+chr13	76718001	.	G	A	59	.	DP=4;AF1=0.5004;CI95=0.5,0.5;DP4=1,0,3,0;MQ=45;PV4=1,1,0.12,1	PL:GT:GQ	89,0,28:0/1:31
+chr13	100912695	.	A	T	23	.	DP=22;AF1=0.5;CI95=0.5,0.5;DP4=0,16,0,6;MQ=31;PV4=1,0.029,1,0.35	PL:GT:GQ	53,0,103:0/1:56
+chr13	101332001	.	G	C	21	.	DP=23;AF1=1;CI95=1,1;DP4=0,0,23,0;MQ=21	PL:GT:GQ	54,69,0:1/1:99
+chr13	102637334	.	C	T	68	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=49	PL:GT:GQ	100,9,0:1/1:63
+chr13	102895627	.	C	T	63	.	DP=9;AF1=1;CI95=1,1;DP4=0,0,9,0;MQ=48	PL:GT:GQ	96,27,0:1/1:99
+chr13	103830322	.	T	C	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=50	PL:GT:GQ	73,6,0:1/1:49
+chr13	112842448	.	G	A	39	.	DP=18;AF1=1;CI95=1,1;DP4=0,0,0,9;MQ=27	PL:GT:GQ	72,27,0:1/1:99
+chr13	113310291	.	C	T	33.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=43	PL:GT:GQ	66,12,0:1/1:72
+chr13	114775162	.	A	G	80	.	DP=17;AF1=1;CI95=1,1;DP4=0,0,17,0;MQ=21	PL:GT:GQ	113,51,0:1/1:99
+chr13	115267482	.	A	G	16.1	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=29	PL:GT:GQ	48,9,0:1/1:63
+chr13	116068676	.	C	T	3.83	.	DP=8;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=27	PL:GT:GQ	34,12,0:1/1:72
+chr13	116455918	.	A	G	33	.	DP=29;AF1=0.5;CI95=0.5,0.5;DP4=13,0,15,0;MQ=42;PV4=1,1.8e-20,0.3,1	PL:GT:GQ	63,0,146:0/1:66
+chr13	116765012	.	G	A	30.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49	PL:GT:GQ	62,6,0:1/1:49
+chr13	116779773	.	C	T	17.1	.	DP=38;AF1=0.5;CI95=0.5,0.5;DP4=27,0,11,0;MQ=24;PV4=1,4.5e-35,1,1	PL:GT:GQ	47,0,106:0/1:50
+chr13	116779791	.	C	T	57	.	DP=38;AF1=0.5;CI95=0.5,0.5;DP4=24,0,14,0;MQ=24;PV4=1,1,1,1	PL:GT:GQ	87,0,103:0/1:90
+chr14	20159250	.	C	T	11.3	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=39	PL:GT:GQ	43,9,0:1/1:63
+chr14	23510676	.	T	C	52	.	DP=22;AF1=1;CI95=1,1;DP4=0,0,22,0;MQ=32	PL:GT:GQ	85,66,0:1/1:99
+chr14	24735256	.	G	A	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49	PL:GT:GQ	40,6,0:1/1:49
+chr14	29525577	.	G	A	21	.	DP=10;AF1=1;CI95=1,1;DP4=0,0,9,0;MQ=16	PL:GT:GQ	54,27,0:1/1:99
+chr14	36186389	.	C	T	6.79	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=20	PL:GT:GQ	37,6,0:1/1:49
+chr14	36186394	.	A	G	6.79	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=20	PL:GT:GQ	37,6,0:1/1:49
+chr14	37440609	.	A	G	13	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=33	PL:GT:GQ	44,6,0:1/1:49
+chr14	40432807	.	A	G	18.6	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=23	PL:GT:GQ	51,12,0:1/1:72
+chr14	59466268	.	T	C	15.1	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=25	PL:GT:GQ	47,9,0:1/1:63
+chr14	61368162	.	G	T	7.18	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=17	PL:GT:GQ	39,15,0:1/1:75
+chr14	65152922	.	G	A	92	.	DP=33;AF1=0.5;CI95=0.5,0.5;DP4=0,18,0,15;MQ=36;PV4=1,0.059,0.35,1	PL:GT:GQ	122,0,144:0/1:99
+chr14	69749148	.	G	T	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=25	PL:GT:GQ	40,6,0:1/1:49
+chr14	74877658	.	C	T	45	.	DP=48;AF1=1;CI95=1,1;DP4=0,1,0,12;MQ=36;PV4=1,0.02,1,0.39	PL:GT:GQ	78,28,0:1/1:99
+chr14	75546678	.	C	T	19.2	.	DP=7;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=17	PL:GT:GQ	52,18,0:1/1:90
+chr14	76439185	.	T	C	67.1	.	DP=7;AF1=0.505;CI95=0.5,0.5;DP4=0,1,0,6;MQ=33;PV4=1,1,0.056,0.29	PL:GT:GQ	97,0,17:0/1:20
+chr14	77313295	.	T	A	99	.	DP=12;AF1=1;CI95=1,1;DP4=0,0,0,10;MQ=48	PL:GT:GQ	191,30,0:1/1:99
+chr14	77673422	.	G	A	11.5	.	DP=7;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=24	PL:GT:GQ	44,18,0:1/1:90
+chr14	78646125	.	T	C	99	.	DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=40	PL:GT:GQ	153,24,0:1/1:96
+chr14	91702449	.	A	G	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47	PL:GT:GQ	40,6,0:1/1:49
+chr14	91769842	.	G	A	63	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=47	PL:GT:GQ	95,9,0:1/1:63
+chr14	91775899	.	C	G	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=45	PL:GT:GQ	73,6,0:1/1:49
+chr14	91775924	.	A	G	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=45	PL:GT:GQ	40,6,0:1/1:49
+chr14	93482918	.	A	C	68	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=49	PL:GT:GQ	100,9,0:1/1:63
+chr14	93665819	.	C	T	75	.	DP=7;AF1=0.5002;CI95=0.5,0.5;DP4=0,3,0,4;MQ=42;PV4=1,1,1,1	PL:GT:GQ	105,0,31:0/1:34
+chr14	95422276	.	A	G	55.1	.	DP=7;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=45	PL:GT:GQ	88,21,0:1/1:84
+chr14	95731986	.	C	T	68	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=49	PL:GT:GQ	100,9,0:1/1:63
+chr14	96045464	.	A	G	13	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=33	PL:GT:GQ	44,6,0:1/1:49
+chr14	97172020	.	C	T	68	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=51	PL:GT:GQ	100,9,0:1/1:63
+chr14	100515480	.	A	G	6.98	.	DP=3;AF1=0.5002;CI95=0.5,0.5;DP4=1,0,2,0;MQ=45;PV4=1,0.14,0.085,0.33	PL:GT:GQ	36,0,30:0/1:32
+chr14	100770214	.	A	T	8.69	.	DP=20;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=16	PL:GT:GQ	41,21,0:1/1:84
+chr14	101258303	.	G	A	82	.	DP=15;AF1=1;CI95=1,1;DP4=0,0,15,0;MQ=26	PL:GT:GQ	115,45,0:1/1:99
+chr14	101701492	.	C	G	66	.	DP=10;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=49	PL:GT:GQ	99,30,0:1/1:99
+chr14	102113772	.	T	C	3.98	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=30	PL:GT:GQ	33,6,0:1/1:49
+chr14	102751431	.	A	C	36.5	.	DP=3;AF1=0.9998;CI95=0.5,1;DP4=1,0,2,0;MQ=35;PV4=1,1,1,1	PL:GT:GQ	66,2,0:1/1:37
+chr14	103708033	.	A	G	99	.	DP=13;AF1=1;CI95=1,1;DP4=0,0,0,12;MQ=27	PL:GT:GQ	141,36,0:1/1:99
+chr14	104744582	.	G	A	3.52	.	DP=8;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=25	PL:GT:GQ	33,9,0:1/1:63
+chr14	105989100	.	C	T	3.14	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=23	PL:GT:GQ	33,15,0:1/1:75
+chr14	105989162	.	C	T	3.65	.	DP=12;AF1=0.7301;CI95=0.5,1;DP4=0,6,0,6;MQ=15;PV4=1,1,1,1	PL:GT:GQ	30,0,2:0/1:3
+chr14	106234810	.	G	A	25.3	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=39	PL:GT:GQ	58,15,0:1/1:75
+chr14	106995572	.	A	G	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49	PL:GT:GQ	40,6,0:1/1:49
+chr14	107283057	.	T	C	5.5	.	DP=8;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=20	PL:GT:GQ	37,21,0:1/1:84
+chr14	107285319	.	T	C	33	.	DP=36;AF1=1;CI95=1,1;DP4=0,0,0,35;MQ=22	PL:GT:GQ	66,105,0:1/1:99
+chr14	107640449	.	A	G	11.8	.	DP=7;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=36	PL:GT:GQ	44,12,0:1/1:72
+chr15	20082092	.	T	G	18.3	.	DP=10;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=24	PL:GT:GQ	51,15,0:1/1:75
+chr15	22955884	.	T	C	67	.	DP=12;AF1=1;CI95=1,1;DP4=0,0,12,0;MQ=48	PL:GT:GQ	100,36,0:1/1:99
+chr15	22971987	.	A	G	5.29	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=22	PL:GT:GQ	35,6,0:1/1:49
+chr15	23233324	.	C	A	47	.	DP=16;AF1=1;CI95=1,1;DP4=0,0,14,0;MQ=31	PL:GT:GQ	80,42,0:1/1:99
+chr15	25175286	.	C	T	36.5	.	DP=3;AF1=0.9998;CI95=0.5,1;DP4=1,0,2,0;MQ=42;PV4=1,1,1,1	PL:GT:GQ	66,2,0:1/1:37
+chr15	25385709	.	G	A	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=48	PL:GT:GQ	40,6,0:1/1:49
+chr15	27372396	.	A	G	44	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=40	PL:GT:GQ	76,9,0:1/1:63
+chr15	35998093	.	C	T	9.53	.	DP=9;AF1=1;CI95=1,1;DP4=0,0,9,0;MQ=17	PL:GT:GQ	42,27,0:1/1:99
+chr15	36716538	.	C	G	13.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=36	PL:GT:GQ	45,6,0:1/1:49
+chr15	36793360	.	G	T	44	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=42	PL:GT:GQ	76,9,0:1/1:63
+chr15	53783097	.	A	G	10.5	.	DP=31;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=16	PL:GT:GQ	43,21,0:1/1:84
+chr15	54180175	.	C	T	10.4	.	DP=7;AF1=0.5001;CI95=0.5,0.5;DP4=4,0,3,0;MQ=27;PV4=1,1.2e-05,1,1	PL:GT:GQ	40,0,32:0/1:34
+chr15	54939306	.	C	T	99	.	DP=34;AF1=0.5;CI95=0.5,0.5;DP4=0,18,0,16;MQ=49;PV4=1,1,0.18,1	PL:GT:GQ	172,0,181:0/1:99
+chr15	59377916	.	C	T	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=50	PL:GT:GQ	73,6,0:1/1:49
+chr15	59685961	.	G	C	68	.	DP=11;AF1=1;CI95=1,1;DP4=0,0,0,11;MQ=36	PL:GT:GQ	101,33,0:1/1:99
+chr15	60306384	.	A	G	18.6	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=25	PL:GT:GQ	51,12,0:1/1:72
+chr15	60345642	.	G	C	14.9	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35	PL:GT:GQ	46,6,0:1/1:49
+chr15	60367387	.	G	A	13.2	.	DP=6;AF1=0.5001;CI95=0.5,0.5;DP4=3,0,3,0;MQ=34;PV4=1,0.098,0.24,1	PL:GT:GQ	43,0,35:0/1:37
+chr15	60367446	.	C	T	44	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=41	PL:GT:GQ	76,9,0:1/1:63
+chr15	61763755	.	G	A	68	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=45	PL:GT:GQ	100,9,0:1/1:63
+chr15	61831362	.	C	G	11.3	.	DP=5;AF1=0.5;CI95=0.5,0.5;DP4=0,2,0,3;MQ=30;PV4=1,0.00077,0.47,1	PL:GT:GQ	41,0,42:0/1:41
+chr15	63978880	.	G	C	60	.	DP=6;AF1=0.9999;CI95=0.5,1;DP4=2,0,4,0;MQ=35;PV4=1,1,1,1	PL:GT:GQ	90,3,0:1/1:41
+chr15	64342445	.	A	G	12.2	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=18	PL:GT:GQ	44,9,0:1/1:63
+chr15	65424859	.	T	C	11.3	.	DP=10;AF1=1;CI95=1,1;DP4=0,0,0,10;MQ=21	PL:GT:GQ	44,30,0:1/1:99
+chr15	65603698	.	C	T	60	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=49	PL:GT:GQ	92,9,0:1/1:63
+chr15	67005078	.	G	A	13.9	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35	PL:GT:GQ	45,6,0:1/1:49
+chr15	71133512	.	G	C	22.3	.	DP=19;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=25	PL:GT:GQ	55,15,0:1/1:75
+chr15	72619009	.	A	G	22	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=48	PL:GT:GQ	54,9,0:1/1:63
+chr15	73272688	.	C	T	70.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=39	PL:GT:GQ	103,15,0:1/1:75
+chr15	73699335	.	T	A	99	.	DP=9;AF1=1;CI95=1,1;DP4=0,0,0,9;MQ=45	PL:GT:GQ	175,27,0:1/1:99
+chr15	74513352	.	C	T	99	.	DP=10;AF1=1;CI95=1,1;DP4=0,0,0,10;MQ=37	PL:GT:GQ	139,30,0:1/1:99
+chr15	75540536	.	G	A	9.31	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=44	PL:GT:GQ	40,6,0:1/1:49
+chr15	75822537	.	C	A	17.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=23	PL:GT:GQ	50,15,0:1/1:75
+chr15	78554005	.	T	C	12	.	DP=18;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=46	PL:GT:GQ	43,6,0:1/1:49
+chr15	80089369	.	G	A	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=28	PL:GT:GQ	40,6,0:1/1:49
+chr15	83089149	.	C	G	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=33	PL:GT:GQ	40,6,0:1/1:49
+chr15	86839307	.	T	C	90.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=43	PL:GT:GQ	123,15,0:1/1:75
+chr15	89836258	.	T	C	99	.	DP=10;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=39	PL:GT:GQ	141,24,0:1/1:96
+chr15	89837706	.	G	A	4.13	.	DP=8;AF1=0.4998;CI95=0.5,0.5;DP4=0,4,0,4;MQ=30;PV4=1,1,0.25,1	PL:GT:GQ	32,0,59:0/1:35
+chr15	89857648	.	T	C	99	.	DP=27;AF1=0.5;CI95=0.5,0.5;DP4=8,0,8,0;MQ=40;PV4=1,1,0.3,1	PL:GT:GQ	133,0,130:0/1:99
+chr15	89864228	.	A	C	32	.	DP=4;AF1=0.5002;CI95=0.5,0.5;DP4=2,0,2,0;MQ=42;PV4=1,1,1,1	PL:GT:GQ	62,0,31:0/1:34
+chr15	91261235	.	G	A	7.8	.	DP=4;AF1=0.5002;CI95=0.5,0.5;DP4=1,0,2,0;MQ=44;PV4=1,1,0.32,1	PL:GT:GQ	37,0,30:0/1:32
+chr16	256990	.	A	C	10.4	.	DP=16;AF1=0.5008;CI95=0.5,0.5;DP4=4,0,3,0;MQ=23;PV4=1,0.34,1,1	PL:GT:GQ	40,0,25:0/1:28
+chr16	260794	.	T	C	3.01	.	DP=19;AF1=0.4999;CI95=0.5,0.5;DP4=13,0,2,0;MQ=24;PV4=1,1,1,1	PL:GT:GQ	30,0,32:0/1:31
+chr16	419905	.	A	G	7.9	.	DP=5;AF1=0.9966;CI95=0.5,1;DP4=0,2,0,3;MQ=22;PV4=1,1,1,1	PL:GT:GQ	36,1,0:1/1:23
+chr16	824086	.	T	C	22	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=48	PL:GT:GQ	54,9,0:1/1:63
+chr16	1085063	.	C	T	52	.	DP=12;AF1=0.5;CI95=0.5,0.5;DP4=6,0,6,0;MQ=42;PV4=1,1,0.014,1	PL:GT:GQ	82,0,128:0/1:85
+chr16	1221305	.	T	C	54	.	DP=7;AF1=0.5;CI95=0.5,0.5;DP4=0,3,0,3;MQ=40;PV4=1,1,1,1	PL:GT:GQ	84,0,60:0/1:63
+chr16	1411728	.	A	G	32.3	.	DP=11;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=35	PL:GT:GQ	65,15,0:1/1:75
+chr16	1443197	.	C	G	64	.	DP=26;AF1=1;CI95=1,1;DP4=0,0,25,0;MQ=36	PL:GT:GQ	97,75,0:1/1:99
+chr16	1478746	.	A	T	32	.	DP=20;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=28	PL:GT:GQ	65,24,0:1/1:96
+chr16	1514438	.	A	C	45	.	DP=49;AF1=1;CI95=1,1;DP4=0,0,48,0;MQ=26	PL:GT:GQ	78,144,0:1/1:99
+chr16	1601989	.	T	C	99	.	DP=13;AF1=1;CI95=1,1;DP4=0,0,13,0;MQ=29	PL:GT:GQ	133,39,0:1/1:99
+chr16	2043883	.	C	T	30	.	DP=33;AF1=1;CI95=1,1;DP4=0,0,0,33;MQ=14	PL:GT:GQ	63,99,0:1/1:99
+chr16	2137470	.	A	C	39	.	DP=38;AF1=0.5016;CI95=0.5,0.5;DP4=4,0,6,0;MQ=34;PV4=1,0.02,1,1	PL:GT:GQ	69,0,22:0/1:25
+chr16	2537260	.	A	G	99	.	DP=11;AF1=1;CI95=1,1;DP4=0,0,11,0;MQ=40	PL:GT:GQ	177,33,0:1/1:99
+chr16	2564737	.	T	C	99	.	DP=25;AF1=1;CI95=1,1;DP4=0,0,0,22;MQ=41	PL:GT:GQ	199,66,0:1/1:99
+chr16	2612605	.	A	T	62.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=28	PL:GT:GQ	95,15,0:1/1:75
+chr16	2704518	.	G	A	41	.	DP=48;AF1=0.5;CI95=0.5,0.5;DP4=0,17,0,12;MQ=48;PV4=1,1.9e-23,0.24,0.034	PL:GT:GQ	71,0,175:0/1:74
+chr16	3274307	.	G	T	68	.	DP=39;AF1=0.5;CI95=0.5,0.5;DP4=0,30,0,8;MQ=37;PV4=1,1,1,1	PL:GT:GQ	98,0,138:0/1:99
+chr16	5467292	.	G	C	37.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49	PL:GT:GQ	69,6,0:1/1:49
+chr16	10079145	.	A	G	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49	PL:GT:GQ	73,6,0:1/1:49
+chr16	11483702	.	A	G	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=44	PL:GT:GQ	40,6,0:1/1:49
+chr16	12038227	.	A	T	23	.	DP=47;AF1=0.5;CI95=0.5,0.5;DP4=0,22,0,23;MQ=32;PV4=1,4.4e-66,0.47,0.028	PL:GT:GQ	53,0,135:0/1:56
+chr16	21336880	.	G	C	55	.	DP=35;AF1=0.5;CI95=0.5,0.5;DP4=0,12,0,19;MQ=47;PV4=1,5.6e-21,1,1	PL:GT:GQ	85,0,121:0/1:88
+chr16	21980241	.	C	T	16.1	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=29	PL:GT:GQ	48,9,0:1/1:63
+chr16	23275383	.	C	G	13	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47	PL:GT:GQ	44,6,0:1/1:49
+chr16	27546495	.	G	T	25	.	DP=35;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=43	PL:GT:GQ	57,9,0:1/1:63
+chr16	27700399	.	A	T	17.6	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=17	PL:GT:GQ	50,12,0:1/1:72
+chr16	28021935	.	A	G	18.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=23	PL:GT:GQ	51,15,0:1/1:75
+chr16	29070016	.	G	T	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47	PL:GT:GQ	40,6,0:1/1:49
+chr16	29478618	.	C	T	11.3	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=42	PL:GT:GQ	43,9,0:1/1:63
+chr16	29718140	.	C	T	46.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=31	PL:GT:GQ	79,15,0:1/1:75
+chr16	30700759	.	T	C	17.1	.	DP=14;AF1=1;CI95=1,1;DP4=0,0,0,14;MQ=14	PL:GT:GQ	50,42,0:1/1:99
+chr16	35139103	.	A	G	46.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=37	PL:GT:GQ	79,12,0:1/1:72
+chr16	35473348	.	G	A	3.83	.	DP=11;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=25	PL:GT:GQ	34,12,0:1/1:72
+chr16	36213667	.	A	G	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49	PL:GT:GQ	73,6,0:1/1:49
+chr16	36705528	.	G	A	14.4	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=32	PL:GT:GQ	47,15,0:1/1:75
+chr16	43831353	.	C	T	69.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=42	PL:GT:GQ	102,12,0:1/1:72
+chr16	44715166	.	A	C	25	.	DP=18;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=32	PL:GT:GQ	58,24,0:1/1:96
+chr16	44957661	.	T	C	7.03	.	DP=23;AF1=1;CI95=1,1;DP4=0,0,0,7;MQ=18	PL:GT:GQ	39,21,0:1/1:84
+chr16	44958698	.	C	T	42.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=49	PL:GT:GQ	75,15,0:1/1:75
+chr16	44959163	.	T	C	33.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=48	PL:GT:GQ	66,12,0:1/1:72
+chr16	45167959	.	C	T	4.45	.	DP=16;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=24	PL:GT:GQ	35,12,0:1/1:72
+chr16	50254956	.	C	T	13.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=36	PL:GT:GQ	45,6,0:1/1:49
+chr16	52383122	.	A	C	46.5	.	DP=19;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=42	PL:GT:GQ	79,12,0:1/1:72
+chr16	55978159	.	C	T	10.7	.	DP=20;AF1=0.5336;CI95=0.5,1;DP4=2,0,5,0;MQ=35;PV4=1,0.038,1,0.059	PL:GT:GQ	40,0,9:0/1:12
+chr16	61358878	.	T	A	15.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=32	PL:GT:GQ	47,6,0:1/1:49
+chr16	61392487	.	G	A	13	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=31	PL:GT:GQ	44,6,0:1/1:49
+chr16	61621603	.	G	T	6.59	.	DP=10;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=22	PL:GT:GQ	38,12,0:1/1:72
+chr16	69120890	.	G	C	51.3	.	DP=36;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=42	PL:GT:GQ	84,15,0:1/1:75
+chr16	70778219	.	A	G	21.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=39	PL:GT:GQ	53,6,0:1/1:49
+chr16	71899519	.	T	C	40	.	DP=11;AF1=1;CI95=1,1;DP4=0,0,11,0;MQ=33	PL:GT:GQ	73,33,0:1/1:99
+chr16	72079251	.	A	G	11.3	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=41	PL:GT:GQ	43,9,0:1/1:63
+chr16	72093003	.	G	C	9.31	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49	PL:GT:GQ	40,6,0:1/1:49
+chr16	72672428	.	A	G	68	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=49	PL:GT:GQ	100,9,0:1/1:63
+chr16	72864515	.	A	G	13.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35	PL:GT:GQ	45,6,0:1/1:49
+chr16	72890560	.	G	A	47.1	.	DP=10;AF1=0.5064;CI95=0.5,0.5;DP4=0,1,0,7;MQ=49;PV4=1,0.0019,0.0033,1	PL:GT:GQ	77,0,16:0/1:19
+chr16	73048929	.	A	G	6.29	.	DP=4;AF1=0.9966;CI95=0.5,1;DP4=1,0,2,0;MQ=27;PV4=1,1,1,0.33	PL:GT:GQ	34,1,0:1/1:23
+chr16	73177179	.	A	G	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49	PL:GT:GQ	40,6,0:1/1:49
+chr16	73191468	.	C	T	69.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=40	PL:GT:GQ	102,12,0:1/1:72
+chr16	73367439	.	A	C	7.41	.	DP=36;AF1=1;CI95=0.5,1;DP4=0,2,0,13;MQ=26;PV4=1,1,0.027,1	PL:GT:GQ	37,4,0:1/1:45
+chr16	74259316	.	C	T	89.5	.	DP=13;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=49	PL:GT:GQ	122,12,0:1/1:72
+chr16	75271450	.	C	G	6.99	.	DP=15;AF1=0.5015;CI95=0.5,0.5;DP4=0,1,0,3;MQ=44;PV4=1,0.065,0.31,1	PL:GT:GQ	36,0,22:0/1:25
+chr16	76199870	.	G	A	26	.	DP=14;AF1=0.5;CI95=0.5,0.5;DP4=8,0,6,0;MQ=47;PV4=1,1.2e-06,0.32,1	PL:GT:GQ	56,0,141:0/1:59
+chr16	77723692	.	A	G	89.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=50	PL:GT:GQ	122,12,0:1/1:72
+chr17	165875	.	G	A	40.8	.	DP=11;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=42	PL:GT:GQ	72,6,0:1/1:49
+chr17	1443809	.	C	G	9.31	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=50	PL:GT:GQ	40,6,0:1/1:49
+chr17	1618253	.	C	T	22	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=39	PL:GT:GQ	54,9,0:1/1:63
+chr17	2815309	.	T	G	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49	PL:GT:GQ	40,6,0:1/1:49
+chr17	3537486	.	T	G	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=50	PL:GT:GQ	73,6,0:1/1:49
+chr17	3734367	.	C	A	23.5	.	DP=10;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=36	PL:GT:GQ	56,12,0:1/1:72
+chr17	5634764	.	T	C	13	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35	PL:GT:GQ	44,6,0:1/1:49
+chr17	6408090	.	C	G	3.54	.	DP=5;AF1=0.4998;CI95=0.5,0.5;DP4=3,0,2,0;MQ=40;PV4=1,1,0.36,1	PL:GT:GQ	31,0,66:0/1:34
+chr17	7089723	.	A	G	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=47	PL:GT:GQ	40,6,0:1/1:49
+chr17	8731503	.	G	C	11.1	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=46	PL:GT:GQ	42,6,0:1/1:49
+chr17	9282935	.	T	C,G	24.5	.	DP=10;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=40	PL:GT:GQ	57,12,61,0,3,61:1/1:72
+chr17	17284831	.	T	C	29	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=25	PL:GT:GQ	61,9,0:1/1:63
+chr17	18439515	.	G	A	4.11	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=25	PL:GT:GQ	34,9,0:1/1:63
+chr17	18602146	.	C	T	4.76	.	DP=20;AF1=1;CI95=1,1;DP4=0,0,0,11;MQ=16	PL:GT:GQ	36,33,0:1/1:99
+chr17	19427888	.	C	T	57	.	DP=104;AF1=0.5;CI95=0.5,0.5;DP4=45,0,29,0;MQ=39;PV4=1,2.2e-12,1,1	PL:GT:GQ	87,0,131:0/1:90
+chr17	19604159	.	T	C	9.31	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=45	PL:GT:GQ	40,6,0:1/1:49
+chr17	19610366	.	C	T	13	.	DP=13;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48	PL:GT:GQ	44,6,0:1/1:49
+chr17	20484706	.	C	G	51	.	DP=35;AF1=0.5001;CI95=0.5,0.5;DP4=0,11,0,21;MQ=21;PV4=1,0.39,0.49,1	PL:GT:GQ	81,0,36:0/1:39
+chr17	20555720	.	A	G	26.3	.	DP=8;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=28	PL:GT:GQ	59,15,0:1/1:75
+chr17	24328984	.	A	C	15.4	.	DP=34;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=25	PL:GT:GQ	48,15,0:1/1:75
+chr17	26237090	.	G	A	41.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=44	PL:GT:GQ	73,6,0:1/1:49
+chr17	28394766	.	C	A	13.9	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=31	PL:GT:GQ	45,6,0:1/1:49
+chr17	31218277	.	A	G	3.62	.	DP=38;AF1=0.5161;CI95=0.5,0.5;DP4=0,1,0,2;MQ=38;PV4=1,0.26,1,1	PL:GT:GQ	31,0,12:0/1:15
+chr17	31254021	.	C	T	15.1	.	DP=10;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=35	PL:GT:GQ	47,9,0:1/1:63
+chr17	32516798	.	G	A	37.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49	PL:GT:GQ	69,6,0:1/1:49
+chr17	32600253	.	A	G	16.6	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=25	PL:GT:GQ	49,12,0:1/1:72
+chr17	34255214	.	G	C	19.2	.	DP=8;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=21	PL:GT:GQ	52,18,0:1/1:90
+chr17	34365900	.	T	C	93.1	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=38	PL:GT:GQ	126,18,0:1/1:90
+chr17	35380386	.	A	T	6.79	.	DP=44;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=46	PL:GT:GQ	37,6,0:1/1:49
+chr17	41993344	.	C	T	64	.	DP=41;AF1=1;CI95=1,1;DP4=0,0,0,41;MQ=16	PL:GT:GQ	97,123,0:1/1:99
+chr17	42128201	.	A	G	4.13	.	DP=5;AF1=0.4998;CI95=0.5,0.5;DP4=0,2,0,2;MQ=52;PV4=1,0.0041,1,1	PL:GT:GQ	32,0,62:0/1:35
+chr17	42984490	.	C	A	56	.	DP=33;AF1=0.5001;CI95=0.5,0.5;DP4=6,0,12,0;MQ=42;PV4=1,0.004,1,1	PL:GT:GQ	86,0,34:0/1:37
+chr17	43419457	.	G	A	99	.	DP=16;AF1=1;CI95=1,1;DP4=0,0,0,14;MQ=45	PL:GT:GQ	185,42,0:1/1:99
+chr17	43421225	.	A	G	65.1	.	DP=31;AF1=1;CI95=0.5,1;DP4=0,6,0,17;MQ=43;PV4=1,0.004,1,1	PL:GT:GQ	98,18,0:1/1:90
+chr17	45206897	.	G	A	22	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=47	PL:GT:GQ	54,9,0:1/1:63
+chr17	45381302	.	T	C	18.6	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=25	PL:GT:GQ	51,12,0:1/1:72
+chr17	45530812	.	C	A	3.54	.	DP=6;AF1=0.4998;CI95=0.5,0.5;DP4=0,3,0,2;MQ=40;PV4=1,1,0.37,1	PL:GT:GQ	31,0,58:0/1:34
+chr17	50242633	.	G	A	44	.	DP=42;AF1=0.5;CI95=0.5,0.5;DP4=0,25,0,13;MQ=32;PV4=1,0.084,0.14,1	PL:GT:GQ	74,0,154:0/1:77
+chr17	51275317	.	G	A	14.9	.	DP=10;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=31	PL:GT:GQ	46,6,0:1/1:49
+chr17	52325530	.	C	T	29	.	DP=19;AF1=1;CI95=1,1;DP4=0,0,0,18;MQ=24	PL:GT:GQ	62,54,0:1/1:99
+chr17	52411748	.	T	G	18.6	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=25	PL:GT:GQ	51,12,0:1/1:72
+chr17	53190746	.	C	G	62.1	.	DP=20;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=40	PL:GT:GQ	95,18,0:1/1:90
+chr17	58289916	.	T	C	18.2	.	DP=8;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=22	PL:GT:GQ	51,18,0:1/1:90
+chr17	59796875	.	C	T	42	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=35	PL:GT:GQ	74,9,0:1/1:63
diff --git a/tests/tabix_data/vcf/README.txt b/tests/tabix_data/vcf/README.txt
new file mode 100644
index 0000000..d6d26ec
--- /dev/null
+++ b/tests/tabix_data/vcf/README.txt
@@ -0,0 +1,11 @@
+Edits that were necessary to parse these files:
+
+23.vcf: change
+##INFO=<ID=MQ0Fraction,Number=1,Type=Integer,Description="Fraction of Mapping Quality Zero Reads">
+to
+##INFO=<ID=MQ0Fraction,Number=1,Type=Float,Description="Fraction of Mapping Quality Zero Reads">
+
+similar changes in 16.vcf and 2.vcf
+
+13.vcf
+Flag should not have a value.
diff --git a/tests/tabix_data/vcf/issue85.vcf b/tests/tabix_data/vcf/issue85.vcf
new file mode 100644
index 0000000..31695cc
--- /dev/null
+++ b/tests/tabix_data/vcf/issue85.vcf
@@ -0,0 +1,26 @@
+##fileformat=VCFv4.1
+##samtoolsVersion=0.1.18 (r982:295)
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">
+##INFO=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
+##INFO=<ID=MQ,Number=1,Type=Integer,Description="Root-mean-square mapping quality of covering reads">
+##INFO=<ID=FQ,Number=1,Type=Float,Description="Phred probability of all samples being the same">
+##INFO=<ID=AF1,Number=1,Type=Float,Description="Max-likelihood estimate of the first ALT allele frequency (assuming HWE)">
+##INFO=<ID=AC1,Number=1,Type=Float,Description="Max-likelihood estimate of the first ALT allele count (no HWE assumption)">
+##INFO=<ID=G3,Number=3,Type=Float,Description="ML estimate of genotype frequencies">
+##INFO=<ID=HWE,Number=1,Type=Float,Description="Chi^2 based HWE test P-value based on G3">
+##INFO=<ID=CLR,Number=1,Type=Integer,Description="Log ratio of genotype likelihoods with and without the constraint">
+##INFO=<ID=UGT,Number=1,Type=String,Description="The most probable unconstrained genotype configuration in the trio">
+##INFO=<ID=CGT,Number=1,Type=String,Description="The most probable constrained genotype configuration in the trio">
+##INFO=<ID=PV4,Number=4,Type=Float,Description="P-values for strand bias, baseQ bias, mapQ bias and tail distance bias">
+##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
+##INFO=<ID=PC2,Number=2,Type=Integer,Description="Phred probability of the nonRef allele frequency in group1 samples being larger (,smaller) than in group2.">
+##INFO=<ID=PCHI2,Number=1,Type=Float,Description="Posterior weighted chi^2 P-value for testing the association between group1 and group2 samples.">
+##INFO=<ID=QCHI2,Number=1,Type=Integer,Description="Phred scaled PCHI2.">
+##INFO=<ID=PR,Number=1,Type=Integer,Description="# permutations yielding a smaller PCHI2.">
+##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=GL,Number=3,Type=Float,Description="Likelihoods for RR,RA,AA genotypes (R=ref,A=alt)">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="# high-quality bases">
+##FORMAT=<ID=SP,Number=1,Type=Integer,Description="Phred-scaled strand bias P-value">
+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
diff --git a/tests/tabix_data/vcf/vcf_v42.vcf b/tests/tabix_data/vcf/vcf_v42.vcf
new file mode 100644
index 0000000..11dbc0a
--- /dev/null
+++ b/tests/tabix_data/vcf/vcf_v42.vcf
@@ -0,0 +1,25 @@
+##fileformat=VCFv4.2
+##fileDate=20090805
+##source=myImputationProgramV3.1
+##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta
+##contig=<ID=20,length=62435964,assembly=B36,md5=f126cdf8a6e0c7f379d618ff66beb2da,species="Homo sapiens",taxonomy=x>
+##phasing=partial
+##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
+##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency">
+##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele">
+##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129">
+##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership">
+##FILTER=<ID=PASS,Description="All filters passed">
+##FILTER=<ID=q10,Description="Quality below 10">
+##FILTER=<ID=s50,Description="Less than 50% of samples have data">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
+##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA00001	NA00002	NA00003
+20	14370	rs6054257	G	A	29	PASS	NS=3;DP=14;AF=0.5;DB;H2	GT:GQ:DP:HQ	0|0:48:1:51,51	1|0:48:8:51,51	1/1:43:5:.,.
+20	17330	.	T	A	3	q10	NS=3;DP=11;AF=0.017	GT:GQ:DP:HQ	0|0:49:3:58,50	0|1:3:5:65,3	0/0:41:3
+20	1110696	rs6040355	A	G,T	67	PASS	NS=2;DP=10;AF=0.333,0.667;AA=T;DB	GT:GQ:DP:HQ	1|2:21:6:23,27	2|1:2:0:18,2	2/2:35:4
+20	1230237	.	T	.	47	PASS	NS=3;DP=13;AA=T	GT:GQ:DP:HQ	0|0:54:7:56,60	0|0:48:4:51,51	0/0:61:2
+20	1234567	microsat1	GTC	G,GTCT	50	PASS	NS=3;DP=9;AA=G	GT:GQ:DP	0/1:35:4	0/2:17:2	1/1:40:3
diff --git a/tests/tabix_test.py b/tests/tabix_test.py
new file mode 100644
index 0000000..12ab4d2
--- /dev/null
+++ b/tests/tabix_test.py
@@ -0,0 +1,1245 @@
+#!/usr/bin/env python
+'''unit testing code for pysam.
+
+Execute in the :file:`tests` directory as it requires the Makefile
+and data files located there.
+'''
+
+import sys
+import os
+import shutil
+import gzip
+import pysam
+import unittest
+import glob
+import re
+from TestUtils import checkBinaryEqual, checkGZBinaryEqual, check_url, \
+    load_and_convert, make_data_files, TABIX_DATADIR, get_temp_filename
+
+IS_PYTHON3 = sys.version_info[0] >= 3
+
+
+def setUpModule():
+    make_data_files(TABIX_DATADIR)
+
+
+def myzip_open(infile, mode="r"):
+    '''open compressed file and decode.'''
+
+    def _convert(f):
+        for l in f:
+            yield l.decode("ascii")
+
+    if IS_PYTHON3:
+        if mode == "r":
+            return _convert(gzip.open(infile, "r"))
+    else:
+        return gzip.open(mode)
+
+
+def splitToBytes(s):
+    '''split string and return list of bytes.'''
+    return [x.encode("ascii") for x in s.split("\t")]
+
+
+class TestIndexing(unittest.TestCase):
+    filename = os.path.join(TABIX_DATADIR, "example.gtf.gz")
+    filename_idx = os.path.join(TABIX_DATADIR, "example.gtf.gz.tbi")
+
+    def setUp(self):
+
+        self.tmpfilename = get_temp_filename(suffix="gtf.gz")
+        shutil.copyfile(self.filename, self.tmpfilename)
+
+    def test_indexing_with_preset_works(self):
+        '''test indexing via preset.'''
+
+        pysam.tabix_index(self.tmpfilename, preset="gff")
+        self.assertTrue(checkGZBinaryEqual(
+            self.tmpfilename + ".tbi", self.filename_idx))
+
+    def test_indexing_to_custom_location_works(self):
+        '''test indexing a file with a non-default location.'''
+
+        index_path = get_temp_filename(suffix='custom.tbi')
+        pysam.tabix_index(self.tmpfilename, preset="gff",
+                          index=index_path, force=True)
+        self.assertTrue(checkGZBinaryEqual(index_path, self.filename_idx))
+        os.unlink(index_path)
+
+    def test_indexing_with_explict_columns_works(self):
+        '''test indexing via preset.'''
+
+        pysam.tabix_index(self.tmpfilename,
+                          seq_col=0,
+                          start_col=3,
+                          end_col=4,
+                          line_skip=0,
+                          zerobased=False)
+        self.assertTrue(checkGZBinaryEqual(
+            self.tmpfilename + ".tbi", self.filename_idx))
+
+    def test_indexing_with_lineskipping_works(self):
+        '''test indexing via preset and lineskip.'''
+        pysam.tabix_index(self.tmpfilename,
+                          seq_col=0,
+                          start_col=3,
+                          end_col=4,
+                          line_skip=1,
+                          zerobased=False)
+        self.assertFalse(checkGZBinaryEqual(
+            self.tmpfilename + ".tbi", self.filename_idx))
+
+    def tearDown(self):
+        os.unlink(self.tmpfilename)
+        if os.path.exists(self.tmpfilename + ".tbi"):
+            os.unlink(self.tmpfilename + ".tbi")
+
+
+class TestCompression(unittest.TestCase):
+    filename = os.path.join(TABIX_DATADIR, "example.gtf.gz")
+    filename_idx = os.path.join(TABIX_DATADIR, "example.gtf.gz.tbi")
+    preset = "gff"
+
+    def setUp(self):
+        self.tmpfilename = get_temp_filename(suffix="gtf")
+        with gzip.open(self.filename, "rb") as infile, \
+                open(self.tmpfilename, "wb") as outfile:
+            outfile.write(infile.read())
+
+    def testCompression(self):
+        '''see also issue 106'''
+        pysam.tabix_compress(self.tmpfilename, self.tmpfilename + ".gz")
+        checkBinaryEqual(self.tmpfilename, self.tmpfilename + ".gz")
+
+    def testIndexPresetUncompressed(self):
+        '''test indexing via preset.'''
+
+        pysam.tabix_index(self.tmpfilename, preset=self.preset)
+        # check if uncompressed file has been removed
+        self.assertEqual(os.path.exists(self.tmpfilename), False)
+        checkBinaryEqual(self.tmpfilename + ".gz", self.filename)
+        checkBinaryEqual(self.tmpfilename + ".gz.tbi", self.filename_idx)
+
+    def testIndexPresetCompressed(self):
+        '''test indexing via preset.'''
+
+        pysam.tabix_compress(self.tmpfilename, self.tmpfilename + ".gz")
+        pysam.tabix_index(self.tmpfilename + ".gz", preset=self.preset)
+        checkBinaryEqual(self.tmpfilename + ".gz", self.filename)
+        checkBinaryEqual(self.tmpfilename + ".gz.tbi", self.filename_idx)
+
+    def tearDown(self):
+        if os.path.exists(self.tmpfilename):
+            os.unlink(self.tmpfilename)
+        if os.path.exists(self.tmpfilename + ".gz"):
+            os.unlink(self.tmpfilename + ".gz")
+        if os.path.exists(self.tmpfilename + ".gz.tbi"):
+            os.unlink(self.tmpfilename + ".gz.tbi")
+
+
+class TestCompressionSam(TestCompression):
+    filename = os.path.join(TABIX_DATADIR, "example.sam.gz")
+    filename_index = os.path.join(TABIX_DATADIR, "example.sam.gz.tbi")
+    preset = "sam"
+
+
+class TestCompressionBed(TestCompression):
+    filename = os.path.join(TABIX_DATADIR, "example.bed.gz")
+    filename_index = os.path.join(TABIX_DATADIR, "example.bed.gz.tbi")
+    preset = "bed"
+
+
+class TestCompressionVCF(TestCompression):
+    filename = os.path.join(TABIX_DATADIR, "example.vcf.gz")
+    filename_index = os.path.join(TABIX_DATADIR, "example.vcf.gz.tbi")
+    preset = "vcf"
+
+
+class IterationTest(unittest.TestCase):
+
+    with_comments = False
+
+    def setUp(self):
+
+        lines = []
+        with gzip.open(self.filename, "rb") as inf:
+            for line in inf:
+                line = line.decode('ascii')
+                if line.startswith("#"):
+                    if not self.with_comments:
+                        continue
+                lines.append(line)
+
+        # creates index of contig, start, end, adds content without newline.
+        self.compare = [
+            (x[0][0], int(x[0][3]), int(x[0][4]), x[1])
+            for x in [(y.split("\t"), y[:-1]) for y in lines
+                      if not y.startswith("#")]]
+
+        self.comments = [x[:-1] for x in lines if x.startswith("#")]
+
+    def getSubset(self, contig=None, start=None, end=None):
+
+        if contig is None:
+            # all lines
+            subset = [x[3] for x in self.compare]
+        else:
+            if start is not None and end is None:
+                # until end of contig
+                subset = [x[3]
+                          for x in self.compare if x[0] == contig and
+                          x[2] > start]
+            elif start is None and end is not None:
+                # from start of contig
+                subset = [x[3]
+                          for x in self.compare if x[0] == contig and
+                          x[1] <= end]
+            elif start is None and end is None:
+                subset = [x[3] for x in self.compare if x[0] == contig]
+            else:
+                # all within interval
+                subset = [x[3] for x in self.compare if x[0] == contig and
+                          min(x[2], end) - max(x[1], start) > 0]
+
+        if self.with_comments:
+            subset.extend(self.comments)
+
+        return subset
+
+    def checkPairwise(self, result, ref):
+        '''check pairwise results.
+        '''
+        result.sort()
+        ref.sort()
+        a = set(result)
+        b = set(ref)
+
+        self.assertEqual(
+            len(result), len(ref),
+            "unexpected number of results: "
+            "result=%i, expected ref=%i, differences are %s: %s"
+            % (len(result), len(ref),
+               a.difference(b),
+               b.difference(a)))
+
+        for x, d in enumerate(list(zip(result, ref))):
+            self.assertEqual(
+                d[0], d[1],
+                "unexpected results in pair %i:\n'%s', expected\n'%s'" %
+                (x, d[0], d[1]))
+
+
+class TestGZFile(IterationTest):
+
+    filename = os.path.join(TABIX_DATADIR, "example.gtf.gz")
+    with_comments = True
+
+    def setUp(self):
+
+        IterationTest.setUp(self)
+        self.gzfile = pysam.GZIterator(self.filename)
+
+    def testAll(self):
+        result = list(self.gzfile)
+        ref = self.getSubset()
+        self.checkPairwise(result, ref)
+
+
+class TestIterationWithoutComments(IterationTest):
+
+    '''test iterating with TabixFile.fetch() when
+    there are no comments in the file.'''
+
+    filename = os.path.join(TABIX_DATADIR,
+                            "example.gtf.gz")
+
+    def setUp(self):
+        IterationTest.setUp(self)
+        self.tabix = pysam.TabixFile(self.filename)
+
+    def tearDown(self):
+        self.tabix.close()
+
+    def testRegionStrings(self):
+        """test if access with various region strings
+        works"""
+
+        self.assertEqual(218, len(list(
+            self.tabix.fetch("chr1"))))
+        self.assertEqual(218, len(list(
+            self.tabix.fetch("chr1", 1000))))
+        self.assertEqual(218, len(list(
+            self.tabix.fetch("chr1", end=1000000))))
+        self.assertEqual(218, len(list(
+            self.tabix.fetch("chr1", 1000, 1000000))))
+
+    def testAll(self):
+        result = list(self.tabix.fetch())
+        ref = self.getSubset()
+        self.checkPairwise(result, ref)
+
+    def testPerContig(self):
+        for contig in ("chr1", "chr2", "chr1", "chr2"):
+            result = list(self.tabix.fetch(contig))
+            ref = self.getSubset(contig)
+            self.checkPairwise(result, ref)
+
+    def testPerContigToEnd(self):
+
+        end = None
+        for contig in ("chr1", "chr2", "chr1", "chr2"):
+            for start in range(0, 200000, 1000):
+                result = list(self.tabix.fetch(contig, start, end))
+                ref = self.getSubset(contig, start, end)
+                self.checkPairwise(result, ref)
+
+    def testPerContigFromStart(self):
+
+        start = None
+        for contig in ("chr1", "chr2", "chr1", "chr2"):
+            for end in range(0, 200000, 1000):
+                result = list(self.tabix.fetch(contig, start, end))
+                ref = self.getSubset(contig, start, end)
+                self.checkPairwise(result, ref)
+
+    def testPerContig2(self):
+
+        start, end = None, None
+        for contig in ("chr1", "chr2", "chr1", "chr2"):
+            result = list(self.tabix.fetch(contig, start, end))
+            ref = self.getSubset(contig, start, end)
+            self.checkPairwise(result, ref)
+
+    def testPerInterval(self):
+
+        start, end = None, None
+        for contig in ("chr1", "chr2", "chr1", "chr2"):
+            for start in range(0, 200000, 2000):
+                for end in range(start, start + 2000, 500):
+                    result = list(self.tabix.fetch(contig, start, end))
+                    ref = self.getSubset(contig, start, end)
+                    self.checkPairwise(result, ref)
+
+    def testInvalidIntervals(self):
+
+        # invalid intervals (start > end)
+        self.assertRaises(ValueError, self.tabix.fetch, "chr1", 0, -10)
+        self.assertRaises(ValueError, self.tabix.fetch, "chr1", 200, 0)
+
+        # out of range intervals
+        self.assertRaises(ValueError, self.tabix.fetch, "chr1", -10, 200)
+        self.assertRaises(ValueError, self.tabix.fetch, "chr1", -10, -20)
+
+        # unknown chromosome
+        self.assertRaises(ValueError, self.tabix.fetch, "chrUn")
+
+        # out of range access
+        # to be implemented
+        # self.assertRaises(IndexError, self.tabix.fetch, "chr1", 1000000, 2000000)
+
+        # raise no error for empty intervals
+        self.tabix.fetch("chr1", 100, 100)
+
+    def testGetContigs(self):
+        self.assertEqual(sorted(self.tabix.contigs), ["chr1", "chr2"])
+        # check that contigs is read-only
+        self.assertRaises(
+            AttributeError, setattr, self.tabix, "contigs", ["chr1", "chr2"])
+
+    def testHeader(self):
+        ref = []
+        with gzip.open(self.filename) as inf:
+            for x in inf:
+                x = x.decode("ascii")
+                if not x.startswith("#"):
+                    break
+                ref.append(x[:-1])
+
+        header = list(self.tabix.header)
+        self.assertEqual(ref, header)
+
+    def testReopening(self):
+        '''test repeated opening of the same file.'''
+        def func1():
+            # opens any tabix file
+            with pysam.TabixFile(self.filename) as inf:
+                pass
+
+        for i in range(1000):
+            func1()
+
+
+class TestIterationWithComments(TestIterationWithoutComments):
+
+    '''test iterating with TabixFile.fetch() when
+    there are comments in the file.
+
+    Tests will create plenty of warnings on stderr.
+    '''
+
+    filename = os.path.join(TABIX_DATADIR, "example_comments.gtf.gz")
+
+    def setUp(self):
+        TestIterationWithoutComments.setUp(self)
+
+
+class TestIterators(unittest.TestCase):
+    filename = os.path.join(TABIX_DATADIR, "example.gtf.gz")
+
+    iterator = pysam.tabix_generic_iterator
+    parser = pysam.asTuple
+    is_compressed = False
+
+    def setUp(self):
+
+        self.tabix = pysam.TabixFile(self.filename)
+        self.compare = load_and_convert(self.filename)
+        self.tmpfilename_uncompressed = 'tmp_TestIterators'
+        with gzip.open(self.filename, "rb") as infile, \
+                open(self.tmpfilename_uncompressed, "wb") as outfile:
+            outfile.write(infile.read())
+
+    def tearDown(self):
+        self.tabix.close()
+        os.unlink(self.tmpfilename_uncompressed)
+
+    def open(self):
+
+        if self.is_compressed:
+            infile = gzip.open(self.filename)
+        else:
+            infile = open(self.tmpfilename_uncompressed)
+        return infile
+
+    def testIteration(self):
+
+        with self.open() as infile:
+            for x, r in enumerate(self.iterator(infile, self.parser())):
+                self.assertEqual(self.compare[x], list(r))
+                self.assertEqual(len(self.compare[x]), len(r))
+
+                # test indexing
+                for c in range(0, len(r)):
+                    self.assertEqual(self.compare[x][c], r[c])
+
+                # test slicing access
+                for c in range(0, len(r) - 1):
+                    for cc in range(c + 1, len(r)):
+                        self.assertEqual(self.compare[x][c:cc],
+                                         r[c:cc])
+
+    def testClosedFile(self):
+        '''test for error when iterating from closed file.'''
+        infile = self.open()
+        infile.close()
+
+        # iterating from a closed file should raise a value error
+        self.assertRaises(ValueError, self.iterator, infile, self.parser())
+
+    def testClosedFileIteration(self):
+        '''test for error when iterating from file that has been closed'''
+
+        infile = self.open()
+
+        i = self.iterator(infile, self.parser())
+        x = i.next()
+        infile.close()
+        # Not implemented
+        # self.assertRaises(ValueError, i.next)
+
+
+class TestIteratorsGenericCompressed(TestIterators):
+    is_compressed = True
+
+
+class TestIteratorsFileCompressed(TestIterators):
+    iterator = pysam.tabix_file_iterator
+    is_compressed = True
+
+
+class TestIteratorsFileUncompressed(TestIterators):
+    iterator = pysam.tabix_file_iterator
+    is_compressed = False
+
+
+class TestIterationMalformattedGTFFiles(unittest.TestCase):
+
+    '''test reading from malformatted gtf files.'''
+
+    iterator = pysam.tabix_generic_iterator
+    parser = pysam.asGTF
+
+    def testGTFTooManyFields(self):
+
+        with gzip.open(os.path.join(
+                TABIX_DATADIR,
+                "gtf_toomany_fields.gtf.gz")) as infile:
+            iterator = self.iterator(
+                infile,
+                parser=self.parser())
+            self.assertRaises(ValueError, iterator.next)
+
+    def testGTFTooFewFields(self):
+
+        with gzip.open(os.path.join(
+                TABIX_DATADIR,
+                "gtf_toofew_fields.gtf.gz")) as infile:
+            iterator = self.iterator(
+                infile,
+                parser=self.parser())
+            self.assertRaises(ValueError, iterator.next)
+
+
+class TestBed(unittest.TestCase):
+    filename = os.path.join(TABIX_DATADIR, "example.bed.gz")
+
+    def setUp(self):
+
+        self.tabix = pysam.TabixFile(self.filename)
+        self.compare = load_and_convert(self.filename)
+
+    def tearDown(self):
+        self.tabix.close()
+
+    def testRead(self):
+
+        for x, r in enumerate(self.tabix.fetch(parser=pysam.asBed())):
+            c = self.compare[x]
+            self.assertEqual(len(c), len(r))
+            self.assertEqual(c, str(r).split("\t"))
+            self.assertEqual(c[0], r.contig)
+            self.assertEqual(int(c[1]), r.start)
+            self.assertEqual(int(c[2]), r.end)
+            self.assertEqual(list(c), list(r))
+            self.assertEqual("\t".join(map(str, c)),
+                             str(r))
+
+    def testWrite(self):
+
+        for x, r in enumerate(self.tabix.fetch(parser=pysam.asBed())):
+            c = self.compare[x]
+            self.assertEqual(c, str(r).split("\t"))
+            self.assertEqual(list(c), list(r))
+
+            r.contig = "test"
+            self.assertEqual("test", r.contig)
+            self.assertEqual("test", r[0])
+
+            r.start += 1
+            self.assertEqual(int(c[1]) + 1, r.start)
+            self.assertEqual(str(int(c[1]) + 1), r[1])
+
+            r.end += 1
+            self.assertEqual(int(c[2]) + 1, r.end)
+            self.assertEqual(str(int(c[2]) + 1), r[2])
+
+
+class TestVCF(unittest.TestCase):
+
+    filename = os.path.join(TABIX_DATADIR, "example.vcf40")
+
+    def setUp(self):
+        self.tmpfilename = get_temp_filename(suffix="vcf")
+        shutil.copyfile(self.filename, self.tmpfilename)
+        pysam.tabix_index(self.tmpfilename, preset="vcf")
+
+    def tearDown(self):
+        os.unlink(self.tmpfilename + ".gz")
+        if os.path.exists(self.tmpfilename + ".gz.tbi"):
+            os.unlink(self.tmpfilename + ".gz.tbi")
+
+
+if IS_PYTHON3:
+    class TestUnicode(unittest.TestCase):
+
+        '''test reading from a file with non-ascii characters.'''
+
+        filename = os.path.join(TABIX_DATADIR, "example_unicode.vcf")
+
+        def setUp(self):
+            self.tmpfilename = get_temp_filename(suffix="vcf")
+            shutil.copyfile(self.filename, self.tmpfilename)
+            pysam.tabix_index(self.tmpfilename, preset="vcf")
+
+        def tearDown(self):
+            os.unlink(self.tmpfilename + ".gz")
+            if os.path.exists(self.tmpfilename + ".gz.tbi"):
+                os.unlink(self.tmpfilename + ".gz.tbi")
+
+        def testFromTabix(self):
+
+            # use ascii encoding - should raise error
+            with pysam.TabixFile(
+                    self.tmpfilename + ".gz", encoding="ascii") as t:
+                results = list(t.fetch(parser=pysam.asVCF()))
+                self.assertRaises(UnicodeDecodeError,
+                                  getattr, results[1], "id")
+
+            with pysam.TabixFile(
+                    self.tmpfilename + ".gz", encoding="utf-8") as t:
+                results = list(t.fetch(parser=pysam.asVCF()))
+                self.assertEqual(getattr(results[1], "id"), u"Rene\xe9")
+
+        def testFromVCF(self):
+            self.vcf = pysam.VCF()
+            self.assertRaises(
+                UnicodeDecodeError,
+                self.vcf.connect,
+                self.tmpfilename + ".gz",
+                "ascii")
+            self.vcf.connect(self.tmpfilename + ".gz", encoding="utf-8")
+            v = self.vcf.getsamples()[0]
+
+
+class TestVCFFromTabix(TestVCF):
+
+    columns = ("contig", "pos", "id",
+               "ref", "alt", "qual",
+               "filter", "info", "format")
+
+    def setUp(self):
+
+        TestVCF.setUp(self)
+
+        self.tabix = pysam.TabixFile(self.tmpfilename + ".gz")
+        self.compare = load_and_convert(self.filename)
+
+    def tearDown(self):
+        self.tabix.close()
+        TestVCF.tearDown(self)
+
+    def testRead(self):
+
+        ncolumns = len(self.columns)
+
+        for x, r in enumerate(self.tabix.fetch(parser=pysam.asVCF())):
+            c = self.compare[x]
+            for y, field in enumerate(self.columns):
+                # it is ok to have a missing format column
+                if y == 8 and y == len(c):
+                    continue
+                if field == "pos":
+                    self.assertEqual(int(c[y]) - 1, getattr(r, field))
+                    self.assertEqual(int(c[y]) - 1, r.pos)
+                else:
+                    self.assertEqual(c[y], getattr(r, field),
+                                     "mismatch in field %s: %s != %s" %
+                                     (field, c[y], getattr(r, field)))
+            if len(c) == 8:
+                self.assertEqual(0, len(r))
+            else:
+                self.assertEqual(len(c), len(r) + ncolumns)
+
+            for y in range(len(c) - ncolumns):
+                self.assertEqual(c[ncolumns + y], r[y])
+            self.assertEqual("\t".join(map(str, c)),
+                             str(r))
+
+    def testWrite(self):
+
+        ncolumns = len(self.columns)
+
+        for x, r in enumerate(self.tabix.fetch(parser=pysam.asVCF())):
+            c = self.compare[x]
+            # check unmodified string
+            cmp_string = str(r)
+            ref_string = "\t".join([x for x in c])
+
+            self.assertEqual(ref_string, cmp_string)
+
+            # set fields and compare field-wise
+            for y, field in enumerate(self.columns):
+                # it is ok to have a missing format column
+                if y == 8 and y == len(c):
+                    continue
+                if field == "pos":
+                    rpos = getattr(r, field)
+                    self.assertEqual(int(c[y]) - 1, rpos)
+                    self.assertEqual(int(c[y]) - 1, r.pos)
+                    # increment pos by 1
+                    setattr(r, field, rpos + 1)
+                    self.assertEqual(getattr(r, field), rpos + 1)
+                    c[y] = str(int(c[y]) + 1)
+                else:
+                    setattr(r, field, "test_%i" % y)
+                    c[y] = "test_%i" % y
+                    self.assertEqual(c[y], getattr(r, field),
+                                     "mismatch in field %s: %s != %s" %
+                                     (field, c[y], getattr(r, field)))
+
+            if len(c) == 8:
+                self.assertEqual(0, len(r))
+            else:
+                self.assertEqual(len(c), len(r) + ncolumns)
+
+            for y in range(len(c) - ncolumns):
+                c[ncolumns + y] = "test_%i" % y
+                r[y] = "test_%i" % y
+                self.assertEqual(c[ncolumns + y], r[y])
+
+
+class TestVCFFromVCF(TestVCF):
+
+    columns = ("chrom", "pos", "id",
+               "ref", "alt", "qual",
+               "filter", "info", "format")
+
+    # tests failing while parsing
+    fail_on_parsing = (
+        (5, "Flag fields should not have a value"),
+        (9, "aouao"),
+        (12, "Error BAD_NUMBER_OF_PARAMETERS"),
+        (13, "aoeu"),
+        (18, "Error BAD_NUMBER_OF_PARAMETERS"),
+        (24, "Error HEADING_NOT_SEPARATED_BY_TABS"))
+
+    # tests failing on opening
+    fail_on_opening = ((24, "Error HEADING_NOT_SEPARATED_BY_TABS"),
+                       )
+
+    fail_on_samples = []
+
+    check_samples = False
+    coordinate_offset = 1
+
+    # value returned for missing values
+    missing_value = "."
+    missing_quality = -1
+
+    def setUp(self):
+
+        TestVCF.setUp(self)
+
+        self.vcf = pysam.VCF()
+        self.compare = load_and_convert(self.filename, encode=False)
+
+    def tearDown(self):
+        TestVCF.tearDown(self)
+        self.vcf.close()
+
+    def open_vcf(self, fn):
+        return self.vcf.connect(fn)
+
+    def get_failure_stage(self):
+
+        fn = os.path.basename(self.filename)
+        for x, msg in self.fail_on_opening:
+            if "{}.vcf".format(x) == fn:
+                return "opening"
+
+        for x, msg in self.fail_on_parsing:
+            if "{}.vcf".format(x) == fn:
+                return "parsing"
+
+        for x, msg in self.fail_on_samples:
+            if "{}.vcf".format(x) == fn:
+                return "samples"
+
+        return None
+
+    def testConnecting(self):
+
+        if self.get_failure_stage() == "opening":
+            self.assertRaises(ValueError,
+                              self.open_vcf,
+                              self.tmpfilename + ".gz")
+        else:
+            self.open_vcf(self.tmpfilename + ".gz")
+
+    def get_iterator(self):
+
+        with open(self.filename) as f:
+            fn = os.path.basename(self.filename)
+            return list(self.vcf.parse(f))
+
+    def get_field_value(self, record, field):
+        return record[field]
+
+    def sample2value(self, r, v):
+        return r, v
+
+    def alt2value(self, r, v):
+        if r == ".":
+            return [], v
+        else:
+            return r.split(","), list(v)
+
+    def filter2value(self, r, v):
+        if r == "PASS":
+            return [], v
+        elif r == ".":
+            return [], v
+        else:
+            return r.split(";"), v
+
+    def testParsing(self):
+
+        if self.get_failure_stage() in ("opening", "parsing"):
+            return
+
+        itr = self.get_iterator()
+        if itr is None:
+            return
+
+        fn = os.path.basename(self.filename)
+
+        check_samples = self.check_samples
+        for vcf_code, msg in self.fail_on_samples:
+            if "%i.vcf" % vcf_code == fn:
+                check_samples = False
+
+        for x, r in enumerate(itr):
+            c = self.compare[x]
+            for y, field in enumerate(self.columns):
+                # it is ok to have a missing format column
+                if y == 8 and y == len(c):
+                    continue
+
+                val = self.get_field_value(r, field)
+                if field == "pos":
+                    self.assertEqual(int(c[y]) - self.coordinate_offset,
+                                     val)
+                elif field == "alt" or field == "alts":
+                    cc, vv = self.alt2value(c[y], val)
+                    if cc != vv:
+                        # import pdb; pdb.set_trace()
+                        pass
+                    self.assertEqual(
+                        cc, vv,
+                        "mismatch in field %s: expected %s, got %s" %
+                        (field, cc, vv))
+
+                elif field == "filter":
+                    cc, vv = self.filter2value(c[y], val)
+                    self.assertEqual(
+                        cc, vv,
+                        "mismatch in field %s: expected %s, got %s" %
+                        (field, cc, vv))
+
+                elif field == "info":
+                    # tests for info field not implemented
+                    pass
+
+                elif field == "qual" and c[y] == ".":
+                    self.assertEqual(
+                        self.missing_quality, val,
+                        "mismatch in field %s: expected %s, got %s" %
+                        (field, c[y], val))
+
+                elif field == "format":
+                    # format field converted to list
+                    self.assertEqual(
+                        c[y].split(":"), list(val),
+                        "mismatch in field %s: expected %s, got %s" %
+                        (field, c[y], val))
+
+                elif type(val) in (int, float):
+                    if c[y] == ".":
+                        self.assertEqual(
+                            None, val,
+                            "mismatch in field %s: expected %s, got %s" %
+                            (field, c[y], val))
+                    else:
+                        self.assertAlmostEqual(
+                            float(c[y]), float(val), 2,
+                            "mismatch in field %s: expected %s, got %s" %
+                            (field, c[y], val))
+                else:
+                    if c[y] == ".":
+                        ref_val = self.missing_value
+                    else:
+                        ref_val = c[y]
+                    self.assertEqual(
+                        ref_val, val,
+                        "mismatch in field %s: expected %s(%s), got %s(%s)" %
+                        (field, ref_val, type(ref_val), val, type(val)))
+            # parse samples
+            if check_samples:
+                if len(c) == 8:
+                    for x, s in enumerate(r.samples):
+                        self.assertEqual(
+                            [], r.samples[s].values(),
+                            "mismatch in sample {}: "
+                            "expected [], got {}, src={}, line={}".format(
+                                s, r.samples[s].values(),
+                                r.samples[s].items(), r))
+                else:
+                    for x, s in enumerate(r.samples):
+                        ref, comp = self.sample2value(
+                            c[9 + x],
+                            r.samples[s])
+                        self.compare_samples(ref, comp, s, r)
+
+    def compare_samples(self, ref, comp, s, r):
+
+        if ref != comp:
+
+            # check if GT not at start, not VCF conform and
+            # not supported by cbcf.pyx
+            k = r.format.keys()
+            if "GT" in k and k[0] != "GT":
+                return
+
+            # perform an element-wise checto work around rounding differences
+            for a, b in zip(re.split("[:,;]", ref),
+                            re.split("[:,;]", comp)):
+                is_float = True
+                try:
+                    a = float(a)
+                    b = float(b)
+                except ValueError:
+                    is_float = False
+
+                if is_float:
+                    self.assertAlmostEqual(
+                        a, b, 2,
+                        "mismatch in sample {}: "
+                        "expected {}, got {}, src={}, line={}"
+                        .format(
+                            s, ref, comp,
+                            r.samples[s].items(), r))
+                else:
+                    self.assertEqual(
+                        a, b,
+                        "mismatch in sample {}: "
+                        "expected {}, got {}, src={}, line={}"
+                        .format(
+                            s, ref, comp,
+                            r.samples[s].items(), r))
+
+
+############################################################################
+# create a test class for each example vcf file.
+# Two samples are created -
+# 1. Testing pysam/tabix access
+# 2. Testing the VCF class
+vcf_files = glob.glob(os.path.join(TABIX_DATADIR, "vcf", "*.vcf"))
+
+for vcf_file in vcf_files:
+    n = "VCFFromTabixTest_%s" % os.path.basename(vcf_file[:-4])
+    globals()[n] = type(n, (TestVCFFromTabix,), dict(filename=vcf_file,))
+    n = "VCFFromVCFTest_%s" % os.path.basename(vcf_file[:-4])
+    globals()[n] = type(n, (TestVCFFromVCF,), dict(filename=vcf_file,))
+
+
+class TestVCFFromVariantFile(TestVCFFromVCF):
+
+    columns = ("chrom", "pos", "id",
+               "ref", "alts", "qual",
+               "filter", "info", "format")
+
+    fail_on_parsing = [
+        (24, 'Could not parse the "#CHROM.." line'),
+        ("issue85", "empty VCF"),
+    ]
+    fail_on_opening = [
+        (24, 'Could not parse the "#CHROM.." line'),
+        ("issue85", "empty VCF"),
+    ]
+    coordinate_offset = 0
+    check_samples = True
+    fail_on_samples = [
+        (9, "PL field not defined. Expected to be scalar, but is array"),
+        (12, "PL field not defined. Expected to be scalar, but is array"),
+        (18, "PL field not defined. Expected to be scalar, but is array"),
+    ]
+
+    # value returned for missing values
+    missing_value = None
+    missing_quality = None
+
+    vcf = None
+
+    def filter2value(self, r, v):
+        if r == "PASS":
+            return ["PASS"], list(v)
+        elif r == ".":
+            return [], list(v)
+        else:
+            return r.split(";"), list(v)
+
+    def alt2value(self, r, v):
+        if r == ".":
+            return None, v
+        else:
+            return r.split(","), list(v)
+
+    def sample2value(self, r, smp):
+
+        def convert_field(f):
+            if f is None:
+                return "."
+            elif isinstance(f, tuple):
+                return ",".join(map(convert_field, f))
+            else:
+                return str(f)
+
+        v = smp.values()
+
+        if 'GT' in smp:
+            alleles = [
+                str(a) if a is not None else '.' for a in smp.allele_indices]
+            v[0] = '/|'[smp.phased].join(alleles)
+
+        comp = ":".join(map(convert_field, v))
+
+        if comp.endswith(":."):
+            comp = comp[:-2]
+
+        return r, comp
+
+    def setUp(self):
+        TestVCF.setUp(self)
+        self.compare = load_and_convert(self.filename, encode=False)
+
+    def tearDown(self):
+        if self.vcf:
+            self.vcf.close()
+        self.vcf = None
+        TestVCF.tearDown(self)
+
+    def get_iterator(self):
+        self.vcf = pysam.VariantFile(self.filename)
+        return self.vcf.fetch()
+
+    def get_field_value(self, record, field):
+        return getattr(record, field)
+
+    def open_vcf(self, fn):
+        with pysam.VariantFile(fn) as inf:
+            pass
+
+
+for vcf_file in vcf_files:
+    p = os.path.basename(vcf_file[:-4])
+    n = "TestVCFFromVariantFile_%s" % p
+    globals()[n] = type(n, (TestVCFFromVariantFile,), dict(filename=vcf_file,))
+
+
+class TestRemoteFileHTTP(unittest.TestCase):
+
+    url = "http://genserv.anat.ox.ac.uk/downloads/pysam/test/example.gtf.gz"
+    region = "chr1:1-1000"
+    local = os.path.join(TABIX_DATADIR, "example.gtf.gz")
+
+    def setUp(self):
+        if not getattr(pysam.config, "HAVE_LIBCURL", 0) or not check_url(self.url):
+            self.remote_file = None
+        else:
+            self.remote_file = pysam.TabixFile(self.url, "r")
+
+        self.local_file = pysam.TabixFile(self.local, "r")
+
+    def tearDown(self):
+        if self.remote_file is None:
+            return
+
+        self.remote_file.close()
+        self.local_file.close()
+
+    def testFetchAll(self):
+        if self.remote_file is None:
+            return
+
+        remote_result = list(self.remote_file.fetch())
+        local_result = list(self.local_file.fetch())
+
+        self.assertEqual(len(remote_result), len(local_result))
+        for x, y in zip(remote_result, local_result):
+            self.assertEqual(x, y)
+
+    def testHeader(self):
+        if self.remote_file is None:
+            return
+
+        self.assertEqual(list(self.local_file.header), [])
+
+
+class TestRemoteFileHTTPWithHeader(TestRemoteFileHTTP):
+
+    url = "http://genserv.anat.ox.ac.uk/downloads/pysam/test/example_comments.gtf.gz"
+    region = "chr1:1-1000"
+    local = os.path.join(TABIX_DATADIR, "example_comments.gtf.gz")
+
+    def setUp(self):
+        if not getattr(pysam.config, "HAVE_LIBCURL", 0) or not check_url(self.url):
+            self.remote_file = None
+        else:
+            self.remote_file = pysam.TabixFile(self.url, "r")
+        self.local_file = pysam.TabixFile(self.local, "r")
+
+    def testHeader(self):
+        if self.remote_file is None:
+            return
+
+        self.assertEqual(list(self.local_file.header), ["# comment at start"])
+        self.assertEqual(list(self.local_file.header), self.remote_file.header)
+
+
+class TestIndexArgument(unittest.TestCase):
+
+    filename_src = os.path.join(TABIX_DATADIR, "example.vcf.gz")
+    filename_dst = "tmp_example.vcf.gz"
+    index_src = os.path.join(TABIX_DATADIR, "example.vcf.gz.tbi")
+    index_dst = "tmp_index_example.vcf.gz.tbi"
+    index_dst_dat = "tmp_index_example.vcf.gz.tbi.dat"
+    preset = "vcf"
+
+    def testFetchAll(self):
+        shutil.copyfile(self.filename_src, self.filename_dst)
+        shutil.copyfile(self.index_src, self.index_dst)
+
+        with pysam.TabixFile(
+                self.filename_src, "r", index=self.index_src) as same_basename_file:
+            same_basename_results = list(same_basename_file.fetch())
+
+        with pysam.TabixFile(
+                self.filename_dst, "r", index=self.index_dst) as diff_index_file:
+            diff_index_result = list(diff_index_file.fetch())
+
+        self.assertEqual(len(same_basename_results), len(diff_index_result))
+        for x, y in zip(same_basename_results, diff_index_result):
+            self.assertEqual(x, y)
+
+        os.unlink(self.filename_dst)
+        os.unlink(self.index_dst)
+
+    def testLoadIndexWithoutTbiExtension(self):
+        shutil.copyfile(self.filename_src, self.filename_dst)
+        shutil.copyfile(self.index_src, self.index_dst_dat)
+
+        with pysam.TabixFile(
+                self.filename_src, "r", index=self.index_src) as same_basename_file:
+            same_basename_results = list(same_basename_file.fetch())
+
+        with pysam.TabixFile(
+            self.filename_dst, "r", index=self.index_dst_dat) as diff_index_file:
+            diff_index_result = list(diff_index_file.fetch())
+
+        self.assertEqual(len(same_basename_results), len(diff_index_result))
+        for x, y in zip(same_basename_results, diff_index_result):
+            self.assertEqual(x, y)
+
+        os.unlink(self.filename_dst)
+        os.unlink(self.index_dst_dat)
+
+
+def _TestMultipleIteratorsHelper(filename, multiple_iterators):
+    '''open file within scope, return iterator.'''
+
+    tabix = pysam.TabixFile(filename)
+    iterator = tabix.fetch(parser=pysam.asGTF(),
+                           multiple_iterators=multiple_iterators)
+    tabix.close()
+    return iterator
+
+
+class TestBackwardsCompatibility(unittest.TestCase):
+    """check if error is raised if a tabix file from an
+    old version is accessed from pysam"""
+
+    def check(self, filename, raises=None):
+        with pysam.TabixFile(filename) as tf:
+            ref = load_and_convert(filename)
+            if raises is None:
+                self.assertEqual(len(list(tf.fetch())), len(ref))
+            else:
+                self.assertRaises(raises, tf.fetch)
+
+    def testVCF0v23(self):
+        self.check(os.path.join(TABIX_DATADIR, "example_0v23.vcf.gz"),
+                   ValueError)
+
+    def testBED0v23(self):
+        self.check(os.path.join(TABIX_DATADIR, "example_0v23.bed.gz"),
+                   ValueError)
+
+    def testVCF0v26(self):
+        self.check(os.path.join(TABIX_DATADIR, "example_0v26.vcf.gz"),
+                   ValueError)
+
+    def testBED0v26(self):
+        self.check(os.path.join(TABIX_DATADIR, "example_0v26.bed.gz"),
+                   ValueError)
+
+    def testVCF(self):
+        self.check(os.path.join(TABIX_DATADIR, "example.vcf.gz"))
+
+    def testBED(self):
+        self.check(os.path.join(TABIX_DATADIR, "example.bed.gz"))
+
+    def testEmpty(self):
+        self.check(os.path.join(TABIX_DATADIR, "empty.bed.gz"))
+
+
+class TestMultipleIterators(unittest.TestCase):
+
+    filename = os.path.join(TABIX_DATADIR, "example.gtf.gz")
+
+    def testJoinedIterators(self):
+
+        # two iterators working on the same file
+        with pysam.TabixFile(self.filename) as tabix:
+            a = tabix.fetch(parser=pysam.asGTF()).next()
+            b = tabix.fetch(parser=pysam.asGTF()).next()
+            # the first two lines differ only by the feature field
+            self.assertEqual(a.feature, "UTR")
+            self.assertEqual(b.feature, "exon")
+            self.assertEqual(re.sub("UTR", "", str(a)),
+                             re.sub("exon", "", str(b)))
+
+    def testDisjointIterators(self):
+        # two iterators working on the same file
+        with pysam.TabixFile(self.filename) as tabix:
+            a = tabix.fetch(parser=pysam.asGTF(),
+                            multiple_iterators=True).next()
+            b = tabix.fetch(parser=pysam.asGTF(),
+                            multiple_iterators=True).next()
+            # both iterators are at top of file
+            self.assertEqual(str(a), str(b))
+
+    def testScope(self):
+        # technically it does not really test if the scope is correct
+        i = _TestMultipleIteratorsHelper(self.filename,
+                                         multiple_iterators=True)
+        self.assertTrue(i.next())
+        i = _TestMultipleIteratorsHelper(self.filename,
+                                         multiple_iterators=False)
+        self.assertRaises(IOError, i.next)
+
+    def testDoubleFetch(self):
+
+        with pysam.TabixFile(self.filename) as f:
+
+            for a, b in zip(f.fetch(multiple_iterators=True),
+                            f.fetch(multiple_iterators=True)):
+                self.assertEqual(str(a), str(b))
+
+
+class TestContextManager(unittest.TestCase):
+
+    filename = os.path.join(TABIX_DATADIR, "example.gtf.gz")
+
+    def testManager(self):
+
+        with pysam.TabixFile(self.filename) as tabixfile:
+            tabixfile.fetch()
+        self.assertEqual(tabixfile.closed, True)
+
+
+class TestMultithreadTabixFile(unittest.TestCase):
+
+    filename = os.path.join(TABIX_DATADIR, "example.gtf.gz")
+
+    def testMultithreadEqualsSinglethread(self):
+        with pysam.TabixFile(self.filename) as tabixfile:
+            single = [r for r in tabixfile.fetch()]
+        with pysam.TabixFile(self.filename, threads=2) as tabixfile:
+            multi = [r for r in tabixfile.fetch()]
+        for r1, r2 in zip(single, multi):
+            assert str(r1) == str(r2)
+
+
+if __name__ == "__main__":
+    unittest.main()
diff --git a/tests/tabixproxies_test.py b/tests/tabixproxies_test.py
new file mode 100644
index 0000000..09cb210
--- /dev/null
+++ b/tests/tabixproxies_test.py
@@ -0,0 +1,398 @@
+import unittest
+import pysam
+import os
+import re
+import copy
+import gzip
+from TestUtils import load_and_convert, make_data_files, TABIX_DATADIR, IS_PYTHON3
+
+
+def setUpModule():
+    make_data_files(TABIX_DATADIR)
+
+
+@unittest.skipUnless(IS_PYTHON3, "Requires Python 3 Extended Iterable Unpacking")
+class TestBED(unittest.TestCase):
+
+    filename = os.path.join(TABIX_DATADIR, "fivecolumns.bed.gz")
+
+    def setUp(self):
+        self.tabix = pysam.TabixFile(self.filename)
+
+    def tearDown(self):
+        self.tabix.close()
+
+    def testAssignmentToTargetList(self):
+        # TODO When we drop Python 2, remove exec() & my and simplify these
+        my = {}
+        for row in self.tabix.fetch(parser=pysam.asTuple()):
+            my['row'] = row
+
+            # Test that *others gets the right columns...
+            exec('contig, start, end, *others = row', globals(), my)
+            self.assertEqual(3 + len(my['others']), len(row))
+
+            # ...and that a TupleProxy can be assigned from more than once
+            exec('contig, *others = row', globals(), my)
+            self.assertEqual(1 + len(my['others']), len(row))
+
+
+class TestParser(unittest.TestCase):
+
+    filename = os.path.join(TABIX_DATADIR, "example.gtf.gz")
+
+    def setUp(self):
+
+        self.tabix = pysam.TabixFile(self.filename)
+        self.compare = load_and_convert(self.filename)
+
+    def tearDown(self):
+        self.tabix.close()
+
+    def testRead(self):
+
+        for x, r in enumerate(self.tabix.fetch(parser=pysam.asTuple())):
+            c = self.compare[x]
+            self.assertEqual(c, list(r))
+            self.assertEqual(len(c), len(r))
+
+            # test indexing
+            for y in range(0, len(r)):
+                self.assertEqual(c[y], r[y])
+
+            # test slicing access
+            for y in range(0, len(r) - 1):
+                for cc in range(y + 1, len(r)):
+                    self.assertEqual(c[y:cc],
+                                     r[y:cc])
+            self.assertEqual("\t".join(map(str, c)),
+                             str(r))
+
+    @unittest.skipUnless(IS_PYTHON3, "Requires Python 3 Extended Iterable Unpacking")
+    def testAssignmentToTargetList(self):
+        for x, r in enumerate(self.tabix.fetch(parser=pysam.asTuple())):
+            my = { 'r': r }
+            exec('col1, col2, *others, colN = r', globals(), my)
+            self.assertEqual(2 + len(my['others']) + 1, len(r))
+
+    def testWrite(self):
+
+        for x, r in enumerate(self.tabix.fetch(parser=pysam.asTuple())):
+            self.assertEqual(self.compare[x], list(r))
+            c = list(r)
+            for y in range(len(r)):
+                r[y] = "test_%05i" % y
+                c[y] = "test_%05i" % y
+            self.assertEqual([x for x in c], list(r))
+            self.assertEqual("\t".join(c), str(r))
+            # check second assignment
+            for y in range(len(r)):
+                r[y] = "test_%05i" % y
+            self.assertEqual([x for x in c], list(r))
+            self.assertEqual("\t".join(c), str(r))
+
+    def testUnset(self):
+        for x, r in enumerate(self.tabix.fetch(parser=pysam.asTuple())):
+            self.assertEqual(self.compare[x], list(r))
+            c = list(r)
+            e = list(r)
+            for y in range(len(r)):
+                r[y] = None
+                c[y] = None
+                e[y] = ""
+                self.assertEqual(c, list(r))
+                self.assertEqual("\t".join(e), str(r))
+
+    def testIteratorCompressed(self):
+        '''test iteration from compressed file.'''
+        with gzip.open(self.filename) as infile:
+            for x, r in enumerate(pysam.tabix_iterator(
+                    infile, pysam.asTuple())):
+                self.assertEqual(self.compare[x], list(r))
+                self.assertEqual(len(self.compare[x]), len(r))
+
+                # test indexing
+                for c in range(0, len(r)):
+                    self.assertEqual(self.compare[x][c], r[c])
+
+                # test slicing access
+                for c in range(0, len(r) - 1):
+                    for cc in range(c + 1, len(r)):
+                        self.assertEqual(self.compare[x][c:cc],
+                                         r[c:cc])
+
+    def testIteratorUncompressed(self):
+        '''test iteration from uncompressed file.'''
+        tmpfilename = 'tmp_testIteratorUncompressed'
+        with gzip.open(self.filename, "rb") as infile, \
+                open(tmpfilename, "wb") as outfile:
+            outfile.write(infile.read())
+
+        with open(tmpfilename) as infile:
+            for x, r in enumerate(pysam.tabix_iterator(
+                    infile, pysam.asTuple())):
+                self.assertEqual(self.compare[x], list(r))
+                self.assertEqual(len(self.compare[x]), len(r))
+
+                # test indexing
+                for c in range(0, len(r)):
+                    self.assertEqual(self.compare[x][c], r[c])
+
+                # test slicing access
+                for c in range(0, len(r) - 1):
+                    for cc in range(c + 1, len(r)):
+                        self.assertEqual(self.compare[x][c:cc],
+                                         r[c:cc])
+
+        os.unlink(tmpfilename)
+
+    def testCopy(self):
+        a = self.tabix.fetch(parser=pysam.asTuple()).next()
+        b = copy.copy(a)
+        self.assertEqual(a, b)
+
+        a = self.tabix.fetch(parser=pysam.asGTF()).next()
+        b = copy.copy(a)
+        self.assertEqual(a, b)
+
+
+class TestGTF(TestParser):
+
+    parser = pysam.asGTF
+
+    def build_attribute_string(self, d):
+        """build attribute string from dictionary d"""
+        s = "; ".join(["{} \"{}\"".format(x, y) for (x, y) in d.items()]) + ";"
+        # remove quotes around numeric values
+        s = re.sub(r'"(\d+)"', r'\1', s)
+        return s
+
+    def testRead(self):
+
+        for x, r in enumerate(self.tabix.fetch(parser=self.parser())):
+            c = self.compare[x]
+            self.assertEqual(len(c), len(r))
+            self.assertEqual(list(c), list(r))
+            self.assertEqual(c, str(r).split("\t"))
+            self.assertTrue(r.gene_id.startswith("ENSG"))
+            if r.feature != 'gene':
+                self.assertTrue(r.transcript_id.startswith("ENST"))
+            self.assertEqual(c[0], r.contig)
+            self.assertEqual("\t".join(map(str, c)),
+                             str(r))
+
+    def test_setting_fields(self):
+
+        r = self.tabix.fetch(parser=self.parser()).next()
+
+        r.contig = r.contig + "_test_contig"
+        r.source = r.source + "_test_source"
+        r.feature = r.feature + "_test_feature"
+        r.start += 10
+        r.end += 10
+        r.score = 20
+        r.strand = "+"
+        r.frame = 0
+        r.attributes = 'gene_id "0001";'
+        r.transcript_id = "0002"
+        sr = str(r)
+        self.assertTrue("_test_contig" in sr)
+        self.assertTrue("_test_source" in sr)
+        self.assertTrue("_test_feature" in sr)
+        self.assertTrue("gene_id \"0001\"" in sr)
+        self.assertTrue("transcript_id \"0002\"" in sr)
+
+    def test_setAttribute_makes_changes(self):
+
+        r = self.tabix.fetch(parser=self.parser()).next()
+        r.setAttribute("transcript_id", "abcd")
+        sr = str(r)
+        self.assertEqual(r.transcript_id, "abcd")
+        self.assertTrue("transcript_id \"abcd\"" in sr)
+
+    def test_added_attribute_is_output(self):
+        r = self.tabix.fetch(parser=self.parser()).next()
+
+        r.new_int_attribute = 12
+        self.assertTrue("new_int_attribute 12" in str(r).split("\t")[8])
+
+        r.new_float_attribute = 12.0
+        self.assertTrue("new_float_attribute 12.0" in str(r).split("\t")[8])
+
+        r.new_text_attribute = "abc"
+        self.assertTrue("new_text_attribute \"abc\"" in str(r).split("\t")[8])
+
+    def test_setting_start_is_one_based(self):
+
+        r = self.tabix.fetch(parser=self.parser()).next()
+        r.start = 1800
+        self.assertEqual(r.start, 1800)
+        self.assertEqual(str(r).split("\t")[3], "1801")
+
+    def test_setting_end_is_one_based(self):
+
+        r = self.tabix.fetch(parser=self.parser()).next()
+        r.end = 2100
+        self.assertEqual(r.end, 2100)
+        self.assertEqual(str(r).split("\t")[4], "2100")
+
+    def test_setting_frame_to_none_produces_dot(self):
+
+        r = self.tabix.fetch(parser=self.parser()).next()
+        r.frame = None
+        self.assertEqual(str(r).split("\t")[7], ".")
+
+        r.frame = 2
+        self.assertEqual(str(r).split("\t")[7], "2")
+
+        r = self.tabix.fetch(parser=self.parser()).next()
+        r.frame = "."
+        self.assertEqual(r.frame, None)
+        self.assertEqual(str(r).split("\t")[7], ".")
+
+    def test_setting_source_to_none_produces_dot(self):
+
+        r = self.tabix.fetch(parser=self.parser()).next()
+        r.source = None
+        self.assertEqual(str(r).split("\t")[1], ".")
+
+        r.source = "source"
+        self.assertEqual(str(r).split("\t")[1], "source")
+
+        r = self.tabix.fetch(parser=self.parser()).next()
+        r.source = "."
+        self.assertEqual(r.source, None)
+        self.assertEqual(str(r).split("\t")[1], ".")
+
+    def test_setting_feature_to_none_produces_dot(self):
+
+        r = self.tabix.fetch(parser=self.parser()).next()
+        r.feature = None
+        self.assertEqual(str(r).split("\t")[2], ".")
+
+        r.feature = "feature"
+        self.assertEqual(str(r).split("\t")[2], "feature")
+
+        r = self.tabix.fetch(parser=self.parser()).next()
+        r.feature = "."
+        self.assertEqual(r.feature, None)
+        self.assertEqual(str(r).split("\t")[2], ".")
+
+    def test_setting_strand_to_none_produces_dot(self):
+
+        r = self.tabix.fetch(parser=self.parser()).next()
+        r.strand = None
+        self.assertEqual(str(r).split("\t")[6], ".")
+
+        r.strand = "-"
+        self.assertEqual(str(r).split("\t")[6], "-")
+
+        r = self.tabix.fetch(parser=self.parser()).next()
+        r.strand = "."
+        self.assertEqual(r.strand, None)
+        self.assertEqual(str(r).split("\t")[6], ".")
+
+    def test_setting_score_to_none_produces_dot(self):
+
+        r = self.tabix.fetch(parser=self.parser()).next()
+        r.score = None
+        self.assertEqual(str(r).split("\t")[5], ".")
+
+        r.score = 12.0
+        self.assertEqual(str(r).split("\t")[5], "12.0")
+
+        r.score = -12.0
+        self.assertEqual(str(r).split("\t")[5], "-12.0")
+
+        r = self.tabix.fetch(parser=self.parser()).next()
+        r.score = "."
+        self.assertEqual(r.score, None)
+        self.assertEqual(str(r).split("\t")[5], ".")
+
+        r.score = 12
+        self.assertEqual(str(r).split("\t")[5], "12")
+
+        r.score = -12
+        self.assertEqual(str(r).split("\t")[5], "-12")
+
+    def test_asdict_contains_attributes(self):
+        r = self.tabix.fetch(parser=self.parser()).next()
+        d = r.to_dict()
+        c = self.compare[0]
+        s = self.build_attribute_string(d)
+        self.assertEqual(s, c[8])
+
+    def test_asdict_can_be_modified(self):
+        r = self.tabix.fetch(parser=self.parser()).next()
+        d = r.to_dict()
+        d["gene_id"] = "new_gene_id"
+        self.assertTrue("gene_id \"new_gene_id\"", str(r))
+
+
+class TestGFF3(TestGTF):
+
+    parser = pysam.asGFF3
+    filename = os.path.join(TABIX_DATADIR, "example.gff3.gz")
+
+    def build_attribute_string(self, d):
+        """build attribute string from dictionary d"""
+        s = ";".join(["{}={}".format(x, y) for (x, y) in d.items()]) + ";"
+        return s
+
+    def build_attribute_string(self, d):
+        """build attribute string from dictionary d"""
+        s = ";".join(["{}={}".format(x, y) for (x, y) in d.items()]) + ";"
+        return s
+
+    def testRead(self):
+        for x, r in enumerate(self.tabix.fetch(parser=self.parser())):
+            c = self.compare[x]
+            self.assertEqual(len(c), len(r))
+            self.assertEqual(list(c), list(r))
+            self.assertEqual(c, str(r).split("\t"))
+            self.assertEqual(c[0], r.contig)
+            self.assertEqual("\t".join(map(str, c)),
+                             str(r))
+            self.assertTrue(r.ID.startswith("MI00"))
+
+    def test_setting_fields(self):
+
+        for r in self.tabix.fetch(parser=self.parser()):
+            r.contig = r.contig + "_test_contig"
+            r.source = "test_source"
+            r.feature = "test_feature"
+            r.start += 10
+            r.end += 10
+            r.score = 20
+            r.strand = "+"
+            r.frame = 0
+            r.ID = "test"
+            sr = str(r)
+            self.assertTrue("test_contig" in sr)
+            self.assertTrue("test_source" in sr)
+            self.assertTrue("test_feature" in sr)
+            self.assertTrue("ID=test" in sr)
+
+    def test_setAttribute_makes_changes(self):
+
+        r = self.tabix.fetch(parser=self.parser()).next()
+        r.setAttribute("transcript_id", "abcd")
+        sr = str(r)
+        self.assertEqual(r.transcript_id, "abcd")
+        self.assertTrue("transcript_id=abcd" in sr)
+
+    def test_added_attribute_is_output(self):
+        r = self.tabix.fetch(parser=self.parser()).next()
+
+        r.new_int_attribute = 12
+        self.assertTrue("new_int_attribute=12" in str(r).split("\t")[8])
+
+        r.new_float_attribute = 12.0
+        self.assertTrue("new_float_attribute=12.0" in str(r).split("\t")[8])
+
+        r.new_text_attribute = "abc"
+        self.assertTrue("new_text_attribute=abc" in str(r).split("\t")[8])
+
+
+if __name__ == "__main__":
+    unittest.main()
diff --git a/tests/test_samtools_python.py b/tests/test_samtools_python.py
new file mode 100644
index 0000000..3a9d841
--- /dev/null
+++ b/tests/test_samtools_python.py
@@ -0,0 +1,50 @@
+import pysam
+import os
+from TestUtils import make_data_files, BAM_DATADIR
+
+
+def setUpModule():
+    make_data_files(BAM_DATADIR)
+
+
+def test_idxstats_parse_split_lines():
+    bam_filename = os.path.join(BAM_DATADIR, "ex2.bam")
+    # Test pysam 0.8.X style output, which returns a list of lines
+    lines = pysam.idxstats(bam_filename, split_lines=True)
+    for line in lines:
+        _seqname, _seqlen, nmapped, _nunmapped = line.split()
+
+
+def test_bedcov_split_lines():
+    bam_filename = os.path.join(BAM_DATADIR, "ex1.bam")
+    bed_filename = os.path.join(BAM_DATADIR, "ex1.bed")
+    # Test pysam 0.8.X style output, which returns a list of lines
+    lines = pysam.bedcov(bed_filename, bam_filename, split_lines=True)
+    for line in lines:
+        fields = line.split('\t')
+        assert len(fields) in [4, 5], \
+            ("bedcov should give tab delimited output with 4 or 5 fields. "
+             "Split line (%s) gives %d fields." % (fields, len(fields)))
+
+
+def test_idxstats_parse():
+    bam_filename = os.path.join(BAM_DATADIR, "ex2.bam")
+    # Test pysam 0.9.X style output, which returns a string that needs to be split by \n
+    idxstats_string = pysam.idxstats(bam_filename, split_lines=False)
+    lines = idxstats_string.splitlines()
+    for line in lines:
+        splt = line.split("\t")
+        _seqname, _seqlen, nmapped, _nunmapped = splt
+
+
+def test_bedcov():
+    bam_filename = os.path.join(BAM_DATADIR, "ex1.bam")
+    bed_filename = os.path.join(BAM_DATADIR, "ex1.bed")
+    # Test pysam 0.9.X style output, which returns a string that needs to be split by \n
+    bedcov_string = pysam.bedcov(bed_filename, bam_filename, split_lines=False)
+    lines = bedcov_string.splitlines()
+    for line in lines:
+        fields = line.split('\t')
+        assert len(fields) in [4, 5], \
+            ("bedcov should give tab delimited output with 4 or 5 fields. "
+             "Split line (%s) gives %d fields." % (fields, len(fields)))
-- 
2.30.2